Multiple sequence alignment - TraesCS2B01G503500

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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 TraesCS2B01G503500 chr2B 100.000 3483 0 0 1 3483 697766362 697769844 0.000000e+00 6433
1 TraesCS2B01G503500 chr2B 93.113 697 39 5 2788 3483 767467663 767466975 0.000000e+00 1013
2 TraesCS2B01G503500 chr2B 92.407 698 39 6 2788 3483 404181690 404182375 0.000000e+00 983
3 TraesCS2B01G503500 chr2D 91.403 1931 82 25 699 2580 579821728 579823623 0.000000e+00 2569
4 TraesCS2B01G503500 chr2A 90.820 1928 89 30 710 2581 717419395 717421290 0.000000e+00 2499
5 TraesCS2B01G503500 chr1A 89.178 961 67 7 847 1807 156549117 156550040 0.000000e+00 1164
6 TraesCS2B01G503500 chr5B 94.901 706 33 2 1 706 16176342 16175640 0.000000e+00 1101
7 TraesCS2B01G503500 chr5B 94.842 698 32 4 2788 3483 51864529 51865224 0.000000e+00 1086
8 TraesCS2B01G503500 chr5B 94.460 704 35 4 1 703 553942788 553942088 0.000000e+00 1081
9 TraesCS2B01G503500 chr5B 94.209 708 37 3 1 708 553182739 553182036 0.000000e+00 1077
10 TraesCS2B01G503500 chr5B 94.051 706 39 3 1 706 579005841 579006543 0.000000e+00 1068
11 TraesCS2B01G503500 chr5B 82.882 701 107 10 2789 3483 665416582 665415889 4.940000e-173 617
12 TraesCS2B01G503500 chr6B 94.602 704 35 3 1 703 657252909 657253610 0.000000e+00 1086
13 TraesCS2B01G503500 chr1B 94.310 703 38 2 1 703 365450805 365450105 0.000000e+00 1075
14 TraesCS2B01G503500 chr1B 94.043 705 40 2 1 705 49438323 49437621 0.000000e+00 1068
15 TraesCS2B01G503500 chr4B 94.068 708 39 2 1 708 413112308 413111604 0.000000e+00 1072
16 TraesCS2B01G503500 chr4B 92.571 700 35 5 2788 3483 667421062 667421748 0.000000e+00 989
17 TraesCS2B01G503500 chr4B 85.390 705 84 14 2788 3483 612203059 612202365 0.000000e+00 713
18 TraesCS2B01G503500 chr7B 94.051 706 38 4 1 705 479235356 479234654 0.000000e+00 1068
19 TraesCS2B01G503500 chr7B 93.840 698 38 4 2788 3483 255997958 255998652 0.000000e+00 1046
20 TraesCS2B01G503500 chr3D 84.429 700 88 18 2788 3482 507775515 507776198 0.000000e+00 669
21 TraesCS2B01G503500 chr7A 84.227 653 90 10 2836 3483 517575712 517575068 1.060000e-174 623


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 TraesCS2B01G503500 chr2B 697766362 697769844 3482 False 6433 6433 100.000 1 3483 1 chr2B.!!$F2 3482
1 TraesCS2B01G503500 chr2B 767466975 767467663 688 True 1013 1013 93.113 2788 3483 1 chr2B.!!$R1 695
2 TraesCS2B01G503500 chr2B 404181690 404182375 685 False 983 983 92.407 2788 3483 1 chr2B.!!$F1 695
3 TraesCS2B01G503500 chr2D 579821728 579823623 1895 False 2569 2569 91.403 699 2580 1 chr2D.!!$F1 1881
4 TraesCS2B01G503500 chr2A 717419395 717421290 1895 False 2499 2499 90.820 710 2581 1 chr2A.!!$F1 1871
5 TraesCS2B01G503500 chr1A 156549117 156550040 923 False 1164 1164 89.178 847 1807 1 chr1A.!!$F1 960
6 TraesCS2B01G503500 chr5B 16175640 16176342 702 True 1101 1101 94.901 1 706 1 chr5B.!!$R1 705
7 TraesCS2B01G503500 chr5B 51864529 51865224 695 False 1086 1086 94.842 2788 3483 1 chr5B.!!$F1 695
8 TraesCS2B01G503500 chr5B 553942088 553942788 700 True 1081 1081 94.460 1 703 1 chr5B.!!$R3 702
9 TraesCS2B01G503500 chr5B 553182036 553182739 703 True 1077 1077 94.209 1 708 1 chr5B.!!$R2 707
10 TraesCS2B01G503500 chr5B 579005841 579006543 702 False 1068 1068 94.051 1 706 1 chr5B.!!$F2 705
11 TraesCS2B01G503500 chr5B 665415889 665416582 693 True 617 617 82.882 2789 3483 1 chr5B.!!$R4 694
12 TraesCS2B01G503500 chr6B 657252909 657253610 701 False 1086 1086 94.602 1 703 1 chr6B.!!$F1 702
13 TraesCS2B01G503500 chr1B 365450105 365450805 700 True 1075 1075 94.310 1 703 1 chr1B.!!$R2 702
14 TraesCS2B01G503500 chr1B 49437621 49438323 702 True 1068 1068 94.043 1 705 1 chr1B.!!$R1 704
15 TraesCS2B01G503500 chr4B 413111604 413112308 704 True 1072 1072 94.068 1 708 1 chr4B.!!$R1 707
16 TraesCS2B01G503500 chr4B 667421062 667421748 686 False 989 989 92.571 2788 3483 1 chr4B.!!$F1 695
17 TraesCS2B01G503500 chr4B 612202365 612203059 694 True 713 713 85.390 2788 3483 1 chr4B.!!$R2 695
18 TraesCS2B01G503500 chr7B 479234654 479235356 702 True 1068 1068 94.051 1 705 1 chr7B.!!$R1 704
19 TraesCS2B01G503500 chr7B 255997958 255998652 694 False 1046 1046 93.840 2788 3483 1 chr7B.!!$F1 695
20 TraesCS2B01G503500 chr3D 507775515 507776198 683 False 669 669 84.429 2788 3482 1 chr3D.!!$F1 694
21 TraesCS2B01G503500 chr7A 517575068 517575712 644 True 623 623 84.227 2836 3483 1 chr7A.!!$R1 647

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
474 477 0.454452 GCATCAAGAAACGGCGGAAC 60.454 55.0 13.24 1.16 0.0 3.62 F
1861 1877 0.179111 TGCCTATGTGTGTAGCGCTC 60.179 55.0 16.34 6.54 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 2000 0.170561 ATCACGCCGTATATCTCCGC 59.829 55.0 0.00 0.00 0.0 5.54 R
