Multiple sequence alignment - TraesCS7D01G003500

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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 TraesCS7D01G003500 chr7D 100.000 4377 0 0 1 4377 2039864 2035488 0.000000e+00 8083.0
1 TraesCS7D01G003500 chr4A 89.140 2256 145 38 1694 3917 742607563 742605376 0.000000e+00 2717.0
2 TraesCS7D01G003500 chr4A 87.522 1146 76 28 561 1688 742608709 742607613 0.000000e+00 1262.0
3 TraesCS7D01G003500 chr4A 87.479 591 50 8 876 1466 742652299 742651733 0.000000e+00 660.0
4 TraesCS7D01G003500 chr4A 96.124 258 10 0 1 258 742609454 742609197 5.230000e-114 422.0
5 TraesCS7D01G003500 chr4A 88.168 262 21 5 255 506 742608980 742608719 1.980000e-78 303.0
6 TraesCS7D01G003500 chr4A 90.741 216 20 0 166 381 742675479 742675264 5.540000e-74 289.0
7 TraesCS7D01G003500 chr4A 94.624 186 10 0 1 186 742707923 742707738 5.540000e-74 289.0
8 TraesCS7D01G003500 chr4A 87.845 181 12 6 3946 4118 644004864 644004686 2.060000e-48 204.0
9 TraesCS7D01G003500 chr4A 80.165 242 31 12 1906 2141 742651468 742651238 9.740000e-37 165.0
10 TraesCS7D01G003500 chr4A 79.710 138 13 9 1624 1754 742651647 742651518 7.800000e-13 86.1
11 TraesCS7D01G003500 chr4A 100.000 31 0 0 1508 1538 742651727 742651697 1.700000e-04 58.4
12 TraesCS7D01G003500 chrUn 89.460 1907 101 43 141 2012 81433459 81435300 0.000000e+00 2316.0
13 TraesCS7D01G003500 chrUn 95.021 1205 41 4 2035 3234 81435364 81436554 0.000000e+00 1875.0
14 TraesCS7D01G003500 chrUn 95.021 1205 41 4 2035 3234 336021926 336023116 0.000000e+00 1875.0
15 TraesCS7D01G003500 chrUn 94.711 605 22 4 30 634 81529367 81529961 0.000000e+00 931.0
16 TraesCS7D01G003500 chrUn 90.746 670 33 12 3196 3859 81436572 81437218 0.000000e+00 867.0
17 TraesCS7D01G003500 chrUn 90.746 670 33 12 3196 3859 336023134 336023780 0.000000e+00 867.0
18 TraesCS7D01G003500 chrUn 88.204 373 36 5 226 594 81527810 81528178 5.200000e-119 438.0
19 TraesCS7D01G003500 chrUn 86.939 245 15 6 4134 4377 81437358 81437586 4.340000e-65 259.0
20 TraesCS7D01G003500 chrUn 86.939 245 15 6 4134 4377 336023920 336024148 4.340000e-65 259.0
21 TraesCS7D01G003500 chrUn 91.875 160 7 5 1857 2012 336021705 336021862 7.370000e-53 219.0
22 TraesCS7D01G003500 chr5B 80.995 1789 206 67 1827 3577 518482444 518484136 0.000000e+00 1297.0
23 TraesCS7D01G003500 chr5B 81.941 814 107 19 2773 3575 518474858 518475642 0.000000e+00 652.0
24 TraesCS7D01G003500 chr5B 79.604 858 110 35 809 1636 518481347 518482169 4.950000e-154 555.0
25 TraesCS7D01G003500 chr5B 77.074 458 72 16 1778 2223 310664230 310663794 2.630000e-57 233.0
26 TraesCS7D01G003500 chr5B 84.916 179 17 7 3945 4118 602937006 602937179 5.820000e-39 172.0
27 TraesCS7D01G003500 chr5B 86.624 157 12 4 2380 2535 518473834 518473982 9.740000e-37 165.0
28 TraesCS7D01G003500 chr5D 81.254 1739 184 63 1881 3577 429290436 429292074 0.000000e+00 1275.0
29 TraesCS7D01G003500 chr5D 78.675 830 107 36 825 1626 429289342 429290129 5.090000e-134 488.0
30 TraesCS7D01G003500 chr5A 80.687 1688 186 64 1827 3464 545074648 545076245 0.000000e+00 1182.0
31 TraesCS7D01G003500 chr5A 78.656 848 112 35 809 1629 545073561 545074366 2.350000e-137 499.0
32 TraesCS7D01G003500 chr5A 83.149 362 42 10 3228 3577 545060725 545061079 3.290000e-81 313.0
33 TraesCS7D01G003500 chr5A 78.723 423 33 15 2243 2644 545059978 545060364 3.400000e-56 230.0
34 TraesCS7D01G003500 chr5A 85.039 127 11 6 2773 2891 545060560 545060686 5.940000e-24 122.0
35 TraesCS7D01G003500 chr7A 94.545 605 23 4 30 634 1574367 1574961 0.000000e+00 926.0
36 TraesCS7D01G003500 chr7A 87.936 373 37 5 226 594 1572811 1573179 2.420000e-117 433.0
37 TraesCS7D01G003500 chr7A 83.721 172 26 2 2053 2223 264052218 264052388 1.260000e-35 161.0
38 TraesCS7D01G003500 chr6D 80.049 411 59 16 1827 2223 429327276 429326875 2.580000e-72 283.0
39 TraesCS7D01G003500 chr1D 79.902 408 57 18 1827 2220 458737328 458737724 4.310000e-70 276.0
40 TraesCS7D01G003500 chr1D 79.661 413 57 20 1827 2223 319556401 319556000 5.580000e-69 272.0
41 TraesCS7D01G003500 chr1B 84.739 249 35 3 4131 4377 288401370 288401123 3.380000e-61 246.0
42 TraesCS7D01G003500 chr7B 91.477 176 11 4 3946 4118 221831361 221831187 5.660000e-59 239.0
43 TraesCS7D01G003500 chr7B 89.032 155 12 5 3956 4107 509600412 509600564 2.080000e-43 187.0
44 TraesCS7D01G003500 chr2A 90.110 182 7 5 3946 4118 774587799 774587620 4.400000e-55 226.0
45 TraesCS7D01G003500 chr2A 85.057 174 21 3 3948 4120 779198220 779198389 5.820000e-39 172.0
46 TraesCS7D01G003500 chr2A 85.629 167 15 6 3960 4118 686175480 686175645 2.710000e-37 167.0
47 TraesCS7D01G003500 chr2A 96.429 56 1 1 4047 4102 3409028 3409082 1.680000e-14 91.6
48 TraesCS7D01G003500 chr3D 88.649 185 8 7 3946 4118 134006617 134006800 3.430000e-51 213.0
