Multiple sequence alignment - TraesCS3D01G487400

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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 TraesCS3D01G487400 chr3D 100.000 3202 0 0 1 3202 582829706 582826505 0.000000e+00 5914.0
1 TraesCS3D01G487400 chr3D 78.457 311 56 8 1014 1320 582056837 582056534 3.260000e-45 193.0
2 TraesCS3D01G487400 chr3D 89.256 121 13 0 2380 2500 335220443 335220563 5.530000e-33 152.0
3 TraesCS3D01G487400 chr3D 77.670 206 31 11 1116 1312 482501469 482501668 9.390000e-21 111.0
4 TraesCS3D01G487400 chr3B 93.433 1477 90 5 1 1476 778452802 778454272 0.000000e+00 2183.0
5 TraesCS3D01G487400 chr3B 91.560 1019 71 9 1490 2499 778454256 778455268 0.000000e+00 1391.0
6 TraesCS3D01G487400 chr3B 90.941 287 16 8 2683 2961 778455261 778455545 8.380000e-101 377.0
7 TraesCS3D01G487400 chr3B 94.608 204 7 3 2999 3202 778455771 778455970 2.400000e-81 313.0
8 TraesCS3D01G487400 chr3B 79.288 309 62 2 1013 1320 778875852 778876159 6.960000e-52 215.0
9 TraesCS3D01G487400 chr3B 78.964 309 63 2 1013 1320 778932578 778932885 3.240000e-50 209.0
10 TraesCS3D01G487400 chr3B 78.387 310 64 3 1013 1320 778704958 778705266 7.010000e-47 198.0
11 TraesCS3D01G487400 chr2A 89.933 149 14 1 2335 2482 771620167 771620315 1.170000e-44 191.0
12 TraesCS3D01G487400 chr2A 80.541 185 28 5 2503 2682 17956665 17956484 5.570000e-28 135.0
13 TraesCS3D01G487400 chr2A 84.000 75 12 0 2693 2767 771620334 771620408 4.430000e-09 73.1
14 TraesCS3D01G487400 chr6A 85.542 166 22 2 2338 2501 601961372 601961207 4.250000e-39 172.0
15 TraesCS3D01G487400 chr2D 82.412 199 31 4 2493 2689 4194061 4194257 1.530000e-38 171.0
16 TraesCS3D01G487400 chr2D 83.889 180 25 4 2504 2682 534132753 534132929 5.490000e-38 169.0
17 TraesCS3D01G487400 chr2D 81.000 100 18 1 2673 2772 645896676 645896774 9.520000e-11 78.7
18 TraesCS3D01G487400 chr6D 85.714 161 21 1 2340 2500 433481398 433481240 5.490000e-38 169.0
19 TraesCS3D01G487400 chr6D 84.259 108 16 1 2664 2771 440639602 440639496 1.570000e-18 104.0
20 TraesCS3D01G487400 chr6D 85.057 87 13 0 2499 2585 367322192 367322278 4.400000e-14 89.8
21 TraesCS3D01G487400 chr7D 83.333 180 25 5 2325 2501 551607308 551607131 9.190000e-36 161.0
22 TraesCS3D01G487400 chr7D 82.927 164 24 4 2325 2486 551503417 551503256 9.260000e-31 145.0
23 TraesCS3D01G487400 chr7D 100.000 29 0 0 2732 2760 593685066 593685038 2.000000e-03 54.7
24 TraesCS3D01G487400 chr4A 84.615 169 19 4 2338 2501 725261123 725260957 9.190000e-36 161.0
25 TraesCS3D01G487400 chr4A 90.566 53 3 2 2537 2589 672195218 672195268 5.730000e-08 69.4
26 TraesCS3D01G487400 chr3A 90.756 119 11 0 2380 2498 453313332 453313450 3.310000e-35 159.0
27 TraesCS3D01G487400 chr3A 79.558 181 23 8 1140 1312 625405628 625405802 2.020000e-22 117.0
28 TraesCS3D01G487400 chr3A 79.208 101 13 3 2674 2773 453313435 453313528 2.670000e-06 63.9
29 TraesCS3D01G487400 chr1A 93.478 46 3 0 2500 2545 586358163 586358118 5.730000e-08 69.4
30 TraesCS3D01G487400 chr1A 96.970 33 1 0 2740 2772 485004558 485004590 4.460000e-04 56.5
31 TraesCS3D01G487400 chr1B 96.970 33 1 0 2740 2772 516953331 516953363 4.460000e-04 56.5


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 TraesCS3D01G487400 chr3D 582826505 582829706 3201 True 5914 5914 100.0000 1 3202 1 chr3D.!!$R2 3201
1 TraesCS3D01G487400 chr3B 778452802 778455970 3168 False 1066 2183 92.6355 1 3202 4 chr3B.!!$F4 3201

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
178 179 0.034960 TGGAAATTCCGCAATCCCGA 60.035 50.0 7.60 0.00 40.17 5.14 F
955 956 0.167908 ACAACACACAAGCACACACG 59.832 50.0 0.00 0.00 0.00 4.49 F
1745 1749 0.107017 GGCATACCTCTGCATGGTGT 60.107 55.0 18.37 11.07 44.12 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1132 1133 0.037303 ATGGGGTTGTGAGTGAGCAG 59.963 55.0 0.0 0.0 0.00 4.24 R
2132 2136 0.445436 CAGAGAACATGGCAACGAGC 59.555 55.0 0.0 0.0 44.65 5.03 R
2997 3015 0.035152 AGCAATGGCATCCGAAGTCA 60.035 50.0 0.0 0.0 44.61 3.41 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
61 62 6.721668 TCTTACTCTTGATTGAGAGGTCTTCA 59.278 38.462 6.82 0.00 45.93 3.02
79 80 7.280205 AGGTCTTCATCGAATTAAACCATGTAC 59.720 37.037 10.92 0.00 0.00 2.90
81 82 7.009815 GTCTTCATCGAATTAAACCATGTACGA 59.990 37.037 0.00 0.00 0.00 3.43
98 99 3.340814 ACGAGATGAGCCAAATGTTCT 57.659 42.857 0.00 0.00 0.00 3.01
107 108 4.276678 TGAGCCAAATGTTCTCTTCTGTTG 59.723 41.667 0.00 0.00 0.00 3.33
110 111 5.827797 AGCCAAATGTTCTCTTCTGTTGTTA 59.172 36.000 0.00 0.00 0.00 2.41
178 179 0.034960 TGGAAATTCCGCAATCCCGA 60.035 50.000 7.60 0.00 40.17 5.14
213 214 6.313519 ACATTCTGCTAATCCCAGACTAAA 57.686 37.500 0.00 0.00 38.93 1.85
255 256 5.682943 TTTAGGTGAACTGAATTTCCGTG 57.317 39.130 0.00 0.00 0.00 4.94
256 257 1.880027 AGGTGAACTGAATTTCCGTGC 59.120 47.619 0.00 0.00 0.00 5.34
336 337 1.333308 CAACGTGGCATGTTCAACTGA 59.667 47.619 21.68 0.00 0.00 3.41
342 343 5.048083 ACGTGGCATGTTCAACTGATTTAAT 60.048 36.000 6.51 0.00 0.00 1.40
383 384 4.141801 CCGGATTTAATCACCACAGACCTA 60.142 45.833 7.29 0.00 0.00 3.08
411 412 9.692325 TTTTAAACAGGGTTTTACTTACCACTA 57.308 29.630 0.00 0.00 37.40 2.74
418 419 6.559921 AGGGTTTTACTTACCACTAGAGGAAA 59.440 38.462 13.71 0.00 37.40 3.13
428 429 5.036916 ACCACTAGAGGAAATATTGGTGGA 58.963 41.667 13.71 0.00 43.72 4.02
429 430 5.491078 ACCACTAGAGGAAATATTGGTGGAA 59.509 40.000 13.71 0.00 43.72 3.53
