Multiple sequence alignment - TraesCS6A01G406700

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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 TraesCS6A01G406700 chr6A 100.000 5902 0 0 1 5902 611862339 611856438 0.000000e+00 10900.0
1 TraesCS6A01G406700 chr6D 95.528 2952 92 15 2226 5160 465211807 465208879 0.000000e+00 4684.0
2 TraesCS6A01G406700 chr6D 88.823 671 45 26 853 1516 465213984 465213337 0.000000e+00 797.0
3 TraesCS6A01G406700 chr6D 92.424 462 26 5 1577 2038 465213054 465212602 0.000000e+00 651.0
4 TraesCS6A01G406700 chr6D 87.912 546 36 11 5210 5726 465208792 465208248 3.020000e-172 616.0
5 TraesCS6A01G406700 chr6D 83.333 360 50 8 5375 5726 78819812 78819455 2.050000e-84 324.0
6 TraesCS6A01G406700 chr6D 90.909 176 4 4 5727 5893 465208288 465208116 5.950000e-55 226.0
7 TraesCS6A01G406700 chr6D 95.238 126 2 2 2031 2155 465211926 465211804 4.670000e-46 196.0
8 TraesCS6A01G406700 chr6B 92.491 2264 111 31 3027 5259 710103993 710101758 0.000000e+00 3184.0
9 TraesCS6A01G406700 chr6B 89.278 1399 111 24 1587 2968 710105527 710104151 0.000000e+00 1716.0
10 TraesCS6A01G406700 chr6B 95.203 542 23 3 1 541 710233864 710234403 0.000000e+00 854.0
11 TraesCS6A01G406700 chr6B 94.843 543 24 4 1 541 710107794 710107254 0.000000e+00 845.0
12 TraesCS6A01G406700 chr6B 84.701 804 66 33 629 1402 710106604 710105828 0.000000e+00 750.0
13 TraesCS6A01G406700 chr3D 87.151 358 36 9 5375 5726 283311257 283311610 1.190000e-106 398.0
14 TraesCS6A01G406700 chr5D 86.034 358 41 6 5375 5726 509542707 509543061 5.580000e-100 375.0
15 TraesCS6A01G406700 chr5D 85.359 362 39 10 5375 5726 350373596 350373953 4.350000e-96 363.0
16 TraesCS6A01G406700 chr5D 93.548 62 4 0 1 62 512403828 512403767 6.300000e-15 93.5
17 TraesCS6A01G406700 chr5D 91.379 58 4 1 5730 5787 278283895 278283951 1.760000e-10 78.7
18 TraesCS6A01G406700 chr5D 88.710 62 4 3 5727 5788 511950665 511950723 8.200000e-09 73.1
19 TraesCS6A01G406700 chr7D 86.111 324 38 5 5409 5726 102958603 102958925 5.660000e-90 342.0
20 TraesCS6A01G406700 chr7D 80.667 150 19 7 1353 1494 438368727 438368874 2.250000e-19 108.0
21 TraesCS6A01G406700 chr7D 88.732 71 4 4 5727 5797 11680273 11680339 3.790000e-12 84.2
22 TraesCS6A01G406700 chr7D 89.394 66 4 3 5728 5793 72176975 72176913 4.900000e-11 80.5
23 TraesCS6A01G406700 chr7B 83.844 359 50 7 5375 5726 181407914 181408271 9.480000e-88 335.0
24 TraesCS6A01G406700 chr7B 80.000 150 20 7 1353 1494 455271944 455271797 1.050000e-17 102.0
25 TraesCS6A01G406700 chr3B 83.889 360 46 9 5375 5726 377419705 377420060 3.410000e-87 333.0
26 TraesCS6A01G406700 chr4A 83.799 358 46 11 5375 5726 550137230 550136879 4.410000e-86 329.0
27 TraesCS6A01G406700 chr1A 83.815 173 24 4 207 377 521260492 521260662 1.700000e-35 161.0
28 TraesCS6A01G406700 chr1D 83.237 173 26 3 207 377 425573045 425573216 7.920000e-34 156.0
29 TraesCS6A01G406700 chr1D 93.548 62 4 0 1 62 51828680 51828741 6.300000e-15 93.5
30 TraesCS6A01G406700 chr1D 93.651 63 1 3 5726 5788 270617877 270617818 2.270000e-14 91.6
31 TraesCS6A01G406700 chr7A 80.667 150 19 7 1353 1494 489163312 489163459 2.250000e-19 108.0
32 TraesCS6A01G406700 chr7A 92.647 68 2 3 5726 5793 77168432 77168368 1.750000e-15 95.3
33 TraesCS6A01G406700 chr4D 91.045 67 2 3 5727 5793 495893679 495893741 2.930000e-13 87.9
34 TraesCS6A01G406700 chr5B 94.340 53 2 1 5741 5793 340615649 340615700 4.900000e-11 80.5
35 TraesCS6A01G406700 chr5B 80.233 86 15 2 1411 1495 461140061 461139977 4.940000e-06 63.9
36 TraesCS6A01G406700 chr2D 94.231 52 3 0 1088 1139 53649072 53649123 4.900000e-11 80.5
37 TraesCS6A01G406700 chr2D 90.164 61 3 2 5728 5788 628591501 628591558 6.340000e-10 76.8
38 TraesCS6A01G406700 chr2D 76.812 138 28 4 1360 1495 636205839 636205974 2.280000e-09 75.0
39 TraesCS6A01G406700 chr2B 92.857 42 1 2 1455 1495 794263924 794263964 6.390000e-05 60.2
40 TraesCS6A01G406700 chr2B 92.500 40 3 0 1 40 39192721 39192682 2.300000e-04 58.4
41 TraesCS6A01G406700 chr5A 79.070 86 16 2 1411 1495 485205889 485205805 2.300000e-04 58.4


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 TraesCS6A01G406700 chr6A 611856438 611862339 5901 True 10900.00 10900 100.000000 1 5902 1 chr6A.!!$R1 5901
1 TraesCS6A01G406700 chr6D 465208116 465213984 5868 True 1195.00 4684 91.805667 853 5893 6 chr6D.!!$R2 5040
2 TraesCS6A01G406700 chr6B 710101758 710107794 6036 True 1623.75 3184 90.328250 1 5259 4 chr6B.!!$R1 5258
3 TraesCS6A01G406700 chr6B 710233864 710234403 539 False 854.00 854 95.203000 1 541 1 chr6B.!!$F1 540

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
639 1204 0.037046 GGCAAACAAAGGATGGCCAG 60.037 55.000 13.05 0.00 41.02 4.85 F
937 1530 0.045469 AATCTTCCTCCTCCCTGCCT 59.955 55.000 0.00 0.00 0.00 4.75 F
1424 2048 0.107654 CCGTGGGGATGAAGAAGACC 60.108 60.000 0.00 0.00 34.06 3.85 F
2230 3767 0.108041 GGGCATTCCTTGTTGCATGG 60.108 55.000 0.00 0.00 40.66 3.66 F
2952 4501 1.209019 CTAGAGCCCAGTTCACATGCT 59.791 52.381 0.00 0.00 34.40 3.79 F
4082 5761 0.250124 TAGTTGCTGGTGTTCACCGG 60.250 55.000 22.25 22.25 39.14 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 3748 0.108041 CCATGCAACAAGGAATGCCC 60.108 55.0 0.00 0.00 41.87 5.36 R