49 TraesCS7D01G003500 chr2B 85.864 191 15 5 3949 4127 179131354 179131164 4.470000e-45 193.0
50 TraesCS7D01G003500 chr2B 85.946 185 14 7 3946 4118 17047372 17047556 2.080000e-43 187.0
51 TraesCS7D01G003500 chr3B 85.714 182 17 4 3946 4118 559755752 559755571 2.690000e-42 183.0
52 TraesCS7D01G003500 chr6B 84.173 139 21 1 4158 4295 455085231 455085093 2.750000e-27 134.0


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 TraesCS7D01G003500 chr7D 2035488 2039864 4376 True 8083.000000 8083 100.000000 1 4377 1 chr7D.!!$R1 4376
1 TraesCS7D01G003500 chr4A 742605376 742609454 4078 True 1176.000000 2717 90.238500 1 3917 4 chr4A.!!$R4 3916
2 TraesCS7D01G003500 chr4A 742651238 742652299 1061 True 242.375000 660 86.838500 876 2141 4 chr4A.!!$R5 1265
3 TraesCS7D01G003500 chrUn 81433459 81437586 4127 False 1329.250000 2316 90.541500 141 4377 4 chrUn.!!$F1 4236
4 TraesCS7D01G003500 chrUn 336021705 336024148 2443 False 805.000000 1875 91.145250 1857 4377 4 chrUn.!!$F3 2520
5 TraesCS7D01G003500 chrUn 81527810 81529961 2151 False 684.500000 931 91.457500 30 634 2 chrUn.!!$F2 604
6 TraesCS7D01G003500 chr5B 518481347 518484136 2789 False 926.000000 1297 80.299500 809 3577 2 chr5B.!!$F3 2768
7 TraesCS7D01G003500 chr5B 518473834 518475642 1808 False 408.500000 652 84.282500 2380 3575 2 chr5B.!!$F2 1195
8 TraesCS7D01G003500 chr5D 429289342 429292074 2732 False 881.500000 1275 79.964500 825 3577 2 chr5D.!!$F1 2752
9 TraesCS7D01G003500 chr5A 545073561 545076245 2684 False 840.500000 1182 79.671500 809 3464 2 chr5A.!!$F2 2655
10 TraesCS7D01G003500 chr5A 545059978 545061079 1101 False 221.666667 313 82.303667 2243 3577 3 chr5A.!!$F1 1334
11 TraesCS7D01G003500 chr7A 1572811 1574961 2150 False 679.500000 926 91.240500 30 634 2 chr7A.!!$F2 604

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
766 2535 0.042535 CGCACGTCTCGAGAGATCTC 60.043 60.0 17.22 15.29 39.97 2.75 F
2347 4458 0.036388 TTTCGCTGCCTCGAGGAATT 60.036 50.0 35.69 0.00 39.82 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2604 5038 0.034670 GAAGGCCCAGCTGAGTGATT 60.035 55.0 17.39 2.95 0.0 2.57 R
4094 7010 0.615331 TGCTCTTTTGATCCCGAGCT 59.385 50.0 17.64 0.00 46.7 4.09 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
149 1678 5.103290 ACGTGCGAATACTCAAAACAAAT 57.897 34.783 0.00 0.00 0.00 2.32
178 1707 0.834612 AAGGGCGATGAATAACCGGA 59.165 50.000 9.46 0.00 0.00 5.14
244 1773 5.925506 TTTATGAGACCTACGATCCACAA 57.074 39.130 0.00 0.00 0.00 3.33
326 2078 2.561478 TGGGGTTTCTTTTCTCTCCG 57.439 50.000 0.00 0.00 0.00 4.63
355 2107 4.640789 AGTCGCCACTACTTATCTCTTG 57.359 45.455 0.00 0.00 0.00 3.02
358 2114 5.297278 AGTCGCCACTACTTATCTCTTGTAG 59.703 44.000 0.00 0.00 39.43 2.74
431 2190 6.294843 GGAGCACCTCTATTTATAGGACTGTC 60.295 46.154 0.00 0.00 36.66 3.51
479 2238 2.033299 GTGACATGTGACACCAACCAAG 59.967 50.000 10.82 0.00 35.29 3.61
492 2251 2.571212 CAACCAAGCTCCACAACACTA 58.429 47.619 0.00 0.00 0.00 2.74
501 2260 5.967088 AGCTCCACAACACTATGTACTAAG 58.033 41.667 0.00 0.00 30.84 2.18
553 2312 8.567285 TCTTTTCTCTCCAACCAAAATATCTC 57.433 34.615 0.00 0.00 0.00 2.75
565 2324 9.613428 CAACCAAAATATCTCCACTACTTATCA 57.387 33.333 0.00 0.00 0.00 2.15
594 2353 8.822652 ATCTTTTGACATAGCCTTTTCTTTTG 57.177 30.769 0.00 0.00 0.00 2.44
595 2354 8.006298 TCTTTTGACATAGCCTTTTCTTTTGA 57.994 30.769 0.00 0.00 0.00 2.69
596 2355 7.920682 TCTTTTGACATAGCCTTTTCTTTTGAC 59.079 33.333 0.00 0.00 0.00 3.18
641 2400 8.825667 AGAGAAAGAGAAATCTCACAAAGTAC 57.174 34.615 12.65 0.00 45.21 2.73
644 2403 6.771188 AAGAGAAATCTCACAAAGTACGTG 57.229 37.500 12.65 0.00 45.21 4.49
646 2405 6.281405 AGAGAAATCTCACAAAGTACGTGTT 58.719 36.000 12.65 0.00 45.21 3.32
647 2406 6.201044 AGAGAAATCTCACAAAGTACGTGTTG 59.799 38.462 12.65 2.42 45.21 3.33
648 2407 5.236478 AGAAATCTCACAAAGTACGTGTTGG 59.764 40.000 0.00 0.00 35.79 3.77
670 2429 5.066246 TGGGACACGTTTTTAAGTAACCAAG 59.934 40.000 0.00 0.00 0.00 3.61
674 2433 7.218773 GGACACGTTTTTAAGTAACCAAGAAAC 59.781 37.037 0.00 0.00 0.00 2.78
675 2434 7.592051 ACACGTTTTTAAGTAACCAAGAAACA 58.408 30.769 0.00 0.00 0.00 2.83
678 2437 9.642327 ACGTTTTTAAGTAACCAAGAAACAAAT 57.358 25.926 0.00 0.00 0.00 2.32
687 2446 3.389221 CCAAGAAACAAATTGGGGTTCG 58.611 45.455 0.00 0.00 41.92 3.95
688 2447 3.181470 CCAAGAAACAAATTGGGGTTCGT 60.181 43.478 0.00 0.00 41.92 3.85
689 2448 3.726291 AGAAACAAATTGGGGTTCGTG 57.274 42.857 0.00 0.00 0.00 4.35
690 2449 3.292460 AGAAACAAATTGGGGTTCGTGA 58.708 40.909 0.00 0.00 0.00 4.35
757 2526 3.713615 CTACCGGACGCACGTCTCG 62.714 68.421 21.19 20.44 44.04 4.04
759 2528 4.813526 CCGGACGCACGTCTCGAG 62.814 72.222 25.05 5.93 44.04 4.04
760 2529 3.785499 CGGACGCACGTCTCGAGA 61.785 66.667 21.19 12.08 44.04 4.04
761 2530 2.098680 GGACGCACGTCTCGAGAG 59.901 66.667 17.22 12.48 44.04 3.20
