Multiple sequence alignment - TraesCS5B01G323700

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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 TraesCS5B01G323700 chr5B 100.000 3326 0 0 1 3326 508063973 508067298 0.000000e+00 6143.0
1 TraesCS5B01G323700 chr5B 78.713 202 41 2 1374 1574 275268418 275268218 2.080000e-27 134.0
2 TraesCS5B01G323700 chr5B 100.000 37 0 0 1 37 61148965 61149001 5.950000e-08 69.4
3 TraesCS5B01G323700 chr5A 92.051 1950 109 26 697 2606 535239527 535241470 0.000000e+00 2700.0
4 TraesCS5B01G323700 chr5A 79.915 234 23 16 364 582 535238562 535238786 2.070000e-32 150.0
5 TraesCS5B01G323700 chr5A 80.180 111 20 2 1172 1281 679722258 679722367 7.650000e-12 82.4
6 TraesCS5B01G323700 chr5A 100.000 37 0 0 1 37 546590259 546590223 5.950000e-08 69.4
7 TraesCS5B01G323700 chr5A 100.000 37 0 0 1 37 562429283 562429319 5.950000e-08 69.4
8 TraesCS5B01G323700 chr5A 97.297 37 1 0 1 37 631255951 631255987 2.770000e-06 63.9
9 TraesCS5B01G323700 chr5D 93.973 1709 75 14 677 2366 421661276 421662975 0.000000e+00 2560.0
10 TraesCS5B01G323700 chr5D 92.500 240 11 5 2371 2606 421663015 421663251 1.480000e-88 337.0
11 TraesCS5B01G323700 chr5D 88.764 89 7 2 400 487 421659796 421659882 4.540000e-19 106.0
12 TraesCS5B01G323700 chr5D 81.203 133 7 3 134 258 421659428 421659550 1.270000e-14 91.6
13 TraesCS5B01G323700 chr5D 100.000 28 0 0 582 609 450372615 450372588 6.000000e-03 52.8
14 TraesCS5B01G323700 chr3B 93.980 598 28 4 2732 3326 358687170 358686578 0.000000e+00 898.0
15 TraesCS5B01G323700 chr3B 96.875 32 1 0 1372 1403 807976163 807976194 2.000000e-03 54.7
16 TraesCS5B01G323700 chr3B 96.875 32 1 0 1372 1403 808043448 808043417 2.000000e-03 54.7
17 TraesCS5B01G323700 chr1B 92.434 608 29 7 2732 3326 201760199 201759596 0.000000e+00 852.0
18 TraesCS5B01G323700 chr1B 91.092 595 47 5 2732 3323 227710607 227711198 0.000000e+00 800.0
19 TraesCS5B01G323700 chr1B 97.297 37 1 0 1 37 551869327 551869291 2.770000e-06 63.9
20 TraesCS5B01G323700 chr3A 92.074 593 44 2 2732 3321 269674114 269673522 0.000000e+00 832.0
21 TraesCS5B01G323700 chr3A 100.000 37 0 0 1 37 631341446 631341410 5.950000e-08 69.4
22 TraesCS5B01G323700 chr3A 96.875 32 1 0 1372 1403 730656572 730656541 2.000000e-03 54.7
23 TraesCS5B01G323700 chr4D 91.419 606 45 6 2725 3326 349921631 349921029 0.000000e+00 824.0
24 TraesCS5B01G323700 chr4D 81.148 122 21 2 1172 1292 498906632 498906752 2.730000e-16 97.1
25 TraesCS5B01G323700 chr6A 91.156 588 47 4 2740 3322 101364185 101364772 0.000000e+00 793.0
26 TraesCS5B01G323700 chr6A 95.161 62 3 0 1226 1287 538494645 538494706 7.590000e-17 99.0
27 TraesCS5B01G323700 chr6D 90.516 601 48 8 2728 3323 356156757 356157353 0.000000e+00 785.0
28 TraesCS5B01G323700 chr7D 90.000 600 52 6 2732 3326 158963989 158963393 0.000000e+00 769.0
29 TraesCS5B01G323700 chr7D 77.686 121 21 5 1171 1288 446919997 446919880 5.950000e-08 69.4
30 TraesCS5B01G323700 chr7D 100.000 33 0 0 1246 1278 37234889 37234857 9.960000e-06 62.1
31 TraesCS5B01G323700 chr7A 89.933 596 51 7 2729 3321 241744164 241744753 0.000000e+00 760.0
32 TraesCS5B01G323700 chr7A 79.339 121 19 5 1171 1288 497776204 497776321 2.750000e-11 80.5
33 TraesCS5B01G323700 chr2D 86.087 115 16 0 1448 1562 635760006 635759892 1.250000e-24 124.0
34 TraesCS5B01G323700 chr2D 81.818 121 20 2 1452 1571 60015818 60015699 2.110000e-17 100.0
35 TraesCS5B01G323700 chr2D 84.314 102 16 0 1470 1571 60166898 60166797 2.110000e-17 100.0
36 TraesCS5B01G323700 chr2B 83.178 107 18 0 1453 1559 263812286 263812180 7.590000e-17 99.0
37 TraesCS5B01G323700 chr2B 83.333 102 17 0 1470 1571 94099228 94099127 9.820000e-16 95.3
38 TraesCS5B01G323700 chr4B 76.166 193 40 6 1374 1563 483951293 483951482 2.730000e-16 97.1
39 TraesCS5B01G323700 chr4B 78.182 110 24 0 1172 1281 641407819 641407928 1.660000e-08 71.3
40 TraesCS5B01G323700 chr7B 100.000 37 0 0 1 37 711172977 711173013 5.950000e-08 69.4
41 TraesCS5B01G323700 chr7B 100.000 30 0 0 580 609 188605775 188605804 4.640000e-04 56.5
42 TraesCS5B01G323700 chr6B 97.297 37 1 0 1 37 707854571 707854607 2.770000e-06 63.9
43 TraesCS5B01G323700 chr2A 97.297 37 1 0 1 37 80238266 80238302 2.770000e-06 63.9
44 TraesCS5B01G323700 chr2A 100.000 29 0 0 581 609 93888986 93889014 2.000000e-03 54.7
45 TraesCS5B01G323700 chr3D 96.875 32 1 0 1372 1403 600632525 600632556 2.000000e-03 54.7
46 TraesCS5B01G323700 chr3D 96.875 32 1 0 1372 1403 600820592 600820561 2.000000e-03 54.7


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 TraesCS5B01G323700 chr5B 508063973 508067298 3325 False 6143.00 6143 100.000 1 3326 1 chr5B.!!$F2 3325
