Multiple sequence alignment - TraesCS5B01G266500

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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 TraesCS5B01G266500 chr5B 100.000 4072 0 0 1 4072 450843116 450839045 0.000000e+00 7520
1 TraesCS5B01G266500 chr5B 85.756 1032 102 25 929 1940 516605667 516604661 0.000000e+00 1050
2 TraesCS5B01G266500 chr5B 92.228 193 12 3 3320 3509 697855055 697854863 1.870000e-68 270
3 TraesCS5B01G266500 chr5D 87.773 2560 182 58 2 2498 377535569 377533078 0.000000e+00 2872
4 TraesCS5B01G266500 chr5D 86.494 733 48 22 2610 3325 377532657 377531959 0.000000e+00 758
5 TraesCS5B01G266500 chr5D 90.462 346 11 12 3741 4072 377531623 377531286 1.740000e-118 436
6 TraesCS5B01G266500 chr5D 91.061 179 11 1 3503 3681 377531963 377531790 1.890000e-58 237
7 TraesCS5B01G266500 chr5D 96.970 66 2 0 3668 3733 377531766 377531701 1.200000e-20 111
8 TraesCS5B01G266500 chr5A 84.738 1697 163 45 1698 3325 478321501 478319832 0.000000e+00 1611
9 TraesCS5B01G266500 chr5A 90.288 1040 64 19 642 1653 478322531 478321501 0.000000e+00 1327
10 TraesCS5B01G266500 chr5A 88.908 586 33 13 3503 4072 478319836 478319267 0.000000e+00 693
11 TraesCS5B01G266500 chr5A 90.253 513 20 10 1 494 478323208 478322707 0.000000e+00 643
12 TraesCS5B01G266500 chr6B 86.058 624 66 13 1136 1744 575575932 575575315 0.000000e+00 651
13 TraesCS5B01G266500 chr6B 92.513 187 11 3 3322 3505 33072779 33072965 8.680000e-67 265
14 TraesCS5B01G266500 chr6D 83.193 357 48 12 1102 1454 427527775 427528123 2.360000e-82 316
15 TraesCS5B01G266500 chr4B 85.953 299 28 10 1007 1298 149735484 149735775 1.420000e-79 307
16 TraesCS5B01G266500 chr7B 85.714 294 28 10 1007 1293 683245404 683245690 8.560000e-77 298
17 TraesCS5B01G266500 chr7B 92.857 196 14 0 988 1183 184299349 184299544 6.660000e-73 285
18 TraesCS5B01G266500 chr7A 94.595 185 10 0 999 1183 229143261 229143077 1.850000e-73 287
19 TraesCS5B01G266500 chr7A 86.325 234 17 7 1711 1940 919588 919366 1.460000e-59 241
20 TraesCS5B01G266500 chr6A 84.512 297 32 9 1007 1296 103975856 103975567 8.620000e-72 281
21 TraesCS5B01G266500 chr7D 92.347 196 15 0 988 1183 216082343 216082148 3.100000e-71 279
22 TraesCS5B01G266500 chr3D 92.553 188 10 4 3320 3504 100466164 100465978 2.410000e-67 267
23 TraesCS5B01G266500 chr1A 92.935 184 10 3 3324 3504 582559482 582559665 8.680000e-67 265
24 TraesCS5B01G266500 chrUn 91.667 192 13 3 3319 3507 255618823 255618632 3.120000e-66 263
25 TraesCS5B01G266500 chrUn 92.063 189 12 3 3319 3504 347383956 347384144 3.120000e-66 263
26 TraesCS5B01G266500 chrUn 92.063 189 12 3 3319 3504 404982492 404982680 3.120000e-66 263
27 TraesCS5B01G266500 chr1B 91.667 192 13 3 3319 3507 528498410 528498219 3.120000e-66 263
28 TraesCS5B01G266500 chr1B 85.897 234 19 9 1711 1940 212226278 212226501 1.890000e-58 237
29 TraesCS5B01G266500 chr1B 85.776 232 20 7 1713 1940 606228897 606229119 2.450000e-57 233
30 TraesCS5B01G266500 chr2D 92.021 188 10 5 3321 3504 591983008 591983194 4.040000e-65 259
31 TraesCS5B01G266500 chr2A 85.897 234 18 7 1711 1940 59861460 59861682 6.800000e-58 235
32 TraesCS5B01G266500 chr4A 85.043 234 20 7 1711 1940 79416443 79416665 1.470000e-54 224
33 TraesCS5B01G266500 chr2B 83.761 234 24 6 1711 1940 321106948 321107171 4.120000e-50 209


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 TraesCS5B01G266500 chr5B 450839045 450843116 4071 True 7520.0 7520 100.00000 1 4072 1 chr5B.!!$R1 4071
1 TraesCS5B01G266500 chr5B 516604661 516605667 1006 True 1050.0 1050 85.75600 929 1940 1 chr5B.!!$R2 1011
2 TraesCS5B01G266500 chr5D 377531286 377535569 4283 True 882.8 2872 90.55200 2 4072 5 chr5D.!!$R1 4070
3 TraesCS5B01G266500 chr5A 478319267 478323208 3941 True 1068.5 1611 88.54675 1 4072 4 chr5A.!!$R1 4071
4 TraesCS5B01G266500 chr6B 575575315 575575932 617 True 651.0 651 86.05800 1136 1744 1 chr6B.!!$R1 608

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
607 676 0.179124 CGGTGCTGCTCCTAGTCTTC 60.179 60.0 17.64 0.0 0.00 2.87 F
1258 1351 0.177141 GTGAGTATGCCCTGGCGTTA 59.823 55.0 8.42 0.0 45.51 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2395 2544 0.752054 ACCAACCACACAAGCCATTG 59.248 50.0 0.0 0.0 42.46 2.82 R
3098 3576 0.175073 CCCTACTTCAGTACACGGCC 59.825 60.0 0.0 0.0 0.00 6.13 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 2.819595 CCGATGAACCAGGGCGTG 60.820 66.667 0.00 0.00 0.00 5.34
155 156 1.617850 CTGGAAGTGAGCTCAGTGTCT 59.382 52.381 24.53 11.70 0.00 3.41
197 198 2.563179 AGTGACCAGCTTGACGTAGAAT 59.437 45.455 0.00 0.00 0.00 2.40
198 199 2.924290 GTGACCAGCTTGACGTAGAATC 59.076 50.000 0.00 0.00 0.00 2.52
212 213 4.142271 ACGTAGAATCCTGAAGCAGAAGAG 60.142 45.833 0.00 0.00 32.44 2.85
213 214 4.097135 CGTAGAATCCTGAAGCAGAAGAGA 59.903 45.833 0.00 0.00 32.44 3.10
