Multiple sequence alignment - TraesCS5A01G525200

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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 TraesCS5A01G525200 chr5A 100.000 5164 0 0 1 5164 685735810 685740973 0.000000e+00 9537.0
1 TraesCS5A01G525200 chr5A 77.439 328 54 13 999 1324 698012692 698012383 1.480000e-40 178.0
2 TraesCS5A01G525200 chr5A 74.631 406 69 23 1966 2363 660428837 660428458 1.160000e-31 148.0
3 TraesCS5A01G525200 chr4B 92.910 2426 129 13 2553 4968 646855991 646858383 0.000000e+00 3487.0
4 TraesCS5A01G525200 chr4B 89.073 1391 114 15 42 1428 646842564 646843920 0.000000e+00 1692.0
5 TraesCS5A01G525200 chr4B 86.266 699 72 13 1874 2555 646855207 646855898 0.000000e+00 737.0
6 TraesCS5A01G525200 chr4B 86.920 237 23 2 1458 1692 646844409 646844639 5.130000e-65 259.0
7 TraesCS5A01G525200 chr4B 92.135 178 14 0 1701 1878 646844890 646845067 8.580000e-63 252.0
8 TraesCS5A01G525200 chr4B 87.963 216 20 4 4953 5164 646858735 646858948 3.090000e-62 250.0
9 TraesCS5A01G525200 chr4B 91.061 179 15 1 1448 1625 646844712 646844890 1.860000e-59 241.0
10 TraesCS5A01G525200 chr4B 76.667 330 66 9 999 1324 657808123 657808445 6.870000e-39 172.0
11 TraesCS5A01G525200 chr4B 100.000 32 0 0 730 761 114439539 114439570 5.580000e-05 60.2
12 TraesCS5A01G525200 chr4D 92.861 2115 100 24 3085 5164 502481860 502483958 0.000000e+00 3022.0
13 TraesCS5A01G525200 chr4D 93.705 1398 75 10 38 1428 502478740 502480131 0.000000e+00 2082.0
14 TraesCS5A01G525200 chr4D 89.104 1083 81 15 1928 2989 502480772 502481838 0.000000e+00 1312.0
15 TraesCS5A01G525200 chr4D 94.886 176 8 1 1712 1887 502480377 502480551 1.830000e-69 274.0
16 TraesCS5A01G525200 chr4D 76.596 329 65 9 999 1324 509239604 509239285 2.470000e-38 171.0
17 TraesCS5A01G525200 chr4A 77.431 576 80 27 79 636 24946268 24946811 1.090000e-76 298.0
18 TraesCS5A01G525200 chr4A 77.658 555 77 33 174 696 590605199 590604660 1.410000e-75 294.0
19 TraesCS5A01G525200 chr6B 74.390 738 138 30 77 787 508829140 508829853 8.520000e-68 268.0
20 TraesCS5A01G525200 chr5D 74.946 459 83 27 1958 2398 269297523 269297079 1.140000e-41 182.0
21 TraesCS5A01G525200 chr3D 80.408 245 36 10 1994 2232 374067289 374067527 5.310000e-40 176.0
22 TraesCS5A01G525200 chr3D 76.172 256 40 13 1039 1294 453209274 453209508 1.180000e-21 115.0
23 TraesCS5A01G525200 chr3D 97.059 34 1 0 44 77 307839937 307839970 2.010000e-04 58.4
24 TraesCS5A01G525200 chr3A 76.647 334 65 10 1004 1335 549257447 549257125 6.870000e-39 172.0
25 TraesCS5A01G525200 chr3A 100.000 36 0 0 42 77 88212354 88212319 3.340000e-07 67.6
26 TraesCS5A01G525200 chr7D 76.308 325 64 10 1004 1325 262860246 262859932 1.490000e-35 161.0
27 TraesCS5A01G525200 chr7D 78.912 147 25 5 90 234 245470804 245470946 1.530000e-15 95.3
28 TraesCS5A01G525200 chr7D 94.118 34 2 0 44 77 72281790 72281823 9.000000e-03 52.8
29 TraesCS5A01G525200 chr2D 75.466 322 68 8 1006 1325 165691238 165690926 4.170000e-31 147.0
30 TraesCS5A01G525200 chr2D 97.222 36 1 0 42 77 638381113 638381078 1.550000e-05 62.1
31 TraesCS5A01G525200 chr5B 85.401 137 20 0 84 220 554524955 554524819 5.390000e-30 143.0
32 TraesCS5A01G525200 chr2B 94.595 37 1 1 44 80 50496600 50496635 7.220000e-04 56.5
33 TraesCS5A01G525200 chr3B 85.455 55 5 3 311 362 676936328 676936382 3.000000e-03 54.7


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 TraesCS5A01G525200 chr5A 685735810 685740973 5163 False 9537.000000 9537 100.000000 1 5164 1 chr5A.!!$F1 5163
1 TraesCS5A01G525200 chr4B 646855207 646858948 3741 False 1491.333333 3487 89.046333 1874 5164 3 chr4B.!!$F4 3290
2 TraesCS5A01G525200 chr4B 646842564 646845067 2503 False 611.000000 1692 89.797250 42 1878 4 chr4B.!!$F3 1836
3 TraesCS5A01G525200 chr4D 502478740 502483958 5218 False 1672.500000 3022 92.639000 38 5164 4 chr4D.!!$F1 5126
4 TraesCS5A01G525200 chr4A 24946268 24946811 543 False 298.000000 298 77.431000 79 636 1 chr4A.!!$F1 557
5 TraesCS5A01G525200 chr4A 590604660 590605199 539 True 294.000000 294 77.658000 174 696 1 chr4A.!!$R1 522
6 TraesCS5A01G525200 chr6B 508829140 508829853 713 False 268.000000 268 74.390000 77 787 1 chr6B.!!$F1 710

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
698 729 0.027848 GTTTGCGGAAAAACGGACGA 59.972 50.0 2.79 0.0 32.76 4.20 F