439 440 6.352737 GGAAATATTGGTGGAACAGAGGTAGA 60.353 42.308 0.00 0.00 41.80 2.59
442 443 3.981071 TGGTGGAACAGAGGTAGATTG 57.019 47.619 0.00 0.00 41.80 2.67
460 461 2.154567 TGGGTTACCGCTGATACTCT 57.845 50.000 0.00 0.00 40.75 3.24
473 474 4.258543 CTGATACTCTTTACCGCCCAAAA 58.741 43.478 0.00 0.00 0.00 2.44
478 479 4.149598 ACTCTTTACCGCCCAAAATTCTT 58.850 39.130 0.00 0.00 0.00 2.52
586 587 1.506028 ATGTGGGGGTGTGGTTAGGG 61.506 60.000 0.00 0.00 0.00 3.53
606 607 3.714391 GGTGTAGCTATAACCCTCGTTG 58.286 50.000 14.74 0.00 33.17 4.10
619 620 2.488153 CCCTCGTTGGAACCAGATTTTC 59.512 50.000 0.00 0.00 38.35 2.29
648 649 5.711976 CCAACATTTGGTTCCTATCTTGACT 59.288 40.000 0.00 0.00 45.93 3.41
682 683 5.288804 ACAAAAATGATTTCACCACTTCCG 58.711 37.500 0.00 0.00 0.00 4.30
685 686 1.808411 TGATTTCACCACTTCCGAGC 58.192 50.000 0.00 0.00 0.00 5.03
779 780 4.215399 CGAGGGCAAGATAAGTTTGTTTGA 59.785 41.667 0.00 0.00 0.00 2.69
801 802 4.843220 ACTTCAAACTTCAAGATGCAGG 57.157 40.909 0.00 0.00 0.00 4.85
804 805 3.819368 TCAAACTTCAAGATGCAGGACA 58.181 40.909 0.00 0.00 0.00 4.02
812 813 6.150140 ACTTCAAGATGCAGGACAAATAAGTC 59.850 38.462 0.00 0.00 37.80 3.01
829 830 9.029243 CAAATAAGTCATAGCTGAGTACTCTTG 57.971 37.037 23.01 16.18 33.81 3.02
845 846 3.772025 ACTCTTGGTCCCATAGAGACAAG 59.228 47.826 21.77 9.54 39.96 3.16
862 863 4.095782 AGACAAGACAGACTCTATCGAAGC 59.904 45.833 0.00 0.00 0.00 3.86
864 865 5.186942 ACAAGACAGACTCTATCGAAGCTA 58.813 41.667 0.00 0.00 0.00 3.32
933 934 8.910351 AGCATCAGTATCCTACTTAAATTTCC 57.090 34.615 0.00 0.00 36.76 3.13
955 956 0.167908 ACAACACACAAGCACACACG 59.832 50.000 0.00 0.00 0.00 4.49
962 963 3.585990 AAGCACACACGCCACAGC 61.586 61.111 0.00 0.00 0.00 4.40
968 969 4.481617 ACACGCCACAGCACCACA 62.482 61.111 0.00 0.00 39.83 4.17
977 978 1.001048 CACAGCACCACACCATTGAAG 60.001 52.381 0.00 0.00 0.00 3.02
982 983 2.233271 CACCACACCATTGAAGAGCTT 58.767 47.619 0.00 0.00 0.00 3.74
988 989 3.005155 ACACCATTGAAGAGCTTGCTTTC 59.995 43.478 0.00 4.05 0.00 2.62
1009 1010 3.152341 CAAGCAAGAAGAATGGGTGAGT 58.848 45.455 0.00 0.00 0.00 3.41
1011 1012 1.734465 GCAAGAAGAATGGGTGAGTCG 59.266 52.381 0.00 0.00 0.00 4.18
1057 1058 3.475774 GTACGTTCAGCCACCGCG 61.476 66.667 0.00 0.00 41.18 6.46
1101 1102 1.153628 GGTGCCGTACGAGCTCATT 60.154 57.895 18.76 1.92 0.00 2.57
1130 1131 0.662619 CTTCGCAACAAGAGCCAACA 59.337 50.000 0.00 0.00 0.00 3.33
1132 1133 1.370900 CGCAACAAGAGCCAACAGC 60.371 57.895 0.00 0.00 44.25 4.40
1192 1193 3.916392 CTCCACGGCGACAGACCAC 62.916 68.421 16.62 0.00 0.00 4.16
1198 1199 2.711922 GGCGACAGACCACCGATCT 61.712 63.158 0.00 0.00 0.00 2.75
1212 1213 0.651031 CGATCTGTGAGTCGCTCGTA 59.349 55.000 5.11 0.00 32.35 3.43
1311 1312 0.532573 TCTGGGCTCACTTCATCGAC 59.467 55.000 0.00 0.00 0.00 4.20
1312 1313 0.803768 CTGGGCTCACTTCATCGACG 60.804 60.000 0.00 0.00 0.00 5.12
1322 1323 5.100259 TCACTTCATCGACGAAAAGGTATC 58.900 41.667 20.73 0.00 0.00 2.24
1371 1372 4.687901 TGTGTTGAGAACTTGAGATCCA 57.312 40.909 0.00 0.00 0.00 3.41
1375 1376 3.272574 TGAGAACTTGAGATCCATGCC 57.727 47.619 0.00 0.00 0.00 4.40
1376 1377 2.573009 TGAGAACTTGAGATCCATGCCA 59.427 45.455 0.00 0.00 0.00 4.92
1378 1379 4.012374 GAGAACTTGAGATCCATGCCAAA 58.988 43.478 0.00 0.00 0.00 3.28
1380 1381 4.219288 AGAACTTGAGATCCATGCCAAAAC 59.781 41.667 0.00 0.00 0.00 2.43
1381 1382 3.771216 ACTTGAGATCCATGCCAAAACT 58.229 40.909 0.00 0.00 0.00 2.66
1382 1383 4.154942 ACTTGAGATCCATGCCAAAACTT 58.845 39.130 0.00 0.00 0.00 2.66
1436 1437 1.266867 TGCAGGCCTAGAGCACATGA 61.267 55.000 12.02 0.00 46.50 3.07
1591 1594 1.536766 ACATGACCATTTCTGCACACG 59.463 47.619 0.00 0.00 0.00 4.49
1592 1595 1.536766 CATGACCATTTCTGCACACGT 59.463 47.619 0.00 0.00 0.00 4.49
1607 1611 5.626211 TGCACACGTTATATTCATGTGTTG 58.374 37.500 9.01 7.17 41.52 3.33
1608 1612 4.495472 GCACACGTTATATTCATGTGTTGC 59.505 41.667 9.01 11.31 41.52 4.17
1609 1613 5.027737 CACACGTTATATTCATGTGTTGCC 58.972 41.667 9.01 0.00 41.52 4.52
1646 1650 9.986833 GTTTCAAGTTCAAATATTGTTTTGCTT 57.013 25.926 0.00 0.00 36.69 3.91
1655 1659 8.825745 TCAAATATTGTTTTGCTTGGAAGAAAC 58.174 29.630 0.00 0.00 36.69 2.78
1660 1664 6.867662 TGTTTTGCTTGGAAGAAACAAAAA 57.132 29.167 0.00 0.00 40.66 1.94
1690 1694 9.160496 AGAAAAATTTCTACAGTGATAGAGCAG 57.840 33.333 6.62 0.00 45.17 4.24
1702 1706 3.776969 TGATAGAGCAGGAACCTTGATGT 59.223 43.478 0.00 0.00 0.00 3.06
1745 1749 0.107017 GGCATACCTCTGCATGGTGT 60.107 55.000 18.37 11.07 44.12 4.16
1777 1781 5.369685 TGGGTATATAATTGCGTGCAATG 57.630 39.130 19.80 0.00 44.86 2.82
1790 1794 1.591183 GCAATGTTGCGGAACCCAT 59.409 52.632 17.64 1.95 45.11 4.00
1805 1809 1.993956 CCCATGGGTGTTCTGAAACA 58.006 50.000 23.93 0.00 43.06 2.83
1883 1887 1.369839 CTAGCGAGGCACAGAGACGA 61.370 60.000 0.00 0.00 0.00 4.20
1887 1891 1.380403 CGAGGCACAGAGACGATCCT 61.380 60.000 0.00 0.00 0.00 3.24
2057 2061 1.111116 TGGTCACGGACGAGGAGTTT 61.111 55.000 0.00 0.00 32.65 2.66
2063 2067 2.654877 GACGAGGAGTTTCCGGCA 59.345 61.111 0.00 0.00 42.75 5.69
2090 2094 2.158813 CCATTGGGCTAGACGGTATGTT 60.159 50.000 0.00 0.00 0.00 2.71
2091 2095 3.070446 CCATTGGGCTAGACGGTATGTTA 59.930 47.826 0.00 0.00 0.00 2.41
2132 2136 3.003173 TTGCCGGAGAGGGGTGAG 61.003 66.667 5.05 0.00 41.48 3.51
2187 2191 1.659335 CGATCAATGGCAATGGCGC 60.659 57.895 0.00 0.00 42.47 6.53
2219 2223 5.277828 GCAGTGAAGTCGTCCACTTTAATTT 60.278 40.000 0.00 0.00 46.10 1.82
2231 2236 8.652463 CGTCCACTTTAATTTGTCTTTTGTTTT 58.348 29.630 0.00 0.00 0.00 2.43
