Multiple sequence alignment - TraesCS5B01G127200

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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 TraesCS5B01G127200 chr5B 100.000 3800 0 0 1 3800 232298436 232294637 0.000000e+00 7018.0
1 TraesCS5B01G127200 chr5B 91.257 183 15 1 1 183 403785413 403785232 8.150000e-62 248.0
2 TraesCS5B01G127200 chr5B 94.444 90 5 0 256 345 307191719 307191630 5.120000e-29 139.0
3 TraesCS5B01G127200 chr5A 97.431 2919 64 6 885 3800 285399432 285396522 0.000000e+00 4964.0
4 TraesCS5B01G127200 chr5D 97.068 2933 75 7 870 3800 216157839 216154916 0.000000e+00 4929.0
5 TraesCS5B01G127200 chr5D 91.935 496 33 4 360 852 351402284 351401793 0.000000e+00 688.0
6 TraesCS5B01G127200 chr5D 89.848 197 17 2 659 852 357769378 357769182 2.270000e-62 250.0
7 TraesCS5B01G127200 chr5D 89.848 197 17 2 659 852 449754432 449754628 2.270000e-62 250.0
8 TraesCS5B01G127200 chr5D 97.674 43 1 0 177 219 216157955 216157913 1.460000e-09 75.0
9 TraesCS5B01G127200 chr7B 88.361 610 46 13 256 852 743550198 743549601 0.000000e+00 710.0
10 TraesCS5B01G127200 chr7B 95.640 344 13 2 334 677 482636337 482635996 5.550000e-153 551.0
11 TraesCS5B01G127200 chr7B 91.304 184 15 1 1 184 162266721 162266903 2.270000e-62 250.0
12 TraesCS5B01G127200 chr1B 96.716 335 11 0 332 666 672032564 672032230 3.320000e-155 558.0
13 TraesCS5B01G127200 chr1B 91.111 180 16 0 1 180 677584725 677584904 1.050000e-60 244.0
14 TraesCS5B01G127200 chr1B 91.908 173 14 0 8 180 17888605 17888433 3.790000e-60 243.0
15 TraesCS5B01G127200 chr1B 90.556 180 16 1 1 180 49671034 49671212 1.760000e-58 237.0
16 TraesCS5B01G127200 chr3D 95.677 347 11 4 334 677 7429105 7428760 4.290000e-154 555.0
17 TraesCS5B01G127200 chr3D 88.830 188 21 0 1 188 290032413 290032600 8.210000e-57 231.0
18 TraesCS5B01G127200 chr6D 93.029 373 21 4 311 681 401304699 401305068 1.200000e-149 540.0
19 TraesCS5B01G127200 chr6D 86.364 506 49 9 263 762 22247269 22246778 5.590000e-148 534.0
20 TraesCS5B01G127200 chr6D 89.848 197 17 2 659 852 426818899 426818703 2.270000e-62 250.0
21 TraesCS5B01G127200 chr4B 93.611 360 21 2 311 669 548626589 548626947 1.550000e-148 536.0
22 TraesCS5B01G127200 chr4B 89.950 199 17 2 659 854 643261073 643261271 1.750000e-63 254.0
23 TraesCS5B01G127200 chr4B 92.222 90 5 2 248 335 165907360 165907449 3.980000e-25 126.0
24 TraesCS5B01G127200 chr4B 92.222 90 5 2 248 335 211719759 211719848 3.980000e-25 126.0
25 TraesCS5B01G127200 chr2B 92.042 377 24 6 311 684 504284335 504283962 3.360000e-145 525.0
26 TraesCS5B01G127200 chr2B 91.257 183 16 0 1 183 571524364 571524182 2.270000e-62 250.0
27 TraesCS5B01G127200 chr2B 90.698 43 3 1 3465 3507 131182248 131182289 5.300000e-04 56.5
28 TraesCS5B01G127200 chr6B 92.778 180 11 2 1 180 617034942 617034765 3.770000e-65 259.0
29 TraesCS5B01G127200 chr6B 86.614 127 16 1 250 376 714078575 714078700 5.120000e-29 139.0
30 TraesCS5B01G127200 chr6B 93.182 88 5 1 249 335 472494602 472494515 1.110000e-25 128.0
31 TraesCS5B01G127200 chr6B 94.118 85 4 1 251 335 621568580 621568497 1.110000e-25 128.0
32 TraesCS5B01G127200 chr4D 89.848 197 17 2 659 852 125200857 125201053 2.270000e-62 250.0
33 TraesCS5B01G127200 chr4D 94.118 85 4 1 251 335 416252938 416253021 1.110000e-25 128.0
34 TraesCS5B01G127200 chr2D 89.848 197 17 2 659 852 149715238 149715434 2.270000e-62 250.0
35 TraesCS5B01G127200 chr2A 89.216 204 16 5 653 852 767301692 767301491 2.270000e-62 250.0
36 TraesCS5B01G127200 chrUn 91.011 178 16 0 3 180 50774127 50773950 1.360000e-59 241.0
37 TraesCS5B01G127200 chr7D 95.294 85 3 1 251 335 381842188 381842105 2.380000e-27 134.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G127200 chr5B 232294637 232298436 3799 True 7018 7018 100.000 1 3800 1 chr5B.!!$R1 3799
1 TraesCS5B01G127200 chr5A 285396522 285399432 2910 True 4964 4964 97.431 885 3800 1 chr5A.!!$R1 2915
2 TraesCS5B01G127200 chr5D 216154916 216157955 3039 True 2502 4929 97.371 177 3800 2 chr5D.!!$R3 3623
3 TraesCS5B01G127200 chr7B 743549601 743550198 597 True 710 710 88.361 256 852 1 chr7B.!!$R2 596

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
128 129 0.100503 AAAGCTGTTTTGCGCGAACT 59.899 45.0 21.89 9.6 38.13 3.01 F
855 868 0.179062 CCACTATGACCAGCCTGAGC 60.179 60.0 0.00 0.0 40.32 4.26 F
897 910 0.381801 AGCTGCACGGTTTCACTTTG 59.618 50.0 1.02 0.0 0.00 2.77 F
2514 2527 0.185175 AAGTGGCGGAGTCCCTTTTT 59.815 50.0 2.80 0.0 0.00 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 1765 0.177604 CTGCCTCATCGAGCCTCTTT 59.822 55.000 0.00 0.00 0.00 2.52 R
2514 2527 0.843309 TGTTTCCAGGCTCCAACTGA 59.157 50.000 0.00 0.00 38.20 3.41 R
