Multiple sequence alignment - TraesCS5A01G192300

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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 TraesCS5A01G192300 chr5A 100.000 6507 0 0 1 6507 395908973 395915479 0.000000e+00 12017.0
1 TraesCS5A01G192300 chr5B 94.460 3628 130 22 2207 5807 344621052 344617469 0.000000e+00 5520.0
2 TraesCS5A01G192300 chr5B 88.574 2118 143 44 1 2096 344623131 344621091 0.000000e+00 2479.0
3 TraesCS5A01G192300 chr5B 88.956 498 20 4 6045 6507 344617018 344616521 3.380000e-162 582.0
4 TraesCS5A01G192300 chr5B 83.028 218 31 4 2707 2922 459483772 459483985 6.660000e-45 193.0
5 TraesCS5A01G192300 chr5B 91.176 102 8 1 2576 2677 212395768 212395668 3.160000e-28 137.0
6 TraesCS5A01G192300 chr5D 95.020 3273 78 18 3283 6507 301579384 301576149 0.000000e+00 5062.0
7 TraesCS5A01G192300 chr5D 93.973 1875 62 18 1428 3284 301581322 301579481 0.000000e+00 2789.0
8 TraesCS5A01G192300 chr5D 88.191 1448 82 49 1 1420 301582792 301581406 0.000000e+00 1644.0
9 TraesCS5A01G192300 chr5D 84.135 208 26 5 2707 2910 383639339 383639543 1.850000e-45 195.0
10 TraesCS5A01G192300 chr5D 89.130 46 5 0 3260 3305 47024564 47024519 2.530000e-04 58.4
11 TraesCS5A01G192300 chr7D 79.775 356 39 15 2576 2929 351590027 351589703 1.830000e-55 228.0
12 TraesCS5A01G192300 chr7D 97.619 42 1 0 972 1013 461650893 461650934 9.050000e-09 73.1
13 TraesCS5A01G192300 chr7B 79.772 351 38 17 2576 2922 354251292 354251613 2.360000e-54 224.0
14 TraesCS5A01G192300 chr7B 81.567 217 37 2 2708 2922 697308656 697308871 6.710000e-40 176.0
15 TraesCS5A01G192300 chr2D 83.539 243 28 9 2688 2925 194457223 194456988 3.950000e-52 217.0
16 TraesCS5A01G192300 chr2D 90.741 54 2 2 971 1024 588509294 588509244 1.170000e-07 69.4
17 TraesCS5A01G192300 chr2D 86.792 53 7 0 3254 3306 649145896 649145948 7.050000e-05 60.2
18 TraesCS5A01G192300 chr2D 100.000 28 0 0 3186 3213 249879447 249879474 1.200000e-02 52.8
19 TraesCS5A01G192300 chr2B 84.211 228 22 7 2707 2925 250264647 250264425 6.610000e-50 209.0
20 TraesCS5A01G192300 chr2B 92.593 108 8 0 2576 2683 275317147 275317040 8.740000e-34 156.0
21 TraesCS5A01G192300 chr2B 93.137 102 7 0 2576 2677 234367961 234367860 4.060000e-32 150.0
22 TraesCS5A01G192300 chr2B 86.792 53 7 0 3254 3306 785136263 785136315 7.050000e-05 60.2
23 TraesCS5A01G192300 chr2B 100.000 28 0 0 3186 3213 338733740 338733767 1.200000e-02 52.8
24 TraesCS5A01G192300 chr3D 82.629 213 26 5 2687 2894 206978748 206978954 1.860000e-40 178.0
25 TraesCS5A01G192300 chr3B 82.407 216 27 4 2687 2897 284678673 284678464 1.860000e-40 178.0
26 TraesCS5A01G192300 chr7A 91.346 104 9 0 2576 2679 341443367 341443470 6.800000e-30 143.0
27 TraesCS5A01G192300 chr3A 87.629 97 12 0 2578 2674 555535193 555535289 5.330000e-21 113.0
28 TraesCS5A01G192300 chr4D 84.337 83 7 3 971 1053 459920266 459920190 7.000000e-10 76.8
29 TraesCS5A01G192300 chr4D 84.746 59 9 0 3254 3312 70234573 70234515 7.050000e-05 60.2
30 TraesCS5A01G192300 chr6B 83.133 83 8 4 971 1053 377866619 377866543 3.260000e-08 71.3
31 TraesCS5A01G192300 chr2A 83.133 83 8 3 971 1053 777559680 777559756 3.260000e-08 71.3
32 TraesCS5A01G192300 chr2A 86.792 53 7 0 3254 3306 775526469 775526417 7.050000e-05 60.2
33 TraesCS5A01G192300 chrUn 93.333 45 1 2 5807 5851 292665421 292665379 1.510000e-06 65.8
34 TraesCS5A01G192300 chrUn 93.333 45 1 2 5807 5851 292670895 292670853 1.510000e-06 65.8
35 TraesCS5A01G192300 chrUn 93.333 45 1 2 5807 5851 350313752 350313710 1.510000e-06 65.8
36 TraesCS5A01G192300 chr4B 100.000 35 0 0 5806 5840 240209819 240209853 1.510000e-06 65.8
37 TraesCS5A01G192300 chr4A 100.000 35 0 0 5806 5840 352494797 352494831 1.510000e-06 65.8
38 TraesCS5A01G192300 chr4A 84.746 59 9 0 3254 3312 522917021 522916963 7.050000e-05 60.2
39 TraesCS5A01G192300 chr1B 95.238 42 0 1 5806 5847 36775740 36775701 1.510000e-06 65.8
40 TraesCS5A01G192300 chr1B 95.238 42 0 1 5806 5847 36781391 36781352 1.510000e-06 65.8
41 TraesCS5A01G192300 chr1B 95.238 42 0 1 5806 5847 36783563 36783524 1.510000e-06 65.8