2262 2267 6.346096 CACTTTCCCACGATCTTATCCTTTA 58.654 40.000 0.00 0.00 0.00 1.85
2286 2292 2.621055 TCCTTGCATTGTAACACGCTTT 59.379 40.909 0.00 0.00 0.00 3.51
2303 2309 6.092748 CACGCTTTTATGGTTTCTGCTAAAT 58.907 36.000 0.00 0.00 0.00 1.40
2344 2350 8.200792 TGAGAGCTTTCTTCAGAATAATACTCC 58.799 37.037 5.77 2.78 33.54 3.85
2352 2358 6.498651 TCTTCAGAATAATACTCCCTCCATCC 59.501 42.308 0.00 0.00 0.00 3.51
2375 2381 5.989777 CCCAATATACAAGGCTACTACACAC 59.010 44.000 0.00 0.00 0.00 3.82
2377 2383 7.272978 CCAATATACAAGGCTACTACACACTT 58.727 38.462 0.00 0.00 0.00 3.16
2429 2439 6.247727 TCAACAAAAAGCGAGTTATATGCA 57.752 33.333 0.00 0.00 0.00 3.96
2442 2452 7.696453 GCGAGTTATATGCAACAAAAAGTATGT 59.304 33.333 0.00 0.00 0.00 2.29
2507 2517 9.952030 TGTTAGATGTCATATAACCAGTGAAAA 57.048 29.630 21.79 4.06 36.41 2.29
2511 2521 9.911788 AGATGTCATATAACCAGTGAAAAAGAT 57.088 29.630 0.00 0.00 0.00 2.40
2514 2524 9.109393 TGTCATATAACCAGTGAAAAAGATAGC 57.891 33.333 0.00 0.00 0.00 2.97
2515 2525 8.276325 GTCATATAACCAGTGAAAAAGATAGCG 58.724 37.037 0.00 0.00 0.00 4.26
2516 2526 3.831715 AACCAGTGAAAAAGATAGCGC 57.168 42.857 0.00 0.00 0.00 5.92
2517 2527 2.778299 ACCAGTGAAAAAGATAGCGCA 58.222 42.857 11.47 0.00 0.00 6.09
2518 2528 2.484264 ACCAGTGAAAAAGATAGCGCAC 59.516 45.455 11.47 0.00 0.00 5.34
2519 2529 2.744202 CCAGTGAAAAAGATAGCGCACT 59.256 45.455 11.47 2.60 37.09 4.40
2520 2530 3.932710 CCAGTGAAAAAGATAGCGCACTA 59.067 43.478 11.47 0.00 35.09 2.74
2521 2531 4.572389 CCAGTGAAAAAGATAGCGCACTAT 59.428 41.667 11.47 0.00 41.98 2.12
2522 2532 5.753438 CCAGTGAAAAAGATAGCGCACTATA 59.247 40.000 11.47 0.00 39.28 1.31
2523 2533 6.074088 CCAGTGAAAAAGATAGCGCACTATAG 60.074 42.308 11.47 0.00 39.28 1.31
2524 2534 5.463724 AGTGAAAAAGATAGCGCACTATAGC 59.536 40.000 11.47 0.00 39.28 2.97
2536 2546 2.847133 GCACTATAGCGTCGCTAATAGC 59.153 50.000 29.13 24.04 44.62 2.97
2537 2547 3.669824 GCACTATAGCGTCGCTAATAGCA 60.670 47.826 29.13 9.37 44.62 3.49
2538 2548 4.663166 CACTATAGCGTCGCTAATAGCAT 58.337 43.478 29.13 15.97 44.62 3.79
2539 2549 4.497251 CACTATAGCGTCGCTAATAGCATG 59.503 45.833 29.13 19.05 44.62 4.06
2540 2550 3.577649 ATAGCGTCGCTAATAGCATGT 57.422 42.857 29.13 8.87 44.62 3.21
2541 2551 2.225068 AGCGTCGCTAATAGCATGTT 57.775 45.000 20.25 1.00 42.58 2.71
2542 2552 3.364889 AGCGTCGCTAATAGCATGTTA 57.635 42.857 20.25 0.00 42.58 2.41
2543 2553 3.914312 AGCGTCGCTAATAGCATGTTAT 58.086 40.909 20.25 0.00 42.58 1.89
2544 2554 5.055642 AGCGTCGCTAATAGCATGTTATA 57.944 39.130 20.25 0.00 42.58 0.98
2545 2555 5.096169 AGCGTCGCTAATAGCATGTTATAG 58.904 41.667 20.25 2.93 42.58 1.31
2546 2556 4.259451 GCGTCGCTAATAGCATGTTATAGC 60.259 45.833 10.68 10.47 42.58 2.97
2549 2559 5.763444 CGCTAATAGCATGTTATAGCGTT 57.237 39.130 26.23 9.82 42.58 4.84
2550 2560 5.776081 CGCTAATAGCATGTTATAGCGTTC 58.224 41.667 26.23 8.45 42.58 3.95
2551 2561 5.573282 CGCTAATAGCATGTTATAGCGTTCT 59.427 40.000 26.23 8.26 42.58 3.01
2552 2562 6.453003 CGCTAATAGCATGTTATAGCGTTCTG 60.453 42.308 26.23 12.17 42.58 3.02
2553 2563 6.586463 GCTAATAGCATGTTATAGCGTTCTGA 59.414 38.462 7.49 0.00 41.89 3.27
2554 2564 7.201393 GCTAATAGCATGTTATAGCGTTCTGAG 60.201 40.741 7.49 0.00 41.89 3.35
2555 2565 3.126831 AGCATGTTATAGCGTTCTGAGC 58.873 45.455 0.00 0.00 35.48 4.26
2556 2566 2.866156 GCATGTTATAGCGTTCTGAGCA 59.134 45.455 0.00 0.00 37.01 4.26
2557 2567 3.309682 GCATGTTATAGCGTTCTGAGCAA 59.690 43.478 0.00 0.00 37.01 3.91
2558 2568 4.024556 GCATGTTATAGCGTTCTGAGCAAT 60.025 41.667 0.00 0.00 37.01 3.56
2559 2569 5.438117 CATGTTATAGCGTTCTGAGCAATG 58.562 41.667 0.00 0.00 37.01 2.82
2560 2570 4.503910 TGTTATAGCGTTCTGAGCAATGT 58.496 39.130 0.00 0.00 37.01 2.71
2561 2571 4.566759 TGTTATAGCGTTCTGAGCAATGTC 59.433 41.667 0.00 0.00 37.01 3.06
2562 2572 3.533606 ATAGCGTTCTGAGCAATGTCT 57.466 42.857 0.00 0.00 37.01 3.41
2563 2573 1.719600 AGCGTTCTGAGCAATGTCTC 58.280 50.000 0.00 0.00 37.01 3.36
2564 2574 1.001293 AGCGTTCTGAGCAATGTCTCA 59.999 47.619 7.06 7.06 40.50 3.27
2565 2575 1.127582 GCGTTCTGAGCAATGTCTCAC 59.872 52.381 3.84 0.00 38.11 3.51
2566 2576 2.681706 CGTTCTGAGCAATGTCTCACT 58.318 47.619 3.84 0.00 38.11 3.41
2567 2577 3.838120 CGTTCTGAGCAATGTCTCACTA 58.162 45.455 3.84 0.00 38.11 2.74
2568 2578 4.237724 CGTTCTGAGCAATGTCTCACTAA 58.762 43.478 3.84 0.69 38.11 2.24
2569 2579 4.686091 CGTTCTGAGCAATGTCTCACTAAA 59.314 41.667 3.84 0.00 38.11 1.85
2570 2580 5.349817 CGTTCTGAGCAATGTCTCACTAAAT 59.650 40.000 3.84 0.00 38.11 1.40
2571 2581 6.128445 CGTTCTGAGCAATGTCTCACTAAATT 60.128 38.462 3.84 0.00 38.11 1.82
2572 2582 7.063426 CGTTCTGAGCAATGTCTCACTAAATTA 59.937 37.037 3.84 0.00 38.11 1.40
2573 2583 8.721478 GTTCTGAGCAATGTCTCACTAAATTAA 58.279 33.333 3.84 0.00 38.11 1.40
2574 2584 9.453572 TTCTGAGCAATGTCTCACTAAATTAAT 57.546 29.630 3.84 0.00 38.11 1.40
2575 2585 9.102757 TCTGAGCAATGTCTCACTAAATTAATC 57.897 33.333 3.84 0.00 38.11 1.75
2576 2586 7.909267 TGAGCAATGTCTCACTAAATTAATCG 58.091 34.615 3.84 0.00 38.11 3.34
2577 2587 7.763985 TGAGCAATGTCTCACTAAATTAATCGA 59.236 33.333 3.84 0.00 38.11 3.59
2578 2588 8.668510 AGCAATGTCTCACTAAATTAATCGAT 57.331 30.769 0.00 0.00 0.00 3.59
2579 2589 8.554528 AGCAATGTCTCACTAAATTAATCGATG 58.445 33.333 0.00 0.00 0.00 3.84
2580 2590 8.338259 GCAATGTCTCACTAAATTAATCGATGT 58.662 33.333 0.00 0.00 0.00 3.06
2584 2594 9.863845 TGTCTCACTAAATTAATCGATGTACAA 57.136 29.630 0.00 0.00 0.00 2.41
2591 2601 9.580916 CTAAATTAATCGATGTACAATGTTCCG 57.419 33.333 0.00 0.00 0.00 4.30