2788 2801 1.006805 GACACTCTCAGCACAGCGT 60.007 57.895 0.00 0.00 0.00 5.07 R
3680 3694 2.125106 ACCCTTCTTGGCGATCGC 60.125 61.111 31.52 31.52 41.06 4.58 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 2.836154 AAGAGCAGACCCCGCAAA 59.164 55.556 0.00 0.00 0.00 3.68
18 19 1.302832 AAGAGCAGACCCCGCAAAG 60.303 57.895 0.00 0.00 0.00 2.77
19 20 3.435186 GAGCAGACCCCGCAAAGC 61.435 66.667 0.00 0.00 0.00 3.51
22 23 4.697756 CAGACCCCGCAAAGCCGA 62.698 66.667 0.00 0.00 0.00 5.54
23 24 4.699522 AGACCCCGCAAAGCCGAC 62.700 66.667 0.00 0.00 0.00 4.79
28 29 4.745751 CCGCAAAGCCGACCCGTA 62.746 66.667 0.00 0.00 0.00 4.02
29 30 2.739287 CGCAAAGCCGACCCGTAA 60.739 61.111 0.00 0.00 0.00 3.18
30 31 2.319096 CGCAAAGCCGACCCGTAAA 61.319 57.895 0.00 0.00 0.00 2.01
31 32 1.843734 CGCAAAGCCGACCCGTAAAA 61.844 55.000 0.00 0.00 0.00 1.52
32 33 0.311477 GCAAAGCCGACCCGTAAAAA 59.689 50.000 0.00 0.00 0.00 1.94
75 76 2.445682 TTTATGGATCCGTTTGGGGG 57.554 50.000 12.82 0.00 36.01 5.40
89 90 3.081554 GGGGGTCTGCATCTGTGT 58.918 61.111 0.00 0.00 0.00 3.72
90 91 1.078143 GGGGGTCTGCATCTGTGTC 60.078 63.158 0.00 0.00 0.00 3.67
91 92 1.679311 GGGGTCTGCATCTGTGTCA 59.321 57.895 0.00 0.00 0.00 3.58
92 93 0.392193 GGGGTCTGCATCTGTGTCAG 60.392 60.000 0.00 0.00 33.55 3.51
93 94 1.023513 GGGTCTGCATCTGTGTCAGC 61.024 60.000 0.00 0.00 32.83 4.26
94 95 1.023513 GGTCTGCATCTGTGTCAGCC 61.024 60.000 0.00 0.00 32.83 4.85
95 96 1.023513 GTCTGCATCTGTGTCAGCCC 61.024 60.000 0.00 0.00 32.83 5.19
96 97 1.002990 CTGCATCTGTGTCAGCCCA 60.003 57.895 0.00 0.00 0.00 5.36
97 98 0.607217 CTGCATCTGTGTCAGCCCAA 60.607 55.000 0.00 0.00 0.00 4.12
98 99 0.178995 TGCATCTGTGTCAGCCCAAA 60.179 50.000 0.00 0.00 0.00 3.28
99 100 0.242017 GCATCTGTGTCAGCCCAAAC 59.758 55.000 0.00 0.00 0.00 2.93
100 101 0.883833 CATCTGTGTCAGCCCAAACC 59.116 55.000 0.00 0.00 0.00 3.27
101 102 0.606401 ATCTGTGTCAGCCCAAACCG 60.606 55.000 0.00 0.00 0.00 4.44
102 103 1.227823 CTGTGTCAGCCCAAACCGA 60.228 57.895 0.00 0.00 0.00 4.69
103 104 1.507141 CTGTGTCAGCCCAAACCGAC 61.507 60.000 0.00 0.00 0.00 4.79
104 105 2.112297 TGTCAGCCCAAACCGACC 59.888 61.111 0.00 0.00 0.00 4.79
105 106 2.671963 GTCAGCCCAAACCGACCC 60.672 66.667 0.00 0.00 0.00 4.46
106 107 4.323477 TCAGCCCAAACCGACCCG 62.323 66.667 0.00 0.00 0.00 5.28
110 111 4.992511 CCCAAACCGACCCGCGAA 62.993 66.667 8.23 0.00 44.57 4.70
111 112 2.973600 CCAAACCGACCCGCGAAA 60.974 61.111 8.23 0.00 44.57 3.46
112 113 2.554272 CAAACCGACCCGCGAAAG 59.446 61.111 8.23 0.00 44.57 2.62
124 125 3.128701 CGAAAGCTGTTTTGCGCG 58.871 55.556 0.00 0.00 38.13 6.86
125 126 1.368731 CGAAAGCTGTTTTGCGCGA 60.369 52.632 12.10 0.00 38.13 5.87
126 127 0.927994 CGAAAGCTGTTTTGCGCGAA 60.928 50.000 12.10 5.81 38.13 4.70
127 128 0.498511 GAAAGCTGTTTTGCGCGAAC 59.501 50.000 12.10 14.23 38.13 3.95
128 129 0.100503 AAAGCTGTTTTGCGCGAACT 59.899 45.000 21.89 9.60 38.13 3.01
129 130 0.592247 AAGCTGTTTTGCGCGAACTG 60.592 50.000 21.89 21.45 38.13 3.16
130 131 2.639000 GCTGTTTTGCGCGAACTGC 61.639 57.895 28.50 28.50 42.09 4.40
131 132 1.298264 CTGTTTTGCGCGAACTGCA 60.298 52.632 21.89 14.94 46.97 4.41
139 140 2.351888 GCGAACTGCAAACGCGTT 60.352 55.556 20.79 20.79 45.45 4.84
140 141 1.937362 GCGAACTGCAAACGCGTTT 60.937 52.632 30.36 30.36 45.45 3.60
141 142 1.468340 GCGAACTGCAAACGCGTTTT 61.468 50.000 33.05 19.44 45.45 2.43
142 143 0.223513 CGAACTGCAAACGCGTTTTG 59.776 50.000 33.05 26.38 46.57 2.44
169 170 3.857038 GGAATGCGGGGTCGGCTA 61.857 66.667 0.00 0.00 36.79 3.93
170 171 2.280186 GAATGCGGGGTCGGCTAG 60.280 66.667 0.00 0.00 36.79 3.42
171 172 2.762459 AATGCGGGGTCGGCTAGA 60.762 61.111 0.00 0.00 36.79 2.43
172 173 2.701163 GAATGCGGGGTCGGCTAGAG 62.701 65.000 0.00 0.00 36.79 2.43
173 174 4.753662 TGCGGGGTCGGCTAGAGT 62.754 66.667 0.00 0.00 36.79 3.24
174 175 3.459063 GCGGGGTCGGCTAGAGTT 61.459 66.667 0.00 0.00 36.79 3.01
175 176 2.494918 CGGGGTCGGCTAGAGTTG 59.505 66.667 0.00 0.00 0.00 3.16
185 186 1.145162 GCTAGAGTTGCTCTCAGCGC 61.145 60.000 0.00 0.00 46.26 5.92
219 220 2.962421 TGAAAGCGAGGGGACAAAAATT 59.038 40.909 0.00 0.00 0.00 1.82
221 222 1.165270 AGCGAGGGGACAAAAATTCG 58.835 50.000 0.00 0.00 0.00 3.34
222 223 1.161843 GCGAGGGGACAAAAATTCGA 58.838 50.000 0.00 0.00 0.00 3.71
243 256 0.384669 GACGATACGAGGAACCCTGG 59.615 60.000 0.00 0.00 35.43 4.45
244 257 0.324091 ACGATACGAGGAACCCTGGT 60.324 55.000 5.97 5.97 44.48 4.00
271 284 2.437281 CCTTGAGGCTGATCATAGTGGT 59.563 50.000 0.00 0.00 0.00 4.16
277 290 4.290093 AGGCTGATCATAGTGGTGAGTAA 58.710 43.478 0.00 0.00 0.00 2.24
279 292 4.100189 GGCTGATCATAGTGGTGAGTAACT 59.900 45.833 0.00 0.00 0.00 2.24
282 295 6.920758 GCTGATCATAGTGGTGAGTAACTTAG 59.079 42.308 0.00 0.00 0.00 2.18
298 311 9.239002 GAGTAACTTAGACTAGTAACATGCATG 57.761 37.037 25.09 25.09 0.00 4.06
