Multiple sequence alignment - TraesCS2B01G477800

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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 TraesCS2B01G477800 chr2B 100.000 3618 0 0 909 4526 675342434 675346051 0.000000e+00 6682
1 TraesCS2B01G477800 chr2B 100.000 646 0 0 1 646 675341526 675342171 0.000000e+00 1194
2 TraesCS2B01G477800 chr2D 94.047 2150 78 15 2418 4526 564083254 564085394 0.000000e+00 3216
3 TraesCS2B01G477800 chr2D 90.421 689 53 4 1650 2335 564082575 564083253 0.000000e+00 894
4 TraesCS2B01G477800 chr2D 94.161 411 17 3 933 1337 564081778 564082187 1.790000e-173 619
5 TraesCS2B01G477800 chr2D 82.353 493 35 19 171 646 564081298 564081755 9.190000e-102 381
6 TraesCS2B01G477800 chr2D 98.246 57 1 0 1 57 564081084 564081140 2.880000e-17 100
7 TraesCS2B01G477800 chr2A 93.898 2147 81 20 2418 4526 704764593 704766727 0.000000e+00 3193
8 TraesCS2B01G477800 chr2A 92.185 755 50 6 1587 2335 704763841 704764592 0.000000e+00 1059
9 TraesCS2B01G477800 chr2A 93.028 459 23 3 933 1391 704763383 704763832 0.000000e+00 662
10 TraesCS2B01G477800 chr2A 83.299 491 31 20 171 646 704762907 704763361 5.450000e-109 405


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 TraesCS2B01G477800 chr2B 675341526 675346051 4525 False 3938.00 6682 100.0000 1 4526 2 chr2B.!!$F1 4525
1 TraesCS2B01G477800 chr2D 564081084 564085394 4310 False 1042.00 3216 91.8456 1 4526 5 chr2D.!!$F1 4525
2 TraesCS2B01G477800 chr2A 704762907 704766727 3820 False 1329.75 3193 90.6025 171 4526 4 chr2A.!!$F1 4355

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
533 620 0.094730 GATCTTCGCCGTCGGTTTTG 59.905 55.0 13.94 0.87 36.13 2.44 F
1554 1726 0.541764 TTGGAGTGAAATGCCCACCC 60.542 55.0 0.00 0.00 35.23 4.61 F
2940 3197 0.105593 CCACCAGATGTCGATCCAGG 59.894 60.0 0.00 0.00 32.79 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 1873 0.327924 CATGTGACTGCTGGGGGTTA 59.672 55.000 0.0 0.0 0.00 2.85 R
3074 3331 1.617839 AAGCCTCTAGCCTTGCCCT 60.618 57.895 0.0 0.0 45.47 5.19 R
4408 4682 2.359975 CGCCCAACCCTCTTCCAC 60.360 66.667 0.0 0.0 0.00 4.02 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
51 52 1.001815 CAGGAACGTCACGGCAAAATT 60.002 47.619 0.35 0.00 0.00 1.82
57 58 2.614983 ACGTCACGGCAAAATTAACTGT 59.385 40.909 0.35 0.00 0.00 3.55
58 59 3.223157 CGTCACGGCAAAATTAACTGTC 58.777 45.455 0.00 0.00 0.00 3.51
59 60 3.059188 CGTCACGGCAAAATTAACTGTCT 60.059 43.478 0.00 0.00 0.00 3.41
60 61 4.219033 GTCACGGCAAAATTAACTGTCTG 58.781 43.478 0.00 0.00 0.00 3.51
61 62 2.979813 CACGGCAAAATTAACTGTCTGC 59.020 45.455 0.00 0.00 0.00 4.26
62 63 2.621055 ACGGCAAAATTAACTGTCTGCA 59.379 40.909 0.00 0.00 0.00 4.41
88 89 3.745332 TGCAGCAACATGTCTAAATCG 57.255 42.857 0.00 0.00 0.00 3.34
89 90 2.159531 TGCAGCAACATGTCTAAATCGC 60.160 45.455 0.00 0.00 0.00 4.58
90 91 2.792542 GCAGCAACATGTCTAAATCGCC 60.793 50.000 0.00 0.00 0.00 5.54
91 92 2.679837 CAGCAACATGTCTAAATCGCCT 59.320 45.455 0.00 0.00 0.00 5.52
92 93 2.679837 AGCAACATGTCTAAATCGCCTG 59.320 45.455 0.00 0.00 0.00 4.85
93 94 2.792542 GCAACATGTCTAAATCGCCTGC 60.793 50.000 0.00 0.00 0.00 4.85
94 95 2.401583 ACATGTCTAAATCGCCTGCA 57.598 45.000 0.00 0.00 0.00 4.41
95 96 2.923121 ACATGTCTAAATCGCCTGCAT 58.077 42.857 0.00 0.00 0.00 3.96
96 97 4.071961 ACATGTCTAAATCGCCTGCATA 57.928 40.909 0.00 0.00 0.00 3.14
97 98 3.809832 ACATGTCTAAATCGCCTGCATAC 59.190 43.478 0.00 0.00 0.00 2.39
98 99 3.535280 TGTCTAAATCGCCTGCATACA 57.465 42.857 0.00 0.00 0.00 2.29
99 100 3.194861 TGTCTAAATCGCCTGCATACAC 58.805 45.455 0.00 0.00 0.00 2.90
100 101 3.194861 GTCTAAATCGCCTGCATACACA 58.805 45.455 0.00 0.00 0.00 3.72
101 102 3.621268 GTCTAAATCGCCTGCATACACAA 59.379 43.478 0.00 0.00 0.00 3.33
102 103 2.919666 AAATCGCCTGCATACACAAC 57.080 45.000 0.00 0.00 0.00 3.32
111 112 3.928211 CTGCATACACAACGCAGTATTC 58.072 45.455 0.00 0.00 45.00 1.75
119 120 4.141680 CACAACGCAGTATTCGTCTTTTC 58.858 43.478 0.00 0.00 45.00 2.29
126 127 4.569564 GCAGTATTCGTCTTTTCCCGTATT 59.430 41.667 0.00 0.00 0.00 1.89
149 179 3.639094 TGGGAGCGAAGGAAAATGAAAAA 59.361 39.130 0.00 0.00 0.00 1.94
153 183 6.159293 GGAGCGAAGGAAAATGAAAAAGATT 58.841 36.000 0.00 0.00 0.00 2.40
159 189 9.334693 CGAAGGAAAATGAAAAAGATTGACTAG 57.665 33.333 0.00 0.00 0.00 2.57
160 190 9.631452 GAAGGAAAATGAAAAAGATTGACTAGG 57.369 33.333 0.00 0.00 0.00 3.02
161 191 8.127150 AGGAAAATGAAAAAGATTGACTAGGG 57.873 34.615 0.00 0.00 0.00 3.53
162 192 6.813649 GGAAAATGAAAAAGATTGACTAGGGC 59.186 38.462 0.00 0.00 0.00 5.19
164 194 6.521151 AATGAAAAAGATTGACTAGGGCTG 57.479 37.500 0.00 0.00 0.00 4.85
165 195 3.758554 TGAAAAAGATTGACTAGGGCTGC 59.241 43.478 0.00 0.00 0.00 5.25
166 196 2.426842 AAAGATTGACTAGGGCTGCC 57.573 50.000 11.05 11.05 0.00 4.85
167 197 0.179000 AAGATTGACTAGGGCTGCCG 59.821 55.000 13.40 1.04 0.00 5.69
168 198 1.227674 GATTGACTAGGGCTGCCGG 60.228 63.158 13.40 0.00 0.00 6.13
169 199 1.686325 GATTGACTAGGGCTGCCGGA 61.686 60.000 13.40 1.41 0.00 5.14
174 243 1.524621 CTAGGGCTGCCGGAACATG 60.525 63.158 13.40 0.00 0.00 3.21
194 263 8.797350 AACATGAATCAACTGAGATACAATCA 57.203 30.769 0.00 0.00 0.00 2.57
229 298 1.074775 ATACCTAGGGCTGCCGGAA 60.075 57.895 14.81 0.00 0.00 4.30
349 419 2.203938 GAGGGAGGTGGGTGGTGA 60.204 66.667 0.00 0.00 0.00 4.02
350 420 2.203998 AGGGAGGTGGGTGGTGAG 60.204 66.667 0.00 0.00 0.00 3.51
351 421 3.330720 GGGAGGTGGGTGGTGAGG 61.331 72.222 0.00 0.00 0.00 3.86
