Multiple sequence alignment - TraesCS2D01G100300

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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 TraesCS2D01G100300 chr2D 100.000 5348 0 0 1 5348 52235913 52230566 0.000000e+00 9877.0
1 TraesCS2D01G100300 chr2D 87.342 237 19 7 574 808 86490861 86490634 1.480000e-65 261.0
2 TraesCS2D01G100300 chr2A 95.003 3382 98 14 1897 5258 53789361 53786031 0.000000e+00 5243.0
3 TraesCS2D01G100300 chr2A 94.984 917 42 4 921 1834 53790255 53789340 0.000000e+00 1435.0
4 TraesCS2D01G100300 chr2A 88.034 351 32 7 1 348 53791150 53790807 1.790000e-109 407.0
5 TraesCS2D01G100300 chr2A 92.562 121 9 0 2554 2674 656707309 656707189 1.980000e-39 174.0
6 TraesCS2D01G100300 chr2A 95.122 41 2 0 1865 1905 697098018 697097978 1.240000e-06 65.8
7 TraesCS2D01G100300 chr2B 91.593 2700 118 32 2705 5345 81761851 81759202 0.000000e+00 3627.0
8 TraesCS2D01G100300 chr2B 88.757 1859 148 42 1 1834 81764281 81762459 0.000000e+00 2218.0
9 TraesCS2D01G100300 chr2B 94.073 658 18 8 1897 2553 81762480 81761843 0.000000e+00 979.0
10 TraesCS2D01G100300 chr2B 100.000 36 0 0 1865 1900 116429839 116429804 3.460000e-07 67.6
11 TraesCS2D01G100300 chr5D 83.750 240 30 7 571 807 380692104 380691871 9.020000e-53 219.0
12 TraesCS2D01G100300 chr4D 83.750 240 30 8 572 808 70326213 70326446 9.020000e-53 219.0
13 TraesCS2D01G100300 chr4D 97.436 39 1 0 1865 1903 259089112 259089074 3.460000e-07 67.6
14 TraesCS2D01G100300 chr4D 95.122 41 1 1 1865 1905 427261655 427261694 4.470000e-06 63.9
15 TraesCS2D01G100300 chr1A 82.845 239 37 4 573 808 9604352 9604115 1.510000e-50 211.0
16 TraesCS2D01G100300 chr6A 89.404 151 16 0 2554 2704 85268915 85268765 1.970000e-44 191.0
17 TraesCS2D01G100300 chr6A 95.238 42 1 1 1865 1905 36257992 36257951 1.240000e-06 65.8
18 TraesCS2D01G100300 chr4B 81.513 238 29 13 573 807 89455029 89454804 1.180000e-41 182.0
19 TraesCS2D01G100300 chr1B 81.624 234 26 13 577 804 613023475 613023697 1.530000e-40 178.0
20 TraesCS2D01G100300 chr1D 84.492 187 20 7 628 810 343883055 343883236 5.500000e-40 176.0
21 TraesCS2D01G100300 chr3B 80.417 240 35 12 577 811 466974130 466973898 7.120000e-39 172.0
22 TraesCS2D01G100300 chr7B 97.561 41 1 0 141 181 468942869 468942829 2.670000e-08 71.3
23 TraesCS2D01G100300 chr7B 90.909 55 2 2 127 181 667118506 667118455 2.670000e-08 71.3
24 TraesCS2D01G100300 chr4A 100.000 37 0 0 1865 1901 359955351 359955315 9.610000e-08 69.4
25 TraesCS2D01G100300 chr3D 100.000 36 0 0 1865 1900 378565365 378565330 3.460000e-07 67.6
26 TraesCS2D01G100300 chr3D 100.000 36 0 0 1865 1900 613784214 613784179 3.460000e-07 67.6
27 TraesCS2D01G100300 chr7D 91.837 49 0 4 1865 1909 100096178 100096130 1.240000e-06 65.8


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 TraesCS2D01G100300 chr2D 52230566 52235913 5347 True 9877.000000 9877 100.000000 1 5348 1 chr2D.!!$R1 5347
1 TraesCS2D01G100300 chr2A 53786031 53791150 5119 True 2361.666667 5243 92.673667 1 5258 3 chr2A.!!$R3 5257
2 TraesCS2D01G100300 chr2B 81759202 81764281 5079 True 2274.666667 3627 91.474333 1 5345 3 chr2B.!!$R2 5344

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
260 265 0.037605 CTACTCCCACCAACGACACC 60.038 60.000 0.00 0.0 0.00 4.16 F
615 842 0.094730 GTGGCACGAAGTAACATCGC 59.905 55.000 0.00 0.0 41.61 4.58 F
1880 2173 0.030909 TTTCAGAGGCCGGGGGTATA 60.031 55.000 2.18 0.0 0.00 1.47 F
2202 2495 0.460722 TTGACGACGGTTGGACTCAA 59.539 50.000 0.00 0.0 0.00 3.02 F
2598 2892 1.268234 GCCAGCTGATAATTGCACGAC 60.268 52.381 17.39 0.0 0.00 4.34 F
2686 2980 1.299165 GTCGTGCACTGTCGTGTCT 60.299 57.895 16.19 0.0 43.16 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 2154 0.030909 TATACCCCCGGCCTCTGAAA 60.031 55.0 0.00 0.0 0.00 2.69 R
2550 2844 0.106167 TCCCTGTAGCGGTGCTCTAT 60.106 55.0 3.95 0.0 40.44 1.98 R
3668 3962 2.198827 TTGATGTACCCCAACTGCTG 57.801 50.0 0.00 0.0 0.00 4.41 R
3951 4245 0.486879 AGGGAGAAACCAATGGCCAA 59.513 50.0 10.96 0.0 41.20 4.52 R
4224 4518 0.373716 GGAACGCTCTAAACATGCCG 59.626 55.0 0.00 0.0 0.00 5.69 R
4463 4758 0.593128 CAGGGAGAAAAACAGCACCG 59.407 55.0 0.00 0.0 0.00 4.94 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
61 64 8.352201 TGAAGAAACAAAGACATCAATAGTTGG 58.648 33.333 0.00 0.00 0.00 3.77
77 80 3.607741 AGTTGGCACTCTCATTCATCTG 58.392 45.455 0.00 0.00 0.00 2.90
109 112 6.102663 AGTCTATTTGATCTTGTTCACTCCG 58.897 40.000 0.00 0.00 0.00 4.63