214 215 4.741321 AGAATCCTGAAGCAGAAGAGAG 57.259 45.455 0.00 0.00 32.44 3.20
215 216 3.451902 AGAATCCTGAAGCAGAAGAGAGG 59.548 47.826 0.00 0.00 32.44 3.69
314 318 2.136728 TGTTTAATGTGTCGTCGTGGG 58.863 47.619 0.00 0.00 0.00 4.61
457 472 1.281577 TGGCTGTGATGCTGATGGTTA 59.718 47.619 0.00 0.00 0.00 2.85
478 493 8.515414 TGGTTATTCTTTTTGGTTTTGGTTTTG 58.485 29.630 0.00 0.00 0.00 2.44
496 558 4.670227 TTTGGTTTTTGCAAGTTTTCCG 57.330 36.364 0.00 0.00 0.00 4.30
522 591 4.578105 GGTATTGCTAATCTTTCTGCTGCT 59.422 41.667 0.00 0.00 0.00 4.24
551 620 4.202151 GCTGATGGTTTTTCTGTTTGGACT 60.202 41.667 0.00 0.00 0.00 3.85
552 621 5.682212 GCTGATGGTTTTTCTGTTTGGACTT 60.682 40.000 0.00 0.00 0.00 3.01
553 622 5.901552 TGATGGTTTTTCTGTTTGGACTTC 58.098 37.500 0.00 0.00 0.00 3.01
554 623 5.656416 TGATGGTTTTTCTGTTTGGACTTCT 59.344 36.000 0.00 0.00 0.00 2.85
555 624 5.993748 TGGTTTTTCTGTTTGGACTTCTT 57.006 34.783 0.00 0.00 0.00 2.52
556 625 6.353404 TGGTTTTTCTGTTTGGACTTCTTT 57.647 33.333 0.00 0.00 0.00 2.52
557 626 6.394809 TGGTTTTTCTGTTTGGACTTCTTTC 58.605 36.000 0.00 0.00 0.00 2.62
558 627 6.210584 TGGTTTTTCTGTTTGGACTTCTTTCT 59.789 34.615 0.00 0.00 0.00 2.52
559 628 6.752351 GGTTTTTCTGTTTGGACTTCTTTCTC 59.248 38.462 0.00 0.00 0.00 2.87
560 629 7.363007 GGTTTTTCTGTTTGGACTTCTTTCTCT 60.363 37.037 0.00 0.00 0.00 3.10
561 630 6.927294 TTTCTGTTTGGACTTCTTTCTCTC 57.073 37.500 0.00 0.00 0.00 3.20
563 632 5.848406 TCTGTTTGGACTTCTTTCTCTCTC 58.152 41.667 0.00 0.00 0.00 3.20
565 634 5.848406 TGTTTGGACTTCTTTCTCTCTCTC 58.152 41.667 0.00 0.00 0.00 3.20
567 636 5.975693 TTGGACTTCTTTCTCTCTCTCTC 57.024 43.478 0.00 0.00 0.00 3.20
607 676 0.179124 CGGTGCTGCTCCTAGTCTTC 60.179 60.000 17.64 0.00 0.00 2.87
612 681 2.107366 GCTGCTCCTAGTCTTCCTCTT 58.893 52.381 0.00 0.00 0.00 2.85
614 683 3.430236 GCTGCTCCTAGTCTTCCTCTTTC 60.430 52.174 0.00 0.00 0.00 2.62
617 686 3.430236 GCTCCTAGTCTTCCTCTTTCTGC 60.430 52.174 0.00 0.00 0.00 4.26
620 689 2.470983 AGTCTTCCTCTTTCTGCTGC 57.529 50.000 0.00 0.00 0.00 5.25
621 690 1.003003 AGTCTTCCTCTTTCTGCTGCC 59.997 52.381 0.00 0.00 0.00 4.85
625 694 0.603707 TCCTCTTTCTGCTGCCGTTG 60.604 55.000 0.00 0.00 0.00 4.10
628 697 1.208614 CTTTCTGCTGCCGTTGCTC 59.791 57.895 0.00 0.00 38.71 4.26
639 708 1.370414 CGTTGCTCGGTTTTGCCAG 60.370 57.895 0.00 0.00 36.97 4.85
658 727 1.211449 CGAGTGCGTCTTCAGCTCT 59.789 57.895 0.00 0.00 40.57 4.09
672 741 2.029290 TCAGCTCTGGTTTACGGTCTTC 60.029 50.000 0.00 0.00 0.00 2.87
705 774 2.603776 AGGAGGAGGCGACGGTTT 60.604 61.111 0.00 0.00 0.00 3.27
726 795 1.305297 AGATCACAGGAGGCGTCCA 60.305 57.895 26.40 6.94 46.80 4.02
747 816 4.803426 GCTGGGTCGTCTCGCTGG 62.803 72.222 0.00 0.00 0.00 4.85
884 959 4.530857 CGGAACCCTAGCCAGCCG 62.531 72.222 0.00 0.00 0.00 5.52
885 960 4.858680 GGAACCCTAGCCAGCCGC 62.859 72.222 0.00 0.00 37.98 6.53
927 1014 2.818274 GCCAGTAGCGGGAAACGG 60.818 66.667 0.00 0.00 44.51 4.44
1242 1335 0.817654 AGTCCGATTCATCTGCGTGA 59.182 50.000 0.00 0.00 0.00 4.35
1254 1347 2.897350 GCGTGAGTATGCCCTGGC 60.897 66.667 0.00 0.00 42.35 4.85
1258 1351 0.177141 GTGAGTATGCCCTGGCGTTA 59.823 55.000 8.42 0.00 45.51 3.18
1260 1353 1.488812 TGAGTATGCCCTGGCGTTAAT 59.511 47.619 8.42 0.00 45.51 1.40
1429 1532 6.287589 TGGTTGAAGGTGTTTGTTATGTTT 57.712 33.333 0.00 0.00 0.00 2.83
1435 1538 5.257082 AGGTGTTTGTTATGTTTGGTGTC 57.743 39.130 0.00 0.00 0.00 3.67
1457 1560 4.974103 GATTAATCAGTAATCGCTGCGT 57.026 40.909 22.48 6.13 38.98 5.24
1483 1586 3.279434 GGAGCAAATTTCCCATCTACGT 58.721 45.455 0.00 0.00 0.00 3.57
1551 1661 3.673594 CGGTAGTCAGTGACTGGATGTTC 60.674 52.174 31.70 14.20 43.30 3.18
1597 1707 5.914635 GCATGAAAATTGGTGGTGATATACG 59.085 40.000 0.00 0.00 0.00 3.06
1610 1720 5.009310 TGGTGATATACGGTAGTGATGTGAC 59.991 44.000 0.00 0.00 0.00 3.67
1662 1772 7.749377 TCTCAATTCTAAGTAATGGGAAGGA 57.251 36.000 0.00 0.00 0.00 3.36
1664 1774 7.403231 TCTCAATTCTAAGTAATGGGAAGGAGT 59.597 37.037 0.00 0.00 31.31 3.85
1670 1780 3.532102 AGTAATGGGAAGGAGTGAGGTT 58.468 45.455 0.00 0.00 0.00 3.50
1766 1881 8.898761 TGAAAATTGCTGTTATGATTACCGTAT 58.101 29.630 0.00 0.00 0.00 3.06
1774 1891 7.359262 TGTTATGATTACCGTATTATGCAGC 57.641 36.000 0.00 0.00 0.00 5.25
1822 1939 4.686554 GCTCGTGTCATAGTTTTCAGTTCT 59.313 41.667 0.00 0.00 0.00 3.01
1839 1956 4.636206 CAGTTCTAAGTAATGTGAAGGGGC 59.364 45.833 0.00 0.00 0.00 5.80
1840 1957 3.926058 TCTAAGTAATGTGAAGGGGCC 57.074 47.619 0.00 0.00 0.00 5.80
1841 1958 3.460825 TCTAAGTAATGTGAAGGGGCCT 58.539 45.455 0.84 0.00 0.00 5.19
1854 1973 4.202673 TGAAGGGGCCTTTTATCTTGTTCT 60.203 41.667 1.09 0.00 36.26 3.01
1858 1977 5.952347 AGGGGCCTTTTATCTTGTTCTAAAG 59.048 40.000 0.84 0.00 0.00 1.85
1895 2014 9.733556 TTTTCTATTGCTAAACTGATAGAACCA 57.266 29.630 4.62 0.00 39.50 3.67
1963 2082 8.827758 GGATTCCCTTAATATAGGAGTAAAGCT 58.172 37.037 0.00 0.00 37.50 3.74
