Multiple sequence alignment - TraesCS7D01G043500

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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 TraesCS7D01G043500 chr7D 100.000 2795 0 0 1 2795 22510756 22507962 0.000000e+00 5162.0
1 TraesCS7D01G043500 chr7D 90.111 991 56 16 760 1726 22270429 22269457 0.000000e+00 1249.0
2 TraesCS7D01G043500 chr7D 88.170 989 81 19 760 1726 22523176 22522202 0.000000e+00 1146.0
3 TraesCS7D01G043500 chr7D 86.559 558 41 9 1722 2248 22522247 22521693 4.010000e-163 584.0
4 TraesCS7D01G043500 chr7D 78.404 727 85 32 59 748 22271591 22270900 9.320000e-110 407.0
5 TraesCS7D01G043500 chr7D 81.230 309 24 10 1663 1945 22269557 22269257 4.690000e-53 219.0
6 TraesCS7D01G043500 chr7D 93.651 63 4 0 1 63 213380299 213380237 8.240000e-16 95.3
7 TraesCS7D01G043500 chr7A 89.474 1520 90 29 761 2260 22916649 22915180 0.000000e+00 1857.0
8 TraesCS7D01G043500 chr7A 89.836 974 51 12 760 1726 22898543 22897611 0.000000e+00 1206.0
9 TraesCS7D01G043500 chr7A 78.175 559 71 25 1718 2237 22897660 22897114 2.700000e-80 309.0
10 TraesCS7D01G043500 chr7A 92.157 51 3 1 1676 1726 22915727 22915678 1.390000e-08 71.3
11 TraesCS7D01G043500 chr4A 87.583 1208 67 25 547 1726 705055531 705054379 0.000000e+00 1323.0
12 TraesCS7D01G043500 chr4A 87.604 1202 65 23 547 1726 704808258 704807119 0.000000e+00 1317.0
13 TraesCS7D01G043500 chr4A 86.996 992 82 22 760 1726 705170665 705169696 0.000000e+00 1074.0
14 TraesCS7D01G043500 chr4A 84.021 388 49 7 1718 2102 705169745 705169368 7.360000e-96 361.0
15 TraesCS7D01G043500 chr4A 88.318 214 17 5 1736 1945 704807150 704806941 1.660000e-62 250.0
16 TraesCS7D01G043500 chr4A 89.630 135 14 0 1968 2102 705054046 705053912 3.700000e-39 172.0
17 TraesCS7D01G043500 chr4A 92.857 70 4 1 2726 2795 705052768 705052700 1.770000e-17 100.0
18 TraesCS7D01G043500 chr4A 91.429 70 5 1 2726 2795 705168189 705168121 8.240000e-16 95.3
19 TraesCS7D01G043500 chr4A 85.915 71 9 1 2182 2252 704806163 704806094 1.070000e-09 75.0
20 TraesCS7D01G043500 chr4A 82.609 92 9 7 2050 2139 704806443 704806357 1.070000e-09 75.0
21 TraesCS7D01G043500 chr5B 90.060 503 39 2 966 1466 469337832 469338325 2.350000e-180 641.0
22 TraesCS7D01G043500 chr5B 96.429 56 2 0 1 56 122835851 122835906 2.960000e-15 93.5
23 TraesCS7D01G043500 chr5B 93.548 62 4 0 1 62 551541220 551541281 2.960000e-15 93.5
24 TraesCS7D01G043500 chr6B 87.665 227 19 4 1099 1325 138522219 138522436 3.570000e-64 255.0
25 TraesCS7D01G043500 chr6B 81.124 249 22 15 1718 1945 138522478 138522722 2.860000e-40 176.0
26 TraesCS7D01G043500 chr6B 88.000 75 6 3 5 78 405863411 405863339 4.960000e-13 86.1
27 TraesCS7D01G043500 chr5D 80.498 241 38 8 196 432 315683896 315684131 2.860000e-40 176.0
28 TraesCS7D01G043500 chr1D 75.595 336 57 15 121 438 487885274 487884946 2.900000e-30 143.0
29 TraesCS7D01G043500 chr7B 76.604 265 47 12 197 456 734690917 734690663 6.280000e-27 132.0
30 TraesCS7D01G043500 chr1A 98.361 61 1 0 1473 1533 27383214 27383154 1.060000e-19 108.0
31 TraesCS7D01G043500 chr1A 96.721 61 2 0 1473 1533 442726932 442726872 4.930000e-18 102.0
32 TraesCS7D01G043500 chr4B 77.841 176 30 7 196 368 568713653 568713484 1.770000e-17 100.0
33 TraesCS7D01G043500 chr4D 96.552 58 2 0 1 58 182067030 182067087 2.290000e-16 97.1
34 TraesCS7D01G043500 chr4D 93.548 62 4 0 1 62 404108688 404108749 2.960000e-15 93.5
35 TraesCS7D01G043500 chr3A 95.082 61 3 0 1 61 641872893 641872953 2.290000e-16 97.1
36 TraesCS7D01G043500 chr3A 95.082 61 2 1 1 61 108026725 108026666 8.240000e-16 95.3
37 TraesCS7D01G043500 chr1B 93.846 65 3 1 1 64 146571502 146571438 2.290000e-16 97.1


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 TraesCS7D01G043500 chr7D 22507962 22510756 2794 True 5162.000000 5162 100.000000 1 2795 1 chr7D.!!$R1 2794
1 TraesCS7D01G043500 chr7D 22521693 22523176 1483 True 865.000000 1146 87.364500 760 2248 2 chr7D.!!$R4 1488
2 TraesCS7D01G043500 chr7D 22269257 22271591 2334 True 625.000000 1249 83.248333 59 1945 3 chr7D.!!$R3 1886
3 TraesCS7D01G043500 chr7A 22915180 22916649 1469 True 964.150000 1857 90.815500 761 2260 2 chr7A.!!$R2 1499
4 TraesCS7D01G043500 chr7A 22897114 22898543 1429 True 757.500000 1206 84.005500 760 2237 2 chr7A.!!$R1 1477
5 TraesCS7D01G043500 chr4A 705052700 705055531 2831 True 531.666667 1323 90.023333 547 2795 3 chr4A.!!$R2 2248
6 TraesCS7D01G043500 chr4A 705168121 705170665 2544 True 510.100000 1074 87.482000 760 2795 3 chr4A.!!$R3 2035
7 TraesCS7D01G043500 chr4A 704806094 704808258 2164 True 429.250000 1317 86.111500 547 2252 4 chr4A.!!$R1 1705
8 TraesCS7D01G043500 chr6B 138522219 138522722 503 False 215.500000 255 84.394500 1099 1945 2 chr6B.!!$F1 846

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
