Multiple sequence alignment - TraesCS1B01G377700

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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 TraesCS1B01G377700 chr1B 100.000 5415 0 0 1 5415 610160206 610165620 0.000000e+00 10000.0
1 TraesCS1B01G377700 chr1B 91.317 1359 85 18 1083 2421 634041062 634042407 0.000000e+00 1825.0
2 TraesCS1B01G377700 chr1B 85.714 63 6 2 4837 4896 606319323 606319261 4.530000e-06 63.9
3 TraesCS1B01G377700 chr1A 92.234 4391 188 68 537 4842 541988362 541992684 0.000000e+00 6078.0
4 TraesCS1B01G377700 chr1A 90.625 416 23 9 5002 5415 541993200 541993601 6.170000e-149 538.0
5 TraesCS1B01G377700 chr1A 90.667 75 7 0 156 230 391943484 391943410 3.450000e-17 100.0
6 TraesCS1B01G377700 chr1D 92.061 4144 184 53 790 4842 446263257 446267346 0.000000e+00 5696.0
7 TraesCS1B01G377700 chr1D 88.174 668 43 13 1 662 446262420 446263057 0.000000e+00 763.0
8 TraesCS1B01G377700 chr1D 92.105 418 25 5 5000 5415 446267433 446267844 2.810000e-162 582.0
9 TraesCS1B01G377700 chr3B 91.538 1359 82 18 1083 2421 47624633 47623288 0.000000e+00 1842.0
10 TraesCS1B01G377700 chr3B 91.023 1359 88 19 1083 2421 702015723 702017067 0.000000e+00 1803.0
11 TraesCS1B01G377700 chr3B 86.000 150 17 4 223 371 2217852 2217998 2.020000e-34 158.0
12 TraesCS1B01G377700 chr3B 87.692 65 4 3 4835 4897 482487893 482487831 7.520000e-09 73.1
13 TraesCS1B01G377700 chr3B 86.441 59 7 1 4826 4883 810609275 810609217 4.530000e-06 63.9
14 TraesCS1B01G377700 chr2B 91.244 1359 86 18 1083 2421 715698150 715699495 0.000000e+00 1820.0
15 TraesCS1B01G377700 chr2B 90.802 1359 91 19 1083 2421 792241081 792242425 0.000000e+00 1786.0
16 TraesCS1B01G377700 chr2B 90.675 1362 84 27 1083 2421 145166055 145167396 0.000000e+00 1772.0
17 TraesCS1B01G377700 chr2B 86.897 145 16 3 223 366 233079367 233079509 5.610000e-35 159.0
18 TraesCS1B01G377700 chr2B 87.500 64 8 0 4845 4908 4941686 4941623 2.090000e-09 75.0
19 TraesCS1B01G377700 chr7B 91.292 1355 85 18 1087 2421 701833580 701834921 0.000000e+00 1818.0
20 TraesCS1B01G377700 chr7B 90.114 1052 76 12 1385 2421 97694159 97695197 0.000000e+00 1341.0
21 TraesCS1B01G377700 chr7B 85.714 154 18 4 217 368 539881264 539881113 5.610000e-35 159.0
22 TraesCS1B01G377700 chr4B 90.445 1392 95 23 1051 2421 499364970 499366344 0.000000e+00 1799.0
23 TraesCS1B01G377700 chr4B 90.114 1052 75 14 1385 2421 134178127 134179164 0.000000e+00 1339.0
24 TraesCS1B01G377700 chr4B 89.412 85 6 3 295 378 212505067 212504985 2.670000e-18 104.0
25 TraesCS1B01G377700 chr6B 90.100 1394 99 24 1051 2421 100474947 100473570 0.000000e+00 1773.0
26 TraesCS1B01G377700 chr2D 82.432 148 21 4 223 368 154172682 154172538 2.050000e-24 124.0
27 TraesCS1B01G377700 chr2D 86.441 118 10 4 250 366 596152649 596152761 2.050000e-24 124.0
28 TraesCS1B01G377700 chr6A 80.392 153 26 4 219 370 155093825 155093974 4.430000e-21 113.0
29 TraesCS1B01G377700 chr6A 84.375 64 6 4 171 232 155093531 155093592 5.860000e-05 60.2
30 TraesCS1B01G377700 chr5D 92.000 75 2 3 296 368 561619899 561619827 9.600000e-18 102.0
31 TraesCS1B01G377700 chr3A 81.250 112 19 1 4836 4945 695051632 695051521 7.470000e-14 89.8
32 TraesCS1B01G377700 chr3A 87.500 56 6 1 4835 4889 491183664 491183719 4.530000e-06 63.9
33 TraesCS1B01G377700 chr7D 96.078 51 2 0 223 273 173115638 173115688 3.480000e-12 84.2
34 TraesCS1B01G377700 chr7A 89.286 56 6 0 4844 4899 229207105 229207050 2.710000e-08 71.3
35 TraesCS1B01G377700 chr5B 93.478 46 3 0 4844 4889 328226256 328226211 9.730000e-08 69.4
36 TraesCS1B01G377700 chr3D 93.478 46 3 0 4844 4889 537165541 537165496 9.730000e-08 69.4


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 TraesCS1B01G377700 chr1B 610160206 610165620 5414 False 10000 10000 100.0000 1 5415 1 chr1B.!!$F1 5414
1 TraesCS1B01G377700 chr1B 634041062 634042407 1345 False 1825 1825 91.3170 1083 2421 1 chr1B.!!$F2 1338
2 TraesCS1B01G377700 chr1A 541988362 541993601 5239 False 3308 6078 91.4295 537 5415 2 chr1A.!!$F1 4878
3 TraesCS1B01G377700 chr1D 446262420 446267844 5424 False 2347 5696 90.7800 1 5415 3 chr1D.!!$F1 5414
4 TraesCS1B01G377700 chr3B 47623288 47624633 1345 True 1842 1842 91.5380 1083 2421 1 chr3B.!!$R1 1338
5 TraesCS1B01G377700 chr3B 702015723 702017067 1344 False 1803 1803 91.0230 1083 2421 1 chr3B.!!$F2 1338
6 TraesCS1B01G377700 chr2B 715698150 715699495 1345 False 1820 1820 91.2440 1083 2421 1 chr2B.!!$F3 1338
7 TraesCS1B01G377700 chr2B 792241081 792242425 1344 False 1786 1786 90.8020 1083 2421 1 chr2B.!!$F4 1338
