Multiple sequence alignment - TraesCS2D01G522400

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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 TraesCS2D01G522400 chr2D 100.000 6742 0 0 1 6742 611165025 611158284 0.000000e+00 12451.0
1 TraesCS2D01G522400 chr2D 87.733 644 58 7 75 697 569851466 569850823 0.000000e+00 732.0
2 TraesCS2D01G522400 chr2D 88.293 615 65 5 75 684 603661439 603660827 0.000000e+00 730.0
3 TraesCS2D01G522400 chr2D 87.023 131 14 3 6447 6575 610411131 610411002 1.960000e-30 145.0
4 TraesCS2D01G522400 chr2A 95.194 3995 120 39 2784 6742 743389578 743385620 0.000000e+00 6248.0
5 TraesCS2D01G522400 chr2A 92.668 1514 66 22 1292 2782 743391591 743390100 0.000000e+00 2139.0
6 TraesCS2D01G522400 chr2A 90.017 581 52 6 117 696 197486942 197486367 0.000000e+00 747.0
7 TraesCS2D01G522400 chr2A 88.645 502 20 14 761 1254 743392329 743391857 1.630000e-160 577.0
8 TraesCS2D01G522400 chr2A 84.615 130 19 1 6447 6575 743324986 743324857 1.970000e-25 128.0
9 TraesCS2D01G522400 chr2A 100.000 28 0 0 6656 6683 743385670 743385643 1.200000e-02 52.8
10 TraesCS2D01G522400 chr2B 95.183 3052 116 18 2784 5823 746039052 746036020 0.000000e+00 4793.0
11 TraesCS2D01G522400 chr2B 90.742 2128 107 37 701 2779 746041664 746039578 0.000000e+00 2756.0
12 TraesCS2D01G522400 chr2B 89.441 805 56 15 5900 6693 746035984 746035198 0.000000e+00 989.0
13 TraesCS2D01G522400 chr2B 88.312 847 67 16 1368 2203 69930879 69931704 0.000000e+00 987.0
14 TraesCS2D01G522400 chr2B 87.839 847 62 21 1368 2203 69982241 69983057 0.000000e+00 955.0
15 TraesCS2D01G522400 chr2B 87.023 131 14 3 6447 6575 745781492 745781363 1.960000e-30 145.0
16 TraesCS2D01G522400 chr4A 91.772 632 45 2 75 699 690100877 690100246 0.000000e+00 872.0
17 TraesCS2D01G522400 chr5B 91.840 625 30 3 95 698 311547870 311547246 0.000000e+00 852.0
18 TraesCS2D01G522400 chr5B 84.354 588 69 7 62 627 571222294 571221708 7.640000e-154 555.0
19 TraesCS2D01G522400 chr6D 89.596 644 55 4 62 696 24828007 24828647 0.000000e+00 808.0
20 TraesCS2D01G522400 chr6D 89.692 650 41 7 72 698 106077252 106077898 0.000000e+00 806.0
21 TraesCS2D01G522400 chr6D 84.667 150 23 0 1095 1244 394555699 394555848 4.210000e-32 150.0
22 TraesCS2D01G522400 chr5D 90.492 610 36 5 92 680 411155286 411155894 0.000000e+00 785.0
23 TraesCS2D01G522400 chr3A 88.940 651 44 11 72 698 507057398 507056752 0.000000e+00 778.0
24 TraesCS2D01G522400 chr6B 92.393 539 28 4 1666 2203 488863915 488864441 0.000000e+00 756.0
25 TraesCS2D01G522400 chr6B 83.750 160 25 1 1095 1254 590444899 590445057 4.210000e-32 150.0
26 TraesCS2D01G522400 chr6B 100.000 41 0 0 2127 2167 488864439 488864479 7.250000e-10 76.8
27 TraesCS2D01G522400 chr6A 84.000 150 24 0 1095 1244 540601575 540601724 1.960000e-30 145.0
28 TraesCS2D01G522400 chr7D 82.407 108 8 4 1034 1141 609066445 609066349 4.330000e-12 84.2
29 TraesCS2D01G522400 chr1D 100.000 30 0 0 6466 6495 479359465 479359436 1.000000e-03 56.5


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 TraesCS2D01G522400 chr2D 611158284 611165025 6741 True 12451.0 12451 100.000000 1 6742 1 chr2D.!!$R4 6741
1 TraesCS2D01G522400 chr2D 569850823 569851466 643 True 732.0 732 87.733000 75 697 1 chr2D.!!$R1 622
2 TraesCS2D01G522400 chr2D 603660827 603661439 612 True 730.0 730 88.293000 75 684 1 chr2D.!!$R2 609
3 TraesCS2D01G522400 chr2A 743385620 743389578 3958 True 3150.4 6248 97.597000 2784 6742 2 chr2A.!!$R3 3958
4 TraesCS2D01G522400 chr2A 743390100 743392329 2229 True 1358.0 2139 90.656500 761 2782 2 chr2A.!!$R4 2021
5 TraesCS2D01G522400 chr2A 197486367 197486942 575 True 747.0 747 90.017000 117 696 1 chr2A.!!$R1 579
6 TraesCS2D01G522400 chr2B 746035198 746041664 6466 True 2846.0 4793 91.788667 701 6693 3 chr2B.!!$R2 5992
7 TraesCS2D01G522400 chr2B 69930879 69931704 825 False 987.0 987 88.312000 1368 2203 1 chr2B.!!$F1 835
8 TraesCS2D01G522400 chr2B 69982241 69983057 816 False 955.0 955 87.839000 1368 2203 1 chr2B.!!$F2 835
9 TraesCS2D01G522400 chr4A 690100246 690100877 631 True 872.0 872 91.772000 75 699 1 chr4A.!!$R1 624
10 TraesCS2D01G522400 chr5B 311547246 311547870 624 True 852.0 852 91.840000 95 698 1 chr5B.!!$R1 603
11 TraesCS2D01G522400 chr5B 571221708 571222294 586 True 555.0 555 84.354000 62 627 1 chr5B.!!$R2 565
12 TraesCS2D01G522400 chr6D 24828007 24828647 640 False 808.0 808 89.596000 62 696 1 chr6D.!!$F1 634
13 TraesCS2D01G522400 chr6D 106077252 106077898 646 False 806.0 806 89.692000 72 698 1 chr6D.!!$F2 626
14 TraesCS2D01G522400 chr5D 411155286 411155894 608 False 785.0 785 90.492000 92 680 1 chr5D.!!$F1 588