441 459 0.175989 TCATATGCCCGTGCGTGTAA 59.824 50.0 0.0 0.0 41.78 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2331 4371 0.036765 TTGTCCGGATCCACGAAAGG 60.037 55.0 7.81 3.47 35.47 3.11 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
49 50 8.904099 AAAAGACAAATATATAGGAACGGAGG 57.096 34.615 0.00 0.00 0.00 4.30
50 51 6.607004 AGACAAATATATAGGAACGGAGGG 57.393 41.667 0.00 0.00 0.00 4.30
51 52 6.320518 AGACAAATATATAGGAACGGAGGGA 58.679 40.000 0.00 0.00 0.00 4.20
52 53 6.437793 AGACAAATATATAGGAACGGAGGGAG 59.562 42.308 0.00 0.00 0.00 4.30
53 54 6.082707 ACAAATATATAGGAACGGAGGGAGT 58.917 40.000 0.00 0.00 0.00 3.85
54 55 7.243824 ACAAATATATAGGAACGGAGGGAGTA 58.756 38.462 0.00 0.00 0.00 2.59
55 56 7.178097 ACAAATATATAGGAACGGAGGGAGTAC 59.822 40.741 0.00 0.00 0.00 2.73
56 57 4.736611 ATATAGGAACGGAGGGAGTACA 57.263 45.455 0.00 0.00 0.00 2.90
57 58 2.905415 TAGGAACGGAGGGAGTACAA 57.095 50.000 0.00 0.00 0.00 2.41
69 70 2.024751 GGGAGTACAATTTAGGGGCCAA 60.025 50.000 4.39 0.00 0.00 4.52
71 72 4.141111 GGGAGTACAATTTAGGGGCCAATA 60.141 45.833 4.39 0.00 0.00 1.90
86 87 3.561725 GGCCAATATAGTGAGAAGTGCAC 59.438 47.826 9.40 9.40 36.53 4.57
87 88 3.246226 GCCAATATAGTGAGAAGTGCACG 59.754 47.826 12.01 0.00 41.04 5.34
90 91 2.656560 ATAGTGAGAAGTGCACGGAC 57.343 50.000 12.01 7.02 41.04 4.79
92 93 2.022129 GTGAGAAGTGCACGGACGG 61.022 63.158 12.01 0.00 0.00 4.79
94 95 1.733399 GAGAAGTGCACGGACGGAC 60.733 63.158 12.01 0.00 0.00 4.79
95 96 2.737376 GAAGTGCACGGACGGACC 60.737 66.667 12.01 0.00 0.00 4.46
99 100 2.680707 TGCACGGACGGACCCATA 60.681 61.111 0.00 0.00 34.64 2.74
102 103 3.152400 ACGGACGGACCCATAGGC 61.152 66.667 0.00 0.00 36.11 3.93
109 110 1.902508 ACGGACCCATAGGCATATGAG 59.097 52.381 19.55 9.20 41.22 2.90
126 127 6.518493 CATATGAGCCCACATTTTAAAGCAT 58.482 36.000 0.00 0.00 0.00 3.79
177 178 2.028658 AGTCTCACACGCACATCTTCAT 60.029 45.455 0.00 0.00 0.00 2.57
191 192 6.587651 CACATCTTCATATTCTATGTGCACG 58.412 40.000 13.13 0.00 40.48 5.34
192 193 6.201615 CACATCTTCATATTCTATGTGCACGT 59.798 38.462 17.19 17.19 40.48 4.49
193 194 6.201615 ACATCTTCATATTCTATGTGCACGTG 59.798 38.462 21.92 12.28 29.93 4.49
273 291 6.917533 ACTCATTTTAGAAGCACTGGAATTG 58.082 36.000 0.00 0.00 0.00 2.32
274 292 6.491403 ACTCATTTTAGAAGCACTGGAATTGT 59.509 34.615 0.00 0.00 0.00 2.71
275 293 7.014615 ACTCATTTTAGAAGCACTGGAATTGTT 59.985 33.333 0.00 0.00 0.00 2.83
277 295 9.023962 TCATTTTAGAAGCACTGGAATTGTTAT 57.976 29.630 0.00 0.00 0.00 1.89
281 299 9.474920 TTTAGAAGCACTGGAATTGTTATTTTG 57.525 29.630 0.00 0.00 0.00 2.44
285 303 4.804108 CACTGGAATTGTTATTTTGGCGA 58.196 39.130 0.00 0.00 0.00 5.54
340 358 2.790586 TGCCGCGCACACATATTG 59.209 55.556 8.75 0.00 31.71 1.90
354 372 4.579454 ACATATTGTGAAGATGCATGCC 57.421 40.909 16.68 0.00 33.51 4.40
368 386 6.938507 AGATGCATGCCTGAAATTTTCTTTA 58.061 32.000 16.68 0.00 0.00 1.85
370 388 6.100404 TGCATGCCTGAAATTTTCTTTAGT 57.900 33.333 16.68 0.00 0.00 2.24
373 391 8.965819 TGCATGCCTGAAATTTTCTTTAGTATA 58.034 29.630 16.68 0.00 0.00 1.47
401 419 9.493206 TTTTGACATTTAAAACGTGTCTAGAAC 57.507 29.630 17.12 0.00 42.03 3.01
403 421 6.696583 TGACATTTAAAACGTGTCTAGAACGA 59.303 34.615 24.46 9.28 43.68 3.85
405 423 8.080083 ACATTTAAAACGTGTCTAGAACGAAT 57.920 30.769 24.46 14.73 43.68 3.34
441 459 0.175989 TCATATGCCCGTGCGTGTAA 59.824 50.000 0.00 0.00 41.78 2.41
455 473 1.805345 CGTGTAAGACGTGTCCTCTCT 59.195 52.381 0.00 0.00 43.50 3.10
465 483 3.890147 ACGTGTCCTCTCTCACTTTAGTT 59.110 43.478 0.00 0.00 33.07 2.24
482 500 9.083080 CACTTTAGTTGGGTTTTTAAGTTCTTG 57.917 33.333 0.00 0.00 0.00 3.02
491 509 9.802039 TGGGTTTTTAAGTTCTTGTATATGACT 57.198 29.630 0.00 0.00 0.00 3.41
498 516 6.155475 AGTTCTTGTATATGACTCTGCTCC 57.845 41.667 0.00 0.00 0.00 4.70
500 518 3.570125 TCTTGTATATGACTCTGCTCCCG 59.430 47.826 0.00 0.00 0.00 5.14
507 525 3.160047 CTCTGCTCCCGCCAGGAT 61.160 66.667 0.00 0.00 46.33 3.24
522 540 6.463331 CCCGCCAGGATAAGTTTATGTACTAA 60.463 42.308 0.00 0.00 41.02 2.24
610 630 7.429636 TTGAATAGACGTCTTGGGTAAAAAG 57.570 36.000 25.44 0.00 0.00 2.27
633 653 2.044806 GATATGACAGCGGGCCCACT 62.045 60.000 24.92 16.30 0.00 4.00
659 687 3.204158 AGAAGAGAGCTGGATAGGTGAGA 59.796 47.826 0.00 0.00 34.13 3.27
660 688 2.944129 AGAGAGCTGGATAGGTGAGAC 58.056 52.381 0.00 0.00 34.13 3.36
661 689 1.960689 GAGAGCTGGATAGGTGAGACC 59.039 57.143 0.00 0.00 38.99 3.85
699 736 0.406750 TAGACAGGAGTGGGAACGGA 59.593 55.000 0.00 0.00 0.00 4.69
726 763 1.375523 GCCAAGTGGTACCCAGACG 60.376 63.158 10.07 0.00 37.57 4.18
733 770 0.533491 TGGTACCCAGACGCATACAC 59.467 55.000 10.07 0.00 0.00 2.90
811 1320 1.904990 GCCAACCCCACCTCTCTCTC 61.905 65.000 0.00 0.00 0.00 3.20
812 1321 0.252467 CCAACCCCACCTCTCTCTCT 60.252 60.000 0.00 0.00 0.00 3.10
813 1322 0.901124 CAACCCCACCTCTCTCTCTG 59.099 60.000 0.00 0.00 0.00 3.35
