Multiple sequence alignment - TraesCS3A01G376800

Loading Multiple Alignment...

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 TraesCS3A01G376800 chr3A 100.000 2538 0 0 1 2538 625532100 625534637 0.000000e+00 4687.0
1 TraesCS3A01G376800 chr3B 91.158 1097 44 15 756 1835 644910135 644911195 0.000000e+00 1439.0
2 TraesCS3A01G376800 chr3B 93.068 577 37 3 177 751 303290432 303289857 0.000000e+00 841.0
3 TraesCS3A01G376800 chr3B 92.882 576 34 6 177 750 498459581 498460151 0.000000e+00 830.0
4 TraesCS3A01G376800 chr3B 87.674 576 21 13 1905 2432 644911285 644911858 2.140000e-175 625.0
5 TraesCS3A01G376800 chr3B 89.333 75 5 2 29 103 752000072 752000143 9.670000e-15 91.6
6 TraesCS3A01G376800 chr3B 89.333 75 5 3 29 103 822798539 822798610 9.670000e-15 91.6
7 TraesCS3A01G376800 chr3B 92.308 52 2 2 1829 1880 644911232 644911281 3.500000e-09 73.1
8 TraesCS3A01G376800 chr3D 88.412 1096 71 33 756 1833 482595731 482596788 0.000000e+00 1269.0
9 TraesCS3A01G376800 chr3D 82.117 548 55 25 1905 2421 482596874 482597409 1.800000e-116 429.0
10 TraesCS3A01G376800 chr2B 95.009 581 26 3 177 755 699176622 699177201 0.000000e+00 909.0
11 TraesCS3A01G376800 chr2B 92.469 571 38 5 182 750 454345171 454345738 0.000000e+00 811.0
12 TraesCS3A01G376800 chr7B 94.295 596 29 5 177 768 110111315 110111909 0.000000e+00 907.0
13 TraesCS3A01G376800 chr5B 94.655 580 28 3 177 754 44469076 44469654 0.000000e+00 896.0
14 TraesCS3A01G376800 chr5B 93.264 579 35 4 179 755 360418305 360417729 0.000000e+00 850.0
15 TraesCS3A01G376800 chr6B 94.435 575 29 3 177 749 578004723 578004150 0.000000e+00 881.0
16 TraesCS3A01G376800 chr6B 93.543 573 32 5 179 749 498853548 498854117 0.000000e+00 848.0
17 TraesCS3A01G376800 chr6B 89.333 75 5 2 29 103 160912482 160912411 9.670000e-15 91.6
18 TraesCS3A01G376800 chr6B 84.783 92 8 4 10 99 274980703 274980790 1.250000e-13 87.9
19 TraesCS3A01G376800 chr6A 85.806 155 19 2 1374 1525 16984423 16984269 7.270000e-36 161.0
20 TraesCS3A01G376800 chr7D 88.312 77 6 3 27 103 526443053 526443126 3.480000e-14 89.8
21 TraesCS3A01G376800 chr7D 86.585 82 6 4 27 107 557088115 557088038 4.500000e-13 86.1
22 TraesCS3A01G376800 chr7A 88.000 75 6 2 29 103 215184576 215184647 4.500000e-13 86.1
23 TraesCS3A01G376800 chr1B 87.013 77 7 2 29 105 546679219 546679146 1.620000e-12 84.2
24 TraesCS3A01G376800 chr1D 84.524 84 8 4 29 112 453108571 453108493 7.530000e-11 78.7


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 TraesCS3A01G376800 chr3A 625532100 625534637 2537 False 4687.000000 4687 100.0000 1 2538 1 chr3A.!!$F1 2537
1 TraesCS3A01G376800 chr3B 303289857 303290432 575 True 841.000000 841 93.0680 177 751 1 chr3B.!!$R1 574
2 TraesCS3A01G376800 chr3B 498459581 498460151 570 False 830.000000 830 92.8820 177 750 1 chr3B.!!$F1 573
3 TraesCS3A01G376800 chr3B 644910135 644911858 1723 False 712.366667 1439 90.3800 756 2432 3 chr3B.!!$F4 1676
4 TraesCS3A01G376800 chr3D 482595731 482597409 1678 False 849.000000 1269 85.2645 756 2421 2 chr3D.!!$F1 1665
5 TraesCS3A01G376800 chr2B 699176622 699177201 579 False 909.000000 909 95.0090 177 755 1 chr2B.!!$F2 578
6 TraesCS3A01G376800 chr2B 454345171 454345738 567 False 811.000000 811 92.4690 182 750 1 chr2B.!!$F1 568
7 TraesCS3A01G376800 chr7B 110111315 110111909 594 False 907.000000 907 94.2950 177 768 1 chr7B.!!$F1 591
8 TraesCS3A01G376800 chr5B 44469076 44469654 578 False 896.000000 896 94.6550 177 754 1 chr5B.!!$F1 577
9 TraesCS3A01G376800 chr5B 360417729 360418305 576 True 850.000000 850 93.2640 179 755 1 chr5B.!!$R1 576
10 TraesCS3A01G376800 chr6B 578004150 578004723 573 True 881.000000 881 94.4350 177 749 1 chr6B.!!$R2 572
11 TraesCS3A01G376800 chr6B 498853548 498854117 569 False 848.000000 848 93.5430 179 749 1 chr6B.!!$F2 570

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
173 174 0.177141 CGATAGGAAAACAGGGCCGA 59.823 55.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1619 1639 0.250038 AGCAGAAGAGCTCGCAAACA 60.25 50.0 8.37 0.0 42.18 2.83 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
22 23 5.982890 AGGATTTGTGAACATAACCCTTG 57.017 39.130 0.00 0.00 0.00 3.61
23 24 5.393866 AGGATTTGTGAACATAACCCTTGT 58.606 37.500 0.00 0.00 0.00 3.16
24 25 5.476945 AGGATTTGTGAACATAACCCTTGTC 59.523 40.000 0.00 0.00 0.00 3.18
25 26 5.242838 GGATTTGTGAACATAACCCTTGTCA 59.757 40.000 0.00 0.00 0.00 3.58