1593 2086 0.250513 AAAGATGAGGCCACTCCGAC 59.749 55.0 5.01 0.0 43.29 4.79 F
1697 2434 0.391597 GAAGACCCCAAGACACGTGA 59.608 55.0 25.01 0.0 0.00 4.35 F
2287 3222 0.534412 TGTGTGTGGTTTTTGCCTGG 59.466 50.0 0.00 0.0 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1981 2904 0.037303 TCGACTTCCACTACCTCCGT 59.963 55.0 0.00 0.0 0.0 4.69 R
2523 3463 0.620556 GCTCTCAGTGGGGAATTGGA 59.379 55.0 0.00 0.0 0.0 3.53 R
3663 4707 0.681733 CTGTCCATGGGGTATCCTCG 59.318 60.0 13.02 0.0 36.2 4.63 R
4189 5233 0.250945 TGGTTGTTGGGCGCTTGATA 60.251 50.0 7.64 0.0 0.0 2.15 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 2.674138 TTGCTCCGGCTATTGGCA 59.326 55.556 0.00 0.00 44.01 4.92
18 19 1.748879 TTGCTCCGGCTATTGGCAC 60.749 57.895 0.00 0.00 44.01 5.01
19 20 3.272334 GCTCCGGCTATTGGCACG 61.272 66.667 0.00 0.00 44.01 5.34
20 21 2.186903 CTCCGGCTATTGGCACGT 59.813 61.111 0.00 0.00 44.01 4.49
21 22 2.125310 TCCGGCTATTGGCACGTG 60.125 61.111 12.28 12.28 44.01 4.49
22 23 2.435938 CCGGCTATTGGCACGTGT 60.436 61.111 18.38 0.00 44.01 4.49
23 24 2.038269 CCGGCTATTGGCACGTGTT 61.038 57.895 18.38 2.64 44.01 3.32
24 25 1.582610 CCGGCTATTGGCACGTGTTT 61.583 55.000 18.38 2.28 44.01 2.83
25 26 0.179200 CGGCTATTGGCACGTGTTTC 60.179 55.000 18.38 8.00 44.01 2.78
26 27 0.170339 GGCTATTGGCACGTGTTTCC 59.830 55.000 18.38 10.60 44.01 3.13
27 28 0.878416 GCTATTGGCACGTGTTTCCA 59.122 50.000 18.38 13.31 41.35 3.53
28 29 1.401018 GCTATTGGCACGTGTTTCCAC 60.401 52.381 18.38 0.00 41.35 4.02
29 30 1.876799 CTATTGGCACGTGTTTCCACA 59.123 47.619 18.38 7.54 41.93 4.17
30 31 0.667993 ATTGGCACGTGTTTCCACAG 59.332 50.000 18.38 0.00 41.93 3.66
31 32 0.678366 TTGGCACGTGTTTCCACAGT 60.678 50.000 18.38 0.00 41.93 3.55
32 33 0.678366 TGGCACGTGTTTCCACAGTT 60.678 50.000 18.38 0.00 41.93 3.16
33 34 1.301423 GGCACGTGTTTCCACAGTTA 58.699 50.000 18.38 0.00 41.93 2.24
34 35 1.003223 GGCACGTGTTTCCACAGTTAC 60.003 52.381 18.38 0.00 41.93 2.50
35 36 1.003223 GCACGTGTTTCCACAGTTACC 60.003 52.381 18.38 0.00 41.93 2.85
36 37 2.281517 CACGTGTTTCCACAGTTACCA 58.718 47.619 7.58 0.00 41.93 3.25
267 284 1.163420 ACCTCGCATCGCACAACAAA 61.163 50.000 0.00 0.00 0.00 2.83
282 299 5.715070 CACAACAAAGTCACCCTTAAACAA 58.285 37.500 0.00 0.00 31.48 2.83
283 300 6.337356 CACAACAAAGTCACCCTTAAACAAT 58.663 36.000 0.00 0.00 31.48 2.71
294 311 4.352893 ACCCTTAAACAATGAGTACCCTGT 59.647 41.667 0.00 0.00 0.00 4.00
305 322 1.623811 AGTACCCTGTCATCGTGCTTT 59.376 47.619 0.00 0.00 0.00 3.51
318 335 6.198966 GTCATCGTGCTTTTCTGAAAAACAAT 59.801 34.615 17.62 8.48 31.23 2.71
360 384 6.545666 TCAATGACATTTGACTAAACACCTGT 59.454 34.615 0.00 0.00 30.82 4.00
409 433 1.880941 GACAGGGGTGAGAAGGGTAT 58.119 55.000 0.00 0.00 0.00 2.73
411 435 1.080498 ACAGGGGTGAGAAGGGTATCA 59.920 52.381 0.00 0.00 0.00 2.15
435 459 1.991230 CGGAGGGATTCTTGGGTGT 59.009 57.895 0.00 0.00 0.00 4.16
520 547 2.288025 GGTGGCCGGAGAGGTACAA 61.288 63.158 5.05 0.00 43.70 2.41
521 548 1.675219 GTGGCCGGAGAGGTACAAA 59.325 57.895 5.05 0.00 43.70 2.83
529 556 3.497031 GAGGTACAAAGGCGGCGC 61.497 66.667 26.17 26.17 0.00 6.53
612 642 2.045885 AGGAGGGGATTTCAGTGAGGTA 59.954 50.000 0.00 0.00 0.00 3.08
653 683 0.539986 GGCTAATGTCCGAACTCCCA 59.460 55.000 0.00 0.00 0.00 4.37
668 698 0.253160 TCCCACACAGCCTCCCTAAT 60.253 55.000 0.00 0.00 0.00 1.73
694 725 2.212579 GCAGTTTGCGGAAAAACGG 58.787 52.632 2.79 0.00 43.39 4.44
698 729 0.027848 GTTTGCGGAAAAACGGACGA 59.972 50.000 2.79 0.00 32.76 4.20
702 733 2.141517 TGCGGAAAAACGGACGATTAA 58.858 42.857 0.00 0.00 0.00 1.40
713 744 1.745768 GACGATTAAACCGGTCCGCG 61.746 60.000 8.04 10.61 0.00 6.46
727 758 3.993103 CGCGGACGGATGAAGTAC 58.007 61.111 0.00 0.00 34.97 2.73
729 760 1.514087 GCGGACGGATGAAGTACCA 59.486 57.895 0.00 0.00 0.00 3.25
748 779 3.243367 ACCACATTGGATGACAAAACACG 60.243 43.478 0.00 0.00 43.46 4.49
750 781 4.358851 CACATTGGATGACAAAACACGTT 58.641 39.130 0.00 0.00 43.46 3.99
761 792 0.878961 AAACACGTTCGGACAGCTCC 60.879 55.000 0.00 0.00 0.00 4.70
792 823 3.817647 GGATGCAGATGGTTTGATAGTCC 59.182 47.826 0.00 0.00 0.00 3.85
793 824 4.445448 GGATGCAGATGGTTTGATAGTCCT 60.445 45.833 0.00 0.00 0.00 3.85
795 826 5.692115 TGCAGATGGTTTGATAGTCCTTA 57.308 39.130 0.00 0.00 0.00 2.69
796 827 6.061022 TGCAGATGGTTTGATAGTCCTTAA 57.939 37.500 0.00 0.00 0.00 1.85
798 829 6.374333 TGCAGATGGTTTGATAGTCCTTAAAC 59.626 38.462 0.00 0.00 33.48 2.01
