Multiple sequence alignment - TraesCS5D01G483200

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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 TraesCS5D01G483200 chr5D 100.000 7959 0 0 1 7959 520124479 520132437 0.000000e+00 14698.0
1 TraesCS5D01G483200 chr5A 97.050 5288 119 17 1943 7209 647362024 647367295 0.000000e+00 8866.0
2 TraesCS5D01G483200 chr5A 92.476 1050 58 11 900 1944 647360938 647361971 0.000000e+00 1482.0
3 TraesCS5D01G483200 chr5A 90.924 628 32 2 7357 7959 647368718 647369345 0.000000e+00 821.0
4 TraesCS5D01G483200 chr5B 95.157 3985 110 32 3305 7255 655145324 655149259 0.000000e+00 6213.0
5 TraesCS5D01G483200 chr5B 95.338 1866 70 9 1450 3307 655143355 655145211 0.000000e+00 2948.0
6 TraesCS5D01G483200 chr5B 90.678 590 29 9 41 625 655142002 655142570 0.000000e+00 761.0
7 TraesCS5D01G483200 chr5B 87.994 658 37 15 778 1413 655142718 655143355 0.000000e+00 739.0
8 TraesCS5D01G483200 chr5B 80.679 383 63 7 7473 7844 655149908 655150290 3.630000e-73 287.0
9 TraesCS5D01G483200 chr5B 77.474 293 59 5 7671 7958 504812717 504813007 1.370000e-37 169.0
10 TraesCS5D01G483200 chr5B 87.500 136 10 5 642 775 655142553 655142683 4.980000e-32 150.0
11 TraesCS5D01G483200 chr5B 94.318 88 4 1 7271 7358 655149368 655149454 5.010000e-27 134.0
12 TraesCS5D01G483200 chrUn 75.902 610 110 27 7365 7959 338402293 338402880 2.190000e-70 278.0
13 TraesCS5D01G483200 chrUn 75.902 610 110 27 7365 7959 443405548 443404961 2.190000e-70 278.0
14 TraesCS5D01G483200 chrUn 78.626 131 23 4 7831 7958 226037830 226037958 1.840000e-11 82.4
15 TraesCS5D01G483200 chrUn 78.626 131 23 4 7831 7958 250213140 250213268 1.840000e-11 82.4
16 TraesCS5D01G483200 chr6A 76.436 505 96 15 7472 7958 94188679 94189178 1.330000e-62 252.0
17 TraesCS5D01G483200 chr1A 76.862 376 75 11 7590 7958 118816468 118816098 1.350000e-47 202.0
18 TraesCS5D01G483200 chr7D 78.521 284 53 7 7681 7958 484347400 484347681 6.350000e-41 180.0
19 TraesCS5D01G483200 chr7D 73.333 285 66 7 7681 7958 39549997 39549716 6.570000e-16 97.1
20 TraesCS5D01G483200 chr7A 74.528 424 88 15 7472 7888 239614236 239613826 4.940000e-37 167.0
21 TraesCS5D01G483200 chr2D 97.619 42 1 0 7917 7958 139497645 139497686 1.110000e-08 73.1
22 TraesCS5D01G483200 chr2D 100.000 30 0 0 3 32 102698699 102698670 1.000000e-03 56.5
23 TraesCS5D01G483200 chr4A 80.233 86 9 5 7876 7958 719146301 719146381 3.100000e-04 58.4


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 TraesCS5D01G483200 chr5D 520124479 520132437 7958 False 14698.000000 14698 100.000000 1 7959 1 chr5D.!!$F1 7958
1 TraesCS5D01G483200 chr5A 647360938 647369345 8407 False 3723.000000 8866 93.483333 900 7959 3 chr5A.!!$F1 7059
2 TraesCS5D01G483200 chr5B 655142002 655150290 8288 False 1604.571429 6213 90.237714 41 7844 7 chr5B.!!$F2 7803
3 TraesCS5D01G483200 chrUn 338402293 338402880 587 False 278.000000 278 75.902000 7365 7959 1 chrUn.!!$F3 594
4 TraesCS5D01G483200 chrUn 443404961 443405548 587 True 278.000000 278 75.902000 7365 7959 1 chrUn.!!$R1 594

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
285 286 0.032130 ACGACATATAGTGCCGGCAG 59.968 55.000 33.73 20.10 38.08 4.85 F
286 287 0.032130 CGACATATAGTGCCGGCAGT 59.968 55.000 37.19 37.19 29.31 4.40 F
1565 1633 0.037326 TGTGAGACACGGCTCAATCC 60.037 55.000 3.63 0.00 45.69 3.01 F
1650 1718 3.718815 TGGTGTCGTATATGCGCAATAA 58.281 40.909 17.11 2.95 0.00 1.40 F
2372 2499 3.586470 GAGGATGAGGTACCTCTCTCA 57.414 52.381 35.83 21.30 46.28 3.27 F
4033 4285 1.946984 AACAGAAGACCGGGGATACA 58.053 50.000 6.32 0.00 39.74 2.29 F
4122 4374 0.036010 CACTCACCAAGTAGGCCAGG 60.036 60.000 5.01 0.47 43.14 4.45 F
4630 4889 0.391130 TATCGCACACAAGGACCTGC 60.391 55.000 0.00 0.00 0.00 4.85 F
6164 6441 0.321653 GACGACCACTGCCCATTTCT 60.322 55.000 0.00 0.00 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1540 1608 0.180406 AGCCGTGTCTCACAAAACCT 59.820 50.000 1.00 0.00 33.40 3.50 R
1582 1650 0.944311 GCGTCAGAACTTGCTTCCGA 60.944 55.000 0.00 0.00 0.00 4.55 R
2372 2499 1.187087 CGGGCCTTTGTAGAGAGAGT 58.813 55.000 0.84 0.00 0.00 3.24 R