762 2531 2.389020 GGACGCACGTCTCGAGAGA 61.389 63.158 17.22 0.00 44.04 3.10
763 2532 1.707239 GGACGCACGTCTCGAGAGAT 61.707 60.000 17.22 3.64 44.04 2.75
764 2533 0.315544 GACGCACGTCTCGAGAGATC 60.316 60.000 17.22 3.11 41.57 2.75
765 2534 0.741574 ACGCACGTCTCGAGAGATCT 60.742 55.000 17.22 0.00 39.97 2.75
766 2535 0.042535 CGCACGTCTCGAGAGATCTC 60.043 60.000 17.22 15.29 39.97 2.75
767 2536 0.306533 GCACGTCTCGAGAGATCTCC 59.693 60.000 17.22 9.79 39.97 3.71
768 2537 1.657822 CACGTCTCGAGAGATCTCCA 58.342 55.000 17.22 2.89 39.97 3.86
769 2538 2.217750 CACGTCTCGAGAGATCTCCAT 58.782 52.381 17.22 1.11 39.97 3.41
770 2539 2.032117 CACGTCTCGAGAGATCTCCATG 60.032 54.545 17.22 9.38 39.97 3.66
975 2759 2.171448 GGTAGATGAATGTGGAGTGCCT 59.829 50.000 0.00 0.00 34.31 4.75
991 2778 2.259818 CTTCACTCTCCGCACGCT 59.740 61.111 0.00 0.00 0.00 5.07
1090 2901 3.138798 TCGTCTACTGCTCCGCCC 61.139 66.667 0.00 0.00 0.00 6.13
1392 3215 4.760047 GCCTGGCTCGCCGAGAAA 62.760 66.667 20.05 3.47 39.42 2.52
1399 3222 4.735132 TCGCCGAGAAACTGCCCG 62.735 66.667 0.00 0.00 0.00 6.13
1440 3263 7.348080 TCAGGTACCTCAACATCTAATACTG 57.652 40.000 12.84 0.00 0.00 2.74
1441 3264 6.895756 TCAGGTACCTCAACATCTAATACTGT 59.104 38.462 12.84 0.00 0.00 3.55
1442 3265 6.980978 CAGGTACCTCAACATCTAATACTGTG 59.019 42.308 12.84 0.00 0.00 3.66
1443 3266 5.753921 GGTACCTCAACATCTAATACTGTGC 59.246 44.000 4.06 0.00 0.00 4.57
1444 3267 5.683876 ACCTCAACATCTAATACTGTGCT 57.316 39.130 0.00 0.00 0.00 4.40
1455 3278 9.507280 CATCTAATACTGTGCTTGGTTAATTTG 57.493 33.333 0.00 0.00 0.00 2.32
1467 3295 7.071414 GCTTGGTTAATTTGCAAATTTCACTC 58.929 34.615 35.18 24.24 39.24 3.51
1470 3298 6.928492 TGGTTAATTTGCAAATTTCACTCCTC 59.072 34.615 35.18 20.64 39.24 3.71
1564 3408 4.094887 GGACAGTTTGATTGCGTGATACAT 59.905 41.667 0.00 0.00 0.00 2.29
1565 3409 5.391950 GGACAGTTTGATTGCGTGATACATT 60.392 40.000 0.00 0.00 0.00 2.71
1566 3410 5.631026 ACAGTTTGATTGCGTGATACATTC 58.369 37.500 0.00 0.00 0.00 2.67
1567 3411 5.412594 ACAGTTTGATTGCGTGATACATTCT 59.587 36.000 0.00 0.00 0.00 2.40
1643 3522 5.440207 TCAAGGGAGAATGATCACAATCA 57.560 39.130 0.00 0.00 45.73 2.57
1669 3559 3.181471 ACAAAGTGAGTGAGAGTGAGTGG 60.181 47.826 0.00 0.00 0.00 4.00
1727 3675 6.368791 TGTGCTATCTGTCTGTGATGTAAAAC 59.631 38.462 0.00 0.00 0.00 2.43
1728 3676 6.368791 GTGCTATCTGTCTGTGATGTAAAACA 59.631 38.462 0.00 0.00 0.00 2.83
1729 3677 6.934083 TGCTATCTGTCTGTGATGTAAAACAA 59.066 34.615 0.00 0.00 0.00 2.83
1730 3678 7.607607 TGCTATCTGTCTGTGATGTAAAACAAT 59.392 33.333 0.00 0.00 0.00 2.71
1760 3712 5.694006 GGAAGATCTCTTTCGTGATACATGG 59.306 44.000 0.00 0.00 36.11 3.66
1788 3802 8.102676 TGTAATGGTGGATCGATGATTAATGAT 58.897 33.333 0.54 0.00 0.00 2.45
1830 3844 4.468765 TCTCCTCTGAAAGATTGCTCAG 57.531 45.455 0.00 0.00 45.62 3.35
1868 3892 4.019501 AGCTTGGATCTTTGTCTGACTGAT 60.020 41.667 9.51 9.70 0.00 2.90
1941 3965 8.188139 AGTTTGACTGTATAAACCACACAAAAG 58.812 33.333 13.36 0.00 37.47 2.27
2003 4093 2.147150 GAACCAGTGAGAAGCCTGAAC 58.853 52.381 0.00 0.00 0.00 3.18
2004 4094 1.131638 ACCAGTGAGAAGCCTGAACA 58.868 50.000 0.00 0.00 0.00 3.18
2005 4095 1.490490 ACCAGTGAGAAGCCTGAACAA 59.510 47.619 0.00 0.00 0.00 2.83
2006 4096 1.876156 CCAGTGAGAAGCCTGAACAAC 59.124 52.381 0.00 0.00 0.00 3.32
2007 4097 2.564771 CAGTGAGAAGCCTGAACAACA 58.435 47.619 0.00 0.00 0.00 3.33
2008 4098 2.945008 CAGTGAGAAGCCTGAACAACAA 59.055 45.455 0.00 0.00 0.00 2.83
2009 4099 3.378112 CAGTGAGAAGCCTGAACAACAAA 59.622 43.478 0.00 0.00 0.00 2.83
2010 4100 4.016444 AGTGAGAAGCCTGAACAACAAAA 58.984 39.130 0.00 0.00 0.00 2.44
2011 4101 4.462483 AGTGAGAAGCCTGAACAACAAAAA 59.538 37.500 0.00 0.00 0.00 1.94
2016 4106 1.587946 GCCTGAACAACAAAAAGCACG 59.412 47.619 0.00 0.00 0.00 5.34
2088 4180 3.521995 TGCTGTTGCAGTCTAGCTC 57.478 52.632 12.58 0.00 45.31 4.09
2130 4226 3.925379 TGCTACATACTTCATATGGGCG 58.075 45.455 2.13 0.00 44.51 6.13
2156 4252 7.105241 AGGCTAATTGTCAATCTTCCAATTC 57.895 36.000 0.00 0.00 39.04 2.17
2158 4254 6.976925 GGCTAATTGTCAATCTTCCAATTCAG 59.023 38.462 0.00 0.00 39.04 3.02
2240 4343 7.938140 TCCCTAATTGAGAAAATTGTACAGG 57.062 36.000 0.00 0.00 0.00 4.00
2347 4458 0.036388 TTTCGCTGCCTCGAGGAATT 60.036 50.000 35.69 0.00 39.82 2.17
2451 4562 4.573607 TGCACTCTCTCAATACATTCATGC 59.426 41.667 0.00 0.00 0.00 4.06
2477 4588 1.674221 GGACCTCAGATATGCGATGCC 60.674 57.143 0.00 0.00 0.00 4.40
2666 5100 2.563179 ACACATACAGACCACTCACTCC 59.437 50.000 0.00 0.00 0.00 3.85
2672 5324 1.206610 CAGACCACTCACTCCCTCATG 59.793 57.143 0.00 0.00 0.00 3.07
2764 5549 7.169140 ACATTGCGAACTTGGTTTAATTTCTTC 59.831 33.333 0.00 0.00 0.00 2.87
2780 5565 0.317603 CTTCACAGCAACAGCAGCAC 60.318 55.000 0.00 0.00 0.00 4.40
2843 5639 6.789457 ACTCATGTTATAATCCATCCTCCTCA 59.211 38.462 0.00 0.00 0.00 3.86