352 422 2.529389 GGAGGTGGGTGGTGAGGT 60.529 66.667 0.00 0.00 0.00 3.85
354 424 2.854032 AGGTGGGTGGTGAGGTGG 60.854 66.667 0.00 0.00 0.00 4.61
355 425 3.966543 GGTGGGTGGTGAGGTGGG 61.967 72.222 0.00 0.00 0.00 4.61
356 426 3.966543 GTGGGTGGTGAGGTGGGG 61.967 72.222 0.00 0.00 0.00 4.96
358 428 4.995058 GGGTGGTGAGGTGGGGGA 62.995 72.222 0.00 0.00 0.00 4.81
359 429 2.856988 GGTGGTGAGGTGGGGGAA 60.857 66.667 0.00 0.00 0.00 3.97
360 430 2.434774 GTGGTGAGGTGGGGGAAC 59.565 66.667 0.00 0.00 0.00 3.62
361 431 3.246112 TGGTGAGGTGGGGGAACG 61.246 66.667 0.00 0.00 0.00 3.95
362 432 2.926242 GGTGAGGTGGGGGAACGA 60.926 66.667 0.00 0.00 0.00 3.85
363 433 2.346365 GTGAGGTGGGGGAACGAC 59.654 66.667 0.00 0.00 0.00 4.34
364 434 2.203182 TGAGGTGGGGGAACGACT 59.797 61.111 0.00 0.00 0.00 4.18
365 435 2.214216 TGAGGTGGGGGAACGACTG 61.214 63.158 0.00 0.00 0.00 3.51
366 436 2.928396 AGGTGGGGGAACGACTGG 60.928 66.667 0.00 0.00 0.00 4.00
367 437 4.717313 GGTGGGGGAACGACTGGC 62.717 72.222 0.00 0.00 0.00 4.85
368 438 4.717313 GTGGGGGAACGACTGGCC 62.717 72.222 0.00 0.00 0.00 5.36
419 489 2.417516 CGCTCGATCCAATCCCGT 59.582 61.111 0.00 0.00 0.00 5.28
462 534 2.016704 CCGTATGCATCGCTCGGTC 61.017 63.158 0.19 0.00 35.15 4.79
463 535 2.016704 CGTATGCATCGCTCGGTCC 61.017 63.158 0.19 0.00 0.00 4.46
464 536 1.067416 GTATGCATCGCTCGGTCCA 59.933 57.895 0.19 0.00 0.00 4.02
465 537 0.941463 GTATGCATCGCTCGGTCCAG 60.941 60.000 0.19 0.00 0.00 3.86
527 614 2.956964 GGCTGATCTTCGCCGTCG 60.957 66.667 5.68 0.00 36.45 5.12
533 620 0.094730 GATCTTCGCCGTCGGTTTTG 59.905 55.000 13.94 0.87 36.13 2.44
536 623 0.656205 CTTCGCCGTCGGTTTTGTTG 60.656 55.000 13.94 0.00 36.13 3.33
576 663 3.798954 CTCCGATGCTTCCGCTCCC 62.799 68.421 0.00 0.00 36.97 4.30
611 698 4.290622 CCCAGGCCCAGTGCAAGT 62.291 66.667 0.00 0.00 43.89 3.16
612 699 2.987547 CCAGGCCCAGTGCAAGTG 60.988 66.667 0.00 0.00 43.89 3.16
613 700 2.113774 CAGGCCCAGTGCAAGTGA 59.886 61.111 0.00 0.00 40.62 3.41
614 701 2.113986 AGGCCCAGTGCAAGTGAC 59.886 61.111 0.00 0.00 40.62 3.67
615 702 2.113986 GGCCCAGTGCAAGTGACT 59.886 61.111 0.00 0.00 40.62 3.41
616 703 2.263741 GGCCCAGTGCAAGTGACTG 61.264 63.158 0.00 0.00 40.62 3.51
618 705 2.610694 CCCAGTGCAAGTGACTGCG 61.611 63.158 0.00 0.00 45.74 5.18
621 708 3.279116 GTGCAAGTGACTGCGCCA 61.279 61.111 4.18 0.00 45.17 5.69
622 709 2.281692 TGCAAGTGACTGCGCCAT 60.282 55.556 4.18 0.00 45.74 4.40
623 710 1.898094 TGCAAGTGACTGCGCCATT 60.898 52.632 4.18 0.00 45.74 3.16
624 711 1.286880 GCAAGTGACTGCGCCATTT 59.713 52.632 4.18 0.00 31.50 2.32
625 712 1.005294 GCAAGTGACTGCGCCATTTG 61.005 55.000 4.18 10.36 35.29 2.32
626 713 1.005294 CAAGTGACTGCGCCATTTGC 61.005 55.000 4.18 0.00 0.00 3.68
1212 1312 4.074526 TCGCTGCCTCCTGCTGTC 62.075 66.667 0.00 0.00 42.00 3.51
1258 1358 5.474532 TCTCTTGCTTGTTATTTCTGCACAT 59.525 36.000 0.00 0.00 33.13 3.21
1391 1562 8.204836 AGATGTAAAGAAGATAGGTTTGCGTAT 58.795 33.333 0.00 0.00 0.00 3.06
1393 1564 8.638685 TGTAAAGAAGATAGGTTTGCGTATAC 57.361 34.615 0.00 0.00 0.00 1.47
1394 1565 8.252417 TGTAAAGAAGATAGGTTTGCGTATACA 58.748 33.333 3.32 0.00 0.00 2.29
1397 1568 8.813643 AAGAAGATAGGTTTGCGTATACATAC 57.186 34.615 3.32 0.00 0.00 2.39
1399 1570 8.082852 AGAAGATAGGTTTGCGTATACATACAG 58.917 37.037 3.32 0.00 32.87 2.74
1401 1572 8.400184 AGATAGGTTTGCGTATACATACAGTA 57.600 34.615 3.32 0.00 37.06 2.74
1452 1624 7.162761 TGAAAATACTCAAATTGTAGACCGGA 58.837 34.615 9.46 0.00 0.00 5.14
1453 1625 7.662258 TGAAAATACTCAAATTGTAGACCGGAA 59.338 33.333 9.46 0.00 0.00 4.30
1457 1629 8.888579 ATACTCAAATTGTAGACCGGAATTAG 57.111 34.615 9.46 1.17 0.00 1.73
1465 1637 4.933400 TGTAGACCGGAATTAGCTTGAAAC 59.067 41.667 9.46 0.00 0.00 2.78
1469 1641 2.739913 CCGGAATTAGCTTGAAACGACA 59.260 45.455 0.00 0.00 0.00 4.35
1475 1647 6.093633 GGAATTAGCTTGAAACGACACCTTAT 59.906 38.462 0.00 0.00 0.00 1.73
1477 1649 4.002906 AGCTTGAAACGACACCTTATCA 57.997 40.909 0.00 0.00 0.00 2.15
1484 1656 7.265647 TGAAACGACACCTTATCAAAATTGA 57.734 32.000 0.00 0.00 42.14 2.57
1488 1660 7.076842 ACGACACCTTATCAAAATTGATCTG 57.923 36.000 11.69 6.62 44.17 2.90
1496 1668 9.294030 CCTTATCAAAATTGATCTGTTTAGTGC 57.706 33.333 11.69 0.00 44.17 4.40
1497 1669 9.294030 CTTATCAAAATTGATCTGTTTAGTGCC 57.706 33.333 11.69 0.00 44.17 5.01
1502 1674 5.886960 ATTGATCTGTTTAGTGCCTTGTC 57.113 39.130 0.00 0.00 0.00 3.18
1521 1693 4.331968 TGTCGAAATGCTAAGTGGGAAAT 58.668 39.130 0.00 0.00 0.00 2.17
1537 1709 3.636764 GGGAAATATGGCCTTGGTACTTG 59.363 47.826 3.32 0.00 0.00 3.16
1544 1716 1.073284 GGCCTTGGTACTTGGAGTGAA 59.927 52.381 0.00 0.00 0.00 3.18
1548 1720 3.191371 CCTTGGTACTTGGAGTGAAATGC 59.809 47.826 0.00 0.00 0.00 3.56
1549 1721 2.790433 TGGTACTTGGAGTGAAATGCC 58.210 47.619 0.00 0.00 0.00 4.40
1550 1722 2.092323 GGTACTTGGAGTGAAATGCCC 58.908 52.381 0.00 0.00 0.00 5.36
1552 1724 1.620822 ACTTGGAGTGAAATGCCCAC 58.379 50.000 0.00 0.00 34.89 4.61
1553 1725 0.890683 CTTGGAGTGAAATGCCCACC 59.109 55.000 0.00 0.00 35.23 4.61
1554 1726 0.541764 TTGGAGTGAAATGCCCACCC 60.542 55.000 0.00 0.00 35.23 4.61
1556 1728 1.250840 GGAGTGAAATGCCCACCCAC 61.251 60.000 0.00 0.00 35.23 4.61
1557 1729 1.228862 AGTGAAATGCCCACCCACC 60.229 57.895 0.00 0.00 35.23 4.61
1558 1730 2.119391 TGAAATGCCCACCCACCC 59.881 61.111 0.00 0.00 0.00 4.61
1559 1731 2.119391 GAAATGCCCACCCACCCA 59.881 61.111 0.00 0.00 0.00 4.51
