Multiple sequence alignment - TraesCS1D01G186100

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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 TraesCS1D01G186100 chr1D 100.000 7005 0 0 1 7005 257005421 256998417 0.000000e+00 12936.0
1 TraesCS1D01G186100 chr1D 88.764 89 10 0 3091 3179 147896324 147896236 7.430000e-20 110.0
2 TraesCS1D01G186100 chr1D 89.873 79 7 1 5481 5558 211633440 211633518 4.470000e-17 100.0
3 TraesCS1D01G186100 chr1A 95.760 3797 106 21 2433 6219 330769982 330766231 0.000000e+00 6069.0
4 TraesCS1D01G186100 chr1A 93.813 1794 54 16 576 2347 330771737 330769979 0.000000e+00 2645.0
5 TraesCS1D01G186100 chr1A 92.990 485 26 4 73 556 330772202 330771725 0.000000e+00 701.0
6 TraesCS1D01G186100 chr1A 93.671 158 9 1 6668 6824 330766209 330766052 1.170000e-57 235.0
7 TraesCS1D01G186100 chr1A 94.118 68 4 0 6938 7005 330765659 330765592 3.460000e-18 104.0
8 TraesCS1D01G186100 chr1B 95.176 2674 84 13 3538 6204 356205742 356208377 0.000000e+00 4181.0
9 TraesCS1D01G186100 chr1B 96.115 1467 32 12 1950 3408 356204296 356205745 0.000000e+00 2370.0
10 TraesCS1D01G186100 chr1B 96.399 1194 35 5 764 1949 356203139 356204332 0.000000e+00 1960.0
11 TraesCS1D01G186100 chr1B 89.474 646 32 13 73 718 356202516 356203125 0.000000e+00 784.0
12 TraesCS1D01G186100 chr1B 92.766 470 22 4 6452 6914 356208904 356209368 0.000000e+00 669.0
13 TraesCS1D01G186100 chr1B 95.279 233 10 1 6217 6448 356208706 356208938 1.110000e-97 368.0
14 TraesCS1D01G186100 chr6D 98.701 231 3 0 1162 1392 245266809 245267039 1.820000e-110 411.0
15 TraesCS1D01G186100 chr6D 95.726 117 4 1 1058 1173 245267039 245267155 3.340000e-43 187.0
16 TraesCS1D01G186100 chr6D 90.909 77 6 1 5483 5558 445217044 445217120 1.240000e-17 102.0
17 TraesCS1D01G186100 chr6D 90.667 75 6 1 5484 5557 47187445 47187519 1.610000e-16 99.0
18 TraesCS1D01G186100 chr6B 97.297 74 2 0 1 74 559511897 559511970 7.380000e-25 126.0
19 TraesCS1D01G186100 chr6B 88.764 89 8 2 3090 3177 85383767 85383680 2.670000e-19 108.0
20 TraesCS1D01G186100 chr6B 90.667 75 6 1 5484 5557 124550587 124550513 1.610000e-16 99.0
21 TraesCS1D01G186100 chr6B 88.608 79 9 0 5470 5548 9661810 9661888 5.780000e-16 97.1
22 TraesCS1D01G186100 chr2B 92.941 85 6 0 3093 3177 247368538 247368622 2.650000e-24 124.0
23 TraesCS1D01G186100 chr4A 91.860 86 7 0 3093 3178 570973516 570973601 3.430000e-23 121.0
24 TraesCS1D01G186100 chr7B 90.698 86 8 0 3093 3178 509568663 509568578 1.600000e-21 115.0
25 TraesCS1D01G186100 chr7B 96.970 66 2 0 5483 5548 559532021 559531956 2.070000e-20 111.0
26 TraesCS1D01G186100 chr5D 89.888 89 6 2 3093 3181 546857278 546857363 2.070000e-20 111.0
27 TraesCS1D01G186100 chr2A 90.476 84 8 0 3093 3176 28816476 28816559 2.070000e-20 111.0
28 TraesCS1D01G186100 chr4B 89.655 87 8 1 3093 3179 612214164 612214249 7.430000e-20 110.0
29 TraesCS1D01G186100 chr7A 90.789 76 6 1 5484 5558 632520559 632520634 4.470000e-17 100.0


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 TraesCS1D01G186100 chr1D 256998417 257005421 7004 True 12936.0 12936 100.0000 1 7005 1 chr1D.!!$R2 7004
1 TraesCS1D01G186100 chr1A 330765592 330772202 6610 True 1950.8 6069 94.0704 73 7005 5 chr1A.!!$R1 6932
2 TraesCS1D01G186100 chr1B 356202516 356209368 6852 False 1722.0 4181 94.2015 73 6914 6 chr1B.!!$F1 6841

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
20 21 0.392193 CCTCGAAGCACCTGAAGCAT 60.392 55.0 0.00 0.0 0.00 3.79 F
1506 1517 0.036732 TCGTTGCTGAGGGATTTGCT 59.963 50.0 0.00 0.0 0.00 3.91 F
2906 2938 0.034089 CCAGAAAAGGCTACTGGGGG 60.034 60.0 20.36 2.9 44.96 5.40 F
3773 3809 0.638292 AATCCCATCACCCATTGCCT 59.362 50.0 0.00 0.0 0.00 4.75 F
3871 3907 0.251341 AAGTGGAATCACACCTGGGC 60.251 55.0 0.00 0.0 45.91 5.36 F
4296 4333 0.615544 TCAAGGGGTATCCGGACGTT 60.616 55.0 6.12 0.0 41.52 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1548 1559 0.544357 CAGGGGAGTGGAGGTACACA 60.544 60.000 0.00 0.0 43.72 3.72 R
2979 3011 0.234625 GCGCAAGTCGTGATGTTTGA 59.765 50.000 0.30 0.0 41.07 2.69 R
3819 3855 0.904865 TCCGCTTCTCCATGAGTGGT 60.905 55.000 10.56 0.0 46.16 4.16 R
5093 5134 1.063717 CCCTGGCCTGGTCATAATTGT 60.064 52.381 25.58 0.0 0.00 2.71 R
5751 5793 1.203994 GCAGAATTGTGAGCATGGCTT 59.796 47.619 6.80 0.0 39.88 4.35 R
6295 6662 4.109050 TGACATGTTTTTCGCAAGGTTTC 58.891 39.130 0.00 0.0 38.47 2.78 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.293498 TCCTCGAAGCACCTGAAGC 59.707 57.895 0.00 0.00 0.00 3.86