3238 6098 8.180920 CGAGTTTGGGTTTCAAATTTGAATTTT 58.819 29.630 29.13 12.48 45.65 1.82
3393 6253 5.119279 CAGGATAAATTCACGAGCGATTAGG 59.881 44.000 0.00 0.00 0.00 2.69
3501 6374 9.658475 TTTGTAGTTACATCTTCATTTTTGTCG 57.342 29.630 0.00 0.00 35.89 4.35
3502 6375 8.596271 TGTAGTTACATCTTCATTTTTGTCGA 57.404 30.769 0.00 0.00 0.00 4.20
3787 6665 4.225042 TCAGCCCTTGTCTATGTGTACATT 59.775 41.667 0.00 0.00 37.76 2.71
3882 6789 8.547967 TTGGTGAATGTATTCTCTGAAAGTAC 57.452 34.615 6.21 0.00 37.67 2.73
3891 6798 9.261180 TGTATTCTCTGAAAGTACTGTTTCTTG 57.739 33.333 0.00 0.00 37.34 3.02
3893 6800 8.964476 ATTCTCTGAAAGTACTGTTTCTTGAA 57.036 30.769 0.00 4.81 37.34 2.69
3917 6824 6.672266 AAAGAGAGACAAATGACTCACCTA 57.328 37.500 13.76 0.00 38.87 3.08
3918 6825 6.672266 AAGAGAGACAAATGACTCACCTAA 57.328 37.500 13.76 0.00 38.87 2.69
3919 6826 6.672266 AGAGAGACAAATGACTCACCTAAA 57.328 37.500 13.76 0.00 38.87 1.85
3920 6827 7.067496 AGAGAGACAAATGACTCACCTAAAA 57.933 36.000 13.76 0.00 38.87 1.52
3922 6829 6.831976 AGAGACAAATGACTCACCTAAAAGT 58.168 36.000 13.76 0.00 38.87 2.66
3929 6845 4.883083 TGACTCACCTAAAAGTACTGCAG 58.117 43.478 13.48 13.48 0.00 4.41
3944 6860 8.982091 AAGTACTGCAGTCTCTATTACTATCA 57.018 34.615 25.56 0.00 0.00 2.15
3945 6861 8.982091 AGTACTGCAGTCTCTATTACTATCAA 57.018 34.615 25.56 0.00 0.00 2.57
3946 6862 9.581289 AGTACTGCAGTCTCTATTACTATCAAT 57.419 33.333 25.56 0.00 0.00 2.57
3947 6863 9.834628 GTACTGCAGTCTCTATTACTATCAATC 57.165 37.037 25.56 0.00 0.00 2.67
3948 6864 7.589395 ACTGCAGTCTCTATTACTATCAATCG 58.411 38.462 15.25 0.00 0.00 3.34
3949 6865 7.445707 ACTGCAGTCTCTATTACTATCAATCGA 59.554 37.037 15.25 0.00 0.00 3.59
3950 6866 8.341892 TGCAGTCTCTATTACTATCAATCGAT 57.658 34.615 0.00 0.00 35.50 3.59
3951 6867 8.797438 TGCAGTCTCTATTACTATCAATCGATT 58.203 33.333 4.39 4.39 32.73 3.34
3952 6868 9.632807 GCAGTCTCTATTACTATCAATCGATTT 57.367 33.333 8.21 0.00 32.73 2.17
3964 6880 9.301153 ACTATCAATCGATTTTGTTATTTTGCC 57.699 29.630 8.21 0.00 32.73 4.52
3965 6881 6.959671 TCAATCGATTTTGTTATTTTGCCC 57.040 33.333 8.21 0.00 0.00 5.36
3966 6882 6.459066 TCAATCGATTTTGTTATTTTGCCCA 58.541 32.000 8.21 0.00 0.00 5.36
3967 6883 6.589523 TCAATCGATTTTGTTATTTTGCCCAG 59.410 34.615 8.21 0.00 0.00 4.45
3968 6884 5.713792 TCGATTTTGTTATTTTGCCCAGA 57.286 34.783 0.00 0.00 0.00 3.86
3969 6885 6.090483 TCGATTTTGTTATTTTGCCCAGAA 57.910 33.333 0.00 0.00 0.00 3.02
3970 6886 5.923684 TCGATTTTGTTATTTTGCCCAGAAC 59.076 36.000 0.00 0.00 0.00 3.01
3971 6887 5.925969 CGATTTTGTTATTTTGCCCAGAACT 59.074 36.000 0.00 0.00 0.00 3.01
3972 6888 6.089417 CGATTTTGTTATTTTGCCCAGAACTC 59.911 38.462 0.00 0.00 0.00 3.01
3973 6889 4.864704 TTGTTATTTTGCCCAGAACTCC 57.135 40.909 0.00 0.00 0.00 3.85
3974 6890 3.838565 TGTTATTTTGCCCAGAACTCCA 58.161 40.909 0.00 0.00 0.00 3.86
3975 6891 3.572255 TGTTATTTTGCCCAGAACTCCAC 59.428 43.478 0.00 0.00 0.00 4.02
3976 6892 2.380064 ATTTTGCCCAGAACTCCACA 57.620 45.000 0.00 0.00 0.00 4.17
3977 6893 2.151502 TTTTGCCCAGAACTCCACAA 57.848 45.000 0.00 0.00 0.00 3.33
3978 6894 2.151502 TTTGCCCAGAACTCCACAAA 57.848 45.000 0.00 0.00 0.00 2.83
3979 6895 2.380064 TTGCCCAGAACTCCACAAAT 57.620 45.000 0.00 0.00 0.00 2.32
3980 6896 1.619654 TGCCCAGAACTCCACAAATG 58.380 50.000 0.00 0.00 0.00 2.32
3981 6897 1.133513 TGCCCAGAACTCCACAAATGT 60.134 47.619 0.00 0.00 0.00 2.71
3982 6898 1.541588 GCCCAGAACTCCACAAATGTC 59.458 52.381 0.00 0.00 0.00 3.06
3983 6899 2.862541 CCCAGAACTCCACAAATGTCA 58.137 47.619 0.00 0.00 0.00 3.58
3984 6900 3.424703 CCCAGAACTCCACAAATGTCAT 58.575 45.455 0.00 0.00 0.00 3.06
3985 6901 3.828451 CCCAGAACTCCACAAATGTCATT 59.172 43.478 0.00 0.00 0.00 2.57
3986 6902 4.281688 CCCAGAACTCCACAAATGTCATTT 59.718 41.667 4.91 4.91 0.00 2.32
3987 6903 5.464168 CCAGAACTCCACAAATGTCATTTC 58.536 41.667 7.87 0.00 0.00 2.17
3988 6904 5.149273 CAGAACTCCACAAATGTCATTTCG 58.851 41.667 7.87 6.94 0.00 3.46
3989 6905 5.049474 CAGAACTCCACAAATGTCATTTCGA 60.049 40.000 7.87 3.98 0.00 3.71
3990 6906 5.707298 AGAACTCCACAAATGTCATTTCGAT 59.293 36.000 7.87 0.00 0.00 3.59
3991 6907 5.551760 ACTCCACAAATGTCATTTCGATC 57.448 39.130 7.87 0.00 0.00 3.69
3992 6908 5.248640 ACTCCACAAATGTCATTTCGATCT 58.751 37.500 7.87 0.00 0.00 2.75
3993 6909 5.122869 ACTCCACAAATGTCATTTCGATCTG 59.877 40.000 7.87 0.00 0.00 2.90
3994 6910 5.244755 TCCACAAATGTCATTTCGATCTGA 58.755 37.500 7.87 0.00 0.00 3.27
3995 6911 5.704978 TCCACAAATGTCATTTCGATCTGAA 59.295 36.000 7.87 0.00 33.85 3.02
4006 6922 3.492421 TCGATCTGAAATTTTGCAGGC 57.508 42.857 6.96 0.00 33.05 4.85
4007 6923 2.819019 TCGATCTGAAATTTTGCAGGCA 59.181 40.909 6.96 0.00 33.05 4.75
4008 6924 3.255395 TCGATCTGAAATTTTGCAGGCAA 59.745 39.130 1.93 1.93 33.05 4.52
4009 6925 4.082081 TCGATCTGAAATTTTGCAGGCAAT 60.082 37.500 7.62 0.00 35.70 3.56