814 1323 0.907230 AACCCCACCTCTCTCTCTGC 60.907 60.000 0.00 0.00 0.00 4.26
815 1324 1.001503 CCCCACCTCTCTCTCTGCT 59.998 63.158 0.00 0.00 0.00 4.24
816 1325 1.042559 CCCCACCTCTCTCTCTGCTC 61.043 65.000 0.00 0.00 0.00 4.26
817 1326 1.383456 CCCACCTCTCTCTCTGCTCG 61.383 65.000 0.00 0.00 0.00 5.03
818 1327 0.393673 CCACCTCTCTCTCTGCTCGA 60.394 60.000 0.00 0.00 0.00 4.04
819 1328 1.679139 CACCTCTCTCTCTGCTCGAT 58.321 55.000 0.00 0.00 0.00 3.59
820 1329 2.023673 CACCTCTCTCTCTGCTCGATT 58.976 52.381 0.00 0.00 0.00 3.34
821 1330 2.426738 CACCTCTCTCTCTGCTCGATTT 59.573 50.000 0.00 0.00 0.00 2.17
822 1331 2.687935 ACCTCTCTCTCTGCTCGATTTC 59.312 50.000 0.00 0.00 0.00 2.17
823 1332 2.034558 CCTCTCTCTCTGCTCGATTTCC 59.965 54.545 0.00 0.00 0.00 3.13
824 1333 2.951642 CTCTCTCTCTGCTCGATTTCCT 59.048 50.000 0.00 0.00 0.00 3.36
919 1443 1.355720 CCTCAACTCCCCACCTTCATT 59.644 52.381 0.00 0.00 0.00 2.57
973 1508 0.827368 ATCAGGCCGAGGAAGAAGTC 59.173 55.000 0.00 0.00 0.00 3.01
974 1509 0.251832 TCAGGCCGAGGAAGAAGTCT 60.252 55.000 0.00 0.00 0.00 3.24
1263 1833 4.404654 GCCAAGGCCGCAAAGTCG 62.405 66.667 0.00 0.00 34.56 4.18
1416 1989 2.800581 CGACGAGGACTCCGAGTCG 61.801 68.421 23.96 23.96 45.96 4.18
1417 1990 1.447489 GACGAGGACTCCGAGTCGA 60.447 63.158 19.95 0.00 45.96 4.20
1731 2370 4.812476 CCGGCGGCGAAGACATCA 62.812 66.667 34.49 0.00 27.25 3.07
1732 2371 3.554692 CGGCGGCGAAGACATCAC 61.555 66.667 29.19 0.00 27.25 3.06
1733 2372 3.195698 GGCGGCGAAGACATCACC 61.196 66.667 12.98 0.00 27.25 4.02
1736 2375 4.590487 GGCGAAGACATCACCGAA 57.410 55.556 0.00 0.00 31.66 4.30
1737 2376 2.373938 GGCGAAGACATCACCGAAG 58.626 57.895 0.00 0.00 31.66 3.79
1738 2377 0.108804 GGCGAAGACATCACCGAAGA 60.109 55.000 0.00 0.00 31.66 2.87
1739 2378 1.272781 GCGAAGACATCACCGAAGAG 58.727 55.000 0.00 0.00 0.00 2.85
1741 2380 1.472878 CGAAGACATCACCGAAGAGGA 59.527 52.381 0.00 0.00 45.00 3.71
1742 2381 2.094700 CGAAGACATCACCGAAGAGGAA 60.095 50.000 0.00 0.00 45.00 3.36
1743 2382 3.516615 GAAGACATCACCGAAGAGGAAG 58.483 50.000 0.00 0.00 45.00 3.46
1744 2383 2.808919 AGACATCACCGAAGAGGAAGA 58.191 47.619 0.00 0.00 45.00 2.87
1745 2384 2.494073 AGACATCACCGAAGAGGAAGAC 59.506 50.000 0.00 0.00 45.00 3.01
1746 2385 1.550976 ACATCACCGAAGAGGAAGACC 59.449 52.381 0.00 0.00 45.00 3.85
1747 2386 0.818296 ATCACCGAAGAGGAAGACCG 59.182 55.000 0.00 0.00 45.00 4.79
1748 2387 1.446272 CACCGAAGAGGAAGACCGC 60.446 63.158 0.00 0.00 45.00 5.68
1750 2389 1.153745 CCGAAGAGGAAGACCGCTG 60.154 63.158 0.00 0.00 45.18 5.18
1751 2390 1.595993 CCGAAGAGGAAGACCGCTGA 61.596 60.000 0.00 0.00 45.18 4.26
1752 2391 0.179150 CGAAGAGGAAGACCGCTGAG 60.179 60.000 0.00 0.00 45.18 3.35
1753 2392 0.174617 GAAGAGGAAGACCGCTGAGG 59.825 60.000 0.00 0.00 45.18 3.86
1754 2393 1.893919 AAGAGGAAGACCGCTGAGGC 61.894 60.000 0.00 0.00 45.18 4.70
1900 2595 2.525750 TCGTCGAAATGCTTGAATGC 57.474 45.000 0.00 0.00 0.00 3.56
1901 2596 2.076100 TCGTCGAAATGCTTGAATGCT 58.924 42.857 0.00 0.00 0.00 3.79
1920 3174 4.194640 TGCTATCTGTCATGCTTCTTTCC 58.805 43.478 0.00 0.00 0.00 3.13
1948 3206 5.565592 TGAATCAAATCCCTCAAATGTCG 57.434 39.130 0.00 0.00 0.00 4.35
1962 3220 2.386661 ATGTCGCTGGTAAACTCTGG 57.613 50.000 0.00 0.00 0.00 3.86
1966 3224 2.673368 GTCGCTGGTAAACTCTGGATTG 59.327 50.000 0.00 0.00 0.00 2.67
2139 4030 5.497464 TGTCTGATCAACCCTGAACATAA 57.503 39.130 0.00 0.00 34.24 1.90
2172 4072 8.408601 TCCCGTACTGTGATCTTAAGTAAATAC 58.591 37.037 1.63 0.00 0.00 1.89
2174 4074 9.234384 CCGTACTGTGATCTTAAGTAAATACTG 57.766 37.037 1.63 3.69 36.50 2.74
2175 4075 9.999009 CGTACTGTGATCTTAAGTAAATACTGA 57.001 33.333 1.63 0.00 36.50 3.41
2260 4300 4.294523 TGGTGCTATGACGCCAAC 57.705 55.556 0.00 0.00 46.95 3.77
2270 4310 0.832135 TGACGCCAACCTCCTCTCTT 60.832 55.000 0.00 0.00 0.00 2.85
2273 4313 1.831652 CGCCAACCTCCTCTCTTGGT 61.832 60.000 0.00 0.00 37.38 3.67
2278 4318 0.191064 ACCTCCTCTCTTGGTCACCA 59.809 55.000 0.00 0.00 0.00 4.17
2279 4319 1.352083 CCTCCTCTCTTGGTCACCAA 58.648 55.000 9.51 9.51 41.69 3.67
2281 4321 1.694150 CTCCTCTCTTGGTCACCAACA 59.306 52.381 4.67 0.00 38.75 3.33
2282 4322 1.416401 TCCTCTCTTGGTCACCAACAC 59.584 52.381 4.67 0.00 38.75 3.32
2283 4323 1.543429 CCTCTCTTGGTCACCAACACC 60.543 57.143 4.67 0.00 38.75 4.16
2284 4324 1.417890 CTCTCTTGGTCACCAACACCT 59.582 52.381 4.67 0.00 38.75 4.00
2285 4325 1.416401 TCTCTTGGTCACCAACACCTC 59.584 52.381 4.67 0.00 38.75 3.85
2286 4326 0.105964 TCTTGGTCACCAACACCTCG 59.894 55.000 4.67 0.00 38.75 4.63
2287 4327 1.507141 CTTGGTCACCAACACCTCGC 61.507 60.000 4.67 0.00 38.75 5.03
2288 4328 3.041940 GGTCACCAACACCTCGCG 61.042 66.667 0.00 0.00 0.00 5.87
2289 4329 3.712881 GTCACCAACACCTCGCGC 61.713 66.667 0.00 0.00 0.00 6.86
2290 4330 4.980805 TCACCAACACCTCGCGCC 62.981 66.667 0.00 0.00 0.00 6.53