15 TraesCS2D01G522400 chr3A 507056752 507057398 646 True 778.0 778 88.940000 72 698 1 chr3A.!!$R1 626
16 TraesCS2D01G522400 chr6B 488863915 488864479 564 False 416.4 756 96.196500 1666 2203 2 chr6B.!!$F2 537

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
32 33 0.173481 TCGTCGGCTTGAATCCTCTG 59.827 55.000 0.00 0.0 0.00 3.35 F
487 524 0.179081 GTTCTACGGGGCCTTAGCAG 60.179 60.000 0.84 0.0 42.56 4.24 F
910 953 0.185175 AACCCAAAAGAACCCGAGCT 59.815 50.000 0.00 0.0 0.00 4.09 F
1601 1926 0.179468 AAAGGGCGCGCTTAATCCTA 59.821 50.000 35.79 0.0 0.00 2.94 F
1812 2137 1.202879 TGCCCTGGTGTAGTTTTGGAG 60.203 52.381 0.00 0.0 0.00 3.86 F
2733 3076 1.279271 GGTAGGTGCTGAAGTGACCAT 59.721 52.381 0.00 0.0 31.61 3.55 F
4075 4956 1.451028 GCGGCTTGCTGAGGAATCT 60.451 57.895 5.52 0.0 41.73 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1387 1672 0.309922 TATCCAGCGACGAATCCGAC 59.690 55.000 0.00 0.00 39.50 4.79 R
1389 1674 0.311165 ACTATCCAGCGACGAATCCG 59.689 55.000 0.00 0.00 42.50 4.18 R
2273 2611 0.824109 TCCCGAAGATGAAGCGACAT 59.176 50.000 0.00 0.00 0.00 3.06 R
2733 3076 1.069513 ACATTATTACGCGGGCTAGCA 59.930 47.619 18.24 0.00 36.85 3.49 R
3772 4653 3.766591 CTCTCCACAGTTCTAGACCATGT 59.233 47.826 0.00 0.00 0.00 3.21 R
4351 5232 0.804989 GCTGGACGAAATCAACAGGG 59.195 55.000 0.00 0.00 0.00 4.45 R
5809 6690 0.182537 AGGCAACAACTGTGGCTACA 59.817 50.000 9.05 1.86 44.30 2.74 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
18 19 2.427360 ACGGACAAAATCGTCGTCG 58.573 52.632 0.00 0.00 36.73 5.12
19 20 1.005294 ACGGACAAAATCGTCGTCGG 61.005 55.000 1.55 0.00 36.73 4.79
20 21 1.418755 GGACAAAATCGTCGTCGGC 59.581 57.895 1.55 0.00 36.73 5.54
21 22 1.012486 GGACAAAATCGTCGTCGGCT 61.012 55.000 1.55 0.00 36.73 5.52
22 23 0.788391 GACAAAATCGTCGTCGGCTT 59.212 50.000 1.55 0.00 37.69 4.35
23 24 0.511221 ACAAAATCGTCGTCGGCTTG 59.489 50.000 1.55 6.25 37.69 4.01
24 25 0.787787 CAAAATCGTCGTCGGCTTGA 59.212 50.000 1.55 0.00 37.69 3.02
25 26 1.193650 CAAAATCGTCGTCGGCTTGAA 59.806 47.619 1.55 0.00 37.69 2.69
26 27 1.722011 AAATCGTCGTCGGCTTGAAT 58.278 45.000 1.55 0.00 37.69 2.57
27 28 1.278238 AATCGTCGTCGGCTTGAATC 58.722 50.000 1.55 0.00 37.69 2.52
28 29 0.527817 ATCGTCGTCGGCTTGAATCC 60.528 55.000 1.55 0.00 37.69 3.01
29 30 1.153823 CGTCGTCGGCTTGAATCCT 60.154 57.895 0.00 0.00 0.00 3.24
30 31 1.140407 CGTCGTCGGCTTGAATCCTC 61.140 60.000 0.00 0.00 0.00 3.71
31 32 0.173708 GTCGTCGGCTTGAATCCTCT 59.826 55.000 0.00 0.00 0.00 3.69
32 33 0.173481 TCGTCGGCTTGAATCCTCTG 59.827 55.000 0.00 0.00 0.00 3.35
33 34 0.807667 CGTCGGCTTGAATCCTCTGG 60.808 60.000 0.00 0.00 0.00 3.86
34 35 0.250513 GTCGGCTTGAATCCTCTGGT 59.749 55.000 0.00 0.00 0.00 4.00
35 36 0.984230 TCGGCTTGAATCCTCTGGTT 59.016 50.000 0.00 0.00 0.00 3.67
36 37 1.089920 CGGCTTGAATCCTCTGGTTG 58.910 55.000 0.00 0.00 0.00 3.77
37 38 1.467920 GGCTTGAATCCTCTGGTTGG 58.532 55.000 0.00 0.00 0.00 3.77
38 39 1.004745 GGCTTGAATCCTCTGGTTGGA 59.995 52.381 0.00 0.00 38.06 3.53
39 40 2.363683 GCTTGAATCCTCTGGTTGGAG 58.636 52.381 0.00 0.00 36.99 3.86
40 41 2.290577 GCTTGAATCCTCTGGTTGGAGT 60.291 50.000 0.00 0.00 36.99 3.85
41 42 3.812167 GCTTGAATCCTCTGGTTGGAGTT 60.812 47.826 0.00 0.00 36.99 3.01
42 43 3.423539 TGAATCCTCTGGTTGGAGTTG 57.576 47.619 0.00 0.00 36.99 3.16
43 44 2.087646 GAATCCTCTGGTTGGAGTTGC 58.912 52.381 0.00 0.00 36.99 4.17
44 45 1.366319 ATCCTCTGGTTGGAGTTGCT 58.634 50.000 0.00 0.00 36.99 3.91
45 46 1.140312 TCCTCTGGTTGGAGTTGCTT 58.860 50.000 0.00 0.00 0.00 3.91
46 47 1.494721 TCCTCTGGTTGGAGTTGCTTT 59.505 47.619 0.00 0.00 0.00 3.51
47 48 2.091885 TCCTCTGGTTGGAGTTGCTTTT 60.092 45.455 0.00 0.00 0.00 2.27
48 49 3.137544 TCCTCTGGTTGGAGTTGCTTTTA 59.862 43.478 0.00 0.00 0.00 1.52
49 50 3.503748 CCTCTGGTTGGAGTTGCTTTTAG 59.496 47.826 0.00 0.00 0.00 1.85
50 51 3.486383 TCTGGTTGGAGTTGCTTTTAGG 58.514 45.455 0.00 0.00 0.00 2.69
51 52 3.117663 TCTGGTTGGAGTTGCTTTTAGGT 60.118 43.478 0.00 0.00 0.00 3.08
52 53 3.636764 CTGGTTGGAGTTGCTTTTAGGTT 59.363 43.478 0.00 0.00 0.00 3.50
53 54 4.027437 TGGTTGGAGTTGCTTTTAGGTTT 58.973 39.130 0.00 0.00 0.00 3.27
54 55 4.142049 TGGTTGGAGTTGCTTTTAGGTTTG 60.142 41.667 0.00 0.00 0.00 2.93
55 56 3.726291 TGGAGTTGCTTTTAGGTTTGC 57.274 42.857 0.00 0.00 0.00 3.68
56 57 3.027412 TGGAGTTGCTTTTAGGTTTGCA 58.973 40.909 0.00 0.00 0.00 4.08
57 58 3.181480 TGGAGTTGCTTTTAGGTTTGCAC 60.181 43.478 0.00 0.00 35.01 4.57
58 59 3.042887 GAGTTGCTTTTAGGTTTGCACG 58.957 45.455 0.00 0.00 35.01 5.34
59 60 2.425668 AGTTGCTTTTAGGTTTGCACGT 59.574 40.909 0.00 0.00 35.01 4.49
60 61 3.119280 AGTTGCTTTTAGGTTTGCACGTT 60.119 39.130 0.00 0.00 35.01 3.99
88 89 1.745320 CTTACCCAGCCGTCGCCTAT 61.745 60.000 0.00 0.00 34.57 2.57