26 27 6.239176 GGATTTGTGAACATAACCCTTGTCAA 60.239 38.462 0.00 0.00 0.00 3.18
27 28 5.766150 TTGTGAACATAACCCTTGTCAAG 57.234 39.130 5.53 5.53 0.00 3.02
28 29 4.787551 TGTGAACATAACCCTTGTCAAGT 58.212 39.130 11.61 0.00 0.00 3.16
29 30 5.931294 TGTGAACATAACCCTTGTCAAGTA 58.069 37.500 11.61 0.00 0.00 2.24
30 31 5.761234 TGTGAACATAACCCTTGTCAAGTAC 59.239 40.000 11.61 0.00 0.00 2.73
31 32 5.995897 GTGAACATAACCCTTGTCAAGTACT 59.004 40.000 11.61 0.00 0.00 2.73
32 33 6.147328 GTGAACATAACCCTTGTCAAGTACTC 59.853 42.308 11.61 0.00 0.00 2.59
33 34 5.818678 ACATAACCCTTGTCAAGTACTCA 57.181 39.130 11.61 0.00 0.00 3.41
34 35 5.548406 ACATAACCCTTGTCAAGTACTCAC 58.452 41.667 11.61 0.00 0.00 3.51
35 36 5.307196 ACATAACCCTTGTCAAGTACTCACT 59.693 40.000 11.61 0.00 36.19 3.41
36 37 4.338379 AACCCTTGTCAAGTACTCACTC 57.662 45.455 11.61 0.00 32.29 3.51
37 38 2.633481 ACCCTTGTCAAGTACTCACTCC 59.367 50.000 11.61 0.00 32.29 3.85
38 39 2.352814 CCCTTGTCAAGTACTCACTCCG 60.353 54.545 11.61 0.00 32.29 4.63
39 40 2.296471 CCTTGTCAAGTACTCACTCCGT 59.704 50.000 11.61 0.00 32.29 4.69
40 41 3.566523 CTTGTCAAGTACTCACTCCGTC 58.433 50.000 4.27 0.00 32.29 4.79
41 42 2.860009 TGTCAAGTACTCACTCCGTCT 58.140 47.619 0.00 0.00 32.29 4.18
42 43 3.220110 TGTCAAGTACTCACTCCGTCTT 58.780 45.455 0.00 0.00 32.29 3.01
43 44 4.392047 TGTCAAGTACTCACTCCGTCTTA 58.608 43.478 0.00 0.00 32.29 2.10
44 45 4.823442 TGTCAAGTACTCACTCCGTCTTAA 59.177 41.667 0.00 0.00 32.29 1.85
45 46 5.300034 TGTCAAGTACTCACTCCGTCTTAAA 59.700 40.000 0.00 0.00 32.29 1.52
46 47 6.183360 TGTCAAGTACTCACTCCGTCTTAAAA 60.183 38.462 0.00 0.00 32.29 1.52
47 48 6.867293 GTCAAGTACTCACTCCGTCTTAAAAT 59.133 38.462 0.00 0.00 32.29 1.82
48 49 8.025445 GTCAAGTACTCACTCCGTCTTAAAATA 58.975 37.037 0.00 0.00 32.29 1.40
49 50 8.579006 TCAAGTACTCACTCCGTCTTAAAATAA 58.421 33.333 0.00 0.00 32.29 1.40
50 51 8.861101 CAAGTACTCACTCCGTCTTAAAATAAG 58.139 37.037 0.00 0.00 32.29 1.73
51 52 8.120140 AGTACTCACTCCGTCTTAAAATAAGT 57.880 34.615 0.00 0.00 0.00 2.24
52 53 8.027771 AGTACTCACTCCGTCTTAAAATAAGTG 58.972 37.037 0.00 0.00 35.20 3.16
53 54 6.756221 ACTCACTCCGTCTTAAAATAAGTGT 58.244 36.000 0.00 0.00 35.37 3.55
54 55 6.867293 ACTCACTCCGTCTTAAAATAAGTGTC 59.133 38.462 0.00 0.00 35.37 3.67
55 56 6.989659 TCACTCCGTCTTAAAATAAGTGTCT 58.010 36.000 0.00 0.00 35.37 3.41
56 57 7.088905 TCACTCCGTCTTAAAATAAGTGTCTC 58.911 38.462 0.00 0.00 35.37 3.36
57 58 6.866770 CACTCCGTCTTAAAATAAGTGTCTCA 59.133 38.462 0.00 0.00 0.00 3.27
58 59 7.384115 CACTCCGTCTTAAAATAAGTGTCTCAA 59.616 37.037 0.00 0.00 0.00 3.02
59 60 7.929785 ACTCCGTCTTAAAATAAGTGTCTCAAA 59.070 33.333 0.00 0.00 0.00 2.69
60 61 8.842358 TCCGTCTTAAAATAAGTGTCTCAAAT 57.158 30.769 0.00 0.00 0.00 2.32
61 62 9.280174 TCCGTCTTAAAATAAGTGTCTCAAATT 57.720 29.630 0.00 0.00 0.00 1.82
62 63 9.893305 CCGTCTTAAAATAAGTGTCTCAAATTT 57.107 29.630 0.00 0.00 0.00 1.82
123 124 9.516314 TTGAGATATTGAGTTATGTACTTGACG 57.484 33.333 0.00 0.00 37.17 4.35
124 125 7.648112 TGAGATATTGAGTTATGTACTTGACGC 59.352 37.037 0.00 0.00 37.17 5.19
125 126 7.717568 AGATATTGAGTTATGTACTTGACGCT 58.282 34.615 8.38 0.00 37.17 5.07
126 127 7.649705 AGATATTGAGTTATGTACTTGACGCTG 59.350 37.037 8.38 0.00 37.17 5.18
127 128 4.776795 TGAGTTATGTACTTGACGCTGA 57.223 40.909 8.38 0.00 37.17 4.26
128 129 5.128992 TGAGTTATGTACTTGACGCTGAA 57.871 39.130 8.38 0.00 37.17 3.02
129 130 5.720202 TGAGTTATGTACTTGACGCTGAAT 58.280 37.500 8.38 0.00 37.17 2.57
130 131 5.805486 TGAGTTATGTACTTGACGCTGAATC 59.195 40.000 8.38 0.00 37.17 2.52
131 132 5.967088 AGTTATGTACTTGACGCTGAATCT 58.033 37.500 0.00 0.00 31.29 2.40
132 133 5.807520 AGTTATGTACTTGACGCTGAATCTG 59.192 40.000 0.00 0.00 31.29 2.90
133 134 3.934457 TGTACTTGACGCTGAATCTGA 57.066 42.857 0.00 0.00 0.00 3.27
134 135 3.838120 TGTACTTGACGCTGAATCTGAG 58.162 45.455 0.00 0.00 0.00 3.35
135 136 3.506067 TGTACTTGACGCTGAATCTGAGA 59.494 43.478 0.00 0.00 0.00 3.27
136 137 2.953020 ACTTGACGCTGAATCTGAGAC 58.047 47.619 0.00 0.00 0.00 3.36
137 138 2.560542 ACTTGACGCTGAATCTGAGACT 59.439 45.455 0.00 0.00 0.00 3.24
138 139 2.643933 TGACGCTGAATCTGAGACTG 57.356 50.000 0.00 0.00 0.00 3.51
139 140 1.203287 TGACGCTGAATCTGAGACTGG 59.797 52.381 0.00 0.00 0.00 4.00
140 141 1.474478 GACGCTGAATCTGAGACTGGA 59.526 52.381 0.00 0.00 0.00 3.86
141 142 1.895798 ACGCTGAATCTGAGACTGGAA 59.104 47.619 0.00 0.00 0.00 3.53
142 143 2.266554 CGCTGAATCTGAGACTGGAAC 58.733 52.381 0.00 0.00 0.00 3.62
