Multiple sequence alignment - TraesCS2D01G073700

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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 TraesCS2D01G073700 chr2D 100.000 2639 0 0 1 2639 30981064 30978426 0.000000e+00 4874.0
1 TraesCS2D01G073700 chr2D 93.282 908 27 7 873 1774 30935696 30934817 0.000000e+00 1308.0
2 TraesCS2D01G073700 chr2D 91.111 180 15 1 2257 2435 30933222 30933043 2.620000e-60 243.0
3 TraesCS2D01G073700 chr2D 90.769 65 5 1 1928 1992 30934820 30934757 4.680000e-13 86.1
4 TraesCS2D01G073700 chr2A 97.790 905 11 3 877 1774 33271147 33270245 0.000000e+00 1552.0
5 TraesCS2D01G073700 chr2A 94.269 506 26 2 10 515 33272623 33272121 0.000000e+00 771.0
6 TraesCS2D01G073700 chr2A 96.899 258 5 2 1928 2184 33270246 33269991 1.880000e-116 429.0
7 TraesCS2D01G073700 chr2A 97.525 202 4 1 2222 2422 33269992 33269791 6.990000e-91 344.0
8 TraesCS2D01G073700 chr2A 98.810 84 1 0 2556 2639 33269650 33269567 1.640000e-32 150.0
9 TraesCS2D01G073700 chr2A 90.566 106 5 2 652 757 33271238 33271138 4.580000e-28 135.0
10 TraesCS2D01G073700 chr2A 100.000 35 0 0 2521 2555 33269715 33269681 6.100000e-07 65.8
11 TraesCS2D01G073700 chr2A 100.000 28 0 0 2413 2440 33269739 33269712 5.000000e-03 52.8
12 TraesCS2D01G073700 chr2B 93.889 900 46 6 877 1774 51228636 51229528 0.000000e+00 1349.0
13 TraesCS2D01G073700 chr2B 91.698 530 26 10 1 515 51227816 51228342 0.000000e+00 719.0
14 TraesCS2D01G073700 chr2B 90.149 335 25 6 1928 2261 51229525 51229852 1.880000e-116 429.0
15 TraesCS2D01G073700 chr2B 91.500 200 7 4 559 753 51228444 51228638 1.560000e-67 267.0
16 TraesCS2D01G073700 chr2B 88.050 159 17 2 1772 1929 310105254 310105411 1.250000e-43 187.0
17 TraesCS2D01G073700 chr2B 84.393 173 19 6 1765 1929 550532679 550532851 2.100000e-36 163.0
18 TraesCS2D01G073700 chr2B 84.211 171 18 5 1768 1930 454845572 454845741 9.780000e-35 158.0
19 TraesCS2D01G073700 chr7D 90.973 709 57 7 934 1640 133327725 133327022 0.000000e+00 948.0
20 TraesCS2D01G073700 chr7D 91.515 165 6 4 1773 1929 412879593 412879757 1.230000e-53 220.0
21 TraesCS2D01G073700 chr7A 90.409 709 61 7 934 1640 131937295 131936592 0.000000e+00 926.0
22 TraesCS2D01G073700 chr7B 88.608 711 70 9 934 1640 94630775 94630072 0.000000e+00 854.0
23 TraesCS2D01G073700 chr1A 90.625 160 13 1 1773 1932 584472134 584471977 7.400000e-51 211.0
24 TraesCS2D01G073700 chr5D 88.535 157 18 0 1773 1929 361671710 361671866 9.640000e-45 191.0
25 TraesCS2D01G073700 chr5D 98.113 53 1 0 786 838 59230352 59230404 2.800000e-15 93.5
26 TraesCS2D01G073700 chr5A 86.957 161 10 6 1772 1928 419674755 419674602 1.260000e-38 171.0
27 TraesCS2D01G073700 chr5A 94.231 52 3 0 2558 2609 689931017 689930966 2.180000e-11 80.5
28 TraesCS2D01G073700 chr5B 85.030 167 16 4 1768 1929 27983541 27983379 7.560000e-36 161.0
29 TraesCS2D01G073700 chr6B 83.708 178 16 9 1764 1931 713154147 713153973 3.520000e-34 156.0
30 TraesCS2D01G073700 chr1B 89.216 102 9 2 778 877 17871546 17871445 2.760000e-25 126.0
31 TraesCS2D01G073700 chr1B 89.109 101 9 2 778 876 547259366 547259466 9.920000e-25 124.0


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 TraesCS2D01G073700 chr2D 30978426 30981064 2638 True 4874.00 4874 100.000000 1 2639 1 chr2D.!!$R1 2638
1 TraesCS2D01G073700 chr2D 30933043 30935696 2653 True 545.70 1308 91.720667 873 2435 3 chr2D.!!$R2 1562
2 TraesCS2D01G073700 chr2A 33269567 33272623 3056 True 437.45 1552 96.982375 10 2639 8 chr2A.!!$R1 2629
3 TraesCS2D01G073700 chr2B 51227816 51229852 2036 False 691.00 1349 91.809000 1 2261 4 chr2B.!!$F4 2260
4 TraesCS2D01G073700 chr7D 133327022 133327725 703 True 948.00 948 90.973000 934 1640 1 chr7D.!!$R1 706
5 TraesCS2D01G073700 chr7A 131936592 131937295 703 True 926.00 926 90.409000 934 1640 1 chr7A.!!$R1 706
6 TraesCS2D01G073700 chr7B 94630072 94630775 703 True 854.00 854 88.608000 934 1640 1 chr7B.!!$R1 706

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
862 1643 0.326264 CCCAGTCTTAACCTGCTGCT 59.674 55.0 0.0 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2457 4581 0.035343 GCCCCTGAACCTCCTGTAAC 60.035 60.0 0.0 0.0 0.0 2.5 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
23 24 5.689383 AATCACAAAATCTACAAGCGTGT 57.311 34.783 10.83 10.83 42.09 4.49
35 36 3.155501 ACAAGCGTGTAGGTCTTAGACT 58.844 45.455 12.41 1.35 35.72 3.24
53 58 8.922676 TCTTAGACTAGCAGTTAAAATTTCACG 58.077 33.333 0.00 0.00 0.00 4.35
109 124 6.401955 TGTTTAGCAAAGCAACAAAAGAAC 57.598 33.333 0.00 0.00 0.00 3.01
116 131 0.572125 GCAACAAAAGAACGCTGCAC 59.428 50.000 0.00 0.00 0.00 4.57
