Multiple sequence alignment - TraesCS6A01G337200

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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 TraesCS6A01G337200 chr6A 100.000 4865 0 0 1 4865 571162304 571167168 0.000000e+00 8985.0
1 TraesCS6A01G337200 chr6A 85.570 395 27 7 4489 4865 571182235 571181853 2.120000e-103 387.0
2 TraesCS6A01G337200 chr6D 93.260 2359 110 20 588 2927 426283479 426285807 0.000000e+00 3430.0
3 TraesCS6A01G337200 chr6D 88.889 738 42 15 3529 4250 426286383 426287096 0.000000e+00 872.0
4 TraesCS6A01G337200 chr6D 88.080 646 63 10 7 651 426282941 426283573 0.000000e+00 754.0
5 TraesCS6A01G337200 chr6D 91.509 424 29 5 2924 3343 426285967 426286387 1.170000e-160 577.0
6 TraesCS6A01G337200 chr6D 89.079 467 36 7 4250 4713 426287052 426287506 2.540000e-157 566.0
7 TraesCS6A01G337200 chr6D 84.910 444 39 15 4250 4692 426333567 426333983 1.620000e-114 424.0
8 TraesCS6A01G337200 chr6D 88.816 304 28 3 3784 4085 426298848 426299147 7.690000e-98 368.0
9 TraesCS6A01G337200 chr6D 88.953 172 13 3 4081 4250 426333443 426333610 1.770000e-49 207.0
10 TraesCS6A01G337200 chr6B 90.801 2522 173 25 7 2511 641885426 641887905 0.000000e+00 3317.0
11 TraesCS6A01G337200 chr6B 90.878 866 54 12 2509 3352 641887986 641888848 0.000000e+00 1138.0
12 TraesCS6A01G337200 chr6B 90.109 829 44 23 3400 4216 641888869 641889671 0.000000e+00 1042.0
13 TraesCS6A01G337200 chr6B 89.313 524 31 8 4357 4865 641889710 641890223 6.870000e-178 634.0
14 TraesCS6A01G337200 chr6B 85.215 629 52 19 4250 4865 641900237 641900837 4.160000e-170 608.0
15 TraesCS6A01G337200 chr6B 88.771 472 39 8 3785 4250 641899819 641900282 2.540000e-157 566.0
16 TraesCS6A01G337200 chr6B 94.872 39 2 0 4274 4312 641889670 641889708 1.460000e-05 62.1
17 TraesCS6A01G337200 chr1A 88.162 321 28 7 2704 3024 489339471 489339161 1.650000e-99 374.0
18 TraesCS6A01G337200 chr1A 86.486 259 29 4 2106 2363 489387770 489387517 3.710000e-71 279.0
19 TraesCS6A01G337200 chr1B 87.227 321 33 4 2704 3024 526276102 526275790 4.630000e-95 359.0
20 TraesCS6A01G337200 chr1B 87.786 131 16 0 2233 2363 526276518 526276388 2.340000e-33 154.0
21 TraesCS6A01G337200 chr1D 88.031 259 28 3 2106 2363 395387361 395387105 2.200000e-78 303.0
22 TraesCS6A01G337200 chr1D 87.645 259 29 3 2106 2363 395072822 395072566 1.020000e-76 298.0
23 TraesCS6A01G337200 chr1D 75.166 451 65 26 2392 2831 395387106 395386692 8.370000e-38 169.0
24 TraesCS6A01G337200 chr3D 87.645 259 28 4 2106 2363 57052707 57052962 1.020000e-76 298.0
25 TraesCS6A01G337200 chr2B 82.450 302 44 2 2137 2438 250519015 250518723 6.250000e-64 255.0
26 TraesCS6A01G337200 chr4B 79.545 308 48 5 2131 2438 78600198 78599906 6.380000e-49 206.0
27 TraesCS6A01G337200 chr7B 96.774 31 1 0 2984 3014 8971846 8971876 9.000000e-03 52.8
28 TraesCS6A01G337200 chr2D 96.774 31 1 0 2984 3014 647192725 647192755 9.000000e-03 52.8


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 TraesCS6A01G337200 chr6A 571162304 571167168 4864 False 8985.00 8985 100.0000 1 4865 1 chr6A.!!$F1 4864
1 TraesCS6A01G337200 chr6D 426282941 426287506 4565 False 1239.80 3430 90.1634 7 4713 5 chr6D.!!$F2 4706
2 TraesCS6A01G337200 chr6D 426333443 426333983 540 False 315.50 424 86.9315 4081 4692 2 chr6D.!!$F3 611
3 TraesCS6A01G337200 chr6B 641885426 641890223 4797 False 1238.62 3317 91.1946 7 4865 5 chr6B.!!$F1 4858
4 TraesCS6A01G337200 chr6B 641899819 641900837 1018 False 587.00 608 86.9930 3785 4865 2 chr6B.!!$F2 1080
5 TraesCS6A01G337200 chr1B 526275790 526276518 728 True 256.50 359 87.5065 2233 3024 2 chr1B.!!$R1 791
6 TraesCS6A01G337200 chr1D 395386692 395387361 669 True 236.00 303 81.5985 2106 2831 2 chr1D.!!$R2 725

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
195 204 0.461961 TTTCTTGGTTGGTTTGGCGG 59.538 50.000 0.00 0.00 0.00 6.13 F
374 383 0.609131 AAGGTGGGATTTCTGTGCCG 60.609 55.000 0.00 0.00 31.23 5.69 F
867 913 0.761187 ACTTCTGTCTGCAAGCAGGA 59.239 50.000 20.78 8.57 43.75 3.86 F
1156 1202 0.813184 CTTTCAGCATCCACGGCATT 59.187 50.000 0.00 0.00 0.00 3.56 F
1165 1211 1.737838 TCCACGGCATTTAAGCTCTG 58.262 50.000 0.00 0.00 34.17 3.35 F
2677 2821 1.834263 ACCTGCTGTCAGTAGATTCCC 59.166 52.381 18.55 0.00 38.66 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1165 1211 0.819259 TGAACTGCACCACTTCCTGC 60.819 55.000 0.00 0.00 0.00 4.85 R
1424 1470 1.003580 GCTCCTCAACCTCATTCCACA 59.996 52.381 0.00 0.00 0.00 4.17 R
2677 2821 1.093159 AACTCGTACGCCCTACAGAG 58.907 55.000 11.24 2.38 34.65 3.35 R
3024 3340 0.793250 GCAGTCGAAAGCCAAGAGAC 59.207 55.000 0.00 0.00 0.00 3.36 R
3081 3400 6.526526 TGTTATGCCTATACGGATAGCAAAA 58.473 36.000 9.35 2.20 34.70 2.44 R
4553 4943 0.035439 AAGTTGGCCCACATAGGTCG 60.035 55.000 10.02 0.00 32.60 4.79 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
88 91 6.040842 TGCTTCTTCCTTCAGCTGTTATTTTT 59.959 34.615 14.67 0.00 34.42 1.94
90 93 6.575162 TCTTCCTTCAGCTGTTATTTTTCC 57.425 37.500 14.67 0.00 0.00 3.13