1560 1732 2.203773 AAATGCCCACCCACCCAC 60.204 61.111 0.00 0.00 0.00 4.61
1602 1802 6.070824 TGGTGATTCTTAGTTCACTGCTCATA 60.071 38.462 14.13 0.00 41.55 2.15
1604 1804 7.334421 GGTGATTCTTAGTTCACTGCTCATAAA 59.666 37.037 14.13 0.00 41.55 1.40
1624 1850 2.662866 ACAATCTCCAATGCATCAGGG 58.337 47.619 15.79 10.98 0.00 4.45
1625 1851 2.242965 ACAATCTCCAATGCATCAGGGA 59.757 45.455 15.79 14.11 0.00 4.20
1626 1852 3.117246 ACAATCTCCAATGCATCAGGGAT 60.117 43.478 15.79 10.92 0.00 3.85
1627 1853 3.895656 CAATCTCCAATGCATCAGGGATT 59.104 43.478 15.09 15.09 38.16 3.01
1628 1854 3.219176 TCTCCAATGCATCAGGGATTC 57.781 47.619 15.79 0.00 35.06 2.52
1629 1855 2.510800 TCTCCAATGCATCAGGGATTCA 59.489 45.455 15.79 2.67 35.06 2.57
1630 1856 3.053470 TCTCCAATGCATCAGGGATTCAA 60.053 43.478 15.79 2.08 35.06 2.69
1631 1857 3.293337 TCCAATGCATCAGGGATTCAAG 58.707 45.455 15.79 0.00 35.06 3.02
1632 1858 2.364324 CCAATGCATCAGGGATTCAAGG 59.636 50.000 0.00 0.00 35.06 3.61
1633 1859 3.293337 CAATGCATCAGGGATTCAAGGA 58.707 45.455 0.00 0.00 35.06 3.36
1634 1860 3.675348 ATGCATCAGGGATTCAAGGAA 57.325 42.857 0.00 0.00 0.00 3.36
1635 1861 2.726821 TGCATCAGGGATTCAAGGAAC 58.273 47.619 0.00 0.00 0.00 3.62
1636 1862 4.571362 AATGCATCAGGGATTCAAGGAACT 60.571 41.667 0.00 0.00 33.25 3.01
1637 1863 2.686915 GCATCAGGGATTCAAGGAACTG 59.313 50.000 0.00 0.00 40.86 3.16
1638 1864 3.285484 CATCAGGGATTCAAGGAACTGG 58.715 50.000 0.00 0.00 40.86 4.00
1639 1865 2.348472 TCAGGGATTCAAGGAACTGGT 58.652 47.619 0.00 0.00 40.86 4.00
1640 1866 2.716424 TCAGGGATTCAAGGAACTGGTT 59.284 45.455 0.00 0.00 40.86 3.67
1641 1867 3.913799 TCAGGGATTCAAGGAACTGGTTA 59.086 43.478 0.00 0.00 40.86 2.85
1642 1868 4.352595 TCAGGGATTCAAGGAACTGGTTAA 59.647 41.667 0.00 0.00 40.86 2.01
1643 1869 5.076873 CAGGGATTCAAGGAACTGGTTAAA 58.923 41.667 0.00 0.00 40.86 1.52
1644 1870 5.716703 CAGGGATTCAAGGAACTGGTTAAAT 59.283 40.000 0.00 0.00 40.86 1.40
1645 1871 6.211384 CAGGGATTCAAGGAACTGGTTAAATT 59.789 38.462 0.00 0.00 40.86 1.82
1646 1872 6.787458 AGGGATTCAAGGAACTGGTTAAATTT 59.213 34.615 0.00 0.00 40.86 1.82
1647 1873 7.292356 AGGGATTCAAGGAACTGGTTAAATTTT 59.708 33.333 0.00 0.00 40.86 1.82
1648 1874 8.590204 GGGATTCAAGGAACTGGTTAAATTTTA 58.410 33.333 0.00 0.00 40.86 1.52
1668 1894 2.605607 CCCCCAGCAGTCACATGGA 61.606 63.158 0.00 0.00 36.09 3.41
1673 1899 2.564062 CCCAGCAGTCACATGGATTTTT 59.436 45.455 0.00 0.00 36.09 1.94
1703 1929 1.001181 GCATTTTGGGCAGCTTGAGAA 59.999 47.619 0.00 0.00 0.00 2.87
1722 1948 8.415950 TTGAGAAATTCTATGTGGCCTTTTTA 57.584 30.769 3.32 0.00 0.00 1.52
1737 1964 8.440059 GTGGCCTTTTTATTTTATTTACAGCAC 58.560 33.333 3.32 0.00 0.00 4.40
1738 1965 7.329717 TGGCCTTTTTATTTTATTTACAGCACG 59.670 33.333 3.32 0.00 0.00 5.34
1741 1971 9.072294 CCTTTTTATTTTATTTACAGCACGAGG 57.928 33.333 0.00 0.00 0.00 4.63
1748 1978 2.088950 TTACAGCACGAGGCCTAAAC 57.911 50.000 4.42 0.00 46.50 2.01
1757 1987 4.680975 GCACGAGGCCTAAACTATCTCTTT 60.681 45.833 4.42 0.00 36.11 2.52
1768 1998 2.431057 ACTATCTCTTTGCCAGTACCCG 59.569 50.000 0.00 0.00 0.00 5.28
1773 2003 2.167693 CTCTTTGCCAGTACCCGATACA 59.832 50.000 0.00 0.00 36.09 2.29
1781 2011 4.817517 CCAGTACCCGATACATTACCATC 58.182 47.826 0.00 0.00 36.09 3.51
1821 2051 9.645059 ATCATATCGTATGTAGTTCCATCTTTG 57.355 33.333 5.36 0.00 0.00 2.77
1890 2120 5.999205 ACATTGGACTAAATTCCATTGCA 57.001 34.783 11.99 0.00 45.42 4.08
1893 2123 2.760092 TGGACTAAATTCCATTGCAGGC 59.240 45.455 0.00 0.00 41.00 4.85
1897 2127 4.088634 ACTAAATTCCATTGCAGGCTTCA 58.911 39.130 0.00 0.00 0.00 3.02
2007 2237 0.531974 TAAGGCGCGGGCATCTAAAG 60.532 55.000 26.61 0.00 42.47 1.85
2057 2287 7.333528 TGCTATCTTGTCAAACTTCAGTTTT 57.666 32.000 2.01 0.00 45.07 2.43
2078 2308 5.682234 TTGATTCTCTTCTGCACTATCCA 57.318 39.130 0.00 0.00 0.00 3.41
2089 2319 5.428253 TCTGCACTATCCACCATAGTTTTC 58.572 41.667 0.00 0.00 44.80 2.29
2155 2386 9.708092 ATTTAAGAAGACAGTACAGAAACCTAC 57.292 33.333 0.00 0.00 0.00 3.18
2180 2411 5.975693 TTCTTGGAATATGTGGTTTGACC 57.024 39.130 0.00 0.00 39.22 4.02
2234 2465 8.306038 TGAATTCATACTCAAATCCACTTTTGG 58.694 33.333 3.38 0.00 45.56 3.28
2246 2477 6.909550 ATCCACTTTTGGTGTTATGCTTTA 57.090 33.333 0.00 0.00 44.35 1.85
2266 2497 9.308318 TGCTTTAGAATTGGTTGTTTTTCTAAC 57.692 29.630 4.05 0.00 39.26 2.34
2338 2569 9.747898 ACTAATATAACTTTTTCATGTGACCCA 57.252 29.630 0.00 0.00 0.00 4.51
2340 2571 5.722021 ATAACTTTTTCATGTGACCCACC 57.278 39.130 0.00 0.00 32.73 4.61
2342 2573 2.693074 ACTTTTTCATGTGACCCACCAC 59.307 45.455 0.00 0.00 37.55 4.16
2343 2574 1.698506 TTTTCATGTGACCCACCACC 58.301 50.000 0.00 0.00 36.26 4.61
2344 2575 0.553333 TTTCATGTGACCCACCACCA 59.447 50.000 0.00 0.00 36.26 4.17
2345 2576 0.776810 TTCATGTGACCCACCACCAT 59.223 50.000 0.00 0.00 36.26 3.55
2346 2577 0.776810 TCATGTGACCCACCACCATT 59.223 50.000 0.00 0.00 36.26 3.16
2347 2578 1.988846 TCATGTGACCCACCACCATTA 59.011 47.619 0.00 0.00 36.26 1.90
2348 2579 2.026356 TCATGTGACCCACCACCATTAG 60.026 50.000 0.00 0.00 36.26 1.73
2349 2580 1.735926 TGTGACCCACCACCATTAGA 58.264 50.000 0.00 0.00 36.26 2.10
2350 2581 1.349688 TGTGACCCACCACCATTAGAC 59.650 52.381 0.00 0.00 36.26 2.59
2351 2582 0.988832 TGACCCACCACCATTAGACC 59.011 55.000 0.00 0.00 0.00 3.85
2352 2583 0.988832 GACCCACCACCATTAGACCA 59.011 55.000 0.00 0.00 0.00 4.02
2353 2584 1.564348 GACCCACCACCATTAGACCAT 59.436 52.381 0.00 0.00 0.00 3.55
2354 2585 2.000048 ACCCACCACCATTAGACCATT 59.000 47.619 0.00 0.00 0.00 3.16