2291 4331 4.988598 CACCAACACCTCGCGCCT 62.989 66.667 0.00 0.00 0.00 5.52
2292 4332 4.681978 ACCAACACCTCGCGCCTC 62.682 66.667 0.00 0.00 0.00 4.70
2315 4355 4.779733 GGCCTCCACTCCCCTCGA 62.780 72.222 0.00 0.00 0.00 4.04
2316 4356 3.151022 GCCTCCACTCCCCTCGAG 61.151 72.222 5.13 5.13 44.95 4.04
2317 4357 3.151022 CCTCCACTCCCCTCGAGC 61.151 72.222 6.99 0.00 43.01 5.03
2318 4358 3.151022 CTCCACTCCCCTCGAGCC 61.151 72.222 6.99 0.00 43.01 4.70
2319 4359 3.965026 CTCCACTCCCCTCGAGCCA 62.965 68.421 6.99 0.00 43.01 4.75
2320 4360 3.465403 CCACTCCCCTCGAGCCAG 61.465 72.222 6.99 4.44 43.01 4.85
2321 4361 2.363018 CACTCCCCTCGAGCCAGA 60.363 66.667 6.99 1.92 43.01 3.86
2322 4362 2.363147 ACTCCCCTCGAGCCAGAC 60.363 66.667 6.99 0.00 43.01 3.51
2323 4363 3.522731 CTCCCCTCGAGCCAGACG 61.523 72.222 6.99 0.00 0.00 4.18
2344 4384 2.582436 TCCGCCTTTCGTGGATCC 59.418 61.111 4.20 4.20 46.59 3.36
2345 4385 2.890474 CCGCCTTTCGTGGATCCG 60.890 66.667 7.39 0.00 45.94 4.18
2346 4386 2.890474 CGCCTTTCGTGGATCCGG 60.890 66.667 7.39 0.00 0.00 5.14
2347 4387 2.582436 GCCTTTCGTGGATCCGGA 59.418 61.111 6.61 6.61 0.00 5.14
2348 4388 1.814169 GCCTTTCGTGGATCCGGAC 60.814 63.158 6.12 0.00 0.00 4.79
2349 4389 1.594833 CCTTTCGTGGATCCGGACA 59.405 57.895 6.12 0.00 0.00 4.02
2350 4390 0.036765 CCTTTCGTGGATCCGGACAA 60.037 55.000 6.12 0.00 0.00 3.18
2351 4391 1.076332 CTTTCGTGGATCCGGACAAC 58.924 55.000 6.12 4.39 0.00 3.32
2352 4392 0.668096 TTTCGTGGATCCGGACAACG 60.668 55.000 22.74 22.74 43.80 4.10
2353 4393 3.186047 CGTGGATCCGGACAACGC 61.186 66.667 18.80 12.39 42.52 4.84
2354 4394 2.264794 GTGGATCCGGACAACGCT 59.735 61.111 6.12 0.00 42.52 5.07
2355 4395 1.810030 GTGGATCCGGACAACGCTC 60.810 63.158 6.12 0.00 42.52 5.03
2356 4396 2.202892 GGATCCGGACAACGCTCC 60.203 66.667 6.12 4.70 42.52 4.70
2357 4397 2.577059 GATCCGGACAACGCTCCA 59.423 61.111 6.12 0.00 42.52 3.86
2358 4398 1.144057 GATCCGGACAACGCTCCAT 59.856 57.895 6.12 0.00 42.52 3.41
2359 4399 1.153369 ATCCGGACAACGCTCCATG 60.153 57.895 6.12 0.00 42.52 3.66
2360 4400 3.499737 CCGGACAACGCTCCATGC 61.500 66.667 0.00 0.00 42.52 4.06
2361 4401 3.499737 CGGACAACGCTCCATGCC 61.500 66.667 0.00 0.00 38.78 4.40
2362 4402 3.134127 GGACAACGCTCCATGCCC 61.134 66.667 0.00 0.00 38.78 5.36
2363 4403 3.134127 GACAACGCTCCATGCCCC 61.134 66.667 0.00 0.00 38.78 5.80
2364 4404 3.918253 GACAACGCTCCATGCCCCA 62.918 63.158 0.00 0.00 38.78 4.96
2365 4405 2.440796 CAACGCTCCATGCCCCAT 60.441 61.111 0.00 0.00 38.78 4.00
2366 4406 2.053865 CAACGCTCCATGCCCCATT 61.054 57.895 0.00 0.00 38.78 3.16
2367 4407 0.751277 CAACGCTCCATGCCCCATTA 60.751 55.000 0.00 0.00 38.78 1.90
2368 4408 0.185901 AACGCTCCATGCCCCATTAT 59.814 50.000 0.00 0.00 38.78 1.28
2369 4409 0.538057 ACGCTCCATGCCCCATTATG 60.538 55.000 0.00 0.00 38.78 1.90
2370 4410 1.870055 CGCTCCATGCCCCATTATGC 61.870 60.000 0.00 0.00 38.78 3.14
2371 4411 1.870055 GCTCCATGCCCCATTATGCG 61.870 60.000 0.00 0.00 35.15 4.73
2372 4412 1.870055 CTCCATGCCCCATTATGCGC 61.870 60.000 0.00 0.00 0.00 6.09
2373 4413 2.652530 CATGCCCCATTATGCGCC 59.347 61.111 4.18 0.00 0.00 6.53
2374 4414 2.601367 ATGCCCCATTATGCGCCC 60.601 61.111 4.18 0.00 0.00 6.13
2375 4415 4.912395 TGCCCCATTATGCGCCCC 62.912 66.667 4.18 0.00 0.00 5.80
2376 4416 4.603535 GCCCCATTATGCGCCCCT 62.604 66.667 4.18 0.00 0.00 4.79
2383 4423 1.344953 ATTATGCGCCCCTCTCCACA 61.345 55.000 4.18 0.00 0.00 4.17
2384 4424 1.971505 TTATGCGCCCCTCTCCACAG 61.972 60.000 4.18 0.00 0.00 3.66
2404 4444 3.387609 ATCGCCCCTCCTCTGCTCT 62.388 63.158 0.00 0.00 0.00 4.09
2418 4458 3.790437 CTCTGGGCCGATGCACCT 61.790 66.667 0.00 0.00 41.56 4.00
2419 4459 4.100084 TCTGGGCCGATGCACCTG 62.100 66.667 0.00 0.00 41.56 4.00
2420 4460 4.100084 CTGGGCCGATGCACCTGA 62.100 66.667 0.00 0.00 41.56 3.86
2438 4503 0.235926 GAGCAAAGGTTGTCACTCGC 59.764 55.000 0.00 0.00 0.00 5.03
2442 4507 0.390124 AAAGGTTGTCACTCGCCGTA 59.610 50.000 0.00 0.00 0.00 4.02
2464 4529 3.329542 TTCAGGCATGGTCCCTCGC 62.330 63.158 0.00 0.00 0.00 5.03
2467 4532 4.101448 GGCATGGTCCCTCGCTGT 62.101 66.667 0.00 0.00 0.00 4.40
2486 4551 3.754965 TGTAGTGATTTGCTTTCAGGCT 58.245 40.909 0.00 0.00 0.00 4.58
2495 4560 1.092345 GCTTTCAGGCTCCACGATCC 61.092 60.000 0.00 0.00 0.00 3.36
2496 4561 0.539051 CTTTCAGGCTCCACGATCCT 59.461 55.000 0.00 0.00 0.00 3.24
2507 4572 2.126071 CGATCCTCGGTGTTGCGT 60.126 61.111 0.00 0.00 36.00 5.24
2509 4574 1.080093 GATCCTCGGTGTTGCGTCA 60.080 57.895 0.00 0.00 0.00 4.35
2510 4575 0.669318 GATCCTCGGTGTTGCGTCAA 60.669 55.000 0.00 0.00 0.00 3.18
2512 4577 0.604073 TCCTCGGTGTTGCGTCAATA 59.396 50.000 0.00 0.00 0.00 1.90
2513 4578 1.001068 TCCTCGGTGTTGCGTCAATAA 59.999 47.619 0.00 0.00 0.00 1.40
2517 4582 1.393539 CGGTGTTGCGTCAATAAGGAG 59.606 52.381 0.00 0.00 0.00 3.69
2539 4604 4.320456 CTGTGCTCTGGCCGTGGT 62.320 66.667 0.00 0.00 37.74 4.16
