Multiple sequence alignment - TraesCS1A01G029600

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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 TraesCS1A01G029600 chr1A 100.000 3114 0 0 1 3114 13829461 13832574 0.000000e+00 5751.0
1 TraesCS1A01G029600 chr1A 87.831 756 61 17 1093 1836 31945739 31946475 0.000000e+00 857.0
2 TraesCS1A01G029600 chr1A 85.827 762 61 22 1093 1836 31909341 31910073 0.000000e+00 765.0
3 TraesCS1A01G029600 chr1A 79.021 143 18 7 2507 2637 244881451 244881309 1.540000e-13 87.9
4 TraesCS1A01G029600 chr1D 87.426 1360 86 44 597 1931 11702481 11703780 0.000000e+00 1485.0
5 TraesCS1A01G029600 chr1D 84.866 859 68 34 1093 1931 33027914 33028730 0.000000e+00 809.0
6 TraesCS1A01G029600 chr1D 83.546 705 60 23 1994 2652 11703806 11704500 2.660000e-170 608.0
7 TraesCS1A01G029600 chr1D 88.571 350 38 2 2655 3003 11704548 11704896 1.030000e-114 424.0
8 TraesCS1A01G029600 chr1D 88.515 357 26 12 242 598 11667847 11667506 4.800000e-113 418.0
9 TraesCS1A01G029600 chr1D 84.919 431 44 10 1412 1836 58816846 58817261 1.730000e-112 416.0
10 TraesCS1A01G029600 chr1D 94.048 84 5 0 2920 3003 11732575 11732658 9.060000e-26 128.0
11 TraesCS1A01G029600 chr1B 87.511 1153 80 28 827 1931 17574552 17575688 0.000000e+00 1273.0
12 TraesCS1A01G029600 chr1B 91.319 599 45 6 1 598 17560579 17561171 0.000000e+00 811.0
13 TraesCS1A01G029600 chr1B 82.780 633 67 21 1253 1856 60534232 60533613 7.650000e-146 527.0
14 TraesCS1A01G029600 chr1B 80.231 693 87 24 1253 1913 60048082 60048756 2.810000e-130 475.0
15 TraesCS1A01G029600 chr1B 80.087 693 88 23 1253 1913 59961646 59962320 1.310000e-128 470.0
16 TraesCS1A01G029600 chr1B 96.923 130 4 0 841 970 17584755 17584626 5.230000e-53 219.0
17 TraesCS1A01G029600 chr1B 100.000 86 0 0 513 598 17561197 17561282 3.210000e-35 159.0
18 TraesCS1A01G029600 chr1B 94.792 96 5 0 607 702 593826201 593826296 1.930000e-32 150.0
19 TraesCS1A01G029600 chr1B 91.026 78 7 0 3035 3112 661629205 661629128 4.250000e-19 106.0
20 TraesCS1A01G029600 chr1B 84.615 104 13 3 1975 2077 17575701 17575802 1.980000e-17 100.0
21 TraesCS1A01G029600 chrUn 80.976 799 78 32 1069 1836 71523377 71524132 1.620000e-157 566.0
22 TraesCS1A01G029600 chrUn 81.030 796 77 32 1072 1836 300096125 300095373 1.620000e-157 566.0
23 TraesCS1A01G029600 chrUn 81.030 796 77 32 1072 1836 310994039 310993287 1.620000e-157 566.0
24 TraesCS1A01G029600 chrUn 79.333 150 22 5 2496 2636 10132100 10131951 2.560000e-16 97.1
25 TraesCS1A01G029600 chr6D 80.453 839 82 36 984 1789 25534051 25533262 1.620000e-157 566.0
26 TraesCS1A01G029600 chr6D 94.000 100 5 1 607 706 435434983 435434885 1.930000e-32 150.0
27 TraesCS1A01G029600 chr6D 85.135 74 9 2 2489 2561 371530208 371530136 1.200000e-09 75.0
28 TraesCS1A01G029600 chr6B 77.510 1036 117 55 984 1976 41418849 41417887 1.660000e-142 516.0
29 TraesCS1A01G029600 chr6B 81.416 226 38 4 1 225 696513030 696513252 6.860000e-42 182.0
30 TraesCS1A01G029600 chr6B 84.932 73 11 0 2491 2563 585810853 585810925 1.200000e-09 75.0
31 TraesCS1A01G029600 chr6B 88.889 63 1 2 1972 2034 41417934 41417878 4.310000e-09 73.1
32 TraesCS1A01G029600 chr3A 87.283 173 19 3 1 172 429658661 429658491 8.810000e-46 195.0
33 TraesCS1A01G029600 chr3A 94.898 98 4 1 607 703 64085333 64085236 5.380000e-33 152.0
34 TraesCS1A01G029600 chr5D 82.648 219 33 5 1 217 345963807 345964022 4.100000e-44 189.0
35 TraesCS1A01G029600 chr5D 87.013 77 8 2 2486 2561 97190536 97190461 5.530000e-13 86.1
36 TraesCS1A01G029600 chr7D 81.938 227 34 7 1 224 635524735 635524513 5.300000e-43 185.0
37 TraesCS1A01G029600 chr4B 81.579 228 34 6 1 226 285576885 285577106 6.860000e-42 182.0
38 TraesCS1A01G029600 chr7A 81.982 222 30 9 1 217 670858476 670858692 2.470000e-41 180.0
39 TraesCS1A01G029600 chr7A 81.223 229 31 11 2 224 164719767 164719545 1.150000e-39 174.0
40 TraesCS1A01G029600 chr5B 81.140 228 37 6 1 226 42253453 42253230 8.870000e-41 178.0
41 TraesCS1A01G029600 chr2D 98.837 86 1 0 607 692 624783173 624783258 1.500000e-33 154.0
42 TraesCS1A01G029600 chr2D 93.137 102 6 1 607 707 62067550 62067449 6.960000e-32 148.0
43 TraesCS1A01G029600 chr2D 92.381 105 5 3 607 710 579754459 579754357 2.500000e-31 147.0
44 TraesCS1A01G029600 chr2B 94.845 97 4 1 608 703 74196853 74196757 1.930000e-32 150.0
45 TraesCS1A01G029600 chr2B 90.805 87 8 0 3028 3114 683778484 683778570 1.960000e-22 117.0
46 TraesCS1A01G029600 chr2B 89.655 87 8 1 3028 3114 683784022 683784107 3.280000e-20 110.0
47 TraesCS1A01G029600 chr2B 85.000 100 6 4 3016 3114 594984872 594984781 3.310000e-15 93.5
48 TraesCS1A01G029600 chr2B 91.228 57 5 0 2490 2546 37886401 37886457 9.260000e-11 78.7
49 TraesCS1A01G029600 chr5A 84.783 138 14 6 607 739 442694564 442694429 7.010000e-27 132.0
50 TraesCS1A01G029600 chr5A 88.235 85 8 2 3030 3114 691977959 691978041 1.980000e-17 100.0
51 TraesCS1A01G029600 chr3D 90.909 88 8 0 3026 3113 477917117 477917204 5.460000e-23 119.0
52 TraesCS1A01G029600 chr3D 87.209 86 9 2 3028 3113 247910028 247910111 2.560000e-16 97.1
53 TraesCS1A01G029600 chr3D 84.932 73 11 0 2491 2563 459077767 459077839 1.200000e-09 75.0
54 TraesCS1A01G029600 chr2A 92.308 78 6 0 3035 3112 683135501 683135578 9.130000e-21 111.0
