Multiple sequence alignment - TraesCS3D01G442800

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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 TraesCS3D01G442800 chr3D 100.000 2606 0 0 1 2606 552628421 552625816 0.000000e+00 4813
1 TraesCS3D01G442800 chr3D 89.783 1243 102 10 604 1833 552610237 552609007 0.000000e+00 1568
2 TraesCS3D01G442800 chr3D 91.220 1082 77 10 555 1633 552571584 552570518 0.000000e+00 1456
3 TraesCS3D01G442800 chr3D 87.142 1221 101 32 653 1841 552576631 552575435 0.000000e+00 1334
4 TraesCS3D01G442800 chr3D 93.345 556 34 3 1 554 30752233 30751679 0.000000e+00 819
5 TraesCS3D01G442800 chr3D 89.017 346 24 8 1849 2190 552563687 552563352 1.440000e-112 416
6 TraesCS3D01G442800 chr3D 85.648 216 28 3 1647 1860 552570473 552570259 9.390000e-55 224
7 TraesCS3D01G442800 chr3B 89.128 1674 124 29 551 2202 733258113 733256476 0.000000e+00 2030
8 TraesCS3D01G442800 chr3B 89.427 1343 106 13 874 2202 733003358 733002038 0.000000e+00 1661
9 TraesCS3D01G442800 chr3B 88.435 882 74 9 972 1851 732998769 732997914 0.000000e+00 1038
10 TraesCS3D01G442800 chr3B 87.101 814 80 18 990 1788 732841640 732840837 0.000000e+00 898
11 TraesCS3D01G442800 chr3B 90.000 410 35 6 2202 2606 777205880 777206288 2.300000e-145 525
12 TraesCS3D01G442800 chr3A 90.399 1302 84 18 653 1933 688987384 688986103 0.000000e+00 1674
13 TraesCS3D01G442800 chr3A 90.312 1187 87 16 551 1728 688978477 688977310 0.000000e+00 1530
14 TraesCS3D01G442800 chr3A 84.010 813 91 31 991 1788 688899002 688898214 0.000000e+00 745
15 TraesCS3D01G442800 chr3A 90.441 408 33 6 2201 2603 614223787 614224193 1.370000e-147 532
16 TraesCS3D01G442800 chr3A 90.024 411 35 6 2201 2606 1874170 1873761 6.390000e-146 527
17 TraesCS3D01G442800 chr3A 86.667 210 9 3 1988 2195 688986101 688985909 5.650000e-52 215
18 TraesCS3D01G442800 chr5D 94.224 554 28 3 1 550 450700111 450700664 0.000000e+00 843
19 TraesCS3D01G442800 chr5D 93.682 554 31 3 1 550 243821788 243821235 0.000000e+00 826
20 TraesCS3D01G442800 chr6D 94.213 553 29 3 1 550 472765176 472765728 0.000000e+00 841
21 TraesCS3D01G442800 chr6D 93.525 556 30 4 1 550 423443205 423443760 0.000000e+00 822
22 TraesCS3D01G442800 chr7D 94.054 555 30 3 1 552 150764048 150764602 0.000000e+00 839
23 TraesCS3D01G442800 chr7D 93.514 555 31 4 1 550 15496587 15496033 0.000000e+00 821
24 TraesCS3D01G442800 chr5B 93.705 556 30 3 1 551 425872411 425871856 0.000000e+00 828
25 TraesCS3D01G442800 chr5B 90.000 410 34 6 2202 2606 449977685 449977278 8.260000e-145 523
26 TraesCS3D01G442800 chr4D 93.694 555 30 3 1 550 413038500 413039054 0.000000e+00 826
27 TraesCS3D01G442800 chr4A 90.976 410 31 6 2202 2606 618461268 618460860 4.900000e-152 547
28 TraesCS3D01G442800 chr7B 90.465 409 34 5 2202 2606 353970752 353970345 3.820000e-148 534
29 TraesCS3D01G442800 chr5A 90.244 410 34 6 2202 2606 75385096 75384688 4.940000e-147 531
30 TraesCS3D01G442800 chr5A 89.563 412 37 6 2200 2606 367068607 367068197 3.840000e-143 518
31 TraesCS3D01G442800 chr2A 90.244 410 34 6 2202 2606 603684185 603684593 4.940000e-147 531


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 TraesCS3D01G442800 chr3D 552625816 552628421 2605 True 4813.000000 4813 100.000000 1 2606 1 chr3D.!!$R4 2605
1 TraesCS3D01G442800 chr3D 552609007 552610237 1230 True 1568.000000 1568 89.783000 604 1833 1 chr3D.!!$R3 1229
2 TraesCS3D01G442800 chr3D 552570259 552576631 6372 True 1004.666667 1456 88.003333 555 1860 3 chr3D.!!$R5 1305
3 TraesCS3D01G442800 chr3D 30751679 30752233 554 True 819.000000 819 93.345000 1 554 1 chr3D.!!$R1 553
4 TraesCS3D01G442800 chr3B 733256476 733258113 1637 True 2030.000000 2030 89.128000 551 2202 1 chr3B.!!$R2 1651
5 TraesCS3D01G442800 chr3B 732997914 733003358 5444 True 1349.500000 1661 88.931000 874 2202 2 chr3B.!!$R3 1328
6 TraesCS3D01G442800 chr3B 732840837 732841640 803 True 898.000000 898 87.101000 990 1788 1 chr3B.!!$R1 798
7 TraesCS3D01G442800 chr3A 688977310 688978477 1167 True 1530.000000 1530 90.312000 551 1728 1 chr3A.!!$R3 1177
8 TraesCS3D01G442800 chr3A 688985909 688987384 1475 True 944.500000 1674 88.533000 653 2195 2 chr3A.!!$R4 1542
9 TraesCS3D01G442800 chr3A 688898214 688899002 788 True 745.000000 745 84.010000 991 1788 1 chr3A.!!$R2 797
10 TraesCS3D01G442800 chr5D 450700111 450700664 553 False 843.000000 843 94.224000 1 550 1 chr5D.!!$F1 549
11 TraesCS3D01G442800 chr5D 243821235 243821788 553 True 826.000000 826 93.682000 1 550 1 chr5D.!!$R1 549
12 TraesCS3D01G442800 chr6D 472765176 472765728 552 False 841.000000 841 94.213000 1 550 1 chr6D.!!$F2 549
13 TraesCS3D01G442800 chr6D 423443205 423443760 555 False 822.000000 822 93.525000 1 550 1 chr6D.!!$F1 549
14 TraesCS3D01G442800 chr7D 150764048 150764602 554 False 839.000000 839 94.054000 1 552 1 chr7D.!!$F1 551
15 TraesCS3D01G442800 chr7D 15496033 15496587 554 True 821.000000 821 93.514000 1 550 1 chr7D.!!$R1 549
16 TraesCS3D01G442800 chr5B 425871856 425872411 555 True 828.000000 828 93.705000 1 551 1 chr5B.!!$R1 550
17 TraesCS3D01G442800 chr4D 413038500 413039054 554 False 826.000000 826 93.694000 1 550 1 chr4D.!!$F1 549

