Multiple sequence alignment - TraesCS2D01G105000

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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 TraesCS2D01G105000 chr2D 100.000 3937 0 0 1 3937 56574634 56578570 0.000000e+00 7271.0
1 TraesCS2D01G105000 chr2D 93.023 172 9 2 2163 2332 32474472 32474302 8.450000e-62 248.0
2 TraesCS2D01G105000 chr2D 93.333 165 8 2 2168 2330 623354521 623354684 1.410000e-59 241.0
3 TraesCS2D01G105000 chr2B 87.198 2898 221 71 708 3546 89550935 89553741 0.000000e+00 3158.0
4 TraesCS2D01G105000 chr2B 94.685 715 35 1 1 712 74040246 74040960 0.000000e+00 1107.0
5 TraesCS2D01G105000 chr2B 91.968 249 9 10 3653 3895 89553899 89554142 4.870000e-89 339.0
6 TraesCS2D01G105000 chr1D 98.177 713 10 1 1 710 41584933 41585645 0.000000e+00 1242.0
7 TraesCS2D01G105000 chr3D 97.361 720 16 1 1 717 11001482 11000763 0.000000e+00 1221.0
8 TraesCS2D01G105000 chr7D 97.350 717 16 1 1 714 142647556 142648272 0.000000e+00 1216.0
9 TraesCS2D01G105000 chr7D 88.947 190 14 6 2149 2335 49173220 49173035 1.100000e-55 228.0
10 TraesCS2D01G105000 chr5D 97.075 718 16 3 1 714 483526102 483525386 0.000000e+00 1205.0
11 TraesCS2D01G105000 chr5D 93.373 166 9 1 2167 2330 6083361 6083526 1.090000e-60 244.0
12 TraesCS2D01G105000 chr4B 94.530 713 36 1 1 710 74914450 74915162 0.000000e+00 1098.0
13 TraesCS2D01G105000 chr4B 91.429 175 12 2 2161 2332 65598031 65597857 1.830000e-58 237.0
14 TraesCS2D01G105000 chr2A 84.072 1218 109 38 2351 3529 57999726 58000897 0.000000e+00 1096.0
15 TraesCS2D01G105000 chr2A 90.891 516 34 8 788 1291 57997971 57998485 0.000000e+00 680.0
16 TraesCS2D01G105000 chr2A 85.185 378 15 10 3586 3937 58001015 58001377 2.250000e-92 350.0
17 TraesCS2D01G105000 chr2A 96.364 55 1 1 712 766 57997861 57997914 5.420000e-14 89.8
18 TraesCS2D01G105000 chr2A 100.000 35 0 0 3591 3625 58000949 58000983 9.130000e-07 65.8
19 TraesCS2D01G105000 chr5B 91.954 174 11 2 2162 2333 694261157 694261329 1.410000e-59 241.0
20 TraesCS2D01G105000 chr7B 91.477 176 10 4 2166 2338 483770604 483770777 1.830000e-58 237.0
21 TraesCS2D01G105000 chr6D 88.083 193 20 2 2152 2342 266773297 266773106 3.960000e-55 226.0
22 TraesCS2D01G105000 chr6D 85.833 120 15 2 1662 1781 379322932 379323049 4.130000e-25 126.0
23 TraesCS2D01G105000 chr6D 87.500 80 8 2 1701 1780 450360924 450361001 1.510000e-14 91.6
24 TraesCS2D01G105000 chr4A 88.083 193 20 2 2152 2342 403382584 403382393 3.960000e-55 226.0
25 TraesCS2D01G105000 chr1A 88.571 70 6 2 1711 1780 489262539 489262472 2.520000e-12 84.2
26 TraesCS2D01G105000 chr1A 87.719 57 6 1 1732 1788 50222127 50222072 9.130000e-07 65.8
27 TraesCS2D01G105000 chr3A 87.143 70 7 2 1711 1780 745526424 745526357 1.170000e-10 78.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G105000 chr2D 56574634 56578570 3936 False 7271.00 7271 100.0000 1 3937 1 chr2D.!!$F1 3936
1 TraesCS2D01G105000 chr2B 89550935 89554142 3207 False 1748.50 3158 89.5830 708 3895 2 chr2B.!!$F2 3187
2 TraesCS2D01G105000 chr2B 74040246 74040960 714 False 1107.00 1107 94.6850 1 712 1 chr2B.!!$F1 711
3 TraesCS2D01G105000 chr1D 41584933 41585645 712 False 1242.00 1242 98.1770 1 710 1 chr1D.!!$F1 709
4 TraesCS2D01G105000 chr3D 11000763 11001482 719 True 1221.00 1221 97.3610 1 717 1 chr3D.!!$R1 716
5 TraesCS2D01G105000 chr7D 142647556 142648272 716 False 1216.00 1216 97.3500 1 714 1 chr7D.!!$F1 713
6 TraesCS2D01G105000 chr5D 483525386 483526102 716 True 1205.00 1205 97.0750 1 714 1 chr5D.!!$R1 713
7 TraesCS2D01G105000 chr4B 74914450 74915162 712 False 1098.00 1098 94.5300 1 710 1 chr4B.!!$F1 709
8 TraesCS2D01G105000 chr2A 57997861 58001377 3516 False 456.32 1096 91.3024 712 3937 5 chr2A.!!$F1 3225

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
212 213 0.252193 CAATGGACACCCCCACCAAT 60.252 55.0 0.00 0.00 39.34 3.16 F
1176 1223 0.111134 TACGCGTTCGATCGTATCCG 60.111 55.0 20.78 15.52 39.79 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1643 2022 0.035317 TAGAAGTGTGCCCTGTGCTG 59.965 55.0 0.00 0.00 42.00 4.41 R
3001 3451 0.251297 TGGCTGGGTTGTCATCCAAG 60.251 55.0 0.32 0.32 30.93 3.61 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
146 147 2.039084 CAGGAGGCAAAGGTAGTCTGTT 59.961 50.000 0.00 0.00 0.00 3.16
177 178 4.197750 CAGAGAGAATATGCAAACCAGCT 58.802 43.478 0.00 0.00 34.99 4.24
212 213 0.252193 CAATGGACACCCCCACCAAT 60.252 55.000 0.00 0.00 39.34 3.16
272 273 1.143684 AGAGTTTGCAAGAGCTTGGGA 59.856 47.619 11.78 0.00 42.74 4.37
296 297 3.461773 AGTCGCCCGGGATCACAG 61.462 66.667 29.31 7.45 0.00 3.66
