Multiple sequence alignment - TraesCS5D01G556800

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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 TraesCS5D01G556800 chr5D 100.000 3416 0 0 1 3416 559729516 559732931 0.000000e+00 6309.0
1 TraesCS5D01G556800 chr5D 83.929 224 25 2 2037 2260 339383466 339383678 1.610000e-48 204.0
2 TraesCS5D01G556800 chr5D 81.553 103 14 2 2890 2992 559832649 559832746 2.830000e-11 80.5
3 TraesCS5D01G556800 chr5B 91.381 1195 56 18 79 1232 693994341 693995529 0.000000e+00 1592.0
4 TraesCS5D01G556800 chr5B 89.124 947 49 18 2036 2948 693996316 693997242 0.000000e+00 1129.0
5 TraesCS5D01G556800 chr5B 84.507 355 44 4 92 445 522054316 522054660 1.170000e-89 340.0
6 TraesCS5D01G556800 chr5B 84.232 241 22 7 1294 1525 693995535 693995768 1.600000e-53 220.0
7 TraesCS5D01G556800 chr5B 94.400 125 6 1 3153 3277 693997347 693997470 1.250000e-44 191.0
8 TraesCS5D01G556800 chr5B 95.455 110 5 0 3010 3119 693997242 693997351 3.500000e-40 176.0
9 TraesCS5D01G556800 chr5B 80.804 224 17 7 627 850 519188689 519188492 5.900000e-33 152.0
10 TraesCS5D01G556800 chr4A 82.407 972 67 38 627 1584 613322077 613322958 0.000000e+00 752.0
11 TraesCS5D01G556800 chr4A 88.480 625 40 15 2036 2648 613325221 613325825 0.000000e+00 726.0
12 TraesCS5D01G556800 chr4A 84.783 414 44 10 163 567 613321593 613321996 6.870000e-107 398.0
13 TraesCS5D01G556800 chr4A 79.393 461 39 23 1618 2040 604195818 604196260 1.210000e-69 274.0
14 TraesCS5D01G556800 chr4A 89.840 187 17 2 3153 3339 613326266 613326450 4.410000e-59 239.0
15 TraesCS5D01G556800 chr4A 92.920 113 7 1 1445 1557 604195689 604195800 2.730000e-36 163.0
16 TraesCS5D01G556800 chr4A 97.143 70 2 0 6 75 613320895 613320964 5.990000e-23 119.0
17 TraesCS5D01G556800 chr4A 80.000 135 15 5 1861 1985 322882833 322882965 4.700000e-14 89.8
18 TraesCS5D01G556800 chr4A 94.444 54 3 0 2814 2867 613325992 613326045 2.180000e-12 84.2
19 TraesCS5D01G556800 chr4A 94.340 53 3 0 3073 3125 613326224 613326276 7.860000e-12 82.4
20 TraesCS5D01G556800 chr2D 80.167 958 102 48 1114 2029 403808644 403809555 1.340000e-178 636.0
21 TraesCS5D01G556800 chr2D 80.628 191 23 9 1850 2035 147702310 147702491 5.950000e-28 135.0
22 TraesCS5D01G556800 chr6A 82.097 782 72 36 1149 1913 307921577 307920847 1.050000e-169 606.0
23 TraesCS5D01G556800 chr6B 79.913 921 95 48 1151 2029 46305749 46306621 8.160000e-166 593.0
24 TraesCS5D01G556800 chr6B 80.818 782 82 31 1149 1913 83867115 83867845 4.980000e-153 551.0
25 TraesCS5D01G556800 chr6B 81.988 322 43 11 1969 2280 667901798 667901482 3.380000e-65 259.0
26 TraesCS5D01G556800 chr6B 77.990 418 41 26 1197 1590 671658618 671659008 7.420000e-52 215.0
27 TraesCS5D01G556800 chr6B 86.364 66 4 2 2642 2707 9570429 9570489 2.200000e-07 67.6
28 TraesCS5D01G556800 chr6B 85.938 64 5 2 2645 2707 501773957 501774017 7.910000e-07 65.8
29 TraesCS5D01G556800 chr1A 81.586 782 76 31 1149 1913 236392083 236392813 4.910000e-163 584.0
30 TraesCS5D01G556800 chr1A 81.790 324 41 10 1969 2280 479639603 479639286 4.370000e-64 255.0
31 TraesCS5D01G556800 chrUn 81.515 779 76 25 1152 1913 87515057 87514330 2.290000e-161 579.0
32 TraesCS5D01G556800 chrUn 80.616 779 81 34 1152 1913 87505231 87504506 3.880000e-149 538.0
33 TraesCS5D01G556800 chr7A 81.458 782 77 33 1149 1913 395514595 395515325 2.290000e-161 579.0
34 TraesCS5D01G556800 chr7A 90.052 191 13 2 380 567 487486142 487485955 3.410000e-60 243.0
35 TraesCS5D01G556800 chr7A 80.804 224 17 7 627 850 487485874 487485677 5.900000e-33 152.0
36 TraesCS5D01G556800 chr4B 81.202 782 79 28 1149 1913 552797100 552797830 4.950000e-158 568.0
37 TraesCS5D01G556800 chr4B 80.946 782 81 35 1149 1913 636566241 636566971 1.070000e-154 556.0
38 TraesCS5D01G556800 chr4B 86.735 98 7 5 326 417 16690006 16689909 1.680000e-18 104.0
39 TraesCS5D01G556800 chr4B 82.906 117 13 4 451 567 16689923 16689814 7.800000e-17 99.0
40 TraesCS5D01G556800 chr4B 87.500 64 5 1 2644 2707 517166900 517166840 1.700000e-08 71.3
41 TraesCS5D01G556800 chr3B 81.202 782 79 33 1149 1913 745498 746228 4.950000e-158 568.0
42 TraesCS5D01G556800 chr3B 81.226 783 77 39 1149 1913 817687415 817688145 4.950000e-158 568.0
43 TraesCS5D01G556800 chr3B 76.611 419 45 27 1197 1590 748486494 748486884 7.530000e-42 182.0
44 TraesCS5D01G556800 chr3B 93.056 72 5 0 492 563 761144107 761144036 4.660000e-19 106.0
45 TraesCS5D01G556800 chr3B 91.429 70 4 2 495 563 761168469 761168401 1.010000e-15 95.3
46 TraesCS5D01G556800 chr3B 84.848 66 5 3 2645 2707 659273917 659273854 1.020000e-05 62.1
47 TraesCS5D01G556800 chr7B 80.946 782 80 34 1149 1913 681954094 681954823 3.850000e-154 555.0
48 TraesCS5D01G556800 chr7B 80.435 782 85 33 1149 1913 695575107 695574377 5.020000e-148 534.0
49 TraesCS5D01G556800 chr7B 89.005 191 15 2 380 567 336661919 336661732 7.370000e-57 231.0
50 TraesCS5D01G556800 chr7B 88.000 100 9 1 627 726 336661651 336661555 7.750000e-22 115.0
