Multiple sequence alignment - TraesCS4D01G196200

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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 TraesCS4D01G196200 chr4D 100.000 3524 0 0 1 3524 340982809 340979286 0.000000e+00 6508
1 TraesCS4D01G196200 chr4D 97.557 696 16 1 1 695 340946373 340945678 0.000000e+00 1190
2 TraesCS4D01G196200 chr4D 88.780 205 21 2 3122 3325 386536702 386536499 2.100000e-62 250
3 TraesCS4D01G196200 chr4D 89.844 128 10 3 697 823 263529877 263530002 1.010000e-35 161
4 TraesCS4D01G196200 chr4D 81.614 223 14 10 697 893 460653882 460653661 3.640000e-35 159
5 TraesCS4D01G196200 chr6B 94.252 1183 42 3 1421 2577 25573198 25574380 0.000000e+00 1784
6 TraesCS4D01G196200 chr6B 92.593 351 20 6 914 1261 25572856 25573203 1.890000e-137 499
7 TraesCS4D01G196200 chr6B 89.100 211 23 0 1408 1618 250786842 250786632 2.700000e-66 263
8 TraesCS4D01G196200 chr6B 89.796 196 18 2 1424 1618 54078527 54078721 2.100000e-62 250
9 TraesCS4D01G196200 chr6B 96.341 82 3 0 1901 1982 168771878 168771959 6.140000e-28 135
10 TraesCS4D01G196200 chr7A 93.981 864 43 4 2639 3501 315512431 315513286 0.000000e+00 1299
11 TraesCS4D01G196200 chr7A 88.834 609 51 7 1922 2515 14167352 14167958 0.000000e+00 732
12 TraesCS4D01G196200 chr1A 95.337 772 35 1 2056 2826 436069684 436070455 0.000000e+00 1225
13 TraesCS4D01G196200 chr1A 88.873 701 61 7 1922 2607 106775387 106776085 0.000000e+00 846
14 TraesCS4D01G196200 chr1A 96.086 511 15 4 3015 3522 436082199 436082707 0.000000e+00 828
15 TraesCS4D01G196200 chr1A 89.163 609 49 7 1922 2515 100356048 100356654 0.000000e+00 743
16 TraesCS4D01G196200 chr1A 92.308 182 13 1 904 1085 436069505 436069685 1.260000e-64 257
17 TraesCS4D01G196200 chr1A 94.702 151 8 0 2822 2972 436082050 436082200 5.880000e-58 235
18 TraesCS4D01G196200 chr1A 93.805 113 7 0 697 809 565754823 565754935 1.680000e-38 171
19 TraesCS4D01G196200 chr1A 92.035 113 9 0 697 809 534643436 534643324 3.640000e-35 159
20 TraesCS4D01G196200 chr1A 88.800 125 12 2 697 819 102990189 102990065 6.090000e-33 152
21 TraesCS4D01G196200 chr2D 95.833 696 28 1 1 695 314543691 314544386 0.000000e+00 1123
22 TraesCS4D01G196200 chr2D 95.402 696 30 2 1 695 45714689 45715383 0.000000e+00 1107
23 TraesCS4D01G196200 chr6D 95.690 696 29 1 1 695 193366171 193366866 0.000000e+00 1118
24 TraesCS4D01G196200 chr6D 95.690 696 29 1 1 695 320104586 320105281 0.000000e+00 1118
25 TraesCS4D01G196200 chr6D 95.115 696 33 1 1 695 242587818 242588513 0.000000e+00 1096
26 TraesCS4D01G196200 chr6D 88.873 701 61 7 1922 2607 374633810 374634508 0.000000e+00 846
27 TraesCS4D01G196200 chr6D 93.902 82 5 0 1901 1982 384290728 384290647 1.330000e-24 124
28 TraesCS4D01G196200 chr1D 95.690 696 29 1 1 695 421472565 421471870 0.000000e+00 1118
29 TraesCS4D01G196200 chr1D 95.115 696 33 1 1 695 97374462 97373767 0.000000e+00 1096
30 TraesCS4D01G196200 chr1D 90.136 294 25 3 3122 3413 45063051 45063342 2.570000e-101 379
31 TraesCS4D01G196200 chr7D 95.259 696 32 1 1 695 207421185 207420490 0.000000e+00 1101
32 TraesCS4D01G196200 chr7D 93.805 113 7 0 697 809 360158597 360158485 1.680000e-38 171
33 TraesCS4D01G196200 chr4A 88.310 710 65 7 1922 2616 182239716 182239010 0.000000e+00 835
34 TraesCS4D01G196200 chr4A 89.527 296 26 3 3122 3416 13061162 13060871 1.550000e-98 370
35 TraesCS4D01G196200 chr5A 88.302 701 61 7 1922 2607 569642804 569643498 0.000000e+00 821
36 TraesCS4D01G196200 chr5A 88.342 609 54 6 1922 2515 147576778 147577384 0.000000e+00 715
37 TraesCS4D01G196200 chr5A 76.852 216 25 4 703 893 547506939 547507154 8.050000e-17 99
38 TraesCS4D01G196200 chr6A 87.623 711 69 9 1922 2616 160697110 160696403 0.000000e+00 808
39 TraesCS4D01G196200 chr6A 90.244 82 8 0 1901 1982 391428327 391428408 1.340000e-19 108
40 TraesCS4D01G196200 chr5B 88.998 609 50 5 1922 2515 38733363 38732757 0.000000e+00 737
41 TraesCS4D01G196200 chr5B 88.136 295 30 3 3122 3413 22316536 22316828 2.600000e-91 346
42 TraesCS4D01G196200 chr1B 88.998 609 50 7 1922 2515 606440918 606440312 0.000000e+00 737
43 TraesCS4D01G196200 chr1B 90.909 187 16 1 2329 2515 51088946 51088761 2.100000e-62 250
44 TraesCS4D01G196200 chr7B 89.527 296 26 3 3122 3416 263138788 263138497 1.550000e-98 370
45 TraesCS4D01G196200 chr7B 95.122 82 4 0 1901 1982 49030124 49030043 2.850000e-26 130
46 TraesCS4D01G196200 chr3B 86.700 203 23 3 3122 3323 805645903 805646102 4.580000e-54 222
47 TraesCS4D01G196200 chr3B 92.105 114 9 0 696 809 279701725 279701612 1.010000e-35 161
48 TraesCS4D01G196200 chr3B 96.341 82 3 0 1901 1982 795067371 795067452 6.140000e-28 135
49 TraesCS4D01G196200 chr4B 90.909 121 9 2 3122 3240 248357322 248357202 1.010000e-35 161
50 TraesCS4D01G196200 chr2A 82.160 213 12 14 705 893 676169591 676169381 3.640000e-35 159
51 TraesCS4D01G196200 chr2A 80.184 217 17 13 701 893 746822261 746822047 4.740000e-29 139
52 TraesCS4D01G196200 chr2A 95.122 82 4 0 1901 1982 405468272 405468353 2.850000e-26 130
53 TraesCS4D01G196200 chr2A 93.902 82 5 0 1901 1982 395712350 395712269 1.330000e-24 124
54 TraesCS4D01G196200 chr3D 89.600 125 11 2 699 821 141537047 141537171 1.310000e-34 158
55 TraesCS4D01G196200 chr3A 92.035 113 7 2 697 809 533842162 533842272 1.310000e-34 158