2988 3121 3.015145 GCAGGGTAGGAAGGGGCA 61.015 66.667 0.00 0.00 0.00 5.36 R
4066 4318 0.789753 CGTGTGTAGTCGTCTCAGCG 60.790 60.000 0.00 0.00 0.00 5.18 R
5839 6116 0.395173 AGGAGAGGACGAAGAGGAGC 60.395 60.000 0.00 0.00 0.00 4.70 R
6164 6441 0.401738 CACTGGAAAGAAGAGCCCCA 59.598 55.000 0.00 0.00 0.00 4.96 R
6304 6581 0.035152 TGGACATGCCGCTTCTCATT 60.035 50.000 0.00 0.00 40.66 2.57 R
7782 9603 0.320421 TAACAGGTTGGCGCAGACTC 60.320 55.000 10.83 1.45 34.59 3.36 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
17 18 4.029472 GCTAGTCCGGGTTCCAGA 57.971 61.111 0.00 0.00 0.00 3.86
18 19 1.817209 GCTAGTCCGGGTTCCAGAG 59.183 63.158 0.00 0.00 0.00 3.35
19 20 1.677637 GCTAGTCCGGGTTCCAGAGG 61.678 65.000 0.00 0.00 0.00 3.69
20 21 1.001248 TAGTCCGGGTTCCAGAGGG 59.999 63.158 0.00 0.00 0.00 4.30
21 22 4.097361 GTCCGGGTTCCAGAGGGC 62.097 72.222 0.00 0.00 0.00 5.19
24 25 3.330720 CGGGTTCCAGAGGGCCTT 61.331 66.667 7.89 0.00 0.00 4.35
25 26 2.907179 CGGGTTCCAGAGGGCCTTT 61.907 63.158 7.89 0.00 0.00 3.11
26 27 1.559065 CGGGTTCCAGAGGGCCTTTA 61.559 60.000 7.89 0.00 0.00 1.85
27 28 0.256177 GGGTTCCAGAGGGCCTTTAG 59.744 60.000 7.89 0.00 0.00 1.85
28 29 0.992695 GGTTCCAGAGGGCCTTTAGT 59.007 55.000 7.89 0.00 0.00 2.24
29 30 1.065345 GGTTCCAGAGGGCCTTTAGTC 60.065 57.143 7.89 0.00 0.00 2.59
30 31 1.065345 GTTCCAGAGGGCCTTTAGTCC 60.065 57.143 7.89 0.00 0.00 3.85
31 32 0.620700 TCCAGAGGGCCTTTAGTCCC 60.621 60.000 7.89 0.00 42.94 4.46
35 36 2.588439 GGGCCTTTAGTCCCGGTC 59.412 66.667 0.84 0.00 32.00 4.79
36 37 2.186125 GGCCTTTAGTCCCGGTCG 59.814 66.667 0.00 0.00 0.00 4.79
37 38 2.186125 GCCTTTAGTCCCGGTCGG 59.814 66.667 0.00 1.86 0.00 4.79
38 39 2.653087 GCCTTTAGTCCCGGTCGGT 61.653 63.158 8.67 0.00 0.00 4.69
39 40 1.514553 CCTTTAGTCCCGGTCGGTC 59.485 63.158 8.67 1.68 0.00 4.79
60 61 5.007724 GGTCCCTGATATTTCAAATCGTGTC 59.992 44.000 0.00 0.00 0.00 3.67
93 94 1.289380 GAAGCACCGAGACCGAAGT 59.711 57.895 0.00 0.00 38.22 3.01
105 106 3.414700 CGAAGTGGTGGCGCTGAC 61.415 66.667 7.64 4.23 0.00 3.51
129 130 1.134901 CTCGAACAGGACCGACTCG 59.865 63.158 5.97 5.97 0.00 4.18
150 151 2.170166 GAACCAGGGACAATGCATCAA 58.830 47.619 0.00 0.00 0.00 2.57
169 170 0.252197 ATTGCGGTGGAGGGAAGTAC 59.748 55.000 0.00 0.00 0.00 2.73
177 178 3.522553 GTGGAGGGAAGTACGAGATTTG 58.477 50.000 0.00 0.00 0.00 2.32
198 199 4.489771 AATTCTGGCGCGGGAGGG 62.490 66.667 8.83 0.00 46.83 4.30
238 239 3.454375 GATTGGATCGTTCGAGGCTTAA 58.546 45.455 0.80 0.00 0.00 1.85
279 280 2.276201 TGGCAACACGACATATAGTGC 58.724 47.619 0.00 0.00 46.17 4.40
280 281 1.597663 GGCAACACGACATATAGTGCC 59.402 52.381 0.00 0.00 41.72 5.01
281 282 1.257936 GCAACACGACATATAGTGCCG 59.742 52.381 0.00 0.00 41.72 5.69
282 283 1.858458 CAACACGACATATAGTGCCGG 59.142 52.381 0.00 0.00 41.72 6.13
283 284 0.249322 ACACGACATATAGTGCCGGC 60.249 55.000 22.73 22.73 41.72 6.13
284 285 0.249280 CACGACATATAGTGCCGGCA 60.249 55.000 29.03 29.03 38.08 5.69
285 286 0.032130 ACGACATATAGTGCCGGCAG 59.968 55.000 33.73 20.10 38.08 4.85
286 287 0.032130 CGACATATAGTGCCGGCAGT 59.968 55.000 37.19 37.19 29.31 4.40
287 288 1.538204 CGACATATAGTGCCGGCAGTT 60.538 52.381 39.78 27.68 29.31 3.16
288 289 2.135933 GACATATAGTGCCGGCAGTTC 58.864 52.381 39.78 26.71 0.00 3.01
289 290 1.202651 ACATATAGTGCCGGCAGTTCC 60.203 52.381 39.78 23.78 0.00 3.62
290 291 0.396811 ATATAGTGCCGGCAGTTCCC 59.603 55.000 39.78 23.38 0.00 3.97
291 292 0.978667 TATAGTGCCGGCAGTTCCCA 60.979 55.000 39.78 23.67 0.00 4.37
292 293 2.536997 ATAGTGCCGGCAGTTCCCAC 62.537 60.000 39.78 21.84 0.00 4.61
334 335 0.250513 GAGATGGAGACCACACACCC 59.749 60.000 0.00 0.00 35.80 4.61
455 461 4.445452 ACATCATGTGCCAGTTTTGATC 57.555 40.909 0.00 0.00 0.00 2.92
510 516 1.634702 GATGTGTCGAGGTCAAGAGC 58.365 55.000 0.00 0.00 0.00 4.09
521 527 1.594331 GTCAAGAGCTGTCCGGTTTT 58.406 50.000 0.00 0.00 0.00 2.43
528 534 2.357952 GAGCTGTCCGGTTTTGAAAGTT 59.642 45.455 0.00 0.00 0.00 2.66
537 543 3.258123 CGGTTTTGAAAGTTGGGGATGAT 59.742 43.478 0.00 0.00 0.00 2.45
565 571 4.756502 ACCGGCTTTAAAGTGTAGAGATC 58.243 43.478 16.38 0.00 0.00 2.75