55 TraesCS1A01G029600 chr2A 88.889 81 7 2 3035 3114 393391526 393391447 7.110000e-17 99.0
56 TraesCS1A01G029600 chr4A 82.178 101 18 0 2491 2591 54407456 54407556 1.540000e-13 87.9
57 TraesCS1A01G029600 chr3B 80.000 105 17 4 2489 2591 53942839 53942737 1.200000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G029600 chr1A 13829461 13832574 3113 False 5751.00 5751 100.000000 1 3114 1 chr1A.!!$F1 3113
1 TraesCS1A01G029600 chr1A 31945739 31946475 736 False 857.00 857 87.831000 1093 1836 1 chr1A.!!$F3 743
2 TraesCS1A01G029600 chr1A 31909341 31910073 732 False 765.00 765 85.827000 1093 1836 1 chr1A.!!$F2 743
3 TraesCS1A01G029600 chr1D 11702481 11704896 2415 False 839.00 1485 86.514333 597 3003 3 chr1D.!!$F4 2406
4 TraesCS1A01G029600 chr1D 33027914 33028730 816 False 809.00 809 84.866000 1093 1931 1 chr1D.!!$F2 838
5 TraesCS1A01G029600 chr1B 17574552 17575802 1250 False 686.50 1273 86.063000 827 2077 2 chr1B.!!$F5 1250
6 TraesCS1A01G029600 chr1B 60533613 60534232 619 True 527.00 527 82.780000 1253 1856 1 chr1B.!!$R2 603
7 TraesCS1A01G029600 chr1B 17560579 17561282 703 False 485.00 811 95.659500 1 598 2 chr1B.!!$F4 597
8 TraesCS1A01G029600 chr1B 60048082 60048756 674 False 475.00 475 80.231000 1253 1913 1 chr1B.!!$F2 660
9 TraesCS1A01G029600 chr1B 59961646 59962320 674 False 470.00 470 80.087000 1253 1913 1 chr1B.!!$F1 660
10 TraesCS1A01G029600 chrUn 71523377 71524132 755 False 566.00 566 80.976000 1069 1836 1 chrUn.!!$F1 767
11 TraesCS1A01G029600 chrUn 300095373 300096125 752 True 566.00 566 81.030000 1072 1836 1 chrUn.!!$R2 764
12 TraesCS1A01G029600 chrUn 310993287 310994039 752 True 566.00 566 81.030000 1072 1836 1 chrUn.!!$R3 764
13 TraesCS1A01G029600 chr6D 25533262 25534051 789 True 566.00 566 80.453000 984 1789 1 chr6D.!!$R1 805
14 TraesCS1A01G029600 chr6B 41417878 41418849 971 True 294.55 516 83.199500 984 2034 2 chr6B.!!$R1 1050

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
314 316 0.033699 AGGAGGAGAATGCCAAAGCC 60.034 55.0 0.00 0.0 38.69 4.35 F
493 495 0.038801 CTTGCGTCACTCTCTCAGCA 60.039 55.0 0.00 0.0 0.00 4.41 F
1297 1431 0.111266 CTGGAACAAGAAACGCGACG 60.111 55.0 15.93 0.0 38.70 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 1784 0.320374 TCTTGTGTAAGTCCCAGCGG 59.680 55.0 0.00 0.0 35.38 5.52 R
1931 2176 0.392461 GAGTAGCATCGGCCAACCAA 60.392 55.0 2.24 0.0 42.56 3.67 R
3094 3434 0.037734 CGGGCTTGGACCTAGGTTTT 59.962 55.0 17.53 0.0 0.00 2.43 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
35 36 5.279255 TGATTTGGCCCATTGTCATATTG 57.721 39.130 0.00 0.00 0.00 1.90
48 49 9.373603 CCATTGTCATATTGATGTCAAATTTGT 57.626 29.630 17.47 0.00 42.03 2.83
66 67 8.368126 CAAATTTGTCATTTTTGTATCTCGAGC 58.632 33.333 7.81 0.00 0.00 5.03
74 75 8.081633 TCATTTTTGTATCTCGAGCAATGTTTT 58.918 29.630 7.81 0.00 0.00 2.43
77 78 6.552859 TTGTATCTCGAGCAATGTTTTGAA 57.447 33.333 7.81 0.00 34.60 2.69
87 88 7.060518 TCGAGCAATGTTTTGAATTTTGATACG 59.939 33.333 0.00 0.00 34.60 3.06
88 89 7.148983 CGAGCAATGTTTTGAATTTTGATACGT 60.149 33.333 0.00 0.00 34.60 3.57
108 109 4.737765 ACGTAATTTTGTGACAACATGCAC 59.262 37.500 0.00 0.00 35.83 4.57
121 122 2.574450 ACATGCACTGATGTTGTGTCA 58.426 42.857 0.00 0.00 37.70 3.58
129 130 3.633525 ACTGATGTTGTGTCAATGTGCTT 59.366 39.130 0.00 0.00 0.00 3.91
130 131 3.967401 TGATGTTGTGTCAATGTGCTTG 58.033 40.909 0.00 0.00 36.09 4.01
131 132 3.380954 TGATGTTGTGTCAATGTGCTTGT 59.619 39.130 0.00 0.00 36.20 3.16
134 135 4.172505 TGTTGTGTCAATGTGCTTGTTTC 58.827 39.130 0.00 0.00 36.20 2.78
182 184 4.939509 AAATGTGCTACAACATACGGTC 57.060 40.909 0.00 0.00 39.89 4.79
196 198 1.138247 CGGTCACCGGTAGCACTAC 59.862 63.158 8.94 0.00 44.15 2.73
225 227 0.986019 TGCACCCGATACATTCCCCT 60.986 55.000 0.00 0.00 0.00 4.79
240 242 3.565764 TCCCCTAGAATGTGCTCAATG 57.434 47.619 0.00 0.00 0.00 2.82
270 272 3.508762 CCAATCAGTTGAATCTTGCAGC 58.491 45.455 0.00 0.00 37.53 5.25
309 311 2.050144 GTATGGAGGAGGAGAATGCCA 58.950 52.381 0.00 0.00 0.00 4.92
314 316 0.033699 AGGAGGAGAATGCCAAAGCC 60.034 55.000 0.00 0.00 38.69 4.35
370 372 0.459934 CGGTGTATTCCGGCGGTAAA 60.460 55.000 27.32 14.66 45.88 2.01
383 385 2.583143 GCGGTAAATAGCCCCTGAAAT 58.417 47.619 0.00 0.00 0.00 2.17
393 395 7.747809 AATAGCCCCTGAAATGGAAATAAAA 57.252 32.000 0.00 0.00 0.00 1.52
394 396 5.682234 AGCCCCTGAAATGGAAATAAAAG 57.318 39.130 0.00 0.00 0.00 2.27
395 397 5.341169 AGCCCCTGAAATGGAAATAAAAGA 58.659 37.500 0.00 0.00 0.00 2.52
396 398 5.966319 AGCCCCTGAAATGGAAATAAAAGAT 59.034 36.000 0.00 0.00 0.00 2.40
397 399 6.098838 AGCCCCTGAAATGGAAATAAAAGATC 59.901 38.462 0.00 0.00 0.00 2.75
398 400 6.098838 GCCCCTGAAATGGAAATAAAAGATCT 59.901 38.462 0.00 0.00 0.00 2.75
399 401 7.365028 GCCCCTGAAATGGAAATAAAAGATCTT 60.365 37.037 0.88 0.88 0.00 2.40
400 402 7.983484 CCCCTGAAATGGAAATAAAAGATCTTG 59.017 37.037 9.17 0.00 0.00 3.02
463 465 2.447244 ACTGCAGCTCTTACAGTGTC 57.553 50.000 15.27 0.00 42.83 3.67
484 486 1.956170 CGCCAACTCTTGCGTCACT 60.956 57.895 0.00 0.00 45.43 3.41
485 487 1.862806 GCCAACTCTTGCGTCACTC 59.137 57.895 0.00 0.00 0.00 3.51
493 495 0.038801 CTTGCGTCACTCTCTCAGCA 60.039 55.000 0.00 0.00 0.00 4.41
598 711 2.827921 GGCTGGTTTCAGATCCAAATGT 59.172 45.455 0.00 0.00 43.49 2.71
614 727 2.667473 ATGTTAGGTGCGTGGTCTAC 57.333 50.000 0.00 0.00 0.00 2.59