56 TraesCS4D01G196200 chr3A 80.543 221 17 13 697 893 556336214 556336432 2.830000e-31 147
57 TraesCS4D01G196200 chr3A 80.180 222 18 13 696 893 575757665 575757884 3.670000e-30 143
58 TraesCS4D01G196200 chr3A 95.122 82 4 0 1901 1982 699162920 699163001 2.850000e-26 130
59 TraesCS4D01G196200 chr2B 96.341 82 3 0 1901 1982 57158555 57158474 6.140000e-28 135
60 TraesCS4D01G196200 chr2B 93.902 82 5 0 1901 1982 241247128 241247209 1.330000e-24 124
61 TraesCS4D01G196200 chr2B 85.849 106 14 1 705 809 237181617 237181722 1.030000e-20 111
62 TraesCS4D01G196200 chr5D 86.667 105 14 0 705 809 66365190 66365294 2.220000e-22 117


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 TraesCS4D01G196200 chr4D 340979286 340982809 3523 True 6508.0 6508 100.0000 1 3524 1 chr4D.!!$R2 3523
1 TraesCS4D01G196200 chr4D 340945678 340946373 695 True 1190.0 1190 97.5570 1 695 1 chr4D.!!$R1 694
2 TraesCS4D01G196200 chr6B 25572856 25574380 1524 False 1141.5 1784 93.4225 914 2577 2 chr6B.!!$F3 1663
3 TraesCS4D01G196200 chr7A 315512431 315513286 855 False 1299.0 1299 93.9810 2639 3501 1 chr7A.!!$F2 862
4 TraesCS4D01G196200 chr7A 14167352 14167958 606 False 732.0 732 88.8340 1922 2515 1 chr7A.!!$F1 593
5 TraesCS4D01G196200 chr1A 106775387 106776085 698 False 846.0 846 88.8730 1922 2607 1 chr1A.!!$F2 685
6 TraesCS4D01G196200 chr1A 100356048 100356654 606 False 743.0 743 89.1630 1922 2515 1 chr1A.!!$F1 593
7 TraesCS4D01G196200 chr1A 436069505 436070455 950 False 741.0 1225 93.8225 904 2826 2 chr1A.!!$F4 1922
8 TraesCS4D01G196200 chr1A 436082050 436082707 657 False 531.5 828 95.3940 2822 3522 2 chr1A.!!$F5 700
9 TraesCS4D01G196200 chr2D 314543691 314544386 695 False 1123.0 1123 95.8330 1 695 1 chr2D.!!$F2 694
10 TraesCS4D01G196200 chr2D 45714689 45715383 694 False 1107.0 1107 95.4020 1 695 1 chr2D.!!$F1 694
11 TraesCS4D01G196200 chr6D 193366171 193366866 695 False 1118.0 1118 95.6900 1 695 1 chr6D.!!$F1 694
12 TraesCS4D01G196200 chr6D 320104586 320105281 695 False 1118.0 1118 95.6900 1 695 1 chr6D.!!$F3 694
13 TraesCS4D01G196200 chr6D 242587818 242588513 695 False 1096.0 1096 95.1150 1 695 1 chr6D.!!$F2 694
14 TraesCS4D01G196200 chr6D 374633810 374634508 698 False 846.0 846 88.8730 1922 2607 1 chr6D.!!$F4 685
15 TraesCS4D01G196200 chr1D 421471870 421472565 695 True 1118.0 1118 95.6900 1 695 1 chr1D.!!$R2 694
16 TraesCS4D01G196200 chr1D 97373767 97374462 695 True 1096.0 1096 95.1150 1 695 1 chr1D.!!$R1 694
17 TraesCS4D01G196200 chr7D 207420490 207421185 695 True 1101.0 1101 95.2590 1 695 1 chr7D.!!$R1 694
18 TraesCS4D01G196200 chr4A 182239010 182239716 706 True 835.0 835 88.3100 1922 2616 1 chr4A.!!$R2 694
19 TraesCS4D01G196200 chr5A 569642804 569643498 694 False 821.0 821 88.3020 1922 2607 1 chr5A.!!$F3 685
20 TraesCS4D01G196200 chr5A 147576778 147577384 606 False 715.0 715 88.3420 1922 2515 1 chr5A.!!$F1 593
21 TraesCS4D01G196200 chr6A 160696403 160697110 707 True 808.0 808 87.6230 1922 2616 1 chr6A.!!$R1 694
22 TraesCS4D01G196200 chr5B 38732757 38733363 606 True 737.0 737 88.9980 1922 2515 1 chr5B.!!$R1 593
23 TraesCS4D01G196200 chr1B 606440312 606440918 606 True 737.0 737 88.9980 1922 2515 1 chr1B.!!$R2 593

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
828 830 0.031857 TAGTTTCGTCGGTCCGCAAA 59.968 50.0 6.34 2.61 0.0 3.68 F
1401 1404 0.036858 AGGGAAACTCGAGAGCAAGC 60.037 55.0 21.68 1.84 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 2205 2.352805 CCCCACAGGACTTGAGCC 59.647 66.667 0.0 0.0 38.24 4.70 R
3169 3214 1.013596 TGCACTTGTTCCAACAGACG 58.986 50.000 0.0 0.0 40.50 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
194 195 2.949177 TGGCCTGTGTGAACAGTTAT 57.051 45.000 3.32 0.00 36.06 1.89
245 246 6.892658 TTTATCACAAGCAAACACCACTAT 57.107 33.333 0.00 0.00 0.00 2.12
424 425 5.579047 TCCAATCAGGTGGTTGAACAATAT 58.421 37.500 4.47 0.00 39.88 1.28
640 642 7.775053 TTTTCTTAATGGCATCAACCTTAGT 57.225 32.000 0.00 0.00 0.00 2.24
695 697 0.804989 GACCCAAGACAATGCCTTCG 59.195 55.000 0.00 0.00 0.00 3.79
696 698 0.110486 ACCCAAGACAATGCCTTCGT 59.890 50.000 0.00 0.00 0.00 3.85
697 699 0.804989 CCCAAGACAATGCCTTCGTC 59.195 55.000 0.00 0.00 0.00 4.20
698 700 1.611673 CCCAAGACAATGCCTTCGTCT 60.612 52.381 0.00 0.00 41.70 4.18
700 702 2.554032 CCAAGACAATGCCTTCGTCTTT 59.446 45.455 13.00 2.60 45.35 2.52
701 703 3.365364 CCAAGACAATGCCTTCGTCTTTC 60.365 47.826 13.00 0.00 45.35 2.62
702 704 2.427506 AGACAATGCCTTCGTCTTTCC 58.572 47.619 0.00 0.00 36.62 3.13
703 705 1.468914 GACAATGCCTTCGTCTTTCCC 59.531 52.381 0.00 0.00 0.00 3.97
704 706 1.073923 ACAATGCCTTCGTCTTTCCCT 59.926 47.619 0.00 0.00 0.00 4.20
705 707 2.304761 ACAATGCCTTCGTCTTTCCCTA 59.695 45.455 0.00 0.00 0.00 3.53
706 708 3.244770 ACAATGCCTTCGTCTTTCCCTAA 60.245 43.478 0.00 0.00 0.00 2.69
707 709 3.933861 ATGCCTTCGTCTTTCCCTAAT 57.066 42.857 0.00 0.00 0.00 1.73
708 710 5.123227 CAATGCCTTCGTCTTTCCCTAATA 58.877 41.667 0.00 0.00 0.00 0.98
709 711 4.829872 TGCCTTCGTCTTTCCCTAATAA 57.170 40.909 0.00 0.00 0.00 1.40
710 712 5.367945 TGCCTTCGTCTTTCCCTAATAAT 57.632 39.130 0.00 0.00 0.00 1.28
711 713 6.488769 TGCCTTCGTCTTTCCCTAATAATA 57.511 37.500 0.00 0.00 0.00 0.98
712 714 6.891388 TGCCTTCGTCTTTCCCTAATAATAA 58.109 36.000 0.00 0.00 0.00 1.40
713 715 7.340256 TGCCTTCGTCTTTCCCTAATAATAAA 58.660 34.615 0.00 0.00 0.00 1.40
