Multiple sequence alignment - TraesCS3B01G329000

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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 TraesCS3B01G329000 chr3B 100.000 8206 0 0 1 8206 531787097 531795302 0.000000e+00 15154.0
1 TraesCS3B01G329000 chr3B 78.753 786 110 27 4608 5350 458162644 458161873 2.680000e-129 473.0
2 TraesCS3B01G329000 chr3B 78.796 731 101 19 4079 4770 657701144 657701859 7.560000e-120 442.0
3 TraesCS3B01G329000 chr3B 90.837 251 19 4 3815 4062 820413618 820413867 4.750000e-87 333.0
4 TraesCS3B01G329000 chr3B 90.688 247 17 4 3815 4059 252593675 252593433 2.860000e-84 324.0
5 TraesCS3B01G329000 chr3B 81.325 166 23 4 4160 4317 825257042 825257207 2.400000e-25 128.0
6 TraesCS3B01G329000 chr3A 91.873 4122 227 55 1 4089 528519520 528523566 0.000000e+00 5657.0
7 TraesCS3B01G329000 chr3A 94.704 1435 46 12 6289 7707 528525814 528527234 0.000000e+00 2202.0
8 TraesCS3B01G329000 chr3A 93.436 1036 36 14 5263 6279 528524703 528525725 0.000000e+00 1507.0
9 TraesCS3B01G329000 chr3A 87.160 514 45 6 7706 8206 528527317 528527822 1.550000e-156 564.0
10 TraesCS3B01G329000 chr3A 86.414 449 50 7 4875 5318 225446278 225446720 1.600000e-131 481.0
11 TraesCS3B01G329000 chr3A 84.989 473 59 4 4886 5351 223531125 223531592 3.470000e-128 470.0
12 TraesCS3B01G329000 chr3D 92.157 2805 156 27 2107 4871 405811967 405814747 0.000000e+00 3903.0
13 TraesCS3B01G329000 chr3D 93.033 1708 80 15 6291 7983 405816213 405817896 0.000000e+00 2459.0
14 TraesCS3B01G329000 chr3D 90.794 1260 72 15 3 1257 405809935 405811155 0.000000e+00 1644.0
15 TraesCS3B01G329000 chr3D 96.573 496 13 2 5788 6279 405815627 405816122 0.000000e+00 819.0
16 TraesCS3B01G329000 chr3D 91.837 539 23 7 5223 5752 405815101 405815627 0.000000e+00 732.0
17 TraesCS3B01G329000 chr3D 90.191 418 20 6 1643 2052 405811556 405811960 7.300000e-145 525.0
18 TraesCS3B01G329000 chr3D 90.411 365 18 9 1300 1654 405811166 405811523 1.610000e-126 464.0
19 TraesCS3B01G329000 chr3D 83.299 491 71 6 4870 5351 6950823 6950335 7.560000e-120 442.0
20 TraesCS3B01G329000 chr3D 91.093 247 16 4 3815 4059 173713165 173712923 6.140000e-86 329.0
21 TraesCS3B01G329000 chr1D 80.693 1010 132 36 4392 5351 420237351 420236355 0.000000e+00 726.0
22 TraesCS3B01G329000 chr5B 87.657 478 52 5 4880 5350 678043313 678042836 4.330000e-152 549.0
23 TraesCS3B01G329000 chr5B 89.062 64 5 1 584 647 425177854 425177915 2.460000e-10 78.7
24 TraesCS3B01G329000 chr2B 87.413 429 46 6 4929 5351 418963640 418963214 3.440000e-133 486.0
25 TraesCS3B01G329000 chr2B 84.330 485 65 6 4872 5349 799282063 799282543 1.610000e-126 464.0
26 TraesCS3B01G329000 chr2B 77.386 765 121 31 4136 4870 775070123 775069381 2.760000e-109 407.0
27 TraesCS3B01G329000 chr2B 83.871 93 14 1 543 634 5817834 5817926 4.080000e-13 87.9
28 TraesCS3B01G329000 chr2B 87.879 66 7 1 543 607 200020689 200020754 8.830000e-10 76.8
29 TraesCS3B01G329000 chr1A 78.344 785 129 28 4591 5351 577507531 577508298 3.470000e-128 470.0
30 TraesCS3B01G329000 chr4A 84.254 489 67 3 4870 5351 72972371 72971886 1.250000e-127 468.0
31 TraesCS3B01G329000 chr4A 83.916 286 38 7 4590 4871 429428985 429428704 4.880000e-67 267.0
32 TraesCS3B01G329000 chr4D 83.943 492 62 13 4870 5351 391100779 391100295 9.710000e-124 455.0
33 TraesCS3B01G329000 chr2D 83.711 485 64 8 4878 5350 7129201 7129682 2.100000e-120 444.0
34 TraesCS3B01G329000 chr7D 91.903 247 13 5 3815 4059 204017348 204017589 1.020000e-88 339.0
35 TraesCS3B01G329000 chr7D 84.000 75 11 1 543 616 188817334 188817408 4.110000e-08 71.3
36 TraesCS3B01G329000 chr7D 78.431 102 16 5 560 658 615407562 615407660 2.470000e-05 62.1
37 TraesCS3B01G329000 chr5D 91.093 247 19 3 3815 4059 217748469 217748224 1.710000e-86 331.0
38 TraesCS3B01G329000 chr5D 86.545 275 35 2 4597 4871 451180090 451179818 1.340000e-77 302.0
39 TraesCS3B01G329000 chr5D 84.249 273 39 4 4601 4871 397023877 397023607 6.320000e-66 263.0
40 TraesCS3B01G329000 chr1B 90.612 245 17 4 3815 4057 497800842 497801082 3.700000e-83 320.0
41 TraesCS3B01G329000 chr4B 80.920 435 55 12 4590 5001 163834376 163833947 1.330000e-82 318.0
42 TraesCS3B01G329000 chr7A 89.600 250 20 4 3815 4062 445250738 445250493 6.180000e-81 313.0
43 TraesCS3B01G329000 chr5A 89.600 250 19 5 3815 4061 366139261 366139016 2.220000e-80 311.0
44 TraesCS3B01G329000 chr6A 81.481 108 17 3 543 649 554782144 554782249 1.470000e-12 86.1
45 TraesCS3B01G329000 chr7B 81.720 93 13 4 578 668 179782018 179781928 3.180000e-09 75.0


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 TraesCS3B01G329000 chr3B 531787097 531795302 8205 False 15154.000000 15154 100.000000 1 8206 1 chr3B.!!$F1 8205
