Multiple sequence alignment - TraesCS4B01G327900

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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 TraesCS4B01G327900 chr4B 100.000 2396 0 0 1 2396 618613356 618615751 0.000000e+00 4425.0
1 TraesCS4B01G327900 chr5A 98.630 1752 19 4 647 2396 522112188 522110440 0.000000e+00 3097.0
2 TraesCS4B01G327900 chr5A 89.474 247 19 5 93 334 666237960 666238204 2.990000e-79 305.0
3 TraesCS4B01G327900 chr5A 83.158 95 12 2 351 441 666246424 666246518 1.530000e-12 84.2
4 TraesCS4B01G327900 chr7A 90.753 1460 107 13 947 2392 44449189 44450634 0.000000e+00 1923.0
5 TraesCS4B01G327900 chr7A 88.820 161 12 3 647 801 44448471 44448631 2.430000e-45 193.0
6 TraesCS4B01G327900 chr3B 97.866 984 18 3 1416 2396 525237489 525238472 0.000000e+00 1698.0
7 TraesCS4B01G327900 chr3B 79.717 848 143 19 1564 2396 68292181 68291348 9.540000e-164 586.0
8 TraesCS4B01G327900 chr3B 97.112 277 7 1 647 922 525236591 525236867 1.300000e-127 466.0
9 TraesCS4B01G327900 chr3B 81.758 455 71 6 1944 2387 53567659 53568112 1.050000e-98 370.0
10 TraesCS4B01G327900 chr2B 82.459 1277 185 23 1134 2396 608200196 608201447 0.000000e+00 1081.0
11 TraesCS4B01G327900 chr2B 86.508 630 56 12 1779 2396 132060424 132059812 0.000000e+00 665.0
12 TraesCS4B01G327900 chr7B 80.339 1475 206 43 981 2396 270535646 270534197 0.000000e+00 1040.0
13 TraesCS4B01G327900 chr6B 89.646 763 65 5 1645 2396 86411644 86410885 0.000000e+00 959.0
14 TraesCS4B01G327900 chr6B 84.728 681 87 9 966 1643 86439872 86439206 0.000000e+00 665.0
15 TraesCS4B01G327900 chr6B 92.105 38 3 0 1030 1067 693951911 693951874 1.000000e-03 54.7
16 TraesCS4B01G327900 chr6B 92.105 38 3 0 1030 1067 693963045 693963008 1.000000e-03 54.7
17 TraesCS4B01G327900 chr6B 92.105 38 3 0 1030 1067 693968992 693968955 1.000000e-03 54.7
18 TraesCS4B01G327900 chr6B 92.105 38 3 0 1030 1067 693975487 693975450 1.000000e-03 54.7
19 TraesCS4B01G327900 chr6B 92.105 38 3 0 1030 1067 693980674 693980637 1.000000e-03 54.7
20 TraesCS4B01G327900 chr6B 92.105 38 3 0 1030 1067 693986232 693986195 1.000000e-03 54.7
21 TraesCS4B01G327900 chr5D 85.330 893 96 15 1519 2396 432215391 432216263 0.000000e+00 891.0
22 TraesCS4B01G327900 chr5D 84.815 270 37 4 1629 1896 480815967 480816234 3.930000e-68 268.0
23 TraesCS4B01G327900 chr4D 86.824 296 23 4 134 413 485404612 485404907 1.380000e-82 316.0
24 TraesCS4B01G327900 chr4D 93.258 89 6 0 556 644 485406269 485406357 5.370000e-27 132.0
25 TraesCS4B01G327900 chr5B 83.230 161 23 3 647 805 625035730 625035888 6.900000e-31 145.0
26 TraesCS4B01G327900 chr5B 85.714 133 19 0 647 779 628606456 628606588 8.930000e-30 141.0


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 TraesCS4B01G327900 chr4B 618613356 618615751 2395 False 4425 4425 100.0000 1 2396 1 chr4B.!!$F1 2395
1 TraesCS4B01G327900 chr5A 522110440 522112188 1748 True 3097 3097 98.6300 647 2396 1 chr5A.!!$R1 1749
2 TraesCS4B01G327900 chr7A 44448471 44450634 2163 False 1058 1923 89.7865 647 2392 2 chr7A.!!$F1 1745
3 TraesCS4B01G327900 chr3B 525236591 525238472 1881 False 1082 1698 97.4890 647 2396 2 chr3B.!!$F2 1749
4 TraesCS4B01G327900 chr3B 68291348 68292181 833 True 586 586 79.7170 1564 2396 1 chr3B.!!$R1 832
5 TraesCS4B01G327900 chr2B 608200196 608201447 1251 False 1081 1081 82.4590 1134 2396 1 chr2B.!!$F1 1262
6 TraesCS4B01G327900 chr2B 132059812 132060424 612 True 665 665 86.5080 1779 2396 1 chr2B.!!$R1 617
7 TraesCS4B01G327900 chr7B 270534197 270535646 1449 True 1040 1040 80.3390 981 2396 1 chr7B.!!$R1 1415
8 TraesCS4B01G327900 chr6B 86410885 86411644 759 True 959 959 89.6460 1645 2396 1 chr6B.!!$R1 751
9 TraesCS4B01G327900 chr6B 86439206 86439872 666 True 665 665 84.7280 966 1643 1 chr6B.!!$R2 677
10 TraesCS4B01G327900 chr5D 432215391 432216263 872 False 891 891 85.3300 1519 2396 1 chr5D.!!$F1 877
11 TraesCS4B01G327900 chr4D 485404612 485406357 1745 False 224 316 90.0410 134 644 2 chr4D.!!$F1 510

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
448 489 0.033781 GGGCTGCTGCATTTTGACAA 59.966 50.0 17.89 0.0 41.91 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2016 3451 0.179029 CCACCCGTTGTCCTTTGAGT 60.179 55.0 0.0 0.0 0.0 3.41 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
22 23 2.989639 TCCAGCAGGAATGGTCGG 59.010 61.111 0.00 0.00 42.23 4.79
23 24 2.825836 CCAGCAGGAATGGTCGGC 60.826 66.667 0.00 0.00 36.89 5.54
24 25 3.197790 CAGCAGGAATGGTCGGCG 61.198 66.667 0.00 0.00 31.88 6.46
25 26 4.473520 AGCAGGAATGGTCGGCGG 62.474 66.667 7.21 0.00 31.88 6.13
39 40 3.544615 GGCGGCCGATGTATTTTTC 57.455 52.632 33.48 6.40 0.00 2.29
40 41 0.736053 GGCGGCCGATGTATTTTTCA 59.264 50.000 33.48 0.00 0.00 2.69