149 164 3.058639 CACAAACTTGCTAAGCCAGAGAC 60.059 47.826 0.00 0.00 0.00 3.36
157 172 2.163815 GCTAAGCCAGAGACGACTAACA 59.836 50.000 0.00 0.00 0.00 2.41
169 184 5.452777 AGACGACTAACAAAGTTACCGTAC 58.547 41.667 10.48 0.00 39.07 3.67
228 244 2.972713 TCAACCCTCTCACACTAAGCTT 59.027 45.455 3.48 3.48 0.00 3.74
233 249 3.381908 CCCTCTCACACTAAGCTTCGTAT 59.618 47.826 0.00 0.00 0.00 3.06
238 254 7.255312 CCTCTCACACTAAGCTTCGTATCTTAT 60.255 40.741 0.00 0.00 0.00 1.73
276 292 8.394971 ACAATGAGTTCATACAAACATCTGAA 57.605 30.769 0.00 0.00 35.10 3.02
539 632 6.675413 TCTAGGTTTGTCCAAGCTAAGTTA 57.325 37.500 0.00 0.00 43.41 2.24
540 633 6.698380 TCTAGGTTTGTCCAAGCTAAGTTAG 58.302 40.000 5.47 5.47 43.41 2.34
541 634 4.072839 AGGTTTGTCCAAGCTAAGTTAGC 58.927 43.478 24.60 24.60 41.66 3.09
542 635 3.818773 GGTTTGTCCAAGCTAAGTTAGCA 59.181 43.478 31.23 12.32 44.28 3.49
543 636 4.459337 GGTTTGTCCAAGCTAAGTTAGCAT 59.541 41.667 31.23 20.40 44.28 3.79
544 637 5.619981 GGTTTGTCCAAGCTAAGTTAGCATG 60.620 44.000 31.23 28.51 46.74 4.06
545 638 8.972074 GGTTTGTCCAAGCTAAGTTAGCATGC 62.972 46.154 31.23 19.54 46.07 4.06
567 660 9.838975 CATGCTGAAGTTAGATAGAGTGTATAG 57.161 37.037 0.00 0.00 0.00 1.31
614 708 7.409697 ACATCAAATCGGTTTCATTAGATTCG 58.590 34.615 0.00 0.00 32.79 3.34
749 1530 1.741706 TGGAGCGAAGGAAGTACTACG 59.258 52.381 0.00 0.00 0.00 3.51
750 1531 1.742268 GGAGCGAAGGAAGTACTACGT 59.258 52.381 0.00 0.00 0.00 3.57
751 1532 2.939103 GGAGCGAAGGAAGTACTACGTA 59.061 50.000 0.00 0.00 0.00 3.57
752 1533 3.242576 GGAGCGAAGGAAGTACTACGTAC 60.243 52.174 0.00 0.00 39.10 3.67
754 1535 3.620821 AGCGAAGGAAGTACTACGTACTC 59.379 47.826 7.09 0.00 46.96 2.59
755 1536 3.372206 GCGAAGGAAGTACTACGTACTCA 59.628 47.826 7.09 0.00 46.96 3.41
756 1537 4.493872 GCGAAGGAAGTACTACGTACTCAG 60.494 50.000 7.09 0.00 46.96 3.35
757 1538 4.629200 CGAAGGAAGTACTACGTACTCAGT 59.371 45.833 7.09 0.00 46.96 3.41
758 1539 5.445673 CGAAGGAAGTACTACGTACTCAGTG 60.446 48.000 7.09 0.00 46.96 3.66
759 1540 4.260170 AGGAAGTACTACGTACTCAGTGG 58.740 47.826 7.09 0.00 46.96 4.00
760 1541 4.006319 GGAAGTACTACGTACTCAGTGGT 58.994 47.826 7.09 1.09 46.96 4.16
761 1542 4.142730 GGAAGTACTACGTACTCAGTGGTG 60.143 50.000 7.09 0.00 46.96 4.17
762 1543 3.341823 AGTACTACGTACTCAGTGGTGG 58.658 50.000 0.00 0.00 44.86 4.61
763 1544 2.574006 ACTACGTACTCAGTGGTGGA 57.426 50.000 0.00 0.00 32.07 4.02
764 1545 2.434428 ACTACGTACTCAGTGGTGGAG 58.566 52.381 0.00 0.00 38.36 3.86
765 1546 2.039480 ACTACGTACTCAGTGGTGGAGA 59.961 50.000 0.00 0.00 36.26 3.71
766 1547 1.245732 ACGTACTCAGTGGTGGAGAC 58.754 55.000 0.00 0.00 36.26 3.36
767 1548 1.244816 CGTACTCAGTGGTGGAGACA 58.755 55.000 0.00 0.00 36.26 3.41
768 1549 1.200252 CGTACTCAGTGGTGGAGACAG 59.800 57.143 0.00 0.00 44.46 3.51
769 1550 1.546476 GTACTCAGTGGTGGAGACAGG 59.454 57.143 0.00 0.00 44.46 4.00
770 1551 1.294780 CTCAGTGGTGGAGACAGGC 59.705 63.158 0.00 0.00 44.46 4.85
771 1552 2.177594 CTCAGTGGTGGAGACAGGCC 62.178 65.000 0.00 0.00 44.46 5.19
772 1553 2.205462 AGTGGTGGAGACAGGCCT 59.795 61.111 0.00 0.00 44.46 5.19
773 1554 0.904865 CAGTGGTGGAGACAGGCCTA 60.905 60.000 3.98 0.00 44.46 3.93
774 1555 0.616111 AGTGGTGGAGACAGGCCTAG 60.616 60.000 3.98 2.19 44.46 3.02
775 1556 1.306141 TGGTGGAGACAGGCCTAGG 60.306 63.158 3.98 3.67 44.46 3.02
776 1557 2.066999 GGTGGAGACAGGCCTAGGG 61.067 68.421 3.98 0.00 44.46 3.53
777 1558 2.365635 TGGAGACAGGCCTAGGGC 60.366 66.667 27.51 27.51 41.93 5.19
791 1572 5.506730 GCCTAGGGCTTCCTTATAATTCT 57.493 43.478 11.72 0.00 46.69 2.40
792 1573 5.882040 GCCTAGGGCTTCCTTATAATTCTT 58.118 41.667 11.72 0.00 46.69 2.52
793 1574 5.707764 GCCTAGGGCTTCCTTATAATTCTTG 59.292 44.000 11.72 0.00 46.69 3.02
794 1575 6.465894 GCCTAGGGCTTCCTTATAATTCTTGA 60.466 42.308 11.72 0.00 46.69 3.02
795 1576 7.694093 CCTAGGGCTTCCTTATAATTCTTGAT 58.306 38.462 0.00 0.00 41.96 2.57
796 1577 8.826765 CCTAGGGCTTCCTTATAATTCTTGATA 58.173 37.037 0.00 0.00 41.96 2.15
799 1580 9.936329 AGGGCTTCCTTATAATTCTTGATAAAA 57.064 29.630 0.00 0.00 37.72 1.52
837 1618 8.668353 TCACAGAAATTTATCAGTCAACATAGC 58.332 33.333 0.00 0.00 0.00 2.97
838 1619 8.453320 CACAGAAATTTATCAGTCAACATAGCA 58.547 33.333 0.00 0.00 0.00 3.49
839 1620 9.182214 ACAGAAATTTATCAGTCAACATAGCAT 57.818 29.630 0.00 0.00 0.00 3.79
843 1624 7.678947 ATTTATCAGTCAACATAGCATAGGC 57.321 36.000 0.00 0.00 41.61 3.93
844 1625 3.475566 TCAGTCAACATAGCATAGGCC 57.524 47.619 0.00 0.00 42.56 5.19
845 1626 2.104792 TCAGTCAACATAGCATAGGCCC 59.895 50.000 0.00 0.00 42.56 5.80
846 1627 2.126882 AGTCAACATAGCATAGGCCCA 58.873 47.619 0.00 0.00 42.56 5.36