8 TraesCS1B01G377700 chr2B 145166055 145167396 1341 False 1772 1772 90.6750 1083 2421 1 chr2B.!!$F1 1338
9 TraesCS1B01G377700 chr7B 701833580 701834921 1341 False 1818 1818 91.2920 1087 2421 1 chr7B.!!$F2 1334
10 TraesCS1B01G377700 chr7B 97694159 97695197 1038 False 1341 1341 90.1140 1385 2421 1 chr7B.!!$F1 1036
11 TraesCS1B01G377700 chr4B 499364970 499366344 1374 False 1799 1799 90.4450 1051 2421 1 chr4B.!!$F2 1370
12 TraesCS1B01G377700 chr4B 134178127 134179164 1037 False 1339 1339 90.1140 1385 2421 1 chr4B.!!$F1 1036
13 TraesCS1B01G377700 chr6B 100473570 100474947 1377 True 1773 1773 90.1000 1051 2421 1 chr6B.!!$R1 1370

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
277 284 0.106918 TGGACACGGCTGGAACTTTT 60.107 50.000 0.00 0.00 0.00 2.27 F
575 583 0.108520 TCCCCGAAAAATCCGAGACG 60.109 55.000 0.00 0.00 0.00 4.18 F
1661 1831 0.319728 GCTCCTCTGCAAGTGAGTGA 59.680 55.000 7.59 1.91 36.66 3.41 F
1705 1882 0.467384 CTCTCGGATGCTTGGGACAT 59.533 55.000 0.00 0.00 39.30 3.06 F
3337 3538 1.211457 CTGGGTCTCTTGCTAGCCATT 59.789 52.381 13.29 0.00 42.09 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 1829 0.323725 GCAAGCCTTCCCAATCCTCA 60.324 55.000 0.00 0.0 0.00 3.86 R
1829 2010 1.129251 CACTGGCAATTCAGTACGCAG 59.871 52.381 0.00 0.0 45.24 5.18 R
3581 3782 1.198408 CACAGCAATGCAGACGTTCAT 59.802 47.619 8.35 0.0 0.00 2.57 R
3595 3796 1.543208 CCAAGTAGGAAGTGCACAGCA 60.543 52.381 21.04 0.0 41.22 4.41 R
4433 4634 0.032912 TGTGTACTATCTCCCGCCCA 60.033 55.000 0.00 0.0 0.00 5.36 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
21 22 4.015406 ACGAGGTGCGGCATGGAA 62.015 61.111 5.72 0.00 46.49 3.53
24 25 4.349503 AGGTGCGGCATGGAAGCA 62.350 61.111 5.72 0.00 38.71 3.91
37 38 1.601759 GAAGCACTGCTGGAAGGCA 60.602 57.895 3.73 0.00 39.62 4.75
257 264 3.009115 TCCTTCCTCGCTTGGGGG 61.009 66.667 0.00 0.00 0.00 5.40
273 280 2.668550 GGTGGACACGGCTGGAAC 60.669 66.667 0.00 0.00 0.00 3.62
274 281 2.426023 GTGGACACGGCTGGAACT 59.574 61.111 0.00 0.00 0.00 3.01
275 282 1.227853 GTGGACACGGCTGGAACTT 60.228 57.895 0.00 0.00 0.00 2.66
276 283 0.818040 GTGGACACGGCTGGAACTTT 60.818 55.000 0.00 0.00 0.00 2.66
277 284 0.106918 TGGACACGGCTGGAACTTTT 60.107 50.000 0.00 0.00 0.00 2.27
278 285 1.029681 GGACACGGCTGGAACTTTTT 58.970 50.000 0.00 0.00 0.00 1.94
352 360 3.003173 CCTGGGAGGGCTCAACGA 61.003 66.667 0.00 0.00 0.00 3.85
354 362 3.316573 CTGGGAGGGCTCAACGACC 62.317 68.421 0.00 0.00 43.35 4.79
365 373 0.965866 TCAACGACCGGAGATGCTCT 60.966 55.000 9.46 0.00 0.00 4.09
386 394 2.695055 CATTCGCTACCGCACACG 59.305 61.111 0.00 0.00 39.67 4.49
399 407 1.383080 CGCACACGATTTTTCATGCAC 59.617 47.619 0.00 0.00 43.93 4.57
426 434 5.779771 TCATAGCCCTTCCATTTCTGTTTTT 59.220 36.000 0.00 0.00 0.00 1.94
487 495 7.511959 AAAAACCAGAGAATTCTACTTCCAC 57.488 36.000 8.25 0.00 30.73 4.02
501 509 6.059484 TCTACTTCCACGAAGGTTTTGAAAT 58.941 36.000 6.37 0.00 43.25 2.17
532 540 6.787085 TCGAGAAGGTTTGAAAAAGAGATC 57.213 37.500 0.00 0.00 0.00 2.75
574 582 2.327200 ATCCCCGAAAAATCCGAGAC 57.673 50.000 0.00 0.00 0.00 3.36
575 583 0.108520 TCCCCGAAAAATCCGAGACG 60.109 55.000 0.00 0.00 0.00 4.18
707 736 2.515057 AAAACGCCCACACGCAGA 60.515 55.556 0.00 0.00 36.19 4.26
857 959 3.061848 CCTGCGCCCCATTCGTTT 61.062 61.111 4.18 0.00 0.00 3.60
884 994 0.594796 GCCCGCGCTTTATTGATTGG 60.595 55.000 5.56 0.00 0.00 3.16
960 1082 4.292178 GAGGATCCAGCGGGCGAG 62.292 72.222 15.82 0.00 0.00 5.03
1618 1788 0.603065 GACTGGGTGGATTTTGGTGC 59.397 55.000 0.00 0.00 0.00 5.01
1636 1806 2.637025 CGGTTGCGGTGTTTCTGG 59.363 61.111 0.00 0.00 0.00 3.86
1659 1829 0.321021 CAGCTCCTCTGCAAGTGAGT 59.679 55.000 7.59 0.00 36.66 3.41
1660 1830 0.321021 AGCTCCTCTGCAAGTGAGTG 59.679 55.000 7.59 0.00 36.66 3.51
1661 1831 0.319728 GCTCCTCTGCAAGTGAGTGA 59.680 55.000 7.59 1.91 36.66 3.41
1662 1832 1.672441 GCTCCTCTGCAAGTGAGTGAG 60.672 57.143 11.98 11.98 36.66 3.51
1705 1882 0.467384 CTCTCGGATGCTTGGGACAT 59.533 55.000 0.00 0.00 39.30 3.06
1814 1995 4.080807 TGTTCTAGTCGGGGATGCAAAATA 60.081 41.667 0.00 0.00 0.00 1.40
1829 2010 3.926527 GCAAAATAAACTACCAAGCCTGC 59.073 43.478 0.00 0.00 0.00 4.85
1881 2062 9.959749 TCAACAATTTGACTTGATAACTTTACC 57.040 29.630 2.79 0.00 36.79 2.85
1906 2087 2.552743 GGAGGACTGCAACCTTGTTTAC 59.447 50.000 12.45 0.80 37.93 2.01
1944 2127 4.379813 CCATGGCATAACTGAACACTTCAC 60.380 45.833 0.00 0.00 35.46 3.18
1949 2132 6.070481 TGGCATAACTGAACACTTCACCTATA 60.070 38.462 0.00 0.00 35.46 1.31
1950 2133 6.992715 GGCATAACTGAACACTTCACCTATAT 59.007 38.462 0.00 0.00 35.46 0.86
