Multiple sequence alignment - TraesCS1A01G270300

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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 TraesCS1A01G270300 chr1A 100.000 5854 0 0 1 5854 464254814 464248961 0.000000e+00 10811.0
1 TraesCS1A01G270300 chr1A 88.785 214 20 4 2255 2467 352130578 352130368 5.820000e-65 259.0
2 TraesCS1A01G270300 chr1A 87.383 214 20 7 2255 2467 7306446 7306653 7.580000e-59 239.0
3 TraesCS1A01G270300 chr1D 95.484 2458 92 11 2713 5159 365438607 365436158 0.000000e+00 3906.0
4 TraesCS1A01G270300 chr1D 92.486 1251 54 18 578 1816 365440745 365439523 0.000000e+00 1753.0
5 TraesCS1A01G270300 chr1D 94.494 672 19 3 5198 5854 365436161 365435493 0.000000e+00 1020.0
6 TraesCS1A01G270300 chr1D 95.279 466 22 0 1769 2234 365439526 365439061 0.000000e+00 739.0
7 TraesCS1A01G270300 chr1D 87.608 347 18 7 2244 2568 365438938 365438595 4.280000e-101 379.0
8 TraesCS1A01G270300 chr1B 96.089 2327 71 10 3538 5854 488821800 488819484 0.000000e+00 3775.0
9 TraesCS1A01G270300 chr1B 97.359 833 20 2 2713 3544 488822750 488821919 0.000000e+00 1415.0
10 TraesCS1A01G270300 chr1B 93.112 842 39 6 979 1816 488824438 488823612 0.000000e+00 1216.0
11 TraesCS1A01G270300 chr1B 93.613 501 31 1 1736 2236 488823647 488823148 0.000000e+00 747.0
12 TraesCS1A01G270300 chr1B 81.494 616 62 32 1 578 488825667 488825066 5.350000e-125 459.0
13 TraesCS1A01G270300 chr1B 88.473 347 16 6 2244 2568 488823082 488822738 1.180000e-106 398.0
14 TraesCS1A01G270300 chr1B 93.750 112 7 0 9 120 488826359 488826248 1.010000e-37 169.0
15 TraesCS1A01G270300 chr7A 82.796 558 78 13 1922 2471 20829328 20828781 3.170000e-132 483.0
16 TraesCS1A01G270300 chr7A 87.742 155 10 7 2564 2718 699308357 699308502 7.800000e-39 172.0
17 TraesCS1A01G270300 chr2A 82.765 557 80 11 1922 2471 17786965 17786418 3.170000e-132 483.0
18 TraesCS1A01G270300 chr2A 89.333 150 8 6 2564 2713 749895209 749895068 1.300000e-41 182.0
19 TraesCS1A01G270300 chr7D 83.460 526 76 6 1924 2442 1522601 1522080 4.100000e-131 479.0
20 TraesCS1A01G270300 chr7D 93.416 243 16 0 2763 3005 414290214 414289972 1.550000e-95 361.0
21 TraesCS1A01G270300 chr5A 91.346 312 25 2 2713 3023 36553684 36553374 5.420000e-115 425.0
22 TraesCS1A01G270300 chr5A 88.182 110 6 1 2560 2669 705939308 705939206 2.210000e-24 124.0
23 TraesCS1A01G270300 chr6D 93.416 243 16 0 2763 3005 468640015 468640257 1.550000e-95 361.0
24 TraesCS1A01G270300 chr5D 93.416 243 16 0 2763 3005 267805712 267805954 1.550000e-95 361.0
25 TraesCS1A01G270300 chr3D 93.416 243 16 0 2763 3005 502142322 502142080 1.550000e-95 361.0
26 TraesCS1A01G270300 chr3D 88.591 149 10 4 2564 2712 606361636 606361495 2.170000e-39 174.0
27 TraesCS1A01G270300 chr4B 82.843 408 63 6 1922 2324 395826770 395827175 5.580000e-95 359.0
28 TraesCS1A01G270300 chr2D 93.004 243 16 1 2763 3005 332504897 332504656 2.600000e-93 353.0
29 TraesCS1A01G270300 chr5B 82.152 409 66 6 1922 2325 505688636 505688230 1.560000e-90 344.0
30 TraesCS1A01G270300 chr7B 81.907 409 67 6 1922 2325 51592141 51591735 7.270000e-89 339.0
31 TraesCS1A01G270300 chr7B 81.907 409 66 7 1922 2325 51618172 51617767 7.270000e-89 339.0
32 TraesCS1A01G270300 chr7B 97.143 35 1 0 2386 2420 179758155 179758189 6.340000e-05 60.2
33 TraesCS1A01G270300 chr6A 88.591 149 10 5 2564 2712 147956952 147956811 2.170000e-39 174.0
34 TraesCS1A01G270300 chr6A 87.097 155 13 5 2564 2718 586301493 586301640 1.010000e-37 169.0
35 TraesCS1A01G270300 chr3A 88.000 150 11 5 2564 2713 225652339 225652197 2.810000e-38 171.0
36 TraesCS1A01G270300 chr4A 87.838 148 10 5 2564 2711 621236463 621236602 3.630000e-37 167.0
37 TraesCS1A01G270300 chr2B 86.842 152 9 7 2564 2715 183060232 183060092 6.070000e-35 159.0
38 TraesCS1A01G270300 chr3B 86.184 152 9 9 2564 2711 464428773 464428916 2.820000e-33 154.0


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 TraesCS1A01G270300 chr1A 464248961 464254814 5853 True 10811.000000 10811 100.000000 1 5854 1 chr1A.!!$R2 5853
1 TraesCS1A01G270300 chr1D 365435493 365440745 5252 True 1559.400000 3906 93.070200 578 5854 5 chr1D.!!$R1 5276
2 TraesCS1A01G270300 chr1B 488819484 488826359 6875 True 1168.428571 3775 91.984286 1 5854 7 chr1B.!!$R1 5853
3 TraesCS1A01G270300 chr7A 20828781 20829328 547 True 483.000000 483 82.796000 1922 2471 1 chr7A.!!$R1 549
4 TraesCS1A01G270300 chr2A 17786418 17786965 547 True 483.000000 483 82.765000 1922 2471 1 chr2A.!!$R1 549
5 TraesCS1A01G270300 chr7D 1522080 1522601 521 True 479.000000 479 83.460000 1924 2442 1 chr7D.!!$R1 518

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
97 790 1.000955 ACACCTGTTGCTCGAACCTAG 59.999 52.381 0.00 0.0 33.07 3.02 F
1486 2469 0.391263 CAAGTAACTGTCCTCCGCCC 60.391 60.000 0.00 0.0 0.00 6.13 F
1562 2545 1.266404 CGCGAACGATAGCAGTCAAAC 60.266 52.381 0.00 0.0 43.93 2.93 F
2597 3809 0.240411 ACGCGAGAGTAGTTGGTCAC 59.760 55.000 15.93 0.0 0.00 3.67 F
2620 3832 0.315568 TATTTGGGTTGTTGCGGCAC 59.684 50.000 0.05 0.0 0.00 5.01 F