671 785 7.040755 TGTTTGTTGTACTACCATGATTGAAGG 60.041 37.037 4.98 0.00 0.00 3.46
683 797 7.348815 ACCATGATTGAAGGTGAATAGATTGA 58.651 34.615 0.00 0.00 33.57 2.57
686 800 9.731819 CATGATTGAAGGTGAATAGATTGAAAG 57.268 33.333 0.00 0.00 0.00 2.62
695 809 9.807921 AGGTGAATAGATTGAAAGTTTTTAGGA 57.192 29.630 0.00 0.00 0.00 2.94
728 842 0.512952 GCTTCGAGCTCTTTTCGCAA 59.487 50.000 12.85 0.00 38.45 4.85
763 877 6.060136 GGTTTTATAGGTAGAATGGGTCCAC 58.940 44.000 0.00 0.00 0.00 4.02
788 904 4.863689 CCATGTACGTACGTATCACCAAAA 59.136 41.667 29.05 4.37 32.82 2.44
789 905 5.348179 CCATGTACGTACGTATCACCAAAAA 59.652 40.000 29.05 3.59 32.82 1.94
790 906 5.820926 TGTACGTACGTATCACCAAAAAC 57.179 39.130 29.05 16.03 32.82 2.43
812 928 1.811965 TCCATCACCAATCGCAAAGTG 59.188 47.619 0.00 0.00 0.00 3.16
815 931 1.080569 CACCAATCGCAAAGTGCCC 60.081 57.895 0.00 0.00 41.12 5.36
893 1009 1.323534 GTTCGATCATTTCCGTGTCCG 59.676 52.381 0.00 0.00 0.00 4.79
900 1016 0.179145 ATTTCCGTGTCCGCTACTCG 60.179 55.000 4.22 4.22 43.08 4.18
912 1028 0.316854 GCTACTCGTCGGATTCGGAC 60.317 60.000 12.91 12.91 36.95 4.79
970 1091 3.694734 CACAGCGGGCAACAATAAATAG 58.305 45.455 0.00 0.00 39.74 1.73
1057 1188 0.179004 ATCGACATCTCCCTCTCGCT 60.179 55.000 0.00 0.00 0.00 4.93
1059 1190 1.652012 GACATCTCCCTCTCGCTCG 59.348 63.158 0.00 0.00 0.00 5.03
1060 1191 1.077357 ACATCTCCCTCTCGCTCGT 60.077 57.895 0.00 0.00 0.00 4.18
1061 1192 0.180642 ACATCTCCCTCTCGCTCGTA 59.819 55.000 0.00 0.00 0.00 3.43
1086 1217 3.531207 TCGCGGCTGATCCAGGAG 61.531 66.667 6.13 0.00 34.01 3.69
1120 1254 1.324005 GGCAGTAGCTCTTCTCCCGT 61.324 60.000 0.00 0.00 41.70 5.28
1297 1431 0.111266 CTGGAACAAGAAACGCGACG 60.111 55.000 15.93 0.00 38.70 5.12
1502 1676 2.421619 GGACAGCAAGAAACTGGAGAG 58.578 52.381 0.00 0.00 39.55 3.20
1506 1680 1.696336 AGCAAGAAACTGGAGAGCTCA 59.304 47.619 17.77 0.00 0.00 4.26
1720 1935 4.096003 GGCCCAGCTTCTACGCCA 62.096 66.667 0.00 0.00 39.50 5.69
1789 2004 1.801913 CCGCGTGCACTCTGTACTC 60.802 63.158 16.19 0.00 30.49 2.59
1807 2033 6.014647 TGTACTCAGTAACTAAGTCCACCAT 58.985 40.000 0.00 0.00 0.00 3.55
1825 2051 3.452627 ACCATGGCGATCTAGTTTCTTCT 59.547 43.478 13.04 0.00 0.00 2.85
1828 2062 3.262420 TGGCGATCTAGTTTCTTCTTGC 58.738 45.455 0.00 0.00 0.00 4.01
1851 2085 2.683867 GAGTAGACGAGTGGTGCTGTAT 59.316 50.000 0.00 0.00 0.00 2.29
1867 2104 3.243002 GCTGTATGTAGTCGTAGGGTGTC 60.243 52.174 0.00 0.00 0.00 3.67
1871 2108 2.079158 TGTAGTCGTAGGGTGTCGAAG 58.921 52.381 0.00 0.00 37.81 3.79
1883 2128 4.162320 AGGGTGTCGAAGTCAATCACATAT 59.838 41.667 0.00 0.00 0.00 1.78
1884 2129 5.362717 AGGGTGTCGAAGTCAATCACATATA 59.637 40.000 0.00 0.00 0.00 0.86
1885 2130 5.692204 GGGTGTCGAAGTCAATCACATATAG 59.308 44.000 0.00 0.00 0.00 1.31
1888 2133 7.919091 GGTGTCGAAGTCAATCACATATAGTAA 59.081 37.037 0.00 0.00 0.00 2.24
1890 2135 8.463607 TGTCGAAGTCAATCACATATAGTAACA 58.536 33.333 0.00 0.00 0.00 2.41
1931 2176 5.494724 TCATCTCAGCTAGTGAAAAGCATT 58.505 37.500 0.00 0.00 42.62 3.56
1932 2177 5.942236 TCATCTCAGCTAGTGAAAAGCATTT 59.058 36.000 0.00 0.00 42.62 2.32
1934 2179 4.456911 TCTCAGCTAGTGAAAAGCATTTGG 59.543 41.667 0.00 0.00 42.62 3.28
1935 2180 4.144297 TCAGCTAGTGAAAAGCATTTGGT 58.856 39.130 0.00 0.00 42.62 3.67
1937 2182 4.682860 CAGCTAGTGAAAAGCATTTGGTTG 59.317 41.667 0.00 0.00 42.62 3.77
1938 2183 3.989817 GCTAGTGAAAAGCATTTGGTTGG 59.010 43.478 0.00 0.00 39.02 3.77
1939 2184 2.837498 AGTGAAAAGCATTTGGTTGGC 58.163 42.857 0.00 0.00 39.02 4.52
1941 2186 1.147473 GAAAAGCATTTGGTTGGCCG 58.853 50.000 0.00 0.00 39.02 6.13
1942 2187 0.755686 AAAAGCATTTGGTTGGCCGA 59.244 45.000 0.00 0.00 39.02 5.54
1943 2188 0.975887 AAAGCATTTGGTTGGCCGAT 59.024 45.000 0.00 0.00 36.60 4.18
1944 2189 0.247185 AAGCATTTGGTTGGCCGATG 59.753 50.000 0.00 0.00 37.67 3.84
1945 2190 1.810853 GCATTTGGTTGGCCGATGC 60.811 57.895 0.00 0.00 44.10 3.91
1946 2191 1.892338 CATTTGGTTGGCCGATGCT 59.108 52.632 0.00 0.00 37.67 3.79
1947 2192 1.102154 CATTTGGTTGGCCGATGCTA 58.898 50.000 0.00 0.00 37.67 3.49
1948 2193 1.102978 ATTTGGTTGGCCGATGCTAC 58.897 50.000 0.00 0.00 37.67 3.58
1949 2194 0.037590 TTTGGTTGGCCGATGCTACT 59.962 50.000 0.00 0.00 37.67 2.57
1950 2195 0.392461 TTGGTTGGCCGATGCTACTC 60.392 55.000 0.00 0.00 37.67 2.59
1951 2196 1.523938 GGTTGGCCGATGCTACTCC 60.524 63.158 0.00 0.00 37.74 3.85
1952 2197 1.883084 GTTGGCCGATGCTACTCCG 60.883 63.158 0.00 0.00 37.74 4.63
1953 2198 3.088941 TTGGCCGATGCTACTCCGG 62.089 63.158 0.00 0.00 45.51 5.14
1954 2199 3.537874 GGCCGATGCTACTCCGGT 61.538 66.667 0.00 0.00 44.63 5.28
1955 2200 2.279517 GCCGATGCTACTCCGGTG 60.280 66.667 0.00 0.00 44.63 4.94
1956 2201 3.077519 GCCGATGCTACTCCGGTGT 62.078 63.158 14.50 14.50 44.63 4.16
1957 2202 1.065928 CCGATGCTACTCCGGTGTC 59.934 63.158 13.38 0.02 38.55 3.67
1958 2203 1.663379 CCGATGCTACTCCGGTGTCA 61.663 60.000 13.38 6.47 38.55 3.58
1959 2204 0.385751 CGATGCTACTCCGGTGTCAT 59.614 55.000 13.38 11.27 0.00 3.06
1960 2205 1.202417 CGATGCTACTCCGGTGTCATT 60.202 52.381 13.38 0.00 0.00 2.57
1961 2206 2.205074 GATGCTACTCCGGTGTCATTG 58.795 52.381 13.38 3.75 0.00 2.82
1962 2207 0.973632 TGCTACTCCGGTGTCATTGT 59.026 50.000 13.38 0.00 0.00 2.71
1963 2208 1.346395 TGCTACTCCGGTGTCATTGTT 59.654 47.619 13.38 0.00 0.00 2.83
