Multiple sequence alignment - TraesCS1B01G213900

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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 TraesCS1B01G213900 chr1B 100.000 5395 0 0 1 5395 388381085 388386479 0.000000e+00 9963.0
1 TraesCS1B01G213900 chr1B 85.801 331 35 9 431 753 263981350 263981676 1.860000e-89 340.0
2 TraesCS1B01G213900 chr1B 84.146 328 43 6 432 752 583978860 583979185 5.250000e-80 309.0
3 TraesCS1B01G213900 chr1B 82.558 86 15 0 1520 1605 487495854 487495769 5.790000e-10 76.8
4 TraesCS1B01G213900 chr1B 92.105 38 1 2 3808 3844 106654750 106654786 1.000000e-02 52.8
5 TraesCS1B01G213900 chr1D 92.046 2967 152 41 376 3316 286088899 286091807 0.000000e+00 4095.0
6 TraesCS1B01G213900 chr1D 91.667 828 41 9 3839 4660 286092284 286093089 0.000000e+00 1122.0
7 TraesCS1B01G213900 chr1D 83.876 645 83 15 2 630 286088216 286088855 3.600000e-166 595.0
8 TraesCS1B01G213900 chr1D 90.086 464 22 11 3313 3760 286091832 286092287 1.010000e-161 580.0
9 TraesCS1B01G213900 chr1D 92.042 377 21 6 4873 5246 286093287 286093657 6.190000e-144 521.0
10 TraesCS1B01G213900 chr1D 80.189 424 64 15 335 750 307448343 307448754 3.160000e-77 300.0
11 TraesCS1B01G213900 chr1D 89.831 177 10 3 4712 4888 286093106 286093274 2.530000e-53 220.0
12 TraesCS1B01G213900 chr1D 94.030 134 8 0 5262 5395 286093645 286093778 2.550000e-48 204.0
13 TraesCS1B01G213900 chr1D 90.476 63 5 1 3757 3818 96486290 96486352 1.250000e-11 82.4
14 TraesCS1B01G213900 chr1A 93.130 2751 119 42 604 3316 357414637 357417355 0.000000e+00 3969.0
15 TraesCS1B01G213900 chr1A 91.552 580 20 11 3839 4416 357417812 357418364 0.000000e+00 773.0
16 TraesCS1B01G213900 chr1A 82.861 776 108 17 1 760 357413705 357414471 0.000000e+00 673.0
17 TraesCS1B01G213900 chr1A 92.248 387 19 4 4471 4855 357418375 357418752 6.150000e-149 538.0
18 TraesCS1B01G213900 chr1A 87.126 435 19 14 3332 3759 357417405 357417809 4.920000e-125 459.0
19 TraesCS1B01G213900 chr1A 76.887 212 42 6 1520 1726 463290368 463290159 4.420000e-21 113.0
20 TraesCS1B01G213900 chr6D 82.160 426 56 15 337 749 316101947 316102365 1.110000e-91 348.0
21 TraesCS1B01G213900 chr6D 82.530 332 45 9 434 753 460563723 460563393 4.110000e-71 279.0
22 TraesCS1B01G213900 chr6D 100.000 28 0 0 3817 3844 38953541 38953568 1.000000e-02 52.8
23 TraesCS1B01G213900 chr6D 100.000 28 0 0 3817 3844 150116232 150116259 1.000000e-02 52.8
24 TraesCS1B01G213900 chr6D 100.000 28 0 0 3817 3844 280567276 280567249 1.000000e-02 52.8
25 TraesCS1B01G213900 chr5B 80.235 425 67 11 337 752 396438763 396438347 2.440000e-78 303.0
26 TraesCS1B01G213900 chr5B 92.188 64 4 1 3757 3819 387175351 387175288 7.440000e-14 89.8
27 TraesCS1B01G213900 chr5B 88.889 63 6 1 3757 3818 50347521 50347583 5.790000e-10 76.8
28 TraesCS1B01G213900 chr5B 100.000 29 0 0 3816 3844 86843343 86843371 3.000000e-03 54.7
29 TraesCS1B01G213900 chr5D 83.183 333 44 8 428 751 7021381 7021710 1.470000e-75 294.0
30 TraesCS1B01G213900 chr2B 91.045 67 5 1 3753 3818 213400312 213400246 7.440000e-14 89.8
31 TraesCS1B01G213900 chr2B 90.476 63 5 1 3757 3818 764910574 764910636 1.250000e-11 82.4
32 TraesCS1B01G213900 chr2B 89.062 64 6 1 3756 3818 107531357 107531294 1.610000e-10 78.7
33 TraesCS1B01G213900 chr7D 88.889 63 6 1 3757 3818 7199042 7199104 5.790000e-10 76.8
34 TraesCS1B01G213900 chr3B 88.889 63 6 1 3757 3818 246158900 246158838 5.790000e-10 76.8
35 TraesCS1B01G213900 chr3B 96.774 31 1 0 3817 3847 562586506 562586476 1.000000e-02 52.8
36 TraesCS1B01G213900 chr2D 88.889 63 6 1 3757 3818 139586621 139586683 5.790000e-10 76.8
37 TraesCS1B01G213900 chr2D 100.000 29 0 0 3816 3844 161245554 161245526 3.000000e-03 54.7
38 TraesCS1B01G213900 chr3D 100.000 29 0 0 3816 3844 310898723 310898695 3.000000e-03 54.7
39 TraesCS1B01G213900 chr7B 100.000 28 0 0 3817 3844 567728734 567728707 1.000000e-02 52.8


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 TraesCS1B01G213900 chr1B 388381085 388386479 5394 False 9963.000000 9963 100.000000 1 5395 1 chr1B.!!$F3 5394
1 TraesCS1B01G213900 chr1D 286088216 286093778 5562 False 1048.142857 4095 90.511143 2 5395 7 chr1D.!!$F3 5393
2 TraesCS1B01G213900 chr1A 357413705 357418752 5047 False 1282.400000 3969 89.383400 1 4855 5 chr1A.!!$F1 4854

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
166 170 0.319211 CCAAGTTGTAGGACGCGTGA 60.319 55.0 20.70 0.0 0.0 4.35 F
1585 2093 0.322322 GGACCGGGACATGTACAACA 59.678 55.0 10.99 0.0 0.0 3.33 F
1871 2383 0.110238 CGTCGAACACCTGCCATTTG 60.110 55.0 0.00 0.0 0.0 2.32 F
2378 2893 0.508641 CGTCGCCTTGCACATATAGC 59.491 55.0 0.00 0.0 0.0 2.97 F
4245 4856 0.179078 TTGTGCTTTGCTTTGCTGGG 60.179 50.0 0.00 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1838 2346 0.389757 TCGACGAAATGTGGGTGTCA 59.610 50.000 0.0 0.0 0.00 3.58 R
2521 3048 0.318107 CCTTGCGTTTGTGCTCTTGG 60.318 55.000 0.0 0.0 35.36 3.61 R
3825 4435 0.113776 ACAAGTACTCCCTCCGTCCA 59.886 55.000 0.0 0.0 0.00 4.02 R
4248 4859 0.535797 TACTCTCCGAGACGAGCTGA 59.464 55.000 0.0 0.0 33.32 4.26 R
5049 5697 1.933181 GGTGCAAAACAAACTTCAGCC 59.067 47.619 0.0 0.0 0.00 4.85 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
48 51 2.224426 ACTCTAACCGACAACAATGGCA 60.224 45.455 0.00 0.00 32.33 4.92
61 64 0.606401 AATGGCAGACCGTCAAGTGG 60.606 55.000 0.40 0.00 39.70 4.00