2626 3838 1.009675 GTTGTTGCGGCACTGTCTG 60.010 57.895 0.05 0.0 0.00 3.51 F
4013 5352 0.756903 ACACTGTACCCGAAAGTGCT 59.243 50.000 9.54 0.0 44.14 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1764 2751 0.318120 ACTCCGGCTGGCAAAATTTG 59.682 50.000 6.73 0.57 34.14 2.32 R
2578 3790 0.240411 GTGACCAACTACTCTCGCGT 59.760 55.000 5.77 0.00 0.00 6.01 R
2719 3931 0.249120 CGAAGATACACACAGCCCCA 59.751 55.000 0.00 0.00 0.00 4.96 R
3934 5273 0.547712 TGAGCTGGGCCTACCTTTCT 60.548 55.000 4.53 0.00 41.11 2.52 R
4013 5352 4.526650 TGCACTCTACTACCAGTGAATTGA 59.473 41.667 3.24 0.00 42.37 2.57 R
4409 5748 9.110502 CTTACCTGAGGTTCTGATATTTTTACC 57.889 37.037 10.53 0.00 37.09 2.85 R
4967 6313 0.110238 GCAAATCGCTCGCAAGTTCA 60.110 50.000 0.00 0.00 37.77 3.18 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
29 722 1.612442 TGGAGGGAACGAGGAAGGG 60.612 63.158 0.00 0.00 0.00 3.95
56 749 7.061326 GTCTCGATAAGTCTCTTGTTGAGTTTC 59.939 40.741 16.98 9.60 43.13 2.78
61 754 2.801111 GTCTCTTGTTGAGTTTCCGGAC 59.199 50.000 1.83 0.00 43.13 4.79
66 759 1.070105 TTGAGTTTCCGGACCCACG 59.930 57.895 1.83 0.00 0.00 4.94
89 782 3.045601 ACATCTACACACCTGTTGCTC 57.954 47.619 0.00 0.00 0.00 4.26
90 783 1.995484 CATCTACACACCTGTTGCTCG 59.005 52.381 0.00 0.00 0.00 5.03
97 790 1.000955 ACACCTGTTGCTCGAACCTAG 59.999 52.381 0.00 0.00 33.07 3.02
126 819 3.200483 ACACAAAGTTACACCGAGGTTC 58.800 45.455 0.00 0.00 0.00 3.62
132 825 2.897969 AGTTACACCGAGGTTCAGACAT 59.102 45.455 0.00 0.00 0.00 3.06
135 828 5.187186 AGTTACACCGAGGTTCAGACATAAT 59.813 40.000 0.00 0.00 0.00 1.28
137 830 4.906618 ACACCGAGGTTCAGACATAATTT 58.093 39.130 0.00 0.00 0.00 1.82
138 831 5.313712 ACACCGAGGTTCAGACATAATTTT 58.686 37.500 0.00 0.00 0.00 1.82
199 892 9.065871 GCTTTGCACTAATAATTTAGACAACTG 57.934 33.333 0.00 2.52 38.56 3.16
201 894 9.891828 TTTGCACTAATAATTTAGACAACTGTG 57.108 29.630 0.00 0.00 38.56 3.66
273 966 1.331447 TCGTTCTCTCACGTTTCGTCA 59.669 47.619 0.00 0.00 38.32 4.35
283 976 1.256895 ACGTTTCGTCACATGTGTTCG 59.743 47.619 24.63 25.95 33.69 3.95
289 982 1.590698 CGTCACATGTGTTCGTCAACA 59.409 47.619 24.63 0.00 40.40 3.33
347 1070 9.490379 AATTGAACAACTAATTACTCGACTTCT 57.510 29.630 0.00 0.00 0.00 2.85
350 1073 7.808381 TGAACAACTAATTACTCGACTTCTCAG 59.192 37.037 0.00 0.00 0.00 3.35
361 1084 5.635700 ACTCGACTTCTCAGAACAATTTAGC 59.364 40.000 0.00 0.00 0.00 3.09
362 1085 5.538118 TCGACTTCTCAGAACAATTTAGCA 58.462 37.500 0.00 0.00 0.00 3.49
365 1088 7.275779 TCGACTTCTCAGAACAATTTAGCATAC 59.724 37.037 0.00 0.00 0.00 2.39
366 1089 7.464710 CGACTTCTCAGAACAATTTAGCATACC 60.465 40.741 0.00 0.00 0.00 2.73
367 1090 7.168219 ACTTCTCAGAACAATTTAGCATACCA 58.832 34.615 0.00 0.00 0.00 3.25
368 1091 6.985188 TCTCAGAACAATTTAGCATACCAC 57.015 37.500 0.00 0.00 0.00 4.16
369 1092 6.472016 TCTCAGAACAATTTAGCATACCACA 58.528 36.000 0.00 0.00 0.00 4.17
370 1093 6.939730 TCTCAGAACAATTTAGCATACCACAA 59.060 34.615 0.00 0.00 0.00 3.33
371 1094 7.611467 TCTCAGAACAATTTAGCATACCACAAT 59.389 33.333 0.00 0.00 0.00 2.71
372 1095 8.121305 TCAGAACAATTTAGCATACCACAATT 57.879 30.769 0.00 0.00 0.00 2.32
373 1096 9.237187 TCAGAACAATTTAGCATACCACAATTA 57.763 29.630 0.00 0.00 0.00 1.40
403 1126 3.109230 GCTCGATGCTAAACACACTTG 57.891 47.619 0.00 0.00 38.95 3.16
444 1179 4.789075 CGACTACACCGTGGGCCG 62.789 72.222 3.03 0.00 0.00 6.13
445 1180 3.688159 GACTACACCGTGGGCCGT 61.688 66.667 3.03 0.00 33.66 5.68
446 1181 2.283101 ACTACACCGTGGGCCGTA 60.283 61.111 3.03 0.00 33.66 4.02
447 1182 2.275547 GACTACACCGTGGGCCGTAG 62.276 65.000 12.32 12.32 37.74 3.51
462 1197 2.464865 CCGTAGAGCTTACATGTCTGC 58.535 52.381 0.00 8.34 0.00 4.26
475 1210 7.872993 GCTTACATGTCTGCCATTAATCTAGTA 59.127 37.037 0.00 0.00 0.00 1.82
476 1211 9.935241 CTTACATGTCTGCCATTAATCTAGTAT 57.065 33.333 0.00 0.00 0.00 2.12
480 1215 8.824781 CATGTCTGCCATTAATCTAGTATATGC 58.175 37.037 0.00 0.00 0.00 3.14
528 1263 6.488769 TGACCCACTTTTAGAACTTAGTGA 57.511 37.500 0.00 0.00 40.24 3.41
533 1268 9.197306 ACCCACTTTTAGAACTTAGTGAAAAAT 57.803 29.630 0.00 0.00 40.24 1.82
602 1386 3.057456 AGTCACAACTACTGTAGCTTCCG 60.057 47.826 14.55 2.09 36.10 4.30
677 1466 9.345517 GAAATTTAACGTAGGTAAATTTCCACC 57.654 33.333 28.22 15.15 45.23 4.61
695 1484 5.947663 TCCACCCAATACCTTTATACATGG 58.052 41.667 0.00 0.00 0.00 3.66
697 1486 6.160636 TCCACCCAATACCTTTATACATGGAA 59.839 38.462 0.00 0.00 0.00 3.53
701 1490 9.500701 ACCCAATACCTTTATACATGGAATTTT 57.499 29.630 0.00 0.00 0.00 1.82
794 1583 4.094887 ACATTCCGAAAGTGAATTCATCCG 59.905 41.667 12.12 11.99 31.56 4.18
799 1588 6.988522 TCCGAAAGTGAATTCATCCGATATA 58.011 36.000 12.12 0.00 0.00 0.86
801 1590 7.384115 TCCGAAAGTGAATTCATCCGATATAAC 59.616 37.037 12.12 0.00 0.00 1.89
822 1611 4.055360 ACTTTCGTCATTGATCACGTTGA 58.945 39.130 0.00 0.00 37.30 3.18
841 1631 3.030291 TGACAGCCAACAACCATCTTTT 58.970 40.909 0.00 0.00 0.00 2.27
842 1632 3.068024 TGACAGCCAACAACCATCTTTTC 59.932 43.478 0.00 0.00 0.00 2.29
868 1658 1.398958 TTTTGACAGCAGCCAACCCC 61.399 55.000 0.00 0.00 0.00 4.95
870 1660 2.203480 GACAGCAGCCAACCCCAA 60.203 61.111 0.00 0.00 0.00 4.12