1951 2134 7.499232 GGCATAACTGAACACTTCACCTATATT 59.501 37.037 0.00 0.00 35.46 1.28
1952 2135 9.542462 GCATAACTGAACACTTCACCTATATTA 57.458 33.333 0.00 0.00 35.46 0.98
2017 2200 3.259876 ACTGGAACATGCTTGCATGAAAT 59.740 39.130 33.52 21.59 38.20 2.17
2018 2201 4.250464 CTGGAACATGCTTGCATGAAATT 58.750 39.130 33.52 21.18 38.20 1.82
2019 2202 4.247258 TGGAACATGCTTGCATGAAATTC 58.753 39.130 33.52 25.97 36.48 2.17
2020 2203 4.020928 TGGAACATGCTTGCATGAAATTCT 60.021 37.500 33.52 13.74 36.48 2.40
2023 2208 6.072893 GGAACATGCTTGCATGAAATTCTTTT 60.073 34.615 33.52 18.79 36.48 2.27
2042 2227 6.964908 TCTTTTGTGCGATTCTGAAATGTAA 58.035 32.000 0.00 0.00 0.00 2.41
2081 2266 4.617530 GCTTCTGAAATGCTGCTGATTTGA 60.618 41.667 0.00 0.00 0.00 2.69
2094 2279 4.527427 TGCTGATTTGATTGATGGTTCCAA 59.473 37.500 0.00 0.00 0.00 3.53
2099 2284 6.930164 TGATTTGATTGATGGTTCCAAACTTG 59.070 34.615 0.00 0.00 30.78 3.16
2104 2289 2.964464 TGATGGTTCCAAACTTGCATGT 59.036 40.909 0.00 0.00 0.00 3.21
2183 2369 5.596836 TGAGTGGATTTGCCCAATAAATC 57.403 39.130 0.00 0.00 41.53 2.17
2201 2388 7.754851 ATAAATCGTTTTTATAAGGCCCGAT 57.245 32.000 0.00 0.00 35.32 4.18
2706 2907 3.776969 AGTGGCTATTTCTGGAGATGTCA 59.223 43.478 0.00 0.00 0.00 3.58
3152 3353 4.079253 GGAAGAATACAAAGAGGTGCCAA 58.921 43.478 0.00 0.00 0.00 4.52
3211 3412 3.326521 TGCCTGGAATGGTATGAGGTAT 58.673 45.455 0.00 0.00 0.00 2.73
3323 3524 1.486726 CCATCTCTGGTTACCTGGGTC 59.513 57.143 8.01 0.00 37.79 4.46
3337 3538 1.211457 CTGGGTCTCTTGCTAGCCATT 59.789 52.381 13.29 0.00 42.09 3.16
3351 3552 2.508526 AGCCATTGTTCTGGTCACTTC 58.491 47.619 0.00 0.00 38.63 3.01
3581 3782 3.069586 CGTGATTGCTCTATTAGGGACCA 59.930 47.826 0.00 0.00 0.00 4.02
3595 3796 1.453155 GGACCATGAACGTCTGCATT 58.547 50.000 0.00 0.00 0.00 3.56
3763 3964 2.496470 GTCGGTCAGGGAGATAGTTGTT 59.504 50.000 0.00 0.00 0.00 2.83
3787 3988 0.469144 GGAACAAAGGCAACCCTCCA 60.469 55.000 0.00 0.00 41.90 3.86
3865 4066 3.181461 ACTCTCTCAACAACAGGTTCAGG 60.181 47.826 0.00 0.00 37.72 3.86
4009 4210 4.266070 CCGCGGATGATCGACGGT 62.266 66.667 24.07 0.00 41.31 4.83
4081 4282 2.729479 CCTGATCCTCACAGGCGCT 61.729 63.158 7.64 0.00 46.30 5.92
4273 4474 1.002624 GGCCATCGACACCTCCAAA 60.003 57.895 0.00 0.00 0.00 3.28
4282 4483 0.969894 ACACCTCCAAACTCTCCTCG 59.030 55.000 0.00 0.00 0.00 4.63
4393 4594 3.944250 ATGGGAGTTTGGCAGGCGG 62.944 63.158 0.00 0.00 0.00 6.13
4433 4634 1.908793 CCCGGACTCTGGACAGTGT 60.909 63.158 0.73 6.73 37.80 3.55
4453 4654 0.674534 GGGCGGGAGATAGTACACAG 59.325 60.000 0.00 0.00 0.00 3.66
4525 4729 1.243342 TTTGCAGCATGGGACGGAAG 61.243 55.000 0.00 0.00 35.86 3.46
4550 4757 5.041940 GCTATAACCTTGGTAGAAGTGTCG 58.958 45.833 0.00 0.00 0.00 4.35
4551 4758 5.393896 GCTATAACCTTGGTAGAAGTGTCGT 60.394 44.000 0.00 0.00 0.00 4.34
4552 4759 3.382048 AACCTTGGTAGAAGTGTCGTC 57.618 47.619 0.00 0.00 0.00 4.20
4592 4800 4.026744 AGCCTAGAGTGCAGTAGATCAAA 58.973 43.478 0.00 0.00 0.00 2.69
4597 4805 7.271511 CCTAGAGTGCAGTAGATCAAAATCTT 58.728 38.462 0.00 0.00 42.39 2.40
4598 4806 7.437862 CCTAGAGTGCAGTAGATCAAAATCTTC 59.562 40.741 0.00 0.00 42.39 2.87
4600 4808 7.393216 AGAGTGCAGTAGATCAAAATCTTCTT 58.607 34.615 0.00 0.00 42.39 2.52
4601 4809 7.548780 AGAGTGCAGTAGATCAAAATCTTCTTC 59.451 37.037 0.00 0.00 42.39 2.87
4602 4810 6.597280 AGTGCAGTAGATCAAAATCTTCTTCC 59.403 38.462 0.00 0.00 42.39 3.46
4603 4811 5.882557 TGCAGTAGATCAAAATCTTCTTCCC 59.117 40.000 0.00 0.00 42.39 3.97
4604 4812 5.298026 GCAGTAGATCAAAATCTTCTTCCCC 59.702 44.000 0.00 0.00 42.39 4.81
4605 4813 5.525378 CAGTAGATCAAAATCTTCTTCCCCG 59.475 44.000 0.00 0.00 42.39 5.73
4606 4814 3.891049 AGATCAAAATCTTCTTCCCCGG 58.109 45.455 0.00 0.00 39.27 5.73
4609 4817 2.107552 TCAAAATCTTCTTCCCCGGTGT 59.892 45.455 0.00 0.00 0.00 4.16
4610 4818 2.488153 CAAAATCTTCTTCCCCGGTGTC 59.512 50.000 0.00 0.00 0.00 3.67
4612 4820 2.544844 ATCTTCTTCCCCGGTGTCTA 57.455 50.000 0.00 0.00 0.00 2.59
4613 4821 2.314071 TCTTCTTCCCCGGTGTCTAA 57.686 50.000 0.00 0.00 0.00 2.10
4614 4822 2.829023 TCTTCTTCCCCGGTGTCTAAT 58.171 47.619 0.00 0.00 0.00 1.73
4615 4823 3.178865 TCTTCTTCCCCGGTGTCTAATT 58.821 45.455 0.00 0.00 0.00 1.40
4619 4827 1.492764 TCCCCGGTGTCTAATTCTCC 58.507 55.000 0.00 0.00 0.00 3.71
4621 4829 1.139058 CCCCGGTGTCTAATTCTCCAG 59.861 57.143 0.00 0.00 0.00 3.86
4631 4839 5.306937 TGTCTAATTCTCCAGGAACTTGTGA 59.693 40.000 0.00 0.00 34.60 3.58
4638 4846 4.347876 TCTCCAGGAACTTGTGAGATCAAA 59.652 41.667 0.00 0.00 34.60 2.69
4689 4898 5.999205 AAGATTCAATTGGGTTGTATGCA 57.001 34.783 5.42 0.00 38.95 3.96