19 20 1.004560 CCTCGAAGCACCTGAAGCA 60.005 57.895 0.00 0.00 0.00 3.91
20 21 0.392193 CCTCGAAGCACCTGAAGCAT 60.392 55.000 0.00 0.00 0.00 3.79
21 22 1.134699 CCTCGAAGCACCTGAAGCATA 60.135 52.381 0.00 0.00 0.00 3.14
22 23 2.200067 CTCGAAGCACCTGAAGCATAG 58.800 52.381 0.00 0.00 0.00 2.23
23 24 0.654683 CGAAGCACCTGAAGCATAGC 59.345 55.000 0.00 0.00 0.00 2.97
24 25 1.020437 GAAGCACCTGAAGCATAGCC 58.980 55.000 0.00 0.00 0.00 3.93
25 26 0.394899 AAGCACCTGAAGCATAGCCC 60.395 55.000 0.00 0.00 0.00 5.19
26 27 2.182842 GCACCTGAAGCATAGCCCG 61.183 63.158 0.00 0.00 0.00 6.13
27 28 1.221840 CACCTGAAGCATAGCCCGT 59.778 57.895 0.00 0.00 0.00 5.28
28 29 1.091771 CACCTGAAGCATAGCCCGTG 61.092 60.000 0.00 0.00 0.00 4.94
29 30 1.524621 CCTGAAGCATAGCCCGTGG 60.525 63.158 0.00 0.00 0.00 4.94
30 31 1.522092 CTGAAGCATAGCCCGTGGA 59.478 57.895 0.00 0.00 0.00 4.02
31 32 0.531532 CTGAAGCATAGCCCGTGGAG 60.532 60.000 0.00 0.00 0.00 3.86
32 33 1.227674 GAAGCATAGCCCGTGGAGG 60.228 63.158 0.00 0.00 40.63 4.30
33 34 1.972660 GAAGCATAGCCCGTGGAGGT 61.973 60.000 0.00 0.00 38.74 3.85
34 35 1.972660 AAGCATAGCCCGTGGAGGTC 61.973 60.000 0.00 0.00 38.74 3.85
35 36 2.822399 CATAGCCCGTGGAGGTCC 59.178 66.667 0.00 0.00 38.74 4.46
36 37 2.838225 ATAGCCCGTGGAGGTCCG 60.838 66.667 0.00 0.00 39.43 4.79
37 38 3.674050 ATAGCCCGTGGAGGTCCGT 62.674 63.158 0.00 0.00 39.43 4.69
43 44 2.758737 GTGGAGGTCCGTCGGGAT 60.759 66.667 12.29 0.00 46.14 3.85
44 45 2.758327 TGGAGGTCCGTCGGGATG 60.758 66.667 12.29 0.00 46.14 3.51
45 46 2.441532 GGAGGTCCGTCGGGATGA 60.442 66.667 12.29 0.00 46.14 2.92
46 47 2.056223 GGAGGTCCGTCGGGATGAA 61.056 63.158 12.29 0.00 46.14 2.57
47 48 1.141234 GAGGTCCGTCGGGATGAAC 59.859 63.158 12.29 1.01 46.14 3.18
48 49 2.186125 GGTCCGTCGGGATGAACC 59.814 66.667 12.29 7.42 46.14 3.62
56 57 3.905249 GGGATGAACCGCAACTCC 58.095 61.111 0.00 0.00 40.11 3.85
57 58 2.106683 GGGATGAACCGCAACTCCG 61.107 63.158 0.00 0.00 40.11 4.63
58 59 1.079405 GGATGAACCGCAACTCCGA 60.079 57.895 0.00 0.00 0.00 4.55
59 60 1.084370 GGATGAACCGCAACTCCGAG 61.084 60.000 0.00 0.00 0.00 4.63
60 61 1.079127 ATGAACCGCAACTCCGAGG 60.079 57.895 0.00 0.00 0.00 4.63
61 62 1.541310 ATGAACCGCAACTCCGAGGA 61.541 55.000 0.00 0.00 0.00 3.71
62 63 1.737008 GAACCGCAACTCCGAGGAC 60.737 63.158 0.00 0.00 0.00 3.85
63 64 2.430382 GAACCGCAACTCCGAGGACA 62.430 60.000 0.00 0.00 0.00 4.02
64 65 2.125912 CCGCAACTCCGAGGACAG 60.126 66.667 0.00 0.00 0.00 3.51
65 66 2.125912 CGCAACTCCGAGGACAGG 60.126 66.667 0.00 0.00 0.00 4.00
66 67 2.266055 GCAACTCCGAGGACAGGG 59.734 66.667 0.00 0.00 0.00 4.45
67 68 2.982130 CAACTCCGAGGACAGGGG 59.018 66.667 0.00 0.00 34.75 4.79
68 69 3.003763 AACTCCGAGGACAGGGGC 61.004 66.667 0.00 0.00 30.64 5.80
136 137 8.417273 TCTCCGGTTGATATATTCAAGACATA 57.583 34.615 0.00 0.00 44.89 2.29
163 164 1.322442 GTCGTAGGGTTAGGCCGTAT 58.678 55.000 0.00 0.00 39.49 3.06
177 178 4.887748 AGGCCGTATCATGAGAACATAAG 58.112 43.478 0.09 0.00 35.09 1.73
349 350 8.526978 TGGTTTGTTGAATTATATTGCTAGCAA 58.473 29.630 31.05 31.05 40.47 3.91
432 434 9.300681 TCACAGAATTTCAAAATGATCCTTACT 57.699 29.630 0.00 0.00 0.00 2.24
482 484 9.378551 GATGGAATTAGTAGACATTGTTGTACA 57.621 33.333 10.97 0.00 35.79 2.90
1209 1217 3.678921 CGATTCCATCGCCTACCAA 57.321 52.632 0.00 0.00 46.55 3.67
1260 1271 3.224324 GGGATCGCGTGGAGGCTA 61.224 66.667 5.77 0.00 0.00 3.93
1281 1292 1.139095 GACGCTCCCCTTCTACGTG 59.861 63.158 0.00 0.00 37.05 4.49
1284 1295 1.885163 CGCTCCCCTTCTACGTGGTT 61.885 60.000 0.00 0.00 0.00 3.67
1377 1388 2.042435 CTCTCCCTCCTCGGCCTT 60.042 66.667 0.00 0.00 0.00 4.35
1506 1517 0.036732 TCGTTGCTGAGGGATTTGCT 59.963 50.000 0.00 0.00 0.00 3.91
1513 1524 1.741770 GAGGGATTTGCTGACGCGT 60.742 57.895 13.85 13.85 39.65 6.01
1548 1559 3.060602 GCGTGAGTACAAGCTTCTCTTT 58.939 45.455 13.15 0.00 45.26 2.52
2018 2034 7.581476 TGTAAAAGGAGTTTGCGATTCTTTAG 58.419 34.615 0.00 0.00 34.77 1.85
2058 2074 3.861276 ATGATGTGTTCATGCAGTTGG 57.139 42.857 0.00 0.00 43.60 3.77
2223 2239 4.655649 TCCTGGAGATGTATATGTGCTGTT 59.344 41.667 0.00 0.00 0.00 3.16
2224 2240 4.753610 CCTGGAGATGTATATGTGCTGTTG 59.246 45.833 0.00 0.00 0.00 3.33
2345 2371 8.970859 ATCAACCTTCCTCTATTGTCTAATTG 57.029 34.615 0.00 0.00 0.00 2.32
2387 2414 9.959749 TGTATTGGAATTTAAAGTTGAGTTGAC 57.040 29.630 0.00 0.00 0.00 3.18
2518 2545 4.664150 TTTCAATTCCAGTCCCAAACAC 57.336 40.909 0.00 0.00 0.00 3.32