1 TraesCS5B01G323700 chr5A 535238562 535241470 2908 False 1425.00 2700 85.983 364 2606 2 chr5A.!!$F4 2242
2 TraesCS5B01G323700 chr5D 421659428 421663251 3823 False 773.65 2560 89.110 134 2606 4 chr5D.!!$F1 2472
3 TraesCS5B01G323700 chr3B 358686578 358687170 592 True 898.00 898 93.980 2732 3326 1 chr3B.!!$R1 594
4 TraesCS5B01G323700 chr1B 201759596 201760199 603 True 852.00 852 92.434 2732 3326 1 chr1B.!!$R1 594
5 TraesCS5B01G323700 chr1B 227710607 227711198 591 False 800.00 800 91.092 2732 3323 1 chr1B.!!$F1 591
6 TraesCS5B01G323700 chr3A 269673522 269674114 592 True 832.00 832 92.074 2732 3321 1 chr3A.!!$R1 589
7 TraesCS5B01G323700 chr4D 349921029 349921631 602 True 824.00 824 91.419 2725 3326 1 chr4D.!!$R1 601
8 TraesCS5B01G323700 chr6A 101364185 101364772 587 False 793.00 793 91.156 2740 3322 1 chr6A.!!$F1 582
9 TraesCS5B01G323700 chr6D 356156757 356157353 596 False 785.00 785 90.516 2728 3323 1 chr6D.!!$F1 595
10 TraesCS5B01G323700 chr7D 158963393 158963989 596 True 769.00 769 90.000 2732 3326 1 chr7D.!!$R2 594
11 TraesCS5B01G323700 chr7A 241744164 241744753 589 False 760.00 760 89.933 2729 3321 1 chr7A.!!$F1 592

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
388 542 0.029567 GCATGCAGCTCTCATTGCTC 59.970 55.0 14.21 0.0 40.87 4.26 F
688 2189 0.039326 ACGGTCACTGGTACTAGCCT 59.961 55.0 6.09 0.0 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2305 3836 0.032952 TAGTTCACCACACGGCAGTC 59.967 55.0 0.0 0.0 34.57 3.51 R
2366 3904 0.753867 TGAAAGCCACTACACACGGA 59.246 50.0 0.0 0.0 0.00 4.69 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
26 27 9.373603 TGTAATTGCGTGTAACTCTTTATATGT 57.626 29.630 0.00 0.00 31.75 2.29
31 32 7.902032 TGCGTGTAACTCTTTATATGTTTAGC 58.098 34.615 0.00 0.00 31.75 3.09
32 33 7.546316 TGCGTGTAACTCTTTATATGTTTAGCA 59.454 33.333 0.00 0.00 31.75 3.49
33 34 8.548721 GCGTGTAACTCTTTATATGTTTAGCAT 58.451 33.333 0.00 0.00 36.70 3.79
45 46 4.916983 TGTTTAGCATTATCATGTGCCC 57.083 40.909 2.63 0.00 42.20 5.36
46 47 3.314913 TGTTTAGCATTATCATGTGCCCG 59.685 43.478 2.63 0.00 42.20 6.13
47 48 1.522668 TAGCATTATCATGTGCCCGC 58.477 50.000 2.63 0.00 42.20 6.13
48 49 0.179009 AGCATTATCATGTGCCCGCT 60.179 50.000 2.63 0.00 42.20 5.52
49 50 0.039798 GCATTATCATGTGCCCGCTG 60.040 55.000 0.00 0.00 35.35 5.18
50 51 0.594602 CATTATCATGTGCCCGCTGG 59.405 55.000 0.00 0.00 0.00 4.85
51 52 0.473755 ATTATCATGTGCCCGCTGGA 59.526 50.000 0.00 0.00 0.00 3.86
52 53 0.463654 TTATCATGTGCCCGCTGGAC 60.464 55.000 0.00 0.00 0.00 4.02
53 54 2.642996 TATCATGTGCCCGCTGGACG 62.643 60.000 0.00 0.00 43.15 4.79
70 71 3.177249 GGTTCACCGACTACGCGC 61.177 66.667 5.73 0.00 38.29 6.86
71 72 3.530104 GTTCACCGACTACGCGCG 61.530 66.667 30.96 30.96 38.29 6.86
77 78 4.564121 CGACTACGCGCGCTCGTA 62.564 66.667 32.58 28.36 43.15 3.43
78 79 3.010145 GACTACGCGCGCTCGTAC 61.010 66.667 32.58 15.59 43.15 3.67
79 80 4.858200 ACTACGCGCGCTCGTACG 62.858 66.667 32.58 22.88 43.15 3.67
80 81 4.858200 CTACGCGCGCTCGTACGT 62.858 66.667 32.58 20.23 43.15 3.57
85 86 2.649662 CGCGCTCGTACGTGCATA 60.650 61.111 33.35 8.16 40.29 3.14
86 87 2.902383 CGCGCTCGTACGTGCATAC 61.902 63.158 33.35 23.20 40.29 2.39
99 100 2.148916 TGCATACGCACTGGTATAGC 57.851 50.000 0.00 0.00 45.36 2.97
100 101 1.410882 TGCATACGCACTGGTATAGCA 59.589 47.619 4.27 4.27 45.36 3.49
101 102 1.792949 GCATACGCACTGGTATAGCAC 59.207 52.381 0.00 0.00 38.36 4.40
102 103 2.545952 GCATACGCACTGGTATAGCACT 60.546 50.000 0.00 0.00 38.36 4.40
103 104 3.309388 CATACGCACTGGTATAGCACTC 58.691 50.000 0.00 0.00 32.04 3.51
104 105 1.182667 ACGCACTGGTATAGCACTCA 58.817 50.000 0.00 0.00 0.00 3.41
105 106 1.548719 ACGCACTGGTATAGCACTCAA 59.451 47.619 0.00 0.00 0.00 3.02
106 107 1.927174 CGCACTGGTATAGCACTCAAC 59.073 52.381 0.00 0.00 0.00 3.18
107 108 2.673893 CGCACTGGTATAGCACTCAACA 60.674 50.000 0.00 0.00 0.00 3.33
108 109 3.334691 GCACTGGTATAGCACTCAACAA 58.665 45.455 0.00 0.00 0.00 2.83
109 110 3.372206 GCACTGGTATAGCACTCAACAAG 59.628 47.826 0.00 0.00 0.00 3.16
110 111 3.372206 CACTGGTATAGCACTCAACAAGC 59.628 47.826 0.00 0.00 0.00 4.01
111 112 2.604914 CTGGTATAGCACTCAACAAGCG 59.395 50.000 0.00 0.00 0.00 4.68
112 113 1.327764 GGTATAGCACTCAACAAGCGC 59.672 52.381 0.00 0.00 33.01 5.92
113 114 1.999735 GTATAGCACTCAACAAGCGCA 59.000 47.619 11.47 0.00 35.41 6.09
114 115 1.081892 ATAGCACTCAACAAGCGCAG 58.918 50.000 11.47 3.78 35.41 5.18
115 116 0.033366 TAGCACTCAACAAGCGCAGA 59.967 50.000 11.47 0.00 35.41 4.26
116 117 1.206072 GCACTCAACAAGCGCAGAG 59.794 57.895 11.47 11.00 33.08 3.35
117 118 1.864862 CACTCAACAAGCGCAGAGG 59.135 57.895 11.47 0.00 32.52 3.69
118 119 0.601046 CACTCAACAAGCGCAGAGGA 60.601 55.000 11.47 4.28 32.52 3.71