110 113 5.869888 GTCTATTTGATCTTGTTCACTCCGT 59.130 40.000 0.00 0.00 0.00 4.69
125 128 1.273606 CTCCGTGGACACATGAGAACT 59.726 52.381 0.00 0.00 35.58 3.01
236 241 5.354234 GGACAAAAACGATACATCCATGACT 59.646 40.000 0.00 0.00 0.00 3.41
249 254 4.603094 TCCATGACTAAGACTACTCCCA 57.397 45.455 0.00 0.00 0.00 4.37
260 265 0.037605 CTACTCCCACCAACGACACC 60.038 60.000 0.00 0.00 0.00 4.16
263 268 2.357034 CCCACCAACGACACCTCG 60.357 66.667 0.00 0.00 46.06 4.63
282 287 2.744741 TCGAACTCAACAAAAGCACACA 59.255 40.909 0.00 0.00 0.00 3.72
284 289 3.543494 CGAACTCAACAAAAGCACACAAG 59.457 43.478 0.00 0.00 0.00 3.16
286 291 2.230992 ACTCAACAAAAGCACACAAGCA 59.769 40.909 0.00 0.00 36.85 3.91
289 294 3.119209 TCAACAAAAGCACACAAGCATCA 60.119 39.130 0.00 0.00 36.85 3.07
301 316 3.925299 CACAAGCATCACAAACACAAACA 59.075 39.130 0.00 0.00 0.00 2.83
302 317 3.925913 ACAAGCATCACAAACACAAACAC 59.074 39.130 0.00 0.00 0.00 3.32
303 318 3.865011 AGCATCACAAACACAAACACA 57.135 38.095 0.00 0.00 0.00 3.72
304 319 3.510719 AGCATCACAAACACAAACACAC 58.489 40.909 0.00 0.00 0.00 3.82
305 320 2.278615 GCATCACAAACACAAACACACG 59.721 45.455 0.00 0.00 0.00 4.49
306 321 2.620779 TCACAAACACAAACACACGG 57.379 45.000 0.00 0.00 0.00 4.94
307 322 1.200252 TCACAAACACAAACACACGGG 59.800 47.619 0.00 0.00 0.00 5.28
308 323 1.200252 CACAAACACAAACACACGGGA 59.800 47.619 0.00 0.00 0.00 5.14
309 324 1.887198 ACAAACACAAACACACGGGAA 59.113 42.857 0.00 0.00 0.00 3.97
310 325 2.296471 ACAAACACAAACACACGGGAAA 59.704 40.909 0.00 0.00 0.00 3.13
311 326 3.056465 ACAAACACAAACACACGGGAAAT 60.056 39.130 0.00 0.00 0.00 2.17
322 337 0.178068 ACGGGAAATCCACTCCATCG 59.822 55.000 1.22 0.00 37.91 3.84
329 344 1.656652 ATCCACTCCATCGAAAAGCG 58.343 50.000 0.00 0.00 42.69 4.68
341 356 2.036217 TCGAAAAGCGGACTTACCAGAA 59.964 45.455 0.00 0.00 41.33 3.02
397 622 4.100498 TCCCTCCGTTCCATATTAAGTCAC 59.900 45.833 0.00 0.00 0.00 3.67
398 623 4.377897 CCTCCGTTCCATATTAAGTCACC 58.622 47.826 0.00 0.00 0.00 4.02
399 624 4.049186 CTCCGTTCCATATTAAGTCACCG 58.951 47.826 0.00 0.00 0.00 4.94
411 636 9.321562 CATATTAAGTCACCGGTTTAGTACAAT 57.678 33.333 2.97 5.60 0.00 2.71
463 689 5.648960 TGAAACGAAGGGAGTAAACAAAAGT 59.351 36.000 0.00 0.00 0.00 2.66
495 722 4.574828 AGCCATATCATCACGTGTTTTACC 59.425 41.667 16.51 0.00 0.00 2.85
569 796 7.763734 TTTTGTGACAATAACGCGTTTATAC 57.236 32.000 31.50 19.15 29.54 1.47
570 797 6.463483 TTGTGACAATAACGCGTTTATACA 57.537 33.333 31.50 21.26 29.54 2.29
572 799 6.298103 TGTGACAATAACGCGTTTATACAAC 58.702 36.000 31.50 20.69 29.54 3.32
573 800 5.729424 GTGACAATAACGCGTTTATACAACC 59.271 40.000 31.50 12.16 29.54 3.77
575 802 4.694509 ACAATAACGCGTTTATACAACCCA 59.305 37.500 31.50 8.12 29.54 4.51
585 812 7.485277 CGCGTTTATACAACCCAAAATGATAAA 59.515 33.333 0.00 0.00 0.00 1.40
591 818 5.244755 ACAACCCAAAATGATAAATGCCAC 58.755 37.500 0.00 0.00 0.00 5.01
594 821 4.285517 ACCCAAAATGATAAATGCCACACA 59.714 37.500 0.00 0.00 0.00 3.72
612 839 2.483877 CACATGTGGCACGAAGTAACAT 59.516 45.455 18.51 0.00 41.61 2.71
615 842 0.094730 GTGGCACGAAGTAACATCGC 59.905 55.000 0.00 0.00 41.61 4.58
619 846 0.999406 CACGAAGTAACATCGCCCTG 59.001 55.000 0.56 0.00 41.61 4.45
640 867 7.861872 GCCCTGACGTTTTTACAACTAAAATTA 59.138 33.333 0.00 0.00 32.90 1.40
641 868 9.902196 CCCTGACGTTTTTACAACTAAAATTAT 57.098 29.630 0.00 0.00 32.90 1.28
664 891 7.587037 ATCACTCAAGAAAGAACAAAATCCA 57.413 32.000 0.00 0.00 0.00 3.41
665 892 7.403312 TCACTCAAGAAAGAACAAAATCCAA 57.597 32.000 0.00 0.00 0.00 3.53
666 893 7.835822 TCACTCAAGAAAGAACAAAATCCAAA 58.164 30.769 0.00 0.00 0.00 3.28
667 894 7.759433 TCACTCAAGAAAGAACAAAATCCAAAC 59.241 33.333 0.00 0.00 0.00 2.93
696 923 9.921637 AAAAACTAAAACTTGACATCAAACAGA 57.078 25.926 0.00 0.00 35.15 3.41
703 930 6.757897 ACTTGACATCAAACAGAAAGTTGA 57.242 33.333 0.00 0.00 41.19 3.18
712 939 5.125257 TCAAACAGAAAGTTGACATGCTTCA 59.875 36.000 0.00 0.00 41.19 3.02
721 948 6.064846 AGTTGACATGCTTCACAACTAAAG 57.935 37.500 15.67 0.00 46.84 1.85
761 988 6.084326 ACTAAATTTGCCATCAGAAAACGT 57.916 33.333 0.00 0.00 0.00 3.99
762 989 6.149633 ACTAAATTTGCCATCAGAAAACGTC 58.850 36.000 0.00 0.00 0.00 4.34
763 990 2.679355 TTTGCCATCAGAAAACGTCG 57.321 45.000 0.00 0.00 0.00 5.12
766 993 1.644786 GCCATCAGAAAACGTCGGGG 61.645 60.000 0.00 0.00 0.00 5.73
768 995 0.953471 CATCAGAAAACGTCGGGGCA 60.953 55.000 0.00 0.00 0.00 5.36
769 996 0.673644 ATCAGAAAACGTCGGGGCAG 60.674 55.000 0.00 0.00 0.00 4.85
785 1012 2.268730 GCAGAATTGCTTAGTGCCAC 57.731 50.000 0.00 0.00 46.95 5.01