41 42 1.533129 GGCGGCCGATGTATTTTTCAC 60.533 52.381 33.48 5.54 0.00 3.18
42 43 1.533129 GCGGCCGATGTATTTTTCACC 60.533 52.381 33.48 0.62 0.00 4.02
43 44 1.740585 CGGCCGATGTATTTTTCACCA 59.259 47.619 24.07 0.00 0.00 4.17
44 45 2.162608 CGGCCGATGTATTTTTCACCAA 59.837 45.455 24.07 0.00 0.00 3.67
45 46 3.366476 CGGCCGATGTATTTTTCACCAAA 60.366 43.478 24.07 0.00 0.00 3.28
46 47 3.924073 GGCCGATGTATTTTTCACCAAAC 59.076 43.478 0.00 0.00 0.00 2.93
47 48 4.321675 GGCCGATGTATTTTTCACCAAACT 60.322 41.667 0.00 0.00 0.00 2.66
48 49 4.857037 GCCGATGTATTTTTCACCAAACTC 59.143 41.667 0.00 0.00 0.00 3.01
49 50 5.086058 CCGATGTATTTTTCACCAAACTCG 58.914 41.667 0.00 0.00 0.00 4.18
50 51 5.106869 CCGATGTATTTTTCACCAAACTCGA 60.107 40.000 0.00 0.00 0.00 4.04
51 52 5.788531 CGATGTATTTTTCACCAAACTCGAC 59.211 40.000 0.00 0.00 0.00 4.20
52 53 6.565060 CGATGTATTTTTCACCAAACTCGACA 60.565 38.462 0.00 0.00 0.00 4.35
53 54 5.812652 TGTATTTTTCACCAAACTCGACAC 58.187 37.500 0.00 0.00 0.00 3.67
54 55 3.392769 TTTTTCACCAAACTCGACACG 57.607 42.857 0.00 0.00 0.00 4.49
55 56 2.296831 TTTCACCAAACTCGACACGA 57.703 45.000 0.00 0.00 0.00 4.35
56 57 2.296831 TTCACCAAACTCGACACGAA 57.703 45.000 0.00 0.00 34.74 3.85
57 58 1.847818 TCACCAAACTCGACACGAAG 58.152 50.000 0.00 0.00 34.74 3.79
58 59 1.406180 TCACCAAACTCGACACGAAGA 59.594 47.619 0.00 0.00 34.74 2.87
59 60 2.035449 TCACCAAACTCGACACGAAGAT 59.965 45.455 0.00 0.00 34.74 2.40
60 61 2.155732 CACCAAACTCGACACGAAGATG 59.844 50.000 0.00 0.00 34.74 2.90
61 62 2.035449 ACCAAACTCGACACGAAGATGA 59.965 45.455 0.00 0.00 34.74 2.92
62 63 3.057019 CCAAACTCGACACGAAGATGAA 58.943 45.455 0.00 0.00 34.74 2.57
63 64 3.121944 CCAAACTCGACACGAAGATGAAG 59.878 47.826 0.00 0.00 34.74 3.02
64 65 2.638556 ACTCGACACGAAGATGAAGG 57.361 50.000 0.00 0.00 34.74 3.46
65 66 1.272781 CTCGACACGAAGATGAAGGC 58.727 55.000 0.00 0.00 34.74 4.35
66 67 0.456142 TCGACACGAAGATGAAGGCG 60.456 55.000 0.00 0.00 31.06 5.52
67 68 1.413767 CGACACGAAGATGAAGGCGG 61.414 60.000 0.00 0.00 0.00 6.13
68 69 0.108804 GACACGAAGATGAAGGCGGA 60.109 55.000 0.00 0.00 0.00 5.54
69 70 0.537188 ACACGAAGATGAAGGCGGAT 59.463 50.000 0.00 0.00 0.00 4.18
70 71 1.066143 ACACGAAGATGAAGGCGGATT 60.066 47.619 0.00 0.00 0.00 3.01
71 72 1.594862 CACGAAGATGAAGGCGGATTC 59.405 52.381 0.00 0.00 0.00 2.52
72 73 1.221414 CGAAGATGAAGGCGGATTCC 58.779 55.000 0.00 0.00 0.00 3.01
107 108 3.746957 GGAGGCCTCCAAGGTCAT 58.253 61.111 41.69 0.00 44.17 3.06
108 109 1.529309 GGAGGCCTCCAAGGTCATC 59.471 63.158 41.69 15.08 44.17 2.92
109 110 1.274703 GGAGGCCTCCAAGGTCATCA 61.275 60.000 41.69 0.00 44.17 3.07
110 111 0.107459 GAGGCCTCCAAGGTCATCAC 60.107 60.000 23.19 0.00 44.17 3.06
111 112 1.077429 GGCCTCCAAGGTCATCACC 60.077 63.158 0.00 0.00 40.51 4.02
112 113 1.077429 GCCTCCAAGGTCATCACCC 60.077 63.158 0.00 0.00 45.12 4.61
113 114 1.566298 GCCTCCAAGGTCATCACCCT 61.566 60.000 0.00 0.00 45.12 4.34
114 115 0.254178 CCTCCAAGGTCATCACCCTG 59.746 60.000 0.00 0.00 45.12 4.45
116 117 2.078452 CCAAGGTCATCACCCTGGT 58.922 57.895 0.00 0.00 46.21 4.00
117 118 0.322816 CCAAGGTCATCACCCTGGTG 60.323 60.000 10.13 10.13 46.21 4.17
118 119 0.962356 CAAGGTCATCACCCTGGTGC 60.962 60.000 11.55 0.00 45.12 5.01
119 120 1.426251 AAGGTCATCACCCTGGTGCA 61.426 55.000 11.55 1.57 45.12 4.57
120 121 1.210204 AGGTCATCACCCTGGTGCAT 61.210 55.000 11.55 3.81 45.12 3.96
121 122 0.323725 GGTCATCACCCTGGTGCATT 60.324 55.000 11.55 0.00 45.04 3.56
122 123 1.549203 GTCATCACCCTGGTGCATTT 58.451 50.000 11.55 0.00 45.04 2.32
123 124 1.895131 GTCATCACCCTGGTGCATTTT 59.105 47.619 11.55 0.00 45.04 1.82
124 125 2.094545 GTCATCACCCTGGTGCATTTTC 60.095 50.000 11.55 0.00 45.04 2.29
125 126 1.894466 CATCACCCTGGTGCATTTTCA 59.106 47.619 11.55 0.00 45.04 2.69
126 127 1.327303 TCACCCTGGTGCATTTTCAC 58.673 50.000 11.55 0.00 45.04 3.18
142 143 3.394836 ACCTCGGAGCAGAAGGGC 61.395 66.667 0.00 0.00 0.00 5.19
152 153 1.202976 AGCAGAAGGGCACTTTCACAT 60.203 47.619 0.84 0.00 36.97 3.21
167 168 2.806434 TCACATGGATCCCACCAAAAG 58.194 47.619 9.90 0.00 43.47 2.27
202 205 0.105039 CAGAGGGATACAAGGACGGC 59.895 60.000 0.00 0.00 39.74 5.68
227 230 4.993945 GCGGCATGCGCGTAATCG 62.994 66.667 23.32 15.62 39.92 3.34
231 234 1.154599 GCATGCGCGTAATCGATGG 60.155 57.895 8.43 0.00 39.71 3.51
265 268 3.909086 AAGAGCGAGCAAGCCCCAC 62.909 63.158 0.00 0.00 38.01 4.61
307 321 0.038166 CCAATGCTACCACCACCAGT 59.962 55.000 0.00 0.00 0.00 4.00
345 359 4.389576 CTCGTTTGGCGCACAGGC 62.390 66.667 10.83 1.11 46.95 4.85
404 421 3.721706 GCACAGCCAGCCTACCCT 61.722 66.667 0.00 0.00 0.00 4.34
406 423 2.689034 ACAGCCAGCCTACCCTCC 60.689 66.667 0.00 0.00 0.00 4.30
441 482 4.728110 TGCTCGGGCTGCTGCATT 62.728 61.111 17.89 0.00 41.91 3.56