4694 4903 3.128415 TCAATTGGGTTGTATGCATGTCG 59.872 43.478 10.16 0.00 38.95 4.35
4703 4915 4.678509 TGTATGCATGTCGTTCTTTTCC 57.321 40.909 10.16 0.00 0.00 3.13
4760 4974 8.531622 TTGTAAATGGTGTGATTTTGCTTATG 57.468 30.769 0.00 0.00 0.00 1.90
4767 4985 6.937465 TGGTGTGATTTTGCTTATGTACAGTA 59.063 34.615 0.33 0.00 0.00 2.74
4769 4987 7.119262 GGTGTGATTTTGCTTATGTACAGTACT 59.881 37.037 12.07 0.00 0.00 2.73
4774 4995 8.943909 ATTTTGCTTATGTACAGTACTAGGAC 57.056 34.615 12.07 0.00 0.00 3.85
4782 5003 7.575414 ATGTACAGTACTAGGACTTCATCTG 57.425 40.000 4.33 0.00 0.00 2.90
4826 5048 2.140792 ACTGGAGTGGACTGCCGTT 61.141 57.895 0.00 0.00 36.79 4.44
4842 5064 2.352960 GCCGTTGCAGGAGAAATTCTAG 59.647 50.000 0.00 0.00 37.47 2.43
4843 5065 3.600388 CCGTTGCAGGAGAAATTCTAGT 58.400 45.455 0.00 0.00 0.00 2.57
4844 5066 4.755411 CCGTTGCAGGAGAAATTCTAGTA 58.245 43.478 0.00 0.00 0.00 1.82
4845 5067 4.567159 CCGTTGCAGGAGAAATTCTAGTAC 59.433 45.833 0.00 0.00 0.00 2.73
4846 5068 5.411781 CGTTGCAGGAGAAATTCTAGTACT 58.588 41.667 0.00 0.00 0.00 2.73
4847 5069 5.517054 CGTTGCAGGAGAAATTCTAGTACTC 59.483 44.000 0.00 0.00 0.00 2.59
4848 5070 5.599999 TGCAGGAGAAATTCTAGTACTCC 57.400 43.478 0.00 0.00 44.97 3.85
4849 5071 4.406003 TGCAGGAGAAATTCTAGTACTCCC 59.594 45.833 0.00 0.00 45.53 4.30
4850 5072 4.651962 GCAGGAGAAATTCTAGTACTCCCT 59.348 45.833 0.00 0.00 45.53 4.20
4851 5073 5.221362 GCAGGAGAAATTCTAGTACTCCCTC 60.221 48.000 0.00 0.00 45.53 4.30
4852 5074 5.303333 CAGGAGAAATTCTAGTACTCCCTCC 59.697 48.000 0.00 6.35 45.53 4.30
4853 5075 5.043281 AGGAGAAATTCTAGTACTCCCTCCA 60.043 44.000 0.00 0.00 45.53 3.86
4854 5076 5.661759 GGAGAAATTCTAGTACTCCCTCCAA 59.338 44.000 0.00 0.00 40.58 3.53
4855 5077 6.327887 GGAGAAATTCTAGTACTCCCTCCAAT 59.672 42.308 0.00 0.00 40.58 3.16
4856 5078 7.368198 AGAAATTCTAGTACTCCCTCCAATC 57.632 40.000 0.00 0.00 0.00 2.67
4857 5079 6.327887 AGAAATTCTAGTACTCCCTCCAATCC 59.672 42.308 0.00 0.00 0.00 3.01
4858 5080 4.620086 TTCTAGTACTCCCTCCAATCCA 57.380 45.455 0.00 0.00 0.00 3.41
4859 5081 4.834406 TCTAGTACTCCCTCCAATCCAT 57.166 45.455 0.00 0.00 0.00 3.41
4860 5082 5.942977 TCTAGTACTCCCTCCAATCCATA 57.057 43.478 0.00 0.00 0.00 2.74
4861 5083 6.485388 TCTAGTACTCCCTCCAATCCATAT 57.515 41.667 0.00 0.00 0.00 1.78
4862 5084 6.875469 TCTAGTACTCCCTCCAATCCATATT 58.125 40.000 0.00 0.00 0.00 1.28
4863 5085 8.008104 TCTAGTACTCCCTCCAATCCATATTA 57.992 38.462 0.00 0.00 0.00 0.98
4864 5086 8.461854 TCTAGTACTCCCTCCAATCCATATTAA 58.538 37.037 0.00 0.00 0.00 1.40
4865 5087 9.273137 CTAGTACTCCCTCCAATCCATATTAAT 57.727 37.037 0.00 0.00 0.00 1.40
4866 5088 8.525729 AGTACTCCCTCCAATCCATATTAATT 57.474 34.615 0.00 0.00 0.00 1.40
4867 5089 8.386264 AGTACTCCCTCCAATCCATATTAATTG 58.614 37.037 0.00 1.40 33.57 2.32
4868 5090 7.406620 ACTCCCTCCAATCCATATTAATTGA 57.593 36.000 7.95 0.00 35.35 2.57
4869 5091 7.234355 ACTCCCTCCAATCCATATTAATTGAC 58.766 38.462 7.95 0.00 35.35 3.18
4870 5092 6.237901 TCCCTCCAATCCATATTAATTGACG 58.762 40.000 7.95 0.00 35.35 4.35
4871 5093 5.106157 CCCTCCAATCCATATTAATTGACGC 60.106 44.000 7.95 0.00 35.35 5.19
4872 5094 5.707298 CCTCCAATCCATATTAATTGACGCT 59.293 40.000 7.95 0.00 35.35 5.07
4873 5095 6.348786 CCTCCAATCCATATTAATTGACGCTG 60.349 42.308 7.95 0.00 35.35 5.18
4874 5096 5.048782 TCCAATCCATATTAATTGACGCTGC 60.049 40.000 7.95 0.00 35.35 5.25
4875 5097 5.048504 CCAATCCATATTAATTGACGCTGCT 60.049 40.000 0.00 0.00 35.35 4.24
4876 5098 6.441274 CAATCCATATTAATTGACGCTGCTT 58.559 36.000 0.00 0.00 35.35 3.91
4877 5099 6.639632 ATCCATATTAATTGACGCTGCTTT 57.360 33.333 0.00 0.00 0.00 3.51
4878 5100 7.744087 ATCCATATTAATTGACGCTGCTTTA 57.256 32.000 0.00 0.00 0.00 1.85
4879 5101 7.561021 TCCATATTAATTGACGCTGCTTTAA 57.439 32.000 0.00 0.00 0.00 1.52
4880 5102 8.165239 TCCATATTAATTGACGCTGCTTTAAT 57.835 30.769 0.00 0.00 0.00 1.40
4881 5103 9.278978 TCCATATTAATTGACGCTGCTTTAATA 57.721 29.630 0.00 5.00 32.39 0.98
4882 5104 9.329913 CCATATTAATTGACGCTGCTTTAATAC 57.670 33.333 0.00 0.00 31.29 1.89
4883 5105 9.877137 CATATTAATTGACGCTGCTTTAATACA 57.123 29.630 0.00 0.00 31.29 2.29
4886 5108 9.801873 ATTAATTGACGCTGCTTTAATACAATT 57.198 25.926 0.00 0.00 39.14 2.32
4887 5109 9.632807 TTAATTGACGCTGCTTTAATACAATTT 57.367 25.926 0.00 0.00 37.67 1.82
4888 5110 8.532977 AATTGACGCTGCTTTAATACAATTTT 57.467 26.923 0.00 0.00 34.54 1.82
4889 5111 9.632807 AATTGACGCTGCTTTAATACAATTTTA 57.367 25.926 0.00 0.00 34.54 1.52
4890 5112 9.801873 ATTGACGCTGCTTTAATACAATTTTAT 57.198 25.926 0.00 0.00 0.00 1.40