2212 3749 0.896923 TCCATGCAACAAGGAATGCC 59.103 50.0 0.00 0.00 41.87 4.40 R
2923 4472 1.123928 CTGGGCTCTAGTTCCCGATT 58.876 55.0 14.41 0.00 45.60 3.34 R
3509 5185 0.695462 ATGATAGGGCCAGCCTGACA 60.695 55.0 6.18 4.94 36.10 3.58 R
4390 6069 0.893270 CTGTGGTTGGCGGGAATTCA 60.893 55.0 7.93 0.00 0.00 2.57 R
5714 7489 0.323087 AAAATACCGCTCCACACCCC 60.323 55.0 0.00 0.00 0.00 4.95 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
111 112 5.940192 AGATGACGCAATGTTCAAGTTTA 57.060 34.783 0.00 0.00 0.00 2.01
115 116 4.576873 TGACGCAATGTTCAAGTTTAAGGA 59.423 37.500 0.00 0.00 0.00 3.36
190 191 9.254133 CAACAATGTAGGTAGTGAAGATATGAG 57.746 37.037 0.00 0.00 0.00 2.90
240 241 6.942576 AGCAGTTAAGGAAGTGATGTTTGTAT 59.057 34.615 0.00 0.00 38.12 2.29
256 257 9.987901 GATGTTTGTATTGTGTGTAATTTTTCG 57.012 29.630 0.00 0.00 0.00 3.46
263 264 9.098746 GTATTGTGTGTAATTTTTCGTGTAGTG 57.901 33.333 0.00 0.00 0.00 2.74
265 266 7.074507 TGTGTGTAATTTTTCGTGTAGTGTT 57.925 32.000 0.00 0.00 0.00 3.32
266 267 7.528307 TGTGTGTAATTTTTCGTGTAGTGTTT 58.472 30.769 0.00 0.00 0.00 2.83
360 361 0.250513 GAAGGTTGACTCGATGGCCT 59.749 55.000 3.32 0.00 0.00 5.19
410 413 4.808767 AAGGGAGTTAAGTTTGAGGGTT 57.191 40.909 0.00 0.00 0.00 4.11
411 414 4.808767 AGGGAGTTAAGTTTGAGGGTTT 57.191 40.909 0.00 0.00 0.00 3.27
545 548 2.441532 CCCGCCCCGTCTCTAGAA 60.442 66.667 0.00 0.00 0.00 2.10
546 549 2.056223 CCCGCCCCGTCTCTAGAAA 61.056 63.158 0.00 0.00 0.00 2.52
547 550 1.400530 CCCGCCCCGTCTCTAGAAAT 61.401 60.000 0.00 0.00 0.00 2.17
548 551 1.325355 CCGCCCCGTCTCTAGAAATA 58.675 55.000 0.00 0.00 0.00 1.40
549 552 1.684983 CCGCCCCGTCTCTAGAAATAA 59.315 52.381 0.00 0.00 0.00 1.40
552 555 2.102588 GCCCCGTCTCTAGAAATAAGCA 59.897 50.000 0.00 0.00 0.00 3.91
553 556 3.244249 GCCCCGTCTCTAGAAATAAGCAT 60.244 47.826 0.00 0.00 0.00 3.79
555 558 4.752101 CCCCGTCTCTAGAAATAAGCATTG 59.248 45.833 0.00 0.00 0.00 2.82
595 1131 5.916661 ATGCGTCTATATCTAATCCGGTT 57.083 39.130 0.00 0.00 0.00 4.44
610 1157 8.726988 TCTAATCCGGTTGAAAATAAGAAGTTG 58.273 33.333 0.00 0.00 0.00 3.16
614 1161 4.973663 CGGTTGAAAATAAGAAGTTGCGTT 59.026 37.500 0.00 0.00 0.00 4.84
639 1204 0.037046 GGCAAACAAAGGATGGCCAG 60.037 55.000 13.05 0.00 41.02 4.85
649 1214 0.106819 GGATGGCCAGAGTGCATTCT 60.107 55.000 13.05 5.80 0.00 2.40
650 1215 1.307097 GATGGCCAGAGTGCATTCTC 58.693 55.000 13.05 2.16 34.96 2.87
651 1216 0.622136 ATGGCCAGAGTGCATTCTCA 59.378 50.000 13.05 5.19 36.97 3.27
666 1231 4.083324 GCATTCTCACAGGAAAATGAACGA 60.083 41.667 0.00 0.00 32.14 3.85
667 1232 5.562696 GCATTCTCACAGGAAAATGAACGAA 60.563 40.000 0.00 0.00 32.14 3.85
668 1233 5.418310 TTCTCACAGGAAAATGAACGAAC 57.582 39.130 0.00 0.00 0.00 3.95
669 1234 3.493129 TCTCACAGGAAAATGAACGAACG 59.507 43.478 0.00 0.00 0.00 3.95
670 1235 2.032377 TCACAGGAAAATGAACGAACGC 60.032 45.455 0.00 0.00 0.00 4.84
671 1236 2.032030 CACAGGAAAATGAACGAACGCT 60.032 45.455 0.00 0.00 0.00 5.07
672 1237 2.032030 ACAGGAAAATGAACGAACGCTG 60.032 45.455 0.00 0.00 0.00 5.18
674 1239 1.069227 GGAAAATGAACGAACGCTGCT 60.069 47.619 0.00 0.00 0.00 4.24
675 1240 2.158841 GGAAAATGAACGAACGCTGCTA 59.841 45.455 0.00 0.00 0.00 3.49
676 1241 2.875080 AAATGAACGAACGCTGCTAC 57.125 45.000 0.00 0.00 0.00 3.58
677 1242 2.080286 AATGAACGAACGCTGCTACT 57.920 45.000 0.00 0.00 0.00 2.57
682 1247 4.735985 TGAACGAACGCTGCTACTATTTA 58.264 39.130 0.00 0.00 0.00 1.40
743 1309 7.944554 ACAGAAAGAGAAATGAAACATCCCTAA 59.055 33.333 0.00 0.00 0.00 2.69
744 1310 8.796475 CAGAAAGAGAAATGAAACATCCCTAAA 58.204 33.333 0.00 0.00 0.00 1.85
746 1312 9.631452 GAAAGAGAAATGAAACATCCCTAAAAG 57.369 33.333 0.00 0.00 0.00 2.27
748 1314 8.572855 AGAGAAATGAAACATCCCTAAAAGAG 57.427 34.615 0.00 0.00 0.00 2.85
798 1370 9.476202 GAAAGCAATATAAATGACCCAATTACC 57.524 33.333 0.00 0.00 0.00 2.85
800 1372 7.305246 AGCAATATAAATGACCCAATTACCCT 58.695 34.615 0.00 0.00 0.00 4.34
801 1373 7.451566 AGCAATATAAATGACCCAATTACCCTC 59.548 37.037 0.00 0.00 0.00 4.30
802 1374 7.232534 GCAATATAAATGACCCAATTACCCTCA 59.767 37.037 0.00 0.00 0.00 3.86
803 1375 9.312904 CAATATAAATGACCCAATTACCCTCAT 57.687 33.333 0.00 0.00 0.00 2.90
804 1376 9.897040 AATATAAATGACCCAATTACCCTCATT 57.103 29.630 0.00 0.00 33.86 2.57
805 1377 9.897040 ATATAAATGACCCAATTACCCTCATTT 57.103 29.630 13.10 13.10 41.89 2.32
806 1378 6.950860 AAATGACCCAATTACCCTCATTTT 57.049 33.333 0.00 0.00 38.01 1.82
808 1380 5.269554 TGACCCAATTACCCTCATTTTCT 57.730 39.130 0.00 0.00 0.00 2.52
810 1382 5.714806 TGACCCAATTACCCTCATTTTCTTC 59.285 40.000 0.00 0.00 0.00 2.87
816 1409 7.394359 CCAATTACCCTCATTTTCTTCAGAGAA 59.606 37.037 0.00 0.00 40.07 2.87
839 1432 1.897560 AAAAGAGCCTTCTGGAACGG 58.102 50.000 0.00 0.00 32.79 4.44
847 1440 3.187313 TCTGGAACGGAGGGAGGA 58.813 61.111 0.00 0.00 39.80 3.71
889 1482 4.890306 GCCTCCCCTCCCTCCCTC 62.890 77.778 0.00 0.00 0.00 4.30
905 1498 4.415332 TCGCACGCCCGAGACTTC 62.415 66.667 0.00 0.00 32.74 3.01
934 1527 1.885049 TCCAATCTTCCTCCTCCCTG 58.115 55.000 0.00 0.00 0.00 4.45
936 1529 0.182299 CAATCTTCCTCCTCCCTGCC 59.818 60.000 0.00 0.00 0.00 4.85
937 1530 0.045469 AATCTTCCTCCTCCCTGCCT 59.955 55.000 0.00 0.00 0.00 4.75
938 1531 0.399806 ATCTTCCTCCTCCCTGCCTC 60.400 60.000 0.00 0.00 0.00 4.70