2592 2602 3.944422 AATCGATGTACAATGTTCCGC 57.056 42.857 0.00 0.00 0.00 5.54
2593 2603 2.665649 TCGATGTACAATGTTCCGCT 57.334 45.000 0.00 0.00 0.00 5.52
2594 2604 3.786516 TCGATGTACAATGTTCCGCTA 57.213 42.857 0.00 0.00 0.00 4.26
2595 2605 4.112716 TCGATGTACAATGTTCCGCTAA 57.887 40.909 0.00 0.00 0.00 3.09
2596 2606 4.689071 TCGATGTACAATGTTCCGCTAAT 58.311 39.130 0.00 0.00 0.00 1.73
2597 2607 5.834169 TCGATGTACAATGTTCCGCTAATA 58.166 37.500 0.00 0.00 0.00 0.98
2598 2608 5.918576 TCGATGTACAATGTTCCGCTAATAG 59.081 40.000 0.00 0.00 0.00 1.73
2599 2609 5.388475 CGATGTACAATGTTCCGCTAATAGC 60.388 44.000 0.00 1.41 38.02 2.97
2600 2610 4.760878 TGTACAATGTTCCGCTAATAGCA 58.239 39.130 13.15 0.00 42.58 3.49
2601 2611 5.364778 TGTACAATGTTCCGCTAATAGCAT 58.635 37.500 13.15 0.00 42.58 3.79
2602 2612 4.818534 ACAATGTTCCGCTAATAGCATG 57.181 40.909 13.15 2.85 42.58 4.06
2603 2613 4.199310 ACAATGTTCCGCTAATAGCATGT 58.801 39.130 13.15 2.83 42.58 3.21
2604 2614 4.640201 ACAATGTTCCGCTAATAGCATGTT 59.360 37.500 13.15 0.00 42.58 2.71
2605 2615 5.820423 ACAATGTTCCGCTAATAGCATGTTA 59.180 36.000 13.15 0.00 42.58 2.41
2606 2616 6.486657 ACAATGTTCCGCTAATAGCATGTTAT 59.513 34.615 13.15 0.00 42.58 1.89
2607 2617 7.659799 ACAATGTTCCGCTAATAGCATGTTATA 59.340 33.333 13.15 0.00 42.58 0.98
2608 2618 7.834068 ATGTTCCGCTAATAGCATGTTATAG 57.166 36.000 13.15 2.93 42.58 1.31
2609 2619 6.755206 TGTTCCGCTAATAGCATGTTATAGT 58.245 36.000 13.15 0.00 42.58 2.12
2610 2620 6.645003 TGTTCCGCTAATAGCATGTTATAGTG 59.355 38.462 13.15 7.33 42.58 2.74
2611 2621 5.168569 TCCGCTAATAGCATGTTATAGTGC 58.831 41.667 13.15 6.84 42.58 4.40
2612 2622 4.031765 CCGCTAATAGCATGTTATAGTGCG 59.968 45.833 23.31 23.31 45.69 5.34
2613 2623 4.857037 CGCTAATAGCATGTTATAGTGCGA 59.143 41.667 24.68 0.00 45.69 5.10
2614 2624 5.516696 CGCTAATAGCATGTTATAGTGCGAT 59.483 40.000 24.68 5.74 45.69 4.58
2615 2625 6.691388 CGCTAATAGCATGTTATAGTGCGATA 59.309 38.462 24.68 6.40 45.69 2.92
2616 2626 7.379797 CGCTAATAGCATGTTATAGTGCGATAT 59.620 37.037 24.68 4.64 45.69 1.63
2617 2627 9.678941 GCTAATAGCATGTTATAGTGCGATATA 57.321 33.333 7.49 0.00 45.69 0.86
2619 2629 8.581057 AATAGCATGTTATAGTGCGATATAGC 57.419 34.615 2.17 0.16 45.69 2.97
2620 2630 5.965922 AGCATGTTATAGTGCGATATAGCA 58.034 37.500 6.39 6.39 45.69 3.49
2635 2645 7.485825 CGATATAGCACGCTAATAGCATATC 57.514 40.000 13.15 14.01 42.58 1.63
2636 2646 7.301789 CGATATAGCACGCTAATAGCATATCT 58.698 38.462 18.82 10.91 42.58 1.98
2637 2647 7.805542 CGATATAGCACGCTAATAGCATATCTT 59.194 37.037 18.82 3.71 42.58 2.40
2640 2650 8.864069 ATAGCACGCTAATAGCATATCTTAAG 57.136 34.615 13.15 0.00 42.58 1.85
2641 2651 6.925211 AGCACGCTAATAGCATATCTTAAGA 58.075 36.000 13.15 7.82 42.58 2.10
2642 2652 7.032580 AGCACGCTAATAGCATATCTTAAGAG 58.967 38.462 13.15 0.00 42.58 2.85
2643 2653 7.030165 GCACGCTAATAGCATATCTTAAGAGA 58.970 38.462 13.15 6.81 42.58 3.10
2644 2654 7.008810 GCACGCTAATAGCATATCTTAAGAGAC 59.991 40.741 13.15 0.44 42.58 3.36
2645 2655 8.023706 CACGCTAATAGCATATCTTAAGAGACA 58.976 37.037 13.15 0.00 42.58 3.41
2646 2656 8.024285 ACGCTAATAGCATATCTTAAGAGACAC 58.976 37.037 13.15 2.42 42.58 3.67
2647 2657 8.023706 CGCTAATAGCATATCTTAAGAGACACA 58.976 37.037 13.15 0.00 42.58 3.72
2648 2658 9.868277 GCTAATAGCATATCTTAAGAGACACAT 57.132 33.333 11.53 0.00 41.89 3.21
2663 2673 8.565896 AAGAGACACATTATTTTGTCATAGCA 57.434 30.769 6.66 0.00 43.94 3.49
2664 2674 8.743085 AGAGACACATTATTTTGTCATAGCAT 57.257 30.769 6.66 0.00 43.94 3.79
2665 2675 8.618677 AGAGACACATTATTTTGTCATAGCATG 58.381 33.333 6.66 0.00 43.94 4.06
2666 2676 7.198390 AGACACATTATTTTGTCATAGCATGC 58.802 34.615 10.51 10.51 43.94 4.06
2667 2677 7.067859 AGACACATTATTTTGTCATAGCATGCT 59.932 33.333 25.99 25.99 43.94 3.79
2668 2678 8.224389 ACACATTATTTTGTCATAGCATGCTA 57.776 30.769 28.72 28.72 0.00 3.49
2669 2679 8.853126 ACACATTATTTTGTCATAGCATGCTAT 58.147 29.630 30.43 30.43 39.60 2.97
2670 2680 9.687210 CACATTATTTTGTCATAGCATGCTATT 57.313 29.630 32.84 20.72 37.16 1.73
2729 2739 9.362151 ACCAAAATAAGAAGTTCCAGTTTGATA 57.638 29.630 20.78 0.00 0.00 2.15
2730 2740 9.626045 CCAAAATAAGAAGTTCCAGTTTGATAC 57.374 33.333 20.78 0.00 0.00 2.24
2745 2755 5.746721 AGTTTGATACGAAAAACAAAGTGGC 59.253 36.000 0.00 0.00 38.48 5.01
2767 2777 4.137543 CCTTGTATACAGAAATGGAGGGC 58.862 47.826 5.56 0.00 0.00 5.19
2791 2801 9.797556 GGCGTATTGTATCACATCAGTATTATA 57.202 33.333 0.00 0.00 0.00 0.98
2852 2864 6.746745 GGTTAACCGAGAAATAACCATTCA 57.253 37.500 9.34 0.00 45.09 2.57
2858 2870 8.608844 AACCGAGAAATAACCATTCATAGATC 57.391 34.615 0.00 0.00 0.00 2.75
2863 2875 9.645059 GAGAAATAACCATTCATAGATCGATGA 57.355 33.333 13.81 13.81 33.96 2.92
2878 2890 2.297315 TCGATGAATCATAGCCGCTCTT 59.703 45.455 0.00 0.00 0.00 2.85
2884 2896 5.182487 TGAATCATAGCCGCTCTTACAAAA 58.818 37.500 0.00 0.00 0.00 2.44
2885 2897 5.822519 TGAATCATAGCCGCTCTTACAAAAT 59.177 36.000 0.00 0.00 0.00 1.82
2889 2901 7.801716 TCATAGCCGCTCTTACAAAATTATT 57.198 32.000 0.00 0.00 0.00 1.40
2937 2951 8.742554 AAAAATCCATAGCTAACAAGAAAACG 57.257 30.769 0.00 0.00 0.00 3.60
2940 2958 7.681939 ATCCATAGCTAACAAGAAAACGAAA 57.318 32.000 0.00 0.00 0.00 3.46
2941 2959 7.681939 TCCATAGCTAACAAGAAAACGAAAT 57.318 32.000 0.00 0.00 0.00 2.17
2944 2962 9.834628 CCATAGCTAACAAGAAAACGAAATAAA 57.165 29.630 0.00 0.00 0.00 1.40
2970 2988 6.961360 ATCCACGATCTACTTTCTATGTCA 57.039 37.500 0.00 0.00 0.00 3.58