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
594 5089 0.519077 GTGCGCTTGGGAAGAAGAAG 59.481 55.0 9.73 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2351 6970 0.035439 CACTTACAAGCGGGACCCAT 60.035 55.0 12.15 0.0 0.0 4.0 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
90 92 1.645034 CGGTGCTTCATCCTACACAG 58.355 55.000 0.00 0.00 34.69 3.66
170 172 2.408241 GGACTCGCGCAGTAGGAGT 61.408 63.158 13.67 13.67 43.32 3.85
294 296 2.035961 ACACATGTAAGTGCGTCAGACT 59.964 45.455 0.00 0.00 43.23 3.24
353 356 3.950395 GCTTCTGGCTTTTGATGATAGGT 59.050 43.478 0.00 0.00 38.06 3.08
527 530 3.473647 CCAGATGCAGAGGCCGGA 61.474 66.667 5.05 0.00 40.13 5.14
528 531 2.202987 CAGATGCAGAGGCCGGAC 60.203 66.667 5.05 0.00 40.13 4.79
541 545 1.120530 GCCGGACTCATCCTCCTTTA 58.879 55.000 5.05 0.00 43.73 1.85
591 5086 1.630244 CTCGTGCGCTTGGGAAGAAG 61.630 60.000 9.73 0.00 0.00 2.85
593 5088 1.227999 CGTGCGCTTGGGAAGAAGAA 61.228 55.000 9.73 0.00 0.00 2.52
594 5089 0.519077 GTGCGCTTGGGAAGAAGAAG 59.481 55.000 9.73 0.00 0.00 2.85
600 5095 4.727475 CGCTTGGGAAGAAGAAGAAAATC 58.273 43.478 0.00 0.00 0.00 2.17
609 5104 3.430218 AGAAGAAGAAAATCACTGACGCG 59.570 43.478 3.53 3.53 0.00 6.01
643 5140 5.543714 TCAGGTACGTGAGAAATAGCAAAA 58.456 37.500 14.05 0.00 0.00 2.44
649 5146 6.715344 ACGTGAGAAATAGCAAAATCGTAA 57.285 33.333 0.00 0.00 0.00 3.18
710 5210 4.142359 CCTCTATCGCTATTCCGTATTGCT 60.142 45.833 0.00 0.00 33.52 3.91
711 5211 4.733850 TCTATCGCTATTCCGTATTGCTG 58.266 43.478 0.00 0.00 33.52 4.41
713 5213 3.994204 TCGCTATTCCGTATTGCTGTA 57.006 42.857 0.00 0.00 33.52 2.74
725 5225 6.202762 TCCGTATTGCTGTATCATGCTAAAAG 59.797 38.462 0.00 0.00 0.00 2.27
780 5293 3.357919 GGCAACTGCATGCTGACA 58.642 55.556 28.74 3.24 45.68 3.58
845 5364 6.039493 CACTATTCTATCCTAACCAGTGACGT 59.961 42.308 0.00 0.00 35.32 4.34
860 5381 0.921347 GACGTGTACAGCGCCATAAG 59.079 55.000 2.29 0.00 0.00 1.73
881 5402 3.776969 AGCTAATGATTCAGACACCCTCA 59.223 43.478 0.00 0.00 0.00 3.86
885 5406 4.581309 ATGATTCAGACACCCTCACATT 57.419 40.909 0.00 0.00 0.00 2.71
886 5407 4.371624 TGATTCAGACACCCTCACATTT 57.628 40.909 0.00 0.00 0.00 2.32
894 5415 5.067153 CAGACACCCTCACATTTGTTAACAA 59.933 40.000 17.01 17.01 0.00 2.83
937 5461 3.414136 AAACCAGCCACTGACGCCA 62.414 57.895 0.00 0.00 32.44 5.69
939 5463 2.360350 CCAGCCACTGACGCCAAT 60.360 61.111 0.00 0.00 32.44 3.16
972 5496 7.541916 TCATCTTAGCTCATCTCATCTCAAT 57.458 36.000 0.00 0.00 0.00 2.57
1021 5545 1.630126 GGCCAAGATCCAGCCTCTCA 61.630 60.000 10.27 0.00 43.62 3.27
1058 5588 2.806237 GTCCTCCGACGATCACCC 59.194 66.667 0.00 0.00 0.00 4.61
1167 5697 2.872925 CGCGTCGACAACTACGGG 60.873 66.667 17.16 5.54 43.90 5.28
1230 5760 0.397675 ACGCCCTCATCAGGATCAGA 60.398 55.000 0.00 0.00 43.65 3.27
1249 5779 2.830370 GCAAGGGCTTCGGGATGG 60.830 66.667 0.00 0.00 36.96 3.51
1263 5793 0.914417 GGATGGTCAGGAGGTGGGAA 60.914 60.000 0.00 0.00 0.00 3.97
1266 5796 0.401395 TGGTCAGGAGGTGGGAAGTT 60.401 55.000 0.00 0.00 0.00 2.66
1575 6114 3.490759 GTCGTGCGTGGCCTCATG 61.491 66.667 3.32 5.20 0.00 3.07
1604 6158 1.496060 ACCGCTCCTTGTGATGGATA 58.504 50.000 0.00 0.00 32.56 2.59
1633 6187 5.965033 ATGGCAATCCTCTTCTTCTCTAA 57.035 39.130 0.00 0.00 0.00 2.10
1674 6275 0.624785 AGAGTACCTGTAGGCGGTCT 59.375 55.000 0.00 0.00 39.32 3.85
1675 6276 1.023502 GAGTACCTGTAGGCGGTCTC 58.976 60.000 0.00 0.00 39.32 3.36
1735 6338 5.860941 TTTTGCCCAAACTGAAGACATTA 57.139 34.783 0.00 0.00 0.00 1.90
1747 6350 9.956720 AAACTGAAGACATTATGACTCTTTTTG 57.043 29.630 0.00 0.00 0.00 2.44
1797 6406 6.556874 AGGGGTTTCAATACCAAAATCTCAAA 59.443 34.615 0.00 0.00 40.09 2.69
1798 6407 7.237471 AGGGGTTTCAATACCAAAATCTCAAAT 59.763 33.333 0.00 0.00 40.09 2.32
1916 6530 2.202987 GACCTGGCCTCTGCATCG 60.203 66.667 3.32 0.00 40.13 3.84
1938 6552 7.210718 TCGTTGTGATGGTATCTTCGTATAT 57.789 36.000 0.00 0.00 0.00 0.86
1939 6553 8.326680 TCGTTGTGATGGTATCTTCGTATATA 57.673 34.615 0.00 0.00 0.00 0.86
1940 6554 8.232513 TCGTTGTGATGGTATCTTCGTATATAC 58.767 37.037 2.53 2.53 0.00 1.47
1941 6555 8.235226 CGTTGTGATGGTATCTTCGTATATACT 58.765 37.037 11.05 0.00 0.00 2.12
1942 6556 9.557338 GTTGTGATGGTATCTTCGTATATACTC 57.443 37.037 11.05 0.00 0.00 2.59
1943 6557 8.277490 TGTGATGGTATCTTCGTATATACTCC 57.723 38.462 11.05 3.35 0.00 3.85
1984 6598 9.889128 TGTCAGAAAAAGATCCAAAAAGATTTT 57.111 25.926 0.00 0.00 0.00 1.82
2018 6633 5.576384 GTCAACATTTCAAGCAGTGACAAAA 59.424 36.000 0.00 0.00 35.39 2.44
2047 6662 6.292328 GCCAAACTGACAAAATTAGACAAAGC 60.292 38.462 0.00 0.00 0.00 3.51
2196 6815 6.860023 CACTGATCCAGAAGTTCATTGTTTTC 59.140 38.462 5.50 0.00 35.18 2.29
2197 6816 6.015940 ACTGATCCAGAAGTTCATTGTTTTCC 60.016 38.462 5.50 0.00 35.18 3.13
2202 6821 6.003950 CCAGAAGTTCATTGTTTTCCCTAGA 58.996 40.000 5.50 0.00 0.00 2.43
2203 6822 6.150140 CCAGAAGTTCATTGTTTTCCCTAGAG 59.850 42.308 5.50 0.00 0.00 2.43
2204 6823 6.150140 CAGAAGTTCATTGTTTTCCCTAGAGG 59.850 42.308 5.50 0.00 0.00 3.69
2218 6837 2.755103 CCTAGAGGGAATTGCACAAACC 59.245 50.000 0.00 0.00 37.23 3.27
2219 6838 2.380064 AGAGGGAATTGCACAAACCA 57.620 45.000 0.00 0.00 0.00 3.67
2221 6840 1.000843 GAGGGAATTGCACAAACCACC 59.999 52.381 0.00 0.00 0.00 4.61
2222 6841 0.755686 GGGAATTGCACAAACCACCA 59.244 50.000 0.00 0.00 0.00 4.17