1 TraesCS3B01G329000 chr3B 458161873 458162644 771 True 473.000000 473 78.753000 4608 5350 1 chr3B.!!$R2 742
2 TraesCS3B01G329000 chr3B 657701144 657701859 715 False 442.000000 442 78.796000 4079 4770 1 chr3B.!!$F2 691
3 TraesCS3B01G329000 chr3A 528519520 528527822 8302 False 2482.500000 5657 91.793250 1 8206 4 chr3A.!!$F3 8205
4 TraesCS3B01G329000 chr3D 405809935 405817896 7961 False 1506.571429 3903 92.142286 3 7983 7 chr3D.!!$F1 7980
5 TraesCS3B01G329000 chr1D 420236355 420237351 996 True 726.000000 726 80.693000 4392 5351 1 chr1D.!!$R1 959
6 TraesCS3B01G329000 chr2B 775069381 775070123 742 True 407.000000 407 77.386000 4136 4870 1 chr2B.!!$R2 734
7 TraesCS3B01G329000 chr1A 577507531 577508298 767 False 470.000000 470 78.344000 4591 5351 1 chr1A.!!$F1 760

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
773 791 0.107831 CCGAAGGCCGATGGGAAATA 59.892 55.000 6.78 0.00 46.14 1.40 F
1292 1311 0.249031 GTGTTTGTGTGCTGGCTTCC 60.249 55.000 0.00 0.00 0.00 3.46 F
1481 1502 0.320374 TCCACTGTTTAGGTGCTCGG 59.680 55.000 0.00 0.00 33.78 4.63 F
1815 1885 0.806868 ATGTTGCGCTGGACATCTTG 59.193 50.000 9.73 0.00 31.07 3.02 F
1922 1997 1.278537 AGGGGACAATTTTGGGCATG 58.721 50.000 0.00 0.00 0.00 4.06 F
2786 2865 2.328099 GGAGCAGAGCAACCAACCG 61.328 63.158 0.00 0.00 0.00 4.44 F
4465 4582 0.039180 TAGGCCTCTTCAGACGGTGA 59.961 55.000 9.68 0.00 0.00 4.02 F
4634 4765 0.108804 GATGGAGGTTCGTCGAGCAA 60.109 55.000 11.35 0.00 0.00 3.91 F
4888 5054 0.390735 TCGACGATGTGGAGTCTCGA 60.391 55.000 6.52 0.88 36.32 4.04 F
4959 5125 0.608856 TACGGAGGTGGCGTTGTCTA 60.609 55.000 0.00 0.00 0.00 2.59 F
6889 7164 0.320073 GCAAAGAAGCTGCCATGCAA 60.320 50.000 13.19 0.00 38.41 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1793 1863 1.002257 ATGTCCAGCGCAACATGGA 60.002 52.632 18.47 15.49 43.34 3.41 R
2757 2836 3.161067 TGCTCTGCTCCCTATAAGCTAG 58.839 50.000 0.00 0.00 40.50 3.42 R
2820 2899 3.509575 AGCCGTTATTTTGCCATTCTTCA 59.490 39.130 0.00 0.00 0.00 3.02 R
3334 3414 5.287226 GGTGTAGACATAAGAATACGTGGG 58.713 45.833 0.00 0.00 0.00 4.61 R
3827 3915 0.988832 GTACATCCACTCCCCCAACA 59.011 55.000 0.00 0.00 0.00 3.33 R
4612 4742 0.179134 CTCGACGAACCTCCATCCAC 60.179 60.000 0.00 0.00 0.00 4.02 R
5300 5473 0.538584 TCAGGACGATGCATGAAGCT 59.461 50.000 2.46 0.00 45.94 3.74 R
6615 6887 2.215942 ACAATAAAGGCCTCACCCAC 57.784 50.000 5.23 0.00 40.58 4.61 R
6760 7035 4.503123 GGCAAAAGTTCCTTAAACATGGCT 60.503 41.667 0.00 0.00 40.56 4.75 R
7059 7345 0.737715 GGCAGCTCTACACCACGAAG 60.738 60.000 0.00 0.00 0.00 3.79 R
8163 8550 1.208293 GACAAGGCCCAACTCTCTAGG 59.792 57.143 0.00 0.00 0.00 3.02 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
100 102 1.831736 GAAGAATCCGTCCCCTTGAGA 59.168 52.381 0.00 0.00 0.00 3.27
114 116 1.801771 CTTGAGACTCTGTCGACGAGT 59.198 52.381 29.82 29.82 43.97 4.18
133 135 1.078426 CGTGGATTTCCTCGCCCTT 60.078 57.895 7.99 0.00 44.38 3.95
147 149 1.776034 GCCCTTTGCCTATCGCTTCG 61.776 60.000 0.00 0.00 38.78 3.79
168 170 1.044790 GGTCAATGAAGGGGCATGGG 61.045 60.000 0.00 0.00 0.00 4.00
210 212 6.464039 CCCAGCTAGTAATTTAGGTTAGGGAC 60.464 46.154 6.13 0.00 36.90 4.46
362 370 0.696501 TTGGGGAGGCAAGGTTAGAC 59.303 55.000 0.00 0.00 0.00 2.59
379 387 5.648092 GGTTAGACTTTCTTGCCATATGTGT 59.352 40.000 1.24 0.00 0.00 3.72
411 419 7.201902 GGTGAGATCTCAGACACTTCAGATATT 60.202 40.741 25.76 0.00 40.75 1.28
440 448 1.002134 CAACATCGGCTCCAAGGGT 60.002 57.895 0.00 0.00 0.00 4.34
441 449 0.609131 CAACATCGGCTCCAAGGGTT 60.609 55.000 0.00 0.00 0.00 4.11
442 450 0.988832 AACATCGGCTCCAAGGGTTA 59.011 50.000 0.00 0.00 0.00 2.85
443 451 1.213296 ACATCGGCTCCAAGGGTTAT 58.787 50.000 0.00 0.00 0.00 1.89
444 452 2.404559 ACATCGGCTCCAAGGGTTATA 58.595 47.619 0.00 0.00 0.00 0.98
445 453 2.775384 ACATCGGCTCCAAGGGTTATAA 59.225 45.455 0.00 0.00 0.00 0.98
446 454 3.201266 ACATCGGCTCCAAGGGTTATAAA 59.799 43.478 0.00 0.00 0.00 1.40
447 455 4.204012 CATCGGCTCCAAGGGTTATAAAA 58.796 43.478 0.00 0.00 0.00 1.52
448 456 4.304048 TCGGCTCCAAGGGTTATAAAAA 57.696 40.909 0.00 0.00 0.00 1.94
498 507 3.195610 TGGATATGTGCACGAAGACTTCT 59.804 43.478 13.13 0.00 0.00 2.85
501 510 1.852942 TGTGCACGAAGACTTCTCAC 58.147 50.000 13.13 15.97 0.00 3.51
519 529 3.021695 TCACCCGTTCTCGACAAGATAT 58.978 45.455 0.00 0.00 39.71 1.63
540 550 1.299976 CGGCAAAGGTAGGGAAGCT 59.700 57.895 0.00 0.00 37.60 3.74
570 580 1.372004 CGACGGTAGCGGTTGTTCA 60.372 57.895 19.72 0.00 0.00 3.18
575 585 0.170339 GGTAGCGGTTGTTCAATGGC 59.830 55.000 0.00 3.72 0.00 4.40
582 592 3.119495 GCGGTTGTTCAATGGCTTAGAAT 60.119 43.478 0.00 0.00 0.00 2.40
759 777 4.214383 CGAGCGCATGTGCCGAAG 62.214 66.667 26.95 12.35 37.91 3.79
771 789 2.270850 CCGAAGGCCGATGGGAAA 59.729 61.111 6.78 0.00 46.14 3.13