166 170 0.319211 CCAAGTTGTAGGACGCGTGA 60.319 55.000 20.70 0.00 0.00 4.35
177 181 3.103911 CGCGTGAGTGGAACGGTC 61.104 66.667 0.00 0.00 45.86 4.79
178 182 2.338984 GCGTGAGTGGAACGGTCT 59.661 61.111 0.00 0.00 45.86 3.85
179 183 1.582968 GCGTGAGTGGAACGGTCTA 59.417 57.895 0.00 0.00 45.86 2.59
183 188 1.884579 GTGAGTGGAACGGTCTAGACA 59.115 52.381 23.91 0.00 45.86 3.41
186 191 0.963962 GTGGAACGGTCTAGACACCA 59.036 55.000 23.91 21.07 36.01 4.17
199 204 0.963355 GACACCAATAAAGCCCGCCA 60.963 55.000 0.00 0.00 0.00 5.69
216 221 0.530288 CCATCGGTTTGCGGGAAAAT 59.470 50.000 0.00 0.00 0.00 1.82
226 239 4.487714 TTGCGGGAAAATAGATCAGTCT 57.512 40.909 0.00 0.00 38.52 3.24
227 240 5.607939 TTGCGGGAAAATAGATCAGTCTA 57.392 39.130 0.00 0.00 41.03 2.59
256 269 2.124151 GGTGCCGCCTTGGATGAT 60.124 61.111 0.00 0.00 42.00 2.45
259 272 0.947244 GTGCCGCCTTGGATGATAAG 59.053 55.000 0.00 0.00 42.00 1.73
268 281 1.107945 TGGATGATAAGTCGCGTCCA 58.892 50.000 5.77 6.33 33.40 4.02
302 315 0.543410 TCGTGGGCAGTTTAGGGAGA 60.543 55.000 0.00 0.00 0.00 3.71
306 319 0.815615 GGGCAGTTTAGGGAGATGCG 60.816 60.000 0.00 0.00 37.76 4.73
316 329 2.308690 AGGGAGATGCGGTAACTCTAC 58.691 52.381 3.63 0.00 0.00 2.59
321 334 4.508124 GGAGATGCGGTAACTCTACAATTG 59.492 45.833 3.24 3.24 0.00 2.32
350 363 2.969443 AACTCGAGAATGGCGTTTTG 57.031 45.000 21.68 0.00 0.00 2.44
423 453 5.886960 AAGTCGATTTCCAAGAAATCTGG 57.113 39.130 21.47 11.41 35.17 3.86
424 454 4.911390 AGTCGATTTCCAAGAAATCTGGT 58.089 39.130 21.47 8.12 35.17 4.00
425 455 5.316987 AGTCGATTTCCAAGAAATCTGGTT 58.683 37.500 21.47 7.51 35.17 3.67
468 498 2.159156 GGATGTGAGGCGTATGTGTGTA 60.159 50.000 0.00 0.00 0.00 2.90
483 513 8.365210 CGTATGTGTGTAAAAATTTCAAGATGC 58.635 33.333 0.00 0.00 0.00 3.91
486 516 8.659925 TGTGTGTAAAAATTTCAAGATGCAAT 57.340 26.923 0.00 0.00 0.00 3.56
499 529 3.683989 AGATGCAATACGTTGAAATGCG 58.316 40.909 0.00 0.00 39.81 4.73
584 1087 4.278170 CAGATTTGTCTTTGCACAACCCTA 59.722 41.667 0.00 0.00 35.97 3.53
598 1101 5.556470 CACAACCCTAATTTCGACGTATTG 58.444 41.667 0.00 0.00 0.00 1.90
600 1103 3.864243 ACCCTAATTTCGACGTATTGCA 58.136 40.909 0.00 0.00 0.00 4.08
619 1122 9.083080 GTATTGCATCCTAAAAATTTACACACC 57.917 33.333 0.00 0.00 0.00 4.16
715 1219 9.869844 CACGAATTTTAAAATTTGCATTTGGTA 57.130 25.926 29.12 0.00 41.44 3.25
739 1243 0.820226 TCATGAAGCTCGGTCTCCAG 59.180 55.000 0.00 0.00 0.00 3.86
771 1275 4.162888 TCCGGATAAAACTCCCTCTTTACC 59.837 45.833 0.00 0.00 31.04 2.85
873 1380 1.467342 GGGTCATACTTTGTGCCGTTC 59.533 52.381 0.00 0.00 0.00 3.95
880 1387 1.074889 ACTTTGTGCCGTTCCCCTATT 59.925 47.619 0.00 0.00 0.00 1.73
881 1388 2.306512 ACTTTGTGCCGTTCCCCTATTA 59.693 45.455 0.00 0.00 0.00 0.98
898 1405 6.152831 CCCCTATTATATAAAACCCAGCAAGC 59.847 42.308 0.00 0.00 0.00 4.01
924 1432 1.805134 GCGAGTGAGCTCAGAGCAC 60.805 63.158 24.64 18.58 45.56 4.40
935 1443 3.619767 AGAGCACAGCAGCGGACA 61.620 61.111 0.00 0.00 40.15 4.02
1002 1510 2.680352 GCTCCACTCCGACTCCCA 60.680 66.667 0.00 0.00 0.00 4.37
1048 1556 4.794648 TCGCCCCCTGCATTTCCG 62.795 66.667 0.00 0.00 41.33 4.30
1055 1563 2.040544 CCTGCATTTCCGCCGAAGT 61.041 57.895 0.00 0.00 0.00 3.01
1218 1726 4.409218 GACTCGTACGTGGCCGCA 62.409 66.667 18.18 0.00 37.70 5.69
1582 2090 0.611200 CAAGGACCGGGACATGTACA 59.389 55.000 10.99 0.00 0.00 2.90
1585 2093 0.322322 GGACCGGGACATGTACAACA 59.678 55.000 10.99 0.00 0.00 3.33
1821 2329 3.227273 GGTAACTCCTCTCCCTCCC 57.773 63.158 0.00 0.00 0.00 4.30
1823 2331 0.398806 GTAACTCCTCTCCCTCCCCC 60.399 65.000 0.00 0.00 0.00 5.40
1838 2346 3.953775 CCCCTTGTCCGTGTGCCT 61.954 66.667 0.00 0.00 0.00 4.75
1840 2348 2.425592 CCTTGTCCGTGTGCCTGA 59.574 61.111 0.00 0.00 0.00 3.86
1841 2349 1.961277 CCTTGTCCGTGTGCCTGAC 60.961 63.158 0.00 0.00 0.00 3.51
1842 2350 1.227527 CTTGTCCGTGTGCCTGACA 60.228 57.895 0.00 0.00 37.24 3.58
1871 2383 0.110238 CGTCGAACACCTGCCATTTG 60.110 55.000 0.00 0.00 0.00 2.32
1884 2396 1.586154 CCATTTGCCTCACACCGTCC 61.586 60.000 0.00 0.00 0.00 4.79
1885 2397 1.671054 ATTTGCCTCACACCGTCCG 60.671 57.895 0.00 0.00 0.00 4.79
1886 2398 2.391724 ATTTGCCTCACACCGTCCGT 62.392 55.000 0.00 0.00 0.00 4.69
2093 2605 4.027572 TCAAGTTTTGCTTTTCCTCGTG 57.972 40.909 0.00 0.00 34.69 4.35
2095 2607 1.681264 AGTTTTGCTTTTCCTCGTGGG 59.319 47.619 3.23 0.00 0.00 4.61
2099 2614 1.375326 GCTTTTCCTCGTGGGTCCT 59.625 57.895 3.23 0.00 36.25 3.85
2128 2643 2.972505 CTGACACGGCGGTTGCTT 60.973 61.111 13.24 0.00 42.25 3.91
2132 2647 2.051345 CACGGCGGTTGCTTGTTC 60.051 61.111 13.24 0.00 42.25 3.18
2137 2652 2.943653 CGGTTGCTTGTTCCCGTC 59.056 61.111 0.00 0.00 35.78 4.79
2251 2766 2.046285 GTTCACCATCAAGGGCGGG 61.046 63.158 0.00 0.00 43.89 6.13
2311 2826 2.824936 TCCCGTTATCCTACACGACAAA 59.175 45.455 0.00 0.00 38.76 2.83
2336 2851 3.157949 CCCCTCCCGAAGCTCTCC 61.158 72.222 0.00 0.00 0.00 3.71
2368 2883 3.930848 AGGAGTAATTTTACGTCGCCTTG 59.069 43.478 0.00 0.00 38.65 3.61
2370 2885 3.068560 AGTAATTTTACGTCGCCTTGCA 58.931 40.909 0.00 0.00 38.65 4.08
2377 2892 1.852942 ACGTCGCCTTGCACATATAG 58.147 50.000 0.00 0.00 0.00 1.31
2378 2893 0.508641 CGTCGCCTTGCACATATAGC 59.491 55.000 0.00 0.00 0.00 2.97
2465 2992 1.607801 CTCGTGCCTGTCTCCATCCA 61.608 60.000 0.00 0.00 0.00 3.41
2519 3046 1.594836 GCCGGTGTGTTCGTTACCA 60.595 57.895 1.90 0.00 34.10 3.25
2521 3048 1.562575 CCGGTGTGTTCGTTACCAGC 61.563 60.000 0.00 0.00 34.10 4.85