714 716 7.497909 TGCCTTCGTCTTTCCCTAATAATAAAG 59.502 37.037 0.00 0.00 0.00 1.85
715 717 7.520131 GCCTTCGTCTTTCCCTAATAATAAAGC 60.520 40.741 0.00 0.00 0.00 3.51
716 718 7.497909 CCTTCGTCTTTCCCTAATAATAAAGCA 59.502 37.037 0.00 0.00 0.00 3.91
717 719 7.781548 TCGTCTTTCCCTAATAATAAAGCAC 57.218 36.000 0.00 0.00 0.00 4.40
718 720 6.477688 TCGTCTTTCCCTAATAATAAAGCACG 59.522 38.462 0.00 0.00 35.83 5.34
719 721 6.292703 CGTCTTTCCCTAATAATAAAGCACGG 60.293 42.308 0.00 0.00 33.69 4.94
720 722 6.764560 GTCTTTCCCTAATAATAAAGCACGGA 59.235 38.462 0.00 0.00 0.00 4.69
721 723 7.444487 GTCTTTCCCTAATAATAAAGCACGGAT 59.556 37.037 0.00 0.00 0.00 4.18
722 724 7.996644 TCTTTCCCTAATAATAAAGCACGGATT 59.003 33.333 0.00 0.00 0.00 3.01
723 725 7.504924 TTCCCTAATAATAAAGCACGGATTG 57.495 36.000 0.00 0.00 0.00 2.67
724 726 6.833041 TCCCTAATAATAAAGCACGGATTGA 58.167 36.000 0.00 0.00 0.00 2.57
725 727 6.708949 TCCCTAATAATAAAGCACGGATTGAC 59.291 38.462 0.00 0.00 0.00 3.18
726 728 6.710744 CCCTAATAATAAAGCACGGATTGACT 59.289 38.462 0.00 0.00 0.00 3.41
727 729 7.095187 CCCTAATAATAAAGCACGGATTGACTC 60.095 40.741 0.00 0.00 0.00 3.36
728 730 6.619801 AATAATAAAGCACGGATTGACTCC 57.380 37.500 0.00 0.00 41.07 3.85
736 738 3.154589 GGATTGACTCCGTGGGTTC 57.845 57.895 0.00 0.00 33.29 3.62
737 739 0.323629 GGATTGACTCCGTGGGTTCA 59.676 55.000 0.00 0.00 33.29 3.18
738 740 1.065418 GGATTGACTCCGTGGGTTCAT 60.065 52.381 0.00 0.00 33.29 2.57
739 741 2.280628 GATTGACTCCGTGGGTTCATC 58.719 52.381 0.00 0.00 0.00 2.92
740 742 0.037697 TTGACTCCGTGGGTTCATCG 60.038 55.000 0.00 0.00 0.00 3.84
741 743 1.183030 TGACTCCGTGGGTTCATCGT 61.183 55.000 0.00 0.00 0.00 3.73
742 744 0.458025 GACTCCGTGGGTTCATCGTC 60.458 60.000 0.00 0.00 0.00 4.20
743 745 1.183030 ACTCCGTGGGTTCATCGTCA 61.183 55.000 0.00 0.00 0.00 4.35
744 746 0.175760 CTCCGTGGGTTCATCGTCAT 59.824 55.000 0.00 0.00 0.00 3.06
745 747 1.407618 CTCCGTGGGTTCATCGTCATA 59.592 52.381 0.00 0.00 0.00 2.15
746 748 1.826096 TCCGTGGGTTCATCGTCATAA 59.174 47.619 0.00 0.00 0.00 1.90
747 749 2.432874 TCCGTGGGTTCATCGTCATAAT 59.567 45.455 0.00 0.00 0.00 1.28
748 750 3.637694 TCCGTGGGTTCATCGTCATAATA 59.362 43.478 0.00 0.00 0.00 0.98
749 751 3.739300 CCGTGGGTTCATCGTCATAATAC 59.261 47.826 0.00 0.00 0.00 1.89
750 752 3.424198 CGTGGGTTCATCGTCATAATACG 59.576 47.826 0.00 0.00 44.19 3.06
751 753 3.183775 GTGGGTTCATCGTCATAATACGC 59.816 47.826 0.00 0.00 42.56 4.42
752 754 3.069016 TGGGTTCATCGTCATAATACGCT 59.931 43.478 0.00 0.00 42.56 5.07
753 755 4.056050 GGGTTCATCGTCATAATACGCTT 58.944 43.478 0.00 0.00 42.56 4.68
754 756 4.150098 GGGTTCATCGTCATAATACGCTTC 59.850 45.833 0.00 0.00 42.56 3.86
755 757 4.982916 GGTTCATCGTCATAATACGCTTCT 59.017 41.667 0.00 0.00 42.56 2.85
756 758 5.462398 GGTTCATCGTCATAATACGCTTCTT 59.538 40.000 0.00 0.00 42.56 2.52
757 759 6.345882 GGTTCATCGTCATAATACGCTTCTTC 60.346 42.308 0.00 0.00 42.56 2.87
758 760 6.073327 TCATCGTCATAATACGCTTCTTCT 57.927 37.500 0.00 0.00 42.56 2.85
759 761 6.143496 TCATCGTCATAATACGCTTCTTCTC 58.857 40.000 0.00 0.00 42.56 2.87
760 762 4.524749 TCGTCATAATACGCTTCTTCTCG 58.475 43.478 0.00 0.00 42.56 4.04
761 763 4.034858 TCGTCATAATACGCTTCTTCTCGT 59.965 41.667 0.00 0.00 42.56 4.18
762 764 4.144902 CGTCATAATACGCTTCTTCTCGTG 59.855 45.833 0.00 0.00 39.46 4.35
763 765 5.271625 GTCATAATACGCTTCTTCTCGTGA 58.728 41.667 0.00 0.00 39.46 4.35
764 766 5.742453 GTCATAATACGCTTCTTCTCGTGAA 59.258 40.000 0.00 0.00 39.46 3.18
765 767 6.418226 GTCATAATACGCTTCTTCTCGTGAAT 59.582 38.462 0.00 0.00 39.46 2.57
766 768 6.978659 TCATAATACGCTTCTTCTCGTGAATT 59.021 34.615 0.00 0.00 39.46 2.17
767 769 7.491372 TCATAATACGCTTCTTCTCGTGAATTT 59.509 33.333 0.00 0.00 39.46 1.82
768 770 8.752254 CATAATACGCTTCTTCTCGTGAATTTA 58.248 33.333 0.00 0.00 39.46 1.40
769 771 7.772332 AATACGCTTCTTCTCGTGAATTTAT 57.228 32.000 0.00 0.00 39.46 1.40
770 772 5.456192 ACGCTTCTTCTCGTGAATTTATG 57.544 39.130 0.00 0.00 37.55 1.90
771 773 4.929808 ACGCTTCTTCTCGTGAATTTATGT 59.070 37.500 0.00 0.00 37.55 2.29
772 774 5.408604 ACGCTTCTTCTCGTGAATTTATGTT 59.591 36.000 0.00 0.00 37.55 2.71
773 775 6.073222 ACGCTTCTTCTCGTGAATTTATGTTT 60.073 34.615 0.00 0.00 37.55 2.83
774 776 6.797033 CGCTTCTTCTCGTGAATTTATGTTTT 59.203 34.615 0.00 0.00 0.00 2.43
775 777 7.323656 CGCTTCTTCTCGTGAATTTATGTTTTT 59.676 33.333 0.00 0.00 0.00 1.94
776 778 9.607285 GCTTCTTCTCGTGAATTTATGTTTTTA 57.393 29.630 0.00 0.00 0.00 1.52
816 818 2.572191 TGCGAGGTGGTATAGTTTCG 57.428 50.000 0.00 0.00 0.00 3.46
817 819 1.820519 TGCGAGGTGGTATAGTTTCGT 59.179 47.619 0.00 0.00 0.00 3.85
818 820 2.159338 TGCGAGGTGGTATAGTTTCGTC 60.159 50.000 0.00 0.00 0.00 4.20
819 821 2.713011 CGAGGTGGTATAGTTTCGTCG 58.287 52.381 0.00 0.00 0.00 5.12
820 822 2.540361 CGAGGTGGTATAGTTTCGTCGG 60.540 54.545 0.00 0.00 34.39 4.79
821 823 2.424956 GAGGTGGTATAGTTTCGTCGGT 59.575 50.000 0.00 0.00 0.00 4.69
822 824 2.424956 AGGTGGTATAGTTTCGTCGGTC 59.575 50.000 0.00 0.00 0.00 4.79
823 825 2.480244 GGTGGTATAGTTTCGTCGGTCC 60.480 54.545 0.00 0.00 0.00 4.46
824 826 1.401552 TGGTATAGTTTCGTCGGTCCG 59.598 52.381 4.39 4.39 0.00 4.79
825 827 1.470940 GTATAGTTTCGTCGGTCCGC 58.529 55.000 6.34 0.60 0.00 5.54
826 828 1.093972 TATAGTTTCGTCGGTCCGCA 58.906 50.000 6.34 0.00 0.00 5.69