787 1014 2.669391 GCAGAATTGCTTAGTGCCACAC 60.669 50.000 0.00 0.00 46.95 3.82
789 1016 1.535462 GAATTGCTTAGTGCCACACGT 59.465 47.619 0.00 0.00 42.00 4.49
790 1017 0.874390 ATTGCTTAGTGCCACACGTG 59.126 50.000 15.48 15.48 42.00 4.49
791 1018 0.462937 TTGCTTAGTGCCACACGTGT 60.463 50.000 17.22 17.22 42.00 4.49
792 1019 1.157257 TGCTTAGTGCCACACGTGTG 61.157 55.000 36.13 36.13 45.23 3.82
793 1020 3.501007 TGCTTAGTGCCACACGTGTGA 62.501 52.381 42.33 25.54 45.30 3.58
813 1040 4.592485 GACACTATCAGGGTCCATACAG 57.408 50.000 0.00 0.00 42.74 2.74
826 1053 4.892934 GGTCCATACAGCCCAAATGATAAA 59.107 41.667 0.00 0.00 0.00 1.40
827 1054 5.362430 GGTCCATACAGCCCAAATGATAAAA 59.638 40.000 0.00 0.00 0.00 1.52
828 1055 6.127196 GGTCCATACAGCCCAAATGATAAAAA 60.127 38.462 0.00 0.00 0.00 1.94
830 1057 6.438741 TCCATACAGCCCAAATGATAAAAACA 59.561 34.615 0.00 0.00 0.00 2.83
831 1058 6.534793 CCATACAGCCCAAATGATAAAAACAC 59.465 38.462 0.00 0.00 0.00 3.32
832 1059 5.543507 ACAGCCCAAATGATAAAAACACA 57.456 34.783 0.00 0.00 0.00 3.72
872 1099 1.301423 CGAACACGGGTGAAAAAGGA 58.699 50.000 5.71 0.00 0.00 3.36
949 1227 2.993899 CGCTTAACACTAAGGACCACAG 59.006 50.000 0.00 0.00 35.90 3.66
981 1259 1.318576 AAAAGTGCAGTAGTGTGGCC 58.681 50.000 0.00 0.00 0.00 5.36
982 1260 0.474184 AAAGTGCAGTAGTGTGGCCT 59.526 50.000 3.32 0.00 0.00 5.19
1030 1308 2.597578 TCTTTTCCCCCTTTGTAGCC 57.402 50.000 0.00 0.00 0.00 3.93
1195 1473 4.080863 TCCCCTCTTCAAAATCTACTCTGC 60.081 45.833 0.00 0.00 0.00 4.26
1284 1562 5.418310 AGGAAATGGTGCGATTTTATACG 57.582 39.130 0.00 0.00 0.00 3.06
1432 1714 5.050363 GCAAGATAAGGCATAATCGTTTCGA 60.050 40.000 0.00 0.00 41.13 3.71
1478 1764 4.822685 ATGCTGGATCTTATCTAGGCAG 57.177 45.455 2.96 0.00 38.22 4.85
1480 1766 3.576118 TGCTGGATCTTATCTAGGCAGTC 59.424 47.826 2.96 0.00 38.22 3.51
1490 1776 0.965866 CTAGGCAGTCGTCCCAGTCA 60.966 60.000 0.00 0.00 0.00 3.41
1520 1806 5.237048 TGCTAATTTTGCATCTTTTGGGAC 58.763 37.500 1.26 0.00 35.31 4.46
1539 1825 4.814771 GGGACGATTGATTAGGTTAGGTTG 59.185 45.833 0.00 0.00 0.00 3.77
1627 1913 2.161609 GGGTTTCGTTTCATGGCTAGTG 59.838 50.000 0.00 0.00 0.00 2.74
1635 1921 3.632643 TTCATGGCTAGTGATTGCAGA 57.367 42.857 0.00 0.00 0.00 4.26
1700 1987 5.836024 TTTGGTGGGTACATATAGGGATC 57.164 43.478 0.00 0.00 0.00 3.36
1706 1993 2.431057 GGTACATATAGGGATCGGCCAG 59.569 54.545 2.24 0.00 38.95 4.85
1727 2020 7.287235 GGCCAGTTCTCTTATCTTACCTAGTTA 59.713 40.741 0.00 0.00 0.00 2.24
1740 2033 8.773404 TCTTACCTAGTTAAGCAGATTTTGAC 57.227 34.615 2.27 0.00 0.00 3.18
1826 2119 7.070074 GGACTCTATCTAAATGGAAACTCCTCA 59.930 40.741 0.00 0.00 37.46 3.86
1827 2120 8.560124 ACTCTATCTAAATGGAAACTCCTCAT 57.440 34.615 0.00 0.00 37.46 2.90
1828 2121 9.661954 ACTCTATCTAAATGGAAACTCCTCATA 57.338 33.333 0.00 0.00 37.46 2.15
1833 2126 9.981460 ATCTAAATGGAAACTCCTCATAAAGTT 57.019 29.630 0.00 0.00 37.46 2.66
1834 2127 9.449719 TCTAAATGGAAACTCCTCATAAAGTTC 57.550 33.333 0.00 0.00 37.46 3.01
1835 2128 9.454859 CTAAATGGAAACTCCTCATAAAGTTCT 57.545 33.333 0.00 0.00 37.46 3.01
1836 2129 7.929941 AATGGAAACTCCTCATAAAGTTCTC 57.070 36.000 0.00 0.00 37.46 2.87
1837 2130 6.688073 TGGAAACTCCTCATAAAGTTCTCT 57.312 37.500 0.00 0.00 37.46 3.10
1838 2131 7.079451 TGGAAACTCCTCATAAAGTTCTCTT 57.921 36.000 0.00 0.00 37.46 2.85
1839 2132 8.202461 TGGAAACTCCTCATAAAGTTCTCTTA 57.798 34.615 0.00 0.00 37.46 2.10
1840 2133 8.826765 TGGAAACTCCTCATAAAGTTCTCTTAT 58.173 33.333 0.00 0.00 37.46 1.73
1841 2134 9.320352 GGAAACTCCTCATAAAGTTCTCTTATC 57.680 37.037 0.00 0.00 34.71 1.75
1842 2135 9.320352 GAAACTCCTCATAAAGTTCTCTTATCC 57.680 37.037 0.00 0.00 34.71 2.59
1843 2136 7.045126 ACTCCTCATAAAGTTCTCTTATCCG 57.955 40.000 0.00 0.00 33.09 4.18
1844 2137 5.844004 TCCTCATAAAGTTCTCTTATCCGC 58.156 41.667 0.00 0.00 33.09 5.54
1845 2138 4.681942 CCTCATAAAGTTCTCTTATCCGCG 59.318 45.833 0.00 0.00 33.09 6.46
1846 2139 5.507482 CCTCATAAAGTTCTCTTATCCGCGA 60.507 44.000 8.23 0.00 33.09 5.87
1847 2140 5.520632 TCATAAAGTTCTCTTATCCGCGAG 58.479 41.667 8.23 0.00 33.09 5.03
1848 2141 3.870633 AAAGTTCTCTTATCCGCGAGT 57.129 42.857 8.23 0.00 33.09 4.18
1849 2142 3.870633 AAGTTCTCTTATCCGCGAGTT 57.129 42.857 8.23 0.00 31.46 3.01
1850 2143 3.870633 AGTTCTCTTATCCGCGAGTTT 57.129 42.857 8.23 0.00 0.00 2.66
1851 2144 3.771798 AGTTCTCTTATCCGCGAGTTTC 58.228 45.455 8.23 0.00 0.00 2.78
1852 2145 2.858941 GTTCTCTTATCCGCGAGTTTCC 59.141 50.000 8.23 0.00 0.00 3.13
1853 2146 2.097036 TCTCTTATCCGCGAGTTTCCA 58.903 47.619 8.23 0.00 0.00 3.53
