Multiple sequence alignment - TraesCS3B01G126200

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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 TraesCS3B01G126200 chr3B 100.000 7144 0 0 1 7144 102600702 102593559 0.000000e+00 13193
1 TraesCS3B01G126200 chr3B 86.726 226 28 2 1323 1547 267284934 267284710 4.280000e-62 250
2 TraesCS3B01G126200 chr3B 76.825 315 53 10 2067 2378 721655421 721655124 7.420000e-35 159
3 TraesCS3B01G126200 chr3A 92.189 4276 193 48 35 4261 72299611 72295428 0.000000e+00 5915
4 TraesCS3B01G126200 chr3A 92.000 1325 73 22 5776 7095 72294113 72292817 0.000000e+00 1829
5 TraesCS3B01G126200 chr3A 94.161 805 28 8 4956 5745 72294907 72294107 0.000000e+00 1208
6 TraesCS3B01G126200 chr3A 93.293 492 30 3 4310 4800 72295435 72294946 0.000000e+00 723
7 TraesCS3B01G126200 chr3A 81.250 208 30 8 2164 2369 620081939 620082139 7.420000e-35 159
8 TraesCS3B01G126200 chr3D 92.748 3861 174 39 134 3956 63248536 63244744 0.000000e+00 5481
9 TraesCS3B01G126200 chr3D 93.902 2509 82 25 4308 6769 63244473 63241989 0.000000e+00 3720
10 TraesCS3B01G126200 chr3D 89.717 389 30 4 6757 7144 63241972 63241593 8.330000e-134 488
11 TraesCS3B01G126200 chr3D 85.900 461 29 15 3805 4262 63244892 63244465 6.530000e-125 459
12 TraesCS3B01G126200 chr6D 86.726 226 28 2 1323 1547 104996298 104996074 4.280000e-62 250
13 TraesCS3B01G126200 chr7D 86.364 220 28 2 1323 1541 289571319 289571537 9.260000e-59 239
14 TraesCS3B01G126200 chr7D 85.398 226 31 2 1323 1547 310370062 310369838 4.310000e-57 233
15 TraesCS3B01G126200 chr7D 84.513 226 33 2 2160 2384 471557083 471557307 9.330000e-54 222
16 TraesCS3B01G126200 chr7A 85.590 229 31 2 2160 2387 526132376 526132149 9.260000e-59 239
17 TraesCS3B01G126200 chr2D 86.364 220 28 2 1323 1541 213033049 213033267 9.260000e-59 239
18 TraesCS3B01G126200 chr1D 86.036 222 29 2 1321 1541 388065040 388064820 3.330000e-58 237
19 TraesCS3B01G126200 chr7B 85.398 226 31 2 2160 2384 495338137 495338361 4.310000e-57 233
20 TraesCS3B01G126200 chr5D 85.398 226 31 2 1323 1547 159720346 159720122 4.310000e-57 233
21 TraesCS3B01G126200 chr5D 77.632 304 51 5 2067 2369 194274634 194274347 1.230000e-37 169
22 TraesCS3B01G126200 chr5A 76.061 330 59 12 2043 2369 288734170 288734482 3.450000e-33 154


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 TraesCS3B01G126200 chr3B 102593559 102600702 7143 True 13193.00 13193 100.00000 1 7144 1 chr3B.!!$R1 7143
1 TraesCS3B01G126200 chr3A 72292817 72299611 6794 True 2418.75 5915 92.91075 35 7095 4 chr3A.!!$R1 7060
2 TraesCS3B01G126200 chr3D 63241593 63248536 6943 True 2537.00 5481 90.56675 134 7144 4 chr3D.!!$R1 7010

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
628 645 0.037590 TACAGCAAGCCGTTCCCATT 59.962 50.0 0.00 0.0 0.00 3.16 F
2010 2042 0.317603 ACACACTCGTACGTGCTCAC 60.318 55.0 16.05 0.0 38.45 3.51 F
3622 3679 0.257039 GGTGATTCCATCCTGCTGGT 59.743 55.0 9.73 0.0 37.57 4.00 F
3720 3779 0.519519 CAACGCAAGAAACCGCCATA 59.480 50.0 0.00 0.0 43.62 2.74 F
5304 5399 1.633852 GAGAGAGCTTTGGTGCTGCG 61.634 60.0 0.00 0.0 44.17 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2563 2597 0.390340 TCAAGTGCTGCATCTCGACC 60.390 55.000 5.27 0.0 0.00 4.79 R
3696 3755 0.941542 CGGTTTCTTGCGTTGGAGAA 59.058 50.000 0.00 0.0 0.00 2.87 R
5192 5287 1.542492 AAAGCTGTCATGCTGAAGGG 58.458 50.000 0.00 0.0 43.24 3.95 R
5650 5757 4.293415 ACTGTAGTAGGACAAAACGAACG 58.707 43.478 0.00 0.0 0.00 3.95 R
6364 6477 0.178973 CCTTTCCCCCAACCGTTCTT 60.179 55.000 0.00 0.0 0.00 2.52 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
28 29 0.543749 GAGGATCTGTCAGGGGTTGG 59.456 60.000 0.00 0.00 0.00 3.77
29 30 0.119155 AGGATCTGTCAGGGGTTGGA 59.881 55.000 0.00 0.00 0.00 3.53
30 31 0.991920 GGATCTGTCAGGGGTTGGAA 59.008 55.000 0.00 0.00 0.00 3.53
31 32 1.566231 GGATCTGTCAGGGGTTGGAAT 59.434 52.381 0.00 0.00 0.00 3.01
32 33 2.024941 GGATCTGTCAGGGGTTGGAATT 60.025 50.000 0.00 0.00 0.00 2.17
33 34 3.202151 GGATCTGTCAGGGGTTGGAATTA 59.798 47.826 0.00 0.00 0.00 1.40
117 123 3.493350 GGTCGTCCATGAGATTGCTATGT 60.493 47.826 0.00 0.00 0.00 2.29
118 124 4.122776 GTCGTCCATGAGATTGCTATGTT 58.877 43.478 0.00 0.00 0.00 2.71
119 125 4.210120 GTCGTCCATGAGATTGCTATGTTC 59.790 45.833 0.00 0.00 0.00 3.18
120 126 3.496130 CGTCCATGAGATTGCTATGTTCC 59.504 47.826 0.00 0.00 0.00 3.62
121 127 4.712476 GTCCATGAGATTGCTATGTTCCT 58.288 43.478 0.00 0.00 0.00 3.36