4010 6926 4.628333 CGATCTGAAATTTTGCAGGCAATT 59.372 37.500 7.62 0.00 35.70 2.32
4011 6927 5.806502 CGATCTGAAATTTTGCAGGCAATTA 59.193 36.000 7.62 0.00 35.70 1.40
4012 6928 6.020121 CGATCTGAAATTTTGCAGGCAATTAG 60.020 38.462 7.62 0.00 35.70 1.73
4013 6929 6.343716 TCTGAAATTTTGCAGGCAATTAGA 57.656 33.333 7.62 2.05 35.70 2.10
4014 6930 6.757237 TCTGAAATTTTGCAGGCAATTAGAA 58.243 32.000 7.62 0.00 35.70 2.10
4015 6931 6.646240 TCTGAAATTTTGCAGGCAATTAGAAC 59.354 34.615 7.62 0.19 35.70 3.01
4016 6932 6.286758 TGAAATTTTGCAGGCAATTAGAACA 58.713 32.000 7.62 2.60 35.70 3.18
4017 6933 6.935771 TGAAATTTTGCAGGCAATTAGAACAT 59.064 30.769 7.62 0.00 35.70 2.71
4018 6934 7.444792 TGAAATTTTGCAGGCAATTAGAACATT 59.555 29.630 7.62 0.00 35.70 2.71
4019 6935 6.973229 ATTTTGCAGGCAATTAGAACATTC 57.027 33.333 7.62 0.00 35.70 2.67
4020 6936 5.465532 TTTGCAGGCAATTAGAACATTCA 57.534 34.783 7.62 0.00 35.70 2.57
4021 6937 5.664294 TTGCAGGCAATTAGAACATTCAT 57.336 34.783 1.93 0.00 0.00 2.57
4022 6938 5.252969 TGCAGGCAATTAGAACATTCATC 57.747 39.130 0.00 0.00 0.00 2.92
4023 6939 4.705991 TGCAGGCAATTAGAACATTCATCA 59.294 37.500 0.00 0.00 0.00 3.07
4024 6940 5.185442 TGCAGGCAATTAGAACATTCATCAA 59.815 36.000 0.00 0.00 0.00 2.57
4025 6941 6.127281 TGCAGGCAATTAGAACATTCATCAAT 60.127 34.615 0.00 0.00 0.00 2.57
4026 6942 6.200286 GCAGGCAATTAGAACATTCATCAATG 59.800 38.462 0.00 0.00 44.57 2.82
4084 7000 7.621832 TTTTTCGATTTTACTGTTCATGCAG 57.378 32.000 0.00 0.00 41.92 4.41
4085 7001 4.944962 TCGATTTTACTGTTCATGCAGG 57.055 40.909 0.00 0.00 40.59 4.85
4086 7002 4.574892 TCGATTTTACTGTTCATGCAGGA 58.425 39.130 0.00 0.00 40.59 3.86
4087 7003 4.631377 TCGATTTTACTGTTCATGCAGGAG 59.369 41.667 0.00 0.00 40.59 3.69
4088 7004 4.666237 GATTTTACTGTTCATGCAGGAGC 58.334 43.478 8.37 8.37 40.59 4.70
4105 7021 1.637338 AGCATATGAGCTCGGGATCA 58.363 50.000 5.33 5.33 42.18 2.92
4106 7022 1.973515 AGCATATGAGCTCGGGATCAA 59.026 47.619 7.61 0.00 42.18 2.57
4107 7023 2.369860 AGCATATGAGCTCGGGATCAAA 59.630 45.455 7.61 0.00 42.18 2.69
4108 7024 3.141398 GCATATGAGCTCGGGATCAAAA 58.859 45.455 7.61 0.00 41.37 2.44
4109 7025 3.188048 GCATATGAGCTCGGGATCAAAAG 59.812 47.826 7.61 0.72 41.37 2.27
4110 7026 4.635223 CATATGAGCTCGGGATCAAAAGA 58.365 43.478 7.61 0.00 41.37 2.52
4111 7027 2.680312 TGAGCTCGGGATCAAAAGAG 57.320 50.000 0.00 0.00 34.74 2.85
4115 7031 2.393271 CTCGGGATCAAAAGAGCACT 57.607 50.000 0.00 0.00 0.00 4.40
4116 7032 2.704572 CTCGGGATCAAAAGAGCACTT 58.295 47.619 0.00 0.00 38.05 3.16
4117 7033 3.077359 CTCGGGATCAAAAGAGCACTTT 58.923 45.455 3.03 3.03 46.64 2.66
4136 7052 7.262048 GCACTTTTGCTCTTCTCTATACTACT 58.738 38.462 0.00 0.00 46.17 2.57
4137 7053 7.762159 GCACTTTTGCTCTTCTCTATACTACTT 59.238 37.037 0.00 0.00 46.17 2.24
4175 7096 7.200455 AGGTTTTATCTTTCACTTGGTTTTCG 58.800 34.615 0.00 0.00 0.00 3.46
4310 7231 4.909696 TGGTATGGCAATAAATTCACGG 57.090 40.909 0.00 0.00 0.00 4.94
4312 7233 4.336993 TGGTATGGCAATAAATTCACGGTC 59.663 41.667 0.00 0.00 0.00 4.79
4313 7234 4.336993 GGTATGGCAATAAATTCACGGTCA 59.663 41.667 0.00 0.00 0.00 4.02
4350 7271 7.945664 TGTTTCTTATGGTAAAACCTGGTACAT 59.054 33.333 0.00 3.21 39.58 2.29
4352 7273 5.883673 TCTTATGGTAAAACCTGGTACATGC 59.116 40.000 0.00 0.00 39.58 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 6.263842 CCTCATACTTGCATGTCCATGTATTT 59.736 38.462 8.74 0.00 40.80 1.40
41 1570 4.265073 AGTTTCCCTCATACTTGCATGTC 58.735 43.478 8.74 0.00 0.00 3.06
92 1621 4.056050 GGTCTGTCGGAATACGCATATTT 58.944 43.478 0.00 0.00 43.86 1.40
149 1678 3.836365 TCATCGCCCTTATCATGTTCA 57.164 42.857 0.00 0.00 0.00 3.18
178 1707 6.213195 ACTCTCCAAGATCAGATCAAGAAACT 59.787 38.462 13.14 0.00 0.00 2.66
244 1773 5.290493 TGTGGAGTTCTATTTGTGTCACT 57.710 39.130 4.27 0.00 0.00 3.41
297 2046 4.890158 AAAGAAACCCCAAAATAGGCAG 57.110 40.909 0.00 0.00 0.00 4.85
431 2190 3.571571 TGAGTCGTCGGTCTTGTAATTG 58.428 45.455 0.00 0.00 0.00 2.32
479 2238 5.962433 TCTTAGTACATAGTGTTGTGGAGC 58.038 41.667 0.00 0.00 0.00 4.70
519 2278 6.833416 TGGTTGGAGAGAAAAGAAATCTCAAA 59.167 34.615 6.35 0.00 44.64 2.69
530 2289 7.176690 GTGGAGATATTTTGGTTGGAGAGAAAA 59.823 37.037 0.00 0.00 0.00 2.29
553 2312 9.166173 TGTCAAAAGATCAATGATAAGTAGTGG 57.834 33.333 0.00 0.00 0.00 4.00
565 2324 8.358582 AGAAAAGGCTATGTCAAAAGATCAAT 57.641 30.769 0.00 0.00 0.00 2.57
594 2353 8.499162 TCTCTTTTCTCTTTTTGATTGATCGTC 58.501 33.333 0.00 0.00 0.00 4.20
595 2354 8.383318 TCTCTTTTCTCTTTTTGATTGATCGT 57.617 30.769 0.00 0.00 0.00 3.73
596 2355 9.669353 TTTCTCTTTTCTCTTTTTGATTGATCG 57.331 29.630 0.00 0.00 0.00 3.69
644 2403 5.163673 TGGTTACTTAAAAACGTGTCCCAAC 60.164 40.000 0.00 0.00 0.00 3.77
646 2405 4.521146 TGGTTACTTAAAAACGTGTCCCA 58.479 39.130 0.00 0.00 0.00 4.37
647 2406 5.296531 TCTTGGTTACTTAAAAACGTGTCCC 59.703 40.000 0.00 0.00 0.00 4.46