2775 2849 0.039798 TGAAGAACTAACGCGCGAGT 60.040 50.0 39.36 27.43 0.0 4.18 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
60 61 1.837051 ATGGAGATCCGGCGCCTTA 60.837 57.895 26.68 12.95 39.43 2.69
70 72 2.349755 GCGCCTTACTGTCCCCAA 59.650 61.111 0.00 0.00 0.00 4.12
198 200 1.079127 CCTTGTTCCGCCTGTCGAT 60.079 57.895 0.00 0.00 41.67 3.59
372 375 3.566261 CATGGCGTGCTTCTTCGT 58.434 55.556 0.00 0.00 0.00 3.85
457 460 0.615331 AGAGATGCGAGGGAAAAGCA 59.385 50.000 0.00 0.00 45.46 3.91
472 475 0.605319 AAGCATCAAGAAACGGCGGA 60.605 50.000 13.24 0.00 0.00 5.54
474 477 0.454452 GCATCAAGAAACGGCGGAAC 60.454 55.000 13.24 1.16 0.00 3.62
609 612 2.017783 CCGAGCCGACGAAAAACGA 61.018 57.895 0.00 0.00 45.77 3.85
628 631 3.468007 CTTCTGGAAGCGCGACTG 58.532 61.111 12.10 0.33 0.00 3.51
667 670 1.079875 GGCGCGGTAAAATCGTCTGA 61.080 55.000 8.83 0.00 0.00 3.27
717 720 2.231380 CCCTAACCCAGCCAGTGGT 61.231 63.158 11.74 0.00 46.37 4.16
718 721 1.002134 CCTAACCCAGCCAGTGGTG 60.002 63.158 11.74 7.84 46.37 4.17
752 755 7.719633 AGAGAACTTGTAAGACATGCCTAAAAA 59.280 33.333 0.00 0.00 0.00 1.94
755 758 6.303839 ACTTGTAAGACATGCCTAAAAAGGA 58.696 36.000 0.00 0.00 0.00 3.36
817 828 3.735591 TCGAAACGGGAAAGAATTGTCT 58.264 40.909 0.00 0.00 34.72 3.41
854 866 1.271840 TATCCGCTCCACCCAGCTTT 61.272 55.000 0.00 0.00 37.25 3.51
971 983 2.740055 CACCCAGCACGAGACAGC 60.740 66.667 0.00 0.00 0.00 4.40
1011 1023 2.860293 GACAACATGGGCGACGTG 59.140 61.111 0.00 0.00 41.98 4.49
1066 1078 4.069232 CTCCGCCGCCAGAACTGA 62.069 66.667 3.19 0.00 0.00 3.41
1227 1239 2.687200 TACCTGGAGCGGGTGCAT 60.687 61.111 0.00 0.00 43.80 3.96
1269 1281 0.976073 AGTGCTACGTGGTGGCCTAT 60.976 55.000 3.32 0.00 39.28 2.57
1426 1438 0.678684 TCCATGCTACTCGACGACCA 60.679 55.000 0.00 0.00 0.00 4.02
1433 1445 1.986378 CTACTCGACGACCAAAGCAAG 59.014 52.381 0.00 0.00 0.00 4.01
1447 1459 5.006386 CCAAAGCAAGAACAGAGTAGGAAT 58.994 41.667 0.00 0.00 0.00 3.01
1468 1481 6.127647 GGAATTCTATCACCATTGCTGTCAAA 60.128 38.462 5.23 0.00 35.56 2.69
1590 1605 1.214175 AGACCAACCATGACCACAACA 59.786 47.619 0.00 0.00 0.00 3.33
1594 1609 2.430332 CCAACCATGACCACAACAAACT 59.570 45.455 0.00 0.00 0.00 2.66
1595 1610 3.118811 CCAACCATGACCACAACAAACTT 60.119 43.478 0.00 0.00 0.00 2.66
1596 1611 4.502962 CAACCATGACCACAACAAACTTT 58.497 39.130 0.00 0.00 0.00 2.66
1597 1612 4.122143 ACCATGACCACAACAAACTTTG 57.878 40.909 0.00 0.00 0.00 2.77
1598 1613 3.118811 ACCATGACCACAACAAACTTTGG 60.119 43.478 6.47 0.00 35.06 3.28
1599 1614 3.131933 CCATGACCACAACAAACTTTGGA 59.868 43.478 6.47 0.00 33.02 3.53
1600 1615 4.362279 CATGACCACAACAAACTTTGGAG 58.638 43.478 6.47 0.98 33.02 3.86
1601 1616 3.691575 TGACCACAACAAACTTTGGAGA 58.308 40.909 6.47 0.00 33.02 3.71
1602 1617 4.082845 TGACCACAACAAACTTTGGAGAA 58.917 39.130 6.47 0.00 33.02 2.87
1603 1618 4.524714 TGACCACAACAAACTTTGGAGAAA 59.475 37.500 6.47 0.00 33.02 2.52
1604 1619 4.816392 ACCACAACAAACTTTGGAGAAAC 58.184 39.130 6.47 0.00 33.02 2.78
1605 1620 4.282195 ACCACAACAAACTTTGGAGAAACA 59.718 37.500 6.47 0.00 33.02 2.83
1606 1621 5.046663 ACCACAACAAACTTTGGAGAAACAT 60.047 36.000 6.47 0.00 33.02 2.71
1607 1622 5.874261 CCACAACAAACTTTGGAGAAACATT 59.126 36.000 6.47 0.00 34.12 2.71
1608 1623 6.183360 CCACAACAAACTTTGGAGAAACATTG 60.183 38.462 6.47 2.06 34.12 2.82
1609 1624 5.351189 ACAACAAACTTTGGAGAAACATTGC 59.649 36.000 6.47 0.00 34.12 3.56
1610 1625 4.441792 ACAAACTTTGGAGAAACATTGCC 58.558 39.130 6.47 0.00 34.12 4.52
1611 1626 4.081198 ACAAACTTTGGAGAAACATTGCCA 60.081 37.500 6.47 0.00 34.12 4.92
1612 1627 3.733443 ACTTTGGAGAAACATTGCCAC 57.267 42.857 0.00 0.00 0.00 5.01
1613 1628 3.030291 ACTTTGGAGAAACATTGCCACA 58.970 40.909 0.00 0.00 0.00 4.17
1614 1629 3.068590 ACTTTGGAGAAACATTGCCACAG 59.931 43.478 0.00 0.00 35.04 3.66
1615 1630 0.961019 TGGAGAAACATTGCCACAGC 59.039 50.000 0.00 0.00 40.48 4.40
1616 1631 1.251251 GGAGAAACATTGCCACAGCT 58.749 50.000 0.00 0.00 40.80 4.24
1617 1632 2.224744 TGGAGAAACATTGCCACAGCTA 60.225 45.455 0.00 0.00 40.80 3.32
1618 1633 2.421424 GGAGAAACATTGCCACAGCTAG 59.579 50.000 0.00 0.00 40.80 3.42
1619 1634 3.077359 GAGAAACATTGCCACAGCTAGT 58.923 45.455 0.00 0.00 40.80 2.57
1658 1674 8.154203 TGGCCACGATAAATAGATCAAAATCTA 58.846 33.333 0.00 0.00 46.09 1.98
1704 1720 3.580895 TGGTACTTTGTATGGCAGTGAGA 59.419 43.478 0.00 0.00 0.00 3.27
1851 1867 3.777465 AGTACGTACACTGCCTATGTG 57.223 47.619 26.55 0.00 40.87 3.21
1861 1877 0.179111 TGCCTATGTGTGTAGCGCTC 60.179 55.000 16.34 6.54 0.00 5.03
1874 1890 1.895231 GCGCTCCATGCATGATCCA 60.895 57.895 28.31 7.75 43.06 3.41
1972 1994 9.254133 CATACATAAAGAACGTCTTGATCAGAT 57.746 33.333 0.00 0.00 36.71 2.90
1990 2012 4.745620 TCAGATAGATCGCGGAGATATACG 59.254 45.833 6.13 0.00 40.26 3.06