2540 4605 3.832237 CTGTGCTCTGGCCGTGGTT 62.832 63.158 0.00 0.00 37.74 3.67
2546 4611 3.052082 CTGGCCGTGGTTGCTCTG 61.052 66.667 0.00 0.00 0.00 3.35
2551 4616 1.210931 CCGTGGTTGCTCTGCATTG 59.789 57.895 0.00 0.00 38.76 2.82
2558 4623 0.329261 TTGCTCTGCATTGGCCTACT 59.671 50.000 3.32 0.00 38.76 2.57
2561 4626 1.950828 CTCTGCATTGGCCTACTCAG 58.049 55.000 3.32 7.72 40.13 3.35
2569 4634 4.943822 GCCTACTCAGGGCTTGTC 57.056 61.111 0.00 0.00 45.57 3.18
2580 4645 0.035915 GGGCTTGTCTCCTGGAGAAC 60.036 60.000 27.19 20.15 40.59 3.01
2581 4646 0.980423 GGCTTGTCTCCTGGAGAACT 59.020 55.000 27.19 0.00 40.59 3.01
2614 4679 2.264480 CAAGCCCGACGATGGTGA 59.736 61.111 0.00 0.00 0.00 4.02
2616 4681 1.153369 AAGCCCGACGATGGTGATG 60.153 57.895 0.00 0.00 0.00 3.07
2620 4685 1.588932 CCGACGATGGTGATGTCCG 60.589 63.158 0.00 0.00 0.00 4.79
2626 4691 1.359848 GATGGTGATGTCCGTGACAC 58.640 55.000 8.60 0.00 45.65 3.67
2629 4694 2.176045 TGGTGATGTCCGTGACACTAT 58.824 47.619 8.60 0.00 45.65 2.12
2631 4696 2.930040 GGTGATGTCCGTGACACTATTG 59.070 50.000 8.60 0.00 45.65 1.90
2636 4701 2.563620 TGTCCGTGACACTATTGCCTTA 59.436 45.455 3.68 0.00 37.67 2.69
2653 4718 1.320555 CTTATTGAAGGCGTCGTCGTG 59.679 52.381 3.66 0.00 39.49 4.35
2672 4737 3.733337 GTGGAGTTTTCTCTTGAGCAGA 58.267 45.455 0.00 0.00 45.52 4.26
2675 4740 3.745458 GGAGTTTTCTCTTGAGCAGACTG 59.255 47.826 0.00 0.00 45.52 3.51
2699 4764 0.841289 TGTCGGGGACTCTTGGTTTT 59.159 50.000 0.00 0.00 33.15 2.43
2700 4765 1.235724 GTCGGGGACTCTTGGTTTTG 58.764 55.000 0.00 0.00 0.00 2.44
2702 4767 1.702957 TCGGGGACTCTTGGTTTTGAT 59.297 47.619 0.00 0.00 0.00 2.57
2714 4779 5.588648 TCTTGGTTTTGATCGAAAGTTCAGT 59.411 36.000 8.45 0.00 40.55 3.41
2721 4786 5.139435 TGATCGAAAGTTCAGTGATGACT 57.861 39.130 0.00 0.00 35.07 3.41
2722 4787 6.267496 TGATCGAAAGTTCAGTGATGACTA 57.733 37.500 0.00 0.00 35.07 2.59
2753 4849 2.844348 AGTACCCCTGTATTCACCCTTG 59.156 50.000 0.00 0.00 0.00 3.61
2761 4857 2.235016 GTATTCACCCTTGCCACAACA 58.765 47.619 0.00 0.00 0.00 3.33
2767 4863 1.138661 ACCCTTGCCACAACAAACATG 59.861 47.619 0.00 0.00 0.00 3.21
2778 4874 1.032014 ACAAACATGGCAGCTTCGTT 58.968 45.000 0.00 0.00 0.00 3.85
2779 4875 1.269206 ACAAACATGGCAGCTTCGTTG 60.269 47.619 0.00 0.00 0.00 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 9.338622 CCTCCGTTCCTATATATTTGTCTTTTT 57.661 33.333 0.00 0.00 0.00 1.94
24 25 7.937394 CCCTCCGTTCCTATATATTTGTCTTTT 59.063 37.037 0.00 0.00 0.00 2.27
25 26 7.291651 TCCCTCCGTTCCTATATATTTGTCTTT 59.708 37.037 0.00 0.00 0.00 2.52
26 27 6.785963 TCCCTCCGTTCCTATATATTTGTCTT 59.214 38.462 0.00 0.00 0.00 3.01
27 28 6.320518 TCCCTCCGTTCCTATATATTTGTCT 58.679 40.000 0.00 0.00 0.00 3.41
28 29 6.210984 ACTCCCTCCGTTCCTATATATTTGTC 59.789 42.308 0.00 0.00 0.00 3.18
29 30 6.082707 ACTCCCTCCGTTCCTATATATTTGT 58.917 40.000 0.00 0.00 0.00 2.83
30 31 6.607004 ACTCCCTCCGTTCCTATATATTTG 57.393 41.667 0.00 0.00 0.00 2.32
31 32 7.243824 TGTACTCCCTCCGTTCCTATATATTT 58.756 38.462 0.00 0.00 0.00 1.40
32 33 6.797707 TGTACTCCCTCCGTTCCTATATATT 58.202 40.000 0.00 0.00 0.00 1.28
33 34 6.398655 TGTACTCCCTCCGTTCCTATATAT 57.601 41.667 0.00 0.00 0.00 0.86
34 35 5.848286 TGTACTCCCTCCGTTCCTATATA 57.152 43.478 0.00 0.00 0.00 0.86
35 36 4.736611 TGTACTCCCTCCGTTCCTATAT 57.263 45.455 0.00 0.00 0.00 0.86
36 37 4.524802 TTGTACTCCCTCCGTTCCTATA 57.475 45.455 0.00 0.00 0.00 1.31
37 38 3.393426 TTGTACTCCCTCCGTTCCTAT 57.607 47.619 0.00 0.00 0.00 2.57
38 39 2.905415 TTGTACTCCCTCCGTTCCTA 57.095 50.000 0.00 0.00 0.00 2.94
39 40 2.249309 ATTGTACTCCCTCCGTTCCT 57.751 50.000 0.00 0.00 0.00 3.36
40 41 3.345508 AAATTGTACTCCCTCCGTTCC 57.654 47.619 0.00 0.00 0.00 3.62
41 42 4.439968 CCTAAATTGTACTCCCTCCGTTC 58.560 47.826 0.00 0.00 0.00 3.95
42 43 3.199289 CCCTAAATTGTACTCCCTCCGTT 59.801 47.826 0.00 0.00 0.00 4.44
43 44 2.770232 CCCTAAATTGTACTCCCTCCGT 59.230 50.000 0.00 0.00 0.00 4.69
44 45 2.104281 CCCCTAAATTGTACTCCCTCCG 59.896 54.545 0.00 0.00 0.00 4.63
45 46 2.158652 GCCCCTAAATTGTACTCCCTCC 60.159 54.545 0.00 0.00 0.00 4.30
46 47 2.158652 GGCCCCTAAATTGTACTCCCTC 60.159 54.545 0.00 0.00 0.00 4.30
47 48 1.850998 GGCCCCTAAATTGTACTCCCT 59.149 52.381 0.00 0.00 0.00 4.20
48 49 1.567175 TGGCCCCTAAATTGTACTCCC 59.433 52.381 0.00 0.00 0.00 4.30
49 50 3.375647 TTGGCCCCTAAATTGTACTCC 57.624 47.619 0.00 0.00 0.00 3.85
50 51 7.390718 CACTATATTGGCCCCTAAATTGTACTC 59.609 40.741 0.00 0.00 0.00 2.59
51 52 7.073215 TCACTATATTGGCCCCTAAATTGTACT 59.927 37.037 0.00 0.00 0.00 2.73
52 53 7.228590 TCACTATATTGGCCCCTAAATTGTAC 58.771 38.462 0.00 0.00 0.00 2.90
53 54 7.293771 TCTCACTATATTGGCCCCTAAATTGTA 59.706 37.037 0.00 0.00 0.00 2.41
54 55 6.102615 TCTCACTATATTGGCCCCTAAATTGT 59.897 38.462 0.00 0.00 0.00 2.71
55 56 6.542821 TCTCACTATATTGGCCCCTAAATTG 58.457 40.000 0.00 0.00 0.00 2.32