2621 2649 4.044065 ACCTGTCATTCCCATTCCTGTTAA 59.956 41.667 0.00 0.00 0.00 2.01
2793 2825 3.005554 AGATTCAAACGAGATGGTGCAG 58.994 45.455 0.00 0.00 0.00 4.41
2836 2868 7.370383 TGAAGATACAGGAATTTGCTTTGTTC 58.630 34.615 0.00 0.00 0.00 3.18
2882 2914 3.498481 CCAGATCCCAGGACTCACAAAAA 60.498 47.826 0.00 0.00 0.00 1.94
2906 2938 0.034089 CCAGAAAAGGCTACTGGGGG 60.034 60.000 20.36 2.90 44.96 5.40
2979 3011 4.461781 CAGGATCTCACCTCATTTTGCTTT 59.538 41.667 0.00 0.00 38.32 3.51
3047 3079 0.790207 AATTGCTCACGTACACTGCG 59.210 50.000 0.00 0.00 0.00 5.18
3120 3152 5.987347 CCATCCGTACCAAAATATAAGACGT 59.013 40.000 0.00 0.00 0.00 4.34
3157 3189 6.991485 ATTGAACTGCAAAAACGTCTTATG 57.009 33.333 0.00 0.00 40.48 1.90
3171 3203 6.092955 ACGTCTTATGTTTTGGTACAGAGA 57.907 37.500 0.00 0.00 42.39 3.10
3199 3231 1.269051 TGGCTGCGTATGTAGATGACG 60.269 52.381 3.98 0.00 39.55 4.35
3462 3496 4.635765 TGTATGATTCCAGCTAAGTTGCAC 59.364 41.667 0.00 0.00 34.99 4.57
3492 3526 7.398829 ACAACAATACAGATACCACAATACCA 58.601 34.615 0.00 0.00 0.00 3.25
3536 3570 9.595823 AAATACGCAGATACGGCTAATAAATAT 57.404 29.630 0.00 0.00 37.37 1.28
3598 3632 3.445805 GGAAAAACGATAATTCAGGGGCA 59.554 43.478 0.00 0.00 0.00 5.36
3599 3633 4.099419 GGAAAAACGATAATTCAGGGGCAT 59.901 41.667 0.00 0.00 0.00 4.40
3608 3642 6.540189 CGATAATTCAGGGGCATCCTTATTAG 59.460 42.308 11.66 0.00 45.47 1.73
3672 3706 1.338389 GCATGGCTGATTTTGGCAAGT 60.338 47.619 0.00 0.00 43.05 3.16
3773 3809 0.638292 AATCCCATCACCCATTGCCT 59.362 50.000 0.00 0.00 0.00 4.75
3785 3821 4.931002 CACCCATTGCCTTTGTAAAATCAG 59.069 41.667 0.00 0.00 0.00 2.90
3819 3855 2.947652 GCATAGAAATGAGCAGAGGCAA 59.052 45.455 0.00 0.00 36.62 4.52
3871 3907 0.251341 AAGTGGAATCACACCTGGGC 60.251 55.000 0.00 0.00 45.91 5.36
3872 3908 1.074775 GTGGAATCACACCTGGGCA 59.925 57.895 0.00 0.00 43.13 5.36
4009 4045 2.185350 CAACGGCCGCTCATCTCT 59.815 61.111 28.58 0.00 0.00 3.10
4024 4060 3.131223 TCATCTCTTTCTCTAGGTTGGCG 59.869 47.826 0.00 0.00 0.00 5.69
4047 4083 2.819608 TGAGCAGTGGTAGATTTTTGGC 59.180 45.455 0.00 0.00 0.00 4.52
4229 4266 4.566837 TCACCAGGTATCTCCACCATATT 58.433 43.478 0.00 0.00 41.40 1.28
4296 4333 0.615544 TCAAGGGGTATCCGGACGTT 60.616 55.000 6.12 0.00 41.52 3.99
4299 4336 1.406903 AGGGGTATCCGGACGTTTAG 58.593 55.000 6.12 0.00 41.52 1.85
4306 4343 1.078918 CCGGACGTTTAGAACCCCC 60.079 63.158 0.00 0.00 0.00 5.40
4307 4344 1.547472 CCGGACGTTTAGAACCCCCT 61.547 60.000 0.00 0.00 0.00 4.79
4437 4475 5.519808 AGTACCACTGGATCTGAGATTGTA 58.480 41.667 0.71 0.00 0.00 2.41
4485 4524 9.875675 GATAGTAAAGTGAAATGATGCATCTTC 57.124 33.333 26.32 21.42 0.00 2.87
4487 4526 5.885230 AAAGTGAAATGATGCATCTTCGA 57.115 34.783 26.32 7.58 0.00 3.71
4539 4578 5.547465 TGGCCACTATGTTTCTTATATCGG 58.453 41.667 0.00 0.00 0.00 4.18
4587 4626 9.646427 TGTTTAATTGCTTCTTTAACACTTTGT 57.354 25.926 0.00 0.00 0.00 2.83
4594 4633 8.850454 TGCTTCTTTAACACTTTGTACAATTC 57.150 30.769 9.56 0.00 0.00 2.17
4660 4699 1.467920 GGCCCAAATCACCTGAAGAG 58.532 55.000 0.00 0.00 0.00 2.85
4678 4717 9.170734 CCTGAAGAGATGATAACAATTCTTCAA 57.829 33.333 21.74 12.68 46.22 2.69
4809 4848 2.926200 CACTTGAAGCTGATCAGGTACG 59.074 50.000 26.71 16.71 37.52 3.67
4874 4915 4.702612 TGTTTGTGCTTTGGTTGTAGAAGA 59.297 37.500 0.00 0.00 0.00 2.87
4875 4916 5.163663 TGTTTGTGCTTTGGTTGTAGAAGAG 60.164 40.000 0.00 0.00 0.00 2.85
4880 4921 5.351740 GTGCTTTGGTTGTAGAAGAGTATCC 59.648 44.000 0.00 0.00 33.66 2.59
5093 5134 8.735692 TTCATGATAGCACTGATTTAATCACA 57.264 30.769 3.20 0.00 35.06 3.58
5143 5184 6.462500 CAGATGAGAGAGGAACAAGAAAGAA 58.538 40.000 0.00 0.00 0.00 2.52
5329 5370 5.345202 ACTCGAGTATGTTTAACGCTCTTTG 59.655 40.000 18.46 0.00 0.00 2.77
5353 5394 2.228822 CGCTATCAACAACCTTTTGCCT 59.771 45.455 0.00 0.00 36.00 4.75
5462 5503 6.659242 AGTGTAGTACCTTATGCTGCATTTTT 59.341 34.615 21.56 5.77 37.90 1.94
5517 5559 6.540205 GTTCCATAATACTTGTCGTGGTTTC 58.460 40.000 0.00 0.00 0.00 2.78
5546 5588 9.658799 TTCAAATTTGAACTAAAACCATGACAA 57.341 25.926 26.01 1.80 41.88 3.18
5547 5589 9.311916 TCAAATTTGAACTAAAACCATGACAAG 57.688 29.630 18.45 0.00 33.55 3.16
5548 5590 7.713764 AATTTGAACTAAAACCATGACAAGC 57.286 32.000 0.00 0.00 0.00 4.01
5549 5591 6.463995 TTTGAACTAAAACCATGACAAGCT 57.536 33.333 0.00 0.00 0.00 3.74
5550 5592 6.463995 TTGAACTAAAACCATGACAAGCTT 57.536 33.333 0.00 0.00 0.00 3.74
5551 5593 7.575414 TTGAACTAAAACCATGACAAGCTTA 57.425 32.000 0.00 0.00 0.00 3.09