301 314 6.936279 ACTTAGACTAGTAACATGCATGTGT 58.064 36.000 31.98 23.82 41.61 3.72
302 315 7.036220 ACTTAGACTAGTAACATGCATGTGTC 58.964 38.462 31.98 29.23 41.61 3.67
309 322 5.171476 AGTAACATGCATGTGTCACTAGTC 58.829 41.667 31.98 13.95 41.61 2.59
314 327 5.105187 ACATGCATGTGTCACTAGTCTATGT 60.105 40.000 30.92 1.32 40.03 2.29
321 334 7.621428 TGTGTCACTAGTCTATGTTACTACC 57.379 40.000 4.27 0.00 0.00 3.18
324 337 7.769970 GTGTCACTAGTCTATGTTACTACCTCT 59.230 40.741 0.00 0.00 0.00 3.69
325 338 8.985922 TGTCACTAGTCTATGTTACTACCTCTA 58.014 37.037 0.00 0.00 0.00 2.43
331 344 8.851541 AGTCTATGTTACTACCTCTATAGTGC 57.148 38.462 0.00 0.00 36.09 4.40
332 345 8.438373 AGTCTATGTTACTACCTCTATAGTGCA 58.562 37.037 0.00 0.00 36.09 4.57
409 422 6.560304 AGATAGATGGTGAGTGGTGGAATATT 59.440 38.462 0.00 0.00 0.00 1.28
451 464 7.212274 AGCACTCAATTAATGCTCTTGTTTTT 58.788 30.769 4.81 0.00 46.68 1.94
534 547 9.807649 ATGCATTGGTCATTTTTCTCTTAATAC 57.192 29.630 0.00 0.00 0.00 1.89
580 593 5.807909 TCTTGGAATCTGAACATGTGATGA 58.192 37.500 0.00 0.00 0.00 2.92
582 595 5.425196 TGGAATCTGAACATGTGATGAGA 57.575 39.130 0.00 0.00 0.00 3.27
646 659 6.488769 TTTGAGATAAGCCCTATAAACCGA 57.511 37.500 0.00 0.00 0.00 4.69
652 665 4.579647 AAGCCCTATAAACCGAAAAGGA 57.420 40.909 0.00 0.00 45.00 3.36
653 666 4.152284 AGCCCTATAAACCGAAAAGGAG 57.848 45.455 0.00 0.00 45.00 3.69
654 667 3.118000 AGCCCTATAAACCGAAAAGGAGG 60.118 47.826 0.00 0.00 45.00 4.30
655 668 3.816994 CCCTATAAACCGAAAAGGAGGG 58.183 50.000 0.00 0.00 45.00 4.30
656 669 3.457012 CCCTATAAACCGAAAAGGAGGGA 59.543 47.826 0.00 0.00 46.86 4.20
657 670 4.444449 CCCTATAAACCGAAAAGGAGGGAG 60.444 50.000 0.00 0.00 46.86 4.30
658 671 4.163649 CCTATAAACCGAAAAGGAGGGAGT 59.836 45.833 0.00 0.00 45.00 3.85
659 672 5.364735 CCTATAAACCGAAAAGGAGGGAGTA 59.635 44.000 0.00 0.00 45.00 2.59
660 673 3.697619 AAACCGAAAAGGAGGGAGTAG 57.302 47.619 0.00 0.00 45.00 2.57
661 674 2.322339 ACCGAAAAGGAGGGAGTAGT 57.678 50.000 0.00 0.00 45.00 2.73
662 675 3.463048 ACCGAAAAGGAGGGAGTAGTA 57.537 47.619 0.00 0.00 45.00 1.82
663 676 3.991683 ACCGAAAAGGAGGGAGTAGTAT 58.008 45.455 0.00 0.00 45.00 2.12
664 677 3.959449 ACCGAAAAGGAGGGAGTAGTATC 59.041 47.826 0.00 0.00 45.00 2.24
665 678 3.958798 CCGAAAAGGAGGGAGTAGTATCA 59.041 47.826 0.00 0.00 45.00 2.15
666 679 4.589374 CCGAAAAGGAGGGAGTAGTATCAT 59.411 45.833 0.00 0.00 45.00 2.45
667 680 5.773680 CCGAAAAGGAGGGAGTAGTATCATA 59.226 44.000 0.00 0.00 45.00 2.15
668 681 6.071840 CCGAAAAGGAGGGAGTAGTATCATAG 60.072 46.154 0.00 0.00 45.00 2.23
669 682 6.715718 CGAAAAGGAGGGAGTAGTATCATAGA 59.284 42.308 0.00 0.00 0.00 1.98
670 683 7.394923 CGAAAAGGAGGGAGTAGTATCATAGAT 59.605 40.741 0.00 0.00 0.00 1.98
671 684 9.095700 GAAAAGGAGGGAGTAGTATCATAGATT 57.904 37.037 0.00 0.00 0.00 2.40
673 686 9.762381 AAAGGAGGGAGTAGTATCATAGATTAG 57.238 37.037 0.00 0.00 0.00 1.73
674 687 8.471302 AGGAGGGAGTAGTATCATAGATTAGT 57.529 38.462 0.00 0.00 0.00 2.24
675 688 9.577337 AGGAGGGAGTAGTATCATAGATTAGTA 57.423 37.037 0.00 0.00 0.00 1.82
688 701 8.712228 TCATAGATTAGTATCATGTGTGGTCT 57.288 34.615 0.00 0.00 32.95 3.85
689 702 8.797438 TCATAGATTAGTATCATGTGTGGTCTC 58.203 37.037 0.00 0.00 32.95 3.36
690 703 8.579863 CATAGATTAGTATCATGTGTGGTCTCA 58.420 37.037 0.00 0.00 32.95 3.27
691 704 7.609097 AGATTAGTATCATGTGTGGTCTCAT 57.391 36.000 0.00 0.00 32.95 2.90
692 705 8.027524 AGATTAGTATCATGTGTGGTCTCATT 57.972 34.615 0.00 0.00 32.95 2.57
693 706 8.489489 AGATTAGTATCATGTGTGGTCTCATTT 58.511 33.333 0.00 0.00 32.95 2.32
694 707 9.764363 GATTAGTATCATGTGTGGTCTCATTTA 57.236 33.333 0.00 0.00 0.00 1.40
697 710 8.442632 AGTATCATGTGTGGTCTCATTTATTG 57.557 34.615 0.00 0.00 0.00 1.90
698 711 5.565592 TCATGTGTGGTCTCATTTATTGC 57.434 39.130 0.00 0.00 0.00 3.56
699 712 4.398988 TCATGTGTGGTCTCATTTATTGCC 59.601 41.667 0.00 0.00 0.00 4.52
700 713 3.760738 TGTGTGGTCTCATTTATTGCCA 58.239 40.909 0.00 0.00 0.00 4.92
701 714 3.758023 TGTGTGGTCTCATTTATTGCCAG 59.242 43.478 0.00 0.00 0.00 4.85
702 715 2.754552 TGTGGTCTCATTTATTGCCAGC 59.245 45.455 0.00 0.00 0.00 4.85
703 716 2.754552 GTGGTCTCATTTATTGCCAGCA 59.245 45.455 0.00 0.00 0.00 4.41
704 717 3.382546 GTGGTCTCATTTATTGCCAGCAT 59.617 43.478 0.00 0.00 0.00 3.79
705 718 3.382227 TGGTCTCATTTATTGCCAGCATG 59.618 43.478 0.00 0.00 0.00 4.06
706 719 3.633525 GGTCTCATTTATTGCCAGCATGA 59.366 43.478 0.00 0.00 39.69 3.07
707 720 4.498682 GGTCTCATTTATTGCCAGCATGAC 60.499 45.833 0.00 0.00 39.69 3.06
708 721 4.096833 GTCTCATTTATTGCCAGCATGACA 59.903 41.667 0.00 0.00 39.69 3.58
709 722 4.096833 TCTCATTTATTGCCAGCATGACAC 59.903 41.667 0.00 0.00 39.69 3.67
710 723 3.762823 TCATTTATTGCCAGCATGACACA 59.237 39.130 0.00 0.00 39.69 3.72