940 1533 1.002274 TTCCTCCTCCCTGCCTCTC 59.998 63.158 0.00 0.00 0.00 3.20
941 1534 1.522917 TTCCTCCTCCCTGCCTCTCT 61.523 60.000 0.00 0.00 0.00 3.10
942 1535 1.457455 CCTCCTCCCTGCCTCTCTC 60.457 68.421 0.00 0.00 0.00 3.20
943 1536 1.827789 CTCCTCCCTGCCTCTCTCG 60.828 68.421 0.00 0.00 0.00 4.04
944 1537 2.043450 CCTCCCTGCCTCTCTCGT 60.043 66.667 0.00 0.00 0.00 4.18
955 1558 2.214181 CTCTCTCGTGTTCCCCACCG 62.214 65.000 0.00 0.00 41.26 4.94
969 1572 0.958876 CCACCGAACCAAACCCTAGC 60.959 60.000 0.00 0.00 0.00 3.42
1011 1635 1.833049 AGCCCCGAACCCTAGATCG 60.833 63.158 0.00 0.00 38.74 3.69
1013 1637 2.039509 CCCCGAACCCTAGATCGAC 58.960 63.158 12.27 0.00 41.43 4.20
1024 1648 2.296814 TAGATCGACCGACCGACCGA 62.297 60.000 1.45 8.05 41.70 4.69
1124 1748 4.180946 CCGACGGACGAGGAGCTG 62.181 72.222 8.64 0.00 45.77 4.24
1370 1994 1.153823 CGGCTACTGGAAGACCACG 60.154 63.158 0.00 0.00 41.77 4.94
1424 2048 0.107654 CCGTGGGGATGAAGAAGACC 60.108 60.000 0.00 0.00 34.06 3.85
1551 2175 2.134789 CCCCCAATCTCCTCTTGTTG 57.865 55.000 0.00 0.00 0.00 3.33
1552 2176 1.467920 CCCCAATCTCCTCTTGTTGC 58.532 55.000 0.00 0.00 0.00 4.17
1553 2177 1.467920 CCCAATCTCCTCTTGTTGCC 58.532 55.000 0.00 0.00 0.00 4.52
1554 2178 1.089920 CCAATCTCCTCTTGTTGCCG 58.910 55.000 0.00 0.00 0.00 5.69
1555 2179 0.449388 CAATCTCCTCTTGTTGCCGC 59.551 55.000 0.00 0.00 0.00 6.53
1556 2180 0.326264 AATCTCCTCTTGTTGCCGCT 59.674 50.000 0.00 0.00 0.00 5.52
1557 2181 0.392193 ATCTCCTCTTGTTGCCGCTG 60.392 55.000 0.00 0.00 0.00 5.18
1558 2182 2.669569 TCCTCTTGTTGCCGCTGC 60.670 61.111 0.00 0.00 38.26 5.25
1559 2183 2.670934 CCTCTTGTTGCCGCTGCT 60.671 61.111 0.70 0.00 38.71 4.24
1560 2184 1.375908 CCTCTTGTTGCCGCTGCTA 60.376 57.895 0.70 0.00 38.71 3.49
1561 2185 0.955428 CCTCTTGTTGCCGCTGCTAA 60.955 55.000 0.70 0.00 38.71 3.09
1562 2186 0.445436 CTCTTGTTGCCGCTGCTAAG 59.555 55.000 0.70 4.14 38.71 2.18
1563 2187 0.250295 TCTTGTTGCCGCTGCTAAGT 60.250 50.000 0.70 0.00 38.71 2.24
1564 2188 0.593128 CTTGTTGCCGCTGCTAAGTT 59.407 50.000 0.70 0.00 38.71 2.66
1565 2189 1.001378 CTTGTTGCCGCTGCTAAGTTT 60.001 47.619 0.70 0.00 38.71 2.66
1566 2190 0.310543 TGTTGCCGCTGCTAAGTTTG 59.689 50.000 0.70 0.00 38.71 2.93
1567 2191 0.310854 GTTGCCGCTGCTAAGTTTGT 59.689 50.000 0.70 0.00 38.71 2.83
1568 2192 1.028905 TTGCCGCTGCTAAGTTTGTT 58.971 45.000 0.70 0.00 38.71 2.83
1569 2193 0.310543 TGCCGCTGCTAAGTTTGTTG 59.689 50.000 0.70 0.00 38.71 3.33
1570 2194 0.310854 GCCGCTGCTAAGTTTGTTGT 59.689 50.000 0.00 0.00 33.53 3.32
1571 2195 1.663161 GCCGCTGCTAAGTTTGTTGTC 60.663 52.381 0.00 0.00 33.53 3.18
1572 2196 1.601903 CCGCTGCTAAGTTTGTTGTCA 59.398 47.619 0.00 0.00 0.00 3.58
1573 2197 2.226437 CCGCTGCTAAGTTTGTTGTCAT 59.774 45.455 0.00 0.00 0.00 3.06
1574 2198 3.228749 CGCTGCTAAGTTTGTTGTCATG 58.771 45.455 0.00 0.00 0.00 3.07
1575 2199 2.982470 GCTGCTAAGTTTGTTGTCATGC 59.018 45.455 0.00 0.00 0.00 4.06
1735 2585 1.885157 TTGCTGTAGCCTGCAATGC 59.115 52.632 0.00 0.00 46.52 3.56
1755 2605 3.758023 TGCGAATCCACACTGAATTTGAT 59.242 39.130 0.00 0.00 0.00 2.57
1761 2611 7.706607 CGAATCCACACTGAATTTGATAGTCTA 59.293 37.037 0.00 0.00 0.00 2.59
1774 2624 6.615264 TTGATAGTCTAGGTGTTAGTAGCG 57.385 41.667 0.00 0.00 0.00 4.26
1784 2634 3.318275 GGTGTTAGTAGCGATGAGGATGA 59.682 47.826 0.00 0.00 0.00 2.92
1793 2643 3.894427 AGCGATGAGGATGAACTGTCTAT 59.106 43.478 0.00 0.00 0.00 1.98
1797 2647 5.240403 CGATGAGGATGAACTGTCTATCTCA 59.760 44.000 0.00 0.00 0.00 3.27
1799 2649 6.214191 TGAGGATGAACTGTCTATCTCAAC 57.786 41.667 0.00 0.00 0.00 3.18
1806 2656 7.895975 TGAACTGTCTATCTCAACAATCTTG 57.104 36.000 0.00 0.00 0.00 3.02
1825 2675 5.003804 TCTTGGTAATTCTTGACCAGAAGC 58.996 41.667 0.00 0.00 46.23 3.86
1858 2708 3.827898 GCGGCTAGTCTCGGTGCT 61.828 66.667 0.00 0.00 0.00 4.40
2023 2873 6.349611 CCAGAGTGGGTTTTAGTTTGATGATG 60.350 42.308 0.00 0.00 32.67 3.07
2024 2874 6.430925 CAGAGTGGGTTTTAGTTTGATGATGA 59.569 38.462 0.00 0.00 0.00 2.92
2025 2875 7.121759 CAGAGTGGGTTTTAGTTTGATGATGAT 59.878 37.037 0.00 0.00 0.00 2.45
2026 2876 7.671398 AGAGTGGGTTTTAGTTTGATGATGATT 59.329 33.333 0.00 0.00 0.00 2.57
2027 2877 7.830739 AGTGGGTTTTAGTTTGATGATGATTC 58.169 34.615 0.00 0.00 0.00 2.52
2029 2879 7.542130 GTGGGTTTTAGTTTGATGATGATTCAC 59.458 37.037 0.00 0.00 33.85 3.18
2135 3670 5.994250 TCCTGAAATCTCAATCTTAGGTGG 58.006 41.667 0.00 0.00 0.00 4.61
2192 3729 4.214993 AGGGGGTAGTGTATCAGCTTAT 57.785 45.455 0.00 0.00 0.00 1.73
2193 3730 4.161102 AGGGGGTAGTGTATCAGCTTATC 58.839 47.826 0.00 0.00 0.00 1.75
2198 3735 5.509840 GGGTAGTGTATCAGCTTATCTGTGG 60.510 48.000 0.00 0.00 43.32 4.17
2202 3739 5.541868 AGTGTATCAGCTTATCTGTGGCTAT 59.458 40.000 0.00 0.00 43.32 2.97
2204 3741 4.970860 ATCAGCTTATCTGTGGCTATGT 57.029 40.909 0.00 0.00 43.32 2.29
2205 3742 6.493458 TGTATCAGCTTATCTGTGGCTATGTA 59.507 38.462 0.00 0.00 43.32 2.29
2206 3743 5.869649 TCAGCTTATCTGTGGCTATGTAA 57.130 39.130 0.00 0.00 43.32 2.41
2207 3744 5.847304 TCAGCTTATCTGTGGCTATGTAAG 58.153 41.667 0.00 0.00 43.32 2.34
2208 3745 4.450419 CAGCTTATCTGTGGCTATGTAAGC 59.550 45.833 6.78 6.78 43.09 3.09
2209 3746 5.970210 CAGCTTATCTGTGGCTATGTAAGCA 60.970 44.000 14.86 0.00 44.37 3.91