772 790 1.152963 CCGAAGGCCGATGGGAAAT 60.153 57.895 6.78 0.00 46.14 2.17
773 791 0.107831 CCGAAGGCCGATGGGAAATA 59.892 55.000 6.78 0.00 46.14 1.40
774 792 1.512926 CGAAGGCCGATGGGAAATAG 58.487 55.000 0.00 0.00 41.76 1.73
775 793 1.202651 CGAAGGCCGATGGGAAATAGT 60.203 52.381 0.00 0.00 41.76 2.12
776 794 2.036733 CGAAGGCCGATGGGAAATAGTA 59.963 50.000 0.00 0.00 41.76 1.82
777 795 3.306780 CGAAGGCCGATGGGAAATAGTAT 60.307 47.826 0.00 0.00 41.76 2.12
984 1003 2.263540 GGCGCCCTTACACGAAGA 59.736 61.111 18.11 0.00 37.33 2.87
1054 1073 0.926846 CGCTCGCTTGATCTTCCTTC 59.073 55.000 0.00 0.00 0.00 3.46
1094 1113 2.302445 CCTTGGCTCTCCCTATCATCAG 59.698 54.545 0.00 0.00 0.00 2.90
1101 1120 2.887783 TCTCCCTATCATCAGCTCGTTC 59.112 50.000 0.00 0.00 0.00 3.95
1112 1131 1.807573 GCTCGTTCTCTCCGCCTTG 60.808 63.158 0.00 0.00 0.00 3.61
1127 1146 3.056607 CCGCCTTGTTTTCAGGATTTGAT 60.057 43.478 0.00 0.00 35.27 2.57
1216 1235 0.603569 GAGCGTCAAGAAGAGGACCA 59.396 55.000 0.00 0.00 34.03 4.02
1267 1286 3.626924 AGGTCCGTGCCCTGTGTC 61.627 66.667 0.00 0.00 0.00 3.67
1268 1287 3.936203 GGTCCGTGCCCTGTGTCA 61.936 66.667 0.00 0.00 0.00 3.58
1269 1288 2.665185 GTCCGTGCCCTGTGTCAC 60.665 66.667 0.00 0.00 0.00 3.67
1270 1289 2.842462 TCCGTGCCCTGTGTCACT 60.842 61.111 4.27 0.00 0.00 3.41
1271 1290 2.666190 CCGTGCCCTGTGTCACTG 60.666 66.667 4.27 3.57 0.00 3.66
1272 1291 2.108976 CGTGCCCTGTGTCACTGT 59.891 61.111 4.27 0.00 0.00 3.55
1273 1292 2.246739 CGTGCCCTGTGTCACTGTG 61.247 63.158 4.27 0.17 0.00 3.66
1274 1293 1.153168 GTGCCCTGTGTCACTGTGT 60.153 57.895 7.79 0.00 0.00 3.72
1275 1294 1.153188 TGCCCTGTGTCACTGTGTG 60.153 57.895 7.79 0.00 34.45 3.82
1276 1295 1.153168 GCCCTGTGTCACTGTGTGT 60.153 57.895 7.79 0.00 34.79 3.72
1282 1301 2.483877 CTGTGTCACTGTGTGTTTGTGT 59.516 45.455 7.79 0.00 34.79 3.72
1289 1308 0.964860 TGTGTGTTTGTGTGCTGGCT 60.965 50.000 0.00 0.00 0.00 4.75
1292 1311 0.249031 GTGTTTGTGTGCTGGCTTCC 60.249 55.000 0.00 0.00 0.00 3.46
1327 1346 1.528076 TGCATGCGGGTGTTCTTGT 60.528 52.632 14.09 0.00 0.00 3.16
1340 1359 2.135933 GTTCTTGTCTGGTCCTGTTCG 58.864 52.381 0.00 0.00 0.00 3.95
1454 1475 9.107367 GTGAGATATTTCTTCGTTTTTGTCTTG 57.893 33.333 0.00 0.00 30.30 3.02
1481 1502 0.320374 TCCACTGTTTAGGTGCTCGG 59.680 55.000 0.00 0.00 33.78 4.63
1482 1503 1.298859 CCACTGTTTAGGTGCTCGGC 61.299 60.000 0.00 0.00 33.78 5.54
1484 1505 2.047655 TGTTTAGGTGCTCGGCGG 60.048 61.111 7.21 0.00 0.00 6.13
1485 1506 2.047560 GTTTAGGTGCTCGGCGGT 60.048 61.111 7.21 0.00 0.00 5.68
1511 1541 5.014202 GGGGTTTGCTTATTAGACCTTGAA 58.986 41.667 0.00 0.00 0.00 2.69
1530 1560 4.730966 TGAACTGTAGGTTTGGGCATTAA 58.269 39.130 0.00 0.00 38.41 1.40
1548 1578 6.242829 GCATTAATTTTGGTGCGAAATGAAG 58.757 36.000 0.00 0.00 29.04 3.02
1560 1590 2.488153 CGAAATGAAGGGGGTTTGACTC 59.512 50.000 0.00 0.00 0.00 3.36
1579 1609 7.369803 TGACTCAGTGAAAGCTATTGATTTC 57.630 36.000 10.37 10.37 45.62 2.17
1654 1724 7.346471 AGTATATATGGCCATTAATGTGGGAC 58.654 38.462 26.37 11.72 39.73 4.46
1655 1725 4.747265 ATATGGCCATTAATGTGGGACT 57.253 40.909 26.37 0.00 39.73 3.85
1793 1863 3.483421 GGTGCCAAACCTTACTAACTGT 58.517 45.455 0.00 0.00 46.55 3.55
1815 1885 0.806868 ATGTTGCGCTGGACATCTTG 59.193 50.000 9.73 0.00 31.07 3.02
1840 1915 8.988934 TGCTTATAGAGTTGTGAAAGTACTTTG 58.011 33.333 25.17 6.86 32.11 2.77
1922 1997 1.278537 AGGGGACAATTTTGGGCATG 58.721 50.000 0.00 0.00 0.00 4.06
1925 2000 3.037549 GGGGACAATTTTGGGCATGATA 58.962 45.455 0.00 0.00 0.00 2.15
1987 2062 9.793259 ACAGTTTCTCATTTCCTGTATAGAAAA 57.207 29.630 0.00 0.00 36.83 2.29
2048 2125 6.145696 GCTATCTTCCGTATGGTAATTGTCAC 59.854 42.308 0.00 0.00 36.30 3.67
2086 2163 4.857037 GGCGTCATCACCAAAAATTCTTAC 59.143 41.667 0.00 0.00 0.00 2.34
2508 2585 7.068226 CCCATAAAGTACCCAAAGTAAGATTGG 59.932 40.741 0.00 0.00 45.62 3.16
2631 2708 3.554934 TCAGCTTCTTTGTGTGATGGTT 58.445 40.909 0.00 0.00 0.00 3.67
2757 2836 7.707104 TCTTGTTCACCTTTCTTTTGATTCTC 58.293 34.615 0.00 0.00 0.00 2.87
2786 2865 2.328099 GGAGCAGAGCAACCAACCG 61.328 63.158 0.00 0.00 0.00 4.44
2802 2881 5.385198 ACCAACCGCAATGAATTATCCTAT 58.615 37.500 0.00 0.00 0.00 2.57
2945 3025 6.870971 TTGTACCCATCACTTTTGTCTAAC 57.129 37.500 0.00 0.00 0.00 2.34
2979 3059 4.906618 ACAGATTGGAAAATGGTAGTCGT 58.093 39.130 0.00 0.00 0.00 4.34
3265 3345 6.533819 TGTAAACTTGTTCCAGATGTTACG 57.466 37.500 0.00 0.00 0.00 3.18
3269 3349 5.717078 ACTTGTTCCAGATGTTACGTCTA 57.283 39.130 6.78 0.00 0.00 2.59
3286 3366 6.452494 ACGTCTACATCTTAGTGCACTTAT 57.548 37.500 27.06 13.55 0.00 1.73
3349 3429 8.899771 ACCTTTTATTTCCCACGTATTCTTATG 58.100 33.333 0.00 0.00 0.00 1.90
3365 3445 3.012502 TCTTATGTCTACACCCTGGGACT 59.987 47.826 22.23 5.91 0.00 3.85
3407 3487 9.317936 TCACTGTATTTTGTAGCAAGAGATATG 57.682 33.333 0.00 0.00 0.00 1.78