4891 5113 9.632807 TTGACGCTGCTTTAATACAATTTTATT 57.367 25.926 0.00 2.60 0.00 1.40
4928 5150 8.079809 ACTAAAAGTGTCAATTAATTTGGACCG 58.920 33.333 13.31 0.00 35.92 4.79
4929 5151 5.385509 AAGTGTCAATTAATTTGGACCGG 57.614 39.130 13.31 0.00 35.92 5.28
4930 5152 4.658063 AGTGTCAATTAATTTGGACCGGA 58.342 39.130 9.46 0.00 35.92 5.14
4931 5153 4.700213 AGTGTCAATTAATTTGGACCGGAG 59.300 41.667 9.46 0.00 35.92 4.63
4932 5154 4.013728 TGTCAATTAATTTGGACCGGAGG 58.986 43.478 9.46 0.00 45.06 4.30
4933 5155 4.263550 TGTCAATTAATTTGGACCGGAGGA 60.264 41.667 9.46 0.00 43.23 3.71
4934 5156 4.703093 GTCAATTAATTTGGACCGGAGGAA 59.297 41.667 9.46 0.00 43.23 3.36
4935 5157 4.947388 TCAATTAATTTGGACCGGAGGAAG 59.053 41.667 9.46 0.00 43.23 3.46
4936 5158 5.515886 TCAATTAATTTGGACCGGAGGAAGT 60.516 40.000 9.46 0.00 43.23 3.01
4937 5159 6.296547 TCAATTAATTTGGACCGGAGGAAGTA 60.297 38.462 9.46 0.00 43.23 2.24
4938 5160 8.278919 TCAATTAATTTGGACCGGAGGAAGTAC 61.279 40.741 9.46 0.00 43.23 2.73
4971 5632 2.126882 TGCAGCCTAGATGGTTGGTAT 58.873 47.619 0.00 0.00 45.70 2.73
4972 5633 2.509548 TGCAGCCTAGATGGTTGGTATT 59.490 45.455 0.00 0.00 45.70 1.89
4980 5641 6.634039 GCCTAGATGGTTGGTATTAGTCCAAA 60.634 42.308 0.00 0.00 44.91 3.28
4993 5654 3.840124 AGTCCAAACTTTCTCCGTCTT 57.160 42.857 0.00 0.00 28.74 3.01
4995 5656 5.286267 AGTCCAAACTTTCTCCGTCTTAA 57.714 39.130 0.00 0.00 28.74 1.85
4996 5657 5.055144 AGTCCAAACTTTCTCCGTCTTAAC 58.945 41.667 0.00 0.00 28.74 2.01
4997 5658 5.055144 GTCCAAACTTTCTCCGTCTTAACT 58.945 41.667 0.00 0.00 0.00 2.24
5009 5683 5.636837 TCCGTCTTAACTAAAATTGCATGC 58.363 37.500 11.82 11.82 0.00 4.06
5014 5688 7.273164 CGTCTTAACTAAAATTGCATGCAATCA 59.727 33.333 38.48 26.53 44.86 2.57
5025 5699 2.745281 GCATGCAATCAACCAAAGCAAT 59.255 40.909 14.21 0.00 38.85 3.56
5029 5703 2.738314 GCAATCAACCAAAGCAATCCAC 59.262 45.455 0.00 0.00 0.00 4.02
5032 5706 1.133199 TCAACCAAAGCAATCCACCCT 60.133 47.619 0.00 0.00 0.00 4.34
5033 5707 2.109128 TCAACCAAAGCAATCCACCCTA 59.891 45.455 0.00 0.00 0.00 3.53
5037 5711 4.167319 ACCAAAGCAATCCACCCTAAAAT 58.833 39.130 0.00 0.00 0.00 1.82
5039 5713 4.937015 CCAAAGCAATCCACCCTAAAATTG 59.063 41.667 0.00 0.00 33.31 2.32
5044 5718 4.892433 CAATCCACCCTAAAATTGCAACA 58.108 39.130 0.00 0.00 0.00 3.33
5045 5719 5.303971 CAATCCACCCTAAAATTGCAACAA 58.696 37.500 0.00 0.00 0.00 2.83
5073 5747 6.540438 TTCTCCATAACAGGAAAGTACGAT 57.460 37.500 0.00 0.00 37.20 3.73
5114 5788 6.769822 AGATGAACAAACATGAGACAGAGTTT 59.230 34.615 0.00 0.00 34.78 2.66
5115 5789 6.757897 TGAACAAACATGAGACAGAGTTTT 57.242 33.333 0.00 0.00 32.34 2.43
5153 5828 9.099454 CTCAAGTCGCTAATTTACCTAATCTTT 57.901 33.333 0.00 0.00 0.00 2.52
5168 5843 4.910746 AATCTTTGAACATGAGACGACG 57.089 40.909 0.00 0.00 0.00 5.12
5209 5884 4.764050 TTTGAGTTACACAACAGGAGGA 57.236 40.909 0.00 0.00 37.10 3.71
5226 5901 2.554032 GAGGAGACTGATCTAGCTGAGC 59.446 54.545 0.00 0.00 44.43 4.26
5228 5903 2.034558 GGAGACTGATCTAGCTGAGCAC 59.965 54.545 7.39 0.00 36.01 4.40
5244 5919 1.859398 CACGCGACTGCAGCTTTTA 59.141 52.632 15.93 0.00 42.97 1.52
5255 5930 1.729149 GCAGCTTTTAGTTCGCGCATT 60.729 47.619 8.75 0.00 0.00 3.56
5302 5977 1.914700 GACTTCGTCTTCTTGCTAGCG 59.085 52.381 10.77 0.00 0.00 4.26
5381 6056 3.181478 TGTGCTGAAATGTTGTCATGCAA 60.181 39.130 0.00 0.00 33.78 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.900498 GTTGCCTTCCAGCAGTGCT 60.900 57.895 13.14 13.14 45.13 4.40
24 25 2.980233 GCGTTGCCTTCCAGCAGT 60.980 61.111 0.00 0.00 45.13 4.40
82 83 4.082523 TACCCGAGCCACAGCAGC 62.083 66.667 0.00 0.00 43.56 5.25
97 98 0.872021 CGCACTCGGCCATCTTCTAC 60.872 60.000 2.24 0.00 40.31 2.59
98 99 1.437573 CGCACTCGGCCATCTTCTA 59.562 57.895 2.24 0.00 40.31 2.10
124 125 4.493747 CGCCCCCGACGAGAAGTC 62.494 72.222 0.00 0.00 46.16 3.01
175 176 4.899239 CCCGAGCTCCATGGACGC 62.899 72.222 21.70 21.70 0.00 5.19
227 228 2.604686 AAGGAGACAGCGAGCCCA 60.605 61.111 0.00 0.00 0.00 5.36
232 233 2.701780 GCGAGGAAGGAGACAGCGA 61.702 63.158 0.00 0.00 0.00 4.93
235 236 0.108424 CCAAGCGAGGAAGGAGACAG 60.108 60.000 0.00 0.00 0.00 3.51
257 264 0.818040 AAAGTTCCAGCCGTGTCCAC 60.818 55.000 0.00 0.00 0.00 4.02
275 282 4.510167 TTTTTGGCTTGGGGATGAAAAA 57.490 36.364 0.00 0.00 0.00 1.94
341 349 3.382832 CTCCGGTCGTTGAGCCCT 61.383 66.667 0.00 0.00 0.00 5.19
342 350 2.722201 ATCTCCGGTCGTTGAGCCC 61.722 63.158 0.00 0.00 0.00 5.19
343 351 1.519455 CATCTCCGGTCGTTGAGCC 60.519 63.158 0.00 0.00 0.00 4.70
386 394 3.727723 GCTATGAGCGTGCATGAAAAATC 59.272 43.478 10.93 0.00 0.00 2.17
399 407 1.876156 GAAATGGAAGGGCTATGAGCG 59.124 52.381 0.00 0.00 43.62 5.03