1854 2147 2.693591 TCTCTTATCCGCGAGTTTCCAT 59.306 45.455 8.23 0.00 0.00 3.41
1855 2148 3.132289 TCTCTTATCCGCGAGTTTCCATT 59.868 43.478 8.23 0.00 0.00 3.16
1856 2149 3.869065 TCTTATCCGCGAGTTTCCATTT 58.131 40.909 8.23 0.00 0.00 2.32
1857 2150 4.258543 TCTTATCCGCGAGTTTCCATTTT 58.741 39.130 8.23 0.00 0.00 1.82
1858 2151 4.698304 TCTTATCCGCGAGTTTCCATTTTT 59.302 37.500 8.23 0.00 0.00 1.94
1876 2169 2.438795 TTTTTCAGAGGCCGGGGG 59.561 61.111 2.18 0.00 0.00 5.40
1877 2170 2.466186 TTTTTCAGAGGCCGGGGGT 61.466 57.895 2.18 0.00 0.00 4.95
1878 2171 1.135068 TTTTTCAGAGGCCGGGGGTA 61.135 55.000 2.18 0.00 0.00 3.69
1879 2172 0.917333 TTTTCAGAGGCCGGGGGTAT 60.917 55.000 2.18 0.00 0.00 2.73
1880 2173 0.030909 TTTCAGAGGCCGGGGGTATA 60.031 55.000 2.18 0.00 0.00 1.47
1881 2174 0.761702 TTCAGAGGCCGGGGGTATAC 60.762 60.000 2.18 0.00 0.00 1.47
1882 2175 2.203466 AGAGGCCGGGGGTATACC 59.797 66.667 13.99 13.99 39.11 2.73
1883 2176 2.203466 GAGGCCGGGGGTATACCT 59.797 66.667 21.25 0.00 40.03 3.08
1884 2177 1.912264 GAGGCCGGGGGTATACCTC 60.912 68.421 21.25 17.88 40.14 3.85
1894 2187 4.529716 GGGGTATACCTCCATTTCCAAA 57.470 45.455 21.25 0.00 40.03 3.28
1895 2188 4.874199 GGGGTATACCTCCATTTCCAAAA 58.126 43.478 21.25 0.00 40.03 2.44
1896 2189 5.274015 GGGGTATACCTCCATTTCCAAAAA 58.726 41.667 21.25 0.00 40.03 1.94
1923 2216 4.767409 GGAAACTCCTCATAAAGTTTGCCT 59.233 41.667 5.31 0.00 43.75 4.75
1925 2218 3.084786 ACTCCTCATAAAGTTTGCCTGC 58.915 45.455 0.00 0.00 0.00 4.85
1937 2230 2.843401 TTGCCTGCTTTGATGCAAAT 57.157 40.000 0.00 0.00 42.83 2.32
2202 2495 0.460722 TTGACGACGGTTGGACTCAA 59.539 50.000 0.00 0.00 0.00 3.02
2236 2529 6.876257 ACTGTGCTTAGTCTCAAATTTCCTAG 59.124 38.462 0.00 0.00 0.00 3.02
2242 2535 8.661257 GCTTAGTCTCAAATTTCCTAGAAGTTC 58.339 37.037 0.00 0.00 0.00 3.01
2430 2724 6.131264 ACAATAGCCATCATCCAGATTCAAA 58.869 36.000 0.00 0.00 33.72 2.69
2550 2844 2.586425 AGCTTGCTGCCTCTTACAAAA 58.414 42.857 0.00 0.00 44.23 2.44
2576 2870 2.564975 CGCTACAGGGACGACGTT 59.435 61.111 0.13 0.00 0.00 3.99
2598 2892 1.268234 GCCAGCTGATAATTGCACGAC 60.268 52.381 17.39 0.00 0.00 4.34
2686 2980 1.299165 GTCGTGCACTGTCGTGTCT 60.299 57.895 16.19 0.00 43.16 3.41
2693 2987 1.921243 CACTGTCGTGTCTTGTGTGA 58.079 50.000 0.00 0.00 36.39 3.58
2694 2988 2.267426 CACTGTCGTGTCTTGTGTGAA 58.733 47.619 0.00 0.00 36.39 3.18
2695 2989 2.282555 CACTGTCGTGTCTTGTGTGAAG 59.717 50.000 0.00 0.00 36.39 3.02
2696 2990 2.094182 ACTGTCGTGTCTTGTGTGAAGT 60.094 45.455 0.00 0.00 0.00 3.01
2697 2991 3.129813 ACTGTCGTGTCTTGTGTGAAGTA 59.870 43.478 0.00 0.00 0.00 2.24
2832 3126 9.931210 GGTGTTATAGCTATGTGTTTATTTCAC 57.069 33.333 16.77 9.23 36.48 3.18
3054 3348 2.891941 ATTCATGCACACCGCCGGAT 62.892 55.000 11.71 0.00 41.33 4.18
3451 3745 3.036429 GCCGCTCCTGGAGGTGATT 62.036 63.158 24.43 0.00 37.22 2.57
3469 3763 4.396166 GTGATTCTTCCGTCATTCCATTGT 59.604 41.667 0.00 0.00 0.00 2.71
3668 3962 3.125316 CCACGGATTGAGTCAGTTAAAGC 59.875 47.826 0.00 0.00 32.67 3.51
3834 4128 2.227036 CCCAGTCCCAGCTGAACCT 61.227 63.158 17.39 4.11 38.70 3.50
3933 4227 1.379843 CCCACCCATTCCTTTCCCG 60.380 63.158 0.00 0.00 0.00 5.14
3951 4245 2.112815 GCTAATGCCGCCTTCCGTT 61.113 57.895 0.00 0.00 34.38 4.44
4089 4383 2.065899 CAGTCCTTGGAAAACACCCA 57.934 50.000 0.00 0.00 0.00 4.51
4224 4518 3.100862 GATTGAACCTGGCGAGCGC 62.101 63.158 6.27 6.27 41.06 5.92
4305 4599 0.674895 GAGTCATGCAAGCGAACCCT 60.675 55.000 0.00 0.00 0.00 4.34
4463 4758 3.005472 TGCAACTGTACTATCGGGATAGC 59.995 47.826 14.13 2.03 43.46 2.97
4468 4763 1.135460 GTACTATCGGGATAGCGGTGC 60.135 57.143 14.13 0.00 43.46 5.01
4476 4771 1.132453 GGGATAGCGGTGCTGTTTTTC 59.868 52.381 0.00 0.00 40.10 2.29
4533 4828 1.154205 CGGGTTCATGATCAGACCGC 61.154 60.000 15.50 7.69 33.01 5.68
4601 4896 4.913376 GCTTAATGCATACAGGTGTTCTG 58.087 43.478 0.00 0.00 44.39 3.02
4602 4897 4.731773 GCTTAATGCATACAGGTGTTCTGC 60.732 45.833 0.00 9.33 43.47 4.26
4603 4898 6.885314 GCTTAATGCATACAGGTGTTCTGCT 61.885 44.000 0.00 3.22 43.47 4.24
4604 4899 8.281533 GCTTAATGCATACAGGTGTTCTGCTT 62.282 42.308 0.00 8.50 43.47 3.91
4605 4900 9.648832 GCTTAATGCATACAGGTGTTCTGCTTT 62.649 40.741 0.00 15.41 43.47 3.51
4675 4970 7.702348 AGAAGCACAAGATTTAGAAACACAAAC 59.298 33.333 0.00 0.00 0.00 2.93
4712 5007 4.675976 TCAACTCTGAAGAAAACCGGTA 57.324 40.909 8.00 0.00 0.00 4.02
4715 5010 4.684484 ACTCTGAAGAAAACCGGTAACT 57.316 40.909 8.00 4.73 0.00 2.24
4720 5015 5.297527 TCTGAAGAAAACCGGTAACTTTTCC 59.702 40.000 20.66 10.70 40.01 3.13