3533 3615 7.148018 CCAAGCTCACATGGTCACTTAATTTAT 60.148 37.037 0.00 0.00 29.74 1.40
3562 3644 7.689299 TCAGAGGATCAGTTTAGAAAATCCAA 58.311 34.615 0.00 0.00 38.69 3.53
3695 3783 5.959583 TGGGGTTTGTTTATTTTCCAGTT 57.040 34.783 0.00 0.00 0.00 3.16
3827 3915 0.247736 CCGAGTGCCTAGCTCAACTT 59.752 55.000 0.00 0.00 33.45 2.66
3874 3962 1.271379 ACACCTGGGTTCAAATCCTCG 60.271 52.381 0.00 0.00 0.00 4.63
3877 3965 0.391130 CTGGGTTCAAATCCTCGCGA 60.391 55.000 9.26 9.26 0.00 5.87
3940 4029 3.449377 TCCTGGTACTCACGCATTTATCA 59.551 43.478 0.00 0.00 0.00 2.15
3965 4054 2.780010 AGGACTAGGCTTGGTGCATAAT 59.220 45.455 6.61 0.00 45.15 1.28
4001 4090 4.288626 TCCTGGTACTCATGCTTAAAAGGT 59.711 41.667 0.00 0.00 0.00 3.50
4031 4121 1.679311 CTAGTTGGTGCAGAGGCCA 59.321 57.895 5.01 0.00 40.13 5.36
4048 4138 2.291217 GGCCAGGAAGTGAAATTCTCCT 60.291 50.000 0.00 0.00 0.00 3.69
4075 4165 0.108992 TTAGAGCTTGCACGTACGGG 60.109 55.000 21.06 18.06 0.00 5.28
4098 4189 1.774300 AAAAAGTGGATCGGCCCCT 59.226 52.632 0.00 0.00 34.97 4.79
4099 4190 0.611896 AAAAAGTGGATCGGCCCCTG 60.612 55.000 0.00 0.00 34.97 4.45
4100 4191 3.645268 AAAGTGGATCGGCCCCTGC 62.645 63.158 0.00 0.00 34.97 4.85
4181 4273 0.614979 CTCCGACCCTTCTCTTCCCA 60.615 60.000 0.00 0.00 0.00 4.37
4182 4274 0.042731 TCCGACCCTTCTCTTCCCAT 59.957 55.000 0.00 0.00 0.00 4.00
4184 4276 0.103208 CGACCCTTCTCTTCCCATCG 59.897 60.000 0.00 0.00 0.00 3.84
4186 4278 1.147153 CCCTTCTCTTCCCATCGCC 59.853 63.158 0.00 0.00 0.00 5.54
4187 4279 1.227380 CCTTCTCTTCCCATCGCCG 60.227 63.158 0.00 0.00 0.00 6.46
4329 4426 4.521062 GATCAGCGCGGCTCAGGT 62.521 66.667 8.83 0.00 36.40 4.00
4330 4427 3.138930 GATCAGCGCGGCTCAGGTA 62.139 63.158 8.83 0.00 36.40 3.08
4381 4492 0.463295 ATCGGTGCAAGGCAGATCAG 60.463 55.000 0.00 0.00 40.08 2.90
4449 4566 0.179062 ATCTTTGCGCTCCTGCTAGG 60.179 55.000 9.73 0.00 36.97 3.02
4465 4582 0.039180 TAGGCCTCTTCAGACGGTGA 59.961 55.000 9.68 0.00 0.00 4.02
4537 4654 1.579429 GCCGCAAACTCCGTTGATT 59.421 52.632 0.00 0.00 0.00 2.57
4560 4677 1.174078 TTCGGGTCAGCGTGTGTCTA 61.174 55.000 0.00 0.00 0.00 2.59
4612 4742 2.125147 ATCCGGTGCACACGATGG 60.125 61.111 23.58 14.72 0.00 3.51
4634 4765 0.108804 GATGGAGGTTCGTCGAGCAA 60.109 55.000 11.35 0.00 0.00 3.91
4678 4809 1.303561 CTAGTTGCCAAGGCCAGCA 60.304 57.895 5.01 8.51 41.09 4.41
4704 4835 1.517832 CGTCCTTCTTCATCGCCCT 59.482 57.895 0.00 0.00 0.00 5.19
4747 4878 1.006519 AGAAGCTCCAGACCTCTAGCA 59.993 52.381 0.00 0.00 37.44 3.49
4791 4926 3.071312 AGACTAGTAGATCGGATGACGGT 59.929 47.826 3.59 0.00 44.45 4.83
4794 4929 1.133884 AGTAGATCGGATGACGGTGGA 60.134 52.381 0.00 0.00 44.45 4.02
4807 4942 2.029844 GGTGGAGCTCTTGTGTCGC 61.030 63.158 14.64 1.91 0.00 5.19
4858 4993 2.190578 CATTGGCTCGAGGGACCC 59.809 66.667 15.58 0.59 0.00 4.46
4888 5054 0.390735 TCGACGATGTGGAGTCTCGA 60.391 55.000 6.52 0.88 36.32 4.04
4937 5103 1.655484 GATGTGTGATGATGGACGCA 58.345 50.000 0.00 0.00 37.03 5.24
4959 5125 0.608856 TACGGAGGTGGCGTTGTCTA 60.609 55.000 0.00 0.00 0.00 2.59
5108 5274 4.572571 GACCGGTGTGTGCCCCAA 62.573 66.667 14.63 0.00 0.00 4.12
5111 5277 2.518349 CGGTGTGTGCCCCAAACT 60.518 61.111 0.00 0.00 31.39 2.66
5120 5288 2.929903 GCCCCAAACTCGCAATGCA 61.930 57.895 5.91 0.00 0.00 3.96
5165 5333 1.895131 GATGTTGGGCTTTGGTGTGAT 59.105 47.619 0.00 0.00 0.00 3.06
5320 5493 0.935898 GCTTCATGCATCGTCCTGAG 59.064 55.000 0.00 0.00 42.31 3.35
5370 5549 2.359900 AGTGATTCCGAGTGCCATTTC 58.640 47.619 0.00 0.00 0.00 2.17
5388 5567 6.525355 CCATTTCGCATTATAGATACGTGTG 58.475 40.000 0.00 0.00 0.00 3.82
5390 5569 4.168922 TCGCATTATAGATACGTGTGGG 57.831 45.455 0.00 0.00 0.00 4.61
5505 5693 5.975693 TTCCCTTGTGTTGCCTATTTAAG 57.024 39.130 0.00 0.00 0.00 1.85
5506 5694 4.993028 TCCCTTGTGTTGCCTATTTAAGT 58.007 39.130 0.00 0.00 0.00 2.24
5507 5695 6.129414 TCCCTTGTGTTGCCTATTTAAGTA 57.871 37.500 0.00 0.00 0.00 2.24
5508 5696 6.727394 TCCCTTGTGTTGCCTATTTAAGTAT 58.273 36.000 0.00 0.00 0.00 2.12
5509 5697 7.179269 TCCCTTGTGTTGCCTATTTAAGTATT 58.821 34.615 0.00 0.00 0.00 1.89
5510 5698 7.672239 TCCCTTGTGTTGCCTATTTAAGTATTT 59.328 33.333 0.00 0.00 0.00 1.40
5511 5699 8.962679 CCCTTGTGTTGCCTATTTAAGTATTTA 58.037 33.333 0.00 0.00 0.00 1.40
5514 5702 9.849166 TTGTGTTGCCTATTTAAGTATTTAAGC 57.151 29.630 0.00 0.00 30.84 3.09
5640 5828 3.372822 CGTGGTGTGTGTTGTTAACTTCT 59.627 43.478 7.22 0.00 0.00 2.85
6143 6335 4.502105 TTTACTGCAGATGGATGGCTTA 57.498 40.909 23.35 0.00 0.00 3.09
6149 6341 3.444742 TGCAGATGGATGGCTTAACAAAG 59.555 43.478 0.00 0.00 0.00 2.77
6191 6383 2.672195 GCTTGCAGCAACAAATCTACCC 60.672 50.000 2.83 0.00 41.89 3.69
6243 6435 0.750850 TGAGAAGCGGGTATGGCTAC 59.249 55.000 0.00 0.00 40.53 3.58
6263 6455 7.502895 TGGCTACTACTGTGTTTTTATTCCAAA 59.497 33.333 0.00 0.00 0.00 3.28