2210 3747 7.402737 CAGCTTATCTGTGGCTATGTAAGCAA 61.403 42.308 14.86 0.00 44.37 3.91
2211 3748 9.106396 CAGCTTATCTGTGGCTATGTAAGCAAG 62.106 44.444 14.86 5.69 44.37 4.01
2230 3767 0.108041 GGGCATTCCTTGTTGCATGG 60.108 55.000 0.00 0.00 40.66 3.66
2275 3812 4.495844 CGTCAGTTTTCTTGTTCCACTTCC 60.496 45.833 0.00 0.00 0.00 3.46
2337 3874 8.484641 TTGCAGATGACAAATTTGTTTTTACA 57.515 26.923 24.02 16.85 42.43 2.41
2480 4027 7.360691 CCTTGTACTTGACAACATTGATCTGAG 60.361 40.741 0.00 0.00 43.30 3.35
2741 4290 2.287584 ACATGGAGGAGGAATGGGAAA 58.712 47.619 0.00 0.00 0.00 3.13
2743 4292 3.273084 ACATGGAGGAGGAATGGGAAAAT 59.727 43.478 0.00 0.00 0.00 1.82
2868 4417 7.113965 GCACATATTTTCTGGAATTAATGAGCG 59.886 37.037 0.00 0.00 0.00 5.03
2884 4433 1.321743 GAGCGTGTGCAAGTAAGATCG 59.678 52.381 0.00 0.00 46.23 3.69
2910 4459 6.875726 TGTCTTTGTTATCCTTCTGTGAGATG 59.124 38.462 0.00 0.00 0.00 2.90
2923 4472 7.067615 CCTTCTGTGAGATGTTAGTTAGCTAGA 59.932 40.741 0.00 0.00 0.00 2.43
2929 4478 6.016192 TGAGATGTTAGTTAGCTAGAATCGGG 60.016 42.308 0.00 0.00 31.54 5.14
2952 4501 1.209019 CTAGAGCCCAGTTCACATGCT 59.791 52.381 0.00 0.00 34.40 3.79
2968 4517 4.206404 CACATGCTACCGTATCTGTTTACG 59.794 45.833 0.00 6.13 43.48 3.18
3205 4881 6.003326 TGCTCTGTGAACCATTTTCTATTGA 58.997 36.000 0.00 0.00 0.00 2.57
3333 5009 4.711355 TCCCCAAGCTCAAGATTTTAATGG 59.289 41.667 0.00 0.00 0.00 3.16
3340 5016 4.949856 GCTCAAGATTTTAATGGGACTGGA 59.050 41.667 0.00 0.00 0.00 3.86
3411 5087 1.436600 CCTGTGTCAGATGTCAGTGC 58.563 55.000 0.00 0.00 32.44 4.40
3509 5185 7.341256 GCCCAAATCAAGATGATGGATATGTAT 59.659 37.037 13.72 0.00 37.15 2.29
3568 5244 5.784398 ATGGTGATCAGGCATATTATCCA 57.216 39.130 0.00 0.00 0.00 3.41
3779 5455 1.340889 GTCTGCCATTTCCACAGCAAA 59.659 47.619 0.00 0.00 34.26 3.68
3913 5589 3.202097 GGCTCTCTTAAATGCCTCAGAC 58.798 50.000 0.00 0.00 41.92 3.51
3952 5628 2.285889 TTTTGGGCCCAGTTGACGGA 62.286 55.000 26.87 4.06 0.00 4.69
4005 5681 4.846779 TTGACCAAAAGGTATGCTTCAC 57.153 40.909 0.00 0.00 0.00 3.18
4009 5685 3.004315 ACCAAAAGGTATGCTTCACAACG 59.996 43.478 0.00 0.00 0.00 4.10
4075 5754 5.755849 AGGCTAATAATTAGTTGCTGGTGT 58.244 37.500 16.57 0.00 35.66 4.16
4078 5757 6.094881 GGCTAATAATTAGTTGCTGGTGTTCA 59.905 38.462 16.57 0.00 35.66 3.18
4079 5758 6.967199 GCTAATAATTAGTTGCTGGTGTTCAC 59.033 38.462 11.25 0.00 35.66 3.18
4080 5759 5.897377 ATAATTAGTTGCTGGTGTTCACC 57.103 39.130 14.31 14.31 0.00 4.02
4081 5760 1.588674 TTAGTTGCTGGTGTTCACCG 58.411 50.000 15.82 11.85 0.00 4.94
4082 5761 0.250124 TAGTTGCTGGTGTTCACCGG 60.250 55.000 22.25 22.25 39.14 5.28
4083 5762 1.525077 GTTGCTGGTGTTCACCGGA 60.525 57.895 28.43 16.22 38.41 5.14
4084 5763 1.098712 GTTGCTGGTGTTCACCGGAA 61.099 55.000 28.43 19.05 38.41 4.30
4252 5931 3.695830 TTCTTCTTAGGCAATCGGTGT 57.304 42.857 0.00 0.00 0.00 4.16
4281 5960 4.028131 ACTGGACGACCTCACCATTTATA 58.972 43.478 5.33 0.00 37.04 0.98
4390 6069 1.304713 CCCACCTGCAATGGCTTCT 60.305 57.895 10.63 0.00 41.91 2.85
4607 6286 4.103103 TCGACGACGAGCCAGCTG 62.103 66.667 6.78 6.78 43.81 4.24
4740 6419 1.065636 GTAAGTTAAGAGCCCGCCCTT 60.066 52.381 0.00 0.00 0.00 3.95
4756 6435 1.618616 CCCTTGGGGCCGTTCTTATTT 60.619 52.381 0.00 0.00 35.35 1.40
4816 6498 2.027625 GTGGGAGCAAACGACTCGG 61.028 63.158 2.98 0.00 34.87 4.63
4888 6571 7.549488 CCTGACTTGGTGAAAGGTATAGTAAAG 59.451 40.741 0.00 0.00 40.51 1.85
4889 6572 6.877322 TGACTTGGTGAAAGGTATAGTAAAGC 59.123 38.462 0.00 0.00 40.51 3.51
4916 6602 1.548269 CTCTCGAACTGGAGAAAGCCT 59.452 52.381 0.00 0.00 42.20 4.58
5017 6703 2.092429 TGCTCAGAGTGTTTGGAAACCT 60.092 45.455 0.00 0.00 38.11 3.50
5021 6707 4.594970 TCAGAGTGTTTGGAAACCTGAAA 58.405 39.130 7.04 0.00 38.11 2.69
5106 6796 3.142838 ACCAATGCTGGATGCGGC 61.143 61.111 11.71 11.71 46.92 6.53
5107 6797 3.908081 CCAATGCTGGATGCGGCC 61.908 66.667 16.14 0.00 46.92 6.13
5134 6832 7.253422 GCTATTTATCAGTGTTGTCTGCATTT 58.747 34.615 0.00 0.00 35.63 2.32
5153 6851 5.460646 CATTTACAGCAACGGAAGATTGTT 58.539 37.500 0.00 0.00 0.00 2.83
5160 6858 4.037923 AGCAACGGAAGATTGTTGATGTTT 59.962 37.500 9.09 0.00 46.45 2.83
5194 6892 7.229106 ACAGTTTTTGCATTTAAGCATCCAATT 59.771 29.630 0.00 0.00 45.19 2.32
5217 6961 4.686191 TTTGGTTCTGTTTGATTGCCAT 57.314 36.364 0.00 0.00 0.00 4.40
5277 7025 0.237761 ACGTTGTTCCTCTCGTCTCG 59.762 55.000 0.00 0.00 30.71 4.04
5279 7027 1.725292 CGTTGTTCCTCTCGTCTCGTC 60.725 57.143 0.00 0.00 0.00 4.20
5282 7030 2.396955 TTCCTCTCGTCTCGTCGCC 61.397 63.158 0.00 0.00 0.00 5.54
5380 7150 5.450818 TCTTGCTGGAAAATATACACCCT 57.549 39.130 0.00 0.00 0.00 4.34
5462 7232 4.610605 TGAAACGTGGGTTCTCAATCTA 57.389 40.909 0.00 0.00 34.62 1.98
5466 7236 3.432378 ACGTGGGTTCTCAATCTACTCT 58.568 45.455 0.00 0.00 0.00 3.24
5467 7237 3.444388 ACGTGGGTTCTCAATCTACTCTC 59.556 47.826 0.00 0.00 0.00 3.20
5511 7281 4.518278 ACCAGGAAATGTATACATGGCA 57.482 40.909 18.94 0.00 38.76 4.92
5566 7336 8.356657 TCCAAACAGTTTTGTTCTATACATTGG 58.643 33.333 0.00 0.00 46.54 3.16
5601 7371 5.798125 TTTCTTGCCACCAATATGTTTCA 57.202 34.783 0.00 0.00 0.00 2.69
5605 7375 3.706183 TGCCACCAATATGTTTCATGGA 58.294 40.909 0.00 0.00 36.75 3.41
5609 7381 5.754890 GCCACCAATATGTTTCATGGATTTC 59.245 40.000 0.00 0.00 36.75 2.17