871 1661 2.203538 ACAGCAGCCAACCCCAAG 60.204 61.111 0.00 0.00 0.00 3.61
872 1662 3.688159 CAGCAGCCAACCCCAAGC 61.688 66.667 0.00 0.00 0.00 4.01
873 1663 4.223125 AGCAGCCAACCCCAAGCA 62.223 61.111 0.00 0.00 0.00 3.91
874 1664 3.688159 GCAGCCAACCCCAAGCAG 61.688 66.667 0.00 0.00 0.00 4.24
875 1665 3.688159 CAGCCAACCCCAAGCAGC 61.688 66.667 0.00 0.00 0.00 5.25
877 1667 3.688159 GCCAACCCCAAGCAGCAG 61.688 66.667 0.00 0.00 0.00 4.24
1026 2004 4.075793 TCCTCCCTCTCCACCCCG 62.076 72.222 0.00 0.00 0.00 5.73
1035 2013 4.753662 TCCACCCCGTCCTCCTCG 62.754 72.222 0.00 0.00 0.00 4.63
1050 2028 4.437587 TCGTCCCCCTCCTCGTCC 62.438 72.222 0.00 0.00 0.00 4.79
1146 2124 1.599240 GCTCTGCCCATCCCGATTC 60.599 63.158 0.00 0.00 0.00 2.52
1482 2465 5.167303 AGGAAATCAAGTAACTGTCCTCC 57.833 43.478 0.00 0.00 27.49 4.30
1483 2466 3.933332 GGAAATCAAGTAACTGTCCTCCG 59.067 47.826 0.00 0.00 0.00 4.63
1484 2467 2.674796 ATCAAGTAACTGTCCTCCGC 57.325 50.000 0.00 0.00 0.00 5.54
1485 2468 0.606604 TCAAGTAACTGTCCTCCGCC 59.393 55.000 0.00 0.00 0.00 6.13
1486 2469 0.391263 CAAGTAACTGTCCTCCGCCC 60.391 60.000 0.00 0.00 0.00 6.13
1548 2531 1.324736 GACATGACTTGGATCGCGAAC 59.675 52.381 15.24 11.28 0.00 3.95
1562 2545 1.266404 CGCGAACGATAGCAGTCAAAC 60.266 52.381 0.00 0.00 43.93 2.93
1594 2577 6.871492 TCAGATTAACTGTATTGAGCGACAAA 59.129 34.615 3.79 0.00 45.86 2.83
1596 2579 7.689812 CAGATTAACTGTATTGAGCGACAAAAG 59.310 37.037 3.79 5.20 40.42 2.27
1629 2612 2.556622 TCGCTTCAAATTCCCCTTTGTC 59.443 45.455 0.00 0.00 37.39 3.18
1672 2655 8.409371 CAGTAGACTTCAGAGTAATGCATTCTA 58.591 37.037 16.86 4.28 35.88 2.10
1705 2688 6.457528 GCCTGCTGTTCTTGTACTATCATTTC 60.458 42.308 0.00 0.00 0.00 2.17
1715 2698 9.213777 TCTTGTACTATCATTTCCCTCTTACAT 57.786 33.333 0.00 0.00 0.00 2.29
1752 2739 5.105595 GGCTTCAGAGTAGCAAAATTGGATT 60.106 40.000 0.00 0.00 40.42 3.01
1753 2740 6.032717 GCTTCAGAGTAGCAAAATTGGATTC 58.967 40.000 0.00 0.00 38.51 2.52
1754 2741 6.349611 GCTTCAGAGTAGCAAAATTGGATTCA 60.350 38.462 0.00 0.00 38.51 2.57
1755 2742 7.630082 GCTTCAGAGTAGCAAAATTGGATTCAT 60.630 37.037 0.00 0.00 38.51 2.57
1764 2751 6.315393 AGCAAAATTGGATTCATTCAGCATTC 59.685 34.615 0.00 0.00 0.00 2.67
1965 3040 1.488393 ACTATGGAGCTGAGGAAAGCC 59.512 52.381 0.00 0.00 44.68 4.35
2201 3276 7.170658 GTGATGAGGTAAAGTTATCATCTCTGC 59.829 40.741 13.42 0.00 45.33 4.26
2206 3281 6.070538 AGGTAAAGTTATCATCTCTGCACACT 60.071 38.462 0.00 0.00 0.00 3.55
2291 3479 4.156556 TGCTTATCCTGCAGTCATTTTGTC 59.843 41.667 13.81 0.00 35.31 3.18
2300 3488 1.880027 AGTCATTTTGTCGTTCCCAGC 59.120 47.619 0.00 0.00 0.00 4.85
2398 3586 9.295825 TGTCATTATTGTGTCTCCTTATTGTTT 57.704 29.630 0.00 0.00 0.00 2.83
2518 3730 6.993786 TGTCACATTCTTTGTAGTTTGTCA 57.006 33.333 0.00 0.00 36.57 3.58
2544 3756 6.073447 TCCTTTTGGCTCCTTGATATTGTA 57.927 37.500 0.00 0.00 40.12 2.41
2584 3796 3.481009 GGATACCTGATGACGCGAG 57.519 57.895 15.93 0.00 0.00 5.03
2585 3797 0.952280 GGATACCTGATGACGCGAGA 59.048 55.000 15.93 0.00 0.00 4.04
2586 3798 1.068885 GGATACCTGATGACGCGAGAG 60.069 57.143 15.93 0.00 0.00 3.20
2587 3799 1.604755 GATACCTGATGACGCGAGAGT 59.395 52.381 15.93 2.38 0.00 3.24
2588 3800 2.320745 TACCTGATGACGCGAGAGTA 57.679 50.000 15.93 1.33 0.00 2.59
2589 3801 1.018148 ACCTGATGACGCGAGAGTAG 58.982 55.000 15.93 5.24 0.00 2.57
2590 3802 1.018148 CCTGATGACGCGAGAGTAGT 58.982 55.000 15.93 0.00 0.00 2.73
2591 3803 1.402259 CCTGATGACGCGAGAGTAGTT 59.598 52.381 15.93 0.00 0.00 2.24
2592 3804 2.445316 CTGATGACGCGAGAGTAGTTG 58.555 52.381 15.93 0.00 0.00 3.16
2593 3805 1.132453 TGATGACGCGAGAGTAGTTGG 59.868 52.381 15.93 0.00 0.00 3.77
2594 3806 1.132643 GATGACGCGAGAGTAGTTGGT 59.867 52.381 15.93 0.00 0.00 3.67
2595 3807 0.520404 TGACGCGAGAGTAGTTGGTC 59.480 55.000 15.93 0.00 0.00 4.02
2596 3808 0.520404 GACGCGAGAGTAGTTGGTCA 59.480 55.000 15.93 0.00 0.00 4.02
2597 3809 0.240411 ACGCGAGAGTAGTTGGTCAC 59.760 55.000 15.93 0.00 0.00 3.67
2598 3810 0.522180 CGCGAGAGTAGTTGGTCACT 59.478 55.000 0.00 0.00 39.87 3.41
2599 3811 1.068472 CGCGAGAGTAGTTGGTCACTT 60.068 52.381 0.00 0.00 36.88 3.16
2600 3812 2.607282 CGCGAGAGTAGTTGGTCACTTT 60.607 50.000 0.00 0.00 36.88 2.66
2601 3813 3.391049 GCGAGAGTAGTTGGTCACTTTT 58.609 45.455 0.00 0.00 36.88 2.27
2602 3814 4.553323 GCGAGAGTAGTTGGTCACTTTTA 58.447 43.478 0.00 0.00 36.88 1.52
2603 3815 5.169295 GCGAGAGTAGTTGGTCACTTTTAT 58.831 41.667 0.00 0.00 36.88 1.40
2604 3816 5.638234 GCGAGAGTAGTTGGTCACTTTTATT 59.362 40.000 0.00 0.00 36.88 1.40
2605 3817 6.147328 GCGAGAGTAGTTGGTCACTTTTATTT 59.853 38.462 0.00 0.00 36.88 1.40
2606 3818 7.510630 CGAGAGTAGTTGGTCACTTTTATTTG 58.489 38.462 0.00 0.00 36.88 2.32
2607 3819 7.360101 CGAGAGTAGTTGGTCACTTTTATTTGG 60.360 40.741 0.00 0.00 36.88 3.28
2608 3820 6.715264 AGAGTAGTTGGTCACTTTTATTTGGG 59.285 38.462 0.00 0.00 36.88 4.12
2609 3821 6.370453 AGTAGTTGGTCACTTTTATTTGGGT 58.630 36.000 0.00 0.00 36.88 4.51
2610 3822 6.837048 AGTAGTTGGTCACTTTTATTTGGGTT 59.163 34.615 0.00 0.00 36.88 4.11
2611 3823 5.912892 AGTTGGTCACTTTTATTTGGGTTG 58.087 37.500 0.00 0.00 27.32 3.77