2610 3137 1.306568 GGTTCCAGCTCCTCCTCCT 60.307 63.158 0.00 0.00 0.00 3.69
2611 3138 1.621672 GGTTCCAGCTCCTCCTCCTG 61.622 65.000 0.00 0.00 0.00 3.86
2612 3139 1.306482 TTCCAGCTCCTCCTCCTGG 60.306 63.158 0.00 0.00 45.88 4.45
2613 3140 2.040278 CCAGCTCCTCCTCCTGGT 59.960 66.667 0.00 0.00 40.92 4.00
2642 3169 6.211785 TGGTTTTTACCTTTTCACCTCAACTT 59.788 34.615 0.00 0.00 0.00 2.66
2647 3174 4.461198 ACCTTTTCACCTCAACTTCGATT 58.539 39.130 0.00 0.00 0.00 3.34
2672 3199 1.912043 GGAGGATAGGCCATGCATACT 59.088 52.381 5.01 0.54 40.02 2.12
2673 3200 3.107601 GGAGGATAGGCCATGCATACTA 58.892 50.000 5.01 3.06 40.02 1.82
2674 3201 3.118592 GGAGGATAGGCCATGCATACTAC 60.119 52.174 5.01 0.00 40.02 2.73
2749 3276 2.979676 CAGTGCCGCATGTGGTGT 60.980 61.111 25.68 8.62 0.00 4.16
2986 3513 1.903404 CGCCTGGAAAAGCTGGGTT 60.903 57.895 0.00 0.00 0.00 4.11
2989 3516 1.272490 GCCTGGAAAAGCTGGGTTTAC 59.728 52.381 0.00 0.00 0.00 2.01
3065 3595 0.591170 CACTCCCGTGAACGCAAAAT 59.409 50.000 0.00 0.00 43.97 1.82
3072 3602 6.127842 ACTCCCGTGAACGCAAAATAATAAAT 60.128 34.615 0.00 0.00 38.18 1.40
3073 3603 7.066043 ACTCCCGTGAACGCAAAATAATAAATA 59.934 33.333 0.00 0.00 38.18 1.40
3095 3625 5.551760 AATTAATCCAACAAGAGACAGCG 57.448 39.130 0.00 0.00 0.00 5.18
3134 3672 1.546029 GGCCAGGTTTGAATGGAGTTC 59.454 52.381 0.00 0.00 39.02 3.01
3140 3678 0.796312 TTTGAATGGAGTTCGCTCGC 59.204 50.000 0.00 0.00 44.99 5.03
3374 3959 3.248602 TGAAAGCGAAAAGAGTGAAGAGC 59.751 43.478 0.00 0.00 0.00 4.09
3392 3994 0.937304 GCGCTCACTGTTCTGTTCAA 59.063 50.000 0.00 0.00 0.00 2.69
3393 3995 1.070309 GCGCTCACTGTTCTGTTCAAG 60.070 52.381 0.00 0.00 0.00 3.02
3394 3996 2.205074 CGCTCACTGTTCTGTTCAAGT 58.795 47.619 0.00 0.00 0.00 3.16
3395 3997 2.033407 CGCTCACTGTTCTGTTCAAGTG 60.033 50.000 0.00 0.00 0.00 3.16
3396 3998 2.286654 GCTCACTGTTCTGTTCAAGTGC 60.287 50.000 0.00 0.00 0.00 4.40
3397 3999 2.938451 CTCACTGTTCTGTTCAAGTGCA 59.062 45.455 0.00 0.00 0.00 4.57
3398 4000 2.677836 TCACTGTTCTGTTCAAGTGCAC 59.322 45.455 9.40 9.40 0.00 4.57
3399 4001 2.679837 CACTGTTCTGTTCAAGTGCACT 59.320 45.455 15.25 15.25 0.00 4.40
3400 4002 3.871006 CACTGTTCTGTTCAAGTGCACTA 59.129 43.478 22.01 1.56 0.00 2.74
3401 4003 4.025396 CACTGTTCTGTTCAAGTGCACTAG 60.025 45.833 22.01 13.62 0.00 2.57
3402 4004 4.122776 CTGTTCTGTTCAAGTGCACTAGT 58.877 43.478 22.01 1.56 0.00 2.57
3419 4021 4.275196 CACTAGTAGTACGCATTAGCAGGA 59.725 45.833 1.57 0.00 42.27 3.86
3582 4191 2.690497 GCTAGGCTAGTGATGTCAGTGA 59.310 50.000 21.92 0.00 0.00 3.41
3678 4287 2.893637 GACTGTACGTCCAATGCTCAT 58.106 47.619 0.00 0.00 36.62 2.90
3679 4288 2.604914 GACTGTACGTCCAATGCTCATG 59.395 50.000 0.00 0.00 36.62 3.07
3680 4289 2.028112 ACTGTACGTCCAATGCTCATGT 60.028 45.455 0.00 0.00 0.00 3.21
3681 4290 3.194755 ACTGTACGTCCAATGCTCATGTA 59.805 43.478 0.00 0.00 0.00 2.29
3682 4291 4.141937 ACTGTACGTCCAATGCTCATGTAT 60.142 41.667 0.00 0.00 0.00 2.29
3743 4353 1.871080 CTTCTGAAGAACACAGGCGT 58.129 50.000 12.01 0.00 36.22 5.68
3759 4369 6.430000 ACACAGGCGTGAAAAAGATAATTACT 59.570 34.615 14.38 0.00 46.80 2.24
3760 4370 6.961554 CACAGGCGTGAAAAAGATAATTACTC 59.038 38.462 14.38 0.00 46.80 2.59
3761 4371 6.093633 ACAGGCGTGAAAAAGATAATTACTCC 59.906 38.462 14.38 0.00 0.00 3.85
3762 4372 5.589050 AGGCGTGAAAAAGATAATTACTCCC 59.411 40.000 0.00 0.00 0.00 4.30
3763 4373 5.589050 GGCGTGAAAAAGATAATTACTCCCT 59.411 40.000 0.00 0.00 0.00 4.20
3764 4374 6.238402 GGCGTGAAAAAGATAATTACTCCCTC 60.238 42.308 0.00 0.00 0.00 4.30
3765 4375 6.315393 GCGTGAAAAAGATAATTACTCCCTCA 59.685 38.462 0.00 0.00 0.00 3.86
3766 4376 7.466050 GCGTGAAAAAGATAATTACTCCCTCAG 60.466 40.741 0.00 0.00 0.00 3.35
3767 4377 7.549488 CGTGAAAAAGATAATTACTCCCTCAGT 59.451 37.037 0.00 0.00 39.41 3.41
3768 4378 8.884726 GTGAAAAAGATAATTACTCCCTCAGTC 58.115 37.037 0.00 0.00 36.43 3.51
3769 4379 8.047310 TGAAAAAGATAATTACTCCCTCAGTCC 58.953 37.037 0.00 0.00 36.43 3.85
3770 4380 5.793030 AAGATAATTACTCCCTCAGTCCG 57.207 43.478 0.00 0.00 36.43 4.79
3771 4381 5.063017 AGATAATTACTCCCTCAGTCCGA 57.937 43.478 0.00 0.00 36.43 4.55
3772 4382 5.455872 AGATAATTACTCCCTCAGTCCGAA 58.544 41.667 0.00 0.00 36.43 4.30
3773 4383 5.897824 AGATAATTACTCCCTCAGTCCGAAA 59.102 40.000 0.00 0.00 36.43 3.46
3774 4384 4.903045 AATTACTCCCTCAGTCCGAAAA 57.097 40.909 0.00 0.00 36.43 2.29
3775 4385 5.437191 AATTACTCCCTCAGTCCGAAAAT 57.563 39.130 0.00 0.00 36.43 1.82
3776 4386 6.555463 AATTACTCCCTCAGTCCGAAAATA 57.445 37.500 0.00 0.00 36.43 1.40
3777 4387 3.889520 ACTCCCTCAGTCCGAAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
3778 4388 3.442076 ACTCCCTCAGTCCGAAAATACT 58.558 45.455 0.00 0.00 0.00 2.12
3779 4389 3.838903 ACTCCCTCAGTCCGAAAATACTT 59.161 43.478 0.00 0.00 0.00 2.24
3780 4390 4.184629 CTCCCTCAGTCCGAAAATACTTG 58.815 47.826 0.00 0.00 0.00 3.16
3781 4391 3.581332 TCCCTCAGTCCGAAAATACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
3782 4392 3.933332 CCCTCAGTCCGAAAATACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
3783 4393 4.322801 CCCTCAGTCCGAAAATACTTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
3784 4394 5.238583 CCTCAGTCCGAAAATACTTGTCTT 58.761 41.667 0.00 0.00 0.00 3.01
3785 4395 5.348997 CCTCAGTCCGAAAATACTTGTCTTC 59.651 44.000 0.00 0.00 0.00 2.87
3786 4396 5.849510 TCAGTCCGAAAATACTTGTCTTCA 58.150 37.500 0.00 0.00 0.00 3.02
3787 4397 6.285224 TCAGTCCGAAAATACTTGTCTTCAA 58.715 36.000 0.00 0.00 0.00 2.69