711 724 4.403113 TCATTTATTGCCAGCATGACACAT 59.597 37.500 0.00 0.00 39.69 3.21
712 725 5.593502 TCATTTATTGCCAGCATGACACATA 59.406 36.000 0.00 0.00 39.69 2.29
713 726 5.503662 TTTATTGCCAGCATGACACATAG 57.496 39.130 0.00 0.00 39.69 2.23
714 727 2.495155 TTGCCAGCATGACACATAGT 57.505 45.000 0.00 0.00 39.69 2.12
715 728 3.625649 TTGCCAGCATGACACATAGTA 57.374 42.857 0.00 0.00 39.69 1.82
716 729 3.183793 TGCCAGCATGACACATAGTAG 57.816 47.619 0.00 0.00 39.69 2.57
717 730 1.869767 GCCAGCATGACACATAGTAGC 59.130 52.381 0.00 0.00 39.69 3.58
718 731 2.742856 GCCAGCATGACACATAGTAGCA 60.743 50.000 0.00 0.00 39.69 3.49
719 732 3.736720 CCAGCATGACACATAGTAGCAT 58.263 45.455 0.00 0.00 39.69 3.79
720 733 3.744942 CCAGCATGACACATAGTAGCATC 59.255 47.826 0.00 0.00 39.69 3.91
721 734 4.374399 CAGCATGACACATAGTAGCATCA 58.626 43.478 0.00 0.00 39.69 3.07
722 735 4.995487 CAGCATGACACATAGTAGCATCAT 59.005 41.667 0.00 0.00 39.69 2.45
723 736 6.161381 CAGCATGACACATAGTAGCATCATA 58.839 40.000 0.00 0.00 39.69 2.15
724 737 6.817140 CAGCATGACACATAGTAGCATCATAT 59.183 38.462 0.00 0.00 39.69 1.78
725 738 7.333672 CAGCATGACACATAGTAGCATCATATT 59.666 37.037 0.00 0.00 39.69 1.28
726 739 7.881751 AGCATGACACATAGTAGCATCATATTT 59.118 33.333 0.00 0.00 0.00 1.40
727 740 9.154847 GCATGACACATAGTAGCATCATATTTA 57.845 33.333 0.00 0.00 0.00 1.40
755 768 8.930846 ATGTTACGGTATCTACCTATGTTACT 57.069 34.615 4.93 0.00 44.25 2.24
761 774 9.454859 ACGGTATCTACCTATGTTACTATAACC 57.545 37.037 4.93 0.00 44.25 2.85
762 775 9.453572 CGGTATCTACCTATGTTACTATAACCA 57.546 37.037 4.93 0.00 44.25 3.67
824 837 8.727100 TTTATGAGTCCCAGATACATGATACT 57.273 34.615 0.00 0.00 0.00 2.12
825 838 9.822727 TTTATGAGTCCCAGATACATGATACTA 57.177 33.333 0.00 0.00 0.00 1.82
826 839 7.953005 ATGAGTCCCAGATACATGATACTAG 57.047 40.000 0.00 0.00 0.00 2.57
827 840 6.853490 TGAGTCCCAGATACATGATACTAGT 58.147 40.000 0.00 0.00 0.00 2.57
828 841 7.298374 TGAGTCCCAGATACATGATACTAGTT 58.702 38.462 0.00 0.00 0.00 2.24
829 842 8.445588 TGAGTCCCAGATACATGATACTAGTTA 58.554 37.037 0.00 0.00 0.00 2.24
830 843 9.469097 GAGTCCCAGATACATGATACTAGTTAT 57.531 37.037 0.00 0.00 0.00 1.89
831 844 9.249053 AGTCCCAGATACATGATACTAGTTATG 57.751 37.037 0.00 6.79 0.00 1.90
832 845 9.026121 GTCCCAGATACATGATACTAGTTATGT 57.974 37.037 18.19 18.19 37.51 2.29
833 846 9.601810 TCCCAGATACATGATACTAGTTATGTT 57.398 33.333 18.91 10.92 35.55 2.71
840 853 8.548880 ACATGATACTAGTTATGTTACCCACT 57.451 34.615 0.00 0.00 30.05 4.00
841 854 9.650714 ACATGATACTAGTTATGTTACCCACTA 57.349 33.333 0.00 0.00 30.05 2.74
844 857 9.871175 TGATACTAGTTATGTTACCCACTATGA 57.129 33.333 0.00 0.00 0.00 2.15
846 859 7.357429 ACTAGTTATGTTACCCACTATGACC 57.643 40.000 0.00 0.00 0.00 4.02
847 860 6.899075 ACTAGTTATGTTACCCACTATGACCA 59.101 38.462 0.00 0.00 0.00 4.02
848 861 6.235231 AGTTATGTTACCCACTATGACCAG 57.765 41.667 0.00 0.00 0.00 4.00
849 862 3.560636 ATGTTACCCACTATGACCAGC 57.439 47.619 0.00 0.00 0.00 4.85
850 863 1.557832 TGTTACCCACTATGACCAGCC 59.442 52.381 0.00 0.00 0.00 4.85
851 864 1.838077 GTTACCCACTATGACCAGCCT 59.162 52.381 0.00 0.00 0.00 4.58
852 865 1.496060 TACCCACTATGACCAGCCTG 58.504 55.000 0.00 0.00 0.00 4.85
853 866 0.252696 ACCCACTATGACCAGCCTGA 60.253 55.000 0.00 0.00 0.00 3.86
854 867 0.467384 CCCACTATGACCAGCCTGAG 59.533 60.000 0.00 0.00 0.00 3.35
855 868 0.179062 CCACTATGACCAGCCTGAGC 60.179 60.000 0.00 0.00 40.32 4.26
856 869 0.529337 CACTATGACCAGCCTGAGCG 60.529 60.000 0.00 0.00 46.67 5.03
857 870 1.593750 CTATGACCAGCCTGAGCGC 60.594 63.158 0.00 0.00 46.67 5.92
858 871 3.430565 TATGACCAGCCTGAGCGCG 62.431 63.158 0.00 0.00 46.67 6.86
876 889 2.339728 CGAGGGTTCGCATCTCTATC 57.660 55.000 0.00 0.00 40.36 2.08
877 890 1.609072 CGAGGGTTCGCATCTCTATCA 59.391 52.381 0.00 0.00 40.36 2.15
878 891 2.034685 CGAGGGTTCGCATCTCTATCAA 59.965 50.000 0.00 0.00 40.36 2.57
879 892 3.648009 GAGGGTTCGCATCTCTATCAAG 58.352 50.000 0.00 0.00 0.00 3.02
880 893 2.139118 GGGTTCGCATCTCTATCAAGC 58.861 52.381 0.00 0.00 0.00 4.01
881 894 2.224161 GGGTTCGCATCTCTATCAAGCT 60.224 50.000 0.00 0.00 0.00 3.74
897 910 0.381801 AGCTGCACGGTTTCACTTTG 59.618 50.000 1.02 0.00 0.00 2.77
902 915 1.133407 GCACGGTTTCACTTTGAACCA 59.867 47.619 6.14 0.00 35.89 3.67
952 965 1.410850 TAGGCAGCATCTGGTAGGGC 61.411 60.000 0.00 0.00 31.21 5.19
989 1002 0.456221 TAGTTGCCGCTACTCTGCTC 59.544 55.000 10.88 0.00 0.00 4.26
990 1003 1.216710 GTTGCCGCTACTCTGCTCT 59.783 57.895 0.00 0.00 0.00 4.09
991 1004 1.080995 GTTGCCGCTACTCTGCTCTG 61.081 60.000 0.00 0.00 0.00 3.35
992 1005 2.584694 GCCGCTACTCTGCTCTGC 60.585 66.667 0.00 0.00 0.00 4.26
993 1006 3.074999 GCCGCTACTCTGCTCTGCT 62.075 63.158 0.00 0.00 0.00 4.24
994 1007 1.515020 CCGCTACTCTGCTCTGCTT 59.485 57.895 0.00 0.00 0.00 3.91