6286 6478 3.637769 TGTTTTTCCAAACAGCTACCCT 58.362 40.909 0.00 0.00 46.06 4.34
6287 6479 4.027437 TGTTTTTCCAAACAGCTACCCTT 58.973 39.130 0.00 0.00 46.06 3.95
6427 6698 4.347360 TGGATGCTTGAGATGTATCCAG 57.653 45.455 8.96 0.00 46.52 3.86
6554 6825 8.783903 AGTTTATCTATACCCAAACCCATTACA 58.216 33.333 0.00 0.00 32.52 2.41
6558 6829 6.419791 TCTATACCCAAACCCATTACAACAG 58.580 40.000 0.00 0.00 0.00 3.16
6615 6887 4.756642 TCAAAGTAGGAAGACATGCTTGTG 59.243 41.667 10.37 0.00 36.83 3.33
6618 6890 1.901591 AGGAAGACATGCTTGTGTGG 58.098 50.000 10.37 0.00 36.83 4.17
6760 7035 0.956633 CTGAAGCTGAAGCAAGGCAA 59.043 50.000 4.90 0.00 45.16 4.52
6847 7122 3.893200 TCGAAAAGACTGAAGGGTACTCA 59.107 43.478 0.00 0.00 0.00 3.41
6889 7164 0.320073 GCAAAGAAGCTGCCATGCAA 60.320 50.000 13.19 0.00 38.41 4.08
6995 7270 8.707449 TCCTAAAACTCTTTGTACTTTCCTGTA 58.293 33.333 0.00 0.00 0.00 2.74
7059 7345 8.883731 CCGATCTGATCAAACATATTATTACCC 58.116 37.037 17.19 0.00 0.00 3.69
7217 7503 6.959639 ATTCTTTCTTAAGAGCAAACCACA 57.040 33.333 5.12 0.00 41.25 4.17
7269 7555 1.745115 TGCCTCGCCAAGCATGTAC 60.745 57.895 0.00 0.00 33.08 2.90
7271 7557 0.179084 GCCTCGCCAAGCATGTACTA 60.179 55.000 0.00 0.00 0.00 1.82
7272 7558 1.858091 CCTCGCCAAGCATGTACTAG 58.142 55.000 0.00 0.00 0.00 2.57
7273 7559 1.137086 CCTCGCCAAGCATGTACTAGT 59.863 52.381 0.00 0.00 0.00 2.57
7274 7560 2.464865 CTCGCCAAGCATGTACTAGTC 58.535 52.381 0.00 0.00 0.00 2.59
7275 7561 1.822371 TCGCCAAGCATGTACTAGTCA 59.178 47.619 0.00 0.00 0.00 3.41
7276 7562 2.232696 TCGCCAAGCATGTACTAGTCAA 59.767 45.455 0.00 0.00 0.00 3.18
7277 7563 3.118775 TCGCCAAGCATGTACTAGTCAAT 60.119 43.478 0.00 0.00 0.00 2.57
7371 7657 0.604243 GTGATGCACGGTGGTGGTTA 60.604 55.000 10.60 0.00 44.54 2.85
7380 7666 2.291190 ACGGTGGTGGTTAATTTGAACG 59.709 45.455 0.00 0.00 0.00 3.95
7443 7732 0.031857 CAAAATGGCCTTGTCGCACA 59.968 50.000 3.32 0.00 0.00 4.57
7455 7745 6.072728 GGCCTTGTCGCACATTATATTTATCA 60.073 38.462 0.00 0.00 0.00 2.15
7456 7746 6.797033 GCCTTGTCGCACATTATATTTATCAC 59.203 38.462 0.00 0.00 0.00 3.06
7551 7841 1.474077 GGGCATCTGATTTTTCTGCGT 59.526 47.619 0.00 0.00 33.69 5.24
7790 8164 9.832445 AAGAATGTTTTCTGTAAGTCTTGTCTA 57.168 29.630 0.00 0.00 41.42 2.59
7866 8240 7.122501 TCTGCATGCAATTTACAAGGAGAATAA 59.877 33.333 22.88 0.00 31.60 1.40
7867 8241 7.784037 TGCATGCAATTTACAAGGAGAATAAT 58.216 30.769 20.30 0.00 0.00 1.28
7868 8242 7.707464 TGCATGCAATTTACAAGGAGAATAATG 59.293 33.333 20.30 0.00 0.00 1.90
7873 8247 9.076596 GCAATTTACAAGGAGAATAATGTTCAC 57.923 33.333 0.00 0.00 0.00 3.18
7880 8254 7.824779 ACAAGGAGAATAATGTTCACTTAGACC 59.175 37.037 0.00 0.00 0.00 3.85
7983 8357 8.378565 TGTCTACCTATACCACTATGTAGTACC 58.621 40.741 0.00 0.00 34.13 3.34
7984 8358 8.378565 GTCTACCTATACCACTATGTAGTACCA 58.621 40.741 0.00 0.00 34.13 3.25
7985 8359 8.378565 TCTACCTATACCACTATGTAGTACCAC 58.621 40.741 0.00 0.00 34.13 4.16
8008 8382 5.126061 ACAACAACTTTGATATGCTCCATCC 59.874 40.000 0.00 0.00 0.00 3.51
8010 8384 4.885907 ACAACTTTGATATGCTCCATCCAG 59.114 41.667 0.00 0.00 0.00 3.86
8011 8385 4.785346 ACTTTGATATGCTCCATCCAGT 57.215 40.909 0.00 0.00 0.00 4.00
8034 8410 4.339530 TGGTTGAGAGATGATCCGTTAGAG 59.660 45.833 0.00 0.00 0.00 2.43
8038 8414 5.441500 TGAGAGATGATCCGTTAGAGAGTT 58.558 41.667 0.00 0.00 0.00 3.01
8048 8424 6.531503 TCCGTTAGAGAGTTTTCATCTCAT 57.468 37.500 5.81 0.00 44.68 2.90
8049 8425 6.936279 TCCGTTAGAGAGTTTTCATCTCATT 58.064 36.000 5.81 0.00 44.68 2.57
8103 8490 7.175347 TGTCTCATAGTGTTCTAGAAGCATT 57.825 36.000 5.12 6.83 0.00 3.56
8104 8491 7.615403 TGTCTCATAGTGTTCTAGAAGCATTT 58.385 34.615 5.12 3.61 0.00 2.32
8106 8493 9.587772 GTCTCATAGTGTTCTAGAAGCATTTTA 57.412 33.333 5.12 3.38 0.00 1.52
8124 8511 8.739972 AGCATTTTATTTCCGTACAAAGAATCT 58.260 29.630 0.00 0.00 0.00 2.40
8174 8561 6.068010 AGATAGTCCATGTCCTAGAGAGTTG 58.932 44.000 0.00 0.00 0.00 3.16
8190 8577 5.191722 AGAGAGTTGGGCCTTGTCAAATATA 59.808 40.000 4.53 0.00 0.00 0.86
8194 8581 8.058847 AGAGTTGGGCCTTGTCAAATATAATTA 58.941 33.333 4.53 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 96 1.801771 ACTCGTCGACAGAGTCTCAAG 59.198 52.381 26.44 11.01 44.87 3.02
147 149 1.754234 ATGCCCCTTCATTGACCGC 60.754 57.895 0.00 0.00 0.00 5.68
362 370 4.669965 CGTCACACACATATGGCAAGAAAG 60.670 45.833 7.80 0.00 0.00 2.62
379 387 1.813178 GTCTGAGATCTCACCGTCACA 59.187 52.381 21.67 0.00 35.46 3.58
411 419 1.611491 GCCGATGTTGAACCCTTGAAA 59.389 47.619 0.00 0.00 0.00 2.69
446 454 4.086706 ACTCCTTGGAGACGATGTTTTT 57.913 40.909 22.10 0.00 0.00 1.94
447 455 3.771577 ACTCCTTGGAGACGATGTTTT 57.228 42.857 22.10 0.00 0.00 2.43
448 456 3.403038 CAACTCCTTGGAGACGATGTTT 58.597 45.455 22.10 2.57 0.00 2.83