3788 4398 6.764085 TCAGTCCGAAAATACTTGTCTTCAAA 59.236 34.615 0.00 0.00 32.87 2.69
3789 4399 7.281324 TCAGTCCGAAAATACTTGTCTTCAAAA 59.719 33.333 0.00 0.00 32.87 2.44
3790 4400 8.076178 CAGTCCGAAAATACTTGTCTTCAAAAT 58.924 33.333 0.00 0.00 32.87 1.82
3791 4401 8.076178 AGTCCGAAAATACTTGTCTTCAAAATG 58.924 33.333 0.00 0.00 32.87 2.32
3792 4402 7.326063 GTCCGAAAATACTTGTCTTCAAAATGG 59.674 37.037 0.00 0.00 32.87 3.16
3793 4403 7.229707 TCCGAAAATACTTGTCTTCAAAATGGA 59.770 33.333 0.00 0.00 32.87 3.41
3794 4404 7.326063 CCGAAAATACTTGTCTTCAAAATGGAC 59.674 37.037 0.00 0.00 32.87 4.02
3795 4405 7.860373 CGAAAATACTTGTCTTCAAAATGGACA 59.140 33.333 0.00 0.00 38.07 4.02
3796 4406 9.528018 GAAAATACTTGTCTTCAAAATGGACAA 57.472 29.630 0.00 0.00 44.35 3.18
3797 4407 9.883142 AAAATACTTGTCTTCAAAATGGACAAA 57.117 25.926 8.67 0.00 45.31 2.83
3798 4408 9.883142 AAATACTTGTCTTCAAAATGGACAAAA 57.117 25.926 8.67 2.16 45.31 2.44
3799 4409 9.533253 AATACTTGTCTTCAAAATGGACAAAAG 57.467 29.630 8.67 2.10 45.31 2.27
3800 4410 6.340522 ACTTGTCTTCAAAATGGACAAAAGG 58.659 36.000 8.67 1.76 45.31 3.11
3801 4411 6.154363 ACTTGTCTTCAAAATGGACAAAAGGA 59.846 34.615 8.67 0.00 45.31 3.36
3802 4412 6.537453 TGTCTTCAAAATGGACAAAAGGAA 57.463 33.333 0.00 0.00 37.10 3.36
3803 4413 7.123355 TGTCTTCAAAATGGACAAAAGGAAT 57.877 32.000 0.00 0.00 37.10 3.01
3804 4414 6.985645 TGTCTTCAAAATGGACAAAAGGAATG 59.014 34.615 0.00 0.00 37.10 2.67
3805 4415 6.986231 GTCTTCAAAATGGACAAAAGGAATGT 59.014 34.615 0.00 0.00 0.00 2.71
3806 4416 8.141268 GTCTTCAAAATGGACAAAAGGAATGTA 58.859 33.333 0.00 0.00 0.00 2.29
3807 4417 8.869109 TCTTCAAAATGGACAAAAGGAATGTAT 58.131 29.630 0.00 0.00 0.00 2.29
3808 4418 9.492973 CTTCAAAATGGACAAAAGGAATGTATT 57.507 29.630 0.00 0.00 0.00 1.89
3809 4419 9.844257 TTCAAAATGGACAAAAGGAATGTATTT 57.156 25.926 0.00 0.00 0.00 1.40
3832 4442 9.729281 ATTTAAAACTAAGTAATTCTGGACGGA 57.271 29.630 0.00 0.00 0.00 4.69
3833 4443 8.767478 TTAAAACTAAGTAATTCTGGACGGAG 57.233 34.615 0.00 0.00 0.00 4.63
3834 4444 5.340439 AACTAAGTAATTCTGGACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
3835 4445 3.705072 ACTAAGTAATTCTGGACGGAGGG 59.295 47.826 0.00 0.00 0.00 4.30
3836 4446 2.544844 AGTAATTCTGGACGGAGGGA 57.455 50.000 0.00 0.00 0.00 4.20
3837 4447 2.389715 AGTAATTCTGGACGGAGGGAG 58.610 52.381 0.00 0.00 0.00 4.30
3859 4469 8.971073 GGGAGTACTTGTATAGTGGTAAAGTAA 58.029 37.037 0.00 0.00 37.73 2.24
3872 4482 8.937634 AGTGGTAAAGTAATAATTGTACTCGG 57.062 34.615 4.61 0.00 31.32 4.63
3886 4496 1.094785 ACTCGGTACATTTGCATGGC 58.905 50.000 0.00 0.00 34.27 4.40
3907 4517 4.351192 GCCATTTGAATACCGATGTGTTC 58.649 43.478 0.00 0.00 41.48 3.18
3914 4524 6.662414 TGAATACCGATGTGTTCTTGATTC 57.338 37.500 4.28 0.00 41.61 2.52
4240 4851 1.216941 CCGGCTTGTGCTTTGCTTTG 61.217 55.000 0.00 0.00 39.59 2.77
4241 4852 1.824272 CGGCTTGTGCTTTGCTTTGC 61.824 55.000 0.00 0.00 39.59 3.68
4242 4853 0.531311 GGCTTGTGCTTTGCTTTGCT 60.531 50.000 0.00 0.00 39.59 3.91
4243 4854 0.580104 GCTTGTGCTTTGCTTTGCTG 59.420 50.000 0.00 0.00 36.03 4.41
4244 4855 1.214367 CTTGTGCTTTGCTTTGCTGG 58.786 50.000 0.00 0.00 0.00 4.85
4245 4856 0.179078 TTGTGCTTTGCTTTGCTGGG 60.179 50.000 0.00 0.00 0.00 4.45
4246 4857 1.957695 GTGCTTTGCTTTGCTGGGC 60.958 57.895 0.00 0.00 0.00 5.36
4247 4858 2.735857 GCTTTGCTTTGCTGGGCG 60.736 61.111 0.00 0.00 0.00 6.13
4248 4859 2.730094 CTTTGCTTTGCTGGGCGT 59.270 55.556 0.00 0.00 0.00 5.68
4249 4860 1.372128 CTTTGCTTTGCTGGGCGTC 60.372 57.895 0.00 0.00 0.00 5.19
4250 4861 2.074230 CTTTGCTTTGCTGGGCGTCA 62.074 55.000 0.00 0.00 0.00 4.35
4379 4990 9.078990 AGATCCTACTTGTCATCATCGTTATAA 57.921 33.333 0.00 0.00 0.00 0.98
4425 5038 5.310451 TGGGAAGTTTACGCTTGTCTATTT 58.690 37.500 0.00 0.00 0.00 1.40
4426 5039 5.766174 TGGGAAGTTTACGCTTGTCTATTTT 59.234 36.000 0.00 0.00 0.00 1.82
4427 5040 6.084277 GGGAAGTTTACGCTTGTCTATTTTG 58.916 40.000 0.00 0.00 0.00 2.44
4428 5041 6.293790 GGGAAGTTTACGCTTGTCTATTTTGT 60.294 38.462 0.00 0.00 0.00 2.83
4429 5042 7.095102 GGGAAGTTTACGCTTGTCTATTTTGTA 60.095 37.037 0.00 0.00 0.00 2.41
4448 5061 6.995511 TTGTAGTATTTACAGATGGCCAAC 57.004 37.500 10.96 7.42 0.00 3.77
4513 5129 6.210584 GGACCATTTCAAGTTGGATTTCCTTA 59.789 38.462 2.34 0.00 36.79 2.69
4575 5191 7.119846 GCAAACCACACAAATTCTAGAGATAGT 59.880 37.037 0.00 0.00 0.00 2.12
4601 5217 1.645710 AACAGGAGGTAGGACCACAG 58.354 55.000 0.00 0.00 41.95 3.66
4622 5238 3.088532 GTTCCTATGTTCCACATGGCAA 58.911 45.455 0.00 0.00 39.53 4.52
4648 5264 4.392921 AATATCAGACACTCCAAGGACG 57.607 45.455 0.00 0.00 0.00 4.79
4653 5269 1.971357 AGACACTCCAAGGACGTCATT 59.029 47.619 18.91 14.64 0.00 2.57
4663 5279 1.574428 GACGTCATTTGTTGCGGCT 59.426 52.632 11.55 0.00 32.38 5.52
4677 5293 3.274067 GGCTTGCCCGTACTTTGG 58.726 61.111 0.00 0.00 0.00 3.28
4704 5320 5.747197 GCAGGATTTTCAAGCACATGAATAG 59.253 40.000 0.00 0.00 38.98 1.73
4721 5339 9.136323 ACATGAATAGGAAAAACATAGGGATTC 57.864 33.333 0.00 0.00 0.00 2.52
4763 5381 2.156117 CGCAAGGTTTCAACAATGCATG 59.844 45.455 0.00 0.00 40.10 4.06
4764 5382 3.391965 GCAAGGTTTCAACAATGCATGA 58.608 40.909 0.00 0.00 39.96 3.07
4765 5383 3.808726 GCAAGGTTTCAACAATGCATGAA 59.191 39.130 0.00 0.00 39.96 2.57
4766 5384 4.084223 GCAAGGTTTCAACAATGCATGAAG 60.084 41.667 0.00 0.00 39.96 3.02
4767 5385 3.656559 AGGTTTCAACAATGCATGAAGC 58.343 40.909 0.00 2.80 45.96 3.86