92 95 5.705609 TCCTTCAGCTGTTATTTTTCCAC 57.294 39.130 14.67 0.00 0.00 4.02
93 96 4.522789 TCCTTCAGCTGTTATTTTTCCACC 59.477 41.667 14.67 0.00 0.00 4.61
131 140 2.069465 CTCGCTCTGGATGGGACGAG 62.069 65.000 0.00 0.00 40.70 4.18
170 179 1.418264 TCAAGTGGTTGATTCGTGGGA 59.582 47.619 0.00 0.00 37.79 4.37
173 182 0.676782 GTGGTTGATTCGTGGGAGGG 60.677 60.000 0.00 0.00 0.00 4.30
174 183 0.838554 TGGTTGATTCGTGGGAGGGA 60.839 55.000 0.00 0.00 0.00 4.20
177 186 2.620627 GGTTGATTCGTGGGAGGGATTT 60.621 50.000 0.00 0.00 0.00 2.17
178 187 3.089284 GTTGATTCGTGGGAGGGATTTT 58.911 45.455 0.00 0.00 0.00 1.82
179 188 2.999331 TGATTCGTGGGAGGGATTTTC 58.001 47.619 0.00 0.00 0.00 2.29
180 189 2.576191 TGATTCGTGGGAGGGATTTTCT 59.424 45.455 0.00 0.00 0.00 2.52
181 190 3.010138 TGATTCGTGGGAGGGATTTTCTT 59.990 43.478 0.00 0.00 0.00 2.52
187 196 2.179427 GGGAGGGATTTTCTTGGTTGG 58.821 52.381 0.00 0.00 0.00 3.77
195 204 0.461961 TTTCTTGGTTGGTTTGGCGG 59.538 50.000 0.00 0.00 0.00 6.13
236 245 3.583882 ATTTGGGGGCGGACTGTGG 62.584 63.158 0.00 0.00 0.00 4.17
292 301 4.899239 CGGAGGCTGCGGGATCAC 62.899 72.222 21.44 0.00 0.00 3.06
303 312 0.882927 CGGGATCACGGTGTGTTTGT 60.883 55.000 10.23 0.00 34.79 2.83
374 383 0.609131 AAGGTGGGATTTCTGTGCCG 60.609 55.000 0.00 0.00 31.23 5.69
414 424 2.131023 GGAGGGGGAATTCTGATCTGT 58.869 52.381 5.23 0.00 0.00 3.41
415 425 3.318313 GGAGGGGGAATTCTGATCTGTA 58.682 50.000 5.23 0.00 0.00 2.74
416 426 3.326297 GGAGGGGGAATTCTGATCTGTAG 59.674 52.174 5.23 0.00 0.00 2.74
417 427 2.708325 AGGGGGAATTCTGATCTGTAGC 59.292 50.000 5.23 0.00 0.00 3.58
418 428 2.708325 GGGGGAATTCTGATCTGTAGCT 59.292 50.000 5.23 0.00 0.00 3.32
419 429 3.495806 GGGGGAATTCTGATCTGTAGCTG 60.496 52.174 5.23 0.00 0.00 4.24
439 449 2.737783 TGGAACCGTTTTGTATGTAGCG 59.262 45.455 0.00 0.00 0.00 4.26
444 454 1.326548 CGTTTTGTATGTAGCGGCTCC 59.673 52.381 5.39 0.00 0.00 4.70
469 480 3.569250 TTTCTGTATTTTCCTTGGCGC 57.431 42.857 0.00 0.00 0.00 6.53
507 519 6.669278 AGATTTCCTTTTCTTTTCGTGCTAC 58.331 36.000 0.00 0.00 0.00 3.58
542 554 3.062042 GGAGCTCCAATTGCTGTTTTTG 58.938 45.455 28.43 0.00 41.30 2.44
580 623 4.023279 TGCTTTGTTATGCCAACTACTGTG 60.023 41.667 0.00 0.00 0.00 3.66
581 624 4.215399 GCTTTGTTATGCCAACTACTGTGA 59.785 41.667 0.00 0.00 0.00 3.58
582 625 5.278266 GCTTTGTTATGCCAACTACTGTGAA 60.278 40.000 0.00 0.00 0.00 3.18
583 626 6.570378 GCTTTGTTATGCCAACTACTGTGAAT 60.570 38.462 0.00 0.00 0.00 2.57
584 627 6.892658 TTGTTATGCCAACTACTGTGAATT 57.107 33.333 0.00 0.00 0.00 2.17
585 628 6.252967 TGTTATGCCAACTACTGTGAATTG 57.747 37.500 0.00 0.00 0.00 2.32
586 629 3.855689 ATGCCAACTACTGTGAATTGC 57.144 42.857 0.00 0.00 0.00 3.56
587 630 2.862541 TGCCAACTACTGTGAATTGCT 58.137 42.857 0.00 0.00 0.00 3.91
588 631 3.221771 TGCCAACTACTGTGAATTGCTT 58.778 40.909 0.00 0.00 0.00 3.91
589 632 3.004629 TGCCAACTACTGTGAATTGCTTG 59.995 43.478 0.00 0.00 0.00 4.01
590 633 3.568538 CCAACTACTGTGAATTGCTTGC 58.431 45.455 0.00 0.00 0.00 4.01
591 634 3.254166 CCAACTACTGTGAATTGCTTGCT 59.746 43.478 0.00 0.00 0.00 3.91
592 635 4.261741 CCAACTACTGTGAATTGCTTGCTT 60.262 41.667 0.00 0.00 0.00 3.91
593 636 4.756084 ACTACTGTGAATTGCTTGCTTC 57.244 40.909 0.00 0.00 0.00 3.86
594 637 2.693797 ACTGTGAATTGCTTGCTTCG 57.306 45.000 0.00 0.00 0.00 3.79
595 638 1.949525 ACTGTGAATTGCTTGCTTCGT 59.050 42.857 0.00 0.00 0.00 3.85
596 639 2.031682 ACTGTGAATTGCTTGCTTCGTC 60.032 45.455 0.00 0.00 0.00 4.20
597 640 1.946081 TGTGAATTGCTTGCTTCGTCA 59.054 42.857 0.00 0.00 0.00 4.35
598 641 2.553602 TGTGAATTGCTTGCTTCGTCAT 59.446 40.909 0.00 0.00 0.00 3.06
599 642 2.912967 GTGAATTGCTTGCTTCGTCATG 59.087 45.455 0.00 0.00 0.00 3.07
600 643 2.553602 TGAATTGCTTGCTTCGTCATGT 59.446 40.909 0.00 0.00 0.00 3.21
601 644 2.907910 ATTGCTTGCTTCGTCATGTC 57.092 45.000 0.00 0.00 0.00 3.06
602 645 1.592064 TTGCTTGCTTCGTCATGTCA 58.408 45.000 0.00 0.00 0.00 3.58
603 646 1.592064 TGCTTGCTTCGTCATGTCAA 58.408 45.000 0.00 0.00 0.00 3.18
604 647 1.264020 TGCTTGCTTCGTCATGTCAAC 59.736 47.619 0.00 0.00 0.00 3.18
605 648 1.532868 GCTTGCTTCGTCATGTCAACT 59.467 47.619 0.00 0.00 0.00 3.16
606 649 2.736721 GCTTGCTTCGTCATGTCAACTA 59.263 45.455 0.00 0.00 0.00 2.24
607 650 3.423645 GCTTGCTTCGTCATGTCAACTAC 60.424 47.826 0.00 0.00 0.00 2.73
608 651 3.660501 TGCTTCGTCATGTCAACTACT 57.339 42.857 0.00 0.00 0.00 2.57
609 652 3.317150 TGCTTCGTCATGTCAACTACTG 58.683 45.455 0.00 0.00 0.00 2.74
610 653 3.243737 TGCTTCGTCATGTCAACTACTGT 60.244 43.478 0.00 0.00 0.00 3.55
611 654 3.121944 GCTTCGTCATGTCAACTACTGTG 59.878 47.826 0.00 0.00 0.00 3.66
641 684 1.394917 CTTCGTCATGCCAACTACTGC 59.605 52.381 0.00 0.00 0.00 4.40
662 705 2.187707 CAATGGCTTGCTTCGTTATGC 58.812 47.619 0.00 0.00 0.00 3.14
687 733 1.668826 ACTGTGGATGGCTTAAGGGA 58.331 50.000 4.29 0.00 0.00 4.20
739 785 5.346181 AGGATGGCTTCTTAGAGTGTAAC 57.654 43.478 0.07 0.00 0.00 2.50
750 796 2.527100 AGAGTGTAACAAGTATCGCGC 58.473 47.619 0.00 0.00 41.43 6.86