464 472 5.701290 CGTGGAAGTAGAATTCTCTGGTTTT 59.299 40.000 12.24 0.00 32.70 2.43
465 473 5.011738 TCGTGGAAGTAGAATTCTCTGGTTT 59.988 40.000 12.24 0.66 32.70 3.27
466 474 4.527038 TCGTGGAAGTAGAATTCTCTGGTT 59.473 41.667 12.24 1.29 32.70 3.67
467 475 4.087182 TCGTGGAAGTAGAATTCTCTGGT 58.913 43.478 12.24 0.00 32.70 4.00
468 476 4.720649 TCGTGGAAGTAGAATTCTCTGG 57.279 45.455 12.24 0.00 32.70 3.86
475 483 5.617252 TCAAAACCTTCGTGGAAGTAGAAT 58.383 37.500 4.82 0.00 37.92 2.40
487 495 4.228912 AGCAGACATTTCAAAACCTTCG 57.771 40.909 0.00 0.00 0.00 3.79
501 509 2.102420 TCAAACCTTCTCGAAGCAGACA 59.898 45.455 1.13 0.00 37.11 3.41
556 564 0.108520 CGTCTCGGATTTTTCGGGGA 60.109 55.000 0.00 0.00 0.00 4.81
574 582 2.186903 CGGACACATTCCCCCTCG 59.813 66.667 0.00 0.00 42.27 4.63
575 583 1.078426 CACGGACACATTCCCCCTC 60.078 63.158 0.00 0.00 42.27 4.30
707 736 2.772191 TGGTGGTGCTGGTGAGGT 60.772 61.111 0.00 0.00 0.00 3.85
854 956 4.174129 CGCGGGCGGAATGGAAAC 62.174 66.667 4.92 0.00 35.56 2.78
884 994 6.016610 TGGGCTCGGCTAATTAATTAATCAAC 60.017 38.462 11.08 3.96 0.00 3.18
917 1027 2.589492 CGCTGGCGGAATTAGAGCG 61.589 63.158 7.12 0.00 45.60 5.03
1596 1765 2.297033 CACCAAAATCCACCCAGTCAAG 59.703 50.000 0.00 0.00 0.00 3.02
1659 1829 0.323725 GCAAGCCTTCCCAATCCTCA 60.324 55.000 0.00 0.00 0.00 3.86
1660 1830 1.379642 CGCAAGCCTTCCCAATCCTC 61.380 60.000 0.00 0.00 0.00 3.71
1661 1831 1.379044 CGCAAGCCTTCCCAATCCT 60.379 57.895 0.00 0.00 0.00 3.24
1662 1832 2.418083 CCGCAAGCCTTCCCAATCC 61.418 63.158 0.00 0.00 0.00 3.01
1705 1882 1.278985 AGACATCGCACTCCCAAATCA 59.721 47.619 0.00 0.00 0.00 2.57
1814 1995 1.237285 CGCAGCAGGCTTGGTAGTTT 61.237 55.000 0.00 0.00 41.67 2.66
1829 2010 1.129251 CACTGGCAATTCAGTACGCAG 59.871 52.381 0.00 0.00 45.24 5.18
1856 2037 9.965824 AGGTAAAGTTATCAAGTCAAATTGTTG 57.034 29.630 0.00 0.00 35.95 3.33
1881 2062 1.783250 AAGGTTGCAGTCCTCCCCAG 61.783 60.000 11.95 0.00 33.76 4.45
2017 2200 5.830912 ACATTTCAGAATCGCACAAAAGAA 58.169 33.333 0.00 0.00 0.00 2.52
2018 2201 5.437289 ACATTTCAGAATCGCACAAAAGA 57.563 34.783 0.00 0.00 0.00 2.52
2019 2202 7.801547 ATTACATTTCAGAATCGCACAAAAG 57.198 32.000 0.00 0.00 0.00 2.27
2020 2203 8.586570 AAATTACATTTCAGAATCGCACAAAA 57.413 26.923 0.00 0.00 0.00 2.44
2023 2208 9.340695 CTTAAAATTACATTTCAGAATCGCACA 57.659 29.630 0.00 0.00 0.00 4.57
2081 2266 4.040706 ACATGCAAGTTTGGAACCATCAAT 59.959 37.500 0.00 0.00 30.51 2.57
2104 2289 5.916661 TGCTTTTGTTTGGTACTTTGGTA 57.083 34.783 0.00 0.00 0.00 3.25
2162 2347 4.097892 ACGATTTATTGGGCAAATCCACTC 59.902 41.667 0.00 0.00 38.58 3.51
2183 2369 4.571580 TGTGTATCGGGCCTTATAAAAACG 59.428 41.667 0.84 0.00 0.00 3.60
2291 2487 5.954150 AGATGGCATTTCTAGGTTGACAAAT 59.046 36.000 0.00 0.00 30.89 2.32
2463 2664 2.097036 TCGCCCTGAGAGACGAATAAA 58.903 47.619 0.00 0.00 0.00 1.40
3152 3353 4.228210 TGGCTCTTCAATCCCAAGTTCTAT 59.772 41.667 0.00 0.00 0.00 1.98
3211 3412 1.737735 CTGCGCGTCCAAGTGATGA 60.738 57.895 8.43 0.00 31.07 2.92
3323 3524 2.681848 CCAGAACAATGGCTAGCAAGAG 59.318 50.000 18.24 4.45 32.48 2.85
3351 3552 2.738321 GCACCTTTCACAAAACCCACAG 60.738 50.000 0.00 0.00 0.00 3.66
3581 3782 1.198408 CACAGCAATGCAGACGTTCAT 59.802 47.619 8.35 0.00 0.00 2.57
3595 3796 1.543208 CCAAGTAGGAAGTGCACAGCA 60.543 52.381 21.04 0.00 41.22 4.41
3763 3964 1.398692 GGTTGCCTTTGTTCCAGACA 58.601 50.000 0.00 0.00 36.19 3.41
3865 4066 2.101082 GGTCTTTATCAGAGGGTCGACC 59.899 54.545 27.04 27.04 40.67 4.79
4009 4210 1.982395 CCTGTACTGCGGAGGGTCA 60.982 63.158 9.36 3.44 0.00 4.02
4078 4279 1.376424 ACTGTCCATGAAGGCAGCG 60.376 57.895 3.77 0.00 42.02 5.18
4081 4282 1.059098 ACTCACTGTCCATGAAGGCA 58.941 50.000 0.00 0.00 37.29 4.75
4084 4285 3.144506 AGCAAACTCACTGTCCATGAAG 58.855 45.455 0.00 0.00 0.00 3.02
4223 4424 1.676635 CGTACTCCACCGTCCTCCA 60.677 63.158 0.00 0.00 0.00 3.86
4273 4474 2.043852 ATGGCGACCGAGGAGAGT 60.044 61.111 0.00 0.00 0.00 3.24
4393 4594 1.188863 ATTTGTCCCAGCCATCTTGC 58.811 50.000 0.00 0.00 0.00 4.01
4433 4634 0.032912 TGTGTACTATCTCCCGCCCA 60.033 55.000 0.00 0.00 0.00 5.36
4453 4654 2.088950 AAGCATTTGCATCTGTTGGC 57.911 45.000 5.20 0.00 45.16 4.52
4484 4687 2.944409 TTCCCACGGGACCAACAACG 62.944 60.000 3.66 0.00 45.11 4.10
4525 4729 5.731591 ACACTTCTACCAAGGTTATAGCAC 58.268 41.667 0.00 0.00 0.00 4.40
4592 4800 1.657804 AGACACCGGGGAAGAAGATT 58.342 50.000 12.96 0.00 0.00 2.40
4597 4805 2.764572 GAGAATTAGACACCGGGGAAGA 59.235 50.000 12.96 0.00 0.00 2.87
4598 4806 2.158943 GGAGAATTAGACACCGGGGAAG 60.159 54.545 12.96 0.00 0.00 3.46