2223 6842 1.270252 GGGAATTGCACAAACCACCAG 60.270 52.381 0.00 0.00 0.00 4.00
2224 6843 1.412343 GGAATTGCACAAACCACCAGT 59.588 47.619 0.00 0.00 0.00 4.00
2225 6844 2.158971 GGAATTGCACAAACCACCAGTT 60.159 45.455 0.00 0.00 41.81 3.16
2226 6845 3.068873 GGAATTGCACAAACCACCAGTTA 59.931 43.478 0.00 0.00 37.88 2.24
2227 6846 4.262420 GGAATTGCACAAACCACCAGTTAT 60.262 41.667 0.00 0.00 37.88 1.89
2228 6847 4.953940 ATTGCACAAACCACCAGTTATT 57.046 36.364 0.00 0.00 37.88 1.40
2229 6848 3.724508 TGCACAAACCACCAGTTATTG 57.275 42.857 0.00 0.00 37.88 1.90
2240 6859 3.366052 CCAGTTATTGGGGCTAGTGTT 57.634 47.619 0.00 0.00 43.75 3.32
2242 6861 2.423538 CAGTTATTGGGGCTAGTGTTGC 59.576 50.000 0.00 0.00 0.00 4.17
2244 6863 2.122783 TATTGGGGCTAGTGTTGCAC 57.877 50.000 0.00 0.00 34.10 4.57
2245 6864 0.112218 ATTGGGGCTAGTGTTGCACA 59.888 50.000 2.01 0.00 36.74 4.57
2246 6865 0.537143 TTGGGGCTAGTGTTGCACAG 60.537 55.000 2.01 0.00 36.74 3.66
2247 6866 1.374947 GGGGCTAGTGTTGCACAGA 59.625 57.895 2.01 0.00 36.74 3.41
2248 6867 0.250727 GGGGCTAGTGTTGCACAGAA 60.251 55.000 2.01 0.00 36.74 3.02
2249 6868 0.875059 GGGCTAGTGTTGCACAGAAC 59.125 55.000 2.01 0.00 36.74 3.01
2256 6875 2.561569 GTGTTGCACAGAACACCTACT 58.438 47.619 7.98 0.00 46.74 2.57
2260 6879 5.347907 GTGTTGCACAGAACACCTACTATAC 59.652 44.000 7.98 0.00 46.74 1.47
2262 6881 3.129813 TGCACAGAACACCTACTATACGG 59.870 47.826 0.00 0.00 0.00 4.02
2263 6882 3.490419 GCACAGAACACCTACTATACGGG 60.490 52.174 0.00 0.00 0.00 5.28
2264 6883 3.698040 CACAGAACACCTACTATACGGGT 59.302 47.826 0.00 0.00 0.00 5.28
2265 6884 4.159135 CACAGAACACCTACTATACGGGTT 59.841 45.833 0.00 0.00 0.00 4.11
2266 6885 4.774200 ACAGAACACCTACTATACGGGTTT 59.226 41.667 0.00 0.00 0.00 3.27
2267 6886 5.107133 CAGAACACCTACTATACGGGTTTG 58.893 45.833 0.00 0.00 0.00 2.93
2268 6887 4.774200 AGAACACCTACTATACGGGTTTGT 59.226 41.667 0.00 0.00 0.00 2.83
2269 6888 5.246883 AGAACACCTACTATACGGGTTTGTT 59.753 40.000 0.00 0.00 0.00 2.83
2270 6889 4.824289 ACACCTACTATACGGGTTTGTTG 58.176 43.478 0.00 0.00 0.00 3.33
2271 6890 3.619929 CACCTACTATACGGGTTTGTTGC 59.380 47.826 0.00 0.00 0.00 4.17
2273 6892 3.869246 CCTACTATACGGGTTTGTTGCAG 59.131 47.826 0.00 0.00 0.00 4.41
2274 6893 3.688694 ACTATACGGGTTTGTTGCAGA 57.311 42.857 0.00 0.00 0.00 4.26
2275 6894 4.010667 ACTATACGGGTTTGTTGCAGAA 57.989 40.909 0.00 0.00 0.00 3.02
2278 6897 2.287393 ACGGGTTTGTTGCAGAAAAC 57.713 45.000 14.68 14.68 35.89 2.43
2279 6898 1.546476 ACGGGTTTGTTGCAGAAAACA 59.454 42.857 21.08 6.73 37.89 2.83
2280 6899 1.923864 CGGGTTTGTTGCAGAAAACAC 59.076 47.619 21.08 18.26 39.70 3.32
2281 6900 2.276201 GGGTTTGTTGCAGAAAACACC 58.724 47.619 21.08 16.85 39.70 4.16
2282 6901 2.354203 GGGTTTGTTGCAGAAAACACCA 60.354 45.455 21.08 0.00 39.70 4.17
2284 6903 3.321497 GTTTGTTGCAGAAAACACCACA 58.679 40.909 16.98 0.47 39.70 4.17
2285 6904 3.883830 TTGTTGCAGAAAACACCACAT 57.116 38.095 0.00 0.00 39.70 3.21
2286 6905 4.991153 TTGTTGCAGAAAACACCACATA 57.009 36.364 0.00 0.00 39.70 2.29
2287 6906 5.528043 TTGTTGCAGAAAACACCACATAT 57.472 34.783 0.00 0.00 39.70 1.78
2288 6907 5.528043 TGTTGCAGAAAACACCACATATT 57.472 34.783 0.00 0.00 35.16 1.28
2289 6908 5.288015 TGTTGCAGAAAACACCACATATTG 58.712 37.500 0.00 0.00 35.16 1.90
2303 6922 6.691754 CCACATATTGGTGTAATACTTGCA 57.308 37.500 0.00 0.00 41.10 4.08
2304 6923 6.728200 CCACATATTGGTGTAATACTTGCAG 58.272 40.000 0.00 0.00 41.10 4.41
2305 6924 6.318648 CCACATATTGGTGTAATACTTGCAGT 59.681 38.462 0.00 0.00 41.10 4.40
2307 6926 8.888716 CACATATTGGTGTAATACTTGCAGTTA 58.111 33.333 0.00 0.00 34.22 2.24
2309 6928 9.935682 CATATTGGTGTAATACTTGCAGTTAAG 57.064 33.333 0.00 0.00 34.22 1.85
2310 6929 7.996098 ATTGGTGTAATACTTGCAGTTAAGT 57.004 32.000 0.00 0.00 43.03 2.24
2311 6930 7.429636 TTGGTGTAATACTTGCAGTTAAGTC 57.570 36.000 0.00 0.00 41.01 3.01
2313 6932 7.898918 TGGTGTAATACTTGCAGTTAAGTCTA 58.101 34.615 0.00 0.00 41.01 2.59
2314 6933 8.369424 TGGTGTAATACTTGCAGTTAAGTCTAA 58.631 33.333 0.00 0.00 41.01 2.10
2322 6941 7.897864 ACTTGCAGTTAAGTCTAATCTAGTGT 58.102 34.615 0.00 0.00 36.16 3.55
2324 6943 9.209175 CTTGCAGTTAAGTCTAATCTAGTGTTT 57.791 33.333 0.00 0.00 0.00 2.83
2326 6945 7.602644 TGCAGTTAAGTCTAATCTAGTGTTTGG 59.397 37.037 0.00 0.00 0.00 3.28
2328 6947 9.877178 CAGTTAAGTCTAATCTAGTGTTTGGAT 57.123 33.333 0.00 0.00 0.00 3.41
2355 6974 8.906867 ACATTAACATAATTTCAGACAGATGGG 58.093 33.333 0.00 0.00 0.00 4.00
2356 6975 8.906867 CATTAACATAATTTCAGACAGATGGGT 58.093 33.333 0.00 0.00 0.00 4.51
2357 6976 8.506168 TTAACATAATTTCAGACAGATGGGTC 57.494 34.615 0.00 0.00 38.08 4.46
2358 6977 5.440610 ACATAATTTCAGACAGATGGGTCC 58.559 41.667 0.00 0.00 38.59 4.46
2359 6978 3.372440 AATTTCAGACAGATGGGTCCC 57.628 47.619 0.00 0.00 38.59 4.46
2360 6979 0.613260 TTTCAGACAGATGGGTCCCG 59.387 55.000 2.65 0.00 38.59 5.14
2361 6980 1.899437 TTCAGACAGATGGGTCCCGC 61.899 60.000 2.65 0.00 38.59 6.13
2363 6982 1.613630 AGACAGATGGGTCCCGCTT 60.614 57.895 2.65 0.00 38.59 4.68
2364 6983 1.450312 GACAGATGGGTCCCGCTTG 60.450 63.158 2.65 3.65 0.00 4.01
2366 6985 0.907704 ACAGATGGGTCCCGCTTGTA 60.908 55.000 2.65 0.00 0.00 2.41
2367 6986 0.251916 CAGATGGGTCCCGCTTGTAA 59.748 55.000 2.65 0.00 0.00 2.41
