Multiple sequence alignment - TraesCS2A01G284900

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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 TraesCS2A01G284900 chr2A 100.000 5406 0 0 1 5406 478762507 478767912 0.000000e+00 9984.0
1 TraesCS2A01G284900 chr2A 76.166 193 40 5 1208 1399 619628187 619628000 4.460000e-16 97.1
2 TraesCS2A01G284900 chr2D 94.294 2138 66 23 839 2953 357702543 357704647 0.000000e+00 3221.0
3 TraesCS2A01G284900 chr2D 93.867 1712 44 13 2580 4262 357704933 357706612 0.000000e+00 2523.0
4 TraesCS2A01G284900 chr2D 96.315 1004 31 1 4260 5263 357706573 357707570 0.000000e+00 1644.0
5 TraesCS2A01G284900 chr2D 94.532 695 22 10 1 683 357701510 357702200 0.000000e+00 1059.0
6 TraesCS2A01G284900 chr2D 85.342 307 44 1 1 306 34988388 34988082 3.140000e-82 316.0
7 TraesCS2A01G284900 chr2D 75.812 277 56 11 1124 1396 357697617 357697886 4.390000e-26 130.0
8 TraesCS2A01G284900 chr2D 79.114 158 28 4 1208 1364 477264635 477264482 2.660000e-18 104.0
9 TraesCS2A01G284900 chr2D 86.420 81 10 1 5280 5359 26493812 26493732 2.680000e-13 87.9
10 TraesCS2A01G284900 chr2B 89.122 1480 105 20 2129 3588 425356698 425358141 0.000000e+00 1790.0
11 TraesCS2A01G284900 chr2B 94.746 1104 44 6 4260 5356 425360088 425361184 0.000000e+00 1705.0
12 TraesCS2A01G284900 chr2B 91.648 886 36 19 864 1736 425354058 425354918 0.000000e+00 1192.0
13 TraesCS2A01G284900 chr2B 91.745 642 18 9 1 619 425353155 425353784 0.000000e+00 859.0
14 TraesCS2A01G284900 chr2B 91.639 598 36 6 3672 4262 425359537 425360127 0.000000e+00 815.0
15 TraesCS2A01G284900 chr2B 84.691 307 46 1 1 306 57664893 57664587 6.800000e-79 305.0
16 TraesCS2A01G284900 chr2B 90.909 132 6 3 716 843 425353847 425353976 7.200000e-39 172.0
17 TraesCS2A01G284900 chr2B 96.703 91 3 0 1779 1869 425356216 425356306 9.380000e-33 152.0
18 TraesCS2A01G284900 chr2B 75.090 277 58 11 1124 1396 425349214 425349483 9.510000e-23 119.0
19 TraesCS2A01G284900 chr2B 76.166 193 41 4 1208 1399 559193125 559192937 4.460000e-16 97.1
20 TraesCS2A01G284900 chr3D 89.474 209 21 1 4342 4549 460524347 460524555 4.150000e-66 263.0
21 TraesCS2A01G284900 chr3D 86.385 213 19 4 3884 4092 460524144 460524350 1.960000e-54 224.0
22 TraesCS2A01G284900 chr5D 88.038 209 24 1 4342 4549 492269993 492270201 4.180000e-61 246.0
23 TraesCS2A01G284900 chr5D 87.324 213 17 4 3884 4092 492274107 492274313 9.050000e-58 235.0
24 TraesCS2A01G284900 chr5D 90.426 94 9 0 5263 5356 561694722 561694815 2.040000e-24 124.0
25 TraesCS2A01G284900 chr3B 82.407 216 12 10 3884 4095 124773603 124773410 1.200000e-36 165.0
26 TraesCS2A01G284900 chr1B 82.629 213 11 10 3884 4092 422555034 422555224 1.200000e-36 165.0
27 TraesCS2A01G284900 chr1B 86.813 91 12 0 5259 5349 364289385 364289295 9.580000e-18 102.0
28 TraesCS2A01G284900 chr1B 85.417 96 14 0 5261 5356 600468103 600468198 3.450000e-17 100.0
29 TraesCS2A01G284900 chr7D 84.000 100 14 2 5257 5356 551930487 551930584 1.600000e-15 95.3
30 TraesCS2A01G284900 chr6D 76.440 191 33 11 1213 1399 304297070 304296888 5.770000e-15 93.5
31 TraesCS2A01G284900 chr6A 75.401 187 37 9 1213 1396 410866425 410866605 1.250000e-11 82.4


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 TraesCS2A01G284900 chr2A 478762507 478767912 5405 False 9984.0 9984 100.00000 1 5406 1 chr2A.!!$F1 5405
1 TraesCS2A01G284900 chr2D 357697617 357707570 9953 False 1715.4 3221 90.96400 1 5263 5 chr2D.!!$F1 5262
2 TraesCS2A01G284900 chr2B 425349214 425361184 11970 False 850.5 1790 90.20025 1 5356 8 chr2B.!!$F1 5355
3 TraesCS2A01G284900 chr5D 492269993 492274313 4320 False 240.5 246 87.68100 3884 4549 2 chr5D.!!$F2 665

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
890 5435 0.608856 ATTGCTGATGCCAACCACGA 60.609 50.000 0.0 0.0 38.71 4.35 F
1402 5965 1.141019 GCGTTCAGCGGTCAGGATA 59.859 57.895 0.0 0.0 41.69 2.59 F
1440 6003 1.312815 AGCTCTTTGCAGTGTTCACC 58.687 50.000 0.0 0.0 45.94 4.02 F
1443 6013 1.369209 CTTTGCAGTGTTCACCGCG 60.369 57.895 0.0 0.0 0.00 6.46 F
3344 10022 1.497991 TTATCGCTACGCAATCTGGC 58.502 50.000 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2129 8138 0.392706 ATCTGGTGACAACAGACGCA 59.607 50.000 25.19 3.54 46.67 5.24 R