143 144 2.626840 GCTGAATCTGAGACTGGAACC 58.373 52.381 0.00 0.00 0.00 3.62
144 145 2.027745 GCTGAATCTGAGACTGGAACCA 60.028 50.000 0.00 0.00 0.00 3.67
172 173 2.690326 CGATAGGAAAACAGGGCCG 58.310 57.895 0.00 0.00 0.00 6.13
173 174 0.177141 CGATAGGAAAACAGGGCCGA 59.823 55.000 0.00 0.00 0.00 5.54
174 175 1.406341 CGATAGGAAAACAGGGCCGAA 60.406 52.381 0.00 0.00 0.00 4.30
175 176 2.718563 GATAGGAAAACAGGGCCGAAA 58.281 47.619 0.00 0.00 0.00 3.46
198 199 4.566004 TCACTATTCTGACCCTTTCAACG 58.434 43.478 0.00 0.00 32.21 4.10
201 202 5.468746 CACTATTCTGACCCTTTCAACGAAA 59.531 40.000 0.00 0.00 32.21 3.46
202 203 4.830826 ATTCTGACCCTTTCAACGAAAC 57.169 40.909 0.00 0.00 32.21 2.78
441 443 1.338389 GCTGCCTTTTCCATGTGCATT 60.338 47.619 0.00 0.00 0.00 3.56
459 461 5.640357 GTGCATTTGAAATGTGGATGAACAT 59.360 36.000 18.12 0.00 42.62 2.71
525 527 1.184970 CCATGGTCCCTTGGCGTTTT 61.185 55.000 2.57 0.00 35.06 2.43
526 528 0.243636 CATGGTCCCTTGGCGTTTTC 59.756 55.000 0.00 0.00 0.00 2.29
617 619 4.330944 TCTTCTTGGTCAGAAACGCTAA 57.669 40.909 0.00 0.00 41.25 3.09
639 641 6.594788 AACTACCTCGGTGTTTCTATGTTA 57.405 37.500 0.00 0.00 0.00 2.41
675 677 0.591170 GCTGTGGCGTTGCTAAAAGA 59.409 50.000 0.00 0.00 0.00 2.52
680 682 2.289547 GTGGCGTTGCTAAAAGAGTCAA 59.710 45.455 0.00 0.00 0.00 3.18
686 688 5.389098 GCGTTGCTAAAAGAGTCAAATCGTA 60.389 40.000 0.00 0.00 0.00 3.43
704 706 9.536558 CAAATCGTAAAATACTTTCACATCGAA 57.463 29.630 0.00 0.00 0.00 3.71
725 727 7.254137 TCGAATTCATTTTGTGACAAAGTTCA 58.746 30.769 10.91 0.00 36.32 3.18
727 729 7.999878 CGAATTCATTTTGTGACAAAGTTCATG 59.000 33.333 10.91 11.58 36.32 3.07
774 776 3.018840 GAAAACAGCGGGCCGTACG 62.019 63.158 28.82 18.05 0.00 3.67
874 878 5.061064 CCAAGAAGCGCACTATAATATCGTC 59.939 44.000 11.47 0.00 0.00 4.20
912 918 0.251916 TGTCACCGTCCATTCCCATC 59.748 55.000 0.00 0.00 0.00 3.51
916 922 1.152963 CCGTCCATTCCCATCCCAC 60.153 63.158 0.00 0.00 0.00 4.61
920 926 2.323758 CCATTCCCATCCCACCCCA 61.324 63.158 0.00 0.00 0.00 4.96
966 972 0.605589 CTCCAGTGAGCTCGAAACCT 59.394 55.000 9.64 0.00 0.00 3.50
1126 1142 0.323542 GGAGGTCGAGGACTTCTCCA 60.324 60.000 13.06 0.00 39.30 3.86
1296 1312 1.209747 GACCGGCCCAGATCTACTTTT 59.790 52.381 0.00 0.00 0.00 2.27
1316 1332 2.841215 TCTTCACGGTTGTTACCTTGG 58.159 47.619 0.00 0.00 42.42 3.61
1327 1343 5.827267 GGTTGTTACCTTGGTGTTAAACCTA 59.173 40.000 15.18 0.00 44.53 3.08
1351 1367 1.596934 GTGGTTCGGAGCAGATGGA 59.403 57.895 0.00 0.00 33.20 3.41
1369 1385 1.133482 GGAGAGGAGAGGAAGGGAGAG 60.133 61.905 0.00 0.00 0.00 3.20
1545 1561 4.222847 GCCTCGCTAAGGGACCGG 62.223 72.222 0.00 0.00 46.32 5.28
1595 1611 6.005823 TCCATCGATCTTGGCATAAATGAAT 58.994 36.000 0.00 0.00 34.06 2.57
1596 1612 6.072342 TCCATCGATCTTGGCATAAATGAATG 60.072 38.462 0.00 0.00 34.06 2.67
1602 1618 7.168637 CGATCTTGGCATAAATGAATGGAAAAG 59.831 37.037 0.00 0.00 0.00 2.27
1603 1619 6.642430 TCTTGGCATAAATGAATGGAAAAGG 58.358 36.000 0.00 0.00 0.00 3.11
1661 1694 7.498900 TGCTCTTAATTAGCTTTGCTTATGCTA 59.501 33.333 10.34 0.00 40.44 3.49
1676 1709 5.220416 GCTTATGCTAAATTTCGTCGTGTCT 60.220 40.000 0.00 0.00 36.03 3.41
1677 1710 4.842139 ATGCTAAATTTCGTCGTGTCTC 57.158 40.909 0.00 0.00 0.00 3.36
1678 1711 2.659757 TGCTAAATTTCGTCGTGTCTCG 59.340 45.455 0.00 0.00 41.41 4.04
1679 1712 2.660236 GCTAAATTTCGTCGTGTCTCGT 59.340 45.455 0.00 0.00 40.80 4.18
1680 1713 3.120782 GCTAAATTTCGTCGTGTCTCGTT 59.879 43.478 0.00 0.00 40.80 3.85
1681 1714 4.375706 GCTAAATTTCGTCGTGTCTCGTTT 60.376 41.667 0.00 0.00 40.80 3.60
1707 1740 5.623368 CGTTCTAGTTTCCAGCTCAAGATCT 60.623 44.000 0.00 0.00 0.00 2.75
1708 1741 6.169800 GTTCTAGTTTCCAGCTCAAGATCTT 58.830 40.000 0.88 0.88 0.00 2.40
1720 1753 4.080863 GCTCAAGATCTTAGGGAGGTTCAA 60.081 45.833 18.12 0.00 0.00 2.69
1722 1755 6.642733 TCAAGATCTTAGGGAGGTTCAATT 57.357 37.500 7.86 0.00 0.00 2.32
1740 1773 0.109039 TTCGCTGCGCTGTGTATGTA 60.109 50.000 24.31 5.03 0.00 2.29
1797 1830 1.456296 TGCAGTGATGCAATGACTCC 58.544 50.000 0.00 0.00 35.15 3.85
1835 1868 2.045561 TCCAGTTTTCGTTGCCTGAA 57.954 45.000 0.00 0.00 0.00 3.02
1837 1870 1.269051 CCAGTTTTCGTTGCCTGAACC 60.269 52.381 0.00 0.00 0.00 3.62
1838 1871 1.403679 CAGTTTTCGTTGCCTGAACCA 59.596 47.619 0.00 0.00 0.00 3.67
1839 1872 1.404035 AGTTTTCGTTGCCTGAACCAC 59.596 47.619 0.00 0.00 0.00 4.16
1840 1873 1.133407 GTTTTCGTTGCCTGAACCACA 59.867 47.619 0.00 0.00 0.00 4.17
1877 1955 0.678395 CTGATGGATCCCACGGAGAG 59.322 60.000 9.90 0.00 35.80 3.20