51 TraesCS5D01G556800 chr7B 93.056 72 4 1 492 563 644283904 644283834 1.680000e-18 104.0
52 TraesCS5D01G556800 chr7B 89.189 74 8 0 359 432 642054148 642054221 3.630000e-15 93.5
53 TraesCS5D01G556800 chr1B 84.211 342 42 6 92 432 337425963 337426293 4.250000e-84 322.0
54 TraesCS5D01G556800 chr1B 82.319 345 50 3 92 435 600850115 600849781 4.310000e-74 289.0
55 TraesCS5D01G556800 chr1B 82.164 342 50 3 92 432 657829562 657829893 2.010000e-72 283.0
56 TraesCS5D01G556800 chr1B 85.646 209 19 2 2055 2263 151148737 151148540 3.450000e-50 209.0
57 TraesCS5D01G556800 chr1B 77.835 194 21 9 1853 2035 151149125 151148943 2.170000e-17 100.0
58 TraesCS5D01G556800 chr2A 81.053 380 42 19 1551 1913 290319740 290320106 3.360000e-70 276.0
59 TraesCS5D01G556800 chr4D 78.696 460 44 26 1618 2040 60090985 60091427 1.220000e-64 257.0
60 TraesCS5D01G556800 chr4D 85.200 250 26 4 197 445 142309258 142309497 2.630000e-61 246.0
61 TraesCS5D01G556800 chr4D 82.379 227 27 4 2036 2260 332130721 332130936 5.820000e-43 185.0
62 TraesCS5D01G556800 chr4D 81.152 191 22 11 1850 2035 332130480 332130661 1.280000e-29 141.0
63 TraesCS5D01G556800 chr3D 78.322 429 58 22 1853 2263 231533007 231532596 9.470000e-61 244.0
64 TraesCS5D01G556800 chr2B 80.702 342 27 16 1717 2035 306849360 306849035 2.650000e-56 230.0
65 TraesCS5D01G556800 chr2B 84.848 66 5 2 2644 2707 794694551 794694489 1.020000e-05 62.1
66 TraesCS5D01G556800 chr2B 84.848 66 5 2 2644 2707 794803452 794803390 1.020000e-05 62.1
67 TraesCS5D01G556800 chr7D 83.929 224 25 2 2037 2260 594651926 594652138 1.610000e-48 204.0
68 TraesCS5D01G556800 chr7D 86.154 65 4 2 2645 2707 234073672 234073733 7.910000e-07 65.8
69 TraesCS5D01G556800 chr6D 83.700 227 26 2 2037 2263 73253394 73253179 1.610000e-48 204.0
70 TraesCS5D01G556800 chr6D 83.125 160 15 11 1853 2006 73253634 73253481 5.950000e-28 135.0
71 TraesCS5D01G556800 chr5A 87.719 171 14 1 275 445 168349739 168349576 3.480000e-45 193.0
72 TraesCS5D01G556800 chr5A 88.889 63 4 1 2645 2707 655994096 655994155 1.310000e-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 TraesCS5D01G556800 chr5D 559729516 559732931 3415 False 6309.000000 6309 100.000000 1 3416 1 chr5D.!!$F2 3415
1 TraesCS5D01G556800 chr5B 693994341 693997470 3129 False 661.600000 1592 90.918400 79 3277 5 chr5B.!!$F2 3198
2 TraesCS5D01G556800 chr4A 613320895 613326450 5555 False 342.942857 752 90.205286 6 3339 7 chr4A.!!$F3 3333
3 TraesCS5D01G556800 chr4A 604195689 604196260 571 False 218.500000 274 86.156500 1445 2040 2 chr4A.!!$F2 595
4 TraesCS5D01G556800 chr2D 403808644 403809555 911 False 636.000000 636 80.167000 1114 2029 1 chr2D.!!$F2 915
5 TraesCS5D01G556800 chr6A 307920847 307921577 730 True 606.000000 606 82.097000 1149 1913 1 chr6A.!!$R1 764
6 TraesCS5D01G556800 chr6B 46305749 46306621 872 False 593.000000 593 79.913000 1151 2029 1 chr6B.!!$F2 878
7 TraesCS5D01G556800 chr6B 83867115 83867845 730 False 551.000000 551 80.818000 1149 1913 1 chr6B.!!$F3 764
8 TraesCS5D01G556800 chr1A 236392083 236392813 730 False 584.000000 584 81.586000 1149 1913 1 chr1A.!!$F1 764
9 TraesCS5D01G556800 chrUn 87514330 87515057 727 True 579.000000 579 81.515000 1152 1913 1 chrUn.!!$R2 761
10 TraesCS5D01G556800 chrUn 87504506 87505231 725 True 538.000000 538 80.616000 1152 1913 1 chrUn.!!$R1 761
11 TraesCS5D01G556800 chr7A 395514595 395515325 730 False 579.000000 579 81.458000 1149 1913 1 chr7A.!!$F1 764
12 TraesCS5D01G556800 chr4B 552797100 552797830 730 False 568.000000 568 81.202000 1149 1913 1 chr4B.!!$F1 764
13 TraesCS5D01G556800 chr4B 636566241 636566971 730 False 556.000000 556 80.946000 1149 1913 1 chr4B.!!$F2 764
14 TraesCS5D01G556800 chr3B 745498 746228 730 False 568.000000 568 81.202000 1149 1913 1 chr3B.!!$F1 764
15 TraesCS5D01G556800 chr3B 817687415 817688145 730 False 568.000000 568 81.226000 1149 1913 1 chr3B.!!$F3 764
16 TraesCS5D01G556800 chr7B 681954094 681954823 729 False 555.000000 555 80.946000 1149 1913 1 chr7B.!!$F2 764
17 TraesCS5D01G556800 chr7B 695574377 695575107 730 True 534.000000 534 80.435000 1149 1913 1 chr7B.!!$R2 764

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
668 1279 1.107538 CGAGCGTATTGAGGGGGAGA 61.108 60.0 0.00 0.00 0.00 3.71 F
1333 2011 0.378257 CGATGTATTGCTGCGGCTTT 59.622 50.0 20.27 8.55 39.59 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1656 2412 0.248621 GCACCCAAATACTCATGCGC 60.249 55.0 0.00 0.0 0.0 6.09 R
3181 5932 0.031616 TGGTTTGGTTTGGAGGCCTT 60.032 50.0 6.77 0.0 0.0 4.35 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
41 42 5.765182 ACCTTCAGTGAACAGGTTAAATCTG 59.235 40.000 10.27 5.76 38.16 2.90
45 46 5.070001 CAGTGAACAGGTTAAATCTGGGAA 58.930 41.667 10.60 0.00 36.62 3.97
80 643 8.040716 AGGCATAACTAATCGCATTATTTACC 57.959 34.615 0.00 0.00 0.00 2.85
117 680 7.217070 GCAGTATCTGATTCGAACAAACAAATC 59.783 37.037 0.00 0.00 32.44 2.17