1964 2209 2.000447 GCTACTCCGGTGTCATTGTTC 59.000 52.381 13.38 0.00 0.00 3.18
1965 2210 2.618053 CTACTCCGGTGTCATTGTTCC 58.382 52.381 13.38 0.00 0.00 3.62
1966 2211 0.762418 ACTCCGGTGTCATTGTTCCA 59.238 50.000 2.61 0.00 0.00 3.53
1967 2212 1.142060 ACTCCGGTGTCATTGTTCCAA 59.858 47.619 2.61 0.00 0.00 3.53
1968 2213 2.224769 ACTCCGGTGTCATTGTTCCAAT 60.225 45.455 2.61 0.00 0.00 3.16
1969 2214 2.158559 TCCGGTGTCATTGTTCCAATG 58.841 47.619 0.00 10.04 0.00 2.82
1970 2215 1.885887 CCGGTGTCATTGTTCCAATGT 59.114 47.619 14.62 0.00 0.00 2.71
1971 2216 3.078097 CCGGTGTCATTGTTCCAATGTA 58.922 45.455 14.62 5.18 0.00 2.29
1978 2223 8.085296 GGTGTCATTGTTCCAATGTAAACATTA 58.915 33.333 14.62 0.00 44.10 1.90
1988 2233 3.275617 TGTAAACATTAGGCCGATGCT 57.724 42.857 18.54 7.06 37.74 3.79
1989 2234 4.409718 TGTAAACATTAGGCCGATGCTA 57.590 40.909 18.54 9.97 37.74 3.49
1990 2235 4.124238 TGTAAACATTAGGCCGATGCTAC 58.876 43.478 18.54 18.36 37.74 3.58
1991 2236 3.560636 AAACATTAGGCCGATGCTACT 57.439 42.857 18.54 0.83 37.74 2.57
1992 2237 2.821991 ACATTAGGCCGATGCTACTC 57.178 50.000 18.54 0.00 37.74 2.59
1995 2240 1.329256 TTAGGCCGATGCTACTCCTC 58.671 55.000 0.00 0.00 37.74 3.71
1999 2244 0.825840 GCCGATGCTACTCCTCCTCT 60.826 60.000 0.00 0.00 33.53 3.69
2034 2280 9.142014 TGATTCCAATGTAACCAAAATATAGGG 57.858 33.333 0.00 0.00 0.00 3.53
2088 2352 2.061028 CATTTTTCTGCAAGGCGTTCC 58.939 47.619 0.00 0.00 0.00 3.62
2091 2355 1.781025 TTTCTGCAAGGCGTTCCGTG 61.781 55.000 0.00 0.00 43.51 4.94
2102 2366 1.862827 GCGTTCCGTGTGAAGTTAACT 59.137 47.619 1.12 1.12 32.37 2.24
2105 2369 4.606894 GCGTTCCGTGTGAAGTTAACTAAC 60.607 45.833 8.92 11.04 32.37 2.34
2109 2373 7.043458 CGTTCCGTGTGAAGTTAACTAACTAAA 60.043 37.037 8.92 2.52 45.17 1.85
2110 2374 8.768019 GTTCCGTGTGAAGTTAACTAACTAAAT 58.232 33.333 8.92 0.00 45.17 1.40
2111 2375 9.979578 TTCCGTGTGAAGTTAACTAACTAAATA 57.020 29.630 8.92 0.00 45.17 1.40
2112 2376 9.979578 TCCGTGTGAAGTTAACTAACTAAATAA 57.020 29.630 8.92 0.00 45.17 1.40
2178 2442 9.515020 ACAGTATTTATGCAAATAACCGAATTG 57.485 29.630 0.00 0.00 38.13 2.32
2182 2446 1.813178 TGCAAATAACCGAATTGCCGA 59.187 42.857 7.19 0.00 46.74 5.54
2207 2471 3.667261 GCACGACCGTATATATGTGTCAC 59.333 47.826 16.92 0.00 0.00 3.67
2218 2482 0.902531 ATGTGTCACGGGGTAGAAGG 59.097 55.000 0.00 0.00 0.00 3.46
2228 2492 1.847088 GGGGTAGAAGGAGAAATGGCT 59.153 52.381 0.00 0.00 0.00 4.75
2229 2493 2.422093 GGGGTAGAAGGAGAAATGGCTG 60.422 54.545 0.00 0.00 0.00 4.85
2230 2494 2.422093 GGGTAGAAGGAGAAATGGCTGG 60.422 54.545 0.00 0.00 0.00 4.85
2231 2495 2.505819 GGTAGAAGGAGAAATGGCTGGA 59.494 50.000 0.00 0.00 0.00 3.86
2245 2509 6.584185 AATGGCTGGAAAAACTAACGTTAT 57.416 33.333 8.76 0.00 31.86 1.89
2246 2510 7.690952 AATGGCTGGAAAAACTAACGTTATA 57.309 32.000 8.76 0.00 31.86 0.98
2247 2511 7.875327 ATGGCTGGAAAAACTAACGTTATAT 57.125 32.000 8.76 0.00 31.86 0.86
2251 2515 7.065443 GGCTGGAAAAACTAACGTTATATGACT 59.935 37.037 8.76 0.00 31.86 3.41
2258 2522 9.555727 AAAACTAACGTTATATGACTGCCATAT 57.444 29.630 8.76 2.08 46.95 1.78
2273 2537 6.008331 ACTGCCATATAACAGATCATTGCAT 58.992 36.000 10.33 0.00 37.35 3.96
2281 2545 4.442401 ACAGATCATTGCATATCCCACA 57.558 40.909 0.00 0.00 0.00 4.17
2289 2553 0.670162 GCATATCCCACACACATGGC 59.330 55.000 0.00 0.00 38.55 4.40
2291 2555 2.377073 CATATCCCACACACATGGCAA 58.623 47.619 0.00 0.00 38.55 4.52
2348 2635 8.776680 AACAAGATATTCAAAAACGTACACAC 57.223 30.769 0.00 0.00 0.00 3.82
2390 2677 5.467399 CCCATGCCATAAAAACTTGCATATG 59.533 40.000 0.00 0.00 40.46 1.78
2391 2678 6.050432 CCATGCCATAAAAACTTGCATATGT 58.950 36.000 4.29 0.00 40.46 2.29
2415 2702 2.007360 TTGCATGCGCCTTTTTATGG 57.993 45.000 14.09 0.00 37.32 2.74
2418 2705 2.028658 TGCATGCGCCTTTTTATGGAAA 60.029 40.909 14.09 0.00 37.32 3.13
2419 2706 2.348362 GCATGCGCCTTTTTATGGAAAC 59.652 45.455 4.18 0.00 0.00 2.78
2420 2707 3.848726 CATGCGCCTTTTTATGGAAACT 58.151 40.909 4.18 0.00 0.00 2.66
2422 2709 4.695217 TGCGCCTTTTTATGGAAACTAG 57.305 40.909 4.18 0.00 0.00 2.57
2423 2710 3.119637 TGCGCCTTTTTATGGAAACTAGC 60.120 43.478 4.18 0.00 0.00 3.42
2424 2711 3.119637 GCGCCTTTTTATGGAAACTAGCA 60.120 43.478 0.00 0.00 0.00 3.49
2425 2712 4.412207 CGCCTTTTTATGGAAACTAGCAC 58.588 43.478 0.00 0.00 0.00 4.40
2454 2741 3.626028 GTGCAAACACTCCCTAAACTG 57.374 47.619 0.00 0.00 43.85 3.16
2461 2748 4.868314 ACACTCCCTAAACTGACTACAC 57.132 45.455 0.00 0.00 0.00 2.90
2475 2762 5.696724 ACTGACTACACATTTTCAGTACAGC 59.303 40.000 1.27 0.00 45.41 4.40
2477 2764 2.969443 ACACATTTTCAGTACAGCGC 57.031 45.000 0.00 0.00 0.00 5.92
2493 2780 2.164219 CAGCGCCATCCAATTTTGTACT 59.836 45.455 2.29 0.00 0.00 2.73
2494 2781 2.825532 AGCGCCATCCAATTTTGTACTT 59.174 40.909 2.29 0.00 0.00 2.24
2495 2782 3.119495 AGCGCCATCCAATTTTGTACTTC 60.119 43.478 2.29 0.00 0.00 3.01
2496 2783 3.769536 CGCCATCCAATTTTGTACTTCC 58.230 45.455 0.00 0.00 0.00 3.46
2497 2784 3.443681 CGCCATCCAATTTTGTACTTCCT 59.556 43.478 0.00 0.00 0.00 3.36
2504 2791 4.378046 CCAATTTTGTACTTCCTCCGTTCG 60.378 45.833 0.00 0.00 0.00 3.95
2516 2803 4.365723 TCCTCCGTTCGCAAATATAAGAC 58.634 43.478 0.00 0.00 0.00 3.01
2521 2808 5.120519 TCCGTTCGCAAATATAAGACGTTTT 59.879 36.000 0.00 0.00 0.00 2.43
2539 2826 9.530633 AGACGTTTTAGATATTTCACTATGGAC 57.469 33.333 0.00 0.00 0.00 4.02