570 576 6.369065 CGGCTTTAAAGTGTAGAGATCAAACT 59.631 38.462 16.38 0.00 0.00 2.66
604 610 7.113658 TGATGAATTGAGGTACTAGAAGGAC 57.886 40.000 0.00 0.00 41.55 3.85
607 613 5.783360 TGAATTGAGGTACTAGAAGGACCAA 59.217 40.000 10.90 0.00 41.55 3.67
608 614 6.271391 TGAATTGAGGTACTAGAAGGACCAAA 59.729 38.462 10.90 5.22 41.55 3.28
609 615 5.740290 TTGAGGTACTAGAAGGACCAAAG 57.260 43.478 10.90 0.00 41.55 2.77
610 616 4.748701 TGAGGTACTAGAAGGACCAAAGT 58.251 43.478 10.90 0.00 41.55 2.66
611 617 5.152934 TGAGGTACTAGAAGGACCAAAGTT 58.847 41.667 10.90 0.00 41.55 2.66
612 618 5.605488 TGAGGTACTAGAAGGACCAAAGTTT 59.395 40.000 10.90 0.00 41.55 2.66
613 619 6.100714 TGAGGTACTAGAAGGACCAAAGTTTT 59.899 38.462 10.90 0.00 41.55 2.43
614 620 6.531923 AGGTACTAGAAGGACCAAAGTTTTC 58.468 40.000 10.90 0.00 36.02 2.29
615 621 6.100714 AGGTACTAGAAGGACCAAAGTTTTCA 59.899 38.462 10.90 0.00 36.02 2.69
616 622 6.940867 GGTACTAGAAGGACCAAAGTTTTCAT 59.059 38.462 3.31 0.00 33.16 2.57
617 623 7.447545 GGTACTAGAAGGACCAAAGTTTTCATT 59.552 37.037 3.31 0.00 33.16 2.57
618 624 9.498176 GTACTAGAAGGACCAAAGTTTTCATTA 57.502 33.333 0.00 0.00 0.00 1.90
619 625 8.622948 ACTAGAAGGACCAAAGTTTTCATTAG 57.377 34.615 0.00 0.00 0.00 1.73
620 626 8.437575 ACTAGAAGGACCAAAGTTTTCATTAGA 58.562 33.333 0.00 0.00 0.00 2.10
621 627 9.454859 CTAGAAGGACCAAAGTTTTCATTAGAT 57.545 33.333 0.00 0.00 0.00 1.98
622 628 8.712228 AGAAGGACCAAAGTTTTCATTAGATT 57.288 30.769 0.00 0.00 0.00 2.40
623 629 9.147732 AGAAGGACCAAAGTTTTCATTAGATTT 57.852 29.630 0.00 0.00 0.00 2.17
624 630 9.411801 GAAGGACCAAAGTTTTCATTAGATTTC 57.588 33.333 0.00 0.00 0.00 2.17
625 631 7.896811 AGGACCAAAGTTTTCATTAGATTTCC 58.103 34.615 0.00 0.00 0.00 3.13
626 632 7.508977 AGGACCAAAGTTTTCATTAGATTTCCA 59.491 33.333 0.00 0.00 0.00 3.53
627 633 8.314021 GGACCAAAGTTTTCATTAGATTTCCAT 58.686 33.333 0.00 0.00 0.00 3.41
628 634 9.358872 GACCAAAGTTTTCATTAGATTTCCATC 57.641 33.333 0.00 0.00 0.00 3.51
629 635 8.028938 ACCAAAGTTTTCATTAGATTTCCATCG 58.971 33.333 0.00 0.00 34.17 3.84
630 636 7.009540 CCAAAGTTTTCATTAGATTTCCATCGC 59.990 37.037 0.00 0.00 34.17 4.58
631 637 6.757897 AGTTTTCATTAGATTTCCATCGCA 57.242 33.333 0.00 0.00 34.17 5.10
632 638 7.156876 AGTTTTCATTAGATTTCCATCGCAA 57.843 32.000 0.00 0.00 34.17 4.85
633 639 7.601856 AGTTTTCATTAGATTTCCATCGCAAA 58.398 30.769 0.00 0.00 34.17 3.68
634 640 8.087750 AGTTTTCATTAGATTTCCATCGCAAAA 58.912 29.630 0.00 0.00 34.17 2.44
635 641 8.707839 GTTTTCATTAGATTTCCATCGCAAAAA 58.292 29.630 0.00 0.00 34.17 1.94
701 707 7.517321 GCAAGAAACTCATCAAAACAAACAAA 58.483 30.769 0.00 0.00 0.00 2.83
762 768 7.506328 ACTTACCATTTTGACTTAAGACACC 57.494 36.000 10.09 0.00 0.00 4.16
775 781 3.845781 AAGACACCAAGACAGACACAT 57.154 42.857 0.00 0.00 0.00 3.21
776 782 4.955811 AAGACACCAAGACAGACACATA 57.044 40.909 0.00 0.00 0.00 2.29
787 825 8.783093 CCAAGACAGACACATACTTTTGATTAA 58.217 33.333 0.00 0.00 0.00 1.40
847 885 2.357075 GAAACGGAGGGAGGATCAAAC 58.643 52.381 0.00 0.00 36.25 2.93
866 904 3.791973 ACGTTTCCATTTTTGCACTCA 57.208 38.095 0.00 0.00 0.00 3.41
1003 1050 3.387050 CCGGAGTAAAACCCTAGCTATGT 59.613 47.826 0.00 0.00 0.00 2.29
1004 1051 4.501058 CCGGAGTAAAACCCTAGCTATGTC 60.501 50.000 0.00 0.00 0.00 3.06
1005 1052 4.501058 CGGAGTAAAACCCTAGCTATGTCC 60.501 50.000 0.00 0.00 0.00 4.02
1288 1341 2.829003 TCTCGCGGCTAGGTGAGG 60.829 66.667 6.13 0.00 43.17 3.86
1354 1419 3.275999 AGCAGGACAGTTTAAAACGTGT 58.724 40.909 0.00 0.00 36.23 4.49
1376 1441 0.179032 TCCCTTGCACACATTGTCGT 60.179 50.000 0.00 0.00 0.00 4.34
1382 1447 2.280628 TGCACACATTGTCGTTGTACA 58.719 42.857 0.00 0.00 0.00 2.90
1395 1461 2.470821 GTTGTACACAACGTGAGAGCT 58.529 47.619 9.31 0.00 45.44 4.09
1403 1469 2.549754 ACAACGTGAGAGCTTGATTTGG 59.450 45.455 0.00 0.00 0.00 3.28
1434 1500 7.647318 TGTAGTTCGTACGTTTGTAAGAAATCA 59.353 33.333 16.05 4.50 45.99 2.57
1445 1511 5.227569 TGTAAGAAATCAGCCTGACAGAA 57.772 39.130 3.32 0.00 0.00 3.02
1479 1545 3.787001 TGGTCGCACCACACCACA 61.787 61.111 4.16 0.00 44.79 4.17
1515 1581 2.295909 TCCCAGTTTTGCGATTTTCCAG 59.704 45.455 0.00 0.00 0.00 3.86
1524 1590 2.557924 TGCGATTTTCCAGCTGAAACAT 59.442 40.909 17.39 0.00 42.56 2.71