2039 2083 2.486203 TGAATTACATTTTGCTCGGCGT 59.514 40.909 6.85 0.00 0.00 5.68
2072 2120 3.181397 CGCATGTTCCATGGTGAAAATC 58.819 45.455 12.58 0.00 0.00 2.17
2075 2123 5.180271 GCATGTTCCATGGTGAAAATCAAT 58.820 37.500 12.58 0.00 0.00 2.57
2076 2124 6.339730 GCATGTTCCATGGTGAAAATCAATA 58.660 36.000 12.58 0.00 0.00 1.90
2077 2125 6.817641 GCATGTTCCATGGTGAAAATCAATAA 59.182 34.615 12.58 0.00 0.00 1.40
2078 2126 7.010738 GCATGTTCCATGGTGAAAATCAATAAG 59.989 37.037 12.58 0.00 0.00 1.73
2079 2127 7.537596 TGTTCCATGGTGAAAATCAATAAGT 57.462 32.000 12.58 0.00 0.00 2.24
2080 2128 7.377398 TGTTCCATGGTGAAAATCAATAAGTG 58.623 34.615 12.58 0.00 0.00 3.16
2108 2156 3.340814 ACTGATTAGCTGAACCCTGTG 57.659 47.619 0.00 0.00 0.00 3.66
2109 2157 2.639839 ACTGATTAGCTGAACCCTGTGT 59.360 45.455 0.00 0.00 0.00 3.72
2110 2158 3.073062 ACTGATTAGCTGAACCCTGTGTT 59.927 43.478 0.00 0.00 40.81 3.32
2111 2159 3.411446 TGATTAGCTGAACCCTGTGTTG 58.589 45.455 0.00 0.00 37.29 3.33
2112 2160 2.270352 TTAGCTGAACCCTGTGTTGG 57.730 50.000 0.00 0.00 37.29 3.77
2113 2161 1.429930 TAGCTGAACCCTGTGTTGGA 58.570 50.000 0.00 0.00 37.29 3.53
2115 2163 0.883833 GCTGAACCCTGTGTTGGATG 59.116 55.000 0.00 0.00 37.29 3.51
2116 2164 1.819305 GCTGAACCCTGTGTTGGATGT 60.819 52.381 0.00 0.00 37.29 3.06
2117 2165 2.586425 CTGAACCCTGTGTTGGATGTT 58.414 47.619 0.00 0.00 37.29 2.71
2118 2166 2.294233 CTGAACCCTGTGTTGGATGTTG 59.706 50.000 0.00 0.00 37.29 3.33
2119 2167 2.092158 TGAACCCTGTGTTGGATGTTGA 60.092 45.455 0.00 0.00 37.29 3.18
2120 2168 1.981256 ACCCTGTGTTGGATGTTGAC 58.019 50.000 0.00 0.00 0.00 3.18
2323 2390 0.953471 CGTCCAACAAGCCGGATCAA 60.953 55.000 5.05 0.00 32.83 2.57
2332 2399 2.735772 GCCGGATCAAGAGCCCTCA 61.736 63.158 5.05 0.00 32.05 3.86
2346 2413 3.744719 CTCAAGGGTCGACGGCGA 61.745 66.667 10.67 10.67 45.71 5.54
2483 2550 2.327244 CGTCGCGGTACTCCTAGC 59.673 66.667 6.13 0.00 0.00 3.42
2537 2611 5.120053 TCGATGTGCACATTAACTAACTGTG 59.880 40.000 31.82 10.94 42.44 3.66
2570 2644 2.543031 CGGATTCGATGTGTATGGACGT 60.543 50.000 0.00 0.00 39.00 4.34
2581 2655 4.394610 TGTGTATGGACGTTGAATGGAATG 59.605 41.667 0.00 0.00 0.00 2.67
2582 2656 3.376859 TGTATGGACGTTGAATGGAATGC 59.623 43.478 0.00 0.00 0.00 3.56
2583 2657 1.902938 TGGACGTTGAATGGAATGCA 58.097 45.000 0.00 0.00 0.00 3.96
2584 2658 1.539388 TGGACGTTGAATGGAATGCAC 59.461 47.619 0.00 0.00 25.18 4.57
2585 2659 1.812571 GGACGTTGAATGGAATGCACT 59.187 47.619 0.00 0.00 25.18 4.40
2586 2660 3.006940 GGACGTTGAATGGAATGCACTA 58.993 45.455 0.00 0.00 25.18 2.74
2587 2661 3.438781 GGACGTTGAATGGAATGCACTAA 59.561 43.478 0.00 0.00 25.18 2.24
2588 2662 4.437390 GGACGTTGAATGGAATGCACTAAG 60.437 45.833 0.00 0.00 25.18 2.18
2589 2663 4.323417 ACGTTGAATGGAATGCACTAAGA 58.677 39.130 0.00 0.00 25.18 2.10
2590 2664 4.154195 ACGTTGAATGGAATGCACTAAGAC 59.846 41.667 0.00 0.00 25.18 3.01
2591 2665 4.393062 CGTTGAATGGAATGCACTAAGACT 59.607 41.667 0.00 0.00 25.18 3.24
2592 2666 5.634896 GTTGAATGGAATGCACTAAGACTG 58.365 41.667 0.00 0.00 25.18 3.51
2593 2667 4.264253 TGAATGGAATGCACTAAGACTGG 58.736 43.478 0.00 0.00 0.00 4.00
2594 2668 4.019411 TGAATGGAATGCACTAAGACTGGA 60.019 41.667 0.00 0.00 0.00 3.86
2595 2669 3.616956 TGGAATGCACTAAGACTGGAG 57.383 47.619 0.00 0.00 0.00 3.86
2596 2670 2.906389 TGGAATGCACTAAGACTGGAGT 59.094 45.455 0.00 0.00 0.00 3.85
2597 2671 3.327757 TGGAATGCACTAAGACTGGAGTT 59.672 43.478 0.00 0.00 0.00 3.01
2598 2672 4.530553 TGGAATGCACTAAGACTGGAGTTA 59.469 41.667 0.00 0.00 0.00 2.24
2599 2673 5.012664 TGGAATGCACTAAGACTGGAGTTAA 59.987 40.000 0.00 0.00 0.00 2.01
2600 2674 5.938125 GGAATGCACTAAGACTGGAGTTAAA 59.062 40.000 0.00 0.00 0.00 1.52
2601 2675 6.599638 GGAATGCACTAAGACTGGAGTTAAAT 59.400 38.462 0.00 0.00 0.00 1.40
2602 2676 7.201652 GGAATGCACTAAGACTGGAGTTAAATC 60.202 40.741 0.00 0.00 0.00 2.17
2603 2677 5.488341 TGCACTAAGACTGGAGTTAAATCC 58.512 41.667 15.06 15.06 40.03 3.01
2604 2678 4.567159 GCACTAAGACTGGAGTTAAATCCG 59.433 45.833 16.64 13.35 42.77 4.18
2610 2684 2.817901 CTGGAGTTAAATCCGGTACCG 58.182 52.381 27.68 27.68 42.77 4.02
2611 2685 2.167075 CTGGAGTTAAATCCGGTACCGT 59.833 50.000 31.24 16.40 42.77 4.83
2612 2686 2.094078 TGGAGTTAAATCCGGTACCGTG 60.094 50.000 31.24 22.29 42.77 4.94
2613 2687 2.094026 GGAGTTAAATCCGGTACCGTGT 60.094 50.000 31.24 17.34 37.81 4.49
2614 2688 3.588955 GAGTTAAATCCGGTACCGTGTT 58.411 45.455 31.24 21.86 37.81 3.32
2615 2689 3.996363 GAGTTAAATCCGGTACCGTGTTT 59.004 43.478 31.24 28.58 37.81 2.83
2616 2690 4.388485 AGTTAAATCCGGTACCGTGTTTT 58.612 39.130 31.24 26.26 37.81 2.43
2617 2691 4.452114 AGTTAAATCCGGTACCGTGTTTTC 59.548 41.667 31.24 22.60 37.81 2.29
2618 2692 2.547299 AATCCGGTACCGTGTTTTCA 57.453 45.000 31.24 8.31 37.81 2.69
2619 2693 2.088950 ATCCGGTACCGTGTTTTCAG 57.911 50.000 31.24 14.39 37.81 3.02