56 57 6.780198 TCTCACTATATTGGCCCCTAAATT 57.220 37.500 0.00 0.00 0.00 1.82
57 58 6.332901 ACTTCTCACTATATTGGCCCCTAAAT 59.667 38.462 0.00 0.00 0.00 1.40
69 70 3.243101 CGTCCGTGCACTTCTCACTATAT 60.243 47.826 16.19 0.00 32.54 0.86
71 72 1.135373 CGTCCGTGCACTTCTCACTAT 60.135 52.381 16.19 0.00 32.54 2.12
86 87 1.183030 TATGCCTATGGGTCCGTCCG 61.183 60.000 0.00 0.00 37.00 4.79
87 88 1.066143 CATATGCCTATGGGTCCGTCC 60.066 57.143 0.00 0.00 32.60 4.79
90 91 1.406069 GCTCATATGCCTATGGGTCCG 60.406 57.143 10.18 0.00 38.01 4.79
102 103 5.904941 TGCTTTAAAATGTGGGCTCATATG 58.095 37.500 0.00 0.00 0.00 1.78
109 110 8.940768 TTAGAAATATGCTTTAAAATGTGGGC 57.059 30.769 0.00 0.00 0.00 5.36
163 164 6.587651 CACATAGAATATGAAGATGTGCGTG 58.412 40.000 3.87 0.00 40.50 5.34
164 165 6.775939 CACATAGAATATGAAGATGTGCGT 57.224 37.500 3.87 0.00 40.50 5.24
237 255 8.289618 GCTTCTAAAATGAGTTGTATGACACAA 58.710 33.333 0.00 0.00 44.97 3.33
238 256 7.443879 TGCTTCTAAAATGAGTTGTATGACACA 59.556 33.333 0.00 0.00 34.51 3.72
246 264 5.376625 TCCAGTGCTTCTAAAATGAGTTGT 58.623 37.500 0.00 0.00 0.00 3.32
247 265 5.947228 TCCAGTGCTTCTAAAATGAGTTG 57.053 39.130 0.00 0.00 0.00 3.16
251 269 6.899393 ACAATTCCAGTGCTTCTAAAATGA 57.101 33.333 0.00 0.00 0.00 2.57
259 277 5.120674 GCCAAAATAACAATTCCAGTGCTTC 59.879 40.000 0.00 0.00 0.00 3.86
273 291 4.739195 TGTTATGCCTTCGCCAAAATAAC 58.261 39.130 0.00 0.00 33.72 1.89
274 292 5.392767 TTGTTATGCCTTCGCCAAAATAA 57.607 34.783 0.00 0.00 0.00 1.40
275 293 5.392767 TTTGTTATGCCTTCGCCAAAATA 57.607 34.783 0.00 0.00 0.00 1.40
277 295 3.735237 TTTGTTATGCCTTCGCCAAAA 57.265 38.095 0.00 0.00 0.00 2.44
281 299 4.993905 ACTATTTTTGTTATGCCTTCGCC 58.006 39.130 0.00 0.00 0.00 5.54
337 355 2.730382 TCAGGCATGCATCTTCACAAT 58.270 42.857 21.36 0.00 0.00 2.71
340 358 3.795623 ATTTCAGGCATGCATCTTCAC 57.204 42.857 21.36 0.00 0.00 3.18
378 396 6.696583 TCGTTCTAGACACGTTTTAAATGTCA 59.303 34.615 18.10 7.39 44.26 3.58
379 397 7.097342 TCGTTCTAGACACGTTTTAAATGTC 57.903 36.000 19.69 10.99 42.54 3.06
380 398 7.467557 TTCGTTCTAGACACGTTTTAAATGT 57.532 32.000 19.69 0.00 38.81 2.71
381 399 8.928844 AATTCGTTCTAGACACGTTTTAAATG 57.071 30.769 19.69 0.00 38.81 2.32
382 400 9.940166 AAAATTCGTTCTAGACACGTTTTAAAT 57.060 25.926 19.69 12.53 38.81 1.40
418 436 2.542907 CGCACGGGCATATGAACCC 61.543 63.158 11.77 7.63 43.25 4.11
441 459 2.279935 AAGTGAGAGAGGACACGTCT 57.720 50.000 0.00 0.00 41.22 4.18
448 466 3.858135 ACCCAACTAAAGTGAGAGAGGA 58.142 45.455 0.00 0.00 0.00 3.71
455 473 8.584063 AGAACTTAAAAACCCAACTAAAGTGA 57.416 30.769 0.00 0.00 0.00 3.41
465 483 9.802039 AGTCATATACAAGAACTTAAAAACCCA 57.198 29.630 0.00 0.00 0.00 4.51
498 516 4.957296 AGTACATAAACTTATCCTGGCGG 58.043 43.478 0.00 0.00 0.00 6.13
500 518 9.338622 ACAATTAGTACATAAACTTATCCTGGC 57.661 33.333 0.00 0.00 0.00 4.85
583 602 7.804843 TTTACCCAAGACGTCTATTCAAAAA 57.195 32.000 20.39 12.26 0.00 1.94
584 603 7.804843 TTTTACCCAAGACGTCTATTCAAAA 57.195 32.000 20.39 17.07 0.00 2.44
585 604 7.716123 TCTTTTTACCCAAGACGTCTATTCAAA 59.284 33.333 20.39 12.43 0.00 2.69
586 605 7.218614 TCTTTTTACCCAAGACGTCTATTCAA 58.781 34.615 20.39 6.95 0.00 2.69
593 612 5.996669 TCTTTCTTTTTACCCAAGACGTC 57.003 39.130 7.70 7.70 29.70 4.34
597 616 9.231297 CTGTCATATCTTTCTTTTTACCCAAGA 57.769 33.333 0.00 0.00 0.00 3.02
610 630 1.230324 GGCCCGCTGTCATATCTTTC 58.770 55.000 0.00 0.00 0.00 2.62
633 653 2.433604 CCTATCCAGCTCTCTTCTGCAA 59.566 50.000 0.00 0.00 0.00 4.08
699 736 2.346284 TACCACTTGGCAGGCCGTTT 62.346 55.000 5.74 0.00 39.32 3.60
726 763 0.464554 GGGAGCCCTTCTGTGTATGC 60.465 60.000 0.00 0.00 0.00 3.14
811 1320 1.699656 CGTGGCAGGAAATCGAGCAG 61.700 60.000 0.00 0.00 0.00 4.24
812 1321 1.741401 CGTGGCAGGAAATCGAGCA 60.741 57.895 0.00 0.00 0.00 4.26
813 1322 3.093278 CGTGGCAGGAAATCGAGC 58.907 61.111 0.00 0.00 0.00 5.03
814 1323 2.802667 CGCGTGGCAGGAAATCGAG 61.803 63.158 12.03 0.00 0.00 4.04
815 1324 2.813474 CGCGTGGCAGGAAATCGA 60.813 61.111 12.03 0.00 0.00 3.59
816 1325 4.520846 GCGCGTGGCAGGAAATCG 62.521 66.667 12.03 5.99 42.87 3.34
817 1326 4.520846 CGCGCGTGGCAGGAAATC 62.521 66.667 24.19 0.00 43.84 2.17
919 1443 0.535797 CTGCTGCTCTGTGGATCTGA 59.464 55.000 0.00 0.00 0.00 3.27
973 1508 1.227497 GAGATCCGGCTGGCTGAAG 60.227 63.158 6.73 0.00 34.14 3.02
974 1509 1.552799 TTGAGATCCGGCTGGCTGAA 61.553 55.000 6.73 0.00 34.14 3.02
1255 1825 2.861006 GCGGACCTTCGACTTTGC 59.139 61.111 0.00 0.00 0.00 3.68
1257 1827 2.737376 GCGCGGACCTTCGACTTT 60.737 61.111 8.83 0.00 0.00 2.66
1395 1968 2.800581 CTCGGAGTCCTCGTCGTCG 61.801 68.421 7.77 0.00 38.55 5.12
1416 1989 2.750637 TCACCCTCCGACTCGCTC 60.751 66.667 0.00 0.00 0.00 5.03
1417 1990 2.752238 CTCACCCTCCGACTCGCT 60.752 66.667 0.00 0.00 0.00 4.93
1689 2328 2.509561 GCGGTCTTCCTCTTCGGC 60.510 66.667 0.00 0.00 0.00 5.54