2368 6987 0.541863 AGATGGGTCCCGCTTGTAAG 59.458 55.000 2.65 0.00 0.00 2.34
2370 6989 0.035439 ATGGGTCCCGCTTGTAAGTG 60.035 55.000 2.65 0.00 36.32 3.16
2372 6991 0.609662 GGGTCCCGCTTGTAAGTGTA 59.390 55.000 0.00 0.00 34.79 2.90
2373 6992 1.673923 GGGTCCCGCTTGTAAGTGTAC 60.674 57.143 0.00 2.89 34.79 2.90
2374 6993 1.001181 GGTCCCGCTTGTAAGTGTACA 59.999 52.381 0.00 0.00 38.49 2.90
2376 6995 2.671396 GTCCCGCTTGTAAGTGTACATG 59.329 50.000 0.00 0.00 39.96 3.21
2377 6996 2.300723 TCCCGCTTGTAAGTGTACATGT 59.699 45.455 2.69 2.69 39.96 3.21
2378 6997 2.415168 CCCGCTTGTAAGTGTACATGTG 59.585 50.000 9.11 6.42 39.96 3.21
2380 6999 2.159707 CGCTTGTAAGTGTACATGTGGC 60.160 50.000 9.11 1.72 39.96 5.01
2381 7000 2.811431 GCTTGTAAGTGTACATGTGGCA 59.189 45.455 9.11 4.65 39.96 4.92
2383 7002 4.613622 GCTTGTAAGTGTACATGTGGCAAG 60.614 45.833 9.11 17.75 39.96 4.01
2385 7004 4.709250 TGTAAGTGTACATGTGGCAAGAA 58.291 39.130 9.11 0.00 35.23 2.52
2386 7005 5.126779 TGTAAGTGTACATGTGGCAAGAAA 58.873 37.500 9.11 0.00 35.23 2.52
2387 7006 5.590663 TGTAAGTGTACATGTGGCAAGAAAA 59.409 36.000 9.11 0.00 35.23 2.29
2388 7007 5.590530 AAGTGTACATGTGGCAAGAAAAA 57.409 34.783 9.11 0.00 0.00 1.94
2389 7008 4.932146 AGTGTACATGTGGCAAGAAAAAC 58.068 39.130 9.11 0.00 0.00 2.43
2390 7009 4.048504 GTGTACATGTGGCAAGAAAAACC 58.951 43.478 9.11 0.00 0.00 3.27
2391 7010 2.507339 ACATGTGGCAAGAAAAACCG 57.493 45.000 0.00 0.00 0.00 4.44
2392 7011 1.068434 ACATGTGGCAAGAAAAACCGG 59.932 47.619 0.00 0.00 0.00 5.28
2394 7013 0.741915 TGTGGCAAGAAAAACCGGTC 59.258 50.000 8.04 0.00 0.00 4.79
2395 7014 0.741915 GTGGCAAGAAAAACCGGTCA 59.258 50.000 8.04 0.00 0.00 4.02
2396 7015 0.741915 TGGCAAGAAAAACCGGTCAC 59.258 50.000 8.04 0.00 0.00 3.67
2397 7016 0.741915 GGCAAGAAAAACCGGTCACA 59.258 50.000 8.04 0.00 0.00 3.58
2399 7018 2.607038 GGCAAGAAAAACCGGTCACATC 60.607 50.000 8.04 4.40 0.00 3.06
2401 7020 3.853307 GCAAGAAAAACCGGTCACATCAG 60.853 47.826 8.04 0.00 0.00 2.90
2402 7021 1.880027 AGAAAAACCGGTCACATCAGC 59.120 47.619 8.04 0.00 0.00 4.26
2403 7022 0.958822 AAAAACCGGTCACATCAGCC 59.041 50.000 8.04 0.00 0.00 4.85
2406 7025 0.889186 AACCGGTCACATCAGCCAAC 60.889 55.000 8.04 0.00 0.00 3.77
2407 7026 1.302431 CCGGTCACATCAGCCAACA 60.302 57.895 0.00 0.00 0.00 3.33
2408 7027 0.677731 CCGGTCACATCAGCCAACAT 60.678 55.000 0.00 0.00 0.00 2.71
2409 7028 1.406751 CCGGTCACATCAGCCAACATA 60.407 52.381 0.00 0.00 0.00 2.29
2410 7029 2.564771 CGGTCACATCAGCCAACATAT 58.435 47.619 0.00 0.00 0.00 1.78
2411 7030 2.945008 CGGTCACATCAGCCAACATATT 59.055 45.455 0.00 0.00 0.00 1.28
2412 7031 4.126437 CGGTCACATCAGCCAACATATTA 58.874 43.478 0.00 0.00 0.00 0.98
2413 7032 4.212004 CGGTCACATCAGCCAACATATTAG 59.788 45.833 0.00 0.00 0.00 1.73
2414 7033 5.368145 GGTCACATCAGCCAACATATTAGA 58.632 41.667 0.00 0.00 0.00 2.10
2415 7034 5.237344 GGTCACATCAGCCAACATATTAGAC 59.763 44.000 0.00 0.00 0.00 2.59
2419 7038 6.986231 CACATCAGCCAACATATTAGACTGTA 59.014 38.462 0.00 0.00 0.00 2.74
2421 7040 8.213679 ACATCAGCCAACATATTAGACTGTATT 58.786 33.333 0.00 0.00 0.00 1.89
2422 7041 9.710900 CATCAGCCAACATATTAGACTGTATTA 57.289 33.333 0.00 0.00 0.00 0.98
2424 7043 9.929180 TCAGCCAACATATTAGACTGTATTATC 57.071 33.333 0.00 0.00 0.00 1.75
2425 7044 9.935241 CAGCCAACATATTAGACTGTATTATCT 57.065 33.333 0.00 0.00 0.00 1.98
2427 7046 9.372369 GCCAACATATTAGACTGTATTATCTCC 57.628 37.037 0.00 0.00 0.00 3.71
2428 7047 9.877178 CCAACATATTAGACTGTATTATCTCCC 57.123 37.037 0.00 0.00 0.00 4.30
2435 7054 9.784531 ATTAGACTGTATTATCTCCCAAACATG 57.215 33.333 0.00 0.00 0.00 3.21
2437 7056 7.050377 AGACTGTATTATCTCCCAAACATGTG 58.950 38.462 0.00 0.00 0.00 3.21
2438 7057 6.122277 ACTGTATTATCTCCCAAACATGTGG 58.878 40.000 0.00 0.00 38.51 4.17
2439 7058 6.073447 TGTATTATCTCCCAAACATGTGGT 57.927 37.500 0.00 0.00 36.90 4.16
2440 7059 6.119536 TGTATTATCTCCCAAACATGTGGTC 58.880 40.000 0.00 0.00 36.90 4.02
2441 7060 2.514458 ATCTCCCAAACATGTGGTCC 57.486 50.000 0.00 0.00 36.90 4.46
2442 7061 1.144691 TCTCCCAAACATGTGGTCCA 58.855 50.000 0.00 0.00 36.90 4.02
2443 7062 1.496857 TCTCCCAAACATGTGGTCCAA 59.503 47.619 0.00 0.00 36.90 3.53
2444 7063 2.109834 TCTCCCAAACATGTGGTCCAAT 59.890 45.455 0.00 0.00 36.90 3.16
2445 7064 2.899256 CTCCCAAACATGTGGTCCAATT 59.101 45.455 0.00 0.00 36.90 2.32
2446 7065 2.632028 TCCCAAACATGTGGTCCAATTG 59.368 45.455 0.00 0.00 36.90 2.32
2447 7066 2.632028 CCCAAACATGTGGTCCAATTGA 59.368 45.455 7.12 0.00 36.90 2.57
2448 7067 3.306225 CCCAAACATGTGGTCCAATTGAG 60.306 47.826 7.12 0.00 36.90 3.02
2449 7068 3.319755 CAAACATGTGGTCCAATTGAGC 58.680 45.455 7.12 3.72 41.96 4.26
2450 7069 1.549203 ACATGTGGTCCAATTGAGCC 58.451 50.000 7.12 9.03 40.88 4.70
2451 7070 0.452987 CATGTGGTCCAATTGAGCCG 59.547 55.000 7.12 0.00 40.88 5.52
2453 7072 0.109532 TGTGGTCCAATTGAGCCGAA 59.890 50.000 7.12 0.00 40.88 4.30
2455 7074 1.068541 GTGGTCCAATTGAGCCGAAAC 60.069 52.381 7.12 0.00 40.88 2.78
2462 7125 3.243704 CCAATTGAGCCGAAACTTTTCCA 60.244 43.478 7.12 0.00 33.68 3.53
2464 7127 4.664150 ATTGAGCCGAAACTTTTCCAAA 57.336 36.364 0.00 0.00 33.68 3.28
2468 7131 6.150396 TGAGCCGAAACTTTTCCAAATTAA 57.850 33.333 0.00 0.00 33.68 1.40
2473 7136 9.150348 AGCCGAAACTTTTCCAAATTAATATTG 57.850 29.630 0.00 0.00 33.68 1.90