2971 2989 6.378710 TCCACGATCTACTTTCTATGTCAG 57.621 41.667 0.00 0.00 0.00 3.51
2972 2990 4.979197 CCACGATCTACTTTCTATGTCAGC 59.021 45.833 0.00 0.00 0.00 4.26
2973 2991 5.450550 CCACGATCTACTTTCTATGTCAGCA 60.451 44.000 0.00 0.00 0.00 4.41
2974 2992 6.036470 CACGATCTACTTTCTATGTCAGCAA 58.964 40.000 0.00 0.00 0.00 3.91
2975 2993 6.020281 CACGATCTACTTTCTATGTCAGCAAC 60.020 42.308 0.00 0.00 0.00 4.17
2976 2994 6.036470 CGATCTACTTTCTATGTCAGCAACA 58.964 40.000 0.00 0.00 43.51 3.33
2977 2995 6.198029 CGATCTACTTTCTATGTCAGCAACAG 59.802 42.308 0.00 0.00 42.37 3.16
2978 2996 5.171476 TCTACTTTCTATGTCAGCAACAGC 58.829 41.667 0.00 0.00 42.37 4.40
2979 2997 3.743521 ACTTTCTATGTCAGCAACAGCA 58.256 40.909 0.00 0.00 42.37 4.41
2980 2998 4.330250 ACTTTCTATGTCAGCAACAGCAT 58.670 39.130 0.00 0.00 42.37 3.79
2981 2999 4.155462 ACTTTCTATGTCAGCAACAGCATG 59.845 41.667 0.00 0.00 42.37 4.06
2988 3006 3.189921 GCAACAGCATGCCGATCA 58.810 55.556 15.66 0.00 42.53 2.92
2991 3009 1.089112 CAACAGCATGCCGATCAAGA 58.911 50.000 15.66 0.00 42.53 3.02
2993 3011 1.825090 ACAGCATGCCGATCAAGAAA 58.175 45.000 15.66 0.00 42.53 2.52
2994 3012 1.470098 ACAGCATGCCGATCAAGAAAC 59.530 47.619 15.66 0.00 42.53 2.78
2997 3015 2.821969 AGCATGCCGATCAAGAAACTTT 59.178 40.909 15.66 0.00 0.00 2.66
3041 3247 5.443693 CGCTTGGAAACGTACACAATAGTAC 60.444 44.000 0.00 0.00 40.68 2.73
3045 3251 7.213216 TGGAAACGTACACAATAGTACTACA 57.787 36.000 4.31 0.00 41.65 2.74
3048 3254 7.594758 GGAAACGTACACAATAGTACTACAACA 59.405 37.037 4.31 0.00 41.65 3.33
3092 3298 4.219033 CAAAGTCACCATCGTTTTGCTAC 58.781 43.478 0.00 0.00 0.00 3.58
3110 3316 9.653287 TTTTGCTACATTATATTATCTCCTCCG 57.347 33.333 0.00 0.00 0.00 4.63
3195 3401 3.487042 GCAGCTGCATCAATAACAGTGAG 60.487 47.826 33.36 0.00 41.59 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.836007 TCTCAATCAAGAGTAAGATGCTCCTA 59.164 38.462 0.00 0.00 36.97 2.94
61 62 7.207383 TCATCTCGTACATGGTTTAATTCGAT 58.793 34.615 0.00 0.00 0.00 3.59
79 80 3.529533 AGAGAACATTTGGCTCATCTCG 58.470 45.455 0.00 0.00 38.60 4.04
81 82 4.942483 CAGAAGAGAACATTTGGCTCATCT 59.058 41.667 0.00 0.00 37.24 2.90
110 111 9.628500 ACTCAGGAAAGTACAGAATTTAACTTT 57.372 29.630 0.00 0.00 43.06 2.66
154 155 2.491693 GGATTGCGGAATTTCCAACTGA 59.508 45.455 15.58 1.55 35.91 3.41
168 169 3.234368 CGGAAATTTCGGGATTGCG 57.766 52.632 15.92 7.02 0.00 4.85
178 179 2.299867 AGCAGAATGTTGCCGGAAATTT 59.700 40.909 5.05 0.00 45.18 1.82
228 229 9.020731 ACGGAAATTCAGTTCACCTAAATTTAT 57.979 29.630 0.00 0.00 31.58 1.40
237 238 1.606668 TGCACGGAAATTCAGTTCACC 59.393 47.619 0.00 0.00 0.00 4.02
255 256 2.808543 AGAGAACAACAAAGGACGATGC 59.191 45.455 0.00 0.00 0.00 3.91
256 257 4.389077 GGTAGAGAACAACAAAGGACGATG 59.611 45.833 0.00 0.00 0.00 3.84
336 337 8.893727 CGGTCCAGTCTCTGATAAAAATTAAAT 58.106 33.333 0.00 0.00 32.44 1.40
342 343 3.835978 TCCGGTCCAGTCTCTGATAAAAA 59.164 43.478 0.00 0.00 32.44 1.94
349 350 3.887621 TTAAATCCGGTCCAGTCTCTG 57.112 47.619 0.00 0.00 0.00 3.35
356 357 2.306219 TGTGGTGATTAAATCCGGTCCA 59.694 45.455 0.00 0.00 0.00 4.02
383 384 8.469200 GTGGTAAGTAAAACCCTGTTTAAAACT 58.531 33.333 0.00 0.00 36.06 2.66
407 408 6.414732 TGTTCCACCAATATTTCCTCTAGTG 58.585 40.000 0.00 0.00 0.00 2.74
411 412 5.339530 CCTCTGTTCCACCAATATTTCCTCT 60.340 44.000 0.00 0.00 0.00 3.69
418 419 6.409695 CCAATCTACCTCTGTTCCACCAATAT 60.410 42.308 0.00 0.00 0.00 1.28
428 429 3.197116 CGGTAACCCAATCTACCTCTGTT 59.803 47.826 0.00 0.00 36.24 3.16
429 430 2.764572 CGGTAACCCAATCTACCTCTGT 59.235 50.000 0.00 0.00 36.24 3.41
439 440 3.039011 AGAGTATCAGCGGTAACCCAAT 58.961 45.455 0.00 0.00 37.82 3.16
442 443 3.538634 AAAGAGTATCAGCGGTAACCC 57.461 47.619 0.00 0.00 37.82 4.11
460 461 5.786264 TGTAAAGAATTTTGGGCGGTAAA 57.214 34.783 0.00 0.00 40.09 2.01
527 528 7.744087 AGCTGCAAAACCATTTCGATATATA 57.256 32.000 1.02 0.00 0.00 0.86
528 529 6.639632 AGCTGCAAAACCATTTCGATATAT 57.360 33.333 1.02 0.00 0.00 0.86
586 587 3.382546 TCCAACGAGGGTTATAGCTACAC 59.617 47.826 0.00 0.00 38.24 2.90
605 606 4.656100 TGGATCTGAAAATCTGGTTCCA 57.344 40.909 0.00 0.00 31.25 3.53
606 607 4.766891 TGTTGGATCTGAAAATCTGGTTCC 59.233 41.667 0.00 0.00 0.00 3.62
676 677 0.179161 CATCGACGAAGCTCGGAAGT 60.179 55.000 0.00 0.00 45.59 3.01
682 683 0.798771 AGCGTTCATCGACGAAGCTC 60.799 55.000 0.00 0.00 45.47 4.09
685 686 0.635731 GTGAGCGTTCATCGACGAAG 59.364 55.000 4.92 0.00 45.47 3.79
779 780 4.889409 TCCTGCATCTTGAAGTTTGAAGTT 59.111 37.500 0.00 0.00 0.00 2.66
789 790 6.003326 TGACTTATTTGTCCTGCATCTTGAA 58.997 36.000 0.00 0.00 36.21 2.69
801 802 8.410141 AGAGTACTCAGCTATGACTTATTTGTC 58.590 37.037 24.44 0.00 37.47 3.18
804 805 8.200792 CCAAGAGTACTCAGCTATGACTTATTT 58.799 37.037 24.44 2.29 0.00 1.40
812 813 3.068873 GGGACCAAGAGTACTCAGCTATG 59.931 52.174 24.44 13.76 0.00 2.23
829 830 3.131400 GTCTGTCTTGTCTCTATGGGACC 59.869 52.174 0.00 0.00 33.22 4.46
933 934 1.468127 TGTGTGCTTGTGTGTTGTCTG 59.532 47.619 0.00 0.00 0.00 3.51
955 956 2.202395 AATGGTGTGGTGCTGTGGC 61.202 57.895 0.00 0.00 39.26 5.01
962 963 1.901591 AGCTCTTCAATGGTGTGGTG 58.098 50.000 0.00 0.00 0.00 4.17
968 969 3.225104 TGAAAGCAAGCTCTTCAATGGT 58.775 40.909 13.42 0.00 0.00 3.55
988 989 3.152341 ACTCACCCATTCTTCTTGCTTG 58.848 45.455 0.00 0.00 0.00 4.01
992 993 1.734465 GCGACTCACCCATTCTTCTTG 59.266 52.381 0.00 0.00 0.00 3.02
1009 1010 2.184322 GATGAGCTTCACCGGCGA 59.816 61.111 9.30 0.00 34.52 5.54
1011 1012 2.467826 GCTGATGAGCTTCACCGGC 61.468 63.158 0.00 0.00 42.52 6.13