146 709 3.817084 ACAATCTCCAGTCACACATGTTG 59.183 43.478 0.00 0.00 0.00 3.33
161 724 6.688385 CACACATGTTGTCTAGAAAACACAAG 59.312 38.462 27.12 21.33 39.00 3.16
230 794 6.709643 CAATACTCATCAAACGACCTTCATC 58.290 40.000 0.00 0.00 0.00 2.92
485 1053 3.677527 GGTTCCTCGACCTCGACA 58.322 61.111 0.00 0.00 44.22 4.35
499 1067 2.358737 GACAACCCCGACCAGCAG 60.359 66.667 0.00 0.00 0.00 4.24
631 1242 2.231235 GACATTTCAACCAAATCGGCCT 59.769 45.455 0.00 0.00 39.03 5.19
634 1245 1.533625 TTCAACCAAATCGGCCTCTG 58.466 50.000 0.00 0.00 39.03 3.35
668 1279 1.107538 CGAGCGTATTGAGGGGGAGA 61.108 60.000 0.00 0.00 0.00 3.71
669 1280 1.343069 GAGCGTATTGAGGGGGAGAT 58.657 55.000 0.00 0.00 0.00 2.75
670 1281 1.694696 GAGCGTATTGAGGGGGAGATT 59.305 52.381 0.00 0.00 0.00 2.40
671 1282 1.417890 AGCGTATTGAGGGGGAGATTG 59.582 52.381 0.00 0.00 0.00 2.67
672 1283 1.543429 GCGTATTGAGGGGGAGATTGG 60.543 57.143 0.00 0.00 0.00 3.16
673 1284 2.047061 CGTATTGAGGGGGAGATTGGA 58.953 52.381 0.00 0.00 0.00 3.53
874 1505 5.603395 TGGACGGACCCAAATGTAATATCTA 59.397 40.000 0.00 0.00 38.00 1.98
876 1507 6.817140 GGACGGACCCAAATGTAATATCTATC 59.183 42.308 0.00 0.00 0.00 2.08
877 1508 7.310485 GGACGGACCCAAATGTAATATCTATCT 60.310 40.741 0.00 0.00 0.00 1.98
893 1528 5.074746 TCTATCTATGGGCCAGAGTGTAA 57.925 43.478 26.25 8.88 0.00 2.41
960 1609 1.610673 TCTTGGGCTTCTCTCGGCT 60.611 57.895 0.00 0.00 0.00 5.52
1240 1908 1.143401 GCCAAGGTACCCTACTCGC 59.857 63.158 8.74 0.00 31.13 5.03
1243 1911 0.686769 CAAGGTACCCTACTCGCCCT 60.687 60.000 8.74 0.00 31.13 5.19
1244 1912 0.686769 AAGGTACCCTACTCGCCCTG 60.687 60.000 8.74 0.00 31.13 4.45
1245 1913 2.794028 GGTACCCTACTCGCCCTGC 61.794 68.421 0.00 0.00 0.00 4.85
1246 1914 2.443390 TACCCTACTCGCCCTGCC 60.443 66.667 0.00 0.00 0.00 4.85
1310 1988 0.451783 CACCAACCCTTAGCGATTGC 59.548 55.000 0.00 0.00 43.24 3.56
1333 2011 0.378257 CGATGTATTGCTGCGGCTTT 59.622 50.000 20.27 8.55 39.59 3.51
1334 2012 1.831343 GATGTATTGCTGCGGCTTTG 58.169 50.000 20.27 0.00 39.59 2.77
1335 2013 1.401552 GATGTATTGCTGCGGCTTTGA 59.598 47.619 20.27 2.40 39.59 2.69
1336 2014 0.521291 TGTATTGCTGCGGCTTTGAC 59.479 50.000 20.27 11.72 39.59 3.18
1505 2192 3.321968 CCTCTTTTTAGTGCCTTGGCTTT 59.678 43.478 13.18 3.73 0.00 3.51
1525 2213 3.110447 TCTTGCATTTGGGAAGCAAAC 57.890 42.857 0.00 0.00 46.30 2.93
1590 2340 7.523380 GCCGTACTCTTGTATATCAATACCAGT 60.523 40.741 0.00 0.00 37.72 4.00
1592 2342 9.181805 CGTACTCTTGTATATCAATACCAGTTG 57.818 37.037 0.00 0.00 37.72 3.16
1656 2412 4.565962 GTGTATGCTCAACTCAGTGATCTG 59.434 45.833 0.00 0.00 42.54 2.90
1657 2413 2.090400 TGCTCAACTCAGTGATCTGC 57.910 50.000 0.00 0.00 41.10 4.26
1680 2436 3.313526 GCATGAGTATTTGGGTGCTACTG 59.686 47.826 0.00 0.00 0.00 2.74
1681 2437 2.985896 TGAGTATTTGGGTGCTACTGC 58.014 47.619 0.00 0.00 40.20 4.40
1682 2438 2.571653 TGAGTATTTGGGTGCTACTGCT 59.428 45.455 0.00 0.00 40.48 4.24
1683 2439 3.772572 TGAGTATTTGGGTGCTACTGCTA 59.227 43.478 0.00 0.00 40.48 3.49
1684 2440 4.141937 TGAGTATTTGGGTGCTACTGCTAG 60.142 45.833 0.00 0.00 40.48 3.42
1685 2441 3.775316 AGTATTTGGGTGCTACTGCTAGT 59.225 43.478 0.00 0.00 40.48 2.57
1691 2450 3.194968 TGGGTGCTACTGCTAGTAAGAAC 59.805 47.826 2.05 0.00 40.48 3.01
1692 2451 3.430513 GGGTGCTACTGCTAGTAAGAACC 60.431 52.174 1.82 1.82 40.48 3.62
1695 2454 5.480205 GTGCTACTGCTAGTAAGAACCTTT 58.520 41.667 2.05 0.00 40.48 3.11
1714 2477 7.354751 ACCTTTTGCAATTAGGTTTTAGTCA 57.645 32.000 21.83 0.00 39.19 3.41
1784 2564 4.850680 AGAGTTGTGGTGAGGTAAACAAA 58.149 39.130 0.00 0.00 34.54 2.83
1789 2569 7.001674 AGTTGTGGTGAGGTAAACAAATGATA 58.998 34.615 0.00 0.00 34.54 2.15
1791 2571 5.708230 TGTGGTGAGGTAAACAAATGATACC 59.292 40.000 10.26 10.26 39.51 2.73
1853 3195 7.860373 TGTTACTGCATGAGTTTGTTATGTTTC 59.140 33.333 0.00 0.00 35.96 2.78
1862 3204 7.771183 TGAGTTTGTTATGTTTCTTCAAAGCT 58.229 30.769 0.00 0.00 0.00 3.74
1864 3206 8.411318 AGTTTGTTATGTTTCTTCAAAGCTTG 57.589 30.769 0.00 0.00 0.00 4.01
1957 3355 1.241165 TGCTCACTTCATGGCACTTG 58.759 50.000 0.00 0.00 31.83 3.16
1966 4330 2.715046 TCATGGCACTTGGAGAACATC 58.285 47.619 0.00 0.00 0.00 3.06
1967 4331 2.040145 TCATGGCACTTGGAGAACATCA 59.960 45.455 0.00 0.00 0.00 3.07
1970 4334 1.541588 GGCACTTGGAGAACATCAACC 59.458 52.381 0.00 0.00 0.00 3.77
1989 4353 8.472413 CATCAACCATCTGTTTTATCCATTCTT 58.528 33.333 0.00 0.00 34.00 2.52
1990 4354 7.829725 TCAACCATCTGTTTTATCCATTCTTG 58.170 34.615 0.00 0.00 34.00 3.02
1992 4356 5.163622 ACCATCTGTTTTATCCATTCTTGCG 60.164 40.000 0.00 0.00 0.00 4.85
2007 4544 2.742053 TCTTGCGTTCTGGCATTCTAAC 59.258 45.455 0.00 0.00 43.52 2.34
2013 4550 5.163447 TGCGTTCTGGCATTCTAACTAGTAT 60.163 40.000 0.00 0.00 38.17 2.12
2041 4628 1.868713 TCTCCCAGTGGCGGTTTATA 58.131 50.000 2.61 0.00 0.00 0.98
2051 4638 5.063944 CAGTGGCGGTTTATATCTATGATGC 59.936 44.000 0.00 0.00 0.00 3.91
2065 4705 9.794685 ATATCTATGATGCGATACTACTGTTTG 57.205 33.333 0.00 0.00 0.00 2.93
2073 4713 9.119329 GATGCGATACTACTGTTTGTATCTAAG 57.881 37.037 20.67 12.58 41.45 2.18