2612 3824 5.423931 AGTTGGTCACTTTTATTTGGGTTGT 59.576 36.000 0.00 0.00 27.32 3.32
2613 3825 5.941555 TGGTCACTTTTATTTGGGTTGTT 57.058 34.783 0.00 0.00 0.00 2.83
2614 3826 5.665459 TGGTCACTTTTATTTGGGTTGTTG 58.335 37.500 0.00 0.00 0.00 3.33
2615 3827 4.509970 GGTCACTTTTATTTGGGTTGTTGC 59.490 41.667 0.00 0.00 0.00 4.17
2616 3828 4.208253 GTCACTTTTATTTGGGTTGTTGCG 59.792 41.667 0.00 0.00 0.00 4.85
2617 3829 3.492756 CACTTTTATTTGGGTTGTTGCGG 59.507 43.478 0.00 0.00 0.00 5.69
2618 3830 2.156343 TTTATTTGGGTTGTTGCGGC 57.844 45.000 0.00 0.00 0.00 6.53
2619 3831 1.040646 TTATTTGGGTTGTTGCGGCA 58.959 45.000 0.00 0.00 0.00 5.69
2620 3832 0.315568 TATTTGGGTTGTTGCGGCAC 59.684 50.000 0.05 0.00 0.00 5.01
2621 3833 1.398958 ATTTGGGTTGTTGCGGCACT 61.399 50.000 0.05 0.00 0.00 4.40
2622 3834 2.290122 TTTGGGTTGTTGCGGCACTG 62.290 55.000 0.05 0.00 0.00 3.66
2623 3835 3.216292 GGGTTGTTGCGGCACTGT 61.216 61.111 0.05 0.00 0.00 3.55
2624 3836 2.331451 GGTTGTTGCGGCACTGTC 59.669 61.111 0.05 0.00 0.00 3.51
2625 3837 2.186826 GGTTGTTGCGGCACTGTCT 61.187 57.895 0.05 0.00 0.00 3.41
2626 3838 1.009675 GTTGTTGCGGCACTGTCTG 60.010 57.895 0.05 0.00 0.00 3.51
2627 3839 1.451207 TTGTTGCGGCACTGTCTGT 60.451 52.632 0.05 0.00 0.00 3.41
2641 3853 6.656314 CACTGTCTGTGTTGTAAGTTGTAA 57.344 37.500 1.84 0.00 41.53 2.41
2642 3854 6.475207 CACTGTCTGTGTTGTAAGTTGTAAC 58.525 40.000 1.84 0.00 41.53 2.50
2643 3855 6.091577 CACTGTCTGTGTTGTAAGTTGTAACA 59.908 38.462 1.84 3.49 41.53 2.41
2648 3860 4.825400 GTGTTGTAAGTTGTAACACGACC 58.175 43.478 16.38 1.35 42.96 4.79
2649 3861 4.329528 GTGTTGTAAGTTGTAACACGACCA 59.670 41.667 16.38 0.00 42.96 4.02
2650 3862 5.006941 GTGTTGTAAGTTGTAACACGACCAT 59.993 40.000 16.38 0.00 42.96 3.55
2651 3863 6.200665 GTGTTGTAAGTTGTAACACGACCATA 59.799 38.462 16.38 0.00 42.96 2.74
2652 3864 6.760298 TGTTGTAAGTTGTAACACGACCATAA 59.240 34.615 0.00 0.00 32.87 1.90
2653 3865 7.279536 TGTTGTAAGTTGTAACACGACCATAAA 59.720 33.333 0.00 0.00 32.87 1.40
2654 3866 7.176285 TGTAAGTTGTAACACGACCATAAAC 57.824 36.000 0.00 0.00 32.87 2.01
2655 3867 6.985645 TGTAAGTTGTAACACGACCATAAACT 59.014 34.615 0.00 0.00 32.87 2.66
2656 3868 6.535274 AAGTTGTAACACGACCATAAACTC 57.465 37.500 0.00 0.00 32.87 3.01
2657 3869 5.850614 AGTTGTAACACGACCATAAACTCT 58.149 37.500 0.00 0.00 32.87 3.24
2658 3870 6.985117 AGTTGTAACACGACCATAAACTCTA 58.015 36.000 0.00 0.00 32.87 2.43
2659 3871 7.609056 AGTTGTAACACGACCATAAACTCTAT 58.391 34.615 0.00 0.00 32.87 1.98
2660 3872 8.092687 AGTTGTAACACGACCATAAACTCTATT 58.907 33.333 0.00 0.00 32.87 1.73
2661 3873 8.378421 GTTGTAACACGACCATAAACTCTATTC 58.622 37.037 0.00 0.00 0.00 1.75
2662 3874 7.037438 TGTAACACGACCATAAACTCTATTCC 58.963 38.462 0.00 0.00 0.00 3.01
2663 3875 5.934402 ACACGACCATAAACTCTATTCCT 57.066 39.130 0.00 0.00 0.00 3.36
2664 3876 5.903810 ACACGACCATAAACTCTATTCCTC 58.096 41.667 0.00 0.00 0.00 3.71
2665 3877 5.657302 ACACGACCATAAACTCTATTCCTCT 59.343 40.000 0.00 0.00 0.00 3.69
2666 3878 6.154706 ACACGACCATAAACTCTATTCCTCTT 59.845 38.462 0.00 0.00 0.00 2.85
2667 3879 7.341256 ACACGACCATAAACTCTATTCCTCTTA 59.659 37.037 0.00 0.00 0.00 2.10
2668 3880 8.361139 CACGACCATAAACTCTATTCCTCTTAT 58.639 37.037 0.00 0.00 0.00 1.73
2669 3881 8.925338 ACGACCATAAACTCTATTCCTCTTATT 58.075 33.333 0.00 0.00 0.00 1.40
2670 3882 9.765795 CGACCATAAACTCTATTCCTCTTATTT 57.234 33.333 0.00 0.00 0.00 1.40
2694 3906 8.761575 TTAATGAATGAGTCAAATCTTTTGCC 57.238 30.769 0.00 0.00 40.50 4.52
2695 3907 6.600882 ATGAATGAGTCAAATCTTTTGCCT 57.399 33.333 0.00 0.00 40.50 4.75
2696 3908 6.017400 TGAATGAGTCAAATCTTTTGCCTC 57.983 37.500 0.00 4.54 31.51 4.70
2697 3909 5.771666 TGAATGAGTCAAATCTTTTGCCTCT 59.228 36.000 11.04 3.46 31.51 3.69
2698 3910 5.893897 ATGAGTCAAATCTTTTGCCTCTC 57.106 39.130 11.04 10.46 0.00 3.20
2699 3911 4.978099 TGAGTCAAATCTTTTGCCTCTCT 58.022 39.130 11.04 0.00 0.00 3.10
2700 3912 5.380043 TGAGTCAAATCTTTTGCCTCTCTT 58.620 37.500 11.04 0.00 0.00 2.85
2701 3913 5.471456 TGAGTCAAATCTTTTGCCTCTCTTC 59.529 40.000 11.04 0.00 0.00 2.87
2702 3914 5.380043 AGTCAAATCTTTTGCCTCTCTTCA 58.620 37.500 0.00 0.00 0.00 3.02
2703 3915 5.829924 AGTCAAATCTTTTGCCTCTCTTCAA 59.170 36.000 0.00 0.00 0.00 2.69
2704 3916 6.322201 AGTCAAATCTTTTGCCTCTCTTCAAA 59.678 34.615 0.00 0.00 0.00 2.69
2705 3917 6.980397 GTCAAATCTTTTGCCTCTCTTCAAAA 59.020 34.615 0.00 0.00 39.13 2.44
2706 3918 7.492344 GTCAAATCTTTTGCCTCTCTTCAAAAA 59.508 33.333 0.00 0.00 40.36 1.94
2707 3919 8.206189 TCAAATCTTTTGCCTCTCTTCAAAAAT 58.794 29.630 0.00 0.00 40.36 1.82
2708 3920 9.480053 CAAATCTTTTGCCTCTCTTCAAAAATA 57.520 29.630 0.00 0.00 40.36 1.40
2776 3988 4.504689 GGGAGGCTTCTCTTCCATTATCTG 60.505 50.000 0.00 0.00 37.65 2.90
3171 4384 1.556911 CCAACAGGCTCTGTGTATCCT 59.443 52.381 8.37 0.00 44.62 3.24
3297 4510 5.308014 TGTGTCAGCAGTTCATCACTATTT 58.692 37.500 0.00 0.00 32.76 1.40
3319 4532 3.889196 TGATGTGTCGTGCTTTTAACC 57.111 42.857 0.00 0.00 0.00 2.85
3414 4627 4.460263 TGCATTACCTGGAATGTATGACC 58.540 43.478 0.00 0.00 38.77 4.02
3434 4647 6.231951 TGACCGAACATTAACTGTAAATGGA 58.768 36.000 0.00 0.00 38.41 3.41