3290 9968 1.002430 CCCCATGATATGACTGACCCG 59.998 57.143 0.00 0.00 0.00 5.28 R
3482 10175 6.097554 TGGAATTGCAACCAAAGAGAAAACTA 59.902 34.615 0.00 0.00 34.05 2.24 R
3515 10208 9.234384 GATGAATTTGAAGATAATTGCAGAGTG 57.766 33.333 0.00 0.00 0.00 3.51 R
5368 13408 0.035056 AAGGCCCGAAAGACAGATGG 60.035 55.000 0.00 0.00 0.00 3.51 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
236 4439 1.009829 GCGTCCCTTCTGCAATACTG 58.990 55.000 0.00 0.00 0.00 2.74
353 4557 4.166725 TGGGATGCCACAATAGAAGAGAAT 59.833 41.667 0.00 0.00 0.00 2.40
383 4587 8.535690 TCGTGTACATATTTATTTCACACACA 57.464 30.769 0.00 0.00 35.65 3.72
384 4588 8.436970 TCGTGTACATATTTATTTCACACACAC 58.563 33.333 0.00 0.00 35.65 3.82
508 4716 5.818857 AGTTTTCACATTTTGCTTGCTTGAT 59.181 32.000 0.00 0.00 0.00 2.57
559 4784 1.727511 TTGCATATGCTTGGGCGCTC 61.728 55.000 27.13 2.47 42.66 5.03
639 4869 2.666317 TCCACTATTCGATGGCTCTGA 58.334 47.619 0.00 0.00 35.81 3.27
649 4879 2.611292 CGATGGCTCTGATCTGAAAACC 59.389 50.000 3.72 6.43 0.00 3.27
699 5149 5.444218 CGAACTAAATCTCACACGCCTAAAC 60.444 44.000 0.00 0.00 0.00 2.01
744 5220 6.321181 AGCTCCACACATTTGAAGAAGTTTAA 59.679 34.615 0.00 0.00 0.00 1.52
745 5221 6.638468 GCTCCACACATTTGAAGAAGTTTAAG 59.362 38.462 0.00 0.00 0.00 1.85
746 5222 7.468631 GCTCCACACATTTGAAGAAGTTTAAGA 60.469 37.037 0.00 0.00 0.00 2.10
796 5272 7.179410 GGCACATTTGAAAACAAACTTTAGTG 58.821 34.615 0.00 0.00 0.00 2.74
818 5294 3.303791 GCTAACACCGTCCTTTGAACAAG 60.304 47.826 0.00 0.00 0.00 3.16
819 5295 2.702592 ACACCGTCCTTTGAACAAGA 57.297 45.000 0.00 0.00 0.00 3.02
820 5296 2.285977 ACACCGTCCTTTGAACAAGAC 58.714 47.619 0.00 0.00 0.00 3.01
821 5297 2.093128 ACACCGTCCTTTGAACAAGACT 60.093 45.455 0.00 0.00 0.00 3.24
888 5433 2.731968 CGTAATTGCTGATGCCAACCAC 60.732 50.000 0.00 0.00 38.71 4.16
890 5435 0.608856 ATTGCTGATGCCAACCACGA 60.609 50.000 0.00 0.00 38.71 4.35
970 5518 3.093717 TCACGAGTCCACTTTGACTTC 57.906 47.619 0.00 0.00 45.41 3.01
973 5521 3.005472 CACGAGTCCACTTTGACTTCCTA 59.995 47.826 0.00 0.00 45.41 2.94
982 5530 5.641209 CCACTTTGACTTCCTACATGAGAAG 59.359 44.000 17.47 17.47 44.14 2.85
994 5545 7.918076 TCCTACATGAGAAGTAGTTCCAAAAT 58.082 34.615 6.68 0.00 37.78 1.82
1011 5562 4.931002 CCAAAATTCCAAATGAGAATGCGT 59.069 37.500 0.00 0.00 34.23 5.24
1027 5578 2.506544 CGTACAGCATCCGAATCCG 58.493 57.895 0.00 0.00 0.00 4.18
1401 5964 2.125512 GCGTTCAGCGGTCAGGAT 60.126 61.111 0.00 0.00 41.69 3.24
1402 5965 1.141019 GCGTTCAGCGGTCAGGATA 59.859 57.895 0.00 0.00 41.69 2.59
1410 5973 2.228582 CAGCGGTCAGGATATCTCTCTG 59.771 54.545 2.05 2.06 0.00 3.35
1437 6000 2.481952 CCAGTAGCTCTTTGCAGTGTTC 59.518 50.000 0.00 0.00 45.94 3.18
1439 6002 3.059325 CAGTAGCTCTTTGCAGTGTTCAC 60.059 47.826 0.00 0.00 45.94 3.18
1440 6003 1.312815 AGCTCTTTGCAGTGTTCACC 58.687 50.000 0.00 0.00 45.94 4.02
1443 6013 1.369209 CTTTGCAGTGTTCACCGCG 60.369 57.895 0.00 0.00 0.00 6.46
1476 6046 5.518847 CCGTGAATTTCTCGAGCATTTAGTA 59.481 40.000 19.31 0.00 35.64 1.82
1477 6047 6.201044 CCGTGAATTTCTCGAGCATTTAGTAT 59.799 38.462 19.31 0.00 35.64 2.12
1478 6048 7.254455 CCGTGAATTTCTCGAGCATTTAGTATT 60.254 37.037 19.31 0.00 35.64 1.89
1479 6049 8.116753 CGTGAATTTCTCGAGCATTTAGTATTT 58.883 33.333 14.00 0.00 35.64 1.40
1480 6050 9.774742 GTGAATTTCTCGAGCATTTAGTATTTT 57.225 29.630 7.81 0.00 0.00 1.82
1516 6086 1.539157 CTCCCCTTCTTGTTCTTGGC 58.461 55.000 0.00 0.00 0.00 4.52
1738 6308 5.287674 TGCAAACATGGATTCTGGAAAAA 57.712 34.783 0.00 0.00 0.00 1.94
1793 7631 8.773136 CGCGTTTATGTTATTGTTTCTTAAGTC 58.227 33.333 0.00 0.00 0.00 3.01
1883 7883 6.624352 TGATTAATAGCTTGCATGGAGAAC 57.376 37.500 0.00 0.00 0.00 3.01
1930 7930 8.664211 ATGGCAATTAGTACTTAGCTAAGTTC 57.336 34.615 36.91 31.66 43.57 3.01
2356 8365 7.199541 AGAGAATTCAGATGTGTGAAACTTG 57.800 36.000 8.44 0.00 39.84 3.16
2357 8366 6.769822 AGAGAATTCAGATGTGTGAAACTTGT 59.230 34.615 8.44 0.00 39.84 3.16
2404 8413 3.848272 ATGGCCACAAACATTTCGTAG 57.152 42.857 8.16 0.00 0.00 3.51
2422 8432 3.119637 CGTAGTAAGTTTGGCCATTTGGG 60.120 47.826 6.09 0.00 40.85 4.12
2479 8489 5.468540 TCTTAGCACAAGTGACACTACAT 57.531 39.130 8.91 0.00 0.00 2.29