1557 1625 3.875134 AGTTTAGGTTTTGTGAGACACGG 59.125 43.478 0.00 0.00 37.14 4.94
1561 1629 1.295792 GTTTTGTGAGACACGGCTCA 58.704 50.000 0.00 0.00 42.31 4.26
1565 1633 0.037326 TGTGAGACACGGCTCAATCC 60.037 55.000 3.63 0.00 45.69 3.01
1579 1647 5.568392 GGCTCAATCCCATCTAGATTTCAT 58.432 41.667 1.33 0.00 31.56 2.57
1582 1650 7.833183 GGCTCAATCCCATCTAGATTTCATATT 59.167 37.037 1.33 0.00 31.56 1.28
1643 1711 4.514781 TCCATACTGGTGTCGTATATGC 57.485 45.455 0.00 0.00 39.03 3.14
1650 1718 3.718815 TGGTGTCGTATATGCGCAATAA 58.281 40.909 17.11 2.95 0.00 1.40
1944 2067 4.268884 GTGCGCAAACAAAAATCAACCTAA 59.731 37.500 14.00 0.00 0.00 2.69
2372 2499 3.586470 GAGGATGAGGTACCTCTCTCA 57.414 52.381 35.83 21.30 46.28 3.27
2497 2624 4.869861 CCGCCTTCCATTTTAAAAATCTGG 59.130 41.667 11.35 11.35 0.00 3.86
2516 2643 5.693961 TCTGGCCAACATCATATACACATT 58.306 37.500 7.01 0.00 0.00 2.71
2688 2815 5.754782 ACACCATAGAATCACTGGCAATTA 58.245 37.500 1.64 0.00 33.12 1.40
2891 3024 7.038941 AGCTACTTGGATAACTACAGAACTTGT 60.039 37.037 0.00 0.00 43.96 3.16
2988 3121 4.319622 CGGAAAATGTGCATGCAAACAATT 60.320 37.500 24.58 13.64 0.00 2.32
3026 3159 2.472695 TCGCTACAATCTGTTGCCTT 57.527 45.000 7.47 0.00 44.21 4.35
3259 3392 3.586470 ACAAGTGTGGTTGGGTTGATA 57.414 42.857 0.00 0.00 0.00 2.15
3758 4004 7.605691 AGCTCAACTCCAATCTATATGTATTGC 59.394 37.037 6.41 0.00 32.79 3.56
3920 4167 4.955925 TGAACGTTGTCAAGTGTTTCAT 57.044 36.364 5.00 0.00 0.00 2.57
4033 4285 1.946984 AACAGAAGACCGGGGATACA 58.053 50.000 6.32 0.00 39.74 2.29
4059 4311 3.009723 AGCACCATGATTAAGAACACCG 58.990 45.455 0.00 0.00 0.00 4.94
4111 4363 1.607148 CACGACTAGACACACTCACCA 59.393 52.381 0.00 0.00 0.00 4.17
4122 4374 0.036010 CACTCACCAAGTAGGCCAGG 60.036 60.000 5.01 0.47 43.14 4.45
4329 4588 1.228124 TGCTGTCCAAAACTCCCCG 60.228 57.895 0.00 0.00 0.00 5.73
4480 4739 5.911838 GTCAAAGAAGAAAAGATGCACTGAC 59.088 40.000 0.00 0.00 0.00 3.51
4630 4889 0.391130 TATCGCACACAAGGACCTGC 60.391 55.000 0.00 0.00 0.00 4.85
4832 5091 4.177026 GTGTGCATCGAAGATAGACAACT 58.823 43.478 0.00 0.00 45.12 3.16
5399 5665 6.086871 GCTCTACCAATAAAAGAACAGCAAC 58.913 40.000 0.00 0.00 0.00 4.17
5582 5851 9.967451 TTATTTATTATCAGTTGTGGAAGGACA 57.033 29.630 0.00 0.00 0.00 4.02
5588 5857 5.042463 TCAGTTGTGGAAGGACATAAACA 57.958 39.130 0.00 0.00 0.00 2.83
5630 5899 3.689569 GCCTTGCTCCTCCTTATTTCCAT 60.690 47.826 0.00 0.00 0.00 3.41
5639 5908 4.166144 CCTCCTTATTTCCATAGTGGTGGT 59.834 45.833 0.00 0.00 39.03 4.16
5835 6112 2.489802 CCTCACCTTCTTTCCCTTGCTT 60.490 50.000 0.00 0.00 0.00 3.91
5839 6116 1.168714 CTTCTTTCCCTTGCTTCGGG 58.831 55.000 0.00 0.00 43.38 5.14
6164 6441 0.321653 GACGACCACTGCCCATTTCT 60.322 55.000 0.00 0.00 0.00 2.52
6183 6460 0.401738 TGGGGCTCTTCTTTCCAGTG 59.598 55.000 0.00 0.00 0.00 3.66
6277 6554 2.493675 CTCGTCCATCAGAAGGTTCAGA 59.506 50.000 0.00 0.00 0.00 3.27
6301 6578 1.873069 GCCTGAATCTCATCTCCAGCG 60.873 57.143 0.00 0.00 0.00 5.18
6302 6579 1.685517 CCTGAATCTCATCTCCAGCGA 59.314 52.381 0.00 0.00 0.00 4.93
6303 6580 2.288334 CCTGAATCTCATCTCCAGCGAG 60.288 54.545 0.00 0.00 37.48 5.03
6361 6645 0.247460 GGCAACTCAAAGGGGATTGC 59.753 55.000 0.00 0.00 43.88 3.56
6697 6981 3.824443 TGATCTGGAAACACTCACTCGTA 59.176 43.478 0.00 0.00 35.60 3.43
6698 6982 4.462834 TGATCTGGAAACACTCACTCGTAT 59.537 41.667 0.00 0.00 35.60 3.06
6699 6983 4.174411 TCTGGAAACACTCACTCGTATG 57.826 45.455 0.00 0.00 35.60 2.39
6708 6993 5.575957 ACACTCACTCGTATGTATTTACCG 58.424 41.667 0.00 0.00 0.00 4.02
6713 6998 6.191661 TCACTCGTATGTATTTACCGTTACG 58.808 40.000 0.00 0.00 33.63 3.18
6729 7014 4.545610 CGTTACGTTTGTAGGTCCAAGTA 58.454 43.478 0.00 0.00 0.00 2.24
6818 7103 6.479006 TCTGCTTGGTGAGTAGTAGTAGTAA 58.521 40.000 0.00 0.00 38.98 2.24
6819 7104 6.944290 TCTGCTTGGTGAGTAGTAGTAGTAAA 59.056 38.462 0.00 0.00 38.98 2.01
6983 7286 2.295472 ATCGCTGGAGCTGCAGAGTC 62.295 60.000 36.18 18.77 39.32 3.36
7037 7340 4.870636 AGAGGAGTTGAGATGATCAGAGT 58.129 43.478 0.09 0.00 39.68 3.24
7045 7348 6.594547 AGTTGAGATGATCAGAGTGTGAAATG 59.405 38.462 0.09 0.00 39.19 2.32