4722 5017 2.291465 AGAAAACCGGTAACTTTTCCGC 59.709 45.455 20.66 3.11 44.63 5.54
4724 5019 1.844771 AACCGGTAACTTTTCCGCGC 61.845 55.000 8.00 0.00 44.63 6.86
4757 5054 1.600013 GCTGATGCATCTGCTTCTCTG 59.400 52.381 37.09 14.63 44.98 3.35
4760 5057 2.433239 TGATGCATCTGCTTCTCTGCTA 59.567 45.455 26.32 0.00 43.23 3.49
4792 5107 4.871933 TGTGTGTATGTGAGTGATGACT 57.128 40.909 0.00 0.00 33.98 3.41
4813 5128 4.530946 ACTAGTGGTGGTTGTAAGCTATGT 59.469 41.667 0.00 0.00 0.00 2.29
4819 5138 4.506654 GGTGGTTGTAAGCTATGTGTATCG 59.493 45.833 0.00 0.00 0.00 2.92
4953 5291 4.436050 GCCGCCTTTATATCAACATCGATG 60.436 45.833 23.68 23.68 0.00 3.84
5110 5450 0.733150 CCAGCAGATGTGTCAGCATG 59.267 55.000 0.00 0.00 39.15 4.06
5132 5472 0.535102 AACTCTGCCACTGAAACGGG 60.535 55.000 0.00 0.00 0.00 5.28
5135 5475 0.034337 TCTGCCACTGAAACGGGTAC 59.966 55.000 0.00 0.00 0.00 3.34
5188 5543 7.094890 TGCACTGAAGTAGAAGTAGTGTAGTAC 60.095 40.741 0.00 0.00 40.52 2.73
5210 5565 0.519077 CTTGCAGGAACTCGAAAGGC 59.481 55.000 0.00 0.00 34.60 4.35
5211 5566 0.179032 TTGCAGGAACTCGAAAGGCA 60.179 50.000 0.00 0.00 34.60 4.75
5215 5570 0.759346 AGGAACTCGAAAGGCACTGT 59.241 50.000 0.00 0.00 40.86 3.55
5230 5585 2.605580 GCACTGTCTGTAAAAAGCCTGC 60.606 50.000 0.00 0.00 0.00 4.85
5302 5657 3.981211 TGCATTTTTGCCTCTTCTGAAC 58.019 40.909 0.00 0.00 0.00 3.18
5332 5695 1.285280 TGGTCGATCCATTGGAGGTT 58.715 50.000 11.78 0.00 41.93 3.50
5333 5696 1.209504 TGGTCGATCCATTGGAGGTTC 59.790 52.381 11.78 3.23 41.93 3.62
5345 5708 3.731652 TGGAGGTTCAGTGCATTTTTG 57.268 42.857 0.00 0.00 0.00 2.44
5346 5709 2.224018 TGGAGGTTCAGTGCATTTTTGC 60.224 45.455 0.00 0.00 0.00 3.68
5347 5710 2.407090 GAGGTTCAGTGCATTTTTGCC 58.593 47.619 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 64 6.374565 AATTAAGCAGATGAATGAGAGTGC 57.625 37.500 0.00 0.00 0.00 4.40
134 137 1.933247 CTTTTGCCTTGGTTTCGCAA 58.067 45.000 0.00 0.00 40.58 4.85
171 176 7.278875 ACCTGGCAATAGATCTTCTTCTTAAG 58.721 38.462 0.00 0.00 0.00 1.85
187 192 5.461032 TTTTTCGTGATTAACCTGGCAAT 57.539 34.783 0.00 0.00 0.00 3.56
216 221 8.041323 AGTCTTAGTCATGGATGTATCGTTTTT 58.959 33.333 0.00 0.00 0.00 1.94
221 226 7.361371 GGAGTAGTCTTAGTCATGGATGTATCG 60.361 44.444 0.00 0.00 31.92 2.92
236 241 2.821969 GTCGTTGGTGGGAGTAGTCTTA 59.178 50.000 0.00 0.00 0.00 2.10
249 254 0.031721 GAGTTCGAGGTGTCGTTGGT 59.968 55.000 0.00 0.00 46.85 3.67
260 265 3.181511 TGTGTGCTTTTGTTGAGTTCGAG 60.182 43.478 0.00 0.00 0.00 4.04
263 268 3.304293 GCTTGTGTGCTTTTGTTGAGTTC 59.696 43.478 0.00 0.00 0.00 3.01
282 287 3.925913 GTGTGTTTGTGTTTGTGATGCTT 59.074 39.130 0.00 0.00 0.00 3.91
284 289 2.278615 CGTGTGTTTGTGTTTGTGATGC 59.721 45.455 0.00 0.00 0.00 3.91
286 291 2.159310 CCCGTGTGTTTGTGTTTGTGAT 60.159 45.455 0.00 0.00 0.00 3.06
289 294 1.535833 TCCCGTGTGTTTGTGTTTGT 58.464 45.000 0.00 0.00 0.00 2.83
301 316 0.991920 ATGGAGTGGATTTCCCGTGT 59.008 50.000 0.00 0.00 37.93 4.49
302 317 1.668419 GATGGAGTGGATTTCCCGTG 58.332 55.000 0.00 0.00 37.93 4.94
303 318 0.178068 CGATGGAGTGGATTTCCCGT 59.822 55.000 0.00 0.00 37.93 5.28
304 319 0.464036 TCGATGGAGTGGATTTCCCG 59.536 55.000 0.00 0.00 37.93 5.14
305 320 2.710096 TTCGATGGAGTGGATTTCCC 57.290 50.000 0.00 0.00 33.62 3.97
306 321 3.181496 GCTTTTCGATGGAGTGGATTTCC 60.181 47.826 0.00 0.00 35.20 3.13
307 322 3.485877 CGCTTTTCGATGGAGTGGATTTC 60.486 47.826 0.00 0.00 41.67 2.17
308 323 2.420022 CGCTTTTCGATGGAGTGGATTT 59.580 45.455 0.00 0.00 41.67 2.17
309 324 2.009774 CGCTTTTCGATGGAGTGGATT 58.990 47.619 0.00 0.00 41.67 3.01
310 325 1.656652 CGCTTTTCGATGGAGTGGAT 58.343 50.000 0.00 0.00 41.67 3.41
311 326 0.391130 CCGCTTTTCGATGGAGTGGA 60.391 55.000 14.27 0.00 42.32 4.02
322 337 4.823790 TTTTCTGGTAAGTCCGCTTTTC 57.176 40.909 0.00 0.00 39.52 2.29
329 344 5.055144 ACGACTTCTTTTTCTGGTAAGTCC 58.945 41.667 0.00 0.00 41.82 3.85
341 356 3.751698 GCAAGGTCCATACGACTTCTTTT 59.248 43.478 0.00 0.00 41.64 2.27
363 588 3.181478 GGAACGGAGGGAGTACATGTTAG 60.181 52.174 2.30 0.00 0.00 2.34
438 664 5.488645 TTTGTTTACTCCCTTCGTTTCAC 57.511 39.130 0.00 0.00 0.00 3.18
495 722 0.744414 AACCATTCATGTCGAGCGGG 60.744 55.000 0.00 0.00 0.00 6.13
544 771 7.854422 TGTATAAACGCGTTATTGTCACAAAAA 59.146 29.630 26.87 0.00 34.18 1.94
557 784 4.564940 TTTTGGGTTGTATAAACGCGTT 57.435 36.364 20.79 20.79 36.08 4.84
568 795 5.221803 TGTGGCATTTATCATTTTGGGTTGT 60.222 36.000 0.00 0.00 0.00 3.32
569 796 5.122082 GTGTGGCATTTATCATTTTGGGTTG 59.878 40.000 0.00 0.00 0.00 3.77