847 1628 2.105477 AGTCAACATAGCATAGGCCCAG 59.895 50.000 0.00 0.00 42.56 4.45
848 1629 2.126882 TCAACATAGCATAGGCCCAGT 58.873 47.619 0.00 0.00 42.56 4.00
849 1630 2.104792 TCAACATAGCATAGGCCCAGTC 59.895 50.000 0.00 0.00 42.56 3.51
850 1631 2.105477 CAACATAGCATAGGCCCAGTCT 59.895 50.000 0.00 0.00 42.56 3.24
851 1632 2.412591 ACATAGCATAGGCCCAGTCTT 58.587 47.619 0.00 0.00 42.56 3.01
852 1633 3.587498 ACATAGCATAGGCCCAGTCTTA 58.413 45.455 0.00 0.00 42.56 2.10
853 1634 3.973973 ACATAGCATAGGCCCAGTCTTAA 59.026 43.478 0.00 0.00 42.56 1.85
854 1635 4.202367 ACATAGCATAGGCCCAGTCTTAAC 60.202 45.833 0.00 0.00 42.56 2.01
855 1636 1.490910 AGCATAGGCCCAGTCTTAACC 59.509 52.381 0.00 0.00 42.56 2.85
856 1637 1.490910 GCATAGGCCCAGTCTTAACCT 59.509 52.381 0.00 0.00 34.42 3.50
857 1638 2.746472 GCATAGGCCCAGTCTTAACCTG 60.746 54.545 0.00 0.00 31.79 4.00
858 1639 0.909623 TAGGCCCAGTCTTAACCTGC 59.090 55.000 0.00 0.00 31.79 4.85
859 1640 0.842467 AGGCCCAGTCTTAACCTGCT 60.842 55.000 0.00 0.00 0.00 4.24
860 1641 0.678048 GGCCCAGTCTTAACCTGCTG 60.678 60.000 0.00 0.00 0.00 4.41
861 1642 1.308783 GCCCAGTCTTAACCTGCTGC 61.309 60.000 0.00 0.00 0.00 5.25
862 1643 0.326264 CCCAGTCTTAACCTGCTGCT 59.674 55.000 0.00 0.00 0.00 4.24
863 1644 1.555075 CCCAGTCTTAACCTGCTGCTA 59.445 52.381 0.00 0.00 0.00 3.49
864 1645 2.027192 CCCAGTCTTAACCTGCTGCTAA 60.027 50.000 0.00 0.00 0.00 3.09
865 1646 3.370953 CCCAGTCTTAACCTGCTGCTAAT 60.371 47.826 0.00 0.00 0.00 1.73
866 1647 4.265073 CCAGTCTTAACCTGCTGCTAATT 58.735 43.478 0.00 0.00 0.00 1.40
867 1648 4.333926 CCAGTCTTAACCTGCTGCTAATTC 59.666 45.833 0.00 0.00 0.00 2.17
868 1649 4.333926 CAGTCTTAACCTGCTGCTAATTCC 59.666 45.833 0.00 0.00 0.00 3.01
869 1650 3.309954 GTCTTAACCTGCTGCTAATTCCG 59.690 47.826 0.00 0.00 0.00 4.30
870 1651 1.663695 TAACCTGCTGCTAATTCCGC 58.336 50.000 0.00 0.00 0.00 5.54
871 1652 1.032114 AACCTGCTGCTAATTCCGCC 61.032 55.000 0.00 0.00 0.00 6.13
1434 2225 0.179000 GCGACATCATGGTCTTCCCT 59.821 55.000 0.00 0.00 35.63 4.20
1718 2509 2.304092 TGTCGGATTACGTGCCTAGAT 58.696 47.619 0.00 0.00 44.69 1.98
1756 2548 2.460757 GGTTTTCTACCGCTACCACA 57.539 50.000 0.00 0.00 37.12 4.17
1778 2570 6.127810 CATGCATGCATGTTATATACTCCC 57.872 41.667 40.30 7.03 46.20 4.30
1779 2571 5.503634 TGCATGCATGTTATATACTCCCT 57.496 39.130 26.79 0.00 0.00 4.20
1780 2572 5.491070 TGCATGCATGTTATATACTCCCTC 58.509 41.667 26.79 6.41 0.00 4.30
1781 2573 4.878397 GCATGCATGTTATATACTCCCTCC 59.122 45.833 26.79 1.51 0.00 4.30
1782 2574 4.801330 TGCATGTTATATACTCCCTCCG 57.199 45.455 0.00 0.00 0.00 4.63
1783 2575 4.157246 TGCATGTTATATACTCCCTCCGT 58.843 43.478 0.00 0.00 0.00 4.69
1784 2576 4.591498 TGCATGTTATATACTCCCTCCGTT 59.409 41.667 0.00 0.00 0.00 4.44
1785 2577 5.169295 GCATGTTATATACTCCCTCCGTTC 58.831 45.833 0.00 0.00 0.00 3.95
1786 2578 5.721232 CATGTTATATACTCCCTCCGTTCC 58.279 45.833 0.00 0.00 0.00 3.62
1787 2579 4.154942 TGTTATATACTCCCTCCGTTCCC 58.845 47.826 0.00 0.00 0.00 3.97
1788 2580 4.154942 GTTATATACTCCCTCCGTTCCCA 58.845 47.826 0.00 0.00 0.00 4.37
1789 2581 2.852714 TATACTCCCTCCGTTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
1790 2582 1.961133 ATACTCCCTCCGTTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
1791 2583 1.961133 TACTCCCTCCGTTCCCAAAT 58.039 50.000 0.00 0.00 0.00 2.32
1792 2584 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
1793 2585 2.488836 ACTCCCTCCGTTCCCAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
1794 2586 3.660959 ACTCCCTCCGTTCCCAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
1795 2587 4.042174 ACTCCCTCCGTTCCCAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
1796 2588 4.102681 ACTCCCTCCGTTCCCAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
1797 2589 4.042174 TCCCTCCGTTCCCAAATATAAGT 58.958 43.478 0.00 0.00 0.00 2.24
1798 2590 4.475747 TCCCTCCGTTCCCAAATATAAGTT 59.524 41.667 0.00 0.00 0.00 2.66
1799 2591 5.044698 TCCCTCCGTTCCCAAATATAAGTTT 60.045 40.000 0.00 0.00 0.00 2.66
1800 2592 5.655090 CCCTCCGTTCCCAAATATAAGTTTT 59.345 40.000 0.00 0.00 0.00 2.43
1801 2593 6.153851 CCCTCCGTTCCCAAATATAAGTTTTT 59.846 38.462 0.00 0.00 0.00 1.94
1802 2594 7.255569 CCTCCGTTCCCAAATATAAGTTTTTC 58.744 38.462 0.00 0.00 0.00 2.29
1803 2595 7.122204 CCTCCGTTCCCAAATATAAGTTTTTCT 59.878 37.037 0.00 0.00 0.00 2.52
1804 2596 9.169592 CTCCGTTCCCAAATATAAGTTTTTCTA 57.830 33.333 0.00 0.00 0.00 2.10
1805 2597 9.169592 TCCGTTCCCAAATATAAGTTTTTCTAG 57.830 33.333 0.00 0.00 0.00 2.43
1806 2598 9.169592 CCGTTCCCAAATATAAGTTTTTCTAGA 57.830 33.333 0.00 0.00 0.00 2.43