1882 1960 1.330655 GGATCCCACGGAGAGAAGCA 61.331 60.000 0.00 0.00 34.05 3.91
1883 1961 0.179097 GATCCCACGGAGAGAAGCAC 60.179 60.000 0.00 0.00 34.05 4.40
1884 1962 0.904865 ATCCCACGGAGAGAAGCACA 60.905 55.000 0.00 0.00 34.05 4.57
1885 1963 1.079543 CCCACGGAGAGAAGCACAG 60.080 63.158 0.00 0.00 0.00 3.66
1886 1964 1.079543 CCACGGAGAGAAGCACAGG 60.080 63.158 0.00 0.00 0.00 4.00
1887 1965 1.668294 CACGGAGAGAAGCACAGGT 59.332 57.895 0.00 0.00 0.00 4.00
1888 1966 0.034059 CACGGAGAGAAGCACAGGTT 59.966 55.000 0.00 0.00 0.00 3.50
1889 1967 0.034059 ACGGAGAGAAGCACAGGTTG 59.966 55.000 0.00 0.00 0.00 3.77
2019 2107 8.959705 AACTAGCTAAACACTTTTTACAGAGT 57.040 30.769 0.00 0.00 0.00 3.24
2062 2152 1.208052 TGAGTGGGTAATGCTGCTCTC 59.792 52.381 0.00 0.00 0.00 3.20
2063 2153 1.208052 GAGTGGGTAATGCTGCTCTCA 59.792 52.381 0.00 0.00 0.00 3.27
2215 2308 0.380378 TTTCAGCGCCACAGAAACAC 59.620 50.000 2.29 0.00 29.67 3.32
2240 2333 4.527944 TGTCTGTGGACCAAAATGTTGTA 58.472 39.130 0.00 0.00 41.47 2.41
2255 2348 5.746307 ATGTTGTACGAAGCTACGAGATA 57.254 39.130 0.00 0.00 37.03 1.98
2292 2393 8.206189 TGAGATGAGAGTGCATCATAAAACATA 58.794 33.333 1.30 0.00 45.52 2.29
2334 2461 9.463443 AACACTAATTCAAAAGTGAAGCAATAC 57.537 29.630 12.05 0.00 46.75 1.89
2345 2472 6.690194 AGTGAAGCAATACAGGAAATGATC 57.310 37.500 0.00 0.00 0.00 2.92
2399 2526 2.130395 CAGGTGCAGTGCTATATGTCG 58.870 52.381 17.60 0.00 0.00 4.35
2421 2548 6.487331 GTCGAAGATAAATCCAGAGTCTAGGA 59.513 42.308 12.05 12.05 40.67 2.94
2423 2550 6.488683 CGAAGATAAATCCAGAGTCTAGGACT 59.511 42.308 11.94 0.00 46.42 3.85
2432 2559 7.209340 TCCAGAGTCTAGGACTGTTAATCTA 57.791 40.000 4.85 0.00 43.53 1.98
2433 2560 7.284074 TCCAGAGTCTAGGACTGTTAATCTAG 58.716 42.308 4.85 0.00 43.53 2.43
2434 2561 6.488683 CCAGAGTCTAGGACTGTTAATCTAGG 59.511 46.154 4.85 0.00 43.53 3.02
2435 2562 7.057894 CAGAGTCTAGGACTGTTAATCTAGGT 58.942 42.308 4.85 0.00 43.53 3.08
2436 2563 7.227910 CAGAGTCTAGGACTGTTAATCTAGGTC 59.772 44.444 4.85 0.00 43.53 3.85
2437 2564 6.056884 AGTCTAGGACTGTTAATCTAGGTCG 58.943 44.000 0.00 0.00 41.76 4.79
2438 2565 5.821995 GTCTAGGACTGTTAATCTAGGTCGT 59.178 44.000 0.00 0.00 32.41 4.34
2439 2566 4.985538 AGGACTGTTAATCTAGGTCGTG 57.014 45.455 0.00 0.00 0.00 4.35
2440 2567 4.597004 AGGACTGTTAATCTAGGTCGTGA 58.403 43.478 0.00 0.00 0.00 4.35
2441 2568 5.202004 AGGACTGTTAATCTAGGTCGTGAT 58.798 41.667 0.00 0.00 0.00 3.06
2442 2569 5.657302 AGGACTGTTAATCTAGGTCGTGATT 59.343 40.000 0.00 0.00 36.87 2.57
2443 2570 6.832384 AGGACTGTTAATCTAGGTCGTGATTA 59.168 38.462 0.00 0.00 35.01 1.75
2444 2571 7.506261 AGGACTGTTAATCTAGGTCGTGATTAT 59.494 37.037 0.00 0.00 35.78 1.28
2445 2572 7.595502 GGACTGTTAATCTAGGTCGTGATTATG 59.404 40.741 0.00 0.00 35.78 1.90
2446 2573 8.008513 ACTGTTAATCTAGGTCGTGATTATGT 57.991 34.615 0.00 0.00 35.78 2.29
2447 2574 8.136165 ACTGTTAATCTAGGTCGTGATTATGTC 58.864 37.037 0.00 0.00 35.78 3.06
2448 2575 7.431249 TGTTAATCTAGGTCGTGATTATGTCC 58.569 38.462 0.00 0.00 35.78 4.02
2449 2576 5.470047 AATCTAGGTCGTGATTATGTCCC 57.530 43.478 0.00 0.00 31.91 4.46
2450 2577 3.905968 TCTAGGTCGTGATTATGTCCCA 58.094 45.455 0.00 0.00 0.00 4.37
2451 2578 3.889538 TCTAGGTCGTGATTATGTCCCAG 59.110 47.826 0.00 0.00 0.00 4.45
2452 2579 1.139058 AGGTCGTGATTATGTCCCAGC 59.861 52.381 0.00 0.00 0.00 4.85
2453 2580 1.583054 GTCGTGATTATGTCCCAGCC 58.417 55.000 0.00 0.00 0.00 4.85
2454 2581 1.139058 GTCGTGATTATGTCCCAGCCT 59.861 52.381 0.00 0.00 0.00 4.58
2455 2582 2.364324 GTCGTGATTATGTCCCAGCCTA 59.636 50.000 0.00 0.00 0.00 3.93
2456 2583 3.035363 TCGTGATTATGTCCCAGCCTAA 58.965 45.455 0.00 0.00 0.00 2.69
2457 2584 3.646162 TCGTGATTATGTCCCAGCCTAAT 59.354 43.478 0.00 0.00 0.00 1.73
2458 2585 4.102524 TCGTGATTATGTCCCAGCCTAATT 59.897 41.667 0.00 0.00 0.00 1.40
2459 2586 4.821805 CGTGATTATGTCCCAGCCTAATTT 59.178 41.667 0.00 0.00 0.00 1.82
2460 2587 5.299279 CGTGATTATGTCCCAGCCTAATTTT 59.701 40.000 0.00 0.00 0.00 1.82
2461 2588 6.183360 CGTGATTATGTCCCAGCCTAATTTTT 60.183 38.462 0.00 0.00 0.00 1.94
2500 2627 8.755696 TGAACCATTGTTATGTTAAGAAATGC 57.244 30.769 0.00 0.00 33.97 3.56
2501 2628 8.584157 TGAACCATTGTTATGTTAAGAAATGCT 58.416 29.630 0.00 0.00 33.97 3.79
2502 2629 8.761575 AACCATTGTTATGTTAAGAAATGCTG 57.238 30.769 0.00 0.00 31.36 4.41
2503 2630 7.895759 ACCATTGTTATGTTAAGAAATGCTGT 58.104 30.769 0.00 0.00 0.00 4.40
2504 2631 8.028938 ACCATTGTTATGTTAAGAAATGCTGTC 58.971 33.333 0.00 0.00 0.00 3.51