119 120 0.106708 ACTCAACAAGCGCAGAGGAA 59.893 50.000 11.47 0.00 32.52 3.36
120 121 0.795085 CTCAACAAGCGCAGAGGAAG 59.205 55.000 11.47 0.00 0.00 3.46
121 122 1.208614 CAACAAGCGCAGAGGAAGC 59.791 57.895 11.47 0.00 0.00 3.86
122 123 1.072159 AACAAGCGCAGAGGAAGCT 59.928 52.632 11.47 0.00 43.90 3.74
123 124 1.233285 AACAAGCGCAGAGGAAGCTG 61.233 55.000 11.47 0.00 41.53 4.24
129 130 3.588336 CAGAGGAAGCTGCTTGCC 58.412 61.111 27.01 21.78 44.23 4.52
130 131 1.002379 CAGAGGAAGCTGCTTGCCT 60.002 57.895 27.01 25.33 44.23 4.75
131 132 1.002379 AGAGGAAGCTGCTTGCCTG 60.002 57.895 27.01 0.00 44.23 4.85
132 133 2.035312 AGGAAGCTGCTTGCCTGG 59.965 61.111 27.01 0.00 44.23 4.45
160 161 2.123248 TTGGATCGGTCAGCCTGCAA 62.123 55.000 0.00 0.00 0.00 4.08
161 162 1.377202 GGATCGGTCAGCCTGCAAA 60.377 57.895 0.00 0.00 0.00 3.68
162 163 1.372087 GGATCGGTCAGCCTGCAAAG 61.372 60.000 0.00 0.00 0.00 2.77
163 164 1.986575 GATCGGTCAGCCTGCAAAGC 61.987 60.000 0.04 0.04 0.00 3.51
164 165 4.093952 CGGTCAGCCTGCAAAGCG 62.094 66.667 2.93 0.00 34.64 4.68
165 166 4.410743 GGTCAGCCTGCAAAGCGC 62.411 66.667 0.00 0.00 42.89 5.92
221 227 0.456221 TCGCCTCGAGTGAAATCTCC 59.544 55.000 12.31 0.00 30.08 3.71
224 230 1.472376 GCCTCGAGTGAAATCTCCCTG 60.472 57.143 12.31 0.00 0.00 4.45
247 256 1.626654 CGCGCGAGTGATTCCAAGTT 61.627 55.000 28.94 0.00 46.66 2.66
251 260 2.159787 CGCGAGTGATTCCAAGTTCAAG 60.160 50.000 0.00 0.00 0.00 3.02
254 263 4.058124 CGAGTGATTCCAAGTTCAAGACA 58.942 43.478 0.00 0.00 0.00 3.41
258 267 5.940470 AGTGATTCCAAGTTCAAGACATACC 59.060 40.000 0.00 0.00 0.00 2.73
260 269 5.705441 TGATTCCAAGTTCAAGACATACCAC 59.295 40.000 0.00 0.00 0.00 4.16
264 273 4.935808 CCAAGTTCAAGACATACCACTACC 59.064 45.833 0.00 0.00 0.00 3.18
265 274 5.512404 CCAAGTTCAAGACATACCACTACCA 60.512 44.000 0.00 0.00 0.00 3.25
266 275 5.148651 AGTTCAAGACATACCACTACCAC 57.851 43.478 0.00 0.00 0.00 4.16
272 416 1.203994 ACATACCACTACCACTGCGAC 59.796 52.381 0.00 0.00 0.00 5.19
294 438 2.411904 GATGATGAGCTTCCACCGATC 58.588 52.381 0.00 0.00 0.00 3.69
295 439 0.465705 TGATGAGCTTCCACCGATCC 59.534 55.000 0.00 0.00 0.00 3.36
297 441 0.911769 ATGAGCTTCCACCGATCCAA 59.088 50.000 0.00 0.00 0.00 3.53
298 442 0.690192 TGAGCTTCCACCGATCCAAA 59.310 50.000 0.00 0.00 0.00 3.28
299 443 1.073125 TGAGCTTCCACCGATCCAAAA 59.927 47.619 0.00 0.00 0.00 2.44
305 449 0.243636 CCACCGATCCAAAAAGTGCC 59.756 55.000 0.00 0.00 0.00 5.01
312 456 2.551912 CCAAAAAGTGCCCGTCGCT 61.552 57.895 0.00 0.00 38.78 4.93
316 460 0.743345 AAAAGTGCCCGTCGCTATCC 60.743 55.000 0.00 0.00 38.78 2.59
320 464 2.048127 GCCCGTCGCTATCCATCC 60.048 66.667 0.00 0.00 0.00 3.51
322 466 1.006102 CCCGTCGCTATCCATCCAC 60.006 63.158 0.00 0.00 0.00 4.02
346 500 2.095969 CGCAGTAAATTTGACCGCTTCA 60.096 45.455 0.00 0.00 0.00 3.02
358 512 2.177531 GCTTCATGCGCACACCAG 59.822 61.111 14.90 7.88 0.00 4.00
359 513 2.177531 CTTCATGCGCACACCAGC 59.822 61.111 14.90 0.00 0.00 4.85
360 514 3.332493 CTTCATGCGCACACCAGCC 62.332 63.158 14.90 0.00 0.00 4.85
368 522 3.941188 CACACCAGCCCAGACCGT 61.941 66.667 0.00 0.00 0.00 4.83
369 523 3.941188 ACACCAGCCCAGACCGTG 61.941 66.667 0.00 0.00 0.00 4.94
388 542 0.029567 GCATGCAGCTCTCATTGCTC 59.970 55.000 14.21 0.00 40.87 4.26
389 543 0.663688 CATGCAGCTCTCATTGCTCC 59.336 55.000 0.00 0.00 40.87 4.70
390 544 0.547075 ATGCAGCTCTCATTGCTCCT 59.453 50.000 0.00 0.00 40.87 3.69
391 545 0.392595 TGCAGCTCTCATTGCTCCTG 60.393 55.000 0.00 0.00 40.87 3.86
450 608 3.862642 GCATAGGCATAGCACTCCACTAC 60.863 52.174 0.00 0.00 40.72 2.73
456 614 1.372582 TAGCACTCCACTACGTACCG 58.627 55.000 0.00 0.00 0.00 4.02
534 729 1.698165 GCGCGTGATTAGCTGCTATA 58.302 50.000 10.64 2.32 33.68 1.31
536 731 1.986378 CGCGTGATTAGCTGCTATACC 59.014 52.381 10.64 3.66 0.00 2.73
544 739 5.999600 TGATTAGCTGCTATACCACGTACTA 59.000 40.000 10.64 0.00 0.00 1.82
545 740 5.679734 TTAGCTGCTATACCACGTACTAC 57.320 43.478 10.64 0.00 0.00 2.73
554 749 3.141002 ACCACGTACTACATGCTTACG 57.859 47.619 15.88 15.88 43.34 3.18
560 755 3.003068 CGTACTACATGCTTACGGCTACT 59.997 47.826 11.60 0.00 42.39 2.57
561 756 3.712091 ACTACATGCTTACGGCTACTC 57.288 47.619 0.00 0.00 42.39 2.59
582 781 7.944729 ACTCTACCATATGAACTGCAAAAAT 57.055 32.000 3.65 0.00 0.00 1.82
583 782 7.765307 ACTCTACCATATGAACTGCAAAAATG 58.235 34.615 3.65 0.00 0.00 2.32
584 783 7.394359 ACTCTACCATATGAACTGCAAAAATGT 59.606 33.333 3.65 0.00 0.00 2.71
586 785 6.594788 ACCATATGAACTGCAAAAATGTCT 57.405 33.333 3.65 0.00 0.00 3.41
588 787 8.121305 ACCATATGAACTGCAAAAATGTCTTA 57.879 30.769 3.65 0.00 0.00 2.10
594 793 7.816640 TGAACTGCAAAAATGTCTTATACTCC 58.183 34.615 0.00 0.00 0.00 3.85
595 794 6.759497 ACTGCAAAAATGTCTTATACTCCC 57.241 37.500 0.00 0.00 0.00 4.30