2620 2694 1.039068 TCCGGTACCGTGTTTTCAGA 58.961 50.000 31.24 16.47 37.81 3.27
2621 2695 1.000060 TCCGGTACCGTGTTTTCAGAG 60.000 52.381 31.24 12.95 37.81 3.35
2622 2696 1.269936 CCGGTACCGTGTTTTCAGAGT 60.270 52.381 31.24 0.00 37.81 3.24
2623 2697 2.056577 CGGTACCGTGTTTTCAGAGTC 58.943 52.381 26.39 0.00 34.35 3.36
2624 2698 2.410939 GGTACCGTGTTTTCAGAGTCC 58.589 52.381 0.00 0.00 0.00 3.85
2625 2699 2.410939 GTACCGTGTTTTCAGAGTCCC 58.589 52.381 0.00 0.00 0.00 4.46
2626 2700 0.108019 ACCGTGTTTTCAGAGTCCCC 59.892 55.000 0.00 0.00 0.00 4.81
2627 2701 0.949105 CCGTGTTTTCAGAGTCCCCG 60.949 60.000 0.00 0.00 0.00 5.73
2628 2702 0.949105 CGTGTTTTCAGAGTCCCCGG 60.949 60.000 0.00 0.00 0.00 5.73
2629 2703 0.108019 GTGTTTTCAGAGTCCCCGGT 59.892 55.000 0.00 0.00 0.00 5.28
2630 2704 0.107831 TGTTTTCAGAGTCCCCGGTG 59.892 55.000 0.00 0.00 0.00 4.94
2631 2705 0.108019 GTTTTCAGAGTCCCCGGTGT 59.892 55.000 0.00 0.00 0.00 4.16
2632 2706 0.841289 TTTTCAGAGTCCCCGGTGTT 59.159 50.000 0.00 0.00 0.00 3.32
2633 2707 0.841289 TTTCAGAGTCCCCGGTGTTT 59.159 50.000 0.00 0.00 0.00 2.83
2634 2708 0.841289 TTCAGAGTCCCCGGTGTTTT 59.159 50.000 0.00 0.00 0.00 2.43
2635 2709 0.841289 TCAGAGTCCCCGGTGTTTTT 59.159 50.000 0.00 0.00 0.00 1.94
2663 2737 8.966155 TTTGGATAGAAAAGGGTTTTATTCCT 57.034 30.769 0.00 0.00 31.94 3.36
2664 2738 8.589701 TTGGATAGAAAAGGGTTTTATTCCTC 57.410 34.615 0.00 0.00 31.94 3.71
2665 2739 6.826741 TGGATAGAAAAGGGTTTTATTCCTCG 59.173 38.462 0.00 0.00 31.94 4.63
2666 2740 7.052248 GGATAGAAAAGGGTTTTATTCCTCGA 58.948 38.462 0.00 0.00 31.94 4.04
2667 2741 7.720074 GGATAGAAAAGGGTTTTATTCCTCGAT 59.280 37.037 0.00 0.00 31.94 3.59
2668 2742 9.774413 GATAGAAAAGGGTTTTATTCCTCGATA 57.226 33.333 0.00 0.00 31.94 2.92
2673 2747 9.916360 AAAAGGGTTTTATTCCTCGATAATAGT 57.084 29.630 0.00 0.00 32.02 2.12
2685 2759 8.041829 TCCTCGATAATAGTATTACAGTCAGC 57.958 38.462 4.71 0.00 0.00 4.26
2686 2760 7.883833 TCCTCGATAATAGTATTACAGTCAGCT 59.116 37.037 4.71 0.00 0.00 4.24
2687 2761 9.163899 CCTCGATAATAGTATTACAGTCAGCTA 57.836 37.037 4.71 0.00 0.00 3.32
2702 2776 8.582657 ACAGTCAGCTAAAATAAGACTAGAGA 57.417 34.615 0.00 0.00 37.45 3.10
2703 2777 9.196139 ACAGTCAGCTAAAATAAGACTAGAGAT 57.804 33.333 0.00 0.00 37.45 2.75
2708 2782 9.405587 CAGCTAAAATAAGACTAGAGATACTGC 57.594 37.037 0.00 0.00 0.00 4.40
2709 2783 8.581578 AGCTAAAATAAGACTAGAGATACTGCC 58.418 37.037 0.00 0.00 0.00 4.85
2710 2784 8.581578 GCTAAAATAAGACTAGAGATACTGCCT 58.418 37.037 0.00 0.00 0.00 4.75
2711 2785 9.906660 CTAAAATAAGACTAGAGATACTGCCTG 57.093 37.037 0.00 0.00 0.00 4.85
2712 2786 8.540507 AAAATAAGACTAGAGATACTGCCTGA 57.459 34.615 0.00 0.00 0.00 3.86
2713 2787 8.540507 AAATAAGACTAGAGATACTGCCTGAA 57.459 34.615 0.00 0.00 0.00 3.02
2714 2788 8.540507 AATAAGACTAGAGATACTGCCTGAAA 57.459 34.615 0.00 0.00 0.00 2.69
2715 2789 5.845391 AGACTAGAGATACTGCCTGAAAC 57.155 43.478 0.00 0.00 0.00 2.78
2716 2790 5.515106 AGACTAGAGATACTGCCTGAAACT 58.485 41.667 0.00 0.00 0.00 2.66
2717 2791 5.955355 AGACTAGAGATACTGCCTGAAACTT 59.045 40.000 0.00 0.00 0.00 2.66
2718 2792 5.971763 ACTAGAGATACTGCCTGAAACTTG 58.028 41.667 0.00 0.00 0.00 3.16
2719 2793 4.213564 AGAGATACTGCCTGAAACTTGG 57.786 45.455 0.00 0.00 0.00 3.61
2720 2794 3.054802 AGAGATACTGCCTGAAACTTGGG 60.055 47.826 0.00 0.00 0.00 4.12
2721 2795 2.025887 AGATACTGCCTGAAACTTGGGG 60.026 50.000 0.00 0.00 0.00 4.96
2722 2796 0.251165 TACTGCCTGAAACTTGGGGC 60.251 55.000 0.00 0.00 44.31 5.80
2724 2798 3.869481 GCCTGAAACTTGGGGCAA 58.131 55.556 0.00 0.00 43.59 4.52
2725 2799 1.367471 GCCTGAAACTTGGGGCAAC 59.633 57.895 0.00 0.00 43.59 4.17
2737 2811 2.049248 GGCAACCAACATGCGGTG 60.049 61.111 8.12 0.00 44.75 4.94
2738 2812 2.734346 GCAACCAACATGCGGTGC 60.734 61.111 8.12 5.32 36.67 5.01
2739 2813 3.041701 CAACCAACATGCGGTGCT 58.958 55.556 8.12 0.00 36.67 4.40
2740 2814 1.861542 GCAACCAACATGCGGTGCTA 61.862 55.000 8.12 0.00 36.67 3.49
2741 2815 0.109781 CAACCAACATGCGGTGCTAC 60.110 55.000 8.12 0.00 36.67 3.58
2742 2816 1.241315 AACCAACATGCGGTGCTACC 61.241 55.000 8.12 0.00 36.67 3.18
2743 2817 1.377202 CCAACATGCGGTGCTACCT 60.377 57.895 0.00 0.00 35.66 3.08
2744 2818 1.647545 CCAACATGCGGTGCTACCTG 61.648 60.000 0.00 0.00 35.66 4.00
2745 2819 2.040544 AACATGCGGTGCTACCTGC 61.041 57.895 0.00 11.87 43.25 4.85
2755 2829 2.624169 GCTACCTGCAAAACGACCA 58.376 52.632 0.00 0.00 42.31 4.02
2756 2830 0.948678 GCTACCTGCAAAACGACCAA 59.051 50.000 0.00 0.00 42.31 3.67
2757 2831 1.539827 GCTACCTGCAAAACGACCAAT 59.460 47.619 0.00 0.00 42.31 3.16
2758 2832 2.745281 GCTACCTGCAAAACGACCAATA 59.255 45.455 0.00 0.00 42.31 1.90
2759 2833 3.377172 GCTACCTGCAAAACGACCAATAT 59.623 43.478 0.00 0.00 42.31 1.28
2760 2834 4.142469 GCTACCTGCAAAACGACCAATATT 60.142 41.667 0.00 0.00 42.31 1.28
