Multiple sequence alignment - TraesCS3B01G424900

Loading Multiple Alignment...

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 TraesCS3B01G424900 chr3B 100.000 4737 0 0 1 4737 662974762 662979498 0.000000e+00 8748
1 TraesCS3B01G424900 chr3B 87.654 243 23 5 1986 2226 662976808 662977045 4.670000e-70 276
2 TraesCS3B01G424900 chr3D 92.319 2721 150 33 1989 4678 501299385 501302077 0.000000e+00 3812
3 TraesCS3B01G424900 chr3D 85.951 2356 171 79 19 2284 501297337 501299622 0.000000e+00 2370
4 TraesCS3B01G424900 chr3D 88.462 286 23 5 2011 2287 501299284 501299568 2.110000e-88 337
5 TraesCS3B01G424900 chr3A 93.328 2518 131 24 1980 4484 640766636 640769129 0.000000e+00 3685
6 TraesCS3B01G424900 chr3A 86.839 2363 171 70 20 2287 640764388 640766705 0.000000e+00 2512
7 TraesCS3B01G424900 chr3A 89.308 318 23 6 1980 2287 640766451 640766767 5.750000e-104 388
8 TraesCS3B01G424900 chr3A 88.387 310 24 7 1989 2287 640766521 640766829 3.480000e-96 363
9 TraesCS3B01G424900 chr3A 87.179 312 31 7 1980 2284 640766574 640766883 3.510000e-91 346


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 TraesCS3B01G424900 chr3B 662974762 662979498 4736 False 4512.0 8748 93.827000 1 4737 2 chr3B.!!$F1 4736
1 TraesCS3B01G424900 chr3D 501297337 501302077 4740 False 2173.0 3812 88.910667 19 4678 3 chr3D.!!$F1 4659
2 TraesCS3B01G424900 chr3A 640764388 640769129 4741 False 1458.8 3685 89.008200 20 4484 5 chr3A.!!$F1 4464

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
475 491 0.110486 AAACCCAGGCAAGTCGTGAT 59.890 50.0 0.0 0.0 32.56 3.06 F
719 820 0.178861 TCCTTCCTCCCCTTGCTTCT 60.179 55.0 0.0 0.0 0.00 2.85 F
1805 1957 0.383949 TGTGAAGTTGCCGAAAAGCC 59.616 50.0 0.0 0.0 0.00 4.35 F
3190 3596 0.109723 TCACCCGTCTTTTCCTTGGG 59.890 55.0 0.0 0.0 45.70 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2258 2658 0.686789 TGAGCTCTAAACCTGCTGCA 59.313 50.0 16.19 0.88 37.16 4.41 R
2371 2772 0.865769 CGAAAAGCTAAGGTGCACGT 59.134 50.0 11.45 8.83 34.99 4.49 R
3505 3911 0.719465 GTTCCGCAACGATCGTCAAT 59.281 50.0 22.98 2.55 0.00 2.57 R
4607 5048 0.322975 CCCGATATTGGCTCCAGGAG 59.677 60.0 12.81 12.81 0.00 3.69 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
44 45 6.538021 ACATATCTTGTTGTTCTCAGCTGATC 59.462 38.462 18.63 11.38 33.74 2.92
82 83 4.322385 GGCGTTGACCGTTGCCAC 62.322 66.667 0.00 0.00 46.76 5.01
116 117 4.811969 TTATACGTGCCTTCCAGAAAGA 57.188 40.909 0.00 0.00 37.12 2.52
123 124 4.681781 CGTGCCTTCCAGAAAGATATCTGT 60.682 45.833 5.86 0.00 44.32 3.41
131 132 7.718334 TCCAGAAAGATATCTGTGTCTGTTA 57.282 36.000 25.21 16.87 44.32 2.41
136 137 8.367911 AGAAAGATATCTGTGTCTGTTACAACA 58.632 33.333 5.86 0.00 40.63 3.33
166 168 5.163478 GCTGAACCTGATTGGCATAGAAAAT 60.163 40.000 0.00 0.00 40.22 1.82
168 170 5.127519 TGAACCTGATTGGCATAGAAAATGG 59.872 40.000 0.00 0.00 40.22 3.16
169 171 4.870636 ACCTGATTGGCATAGAAAATGGA 58.129 39.130 0.00 0.00 40.22 3.41
177 179 4.352001 TGGCATAGAAAATGGAGAGGCTAT 59.648 41.667 0.00 0.00 0.00 2.97
183 185 6.168270 AGAAAATGGAGAGGCTATGACTAC 57.832 41.667 0.00 0.00 0.00 2.73