7157 7460 1.134907 CCCGCGTTGAGGTATGTACTT 60.135 52.381 4.92 0.00 0.00 2.24
7210 7514 3.692791 AACAAAACGAAGCTTGTCTCC 57.307 42.857 2.10 0.00 36.11 3.71
7255 8595 6.741992 TGGCAATGTTTAGAAGATGTGTAG 57.258 37.500 0.00 0.00 0.00 2.74
7256 8596 5.647658 TGGCAATGTTTAGAAGATGTGTAGG 59.352 40.000 0.00 0.00 0.00 3.18
7258 8598 5.355350 GCAATGTTTAGAAGATGTGTAGGCT 59.645 40.000 0.00 0.00 0.00 4.58
7259 8599 6.127897 GCAATGTTTAGAAGATGTGTAGGCTT 60.128 38.462 0.00 0.00 0.00 4.35
7261 8601 8.299570 CAATGTTTAGAAGATGTGTAGGCTTTT 58.700 33.333 0.00 0.00 0.00 2.27
7342 8775 4.762765 AGTTCACTGTCTCAGATAGTCGTT 59.237 41.667 0.06 0.00 31.86 3.85
7343 8776 4.686839 TCACTGTCTCAGATAGTCGTTG 57.313 45.455 0.06 0.00 31.86 4.10
7468 9251 2.755469 GTTGACGGGCATGGGCAT 60.755 61.111 0.00 0.00 43.71 4.40
7525 9334 1.003839 GTGACCATTCGGCCTGTGA 60.004 57.895 0.00 0.00 34.57 3.58
7571 9380 1.943340 GGCCATCGAAAGGTCTTCATC 59.057 52.381 0.00 0.00 0.00 2.92
7579 9388 3.307059 CGAAAGGTCTTCATCAGGGTTCT 60.307 47.826 0.00 0.00 0.00 3.01
7653 9462 1.327690 GCCTGACGTGGAGGGTATGA 61.328 60.000 11.36 0.00 0.00 2.15
7662 9471 3.244215 CGTGGAGGGTATGATTATGCAGT 60.244 47.826 0.00 0.00 0.00 4.40
7812 9633 3.426615 CCAACCTGTTATACCTGGCAAA 58.573 45.455 0.00 0.00 0.00 3.68
7867 9692 0.387929 TGCTCGGATATGTTCGGACC 59.612 55.000 0.00 0.00 31.13 4.46
7869 9694 0.039437 CTCGGATATGTTCGGACCGG 60.039 60.000 15.25 0.00 43.14 5.28
7885 9712 0.821711 CCGGCTCTTGGGTGAAAACA 60.822 55.000 0.00 0.00 0.00 2.83
7915 9742 2.235402 GGTCTTCGGTGGTTGGATAGAA 59.765 50.000 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.677637 CCTCTGGAACCCGGACTAGC 61.678 65.000 0.73 0.00 33.41 3.42
1 2 1.043673 CCCTCTGGAACCCGGACTAG 61.044 65.000 0.73 1.32 33.41 2.57
2 3 1.001248 CCCTCTGGAACCCGGACTA 59.999 63.158 0.73 0.00 33.41 2.59
3 4 2.284699 CCCTCTGGAACCCGGACT 60.285 66.667 0.73 0.00 33.41 3.85
4 5 4.097361 GCCCTCTGGAACCCGGAC 62.097 72.222 0.73 0.00 33.41 4.79
7 8 1.559065 TAAAGGCCCTCTGGAACCCG 61.559 60.000 0.00 0.00 0.00 5.28
8 9 0.256177 CTAAAGGCCCTCTGGAACCC 59.744 60.000 0.00 0.00 0.00 4.11
9 10 0.992695 ACTAAAGGCCCTCTGGAACC 59.007 55.000 0.00 0.00 0.00 3.62
10 11 1.065345 GGACTAAAGGCCCTCTGGAAC 60.065 57.143 0.00 0.00 0.00 3.62
11 12 1.286248 GGACTAAAGGCCCTCTGGAA 58.714 55.000 0.00 0.00 0.00 3.53
12 13 0.620700 GGGACTAAAGGCCCTCTGGA 60.621 60.000 14.19 0.00 41.31 3.86
13 14 1.915983 GGGACTAAAGGCCCTCTGG 59.084 63.158 14.19 0.00 41.31 3.86
14 15 1.522569 CGGGACTAAAGGCCCTCTG 59.477 63.158 18.97 0.00 42.40 3.35
15 16 1.689582 CCGGGACTAAAGGCCCTCT 60.690 63.158 18.97 0.00 42.40 3.69
16 17 1.969200 GACCGGGACTAAAGGCCCTC 61.969 65.000 18.97 6.86 42.40 4.30
17 18 1.993948 GACCGGGACTAAAGGCCCT 60.994 63.158 18.97 0.25 42.40 5.19
18 19 2.588439 GACCGGGACTAAAGGCCC 59.412 66.667 11.29 11.29 41.11 5.80
19 20 2.186125 CGACCGGGACTAAAGGCC 59.814 66.667 6.32 0.00 0.00 5.19
20 21 2.186125 CCGACCGGGACTAAAGGC 59.814 66.667 6.32 0.00 38.47 4.35
21 22 1.514553 GACCGACCGGGACTAAAGG 59.485 63.158 13.43 0.16 39.97 3.11
22 23 1.514553 GGACCGACCGGGACTAAAG 59.485 63.158 13.43 0.00 39.97 1.85
23 24 1.984026 GGGACCGACCGGGACTAAA 60.984 63.158 13.43 0.00 39.97 1.85
24 25 2.362889 GGGACCGACCGGGACTAA 60.363 66.667 13.43 0.00 39.97 2.24
25 26 3.341629 AGGGACCGACCGGGACTA 61.342 66.667 13.43 0.00 39.97 2.59
27 28 2.916527 TATCAGGGACCGACCGGGAC 62.917 65.000 13.43 6.40 39.97 4.46
28 29 2.015243 ATATCAGGGACCGACCGGGA 62.015 60.000 13.43 0.26 39.97 5.14
29 30 1.119574 AATATCAGGGACCGACCGGG 61.120 60.000 13.43 0.00 43.62 5.73
30 31 0.756903 AAATATCAGGGACCGACCGG 59.243 55.000 6.94 6.94 40.11 5.28
31 32 1.411246 TGAAATATCAGGGACCGACCG 59.589 52.381 0.00 0.00 40.11 4.79
32 33 3.553828 TTGAAATATCAGGGACCGACC 57.446 47.619 0.00 0.00 36.78 4.79
33 34 4.211374 CGATTTGAAATATCAGGGACCGAC 59.789 45.833 0.00 0.00 36.78 4.79
34 35 4.141801 ACGATTTGAAATATCAGGGACCGA 60.142 41.667 0.00 0.00 36.78 4.69
35 36 4.024893 CACGATTTGAAATATCAGGGACCG 60.025 45.833 0.00 0.00 36.78 4.79
36 37 4.881850 ACACGATTTGAAATATCAGGGACC 59.118 41.667 0.00 0.00 36.78 4.46