5552 5594 7.759489 TGAACTAAAACCATGACAAGCTTAT 57.241 32.000 0.00 0.00 0.00 1.73
5553 5595 7.592938 TGAACTAAAACCATGACAAGCTTATG 58.407 34.615 0.00 0.00 0.00 1.90
5554 5596 6.515272 ACTAAAACCATGACAAGCTTATGG 57.485 37.500 20.58 20.58 45.37 2.74
5630 5672 3.506067 GGGACACATCGTTCCTGAATTTT 59.494 43.478 0.00 0.00 40.69 1.82
5751 5793 4.407621 TCACAGGTCTTTGAACTAACTCCA 59.592 41.667 0.00 0.00 0.00 3.86
6011 6053 6.471233 TCGAGATAGAACAATGAATGTCCT 57.529 37.500 0.00 0.00 42.99 3.85
6119 6161 5.293569 GCTGTACGGCAATATACTTGACTTT 59.706 40.000 21.95 0.00 0.00 2.66
6145 6187 3.196463 CAAATGCTGCTTTTGTGGTTCA 58.804 40.909 24.65 0.00 31.05 3.18
6243 6610 5.499139 TTCTGTGGTTGTGTTCTTGAATC 57.501 39.130 0.00 0.00 0.00 2.52
6244 6611 4.780815 TCTGTGGTTGTGTTCTTGAATCT 58.219 39.130 0.00 0.00 0.00 2.40
6324 6691 4.707563 TGCGAAAAACATGTCAGTAATCG 58.292 39.130 0.00 5.52 0.00 3.34
6375 6742 0.108472 TTGCGGATCTGTGCTGAGAG 60.108 55.000 2.89 0.00 0.00 3.20
6386 6753 0.468226 TGCTGAGAGGTTGAACGGTT 59.532 50.000 0.00 0.00 0.00 4.44
6387 6754 0.868406 GCTGAGAGGTTGAACGGTTG 59.132 55.000 0.00 0.00 0.00 3.77
6396 6763 5.047590 AGAGGTTGAACGGTTGAAAGTTTTT 60.048 36.000 0.00 0.00 0.00 1.94
6410 6777 5.928839 TGAAAGTTTTTGCACTTGTGCTTTA 59.071 32.000 23.53 8.93 37.07 1.85
6411 6778 6.090628 TGAAAGTTTTTGCACTTGTGCTTTAG 59.909 34.615 23.53 0.00 37.07 1.85
6412 6779 3.865164 AGTTTTTGCACTTGTGCTTTAGC 59.135 39.130 23.53 12.58 42.50 3.09
6413 6780 6.082027 AAGTTTTTGCACTTGTGCTTTAGCA 61.082 36.000 23.53 0.00 41.18 3.49
6414 6781 7.508741 AAGTTTTTGCACTTGTGCTTTAGCAA 61.509 34.615 23.53 8.26 40.81 3.91
6415 6782 8.904306 AAGTTTTTGCACTTGTGCTTTAGCAAA 61.904 33.333 23.53 13.08 46.38 3.68
6424 6791 1.128513 GCTTTAGCAAACGGTTGTGC 58.871 50.000 15.84 15.50 41.59 4.57
6428 6795 2.412937 GCAAACGGTTGTGCTGCT 59.587 55.556 15.84 0.00 37.78 4.24
6429 6796 1.658409 GCAAACGGTTGTGCTGCTC 60.658 57.895 15.84 0.00 37.78 4.26
6430 6797 2.024918 CAAACGGTTGTGCTGCTCT 58.975 52.632 4.63 0.00 0.00 4.09
6431 6798 1.225855 CAAACGGTTGTGCTGCTCTA 58.774 50.000 4.63 0.00 0.00 2.43
6432 6799 1.195448 CAAACGGTTGTGCTGCTCTAG 59.805 52.381 4.63 0.00 0.00 2.43
6433 6800 0.393077 AACGGTTGTGCTGCTCTAGT 59.607 50.000 0.00 0.00 0.00 2.57
6434 6801 0.319900 ACGGTTGTGCTGCTCTAGTG 60.320 55.000 0.00 0.00 0.00 2.74
6435 6802 0.038251 CGGTTGTGCTGCTCTAGTGA 60.038 55.000 0.00 0.00 0.00 3.41
6436 6803 1.404717 CGGTTGTGCTGCTCTAGTGAT 60.405 52.381 0.00 0.00 0.00 3.06
6437 6804 2.005451 GGTTGTGCTGCTCTAGTGATG 58.995 52.381 0.00 0.00 0.00 3.07
6438 6805 2.005451 GTTGTGCTGCTCTAGTGATGG 58.995 52.381 0.00 0.00 0.00 3.51
6439 6806 1.560505 TGTGCTGCTCTAGTGATGGA 58.439 50.000 0.00 0.00 0.00 3.41
6440 6807 2.113807 TGTGCTGCTCTAGTGATGGAT 58.886 47.619 0.00 0.00 0.00 3.41
6441 6808 2.159000 TGTGCTGCTCTAGTGATGGATG 60.159 50.000 0.00 0.00 0.00 3.51
6442 6809 2.102084 GTGCTGCTCTAGTGATGGATGA 59.898 50.000 0.00 0.00 0.00 2.92
6443 6810 2.767960 TGCTGCTCTAGTGATGGATGAA 59.232 45.455 0.00 0.00 0.00 2.57
6444 6811 3.181468 TGCTGCTCTAGTGATGGATGAAG 60.181 47.826 0.00 0.00 0.00 3.02
6445 6812 3.069300 GCTGCTCTAGTGATGGATGAAGA 59.931 47.826 0.00 0.00 0.00 2.87
6446 6813 4.619973 CTGCTCTAGTGATGGATGAAGAC 58.380 47.826 0.00 0.00 0.00 3.01
6447 6814 4.285020 TGCTCTAGTGATGGATGAAGACT 58.715 43.478 0.00 0.00 0.00 3.24
6448 6815 5.449553 TGCTCTAGTGATGGATGAAGACTA 58.550 41.667 0.00 0.00 0.00 2.59
6449 6816 5.893824 TGCTCTAGTGATGGATGAAGACTAA 59.106 40.000 0.00 0.00 0.00 2.24
6450 6817 6.552725 TGCTCTAGTGATGGATGAAGACTAAT 59.447 38.462 0.00 0.00 0.00 1.73
6535 6903 1.447317 AAACGGTTGTGCTGCTCCAG 61.447 55.000 0.00 0.00 34.12 3.86
6546 6914 2.284190 GCTGCTCCAGTAATGAAGACC 58.716 52.381 0.00 0.00 33.43 3.85
6556 6924 6.761242 TCCAGTAATGAAGACCACGAATAATG 59.239 38.462 0.00 0.00 0.00 1.90
6581 6949 4.144297 TCTGGAGGGTCAACAAATTCTTG 58.856 43.478 0.00 0.00 38.61 3.02
6641 7009 7.554211 TGCATGTAAATCTTCATTGGCAATTA 58.446 30.769 10.65 0.00 0.00 1.40
6712 7080 9.436957 TTGTTCTTTAGGAGCTAAACTATTCTG 57.563 33.333 0.00 0.00 33.19 3.02
6718 7086 4.049869 GGAGCTAAACTATTCTGTACGCC 58.950 47.826 0.00 0.00 0.00 5.68
6838 7400 7.773224 TGTTTTTGACCTTCTCAGACATTCTTA 59.227 33.333 0.00 0.00 0.00 2.10
6841 7403 5.087323 TGACCTTCTCAGACATTCTTAGGT 58.913 41.667 0.00 0.00 0.00 3.08
6863 7426 1.069227 GCAGTTTCAAGTTACCCGCTG 60.069 52.381 0.00 0.00 0.00 5.18