761 807 4.035558 ACAAGTATCGCGCAATGATGAATT 59.964 37.500 8.75 0.00 0.00 2.17
822 868 8.677300 GTTGGAGATTAGCTCATACATTTTGAA 58.323 33.333 0.00 0.00 45.81 2.69
852 898 2.787129 GCAAACACTGCCGTAAAACTTC 59.213 45.455 0.00 0.00 46.13 3.01
867 913 0.761187 ACTTCTGTCTGCAAGCAGGA 59.239 50.000 20.78 8.57 43.75 3.86
907 953 1.425066 TGTGCCCTGATTCAGTTCCTT 59.575 47.619 12.54 0.00 0.00 3.36
930 976 2.401583 TCCAATTGACAGATCCGGTG 57.598 50.000 7.12 0.00 0.00 4.94
1008 1054 1.544724 TTGGCAGCACTATGAAACCC 58.455 50.000 0.00 0.00 0.00 4.11
1080 1126 4.362677 AGTTTCCACTAGGCTCTCCAATA 58.637 43.478 0.00 0.00 33.74 1.90
1089 1135 2.570752 AGGCTCTCCAATATCGCATGAT 59.429 45.455 0.00 0.00 35.05 2.45
1119 1165 7.054124 GGTTAGGATTGATATCACAAGTTGGA 58.946 38.462 4.48 2.22 33.22 3.53
1149 1195 2.354103 CGAGAGTTCCTTTCAGCATCCA 60.354 50.000 0.00 0.00 0.00 3.41
1156 1202 0.813184 CTTTCAGCATCCACGGCATT 59.187 50.000 0.00 0.00 0.00 3.56
1159 1205 2.121291 TCAGCATCCACGGCATTTAA 57.879 45.000 0.00 0.00 0.00 1.52
1165 1211 1.737838 TCCACGGCATTTAAGCTCTG 58.262 50.000 0.00 0.00 34.17 3.35
1470 1516 5.297527 TCATGCCTGTAACATTCTTATGCTG 59.702 40.000 0.00 0.00 35.03 4.41
1515 1561 6.983307 CACCATTTGAAAACATGTAAGGTTCA 59.017 34.615 0.00 4.51 41.66 3.18
1577 1623 9.645059 CTATCGTGATATATCTTGTTGGATTGT 57.355 33.333 13.79 0.00 0.00 2.71
1585 1631 5.886960 ATCTTGTTGGATTGTTACTGCTC 57.113 39.130 0.00 0.00 0.00 4.26
1680 1727 1.866601 TGTGCATTGATAAGATCGCCG 59.133 47.619 0.00 0.00 0.00 6.46
1682 1729 2.738846 GTGCATTGATAAGATCGCCGAT 59.261 45.455 0.00 0.00 0.00 4.18
1808 1858 3.367703 GCTGTGCCAAGAACAATATTGCT 60.368 43.478 15.48 2.79 0.00 3.91
1957 2008 6.071952 TCCTTCTTGCCAGTCAAATATTGTTC 60.072 38.462 0.00 0.00 33.65 3.18
1966 2017 6.211384 CCAGTCAAATATTGTTCCCTTTCCTT 59.789 38.462 0.00 0.00 0.00 3.36
2049 2100 7.792925 TGTATCTTGTTATTTTGACAGTGTCG 58.207 34.615 18.17 0.33 34.95 4.35
2051 2102 3.513462 TGTTATTTTGACAGTGTCGCG 57.487 42.857 18.17 0.00 34.95 5.87
2151 2202 1.979308 TGTCGGGATGGGTTACAGAAA 59.021 47.619 0.00 0.00 0.00 2.52
2275 2326 4.021016 CAGACTGAGGTACTGCTTAAAGGT 60.021 45.833 0.00 0.00 41.55 3.50
2293 2344 5.729974 AAGGTTGTTCGTTTGAGTTACTC 57.270 39.130 5.27 5.27 0.00 2.59
2344 2395 3.535561 ACAACCGGATTCTATCTGCAAG 58.464 45.455 9.46 0.00 34.26 4.01
2419 2470 6.782988 ACCCGGATTTCTATGAAGATCTTCTA 59.217 38.462 30.45 19.53 40.14 2.10
2556 2690 1.978580 AGAGAAACGGTTCCATCTGGT 59.021 47.619 10.19 0.00 33.92 4.00
2589 2723 4.025647 GGAAATCGTCAAGAAAGATAGCCG 60.026 45.833 0.00 0.00 0.00 5.52
2622 2756 5.794894 TCTGTTCATAGAGAAACAGTTCCC 58.205 41.667 13.22 0.00 38.13 3.97
2647 2785 8.071368 CCAACCAATTCTTTCATGTCATTTTTG 58.929 33.333 0.00 0.00 0.00 2.44
2677 2821 1.834263 ACCTGCTGTCAGTAGATTCCC 59.166 52.381 18.55 0.00 38.66 3.97
2791 2944 4.157289 ACTCATTTGCCTCTGTTGCTAATG 59.843 41.667 15.70 15.70 46.34 1.90
2794 2947 5.927281 ATTTGCCTCTGTTGCTAATGAAT 57.073 34.783 0.00 0.00 33.88 2.57
2815 2968 3.799281 TTTGCATTATACTTGCCCTGC 57.201 42.857 4.78 0.00 39.39 4.85
2899 3052 2.557056 AGTGCAGTGCGAGAGTAAGTAA 59.443 45.455 11.20 0.00 0.00 2.24
3024 3340 6.532657 ACAAACTTTTCAGTGCATTTGAGAAG 59.467 34.615 22.14 22.14 40.60 2.85
3109 3428 5.125739 GCTATCCGTATAGGCATAACAGAGT 59.874 44.000 0.00 0.00 40.77 3.24
3160 3479 7.741785 TGAATCCTAATACCGATTACCATTGT 58.258 34.615 0.00 0.00 0.00 2.71
3161 3480 8.215050 TGAATCCTAATACCGATTACCATTGTT 58.785 33.333 0.00 0.00 0.00 2.83
3166 3485 8.679100 CCTAATACCGATTACCATTGTTTGAAA 58.321 33.333 0.00 0.00 0.00 2.69
3207 3526 2.872858 GGGAAGACATTCGAATACCTGC 59.127 50.000 10.97 9.10 36.19 4.85
3208 3527 3.531538 GGAAGACATTCGAATACCTGCA 58.468 45.455 10.97 0.00 36.19 4.41
3213 3532 5.352284 AGACATTCGAATACCTGCAGTAAG 58.648 41.667 10.97 0.00 33.70 2.34
3214 3533 5.086104 ACATTCGAATACCTGCAGTAAGT 57.914 39.130 10.97 6.14 33.70 2.24
3215 3534 5.488341 ACATTCGAATACCTGCAGTAAGTT 58.512 37.500 10.97 1.73 33.70 2.66
3217 3536 6.092259 ACATTCGAATACCTGCAGTAAGTTTC 59.908 38.462 10.97 7.39 33.70 2.78
3243 3564 8.781196 CAGTCTCATCTGGTTAATATGATTTGG 58.219 37.037 0.00 0.00 0.00 3.28
3253 3574 6.915843 GGTTAATATGATTTGGTGCGTTTAGG 59.084 38.462 0.00 0.00 0.00 2.69
3268 3589 6.089551 GTGCGTTTAGGCATGTGATACTATAG 59.910 42.308 0.00 0.00 45.99 1.31
3273 3594 3.193691 AGGCATGTGATACTATAGTCGGC 59.806 47.826 9.12 3.34 0.00 5.54
3276 3597 4.859798 GCATGTGATACTATAGTCGGCTTC 59.140 45.833 9.12 1.31 0.00 3.86
3364 3685 4.801164 ACATACGTATGTACTCCCTCCTT 58.199 43.478 34.01 9.83 44.54 3.36
3366 3687 2.664015 ACGTATGTACTCCCTCCTTCC 58.336 52.381 0.00 0.00 0.00 3.46
3368 3689 2.688817 CGTATGTACTCCCTCCTTCCCA 60.689 54.545 0.00 0.00 0.00 4.37
3369 3690 2.182516 ATGTACTCCCTCCTTCCCAG 57.817 55.000 0.00 0.00 0.00 4.45
3370 3691 1.089978 TGTACTCCCTCCTTCCCAGA 58.910 55.000 0.00 0.00 0.00 3.86
3371 3692 1.435563 TGTACTCCCTCCTTCCCAGAA 59.564 52.381 0.00 0.00 0.00 3.02
3372 3693 2.158066 TGTACTCCCTCCTTCCCAGAAA 60.158 50.000 0.00 0.00 0.00 2.52
3373 3694 2.367947 ACTCCCTCCTTCCCAGAAAT 57.632 50.000 0.00 0.00 0.00 2.17