2016 2139 4.881019 ATTGTTGTGAGAGAGCAGTAGT 57.119 40.909 0.00 0.00 0.00 2.73
2047 2170 1.471676 CCTGTGGCTCAGTCCGTATTC 60.472 57.143 14.80 0.00 42.19 1.75
2063 2186 2.604046 ATTCGGGATTCCTTCTGACG 57.396 50.000 2.01 0.00 0.00 4.35
2108 2246 2.196595 AGCACCAGCCAAAGATACCTA 58.803 47.619 0.00 0.00 43.56 3.08
2134 2272 5.125356 TCTCTTGTTGATTGACTGCTGAAA 58.875 37.500 0.00 0.00 0.00 2.69
2139 2277 8.412456 TCTTGTTGATTGACTGCTGAAATTTTA 58.588 29.630 0.00 0.00 0.00 1.52
2149 2287 9.598517 TGACTGCTGAAATTTTATTTTCTTTGT 57.401 25.926 0.00 0.00 36.71 2.83
2174 2312 9.185192 GTTGGAAAATGACTACTGAAATTGAAG 57.815 33.333 0.00 0.00 0.00 3.02
2180 2318 4.202461 TGACTACTGAAATTGAAGGCACCT 60.202 41.667 0.00 0.00 0.00 4.00
2186 2324 5.070847 ACTGAAATTGAAGGCACCTTTTGAT 59.929 36.000 2.89 0.00 36.26 2.57
2241 2379 4.273480 GCTATTGTTGTTATGTCTCGGCAT 59.727 41.667 0.00 0.00 0.00 4.40
2246 2384 3.326836 TGTTATGTCTCGGCATGTTGA 57.673 42.857 0.00 0.00 0.00 3.18
2260 2398 3.875727 GCATGTTGAGCTCATGTCTATGT 59.124 43.478 19.04 0.00 42.94 2.29
2299 2437 9.499479 CCAGCAACTCATAGAAATACTGAATAT 57.501 33.333 0.00 0.00 0.00 1.28
2375 2521 4.331168 GTGTCTTGTCATATTCTGAGCACC 59.669 45.833 0.00 0.00 33.51 5.01
2381 2530 4.696877 TGTCATATTCTGAGCACCAAGTTG 59.303 41.667 0.00 0.00 33.51 3.16
2429 2578 2.482721 GGTTGGTACACACGATTTCAGG 59.517 50.000 0.00 0.00 39.29 3.86
2455 2607 7.306749 GGTGTCATGTGCATCTTAAAACAAAAG 60.307 37.037 0.00 0.00 0.00 2.27
2486 2639 2.361757 TCCAACATTTGACCTGCAACAG 59.638 45.455 0.00 0.00 35.91 3.16
2515 2668 4.248058 CAAAAATTGTCCAGGGAGAATGC 58.752 43.478 11.04 0.00 38.01 3.56
2518 2671 2.673775 TTGTCCAGGGAGAATGCAAA 57.326 45.000 0.00 0.00 0.00 3.68
2521 2674 3.091545 TGTCCAGGGAGAATGCAAATTC 58.908 45.455 0.00 0.00 0.00 2.17
2522 2675 3.091545 GTCCAGGGAGAATGCAAATTCA 58.908 45.455 3.04 0.00 33.16 2.57
2523 2676 3.091545 TCCAGGGAGAATGCAAATTCAC 58.908 45.455 3.04 0.00 33.16 3.18
2528 2681 6.206243 CCAGGGAGAATGCAAATTCACTATAG 59.794 42.308 0.00 0.00 33.16 1.31
2551 2717 6.769512 AGTTATCTTTCTGGCTGTAACAAGA 58.230 36.000 0.00 0.00 0.00 3.02
2565 2731 9.849166 GGCTGTAACAAGATATCTAATAGAGAC 57.151 37.037 5.46 6.19 36.87 3.36
2594 2761 9.341078 TGTTATGCTTTATCATTTATGCTCTCA 57.659 29.630 0.00 0.00 0.00 3.27
2596 2763 6.309712 TGCTTTATCATTTATGCTCTCAGC 57.690 37.500 0.00 0.00 42.82 4.26
2604 2771 7.725818 TCATTTATGCTCTCAGCTTCATTAG 57.274 36.000 0.00 0.00 42.97 1.73
2613 2780 6.073112 GCTCTCAGCTTCATTAGGAATGATTC 60.073 42.308 2.87 0.00 46.50 2.52
2615 2782 8.255111 TCTCAGCTTCATTAGGAATGATTCTA 57.745 34.615 5.03 0.00 46.50 2.10
2648 3111 1.004918 GTAGTGAGCCCTGTTGCGT 60.005 57.895 0.00 0.00 36.02 5.24
2652 3115 1.073025 TGAGCCCTGTTGCGTTGAT 59.927 52.632 0.00 0.00 36.02 2.57
2656 3119 2.017049 AGCCCTGTTGCGTTGATTATC 58.983 47.619 0.00 0.00 36.02 1.75
2661 3124 5.095490 CCCTGTTGCGTTGATTATCTTTTC 58.905 41.667 0.00 0.00 0.00 2.29
2698 3161 6.868339 GCAGGATAAGTTAAGTGCACATTTTT 59.132 34.615 21.04 6.97 0.00 1.94
2746 3211 4.811024 TGAACTGTGTTAGAAGCAGACTTG 59.189 41.667 0.00 0.00 35.82 3.16
2805 3272 2.616842 AGGTAAAAAGTGAAGTGTGCCG 59.383 45.455 0.00 0.00 0.00 5.69
2809 3276 4.385358 AAAAAGTGAAGTGTGCCGAATT 57.615 36.364 0.00 0.00 0.00 2.17
2857 3335 6.205464 TCCTTCTGAAATGACATCAGTGTTTC 59.795 38.462 6.07 0.00 43.77 2.78
2873 3351 4.154195 AGTGTTTCGTTATCATGGCTTGAC 59.846 41.667 5.09 0.00 37.11 3.18
2880 3358 4.507710 GTTATCATGGCTTGACTGACAGA 58.492 43.478 10.08 0.00 37.11 3.41
2884 3362 3.194329 TCATGGCTTGACTGACAGACTAG 59.806 47.826 10.08 10.56 0.00 2.57
3073 3551 0.756294 TCCAAGGCGAAGAAGTGACA 59.244 50.000 0.00 0.00 0.00 3.58
3112 3590 0.456312 GAGACGGCCGTGTACTGAAG 60.456 60.000 39.65 0.00 0.00 3.02
3117 3595 0.175073 GGCCGTGTACTGAAGTAGGG 59.825 60.000 0.00 0.00 0.00 3.53
3118 3596 0.175073 GCCGTGTACTGAAGTAGGGG 59.825 60.000 0.00 0.00 0.00 4.79
3138 3619 4.369182 GGGTAGATCTGTGTACCAAATCG 58.631 47.826 13.25 0.00 44.10 3.34
3157 3638 1.978617 CCAGCGTTGGGCCTGATTT 60.979 57.895 10.99 0.00 45.17 2.17
3158 3639 1.535204 CCAGCGTTGGGCCTGATTTT 61.535 55.000 10.99 0.00 45.17 1.82
3170 3651 4.637091 GGGCCTGATTTTGATTCAAATTGG 59.363 41.667 12.39 12.21 33.19 3.16
3194 3675 6.887002 GGATTCTTTCTGTACAGGGAATTCTT 59.113 38.462 25.24 14.06 0.00 2.52
3205 3686 3.941483 CAGGGAATTCTTAAGATGTGCGT 59.059 43.478 5.89 1.75 0.00 5.24
3206 3687 4.396166 CAGGGAATTCTTAAGATGTGCGTT 59.604 41.667 5.89 0.00 0.00 4.84
3207 3688 4.396166 AGGGAATTCTTAAGATGTGCGTTG 59.604 41.667 5.89 0.00 0.00 4.10
3208 3689 4.156008 GGGAATTCTTAAGATGTGCGTTGT 59.844 41.667 5.89 0.00 0.00 3.32
3209 3690 5.088739 GGAATTCTTAAGATGTGCGTTGTG 58.911 41.667 5.89 0.00 0.00 3.33
3210 3691 3.536158 TTCTTAAGATGTGCGTTGTGC 57.464 42.857 5.89 0.00 46.70 4.57