6870 7433 4.832608 GTTACCCGCTGCTCCCGG 62.833 72.222 0.00 0.00 45.17 5.73
6887 7455 1.128692 CCGGAAACTCGAAAGATGTGC 59.871 52.381 0.00 0.00 40.84 4.57
6918 7486 8.856153 TTAGACATATTTGAAACTTAGCCACA 57.144 30.769 0.00 0.00 0.00 4.17
6919 7487 7.759489 AGACATATTTGAAACTTAGCCACAA 57.241 32.000 0.00 0.00 0.00 3.33
6925 7493 9.905713 ATATTTGAAACTTAGCCACAATCTAGA 57.094 29.630 0.00 0.00 0.00 2.43
6926 7494 7.672983 TTTGAAACTTAGCCACAATCTAGAG 57.327 36.000 0.00 0.00 0.00 2.43
6930 7498 6.360370 AACTTAGCCACAATCTAGAGACAA 57.640 37.500 0.00 0.00 0.00 3.18
6934 7502 5.426689 AGCCACAATCTAGAGACAATCAA 57.573 39.130 0.00 0.00 0.00 2.57
6935 7503 5.426504 AGCCACAATCTAGAGACAATCAAG 58.573 41.667 0.00 0.00 0.00 3.02
6936 7504 4.574013 GCCACAATCTAGAGACAATCAAGG 59.426 45.833 0.00 0.00 0.00 3.61
6962 7616 1.459592 CTTACTGTTGCCGTCGGAAAG 59.540 52.381 17.49 1.76 0.00 2.62
7002 7656 3.328505 CCCATGACAAAAGAAATGCCAC 58.671 45.455 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.293498 GCTTCAGGTGCTTCGAGGA 59.707 57.895 0.00 0.00 0.00 3.71
1 2 0.392193 ATGCTTCAGGTGCTTCGAGG 60.392 55.000 0.00 0.00 0.00 4.63
2 3 2.200067 CTATGCTTCAGGTGCTTCGAG 58.800 52.381 0.00 0.00 0.00 4.04
3 4 1.740380 GCTATGCTTCAGGTGCTTCGA 60.740 52.381 0.00 0.00 0.00 3.71
4 5 0.654683 GCTATGCTTCAGGTGCTTCG 59.345 55.000 0.00 0.00 0.00 3.79
5 6 1.020437 GGCTATGCTTCAGGTGCTTC 58.980 55.000 0.00 0.00 0.00 3.86
6 7 0.394899 GGGCTATGCTTCAGGTGCTT 60.395 55.000 0.00 0.00 0.00 3.91
7 8 1.225704 GGGCTATGCTTCAGGTGCT 59.774 57.895 0.00 0.00 0.00 4.40
8 9 2.182842 CGGGCTATGCTTCAGGTGC 61.183 63.158 0.00 0.00 0.00 5.01
9 10 1.091771 CACGGGCTATGCTTCAGGTG 61.092 60.000 0.00 0.00 0.00 4.00
10 11 1.221840 CACGGGCTATGCTTCAGGT 59.778 57.895 0.00 0.00 0.00 4.00
11 12 1.524621 CCACGGGCTATGCTTCAGG 60.525 63.158 0.00 0.00 0.00 3.86
12 13 0.531532 CTCCACGGGCTATGCTTCAG 60.532 60.000 0.00 0.00 0.00 3.02
13 14 1.522092 CTCCACGGGCTATGCTTCA 59.478 57.895 0.00 0.00 0.00 3.02
14 15 1.227674 CCTCCACGGGCTATGCTTC 60.228 63.158 0.00 0.00 0.00 3.86
15 16 1.972660 GACCTCCACGGGCTATGCTT 61.973 60.000 0.00 0.00 38.04 3.91
16 17 2.365635 ACCTCCACGGGCTATGCT 60.366 61.111 0.00 0.00 36.97 3.79
17 18 2.109181 GACCTCCACGGGCTATGC 59.891 66.667 0.00 0.00 38.04 3.14
18 19 2.822399 GGACCTCCACGGGCTATG 59.178 66.667 0.00 0.00 42.26 2.23
19 20 2.838225 CGGACCTCCACGGGCTAT 60.838 66.667 0.00 0.00 42.26 2.97
20 21 4.371417 ACGGACCTCCACGGGCTA 62.371 66.667 0.00 0.00 42.26 3.93
26 27 2.758737 ATCCCGACGGACCTCCAC 60.759 66.667 17.49 0.00 42.48 4.02
27 28 2.758327 CATCCCGACGGACCTCCA 60.758 66.667 17.49 0.00 42.48 3.86
28 29 2.056223 TTCATCCCGACGGACCTCC 61.056 63.158 17.49 0.00 42.48 4.30
29 30 1.141234 GTTCATCCCGACGGACCTC 59.859 63.158 17.49 0.00 42.48 3.85
30 31 2.356780 GGTTCATCCCGACGGACCT 61.357 63.158 17.49 0.00 42.48 3.85
31 32 2.186125 GGTTCATCCCGACGGACC 59.814 66.667 17.49 10.93 42.48 4.46
39 40 2.106683 CGGAGTTGCGGTTCATCCC 61.107 63.158 0.00 0.00 0.00 3.85
40 41 1.079405 TCGGAGTTGCGGTTCATCC 60.079 57.895 0.00 0.00 0.00 3.51
41 42 1.084370 CCTCGGAGTTGCGGTTCATC 61.084 60.000 4.02 0.00 0.00 2.92
42 43 1.079127 CCTCGGAGTTGCGGTTCAT 60.079 57.895 4.02 0.00 0.00 2.57
43 44 2.204461 TCCTCGGAGTTGCGGTTCA 61.204 57.895 4.02 0.00 0.00 3.18
44 45 1.737008 GTCCTCGGAGTTGCGGTTC 60.737 63.158 4.02 0.00 0.00 3.62
45 46 2.342648 GTCCTCGGAGTTGCGGTT 59.657 61.111 4.02 0.00 0.00 4.44
46 47 2.915659 TGTCCTCGGAGTTGCGGT 60.916 61.111 4.02 0.00 0.00 5.68
47 48 2.125912 CTGTCCTCGGAGTTGCGG 60.126 66.667 4.02 0.00 0.00 5.69
48 49 2.125912 CCTGTCCTCGGAGTTGCG 60.126 66.667 4.02 0.00 0.00 4.85
49 50 2.266055 CCCTGTCCTCGGAGTTGC 59.734 66.667 4.02 0.00 0.00 4.17
50 51 2.982130 CCCCTGTCCTCGGAGTTG 59.018 66.667 4.02 0.00 0.00 3.16
51 52 3.003763 GCCCCTGTCCTCGGAGTT 61.004 66.667 4.02 0.00 0.00 3.01
65 66 3.244281 AACTACAACCGGGTCGCCC 62.244 63.158 6.32 4.96 41.09 6.13
66 67 1.739196 GAACTACAACCGGGTCGCC 60.739 63.158 6.32 0.00 0.00 5.54
67 68 0.320160 AAGAACTACAACCGGGTCGC 60.320 55.000 6.32 0.00 0.00 5.19
68 69 1.670967 GGAAGAACTACAACCGGGTCG 60.671 57.143 6.32 0.00 0.00 4.79
69 70 1.622312 AGGAAGAACTACAACCGGGTC 59.378 52.381 6.32 0.00 0.00 4.46
70 71 1.346722 CAGGAAGAACTACAACCGGGT 59.653 52.381 6.32 0.00 0.00 5.28
71 72 1.346722 ACAGGAAGAACTACAACCGGG 59.653 52.381 6.32 0.00 0.00 5.73
136 137 3.754850 GCCTAACCCTACGACATTGTTTT 59.245 43.478 0.00 0.00 0.00 2.43