2560 2847 3.969976 ACTACATATGGGCTGACATGAGT 59.030 43.478 7.80 0.00 32.39 3.41
2572 2859 5.213913 CTGACATGAGTGAGCAAACATAC 57.786 43.478 0.00 0.00 0.00 2.39
2581 2868 6.310467 TGAGTGAGCAAACATACTAAATCGTC 59.690 38.462 0.00 0.00 0.00 4.20
2582 2869 6.398918 AGTGAGCAAACATACTAAATCGTCT 58.601 36.000 0.00 0.00 0.00 4.18
2592 2879 9.985318 AACATACTAAATCGTCTCTATATACGC 57.015 33.333 0.00 0.00 38.94 4.42
2593 2880 9.159364 ACATACTAAATCGTCTCTATATACGCA 57.841 33.333 0.00 0.00 38.94 5.24
2594 2881 9.983804 CATACTAAATCGTCTCTATATACGCAA 57.016 33.333 0.00 0.00 38.94 4.85
2597 2884 9.740239 ACTAAATCGTCTCTATATACGCAAAAA 57.260 29.630 0.00 0.00 38.94 1.94
2641 2936 6.524101 TTGTGAACAAAGGAAGTAGCTTTT 57.476 33.333 0.00 0.00 32.11 2.27
2642 2937 7.633193 TTGTGAACAAAGGAAGTAGCTTTTA 57.367 32.000 0.00 0.00 32.11 1.52
2690 3030 7.527457 ACTAGAAATTGTATCGGCAAAAAGAC 58.473 34.615 0.00 0.00 31.63 3.01
2696 3036 5.957842 TGTATCGGCAAAAAGACAAATCT 57.042 34.783 0.00 0.00 36.42 2.40
2704 3044 6.226052 GGCAAAAAGACAAATCTTCCAAGAT 58.774 36.000 0.00 0.00 44.82 2.40
2726 3066 3.577649 ACATAGTTCGTCTCCTGTGTG 57.422 47.619 0.00 0.00 32.65 3.82
2741 3081 2.469826 TGTGTGTTCTAGTGCTTGTCG 58.530 47.619 0.00 0.00 0.00 4.35
2745 3085 1.684450 TGTTCTAGTGCTTGTCGGTCA 59.316 47.619 0.00 0.00 0.00 4.02
2749 3089 0.317160 TAGTGCTTGTCGGTCACCAG 59.683 55.000 0.00 0.00 0.00 4.00
2761 3101 3.921257 TCACCAGTGTGATCTGCAG 57.079 52.632 7.63 7.63 46.40 4.41
2771 3111 6.149308 CCAGTGTGATCTGCAGTACAAATTAA 59.851 38.462 14.67 0.00 34.47 1.40
2774 3114 7.228507 AGTGTGATCTGCAGTACAAATTAAACA 59.771 33.333 14.67 5.11 0.00 2.83
2775 3115 8.023128 GTGTGATCTGCAGTACAAATTAAACAT 58.977 33.333 14.67 0.00 0.00 2.71
2799 3139 9.030301 CATAACAAAGAAAAATCGAGTGGTTTT 57.970 29.630 0.00 0.00 0.00 2.43
2808 3148 9.124807 GAAAAATCGAGTGGTTTTAATACCTTG 57.875 33.333 15.06 1.89 39.04 3.61
2811 3151 7.754851 ATCGAGTGGTTTTAATACCTTGTTT 57.245 32.000 15.06 0.00 39.04 2.83
2834 3174 3.239449 GGGTCCATTTTCACCTTCCTTT 58.761 45.455 0.00 0.00 32.69 3.11
2869 3209 2.476619 ACGAAGATCACAAGAGCAAACG 59.523 45.455 0.00 0.00 30.99 3.60
2888 3228 5.352643 AACGAACCAAACGGAAAGAATAG 57.647 39.130 0.00 0.00 34.93 1.73
2889 3229 3.749609 ACGAACCAAACGGAAAGAATAGG 59.250 43.478 0.00 0.00 34.93 2.57
2891 3231 4.931002 CGAACCAAACGGAAAGAATAGGTA 59.069 41.667 0.00 0.00 0.00 3.08
2927 3267 7.807977 ATTACTGCACTAAATACCATCTTGG 57.192 36.000 0.00 0.00 45.02 3.61
2940 3280 3.729274 CCATCTTGGAGCCAGGTTTTGG 61.729 54.545 0.00 2.10 45.04 3.28
2957 3297 3.294038 TTGGGACGAAAACTTTACCCA 57.706 42.857 0.00 0.00 44.39 4.51
2960 3300 2.490509 GGGACGAAAACTTTACCCATGG 59.509 50.000 4.14 4.14 37.50 3.66
2965 3305 4.520111 ACGAAAACTTTACCCATGGTAACC 59.480 41.667 11.73 0.00 46.28 2.85
3036 3376 8.677148 ATTTGATTATACCATGTGAGTACACC 57.323 34.615 0.00 0.00 45.40 4.16
3037 3377 7.432148 TTGATTATACCATGTGAGTACACCT 57.568 36.000 0.00 0.00 45.40 4.00
3038 3378 6.816136 TGATTATACCATGTGAGTACACCTG 58.184 40.000 0.00 0.00 45.40 4.00
3041 3381 3.159298 CATGTGAGTACACCTGGCC 57.841 57.895 0.00 0.00 45.40 5.36
3042 3382 0.324614 CATGTGAGTACACCTGGCCA 59.675 55.000 4.71 4.71 45.40 5.36
3043 3383 1.065199 CATGTGAGTACACCTGGCCAT 60.065 52.381 5.51 0.00 45.40 4.40
3044 3384 0.613260 TGTGAGTACACCTGGCCATC 59.387 55.000 5.51 0.00 45.40 3.51
3045 3385 0.905357 GTGAGTACACCTGGCCATCT 59.095 55.000 5.51 0.00 40.74 2.90
3046 3386 0.904649 TGAGTACACCTGGCCATCTG 59.095 55.000 5.51 7.12 0.00 2.90
3047 3387 0.462759 GAGTACACCTGGCCATCTGC 60.463 60.000 5.51 0.00 40.16 4.26
3089 3429 2.124695 GGCCTACCAAAGCCCGAG 60.125 66.667 0.00 0.00 43.76 4.63
3090 3430 2.124695 GCCTACCAAAGCCCGAGG 60.125 66.667 0.00 0.00 0.00 4.63
3102 3442 3.460648 CCCGAGGCAGAAAACCTAG 57.539 57.895 0.00 0.00 37.77 3.02
3103 3443 0.107654 CCCGAGGCAGAAAACCTAGG 60.108 60.000 7.41 7.41 46.56 3.02
3104 3444 0.613777 CCGAGGCAGAAAACCTAGGT 59.386 55.000 9.21 9.21 43.16 3.08
3105 3445 1.405661 CCGAGGCAGAAAACCTAGGTC 60.406 57.143 16.64 2.44 43.16 3.85
3106 3446 1.405661 CGAGGCAGAAAACCTAGGTCC 60.406 57.143 16.64 11.03 37.77 4.46
3107 3447 1.628846 GAGGCAGAAAACCTAGGTCCA 59.371 52.381 16.64 0.00 37.77 4.02
3108 3448 2.039879 GAGGCAGAAAACCTAGGTCCAA 59.960 50.000 16.64 0.00 37.77 3.53
3109 3449 2.040412 AGGCAGAAAACCTAGGTCCAAG 59.960 50.000 16.64 5.94 35.10 3.61
3110 3450 1.813178 GCAGAAAACCTAGGTCCAAGC 59.187 52.381 16.64 12.27 0.00 4.01
3111 3451 2.437413 CAGAAAACCTAGGTCCAAGCC 58.563 52.381 16.64 1.90 0.00 4.35
3112 3452 1.354705 AGAAAACCTAGGTCCAAGCCC 59.645 52.381 16.64 0.82 0.00 5.19
3113 3453 0.037734 AAAACCTAGGTCCAAGCCCG 59.962 55.000 16.64 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.086094 CAATGGGCCAAATCAAAAGCC 58.914 47.619 11.89 0.00 44.99 4.35
48 49 6.741992 ACATTGCTCGAGATACAAAAATGA 57.258 33.333 18.75 0.00 0.00 2.57
51 52 7.421599 TCAAAACATTGCTCGAGATACAAAAA 58.578 30.769 18.75 0.00 0.00 1.94
54 55 6.552859 TTCAAAACATTGCTCGAGATACAA 57.447 33.333 18.75 11.56 0.00 2.41
62 63 7.148983 ACGTATCAAAATTCAAAACATTGCTCG 60.149 33.333 0.00 0.00 0.00 5.03
74 75 9.952188 TGTCACAAAATTACGTATCAAAATTCA 57.048 25.926 0.00 0.00 0.00 2.57
77 78 9.737427 TGTTGTCACAAAATTACGTATCAAAAT 57.263 25.926 0.00 0.00 0.00 1.82
87 88 5.976534 TCAGTGCATGTTGTCACAAAATTAC 59.023 36.000 0.00 0.00 36.16 1.89