2761 2835 5.065474 GCTACCTGCAAAACGACCAATATTA 59.935 40.000 0.00 0.00 42.31 0.98
2762 2836 5.560966 ACCTGCAAAACGACCAATATTAG 57.439 39.130 0.00 0.00 0.00 1.73
2763 2837 4.142469 ACCTGCAAAACGACCAATATTAGC 60.142 41.667 0.00 0.00 0.00 3.09
2764 2838 4.096382 CCTGCAAAACGACCAATATTAGCT 59.904 41.667 0.00 0.00 0.00 3.32
2765 2839 5.295787 CCTGCAAAACGACCAATATTAGCTA 59.704 40.000 0.00 0.00 0.00 3.32
2766 2840 6.358118 TGCAAAACGACCAATATTAGCTAG 57.642 37.500 0.00 0.00 0.00 3.42
2767 2841 6.110033 TGCAAAACGACCAATATTAGCTAGA 58.890 36.000 0.00 0.00 0.00 2.43
2768 2842 6.596106 TGCAAAACGACCAATATTAGCTAGAA 59.404 34.615 0.00 0.00 0.00 2.10
2769 2843 6.905609 GCAAAACGACCAATATTAGCTAGAAC 59.094 38.462 0.00 0.00 0.00 3.01
2770 2844 7.201617 GCAAAACGACCAATATTAGCTAGAACT 60.202 37.037 0.00 0.00 0.00 3.01
2771 2845 9.309516 CAAAACGACCAATATTAGCTAGAACTA 57.690 33.333 0.00 0.00 0.00 2.24
2772 2846 9.530633 AAAACGACCAATATTAGCTAGAACTAG 57.469 33.333 0.00 4.67 36.29 2.57
2773 2847 8.461249 AACGACCAATATTAGCTAGAACTAGA 57.539 34.615 12.33 0.00 35.21 2.43
2774 2848 8.101654 ACGACCAATATTAGCTAGAACTAGAG 57.898 38.462 12.33 0.00 35.21 2.43
2775 2849 7.937942 ACGACCAATATTAGCTAGAACTAGAGA 59.062 37.037 12.33 0.00 35.21 3.10
2776 2850 8.231837 CGACCAATATTAGCTAGAACTAGAGAC 58.768 40.741 12.33 0.00 35.21 3.36
2777 2851 9.292195 GACCAATATTAGCTAGAACTAGAGACT 57.708 37.037 12.33 3.60 35.21 3.24
2778 2852 9.292195 ACCAATATTAGCTAGAACTAGAGACTC 57.708 37.037 12.33 0.00 35.21 3.36
2779 2853 8.447833 CCAATATTAGCTAGAACTAGAGACTCG 58.552 40.741 12.33 0.00 35.21 4.18
2780 2854 5.934935 ATTAGCTAGAACTAGAGACTCGC 57.065 43.478 12.33 0.73 35.21 5.03
2781 2855 2.206750 AGCTAGAACTAGAGACTCGCG 58.793 52.381 12.33 0.00 35.21 5.87
2782 2856 1.333435 GCTAGAACTAGAGACTCGCGC 60.333 57.143 12.33 0.00 35.21 6.86
2783 2857 0.928922 TAGAACTAGAGACTCGCGCG 59.071 55.000 26.76 26.76 0.00 6.86
2784 2858 1.020333 AGAACTAGAGACTCGCGCGT 61.020 55.000 30.98 12.05 0.00 6.01
2785 2859 0.179194 GAACTAGAGACTCGCGCGTT 60.179 55.000 30.98 18.38 0.00 4.84
2786 2860 1.061711 GAACTAGAGACTCGCGCGTTA 59.938 52.381 30.98 10.85 0.00 3.18
3062 3144 8.336235 TGGGAGATCTTATTTCATGTTAAACCT 58.664 33.333 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 124 1.949631 CGGCGTCTTCCTAATCGGC 60.950 63.158 0.00 0.00 43.44 5.54
338 341 2.126189 GCCGCCGAAGAAGTACGT 60.126 61.111 0.00 0.00 0.00 3.57
457 460 1.535462 CTTGTTCCGCCGTTTCTTGAT 59.465 47.619 0.00 0.00 0.00 2.57
472 475 4.016706 CGACCCGAGGGCCTTGTT 62.017 66.667 19.53 5.94 39.32 2.83
752 755 5.339423 TCCTTCATTTCTTTCCCTTTCCT 57.661 39.130 0.00 0.00 0.00 3.36
755 758 8.267620 AGAAAATCCTTCATTTCTTTCCCTTT 57.732 30.769 0.00 0.00 41.79 3.11
854 866 3.770040 CACGATGTCGGCCTCCCA 61.770 66.667 0.00 0.00 44.95 4.37
983 995 3.567478 ATGTTGTCGGCTCGTCGCA 62.567 57.895 0.00 0.00 41.67 5.10
1050 1062 4.069232 CTCAGTTCTGGCGGCGGA 62.069 66.667 17.78 17.78 0.00 5.54
1059 1071 1.376424 CGCCACCATGCTCAGTTCT 60.376 57.895 0.00 0.00 0.00 3.01
1145 1157 4.853142 TCCCGGTGATCCCCTCGG 62.853 72.222 0.00 0.00 41.90 4.63
1314 1326 2.202946 TGCACGTTCTTGGACGCA 60.203 55.556 0.86 0.00 46.47 5.24
1426 1438 6.538263 AGAATTCCTACTCTGTTCTTGCTTT 58.462 36.000 0.65 0.00 0.00 3.51
1433 1445 7.113658 TGGTGATAGAATTCCTACTCTGTTC 57.886 40.000 0.65 0.00 0.00 3.18
1447 1459 5.316167 AGTTTGACAGCAATGGTGATAGAA 58.684 37.500 19.98 5.48 34.87 2.10
1468 1481 4.689612 TCTTTGGCTGTTCTTGTCTAGT 57.310 40.909 0.00 0.00 0.00 2.57
1516 1529 7.095910 CGGCACTATCTTAGTAGCTAGTAGTA 58.904 42.308 8.29 2.10 37.23 1.82
1517 1530 5.933463 CGGCACTATCTTAGTAGCTAGTAGT 59.067 44.000 8.29 2.16 37.23 2.73
1518 1531 5.933463 ACGGCACTATCTTAGTAGCTAGTAG 59.067 44.000 8.29 1.56 37.23 2.57
1590 1605 4.081198 TGTGGCAATGTTTCTCCAAAGTTT 60.081 37.500 0.00 0.00 0.00 2.66
1594 1609 2.224018 GCTGTGGCAATGTTTCTCCAAA 60.224 45.455 0.00 0.00 38.54 3.28
1595 1610 1.340889 GCTGTGGCAATGTTTCTCCAA 59.659 47.619 0.00 0.00 38.54 3.53
1596 1611 0.961019 GCTGTGGCAATGTTTCTCCA 59.039 50.000 0.00 0.00 38.54 3.86
1597 1612 1.251251 AGCTGTGGCAATGTTTCTCC 58.749 50.000 0.00 0.00 41.70 3.71
1598 1613 3.077359 ACTAGCTGTGGCAATGTTTCTC 58.923 45.455 0.00 0.00 41.70 2.87
1599 1614 3.146104 ACTAGCTGTGGCAATGTTTCT 57.854 42.857 0.00 0.00 41.70 2.52
1600 1615 3.923017 AACTAGCTGTGGCAATGTTTC 57.077 42.857 0.00 0.00 41.70 2.78
1601 1616 4.370917 CAAAACTAGCTGTGGCAATGTTT 58.629 39.130 0.00 0.00 41.70 2.83
1602 1617 3.243839 CCAAAACTAGCTGTGGCAATGTT 60.244 43.478 0.00 0.00 41.70 2.71
1603 1618 2.297033 CCAAAACTAGCTGTGGCAATGT 59.703 45.455 0.00 0.00 41.70 2.71
1604 1619 2.557924 TCCAAAACTAGCTGTGGCAATG 59.442 45.455 0.00 0.00 41.70 2.82
1605 1620 2.875296 TCCAAAACTAGCTGTGGCAAT 58.125 42.857 0.00 0.00 41.70 3.56
1606 1621 2.356665 TCCAAAACTAGCTGTGGCAA 57.643 45.000 0.00 0.00 41.70 4.52