122 128 5.128919 GTCCATGAGATTGCTATGTTCCTT 58.871 41.667 0.00 0.00 0.00 3.36
123 129 6.291377 GTCCATGAGATTGCTATGTTCCTTA 58.709 40.000 0.00 0.00 0.00 2.69
124 130 6.767902 GTCCATGAGATTGCTATGTTCCTTAA 59.232 38.462 0.00 0.00 0.00 1.85
125 131 6.994496 TCCATGAGATTGCTATGTTCCTTAAG 59.006 38.462 0.00 0.00 0.00 1.85
126 132 6.994496 CCATGAGATTGCTATGTTCCTTAAGA 59.006 38.462 3.36 0.00 0.00 2.10
127 133 7.172875 CCATGAGATTGCTATGTTCCTTAAGAG 59.827 40.741 3.36 0.00 0.00 2.85
128 134 7.187824 TGAGATTGCTATGTTCCTTAAGAGT 57.812 36.000 3.36 0.00 0.00 3.24
129 135 7.044181 TGAGATTGCTATGTTCCTTAAGAGTG 58.956 38.462 3.36 0.00 0.00 3.51
130 136 6.951971 AGATTGCTATGTTCCTTAAGAGTGT 58.048 36.000 3.36 0.00 0.00 3.55
131 137 7.398024 AGATTGCTATGTTCCTTAAGAGTGTT 58.602 34.615 3.36 0.00 0.00 3.32
132 138 8.540388 AGATTGCTATGTTCCTTAAGAGTGTTA 58.460 33.333 3.36 0.00 0.00 2.41
160 166 5.975988 ATATATGAGTTGGGGTCTGTTGT 57.024 39.130 0.00 0.00 0.00 3.32
168 174 1.695242 TGGGGTCTGTTGTACGATGTT 59.305 47.619 0.00 0.00 0.00 2.71
170 176 1.463444 GGGTCTGTTGTACGATGTTGC 59.537 52.381 0.00 0.00 0.00 4.17
201 207 6.073385 CGTGAATGTTATGCTCAGCTATGATT 60.073 38.462 0.00 0.00 34.12 2.57
219 228 6.764308 ATGATTGTCAGAATGTTGGTTAGG 57.236 37.500 0.00 0.00 37.40 2.69
226 235 8.731275 TGTCAGAATGTTGGTTAGGTAATATG 57.269 34.615 0.00 0.00 37.40 1.78
235 244 7.335924 TGTTGGTTAGGTAATATGAGTTGCTTC 59.664 37.037 0.00 0.00 0.00 3.86
236 245 7.195374 TGGTTAGGTAATATGAGTTGCTTCT 57.805 36.000 0.00 0.00 0.00 2.85
285 295 1.031571 TCCGTTTGAGATGCATGGCC 61.032 55.000 2.46 0.00 0.00 5.36
305 315 0.981277 ATGCTACGGTGCTACCCCTT 60.981 55.000 3.74 0.00 33.75 3.95
312 322 0.400594 GGTGCTACCCCTTGTTGAGT 59.599 55.000 0.00 0.00 30.04 3.41
314 324 1.348036 GTGCTACCCCTTGTTGAGTCT 59.652 52.381 0.00 0.00 0.00 3.24
315 325 2.565834 GTGCTACCCCTTGTTGAGTCTA 59.434 50.000 0.00 0.00 0.00 2.59
316 326 2.832129 TGCTACCCCTTGTTGAGTCTAG 59.168 50.000 0.00 0.00 0.00 2.43
334 344 6.240145 AGTCTAGTACTATAGTTGCTAGGCC 58.760 44.000 27.26 21.44 37.55 5.19
335 345 6.044637 AGTCTAGTACTATAGTTGCTAGGCCT 59.955 42.308 27.26 22.49 37.55 5.19
336 346 7.237263 AGTCTAGTACTATAGTTGCTAGGCCTA 59.763 40.741 27.26 13.09 37.55 3.93
383 394 3.418684 TTAAGCTCGCCCTTCTCTTTT 57.581 42.857 0.00 0.00 0.00 2.27
444 455 0.603707 TCTGCAGTAACAGCTGTGGC 60.604 55.000 22.49 20.90 38.65 5.01
496 507 4.470334 TCTTCTTGCCTTTTGCTTTTGT 57.530 36.364 0.00 0.00 42.00 2.83
500 511 3.688673 TCTTGCCTTTTGCTTTTGTTTGG 59.311 39.130 0.00 0.00 42.00 3.28
552 564 9.559732 CATCTCAAGTCCCATAAAACATACATA 57.440 33.333 0.00 0.00 0.00 2.29
560 572 8.349983 GTCCCATAAAACATACATACATCAACC 58.650 37.037 0.00 0.00 0.00 3.77
577 589 7.458397 ACATCAACCCTAAACATCTTACTGAA 58.542 34.615 0.00 0.00 0.00 3.02
579 591 7.311092 TCAACCCTAAACATCTTACTGAAGA 57.689 36.000 0.00 0.00 45.75 2.87
597 609 2.274437 AGATGCTTATGTGCACTGTCG 58.726 47.619 19.41 5.46 46.33 4.35
599 611 1.147473 TGCTTATGTGCACTGTCGTG 58.853 50.000 19.41 4.74 44.07 4.35
615 632 1.206849 TCGTGCCATCATCTTACAGCA 59.793 47.619 0.00 0.00 0.00 4.41
628 645 0.037590 TACAGCAAGCCGTTCCCATT 59.962 50.000 0.00 0.00 0.00 3.16
635 653 3.616821 GCAAGCCGTTCCCATTAAAAATC 59.383 43.478 0.00 0.00 0.00 2.17
669 687 3.873910 TCTTACAGCCAGATTAACCTGC 58.126 45.455 0.00 0.00 32.97 4.85
723 749 3.587498 TGGGTGAGAGAGGAAGAAAAGA 58.413 45.455 0.00 0.00 0.00 2.52
795 821 2.253513 GCTTGAGTTAAAGCGGCCA 58.746 52.632 2.24 0.00 42.86 5.36
889 916 2.760385 CCCTCCCCCTCACTCGTC 60.760 72.222 0.00 0.00 0.00 4.20
1006 1033 3.223661 GATCTCATCGGCATGGTCC 57.776 57.895 0.00 0.00 0.00 4.46
1360 1392 1.888512 TCAACTGCAAGAAGGATTGGC 59.111 47.619 0.00 0.00 37.43 4.52
1386 1418 4.157607 CCGGCTGGTGTCAAGTTT 57.842 55.556 2.29 0.00 0.00 2.66
1465 1497 2.173569 TCGAGATCTCACCCTCTCATCA 59.826 50.000 22.31 0.00 38.22 3.07
1562 1594 3.491342 TGTTCGAGATGGCTAGCTAGAT 58.509 45.455 25.15 9.82 0.00 1.98
1627 1659 5.879237 TGTATATTCCTTGCTTTTCTTGCG 58.121 37.500 0.00 0.00 0.00 4.85
1658 1690 1.002069 TGCTTTCCATGGGGTGATCT 58.998 50.000 13.02 0.00 34.93 2.75
1678 1710 9.896645 GTGATCTGTATATCATATGTTGGGATT 57.103 33.333 1.90 0.00 38.13 3.01
1917 1949 6.894339 TCTGAAGTTTCCAAATAGGTTTCC 57.106 37.500 0.00 0.00 39.02 3.13
2010 2042 0.317603 ACACACTCGTACGTGCTCAC 60.318 55.000 16.05 0.00 38.45 3.51
2050 2084 1.834188 TCTCGTCATGAGCAGGTGTA 58.166 50.000 0.00 0.00 44.86 2.90
2062 2096 1.448985 CAGGTGTAACAATGGACGGG 58.551 55.000 0.00 0.00 39.98 5.28