995 1008 0.805322 CCGCTACTCTGCTCTGCTTG 60.805 60.000 0.00 0.00 0.00 4.01
1392 1405 3.801997 CCTGCCCCCTCTCGCAAT 61.802 66.667 0.00 0.00 33.87 3.56
1649 1662 1.208535 CAATGCAATGGTGGATGCCTT 59.791 47.619 0.00 0.00 41.87 4.35
1650 1663 1.575419 ATGCAATGGTGGATGCCTTT 58.425 45.000 0.00 0.00 41.87 3.11
1692 1705 0.534203 ACGCCAGGACGTTGTTCAAT 60.534 50.000 3.38 0.00 45.75 2.57
1848 1861 3.512516 GGGCACGAGCAGAATGGC 61.513 66.667 7.26 0.00 44.61 4.40
2098 2111 2.892852 ACTGCCATGTTAGTGTTTGCAT 59.107 40.909 0.00 0.00 0.00 3.96
2514 2527 0.185175 AAGTGGCGGAGTCCCTTTTT 59.815 50.000 2.80 0.00 0.00 1.94
2788 2801 3.055094 GGATCCTGTTGAAGACCAGCTTA 60.055 47.826 3.84 0.00 36.83 3.09
2814 2827 1.072806 TGCTGAGAGTGTCATGCCTTT 59.927 47.619 8.51 0.00 33.51 3.11
2860 2873 2.826428 CTACACGAAGCATGCCAGTAT 58.174 47.619 15.66 3.84 0.00 2.12
2873 2886 5.504665 GCATGCCAGTATATGTTCACTGTTC 60.505 44.000 6.36 0.00 40.47 3.18
3039 3053 1.078497 CCCACCGCTTCAGCATACA 60.078 57.895 0.00 0.00 42.21 2.29
3054 3068 6.526526 TCAGCATACAACTAAACACCACTAA 58.473 36.000 0.00 0.00 0.00 2.24
3059 3073 5.473796 ACAACTAAACACCACTAACAACG 57.526 39.130 0.00 0.00 0.00 4.10
3111 3125 7.447545 AGCAATCCGTATACAGTTCAGTATCTA 59.552 37.037 3.32 0.00 36.23 1.98
3117 3131 9.270640 CCGTATACAGTTCAGTATCTACTAAGT 57.729 37.037 3.32 0.00 36.23 2.24
3298 3312 4.141824 TGCCTACATCGTGGATCATTGTTA 60.142 41.667 0.00 0.00 0.00 2.41
3402 3416 0.768221 TCCACTGAGAGCCAAAGGGT 60.768 55.000 0.00 0.00 36.17 4.34
3428 3442 2.483188 CCCGTGTTATCCTAGGAAGTGC 60.483 54.545 17.30 7.27 0.00 4.40
3750 3764 6.460781 ACTAGAACACGTGTGAAATAATGGA 58.539 36.000 24.16 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.302832 CTTTGCGGGGTCTGCTCTT 60.303 57.895 0.30 0.00 0.00 2.85
1 2 2.348998 CTTTGCGGGGTCTGCTCT 59.651 61.111 0.30 0.00 0.00 4.09
2 3 3.435186 GCTTTGCGGGGTCTGCTC 61.435 66.667 0.30 0.00 0.00 4.26
5 6 4.697756 TCGGCTTTGCGGGGTCTG 62.698 66.667 0.00 0.00 0.00 3.51
6 7 4.699522 GTCGGCTTTGCGGGGTCT 62.700 66.667 0.00 0.00 0.00 3.85
11 12 4.745751 TACGGGTCGGCTTTGCGG 62.746 66.667 0.00 0.00 0.00 5.69
12 13 1.843734 TTTTACGGGTCGGCTTTGCG 61.844 55.000 0.00 0.00 0.00 4.85
13 14 0.311477 TTTTTACGGGTCGGCTTTGC 59.689 50.000 0.00 0.00 0.00 3.68
54 55 3.100671 CCCCCAAACGGATCCATAAAAA 58.899 45.455 13.41 0.00 0.00 1.94
55 56 2.741145 CCCCCAAACGGATCCATAAAA 58.259 47.619 13.41 0.00 0.00 1.52
56 57 2.445682 CCCCCAAACGGATCCATAAA 57.554 50.000 13.41 0.00 0.00 1.40
72 73 1.078143 GACACAGATGCAGACCCCC 60.078 63.158 0.00 0.00 0.00 5.40
73 74 0.392193 CTGACACAGATGCAGACCCC 60.392 60.000 0.00 0.00 34.03 4.95
74 75 1.023513 GCTGACACAGATGCAGACCC 61.024 60.000 2.81 0.00 34.03 4.46
75 76 1.023513 GGCTGACACAGATGCAGACC 61.024 60.000 2.81 0.00 34.00 3.85
76 77 1.023513 GGGCTGACACAGATGCAGAC 61.024 60.000 2.81 0.00 37.30 3.51
77 78 1.297689 GGGCTGACACAGATGCAGA 59.702 57.895 2.81 0.00 34.03 4.26
78 79 0.607217 TTGGGCTGACACAGATGCAG 60.607 55.000 2.81 0.00 34.79 4.41
79 80 0.178995 TTTGGGCTGACACAGATGCA 60.179 50.000 2.81 0.00 32.44 3.96
80 81 0.242017 GTTTGGGCTGACACAGATGC 59.758 55.000 2.81 0.00 32.44 3.91
81 82 0.883833 GGTTTGGGCTGACACAGATG 59.116 55.000 2.81 0.00 32.44 2.90
82 83 0.606401 CGGTTTGGGCTGACACAGAT 60.606 55.000 2.81 0.00 32.44 2.90
83 84 1.227823 CGGTTTGGGCTGACACAGA 60.228 57.895 2.81 0.00 32.44 3.41
84 85 1.227823 TCGGTTTGGGCTGACACAG 60.228 57.895 0.00 0.00 34.12 3.66
85 86 1.525077 GTCGGTTTGGGCTGACACA 60.525 57.895 0.00 0.00 42.63 3.72
86 87 2.258726 GGTCGGTTTGGGCTGACAC 61.259 63.158 7.26 0.00 44.33 3.67
87 88 2.112297 GGTCGGTTTGGGCTGACA 59.888 61.111 7.26 0.00 44.33 3.58
88 89 2.671963 GGGTCGGTTTGGGCTGAC 60.672 66.667 0.00 0.00 42.43 3.51
89 90 4.323477 CGGGTCGGTTTGGGCTGA 62.323 66.667 0.00 0.00 0.00 4.26
93 94 4.992511 TTCGCGGGTCGGTTTGGG 62.993 66.667 6.13 0.00 39.05 4.12
94 95 2.961669 CTTTCGCGGGTCGGTTTGG 61.962 63.158 6.13 0.00 39.05 3.28
95 96 2.554272 CTTTCGCGGGTCGGTTTG 59.446 61.111 6.13 0.00 39.05 2.93
96 97 3.351416 GCTTTCGCGGGTCGGTTT 61.351 61.111 6.13 0.00 39.05 3.27
97 98 4.309950 AGCTTTCGCGGGTCGGTT 62.310 61.111 6.13 0.00 42.32 4.44
100 101 2.113131 AAAACAGCTTTCGCGGGTCG 62.113 55.000 6.13 0.00 42.32 4.79
101 102 0.660300 CAAAACAGCTTTCGCGGGTC 60.660 55.000 6.13 0.00 42.32 4.46
102 103 1.358759 CAAAACAGCTTTCGCGGGT 59.641 52.632 6.13 0.00 42.32 5.28
103 104 2.016165 GCAAAACAGCTTTCGCGGG 61.016 57.895 6.13 0.00 42.32 6.13
104 105 2.356796 CGCAAAACAGCTTTCGCGG 61.357 57.895 6.13 0.00 42.32 6.46
105 106 2.976032 GCGCAAAACAGCTTTCGCG 61.976 57.895 0.30 0.00 42.40 5.87
106 107 2.839330 GCGCAAAACAGCTTTCGC 59.161 55.556 0.30 0.00 36.84 4.70
107 108 0.927994 TTCGCGCAAAACAGCTTTCG 60.928 50.000 8.75 0.00 0.00 3.46