177 178 1.594836 TGGTGACGCGGGTAAACAC 60.595 57.895 12.47 8.87 0.00 3.32
185 186 2.202878 CTATGGGTGGTGACGCGG 60.203 66.667 12.47 0.00 43.50 6.46
431 433 9.214957 TCAACACCTTTGTTACATATTGAGTAG 57.785 33.333 0.00 0.00 44.57 2.57
432 434 9.733556 ATCAACACCTTTGTTACATATTGAGTA 57.266 29.630 0.00 0.00 44.57 2.59
433 435 8.514594 CATCAACACCTTTGTTACATATTGAGT 58.485 33.333 0.00 0.00 44.57 3.41
434 436 7.970061 CCATCAACACCTTTGTTACATATTGAG 59.030 37.037 0.00 0.00 44.57 3.02
435 437 7.667635 TCCATCAACACCTTTGTTACATATTGA 59.332 33.333 0.00 0.00 44.57 2.57
436 438 7.825681 TCCATCAACACCTTTGTTACATATTG 58.174 34.615 0.00 0.00 44.57 1.90
437 439 8.415950 TTCCATCAACACCTTTGTTACATATT 57.584 30.769 0.00 0.00 44.57 1.28
438 440 8.593945 ATTCCATCAACACCTTTGTTACATAT 57.406 30.769 0.00 0.00 44.57 1.78
482 484 8.608844 TCCCGCAACAAAATAACAATTTAATT 57.391 26.923 0.00 0.00 0.00 1.40
562 564 4.401837 ACTGTTACTTGGCCCGTTTAAAAA 59.598 37.500 0.00 0.00 0.00 1.94
563 565 3.952967 ACTGTTACTTGGCCCGTTTAAAA 59.047 39.130 0.00 0.00 0.00 1.52
564 566 3.553904 ACTGTTACTTGGCCCGTTTAAA 58.446 40.909 0.00 0.00 0.00 1.52
565 567 3.211718 ACTGTTACTTGGCCCGTTTAA 57.788 42.857 0.00 0.00 0.00 1.52
566 568 2.934886 ACTGTTACTTGGCCCGTTTA 57.065 45.000 0.00 0.00 0.00 2.01
567 569 2.369532 TCTACTGTTACTTGGCCCGTTT 59.630 45.455 0.00 0.00 0.00 3.60
568 570 1.972795 TCTACTGTTACTTGGCCCGTT 59.027 47.619 0.00 0.00 0.00 4.44
569 571 1.636148 TCTACTGTTACTTGGCCCGT 58.364 50.000 0.00 0.00 0.00 5.28
570 572 2.754946 TTCTACTGTTACTTGGCCCG 57.245 50.000 0.00 0.00 0.00 6.13
571 573 4.216411 TGATTCTACTGTTACTTGGCCC 57.784 45.455 0.00 0.00 0.00 5.80
572 574 4.092968 CGTTGATTCTACTGTTACTTGGCC 59.907 45.833 0.00 0.00 0.00 5.36
573 575 4.092968 CCGTTGATTCTACTGTTACTTGGC 59.907 45.833 0.00 0.00 0.00 4.52
574 576 5.475719 TCCGTTGATTCTACTGTTACTTGG 58.524 41.667 0.00 0.00 0.00 3.61
575 577 6.387465 TCTCCGTTGATTCTACTGTTACTTG 58.613 40.000 0.00 0.00 0.00 3.16
576 578 6.585695 TCTCCGTTGATTCTACTGTTACTT 57.414 37.500 0.00 0.00 0.00 2.24
580 582 5.209818 TGTTCTCCGTTGATTCTACTGTT 57.790 39.130 0.00 0.00 0.00 3.16
654 656 8.731275 TTCTGTTGAATTCTTTGAGTAGAACA 57.269 30.769 7.05 4.75 37.00 3.18
1110 1118 2.359169 GGTGATGGAGGAGACGGCA 61.359 63.158 0.00 0.00 0.00 5.69
1260 1271 1.313812 CGTAGAAGGGGAGCGTCACT 61.314 60.000 0.00 0.00 0.00 3.41
1548 1559 0.544357 CAGGGGAGTGGAGGTACACA 60.544 60.000 0.00 0.00 43.72 3.72
1778 1789 4.924305 AATTGATGAGCACAACAACACT 57.076 36.364 8.88 0.00 40.49 3.55
2058 2074 9.088512 CCACAGATCTGTAACTATTGTTCTAAC 57.911 37.037 27.44 0.00 42.83 2.34
2152 2168 7.522236 GCAATTATATTCTGAAGGTAGGCCAAC 60.522 40.741 5.01 0.00 37.19 3.77
2387 2414 6.992063 AACTGCACTATTTAATCTCACCTG 57.008 37.500 0.00 0.00 0.00 4.00
2518 2545 3.766545 TCCCAAGGGAGAACATTTCAAG 58.233 45.455 3.04 0.00 39.76 3.02
2621 2649 9.253832 TGGTATGTTAGATTCATTCAAATTGGT 57.746 29.630 0.00 0.00 0.00 3.67
2793 2825 6.877611 TCTTCAGAAATAAAGTCCCACAAC 57.122 37.500 0.00 0.00 0.00 3.32
2836 2868 7.729881 TGGATTGATAAAAATATCTTGGGGAGG 59.270 37.037 0.00 0.00 0.00 4.30
2948 2980 1.008815 AGGTGAGATCCTGGACCATGA 59.991 52.381 0.00 1.58 36.35 3.07
2979 3011 0.234625 GCGCAAGTCGTGATGTTTGA 59.765 50.000 0.30 0.00 41.07 2.69
3047 3079 4.270325 GGTAGTAATTGGACGCAATCAGAC 59.730 45.833 0.00 0.00 0.00 3.51
3157 3189 6.702282 GCCATCTACTATCTCTGTACCAAAAC 59.298 42.308 0.00 0.00 0.00 2.43
3171 3203 5.254115 TCTACATACGCAGCCATCTACTAT 58.746 41.667 0.00 0.00 0.00 2.12
3462 3496 6.277605 TGTGGTATCTGTATTGTTGTATCCG 58.722 40.000 0.00 0.00 0.00 4.18
3546 3580 7.175467 TCCCATGTGCAAATCATCAATATCTAC 59.825 37.037 0.00 0.00 0.00 2.59
3608 3642 7.703621 AGCAAGCAACATCATAACAATTATCAC 59.296 33.333 0.00 0.00 0.00 3.06
3672 3706 4.090819 GGGCTTAGAAACAATGGGGTTTA 58.909 43.478 0.00 0.00 40.85 2.01
3801 3837 2.305635 TGGTTGCCTCTGCTCATTTCTA 59.694 45.455 0.00 0.00 38.71 2.10
3819 3855 0.904865 TCCGCTTCTCCATGAGTGGT 60.905 55.000 10.56 0.00 46.16 4.16
3871 3907 1.153208 GCTCCATCTCACCCAGCTG 60.153 63.158 6.78 6.78 0.00 4.24
3872 3908 1.614525 TGCTCCATCTCACCCAGCT 60.615 57.895 0.00 0.00 0.00 4.24
3997 4033 2.288152 CCTAGAGAAAGAGATGAGCGGC 60.288 54.545 0.00 0.00 0.00 6.53
4009 4045 2.870435 GCTCAACGCCAACCTAGAGAAA 60.870 50.000 0.00 0.00 0.00 2.52
4024 4060 4.798574 CCAAAAATCTACCACTGCTCAAC 58.201 43.478 0.00 0.00 0.00 3.18
4033 4069 4.794655 GCAACGAAAGCCAAAAATCTACCA 60.795 41.667 0.00 0.00 0.00 3.25