2355 2586 2.291540 ACCCACCACCATTAGACCATTG 60.292 50.000 0.00 0.00 0.00 2.82
2356 2587 2.025416 CCCACCACCATTAGACCATTGA 60.025 50.000 0.00 0.00 0.00 2.57
2357 2588 3.373001 CCCACCACCATTAGACCATTGAT 60.373 47.826 0.00 0.00 0.00 2.57
2358 2589 3.633525 CCACCACCATTAGACCATTGATG 59.366 47.826 0.00 0.00 0.00 3.07
2359 2590 3.067180 CACCACCATTAGACCATTGATGC 59.933 47.826 0.00 0.00 0.00 3.91
2360 2591 2.624838 CCACCATTAGACCATTGATGCC 59.375 50.000 0.00 0.00 0.00 4.40
2361 2592 3.559069 CACCATTAGACCATTGATGCCT 58.441 45.455 0.00 0.00 0.00 4.75
2362 2593 3.567164 CACCATTAGACCATTGATGCCTC 59.433 47.826 0.00 0.00 0.00 4.70
2363 2594 3.202818 ACCATTAGACCATTGATGCCTCA 59.797 43.478 0.00 0.00 0.00 3.86
2364 2595 4.141088 ACCATTAGACCATTGATGCCTCAT 60.141 41.667 0.00 0.00 0.00 2.90
2365 2596 4.217767 CCATTAGACCATTGATGCCTCATG 59.782 45.833 0.00 0.00 0.00 3.07
2366 2597 4.508551 TTAGACCATTGATGCCTCATGT 57.491 40.909 0.00 0.00 0.00 3.21
2367 2598 2.928334 AGACCATTGATGCCTCATGTC 58.072 47.619 0.00 1.30 0.00 3.06
2368 2599 2.240414 AGACCATTGATGCCTCATGTCA 59.760 45.455 14.58 0.00 31.93 3.58
2369 2600 3.117625 AGACCATTGATGCCTCATGTCAT 60.118 43.478 14.58 0.00 31.93 3.06
2370 2601 2.956333 ACCATTGATGCCTCATGTCATG 59.044 45.455 6.47 6.47 0.00 3.07
2371 2602 3.219281 CCATTGATGCCTCATGTCATGA 58.781 45.455 14.76 14.76 37.76 3.07
2372 2603 3.826729 CCATTGATGCCTCATGTCATGAT 59.173 43.478 15.84 1.07 38.85 2.45
2373 2604 5.007682 CCATTGATGCCTCATGTCATGATA 58.992 41.667 15.84 6.52 38.85 2.15
2374 2605 5.652452 CCATTGATGCCTCATGTCATGATAT 59.348 40.000 15.84 10.65 38.85 1.63
2375 2606 6.183360 CCATTGATGCCTCATGTCATGATATC 60.183 42.308 15.84 17.62 38.85 1.63
2376 2607 5.492855 TGATGCCTCATGTCATGATATCA 57.507 39.130 21.57 21.57 38.85 2.15
2377 2608 5.243207 TGATGCCTCATGTCATGATATCAC 58.757 41.667 21.57 13.47 38.85 3.06
2378 2609 4.968971 TGCCTCATGTCATGATATCACT 57.031 40.909 15.84 0.00 38.85 3.41
2379 2610 5.300411 TGCCTCATGTCATGATATCACTT 57.700 39.130 15.84 0.00 38.85 3.16
2380 2611 5.687780 TGCCTCATGTCATGATATCACTTT 58.312 37.500 15.84 0.00 38.85 2.66
2381 2612 6.829849 TGCCTCATGTCATGATATCACTTTA 58.170 36.000 15.84 0.00 38.85 1.85
2382 2613 7.455891 TGCCTCATGTCATGATATCACTTTAT 58.544 34.615 15.84 0.00 38.85 1.40
2383 2614 8.596293 TGCCTCATGTCATGATATCACTTTATA 58.404 33.333 15.84 0.00 38.85 0.98
2384 2615 9.610705 GCCTCATGTCATGATATCACTTTATAT 57.389 33.333 15.84 0.00 38.85 0.86
2396 2627 9.846248 GATATCACTTTATATGATTTGGTTGCC 57.154 33.333 0.00 0.00 37.89 4.52
2397 2628 6.463995 TCACTTTATATGATTTGGTTGCCC 57.536 37.500 0.00 0.00 0.00 5.36
2398 2629 6.194235 TCACTTTATATGATTTGGTTGCCCT 58.806 36.000 0.00 0.00 0.00 5.19
2399 2630 6.667414 TCACTTTATATGATTTGGTTGCCCTT 59.333 34.615 0.00 0.00 0.00 3.95
2400 2631 6.980397 CACTTTATATGATTTGGTTGCCCTTC 59.020 38.462 0.00 0.00 0.00 3.46
2401 2632 6.897413 ACTTTATATGATTTGGTTGCCCTTCT 59.103 34.615 0.00 0.00 0.00 2.85
2402 2633 8.058847 ACTTTATATGATTTGGTTGCCCTTCTA 58.941 33.333 0.00 0.00 0.00 2.10
2403 2634 8.830915 TTTATATGATTTGGTTGCCCTTCTAA 57.169 30.769 0.00 0.00 0.00 2.10
2404 2635 6.966534 ATATGATTTGGTTGCCCTTCTAAG 57.033 37.500 0.00 0.00 0.00 2.18
2405 2636 4.112634 TGATTTGGTTGCCCTTCTAAGT 57.887 40.909 0.00 0.00 0.00 2.24
2406 2637 4.479158 TGATTTGGTTGCCCTTCTAAGTT 58.521 39.130 0.00 0.00 0.00 2.66
2407 2638 4.522789 TGATTTGGTTGCCCTTCTAAGTTC 59.477 41.667 0.00 0.00 0.00 3.01
2408 2639 3.876309 TTGGTTGCCCTTCTAAGTTCT 57.124 42.857 0.00 0.00 0.00 3.01
2409 2640 4.986054 TTGGTTGCCCTTCTAAGTTCTA 57.014 40.909 0.00 0.00 0.00 2.10
2410 2641 4.986054 TGGTTGCCCTTCTAAGTTCTAA 57.014 40.909 0.00 0.00 0.00 2.10
2411 2642 5.514500 TGGTTGCCCTTCTAAGTTCTAAT 57.486 39.130 0.00 0.00 0.00 1.73
2412 2643 5.253330 TGGTTGCCCTTCTAAGTTCTAATG 58.747 41.667 0.00 0.00 0.00 1.90
2413 2644 4.640647 GGTTGCCCTTCTAAGTTCTAATGG 59.359 45.833 0.00 0.00 0.00 3.16
2414 2645 5.254115 GTTGCCCTTCTAAGTTCTAATGGT 58.746 41.667 0.00 0.00 0.00 3.55
2415 2646 5.099042 TGCCCTTCTAAGTTCTAATGGTC 57.901 43.478 0.00 0.00 0.00 4.02
2416 2647 4.783227 TGCCCTTCTAAGTTCTAATGGTCT 59.217 41.667 0.00 0.00 0.00 3.85
2417 2648 5.962031 TGCCCTTCTAAGTTCTAATGGTCTA 59.038 40.000 0.00 0.00 0.00 2.59
2418 2649 6.442564 TGCCCTTCTAAGTTCTAATGGTCTAA 59.557 38.462 0.00 0.00 0.00 2.10
2419 2650 6.762187 GCCCTTCTAAGTTCTAATGGTCTAAC 59.238 42.308 0.00 0.00 0.00 2.34
2420 2651 7.364851 GCCCTTCTAAGTTCTAATGGTCTAACT 60.365 40.741 0.00 0.00 33.72 2.24
2421 2652 9.198475 CCCTTCTAAGTTCTAATGGTCTAACTA 57.802 37.037 0.00 0.00 32.09 2.24
2445 2676 2.092699 GGGGTGAATTCTTCTCTGAGGG 60.093 54.545 7.05 0.00 0.00 4.30
2475 2706 5.423015 TGTCATCTTCTCCATTTGTCTAGC 58.577 41.667 0.00 0.00 0.00 3.42
2505 2736 7.193595 AGCTTTATAACATTGTAAATCCACGC 58.806 34.615 0.00 0.00 0.00 5.34
2519 2750 0.249868 CCACGCCTCACTCTTGTTGA 60.250 55.000 0.00 0.00 0.00 3.18
2529 2760 2.417933 CACTCTTGTTGACTGCTATGGC 59.582 50.000 0.00 0.00 39.26 4.40
2631 2862 5.769367 CTGGTTTCCAAGCCTACTTTTAAC 58.231 41.667 0.00 0.00 32.29 2.01
2632 2863 4.585581 TGGTTTCCAAGCCTACTTTTAACC 59.414 41.667 0.00 0.00 37.92 2.85
2636 2867 7.270047 GTTTCCAAGCCTACTTTTAACCTTTT 58.730 34.615 0.00 0.00 32.29 2.27
2637 2868 7.426606 TTCCAAGCCTACTTTTAACCTTTTT 57.573 32.000 0.00 0.00 32.29 1.94
2696 2953 9.134734 TCTTTAAATCGTGCAATAATTTTGACC 57.865 29.630 7.31 0.00 0.00 4.02