3374 3695 2.648838 ACTCCCTCCTTCCCAGAAATT 58.351 47.619 0.00 0.00 0.00 1.82
3375 3696 3.815507 ACTCCCTCCTTCCCAGAAATTA 58.184 45.455 0.00 0.00 0.00 1.40
3376 3697 4.183916 ACTCCCTCCTTCCCAGAAATTAA 58.816 43.478 0.00 0.00 0.00 1.40
3377 3698 4.228438 ACTCCCTCCTTCCCAGAAATTAAG 59.772 45.833 0.00 0.00 0.00 1.85
3378 3699 4.183916 TCCCTCCTTCCCAGAAATTAAGT 58.816 43.478 0.00 0.00 0.00 2.24
3379 3700 4.227527 TCCCTCCTTCCCAGAAATTAAGTC 59.772 45.833 0.00 0.00 0.00 3.01
3380 3701 4.527944 CCTCCTTCCCAGAAATTAAGTCC 58.472 47.826 0.00 0.00 0.00 3.85
3381 3702 4.228438 CCTCCTTCCCAGAAATTAAGTCCT 59.772 45.833 0.00 0.00 0.00 3.85
3382 3703 5.281245 CCTCCTTCCCAGAAATTAAGTCCTT 60.281 44.000 0.00 0.00 0.00 3.36
3383 3704 6.069615 CCTCCTTCCCAGAAATTAAGTCCTTA 60.070 42.308 0.00 0.00 0.00 2.69
3384 3705 7.337826 TCCTTCCCAGAAATTAAGTCCTTAA 57.662 36.000 2.21 2.21 39.12 1.85
3385 3706 7.761608 TCCTTCCCAGAAATTAAGTCCTTAAA 58.238 34.615 3.78 0.00 38.38 1.52
3386 3707 8.228905 TCCTTCCCAGAAATTAAGTCCTTAAAA 58.771 33.333 3.78 0.00 38.38 1.52
3387 3708 9.035890 CCTTCCCAGAAATTAAGTCCTTAAAAT 57.964 33.333 3.78 0.00 38.38 1.82
3402 3723 9.946165 AGTCCTTAAAATTTTGTCTTAAAGTCG 57.054 29.630 13.76 0.00 0.00 4.18
3479 3800 8.985315 ACATCACCAAATCAGTATCATTATGT 57.015 30.769 0.00 0.00 0.00 2.29
3485 3806 8.219868 ACCAAATCAGTATCATTATGTCCATCA 58.780 33.333 0.00 0.00 0.00 3.07
3562 3887 7.857569 TGTTCCTTTTAGTACGATTTGAGTTG 58.142 34.615 0.00 0.00 0.00 3.16
3874 4212 3.321950 AGAAGATGCTAGGGTAATGGCT 58.678 45.455 0.00 0.00 0.00 4.75
3895 4233 0.463116 ACTAAATAGCCGGCGGTTGG 60.463 55.000 28.82 19.55 0.00 3.77
4090 4432 6.719301 TGATTTTCATATGGGTTGGCATTTT 58.281 32.000 2.13 0.00 0.00 1.82
4164 4508 1.796151 CGCGTGTTTCCTGCATCAT 59.204 52.632 0.00 0.00 0.00 2.45
4165 4509 0.247814 CGCGTGTTTCCTGCATCATC 60.248 55.000 0.00 0.00 0.00 2.92
4166 4510 0.804364 GCGTGTTTCCTGCATCATCA 59.196 50.000 0.00 0.00 0.00 3.07
4170 4514 4.261322 GCGTGTTTCCTGCATCATCAATAT 60.261 41.667 0.00 0.00 0.00 1.28
4193 4537 5.167845 TCAAAATAATGGCTTCGGCTTTTC 58.832 37.500 0.00 0.00 41.44 2.29
4216 4561 2.265683 CGACTGATATCCATGATGCGG 58.734 52.381 0.00 0.00 0.00 5.69
4222 4567 6.061441 ACTGATATCCATGATGCGGTTTTTA 58.939 36.000 0.00 0.00 0.00 1.52
4223 4568 6.545666 ACTGATATCCATGATGCGGTTTTTAA 59.454 34.615 0.00 0.00 0.00 1.52
4224 4569 7.068103 ACTGATATCCATGATGCGGTTTTTAAA 59.932 33.333 0.00 0.00 0.00 1.52
4225 4570 7.776107 TGATATCCATGATGCGGTTTTTAAAA 58.224 30.769 0.00 0.00 0.00 1.52
4226 4571 7.704472 TGATATCCATGATGCGGTTTTTAAAAC 59.296 33.333 11.71 11.71 0.00 2.43
4227 4572 5.461032 TCCATGATGCGGTTTTTAAAACT 57.539 34.783 18.31 0.59 0.00 2.66
4228 4573 5.226396 TCCATGATGCGGTTTTTAAAACTG 58.774 37.500 21.22 21.22 0.00 3.16
4229 4574 5.010112 TCCATGATGCGGTTTTTAAAACTGA 59.990 36.000 27.45 15.48 0.00 3.41
4230 4575 5.118510 CCATGATGCGGTTTTTAAAACTGAC 59.881 40.000 27.45 19.56 0.00 3.51
4231 4576 4.612943 TGATGCGGTTTTTAAAACTGACC 58.387 39.130 27.45 16.83 0.00 4.02
4232 4577 3.439895 TGCGGTTTTTAAAACTGACCC 57.560 42.857 27.45 13.76 0.00 4.46
4233 4578 3.025262 TGCGGTTTTTAAAACTGACCCT 58.975 40.909 27.45 0.00 0.00 4.34
4234 4579 3.067040 TGCGGTTTTTAAAACTGACCCTC 59.933 43.478 27.45 13.17 0.00 4.30
4235 4580 3.551454 GCGGTTTTTAAAACTGACCCTCC 60.551 47.826 27.45 9.39 0.00 4.30
4236 4581 3.005050 CGGTTTTTAAAACTGACCCTCCC 59.995 47.826 21.03 1.44 0.00 4.30
4237 4582 3.962063 GGTTTTTAAAACTGACCCTCCCA 59.038 43.478 18.31 0.00 0.00 4.37
4238 4583 4.591498 GGTTTTTAAAACTGACCCTCCCAT 59.409 41.667 18.31 0.00 0.00 4.00
4239 4584 5.071250 GGTTTTTAAAACTGACCCTCCCATT 59.929 40.000 18.31 0.00 0.00 3.16
4240 4585 6.408776 GGTTTTTAAAACTGACCCTCCCATTT 60.409 38.462 18.31 0.00 0.00 2.32
4241 4586 6.816616 TTTTAAAACTGACCCTCCCATTTT 57.183 33.333 0.00 0.00 0.00 1.82
4242 4587 6.413783 TTTAAAACTGACCCTCCCATTTTC 57.586 37.500 0.00 0.00 0.00 2.29
4243 4588 3.611025 AAACTGACCCTCCCATTTTCA 57.389 42.857 0.00 0.00 0.00 2.69
4244 4589 2.887151 ACTGACCCTCCCATTTTCAG 57.113 50.000 0.00 0.00 39.72 3.02
4245 4590 2.065799 ACTGACCCTCCCATTTTCAGT 58.934 47.619 0.00 0.00 41.63 3.41
4246 4591 3.256704 ACTGACCCTCCCATTTTCAGTA 58.743 45.455 0.74 0.00 43.97 2.74
4247 4592 3.655777 ACTGACCCTCCCATTTTCAGTAA 59.344 43.478 0.74 0.00 43.97 2.24
4248 4593 4.263506 ACTGACCCTCCCATTTTCAGTAAG 60.264 45.833 0.74 0.00 43.97 2.34
4249 4594 3.017442 GACCCTCCCATTTTCAGTAAGC 58.983 50.000 0.00 0.00 0.00 3.09
4250 4595 2.291605 ACCCTCCCATTTTCAGTAAGCC 60.292 50.000 0.00 0.00 0.00 4.35
4251 4596 2.291540 CCCTCCCATTTTCAGTAAGCCA 60.292 50.000 0.00 0.00 0.00 4.75
4252 4597 3.628257 CCCTCCCATTTTCAGTAAGCCAT 60.628 47.826 0.00 0.00 0.00 4.40
4253 4598 3.382546 CCTCCCATTTTCAGTAAGCCATG 59.617 47.826 0.00 0.00 0.00 3.66
4254 4599 4.272489 CTCCCATTTTCAGTAAGCCATGA 58.728 43.478 0.00 0.00 0.00 3.07
4255 4600 4.870636 TCCCATTTTCAGTAAGCCATGAT 58.129 39.130 0.00 0.00 0.00 2.45
4256 4601 4.646040 TCCCATTTTCAGTAAGCCATGATG 59.354 41.667 0.00 0.00 0.00 3.07