2065 2099 0.802494 GTGTAACAATGGACGGGCTG 59.198 55.000 0.00 0.00 36.32 4.85
2137 2171 1.141019 GCGGCGGAAGATACAGACA 59.859 57.895 9.78 0.00 0.00 3.41
2236 2270 1.885049 AGGGCTGCAAGAAGATCCTA 58.115 50.000 0.50 0.00 34.07 2.94
2275 2309 4.947147 AAGCACCGCAAGCCCGAA 62.947 61.111 0.00 0.00 0.00 4.30
2278 2312 2.255252 CACCGCAAGCCCGAAAAG 59.745 61.111 0.00 0.00 0.00 2.27
2347 2381 3.827898 GAGGGGGAGCTCGTCGTG 61.828 72.222 7.83 0.00 0.00 4.35
2674 2708 3.058639 TCGTCTCTGCATCTCGACATATG 60.059 47.826 0.00 0.00 0.00 1.78
2683 2717 1.208535 TCTCGACATATGGCCGGTTTT 59.791 47.619 16.23 0.00 0.00 2.43
2694 2728 5.568620 ATGGCCGGTTTTCTTAGATCTAT 57.431 39.130 1.90 0.00 0.00 1.98
2701 2735 9.007901 GCCGGTTTTCTTAGATCTATACTACTA 57.992 37.037 1.90 0.00 0.00 1.82
2772 2806 3.428870 AGATCACGCGAAAGTACAGTTTG 59.571 43.478 15.93 0.00 0.00 2.93
2773 2807 1.259507 TCACGCGAAAGTACAGTTTGC 59.740 47.619 15.93 10.20 0.00 3.68
2774 2808 1.260561 CACGCGAAAGTACAGTTTGCT 59.739 47.619 15.93 4.73 0.00 3.91
2826 2866 1.084370 ATGCCGCTACAGTTTCGAGC 61.084 55.000 0.00 0.00 0.00 5.03
2832 2872 1.135460 GCTACAGTTTCGAGCTACGGT 60.135 52.381 5.87 1.28 42.82 4.83
2858 2900 5.661056 AGTAGATCGATGGTTTCTGTTCA 57.339 39.130 0.54 0.00 0.00 3.18
3080 3129 0.381801 ACTCAAACTGCAAGCAACGG 59.618 50.000 0.00 0.00 37.60 4.44
3119 3168 0.310854 CCCACCGTGAAAGCAAGAAC 59.689 55.000 0.00 0.00 0.00 3.01
3282 3331 7.676683 AAAGGAGACTAGCCATGTAGATTTA 57.323 36.000 0.00 0.00 42.68 1.40
3283 3332 7.676683 AAGGAGACTAGCCATGTAGATTTAA 57.323 36.000 0.00 0.00 42.68 1.52
3284 3333 7.676683 AGGAGACTAGCCATGTAGATTTAAA 57.323 36.000 0.00 0.00 40.61 1.52
3495 3552 4.007644 CTGGTCAGCAGGCCGACA 62.008 66.667 9.60 0.00 33.66 4.35
3543 3600 1.217001 CGTTGCAGCACACTTCTGTA 58.783 50.000 0.00 0.00 34.21 2.74
3594 3651 2.955660 AGCAATTTTTCTCCACCACGAA 59.044 40.909 0.00 0.00 0.00 3.85
3619 3676 1.588239 TCAGGTGATTCCATCCTGCT 58.412 50.000 12.04 0.00 45.67 4.24
3620 3677 1.211212 TCAGGTGATTCCATCCTGCTG 59.789 52.381 12.04 0.00 45.67 4.41
3621 3678 0.549950 AGGTGATTCCATCCTGCTGG 59.450 55.000 2.58 2.58 39.02 4.85
3622 3679 0.257039 GGTGATTCCATCCTGCTGGT 59.743 55.000 9.73 0.00 37.57 4.00
3623 3680 1.341383 GGTGATTCCATCCTGCTGGTT 60.341 52.381 9.73 0.00 37.57 3.67
3624 3681 2.450476 GTGATTCCATCCTGCTGGTTT 58.550 47.619 9.73 0.00 37.57 3.27
3625 3682 2.165030 GTGATTCCATCCTGCTGGTTTG 59.835 50.000 9.73 8.63 37.57 2.93
3626 3683 2.225091 TGATTCCATCCTGCTGGTTTGT 60.225 45.455 9.73 0.00 37.57 2.83
3627 3684 2.380064 TTCCATCCTGCTGGTTTGTT 57.620 45.000 9.73 0.00 37.57 2.83
3628 3685 2.380064 TCCATCCTGCTGGTTTGTTT 57.620 45.000 9.73 0.00 37.57 2.83
3629 3686 2.676748 TCCATCCTGCTGGTTTGTTTT 58.323 42.857 9.73 0.00 37.57 2.43
3630 3687 2.627699 TCCATCCTGCTGGTTTGTTTTC 59.372 45.455 9.73 0.00 37.57 2.29
3631 3688 2.629617 CCATCCTGCTGGTTTGTTTTCT 59.370 45.455 9.73 0.00 34.23 2.52
3632 3689 3.553508 CCATCCTGCTGGTTTGTTTTCTG 60.554 47.826 9.73 0.00 34.23 3.02
3633 3690 2.031120 TCCTGCTGGTTTGTTTTCTGG 58.969 47.619 9.73 0.00 34.23 3.86
3634 3691 1.538849 CCTGCTGGTTTGTTTTCTGGC 60.539 52.381 0.51 0.00 0.00 4.85
3635 3692 1.410153 CTGCTGGTTTGTTTTCTGGCT 59.590 47.619 0.00 0.00 0.00 4.75
3636 3693 2.622942 CTGCTGGTTTGTTTTCTGGCTA 59.377 45.455 0.00 0.00 0.00 3.93
3661 3718 4.697352 AGCTTGTACACATTCATCTGGAAC 59.303 41.667 0.00 0.00 38.60 3.62
3675 3734 5.711506 TCATCTGGAACATATGTTGCTTGTT 59.288 36.000 31.84 19.76 45.06 2.83
3695 3754 8.721478 GCTTGTTTATATTCTTGAGTGACTGAA 58.279 33.333 0.00 0.00 0.00 3.02
3704 3763 5.300752 TCTTGAGTGACTGAATTCTCCAAC 58.699 41.667 7.05 0.87 0.00 3.77
3710 3769 3.067106 GACTGAATTCTCCAACGCAAGA 58.933 45.455 7.05 0.00 43.62 3.02
3711 3770 3.476552 ACTGAATTCTCCAACGCAAGAA 58.523 40.909 7.05 0.00 43.62 2.52
3712 3771 3.882888 ACTGAATTCTCCAACGCAAGAAA 59.117 39.130 7.05 0.00 43.62 2.52
3713 3772 4.222114 CTGAATTCTCCAACGCAAGAAAC 58.778 43.478 7.05 0.00 43.62 2.78
3715 3774 0.941542 TTCTCCAACGCAAGAAACCG 59.058 50.000 0.00 0.00 43.62 4.44
3716 3775 1.082104 CTCCAACGCAAGAAACCGC 60.082 57.895 0.00 0.00 43.62 5.68
3718 3777 2.718731 CAACGCAAGAAACCGCCA 59.281 55.556 0.00 0.00 43.62 5.69
3719 3778 1.285641 CAACGCAAGAAACCGCCAT 59.714 52.632 0.00 0.00 43.62 4.40
3720 3779 0.519519 CAACGCAAGAAACCGCCATA 59.480 50.000 0.00 0.00 43.62 2.74
3722 3781 2.319136 ACGCAAGAAACCGCCATATA 57.681 45.000 0.00 0.00 43.62 0.86
3741 3800 7.692291 GCCATATATATGAACGCATGTGTTTAC 59.308 37.037 24.53 13.92 35.75 2.01