89 90 1.332144 TTACCCAGCCGTCGCCTATT 61.332 55.000 0.00 0.00 34.57 1.73
90 91 2.023414 TACCCAGCCGTCGCCTATTG 62.023 60.000 0.00 0.00 34.57 1.90
151 166 2.125673 CCGTCTACCGTGGCCTTG 60.126 66.667 3.32 0.00 33.66 3.61
342 364 3.365291 TAGCATCGTCGGTGGGCAC 62.365 63.158 7.76 0.00 0.00 5.01
357 379 1.663739 GCACGTGGAGGTGTGTCTA 59.336 57.895 18.88 0.00 40.08 2.59
391 428 1.694639 GGATCTGTTCGTCGTTCGTT 58.305 50.000 0.00 0.00 40.80 3.85
405 442 4.146788 GTCGTTCGTTTTTGTTTGTGTGTT 59.853 37.500 0.00 0.00 0.00 3.32
487 524 0.179081 GTTCTACGGGGCCTTAGCAG 60.179 60.000 0.84 0.00 42.56 4.24
526 563 4.820173 GTCTACTACAACAAAGTTTGCCCT 59.180 41.667 15.59 0.55 0.00 5.19
746 783 3.186119 AGAAAAACAATGTGGCGTGTTG 58.814 40.909 0.00 0.00 37.99 3.33
753 790 2.704725 ATGTGGCGTGTTGATGTTTC 57.295 45.000 0.00 0.00 0.00 2.78
805 842 2.415776 GAATACGAACGTGGGTCCAAA 58.584 47.619 10.14 0.00 0.00 3.28
830 872 4.047059 GAACCCGAGACGGCGTGA 62.047 66.667 21.19 0.00 46.86 4.35
845 887 3.621805 TGACCCGAAGCGCCAGAA 61.622 61.111 2.29 0.00 0.00 3.02
856 898 2.907407 GCCAGAAATAGGGGCGGC 60.907 66.667 0.00 0.00 38.04 6.53
857 899 2.203351 CCAGAAATAGGGGCGGCC 60.203 66.667 22.00 22.00 0.00 6.13
858 900 2.203351 CAGAAATAGGGGCGGCCC 60.203 66.667 38.87 38.87 44.51 5.80
892 935 1.202604 GGATATCCACCGAGGCGAAAA 60.203 52.381 17.34 0.00 37.29 2.29
903 946 2.739292 GAGGCGAAAACCCAAAAGAAC 58.261 47.619 0.00 0.00 0.00 3.01
907 950 1.677052 CGAAAACCCAAAAGAACCCGA 59.323 47.619 0.00 0.00 0.00 5.14
908 951 2.287368 CGAAAACCCAAAAGAACCCGAG 60.287 50.000 0.00 0.00 0.00 4.63
909 952 1.037493 AAACCCAAAAGAACCCGAGC 58.963 50.000 0.00 0.00 0.00 5.03
910 953 0.185175 AACCCAAAAGAACCCGAGCT 59.815 50.000 0.00 0.00 0.00 4.09
911 954 0.185175 ACCCAAAAGAACCCGAGCTT 59.815 50.000 0.00 0.00 0.00 3.74
912 955 1.422402 ACCCAAAAGAACCCGAGCTTA 59.578 47.619 0.00 0.00 0.00 3.09
913 956 2.041216 ACCCAAAAGAACCCGAGCTTAT 59.959 45.455 0.00 0.00 0.00 1.73
914 957 3.264964 ACCCAAAAGAACCCGAGCTTATA 59.735 43.478 0.00 0.00 0.00 0.98
915 958 4.263594 ACCCAAAAGAACCCGAGCTTATAA 60.264 41.667 0.00 0.00 0.00 0.98
916 959 4.335594 CCCAAAAGAACCCGAGCTTATAAG 59.664 45.833 8.20 8.20 0.00 1.73
917 960 4.335594 CCAAAAGAACCCGAGCTTATAAGG 59.664 45.833 14.28 0.52 0.00 2.69
918 961 5.183228 CAAAAGAACCCGAGCTTATAAGGA 58.817 41.667 14.28 0.00 0.00 3.36
964 1016 5.495502 CGTGCGAAACAAAATACCTATACC 58.504 41.667 0.00 0.00 0.00 2.73
991 1043 3.140225 GAGGCCCATCGTCTCGTCC 62.140 68.421 0.00 0.00 0.00 4.79
992 1044 3.148279 GGCCCATCGTCTCGTCCT 61.148 66.667 0.00 0.00 0.00 3.85
993 1045 2.413765 GCCCATCGTCTCGTCCTC 59.586 66.667 0.00 0.00 0.00 3.71
994 1046 2.415608 GCCCATCGTCTCGTCCTCA 61.416 63.158 0.00 0.00 0.00 3.86
995 1047 1.433879 CCCATCGTCTCGTCCTCAC 59.566 63.158 0.00 0.00 0.00 3.51
996 1048 1.433879 CCATCGTCTCGTCCTCACC 59.566 63.158 0.00 0.00 0.00 4.02
997 1049 1.032657 CCATCGTCTCGTCCTCACCT 61.033 60.000 0.00 0.00 0.00 4.00
1048 1103 2.844362 CAGCAGGGAGGGCGGATA 60.844 66.667 0.00 0.00 36.08 2.59
1356 1641 2.343101 CGACGGTACATGTGTTGGATT 58.657 47.619 9.11 0.00 0.00 3.01
1383 1668 1.315690 TCGGGATTCGTCGCTAGATT 58.684 50.000 0.00 0.00 40.32 2.40
1384 1669 1.266175 TCGGGATTCGTCGCTAGATTC 59.734 52.381 0.00 0.00 40.32 2.52
1385 1670 1.687628 GGGATTCGTCGCTAGATTCG 58.312 55.000 0.00 0.00 0.00 3.34
1386 1671 1.666311 GGGATTCGTCGCTAGATTCGG 60.666 57.143 0.00 0.00 0.00 4.30
1387 1672 1.666311 GGATTCGTCGCTAGATTCGGG 60.666 57.143 0.00 0.00 0.00 5.14
1388 1673 1.001597 GATTCGTCGCTAGATTCGGGT 60.002 52.381 0.00 0.00 0.00 5.28
1389 1674 0.379669 TTCGTCGCTAGATTCGGGTC 59.620 55.000 0.00 0.00 0.00 4.46
1424 1730 3.546417 GGATAGTGTGTCGATCGTGTCTC 60.546 52.174 15.94 8.53 0.00 3.36
1550 1866 3.889196 TGTATGCGAGTTTGTGGTTTC 57.111 42.857 0.00 0.00 0.00 2.78
1596 1921 1.873165 CTTGAAAGGGCGCGCTTAA 59.127 52.632 35.79 26.14 0.00 1.85
1601 1926 0.179468 AAAGGGCGCGCTTAATCCTA 59.821 50.000 35.79 0.00 0.00 2.94
1640 1965 4.700365 GTTTTCCCGTGCTGGCGC 62.700 66.667 0.00 0.00 35.87 6.53
1655 1980 3.349006 CGCGGCTGTGACTTGCTT 61.349 61.111 0.00 0.00 0.00 3.91
1704 2029 4.202441 GGGATGTGTTGCTCTGATTGTAT 58.798 43.478 0.00 0.00 0.00 2.29
1772 2097 2.080693 CATGGGTTTTAGCACGCTGTA 58.919 47.619 0.72 0.00 0.00 2.74
1812 2137 1.202879 TGCCCTGGTGTAGTTTTGGAG 60.203 52.381 0.00 0.00 0.00 3.86
2273 2611 6.430000 GGCAGTATTTTGTTTCTAGGTTCTGA 59.570 38.462 0.00 0.00 0.00 3.27
2320 2658 7.710907 GCCCCTTATTAATTTTTGTTCCAGATC 59.289 37.037 0.00 0.00 0.00 2.75
2411 2750 7.067615 TGAGCAAAGTCCTTGTGTTGTTATAAA 59.932 33.333 0.00 0.00 37.36 1.40
2476 2815 6.048732 TCAATAGCTGTAAACTCATCCACA 57.951 37.500 0.00 0.00 0.00 4.17
2556 2896 7.414436 TGCTGTTCACATTGTTTTAGTACTTC 58.586 34.615 0.00 0.00 0.00 3.01