2505 2632 8.028354 CCATTGTTATGTTAAGAAATGCTGTCA 58.972 33.333 0.00 0.00 0.00 3.58
2506 2633 9.409312 CATTGTTATGTTAAGAAATGCTGTCAA 57.591 29.630 0.00 0.00 0.00 3.18
2507 2634 9.979578 ATTGTTATGTTAAGAAATGCTGTCAAA 57.020 25.926 0.00 0.00 0.00 2.69
2508 2635 9.809096 TTGTTATGTTAAGAAATGCTGTCAAAA 57.191 25.926 0.00 0.00 0.00 2.44
2509 2636 9.809096 TGTTATGTTAAGAAATGCTGTCAAAAA 57.191 25.926 0.00 0.00 0.00 1.94
2511 2638 6.804534 TGTTAAGAAATGCTGTCAAAAACG 57.195 33.333 0.00 0.00 0.00 3.60
2512 2639 6.556212 TGTTAAGAAATGCTGTCAAAAACGA 58.444 32.000 0.00 0.00 0.00 3.85
2513 2640 6.690957 TGTTAAGAAATGCTGTCAAAAACGAG 59.309 34.615 0.00 0.00 0.00 4.18
2514 2641 5.499139 AAGAAATGCTGTCAAAAACGAGA 57.501 34.783 0.00 0.00 0.00 4.04
2515 2642 5.499139 AGAAATGCTGTCAAAAACGAGAA 57.501 34.783 0.00 0.00 0.00 2.87
2516 2643 5.273944 AGAAATGCTGTCAAAAACGAGAAC 58.726 37.500 0.00 0.00 0.00 3.01
2517 2644 4.900635 AATGCTGTCAAAAACGAGAACT 57.099 36.364 0.00 0.00 0.00 3.01
2518 2645 6.260050 AGAAATGCTGTCAAAAACGAGAACTA 59.740 34.615 0.00 0.00 0.00 2.24
2519 2646 6.371809 AATGCTGTCAAAAACGAGAACTAA 57.628 33.333 0.00 0.00 0.00 2.24
2520 2647 5.804692 TGCTGTCAAAAACGAGAACTAAA 57.195 34.783 0.00 0.00 0.00 1.85
2521 2648 5.565695 TGCTGTCAAAAACGAGAACTAAAC 58.434 37.500 0.00 0.00 0.00 2.01
2522 2649 5.353123 TGCTGTCAAAAACGAGAACTAAACT 59.647 36.000 0.00 0.00 0.00 2.66
2523 2650 6.535865 TGCTGTCAAAAACGAGAACTAAACTA 59.464 34.615 0.00 0.00 0.00 2.24
2524 2651 7.225931 TGCTGTCAAAAACGAGAACTAAACTAT 59.774 33.333 0.00 0.00 0.00 2.12
2525 2652 8.706035 GCTGTCAAAAACGAGAACTAAACTATA 58.294 33.333 0.00 0.00 0.00 1.31
2527 2654 9.754382 TGTCAAAAACGAGAACTAAACTATAGT 57.246 29.630 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.393866 ACAAGGGTTATGTTCACAAATCCT 58.606 37.500 2.55 2.55 0.00 3.24
1 2 5.242838 TGACAAGGGTTATGTTCACAAATCC 59.757 40.000 0.00 0.00 0.00 3.01
2 3 6.325919 TGACAAGGGTTATGTTCACAAATC 57.674 37.500 0.00 0.00 0.00 2.17
3 4 6.323739 ACTTGACAAGGGTTATGTTCACAAAT 59.676 34.615 19.16 0.00 0.00 2.32
4 5 5.654650 ACTTGACAAGGGTTATGTTCACAAA 59.345 36.000 19.16 0.00 0.00 2.83
5 6 5.197451 ACTTGACAAGGGTTATGTTCACAA 58.803 37.500 19.16 0.00 0.00 3.33
6 7 4.787551 ACTTGACAAGGGTTATGTTCACA 58.212 39.130 19.16 0.00 0.00 3.58
7 8 5.995897 AGTACTTGACAAGGGTTATGTTCAC 59.004 40.000 19.16 2.15 0.00 3.18
8 9 6.182507 AGTACTTGACAAGGGTTATGTTCA 57.817 37.500 19.16 0.00 0.00 3.18
9 10 6.147328 GTGAGTACTTGACAAGGGTTATGTTC 59.853 42.308 19.16 6.10 0.00 3.18
10 11 5.995897 GTGAGTACTTGACAAGGGTTATGTT 59.004 40.000 19.16 0.00 0.00 2.71
11 12 5.307196 AGTGAGTACTTGACAAGGGTTATGT 59.693 40.000 19.16 0.00 31.66 2.29
12 13 5.794894 AGTGAGTACTTGACAAGGGTTATG 58.205 41.667 19.16 0.00 31.66 1.90
13 14 5.046520 GGAGTGAGTACTTGACAAGGGTTAT 60.047 44.000 19.16 0.52 37.25 1.89
14 15 4.282703 GGAGTGAGTACTTGACAAGGGTTA 59.717 45.833 19.16 0.27 37.25 2.85
15 16 3.071167 GGAGTGAGTACTTGACAAGGGTT 59.929 47.826 19.16 3.95 37.25 4.11
16 17 2.633481 GGAGTGAGTACTTGACAAGGGT 59.367 50.000 19.16 2.85 37.25 4.34
17 18 2.352814 CGGAGTGAGTACTTGACAAGGG 60.353 54.545 19.16 0.00 37.25 3.95
18 19 2.296471 ACGGAGTGAGTACTTGACAAGG 59.704 50.000 19.16 2.01 42.51 3.61
19 20 3.644884 ACGGAGTGAGTACTTGACAAG 57.355 47.619 13.77 13.77 42.51 3.16
34 35 7.884816 TTGAGACACTTATTTTAAGACGGAG 57.115 36.000 1.47 0.00 0.00 4.63
35 36 8.842358 ATTTGAGACACTTATTTTAAGACGGA 57.158 30.769 1.47 0.00 0.00 4.69
36 37 9.893305 AAATTTGAGACACTTATTTTAAGACGG 57.107 29.630 1.47 0.00 0.00 4.79
97 98 9.516314 CGTCAAGTACATAACTCAATATCTCAA 57.484 33.333 0.00 0.00 37.50 3.02
98 99 7.648112 GCGTCAAGTACATAACTCAATATCTCA 59.352 37.037 0.00 0.00 37.50 3.27
99 100 7.863375 AGCGTCAAGTACATAACTCAATATCTC 59.137 37.037 0.00 0.00 37.50 2.75
100 101 7.649705 CAGCGTCAAGTACATAACTCAATATCT 59.350 37.037 0.00 0.00 37.50 1.98
101 102 7.648112 TCAGCGTCAAGTACATAACTCAATATC 59.352 37.037 0.00 0.00 37.50 1.63
102 103 7.489160 TCAGCGTCAAGTACATAACTCAATAT 58.511 34.615 0.00 0.00 37.50 1.28
103 104 6.859017 TCAGCGTCAAGTACATAACTCAATA 58.141 36.000 0.00 0.00 37.50 1.90
104 105 5.720202 TCAGCGTCAAGTACATAACTCAAT 58.280 37.500 0.00 0.00 37.50 2.57
105 106 5.128992 TCAGCGTCAAGTACATAACTCAA 57.871 39.130 0.00 0.00 37.50 3.02
106 107 4.776795 TCAGCGTCAAGTACATAACTCA 57.223 40.909 0.00 0.00 37.50 3.41
107 108 6.020281 CAGATTCAGCGTCAAGTACATAACTC 60.020 42.308 0.00 0.00 37.50 3.01