1032 1033 1.623973 GGCTGAACGTACTGCCGAAC 61.624 60.000 9.32 0.00 42.86 3.95
1083 1084 1.153628 AATGAGCTCGTACGGCACC 60.154 57.895 24.11 17.27 0.00 5.01
1115 1116 4.641777 GCTGTTGGCTCTTGTTGC 57.358 55.556 0.00 0.00 38.06 4.17
1130 1131 1.072159 GGGTTGTGAGTGAGCAGCT 59.928 57.895 0.00 0.00 0.00 4.24
1132 1133 0.037303 ATGGGGTTGTGAGTGAGCAG 59.963 55.000 0.00 0.00 0.00 4.24
1140 1141 1.144691 TCTTGTGGATGGGGTTGTGA 58.855 50.000 0.00 0.00 0.00 3.58
1192 1193 1.297967 CGAGCGACTCACAGATCGG 60.298 63.158 7.47 0.00 38.78 4.18
1198 1199 3.310501 TCGATAATTACGAGCGACTCACA 59.689 43.478 0.00 0.00 34.85 3.58
1212 1213 4.558898 GCCTCATCCACGTACTCGATAATT 60.559 45.833 0.00 0.00 40.62 1.40
1251 1252 4.716977 GGGTCGGTGGGGAGGAGT 62.717 72.222 0.00 0.00 0.00 3.85
1311 1312 3.189287 ACAGCTTTGCAGATACCTTTTCG 59.811 43.478 0.00 0.00 0.00 3.46
1312 1313 4.773323 ACAGCTTTGCAGATACCTTTTC 57.227 40.909 0.00 0.00 0.00 2.29
1322 1323 1.532868 AGCTCGTTTACAGCTTTGCAG 59.467 47.619 0.00 0.00 45.34 4.41
1388 1389 8.755018 GTTCAAATGTATTCCTTTTGTTGACAG 58.245 33.333 0.00 0.00 38.61 3.51
1390 1391 8.871686 AGTTCAAATGTATTCCTTTTGTTGAC 57.128 30.769 0.00 0.00 38.61 3.18
1395 1396 8.140677 TGCAAAGTTCAAATGTATTCCTTTTG 57.859 30.769 0.00 0.00 38.76 2.44
1401 1402 4.627035 GGCCTGCAAAGTTCAAATGTATTC 59.373 41.667 0.00 0.00 0.00 1.75
1569 1570 3.550639 CGTGTGCAGAAATGGTCATGTTT 60.551 43.478 0.00 0.00 0.00 2.83
1571 1572 1.536766 CGTGTGCAGAAATGGTCATGT 59.463 47.619 0.00 0.00 0.00 3.21
1591 1594 4.339247 AGGCAGGCAACACATGAATATAAC 59.661 41.667 0.00 0.00 41.41 1.89
1592 1595 4.338964 CAGGCAGGCAACACATGAATATAA 59.661 41.667 0.00 0.00 41.41 0.98
1607 1611 1.000171 CTTGAAACTTTCCAGGCAGGC 60.000 52.381 0.00 0.00 37.29 4.85
1608 1612 2.310538 ACTTGAAACTTTCCAGGCAGG 58.689 47.619 7.36 0.00 39.47 4.85
1609 1613 3.381272 TGAACTTGAAACTTTCCAGGCAG 59.619 43.478 7.36 0.00 0.00 4.85
1665 1669 8.394121 CCTGCTCTATCACTGTAGAAATTTTTC 58.606 37.037 0.00 0.00 37.45 2.29
1668 1672 7.187824 TCCTGCTCTATCACTGTAGAAATTT 57.812 36.000 0.00 0.00 30.74 1.82
1669 1673 6.798427 TCCTGCTCTATCACTGTAGAAATT 57.202 37.500 0.00 0.00 30.74 1.82
1670 1674 6.407525 GGTTCCTGCTCTATCACTGTAGAAAT 60.408 42.308 0.00 0.00 30.74 2.17
1671 1675 5.105310 GGTTCCTGCTCTATCACTGTAGAAA 60.105 44.000 0.00 0.00 30.74 2.52
1682 1686 5.957771 TTACATCAAGGTTCCTGCTCTAT 57.042 39.130 0.00 0.00 0.00 1.98
1684 1688 4.640771 TTTACATCAAGGTTCCTGCTCT 57.359 40.909 0.00 0.00 0.00 4.09
1687 1691 7.391148 TCTAAATTTACATCAAGGTTCCTGC 57.609 36.000 0.00 0.00 0.00 4.85
1690 1694 7.258441 GCCTTCTAAATTTACATCAAGGTTCC 58.742 38.462 15.47 0.00 32.92 3.62
1702 1706 6.465321 CCTTCTATCCGGGCCTTCTAAATTTA 60.465 42.308 0.84 0.00 0.00 1.40
1756 1760 5.371115 ACATTGCACGCAATTATATACCC 57.629 39.130 14.41 0.00 43.32 3.69
1757 1761 6.674005 CAACATTGCACGCAATTATATACC 57.326 37.500 14.41 0.00 43.32 2.73
1790 1794 5.830457 TCAACATATTGTTTCAGAACACCCA 59.170 36.000 0.00 0.00 45.01 4.51
1804 1808 9.465985 TGCACTGCATATTTAATCAACATATTG 57.534 29.630 0.00 0.00 33.19 1.90
1853 1857 1.051812 CCTCGCTAGGTTCCATCCAT 58.948 55.000 0.00 0.00 38.19 3.41
1883 1887 1.566231 CCCTTTGCCTCTACCAAGGAT 59.434 52.381 0.00 0.00 38.87 3.24
1887 1891 0.991920 CTCCCCTTTGCCTCTACCAA 59.008 55.000 0.00 0.00 0.00 3.67
2045 2049 2.125633 GCCGGAAACTCCTCGTCC 60.126 66.667 5.05 0.00 33.30 4.79
2046 2050 1.737008 GTGCCGGAAACTCCTCGTC 60.737 63.158 5.05 0.00 33.30 4.20
2048 2052 0.602905 AAAGTGCCGGAAACTCCTCG 60.603 55.000 5.05 0.00 33.30 4.63
2076 2080 5.434352 TCATCACTAACATACCGTCTAGC 57.566 43.478 0.00 0.00 0.00 3.42
2090 2094 5.683249 GCATGTCTTCACATCCTCATCACTA 60.683 44.000 0.00 0.00 41.69 2.74
2091 2095 4.767478 CATGTCTTCACATCCTCATCACT 58.233 43.478 0.00 0.00 41.69 3.41
2132 2136 0.445436 CAGAGAACATGGCAACGAGC 59.555 55.000 0.00 0.00 44.65 5.03
2188 2192 2.661566 CGACTTCACTGCTGTGGCG 61.662 63.158 21.80 16.08 43.94 5.69
2196 2200 5.924475 AATTAAAGTGGACGACTTCACTG 57.076 39.130 3.11 0.00 44.68 3.66
2205 2209 7.749539 AACAAAAGACAAATTAAAGTGGACG 57.250 32.000 0.00 0.00 0.00 4.79
2231 2236 3.581332 AGATCGTGGGAAAGTGGTAGAAA 59.419 43.478 0.00 0.00 0.00 2.52
2234 2239 3.611766 AAGATCGTGGGAAAGTGGTAG 57.388 47.619 0.00 0.00 0.00 3.18
2247 2252 7.054124 TGCAAGGAAATAAAGGATAAGATCGT 58.946 34.615 0.00 0.00 0.00 3.73
2262 2267 3.255642 AGCGTGTTACAATGCAAGGAAAT 59.744 39.130 12.26 0.00 0.00 2.17
2286 2292 7.732222 AATCCCAATTTAGCAGAAACCATAA 57.268 32.000 0.00 0.00 0.00 1.90
2303 2309 8.109634 AGAAAGCTCTCACTTTATTAATCCCAA 58.890 33.333 0.00 0.00 39.93 4.12
2344 2350 3.331889 AGCCTTGTATATTGGGATGGAGG 59.668 47.826 0.00 0.00 0.00 4.30
2352 2358 6.817184 AGTGTGTAGTAGCCTTGTATATTGG 58.183 40.000 0.00 0.00 0.00 3.16
2406 2416 6.247727 TGCATATAACTCGCTTTTTGTTGA 57.752 33.333 0.00 0.00 0.00 3.18
2429 2439 6.646240 GTGCATCCAATGACATACTTTTTGTT 59.354 34.615 0.00 0.00 0.00 2.83
2442 2452 5.725325 TCTTTCAAATGTGCATCCAATGA 57.275 34.783 0.00 0.00 0.00 2.57
2498 2508 2.744202 AGTGCGCTATCTTTTTCACTGG 59.256 45.455 9.73 0.00 34.00 4.00
2499 2509 5.725110 ATAGTGCGCTATCTTTTTCACTG 57.275 39.130 14.10 0.00 36.37 3.66
2500 2510 5.463724 GCTATAGTGCGCTATCTTTTTCACT 59.536 40.000 22.65 1.47 38.71 3.41
2501 2511 5.671074 GCTATAGTGCGCTATCTTTTTCAC 58.329 41.667 22.65 2.33 38.71 3.18
2502 2512 5.907197 GCTATAGTGCGCTATCTTTTTCA 57.093 39.130 22.65 3.45 38.71 2.69
2515 2525 2.847133 GCTATTAGCGACGCTATAGTGC 59.153 50.000 28.67 23.61 41.01 4.40