2637 2979 6.589523 TGACATATGGTGTAATTTTTGCAAGC 59.410 34.615 7.80 0.00 42.36 4.01
2694 3037 2.226330 TGCACTTGAACCGCTGTATTT 58.774 42.857 0.00 0.00 0.00 1.40
2733 3076 1.279271 GGTAGGTGCTGAAGTGACCAT 59.721 52.381 0.00 0.00 31.61 3.55
2768 3112 9.793245 GCGTAATAATGTTGTAGTTAGCTAATG 57.207 33.333 9.88 0.00 0.00 1.90
2837 3702 2.027192 AGTCATGCGTATGTGGTCCTTT 60.027 45.455 13.39 0.00 35.73 3.11
3196 4074 9.950680 CACTTTTCTACAAACAAACTGTATGAT 57.049 29.630 0.00 0.00 0.00 2.45
3289 4168 2.552093 TTTTGGGAGTTGGTTTGGGA 57.448 45.000 0.00 0.00 0.00 4.37
3313 4193 8.821894 GGATTTCTTAGTGTGCTTATTGACTAG 58.178 37.037 0.00 0.00 0.00 2.57
3493 4374 9.853555 TGGTTTGTGCAGATATTGTTATTTAAG 57.146 29.630 0.00 0.00 0.00 1.85
3715 4596 8.148437 AGGCATTACAGATGATCAGAGATATT 57.852 34.615 0.09 0.00 0.00 1.28
4051 4932 2.633488 GGTGAGTACCTGAAGAATGCC 58.367 52.381 0.00 0.00 43.97 4.40
4075 4956 1.451028 GCGGCTTGCTGAGGAATCT 60.451 57.895 5.52 0.00 41.73 2.40
4303 5184 3.815856 TCTCTCATGGCTTCTCATGTC 57.184 47.619 0.00 0.00 43.52 3.06
4351 5232 3.375699 TGACCCAGAGAGATTAAGGGAC 58.624 50.000 2.29 0.00 42.25 4.46
4751 5632 2.480845 GCTACCAGTTCACGTCAAAGT 58.519 47.619 0.00 0.00 0.00 2.66
4817 5698 5.012239 TGCAAAGTTTCTATGCCAATCTCT 58.988 37.500 0.00 0.00 39.31 3.10
4855 5736 4.210331 GCCCAACAATATCTGTCCAGATT 58.790 43.478 14.54 0.00 45.31 2.40
4932 5813 2.641815 AGATCCTTGGTGTTTCTGAGCT 59.358 45.455 0.00 0.00 0.00 4.09
4939 5820 1.583054 GTGTTTCTGAGCTGTTCCGT 58.417 50.000 0.00 0.00 0.00 4.69
4945 5826 0.952497 CTGAGCTGTTCCGTGCACAT 60.952 55.000 18.64 0.00 0.00 3.21
4973 5854 1.028330 CACGCACAATGGCAGGAGAT 61.028 55.000 0.00 0.00 0.00 2.75
5005 5886 4.831155 CAGACAAATATGGGGAATGCAGAT 59.169 41.667 0.00 0.00 0.00 2.90
5077 5958 2.007608 CAGATGTGTGTCCTGATGCTG 58.992 52.381 0.00 0.00 0.00 4.41
5248 6129 0.517316 GCGACGCTTTCCACTTCAAT 59.483 50.000 13.73 0.00 0.00 2.57
5299 6180 2.520500 ATTGGCACGGTGGTTGCA 60.521 55.556 10.60 0.00 0.00 4.08
5311 6192 1.131638 TGGTTGCACAGAAGGAGTCT 58.868 50.000 0.00 0.00 36.88 3.24
5768 6649 2.697751 TGTTTATGCTTGGGTTGTTGCT 59.302 40.909 0.00 0.00 0.00 3.91
5800 6681 1.755959 TGTGGTTTGATGCTTGCTTGT 59.244 42.857 0.00 0.00 0.00 3.16
5801 6682 2.129607 GTGGTTTGATGCTTGCTTGTG 58.870 47.619 0.00 0.00 0.00 3.33
5809 6690 0.901124 TGCTTGCTTGTGGTTTGGTT 59.099 45.000 0.00 0.00 0.00 3.67
5838 6719 0.109597 GTTGTTGCCTGATGCTTCCG 60.110 55.000 0.00 0.00 42.00 4.30
5840 6721 1.675641 GTTGCCTGATGCTTCCGGT 60.676 57.895 0.00 0.00 42.00 5.28
5845 6726 1.377725 CTGATGCTTCCGGTTGCCT 60.378 57.895 16.21 8.52 0.00 4.75
5869 6750 8.499162 CCTTTTTCTGTGTAGTGTTTGAGATAG 58.501 37.037 0.00 0.00 0.00 2.08
5873 6754 9.778741 TTTCTGTGTAGTGTTTGAGATAGATTT 57.221 29.630 0.00 0.00 0.00 2.17
5874 6755 9.778741 TTCTGTGTAGTGTTTGAGATAGATTTT 57.221 29.630 0.00 0.00 0.00 1.82
5878 6759 9.099454 GTGTAGTGTTTGAGATAGATTTTAGGG 57.901 37.037 0.00 0.00 0.00 3.53
5879 6760 8.822805 TGTAGTGTTTGAGATAGATTTTAGGGT 58.177 33.333 0.00 0.00 0.00 4.34
5892 6773 7.130681 AGATTTTAGGGTCTTAGATGAGTGG 57.869 40.000 0.00 0.00 0.00 4.00
5894 6775 6.697641 TTTTAGGGTCTTAGATGAGTGGTT 57.302 37.500 0.00 0.00 0.00 3.67
5896 6777 3.791320 AGGGTCTTAGATGAGTGGTTCA 58.209 45.455 0.00 0.00 40.85 3.18
5912 6793 3.069872 TGGTTCAGTTTAGGACGTGCTTA 59.930 43.478 16.89 2.36 0.00 3.09
5914 6795 4.329256 GGTTCAGTTTAGGACGTGCTTATC 59.671 45.833 16.89 5.39 0.00 1.75
5921 6802 2.350522 AGGACGTGCTTATCTTGCTTG 58.649 47.619 2.68 0.00 0.00 4.01
5930 6811 4.830046 TGCTTATCTTGCTTGGGTTGTTAA 59.170 37.500 0.00 0.00 0.00 2.01
5931 6812 5.048083 TGCTTATCTTGCTTGGGTTGTTAAG 60.048 40.000 0.00 0.00 0.00 1.85
5932 6813 5.622233 GCTTATCTTGCTTGGGTTGTTAAGG 60.622 44.000 0.00 0.00 0.00 2.69
5933 6814 3.306472 TCTTGCTTGGGTTGTTAAGGT 57.694 42.857 0.00 0.00 0.00 3.50
5934 6815 4.440826 TCTTGCTTGGGTTGTTAAGGTA 57.559 40.909 0.00 0.00 0.00 3.08
5935 6816 4.394729 TCTTGCTTGGGTTGTTAAGGTAG 58.605 43.478 0.00 0.00 0.00 3.18
5936 6817 2.510613 TGCTTGGGTTGTTAAGGTAGC 58.489 47.619 0.00 0.00 0.00 3.58
5937 6818 2.107552 TGCTTGGGTTGTTAAGGTAGCT 59.892 45.455 0.00 0.00 0.00 3.32
5938 6819 3.154710 GCTTGGGTTGTTAAGGTAGCTT 58.845 45.455 12.54 12.54 0.00 3.74
5939 6820 4.202482 TGCTTGGGTTGTTAAGGTAGCTTA 60.202 41.667 10.31 10.31 0.00 3.09
5940 6821 4.763279 GCTTGGGTTGTTAAGGTAGCTTAA 59.237 41.667 20.42 20.42 0.00 1.85
5941 6822 5.335426 GCTTGGGTTGTTAAGGTAGCTTAAC 60.335 44.000 34.82 34.82 45.17 2.01
5990 6885 9.975218 AGGTGATAACTTTTAGGTAAATGATGT 57.025 29.630 3.16 0.00 0.00 3.06
5997 6892 8.842358 ACTTTTAGGTAAATGATGTCTTTCGA 57.158 30.769 3.16 0.00 0.00 3.71