2608 8623 2.234143 GCCTTGCAGAAAGAAAGTCCT 58.766 47.619 0.00 0.00 38.24 3.85
2954 9632 1.540435 GGGGAGGATCTGAGATCCGC 61.540 65.000 29.88 29.88 42.87 5.54
3095 9773 4.085357 TCAATGACTAGTTTGCCACACT 57.915 40.909 0.00 0.00 0.00 3.55
3141 9819 8.535690 AACTTGAGCTTGACTATAAGTTGTAC 57.464 34.615 0.00 0.00 41.08 2.90
3245 9923 5.255397 ACTTCAATCCCAGTTATGTTGGA 57.745 39.130 0.00 0.00 37.96 3.53
3334 10012 4.893424 TTCTTTGGCCATTTATCGCTAC 57.107 40.909 6.09 0.00 0.00 3.58
3344 10022 1.497991 TTATCGCTACGCAATCTGGC 58.502 50.000 0.00 0.00 0.00 4.85
3482 10175 7.470935 TTCACAGATTCATTTGGTTGATGAT 57.529 32.000 0.00 0.00 33.82 2.45
3515 10208 6.928492 TCTTTGGTTGCAATTCCACTAAATTC 59.072 34.615 8.23 0.00 33.12 2.17
3541 10234 9.234384 CACTCTGCAATTATCTTCAAATTCATC 57.766 33.333 0.00 0.00 0.00 2.92
3637 10331 1.212751 GGGCTGCACGTGGATTTTC 59.787 57.895 18.88 4.07 0.00 2.29
3641 10335 2.545742 GGCTGCACGTGGATTTTCTTTT 60.546 45.455 18.88 0.00 0.00 2.27
3643 10337 3.182372 GCTGCACGTGGATTTTCTTTTTC 59.818 43.478 18.88 0.00 0.00 2.29
3644 10338 4.610945 CTGCACGTGGATTTTCTTTTTCT 58.389 39.130 18.88 0.00 0.00 2.52
3792 11822 2.237392 AGATGGCCTCTACAACTTGGTC 59.763 50.000 3.32 0.00 30.26 4.02
3861 11891 3.446442 AAAGGTGATCAGCCTGTTCAT 57.554 42.857 20.92 0.00 36.30 2.57
3904 11934 8.602328 TCAGCAATTCTTGTTGTACAATTTTTG 58.398 29.630 12.26 10.79 41.82 2.44
3905 11935 8.389603 CAGCAATTCTTGTTGTACAATTTTTGT 58.610 29.630 12.26 0.00 37.48 2.83
3918 11948 4.034975 ACAATTTTTGTTGCCCATTCAACG 59.965 37.500 2.76 0.00 46.85 4.10
4120 12154 3.555527 TCAAGGGATGATGAGCTTCAG 57.444 47.619 0.00 0.00 31.50 3.02
4225 12259 0.261402 TGCCCACCATATTTCCCCAG 59.739 55.000 0.00 0.00 0.00 4.45
4226 12260 1.115326 GCCCACCATATTTCCCCAGC 61.115 60.000 0.00 0.00 0.00 4.85
4227 12261 0.557729 CCCACCATATTTCCCCAGCT 59.442 55.000 0.00 0.00 0.00 4.24
4228 12262 1.696063 CCACCATATTTCCCCAGCTG 58.304 55.000 6.78 6.78 0.00 4.24
4229 12263 1.215173 CCACCATATTTCCCCAGCTGA 59.785 52.381 17.39 0.00 0.00 4.26
4230 12264 2.358090 CCACCATATTTCCCCAGCTGAA 60.358 50.000 17.39 0.80 0.00 3.02
4231 12265 2.954318 CACCATATTTCCCCAGCTGAAG 59.046 50.000 17.39 5.89 0.00 3.02
4232 12266 2.582636 ACCATATTTCCCCAGCTGAAGT 59.417 45.455 17.39 0.71 0.00 3.01
4233 12267 2.954318 CCATATTTCCCCAGCTGAAGTG 59.046 50.000 17.39 4.88 0.00 3.16
4234 12268 2.806945 TATTTCCCCAGCTGAAGTGG 57.193 50.000 17.39 7.60 34.52 4.00
4235 12269 0.779997 ATTTCCCCAGCTGAAGTGGT 59.220 50.000 17.39 0.00 32.62 4.16
4236 12270 1.440618 TTTCCCCAGCTGAAGTGGTA 58.559 50.000 17.39 1.03 32.62 3.25
4237 12271 1.668826 TTCCCCAGCTGAAGTGGTAT 58.331 50.000 17.39 0.00 32.62 2.73
4238 12272 0.911769 TCCCCAGCTGAAGTGGTATG 59.088 55.000 17.39 0.00 32.62 2.39
4239 12273 0.620556 CCCCAGCTGAAGTGGTATGT 59.379 55.000 17.39 0.00 32.62 2.29
4240 12274 1.679944 CCCCAGCTGAAGTGGTATGTG 60.680 57.143 17.39 0.00 32.62 3.21
4241 12275 1.089920 CCAGCTGAAGTGGTATGTGC 58.910 55.000 17.39 0.00 0.00 4.57
4242 12276 1.339438 CCAGCTGAAGTGGTATGTGCT 60.339 52.381 17.39 0.00 0.00 4.40
4243 12277 2.430465 CAGCTGAAGTGGTATGTGCTT 58.570 47.619 8.42 0.00 0.00 3.91
4244 12278 2.161012 CAGCTGAAGTGGTATGTGCTTG 59.839 50.000 8.42 0.00 0.00 4.01
4245 12279 2.154462 GCTGAAGTGGTATGTGCTTGT 58.846 47.619 0.00 0.00 0.00 3.16
4246 12280 2.160417 GCTGAAGTGGTATGTGCTTGTC 59.840 50.000 0.00 0.00 0.00 3.18
4247 12281 3.668447 CTGAAGTGGTATGTGCTTGTCT 58.332 45.455 0.00 0.00 0.00 3.41
4248 12282 3.402110 TGAAGTGGTATGTGCTTGTCTG 58.598 45.455 0.00 0.00 0.00 3.51
4249 12283 1.813513 AGTGGTATGTGCTTGTCTGC 58.186 50.000 0.00 0.00 0.00 4.26
4250 12284 1.349026 AGTGGTATGTGCTTGTCTGCT 59.651 47.619 0.00 0.00 0.00 4.24
4251 12285 2.567169 AGTGGTATGTGCTTGTCTGCTA 59.433 45.455 0.00 0.00 0.00 3.49
4252 12286 2.673368 GTGGTATGTGCTTGTCTGCTAC 59.327 50.000 0.00 0.00 0.00 3.58
4253 12287 2.567169 TGGTATGTGCTTGTCTGCTACT 59.433 45.455 0.00 0.00 0.00 2.57
4254 12288 3.007940 TGGTATGTGCTTGTCTGCTACTT 59.992 43.478 0.00 0.00 0.00 2.24
4255 12289 4.221924 TGGTATGTGCTTGTCTGCTACTTA 59.778 41.667 0.00 0.00 0.00 2.24
4256 12290 4.567159 GGTATGTGCTTGTCTGCTACTTAC 59.433 45.833 0.00 0.00 31.87 2.34