2104 4744 8.746530 AGCTTGTGATTTGAAGATCATGTAATT 58.253 29.630 0.00 0.00 38.25 1.40
2292 4932 3.256136 ACACCAAGAAGTTCCTCTACTCG 59.744 47.826 0.00 0.00 0.00 4.18
2310 4950 2.125673 CCGTTCACCGCCGAAGAT 60.126 61.111 0.00 0.00 34.38 2.40
2311 4951 1.140161 CCGTTCACCGCCGAAGATA 59.860 57.895 0.00 0.00 34.38 1.98
2313 4953 0.457166 CGTTCACCGCCGAAGATACA 60.457 55.000 0.00 0.00 0.00 2.29
2322 4962 1.736586 CGAAGATACAGAGGCGGCT 59.263 57.895 13.09 13.09 0.00 5.52
2351 4997 2.103934 CGAGGAGCAGCCGAAGAG 59.896 66.667 0.00 0.00 43.43 2.85
2404 5050 1.452145 GACCAAGAAACAGCCGGCAA 61.452 55.000 31.54 0.00 0.00 4.52
2472 5118 1.298157 TTTCGCGCTGCTGCTGTTAT 61.298 50.000 14.03 0.00 36.97 1.89
2580 5232 1.304052 AAATTACGCTGGCAGGCCA 60.304 52.632 17.64 13.18 45.02 5.36
2588 5240 2.842801 TGGCAGGCCAGTTTGCTA 59.157 55.556 9.35 5.68 41.89 3.49
2612 5266 1.954382 TCTGTGTTGTAGACTCGCTGT 59.046 47.619 0.00 0.00 0.00 4.40
2613 5267 2.031069 TCTGTGTTGTAGACTCGCTGTC 60.031 50.000 1.00 1.00 45.67 3.51
2626 5280 6.315091 GACTCGCTGTCTGGTAGAATAATA 57.685 41.667 1.94 0.00 42.21 0.98
2627 5281 6.902771 ACTCGCTGTCTGGTAGAATAATAT 57.097 37.500 0.00 0.00 0.00 1.28
2628 5282 6.682746 ACTCGCTGTCTGGTAGAATAATATG 58.317 40.000 0.00 0.00 0.00 1.78
2629 5283 6.490381 ACTCGCTGTCTGGTAGAATAATATGA 59.510 38.462 0.00 0.00 0.00 2.15
2630 5284 7.177568 ACTCGCTGTCTGGTAGAATAATATGAT 59.822 37.037 0.00 0.00 0.00 2.45
2631 5285 7.315890 TCGCTGTCTGGTAGAATAATATGATG 58.684 38.462 0.00 0.00 0.00 3.07
2656 5314 5.946972 ACATGATAATCTAGTACTCCCTCCG 59.053 44.000 0.00 0.00 0.00 4.63
2671 5329 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
2672 5330 8.315220 ACTCCCTCCGTAAAGAAATATAAGAA 57.685 34.615 0.00 0.00 0.00 2.52
2673 5331 8.202811 ACTCCCTCCGTAAAGAAATATAAGAAC 58.797 37.037 0.00 0.00 0.00 3.01
2736 5408 7.753309 AGTATCTATCAGTCTTAAGATGCGT 57.247 36.000 8.75 0.00 36.54 5.24
2789 5469 3.324108 GTAACCGGGGTGAGGCCA 61.324 66.667 6.32 0.00 39.65 5.36
2802 5510 1.274069 TGAGGCCAGAAAGGAGGATCT 60.274 52.381 5.01 0.00 41.22 2.75
2933 5684 1.003718 AAGCAAGAGGTGTACCGCC 60.004 57.895 0.95 0.00 42.08 6.13
2966 5717 1.652563 GCGTTCCCTTTGGTCACAC 59.347 57.895 0.00 0.00 0.00 3.82
2969 5720 1.890041 TTCCCTTTGGTCACACGCG 60.890 57.895 3.53 3.53 0.00 6.01
2970 5721 3.353836 CCCTTTGGTCACACGCGG 61.354 66.667 12.47 1.27 0.00 6.46
2973 5724 2.280524 TTTGGTCACACGCGGGAG 60.281 61.111 19.19 7.73 0.00 4.30
2989 5740 1.749033 GAGGATAGACGGCAAGGGG 59.251 63.158 0.00 0.00 0.00 4.79
3001 5752 1.908619 GGCAAGGGGTTCATTGGATTT 59.091 47.619 0.00 0.00 35.45 2.17
3002 5753 2.305635 GGCAAGGGGTTCATTGGATTTT 59.694 45.455 0.00 0.00 35.45 1.82
3003 5754 3.244875 GGCAAGGGGTTCATTGGATTTTT 60.245 43.478 0.00 0.00 35.45 1.94
3004 5755 4.019771 GGCAAGGGGTTCATTGGATTTTTA 60.020 41.667 0.00 0.00 35.45 1.52
3005 5756 5.178061 GCAAGGGGTTCATTGGATTTTTAG 58.822 41.667 0.00 0.00 35.45 1.85
3006 5757 5.046663 GCAAGGGGTTCATTGGATTTTTAGA 60.047 40.000 0.00 0.00 35.45 2.10
3007 5758 6.633856 CAAGGGGTTCATTGGATTTTTAGAG 58.366 40.000 0.00 0.00 31.71 2.43
3008 5759 4.711846 AGGGGTTCATTGGATTTTTAGAGC 59.288 41.667 0.00 0.00 0.00 4.09
3009 5760 4.141937 GGGGTTCATTGGATTTTTAGAGCC 60.142 45.833 0.00 0.00 0.00 4.70
3059 5810 3.058016 ACAGAATCGCCAACATTTGACAG 60.058 43.478 0.00 0.00 0.00 3.51
3069 5820 4.022068 CCAACATTTGACAGTTGTGGCTAT 60.022 41.667 0.00 0.00 42.62 2.97
3115 5866 7.362574 CCAAAAATTAGAGCCTAACAAATCGGA 60.363 37.037 0.00 0.00 0.00 4.55
3116 5867 7.881775 AAAATTAGAGCCTAACAAATCGGAT 57.118 32.000 0.00 0.00 0.00 4.18
3117 5868 6.867662 AATTAGAGCCTAACAAATCGGATG 57.132 37.500 0.00 0.00 0.00 3.51
3118 5869 2.565841 AGAGCCTAACAAATCGGATGC 58.434 47.619 0.00 0.00 0.00 3.91
3119 5870 1.604278 GAGCCTAACAAATCGGATGCC 59.396 52.381 0.00 0.00 0.00 4.40
3120 5871 1.064758 AGCCTAACAAATCGGATGCCA 60.065 47.619 0.00 0.00 0.00 4.92
3121 5872 1.956477 GCCTAACAAATCGGATGCCAT 59.044 47.619 0.00 0.00 0.00 4.40
3122 5873 2.362077 GCCTAACAAATCGGATGCCATT 59.638 45.455 0.00 0.00 0.00 3.16
3123 5874 3.181476 GCCTAACAAATCGGATGCCATTT 60.181 43.478 0.00 0.00 0.00 2.32
3124 5875 4.680440 GCCTAACAAATCGGATGCCATTTT 60.680 41.667 0.00 0.00 0.00 1.82
3125 5876 5.418676 CCTAACAAATCGGATGCCATTTTT 58.581 37.500 0.00 0.00 0.00 1.94
3174 5925 5.449553 AGCTGCTAATTTATTAGGGTTGCT 58.550 37.500 0.00 0.00 40.01 3.91
3218 5969 1.367659 CAAGCAGGCTCTAAGTGCTC 58.632 55.000 0.00 0.00 46.86 4.26
3255 6006 1.984990 CATGGCGTGTGTGCAAATTAC 59.015 47.619 0.00 0.00 36.28 1.89
3273 6024 1.151777 ACGAGTGTCACGGCTTGTTG 61.152 55.000 0.00 0.00 34.93 3.33
3276 6027 0.732571 AGTGTCACGGCTTGTTGTTG 59.267 50.000 0.00 0.00 0.00 3.33
3285 6036 2.159503 CGGCTTGTTGTTGTGTGTACAA 60.160 45.455 0.00 0.00 44.17 2.41
3302 6053 0.744414 CAATACACTGTGCCTCCCGG 60.744 60.000 7.90 0.00 0.00 5.73
3320 6071 2.986479 CCGGTGCTTCTGTAATTTTTGC 59.014 45.455 0.00 0.00 0.00 3.68
3339 6090 1.695788 GCGGGGGTAAAATAGCTAGGA 59.304 52.381 0.00 0.00 0.00 2.94