6002 6897 9.667107 TTAGGTAAATGATGTCTTTCGAAATCT 57.333 29.630 11.70 0.00 35.33 2.40
6011 6906 9.435688 TGATGTCTTTCGAAATCTAATTTGAGA 57.564 29.630 11.70 1.57 35.33 3.27
6015 6910 8.599774 GTCTTTCGAAATCTAATTTGAGAGAGG 58.400 37.037 11.70 0.00 29.92 3.69
6017 6912 9.587772 CTTTCGAAATCTAATTTGAGAGAGGTA 57.412 33.333 11.70 0.00 31.47 3.08
6076 6984 5.221244 GCCCAATCGAGCTAATAAACCAAAT 60.221 40.000 0.00 0.00 0.00 2.32
6082 6990 7.681939 TCGAGCTAATAAACCAAATTGAAGT 57.318 32.000 0.00 0.00 0.00 3.01
6105 7014 8.268850 AGTTGCTAAAATGACGAGTAATTCAT 57.731 30.769 0.00 0.00 0.00 2.57
6119 7028 6.128172 CGAGTAATTCATTCATGGGCTAATCC 60.128 42.308 0.00 0.00 0.00 3.01
6168 7080 3.243359 ACATGAACAAGGTGACCCATT 57.757 42.857 0.00 0.00 0.00 3.16
6174 7086 3.425162 ACAAGGTGACCCATTCTCTTC 57.575 47.619 0.00 0.00 0.00 2.87
6258 7170 2.160205 GGCACCCTAAAGAACTGAACC 58.840 52.381 0.00 0.00 0.00 3.62
6343 7255 0.101399 CATCGCCGTAGAGCTTGAGT 59.899 55.000 0.00 0.00 0.00 3.41
6693 7644 2.745785 CGCTGCCGCCGTAAATCAA 61.746 57.895 0.00 0.00 0.00 2.57
6694 7645 1.226295 GCTGCCGCCGTAAATCAAC 60.226 57.895 0.00 0.00 0.00 3.18
6695 7646 1.644786 GCTGCCGCCGTAAATCAACT 61.645 55.000 0.00 0.00 0.00 3.16
6696 7647 0.802494 CTGCCGCCGTAAATCAACTT 59.198 50.000 0.00 0.00 0.00 2.66
6697 7648 0.519519 TGCCGCCGTAAATCAACTTG 59.480 50.000 0.00 0.00 0.00 3.16
6698 7649 0.796870 GCCGCCGTAAATCAACTTGC 60.797 55.000 0.00 0.00 0.00 4.01
6699 7650 0.179174 CCGCCGTAAATCAACTTGCC 60.179 55.000 0.00 0.00 0.00 4.52
6700 7651 0.519519 CGCCGTAAATCAACTTGCCA 59.480 50.000 0.00 0.00 0.00 4.92
6701 7652 1.465689 CGCCGTAAATCAACTTGCCAG 60.466 52.381 0.00 0.00 0.00 4.85
6702 7653 1.135402 GCCGTAAATCAACTTGCCAGG 60.135 52.381 0.00 0.00 0.00 4.45
6703 7654 2.159382 CCGTAAATCAACTTGCCAGGT 58.841 47.619 0.00 0.00 0.00 4.00
6704 7655 2.556622 CCGTAAATCAACTTGCCAGGTT 59.443 45.455 0.00 0.00 0.00 3.50
6705 7656 3.005367 CCGTAAATCAACTTGCCAGGTTT 59.995 43.478 0.00 0.00 0.00 3.27
6706 7657 3.980775 CGTAAATCAACTTGCCAGGTTTG 59.019 43.478 0.00 0.00 0.00 2.93
6707 7658 4.261405 CGTAAATCAACTTGCCAGGTTTGA 60.261 41.667 0.00 0.00 0.00 2.69
6708 7659 4.961438 AAATCAACTTGCCAGGTTTGAT 57.039 36.364 0.00 0.00 0.00 2.57
6709 7660 3.947910 ATCAACTTGCCAGGTTTGATG 57.052 42.857 3.64 0.00 0.00 3.07
6710 7661 1.340889 TCAACTTGCCAGGTTTGATGC 59.659 47.619 0.00 0.00 0.00 3.91
6711 7662 0.681175 AACTTGCCAGGTTTGATGCC 59.319 50.000 0.00 0.00 0.00 4.40
6712 7663 1.213537 CTTGCCAGGTTTGATGCCG 59.786 57.895 0.00 0.00 0.00 5.69
6713 7664 2.824071 CTTGCCAGGTTTGATGCCGC 62.824 60.000 0.00 0.00 0.00 6.53
6714 7665 3.064324 GCCAGGTTTGATGCCGCT 61.064 61.111 0.00 0.00 0.00 5.52
6715 7666 2.879907 CCAGGTTTGATGCCGCTG 59.120 61.111 0.00 0.00 0.00 5.18
6716 7667 2.180017 CAGGTTTGATGCCGCTGC 59.820 61.111 0.00 0.00 38.26 5.25
6717 7668 3.064324 AGGTTTGATGCCGCTGCC 61.064 61.111 0.00 0.00 36.33 4.85
6718 7669 4.481112 GGTTTGATGCCGCTGCCG 62.481 66.667 0.00 0.00 36.33 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.005294 CCGACGACGATTTTGTCCGT 61.005 55.000 9.28 0.00 42.66 4.69
1 2 1.700029 CCGACGACGATTTTGTCCG 59.300 57.895 9.28 0.00 42.66 4.79
2 3 1.012486 AGCCGACGACGATTTTGTCC 61.012 55.000 9.28 0.00 42.66 4.02
3 4 0.788391 AAGCCGACGACGATTTTGTC 59.212 50.000 9.28 0.00 42.66 3.18
4 5 0.511221 CAAGCCGACGACGATTTTGT 59.489 50.000 9.28 0.00 42.66 2.83
5 6 0.787787 TCAAGCCGACGACGATTTTG 59.212 50.000 9.28 9.88 42.66 2.44
6 7 1.504359 TTCAAGCCGACGACGATTTT 58.496 45.000 9.28 0.00 42.66 1.82
7 8 1.659098 GATTCAAGCCGACGACGATTT 59.341 47.619 9.28 0.00 42.66 2.17
8 9 1.278238 GATTCAAGCCGACGACGATT 58.722 50.000 9.28 0.21 42.66 3.34
9 10 0.527817 GGATTCAAGCCGACGACGAT 60.528 55.000 9.28 0.00 42.66 3.73
10 11 1.153901 GGATTCAAGCCGACGACGA 60.154 57.895 9.28 0.00 42.66 4.20
11 12 1.140407 GAGGATTCAAGCCGACGACG 61.140 60.000 0.00 0.00 39.43 5.12
12 13 0.173708 AGAGGATTCAAGCCGACGAC 59.826 55.000 0.00 0.00 0.00 4.34
13 14 0.173481 CAGAGGATTCAAGCCGACGA 59.827 55.000 0.00 0.00 0.00 4.20
14 15 0.807667 CCAGAGGATTCAAGCCGACG 60.808 60.000 0.00 0.00 0.00 5.12
15 16 0.250513 ACCAGAGGATTCAAGCCGAC 59.749 55.000 0.00 0.00 0.00 4.79
16 17 0.984230 AACCAGAGGATTCAAGCCGA 59.016 50.000 0.00 0.00 0.00 5.54
17 18 1.089920 CAACCAGAGGATTCAAGCCG 58.910 55.000 0.00 0.00 0.00 5.52
18 19 1.004745 TCCAACCAGAGGATTCAAGCC 59.995 52.381 0.00 0.00 0.00 4.35
19 20 2.290577 ACTCCAACCAGAGGATTCAAGC 60.291 50.000 0.00 0.00 38.26 4.01
20 21 3.710209 ACTCCAACCAGAGGATTCAAG 57.290 47.619 0.00 0.00 38.26 3.02
21 22 3.754965 CAACTCCAACCAGAGGATTCAA 58.245 45.455 0.00 0.00 38.26 2.69
22 23 2.553028 GCAACTCCAACCAGAGGATTCA 60.553 50.000 0.00 0.00 38.26 2.57
23 24 2.087646 GCAACTCCAACCAGAGGATTC 58.912 52.381 0.00 0.00 38.26 2.52