3260 3758 5.765182 CCGAGCTAAGGATTTTCATTATGGT 59.235 40.000 1.60 0.00 0.00 3.55
3261 3759 6.073003 CCGAGCTAAGGATTTTCATTATGGTC 60.073 42.308 1.60 0.00 0.00 4.02
3320 3822 3.502237 CAACTGCTGCAAATGGGAC 57.498 52.632 3.02 0.00 0.00 4.46
3321 3823 0.963962 CAACTGCTGCAAATGGGACT 59.036 50.000 3.02 0.00 0.00 3.85
3322 3824 1.068055 CAACTGCTGCAAATGGGACTC 60.068 52.381 3.02 0.00 0.00 3.36
3323 3825 0.111061 ACTGCTGCAAATGGGACTCA 59.889 50.000 3.02 0.00 0.00 3.41
3324 3826 0.809385 CTGCTGCAAATGGGACTCAG 59.191 55.000 3.02 0.00 0.00 3.35
3325 3827 0.609957 TGCTGCAAATGGGACTCAGG 60.610 55.000 0.00 0.00 0.00 3.86
3326 3828 1.318158 GCTGCAAATGGGACTCAGGG 61.318 60.000 0.00 0.00 0.00 4.45
3327 3829 0.682209 CTGCAAATGGGACTCAGGGG 60.682 60.000 0.00 0.00 0.00 4.79
3328 3830 1.380380 GCAAATGGGACTCAGGGGG 60.380 63.158 0.00 0.00 0.00 5.40
3329 3831 2.087248 CAAATGGGACTCAGGGGGT 58.913 57.895 0.00 0.00 0.00 4.95
3330 3832 0.323725 CAAATGGGACTCAGGGGGTG 60.324 60.000 0.00 0.00 0.00 4.61
3331 3833 0.776080 AAATGGGACTCAGGGGGTGT 60.776 55.000 0.00 0.00 0.00 4.16
3332 3834 0.776080 AATGGGACTCAGGGGGTGTT 60.776 55.000 0.00 0.00 0.00 3.32
3333 3835 0.776080 ATGGGACTCAGGGGGTGTTT 60.776 55.000 0.00 0.00 0.00 2.83
3334 3836 1.074951 GGGACTCAGGGGGTGTTTG 59.925 63.158 0.00 0.00 0.00 2.93
3335 3837 1.074951 GGACTCAGGGGGTGTTTGG 59.925 63.158 0.00 0.00 0.00 3.28
3336 3838 1.716028 GGACTCAGGGGGTGTTTGGT 61.716 60.000 0.00 0.00 0.00 3.67
3337 3839 0.185175 GACTCAGGGGGTGTTTGGTT 59.815 55.000 0.00 0.00 0.00 3.67
3338 3840 0.185175 ACTCAGGGGGTGTTTGGTTC 59.815 55.000 0.00 0.00 0.00 3.62
3339 3841 0.184933 CTCAGGGGGTGTTTGGTTCA 59.815 55.000 0.00 0.00 0.00 3.18
3340 3842 0.184933 TCAGGGGGTGTTTGGTTCAG 59.815 55.000 0.00 0.00 0.00 3.02
3341 3843 0.827507 CAGGGGGTGTTTGGTTCAGG 60.828 60.000 0.00 0.00 0.00 3.86
3342 3844 1.533033 GGGGGTGTTTGGTTCAGGG 60.533 63.158 0.00 0.00 0.00 4.45
3343 3845 1.539665 GGGGTGTTTGGTTCAGGGA 59.460 57.895 0.00 0.00 0.00 4.20
3344 3846 0.826256 GGGGTGTTTGGTTCAGGGAC 60.826 60.000 0.00 0.00 0.00 4.46
3345 3847 0.185175 GGGTGTTTGGTTCAGGGACT 59.815 55.000 0.00 0.00 43.88 3.85
3346 3848 1.411074 GGGTGTTTGGTTCAGGGACTT 60.411 52.381 0.00 0.00 34.60 3.01
3347 3849 2.384828 GGTGTTTGGTTCAGGGACTTT 58.615 47.619 0.00 0.00 34.60 2.66
3348 3850 2.764010 GGTGTTTGGTTCAGGGACTTTT 59.236 45.455 0.00 0.00 34.60 2.27
3349 3851 3.196901 GGTGTTTGGTTCAGGGACTTTTT 59.803 43.478 0.00 0.00 34.60 1.94
3350 3852 4.403113 GGTGTTTGGTTCAGGGACTTTTTA 59.597 41.667 0.00 0.00 34.60 1.52
3351 3853 5.451381 GGTGTTTGGTTCAGGGACTTTTTAG 60.451 44.000 0.00 0.00 34.60 1.85
3352 3854 5.126545 GTGTTTGGTTCAGGGACTTTTTAGT 59.873 40.000 0.00 0.00 34.60 2.24
3353 3855 5.358725 TGTTTGGTTCAGGGACTTTTTAGTC 59.641 40.000 0.00 0.00 34.60 2.59
3385 3887 9.543783 GACTAGAAAAAGTCTCTAAAAAGTCCA 57.456 33.333 0.00 0.00 42.21 4.02
3389 3891 9.508642 AGAAAAAGTCTCTAAAAAGTCCATAGG 57.491 33.333 0.00 0.00 0.00 2.57
3390 3892 9.503399 GAAAAAGTCTCTAAAAAGTCCATAGGA 57.497 33.333 0.00 0.00 0.00 2.94
3391 3893 9.862149 AAAAAGTCTCTAAAAAGTCCATAGGAA 57.138 29.630 0.00 0.00 31.38 3.36
3393 3895 9.674068 AAAGTCTCTAAAAAGTCCATAGGAATC 57.326 33.333 0.00 0.00 31.38 2.52
3394 3896 8.380742 AGTCTCTAAAAAGTCCATAGGAATCA 57.619 34.615 0.00 0.00 31.38 2.57
3395 3897 8.826765 AGTCTCTAAAAAGTCCATAGGAATCAA 58.173 33.333 0.00 0.00 31.38 2.57
3396 3898 9.449719 GTCTCTAAAAAGTCCATAGGAATCAAA 57.550 33.333 0.00 0.00 31.38 2.69
3397 3899 9.449719 TCTCTAAAAAGTCCATAGGAATCAAAC 57.550 33.333 0.00 0.00 31.38 2.93
3398 3900 8.263940 TCTAAAAAGTCCATAGGAATCAAACG 57.736 34.615 0.00 0.00 31.38 3.60
3399 3901 5.897377 AAAAGTCCATAGGAATCAAACGG 57.103 39.130 0.00 0.00 31.38 4.44
3400 3902 4.837093 AAGTCCATAGGAATCAAACGGA 57.163 40.909 0.00 0.00 31.38 4.69
3401 3903 4.837093 AGTCCATAGGAATCAAACGGAA 57.163 40.909 0.00 0.00 31.38 4.30
3402 3904 4.770795 AGTCCATAGGAATCAAACGGAAG 58.229 43.478 0.00 0.00 31.38 3.46
3403 3905 3.877508 GTCCATAGGAATCAAACGGAAGG 59.122 47.826 0.00 0.00 31.38 3.46
3404 3906 3.118038 TCCATAGGAATCAAACGGAAGGG 60.118 47.826 0.00 0.00 0.00 3.95
3405 3907 3.118038 CCATAGGAATCAAACGGAAGGGA 60.118 47.826 0.00 0.00 0.00 4.20
3406 3908 2.491675 AGGAATCAAACGGAAGGGAC 57.508 50.000 0.00 0.00 0.00 4.46
3425 3927 7.569599 AGGGACTTTTTCTACAGGATTAGAA 57.430 36.000 0.00 0.00 33.39 2.10
3426 3928 7.985589 AGGGACTTTTTCTACAGGATTAGAAA 58.014 34.615 1.96 1.96 43.34 2.52
3437 3939 9.756571 TCTACAGGATTAGAAAAAGACTCTACT 57.243 33.333 0.00 0.00 0.00 2.57
3438 3940 9.796120 CTACAGGATTAGAAAAAGACTCTACTG 57.204 37.037 0.00 0.00 0.00 2.74
3439 3941 8.423906 ACAGGATTAGAAAAAGACTCTACTGA 57.576 34.615 0.00 0.00 0.00 3.41
3440 3942 8.871125 ACAGGATTAGAAAAAGACTCTACTGAA 58.129 33.333 0.00 0.00 0.00 3.02
3441 3943 9.364989 CAGGATTAGAAAAAGACTCTACTGAAG 57.635 37.037 0.00 0.00 0.00 3.02