4600 4808 1.273381 TGGAGAATTAGACACCGGGGA 60.273 52.381 12.96 0.00 0.00 4.81
4601 4809 1.139058 CTGGAGAATTAGACACCGGGG 59.861 57.143 0.00 0.00 0.00 5.73
4602 4810 1.139058 CCTGGAGAATTAGACACCGGG 59.861 57.143 6.32 0.00 37.96 5.73
4603 4811 2.108168 TCCTGGAGAATTAGACACCGG 58.892 52.381 0.00 0.00 0.00 5.28
4604 4812 3.195825 AGTTCCTGGAGAATTAGACACCG 59.804 47.826 0.00 0.00 36.69 4.94
4605 4813 4.828072 AGTTCCTGGAGAATTAGACACC 57.172 45.455 0.00 0.00 36.69 4.16
4606 4814 5.409826 CACAAGTTCCTGGAGAATTAGACAC 59.590 44.000 0.00 0.00 36.69 3.67
4609 4817 5.780282 TCTCACAAGTTCCTGGAGAATTAGA 59.220 40.000 0.00 0.00 36.69 2.10
4610 4818 6.042638 TCTCACAAGTTCCTGGAGAATTAG 57.957 41.667 0.00 0.00 36.69 1.73
4612 4820 4.982241 TCTCACAAGTTCCTGGAGAATT 57.018 40.909 0.00 0.00 36.69 2.17
4613 4821 4.533707 TGATCTCACAAGTTCCTGGAGAAT 59.466 41.667 0.00 0.00 38.05 2.40
4614 4822 3.903714 TGATCTCACAAGTTCCTGGAGAA 59.096 43.478 0.00 0.00 38.05 2.87
4615 4823 3.510459 TGATCTCACAAGTTCCTGGAGA 58.490 45.455 0.00 0.00 38.80 3.71
4619 4827 4.458295 AGCATTTGATCTCACAAGTTCCTG 59.542 41.667 0.00 0.00 0.00 3.86
4621 4829 4.456911 TGAGCATTTGATCTCACAAGTTCC 59.543 41.667 0.00 0.00 34.69 3.62
4631 4839 5.498393 CTGGCCTATATGAGCATTTGATCT 58.502 41.667 3.32 0.00 0.00 2.75
4638 4846 1.339824 GCAGCTGGCCTATATGAGCAT 60.340 52.381 17.12 0.00 36.11 3.79
4689 4898 5.745227 ACATCTATGGGAAAAGAACGACAT 58.255 37.500 0.00 0.00 0.00 3.06
4694 4903 9.196552 CAAAAAGAACATCTATGGGAAAAGAAC 57.803 33.333 0.00 0.00 0.00 3.01
4703 4915 6.449698 ACAAGTGCAAAAAGAACATCTATGG 58.550 36.000 0.00 0.00 0.00 2.74
4760 4974 6.120905 TCCAGATGAAGTCCTAGTACTGTAC 58.879 44.000 9.93 9.93 0.00 2.90
4767 4985 5.485353 TGAAACATCCAGATGAAGTCCTAGT 59.515 40.000 14.42 0.00 41.20 2.57
4769 4987 5.248248 TGTGAAACATCCAGATGAAGTCCTA 59.752 40.000 14.42 0.00 45.67 2.94
4826 5048 4.406003 GGGAGTACTAGAATTTCTCCTGCA 59.594 45.833 1.27 0.00 42.76 4.41
4842 5064 8.383175 TCAATTAATATGGATTGGAGGGAGTAC 58.617 37.037 9.98 0.00 34.74 2.73
4843 5065 8.383175 GTCAATTAATATGGATTGGAGGGAGTA 58.617 37.037 9.98 0.00 34.74 2.59
4844 5066 7.234355 GTCAATTAATATGGATTGGAGGGAGT 58.766 38.462 9.98 0.00 34.74 3.85
4845 5067 6.372659 CGTCAATTAATATGGATTGGAGGGAG 59.627 42.308 9.98 0.00 34.74 4.30
4846 5068 6.237901 CGTCAATTAATATGGATTGGAGGGA 58.762 40.000 9.98 0.00 34.74 4.20
4847 5069 5.106157 GCGTCAATTAATATGGATTGGAGGG 60.106 44.000 9.98 2.10 34.74 4.30
4848 5070 5.707298 AGCGTCAATTAATATGGATTGGAGG 59.293 40.000 9.98 0.00 34.74 4.30
4849 5071 6.605849 CAGCGTCAATTAATATGGATTGGAG 58.394 40.000 9.98 6.87 34.74 3.86
4850 5072 5.048782 GCAGCGTCAATTAATATGGATTGGA 60.049 40.000 9.98 0.00 34.74 3.53
4851 5073 5.048504 AGCAGCGTCAATTAATATGGATTGG 60.049 40.000 9.98 0.21 34.74 3.16
4852 5074 6.005583 AGCAGCGTCAATTAATATGGATTG 57.994 37.500 5.39 5.39 35.18 2.67
4853 5075 6.639632 AAGCAGCGTCAATTAATATGGATT 57.360 33.333 0.00 0.00 0.00 3.01
4854 5076 6.639632 AAAGCAGCGTCAATTAATATGGAT 57.360 33.333 0.00 0.00 0.00 3.41
4855 5077 7.561021 TTAAAGCAGCGTCAATTAATATGGA 57.439 32.000 0.00 0.00 0.00 3.41
4856 5078 9.329913 GTATTAAAGCAGCGTCAATTAATATGG 57.670 33.333 10.66 0.00 33.49 2.74
4857 5079 9.877137 TGTATTAAAGCAGCGTCAATTAATATG 57.123 29.630 10.66 0.00 33.49 1.78
4860 5082 9.801873 AATTGTATTAAAGCAGCGTCAATTAAT 57.198 25.926 3.98 6.05 34.16 1.40
4861 5083 9.632807 AAATTGTATTAAAGCAGCGTCAATTAA 57.367 25.926 5.69 1.10 34.60 1.40
4862 5084 9.632807 AAAATTGTATTAAAGCAGCGTCAATTA 57.367 25.926 5.69 0.00 34.60 1.40
4863 5085 8.532977 AAAATTGTATTAAAGCAGCGTCAATT 57.467 26.923 0.00 0.00 36.34 2.32
4864 5086 9.801873 ATAAAATTGTATTAAAGCAGCGTCAAT 57.198 25.926 0.00 0.00 0.00 2.57
4865 5087 9.632807 AATAAAATTGTATTAAAGCAGCGTCAA 57.367 25.926 0.00 0.00 0.00 3.18
4902 5124 8.079809 CGGTCCAAATTAATTGACACTTTTAGT 58.920 33.333 16.30 0.00 41.85 2.24
4903 5125 7.540745 CCGGTCCAAATTAATTGACACTTTTAG 59.459 37.037 16.30 3.67 41.85 1.85
4904 5126 7.230913 TCCGGTCCAAATTAATTGACACTTTTA 59.769 33.333 16.30 0.00 41.85 1.52
4905 5127 6.041069 TCCGGTCCAAATTAATTGACACTTTT 59.959 34.615 16.30 0.00 41.85 2.27
4906 5128 5.536916 TCCGGTCCAAATTAATTGACACTTT 59.463 36.000 16.30 0.00 41.85 2.66
4907 5129 5.074115 TCCGGTCCAAATTAATTGACACTT 58.926 37.500 16.30 0.00 41.85 3.16
4908 5130 4.658063 TCCGGTCCAAATTAATTGACACT 58.342 39.130 16.30 0.00 41.85 3.55
4909 5131 4.142469 CCTCCGGTCCAAATTAATTGACAC 60.142 45.833 16.30 7.64 41.85 3.67
4910 5132 4.013728 CCTCCGGTCCAAATTAATTGACA 58.986 43.478 16.30 1.21 41.85 3.58
4911 5133 4.266714 TCCTCCGGTCCAAATTAATTGAC 58.733 43.478 0.00 5.85 41.85 3.18