4257 12291 4.543590 ATGTGCTTGTCTGCTACTTACT 57.456 40.909 0.00 0.00 0.00 2.24
4258 12292 4.336889 TGTGCTTGTCTGCTACTTACTT 57.663 40.909 0.00 0.00 0.00 2.24
4297 12331 3.433615 GTGCTTGTCTGCTACTTACTTGG 59.566 47.826 0.00 0.00 0.00 3.61
4427 12461 2.108514 CGATGGTGGCGTCATTGCT 61.109 57.895 0.00 0.00 34.52 3.91
4574 12608 1.299089 CGTGCTCGGATGCGTCATA 60.299 57.895 6.49 0.00 35.36 2.15
4604 12638 2.149383 ACTGTGGCTCTTCTGGGCA 61.149 57.895 0.00 0.00 36.92 5.36
4616 12650 1.131638 TCTGGGCAGCCTTCGATATT 58.868 50.000 12.43 0.00 0.00 1.28
4619 12653 0.179018 GGGCAGCCTTCGATATTGGT 60.179 55.000 12.43 0.00 0.00 3.67
4691 12725 1.032114 CCATTCTTGGGGTCGAAGGC 61.032 60.000 0.00 0.00 39.56 4.35
4692 12726 0.322456 CATTCTTGGGGTCGAAGGCA 60.322 55.000 0.00 0.00 0.00 4.75
4724 12758 1.220206 CCAGCACTGCCTCGAGATT 59.780 57.895 15.71 0.00 0.00 2.40
4811 12845 1.128200 CGAGGTTCATCCCCATACCA 58.872 55.000 0.00 0.00 36.75 3.25
4844 12878 2.701006 CCGTTCTACATTGGCGCG 59.299 61.111 0.00 0.00 0.00 6.86
4865 12899 0.604073 TCTTCGGCGTGGACATGTTA 59.396 50.000 6.85 0.00 0.00 2.41
4993 13027 2.159421 GCATTCCATCTGCTGTTCTGTG 60.159 50.000 0.00 0.00 36.68 3.66
5030 13064 2.361610 CCGGTCTGCATGGCCTTT 60.362 61.111 3.32 0.00 38.58 3.11
5071 13105 2.104451 CCAGGTGAGAAGATGGATCCAG 59.896 54.545 21.33 1.30 34.60 3.86
5145 13179 3.628017 TCATACGTACAGATGTGCATCG 58.372 45.455 0.00 4.95 42.48 3.84
5186 13220 0.738389 AACGAACCACAGCACTTTGG 59.262 50.000 1.23 1.23 39.00 3.28
5187 13221 0.107410 ACGAACCACAGCACTTTGGA 60.107 50.000 9.78 0.00 36.28 3.53
5188 13222 1.238439 CGAACCACAGCACTTTGGAT 58.762 50.000 9.78 0.00 36.28 3.41
5189 13223 1.608590 CGAACCACAGCACTTTGGATT 59.391 47.619 9.78 1.00 36.28 3.01
5190 13224 2.034558 CGAACCACAGCACTTTGGATTT 59.965 45.455 9.78 0.00 36.28 2.17
5191 13225 3.383761 GAACCACAGCACTTTGGATTTG 58.616 45.455 9.78 0.00 36.28 2.32
5285 13325 1.895020 TTGAACGGTCATCGGGGGAG 61.895 60.000 2.76 0.00 44.45 4.30
5313 13353 3.916349 CCCTCCCCACCTGAATATATTGA 59.084 47.826 1.78 0.00 0.00 2.57
5343 13383 1.144913 TGCCAAAGCCAAGAGTTACCT 59.855 47.619 0.00 0.00 38.69 3.08
5344 13384 1.813178 GCCAAAGCCAAGAGTTACCTC 59.187 52.381 0.00 0.00 38.04 3.85
5345 13385 2.076863 CCAAAGCCAAGAGTTACCTCG 58.923 52.381 0.00 0.00 42.86 4.63
5346 13386 2.550208 CCAAAGCCAAGAGTTACCTCGT 60.550 50.000 0.00 0.00 42.86 4.18
5356 13396 5.541953 AGAGTTACCTCGTAAACTTTGGT 57.458 39.130 0.00 0.00 42.86 3.67
5357 13397 5.922053 AGAGTTACCTCGTAAACTTTGGTT 58.078 37.500 0.00 0.00 42.86 3.67
5358 13398 5.756833 AGAGTTACCTCGTAAACTTTGGTTG 59.243 40.000 0.00 0.00 42.86 3.77
5359 13399 5.430886 AGTTACCTCGTAAACTTTGGTTGT 58.569 37.500 0.00 0.00 35.63 3.32
5360 13400 5.882000 AGTTACCTCGTAAACTTTGGTTGTT 59.118 36.000 0.00 0.00 35.63 2.83
5361 13401 6.375174 AGTTACCTCGTAAACTTTGGTTGTTT 59.625 34.615 0.00 0.00 40.27 2.83
5362 13402 5.648178 ACCTCGTAAACTTTGGTTGTTTT 57.352 34.783 0.00 0.00 38.41 2.43
5363 13403 6.756299 ACCTCGTAAACTTTGGTTGTTTTA 57.244 33.333 0.00 0.00 38.41 1.52
5364 13404 7.337480 ACCTCGTAAACTTTGGTTGTTTTAT 57.663 32.000 0.00 0.00 38.41 1.40
5365 13405 7.420002 ACCTCGTAAACTTTGGTTGTTTTATC 58.580 34.615 0.00 0.00 38.41 1.75
5366 13406 7.283807 ACCTCGTAAACTTTGGTTGTTTTATCT 59.716 33.333 0.00 0.00 38.41 1.98
5367 13407 8.132995 CCTCGTAAACTTTGGTTGTTTTATCTT 58.867 33.333 0.00 0.00 38.41 2.40
5368 13408 9.166126 CTCGTAAACTTTGGTTGTTTTATCTTC 57.834 33.333 0.00 0.00 38.41 2.87
5369 13409 8.130469 TCGTAAACTTTGGTTGTTTTATCTTCC 58.870 33.333 0.00 0.00 38.41 3.46
5370 13410 7.916450 CGTAAACTTTGGTTGTTTTATCTTCCA 59.084 33.333 0.00 0.00 38.41 3.53
5371 13411 9.758651 GTAAACTTTGGTTGTTTTATCTTCCAT 57.241 29.630 0.00 0.00 38.41 3.41
5372 13412 8.887036 AAACTTTGGTTGTTTTATCTTCCATC 57.113 30.769 0.00 0.00 34.40 3.51
5373 13413 7.839680 ACTTTGGTTGTTTTATCTTCCATCT 57.160 32.000 0.00 0.00 0.00 2.90
5374 13414 7.661040 ACTTTGGTTGTTTTATCTTCCATCTG 58.339 34.615 0.00 0.00 0.00 2.90
5375 13415 7.287696 ACTTTGGTTGTTTTATCTTCCATCTGT 59.712 33.333 0.00 0.00 0.00 3.41
5376 13416 6.817765 TGGTTGTTTTATCTTCCATCTGTC 57.182 37.500 0.00 0.00 0.00 3.51
5377 13417 6.542821 TGGTTGTTTTATCTTCCATCTGTCT 58.457 36.000 0.00 0.00 0.00 3.41