597 796 6.599638 ACTGCAAAAATGTCTTATACTCCCTC 59.400 38.462 0.00 0.00 0.00 4.30
598 797 5.885912 TGCAAAAATGTCTTATACTCCCTCC 59.114 40.000 0.00 0.00 0.00 4.30
602 2042 2.941480 TGTCTTATACTCCCTCCGTCC 58.059 52.381 0.00 0.00 0.00 4.79
605 2045 0.846015 TTATACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
614 2054 0.535335 CTCCGTCCGGAAATCTCCAA 59.465 55.000 5.23 0.00 44.66 3.53
618 2058 2.102588 CCGTCCGGAAATCTCCAAGTAT 59.897 50.000 5.23 0.00 42.58 2.12
623 2063 6.445475 GTCCGGAAATCTCCAAGTATAGTAC 58.555 44.000 5.23 0.00 42.58 2.73
660 2100 1.067142 TGGCAGTAGCTTACCAGAACG 60.067 52.381 0.00 0.00 41.70 3.95
670 2134 2.373540 TACCAGAACGTACCATGCAC 57.626 50.000 0.00 0.00 0.00 4.57
675 2176 1.368209 AACGTACCATGCACGGTCA 59.632 52.632 8.24 0.00 43.59 4.02
677 2178 1.080093 CGTACCATGCACGGTCACT 60.080 57.895 8.24 0.00 40.67 3.41
678 2179 1.351430 CGTACCATGCACGGTCACTG 61.351 60.000 8.24 0.00 40.67 3.66
679 2180 1.019278 GTACCATGCACGGTCACTGG 61.019 60.000 8.24 2.56 40.67 4.00
686 2187 0.458025 GCACGGTCACTGGTACTAGC 60.458 60.000 6.09 0.00 0.00 3.42
688 2189 0.039326 ACGGTCACTGGTACTAGCCT 59.961 55.000 6.09 0.00 0.00 4.58
701 2204 0.867086 CTAGCCTACTAGGACGACGC 59.133 60.000 6.26 0.00 41.99 5.19
756 2262 5.048782 TCTCTTGTACAACACATTCCAATGC 60.049 40.000 3.59 0.00 40.04 3.56
779 2285 0.788391 GCACTGTACGTACACAAGGC 59.212 55.000 24.10 19.09 31.93 4.35
794 2300 0.613777 AAGGCCAGAACTTAGGACCG 59.386 55.000 5.01 0.00 31.34 4.79
796 2302 0.108281 GGCCAGAACTTAGGACCGAC 60.108 60.000 0.00 0.00 0.00 4.79
797 2303 0.896226 GCCAGAACTTAGGACCGACT 59.104 55.000 0.00 0.00 0.00 4.18
805 2311 2.686915 ACTTAGGACCGACTATTCCACG 59.313 50.000 0.00 0.00 33.92 4.94
846 2352 1.673665 CTGCCACTTCACCTGCTCC 60.674 63.158 0.00 0.00 0.00 4.70
857 2363 0.476611 ACCTGCTCCCCCTCTCTTTT 60.477 55.000 0.00 0.00 0.00 2.27
912 2418 1.956869 TCCTCATCACCATCACCACT 58.043 50.000 0.00 0.00 0.00 4.00
1300 2808 4.219944 TCAATGTACGTACTCCAAGAGCTT 59.780 41.667 25.12 3.96 32.04 3.74
1315 2823 2.105466 GCTTCTGGCTGAGCTTCCG 61.105 63.158 3.72 0.00 38.06 4.30
1329 2838 3.509137 TTCCGGCGCACGTTCTCTT 62.509 57.895 10.83 0.00 42.24 2.85
1378 2888 1.080298 GTTGCTTGTGATGCAGGGC 60.080 57.895 0.00 0.00 41.71 5.19
1590 3102 5.321516 CGTATGTTACCTTGCTTTGCTTAC 58.678 41.667 0.00 0.00 0.00 2.34
1591 3103 5.121768 CGTATGTTACCTTGCTTTGCTTACT 59.878 40.000 0.00 0.00 0.00 2.24
1602 3114 5.556915 TGCTTTGCTTACTATACACTGGTT 58.443 37.500 0.00 0.00 0.00 3.67
1623 3139 1.210545 CGGCGTACACACTCACGTTT 61.211 55.000 0.00 0.00 40.25 3.60
1745 3266 3.365265 GCCAACAGCAACCTCCCG 61.365 66.667 0.00 0.00 42.97 5.14
1861 3386 5.441872 CGTCGTTGAATCATTGCACATTTTC 60.442 40.000 0.00 0.00 0.00 2.29
1862 3387 5.401972 GTCGTTGAATCATTGCACATTTTCA 59.598 36.000 0.00 0.00 0.00 2.69
1877 3408 4.083110 ACATTTTCATGGAGAGAAAGCACG 60.083 41.667 0.00 0.00 36.45 5.34
1888 3419 6.479990 TGGAGAGAAAGCACGATTGTATATTG 59.520 38.462 0.00 0.00 0.00 1.90
1895 3426 8.889849 AAAGCACGATTGTATATTGTTGTAAC 57.110 30.769 0.00 0.00 0.00 2.50
2112 3643 2.949451 ACTACATCAACCTGCTCTCG 57.051 50.000 0.00 0.00 0.00 4.04
2440 4013 9.418045 GAAATAAGCTGCTAGATTCTAACTAGG 57.582 37.037 0.90 0.00 38.11 3.02
2482 4061 1.146041 TATCTGGTGATGTGCGGCC 59.854 57.895 0.00 0.00 34.32 6.13
2513 4092 9.213799 TGGCTTGTCAAAATAATTAATTTCACC 57.786 29.630 5.91 0.00 36.76 4.02
2563 4146 3.496884 TGTGCTTTTCTCCGTGTATTCAC 59.503 43.478 0.00 0.00 40.79 3.18
2583 4166 2.037121 ACGTTGGTGAGTGTCATGATGA 59.963 45.455 0.00 0.00 0.00 2.92
2588 4171 5.169992 TGGTGAGTGTCATGATGATTTCT 57.830 39.130 0.00 0.00 0.00 2.52
2624 4207 7.848716 CAAAAAGAGTTTTGCTATGTCTCTG 57.151 36.000 0.00 0.00 45.20 3.35
2625 4208 7.420800 CAAAAAGAGTTTTGCTATGTCTCTGT 58.579 34.615 0.00 0.00 45.20 3.41
2626 4209 6.793492 AAAGAGTTTTGCTATGTCTCTGTC 57.207 37.500 0.00 0.00 35.94 3.51
2627 4210 5.474578 AGAGTTTTGCTATGTCTCTGTCA 57.525 39.130 0.00 0.00 34.74 3.58
2628 4211 6.047511 AGAGTTTTGCTATGTCTCTGTCAT 57.952 37.500 0.00 0.00 34.74 3.06
2629 4212 6.471146 AGAGTTTTGCTATGTCTCTGTCATT 58.529 36.000 0.00 0.00 34.74 2.57
2630 4213 6.939163 AGAGTTTTGCTATGTCTCTGTCATTT 59.061 34.615 0.00 0.00 34.74 2.32
2631 4214 6.906659 AGTTTTGCTATGTCTCTGTCATTTG 58.093 36.000 0.00 0.00 0.00 2.32
2632 4215 6.712095 AGTTTTGCTATGTCTCTGTCATTTGA 59.288 34.615 0.00 0.00 0.00 2.69
2633 4216 6.732531 TTTGCTATGTCTCTGTCATTTGAG 57.267 37.500 0.00 0.00 0.00 3.02
2634 4217 5.665916 TGCTATGTCTCTGTCATTTGAGA 57.334 39.130 0.00 0.00 37.03 3.27
2644 4227 8.315391 TCTCTGTCATTTGAGACTTTGTTATG 57.685 34.615 0.00 0.00 39.27 1.90
2645 4228 7.933577 TCTCTGTCATTTGAGACTTTGTTATGT 59.066 33.333 0.00 0.00 39.27 2.29