3836 3895 9.081204 TGTCTACATAAACTTAGACACTTACCA 57.919 33.333 7.25 0.00 45.96 3.25
3867 3926 8.795786 TGCTAACAACTGAAAAACACATATTC 57.204 30.769 0.00 0.00 0.00 1.75
3871 3930 6.668323 ACAACTGAAAAACACATATTCTCCG 58.332 36.000 0.00 0.00 0.00 4.63
3872 3931 6.262273 ACAACTGAAAAACACATATTCTCCGT 59.738 34.615 0.00 0.00 0.00 4.69
3878 3937 6.834168 AAAACACATATTCTCCGTCCAATT 57.166 33.333 0.00 0.00 0.00 2.32
3886 3945 7.993183 ACATATTCTCCGTCCAATTTAACATCT 59.007 33.333 0.00 0.00 0.00 2.90
3887 3946 6.927294 ATTCTCCGTCCAATTTAACATCTC 57.073 37.500 0.00 0.00 0.00 2.75
3911 3970 9.395707 CTCTTTTCTTTCTCAAGATTTCACATG 57.604 33.333 0.00 0.00 38.89 3.21
3921 3980 9.897744 TCTCAAGATTTCACATGAATTTTGTAC 57.102 29.630 0.00 0.00 33.54 2.90
3938 3997 5.957771 TTGTACTGGGATTCTCAAGCTAT 57.042 39.130 0.00 0.00 0.00 2.97
3942 4001 5.184892 ACTGGGATTCTCAAGCTATGTTT 57.815 39.130 0.00 0.00 0.00 2.83
4012 4071 6.952773 TTAACTCCACTTACAAAAGCACAT 57.047 33.333 0.00 0.00 36.05 3.21
4027 4086 9.630098 ACAAAAGCACATCTAAAATGTCATAAG 57.370 29.630 0.00 0.00 0.00 1.73
4056 4115 6.819146 TCCTTTCGTTTTGCATTTAAAAGGTT 59.181 30.769 19.27 0.00 41.18 3.50
4098 4157 8.257306 ACAAATAAACCAGCCTATGTAAAATGG 58.743 33.333 0.00 0.00 0.00 3.16
4149 4209 9.903682 ATTGTTTCATAGAATTTCTGAACACAG 57.096 29.630 9.22 0.00 29.93 3.66
4150 4210 7.874940 TGTTTCATAGAATTTCTGAACACAGG 58.125 34.615 9.22 0.00 33.04 4.00
4165 4225 6.684686 TGAACACAGGCGGTTACTATATATC 58.315 40.000 0.00 0.00 0.00 1.63
4208 4270 7.601856 CACACATATGTTCCACCAACTTTATT 58.398 34.615 5.37 0.00 36.72 1.40
4529 4591 6.563422 TGTTAATGCAATACCAGCTCATTTC 58.437 36.000 0.00 0.00 0.00 2.17
4536 4599 7.839907 TGCAATACCAGCTCATTTCTTTATTT 58.160 30.769 0.00 0.00 0.00 1.40
4537 4600 8.965819 TGCAATACCAGCTCATTTCTTTATTTA 58.034 29.630 0.00 0.00 0.00 1.40
4645 4709 8.546244 ACTAAAAGAACGCTTTAGTTACTGTTC 58.454 33.333 0.00 0.00 43.32 3.18
4684 4748 3.304026 CACAGAACATGCAACAACAACAC 59.696 43.478 0.00 0.00 0.00 3.32
4804 4868 5.453567 ACTTGTATTTGTTTTGCCTCCTC 57.546 39.130 0.00 0.00 0.00 3.71
4820 4884 2.673368 CTCCTCTGCGTGTATGAAAACC 59.327 50.000 0.00 0.00 0.00 3.27
4898 4987 7.802117 TCTTATAATGGAAATCGAAGAGGGTT 58.198 34.615 0.00 0.00 43.63 4.11
5001 5092 7.492344 GCATGGTTTAAGCTAAGCACATTAATT 59.508 33.333 3.33 0.00 38.23 1.40
5046 5137 8.737175 CCTCAATTGGTTATCTTGATCCATATG 58.263 37.037 5.42 0.00 0.00 1.78
5304 5399 1.633852 GAGAGAGCTTTGGTGCTGCG 61.634 60.000 0.00 0.00 44.17 5.18
5448 5543 2.154462 ACTTTCCTGCTTTCATCACCG 58.846 47.619 0.00 0.00 0.00 4.94
5505 5600 4.697756 TCGCCCGGCCTTCTTGTG 62.698 66.667 3.10 0.00 0.00 3.33
5540 5647 8.779354 AGAGTTGTTTACCATTATCTCTTGTC 57.221 34.615 0.00 0.00 0.00 3.18
5650 5757 5.407387 GCATGGCATTTGTTATCATTGATCC 59.593 40.000 1.55 0.00 0.00 3.36
5772 5882 4.043100 GCCCCCACCACCACTACC 62.043 72.222 0.00 0.00 0.00 3.18
5871 5982 7.730364 TGTATCTTTTCTCACTTGAACCTTC 57.270 36.000 0.00 0.00 0.00 3.46
5894 6005 5.877012 TCATGTCTTCTGGAGCTTAAATGTC 59.123 40.000 0.00 0.00 0.00 3.06
5921 6032 7.559335 TGCTAGACAGTTGGATCCATATATT 57.441 36.000 17.06 2.94 0.00 1.28
5976 6088 2.436911 ACATGCATGTATCCTGCTCTCA 59.563 45.455 30.50 0.00 39.68 3.27
5985 6097 4.467438 TGTATCCTGCTCTCATTCAAGTGA 59.533 41.667 0.00 0.00 0.00 3.41
5986 6098 4.564782 ATCCTGCTCTCATTCAAGTGAA 57.435 40.909 0.00 0.00 38.56 3.18
6026 6138 0.675633 AATGTTGCACTTCACTGGGC 59.324 50.000 0.00 0.00 0.00 5.36
6047 6160 4.112634 GCTGTTCCTTTTTGACCACTTTC 58.887 43.478 0.00 0.00 0.00 2.62
6235 6348 3.507411 TCTCCCTCCTTGAATATACGGG 58.493 50.000 0.00 0.00 0.00 5.28
6241 6354 2.035449 TCCTTGAATATACGGGACTGCG 59.965 50.000 0.00 0.00 0.00 5.18
6354 6467 2.031120 CTTTGCAAAGGTGTTGAGGGA 58.969 47.619 28.12 0.00 32.40 4.20
6364 6477 2.372172 GGTGTTGAGGGAAAAGAGGAGA 59.628 50.000 0.00 0.00 0.00 3.71
6378 6492 1.002502 GGAGAAGAACGGTTGGGGG 60.003 63.158 0.00 0.00 0.00 5.40
6381 6495 0.848053 AGAAGAACGGTTGGGGGAAA 59.152 50.000 0.00 0.00 0.00 3.13
6383 6497 0.178973 AAGAACGGTTGGGGGAAAGG 60.179 55.000 0.00 0.00 0.00 3.11
6384 6498 1.152138 GAACGGTTGGGGGAAAGGT 59.848 57.895 0.00 0.00 0.00 3.50
6439 6553 6.662414 TCGAAGCATAACTAATGAACCTTG 57.338 37.500 0.00 0.00 37.86 3.61
6467 6581 8.623903 TCCAAGTTTGATTATAAGCACATCATC 58.376 33.333 2.18 0.00 0.00 2.92
6480 6594 3.554524 CACATCATCGTTTGTCACAACC 58.445 45.455 0.00 0.00 0.00 3.77
6548 6663 8.709386 TGTTTGCATGTACATTAACTTTGTTT 57.291 26.923 5.37 0.00 0.00 2.83