2733 2990 1.398739 TGCAAAACCACGTGTGTACAG 59.601 47.619 15.65 0.00 0.00 2.74
2844 3101 3.004315 CGGCTTACAAATGAACAACAGGT 59.996 43.478 0.00 0.00 0.00 4.00
2845 3102 4.546570 GGCTTACAAATGAACAACAGGTC 58.453 43.478 0.00 0.00 0.00 3.85
2940 3197 0.105593 CCACCAGATGTCGATCCAGG 59.894 60.000 0.00 0.00 32.79 4.45
3037 3294 7.797121 AAGGAATGTTTATCAAAAGGATGGT 57.203 32.000 0.00 0.00 36.72 3.55
3074 3331 1.896220 AGCCGAACATGAAGCTTTGA 58.104 45.000 0.00 0.00 29.27 2.69
3108 3365 2.490903 AGGCTTCAAATGATGTGAGTGC 59.509 45.455 4.71 4.71 0.00 4.40
3120 3377 4.277921 TGATGTGAGTGCTTGCAATTAACA 59.722 37.500 0.00 12.34 0.00 2.41
3123 3380 4.277921 TGTGAGTGCTTGCAATTAACATGA 59.722 37.500 0.00 0.00 0.00 3.07
3131 3388 9.090692 GTGCTTGCAATTAACATGATATTCTTT 57.909 29.630 0.00 0.00 0.00 2.52
3233 3490 7.601856 CAGGCAGGATAAATGAGTTGTTTTAA 58.398 34.615 0.00 0.00 0.00 1.52
3265 3522 8.314021 TCAAGCTCAATCTGATAACTGAACTAA 58.686 33.333 0.00 0.00 0.00 2.24
3308 3567 3.515502 CCACTGTCTGGAATAACTCTCCA 59.484 47.826 0.00 0.00 43.95 3.86
3346 3605 2.301870 TCGCAGGTAACACCATTCTCTT 59.698 45.455 0.00 0.00 41.95 2.85
3347 3606 2.673368 CGCAGGTAACACCATTCTCTTC 59.327 50.000 0.00 0.00 41.95 2.87
3522 3793 5.833131 ACTATCAAAAAGCTTGGAAGGACAA 59.167 36.000 0.00 0.00 0.00 3.18
3527 3798 6.323739 TCAAAAAGCTTGGAAGGACAATAACT 59.676 34.615 0.00 0.00 0.00 2.24
3607 3878 9.438228 GTTTTAGCTGTAGATAGAGGAGTTTTT 57.562 33.333 0.00 0.00 0.00 1.94
3655 3926 5.118990 ACACATGATATGGAGCACTGTTAC 58.881 41.667 0.00 0.00 33.60 2.50
3777 4048 6.231951 AGGATGCTCTCATTTATCACTCATG 58.768 40.000 0.00 0.00 31.96 3.07
3785 4057 6.149308 TCTCATTTATCACTCATGTTTTGCGT 59.851 34.615 0.00 0.00 0.00 5.24
3804 4076 9.900710 TTTTGCGTAATTCAACAGTAACATAAT 57.099 25.926 0.00 0.00 0.00 1.28
3892 4164 6.477253 TGATACAGCACAAACCCTATAACAA 58.523 36.000 0.00 0.00 0.00 2.83
4106 4380 1.203441 AGACAGCATGGAAGCCCTCA 61.203 55.000 0.00 0.00 43.62 3.86
4250 4524 3.428725 GCTCCAGATCATCTACGCCATAG 60.429 52.174 0.00 0.00 0.00 2.23
4270 4544 4.630644 AGTGATCATCCTCAAACAGTGT 57.369 40.909 0.00 0.00 0.00 3.55
4273 4547 6.344500 AGTGATCATCCTCAAACAGTGTATC 58.656 40.000 0.00 0.00 0.00 2.24
4274 4548 6.070596 AGTGATCATCCTCAAACAGTGTATCA 60.071 38.462 0.00 0.00 0.00 2.15
4304 4578 1.079750 GTCAGTTCGCTGGTCCTCC 60.080 63.158 0.00 0.00 45.04 4.30
4305 4579 1.228894 TCAGTTCGCTGGTCCTCCT 60.229 57.895 0.00 0.00 45.04 3.69
4306 4580 1.216710 CAGTTCGCTGGTCCTCCTC 59.783 63.158 0.00 0.00 41.40 3.71
4384 4658 7.442666 GTGACTCTGAGTTACAGGATTTTCTTT 59.557 37.037 23.11 0.00 45.76 2.52
4385 4659 7.442364 TGACTCTGAGTTACAGGATTTTCTTTG 59.558 37.037 12.27 0.00 45.76 2.77
4408 4682 4.118410 GCAGGTTCTGTAGATCTGTCATG 58.882 47.826 5.18 1.46 33.43 3.07
4428 4702 4.344865 GAAGAGGGTTGGGCGCCA 62.345 66.667 30.85 12.04 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 2.710377 TGCAGGCGATTTAGACATGTT 58.290 42.857 0.00 0.00 0.00 2.71
75 76 2.401583 TGCAGGCGATTTAGACATGT 57.598 45.000 0.00 0.00 0.00 3.21
76 77 3.809279 TGTATGCAGGCGATTTAGACATG 59.191 43.478 0.00 0.00 0.00 3.21
77 78 3.809832 GTGTATGCAGGCGATTTAGACAT 59.190 43.478 0.00 0.00 0.00 3.06
78 79 3.194861 GTGTATGCAGGCGATTTAGACA 58.805 45.455 0.00 0.00 0.00 3.41
79 80 3.194861 TGTGTATGCAGGCGATTTAGAC 58.805 45.455 0.00 0.00 0.00 2.59
80 81 3.535280 TGTGTATGCAGGCGATTTAGA 57.465 42.857 0.00 0.00 0.00 2.10
81 82 3.544048 CGTTGTGTATGCAGGCGATTTAG 60.544 47.826 0.00 0.00 0.00 1.85
83 84 1.130373 CGTTGTGTATGCAGGCGATTT 59.870 47.619 0.00 0.00 0.00 2.17
84 85 0.726827 CGTTGTGTATGCAGGCGATT 59.273 50.000 0.00 0.00 0.00 3.34
85 86 1.705337 GCGTTGTGTATGCAGGCGAT 61.705 55.000 0.00 0.00 38.70 4.58
86 87 2.387445 GCGTTGTGTATGCAGGCGA 61.387 57.895 0.00 0.00 38.70 5.54
87 88 2.098298 GCGTTGTGTATGCAGGCG 59.902 61.111 0.00 0.00 38.70 5.52
88 89 3.262936 TGCGTTGTGTATGCAGGC 58.737 55.556 0.00 0.00 43.72 4.85
91 92 2.347150 CGAATACTGCGTTGTGTATGCA 59.653 45.455 0.00 0.00 46.32 3.96
92 93 2.347452 ACGAATACTGCGTTGTGTATGC 59.653 45.455 0.00 0.00 39.18 3.14
93 94 3.857665 AGACGAATACTGCGTTGTGTATG 59.142 43.478 0.00 0.00 42.77 2.39
94 95 4.106029 AGACGAATACTGCGTTGTGTAT 57.894 40.909 0.00 0.00 42.77 2.29
95 96 3.564235 AGACGAATACTGCGTTGTGTA 57.436 42.857 0.00 0.00 42.77 2.90
96 97 2.433868 AGACGAATACTGCGTTGTGT 57.566 45.000 0.00 0.00 42.77 3.72
97 98 3.788434 AAAGACGAATACTGCGTTGTG 57.212 42.857 0.00 0.00 42.77 3.33
98 99 3.185797 GGAAAAGACGAATACTGCGTTGT 59.814 43.478 0.00 0.00 42.77 3.32
99 100 3.424433 GGGAAAAGACGAATACTGCGTTG 60.424 47.826 0.00 0.00 42.77 4.10
100 101 2.740447 GGGAAAAGACGAATACTGCGTT 59.260 45.455 0.00 0.00 42.77 4.84
101 102 2.344025 GGGAAAAGACGAATACTGCGT 58.656 47.619 0.00 0.00 45.79 5.24
102 103 1.323534 CGGGAAAAGACGAATACTGCG 59.676 52.381 0.00 0.00 0.00 5.18
108 109 4.957759 CCAAATACGGGAAAAGACGAAT 57.042 40.909 0.00 0.00 0.00 3.34
126 127 2.577606 TCATTTTCCTTCGCTCCCAA 57.422 45.000 0.00 0.00 0.00 4.12
149 179 1.690219 CCGGCAGCCCTAGTCAATCT 61.690 60.000 5.63 0.00 0.00 2.40
153 183 2.284331 TTCCGGCAGCCCTAGTCA 60.284 61.111 5.63 0.00 0.00 3.41
159 189 1.728490 GATTCATGTTCCGGCAGCCC 61.728 60.000 5.63 0.00 0.00 5.19
160 190 1.031571 TGATTCATGTTCCGGCAGCC 61.032 55.000 0.00 0.00 0.00 4.85
161 191 0.810648 TTGATTCATGTTCCGGCAGC 59.189 50.000 0.00 0.00 0.00 5.25
162 192 2.086869 AGTTGATTCATGTTCCGGCAG 58.913 47.619 0.00 0.00 0.00 4.85