799 830 6.456988 GCAGATGGTTTGATAGTCCTTAAACG 60.457 42.308 0.00 0.00 34.68 3.60
917 949 3.833645 TCCGGATTGTCTCGCCCG 61.834 66.667 0.00 0.00 41.47 6.13
947 979 2.830104 TGCATGAATCTGATCGTCCAG 58.170 47.619 0.00 1.37 35.55 3.86
1175 1207 6.955364 TGATTCTCAATCCACTGATCTCTTT 58.045 36.000 0.00 0.00 37.09 2.52
1330 1363 4.232221 CCCGCGATCTGTACGTAATTAAT 58.768 43.478 8.23 0.00 0.00 1.40
1406 1439 3.489416 GGAGAAAACAAAAACGATGTGGC 59.511 43.478 0.00 0.00 0.00 5.01
1455 1544 6.286758 TCAGAATAGTTCTCTCCATTCATGC 58.713 40.000 0.00 0.00 38.11 4.06
1462 1955 2.842496 TCTCTCCATTCATGCTCTTGGT 59.158 45.455 0.00 0.00 0.00 3.67
1491 1984 1.811965 CCATTTGATCTTGGTGTCGCA 59.188 47.619 0.00 0.00 0.00 5.10
1492 1985 2.159476 CCATTTGATCTTGGTGTCGCAG 60.159 50.000 0.00 0.00 0.00 5.18
1501 1994 2.760634 TGGTGTCGCAGATGTTGTAT 57.239 45.000 0.00 0.00 40.67 2.29
1503 1996 2.028567 TGGTGTCGCAGATGTTGTATGA 60.029 45.455 0.00 0.00 40.67 2.15
1507 2000 2.029728 GTCGCAGATGTTGTATGACAGC 59.970 50.000 0.00 0.00 40.67 4.40
1510 2003 2.681976 GCAGATGTTGTATGACAGCCCT 60.682 50.000 0.00 0.00 36.64 5.19
1513 2006 1.262417 TGTTGTATGACAGCCCTCGA 58.738 50.000 0.00 0.00 0.00 4.04
1519 2012 2.048127 GACAGCCCTCGACCACAC 60.048 66.667 0.00 0.00 0.00 3.82
1565 2058 9.825972 AACAATCACATAAAAGATGTAGTTTCG 57.174 29.630 0.00 0.00 0.00 3.46
1567 2060 9.825972 CAATCACATAAAAGATGTAGTTTCGTT 57.174 29.630 0.00 0.00 0.00 3.85
1573 2066 9.329913 CATAAAAGATGTAGTTTCGTTCTTTGG 57.670 33.333 0.00 0.00 0.00 3.28
1584 2077 3.074412 TCGTTCTTTGGAAAGATGAGGC 58.926 45.455 2.71 0.00 43.92 4.70
1590 2083 0.620556 TGGAAAGATGAGGCCACTCC 59.379 55.000 5.01 1.44 43.29 3.85
1593 2086 0.250513 AAAGATGAGGCCACTCCGAC 59.749 55.000 5.01 0.00 43.29 4.79
1610 2105 4.566004 TCCGACAAAACAAGATAGACCAG 58.434 43.478 0.00 0.00 0.00 4.00
1615 2110 7.333423 CCGACAAAACAAGATAGACCAGAATAA 59.667 37.037 0.00 0.00 0.00 1.40
1654 2149 9.261180 CACAAAAATTGAGAGTGTAGAGACTTA 57.739 33.333 0.00 0.00 0.00 2.24
1661 2156 7.147143 TGAGAGTGTAGAGACTTATCAACAC 57.853 40.000 0.00 0.00 36.36 3.32
1666 2161 6.591834 AGTGTAGAGACTTATCAACACATTGC 59.408 38.462 6.23 0.00 37.54 3.56
1674 2169 7.013655 AGACTTATCAACACATTGCAAAGAAGT 59.986 33.333 8.96 6.72 35.63 3.01
1692 2187 2.930826 GTCAAGAAGACCCCAAGACA 57.069 50.000 0.00 0.00 41.56 3.41
1693 2188 2.495084 GTCAAGAAGACCCCAAGACAC 58.505 52.381 0.00 0.00 41.56 3.67
1697 2434 0.391597 GAAGACCCCAAGACACGTGA 59.608 55.000 25.01 0.00 0.00 4.35
1699 2436 1.046472 AGACCCCAAGACACGTGACA 61.046 55.000 25.01 0.00 0.00 3.58
1710 2447 6.809689 CCAAGACACGTGACATACTTACATAA 59.190 38.462 25.01 0.00 0.00 1.90
1790 2527 0.753262 AGAATTCGATGCCCGCTACT 59.247 50.000 0.00 0.00 38.37 2.57
1849 2586 9.874205 AATATTGACCAATAAATGTTTGTCCAG 57.126 29.630 6.55 0.00 36.90 3.86
1898 2635 1.270907 ACAGAGGTGATGGTGGAGTC 58.729 55.000 0.00 0.00 0.00 3.36
1902 2639 2.304180 AGAGGTGATGGTGGAGTCTTTG 59.696 50.000 0.00 0.00 0.00 2.77
1905 2642 2.224523 GGTGATGGTGGAGTCTTTGTCA 60.225 50.000 0.00 0.00 0.00 3.58
1906 2643 2.808543 GTGATGGTGGAGTCTTTGTCAC 59.191 50.000 0.00 0.00 0.00 3.67
1981 2904 2.131972 CGTGTTGATTGGTCTCGTTGA 58.868 47.619 0.00 0.00 0.00 3.18
2036 2959 4.424711 GCTGGTTGGATGCCGGGA 62.425 66.667 2.18 0.00 33.10 5.14
2081 3005 4.918360 TGGCCCTGTGAGTGGGGT 62.918 66.667 0.00 0.00 44.71 4.95
2091 3015 2.847234 AGTGGGGTCGTGGCTTCA 60.847 61.111 0.00 0.00 0.00 3.02
2121 3045 4.179579 GGCATTCCGGCGCTTCAC 62.180 66.667 7.64 0.00 33.57 3.18
2141 3066 2.125106 GCGGTGGGGTCTGTCATC 60.125 66.667 0.00 0.00 0.00 2.92
2148 3073 1.298859 GGGGTCTGTCATCGTTGTGC 61.299 60.000 0.00 0.00 0.00 4.57
2190 3115 3.141398 CCTAATCAATCATGTGGTCGGG 58.859 50.000 0.00 0.00 0.00 5.14
2228 3153 2.124736 CATCAATCGTGGGGGCGT 60.125 61.111 0.00 0.00 0.00 5.68
2285 3220 0.534873 GGTGTGTGTGGTTTTTGCCT 59.465 50.000 0.00 0.00 0.00 4.75
2287 3222 0.534412 TGTGTGTGGTTTTTGCCTGG 59.466 50.000 0.00 0.00 0.00 4.45
2302 3237 6.478512 TTTGCCTGGTTTTCTCAATTAACT 57.521 33.333 0.00 0.00 0.00 2.24
2319 3254 0.614979 ACTGTGCCTCTGTATCGGGT 60.615 55.000 0.00 0.00 0.00 5.28
2373 3308 7.308469 GGGCAATTCTCTTCTTCTATAATGCAG 60.308 40.741 0.00 0.00 0.00 4.41
2380 3315 6.051717 TCTTCTTCTATAATGCAGTGAAGGC 58.948 40.000 11.37 0.00 35.98 4.35
2446 3386 8.754080 AGTGGCATATCTATTCTGTAGGTATTC 58.246 37.037 0.00 0.00 0.00 1.75