3675 5013 6.268387 TGTCCATGTTCTCTAGATATGCATGA 59.732 38.462 10.16 0.00 35.58 3.07
3813 5151 2.555227 GGAAAGATCCAAAGCCAGGTGA 60.555 50.000 0.00 0.00 45.79 4.02
3965 5304 1.412217 CCCAGCTCACCAGAGATCCTA 60.412 57.143 0.00 0.00 44.98 2.94
3973 5312 5.407407 TCACCAGAGATCCTAAGTTTGTC 57.593 43.478 0.00 0.00 0.00 3.18
4013 5352 0.756903 ACACTGTACCCGAAAGTGCT 59.243 50.000 9.54 0.00 44.14 4.40
4037 5376 4.727507 ATTCACTGGTAGTAGAGTGCAG 57.272 45.455 0.00 0.00 39.61 4.41
4100 5439 5.161943 GTCCAGTACCACCATCTTTACTT 57.838 43.478 0.00 0.00 0.00 2.24
4202 5541 8.978874 ATGTTGTAGAAATTGGCTCACATATA 57.021 30.769 0.00 0.00 0.00 0.86
4214 5553 5.545335 TGGCTCACATATATCCAGTCTTGAT 59.455 40.000 0.00 0.00 0.00 2.57
4215 5554 6.043590 TGGCTCACATATATCCAGTCTTGATT 59.956 38.462 0.00 0.00 0.00 2.57
4724 6070 4.379243 CAGGTCGCGCTTGTCCCT 62.379 66.667 5.56 0.00 0.00 4.20
4739 6085 0.259647 TCCCTGGAGATGCATTTGGG 59.740 55.000 0.00 8.69 34.76 4.12
4751 6097 0.826062 CATTTGGGGATGACAAGGGC 59.174 55.000 0.00 0.00 0.00 5.19
4752 6098 0.413037 ATTTGGGGATGACAAGGGCA 59.587 50.000 0.00 0.00 0.00 5.36
4853 6199 1.747367 CCCTGCCGCGGTTCAATAA 60.747 57.895 28.70 2.98 0.00 1.40
4959 6305 8.094798 TGTACAACAGATAGTTCACCATTTTC 57.905 34.615 0.00 0.00 38.74 2.29
5114 6460 4.177537 TCACTGATTTGGGTGGAAAAGA 57.822 40.909 0.00 0.00 34.57 2.52
5153 6500 9.667107 TTTATGGAGAAGTACTTAACATCCTTG 57.333 33.333 20.61 0.00 31.87 3.61
5251 6598 4.005650 CTGATACAATTGACCACTGCAGT 58.994 43.478 15.25 15.25 0.00 4.40
5572 6934 4.098044 TCCTCCTGAATAAGTAAGAGTGCG 59.902 45.833 0.00 0.00 0.00 5.34
5615 6977 3.933332 GACGCCTAATCTAGTTTGCAACT 59.067 43.478 0.00 2.51 45.40 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.547954 GTTCCCTCCACCCCTTCTCT 60.548 60.000 0.00 0.00 0.00 3.10
3 4 1.918800 CGTTCCCTCCACCCCTTCT 60.919 63.158 0.00 0.00 0.00 2.85
29 722 5.312120 TCAACAAGAGACTTATCGAGACC 57.688 43.478 0.00 0.00 0.00 3.85
56 749 1.105457 TAGATGTAACGTGGGTCCGG 58.895 55.000 0.00 0.00 0.00 5.14
61 754 2.232941 AGGTGTGTAGATGTAACGTGGG 59.767 50.000 0.00 0.00 0.00 4.61
66 759 4.315803 AGCAACAGGTGTGTAGATGTAAC 58.684 43.478 0.00 0.00 35.08 2.50
89 782 1.601903 TGTGTTGCAAAGCTAGGTTCG 59.398 47.619 7.80 0.00 0.00 3.95
90 783 3.708563 TTGTGTTGCAAAGCTAGGTTC 57.291 42.857 7.80 0.00 33.53 3.62
199 892 7.440523 ACCTTGTTTATGAAGAGATCAACAC 57.559 36.000 0.00 0.00 42.54 3.32
201 894 9.606631 ATCTACCTTGTTTATGAAGAGATCAAC 57.393 33.333 0.00 0.00 42.54 3.18
230 923 9.974980 ACGAACTATTATTGGTTCAATTTGTTT 57.025 25.926 12.49 0.00 41.89 2.83
233 926 9.840427 AGAACGAACTATTATTGGTTCAATTTG 57.160 29.630 13.48 0.00 44.92 2.32
246 939 5.791974 CGAAACGTGAGAGAACGAACTATTA 59.208 40.000 3.45 0.00 46.49 0.98
250 943 2.223433 ACGAAACGTGAGAGAACGAACT 60.223 45.455 3.45 0.00 46.49 3.01
251 944 2.114825 ACGAAACGTGAGAGAACGAAC 58.885 47.619 3.45 0.00 46.49 3.95
252 945 2.223317 TGACGAAACGTGAGAGAACGAA 60.223 45.455 3.45 0.00 46.49 3.85
253 946 1.331447 TGACGAAACGTGAGAGAACGA 59.669 47.619 3.45 0.00 46.49 3.85
273 966 4.955925 TTCTTTGTTGACGAACACATGT 57.044 36.364 0.00 0.00 41.92 3.21
323 1046 8.139350 TGAGAAGTCGAGTAATTAGTTGTTCAA 58.861 33.333 7.32 0.00 0.00 2.69
324 1047 7.654568 TGAGAAGTCGAGTAATTAGTTGTTCA 58.345 34.615 7.32 3.68 0.00 3.18
325 1048 8.021973 TCTGAGAAGTCGAGTAATTAGTTGTTC 58.978 37.037 7.32 5.47 0.00 3.18
342 1065 7.119846 GTGGTATGCTAAATTGTTCTGAGAAGT 59.880 37.037 0.00 0.00 0.00 3.01
343 1066 7.119699 TGTGGTATGCTAAATTGTTCTGAGAAG 59.880 37.037 0.00 0.00 0.00 2.85
347 1070 7.701539 ATTGTGGTATGCTAAATTGTTCTGA 57.298 32.000 0.00 0.00 0.00 3.27
383 1106 2.726066 GCAAGTGTGTTTAGCATCGAGC 60.726 50.000 0.00 0.00 46.19 5.03
396 1119 9.961265 ATATCATTCATAATCTTTGCAAGTGTG 57.039 29.630 0.00 0.00 0.00 3.82
417 1152 5.181811 CCCACGGTGTAGTCGTAATATATCA 59.818 44.000 7.45 0.00 38.94 2.15
420 1155 3.253188 GCCCACGGTGTAGTCGTAATATA 59.747 47.826 7.45 0.00 38.94 0.86
423 1158 0.174162 GCCCACGGTGTAGTCGTAAT 59.826 55.000 7.45 0.00 38.94 1.89
444 1179 3.526931 TGGCAGACATGTAAGCTCTAC 57.473 47.619 18.17 5.76 0.00 2.59
445 1180 4.760530 AATGGCAGACATGTAAGCTCTA 57.239 40.909 18.17 8.51 40.44 2.43
446 1181 3.641434 AATGGCAGACATGTAAGCTCT 57.359 42.857 18.17 0.52 40.44 4.09
447 1182 5.762218 AGATTAATGGCAGACATGTAAGCTC 59.238 40.000 18.17 10.93 40.44 4.09
500 1235 8.603304 ACTAAGTTCTAAAAGTGGGTCATATGT 58.397 33.333 1.90 0.00 0.00 2.29
501 1236 8.883731 CACTAAGTTCTAAAAGTGGGTCATATG 58.116 37.037 0.00 0.00 36.53 1.78
502 1237 8.822805 TCACTAAGTTCTAAAAGTGGGTCATAT 58.177 33.333 3.50 0.00 39.80 1.78
503 1238 8.197592 TCACTAAGTTCTAAAAGTGGGTCATA 57.802 34.615 3.50 0.00 39.80 2.15
504 1239 7.074653 TCACTAAGTTCTAAAAGTGGGTCAT 57.925 36.000 3.50 0.00 39.80 3.06
505 1240 6.488769 TCACTAAGTTCTAAAAGTGGGTCA 57.511 37.500 3.50 0.00 39.80 4.02
506 1241 7.797038 TTTCACTAAGTTCTAAAAGTGGGTC 57.203 36.000 3.50 0.00 39.80 4.46
558 1293 7.985184 TGACTACACCCAATACATGAACTATTC 59.015 37.037 0.00 0.00 0.00 1.75
567 1302 5.499004 AGTTGTGACTACACCCAATACAT 57.501 39.130 0.00 0.00 45.40 2.29