108 109 5.807520 CAGATTCAGCGTCAAGTACATAACT 59.192 40.000 0.00 0.00 41.49 2.24
109 110 5.805486 TCAGATTCAGCGTCAAGTACATAAC 59.195 40.000 0.00 0.00 0.00 1.89
110 111 5.961272 TCAGATTCAGCGTCAAGTACATAA 58.039 37.500 0.00 0.00 0.00 1.90
111 112 5.357032 TCTCAGATTCAGCGTCAAGTACATA 59.643 40.000 0.00 0.00 0.00 2.29
112 113 4.158579 TCTCAGATTCAGCGTCAAGTACAT 59.841 41.667 0.00 0.00 0.00 2.29
113 114 3.506067 TCTCAGATTCAGCGTCAAGTACA 59.494 43.478 0.00 0.00 0.00 2.90
114 115 3.854809 GTCTCAGATTCAGCGTCAAGTAC 59.145 47.826 0.00 0.00 0.00 2.73
115 116 3.759086 AGTCTCAGATTCAGCGTCAAGTA 59.241 43.478 0.00 0.00 0.00 2.24
116 117 2.560542 AGTCTCAGATTCAGCGTCAAGT 59.439 45.455 0.00 0.00 0.00 3.16
117 118 2.922387 CAGTCTCAGATTCAGCGTCAAG 59.078 50.000 0.00 0.00 0.00 3.02
118 119 2.353109 CCAGTCTCAGATTCAGCGTCAA 60.353 50.000 0.00 0.00 0.00 3.18
119 120 1.203287 CCAGTCTCAGATTCAGCGTCA 59.797 52.381 0.00 0.00 0.00 4.35
120 121 1.474478 TCCAGTCTCAGATTCAGCGTC 59.526 52.381 0.00 0.00 0.00 5.19
121 122 1.550327 TCCAGTCTCAGATTCAGCGT 58.450 50.000 0.00 0.00 0.00 5.07
122 123 2.266554 GTTCCAGTCTCAGATTCAGCG 58.733 52.381 0.00 0.00 0.00 5.18
123 124 2.027745 TGGTTCCAGTCTCAGATTCAGC 60.028 50.000 0.00 0.00 0.00 4.26
124 125 3.859443 CTGGTTCCAGTCTCAGATTCAG 58.141 50.000 10.40 0.00 0.00 3.02
125 126 2.027745 GCTGGTTCCAGTCTCAGATTCA 60.028 50.000 18.42 0.00 36.52 2.57
126 127 2.027745 TGCTGGTTCCAGTCTCAGATTC 60.028 50.000 18.42 1.54 36.52 2.52
127 128 1.980765 TGCTGGTTCCAGTCTCAGATT 59.019 47.619 18.42 0.00 36.52 2.40
128 129 1.277557 GTGCTGGTTCCAGTCTCAGAT 59.722 52.381 18.42 0.00 36.52 2.90
129 130 0.681733 GTGCTGGTTCCAGTCTCAGA 59.318 55.000 18.42 0.00 36.52 3.27
130 131 0.668706 CGTGCTGGTTCCAGTCTCAG 60.669 60.000 18.42 4.69 36.52 3.35
131 132 1.367471 CGTGCTGGTTCCAGTCTCA 59.633 57.895 18.42 7.05 36.52 3.27
132 133 2.029844 GCGTGCTGGTTCCAGTCTC 61.030 63.158 18.42 11.18 36.52 3.36
133 134 2.031163 GCGTGCTGGTTCCAGTCT 59.969 61.111 18.42 0.00 36.52 3.24
134 135 3.050275 GGCGTGCTGGTTCCAGTC 61.050 66.667 18.42 11.93 36.52 3.51
135 136 4.988598 CGGCGTGCTGGTTCCAGT 62.989 66.667 18.42 0.00 36.52 4.00
145 146 4.884257 TTCCTATCGGCGGCGTGC 62.884 66.667 31.06 0.00 45.38 5.34
146 147 1.812093 TTTTCCTATCGGCGGCGTG 60.812 57.895 31.06 20.51 0.00 5.34
147 148 1.812507 GTTTTCCTATCGGCGGCGT 60.813 57.895 31.06 19.95 0.00 5.68
148 149 1.762222 CTGTTTTCCTATCGGCGGCG 61.762 60.000 27.15 27.15 0.00 6.46
149 150 1.436983 CCTGTTTTCCTATCGGCGGC 61.437 60.000 7.21 0.00 0.00 6.53
150 151 0.814010 CCCTGTTTTCCTATCGGCGG 60.814 60.000 7.21 0.00 0.00 6.13
151 152 1.436983 GCCCTGTTTTCCTATCGGCG 61.437 60.000 0.00 0.00 0.00 6.46
152 153 1.101635 GGCCCTGTTTTCCTATCGGC 61.102 60.000 0.00 0.00 0.00 5.54
153 154 0.814010 CGGCCCTGTTTTCCTATCGG 60.814 60.000 0.00 0.00 0.00 4.18
154 155 0.177141 TCGGCCCTGTTTTCCTATCG 59.823 55.000 0.00 0.00 0.00 2.92
155 156 2.413310 TTCGGCCCTGTTTTCCTATC 57.587 50.000 0.00 0.00 0.00 2.08
156 157 2.891191 TTTCGGCCCTGTTTTCCTAT 57.109 45.000 0.00 0.00 0.00 2.57
157 158 2.040545 TGATTTCGGCCCTGTTTTCCTA 59.959 45.455 0.00 0.00 0.00 2.94
158 159 1.203001 TGATTTCGGCCCTGTTTTCCT 60.203 47.619 0.00 0.00 0.00 3.36
159 160 1.067846 GTGATTTCGGCCCTGTTTTCC 60.068 52.381 0.00 0.00 0.00 3.13
160 161 1.886542 AGTGATTTCGGCCCTGTTTTC 59.113 47.619 0.00 0.00 0.00 2.29
161 162 1.995376 AGTGATTTCGGCCCTGTTTT 58.005 45.000 0.00 0.00 0.00 2.43
162 163 2.871096 TAGTGATTTCGGCCCTGTTT 57.129 45.000 0.00 0.00 0.00 2.83
163 164 3.054361 AGAATAGTGATTTCGGCCCTGTT 60.054 43.478 0.00 0.00 0.00 3.16
164 165 2.505819 AGAATAGTGATTTCGGCCCTGT 59.494 45.455 0.00 0.00 0.00 4.00
165 166 2.874701 CAGAATAGTGATTTCGGCCCTG 59.125 50.000 0.00 0.00 0.00 4.45
166 167 2.771943 TCAGAATAGTGATTTCGGCCCT 59.228 45.455 0.00 0.00 0.00 5.19
167 168 2.872858 GTCAGAATAGTGATTTCGGCCC 59.127 50.000 0.00 0.00 0.00 5.80
168 169 2.872858 GGTCAGAATAGTGATTTCGGCC 59.127 50.000 0.00 0.00 0.00 6.13
169 170 2.872858 GGGTCAGAATAGTGATTTCGGC 59.127 50.000 0.00 0.00 0.00 5.54
170 171 4.408182 AGGGTCAGAATAGTGATTTCGG 57.592 45.455 0.00 0.00 0.00 4.30
171 172 5.874810 TGAAAGGGTCAGAATAGTGATTTCG 59.125 40.000 0.00 0.00 30.52 3.46
172 173 7.530863 GTTGAAAGGGTCAGAATAGTGATTTC 58.469 38.462 0.00 0.00 37.61 2.17
173 174 6.149474 CGTTGAAAGGGTCAGAATAGTGATTT 59.851 38.462 0.00 0.00 37.61 2.17
174 175 5.643777 CGTTGAAAGGGTCAGAATAGTGATT 59.356 40.000 0.00 0.00 37.61 2.57