2459 3399 6.271391 TCTGTAGGTATTCAAAACTTCCTCCA 59.729 38.462 0.00 0.00 0.00 3.86
2483 3423 7.043854 CCATAATTAGCTTGAGCAACATTTTCG 60.044 37.037 5.70 0.00 45.16 3.46
2487 3427 4.537015 AGCTTGAGCAACATTTTCGTAAC 58.463 39.130 5.70 0.00 45.16 2.50
2488 3428 4.275936 AGCTTGAGCAACATTTTCGTAACT 59.724 37.500 5.70 0.00 45.16 2.24
2489 3429 4.379793 GCTTGAGCAACATTTTCGTAACTG 59.620 41.667 0.00 0.00 41.59 3.16
2523 3463 3.588842 TGTTGGATCAAGGTCCTGAATCT 59.411 43.478 11.64 0.00 39.12 2.40
2537 3477 3.285484 CTGAATCTCCAATTCCCCACTG 58.715 50.000 0.00 0.00 0.00 3.66
2650 3685 6.445451 ACTTCCCATCTGTGCAGATAATAT 57.555 37.500 13.60 0.00 45.78 1.28
2736 3772 3.476552 TGTTCCTAAGCAACCTTGAGTG 58.523 45.455 0.00 0.00 32.47 3.51
2739 3775 3.244582 TCCTAAGCAACCTTGAGTGGTA 58.755 45.455 0.00 0.00 39.83 3.25
2742 3778 5.010282 CCTAAGCAACCTTGAGTGGTAAAT 58.990 41.667 0.00 0.00 39.83 1.40
2782 3818 8.367911 TGTTATATTAAGTGCCTCACCTATCTG 58.632 37.037 0.00 0.00 34.49 2.90
2989 4025 4.464008 CAGTTATGCATATCCACACCCTT 58.536 43.478 7.36 0.00 0.00 3.95
2990 4026 4.516698 CAGTTATGCATATCCACACCCTTC 59.483 45.833 7.36 0.00 0.00 3.46
3008 4044 5.014123 ACCCTTCTTGAACATAAGTGGATCA 59.986 40.000 0.00 0.00 0.00 2.92
3009 4045 6.125029 CCCTTCTTGAACATAAGTGGATCAT 58.875 40.000 0.00 0.00 0.00 2.45
3092 4132 4.469945 CCACCCTCTCCTACATAGTCAAAA 59.530 45.833 0.00 0.00 0.00 2.44
3099 4139 7.497249 CCTCTCCTACATAGTCAAAATTTCAGG 59.503 40.741 0.00 0.00 0.00 3.86
3174 4214 7.120579 TGTTCGTTTTGACTATTTGCATCCTAT 59.879 33.333 0.00 0.00 0.00 2.57
3286 4326 1.094785 GGTGTGCACTGTCAAGTTGT 58.905 50.000 19.41 0.00 32.98 3.32
3327 4367 7.123247 ACCTATTTATTTCTGCTGACATTTGCT 59.877 33.333 0.00 0.00 0.00 3.91
3343 4383 6.276847 ACATTTGCTATAGCTGTAGTGTCTC 58.723 40.000 24.61 2.80 42.66 3.36
3537 4577 3.845781 TGTATCCTTCTTGATGAGGCC 57.154 47.619 0.00 0.00 0.00 5.19
3560 4600 3.146066 TGTCTAGCATGTTGTTTCCACC 58.854 45.455 0.00 0.00 0.00 4.61
3575 4615 2.316108 TCCACCGAATGCTAGCTGATA 58.684 47.619 17.23 0.00 0.00 2.15
3663 4707 1.617740 GCAATGTTGCGGCTCTTAAC 58.382 50.000 0.00 0.00 45.11 2.01
3912 4956 6.353404 TCACTACATTCTGTGGTTATGTCA 57.647 37.500 0.00 0.00 39.06 3.58
3913 4957 6.398095 TCACTACATTCTGTGGTTATGTCAG 58.602 40.000 0.00 0.00 39.06 3.51
4166 5210 1.515020 GTCGTGCTGCCTCTGATCT 59.485 57.895 0.00 0.00 0.00 2.75
4168 5212 1.028130 TCGTGCTGCCTCTGATCTAG 58.972 55.000 0.00 0.00 0.00 2.43
4188 5232 4.476752 GTGCCCGGCCGGAATACA 62.477 66.667 45.44 31.31 37.50 2.29
4189 5233 3.484806 TGCCCGGCCGGAATACAT 61.485 61.111 45.44 0.00 37.50 2.29
4190 5234 2.141448 TGCCCGGCCGGAATACATA 61.141 57.895 45.44 19.03 37.50 2.29
4191 5235 1.298667 GCCCGGCCGGAATACATAT 59.701 57.895 45.44 0.00 37.50 1.78
4192 5236 0.743345 GCCCGGCCGGAATACATATC 60.743 60.000 45.44 17.05 37.50 1.63
4195 5239 2.346803 CCGGCCGGAATACATATCAAG 58.653 52.381 41.82 6.03 37.50 3.02
4196 5240 1.732259 CGGCCGGAATACATATCAAGC 59.268 52.381 20.10 0.00 0.00 4.01
4197 5241 1.732259 GGCCGGAATACATATCAAGCG 59.268 52.381 5.05 0.00 0.00 4.68
4200 5244 1.732259 CGGAATACATATCAAGCGCCC 59.268 52.381 2.29 0.00 0.00 6.13
4202 5246 3.146066 GGAATACATATCAAGCGCCCAA 58.854 45.455 2.29 0.00 0.00 4.12
4203 5247 3.058224 GGAATACATATCAAGCGCCCAAC 60.058 47.826 2.29 0.00 0.00 3.77
4204 5248 2.700722 TACATATCAAGCGCCCAACA 57.299 45.000 2.29 0.00 0.00 3.33
4205 5249 1.832883 ACATATCAAGCGCCCAACAA 58.167 45.000 2.29 0.00 0.00 2.83
4206 5250 1.472480 ACATATCAAGCGCCCAACAAC 59.528 47.619 2.29 0.00 0.00 3.32
4216 5260 0.389025 GCCCAACAACCAACCAAGAG 59.611 55.000 0.00 0.00 0.00 2.85
4326 5370 2.169769 GGTAGGTAGGCATGCTGTTACA 59.830 50.000 18.92 1.30 0.00 2.41
4383 5428 9.897744 CAAATGTTTTATGTCATGTAGAACTGT 57.102 29.630 0.00 0.00 0.00 3.55
4401 5446 8.200024 AGAACTGTTGATGACCTGCTATATAT 57.800 34.615 0.00 0.00 0.00 0.86
4462 5511 9.159254 TCTCTATTTAATATCCCTTTGAGCAGA 57.841 33.333 0.00 0.00 0.00 4.26
4476 5525 3.120792 TGAGCAGACGTGAACTGTTAAC 58.879 45.455 0.00 0.00 37.64 2.01
4496 5545 9.372369 TGTTAACTTTTTGGGTAAATTGTGAAG 57.628 29.630 7.22 0.00 0.00 3.02
4501 5550 8.532819 ACTTTTTGGGTAAATTGTGAAGTGTTA 58.467 29.630 0.00 0.00 0.00 2.41
4567 5620 7.855904 AGTACATCAAATCGAACAAACTGAAAC 59.144 33.333 0.00 0.00 0.00 2.78
4569 5622 7.202526 ACATCAAATCGAACAAACTGAAACAT 58.797 30.769 0.00 0.00 0.00 2.71