449 457 3.045601 CAACTCCTTGGAGACGATGTT 57.954 47.619 22.10 4.06 0.00 2.71
450 458 2.751166 CAACTCCTTGGAGACGATGT 57.249 50.000 22.10 0.00 0.00 3.06
460 468 2.276732 TCCAAAGAGCCAACTCCTTG 57.723 50.000 0.00 0.00 44.65 3.61
461 469 4.018050 ACATATCCAAAGAGCCAACTCCTT 60.018 41.667 0.00 0.00 44.65 3.36
462 470 3.525199 ACATATCCAAAGAGCCAACTCCT 59.475 43.478 0.00 0.00 44.65 3.69
463 471 3.629398 CACATATCCAAAGAGCCAACTCC 59.371 47.826 0.00 0.00 44.65 3.85
464 472 3.065925 GCACATATCCAAAGAGCCAACTC 59.934 47.826 0.00 0.00 43.82 3.01
465 473 3.019564 GCACATATCCAAAGAGCCAACT 58.980 45.455 0.00 0.00 0.00 3.16
498 507 1.254026 ATCTTGTCGAGAACGGGTGA 58.746 50.000 0.00 0.00 38.06 4.02
501 510 2.128035 GCATATCTTGTCGAGAACGGG 58.872 52.381 0.00 0.00 38.06 5.28
519 529 2.478335 CTTCCCTACCTTTGCCGGCA 62.478 60.000 29.03 29.03 0.00 5.69
692 704 1.024271 CTCACCAACCACACCAACAG 58.976 55.000 0.00 0.00 0.00 3.16
695 707 0.106918 GGACTCACCAACCACACCAA 60.107 55.000 0.00 0.00 38.79 3.67
759 777 2.618053 CGATACTATTTCCCATCGGCC 58.382 52.381 0.00 0.00 37.28 6.13
760 778 2.000447 GCGATACTATTTCCCATCGGC 59.000 52.381 5.15 0.00 40.39 5.54
761 779 2.259618 CGCGATACTATTTCCCATCGG 58.740 52.381 0.00 0.00 40.39 4.18
762 780 2.661675 CACGCGATACTATTTCCCATCG 59.338 50.000 15.93 0.00 42.36 3.84
763 781 2.993899 CCACGCGATACTATTTCCCATC 59.006 50.000 15.93 0.00 0.00 3.51
766 784 2.806608 TCCACGCGATACTATTTCCC 57.193 50.000 15.93 0.00 0.00 3.97
767 785 3.251571 GGATCCACGCGATACTATTTCC 58.748 50.000 15.93 4.04 0.00 3.13
768 786 3.909430 TGGATCCACGCGATACTATTTC 58.091 45.455 15.93 0.00 32.29 2.17
769 787 3.572682 TCTGGATCCACGCGATACTATTT 59.427 43.478 15.93 0.00 32.29 1.40
770 788 3.154710 TCTGGATCCACGCGATACTATT 58.845 45.455 15.93 0.00 32.29 1.73
771 789 2.791655 TCTGGATCCACGCGATACTAT 58.208 47.619 15.93 0.00 32.29 2.12
772 790 2.265589 TCTGGATCCACGCGATACTA 57.734 50.000 15.93 0.00 32.29 1.82
773 791 1.542030 GATCTGGATCCACGCGATACT 59.458 52.381 15.93 0.00 32.29 2.12
774 792 1.983972 GATCTGGATCCACGCGATAC 58.016 55.000 15.93 0.00 31.57 2.24
974 993 1.135199 GGATCTGCCGTCTTCGTGTAA 60.135 52.381 0.00 0.00 35.01 2.41
977 996 0.389817 TTGGATCTGCCGTCTTCGTG 60.390 55.000 0.00 0.00 40.66 4.35
981 1000 0.036732 TTGCTTGGATCTGCCGTCTT 59.963 50.000 0.00 0.00 40.66 3.01
984 1003 2.485677 CATTGCTTGGATCTGCCGT 58.514 52.632 0.00 0.00 40.66 5.68
1022 1041 4.847444 GAGCGGGGCCAGAGAAGC 62.847 72.222 8.22 1.41 0.00 3.86
1045 1064 1.751351 TCACGAGATGCGAAGGAAGAT 59.249 47.619 0.00 0.00 44.57 2.40
1054 1073 3.032609 GCGGGATCACGAGATGCG 61.033 66.667 24.26 5.33 42.90 4.73
1086 1105 2.550180 CGGAGAGAACGAGCTGATGATA 59.450 50.000 0.00 0.00 0.00 2.15
1094 1113 1.807573 CAAGGCGGAGAGAACGAGC 60.808 63.158 0.00 0.00 0.00 5.03
1101 1120 1.160137 CCTGAAAACAAGGCGGAGAG 58.840 55.000 0.00 0.00 0.00 3.20
1112 1131 3.575965 ACGCCATCAAATCCTGAAAAC 57.424 42.857 0.00 0.00 37.67 2.43
1198 1217 0.318762 GTGGTCCTCTTCTTGACGCT 59.681 55.000 0.00 0.00 32.19 5.07
1216 1235 0.828022 TCGTAGATGGCCAAATCGGT 59.172 50.000 10.96 0.00 36.97 4.69
1267 1286 1.467883 CCAGCACACAAACACACAGTG 60.468 52.381 0.00 0.00 39.75 3.66
1268 1287 0.810648 CCAGCACACAAACACACAGT 59.189 50.000 0.00 0.00 0.00 3.55
1269 1288 0.526096 GCCAGCACACAAACACACAG 60.526 55.000 0.00 0.00 0.00 3.66
1270 1289 0.964860 AGCCAGCACACAAACACACA 60.965 50.000 0.00 0.00 0.00 3.72
1271 1290 0.173255 AAGCCAGCACACAAACACAC 59.827 50.000 0.00 0.00 0.00 3.82
1272 1291 0.455410 GAAGCCAGCACACAAACACA 59.545 50.000 0.00 0.00 0.00 3.72
1273 1292 0.249031 GGAAGCCAGCACACAAACAC 60.249 55.000 0.00 0.00 0.00 3.32
1274 1293 0.395586 AGGAAGCCAGCACACAAACA 60.396 50.000 0.00 0.00 0.00 2.83
1275 1294 0.746659 AAGGAAGCCAGCACACAAAC 59.253 50.000 0.00 0.00 0.00 2.93
1276 1295 0.746063 CAAGGAAGCCAGCACACAAA 59.254 50.000 0.00 0.00 0.00 2.83
1282 1301 3.272364 ATCGCCAAGGAAGCCAGCA 62.272 57.895 0.00 0.00 0.00 4.41
1289 1308 1.135527 ACGTAATCGATCGCCAAGGAA 59.864 47.619 11.09 0.00 40.62 3.36
1292 1311 0.229753 GCACGTAATCGATCGCCAAG 59.770 55.000 11.09 3.14 40.62 3.61
1327 1346 0.033504 GTCAAGCGAACAGGACCAGA 59.966 55.000 0.00 0.00 0.00 3.86
1340 1359 2.814913 AAACGGGATCGGGGTCAAGC 62.815 60.000 0.00 0.00 41.39 4.01
1401 1422 0.236711 CAGCATTCCCATCGCGAATC 59.763 55.000 15.24 0.00 0.00 2.52
1454 1475 4.870991 GCACCTAAACAGTGGATCTTAGTC 59.129 45.833 0.00 0.00 35.71 2.59
1501 1531 4.041198 CCCAAACCTACAGTTCAAGGTCTA 59.959 45.833 0.00 0.00 45.51 2.59
1505 1535 1.886542 GCCCAAACCTACAGTTCAAGG 59.113 52.381 0.00 0.00 37.88 3.61
1511 1541 6.463360 CAAAATTAATGCCCAAACCTACAGT 58.537 36.000 0.00 0.00 0.00 3.55
1530 1560 2.028203 CCCCTTCATTTCGCACCAAAAT 60.028 45.455 0.00 0.00 0.00 1.82
1548 1578 2.230660 CTTTCACTGAGTCAAACCCCC 58.769 52.381 0.00 0.00 0.00 5.40