175 176 5.046591 TCGTTGAAAGGGTCAGAATAGTGAT 60.047 40.000 0.00 0.00 37.61 3.06
198 199 6.194692 GTCGAGTTCATTTTGTGACAAGTTTC 59.805 38.462 0.00 0.00 36.32 2.78
201 202 4.260212 CGTCGAGTTCATTTTGTGACAAGT 60.260 41.667 0.00 0.00 36.32 3.16
202 203 4.203828 CGTCGAGTTCATTTTGTGACAAG 58.796 43.478 0.00 0.00 36.32 3.16
283 284 0.463116 ACCTCGGCGTTTCTGTGTTT 60.463 50.000 6.85 0.00 0.00 2.83
288 289 0.454600 TAGCTACCTCGGCGTTTCTG 59.545 55.000 6.85 0.00 34.52 3.02
392 393 0.243636 GTCCCTTGGCGTTTCAATGG 59.756 55.000 0.00 0.00 34.90 3.16
441 443 6.947733 AGTTAGGATGTTCATCCACATTTCAA 59.052 34.615 26.92 10.78 43.14 2.69
485 487 1.439679 GTTGCTACCCTCTTTGGTCG 58.560 55.000 0.00 0.00 39.91 4.79
525 527 2.409055 GCGTTGCTGCCCATCATGA 61.409 57.895 0.00 0.00 0.00 3.07
526 528 2.103538 GCGTTGCTGCCCATCATG 59.896 61.111 0.00 0.00 0.00 3.07
617 619 6.594788 TTAACATAGAAACACCGAGGTAGT 57.405 37.500 0.00 0.00 0.00 2.73
704 706 7.499292 TCCATGAACTTTGTCACAAAATGAAT 58.501 30.769 12.41 0.00 39.72 2.57
725 727 5.983333 ATCACTATTCTGACCCTTTCCAT 57.017 39.130 0.00 0.00 0.00 3.41
727 729 6.434340 ACAAAATCACTATTCTGACCCTTTCC 59.566 38.462 0.00 0.00 0.00 3.13
774 776 2.304516 ATTACCACGTTGCGCGATGC 62.305 55.000 16.99 0.00 44.77 3.91
840 843 1.812571 GCGCTTCTTGGATCTTTTGGA 59.187 47.619 0.00 0.00 0.00 3.53
874 878 2.510691 GTACGGCGTGGGGTGATG 60.511 66.667 24.86 0.00 0.00 3.07
912 918 3.650950 CTGGTGGAGTGGGGTGGG 61.651 72.222 0.00 0.00 0.00 4.61
916 922 2.529136 TGGACTGGTGGAGTGGGG 60.529 66.667 0.00 0.00 33.83 4.96
920 926 2.507854 CGGTGTGGACTGGTGGAGT 61.508 63.158 0.00 0.00 37.76 3.85
966 972 3.579534 ACTGTATCGCTTCCTCCTCTA 57.420 47.619 0.00 0.00 0.00 2.43
1224 1240 4.719369 AAGGCGTCGCTGTCGTCC 62.719 66.667 18.11 0.00 36.96 4.79
1296 1312 2.171027 ACCAAGGTAACAACCGTGAAGA 59.829 45.455 11.38 0.00 40.87 2.87
1316 1332 2.145536 CCACGGTGGTAGGTTTAACAC 58.854 52.381 19.15 0.00 45.01 3.32
1351 1367 0.933700 CCTCTCCCTTCCTCTCCTCT 59.066 60.000 0.00 0.00 0.00 3.69
1369 1385 2.815647 CTCTTCTTGACGGCGGCC 60.816 66.667 11.74 9.54 0.00 6.13
1545 1561 3.567797 GAACGCGATGAGGCTGGC 61.568 66.667 15.93 0.00 0.00 4.85
1619 1639 0.250038 AGCAGAAGAGCTCGCAAACA 60.250 50.000 8.37 0.00 42.18 2.83
1661 1694 4.511734 GAAAACGAGACACGACGAAATTT 58.488 39.130 0.00 0.00 45.77 1.82
1676 1709 3.492011 GCTGGAAACTAGAACGAAAACGA 59.508 43.478 0.00 0.00 0.00 3.85
1677 1710 3.493503 AGCTGGAAACTAGAACGAAAACG 59.506 43.478 0.00 0.00 0.00 3.60
1678 1711 4.510340 TGAGCTGGAAACTAGAACGAAAAC 59.490 41.667 0.00 0.00 0.00 2.43
1679 1712 4.699637 TGAGCTGGAAACTAGAACGAAAA 58.300 39.130 0.00 0.00 0.00 2.29
1680 1713 4.330944 TGAGCTGGAAACTAGAACGAAA 57.669 40.909 0.00 0.00 0.00 3.46
1681 1714 4.038763 TCTTGAGCTGGAAACTAGAACGAA 59.961 41.667 0.00 0.00 0.00 3.85
1707 1740 2.939640 GCAGCGAATTGAACCTCCCTAA 60.940 50.000 0.00 0.00 0.00 2.69
1708 1741 1.406887 GCAGCGAATTGAACCTCCCTA 60.407 52.381 0.00 0.00 0.00 3.53
1744 1777 7.027760 CACACTAGTACATCATTTACAGACGT 58.972 38.462 0.00 0.00 0.00 4.34
1745 1778 7.027760 ACACACTAGTACATCATTTACAGACG 58.972 38.462 0.00 0.00 0.00 4.18
1760 1793 8.288689 TCACTGCATCTTATTACACACTAGTA 57.711 34.615 0.00 0.00 0.00 1.82
1761 1794 7.170393 TCACTGCATCTTATTACACACTAGT 57.830 36.000 0.00 0.00 0.00 2.57
1762 1795 8.070007 CATCACTGCATCTTATTACACACTAG 57.930 38.462 0.00 0.00 0.00 2.57
1797 1830 2.736192 GGAAAACCATTTGCACCGAATG 59.264 45.455 3.08 3.08 36.90 2.67
1819 1852 1.404035 GTGGTTCAGGCAACGAAAACT 59.596 47.619 0.00 0.00 46.39 2.66
1835 1868 2.495155 TCTACATGCAGCATTGTGGT 57.505 45.000 4.69 3.06 0.00 4.16
1837 1870 5.034797 CAGAAATCTACATGCAGCATTGTG 58.965 41.667 4.69 0.00 0.00 3.33
1838 1871 4.945543 TCAGAAATCTACATGCAGCATTGT 59.054 37.500 4.69 10.12 0.00 2.71
1839 1872 5.494632 TCAGAAATCTACATGCAGCATTG 57.505 39.130 4.69 4.23 0.00 2.82
1840 1873 5.009710 CCATCAGAAATCTACATGCAGCATT 59.990 40.000 4.69 0.15 0.00 3.56
1889 1967 0.313672 CCTCTACAGATGCCGAGAGC 59.686 60.000 0.00 0.00 44.14 4.09
1890 1968 1.686355 ACCTCTACAGATGCCGAGAG 58.314 55.000 0.00 0.00 36.08 3.20
1891 1969 2.025155 GAACCTCTACAGATGCCGAGA 58.975 52.381 0.00 0.00 0.00 4.04
1892 1970 1.751351 TGAACCTCTACAGATGCCGAG 59.249 52.381 0.00 0.00 0.00 4.63
1893 1971 1.751351 CTGAACCTCTACAGATGCCGA 59.249 52.381 0.00 0.00 36.38 5.54
1894 1972 1.804372 GCTGAACCTCTACAGATGCCG 60.804 57.143 0.00 0.00 36.38 5.69
1895 1973 1.208052 TGCTGAACCTCTACAGATGCC 59.792 52.381 0.00 0.00 36.38 4.40