4577 5630 8.555166 TCGAACAAACTGAAACATAAATGAAC 57.445 30.769 0.00 0.00 0.00 3.18
4664 5718 3.976942 CACCTTTTGCATCTCAACTTTCG 59.023 43.478 0.00 0.00 33.73 3.46
4696 5750 5.630415 TGGGTTATGAATCCGAAGAAGAT 57.370 39.130 0.00 0.00 0.00 2.40
4721 5775 5.880332 GGAAATTACATTGAGCCACAGACTA 59.120 40.000 0.00 0.00 0.00 2.59
4722 5776 6.037610 GGAAATTACATTGAGCCACAGACTAG 59.962 42.308 0.00 0.00 0.00 2.57
4732 5786 7.839680 TGAGCCACAGACTAGAATAATATCA 57.160 36.000 0.00 0.00 0.00 2.15
4735 5789 9.547753 GAGCCACAGACTAGAATAATATCAAAA 57.452 33.333 0.00 0.00 0.00 2.44
4760 5814 1.291132 GAAGAGCCGCATAAGTCCAC 58.709 55.000 0.00 0.00 0.00 4.02
4787 5854 8.242053 GCCAGAATCTATAATCATTGAACATGG 58.758 37.037 0.00 0.00 0.00 3.66
4825 5892 1.477558 CCCTCACAAGGCAAGTTGTCT 60.478 52.381 3.55 3.55 41.85 3.41
4844 5918 4.117685 GTCTAACCGTTGATTTATCGCCT 58.882 43.478 0.00 0.00 0.00 5.52
4852 5926 4.317139 CGTTGATTTATCGCCTAACTGTCG 60.317 45.833 0.00 0.00 0.00 4.35
4865 5939 4.082190 CCTAACTGTCGGTCAAGAAGATCA 60.082 45.833 0.00 0.00 0.00 2.92
4870 5944 3.254892 GTCGGTCAAGAAGATCAGGAAC 58.745 50.000 0.00 0.00 0.00 3.62
4892 5966 3.809832 CACATAAGATCGAAGCGGGAATT 59.190 43.478 0.00 0.00 0.00 2.17
4903 5977 4.674101 CGAAGCGGGAATTTAATCAAAGCA 60.674 41.667 0.00 0.00 0.00 3.91
4907 5981 3.851403 CGGGAATTTAATCAAAGCACACG 59.149 43.478 0.00 0.00 0.00 4.49
4909 5983 4.857037 GGGAATTTAATCAAAGCACACGTC 59.143 41.667 0.00 0.00 0.00 4.34
4924 5998 0.102481 ACGTCACACTTCTTCGCTGT 59.898 50.000 0.00 0.00 0.00 4.40
4931 6005 0.034059 ACTTCTTCGCTGTCCACCAG 59.966 55.000 0.00 0.00 44.53 4.00
4962 6404 1.701847 AGGTCAAAGCATGAGACACCT 59.298 47.619 0.00 0.00 39.19 4.00
4975 6417 6.401394 CATGAGACACCTAACTTCAAGATCA 58.599 40.000 0.00 0.00 0.00 2.92
4979 6421 3.910627 ACACCTAACTTCAAGATCAGGGT 59.089 43.478 0.00 0.00 0.00 4.34
4985 6427 2.108952 ACTTCAAGATCAGGGTTTGCCT 59.891 45.455 0.00 0.00 34.45 4.75
5009 6451 0.250901 GCGGGGCTCCAATATCACAT 60.251 55.000 1.96 0.00 0.00 3.21
5010 6452 1.527034 CGGGGCTCCAATATCACATG 58.473 55.000 1.96 0.00 0.00 3.21
5022 6464 5.105635 CCAATATCACATGCTCTTTGGTGTT 60.106 40.000 0.00 0.00 33.17 3.32
5026 6468 2.559668 CACATGCTCTTTGGTGTTGGAT 59.440 45.455 0.00 0.00 0.00 3.41
5033 6475 3.229293 TCTTTGGTGTTGGATGCATTGA 58.771 40.909 0.00 0.00 0.00 2.57
5034 6476 3.005684 TCTTTGGTGTTGGATGCATTGAC 59.994 43.478 0.00 0.71 0.00 3.18
5035 6477 1.992538 TGGTGTTGGATGCATTGACA 58.007 45.000 0.00 3.59 0.00 3.58
5106 6552 1.905894 ACTTCTCTTTCCCTCTCCAGC 59.094 52.381 0.00 0.00 0.00 4.85
5122 6568 2.352805 GCTTGTGGCAGCTAGGGT 59.647 61.111 0.00 0.00 41.35 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.748879 GTGCCAATAGCCGGAGCAA 60.749 57.895 5.05 0.00 43.56 3.91
1 2 2.124736 GTGCCAATAGCCGGAGCA 60.125 61.111 5.05 0.00 43.56 4.26
2 3 3.272334 CGTGCCAATAGCCGGAGC 61.272 66.667 5.05 0.00 42.71 4.70
3 4 2.173669 CACGTGCCAATAGCCGGAG 61.174 63.158 5.05 0.00 42.71 4.63
4 5 2.125310 CACGTGCCAATAGCCGGA 60.125 61.111 5.05 0.00 42.71 5.14
5 6 1.582610 AAACACGTGCCAATAGCCGG 61.583 55.000 17.22 0.00 42.71 6.13
6 7 0.179200 GAAACACGTGCCAATAGCCG 60.179 55.000 17.22 0.00 42.71 5.52
7 8 0.170339 GGAAACACGTGCCAATAGCC 59.830 55.000 17.22 3.98 42.71 3.93
8 9 0.878416 TGGAAACACGTGCCAATAGC 59.122 50.000 17.22 0.00 37.46 2.97
20 21 2.093075 TCGGTTGGTAACTGTGGAAACA 60.093 45.455 0.00 0.00 38.89 2.83
21 22 2.288729 GTCGGTTGGTAACTGTGGAAAC 59.711 50.000 0.00 0.00 38.89 2.78
22 23 2.093075 TGTCGGTTGGTAACTGTGGAAA 60.093 45.455 0.00 0.00 38.89 3.13
23 24 1.485480 TGTCGGTTGGTAACTGTGGAA 59.515 47.619 0.00 0.00 38.89 3.53
24 25 1.121378 TGTCGGTTGGTAACTGTGGA 58.879 50.000 0.00 0.00 38.89 4.02
25 26 1.202604 AGTGTCGGTTGGTAACTGTGG 60.203 52.381 0.00 0.00 38.89 4.17
26 27 2.234300 AGTGTCGGTTGGTAACTGTG 57.766 50.000 0.00 0.00 38.89 3.66
27 28 2.994186 AAGTGTCGGTTGGTAACTGT 57.006 45.000 0.00 0.00 38.89 3.55
28 29 4.562082 TCATAAGTGTCGGTTGGTAACTG 58.438 43.478 0.00 0.00 39.17 3.16
29 30 4.877378 TCATAAGTGTCGGTTGGTAACT 57.123 40.909 0.00 0.00 37.61 2.24
30 31 5.416947 AGATCATAAGTGTCGGTTGGTAAC 58.583 41.667 0.00 0.00 0.00 2.50
31 32 5.394883 GGAGATCATAAGTGTCGGTTGGTAA 60.395 44.000 0.00 0.00 0.00 2.85
32 33 4.098960 GGAGATCATAAGTGTCGGTTGGTA 59.901 45.833 0.00 0.00 0.00 3.25
33 34 3.118738 GGAGATCATAAGTGTCGGTTGGT 60.119 47.826 0.00 0.00 0.00 3.67