2646 4229 8.450578 TCTGTCATTTGAGACTTTGTTATGTT 57.549 30.769 0.00 0.00 39.27 2.71
2647 4230 8.902806 TCTGTCATTTGAGACTTTGTTATGTTT 58.097 29.630 0.00 0.00 39.27 2.83
2648 4231 9.173939 CTGTCATTTGAGACTTTGTTATGTTTC 57.826 33.333 0.00 0.00 39.27 2.78
2649 4232 8.681806 TGTCATTTGAGACTTTGTTATGTTTCA 58.318 29.630 0.00 0.00 39.27 2.69
2650 4233 9.173939 GTCATTTGAGACTTTGTTATGTTTCAG 57.826 33.333 0.00 0.00 35.65 3.02
2651 4234 8.902806 TCATTTGAGACTTTGTTATGTTTCAGT 58.097 29.630 0.00 0.00 30.81 3.41
2652 4235 9.173939 CATTTGAGACTTTGTTATGTTTCAGTC 57.826 33.333 0.00 0.00 30.81 3.51
2653 4236 6.525121 TGAGACTTTGTTATGTTTCAGTCG 57.475 37.500 0.00 0.00 0.00 4.18
2654 4237 6.277605 TGAGACTTTGTTATGTTTCAGTCGA 58.722 36.000 0.00 0.00 0.00 4.20
2655 4238 6.929049 TGAGACTTTGTTATGTTTCAGTCGAT 59.071 34.615 0.00 0.00 0.00 3.59
2656 4239 8.085909 TGAGACTTTGTTATGTTTCAGTCGATA 58.914 33.333 0.00 0.00 0.00 2.92
2657 4240 8.467402 AGACTTTGTTATGTTTCAGTCGATAG 57.533 34.615 0.00 0.00 0.00 2.08
2658 4241 8.088981 AGACTTTGTTATGTTTCAGTCGATAGT 58.911 33.333 0.00 0.00 37.40 2.12
2659 4242 9.350357 GACTTTGTTATGTTTCAGTCGATAGTA 57.650 33.333 0.00 0.00 37.40 1.82
2660 4243 9.871238 ACTTTGTTATGTTTCAGTCGATAGTAT 57.129 29.630 0.00 0.00 37.40 2.12
2664 4247 9.731819 TGTTATGTTTCAGTCGATAGTATCTTC 57.268 33.333 8.49 1.74 37.40 2.87
2665 4248 9.182933 GTTATGTTTCAGTCGATAGTATCTTCC 57.817 37.037 8.49 0.00 37.40 3.46
2666 4249 7.589958 ATGTTTCAGTCGATAGTATCTTCCT 57.410 36.000 8.49 0.00 37.40 3.36
2667 4250 7.406031 TGTTTCAGTCGATAGTATCTTCCTT 57.594 36.000 8.49 0.00 37.40 3.36
2668 4251 7.837863 TGTTTCAGTCGATAGTATCTTCCTTT 58.162 34.615 8.49 0.00 37.40 3.11
2669 4252 8.963725 TGTTTCAGTCGATAGTATCTTCCTTTA 58.036 33.333 8.49 0.00 37.40 1.85
2670 4253 9.798994 GTTTCAGTCGATAGTATCTTCCTTTAA 57.201 33.333 8.49 0.00 37.40 1.52
2687 4270 9.774742 CTTCCTTTAATTTTACAAGGAGATTCG 57.225 33.333 0.42 0.00 45.45 3.34
2688 4271 8.857694 TCCTTTAATTTTACAAGGAGATTCGT 57.142 30.769 0.00 0.00 41.02 3.85
2689 4272 8.726988 TCCTTTAATTTTACAAGGAGATTCGTG 58.273 33.333 0.00 0.00 41.02 4.35
2690 4273 8.512138 CCTTTAATTTTACAAGGAGATTCGTGT 58.488 33.333 0.00 0.00 39.73 4.49
2815 4398 5.888161 CAGTACAATTTCATTTAGGGGCTCT 59.112 40.000 0.00 0.00 0.00 4.09
2834 4417 3.717707 TCTTCAAACCAGTCTGAAGTCG 58.282 45.455 12.35 0.00 45.75 4.18
2837 4420 4.131649 TCAAACCAGTCTGAAGTCGAAA 57.868 40.909 0.00 0.00 0.00 3.46
2927 4512 5.711506 AGTCATGACAAAATCACAGGCATAA 59.288 36.000 27.02 0.00 41.24 1.90
2999 4589 1.911357 TCCTGCATGGTCTCAATCACT 59.089 47.619 0.00 0.00 37.07 3.41
3039 4630 3.847671 TGATTATGCGATTACACCCCA 57.152 42.857 0.00 0.00 0.00 4.96
3109 4700 3.937814 TCAGAACATCCGCACAATAGTT 58.062 40.909 0.00 0.00 0.00 2.24
3110 4701 4.323417 TCAGAACATCCGCACAATAGTTT 58.677 39.130 0.00 0.00 0.00 2.66
3212 4811 4.158949 TGATCAAAGGAGGCATCAACATTG 59.841 41.667 0.00 0.00 0.00 2.82
3323 4924 6.097412 AGTGCTATGATCGCCATTGATATCTA 59.903 38.462 3.98 0.00 36.71 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.385111 GCTAAACATATAAAGAGTTACACGCAA 58.615 33.333 0.00 0.00 0.00 4.85
7 8 7.902032 TGCTAAACATATAAAGAGTTACACGC 58.098 34.615 0.00 0.00 0.00 5.34
19 20 8.739039 GGGCACATGATAATGCTAAACATATAA 58.261 33.333 0.00 0.00 41.74 0.98
20 21 7.065683 CGGGCACATGATAATGCTAAACATATA 59.934 37.037 0.00 0.00 41.74 0.86
21 22 6.127925 CGGGCACATGATAATGCTAAACATAT 60.128 38.462 0.00 0.00 41.74 1.78
22 23 5.181056 CGGGCACATGATAATGCTAAACATA 59.819 40.000 0.00 0.00 41.74 2.29
23 24 4.022935 CGGGCACATGATAATGCTAAACAT 60.023 41.667 0.00 0.00 41.74 2.71
24 25 3.314913 CGGGCACATGATAATGCTAAACA 59.685 43.478 0.00 0.00 41.74 2.83
25 26 3.853307 GCGGGCACATGATAATGCTAAAC 60.853 47.826 0.00 0.00 41.74 2.01
26 27 2.293122 GCGGGCACATGATAATGCTAAA 59.707 45.455 0.00 0.00 41.74 1.85
27 28 1.879380 GCGGGCACATGATAATGCTAA 59.121 47.619 0.00 0.00 41.74 3.09
28 29 1.072173 AGCGGGCACATGATAATGCTA 59.928 47.619 0.00 0.00 41.74 3.49
29 30 0.179009 AGCGGGCACATGATAATGCT 60.179 50.000 0.00 0.00 41.74 3.79
30 31 0.039798 CAGCGGGCACATGATAATGC 60.040 55.000 0.00 0.00 41.29 3.56
31 32 0.594602 CCAGCGGGCACATGATAATG 59.405 55.000 0.00 0.00 0.00 1.90
32 33 0.473755 TCCAGCGGGCACATGATAAT 59.526 50.000 0.00 0.00 0.00 1.28
33 34 0.463654 GTCCAGCGGGCACATGATAA 60.464 55.000 0.00 0.00 0.00 1.75
34 35 1.146041 GTCCAGCGGGCACATGATA 59.854 57.895 0.00 0.00 0.00 2.15
35 36 2.124570 GTCCAGCGGGCACATGAT 60.125 61.111 0.00 0.00 0.00 2.45
36 37 4.758251 CGTCCAGCGGGCACATGA 62.758 66.667 0.00 0.00 36.85 3.07
53 54 3.177249 GCGCGTAGTCGGTGAACC 61.177 66.667 8.43 0.00 37.56 3.62
54 55 3.530104 CGCGCGTAGTCGGTGAAC 61.530 66.667 24.19 0.00 37.56 3.18