1607 1622 2.356665 TTCCAAAACTAGCTGTGGCA 57.643 45.000 0.00 0.00 41.70 4.92
1608 1623 3.726291 TTTTCCAAAACTAGCTGTGGC 57.274 42.857 0.00 0.00 39.06 5.01
1609 1624 5.004922 TGTTTTTCCAAAACTAGCTGTGG 57.995 39.130 12.15 0.00 0.00 4.17
1610 1625 5.463061 CCATGTTTTTCCAAAACTAGCTGTG 59.537 40.000 12.15 0.00 0.00 3.66
1611 1626 5.600696 CCATGTTTTTCCAAAACTAGCTGT 58.399 37.500 12.15 0.00 0.00 4.40
1612 1627 4.448732 GCCATGTTTTTCCAAAACTAGCTG 59.551 41.667 12.15 5.93 0.00 4.24
1613 1628 4.503123 GGCCATGTTTTTCCAAAACTAGCT 60.503 41.667 12.15 0.00 0.00 3.32
1614 1629 3.745975 GGCCATGTTTTTCCAAAACTAGC 59.254 43.478 12.15 11.22 0.00 3.42
1615 1630 4.749598 GTGGCCATGTTTTTCCAAAACTAG 59.250 41.667 9.72 0.00 0.00 2.57
1616 1631 4.698575 GTGGCCATGTTTTTCCAAAACTA 58.301 39.130 9.72 1.68 0.00 2.24
1617 1632 3.540617 GTGGCCATGTTTTTCCAAAACT 58.459 40.909 9.72 0.00 0.00 2.66
1618 1633 2.286563 CGTGGCCATGTTTTTCCAAAAC 59.713 45.455 17.42 5.33 0.00 2.43
1619 1634 2.168521 TCGTGGCCATGTTTTTCCAAAA 59.831 40.909 24.24 0.00 0.00 2.44
1658 1674 3.034635 AGTATTCTCCATTGCCGTCTCT 58.965 45.455 0.00 0.00 0.00 3.10
1812 1828 5.065218 CGTACTACACCTACCAGTCGTTATT 59.935 44.000 0.00 0.00 0.00 1.40
1844 1860 0.459899 TGGAGCGCTACACACATAGG 59.540 55.000 21.07 0.00 0.00 2.57
1861 1877 2.477845 TACGGATGGATCATGCATGG 57.522 50.000 25.97 10.03 31.64 3.66
1874 1890 7.140705 TGACGACGACATAATTAAATACGGAT 58.859 34.615 0.00 0.00 0.00 4.18
1950 1972 9.689976 ATCTATCTGATCAAGACGTTCTTTATG 57.310 33.333 0.00 0.00 37.88 1.90
1972 1994 1.938577 GCCGTATATCTCCGCGATCTA 59.061 52.381 8.23 0.00 33.48 1.98
1978 2000 0.170561 ATCACGCCGTATATCTCCGC 59.829 55.000 0.00 0.00 0.00 5.54
1990 2012 2.202171 CGTCGCAACAATCACGCC 60.202 61.111 0.00 0.00 0.00 5.68
2023 2055 3.357166 AAAAACGCCGAGCAAAATGTA 57.643 38.095 0.00 0.00 0.00 2.29
2076 2124 8.989980 GTTCAGCTAATCAGTTTACTTACACTT 58.010 33.333 0.00 0.00 0.00 3.16
2077 2125 7.603024 GGTTCAGCTAATCAGTTTACTTACACT 59.397 37.037 0.00 0.00 0.00 3.55
2078 2126 7.148457 GGGTTCAGCTAATCAGTTTACTTACAC 60.148 40.741 0.00 0.00 0.00 2.90
2079 2127 6.877322 GGGTTCAGCTAATCAGTTTACTTACA 59.123 38.462 0.00 0.00 0.00 2.41
2080 2128 7.064728 CAGGGTTCAGCTAATCAGTTTACTTAC 59.935 40.741 0.00 0.00 0.00 2.34
2096 2144 0.883833 CATCCAACACAGGGTTCAGC 59.116 55.000 0.00 0.00 37.72 4.26
2108 2156 0.384230 CACGCGTGTCAACATCCAAC 60.384 55.000 30.50 0.00 0.00 3.77
2109 2157 1.938125 CACGCGTGTCAACATCCAA 59.062 52.632 30.50 0.00 0.00 3.53
2110 2158 2.603247 GCACGCGTGTCAACATCCA 61.603 57.895 36.80 0.00 0.00 3.41
2111 2159 2.173382 GCACGCGTGTCAACATCC 59.827 61.111 36.80 16.46 0.00 3.51
2112 2160 1.154599 CTGCACGCGTGTCAACATC 60.155 57.895 36.80 20.52 0.00 3.06
2113 2161 2.938253 CTGCACGCGTGTCAACAT 59.062 55.556 36.80 0.00 0.00 2.71
2115 2163 4.666532 GGCTGCACGCGTGTCAAC 62.667 66.667 36.80 27.76 40.44 3.18
2295 2362 2.101209 CTTGTTGGACGTGTCGTGGC 62.101 60.000 0.00 0.00 41.37 5.01
2346 2413 0.395862 ATCATCGTGGTCCTCCTCGT 60.396 55.000 8.21 0.00 46.59 4.18
2362 2429 2.104132 CGCGTGATCCGGTCATCA 59.896 61.111 0.00 0.58 39.48 3.07
2386 2453 1.373748 GTACCGCAAGACGCCTTCA 60.374 57.895 0.00 0.00 41.76 3.02
2537 2611 1.328680 TCGAATCCGAGCAGTACGTAC 59.671 52.381 18.10 18.10 40.30 3.67
2570 2644 4.701651 CCAGTCTTAGTGCATTCCATTCAA 59.298 41.667 0.00 0.00 0.00 2.69
2581 2655 4.567159 CGGATTTAACTCCAGTCTTAGTGC 59.433 45.833 11.97 0.00 34.78 4.40
2582 2656 5.109903 CCGGATTTAACTCCAGTCTTAGTG 58.890 45.833 11.97 0.00 34.78 2.74
2583 2657 4.776308 ACCGGATTTAACTCCAGTCTTAGT 59.224 41.667 9.46 0.00 34.78 2.24
2584 2658 5.340439 ACCGGATTTAACTCCAGTCTTAG 57.660 43.478 9.46 0.00 34.78 2.18
2585 2659 5.127682 GGTACCGGATTTAACTCCAGTCTTA 59.872 44.000 9.46 0.00 34.78 2.10
2586 2660 4.081254 GGTACCGGATTTAACTCCAGTCTT 60.081 45.833 9.46 0.00 34.78 3.01
2587 2661 3.450096 GGTACCGGATTTAACTCCAGTCT 59.550 47.826 9.46 0.00 34.78 3.24
2588 2662 3.736126 CGGTACCGGATTTAACTCCAGTC 60.736 52.174 27.00 2.19 34.78 3.51
2589 2663 2.167075 CGGTACCGGATTTAACTCCAGT 59.833 50.000 27.00 8.96 34.78 4.00
2590 2664 2.167075 ACGGTACCGGATTTAACTCCAG 59.833 50.000 35.86 5.70 44.69 3.86
2591 2665 2.094078 CACGGTACCGGATTTAACTCCA 60.094 50.000 35.86 0.00 44.69 3.86
2592 2666 2.094026 ACACGGTACCGGATTTAACTCC 60.094 50.000 35.86 1.73 44.69 3.85
2593 2667 3.236632 ACACGGTACCGGATTTAACTC 57.763 47.619 35.86 0.00 44.69 3.01
2594 2668 3.683365 AACACGGTACCGGATTTAACT 57.317 42.857 35.86 11.64 44.69 2.24
2595 2669 4.213059 TGAAAACACGGTACCGGATTTAAC 59.787 41.667 35.86 26.69 44.69 2.01
2596 2670 4.384056 TGAAAACACGGTACCGGATTTAA 58.616 39.130 35.86 22.61 44.69 1.52
2597 2671 3.995705 CTGAAAACACGGTACCGGATTTA 59.004 43.478 35.86 19.48 44.69 1.40
2598 2672 2.809696 CTGAAAACACGGTACCGGATTT 59.190 45.455 35.86 29.42 44.69 2.17