34 35 3.118775 TGGAGATCATAAGTGTCGGTTGG 60.119 47.826 0.00 0.00 0.00 3.77
35 36 4.123497 TGGAGATCATAAGTGTCGGTTG 57.877 45.455 0.00 0.00 0.00 3.77
36 37 4.443457 CCATGGAGATCATAAGTGTCGGTT 60.443 45.833 5.56 0.00 34.12 4.44
267 284 5.514310 GGGTACTCATTGTTTAAGGGTGACT 60.514 44.000 0.00 0.00 0.00 3.41
282 299 1.137086 GCACGATGACAGGGTACTCAT 59.863 52.381 0.00 0.00 0.00 2.90
283 300 0.530744 GCACGATGACAGGGTACTCA 59.469 55.000 0.00 0.00 0.00 3.41
294 311 5.242069 TGTTTTTCAGAAAAGCACGATGA 57.758 34.783 18.34 0.00 36.80 2.92
360 384 4.221422 GGCAGATACCGCGCCTGA 62.221 66.667 13.81 0.00 42.78 3.86
409 433 0.324738 AGAATCCCTCCGCAGTCTGA 60.325 55.000 3.32 0.00 0.00 3.27
411 435 0.539051 CAAGAATCCCTCCGCAGTCT 59.461 55.000 0.00 0.00 0.00 3.24
435 459 0.742505 CCTTGGACTACGCCGATGTA 59.257 55.000 0.00 0.00 0.00 2.29
612 642 1.019650 ATAGGACTCTGACACCCCCT 58.980 55.000 0.00 0.00 0.00 4.79
653 683 1.065126 GCAAGATTAGGGAGGCTGTGT 60.065 52.381 0.00 0.00 0.00 3.72
668 698 2.554636 CCGCAAACTGCAGGCAAGA 61.555 57.895 19.93 0.00 45.36 3.02
686 717 3.058983 ACCGGTTTAATCGTCCGTTTTTC 60.059 43.478 0.00 0.00 42.30 2.29
694 725 1.745768 CGCGGACCGGTTTAATCGTC 61.746 60.000 17.22 0.00 0.00 4.20
713 744 2.936498 CAATGTGGTACTTCATCCGTCC 59.064 50.000 0.00 0.00 0.00 4.79
727 758 3.243367 ACGTGTTTTGTCATCCAATGTGG 60.243 43.478 0.00 0.00 39.43 4.17
729 760 4.606961 GAACGTGTTTTGTCATCCAATGT 58.393 39.130 0.00 0.00 31.81 2.71
776 807 6.113411 CCGTTTAAGGACTATCAAACCATCT 58.887 40.000 0.00 0.00 0.00 2.90
792 823 3.127030 GGAGTTCATTCTGCCCGTTTAAG 59.873 47.826 0.00 0.00 0.00 1.85
793 824 3.078837 GGAGTTCATTCTGCCCGTTTAA 58.921 45.455 0.00 0.00 0.00 1.52
795 826 1.534729 GGAGTTCATTCTGCCCGTTT 58.465 50.000 0.00 0.00 0.00 3.60
796 827 0.322546 GGGAGTTCATTCTGCCCGTT 60.323 55.000 0.00 0.00 39.52 4.44
798 829 4.225497 GGGAGTTCATTCTGCCCG 57.775 61.111 0.00 0.00 39.52 6.13
917 949 6.904011 CGATCAGATTCATGCAAAGTAGTTTC 59.096 38.462 0.00 0.00 0.00 2.78
1175 1207 5.245977 TGCATCGACCAGATCAAATATAGGA 59.754 40.000 0.00 0.00 37.52 2.94
1315 1348 5.864418 AGGCAGGATTAATTACGTACAGA 57.136 39.130 0.00 0.00 0.00 3.41
1330 1363 0.918983 ATCGAAATGGGAAGGCAGGA 59.081 50.000 0.00 0.00 0.00 3.86
1439 1528 3.626670 CCAAGAGCATGAATGGAGAGAAC 59.373 47.826 0.00 0.00 34.82 3.01
1455 1544 1.004560 TGGAGCTTCGCACCAAGAG 60.005 57.895 2.50 0.00 45.44 2.85
1462 1955 2.408271 AGATCAAATGGAGCTTCGCA 57.592 45.000 0.00 0.00 39.85 5.10
1491 1984 2.159043 CGAGGGCTGTCATACAACATCT 60.159 50.000 0.00 0.00 0.00 2.90
1492 1985 2.159099 TCGAGGGCTGTCATACAACATC 60.159 50.000 0.00 0.00 0.00 3.06
1501 1994 2.523168 TGTGGTCGAGGGCTGTCA 60.523 61.111 0.00 0.00 0.00 3.58
1503 1996 3.626924 GGTGTGGTCGAGGGCTGT 61.627 66.667 0.00 0.00 0.00 4.40
1507 2000 0.459585 CAATACGGTGTGGTCGAGGG 60.460 60.000 0.00 0.00 0.00 4.30
1519 2012 7.837202 TTGTTTCTCTTATGTACCAATACGG 57.163 36.000 0.00 0.00 42.50 4.02
1522 2015 9.952030 TGTGATTGTTTCTCTTATGTACCAATA 57.048 29.630 0.00 0.00 0.00 1.90
1567 2060 6.631620 GGAGTGGCCTCATCTTTCCAAAGA 62.632 50.000 3.32 4.24 40.49 2.52
1573 2066 0.537188 TCGGAGTGGCCTCATCTTTC 59.463 55.000 3.32 0.00 39.64 2.62
1584 2077 4.389077 GTCTATCTTGTTTTGTCGGAGTGG 59.611 45.833 0.00 0.00 0.00 4.00
1590 2083 6.727824 ATTCTGGTCTATCTTGTTTTGTCG 57.272 37.500 0.00 0.00 0.00 4.35
1593 2086 9.994432 GATGTTATTCTGGTCTATCTTGTTTTG 57.006 33.333 0.00 0.00 0.00 2.44
1610 2105 1.329599 GTGGGAACGGCGATGTTATTC 59.670 52.381 16.62 5.39 30.75 1.75
1615 2110 0.820074 TTTTGTGGGAACGGCGATGT 60.820 50.000 16.62 0.00 0.00 3.06
1654 2149 5.518848 TGACTTCTTTGCAATGTGTTGAT 57.481 34.783 11.67 0.00 37.53 2.57
1661 2156 5.218139 GGTCTTCTTGACTTCTTTGCAATG 58.782 41.667 0.00 2.27 44.74 2.82
1666 2161 3.820557 TGGGGTCTTCTTGACTTCTTTG 58.179 45.455 0.00 0.00 44.74 2.77
1674 2169 1.070134 CGTGTCTTGGGGTCTTCTTGA 59.930 52.381 0.00 0.00 0.00 3.02
1692 2187 7.923878 TGCACATATTATGTAAGTATGTCACGT 59.076 33.333 8.95 0.00 42.70 4.49
1693 2188 8.293114 TGCACATATTATGTAAGTATGTCACG 57.707 34.615 8.95 0.00 42.70 4.35
1710 2447 5.121380 AGAGGGACATTTTCTGCACATAT 57.879 39.130 0.00 0.00 0.00 1.78
1774 2511 1.134521 TCAAAGTAGCGGGCATCGAAT 60.135 47.619 2.84 0.00 42.43 3.34
1790 2527 8.721133 TTGGCATAGGATAGATAGTACTCAAA 57.279 34.615 0.00 0.00 0.00 2.69
1826 2563 7.537596 TCTGGACAAACATTTATTGGTCAAT 57.462 32.000 1.65 1.65 34.93 2.57