648 2407 6.362210 TCTTGGTTACTTAAAAACGTGTCC 57.638 37.500 0.00 0.00 0.00 4.02
670 2429 3.552068 CCTCACGAACCCCAATTTGTTTC 60.552 47.826 0.00 0.00 0.00 2.78
674 2433 0.887933 CCCTCACGAACCCCAATTTG 59.112 55.000 0.00 0.00 0.00 2.32
675 2434 0.481128 ACCCTCACGAACCCCAATTT 59.519 50.000 0.00 0.00 0.00 1.82
678 2437 2.522367 GGACCCTCACGAACCCCAA 61.522 63.158 0.00 0.00 0.00 4.12
680 2439 4.078516 CGGACCCTCACGAACCCC 62.079 72.222 0.00 0.00 0.00 4.95
682 2441 2.260743 GACGGACCCTCACGAACC 59.739 66.667 0.00 0.00 0.00 3.62
683 2442 2.126580 CGACGGACCCTCACGAAC 60.127 66.667 0.00 0.00 0.00 3.95
684 2443 3.367743 CCGACGGACCCTCACGAA 61.368 66.667 8.64 0.00 0.00 3.85
687 2446 3.450115 CTCCCGACGGACCCTCAC 61.450 72.222 17.49 0.00 33.32 3.51
688 2447 3.975591 ACTCCCGACGGACCCTCA 61.976 66.667 17.49 0.00 33.32 3.86
689 2448 3.450115 CACTCCCGACGGACCCTC 61.450 72.222 17.49 0.00 33.32 4.30
743 2502 3.703939 CTCTCGAGACGTGCGTCCG 62.704 68.421 19.35 20.16 45.59 4.79
757 2526 2.144730 GTGCATGCATGGAGATCTCTC 58.855 52.381 25.64 12.59 42.14 3.20
758 2527 1.540580 CGTGCATGCATGGAGATCTCT 60.541 52.381 28.79 0.23 0.00 3.10
759 2528 0.866427 CGTGCATGCATGGAGATCTC 59.134 55.000 28.79 14.75 0.00 2.75
760 2529 1.164662 GCGTGCATGCATGGAGATCT 61.165 55.000 34.64 0.00 33.81 2.75
761 2530 1.164662 AGCGTGCATGCATGGAGATC 61.165 55.000 34.64 20.71 37.31 2.75
762 2531 0.107268 TAGCGTGCATGCATGGAGAT 59.893 50.000 34.64 21.89 37.31 2.75
763 2532 0.811219 GTAGCGTGCATGCATGGAGA 60.811 55.000 34.64 13.84 37.31 3.71
764 2533 1.645455 GTAGCGTGCATGCATGGAG 59.355 57.895 34.64 21.90 37.31 3.86
765 2534 1.819208 GGTAGCGTGCATGCATGGA 60.819 57.895 34.64 22.97 37.31 3.41
766 2535 1.820906 AGGTAGCGTGCATGCATGG 60.821 57.895 34.64 24.94 37.31 3.66
767 2536 1.354155 CAGGTAGCGTGCATGCATG 59.646 57.895 31.36 31.36 37.31 4.06
768 2537 1.078214 ACAGGTAGCGTGCATGCAT 60.078 52.632 31.36 18.67 37.31 3.96
769 2538 1.741401 GACAGGTAGCGTGCATGCA 60.741 57.895 31.36 18.46 37.31 3.96
770 2539 2.802667 CGACAGGTAGCGTGCATGC 61.803 63.158 23.58 23.58 0.00 4.06
942 2723 1.300465 ATCTACCAGCAGCGCATCG 60.300 57.895 11.47 0.00 0.00 3.84
975 2759 2.258591 GAGCGTGCGGAGAGTGAA 59.741 61.111 0.00 0.00 0.00 3.18
1282 3096 0.460311 GTGTACTCCTCCACGATGGG 59.540 60.000 0.00 0.00 38.32 4.00
1389 3212 1.202114 TGCATGATTTCGGGCAGTTTC 59.798 47.619 0.00 0.00 0.00 2.78
1392 3215 2.485677 CTGCATGATTTCGGGCAGT 58.514 52.632 12.49 0.00 46.47 4.40
1399 3222 2.686915 CCTGAACCTCCTGCATGATTTC 59.313 50.000 0.00 0.00 0.00 2.17
1440 3263 6.632434 GTGAAATTTGCAAATTAACCAAGCAC 59.368 34.615 31.87 24.08 37.62 4.40
1441 3264 6.541641 AGTGAAATTTGCAAATTAACCAAGCA 59.458 30.769 31.87 19.22 37.62 3.91
1442 3265 6.958255 AGTGAAATTTGCAAATTAACCAAGC 58.042 32.000 31.87 19.28 37.62 4.01
1443 3266 7.442062 AGGAGTGAAATTTGCAAATTAACCAAG 59.558 33.333 31.87 0.00 37.62 3.61
1444 3267 7.278875 AGGAGTGAAATTTGCAAATTAACCAA 58.721 30.769 31.87 16.11 37.62 3.67
1478 3306 2.149578 AGTGTGTCTCTCAATTGCAGC 58.850 47.619 0.00 0.00 0.00 5.25
1639 3518 6.648310 CACTCTCACTCACTTTGTATGTGATT 59.352 38.462 0.00 0.00 42.57 2.57
1640 3519 6.015095 TCACTCTCACTCACTTTGTATGTGAT 60.015 38.462 0.00 0.00 42.57 3.06
1641 3520 5.301805 TCACTCTCACTCACTTTGTATGTGA 59.698 40.000 0.00 0.00 41.48 3.58
1642 3521 5.532557 TCACTCTCACTCACTTTGTATGTG 58.467 41.667 0.00 0.00 36.82 3.21
1643 3522 5.303078 ACTCACTCTCACTCACTTTGTATGT 59.697 40.000 0.00 0.00 0.00 2.29
1669 3559 8.099537 ACTCCATATATTGTCATCATTCTCACC 58.900 37.037 0.00 0.00 0.00 4.02
1727 3675 9.534565 TCACGAAAGAGATCTTCCTTATTATTG 57.465 33.333 0.00 0.00 34.61 1.90
1733 3681 7.640597 TGTATCACGAAAGAGATCTTCCTTA 57.359 36.000 0.00 0.00 40.61 2.69
1750 3702 5.620206 TCCACCATTACATCCATGTATCAC 58.380 41.667 0.21 0.00 42.32 3.06
1760 3712 7.905604 TTAATCATCGATCCACCATTACATC 57.094 36.000 0.00 0.00 0.00 3.06
1788 3802 4.165950 AGAACTGAATATGCATGGTACCCA 59.834 41.667 10.16 0.00 38.19 4.51
1830 3844 1.665169 CAAGCTTGGCACCACAAAAAC 59.335 47.619 19.14 0.00 0.00 2.43
1868 3892 9.237187 AGCGATTAGAAGATAATCTCAGTCATA 57.763 33.333 6.17 0.00 33.12 2.15
1898 3922 6.651643 AGTCAAACTAACCAACATATGCGTTA 59.348 34.615 1.58 6.55 0.00 3.18
2003 4093 1.854126 CTTCAGGCGTGCTTTTTGTTG 59.146 47.619 0.35 0.00 0.00 3.33
2004 4094 1.202405 CCTTCAGGCGTGCTTTTTGTT 60.202 47.619 0.35 0.00 0.00 2.83
2005 4095 0.385390 CCTTCAGGCGTGCTTTTTGT 59.615 50.000 0.35 0.00 0.00 2.83
2006 4096 0.318955 CCCTTCAGGCGTGCTTTTTG 60.319 55.000 0.35 0.00 0.00 2.44
2007 4097 1.463553 CCCCTTCAGGCGTGCTTTTT 61.464 55.000 0.35 0.00 0.00 1.94
2008 4098 1.903404 CCCCTTCAGGCGTGCTTTT 60.903 57.895 0.35 0.00 0.00 2.27
2009 4099 2.282462 CCCCTTCAGGCGTGCTTT 60.282 61.111 0.35 0.00 0.00 3.51
2010 4100 2.640581 AAACCCCTTCAGGCGTGCTT 62.641 55.000 0.35 0.00 0.00 3.91