1827 2619 9.671279 TCTAGAGATTGCAACAAATAAAGATCA 57.329 29.630 0.00 0.00 0.00 2.92
1832 2624 9.079833 AGATTGCAACAAATAAAGATCAAATCG 57.920 29.630 0.00 0.00 0.00 3.34
1833 2625 8.984891 ATTGCAACAAATAAAGATCAAATCGA 57.015 26.923 0.00 0.00 0.00 3.59
1834 2626 8.809159 TTGCAACAAATAAAGATCAAATCGAA 57.191 26.923 0.00 0.00 0.00 3.71
1835 2627 8.984891 TGCAACAAATAAAGATCAAATCGAAT 57.015 26.923 0.00 0.00 0.00 3.34
1836 2628 8.862074 TGCAACAAATAAAGATCAAATCGAATG 58.138 29.630 0.00 0.00 0.00 2.67
1837 2629 9.075519 GCAACAAATAAAGATCAAATCGAATGA 57.924 29.630 6.72 6.72 0.00 2.57
1846 2638 8.954950 AAGATCAAATCGAATGAATCTACACT 57.045 30.769 8.16 0.00 0.00 3.55
1847 2639 8.954950 AGATCAAATCGAATGAATCTACACTT 57.045 30.769 8.16 0.00 0.00 3.16
1848 2640 9.388506 AGATCAAATCGAATGAATCTACACTTT 57.611 29.630 8.16 0.00 0.00 2.66
1881 2673 9.511272 TGTCTACATACATCCGTATATTGTAGT 57.489 33.333 0.00 0.00 38.60 2.73
1882 2674 9.985318 GTCTACATACATCCGTATATTGTAGTC 57.015 37.037 0.00 0.00 38.60 2.59
1883 2675 9.955102 TCTACATACATCCGTATATTGTAGTCT 57.045 33.333 0.00 0.00 38.60 3.24
1923 2715 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
1924 2716 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
1925 2717 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
1926 2718 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2125 3007 9.974750 GAGCTTGTATACTTTATTTCTGTCAAC 57.025 33.333 4.17 0.00 0.00 3.18
2215 3551 2.277969 GATCCTCATGCCATATCGCTG 58.722 52.381 0.00 0.00 0.00 5.18
2314 4376 3.384668 GCTTTCTTCCAAAGCTTGAACC 58.615 45.455 0.00 0.00 46.64 3.62
2437 4561 8.624776 CAACTTAACAAGAGAATCAAAGACCTT 58.375 33.333 0.00 0.00 37.82 3.50
2438 4562 8.753497 ACTTAACAAGAGAATCAAAGACCTTT 57.247 30.769 0.00 0.00 37.82 3.11
2439 4563 9.190317 ACTTAACAAGAGAATCAAAGACCTTTT 57.810 29.630 0.00 0.00 37.82 2.27
2440 4564 9.455847 CTTAACAAGAGAATCAAAGACCTTTTG 57.544 33.333 0.00 0.00 37.82 2.44
2441 4565 5.836347 ACAAGAGAATCAAAGACCTTTTGC 58.164 37.500 0.00 0.00 37.82 3.68
2442 4566 5.595952 ACAAGAGAATCAAAGACCTTTTGCT 59.404 36.000 0.00 0.00 37.82 3.91
2443 4567 6.772716 ACAAGAGAATCAAAGACCTTTTGCTA 59.227 34.615 0.00 0.00 37.82 3.49
2444 4568 7.285401 ACAAGAGAATCAAAGACCTTTTGCTAA 59.715 33.333 0.00 0.00 37.82 3.09
2445 4569 7.823745 AGAGAATCAAAGACCTTTTGCTAAA 57.176 32.000 0.00 0.00 37.82 1.85
2446 4570 7.652727 AGAGAATCAAAGACCTTTTGCTAAAC 58.347 34.615 0.00 0.00 37.82 2.01
2447 4571 6.749139 AGAATCAAAGACCTTTTGCTAAACC 58.251 36.000 0.00 0.00 0.00 3.27
2448 4572 4.929819 TCAAAGACCTTTTGCTAAACCC 57.070 40.909 0.00 0.00 0.00 4.11
2449 4573 4.282496 TCAAAGACCTTTTGCTAAACCCA 58.718 39.130 0.00 0.00 0.00 4.51
2450 4574 4.098807 TCAAAGACCTTTTGCTAAACCCAC 59.901 41.667 0.00 0.00 0.00 4.61
2451 4575 2.227194 AGACCTTTTGCTAAACCCACG 58.773 47.619 0.00 0.00 0.00 4.94
2452 4576 1.268625 GACCTTTTGCTAAACCCACGG 59.731 52.381 0.00 0.00 0.00 4.94
2453 4577 1.133730 ACCTTTTGCTAAACCCACGGA 60.134 47.619 3.52 0.00 0.00 4.69
2454 4578 2.167662 CCTTTTGCTAAACCCACGGAT 58.832 47.619 0.00 0.00 0.00 4.18
2455 4579 2.094752 CCTTTTGCTAAACCCACGGATG 60.095 50.000 0.00 0.00 0.00 3.51
2456 4580 1.540267 TTTGCTAAACCCACGGATGG 58.460 50.000 0.00 0.00 46.81 3.51
2464 4588 4.954933 CCACGGATGGGTTACAGG 57.045 61.111 0.00 0.00 43.04 4.00
2465 4589 2.292866 CCACGGATGGGTTACAGGA 58.707 57.895 0.00 0.00 43.04 3.86
2466 4590 0.178068 CCACGGATGGGTTACAGGAG 59.822 60.000 0.00 0.00 43.04 3.69
2467 4591 0.178068 CACGGATGGGTTACAGGAGG 59.822 60.000 0.00 0.00 0.00 4.30
2468 4592 0.252558 ACGGATGGGTTACAGGAGGT 60.253 55.000 0.00 0.00 0.00 3.85
2469 4593 0.909623 CGGATGGGTTACAGGAGGTT 59.090 55.000 0.00 0.00 0.00 3.50
2470 4594 1.134491 CGGATGGGTTACAGGAGGTTC 60.134 57.143 0.00 0.00 0.00 3.62
2471 4595 1.913419 GGATGGGTTACAGGAGGTTCA 59.087 52.381 0.00 0.00 0.00 3.18
2472 4596 2.092914 GGATGGGTTACAGGAGGTTCAG 60.093 54.545 0.00 0.00 0.00 3.02
2473 4597 1.358152 TGGGTTACAGGAGGTTCAGG 58.642 55.000 0.00 0.00 0.00 3.86
2474 4598 0.618981 GGGTTACAGGAGGTTCAGGG 59.381 60.000 0.00 0.00 0.00 4.45
2475 4599 0.618981 GGTTACAGGAGGTTCAGGGG 59.381 60.000 0.00 0.00 0.00 4.79
2476 4600 0.035343 GTTACAGGAGGTTCAGGGGC 60.035 60.000 0.00 0.00 0.00 5.80
2477 4601 0.178873 TTACAGGAGGTTCAGGGGCT 60.179 55.000 0.00 0.00 0.00 5.19
2478 4602 0.617820 TACAGGAGGTTCAGGGGCTC 60.618 60.000 0.00 0.00 0.00 4.70
2479 4603 2.285743 AGGAGGTTCAGGGGCTCC 60.286 66.667 0.00 0.00 34.61 4.70
2480 4604 2.285743 GGAGGTTCAGGGGCTCCT 60.286 66.667 0.00 0.00 46.26 3.69
2481 4605 1.925972 GGAGGTTCAGGGGCTCCTT 60.926 63.158 0.00 0.00 42.67 3.36