827 829 0.244450 ATAGTTTCGTCGGTCCGCAA 59.756 50.000 6.34 0.00 0.00 4.85
828 830 0.031857 TAGTTTCGTCGGTCCGCAAA 59.968 50.000 6.34 2.61 0.00 3.68
829 831 0.810823 AGTTTCGTCGGTCCGCAAAA 60.811 50.000 6.34 4.01 0.00 2.44
830 832 0.236449 GTTTCGTCGGTCCGCAAAAT 59.764 50.000 6.34 0.00 0.00 1.82
831 833 0.945813 TTTCGTCGGTCCGCAAAATT 59.054 45.000 6.34 0.00 0.00 1.82
832 834 0.945813 TTCGTCGGTCCGCAAAATTT 59.054 45.000 6.34 0.00 0.00 1.82
833 835 0.513820 TCGTCGGTCCGCAAAATTTC 59.486 50.000 6.34 0.00 0.00 2.17
834 836 0.515564 CGTCGGTCCGCAAAATTTCT 59.484 50.000 6.34 0.00 0.00 2.52
835 837 1.724654 CGTCGGTCCGCAAAATTTCTG 60.725 52.381 6.34 0.00 0.00 3.02
836 838 1.265905 GTCGGTCCGCAAAATTTCTGT 59.734 47.619 6.34 0.00 0.00 3.41
837 839 2.481185 GTCGGTCCGCAAAATTTCTGTA 59.519 45.455 6.34 0.00 0.00 2.74
838 840 2.739913 TCGGTCCGCAAAATTTCTGTAG 59.260 45.455 6.34 0.00 0.00 2.74
839 841 2.159572 CGGTCCGCAAAATTTCTGTAGG 60.160 50.000 0.00 1.95 0.00 3.18
840 842 2.817844 GGTCCGCAAAATTTCTGTAGGT 59.182 45.455 0.00 0.00 0.00 3.08
841 843 3.119955 GGTCCGCAAAATTTCTGTAGGTC 60.120 47.826 0.00 0.30 0.00 3.85
842 844 2.739913 TCCGCAAAATTTCTGTAGGTCG 59.260 45.455 0.00 0.00 0.00 4.79
843 845 2.505866 CGCAAAATTTCTGTAGGTCGC 58.494 47.619 0.00 0.00 0.00 5.19
844 846 2.159627 CGCAAAATTTCTGTAGGTCGCT 59.840 45.455 0.00 0.00 0.00 4.93
845 847 3.492313 GCAAAATTTCTGTAGGTCGCTG 58.508 45.455 0.00 0.00 0.00 5.18
846 848 3.058224 GCAAAATTTCTGTAGGTCGCTGT 60.058 43.478 0.00 0.00 0.00 4.40
847 849 4.556699 GCAAAATTTCTGTAGGTCGCTGTT 60.557 41.667 0.00 0.00 0.00 3.16
848 850 4.749245 AAATTTCTGTAGGTCGCTGTTG 57.251 40.909 0.00 0.00 0.00 3.33
849 851 2.902705 TTTCTGTAGGTCGCTGTTGT 57.097 45.000 0.00 0.00 0.00 3.32
850 852 2.902705 TTCTGTAGGTCGCTGTTGTT 57.097 45.000 0.00 0.00 0.00 2.83
851 853 2.902705 TCTGTAGGTCGCTGTTGTTT 57.097 45.000 0.00 0.00 0.00 2.83
852 854 3.188159 TCTGTAGGTCGCTGTTGTTTT 57.812 42.857 0.00 0.00 0.00 2.43
853 855 4.325028 TCTGTAGGTCGCTGTTGTTTTA 57.675 40.909 0.00 0.00 0.00 1.52
854 856 4.695396 TCTGTAGGTCGCTGTTGTTTTAA 58.305 39.130 0.00 0.00 0.00 1.52
855 857 4.508861 TCTGTAGGTCGCTGTTGTTTTAAC 59.491 41.667 0.00 0.00 0.00 2.01
856 858 4.444536 TGTAGGTCGCTGTTGTTTTAACT 58.555 39.130 0.00 0.00 0.00 2.24
857 859 3.963383 AGGTCGCTGTTGTTTTAACTG 57.037 42.857 0.00 0.00 0.00 3.16
858 860 3.537580 AGGTCGCTGTTGTTTTAACTGA 58.462 40.909 0.00 0.00 0.00 3.41
859 861 3.311596 AGGTCGCTGTTGTTTTAACTGAC 59.688 43.478 0.00 0.00 0.00 3.51
860 862 3.311596 GGTCGCTGTTGTTTTAACTGACT 59.688 43.478 0.00 0.00 0.00 3.41
861 863 4.201881 GGTCGCTGTTGTTTTAACTGACTT 60.202 41.667 0.00 0.00 0.00 3.01
862 864 4.962151 GTCGCTGTTGTTTTAACTGACTTC 59.038 41.667 0.00 0.00 0.00 3.01
863 865 4.873827 TCGCTGTTGTTTTAACTGACTTCT 59.126 37.500 0.00 0.00 0.00 2.85
864 866 5.006358 TCGCTGTTGTTTTAACTGACTTCTC 59.994 40.000 0.00 0.00 0.00 2.87
865 867 5.511571 GCTGTTGTTTTAACTGACTTCTCC 58.488 41.667 0.00 0.00 0.00 3.71
866 868 5.505819 GCTGTTGTTTTAACTGACTTCTCCC 60.506 44.000 0.00 0.00 0.00 4.30
867 869 4.885325 TGTTGTTTTAACTGACTTCTCCCC 59.115 41.667 0.00 0.00 0.00 4.81
868 870 5.131067 GTTGTTTTAACTGACTTCTCCCCT 58.869 41.667 0.00 0.00 0.00 4.79
869 871 4.714632 TGTTTTAACTGACTTCTCCCCTG 58.285 43.478 0.00 0.00 0.00 4.45
870 872 4.410883 TGTTTTAACTGACTTCTCCCCTGA 59.589 41.667 0.00 0.00 0.00 3.86
871 873 5.073144 TGTTTTAACTGACTTCTCCCCTGAT 59.927 40.000 0.00 0.00 0.00 2.90
872 874 5.422214 TTTAACTGACTTCTCCCCTGATC 57.578 43.478 0.00 0.00 0.00 2.92
873 875 1.872773 ACTGACTTCTCCCCTGATCC 58.127 55.000 0.00 0.00 0.00 3.36
874 876 0.749649 CTGACTTCTCCCCTGATCCG 59.250 60.000 0.00 0.00 0.00 4.18
875 877 0.041238 TGACTTCTCCCCTGATCCGT 59.959 55.000 0.00 0.00 0.00 4.69
876 878 0.747852 GACTTCTCCCCTGATCCGTC 59.252 60.000 0.00 0.00 0.00 4.79
877 879 0.336737 ACTTCTCCCCTGATCCGTCT 59.663 55.000 0.00 0.00 0.00 4.18
878 880 0.749649 CTTCTCCCCTGATCCGTCTG 59.250 60.000 0.00 0.00 0.00 3.51
879 881 0.687757 TTCTCCCCTGATCCGTCTGG 60.688 60.000 0.00 0.00 41.68 3.86
883 885 2.765807 CCTGATCCGTCTGGGCCT 60.766 66.667 4.53 0.00 39.18 5.19
884 886 2.801631 CCTGATCCGTCTGGGCCTC 61.802 68.421 4.53 0.00 39.18 4.70
885 887 2.038813 TGATCCGTCTGGGCCTCA 59.961 61.111 4.53 0.00 35.24 3.86
886 888 2.025767 CTGATCCGTCTGGGCCTCAG 62.026 65.000 13.43 13.43 44.68 3.35
887 889 3.453070 GATCCGTCTGGGCCTCAGC 62.453 68.421 14.49 9.75 43.06 4.26
897 899 4.468689 GCCTCAGCCCACCGGTAC 62.469 72.222 6.87 0.00 0.00 3.34
898 900 3.782443 CCTCAGCCCACCGGTACC 61.782 72.222 6.87 0.16 0.00 3.34
899 901 3.782443 CTCAGCCCACCGGTACCC 61.782 72.222 6.87 0.00 0.00 3.69
900 902 4.326227 TCAGCCCACCGGTACCCT 62.326 66.667 6.87 0.00 0.00 4.34
901 903 3.327404 CAGCCCACCGGTACCCTT 61.327 66.667 6.87 0.00 0.00 3.95
902 904 3.327404 AGCCCACCGGTACCCTTG 61.327 66.667 6.87 3.22 0.00 3.61
948 950 2.521224 GACCTCCGCCGGTCCTAT 60.521 66.667 1.63 0.00 46.19 2.57
983 985 2.358737 CAGACGGTGCCCTTGTCC 60.359 66.667 0.00 0.00 33.09 4.02
984 986 2.526873 AGACGGTGCCCTTGTCCT 60.527 61.111 0.00 0.00 33.09 3.85
985 987 2.358737 GACGGTGCCCTTGTCCTG 60.359 66.667 0.00 0.00 0.00 3.86
986 988 3.168528 ACGGTGCCCTTGTCCTGT 61.169 61.111 0.00 0.00 0.00 4.00
1119 1121 2.919856 AGCGGCGGAGATGGCTAT 60.920 61.111 9.78 0.00 33.19 2.97
1120 1122 2.740055 GCGGCGGAGATGGCTATG 60.740 66.667 9.78 0.00 0.00 2.23