5378 13418 7.004086 TGGTTGTTTTATCTTCCATCTGTCTT 58.996 34.615 0.00 0.00 0.00 3.01
5379 13419 7.505585 TGGTTGTTTTATCTTCCATCTGTCTTT 59.494 33.333 0.00 0.00 0.00 2.52
5380 13420 8.023706 GGTTGTTTTATCTTCCATCTGTCTTTC 58.976 37.037 0.00 0.00 0.00 2.62
5381 13421 7.364522 TGTTTTATCTTCCATCTGTCTTTCG 57.635 36.000 0.00 0.00 0.00 3.46
5382 13422 6.371548 TGTTTTATCTTCCATCTGTCTTTCGG 59.628 38.462 0.00 0.00 0.00 4.30
5383 13423 3.550437 ATCTTCCATCTGTCTTTCGGG 57.450 47.619 0.00 0.00 0.00 5.14
5384 13424 1.066143 TCTTCCATCTGTCTTTCGGGC 60.066 52.381 0.00 0.00 0.00 6.13
5385 13425 0.035439 TTCCATCTGTCTTTCGGGCC 60.035 55.000 0.00 0.00 0.00 5.80
5386 13426 0.909610 TCCATCTGTCTTTCGGGCCT 60.910 55.000 0.84 0.00 0.00 5.19
5387 13427 0.035056 CCATCTGTCTTTCGGGCCTT 60.035 55.000 0.84 0.00 0.00 4.35
5388 13428 1.373570 CATCTGTCTTTCGGGCCTTC 58.626 55.000 0.84 0.00 0.00 3.46
5389 13429 0.253327 ATCTGTCTTTCGGGCCTTCC 59.747 55.000 0.84 0.00 0.00 3.46
5390 13430 1.125093 TCTGTCTTTCGGGCCTTCCA 61.125 55.000 0.84 0.00 34.36 3.53
5391 13431 0.035056 CTGTCTTTCGGGCCTTCCAT 60.035 55.000 0.84 0.00 34.36 3.41
5392 13432 0.322456 TGTCTTTCGGGCCTTCCATG 60.322 55.000 0.84 0.00 34.36 3.66
5393 13433 0.322546 GTCTTTCGGGCCTTCCATGT 60.323 55.000 0.84 0.00 34.36 3.21
5394 13434 0.404040 TCTTTCGGGCCTTCCATGTT 59.596 50.000 0.84 0.00 34.36 2.71
5395 13435 1.203001 TCTTTCGGGCCTTCCATGTTT 60.203 47.619 0.84 0.00 34.36 2.83
5396 13436 1.202348 CTTTCGGGCCTTCCATGTTTC 59.798 52.381 0.84 0.00 34.36 2.78
5397 13437 0.111446 TTCGGGCCTTCCATGTTTCA 59.889 50.000 0.84 0.00 34.36 2.69
5398 13438 0.608035 TCGGGCCTTCCATGTTTCAC 60.608 55.000 0.84 0.00 34.36 3.18
5399 13439 0.609131 CGGGCCTTCCATGTTTCACT 60.609 55.000 0.84 0.00 34.36 3.41
5400 13440 1.339631 CGGGCCTTCCATGTTTCACTA 60.340 52.381 0.84 0.00 34.36 2.74
5401 13441 2.369394 GGGCCTTCCATGTTTCACTAG 58.631 52.381 0.84 0.00 35.00 2.57
5402 13442 2.290960 GGGCCTTCCATGTTTCACTAGT 60.291 50.000 0.84 0.00 35.00 2.57
5403 13443 3.010420 GGCCTTCCATGTTTCACTAGTC 58.990 50.000 0.00 0.00 0.00 2.59
5404 13444 3.559171 GGCCTTCCATGTTTCACTAGTCA 60.559 47.826 0.00 0.00 0.00 3.41
5405 13445 4.265073 GCCTTCCATGTTTCACTAGTCAT 58.735 43.478 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.113617 CGTCCCTCAGGAGGTTGA 57.886 61.111 14.00 2.71 45.21 3.18
119 4322 2.304180 CTCCCAGACAAACAGGATGACT 59.696 50.000 0.00 0.00 39.69 3.41
171 4374 2.664851 CGAAGCAACCGCACCTGA 60.665 61.111 0.00 0.00 42.27 3.86
176 4379 2.517402 AAACCCGAAGCAACCGCA 60.517 55.556 0.00 0.00 42.27 5.69
209 4412 1.403814 CAGAAGGGACGCTCCAGATA 58.596 55.000 6.41 0.00 38.64 1.98
236 4439 3.862642 GCGGGTCAATCCTCATGATAGAC 60.863 52.174 0.00 0.51 36.25 2.59
353 4557 7.222999 TGTGAAATAAATATGTACACGATGCGA 59.777 33.333 0.00 0.00 0.00 5.10
383 4587 1.931172 GCCGCAGTATGATTTACACGT 59.069 47.619 0.00 0.00 39.69 4.49
384 4588 1.930503 TGCCGCAGTATGATTTACACG 59.069 47.619 0.00 0.00 39.69 4.49
387 4591 6.142320 GCTATTTTTGCCGCAGTATGATTTAC 59.858 38.462 0.00 0.00 39.69 2.01
388 4592 6.183360 TGCTATTTTTGCCGCAGTATGATTTA 60.183 34.615 0.00 0.00 39.69 1.40
390 4594 4.097741 TGCTATTTTTGCCGCAGTATGATT 59.902 37.500 0.00 0.00 39.69 2.57
391 4595 3.631686 TGCTATTTTTGCCGCAGTATGAT 59.368 39.130 0.00 0.00 39.69 2.45
392 4596 3.013219 TGCTATTTTTGCCGCAGTATGA 58.987 40.909 0.00 0.00 39.69 2.15
393 4597 3.365832 CTGCTATTTTTGCCGCAGTATG 58.634 45.455 0.00 0.00 43.53 2.39
421 4625 5.174035 GGTCGAGATATCAACAGAATGAACG 59.826 44.000 5.32 0.00 39.69 3.95
508 4716 0.730155 CGTACCGCGCAAACACTAGA 60.730 55.000 8.75 0.00 0.00 2.43
537 4762 1.774639 CGCCCAAGCATATGCAATTC 58.225 50.000 28.62 12.52 45.16 2.17
608 4838 7.667557 CCATCGAATAGTGGATTTCCTACTTA 58.332 38.462 0.00 0.00 37.72 2.24
639 4869 5.279156 GCAAGTTCTGGAATGGTTTTCAGAT 60.279 40.000 0.00 0.00 45.05 2.90
649 4879 6.320672 AGGATAATCAAGCAAGTTCTGGAATG 59.679 38.462 0.00 0.00 0.00 2.67
699 5149 0.456142 TTGAGATTCGTCGGCGTCAG 60.456 55.000 10.18 0.00 39.49 3.51
744 5220 7.011763 CACAATTCGAACCATCACAAGATATCT 59.988 37.037 0.00 0.00 31.88 1.98
745 5221 7.128331 CACAATTCGAACCATCACAAGATATC 58.872 38.462 0.00 0.00 31.88 1.63