4812 5430 4.409574 TGACTTGGGTTTAGTCACTTGGTA 59.590 41.667 0.00 0.00 45.15 3.25
4827 5445 3.564225 ACTTGGTAGTCTTTTTCCGCTTG 59.436 43.478 0.00 0.00 0.00 4.01
4843 5461 6.024552 TCCGCTTGCTTTTTATGATTTCTT 57.975 33.333 0.00 0.00 0.00 2.52
4855 5473 8.696410 TTTTATGATTTCTTTTGGGCGTATTC 57.304 30.769 0.00 0.00 0.00 1.75
4866 5484 0.027586 GGCGTATTCGTGATGTTGCC 59.972 55.000 0.00 0.00 39.49 4.52
4907 5553 0.740737 AGTGCAACACTTGACTTGGC 59.259 50.000 0.00 0.00 42.59 4.52
4919 5565 3.488778 TGACTTGGCTACCCGTAAAAA 57.511 42.857 0.00 0.00 0.00 1.94
5001 5649 9.630098 AAGCTTGTTTCAAGACATAAATACATG 57.370 29.630 12.77 0.00 0.00 3.21
5006 5654 8.738106 TGTTTCAAGACATAAATACATGATGCA 58.262 29.630 0.00 0.00 0.00 3.96
5053 5701 9.190317 TCTATATATAGGATTATATGCGGGCTG 57.810 37.037 17.81 0.00 34.88 4.85
5065 5713 1.208259 GCGGGCTGAAGTTTGTTTTG 58.792 50.000 0.00 0.00 0.00 2.44
5153 5802 9.362539 ACATAATGCAAAAGAATGCTAAGAAAG 57.637 29.630 0.00 0.00 46.54 2.62
5198 5847 8.205512 TCCTACAAGTCAAACAACTTACATACA 58.794 33.333 0.00 0.00 37.38 2.29
5295 5944 4.587262 ACCCTTTGACTTGGTAAATTCCAC 59.413 41.667 0.00 0.00 37.20 4.02
5305 5954 7.590279 ACTTGGTAAATTCCACTGATTTTACG 58.410 34.615 11.10 0.00 42.63 3.18
5306 5955 7.229907 ACTTGGTAAATTCCACTGATTTTACGT 59.770 33.333 0.00 0.00 42.63 3.57
5317 5966 6.872020 CCACTGATTTTACGTATTCGGGATAT 59.128 38.462 0.00 0.00 41.85 1.63
5325 5974 5.326200 ACGTATTCGGGATATCCAAGATC 57.674 43.478 23.27 12.84 41.85 2.75
5352 6001 4.468765 AGGAGTGTCATGTCATCTTGAG 57.531 45.455 0.00 0.00 0.00 3.02
5381 6030 9.613428 CTAGTATATGGTTGTTGATTCCAAGAA 57.387 33.333 0.00 0.00 33.79 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 10 0.319641 GACACGATCGGATAAGGGGC 60.320 60.000 20.98 0.00 0.00 5.80
10 13 2.619177 AGAGTGACACGATCGGATAAGG 59.381 50.000 20.98 4.01 0.00 2.69
13 16 3.562973 GGTTAGAGTGACACGATCGGATA 59.437 47.826 20.98 0.00 0.00 2.59
48 51 0.535102 CAAAGCCCACTTGACGGTCT 60.535 55.000 9.88 0.00 35.85 3.85
61 64 1.674322 TTAGTGCCGCTCCAAAGCC 60.674 57.895 0.00 0.00 46.34 4.35
137 141 1.746322 TACAACTTGGTCCCGCACGA 61.746 55.000 0.00 0.00 0.00 4.35
166 170 1.254954 GGTGTCTAGACCGTTCCACT 58.745 55.000 20.11 0.00 0.00 4.00
171 175 4.251268 GCTTTATTGGTGTCTAGACCGTT 58.749 43.478 20.11 3.65 39.07 4.44
173 177 3.195661 GGCTTTATTGGTGTCTAGACCG 58.804 50.000 20.11 0.00 39.07 4.79
174 178 3.542648 GGGCTTTATTGGTGTCTAGACC 58.457 50.000 20.11 11.08 36.43 3.85
176 180 2.419574 GCGGGCTTTATTGGTGTCTAGA 60.420 50.000 0.00 0.00 0.00 2.43
177 181 1.940613 GCGGGCTTTATTGGTGTCTAG 59.059 52.381 0.00 0.00 0.00 2.43
178 182 1.407712 GGCGGGCTTTATTGGTGTCTA 60.408 52.381 0.00 0.00 0.00 2.59
179 183 0.679960 GGCGGGCTTTATTGGTGTCT 60.680 55.000 0.00 0.00 0.00 3.41
183 188 1.101049 CGATGGCGGGCTTTATTGGT 61.101 55.000 2.38 0.00 0.00 3.67
199 204 2.993937 TCTATTTTCCCGCAAACCGAT 58.006 42.857 0.00 0.00 40.02 4.18
226 239 2.372074 GGCACCCCATCGGTCCTTA 61.372 63.158 0.00 0.00 43.58 2.69
227 240 3.728373 GGCACCCCATCGGTCCTT 61.728 66.667 0.00 0.00 43.58 3.36
256 269 2.031314 CGAATAGTCTGGACGCGACTTA 59.969 50.000 15.93 0.00 41.62 2.24
259 272 0.376152 TCGAATAGTCTGGACGCGAC 59.624 55.000 15.93 6.56 36.20 5.19
268 281 0.377554 CACGACCGCTCGAATAGTCT 59.622 55.000 7.21 0.00 43.06 3.24
272 285 2.802792 CCCACGACCGCTCGAATA 59.197 61.111 7.21 0.00 43.06 1.75
273 286 4.814294 GCCCACGACCGCTCGAAT 62.814 66.667 7.21 0.00 43.06 3.34
302 315 4.816385 CCATCAATTGTAGAGTTACCGCAT 59.184 41.667 5.13 0.00 0.00 4.73
306 319 8.974060 TTTATCCCATCAATTGTAGAGTTACC 57.026 34.615 5.13 0.00 0.00 2.85
316 329 6.925610 TCTCGAGTTTTATCCCATCAATTG 57.074 37.500 13.13 0.00 0.00 2.32
321 334 4.214332 GCCATTCTCGAGTTTTATCCCATC 59.786 45.833 13.13 0.00 0.00 3.51
350 363 1.743321 CTCCATGGAGGACGAGAGCC 61.743 65.000 31.14 0.00 43.07 4.70
403 433 5.629079 AACCAGATTTCTTGGAAATCGAC 57.371 39.130 20.21 5.25 40.56 4.20
468 498 8.586570 TCAACGTATTGCATCTTGAAATTTTT 57.413 26.923 0.00 0.00 35.63 1.94
483 513 3.120338 ACAGGTCGCATTTCAACGTATTG 60.120 43.478 0.00 0.00 37.14 1.90
486 516 2.157834 ACAGGTCGCATTTCAACGTA 57.842 45.000 0.00 0.00 0.00 3.57
540 572 8.635765 ATCTGGAGCTTTTTAACACTTGATAA 57.364 30.769 0.00 0.00 0.00 1.75
546 578 6.547510 AGACAAATCTGGAGCTTTTTAACACT 59.452 34.615 0.00 0.00 32.29 3.55
561 593 3.068590 AGGGTTGTGCAAAGACAAATCTG 59.931 43.478 0.00 0.00 37.58 2.90
584 1087 6.671614 TTTAGGATGCAATACGTCGAAATT 57.328 33.333 0.00 0.00 34.88 1.82
598 1101 6.586082 CACAGGTGTGTAAATTTTTAGGATGC 59.414 38.462 0.00 0.00 40.96 3.91
619 1122 9.926158 AAAGATAGATGAAGATATAGTGCACAG 57.074 33.333 21.04 0.00 0.00 3.66
691 1195 9.049974 GCTACCAAATGCAAATTTTAAAATTCG 57.950 29.630 22.96 15.32 37.62 3.34
715 1219 0.107945 GACCGAGCTTCATGAAGGCT 60.108 55.000 31.41 27.18 38.80 4.58
739 1243 5.340803 GGAGTTTTATCCGGAAATTGCTTC 58.659 41.667 9.01 0.00 0.00 3.86
771 1275 3.906008 CGATGTGGCGTTTTCTTTAACAG 59.094 43.478 0.00 0.00 0.00 3.16
783 1287 0.881118 AAAGAATTGCGATGTGGCGT 59.119 45.000 0.00 0.00 35.06 5.68
784 1288 1.981254 AAAAGAATTGCGATGTGGCG 58.019 45.000 0.00 0.00 35.06 5.69
785 1289 4.683781 TGTTAAAAAGAATTGCGATGTGGC 59.316 37.500 0.00 0.00 0.00 5.01
786 1290 6.761731 TTGTTAAAAAGAATTGCGATGTGG 57.238 33.333 0.00 0.00 0.00 4.17
873 1380 6.152831 GCTTGCTGGGTTTTATATAATAGGGG 59.847 42.308 0.00 0.00 0.00 4.79
880 1387 5.031066 ACTCGCTTGCTGGGTTTTATATA 57.969 39.130 0.00 0.00 0.00 0.86