108 109 0.498511 GTTCGCGCAAAACAGCTTTC 59.501 50.000 8.75 0.00 0.00 2.62
109 110 0.100503 AGTTCGCGCAAAACAGCTTT 59.899 45.000 20.74 1.54 0.00 3.51
110 111 0.592247 CAGTTCGCGCAAAACAGCTT 60.592 50.000 20.74 1.86 0.00 3.74
111 112 1.009675 CAGTTCGCGCAAAACAGCT 60.010 52.632 20.74 2.17 0.00 4.24
112 113 2.639000 GCAGTTCGCGCAAAACAGC 61.639 57.895 19.26 19.26 33.04 4.40
113 114 0.865218 TTGCAGTTCGCGCAAAACAG 60.865 50.000 20.74 15.30 45.91 3.16
114 115 1.137614 TTGCAGTTCGCGCAAAACA 59.862 47.368 20.74 3.47 45.91 2.83
115 116 3.990141 TTGCAGTTCGCGCAAAAC 58.010 50.000 8.75 11.52 45.91 2.43
119 120 4.954680 GCGTTTGCAGTTCGCGCA 62.955 61.111 8.75 0.00 46.97 6.09
122 123 1.468340 AAAACGCGTTTGCAGTTCGC 61.468 50.000 35.31 17.67 45.28 4.70
123 124 0.223513 CAAAACGCGTTTGCAGTTCG 59.776 50.000 35.31 15.11 40.25 3.95
152 153 3.809374 CTAGCCGACCCCGCATTCC 62.809 68.421 0.00 0.00 0.00 3.01
153 154 2.280186 CTAGCCGACCCCGCATTC 60.280 66.667 0.00 0.00 0.00 2.67
154 155 2.762459 TCTAGCCGACCCCGCATT 60.762 61.111 0.00 0.00 0.00 3.56
155 156 3.227276 CTCTAGCCGACCCCGCAT 61.227 66.667 0.00 0.00 0.00 4.73
156 157 4.753662 ACTCTAGCCGACCCCGCA 62.754 66.667 0.00 0.00 0.00 5.69
157 158 3.459063 AACTCTAGCCGACCCCGC 61.459 66.667 0.00 0.00 0.00 6.13
158 159 2.494918 CAACTCTAGCCGACCCCG 59.505 66.667 0.00 0.00 0.00 5.73
159 160 2.187163 GCAACTCTAGCCGACCCC 59.813 66.667 0.00 0.00 0.00 4.95
160 161 1.142097 GAGCAACTCTAGCCGACCC 59.858 63.158 0.00 0.00 0.00 4.46
161 162 0.101579 GAGAGCAACTCTAGCCGACC 59.898 60.000 0.00 0.00 41.35 4.79
162 163 0.811915 TGAGAGCAACTCTAGCCGAC 59.188 55.000 11.18 0.00 41.35 4.79
163 164 1.098869 CTGAGAGCAACTCTAGCCGA 58.901 55.000 11.18 0.00 41.35 5.54
164 165 0.527385 GCTGAGAGCAACTCTAGCCG 60.527 60.000 16.28 0.00 41.35 5.52
165 166 0.527385 CGCTGAGAGCAACTCTAGCC 60.527 60.000 18.74 0.05 41.35 3.93
166 167 1.145162 GCGCTGAGAGCAACTCTAGC 61.145 60.000 2.54 16.72 41.35 3.42
167 168 0.527385 GGCGCTGAGAGCAACTCTAG 60.527 60.000 10.93 8.41 41.35 2.43
168 169 1.250840 TGGCGCTGAGAGCAACTCTA 61.251 55.000 10.93 0.00 41.35 2.43
169 170 2.104572 TTGGCGCTGAGAGCAACTCT 62.105 55.000 10.93 0.00 44.28 3.24
170 171 1.633852 CTTGGCGCTGAGAGCAACTC 61.634 60.000 10.93 4.35 42.58 3.01
171 172 1.670406 CTTGGCGCTGAGAGCAACT 60.670 57.895 10.93 0.00 42.58 3.16
172 173 2.684843 CCTTGGCGCTGAGAGCAAC 61.685 63.158 10.93 0.00 42.58 4.17
173 174 2.359107 CCTTGGCGCTGAGAGCAA 60.359 61.111 10.93 0.00 42.58 3.91
174 175 3.630013 ACCTTGGCGCTGAGAGCA 61.630 61.111 10.93 0.00 42.58 4.26
175 176 3.123620 CACCTTGGCGCTGAGAGC 61.124 66.667 7.64 0.00 38.02 4.09
185 186 1.962144 CTTTCAGCTGCCACCTTGG 59.038 57.895 9.47 0.00 41.55 3.61
221 222 2.022934 AGGGTTCCTCGTATCGTCTTC 58.977 52.381 0.00 0.00 0.00 2.87
222 223 1.749634 CAGGGTTCCTCGTATCGTCTT 59.250 52.381 0.00 0.00 0.00 3.01
228 241 1.761198 GCTAACCAGGGTTCCTCGTAT 59.239 52.381 7.04 0.00 39.31 3.06
235 248 0.323451 CAAGGGGCTAACCAGGGTTC 60.323 60.000 7.04 0.00 42.91 3.62
271 284 8.344446 TGCATGTTACTAGTCTAAGTTACTCA 57.656 34.615 0.00 0.00 31.82 3.41
277 290 6.936279 ACACATGCATGTTACTAGTCTAAGT 58.064 36.000 29.48 16.14 39.39 2.24
279 292 6.811665 GTGACACATGCATGTTACTAGTCTAA 59.188 38.462 31.08 18.83 39.39 2.10
282 295 5.171476 AGTGACACATGCATGTTACTAGTC 58.829 41.667 29.48 28.39 44.90 2.59
290 303 3.969287 AGACTAGTGACACATGCATGT 57.031 42.857 26.61 26.61 42.84 3.21
298 311 7.769970 AGAGGTAGTAACATAGACTAGTGACAC 59.230 40.741 0.00 0.00 30.08 3.67
314 327 7.018349 AGGGAGTATGCACTATAGAGGTAGTAA 59.982 40.741 6.78 0.00 34.21 2.24
321 334 4.929479 AGGAGGGAGTATGCACTATAGAG 58.071 47.826 6.78 0.00 34.21 2.43
324 337 4.838986 GGAAAGGAGGGAGTATGCACTATA 59.161 45.833 0.00 0.00 34.21 1.31
325 338 3.648545 GGAAAGGAGGGAGTATGCACTAT 59.351 47.826 0.00 0.00 34.21 2.12
326 339 3.039011 GGAAAGGAGGGAGTATGCACTA 58.961 50.000 0.00 0.00 34.21 2.74
327 340 1.840635 GGAAAGGAGGGAGTATGCACT 59.159 52.381 0.00 0.00 37.87 4.40
328 341 1.473434 CGGAAAGGAGGGAGTATGCAC 60.473 57.143 0.00 0.00 0.00 4.57
329 342 0.830648 CGGAAAGGAGGGAGTATGCA 59.169 55.000 0.00 0.00 0.00 3.96
330 343 0.106894 CCGGAAAGGAGGGAGTATGC 59.893 60.000 0.00 0.00 45.00 3.14
331 344 1.497161 ACCGGAAAGGAGGGAGTATG 58.503 55.000 9.46 0.00 45.00 2.39
332 345 2.265526 AACCGGAAAGGAGGGAGTAT 57.734 50.000 9.46 0.00 45.00 2.12
431 444 9.814899 TTTGAGAAAAACAAGAGCATTAATTGA 57.185 25.926 0.00 0.00 0.00 2.57
520 533 9.142515 CATTGCATGCAAGTATTAAGAGAAAAA 57.857 29.630 34.15 9.13 39.47 1.94
534 547 5.726729 TGCATTAAATCATTGCATGCAAG 57.273 34.783 34.15 25.40 40.64 4.01
546 559 8.192774 TGTTCAGATTCCAAGATGCATTAAATC 58.807 33.333 0.00 6.51 0.00 2.17