3442 3944 9.315363 AGGATTAGAAAAAGACTCTACTGAAGA 57.685 33.333 0.00 0.00 0.00 2.87
3499 4001 8.624701 GTCCTAGGACTTTTAAACAAAACAAC 57.375 34.615 31.12 1.86 41.57 3.32
3500 4002 7.703621 GTCCTAGGACTTTTAAACAAAACAACC 59.296 37.037 31.12 0.93 41.57 3.77
3501 4003 6.982141 CCTAGGACTTTTAAACAAAACAACCC 59.018 38.462 1.05 0.00 0.00 4.11
3544 4046 2.874086 TGTCAGCTGTCATTGTCTTGTG 59.126 45.455 14.67 0.00 0.00 3.33
3547 4049 2.031420 CAGCTGTCATTGTCTTGTGTGG 60.031 50.000 5.25 0.00 0.00 4.17
3548 4050 1.949525 GCTGTCATTGTCTTGTGTGGT 59.050 47.619 0.00 0.00 0.00 4.16
3549 4051 3.138304 GCTGTCATTGTCTTGTGTGGTA 58.862 45.455 0.00 0.00 0.00 3.25
3550 4052 3.058914 GCTGTCATTGTCTTGTGTGGTAC 60.059 47.826 0.00 0.00 0.00 3.34
3551 4053 4.126437 CTGTCATTGTCTTGTGTGGTACA 58.874 43.478 0.00 0.00 37.56 2.90
3612 4114 3.494332 AGTCGTTAACCACTAGACCAGT 58.506 45.455 3.85 0.00 38.32 4.00
3652 4154 5.490139 AATGTTGCAGTATTGATTCTCCG 57.510 39.130 0.00 0.00 0.00 4.63
3659 4161 5.647658 TGCAGTATTGATTCTCCGATGTTTT 59.352 36.000 0.00 0.00 0.00 2.43
3666 4168 3.780804 TTCTCCGATGTTTTCCCTTGA 57.219 42.857 0.00 0.00 0.00 3.02
3699 4238 2.747989 CCAGCATTAGCATATCAGGCTG 59.252 50.000 8.58 8.58 45.49 4.85
3701 4240 3.436015 CAGCATTAGCATATCAGGCTGTC 59.564 47.826 15.27 0.29 45.49 3.51
3759 4368 2.202987 GCCATGACAGCCTCTCGG 60.203 66.667 0.00 0.00 0.00 4.63
3872 4492 6.919115 GGAAATTTCCTTGTAAACAAAGCGTA 59.081 34.615 26.94 0.00 44.11 4.42
3919 4539 0.957395 CCGAATGTGAGCAACAGCCT 60.957 55.000 0.00 0.00 43.64 4.58
3920 4540 0.167470 CGAATGTGAGCAACAGCCTG 59.833 55.000 0.00 0.00 43.64 4.85
3921 4541 1.242076 GAATGTGAGCAACAGCCTGT 58.758 50.000 0.00 0.00 43.64 4.00
3922 4542 0.956633 AATGTGAGCAACAGCCTGTG 59.043 50.000 0.00 0.00 43.64 3.66
3923 4543 0.179009 ATGTGAGCAACAGCCTGTGT 60.179 50.000 0.00 0.00 43.64 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 156 1.810853 CGACGATGGCATGCAGACA 60.811 57.895 21.36 8.94 41.62 3.41
197 198 1.077828 TCCCTCTCTTCTGCTTCAGGA 59.922 52.381 0.00 0.00 31.51 3.86
198 199 1.566211 TCCCTCTCTTCTGCTTCAGG 58.434 55.000 0.00 0.00 31.51 3.86
314 318 1.467342 GACATCCGGGCTAACAACAAC 59.533 52.381 0.00 0.00 0.00 3.32
412 426 2.375174 ACCCAGCAGAGAACACCAATTA 59.625 45.455 0.00 0.00 0.00 1.40
414 428 0.773644 ACCCAGCAGAGAACACCAAT 59.226 50.000 0.00 0.00 0.00 3.16
457 472 7.531857 AACCAAAACCAAAACCAAAAAGAAT 57.468 28.000 0.00 0.00 0.00 2.40
478 493 2.350192 CACCGGAAAACTTGCAAAAACC 59.650 45.455 9.46 0.00 0.00 3.27
496 558 4.884164 AGCAGAAAGATTAGCAATACCACC 59.116 41.667 0.00 0.00 0.00 4.61
522 591 3.890756 ACAGAAAAACCATCAGCATCACA 59.109 39.130 0.00 0.00 0.00 3.58
582 651 0.618458 TAGGAGCAGCACCGGAAAAT 59.382 50.000 9.46 0.00 0.00 1.82
589 658 0.176910 GGAAGACTAGGAGCAGCACC 59.823 60.000 0.00 0.00 0.00 5.01
607 676 1.871772 CAACGGCAGCAGAAAGAGG 59.128 57.895 0.00 0.00 0.00 3.69
612 681 3.043713 CGAGCAACGGCAGCAGAA 61.044 61.111 0.00 0.00 44.61 3.02
621 690 1.370414 CTGGCAAAACCGAGCAACG 60.370 57.895 0.00 0.00 43.94 4.10
625 694 3.314388 CTCGCTGGCAAAACCGAGC 62.314 63.158 11.63 0.00 43.94 5.03
628 697 2.252260 CACTCGCTGGCAAAACCG 59.748 61.111 0.00 0.00 43.94 4.44
639 708 2.431601 AGCTGAAGACGCACTCGC 60.432 61.111 0.00 0.00 39.84 5.03
674 743 4.462133 CCTCCTCCTGAAGACGTATTCTA 58.538 47.826 22.26 9.17 32.51 2.10
693 762 1.404391 TGATCTCTAAACCGTCGCCTC 59.596 52.381 0.00 0.00 0.00 4.70
705 774 1.681538 GACGCCTCCTGTGATCTCTA 58.318 55.000 0.00 0.00 0.00 2.43
726 795 3.069980 GCGAGACGACCCAGCATCT 62.070 63.158 0.00 0.00 0.00 2.90
747 816 0.678048 GAAGATGTGGGACCCAGCAC 60.678 60.000 15.52 8.06 32.34 4.40
885 960 3.238497 TCCGGCGATACCCATGGG 61.238 66.667 30.23 30.23 42.03 4.00
923 1010 2.231540 CTCCTCCTCCTCCTCCCGTT 62.232 65.000 0.00 0.00 0.00 4.44
927 1014 0.996762 TCTCCTCCTCCTCCTCCTCC 60.997 65.000 0.00 0.00 0.00 4.30
967 1057 0.314302 CCCTCCTAATCTACACCGCG 59.686 60.000 0.00 0.00 0.00 6.46
968 1058 0.680061 CCCCTCCTAATCTACACCGC 59.320 60.000 0.00 0.00 0.00 5.68
969 1059 2.240279 CTCCCCTCCTAATCTACACCG 58.760 57.143 0.00 0.00 0.00 4.94
970 1060 2.179424 TCCTCCCCTCCTAATCTACACC 59.821 54.545 0.00 0.00 0.00 4.16
1242 1335 2.092646 TGAATTAACGCCAGGGCATACT 60.093 45.455 11.42 0.00 42.06 2.12
1254 1347 2.882137 ACCACCACCAACTGAATTAACG 59.118 45.455 0.00 0.00 0.00 3.18
1258 1351 2.306847 GACACCACCACCAACTGAATT 58.693 47.619 0.00 0.00 0.00 2.17
1260 1353 0.106918 GGACACCACCACCAACTGAA 60.107 55.000 0.00 0.00 0.00 3.02
1346 1440 5.348997 CAGCGACTATACGAGATCACTGATA 59.651 44.000 0.00 0.00 35.09 2.15
1361 1463 5.105146 ACTTCAGAATTCCTTCAGCGACTAT 60.105 40.000 0.65 0.00 33.56 2.12
1483 1586 7.044181 CAGACCTCAAAGATGCTCATAGTAAA 58.956 38.462 0.00 0.00 0.00 2.01
1551 1661 0.801251 GTGCAAGAAGCTGGCTAGTG 59.199 55.000 0.00 0.00 45.94 2.74
1597 1707 2.180276 AGTCCCAGTCACATCACTACC 58.820 52.381 0.00 0.00 0.00 3.18