364 372 1.004440 GTGGAAGCAGAAGCCTCGT 60.004 57.895 0.00 0.00 43.56 4.18
484 492 4.925861 GGAGCAGATCGCCCTGGC 62.926 72.222 0.00 0.00 44.04 4.85
782 790 5.335897 CGTCATTCCACCAATCTTTGACATT 60.336 40.000 0.00 0.00 33.38 2.71
792 835 5.172934 CAATCTTTGACATTGTGGAATGGG 58.827 41.667 0.00 0.00 43.00 4.00
800 843 2.119391 GTGGAATGGGTTGGGCCA 59.881 61.111 0.00 0.00 39.65 5.36
857 900 3.349304 ATGGACTGGCCCCATGCA 61.349 61.111 10.91 3.05 42.45 3.96
858 901 2.859525 GATGGACTGGCCCCATGCAA 62.860 60.000 15.95 0.00 43.96 4.08
859 902 3.070576 GGACTGGCCCCATGCAAC 61.071 66.667 0.00 0.00 43.89 4.17
901 946 2.753966 CCCATCAGAACGCGCAAGG 61.754 63.158 5.73 0.00 38.28 3.61
921 966 5.966742 AGGAGCATTTTAACAAGTCTTCC 57.033 39.130 0.00 0.00 0.00 3.46
973 1020 3.704061 CCCCGAGAAGAGAGAGAGAAAAT 59.296 47.826 0.00 0.00 0.00 1.82
1138 1185 1.372997 CTCGTCCAGGTCCGTGTTG 60.373 63.158 1.99 0.00 0.00 3.33
1147 1194 0.942252 GGTCCGTGTTGAAACTGTCC 59.058 55.000 0.00 0.00 0.00 4.02
1176 1223 0.111134 TACGCGTTCGATCGTATCCG 60.111 55.000 20.78 15.52 39.79 4.18
1205 1260 0.606673 ACTTTCGAGCCTTGCTTCCC 60.607 55.000 0.00 0.00 39.88 3.97
1230 1285 4.619140 CCGTCGCCCGATCCGTAC 62.619 72.222 0.00 0.00 39.56 3.67
1234 1289 0.524862 GTCGCCCGATCCGTACATAT 59.475 55.000 0.00 0.00 0.00 1.78
1235 1290 0.524414 TCGCCCGATCCGTACATATG 59.476 55.000 0.00 0.00 0.00 1.78
1238 1293 2.762745 GCCCGATCCGTACATATGTTT 58.237 47.619 14.77 0.00 0.00 2.83
1239 1294 2.478894 GCCCGATCCGTACATATGTTTG 59.521 50.000 14.77 6.85 0.00 2.93
1240 1295 3.064207 CCCGATCCGTACATATGTTTGG 58.936 50.000 14.77 15.66 0.00 3.28
1241 1296 3.493699 CCCGATCCGTACATATGTTTGGT 60.494 47.826 14.77 7.15 0.00 3.67
1242 1297 3.739300 CCGATCCGTACATATGTTTGGTC 59.261 47.826 14.77 13.56 0.00 4.02
1243 1298 4.500887 CCGATCCGTACATATGTTTGGTCT 60.501 45.833 14.77 8.28 0.00 3.85
1244 1299 4.680110 CGATCCGTACATATGTTTGGTCTC 59.320 45.833 14.77 14.48 0.00 3.36
1291 1346 1.452651 CCGATCTTGCCATGCCTGT 60.453 57.895 0.00 0.00 0.00 4.00
1292 1347 1.721664 CCGATCTTGCCATGCCTGTG 61.722 60.000 0.00 0.00 0.00 3.66
1293 1348 1.028330 CGATCTTGCCATGCCTGTGT 61.028 55.000 0.00 0.00 0.00 3.72
1294 1349 1.743431 CGATCTTGCCATGCCTGTGTA 60.743 52.381 0.00 0.00 0.00 2.90
1295 1350 1.672881 GATCTTGCCATGCCTGTGTAC 59.327 52.381 0.00 0.00 0.00 2.90
1306 1361 2.001812 CCTGTGTACTGTAGCTGCTG 57.998 55.000 13.43 7.14 0.00 4.41
1324 1379 3.263170 TGCTGGTTGTTTGCCTAGATCTA 59.737 43.478 1.69 1.69 0.00 1.98
1347 1402 1.078759 CGTGCTGGATCGGTCTTCAC 61.079 60.000 0.00 0.72 0.00 3.18
1369 1424 4.933064 GGCGATCCGAGCGAGGTG 62.933 72.222 10.84 0.00 35.00 4.00
1370 1425 3.889044 GCGATCCGAGCGAGGTGA 61.889 66.667 10.84 0.00 0.00 4.02
1392 1448 3.940335 TGTGATCTGGGAGGGATTATCA 58.060 45.455 0.00 0.00 0.00 2.15
1441 1813 7.168219 TGTTGTTTGGATCTAATTAGTGCTCT 58.832 34.615 12.19 0.00 0.00 4.09
1445 1817 9.330063 TGTTTGGATCTAATTAGTGCTCTATTG 57.670 33.333 12.19 0.00 0.00 1.90
1449 1821 8.807118 TGGATCTAATTAGTGCTCTATTGGTAG 58.193 37.037 12.19 0.00 0.00 3.18
1469 1841 1.202722 GGGTGGGATTGTATACGGTGG 60.203 57.143 0.00 0.00 0.00 4.61
1481 1853 0.406750 TACGGTGGAGGAGAAGACCA 59.593 55.000 0.00 0.00 0.00 4.02
1493 1865 5.189180 AGGAGAAGACCAAAGTGATTATGC 58.811 41.667 0.00 0.00 0.00 3.14
1643 2022 6.545504 TGATAGTCTTTGACAAGCAAGTTC 57.454 37.500 0.46 0.00 37.87 3.01
1663 2042 3.558674 GCACAGGGCACACTTCTAT 57.441 52.632 0.00 0.00 43.97 1.98
1687 2066 2.009774 CTCTGCCCCGAATTACTTGTG 58.990 52.381 0.00 0.00 0.00 3.33
1688 2067 1.094785 CTGCCCCGAATTACTTGTGG 58.905 55.000 0.00 0.00 0.00 4.17
1700 2111 6.038161 CGAATTACTTGTGGCAGAAATGGATA 59.962 38.462 0.00 0.00 0.00 2.59
1701 2112 6.949352 ATTACTTGTGGCAGAAATGGATAG 57.051 37.500 0.00 0.00 0.00 2.08
1702 2113 4.574674 ACTTGTGGCAGAAATGGATAGA 57.425 40.909 0.00 0.00 0.00 1.98
1703 2114 4.922206 ACTTGTGGCAGAAATGGATAGAA 58.078 39.130 0.00 0.00 0.00 2.10
1704 2115 5.324409 ACTTGTGGCAGAAATGGATAGAAA 58.676 37.500 0.00 0.00 0.00 2.52
1705 2116 5.954150 ACTTGTGGCAGAAATGGATAGAAAT 59.046 36.000 0.00 0.00 0.00 2.17
1706 2117 5.840243 TGTGGCAGAAATGGATAGAAATG 57.160 39.130 0.00 0.00 0.00 2.32
1707 2118 4.646040 TGTGGCAGAAATGGATAGAAATGG 59.354 41.667 0.00 0.00 0.00 3.16
1708 2119 4.038402 GTGGCAGAAATGGATAGAAATGGG 59.962 45.833 0.00 0.00 0.00 4.00
1709 2120 3.006217 GGCAGAAATGGATAGAAATGGGC 59.994 47.826 0.00 0.00 0.00 5.36
1729 2140 8.828688 ATGGGCGTATCTAGAACTAAAAATAC 57.171 34.615 0.00 0.00 0.00 1.89
1754 2165 5.406780 GTCTAAGATACATCCATTTCTGCGG 59.593 44.000 0.00 0.00 0.00 5.69