42 TraesCS5A01G192300 chr1B 85.000 60 7 2 3254 3311 609304930 609304871 7.050000e-05 60.2


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 TraesCS5A01G192300 chr5A 395908973 395915479 6506 False 12017.000000 12017 100.000000 1 6507 1 chr5A.!!$F1 6506
1 TraesCS5A01G192300 chr5B 344616521 344623131 6610 True 2860.333333 5520 90.663333 1 6507 3 chr5B.!!$R2 6506
2 TraesCS5A01G192300 chr5D 301576149 301582792 6643 True 3165.000000 5062 92.394667 1 6507 3 chr5D.!!$R2 6506

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
624 649 0.107017 AACTGGGAAGGATGGATGCG 60.107 55.000 0.00 0.00 0.00 4.73 F
1110 1154 0.177604 GCCTCACCTCTGACTCCATG 59.822 60.000 0.00 0.00 0.00 3.66 F
2069 2206 0.179189 GCTCAAGGTACGCAATGCAC 60.179 55.000 5.91 0.00 0.00 4.57 F
2966 3124 1.066908 TGTAGTTGCAAAACTGGCAGC 59.933 47.619 15.89 0.75 43.05 5.25 F
3916 4175 0.548682 ACCTGAGGGTCCTGCTTCAT 60.549 55.000 2.38 0.00 43.38 2.57 F
4430 4689 1.391157 GCAGTGGTTTTGGCCAGTCA 61.391 55.000 5.11 0.00 40.01 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 1772 1.276415 TTGCTCGCTTTGTTTGTTGC 58.724 45.000 0.00 0.00 0.00 4.17 R
3060 3219 0.605319 TACCAAAGCCGAGGCACTTG 60.605 55.000 17.18 17.11 41.55 3.16 R
3633 3892 0.957395 ATCCTGCACGAAGCTGTTGG 60.957 55.000 6.22 4.08 45.94 3.77 R
4307 4566 0.036164 TGGAGTTCATGGGGTTGTCG 59.964 55.000 0.00 0.00 0.00 4.35 R
5238 5500 0.178068 CGACCACCTTCCCTACATGG 59.822 60.000 0.00 0.00 36.46 3.66 R
5804 6070 1.071471 GCTACATGCACCGGGCTAT 59.929 57.895 6.32 0.53 45.15 2.97 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
66 67 6.016777 CACTTCAAATCTGTTCTGCCTTTAGT 60.017 38.462 0.00 0.00 0.00 2.24
78 81 8.400186 TGTTCTGCCTTTAGTTTACTGTAAAAC 58.600 33.333 14.10 9.02 39.22 2.43
96 99 7.363431 TGTAAAACGCATCATATTGTCACAAA 58.637 30.769 0.00 0.00 0.00 2.83
97 100 7.862873 TGTAAAACGCATCATATTGTCACAAAA 59.137 29.630 0.00 0.00 0.00 2.44
132 143 4.158579 GGAAGGAGGAAGTATTTTGCAAGG 59.841 45.833 0.00 0.00 0.00 3.61
142 153 7.040686 GGAAGTATTTTGCAAGGAGAAACACTA 60.041 37.037 0.00 0.00 0.00 2.74
145 156 2.859165 TGCAAGGAGAAACACTAGGG 57.141 50.000 0.00 0.00 0.00 3.53
220 234 1.197721 GTTTGCACCGATGAACTGGAG 59.802 52.381 0.00 0.00 0.00 3.86
221 235 0.396435 TTGCACCGATGAACTGGAGT 59.604 50.000 0.00 0.00 0.00 3.85
222 236 1.262417 TGCACCGATGAACTGGAGTA 58.738 50.000 0.00 0.00 0.00 2.59
223 237 1.204704 TGCACCGATGAACTGGAGTAG 59.795 52.381 0.00 0.00 0.00 2.57
239 253 8.418597 ACTGGAGTAGTACAAGAAGTCAATAA 57.581 34.615 2.52 0.00 38.04 1.40
304 322 1.292242 TGAAGCCACCTAGAGGGAGAT 59.708 52.381 0.00 0.00 40.27 2.75
305 323 2.518407 TGAAGCCACCTAGAGGGAGATA 59.482 50.000 0.00 0.00 40.27 1.98
306 324 2.687003 AGCCACCTAGAGGGAGATAC 57.313 55.000 0.00 0.00 40.27 2.24
307 325 1.202952 AGCCACCTAGAGGGAGATACG 60.203 57.143 0.00 0.00 40.27 3.06
322 340 2.117137 GATACGTACGTCAGCATGGTG 58.883 52.381 26.53 18.87 36.16 4.17
392 410 2.203337 AGCACGCCCTTTCTGCAA 60.203 55.556 0.00 0.00 33.06 4.08
429 448 2.159462 GCACAGTGCATTTTCTAGAGCC 60.159 50.000 21.22 0.00 44.26 4.70
434 453 0.748005 GCATTTTCTAGAGCCGGCCA 60.748 55.000 26.15 7.96 0.00 5.36
450 469 4.220602 GCCGGCCATTTTCTATGGAATAAT 59.779 41.667 18.11 0.00 41.64 1.28
451 470 5.713025 CCGGCCATTTTCTATGGAATAATG 58.287 41.667 2.24 14.23 41.64 1.90
502 521 2.386661 ACAGGACTGTCGCCATTAAG 57.613 50.000 0.00 0.00 40.24 1.85
511 530 6.349363 GGACTGTCGCCATTAAGAAAAGAAAT 60.349 38.462 1.07 0.00 0.00 2.17
515 534 5.287035 GTCGCCATTAAGAAAAGAAATGCAG 59.713 40.000 0.00 0.00 30.81 4.41
522 541 4.184079 AGAAAAGAAATGCAGCATCCAC 57.816 40.909 8.77 3.44 0.00 4.02
525 544 1.913778 AGAAATGCAGCATCCACACA 58.086 45.000 8.77 0.00 0.00 3.72
526 545 2.453521 AGAAATGCAGCATCCACACAT 58.546 42.857 8.77 0.00 0.00 3.21
527 546 3.623703 AGAAATGCAGCATCCACACATA 58.376 40.909 8.77 0.00 0.00 2.29
529 548 4.647853 AGAAATGCAGCATCCACACATATT 59.352 37.500 8.77 0.00 0.00 1.28
530 549 4.579454 AATGCAGCATCCACACATATTC 57.421 40.909 8.77 0.00 0.00 1.75
539 564 5.345702 CATCCACACATATTCTTTGCCAAG 58.654 41.667 0.00 0.00 0.00 3.61
554 579 2.297033 TGCCAAGAAGACAGAAAATGCC 59.703 45.455 0.00 0.00 0.00 4.40