1202 1205 3.285215 GGCAGATCCATGGCAGCG 61.285 66.667 6.96 0.00 44.71 5.18
1224 1227 2.606587 GCTTCTGGGCAGGAAGGGA 61.607 63.158 16.46 0.00 40.13 4.20
1242 1245 2.107366 GGAGGTGAGGGAGAGAAGAAG 58.893 57.143 0.00 0.00 0.00 2.85
1258 1261 2.911484 AGAAGGCAGAAAATAGGAGCG 58.089 47.619 0.00 0.00 0.00 5.03
1259 1262 1.943340 GAAGGCAGAAAATAGGAGCGG 59.057 52.381 0.00 0.00 0.00 5.52
1260 1263 0.912486 AGGCAGAAAATAGGAGCGGT 59.088 50.000 0.00 0.00 0.00 5.68
1261 1264 1.017387 GGCAGAAAATAGGAGCGGTG 58.983 55.000 0.00 0.00 0.00 4.94
1262 1265 0.378610 GCAGAAAATAGGAGCGGTGC 59.621 55.000 0.00 0.00 0.00 5.01
1263 1266 1.017387 CAGAAAATAGGAGCGGTGCC 58.983 55.000 1.29 0.00 0.00 5.01
1264 1267 0.462047 AGAAAATAGGAGCGGTGCCG 60.462 55.000 6.22 6.22 43.09 5.69
1282 1285 4.200283 CGACCGAGGCAGGAGCTC 62.200 72.222 4.71 4.71 41.70 4.09
1283 1286 4.200283 GACCGAGGCAGGAGCTCG 62.200 72.222 7.83 0.00 41.70 5.03
1285 1288 4.200283 CCGAGGCAGGAGCTCGTC 62.200 72.222 5.82 0.00 41.70 4.20
1286 1289 4.544689 CGAGGCAGGAGCTCGTCG 62.545 72.222 5.82 3.36 41.70 5.12
1287 1290 4.200283 GAGGCAGGAGCTCGTCGG 62.200 72.222 5.82 0.00 41.70 4.79
1288 1291 4.742649 AGGCAGGAGCTCGTCGGA 62.743 66.667 5.82 0.00 41.70 4.55
1289 1292 4.200283 GGCAGGAGCTCGTCGGAG 62.200 72.222 5.82 0.00 43.46 4.63
1297 1300 3.062466 CTCGTCGGAGCTGGGTGA 61.062 66.667 0.00 0.00 32.61 4.02
1298 1301 3.343788 CTCGTCGGAGCTGGGTGAC 62.344 68.421 0.00 0.00 32.61 3.67
1299 1302 4.778415 CGTCGGAGCTGGGTGACG 62.778 72.222 10.83 10.83 46.57 4.35
1300 1303 4.436998 GTCGGAGCTGGGTGACGG 62.437 72.222 0.00 0.00 0.00 4.79
1366 1369 3.299190 CCTCTCCTCGGGCGGATC 61.299 72.222 0.00 0.00 31.43 3.36
1367 1370 3.665226 CTCTCCTCGGGCGGATCG 61.665 72.222 0.00 0.00 31.43 3.69
1379 1382 3.299190 GGATCGGGAGGGAGCGAG 61.299 72.222 0.00 0.00 0.00 5.03
1380 1383 3.299190 GATCGGGAGGGAGCGAGG 61.299 72.222 0.00 0.00 0.00 4.63
1381 1384 4.924187 ATCGGGAGGGAGCGAGGG 62.924 72.222 0.00 0.00 0.00 4.30
1386 1389 4.144727 GAGGGAGCGAGGGAGGGA 62.145 72.222 0.00 0.00 0.00 4.20
1387 1390 3.680920 GAGGGAGCGAGGGAGGGAA 62.681 68.421 0.00 0.00 0.00 3.97
1388 1391 2.687566 GGGAGCGAGGGAGGGAAA 60.688 66.667 0.00 0.00 0.00 3.13
1389 1392 2.585153 GGAGCGAGGGAGGGAAAC 59.415 66.667 0.00 0.00 0.00 2.78
1390 1393 1.990614 GGAGCGAGGGAGGGAAACT 60.991 63.158 0.00 0.00 0.00 2.66
1391 1394 1.518302 GAGCGAGGGAGGGAAACTC 59.482 63.158 0.00 0.00 45.84 3.01
1400 1403 2.003196 GAGGGAAACTCGAGAGCAAG 57.997 55.000 21.68 0.00 36.29 4.01
1401 1404 0.036858 AGGGAAACTCGAGAGCAAGC 60.037 55.000 21.68 1.84 0.00 4.01
1402 1405 0.036858 GGGAAACTCGAGAGCAAGCT 60.037 55.000 21.68 0.00 0.00 3.74
1403 1406 1.355005 GGAAACTCGAGAGCAAGCTC 58.645 55.000 21.68 14.00 43.03 4.09
1404 1407 1.355005 GAAACTCGAGAGCAAGCTCC 58.645 55.000 21.68 9.04 43.70 4.70
1405 1408 0.036858 AAACTCGAGAGCAAGCTCCC 60.037 55.000 21.68 5.97 43.70 4.30
1406 1409 2.103934 CTCGAGAGCAAGCTCCCG 59.896 66.667 18.16 18.16 43.97 5.14
1407 1410 4.135153 TCGAGAGCAAGCTCCCGC 62.135 66.667 19.21 8.67 42.66 6.13
1443 1446 3.456431 TTGGTTCGGCGCACAAACG 62.456 57.895 10.83 2.53 0.00 3.60
1465 1468 2.202932 CCTTGGCCGTCTCCGATG 60.203 66.667 0.00 0.00 35.63 3.84
1536 1539 3.429141 CTGCAGCGGCTGGAACTG 61.429 66.667 29.44 12.96 41.91 3.16
1547 1550 0.742281 CTGGAACTGGCTGATGGTCG 60.742 60.000 0.00 0.00 0.00 4.79
1577 1580 1.476891 CTCGACTTCATCCTTTCCCGA 59.523 52.381 0.00 0.00 0.00 5.14
1604 1607 2.682594 CTCCATCCATGACCTCTGGTA 58.317 52.381 0.00 0.00 35.25 3.25
1608 1611 2.623418 TCCATGACCTCTGGTACACT 57.377 50.000 0.00 0.00 35.25 3.55
1649 1652 7.896811 ACTTCAGTTAGATGTTAGTCATGTCA 58.103 34.615 0.00 0.00 36.83 3.58
1674 1700 6.563222 TTTCGATAAAAGGGACGAAAATGT 57.437 33.333 0.00 0.00 46.40 2.71
1699 1725 4.582973 TTGGGATACATCAACACCATCA 57.417 40.909 0.00 0.00 39.74 3.07
1760 1786 5.410602 AGAAGCAGAATCCTACATCCCTAT 58.589 41.667 0.00 0.00 0.00 2.57
1761 1787 6.565974 AGAAGCAGAATCCTACATCCCTATA 58.434 40.000 0.00 0.00 0.00 1.31
1794 1822 4.519540 ATCAAAGTATGCCAAAACGCTT 57.480 36.364 0.00 0.00 0.00 4.68
1834 1862 3.008330 GAGTCTTGTCGGCAGAGTACTA 58.992 50.000 0.00 0.00 0.00 1.82
1943 1971 7.875971 ACAGAACTTTGAAATCCACTTCATAC 58.124 34.615 0.00 0.00 35.31 2.39
2072 2114 5.243730 CAGTTGGGAACTTGGTGTATCATTT 59.756 40.000 0.00 0.00 40.46 2.32
2082 2124 6.266558 ACTTGGTGTATCATTTTTGGCTGTTA 59.733 34.615 0.00 0.00 0.00 2.41
2163 2205 4.633126 CACTAAGAGATTGATGTGTGGGTG 59.367 45.833 0.00 0.00 0.00 4.61
2256 2298 5.710513 TTCTCTGCATGCACAAGTAAAAT 57.289 34.783 18.46 0.00 0.00 1.82
2258 2300 4.761227 TCTCTGCATGCACAAGTAAAATCA 59.239 37.500 18.46 0.00 0.00 2.57
2607 2652 2.765689 ATGAAACCAAACCAGGTGGA 57.234 45.000 2.10 0.00 42.25 4.02
2611 2656 2.067365 AACCAAACCAGGTGGACTTC 57.933 50.000 2.10 0.00 42.25 3.01
2820 2865 7.773489 TTTCATGTACATGGAAAAGGAATCA 57.227 32.000 30.56 8.43 39.24 2.57
2862 2907 8.627208 AGTTGAGAAATCTTTTCTTGCTATCA 57.373 30.769 4.16 0.00 0.00 2.15
2888 2933 1.541147 GCAAGCTCAATGTAAGCACCA 59.459 47.619 0.00 0.00 42.35 4.17
3331 3377 6.982141 TGTATTAACGAATCTAGCATCGGTTT 59.018 34.615 17.50 8.96 43.11 3.27
3522 3570 5.952347 ACTCCCTCCGTTCAAATATAAGT 57.048 39.130 0.00 0.00 0.00 2.24
3523 3571 5.915175 ACTCCCTCCGTTCAAATATAAGTC 58.085 41.667 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