2482 4606 1.604915 GAGGTTCAGGGGCTCCTTC 59.395 63.158 0.00 0.00 42.67 3.46
2483 4607 1.151810 AGGTTCAGGGGCTCCTTCA 60.152 57.895 0.00 0.00 42.67 3.02
2484 4608 0.551131 AGGTTCAGGGGCTCCTTCAT 60.551 55.000 0.00 0.00 42.67 2.57
2485 4609 0.106967 GGTTCAGGGGCTCCTTCATC 60.107 60.000 0.00 0.00 42.67 2.92
2486 4610 0.915364 GTTCAGGGGCTCCTTCATCT 59.085 55.000 0.00 0.00 42.67 2.90
2487 4611 2.119495 GTTCAGGGGCTCCTTCATCTA 58.881 52.381 0.00 0.00 42.67 1.98
2488 4612 2.505819 GTTCAGGGGCTCCTTCATCTAA 59.494 50.000 0.00 0.00 42.67 2.10
2489 4613 3.066208 TCAGGGGCTCCTTCATCTAAT 57.934 47.619 0.00 0.00 42.67 1.73
2490 4614 3.397527 TCAGGGGCTCCTTCATCTAATT 58.602 45.455 0.00 0.00 42.67 1.40
2491 4615 3.392616 TCAGGGGCTCCTTCATCTAATTC 59.607 47.826 0.00 0.00 42.67 2.17
2492 4616 3.393941 CAGGGGCTCCTTCATCTAATTCT 59.606 47.826 0.00 0.00 42.67 2.40
2493 4617 3.650461 AGGGGCTCCTTCATCTAATTCTC 59.350 47.826 0.00 0.00 41.56 2.87
2494 4618 3.650461 GGGGCTCCTTCATCTAATTCTCT 59.350 47.826 0.00 0.00 0.00 3.10
2495 4619 4.262851 GGGGCTCCTTCATCTAATTCTCTC 60.263 50.000 0.00 0.00 0.00 3.20
2496 4620 4.262851 GGGCTCCTTCATCTAATTCTCTCC 60.263 50.000 0.00 0.00 0.00 3.71
2497 4621 4.346418 GGCTCCTTCATCTAATTCTCTCCA 59.654 45.833 0.00 0.00 0.00 3.86
2498 4622 5.012975 GGCTCCTTCATCTAATTCTCTCCAT 59.987 44.000 0.00 0.00 0.00 3.41
2499 4623 6.165577 GCTCCTTCATCTAATTCTCTCCATC 58.834 44.000 0.00 0.00 0.00 3.51
2500 4624 6.678568 TCCTTCATCTAATTCTCTCCATCC 57.321 41.667 0.00 0.00 0.00 3.51
2501 4625 5.545723 TCCTTCATCTAATTCTCTCCATCCC 59.454 44.000 0.00 0.00 0.00 3.85
2502 4626 5.280419 CCTTCATCTAATTCTCTCCATCCCC 60.280 48.000 0.00 0.00 0.00 4.81
2503 4627 4.171234 TCATCTAATTCTCTCCATCCCCC 58.829 47.826 0.00 0.00 0.00 5.40
2504 4628 2.609747 TCTAATTCTCTCCATCCCCCG 58.390 52.381 0.00 0.00 0.00 5.73
2505 4629 1.002544 CTAATTCTCTCCATCCCCCGC 59.997 57.143 0.00 0.00 0.00 6.13
2506 4630 1.709994 AATTCTCTCCATCCCCCGCC 61.710 60.000 0.00 0.00 0.00 6.13
2507 4631 4.880426 TCTCTCCATCCCCCGCCC 62.880 72.222 0.00 0.00 0.00 6.13
2565 4719 1.072965 GGGGCCTCTCAGTCATAATGG 59.927 57.143 0.84 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.851976 AGTCTAAGACCTACACGCTTG 57.148 47.619 0.00 0.00 32.18 4.01
53 58 3.936453 TGACCTGGTGCGTAATTAATCAC 59.064 43.478 2.82 8.91 0.00 3.06
109 124 0.662619 TGGAGACAAAAAGTGCAGCG 59.337 50.000 0.00 0.00 37.44 5.18
149 164 4.545610 TGGTACGGTAACTTTGTTAGTCG 58.454 43.478 4.63 9.74 35.54 4.18
157 172 4.383173 CCAGAACTTGGTACGGTAACTTT 58.617 43.478 4.63 0.00 42.41 2.66
238 254 8.797350 ATGAACTCATTGTCTCAATTATCACA 57.203 30.769 0.00 0.00 31.37 3.58
434 450 1.002857 AGGATTTGTGGGGAGAAGGG 58.997 55.000 0.00 0.00 0.00 3.95
539 632 5.128499 ACACTCTATCTAACTTCAGCATGCT 59.872 40.000 16.30 16.30 34.76 3.79
540 633 5.355596 ACACTCTATCTAACTTCAGCATGC 58.644 41.667 10.51 10.51 34.76 4.06
541 634 9.838975 CTATACACTCTATCTAACTTCAGCATG 57.161 37.037 0.00 0.00 37.54 4.06
542 635 9.800572 TCTATACACTCTATCTAACTTCAGCAT 57.199 33.333 0.00 0.00 0.00 3.79
543 636 9.628500 TTCTATACACTCTATCTAACTTCAGCA 57.372 33.333 0.00 0.00 0.00 4.41
544 637 9.887406 GTTCTATACACTCTATCTAACTTCAGC 57.113 37.037 0.00 0.00 0.00 4.26
717 1498 6.920569 TCCTTCGCTCCAAATTAAATACTC 57.079 37.500 0.00 0.00 0.00 2.59
723 1504 5.801380 AGTACTTCCTTCGCTCCAAATTAA 58.199 37.500 0.00 0.00 0.00 1.40
724 1505 5.416271 AGTACTTCCTTCGCTCCAAATTA 57.584 39.130 0.00 0.00 0.00 1.40
725 1506 4.287766 AGTACTTCCTTCGCTCCAAATT 57.712 40.909 0.00 0.00 0.00 1.82
726 1507 3.983044 AGTACTTCCTTCGCTCCAAAT 57.017 42.857 0.00 0.00 0.00 2.32
749 1530 1.546476 CCTGTCTCCACCACTGAGTAC 59.454 57.143 0.00 0.00 0.00 2.73
750 1531 1.924731 CCTGTCTCCACCACTGAGTA 58.075 55.000 0.00 0.00 0.00 2.59
751 1532 1.476007 GCCTGTCTCCACCACTGAGT 61.476 60.000 0.00 0.00 0.00 3.41
752 1533 1.294780 GCCTGTCTCCACCACTGAG 59.705 63.158 0.00 0.00 0.00 3.35
753 1534 2.217038 GGCCTGTCTCCACCACTGA 61.217 63.158 0.00 0.00 0.00 3.41
754 1535 0.904865 TAGGCCTGTCTCCACCACTG 60.905 60.000 17.99 0.00 0.00 3.66
755 1536 0.616111 CTAGGCCTGTCTCCACCACT 60.616 60.000 17.99 0.00 0.00 4.00
756 1537 1.617947 CCTAGGCCTGTCTCCACCAC 61.618 65.000 17.99 0.00 0.00 4.16
757 1538 1.306141 CCTAGGCCTGTCTCCACCA 60.306 63.158 17.99 0.00 0.00 4.17
758 1539 2.066999 CCCTAGGCCTGTCTCCACC 61.067 68.421 17.99 0.00 0.00 4.61
759 1540 2.736826 GCCCTAGGCCTGTCTCCAC 61.737 68.421 17.99 0.00 44.06 4.02
760 1541 2.365635 GCCCTAGGCCTGTCTCCA 60.366 66.667 17.99 0.00 44.06 3.86
770 1551 7.079451 TCAAGAATTATAAGGAAGCCCTAGG 57.921 40.000 0.06 0.06 43.48 3.02
811 1592 8.668353 GCTATGTTGACTGATAAATTTCTGTGA 58.332 33.333 0.00 0.00 0.00 3.58