24 25 1.707427 AGCAACTCCAACCAGAGGATT 59.293 47.619 0.00 0.00 38.26 3.01
25 26 1.366319 AGCAACTCCAACCAGAGGAT 58.634 50.000 0.00 0.00 38.26 3.24
26 27 1.140312 AAGCAACTCCAACCAGAGGA 58.860 50.000 0.00 0.00 38.26 3.71
27 28 1.986882 AAAGCAACTCCAACCAGAGG 58.013 50.000 0.00 0.00 38.26 3.69
28 29 3.503748 CCTAAAAGCAACTCCAACCAGAG 59.496 47.826 0.00 0.00 39.91 3.35
29 30 3.117663 ACCTAAAAGCAACTCCAACCAGA 60.118 43.478 0.00 0.00 0.00 3.86
30 31 3.222603 ACCTAAAAGCAACTCCAACCAG 58.777 45.455 0.00 0.00 0.00 4.00
31 32 3.306472 ACCTAAAAGCAACTCCAACCA 57.694 42.857 0.00 0.00 0.00 3.67
32 33 4.368315 CAAACCTAAAAGCAACTCCAACC 58.632 43.478 0.00 0.00 0.00 3.77
33 34 3.802139 GCAAACCTAAAAGCAACTCCAAC 59.198 43.478 0.00 0.00 0.00 3.77
34 35 3.449018 TGCAAACCTAAAAGCAACTCCAA 59.551 39.130 0.00 0.00 33.48 3.53
35 36 3.027412 TGCAAACCTAAAAGCAACTCCA 58.973 40.909 0.00 0.00 33.48 3.86
36 37 3.381045 GTGCAAACCTAAAAGCAACTCC 58.619 45.455 0.00 0.00 38.91 3.85
37 38 3.042887 CGTGCAAACCTAAAAGCAACTC 58.957 45.455 0.00 0.00 38.91 3.01
38 39 2.425668 ACGTGCAAACCTAAAAGCAACT 59.574 40.909 0.00 0.00 38.91 3.16
39 40 2.804647 ACGTGCAAACCTAAAAGCAAC 58.195 42.857 0.00 0.00 38.91 4.17
40 41 3.182967 CAACGTGCAAACCTAAAAGCAA 58.817 40.909 0.00 0.00 38.91 3.91
41 42 2.803451 CAACGTGCAAACCTAAAAGCA 58.197 42.857 0.00 0.00 34.10 3.91
42 43 1.521006 GCAACGTGCAAACCTAAAAGC 59.479 47.619 0.00 0.00 44.26 3.51
43 44 1.778591 CGCAACGTGCAAACCTAAAAG 59.221 47.619 9.95 0.00 45.36 2.27
44 45 1.400846 TCGCAACGTGCAAACCTAAAA 59.599 42.857 9.95 0.00 45.36 1.52
45 46 1.003331 CTCGCAACGTGCAAACCTAAA 60.003 47.619 9.95 0.00 45.36 1.85
46 47 0.584396 CTCGCAACGTGCAAACCTAA 59.416 50.000 9.95 0.00 45.36 2.69
47 48 0.249531 TCTCGCAACGTGCAAACCTA 60.250 50.000 9.95 0.00 45.36 3.08
48 49 1.522806 TCTCGCAACGTGCAAACCT 60.523 52.632 9.95 0.00 45.36 3.50
49 50 1.368850 GTCTCGCAACGTGCAAACC 60.369 57.895 9.95 0.00 45.36 3.27
50 51 1.717728 CGTCTCGCAACGTGCAAAC 60.718 57.895 9.95 4.42 45.36 2.93
51 52 2.623718 CGTCTCGCAACGTGCAAA 59.376 55.556 9.95 0.00 45.36 3.68
70 71 1.332144 AATAGGCGACGGCTGGGTAA 61.332 55.000 31.73 13.60 39.30 2.85
157 172 2.732619 GGATCCACTCCGTCCCCAC 61.733 68.421 6.95 0.00 33.29 4.61
318 340 2.722548 CCGACGATGCTAGACGCG 60.723 66.667 3.53 3.53 43.27 6.01
342 364 0.895530 ACCATAGACACACCTCCACG 59.104 55.000 0.00 0.00 0.00 4.94
357 379 1.492176 AGATCCGAGCAAATCCACCAT 59.508 47.619 0.00 0.00 0.00 3.55
391 428 5.237344 CCAACCTGAAAACACACAAACAAAA 59.763 36.000 0.00 0.00 0.00 2.44
405 442 6.642733 AGATAAGAAGGATCCAACCTGAAA 57.357 37.500 15.82 0.00 40.49 2.69
699 736 0.809385 CGAGAACGGACCTAAGAGCA 59.191 55.000 0.00 0.00 35.72 4.26
719 756 4.328712 ACGCCACATTGTTTTTCTTTTCAC 59.671 37.500 0.00 0.00 0.00 3.18
753 790 8.615585 GTTCACGTTTTATATTCAAACTTCACG 58.384 33.333 0.00 0.00 32.79 4.35
798 835 1.338973 GGGTTCGTTTTCCTTTGGACC 59.661 52.381 0.00 0.00 0.00 4.46
805 842 0.319297 CGTCTCGGGTTCGTTTTCCT 60.319 55.000 0.00 0.00 37.69 3.36
828 870 2.463589 ATTTCTGGCGCTTCGGGTCA 62.464 55.000 7.64 0.00 0.00 4.02
830 872 0.462047 CTATTTCTGGCGCTTCGGGT 60.462 55.000 7.64 0.00 0.00 5.28
892 935 0.185175 AAGCTCGGGTTCTTTTGGGT 59.815 50.000 0.00 0.00 0.00 4.51
909 952 9.382244 GTGTGCGCTTATATTTTTCCTTATAAG 57.618 33.333 9.73 5.43 39.65 1.73
910 953 8.065407 CGTGTGCGCTTATATTTTTCCTTATAA 58.935 33.333 9.73 0.00 0.00 0.98
911 954 7.569297 CGTGTGCGCTTATATTTTTCCTTATA 58.431 34.615 9.73 0.00 0.00 0.98
912 955 6.427150 CGTGTGCGCTTATATTTTTCCTTAT 58.573 36.000 9.73 0.00 0.00 1.73
913 956 5.802064 CGTGTGCGCTTATATTTTTCCTTA 58.198 37.500 9.73 0.00 0.00 2.69
914 957 4.658071 CGTGTGCGCTTATATTTTTCCTT 58.342 39.130 9.73 0.00 0.00 3.36
915 958 4.273005 CGTGTGCGCTTATATTTTTCCT 57.727 40.909 9.73 0.00 0.00 3.36
943 988 4.034279 GCGGTATAGGTATTTTGTTTCGCA 59.966 41.667 0.00 0.00 38.40 5.10
991 1043 1.768077 GGAGGGGATGGGAGGTGAG 60.768 68.421 0.00 0.00 0.00 3.51
992 1044 2.372688 GGAGGGGATGGGAGGTGA 59.627 66.667 0.00 0.00 0.00 4.02
993 1045 2.774351 GGGAGGGGATGGGAGGTG 60.774 72.222 0.00 0.00 0.00 4.00
994 1046 4.124126 GGGGAGGGGATGGGAGGT 62.124 72.222 0.00 0.00 0.00 3.85
995 1047 3.795924 AGGGGAGGGGATGGGAGG 61.796 72.222 0.00 0.00 0.00 4.30
996 1048 2.122189 GAGGGGAGGGGATGGGAG 60.122 72.222 0.00 0.00 0.00 4.30
997 1049 3.791076 GGAGGGGAGGGGATGGGA 61.791 72.222 0.00 0.00 0.00 4.37
1344 1629 1.024046 TCGGCGGAATCCAACACATG 61.024 55.000 7.21 0.00 0.00 3.21
1383 1668 4.183686 GCGACGAATCCGACCCGA 62.184 66.667 0.00 0.00 39.50 5.14
1384 1669 4.189188 AGCGACGAATCCGACCCG 62.189 66.667 0.00 0.00 39.50 5.28
1385 1670 2.582498 CAGCGACGAATCCGACCC 60.582 66.667 0.00 0.00 39.50 4.46