164 194 2.083774 TCAGTTGATTCATGTTCCGGC 58.916 47.619 0.00 0.00 0.00 6.13
165 195 3.599343 TCTCAGTTGATTCATGTTCCGG 58.401 45.455 0.00 0.00 0.00 5.14
166 196 5.812127 TGTATCTCAGTTGATTCATGTTCCG 59.188 40.000 0.00 0.00 0.00 4.30
167 197 7.615582 TTGTATCTCAGTTGATTCATGTTCC 57.384 36.000 0.00 0.00 0.00 3.62
168 198 8.886719 TGATTGTATCTCAGTTGATTCATGTTC 58.113 33.333 0.00 0.00 0.00 3.18
169 199 8.797350 TGATTGTATCTCAGTTGATTCATGTT 57.203 30.769 0.00 0.00 0.00 2.71
174 243 8.429493 TCACATGATTGTATCTCAGTTGATTC 57.571 34.615 0.00 0.00 33.76 2.52
347 417 2.203182 AGTCGTTCCCCCACCTCA 59.797 61.111 0.00 0.00 0.00 3.86
349 419 2.928396 CCAGTCGTTCCCCCACCT 60.928 66.667 0.00 0.00 0.00 4.00
350 420 4.717313 GCCAGTCGTTCCCCCACC 62.717 72.222 0.00 0.00 0.00 4.61
351 421 4.717313 GGCCAGTCGTTCCCCCAC 62.717 72.222 0.00 0.00 0.00 4.61
378 448 3.081409 ATCCCGTCCCGTCCCTTG 61.081 66.667 0.00 0.00 0.00 3.61
379 449 3.081409 CATCCCGTCCCGTCCCTT 61.081 66.667 0.00 0.00 0.00 3.95
419 489 4.709886 TGGAGAGAGATGAACCAAACGATA 59.290 41.667 0.00 0.00 0.00 2.92
462 534 1.540267 GAATATGCTGATGCTGGCTGG 59.460 52.381 0.00 0.00 40.48 4.85
463 535 1.540267 GGAATATGCTGATGCTGGCTG 59.460 52.381 0.00 0.00 40.48 4.85
464 536 1.424302 AGGAATATGCTGATGCTGGCT 59.576 47.619 0.00 0.00 40.48 4.75
465 537 1.811359 GAGGAATATGCTGATGCTGGC 59.189 52.381 0.00 0.00 40.48 4.85
527 614 1.096416 TGACCGTCCACAACAAAACC 58.904 50.000 0.00 0.00 0.00 3.27
533 620 1.897398 GCATCGTGACCGTCCACAAC 61.897 60.000 0.00 0.00 36.89 3.32
536 623 3.179265 CGCATCGTGACCGTCCAC 61.179 66.667 0.00 0.00 35.01 4.02
597 684 2.113986 GTCACTTGCACTGGGCCT 59.886 61.111 4.53 0.00 43.89 5.19
598 685 2.113986 AGTCACTTGCACTGGGCC 59.886 61.111 0.00 0.00 43.89 5.80
599 686 2.912624 GCAGTCACTTGCACTGGGC 61.913 63.158 0.00 0.00 43.53 5.36
600 687 2.610694 CGCAGTCACTTGCACTGGG 61.611 63.158 4.32 4.32 45.17 4.45
601 688 2.941333 CGCAGTCACTTGCACTGG 59.059 61.111 3.73 0.00 44.28 4.00
603 690 2.974698 GGCGCAGTCACTTGCACT 60.975 61.111 10.83 0.00 44.28 4.40
618 705 1.514553 GGAGGAAGCAGCAAATGGC 59.485 57.895 0.00 0.00 45.30 4.40
619 706 0.962356 ACGGAGGAAGCAGCAAATGG 60.962 55.000 0.00 0.00 0.00 3.16
621 708 0.326264 AGACGGAGGAAGCAGCAAAT 59.674 50.000 0.00 0.00 0.00 2.32
622 709 0.108585 AAGACGGAGGAAGCAGCAAA 59.891 50.000 0.00 0.00 0.00 3.68
623 710 0.320771 GAAGACGGAGGAAGCAGCAA 60.321 55.000 0.00 0.00 0.00 3.91
624 711 1.188219 AGAAGACGGAGGAAGCAGCA 61.188 55.000 0.00 0.00 0.00 4.41
625 712 0.459411 GAGAAGACGGAGGAAGCAGC 60.459 60.000 0.00 0.00 0.00 5.25
626 713 0.174617 GGAGAAGACGGAGGAAGCAG 59.825 60.000 0.00 0.00 0.00 4.24
925 1019 2.108952 AGTGCTCAGGGATGGAGTTTTT 59.891 45.455 0.00 0.00 34.83 1.94
926 1020 1.707427 AGTGCTCAGGGATGGAGTTTT 59.293 47.619 0.00 0.00 34.83 2.43
927 1021 1.280421 GAGTGCTCAGGGATGGAGTTT 59.720 52.381 0.00 0.00 34.83 2.66
928 1022 0.908198 GAGTGCTCAGGGATGGAGTT 59.092 55.000 0.00 0.00 34.83 3.01
929 1023 0.980231 GGAGTGCTCAGGGATGGAGT 60.980 60.000 1.41 0.00 34.83 3.85
930 1024 1.694133 GGGAGTGCTCAGGGATGGAG 61.694 65.000 1.41 0.00 35.47 3.86
931 1025 1.690633 GGGAGTGCTCAGGGATGGA 60.691 63.158 1.41 0.00 0.00 3.41
1045 1145 0.474184 CTGGGCGGGATTAAGTGGAT 59.526 55.000 0.00 0.00 0.00 3.41
1049 1149 0.179018 GCATCTGGGCGGGATTAAGT 60.179 55.000 0.00 0.00 0.00 2.24
1101 1201 2.882876 GTGTCGCTCGAAGCCCTA 59.117 61.111 0.00 0.00 38.18 3.53
1132 1232 3.607661 GATCCTCCGCTCCCCGTC 61.608 72.222 0.00 0.00 34.38 4.79
1154 1254 1.081092 CCCACCCTCCTCTCCAGAA 59.919 63.158 0.00 0.00 0.00 3.02
1258 1358 2.026905 GCCAACCCTCACAGTCCAAAA 61.027 52.381 0.00 0.00 0.00 2.44
1348 1518 0.961019 TCTGCCACATTTTGCTCACC 59.039 50.000 0.00 0.00 0.00 4.02
1441 1613 4.811969 TCAAGCTAATTCCGGTCTACAA 57.188 40.909 0.00 0.00 0.00 2.41
1447 1619 2.740447 GTCGTTTCAAGCTAATTCCGGT 59.260 45.455 0.00 0.00 0.00 5.28
1449 1621 3.424433 GGTGTCGTTTCAAGCTAATTCCG 60.424 47.826 0.00 0.00 0.00 4.30
1452 1624 6.653320 TGATAAGGTGTCGTTTCAAGCTAATT 59.347 34.615 0.00 0.00 0.00 1.40
1453 1625 6.170506 TGATAAGGTGTCGTTTCAAGCTAAT 58.829 36.000 0.00 0.00 0.00 1.73
1457 1629 4.742438 TTGATAAGGTGTCGTTTCAAGC 57.258 40.909 0.00 0.00 0.00 4.01
1475 1647 6.899393 AGGCACTAAACAGATCAATTTTGA 57.101 33.333 0.00 0.00 38.34 2.69
1477 1649 7.054491 ACAAGGCACTAAACAGATCAATTTT 57.946 32.000 0.00 0.00 38.49 1.82
1484 1656 3.678056 TCGACAAGGCACTAAACAGAT 57.322 42.857 0.00 0.00 38.49 2.90
1488 1660 3.058224 AGCATTTCGACAAGGCACTAAAC 60.058 43.478 15.56 0.00 38.49 2.01
1493 1665 2.484264 ACTTAGCATTTCGACAAGGCAC 59.516 45.455 15.56 0.00 0.00 5.01
1496 1668 2.420022 CCCACTTAGCATTTCGACAAGG 59.580 50.000 0.00 0.00 0.00 3.61
1497 1669 3.334691 TCCCACTTAGCATTTCGACAAG 58.665 45.455 0.00 0.00 0.00 3.16
1502 1674 5.762045 CCATATTTCCCACTTAGCATTTCG 58.238 41.667 0.00 0.00 0.00 3.46
1521 1693 2.238646 CACTCCAAGTACCAAGGCCATA 59.761 50.000 5.01 0.00 0.00 2.74
1537 1709 1.076549 TGGGTGGGCATTTCACTCC 59.923 57.895 0.00 0.00 34.87 3.85
1544 1716 3.192630 AGTGGGTGGGTGGGCATT 61.193 61.111 0.00 0.00 0.00 3.56
1548 1720 0.689412 AAAAACAGTGGGTGGGTGGG 60.689 55.000 0.00 0.00 0.00 4.61
1549 1721 2.909140 AAAAACAGTGGGTGGGTGG 58.091 52.632 0.00 0.00 0.00 4.61
1583 1783 8.621532 ATTGTTTATGAGCAGTGAACTAAGAA 57.378 30.769 0.00 0.00 0.00 2.52
1585 1785 8.261492 AGATTGTTTATGAGCAGTGAACTAAG 57.739 34.615 0.00 0.00 0.00 2.18
1602 1802 3.449737 CCCTGATGCATTGGAGATTGTTT 59.550 43.478 17.86 0.00 0.00 2.83