3340 6091 2.305052 GCGGGGGTAAAATAGCTAGGAT 59.695 50.000 0.00 0.00 0.00 3.24
3341 6092 3.244805 GCGGGGGTAAAATAGCTAGGATT 60.245 47.826 0.00 0.00 0.00 3.01
3342 6093 4.324267 CGGGGGTAAAATAGCTAGGATTG 58.676 47.826 0.00 0.00 0.00 2.67
3343 6094 4.202430 CGGGGGTAAAATAGCTAGGATTGT 60.202 45.833 0.00 0.00 0.00 2.71
3344 6095 5.314529 GGGGGTAAAATAGCTAGGATTGTC 58.685 45.833 0.00 0.00 0.00 3.18
3345 6096 5.073280 GGGGGTAAAATAGCTAGGATTGTCT 59.927 44.000 0.00 0.00 0.00 3.41
3346 6097 6.410504 GGGGGTAAAATAGCTAGGATTGTCTT 60.411 42.308 0.00 0.00 0.00 3.01
3347 6098 6.711194 GGGGTAAAATAGCTAGGATTGTCTTC 59.289 42.308 0.00 0.00 0.00 2.87
3348 6099 7.420330 GGGGTAAAATAGCTAGGATTGTCTTCT 60.420 40.741 0.00 0.00 0.00 2.85
3349 6100 7.993758 GGGTAAAATAGCTAGGATTGTCTTCTT 59.006 37.037 0.00 0.00 0.00 2.52
3350 6101 9.047371 GGTAAAATAGCTAGGATTGTCTTCTTC 57.953 37.037 0.00 0.00 0.00 2.87
3351 6102 9.047371 GTAAAATAGCTAGGATTGTCTTCTTCC 57.953 37.037 0.00 0.00 0.00 3.46
3352 6103 7.444703 AAATAGCTAGGATTGTCTTCTTCCT 57.555 36.000 0.00 0.00 42.49 3.36
3353 6104 7.444703 AATAGCTAGGATTGTCTTCTTCCTT 57.555 36.000 0.00 0.00 40.37 3.36
3354 6105 5.770685 AGCTAGGATTGTCTTCTTCCTTT 57.229 39.130 0.00 0.00 40.37 3.11
3355 6106 6.133253 AGCTAGGATTGTCTTCTTCCTTTT 57.867 37.500 0.00 0.00 40.37 2.27
3356 6107 6.176896 AGCTAGGATTGTCTTCTTCCTTTTC 58.823 40.000 0.00 0.00 40.37 2.29
3357 6108 5.940470 GCTAGGATTGTCTTCTTCCTTTTCA 59.060 40.000 0.00 0.00 40.37 2.69
3358 6109 6.128145 GCTAGGATTGTCTTCTTCCTTTTCAC 60.128 42.308 0.00 0.00 40.37 3.18
3359 6110 4.757149 AGGATTGTCTTCTTCCTTTTCACG 59.243 41.667 0.00 0.00 36.46 4.35
3360 6111 4.755123 GGATTGTCTTCTTCCTTTTCACGA 59.245 41.667 0.00 0.00 0.00 4.35
3361 6112 5.106908 GGATTGTCTTCTTCCTTTTCACGAG 60.107 44.000 0.00 0.00 0.00 4.18
3362 6113 3.131396 TGTCTTCTTCCTTTTCACGAGC 58.869 45.455 0.00 0.00 0.00 5.03
3363 6114 3.131396 GTCTTCTTCCTTTTCACGAGCA 58.869 45.455 0.00 0.00 0.00 4.26
3364 6115 3.560068 GTCTTCTTCCTTTTCACGAGCAA 59.440 43.478 0.00 0.00 0.00 3.91
3365 6116 3.809832 TCTTCTTCCTTTTCACGAGCAAG 59.190 43.478 0.00 0.00 0.00 4.01
3366 6117 3.469008 TCTTCCTTTTCACGAGCAAGA 57.531 42.857 0.00 0.00 0.00 3.02
3367 6118 3.393800 TCTTCCTTTTCACGAGCAAGAG 58.606 45.455 0.00 0.00 0.00 2.85
3368 6119 2.910688 TCCTTTTCACGAGCAAGAGT 57.089 45.000 0.00 0.00 0.00 3.24
3369 6120 3.194005 TCCTTTTCACGAGCAAGAGTT 57.806 42.857 0.00 0.00 0.00 3.01
3370 6121 2.872245 TCCTTTTCACGAGCAAGAGTTG 59.128 45.455 0.00 0.00 0.00 3.16
3371 6122 2.614057 CCTTTTCACGAGCAAGAGTTGT 59.386 45.455 0.00 0.00 0.00 3.32
3372 6123 3.807622 CCTTTTCACGAGCAAGAGTTGTA 59.192 43.478 0.00 0.00 0.00 2.41
3373 6124 4.318831 CCTTTTCACGAGCAAGAGTTGTAC 60.319 45.833 0.00 0.00 0.00 2.90
3374 6125 3.446310 TTCACGAGCAAGAGTTGTACA 57.554 42.857 0.00 0.00 0.00 2.90
3375 6126 3.446310 TCACGAGCAAGAGTTGTACAA 57.554 42.857 3.59 3.59 0.00 2.41
3376 6127 3.381045 TCACGAGCAAGAGTTGTACAAG 58.619 45.455 8.98 0.00 0.00 3.16
3377 6128 2.096713 CACGAGCAAGAGTTGTACAAGC 60.097 50.000 8.98 8.60 0.00 4.01
3378 6129 2.135139 CGAGCAAGAGTTGTACAAGCA 58.865 47.619 8.98 0.00 0.00 3.91
3379 6130 2.096713 CGAGCAAGAGTTGTACAAGCAC 60.097 50.000 8.98 6.36 0.00 4.40
3380 6131 1.867233 AGCAAGAGTTGTACAAGCACG 59.133 47.619 8.98 0.00 0.00 5.34
3381 6132 1.864711 GCAAGAGTTGTACAAGCACGA 59.135 47.619 8.98 0.00 0.00 4.35
3382 6133 2.286833 GCAAGAGTTGTACAAGCACGAA 59.713 45.455 8.98 0.00 0.00 3.85
3383 6134 3.058914 GCAAGAGTTGTACAAGCACGAAT 60.059 43.478 8.98 0.00 0.00 3.34
3384 6135 4.554723 GCAAGAGTTGTACAAGCACGAATT 60.555 41.667 8.98 0.00 0.00 2.17
3385 6136 4.992381 AGAGTTGTACAAGCACGAATTC 57.008 40.909 8.98 0.00 0.00 2.17
3386 6137 3.428870 AGAGTTGTACAAGCACGAATTCG 59.571 43.478 25.64 25.64 46.33 3.34
3387 6138 2.478894 AGTTGTACAAGCACGAATTCGG 59.521 45.455 29.79 19.63 44.95 4.30
3388 6139 0.793861 TGTACAAGCACGAATTCGGC 59.206 50.000 29.79 26.91 44.95 5.54
3389 6140 0.247145 GTACAAGCACGAATTCGGCG 60.247 55.000 29.79 21.17 44.95 6.46
3390 6141 1.962092 TACAAGCACGAATTCGGCGC 61.962 55.000 29.79 28.44 44.95 6.53
3391 6142 3.047280 AAGCACGAATTCGGCGCA 61.047 55.556 32.44 0.00 44.95 6.09
3392 6143 3.308878 AAGCACGAATTCGGCGCAC 62.309 57.895 32.44 18.42 44.95 5.34
3394 6145 4.499023 CACGAATTCGGCGCACGG 62.499 66.667 29.79 7.98 44.95 4.94
3397 6148 4.096558 GAATTCGGCGCACGGCAA 62.097 61.111 17.00 10.07 46.16 4.52
3398 6149 4.101790 AATTCGGCGCACGGCAAG 62.102 61.111 17.00 1.33 46.16 4.01
3406 6157 2.676471 GCACGGCAAGGGGTTGAT 60.676 61.111 0.00 0.00 0.00 2.57
3407 6158 2.275380 GCACGGCAAGGGGTTGATT 61.275 57.895 0.00 0.00 0.00 2.57
3408 6159 1.586028 CACGGCAAGGGGTTGATTG 59.414 57.895 0.00 0.00 0.00 2.67
3409 6160 1.606313 ACGGCAAGGGGTTGATTGG 60.606 57.895 0.00 0.00 0.00 3.16
3410 6161 1.606313 CGGCAAGGGGTTGATTGGT 60.606 57.895 0.00 0.00 0.00 3.67
3411 6162 1.184970 CGGCAAGGGGTTGATTGGTT 61.185 55.000 0.00 0.00 0.00 3.67