6566 6681 6.385649 TTGTTTTTCCGCTTAGTTTGAGAT 57.614 33.333 0.00 0.00 0.00 2.75
6591 6706 5.732247 GCCTTCTTTTTCTTTTAGTGACGCA 60.732 40.000 0.00 0.00 0.00 5.24
6647 6762 8.217131 ACTTTACTTTGTAACGAGTTGGATTT 57.783 30.769 0.00 0.00 0.00 2.17
6714 6831 5.956068 TTGTTTATGCTGACTTATGCACA 57.044 34.783 0.00 0.00 42.26 4.57
6716 6833 6.324561 TGTTTATGCTGACTTATGCACAAA 57.675 33.333 0.00 0.00 42.26 2.83
6717 6834 6.923012 TGTTTATGCTGACTTATGCACAAAT 58.077 32.000 0.00 0.00 37.78 2.32
6719 6836 8.518702 TGTTTATGCTGACTTATGCACAAATAA 58.481 29.630 0.00 0.00 37.78 1.40
6722 6839 7.997107 ATGCTGACTTATGCACAAATAAATG 57.003 32.000 0.00 0.00 42.26 2.32
6724 6841 7.377398 TGCTGACTTATGCACAAATAAATGTT 58.623 30.769 0.00 0.00 33.94 2.71
6725 6842 7.328982 TGCTGACTTATGCACAAATAAATGTTG 59.671 33.333 0.00 0.00 33.94 3.33
6726 6843 7.541783 GCTGACTTATGCACAAATAAATGTTGA 59.458 33.333 0.00 0.00 0.00 3.18
6727 6844 9.409312 CTGACTTATGCACAAATAAATGTTGAA 57.591 29.630 0.00 0.00 0.00 2.69
6728 6845 9.755804 TGACTTATGCACAAATAAATGTTGAAA 57.244 25.926 0.00 0.00 0.00 2.69
6755 6872 8.232913 TCCTTTATTTTATTTTAGCGCTCCAT 57.767 30.769 16.34 7.21 0.00 3.41
6820 6967 8.342634 GCTAATTTGTTGTGAACTGAACTCTAA 58.657 33.333 0.00 0.00 0.00 2.10
6869 7016 4.351192 CATATCCGCAAAAGGCTGTTAAC 58.649 43.478 0.00 0.00 41.67 2.01
6899 7046 6.539649 TTAGTATTGCATGTTAGATTCGGC 57.460 37.500 0.00 0.00 0.00 5.54
6902 7049 4.717233 ATTGCATGTTAGATTCGGCAAA 57.283 36.364 0.00 0.00 43.44 3.68
6916 7063 7.264947 AGATTCGGCAAAACAATAATTTAGGG 58.735 34.615 0.00 0.00 0.00 3.53
6936 7083 5.960704 AGGGTTGGTCAAAAGGTATTTAGT 58.039 37.500 0.00 0.00 0.00 2.24
6939 7086 6.452242 GGTTGGTCAAAAGGTATTTAGTTGG 58.548 40.000 0.00 0.00 0.00 3.77
7063 7211 4.100373 TCCCATAACCCCATTCAAAAAGG 58.900 43.478 0.00 0.00 0.00 3.11
7104 7252 3.561725 ACTAACACTGCTTTGCTCTGTTC 59.438 43.478 8.07 0.00 33.44 3.18
7113 7261 6.370166 ACTGCTTTGCTCTGTTCTAATCTAAC 59.630 38.462 0.00 0.00 0.00 2.34
7118 7266 9.515020 CTTTGCTCTGTTCTAATCTAACTAGAG 57.485 37.037 0.00 0.00 36.39 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.005684 CCTGACAGATCCTCTATCACTGC 59.994 52.174 3.32 0.00 37.03 4.40
1 2 3.573538 CCCTGACAGATCCTCTATCACTG 59.426 52.174 3.32 0.00 37.03 3.66
2 3 3.437784 CCCCTGACAGATCCTCTATCACT 60.438 52.174 3.32 0.00 37.03 3.41
3 4 2.896685 CCCCTGACAGATCCTCTATCAC 59.103 54.545 3.32 0.00 37.03 3.06
4 5 2.520120 ACCCCTGACAGATCCTCTATCA 59.480 50.000 3.32 0.00 37.03 2.15
5 6 3.252554 ACCCCTGACAGATCCTCTATC 57.747 52.381 3.32 0.00 34.52 2.08
6 7 3.312890 CAACCCCTGACAGATCCTCTAT 58.687 50.000 3.32 0.00 0.00 1.98
7 8 2.626950 CCAACCCCTGACAGATCCTCTA 60.627 54.545 3.32 0.00 0.00 2.43
8 9 1.577736 CAACCCCTGACAGATCCTCT 58.422 55.000 3.32 0.00 0.00 3.69
9 10 0.543749 CCAACCCCTGACAGATCCTC 59.456 60.000 3.32 0.00 0.00 3.71
10 11 0.119155 TCCAACCCCTGACAGATCCT 59.881 55.000 3.32 0.00 0.00 3.24
11 12 0.991920 TTCCAACCCCTGACAGATCC 59.008 55.000 3.32 0.00 0.00 3.36
12 13 3.372440 AATTCCAACCCCTGACAGATC 57.628 47.619 3.32 0.00 0.00 2.75
13 14 4.478317 TGATAATTCCAACCCCTGACAGAT 59.522 41.667 3.32 0.00 0.00 2.90
14 15 3.849574 TGATAATTCCAACCCCTGACAGA 59.150 43.478 3.32 0.00 0.00 3.41
15 16 4.235079 TGATAATTCCAACCCCTGACAG 57.765 45.455 0.00 0.00 0.00 3.51
16 17 4.666412 TTGATAATTCCAACCCCTGACA 57.334 40.909 0.00 0.00 0.00 3.58
17 18 5.993748 TTTTGATAATTCCAACCCCTGAC 57.006 39.130 0.00 0.00 0.00 3.51
18 19 6.259893 TGATTTTGATAATTCCAACCCCTGA 58.740 36.000 0.00 0.00 0.00 3.86
19 20 6.155049 ACTGATTTTGATAATTCCAACCCCTG 59.845 38.462 0.00 0.00 0.00 4.45
20 21 6.263754 ACTGATTTTGATAATTCCAACCCCT 58.736 36.000 0.00 0.00 0.00 4.79
21 22 6.544928 ACTGATTTTGATAATTCCAACCCC 57.455 37.500 0.00 0.00 0.00 4.95
22 23 7.559897 TCCTACTGATTTTGATAATTCCAACCC 59.440 37.037 0.00 0.00 0.00 4.11
23 24 8.519799 TCCTACTGATTTTGATAATTCCAACC 57.480 34.615 0.00 0.00 0.00 3.77
26 27 9.699410 ACATTCCTACTGATTTTGATAATTCCA 57.301 29.630 0.00 0.00 0.00 3.53
70 76 8.539544 CCCCATTAAACATTCCTAGTGATTTTT 58.460 33.333 0.00 0.00 0.00 1.94
78 84 4.777463 ACGACCCCATTAAACATTCCTAG 58.223 43.478 0.00 0.00 0.00 3.02
87 93 2.841266 TCTCATGGACGACCCCATTAAA 59.159 45.455 0.34 0.00 44.11 1.52
150 156 1.463444 GCAACATCGTACAACAGACCC 59.537 52.381 0.00 0.00 0.00 4.46
154 160 2.413112 CAGGAGCAACATCGTACAACAG 59.587 50.000 0.00 0.00 0.00 3.16
160 166 0.735978 CACGCAGGAGCAACATCGTA 60.736 55.000 0.00 0.00 42.27 3.43
168 174 2.009051 CATAACATTCACGCAGGAGCA 58.991 47.619 0.00 0.00 42.27 4.26