37 38 5.584649 TGACACGATTTGAAATATCAGGGAC 59.415 40.000 0.00 0.00 36.78 4.46
38 39 5.739959 TGACACGATTTGAAATATCAGGGA 58.260 37.500 0.00 0.00 36.78 4.20
39 40 5.586243 ACTGACACGATTTGAAATATCAGGG 59.414 40.000 17.68 5.08 37.29 4.45
60 61 0.179189 GCTTCGCCCAAAATCGACTG 60.179 55.000 0.00 0.00 34.16 3.51
128 129 0.680921 ATGCATTGTCCCTGGTTCCG 60.681 55.000 0.00 0.00 0.00 4.30
129 130 1.106285 GATGCATTGTCCCTGGTTCC 58.894 55.000 0.00 0.00 0.00 3.62
150 151 0.252197 GTACTTCCCTCCACCGCAAT 59.748 55.000 0.00 0.00 0.00 3.56
155 156 1.777941 ATCTCGTACTTCCCTCCACC 58.222 55.000 0.00 0.00 0.00 4.61
169 170 3.786818 GCGCCAGAATTCTTCAAATCTCG 60.787 47.826 4.86 2.28 0.00 4.04
177 178 1.432270 CTCCCGCGCCAGAATTCTTC 61.432 60.000 4.86 0.00 0.00 2.87
198 199 1.213799 GTCGACAACCTCCCCGTAC 59.786 63.158 11.55 0.00 0.00 3.67
256 257 4.119136 CACTATATGTCGTGTTGCCATCA 58.881 43.478 0.00 0.00 0.00 3.07
268 269 2.135933 GAACTGCCGGCACTATATGTC 58.864 52.381 29.03 10.99 0.00 3.06
269 270 1.202651 GGAACTGCCGGCACTATATGT 60.203 52.381 29.03 18.70 0.00 2.29
270 271 1.512926 GGAACTGCCGGCACTATATG 58.487 55.000 29.03 17.92 0.00 1.78
271 272 0.396811 GGGAACTGCCGGCACTATAT 59.603 55.000 29.03 9.90 37.63 0.86
272 273 0.978667 TGGGAACTGCCGGCACTATA 60.979 55.000 29.03 3.50 37.63 1.31
273 274 2.297895 TGGGAACTGCCGGCACTAT 61.298 57.895 29.03 14.93 37.63 2.12
274 275 2.925706 TGGGAACTGCCGGCACTA 60.926 61.111 29.03 11.45 37.63 2.74
275 276 4.643387 GTGGGAACTGCCGGCACT 62.643 66.667 29.03 16.52 37.63 4.40
276 277 4.947147 TGTGGGAACTGCCGGCAC 62.947 66.667 29.03 16.90 37.63 5.01
277 278 4.641645 CTGTGGGAACTGCCGGCA 62.642 66.667 30.59 30.59 37.63 5.69
279 280 3.491598 AACCTGTGGGAACTGCCGG 62.492 63.158 0.00 0.00 37.63 6.13
280 281 2.113139 AACCTGTGGGAACTGCCG 59.887 61.111 0.00 0.00 37.63 5.69
281 282 2.564721 GCAACCTGTGGGAACTGCC 61.565 63.158 0.00 0.00 33.49 4.85
282 283 2.564721 GGCAACCTGTGGGAACTGC 61.565 63.158 0.00 0.00 36.37 4.40
283 284 1.152777 TGGCAACCTGTGGGAACTG 60.153 57.895 0.00 0.00 36.25 3.16
284 285 1.151450 CTGGCAACCTGTGGGAACT 59.849 57.895 0.00 0.00 36.25 3.01
285 286 1.903404 CCTGGCAACCTGTGGGAAC 60.903 63.158 0.00 0.00 36.25 3.62
286 287 2.351924 GACCTGGCAACCTGTGGGAA 62.352 60.000 0.00 0.00 36.25 3.97
287 288 2.776526 ACCTGGCAACCTGTGGGA 60.777 61.111 0.00 0.00 36.25 4.37
288 289 2.282462 GACCTGGCAACCTGTGGG 60.282 66.667 0.00 0.00 38.88 4.61
289 290 0.540365 AATGACCTGGCAACCTGTGG 60.540 55.000 0.00 0.00 0.00 4.17
290 291 0.599558 CAATGACCTGGCAACCTGTG 59.400 55.000 0.00 0.00 0.00 3.66
291 292 0.540365 CCAATGACCTGGCAACCTGT 60.540 55.000 0.00 0.00 0.00 4.00
292 293 1.252904 CCCAATGACCTGGCAACCTG 61.253 60.000 0.00 0.00 34.88 4.00
334 335 0.179215 GCATTTCGTCGAGCTGTTGG 60.179 55.000 0.00 0.00 0.00 3.77
436 442 5.471556 TTTGATCAAAACTGGCACATGAT 57.528 34.783 18.45 0.00 37.09 2.45
461 467 3.650281 TTCACCTATGGCATGACATGT 57.350 42.857 24.86 11.60 32.39 3.21
462 468 3.067180 GGTTTCACCTATGGCATGACATG 59.933 47.826 24.86 10.88 34.73 3.21
510 516 2.223711 CCCAACTTTCAAAACCGGACAG 60.224 50.000 9.46 0.00 0.00 3.51
521 527 4.280677 GTCAACAATCATCCCCAACTTTCA 59.719 41.667 0.00 0.00 0.00 2.69
528 534 0.034574 CCGGTCAACAATCATCCCCA 60.035 55.000 0.00 0.00 0.00 4.96
537 543 3.018149 ACACTTTAAAGCCGGTCAACAA 58.982 40.909 15.24 0.00 0.00 2.83
565 571 3.574284 TCATCAATCCGCCAAAGTTTG 57.426 42.857 8.73 8.73 0.00 2.93
570 576 3.130869 CCTCAATTCATCAATCCGCCAAA 59.869 43.478 0.00 0.00 0.00 3.28
604 610 7.009540 GCGATGGAAATCTAATGAAAACTTTGG 59.990 37.037 0.00 0.00 0.00 3.28
607 613 7.156876 TGCGATGGAAATCTAATGAAAACTT 57.843 32.000 0.00 0.00 0.00 2.66
608 614 6.757897 TGCGATGGAAATCTAATGAAAACT 57.242 33.333 0.00 0.00 0.00 2.66
609 615 7.810766 TTTGCGATGGAAATCTAATGAAAAC 57.189 32.000 0.00 0.00 0.00 2.43
610 616 8.824159 TTTTTGCGATGGAAATCTAATGAAAA 57.176 26.923 0.00 0.00 0.00 2.29
638 644 9.793259 TGTAGTGAAATCTAATGAAACCTTCTT 57.207 29.630 0.00 0.00 0.00 2.52
639 645 9.965902 ATGTAGTGAAATCTAATGAAACCTTCT 57.034 29.630 0.00 0.00 0.00 2.85
640 646 9.994432 CATGTAGTGAAATCTAATGAAACCTTC 57.006 33.333 0.00 0.00 0.00 3.46