570 797 5.221803 TGTGTGGCATTTATCATTTTGGGTT 60.222 36.000 0.00 0.00 0.00 4.11
572 799 4.829968 TGTGTGGCATTTATCATTTTGGG 58.170 39.130 0.00 0.00 0.00 4.12
573 800 5.875910 ACATGTGTGGCATTTATCATTTTGG 59.124 36.000 0.00 0.00 35.19 3.28
575 802 6.971527 CACATGTGTGGCATTTATCATTTT 57.028 33.333 18.03 0.00 42.10 1.82
591 818 1.870402 TGTTACTTCGTGCCACATGTG 59.130 47.619 19.31 19.31 0.00 3.21
594 821 1.999735 CGATGTTACTTCGTGCCACAT 59.000 47.619 11.67 0.00 32.08 3.21
612 839 1.598601 GTTGTAAAAACGTCAGGGCGA 59.401 47.619 0.00 0.00 35.59 5.54
615 842 9.902196 ATAATTTTAGTTGTAAAAACGTCAGGG 57.098 29.630 0.00 0.00 40.65 4.45
640 867 7.587037 TGGATTTTGTTCTTTCTTGAGTGAT 57.413 32.000 0.00 0.00 0.00 3.06
641 868 7.403312 TTGGATTTTGTTCTTTCTTGAGTGA 57.597 32.000 0.00 0.00 0.00 3.41
644 871 8.477984 TTGTTTGGATTTTGTTCTTTCTTGAG 57.522 30.769 0.00 0.00 0.00 3.02
645 872 8.839310 TTTGTTTGGATTTTGTTCTTTCTTGA 57.161 26.923 0.00 0.00 0.00 3.02
646 873 9.890352 TTTTTGTTTGGATTTTGTTCTTTCTTG 57.110 25.926 0.00 0.00 0.00 3.02
677 904 8.087750 TCAACTTTCTGTTTGATGTCAAGTTTT 58.912 29.630 0.00 0.00 36.63 2.43
684 911 5.400485 GCATGTCAACTTTCTGTTTGATGTC 59.600 40.000 0.00 0.00 36.63 3.06
685 912 5.068198 AGCATGTCAACTTTCTGTTTGATGT 59.932 36.000 0.00 0.00 36.63 3.06
688 915 5.125257 TGAAGCATGTCAACTTTCTGTTTGA 59.875 36.000 0.00 0.00 36.63 2.69
696 923 4.989279 AGTTGTGAAGCATGTCAACTTT 57.011 36.364 10.13 0.00 45.01 2.66
721 948 7.923414 AATTTAGTTACCTGAGGATGACAAC 57.077 36.000 4.99 1.21 0.00 3.32
725 952 5.885912 GGCAAATTTAGTTACCTGAGGATGA 59.114 40.000 4.99 0.00 0.00 2.92
732 959 6.757897 TCTGATGGCAAATTTAGTTACCTG 57.242 37.500 0.00 0.00 0.00 4.00
735 962 7.593644 ACGTTTTCTGATGGCAAATTTAGTTAC 59.406 33.333 0.00 0.00 0.00 2.50
744 971 1.265635 CCGACGTTTTCTGATGGCAAA 59.734 47.619 0.00 0.00 0.00 3.68
752 979 0.882927 TTCTGCCCCGACGTTTTCTG 60.883 55.000 0.00 0.00 0.00 3.02
754 981 0.879090 AATTCTGCCCCGACGTTTTC 59.121 50.000 0.00 0.00 0.00 2.29
785 1012 1.272490 ACCCTGATAGTGTCACACGTG 59.728 52.381 15.48 15.48 39.64 4.49
787 1014 1.135083 GGACCCTGATAGTGTCACACG 60.135 57.143 1.22 0.00 39.64 4.49
789 1016 2.319025 TGGACCCTGATAGTGTCACA 57.681 50.000 5.62 0.00 32.22 3.58
790 1017 3.704566 TGTATGGACCCTGATAGTGTCAC 59.295 47.826 0.00 0.00 32.22 3.67
791 1018 3.960755 CTGTATGGACCCTGATAGTGTCA 59.039 47.826 0.00 0.00 35.05 3.58
792 1019 3.243907 GCTGTATGGACCCTGATAGTGTC 60.244 52.174 0.00 0.00 0.00 3.67
793 1020 2.700897 GCTGTATGGACCCTGATAGTGT 59.299 50.000 0.00 0.00 0.00 3.55
794 1021 2.037772 GGCTGTATGGACCCTGATAGTG 59.962 54.545 0.00 0.00 0.00 2.74
795 1022 2.330216 GGCTGTATGGACCCTGATAGT 58.670 52.381 0.00 0.00 0.00 2.12
813 1040 8.316640 TGTATTTGTGTTTTTATCATTTGGGC 57.683 30.769 0.00 0.00 0.00 5.36
826 1053 7.169308 TGTTCGTTTGTGTTTGTATTTGTGTTT 59.831 29.630 0.00 0.00 0.00 2.83
827 1054 6.641314 TGTTCGTTTGTGTTTGTATTTGTGTT 59.359 30.769 0.00 0.00 0.00 3.32
828 1055 6.088350 GTGTTCGTTTGTGTTTGTATTTGTGT 59.912 34.615 0.00 0.00 0.00 3.72
830 1057 5.284188 CGTGTTCGTTTGTGTTTGTATTTGT 59.716 36.000 0.00 0.00 0.00 2.83
831 1058 5.508573 TCGTGTTCGTTTGTGTTTGTATTTG 59.491 36.000 0.00 0.00 38.33 2.32
832 1059 5.629097 TCGTGTTCGTTTGTGTTTGTATTT 58.371 33.333 0.00 0.00 38.33 1.40
889 1118 3.324846 TGGATATCCTGCTTTCGCACTAT 59.675 43.478 22.35 0.00 42.25 2.12
890 1119 2.698274 TGGATATCCTGCTTTCGCACTA 59.302 45.455 22.35 0.00 42.25 2.74
949 1227 3.462021 TGCACTTTTTGGGTAATTGCAC 58.538 40.909 0.00 0.00 36.60 4.57
982 1260 1.940883 ATTTAGCCTCGCGTCCGTGA 61.941 55.000 5.77 2.72 35.54 4.35
1145 1423 0.803117 CTCGCGTGACTTCACCTCTA 59.197 55.000 5.77 0.00 43.66 2.43
1195 1473 1.981495 ACTGAAAGGGGGAGAACAGAG 59.019 52.381 0.00 0.00 39.30 3.35
1284 1562 9.654663 AAGAAACAGAAGACATATACTTGTACC 57.345 33.333 0.00 0.00 0.00 3.34
1432 1714 5.191426 TGACTAGATTACCGACTGCTAAGT 58.809 41.667 0.00 0.00 40.21 2.24
1478 1764 0.613777 AGGGATTTGACTGGGACGAC 59.386 55.000 0.00 0.00 0.00 4.34
1480 1766 1.026718 GCAGGGATTTGACTGGGACG 61.027 60.000 0.00 0.00 35.30 4.79
1490 1776 5.945144 AGATGCAAAATTAGCAGGGATTT 57.055 34.783 10.69 0.00 46.36 2.17
1520 1806 7.270047 TCTAACCAACCTAACCTAATCAATCG 58.730 38.462 0.00 0.00 0.00 3.34
1539 1825 4.743955 GCTTGACATGGTCCCTATCTAACC 60.744 50.000 0.00 0.00 0.00 2.85
1627 1913 1.814394 TCACACAGCCATTCTGCAATC 59.186 47.619 0.00 0.00 46.76 2.67
1635 1921 0.606130 TGACGCATCACACAGCCATT 60.606 50.000 0.00 0.00 0.00 3.16