1769 2201 1.300697 GCGGCGAGTAATTCCGGAT 60.301 57.895 12.98 0.00 43.11 4.18
1781 2213 1.232216 TCCGGATGGAGGGAGTACC 59.768 63.158 0.00 0.00 40.17 3.34
1793 2225 1.205655 GGGAGTACCGGTTAGAACACC 59.794 57.143 15.04 13.05 36.97 4.16
1798 2230 0.683412 ACCGGTTAGAACACCTGACC 59.317 55.000 0.00 0.00 45.34 4.02
1824 2256 4.037446 GTGTAACAGAACCTGGATGCAAAA 59.963 41.667 0.00 0.00 35.51 2.44
1995 2432 2.694397 TGTGCCTAATAGCTCCTGGAT 58.306 47.619 0.00 0.00 0.00 3.41
2009 2446 2.644299 TCCTGGATGGTCTCAAACATGT 59.356 45.455 0.00 0.00 37.07 3.21
2010 2447 3.012518 CCTGGATGGTCTCAAACATGTC 58.987 50.000 0.00 0.00 0.00 3.06
2011 2448 3.559811 CCTGGATGGTCTCAAACATGTCA 60.560 47.826 0.00 0.00 0.00 3.58
2012 2449 3.678289 TGGATGGTCTCAAACATGTCAG 58.322 45.455 0.00 0.00 0.00 3.51
2013 2450 2.421424 GGATGGTCTCAAACATGTCAGC 59.579 50.000 0.00 0.00 0.00 4.26
2031 2472 5.066634 TGTCAGCGTAGATCCTCTCTAAAAG 59.933 44.000 0.00 0.00 38.20 2.27
2050 2491 6.670695 AAAAGGGCACTTCTGTTGAATATT 57.329 33.333 0.00 0.00 35.41 1.28
2080 2521 4.531332 GCGCATTCCATTATTTCTGACTC 58.469 43.478 0.30 0.00 0.00 3.36
2101 2542 7.177216 TGACTCTTATGCATGAAAATTTGGAGT 59.823 33.333 10.16 8.14 32.85 3.85
2104 2545 8.347004 TCTTATGCATGAAAATTTGGAGTACA 57.653 30.769 10.16 0.00 0.00 2.90
2147 2588 4.031765 GTGTCACTGTCATGTATGCTTACG 59.968 45.833 5.40 0.00 0.00 3.18
2182 2623 2.784682 AGTATCTACTCCCTCCGTTCCT 59.215 50.000 0.00 0.00 0.00 3.36
2185 2626 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
2188 2629 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
2196 2637 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2197 2638 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
2198 2639 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2199 2640 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2200 2641 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2201 2642 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2240 2681 9.511272 ACTACAATATACGGATGTACATAGACA 57.489 33.333 8.71 1.12 32.26 3.41
2251 2692 9.692749 CGGATGTACATAGACATATTTTAGTGT 57.307 33.333 8.71 0.00 40.18 3.55
2272 2713 7.246311 AGTGTAGATTCATTCATTTTGCTTCG 58.754 34.615 0.00 0.00 0.00 3.79
2273 2714 7.023575 GTGTAGATTCATTCATTTTGCTTCGT 58.976 34.615 0.00 0.00 0.00 3.85
2275 2716 8.892723 TGTAGATTCATTCATTTTGCTTCGTAT 58.107 29.630 0.00 0.00 0.00 3.06
2276 2717 9.162793 GTAGATTCATTCATTTTGCTTCGTATG 57.837 33.333 0.00 0.00 0.00 2.39
2277 2718 7.765307 AGATTCATTCATTTTGCTTCGTATGT 58.235 30.769 0.00 0.00 0.00 2.29
2278 2719 8.892723 AGATTCATTCATTTTGCTTCGTATGTA 58.107 29.630 0.00 0.00 0.00 2.29
2279 2720 9.162793 GATTCATTCATTTTGCTTCGTATGTAG 57.837 33.333 0.00 0.00 0.00 2.74
2280 2721 7.609760 TCATTCATTTTGCTTCGTATGTAGT 57.390 32.000 0.00 0.00 0.00 2.73
2281 2722 7.684670 TCATTCATTTTGCTTCGTATGTAGTC 58.315 34.615 0.00 0.00 0.00 2.59
2282 2723 7.333174 TCATTCATTTTGCTTCGTATGTAGTCA 59.667 33.333 0.00 0.00 0.00 3.41
2283 2724 7.609760 TTCATTTTGCTTCGTATGTAGTCAT 57.390 32.000 0.00 0.00 38.00 3.06
2284 2725 7.609760 TCATTTTGCTTCGTATGTAGTCATT 57.390 32.000 0.00 0.00 35.70 2.57
2285 2726 8.039603 TCATTTTGCTTCGTATGTAGTCATTT 57.960 30.769 0.00 0.00 35.70 2.32
2286 2727 7.962373 TCATTTTGCTTCGTATGTAGTCATTTG 59.038 33.333 0.00 0.00 35.70 2.32
2287 2728 6.795098 TTTGCTTCGTATGTAGTCATTTGT 57.205 33.333 0.00 0.00 35.70 2.83
2288 2729 6.795098 TTGCTTCGTATGTAGTCATTTGTT 57.205 33.333 0.00 0.00 35.70 2.83
2289 2730 6.164408 TGCTTCGTATGTAGTCATTTGTTG 57.836 37.500 0.00 0.00 35.70 3.33
2290 2731 5.929415 TGCTTCGTATGTAGTCATTTGTTGA 59.071 36.000 0.00 0.00 35.70 3.18
2291 2732 6.425417 TGCTTCGTATGTAGTCATTTGTTGAA 59.575 34.615 0.00 0.00 35.70 2.69
2292 2733 7.041712 TGCTTCGTATGTAGTCATTTGTTGAAA 60.042 33.333 0.00 0.00 35.70 2.69
2293 2734 7.962918 GCTTCGTATGTAGTCATTTGTTGAAAT 59.037 33.333 0.00 0.00 35.70 2.17
2294 2735 9.478019 CTTCGTATGTAGTCATTTGTTGAAATC 57.522 33.333 0.00 0.00 35.70 2.17
2295 2736 8.771920 TCGTATGTAGTCATTTGTTGAAATCT 57.228 30.769 0.00 0.00 35.70 2.40
2296 2737 9.214957 TCGTATGTAGTCATTTGTTGAAATCTT 57.785 29.630 0.00 0.00 35.70 2.40
2297 2738 9.825972 CGTATGTAGTCATTTGTTGAAATCTTT 57.174 29.630 0.00 0.00 35.70 2.52
2323 2764 7.947282 AGAAAGACAAATATTTGGAAACGGAA 58.053 30.769 27.43 0.00 42.34 4.30
2336 2777 2.745515 AACGGAAGGAGTAGTTCTGC 57.254 50.000 0.00 0.00 34.15 4.26
2341 2782 3.526534 GGAAGGAGTAGTTCTGCACATC 58.473 50.000 0.00 0.00 36.95 3.06
2433 2874 1.900486 ACTGGTACCTACTGCCTTGTC 59.100 52.381 14.36 0.00 0.00 3.18