88 89 6.141560 TCAGTGCATGTTGTCACAAAATTA 57.858 33.333 0.00 0.00 36.16 1.40
101 102 2.574450 TGACACAACATCAGTGCATGT 58.426 42.857 0.00 3.29 40.59 3.21
108 109 3.909776 AGCACATTGACACAACATCAG 57.090 42.857 0.00 0.00 0.00 2.90
121 122 7.671495 AAACTGAAAAAGAAACAAGCACATT 57.329 28.000 0.00 0.00 0.00 2.71
158 160 6.091577 TGACCGTATGTTGTAGCACATTTTAG 59.908 38.462 0.00 0.00 38.40 1.85
168 170 1.203052 ACCGGTGACCGTATGTTGTAG 59.797 52.381 23.73 6.43 46.80 2.74
177 179 1.303561 TAGTGCTACCGGTGACCGT 60.304 57.895 23.73 13.32 46.80 4.83
182 184 0.108329 CCCTTGTAGTGCTACCGGTG 60.108 60.000 19.93 8.61 35.26 4.94
187 189 0.981943 ACCCACCCTTGTAGTGCTAC 59.018 55.000 2.60 2.60 33.75 3.58
225 227 6.767902 GGGTAAGATTCATTGAGCACATTCTA 59.232 38.462 0.00 0.00 0.00 2.10
240 242 7.872113 AGATTCAACTGATTGGGTAAGATTC 57.128 36.000 0.00 0.00 36.39 2.52
270 272 3.340814 ACCATTAGCAAGTCAGGACTG 57.659 47.619 2.15 0.00 41.58 3.51
341 343 2.288825 CGGAATACACCGCAGATGGTAT 60.289 50.000 0.00 0.00 46.20 2.73
353 355 2.477754 GCTATTTACCGCCGGAATACAC 59.522 50.000 11.71 0.00 0.00 2.90
364 366 2.884639 CCATTTCAGGGGCTATTTACCG 59.115 50.000 0.00 0.00 0.00 4.02
370 372 7.132128 TCTTTTATTTCCATTTCAGGGGCTAT 58.868 34.615 0.00 0.00 0.00 2.97
393 395 8.386264 TCCTTCTTCTCAATTTTACCAAGATCT 58.614 33.333 0.00 0.00 0.00 2.75
394 396 8.567285 TCCTTCTTCTCAATTTTACCAAGATC 57.433 34.615 0.00 0.00 0.00 2.75
395 397 8.940397 TTCCTTCTTCTCAATTTTACCAAGAT 57.060 30.769 0.00 0.00 0.00 2.40
396 398 8.630037 GTTTCCTTCTTCTCAATTTTACCAAGA 58.370 33.333 0.00 0.00 0.00 3.02
397 399 8.413229 TGTTTCCTTCTTCTCAATTTTACCAAG 58.587 33.333 0.00 0.00 0.00 3.61
398 400 8.299990 TGTTTCCTTCTTCTCAATTTTACCAA 57.700 30.769 0.00 0.00 0.00 3.67
399 401 7.889873 TGTTTCCTTCTTCTCAATTTTACCA 57.110 32.000 0.00 0.00 0.00 3.25
400 402 8.630037 TCTTGTTTCCTTCTTCTCAATTTTACC 58.370 33.333 0.00 0.00 0.00 2.85
438 440 5.047306 ACACTGTAAGAGCTGCAGTTATACA 60.047 40.000 20.25 20.25 40.99 2.29
439 441 5.411781 ACACTGTAAGAGCTGCAGTTATAC 58.588 41.667 16.64 15.65 40.99 1.47
484 486 3.773667 AGGATGAAGATGTTGCTGAGAGA 59.226 43.478 0.00 0.00 0.00 3.10
485 487 4.139859 AGGATGAAGATGTTGCTGAGAG 57.860 45.455 0.00 0.00 0.00 3.20
493 495 7.771927 ACTGAATCAAAAGGATGAAGATGTT 57.228 32.000 0.00 0.00 36.02 2.71
641 754 8.443160 CAATCATGGTAGTACAACAAACACTAG 58.557 37.037 2.06 0.00 0.00 2.57
642 755 8.151596 TCAATCATGGTAGTACAACAAACACTA 58.848 33.333 2.06 0.00 0.00 2.74
643 756 6.995686 TCAATCATGGTAGTACAACAAACACT 59.004 34.615 2.06 0.00 0.00 3.55
649 763 5.937540 CACCTTCAATCATGGTAGTACAACA 59.062 40.000 2.06 0.00 31.11 3.33
721 835 3.897141 ACCCCTTTTCTTTTTGCGAAA 57.103 38.095 0.00 0.00 0.00 3.46
728 842 9.886337 TTCTACCTATAAAACCCCTTTTCTTTT 57.114 29.630 0.00 0.00 31.74 2.27
732 846 7.287005 CCCATTCTACCTATAAAACCCCTTTTC 59.713 40.741 0.00 0.00 31.74 2.29
738 852 5.133153 TGGACCCATTCTACCTATAAAACCC 59.867 44.000 0.00 0.00 0.00 4.11
763 877 3.313249 TGGTGATACGTACGTACATGGAG 59.687 47.826 28.99 10.79 33.01 3.86
788 904 2.127271 TGCGATTGGTGATGGATGTT 57.873 45.000 0.00 0.00 0.00 2.71
789 905 2.127271 TTGCGATTGGTGATGGATGT 57.873 45.000 0.00 0.00 0.00 3.06
790 906 2.424601 ACTTTGCGATTGGTGATGGATG 59.575 45.455 0.00 0.00 0.00 3.51
812 928 1.148273 TATCCAATCCGCACTGGGC 59.852 57.895 0.00 0.00 38.76 5.36
815 931 1.209128 GTCGTATCCAATCCGCACTG 58.791 55.000 0.00 0.00 0.00 3.66
893 1009 0.316854 GTCCGAATCCGACGAGTAGC 60.317 60.000 0.00 0.00 38.22 3.58
1008 1132 6.360618 GGTAGATCCCTTGTTTGATGAAGAT 58.639 40.000 0.00 0.00 0.00 2.40
1057 1188 3.566853 CCGCGACGCCTACTACGA 61.567 66.667 15.34 0.00 0.00 3.43
1059 1190 3.885521 AGCCGCGACGCCTACTAC 61.886 66.667 15.34 0.00 0.00 2.73
1060 1191 3.884350 CAGCCGCGACGCCTACTA 61.884 66.667 15.34 0.00 0.00 1.82
1086 1217 4.261781 GCCGCCATTGCTAGCTGC 62.262 66.667 17.23 12.01 43.25 5.25
1091 1222 1.523711 GCTACTGCCGCCATTGCTA 60.524 57.895 0.00 0.00 34.43 3.49
1106 1240 1.077644 AGCGACGGGAGAAGAGCTA 60.078 57.895 0.00 0.00 32.73 3.32
1297 1431 5.298197 CAGATTGAGCTGCATGGATTATC 57.702 43.478 1.02 0.00 0.00 1.75
1541 1733 3.044059 CTAGGCAGGCGCTTGTTGC 62.044 63.158 21.36 17.66 38.60 4.17
1542 1734 3.044059 GCTAGGCAGGCGCTTGTTG 62.044 63.158 21.36 9.13 38.60 3.33
1584 1784 0.320374 TCTTGTGTAAGTCCCAGCGG 59.680 55.000 0.00 0.00 35.38 5.52
1673 1888 1.965930 GCCTTGTGCGGTGTCATCA 60.966 57.895 0.00 0.00 0.00 3.07
1674 1889 2.690778 GGCCTTGTGCGGTGTCATC 61.691 63.158 0.00 0.00 42.61 2.92
1675 1890 2.672996 GGCCTTGTGCGGTGTCAT 60.673 61.111 0.00 0.00 42.61 3.06
1720 1935 2.107750 CATGCTCGGATCAGGCGT 59.892 61.111 0.00 0.00 0.00 5.68
1789 2004 3.270877 GCCATGGTGGACTTAGTTACTG 58.729 50.000 14.67 0.00 40.96 2.74
1807 2033 3.262420 GCAAGAAGAAACTAGATCGCCA 58.738 45.455 0.00 0.00 0.00 5.69
1825 2051 0.892358 ACCACTCGTCTACTCCGCAA 60.892 55.000 0.00 0.00 0.00 4.85
1828 2062 1.136984 GCACCACTCGTCTACTCCG 59.863 63.158 0.00 0.00 0.00 4.63
1851 2085 2.079158 CTTCGACACCCTACGACTACA 58.921 52.381 0.00 0.00 38.24 2.74
1892 2137 9.055689 AGCTGAGATGAAATAATAGGGATACAT 57.944 33.333 0.00 0.00 39.74 2.29
1895 2140 9.775539 ACTAGCTGAGATGAAATAATAGGGATA 57.224 33.333 0.00 0.00 0.00 2.59
1902 2147 8.619546 GCTTTTCACTAGCTGAGATGAAATAAT 58.380 33.333 13.73 0.00 39.94 1.28