611 636 4.142513 GCAGAGAAGCATAAGAAAACTGGG 60.143 45.833 0.00 0.00 0.00 4.45
615 640 5.012893 AGAAGCATAAGAAAACTGGGAAGG 58.987 41.667 0.00 0.00 0.00 3.46
616 641 4.657814 AGCATAAGAAAACTGGGAAGGA 57.342 40.909 0.00 0.00 0.00 3.36
617 642 5.198602 AGCATAAGAAAACTGGGAAGGAT 57.801 39.130 0.00 0.00 0.00 3.24
619 644 4.098501 GCATAAGAAAACTGGGAAGGATGG 59.901 45.833 0.00 0.00 0.00 3.51
620 645 5.509498 CATAAGAAAACTGGGAAGGATGGA 58.491 41.667 0.00 0.00 0.00 3.41
621 646 4.682021 AAGAAAACTGGGAAGGATGGAT 57.318 40.909 0.00 0.00 0.00 3.41
622 647 3.973425 AGAAAACTGGGAAGGATGGATG 58.027 45.455 0.00 0.00 0.00 3.51
623 648 2.149973 AAACTGGGAAGGATGGATGC 57.850 50.000 0.00 0.00 0.00 3.91
624 649 0.107017 AACTGGGAAGGATGGATGCG 60.107 55.000 0.00 0.00 0.00 4.73
625 650 0.982852 ACTGGGAAGGATGGATGCGA 60.983 55.000 0.00 0.00 0.00 5.10
626 651 0.533755 CTGGGAAGGATGGATGCGAC 60.534 60.000 0.00 0.00 0.00 5.19
627 652 1.271127 TGGGAAGGATGGATGCGACA 61.271 55.000 0.00 0.00 0.00 4.35
628 653 0.533755 GGGAAGGATGGATGCGACAG 60.534 60.000 0.00 0.00 0.00 3.51
629 654 0.179000 GGAAGGATGGATGCGACAGT 59.821 55.000 0.00 0.00 0.00 3.55
632 657 1.126488 AGGATGGATGCGACAGTCAT 58.874 50.000 0.41 0.00 0.00 3.06
676 702 2.031465 GGTGTGGGTGTGGGTACG 59.969 66.667 0.00 0.00 0.00 3.67
677 703 2.810410 GGTGTGGGTGTGGGTACGT 61.810 63.158 0.00 0.00 0.00 3.57
678 704 1.470996 GGTGTGGGTGTGGGTACGTA 61.471 60.000 0.00 0.00 0.00 3.57
679 705 0.319813 GTGTGGGTGTGGGTACGTAC 60.320 60.000 17.56 17.56 0.00 3.67
680 706 1.293179 GTGGGTGTGGGTACGTACC 59.707 63.158 32.59 32.59 45.71 3.34
681 707 1.155859 TGGGTGTGGGTACGTACCT 59.844 57.895 36.70 0.00 45.72 3.08
682 708 1.186917 TGGGTGTGGGTACGTACCTG 61.187 60.000 36.70 0.00 45.72 4.00
683 709 1.187567 GGGTGTGGGTACGTACCTGT 61.188 60.000 36.70 0.00 45.72 4.00
684 710 1.544724 GGTGTGGGTACGTACCTGTA 58.455 55.000 36.70 23.50 45.72 2.74
835 861 2.677228 CATTGGCCTCCGGTCCTT 59.323 61.111 3.32 0.00 0.00 3.36
914 940 0.532573 CAGCGAGCTGGAAGGAAGTA 59.467 55.000 16.69 0.00 40.17 2.24
915 941 0.820871 AGCGAGCTGGAAGGAAGTAG 59.179 55.000 0.00 0.00 0.00 2.57
916 942 0.533032 GCGAGCTGGAAGGAAGTAGT 59.467 55.000 0.00 0.00 0.00 2.73
929 955 2.691011 GGAAGTAGTGGACAGCTAGAGG 59.309 54.545 0.00 0.00 0.00 3.69
930 956 1.770294 AGTAGTGGACAGCTAGAGGC 58.230 55.000 0.00 0.00 42.19 4.70
1055 1098 1.703438 CTCTGCATCAAGCTCGTGGC 61.703 60.000 0.00 0.00 45.94 5.01
1107 1151 2.363172 GGGCCTCACCTCTGACTCC 61.363 68.421 0.84 0.00 39.10 3.85
1108 1152 1.610673 GGCCTCACCTCTGACTCCA 60.611 63.158 0.00 0.00 34.51 3.86
1109 1153 0.980231 GGCCTCACCTCTGACTCCAT 60.980 60.000 0.00 0.00 34.51 3.41
1110 1154 0.177604 GCCTCACCTCTGACTCCATG 59.822 60.000 0.00 0.00 0.00 3.66
1134 1178 0.508641 CTGTCCGTGTTTCTTGAGCG 59.491 55.000 0.00 0.00 0.00 5.03
1167 1211 0.890996 CCAAACACCTCTGCTCCACC 60.891 60.000 0.00 0.00 0.00 4.61
1260 1304 1.265365 GCGCTTCTCAGCTTCTGTTTT 59.735 47.619 0.00 0.00 44.85 2.43
1272 1317 3.504134 GCTTCTGTTTTCCTTCTTCTCCC 59.496 47.826 0.00 0.00 0.00 4.30
1301 1346 3.485381 CGCTTGCTCATTCAGATTCAGTG 60.485 47.826 0.00 0.00 0.00 3.66
1306 1351 4.080751 TGCTCATTCAGATTCAGTGGATGA 60.081 41.667 0.00 0.00 37.55 2.92
1318 1363 3.766591 TCAGTGGATGAACTTCTCTCCTC 59.233 47.826 10.51 7.98 34.02 3.71
1341 1386 3.759618 GGACATTTTGGTTCCGGTCATTA 59.240 43.478 0.00 0.00 0.00 1.90
1467 1588 7.275920 ACACAAAGGAATGGACAGAGTATATC 58.724 38.462 0.00 0.00 0.00 1.63
1506 1629 5.482526 TGTACCTGTTTATCTGGAGTAGCAA 59.517 40.000 0.00 0.00 38.33 3.91
1507 1630 5.700402 ACCTGTTTATCTGGAGTAGCAAT 57.300 39.130 0.00 0.00 38.33 3.56
1508 1631 5.431765 ACCTGTTTATCTGGAGTAGCAATG 58.568 41.667 0.00 0.00 38.33 2.82
1509 1632 5.045578 ACCTGTTTATCTGGAGTAGCAATGT 60.046 40.000 0.00 0.00 38.33 2.71
1510 1633 6.156256 ACCTGTTTATCTGGAGTAGCAATGTA 59.844 38.462 0.00 0.00 38.33 2.29
1511 1634 6.703607 CCTGTTTATCTGGAGTAGCAATGTAG 59.296 42.308 0.00 0.00 37.33 2.74
1512 1635 6.049149 TGTTTATCTGGAGTAGCAATGTAGC 58.951 40.000 0.00 0.00 0.00 3.58
1513 1636 5.869649 TTATCTGGAGTAGCAATGTAGCA 57.130 39.130 0.00 0.00 36.85 3.49
1531 1654 3.928754 AGCATAATACCAGGAGACCAGA 58.071 45.455 0.00 0.00 0.00 3.86