1610 1720 1.752683 ACGAGCAGTAGTAGTCCCAG 58.247 55.000 0.00 0.00 0.00 4.45
1655 1765 2.112190 CCTCTAACCTCACTCCTTCCC 58.888 57.143 0.00 0.00 0.00 3.97
1662 1772 1.903183 GCCTGAACCTCTAACCTCACT 59.097 52.381 0.00 0.00 0.00 3.41
1664 1774 0.895530 CGCCTGAACCTCTAACCTCA 59.104 55.000 0.00 0.00 0.00 3.86
1670 1780 1.591703 CAGTGCGCCTGAACCTCTA 59.408 57.895 17.75 0.00 44.49 2.43
1696 1806 7.446625 GGCTAGTTCATATCCAATCACTGAATT 59.553 37.037 0.00 0.00 0.00 2.17
1749 1861 7.117667 TGCTGCATAATACGGTAATCATAACAG 59.882 37.037 0.00 0.00 0.00 3.16
1766 1881 3.004862 CACTCACATCACTGCTGCATAA 58.995 45.455 1.31 0.00 0.00 1.90
1774 1891 2.828520 AGTAGTCCCACTCACATCACTG 59.171 50.000 0.00 0.00 0.00 3.66
1822 1939 4.668138 AAAGGCCCCTTCACATTACTTA 57.332 40.909 0.00 0.00 34.84 2.24
1895 2014 4.334552 TGACATTTGCACCACATCACTAT 58.665 39.130 0.00 0.00 0.00 2.12
1910 2029 5.047164 TGCATAGGCTCACAATTTGACATTT 60.047 36.000 2.79 0.00 41.91 2.32
1942 2061 6.651225 GCACAGCTTTACTCCTATATTAAGGG 59.349 42.308 0.00 0.00 37.24 3.95
1995 2118 4.881019 ACTACTGCTCTCTCACAACAAT 57.119 40.909 0.00 0.00 0.00 2.71
2042 2165 3.067742 TCGTCAGAAGGAATCCCGAATAC 59.932 47.826 0.00 0.00 37.58 1.89
2047 2170 2.271800 CTTTCGTCAGAAGGAATCCCG 58.728 52.381 0.00 0.00 37.70 5.14
2063 2186 5.353678 AGTCATGCAAGATAAGAGCACTTTC 59.646 40.000 0.55 0.38 41.60 2.62
2108 2246 3.072184 AGCAGTCAATCAACAAGAGAGGT 59.928 43.478 0.00 0.00 0.00 3.85
2149 2287 8.359642 CCTTCAATTTCAGTAGTCATTTTCCAA 58.640 33.333 0.00 0.00 0.00 3.53
2150 2288 7.523709 GCCTTCAATTTCAGTAGTCATTTTCCA 60.524 37.037 0.00 0.00 0.00 3.53
2156 2294 4.702131 GGTGCCTTCAATTTCAGTAGTCAT 59.298 41.667 0.00 0.00 0.00 3.06
2174 2312 4.450976 AGGAAAACAAATCAAAAGGTGCC 58.549 39.130 0.00 0.00 0.00 5.01
2212 2350 7.224753 CCGAGACATAACAACAATAGCTACAAT 59.775 37.037 0.00 0.00 0.00 2.71
2217 2355 3.871594 GCCGAGACATAACAACAATAGCT 59.128 43.478 0.00 0.00 0.00 3.32
2222 2360 3.407698 ACATGCCGAGACATAACAACAA 58.592 40.909 0.00 0.00 0.00 2.83
2241 2379 6.982724 CAGAATACATAGACATGAGCTCAACA 59.017 38.462 22.50 4.54 35.96 3.33
2246 2384 5.837979 AGACCAGAATACATAGACATGAGCT 59.162 40.000 0.00 0.00 35.96 4.09
2375 2521 7.064490 GCCATTGTATTTTACCCAATCAACTTG 59.936 37.037 0.00 0.00 34.42 3.16
2395 2544 0.752054 ACCAACCACACAAGCCATTG 59.248 50.000 0.00 0.00 42.46 2.82
2396 2545 1.960689 GTACCAACCACACAAGCCATT 59.039 47.619 0.00 0.00 0.00 3.16
2420 2569 1.131126 GCACATGACACCCTGAAATCG 59.869 52.381 0.00 0.00 0.00 3.34
2429 2578 5.119931 TGTTTTAAGATGCACATGACACC 57.880 39.130 0.00 0.00 0.00 4.16
2498 2651 2.905415 TTGCATTCTCCCTGGACAAT 57.095 45.000 0.00 0.00 0.00 2.71
2518 2671 8.709308 ACAGCCAGAAAGATAACTATAGTGAAT 58.291 33.333 6.06 3.41 0.00 2.57
2521 2674 9.250624 GTTACAGCCAGAAAGATAACTATAGTG 57.749 37.037 6.06 0.00 0.00 2.74
2522 2675 8.978472 TGTTACAGCCAGAAAGATAACTATAGT 58.022 33.333 0.00 0.00 0.00 2.12
2523 2676 9.817809 TTGTTACAGCCAGAAAGATAACTATAG 57.182 33.333 0.00 0.00 0.00 1.31
2528 2681 7.617041 ATCTTGTTACAGCCAGAAAGATAAC 57.383 36.000 0.00 0.00 33.71 1.89
2565 2731 9.390795 GAGCATAAATGATAAAGCATAACAGTG 57.609 33.333 0.00 0.00 0.00 3.66
2567 2733 9.823098 GAGAGCATAAATGATAAAGCATAACAG 57.177 33.333 0.00 0.00 0.00 3.16
2572 2739 6.715718 AGCTGAGAGCATAAATGATAAAGCAT 59.284 34.615 10.16 0.00 45.56 3.79
2604 2771 6.315891 GCTGATATCAAGCCTAGAATCATTCC 59.684 42.308 6.90 0.00 0.00 3.01
2613 2780 4.216472 TCACTACGCTGATATCAAGCCTAG 59.784 45.833 19.35 19.35 0.00 3.02
2615 2782 2.959030 TCACTACGCTGATATCAAGCCT 59.041 45.455 6.90 5.61 0.00 4.58
2652 3115 9.159254 TCCTGCTCCTAATATGAGAAAAGATAA 57.841 33.333 0.00 0.00 31.26 1.75
2656 3119 9.434420 CTTATCCTGCTCCTAATATGAGAAAAG 57.566 37.037 0.00 0.00 31.26 2.27
2661 3124 9.868277 CTTAACTTATCCTGCTCCTAATATGAG 57.132 37.037 0.00 0.00 0.00 2.90
2704 3167 9.912634 ACAGTTCAAATAAATGTCTTTGGTATG 57.087 29.630 0.00 0.00 34.01 2.39
2705 3168 9.912634 CACAGTTCAAATAAATGTCTTTGGTAT 57.087 29.630 0.00 0.00 34.01 2.73
2706 3169 8.908903 ACACAGTTCAAATAAATGTCTTTGGTA 58.091 29.630 0.00 0.00 34.01 3.25
2779 3246 3.875134 ACACTTCACTTTTTACCTGTCCG 59.125 43.478 0.00 0.00 0.00 4.79
2780 3247 4.497507 GCACACTTCACTTTTTACCTGTCC 60.498 45.833 0.00 0.00 0.00 4.02
2786 3253 3.955771 TCGGCACACTTCACTTTTTAC 57.044 42.857 0.00 0.00 0.00 2.01
2792 3259 2.254546 TCAATTCGGCACACTTCACT 57.745 45.000 0.00 0.00 0.00 3.41
2809 3276 8.732854 AGGAATGGATATGTTTTAGGGTTATCA 58.267 33.333 0.00 0.00 0.00 2.15
2857 3335 3.261580 TGTCAGTCAAGCCATGATAACG 58.738 45.455 0.00 0.00 40.97 3.18
3096 3574 0.524862 CTACTTCAGTACACGGCCGT 59.475 55.000 28.70 28.70 0.00 5.68
3098 3576 0.175073 CCCTACTTCAGTACACGGCC 59.825 60.000 0.00 0.00 0.00 6.13
3112 3590 3.907221 TGGTACACAGATCTACCCCTAC 58.093 50.000 9.45 0.00 32.68 3.18