1716 2355 3.195698 GGTGATGTCTTCGCCGCC 61.196 66.667 2.79 0.00 44.79 6.13
1720 2359 1.272781 CTCTTCGGTGATGTCTTCGC 58.727 55.000 0.00 0.00 0.00 4.70
1721 2360 1.472878 TCCTCTTCGGTGATGTCTTCG 59.527 52.381 0.00 0.00 0.00 3.79
1722 2361 3.193691 TCTTCCTCTTCGGTGATGTCTTC 59.806 47.826 0.00 0.00 0.00 2.87
1723 2362 3.056465 GTCTTCCTCTTCGGTGATGTCTT 60.056 47.826 0.00 0.00 0.00 3.01
1724 2363 2.494073 GTCTTCCTCTTCGGTGATGTCT 59.506 50.000 0.00 0.00 0.00 3.41
1725 2364 2.417515 GGTCTTCCTCTTCGGTGATGTC 60.418 54.545 0.00 0.00 0.00 3.06
1726 2365 1.550976 GGTCTTCCTCTTCGGTGATGT 59.449 52.381 0.00 0.00 0.00 3.06
1727 2366 1.469940 CGGTCTTCCTCTTCGGTGATG 60.470 57.143 0.00 0.00 0.00 3.07
1728 2367 0.818296 CGGTCTTCCTCTTCGGTGAT 59.182 55.000 0.00 0.00 0.00 3.06
1729 2368 1.874345 GCGGTCTTCCTCTTCGGTGA 61.874 60.000 0.00 0.00 0.00 4.02
1730 2369 1.446272 GCGGTCTTCCTCTTCGGTG 60.446 63.158 0.00 0.00 0.00 4.94
1731 2370 1.606889 AGCGGTCTTCCTCTTCGGT 60.607 57.895 0.00 0.00 0.00 4.69
1732 2371 1.153745 CAGCGGTCTTCCTCTTCGG 60.154 63.158 0.00 0.00 0.00 4.30
1733 2372 0.179150 CTCAGCGGTCTTCCTCTTCG 60.179 60.000 0.00 0.00 0.00 3.79
1734 2373 0.174617 CCTCAGCGGTCTTCCTCTTC 59.825 60.000 0.00 0.00 0.00 2.87
1735 2374 1.893919 GCCTCAGCGGTCTTCCTCTT 61.894 60.000 0.00 0.00 34.25 2.85
1736 2375 2.355193 GCCTCAGCGGTCTTCCTCT 61.355 63.158 0.00 0.00 34.25 3.69
1737 2376 2.185608 GCCTCAGCGGTCTTCCTC 59.814 66.667 0.00 0.00 34.25 3.71
1756 2395 4.785453 GGTCCTCCTTGCCGCCAG 62.785 72.222 0.00 0.00 0.00 4.85
1900 2595 4.437239 ACGGAAAGAAGCATGACAGATAG 58.563 43.478 0.00 0.00 0.00 2.08
1901 2596 4.471904 ACGGAAAGAAGCATGACAGATA 57.528 40.909 0.00 0.00 0.00 1.98
1920 3174 8.786898 ACATTTGAGGGATTTGATTCATATACG 58.213 33.333 0.00 0.00 0.00 3.06
1948 3206 3.944087 AGACAATCCAGAGTTTACCAGC 58.056 45.455 0.00 0.00 0.00 4.85
1962 3220 8.677300 TGCAGGAACTATTATTTCAAGACAATC 58.323 33.333 0.00 0.00 36.02 2.67
1966 3224 7.334421 TCAGTGCAGGAACTATTATTTCAAGAC 59.666 37.037 0.00 0.00 36.02 3.01
2139 4030 4.279145 AGATCACAGTACGGGAACATACT 58.721 43.478 0.00 0.00 32.95 2.12
2239 4139 0.899019 TGGCGTCATAGCACCAACTA 59.101 50.000 0.00 0.00 39.27 2.24
2260 4300 1.002544 GTTGGTGACCAAGAGAGGAGG 59.997 57.143 18.89 0.00 44.82 4.30
2270 4310 2.110213 GCGAGGTGTTGGTGACCA 59.890 61.111 0.00 0.00 35.76 4.02
2273 4313 4.980805 GGCGCGAGGTGTTGGTGA 62.981 66.667 12.10 0.00 0.00 4.02
2298 4338 4.779733 TCGAGGGGAGTGGAGGCC 62.780 72.222 0.00 0.00 0.00 5.19
2299 4339 3.151022 CTCGAGGGGAGTGGAGGC 61.151 72.222 3.91 0.00 38.02 4.70
2300 4340 3.151022 GCTCGAGGGGAGTGGAGG 61.151 72.222 15.58 0.00 45.03 4.30
2301 4341 3.151022 GGCTCGAGGGGAGTGGAG 61.151 72.222 15.58 0.00 45.03 3.86
2302 4342 3.965026 CTGGCTCGAGGGGAGTGGA 62.965 68.421 15.58 0.00 45.03 4.02
2303 4343 3.465403 CTGGCTCGAGGGGAGTGG 61.465 72.222 15.58 0.00 45.03 4.00
2304 4344 2.363018 TCTGGCTCGAGGGGAGTG 60.363 66.667 15.58 0.00 45.03 3.51
2305 4345 2.363147 GTCTGGCTCGAGGGGAGT 60.363 66.667 15.58 0.00 45.03 3.85
2306 4346 3.522731 CGTCTGGCTCGAGGGGAG 61.523 72.222 15.58 0.00 46.06 4.30
2325 4365 1.521681 GATCCACGAAAGGCGGAGG 60.522 63.158 0.00 0.00 46.49 4.30
2326 4366 1.521681 GGATCCACGAAAGGCGGAG 60.522 63.158 6.95 0.00 46.49 4.63
2327 4367 2.582436 GGATCCACGAAAGGCGGA 59.418 61.111 6.95 0.00 46.49 5.54
2328 4368 2.890474 CGGATCCACGAAAGGCGG 60.890 66.667 13.41 0.00 46.49 6.13
2330 4370 1.814169 GTCCGGATCCACGAAAGGC 60.814 63.158 7.81 0.00 35.47 4.35
2331 4371 0.036765 TTGTCCGGATCCACGAAAGG 60.037 55.000 7.81 3.47 35.47 3.11
2332 4372 1.076332 GTTGTCCGGATCCACGAAAG 58.924 55.000 7.81 0.00 35.47 2.62
2333 4373 0.668096 CGTTGTCCGGATCCACGAAA 60.668 55.000 21.95 0.36 35.47 3.46
2334 4374 1.080366 CGTTGTCCGGATCCACGAA 60.080 57.895 21.95 0.00 35.47 3.85
2335 4375 2.569657 CGTTGTCCGGATCCACGA 59.430 61.111 21.95 5.15 35.47 4.35
2336 4376 3.186047 GCGTTGTCCGGATCCACG 61.186 66.667 22.07 22.07 36.94 4.94
2337 4377 1.810030 GAGCGTTGTCCGGATCCAC 60.810 63.158 7.81 3.70 36.94 4.02
2338 4378 2.577059 GAGCGTTGTCCGGATCCA 59.423 61.111 7.81 0.00 36.94 3.41
2339 4379 2.202892 GGAGCGTTGTCCGGATCC 60.203 66.667 7.81 5.42 36.94 3.36
2340 4380 1.144057 ATGGAGCGTTGTCCGGATC 59.856 57.895 7.81 0.00 39.81 3.36
2341 4381 1.153369 CATGGAGCGTTGTCCGGAT 60.153 57.895 7.81 0.00 39.81 4.18
2342 4382 2.264480 CATGGAGCGTTGTCCGGA 59.736 61.111 0.00 0.00 39.81 5.14
2343 4383 3.499737 GCATGGAGCGTTGTCCGG 61.500 66.667 0.00 0.00 39.81 5.14
2352 4392 1.870055 CGCATAATGGGGCATGGAGC 61.870 60.000 0.00 0.00 44.65 4.70
2353 4393 1.870055 GCGCATAATGGGGCATGGAG 61.870 60.000 0.30 0.00 45.15 3.86
2354 4394 1.902918 GCGCATAATGGGGCATGGA 60.903 57.895 0.30 0.00 45.15 3.41
2355 4395 2.652530 GCGCATAATGGGGCATGG 59.347 61.111 0.30 0.00 45.15 3.66