812 1593 8.453320 TGCTATGTTGACTGATAAATTTCTGTG 58.547 33.333 0.00 0.00 0.00 3.66
813 1594 8.565896 TGCTATGTTGACTGATAAATTTCTGT 57.434 30.769 0.00 0.00 0.00 3.41
817 1598 8.571336 GCCTATGCTATGTTGACTGATAAATTT 58.429 33.333 0.00 0.00 33.53 1.82
818 1599 7.175641 GGCCTATGCTATGTTGACTGATAAATT 59.824 37.037 0.00 0.00 37.74 1.82
819 1600 6.656693 GGCCTATGCTATGTTGACTGATAAAT 59.343 38.462 0.00 0.00 37.74 1.40
820 1601 5.997746 GGCCTATGCTATGTTGACTGATAAA 59.002 40.000 0.00 0.00 37.74 1.40
821 1602 5.513094 GGGCCTATGCTATGTTGACTGATAA 60.513 44.000 0.84 0.00 37.74 1.75
822 1603 4.020218 GGGCCTATGCTATGTTGACTGATA 60.020 45.833 0.84 0.00 37.74 2.15
823 1604 3.244700 GGGCCTATGCTATGTTGACTGAT 60.245 47.826 0.84 0.00 37.74 2.90
824 1605 2.104792 GGGCCTATGCTATGTTGACTGA 59.895 50.000 0.84 0.00 37.74 3.41
825 1606 2.158769 TGGGCCTATGCTATGTTGACTG 60.159 50.000 4.53 0.00 37.74 3.51
826 1607 2.105477 CTGGGCCTATGCTATGTTGACT 59.895 50.000 4.53 0.00 37.74 3.41
827 1608 2.158755 ACTGGGCCTATGCTATGTTGAC 60.159 50.000 4.53 0.00 37.74 3.18
828 1609 2.104792 GACTGGGCCTATGCTATGTTGA 59.895 50.000 4.53 0.00 37.74 3.18
829 1610 2.105477 AGACTGGGCCTATGCTATGTTG 59.895 50.000 4.53 0.00 37.74 3.33
830 1611 2.412591 AGACTGGGCCTATGCTATGTT 58.587 47.619 4.53 0.00 37.74 2.71
831 1612 2.109229 AGACTGGGCCTATGCTATGT 57.891 50.000 4.53 0.00 37.74 2.29
832 1613 4.319177 GTTAAGACTGGGCCTATGCTATG 58.681 47.826 4.53 0.00 37.74 2.23
833 1614 3.328050 GGTTAAGACTGGGCCTATGCTAT 59.672 47.826 4.53 0.00 37.74 2.97
834 1615 2.704065 GGTTAAGACTGGGCCTATGCTA 59.296 50.000 4.53 0.00 37.74 3.49
835 1616 1.490910 GGTTAAGACTGGGCCTATGCT 59.509 52.381 4.53 0.00 37.74 3.79
836 1617 1.490910 AGGTTAAGACTGGGCCTATGC 59.509 52.381 4.53 0.00 0.00 3.14
837 1618 2.746472 GCAGGTTAAGACTGGGCCTATG 60.746 54.545 4.53 0.00 36.48 2.23
838 1619 1.490910 GCAGGTTAAGACTGGGCCTAT 59.509 52.381 4.53 0.00 36.48 2.57
839 1620 0.909623 GCAGGTTAAGACTGGGCCTA 59.090 55.000 4.53 0.00 36.48 3.93
840 1621 0.842467 AGCAGGTTAAGACTGGGCCT 60.842 55.000 4.53 0.00 36.48 5.19
841 1622 0.678048 CAGCAGGTTAAGACTGGGCC 60.678 60.000 0.00 0.00 36.48 5.80
842 1623 1.308783 GCAGCAGGTTAAGACTGGGC 61.309 60.000 8.66 0.00 36.48 5.36
843 1624 0.326264 AGCAGCAGGTTAAGACTGGG 59.674 55.000 8.66 0.00 36.48 4.45
844 1625 3.334583 TTAGCAGCAGGTTAAGACTGG 57.665 47.619 8.66 0.00 36.48 4.00
845 1626 4.333926 GGAATTAGCAGCAGGTTAAGACTG 59.666 45.833 0.00 3.32 38.95 3.51
846 1627 4.518249 GGAATTAGCAGCAGGTTAAGACT 58.482 43.478 0.00 0.00 0.00 3.24
847 1628 3.309954 CGGAATTAGCAGCAGGTTAAGAC 59.690 47.826 0.00 0.00 0.00 3.01
848 1629 3.531538 CGGAATTAGCAGCAGGTTAAGA 58.468 45.455 0.00 0.00 0.00 2.10
849 1630 2.032178 GCGGAATTAGCAGCAGGTTAAG 59.968 50.000 0.00 0.00 34.19 1.85
850 1631 2.014128 GCGGAATTAGCAGCAGGTTAA 58.986 47.619 0.00 0.00 34.19 2.01
851 1632 1.663695 GCGGAATTAGCAGCAGGTTA 58.336 50.000 0.00 0.00 34.19 2.85
852 1633 1.032114 GGCGGAATTAGCAGCAGGTT 61.032 55.000 7.55 0.00 36.08 3.50
853 1634 1.452108 GGCGGAATTAGCAGCAGGT 60.452 57.895 7.55 0.00 36.08 4.00
854 1635 1.451927 TGGCGGAATTAGCAGCAGG 60.452 57.895 7.55 0.00 36.08 4.85
855 1636 0.745845 AGTGGCGGAATTAGCAGCAG 60.746 55.000 7.55 0.00 36.08 4.24
856 1637 1.026182 CAGTGGCGGAATTAGCAGCA 61.026 55.000 7.55 0.00 36.08 4.41
857 1638 1.026718 ACAGTGGCGGAATTAGCAGC 61.027 55.000 7.55 0.00 36.08 5.25
858 1639 1.933853 GTACAGTGGCGGAATTAGCAG 59.066 52.381 7.55 0.00 36.08 4.24
859 1640 1.737696 CGTACAGTGGCGGAATTAGCA 60.738 52.381 7.55 0.00 36.08 3.49
860 1641 0.928229 CGTACAGTGGCGGAATTAGC 59.072 55.000 0.00 0.00 0.00 3.09
861 1642 2.288961 ACGTACAGTGGCGGAATTAG 57.711 50.000 12.68 0.00 0.00 1.73
862 1643 2.159254 GGTACGTACAGTGGCGGAATTA 60.159 50.000 26.02 0.00 0.00 1.40
863 1644 1.404583 GGTACGTACAGTGGCGGAATT 60.405 52.381 26.02 0.00 0.00 2.17
864 1645 0.174162 GGTACGTACAGTGGCGGAAT 59.826 55.000 26.02 0.00 0.00 3.01
865 1646 1.177895 TGGTACGTACAGTGGCGGAA 61.178 55.000 26.02 0.00 0.00 4.30
866 1647 1.588824 CTGGTACGTACAGTGGCGGA 61.589 60.000 26.02 2.67 0.00 5.54
867 1648 1.153901 CTGGTACGTACAGTGGCGG 60.154 63.158 26.02 10.25 0.00 6.13
868 1649 1.804326 GCTGGTACGTACAGTGGCG 60.804 63.158 26.02 8.91 38.22 5.69
869 1650 0.736325 CAGCTGGTACGTACAGTGGC 60.736 60.000 26.02 20.98 38.22 5.01
870 1651 0.601558 ACAGCTGGTACGTACAGTGG 59.398 55.000 26.02 17.34 38.22 4.00
871 1652 2.860062 GTACAGCTGGTACGTACAGTG 58.140 52.381 26.02 17.98 42.69 3.66
1434 2225 1.990060 GTAGTGGAGCAGGCCCTGA 60.990 63.158 16.85 0.00 32.44 3.86
1506 2297 2.690881 ATCTGCAGGCCGGGGTTA 60.691 61.111 15.13 0.00 0.00 2.85