170 176 2.283298 AGCATAACATTCACGCAGGAG 58.717 47.619 0.00 0.00 0.00 3.69
201 207 8.544622 TCATATTACCTAACCAACATTCTGACA 58.455 33.333 0.00 0.00 0.00 3.58
255 265 5.743872 GCATCTCAAACGGAAACATAATTCC 59.256 40.000 0.00 0.00 44.50 3.01
285 295 1.227556 GGGGTAGCACCGTAGCATG 60.228 63.158 0.00 0.00 39.83 4.06
290 300 0.322322 CAACAAGGGGTAGCACCGTA 59.678 55.000 0.00 0.00 39.83 4.02
292 302 0.673644 CTCAACAAGGGGTAGCACCG 60.674 60.000 0.00 0.00 39.83 4.94
293 303 0.400594 ACTCAACAAGGGGTAGCACC 59.599 55.000 0.00 0.00 37.60 5.01
294 304 1.348036 AGACTCAACAAGGGGTAGCAC 59.652 52.381 0.00 0.00 0.00 4.40
305 315 9.327628 CTAGCAACTATAGTACTAGACTCAACA 57.672 37.037 25.24 4.14 39.81 3.33
312 322 6.451292 AGGCCTAGCAACTATAGTACTAGA 57.549 41.667 28.36 2.62 37.23 2.43
314 324 8.492782 CCTATAGGCCTAGCAACTATAGTACTA 58.507 40.741 19.33 4.77 42.28 1.82
315 325 7.036717 ACCTATAGGCCTAGCAACTATAGTACT 60.037 40.741 19.33 9.46 42.28 2.73
316 326 7.118060 ACCTATAGGCCTAGCAACTATAGTAC 58.882 42.308 19.33 1.66 42.28 2.73
334 344 4.641094 CCTACGAATGGAGGCTACCTATAG 59.359 50.000 0.00 0.00 31.76 1.31
335 345 4.569228 CCCTACGAATGGAGGCTACCTATA 60.569 50.000 0.00 0.00 31.76 1.31
336 346 3.432378 CCTACGAATGGAGGCTACCTAT 58.568 50.000 0.00 0.00 31.76 2.57
383 394 3.266636 TCACTCACACGCAGAAAGAAAA 58.733 40.909 0.00 0.00 0.00 2.29
388 399 1.570813 CACTCACTCACACGCAGAAA 58.429 50.000 0.00 0.00 0.00 2.52
451 462 3.039588 GTACCGCCACACCACACG 61.040 66.667 0.00 0.00 0.00 4.49
455 466 3.551407 TGCTGTACCGCCACACCA 61.551 61.111 6.82 0.00 0.00 4.17
500 511 7.415229 GTTAGCATATAAGCTGGTGGTAAAAC 58.585 38.462 12.62 2.97 46.11 2.43
517 528 4.037222 TGGGACTTGAGATGGTTAGCATA 58.963 43.478 0.00 0.00 0.00 3.14
518 529 2.846206 TGGGACTTGAGATGGTTAGCAT 59.154 45.455 0.00 0.00 0.00 3.79
552 564 7.016153 TCAGTAAGATGTTTAGGGTTGATGT 57.984 36.000 0.00 0.00 0.00 3.06
597 609 2.223433 GCTTGCTGTAAGATGATGGCAC 60.223 50.000 9.78 0.00 38.76 5.01
599 611 1.336125 GGCTTGCTGTAAGATGATGGC 59.664 52.381 9.78 0.00 38.76 4.40
600 612 1.600957 CGGCTTGCTGTAAGATGATGG 59.399 52.381 9.78 0.00 38.76 3.51
607 624 0.605319 TGGGAACGGCTTGCTGTAAG 60.605 55.000 7.56 0.75 39.49 2.34
615 632 4.526650 ACTGATTTTTAATGGGAACGGCTT 59.473 37.500 0.00 0.00 0.00 4.35
635 653 7.492524 TCTGGCTGTAAGATTAACTATCACTG 58.507 38.462 0.00 0.00 35.59 3.66
795 821 2.240921 GGAGAGAGGGCAGAATTTCCTT 59.759 50.000 0.00 0.00 0.00 3.36
889 916 1.691196 AGGAAGGAGATCGAGAGCAG 58.309 55.000 0.00 0.00 0.00 4.24
1006 1033 0.371645 GCAGAATTCAGAACGCGAGG 59.628 55.000 15.93 0.00 0.00 4.63
1077 1108 3.611674 TCTCCTGGTTCACGCGCA 61.612 61.111 5.73 0.00 0.00 6.09
1323 1355 5.393027 GCAGTTGACATCGGTTAATTCCATT 60.393 40.000 0.00 0.00 0.00 3.16
1377 1409 1.341852 TCCGTCGGATCAAACTTGACA 59.658 47.619 10.71 0.00 40.49 3.58
1386 1418 1.753078 CTCCTGGTCCGTCGGATCA 60.753 63.158 25.32 25.32 40.99 2.92
1465 1497 6.463897 CCGTCTATGGTGGGTATAAACTCATT 60.464 42.308 0.00 0.00 38.69 2.57
1562 1594 5.869649 TCTGTTCATGGCTAGCATAGTTA 57.130 39.130 18.24 0.00 41.93 2.24
1627 1659 4.925646 CCATGGAAAGCAAAGCTAAAGTTC 59.074 41.667 5.56 0.00 38.25 3.01
1678 1710 9.051679 CCCTCACAATTTATGACGAAATACATA 57.948 33.333 0.00 0.00 0.00 2.29
1917 1949 5.501156 AGAAGGCATGTAAAAGGTAGGAAG 58.499 41.667 0.00 0.00 0.00 3.46
2010 2042 6.303970 CGAGATGCAAAAATTAACAGTCAGTG 59.696 38.462 0.00 0.00 0.00 3.66
2050 2084 1.675641 GCTCAGCCCGTCCATTGTT 60.676 57.895 0.00 0.00 0.00 2.83
2065 2099 2.793933 GCGATGGAAGAAATGCTTGCTC 60.794 50.000 0.00 0.00 44.44 4.26
2125 2159 3.766676 TCGCACTCTGTCTGTATCTTC 57.233 47.619 0.00 0.00 0.00 2.87
2236 2270 1.000955 CCGAAGTTGGTGTAGAGCACT 59.999 52.381 0.00 0.00 46.86 4.40
2347 2381 3.182967 CGTCTGGTAGAAGATCTTGCAC 58.817 50.000 14.00 9.88 0.00 4.57
2527 2561 4.487412 CCAGCCGGGTACGACGTC 62.487 72.222 5.47 5.18 44.60 4.34
2563 2597 0.390340 TCAAGTGCTGCATCTCGACC 60.390 55.000 5.27 0.00 0.00 4.79
2674 2708 6.099159 AGTATAGATCTAAGAAAACCGGCC 57.901 41.667 6.52 0.00 0.00 6.13
2694 2728 9.080915 CGTTAGCTATGTCGACATATAGTAGTA 57.919 37.037 32.46 14.57 38.09 1.82
2773 2807 1.686325 ATGGGAATGGTCGGACCGAG 61.686 60.000 18.98 0.00 42.58 4.63
2774 2808 1.687840 ATGGGAATGGTCGGACCGA 60.688 57.895 21.52 13.88 42.58 4.69
2826 2866 6.981762 ACCATCGATCTACTATAACCGTAG 57.018 41.667 0.00 0.00 36.53 3.51
2832 2872 8.909923 TGAACAGAAACCATCGATCTACTATAA 58.090 33.333 0.00 0.00 0.00 0.98
3080 3129 3.532542 GGTGTGGATGGTTTCTAGCTAC 58.467 50.000 0.00 0.00 0.00 3.58