1896 1974 2.680312 TGCTGAACCTCTACAGATGC 57.320 50.000 0.00 0.00 36.38 3.91
1897 1975 3.379240 CGATGCTGAACCTCTACAGATG 58.621 50.000 0.00 0.00 36.38 2.90
1898 1976 2.223923 GCGATGCTGAACCTCTACAGAT 60.224 50.000 0.00 0.00 36.38 2.90
1899 1977 1.135139 GCGATGCTGAACCTCTACAGA 59.865 52.381 0.00 0.00 36.38 3.41
1900 1978 1.134995 TGCGATGCTGAACCTCTACAG 60.135 52.381 0.00 0.00 37.22 2.74
1901 1979 0.894835 TGCGATGCTGAACCTCTACA 59.105 50.000 0.00 0.00 0.00 2.74
1902 1980 2.010145 TTGCGATGCTGAACCTCTAC 57.990 50.000 0.00 0.00 0.00 2.59
1903 1981 2.483714 GGATTGCGATGCTGAACCTCTA 60.484 50.000 0.00 0.00 0.00 2.43
1958 2046 2.410053 CGAGAGCAAACTGTCTAGTTGC 59.590 50.000 6.79 6.79 46.14 4.17
1959 2047 2.989840 CCGAGAGCAAACTGTCTAGTTG 59.010 50.000 0.00 0.00 46.14 3.16
2019 2107 4.274147 TCTTCCAAGTGTGCAGGTTTTAA 58.726 39.130 0.00 0.00 0.00 1.52
2062 2152 7.443272 TGGAATGTATAGTGAAGATTGATGCTG 59.557 37.037 0.00 0.00 0.00 4.41
2063 2153 7.512130 TGGAATGTATAGTGAAGATTGATGCT 58.488 34.615 0.00 0.00 0.00 3.79
2215 2308 3.480470 ACATTTTGGTCCACAGACAGAG 58.520 45.455 0.00 0.00 45.48 3.35
2240 2333 2.915349 TGGTCTATCTCGTAGCTTCGT 58.085 47.619 12.66 0.00 0.00 3.85
2255 2348 5.303971 CACTCTCATCTCAGTTTTTGGTCT 58.696 41.667 0.00 0.00 0.00 3.85
2292 2393 3.873910 AGTGTTGCAAGTACACAGAAGT 58.126 40.909 19.47 0.00 46.42 3.01
2334 2461 6.405176 GGGAAGCACTAAAAGATCATTTCCTG 60.405 42.308 0.00 0.00 33.73 3.86
2345 2472 2.893489 AGCCTTTGGGAAGCACTAAAAG 59.107 45.455 0.00 0.00 33.58 2.27
2399 2526 7.286775 ACAGTCCTAGACTCTGGATTTATCTTC 59.713 40.741 11.38 0.00 41.37 2.87
2421 2548 8.008513 ACATAATCACGACCTAGATTAACAGT 57.991 34.615 0.00 0.00 39.40 3.55
2423 2550 7.431249 GGACATAATCACGACCTAGATTAACA 58.569 38.462 0.00 0.00 39.40 2.41
2432 2559 1.139058 GCTGGGACATAATCACGACCT 59.861 52.381 0.00 0.00 38.20 3.85
2433 2560 1.583054 GCTGGGACATAATCACGACC 58.417 55.000 0.00 0.00 38.20 4.79
2434 2561 1.139058 AGGCTGGGACATAATCACGAC 59.861 52.381 0.00 0.00 38.20 4.34
2435 2562 1.496060 AGGCTGGGACATAATCACGA 58.504 50.000 0.00 0.00 38.20 4.35
2436 2563 3.469008 TTAGGCTGGGACATAATCACG 57.531 47.619 0.00 0.00 38.20 4.35
2437 2564 6.715347 AAAATTAGGCTGGGACATAATCAC 57.285 37.500 0.00 0.00 38.20 3.06
2474 2601 9.369904 GCATTTCTTAACATAACAATGGTTCAT 57.630 29.630 0.00 0.00 38.45 2.57
2475 2602 8.584157 AGCATTTCTTAACATAACAATGGTTCA 58.416 29.630 0.00 0.00 38.45 3.18
2476 2603 8.863049 CAGCATTTCTTAACATAACAATGGTTC 58.137 33.333 0.00 0.00 38.45 3.62
2477 2604 8.367156 ACAGCATTTCTTAACATAACAATGGTT 58.633 29.630 0.00 0.00 41.06 3.67
2478 2605 7.895759 ACAGCATTTCTTAACATAACAATGGT 58.104 30.769 0.00 0.00 33.72 3.55
2479 2606 8.028354 TGACAGCATTTCTTAACATAACAATGG 58.972 33.333 0.00 0.00 0.00 3.16
2480 2607 8.969121 TGACAGCATTTCTTAACATAACAATG 57.031 30.769 0.00 0.00 0.00 2.82
2481 2608 9.979578 TTTGACAGCATTTCTTAACATAACAAT 57.020 25.926 0.00 0.00 0.00 2.71
2482 2609 9.809096 TTTTGACAGCATTTCTTAACATAACAA 57.191 25.926 0.00 0.00 0.00 2.83
2483 2610 9.809096 TTTTTGACAGCATTTCTTAACATAACA 57.191 25.926 0.00 0.00 0.00 2.41
2485 2612 8.963130 CGTTTTTGACAGCATTTCTTAACATAA 58.037 29.630 0.00 0.00 0.00 1.90
2486 2613 8.346300 TCGTTTTTGACAGCATTTCTTAACATA 58.654 29.630 0.00 0.00 0.00 2.29
2487 2614 7.199766 TCGTTTTTGACAGCATTTCTTAACAT 58.800 30.769 0.00 0.00 0.00 2.71
2488 2615 6.556212 TCGTTTTTGACAGCATTTCTTAACA 58.444 32.000 0.00 0.00 0.00 2.41
2489 2616 6.910433 TCTCGTTTTTGACAGCATTTCTTAAC 59.090 34.615 0.00 0.00 0.00 2.01
2490 2617 7.022055 TCTCGTTTTTGACAGCATTTCTTAA 57.978 32.000 0.00 0.00 0.00 1.85
2491 2618 6.612247 TCTCGTTTTTGACAGCATTTCTTA 57.388 33.333 0.00 0.00 0.00 2.10
2492 2619 5.499139 TCTCGTTTTTGACAGCATTTCTT 57.501 34.783 0.00 0.00 0.00 2.52
2493 2620 5.066505 AGTTCTCGTTTTTGACAGCATTTCT 59.933 36.000 0.00 0.00 0.00 2.52
2494 2621 5.273944 AGTTCTCGTTTTTGACAGCATTTC 58.726 37.500 0.00 0.00 0.00 2.17
2495 2622 5.248870 AGTTCTCGTTTTTGACAGCATTT 57.751 34.783 0.00 0.00 0.00 2.32
2496 2623 4.900635 AGTTCTCGTTTTTGACAGCATT 57.099 36.364 0.00 0.00 0.00 3.56
2497 2624 6.038271 AGTTTAGTTCTCGTTTTTGACAGCAT 59.962 34.615 0.00 0.00 0.00 3.79
2498 2625 5.353123 AGTTTAGTTCTCGTTTTTGACAGCA 59.647 36.000 0.00 0.00 0.00 4.41
2499 2626 5.807344 AGTTTAGTTCTCGTTTTTGACAGC 58.193 37.500 0.00 0.00 0.00 4.40
2501 2628 9.754382 ACTATAGTTTAGTTCTCGTTTTTGACA 57.246 29.630 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.