746 5222 6.038603 CCACAATTCGAACCATCACAAGATAT 59.961 38.462 0.00 0.00 31.88 1.63
796 5272 2.215196 TGTTCAAAGGACGGTGTTAGC 58.785 47.619 0.00 0.00 0.00 3.09
808 5284 5.218139 GGAAGATTGCAGTCTTGTTCAAAG 58.782 41.667 27.02 0.00 38.51 2.77
818 5294 4.094590 CACATCTCTTGGAAGATTGCAGTC 59.905 45.833 0.00 0.00 33.68 3.51
819 5295 4.008330 CACATCTCTTGGAAGATTGCAGT 58.992 43.478 0.00 0.00 33.68 4.40
820 5296 4.259356 TCACATCTCTTGGAAGATTGCAG 58.741 43.478 0.00 0.00 33.68 4.41
821 5297 4.290711 TCACATCTCTTGGAAGATTGCA 57.709 40.909 0.00 0.00 33.68 4.08
858 5345 6.987404 TGGCATCAGCAATTACGTATACTTTA 59.013 34.615 0.00 0.00 44.61 1.85
859 5346 5.820423 TGGCATCAGCAATTACGTATACTTT 59.180 36.000 0.00 0.00 44.61 2.66
860 5347 5.364778 TGGCATCAGCAATTACGTATACTT 58.635 37.500 0.00 0.00 44.61 2.24
861 5348 4.956085 TGGCATCAGCAATTACGTATACT 58.044 39.130 0.00 0.00 44.61 2.12
888 5433 1.004185 CAAGAAATCATCGCAGCCTCG 60.004 52.381 0.00 0.00 0.00 4.63
890 5435 2.119801 ACAAGAAATCATCGCAGCCT 57.880 45.000 0.00 0.00 0.00 4.58
893 5438 4.840401 TCGTTACAAGAAATCATCGCAG 57.160 40.909 0.00 0.00 0.00 5.18
895 5440 5.053025 GCAAATCGTTACAAGAAATCATCGC 60.053 40.000 0.00 0.00 0.00 4.58
970 5518 8.567285 AATTTTGGAACTACTTCTCATGTAGG 57.433 34.615 0.00 0.00 41.03 3.18
973 5521 7.004086 TGGAATTTTGGAACTACTTCTCATGT 58.996 34.615 0.00 0.00 0.00 3.21
982 5530 9.143631 CATTCTCATTTGGAATTTTGGAACTAC 57.856 33.333 0.00 0.00 31.90 2.73
994 5545 3.126858 GCTGTACGCATTCTCATTTGGAA 59.873 43.478 5.07 0.00 38.92 3.53
1011 5562 1.605457 GCATCGGATTCGGATGCTGTA 60.605 52.381 34.25 1.54 41.74 2.74
1018 5569 2.483876 GATTTCAGCATCGGATTCGGA 58.516 47.619 0.00 0.00 36.95 4.55
1022 5573 3.131046 GGTTTGGATTTCAGCATCGGATT 59.869 43.478 0.00 0.00 0.00 3.01
1023 5574 2.689983 GGTTTGGATTTCAGCATCGGAT 59.310 45.455 0.00 0.00 0.00 4.18
1024 5575 2.091541 GGTTTGGATTTCAGCATCGGA 58.908 47.619 0.00 0.00 0.00 4.55
1025 5576 1.134946 GGGTTTGGATTTCAGCATCGG 59.865 52.381 0.00 0.00 0.00 4.18
1026 5577 2.094675 AGGGTTTGGATTTCAGCATCG 58.905 47.619 0.00 0.00 0.00 3.84
1027 5578 3.853475 CAAGGGTTTGGATTTCAGCATC 58.147 45.455 0.00 0.00 0.00 3.91
1443 6013 1.732259 AGAAATTCACGGCGACATGTC 59.268 47.619 16.62 16.21 0.00 3.06
1476 6046 5.355071 GGAGGGACGTTCCGTAAAATAAAAT 59.645 40.000 7.39 0.00 41.37 1.82
1477 6047 4.694982 GGAGGGACGTTCCGTAAAATAAAA 59.305 41.667 7.39 0.00 41.37 1.52
1478 6048 4.252878 GGAGGGACGTTCCGTAAAATAAA 58.747 43.478 7.39 0.00 41.37 1.40
1479 6049 3.369366 GGGAGGGACGTTCCGTAAAATAA 60.369 47.826 7.39 0.00 41.37 1.40
1480 6050 2.168313 GGGAGGGACGTTCCGTAAAATA 59.832 50.000 7.39 0.00 41.37 1.40
1481 6051 1.065926 GGGAGGGACGTTCCGTAAAAT 60.066 52.381 7.39 0.00 41.37 1.82
1482 6052 0.321346 GGGAGGGACGTTCCGTAAAA 59.679 55.000 7.39 0.00 41.37 1.52
1483 6053 1.543944 GGGGAGGGACGTTCCGTAAA 61.544 60.000 7.39 0.00 41.37 2.01
1487 6057 3.001406 AAGGGGAGGGACGTTCCG 61.001 66.667 7.39 0.00 37.43 4.30
1502 6072 1.610522 CACCCTGCCAAGAACAAGAAG 59.389 52.381 0.00 0.00 0.00 2.85
1516 6086 3.076258 TACGATGCCGAGCACCCTG 62.076 63.158 0.50 0.00 43.04 4.45
1738 6308 9.503399 CTTTAACTCTGTAGTCAAGGGTAATTT 57.497 33.333 0.00 0.00 33.75 1.82
1739 6309 8.657712 ACTTTAACTCTGTAGTCAAGGGTAATT 58.342 33.333 0.00 0.00 33.75 1.40
1740 6310 8.203681 ACTTTAACTCTGTAGTCAAGGGTAAT 57.796 34.615 0.00 0.00 33.75 1.89
1750 7588 2.555757 ACGCGGACTTTAACTCTGTAGT 59.444 45.455 12.47 0.00 37.65 2.73
1793 7631 1.200716 CACCAATACCTGCAGCACTTG 59.799 52.381 8.66 10.40 0.00 3.16
1855 7693 6.301486 TCCATGCAAGCTATTAATCATCAGT 58.699 36.000 0.00 0.00 0.00 3.41
1883 7883 3.679389 ACCCTGTAACATCAGCTTCTTG 58.321 45.455 0.00 0.00 34.47 3.02
1930 7930 1.014044 CACCGTGTCCACATTCTCGG 61.014 60.000 5.24 5.24 43.38 4.63
2129 8138 0.392706 ATCTGGTGACAACAGACGCA 59.607 50.000 25.19 3.54 46.67 5.24
2131 8140 3.859961 GTCATATCTGGTGACAACAGACG 59.140 47.826 25.19 16.10 46.67 4.18
2183 8192 5.822519 CAGGCTCCATTTTAGCATAAGTGTA 59.177 40.000 0.00 0.00 41.93 2.90
2256 8265 5.001232 GTGAATAGTGGAGGTGCTAAAACA 58.999 41.667 0.00 0.00 0.00 2.83
2356 8365 4.142403 TGGCTCGATGAAAATGGATTGAAC 60.142 41.667 0.00 0.00 0.00 3.18