2011 4101 2.640581 AAAACCCCTTCAGGCGTGCT 62.641 55.000 0.35 0.00 0.00 4.40
2048 4138 6.369615 AGCACATTTTTCATGCTCAAATTACC 59.630 34.615 0.00 0.00 46.68 2.85
2088 4180 3.319122 CAGTCCCCTGTTTTCCTTGAAAG 59.681 47.826 0.00 0.00 32.93 2.62
2130 4226 4.526970 TGGAAGATTGACAATTAGCCTCC 58.473 43.478 1.39 5.35 0.00 4.30
2208 4311 8.477256 CAATTTTCTCAATTAGGGAAAGGCATA 58.523 33.333 4.04 0.00 31.88 3.14
2240 4343 9.129209 GAAGGTTTTTAGTTGATTCAGTTATGC 57.871 33.333 0.00 0.00 0.00 3.14
2347 4458 7.375834 AGATATTCAATCGTAATTAGCCGTCA 58.624 34.615 0.00 0.00 0.00 4.35
2477 4588 5.890334 ACTATTGTTGTTGTTGTTCCACTG 58.110 37.500 0.00 0.00 0.00 3.66
2603 5037 0.407139 AAGGCCCAGCTGAGTGATTT 59.593 50.000 17.39 0.00 0.00 2.17
2604 5038 0.034670 GAAGGCCCAGCTGAGTGATT 60.035 55.000 17.39 2.95 0.00 2.57
2764 5549 2.191513 AGGTGCTGCTGTTGCTGTG 61.192 57.895 0.00 0.00 39.81 3.66
2780 5565 1.890979 GCAGATCGATGGTGGCAGG 60.891 63.158 0.54 0.00 0.00 4.85
2843 5639 1.527611 CATGACCGGCTGGCATGAT 60.528 57.895 30.03 7.19 45.13 2.45
3169 5968 9.182214 ACATCTGCATATTAAAGAGTTGTCAAT 57.818 29.630 0.00 0.00 0.00 2.57
3205 6009 4.561735 TGAAACCCAAACTCGAATCAAC 57.438 40.909 0.00 0.00 0.00 3.18
3517 6392 6.101650 AGGCATGATCGACTGTAATATTGA 57.898 37.500 0.00 0.00 0.00 2.57
3518 6393 6.533012 CCTAGGCATGATCGACTGTAATATTG 59.467 42.308 0.00 0.00 0.00 1.90
3697 6572 7.918076 AGAAGAATGTGTCCCAAAACTATCTA 58.082 34.615 0.00 0.00 0.00 1.98
3837 6715 9.513906 TCACCAAAATCAGATAGTATTGACAAA 57.486 29.630 0.00 0.00 0.00 2.83
3846 6724 9.911788 AGAATACATTCACCAAAATCAGATAGT 57.088 29.630 4.85 0.00 39.23 2.12
3851 6729 8.272545 TCAGAGAATACATTCACCAAAATCAG 57.727 34.615 4.85 0.00 39.23 2.90
3882 6789 9.017669 CATTTGTCTCTCTTTTTCAAGAAACAG 57.982 33.333 3.00 3.00 38.63 3.16
3891 6798 6.484977 AGGTGAGTCATTTGTCTCTCTTTTTC 59.515 38.462 0.00 0.00 32.65 2.29
3893 6800 5.934781 AGGTGAGTCATTTGTCTCTCTTTT 58.065 37.500 0.00 0.00 32.65 2.27
3918 6825 9.409918 TGATAGTAATAGAGACTGCAGTACTTT 57.590 33.333 21.73 15.45 0.00 2.66
3919 6826 8.982091 TGATAGTAATAGAGACTGCAGTACTT 57.018 34.615 21.73 8.63 0.00 2.24
3920 6827 8.982091 TTGATAGTAATAGAGACTGCAGTACT 57.018 34.615 21.73 22.67 0.00 2.73
3922 6829 8.722394 CGATTGATAGTAATAGAGACTGCAGTA 58.278 37.037 21.73 4.02 0.00 2.74
3941 6857 7.102346 TGGGCAAAATAACAAAATCGATTGAT 58.898 30.769 12.25 0.77 35.98 2.57
3942 6858 6.459066 TGGGCAAAATAACAAAATCGATTGA 58.541 32.000 12.25 0.00 34.38 2.57
3943 6859 6.589523 TCTGGGCAAAATAACAAAATCGATTG 59.410 34.615 12.25 4.12 36.37 2.67
3944 6860 6.696411 TCTGGGCAAAATAACAAAATCGATT 58.304 32.000 4.39 4.39 0.00 3.34
3945 6861 6.279513 TCTGGGCAAAATAACAAAATCGAT 57.720 33.333 0.00 0.00 0.00 3.59
3946 6862 5.713792 TCTGGGCAAAATAACAAAATCGA 57.286 34.783 0.00 0.00 0.00 3.59
3947 6863 5.925969 AGTTCTGGGCAAAATAACAAAATCG 59.074 36.000 0.00 0.00 0.00 3.34
3948 6864 6.368791 GGAGTTCTGGGCAAAATAACAAAATC 59.631 38.462 0.00 0.00 0.00 2.17
3949 6865 6.183361 TGGAGTTCTGGGCAAAATAACAAAAT 60.183 34.615 0.00 0.00 0.00 1.82
3950 6866 5.129485 TGGAGTTCTGGGCAAAATAACAAAA 59.871 36.000 0.00 0.00 0.00 2.44
3951 6867 4.651503 TGGAGTTCTGGGCAAAATAACAAA 59.348 37.500 0.00 0.00 0.00 2.83
3952 6868 4.038642 GTGGAGTTCTGGGCAAAATAACAA 59.961 41.667 0.00 0.00 0.00 2.83
3953 6869 3.572255 GTGGAGTTCTGGGCAAAATAACA 59.428 43.478 0.00 0.00 0.00 2.41
3954 6870 3.572255 TGTGGAGTTCTGGGCAAAATAAC 59.428 43.478 0.00 0.00 0.00 1.89
3955 6871 3.838565 TGTGGAGTTCTGGGCAAAATAA 58.161 40.909 0.00 0.00 0.00 1.40
3956 6872 3.517296 TGTGGAGTTCTGGGCAAAATA 57.483 42.857 0.00 0.00 0.00 1.40
3957 6873 2.380064 TGTGGAGTTCTGGGCAAAAT 57.620 45.000 0.00 0.00 0.00 1.82
3958 6874 2.151502 TTGTGGAGTTCTGGGCAAAA 57.848 45.000 0.00 0.00 0.00 2.44
3959 6875 2.151502 TTTGTGGAGTTCTGGGCAAA 57.848 45.000 0.00 0.00 0.00 3.68
3960 6876 1.962807 CATTTGTGGAGTTCTGGGCAA 59.037 47.619 0.00 0.00 0.00 4.52
3961 6877 1.133513 ACATTTGTGGAGTTCTGGGCA 60.134 47.619 0.00 0.00 0.00 5.36
3962 6878 1.541588 GACATTTGTGGAGTTCTGGGC 59.458 52.381 0.00 0.00 0.00 5.36
3963 6879 2.862541 TGACATTTGTGGAGTTCTGGG 58.137 47.619 0.00 0.00 0.00 4.45
3964 6880 5.458041 AAATGACATTTGTGGAGTTCTGG 57.542 39.130 12.62 0.00 0.00 3.86
3965 6881 5.049474 TCGAAATGACATTTGTGGAGTTCTG 60.049 40.000 18.00 0.00 31.47 3.02
3966 6882 5.063204 TCGAAATGACATTTGTGGAGTTCT 58.937 37.500 18.00 0.00 31.47 3.01
3967 6883 5.356882 TCGAAATGACATTTGTGGAGTTC 57.643 39.130 18.00 0.56 31.47 3.01
3968 6884 5.707298 AGATCGAAATGACATTTGTGGAGTT 59.293 36.000 18.00 0.00 31.47 3.01
3969 6885 5.122869 CAGATCGAAATGACATTTGTGGAGT 59.877 40.000 18.00 2.70 31.47 3.85
3970 6886 5.352293 TCAGATCGAAATGACATTTGTGGAG 59.648 40.000 18.00 4.29 31.47 3.86
3971 6887 5.244755 TCAGATCGAAATGACATTTGTGGA 58.755 37.500 18.00 12.01 31.47 4.02
3972 6888 5.550232 TCAGATCGAAATGACATTTGTGG 57.450 39.130 18.00 7.37 31.47 4.17