1700 1987 3.385111 AGGTAAGATAAGAGAACTGGCCG 59.615 47.826 0.00 0.00 0.00 6.13
1706 1993 9.738832 CTGCTTAACTAGGTAAGATAAGAGAAC 57.261 37.037 28.14 9.75 41.03 3.01
1727 2020 3.880490 TGTAACCACGTCAAAATCTGCTT 59.120 39.130 0.00 0.00 0.00 3.91
1826 2119 5.517322 ACTCGCGGATAAGAGAACTTTAT 57.483 39.130 6.13 0.00 37.87 1.40
1827 2120 4.978083 ACTCGCGGATAAGAGAACTTTA 57.022 40.909 6.13 0.00 37.87 1.85
1828 2121 3.870633 ACTCGCGGATAAGAGAACTTT 57.129 42.857 6.13 0.00 37.87 2.66
1829 2122 3.870633 AACTCGCGGATAAGAGAACTT 57.129 42.857 6.13 0.00 37.87 2.66
1830 2123 3.429135 GGAAACTCGCGGATAAGAGAACT 60.429 47.826 6.13 0.00 37.87 3.01
1831 2124 2.858941 GGAAACTCGCGGATAAGAGAAC 59.141 50.000 6.13 0.00 37.87 3.01
1832 2125 2.494471 TGGAAACTCGCGGATAAGAGAA 59.506 45.455 6.13 0.00 37.87 2.87
1833 2126 2.097036 TGGAAACTCGCGGATAAGAGA 58.903 47.619 6.13 0.00 37.87 3.10
1834 2127 2.579207 TGGAAACTCGCGGATAAGAG 57.421 50.000 6.13 0.00 40.16 2.85
1835 2128 3.536956 AATGGAAACTCGCGGATAAGA 57.463 42.857 6.13 0.00 0.00 2.10
1836 2129 4.616181 AAAATGGAAACTCGCGGATAAG 57.384 40.909 6.13 0.00 0.00 1.73
1859 2152 1.135068 TACCCCCGGCCTCTGAAAAA 61.135 55.000 0.00 0.00 0.00 1.94
1860 2153 0.917333 ATACCCCCGGCCTCTGAAAA 60.917 55.000 0.00 0.00 0.00 2.29
1861 2154 0.030909 TATACCCCCGGCCTCTGAAA 60.031 55.000 0.00 0.00 0.00 2.69
1862 2155 0.761702 GTATACCCCCGGCCTCTGAA 60.762 60.000 0.00 0.00 0.00 3.02
1863 2156 1.152398 GTATACCCCCGGCCTCTGA 60.152 63.158 0.00 0.00 0.00 3.27
1864 2157 2.214920 GGTATACCCCCGGCCTCTG 61.215 68.421 11.17 0.00 0.00 3.35
1865 2158 2.203466 GGTATACCCCCGGCCTCT 59.797 66.667 11.17 0.00 0.00 3.69
1866 2159 1.912264 GAGGTATACCCCCGGCCTC 60.912 68.421 18.65 6.31 38.89 4.70
1867 2160 2.203466 GAGGTATACCCCCGGCCT 59.797 66.667 18.65 0.00 36.42 5.19
1868 2161 2.926779 GGAGGTATACCCCCGGCC 60.927 72.222 18.65 8.67 36.42 6.13
1869 2162 1.131928 AATGGAGGTATACCCCCGGC 61.132 60.000 18.65 3.34 36.42 6.13
1870 2163 1.350019 GAAATGGAGGTATACCCCCGG 59.650 57.143 18.65 0.00 36.42 5.73
1871 2164 1.350019 GGAAATGGAGGTATACCCCCG 59.650 57.143 18.65 0.00 36.42 5.73
1872 2165 2.424793 TGGAAATGGAGGTATACCCCC 58.575 52.381 18.65 17.04 36.42 5.40
1873 2166 4.529716 TTTGGAAATGGAGGTATACCCC 57.470 45.455 18.65 18.25 36.42 4.95
1894 2187 9.546428 CAAACTTTATGAGGAGTTTCCATTTTT 57.454 29.630 0.00 0.00 42.47 1.94
1895 2188 7.657354 GCAAACTTTATGAGGAGTTTCCATTTT 59.343 33.333 0.00 0.00 42.47 1.82
1896 2189 7.154656 GCAAACTTTATGAGGAGTTTCCATTT 58.845 34.615 0.00 0.00 42.47 2.32
1897 2190 6.295292 GGCAAACTTTATGAGGAGTTTCCATT 60.295 38.462 0.00 0.00 42.47 3.16
1898 2191 5.185828 GGCAAACTTTATGAGGAGTTTCCAT 59.814 40.000 0.00 0.00 42.47 3.41
1899 2192 4.522789 GGCAAACTTTATGAGGAGTTTCCA 59.477 41.667 0.00 0.00 42.47 3.53
1900 2193 4.767409 AGGCAAACTTTATGAGGAGTTTCC 59.233 41.667 0.00 4.64 42.47 3.13
1901 2194 5.703876 CAGGCAAACTTTATGAGGAGTTTC 58.296 41.667 0.00 0.00 42.47 2.78
1902 2195 4.021981 GCAGGCAAACTTTATGAGGAGTTT 60.022 41.667 0.00 0.00 44.50 2.66
1903 2196 3.507622 GCAGGCAAACTTTATGAGGAGTT 59.492 43.478 0.00 0.00 37.69 3.01
1904 2197 3.084786 GCAGGCAAACTTTATGAGGAGT 58.915 45.455 0.00 0.00 0.00 3.85
1905 2198 3.350833 AGCAGGCAAACTTTATGAGGAG 58.649 45.455 0.00 0.00 0.00 3.69
1906 2199 3.439857 AGCAGGCAAACTTTATGAGGA 57.560 42.857 0.00 0.00 0.00 3.71
1907 2200 4.022068 TCAAAGCAGGCAAACTTTATGAGG 60.022 41.667 0.00 0.00 34.42 3.86
1908 2201 5.125100 TCAAAGCAGGCAAACTTTATGAG 57.875 39.130 0.00 0.00 34.42 2.90
1909 2202 5.472148 CATCAAAGCAGGCAAACTTTATGA 58.528 37.500 0.00 0.00 34.42 2.15
1910 2203 4.092383 GCATCAAAGCAGGCAAACTTTATG 59.908 41.667 0.00 5.92 34.42 1.90
1911 2204 4.248058 GCATCAAAGCAGGCAAACTTTAT 58.752 39.130 0.00 0.00 34.42 1.40
1923 2216 4.859304 AAGTGAGATTTGCATCAAAGCA 57.141 36.364 9.70 0.00 41.45 3.91
1925 2218 9.334693 GTAACTAAAGTGAGATTTGCATCAAAG 57.665 33.333 0.00 0.00 36.76 2.77
1937 2230 6.000219 AGTACAGACGGTAACTAAAGTGAGA 59.000 40.000 0.00 0.00 32.72 3.27
2202 2495 0.250467 CTAAGCACAGTGGGCACAGT 60.250 55.000 21.75 4.05 0.00 3.55
2550 2844 0.106167 TCCCTGTAGCGGTGCTCTAT 60.106 55.000 3.95 0.00 40.44 1.98
2576 2870 1.132834 CGTGCAATTATCAGCTGGCAA 59.867 47.619 15.13 8.62 32.50 4.52
2696 2990 9.926158 TGTAACATCTTATTTTGTACGGAAGTA 57.074 29.630 0.00 0.00 46.88 2.24
2697 2991 8.715088 GTGTAACATCTTATTTTGTACGGAAGT 58.285 33.333 0.00 0.00 43.06 3.01
2798 3092 6.260936 ACACATAGCTATAACACCATTTGAGC 59.739 38.462 5.77 0.00 0.00 4.26
3451 3745 3.981071 AGACAATGGAATGACGGAAGA 57.019 42.857 0.00 0.00 0.00 2.87