5726 7501 1.105167 TCGTATAGGGGTGTGGAGCG 61.105 60.000 0.00 0.00 0.00 5.03
5727 7502 1.746517 GTATAGGGGTGTGGAGCGG 59.253 63.158 0.00 0.00 0.00 5.52
5728 7503 1.047034 GTATAGGGGTGTGGAGCGGT 61.047 60.000 0.00 0.00 0.00 5.68
5729 7504 0.557238 TATAGGGGTGTGGAGCGGTA 59.443 55.000 0.00 0.00 0.00 4.02
5730 7505 0.105142 ATAGGGGTGTGGAGCGGTAT 60.105 55.000 0.00 0.00 0.00 2.73
5731 7506 0.325860 TAGGGGTGTGGAGCGGTATT 60.326 55.000 0.00 0.00 0.00 1.89
5732 7507 1.205460 AGGGGTGTGGAGCGGTATTT 61.205 55.000 0.00 0.00 0.00 1.40
5733 7508 0.323087 GGGGTGTGGAGCGGTATTTT 60.323 55.000 0.00 0.00 0.00 1.82
5734 7509 1.541379 GGGTGTGGAGCGGTATTTTT 58.459 50.000 0.00 0.00 0.00 1.94
5765 7540 8.477419 AATTTAATGTTCATATAGGGGTGTGG 57.523 34.615 0.00 0.00 0.00 4.17
5766 7541 6.833346 TTAATGTTCATATAGGGGTGTGGA 57.167 37.500 0.00 0.00 0.00 4.02
5767 7542 4.982241 ATGTTCATATAGGGGTGTGGAG 57.018 45.455 0.00 0.00 0.00 3.86
5768 7543 2.438021 TGTTCATATAGGGGTGTGGAGC 59.562 50.000 0.00 0.00 0.00 4.70
5769 7544 2.438021 GTTCATATAGGGGTGTGGAGCA 59.562 50.000 0.00 0.00 0.00 4.26
5770 7545 2.047061 TCATATAGGGGTGTGGAGCAC 58.953 52.381 0.00 0.00 46.97 4.40
5796 7580 1.135286 GTGCTACAAATCTGCTTGCCC 60.135 52.381 0.00 0.00 0.00 5.36
5822 7606 7.427214 TGTTATTTAGTTTTGGGTGCTTACAC 58.573 34.615 0.00 0.00 46.66 2.90
5893 7677 0.765510 GTCTGGAGTCCAAACCCTGT 59.234 55.000 14.17 0.00 30.80 4.00
5894 7678 0.764890 TCTGGAGTCCAAACCCTGTG 59.235 55.000 14.17 0.00 30.80 3.66
5895 7679 0.890996 CTGGAGTCCAAACCCTGTGC 60.891 60.000 14.17 0.00 30.80 4.57
5896 7680 1.150536 GGAGTCCAAACCCTGTGCA 59.849 57.895 3.60 0.00 0.00 4.57
5897 7681 0.251341 GGAGTCCAAACCCTGTGCAT 60.251 55.000 3.60 0.00 0.00 3.96
5898 7682 1.168714 GAGTCCAAACCCTGTGCATC 58.831 55.000 0.00 0.00 0.00 3.91
5899 7683 0.251341 AGTCCAAACCCTGTGCATCC 60.251 55.000 0.00 0.00 0.00 3.51
5900 7684 0.251341 GTCCAAACCCTGTGCATCCT 60.251 55.000 0.00 0.00 0.00 3.24
5901 7685 0.038166 TCCAAACCCTGTGCATCCTC 59.962 55.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.297033 GCAAGTGGAAATCCTTCTGCAA 59.703 45.455 12.37 0.00 36.82 4.08
10 11 1.740025 CCGAGCAAGTGGAAATCCTTC 59.260 52.381 0.44 0.00 36.82 3.46
18 19 0.396435 ACATTCACCGAGCAAGTGGA 59.604 50.000 1.59 0.00 35.87 4.02
20 21 1.800805 AGACATTCACCGAGCAAGTG 58.199 50.000 0.00 0.00 36.54 3.16
21 22 2.146342 CAAGACATTCACCGAGCAAGT 58.854 47.619 0.00 0.00 0.00 3.16
111 112 3.558958 GCTTCTTTCTTCTCTGCCTCCTT 60.559 47.826 0.00 0.00 0.00 3.36
115 116 1.346068 ACGCTTCTTTCTTCTCTGCCT 59.654 47.619 0.00 0.00 0.00 4.75
190 191 6.489361 TCCTACTAGTCCGATCAATACTTTCC 59.511 42.308 0.00 0.00 0.00 3.13
240 241 7.074507 ACACTACACGAAAAATTACACACAA 57.925 32.000 0.00 0.00 0.00 3.33
256 257 7.920738 AGAGAACTGATTCAAAAACACTACAC 58.079 34.615 0.00 0.00 37.29 2.90
263 264 6.888430 TCGCTAAGAGAACTGATTCAAAAAC 58.112 36.000 0.00 0.00 37.29 2.43
265 266 7.672983 ATTCGCTAAGAGAACTGATTCAAAA 57.327 32.000 0.00 0.00 37.29 2.44
266 267 8.656849 GTTATTCGCTAAGAGAACTGATTCAAA 58.343 33.333 0.00 0.00 37.29 2.69
384 386 7.127405 ACCCTCAAACTTAACTCCCTTAAAAA 58.873 34.615 0.00 0.00 0.00 1.94
385 388 6.675565 ACCCTCAAACTTAACTCCCTTAAAA 58.324 36.000 0.00 0.00 0.00 1.52
541 544 4.202141 GGCCATGCACAATGCTTATTTCTA 60.202 41.667 0.00 0.00 45.31 2.10
543 546 2.867975 GGCCATGCACAATGCTTATTTC 59.132 45.455 0.00 0.00 45.31 2.17
544 547 2.739287 CGGCCATGCACAATGCTTATTT 60.739 45.455 2.24 0.00 45.31 1.40
545 548 1.202440 CGGCCATGCACAATGCTTATT 60.202 47.619 2.24 0.00 45.31 1.40
546 549 0.386476 CGGCCATGCACAATGCTTAT 59.614 50.000 2.24 0.00 45.31 1.73
547 550 1.808546 CGGCCATGCACAATGCTTA 59.191 52.632 2.24 0.00 45.31 3.09
548 551 2.574929 CGGCCATGCACAATGCTT 59.425 55.556 2.24 0.00 45.31 3.91
549 552 4.137872 GCGGCCATGCACAATGCT 62.138 61.111 2.24 0.00 45.31 3.79
595 1131 5.529430 TCTCCAACGCAACTTCTTATTTTCA 59.471 36.000 0.00 0.00 0.00 2.69
610 1157 0.383949 TTTGTTTGCCTCTCCAACGC 59.616 50.000 0.00 0.00 0.00 4.84
614 1161 2.517959 CATCCTTTGTTTGCCTCTCCA 58.482 47.619 0.00 0.00 0.00 3.86
639 1204 4.456911 TCATTTTCCTGTGAGAATGCACTC 59.543 41.667 0.00 0.00 40.89 3.51
649 1214 2.032377 GCGTTCGTTCATTTTCCTGTGA 60.032 45.455 0.00 0.00 0.00 3.58
650 1215 2.032030 AGCGTTCGTTCATTTTCCTGTG 60.032 45.455 0.00 0.00 0.00 3.66
651 1216 2.032030 CAGCGTTCGTTCATTTTCCTGT 60.032 45.455 0.00 0.00 0.00 4.00
714 1279 8.743714 GGGATGTTTCATTTCTCTTTCTGTATT 58.256 33.333 0.00 0.00 0.00 1.89
718 1283 6.830873 AGGGATGTTTCATTTCTCTTTCTG 57.169 37.500 0.00 0.00 0.00 3.02
743 1309 9.883142 CTTGAATACAACTTCTCTATCCTCTTT 57.117 33.333 0.00 0.00 32.27 2.52
744 1310 9.041354 ACTTGAATACAACTTCTCTATCCTCTT 57.959 33.333 0.00 0.00 32.27 2.85
746 1312 9.092876 CAACTTGAATACAACTTCTCTATCCTC 57.907 37.037 0.00 0.00 32.27 3.71
748 1314 9.436957 TTCAACTTGAATACAACTTCTCTATCC 57.563 33.333 0.00 0.00 30.26 2.59
785 1357 5.842339 AGAAAATGAGGGTAATTGGGTCAT 58.158 37.500 0.00 0.00 0.00 3.06
820 1413 1.420138 TCCGTTCCAGAAGGCTCTTTT 59.580 47.619 0.00 0.00 33.74 2.27
833 1426 0.748367 GCAAATCCTCCCTCCGTTCC 60.748 60.000 0.00 0.00 0.00 3.62
838 1431 2.897350 CGCGCAAATCCTCCCTCC 60.897 66.667 8.75 0.00 0.00 4.30
839 1432 2.125106 ACGCGCAAATCCTCCCTC 60.125 61.111 5.73 0.00 0.00 4.30