3119 3168 3.441496 TGAAAAGAAACTTGCTGGCAG 57.559 42.857 10.94 10.94 0.00 4.85
3234 3283 2.621338 TCTCACTCATCAATTCGTGCC 58.379 47.619 0.00 0.00 0.00 5.01
3495 3552 2.269940 ACTGTAGCTGAGATGGGGTTT 58.730 47.619 0.00 0.00 0.00 3.27
3543 3600 1.283347 ACTGATCATGGTCCAGCACT 58.717 50.000 2.86 0.00 0.00 4.40
3619 3676 4.662278 AGCTATAGCCAGAAAACAAACCA 58.338 39.130 21.17 0.00 43.38 3.67
3620 3677 5.048013 ACAAGCTATAGCCAGAAAACAAACC 60.048 40.000 21.17 0.00 43.38 3.27
3621 3678 6.013842 ACAAGCTATAGCCAGAAAACAAAC 57.986 37.500 21.17 0.00 43.38 2.93
3622 3679 6.712998 TGTACAAGCTATAGCCAGAAAACAAA 59.287 34.615 21.17 0.00 43.38 2.83
3623 3680 6.148811 GTGTACAAGCTATAGCCAGAAAACAA 59.851 38.462 21.17 0.00 43.38 2.83
3624 3681 5.642063 GTGTACAAGCTATAGCCAGAAAACA 59.358 40.000 21.17 14.41 43.38 2.83
3625 3682 5.642063 TGTGTACAAGCTATAGCCAGAAAAC 59.358 40.000 21.17 13.31 43.38 2.43
3626 3683 5.800296 TGTGTACAAGCTATAGCCAGAAAA 58.200 37.500 21.17 0.96 43.38 2.29
3627 3684 5.414789 TGTGTACAAGCTATAGCCAGAAA 57.585 39.130 21.17 5.61 43.38 2.52
3628 3685 5.614324 ATGTGTACAAGCTATAGCCAGAA 57.386 39.130 21.17 2.29 43.38 3.02
3629 3686 5.128663 TGAATGTGTACAAGCTATAGCCAGA 59.871 40.000 21.17 10.30 43.38 3.86
3630 3687 5.359756 TGAATGTGTACAAGCTATAGCCAG 58.640 41.667 21.17 15.72 43.38 4.85
3631 3688 5.351948 TGAATGTGTACAAGCTATAGCCA 57.648 39.130 21.17 10.29 43.38 4.75
3632 3689 6.146837 CAGATGAATGTGTACAAGCTATAGCC 59.853 42.308 21.17 6.06 43.38 3.93
3633 3690 6.146837 CCAGATGAATGTGTACAAGCTATAGC 59.853 42.308 17.33 17.33 42.49 2.97
3634 3691 7.436933 TCCAGATGAATGTGTACAAGCTATAG 58.563 38.462 0.00 0.00 0.00 1.31
3635 3692 7.360113 TCCAGATGAATGTGTACAAGCTATA 57.640 36.000 0.00 0.00 0.00 1.31
3636 3693 6.239217 TCCAGATGAATGTGTACAAGCTAT 57.761 37.500 0.00 0.00 0.00 2.97
3675 3734 9.823647 GGAGAATTCAGTCACTCAAGAATATAA 57.176 33.333 8.44 0.00 31.01 0.98
3689 3748 3.067106 TCTTGCGTTGGAGAATTCAGTC 58.933 45.455 8.44 0.00 0.00 3.51
3695 3754 1.535462 CGGTTTCTTGCGTTGGAGAAT 59.465 47.619 0.00 0.00 32.40 2.40
3696 3755 0.941542 CGGTTTCTTGCGTTGGAGAA 59.058 50.000 0.00 0.00 0.00 2.87
3704 3763 4.629634 TCATATATATGGCGGTTTCTTGCG 59.370 41.667 20.18 0.00 34.50 4.85
3710 3769 4.320023 TGCGTTCATATATATGGCGGTTT 58.680 39.130 26.32 0.00 35.10 3.27
3711 3770 3.932822 TGCGTTCATATATATGGCGGTT 58.067 40.909 26.32 0.00 35.10 4.44
3712 3771 3.603158 TGCGTTCATATATATGGCGGT 57.397 42.857 26.32 0.00 35.10 5.68
3713 3772 3.871006 ACATGCGTTCATATATATGGCGG 59.129 43.478 26.32 18.41 35.10 6.13
3715 3774 5.801350 ACACATGCGTTCATATATATGGC 57.199 39.130 20.18 16.18 34.50 4.40
3716 3775 8.935844 AGTAAACACATGCGTTCATATATATGG 58.064 33.333 20.18 7.75 34.50 2.74
3718 3777 9.705290 TGAGTAAACACATGCGTTCATATATAT 57.295 29.630 0.00 0.00 0.00 0.86
3719 3778 8.974408 GTGAGTAAACACATGCGTTCATATATA 58.026 33.333 0.00 0.00 40.11 0.86
3720 3779 7.494298 TGTGAGTAAACACATGCGTTCATATAT 59.506 33.333 0.00 0.00 44.29 0.86
3722 3781 5.641636 TGTGAGTAAACACATGCGTTCATAT 59.358 36.000 0.00 0.00 44.29 1.78
3798 3857 9.780186 AAGTTTATGTAGACAAGAAGCTAACTT 57.220 29.630 0.00 0.00 39.43 2.66
3803 3862 8.989653 GTCTAAGTTTATGTAGACAAGAAGCT 57.010 34.615 6.07 0.00 43.77 3.74
3818 3877 6.368779 AGCCATGGTAAGTGTCTAAGTTTA 57.631 37.500 14.67 0.00 0.00 2.01
3822 3881 3.375299 GCAAGCCATGGTAAGTGTCTAAG 59.625 47.826 14.67 0.00 0.00 2.18
3827 3886 3.433306 TTAGCAAGCCATGGTAAGTGT 57.567 42.857 14.67 0.00 44.72 3.55
3836 3895 4.935352 TTTTCAGTTGTTAGCAAGCCAT 57.065 36.364 0.00 0.00 34.94 4.40
3837 3896 4.081972 TGTTTTTCAGTTGTTAGCAAGCCA 60.082 37.500 0.00 0.00 34.94 4.75
3867 3926 6.743575 AAAGAGATGTTAAATTGGACGGAG 57.256 37.500 0.00 0.00 0.00 4.63
3886 3945 9.123902 TCATGTGAAATCTTGAGAAAGAAAAGA 57.876 29.630 0.00 0.00 34.61 2.52
3887 3946 9.740239 TTCATGTGAAATCTTGAGAAAGAAAAG 57.260 29.630 0.00 0.00 31.77 2.27
3911 3970 6.151817 AGCTTGAGAATCCCAGTACAAAATTC 59.848 38.462 0.00 0.00 0.00 2.17
3921 3980 4.201990 GCAAACATAGCTTGAGAATCCCAG 60.202 45.833 0.00 0.00 0.00 4.45
4012 4071 9.582431 CGAAAGGACTACTTATGACATTTTAGA 57.418 33.333 0.00 0.00 38.85 2.10
4027 4086 7.917720 TTTAAATGCAAAACGAAAGGACTAC 57.082 32.000 0.00 0.00 0.00 2.73
4165 4225 3.063452 GTGTGCCGTACCATGAACATTAG 59.937 47.826 0.00 0.00 0.00 1.73
4208 4270 6.704493 GCATCTTCCACTATAAATTACACGGA 59.296 38.462 0.00 0.00 0.00 4.69
4222 4284 4.546829 AAATTGCAATGCATCTTCCACT 57.453 36.364 13.82 0.00 38.76 4.00