1386 1671 2.351336 ATCCAGCGACGAATCCGACC 62.351 60.000 0.00 0.00 39.50 4.79
1387 1672 0.309922 TATCCAGCGACGAATCCGAC 59.690 55.000 0.00 0.00 39.50 4.79
1388 1673 0.591659 CTATCCAGCGACGAATCCGA 59.408 55.000 0.00 0.00 39.50 4.55
1389 1674 0.311165 ACTATCCAGCGACGAATCCG 59.689 55.000 0.00 0.00 42.50 4.18
1424 1730 5.660460 ACAGCAAAACCTAAGAAAAACAGG 58.340 37.500 0.00 0.00 35.45 4.00
1550 1866 3.426695 GCACATCCCGATTTCTTGACAAG 60.427 47.826 9.03 9.03 0.00 3.16
1596 1921 6.344500 CATGCAACTCAGTTTCTACTAGGAT 58.656 40.000 0.00 0.00 31.96 3.24
1601 1926 3.560025 CCCCATGCAACTCAGTTTCTACT 60.560 47.826 0.00 0.00 34.00 2.57
1640 1965 1.512926 ACTTAAGCAAGTCACAGCCG 58.487 50.000 1.29 0.00 41.25 5.52
1704 2029 4.411256 AACTACGTCCAGACTCCAAAAA 57.589 40.909 0.00 0.00 0.00 1.94
1772 2097 3.689649 GCAAGACATACCAATTTCCGACT 59.310 43.478 0.00 0.00 0.00 4.18
2215 2553 4.586001 CAGGGCAAAGTAAAGATATGGCAT 59.414 41.667 4.88 4.88 38.21 4.40
2216 2554 3.953612 CAGGGCAAAGTAAAGATATGGCA 59.046 43.478 0.00 0.00 38.21 4.92
2273 2611 0.824109 TCCCGAAGATGAAGCGACAT 59.176 50.000 0.00 0.00 0.00 3.06
2411 2750 5.823045 GCAAGTAGCACTGGTATTAAATCCT 59.177 40.000 0.00 0.00 44.79 3.24
2476 2815 4.151883 ACACCAATGTTTCCATGCTAGTT 58.848 39.130 0.00 0.00 34.46 2.24
2637 2979 9.429359 CTTTTCCAGTAGATATAGCCATTACTG 57.571 37.037 8.27 8.27 40.37 2.74
2733 3076 1.069513 ACATTATTACGCGGGCTAGCA 59.930 47.619 18.24 0.00 36.85 3.49
2782 3126 8.865090 TGGGCTAAATTCTTTCTTGTATTTCAA 58.135 29.630 0.00 0.00 34.61 2.69
2837 3702 7.610580 AACAACCAGGATTTCCTAAATTCAA 57.389 32.000 0.00 0.00 46.65 2.69
2940 3806 6.624352 ACATAAGCAAAGCCATATGTACAG 57.376 37.500 13.18 0.00 38.98 2.74
3289 4168 9.593134 CTCTAGTCAATAAGCACACTAAGAAAT 57.407 33.333 0.00 0.00 0.00 2.17
3313 4193 5.866633 GTCTGCACTATACTTATGGCATCTC 59.133 44.000 1.65 0.00 0.00 2.75
3493 4374 8.739972 ACAAAAGGGAGTATTACATCATGAAAC 58.260 33.333 0.00 0.00 0.00 2.78
3772 4653 3.766591 CTCTCCACAGTTCTAGACCATGT 59.233 47.826 0.00 0.00 0.00 3.21
3829 4710 1.202486 TCCAGAAGTGTGTCGACCAAC 60.202 52.381 14.12 11.24 0.00 3.77
4075 4956 3.615056 CCATATACAGCGAAACACGTTCA 59.385 43.478 0.00 0.00 44.60 3.18
4152 5033 3.554934 AGAAACAACCTCTGCATGTGAA 58.445 40.909 0.00 0.00 0.00 3.18
4303 5184 4.829492 ACCAAAATCTTTCCAGTCTCCTTG 59.171 41.667 0.00 0.00 0.00 3.61
4351 5232 0.804989 GCTGGACGAAATCAACAGGG 59.195 55.000 0.00 0.00 0.00 4.45
4429 5310 6.469782 TTCAAAGCATTCTGGAAAGTCTTT 57.530 33.333 0.00 0.00 0.00 2.52
4741 5622 2.842208 TGCTTTCCAACTTTGACGTG 57.158 45.000 0.00 0.00 0.00 4.49
4751 5632 5.068855 TCAAATCAGTGAACATGCTTTCCAA 59.931 36.000 0.00 0.00 0.00 3.53
4817 5698 1.679311 GGCCATCACTGTCACCAGA 59.321 57.895 0.00 0.00 41.50 3.86
4855 5736 0.615331 GCCAAGATCCAGTGGTGAGA 59.385 55.000 9.54 0.00 37.23 3.27
4932 5813 1.518325 CAGGTAATGTGCACGGAACA 58.482 50.000 13.13 0.00 0.00 3.18
4939 5820 1.673993 CGTGCCCAGGTAATGTGCA 60.674 57.895 0.00 0.00 40.23 4.57
4945 5826 1.074072 ATTGTGCGTGCCCAGGTAA 59.926 52.632 0.00 0.00 0.00 2.85
4973 5854 3.700539 CCCATATTTGTCTGCCATGTCAA 59.299 43.478 0.00 0.00 0.00 3.18
5005 5886 4.016444 GGTCTCCAAATGTTGCCTTGATA 58.984 43.478 0.00 0.00 0.00 2.15
5077 5958 6.483640 AGGTCAAAGTATCTGTTGAGTTGAAC 59.516 38.462 0.00 0.00 34.52 3.18
5248 6129 2.042686 ACTTGCTGCTGAACTTGTCA 57.957 45.000 0.00 0.00 34.17 3.58
5311 6192 2.283894 TCCTGCTTCTCCGGCTCA 60.284 61.111 0.00 0.00 0.00 4.26
5317 6198 2.896443 CGGGTCTCCTGCTTCTCC 59.104 66.667 0.00 0.00 0.00 3.71
5374 6255 1.417288 TCATGATCCTCACGATGGCT 58.583 50.000 0.00 0.00 0.00 4.75
5800 6681 1.064314 ACTGTGGCTACAACCAAACCA 60.064 47.619 3.88 0.00 42.70 3.67
5801 6682 1.687563 ACTGTGGCTACAACCAAACC 58.312 50.000 3.88 0.00 42.70 3.27
5809 6690 0.182537 AGGCAACAACTGTGGCTACA 59.817 50.000 9.05 1.86 44.30 2.74
5838 6719 3.380320 ACACTACACAGAAAAAGGCAACC 59.620 43.478 0.00 0.00 37.17 3.77
5840 6721 5.184096 TCAAACACTACACAGAAAAAGGCAA 59.816 36.000 0.00 0.00 0.00 4.52
5845 6726 9.778741 ATCTATCTCAAACACTACACAGAAAAA 57.221 29.630 0.00 0.00 0.00 1.94
5869 6750 6.890293 ACCACTCATCTAAGACCCTAAAATC 58.110 40.000 0.00 0.00 0.00 2.17
5873 6754 5.338632 TGAACCACTCATCTAAGACCCTAA 58.661 41.667 0.00 0.00 0.00 2.69
5874 6755 4.942944 TGAACCACTCATCTAAGACCCTA 58.057 43.478 0.00 0.00 0.00 3.53
5878 6759 6.814146 CCTAAACTGAACCACTCATCTAAGAC 59.186 42.308 0.00 0.00 32.14 3.01
5879 6760 6.724441 TCCTAAACTGAACCACTCATCTAAGA 59.276 38.462 0.00 0.00 32.14 2.10
5886 6767 2.696707 ACGTCCTAAACTGAACCACTCA 59.303 45.455 0.00 0.00 0.00 3.41
5892 6773 5.169295 AGATAAGCACGTCCTAAACTGAAC 58.831 41.667 0.00 0.00 0.00 3.18
5894 6775 5.168569 CAAGATAAGCACGTCCTAAACTGA 58.831 41.667 0.00 0.00 0.00 3.41