442 483 3.446570 GCTCGGGCTGCTGCATTT 61.447 61.111 17.89 0.00 41.91 2.32
443 484 2.998279 GCTCGGGCTGCTGCATTTT 61.998 57.895 17.89 0.00 41.91 1.82
444 485 1.153901 CTCGGGCTGCTGCATTTTG 60.154 57.895 17.89 2.07 41.91 2.44
445 486 1.588824 CTCGGGCTGCTGCATTTTGA 61.589 55.000 17.89 6.17 41.91 2.69
448 489 0.033781 GGGCTGCTGCATTTTGACAA 59.966 50.000 17.89 0.00 41.91 3.18
450 491 1.142474 GCTGCTGCATTTTGACAACC 58.858 50.000 11.11 0.00 39.41 3.77
451 492 1.538634 GCTGCTGCATTTTGACAACCA 60.539 47.619 11.11 0.00 39.41 3.67
452 493 2.868839 GCTGCTGCATTTTGACAACCAT 60.869 45.455 11.11 0.00 39.41 3.55
453 494 3.395639 CTGCTGCATTTTGACAACCATT 58.604 40.909 1.31 0.00 0.00 3.16
454 495 3.806380 TGCTGCATTTTGACAACCATTT 58.194 36.364 0.00 0.00 0.00 2.32
455 496 3.808726 TGCTGCATTTTGACAACCATTTC 59.191 39.130 0.00 0.00 0.00 2.17
456 497 3.187022 GCTGCATTTTGACAACCATTTCC 59.813 43.478 0.00 0.00 0.00 3.13
457 498 4.378774 CTGCATTTTGACAACCATTTCCA 58.621 39.130 0.00 0.00 0.00 3.53
458 499 4.970711 TGCATTTTGACAACCATTTCCAT 58.029 34.783 0.00 0.00 0.00 3.41
459 500 5.374921 TGCATTTTGACAACCATTTCCATT 58.625 33.333 0.00 0.00 0.00 3.16
460 501 5.238868 TGCATTTTGACAACCATTTCCATTG 59.761 36.000 0.00 0.00 0.00 2.82
462 503 2.721274 TGACAACCATTTCCATTGCG 57.279 45.000 0.00 0.00 0.00 4.85
463 504 1.271934 TGACAACCATTTCCATTGCGG 59.728 47.619 0.00 0.00 0.00 5.69
464 505 0.037419 ACAACCATTTCCATTGCGGC 60.037 50.000 0.00 0.00 33.14 6.53
465 506 1.077645 CAACCATTTCCATTGCGGCG 61.078 55.000 0.51 0.51 33.14 6.46
466 507 1.247419 AACCATTTCCATTGCGGCGA 61.247 50.000 12.98 0.00 33.14 5.54
467 508 1.037030 ACCATTTCCATTGCGGCGAT 61.037 50.000 12.98 0.00 33.14 4.58
468 509 0.595567 CCATTTCCATTGCGGCGATG 60.596 55.000 21.00 21.00 33.14 3.84
469 510 1.066257 ATTTCCATTGCGGCGATGC 59.934 52.632 22.25 0.00 33.14 3.91
470 511 2.666715 ATTTCCATTGCGGCGATGCG 62.667 55.000 22.25 15.84 37.81 4.73
481 522 3.566261 CGATGCGCTGACAACCTT 58.434 55.556 9.73 0.00 0.00 3.50
484 525 0.370273 GATGCGCTGACAACCTTACG 59.630 55.000 9.73 0.00 0.00 3.18
485 526 1.635663 ATGCGCTGACAACCTTACGC 61.636 55.000 9.73 0.00 46.05 4.42
486 527 2.314647 GCGCTGACAACCTTACGCA 61.315 57.895 0.00 0.00 45.25 5.24
487 528 1.491563 CGCTGACAACCTTACGCAC 59.508 57.895 0.00 0.00 0.00 5.34
488 529 1.491563 GCTGACAACCTTACGCACG 59.508 57.895 0.00 0.00 0.00 5.34
489 530 1.219522 GCTGACAACCTTACGCACGT 61.220 55.000 0.00 0.00 0.00 4.49
490 531 1.214367 CTGACAACCTTACGCACGTT 58.786 50.000 0.00 0.00 0.00 3.99
492 533 3.068574 ACAACCTTACGCACGTTGT 57.931 47.368 0.00 5.39 43.91 3.32
493 534 0.932399 ACAACCTTACGCACGTTGTC 59.068 50.000 0.00 0.00 45.16 3.18
494 535 0.931702 CAACCTTACGCACGTTGTCA 59.068 50.000 0.00 0.00 33.72 3.58
495 536 1.070843 CAACCTTACGCACGTTGTCAG 60.071 52.381 0.00 0.00 33.72 3.51
496 537 1.219522 ACCTTACGCACGTTGTCAGC 61.220 55.000 0.00 0.00 0.00 4.26
500 541 3.226712 CGCACGTTGTCAGCGTTA 58.773 55.556 12.37 0.00 45.82 3.18
503 544 0.111266 GCACGTTGTCAGCGTTAGTG 60.111 55.000 12.37 2.67 40.90 2.74
505 546 1.127817 CGTTGTCAGCGTTAGTGCG 59.872 57.895 0.28 0.00 40.67 5.34
506 547 1.272784 CGTTGTCAGCGTTAGTGCGA 61.273 55.000 0.28 0.00 40.67 5.10
507 548 0.435008 GTTGTCAGCGTTAGTGCGAG 59.565 55.000 0.00 0.00 40.67 5.03
508 549 0.312729 TTGTCAGCGTTAGTGCGAGA 59.687 50.000 0.00 0.00 40.67 4.04
509 550 0.109735 TGTCAGCGTTAGTGCGAGAG 60.110 55.000 0.00 0.00 40.67 3.20
510 551 0.109689 GTCAGCGTTAGTGCGAGAGT 60.110 55.000 0.00 0.00 40.67 3.24
511 552 0.596577 TCAGCGTTAGTGCGAGAGTT 59.403 50.000 0.00 0.00 40.67 3.01
513 554 0.314302 AGCGTTAGTGCGAGAGTTGT 59.686 50.000 0.00 0.00 40.67 3.32
514 555 0.435008 GCGTTAGTGCGAGAGTTGTG 59.565 55.000 0.00 0.00 0.00 3.33
516 557 0.790814 GTTAGTGCGAGAGTTGTGGC 59.209 55.000 0.00 0.00 0.00 5.01
519 560 2.661537 TGCGAGAGTTGTGGCACG 60.662 61.111 13.77 0.00 0.00 5.34
520 561 3.414700 GCGAGAGTTGTGGCACGG 61.415 66.667 13.77 0.00 0.00 4.94
521 562 2.338620 CGAGAGTTGTGGCACGGA 59.661 61.111 13.77 0.76 0.00 4.69
523 564 1.069090 GAGAGTTGTGGCACGGACA 59.931 57.895 21.10 0.00 0.00 4.02
524 565 0.946221 GAGAGTTGTGGCACGGACAG 60.946 60.000 21.10 0.00 0.00 3.51
525 566 1.227556 GAGTTGTGGCACGGACAGT 60.228 57.895 21.10 6.40 0.00 3.55
526 567 0.814010 GAGTTGTGGCACGGACAGTT 60.814 55.000 21.10 5.59 0.00 3.16
527 568 0.393808 AGTTGTGGCACGGACAGTTT 60.394 50.000 21.10 3.10 0.00 2.66
528 569 1.134340 AGTTGTGGCACGGACAGTTTA 60.134 47.619 21.10 0.00 0.00 2.01
529 570 1.003223 GTTGTGGCACGGACAGTTTAC 60.003 52.381 13.77 0.00 0.00 2.01
530 571 0.466543 TGTGGCACGGACAGTTTACT 59.533 50.000 13.77 0.00 0.00 2.24
531 572 1.145803 GTGGCACGGACAGTTTACTC 58.854 55.000 0.00 0.00 0.00 2.59
532 573 0.034337 TGGCACGGACAGTTTACTCC 59.966 55.000 0.00 0.00 0.00 3.85