881 1388 3.877508 GACTCGCTTGCTGGGTTTTATAT 59.122 43.478 0.00 0.00 0.00 0.86
898 1405 2.276994 GCTCACTCGCTCGACTCG 60.277 66.667 0.00 0.00 0.00 4.18
941 1449 4.624364 TGAGCGTGGTGTGGCCTG 62.624 66.667 3.32 0.00 38.35 4.85
942 1450 4.626081 GTGAGCGTGGTGTGGCCT 62.626 66.667 3.32 0.00 38.35 5.19
1002 1510 2.977169 CGTTTTTGAAATGGAACGCGAT 59.023 40.909 15.93 0.00 38.44 4.58
1048 1556 1.534175 CGGAGACATGTAGACTTCGGC 60.534 57.143 0.00 0.00 37.36 5.54
1353 1861 0.390472 GGAGGAACTTGAGGAGCACG 60.390 60.000 0.00 0.00 41.55 5.34
1472 1980 2.185310 CTCCAGGTCCTTGAACCCGG 62.185 65.000 0.00 0.00 40.42 5.73
1582 2090 2.280592 GTCGCCGAACACCCTGTT 60.281 61.111 0.00 0.00 44.37 3.16
1821 2329 3.953775 AGGCACACGGACAAGGGG 61.954 66.667 0.00 0.00 0.00 4.79
1823 2331 1.961277 GTCAGGCACACGGACAAGG 60.961 63.158 0.00 0.00 42.84 3.61
1824 2332 3.642755 GTCAGGCACACGGACAAG 58.357 61.111 0.00 0.00 42.84 3.16
1833 2341 0.598065 GAAATGTGGGTGTCAGGCAC 59.402 55.000 0.00 0.00 46.97 5.01
1834 2342 0.888736 CGAAATGTGGGTGTCAGGCA 60.889 55.000 0.00 0.00 0.00 4.75
1835 2343 0.889186 ACGAAATGTGGGTGTCAGGC 60.889 55.000 0.00 0.00 0.00 4.85
1836 2344 1.156736 GACGAAATGTGGGTGTCAGG 58.843 55.000 0.00 0.00 0.00 3.86
1837 2345 0.790207 CGACGAAATGTGGGTGTCAG 59.210 55.000 0.00 0.00 0.00 3.51
1838 2346 0.389757 TCGACGAAATGTGGGTGTCA 59.610 50.000 0.00 0.00 0.00 3.58
1840 2348 1.223187 GTTCGACGAAATGTGGGTGT 58.777 50.000 12.67 0.00 0.00 4.16
1841 2349 1.070175 GTGTTCGACGAAATGTGGGTG 60.070 52.381 12.67 0.00 0.00 4.61
1842 2350 1.223187 GTGTTCGACGAAATGTGGGT 58.777 50.000 12.67 0.00 0.00 4.51
1843 2351 0.515564 GGTGTTCGACGAAATGTGGG 59.484 55.000 12.67 0.00 0.00 4.61
1844 2352 1.194547 CAGGTGTTCGACGAAATGTGG 59.805 52.381 12.67 0.00 0.00 4.17
1845 2353 1.398451 GCAGGTGTTCGACGAAATGTG 60.398 52.381 12.67 8.71 0.00 3.21
2062 2574 2.481952 AGCAAAACTTGAGCTCATCGAC 59.518 45.455 19.04 3.96 32.05 4.20
2095 2607 0.537188 TCAGCATTCTCGGGAAGGAC 59.463 55.000 15.01 4.93 35.53 3.85
2099 2614 0.389817 CGTGTCAGCATTCTCGGGAA 60.390 55.000 0.00 0.00 35.78 3.97
2128 2643 1.364901 GAACCTGTCGACGGGAACA 59.635 57.895 42.84 11.33 45.36 3.18
2137 2652 2.511600 GGCCGGATGAACCTGTCG 60.512 66.667 5.05 0.00 36.31 4.35
2251 2766 3.818773 CGATCTCTAGGAAGACCTTCTCC 59.181 52.174 9.35 0.00 45.36 3.71
2336 2851 1.076533 AATTACTCCTGTGCGACGCG 61.077 55.000 16.14 3.53 0.00 6.01
2519 3046 1.383456 TTGCGTTTGTGCTCTTGGCT 61.383 50.000 0.00 0.00 42.39 4.75
2521 3048 0.318107 CCTTGCGTTTGTGCTCTTGG 60.318 55.000 0.00 0.00 35.36 3.61
2610 3137 5.024118 TGAAAAGGTAAAAACCAGGAACCA 58.976 37.500 0.00 0.00 32.43 3.67
2611 3138 5.353938 GTGAAAAGGTAAAAACCAGGAACC 58.646 41.667 0.00 0.00 0.00 3.62
2612 3139 5.128171 AGGTGAAAAGGTAAAAACCAGGAAC 59.872 40.000 0.00 0.00 0.00 3.62
2613 3140 5.274015 AGGTGAAAAGGTAAAAACCAGGAA 58.726 37.500 0.00 0.00 0.00 3.36
2642 3169 2.520069 GCCTATCCTCCTCTCAATCGA 58.480 52.381 0.00 0.00 0.00 3.59
2647 3174 2.021262 CATGGCCTATCCTCCTCTCA 57.979 55.000 3.32 0.00 35.26 3.27
2672 3199 3.054434 TGCTACTTCTACCGTGGTAGGTA 60.054 47.826 22.53 16.63 45.82 3.08
2673 3200 2.291153 TGCTACTTCTACCGTGGTAGGT 60.291 50.000 22.53 16.43 45.82 3.08
2674 3201 2.372264 TGCTACTTCTACCGTGGTAGG 58.628 52.381 22.53 12.11 45.82 3.18
2749 3276 3.249189 AAAGGGTGGCCTCGCTCA 61.249 61.111 22.86 0.00 0.00 4.26
2986 3513 0.457035 CCGGCGTTACAGCTAGGTAA 59.543 55.000 6.01 0.00 37.29 2.85
2989 3516 1.226888 GACCGGCGTTACAGCTAGG 60.227 63.158 6.01 10.28 39.44 3.02
3072 3602 5.584649 CCGCTGTCTCTTGTTGGATTAATTA 59.415 40.000 0.00 0.00 0.00 1.40
3073 3603 4.396166 CCGCTGTCTCTTGTTGGATTAATT 59.604 41.667 0.00 0.00 0.00 1.40
3080 3610 1.230635 CCACCGCTGTCTCTTGTTGG 61.231 60.000 0.00 0.00 0.00 3.77
3081 3611 1.845809 GCCACCGCTGTCTCTTGTTG 61.846 60.000 0.00 0.00 0.00 3.33
3084 3614 1.376424 ATGCCACCGCTGTCTCTTG 60.376 57.895 0.00 0.00 35.36 3.02
3091 3621 1.518056 AAACTCACATGCCACCGCTG 61.518 55.000 0.00 0.00 35.36 5.18
3092 3622 1.228245 AAACTCACATGCCACCGCT 60.228 52.632 0.00 0.00 35.36 5.52
3094 3624 0.798776 GAGAAACTCACATGCCACCG 59.201 55.000 0.00 0.00 0.00 4.94
3095 3625 0.798776 CGAGAAACTCACATGCCACC 59.201 55.000 0.00 0.00 0.00 4.61
3134 3672 2.530001 GAAACGAAACGGAGCGAGCG 62.530 60.000 0.00 0.00 0.00 5.03
3140 3678 1.719780 CCGAGAAGAAACGAAACGGAG 59.280 52.381 0.00 0.00 41.09 4.63
3221 3767 2.673368 CGTAAAACTCTCACATCAGCCC 59.327 50.000 0.00 0.00 0.00 5.19
3374 3959 2.033407 CACTTGAACAGAACAGTGAGCG 60.033 50.000 0.00 0.00 0.00 5.03
3392 3994 4.497674 GCTAATGCGTACTACTAGTGCACT 60.498 45.833 25.12 25.12 38.54 4.40
3393 3995 3.729716 GCTAATGCGTACTACTAGTGCAC 59.270 47.826 9.40 9.40 38.54 4.57
3394 3996 3.379057 TGCTAATGCGTACTACTAGTGCA 59.621 43.478 5.39 6.46 43.34 4.57
3395 3997 3.961182 TGCTAATGCGTACTACTAGTGC 58.039 45.455 5.39 0.00 43.34 4.40
3396 3998 4.275196 TCCTGCTAATGCGTACTACTAGTG 59.725 45.833 5.39 0.00 43.34 2.74
3397 3999 4.458397 TCCTGCTAATGCGTACTACTAGT 58.542 43.478 0.00 0.00 43.34 2.57
3398 4000 5.008811 AGTTCCTGCTAATGCGTACTACTAG 59.991 44.000 0.00 0.00 43.34 2.57
3399 4001 4.885907 AGTTCCTGCTAATGCGTACTACTA 59.114 41.667 0.00 0.00 43.34 1.82
3400 4002 3.700038 AGTTCCTGCTAATGCGTACTACT 59.300 43.478 0.00 0.00 43.34 2.57
3401 4003 3.797256 CAGTTCCTGCTAATGCGTACTAC 59.203 47.826 0.00 0.00 43.34 2.73
3402 4004 3.446161 ACAGTTCCTGCTAATGCGTACTA 59.554 43.478 0.00 0.00 43.34 1.82