2474 7137 9.145865 GCCGAAACTTTTCCAAATTAATATTGA 57.854 29.630 0.00 0.00 33.68 2.57
2513 9992 9.748708 TTACTGGATTTGTTTCTCATTTTTCTG 57.251 29.630 0.00 0.00 0.00 3.02
2517 9996 9.664332 TGGATTTGTTTCTCATTTTTCTGAAAA 57.336 25.926 11.33 11.33 38.96 2.29
2535 10014 8.783833 TCTGAAAATGTCAAAATTTGAACCAA 57.216 26.923 10.27 0.00 42.15 3.67
2536 10015 9.224267 TCTGAAAATGTCAAAATTTGAACCAAA 57.776 25.926 10.27 0.00 42.15 3.28
2537 10016 9.837525 CTGAAAATGTCAAAATTTGAACCAAAA 57.162 25.926 10.27 0.00 42.15 2.44
2562 10041 9.923143 AAAATAGTATGGGCAAACTAAAACTTC 57.077 29.630 0.00 0.00 32.24 3.01
2563 10042 5.977489 AGTATGGGCAAACTAAAACTTCC 57.023 39.130 0.00 0.00 0.00 3.46
2564 10043 5.390387 AGTATGGGCAAACTAAAACTTCCA 58.610 37.500 0.00 0.00 0.00 3.53
2565 10044 4.600692 ATGGGCAAACTAAAACTTCCAC 57.399 40.909 0.00 0.00 0.00 4.02
2568 10047 3.323691 GGGCAAACTAAAACTTCCACCAT 59.676 43.478 0.00 0.00 0.00 3.55
2570 10049 4.280929 GGCAAACTAAAACTTCCACCATCT 59.719 41.667 0.00 0.00 0.00 2.90
2571 10050 5.475564 GGCAAACTAAAACTTCCACCATCTA 59.524 40.000 0.00 0.00 0.00 1.98
2572 10051 6.349363 GGCAAACTAAAACTTCCACCATCTAG 60.349 42.308 0.00 0.00 0.00 2.43
2573 10052 6.612306 CAAACTAAAACTTCCACCATCTAGC 58.388 40.000 0.00 0.00 0.00 3.42
2574 10053 5.499004 ACTAAAACTTCCACCATCTAGCA 57.501 39.130 0.00 0.00 0.00 3.49
2576 10055 6.303839 ACTAAAACTTCCACCATCTAGCAAA 58.696 36.000 0.00 0.00 0.00 3.68
2578 10057 3.073274 ACTTCCACCATCTAGCAAACC 57.927 47.619 0.00 0.00 0.00 3.27
2579 10058 2.375174 ACTTCCACCATCTAGCAAACCA 59.625 45.455 0.00 0.00 0.00 3.67
2580 10059 3.010584 ACTTCCACCATCTAGCAAACCAT 59.989 43.478 0.00 0.00 0.00 3.55
2581 10060 3.737559 TCCACCATCTAGCAAACCATT 57.262 42.857 0.00 0.00 0.00 3.16
2585 10768 3.129287 CACCATCTAGCAAACCATTGGTC 59.871 47.826 9.22 0.00 43.50 4.02
2588 10771 3.517296 TCTAGCAAACCATTGGTCCAA 57.483 42.857 9.22 6.80 43.50 3.53
2605 10788 4.262721 GGTCCAAATGGGTAAAACTTTCCC 60.263 45.833 0.00 0.00 41.41 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 92 1.658717 CGAGATCCGCCGTCATCAC 60.659 63.158 0.00 0.00 0.00 3.06
294 296 0.834612 CCGGGTCTGGGCATAAACTA 59.165 55.000 0.00 0.00 0.00 2.24
353 356 2.112279 ACCCAGTCCACTCACCTAAA 57.888 50.000 0.00 0.00 0.00 1.85
432 435 2.559668 CAATATGCCTGAATCCGCCATT 59.440 45.455 0.00 0.00 0.00 3.16
559 5053 2.276869 CACGAGATGTGGAGGTCCA 58.723 57.895 0.00 0.00 45.21 4.02
591 5086 2.475111 TGTCGCGTCAGTGATTTTCTTC 59.525 45.455 5.77 0.00 39.30 2.87
593 5088 2.148916 TGTCGCGTCAGTGATTTTCT 57.851 45.000 5.77 0.00 39.30 2.52
594 5089 2.941891 TTGTCGCGTCAGTGATTTTC 57.058 45.000 5.77 0.00 39.30 2.29
677 5175 7.170998 CGGAATAGCGATAGAGGTTAACAAAAT 59.829 37.037 8.10 0.00 39.76 1.82
700 5200 3.751479 AGCATGATACAGCAATACGGA 57.249 42.857 0.00 0.00 0.00 4.69
725 5225 6.035220 GTGTGTTGTTTGTTTAGGCTAAAACC 59.965 38.462 20.57 10.46 38.35 3.27
735 5238 7.909121 CCACGTTTATAGTGTGTTGTTTGTTTA 59.091 33.333 0.00 0.00 37.88 2.01
780 5293 3.099905 TGCTCCATCTAGTACTGCACTT 58.900 45.455 5.39 0.00 38.80 3.16
860 5381 3.873952 GTGAGGGTGTCTGAATCATTAGC 59.126 47.826 0.00 0.00 0.00 3.09
881 5402 5.519927 GTGCTTCTGCTTTGTTAACAAATGT 59.480 36.000 28.88 0.00 43.92 2.71
885 5406 3.699038 AGGTGCTTCTGCTTTGTTAACAA 59.301 39.130 17.01 17.01 40.48 2.83
886 5407 3.287222 AGGTGCTTCTGCTTTGTTAACA 58.713 40.909 3.59 3.59 40.48 2.41
937 5461 6.196918 TGAGCTAAGATGATTGGGATGATT 57.803 37.500 0.00 0.00 0.00 2.57
939 5463 5.546887 AGATGAGCTAAGATGATTGGGATGA 59.453 40.000 0.00 0.00 0.00 2.92
972 5496 6.433404 ACGAGAGAGATTGGTCTACTTTAACA 59.567 38.462 0.00 0.00 33.97 2.41
1050 5577 4.147449 TGCTGGCTCGGGTGATCG 62.147 66.667 0.00 0.00 0.00 3.69
1230 5760 3.717294 ATCCCGAAGCCCTTGCGT 61.717 61.111 0.00 0.00 44.33 5.24
1249 5779 1.143073 ACAAACTTCCCACCTCCTGAC 59.857 52.381 0.00 0.00 0.00 3.51
1569 6108 0.816825 CGGTTGATGAGGGCATGAGG 60.817 60.000 0.00 0.00 34.11 3.86
1570 6109 1.442526 GCGGTTGATGAGGGCATGAG 61.443 60.000 0.00 0.00 34.11 2.90
1571 6110 1.451927 GCGGTTGATGAGGGCATGA 60.452 57.895 0.00 0.00 34.11 3.07
1572 6111 1.442526 GAGCGGTTGATGAGGGCATG 61.443 60.000 0.00 0.00 34.11 4.06
1573 6112 1.153086 GAGCGGTTGATGAGGGCAT 60.153 57.895 0.00 0.00 37.47 4.40
1574 6113 2.268920 GAGCGGTTGATGAGGGCA 59.731 61.111 0.00 0.00 0.00 5.36
1575 6114 2.514824 GGAGCGGTTGATGAGGGC 60.515 66.667 0.00 0.00 0.00 5.19
1576 6115 0.745845 CAAGGAGCGGTTGATGAGGG 60.746 60.000 0.00 0.00 0.00 4.30
1604 6158 2.822707 AGAGGATTGCCATTTCAGCT 57.177 45.000 0.00 0.00 36.29 4.24
1633 6187 6.354938 TCTCATCATGTACTACGTTCCTAGT 58.645 40.000 0.00 0.00 0.00 2.57
1674 6275 7.857734 TTGTCTGAAAAACAATAGTCACAGA 57.142 32.000 0.00 0.00 31.90 3.41
1675 6276 8.909708 TTTTGTCTGAAAAACAATAGTCACAG 57.090 30.769 0.00 0.00 36.57 3.66
1735 6338 4.942761 AACATGCACCAAAAAGAGTCAT 57.057 36.364 0.00 0.00 0.00 3.06
1747 6350 4.038642 TGAGAAAGGGTAAAAACATGCACC 59.961 41.667 0.00 0.00 0.00 5.01
1798 6407 9.906660 GTGAACAACCTTGTATAAATTCATTGA 57.093 29.630 0.00 0.00 41.31 2.57
1916 6530 9.557338 GAGTATATACGAAGATACCATCACAAC 57.443 37.037 7.23 0.00 31.39 3.32
2001 6616 5.163468 TGGCTATTTTTGTCACTGCTTGAAA 60.163 36.000 0.00 0.00 35.39 2.69
2018 6633 8.177119 TGTCTAATTTTGTCAGTTTGGCTATT 57.823 30.769 0.00 0.00 0.00 1.73