4204 4241 4.002256 TGGTGGAGATACCTGGTGATAA 57.998 45.455 10.23 0.00 41.43 1.75
4248 4285 4.093011 TCGGGTCATTTTCCATTTTCCAT 58.907 39.130 0.00 0.00 0.00 3.41
4296 4333 2.840511 TCAGCATACAGGGGGTTCTAA 58.159 47.619 0.00 0.00 0.00 2.10
4299 4336 2.736670 AATCAGCATACAGGGGGTTC 57.263 50.000 0.00 0.00 0.00 3.62
4306 4343 2.162208 ACGGCACAAAATCAGCATACAG 59.838 45.455 0.00 0.00 0.00 2.74
4307 4344 2.158559 ACGGCACAAAATCAGCATACA 58.841 42.857 0.00 0.00 0.00 2.29
4485 4524 3.991773 TCCAAACGACCACTATTCTTTCG 59.008 43.478 0.00 0.00 35.80 3.46
4487 4526 6.894339 AAATCCAAACGACCACTATTCTTT 57.106 33.333 0.00 0.00 0.00 2.52
4494 4533 4.755123 CAGTTCTAAATCCAAACGACCACT 59.245 41.667 0.00 0.00 0.00 4.00
4539 4578 5.350640 ACAACAGTCTAACGCTTTAATAGGC 59.649 40.000 0.00 0.00 0.00 3.93
4587 4626 5.688823 CATGAGCAAAACTGACGAATTGTA 58.311 37.500 0.00 0.00 0.00 2.41
4588 4627 4.539870 CATGAGCAAAACTGACGAATTGT 58.460 39.130 0.00 0.00 0.00 2.71
4589 4628 3.362831 GCATGAGCAAAACTGACGAATTG 59.637 43.478 0.00 0.00 41.58 2.32
4590 4629 3.568538 GCATGAGCAAAACTGACGAATT 58.431 40.909 0.00 0.00 41.58 2.17
4621 4660 2.359900 CCCTCAACCTTTGGAAGATCG 58.640 52.381 0.00 0.00 0.00 3.69
4678 4717 5.050091 CGTAGTGCATTCTTCAACAACTCTT 60.050 40.000 0.00 0.00 0.00 2.85
4880 4921 7.338710 TCCTTTCTTACCATTAGACAGGAATG 58.661 38.462 5.52 0.00 42.64 2.67
5093 5134 1.063717 CCCTGGCCTGGTCATAATTGT 60.064 52.381 25.58 0.00 0.00 2.71
5143 5184 1.450312 CCGCGGCCTCTCTTTCAAT 60.450 57.895 14.67 0.00 0.00 2.57
5329 5370 2.979813 CAAAAGGTTGTTGATAGCGTGC 59.020 45.455 0.00 0.00 0.00 5.34
5536 5578 3.763897 GGTTCCATAAGCTTGTCATGGTT 59.236 43.478 21.03 8.09 40.18 3.67
5537 5579 3.245229 TGGTTCCATAAGCTTGTCATGGT 60.245 43.478 21.03 0.00 40.18 3.55
5538 5580 3.355378 TGGTTCCATAAGCTTGTCATGG 58.645 45.455 17.40 17.40 40.55 3.66
5539 5581 4.641541 TCATGGTTCCATAAGCTTGTCATG 59.358 41.667 9.86 11.70 38.62 3.07
5540 5582 4.641989 GTCATGGTTCCATAAGCTTGTCAT 59.358 41.667 9.86 0.00 38.62 3.06
5541 5583 4.009675 GTCATGGTTCCATAAGCTTGTCA 58.990 43.478 9.86 0.00 38.62 3.58
5542 5584 4.009675 TGTCATGGTTCCATAAGCTTGTC 58.990 43.478 9.86 0.00 38.62 3.18
5543 5585 4.032960 TGTCATGGTTCCATAAGCTTGT 57.967 40.909 9.86 0.00 38.62 3.16
5544 5586 4.676196 GCTTGTCATGGTTCCATAAGCTTG 60.676 45.833 21.13 6.05 38.77 4.01
5545 5587 3.445096 GCTTGTCATGGTTCCATAAGCTT 59.555 43.478 21.13 3.48 34.91 3.74
5546 5588 3.019564 GCTTGTCATGGTTCCATAAGCT 58.980 45.455 21.13 0.00 34.91 3.74
5547 5589 2.754552 TGCTTGTCATGGTTCCATAAGC 59.245 45.455 21.40 21.40 36.69 3.09
5548 5590 5.587388 AATGCTTGTCATGGTTCCATAAG 57.413 39.130 3.88 6.30 35.13 1.73
5549 5591 6.040729 CCATAATGCTTGTCATGGTTCCATAA 59.959 38.462 3.88 0.00 35.13 1.90
5550 5592 5.535783 CCATAATGCTTGTCATGGTTCCATA 59.464 40.000 3.88 0.00 35.13 2.74
5551 5593 4.342951 CCATAATGCTTGTCATGGTTCCAT 59.657 41.667 0.00 0.00 35.13 3.41
5552 5594 3.700539 CCATAATGCTTGTCATGGTTCCA 59.299 43.478 0.00 0.00 35.13 3.53
5553 5595 3.953612 TCCATAATGCTTGTCATGGTTCC 59.046 43.478 0.00 0.00 39.21 3.62
5554 5596 5.343249 GTTCCATAATGCTTGTCATGGTTC 58.657 41.667 0.00 0.00 39.21 3.62
5630 5672 8.088365 GCAGGTCATGTGTACACAGATAATATA 58.912 37.037 30.65 7.07 45.48 0.86
5640 5682 5.007039 CAGATAATGCAGGTCATGTGTACAC 59.993 44.000 19.36 19.36 35.13 2.90
5709 5751 5.968254 TGTGACCAAATTATGACGCTACTA 58.032 37.500 0.00 0.00 0.00 1.82
5711 5753 4.034048 CCTGTGACCAAATTATGACGCTAC 59.966 45.833 0.00 0.00 0.00 3.58
5712 5754 4.188462 CCTGTGACCAAATTATGACGCTA 58.812 43.478 0.00 0.00 0.00 4.26
5713 5755 3.009723 CCTGTGACCAAATTATGACGCT 58.990 45.455 0.00 0.00 0.00 5.07
5714 5756 2.747446 ACCTGTGACCAAATTATGACGC 59.253 45.455 0.00 0.00 0.00 5.19
5751 5793 1.203994 GCAGAATTGTGAGCATGGCTT 59.796 47.619 6.80 0.00 39.88 4.35
6145 6187 7.968405 GCAGAAGGTGAATTTATTAACGAATGT 59.032 33.333 0.00 0.00 0.00 2.71
6295 6662 4.109050 TGACATGTTTTTCGCAAGGTTTC 58.891 39.130 0.00 0.00 38.47 2.78
6324 6691 5.634896 ACAAAATCACAAATCTCATCGCTC 58.365 37.500 0.00 0.00 0.00 5.03
6375 6742 4.434989 GCAAAAACTTTCAACCGTTCAACC 60.435 41.667 0.00 0.00 0.00 3.77
6411 6778 1.658409 GAGCAGCACAACCGTTTGC 60.658 57.895 0.00 9.20 36.00 3.68
6412 6779 1.195448 CTAGAGCAGCACAACCGTTTG 59.805 52.381 0.00 0.00 38.83 2.93
6413 6780 1.202651 ACTAGAGCAGCACAACCGTTT 60.203 47.619 0.00 0.00 0.00 3.60
6414 6781 0.393077 ACTAGAGCAGCACAACCGTT 59.607 50.000 0.00 0.00 0.00 4.44
6415 6782 0.319900 CACTAGAGCAGCACAACCGT 60.320 55.000 0.00 0.00 0.00 4.83