1533 1656 3.388024 GCATAATACCAGGAGACCAGACA 59.612 47.826 0.00 0.00 0.00 3.41
1551 1674 7.450074 ACCAGACACTGATGAAATAGTTAACA 58.550 34.615 8.61 0.00 32.44 2.41
1638 1772 1.734465 CTTGCGAACTTTAGAGCCCAG 59.266 52.381 0.00 0.00 0.00 4.45
1640 1774 0.673644 GCGAACTTTAGAGCCCAGCA 60.674 55.000 0.00 0.00 0.00 4.41
1643 1777 2.504367 GAACTTTAGAGCCCAGCAACA 58.496 47.619 0.00 0.00 0.00 3.33
1652 1786 1.489881 GCCCAGCAACAAACAAAGCG 61.490 55.000 0.00 0.00 0.00 4.68
1727 1864 1.796796 GCCATTCACGCTGAGGAAC 59.203 57.895 0.00 0.00 0.00 3.62
1988 2125 1.809619 CACCGACGGCGTCATCAAT 60.810 57.895 35.62 15.44 35.23 2.57
2069 2206 0.179189 GCTCAAGGTACGCAATGCAC 60.179 55.000 5.91 0.00 0.00 4.57
2096 2233 6.724893 TGAGGTTCCGTATCATCATTCTTA 57.275 37.500 0.00 0.00 0.00 2.10
2097 2234 7.119709 TGAGGTTCCGTATCATCATTCTTAA 57.880 36.000 0.00 0.00 0.00 1.85
2098 2235 7.210174 TGAGGTTCCGTATCATCATTCTTAAG 58.790 38.462 0.00 0.00 0.00 1.85
2100 2237 7.437748 AGGTTCCGTATCATCATTCTTAAGAG 58.562 38.462 5.12 0.00 0.00 2.85
2102 2239 7.711339 GGTTCCGTATCATCATTCTTAAGAGTT 59.289 37.037 5.12 0.00 0.00 3.01
2105 2242 8.909923 TCCGTATCATCATTCTTAAGAGTTGTA 58.090 33.333 5.12 0.00 0.00 2.41
2135 2272 2.499289 TCATTCTTCCCTCTGTCTCTGC 59.501 50.000 0.00 0.00 0.00 4.26
2199 2336 3.897239 TCAACAACACTGTCCCTTTCAT 58.103 40.909 0.00 0.00 33.45 2.57
2323 2460 1.098050 GGTAAATGCAGGGCAGTGAG 58.902 55.000 0.00 0.00 43.65 3.51
2354 2492 2.033801 CGCCAGGAGGAAATAAATGCAG 59.966 50.000 0.00 0.00 36.89 4.41
2473 2627 7.711846 ACTGTTCTTACATGCACAAAATAACA 58.288 30.769 0.00 0.00 32.86 2.41
2518 2672 7.054751 AGTACTAAGATTACCCTGCCAAAATC 58.945 38.462 0.00 0.00 0.00 2.17
2662 2820 5.465724 AGCAAGTTTGTTAGGAAAGAGTACG 59.534 40.000 0.00 0.00 0.00 3.67
2679 2837 6.505272 AGAGTACGGTCAGTTTAGATATTGC 58.495 40.000 0.00 0.00 0.00 3.56
2700 2858 3.688272 CATTCATCATCAAACGTGGAGC 58.312 45.455 0.00 0.00 0.00 4.70
2823 2981 3.319405 CGGTCAAGTCCTGTCTGCTATAT 59.681 47.826 0.00 0.00 0.00 0.86
2966 3124 1.066908 TGTAGTTGCAAAACTGGCAGC 59.933 47.619 15.89 0.75 43.05 5.25
3020 3178 2.422597 CACTCGTGGGCAACTTGATAA 58.577 47.619 0.00 0.00 0.00 1.75
3021 3179 2.159627 CACTCGTGGGCAACTTGATAAC 59.840 50.000 0.00 0.00 0.00 1.89
3023 3181 3.009723 CTCGTGGGCAACTTGATAACAT 58.990 45.455 0.00 0.00 0.00 2.71
3025 3183 4.580868 TCGTGGGCAACTTGATAACATAA 58.419 39.130 0.00 0.00 0.00 1.90
3218 3377 7.521871 ACCTCCGTTCCTAAATATAGTACTG 57.478 40.000 5.39 0.00 0.00 2.74
3221 3380 7.230108 CCTCCGTTCCTAAATATAGTACTGTCA 59.770 40.741 5.39 0.00 0.00 3.58
3327 3584 3.131046 ACTGAAGGAGGCAACAAAACAAG 59.869 43.478 0.00 0.00 41.41 3.16
3477 3736 4.832019 TGACATATCGCATTAGCAAAACG 58.168 39.130 0.00 0.00 42.27 3.60
3506 3765 6.700081 CCCATGAAGATGAATTAGCAAACATG 59.300 38.462 0.00 0.00 33.61 3.21
3541 3800 5.528690 TGATAAGCATGCCATAGTGTCTTTC 59.471 40.000 15.66 1.86 0.00 2.62
3633 3892 6.485648 ACTTACATACCTTGTGTTTCTTGGAC 59.514 38.462 0.00 0.00 39.48 4.02
3916 4175 0.548682 ACCTGAGGGTCCTGCTTCAT 60.549 55.000 2.38 0.00 43.38 2.57
3941 4200 3.059884 AGTGTGCACAAGATAGTGTTCG 58.940 45.455 23.59 0.00 41.52 3.95
3995 4254 6.378710 AAGCTTACTTCTCTTCCAAAACAC 57.621 37.500 0.00 0.00 0.00 3.32
4040 4299 9.640963 GAAAGTGTAGATACTACAACAGACATT 57.359 33.333 12.22 1.43 0.00 2.71
4121 4380 2.572290 GCTATCGGGGTACAATTTGCT 58.428 47.619 0.00 0.00 0.00 3.91
4307 4566 2.042944 GTGGGGAAAGGGATGGCC 60.043 66.667 0.00 0.00 0.00 5.36
4379 4638 1.546029 TCACTGATTGAGACTGTCGGG 59.454 52.381 1.52 0.00 0.00 5.14
4430 4689 1.391157 GCAGTGGTTTTGGCCAGTCA 61.391 55.000 5.11 0.00 40.01 3.41
4542 4804 9.685276 TGTAATATCACCACAAGATTCAGATTT 57.315 29.630 0.00 0.00 0.00 2.17
4563 4825 8.186821 AGATTTGCACTGTATGAAGCTTTATTC 58.813 33.333 9.23 5.00 0.00 1.75
4565 4827 7.452880 TTGCACTGTATGAAGCTTTATTCTT 57.547 32.000 9.23 0.00 0.00 2.52
4606 4868 3.523972 TGGGTAGTTGGGTATGCAACATA 59.476 43.478 0.00 0.00 34.04 2.29
4607 4869 4.167113 TGGGTAGTTGGGTATGCAACATAT 59.833 41.667 0.00 0.00 34.04 1.78
4896 5158 2.034221 GAGGTGTTCCAGGGTGGC 59.966 66.667 0.00 0.00 37.47 5.01