1718 2509 2.276201 CCATTTCTCGCGGTGTTATCA 58.724 47.619 6.13 0.00 0.00 2.15
1756 2548 6.070951 AGGGAGTATATAACATGCATGCAT 57.929 37.500 27.46 27.46 37.08 3.96
1772 2564 1.961133 ATTTGGGAACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
1773 2565 1.961133 TATTTGGGAACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
1774 2566 4.102681 ACTTATATTTGGGAACGGAGGGAG 59.897 45.833 0.00 0.00 0.00 4.30
1775 2567 4.042174 ACTTATATTTGGGAACGGAGGGA 58.958 43.478 0.00 0.00 0.00 4.20
1776 2568 4.432980 ACTTATATTTGGGAACGGAGGG 57.567 45.455 0.00 0.00 0.00 4.30
1777 2569 6.769134 AAAACTTATATTTGGGAACGGAGG 57.231 37.500 0.00 0.00 0.00 4.30
1778 2570 8.051901 AGAAAAACTTATATTTGGGAACGGAG 57.948 34.615 0.00 0.00 0.00 4.63
1779 2571 9.169592 CTAGAAAAACTTATATTTGGGAACGGA 57.830 33.333 0.00 0.00 0.00 4.69
1780 2572 9.169592 TCTAGAAAAACTTATATTTGGGAACGG 57.830 33.333 0.00 0.00 0.00 4.44
1801 2593 9.671279 TGATCTTTATTTGTTGCAATCTCTAGA 57.329 29.630 0.59 0.97 0.00 2.43
1806 2598 9.079833 CGATTTGATCTTTATTTGTTGCAATCT 57.920 29.630 0.59 0.00 0.00 2.40
1807 2599 9.075519 TCGATTTGATCTTTATTTGTTGCAATC 57.924 29.630 0.59 0.00 0.00 2.67
1808 2600 8.984891 TCGATTTGATCTTTATTTGTTGCAAT 57.015 26.923 0.59 0.00 0.00 3.56
1809 2601 8.809159 TTCGATTTGATCTTTATTTGTTGCAA 57.191 26.923 0.00 0.00 0.00 4.08
1810 2602 8.862074 CATTCGATTTGATCTTTATTTGTTGCA 58.138 29.630 0.00 0.00 0.00 4.08
1811 2603 9.075519 TCATTCGATTTGATCTTTATTTGTTGC 57.924 29.630 0.00 0.00 0.00 4.17
1820 2612 9.388506 AGTGTAGATTCATTCGATTTGATCTTT 57.611 29.630 7.04 0.00 0.00 2.52
1821 2613 8.954950 AGTGTAGATTCATTCGATTTGATCTT 57.045 30.769 7.04 0.00 0.00 2.40
1822 2614 8.954950 AAGTGTAGATTCATTCGATTTGATCT 57.045 30.769 0.00 3.95 0.00 2.75
1855 2647 9.511272 ACTACAATATACGGATGTATGTAGACA 57.489 33.333 24.44 0.00 40.69 3.41
1856 2648 9.985318 GACTACAATATACGGATGTATGTAGAC 57.015 37.037 24.44 18.37 40.69 2.59
1857 2649 9.955102 AGACTACAATATACGGATGTATGTAGA 57.045 33.333 24.44 2.20 40.69 2.59
1898 2690 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
1899 2691 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
1900 2692 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
1901 2693 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
1902 2694 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
1903 2695 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
1904 2696 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
1905 2697 9.827198 TTATACTCCCTCCGTTCCTAAATATAA 57.173 33.333 0.00 0.00 0.00 0.98
1907 2699 8.912614 ATTATACTCCCTCCGTTCCTAAATAT 57.087 34.615 0.00 0.00 0.00 1.28
1908 2700 9.471702 CTATTATACTCCCTCCGTTCCTAAATA 57.528 37.037 0.00 0.00 0.00 1.40
1909 2701 7.954620 ACTATTATACTCCCTCCGTTCCTAAAT 59.045 37.037 0.00 0.00 0.00 1.40
1910 2702 7.232127 CACTATTATACTCCCTCCGTTCCTAAA 59.768 40.741 0.00 0.00 0.00 1.85
1911 2703 6.718454 CACTATTATACTCCCTCCGTTCCTAA 59.282 42.308 0.00 0.00 0.00 2.69
1912 2704 6.183361 ACACTATTATACTCCCTCCGTTCCTA 60.183 42.308 0.00 0.00 0.00 2.94
1913 2705 5.078256 CACTATTATACTCCCTCCGTTCCT 58.922 45.833 0.00 0.00 0.00 3.36
1914 2706 4.831710 ACACTATTATACTCCCTCCGTTCC 59.168 45.833 0.00 0.00 0.00 3.62
1915 2707 5.770417 CACACTATTATACTCCCTCCGTTC 58.230 45.833 0.00 0.00 0.00 3.95
1916 2708 4.038883 GCACACTATTATACTCCCTCCGTT 59.961 45.833 0.00 0.00 0.00 4.44
1917 2709 3.573110 GCACACTATTATACTCCCTCCGT 59.427 47.826 0.00 0.00 0.00 4.69
1918 2710 3.572682 TGCACACTATTATACTCCCTCCG 59.427 47.826 0.00 0.00 0.00 4.63
1919 2711 5.482908 CATGCACACTATTATACTCCCTCC 58.517 45.833 0.00 0.00 0.00 4.30
1920 2712 4.932200 GCATGCACACTATTATACTCCCTC 59.068 45.833 14.21 0.00 0.00 4.30
1921 2713 4.347876 TGCATGCACACTATTATACTCCCT 59.652 41.667 18.46 0.00 0.00 4.20
1922 2714 4.641396 TGCATGCACACTATTATACTCCC 58.359 43.478 18.46 0.00 0.00 4.30
1923 2715 5.352569 GGATGCATGCACACTATTATACTCC 59.647 44.000 25.37 17.13 0.00 3.85
1924 2716 5.934043 TGGATGCATGCACACTATTATACTC 59.066 40.000 25.37 11.70 0.00 2.59
1925 2717 5.868454 TGGATGCATGCACACTATTATACT 58.132 37.500 25.37 1.30 0.00 2.12
1926 2718 6.372381 TGATGGATGCATGCACACTATTATAC 59.628 38.462 25.37 5.64 0.00 1.47
2186 3522 5.848286 ATGGCATGAGGATCCTATAAACA 57.152 39.130 16.16 12.05 0.00 2.83
2187 3523 6.703607 CGATATGGCATGAGGATCCTATAAAC 59.296 42.308 16.16 6.27 0.00 2.01
2193 3529 1.209019 GCGATATGGCATGAGGATCCT 59.791 52.381 16.13 16.13 0.00 3.24
2198 3534 2.850439 CCAGCGATATGGCATGAGG 58.150 57.895 10.98 4.56 32.48 3.86
2215 3551 3.385755 TGAGTAAACCCTACCTTATCGCC 59.614 47.826 0.00 0.00 0.00 5.54