2357 8366 4.015764 TGGCTCGATGAAAATGGATTGAA 58.984 39.130 0.00 0.00 0.00 2.69
2404 8413 1.338674 GCCCCAAATGGCCAAACTTAC 60.339 52.381 10.96 0.00 46.11 2.34
2608 8623 4.217550 GGCTCATGTACTTTACAAGGCAAA 59.782 41.667 6.68 0.00 42.76 3.68
2716 8731 3.609103 ACGTGTTCTTAAAAGCTGCAG 57.391 42.857 10.11 10.11 0.00 4.41
3075 9753 4.275689 TGAAGTGTGGCAAACTAGTCATTG 59.724 41.667 11.49 0.00 0.00 2.82
3095 9773 9.474920 CAAGTTTGAATAGGTAAAAAGCATGAA 57.525 29.630 0.00 0.00 0.00 2.57
3162 9840 7.297936 TCAGACAACTGGACATTCTTAACTA 57.702 36.000 0.00 0.00 43.60 2.24
3290 9968 1.002430 CCCCATGATATGACTGACCCG 59.998 57.143 0.00 0.00 0.00 5.28
3482 10175 6.097554 TGGAATTGCAACCAAAGAGAAAACTA 59.902 34.615 0.00 0.00 34.05 2.24
3515 10208 9.234384 GATGAATTTGAAGATAATTGCAGAGTG 57.766 33.333 0.00 0.00 0.00 3.51
3541 10234 5.362556 TCTCTTCAAAAGAAATGCTTCGG 57.637 39.130 0.00 0.00 37.02 4.30
3683 11689 5.019470 TCAACCATGGCCATGTTACATTAA 58.981 37.500 37.30 15.92 37.11 1.40
3792 11822 7.223193 TCTCTTGCAATGACAACAAAGATTTTG 59.777 33.333 0.00 0.28 0.00 2.44
3861 11891 3.244526 TGCTGATGTTACCTTGAAGAGCA 60.245 43.478 0.00 0.00 0.00 4.26
3904 11934 0.596341 AAACGCGTTGAATGGGCAAC 60.596 50.000 27.34 0.00 43.53 4.17
3905 11935 0.952280 TAAACGCGTTGAATGGGCAA 59.048 45.000 27.34 0.00 0.00 4.52
3918 11948 8.460831 AATTCAAGTCATAAAATGGTAAACGC 57.539 30.769 0.00 0.00 0.00 4.84
4120 12154 8.954950 TCCTATCTTTGAAGAACATCTCAATC 57.045 34.615 0.00 0.00 38.77 2.67
4225 12259 2.154462 ACAAGCACATACCACTTCAGC 58.846 47.619 0.00 0.00 0.00 4.26
4226 12260 3.434641 CAGACAAGCACATACCACTTCAG 59.565 47.826 0.00 0.00 0.00 3.02
4227 12261 3.402110 CAGACAAGCACATACCACTTCA 58.598 45.455 0.00 0.00 0.00 3.02
4228 12262 2.160417 GCAGACAAGCACATACCACTTC 59.840 50.000 0.00 0.00 0.00 3.01
4229 12263 2.154462 GCAGACAAGCACATACCACTT 58.846 47.619 0.00 0.00 0.00 3.16
4230 12264 1.349026 AGCAGACAAGCACATACCACT 59.651 47.619 0.00 0.00 36.85 4.00
4231 12265 1.813513 AGCAGACAAGCACATACCAC 58.186 50.000 0.00 0.00 36.85 4.16
4232 12266 2.567169 AGTAGCAGACAAGCACATACCA 59.433 45.455 0.00 0.00 36.85 3.25
4233 12267 3.252974 AGTAGCAGACAAGCACATACC 57.747 47.619 0.00 0.00 36.85 2.73
4234 12268 5.411781 AGTAAGTAGCAGACAAGCACATAC 58.588 41.667 0.00 0.00 36.85 2.39
4235 12269 5.661056 AGTAAGTAGCAGACAAGCACATA 57.339 39.130 0.00 0.00 36.85 2.29
4236 12270 4.543590 AGTAAGTAGCAGACAAGCACAT 57.456 40.909 0.00 0.00 36.85 3.21
4237 12271 4.058124 CAAGTAAGTAGCAGACAAGCACA 58.942 43.478 0.00 0.00 36.85 4.57
4238 12272 3.120511 GCAAGTAAGTAGCAGACAAGCAC 60.121 47.826 0.00 0.00 36.85 4.40
4239 12273 3.067106 GCAAGTAAGTAGCAGACAAGCA 58.933 45.455 0.00 0.00 36.85 3.91
4240 12274 3.124297 CAGCAAGTAAGTAGCAGACAAGC 59.876 47.826 0.00 0.00 0.00 4.01
4241 12275 4.560128 TCAGCAAGTAAGTAGCAGACAAG 58.440 43.478 0.00 0.00 0.00 3.16
4242 12276 4.600692 TCAGCAAGTAAGTAGCAGACAA 57.399 40.909 0.00 0.00 0.00 3.18
4243 12277 4.039245 ACTTCAGCAAGTAAGTAGCAGACA 59.961 41.667 0.00 0.00 41.39 3.41
4244 12278 4.387256 CACTTCAGCAAGTAAGTAGCAGAC 59.613 45.833 0.00 0.00 41.24 3.51
4245 12279 4.560128 CACTTCAGCAAGTAAGTAGCAGA 58.440 43.478 0.00 0.00 41.24 4.26
4246 12280 3.681897 CCACTTCAGCAAGTAAGTAGCAG 59.318 47.826 0.00 0.00 41.24 4.24
4247 12281 3.071023 ACCACTTCAGCAAGTAAGTAGCA 59.929 43.478 0.00 0.00 41.24 3.49
4248 12282 3.665190 ACCACTTCAGCAAGTAAGTAGC 58.335 45.455 0.00 0.00 41.24 3.58
4249 12283 6.868622 AGATACCACTTCAGCAAGTAAGTAG 58.131 40.000 0.00 0.00 41.24 2.57
4250 12284 6.852420 AGATACCACTTCAGCAAGTAAGTA 57.148 37.500 0.00 0.00 41.24 2.24
4251 12285 5.746990 AGATACCACTTCAGCAAGTAAGT 57.253 39.130 0.00 0.00 41.24 2.24
4252 12286 5.934625 ACAAGATACCACTTCAGCAAGTAAG 59.065 40.000 0.00 0.00 41.24 2.34
4253 12287 5.700832 CACAAGATACCACTTCAGCAAGTAA 59.299 40.000 0.00 0.00 41.24 2.24
4254 12288 5.237815 CACAAGATACCACTTCAGCAAGTA 58.762 41.667 0.00 0.00 41.24 2.24
4255 12289 4.067896 CACAAGATACCACTTCAGCAAGT 58.932 43.478 0.00 0.00 44.26 3.16
4256 12290 3.120060 GCACAAGATACCACTTCAGCAAG 60.120 47.826 0.00 0.00 35.50 4.01
4257 12291 2.813754 GCACAAGATACCACTTCAGCAA 59.186 45.455 0.00 0.00 31.48 3.91
4258 12292 2.038952 AGCACAAGATACCACTTCAGCA 59.961 45.455 0.00 0.00 32.67 4.41