841 1434 4.179579 GCACGCGCAAATCCTCCC 62.180 66.667 5.73 0.00 38.36 4.30
842 1435 4.179579 GGCACGCGCAAATCCTCC 62.180 66.667 5.73 0.00 41.24 4.30
843 1436 4.179579 GGGCACGCGCAAATCCTC 62.180 66.667 5.73 0.00 41.24 3.71
844 1437 4.722700 AGGGCACGCGCAAATCCT 62.723 61.111 5.73 5.82 41.24 3.24
845 1438 2.763627 AAAAGGGCACGCGCAAATCC 62.764 55.000 5.73 3.19 41.24 3.01
846 1439 1.344226 GAAAAGGGCACGCGCAAATC 61.344 55.000 5.73 0.00 41.24 2.17
847 1440 1.372872 GAAAAGGGCACGCGCAAAT 60.373 52.632 5.73 0.00 41.24 2.32
888 1481 4.415332 GAAGTCTCGGGCGTGCGA 62.415 66.667 0.00 0.00 0.00 5.10
889 1482 4.421479 AGAAGTCTCGGGCGTGCG 62.421 66.667 0.00 0.00 0.00 5.34
898 1491 6.935167 AGATTGGAAGAAGAAGAGAAGTCTC 58.065 40.000 0.00 0.00 43.17 3.36
899 1492 6.933514 AGATTGGAAGAAGAAGAGAAGTCT 57.066 37.500 0.00 0.00 32.81 3.24
905 1498 5.189539 AGGAGGAAGATTGGAAGAAGAAGAG 59.810 44.000 0.00 0.00 0.00 2.85
934 1527 2.283529 TGGGGAACACGAGAGAGGC 61.284 63.158 0.00 0.00 0.00 4.70
943 1536 0.752376 TTTGGTTCGGTGGGGAACAC 60.752 55.000 7.62 0.00 46.34 3.32
944 1537 0.752376 GTTTGGTTCGGTGGGGAACA 60.752 55.000 7.62 0.00 46.34 3.18
955 1558 0.321298 TGCGAGCTAGGGTTTGGTTC 60.321 55.000 0.00 0.00 0.00 3.62
969 1572 4.247380 GGGGCTGGGATCTGCGAG 62.247 72.222 0.00 0.00 38.51 5.03
1001 1625 1.525535 CGGTCGGTCGATCTAGGGT 60.526 63.158 2.11 0.00 0.00 4.34
1013 1637 4.247612 GATCGGTCGGTCGGTCGG 62.248 72.222 0.00 0.00 30.36 4.79
1031 1655 4.955089 GAGCTCATCGGATCCGTC 57.045 61.111 32.15 18.19 40.74 4.79
1124 1748 1.734748 GCGCAGGTAGTAGGAGACC 59.265 63.158 0.30 0.00 35.83 3.85
1409 2033 0.466124 CGAGGGTCTTCTTCATCCCC 59.534 60.000 0.00 0.00 40.70 4.81
1532 2156 1.957113 GCAACAAGAGGAGATTGGGGG 60.957 57.143 0.00 0.00 31.76 5.40
1533 2157 1.467920 GCAACAAGAGGAGATTGGGG 58.532 55.000 0.00 0.00 31.76 4.96
1534 2158 1.467920 GGCAACAAGAGGAGATTGGG 58.532 55.000 0.00 0.00 31.76 4.12
1535 2159 1.089920 CGGCAACAAGAGGAGATTGG 58.910 55.000 0.00 0.00 31.76 3.16
1536 2160 0.449388 GCGGCAACAAGAGGAGATTG 59.551 55.000 0.00 0.00 0.00 2.67
1537 2161 0.326264 AGCGGCAACAAGAGGAGATT 59.674 50.000 1.45 0.00 0.00 2.40
1538 2162 0.392193 CAGCGGCAACAAGAGGAGAT 60.392 55.000 1.45 0.00 0.00 2.75
1539 2163 1.004560 CAGCGGCAACAAGAGGAGA 60.005 57.895 1.45 0.00 0.00 3.71
1540 2164 2.684843 GCAGCGGCAACAAGAGGAG 61.685 63.158 3.18 0.00 40.72 3.69
1541 2165 1.826340 TAGCAGCGGCAACAAGAGGA 61.826 55.000 12.44 0.00 44.61 3.71
1542 2166 0.955428 TTAGCAGCGGCAACAAGAGG 60.955 55.000 12.44 0.00 44.61 3.69
1543 2167 0.445436 CTTAGCAGCGGCAACAAGAG 59.555 55.000 12.44 0.00 44.61 2.85
1544 2168 0.250295 ACTTAGCAGCGGCAACAAGA 60.250 50.000 19.20 0.00 44.61 3.02
1545 2169 0.593128 AACTTAGCAGCGGCAACAAG 59.407 50.000 12.44 13.07 44.61 3.16
1546 2170 1.028905 AAACTTAGCAGCGGCAACAA 58.971 45.000 12.44 0.98 44.61 2.83
1547 2171 0.310543 CAAACTTAGCAGCGGCAACA 59.689 50.000 12.44 0.00 44.61 3.33
1548 2172 0.310854 ACAAACTTAGCAGCGGCAAC 59.689 50.000 12.44 0.00 44.61 4.17
1549 2173 1.028905 AACAAACTTAGCAGCGGCAA 58.971 45.000 12.44 2.66 44.61 4.52
1550 2174 0.310543 CAACAAACTTAGCAGCGGCA 59.689 50.000 12.44 0.00 44.61 5.69
1551 2175 0.310854 ACAACAAACTTAGCAGCGGC 59.689 50.000 0.00 0.00 41.61 6.53
1552 2176 1.601903 TGACAACAAACTTAGCAGCGG 59.398 47.619 0.00 0.00 0.00 5.52
1553 2177 3.228749 CATGACAACAAACTTAGCAGCG 58.771 45.455 0.00 0.00 0.00 5.18
1554 2178 2.982470 GCATGACAACAAACTTAGCAGC 59.018 45.455 0.00 0.00 0.00 5.25
1555 2179 4.224433 CTGCATGACAACAAACTTAGCAG 58.776 43.478 0.00 0.00 40.57 4.24
1556 2180 3.550639 GCTGCATGACAACAAACTTAGCA 60.551 43.478 0.00 0.00 0.00 3.49
1557 2181 2.982470 GCTGCATGACAACAAACTTAGC 59.018 45.455 0.00 0.00 0.00 3.09
1558 2182 3.568538 GGCTGCATGACAACAAACTTAG 58.431 45.455 0.50 0.00 0.00 2.18
1559 2183 2.295909 GGGCTGCATGACAACAAACTTA 59.704 45.455 0.50 0.00 0.00 2.24
1560 2184 1.069049 GGGCTGCATGACAACAAACTT 59.931 47.619 0.50 0.00 0.00 2.66
1561 2185 0.675633 GGGCTGCATGACAACAAACT 59.324 50.000 0.50 0.00 0.00 2.66
1562 2186 0.675633 AGGGCTGCATGACAACAAAC 59.324 50.000 0.50 0.00 0.00 2.93
1563 2187 0.675083 CAGGGCTGCATGACAACAAA 59.325 50.000 0.50 0.00 0.00 2.83
1564 2188 0.467844 ACAGGGCTGCATGACAACAA 60.468 50.000 10.56 0.00 0.00 2.83
1565 2189 0.890542 GACAGGGCTGCATGACAACA 60.891 55.000 10.56 0.00 0.00 3.33
1566 2190 0.607489 AGACAGGGCTGCATGACAAC 60.607 55.000 10.56 0.00 0.00 3.32
1567 2191 0.607217 CAGACAGGGCTGCATGACAA 60.607 55.000 10.56 0.00 0.00 3.18
1568 2192 1.002990 CAGACAGGGCTGCATGACA 60.003 57.895 10.56 0.00 0.00 3.58
1569 2193 0.743701 CTCAGACAGGGCTGCATGAC 60.744 60.000 10.56 5.05 35.86 3.06
1570 2194 1.600638 CTCAGACAGGGCTGCATGA 59.399 57.895 10.56 0.00 35.86 3.07
1571 2195 1.451567 CCTCAGACAGGGCTGCATG 60.452 63.158 0.50 1.94 38.91 4.06
1572 2196 0.987081 ATCCTCAGACAGGGCTGCAT 60.987 55.000 0.50 0.00 43.67 3.96
1573 2197 1.614525 ATCCTCAGACAGGGCTGCA 60.615 57.895 0.50 0.00 43.67 4.41
1574 2198 1.153208 CATCCTCAGACAGGGCTGC 60.153 63.158 0.00 0.00 43.67 5.25
1575 2199 0.907486 TTCATCCTCAGACAGGGCTG 59.093 55.000 0.00 0.00 43.67 4.85
1599 2445 5.246307 ACCCACTCTAGCAAGTAAATCAAC 58.754 41.667 0.00 0.00 0.00 3.18
1707 2557 2.806244 AGGCTACAGCAAACTTAACACG 59.194 45.455 3.24 0.00 44.36 4.49