580 593 6.670695 ATAAGGCTCAATTTGGTTGTTTCT 57.329 33.333 0.00 0.00 38.95 2.52
582 595 9.791801 ATTTTATAAGGCTCAATTTGGTTGTTT 57.208 25.926 0.00 0.00 38.95 2.83
662 675 9.319060 AGACCACACATGATACTAATCTATGAT 57.681 33.333 0.00 0.00 32.93 2.45
663 676 8.712228 AGACCACACATGATACTAATCTATGA 57.288 34.615 0.00 0.00 32.93 2.15
664 677 8.579863 TGAGACCACACATGATACTAATCTATG 58.420 37.037 0.00 0.00 32.93 2.23
665 678 8.712228 TGAGACCACACATGATACTAATCTAT 57.288 34.615 0.00 0.00 32.93 1.98
666 679 8.712228 ATGAGACCACACATGATACTAATCTA 57.288 34.615 0.00 0.00 32.93 1.98
667 680 7.609097 ATGAGACCACACATGATACTAATCT 57.391 36.000 0.00 0.00 32.93 2.40
668 681 8.668510 AAATGAGACCACACATGATACTAATC 57.331 34.615 0.00 0.00 0.00 1.75
671 684 9.546428 CAATAAATGAGACCACACATGATACTA 57.454 33.333 0.00 0.00 0.00 1.82
672 685 7.012704 GCAATAAATGAGACCACACATGATACT 59.987 37.037 0.00 0.00 0.00 2.12
673 686 7.134815 GCAATAAATGAGACCACACATGATAC 58.865 38.462 0.00 0.00 0.00 2.24
674 687 6.262944 GGCAATAAATGAGACCACACATGATA 59.737 38.462 0.00 0.00 0.00 2.15
675 688 5.068198 GGCAATAAATGAGACCACACATGAT 59.932 40.000 0.00 0.00 0.00 2.45
676 689 4.398988 GGCAATAAATGAGACCACACATGA 59.601 41.667 0.00 0.00 0.00 3.07
677 690 4.158209 TGGCAATAAATGAGACCACACATG 59.842 41.667 0.00 0.00 0.00 3.21
678 691 4.343231 TGGCAATAAATGAGACCACACAT 58.657 39.130 0.00 0.00 0.00 3.21
679 692 3.758023 CTGGCAATAAATGAGACCACACA 59.242 43.478 0.00 0.00 0.00 3.72
680 693 3.428045 GCTGGCAATAAATGAGACCACAC 60.428 47.826 0.00 0.00 0.00 3.82
681 694 2.754552 GCTGGCAATAAATGAGACCACA 59.245 45.455 0.00 0.00 0.00 4.17
682 695 2.754552 TGCTGGCAATAAATGAGACCAC 59.245 45.455 0.00 0.00 0.00 4.16
683 696 3.084536 TGCTGGCAATAAATGAGACCA 57.915 42.857 0.00 0.00 0.00 4.02
684 697 3.633525 TCATGCTGGCAATAAATGAGACC 59.366 43.478 0.00 0.00 0.00 3.85
685 698 4.096833 TGTCATGCTGGCAATAAATGAGAC 59.903 41.667 0.00 0.00 0.00 3.36
686 699 4.096833 GTGTCATGCTGGCAATAAATGAGA 59.903 41.667 0.00 0.00 31.67 3.27
687 700 4.142337 TGTGTCATGCTGGCAATAAATGAG 60.142 41.667 0.00 0.00 31.67 2.90
688 701 3.762823 TGTGTCATGCTGGCAATAAATGA 59.237 39.130 0.00 0.00 31.67 2.57
689 702 4.112716 TGTGTCATGCTGGCAATAAATG 57.887 40.909 0.00 0.00 31.67 2.32
690 703 5.595542 ACTATGTGTCATGCTGGCAATAAAT 59.404 36.000 0.00 0.00 31.67 1.40
691 704 4.949238 ACTATGTGTCATGCTGGCAATAAA 59.051 37.500 0.00 0.00 31.67 1.40
692 705 4.525996 ACTATGTGTCATGCTGGCAATAA 58.474 39.130 0.00 0.00 31.67 1.40
693 706 4.155063 ACTATGTGTCATGCTGGCAATA 57.845 40.909 0.00 0.00 31.67 1.90
694 707 3.008835 ACTATGTGTCATGCTGGCAAT 57.991 42.857 0.00 0.00 31.67 3.56
695 708 2.495155 ACTATGTGTCATGCTGGCAA 57.505 45.000 0.00 0.00 31.67 4.52
696 709 2.742856 GCTACTATGTGTCATGCTGGCA 60.743 50.000 0.00 0.00 0.00 4.92
697 710 1.869767 GCTACTATGTGTCATGCTGGC 59.130 52.381 0.00 0.00 0.00 4.85
698 711 3.183793 TGCTACTATGTGTCATGCTGG 57.816 47.619 0.00 0.00 0.00 4.85
699 712 4.374399 TGATGCTACTATGTGTCATGCTG 58.626 43.478 0.00 0.00 0.00 4.41
700 713 4.677673 TGATGCTACTATGTGTCATGCT 57.322 40.909 0.00 0.00 0.00 3.79
701 714 7.606858 AATATGATGCTACTATGTGTCATGC 57.393 36.000 0.00 0.00 0.00 4.06
798 811 9.331466 AGTATCATGTATCTGGGACTCATAAAT 57.669 33.333 0.00 0.00 0.00 1.40
799 812 8.727100 AGTATCATGTATCTGGGACTCATAAA 57.273 34.615 0.00 0.00 0.00 1.40
800 813 9.467796 CTAGTATCATGTATCTGGGACTCATAA 57.532 37.037 0.00 0.00 0.00 1.90
801 814 8.615705 ACTAGTATCATGTATCTGGGACTCATA 58.384 37.037 0.00 0.00 0.00 2.15
802 815 7.474445 ACTAGTATCATGTATCTGGGACTCAT 58.526 38.462 0.00 0.00 0.00 2.90
803 816 6.853490 ACTAGTATCATGTATCTGGGACTCA 58.147 40.000 0.00 0.00 0.00 3.41
804 817 7.768807 AACTAGTATCATGTATCTGGGACTC 57.231 40.000 0.00 0.00 0.00 3.36
805 818 9.249053 CATAACTAGTATCATGTATCTGGGACT 57.751 37.037 0.00 0.00 0.00 3.85
806 819 9.026121 ACATAACTAGTATCATGTATCTGGGAC 57.974 37.037 13.27 0.00 30.04 4.46
807 820 9.601810 AACATAACTAGTATCATGTATCTGGGA 57.398 33.333 14.59 0.00 31.55 4.37
814 827 9.650714 AGTGGGTAACATAACTAGTATCATGTA 57.349 33.333 14.59 0.00 39.74 2.29
815 828 8.548880 AGTGGGTAACATAACTAGTATCATGT 57.451 34.615 10.40 10.40 39.74 3.21
818 831 9.871175 TCATAGTGGGTAACATAACTAGTATCA 57.129 33.333 0.00 0.00 33.69 2.15
820 833 9.086758 GGTCATAGTGGGTAACATAACTAGTAT 57.913 37.037 0.00 0.00 33.69 2.12
821 834 8.060689 TGGTCATAGTGGGTAACATAACTAGTA 58.939 37.037 0.00 0.00 33.69 1.82
822 835 6.899075 TGGTCATAGTGGGTAACATAACTAGT 59.101 38.462 0.00 0.00 33.69 2.57
823 836 7.356089 TGGTCATAGTGGGTAACATAACTAG 57.644 40.000 0.00 0.00 33.69 2.57
824 837 6.183360 GCTGGTCATAGTGGGTAACATAACTA 60.183 42.308 0.00 0.00 39.74 2.24
825 838 5.396436 GCTGGTCATAGTGGGTAACATAACT 60.396 44.000 0.00 0.00 39.74 2.24
826 839 4.814771 GCTGGTCATAGTGGGTAACATAAC 59.185 45.833 0.00 0.00 39.74 1.89