4257 4602 4.365723 CCATTTTCAGTAAGCCATGATGC 58.634 43.478 0.00 0.00 0.00 3.91
4258 4603 3.763097 TTTTCAGTAAGCCATGATGCG 57.237 42.857 0.00 0.00 36.02 4.73
4259 4604 2.401583 TTCAGTAAGCCATGATGCGT 57.598 45.000 0.00 0.00 36.02 5.24
4260 4605 2.401583 TCAGTAAGCCATGATGCGTT 57.598 45.000 0.00 0.00 36.02 4.84
4261 4606 2.710377 TCAGTAAGCCATGATGCGTTT 58.290 42.857 0.00 0.00 36.02 3.60
4262 4607 3.081061 TCAGTAAGCCATGATGCGTTTT 58.919 40.909 0.00 0.00 36.02 2.43
4263 4608 3.505680 TCAGTAAGCCATGATGCGTTTTT 59.494 39.130 0.00 0.00 36.02 1.94
4302 4647 4.218417 TCCCATTTTCAGTAAGCAAAGCTC 59.782 41.667 0.00 0.00 38.25 4.09
4312 4657 1.208614 GCAAAGCTCTGGCGACAAG 59.791 57.895 0.00 0.00 44.37 3.16
4319 4664 1.115467 CTCTGGCGACAAGGGTAGAT 58.885 55.000 0.00 0.00 42.06 1.98
4335 4680 4.336280 GGTAGATTGTCCTGAGCCTTTTT 58.664 43.478 0.00 0.00 0.00 1.94
4360 4748 3.967203 TTTTTACCTGTAACGTGCACC 57.033 42.857 12.15 0.00 0.00 5.01
4367 4755 0.869068 TGTAACGTGCACCGGATTTG 59.131 50.000 9.46 0.00 42.24 2.32
4409 4797 2.970974 GACGCCACTCTTTGCAGGC 61.971 63.158 2.38 2.38 43.61 4.85
4468 4858 1.069227 GGTGATGAAACAACACTCGGC 60.069 52.381 10.79 0.00 37.33 5.54
4553 4943 4.199310 TCAGACGAATTCCATTGATTCCC 58.801 43.478 0.00 0.00 0.00 3.97
4640 5032 2.284699 AGGTTACGCCTCAGGCCT 60.285 61.111 11.12 0.00 46.96 5.19
4668 5060 3.970410 CCTGGTTGGGGAGCTGCA 61.970 66.667 7.79 0.00 0.00 4.41
4684 5076 2.606795 GCTGCAAAGCAAATCGGTACAA 60.607 45.455 0.00 0.00 38.41 2.41
4695 5087 6.536941 AGCAAATCGGTACAATTTGTTTGTTT 59.463 30.769 23.19 0.88 46.51 2.83
4775 5182 0.611200 GTAAAACCACCCCCATTGCC 59.389 55.000 0.00 0.00 0.00 4.52
4788 5195 2.424667 CCCATTGCCCCATTCATAGTCA 60.425 50.000 0.00 0.00 0.00 3.41
4793 5200 2.301346 GCCCCATTCATAGTCAGTTGG 58.699 52.381 0.00 0.00 0.00 3.77
4797 5204 4.567537 CCCCATTCATAGTCAGTTGGTTCA 60.568 45.833 0.00 0.00 0.00 3.18
4813 5220 9.643693 CAGTTGGTTCAATATTTAAGCAATCTT 57.356 29.630 22.78 13.07 42.85 2.40
4843 5250 2.119801 AGGCACTGCTGAACATTAGG 57.880 50.000 0.00 0.00 37.18 2.69
4845 5252 1.614317 GGCACTGCTGAACATTAGGGT 60.614 52.381 0.00 0.00 0.00 4.34
4856 5263 5.640147 TGAACATTAGGGTGTTTTCCTGAT 58.360 37.500 0.00 0.00 42.08 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.124695 GATCGGGGAGGTGGCAAC 60.125 66.667 0.00 0.00 0.00 4.17
4 5 3.407967 GGATCGGGGAGGTGGCAA 61.408 66.667 0.00 0.00 0.00 4.52
88 91 1.209504 CGCATAAAGAAGGGAGGTGGA 59.790 52.381 0.00 0.00 0.00 4.02
90 93 1.017387 GCGCATAAAGAAGGGAGGTG 58.983 55.000 0.30 0.00 0.00 4.00
92 95 0.462047 ACGCGCATAAAGAAGGGAGG 60.462 55.000 5.73 0.00 0.00 4.30
93 96 0.931005 GACGCGCATAAAGAAGGGAG 59.069 55.000 5.73 0.00 0.00 4.30
150 159 1.418264 TCCCACGAATCAACCACTTGA 59.582 47.619 0.00 0.00 40.77 3.02
151 160 1.806542 CTCCCACGAATCAACCACTTG 59.193 52.381 0.00 0.00 0.00 3.16
170 179 3.390967 CCAAACCAACCAAGAAAATCCCT 59.609 43.478 0.00 0.00 0.00 4.20
173 182 2.799978 CGCCAAACCAACCAAGAAAATC 59.200 45.455 0.00 0.00 0.00 2.17
174 183 2.484594 CCGCCAAACCAACCAAGAAAAT 60.485 45.455 0.00 0.00 0.00 1.82
177 186 1.395826 CCCGCCAAACCAACCAAGAA 61.396 55.000 0.00 0.00 0.00 2.52
178 187 1.830408 CCCGCCAAACCAACCAAGA 60.830 57.895 0.00 0.00 0.00 3.02
179 188 2.733945 CCCGCCAAACCAACCAAG 59.266 61.111 0.00 0.00 0.00 3.61
180 189 2.840102 CCCCGCCAAACCAACCAA 60.840 61.111 0.00 0.00 0.00 3.67
181 190 4.924187 CCCCCGCCAAACCAACCA 62.924 66.667 0.00 0.00 0.00 3.67
236 245 1.923356 ACACCACCAAACCCATCATC 58.077 50.000 0.00 0.00 0.00 2.92
292 301 1.334960 GGATCAGCAACAAACACACCG 60.335 52.381 0.00 0.00 0.00 4.94
295 304 0.950836 CCGGATCAGCAACAAACACA 59.049 50.000 0.00 0.00 0.00 3.72
303 312 2.435938 GAACGCCCGGATCAGCAA 60.436 61.111 0.73 0.00 0.00 3.91
374 383 1.687494 CTCGCCGCAACTAAGCACTC 61.687 60.000 0.00 0.00 0.00 3.51
401 411 4.813697 GGTTCCAGCTACAGATCAGAATTC 59.186 45.833 0.00 0.00 0.00 2.17
414 424 4.010667 ACATACAAAACGGTTCCAGCTA 57.989 40.909 0.00 0.00 0.00 3.32
415 425 2.858745 ACATACAAAACGGTTCCAGCT 58.141 42.857 0.00 0.00 0.00 4.24
416 426 3.425758 GCTACATACAAAACGGTTCCAGC 60.426 47.826 0.00 0.00 0.00 4.85
417 427 3.181524 CGCTACATACAAAACGGTTCCAG 60.182 47.826 0.00 0.00 0.00 3.86
418 428 2.737783 CGCTACATACAAAACGGTTCCA 59.262 45.455 0.00 0.00 0.00 3.53
419 429 2.094734 CCGCTACATACAAAACGGTTCC 59.905 50.000 0.00 0.00 35.99 3.62
444 454 3.911964 CCAAGGAAAATACAGAAAACGCG 59.088 43.478 3.53 3.53 0.00 6.01
469 480 8.517062 AAAAGGAAATCTTATGATCTCACTGG 57.483 34.615 0.00 0.00 34.78 4.00
507 519 2.692041 GGAGCTCCCAAAAATCATCCAG 59.308 50.000 23.19 0.00 34.14 3.86
542 554 5.914898 ACAAAGCAATAACTAACCATCCC 57.085 39.130 0.00 0.00 0.00 3.85
580 623 3.166657 GACATGACGAAGCAAGCAATTC 58.833 45.455 0.00 0.00 0.00 2.17
581 624 2.553602 TGACATGACGAAGCAAGCAATT 59.446 40.909 0.00 0.00 0.00 2.32
582 625 2.153645 TGACATGACGAAGCAAGCAAT 58.846 42.857 0.00 0.00 0.00 3.56
583 626 1.592064 TGACATGACGAAGCAAGCAA 58.408 45.000 0.00 0.00 0.00 3.91