3412 6163 1.055849 GGCAAGGGGTTGATTGGTTT 58.944 50.000 0.00 0.00 0.00 3.27
3413 6164 1.270785 GGCAAGGGGTTGATTGGTTTG 60.271 52.381 0.00 0.00 0.00 2.93
3414 6165 1.270785 GCAAGGGGTTGATTGGTTTGG 60.271 52.381 0.00 0.00 0.00 3.28
3415 6166 2.324541 CAAGGGGTTGATTGGTTTGGA 58.675 47.619 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.001449 TGAAGGTTGATGTCCTTATTAGGG 57.999 41.667 0.00 0.00 44.19 3.53
1 2 6.540189 CACTGAAGGTTGATGTCCTTATTAGG 59.460 42.308 0.00 0.00 44.19 2.69
2 3 7.331026 TCACTGAAGGTTGATGTCCTTATTAG 58.669 38.462 0.00 0.00 44.19 1.73
3 4 7.252612 TCACTGAAGGTTGATGTCCTTATTA 57.747 36.000 0.00 0.00 44.19 0.98
4 5 6.126863 TCACTGAAGGTTGATGTCCTTATT 57.873 37.500 0.00 0.00 44.19 1.40
41 42 5.752650 AGTTATGCCTAACCTAAGTTTCCC 58.247 41.667 8.11 0.00 38.40 3.97
45 46 6.704937 GCGATTAGTTATGCCTAACCTAAGTT 59.295 38.462 8.11 0.00 38.40 2.66
80 643 0.104304 AGATACTGCGGCGTTTAGGG 59.896 55.000 9.37 0.00 0.00 3.53
117 680 3.745975 TGTGACTGGAGATTGTTAAAGCG 59.254 43.478 0.00 0.00 0.00 4.68
146 709 6.903883 TGTTCAGTCTTGTGTTTTCTAGAC 57.096 37.500 0.00 0.00 37.79 2.59
512 1080 3.982372 GAGCCGTCCATTCGTCGCA 62.982 63.158 0.00 0.00 0.00 5.10
520 1088 3.329889 TGCAAGGGAGCCGTCCAT 61.330 61.111 0.00 0.00 46.07 3.41
583 1151 1.231221 TTTTGGTCGAATCCCGTGTG 58.769 50.000 0.00 0.00 39.75 3.82
615 1183 1.073125 TCAGAGGCCGATTTGGTTGAA 59.927 47.619 0.00 0.00 41.21 2.69
617 1185 0.804989 GTCAGAGGCCGATTTGGTTG 59.195 55.000 0.00 0.00 41.21 3.77
668 1279 1.687612 CACCTGCACCTCCTCCAAT 59.312 57.895 0.00 0.00 0.00 3.16
669 1280 2.528818 CCACCTGCACCTCCTCCAA 61.529 63.158 0.00 0.00 0.00 3.53
670 1281 2.770868 ATCCACCTGCACCTCCTCCA 62.771 60.000 0.00 0.00 0.00 3.86
671 1282 1.566298 AATCCACCTGCACCTCCTCC 61.566 60.000 0.00 0.00 0.00 4.30
672 1283 1.134371 GTAATCCACCTGCACCTCCTC 60.134 57.143 0.00 0.00 0.00 3.71
673 1284 0.912486 GTAATCCACCTGCACCTCCT 59.088 55.000 0.00 0.00 0.00 3.69
758 1389 0.179004 ATCTCTCTCCGCCGATGACT 60.179 55.000 0.00 0.00 0.00 3.41
805 1436 4.457496 CACTGTCTCGGCGGCCAT 62.457 66.667 20.71 0.00 0.00 4.40
874 1505 3.658725 AGTTACACTCTGGCCCATAGAT 58.341 45.455 2.71 0.00 0.00 1.98
876 1507 3.704566 TGTAGTTACACTCTGGCCCATAG 59.295 47.826 0.00 0.00 0.00 2.23
877 1508 3.715287 TGTAGTTACACTCTGGCCCATA 58.285 45.455 0.00 0.00 0.00 2.74
893 1528 6.097981 GGAAGCCCTAGTAATGTAGTTGTAGT 59.902 42.308 0.00 0.00 0.00 2.73
897 1532 4.704965 GGGAAGCCCTAGTAATGTAGTTG 58.295 47.826 0.00 0.00 41.34 3.16
960 1609 2.668212 CGCTTCGCTGGGGTTTCA 60.668 61.111 0.00 0.00 0.00 2.69
1208 1874 4.947147 TGGCGTGGTTCCAGGTGC 62.947 66.667 12.15 7.51 0.00 5.01
1257 1925 2.125912 CCGAGCCGAGTGAGTTGG 60.126 66.667 0.00 0.00 0.00 3.77
1258 1926 2.811317 GCCGAGCCGAGTGAGTTG 60.811 66.667 0.00 0.00 0.00 3.16
1259 1927 2.992114 AGCCGAGCCGAGTGAGTT 60.992 61.111 0.00 0.00 0.00 3.01
1260 1928 3.753434 CAGCCGAGCCGAGTGAGT 61.753 66.667 0.00 0.00 0.00 3.41
1293 1971 1.721487 CGCAATCGCTAAGGGTTGG 59.279 57.895 0.00 0.00 35.30 3.77
1310 1988 1.200103 CGCAGCAATACATCGAGCG 59.800 57.895 0.00 0.00 37.68 5.03
1505 2192 2.433604 TGTTTGCTTCCCAAATGCAAGA 59.566 40.909 0.00 0.00 45.52 3.02
1656 2412 0.248621 GCACCCAAATACTCATGCGC 60.249 55.000 0.00 0.00 0.00 6.09
1657 2413 1.382522 AGCACCCAAATACTCATGCG 58.617 50.000 0.00 0.00 38.12 4.73
1680 2436 7.094334 ACCTAATTGCAAAAGGTTCTTACTAGC 60.094 37.037 24.17 0.00 40.82 3.42
1681 2437 8.336801 ACCTAATTGCAAAAGGTTCTTACTAG 57.663 34.615 24.17 1.25 40.82 2.57
1691 2450 7.545615 GGATGACTAAAACCTAATTGCAAAAGG 59.454 37.037 23.09 23.09 36.42 3.11
1692 2451 8.087750 TGGATGACTAAAACCTAATTGCAAAAG 58.912 33.333 1.71 4.05 0.00 2.27
1695 2454 7.716799 ATGGATGACTAAAACCTAATTGCAA 57.283 32.000 0.00 0.00 0.00 4.08
1709 2471 4.753516 ATTCGGTGACAATGGATGACTA 57.246 40.909 0.00 0.00 0.00 2.59
1711 2474 4.260784 GCTTATTCGGTGACAATGGATGAC 60.261 45.833 0.00 0.00 0.00 3.06
1712 2475 3.876914 GCTTATTCGGTGACAATGGATGA 59.123 43.478 0.00 0.00 0.00 2.92
1713 2476 3.879295 AGCTTATTCGGTGACAATGGATG 59.121 43.478 0.00 0.00 0.00 3.51
1714 2477 3.879295 CAGCTTATTCGGTGACAATGGAT 59.121 43.478 0.00 0.00 34.46 3.41
1762 2542 4.497291 TTGTTTACCTCACCACAACTCT 57.503 40.909 0.00 0.00 0.00 3.24
1763 2543 5.298276 TCATTTGTTTACCTCACCACAACTC 59.702 40.000 0.00 0.00 0.00 3.01
1764 2544 5.197451 TCATTTGTTTACCTCACCACAACT 58.803 37.500 0.00 0.00 0.00 3.16
1765 2545 5.508200 TCATTTGTTTACCTCACCACAAC 57.492 39.130 0.00 0.00 0.00 3.32
1766 2546 6.207810 GGTATCATTTGTTTACCTCACCACAA 59.792 38.462 0.00 0.00 33.95 3.33
1767 2547 5.708230 GGTATCATTTGTTTACCTCACCACA 59.292 40.000 0.00 0.00 33.95 4.17
1784 2564 5.824624 CAGAAGTGGCATAAACAGGTATCAT 59.175 40.000 0.00 0.00 0.00 2.45
1789 2569 3.508845 ACAGAAGTGGCATAAACAGGT 57.491 42.857 0.00 0.00 0.00 4.00
1791 2571 7.202016 TCTAAAACAGAAGTGGCATAAACAG 57.798 36.000 0.00 0.00 0.00 3.16
1796 2577 5.500234 AGCATCTAAAACAGAAGTGGCATA 58.500 37.500 0.00 0.00 36.67 3.14
1853 3195 2.613725 GGCCATTTCCCAAGCTTTGAAG 60.614 50.000 0.00 0.00 0.00 3.02