5085 5347 2.094286 CAGTTTCGCTCATCTGACTCCT 60.094 50.000 0.00 0.00 0.00 3.69
5086 5348 2.094286 AGTTTCGCTCATCTGACTCCTG 60.094 50.000 0.00 0.00 0.00 3.86
5087 5349 1.839424 TTCGCTCATCTGACTCCTGA 58.161 50.000 0.00 0.00 0.00 3.86
5109 5371 7.773690 CCTGATGATGATGCTGGATATGAAATA 59.226 37.037 0.00 0.00 0.00 1.40
5238 5500 2.046285 GCACTACCATGGTGGGTGC 61.046 63.158 37.60 37.60 43.37 5.01
5477 5743 5.249420 ACTTTGGAGTGAAGATCTTAAGGC 58.751 41.667 8.25 0.00 33.99 4.35
5479 5745 4.478206 TGGAGTGAAGATCTTAAGGCAG 57.522 45.455 8.25 0.00 0.00 4.85
5500 5766 2.811101 CTAGGACGAGCAGCTGGG 59.189 66.667 17.12 0.00 0.00 4.45
5647 5913 3.549070 CCCAGTAACTATTTGTCGCGTAC 59.451 47.826 5.77 3.66 0.00 3.67
5697 5963 7.995488 TCAACTCATCTTTCTTCCTTTTCTTCT 59.005 33.333 0.00 0.00 0.00 2.85
5743 6009 5.049129 GCCCTGATGAATTGCTTCAGTATAC 60.049 44.000 6.76 0.00 44.32 1.47
5759 6025 6.845908 TCAGTATACGGTCCCTAATCTTACT 58.154 40.000 2.86 0.00 0.00 2.24
5817 6083 1.423541 TCCATTAATAGCCCGGTGCAT 59.576 47.619 15.92 6.03 44.83 3.96
5859 6125 2.366972 CAGGGTCCGGGGAAGGAT 60.367 66.667 0.00 0.00 43.04 3.24
5891 6157 8.588290 TTTAAATCCATTAATAGTGGTGCAGT 57.412 30.769 1.68 0.00 37.96 4.40
5892 6158 9.688091 TTTAAATCCATTAATAGTGGTGCAGTA 57.312 29.630 1.68 0.00 37.96 2.74
5893 6159 9.860650 TTAAATCCATTAATAGTGGTGCAGTAT 57.139 29.630 1.68 0.00 37.96 2.12
5895 6161 8.848474 AATCCATTAATAGTGGTGCAGTATAC 57.152 34.615 1.68 0.00 37.96 1.47
5896 6162 6.765403 TCCATTAATAGTGGTGCAGTATACC 58.235 40.000 0.00 0.00 37.96 2.73
5938 6212 7.927048 ACTACAGAAAGTATGAAACAAACCAC 58.073 34.615 0.00 0.00 30.93 4.16
6019 6293 2.915349 CTCTGTTGATGAGGATGGGTG 58.085 52.381 0.00 0.00 0.00 4.61
6084 6638 5.049680 AGTTCAACGGATTACATGTTGTGAC 60.050 40.000 2.30 0.00 42.65 3.67
6138 6693 2.551912 CCACCGTTCAACAGTGCCC 61.552 63.158 0.00 0.00 0.00 5.36
6141 6696 0.681564 ACCGTTCAACAGTGCCCAAA 60.682 50.000 0.00 0.00 0.00 3.28
6149 6704 4.211125 TCAACAGTGCCCAAAAGATAACA 58.789 39.130 0.00 0.00 0.00 2.41
6152 6707 6.663093 TCAACAGTGCCCAAAAGATAACATAT 59.337 34.615 0.00 0.00 0.00 1.78
6154 6709 5.296780 ACAGTGCCCAAAAGATAACATATCG 59.703 40.000 0.00 0.00 0.00 2.92
6155 6710 5.296780 CAGTGCCCAAAAGATAACATATCGT 59.703 40.000 0.00 0.00 0.00 3.73
6187 6742 6.276847 CAATAGTTCTAGAGCCTTACAGGTG 58.723 44.000 2.55 0.00 37.80 4.00
6189 6744 3.511934 AGTTCTAGAGCCTTACAGGTGTG 59.488 47.826 2.55 0.00 37.80 3.82
6383 6972 7.123247 CCCATAGTTCCATGTCAAGAAGAAAAT 59.877 37.037 0.00 0.00 0.00 1.82
6444 7033 7.671827 TCAATAATTATGAACTGTGTTCGACG 58.328 34.615 0.00 0.00 0.00 5.12
6474 7063 3.126858 TGAGATTTAATGTGTTCAGGCGC 59.873 43.478 0.00 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.201884 GGTGTCCAATCTATAGCAGTACTACAA 60.202 40.741 0.00 0.00 32.32 2.41
10 11 5.069251 AGTGGTGTCCAATCTATAGCAGTAC 59.931 44.000 0.00 0.00 34.18 2.73
15 16 5.934625 CCAATAGTGGTGTCCAATCTATAGC 59.065 44.000 0.00 0.00 40.42 2.97
43 44 6.566197 ACTAAAGGCAGAACAGATTTGAAG 57.434 37.500 0.00 0.00 0.00 3.02
66 67 8.722394 TGACAATATGATGCGTTTTACAGTAAA 58.278 29.630 1.26 1.26 0.00 2.01
96 99 4.098894 TCCTCCTTCCGGTGTAGTATTTT 58.901 43.478 0.00 0.00 0.00 1.82
97 100 3.716431 TCCTCCTTCCGGTGTAGTATTT 58.284 45.455 0.00 0.00 0.00 1.40
102 105 1.558233 ACTTCCTCCTTCCGGTGTAG 58.442 55.000 0.00 0.00 0.00 2.74
103 106 2.905415 TACTTCCTCCTTCCGGTGTA 57.095 50.000 0.00 0.00 0.00 2.90
104 107 2.249309 ATACTTCCTCCTTCCGGTGT 57.751 50.000 0.00 0.00 0.00 4.16
105 108 3.629142 AAATACTTCCTCCTTCCGGTG 57.371 47.619 0.00 0.00 0.00 4.94
106 109 3.872630 GCAAAATACTTCCTCCTTCCGGT 60.873 47.826 0.00 0.00 0.00 5.28
112 123 4.289672 TCTCCTTGCAAAATACTTCCTCCT 59.710 41.667 0.00 0.00 0.00 3.69
113 124 4.589908 TCTCCTTGCAAAATACTTCCTCC 58.410 43.478 0.00 0.00 0.00 4.30
222 236 9.269453 GGTGTTAAGTTATTGACTTCTTGTACT 57.731 33.333 0.00 0.00 45.40 2.73
223 237 9.048446 TGGTGTTAAGTTATTGACTTCTTGTAC 57.952 33.333 0.00 0.00 45.40 2.90
239 253 7.442364 CGATGAAGATAATCCATGGTGTTAAGT 59.558 37.037 12.58 0.00 0.00 2.24
244 258 4.347876 TCCGATGAAGATAATCCATGGTGT 59.652 41.667 12.58 3.25 0.00 4.16
304 322 0.457166 GCACCATGCTGACGTACGTA 60.457 55.000 22.87 5.89 40.96 3.57