1604 1804 2.242965 TCCCTGATGCATTGGAGATTGT 59.757 45.455 17.86 0.00 0.00 2.71
1625 1851 9.772973 GGTTAAAATTTAACCAGTTCCTTGAAT 57.227 29.630 31.68 0.00 44.72 2.57
1626 1852 8.205512 GGGTTAAAATTTAACCAGTTCCTTGAA 58.794 33.333 34.87 0.00 46.58 2.69
1627 1853 7.202020 GGGGTTAAAATTTAACCAGTTCCTTGA 60.202 37.037 34.87 0.00 46.58 3.02
1628 1854 6.932400 GGGGTTAAAATTTAACCAGTTCCTTG 59.068 38.462 34.87 0.00 46.58 3.61
1629 1855 6.043474 GGGGGTTAAAATTTAACCAGTTCCTT 59.957 38.462 34.87 0.00 46.58 3.36
1630 1856 5.544948 GGGGGTTAAAATTTAACCAGTTCCT 59.455 40.000 34.87 0.00 46.58 3.36
1631 1857 5.307456 TGGGGGTTAAAATTTAACCAGTTCC 59.693 40.000 34.87 29.11 46.58 3.62
1632 1858 6.422344 TGGGGGTTAAAATTTAACCAGTTC 57.578 37.500 34.87 23.10 46.58 3.01
1633 1859 5.221762 GCTGGGGGTTAAAATTTAACCAGTT 60.222 40.000 34.87 0.00 46.58 3.16
1634 1860 4.285003 GCTGGGGGTTAAAATTTAACCAGT 59.715 41.667 34.87 0.00 46.58 4.00
1635 1861 4.284746 TGCTGGGGGTTAAAATTTAACCAG 59.715 41.667 34.87 27.41 46.58 4.00
1636 1862 4.232091 TGCTGGGGGTTAAAATTTAACCA 58.768 39.130 34.87 21.28 46.58 3.67
1637 1863 4.285003 ACTGCTGGGGGTTAAAATTTAACC 59.715 41.667 29.90 29.90 44.64 2.85
1638 1864 5.011227 TGACTGCTGGGGGTTAAAATTTAAC 59.989 40.000 17.64 17.64 0.00 2.01
1639 1865 5.011227 GTGACTGCTGGGGGTTAAAATTTAA 59.989 40.000 0.00 0.00 0.00 1.52
1640 1866 4.525100 GTGACTGCTGGGGGTTAAAATTTA 59.475 41.667 0.00 0.00 0.00 1.40
1641 1867 3.323691 GTGACTGCTGGGGGTTAAAATTT 59.676 43.478 0.00 0.00 0.00 1.82
1642 1868 2.897326 GTGACTGCTGGGGGTTAAAATT 59.103 45.455 0.00 0.00 0.00 1.82
1643 1869 2.158385 TGTGACTGCTGGGGGTTAAAAT 60.158 45.455 0.00 0.00 0.00 1.82
1644 1870 1.215673 TGTGACTGCTGGGGGTTAAAA 59.784 47.619 0.00 0.00 0.00 1.52
1645 1871 0.847373 TGTGACTGCTGGGGGTTAAA 59.153 50.000 0.00 0.00 0.00 1.52
1646 1872 1.072266 ATGTGACTGCTGGGGGTTAA 58.928 50.000 0.00 0.00 0.00 2.01
1647 1873 0.327924 CATGTGACTGCTGGGGGTTA 59.672 55.000 0.00 0.00 0.00 2.85
1648 1874 1.075482 CATGTGACTGCTGGGGGTT 59.925 57.895 0.00 0.00 0.00 4.11
1668 1894 7.449704 TGCCCAAAATGCCTAAAATGTAAAAAT 59.550 29.630 0.00 0.00 0.00 1.82
1673 1899 4.622695 GCTGCCCAAAATGCCTAAAATGTA 60.623 41.667 0.00 0.00 0.00 2.29
1722 1948 4.270008 AGGCCTCGTGCTGTAAATAAAAT 58.730 39.130 0.00 0.00 40.92 1.82
1727 1954 3.007635 GTTTAGGCCTCGTGCTGTAAAT 58.992 45.455 9.68 0.00 40.92 1.40
1737 1964 3.804873 GCAAAGAGATAGTTTAGGCCTCG 59.195 47.826 9.68 0.00 0.00 4.63
1738 1965 4.130857 GGCAAAGAGATAGTTTAGGCCTC 58.869 47.826 9.68 0.00 36.04 4.70
1741 1971 4.518249 ACTGGCAAAGAGATAGTTTAGGC 58.482 43.478 0.00 0.00 0.00 3.93
1748 1978 2.693591 TCGGGTACTGGCAAAGAGATAG 59.306 50.000 0.00 0.00 33.92 2.08
1757 1987 2.366266 GGTAATGTATCGGGTACTGGCA 59.634 50.000 0.00 0.00 34.27 4.92
1800 2030 5.670485 TGCAAAGATGGAACTACATACGAT 58.330 37.500 0.00 0.00 0.00 3.73
1846 2076 5.984926 TGTTTTTCCTGATCTGCATGAAAAC 59.015 36.000 0.00 13.95 44.92 2.43
1890 2120 0.883833 CAATGCCGAAACTGAAGCCT 59.116 50.000 0.00 0.00 0.00 4.58
1893 2123 2.642139 ATGCAATGCCGAAACTGAAG 57.358 45.000 1.53 0.00 0.00 3.02
1897 2127 2.807392 CCAAAAATGCAATGCCGAAACT 59.193 40.909 1.53 0.00 0.00 2.66
2007 2237 2.040544 CATCCCACGTTGCCCAGAC 61.041 63.158 0.00 0.00 0.00 3.51
2057 2287 4.141846 GGTGGATAGTGCAGAAGAGAATCA 60.142 45.833 0.00 0.00 37.82 2.57
2078 2308 7.013274 CCAAATCGTCATATGGAAAACTATGGT 59.987 37.037 2.13 0.00 34.82 3.55
2089 2319 4.641396 TCTAAGCCCAAATCGTCATATGG 58.359 43.478 2.13 0.00 0.00 2.74
2134 2365 6.980416 AAGTAGGTTTCTGTACTGTCTTCT 57.020 37.500 0.00 0.00 29.71 2.85
2155 2386 6.868339 GGTCAAACCACATATTCCAAGAAAAG 59.132 38.462 0.00 0.00 38.42 2.27
2207 2438 9.695526 CAAAAGTGGATTTGAGTATGAATTCAA 57.304 29.630 13.09 0.00 41.73 2.69
2234 2465 8.587952 AAACAACCAATTCTAAAGCATAACAC 57.412 30.769 0.00 0.00 0.00 3.32
2325 2556 0.553333 TGGTGGTGGGTCACATGAAA 59.447 50.000 0.00 0.00 39.27 2.69
2335 2566 2.025416 TCAATGGTCTAATGGTGGTGGG 60.025 50.000 0.00 0.00 0.00 4.61
2336 2567 3.364460 TCAATGGTCTAATGGTGGTGG 57.636 47.619 0.00 0.00 0.00 4.61
2338 2569 3.290710 GCATCAATGGTCTAATGGTGGT 58.709 45.455 0.00 0.00 0.00 4.16
2339 2570 2.624838 GGCATCAATGGTCTAATGGTGG 59.375 50.000 0.00 0.00 0.00 4.61
2340 2571 3.559069 AGGCATCAATGGTCTAATGGTG 58.441 45.455 0.00 0.00 0.00 4.17
2342 2573 3.824133 TGAGGCATCAATGGTCTAATGG 58.176 45.455 0.00 0.00 30.61 3.16
2343 2574 4.825634 ACATGAGGCATCAATGGTCTAATG 59.174 41.667 4.62 0.00 39.39 1.90
2344 2575 5.057843 ACATGAGGCATCAATGGTCTAAT 57.942 39.130 4.62 0.00 39.39 1.73
2345 2576 4.080413 TGACATGAGGCATCAATGGTCTAA 60.080 41.667 22.73 8.85 39.39 2.10
2346 2577 3.455543 TGACATGAGGCATCAATGGTCTA 59.544 43.478 22.73 12.38 39.39 2.59
2347 2578 2.240414 TGACATGAGGCATCAATGGTCT 59.760 45.455 22.73 0.00 39.39 3.85
2348 2579 2.646930 TGACATGAGGCATCAATGGTC 58.353 47.619 18.41 18.41 39.39 4.02
2349 2580 2.812836 TGACATGAGGCATCAATGGT 57.187 45.000 4.62 4.12 39.39 3.55
2350 2581 3.219281 TCATGACATGAGGCATCAATGG 58.781 45.455 14.24 0.42 39.39 3.16
2351 2582 6.374333 TGATATCATGACATGAGGCATCAATG 59.626 38.462 24.14 4.69 43.53 2.82
2352 2583 6.374613 GTGATATCATGACATGAGGCATCAAT 59.625 38.462 26.11 12.62 43.53 2.57
2353 2584 5.704053 GTGATATCATGACATGAGGCATCAA 59.296 40.000 26.11 15.87 43.53 2.57
2354 2585 5.012768 AGTGATATCATGACATGAGGCATCA 59.987 40.000 23.31 23.31 43.53 3.07
2355 2586 5.489249 AGTGATATCATGACATGAGGCATC 58.511 41.667 22.00 21.00 43.53 3.91