1735 2585 6.536582 AGACTATCAAATTCAGTGTGGATTCG 59.463 38.462 0.00 0.00 0.00 3.34
1755 2605 5.922053 TCATCGCTACTAACACCTAGACTA 58.078 41.667 0.00 0.00 0.00 2.59
1761 2611 3.014304 TCCTCATCGCTACTAACACCT 57.986 47.619 0.00 0.00 0.00 4.00
1774 2624 6.647334 TGAGATAGACAGTTCATCCTCATC 57.353 41.667 0.00 0.00 0.00 2.92
1784 2634 6.773638 ACCAAGATTGTTGAGATAGACAGTT 58.226 36.000 0.00 0.00 0.00 3.16
1793 2643 7.174946 GGTCAAGAATTACCAAGATTGTTGAGA 59.825 37.037 8.94 0.00 43.21 3.27
1797 2647 7.004086 TCTGGTCAAGAATTACCAAGATTGTT 58.996 34.615 0.00 0.00 44.92 2.83
1799 2649 7.452880 TTCTGGTCAAGAATTACCAAGATTG 57.547 36.000 0.00 0.00 44.92 2.67
1806 2656 4.762251 ACAAGCTTCTGGTCAAGAATTACC 59.238 41.667 0.00 0.00 44.02 2.85
1825 2675 1.938814 CGCACGGCACAAACACAAG 60.939 57.895 0.00 0.00 0.00 3.16
1858 2708 5.958380 AGGTCCATCCTCATCGCTAATATTA 59.042 40.000 0.00 0.00 44.42 0.98
1867 2717 3.678252 GCATATCAGGTCCATCCTCATCG 60.678 52.174 0.00 0.00 46.24 3.84
1954 2804 6.183360 CCTCTGAAAAACACAATCTTCTGGTT 60.183 38.462 0.00 0.00 0.00 3.67
1963 2813 5.420104 GGATCCATCCTCTGAAAAACACAAT 59.580 40.000 6.95 0.00 43.73 2.71
1987 2837 4.156455 ACCCACTCTGGCAATTATACAG 57.844 45.455 0.00 0.00 35.79 2.74
2023 2873 7.825681 TGCAAGATAGAGCTAGATAGTGAATC 58.174 38.462 0.00 0.00 34.52 2.52
2024 2874 7.773489 TGCAAGATAGAGCTAGATAGTGAAT 57.227 36.000 0.00 0.00 0.00 2.57
2025 2875 7.309683 CCATGCAAGATAGAGCTAGATAGTGAA 60.310 40.741 0.00 0.00 0.00 3.18
2026 2876 6.152492 CCATGCAAGATAGAGCTAGATAGTGA 59.848 42.308 0.00 0.00 0.00 3.41
2027 2877 6.152492 TCCATGCAAGATAGAGCTAGATAGTG 59.848 42.308 0.00 0.00 0.00 2.74
2029 2879 6.377996 ACTCCATGCAAGATAGAGCTAGATAG 59.622 42.308 0.00 0.00 0.00 2.08
2135 3670 5.306678 AGATGATGATTTAGTGAGGGGTCTC 59.693 44.000 0.00 0.00 40.36 3.36
2170 3705 2.570386 AGCTGATACACTACCCCCTT 57.430 50.000 0.00 0.00 0.00 3.95
2182 3717 7.792174 GCTTACATAGCCACAGATAAGCTGATA 60.792 40.741 0.00 0.00 44.76 2.15
2185 3722 4.450419 GCTTACATAGCCACAGATAAGCTG 59.550 45.833 6.56 0.00 46.13 4.24
2198 3735 4.000453 AGGAATGCCCTTGCTTACATAGC 61.000 47.826 0.00 0.00 44.85 2.97
2211 3748 0.108041 CCATGCAACAAGGAATGCCC 60.108 55.000 0.00 0.00 41.87 5.36
2212 3749 0.896923 TCCATGCAACAAGGAATGCC 59.103 50.000 0.00 0.00 41.87 4.40
2213 3750 2.028748 ACTTCCATGCAACAAGGAATGC 60.029 45.455 11.96 0.00 39.87 3.56
2214 3751 3.006110 ACACTTCCATGCAACAAGGAATG 59.994 43.478 11.96 13.27 39.87 2.67
2215 3752 3.233507 ACACTTCCATGCAACAAGGAAT 58.766 40.909 11.96 3.25 39.87 3.01
2216 3753 2.665165 ACACTTCCATGCAACAAGGAA 58.335 42.857 11.29 11.29 38.63 3.36
2230 3767 3.997681 GCAAAAGACCTCCTCTACACTTC 59.002 47.826 0.00 0.00 0.00 3.01
2275 3812 9.283420 CTTCATTATGATACTACTGATGCTACG 57.717 37.037 0.00 0.00 0.00 3.51
2337 3874 4.326826 CATGTTCCGAGCCATATAACCAT 58.673 43.478 0.00 0.00 0.00 3.55
2344 3881 2.016318 CAAAGCATGTTCCGAGCCATA 58.984 47.619 0.00 0.00 0.00 2.74
2429 3968 7.764443 GGAATATGTGCAGTGAGTTAAAGTAGA 59.236 37.037 0.00 0.00 0.00 2.59
2436 3975 5.804639 ACAAGGAATATGTGCAGTGAGTTA 58.195 37.500 0.00 0.00 0.00 2.24
2741 4290 6.978674 ATTCTCAATTGCATCATCCTCATT 57.021 33.333 0.00 0.00 0.00 2.57
2743 4292 6.261603 GTGTATTCTCAATTGCATCATCCTCA 59.738 38.462 0.00 0.00 0.00 3.86
2827 4376 7.414222 AAATATGTGCTCATCTTCCACATTT 57.586 32.000 4.19 1.62 45.11 2.32
2868 4417 3.318017 AGACACGATCTTACTTGCACAC 58.682 45.455 0.00 0.00 31.62 3.82
2884 4433 6.223852 TCTCACAGAAGGATAACAAAGACAC 58.776 40.000 0.00 0.00 0.00 3.67
2910 4459 6.146601 AGTTCCCGATTCTAGCTAACTAAC 57.853 41.667 0.00 0.00 0.00 2.34
2923 4472 1.123928 CTGGGCTCTAGTTCCCGATT 58.876 55.000 14.41 0.00 45.60 3.34
2952 4501 3.266636 TCGGTCGTAAACAGATACGGTA 58.733 45.455 6.97 0.00 46.52 4.02
2968 4517 8.739649 ATTAGCTAAACTATTATCGTTCGGTC 57.260 34.615 10.85 0.00 0.00 4.79
3333 5009 2.843701 CATAGCTGACCATTCCAGTCC 58.156 52.381 0.00 0.00 34.29 3.85
3509 5185 0.695462 ATGATAGGGCCAGCCTGACA 60.695 55.000 6.18 4.94 36.10 3.58
3568 5244 7.827236 TGGTTTCGATTACCATAAGTTCTCATT 59.173 33.333 14.10 0.00 40.65 2.57
3779 5455 3.195002 CGGCGCGTTGTCATCCAT 61.195 61.111 8.43 0.00 0.00 3.41
3913 5589 7.538678 CCCAAAAGATCTAAACTGAAATCGTTG 59.461 37.037 0.00 0.00 0.00 4.10
3952 5628 4.880696 GCTGCTGGAAGTTGAGAATTAGAT 59.119 41.667 0.00 0.00 35.30 1.98
4005 5681 6.839820 AGTAAGAGAAACTTGTTACCGTTG 57.160 37.500 0.00 0.00 39.38 4.10
4081 5760 3.937079 CCATAGGTAAACACGGAAGTTCC 59.063 47.826 12.27 12.27 46.40 3.62
4082 5761 4.390909 CACCATAGGTAAACACGGAAGTTC 59.609 45.833 0.00 0.00 36.54 3.01
4083 5762 4.320870 CACCATAGGTAAACACGGAAGTT 58.679 43.478 0.00 0.00 36.54 2.66
4084 5763 3.867216 GCACCATAGGTAAACACGGAAGT 60.867 47.826 0.00 0.00 38.87 3.01
4085 5764 2.676342 GCACCATAGGTAAACACGGAAG 59.324 50.000 0.00 0.00 32.11 3.46
4086 5765 2.303600 AGCACCATAGGTAAACACGGAA 59.696 45.455 0.00 0.00 32.11 4.30
4087 5766 1.903860 AGCACCATAGGTAAACACGGA 59.096 47.619 0.00 0.00 32.11 4.69
4088 5767 2.396590 AGCACCATAGGTAAACACGG 57.603 50.000 0.00 0.00 32.11 4.94
4089 5768 4.119442 AGTAGCACCATAGGTAAACACG 57.881 45.455 0.00 0.00 32.11 4.49
4090 5769 5.731591 AGAAGTAGCACCATAGGTAAACAC 58.268 41.667 0.00 0.00 32.11 3.32
4091 5770 5.720041 AGAGAAGTAGCACCATAGGTAAACA 59.280 40.000 0.00 0.00 32.11 2.83