1560 1590 7.149569 TCCAAGAAATCAATAGCTTTCACTG 57.850 36.000 0.00 0.00 33.44 3.66
1579 1609 2.126467 CCACAACAAACGCATTCCAAG 58.874 47.619 0.00 0.00 0.00 3.61
1654 1724 6.536582 ACCAGTCGAAATAACATGAATCAGAG 59.463 38.462 0.00 0.00 0.00 3.35
1655 1725 6.406370 ACCAGTCGAAATAACATGAATCAGA 58.594 36.000 0.00 0.00 0.00 3.27
1793 1863 1.002257 ATGTCCAGCGCAACATGGA 60.002 52.632 18.47 15.49 43.34 3.41
1815 1885 8.443937 CCAAAGTACTTTCACAACTCTATAAGC 58.556 37.037 18.00 0.00 0.00 3.09
1840 1915 5.382618 AATTCTCTTGCAAGACACATTCC 57.617 39.130 25.16 0.00 0.00 3.01
1922 1997 3.498777 GCTCCAGCTAAAACCCGAATATC 59.501 47.826 0.00 0.00 38.21 1.63
1925 2000 1.004277 TGCTCCAGCTAAAACCCGAAT 59.996 47.619 0.00 0.00 42.66 3.34
2048 2125 1.727335 GACGCCTTTTCTTTCTCTCCG 59.273 52.381 0.00 0.00 0.00 4.63
2052 2129 3.120165 GGTGATGACGCCTTTTCTTTCTC 60.120 47.826 0.00 0.00 42.77 2.87
2086 2163 6.260714 TCCATATGTTAGTTTGCTGTGCTATG 59.739 38.462 1.24 0.00 0.00 2.23
2650 2727 6.126863 TGCCTTCCTTCTCTGAATTTCTTA 57.873 37.500 0.00 0.00 0.00 2.10
2653 2730 4.155644 CACTGCCTTCCTTCTCTGAATTTC 59.844 45.833 0.00 0.00 0.00 2.17
2757 2836 3.161067 TGCTCTGCTCCCTATAAGCTAG 58.839 50.000 0.00 0.00 40.50 3.42
2820 2899 3.509575 AGCCGTTATTTTGCCATTCTTCA 59.490 39.130 0.00 0.00 0.00 3.02
2908 2987 9.391006 GTGATGGGTACAATTTGATAGAAGTAA 57.609 33.333 2.79 0.00 0.00 2.24
2920 2999 7.504238 TGTTAGACAAAAGTGATGGGTACAATT 59.496 33.333 0.00 0.00 0.00 2.32
2945 3025 8.875803 CATTTTCCAATCTGTTCCAATTATGTG 58.124 33.333 0.00 0.00 0.00 3.21
3265 3345 9.021863 GTGTAATAAGTGCACTAAGATGTAGAC 57.978 37.037 22.01 11.18 39.57 2.59
3269 3349 8.615878 TTTGTGTAATAAGTGCACTAAGATGT 57.384 30.769 22.01 5.66 42.85 3.06
3334 3414 5.287226 GGTGTAGACATAAGAATACGTGGG 58.713 45.833 0.00 0.00 0.00 4.61
3349 3429 5.945144 TTATAAAGTCCCAGGGTGTAGAC 57.055 43.478 5.01 0.00 0.00 2.59
3751 3839 7.658982 TCTTCCAATATTCTCACATGTAGATGC 59.341 37.037 0.00 0.00 32.14 3.91
3827 3915 0.988832 GTACATCCACTCCCCCAACA 59.011 55.000 0.00 0.00 0.00 3.33
3874 3962 1.063616 GGAACCTAAATTCGCCTTCGC 59.936 52.381 0.00 0.00 35.26 4.70
3877 3965 7.396339 AGAATAAAAGGAACCTAAATTCGCCTT 59.604 33.333 12.61 0.00 37.34 4.35
3940 4029 1.065126 GCACCAAGCCTAGTCCTCAAT 60.065 52.381 0.00 0.00 37.23 2.57
3965 4054 9.177608 CATGAGTACCAGGATTTTTAATCTTGA 57.822 33.333 11.66 0.00 0.00 3.02
4001 4090 1.423541 ACCAACTAGGGATGCACACAA 59.576 47.619 0.00 0.00 43.89 3.33
4031 4121 3.260205 TGGGAGGAGAATTTCACTTCCT 58.740 45.455 19.38 13.11 0.00 3.36
4048 4138 2.487762 CGTGCAAGCTCTAAAATTGGGA 59.512 45.455 0.00 0.00 0.00 4.37
4167 4258 1.627297 GGCGATGGGAAGAGAAGGGT 61.627 60.000 0.00 0.00 0.00 4.34
4326 4423 3.454573 TGCCGATCCGCGTTACCT 61.455 61.111 4.92 0.00 38.67 3.08
4329 4426 3.709880 CTGGTGCCGATCCGCGTTA 62.710 63.158 4.92 0.00 38.67 3.18
4422 4539 2.435938 GCGCAAAGATCCCCACGA 60.436 61.111 0.30 0.00 0.00 4.35
4423 4540 2.436646 AGCGCAAAGATCCCCACG 60.437 61.111 11.47 0.00 0.00 4.94
4449 4566 1.066858 TGAATCACCGTCTGAAGAGGC 60.067 52.381 0.00 0.00 30.60 4.70
4513 4630 2.676471 GGAGTTTGCGGCCATGGT 60.676 61.111 14.67 0.00 0.00 3.55
4537 4654 4.351938 CACGCTGACCCGAACCGA 62.352 66.667 0.00 0.00 0.00 4.69
4560 4677 0.968901 TCTCGACTACGGCCACCATT 60.969 55.000 2.24 0.00 40.21 3.16
4612 4742 0.179134 CTCGACGAACCTCCATCCAC 60.179 60.000 0.00 0.00 0.00 4.02
4678 4809 1.745489 GAAGAAGGACGCCGCCATT 60.745 57.895 0.70 0.00 0.00 3.16
4704 4835 3.159298 GGCGATGCCTTCAAGAAGA 57.841 52.632 11.25 0.00 46.69 2.87
4726 4857 2.107366 GCTAGAGGTCTGGAGCTTCTT 58.893 52.381 3.79 0.00 39.57 2.52
4747 4878 0.914902 GGTTTCCCCTGGAGGTAGCT 60.915 60.000 0.00 0.00 31.21 3.32
4772 4903 2.484651 CCACCGTCATCCGATCTACTAG 59.515 54.545 0.00 0.00 39.56 2.57
4777 4908 1.739338 GCTCCACCGTCATCCGATCT 61.739 60.000 0.00 0.00 39.56 2.75
4791 4926 3.459823 AGCGACACAAGAGCTCCA 58.540 55.556 10.93 0.00 36.33 3.86
4858 4993 1.443194 ATCGTCGAAACCGTCCACG 60.443 57.895 0.00 0.00 39.44 4.94
4937 5103 3.297620 AACGCCACCTCCGTACGT 61.298 61.111 15.21 0.00 38.06 3.57
4983 5149 2.046023 CATCGACCTTGCCAGCCA 60.046 61.111 0.00 0.00 0.00 4.75
5057 5223 2.317609 GGTCACTGAATGCGCACGT 61.318 57.895 14.90 2.74 0.00 4.49
5067 5233 1.806461 GCACTCTCGGTGGTCACTGA 61.806 60.000 11.58 11.58 45.44 3.41
5108 5274 1.174712 ACCAAGCTGCATTGCGAGTT 61.175 50.000 1.02 0.00 38.13 3.01
5111 5277 1.286570 CAACCAAGCTGCATTGCGA 59.713 52.632 1.02 0.00 38.13 5.10
5120 5288 3.984732 GGAGGCCCCAACCAAGCT 61.985 66.667 0.00 0.00 34.14 3.74
5165 5333 1.960040 CTGAGCCGCATACCCAGACA 61.960 60.000 0.00 0.00 0.00 3.41
5234 5406 1.649321 AGTCTGAAGCCACCATCTCA 58.351 50.000 0.00 0.00 0.00 3.27
5300 5473 0.538584 TCAGGACGATGCATGAAGCT 59.461 50.000 2.46 0.00 45.94 3.74