424 425 7.119699 CACTCAAGAAAACCTTATATCTGCACA 59.880 37.037 0.00 0.00 32.86 4.57
560 562 3.806949 TTCCTAGGTCATGCTGGTTTT 57.193 42.857 9.08 0.00 0.00 2.43
613 615 6.855763 AGGTTGATGCCATTAAGAAAATGA 57.144 33.333 0.00 0.00 0.00 2.57
622 624 5.329399 ACCAAACTAAGGTTGATGCCATTA 58.671 37.500 0.00 0.00 35.33 1.90
640 642 4.993705 AGAGGTATTGAAGTGGACCAAA 57.006 40.909 0.00 0.00 34.18 3.28
695 697 6.764560 TCCGTGCTTTATTATTAGGGAAAGAC 59.235 38.462 0.00 0.00 31.83 3.01
696 698 6.891388 TCCGTGCTTTATTATTAGGGAAAGA 58.109 36.000 0.00 0.00 31.83 2.52
697 699 7.745620 ATCCGTGCTTTATTATTAGGGAAAG 57.254 36.000 0.00 0.00 33.05 2.62
698 700 7.776030 TCAATCCGTGCTTTATTATTAGGGAAA 59.224 33.333 0.00 0.00 0.00 3.13
699 701 7.227910 GTCAATCCGTGCTTTATTATTAGGGAA 59.772 37.037 0.00 0.00 0.00 3.97
700 702 6.708949 GTCAATCCGTGCTTTATTATTAGGGA 59.291 38.462 0.00 0.00 0.00 4.20
701 703 6.710744 AGTCAATCCGTGCTTTATTATTAGGG 59.289 38.462 0.00 0.00 0.00 3.53
702 704 7.095187 GGAGTCAATCCGTGCTTTATTATTAGG 60.095 40.741 0.00 0.00 38.67 2.69
703 705 7.797819 GGAGTCAATCCGTGCTTTATTATTAG 58.202 38.462 0.00 0.00 38.67 1.73
704 706 7.724305 GGAGTCAATCCGTGCTTTATTATTA 57.276 36.000 0.00 0.00 38.67 0.98
705 707 6.619801 GGAGTCAATCCGTGCTTTATTATT 57.380 37.500 0.00 0.00 38.67 1.40
718 720 0.323629 TGAACCCACGGAGTCAATCC 59.676 55.000 0.00 0.00 41.61 3.01
719 721 2.280628 GATGAACCCACGGAGTCAATC 58.719 52.381 0.00 0.00 41.61 2.67
720 722 1.405526 CGATGAACCCACGGAGTCAAT 60.406 52.381 0.00 0.00 41.61 2.57
721 723 0.037697 CGATGAACCCACGGAGTCAA 60.038 55.000 0.00 0.00 41.61 3.18
722 724 1.183030 ACGATGAACCCACGGAGTCA 61.183 55.000 0.00 0.00 41.61 3.41
723 725 0.458025 GACGATGAACCCACGGAGTC 60.458 60.000 0.00 0.00 41.61 3.36
725 727 0.175760 ATGACGATGAACCCACGGAG 59.824 55.000 0.00 0.00 0.00 4.63
726 728 1.476477 TATGACGATGAACCCACGGA 58.524 50.000 0.00 0.00 0.00 4.69
727 729 2.303163 TTATGACGATGAACCCACGG 57.697 50.000 0.00 0.00 0.00 4.94
728 730 3.424198 CGTATTATGACGATGAACCCACG 59.576 47.826 0.00 0.00 45.82 4.94
729 731 3.183775 GCGTATTATGACGATGAACCCAC 59.816 47.826 0.00 0.00 45.82 4.61
730 732 3.069016 AGCGTATTATGACGATGAACCCA 59.931 43.478 0.00 0.00 45.82 4.51
731 733 3.650139 AGCGTATTATGACGATGAACCC 58.350 45.455 0.00 0.00 45.82 4.11
732 734 4.982916 AGAAGCGTATTATGACGATGAACC 59.017 41.667 0.00 0.00 45.82 3.62
733 735 6.418226 AGAAGAAGCGTATTATGACGATGAAC 59.582 38.462 0.00 0.00 45.82 3.18
734 736 6.504398 AGAAGAAGCGTATTATGACGATGAA 58.496 36.000 0.00 0.00 45.82 2.57
735 737 6.073327 AGAAGAAGCGTATTATGACGATGA 57.927 37.500 0.00 0.00 45.82 2.92
736 738 5.058613 CGAGAAGAAGCGTATTATGACGATG 59.941 44.000 0.00 0.00 45.82 3.84
737 739 5.147865 CGAGAAGAAGCGTATTATGACGAT 58.852 41.667 0.00 0.00 45.82 3.73
738 740 4.034858 ACGAGAAGAAGCGTATTATGACGA 59.965 41.667 0.00 0.00 45.82 4.20
739 741 4.144902 CACGAGAAGAAGCGTATTATGACG 59.855 45.833 0.00 0.00 45.70 4.35
740 742 5.271625 TCACGAGAAGAAGCGTATTATGAC 58.728 41.667 0.00 0.00 38.92 3.06
741 743 5.494632 TCACGAGAAGAAGCGTATTATGA 57.505 39.130 0.00 0.00 38.92 2.15
742 744 6.755461 ATTCACGAGAAGAAGCGTATTATG 57.245 37.500 1.01 0.00 38.92 1.90
743 745 7.772332 AAATTCACGAGAAGAAGCGTATTAT 57.228 32.000 1.01 0.00 38.92 1.28
744 746 8.752254 CATAAATTCACGAGAAGAAGCGTATTA 58.248 33.333 1.01 0.00 38.92 0.98
745 747 7.277981 ACATAAATTCACGAGAAGAAGCGTATT 59.722 33.333 1.01 0.00 38.92 1.89
746 748 6.757010 ACATAAATTCACGAGAAGAAGCGTAT 59.243 34.615 1.01 0.00 38.92 3.06
747 749 6.097356 ACATAAATTCACGAGAAGAAGCGTA 58.903 36.000 1.01 0.00 38.92 4.42
748 750 4.929808 ACATAAATTCACGAGAAGAAGCGT 59.070 37.500 1.01 0.00 42.11 5.07
749 751 5.456192 ACATAAATTCACGAGAAGAAGCG 57.544 39.130 1.01 0.00 37.14 4.68
750 752 8.507470 AAAAACATAAATTCACGAGAAGAAGC 57.493 30.769 1.01 0.00 37.14 3.86
790 792 8.350722 CGAAACTATACCACCTCGCATATATAT 58.649 37.037 0.00 0.00 0.00 0.86
791 793 7.337689 ACGAAACTATACCACCTCGCATATATA 59.662 37.037 0.00 0.00 0.00 0.86
792 794 6.152323 ACGAAACTATACCACCTCGCATATAT 59.848 38.462 0.00 0.00 0.00 0.86
793 795 5.474532 ACGAAACTATACCACCTCGCATATA 59.525 40.000 0.00 0.00 0.00 0.86
794 796 4.280174 ACGAAACTATACCACCTCGCATAT 59.720 41.667 0.00 0.00 0.00 1.78
795 797 3.633525 ACGAAACTATACCACCTCGCATA 59.366 43.478 0.00 0.00 0.00 3.14
796 798 2.429610 ACGAAACTATACCACCTCGCAT 59.570 45.455 0.00 0.00 0.00 4.73
797 799 1.820519 ACGAAACTATACCACCTCGCA 59.179 47.619 0.00 0.00 0.00 5.10
798 800 2.457970 GACGAAACTATACCACCTCGC 58.542 52.381 0.00 0.00 0.00 5.03
799 801 2.540361 CCGACGAAACTATACCACCTCG 60.540 54.545 0.00 0.00 0.00 4.63
800 802 2.424956 ACCGACGAAACTATACCACCTC 59.575 50.000 0.00 0.00 0.00 3.85
801 803 2.424956 GACCGACGAAACTATACCACCT 59.575 50.000 0.00 0.00 0.00 4.00
802 804 2.480244 GGACCGACGAAACTATACCACC 60.480 54.545 0.00 0.00 0.00 4.61
803 805 2.792542 CGGACCGACGAAACTATACCAC 60.793 54.545 8.64 0.00 35.47 4.16
804 806 1.401552 CGGACCGACGAAACTATACCA 59.598 52.381 8.64 0.00 35.47 3.25
805 807 1.861605 GCGGACCGACGAAACTATACC 60.862 57.143 20.50 0.00 35.47 2.73
806 808 1.202177 TGCGGACCGACGAAACTATAC 60.202 52.381 20.50 0.00 35.47 1.47
807 809 1.093972 TGCGGACCGACGAAACTATA 58.906 50.000 20.50 0.00 35.47 1.31
808 810 0.244450 TTGCGGACCGACGAAACTAT 59.756 50.000 20.50 0.00 35.47 2.12
809 811 0.031857 TTTGCGGACCGACGAAACTA 59.968 50.000 20.50 0.00 29.56 2.24