3983 6899 8.273635 ATTGCCTGCAAAATTTCAGATCGAAAT 61.274 33.333 8.84 15.30 44.88 2.17
3984 6900 5.738495 TTGCCTGCAAAATTTCAGATCGAAA 60.738 36.000 12.77 12.77 39.25 3.46
3985 6901 3.255395 TGCCTGCAAAATTTCAGATCGAA 59.745 39.130 8.15 0.00 32.26 3.71
3986 6902 2.819019 TGCCTGCAAAATTTCAGATCGA 59.181 40.909 8.15 0.00 32.26 3.59
3987 6903 3.220507 TGCCTGCAAAATTTCAGATCG 57.779 42.857 8.15 0.00 32.26 3.69
3988 6904 7.037438 TCTAATTGCCTGCAAAATTTCAGATC 58.963 34.615 8.84 0.00 39.55 2.75
3989 6905 6.938507 TCTAATTGCCTGCAAAATTTCAGAT 58.061 32.000 8.84 0.00 39.55 2.90
3990 6906 6.343716 TCTAATTGCCTGCAAAATTTCAGA 57.656 33.333 8.84 3.21 39.55 3.27
3991 6907 6.424509 TGTTCTAATTGCCTGCAAAATTTCAG 59.575 34.615 8.84 0.00 39.55 3.02
3992 6908 6.286758 TGTTCTAATTGCCTGCAAAATTTCA 58.713 32.000 8.84 2.51 39.55 2.69
3993 6909 6.783892 TGTTCTAATTGCCTGCAAAATTTC 57.216 33.333 8.84 0.09 39.55 2.17
3994 6910 7.444792 TGAATGTTCTAATTGCCTGCAAAATTT 59.555 29.630 8.84 1.77 39.55 1.82
3995 6911 6.935771 TGAATGTTCTAATTGCCTGCAAAATT 59.064 30.769 8.84 2.49 39.55 1.82
3996 6912 6.465948 TGAATGTTCTAATTGCCTGCAAAAT 58.534 32.000 8.84 3.93 39.55 1.82
3997 6913 5.851720 TGAATGTTCTAATTGCCTGCAAAA 58.148 33.333 8.84 0.00 39.55 2.44
3998 6914 5.465532 TGAATGTTCTAATTGCCTGCAAA 57.534 34.783 8.84 0.00 39.55 3.68
3999 6915 5.185442 TGATGAATGTTCTAATTGCCTGCAA 59.815 36.000 7.06 7.06 40.47 4.08
4000 6916 4.705991 TGATGAATGTTCTAATTGCCTGCA 59.294 37.500 0.00 0.00 0.00 4.41
4001 6917 5.252969 TGATGAATGTTCTAATTGCCTGC 57.747 39.130 0.00 0.00 0.00 4.85
4002 6918 7.694388 CATTGATGAATGTTCTAATTGCCTG 57.306 36.000 0.00 0.00 35.19 4.85
4060 6976 6.640499 CCTGCATGAACAGTAAAATCGAAAAA 59.360 34.615 0.00 0.00 35.83 1.94
4061 6977 6.016693 TCCTGCATGAACAGTAAAATCGAAAA 60.017 34.615 0.00 0.00 35.83 2.29
4062 6978 5.471797 TCCTGCATGAACAGTAAAATCGAAA 59.528 36.000 0.00 0.00 35.83 3.46
4063 6979 5.000591 TCCTGCATGAACAGTAAAATCGAA 58.999 37.500 0.00 0.00 35.83 3.71
4064 6980 4.574892 TCCTGCATGAACAGTAAAATCGA 58.425 39.130 0.00 0.00 35.83 3.59
4065 6981 4.728882 GCTCCTGCATGAACAGTAAAATCG 60.729 45.833 0.00 0.00 39.41 3.34
4066 6982 4.156556 TGCTCCTGCATGAACAGTAAAATC 59.843 41.667 0.00 0.00 45.31 2.17
4067 6983 4.081406 TGCTCCTGCATGAACAGTAAAAT 58.919 39.130 0.00 0.00 45.31 1.82
4068 6984 3.485394 TGCTCCTGCATGAACAGTAAAA 58.515 40.909 0.00 0.00 45.31 1.52
4069 6985 3.138884 TGCTCCTGCATGAACAGTAAA 57.861 42.857 0.00 0.00 45.31 2.01
4070 6986 2.857186 TGCTCCTGCATGAACAGTAA 57.143 45.000 0.00 0.00 45.31 2.24
4087 7003 2.462456 TTGATCCCGAGCTCATATGC 57.538 50.000 15.40 0.11 0.00 3.14
4088 7004 4.635223 TCTTTTGATCCCGAGCTCATATG 58.365 43.478 15.40 0.00 0.00 1.78
4089 7005 4.802248 GCTCTTTTGATCCCGAGCTCATAT 60.802 45.833 15.40 3.21 44.04 1.78
4090 7006 3.493350 GCTCTTTTGATCCCGAGCTCATA 60.493 47.826 15.40 0.00 44.04 2.15
4091 7007 2.744494 GCTCTTTTGATCCCGAGCTCAT 60.744 50.000 15.40 0.00 44.04 2.90
4092 7008 1.406069 GCTCTTTTGATCCCGAGCTCA 60.406 52.381 15.40 0.00 44.04 4.26
4093 7009 1.294857 GCTCTTTTGATCCCGAGCTC 58.705 55.000 2.73 2.73 44.04 4.09
4094 7010 0.615331 TGCTCTTTTGATCCCGAGCT 59.385 50.000 17.64 0.00 46.70 4.09
4095 7011 0.729690 GTGCTCTTTTGATCCCGAGC 59.270 55.000 12.80 12.80 46.74 5.03
4096 7012 2.393271 AGTGCTCTTTTGATCCCGAG 57.607 50.000 0.00 0.00 0.00 4.63
4097 7013 2.859165 AAGTGCTCTTTTGATCCCGA 57.141 45.000 0.00 0.00 0.00 5.14
4149 7070 7.704899 CGAAAACCAAGTGAAAGATAAAACCTT 59.295 33.333 0.00 0.00 0.00 3.50
4162 7083 1.104577 GTGGGGCGAAAACCAAGTGA 61.105 55.000 0.00 0.00 38.73 3.41
4167 7088 2.519780 GTGGTGGGGCGAAAACCA 60.520 61.111 0.00 0.00 41.66 3.67
4168 7089 3.299977 GGTGGTGGGGCGAAAACC 61.300 66.667 0.00 0.00 34.38 3.27
4212 7133 5.606329 AGGGATGAAAAACCAGGAAAAATCA 59.394 36.000 0.00 0.00 0.00 2.57
4221 7142 1.547372 CCAGCAGGGATGAAAAACCAG 59.453 52.381 0.00 0.00 40.01 4.00
4222 7143 1.133199 ACCAGCAGGGATGAAAAACCA 60.133 47.619 0.00 0.00 41.15 3.67
4224 7145 3.751479 AAACCAGCAGGGATGAAAAAC 57.249 42.857 0.00 0.00 41.15 2.43
4265 7186 9.889128 CCATAGATTGATTTGGTTTATTGGTTT 57.111 29.630 0.00 0.00 0.00 3.27
4266 7187 9.045745 ACCATAGATTGATTTGGTTTATTGGTT 57.954 29.630 0.00 0.00 39.41 3.67
4267 7188 8.608185 ACCATAGATTGATTTGGTTTATTGGT 57.392 30.769 0.00 0.00 39.41 3.67
4271 7192 8.806146 GCCATACCATAGATTGATTTGGTTTAT 58.194 33.333 0.00 0.00 42.35 1.40
4272 7193 7.782168 TGCCATACCATAGATTGATTTGGTTTA 59.218 33.333 0.00 0.00 42.35 2.01
4273 7194 6.610830 TGCCATACCATAGATTGATTTGGTTT 59.389 34.615 0.00 0.00 42.35 3.27
4292 7213 5.189928 ACTGACCGTGAATTTATTGCCATA 58.810 37.500 0.00 0.00 0.00 2.74
4350 7271 3.585289 TGGGTTACCAAAGATGTCTAGCA 59.415 43.478 2.98 0.00 45.87 3.49


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

AutoCloner maintained by Alex Coulton.