5354 5533 0.676466 TGCGAAATGGCACTCGGAAT 60.676 50.000 18.96 0.00 38.17 3.01
5370 5549 3.909430 ACCCACACGTATCTATAATGCG 58.091 45.455 0.00 0.00 0.00 4.73
5409 5596 8.612145 ACTCTAAAATGTATACAAAAGACCCCT 58.388 33.333 10.14 0.00 0.00 4.79
5513 5701 7.118390 TGTCTGAAAATAGAAAAGAGCTACTGC 59.882 37.037 0.00 0.00 40.05 4.40
5514 5702 8.539770 TGTCTGAAAATAGAAAAGAGCTACTG 57.460 34.615 0.00 0.00 0.00 2.74
5640 5828 5.939764 AATAACTGTATGCAGGACAGAGA 57.060 39.130 28.98 19.18 46.01 3.10
5677 5865 8.832521 CCTAAATTACCAGTTGTTATGCGATTA 58.167 33.333 0.00 0.00 0.00 1.75
5681 5869 5.163703 TGCCTAAATTACCAGTTGTTATGCG 60.164 40.000 0.00 0.00 0.00 4.73
5761 5949 8.348285 ACCTTAACTATGTTGCACATAACAAT 57.652 30.769 9.33 0.00 43.13 2.71
5772 5960 9.743057 TTCATCAAACAAACCTTAACTATGTTG 57.257 29.630 0.00 0.00 34.67 3.33
5826 6014 2.902486 TCTCAGAATCTCCTGCACTTGT 59.098 45.455 0.00 0.00 34.28 3.16
6084 6276 7.992754 ATGACTAAACTGAAATCAGAAGCTT 57.007 32.000 16.93 0.00 46.59 3.74
6111 6303 6.663093 TCCATCTGCAGTAAAAATTGGTGTAT 59.337 34.615 14.67 0.00 0.00 2.29
6143 6335 7.223387 ACAAATACTAAGTCGTTCGTCTTTGTT 59.777 33.333 18.29 8.74 36.27 2.83
6149 6341 4.620184 AGCACAAATACTAAGTCGTTCGTC 59.380 41.667 0.00 0.00 0.00 4.20
6263 6455 4.653801 AGGGTAGCTGTTTGGAAAAACAAT 59.346 37.500 0.00 1.11 41.55 2.71
6279 6471 4.439289 GCATGACTGAAATGAAAGGGTAGC 60.439 45.833 0.00 0.00 0.00 3.58
6280 6472 4.096984 GGCATGACTGAAATGAAAGGGTAG 59.903 45.833 0.00 0.00 0.00 3.18
6281 6473 4.016444 GGCATGACTGAAATGAAAGGGTA 58.984 43.478 0.00 0.00 0.00 3.69
6283 6475 3.094572 AGGCATGACTGAAATGAAAGGG 58.905 45.455 0.00 0.00 0.00 3.95
6284 6476 4.491676 CAAGGCATGACTGAAATGAAAGG 58.508 43.478 0.00 0.00 0.00 3.11
6285 6477 4.021719 ACCAAGGCATGACTGAAATGAAAG 60.022 41.667 0.00 0.00 0.00 2.62
6286 6478 3.896888 ACCAAGGCATGACTGAAATGAAA 59.103 39.130 0.00 0.00 0.00 2.69
6287 6479 3.499338 ACCAAGGCATGACTGAAATGAA 58.501 40.909 0.00 0.00 0.00 2.57
6402 6673 6.131264 TGGATACATCTCAAGCATCCATTTT 58.869 36.000 0.00 0.00 46.17 1.82
6554 6825 4.508861 GCAGTTGCAAATCAATGTTCTGTT 59.491 37.500 0.00 0.00 41.59 3.16
6615 6887 2.215942 ACAATAAAGGCCTCACCCAC 57.784 50.000 5.23 0.00 40.58 4.61
6618 6890 6.584185 TCTTTTTACAATAAAGGCCTCACC 57.416 37.500 5.23 0.00 34.22 4.02
6760 7035 4.503123 GGCAAAAGTTCCTTAAACATGGCT 60.503 41.667 0.00 0.00 40.56 4.75
7059 7345 0.737715 GGCAGCTCTACACCACGAAG 60.738 60.000 0.00 0.00 0.00 3.79
7217 7503 3.072184 ACAACTGACCTGAGAAGCTGATT 59.928 43.478 0.00 0.00 0.00 2.57
7324 7610 0.031178 CCTGCAGACCACAACAAAGC 59.969 55.000 17.39 0.00 0.00 3.51
7325 7611 1.392589 ACCTGCAGACCACAACAAAG 58.607 50.000 17.39 0.00 0.00 2.77
7371 7657 6.680874 TTTGTACCAGTACACGTTCAAATT 57.319 33.333 10.11 0.00 44.81 1.82
7380 7666 5.063564 GCAAGATAGCTTTGTACCAGTACAC 59.936 44.000 10.11 0.13 44.81 2.90
7551 7841 2.491298 CAGTCTAGTCAAGCAGAGCTGA 59.509 50.000 0.85 0.00 39.62 4.26
7659 7949 6.150976 GGACTGTAATGTTCCATTCAACATGA 59.849 38.462 0.00 0.00 44.62 3.07
7853 8227 9.871238 GTCTAAGTGAACATTATTCTCCTTGTA 57.129 33.333 0.00 0.00 0.00 2.41
7936 8310 5.684704 ACAAGTCAGGAATCTCTGTGAAAA 58.315 37.500 0.00 0.00 36.25 2.29
7942 8316 4.709397 AGGTAGACAAGTCAGGAATCTCTG 59.291 45.833 2.72 0.00 36.17 3.35
7946 8320 6.550108 TGGTATAGGTAGACAAGTCAGGAATC 59.450 42.308 2.72 0.00 0.00 2.52
7983 8357 5.375417 TGGAGCATATCAAAGTTGTTGTG 57.625 39.130 0.00 0.00 0.00 3.33
7984 8358 5.126061 GGATGGAGCATATCAAAGTTGTTGT 59.874 40.000 0.00 0.00 0.00 3.32
7985 8359 5.125900 TGGATGGAGCATATCAAAGTTGTTG 59.874 40.000 0.00 0.00 0.00 3.33
8008 8382 2.167281 ACGGATCATCTCTCAACCACTG 59.833 50.000 0.00 0.00 0.00 3.66
8010 8384 2.969628 ACGGATCATCTCTCAACCAC 57.030 50.000 0.00 0.00 0.00 4.16
8011 8385 4.278310 TCTAACGGATCATCTCTCAACCA 58.722 43.478 0.00 0.00 0.00 3.67
8034 8410 6.237969 GGCGAAGTCTAATGAGATGAAAACTC 60.238 42.308 0.00 0.00 36.12 3.01
8038 8414 4.870426 GTGGCGAAGTCTAATGAGATGAAA 59.130 41.667 0.00 0.00 33.14 2.69
8048 8424 2.037902 TGGTTCATGTGGCGAAGTCTAA 59.962 45.455 0.00 0.00 0.00 2.10
8049 8425 1.621317 TGGTTCATGTGGCGAAGTCTA 59.379 47.619 0.00 0.00 0.00 2.59
8056 8432 1.577328 GAGTGGTGGTTCATGTGGCG 61.577 60.000 0.00 0.00 0.00 5.69
8142 8529 8.674173 TCTAGGACATGGACTATCTTATCTCTT 58.326 37.037 0.00 0.00 0.00 2.85
8143 8530 8.225863 TCTAGGACATGGACTATCTTATCTCT 57.774 38.462 0.00 0.00 0.00 3.10
8146 8533 8.107095 ACTCTCTAGGACATGGACTATCTTATC 58.893 40.741 0.00 0.00 0.00 1.75
8153 8540 4.537751 CCAACTCTCTAGGACATGGACTA 58.462 47.826 0.00 0.00 30.33 2.59
8163 8550 1.208293 GACAAGGCCCAACTCTCTAGG 59.792 57.143 0.00 0.00 0.00 3.02
8174 8561 7.872483 CCATGTTAATTATATTTGACAAGGCCC 59.128 37.037 0.00 0.00 30.55 5.80


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

AutoCloner maintained by Alex Coulton.