4912 5134 4.577988 TCCTCCGGTCCAAATTAATTGA 57.422 40.909 0.00 0.00 41.85 2.57
4913 5135 4.705023 ACTTCCTCCGGTCCAAATTAATTG 59.295 41.667 0.00 0.00 38.84 2.32
4914 5136 4.930696 ACTTCCTCCGGTCCAAATTAATT 58.069 39.130 0.00 0.00 0.00 1.40
4915 5137 4.586306 ACTTCCTCCGGTCCAAATTAAT 57.414 40.909 0.00 0.00 0.00 1.40
4916 5138 4.323715 GGTACTTCCTCCGGTCCAAATTAA 60.324 45.833 0.00 0.00 0.00 1.40
4917 5139 3.198417 GGTACTTCCTCCGGTCCAAATTA 59.802 47.826 0.00 0.00 0.00 1.40
4918 5140 2.026542 GGTACTTCCTCCGGTCCAAATT 60.027 50.000 0.00 0.00 0.00 1.82
4919 5141 1.558294 GGTACTTCCTCCGGTCCAAAT 59.442 52.381 0.00 0.00 0.00 2.32
4920 5142 0.978907 GGTACTTCCTCCGGTCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
4921 5143 0.178926 TGGTACTTCCTCCGGTCCAA 60.179 55.000 0.00 0.00 37.07 3.53
4922 5144 0.042131 ATGGTACTTCCTCCGGTCCA 59.958 55.000 0.00 0.00 37.07 4.02
4923 5145 1.201424 AATGGTACTTCCTCCGGTCC 58.799 55.000 0.00 0.00 37.07 4.46
4924 5146 3.007635 CAAAATGGTACTTCCTCCGGTC 58.992 50.000 0.00 0.00 37.07 4.79
4925 5147 2.374170 ACAAAATGGTACTTCCTCCGGT 59.626 45.455 0.00 0.00 37.07 5.28
4926 5148 2.747446 CACAAAATGGTACTTCCTCCGG 59.253 50.000 0.00 0.00 37.07 5.14
4927 5149 2.747446 CCACAAAATGGTACTTCCTCCG 59.253 50.000 0.00 0.00 44.46 4.63
4939 5161 3.541191 GCTGCACGCCACAAAATG 58.459 55.556 0.00 0.00 0.00 2.32
4954 5176 4.593634 GGACTAATACCAACCATCTAGGCT 59.406 45.833 0.00 0.00 43.14 4.58
4961 5622 7.238710 AGAAAGTTTGGACTAATACCAACCAT 58.761 34.615 0.00 0.00 45.38 3.55
4962 5623 6.607019 AGAAAGTTTGGACTAATACCAACCA 58.393 36.000 0.00 0.00 45.38 3.67
4971 5632 4.950205 AGACGGAGAAAGTTTGGACTAA 57.050 40.909 0.00 0.00 34.21 2.24
4972 5633 4.950205 AAGACGGAGAAAGTTTGGACTA 57.050 40.909 0.00 0.00 34.21 2.59
4980 5641 7.227910 TGCAATTTTAGTTAAGACGGAGAAAGT 59.772 33.333 0.00 0.00 0.00 2.66
4985 5646 5.739161 GCATGCAATTTTAGTTAAGACGGAG 59.261 40.000 14.21 0.00 0.00 4.63
4986 5647 5.182190 TGCATGCAATTTTAGTTAAGACGGA 59.818 36.000 20.30 0.00 0.00 4.69
4993 5654 7.157347 TGGTTGATTGCATGCAATTTTAGTTA 58.843 30.769 38.66 22.26 45.50 2.24
4995 5656 5.549347 TGGTTGATTGCATGCAATTTTAGT 58.451 33.333 38.66 22.32 45.50 2.24
4996 5657 6.483385 TTGGTTGATTGCATGCAATTTTAG 57.517 33.333 38.66 0.00 45.50 1.85
4997 5658 6.568081 GCTTTGGTTGATTGCATGCAATTTTA 60.568 34.615 38.66 26.96 45.50 1.52
5009 5683 3.328505 GGTGGATTGCTTTGGTTGATTG 58.671 45.455 0.00 0.00 0.00 2.67
5012 5686 1.133199 AGGGTGGATTGCTTTGGTTGA 60.133 47.619 0.00 0.00 0.00 3.18
5014 5688 2.990740 TAGGGTGGATTGCTTTGGTT 57.009 45.000 0.00 0.00 0.00 3.67
5025 5699 4.590647 TCATTGTTGCAATTTTAGGGTGGA 59.409 37.500 0.59 0.00 0.00 4.02
5029 5703 7.064966 GGAGAATTCATTGTTGCAATTTTAGGG 59.935 37.037 8.44 0.00 0.00 3.53
5033 5707 7.989416 ATGGAGAATTCATTGTTGCAATTTT 57.011 28.000 8.44 0.00 18.61 1.82
5037 5711 6.990798 TGTTATGGAGAATTCATTGTTGCAA 58.009 32.000 8.44 0.00 34.80 4.08
5039 5713 6.038356 CCTGTTATGGAGAATTCATTGTTGC 58.962 40.000 8.44 0.00 34.80 4.17
5040 5714 7.395190 TCCTGTTATGGAGAATTCATTGTTG 57.605 36.000 8.44 0.00 34.80 3.33
5041 5715 8.421249 TTTCCTGTTATGGAGAATTCATTGTT 57.579 30.769 8.44 0.00 34.80 2.83
5042 5716 7.671398 ACTTTCCTGTTATGGAGAATTCATTGT 59.329 33.333 8.44 0.00 34.80 2.71
5043 5717 8.059798 ACTTTCCTGTTATGGAGAATTCATTG 57.940 34.615 8.44 0.00 34.80 2.82
5044 5718 9.178758 GTACTTTCCTGTTATGGAGAATTCATT 57.821 33.333 8.44 0.00 34.80 2.57
5045 5719 7.495934 CGTACTTTCCTGTTATGGAGAATTCAT 59.504 37.037 8.44 0.00 38.41 2.57
5058 5732 5.245526 AGTTGTAGGATCGTACTTTCCTGTT 59.754 40.000 22.37 1.65 42.38 3.16
5073 5747 5.422012 TGTTCATCTGCTGATAGTTGTAGGA 59.578 40.000 5.70 0.00 32.72 2.94
5114 5788 3.066203 GCGACTTGAGAAGGGAAAAACAA 59.934 43.478 0.00 0.00 0.00 2.83
5115 5789 2.616842 GCGACTTGAGAAGGGAAAAACA 59.383 45.455 0.00 0.00 0.00 2.83
5153 5828 2.416893 CTCTCTCGTCGTCTCATGTTCA 59.583 50.000 0.00 0.00 0.00 3.18
5168 5843 2.440539 TCTTTGTTCGGTGCTCTCTC 57.559 50.000 0.00 0.00 0.00 3.20
5209 5884 1.675483 CGTGCTCAGCTAGATCAGTCT 59.325 52.381 0.00 0.00 38.52 3.24
5226 5901 0.179240 CTAAAAGCTGCAGTCGCGTG 60.179 55.000 16.64 0.00 42.97 5.34
5228 5903 0.512952 AACTAAAAGCTGCAGTCGCG 59.487 50.000 16.64 0.00 42.97 5.87
5244 5919 4.154195 AGAAATAAGTTGAATGCGCGAACT 59.846 37.500 12.10 7.41 0.00 3.01
5255 5930 3.682858 CGCGGAAGGAAGAAATAAGTTGA 59.317 43.478 0.00 0.00 0.00 3.18
5302 5977 2.914097 AAACCAGCCAGTGCAGCC 60.914 61.111 0.00 0.00 41.13 4.85


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

AutoCloner maintained by Alex Coulton.