3472 4075 4.024670 AGAAGCTTTGTACTCCTATCCGT 58.975 43.478 0.00 0.00 0.00 4.69
3480 4086 3.925299 GGGAACGTAGAAGCTTTGTACTC 59.075 47.826 0.00 1.18 0.00 2.59
3582 4191 8.206189 TGCTGGAAAAGAAAGAAAAGAATTGAT 58.794 29.630 0.00 0.00 0.00 2.57
3678 4287 1.203758 CCTACCACGTGCTCACATACA 59.796 52.381 10.91 0.00 0.00 2.29
3679 4288 1.470979 CCCTACCACGTGCTCACATAC 60.471 57.143 10.91 0.00 0.00 2.39
3680 4289 0.821517 CCCTACCACGTGCTCACATA 59.178 55.000 10.91 0.00 0.00 2.29
3681 4290 1.596934 CCCTACCACGTGCTCACAT 59.403 57.895 10.91 0.00 0.00 3.21
3682 4291 3.056458 CCCTACCACGTGCTCACA 58.944 61.111 10.91 0.00 0.00 3.58
3743 4353 8.047310 GGACTGAGGGAGTAATTATCTTTTTCA 58.953 37.037 0.00 0.00 33.83 2.69
3759 4369 3.581332 ACAAGTATTTTCGGACTGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
3760 4370 3.933332 GACAAGTATTTTCGGACTGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
3761 4371 4.822026 AGACAAGTATTTTCGGACTGAGG 58.178 43.478 0.00 0.00 0.00 3.86
3762 4372 5.926542 TGAAGACAAGTATTTTCGGACTGAG 59.073 40.000 0.00 0.00 0.00 3.35
3763 4373 5.849510 TGAAGACAAGTATTTTCGGACTGA 58.150 37.500 0.00 0.00 0.00 3.41
3764 4374 6.539649 TTGAAGACAAGTATTTTCGGACTG 57.460 37.500 0.00 0.00 0.00 3.51
3765 4375 7.562454 TTTTGAAGACAAGTATTTTCGGACT 57.438 32.000 0.00 0.00 37.32 3.85
3766 4376 7.326063 CCATTTTGAAGACAAGTATTTTCGGAC 59.674 37.037 0.00 0.00 37.32 4.79
3767 4377 7.229707 TCCATTTTGAAGACAAGTATTTTCGGA 59.770 33.333 0.00 0.00 37.32 4.55
3768 4378 7.326063 GTCCATTTTGAAGACAAGTATTTTCGG 59.674 37.037 0.00 0.00 37.32 4.30
3769 4379 7.860373 TGTCCATTTTGAAGACAAGTATTTTCG 59.140 33.333 0.00 0.00 37.58 3.46
3770 4380 9.528018 TTGTCCATTTTGAAGACAAGTATTTTC 57.472 29.630 0.90 0.00 43.60 2.29
3778 4388 6.537453 TCCTTTTGTCCATTTTGAAGACAA 57.463 33.333 0.90 0.90 45.99 3.18
3779 4389 6.537453 TTCCTTTTGTCCATTTTGAAGACA 57.463 33.333 0.00 0.00 38.70 3.41
3780 4390 6.986231 ACATTCCTTTTGTCCATTTTGAAGAC 59.014 34.615 0.00 0.00 0.00 3.01
3781 4391 7.123355 ACATTCCTTTTGTCCATTTTGAAGA 57.877 32.000 0.00 0.00 0.00 2.87
3782 4392 9.492973 AATACATTCCTTTTGTCCATTTTGAAG 57.507 29.630 0.00 0.00 0.00 3.02
3783 4393 9.844257 AAATACATTCCTTTTGTCCATTTTGAA 57.156 25.926 0.00 0.00 0.00 2.69
3806 4416 9.729281 TCCGTCCAGAATTACTTAGTTTTAAAT 57.271 29.630 0.00 0.00 0.00 1.40
3807 4417 9.211485 CTCCGTCCAGAATTACTTAGTTTTAAA 57.789 33.333 0.00 0.00 0.00 1.52
3808 4418 7.820872 CCTCCGTCCAGAATTACTTAGTTTTAA 59.179 37.037 0.00 0.00 0.00 1.52
3809 4419 7.325694 CCTCCGTCCAGAATTACTTAGTTTTA 58.674 38.462 0.00 0.00 0.00 1.52
3810 4420 6.171213 CCTCCGTCCAGAATTACTTAGTTTT 58.829 40.000 0.00 0.00 0.00 2.43
3811 4421 5.338137 CCCTCCGTCCAGAATTACTTAGTTT 60.338 44.000 0.00 0.00 0.00 2.66
3812 4422 4.161754 CCCTCCGTCCAGAATTACTTAGTT 59.838 45.833 0.00 0.00 0.00 2.24
3813 4423 3.705072 CCCTCCGTCCAGAATTACTTAGT 59.295 47.826 0.00 0.00 0.00 2.24
3814 4424 3.958798 TCCCTCCGTCCAGAATTACTTAG 59.041 47.826 0.00 0.00 0.00 2.18
3815 4425 3.958798 CTCCCTCCGTCCAGAATTACTTA 59.041 47.826 0.00 0.00 0.00 2.24
3816 4426 2.766828 CTCCCTCCGTCCAGAATTACTT 59.233 50.000 0.00 0.00 0.00 2.24
3817 4427 2.292323 ACTCCCTCCGTCCAGAATTACT 60.292 50.000 0.00 0.00 0.00 2.24
3818 4428 2.108970 ACTCCCTCCGTCCAGAATTAC 58.891 52.381 0.00 0.00 0.00 1.89
3819 4429 2.544844 ACTCCCTCCGTCCAGAATTA 57.455 50.000 0.00 0.00 0.00 1.40
3820 4430 2.108970 GTACTCCCTCCGTCCAGAATT 58.891 52.381 0.00 0.00 0.00 2.17
3821 4431 1.288335 AGTACTCCCTCCGTCCAGAAT 59.712 52.381 0.00 0.00 0.00 2.40
3822 4432 0.702902 AGTACTCCCTCCGTCCAGAA 59.297 55.000 0.00 0.00 0.00 3.02
3823 4433 0.702902 AAGTACTCCCTCCGTCCAGA 59.297 55.000 0.00 0.00 0.00 3.86
3824 4434 0.818296 CAAGTACTCCCTCCGTCCAG 59.182 60.000 0.00 0.00 0.00 3.86
3825 4435 0.113776 ACAAGTACTCCCTCCGTCCA 59.886 55.000 0.00 0.00 0.00 4.02
3826 4436 2.134789 TACAAGTACTCCCTCCGTCC 57.865 55.000 0.00 0.00 0.00 4.79
3827 4437 4.275443 CACTATACAAGTACTCCCTCCGTC 59.725 50.000 0.00 0.00 35.76 4.79
3828 4438 4.205587 CACTATACAAGTACTCCCTCCGT 58.794 47.826 0.00 0.00 35.76 4.69
3829 4439 3.568853 CCACTATACAAGTACTCCCTCCG 59.431 52.174 0.00 0.00 35.76 4.63
3830 4440 4.544683 ACCACTATACAAGTACTCCCTCC 58.455 47.826 0.00 0.00 35.76 4.30
3831 4441 7.341512 ACTTTACCACTATACAAGTACTCCCTC 59.658 40.741 0.00 0.00 35.76 4.30
3832 4442 7.187676 ACTTTACCACTATACAAGTACTCCCT 58.812 38.462 0.00 0.00 35.76 4.20
3833 4443 7.415592 ACTTTACCACTATACAAGTACTCCC 57.584 40.000 0.00 0.00 35.76 4.30
3872 4482 3.859443 TCAAATGGCCATGCAAATGTAC 58.141 40.909 21.63 0.00 0.00 2.90
3886 4496 5.818136 AGAACACATCGGTATTCAAATGG 57.182 39.130 0.00 0.00 32.81 3.16
3907 4517 2.436646 ACCGGCCTGCGAATCAAG 60.437 61.111 0.00 0.00 0.00 3.02
3966 4576 2.124151 TACTCCGCCCCGTACTCC 60.124 66.667 0.00 0.00 0.00 3.85
4241 4852 3.691744 GAGACGAGCTGACGCCCAG 62.692 68.421 0.00 1.43 45.67 4.45
4242 4853 3.749064 GAGACGAGCTGACGCCCA 61.749 66.667 0.00 0.00 36.60 5.36
4243 4854 4.838486 CGAGACGAGCTGACGCCC 62.838 72.222 0.00 0.00 36.60 6.13
4244 4855 4.838486 CCGAGACGAGCTGACGCC 62.838 72.222 0.00 0.00 36.60 5.68
4245 4856 3.726631 CTCCGAGACGAGCTGACGC 62.727 68.421 0.00 0.00 36.70 5.19
4246 4857 2.031044 CTCTCCGAGACGAGCTGACG 62.031 65.000 0.00 0.00 39.31 4.35
4247 4858 1.022451 ACTCTCCGAGACGAGCTGAC 61.022 60.000 0.00 0.00 33.32 3.51
4248 4859 0.535797 TACTCTCCGAGACGAGCTGA 59.464 55.000 0.00 0.00 33.32 4.26