3469 3763 7.175104 ACTGCTGGTTGATTTTCCTTTATAGA 58.825 34.615 0.00 0.00 0.00 1.98
3668 3962 2.198827 TTGATGTACCCCAACTGCTG 57.801 50.000 0.00 0.00 0.00 4.41
3834 4128 3.814283 GGCCATTTTCTGAACAATTTGCA 59.186 39.130 0.00 0.00 0.00 4.08
3933 4227 1.654023 AAACGGAAGGCGGCATTAGC 61.654 55.000 13.08 0.00 41.10 3.09
3951 4245 0.486879 AGGGAGAAACCAATGGCCAA 59.513 50.000 10.96 0.00 41.20 4.52
4008 4302 3.002042 GTGCTGCTGACATGCTATAACTG 59.998 47.826 0.00 0.00 0.00 3.16
4009 4303 3.201290 GTGCTGCTGACATGCTATAACT 58.799 45.455 0.00 0.00 0.00 2.24
4106 4400 1.981256 TTCTGCCTTTTCACCACCTC 58.019 50.000 0.00 0.00 0.00 3.85
4224 4518 0.373716 GGAACGCTCTAAACATGCCG 59.626 55.000 0.00 0.00 0.00 5.69
4275 4569 2.434884 ATGACTCGGGCTGCGTTG 60.435 61.111 0.00 0.00 0.00 4.10
4305 4599 1.077787 AAATCGGGATTGAGCCGCA 60.078 52.632 0.00 0.00 0.00 5.69
4463 4758 0.593128 CAGGGAGAAAAACAGCACCG 59.407 55.000 0.00 0.00 0.00 4.94
4468 4763 8.197439 ACAAGAAAATTACAGGGAGAAAAACAG 58.803 33.333 0.00 0.00 0.00 3.16
4476 4771 5.586643 GGCTCTACAAGAAAATTACAGGGAG 59.413 44.000 0.00 0.00 0.00 4.30
4533 4828 2.360483 TGTACAACCAAACACATGCTGG 59.640 45.455 0.00 0.00 36.24 4.85
4599 4894 5.391736 CCATTAAGCAGAACTCTGAAAGCAG 60.392 44.000 10.95 0.00 46.59 4.24
4600 4895 4.456911 CCATTAAGCAGAACTCTGAAAGCA 59.543 41.667 10.95 0.00 46.59 3.91
4601 4896 4.673841 GCCATTAAGCAGAACTCTGAAAGC 60.674 45.833 10.95 0.00 46.59 3.51
4602 4897 4.142513 GGCCATTAAGCAGAACTCTGAAAG 60.143 45.833 10.95 0.00 46.59 2.62
4603 4898 3.758554 GGCCATTAAGCAGAACTCTGAAA 59.241 43.478 10.95 2.14 46.59 2.69
4604 4899 3.244875 TGGCCATTAAGCAGAACTCTGAA 60.245 43.478 0.00 0.00 46.59 3.02
4605 4900 2.305635 TGGCCATTAAGCAGAACTCTGA 59.694 45.455 0.00 0.00 46.59 3.27
4606 4901 2.421424 GTGGCCATTAAGCAGAACTCTG 59.579 50.000 9.72 2.17 46.40 3.35
4607 4902 2.040278 TGTGGCCATTAAGCAGAACTCT 59.960 45.455 9.72 0.00 0.00 3.24
4608 4903 2.436417 TGTGGCCATTAAGCAGAACTC 58.564 47.619 9.72 0.00 0.00 3.01
4609 4904 2.584835 TGTGGCCATTAAGCAGAACT 57.415 45.000 9.72 0.00 0.00 3.01
4610 4905 2.819608 TCTTGTGGCCATTAAGCAGAAC 59.180 45.455 21.58 2.32 0.00 3.01
4611 4906 3.153369 TCTTGTGGCCATTAAGCAGAA 57.847 42.857 21.58 7.48 0.00 3.02
4612 4907 2.819608 GTTCTTGTGGCCATTAAGCAGA 59.180 45.455 21.58 10.01 0.00 4.26
4653 4948 6.039616 TGGTTTGTGTTTCTAAATCTTGTGC 58.960 36.000 0.00 0.00 0.00 4.57
4675 4970 1.795286 GTTGAACTTCTCGTCAGCTGG 59.205 52.381 15.13 0.00 0.00 4.85
4712 5007 1.305201 TCAAGAAGCGCGGAAAAGTT 58.695 45.000 8.83 0.00 0.00 2.66
4715 5010 4.411327 CAAATATCAAGAAGCGCGGAAAA 58.589 39.130 8.83 0.00 0.00 2.29
4720 5015 2.030823 TCAGCAAATATCAAGAAGCGCG 59.969 45.455 0.00 0.00 0.00 6.86
4722 5017 3.973135 GCATCAGCAAATATCAAGAAGCG 59.027 43.478 0.00 0.00 41.58 4.68
4757 5054 6.968904 CACATACACACAAATTCCATTCTAGC 59.031 38.462 0.00 0.00 0.00 3.42
4760 5057 6.716628 ACTCACATACACACAAATTCCATTCT 59.283 34.615 0.00 0.00 0.00 2.40
4792 5107 4.285003 ACACATAGCTTACAACCACCACTA 59.715 41.667 0.00 0.00 0.00 2.74
4866 5201 1.471119 AATCAGAATGCAGGCCACAG 58.529 50.000 5.01 0.00 34.76 3.66
4953 5291 2.093921 GGGAGACTTCCTGAGCTTACAC 60.094 54.545 0.00 0.00 43.49 2.90
5110 5450 1.461127 CGTTTCAGTGGCAGAGTTAGC 59.539 52.381 0.00 0.00 0.00 3.09
5132 5472 6.292328 GCAAGCATTTTCAGGAACAAAAGTAC 60.292 38.462 0.00 0.00 0.00 2.73
5135 5475 4.812626 AGCAAGCATTTTCAGGAACAAAAG 59.187 37.500 0.00 0.00 0.00 2.27
5210 5565 2.030805 GGCAGGCTTTTTACAGACAGTG 60.031 50.000 0.00 0.00 0.00 3.66
5211 5566 2.230660 GGCAGGCTTTTTACAGACAGT 58.769 47.619 0.00 0.00 0.00 3.55
5215 5570 2.656947 AGTGGCAGGCTTTTTACAGA 57.343 45.000 0.00 0.00 0.00 3.41
5230 5585 4.013050 TGACAGTGAGAGTGATCTAGTGG 58.987 47.826 0.00 0.00 0.00 4.00
5273 5628 2.297033 GAGGCAAAAATGCAGGAGAACA 59.703 45.455 2.97 0.00 36.33 3.18
5274 5629 2.560105 AGAGGCAAAAATGCAGGAGAAC 59.440 45.455 2.97 0.00 36.33 3.01
5276 5631 2.592102 AGAGGCAAAAATGCAGGAGA 57.408 45.000 2.97 0.00 36.33 3.71
5277 5632 2.824341 AGAAGAGGCAAAAATGCAGGAG 59.176 45.455 2.97 0.00 36.33 3.69
5278 5633 2.559668 CAGAAGAGGCAAAAATGCAGGA 59.440 45.455 2.97 0.00 36.33 3.86
5279 5634 2.559668 TCAGAAGAGGCAAAAATGCAGG 59.440 45.455 2.97 0.00 36.33 4.85
5302 5657 1.916000 GGATCGACCAAACGTTACTCG 59.084 52.381 0.00 8.47 41.11 4.18
5317 5680 2.283298 CACTGAACCTCCAATGGATCG 58.717 52.381 0.87 0.00 32.39 3.69


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

AutoCloner maintained by Alex Coulton.