2437 2878 2.420129 GGTACCTACTGCCTTGTCATGG 60.420 54.545 4.06 0.22 0.00 3.66
2460 2902 7.136885 TGGGATGGACTTTATTTCCTCTACTA 58.863 38.462 0.00 0.00 33.84 1.82
2462 2904 8.315482 GGGATGGACTTTATTTCCTCTACTATC 58.685 40.741 0.00 0.00 33.84 2.08
2493 2936 2.875094 AGGATCCATTCTGCCATAGC 57.125 50.000 15.82 0.00 40.48 2.97
2541 2984 3.828875 ATGACTTGGCCTAGCTACTTC 57.171 47.619 14.60 4.55 0.00 3.01
2550 2993 3.243907 GGCCTAGCTACTTCACATAGTGG 60.244 52.174 0.00 0.00 33.87 4.00
2553 2996 2.187958 AGCTACTTCACATAGTGGGCA 58.812 47.619 0.00 0.00 33.87 5.36
2556 2999 1.826385 ACTTCACATAGTGGGCAAGC 58.174 50.000 0.00 0.00 33.87 4.01
2559 3002 0.698238 TCACATAGTGGGCAAGCCTT 59.302 50.000 11.40 0.10 33.87 4.35
2623 3066 2.225019 GTGATGTCTGGTCTTTGCTGTG 59.775 50.000 0.00 0.00 0.00 3.66
2630 3073 0.385390 GGTCTTTGCTGTGTTGGTGG 59.615 55.000 0.00 0.00 0.00 4.61
2651 3095 6.981722 GTGGAACCTGAAACTAAAATCATGT 58.018 36.000 0.00 0.00 0.00 3.21
2707 3151 8.456471 GTGTTAACTCTATTTAACCCATTCCAC 58.544 37.037 7.22 0.00 40.03 4.02
2733 3177 6.006449 AGTTGCTTGATCAATTCCAAGTACT 58.994 36.000 8.96 5.09 41.21 2.73
2743 3190 6.711277 TCAATTCCAAGTACTGTATCTTGCT 58.289 36.000 17.31 7.67 39.47 3.91
2745 3192 8.318412 TCAATTCCAAGTACTGTATCTTGCTTA 58.682 33.333 17.31 9.69 39.47 3.09
2816 3266 5.814188 TCTCTGAATTTTCCTGTCATGATCG 59.186 40.000 0.00 0.00 0.00 3.69
2859 3309 6.471233 TTCTCGGTCTACATGATTCTGAAT 57.529 37.500 1.81 1.81 0.00 2.57
2942 3392 4.509756 CCAGAGGCATGAGTGTCG 57.490 61.111 0.00 0.00 34.36 4.35
2944 3394 0.459237 CCAGAGGCATGAGTGTCGTC 60.459 60.000 0.00 0.00 34.36 4.20
2946 3396 0.613292 AGAGGCATGAGTGTCGTCCT 60.613 55.000 0.00 0.00 34.36 3.85
2950 3400 1.448540 CATGAGTGTCGTCCTGGGC 60.449 63.158 0.00 0.00 0.00 5.36
2951 3401 1.913262 ATGAGTGTCGTCCTGGGCA 60.913 57.895 0.00 0.00 0.00 5.36
2952 3402 1.267574 ATGAGTGTCGTCCTGGGCAT 61.268 55.000 0.00 0.00 0.00 4.40
2953 3403 1.448540 GAGTGTCGTCCTGGGCATG 60.449 63.158 0.00 0.00 0.00 4.06
2954 3404 2.436646 GTGTCGTCCTGGGCATGG 60.437 66.667 0.00 0.00 0.00 3.66
2955 3405 2.606213 TGTCGTCCTGGGCATGGA 60.606 61.111 0.00 0.00 0.00 3.41
3214 3665 2.951642 TCACCAAAGAGTGAGCTTTTGG 59.048 45.455 20.45 20.45 41.78 3.28
3246 3710 1.135517 GCGTGGTGTTTTGTGTTCAGT 60.136 47.619 0.00 0.00 0.00 3.41
3261 3725 4.024556 GTGTTCAGTCTGGTGTCATTTCTG 60.025 45.833 0.00 0.00 0.00 3.02
3282 3746 1.280206 AACTAACTCACCGCGAACGC 61.280 55.000 8.23 9.20 38.22 4.84
3313 3800 5.786121 TGAGATTCCCTTCCAAGATTCTT 57.214 39.130 0.00 0.00 0.00 2.52
3341 3829 7.962964 AACTCGAGATTGAAATCACTTGTAA 57.037 32.000 21.68 0.00 37.89 2.41
3342 3830 7.588143 ACTCGAGATTGAAATCACTTGTAAG 57.412 36.000 21.68 0.00 37.89 2.34
3347 3835 7.543868 CGAGATTGAAATCACTTGTAAGACTCT 59.456 37.037 5.86 0.00 37.89 3.24
3348 3836 8.545229 AGATTGAAATCACTTGTAAGACTCTG 57.455 34.615 5.86 0.00 37.89 3.35
3349 3837 8.370940 AGATTGAAATCACTTGTAAGACTCTGA 58.629 33.333 5.86 0.00 37.89 3.27
3350 3838 7.715265 TTGAAATCACTTGTAAGACTCTGAC 57.285 36.000 0.00 0.00 0.00 3.51
3356 3847 8.682936 ATCACTTGTAAGACTCTGACAAAATT 57.317 30.769 9.85 0.00 32.94 1.82
3358 3849 9.778741 TCACTTGTAAGACTCTGACAAAATTAT 57.221 29.630 9.85 0.00 32.94 1.28
3367 3858 7.870954 AGACTCTGACAAAATTATGACGTGTTA 59.129 33.333 0.00 0.00 0.00 2.41
3369 3860 8.443160 ACTCTGACAAAATTATGACGTGTTATG 58.557 33.333 0.00 0.00 0.00 1.90
3374 3865 5.499139 AAATTATGACGTGTTATGCCCTG 57.501 39.130 0.00 0.00 0.00 4.45
3379 3870 3.215151 TGACGTGTTATGCCCTGAAAAA 58.785 40.909 0.00 0.00 0.00 1.94
3395 3888 7.275183 CCCTGAAAAAGAAAAAGGTTGAGAAT 58.725 34.615 0.00 0.00 0.00 2.40
3402 3895 5.776744 AGAAAAAGGTTGAGAATGATGTGC 58.223 37.500 0.00 0.00 0.00 4.57
3403 3896 5.537674 AGAAAAAGGTTGAGAATGATGTGCT 59.462 36.000 0.00 0.00 0.00 4.40
3409 3902 4.479619 GTTGAGAATGATGTGCTCCAAAC 58.520 43.478 0.00 0.00 0.00 2.93
3410 3903 3.753815 TGAGAATGATGTGCTCCAAACA 58.246 40.909 0.00 0.00 0.00 2.83
3411 3904 3.503363 TGAGAATGATGTGCTCCAAACAC 59.497 43.478 0.00 0.00 38.55 3.32
3413 3906 4.147321 AGAATGATGTGCTCCAAACACTT 58.853 39.130 0.00 0.00 38.86 3.16
3415 3908 2.653726 TGATGTGCTCCAAACACTTGT 58.346 42.857 0.00 0.00 38.86 3.16
3416 3909 2.618241 TGATGTGCTCCAAACACTTGTC 59.382 45.455 0.00 0.00 38.86 3.18
3417 3910 2.121291 TGTGCTCCAAACACTTGTCA 57.879 45.000 0.00 0.00 38.86 3.58
3429 3931 3.735237 CACTTGTCAGTGGTAGTCTGT 57.265 47.619 0.00 0.00 46.10 3.41
3436 3938 4.519350 TGTCAGTGGTAGTCTGTACTCTTG 59.481 45.833 0.00 0.00 37.15 3.02
3437 3939 4.079970 TCAGTGGTAGTCTGTACTCTTGG 58.920 47.826 0.00 0.00 37.15 3.61