1862 3204 2.036572 GGACGGGCCATTTCCCAA 59.963 61.111 4.39 0.00 46.92 4.12
1864 3206 1.753078 GAAGGACGGGCCATTTCCC 60.753 63.158 4.39 0.00 43.02 3.97
1957 3355 5.712152 AAAACAGATGGTTGATGTTCTCC 57.288 39.130 0.00 0.00 40.35 3.71
1966 4330 6.532657 GCAAGAATGGATAAAACAGATGGTTG 59.467 38.462 0.00 0.00 40.35 3.77
1967 4331 6.625740 CGCAAGAATGGATAAAACAGATGGTT 60.626 38.462 0.00 0.00 40.59 3.67
1970 4334 5.883661 ACGCAAGAATGGATAAAACAGATG 58.116 37.500 0.00 0.00 43.62 2.90
1989 4353 2.472695 AGTTAGAATGCCAGAACGCA 57.527 45.000 0.00 0.00 44.35 5.24
1990 4354 3.522553 ACTAGTTAGAATGCCAGAACGC 58.477 45.455 0.00 0.00 0.00 4.84
1992 4356 8.950208 AGAAATACTAGTTAGAATGCCAGAAC 57.050 34.615 0.00 0.00 0.00 3.01
2007 4544 7.437748 CCACTGGGAGATTGTAGAAATACTAG 58.562 42.308 0.00 0.00 35.59 2.57
2013 4550 2.354704 CGCCACTGGGAGATTGTAGAAA 60.355 50.000 0.00 0.00 35.76 2.52
2041 4628 7.661968 ACAAACAGTAGTATCGCATCATAGAT 58.338 34.615 0.00 0.00 0.00 1.98
2051 4638 8.851960 TTGCTTAGATACAAACAGTAGTATCG 57.148 34.615 15.34 7.33 46.95 2.92
2073 4713 4.494350 TCTTCAAATCACAAGCTCTTGC 57.506 40.909 9.36 0.00 44.03 4.01
2104 4744 8.023021 ACACTTGATTAGATATAAGCAGTGGA 57.977 34.615 21.02 1.86 33.32 4.02
2268 4908 5.048224 CGAGTAGAGGAACTTCTTGGTGTTA 60.048 44.000 0.00 0.00 41.55 2.41
2307 4947 1.112315 CCTCAGCCGCCTCTGTATCT 61.112 60.000 0.54 0.00 35.63 1.98
2310 4950 1.754621 CTCCTCAGCCGCCTCTGTA 60.755 63.158 0.54 0.00 35.63 2.74
2311 4951 3.073735 CTCCTCAGCCGCCTCTGT 61.074 66.667 0.54 0.00 35.63 3.41
2322 4962 4.382541 TCCTCGGCTGGCTCCTCA 62.383 66.667 0.00 0.00 0.00 3.86
2351 4997 1.968493 GTTTCCCTTTCCACCCTTTCC 59.032 52.381 0.00 0.00 0.00 3.13
2404 5050 4.335647 CCAGGGTCAAGCCGCTGT 62.336 66.667 0.00 0.00 38.44 4.40
2580 5232 2.158755 ACAACACAGAGCCTAGCAAACT 60.159 45.455 0.00 0.00 0.00 2.66
2588 5240 1.542030 CGAGTCTACAACACAGAGCCT 59.458 52.381 0.00 0.00 0.00 4.58
2626 5280 8.976353 GGGAGTACTAGATTATCATGTCATCAT 58.024 37.037 0.00 0.00 34.21 2.45
2627 5281 8.173412 AGGGAGTACTAGATTATCATGTCATCA 58.827 37.037 0.00 0.00 0.00 3.07
2628 5282 8.588290 AGGGAGTACTAGATTATCATGTCATC 57.412 38.462 0.00 0.00 0.00 2.92
2629 5283 7.617723 GGAGGGAGTACTAGATTATCATGTCAT 59.382 40.741 0.00 0.00 0.00 3.06
2630 5284 6.948886 GGAGGGAGTACTAGATTATCATGTCA 59.051 42.308 0.00 0.00 0.00 3.58
2631 5285 6.094325 CGGAGGGAGTACTAGATTATCATGTC 59.906 46.154 0.00 0.00 0.00 3.06
2671 5329 7.972832 TTAGATCACTAATCCAAACGTTGTT 57.027 32.000 0.00 0.00 34.21 2.83
2672 5330 7.972832 TTTAGATCACTAATCCAAACGTTGT 57.027 32.000 0.00 0.00 38.23 3.32
2673 5331 7.429340 GCATTTAGATCACTAATCCAAACGTTG 59.571 37.037 0.00 0.00 38.23 4.10
2708 5366 9.231297 GCATCTTAAGACTGATAGATACTCTCT 57.769 37.037 7.48 0.00 38.06 3.10
2710 5368 7.663905 ACGCATCTTAAGACTGATAGATACTCT 59.336 37.037 7.48 0.00 0.00 3.24
2712 5370 7.753309 ACGCATCTTAAGACTGATAGATACT 57.247 36.000 7.48 0.00 0.00 2.12
2728 5400 4.516698 ACAAATCTCAGACAAACGCATCTT 59.483 37.500 0.00 0.00 0.00 2.40
2735 5407 5.505286 CAGTCACACAAATCTCAGACAAAC 58.495 41.667 0.00 0.00 0.00 2.93
2736 5408 4.035558 GCAGTCACACAAATCTCAGACAAA 59.964 41.667 0.00 0.00 0.00 2.83
2772 5444 3.324108 TGGCCTCACCCCGGTTAC 61.324 66.667 3.32 0.00 37.83 2.50
2779 5451 1.301293 CTCCTTTCTGGCCTCACCC 59.699 63.158 3.32 0.00 37.83 4.61
2789 5469 3.100671 ACGCTAACAGATCCTCCTTTCT 58.899 45.455 0.00 0.00 0.00 2.52
2802 5510 3.244630 ACCCATTTCACCTTACGCTAACA 60.245 43.478 0.00 0.00 0.00 2.41
2894 5645 5.125578 GCTTGTAATGGTAAAAGGAAGGGAG 59.874 44.000 0.00 0.00 0.00 4.30
2948 5699 1.652563 GTGTGACCAAAGGGAACGC 59.347 57.895 0.00 0.00 38.05 4.84
2951 5702 1.890041 CGCGTGTGACCAAAGGGAA 60.890 57.895 0.00 0.00 38.05 3.97
2966 5717 4.344474 GCCGTCTATCCTCCCGCG 62.344 72.222 0.00 0.00 0.00 6.46
2969 5720 1.749033 CCTTGCCGTCTATCCTCCC 59.251 63.158 0.00 0.00 0.00 4.30
2970 5721 1.749033 CCCTTGCCGTCTATCCTCC 59.251 63.158 0.00 0.00 0.00 4.30
2973 5724 0.179054 GAACCCCTTGCCGTCTATCC 60.179 60.000 0.00 0.00 0.00 2.59
2989 5740 7.961325 TTTTGGCTCTAAAAATCCAATGAAC 57.039 32.000 0.00 0.00 38.27 3.18
3009 5760 7.040823 AGTCAGAGAGAGCTTTACCAAATTTTG 60.041 37.037 1.99 1.99 0.00 2.44
3046 5797 2.101249 AGCCACAACTGTCAAATGTTGG 59.899 45.455 10.03 5.58 45.36 3.77
3059 5810 7.816640 TCTTCTAATCAAACAATAGCCACAAC 58.183 34.615 0.00 0.00 0.00 3.32
3069 5820 8.954950 TTTTGGCAATTCTTCTAATCAAACAA 57.045 26.923 0.00 0.00 0.00 2.83
3139 5890 0.037017 TAGCAGCTACCCCGCAAAAA 59.963 50.000 0.00 0.00 0.00 1.94
3140 5891 0.037017 TTAGCAGCTACCCCGCAAAA 59.963 50.000 0.00 0.00 0.00 2.44
3141 5892 0.254747 ATTAGCAGCTACCCCGCAAA 59.745 50.000 0.00 0.00 0.00 3.68
3142 5893 0.254747 AATTAGCAGCTACCCCGCAA 59.745 50.000 0.00 0.00 0.00 4.85
3143 5894 0.254747 AAATTAGCAGCTACCCCGCA 59.745 50.000 0.00 0.00 0.00 5.69
3144 5895 2.249844 TAAATTAGCAGCTACCCCGC 57.750 50.000 0.00 0.00 0.00 6.13
3145 5896 4.935808 CCTAATAAATTAGCAGCTACCCCG 59.064 45.833 0.00 0.00 38.69 5.73