60 61 4.564121 TACGAGCGCGCGTAGTCG 62.564 66.667 36.53 33.72 43.61 4.18
61 62 3.010145 GTACGAGCGCGCGTAGTC 61.010 66.667 39.67 27.50 46.11 2.59
62 63 4.858200 CGTACGAGCGCGCGTAGT 62.858 66.667 39.67 27.57 46.11 2.73
63 64 4.858200 ACGTACGAGCGCGCGTAG 62.858 66.667 39.67 32.48 46.11 3.51
68 69 2.649662 TATGCACGTACGAGCGCG 60.650 61.111 27.99 8.75 44.79 6.86
69 70 2.911280 GTATGCACGTACGAGCGC 59.089 61.111 27.99 22.59 34.50 5.92
81 82 1.792949 GTGCTATACCAGTGCGTATGC 59.207 52.381 0.00 0.00 43.20 3.14
82 83 3.243401 TGAGTGCTATACCAGTGCGTATG 60.243 47.826 12.09 6.02 31.42 2.39
83 84 2.956333 TGAGTGCTATACCAGTGCGTAT 59.044 45.455 8.65 8.65 33.52 3.06
84 85 2.371306 TGAGTGCTATACCAGTGCGTA 58.629 47.619 0.00 0.00 0.00 4.42
85 86 1.182667 TGAGTGCTATACCAGTGCGT 58.817 50.000 0.00 0.00 0.00 5.24
86 87 1.927174 GTTGAGTGCTATACCAGTGCG 59.073 52.381 0.00 0.00 0.00 5.34
87 88 2.972625 TGTTGAGTGCTATACCAGTGC 58.027 47.619 0.00 0.00 0.00 4.40
88 89 3.372206 GCTTGTTGAGTGCTATACCAGTG 59.628 47.826 0.00 0.00 0.00 3.66
89 90 3.600388 GCTTGTTGAGTGCTATACCAGT 58.400 45.455 0.00 0.00 0.00 4.00
90 91 2.604914 CGCTTGTTGAGTGCTATACCAG 59.395 50.000 0.00 0.00 0.00 4.00
91 92 2.616960 CGCTTGTTGAGTGCTATACCA 58.383 47.619 0.00 0.00 0.00 3.25
99 100 0.601046 TCCTCTGCGCTTGTTGAGTG 60.601 55.000 9.73 0.00 38.94 3.51
100 101 0.106708 TTCCTCTGCGCTTGTTGAGT 59.893 50.000 9.73 0.00 0.00 3.41
101 102 0.795085 CTTCCTCTGCGCTTGTTGAG 59.205 55.000 9.73 8.30 0.00 3.02
102 103 1.230635 GCTTCCTCTGCGCTTGTTGA 61.231 55.000 9.73 0.00 0.00 3.18
103 104 1.208614 GCTTCCTCTGCGCTTGTTG 59.791 57.895 9.73 0.00 0.00 3.33
104 105 1.072159 AGCTTCCTCTGCGCTTGTT 59.928 52.632 9.73 0.00 35.28 2.83
105 106 1.670406 CAGCTTCCTCTGCGCTTGT 60.670 57.895 9.73 0.00 35.28 3.16
106 107 3.175724 CAGCTTCCTCTGCGCTTG 58.824 61.111 9.73 1.08 35.28 4.01
112 113 1.002379 AGGCAAGCAGCTTCCTCTG 60.002 57.895 16.35 3.92 44.79 3.35
113 114 1.002379 CAGGCAAGCAGCTTCCTCT 60.002 57.895 18.28 8.73 44.79 3.69
114 115 2.045131 CCAGGCAAGCAGCTTCCTC 61.045 63.158 18.28 6.90 44.79 3.71
115 116 2.035312 CCAGGCAAGCAGCTTCCT 59.965 61.111 16.35 16.35 44.79 3.36
116 117 1.604593 TTCCAGGCAAGCAGCTTCC 60.605 57.895 4.07 9.90 44.79 3.46
117 118 1.583477 GTTCCAGGCAAGCAGCTTC 59.417 57.895 4.07 0.23 44.79 3.86
118 119 1.905354 GGTTCCAGGCAAGCAGCTT 60.905 57.895 0.21 0.21 44.79 3.74
119 120 2.282745 GGTTCCAGGCAAGCAGCT 60.283 61.111 0.00 0.00 44.79 4.24
120 121 1.466851 AAAGGTTCCAGGCAAGCAGC 61.467 55.000 0.00 0.00 44.65 5.25
121 122 0.600057 GAAAGGTTCCAGGCAAGCAG 59.400 55.000 0.00 0.00 0.00 4.24
122 123 0.185901 AGAAAGGTTCCAGGCAAGCA 59.814 50.000 0.00 0.00 0.00 3.91
123 124 1.000171 CAAGAAAGGTTCCAGGCAAGC 60.000 52.381 0.00 0.00 0.00 4.01
124 125 1.615392 CCAAGAAAGGTTCCAGGCAAG 59.385 52.381 0.00 0.00 0.00 4.01
125 126 1.216678 TCCAAGAAAGGTTCCAGGCAA 59.783 47.619 0.00 0.00 0.00 4.52
126 127 0.850100 TCCAAGAAAGGTTCCAGGCA 59.150 50.000 0.00 0.00 0.00 4.75
127 128 2.095461 GATCCAAGAAAGGTTCCAGGC 58.905 52.381 0.00 0.00 0.00 4.85
128 129 2.359900 CGATCCAAGAAAGGTTCCAGG 58.640 52.381 0.00 0.00 0.00 4.45
129 130 2.290323 ACCGATCCAAGAAAGGTTCCAG 60.290 50.000 0.00 0.00 0.00 3.86
130 131 1.702957 ACCGATCCAAGAAAGGTTCCA 59.297 47.619 0.00 0.00 0.00 3.53
131 132 2.290071 TGACCGATCCAAGAAAGGTTCC 60.290 50.000 0.00 0.00 35.00 3.62
132 133 3.003480 CTGACCGATCCAAGAAAGGTTC 58.997 50.000 0.00 0.00 35.00 3.62
178 179 4.430423 CTTGCTCACGCCGTTCGC 62.430 66.667 0.00 0.00 43.23 4.70
207 208 0.537188 GGCAGGGAGATTTCACTCGA 59.463 55.000 0.00 0.00 33.82 4.04
247 256 3.056107 GCAGTGGTAGTGGTATGTCTTGA 60.056 47.826 0.00 0.00 0.00 3.02
251 260 1.475280 TCGCAGTGGTAGTGGTATGTC 59.525 52.381 0.00 0.00 0.00 3.06
254 263 0.822164 GGTCGCAGTGGTAGTGGTAT 59.178 55.000 0.00 0.00 0.00 2.73
258 267 0.802222 CATCGGTCGCAGTGGTAGTG 60.802 60.000 0.00 0.00 0.00 2.74
260 269 0.385751 ATCATCGGTCGCAGTGGTAG 59.614 55.000 0.00 0.00 0.00 3.18
264 273 1.485838 GCTCATCATCGGTCGCAGTG 61.486 60.000 0.00 0.00 0.00 3.66
265 274 1.227089 GCTCATCATCGGTCGCAGT 60.227 57.895 0.00 0.00 0.00 4.40
266 275 0.529337 AAGCTCATCATCGGTCGCAG 60.529 55.000 0.00 0.00 0.00 5.18
272 416 0.877649 CGGTGGAAGCTCATCATCGG 60.878 60.000 8.19 0.00 32.11 4.18
294 438 2.050442 GCGACGGGCACTTTTTGG 60.050 61.111 0.00 0.00 42.87 3.28
305 449 1.006102 GGTGGATGGATAGCGACGG 60.006 63.158 0.00 0.00 0.00 4.79
312 456 2.375014 TACTGCGAGGTGGATGGATA 57.625 50.000 0.00 0.00 0.00 2.59
316 460 3.689161 TCAAATTTACTGCGAGGTGGATG 59.311 43.478 0.00 0.00 0.00 3.51
320 464 2.159707 CGGTCAAATTTACTGCGAGGTG 60.160 50.000 0.00 0.00 0.00 4.00
322 466 1.202031 GCGGTCAAATTTACTGCGAGG 60.202 52.381 12.65 0.00 39.29 4.63