2360 4400 2.282462 GAGGGGCGCATAATGGGG 60.282 66.667 10.83 0.00 0.00 4.96
2361 4401 1.302832 GAGAGGGGCGCATAATGGG 60.303 63.158 10.83 0.00 0.00 4.00
2362 4402 1.302832 GGAGAGGGGCGCATAATGG 60.303 63.158 10.83 0.00 0.00 3.16
2363 4403 0.886490 GTGGAGAGGGGCGCATAATG 60.886 60.000 10.83 0.00 0.00 1.90
2364 4404 1.344953 TGTGGAGAGGGGCGCATAAT 61.345 55.000 10.83 0.00 0.00 1.28
2365 4405 1.971505 CTGTGGAGAGGGGCGCATAA 61.972 60.000 10.83 0.00 0.00 1.90
2366 4406 2.364973 TGTGGAGAGGGGCGCATA 60.365 61.111 10.83 0.00 0.00 3.14
2367 4407 3.790437 CTGTGGAGAGGGGCGCAT 61.790 66.667 10.83 0.00 0.00 4.73
2370 4410 3.746949 GATGCTGTGGAGAGGGGCG 62.747 68.421 0.00 0.00 0.00 6.13
2371 4411 2.191641 GATGCTGTGGAGAGGGGC 59.808 66.667 0.00 0.00 0.00 5.80
2372 4412 2.503061 CGATGCTGTGGAGAGGGG 59.497 66.667 0.00 0.00 0.00 4.79
2373 4413 2.202987 GCGATGCTGTGGAGAGGG 60.203 66.667 0.00 0.00 0.00 4.30
2374 4414 2.202987 GGCGATGCTGTGGAGAGG 60.203 66.667 0.00 0.00 0.00 3.69
2375 4415 2.202987 GGGCGATGCTGTGGAGAG 60.203 66.667 0.00 0.00 0.00 3.20
2376 4416 3.785859 GGGGCGATGCTGTGGAGA 61.786 66.667 0.00 0.00 0.00 3.71
2383 4423 3.160047 CAGAGGAGGGGCGATGCT 61.160 66.667 0.00 0.00 0.00 3.79
2384 4424 4.925861 GCAGAGGAGGGGCGATGC 62.926 72.222 0.00 0.00 0.00 3.91
2404 4444 4.100084 CTCAGGTGCATCGGCCCA 62.100 66.667 0.00 0.00 40.13 5.36
2417 4457 1.528586 CGAGTGACAACCTTTGCTCAG 59.471 52.381 0.00 0.00 0.00 3.35
2418 4458 1.581934 CGAGTGACAACCTTTGCTCA 58.418 50.000 0.00 0.00 0.00 4.26
2419 4459 0.235926 GCGAGTGACAACCTTTGCTC 59.764 55.000 0.00 0.00 0.00 4.26
2420 4460 1.166531 GGCGAGTGACAACCTTTGCT 61.167 55.000 0.00 0.00 0.00 3.91
2433 4498 2.711922 CCTGAAGGCTACGGCGAGT 61.712 63.158 16.62 0.00 39.81 4.18
2452 4517 0.179100 CACTACAGCGAGGGACCATG 60.179 60.000 0.00 0.00 0.00 3.66
2464 4529 3.755378 AGCCTGAAAGCAAATCACTACAG 59.245 43.478 0.00 0.00 34.23 2.74
2467 4532 3.244875 TGGAGCCTGAAAGCAAATCACTA 60.245 43.478 0.00 0.00 34.23 2.74
2495 4560 1.393539 CCTTATTGACGCAACACCGAG 59.606 52.381 0.00 0.00 0.00 4.63
2496 4561 1.001068 TCCTTATTGACGCAACACCGA 59.999 47.619 0.00 0.00 0.00 4.69
2507 4572 1.210478 GCACAGGAGCCTCCTTATTGA 59.790 52.381 11.57 0.00 46.91 2.57
2509 4574 1.488393 GAGCACAGGAGCCTCCTTATT 59.512 52.381 11.57 0.00 46.91 1.40
2510 4575 1.127343 GAGCACAGGAGCCTCCTTAT 58.873 55.000 11.57 0.00 46.91 1.73
2512 4577 1.229464 AGAGCACAGGAGCCTCCTT 60.229 57.895 11.57 0.00 46.91 3.36
2517 4582 4.792804 GGCCAGAGCACAGGAGCC 62.793 72.222 0.00 0.00 42.56 4.70
2535 4600 1.080298 GCCAATGCAGAGCAACCAC 60.080 57.895 0.00 0.00 43.62 4.16
2539 4604 0.329261 AGTAGGCCAATGCAGAGCAA 59.671 50.000 5.01 0.00 43.62 3.91
2540 4605 0.107508 GAGTAGGCCAATGCAGAGCA 60.108 55.000 5.01 0.00 44.86 4.26
2546 4611 1.825622 GCCCTGAGTAGGCCAATGC 60.826 63.158 5.01 0.00 45.16 3.56
2561 4626 0.035915 GTTCTCCAGGAGACAAGCCC 60.036 60.000 19.75 0.00 38.51 5.19
2569 4634 3.370315 CCAAATCAGGAGTTCTCCAGGAG 60.370 52.174 19.28 10.70 0.00 3.69
2574 4639 4.218635 GGAAAACCAAATCAGGAGTTCTCC 59.781 45.833 10.57 10.57 0.00 3.71
2580 4645 3.306294 GGCTTGGAAAACCAAATCAGGAG 60.306 47.826 0.00 0.00 0.00 3.69
2581 4646 2.632512 GGCTTGGAAAACCAAATCAGGA 59.367 45.455 0.00 0.00 0.00 3.86
2583 4648 2.610232 CGGGCTTGGAAAACCAAATCAG 60.610 50.000 0.00 0.00 0.00 2.90
2584 4649 1.342819 CGGGCTTGGAAAACCAAATCA 59.657 47.619 0.00 0.00 0.00 2.57
2585 4650 1.616374 TCGGGCTTGGAAAACCAAATC 59.384 47.619 0.00 0.00 0.00 2.17
2601 4666 1.227263 GGACATCACCATCGTCGGG 60.227 63.158 0.00 0.00 0.00 5.14
2603 4668 1.138883 ACGGACATCACCATCGTCG 59.861 57.895 0.00 0.00 0.00 5.12
2605 4670 0.108804 GTCACGGACATCACCATCGT 60.109 55.000 0.00 0.00 32.09 3.73
2614 4679 1.555075 AGGCAATAGTGTCACGGACAT 59.445 47.619 9.47 3.34 44.63 3.06
2616 4681 2.094762 AAGGCAATAGTGTCACGGAC 57.905 50.000 0.00 0.00 0.00 4.79
2620 4685 6.124088 CCTTCAATAAGGCAATAGTGTCAC 57.876 41.667 0.00 0.00 45.78 3.67
2636 4701 1.736645 CCACGACGACGCCTTCAAT 60.737 57.895 7.30 0.00 43.96 2.57
2653 4718 3.745458 CAGTCTGCTCAAGAGAAAACTCC 59.255 47.826 0.32 0.00 34.84 3.85
2678 4743 2.113243 AACCAAGAGTCCCCGACAGC 62.113 60.000 0.00 0.00 34.60 4.40
2699 4764 5.139435 AGTCATCACTGAACTTTCGATCA 57.861 39.130 0.00 0.00 31.85 2.92
2700 4765 6.326375 AGTAGTCATCACTGAACTTTCGATC 58.674 40.000 0.00 0.00 33.62 3.69
2702 4767 5.707242 AGTAGTCATCACTGAACTTTCGA 57.293 39.130 0.00 0.00 33.62 3.71
2714 4779 6.097839 GGGGTACTCAACAATAGTAGTCATCA 59.902 42.308 0.00 0.00 30.26 3.07
2721 4786 7.620491 TGAATACAGGGGTACTCAACAATAGTA 59.380 37.037 0.00 0.00 33.20 1.82
2722 4787 6.442564 TGAATACAGGGGTACTCAACAATAGT 59.557 38.462 0.00 0.00 33.20 2.12
2761 4857 0.314935 CCAACGAAGCTGCCATGTTT 59.685 50.000 0.00 0.00 0.00 2.83
2767 4863 0.040067 CTTGTTCCAACGAAGCTGCC 60.040 55.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.