810 812 0.810823 TTTTGCGGACCGACGAAACT 60.811 50.000 20.50 0.00 29.56 2.66
811 813 0.236449 ATTTTGCGGACCGACGAAAC 59.764 50.000 20.50 0.00 29.56 2.78
812 814 0.945813 AATTTTGCGGACCGACGAAA 59.054 45.000 20.50 19.74 35.47 3.46
813 815 0.945813 AAATTTTGCGGACCGACGAA 59.054 45.000 20.50 12.19 35.47 3.85
814 816 0.513820 GAAATTTTGCGGACCGACGA 59.486 50.000 20.50 6.09 35.47 4.20
815 817 0.515564 AGAAATTTTGCGGACCGACG 59.484 50.000 20.50 0.00 0.00 5.12
816 818 1.265905 ACAGAAATTTTGCGGACCGAC 59.734 47.619 20.50 9.82 0.00 4.79
817 819 1.600023 ACAGAAATTTTGCGGACCGA 58.400 45.000 20.50 0.00 0.00 4.69
818 820 2.159572 CCTACAGAAATTTTGCGGACCG 60.160 50.000 10.29 10.29 0.00 4.79
819 821 2.817844 ACCTACAGAAATTTTGCGGACC 59.182 45.455 0.00 0.00 0.00 4.46
820 822 3.424433 CGACCTACAGAAATTTTGCGGAC 60.424 47.826 0.00 0.00 0.00 4.79
821 823 2.739913 CGACCTACAGAAATTTTGCGGA 59.260 45.455 0.00 0.00 0.00 5.54
822 824 2.727916 GCGACCTACAGAAATTTTGCGG 60.728 50.000 0.00 1.06 0.00 5.69
823 825 2.159627 AGCGACCTACAGAAATTTTGCG 59.840 45.455 0.00 0.00 0.00 4.85
824 826 3.058224 ACAGCGACCTACAGAAATTTTGC 60.058 43.478 0.00 0.00 0.00 3.68
825 827 4.749245 ACAGCGACCTACAGAAATTTTG 57.251 40.909 0.00 0.00 0.00 2.44
826 828 4.578928 ACAACAGCGACCTACAGAAATTTT 59.421 37.500 0.00 0.00 0.00 1.82
827 829 4.134563 ACAACAGCGACCTACAGAAATTT 58.865 39.130 0.00 0.00 0.00 1.82
828 830 3.740115 ACAACAGCGACCTACAGAAATT 58.260 40.909 0.00 0.00 0.00 1.82
829 831 3.402628 ACAACAGCGACCTACAGAAAT 57.597 42.857 0.00 0.00 0.00 2.17
830 832 2.902705 ACAACAGCGACCTACAGAAA 57.097 45.000 0.00 0.00 0.00 2.52
831 833 2.902705 AACAACAGCGACCTACAGAA 57.097 45.000 0.00 0.00 0.00 3.02
832 834 2.902705 AAACAACAGCGACCTACAGA 57.097 45.000 0.00 0.00 0.00 3.41
833 835 4.510340 AGTTAAAACAACAGCGACCTACAG 59.490 41.667 0.00 0.00 0.00 2.74
834 836 4.271533 CAGTTAAAACAACAGCGACCTACA 59.728 41.667 0.00 0.00 0.00 2.74
835 837 4.508861 TCAGTTAAAACAACAGCGACCTAC 59.491 41.667 0.00 0.00 0.00 3.18
836 838 4.508861 GTCAGTTAAAACAACAGCGACCTA 59.491 41.667 0.00 0.00 0.00 3.08
837 839 3.311596 GTCAGTTAAAACAACAGCGACCT 59.688 43.478 0.00 0.00 0.00 3.85
838 840 3.311596 AGTCAGTTAAAACAACAGCGACC 59.688 43.478 0.00 0.00 0.00 4.79
839 841 4.531659 AGTCAGTTAAAACAACAGCGAC 57.468 40.909 0.00 0.00 0.00 5.19
840 842 4.873827 AGAAGTCAGTTAAAACAACAGCGA 59.126 37.500 0.00 0.00 0.00 4.93
841 843 5.156804 AGAAGTCAGTTAAAACAACAGCG 57.843 39.130 0.00 0.00 0.00 5.18
842 844 5.505819 GGGAGAAGTCAGTTAAAACAACAGC 60.506 44.000 0.00 0.00 0.00 4.40
843 845 5.008712 GGGGAGAAGTCAGTTAAAACAACAG 59.991 44.000 0.00 0.00 0.00 3.16
844 846 4.885325 GGGGAGAAGTCAGTTAAAACAACA 59.115 41.667 0.00 0.00 0.00 3.33
845 847 5.008712 CAGGGGAGAAGTCAGTTAAAACAAC 59.991 44.000 0.00 0.00 0.00 3.32
846 848 5.104277 TCAGGGGAGAAGTCAGTTAAAACAA 60.104 40.000 0.00 0.00 0.00 2.83
847 849 4.410883 TCAGGGGAGAAGTCAGTTAAAACA 59.589 41.667 0.00 0.00 0.00 2.83
848 850 4.969484 TCAGGGGAGAAGTCAGTTAAAAC 58.031 43.478 0.00 0.00 0.00 2.43
849 851 5.280521 GGATCAGGGGAGAAGTCAGTTAAAA 60.281 44.000 0.00 0.00 0.00 1.52
850 852 4.225267 GGATCAGGGGAGAAGTCAGTTAAA 59.775 45.833 0.00 0.00 0.00 1.52
851 853 3.775316 GGATCAGGGGAGAAGTCAGTTAA 59.225 47.826 0.00 0.00 0.00 2.01
852 854 3.375699 GGATCAGGGGAGAAGTCAGTTA 58.624 50.000 0.00 0.00 0.00 2.24
853 855 2.192263 GGATCAGGGGAGAAGTCAGTT 58.808 52.381 0.00 0.00 0.00 3.16
854 856 1.872773 GGATCAGGGGAGAAGTCAGT 58.127 55.000 0.00 0.00 0.00 3.41
855 857 0.749649 CGGATCAGGGGAGAAGTCAG 59.250 60.000 0.00 0.00 0.00 3.51
856 858 0.041238 ACGGATCAGGGGAGAAGTCA 59.959 55.000 0.00 0.00 0.00 3.41
857 859 0.747852 GACGGATCAGGGGAGAAGTC 59.252 60.000 0.00 0.00 0.00 3.01
858 860 0.336737 AGACGGATCAGGGGAGAAGT 59.663 55.000 0.00 0.00 0.00 3.01
859 861 0.749649 CAGACGGATCAGGGGAGAAG 59.250 60.000 0.00 0.00 0.00 2.85
860 862 0.687757 CCAGACGGATCAGGGGAGAA 60.688 60.000 0.00 0.00 0.00 2.87
861 863 1.075970 CCAGACGGATCAGGGGAGA 60.076 63.158 0.00 0.00 0.00 3.71
862 864 2.136878 CCCAGACGGATCAGGGGAG 61.137 68.421 0.26 0.00 45.95 4.30
863 865 2.041922 CCCAGACGGATCAGGGGA 60.042 66.667 0.26 0.00 45.95 4.81
866 868 2.765807 AGGCCCAGACGGATCAGG 60.766 66.667 0.00 0.00 0.00 3.86
867 869 2.025767 CTGAGGCCCAGACGGATCAG 62.026 65.000 14.21 7.57 45.78 2.90
868 870 2.038813 TGAGGCCCAGACGGATCA 59.961 61.111 0.00 0.00 0.00 2.92
869 871 2.818132 CTGAGGCCCAGACGGATC 59.182 66.667 14.21 0.00 45.78 3.36
870 872 3.474570 GCTGAGGCCCAGACGGAT 61.475 66.667 21.37 0.00 45.78 4.18
880 882 4.468689 GTACCGGTGGGCTGAGGC 62.469 72.222 19.93 0.00 36.48 4.70
881 883 3.782443 GGTACCGGTGGGCTGAGG 61.782 72.222 19.93 0.00 36.48 3.86
882 884 3.782443 GGGTACCGGTGGGCTGAG 61.782 72.222 19.93 0.00 40.86 3.35
915 917 4.671590 TCGGAGTGGACTGCCGGA 62.672 66.667 5.05 0.00 44.87 5.14
983 985 1.003355 ATGGCCGTCTTCACCACAG 60.003 57.895 0.00 0.00 35.99 3.66
984 986 1.302431 CATGGCCGTCTTCACCACA 60.302 57.895 0.00 0.00 35.99 4.17
985 987 2.040544 CCATGGCCGTCTTCACCAC 61.041 63.158 0.00 0.00 35.99 4.16
986 988 2.350895 CCATGGCCGTCTTCACCA 59.649 61.111 0.00 0.00 37.99 4.17
1102 1104 2.919856 ATAGCCATCTCCGCCGCT 60.920 61.111 0.00 0.00 35.34 5.52
1209 1212 2.285668 CCTCCCTTCCTGCCCAGA 60.286 66.667 0.00 0.00 0.00 3.86
1224 1227 1.899438 GCCTTCTTCTCTCCCTCACCT 60.899 57.143 0.00 0.00 0.00 4.00