584 627 1.264020 GTTGACATGACGAAGCAAGCA 59.736 47.619 0.00 0.00 0.00 3.91
585 628 1.532868 AGTTGACATGACGAAGCAAGC 59.467 47.619 0.00 0.00 0.00 4.01
586 629 3.990469 AGTAGTTGACATGACGAAGCAAG 59.010 43.478 0.00 0.00 0.00 4.01
587 630 3.740832 CAGTAGTTGACATGACGAAGCAA 59.259 43.478 0.00 0.00 0.00 3.91
588 631 3.243737 ACAGTAGTTGACATGACGAAGCA 60.244 43.478 0.00 0.00 0.00 3.91
589 632 3.121944 CACAGTAGTTGACATGACGAAGC 59.878 47.826 0.00 0.00 0.00 3.86
590 633 4.546570 TCACAGTAGTTGACATGACGAAG 58.453 43.478 0.00 0.00 0.00 3.79
591 634 4.577834 TCACAGTAGTTGACATGACGAA 57.422 40.909 0.00 0.00 0.00 3.85
592 635 4.577834 TTCACAGTAGTTGACATGACGA 57.422 40.909 0.00 0.00 0.00 4.20
593 636 4.091945 CCATTCACAGTAGTTGACATGACG 59.908 45.833 0.00 0.00 0.00 4.35
594 637 4.142816 GCCATTCACAGTAGTTGACATGAC 60.143 45.833 0.00 0.00 0.00 3.06
595 638 4.002982 GCCATTCACAGTAGTTGACATGA 58.997 43.478 0.00 0.00 0.00 3.07
596 639 4.005650 AGCCATTCACAGTAGTTGACATG 58.994 43.478 0.00 0.00 0.00 3.21
597 640 4.292186 AGCCATTCACAGTAGTTGACAT 57.708 40.909 0.00 0.00 0.00 3.06
598 641 3.769739 AGCCATTCACAGTAGTTGACA 57.230 42.857 0.00 0.00 0.00 3.58
599 642 3.365364 GCAAGCCATTCACAGTAGTTGAC 60.365 47.826 0.00 0.00 0.00 3.18
600 643 2.813754 GCAAGCCATTCACAGTAGTTGA 59.186 45.455 0.00 0.00 0.00 3.18
601 644 2.816087 AGCAAGCCATTCACAGTAGTTG 59.184 45.455 0.00 0.00 0.00 3.16
602 645 3.146104 AGCAAGCCATTCACAGTAGTT 57.854 42.857 0.00 0.00 0.00 2.24
603 646 2.867109 AGCAAGCCATTCACAGTAGT 57.133 45.000 0.00 0.00 0.00 2.73
604 647 2.094894 CGAAGCAAGCCATTCACAGTAG 59.905 50.000 0.00 0.00 0.00 2.57
605 648 2.076100 CGAAGCAAGCCATTCACAGTA 58.924 47.619 0.00 0.00 0.00 2.74
606 649 0.877071 CGAAGCAAGCCATTCACAGT 59.123 50.000 0.00 0.00 0.00 3.55
607 650 0.877071 ACGAAGCAAGCCATTCACAG 59.123 50.000 0.00 0.00 0.00 3.66
608 651 0.874390 GACGAAGCAAGCCATTCACA 59.126 50.000 0.00 0.00 0.00 3.58
609 652 0.874390 TGACGAAGCAAGCCATTCAC 59.126 50.000 0.00 0.00 0.00 3.18
610 653 1.469703 CATGACGAAGCAAGCCATTCA 59.530 47.619 0.00 0.00 0.00 2.57
611 654 1.796617 GCATGACGAAGCAAGCCATTC 60.797 52.381 0.00 0.00 0.00 2.67
641 684 2.801063 CATAACGAAGCAAGCCATTGG 58.199 47.619 0.00 0.00 36.88 3.16
655 698 2.967362 TCCACAGTAGTTGGCATAACG 58.033 47.619 0.00 0.00 0.00 3.18
662 705 2.496899 AAGCCATCCACAGTAGTTGG 57.503 50.000 0.00 0.00 0.00 3.77
739 785 3.590720 TTCATCATTGCGCGATACTTG 57.409 42.857 12.10 8.39 0.00 3.16
761 807 9.748708 CATGTTCTCTTGAAAAATTACTTTCCA 57.251 29.630 1.18 0.00 34.91 3.53
822 868 1.302511 CAGTGTTTGCGCCTACCCT 60.303 57.895 4.18 0.00 0.00 4.34
841 887 3.607078 GCTTGCAGACAGAAGTTTTACGG 60.607 47.826 0.00 0.00 0.00 4.02
852 898 0.873054 CAGTTCCTGCTTGCAGACAG 59.127 55.000 22.50 10.31 0.00 3.51
867 913 5.522456 CACAGTTGCAACACATATTCAGTT 58.478 37.500 30.11 3.00 0.00 3.16
885 931 1.271597 GGAACTGAATCAGGGCACAGT 60.272 52.381 15.38 0.00 43.92 3.55
930 976 2.952310 AGTTTGCCAACAGGAGAAGTTC 59.048 45.455 3.22 0.00 35.05 3.01
1008 1054 4.082571 AGCTTGGAGAAAATGAACCAATCG 60.083 41.667 0.00 0.00 40.78 3.34
1080 1126 3.096852 TCCTAACCCGATATCATGCGAT 58.903 45.455 3.12 0.00 35.50 4.58
1089 1135 7.234782 ACTTGTGATATCAATCCTAACCCGATA 59.765 37.037 7.07 0.00 0.00 2.92
1119 1165 4.281182 TGAAAGGAACTCTCGACTAAAGCT 59.719 41.667 0.00 0.00 38.49 3.74
1149 1195 1.089920 CTGCAGAGCTTAAATGCCGT 58.910 50.000 8.42 0.00 39.22 5.68
1156 1202 1.699634 ACCACTTCCTGCAGAGCTTAA 59.300 47.619 17.39 0.40 0.00 1.85
1159 1205 1.374190 CACCACTTCCTGCAGAGCT 59.626 57.895 17.39 0.00 0.00 4.09
1165 1211 0.819259 TGAACTGCACCACTTCCTGC 60.819 55.000 0.00 0.00 0.00 4.85
1199 1245 4.222309 GCTCCAGCAACCTTGTTGAAGG 62.222 54.545 10.94 10.50 46.61 3.46
1279 1325 1.856265 CTTGAACCAGAGCCCGCAAC 61.856 60.000 0.00 0.00 0.00 4.17
1424 1470 1.003580 GCTCCTCAACCTCATTCCACA 59.996 52.381 0.00 0.00 0.00 4.17
1470 1516 1.499049 GTATTACACTAGCGGCAGCC 58.501 55.000 4.82 0.00 46.67 4.85
1515 1561 5.483937 CCCTTTCTATAAAAAGCAGGGGTTT 59.516 40.000 0.00 0.00 34.99 3.27
1577 1623 2.567615 GGACAGAGAAAGGGAGCAGTAA 59.432 50.000 0.00 0.00 0.00 2.24
1585 1631 3.214696 ACAAACAGGACAGAGAAAGGG 57.785 47.619 0.00 0.00 0.00 3.95
1660 1707 1.866601 CGGCGATCTTATCAATGCACA 59.133 47.619 0.00 0.00 0.00 4.57
1661 1708 2.135139 TCGGCGATCTTATCAATGCAC 58.865 47.619 4.99 0.00 0.00 4.57
1680 1727 3.004002 TCATTGAATCCGCAAGCATCATC 59.996 43.478 0.00 0.00 0.00 2.92
1682 1729 2.367486 TCATTGAATCCGCAAGCATCA 58.633 42.857 0.00 0.00 0.00 3.07
1766 1816 2.111043 CACGAGCACAACCTGGGT 59.889 61.111 0.00 0.00 0.00 4.51
1808 1858 3.903714 TCTTGGTTCTGTCAGATCTTCCA 59.096 43.478 2.68 7.74 0.00 3.53
1957 2008 4.349365 TGTAATAGGGCAAAAGGAAAGGG 58.651 43.478 0.00 0.00 0.00 3.95
1966 2017 2.951642 GCAGAGCATGTAATAGGGCAAA 59.048 45.455 0.00 0.00 0.00 3.68
1996 2047 4.789012 AGTGTCCAAATAATTGCCACAG 57.211 40.909 11.71 0.00 38.40 3.66
2035 2086 2.143122 ACATCGCGACACTGTCAAAAT 58.857 42.857 12.93 0.00 32.09 1.82
2151 2202 7.425606 GTTTTTGACCTTCATTATCCGCATAT 58.574 34.615 0.00 0.00 0.00 1.78