3448 3950 2.173782 TGTACTCTTGGGCCAGAAAACA 59.826 45.455 6.23 10.33 0.00 2.83
3451 3953 1.172180 TCTTGGGCCAGAAAACAGCG 61.172 55.000 6.23 0.00 0.00 5.18
3529 4034 9.378551 GAACCATATTTGTTGTGTAGAGTCATA 57.621 33.333 0.00 0.00 0.00 2.15
3530 4035 9.733556 AACCATATTTGTTGTGTAGAGTCATAA 57.266 29.630 0.00 0.00 0.00 1.90
3531 4036 9.905713 ACCATATTTGTTGTGTAGAGTCATAAT 57.094 29.630 0.00 0.00 0.00 1.28
3547 4052 9.213777 AGAGTCATAATAATCCTAACAACTCCA 57.786 33.333 0.00 0.00 31.94 3.86
3550 4055 8.211629 GTCATAATAATCCTAACAACTCCACCT 58.788 37.037 0.00 0.00 0.00 4.00
3552 4057 6.636454 AATAATCCTAACAACTCCACCTCA 57.364 37.500 0.00 0.00 0.00 3.86
3559 4064 0.105964 CAACTCCACCTCACCACGAA 59.894 55.000 0.00 0.00 0.00 3.85
3560 4065 0.106149 AACTCCACCTCACCACGAAC 59.894 55.000 0.00 0.00 0.00 3.95
3562 4067 0.105964 CTCCACCTCACCACGAACAA 59.894 55.000 0.00 0.00 0.00 2.83
3564 4069 0.884704 CCACCTCACCACGAACAAGG 60.885 60.000 0.00 0.00 0.00 3.61
3582 4143 1.604147 GGAAAAATCCACCTGCCCGG 61.604 60.000 0.00 0.00 39.35 5.73
3658 4268 2.562912 CGGAAGCCACACATGCAC 59.437 61.111 0.00 0.00 0.00 4.57
3659 4269 2.562912 GGAAGCCACACATGCACG 59.437 61.111 0.00 0.00 0.00 5.34
3776 4391 2.024022 CACGGCCACAAACACACG 59.976 61.111 2.24 0.00 0.00 4.49
3858 4473 4.806339 CTCGCCCTCCCCCTTCCT 62.806 72.222 0.00 0.00 0.00 3.36
3859 4474 4.798682 TCGCCCTCCCCCTTCCTC 62.799 72.222 0.00 0.00 0.00 3.71
3860 4475 4.806339 CGCCCTCCCCCTTCCTCT 62.806 72.222 0.00 0.00 0.00 3.69
3861 4476 2.770475 GCCCTCCCCCTTCCTCTC 60.770 72.222 0.00 0.00 0.00 3.20
3862 4477 3.124088 CCCTCCCCCTTCCTCTCT 58.876 66.667 0.00 0.00 0.00 3.10
3863 4478 1.074850 CCCTCCCCCTTCCTCTCTC 60.075 68.421 0.00 0.00 0.00 3.20
3864 4479 1.706575 CCTCCCCCTTCCTCTCTCA 59.293 63.158 0.00 0.00 0.00 3.27
3865 4480 0.689412 CCTCCCCCTTCCTCTCTCAC 60.689 65.000 0.00 0.00 0.00 3.51
3866 4481 0.041833 CTCCCCCTTCCTCTCTCACA 59.958 60.000 0.00 0.00 0.00 3.58
3867 4482 0.719015 TCCCCCTTCCTCTCTCACAT 59.281 55.000 0.00 0.00 0.00 3.21
3868 4483 1.127343 CCCCCTTCCTCTCTCACATC 58.873 60.000 0.00 0.00 0.00 3.06
3869 4484 1.343884 CCCCCTTCCTCTCTCACATCT 60.344 57.143 0.00 0.00 0.00 2.90
3870 4485 2.038659 CCCCTTCCTCTCTCACATCTC 58.961 57.143 0.00 0.00 0.00 2.75
3871 4486 2.359143 CCCCTTCCTCTCTCACATCTCT 60.359 54.545 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 147 6.655078 TGCATATTCTCTCTGCATACACTA 57.345 37.500 0.00 0.00 40.75 2.74
177 178 2.692557 CCATTGGTTTGTTCCAGACACA 59.307 45.455 0.00 0.00 38.18 3.72
364 372 5.452341 TCATCTAGACCCAGTAGAACAGA 57.548 43.478 0.00 0.00 30.33 3.41
484 492 7.262772 TCCTTTATGTCTGTTATTACTCCACG 58.737 38.462 0.00 0.00 0.00 4.94
782 790 2.104359 ATGGCCCAACCCATTCCACA 62.104 55.000 0.00 0.00 42.92 4.17
857 900 4.982241 TTCAGAGACAAGGAAGGATGTT 57.018 40.909 0.00 0.00 0.00 2.71
858 901 5.130145 CCTATTCAGAGACAAGGAAGGATGT 59.870 44.000 0.00 0.00 0.00 3.06
859 902 5.609423 CCTATTCAGAGACAAGGAAGGATG 58.391 45.833 0.00 0.00 0.00 3.51
901 946 4.767409 AGGGGAAGACTTGTTAAAATGCTC 59.233 41.667 0.00 0.00 0.00 4.26
921 966 0.034089 AAATTGGGCGAGAGGAAGGG 60.034 55.000 0.00 0.00 0.00 3.95
1138 1185 4.724036 GCGTAATCGTGAATGGACAGTTTC 60.724 45.833 0.00 0.00 39.49 2.78
1191 1246 2.124942 GAGGGGAAGCAAGGCTCG 60.125 66.667 0.00 0.00 38.25 5.03
1220 1275 3.724374 ACCAAACATATGTACGGATCGG 58.276 45.455 23.63 12.85 0.00 4.18
1230 1285 3.861840 ACACCGAGAGACCAAACATATG 58.138 45.455 0.00 0.00 0.00 1.78
1234 1289 2.036733 CCTAACACCGAGAGACCAAACA 59.963 50.000 0.00 0.00 0.00 2.83
1235 1290 2.612221 CCCTAACACCGAGAGACCAAAC 60.612 54.545 0.00 0.00 0.00 2.93
1238 1293 0.113776 ACCCTAACACCGAGAGACCA 59.886 55.000 0.00 0.00 0.00 4.02
1239 1294 1.264295 AACCCTAACACCGAGAGACC 58.736 55.000 0.00 0.00 0.00 3.85
1240 1295 2.612221 CCAAACCCTAACACCGAGAGAC 60.612 54.545 0.00 0.00 0.00 3.36
1241 1296 1.621814 CCAAACCCTAACACCGAGAGA 59.378 52.381 0.00 0.00 0.00 3.10
1242 1297 1.346722 ACCAAACCCTAACACCGAGAG 59.653 52.381 0.00 0.00 0.00 3.20
1243 1298 1.426751 ACCAAACCCTAACACCGAGA 58.573 50.000 0.00 0.00 0.00 4.04
1244 1299 2.265589 AACCAAACCCTAACACCGAG 57.734 50.000 0.00 0.00 0.00 4.63
1291 1346 1.691976 ACAACCAGCAGCTACAGTACA 59.308 47.619 0.00 0.00 0.00 2.90
1292 1347 2.457366 ACAACCAGCAGCTACAGTAC 57.543 50.000 0.00 0.00 0.00 2.73
1293 1348 3.138304 CAAACAACCAGCAGCTACAGTA 58.862 45.455 0.00 0.00 0.00 2.74
1294 1349 1.949525 CAAACAACCAGCAGCTACAGT 59.050 47.619 0.00 0.00 0.00 3.55
1295 1350 1.335324 GCAAACAACCAGCAGCTACAG 60.335 52.381 0.00 0.00 0.00 2.74
1306 1361 3.195661 CCGTAGATCTAGGCAAACAACC 58.804 50.000 15.55 0.00 0.00 3.77