1931 2176 0.392461 GAGTAGCATCGGCCAACCAA 60.392 55.000 2.24 0.00 42.56 3.67
1932 2177 1.220749 GAGTAGCATCGGCCAACCA 59.779 57.895 2.24 0.00 42.56 3.67
1934 2179 1.883084 CGGAGTAGCATCGGCCAAC 60.883 63.158 2.24 0.00 42.56 3.77
1935 2180 2.499205 CGGAGTAGCATCGGCCAA 59.501 61.111 2.24 0.00 42.56 4.52
1937 2182 3.537874 ACCGGAGTAGCATCGGCC 61.538 66.667 9.46 0.00 46.87 6.13
1938 2183 2.279517 CACCGGAGTAGCATCGGC 60.280 66.667 9.46 0.00 46.87 5.54
1941 2186 2.205074 CAATGACACCGGAGTAGCATC 58.795 52.381 9.46 0.00 0.00 3.91
1942 2187 1.555075 ACAATGACACCGGAGTAGCAT 59.445 47.619 9.46 4.16 0.00 3.79
1943 2188 0.973632 ACAATGACACCGGAGTAGCA 59.026 50.000 9.46 1.28 0.00 3.49
1944 2189 2.000447 GAACAATGACACCGGAGTAGC 59.000 52.381 9.46 0.00 0.00 3.58
1945 2190 2.028476 TGGAACAATGACACCGGAGTAG 60.028 50.000 9.46 0.00 31.92 2.57
1946 2191 1.972075 TGGAACAATGACACCGGAGTA 59.028 47.619 9.46 0.00 31.92 2.59
1947 2192 0.762418 TGGAACAATGACACCGGAGT 59.238 50.000 9.46 6.23 31.92 3.85
1948 2193 3.623848 TGGAACAATGACACCGGAG 57.376 52.632 9.46 1.26 31.92 4.63
1960 2205 4.156922 CGGCCTAATGTTTACATTGGAACA 59.843 41.667 17.33 9.38 44.45 3.18
1961 2206 4.396790 TCGGCCTAATGTTTACATTGGAAC 59.603 41.667 17.33 10.40 44.45 3.62
1962 2207 4.590918 TCGGCCTAATGTTTACATTGGAA 58.409 39.130 17.33 0.00 44.45 3.53
1963 2208 4.223556 TCGGCCTAATGTTTACATTGGA 57.776 40.909 17.33 6.02 44.45 3.53
1964 2209 4.792704 GCATCGGCCTAATGTTTACATTGG 60.793 45.833 16.31 13.52 45.34 3.16
1965 2210 4.036734 AGCATCGGCCTAATGTTTACATTG 59.963 41.667 16.31 7.80 42.98 2.82
1966 2211 4.207165 AGCATCGGCCTAATGTTTACATT 58.793 39.130 12.30 12.30 44.28 2.71
1967 2212 3.820557 AGCATCGGCCTAATGTTTACAT 58.179 40.909 14.40 0.00 42.56 2.29
1968 2213 3.275617 AGCATCGGCCTAATGTTTACA 57.724 42.857 14.40 0.00 42.56 2.41
1969 2214 4.377897 AGTAGCATCGGCCTAATGTTTAC 58.622 43.478 14.40 15.21 42.56 2.01
1970 2215 4.502604 GGAGTAGCATCGGCCTAATGTTTA 60.503 45.833 14.40 6.92 42.56 2.01
1971 2216 3.467803 GAGTAGCATCGGCCTAATGTTT 58.532 45.455 14.40 7.67 42.56 2.83
1978 2223 1.834822 GGAGGAGTAGCATCGGCCT 60.835 63.158 0.00 0.00 42.56 5.19
1988 2233 4.942944 TCATAACACCAAGAGGAGGAGTA 58.057 43.478 0.00 0.00 38.69 2.59
1989 2234 3.791320 TCATAACACCAAGAGGAGGAGT 58.209 45.455 0.00 0.00 38.69 3.85
1990 2235 5.363939 GAATCATAACACCAAGAGGAGGAG 58.636 45.833 0.00 0.00 38.69 3.69
1991 2236 4.164221 GGAATCATAACACCAAGAGGAGGA 59.836 45.833 0.00 0.00 38.69 3.71
1992 2237 4.080356 TGGAATCATAACACCAAGAGGAGG 60.080 45.833 0.00 0.00 38.69 4.30
1995 2240 5.653769 ACATTGGAATCATAACACCAAGAGG 59.346 40.000 0.00 0.00 43.93 3.69
1999 2244 6.721668 TGGTTACATTGGAATCATAACACCAA 59.278 34.615 0.00 0.00 44.63 3.67
2034 2280 9.696917 ACAAATTCATGAAAACTAAACATCCTC 57.303 29.630 13.09 0.00 0.00 3.71
2112 2376 2.879646 TCATTCGGTAAGTGCGGTTTTT 59.120 40.909 0.00 0.00 0.00 1.94
2113 2377 2.224784 GTCATTCGGTAAGTGCGGTTTT 59.775 45.455 0.00 0.00 0.00 2.43
2119 2383 1.922545 GTACGGTCATTCGGTAAGTGC 59.077 52.381 0.00 0.00 34.51 4.40
2122 2386 3.378112 TGGTAGTACGGTCATTCGGTAAG 59.622 47.826 0.00 0.00 34.51 2.34
2162 2426 1.813178 TCGGCAATTCGGTTATTTGCA 59.187 42.857 8.86 0.00 43.25 4.08
2182 2446 3.319972 ACACATATATACGGTCGTGCCTT 59.680 43.478 6.25 0.00 34.25 4.35
2207 2471 1.475213 GCCATTTCTCCTTCTACCCCG 60.475 57.143 0.00 0.00 0.00 5.73
2218 2482 5.154222 CGTTAGTTTTTCCAGCCATTTCTC 58.846 41.667 0.00 0.00 0.00 2.87
2228 2492 7.148373 GGCAGTCATATAACGTTAGTTTTTCCA 60.148 37.037 14.25 0.00 41.49 3.53
2229 2493 7.148373 TGGCAGTCATATAACGTTAGTTTTTCC 60.148 37.037 14.25 8.33 41.49 3.13
2230 2494 7.745015 TGGCAGTCATATAACGTTAGTTTTTC 58.255 34.615 14.25 3.17 41.49 2.29
2231 2495 7.675962 TGGCAGTCATATAACGTTAGTTTTT 57.324 32.000 14.25 0.00 41.49 1.94
2245 2509 7.335171 GCAATGATCTGTTATATGGCAGTCATA 59.665 37.037 0.00 0.00 42.00 2.15
2246 2510 6.150641 GCAATGATCTGTTATATGGCAGTCAT 59.849 38.462 0.00 0.00 36.27 3.06
2247 2511 5.471116 GCAATGATCTGTTATATGGCAGTCA 59.529 40.000 0.00 10.06 34.57 3.41
2251 2515 7.283807 GGATATGCAATGATCTGTTATATGGCA 59.716 37.037 0.00 0.00 0.00 4.92
2258 2522 5.764686 GTGTGGGATATGCAATGATCTGTTA 59.235 40.000 0.00 0.00 0.00 2.41
2268 2532 2.377073 CCATGTGTGTGGGATATGCAA 58.623 47.619 0.00 0.00 35.55 4.08
2273 2537 1.354031 ACTTGCCATGTGTGTGGGATA 59.646 47.619 0.00 0.00 39.48 2.59
2281 2545 1.956477 GTTGAGGAACTTGCCATGTGT 59.044 47.619 0.00 0.00 41.55 3.72
2289 2553 6.075762 TCATGTTGAATGTTGAGGAACTTG 57.924 37.500 0.00 0.00 41.55 3.16
2341 2628 4.808895 TGCTTATCAATGGATCGTGTGTAC 59.191 41.667 0.00 0.00 34.89 2.90
2343 2630 3.872696 TGCTTATCAATGGATCGTGTGT 58.127 40.909 0.00 0.00 34.89 3.72
2344 2631 4.496341 GGTTGCTTATCAATGGATCGTGTG 60.496 45.833 0.00 0.00 36.99 3.82
2348 2635 3.213506 TGGGTTGCTTATCAATGGATCG 58.786 45.455 0.00 0.00 36.99 3.69
2390 2677 4.403015 AAAAAGGCGCATGCAATTTTAC 57.597 36.364 19.57 0.00 45.35 2.01
2391 2678 5.064452 CCATAAAAAGGCGCATGCAATTTTA 59.936 36.000 19.57 19.82 45.35 1.52
2415 2702 4.327854 CACTGAAATCCGTGCTAGTTTC 57.672 45.455 0.00 0.00 0.00 2.78
2423 2710 2.384382 GTGTTTGCACTGAAATCCGTG 58.616 47.619 0.00 1.14 42.13 4.94
2424 2711 2.774439 GTGTTTGCACTGAAATCCGT 57.226 45.000 0.00 0.00 42.13 4.69
2440 2727 4.220724 TGTGTAGTCAGTTTAGGGAGTGT 58.779 43.478 0.00 0.00 0.00 3.55