1242 1245 1.017387 CACCGCTCCTATTTTCTGCC 58.983 55.000 0.00 0.00 0.00 4.85
1265 1268 4.200283 GAGCTCCTGCCTCGGTCG 62.200 72.222 0.87 0.00 40.80 4.79
1266 1269 4.200283 CGAGCTCCTGCCTCGGTC 62.200 72.222 8.47 0.00 40.80 4.79
1268 1271 4.200283 GACGAGCTCCTGCCTCGG 62.200 72.222 8.47 0.00 40.99 4.63
1269 1272 4.544689 CGACGAGCTCCTGCCTCG 62.545 72.222 8.47 9.01 41.76 4.63
1270 1273 4.200283 CCGACGAGCTCCTGCCTC 62.200 72.222 8.47 0.00 40.80 4.70
1271 1274 4.742649 TCCGACGAGCTCCTGCCT 62.743 66.667 8.47 0.00 40.80 4.75
1272 1275 4.200283 CTCCGACGAGCTCCTGCC 62.200 72.222 8.47 0.00 40.80 4.85
1280 1283 3.062466 TCACCCAGCTCCGACGAG 61.062 66.667 0.00 0.00 39.33 4.18
1281 1284 3.371063 GTCACCCAGCTCCGACGA 61.371 66.667 0.00 0.00 0.00 4.20
1282 1285 4.778415 CGTCACCCAGCTCCGACG 62.778 72.222 8.72 8.72 44.34 5.12
1283 1286 4.436998 CCGTCACCCAGCTCCGAC 62.437 72.222 0.00 0.00 0.00 4.79
1349 1352 3.299190 GATCCGCCCGAGGAGAGG 61.299 72.222 0.00 0.00 44.55 3.69
1350 1353 3.665226 CGATCCGCCCGAGGAGAG 61.665 72.222 0.00 0.00 44.55 3.20
1362 1365 3.299190 CTCGCTCCCTCCCGATCC 61.299 72.222 0.00 0.00 32.52 3.36
1363 1366 3.299190 CCTCGCTCCCTCCCGATC 61.299 72.222 0.00 0.00 32.52 3.69
1364 1367 4.924187 CCCTCGCTCCCTCCCGAT 62.924 72.222 0.00 0.00 32.52 4.18
1369 1372 3.680920 TTCCCTCCCTCGCTCCCTC 62.681 68.421 0.00 0.00 0.00 4.30
1370 1373 3.254035 TTTCCCTCCCTCGCTCCCT 62.254 63.158 0.00 0.00 0.00 4.20
1371 1374 2.687566 TTTCCCTCCCTCGCTCCC 60.688 66.667 0.00 0.00 0.00 4.30
1372 1375 1.962321 GAGTTTCCCTCCCTCGCTCC 61.962 65.000 0.00 0.00 33.79 4.70
1373 1376 1.518302 GAGTTTCCCTCCCTCGCTC 59.482 63.158 0.00 0.00 33.79 5.03
1374 1377 2.352032 CGAGTTTCCCTCCCTCGCT 61.352 63.158 0.00 0.00 41.21 4.93
1375 1378 2.184579 CGAGTTTCCCTCCCTCGC 59.815 66.667 0.00 0.00 41.21 5.03
1377 1380 1.107945 CTCTCGAGTTTCCCTCCCTC 58.892 60.000 13.13 0.00 36.82 4.30
1378 1381 0.973496 GCTCTCGAGTTTCCCTCCCT 60.973 60.000 13.13 0.00 36.82 4.20
1379 1382 1.258445 TGCTCTCGAGTTTCCCTCCC 61.258 60.000 13.13 0.00 36.82 4.30
1380 1383 0.608640 TTGCTCTCGAGTTTCCCTCC 59.391 55.000 13.13 0.00 36.82 4.30
1381 1384 2.003196 CTTGCTCTCGAGTTTCCCTC 57.997 55.000 13.13 0.00 36.80 4.30
1382 1385 0.036858 GCTTGCTCTCGAGTTTCCCT 60.037 55.000 13.13 0.00 0.00 4.20
1383 1386 0.036858 AGCTTGCTCTCGAGTTTCCC 60.037 55.000 13.13 0.00 0.00 3.97
1384 1387 1.355005 GAGCTTGCTCTCGAGTTTCC 58.645 55.000 13.13 0.13 0.00 3.13
1385 1388 1.355005 GGAGCTTGCTCTCGAGTTTC 58.645 55.000 20.12 3.48 33.98 2.78
1386 1389 0.036858 GGGAGCTTGCTCTCGAGTTT 60.037 55.000 20.12 0.00 33.98 2.66
1387 1390 1.594310 GGGAGCTTGCTCTCGAGTT 59.406 57.895 20.12 0.00 33.98 3.01
1388 1391 3.293702 GGGAGCTTGCTCTCGAGT 58.706 61.111 20.12 0.00 33.98 4.18
1416 1419 3.726517 CCGAACCAACCAGCGCAG 61.727 66.667 11.47 0.00 0.00 5.18
1421 1424 4.025401 GTGCGCCGAACCAACCAG 62.025 66.667 4.18 0.00 0.00 4.00
1530 1533 0.741221 GACGACCATCAGCCAGTTCC 60.741 60.000 0.00 0.00 0.00 3.62
1547 1550 1.227002 GAAGTCGAGGATGCGGGAC 60.227 63.158 3.16 3.16 0.00 4.46
1577 1580 1.059006 GTCATGGATGGAGGAGGGCT 61.059 60.000 0.00 0.00 0.00 5.19
1604 1607 6.210784 TGAAGTTAATACAGGAGCAGTAGTGT 59.789 38.462 0.00 0.00 0.00 3.55
1608 1611 6.852420 ACTGAAGTTAATACAGGAGCAGTA 57.148 37.500 0.00 0.00 36.17 2.74
1646 1649 5.789710 TCGTCCCTTTTATCGAAAATGAC 57.210 39.130 0.00 0.00 34.08 3.06
1674 1700 5.506730 TGGTGTTGATGTATCCCAAACTA 57.493 39.130 0.00 0.00 0.00 2.24
1699 1725 6.428385 GCATCTTTGCTGAGTAGTGTAATT 57.572 37.500 0.00 0.00 45.77 1.40
1760 1786 8.655901 TGGCATACTTTGATATGGTTAGATGTA 58.344 33.333 0.00 0.00 33.79 2.29
1761 1787 7.517320 TGGCATACTTTGATATGGTTAGATGT 58.483 34.615 0.00 0.00 33.79 3.06
1794 1822 4.614475 ACTCACATCTCATTCCTGTAGGA 58.386 43.478 0.00 0.00 43.73 2.94
1834 1862 3.134804 CGGAATGGAAGGAGGTCTACAAT 59.865 47.826 0.00 0.00 0.00 2.71
1943 1971 5.366829 TTCTGTCAAGTCATGAGCAATTG 57.633 39.130 0.00 0.00 39.19 2.32
2072 2114 8.033038 CGCTAGTATCCTAATATAACAGCCAAA 58.967 37.037 0.00 0.00 0.00 3.28
2082 2124 7.610692 TGTAAGTGCTCGCTAGTATCCTAATAT 59.389 37.037 0.00 0.00 0.00 1.28
2163 2205 2.352805 CCCCACAGGACTTGAGCC 59.647 66.667 0.00 0.00 38.24 4.70
2256 2298 3.145286 TGGATCGTTCACTTTGCATTGA 58.855 40.909 0.00 0.00 0.00 2.57
2258 2300 4.943705 ACTATGGATCGTTCACTTTGCATT 59.056 37.500 0.00 0.00 0.00 3.56
2331 2374 8.321650 AGAGTTGCAGAATTAGAGAAAGAAAG 57.678 34.615 0.00 0.00 0.00 2.62
2561 2606 5.559148 AGATTGGAGTACCATCTTGATCC 57.441 43.478 0.00 0.00 46.34 3.36
2607 2652 3.021695 CCATGTTGGCTGATCATGAAGT 58.978 45.455 0.00 0.00 40.64 3.01
2658 2703 7.907194 GGTAACTAAGCAGCAAGAGTTATTAC 58.093 38.462 13.78 6.88 36.91 1.89
2820 2865 7.921786 TCTCAACTCCGAAATAACAATTGAT 57.078 32.000 13.59 2.25 0.00 2.57
2835 2880 6.324561 AGCAAGAAAAGATTTCTCAACTCC 57.675 37.500 5.86 0.00 0.00 3.85
2862 2907 2.133281 TACATTGAGCTTGCAGCCAT 57.867 45.000 4.77 0.00 43.77 4.40
2915 2960 1.955778 CACAAGGCTCCATGTTCACAA 59.044 47.619 0.00 0.00 0.00 3.33
2991 3036 5.471456 GCTTGGCAAGTAATAGCACTATGAT 59.529 40.000 26.71 0.00 0.00 2.45
3169 3214 1.013596 TGCACTTGTTCCAACAGACG 58.986 50.000 0.00 0.00 40.50 4.18
3483 3529 4.723789 AGGGAGTATCATCCAAACTGATGT 59.276 41.667 0.00 0.00 42.24 3.06


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

AutoCloner maintained by Alex Coulton.