1838 2575 7.064609 CGTACACTATTGATTCTGGACAAACAT 59.935 37.037 0.00 0.00 0.00 2.71
1849 2586 9.900710 AGATTGAGTATCGTACACTATTGATTC 57.099 33.333 0.00 0.00 38.61 2.52
1898 2635 1.620822 CCAAGGGGGAAGTGACAAAG 58.379 55.000 0.00 0.00 40.01 2.77
1944 2861 0.465460 ACGGCACAACCAACAGATGT 60.465 50.000 0.00 0.00 39.03 3.06
1981 2904 0.037303 TCGACTTCCACTACCTCCGT 59.963 55.000 0.00 0.00 0.00 4.69
2061 2984 4.704833 CCACTCACAGGGCCACCG 62.705 72.222 6.18 0.00 43.47 4.94
2071 2994 3.178540 AAGCCACGACCCCACTCAC 62.179 63.158 0.00 0.00 0.00 3.51
2091 3015 3.842925 AATGCCACCAACGCGGAGT 62.843 57.895 12.47 0.65 38.63 3.85
2170 3095 3.808728 ACCCGACCACATGATTGATTAG 58.191 45.455 0.00 0.00 0.00 1.73
2211 3136 1.312371 AAACGCCCCCACGATTGATG 61.312 55.000 0.00 0.00 36.70 3.07
2234 3161 2.888834 AAGGGACAACATGCAACAAC 57.111 45.000 0.00 0.00 0.00 3.32
2236 3163 4.148079 TGATAAAGGGACAACATGCAACA 58.852 39.130 0.00 0.00 0.00 3.33
2237 3164 4.218417 ACTGATAAAGGGACAACATGCAAC 59.782 41.667 0.00 0.00 0.00 4.17
2238 3165 4.406456 ACTGATAAAGGGACAACATGCAA 58.594 39.130 0.00 0.00 0.00 4.08
2241 3168 4.093408 CACGACTGATAAAGGGACAACATG 59.907 45.833 0.00 0.00 0.00 3.21
2242 3169 4.253685 CACGACTGATAAAGGGACAACAT 58.746 43.478 0.00 0.00 0.00 2.71
2243 3170 3.070446 ACACGACTGATAAAGGGACAACA 59.930 43.478 0.00 0.00 0.00 3.33
2285 3220 4.892934 AGGCACAGTTAATTGAGAAAACCA 59.107 37.500 4.81 0.00 0.00 3.67
2287 3222 6.145535 CAGAGGCACAGTTAATTGAGAAAAC 58.854 40.000 4.81 0.00 0.00 2.43
2302 3237 0.981183 AAACCCGATACAGAGGCACA 59.019 50.000 0.00 0.00 0.00 4.57
2373 3308 0.681243 GGGACAGGGAATGCCTTCAC 60.681 60.000 4.06 0.00 34.81 3.18
2380 3315 2.307098 AGAACAAGAGGGACAGGGAATG 59.693 50.000 0.00 0.00 0.00 2.67
2411 3351 0.941463 GATATGCCACTGTCGCCTCG 60.941 60.000 0.00 0.00 0.00 4.63
2419 3359 6.352016 ACCTACAGAATAGATATGCCACTG 57.648 41.667 0.00 0.00 0.00 3.66
2446 3386 8.055279 TCAAGCTAATTATGGAGGAAGTTTTG 57.945 34.615 0.00 0.00 0.00 2.44
2459 3399 7.538575 ACGAAAATGTTGCTCAAGCTAATTAT 58.461 30.769 3.32 0.00 42.66 1.28
2483 3423 5.010213 TCCAACAAAATAAGTGCCCAGTTAC 59.990 40.000 0.00 0.00 0.00 2.50
2487 3427 4.220382 TGATCCAACAAAATAAGTGCCCAG 59.780 41.667 0.00 0.00 0.00 4.45
2488 3428 4.155709 TGATCCAACAAAATAAGTGCCCA 58.844 39.130 0.00 0.00 0.00 5.36
2489 3429 4.799564 TGATCCAACAAAATAAGTGCCC 57.200 40.909 0.00 0.00 0.00 5.36
2523 3463 0.620556 GCTCTCAGTGGGGAATTGGA 59.379 55.000 0.00 0.00 0.00 3.53
2600 3635 6.668283 AGTGTTCCCTTACTCTCTAAGCATAA 59.332 38.462 0.00 0.00 0.00 1.90
2607 3642 6.662663 GGAAGTTAGTGTTCCCTTACTCTCTA 59.337 42.308 0.00 0.00 38.03 2.43
2695 3731 8.784043 AGGAACAATTTCAGACATTGTAAGTAC 58.216 33.333 14.10 1.91 42.80 2.73
2768 3804 1.555075 GGTGAACAGATAGGTGAGGCA 59.445 52.381 0.00 0.00 0.00 4.75
2782 3818 5.938125 ACTAATATATGGGCGAATGGTGAAC 59.062 40.000 0.00 0.00 0.00 3.18
2834 3870 4.500127 TCCTGATCTGCATTGCAAATTTG 58.500 39.130 14.03 14.03 38.41 2.32
2835 3871 4.811969 TCCTGATCTGCATTGCAAATTT 57.188 36.364 13.18 0.00 38.41 1.82
2836 3872 6.474140 TTATCCTGATCTGCATTGCAAATT 57.526 33.333 13.18 0.03 38.41 1.82
2837 3873 6.474140 TTTATCCTGATCTGCATTGCAAAT 57.526 33.333 13.18 4.74 38.41 2.32
2838 3874 5.918426 TTTATCCTGATCTGCATTGCAAA 57.082 34.783 13.18 0.00 38.41 3.68
3099 4139 9.724839 TTAAGGCAAACGTAAAATCATATAAGC 57.275 29.630 0.00 0.00 0.00 3.09
3109 4149 7.266922 AGAAGACATTAAGGCAAACGTAAAA 57.733 32.000 0.00 0.00 0.00 1.52
3115 4155 7.649057 AGTGTAAAGAAGACATTAAGGCAAAC 58.351 34.615 0.00 0.00 0.00 2.93
3246 4286 6.715264 ACACCTTGTTTTCTCGATAAAGGAAT 59.285 34.615 6.27 0.00 38.04 3.01
3248 4288 5.468746 CACACCTTGTTTTCTCGATAAAGGA 59.531 40.000 6.27 0.00 38.04 3.36
3327 4367 6.316640 GTCAAGTCAGAGACACTACAGCTATA 59.683 42.308 0.00 0.00 34.60 1.31
3482 4522 6.916360 ATGGAAGACAAAAATTAGAAGCCA 57.084 33.333 0.00 0.00 0.00 4.75
3560 4600 6.920758 AGAGTTTTACTATCAGCTAGCATTCG 59.079 38.462 18.83 2.15 0.00 3.34
3575 4615 7.013655 ACACATGAAGAAATGCAGAGTTTTACT 59.986 33.333 0.00 0.00 0.00 2.24
3663 4707 0.681733 CTGTCCATGGGGTATCCTCG 59.318 60.000 13.02 0.00 36.20 4.63
3912 4956 2.845659 TGACCCAACATATGAGGACCT 58.154 47.619 10.38 0.00 0.00 3.85
3913 4957 3.644966 TTGACCCAACATATGAGGACC 57.355 47.619 10.38 6.65 0.00 4.46
4076 5120 0.252881 TCTGCACTCCATCCTCCCTT 60.253 55.000 0.00 0.00 0.00 3.95
4184 5228 3.207265 TGTTGGGCGCTTGATATGTAT 57.793 42.857 7.64 0.00 0.00 2.29