5896 6777 3.933332 GCAAGATAAGCACGTCCTAAACT 59.067 43.478 0.00 0.00 0.00 2.66
5912 6793 3.844640 ACCTTAACAACCCAAGCAAGAT 58.155 40.909 0.00 0.00 0.00 2.40
5914 6795 3.057526 GCTACCTTAACAACCCAAGCAAG 60.058 47.826 0.00 0.00 0.00 4.01
5930 6811 8.352942 GCAAAAGCAATATATGTTAAGCTACCT 58.647 33.333 0.00 0.00 0.00 3.08
5931 6812 8.134895 TGCAAAAGCAATATATGTTAAGCTACC 58.865 33.333 0.00 0.00 0.00 3.18
5932 6813 9.683069 ATGCAAAAGCAATATATGTTAAGCTAC 57.317 29.630 0.00 0.00 0.00 3.58
5940 6821 9.701098 CCTTCAATATGCAAAAGCAATATATGT 57.299 29.630 0.00 0.00 0.00 2.29
5941 6822 9.701098 ACCTTCAATATGCAAAAGCAATATATG 57.299 29.630 0.00 0.00 0.00 1.78
5942 6823 9.701098 CACCTTCAATATGCAAAAGCAATATAT 57.299 29.630 0.00 0.00 0.00 0.86
5943 6824 8.911965 TCACCTTCAATATGCAAAAGCAATATA 58.088 29.630 0.00 0.00 0.00 0.86
5989 6884 8.599774 CCTCTCTCAAATTAGATTTCGAAAGAC 58.400 37.037 16.80 12.39 41.84 3.01
5990 6885 8.314751 ACCTCTCTCAAATTAGATTTCGAAAGA 58.685 33.333 16.80 4.56 39.20 2.52
5995 6890 8.983724 GGAATACCTCTCTCAAATTAGATTTCG 58.016 37.037 0.00 0.00 0.00 3.46
5997 6892 8.781951 TGGGAATACCTCTCTCAAATTAGATTT 58.218 33.333 0.00 0.00 41.11 2.17
5999 6894 7.937700 TGGGAATACCTCTCTCAAATTAGAT 57.062 36.000 0.00 0.00 41.11 1.98
6000 6895 7.937700 ATGGGAATACCTCTCTCAAATTAGA 57.062 36.000 0.00 0.00 41.11 2.10
6001 6896 7.040823 GCAATGGGAATACCTCTCTCAAATTAG 60.041 40.741 0.00 0.00 41.11 1.73
6002 6897 6.772716 GCAATGGGAATACCTCTCTCAAATTA 59.227 38.462 0.00 0.00 41.11 1.40
6003 6898 5.595952 GCAATGGGAATACCTCTCTCAAATT 59.404 40.000 0.00 0.00 41.11 1.82
6011 6906 3.682718 CGAGTTGCAATGGGAATACCTCT 60.683 47.826 0.59 0.00 41.11 3.69
6015 6910 4.900635 AATCGAGTTGCAATGGGAATAC 57.099 40.909 0.59 0.00 0.00 1.89
6017 6912 7.581213 TTATAAATCGAGTTGCAATGGGAAT 57.419 32.000 8.63 0.00 0.00 3.01
6076 6984 7.485418 TTACTCGTCATTTTAGCAACTTCAA 57.515 32.000 0.00 0.00 0.00 2.69
6082 6990 8.726068 TGAATGAATTACTCGTCATTTTAGCAA 58.274 29.630 0.82 0.00 42.98 3.91
6105 7014 3.269381 AGACCAAAGGATTAGCCCATGAA 59.731 43.478 0.00 0.00 37.37 2.57
6119 7028 7.687941 ATTTGTAGGTGATGTTAGACCAAAG 57.312 36.000 0.00 0.00 34.36 2.77
6168 7080 9.496873 TTTGTTAAAATCAATAGGTCGAAGAGA 57.503 29.630 0.00 0.00 36.95 3.10
6216 7128 2.700897 CGTCAGGTCTCTTTGGGGATAT 59.299 50.000 0.00 0.00 0.00 1.63
6217 7129 2.108168 CGTCAGGTCTCTTTGGGGATA 58.892 52.381 0.00 0.00 0.00 2.59
6222 7134 1.376037 GCCCGTCAGGTCTCTTTGG 60.376 63.158 0.00 0.00 38.26 3.28
6258 7170 1.139989 CGCCGGCAATGTAGATACTG 58.860 55.000 28.98 0.12 0.00 2.74
6343 7255 0.693049 GGGAGAAGAAGGTGAAGGCA 59.307 55.000 0.00 0.00 0.00 4.75
6693 7644 1.526575 CGGCATCAAACCTGGCAAGT 61.527 55.000 0.00 0.00 39.00 3.16
6694 7645 1.213537 CGGCATCAAACCTGGCAAG 59.786 57.895 0.00 0.00 39.00 4.01
6695 7646 2.929903 GCGGCATCAAACCTGGCAA 61.930 57.895 0.00 0.00 39.00 4.52
6696 7647 3.372730 GCGGCATCAAACCTGGCA 61.373 61.111 0.00 0.00 39.00 4.92
6697 7648 3.064324 AGCGGCATCAAACCTGGC 61.064 61.111 1.45 0.00 35.94 4.85
6698 7649 2.879907 CAGCGGCATCAAACCTGG 59.120 61.111 1.45 0.00 0.00 4.45
6699 7650 2.180017 GCAGCGGCATCAAACCTG 59.820 61.111 3.18 0.00 40.72 4.00
6700 7651 3.064324 GGCAGCGGCATCAAACCT 61.064 61.111 11.88 0.00 43.71 3.50
6701 7652 4.481112 CGGCAGCGGCATCAAACC 62.481 66.667 11.88 0.00 43.71 3.27
6702 7653 1.917782 TTACGGCAGCGGCATCAAAC 61.918 55.000 11.88 0.00 43.71 2.93
6703 7654 1.672682 TTACGGCAGCGGCATCAAA 60.673 52.632 11.88 0.00 43.71 2.69
6704 7655 2.046796 TTACGGCAGCGGCATCAA 60.047 55.556 11.88 0.00 43.71 2.57
6705 7656 2.817834 GTTACGGCAGCGGCATCA 60.818 61.111 11.88 0.00 43.71 3.07
6706 7657 2.511600 AGTTACGGCAGCGGCATC 60.512 61.111 11.88 0.00 43.71 3.91
6707 7658 2.796483 TTCAGTTACGGCAGCGGCAT 62.796 55.000 11.88 0.04 43.71 4.40
6708 7659 3.523087 TTCAGTTACGGCAGCGGCA 62.523 57.895 11.88 0.00 43.71 5.69
6709 7660 2.740826 TTCAGTTACGGCAGCGGC 60.741 61.111 0.00 0.00 40.13 6.53
6710 7661 1.666553 TGTTCAGTTACGGCAGCGG 60.667 57.895 0.00 0.00 0.00 5.52
6711 7662 1.491563 GTGTTCAGTTACGGCAGCG 59.508 57.895 0.00 0.00 0.00 5.18
6712 7663 1.574702 GGGTGTTCAGTTACGGCAGC 61.575 60.000 0.00 0.00 0.00 5.25
6713 7664 0.953960 GGGGTGTTCAGTTACGGCAG 60.954 60.000 0.00 0.00 0.00 4.85
6714 7665 1.071814 GGGGTGTTCAGTTACGGCA 59.928 57.895 0.00 0.00 0.00 5.69
6715 7666 2.030958 CGGGGTGTTCAGTTACGGC 61.031 63.158 0.00 0.00 0.00 5.68
6716 7667 1.375013 CCGGGGTGTTCAGTTACGG 60.375 63.158 0.00 0.00 0.00 4.02
6717 7668 2.030958 GCCGGGGTGTTCAGTTACG 61.031 63.158 2.18 0.00 0.00 3.18
6718 7669 2.030958 CGCCGGGGTGTTCAGTTAC 61.031 63.158 11.01 0.00 0.00 2.50


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

AutoCloner maintained by Alex Coulton.