2516 2526 4.079665 TGCTATTAGCGACGCTATAGTG 57.920 45.455 28.67 19.03 46.26 2.74
2517 2527 4.156190 ACATGCTATTAGCGACGCTATAGT 59.844 41.667 28.67 19.42 46.26 2.12
2518 2528 4.663166 ACATGCTATTAGCGACGCTATAG 58.337 43.478 28.67 26.76 46.26 1.31
2519 2529 4.696899 ACATGCTATTAGCGACGCTATA 57.303 40.909 28.67 19.32 46.26 1.31
2520 2530 3.577649 ACATGCTATTAGCGACGCTAT 57.422 42.857 28.67 19.98 46.26 2.97
2521 2531 3.364889 AACATGCTATTAGCGACGCTA 57.635 42.857 25.04 25.04 46.26 4.26
2522 2532 2.225068 AACATGCTATTAGCGACGCT 57.775 45.000 27.45 27.45 46.26 5.07
2523 2533 4.259451 GCTATAACATGCTATTAGCGACGC 60.259 45.833 13.03 13.03 46.26 5.19
2524 2534 5.362987 GCTATAACATGCTATTAGCGACG 57.637 43.478 10.94 4.54 46.26 5.12
2528 2538 6.586463 TCAGAACGCTATAACATGCTATTAGC 59.414 38.462 8.80 8.80 42.82 3.09
2529 2539 7.201393 GCTCAGAACGCTATAACATGCTATTAG 60.201 40.741 0.00 0.00 0.00 1.73
2530 2540 6.586463 GCTCAGAACGCTATAACATGCTATTA 59.414 38.462 0.00 0.00 0.00 0.98
2531 2541 5.406780 GCTCAGAACGCTATAACATGCTATT 59.593 40.000 0.00 0.00 0.00 1.73
2532 2542 4.926238 GCTCAGAACGCTATAACATGCTAT 59.074 41.667 0.00 0.00 0.00 2.97
2533 2543 4.202111 TGCTCAGAACGCTATAACATGCTA 60.202 41.667 0.00 0.00 0.00 3.49
2534 2544 3.126831 GCTCAGAACGCTATAACATGCT 58.873 45.455 0.00 0.00 0.00 3.79
2535 2545 2.866156 TGCTCAGAACGCTATAACATGC 59.134 45.455 0.00 0.00 0.00 4.06
2536 2546 5.007039 ACATTGCTCAGAACGCTATAACATG 59.993 40.000 0.00 0.00 0.00 3.21
2537 2547 5.118990 ACATTGCTCAGAACGCTATAACAT 58.881 37.500 0.00 0.00 0.00 2.71
2538 2548 4.503910 ACATTGCTCAGAACGCTATAACA 58.496 39.130 0.00 0.00 0.00 2.41
2539 2549 4.806247 AGACATTGCTCAGAACGCTATAAC 59.194 41.667 0.00 0.00 0.00 1.89
2540 2550 5.011090 AGACATTGCTCAGAACGCTATAA 57.989 39.130 0.00 0.00 0.00 0.98
2541 2551 4.097892 TGAGACATTGCTCAGAACGCTATA 59.902 41.667 6.68 0.00 39.84 1.31
2542 2552 3.118992 TGAGACATTGCTCAGAACGCTAT 60.119 43.478 6.68 0.00 39.84 2.97
2543 2553 2.231235 TGAGACATTGCTCAGAACGCTA 59.769 45.455 6.68 0.00 39.84 4.26
2544 2554 1.001293 TGAGACATTGCTCAGAACGCT 59.999 47.619 6.68 0.00 39.84 5.07
2545 2555 1.127582 GTGAGACATTGCTCAGAACGC 59.872 52.381 9.95 0.00 44.92 4.84
2546 2556 2.681706 AGTGAGACATTGCTCAGAACG 58.318 47.619 9.95 0.00 44.92 3.95
2547 2557 6.734104 ATTTAGTGAGACATTGCTCAGAAC 57.266 37.500 9.95 1.95 44.92 3.01
2548 2558 8.846943 TTAATTTAGTGAGACATTGCTCAGAA 57.153 30.769 9.95 6.30 44.92 3.02
2549 2559 9.102757 GATTAATTTAGTGAGACATTGCTCAGA 57.897 33.333 9.95 1.72 44.92 3.27
2550 2560 8.060679 CGATTAATTTAGTGAGACATTGCTCAG 58.939 37.037 9.95 0.00 44.92 3.35
2551 2561 7.763985 TCGATTAATTTAGTGAGACATTGCTCA 59.236 33.333 6.68 6.68 42.31 4.26
2552 2562 8.131455 TCGATTAATTTAGTGAGACATTGCTC 57.869 34.615 0.00 0.00 35.46 4.26
2553 2563 8.554528 CATCGATTAATTTAGTGAGACATTGCT 58.445 33.333 0.00 0.00 0.00 3.91
2554 2564 8.338259 ACATCGATTAATTTAGTGAGACATTGC 58.662 33.333 0.00 0.00 0.00 3.56
2558 2568 9.863845 TTGTACATCGATTAATTTAGTGAGACA 57.136 29.630 0.00 0.00 0.00 3.41
2565 2575 9.580916 CGGAACATTGTACATCGATTAATTTAG 57.419 33.333 0.00 0.00 0.00 1.85
2566 2576 8.065407 GCGGAACATTGTACATCGATTAATTTA 58.935 33.333 0.00 0.00 0.00 1.40
2567 2577 6.910433 GCGGAACATTGTACATCGATTAATTT 59.090 34.615 0.00 0.00 0.00 1.82
2568 2578 6.260050 AGCGGAACATTGTACATCGATTAATT 59.740 34.615 0.00 0.00 0.00 1.40
2569 2579 5.758296 AGCGGAACATTGTACATCGATTAAT 59.242 36.000 0.00 0.00 0.00 1.40
2570 2580 5.113383 AGCGGAACATTGTACATCGATTAA 58.887 37.500 0.00 0.00 0.00 1.40
2571 2581 4.689071 AGCGGAACATTGTACATCGATTA 58.311 39.130 0.00 0.00 0.00 1.75
2572 2582 3.531538 AGCGGAACATTGTACATCGATT 58.468 40.909 0.00 0.00 0.00 3.34
2573 2583 3.179443 AGCGGAACATTGTACATCGAT 57.821 42.857 0.00 0.00 0.00 3.59
2574 2584 2.665649 AGCGGAACATTGTACATCGA 57.334 45.000 0.00 0.00 0.00 3.59
2575 2585 5.388475 GCTATTAGCGGAACATTGTACATCG 60.388 44.000 0.00 0.00 0.00 3.84
2576 2586 5.465390 TGCTATTAGCGGAACATTGTACATC 59.535 40.000 10.94 0.00 46.26 3.06
2577 2587 5.364778 TGCTATTAGCGGAACATTGTACAT 58.635 37.500 10.94 0.00 46.26 2.29
2578 2588 4.760878 TGCTATTAGCGGAACATTGTACA 58.239 39.130 10.94 0.00 46.26 2.90
2579 2589 5.236478 ACATGCTATTAGCGGAACATTGTAC 59.764 40.000 10.94 0.00 46.26 2.90
2580 2590 5.364778 ACATGCTATTAGCGGAACATTGTA 58.635 37.500 10.94 0.00 46.26 2.41
2581 2591 4.199310 ACATGCTATTAGCGGAACATTGT 58.801 39.130 10.94 3.70 46.26 2.71
2582 2592 4.818534 ACATGCTATTAGCGGAACATTG 57.181 40.909 10.94 3.18 46.26 2.82
2583 2593 7.878127 ACTATAACATGCTATTAGCGGAACATT 59.122 33.333 10.94 2.85 46.26 2.71
2584 2594 7.331934 CACTATAACATGCTATTAGCGGAACAT 59.668 37.037 10.94 4.62 46.26 2.71
2585 2595 6.645003 CACTATAACATGCTATTAGCGGAACA 59.355 38.462 10.94 0.00 46.26 3.18
2586 2596 6.401153 GCACTATAACATGCTATTAGCGGAAC 60.401 42.308 10.94 0.00 46.26 3.62
2587 2597 5.637810 GCACTATAACATGCTATTAGCGGAA 59.362 40.000 10.94 0.00 46.26 4.30
2588 2598 5.168569 GCACTATAACATGCTATTAGCGGA 58.831 41.667 10.94 0.00 46.26 5.54
2589 2599 4.031765 CGCACTATAACATGCTATTAGCGG 59.968 45.833 10.94 8.16 46.26 5.52
2590 2600 4.857037 TCGCACTATAACATGCTATTAGCG 59.143 41.667 16.61 16.61 46.26 4.26
2591 2601 6.893958 ATCGCACTATAACATGCTATTAGC 57.106 37.500 8.80 8.80 42.82 3.09
2593 2603 9.678941 GCTATATCGCACTATAACATGCTATTA 57.321 33.333 0.00 0.00 39.79 0.98
2594 2604 8.197439 TGCTATATCGCACTATAACATGCTATT 58.803 33.333 0.00 0.00 39.79 1.73