533 574 0.034337 GGCACGGACAGTTTACTCCA 59.966 55.000 0.00 0.00 0.00 3.86
534 575 1.429463 GCACGGACAGTTTACTCCAG 58.571 55.000 0.00 0.00 0.00 3.86
535 576 1.000506 GCACGGACAGTTTACTCCAGA 59.999 52.381 0.00 0.00 0.00 3.86
536 577 2.673833 CACGGACAGTTTACTCCAGAC 58.326 52.381 0.00 0.00 0.00 3.51
537 578 2.035449 CACGGACAGTTTACTCCAGACA 59.965 50.000 0.00 0.00 0.00 3.41
538 579 2.035576 ACGGACAGTTTACTCCAGACAC 59.964 50.000 0.00 0.00 0.00 3.67
539 580 2.673833 GGACAGTTTACTCCAGACACG 58.326 52.381 0.00 0.00 0.00 4.49
540 581 2.609737 GGACAGTTTACTCCAGACACGG 60.610 54.545 0.00 0.00 0.00 4.94
541 582 2.035576 GACAGTTTACTCCAGACACGGT 59.964 50.000 0.00 0.00 0.00 4.83
542 583 2.223971 ACAGTTTACTCCAGACACGGTG 60.224 50.000 6.58 6.58 0.00 4.94
543 584 1.343465 AGTTTACTCCAGACACGGTGG 59.657 52.381 13.48 0.00 36.28 4.61
544 585 1.069668 GTTTACTCCAGACACGGTGGT 59.930 52.381 13.48 2.01 36.37 4.16
553 594 3.357079 CACGGTGGTGGCTTGAGC 61.357 66.667 0.00 0.00 40.58 4.26
563 604 4.683432 GCTTGAGCCTTGACGTCT 57.317 55.556 17.92 0.00 34.31 4.18
564 605 2.450619 GCTTGAGCCTTGACGTCTC 58.549 57.895 17.92 5.95 34.31 3.36
565 606 1.016653 GCTTGAGCCTTGACGTCTCC 61.017 60.000 17.92 2.32 34.31 3.71
566 607 0.390472 CTTGAGCCTTGACGTCTCCC 60.390 60.000 17.92 2.68 0.00 4.30
567 608 0.832135 TTGAGCCTTGACGTCTCCCT 60.832 55.000 17.92 7.64 0.00 4.20
568 609 1.251527 TGAGCCTTGACGTCTCCCTC 61.252 60.000 17.92 15.90 0.00 4.30
569 610 0.968393 GAGCCTTGACGTCTCCCTCT 60.968 60.000 17.92 7.31 0.00 3.69
570 611 0.331954 AGCCTTGACGTCTCCCTCTA 59.668 55.000 17.92 0.00 0.00 2.43
571 612 1.183549 GCCTTGACGTCTCCCTCTAA 58.816 55.000 17.92 0.00 0.00 2.10
572 613 1.757699 GCCTTGACGTCTCCCTCTAAT 59.242 52.381 17.92 0.00 0.00 1.73
573 614 2.223852 GCCTTGACGTCTCCCTCTAATC 60.224 54.545 17.92 0.00 0.00 1.75
574 615 3.024547 CCTTGACGTCTCCCTCTAATCA 58.975 50.000 17.92 0.00 0.00 2.57
584 625 3.047857 TCCCTCTAATCACCATGCATGA 58.952 45.455 28.31 9.85 0.00 3.07
585 626 3.654321 TCCCTCTAATCACCATGCATGAT 59.346 43.478 28.31 8.39 38.47 2.45
586 627 4.008330 CCCTCTAATCACCATGCATGATC 58.992 47.826 28.31 0.00 35.72 2.92
587 628 3.683340 CCTCTAATCACCATGCATGATCG 59.317 47.826 28.31 13.75 35.72 3.69
588 629 3.667360 TCTAATCACCATGCATGATCGG 58.333 45.455 28.31 13.71 35.72 4.18
589 630 2.643995 AATCACCATGCATGATCGGA 57.356 45.000 28.31 17.90 35.72 4.55
590 631 1.888215 ATCACCATGCATGATCGGAC 58.112 50.000 28.31 0.00 30.81 4.79
591 632 0.530431 TCACCATGCATGATCGGACG 60.530 55.000 28.31 11.52 0.00 4.79
592 633 1.227645 ACCATGCATGATCGGACGG 60.228 57.895 28.31 11.01 0.00 4.79
593 634 2.610694 CCATGCATGATCGGACGGC 61.611 63.158 28.31 0.00 0.00 5.68
594 635 1.596203 CATGCATGATCGGACGGCT 60.596 57.895 22.59 0.00 0.00 5.52
595 636 1.301244 ATGCATGATCGGACGGCTC 60.301 57.895 0.00 0.00 0.00 4.70
596 637 2.031674 ATGCATGATCGGACGGCTCA 62.032 55.000 0.00 0.00 0.00 4.26
598 639 1.300465 CATGATCGGACGGCTCAGG 60.300 63.158 0.00 0.00 0.00 3.86
599 640 1.455773 ATGATCGGACGGCTCAGGA 60.456 57.895 0.00 0.00 0.00 3.86
608 649 3.502572 GGCTCAGGACGCCAAATC 58.497 61.111 0.00 0.00 46.77 2.17
609 650 1.078143 GGCTCAGGACGCCAAATCT 60.078 57.895 0.00 0.00 46.77 2.40
610 651 1.092345 GGCTCAGGACGCCAAATCTC 61.092 60.000 0.00 0.00 46.77 2.75
611 652 0.107945 GCTCAGGACGCCAAATCTCT 60.108 55.000 0.00 0.00 0.00 3.10
612 653 1.649664 CTCAGGACGCCAAATCTCTG 58.350 55.000 0.00 0.00 0.00 3.35
613 654 0.976641 TCAGGACGCCAAATCTCTGT 59.023 50.000 0.00 0.00 0.00 3.41
614 655 1.081892 CAGGACGCCAAATCTCTGTG 58.918 55.000 0.00 0.00 0.00 3.66
615 656 0.036010 AGGACGCCAAATCTCTGTGG 60.036 55.000 0.00 0.00 38.00 4.17
616 657 0.036388 GGACGCCAAATCTCTGTGGA 60.036 55.000 0.00 0.00 37.03 4.02
617 658 1.610624 GGACGCCAAATCTCTGTGGAA 60.611 52.381 0.00 0.00 37.03 3.53
618 659 1.734465 GACGCCAAATCTCTGTGGAAG 59.266 52.381 0.00 0.00 37.03 3.46
619 660 1.089920 CGCCAAATCTCTGTGGAAGG 58.910 55.000 0.00 0.00 37.03 3.46
620 661 0.813821 GCCAAATCTCTGTGGAAGGC 59.186 55.000 0.00 0.00 37.03 4.35
621 662 1.467920 CCAAATCTCTGTGGAAGGCC 58.532 55.000 0.00 0.00 37.03 5.19
622 663 1.089920 CAAATCTCTGTGGAAGGCCG 58.910 55.000 0.00 0.00 36.79 6.13
623 664 0.693049 AAATCTCTGTGGAAGGCCGT 59.307 50.000 0.00 0.00 36.79 5.68
624 665 1.568504 AATCTCTGTGGAAGGCCGTA 58.431 50.000 0.00 0.00 36.79 4.02
625 666 1.568504 ATCTCTGTGGAAGGCCGTAA 58.431 50.000 0.00 0.00 36.79 3.18
626 667 1.568504 TCTCTGTGGAAGGCCGTAAT 58.431 50.000 0.00 0.00 36.79 1.89
627 668 2.742348 TCTCTGTGGAAGGCCGTAATA 58.258 47.619 0.00 0.00 36.79 0.98
628 669 2.693591 TCTCTGTGGAAGGCCGTAATAG 59.306 50.000 0.00 0.00 36.79 1.73
629 670 1.138266 TCTGTGGAAGGCCGTAATAGC 59.862 52.381 0.00 0.00 36.79 2.97