204 210 1.374758 CCGACACAACAGAGGAGGC 60.375 63.158 0.00 0.00 0.00 4.70
226 232 3.923273 AAAAATGAAGGGGGAAGACCT 57.077 42.857 0.00 0.00 40.96 3.85
228 234 5.552430 AAAAATGAAGGGGGAAGACCTAT 57.448 39.130 0.00 0.00 37.35 2.57
230 236 4.526438 AATGAAGGGGGAAGACCTATTG 57.474 45.455 0.00 0.00 37.35 1.90
231 237 2.929301 TGAAGGGGGAAGACCTATTGT 58.071 47.619 0.00 0.00 37.35 2.71
232 238 3.265489 TGAAGGGGGAAGACCTATTGTT 58.735 45.455 0.00 0.00 37.35 2.83
234 240 4.263771 TGAAGGGGGAAGACCTATTGTTTC 60.264 45.833 0.00 0.00 37.35 2.78
235 241 3.265489 AGGGGGAAGACCTATTGTTTCA 58.735 45.455 0.00 0.00 40.03 2.69
236 242 3.010250 AGGGGGAAGACCTATTGTTTCAC 59.990 47.826 0.00 0.00 40.03 3.18
238 244 4.569865 GGGGGAAGACCTATTGTTTCACAT 60.570 45.833 0.00 0.00 40.03 3.21
241 247 6.661805 GGGGAAGACCTATTGTTTCACATAAA 59.338 38.462 0.00 0.00 40.03 1.40
242 248 7.148069 GGGGAAGACCTATTGTTTCACATAAAG 60.148 40.741 0.00 0.00 40.03 1.85
243 249 7.610305 GGGAAGACCTATTGTTTCACATAAAGA 59.390 37.037 0.00 0.00 35.85 2.52
264 271 7.530426 AAGATTTCCATAAAGAAGTGCTTGT 57.470 32.000 0.00 0.00 36.80 3.16
295 302 4.020617 CGCACCAGCTTGGGAGGA 62.021 66.667 0.00 0.00 43.37 3.71
326 333 0.181350 AACCGATGGAATCTGGGAGC 59.819 55.000 0.00 0.00 42.58 4.70
427 443 2.283604 TCGCTCCACCACTAGGCA 60.284 61.111 0.00 0.00 39.06 4.75
428 444 2.185350 CGCTCCACCACTAGGCAG 59.815 66.667 0.00 0.00 39.06 4.85
453 469 1.333619 TGAGAACGGAAACTGCAAAGC 59.666 47.619 0.00 0.00 0.00 3.51
465 481 2.356194 CAAAGCGCAAACCCAGGC 60.356 61.111 11.47 0.00 0.00 4.85
466 482 2.837291 AAAGCGCAAACCCAGGCA 60.837 55.556 11.47 0.00 0.00 4.75
467 483 2.430610 AAAGCGCAAACCCAGGCAA 61.431 52.632 11.47 0.00 0.00 4.52
468 484 2.367868 AAAGCGCAAACCCAGGCAAG 62.368 55.000 11.47 0.00 0.00 4.01
469 485 3.605664 GCGCAAACCCAGGCAAGT 61.606 61.111 0.30 0.00 0.00 3.16
470 486 2.644992 CGCAAACCCAGGCAAGTC 59.355 61.111 0.00 0.00 0.00 3.01
471 487 2.644992 GCAAACCCAGGCAAGTCG 59.355 61.111 0.00 0.00 0.00 4.18
472 488 2.193536 GCAAACCCAGGCAAGTCGT 61.194 57.895 0.00 0.00 0.00 4.34
473 489 1.654220 CAAACCCAGGCAAGTCGTG 59.346 57.895 0.00 0.00 0.00 4.35
474 490 0.817634 CAAACCCAGGCAAGTCGTGA 60.818 55.000 0.00 0.00 32.56 4.35
475 491 0.110486 AAACCCAGGCAAGTCGTGAT 59.890 50.000 0.00 0.00 32.56 3.06
476 492 0.981183 AACCCAGGCAAGTCGTGATA 59.019 50.000 0.00 0.00 32.56 2.15
477 493 0.249398 ACCCAGGCAAGTCGTGATAC 59.751 55.000 0.00 0.00 32.56 2.24
478 494 0.249120 CCCAGGCAAGTCGTGATACA 59.751 55.000 0.00 0.00 32.56 2.29
479 495 1.645034 CCAGGCAAGTCGTGATACAG 58.355 55.000 0.00 0.00 32.56 2.74
480 496 1.002366 CAGGCAAGTCGTGATACAGC 58.998 55.000 0.00 0.00 32.56 4.40
481 497 0.898320 AGGCAAGTCGTGATACAGCT 59.102 50.000 0.00 0.00 0.00 4.24
482 498 2.100197 AGGCAAGTCGTGATACAGCTA 58.900 47.619 0.00 0.00 0.00 3.32
483 499 2.159226 AGGCAAGTCGTGATACAGCTAC 60.159 50.000 0.00 0.00 0.00 3.58
484 500 2.159226 GGCAAGTCGTGATACAGCTACT 60.159 50.000 0.00 0.00 0.00 2.57
489 505 6.420588 CAAGTCGTGATACAGCTACTACTAC 58.579 44.000 0.00 0.00 0.00 2.73