305 323 1.736645 GCACCATGCTGACGTACGT 60.737 57.895 23.04 23.04 40.96 3.57
306 324 2.788176 CGCACCATGCTGACGTACG 61.788 63.158 15.01 15.01 42.25 3.67
307 325 1.683790 GACGCACCATGCTGACGTAC 61.684 60.000 9.44 0.00 42.25 3.67
322 340 2.126734 GTGCTGCCATGTTGACGC 60.127 61.111 0.00 0.00 0.00 5.19
359 377 2.216898 GTGCTGCTGTGAGTCTTCTTT 58.783 47.619 0.00 0.00 0.00 2.52
367 385 4.694233 AGGGCGTGCTGCTGTGAG 62.694 66.667 0.00 0.00 45.43 3.51
368 386 3.772853 AAAGGGCGTGCTGCTGTGA 62.773 57.895 0.00 0.00 45.43 3.58
369 387 3.259425 GAAAGGGCGTGCTGCTGTG 62.259 63.158 0.00 0.00 45.43 3.66
370 388 2.980233 GAAAGGGCGTGCTGCTGT 60.980 61.111 0.00 0.00 45.43 4.40
371 389 2.670934 AGAAAGGGCGTGCTGCTG 60.671 61.111 0.00 0.00 45.43 4.41
425 444 0.954452 CCATAGAAAATGGCCGGCTC 59.046 55.000 28.56 15.93 31.75 4.70
429 448 5.336690 CCCATTATTCCATAGAAAATGGCCG 60.337 44.000 15.56 6.25 42.22 6.13
434 453 8.495160 TGAATGCCCATTATTCCATAGAAAAT 57.505 30.769 0.00 0.00 35.09 1.82
502 521 3.676646 GTGTGGATGCTGCATTTCTTTTC 59.323 43.478 17.36 2.45 0.00 2.29
511 530 3.286329 AGAATATGTGTGGATGCTGCA 57.714 42.857 4.13 4.13 0.00 4.41
515 534 3.130869 TGGCAAAGAATATGTGTGGATGC 59.869 43.478 0.00 0.00 0.00 3.91
529 548 5.737063 GCATTTTCTGTCTTCTTGGCAAAGA 60.737 40.000 0.00 0.00 40.76 2.52
530 549 4.446719 GCATTTTCTGTCTTCTTGGCAAAG 59.553 41.667 0.00 0.00 34.45 2.77
539 564 0.794605 GCGCGGCATTTTCTGTCTTC 60.795 55.000 8.83 0.00 0.00 2.87
544 569 2.202518 CCAGCGCGGCATTTTCTG 60.203 61.111 8.83 4.28 0.00 3.02
588 613 4.142513 CCCAGTTTTCTTATGCTTCTCTGC 60.143 45.833 0.00 0.00 0.00 4.26
596 621 4.098501 CCATCCTTCCCAGTTTTCTTATGC 59.901 45.833 0.00 0.00 0.00 3.14
611 636 1.134699 TGACTGTCGCATCCATCCTTC 60.135 52.381 2.98 0.00 0.00 3.46
615 640 2.554142 TGAATGACTGTCGCATCCATC 58.446 47.619 2.98 0.00 0.00 3.51
616 641 2.696989 TGAATGACTGTCGCATCCAT 57.303 45.000 2.98 0.00 0.00 3.41
617 642 2.696989 ATGAATGACTGTCGCATCCA 57.303 45.000 2.98 0.00 0.00 3.41
619 644 4.093998 ACAAGAATGAATGACTGTCGCATC 59.906 41.667 2.98 2.24 0.00 3.91
620 645 4.005650 ACAAGAATGAATGACTGTCGCAT 58.994 39.130 2.98 4.31 0.00 4.73
621 646 3.402110 ACAAGAATGAATGACTGTCGCA 58.598 40.909 2.98 2.04 0.00 5.10
622 647 5.530519 TTACAAGAATGAATGACTGTCGC 57.469 39.130 2.98 0.00 0.00 5.19
623 648 6.963242 CCATTTACAAGAATGAATGACTGTCG 59.037 38.462 2.98 0.00 38.93 4.35
624 649 8.044060 TCCATTTACAAGAATGAATGACTGTC 57.956 34.615 0.00 0.00 38.93 3.51
625 650 7.121759 CCTCCATTTACAAGAATGAATGACTGT 59.878 37.037 0.00 0.00 38.93 3.55
626 651 7.415989 CCCTCCATTTACAAGAATGAATGACTG 60.416 40.741 0.00 0.00 38.93 3.51
627 652 6.604795 CCCTCCATTTACAAGAATGAATGACT 59.395 38.462 0.00 0.00 38.93 3.41
628 653 6.183360 CCCCTCCATTTACAAGAATGAATGAC 60.183 42.308 0.00 0.00 38.93 3.06
629 654 5.893255 CCCCTCCATTTACAAGAATGAATGA 59.107 40.000 0.00 0.00 38.93 2.57
632 657 4.609301 CCCCCTCCATTTACAAGAATGAA 58.391 43.478 0.00 0.00 38.93 2.57
676 702 1.299926 CTGCGCCGGATACAGGTAC 60.300 63.158 5.05 0.00 33.54 3.34
677 703 3.125607 CTGCGCCGGATACAGGTA 58.874 61.111 5.05 0.00 33.54 3.08
678 704 4.530857 GCTGCGCCGGATACAGGT 62.531 66.667 5.05 0.00 33.54 4.00
760 786 2.789208 CAGTAAGTGCCATTGAATGCG 58.211 47.619 0.00 0.00 0.00 4.73
812 838 1.447643 CCGGAGGCCAATGGAGTAG 59.552 63.158 5.01 0.00 46.14 2.57
895 921 0.532573 TACTTCCTTCCAGCTCGCTG 59.467 55.000 11.83 11.83 43.26 5.18
914 940 0.034380 TACGCCTCTAGCTGTCCACT 60.034 55.000 0.00 0.00 40.39 4.00
915 941 0.382515 CTACGCCTCTAGCTGTCCAC 59.617 60.000 0.00 0.00 40.39 4.02
916 942 0.255033 TCTACGCCTCTAGCTGTCCA 59.745 55.000 0.00 0.00 40.39 4.02
929 955 4.082523 TGGTGGCTGGCTCTACGC 62.083 66.667 2.00 0.00 38.13 4.42
930 956 2.125512 GTGGTGGCTGGCTCTACG 60.126 66.667 2.00 0.00 0.00 3.51
931 957 2.269241 GGTGGTGGCTGGCTCTAC 59.731 66.667 10.55 10.55 0.00 2.59
932 958 3.390521 CGGTGGTGGCTGGCTCTA 61.391 66.667 2.00 0.00 0.00 2.43
1029 1072 1.427592 GCTTGATGCAGAGCGAGGAC 61.428 60.000 4.08 0.00 42.31 3.85
1034 1077 1.808799 ACGAGCTTGATGCAGAGCG 60.809 57.895 8.31 0.00 45.94 5.03
1055 1098 2.186384 CGAGGAAGCAGAGGCAGG 59.814 66.667 0.00 0.00 44.61 4.85