2047 6662 4.271776 CCTAAATTAAACTTCCTACGGCCG 59.728 45.833 26.86 26.86 0.00 6.13
2197 6816 2.755103 GGTTTGTGCAATTCCCTCTAGG 59.245 50.000 0.00 0.00 0.00 3.02
2202 6821 1.047801 GGTGGTTTGTGCAATTCCCT 58.952 50.000 0.00 0.00 0.00 4.20
2203 6822 0.755686 TGGTGGTTTGTGCAATTCCC 59.244 50.000 0.00 0.00 0.00 3.97
2204 6823 1.412343 ACTGGTGGTTTGTGCAATTCC 59.588 47.619 0.00 0.00 0.00 3.01
2205 6824 2.888834 ACTGGTGGTTTGTGCAATTC 57.111 45.000 0.00 0.00 0.00 2.17
2208 6827 3.181471 CCAATAACTGGTGGTTTGTGCAA 60.181 43.478 0.00 0.00 40.78 4.08
2209 6828 2.363680 CCAATAACTGGTGGTTTGTGCA 59.636 45.455 0.00 0.00 40.78 4.57
2210 6829 2.288763 CCCAATAACTGGTGGTTTGTGC 60.289 50.000 0.00 0.00 44.76 4.57
2211 6830 2.298729 CCCCAATAACTGGTGGTTTGTG 59.701 50.000 0.00 0.00 44.76 3.33
2212 6831 2.604139 CCCCAATAACTGGTGGTTTGT 58.396 47.619 0.00 0.00 44.76 2.83
2213 6832 1.275010 GCCCCAATAACTGGTGGTTTG 59.725 52.381 0.00 0.00 44.76 2.93
2214 6833 1.149077 AGCCCCAATAACTGGTGGTTT 59.851 47.619 0.00 0.00 44.76 3.27
2215 6834 0.783850 AGCCCCAATAACTGGTGGTT 59.216 50.000 0.00 0.00 44.76 3.67
2216 6835 1.564348 CTAGCCCCAATAACTGGTGGT 59.436 52.381 0.00 0.00 44.76 4.16
2217 6836 1.564348 ACTAGCCCCAATAACTGGTGG 59.436 52.381 0.00 0.00 44.76 4.61
2218 6837 2.026262 ACACTAGCCCCAATAACTGGTG 60.026 50.000 4.47 4.47 44.76 4.17
2219 6838 2.275466 ACACTAGCCCCAATAACTGGT 58.725 47.619 0.00 0.00 44.76 4.00
2221 6840 2.423538 GCAACACTAGCCCCAATAACTG 59.576 50.000 0.00 0.00 0.00 3.16
2222 6841 2.041081 TGCAACACTAGCCCCAATAACT 59.959 45.455 0.00 0.00 0.00 2.24
2223 6842 2.163613 GTGCAACACTAGCCCCAATAAC 59.836 50.000 0.00 0.00 36.32 1.89
2224 6843 2.224892 TGTGCAACACTAGCCCCAATAA 60.225 45.455 0.00 0.00 45.67 1.40
2225 6844 1.352687 TGTGCAACACTAGCCCCAATA 59.647 47.619 0.00 0.00 45.67 1.90
2226 6845 0.112218 TGTGCAACACTAGCCCCAAT 59.888 50.000 0.00 0.00 45.67 3.16
2227 6846 0.537143 CTGTGCAACACTAGCCCCAA 60.537 55.000 0.00 0.00 45.67 4.12
2228 6847 1.073025 CTGTGCAACACTAGCCCCA 59.927 57.895 0.00 0.00 45.67 4.96
2229 6848 0.250727 TTCTGTGCAACACTAGCCCC 60.251 55.000 0.00 0.00 45.67 5.80
2230 6849 0.875059 GTTCTGTGCAACACTAGCCC 59.125 55.000 0.00 0.00 45.67 5.19
2231 6850 1.593196 TGTTCTGTGCAACACTAGCC 58.407 50.000 0.00 0.00 45.67 3.93
2238 6857 4.561606 CGTATAGTAGGTGTTCTGTGCAAC 59.438 45.833 0.00 0.00 37.35 4.17
2239 6858 4.381185 CCGTATAGTAGGTGTTCTGTGCAA 60.381 45.833 0.00 0.00 0.00 4.08
2240 6859 3.129813 CCGTATAGTAGGTGTTCTGTGCA 59.870 47.826 0.00 0.00 0.00 4.57
2242 6861 3.698040 ACCCGTATAGTAGGTGTTCTGTG 59.302 47.826 0.00 0.00 30.97 3.66
2244 6863 4.996788 AACCCGTATAGTAGGTGTTCTG 57.003 45.455 0.00 0.00 33.05 3.02
2245 6864 4.774200 ACAAACCCGTATAGTAGGTGTTCT 59.226 41.667 0.00 0.00 33.05 3.01
2246 6865 5.077134 ACAAACCCGTATAGTAGGTGTTC 57.923 43.478 0.00 0.00 33.05 3.18
2247 6866 5.240121 CAACAAACCCGTATAGTAGGTGTT 58.760 41.667 0.00 0.00 33.05 3.32
2248 6867 4.824289 CAACAAACCCGTATAGTAGGTGT 58.176 43.478 0.00 0.00 33.05 4.16
2249 6868 3.619929 GCAACAAACCCGTATAGTAGGTG 59.380 47.826 0.00 0.00 33.05 4.00
2251 6870 3.864243 TGCAACAAACCCGTATAGTAGG 58.136 45.455 0.00 0.00 0.00 3.18
2252 6871 4.751060 TCTGCAACAAACCCGTATAGTAG 58.249 43.478 0.00 0.00 0.00 2.57
2253 6872 4.804868 TCTGCAACAAACCCGTATAGTA 57.195 40.909 0.00 0.00 0.00 1.82
2254 6873 3.688694 TCTGCAACAAACCCGTATAGT 57.311 42.857 0.00 0.00 0.00 2.12
2256 6875 4.579340 TGTTTTCTGCAACAAACCCGTATA 59.421 37.500 14.75 0.00 33.60 1.47
2260 6879 1.923864 GTGTTTTCTGCAACAAACCCG 59.076 47.619 14.75 0.00 38.40 5.28
2262 6881 2.670905 GTGGTGTTTTCTGCAACAAACC 59.329 45.455 14.75 6.89 38.40 3.27
2263 6882 3.321497 TGTGGTGTTTTCTGCAACAAAC 58.679 40.909 11.76 11.76 38.40 2.93
2264 6883 3.667497 TGTGGTGTTTTCTGCAACAAA 57.333 38.095 0.00 0.00 38.40 2.83
2265 6884 3.883830 ATGTGGTGTTTTCTGCAACAA 57.116 38.095 0.00 0.00 38.40 2.83
2266 6885 5.288015 CAATATGTGGTGTTTTCTGCAACA 58.712 37.500 0.00 0.00 34.15 3.33
2267 6886 4.685628 CCAATATGTGGTGTTTTCTGCAAC 59.314 41.667 0.00 0.00 43.20 4.17
2268 6887 4.880759 CCAATATGTGGTGTTTTCTGCAA 58.119 39.130 0.00 0.00 43.20 4.08
2269 6888 4.517952 CCAATATGTGGTGTTTTCTGCA 57.482 40.909 0.00 0.00 43.20 4.41
2298 6917 8.764524 AACACTAGATTAGACTTAACTGCAAG 57.235 34.615 0.00 0.00 42.29 4.01
2299 6918 8.988934 CAAACACTAGATTAGACTTAACTGCAA 58.011 33.333 0.00 0.00 0.00 4.08
2300 6919 7.602644 CCAAACACTAGATTAGACTTAACTGCA 59.397 37.037 0.00 0.00 0.00 4.41
2301 6920 7.817962 TCCAAACACTAGATTAGACTTAACTGC 59.182 37.037 0.00 0.00 0.00 4.40
2302 6921 9.877178 ATCCAAACACTAGATTAGACTTAACTG 57.123 33.333 0.00 0.00 0.00 3.16
2329 6948 8.906867 CCCATCTGTCTGAAATTATGTTAATGT 58.093 33.333 0.00 0.00 0.00 2.71
2330 6949 8.906867 ACCCATCTGTCTGAAATTATGTTAATG 58.093 33.333 0.00 0.00 0.00 1.90
2331 6950 9.125026 GACCCATCTGTCTGAAATTATGTTAAT 57.875 33.333 0.00 0.00 32.39 1.40
2332 6951 7.556275 GGACCCATCTGTCTGAAATTATGTTAA 59.444 37.037 0.00 0.00 35.54 2.01
2333 6952 7.054124 GGACCCATCTGTCTGAAATTATGTTA 58.946 38.462 0.00 0.00 35.54 2.41
2335 6954 5.440610 GGACCCATCTGTCTGAAATTATGT 58.559 41.667 0.00 0.00 35.54 2.29
2336 6955 4.823989 GGGACCCATCTGTCTGAAATTATG 59.176 45.833 5.33 0.00 35.54 1.90