827 840 4.141574 GGCTGGTCATAGTGGGTAACATAA 60.142 45.833 0.00 0.00 39.74 1.90
828 841 3.389983 GGCTGGTCATAGTGGGTAACATA 59.610 47.826 0.00 0.00 39.74 2.29
829 842 2.172717 GGCTGGTCATAGTGGGTAACAT 59.827 50.000 0.00 0.00 39.74 2.71
830 843 1.557832 GGCTGGTCATAGTGGGTAACA 59.442 52.381 0.00 0.00 39.74 2.41
831 844 1.838077 AGGCTGGTCATAGTGGGTAAC 59.162 52.381 0.00 0.00 0.00 2.50
832 845 1.837439 CAGGCTGGTCATAGTGGGTAA 59.163 52.381 6.61 0.00 0.00 2.85
833 846 1.007842 TCAGGCTGGTCATAGTGGGTA 59.992 52.381 15.73 0.00 0.00 3.69
834 847 0.252696 TCAGGCTGGTCATAGTGGGT 60.253 55.000 15.73 0.00 0.00 4.51
835 848 0.467384 CTCAGGCTGGTCATAGTGGG 59.533 60.000 15.73 0.00 0.00 4.61
836 849 0.179062 GCTCAGGCTGGTCATAGTGG 60.179 60.000 15.73 0.00 35.22 4.00
837 850 0.529337 CGCTCAGGCTGGTCATAGTG 60.529 60.000 15.73 6.99 36.09 2.74
838 851 1.819229 CGCTCAGGCTGGTCATAGT 59.181 57.895 15.73 0.00 36.09 2.12
839 852 1.593750 GCGCTCAGGCTGGTCATAG 60.594 63.158 15.73 5.17 36.09 2.23
840 853 2.501128 GCGCTCAGGCTGGTCATA 59.499 61.111 15.73 0.00 36.09 2.15
841 854 4.827087 CGCGCTCAGGCTGGTCAT 62.827 66.667 15.73 0.00 36.09 3.06
858 871 3.648009 CTTGATAGAGATGCGAACCCTC 58.352 50.000 0.00 0.00 0.00 4.30
859 872 2.224161 GCTTGATAGAGATGCGAACCCT 60.224 50.000 0.00 0.00 0.00 4.34
860 873 2.139118 GCTTGATAGAGATGCGAACCC 58.861 52.381 0.00 0.00 0.00 4.11
861 874 2.799412 CAGCTTGATAGAGATGCGAACC 59.201 50.000 0.00 0.00 0.00 3.62
867 880 2.133553 CCGTGCAGCTTGATAGAGATG 58.866 52.381 0.00 0.00 36.18 2.90
868 881 1.759445 ACCGTGCAGCTTGATAGAGAT 59.241 47.619 0.00 0.00 0.00 2.75
869 882 1.186200 ACCGTGCAGCTTGATAGAGA 58.814 50.000 0.00 0.00 0.00 3.10
870 883 2.015736 AACCGTGCAGCTTGATAGAG 57.984 50.000 0.00 0.00 0.00 2.43
871 884 2.289382 TGAAACCGTGCAGCTTGATAGA 60.289 45.455 0.00 0.00 0.00 1.98
872 885 2.076100 TGAAACCGTGCAGCTTGATAG 58.924 47.619 0.00 0.00 0.00 2.08
873 886 1.804151 GTGAAACCGTGCAGCTTGATA 59.196 47.619 0.00 0.00 0.00 2.15
874 887 0.593128 GTGAAACCGTGCAGCTTGAT 59.407 50.000 0.00 0.00 0.00 2.57
875 888 0.463654 AGTGAAACCGTGCAGCTTGA 60.464 50.000 0.00 0.00 37.80 3.02
876 889 0.381801 AAGTGAAACCGTGCAGCTTG 59.618 50.000 0.00 0.00 37.80 4.01
877 890 1.102978 AAAGTGAAACCGTGCAGCTT 58.897 45.000 0.00 0.00 37.80 3.74
878 891 0.381801 CAAAGTGAAACCGTGCAGCT 59.618 50.000 0.00 0.00 37.80 4.24
879 892 0.380378 TCAAAGTGAAACCGTGCAGC 59.620 50.000 0.00 0.00 37.80 5.25
880 893 2.450160 GTTCAAAGTGAAACCGTGCAG 58.550 47.619 0.00 0.00 38.22 4.41
881 894 1.133407 GGTTCAAAGTGAAACCGTGCA 59.867 47.619 0.00 0.00 38.10 4.57
897 910 1.570813 GCTGGCACAAACTTTGGTTC 58.429 50.000 6.47 0.00 38.70 3.62
902 915 1.455383 CGAGGGCTGGCACAAACTTT 61.455 55.000 2.88 0.00 38.70 2.66
934 947 2.750657 GCCCTACCAGATGCTGCCT 61.751 63.158 0.00 0.00 0.00 4.75
1649 1662 1.692749 ATCCTCCCGGCCTTGCTAA 60.693 57.895 0.00 0.00 0.00 3.09
1650 1663 2.040884 ATCCTCCCGGCCTTGCTA 60.041 61.111 0.00 0.00 0.00 3.49
1692 1705 0.687427 TGTCCCGGATGCTCATCTGA 60.687 55.000 17.74 6.70 44.92 3.27
1752 1765 0.177604 CTGCCTCATCGAGCCTCTTT 59.822 55.000 0.00 0.00 0.00 2.52
1848 1861 3.222855 AGAGCGGCATCCTCCTCG 61.223 66.667 1.45 0.00 0.00 4.63
2098 2111 1.488705 AAGTCCCGTTCAGGCATCCA 61.489 55.000 0.00 0.00 39.21 3.41
2514 2527 0.843309 TGTTTCCAGGCTCCAACTGA 59.157 50.000 0.00 0.00 38.20 3.41
2788 2801 1.006805 GACACTCTCAGCACAGCGT 60.007 57.895 0.00 0.00 0.00 5.07
2814 2827 7.576287 GCATTCTTGTTCTGATGATTCTTTGGA 60.576 37.037 0.00 0.00 0.00 3.53
2860 2873 4.318332 CTGAAGGCAGAACAGTGAACATA 58.682 43.478 0.00 0.00 45.17 2.29
2873 2886 1.229428 TTCAAAGACGCTGAAGGCAG 58.771 50.000 0.00 0.00 45.13 4.85
2884 2897 4.540824 GAACACTCTGCCATTTCAAAGAC 58.459 43.478 0.00 0.00 0.00 3.01
3039 3053 3.940221 TGCGTTGTTAGTGGTGTTTAGTT 59.060 39.130 0.00 0.00 0.00 2.24
3054 3068 0.662619 CACACACTTCCATGCGTTGT 59.337 50.000 0.00 0.00 0.00 3.32
3059 3073 5.572211 CATATAACACACACACTTCCATGC 58.428 41.667 0.00 0.00 0.00 4.06
3111 3125 8.157476 AGTCAAACAGATATCCAACAACTTAGT 58.843 33.333 0.00 0.00 0.00 2.24
3298 3312 4.037208 CAGGAAAATTGACTTGCACAGAGT 59.963 41.667 0.00 0.00 0.00 3.24
3340 3354 6.706055 TCGCAGAAGTAGTTTCAAACATAG 57.294 37.500 2.41 0.00 38.31 2.23
3385 3399 3.356529 AATACCCTTTGGCTCTCAGTG 57.643 47.619 0.00 0.00 33.59 3.66
3402 3416 5.901276 ACTTCCTAGGATAACACGGGAAATA 59.099 40.000 13.57 0.00 33.31 1.40
3428 3442 5.472478 CCACCTCATCATTTATCTCACATGG 59.528 44.000 0.00 0.00 0.00 3.66
3630 3644 6.714810 TGGGCATGTATAATGGTTGATAAGTC 59.285 38.462 0.00 0.00 0.00 3.01
3680 3694 2.125106 ACCCTTCTTGGCGATCGC 60.125 61.111 31.52 31.52 41.06 4.58


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

AutoCloner maintained by Alex Coulton.