3117 3595 3.802685 GCGATTTGGTACACAGATCTACC 59.197 47.826 5.56 5.56 39.29 3.18
3118 3596 3.802685 GGCGATTTGGTACACAGATCTAC 59.197 47.826 0.00 0.00 39.29 2.59
3157 3638 9.912634 GTACAGAAAGAATCCAATTTGAATCAA 57.087 29.630 0.00 0.00 0.00 2.57
3158 3639 9.076781 TGTACAGAAAGAATCCAATTTGAATCA 57.923 29.630 0.00 0.00 0.00 2.57
3170 3651 7.929941 AAGAATTCCCTGTACAGAAAGAATC 57.070 36.000 24.68 18.25 0.00 2.52
3205 3686 3.551082 GCTATGCATTTTATTGCGCACAA 59.449 39.130 11.12 4.15 45.77 3.33
3206 3687 3.114809 GCTATGCATTTTATTGCGCACA 58.885 40.909 11.12 1.63 45.77 4.57
3207 3688 3.114809 TGCTATGCATTTTATTGCGCAC 58.885 40.909 11.12 0.00 45.77 5.34
3208 3689 3.373849 CTGCTATGCATTTTATTGCGCA 58.626 40.909 5.66 5.66 45.77 6.09
3209 3690 2.154389 GCTGCTATGCATTTTATTGCGC 59.846 45.455 3.54 0.00 45.77 6.09
3210 3691 3.635331 AGCTGCTATGCATTTTATTGCG 58.365 40.909 3.54 0.00 45.77 4.85
3211 3692 4.613944 TGAGCTGCTATGCATTTTATTGC 58.386 39.130 3.54 2.77 43.07 3.56
3320 3822 0.184933 TGAACCAAACACCCCCTGAG 59.815 55.000 0.00 0.00 0.00 3.35
3321 3823 0.184933 CTGAACCAAACACCCCCTGA 59.815 55.000 0.00 0.00 0.00 3.86
3322 3824 0.827507 CCTGAACCAAACACCCCCTG 60.828 60.000 0.00 0.00 0.00 4.45
3323 3825 1.541672 CCTGAACCAAACACCCCCT 59.458 57.895 0.00 0.00 0.00 4.79
3324 3826 1.533033 CCCTGAACCAAACACCCCC 60.533 63.158 0.00 0.00 0.00 5.40
3325 3827 0.826256 GTCCCTGAACCAAACACCCC 60.826 60.000 0.00 0.00 0.00 4.95
3326 3828 0.185175 AGTCCCTGAACCAAACACCC 59.815 55.000 0.00 0.00 0.00 4.61
3327 3829 2.067365 AAGTCCCTGAACCAAACACC 57.933 50.000 0.00 0.00 0.00 4.16
3328 3830 4.465632 AAAAAGTCCCTGAACCAAACAC 57.534 40.909 0.00 0.00 0.00 3.32
3329 3831 5.265989 ACTAAAAAGTCCCTGAACCAAACA 58.734 37.500 0.00 0.00 0.00 2.83
3330 3832 5.828747 GACTAAAAAGTCCCTGAACCAAAC 58.171 41.667 0.00 0.00 32.97 2.93
3359 3861 9.543783 TGGACTTTTTAGAGACTTTTTCTAGTC 57.456 33.333 0.00 0.00 43.90 2.59
3363 3865 9.508642 CCTATGGACTTTTTAGAGACTTTTTCT 57.491 33.333 0.00 0.00 37.23 2.52
3364 3866 9.503399 TCCTATGGACTTTTTAGAGACTTTTTC 57.497 33.333 0.00 0.00 0.00 2.29
3365 3867 9.862149 TTCCTATGGACTTTTTAGAGACTTTTT 57.138 29.630 0.00 0.00 0.00 1.94
3367 3869 9.674068 GATTCCTATGGACTTTTTAGAGACTTT 57.326 33.333 0.00 0.00 0.00 2.66
3368 3870 8.826765 TGATTCCTATGGACTTTTTAGAGACTT 58.173 33.333 0.00 0.00 0.00 3.01
3369 3871 8.380742 TGATTCCTATGGACTTTTTAGAGACT 57.619 34.615 0.00 0.00 0.00 3.24
3370 3872 9.449719 TTTGATTCCTATGGACTTTTTAGAGAC 57.550 33.333 0.00 0.00 0.00 3.36
3371 3873 9.449719 GTTTGATTCCTATGGACTTTTTAGAGA 57.550 33.333 0.00 0.00 0.00 3.10
3372 3874 8.391106 CGTTTGATTCCTATGGACTTTTTAGAG 58.609 37.037 0.00 0.00 0.00 2.43
3373 3875 7.335924 CCGTTTGATTCCTATGGACTTTTTAGA 59.664 37.037 0.00 0.00 0.00 2.10
3374 3876 7.335924 TCCGTTTGATTCCTATGGACTTTTTAG 59.664 37.037 0.00 0.00 0.00 1.85
3375 3877 7.169591 TCCGTTTGATTCCTATGGACTTTTTA 58.830 34.615 0.00 0.00 0.00 1.52
3376 3878 6.007703 TCCGTTTGATTCCTATGGACTTTTT 58.992 36.000 0.00 0.00 0.00 1.94
3377 3879 5.566469 TCCGTTTGATTCCTATGGACTTTT 58.434 37.500 0.00 0.00 0.00 2.27
3378 3880 5.174037 TCCGTTTGATTCCTATGGACTTT 57.826 39.130 0.00 0.00 0.00 2.66
3379 3881 4.837093 TCCGTTTGATTCCTATGGACTT 57.163 40.909 0.00 0.00 0.00 3.01
3380 3882 4.384208 CCTTCCGTTTGATTCCTATGGACT 60.384 45.833 0.00 0.00 0.00 3.85
3381 3883 3.877508 CCTTCCGTTTGATTCCTATGGAC 59.122 47.826 0.00 0.00 0.00 4.02
3382 3884 3.118038 CCCTTCCGTTTGATTCCTATGGA 60.118 47.826 0.00 0.00 0.00 3.41
3383 3885 3.118038 TCCCTTCCGTTTGATTCCTATGG 60.118 47.826 0.00 0.00 0.00 2.74
3384 3886 3.877508 GTCCCTTCCGTTTGATTCCTATG 59.122 47.826 0.00 0.00 0.00 2.23
3385 3887 3.780850 AGTCCCTTCCGTTTGATTCCTAT 59.219 43.478 0.00 0.00 0.00 2.57
3386 3888 3.178865 AGTCCCTTCCGTTTGATTCCTA 58.821 45.455 0.00 0.00 0.00 2.94
3387 3889 1.985895 AGTCCCTTCCGTTTGATTCCT 59.014 47.619 0.00 0.00 0.00 3.36
3388 3890 2.491675 AGTCCCTTCCGTTTGATTCC 57.508 50.000 0.00 0.00 0.00 3.01
3389 3891 4.848562 AAAAGTCCCTTCCGTTTGATTC 57.151 40.909 0.00 0.00 0.00 2.52
3390 3892 4.893524 AGAAAAAGTCCCTTCCGTTTGATT 59.106 37.500 0.00 0.00 0.00 2.57
3391 3893 4.470602 AGAAAAAGTCCCTTCCGTTTGAT 58.529 39.130 0.00 0.00 0.00 2.57
3392 3894 3.893521 AGAAAAAGTCCCTTCCGTTTGA 58.106 40.909 0.00 0.00 0.00 2.69
3393 3895 4.577283 TGTAGAAAAAGTCCCTTCCGTTTG 59.423 41.667 0.00 0.00 0.00 2.93
3394 3896 4.784177 TGTAGAAAAAGTCCCTTCCGTTT 58.216 39.130 0.00 0.00 0.00 3.60
3395 3897 4.386711 CTGTAGAAAAAGTCCCTTCCGTT 58.613 43.478 0.00 0.00 0.00 4.44
3396 3898 3.244457 CCTGTAGAAAAAGTCCCTTCCGT 60.244 47.826 0.00 0.00 0.00 4.69
3397 3899 3.007614 TCCTGTAGAAAAAGTCCCTTCCG 59.992 47.826 0.00 0.00 0.00 4.30
3398 3900 4.635699 TCCTGTAGAAAAAGTCCCTTCC 57.364 45.455 0.00 0.00 0.00 3.46
3399 3901 7.621796 TCTAATCCTGTAGAAAAAGTCCCTTC 58.378 38.462 0.00 0.00 0.00 3.46
3400 3902 7.569599 TCTAATCCTGTAGAAAAAGTCCCTT 57.430 36.000 0.00 0.00 0.00 3.95