2338 6957 3.118408 CGGGACCCATCTGTCTGAAATTA 60.118 47.826 12.15 0.00 35.54 1.40
2339 6958 2.356125 CGGGACCCATCTGTCTGAAATT 60.356 50.000 12.15 0.00 35.54 1.82
2340 6959 1.210478 CGGGACCCATCTGTCTGAAAT 59.790 52.381 12.15 0.00 35.54 2.17
2341 6960 0.613260 CGGGACCCATCTGTCTGAAA 59.387 55.000 12.15 0.00 35.54 2.69
2342 6961 1.899437 GCGGGACCCATCTGTCTGAA 61.899 60.000 12.15 0.00 35.54 3.02
2343 6962 2.359169 GCGGGACCCATCTGTCTGA 61.359 63.158 12.15 0.00 35.54 3.27
2345 6964 1.613630 AAGCGGGACCCATCTGTCT 60.614 57.895 12.15 0.00 35.54 3.41
2346 6965 1.450312 CAAGCGGGACCCATCTGTC 60.450 63.158 12.15 0.00 34.42 3.51
2347 6966 0.907704 TACAAGCGGGACCCATCTGT 60.908 55.000 12.15 11.99 0.00 3.41
2348 6967 0.251916 TTACAAGCGGGACCCATCTG 59.748 55.000 12.15 6.26 0.00 2.90
2349 6968 0.541863 CTTACAAGCGGGACCCATCT 59.458 55.000 12.15 3.69 0.00 2.90
2351 6970 0.035439 CACTTACAAGCGGGACCCAT 60.035 55.000 12.15 0.00 0.00 4.00
2352 6971 1.373435 CACTTACAAGCGGGACCCA 59.627 57.895 12.15 0.00 0.00 4.51
2353 6972 0.609662 TACACTTACAAGCGGGACCC 59.390 55.000 0.00 0.00 0.00 4.46
2354 6973 1.001181 TGTACACTTACAAGCGGGACC 59.999 52.381 0.00 0.00 35.14 4.46
2355 6974 2.443887 TGTACACTTACAAGCGGGAC 57.556 50.000 0.00 0.00 35.14 4.46
2356 6975 2.300723 ACATGTACACTTACAAGCGGGA 59.699 45.455 0.00 0.00 41.64 5.14
2357 6976 2.415168 CACATGTACACTTACAAGCGGG 59.585 50.000 0.00 0.00 41.64 6.13
2358 6977 2.415168 CCACATGTACACTTACAAGCGG 59.585 50.000 0.00 0.00 41.64 5.52
2359 6978 2.159707 GCCACATGTACACTTACAAGCG 60.160 50.000 0.00 0.00 41.64 4.68
2360 6979 2.811431 TGCCACATGTACACTTACAAGC 59.189 45.455 0.00 0.00 41.64 4.01
2361 6980 4.754618 TCTTGCCACATGTACACTTACAAG 59.245 41.667 15.85 15.85 41.64 3.16
2363 6982 4.344359 TCTTGCCACATGTACACTTACA 57.656 40.909 0.00 0.00 42.53 2.41
2364 6983 5.682943 TTTCTTGCCACATGTACACTTAC 57.317 39.130 0.00 0.00 0.00 2.34
2366 6985 5.348164 GTTTTTCTTGCCACATGTACACTT 58.652 37.500 0.00 0.00 0.00 3.16
2367 6986 4.202111 GGTTTTTCTTGCCACATGTACACT 60.202 41.667 0.00 0.00 0.00 3.55
2368 6987 4.048504 GGTTTTTCTTGCCACATGTACAC 58.951 43.478 0.00 0.00 0.00 2.90
2370 6989 3.305110 CGGTTTTTCTTGCCACATGTAC 58.695 45.455 0.00 0.00 0.00 2.90
2372 6991 1.068434 CCGGTTTTTCTTGCCACATGT 59.932 47.619 0.00 0.00 0.00 3.21
2373 6992 1.068434 ACCGGTTTTTCTTGCCACATG 59.932 47.619 0.00 0.00 0.00 3.21
2374 6993 1.339929 GACCGGTTTTTCTTGCCACAT 59.660 47.619 9.42 0.00 0.00 3.21
2376 6995 0.741915 TGACCGGTTTTTCTTGCCAC 59.258 50.000 9.42 0.00 0.00 5.01
2377 6996 0.741915 GTGACCGGTTTTTCTTGCCA 59.258 50.000 9.42 0.00 0.00 4.92
2378 6997 0.741915 TGTGACCGGTTTTTCTTGCC 59.258 50.000 9.42 0.00 0.00 4.52
2380 6999 3.853307 GCTGATGTGACCGGTTTTTCTTG 60.853 47.826 9.42 0.00 0.00 3.02
2381 7000 2.293399 GCTGATGTGACCGGTTTTTCTT 59.707 45.455 9.42 0.00 0.00 2.52
2383 7002 1.068541 GGCTGATGTGACCGGTTTTTC 60.069 52.381 9.42 4.63 0.00 2.29
2385 7004 0.179004 TGGCTGATGTGACCGGTTTT 60.179 50.000 9.42 0.00 0.00 2.43
2386 7005 0.179004 TTGGCTGATGTGACCGGTTT 60.179 50.000 9.42 0.00 0.00 3.27
2387 7006 0.889186 GTTGGCTGATGTGACCGGTT 60.889 55.000 9.42 0.00 0.00 4.44
2388 7007 1.302511 GTTGGCTGATGTGACCGGT 60.303 57.895 6.92 6.92 0.00 5.28
2389 7008 0.677731 ATGTTGGCTGATGTGACCGG 60.678 55.000 0.00 0.00 0.00 5.28
2390 7009 2.022764 TATGTTGGCTGATGTGACCG 57.977 50.000 0.00 0.00 0.00 4.79
2391 7010 5.237344 GTCTAATATGTTGGCTGATGTGACC 59.763 44.000 0.00 0.00 0.00 4.02
2392 7011 6.018425 CAGTCTAATATGTTGGCTGATGTGAC 60.018 42.308 4.82 0.00 0.00 3.67
2394 7013 5.819379 ACAGTCTAATATGTTGGCTGATGTG 59.181 40.000 13.44 0.00 0.00 3.21
2395 7014 5.994250 ACAGTCTAATATGTTGGCTGATGT 58.006 37.500 13.44 0.44 0.00 3.06
2396 7015 8.613060 AATACAGTCTAATATGTTGGCTGATG 57.387 34.615 13.44 0.00 0.00 3.07
2399 7018 9.935241 AGATAATACAGTCTAATATGTTGGCTG 57.065 33.333 7.85 7.85 0.00 4.85
2401 7020 9.372369 GGAGATAATACAGTCTAATATGTTGGC 57.628 37.037 0.00 0.00 0.00 4.52
2402 7021 9.877178 GGGAGATAATACAGTCTAATATGTTGG 57.123 37.037 0.00 0.00 0.00 3.77
2409 7028 9.784531 CATGTTTGGGAGATAATACAGTCTAAT 57.215 33.333 0.00 0.00 0.00 1.73
2410 7029 8.768397 ACATGTTTGGGAGATAATACAGTCTAA 58.232 33.333 0.00 0.00 0.00 2.10
2411 7030 8.204160 CACATGTTTGGGAGATAATACAGTCTA 58.796 37.037 0.00 0.00 0.00 2.59
2412 7031 7.050377 CACATGTTTGGGAGATAATACAGTCT 58.950 38.462 0.00 0.00 0.00 3.24
2413 7032 6.260936 CCACATGTTTGGGAGATAATACAGTC 59.739 42.308 0.00 0.00 32.35 3.51
2414 7033 6.122277 CCACATGTTTGGGAGATAATACAGT 58.878 40.000 0.00 0.00 32.35 3.55
2415 7034 6.122277 ACCACATGTTTGGGAGATAATACAG 58.878 40.000 7.66 0.00 41.49 2.74
2419 7038 4.017591 TGGACCACATGTTTGGGAGATAAT 60.018 41.667 7.66 0.00 41.49 1.28
2421 7040 2.916269 TGGACCACATGTTTGGGAGATA 59.084 45.455 7.66 0.00 41.49 1.98
2422 7041 1.710244 TGGACCACATGTTTGGGAGAT 59.290 47.619 7.66 0.00 41.49 2.75
2423 7042 1.144691 TGGACCACATGTTTGGGAGA 58.855 50.000 7.66 0.00 41.49 3.71
2424 7043 1.993956 TTGGACCACATGTTTGGGAG 58.006 50.000 7.66 0.00 41.49 4.30
2425 7044 2.632028 CAATTGGACCACATGTTTGGGA 59.368 45.455 7.66 0.00 41.49 4.37
2426 7045 2.632028 TCAATTGGACCACATGTTTGGG 59.368 45.455 5.42 3.41 41.49 4.12
2427 7046 3.861886 GCTCAATTGGACCACATGTTTGG 60.862 47.826 5.42 0.00 43.04 3.28