2275 2326 6.092944 ACAACATGAGTAACTCAAACGAACAA 59.907 34.615 0.00 0.00 44.04 2.83
2329 2380 3.814283 CCAGCTTCTTGCAGATAGAATCC 59.186 47.826 0.00 0.00 45.94 3.01
2344 2395 3.084786 AGCATACTTTGAACCCAGCTTC 58.915 45.455 0.00 0.00 0.00 3.86
2419 2470 6.839124 TGATCAATAAAGCATTCACACCTT 57.161 33.333 0.00 0.00 0.00 3.50
2589 2723 9.366513 GTTTCTCTATGAACAGAAACGTTAAAC 57.633 33.333 0.00 0.00 45.17 2.01
2616 2750 4.901250 ACATGAAAGAATTGGTTGGGAACT 59.099 37.500 0.00 0.00 0.00 3.01
2622 2756 8.071368 CCAAAAATGACATGAAAGAATTGGTTG 58.929 33.333 0.00 1.45 31.31 3.77
2647 2785 1.306226 ACAGCAGGTAGGGAGTCCC 60.306 63.158 21.81 21.81 45.90 4.46
2677 2821 1.093159 AACTCGTACGCCCTACAGAG 58.907 55.000 11.24 2.38 34.65 3.35
2686 2830 3.122948 ACACATCATCAAAACTCGTACGC 59.877 43.478 11.24 0.00 0.00 4.42
2791 2944 5.234972 GCAGGGCAAGTATAATGCAAAATTC 59.765 40.000 12.37 0.00 45.60 2.17
2794 2947 3.768757 AGCAGGGCAAGTATAATGCAAAA 59.231 39.130 12.37 0.00 45.60 2.44
2815 2968 9.234827 TGTCATATGAATATTTTCCCTGCATAG 57.765 33.333 7.07 0.00 0.00 2.23
2942 3258 7.229306 GCATTGACCATATCTTCTGAACCATAA 59.771 37.037 0.00 0.00 0.00 1.90
2962 3278 9.545105 AAACAATTAACTTCAATCTTGCATTGA 57.455 25.926 0.00 0.00 36.37 2.57
3024 3340 0.793250 GCAGTCGAAAGCCAAGAGAC 59.207 55.000 0.00 0.00 0.00 3.36
3081 3400 6.526526 TGTTATGCCTATACGGATAGCAAAA 58.473 36.000 9.35 2.20 34.70 2.44
3124 3443 9.255029 TCGGTATTAGGATTCATCTGATCATAA 57.745 33.333 0.00 0.00 0.00 1.90
3127 3446 7.724490 ATCGGTATTAGGATTCATCTGATCA 57.276 36.000 0.00 0.00 0.00 2.92
3160 3479 9.748708 CTGAAGTAAGATCCAAATGTTTTCAAA 57.251 29.630 0.00 0.00 0.00 2.69
3161 3480 8.359642 CCTGAAGTAAGATCCAAATGTTTTCAA 58.640 33.333 0.00 0.00 0.00 2.69
3166 3485 6.139679 TCCCTGAAGTAAGATCCAAATGTT 57.860 37.500 0.00 0.00 0.00 2.71
3175 3494 5.422331 TCGAATGTCTTCCCTGAAGTAAGAT 59.578 40.000 3.95 0.00 40.24 2.40
3207 3526 5.788450 ACCAGATGAGACTGAAACTTACTG 58.212 41.667 0.00 0.00 39.94 2.74
3208 3527 6.426646 AACCAGATGAGACTGAAACTTACT 57.573 37.500 0.00 0.00 39.94 2.24
3213 3532 8.948631 TCATATTAACCAGATGAGACTGAAAC 57.051 34.615 0.00 0.00 39.94 2.78
3217 3536 8.781196 CCAAATCATATTAACCAGATGAGACTG 58.219 37.037 0.00 0.00 33.29 3.51
3243 3564 2.936498 AGTATCACATGCCTAAACGCAC 59.064 45.455 0.00 0.00 42.70 5.34
3253 3574 4.442375 AGCCGACTATAGTATCACATGC 57.558 45.455 5.09 1.57 0.00 4.06
3268 3589 2.167398 TACCCTGCAGTGAAGCCGAC 62.167 60.000 13.81 0.00 0.00 4.79
3273 3594 3.126001 TCTTTGTACCCTGCAGTGAAG 57.874 47.619 13.81 7.20 0.00 3.02
3276 3597 2.002586 CGATCTTTGTACCCTGCAGTG 58.997 52.381 13.81 3.15 0.00 3.66
3352 3673 2.249309 TTCTGGGAAGGAGGGAGTAC 57.751 55.000 0.00 0.00 0.00 2.73
3355 3676 4.228438 ACTTAATTTCTGGGAAGGAGGGAG 59.772 45.833 0.00 0.00 0.00 4.30
3356 3677 4.183916 ACTTAATTTCTGGGAAGGAGGGA 58.816 43.478 0.00 0.00 0.00 4.20
3357 3678 4.527944 GACTTAATTTCTGGGAAGGAGGG 58.472 47.826 0.00 0.00 0.00 4.30
3358 3679 4.228438 AGGACTTAATTTCTGGGAAGGAGG 59.772 45.833 0.00 0.00 0.00 4.30
3359 3680 5.443230 AGGACTTAATTTCTGGGAAGGAG 57.557 43.478 0.00 0.00 0.00 3.69
3360 3681 5.860648 AAGGACTTAATTTCTGGGAAGGA 57.139 39.130 0.00 0.00 0.00 3.36
3361 3682 8.417273 TTTTAAGGACTTAATTTCTGGGAAGG 57.583 34.615 5.44 0.00 35.27 3.46
3376 3697 9.946165 CGACTTTAAGACAAAATTTTAAGGACT 57.054 29.630 2.44 0.00 0.00 3.85
3377 3698 9.940166 TCGACTTTAAGACAAAATTTTAAGGAC 57.060 29.630 2.44 1.94 0.00 3.85
3386 3707 9.543783 AGAACTAGTTCGACTTTAAGACAAAAT 57.456 29.630 25.92 3.52 43.97 1.82
3387 3708 8.937634 AGAACTAGTTCGACTTTAAGACAAAA 57.062 30.769 25.92 0.00 43.97 2.44
3388 3709 8.937634 AAGAACTAGTTCGACTTTAAGACAAA 57.062 30.769 25.92 0.00 43.97 2.83
3390 3711 9.674824 CTTAAGAACTAGTTCGACTTTAAGACA 57.325 33.333 29.52 12.69 43.97 3.41
3391 3712 9.676195 ACTTAAGAACTAGTTCGACTTTAAGAC 57.324 33.333 34.26 14.37 43.97 3.01
3396 3717 8.815189 GTCAAACTTAAGAACTAGTTCGACTTT 58.185 33.333 25.92 18.14 43.97 2.66
3397 3718 7.437565 GGTCAAACTTAAGAACTAGTTCGACTT 59.562 37.037 25.92 18.45 43.97 3.01
3398 3719 6.922407 GGTCAAACTTAAGAACTAGTTCGACT 59.078 38.462 25.92 17.92 43.97 4.18
3440 3761 6.839124 TTGGTGATGTAGATGCTGATTTTT 57.161 33.333 0.00 0.00 0.00 1.94
3444 3765 5.687780 TGATTTGGTGATGTAGATGCTGAT 58.312 37.500 0.00 0.00 0.00 2.90
3448 3769 6.707608 TGATACTGATTTGGTGATGTAGATGC 59.292 38.462 0.00 0.00 0.00 3.91
3541 3866 9.166126 GAAAACAACTCAAATCGTACTAAAAGG 57.834 33.333 0.00 0.00 0.00 3.11
3741 4079 9.450807 CCTGTTTGTAAAGACAGAGTTTAATTG 57.549 33.333 5.14 0.00 44.65 2.32
3742 4080 8.630037 CCCTGTTTGTAAAGACAGAGTTTAATT 58.370 33.333 5.14 0.00 44.65 1.40
3743 4081 7.230712 CCCCTGTTTGTAAAGACAGAGTTTAAT 59.769 37.037 5.14 0.00 44.65 1.40
3750 4088 2.441750 AGCCCCTGTTTGTAAAGACAGA 59.558 45.455 5.14 0.00 44.65 3.41
3761 4099 2.586648 ATCGAAGAAAGCCCCTGTTT 57.413 45.000 0.00 0.00 43.58 2.83
3798 4136 0.108585 TGGTCTCCACTGAAACAGGC 59.891 55.000 0.00 0.00 35.51 4.85
3874 4212 2.553086 CAACCGCCGGCTATTTAGTTA 58.447 47.619 26.68 0.00 0.00 2.24