4092 5771 6.043411 CAGAGAAGTAGCACCATAGGTAAAC 58.957 44.000 0.00 0.00 32.11 2.01
4093 5772 5.395324 GCAGAGAAGTAGCACCATAGGTAAA 60.395 44.000 0.00 0.00 32.11 2.01
4094 5773 4.099573 GCAGAGAAGTAGCACCATAGGTAA 59.900 45.833 0.00 0.00 32.11 2.85
4095 5774 3.637229 GCAGAGAAGTAGCACCATAGGTA 59.363 47.826 0.00 0.00 32.11 3.08
4252 5931 2.751259 GTGAGGTCGTCCAGTGTGTATA 59.249 50.000 0.51 0.00 35.89 1.47
4281 5960 7.271511 TGGAGCAACAAAATACACAGAATTTT 58.728 30.769 0.00 0.00 37.08 1.82
4390 6069 0.893270 CTGTGGTTGGCGGGAATTCA 60.893 55.000 7.93 0.00 0.00 2.57
4433 6112 1.751924 GACACGAATCTGACTAGGCCT 59.248 52.381 11.78 11.78 0.00 5.19
4606 6285 2.342279 GTGCTCACCCGTGTAGCA 59.658 61.111 14.10 14.10 39.53 3.49
4607 6286 2.434359 GGTGCTCACCCGTGTAGC 60.434 66.667 7.82 10.47 45.68 3.58
4651 6330 2.168728 GGCCGAGACAAAGAAGAGGTAT 59.831 50.000 0.00 0.00 0.00 2.73
4740 6419 1.203075 ACCAAAATAAGAACGGCCCCA 60.203 47.619 0.00 0.00 0.00 4.96
4756 6435 5.120399 CCATGTATAGTTCCGCTAAACCAA 58.880 41.667 0.00 0.00 32.72 3.67
4816 6498 6.712549 AGTGCGTAAAAGTAAAACTGTCTTC 58.287 36.000 0.00 0.00 0.00 2.87
4888 6571 2.863137 CTCCAGTTCGAGAGCTTATTGC 59.137 50.000 0.00 0.00 43.29 3.56
4889 6572 4.377839 TCTCCAGTTCGAGAGCTTATTG 57.622 45.455 0.00 0.00 33.91 1.90
5104 6794 2.256117 ACACTGATAAATAGCCGGCC 57.744 50.000 26.15 6.18 0.00 6.13
5106 6796 4.271049 CAGACAACACTGATAAATAGCCGG 59.729 45.833 0.00 0.00 39.94 6.13
5107 6797 4.260375 GCAGACAACACTGATAAATAGCCG 60.260 45.833 0.00 0.00 39.94 5.52
5112 6802 8.109705 TGTAAATGCAGACAACACTGATAAAT 57.890 30.769 0.00 0.00 39.94 1.40
5134 6832 3.734463 TCAACAATCTTCCGTTGCTGTA 58.266 40.909 0.00 0.00 41.80 2.74
5153 6851 6.922957 GCAAAAACTGTTATCCAGAAACATCA 59.077 34.615 0.00 0.00 44.49 3.07
5160 6858 7.598493 GCTTAAATGCAAAAACTGTTATCCAGA 59.402 33.333 0.00 0.00 44.49 3.86
5194 6892 4.836825 TGGCAATCAAACAGAACCAAAAA 58.163 34.783 0.00 0.00 0.00 1.94
5217 6961 1.371467 TTCCCTCTTCCATGGCTTCA 58.629 50.000 6.96 0.00 0.00 3.02
5282 7030 2.026449 AGGAGCAATGGACTCAAAGGAG 60.026 50.000 0.00 0.00 46.96 3.69
5337 7086 2.550830 ATGACCTACATCGGCAATCC 57.449 50.000 0.00 0.00 33.46 3.01
5410 7180 9.506018 CCCAAATGTTAGATTCTTTCCATTTTT 57.494 29.630 11.85 0.00 32.00 1.94
5411 7181 8.102676 CCCCAAATGTTAGATTCTTTCCATTTT 58.897 33.333 11.85 0.00 32.00 1.82
5412 7182 7.457535 TCCCCAAATGTTAGATTCTTTCCATTT 59.542 33.333 9.98 9.98 33.97 2.32
5413 7183 6.959366 TCCCCAAATGTTAGATTCTTTCCATT 59.041 34.615 0.00 0.00 0.00 3.16
5414 7184 6.502138 TCCCCAAATGTTAGATTCTTTCCAT 58.498 36.000 0.00 0.00 0.00 3.41
5416 7186 8.579863 CATATCCCCAAATGTTAGATTCTTTCC 58.420 37.037 0.00 0.00 0.00 3.13
5417 7187 9.354673 TCATATCCCCAAATGTTAGATTCTTTC 57.645 33.333 0.00 0.00 0.00 2.62
5429 7199 3.068024 CCCACGTTTCATATCCCCAAATG 59.932 47.826 0.00 0.00 0.00 2.32
5488 7258 6.199557 TGCCATGTATACATTTCCTGGTAT 57.800 37.500 15.85 0.00 33.61 2.73
5499 7269 8.532186 ACAATATTTCCTTTGCCATGTATACA 57.468 30.769 8.27 8.27 0.00 2.29
5504 7274 4.142182 CGGACAATATTTCCTTTGCCATGT 60.142 41.667 12.12 0.00 0.00 3.21
5506 7276 4.277476 TCGGACAATATTTCCTTTGCCAT 58.723 39.130 12.12 0.00 0.00 4.40
5511 7281 9.203421 GATTTTTGTTCGGACAATATTTCCTTT 57.797 29.630 10.76 0.00 44.71 3.11
5579 7349 5.798125 TGAAACATATTGGTGGCAAGAAA 57.202 34.783 0.00 0.00 0.00 2.52
5582 7352 4.160065 TCCATGAAACATATTGGTGGCAAG 59.840 41.667 0.00 0.00 0.00 4.01
5609 7381 8.717821 TCTACTTCCATGTGAAATTTCGTTAAG 58.282 33.333 13.34 11.93 31.06 1.85
5620 7392 3.132289 GTCCCGATCTACTTCCATGTGAA 59.868 47.826 0.00 0.00 0.00 3.18
5626 7398 0.398098 GGGGTCCCGATCTACTTCCA 60.398 60.000 0.48 0.00 0.00 3.53
5696 7471 7.716123 CCACACCCCTATACGAACATTAAATTA 59.284 37.037 0.00 0.00 0.00 1.40
5714 7489 0.323087 AAAATACCGCTCCACACCCC 60.323 55.000 0.00 0.00 0.00 4.95
5739 7514 8.923270 CCACACCCCTATATGAACATTAAATTT 58.077 33.333 0.00 0.00 0.00 1.82
5740 7515 8.285891 TCCACACCCCTATATGAACATTAAATT 58.714 33.333 0.00 0.00 0.00 1.82
5741 7516 7.821566 TCCACACCCCTATATGAACATTAAAT 58.178 34.615 0.00 0.00 0.00 1.40
5742 7517 7.214460 TCCACACCCCTATATGAACATTAAA 57.786 36.000 0.00 0.00 0.00 1.52
5743 7518 6.690460 GCTCCACACCCCTATATGAACATTAA 60.690 42.308 0.00 0.00 0.00 1.40
5744 7519 5.221843 GCTCCACACCCCTATATGAACATTA 60.222 44.000 0.00 0.00 0.00 1.90
5745 7520 4.446311 GCTCCACACCCCTATATGAACATT 60.446 45.833 0.00 0.00 0.00 2.71
5746 7521 3.073062 GCTCCACACCCCTATATGAACAT 59.927 47.826 0.00 0.00 0.00 2.71
5747 7522 2.438021 GCTCCACACCCCTATATGAACA 59.562 50.000 0.00 0.00 0.00 3.18
5748 7523 2.438021 TGCTCCACACCCCTATATGAAC 59.562 50.000 0.00 0.00 0.00 3.18
5749 7524 2.438021 GTGCTCCACACCCCTATATGAA 59.562 50.000 0.00 0.00 44.02 2.57
5750 7525 2.047061 GTGCTCCACACCCCTATATGA 58.953 52.381 0.00 0.00 44.02 2.15
5751 7526 2.550830 GTGCTCCACACCCCTATATG 57.449 55.000 0.00 0.00 44.02 1.78
5769 7544 1.205460 AGATTTGTAGCACCCGGGGT 61.205 55.000 27.92 14.51 35.62 4.95
5770 7545 0.748005 CAGATTTGTAGCACCCGGGG 60.748 60.000 27.92 12.73 0.00 5.73
5796 7580 7.593644 GTGTAAGCACCCAAAACTAAATAACAG 59.406 37.037 0.00 0.00 39.61 3.16
5822 7606 2.031333 GCAGGAAGAACTTGAGCTGTTG 60.031 50.000 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.