2428 7047 3.319755 GCTCAATTGGACCACATGTTTG 58.680 45.455 5.42 0.00 0.00 2.93
2429 7048 2.299867 GGCTCAATTGGACCACATGTTT 59.700 45.455 5.42 0.00 0.00 2.83
2430 7049 1.895131 GGCTCAATTGGACCACATGTT 59.105 47.619 5.42 0.00 0.00 2.71
2432 7051 0.452987 CGGCTCAATTGGACCACATG 59.547 55.000 15.25 0.00 0.00 3.21
2433 7052 0.327924 TCGGCTCAATTGGACCACAT 59.672 50.000 15.25 0.00 0.00 3.21
2434 7053 0.109532 TTCGGCTCAATTGGACCACA 59.890 50.000 15.25 1.80 0.00 4.17
2435 7054 1.068541 GTTTCGGCTCAATTGGACCAC 60.069 52.381 15.25 5.18 0.00 4.16
2437 7056 1.534729 AGTTTCGGCTCAATTGGACC 58.465 50.000 5.42 6.60 0.00 4.46
2438 7057 3.643159 AAAGTTTCGGCTCAATTGGAC 57.357 42.857 5.42 0.00 0.00 4.02
2439 7058 3.005367 GGAAAAGTTTCGGCTCAATTGGA 59.995 43.478 5.42 0.00 38.06 3.53
2440 7059 3.243704 TGGAAAAGTTTCGGCTCAATTGG 60.244 43.478 5.42 0.00 38.06 3.16
2441 7060 3.976169 TGGAAAAGTTTCGGCTCAATTG 58.024 40.909 0.00 0.00 38.06 2.32
2442 7061 4.664150 TTGGAAAAGTTTCGGCTCAATT 57.336 36.364 0.00 0.00 38.06 2.32
2443 7062 4.664150 TTTGGAAAAGTTTCGGCTCAAT 57.336 36.364 0.00 0.00 38.06 2.57
2444 7063 4.664150 ATTTGGAAAAGTTTCGGCTCAA 57.336 36.364 0.00 0.00 38.06 3.02
2445 7064 4.664150 AATTTGGAAAAGTTTCGGCTCA 57.336 36.364 0.00 0.00 38.06 4.26
2446 7065 8.926715 ATATTAATTTGGAAAAGTTTCGGCTC 57.073 30.769 0.00 0.00 38.06 4.70
2447 7066 9.150348 CAATATTAATTTGGAAAAGTTTCGGCT 57.850 29.630 0.00 0.00 38.06 5.52
2448 7067 9.145865 TCAATATTAATTTGGAAAAGTTTCGGC 57.854 29.630 0.00 0.00 38.06 5.54
2477 7140 9.520515 AGAAACAAATCCAGTAAATACTCATGT 57.479 29.630 0.00 0.00 33.46 3.21
2478 7141 9.994432 GAGAAACAAATCCAGTAAATACTCATG 57.006 33.333 0.00 0.00 33.46 3.07
2479 7142 9.739276 TGAGAAACAAATCCAGTAAATACTCAT 57.261 29.630 0.00 0.00 33.46 2.90
2480 7143 9.739276 ATGAGAAACAAATCCAGTAAATACTCA 57.261 29.630 0.00 0.00 33.46 3.41
2488 7151 9.130661 TCAGAAAAATGAGAAACAAATCCAGTA 57.869 29.630 0.00 0.00 0.00 2.74
2489 7152 8.010733 TCAGAAAAATGAGAAACAAATCCAGT 57.989 30.769 0.00 0.00 0.00 4.00
2490 7153 8.876275 TTCAGAAAAATGAGAAACAAATCCAG 57.124 30.769 0.00 0.00 0.00 3.86
2509 7762 8.783833 TGGTTCAAATTTTGACATTTTCAGAA 57.216 26.923 11.30 0.00 39.87 3.02
2511 7764 9.837525 TTTTGGTTCAAATTTTGACATTTTCAG 57.162 25.926 11.30 0.00 39.87 3.02
2536 10015 9.923143 GAAGTTTTAGTTTGCCCATACTATTTT 57.077 29.630 0.56 0.00 0.00 1.82
2537 10016 8.528643 GGAAGTTTTAGTTTGCCCATACTATTT 58.471 33.333 0.56 0.00 0.00 1.40
2538 10017 7.672239 TGGAAGTTTTAGTTTGCCCATACTATT 59.328 33.333 0.56 0.00 0.00 1.73
2539 10018 7.122204 GTGGAAGTTTTAGTTTGCCCATACTAT 59.878 37.037 0.56 0.00 0.00 2.12
2541 10020 5.243060 GTGGAAGTTTTAGTTTGCCCATACT 59.757 40.000 0.00 0.00 0.00 2.12
2543 10022 4.525100 GGTGGAAGTTTTAGTTTGCCCATA 59.475 41.667 0.00 0.00 0.00 2.74
2544 10023 3.323691 GGTGGAAGTTTTAGTTTGCCCAT 59.676 43.478 0.00 0.00 0.00 4.00
2546 10025 2.696187 TGGTGGAAGTTTTAGTTTGCCC 59.304 45.455 0.00 0.00 0.00 5.36
2548 10027 5.453567 AGATGGTGGAAGTTTTAGTTTGC 57.546 39.130 0.00 0.00 0.00 3.68
2549 10028 6.206634 TGCTAGATGGTGGAAGTTTTAGTTTG 59.793 38.462 0.00 0.00 0.00 2.93
2550 10029 6.303839 TGCTAGATGGTGGAAGTTTTAGTTT 58.696 36.000 0.00 0.00 0.00 2.66
2551 10030 5.876357 TGCTAGATGGTGGAAGTTTTAGTT 58.124 37.500 0.00 0.00 0.00 2.24
2552 10031 5.499004 TGCTAGATGGTGGAAGTTTTAGT 57.501 39.130 0.00 0.00 0.00 2.24
2553 10032 6.349363 GGTTTGCTAGATGGTGGAAGTTTTAG 60.349 42.308 0.00 0.00 0.00 1.85
2554 10033 5.475564 GGTTTGCTAGATGGTGGAAGTTTTA 59.524 40.000 0.00 0.00 0.00 1.52
2555 10034 4.280929 GGTTTGCTAGATGGTGGAAGTTTT 59.719 41.667 0.00 0.00 0.00 2.43
2557 10036 3.181434 TGGTTTGCTAGATGGTGGAAGTT 60.181 43.478 0.00 0.00 0.00 2.66
2559 10038 3.071874 TGGTTTGCTAGATGGTGGAAG 57.928 47.619 0.00 0.00 0.00 3.46
2560 10039 3.737559 ATGGTTTGCTAGATGGTGGAA 57.262 42.857 0.00 0.00 0.00 3.53
2561 10040 3.355378 CAATGGTTTGCTAGATGGTGGA 58.645 45.455 0.00 0.00 0.00 4.02
2562 10041 2.428171 CCAATGGTTTGCTAGATGGTGG 59.572 50.000 0.00 0.00 0.00 4.61
2563 10042 3.091545 ACCAATGGTTTGCTAGATGGTG 58.908 45.455 0.00 0.00 38.22 4.17
2564 10043 3.356290 GACCAATGGTTTGCTAGATGGT 58.644 45.455 6.30 0.00 42.09 3.55
2565 10044 2.689983 GGACCAATGGTTTGCTAGATGG 59.310 50.000 6.30 0.00 35.25 3.51
2568 10047 3.517296 TTGGACCAATGGTTTGCTAGA 57.483 42.857 6.30 0.00 35.25 2.43
2570 10049 3.260380 CCATTTGGACCAATGGTTTGCTA 59.740 43.478 19.68 0.00 35.25 3.49
2571 10050 2.038820 CCATTTGGACCAATGGTTTGCT 59.961 45.455 19.68 0.00 35.25 3.91
2572 10051 2.425539 CCATTTGGACCAATGGTTTGC 58.574 47.619 19.68 0.00 35.25 3.68
2573 10052 2.371510 ACCCATTTGGACCAATGGTTTG 59.628 45.455 23.20 15.53 35.25 2.93
2574 10053 2.700354 ACCCATTTGGACCAATGGTTT 58.300 42.857 23.20 13.52 35.25 3.27
2576 10055 3.551635 TTACCCATTTGGACCAATGGT 57.448 42.857 23.20 22.11 39.44 3.55
2578 10057 5.482163 AGTTTTACCCATTTGGACCAATG 57.518 39.130 7.99 8.48 37.39 2.82
2579 10058 6.465178 GGAAAGTTTTACCCATTTGGACCAAT 60.465 38.462 7.99 0.00 37.39 3.16
2580 10059 5.163290 GGAAAGTTTTACCCATTTGGACCAA 60.163 40.000 1.69 1.69 37.39 3.67
2581 10060 4.345547 GGAAAGTTTTACCCATTTGGACCA 59.654 41.667 0.00 0.00 37.39 4.02


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

AutoCloner maintained by Alex Coulton.