4185 5229 2.680841 GTTGTTGGGCGCTTGATATGTA 59.319 45.455 7.64 0.00 0.00 2.29
4186 5230 1.472480 GTTGTTGGGCGCTTGATATGT 59.528 47.619 7.64 0.00 0.00 2.29
4187 5231 1.202290 GGTTGTTGGGCGCTTGATATG 60.202 52.381 7.64 0.00 0.00 1.78
4188 5232 1.102978 GGTTGTTGGGCGCTTGATAT 58.897 50.000 7.64 0.00 0.00 1.63
4189 5233 0.250945 TGGTTGTTGGGCGCTTGATA 60.251 50.000 7.64 0.00 0.00 2.15
4190 5234 1.112315 TTGGTTGTTGGGCGCTTGAT 61.112 50.000 7.64 0.00 0.00 2.57
4191 5235 1.754621 TTGGTTGTTGGGCGCTTGA 60.755 52.632 7.64 0.00 0.00 3.02
4192 5236 1.591327 GTTGGTTGTTGGGCGCTTG 60.591 57.895 7.64 0.00 0.00 4.01
4195 5239 2.969677 CTTGGTTGGTTGTTGGGCGC 62.970 60.000 0.00 0.00 0.00 6.53
4196 5240 1.067250 CTTGGTTGGTTGTTGGGCG 59.933 57.895 0.00 0.00 0.00 6.13
4197 5241 0.389025 CTCTTGGTTGGTTGTTGGGC 59.611 55.000 0.00 0.00 0.00 5.36
4200 5244 6.633500 TTTATCTCTCTTGGTTGGTTGTTG 57.367 37.500 0.00 0.00 0.00 3.33
4202 5246 6.542821 TGATTTATCTCTCTTGGTTGGTTGT 58.457 36.000 0.00 0.00 0.00 3.32
4203 5247 6.094603 CCTGATTTATCTCTCTTGGTTGGTTG 59.905 42.308 0.00 0.00 0.00 3.77
4204 5248 6.012508 TCCTGATTTATCTCTCTTGGTTGGTT 60.013 38.462 0.00 0.00 0.00 3.67
4205 5249 5.488919 TCCTGATTTATCTCTCTTGGTTGGT 59.511 40.000 0.00 0.00 0.00 3.67
4206 5250 5.994250 TCCTGATTTATCTCTCTTGGTTGG 58.006 41.667 0.00 0.00 0.00 3.77
4326 5370 1.884579 CAGCAGTTCAGTTCAGCCAAT 59.115 47.619 0.00 0.00 0.00 3.16
4462 5511 4.460034 ACCCAAAAAGTTAACAGTTCACGT 59.540 37.500 8.61 0.00 0.00 4.49
4476 5525 7.841915 AACACTTCACAATTTACCCAAAAAG 57.158 32.000 0.00 0.00 0.00 2.27
4537 5590 9.825972 CAGTTTGTTCGATTTGATGTACTTTAT 57.174 29.630 0.00 0.00 0.00 1.40
4567 5620 7.696755 TCATGGATCTTTGTCGTTCATTTATG 58.303 34.615 0.00 0.00 0.00 1.90
4569 5622 7.864108 ATCATGGATCTTTGTCGTTCATTTA 57.136 32.000 0.00 0.00 0.00 1.40
4605 5658 4.094090 ACTTCGAAGAATCCGAGTGTAC 57.906 45.455 31.08 0.00 45.90 2.90
4696 5750 4.458989 GTCTGTGGCTCAATGTAATTTCCA 59.541 41.667 0.00 0.00 31.22 3.53
4732 5786 3.733443 ATGCGGCTCTTCAAAACTTTT 57.267 38.095 0.00 0.00 0.00 2.27
4735 5789 3.412386 ACTTATGCGGCTCTTCAAAACT 58.588 40.909 0.00 0.00 0.00 2.66
4739 5793 1.277842 TGGACTTATGCGGCTCTTCAA 59.722 47.619 0.00 0.00 0.00 2.69
4760 5814 7.425577 TGTTCAATGATTATAGATTCTGGCG 57.574 36.000 0.00 0.00 0.00 5.69
4787 5854 3.259592 GGTGTATCCCCAACCACAC 57.740 57.895 0.00 0.00 40.40 3.82
4825 5892 5.521010 CAGTTAGGCGATAAATCAACGGTTA 59.479 40.000 0.00 0.00 0.00 2.85
4844 5918 4.082190 CCTGATCTTCTTGACCGACAGTTA 60.082 45.833 0.00 0.00 0.00 2.24
4852 5926 4.008074 TGTGTTCCTGATCTTCTTGACC 57.992 45.455 0.00 0.00 0.00 4.02
4865 5939 3.448686 CGCTTCGATCTTATGTGTTCCT 58.551 45.455 0.00 0.00 0.00 3.36
4870 5944 2.509052 TCCCGCTTCGATCTTATGTG 57.491 50.000 0.00 0.00 0.00 3.21
4892 5966 3.874543 AGTGTGACGTGTGCTTTGATTAA 59.125 39.130 0.00 0.00 0.00 1.40
4903 5977 0.102481 AGCGAAGAAGTGTGACGTGT 59.898 50.000 0.00 0.00 0.00 4.49
4907 5981 1.140816 GGACAGCGAAGAAGTGTGAC 58.859 55.000 0.00 0.00 0.00 3.67
4909 5983 0.861837 GTGGACAGCGAAGAAGTGTG 59.138 55.000 0.00 0.00 0.00 3.82
4934 6008 0.901580 ATGCTTTGACCTGCCTTGGG 60.902 55.000 0.00 0.00 0.00 4.12
4962 6404 4.079253 GGCAAACCCTGATCTTGAAGTTA 58.921 43.478 0.00 0.00 0.00 2.24
4979 6421 2.124320 GCCCCGCAGATAGGCAAA 60.124 61.111 0.00 0.00 46.34 3.68
4985 6427 1.555075 GATATTGGAGCCCCGCAGATA 59.445 52.381 0.00 0.00 34.29 1.98
5009 6451 0.961019 GCATCCAACACCAAAGAGCA 59.039 50.000 0.00 0.00 0.00 4.26
5010 6452 0.961019 TGCATCCAACACCAAAGAGC 59.039 50.000 0.00 0.00 0.00 4.09
5022 6464 0.612744 TCTCGGTGTCAATGCATCCA 59.387 50.000 0.00 0.00 0.00 3.41
5026 6468 1.225855 GTGTTCTCGGTGTCAATGCA 58.774 50.000 0.00 0.00 0.00 3.96
5033 6475 2.613026 TGTTCATGTGTTCTCGGTGT 57.387 45.000 0.00 0.00 0.00 4.16
5034 6476 3.062639 GCTATGTTCATGTGTTCTCGGTG 59.937 47.826 0.00 0.00 0.00 4.94
5035 6477 3.262420 GCTATGTTCATGTGTTCTCGGT 58.738 45.455 0.00 0.00 0.00 4.69
5086 6532 1.905894 GCTGGAGAGGGAAAGAGAAGT 59.094 52.381 0.00 0.00 0.00 3.01
5106 6552 0.107654 GGTACCCTAGCTGCCACAAG 60.108 60.000 0.00 0.00 0.00 3.16
5122 6568 0.253630 AAGCTTGGAGGGGATGGGTA 60.254 55.000 0.00 0.00 0.00 3.69
5132 6578 1.901591 TCTTGCCAAGAAGCTTGGAG 58.098 50.000 25.86 16.43 42.06 3.86


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

AutoCloner maintained by Alex Coulton.