1364 1419 1.415659 CCTCCCAGATCACATCACCTC 59.584 57.143 0.00 0.00 0.00 3.85
1365 1420 1.504912 CCTCCCAGATCACATCACCT 58.495 55.000 0.00 0.00 0.00 4.00
1366 1421 0.471617 CCCTCCCAGATCACATCACC 59.528 60.000 0.00 0.00 0.00 4.02
1368 1423 2.502068 ATCCCTCCCAGATCACATCA 57.498 50.000 0.00 0.00 0.00 3.07
1369 1424 4.533707 TGATAATCCCTCCCAGATCACATC 59.466 45.833 0.00 0.00 0.00 3.06
1370 1425 4.506354 TGATAATCCCTCCCAGATCACAT 58.494 43.478 0.00 0.00 0.00 3.21
1392 1448 7.281549 ACAAGTTTGACCACGTAATAAACTTCT 59.718 33.333 20.02 11.99 44.88 2.85
1441 1813 5.246656 CGTATACAATCCCACCCTACCAATA 59.753 44.000 3.32 0.00 0.00 1.90
1445 1817 2.301009 CCGTATACAATCCCACCCTACC 59.699 54.545 3.32 0.00 0.00 3.18
1449 1821 1.202722 CCACCGTATACAATCCCACCC 60.203 57.143 3.32 0.00 0.00 4.61
1469 1841 5.295540 GCATAATCACTTTGGTCTTCTCCTC 59.704 44.000 0.00 0.00 0.00 3.71
1481 1853 3.443329 TGTTGCCATCGCATAATCACTTT 59.557 39.130 0.00 0.00 46.67 2.66
1593 1972 5.417754 AGCATGATGTAGATAGGACCATG 57.582 43.478 0.00 0.00 34.66 3.66
1627 2006 3.111098 GTGCTGAACTTGCTTGTCAAAG 58.889 45.455 0.00 0.00 33.65 2.77
1643 2022 0.035317 TAGAAGTGTGCCCTGTGCTG 59.965 55.000 0.00 0.00 42.00 4.41
1663 2042 0.544697 GTAATTCGGGGCAGAGGGAA 59.455 55.000 0.00 0.00 0.00 3.97
1687 2066 3.006217 GCCCATTTCTATCCATTTCTGCC 59.994 47.826 0.00 0.00 0.00 4.85
1688 2067 3.304928 CGCCCATTTCTATCCATTTCTGC 60.305 47.826 0.00 0.00 0.00 4.26
1700 2111 6.726490 TTAGTTCTAGATACGCCCATTTCT 57.274 37.500 0.00 0.00 0.00 2.52
1701 2112 7.781548 TTTTAGTTCTAGATACGCCCATTTC 57.218 36.000 0.00 0.00 0.00 2.17
1702 2113 8.747538 ATTTTTAGTTCTAGATACGCCCATTT 57.252 30.769 0.00 0.00 0.00 2.32
1703 2114 9.269453 GTATTTTTAGTTCTAGATACGCCCATT 57.731 33.333 0.00 0.00 0.00 3.16
1704 2115 7.597743 CGTATTTTTAGTTCTAGATACGCCCAT 59.402 37.037 5.60 0.00 36.89 4.00
1705 2116 6.919662 CGTATTTTTAGTTCTAGATACGCCCA 59.080 38.462 5.60 0.00 36.89 5.36
1706 2117 6.920210 ACGTATTTTTAGTTCTAGATACGCCC 59.080 38.462 14.84 0.00 43.43 6.13
1707 2118 7.859875 AGACGTATTTTTAGTTCTAGATACGCC 59.140 37.037 14.84 7.15 43.43 5.68
1708 2119 8.779603 AGACGTATTTTTAGTTCTAGATACGC 57.220 34.615 14.84 9.72 43.43 4.42
1729 2140 5.117745 CGCAGAAATGGATGTATCTTAGACG 59.882 44.000 0.00 0.00 0.00 4.18
1736 2147 1.195448 CGCCGCAGAAATGGATGTATC 59.805 52.381 0.00 0.00 0.00 2.24
1754 2165 1.605712 CCTCCATCCGGAATTACTCGC 60.606 57.143 9.01 0.00 42.21 5.03
1769 2201 1.002069 TCTAACCGGTACTCCCTCCA 58.998 55.000 8.00 0.00 0.00 3.86
1781 2213 0.682852 TGGGTCAGGTGTTCTAACCG 59.317 55.000 0.00 0.00 45.53 4.44
1793 2225 2.368875 AGGTTCTGTTACACTGGGTCAG 59.631 50.000 0.00 0.00 37.52 3.51
1824 2256 9.719279 CAAAATGTTGCAAAACTGAAATTGTAT 57.281 25.926 0.00 0.00 0.00 2.29
1864 2299 6.695713 GTCACCAAGATTGAACAACTAAAACC 59.304 38.462 0.00 0.00 0.00 3.27
1871 2306 5.437289 TCATGTCACCAAGATTGAACAAC 57.563 39.130 0.00 0.00 0.00 3.32
1938 2373 4.773323 ATGTGAAGCTAAAGGCAAAGAC 57.227 40.909 0.00 0.00 44.79 3.01
1995 2432 1.202639 ACGCTGACATGTTTGAGACCA 60.203 47.619 0.00 0.00 0.00 4.02
2050 2491 4.734398 ATAATGGAATGCGCCAGAAAAA 57.266 36.364 4.18 0.00 42.15 1.94
2061 2502 8.843262 TGCATAAGAGTCAGAAATAATGGAATG 58.157 33.333 0.00 0.00 0.00 2.67
2120 2561 5.982356 AGCATACATGACAGTGACACTATT 58.018 37.500 8.02 0.00 0.00 1.73
2122 2563 5.405935 AAGCATACATGACAGTGACACTA 57.594 39.130 8.02 0.00 0.00 2.74
2123 2564 3.969287 AGCATACATGACAGTGACACT 57.031 42.857 1.07 1.07 0.00 3.55
2124 2565 4.031765 CGTAAGCATACATGACAGTGACAC 59.968 45.833 0.00 0.00 32.02 3.67
2125 2566 4.173256 CGTAAGCATACATGACAGTGACA 58.827 43.478 0.00 0.00 32.02 3.58
2126 2567 4.761910 CGTAAGCATACATGACAGTGAC 57.238 45.455 0.00 0.00 32.02 3.67
2147 2588 7.309920 GGAGTAGATACTAAGTTCATAGCAGC 58.690 42.308 0.00 0.00 36.50 5.25
2214 2655 9.511272 TGTCTATGTACATCCGTATATTGTAGT 57.489 33.333 12.68 0.00 32.34 2.73
2251 2692 8.892723 ACATACGAAGCAAAATGAATGAATCTA 58.107 29.630 0.00 0.00 0.00 1.98
2252 2693 7.765307 ACATACGAAGCAAAATGAATGAATCT 58.235 30.769 0.00 0.00 0.00 2.40
2253 2694 7.975866 ACATACGAAGCAAAATGAATGAATC 57.024 32.000 0.00 0.00 0.00 2.52
2254 2695 8.677300 ACTACATACGAAGCAAAATGAATGAAT 58.323 29.630 0.00 0.00 0.00 2.57
2255 2696 8.039603 ACTACATACGAAGCAAAATGAATGAA 57.960 30.769 0.00 0.00 0.00 2.57
2257 2698 7.463544 TGACTACATACGAAGCAAAATGAATG 58.536 34.615 0.00 0.00 0.00 2.67
2258 2699 7.609760 TGACTACATACGAAGCAAAATGAAT 57.390 32.000 0.00 0.00 0.00 2.57
2259 2700 7.609760 ATGACTACATACGAAGCAAAATGAA 57.390 32.000 0.00 0.00 34.71 2.57