2217 3553 5.809051 GTGTTGAGTAAACCCTACCTTATCG 59.191 44.000 0.00 0.00 38.06 2.92
2220 3556 4.906664 TGGTGTTGAGTAAACCCTACCTTA 59.093 41.667 0.00 0.00 38.06 2.69
2225 3561 6.043474 AGTTGTATGGTGTTGAGTAAACCCTA 59.957 38.462 0.00 0.00 38.06 3.53
2314 4376 3.298619 TGGTGGCTCAAATAATGGATGG 58.701 45.455 0.00 0.00 0.00 3.51
2437 4561 1.540267 CCATCCGTGGGTTTAGCAAA 58.460 50.000 0.00 0.00 42.11 3.68
2438 4562 3.257935 CCATCCGTGGGTTTAGCAA 57.742 52.632 0.00 0.00 42.11 3.91
2447 4571 0.178068 CTCCTGTAACCCATCCGTGG 59.822 60.000 0.00 0.00 45.61 4.94
2448 4572 0.178068 CCTCCTGTAACCCATCCGTG 59.822 60.000 0.00 0.00 0.00 4.94
2449 4573 0.252558 ACCTCCTGTAACCCATCCGT 60.253 55.000 0.00 0.00 0.00 4.69
2450 4574 0.909623 AACCTCCTGTAACCCATCCG 59.090 55.000 0.00 0.00 0.00 4.18
2451 4575 1.913419 TGAACCTCCTGTAACCCATCC 59.087 52.381 0.00 0.00 0.00 3.51
2452 4576 2.092914 CCTGAACCTCCTGTAACCCATC 60.093 54.545 0.00 0.00 0.00 3.51
2453 4577 1.916181 CCTGAACCTCCTGTAACCCAT 59.084 52.381 0.00 0.00 0.00 4.00
2454 4578 1.358152 CCTGAACCTCCTGTAACCCA 58.642 55.000 0.00 0.00 0.00 4.51
2455 4579 0.618981 CCCTGAACCTCCTGTAACCC 59.381 60.000 0.00 0.00 0.00 4.11
2456 4580 0.618981 CCCCTGAACCTCCTGTAACC 59.381 60.000 0.00 0.00 0.00 2.85
2457 4581 0.035343 GCCCCTGAACCTCCTGTAAC 60.035 60.000 0.00 0.00 0.00 2.50
2458 4582 0.178873 AGCCCCTGAACCTCCTGTAA 60.179 55.000 0.00 0.00 0.00 2.41
2459 4583 0.617820 GAGCCCCTGAACCTCCTGTA 60.618 60.000 0.00 0.00 0.00 2.74
2460 4584 1.920835 GAGCCCCTGAACCTCCTGT 60.921 63.158 0.00 0.00 0.00 4.00
2461 4585 2.674220 GGAGCCCCTGAACCTCCTG 61.674 68.421 0.00 0.00 41.50 3.86
2462 4586 2.285743 GGAGCCCCTGAACCTCCT 60.286 66.667 0.00 0.00 41.50 3.69
2463 4587 1.916206 GAAGGAGCCCCTGAACCTCC 61.916 65.000 0.00 0.00 43.48 4.30
2464 4588 1.201429 TGAAGGAGCCCCTGAACCTC 61.201 60.000 0.00 0.00 43.48 3.85
2465 4589 0.551131 ATGAAGGAGCCCCTGAACCT 60.551 55.000 0.00 0.00 43.48 3.50
2466 4590 0.106967 GATGAAGGAGCCCCTGAACC 60.107 60.000 0.00 0.00 43.48 3.62
2467 4591 0.915364 AGATGAAGGAGCCCCTGAAC 59.085 55.000 0.00 0.00 43.48 3.18
2468 4592 2.568546 TAGATGAAGGAGCCCCTGAA 57.431 50.000 0.00 0.00 43.48 3.02
2469 4593 2.568546 TTAGATGAAGGAGCCCCTGA 57.431 50.000 0.00 0.00 43.48 3.86
2470 4594 3.393941 AGAATTAGATGAAGGAGCCCCTG 59.606 47.826 0.00 0.00 43.48 4.45
2472 4596 3.650461 AGAGAATTAGATGAAGGAGCCCC 59.350 47.826 0.00 0.00 0.00 5.80
2473 4597 4.262851 GGAGAGAATTAGATGAAGGAGCCC 60.263 50.000 0.00 0.00 0.00 5.19
2474 4598 4.346418 TGGAGAGAATTAGATGAAGGAGCC 59.654 45.833 0.00 0.00 0.00 4.70
2475 4599 5.543507 TGGAGAGAATTAGATGAAGGAGC 57.456 43.478 0.00 0.00 0.00 4.70
2476 4600 6.295802 GGGATGGAGAGAATTAGATGAAGGAG 60.296 46.154 0.00 0.00 0.00 3.69
2477 4601 5.545723 GGGATGGAGAGAATTAGATGAAGGA 59.454 44.000 0.00 0.00 0.00 3.36
2478 4602 5.280419 GGGGATGGAGAGAATTAGATGAAGG 60.280 48.000 0.00 0.00 0.00 3.46
2479 4603 5.280419 GGGGGATGGAGAGAATTAGATGAAG 60.280 48.000 0.00 0.00 0.00 3.02
2480 4604 4.599241 GGGGGATGGAGAGAATTAGATGAA 59.401 45.833 0.00 0.00 0.00 2.57
2481 4605 4.171234 GGGGGATGGAGAGAATTAGATGA 58.829 47.826 0.00 0.00 0.00 2.92
2482 4606 3.055530 CGGGGGATGGAGAGAATTAGATG 60.056 52.174 0.00 0.00 0.00 2.90
2483 4607 3.177228 CGGGGGATGGAGAGAATTAGAT 58.823 50.000 0.00 0.00 0.00 1.98
2484 4608 2.609747 CGGGGGATGGAGAGAATTAGA 58.390 52.381 0.00 0.00 0.00 2.10
2485 4609 1.002544 GCGGGGGATGGAGAGAATTAG 59.997 57.143 0.00 0.00 0.00 1.73
2486 4610 1.056660 GCGGGGGATGGAGAGAATTA 58.943 55.000 0.00 0.00 0.00 1.40
2487 4611 1.709994 GGCGGGGGATGGAGAGAATT 61.710 60.000 0.00 0.00 0.00 2.17
2488 4612 2.150051 GGCGGGGGATGGAGAGAAT 61.150 63.158 0.00 0.00 0.00 2.40
2489 4613 2.768344 GGCGGGGGATGGAGAGAA 60.768 66.667 0.00 0.00 0.00 2.87
2490 4614 4.880426 GGGCGGGGGATGGAGAGA 62.880 72.222 0.00 0.00 0.00 3.10
2513 4637 7.309316 CCTGAAAATGAAAATGAAAATTGGGGG 60.309 37.037 0.00 0.00 0.00 5.40
2514 4638 7.231115 ACCTGAAAATGAAAATGAAAATTGGGG 59.769 33.333 0.00 0.00 0.00 4.96
2515 4639 8.077386 CACCTGAAAATGAAAATGAAAATTGGG 58.923 33.333 0.00 0.00 0.00 4.12
2516 4640 8.077386 CCACCTGAAAATGAAAATGAAAATTGG 58.923 33.333 0.00 0.00 0.00 3.16
2517 4641 8.077386 CCCACCTGAAAATGAAAATGAAAATTG 58.923 33.333 0.00 0.00 0.00 2.32
2518 4642 7.255555 GCCCACCTGAAAATGAAAATGAAAATT 60.256 33.333 0.00 0.00 0.00 1.82
2519 4643 6.207221 GCCCACCTGAAAATGAAAATGAAAAT 59.793 34.615 0.00 0.00 0.00 1.82
2520 4644 5.530543 GCCCACCTGAAAATGAAAATGAAAA 59.469 36.000 0.00 0.00 0.00 2.29
2565 4719 2.477845 TTACGGAGGTTTTACAGGGC 57.522 50.000 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.