2454 2741 4.434330 GCGCTGTACTGAAAATGTGTAGTC 60.434 45.833 0.00 0.00 0.00 2.59
2461 2748 2.223340 GGATGGCGCTGTACTGAAAATG 60.223 50.000 7.64 0.00 0.00 2.32
2475 2762 3.443681 AGGAAGTACAAAATTGGATGGCG 59.556 43.478 0.00 0.00 0.00 5.69
2477 2764 4.096382 CGGAGGAAGTACAAAATTGGATGG 59.904 45.833 0.00 0.00 0.00 3.51
2493 2780 4.807304 GTCTTATATTTGCGAACGGAGGAA 59.193 41.667 0.00 0.00 0.00 3.36
2494 2781 4.365723 GTCTTATATTTGCGAACGGAGGA 58.634 43.478 0.00 0.00 0.00 3.71
2495 2782 3.181774 CGTCTTATATTTGCGAACGGAGG 59.818 47.826 0.00 0.00 0.00 4.30
2496 2783 3.795101 ACGTCTTATATTTGCGAACGGAG 59.205 43.478 0.00 0.00 0.00 4.63
2497 2784 3.772932 ACGTCTTATATTTGCGAACGGA 58.227 40.909 0.00 0.00 0.00 4.69
2539 2826 4.039609 TCACTCATGTCAGCCCATATGTAG 59.960 45.833 1.24 0.00 0.00 2.74
2546 2833 1.297689 GCTCACTCATGTCAGCCCA 59.702 57.895 0.00 0.00 0.00 5.36
2547 2834 0.321919 TTGCTCACTCATGTCAGCCC 60.322 55.000 0.00 0.00 0.00 5.19
2560 2847 6.631016 AGAGACGATTTAGTATGTTTGCTCA 58.369 36.000 0.00 0.00 0.00 4.26
2567 2854 9.159364 TGCGTATATAGAGACGATTTAGTATGT 57.841 33.333 8.96 0.00 42.96 2.29
2657 2952 9.615295 TGCCGATACAATTTCTAGTTTAAAAAC 57.385 29.630 0.00 0.00 39.17 2.43
2674 3014 5.957842 AGATTTGTCTTTTTGCCGATACA 57.042 34.783 0.00 0.00 0.00 2.29
2677 3017 4.280677 TGGAAGATTTGTCTTTTTGCCGAT 59.719 37.500 0.00 0.00 0.00 4.18
2680 3020 5.600696 TCTTGGAAGATTTGTCTTTTTGCC 58.399 37.500 0.00 0.00 0.00 4.52
2696 3036 6.380274 AGGAGACGAACTATGTAATCTTGGAA 59.620 38.462 0.00 0.00 0.00 3.53
2697 3037 5.892119 AGGAGACGAACTATGTAATCTTGGA 59.108 40.000 0.00 0.00 0.00 3.53
2704 3044 4.521639 ACACACAGGAGACGAACTATGTAA 59.478 41.667 0.00 0.00 30.65 2.41
2711 3051 2.510768 AGAACACACAGGAGACGAAC 57.489 50.000 0.00 0.00 0.00 3.95
2726 3066 2.059541 GTGACCGACAAGCACTAGAAC 58.940 52.381 0.00 0.00 0.00 3.01
2745 3085 1.970640 TGTACTGCAGATCACACTGGT 59.029 47.619 23.35 0.00 38.22 4.00
2749 3089 7.359595 TGTTTAATTTGTACTGCAGATCACAC 58.640 34.615 23.35 10.09 0.00 3.82
2771 3111 7.712797 ACCACTCGATTTTTCTTTGTTATGTT 58.287 30.769 0.00 0.00 0.00 2.71
2789 3129 6.075280 CGAAACAAGGTATTAAAACCACTCG 58.925 40.000 0.00 0.00 42.40 4.18
2799 3139 4.847990 ATGGACCCGAAACAAGGTATTA 57.152 40.909 0.00 0.00 36.17 0.98
2800 3140 3.732048 ATGGACCCGAAACAAGGTATT 57.268 42.857 0.00 0.00 36.17 1.89
2808 3148 2.235891 AGGTGAAAATGGACCCGAAAC 58.764 47.619 0.00 0.00 32.03 2.78
2811 3151 1.271707 GGAAGGTGAAAATGGACCCGA 60.272 52.381 0.00 0.00 32.03 5.14
2869 3209 6.997239 ATACCTATTCTTTCCGTTTGGTTC 57.003 37.500 0.00 0.00 36.30 3.62
2904 3244 6.953101 TCCAAGATGGTATTTAGTGCAGTAA 58.047 36.000 10.00 10.00 39.03 2.24
2907 3247 4.274459 GCTCCAAGATGGTATTTAGTGCAG 59.726 45.833 0.00 0.00 39.03 4.41
2908 3248 4.199310 GCTCCAAGATGGTATTTAGTGCA 58.801 43.478 0.00 0.00 39.03 4.57
2909 3249 3.565902 GGCTCCAAGATGGTATTTAGTGC 59.434 47.826 0.00 0.00 39.03 4.40
2916 3256 1.898863 ACCTGGCTCCAAGATGGTAT 58.101 50.000 0.00 0.00 39.03 2.73
2927 3267 0.536460 TTCGTCCCAAAACCTGGCTC 60.536 55.000 0.00 0.00 44.90 4.70
2940 3280 3.151554 ACCATGGGTAAAGTTTTCGTCC 58.848 45.455 18.09 0.00 32.11 4.79
2957 3297 4.723309 CCTAGGTAGTCGTAGGTTACCAT 58.277 47.826 3.51 0.00 43.32 3.55
2965 3305 3.801698 TGTAGCACCTAGGTAGTCGTAG 58.198 50.000 15.80 0.89 33.43 3.51
3010 3350 9.772973 GGTGTACTCACATGGTATAATCAAATA 57.227 33.333 0.00 0.00 45.45 1.40
3011 3351 8.494433 AGGTGTACTCACATGGTATAATCAAAT 58.506 33.333 0.00 0.00 45.45 2.32
3012 3352 7.857456 AGGTGTACTCACATGGTATAATCAAA 58.143 34.615 0.00 0.00 45.45 2.69
3013 3353 7.432148 AGGTGTACTCACATGGTATAATCAA 57.568 36.000 0.00 0.00 45.45 2.57
3024 3364 1.210478 GATGGCCAGGTGTACTCACAT 59.790 52.381 13.05 0.00 45.45 3.21
3025 3365 0.613260 GATGGCCAGGTGTACTCACA 59.387 55.000 13.05 0.00 45.45 3.58
3026 3366 0.905357 AGATGGCCAGGTGTACTCAC 59.095 55.000 13.05 0.00 43.19 3.51
3027 3367 0.904649 CAGATGGCCAGGTGTACTCA 59.095 55.000 13.05 0.00 0.00 3.41
3028 3368 0.462759 GCAGATGGCCAGGTGTACTC 60.463 60.000 13.05 1.02 36.11 2.59
3029 3369 1.604378 GCAGATGGCCAGGTGTACT 59.396 57.895 13.05 0.45 36.11 2.73
3030 3370 4.225497 GCAGATGGCCAGGTGTAC 57.775 61.111 13.05 0.00 36.11 2.90
3074 3414 2.124695 GCCTCGGGCTTTGGTAGG 60.125 66.667 7.58 0.00 46.69 3.18
3084 3424 0.107654 CCTAGGTTTTCTGCCTCGGG 60.108 60.000 0.00 0.00 35.87 5.14
3085 3425 0.613777 ACCTAGGTTTTCTGCCTCGG 59.386 55.000 9.21 0.00 42.68 4.63
3086 3426 1.405661 GGACCTAGGTTTTCTGCCTCG 60.406 57.143 17.53 0.00 37.54 4.63
3087 3427 1.628846 TGGACCTAGGTTTTCTGCCTC 59.371 52.381 17.53 0.00 37.54 4.70
3088 3428 1.742308 TGGACCTAGGTTTTCTGCCT 58.258 50.000 17.53 0.00 40.00 4.75
3089 3429 2.437413 CTTGGACCTAGGTTTTCTGCC 58.563 52.381 17.53 11.98 0.00 4.85
3090 3430 1.813178 GCTTGGACCTAGGTTTTCTGC 59.187 52.381 17.53 13.14 0.00 4.26
3091 3431 2.437413 GGCTTGGACCTAGGTTTTCTG 58.563 52.381 17.53 7.15 0.00 3.02
3092 3432 1.354705 GGGCTTGGACCTAGGTTTTCT 59.645 52.381 17.53 0.00 0.00 2.52
3093 3433 1.835494 GGGCTTGGACCTAGGTTTTC 58.165 55.000 17.53 9.69 0.00 2.29
3094 3434 0.037734 CGGGCTTGGACCTAGGTTTT 59.962 55.000 17.53 0.00 0.00 2.43
3095 3435 1.683441 CGGGCTTGGACCTAGGTTT 59.317 57.895 17.53 0.00 0.00 3.27
3096 3436 3.400188 CGGGCTTGGACCTAGGTT 58.600 61.111 17.53 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.