2262 2703 7.816640 ACAAATGACTACATACGAAGCAAAAT 58.183 30.769 0.00 0.00 35.50 1.82
2263 2704 7.197071 ACAAATGACTACATACGAAGCAAAA 57.803 32.000 0.00 0.00 35.50 2.44
2265 2706 6.425417 TCAACAAATGACTACATACGAAGCAA 59.575 34.615 0.00 0.00 35.50 3.91
2267 2708 6.403333 TCAACAAATGACTACATACGAAGC 57.597 37.500 0.00 0.00 35.50 3.86
2268 2709 9.478019 GATTTCAACAAATGACTACATACGAAG 57.522 33.333 0.00 0.00 37.92 3.79
2269 2710 9.214957 AGATTTCAACAAATGACTACATACGAA 57.785 29.630 0.00 0.00 37.92 3.85
2270 2711 8.771920 AGATTTCAACAAATGACTACATACGA 57.228 30.769 0.00 0.00 37.92 3.43
2271 2712 9.825972 AAAGATTTCAACAAATGACTACATACG 57.174 29.630 0.00 0.00 37.92 3.06
2295 2736 9.685828 CCGTTTCCAAATATTTGTCTTTCTAAA 57.314 29.630 23.24 10.85 36.45 1.85
2296 2737 9.069082 TCCGTTTCCAAATATTTGTCTTTCTAA 57.931 29.630 23.24 6.95 36.45 2.10
2297 2738 8.624367 TCCGTTTCCAAATATTTGTCTTTCTA 57.376 30.769 23.24 5.03 36.45 2.10
2298 2739 7.519032 TCCGTTTCCAAATATTTGTCTTTCT 57.481 32.000 23.24 0.00 36.45 2.52
2299 2740 7.328493 CCTTCCGTTTCCAAATATTTGTCTTTC 59.672 37.037 23.24 10.84 36.45 2.62
2300 2741 7.014808 TCCTTCCGTTTCCAAATATTTGTCTTT 59.985 33.333 23.24 0.00 36.45 2.52
2308 2749 6.309389 ACTACTCCTTCCGTTTCCAAATAT 57.691 37.500 0.00 0.00 0.00 1.28
2311 2752 4.102054 AGAACTACTCCTTCCGTTTCCAAA 59.898 41.667 0.00 0.00 0.00 3.28
2314 2755 3.586892 CAGAACTACTCCTTCCGTTTCC 58.413 50.000 0.00 0.00 0.00 3.13
2316 2757 2.367567 TGCAGAACTACTCCTTCCGTTT 59.632 45.455 0.00 0.00 0.00 3.60
2323 2764 2.499289 CAGGATGTGCAGAACTACTCCT 59.501 50.000 0.00 0.00 34.92 3.69
2341 2782 4.945543 AGCCCGTAAAACCTAATAAACAGG 59.054 41.667 0.00 0.00 39.25 4.00
2433 2874 5.699143 AGAGGAAATAAAGTCCATCCCATG 58.301 41.667 0.00 0.00 37.65 3.66
2437 2878 8.871125 TGATAGTAGAGGAAATAAAGTCCATCC 58.129 37.037 0.00 0.00 37.65 3.51
2460 2902 8.910944 CAGAATGGATCCTTAGATTTTGTTGAT 58.089 33.333 14.23 0.00 30.90 2.57
2462 2904 6.976925 GCAGAATGGATCCTTAGATTTTGTTG 59.023 38.462 14.23 3.85 35.86 3.33
2464 2906 5.595952 GGCAGAATGGATCCTTAGATTTTGT 59.404 40.000 14.23 0.00 35.86 2.83
2493 2936 2.821378 TGCCTCAATCACTGAATGTTGG 59.179 45.455 0.00 0.70 32.17 3.77
2541 2984 1.098050 GAAGGCTTGCCCACTATGTG 58.902 55.000 3.46 0.00 35.39 3.21
2550 2993 1.676967 CCAGACAGGAAGGCTTGCC 60.677 63.158 15.60 10.94 41.22 4.52
2553 2996 1.729586 TGTACCAGACAGGAAGGCTT 58.270 50.000 0.00 0.00 41.22 4.35
2556 2999 5.770162 AGAATTTTTGTACCAGACAGGAAGG 59.230 40.000 0.00 0.00 39.88 3.46
2559 3002 5.768164 GGAAGAATTTTTGTACCAGACAGGA 59.232 40.000 0.00 0.00 39.88 3.86
2623 3066 5.585820 TTTTAGTTTCAGGTTCCACCAAC 57.414 39.130 0.00 0.00 41.95 3.77
2630 3073 9.185192 CTTCAACATGATTTTAGTTTCAGGTTC 57.815 33.333 0.00 0.00 42.87 3.62
2637 3081 9.865321 CATGGATCTTCAACATGATTTTAGTTT 57.135 29.630 0.00 0.00 43.46 2.66
2651 3095 1.355381 AGGCACACCATGGATCTTCAA 59.645 47.619 21.47 0.00 39.06 2.69
2707 3151 6.506500 ACTTGGAATTGATCAAGCAACTAG 57.493 37.500 14.54 11.71 42.82 2.57
2733 3177 7.014230 GGAGGGCAAATAAATAAGCAAGATACA 59.986 37.037 0.00 0.00 0.00 2.29
2743 3190 6.951198 TGACTTTGAGGAGGGCAAATAAATAA 59.049 34.615 0.00 0.00 35.00 1.40
2745 3192 5.332743 TGACTTTGAGGAGGGCAAATAAAT 58.667 37.500 0.00 0.00 35.00 1.40
2805 3255 2.475200 TAGTGCGACGATCATGACAG 57.525 50.000 0.00 0.00 0.00 3.51
2816 3266 6.452611 CGAGAAACTGAAACTAATAGTGCGAC 60.453 42.308 0.00 0.00 0.00 5.19
2859 3309 6.165577 GCTGCAAAGGAAAATCAAAAGGATA 58.834 36.000 0.00 0.00 34.28 2.59
2950 3400 0.314935 AAAAGTTGCAGCCGTCCATG 59.685 50.000 0.00 0.00 0.00 3.66
2951 3401 0.314935 CAAAAGTTGCAGCCGTCCAT 59.685 50.000 0.00 0.00 0.00 3.41
2952 3402 0.749818 TCAAAAGTTGCAGCCGTCCA 60.750 50.000 0.00 0.00 0.00 4.02
2953 3403 0.598065 ATCAAAAGTTGCAGCCGTCC 59.402 50.000 0.00 0.00 0.00 4.79
2954 3404 1.689959 CATCAAAAGTTGCAGCCGTC 58.310 50.000 0.00 0.00 0.00 4.79
2955 3405 0.318955 GCATCAAAAGTTGCAGCCGT 60.319 50.000 0.00 0.00 38.72 5.68
2956 3406 1.339235 CGCATCAAAAGTTGCAGCCG 61.339 55.000 0.00 0.00 38.80 5.52
2957 3407 0.318955 ACGCATCAAAAGTTGCAGCC 60.319 50.000 0.00 0.00 38.80 4.85
2958 3408 1.978782 GTACGCATCAAAAGTTGCAGC 59.021 47.619 0.00 0.00 38.80 5.25
2959 3409 3.266541 TGTACGCATCAAAAGTTGCAG 57.733 42.857 0.00 0.00 38.80 4.41
3001 3451 0.251297 TGGCTGGGTTGTCATCCAAG 60.251 55.000 0.32 0.32 30.93 3.61
3246 3710 5.071788 AGTTAGTTCCAGAAATGACACCAGA 59.928 40.000 5.70 0.00 29.09 3.86
3261 3725 1.066136 GTTCGCGGTGAGTTAGTTCC 58.934 55.000 6.13 0.00 0.00 3.62
3282 3746 2.449137 AGGGAATCTCATGGGCTTTG 57.551 50.000 0.00 0.00 0.00 2.77
3313 3800 7.872993 ACAAGTGATTTCAATCTCGAGTTTCTA 59.127 33.333 13.13 0.00 36.39 2.10