602 1386 7.307694 TGACATGTGTAAAGATGAGAAAATGC 58.692 34.615 1.15 0.00 0.00 3.56
657 1446 5.495926 TGGGTGGAAATTTACCTACGTTA 57.504 39.130 9.48 0.00 37.15 3.18
658 1447 4.370094 TGGGTGGAAATTTACCTACGTT 57.630 40.909 9.48 0.00 37.15 3.99
659 1448 4.370094 TTGGGTGGAAATTTACCTACGT 57.630 40.909 9.48 0.00 37.15 3.57
660 1449 5.297527 GGTATTGGGTGGAAATTTACCTACG 59.702 44.000 9.48 0.00 37.15 3.51
661 1450 6.429151 AGGTATTGGGTGGAAATTTACCTAC 58.571 40.000 9.48 5.26 37.15 3.18
663 1452 5.546035 AGGTATTGGGTGGAAATTTACCT 57.454 39.130 9.48 4.30 37.15 3.08
664 1453 6.614694 AAAGGTATTGGGTGGAAATTTACC 57.385 37.500 0.00 0.00 36.21 2.85
666 1455 9.992442 TGTATAAAGGTATTGGGTGGAAATTTA 57.008 29.630 0.00 0.00 0.00 1.40
667 1456 8.903059 TGTATAAAGGTATTGGGTGGAAATTT 57.097 30.769 0.00 0.00 0.00 1.82
677 1466 9.981114 GGAAAATTCCATGTATAAAGGTATTGG 57.019 33.333 7.32 0.00 46.76 3.16
701 1490 8.458573 TCATGCTTAGTTTCAAAAACTTAGGA 57.541 30.769 16.05 14.48 33.21 2.94
720 1509 8.641541 TCAAAACTTAGGAAAGAAAATCATGCT 58.358 29.630 0.00 0.00 36.50 3.79
762 1551 6.928979 TCACTTTCGGAATGTAGTGAAAAA 57.071 33.333 17.15 0.55 42.76 1.94
801 1590 4.084589 TGTCAACGTGATCAATGACGAAAG 60.085 41.667 22.41 9.20 43.91 2.62
822 1611 3.299503 AGAAAAGATGGTTGTTGGCTGT 58.700 40.909 0.00 0.00 0.00 4.40
841 1631 3.446873 TGGCTGCTGTCAAAAAGAAAAGA 59.553 39.130 0.00 0.00 0.00 2.52
842 1632 3.784338 TGGCTGCTGTCAAAAAGAAAAG 58.216 40.909 0.00 0.00 0.00 2.27
872 1662 3.273080 GAGTTTTGCGGGCCTGCTG 62.273 63.158 35.60 9.24 35.36 4.41
873 1663 2.985847 GAGTTTTGCGGGCCTGCT 60.986 61.111 35.60 16.94 35.36 4.24
874 1664 4.056125 GGAGTTTTGCGGGCCTGC 62.056 66.667 30.57 30.57 0.00 4.85
875 1665 3.737172 CGGAGTTTTGCGGGCCTG 61.737 66.667 7.41 7.41 34.17 4.85
949 1739 1.268079 GAAGTTGCAGGTTCTTCAGGC 59.732 52.381 13.89 0.00 37.89 4.85
1026 2004 2.442458 GAGGGGGACGAGGAGGAC 60.442 72.222 0.00 0.00 0.00 3.85
1035 2013 2.039137 AAGGACGAGGAGGGGGAC 59.961 66.667 0.00 0.00 0.00 4.46
1050 2028 1.380302 CTTGGTGGGGAGGGTGAAG 59.620 63.158 0.00 0.00 0.00 3.02
1146 2124 2.434884 AACGGCAGCGGACAGATG 60.435 61.111 7.02 0.00 39.70 2.90
1211 2189 2.190578 CATCCTGAACCTCCCCGC 59.809 66.667 0.00 0.00 0.00 6.13
1408 2386 3.236003 AAGAACGGCGGTCACCTCC 62.236 63.158 28.44 0.00 0.00 4.30
1455 2438 3.270877 CAGTTACTTGATTTCCTCCCCG 58.729 50.000 0.00 0.00 0.00 5.73
1486 2469 2.876368 GATCCAGGCACCAGGAACGG 62.876 65.000 4.76 0.00 36.63 4.44
1548 2531 4.106197 GACTGGTAGTTTGACTGCTATCG 58.894 47.826 0.00 0.00 31.18 2.92
1562 2545 7.436673 GCTCAATACAGTTAATCTGACTGGTAG 59.563 40.741 8.86 1.08 46.77 3.18
1594 2577 4.193826 TGAAGCGAGCTAACAATCTCTT 57.806 40.909 0.00 0.00 0.00 2.85
1596 2579 4.928661 TTTGAAGCGAGCTAACAATCTC 57.071 40.909 14.56 2.28 0.00 2.75
1705 2688 9.924010 AGCCTACTAGTATTATATGTAAGAGGG 57.076 37.037 2.33 0.00 0.00 4.30
1715 2698 9.669887 GCTACTCTGAAGCCTACTAGTATTATA 57.330 37.037 2.33 0.00 33.73 0.98
1716 2699 8.164733 TGCTACTCTGAAGCCTACTAGTATTAT 58.835 37.037 2.33 0.00 39.30 1.28
1722 2708 5.584253 TTTGCTACTCTGAAGCCTACTAG 57.416 43.478 0.00 0.00 39.30 2.57
1729 2715 5.573337 ATCCAATTTTGCTACTCTGAAGC 57.427 39.130 0.00 0.00 40.50 3.86
1752 2739 5.306394 TGGCAAAATTTGAATGCTGAATGA 58.694 33.333 10.26 0.00 39.94 2.57
1753 2740 5.614923 TGGCAAAATTTGAATGCTGAATG 57.385 34.783 10.26 0.00 39.94 2.67
1754 2741 4.155280 GCTGGCAAAATTTGAATGCTGAAT 59.845 37.500 10.26 0.00 39.94 2.57
1755 2742 3.499157 GCTGGCAAAATTTGAATGCTGAA 59.501 39.130 10.26 0.56 39.94 3.02
1764 2751 0.318120 ACTCCGGCTGGCAAAATTTG 59.682 50.000 6.73 0.57 34.14 2.32
1836 2911 9.442047 AATCCAATTTTACTACTCTGAAGTCTG 57.558 33.333 0.00 0.00 36.92 3.51
1965 3040 1.201647 CCCTGAAGCTTGTTGCAGATG 59.798 52.381 2.10 0.00 45.94 2.90
2001 3076 9.414295 TCTGAATATTCTGCAAACAAGAAATTG 57.586 29.630 16.24 0.00 0.00 2.32
2164 3239 0.107800 CCTCATCACCAGGTGAGCAG 60.108 60.000 26.56 21.97 46.04 4.24
2201 3276 5.437289 TTCTCCTAACAAATTGCAGTGTG 57.563 39.130 0.00 0.00 0.00 3.82
2236 3311 4.955450 TGCTATTTTCATGGTATGGCACTT 59.045 37.500 8.69 0.00 31.95 3.16
2237 3312 4.535781 TGCTATTTTCATGGTATGGCACT 58.464 39.130 8.69 0.00 31.95 4.40
2238 3313 4.794003 GCTGCTATTTTCATGGTATGGCAC 60.794 45.833 8.69 4.77 33.17 5.01
2239 3314 3.318839 GCTGCTATTTTCATGGTATGGCA 59.681 43.478 11.11 11.11 35.05 4.92
2240 3315 3.318839 TGCTGCTATTTTCATGGTATGGC 59.681 43.478 0.00 0.00 0.00 4.40
2241 3316 4.261741 GGTGCTGCTATTTTCATGGTATGG 60.262 45.833 0.00 0.00 0.00 2.74
2279 3467 2.350772 GCTGGGAACGACAAAATGACTG 60.351 50.000 0.00 0.00 0.00 3.51
2291 3479 1.834188 ACTTTTATGGGCTGGGAACG 58.166 50.000 0.00 0.00 0.00 3.95
2300 3488 3.964909 GCAATCCGCTAACTTTTATGGG 58.035 45.455 0.00 0.00 37.77 4.00
2398 3586 4.824537 GCTCAGTAGAGATAGGATCACACA 59.175 45.833 0.00 0.00 44.98 3.72
2496 3708 7.016361 AGTGACAAACTACAAAGAATGTGAC 57.984 36.000 0.00 0.00 43.77 3.67
2502 3714 7.696992 AAAGGAAGTGACAAACTACAAAGAA 57.303 32.000 0.00 0.00 38.56 2.52
2504 3716 6.751888 CCAAAAGGAAGTGACAAACTACAAAG 59.248 38.462 0.00 0.00 38.56 2.77