3927 4265 8.777578 TGGTTTCCCGTATCTATATATATGCT 57.222 34.615 5.44 0.00 0.00 3.79
3941 4279 2.314071 TCTTCTCCTGGTTTCCCGTA 57.686 50.000 0.00 0.00 0.00 4.02
4090 4432 4.299586 TGATACAATCCAGGAAACAGCA 57.700 40.909 0.00 0.00 0.00 4.41
4164 4508 6.265196 AGCCGAAGCCATTATTTTGATATTGA 59.735 34.615 0.00 0.00 41.25 2.57
4165 4509 6.449698 AGCCGAAGCCATTATTTTGATATTG 58.550 36.000 0.00 0.00 41.25 1.90
4166 4510 6.655078 AGCCGAAGCCATTATTTTGATATT 57.345 33.333 0.00 0.00 41.25 1.28
4170 4514 4.799564 AAAGCCGAAGCCATTATTTTGA 57.200 36.364 0.00 0.00 41.25 2.69
4193 4537 3.519579 GCATCATGGATATCAGTCGGAG 58.480 50.000 4.83 0.00 0.00 4.63
4216 4561 5.801531 ATGGGAGGGTCAGTTTTAAAAAC 57.198 39.130 1.31 0.00 0.00 2.43
4222 4567 3.897505 CTGAAAATGGGAGGGTCAGTTTT 59.102 43.478 0.00 0.00 33.44 2.43
4223 4568 3.117131 ACTGAAAATGGGAGGGTCAGTTT 60.117 43.478 0.00 0.00 45.00 2.66
4224 4569 2.447047 ACTGAAAATGGGAGGGTCAGTT 59.553 45.455 0.00 0.00 45.00 3.16
4225 4570 2.065799 ACTGAAAATGGGAGGGTCAGT 58.934 47.619 0.00 0.00 43.09 3.41
4226 4571 2.887151 ACTGAAAATGGGAGGGTCAG 57.113 50.000 0.00 0.00 41.21 3.51
4227 4572 3.561313 GCTTACTGAAAATGGGAGGGTCA 60.561 47.826 0.00 0.00 0.00 4.02
4228 4573 3.017442 GCTTACTGAAAATGGGAGGGTC 58.983 50.000 0.00 0.00 0.00 4.46
4229 4574 2.291605 GGCTTACTGAAAATGGGAGGGT 60.292 50.000 0.00 0.00 0.00 4.34
4230 4575 2.291540 TGGCTTACTGAAAATGGGAGGG 60.292 50.000 0.00 0.00 0.00 4.30
4231 4576 3.085952 TGGCTTACTGAAAATGGGAGG 57.914 47.619 0.00 0.00 0.00 4.30
4232 4577 4.272489 TCATGGCTTACTGAAAATGGGAG 58.728 43.478 0.00 0.00 0.00 4.30
4233 4578 4.314522 TCATGGCTTACTGAAAATGGGA 57.685 40.909 0.00 0.00 0.00 4.37
4234 4579 4.738541 GCATCATGGCTTACTGAAAATGGG 60.739 45.833 0.00 0.00 0.00 4.00
4235 4580 4.365723 GCATCATGGCTTACTGAAAATGG 58.634 43.478 0.00 0.00 0.00 3.16
4236 4581 4.039703 CGCATCATGGCTTACTGAAAATG 58.960 43.478 0.00 0.00 0.00 2.32
4237 4582 3.696051 ACGCATCATGGCTTACTGAAAAT 59.304 39.130 0.00 0.00 0.00 1.82
4238 4583 3.081061 ACGCATCATGGCTTACTGAAAA 58.919 40.909 0.00 0.00 0.00 2.29
4239 4584 2.710377 ACGCATCATGGCTTACTGAAA 58.290 42.857 0.00 0.00 0.00 2.69
4240 4585 2.401583 ACGCATCATGGCTTACTGAA 57.598 45.000 0.00 0.00 0.00 3.02
4241 4586 2.401583 AACGCATCATGGCTTACTGA 57.598 45.000 0.00 0.00 0.00 3.41
4242 4587 3.492421 AAAACGCATCATGGCTTACTG 57.508 42.857 0.00 0.00 0.00 2.74
4262 4607 6.673839 AATGGGAGGATCGGTTTTTAAAAA 57.326 33.333 9.31 9.31 34.37 1.94
4263 4608 6.673839 AAATGGGAGGATCGGTTTTTAAAA 57.326 33.333 0.00 0.00 34.37 1.52
4264 4609 6.267928 TGAAAATGGGAGGATCGGTTTTTAAA 59.732 34.615 0.00 0.00 34.37 1.52
4265 4610 5.775701 TGAAAATGGGAGGATCGGTTTTTAA 59.224 36.000 0.00 0.00 34.37 1.52
4266 4611 5.326069 TGAAAATGGGAGGATCGGTTTTTA 58.674 37.500 0.00 0.00 34.37 1.52
4267 4612 4.156477 TGAAAATGGGAGGATCGGTTTTT 58.844 39.130 0.00 0.00 34.37 1.94
4268 4613 3.763897 CTGAAAATGGGAGGATCGGTTTT 59.236 43.478 0.00 0.00 34.37 2.43
4302 4647 1.066143 ACAATCTACCCTTGTCGCCAG 60.066 52.381 0.00 0.00 31.29 4.85
4312 4657 1.501582 AGGCTCAGGACAATCTACCC 58.498 55.000 0.00 0.00 0.00 3.69
4319 4664 1.499007 AGGGAAAAAGGCTCAGGACAA 59.501 47.619 0.00 0.00 0.00 3.18
4353 4698 4.459331 CCGCAAATCCGGTGCACG 62.459 66.667 15.05 6.23 43.24 5.34
4360 4748 4.556233 TGATCTTATCTACCGCAAATCCG 58.444 43.478 0.00 0.00 0.00 4.18
4367 4755 3.495001 GGCAACTTGATCTTATCTACCGC 59.505 47.826 0.00 0.00 0.00 5.68
4409 4797 0.588252 AGCACGCTACTGCACAAAAG 59.412 50.000 0.00 0.00 39.86 2.27
4468 4858 2.742589 GTTCTAGAACAGAAAAGGGCCG 59.257 50.000 27.12 0.00 44.89 6.13
4512 4902 9.232473 TCGTCTGATATGCTATGTCTACTTTAT 57.768 33.333 0.00 0.00 0.00 1.40
4513 4903 8.617290 TCGTCTGATATGCTATGTCTACTTTA 57.383 34.615 0.00 0.00 0.00 1.85
4530 4920 4.823989 GGGAATCAATGGAATTCGTCTGAT 59.176 41.667 0.00 4.42 31.22 2.90
4553 4943 0.035439 AAGTTGGCCCACATAGGTCG 60.035 55.000 10.02 0.00 32.60 4.79
4634 5026 2.583520 GGAGAGCAGTGAGGCCTG 59.416 66.667 12.00 0.00 35.49 4.85
4635 5027 2.686835 GGGAGAGCAGTGAGGCCT 60.687 66.667 3.86 3.86 0.00 5.19
4636 5028 2.686835 AGGGAGAGCAGTGAGGCC 60.687 66.667 0.00 0.00 0.00 5.19
4637 5029 2.583520 CAGGGAGAGCAGTGAGGC 59.416 66.667 0.00 0.00 0.00 4.70
4638 5030 1.197430 AACCAGGGAGAGCAGTGAGG 61.197 60.000 0.00 0.00 0.00 3.86
4639 5031 0.036577 CAACCAGGGAGAGCAGTGAG 60.037 60.000 0.00 0.00 0.00 3.51
4640 5032 1.483595 CCAACCAGGGAGAGCAGTGA 61.484 60.000 0.00 0.00 0.00 3.41
4668 5060 6.942891 CAAACAAATTGTACCGATTTGCTTT 58.057 32.000 22.03 18.64 44.58 3.51
4684 5076 8.032451 AGTACTGTTGCAACTAAACAAACAAAT 58.968 29.630 28.61 5.21 37.10 2.32
4695 5087 5.184479 CAGTAGGGTAGTACTGTTGCAACTA 59.816 44.000 28.61 12.39 43.39 2.24
4775 5182 4.588899 TGAACCAACTGACTATGAATGGG 58.411 43.478 0.00 0.00 32.21 4.00
4813 5220 2.028112 CAGCAGTGCCTACTTTCCACTA 60.028 50.000 12.58 0.00 37.70 2.74
4843 5250 4.664150 TTCCAACAATCAGGAAAACACC 57.336 40.909 0.00 0.00 40.76 4.16


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

AutoCloner maintained by Alex Coulton.