630 671 1.139058 CTGTGGAAGGCCGTAATAGCT 59.861 52.381 0.00 0.00 36.79 3.32
631 672 2.364324 CTGTGGAAGGCCGTAATAGCTA 59.636 50.000 0.00 0.00 36.79 3.32
632 673 2.364324 TGTGGAAGGCCGTAATAGCTAG 59.636 50.000 0.00 0.00 36.79 3.42
633 674 1.343465 TGGAAGGCCGTAATAGCTAGC 59.657 52.381 6.62 6.62 36.79 3.42
634 675 1.619332 GGAAGGCCGTAATAGCTAGCT 59.381 52.381 23.12 23.12 0.00 3.32
635 676 2.610727 GGAAGGCCGTAATAGCTAGCTG 60.611 54.545 27.68 10.31 0.00 4.24
636 677 0.969894 AGGCCGTAATAGCTAGCTGG 59.030 55.000 27.68 19.48 0.00 4.85
637 678 0.966920 GGCCGTAATAGCTAGCTGGA 59.033 55.000 27.68 8.78 0.00 3.86
638 679 1.550976 GGCCGTAATAGCTAGCTGGAT 59.449 52.381 27.68 10.99 0.00 3.41
639 680 2.028020 GGCCGTAATAGCTAGCTGGATT 60.028 50.000 27.68 20.68 0.00 3.01
640 681 3.557264 GGCCGTAATAGCTAGCTGGATTT 60.557 47.826 27.68 16.31 0.00 2.17
641 682 4.065789 GCCGTAATAGCTAGCTGGATTTT 58.934 43.478 27.68 14.05 0.00 1.82
642 683 5.235516 GCCGTAATAGCTAGCTGGATTTTA 58.764 41.667 27.68 13.14 0.00 1.52
643 684 5.120363 GCCGTAATAGCTAGCTGGATTTTAC 59.880 44.000 27.68 20.99 0.00 2.01
644 685 6.456501 CCGTAATAGCTAGCTGGATTTTACT 58.543 40.000 27.68 0.00 0.00 2.24
645 686 6.929606 CCGTAATAGCTAGCTGGATTTTACTT 59.070 38.462 27.68 8.55 0.00 2.24
688 733 1.446099 CTCGCCTGCTCACGCTAAA 60.446 57.895 0.00 0.00 36.97 1.85
901 1333 3.439857 ACTCAAATGCCTATGTGGTGT 57.560 42.857 0.00 0.00 38.35 4.16
1057 1518 0.523546 CTTGTCAGATCCCGTCGACG 60.524 60.000 30.33 30.33 34.95 5.12
1973 3408 6.040054 GGGTGTACCAAAAAGAAGTAACACAT 59.960 38.462 3.11 0.00 39.85 3.21
2016 3451 5.132502 CCCATCAATGATAAGGTTGCTACA 58.867 41.667 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.747467 CGACCATTCCTGCTGGATGAAT 60.747 50.000 13.72 1.15 42.81 2.57
1 2 1.407299 CGACCATTCCTGCTGGATGAA 60.407 52.381 13.72 0.00 42.81 2.57
2 3 0.178767 CGACCATTCCTGCTGGATGA 59.821 55.000 13.72 0.00 42.81 2.92
3 4 0.816825 CCGACCATTCCTGCTGGATG 60.817 60.000 13.72 12.77 42.81 3.51
4 5 1.528824 CCGACCATTCCTGCTGGAT 59.471 57.895 13.72 0.00 42.81 3.41
5 6 2.989639 CCGACCATTCCTGCTGGA 59.010 61.111 8.48 8.48 41.36 3.86
8 9 4.473520 CCGCCGACCATTCCTGCT 62.474 66.667 0.00 0.00 0.00 4.24
21 22 0.736053 TGAAAAATACATCGGCCGCC 59.264 50.000 23.51 0.00 0.00 6.13
22 23 1.533129 GGTGAAAAATACATCGGCCGC 60.533 52.381 23.51 2.12 0.00 6.53
23 24 1.740585 TGGTGAAAAATACATCGGCCG 59.259 47.619 22.12 22.12 0.00 6.13
24 25 3.859411 TTGGTGAAAAATACATCGGCC 57.141 42.857 0.00 0.00 0.00 6.13
25 26 4.805219 AGTTTGGTGAAAAATACATCGGC 58.195 39.130 0.00 0.00 0.00 5.54
26 27 5.086058 CGAGTTTGGTGAAAAATACATCGG 58.914 41.667 0.00 0.00 0.00 4.18
27 28 5.788531 GTCGAGTTTGGTGAAAAATACATCG 59.211 40.000 0.00 0.00 0.00 3.84
28 29 6.577427 GTGTCGAGTTTGGTGAAAAATACATC 59.423 38.462 0.00 0.00 0.00 3.06
29 30 6.435428 GTGTCGAGTTTGGTGAAAAATACAT 58.565 36.000 0.00 0.00 0.00 2.29
30 31 5.502706 CGTGTCGAGTTTGGTGAAAAATACA 60.503 40.000 0.00 0.00 0.00 2.29
31 32 4.901881 CGTGTCGAGTTTGGTGAAAAATAC 59.098 41.667 0.00 0.00 0.00 1.89
32 33 4.809958 TCGTGTCGAGTTTGGTGAAAAATA 59.190 37.500 0.00 0.00 0.00 1.40
33 34 3.623960 TCGTGTCGAGTTTGGTGAAAAAT 59.376 39.130 0.00 0.00 0.00 1.82
34 35 3.001414 TCGTGTCGAGTTTGGTGAAAAA 58.999 40.909 0.00 0.00 0.00 1.94
35 36 2.619147 TCGTGTCGAGTTTGGTGAAAA 58.381 42.857 0.00 0.00 0.00 2.29
36 37 2.296831 TCGTGTCGAGTTTGGTGAAA 57.703 45.000 0.00 0.00 0.00 2.69
37 38 2.159212 TCTTCGTGTCGAGTTTGGTGAA 60.159 45.455 0.00 0.00 37.14 3.18
38 39 1.406180 TCTTCGTGTCGAGTTTGGTGA 59.594 47.619 0.00 0.00 37.14 4.02
39 40 1.847818 TCTTCGTGTCGAGTTTGGTG 58.152 50.000 0.00 0.00 37.14 4.17
40 41 2.035449 TCATCTTCGTGTCGAGTTTGGT 59.965 45.455 0.00 0.00 37.14 3.67
41 42 2.672714 TCATCTTCGTGTCGAGTTTGG 58.327 47.619 0.00 0.00 37.14 3.28
42 43 3.121944 CCTTCATCTTCGTGTCGAGTTTG 59.878 47.826 0.00 0.00 37.14 2.93
43 44 3.318017 CCTTCATCTTCGTGTCGAGTTT 58.682 45.455 0.00 0.00 37.14 2.66
44 45 2.927014 GCCTTCATCTTCGTGTCGAGTT 60.927 50.000 0.00 0.00 37.14 3.01
45 46 1.402984 GCCTTCATCTTCGTGTCGAGT 60.403 52.381 0.00 0.00 37.14 4.18
46 47 1.272781 GCCTTCATCTTCGTGTCGAG 58.727 55.000 0.00 0.00 37.14 4.04
47 48 0.456142 CGCCTTCATCTTCGTGTCGA 60.456 55.000 0.00 0.00 0.00 4.20
48 49 1.413767 CCGCCTTCATCTTCGTGTCG 61.414 60.000 0.00 0.00 0.00 4.35
49 50 0.108804 TCCGCCTTCATCTTCGTGTC 60.109 55.000 0.00 0.00 0.00 3.67
50 51 0.537188 ATCCGCCTTCATCTTCGTGT 59.463 50.000 0.00 0.00 0.00 4.49
51 52 1.594862 GAATCCGCCTTCATCTTCGTG 59.405 52.381 0.00 0.00 0.00 4.35
52 53 1.473434 GGAATCCGCCTTCATCTTCGT 60.473 52.381 0.00 0.00 0.00 3.85
53 54 1.221414 GGAATCCGCCTTCATCTTCG 58.779 55.000 0.00 0.00 0.00 3.79
54 55 1.221414 CGGAATCCGCCTTCATCTTC 58.779 55.000 9.39 0.00 41.17 2.87