1103 1147 1.450848 CGGACAGCATGCATGGAGT 60.451 57.895 27.34 9.85 42.53 3.85
1107 1151 0.241749 AAACACGGACAGCATGCATG 59.758 50.000 22.70 22.70 42.53 4.06
1108 1152 0.523072 GAAACACGGACAGCATGCAT 59.477 50.000 21.98 7.42 42.53 3.96
1109 1153 0.534877 AGAAACACGGACAGCATGCA 60.535 50.000 21.98 0.00 42.53 3.96
1110 1154 0.593128 AAGAAACACGGACAGCATGC 59.407 50.000 10.51 10.51 42.53 4.06
1134 1178 3.552890 GGTGTTTGGATGGAAGCAGAAAC 60.553 47.826 0.00 0.00 0.00 2.78
1243 1287 5.062528 AGAAGGAAAACAGAAGCTGAGAAG 58.937 41.667 0.82 0.00 35.18 2.85
1260 1304 2.724454 CGACTACTGGGAGAAGAAGGA 58.276 52.381 0.00 0.00 0.00 3.36
1272 1317 2.602211 CTGAATGAGCAAGCGACTACTG 59.398 50.000 0.00 0.00 0.00 2.74
1301 1346 2.100087 GTCCGAGGAGAGAAGTTCATCC 59.900 54.545 15.86 15.86 0.00 3.51
1306 1351 4.319177 CAAAATGTCCGAGGAGAGAAGTT 58.681 43.478 0.00 0.00 0.00 2.66
1318 1363 0.519961 GACCGGAACCAAAATGTCCG 59.480 55.000 9.46 4.37 42.91 4.79
1341 1386 2.439507 ACATAATCCGAGGGCACAAGAT 59.560 45.455 0.00 0.00 0.00 2.40
1374 1419 4.030216 TGCATGGTCCTCTATCTGTTACA 58.970 43.478 0.00 0.00 0.00 2.41
1375 1420 4.100189 AGTGCATGGTCCTCTATCTGTTAC 59.900 45.833 0.00 0.00 0.00 2.50
1376 1421 4.290093 AGTGCATGGTCCTCTATCTGTTA 58.710 43.478 0.00 0.00 0.00 2.41
1378 1423 2.756907 AGTGCATGGTCCTCTATCTGT 58.243 47.619 0.00 0.00 0.00 3.41
1379 1424 5.011431 TGAATAGTGCATGGTCCTCTATCTG 59.989 44.000 0.00 0.00 0.00 2.90
1467 1588 7.391148 AACAGGTACACCTTTTTATAGCATG 57.609 36.000 0.00 0.00 46.09 4.06
1482 1605 5.020795 TGCTACTCCAGATAAACAGGTACA 58.979 41.667 0.00 0.00 0.00 2.90
1506 1629 5.155161 TGGTCTCCTGGTATTATGCTACAT 58.845 41.667 0.00 0.00 0.00 2.29
1507 1630 4.552674 TGGTCTCCTGGTATTATGCTACA 58.447 43.478 0.00 0.00 0.00 2.74
1508 1631 4.833380 TCTGGTCTCCTGGTATTATGCTAC 59.167 45.833 0.00 0.00 0.00 3.58
1509 1632 4.833380 GTCTGGTCTCCTGGTATTATGCTA 59.167 45.833 0.00 0.00 0.00 3.49
1510 1633 3.643792 GTCTGGTCTCCTGGTATTATGCT 59.356 47.826 0.00 0.00 0.00 3.79
1511 1634 3.388024 TGTCTGGTCTCCTGGTATTATGC 59.612 47.826 0.00 0.00 0.00 3.14
1512 1635 4.651503 AGTGTCTGGTCTCCTGGTATTATG 59.348 45.833 0.00 0.00 0.00 1.90
1513 1636 4.651503 CAGTGTCTGGTCTCCTGGTATTAT 59.348 45.833 0.00 0.00 0.00 1.28
1531 1654 9.772973 TGTACTTGTTAACTATTTCATCAGTGT 57.227 29.630 7.22 0.00 0.00 3.55
1551 1674 3.009033 TGAGCACTTGGGCTAATGTACTT 59.991 43.478 0.00 0.00 45.99 2.24
1611 1745 4.924462 GCTCTAAAGTTCGCAAGTTCTAGT 59.076 41.667 0.00 0.00 39.48 2.57
1638 1772 1.276415 TTGCTCGCTTTGTTTGTTGC 58.724 45.000 0.00 0.00 0.00 4.17
1640 1774 4.677584 TGTTATTGCTCGCTTTGTTTGTT 58.322 34.783 0.00 0.00 0.00 2.83
1643 1777 5.105752 TGTTTGTTATTGCTCGCTTTGTTT 58.894 33.333 0.00 0.00 0.00 2.83
1652 1786 6.801862 GTGTTCCATACTGTTTGTTATTGCTC 59.198 38.462 0.00 0.00 0.00 4.26
1727 1864 1.456705 CTTCTCGAGGGGAGGGAGG 60.457 68.421 13.56 0.00 43.34 4.30
2069 2206 2.101415 TGATGATACGGAACCTCAGCAG 59.899 50.000 0.00 0.00 30.98 4.24
2098 2235 9.646427 GGGAAGAATGATGATATACTACAACTC 57.354 37.037 0.00 0.00 0.00 3.01
2100 2237 9.646427 GAGGGAAGAATGATGATATACTACAAC 57.354 37.037 0.00 0.00 0.00 3.32
2102 2239 9.029368 CAGAGGGAAGAATGATGATATACTACA 57.971 37.037 0.00 0.00 0.00 2.74
2105 2242 7.955185 AGACAGAGGGAAGAATGATGATATACT 59.045 37.037 0.00 0.00 0.00 2.12
2135 2272 3.093574 CTGCTTTCACGTTTATCATGCG 58.906 45.455 0.00 0.00 0.00 4.73
2199 2336 5.876357 AGCTAACTTGATTCTGGGTTAACA 58.124 37.500 8.10 0.00 0.00 2.41
2323 2460 1.593750 CTCCTGGCGCTATCACTGC 60.594 63.158 7.64 0.00 0.00 4.40
2354 2492 1.297456 GCAGCACTCAAGCAGACCTC 61.297 60.000 0.00 0.00 36.85 3.85
2402 2543 2.564471 GCAAATGCAGAGAGCTGGT 58.436 52.632 0.00 0.00 45.94 4.00
2473 2627 4.226384 ACTTTGGGGAGAAATTTGAGCTT 58.774 39.130 0.00 0.00 0.00 3.74
2662 2820 8.158169 TGATGAATGCAATATCTAAACTGACC 57.842 34.615 0.00 0.00 0.00 4.02
2679 2837 3.488047 GGCTCCACGTTTGATGATGAATG 60.488 47.826 0.00 0.00 0.00 2.67
2886 3044 9.095065 GTACTACTGACATAACCCAAATTACTG 57.905 37.037 0.00 0.00 0.00 2.74
2966 3124 4.843984 CGCAGGTACTCATTGTTAAAAACG 59.156 41.667 0.00 0.00 34.60 3.60
3020 3178 8.135529 GCAGTACCTTCTTGTTTTTCTTTATGT 58.864 33.333 0.00 0.00 0.00 2.29