6416 6783 0.038251 TCACTAGAGCAGCACAACCG 60.038 55.000 0.00 0.00 0.00 4.44
6417 6784 2.005451 CATCACTAGAGCAGCACAACC 58.995 52.381 0.00 0.00 0.00 3.77
6418 6785 2.005451 CCATCACTAGAGCAGCACAAC 58.995 52.381 0.00 0.00 0.00 3.32
6419 6786 1.901833 TCCATCACTAGAGCAGCACAA 59.098 47.619 0.00 0.00 0.00 3.33
6420 6787 1.560505 TCCATCACTAGAGCAGCACA 58.439 50.000 0.00 0.00 0.00 4.57
6421 6788 2.102084 TCATCCATCACTAGAGCAGCAC 59.898 50.000 0.00 0.00 0.00 4.40
6422 6789 2.391678 TCATCCATCACTAGAGCAGCA 58.608 47.619 0.00 0.00 0.00 4.41
6423 6790 3.069300 TCTTCATCCATCACTAGAGCAGC 59.931 47.826 0.00 0.00 0.00 5.25
6424 6791 4.341806 AGTCTTCATCCATCACTAGAGCAG 59.658 45.833 0.00 0.00 0.00 4.24
6425 6792 4.285020 AGTCTTCATCCATCACTAGAGCA 58.715 43.478 0.00 0.00 0.00 4.26
6426 6793 4.935352 AGTCTTCATCCATCACTAGAGC 57.065 45.455 0.00 0.00 0.00 4.09
6429 6796 9.186323 CGTTTATTAGTCTTCATCCATCACTAG 57.814 37.037 0.00 0.00 0.00 2.57
6430 6797 8.141909 CCGTTTATTAGTCTTCATCCATCACTA 58.858 37.037 0.00 0.00 0.00 2.74
6431 6798 6.986817 CCGTTTATTAGTCTTCATCCATCACT 59.013 38.462 0.00 0.00 0.00 3.41
6432 6799 6.761714 ACCGTTTATTAGTCTTCATCCATCAC 59.238 38.462 0.00 0.00 0.00 3.06
6433 6800 6.884832 ACCGTTTATTAGTCTTCATCCATCA 58.115 36.000 0.00 0.00 0.00 3.07
6434 6801 7.280205 ACAACCGTTTATTAGTCTTCATCCATC 59.720 37.037 0.00 0.00 0.00 3.51
6435 6802 7.065803 CACAACCGTTTATTAGTCTTCATCCAT 59.934 37.037 0.00 0.00 0.00 3.41
6436 6803 6.370442 CACAACCGTTTATTAGTCTTCATCCA 59.630 38.462 0.00 0.00 0.00 3.41
6437 6804 6.674760 GCACAACCGTTTATTAGTCTTCATCC 60.675 42.308 0.00 0.00 0.00 3.51
6438 6805 6.092259 AGCACAACCGTTTATTAGTCTTCATC 59.908 38.462 0.00 0.00 0.00 2.92
6439 6806 5.938125 AGCACAACCGTTTATTAGTCTTCAT 59.062 36.000 0.00 0.00 0.00 2.57
6440 6807 5.178623 CAGCACAACCGTTTATTAGTCTTCA 59.821 40.000 0.00 0.00 0.00 3.02
6441 6808 5.618561 CAGCACAACCGTTTATTAGTCTTC 58.381 41.667 0.00 0.00 0.00 2.87
6442 6809 4.083484 GCAGCACAACCGTTTATTAGTCTT 60.083 41.667 0.00 0.00 0.00 3.01
6443 6810 3.435671 GCAGCACAACCGTTTATTAGTCT 59.564 43.478 0.00 0.00 0.00 3.24
6444 6811 3.435671 AGCAGCACAACCGTTTATTAGTC 59.564 43.478 0.00 0.00 0.00 2.59
6445 6812 3.408634 AGCAGCACAACCGTTTATTAGT 58.591 40.909 0.00 0.00 0.00 2.24
6446 6813 3.684788 AGAGCAGCACAACCGTTTATTAG 59.315 43.478 0.00 0.00 0.00 1.73
6447 6814 3.670625 AGAGCAGCACAACCGTTTATTA 58.329 40.909 0.00 0.00 0.00 0.98
6448 6815 2.504367 AGAGCAGCACAACCGTTTATT 58.496 42.857 0.00 0.00 0.00 1.40
6449 6816 2.185004 AGAGCAGCACAACCGTTTAT 57.815 45.000 0.00 0.00 0.00 1.40
6450 6817 2.036733 ACTAGAGCAGCACAACCGTTTA 59.963 45.455 0.00 0.00 0.00 2.01
6535 6903 6.358118 TGCATTATTCGTGGTCTTCATTAC 57.642 37.500 0.00 0.00 0.00 1.89
6546 6914 2.810274 CCCTCCAGATGCATTATTCGTG 59.190 50.000 0.00 0.00 0.00 4.35
6556 6924 1.909700 TTTGTTGACCCTCCAGATGC 58.090 50.000 0.00 0.00 0.00 3.91
6633 7001 1.539157 TGGACGCAACATAATTGCCA 58.461 45.000 6.08 0.00 42.10 4.92
6635 7003 2.282290 GCATTGGACGCAACATAATTGC 59.718 45.455 1.48 1.48 41.71 3.56
6712 7080 1.003851 TATTTCTTGCGCTGGCGTAC 58.996 50.000 16.21 1.51 44.10 3.67
6718 7086 7.273164 TCACATAAAACAATATTTCTTGCGCTG 59.727 33.333 9.73 1.08 0.00 5.18
6811 7180 6.603201 AGAATGTCTGAGAAGGTCAAAAACAA 59.397 34.615 0.00 0.00 33.60 2.83
6838 7400 2.583143 GGTAACTTGAAACTGCCACCT 58.417 47.619 0.00 0.00 0.00 4.00
6841 7403 1.600023 CGGGTAACTTGAAACTGCCA 58.400 50.000 0.00 0.00 0.00 4.92
6863 7426 0.037605 TCTTTCGAGTTTCCGGGAGC 60.038 55.000 0.00 0.00 0.00 4.70
6870 7433 4.489679 AAAGGCACATCTTTCGAGTTTC 57.510 40.909 0.00 0.00 32.01 2.78
6871 7434 4.918810 AAAAGGCACATCTTTCGAGTTT 57.081 36.364 0.00 0.00 36.09 2.66
6894 7462 8.856153 TTGTGGCTAAGTTTCAAATATGTCTA 57.144 30.769 0.00 0.00 0.00 2.59
6917 7485 5.814705 GTGGTCCTTGATTGTCTCTAGATTG 59.185 44.000 0.00 0.00 0.00 2.67
6918 7486 5.104735 GGTGGTCCTTGATTGTCTCTAGATT 60.105 44.000 0.00 0.00 0.00 2.40
6919 7487 4.407296 GGTGGTCCTTGATTGTCTCTAGAT 59.593 45.833 0.00 0.00 0.00 1.98
6935 7503 0.953960 CGGCAACAGTAAGGTGGTCC 60.954 60.000 0.00 0.00 34.69 4.46
6936 7504 0.250166 ACGGCAACAGTAAGGTGGTC 60.250 55.000 0.00 0.00 34.69 4.02
6947 7601 1.301401 CCTCTTTCCGACGGCAACA 60.301 57.895 9.66 0.00 0.00 3.33
6950 7604 1.595993 CTCTCCTCTTTCCGACGGCA 61.596 60.000 9.66 0.00 0.00 5.69
6962 7616 1.677217 GGCATGTTGGTGTCTCTCCTC 60.677 57.143 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.