55 56 3.386543 CGGAATCCGCCTTCATCTT 57.613 52.632 9.39 0.00 41.17 2.40
66 67 1.066587 CTGCTCCTCGTCGGAATCC 59.933 63.158 0.00 0.00 42.53 3.01
67 68 1.590259 GCTGCTCCTCGTCGGAATC 60.590 63.158 0.00 0.00 42.53 2.52
68 69 2.496817 GCTGCTCCTCGTCGGAAT 59.503 61.111 0.00 0.00 42.53 3.01
69 70 3.760035 GGCTGCTCCTCGTCGGAA 61.760 66.667 0.00 0.00 42.53 4.30
76 77 4.527583 CTCCTGCGGCTGCTCCTC 62.528 72.222 20.27 0.00 43.34 3.71
91 92 0.107459 GTGATGACCTTGGAGGCCTC 60.107 60.000 25.59 25.59 39.63 4.70
92 93 1.566298 GGTGATGACCTTGGAGGCCT 61.566 60.000 3.86 3.86 39.63 5.19
93 94 1.077429 GGTGATGACCTTGGAGGCC 60.077 63.158 0.00 0.00 39.63 5.19
94 95 1.077429 GGGTGATGACCTTGGAGGC 60.077 63.158 0.00 0.00 42.66 4.70
95 96 0.254178 CAGGGTGATGACCTTGGAGG 59.746 60.000 5.50 0.00 44.03 4.30
96 97 3.869623 CAGGGTGATGACCTTGGAG 57.130 57.895 5.50 0.00 44.03 3.86
115 116 0.169009 GCTCCGAGGTGAAAATGCAC 59.831 55.000 0.00 0.00 38.05 4.57
116 117 0.250684 TGCTCCGAGGTGAAAATGCA 60.251 50.000 0.00 0.00 0.00 3.96
117 118 0.449388 CTGCTCCGAGGTGAAAATGC 59.551 55.000 0.00 0.00 0.00 3.56
118 119 2.099141 TCTGCTCCGAGGTGAAAATG 57.901 50.000 0.00 0.00 0.00 2.32
119 120 2.616510 CCTTCTGCTCCGAGGTGAAAAT 60.617 50.000 0.00 0.00 0.00 1.82
120 121 1.270839 CCTTCTGCTCCGAGGTGAAAA 60.271 52.381 0.00 0.00 0.00 2.29
121 122 0.321671 CCTTCTGCTCCGAGGTGAAA 59.678 55.000 0.00 0.00 0.00 2.69
122 123 1.544825 CCCTTCTGCTCCGAGGTGAA 61.545 60.000 0.00 0.00 0.00 3.18
123 124 1.984570 CCCTTCTGCTCCGAGGTGA 60.985 63.158 0.00 0.00 0.00 4.02
124 125 2.581354 CCCTTCTGCTCCGAGGTG 59.419 66.667 0.00 0.00 0.00 4.00
125 126 3.394836 GCCCTTCTGCTCCGAGGT 61.395 66.667 0.00 0.00 0.00 3.85
126 127 3.393970 TGCCCTTCTGCTCCGAGG 61.394 66.667 0.00 0.00 0.00 4.63
127 128 2.125350 GTGCCCTTCTGCTCCGAG 60.125 66.667 0.00 0.00 0.00 4.63
128 129 1.768684 AAAGTGCCCTTCTGCTCCGA 61.769 55.000 0.00 0.00 0.00 4.55
129 130 1.301677 GAAAGTGCCCTTCTGCTCCG 61.302 60.000 0.00 0.00 0.00 4.63
130 131 0.250901 TGAAAGTGCCCTTCTGCTCC 60.251 55.000 0.00 0.00 0.00 4.70
131 132 0.877743 GTGAAAGTGCCCTTCTGCTC 59.122 55.000 0.00 0.00 0.00 4.26
132 133 0.183492 TGTGAAAGTGCCCTTCTGCT 59.817 50.000 0.00 0.00 0.00 4.24
142 143 2.094675 GGTGGGATCCATGTGAAAGTG 58.905 52.381 15.23 0.00 35.28 3.16
152 153 0.541764 GTGGCTTTTGGTGGGATCCA 60.542 55.000 15.23 0.00 35.49 3.41
167 168 1.966451 CTGACGGGGAAGTTGTGGC 60.966 63.158 0.00 0.00 0.00 5.01
191 194 4.382320 GGTGGCGCCGTCCTTGTA 62.382 66.667 26.46 4.00 0.00 2.41
217 220 4.059459 CCGCCATCGATTACGCGC 62.059 66.667 20.31 0.00 43.16 6.86
227 230 0.375106 CTTTCGCTTCTTCCGCCATC 59.625 55.000 0.00 0.00 0.00 3.51
231 234 1.391826 CTCTTCTTTCGCTTCTTCCGC 59.608 52.381 0.00 0.00 0.00 5.54
265 268 2.707849 GCTCTTGCCAGTGCCCATG 61.708 63.158 0.53 0.00 34.03 3.66
270 273 2.595463 TGGTGCTCTTGCCAGTGC 60.595 61.111 4.97 4.97 39.57 4.40
307 321 6.261381 ACGAGGCTTTTGTAACTTTGTTCATA 59.739 34.615 0.00 0.00 0.00 2.15
394 411 3.483869 GGCTGGGAGGGTAGGCTG 61.484 72.222 0.00 0.00 36.63 4.85
404 421 3.884704 ATTTTGCAGGCGGCTGGGA 62.885 57.895 36.25 18.23 45.15 4.37
406 423 2.125832 CATTTTGCAGGCGGCTGG 60.126 61.111 36.25 20.25 45.15 4.85
430 471 1.142474 GTTGTCAAAATGCAGCAGCC 58.858 50.000 0.00 0.00 41.13 4.85
441 482 3.388308 CGCAATGGAAATGGTTGTCAAA 58.612 40.909 0.00 0.00 0.00 2.69
442 483 2.288702 CCGCAATGGAAATGGTTGTCAA 60.289 45.455 0.00 0.00 42.00 3.18
443 484 1.271934 CCGCAATGGAAATGGTTGTCA 59.728 47.619 0.00 0.00 42.00 3.58
444 485 1.994916 CCGCAATGGAAATGGTTGTC 58.005 50.000 0.00 0.00 42.00 3.18
445 486 0.037419 GCCGCAATGGAAATGGTTGT 60.037 50.000 0.00 0.00 42.00 3.32
448 489 1.037030 ATCGCCGCAATGGAAATGGT 61.037 50.000 0.00 0.00 42.00 3.55
450 491 1.210545 GCATCGCCGCAATGGAAATG 61.211 55.000 0.00 0.00 42.00 2.32
451 492 1.066257 GCATCGCCGCAATGGAAAT 59.934 52.632 0.00 0.00 42.00 2.17
452 493 2.489285 GCATCGCCGCAATGGAAA 59.511 55.556 0.00 0.00 42.00 3.13
453 494 3.875039 CGCATCGCCGCAATGGAA 61.875 61.111 0.00 0.00 42.00 3.53
464 505 0.370273 GTAAGGTTGTCAGCGCATCG 59.630 55.000 11.47 0.00 0.00 3.84
465 506 0.370273 CGTAAGGTTGTCAGCGCATC 59.630 55.000 11.47 0.00 0.00 3.91
466 507 1.635663 GCGTAAGGTTGTCAGCGCAT 61.636 55.000 11.47 0.00 43.62 4.73
467 508 2.314647 GCGTAAGGTTGTCAGCGCA 61.315 57.895 11.47 0.00 43.62 6.09
468 509 2.314647 TGCGTAAGGTTGTCAGCGC 61.315 57.895 0.00 0.00 44.29 5.92
469 510 1.491563 GTGCGTAAGGTTGTCAGCG 59.508 57.895 0.00 0.00 38.28 5.18
470 511 1.219522 ACGTGCGTAAGGTTGTCAGC 61.220 55.000 0.00 0.00 38.28 4.26
471 512 1.070843 CAACGTGCGTAAGGTTGTCAG 60.071 52.381 13.99 0.00 45.43 3.51
472 513 0.931702 CAACGTGCGTAAGGTTGTCA 59.068 50.000 13.99 0.00 45.43 3.58
473 514 3.721466 CAACGTGCGTAAGGTTGTC 57.279 52.632 13.99 0.00 45.43 3.18