3146 5897 5.222068 ACCCTAATAAATTAGCAGCTACCCC 60.222 44.000 0.00 0.00 38.69 4.95
3147 5898 5.877491 ACCCTAATAAATTAGCAGCTACCC 58.123 41.667 0.00 0.00 38.69 3.69
3148 5899 6.294010 GCAACCCTAATAAATTAGCAGCTACC 60.294 42.308 0.00 0.00 38.69 3.18
3149 5900 6.486993 AGCAACCCTAATAAATTAGCAGCTAC 59.513 38.462 0.00 0.00 38.69 3.58
3150 5901 6.486657 CAGCAACCCTAATAAATTAGCAGCTA 59.513 38.462 0.00 0.00 38.69 3.32
3151 5902 5.300286 CAGCAACCCTAATAAATTAGCAGCT 59.700 40.000 0.00 0.00 38.69 4.24
3152 5903 5.299279 TCAGCAACCCTAATAAATTAGCAGC 59.701 40.000 4.49 5.46 38.69 5.25
3181 5932 0.031616 TGGTTTGGTTTGGAGGCCTT 60.032 50.000 6.77 0.00 0.00 4.35
3183 5934 0.392706 CTTGGTTTGGTTTGGAGGCC 59.607 55.000 0.00 0.00 0.00 5.19
3218 5969 1.679680 CATGGATTTAGCAGCACCCAG 59.320 52.381 0.00 0.00 0.00 4.45
3255 6006 1.151777 ACAACAAGCCGTGACACTCG 61.152 55.000 3.68 0.00 0.00 4.18
3296 6047 2.403252 AATTACAGAAGCACCGGGAG 57.597 50.000 6.32 0.00 0.00 4.30
3298 6049 3.574614 CAAAAATTACAGAAGCACCGGG 58.425 45.455 6.32 0.00 0.00 5.73
3302 6053 2.986479 CCCGCAAAAATTACAGAAGCAC 59.014 45.455 0.00 0.00 0.00 4.40
3320 6071 4.202430 ACAATCCTAGCTATTTTACCCCCG 60.202 45.833 0.00 0.00 0.00 5.73
3339 6090 4.214332 GCTCGTGAAAAGGAAGAAGACAAT 59.786 41.667 0.00 0.00 0.00 2.71
3340 6091 3.560068 GCTCGTGAAAAGGAAGAAGACAA 59.440 43.478 0.00 0.00 0.00 3.18
3341 6092 3.131396 GCTCGTGAAAAGGAAGAAGACA 58.869 45.455 0.00 0.00 0.00 3.41
3342 6093 3.131396 TGCTCGTGAAAAGGAAGAAGAC 58.869 45.455 0.00 0.00 0.00 3.01
3343 6094 3.469008 TGCTCGTGAAAAGGAAGAAGA 57.531 42.857 0.00 0.00 0.00 2.87
3344 6095 3.809832 TCTTGCTCGTGAAAAGGAAGAAG 59.190 43.478 4.84 0.00 44.85 2.85
3345 6096 3.804036 TCTTGCTCGTGAAAAGGAAGAA 58.196 40.909 4.84 0.00 44.85 2.52
3346 6097 3.181465 ACTCTTGCTCGTGAAAAGGAAGA 60.181 43.478 6.86 6.86 45.38 2.87
3347 6098 3.134458 ACTCTTGCTCGTGAAAAGGAAG 58.866 45.455 0.00 0.00 41.86 3.46
3348 6099 3.194005 ACTCTTGCTCGTGAAAAGGAA 57.806 42.857 0.00 0.00 0.00 3.36
3349 6100 2.872245 CAACTCTTGCTCGTGAAAAGGA 59.128 45.455 0.00 0.00 0.00 3.36
3350 6101 2.614057 ACAACTCTTGCTCGTGAAAAGG 59.386 45.455 0.00 0.00 0.00 3.11
3351 6102 3.951979 ACAACTCTTGCTCGTGAAAAG 57.048 42.857 0.00 0.00 0.00 2.27
3352 6103 4.185394 TGTACAACTCTTGCTCGTGAAAA 58.815 39.130 0.00 0.00 0.00 2.29
3353 6104 3.787785 TGTACAACTCTTGCTCGTGAAA 58.212 40.909 0.00 0.00 0.00 2.69
3354 6105 3.446310 TGTACAACTCTTGCTCGTGAA 57.554 42.857 0.00 0.00 0.00 3.18
3355 6106 3.381045 CTTGTACAACTCTTGCTCGTGA 58.619 45.455 3.59 0.00 0.00 4.35
3356 6107 2.096713 GCTTGTACAACTCTTGCTCGTG 60.097 50.000 3.59 0.00 0.00 4.35
3357 6108 2.135933 GCTTGTACAACTCTTGCTCGT 58.864 47.619 3.59 0.00 0.00 4.18
3358 6109 2.096713 GTGCTTGTACAACTCTTGCTCG 60.097 50.000 15.28 0.93 0.00 5.03
3359 6110 2.096713 CGTGCTTGTACAACTCTTGCTC 60.097 50.000 15.28 11.62 0.00 4.26
3360 6111 1.867233 CGTGCTTGTACAACTCTTGCT 59.133 47.619 15.28 0.00 0.00 3.91
3361 6112 1.864711 TCGTGCTTGTACAACTCTTGC 59.135 47.619 3.59 7.01 0.00 4.01
3362 6113 4.732285 ATTCGTGCTTGTACAACTCTTG 57.268 40.909 3.59 0.00 0.00 3.02
3363 6114 4.084537 CGAATTCGTGCTTGTACAACTCTT 60.085 41.667 19.67 0.00 34.11 2.85
3364 6115 3.428870 CGAATTCGTGCTTGTACAACTCT 59.571 43.478 19.67 0.00 34.11 3.24
3365 6116 3.423123 CCGAATTCGTGCTTGTACAACTC 60.423 47.826 25.10 0.16 37.74 3.01
3366 6117 2.478894 CCGAATTCGTGCTTGTACAACT 59.521 45.455 25.10 0.00 37.74 3.16
3367 6118 2.834689 CCGAATTCGTGCTTGTACAAC 58.165 47.619 25.10 2.86 37.74 3.32
3368 6119 1.195900 GCCGAATTCGTGCTTGTACAA 59.804 47.619 25.10 8.28 37.74 2.41
3369 6120 0.793861 GCCGAATTCGTGCTTGTACA 59.206 50.000 25.10 0.00 37.74 2.90
3370 6121 0.247145 CGCCGAATTCGTGCTTGTAC 60.247 55.000 27.14 9.28 37.74 2.90
3371 6122 1.962092 GCGCCGAATTCGTGCTTGTA 61.962 55.000 27.14 0.00 36.39 2.41
3372 6123 2.860293 CGCCGAATTCGTGCTTGT 59.140 55.556 27.14 0.00 37.74 3.16
3373 6124 2.574212 GCGCCGAATTCGTGCTTG 60.574 61.111 27.14 18.59 36.39 4.01
3374 6125 3.047280 TGCGCCGAATTCGTGCTT 61.047 55.556 30.04 0.00 38.87 3.91
3375 6126 3.788766 GTGCGCCGAATTCGTGCT 61.789 61.111 30.04 0.00 38.87 4.40
3377 6128 4.499023 CCGTGCGCCGAATTCGTG 62.499 66.667 25.10 17.99 39.56 4.35
3380 6131 4.096558 TTGCCGTGCGCCGAATTC 62.097 61.111 17.96 0.00 39.56 2.17
3381 6132 4.101790 CTTGCCGTGCGCCGAATT 62.102 61.111 17.96 0.00 39.56 2.17
3389 6140 2.275380 AATCAACCCCTTGCCGTGC 61.275 57.895 0.00 0.00 0.00 5.34
3390 6141 1.586028 CAATCAACCCCTTGCCGTG 59.414 57.895 0.00 0.00 0.00 4.94
3391 6142 1.606313 CCAATCAACCCCTTGCCGT 60.606 57.895 0.00 0.00 0.00 5.68
3392 6143 1.184970 AACCAATCAACCCCTTGCCG 61.185 55.000 0.00 0.00 0.00 5.69
3393 6144 1.055849 AAACCAATCAACCCCTTGCC 58.944 50.000 0.00 0.00 0.00 4.52
3394 6145 1.270785 CCAAACCAATCAACCCCTTGC 60.271 52.381 0.00 0.00 0.00 4.01
3395 6146 2.324541 TCCAAACCAATCAACCCCTTG 58.675 47.619 0.00 0.00 0.00 3.61
3396 6147 2.785357 TCCAAACCAATCAACCCCTT 57.215 45.000 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.