675 681 5.288232 TGTTTGTTTTGATGAGTTTCTTGCG 59.712 36.000 0.00 0.00 0.00 4.85
746 752 6.315393 GTCTGTCTTGGTGTCTTAAGTCAAAA 59.685 38.462 3.91 2.31 0.00 2.44
775 781 8.093307 TGCTGCATTCCAAATTAATCAAAAGTA 58.907 29.630 0.00 0.00 0.00 2.24
776 782 6.935771 TGCTGCATTCCAAATTAATCAAAAGT 59.064 30.769 0.00 0.00 0.00 2.66
817 855 2.830923 TCCCTCCGTTTCCAAATACGTA 59.169 45.455 0.00 0.00 36.09 3.57
818 856 1.624813 TCCCTCCGTTTCCAAATACGT 59.375 47.619 0.00 0.00 36.09 3.57
819 857 2.277084 CTCCCTCCGTTTCCAAATACG 58.723 52.381 0.00 0.00 37.50 3.06
820 858 2.237893 TCCTCCCTCCGTTTCCAAATAC 59.762 50.000 0.00 0.00 0.00 1.89
833 871 2.290071 TGGAAACGTTTGATCCTCCCTC 60.290 50.000 20.10 0.00 34.24 4.30
893 931 0.179105 CTTGTGTGCAGCTTGCCAAA 60.179 50.000 5.82 0.00 44.23 3.28
966 1013 2.026014 CGGCTTTGCGCTGTGTTT 59.974 55.556 9.73 0.00 40.25 2.83
967 1014 3.964875 CCGGCTTTGCGCTGTGTT 61.965 61.111 9.73 0.00 43.75 3.32
968 1015 4.927782 TCCGGCTTTGCGCTGTGT 62.928 61.111 9.73 0.00 43.75 3.72
1089 1142 2.437359 CGGAGGCTGAAGGCAAGG 60.437 66.667 6.65 0.00 44.01 3.61
1288 1341 0.614979 TAGTGACAGGGAGAGGGTGC 60.615 60.000 0.00 0.00 0.00 5.01
1292 1349 2.114616 AGCATTAGTGACAGGGAGAGG 58.885 52.381 0.00 0.00 0.00 3.69
1354 1419 1.680735 GACAATGTGTGCAAGGGACAA 59.319 47.619 0.00 0.00 0.00 3.18
1376 1441 2.863740 CAAGCTCTCACGTTGTGTACAA 59.136 45.455 0.00 0.00 34.79 2.41
1382 1447 2.549754 CCAAATCAAGCTCTCACGTTGT 59.450 45.455 0.00 0.00 0.00 3.32
1395 1461 6.128499 CGTACGAACTACATTTCCCAAATCAA 60.128 38.462 10.44 0.00 0.00 2.57
1403 1469 5.580911 ACAAACGTACGAACTACATTTCC 57.419 39.130 24.41 0.00 0.00 3.13
1434 1500 1.048601 TCTTCCGTTTCTGTCAGGCT 58.951 50.000 0.00 0.00 0.00 4.58
1445 1511 3.074412 GACCATGTCAATGTCTTCCGTT 58.926 45.455 0.00 0.00 32.09 4.44
1474 1540 4.022329 GGGAAATTCACGAAATTCTGTGGT 60.022 41.667 14.39 5.24 36.54 4.16
1475 1541 4.022416 TGGGAAATTCACGAAATTCTGTGG 60.022 41.667 14.39 0.00 36.54 4.17
1476 1542 5.119931 TGGGAAATTCACGAAATTCTGTG 57.880 39.130 10.23 10.23 36.54 3.66
1477 1543 4.827284 ACTGGGAAATTCACGAAATTCTGT 59.173 37.500 7.35 3.06 36.54 3.41
1478 1544 5.376854 ACTGGGAAATTCACGAAATTCTG 57.623 39.130 7.35 2.59 36.54 3.02
1479 1545 6.405278 AAACTGGGAAATTCACGAAATTCT 57.595 33.333 7.35 0.00 36.54 2.40
1540 1608 0.180406 AGCCGTGTCTCACAAAACCT 59.820 50.000 1.00 0.00 33.40 3.50
1548 1616 1.191489 TGGGATTGAGCCGTGTCTCA 61.191 55.000 0.00 0.00 40.99 3.27
1557 1625 8.804912 AATATGAAATCTAGATGGGATTGAGC 57.195 34.615 5.86 0.00 34.19 4.26
1561 1629 8.150827 TCCGAATATGAAATCTAGATGGGATT 57.849 34.615 5.86 0.00 35.25 3.01
1565 1633 6.875726 TGCTTCCGAATATGAAATCTAGATGG 59.124 38.462 5.86 0.00 0.00 3.51
1579 1647 3.250744 CGTCAGAACTTGCTTCCGAATA 58.749 45.455 0.00 0.00 0.00 1.75
1582 1650 0.944311 GCGTCAGAACTTGCTTCCGA 60.944 55.000 0.00 0.00 0.00 4.55
1599 1667 4.651994 ACAATTCAGAATTTAGAAGCGCG 58.348 39.130 5.58 0.00 0.00 6.86
1643 1711 8.900511 TTTTCTGAATCTTGAATCTTATTGCG 57.099 30.769 0.00 0.00 0.00 4.85
1859 1928 9.988815 ATAATCACCACTATAAGCTGAAAGTAG 57.011 33.333 0.00 0.00 35.30 2.57
1909 1978 4.919206 TGTTTGCGCACCATAAATCATAG 58.081 39.130 11.12 0.00 0.00 2.23
1944 2067 6.784031 ACTCAGAGGGTGAATGACTAAAAAT 58.216 36.000 1.53 0.00 33.60 1.82
2372 2499 1.187087 CGGGCCTTTGTAGAGAGAGT 58.813 55.000 0.84 0.00 0.00 3.24
2497 2624 6.418819 GCTGAAAATGTGTATATGATGTTGGC 59.581 38.462 0.00 0.00 0.00 4.52
2688 2815 4.917906 ACTCTACCCTTTTCTCAGCATT 57.082 40.909 0.00 0.00 0.00 3.56
2988 3121 3.015145 GCAGGGTAGGAAGGGGCA 61.015 66.667 0.00 0.00 0.00 5.36
3259 3392 7.285858 GTCTGGAACTCATACTGTAGAAGGTAT 59.714 40.741 0.00 0.00 0.00 2.73
3881 4128 8.635124 CAACGTTCAACAAAATACATGTATTCC 58.365 33.333 27.07 10.02 34.90 3.01
3920 4167 2.223066 CGTTTGTGCTCACCGTGTTTTA 60.223 45.455 0.00 0.00 0.00 1.52
4033 4285 3.370840 TCTTAATCATGGTGCTTGCCT 57.629 42.857 0.00 0.00 0.00 4.75
4066 4318 0.789753 CGTGTGTAGTCGTCTCAGCG 60.790 60.000 0.00 0.00 0.00 5.18
4111 4363 1.765314 CATGCTAGACCTGGCCTACTT 59.235 52.381 3.32 0.00 36.12 2.24
4122 4374 2.009042 GCTGTGTGGGTCATGCTAGAC 61.009 57.143 0.00 1.13 37.80 2.59