476 517 1.214367 CTGACAACGTGCGTAAGGTT 58.786 50.000 0.00 0.00 37.36 3.50
477 518 1.219522 GCTGACAACGTGCGTAAGGT 61.220 55.000 0.00 0.00 38.28 3.50
478 519 1.491563 GCTGACAACGTGCGTAAGG 59.508 57.895 0.00 0.00 38.28 2.69
479 520 1.127817 CGCTGACAACGTGCGTAAG 59.872 57.895 8.85 3.99 44.00 2.34
480 521 3.226712 CGCTGACAACGTGCGTAA 58.773 55.556 8.85 0.00 44.00 3.18
484 525 0.111266 CACTAACGCTGACAACGTGC 60.111 55.000 4.40 0.00 44.30 5.34
485 526 0.111266 GCACTAACGCTGACAACGTG 60.111 55.000 4.40 0.00 44.30 4.49
487 528 1.127817 CGCACTAACGCTGACAACG 59.872 57.895 0.00 0.00 0.00 4.10
488 529 0.435008 CTCGCACTAACGCTGACAAC 59.565 55.000 0.00 0.00 0.00 3.32
489 530 0.312729 TCTCGCACTAACGCTGACAA 59.687 50.000 0.00 0.00 0.00 3.18
490 531 0.109735 CTCTCGCACTAACGCTGACA 60.110 55.000 0.00 0.00 0.00 3.58
492 533 0.596577 AACTCTCGCACTAACGCTGA 59.403 50.000 0.00 0.00 0.00 4.26
493 534 0.710567 CAACTCTCGCACTAACGCTG 59.289 55.000 0.00 0.00 0.00 5.18
494 535 0.314302 ACAACTCTCGCACTAACGCT 59.686 50.000 0.00 0.00 0.00 5.07
495 536 0.435008 CACAACTCTCGCACTAACGC 59.565 55.000 0.00 0.00 0.00 4.84
496 537 1.060713 CCACAACTCTCGCACTAACG 58.939 55.000 0.00 0.00 0.00 3.18
498 539 0.391228 TGCCACAACTCTCGCACTAA 59.609 50.000 0.00 0.00 0.00 2.24
500 541 1.595382 GTGCCACAACTCTCGCACT 60.595 57.895 3.88 0.00 46.32 4.40
503 544 3.414700 CCGTGCCACAACTCTCGC 61.415 66.667 0.00 0.00 0.00 5.03
505 546 0.946221 CTGTCCGTGCCACAACTCTC 60.946 60.000 0.00 0.00 0.00 3.20
506 547 1.069765 CTGTCCGTGCCACAACTCT 59.930 57.895 0.00 0.00 0.00 3.24
507 548 0.814010 AACTGTCCGTGCCACAACTC 60.814 55.000 0.00 0.00 0.00 3.01
508 549 0.393808 AAACTGTCCGTGCCACAACT 60.394 50.000 0.00 0.00 0.00 3.16
509 550 1.003223 GTAAACTGTCCGTGCCACAAC 60.003 52.381 0.00 0.00 0.00 3.32
510 551 1.134340 AGTAAACTGTCCGTGCCACAA 60.134 47.619 0.00 0.00 0.00 3.33
511 552 0.466543 AGTAAACTGTCCGTGCCACA 59.533 50.000 0.00 0.00 0.00 4.17
513 554 0.034337 GGAGTAAACTGTCCGTGCCA 59.966 55.000 0.00 0.00 0.00 4.92
514 555 0.034337 TGGAGTAAACTGTCCGTGCC 59.966 55.000 0.00 0.00 35.37 5.01
516 557 2.035449 TGTCTGGAGTAAACTGTCCGTG 59.965 50.000 0.00 0.00 35.37 4.94
519 560 2.609737 CCGTGTCTGGAGTAAACTGTCC 60.610 54.545 0.00 0.00 0.00 4.02
520 561 2.035576 ACCGTGTCTGGAGTAAACTGTC 59.964 50.000 0.00 0.00 0.00 3.51
521 562 2.037144 ACCGTGTCTGGAGTAAACTGT 58.963 47.619 0.00 0.00 0.00 3.55
523 564 1.343465 CCACCGTGTCTGGAGTAAACT 59.657 52.381 0.00 0.00 0.00 2.66
524 565 1.069668 ACCACCGTGTCTGGAGTAAAC 59.930 52.381 0.00 0.00 32.55 2.01
525 566 1.069513 CACCACCGTGTCTGGAGTAAA 59.930 52.381 0.00 0.00 35.10 2.01
526 567 0.677288 CACCACCGTGTCTGGAGTAA 59.323 55.000 0.00 0.00 35.10 2.24
527 568 1.183030 CCACCACCGTGTCTGGAGTA 61.183 60.000 6.63 0.00 38.41 2.59
528 569 2.507854 CCACCACCGTGTCTGGAGT 61.508 63.158 6.63 0.00 38.41 3.85
529 570 2.343758 CCACCACCGTGTCTGGAG 59.656 66.667 6.63 0.00 38.41 3.86
530 571 3.936203 GCCACCACCGTGTCTGGA 61.936 66.667 14.17 0.00 38.41 3.86
531 572 3.476031 AAGCCACCACCGTGTCTGG 62.476 63.158 7.77 7.77 38.41 3.86
532 573 2.111043 AAGCCACCACCGTGTCTG 59.889 61.111 0.00 0.00 38.41 3.51
533 574 2.111043 CAAGCCACCACCGTGTCT 59.889 61.111 0.00 0.00 38.41 3.41
534 575 1.961277 CTCAAGCCACCACCGTGTC 60.961 63.158 0.00 0.00 38.41 3.67
535 576 2.111043 CTCAAGCCACCACCGTGT 59.889 61.111 0.00 0.00 38.41 4.49
536 577 3.357079 GCTCAAGCCACCACCGTG 61.357 66.667 0.00 0.00 39.91 4.94
546 587 4.683432 AGACGTCAAGGCTCAAGC 57.317 55.556 19.50 0.00 25.16 4.01
551 592 3.701454 GAGGGAGACGTCAAGGCT 58.299 61.111 19.50 0.00 44.42 4.58
557 598 2.376109 TGGTGATTAGAGGGAGACGTC 58.624 52.381 7.70 7.70 45.47 4.34
558 599 2.526888 TGGTGATTAGAGGGAGACGT 57.473 50.000 0.00 0.00 0.00 4.34
559 600 2.546795 GCATGGTGATTAGAGGGAGACG 60.547 54.545 0.00 0.00 0.00 4.18
560 601 2.435805 TGCATGGTGATTAGAGGGAGAC 59.564 50.000 0.00 0.00 0.00 3.36
561 602 2.763039 TGCATGGTGATTAGAGGGAGA 58.237 47.619 0.00 0.00 0.00 3.71
562 603 3.072038 TCATGCATGGTGATTAGAGGGAG 59.928 47.826 25.97 0.00 0.00 4.30
563 604 3.047857 TCATGCATGGTGATTAGAGGGA 58.952 45.455 25.97 0.00 0.00 4.20
564 605 3.497103 TCATGCATGGTGATTAGAGGG 57.503 47.619 25.97 0.00 0.00 4.30
565 606 3.683340 CGATCATGCATGGTGATTAGAGG 59.317 47.826 25.97 0.00 36.49 3.69
566 607 3.683340 CCGATCATGCATGGTGATTAGAG 59.317 47.826 25.97 7.82 36.49 2.43
567 608 3.324556 TCCGATCATGCATGGTGATTAGA 59.675 43.478 25.97 11.20 36.49 2.10
568 609 3.434641 GTCCGATCATGCATGGTGATTAG 59.565 47.826 25.97 11.36 36.49 1.73
569 610 3.402110 GTCCGATCATGCATGGTGATTA 58.598 45.455 25.97 6.40 36.49 1.75
570 611 2.224606 GTCCGATCATGCATGGTGATT 58.775 47.619 25.97 6.76 36.49 2.57
571 612 1.875157 CGTCCGATCATGCATGGTGAT 60.875 52.381 25.97 13.83 38.94 3.06