4348 4410 5.808042 AAGCTGAATATGCTACAACACAG 57.192 39.130 0.00 0.00 40.22 3.66
4432 4494 4.404394 TGAAGGACGGAATTATAGAGCACA 59.596 41.667 0.00 0.00 0.00 4.57
4498 4560 6.317642 AGCTGGTATTGCATTAACATCGTTAA 59.682 34.615 6.80 2.07 0.00 2.01
4645 4709 7.825681 TGTTCTGTGGTAATAATGTTGAATGG 58.174 34.615 0.00 0.00 0.00 3.16
4684 4748 1.614903 TCAATCTTTTGCTGGTGCTGG 59.385 47.619 0.00 0.00 40.48 4.85
4804 4868 4.565166 TCTTATCGGTTTTCATACACGCAG 59.435 41.667 0.00 0.00 0.00 5.18
5022 5113 7.946219 AGCATATGGATCAAGATAACCAATTGA 59.054 33.333 7.12 0.00 37.36 2.57
5025 5116 6.888632 GGAGCATATGGATCAAGATAACCAAT 59.111 38.462 4.56 0.00 36.00 3.16
5027 5118 5.549228 AGGAGCATATGGATCAAGATAACCA 59.451 40.000 4.56 0.00 32.12 3.67
5046 5137 4.081365 GCTTTCCCACCTATATCTAGGAGC 60.081 50.000 10.99 4.68 46.66 4.70
5175 5270 2.616524 AGGGCTTGTTCCACAGTACTA 58.383 47.619 0.00 0.00 0.00 1.82
5192 5287 1.542492 AAAGCTGTCATGCTGAAGGG 58.458 50.000 0.00 0.00 43.24 3.95
5304 5399 5.411669 GTCTCTTCTATCTCACTAGCTAGGC 59.588 48.000 24.35 0.00 0.00 3.93
5448 5543 4.623595 GCTCTCATTTTCGCCTAGCTATAC 59.376 45.833 0.00 0.00 0.00 1.47
5505 5600 8.788325 AATGGTAAACAACTCTAGGACATAAC 57.212 34.615 0.00 0.00 0.00 1.89
5540 5647 4.441087 GCTCCGTTTTACTTTGCTCTTTTG 59.559 41.667 0.00 0.00 0.00 2.44
5650 5757 4.293415 ACTGTAGTAGGACAAAACGAACG 58.707 43.478 0.00 0.00 0.00 3.95
5791 5901 8.682710 AGAAAGCAGTTTGTTCTGTTGTAATAA 58.317 29.630 0.00 0.00 37.70 1.40
5796 5906 5.391312 AAGAAAGCAGTTTGTTCTGTTGT 57.609 34.783 0.00 0.00 37.70 3.32
5871 5982 5.879223 AGACATTTAAGCTCCAGAAGACATG 59.121 40.000 0.00 0.00 0.00 3.21
5894 6005 4.944619 TGGATCCAACTGTCTAGCATAG 57.055 45.455 13.46 0.00 41.04 2.23
5976 6088 7.992754 AATGAGAAAGCTACTTCACTTGAAT 57.007 32.000 1.17 0.00 33.01 2.57
5985 6097 8.800332 ACATTGATTCAAATGAGAAAGCTACTT 58.200 29.630 2.68 0.00 39.46 2.24
5986 6098 8.345724 ACATTGATTCAAATGAGAAAGCTACT 57.654 30.769 2.68 0.00 39.46 2.57
6026 6138 4.441495 GGGAAAGTGGTCAAAAAGGAACAG 60.441 45.833 0.00 0.00 34.61 3.16
6047 6160 0.969894 CCTCCTGCGGTAGAATAGGG 59.030 60.000 0.00 0.00 0.00 3.53
6066 6179 0.537188 TGGGAGTGAGGAATCGAAGC 59.463 55.000 0.00 0.00 0.00 3.86
6235 6348 1.129437 GCATTCTCCAAGAACGCAGTC 59.871 52.381 3.13 0.00 42.39 3.51
6241 6354 4.319177 ACAGTAGTGCATTCTCCAAGAAC 58.681 43.478 0.00 0.00 37.00 3.01
6354 6467 3.477530 CCAACCGTTCTTCTCCTCTTTT 58.522 45.455 0.00 0.00 0.00 2.27
6364 6477 0.178973 CCTTTCCCCCAACCGTTCTT 60.179 55.000 0.00 0.00 0.00 2.52
6378 6492 4.829064 TGTCAGCACAACAATACCTTTC 57.171 40.909 0.00 0.00 0.00 2.62
6381 6495 4.005650 CTGATGTCAGCACAACAATACCT 58.994 43.478 0.00 0.00 35.09 3.08
6383 6497 5.611796 TTCTGATGTCAGCACAACAATAC 57.388 39.130 5.14 0.00 43.46 1.89
6384 6498 5.124297 CCATTCTGATGTCAGCACAACAATA 59.876 40.000 5.14 0.00 43.46 1.90
6439 6553 8.623903 TGATGTGCTTATAATCAAACTTGGATC 58.376 33.333 0.00 0.00 0.00 3.36
6467 6581 3.790820 CACATCAAAGGTTGTGACAAACG 59.209 43.478 7.83 0.00 44.04 3.60
6548 6663 2.747446 GGCATCTCAAACTAAGCGGAAA 59.253 45.455 0.00 0.00 0.00 3.13
6551 6666 2.029838 AGGCATCTCAAACTAAGCGG 57.970 50.000 0.00 0.00 0.00 5.52
6566 6681 5.732247 GCGTCACTAAAAGAAAAAGAAGGCA 60.732 40.000 0.00 0.00 0.00 4.75
6727 6844 9.529325 GGAGCGCTAAAATAAAATAAAGGATTT 57.471 29.630 11.50 0.00 43.42 2.17
6728 6845 8.691797 TGGAGCGCTAAAATAAAATAAAGGATT 58.308 29.630 11.50 0.00 0.00 3.01
6729 6846 8.232913 TGGAGCGCTAAAATAAAATAAAGGAT 57.767 30.769 11.50 0.00 0.00 3.24
6730 6847 7.633193 TGGAGCGCTAAAATAAAATAAAGGA 57.367 32.000 11.50 0.00 0.00 3.36
6731 6848 9.394477 GTATGGAGCGCTAAAATAAAATAAAGG 57.606 33.333 11.50 0.00 0.00 3.11
6732 6849 9.944663 TGTATGGAGCGCTAAAATAAAATAAAG 57.055 29.630 11.50 0.00 0.00 1.85
6776 6922 8.335356 CAAATTAGCGTGCAACAGTAAGTATAT 58.665 33.333 0.00 0.00 35.74 0.86
6788 6934 3.699779 TCACAACAAATTAGCGTGCAA 57.300 38.095 0.00 0.00 0.00 4.08
6897 7044 6.234920 ACCAACCCTAAATTATTGTTTTGCC 58.765 36.000 0.00 0.00 0.00 4.52
6899 7046 8.894768 TTGACCAACCCTAAATTATTGTTTTG 57.105 30.769 0.00 0.00 0.00 2.44
6902 7049 8.154203 CCTTTTGACCAACCCTAAATTATTGTT 58.846 33.333 0.00 0.00 0.00 2.83
6916 7063 5.924254 GCCAACTAAATACCTTTTGACCAAC 59.076 40.000 0.00 0.00 0.00 3.77
7040 7188 4.721274 CCTTTTTGAATGGGGTTATGGGAT 59.279 41.667 0.00 0.00 0.00 3.85
7063 7211 6.708949 TGTTAGTTAGTTCATGGTGTTCCTTC 59.291 38.462 0.00 0.00 34.23 3.46


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

AutoCloner maintained by Alex Coulton.