4169 4428 1.300963 GGCATTGTGCTCCTCCTCA 59.699 57.895 1.64 0.00 44.28 3.86
4226 4485 0.899019 GGTGGACCTGACTTCTCTCC 59.101 60.000 0.00 0.00 0.00 3.71
4264 4523 2.398498 CGTCTTGGCTAGAATGGATCG 58.602 52.381 0.00 0.00 33.81 3.69
4329 4588 2.740714 GCGGTCCTGACAATGCGTC 61.741 63.158 0.00 0.00 45.61 5.19
4399 4658 4.855715 TGGACGCAATTTGTGGATTTTA 57.144 36.364 14.06 0.00 30.87 1.52
4630 4889 7.959733 TGCAGTGTTTATAAGTATGAGAAACG 58.040 34.615 0.00 0.00 33.31 3.60
5399 5665 1.651240 CTGGGCAGCTGAATGGTTCG 61.651 60.000 20.43 0.00 0.00 3.95
5582 5851 8.299570 CCACAAGCTTTATCTTCAGTTGTTTAT 58.700 33.333 0.00 0.00 0.00 1.40
5588 5857 3.507622 GGCCACAAGCTTTATCTTCAGTT 59.492 43.478 0.00 0.00 43.05 3.16
5630 5899 2.502538 GTTGCCTACCATACCACCACTA 59.497 50.000 0.00 0.00 0.00 2.74
5835 6112 2.754658 GGACGAAGAGGAGCCCGA 60.755 66.667 0.00 0.00 0.00 5.14
5839 6116 0.395173 AGGAGAGGACGAAGAGGAGC 60.395 60.000 0.00 0.00 0.00 4.70
6164 6441 0.401738 CACTGGAAAGAAGAGCCCCA 59.598 55.000 0.00 0.00 0.00 4.96
6204 6481 1.265365 GATAAAAGCTCGCTGATGCCC 59.735 52.381 0.00 0.00 35.36 5.36
6277 6554 1.767681 GGAGATGAGATTCAGGCCAGT 59.232 52.381 5.01 0.00 0.00 4.00
6301 6578 1.596727 GACATGCCGCTTCTCATTCTC 59.403 52.381 0.00 0.00 0.00 2.87
6302 6579 1.661341 GACATGCCGCTTCTCATTCT 58.339 50.000 0.00 0.00 0.00 2.40
6303 6580 0.659957 GGACATGCCGCTTCTCATTC 59.340 55.000 0.00 0.00 0.00 2.67
6304 6581 0.035152 TGGACATGCCGCTTCTCATT 60.035 50.000 0.00 0.00 40.66 2.57
6305 6582 0.463295 CTGGACATGCCGCTTCTCAT 60.463 55.000 0.00 0.00 40.66 2.90
6306 6583 1.078918 CTGGACATGCCGCTTCTCA 60.079 57.895 0.00 0.00 40.66 3.27
6401 6685 6.074648 TCAGGTTATCATGTTTTGTCCCTTT 58.925 36.000 0.00 0.00 0.00 3.11
6697 6981 7.096551 ACCTACAAACGTAACGGTAAATACAT 58.903 34.615 0.00 0.00 0.00 2.29
6698 6982 6.451393 ACCTACAAACGTAACGGTAAATACA 58.549 36.000 0.00 0.00 0.00 2.29
6699 6983 6.034577 GGACCTACAAACGTAACGGTAAATAC 59.965 42.308 0.00 0.00 0.00 1.89
6708 6993 8.193438 AGATATACTTGGACCTACAAACGTAAC 58.807 37.037 0.00 0.00 0.00 2.50
6713 6998 7.120923 TGGAGATATACTTGGACCTACAAAC 57.879 40.000 0.00 0.00 0.00 2.93
6729 7014 6.012771 TGGATCTCATTGCATCTTGGAGATAT 60.013 38.462 12.90 0.00 43.36 1.63
6818 7103 3.828451 CACCAACCAGAGTGGATGAAATT 59.172 43.478 4.86 0.00 42.23 1.82
6819 7104 3.181429 ACACCAACCAGAGTGGATGAAAT 60.181 43.478 4.86 0.00 42.23 2.17
6983 7286 4.459337 CCAAAGTAAAAGTAGAGGGCCAAG 59.541 45.833 6.18 0.00 0.00 3.61
7037 7340 8.514594 CAAAAAGAATAGAGCCTACATTTCACA 58.485 33.333 0.00 0.00 0.00 3.58
7045 7348 7.557724 AGGTAGACAAAAAGAATAGAGCCTAC 58.442 38.462 0.00 0.00 0.00 3.18
7157 7460 6.993786 TCGATTGTATTTTAAGATGCCACA 57.006 33.333 0.00 0.00 0.00 4.17
7210 7514 4.403015 TGTTTGTATGTGCACATCTTCG 57.597 40.909 34.54 0.00 37.76 3.79
7281 8714 9.571810 CACAAATGCACATATAAACTACACATT 57.428 29.630 0.00 0.00 0.00 2.71
7349 8782 1.187087 CTAGACAAGGAGCTTCGGGT 58.813 55.000 0.00 0.00 0.00 5.28
7352 8785 0.526524 CCGCTAGACAAGGAGCTTCG 60.527 60.000 0.00 0.00 36.50 3.79
7353 8786 0.533032 ACCGCTAGACAAGGAGCTTC 59.467 55.000 0.00 0.00 36.50 3.86
7355 8788 1.608717 CCACCGCTAGACAAGGAGCT 61.609 60.000 0.00 0.00 36.50 4.09
7468 9251 2.111669 CAGAGCACACCACCAGCA 59.888 61.111 0.00 0.00 0.00 4.41
7579 9388 3.073356 ACAACCACCGAATCTAAAGGGAA 59.927 43.478 0.00 0.00 0.00 3.97
7586 9395 3.616560 GCTGAAGACAACCACCGAATCTA 60.617 47.826 0.00 0.00 0.00 1.98
7623 9432 2.654912 CGTCAGGCCGTTGTTCGTC 61.655 63.158 0.00 0.00 37.94 4.20
7642 9451 3.072915 CCACTGCATAATCATACCCTCCA 59.927 47.826 0.00 0.00 0.00 3.86
7653 9462 1.484653 TGACTACCGCCACTGCATAAT 59.515 47.619 0.00 0.00 37.32 1.28
7662 9471 2.290008 ACATGTGATTTGACTACCGCCA 60.290 45.455 0.00 0.00 0.00 5.69
7782 9603 0.320421 TAACAGGTTGGCGCAGACTC 60.320 55.000 10.83 1.45 34.59 3.36
7812 9633 0.383949 AACACGCAAAAACATCGCCT 59.616 45.000 0.00 0.00 0.00 5.52
7867 9692 1.247567 ATGTTTTCACCCAAGAGCCG 58.752 50.000 0.00 0.00 0.00 5.52
7869 9694 6.587608 CAGATTTTATGTTTTCACCCAAGAGC 59.412 38.462 0.00 0.00 0.00 4.09
7885 9712 4.569719 ACCACCGAAGACCAGATTTTAT 57.430 40.909 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.