356 510 3.129502 CATGCACGGTCTGGGCTG 61.130 66.667 7.57 0.00 0.00 4.85
359 513 3.129502 CTGCATGCACGGTCTGGG 61.130 66.667 18.46 0.00 0.00 4.45
360 514 3.807538 GCTGCATGCACGGTCTGG 61.808 66.667 18.46 6.37 42.31 3.86
361 515 2.745100 AGCTGCATGCACGGTCTG 60.745 61.111 18.46 7.18 45.94 3.51
362 516 2.435586 GAGCTGCATGCACGGTCT 60.436 61.111 27.37 18.55 45.94 3.85
363 517 2.435586 AGAGCTGCATGCACGGTC 60.436 61.111 27.39 27.39 45.94 4.79
364 518 2.435586 GAGAGCTGCATGCACGGT 60.436 61.111 18.46 18.01 45.94 4.83
365 519 1.374343 AATGAGAGCTGCATGCACGG 61.374 55.000 18.46 9.68 45.94 4.94
366 520 0.248094 CAATGAGAGCTGCATGCACG 60.248 55.000 18.46 14.14 45.94 5.34
367 521 0.525668 GCAATGAGAGCTGCATGCAC 60.526 55.000 18.46 13.93 45.94 4.57
368 522 0.679960 AGCAATGAGAGCTGCATGCA 60.680 50.000 21.29 21.29 45.94 3.96
369 523 0.029567 GAGCAATGAGAGCTGCATGC 59.970 55.000 11.82 11.82 43.58 4.06
520 715 4.825634 AGTACGTGGTATAGCAGCTAATCA 59.174 41.667 6.13 2.57 0.00 2.57
534 729 2.159338 CCGTAAGCATGTAGTACGTGGT 60.159 50.000 19.16 19.16 46.57 4.16
536 731 1.850441 GCCGTAAGCATGTAGTACGTG 59.150 52.381 16.78 16.78 42.97 4.49
554 749 4.039245 TGCAGTTCATATGGTAGAGTAGCC 59.961 45.833 2.13 0.00 0.00 3.93
560 755 7.611467 AGACATTTTTGCAGTTCATATGGTAGA 59.389 33.333 2.13 0.00 0.00 2.59
561 756 7.765307 AGACATTTTTGCAGTTCATATGGTAG 58.235 34.615 2.13 0.00 0.00 3.18
582 781 2.747467 CGGACGGAGGGAGTATAAGACA 60.747 54.545 0.00 0.00 0.00 3.41
583 782 1.878734 CGGACGGAGGGAGTATAAGAC 59.121 57.143 0.00 0.00 0.00 3.01
584 783 1.202855 CCGGACGGAGGGAGTATAAGA 60.203 57.143 4.40 0.00 37.50 2.10
586 785 0.846015 TCCGGACGGAGGGAGTATAA 59.154 55.000 9.76 0.00 39.76 0.98
588 787 0.032813 TTTCCGGACGGAGGGAGTAT 60.033 55.000 13.64 0.00 46.06 2.12
590 789 1.305887 ATTTCCGGACGGAGGGAGT 60.306 57.895 13.64 0.00 46.06 3.85
591 790 1.043673 AGATTTCCGGACGGAGGGAG 61.044 60.000 13.64 0.00 46.06 4.30
593 792 1.442148 GAGATTTCCGGACGGAGGG 59.558 63.158 13.64 0.00 46.06 4.30
594 793 1.442148 GGAGATTTCCGGACGGAGG 59.558 63.158 13.64 0.00 46.06 4.30
602 2042 9.538298 AGTGCGTACTATACTTGGAGATTTCCG 62.538 44.444 3.62 0.00 39.99 4.30
605 2045 6.466885 AGTGCGTACTATACTTGGAGATTT 57.533 37.500 3.62 0.00 34.74 2.17
614 2054 2.498481 TGCCCAAAGTGCGTACTATACT 59.502 45.455 6.58 0.00 35.69 2.12
618 2058 0.672401 GCTGCCCAAAGTGCGTACTA 60.672 55.000 6.58 0.00 35.69 1.82
623 2063 3.376078 ATGGCTGCCCAAAGTGCG 61.376 61.111 17.53 0.00 46.14 5.34
643 2083 3.192001 TGGTACGTTCTGGTAAGCTACTG 59.808 47.826 0.00 0.00 0.00 2.74
646 2086 3.429822 GCATGGTACGTTCTGGTAAGCTA 60.430 47.826 0.00 0.00 0.00 3.32
649 2089 2.671396 GTGCATGGTACGTTCTGGTAAG 59.329 50.000 0.00 0.00 0.00 2.34
660 2100 1.019278 CCAGTGACCGTGCATGGTAC 61.019 60.000 30.40 24.60 44.01 3.34
670 2134 1.674962 GTAGGCTAGTACCAGTGACCG 59.325 57.143 0.00 0.00 0.00 4.79
675 2176 3.181456 CGTCCTAGTAGGCTAGTACCAGT 60.181 52.174 11.75 0.00 42.35 4.00
677 2178 3.041211 TCGTCCTAGTAGGCTAGTACCA 58.959 50.000 11.75 0.00 42.35 3.25
678 2179 3.398406 GTCGTCCTAGTAGGCTAGTACC 58.602 54.545 11.75 0.00 42.35 3.34
679 2180 3.056304 CGTCGTCCTAGTAGGCTAGTAC 58.944 54.545 11.75 3.22 42.35 2.73
686 2187 2.023318 CAGGCGTCGTCCTAGTAGG 58.977 63.158 10.24 10.24 33.95 3.18
688 2189 1.077930 AGCAGGCGTCGTCCTAGTA 60.078 57.895 7.72 0.00 33.95 1.82
695 2196 3.986006 TTTCGGAGCAGGCGTCGT 61.986 61.111 0.00 0.00 0.00 4.34
701 2204 1.028905 TGTTTTGGTTTCGGAGCAGG 58.971 50.000 0.00 0.00 37.03 4.85
756 2262 2.599739 TGTGTACGTACAGTGCTACG 57.400 50.000 28.02 17.83 44.21 3.51
779 2285 4.202131 GGAATAGTCGGTCCTAAGTTCTGG 60.202 50.000 0.00 0.00 0.00 3.86
794 2300 0.108992 TGCGTGACCGTGGAATAGTC 60.109 55.000 0.00 0.00 36.15 2.59
796 2302 0.999406 CTTGCGTGACCGTGGAATAG 59.001 55.000 0.00 0.00 36.15 1.73
797 2303 0.604073 TCTTGCGTGACCGTGGAATA 59.396 50.000 0.00 0.00 36.15 1.75
846 2352 7.652507 GTCACGTTTATATAGAAAAGAGAGGGG 59.347 40.741 11.86 0.00 0.00 4.79
857 2363 5.008019 GTGGTCTCGGTCACGTTTATATAGA 59.992 44.000 0.00 0.00 41.85 1.98
912 2418 0.613260 CAGTTGCTGGCCAGTACCTA 59.387 55.000 32.81 12.26 0.00 3.08
937 2445 0.741927 TGACGCGGTCGATCAGTCTA 60.742 55.000 12.47 6.24 39.41 2.59
1300 2808 4.087892 GCCGGAAGCTCAGCCAGA 62.088 66.667 5.05 0.00 38.99 3.86
1315 2823 1.618640 GAGACAAGAGAACGTGCGCC 61.619 60.000 4.18 0.00 0.00 6.53
1329 2838 0.392706 ACACTCACAATGGCGAGACA 59.607 50.000 8.61 0.00 33.33 3.41
1590 3102 2.857592 ACGCCGTAACCAGTGTATAG 57.142 50.000 0.00 0.00 0.00 1.31
1591 3103 3.013219 TGTACGCCGTAACCAGTGTATA 58.987 45.455 0.00 0.00 32.10 1.47
1602 3114 1.207339 CGTGAGTGTGTACGCCGTA 59.793 57.895 3.51 0.00 33.25 4.02
1623 3139 2.029380 CGGCCATCCATTAGTGATCGTA 60.029 50.000 2.24 0.00 0.00 3.43