3401 3903 7.569599 TTCTAATCCTGTAGAAAAAGTCCCT 57.430 36.000 0.00 0.00 37.20 4.20
3411 3913 9.756571 AGTAGAGTCTTTTTCTAATCCTGTAGA 57.243 33.333 0.00 0.00 0.00 2.59
3412 3914 9.796120 CAGTAGAGTCTTTTTCTAATCCTGTAG 57.204 37.037 0.00 0.00 0.00 2.74
3413 3915 9.529823 TCAGTAGAGTCTTTTTCTAATCCTGTA 57.470 33.333 0.00 0.00 0.00 2.74
3414 3916 8.423906 TCAGTAGAGTCTTTTTCTAATCCTGT 57.576 34.615 0.00 0.00 0.00 4.00
3415 3917 9.364989 CTTCAGTAGAGTCTTTTTCTAATCCTG 57.635 37.037 0.00 0.00 0.00 3.86
3416 3918 9.315363 TCTTCAGTAGAGTCTTTTTCTAATCCT 57.685 33.333 0.00 0.00 0.00 3.24
3417 3919 9.581099 CTCTTCAGTAGAGTCTTTTTCTAATCC 57.419 37.037 0.00 0.00 44.54 3.01
3447 3949 3.745799 TGTCCCAGCGACTAATCAAAAA 58.254 40.909 0.00 0.00 42.49 1.94
3448 3950 3.410631 TGTCCCAGCGACTAATCAAAA 57.589 42.857 0.00 0.00 42.49 2.44
3449 3951 3.410631 TTGTCCCAGCGACTAATCAAA 57.589 42.857 0.00 0.00 42.49 2.69
3450 3952 3.410631 TTTGTCCCAGCGACTAATCAA 57.589 42.857 0.00 0.00 42.49 2.57
3451 3953 3.410631 TTTTGTCCCAGCGACTAATCA 57.589 42.857 0.00 0.00 42.49 2.57
3474 3976 7.703621 GGTTGTTTTGTTTAAAAGTCCTAGGAC 59.296 37.037 31.29 31.29 44.86 3.85
3475 3977 7.147863 GGGTTGTTTTGTTTAAAAGTCCTAGGA 60.148 37.037 7.62 7.62 36.51 2.94
3476 3978 6.982141 GGGTTGTTTTGTTTAAAAGTCCTAGG 59.018 38.462 0.82 0.82 36.51 3.02
3477 3979 6.982141 GGGGTTGTTTTGTTTAAAAGTCCTAG 59.018 38.462 0.00 0.00 36.51 3.02
3478 3980 6.668718 AGGGGTTGTTTTGTTTAAAAGTCCTA 59.331 34.615 0.00 0.00 36.51 2.94
3479 3981 5.486063 AGGGGTTGTTTTGTTTAAAAGTCCT 59.514 36.000 0.00 0.00 36.51 3.85
3480 3982 5.736813 AGGGGTTGTTTTGTTTAAAAGTCC 58.263 37.500 0.00 0.00 36.51 3.85
3481 3983 6.399743 TGAGGGGTTGTTTTGTTTAAAAGTC 58.600 36.000 0.00 0.00 36.51 3.01
3482 3984 6.361768 TGAGGGGTTGTTTTGTTTAAAAGT 57.638 33.333 0.00 0.00 36.51 2.66
3483 3985 5.293324 GCTGAGGGGTTGTTTTGTTTAAAAG 59.707 40.000 0.00 0.00 36.51 2.27
3484 3986 5.179533 GCTGAGGGGTTGTTTTGTTTAAAA 58.820 37.500 0.00 0.00 33.57 1.52
3485 3987 4.383226 GGCTGAGGGGTTGTTTTGTTTAAA 60.383 41.667 0.00 0.00 0.00 1.52
3486 3988 3.133183 GGCTGAGGGGTTGTTTTGTTTAA 59.867 43.478 0.00 0.00 0.00 1.52
3487 3989 2.696187 GGCTGAGGGGTTGTTTTGTTTA 59.304 45.455 0.00 0.00 0.00 2.01
3488 3990 1.484653 GGCTGAGGGGTTGTTTTGTTT 59.515 47.619 0.00 0.00 0.00 2.83
3489 3991 1.119684 GGCTGAGGGGTTGTTTTGTT 58.880 50.000 0.00 0.00 0.00 2.83
3490 3992 1.106944 CGGCTGAGGGGTTGTTTTGT 61.107 55.000 0.00 0.00 0.00 2.83
3491 3993 0.821711 TCGGCTGAGGGGTTGTTTTG 60.822 55.000 0.00 0.00 0.00 2.44
3492 3994 0.112412 ATCGGCTGAGGGGTTGTTTT 59.888 50.000 0.00 0.00 0.00 2.43
3493 3995 0.609131 CATCGGCTGAGGGGTTGTTT 60.609 55.000 0.00 0.00 0.00 2.83
3494 3996 1.002134 CATCGGCTGAGGGGTTGTT 60.002 57.895 0.00 0.00 0.00 2.83
3495 3997 2.671070 CATCGGCTGAGGGGTTGT 59.329 61.111 0.00 0.00 0.00 3.32
3496 3998 2.124570 CCATCGGCTGAGGGGTTG 60.125 66.667 18.78 1.98 42.40 3.77
3497 3999 2.285368 TCCATCGGCTGAGGGGTT 60.285 61.111 25.34 0.00 46.14 4.11
3498 4000 2.765807 CTCCATCGGCTGAGGGGT 60.766 66.667 25.34 0.00 46.14 4.95
3499 4001 3.554342 CCTCCATCGGCTGAGGGG 61.554 72.222 25.34 16.98 46.14 4.79
3500 4002 4.247380 GCCTCCATCGGCTGAGGG 62.247 72.222 20.43 20.43 46.79 4.30
3529 4031 4.126437 TGTACCACACAAGACAATGACAG 58.874 43.478 0.00 0.00 32.95 3.51
3547 4049 2.159000 GGCCTGGTATGGTGTACTGTAC 60.159 54.545 10.98 10.98 0.00 2.90
3548 4050 2.112998 GGCCTGGTATGGTGTACTGTA 58.887 52.381 0.00 0.00 0.00 2.74
3549 4051 0.909623 GGCCTGGTATGGTGTACTGT 59.090 55.000 0.00 0.00 0.00 3.55
3550 4052 0.180406 GGGCCTGGTATGGTGTACTG 59.820 60.000 0.84 0.00 0.00 2.74
3551 4053 0.252974 TGGGCCTGGTATGGTGTACT 60.253 55.000 4.53 0.00 0.00 2.73
3612 4114 2.048597 CGTACCGCCAGCACTGAA 60.049 61.111 0.00 0.00 0.00 3.02
3644 4146 4.261801 TCAAGGGAAAACATCGGAGAATC 58.738 43.478 0.00 0.00 43.58 2.52
3652 4154 7.629437 GCCTAGAAGAAATCAAGGGAAAACATC 60.629 40.741 0.00 0.00 0.00 3.06
3659 4161 3.189606 TGGCCTAGAAGAAATCAAGGGA 58.810 45.455 3.32 0.00 0.00 4.20
3666 4168 4.140536 GCTAATGCTGGCCTAGAAGAAAT 58.859 43.478 3.32 0.00 36.03 2.17
3699 4238 2.673368 CAATTAGCTGGAACACCGAGAC 59.327 50.000 0.00 0.00 0.00 3.36
3701 4240 2.009774 CCAATTAGCTGGAACACCGAG 58.990 52.381 0.00 0.00 38.96 4.63
3784 4393 1.286248 ACGGGGAGCTTGGTTAAGAT 58.714 50.000 0.00 0.00 35.92 2.40
3792 4412 2.076863 CTGTTAAGAACGGGGAGCTTG 58.923 52.381 0.00 0.00 34.07 4.01
3919 4539 1.484653 AGTGCTCTGGTACACAACACA 59.515 47.619 0.00 0.00 39.30 3.72
3920 4540 2.240493 AGTGCTCTGGTACACAACAC 57.760 50.000 0.00 0.00 39.30 3.32
3921 4541 3.275617 AAAGTGCTCTGGTACACAACA 57.724 42.857 0.00 0.00 39.30 3.33
3922 4542 5.283060 CATAAAGTGCTCTGGTACACAAC 57.717 43.478 0.00 0.00 39.30 3.32


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

AutoCloner maintained by Alex Coulton.