2599 2673 2.037511 TCTGAAAACACGGTACCGGATT 59.962 45.455 35.86 25.90 44.69 3.01
2600 2674 1.619827 TCTGAAAACACGGTACCGGAT 59.380 47.619 35.86 21.74 44.69 4.18
2601 2675 1.000060 CTCTGAAAACACGGTACCGGA 60.000 52.381 35.86 20.01 44.69 5.14
2602 2676 1.269936 ACTCTGAAAACACGGTACCGG 60.270 52.381 35.86 26.14 44.69 5.28
2603 2677 2.056577 GACTCTGAAAACACGGTACCG 58.943 52.381 32.22 32.22 46.03 4.02
2604 2678 2.410939 GGACTCTGAAAACACGGTACC 58.589 52.381 0.16 0.16 0.00 3.34
2605 2679 2.410939 GGGACTCTGAAAACACGGTAC 58.589 52.381 0.00 0.00 0.00 3.34
2606 2680 1.345415 GGGGACTCTGAAAACACGGTA 59.655 52.381 0.00 0.00 0.00 4.02
2607 2681 0.108019 GGGGACTCTGAAAACACGGT 59.892 55.000 0.00 0.00 0.00 4.83
2608 2682 0.949105 CGGGGACTCTGAAAACACGG 60.949 60.000 0.00 0.00 0.00 4.94
2609 2683 0.949105 CCGGGGACTCTGAAAACACG 60.949 60.000 0.00 0.00 0.00 4.49
2610 2684 0.108019 ACCGGGGACTCTGAAAACAC 59.892 55.000 6.32 0.00 0.00 3.32
2611 2685 0.107831 CACCGGGGACTCTGAAAACA 59.892 55.000 6.32 0.00 0.00 2.83
2612 2686 0.108019 ACACCGGGGACTCTGAAAAC 59.892 55.000 12.96 0.00 0.00 2.43
2613 2687 0.841289 AACACCGGGGACTCTGAAAA 59.159 50.000 12.96 0.00 0.00 2.29
2614 2688 0.841289 AAACACCGGGGACTCTGAAA 59.159 50.000 12.96 0.00 0.00 2.69
2615 2689 0.841289 AAAACACCGGGGACTCTGAA 59.159 50.000 12.96 0.00 0.00 3.02
2616 2690 0.841289 AAAAACACCGGGGACTCTGA 59.159 50.000 12.96 0.00 0.00 3.27
2617 2691 3.414486 AAAAACACCGGGGACTCTG 57.586 52.632 12.96 0.00 0.00 3.35
2637 2711 9.387397 AGGAATAAAACCCTTTTCTATCCAAAA 57.613 29.630 0.00 0.00 34.14 2.44
2638 2712 8.966155 AGGAATAAAACCCTTTTCTATCCAAA 57.034 30.769 0.00 0.00 34.14 3.28
2639 2713 7.338449 CGAGGAATAAAACCCTTTTCTATCCAA 59.662 37.037 0.00 0.00 34.14 3.53
2640 2714 6.826741 CGAGGAATAAAACCCTTTTCTATCCA 59.173 38.462 0.00 0.00 34.14 3.41
2641 2715 7.052248 TCGAGGAATAAAACCCTTTTCTATCC 58.948 38.462 0.00 0.00 34.19 2.59
2642 2716 8.678593 ATCGAGGAATAAAACCCTTTTCTATC 57.321 34.615 0.00 0.00 34.19 2.08
2647 2721 9.916360 ACTATTATCGAGGAATAAAACCCTTTT 57.084 29.630 0.00 0.00 36.67 2.27
2659 2733 8.512956 GCTGACTGTAATACTATTATCGAGGAA 58.487 37.037 0.00 0.00 0.00 3.36
2660 2734 7.883833 AGCTGACTGTAATACTATTATCGAGGA 59.116 37.037 0.00 0.00 0.00 3.71
2661 2735 8.046294 AGCTGACTGTAATACTATTATCGAGG 57.954 38.462 0.00 0.00 0.00 4.63
2676 2750 9.682465 TCTCTAGTCTTATTTTAGCTGACTGTA 57.318 33.333 10.08 0.00 38.30 2.74
2677 2751 8.582657 TCTCTAGTCTTATTTTAGCTGACTGT 57.417 34.615 10.08 0.00 38.30 3.55
2682 2756 9.405587 GCAGTATCTCTAGTCTTATTTTAGCTG 57.594 37.037 0.00 0.00 0.00 4.24
2683 2757 8.581578 GGCAGTATCTCTAGTCTTATTTTAGCT 58.418 37.037 0.00 0.00 0.00 3.32
2684 2758 8.581578 AGGCAGTATCTCTAGTCTTATTTTAGC 58.418 37.037 0.00 0.00 0.00 3.09
2685 2759 9.906660 CAGGCAGTATCTCTAGTCTTATTTTAG 57.093 37.037 0.00 0.00 0.00 1.85
2686 2760 9.642343 TCAGGCAGTATCTCTAGTCTTATTTTA 57.358 33.333 0.00 0.00 0.00 1.52
2687 2761 8.540507 TCAGGCAGTATCTCTAGTCTTATTTT 57.459 34.615 0.00 0.00 0.00 1.82
2688 2762 8.540507 TTCAGGCAGTATCTCTAGTCTTATTT 57.459 34.615 0.00 0.00 0.00 1.40
2689 2763 8.417884 GTTTCAGGCAGTATCTCTAGTCTTATT 58.582 37.037 0.00 0.00 0.00 1.40
2690 2764 7.782644 AGTTTCAGGCAGTATCTCTAGTCTTAT 59.217 37.037 0.00 0.00 0.00 1.73
2691 2765 7.120051 AGTTTCAGGCAGTATCTCTAGTCTTA 58.880 38.462 0.00 0.00 0.00 2.10
2692 2766 5.955355 AGTTTCAGGCAGTATCTCTAGTCTT 59.045 40.000 0.00 0.00 0.00 3.01
2693 2767 5.515106 AGTTTCAGGCAGTATCTCTAGTCT 58.485 41.667 0.00 0.00 0.00 3.24
2694 2768 5.845391 AGTTTCAGGCAGTATCTCTAGTC 57.155 43.478 0.00 0.00 0.00 2.59
2695 2769 5.105146 CCAAGTTTCAGGCAGTATCTCTAGT 60.105 44.000 0.00 0.00 0.00 2.57
2696 2770 5.355596 CCAAGTTTCAGGCAGTATCTCTAG 58.644 45.833 0.00 0.00 0.00 2.43
2697 2771 4.162320 CCCAAGTTTCAGGCAGTATCTCTA 59.838 45.833 0.00 0.00 0.00 2.43
2698 2772 3.054802 CCCAAGTTTCAGGCAGTATCTCT 60.055 47.826 0.00 0.00 0.00 3.10
2699 2773 3.274288 CCCAAGTTTCAGGCAGTATCTC 58.726 50.000 0.00 0.00 0.00 2.75
2700 2774 2.025887 CCCCAAGTTTCAGGCAGTATCT 60.026 50.000 0.00 0.00 0.00 1.98
2701 2775 2.369394 CCCCAAGTTTCAGGCAGTATC 58.631 52.381 0.00 0.00 0.00 2.24
2702 2776 1.616994 GCCCCAAGTTTCAGGCAGTAT 60.617 52.381 3.25 0.00 45.07 2.12
2703 2777 0.251165 GCCCCAAGTTTCAGGCAGTA 60.251 55.000 3.25 0.00 45.07 2.74
2704 2778 1.531602 GCCCCAAGTTTCAGGCAGT 60.532 57.895 3.25 0.00 45.07 4.40
2705 2779 3.369921 GCCCCAAGTTTCAGGCAG 58.630 61.111 3.25 0.00 45.07 4.85
2707 2781 1.367471 GTTGCCCCAAGTTTCAGGC 59.633 57.895 0.00 0.00 45.96 4.85
2708 2782 0.758685 TGGTTGCCCCAAGTTTCAGG 60.759 55.000 0.00 0.00 41.50 3.86
2709 2783 2.819477 TGGTTGCCCCAAGTTTCAG 58.181 52.632 0.00 0.00 41.50 3.02
2717 2791 3.301554 CGCATGTTGGTTGCCCCA 61.302 61.111 0.00 0.00 43.27 4.96