2595 2605 7.716612 TGCTATATCGCACTATAACATGCTAT 58.283 34.615 0.00 0.00 39.79 2.97
2596 2606 7.095695 TGCTATATCGCACTATAACATGCTA 57.904 36.000 0.00 0.00 39.79 3.49
2597 2607 5.965922 TGCTATATCGCACTATAACATGCT 58.034 37.500 0.00 0.00 39.79 3.79
2610 2620 3.435566 TGCTATTAGCGTGCTATATCGC 58.564 45.455 10.94 7.67 46.26 4.58
2611 2621 7.301789 AGATATGCTATTAGCGTGCTATATCG 58.698 38.462 18.61 0.00 46.26 2.92
2614 2624 9.952188 CTTAAGATATGCTATTAGCGTGCTATA 57.048 33.333 18.61 7.66 46.26 1.31
2615 2625 8.687242 TCTTAAGATATGCTATTAGCGTGCTAT 58.313 33.333 18.61 6.08 46.26 2.97
2616 2626 8.051901 TCTTAAGATATGCTATTAGCGTGCTA 57.948 34.615 18.61 0.00 46.26 3.49
2617 2627 6.925211 TCTTAAGATATGCTATTAGCGTGCT 58.075 36.000 18.61 13.02 46.26 4.40
2618 2628 7.008810 GTCTCTTAAGATATGCTATTAGCGTGC 59.991 40.741 18.61 11.25 41.27 5.34
2619 2629 8.023706 TGTCTCTTAAGATATGCTATTAGCGTG 58.976 37.037 18.61 2.44 41.27 5.34
2620 2630 8.024285 GTGTCTCTTAAGATATGCTATTAGCGT 58.976 37.037 14.53 14.53 43.91 5.07
2621 2631 8.023706 TGTGTCTCTTAAGATATGCTATTAGCG 58.976 37.037 5.44 0.00 37.74 4.26
2622 2632 9.868277 ATGTGTCTCTTAAGATATGCTATTAGC 57.132 33.333 5.44 8.80 36.32 3.09
2637 2647 9.665719 TGCTATGACAAAATAATGTGTCTCTTA 57.334 29.630 2.81 0.00 43.73 2.10
2638 2648 8.565896 TGCTATGACAAAATAATGTGTCTCTT 57.434 30.769 2.81 0.00 43.73 2.85
2639 2649 8.618677 CATGCTATGACAAAATAATGTGTCTCT 58.381 33.333 2.81 0.00 43.73 3.10
2640 2650 7.377928 GCATGCTATGACAAAATAATGTGTCTC 59.622 37.037 11.37 0.00 43.73 3.36
2641 2651 7.067859 AGCATGCTATGACAAAATAATGTGTCT 59.932 33.333 21.21 0.00 43.73 3.41
2642 2652 7.198390 AGCATGCTATGACAAAATAATGTGTC 58.802 34.615 21.21 0.00 43.66 3.67
2643 2653 7.104043 AGCATGCTATGACAAAATAATGTGT 57.896 32.000 21.21 0.00 32.57 3.72
2644 2654 9.687210 AATAGCATGCTATGACAAAATAATGTG 57.313 29.630 34.88 0.00 39.03 3.21
2705 2715 9.329913 CGTATCAAACTGGAACTTCTTATTTTG 57.670 33.333 0.00 0.00 0.00 2.44
2729 2739 2.232696 ACAAGGCCACTTTGTTTTTCGT 59.767 40.909 5.01 0.00 33.81 3.85
2730 2740 2.887337 ACAAGGCCACTTTGTTTTTCG 58.113 42.857 5.01 0.00 33.81 3.46
2745 2755 4.137543 GCCCTCCATTTCTGTATACAAGG 58.862 47.826 7.06 8.57 0.00 3.61
2851 2863 4.443725 GCGGCTATGATTCATCGATCTATG 59.556 45.833 1.55 0.77 0.00 2.23
2852 2864 4.340666 AGCGGCTATGATTCATCGATCTAT 59.659 41.667 0.00 0.00 0.00 1.98
2858 2870 2.360553 AGAGCGGCTATGATTCATCG 57.639 50.000 0.60 2.27 0.00 3.84
2863 2875 6.699575 AATTTTGTAAGAGCGGCTATGATT 57.300 33.333 0.60 0.00 0.00 2.57
2944 2962 8.258007 TGACATAGAAAGTAGATCGTGGATTTT 58.742 33.333 0.00 0.00 0.00 1.82
2946 2964 7.348080 TGACATAGAAAGTAGATCGTGGATT 57.652 36.000 0.00 0.00 0.00 3.01
2961 2979 2.421073 GCATGCTGTTGCTGACATAGAA 59.579 45.455 11.37 0.00 39.57 2.10
2962 2980 2.011947 GCATGCTGTTGCTGACATAGA 58.988 47.619 11.37 0.00 39.57 1.98
2965 2983 1.888018 GGCATGCTGTTGCTGACAT 59.112 52.632 18.92 0.00 42.38 3.06
2966 2984 3.357919 GGCATGCTGTTGCTGACA 58.642 55.556 18.92 0.00 42.38 3.58
2970 2988 0.961857 TTGATCGGCATGCTGTTGCT 60.962 50.000 25.42 9.55 42.38 3.91
2971 2989 0.524816 CTTGATCGGCATGCTGTTGC 60.525 55.000 25.42 15.83 42.01 4.17
2972 2990 1.089112 TCTTGATCGGCATGCTGTTG 58.911 50.000 25.42 12.20 0.00 3.33
2973 2991 1.825090 TTCTTGATCGGCATGCTGTT 58.175 45.000 25.42 17.96 0.00 3.16
2974 2992 1.470098 GTTTCTTGATCGGCATGCTGT 59.530 47.619 25.42 13.32 0.00 4.40
2975 2993 1.741706 AGTTTCTTGATCGGCATGCTG 59.258 47.619 21.02 21.02 0.00 4.41
2976 2994 2.119801 AGTTTCTTGATCGGCATGCT 57.880 45.000 18.92 0.00 0.00 3.79
2977 2995 2.919229 CAAAGTTTCTTGATCGGCATGC 59.081 45.455 9.90 9.90 0.00 4.06
2978 2996 4.083110 AGTCAAAGTTTCTTGATCGGCATG 60.083 41.667 0.00 0.00 37.63 4.06
2979 2997 4.074970 AGTCAAAGTTTCTTGATCGGCAT 58.925 39.130 0.00 0.00 37.63 4.40
2980 2998 3.476552 AGTCAAAGTTTCTTGATCGGCA 58.523 40.909 0.00 0.00 37.63 5.69
2981 2999 4.467735 GAAGTCAAAGTTTCTTGATCGGC 58.532 43.478 0.00 0.00 37.63 5.54
2984 3002 5.924475 TCCGAAGTCAAAGTTTCTTGATC 57.076 39.130 0.00 0.00 37.63 2.92
2985 3003 5.335191 GCATCCGAAGTCAAAGTTTCTTGAT 60.335 40.000 0.00 0.00 37.63 2.57
2986 3004 4.024048 GCATCCGAAGTCAAAGTTTCTTGA 60.024 41.667 0.00 0.00 32.89 3.02
2987 3005 4.222114 GCATCCGAAGTCAAAGTTTCTTG 58.778 43.478 0.00 0.00 0.00 3.02
2988 3006 3.253432 GGCATCCGAAGTCAAAGTTTCTT 59.747 43.478 0.00 0.00 0.00 2.52
2991 3009 2.582052 TGGCATCCGAAGTCAAAGTTT 58.418 42.857 0.00 0.00 0.00 2.66
2993 3011 2.489329 CAATGGCATCCGAAGTCAAAGT 59.511 45.455 0.00 0.00 0.00 2.66
2994 3012 2.733227 GCAATGGCATCCGAAGTCAAAG 60.733 50.000 0.00 0.00 40.72 2.77
2997 3015 0.035152 AGCAATGGCATCCGAAGTCA 60.035 50.000 0.00 0.00 44.61 3.41
3041 3247 8.334632 TGACATGCGTATCAATTAATGTTGTAG 58.665 33.333 0.00 0.00 0.00 2.74
3045 3251 8.026026 TGTTTGACATGCGTATCAATTAATGTT 58.974 29.630 0.00 0.00 34.87 2.71
3048 3254 8.978564 TTTGTTTGACATGCGTATCAATTAAT 57.021 26.923 0.00 0.00 34.87 1.40
3059 3265 2.223456 TGGTGACTTTGTTTGACATGCG 60.223 45.455 0.00 0.00 0.00 4.73
3106 3312 0.036010 AGTGGGCAGATCAAACGGAG 60.036 55.000 0.00 0.00 0.00 4.63
3107 3313 0.321564 CAGTGGGCAGATCAAACGGA 60.322 55.000 0.00 0.00 0.00 4.69
3108 3314 1.926511 GCAGTGGGCAGATCAAACGG 61.927 60.000 0.00 0.00 43.97 4.44
3109 3315 1.503542 GCAGTGGGCAGATCAAACG 59.496 57.895 0.00 0.00 43.97 3.60
3160 3366 1.072159 AGCTGCAGGTCAGACAACC 59.928 57.895 13.85 0.00 45.72 3.77


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

AutoCloner maintained by Alex Coulton.