4403 12437 3.716539 GACGCCACCATCGCTGCTA 62.717 63.158 0.00 0.00 0.00 3.49
4442 12476 2.352030 GGCAATGGACATGATTATGCCG 60.352 50.000 14.81 0.00 41.97 5.69
4604 12638 1.141053 GGGTCACCAATATCGAAGGCT 59.859 52.381 0.00 0.00 36.50 4.58
4692 12726 4.809496 CTGGGGCAGAGCGGCAAT 62.809 66.667 1.45 0.00 43.60 3.56
4724 12758 1.602668 GCCAAGAAGAATGCGCAACAA 60.603 47.619 17.11 0.00 0.00 2.83
4844 12878 0.949105 ACATGTCCACGCCGAAGAAC 60.949 55.000 0.00 0.00 0.00 3.01
4865 12899 3.687698 CGAACAAGATTACCGTCCCAATT 59.312 43.478 0.00 0.00 0.00 2.32
4993 13027 2.883386 GGTGGATCAATTCTCAGGATGC 59.117 50.000 0.00 0.00 34.76 3.91
5071 13105 0.755686 CCATGTCCTAGAGTGAGCCC 59.244 60.000 0.00 0.00 0.00 5.19
5145 13179 6.908820 CGTTTTCCTTTGTACAGGAGTAAAAC 59.091 38.462 20.30 20.30 44.18 2.43
5268 13302 2.499685 CTCCCCCGATGACCGTTC 59.500 66.667 0.00 0.00 36.31 3.95
5269 13303 3.081409 CCTCCCCCGATGACCGTT 61.081 66.667 0.00 0.00 36.31 4.44
5272 13306 3.794149 ATCCCCTCCCCCGATGACC 62.794 68.421 0.00 0.00 0.00 4.02
5274 13308 2.204319 GATCCCCTCCCCCGATGA 59.796 66.667 0.00 0.00 0.00 2.92
5275 13309 2.930562 GGATCCCCTCCCCCGATG 60.931 72.222 0.00 0.00 38.19 3.84
5295 13335 7.838079 TTTTGATCAATATATTCAGGTGGGG 57.162 36.000 9.40 0.00 0.00 4.96
5300 13340 7.597743 GGCAGCTTTTTGATCAATATATTCAGG 59.402 37.037 9.40 0.00 0.00 3.86
5301 13341 8.139350 TGGCAGCTTTTTGATCAATATATTCAG 58.861 33.333 9.40 0.00 0.00 3.02
5339 13379 6.756299 AAAACAACCAAAGTTTACGAGGTA 57.244 33.333 0.00 0.00 38.17 3.08
5343 13383 8.130469 GGAAGATAAAACAACCAAAGTTTACGA 58.870 33.333 0.00 0.00 38.17 3.43
5344 13384 7.916450 TGGAAGATAAAACAACCAAAGTTTACG 59.084 33.333 0.00 0.00 38.17 3.18
5345 13385 9.758651 ATGGAAGATAAAACAACCAAAGTTTAC 57.241 29.630 0.00 0.00 38.17 2.01
5346 13386 9.974980 GATGGAAGATAAAACAACCAAAGTTTA 57.025 29.630 0.00 0.00 38.17 2.01
5356 13396 7.094805 CCGAAAGACAGATGGAAGATAAAACAA 60.095 37.037 0.00 0.00 0.00 2.83
5357 13397 6.371548 CCGAAAGACAGATGGAAGATAAAACA 59.628 38.462 0.00 0.00 0.00 2.83
5358 13398 6.183360 CCCGAAAGACAGATGGAAGATAAAAC 60.183 42.308 0.00 0.00 0.00 2.43
5359 13399 5.880332 CCCGAAAGACAGATGGAAGATAAAA 59.120 40.000 0.00 0.00 0.00 1.52
5360 13400 5.428253 CCCGAAAGACAGATGGAAGATAAA 58.572 41.667 0.00 0.00 0.00 1.40
5361 13401 4.683400 GCCCGAAAGACAGATGGAAGATAA 60.683 45.833 0.00 0.00 0.00 1.75
5362 13402 3.181465 GCCCGAAAGACAGATGGAAGATA 60.181 47.826 0.00 0.00 0.00 1.98
5363 13403 2.420687 GCCCGAAAGACAGATGGAAGAT 60.421 50.000 0.00 0.00 0.00 2.40
5364 13404 1.066143 GCCCGAAAGACAGATGGAAGA 60.066 52.381 0.00 0.00 0.00 2.87
5365 13405 1.373570 GCCCGAAAGACAGATGGAAG 58.626 55.000 0.00 0.00 0.00 3.46
5366 13406 0.035439 GGCCCGAAAGACAGATGGAA 60.035 55.000 0.00 0.00 0.00 3.53
5367 13407 0.909610 AGGCCCGAAAGACAGATGGA 60.910 55.000 0.00 0.00 0.00 3.41
5368 13408 0.035056 AAGGCCCGAAAGACAGATGG 60.035 55.000 0.00 0.00 0.00 3.51
5369 13409 1.373570 GAAGGCCCGAAAGACAGATG 58.626 55.000 0.00 0.00 0.00 2.90
5370 13410 0.253327 GGAAGGCCCGAAAGACAGAT 59.747 55.000 0.00 0.00 0.00 2.90
5371 13411 1.125093 TGGAAGGCCCGAAAGACAGA 61.125 55.000 0.00 0.00 37.93 3.41
5372 13412 0.035056 ATGGAAGGCCCGAAAGACAG 60.035 55.000 0.00 0.00 37.93 3.51
5373 13413 0.322456 CATGGAAGGCCCGAAAGACA 60.322 55.000 0.00 0.00 37.93 3.41
5374 13414 0.322546 ACATGGAAGGCCCGAAAGAC 60.323 55.000 0.00 0.00 37.93 3.01
5375 13415 0.404040 AACATGGAAGGCCCGAAAGA 59.596 50.000 0.00 0.00 37.93 2.52
5376 13416 1.202348 GAAACATGGAAGGCCCGAAAG 59.798 52.381 0.00 0.00 37.93 2.62
5377 13417 1.253100 GAAACATGGAAGGCCCGAAA 58.747 50.000 0.00 0.00 37.93 3.46
5378 13418 0.111446 TGAAACATGGAAGGCCCGAA 59.889 50.000 0.00 0.00 37.93 4.30
5379 13419 0.608035 GTGAAACATGGAAGGCCCGA 60.608 55.000 0.00 0.00 35.11 5.14
5380 13420 0.609131 AGTGAAACATGGAAGGCCCG 60.609 55.000 0.00 0.00 41.43 6.13
5381 13421 2.290960 ACTAGTGAAACATGGAAGGCCC 60.291 50.000 0.00 0.00 41.43 5.80
5382 13422 3.010420 GACTAGTGAAACATGGAAGGCC 58.990 50.000 0.00 0.00 41.43 5.19
5383 13423 3.674997 TGACTAGTGAAACATGGAAGGC 58.325 45.455 0.00 0.00 41.43 4.35


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

AutoCloner maintained by Alex Coulton.