2718 2792 4.067913 CCGCATGTTGGTTGCCCC 62.068 66.667 0.00 0.00 36.75 5.80
2719 2793 3.302344 ACCGCATGTTGGTTGCCC 61.302 61.111 6.00 0.00 35.82 5.36
2720 2794 2.049248 CACCGCATGTTGGTTGCC 60.049 61.111 8.81 0.00 37.72 4.52
2721 2795 1.861542 TAGCACCGCATGTTGGTTGC 61.862 55.000 17.43 17.43 37.72 4.17
2722 2796 0.109781 GTAGCACCGCATGTTGGTTG 60.110 55.000 8.81 6.67 37.72 3.77
2723 2797 1.241315 GGTAGCACCGCATGTTGGTT 61.241 55.000 8.81 0.00 37.72 3.67
2724 2798 1.674322 GGTAGCACCGCATGTTGGT 60.674 57.895 6.00 6.00 41.47 3.67
2725 2799 1.377202 AGGTAGCACCGCATGTTGG 60.377 57.895 4.76 4.76 44.90 3.77
2726 2800 1.796151 CAGGTAGCACCGCATGTTG 59.204 57.895 0.00 0.00 44.90 3.33
2727 2801 2.040544 GCAGGTAGCACCGCATGTT 61.041 57.895 13.04 0.00 44.90 2.71
2728 2802 2.436646 GCAGGTAGCACCGCATGT 60.437 61.111 13.04 0.00 44.90 3.21
2737 2811 0.948678 TTGGTCGTTTTGCAGGTAGC 59.051 50.000 0.00 0.00 45.96 3.58
2738 2812 5.560966 AATATTGGTCGTTTTGCAGGTAG 57.439 39.130 0.00 0.00 0.00 3.18
2739 2813 5.065474 GCTAATATTGGTCGTTTTGCAGGTA 59.935 40.000 0.00 0.00 0.00 3.08
2740 2814 4.142469 GCTAATATTGGTCGTTTTGCAGGT 60.142 41.667 0.00 0.00 0.00 4.00
2741 2815 4.096382 AGCTAATATTGGTCGTTTTGCAGG 59.904 41.667 0.00 0.00 0.00 4.85
2742 2816 5.235305 AGCTAATATTGGTCGTTTTGCAG 57.765 39.130 0.00 0.00 0.00 4.41
2743 2817 6.110033 TCTAGCTAATATTGGTCGTTTTGCA 58.890 36.000 0.00 0.00 0.00 4.08
2744 2818 6.598753 TCTAGCTAATATTGGTCGTTTTGC 57.401 37.500 0.00 0.00 0.00 3.68
2745 2819 8.197988 AGTTCTAGCTAATATTGGTCGTTTTG 57.802 34.615 0.00 0.00 0.00 2.44
2746 2820 9.530633 CTAGTTCTAGCTAATATTGGTCGTTTT 57.469 33.333 0.00 0.00 0.00 2.43
2747 2821 8.910944 TCTAGTTCTAGCTAATATTGGTCGTTT 58.089 33.333 0.00 0.00 0.00 3.60
2748 2822 8.461249 TCTAGTTCTAGCTAATATTGGTCGTT 57.539 34.615 0.00 0.00 0.00 3.85
2749 2823 7.937942 TCTCTAGTTCTAGCTAATATTGGTCGT 59.062 37.037 0.00 0.00 0.00 4.34
2750 2824 8.231837 GTCTCTAGTTCTAGCTAATATTGGTCG 58.768 40.741 0.00 0.00 0.00 4.79
2751 2825 9.292195 AGTCTCTAGTTCTAGCTAATATTGGTC 57.708 37.037 0.00 0.00 0.00 4.02
2752 2826 9.292195 GAGTCTCTAGTTCTAGCTAATATTGGT 57.708 37.037 0.00 0.00 0.00 3.67
2753 2827 8.447833 CGAGTCTCTAGTTCTAGCTAATATTGG 58.552 40.741 0.00 0.00 0.00 3.16
2754 2828 7.960738 GCGAGTCTCTAGTTCTAGCTAATATTG 59.039 40.741 0.00 0.00 0.00 1.90
2755 2829 7.148540 CGCGAGTCTCTAGTTCTAGCTAATATT 60.149 40.741 0.00 0.00 0.00 1.28
2756 2830 6.311935 CGCGAGTCTCTAGTTCTAGCTAATAT 59.688 42.308 0.00 0.00 0.00 1.28
2757 2831 5.634439 CGCGAGTCTCTAGTTCTAGCTAATA 59.366 44.000 0.00 0.00 0.00 0.98
2758 2832 4.449743 CGCGAGTCTCTAGTTCTAGCTAAT 59.550 45.833 0.00 0.00 0.00 1.73
2759 2833 3.803231 CGCGAGTCTCTAGTTCTAGCTAA 59.197 47.826 0.00 0.00 0.00 3.09
2760 2834 3.382855 CGCGAGTCTCTAGTTCTAGCTA 58.617 50.000 0.00 0.00 0.00 3.32
2761 2835 2.206750 CGCGAGTCTCTAGTTCTAGCT 58.793 52.381 0.00 0.00 0.00 3.32
2762 2836 1.333435 GCGCGAGTCTCTAGTTCTAGC 60.333 57.143 12.10 0.00 0.00 3.42
2763 2837 1.071107 CGCGCGAGTCTCTAGTTCTAG 60.071 57.143 28.94 0.83 0.00 2.43
2764 2838 0.928922 CGCGCGAGTCTCTAGTTCTA 59.071 55.000 28.94 0.00 0.00 2.10
2765 2839 1.020333 ACGCGCGAGTCTCTAGTTCT 61.020 55.000 39.36 5.70 0.00 3.01
2766 2840 0.179194 AACGCGCGAGTCTCTAGTTC 60.179 55.000 39.36 0.00 0.00 3.01
2767 2841 1.062294 CTAACGCGCGAGTCTCTAGTT 59.938 52.381 39.36 19.09 0.00 2.24
2768 2842 0.651551 CTAACGCGCGAGTCTCTAGT 59.348 55.000 39.36 7.53 0.00 2.57
2769 2843 0.651551 ACTAACGCGCGAGTCTCTAG 59.348 55.000 39.36 24.40 0.00 2.43
2770 2844 1.061711 GAACTAACGCGCGAGTCTCTA 59.938 52.381 39.36 15.26 0.00 2.43
2771 2845 0.179194 GAACTAACGCGCGAGTCTCT 60.179 55.000 39.36 15.42 0.00 3.10
2772 2846 0.179194 AGAACTAACGCGCGAGTCTC 60.179 55.000 39.36 25.20 0.00 3.36
2773 2847 0.240411 AAGAACTAACGCGCGAGTCT 59.760 50.000 39.36 24.86 0.00 3.24
2774 2848 0.634232 GAAGAACTAACGCGCGAGTC 59.366 55.000 39.36 23.12 0.00 3.36
2775 2849 0.039798 TGAAGAACTAACGCGCGAGT 60.040 50.000 39.36 27.43 0.00 4.18
2776 2850 0.362512 GTGAAGAACTAACGCGCGAG 59.637 55.000 39.36 26.68 0.00 5.03
2777 2851 0.039798 AGTGAAGAACTAACGCGCGA 60.040 50.000 39.36 14.99 37.36 5.87
2778 2852 0.362512 GAGTGAAGAACTAACGCGCG 59.637 55.000 30.96 30.96 40.07 6.86
2779 2853 0.362512 CGAGTGAAGAACTAACGCGC 59.637 55.000 5.73 0.00 40.07 6.86
2780 2854 1.382419 CACGAGTGAAGAACTAACGCG 59.618 52.381 3.53 3.53 40.07 6.01
2781 2855 2.658285 TCACGAGTGAAGAACTAACGC 58.342 47.619 3.11 0.00 40.07 4.84
2894 2970 7.124347 ACACGATATACGAACAAAACAACAT 57.876 32.000 0.00 0.00 45.77 2.71
2966 3046 8.722394 TGTGTAAAGATTTCACAAATACGCATA 58.278 29.630 0.84 0.00 38.80 3.14
3062 3144 5.006153 AGCGTGACTGTAGCAATTACATA 57.994 39.130 5.44 0.00 41.30 2.29
3066 3148 3.250744 GTGAGCGTGACTGTAGCAATTA 58.749 45.455 5.44 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.