2506 3718 5.393678 GCCAAAAGGAAGTGACAAACTACAA 60.394 40.000 0.00 0.00 38.56 2.41
2518 3730 3.532641 ATCAAGGAGCCAAAAGGAAGT 57.467 42.857 0.00 0.00 0.00 3.01
2568 3780 1.681538 ACTCTCGCGTCATCAGGTAT 58.318 50.000 5.77 0.00 0.00 2.73
2569 3781 2.210961 CTACTCTCGCGTCATCAGGTA 58.789 52.381 5.77 0.05 0.00 3.08
2570 3782 1.018148 CTACTCTCGCGTCATCAGGT 58.982 55.000 5.77 0.00 0.00 4.00
2571 3783 1.018148 ACTACTCTCGCGTCATCAGG 58.982 55.000 5.77 0.00 0.00 3.86
2572 3784 2.445316 CAACTACTCTCGCGTCATCAG 58.555 52.381 5.77 1.98 0.00 2.90
2573 3785 1.132453 CCAACTACTCTCGCGTCATCA 59.868 52.381 5.77 0.00 0.00 3.07
2574 3786 1.132643 ACCAACTACTCTCGCGTCATC 59.867 52.381 5.77 0.00 0.00 2.92
2575 3787 1.132643 GACCAACTACTCTCGCGTCAT 59.867 52.381 5.77 0.00 0.00 3.06
2576 3788 0.520404 GACCAACTACTCTCGCGTCA 59.480 55.000 5.77 0.00 0.00 4.35
2577 3789 0.520404 TGACCAACTACTCTCGCGTC 59.480 55.000 5.77 0.00 0.00 5.19
2578 3790 0.240411 GTGACCAACTACTCTCGCGT 59.760 55.000 5.77 0.00 0.00 6.01
2579 3791 0.522180 AGTGACCAACTACTCTCGCG 59.478 55.000 0.00 0.00 37.36 5.87
2580 3792 2.726832 AAGTGACCAACTACTCTCGC 57.273 50.000 0.00 0.00 38.56 5.03
2581 3793 7.360101 CCAAATAAAAGTGACCAACTACTCTCG 60.360 40.741 0.00 0.00 38.56 4.04
2582 3794 7.094762 CCCAAATAAAAGTGACCAACTACTCTC 60.095 40.741 0.00 0.00 38.56 3.20
2583 3795 6.715264 CCCAAATAAAAGTGACCAACTACTCT 59.285 38.462 0.00 0.00 38.56 3.24
2584 3796 6.489022 ACCCAAATAAAAGTGACCAACTACTC 59.511 38.462 0.00 0.00 38.56 2.59
2585 3797 6.370453 ACCCAAATAAAAGTGACCAACTACT 58.630 36.000 0.00 0.00 38.56 2.57
2586 3798 6.644248 ACCCAAATAAAAGTGACCAACTAC 57.356 37.500 0.00 0.00 38.56 2.73
2587 3799 6.608002 ACAACCCAAATAAAAGTGACCAACTA 59.392 34.615 0.00 0.00 38.56 2.24
2588 3800 5.423931 ACAACCCAAATAAAAGTGACCAACT 59.576 36.000 0.00 0.00 42.60 3.16
2589 3801 5.666462 ACAACCCAAATAAAAGTGACCAAC 58.334 37.500 0.00 0.00 0.00 3.77
2590 3802 5.941555 ACAACCCAAATAAAAGTGACCAA 57.058 34.783 0.00 0.00 0.00 3.67
2591 3803 5.665459 CAACAACCCAAATAAAAGTGACCA 58.335 37.500 0.00 0.00 0.00 4.02
2592 3804 4.509970 GCAACAACCCAAATAAAAGTGACC 59.490 41.667 0.00 0.00 0.00 4.02
2593 3805 4.208253 CGCAACAACCCAAATAAAAGTGAC 59.792 41.667 0.00 0.00 0.00 3.67
2594 3806 4.363999 CGCAACAACCCAAATAAAAGTGA 58.636 39.130 0.00 0.00 0.00 3.41
2595 3807 3.492756 CCGCAACAACCCAAATAAAAGTG 59.507 43.478 0.00 0.00 0.00 3.16
2596 3808 3.723260 CCGCAACAACCCAAATAAAAGT 58.277 40.909 0.00 0.00 0.00 2.66
2597 3809 2.478514 GCCGCAACAACCCAAATAAAAG 59.521 45.455 0.00 0.00 0.00 2.27
2598 3810 2.158957 TGCCGCAACAACCCAAATAAAA 60.159 40.909 0.00 0.00 0.00 1.52
2599 3811 1.412710 TGCCGCAACAACCCAAATAAA 59.587 42.857 0.00 0.00 0.00 1.40
2600 3812 1.040646 TGCCGCAACAACCCAAATAA 58.959 45.000 0.00 0.00 0.00 1.40
2601 3813 0.315568 GTGCCGCAACAACCCAAATA 59.684 50.000 0.00 0.00 0.00 1.40
2602 3814 1.068921 GTGCCGCAACAACCCAAAT 59.931 52.632 0.00 0.00 0.00 2.32
2603 3815 2.055042 AGTGCCGCAACAACCCAAA 61.055 52.632 0.00 0.00 0.00 3.28
2604 3816 2.441164 AGTGCCGCAACAACCCAA 60.441 55.556 0.00 0.00 0.00 4.12
2605 3817 3.215568 CAGTGCCGCAACAACCCA 61.216 61.111 0.00 0.00 0.00 4.51
2606 3818 3.194272 GACAGTGCCGCAACAACCC 62.194 63.158 0.00 0.00 0.00 4.11
2607 3819 2.186826 AGACAGTGCCGCAACAACC 61.187 57.895 0.00 0.00 0.00 3.77
2608 3820 1.009675 CAGACAGTGCCGCAACAAC 60.010 57.895 0.00 0.00 0.00 3.32
2609 3821 1.451207 ACAGACAGTGCCGCAACAA 60.451 52.632 0.00 0.00 0.00 2.83
2610 3822 2.179547 CACAGACAGTGCCGCAACA 61.180 57.895 0.00 0.00 42.15 3.33
2611 3823 2.633657 CACAGACAGTGCCGCAAC 59.366 61.111 0.00 0.00 42.15 4.17
2619 3831 6.167685 TGTTACAACTTACAACACAGACAGT 58.832 36.000 0.00 0.00 0.00 3.55
2620 3832 6.656314 TGTTACAACTTACAACACAGACAG 57.344 37.500 0.00 0.00 0.00 3.51
2626 3838 4.329528 TGGTCGTGTTACAACTTACAACAC 59.670 41.667 6.73 6.73 45.41 3.32
2627 3839 4.502016 TGGTCGTGTTACAACTTACAACA 58.498 39.130 0.00 0.00 0.00 3.33
2628 3840 5.662211 ATGGTCGTGTTACAACTTACAAC 57.338 39.130 0.00 0.00 0.00 3.32
2629 3841 7.495279 AGTTTATGGTCGTGTTACAACTTACAA 59.505 33.333 0.00 0.00 0.00 2.41
2630 3842 6.985645 AGTTTATGGTCGTGTTACAACTTACA 59.014 34.615 0.00 0.00 0.00 2.41
2631 3843 7.383300 AGAGTTTATGGTCGTGTTACAACTTAC 59.617 37.037 0.00 0.00 0.00 2.34
2632 3844 7.436118 AGAGTTTATGGTCGTGTTACAACTTA 58.564 34.615 0.00 0.00 0.00 2.24
2633 3845 6.285990 AGAGTTTATGGTCGTGTTACAACTT 58.714 36.000 0.00 0.00 0.00 2.66
2634 3846 5.850614 AGAGTTTATGGTCGTGTTACAACT 58.149 37.500 0.00 0.00 0.00 3.16
2635 3847 7.823149 ATAGAGTTTATGGTCGTGTTACAAC 57.177 36.000 0.00 0.00 0.00 3.32
2636 3848 7.546667 GGAATAGAGTTTATGGTCGTGTTACAA 59.453 37.037 0.00 0.00 0.00 2.41
2637 3849 7.037438 GGAATAGAGTTTATGGTCGTGTTACA 58.963 38.462 0.00 0.00 0.00 2.41
2638 3850 7.263496 AGGAATAGAGTTTATGGTCGTGTTAC 58.737 38.462 0.00 0.00 0.00 2.50
2639 3851 7.341256 AGAGGAATAGAGTTTATGGTCGTGTTA 59.659 37.037 0.00 0.00 0.00 2.41
2640 3852 6.154706 AGAGGAATAGAGTTTATGGTCGTGTT 59.845 38.462 0.00 0.00 0.00 3.32
2641 3853 5.657302 AGAGGAATAGAGTTTATGGTCGTGT 59.343 40.000 0.00 0.00 0.00 4.49