3341 3829 6.223852 ACACGTCATAATTTTGTCAGAGTCT 58.776 36.000 0.00 0.00 0.00 3.24
3342 3830 6.467723 ACACGTCATAATTTTGTCAGAGTC 57.532 37.500 0.00 0.00 0.00 3.36
3347 3835 6.318628 GGCATAACACGTCATAATTTTGTCA 58.681 36.000 0.00 0.00 0.00 3.58
3348 3836 5.741982 GGGCATAACACGTCATAATTTTGTC 59.258 40.000 0.00 0.00 0.00 3.18
3349 3837 5.417580 AGGGCATAACACGTCATAATTTTGT 59.582 36.000 0.00 0.00 0.00 2.83
3350 3838 5.743398 CAGGGCATAACACGTCATAATTTTG 59.257 40.000 0.00 0.00 0.00 2.44
3356 3847 3.897141 TTCAGGGCATAACACGTCATA 57.103 42.857 0.00 0.00 0.00 2.15
3358 3849 2.552599 TTTCAGGGCATAACACGTCA 57.447 45.000 0.00 0.00 0.00 4.35
3367 3858 5.104569 TCAACCTTTTTCTTTTTCAGGGCAT 60.105 36.000 0.00 0.00 0.00 4.40
3369 3860 4.765273 TCAACCTTTTTCTTTTTCAGGGC 58.235 39.130 0.00 0.00 0.00 5.19
3374 3865 9.317936 ACATCATTCTCAACCTTTTTCTTTTTC 57.682 29.630 0.00 0.00 0.00 2.29
3379 3870 5.537674 AGCACATCATTCTCAACCTTTTTCT 59.462 36.000 0.00 0.00 0.00 2.52
3395 3888 2.618241 GACAAGTGTTTGGAGCACATCA 59.382 45.455 0.00 0.00 38.66 3.07
3409 3902 4.278669 AGTACAGACTACCACTGACAAGTG 59.721 45.833 0.00 0.00 43.15 3.16
3410 3903 4.471548 AGTACAGACTACCACTGACAAGT 58.528 43.478 0.00 0.00 38.55 3.16
3411 3904 4.762765 AGAGTACAGACTACCACTGACAAG 59.237 45.833 0.00 0.00 35.45 3.16
3413 3906 4.368565 AGAGTACAGACTACCACTGACA 57.631 45.455 0.00 0.00 35.45 3.58
3415 3908 4.079970 CCAAGAGTACAGACTACCACTGA 58.920 47.826 0.00 0.00 35.45 3.41
3416 3909 3.193691 CCCAAGAGTACAGACTACCACTG 59.806 52.174 0.00 0.00 35.45 3.66
3417 3910 3.432378 CCCAAGAGTACAGACTACCACT 58.568 50.000 0.00 0.00 35.45 4.00
3429 3931 2.814097 GCTGTTTTCTGGCCCAAGAGTA 60.814 50.000 0.00 0.00 0.00 2.59
3436 3938 4.056125 GGCGCTGTTTTCTGGCCC 62.056 66.667 7.64 0.00 37.82 5.80
3437 3939 2.087462 AAAGGCGCTGTTTTCTGGCC 62.087 55.000 7.64 0.00 44.07 5.36
3448 3950 0.969894 ACTGAGACTACAAAGGCGCT 59.030 50.000 7.64 0.00 35.06 5.92
3451 3953 5.054477 TGTTGTAACTGAGACTACAAAGGC 58.946 41.667 11.47 3.81 39.17 4.35
3529 4034 6.415573 GTGAGGTGGAGTTGTTAGGATTATT 58.584 40.000 0.00 0.00 0.00 1.40
3530 4035 5.104485 GGTGAGGTGGAGTTGTTAGGATTAT 60.104 44.000 0.00 0.00 0.00 1.28
3531 4036 4.224370 GGTGAGGTGGAGTTGTTAGGATTA 59.776 45.833 0.00 0.00 0.00 1.75
3533 4038 2.572104 GGTGAGGTGGAGTTGTTAGGAT 59.428 50.000 0.00 0.00 0.00 3.24
3537 4042 1.069513 CGTGGTGAGGTGGAGTTGTTA 59.930 52.381 0.00 0.00 0.00 2.41
3546 4051 0.105964 TCCTTGTTCGTGGTGAGGTG 59.894 55.000 0.00 0.00 0.00 4.00
3547 4052 0.834612 TTCCTTGTTCGTGGTGAGGT 59.165 50.000 0.00 0.00 0.00 3.85
3550 4055 3.316868 GGATTTTTCCTTGTTCGTGGTGA 59.683 43.478 0.00 0.00 0.00 4.02
3552 4057 3.067601 GTGGATTTTTCCTTGTTCGTGGT 59.932 43.478 0.00 0.00 0.00 4.16
3559 4064 1.970640 GGCAGGTGGATTTTTCCTTGT 59.029 47.619 0.00 0.00 0.00 3.16
3560 4065 1.276138 GGGCAGGTGGATTTTTCCTTG 59.724 52.381 0.00 0.00 0.00 3.61
3562 4067 0.611896 CGGGCAGGTGGATTTTTCCT 60.612 55.000 0.00 0.00 0.00 3.36
3564 4069 1.890174 CCGGGCAGGTGGATTTTTC 59.110 57.895 0.00 0.00 34.51 2.29
3582 4143 2.528743 CCAGCATCGATCGGCACAC 61.529 63.158 16.41 0.89 0.00 3.82
3668 4278 2.755655 CCGAGGAGAAAGTAAGAGAGCA 59.244 50.000 0.00 0.00 0.00 4.26
3676 4286 2.735151 TGCTCATCCGAGGAGAAAGTA 58.265 47.619 14.18 0.00 39.88 2.24
3677 4287 1.561643 TGCTCATCCGAGGAGAAAGT 58.438 50.000 14.18 0.00 39.88 2.66
3776 4391 2.259511 CCGCCTTTTGCTTCTGGC 59.740 61.111 0.00 0.00 41.76 4.85
3857 4472 5.070180 AGAGAGAGAGAGAGATGTGAGAGAG 59.930 48.000 0.00 0.00 0.00 3.20
3858 4473 4.964897 AGAGAGAGAGAGAGATGTGAGAGA 59.035 45.833 0.00 0.00 0.00 3.10
3859 4474 5.070180 AGAGAGAGAGAGAGAGATGTGAGAG 59.930 48.000 0.00 0.00 0.00 3.20
3860 4475 4.964897 AGAGAGAGAGAGAGAGATGTGAGA 59.035 45.833 0.00 0.00 0.00 3.27
3861 4476 5.070180 AGAGAGAGAGAGAGAGAGATGTGAG 59.930 48.000 0.00 0.00 0.00 3.51
3862 4477 4.964897 AGAGAGAGAGAGAGAGAGATGTGA 59.035 45.833 0.00 0.00 0.00 3.58
3863 4478 5.070180 AGAGAGAGAGAGAGAGAGAGATGTG 59.930 48.000 0.00 0.00 0.00 3.21
3864 4479 5.215069 AGAGAGAGAGAGAGAGAGAGATGT 58.785 45.833 0.00 0.00 0.00 3.06
3865 4480 5.539574 AGAGAGAGAGAGAGAGAGAGAGATG 59.460 48.000 0.00 0.00 0.00 2.90
3866 4481 5.714863 AGAGAGAGAGAGAGAGAGAGAGAT 58.285 45.833 0.00 0.00 0.00 2.75
3867 4482 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3868 4483 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3869 4484 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3870 4485 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3871 4486 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.