1861 3386 3.005554 ACAATCGTGCTTTCTCTCCATG 58.994 45.455 0.00 0.00 0.00 3.66
1862 3387 3.340814 ACAATCGTGCTTTCTCTCCAT 57.659 42.857 0.00 0.00 0.00 3.41
1877 3408 6.406896 CGTGCACGTTACAACAATATACAATC 59.593 38.462 30.50 0.00 34.11 2.67
1888 3419 1.459624 CGTCATCGTGCACGTTACAAC 60.460 52.381 35.74 24.58 40.80 3.32
1895 3426 1.070471 TGTGATCGTCATCGTGCACG 61.070 55.000 32.76 32.76 41.18 5.34
1932 3463 3.712881 GTCGTGCACCGTGCCTTC 61.713 66.667 20.67 10.11 44.23 3.46
2305 3836 0.032952 TAGTTCACCACACGGCAGTC 59.967 55.000 0.00 0.00 34.57 3.51
2335 3870 2.932614 CTGCTTAATCGACCTGACCTTG 59.067 50.000 0.00 0.00 0.00 3.61
2366 3904 0.753867 TGAAAGCCACTACACACGGA 59.246 50.000 0.00 0.00 0.00 4.69
2368 3906 1.865865 ACTGAAAGCCACTACACACG 58.134 50.000 0.00 0.00 37.60 4.49
2451 4030 8.262933 CACATCACCAGATACACCATATATCAT 58.737 37.037 0.00 0.00 32.37 2.45
2452 4031 7.614494 CACATCACCAGATACACCATATATCA 58.386 38.462 0.00 0.00 32.37 2.15
2453 4032 6.536582 GCACATCACCAGATACACCATATATC 59.463 42.308 0.00 0.00 31.88 1.63
2456 4035 4.645535 GCACATCACCAGATACACCATAT 58.354 43.478 0.00 0.00 31.88 1.78
2513 4092 0.944386 CAACCGAACACCTCCAACAG 59.056 55.000 0.00 0.00 0.00 3.16
2563 4146 2.687370 TCATCATGACACTCACCAACG 58.313 47.619 0.00 0.00 0.00 4.10
2606 4189 6.734104 AATGACAGAGACATAGCAAAACTC 57.266 37.500 0.00 0.00 0.00 3.01
2607 4190 6.712095 TCAAATGACAGAGACATAGCAAAACT 59.288 34.615 0.00 0.00 0.00 2.66
2608 4191 6.902341 TCAAATGACAGAGACATAGCAAAAC 58.098 36.000 0.00 0.00 0.00 2.43
2609 4192 6.936335 TCTCAAATGACAGAGACATAGCAAAA 59.064 34.615 0.00 0.00 36.05 2.44
2610 4193 6.466812 TCTCAAATGACAGAGACATAGCAAA 58.533 36.000 0.00 0.00 36.05 3.68
2611 4194 6.041423 TCTCAAATGACAGAGACATAGCAA 57.959 37.500 0.00 0.00 36.05 3.91
2612 4195 5.665916 TCTCAAATGACAGAGACATAGCA 57.334 39.130 0.00 0.00 36.05 3.49
2619 4202 7.933577 ACATAACAAAGTCTCAAATGACAGAGA 59.066 33.333 0.00 0.00 39.27 3.10
2620 4203 8.092521 ACATAACAAAGTCTCAAATGACAGAG 57.907 34.615 0.00 0.00 39.27 3.35
2621 4204 8.450578 AACATAACAAAGTCTCAAATGACAGA 57.549 30.769 0.00 0.00 39.27 3.41
2622 4205 9.173939 GAAACATAACAAAGTCTCAAATGACAG 57.826 33.333 0.00 0.00 39.27 3.51
2623 4206 8.681806 TGAAACATAACAAAGTCTCAAATGACA 58.318 29.630 0.00 0.00 39.27 3.58
2624 4207 9.173939 CTGAAACATAACAAAGTCTCAAATGAC 57.826 33.333 0.00 0.00 37.23 3.06
2625 4208 8.902806 ACTGAAACATAACAAAGTCTCAAATGA 58.097 29.630 0.00 0.00 0.00 2.57
2626 4209 9.173939 GACTGAAACATAACAAAGTCTCAAATG 57.826 33.333 0.00 0.00 33.02 2.32
2627 4210 8.070171 CGACTGAAACATAACAAAGTCTCAAAT 58.930 33.333 0.00 0.00 33.49 2.32
2628 4211 7.279090 TCGACTGAAACATAACAAAGTCTCAAA 59.721 33.333 0.00 0.00 33.49 2.69
2629 4212 6.759356 TCGACTGAAACATAACAAAGTCTCAA 59.241 34.615 0.00 0.00 33.49 3.02
2630 4213 6.277605 TCGACTGAAACATAACAAAGTCTCA 58.722 36.000 0.00 0.00 33.49 3.27
2631 4214 6.764877 TCGACTGAAACATAACAAAGTCTC 57.235 37.500 0.00 0.00 33.49 3.36
2632 4215 8.088981 ACTATCGACTGAAACATAACAAAGTCT 58.911 33.333 0.00 0.00 33.49 3.24
2633 4216 8.240883 ACTATCGACTGAAACATAACAAAGTC 57.759 34.615 0.00 0.00 0.00 3.01
2634 4217 9.871238 ATACTATCGACTGAAACATAACAAAGT 57.129 29.630 0.00 0.00 0.00 2.66
2638 4221 9.731819 GAAGATACTATCGACTGAAACATAACA 57.268 33.333 0.00 0.00 0.00 2.41
2639 4222 9.182933 GGAAGATACTATCGACTGAAACATAAC 57.817 37.037 0.00 0.00 0.00 1.89
2640 4223 9.132923 AGGAAGATACTATCGACTGAAACATAA 57.867 33.333 0.00 0.00 0.00 1.90
2641 4224 8.693120 AGGAAGATACTATCGACTGAAACATA 57.307 34.615 0.00 0.00 0.00 2.29
2642 4225 7.589958 AGGAAGATACTATCGACTGAAACAT 57.410 36.000 0.00 0.00 0.00 2.71
2643 4226 7.406031 AAGGAAGATACTATCGACTGAAACA 57.594 36.000 0.00 0.00 0.00 2.83
2644 4227 9.798994 TTAAAGGAAGATACTATCGACTGAAAC 57.201 33.333 0.00 0.00 0.00 2.78
2661 4244 9.774742 CGAATCTCCTTGTAAAATTAAAGGAAG 57.225 33.333 5.02 0.90 46.70 3.46
2662 4245 9.292195 ACGAATCTCCTTGTAAAATTAAAGGAA 57.708 29.630 5.02 0.00 46.70 3.36
2663 4246 8.726988 CACGAATCTCCTTGTAAAATTAAAGGA 58.273 33.333 3.53 3.53 45.63 3.36
2664 4247 8.512138 ACACGAATCTCCTTGTAAAATTAAAGG 58.488 33.333 0.00 0.00 41.60 3.11
2815 4398 3.812156 TCGACTTCAGACTGGTTTGAA 57.188 42.857 1.81 6.54 33.46 2.69
2871 4454 7.653713 CGAACACTGTAATAGAGAGGCAAATAT 59.346 37.037 0.00 0.00 0.00 1.28
2927 4512 4.992951 GCAATTTTTGAGGACTGCTTTCAT 59.007 37.500 0.00 0.00 0.00 2.57
2999 4589 5.488262 TCATCAACTCAGACAATCTGGAA 57.512 39.130 6.01 0.00 44.39 3.53
3039 4630 0.889186 CTAACACTGGCGCAAAGGGT 60.889 55.000 10.83 11.02 30.72 4.34
3212 4811 3.154710 CCCTAGGGGTTTTGTGAAACTC 58.845 50.000 21.44 0.00 44.00 3.01


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

AutoCloner maintained by Alex Coulton.