2356 2587 5.500546 AGTGATATCATGACATGAGGCAT 57.499 39.130 22.00 14.79 43.53 4.40
2357 2588 4.968971 AGTGATATCATGACATGAGGCA 57.031 40.909 22.00 16.13 43.53 4.75
2358 2589 7.918536 ATAAAGTGATATCATGACATGAGGC 57.081 36.000 22.00 14.05 43.53 4.70
2370 2601 9.846248 GGCAACCAAATCATATAAAGTGATATC 57.154 33.333 0.00 0.00 35.35 1.63
2391 2622 5.254115 ACCATTAGAACTTAGAAGGGCAAC 58.746 41.667 0.00 0.00 0.00 4.17
2392 2623 5.250774 AGACCATTAGAACTTAGAAGGGCAA 59.749 40.000 0.00 0.00 0.00 4.52
2393 2624 4.783227 AGACCATTAGAACTTAGAAGGGCA 59.217 41.667 0.00 0.00 0.00 5.36
2394 2625 5.360649 AGACCATTAGAACTTAGAAGGGC 57.639 43.478 0.00 0.00 0.00 5.19
2395 2626 8.080363 AGTTAGACCATTAGAACTTAGAAGGG 57.920 38.462 0.00 0.00 0.00 3.95
2401 2632 9.597681 CCCCTATAGTTAGACCATTAGAACTTA 57.402 37.037 0.00 0.00 34.15 2.24
2402 2633 8.072480 ACCCCTATAGTTAGACCATTAGAACTT 58.928 37.037 0.00 0.00 34.15 2.66
2403 2634 7.509659 CACCCCTATAGTTAGACCATTAGAACT 59.490 40.741 0.00 0.00 36.21 3.01
2404 2635 7.508296 TCACCCCTATAGTTAGACCATTAGAAC 59.492 40.741 0.00 0.00 0.00 3.01
2405 2636 7.598248 TCACCCCTATAGTTAGACCATTAGAA 58.402 38.462 0.00 0.00 0.00 2.10
2406 2637 7.170554 TCACCCCTATAGTTAGACCATTAGA 57.829 40.000 0.00 0.00 0.00 2.10
2407 2638 7.850935 TTCACCCCTATAGTTAGACCATTAG 57.149 40.000 0.00 0.00 0.00 1.73
2408 2639 8.808240 AATTCACCCCTATAGTTAGACCATTA 57.192 34.615 0.00 0.00 0.00 1.90
2409 2640 7.572861 AGAATTCACCCCTATAGTTAGACCATT 59.427 37.037 8.44 0.00 0.00 3.16
2410 2641 7.082972 AGAATTCACCCCTATAGTTAGACCAT 58.917 38.462 8.44 0.00 0.00 3.55
2411 2642 6.449956 AGAATTCACCCCTATAGTTAGACCA 58.550 40.000 8.44 0.00 0.00 4.02
2412 2643 6.997942 AGAATTCACCCCTATAGTTAGACC 57.002 41.667 8.44 0.00 0.00 3.85
2445 2676 7.824672 ACAAATGGAGAAGATGACAATTCTTC 58.175 34.615 9.80 9.80 46.15 2.87
2451 2682 5.877012 GCTAGACAAATGGAGAAGATGACAA 59.123 40.000 0.00 0.00 0.00 3.18
2488 2719 3.190535 GTGAGGCGTGGATTTACAATGTT 59.809 43.478 0.00 0.00 0.00 2.71
2489 2720 2.747446 GTGAGGCGTGGATTTACAATGT 59.253 45.455 0.00 0.00 0.00 2.71
2519 2750 8.924511 AGTAATATTACAATTGCCATAGCAGT 57.075 30.769 24.05 0.00 42.27 4.40
2548 2779 6.191315 ACCTTGATCACTATCACTAGTCACT 58.809 40.000 0.00 0.00 41.87 3.41
2600 2831 2.497273 GGCTTGGAAACCAGCATAACAT 59.503 45.455 0.00 0.00 33.81 2.71
2636 2867 7.286775 AGACAATTGCAGTAGAAGGGTTTAAAA 59.713 33.333 5.05 0.00 0.00 1.52
2637 2868 6.775629 AGACAATTGCAGTAGAAGGGTTTAAA 59.224 34.615 5.05 0.00 0.00 1.52
2638 2869 6.303839 AGACAATTGCAGTAGAAGGGTTTAA 58.696 36.000 5.05 0.00 0.00 1.52
2639 2870 5.876357 AGACAATTGCAGTAGAAGGGTTTA 58.124 37.500 5.05 0.00 0.00 2.01
2644 2901 9.553064 AGAATATTAGACAATTGCAGTAGAAGG 57.447 33.333 5.05 0.00 0.00 3.46
2733 2990 8.879759 TGACTAACGAATTATTGAAAGGATCAC 58.120 33.333 0.00 0.00 37.92 3.06
2844 3101 4.880120 GTGATCTCCTTTTCTGATGCATGA 59.120 41.667 2.46 0.00 0.00 3.07
2845 3102 4.638865 TGTGATCTCCTTTTCTGATGCATG 59.361 41.667 2.46 0.00 0.00 4.06
2940 3197 4.762289 ACTGGAATCCATCTAACTGTCC 57.238 45.455 0.87 0.00 30.82 4.02
3074 3331 1.617839 AAGCCTCTAGCCTTGCCCT 60.618 57.895 0.00 0.00 45.47 5.19
3120 3377 5.690865 TCGGGGCAAGTTAAAGAATATCAT 58.309 37.500 0.00 0.00 0.00 2.45
3123 3380 4.278419 GCATCGGGGCAAGTTAAAGAATAT 59.722 41.667 0.00 0.00 0.00 1.28
3137 3394 3.219198 GGATTGTGGCATCGGGGC 61.219 66.667 0.00 0.00 43.73 5.80
3138 3395 1.825191 CTGGATTGTGGCATCGGGG 60.825 63.158 0.00 0.00 0.00 5.73
3205 3462 3.370840 ACTCATTTATCCTGCCTGCAA 57.629 42.857 0.00 0.00 0.00 4.08
3233 3490 8.295288 CAGTTATCAGATTGAGCTTGAAACTTT 58.705 33.333 0.00 0.00 0.00 2.66
3240 3497 6.981762 AGTTCAGTTATCAGATTGAGCTTG 57.018 37.500 0.00 0.00 28.50 4.01
3265 3522 8.567948 CAGTGGTAAAACAAATCAGACTATTGT 58.432 33.333 0.00 0.00 38.85 2.71
3273 3530 5.762045 CCAGACAGTGGTAAAACAAATCAG 58.238 41.667 0.00 0.00 42.17 2.90
3308 3567 4.375272 CTGCGAAACATGGTAGAGATCAT 58.625 43.478 0.00 0.00 0.00 2.45
3346 3605 2.372074 GCATACCCCTTGGACCGGA 61.372 63.158 9.46 0.00 34.81 5.14
3347 3606 2.192175 GCATACCCCTTGGACCGG 59.808 66.667 0.00 0.00 34.81 5.28
3522 3793 8.113462 AGGGGTTTATACAATTCACACAGTTAT 58.887 33.333 0.00 0.00 0.00 1.89
3527 3798 5.478679 CCAAGGGGTTTATACAATTCACACA 59.521 40.000 0.00 0.00 0.00 3.72
3607 3878 7.218228 TCAGTACGTAAAGTCTATTGTTCCA 57.782 36.000 0.00 0.00 0.00 3.53
3619 3890 7.704899 TCCATATCATGTGTTCAGTACGTAAAG 59.295 37.037 0.00 0.00 0.00 1.85
3655 3926 8.599055 ATCAGATATACAACAGCACATAACAG 57.401 34.615 0.00 0.00 0.00 3.16
3693 3964 2.190538 TGGTGCATCTGGAGATCTTCA 58.809 47.619 3.02 3.02 31.21 3.02
3777 4048 7.617533 ATGTTACTGTTGAATTACGCAAAAC 57.382 32.000 0.00 0.00 0.00 2.43
3950 4222 5.394663 CCACCAACACAAATTTTGTACCTCA 60.395 40.000 14.13 0.00 43.23 3.86
4106 4380 4.191544 CCATGTTTGGTGATAGTGACGAT 58.808 43.478 0.00 0.00 38.30 3.73
4250 4524 6.108687 TGATACACTGTTTGAGGATGATCAC 58.891 40.000 0.00 0.00 0.00 3.06
4341 4615 7.230712 TCAGAGTCACACAACTGAAGATAGTAA 59.769 37.037 0.00 0.00 36.63 2.24
4384 4658 2.497675 GACAGATCTACAGAACCTGCCA 59.502 50.000 0.00 0.00 34.37 4.92
4385 4659 2.497675 TGACAGATCTACAGAACCTGCC 59.502 50.000 0.00 3.09 34.37 4.85
4408 4682 2.359975 CGCCCAACCCTCTTCCAC 60.360 66.667 0.00 0.00 0.00 4.02
4428 4702 3.058224 GTGAACGGCAATGCTAGTTCTTT 60.058 43.478 30.06 8.61 41.98 2.52


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

AutoCloner maintained by Alex Coulton.