572 613 0.530431 CGTCCGATCATGCATGGTGA 60.530 55.000 25.97 11.24 0.00 4.02
573 614 1.501337 CCGTCCGATCATGCATGGTG 61.501 60.000 25.97 15.31 0.00 4.17
574 615 1.227645 CCGTCCGATCATGCATGGT 60.228 57.895 25.97 20.58 0.00 3.55
584 625 3.518998 CGTCCTGAGCCGTCCGAT 61.519 66.667 0.00 0.00 0.00 4.18
592 633 0.107945 AGAGATTTGGCGTCCTGAGC 60.108 55.000 0.00 0.00 0.00 4.26
593 634 1.066573 ACAGAGATTTGGCGTCCTGAG 60.067 52.381 0.00 0.00 0.00 3.35
594 635 0.976641 ACAGAGATTTGGCGTCCTGA 59.023 50.000 0.00 0.00 0.00 3.86
595 636 1.081892 CACAGAGATTTGGCGTCCTG 58.918 55.000 0.00 0.00 0.00 3.86
596 637 0.036010 CCACAGAGATTTGGCGTCCT 60.036 55.000 0.00 0.00 0.00 3.85
598 639 1.734465 CTTCCACAGAGATTTGGCGTC 59.266 52.381 0.00 0.00 32.37 5.19
599 640 1.611673 CCTTCCACAGAGATTTGGCGT 60.612 52.381 0.00 0.00 32.37 5.68
601 642 0.813821 GCCTTCCACAGAGATTTGGC 59.186 55.000 0.00 0.00 32.37 4.52
604 645 0.693049 ACGGCCTTCCACAGAGATTT 59.307 50.000 0.00 0.00 0.00 2.17
605 646 1.568504 TACGGCCTTCCACAGAGATT 58.431 50.000 0.00 0.00 0.00 2.40
606 647 1.568504 TTACGGCCTTCCACAGAGAT 58.431 50.000 0.00 0.00 0.00 2.75
607 648 1.568504 ATTACGGCCTTCCACAGAGA 58.431 50.000 0.00 0.00 0.00 3.10
608 649 2.803492 GCTATTACGGCCTTCCACAGAG 60.803 54.545 0.00 0.00 0.00 3.35
609 650 1.138266 GCTATTACGGCCTTCCACAGA 59.862 52.381 0.00 0.00 0.00 3.41
610 651 1.139058 AGCTATTACGGCCTTCCACAG 59.861 52.381 0.00 0.00 0.00 3.66
611 652 1.200519 AGCTATTACGGCCTTCCACA 58.799 50.000 0.00 0.00 0.00 4.17
612 653 2.866855 GCTAGCTATTACGGCCTTCCAC 60.867 54.545 7.70 0.00 0.00 4.02
613 654 1.343465 GCTAGCTATTACGGCCTTCCA 59.657 52.381 7.70 0.00 0.00 3.53
614 655 1.619332 AGCTAGCTATTACGGCCTTCC 59.381 52.381 17.69 0.00 0.00 3.46
615 656 2.610727 CCAGCTAGCTATTACGGCCTTC 60.611 54.545 18.86 0.00 0.00 3.46
616 657 1.344763 CCAGCTAGCTATTACGGCCTT 59.655 52.381 18.86 0.00 0.00 4.35
617 658 0.969894 CCAGCTAGCTATTACGGCCT 59.030 55.000 18.86 0.00 0.00 5.19
618 659 0.966920 TCCAGCTAGCTATTACGGCC 59.033 55.000 18.86 0.00 0.00 6.13
619 660 3.320673 AATCCAGCTAGCTATTACGGC 57.679 47.619 18.86 0.00 0.00 5.68
620 661 6.456501 AGTAAAATCCAGCTAGCTATTACGG 58.543 40.000 18.86 14.33 0.00 4.02
621 662 7.652105 TCAAGTAAAATCCAGCTAGCTATTACG 59.348 37.037 18.86 4.28 0.00 3.18
622 663 8.888579 TCAAGTAAAATCCAGCTAGCTATTAC 57.111 34.615 18.86 18.85 0.00 1.89
623 664 8.924303 TCTCAAGTAAAATCCAGCTAGCTATTA 58.076 33.333 18.86 6.09 0.00 0.98
624 665 7.796054 TCTCAAGTAAAATCCAGCTAGCTATT 58.204 34.615 18.86 11.99 0.00 1.73
625 666 7.366847 TCTCAAGTAAAATCCAGCTAGCTAT 57.633 36.000 18.86 5.42 0.00 2.97
626 667 6.684111 GCTCTCAAGTAAAATCCAGCTAGCTA 60.684 42.308 18.86 2.62 0.00 3.32
627 668 5.669477 CTCTCAAGTAAAATCCAGCTAGCT 58.331 41.667 12.68 12.68 0.00 3.32
628 669 4.272261 GCTCTCAAGTAAAATCCAGCTAGC 59.728 45.833 6.62 6.62 0.00 3.42
629 670 4.505922 CGCTCTCAAGTAAAATCCAGCTAG 59.494 45.833 0.00 0.00 0.00 3.42
630 671 4.433615 CGCTCTCAAGTAAAATCCAGCTA 58.566 43.478 0.00 0.00 0.00 3.32
631 672 3.265791 CGCTCTCAAGTAAAATCCAGCT 58.734 45.455 0.00 0.00 0.00 4.24
632 673 2.352960 CCGCTCTCAAGTAAAATCCAGC 59.647 50.000 0.00 0.00 0.00 4.85
633 674 2.352960 GCCGCTCTCAAGTAAAATCCAG 59.647 50.000 0.00 0.00 0.00 3.86
634 675 2.356135 GCCGCTCTCAAGTAAAATCCA 58.644 47.619 0.00 0.00 0.00 3.41
635 676 1.327764 CGCCGCTCTCAAGTAAAATCC 59.672 52.381 0.00 0.00 0.00 3.01
636 677 2.268298 TCGCCGCTCTCAAGTAAAATC 58.732 47.619 0.00 0.00 0.00 2.17
637 678 2.380084 TCGCCGCTCTCAAGTAAAAT 57.620 45.000 0.00 0.00 0.00 1.82
638 679 1.999735 CATCGCCGCTCTCAAGTAAAA 59.000 47.619 0.00 0.00 0.00 1.52
639 680 1.640428 CATCGCCGCTCTCAAGTAAA 58.360 50.000 0.00 0.00 0.00 2.01
640 681 0.179111 CCATCGCCGCTCTCAAGTAA 60.179 55.000 0.00 0.00 0.00 2.24
641 682 1.320344 ACCATCGCCGCTCTCAAGTA 61.320 55.000 0.00 0.00 0.00 2.24
642 683 2.185350 CCATCGCCGCTCTCAAGT 59.815 61.111 0.00 0.00 0.00 3.16
643 684 2.169789 CACCATCGCCGCTCTCAAG 61.170 63.158 0.00 0.00 0.00 3.02
644 685 2.125552 CACCATCGCCGCTCTCAA 60.126 61.111 0.00 0.00 0.00 3.02
645 686 4.819761 GCACCATCGCCGCTCTCA 62.820 66.667 0.00 0.00 0.00 3.27
688 733 1.950484 GCCAGTGTTCGATTGGGACAT 60.950 52.381 7.57 0.00 39.30 3.06
901 1333 1.215382 CGCAGACAAGGATCCGACA 59.785 57.895 5.98 0.00 0.00 4.35
1057 1518 8.787852 GGAAATCATGAAATACTGAAGGTATCC 58.212 37.037 0.00 0.00 39.94 2.59
1732 3162 9.908747 TCCGAACCTAATTTTCCAAGAATATAA 57.091 29.630 0.00 0.00 0.00 0.98
1744 3174 8.711170 TCCATATCTAACTCCGAACCTAATTTT 58.289 33.333 0.00 0.00 0.00 1.82
1973 3408 1.473257 GCATCTACATCGGCAAGACCA 60.473 52.381 0.00 0.00 39.03 4.02
2016 3451 0.179029 CCACCCGTTGTCCTTTGAGT 60.179 55.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.