3021 3179 8.134895 TGCAGTACCTTCTTGTTTTTCTTTATG 58.865 33.333 0.00 0.00 0.00 1.90
3023 3181 7.633193 TGCAGTACCTTCTTGTTTTTCTTTA 57.367 32.000 0.00 0.00 0.00 1.85
3025 3183 6.715347 ATGCAGTACCTTCTTGTTTTTCTT 57.285 33.333 0.00 0.00 0.00 2.52
3060 3219 0.605319 TACCAAAGCCGAGGCACTTG 60.605 55.000 17.18 17.11 41.55 3.16
3146 3305 7.438757 TCCAACATGAAACATGAGTCATTTTTG 59.561 33.333 19.40 10.30 32.06 2.44
3152 3311 5.769162 TGATTCCAACATGAAACATGAGTCA 59.231 36.000 16.86 2.27 0.00 3.41
3218 3377 4.278170 TGATTCCAACAGGAAACATGTGAC 59.722 41.667 0.00 0.00 44.20 3.67
3273 3432 8.652290 ACCCTCTGTTCCTAAATATAAGACATC 58.348 37.037 0.00 0.00 0.00 3.06
3327 3584 5.717078 ATTGTTGATATGCCCATGTGATC 57.283 39.130 0.00 0.00 0.00 2.92
3477 3736 6.455360 TGCTAATTCATCTTCATGGGTTTC 57.545 37.500 0.00 0.00 0.00 2.78
3506 3765 5.754406 TGGCATGCTTATCAATTACAAATGC 59.246 36.000 18.92 0.00 37.70 3.56
3633 3892 0.957395 ATCCTGCACGAAGCTGTTGG 60.957 55.000 6.22 4.08 45.94 3.77
3826 4085 3.554692 GCGTCGAAGATGGTGCCG 61.555 66.667 1.37 0.00 45.11 5.69
3916 4175 3.006859 ACACTATCTTGTGCACACTAGCA 59.993 43.478 21.56 3.05 43.35 3.49
3941 4200 2.000447 GGATGTACCTTGTTGCGAGTC 59.000 52.381 0.00 0.00 35.41 3.36
4040 4299 2.917713 AAAAGGGTACATGATGGCCA 57.082 45.000 8.56 8.56 0.00 5.36
4121 4380 0.395862 GGAGTCTCCCGTCCTCATCA 60.396 60.000 7.78 0.00 0.00 3.07
4307 4566 0.036164 TGGAGTTCATGGGGTTGTCG 59.964 55.000 0.00 0.00 0.00 4.35
4379 4638 2.094762 ACACACCGGCTTCAGTTATC 57.905 50.000 0.00 0.00 0.00 1.75
4542 4804 6.654582 TCAAGAATAAAGCTTCATACAGTGCA 59.345 34.615 0.00 0.00 0.00 4.57
4644 4906 9.495754 GACATAAGTTTCATTTTGACTCATAGC 57.504 33.333 0.00 0.00 0.00 2.97
4755 5017 3.727726 TGTAGTATGGTGCATTGGATCG 58.272 45.455 0.00 0.00 0.00 3.69
4896 5158 6.520272 ACCATCGATCTTCTCAAGGATAAAG 58.480 40.000 0.00 0.00 0.00 1.85
5085 5347 8.545472 TCTATTTCATATCCAGCATCATCATCA 58.455 33.333 0.00 0.00 0.00 3.07
5086 5348 8.959705 TCTATTTCATATCCAGCATCATCATC 57.040 34.615 0.00 0.00 0.00 2.92
5087 5349 9.749340 TTTCTATTTCATATCCAGCATCATCAT 57.251 29.630 0.00 0.00 0.00 2.45
5109 5371 2.787994 CTCATGTTGAGCACCCTTTCT 58.212 47.619 0.00 0.00 37.72 2.52
5238 5500 0.178068 CGACCACCTTCCCTACATGG 59.822 60.000 0.00 0.00 36.46 3.66
5477 5743 3.764810 CTGCTCGTCCTAGCCGCTG 62.765 68.421 2.16 0.00 42.05 5.18
5500 5766 4.756502 GGTGTTCAGGAATCTACTACACC 58.243 47.826 0.00 0.00 44.80 4.16
5647 5913 9.689976 TGATAAACAATTTAATGGGCAATATCG 57.310 29.630 0.00 0.00 0.00 2.92
5697 5963 6.127423 GGGCTTGTGTCTCATACTCTACTTAA 60.127 42.308 0.00 0.00 0.00 1.85
5743 6009 5.057149 CCATTCAAGTAAGATTAGGGACCG 58.943 45.833 0.00 0.00 0.00 4.79
5802 6068 1.270625 GCTACATGCACCGGGCTATTA 60.271 52.381 6.32 0.00 45.15 0.98
5804 6070 1.071471 GCTACATGCACCGGGCTAT 59.929 57.895 6.32 0.53 45.15 2.97
5805 6071 2.028125 GAGCTACATGCACCGGGCTA 62.028 60.000 6.32 0.00 45.94 3.93
5806 6072 3.391665 GAGCTACATGCACCGGGCT 62.392 63.158 6.32 0.81 45.94 5.19
5807 6073 2.897350 GAGCTACATGCACCGGGC 60.897 66.667 6.32 7.25 45.94 6.13
5808 6074 2.203070 GGAGCTACATGCACCGGG 60.203 66.667 6.32 0.00 42.21 5.73
5841 6107 2.891307 GATCCTTCCCCGGACCCTGA 62.891 65.000 0.73 0.00 35.52 3.86
5904 6178 9.832445 TTTCATACTTTCTGTAGTTGAGACTTT 57.168 29.630 0.00 0.00 37.33 2.66
5916 6190 6.377146 ACAGTGGTTTGTTTCATACTTTCTGT 59.623 34.615 0.00 0.00 0.00 3.41
6138 6693 7.148490 TGGACACACACGATATGTTATCTTTTG 60.148 37.037 0.00 0.00 40.64 2.44
6141 6696 5.972935 TGGACACACACGATATGTTATCTT 58.027 37.500 0.00 0.00 40.64 2.40
6149 6704 6.222038 AGAACTATTGGACACACACGATAT 57.778 37.500 0.00 0.00 0.00 1.63
6152 6707 4.763279 TCTAGAACTATTGGACACACACGA 59.237 41.667 0.00 0.00 0.00 4.35
6154 6709 4.865365 GCTCTAGAACTATTGGACACACAC 59.135 45.833 0.00 0.00 0.00 3.82
6155 6710 4.081642 GGCTCTAGAACTATTGGACACACA 60.082 45.833 0.00 0.00 0.00 3.72
6187 6742 2.906691 AGCTATGATGGTCTCAGCAC 57.093 50.000 0.00 0.00 42.46 4.40
6189 6744 3.006752 AGCTTAGCTATGATGGTCTCAGC 59.993 47.826 4.30 4.87 36.99 4.26
6383 6972 6.315393 GGAGTCTTGGAAACTTTATCGCAATA 59.685 38.462 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.