2642 3854 6.150396 AGAGGAATAGAGTTTATGGTCGTG 57.850 41.667 0.00 0.00 0.00 4.35
2643 3855 6.793505 AAGAGGAATAGAGTTTATGGTCGT 57.206 37.500 0.00 0.00 0.00 4.34
2644 3856 9.765795 AAATAAGAGGAATAGAGTTTATGGTCG 57.234 33.333 0.00 0.00 0.00 4.79
2668 3880 9.206870 GGCAAAAGATTTGACTCATTCATTAAA 57.793 29.630 6.99 0.00 32.84 1.52
2669 3881 8.587608 AGGCAAAAGATTTGACTCATTCATTAA 58.412 29.630 5.37 0.00 30.52 1.40
2670 3882 8.125978 AGGCAAAAGATTTGACTCATTCATTA 57.874 30.769 5.37 0.00 30.52 1.90
2671 3883 7.001099 AGGCAAAAGATTTGACTCATTCATT 57.999 32.000 5.37 0.00 30.52 2.57
2672 3884 6.600882 AGGCAAAAGATTTGACTCATTCAT 57.399 33.333 5.37 0.00 30.52 2.57
2679 3891 5.380043 TGAAGAGAGGCAAAAGATTTGACT 58.620 37.500 10.82 10.82 41.23 3.41
2680 3892 5.695851 TGAAGAGAGGCAAAAGATTTGAC 57.304 39.130 6.99 3.80 0.00 3.18
2681 3893 6.713762 TTTGAAGAGAGGCAAAAGATTTGA 57.286 33.333 6.99 0.00 31.64 2.69
2682 3894 7.775397 TTTTTGAAGAGAGGCAAAAGATTTG 57.225 32.000 0.00 0.00 42.71 2.32
2703 3915 9.360901 ACACAGCCCCAAATTTTATTTTATTTT 57.639 25.926 0.00 0.00 0.00 1.82
2704 3916 8.791675 CACACAGCCCCAAATTTTATTTTATTT 58.208 29.630 0.00 0.00 0.00 1.40
2705 3917 7.941790 ACACACAGCCCCAAATTTTATTTTATT 59.058 29.630 0.00 0.00 0.00 1.40
2706 3918 7.457561 ACACACAGCCCCAAATTTTATTTTAT 58.542 30.769 0.00 0.00 0.00 1.40
2707 3919 6.831976 ACACACAGCCCCAAATTTTATTTTA 58.168 32.000 0.00 0.00 0.00 1.52
2708 3920 5.689835 ACACACAGCCCCAAATTTTATTTT 58.310 33.333 0.00 0.00 0.00 1.82
2709 3921 5.303259 ACACACAGCCCCAAATTTTATTT 57.697 34.783 0.00 0.00 0.00 1.40
2710 3922 4.972751 ACACACAGCCCCAAATTTTATT 57.027 36.364 0.00 0.00 0.00 1.40
2711 3923 5.957774 AGATACACACAGCCCCAAATTTTAT 59.042 36.000 0.00 0.00 0.00 1.40
2712 3924 5.329399 AGATACACACAGCCCCAAATTTTA 58.671 37.500 0.00 0.00 0.00 1.52
2713 3925 4.159557 AGATACACACAGCCCCAAATTTT 58.840 39.130 0.00 0.00 0.00 1.82
2714 3926 3.778265 AGATACACACAGCCCCAAATTT 58.222 40.909 0.00 0.00 0.00 1.82
2715 3927 3.456380 AGATACACACAGCCCCAAATT 57.544 42.857 0.00 0.00 0.00 1.82
2716 3928 3.356290 GAAGATACACACAGCCCCAAAT 58.644 45.455 0.00 0.00 0.00 2.32
2717 3929 2.790433 GAAGATACACACAGCCCCAAA 58.210 47.619 0.00 0.00 0.00 3.28
2718 3930 1.338674 CGAAGATACACACAGCCCCAA 60.339 52.381 0.00 0.00 0.00 4.12
2719 3931 0.249120 CGAAGATACACACAGCCCCA 59.751 55.000 0.00 0.00 0.00 4.96
2720 3932 0.462047 CCGAAGATACACACAGCCCC 60.462 60.000 0.00 0.00 0.00 5.80
2721 3933 0.535335 TCCGAAGATACACACAGCCC 59.465 55.000 0.00 0.00 0.00 5.19
2722 3934 2.205074 CATCCGAAGATACACACAGCC 58.795 52.381 0.00 0.00 0.00 4.85
2723 3935 1.594862 GCATCCGAAGATACACACAGC 59.405 52.381 0.00 0.00 0.00 4.40
2790 4003 9.487442 AACCTGCAGGGATATTTTCTAAAATAA 57.513 29.630 35.42 0.00 40.40 1.40
3171 4384 2.238084 TCTCCTCAAGCAGCTCCTTA 57.762 50.000 0.00 0.00 0.00 2.69
3276 4489 6.486320 TCAAAAATAGTGATGAACTGCTGACA 59.514 34.615 0.00 0.00 40.26 3.58
3297 4510 4.096532 TGGTTAAAAGCACGACACATCAAA 59.903 37.500 0.00 0.00 0.00 2.69
3304 4517 4.268884 GCAAAAATGGTTAAAAGCACGACA 59.731 37.500 0.00 0.00 39.48 4.35
3305 4518 4.268884 TGCAAAAATGGTTAAAAGCACGAC 59.731 37.500 0.00 0.00 39.48 4.34
3319 4532 7.066645 TCTCATCAGATAGAACCTGCAAAAATG 59.933 37.037 0.00 0.00 0.00 2.32
3414 4627 9.840427 AGAAAATCCATTTACAGTTAATGTTCG 57.160 29.630 10.61 0.00 39.96 3.95
3434 4647 6.947644 AACAACCGTGTTACCTTAGAAAAT 57.052 33.333 0.00 0.00 46.33 1.82
3499 4712 5.878406 TGGGTTATGTTCCACAAAATTGT 57.122 34.783 0.00 0.00 43.36 2.71
3543 4881 7.838045 TTGATTACTCAAATCCAAGCATTGACG 60.838 37.037 0.00 0.00 44.44 4.35
3675 5013 8.027524 TCAAGATATTCCAACTTGAGCTAGAT 57.972 34.615 0.00 0.00 42.91 1.98
3934 5273 0.547712 TGAGCTGGGCCTACCTTTCT 60.548 55.000 4.53 0.00 41.11 2.52
3973 5312 7.820648 AGTGTTGCTGAATTAAGGATGTAAAG 58.179 34.615 0.00 0.00 0.00 1.85
4013 5352 4.526650 TGCACTCTACTACCAGTGAATTGA 59.473 41.667 3.24 0.00 42.37 2.57
4037 5376 9.174166 TGTTTAAATAATTTAGAGACTCAGGGC 57.826 33.333 5.02 0.00 0.00 5.19
4409 5748 9.110502 CTTACCTGAGGTTCTGATATTTTTACC 57.889 37.037 10.53 0.00 37.09 2.85
4724 6070 1.570024 TCATCCCCAAATGCATCTCCA 59.430 47.619 0.00 0.00 0.00 3.86
4739 6085 2.325583 TACGAATGCCCTTGTCATCC 57.674 50.000 0.00 0.00 0.00 3.51
4853 6199 2.636768 GCCTTCAGCACGCTATTTTT 57.363 45.000 0.00 0.00 42.97 1.94
4875 6221 6.437928 TGCTTTTAATATAATGCTGGCGAAG 58.562 36.000 0.00 0.00 0.00 3.79
4879 6225 5.349543 GGCATGCTTTTAATATAATGCTGGC 59.650 40.000 18.92 0.00 40.15 4.85
4959 6305 1.597937 GCTCGCAAGTTCACAACCAAG 60.598 52.381 0.00 0.00 39.48 3.61
4967 6313 0.110238 GCAAATCGCTCGCAAGTTCA 60.110 50.000 0.00 0.00 37.77 3.18
4968 6314 2.630137 GCAAATCGCTCGCAAGTTC 58.370 52.632 0.00 0.00 37.77 3.01
5190 6537 6.569693 GCACAAAACTTGCGTAAAAATTCATC 59.430 34.615 0.00 0.00 0.00 2.92
5251 6598 5.170021 GCATTTCTTTGCCACATGATAACA 58.830 37.500 0.00 0.00 36.60 2.41
5572 6934 1.177401 GCTGTTCCCAGTTGGATTCC 58.823 55.000 0.00 0.00 44.66 3.01
5615 6977 3.244422 ACTGGAACTTTGATGAAGCCGTA 60.244 43.478 0.00 0.00 39.04 4.02


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

AutoCloner maintained by Alex Coulton.