4249 4860 0.934496 CTACTCTCCGAGACGAGCTG 59.066 60.000 0.00 0.00 33.32 4.24
4250 4861 0.825410 TCTACTCTCCGAGACGAGCT 59.175 55.000 0.00 0.00 33.32 4.09
4290 4901 9.106070 ACATGCATATCACATTATATAGCACTG 57.894 33.333 0.00 0.00 33.14 3.66
4339 4950 2.603021 AGGATCTCACGGCTCATACAT 58.397 47.619 0.00 0.00 0.00 2.29
4425 5038 5.583061 CGTTGGCCATCTGTAAATACTACAA 59.417 40.000 6.09 0.00 0.00 2.41
4426 5039 5.113383 CGTTGGCCATCTGTAAATACTACA 58.887 41.667 6.09 0.00 0.00 2.74
4427 5040 4.025145 GCGTTGGCCATCTGTAAATACTAC 60.025 45.833 6.09 0.00 0.00 2.73
4428 5041 4.124238 GCGTTGGCCATCTGTAAATACTA 58.876 43.478 6.09 0.00 0.00 1.82
4429 5042 2.943033 GCGTTGGCCATCTGTAAATACT 59.057 45.455 6.09 0.00 0.00 2.12
4448 5061 9.003658 ACATATAGAATTAAGGAATCCAAAGCG 57.996 33.333 0.61 0.00 0.00 4.68
4467 5080 8.258007 TGGTCCTACTCAAAACAGAACATATAG 58.742 37.037 0.00 0.00 0.00 1.31
4476 5089 6.263168 ACTTGAAATGGTCCTACTCAAAACAG 59.737 38.462 0.00 0.00 0.00 3.16
4513 5129 0.698818 CAGGGCCTAGAAGGTGGTTT 59.301 55.000 5.28 0.00 37.80 3.27
4575 5191 3.263425 GGTCCTACCTCCTGTTTTCATCA 59.737 47.826 0.00 0.00 34.73 3.07
4622 5238 5.964477 TCCTTGGAGTGTCTGATATTTAGGT 59.036 40.000 0.00 0.00 0.00 3.08
4648 5264 1.284297 GGCAAGCCGCAACAAATGAC 61.284 55.000 0.00 0.00 45.17 3.06
4663 5279 0.752009 TGCAACCAAAGTACGGGCAA 60.752 50.000 0.00 0.00 0.00 4.52
4677 5293 3.096489 TGTGCTTGAAAATCCTGCAAC 57.904 42.857 0.00 0.00 35.34 4.17
4704 5320 2.032924 CGGCGAATCCCTATGTTTTTCC 59.967 50.000 0.00 0.00 0.00 3.13
4735 5353 1.798813 GTTGAAACCTTGCGATCGAGT 59.201 47.619 21.57 7.01 0.00 4.18
4764 5382 9.976511 CATCCTATATTTTTCATGTTCATGCTT 57.023 29.630 7.80 0.00 0.00 3.91
4765 5383 9.358406 TCATCCTATATTTTTCATGTTCATGCT 57.642 29.630 7.80 0.00 0.00 3.79
4766 5384 9.403110 GTCATCCTATATTTTTCATGTTCATGC 57.597 33.333 7.80 0.00 0.00 4.06
4812 5430 3.801114 AAAAGCAAGCGGAAAAAGACT 57.199 38.095 0.00 0.00 0.00 3.24
4827 5445 5.408299 ACGCCCAAAAGAAATCATAAAAAGC 59.592 36.000 0.00 0.00 0.00 3.51
4843 5461 2.102070 ACATCACGAATACGCCCAAA 57.898 45.000 0.00 0.00 43.96 3.28
4855 5473 3.970721 TGCTGAGGCAACATCACG 58.029 55.556 0.00 0.00 46.36 4.35
4866 5484 8.642020 GCACTGAAAATAAAATAGTTTGCTGAG 58.358 33.333 0.00 0.00 0.00 3.35
4919 5565 4.340617 TGTCCAAACAACCTTGTCTCTTT 58.659 39.130 0.00 0.00 41.31 2.52
4922 5568 3.632145 ACATGTCCAAACAACCTTGTCTC 59.368 43.478 0.00 0.00 41.31 3.36
4927 5573 5.358922 CAATCAACATGTCCAAACAACCTT 58.641 37.500 0.00 0.00 39.30 3.50
4928 5574 4.740334 GCAATCAACATGTCCAAACAACCT 60.740 41.667 0.00 0.00 39.30 3.50
5001 5649 7.928908 TTCAAAAGAACACAATAGTTGCATC 57.071 32.000 0.00 0.00 0.00 3.91
5033 5681 5.661312 ACTTCAGCCCGCATATAATCCTATA 59.339 40.000 0.00 0.00 0.00 1.31
5034 5682 4.471386 ACTTCAGCCCGCATATAATCCTAT 59.529 41.667 0.00 0.00 0.00 2.57
5035 5683 3.838317 ACTTCAGCCCGCATATAATCCTA 59.162 43.478 0.00 0.00 0.00 2.94
5036 5684 2.639839 ACTTCAGCCCGCATATAATCCT 59.360 45.455 0.00 0.00 0.00 3.24
5044 5692 1.039856 AAACAAACTTCAGCCCGCAT 58.960 45.000 0.00 0.00 0.00 4.73
5049 5697 1.933181 GGTGCAAAACAAACTTCAGCC 59.067 47.619 0.00 0.00 0.00 4.85
5053 5701 5.793026 TTTCATGGTGCAAAACAAACTTC 57.207 34.783 0.00 0.00 0.00 3.01
5122 5771 9.656040 TTAGCATTCTTTTGCATTATGTTTCAT 57.344 25.926 0.00 0.00 45.23 2.57
5163 5812 6.533730 TGTTTGACTTGTAGGACTGAATCAT 58.466 36.000 0.00 0.00 0.00 2.45
5164 5813 5.924356 TGTTTGACTTGTAGGACTGAATCA 58.076 37.500 0.00 0.00 0.00 2.57
5206 5855 7.888021 TGTTGGAGCCATAGAATCTTTAGAAAA 59.112 33.333 0.00 0.00 0.00 2.29
5259 5908 9.771534 CCAAGTCAAAGGGTTTTCATATAAAAA 57.228 29.630 0.00 0.00 0.00 1.94
5260 5909 8.929487 ACCAAGTCAAAGGGTTTTCATATAAAA 58.071 29.630 0.00 0.00 0.00 1.52
5261 5910 8.485578 ACCAAGTCAAAGGGTTTTCATATAAA 57.514 30.769 0.00 0.00 0.00 1.40
5262 5911 9.589461 TTACCAAGTCAAAGGGTTTTCATATAA 57.411 29.630 0.00 0.00 36.14 0.98
5263 5912 9.589461 TTTACCAAGTCAAAGGGTTTTCATATA 57.411 29.630 0.00 0.00 36.14 0.86
5264 5913 8.485578 TTTACCAAGTCAAAGGGTTTTCATAT 57.514 30.769 0.00 0.00 36.14 1.78
5265 5914 7.899648 TTTACCAAGTCAAAGGGTTTTCATA 57.100 32.000 0.00 0.00 36.14 2.15
5266 5915 6.800072 TTTACCAAGTCAAAGGGTTTTCAT 57.200 33.333 0.00 0.00 36.14 2.57
5267 5916 6.800072 ATTTACCAAGTCAAAGGGTTTTCA 57.200 33.333 0.00 0.00 36.14 2.69
5268 5917 6.704493 GGAATTTACCAAGTCAAAGGGTTTTC 59.296 38.462 0.00 0.00 36.14 2.29
5269 5918 6.157123 TGGAATTTACCAAGTCAAAGGGTTTT 59.843 34.615 0.00 0.00 36.96 2.43
5270 5919 5.663556 TGGAATTTACCAAGTCAAAGGGTTT 59.336 36.000 0.00 0.00 36.96 3.27
5271 5920 5.069914 GTGGAATTTACCAAGTCAAAGGGTT 59.930 40.000 0.00 0.00 41.87 4.11
5272 5921 4.587262 GTGGAATTTACCAAGTCAAAGGGT 59.413 41.667 0.00 0.00 41.87 4.34
5273 5922 4.832823 AGTGGAATTTACCAAGTCAAAGGG 59.167 41.667 0.00 0.00 41.87 3.95
5295 5944 7.094631 TGGATATCCCGAATACGTAAAATCAG 58.905 38.462 19.34 0.00 37.93 2.90
5305 5954 5.677319 TGGATCTTGGATATCCCGAATAC 57.323 43.478 19.34 10.34 42.00 1.89
5306 5955 6.891306 AATGGATCTTGGATATCCCGAATA 57.109 37.500 19.34 1.08 42.00 1.75
5317 5966 4.782691 TGACACTCCTAAATGGATCTTGGA 59.217 41.667 0.00 0.00 45.16 3.53
5325 5974 5.678583 AGATGACATGACACTCCTAAATGG 58.321 41.667 0.00 0.00 37.10 3.16
5352 6001 9.826574 TTGGAATCAACAACCATATACTAGTAC 57.173 33.333 4.31 0.00 33.56 2.73


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

AutoCloner maintained by Alex Coulton.