491 507 6.347696 AGTCGTGATACAGCTACTACTACTT 58.652 40.000 0.00 0.00 0.00 2.24
516 573 4.974721 CACCACCACCACCAGGCC 62.975 72.222 0.00 0.00 39.06 5.19
542 599 1.227141 GAATTTGAACGACGAACGCG 58.773 50.000 3.53 3.53 46.94 6.01
576 655 4.168291 GCAGGGGGCCGAGAGAAG 62.168 72.222 0.00 0.00 36.11 2.85
577 656 2.364317 CAGGGGGCCGAGAGAAGA 60.364 66.667 0.00 0.00 0.00 2.87
578 657 2.042435 AGGGGGCCGAGAGAAGAG 60.042 66.667 0.00 0.00 0.00 2.85
579 658 3.157949 GGGGGCCGAGAGAAGAGG 61.158 72.222 0.00 0.00 0.00 3.69
639 735 2.102578 CAAAAATCCCCATCGCTTCCT 58.897 47.619 0.00 0.00 0.00 3.36
708 809 1.801309 CGCCCTCTCGATCCTTCCTC 61.801 65.000 0.00 0.00 0.00 3.71
711 812 0.830023 CCTCTCGATCCTTCCTCCCC 60.830 65.000 0.00 0.00 0.00 4.81
712 813 0.187361 CTCTCGATCCTTCCTCCCCT 59.813 60.000 0.00 0.00 0.00 4.79
713 814 0.637195 TCTCGATCCTTCCTCCCCTT 59.363 55.000 0.00 0.00 0.00 3.95
714 815 0.755686 CTCGATCCTTCCTCCCCTTG 59.244 60.000 0.00 0.00 0.00 3.61
715 816 1.147153 CGATCCTTCCTCCCCTTGC 59.853 63.158 0.00 0.00 0.00 4.01
718 819 0.922626 ATCCTTCCTCCCCTTGCTTC 59.077 55.000 0.00 0.00 0.00 3.86
719 820 0.178861 TCCTTCCTCCCCTTGCTTCT 60.179 55.000 0.00 0.00 0.00 2.85
721 822 1.284313 CTTCCTCCCCTTGCTTCTCT 58.716 55.000 0.00 0.00 0.00 3.10
722 823 1.209261 CTTCCTCCCCTTGCTTCTCTC 59.791 57.143 0.00 0.00 0.00 3.20
724 825 0.829990 CCTCCCCTTGCTTCTCTCTC 59.170 60.000 0.00 0.00 0.00 3.20
727 828 1.519719 CCCTTGCTTCTCTCTCCCG 59.480 63.158 0.00 0.00 0.00 5.14
733 837 0.741915 GCTTCTCTCTCCCGTACCAG 59.258 60.000 0.00 0.00 0.00 4.00
737 841 1.077930 TCTCTCCCGTACCAGACCG 60.078 63.158 0.00 0.00 0.00 4.79
763 877 1.153309 CTGCTGCCATCATCCGTCA 60.153 57.895 0.00 0.00 0.00 4.35
864 983 1.293683 AATCCGGCCCCATTAACCCT 61.294 55.000 0.00 0.00 0.00 4.34
910 1029 4.637489 CCGCCAGCTCCGATCGAG 62.637 72.222 18.66 13.00 42.04 4.04
911 1030 4.637489 CGCCAGCTCCGATCGAGG 62.637 72.222 18.66 10.99 39.22 4.63
913 1032 3.531207 CCAGCTCCGATCGAGGCA 61.531 66.667 25.41 5.69 39.22 4.75
914 1033 2.027314 CAGCTCCGATCGAGGCAG 59.973 66.667 25.41 17.76 39.22 4.85
917 1036 3.610669 CTCCGATCGAGGCAGGGG 61.611 72.222 18.66 0.00 34.67 4.79
920 1039 2.919856 CGATCGAGGCAGGGGGAT 60.920 66.667 10.26 0.00 0.00 3.85
921 1040 2.511452 CGATCGAGGCAGGGGGATT 61.511 63.158 10.26 0.00 0.00 3.01
1047 1188 0.441921 GCGTCTTCTTCAAGCTGCTC 59.558 55.000 1.00 0.00 30.77 4.26
1209 1356 2.266055 GTCGCCTCCAAGGACCTG 59.734 66.667 0.00 0.00 37.67 4.00
1715 1862 9.059260 GGCAAGGTATAATTTAATTCGGTTCTA 57.941 33.333 0.00 0.00 0.00 2.10
1767 1919 3.939592 GCTTCGACTTTACTAAATGGCCT 59.060 43.478 3.32 0.00 0.00 5.19
1798 1950 1.280746 CTGCAGTGTGAAGTTGCCG 59.719 57.895 5.25 0.00 37.03 5.69
1805 1957 0.383949 TGTGAAGTTGCCGAAAAGCC 59.616 50.000 0.00 0.00 0.00 4.35
1891 2043 4.768968 ACCAGCATTATTTCAGAAACTGCT 59.231 37.500 17.67 17.67 35.57 4.24
1895 2047 7.307694 CAGCATTATTTCAGAAACTGCTAACA 58.692 34.615 20.78 0.00 34.31 2.41
1931 2083 7.908193 AATTAAGTGAACATGTCAAAACGAC 57.092 32.000 0.00 0.00 45.61 4.34
1968 2121 8.067751 TCCCTATCTATTCGATCTGTTATTGG 57.932 38.462 0.00 0.00 33.48 3.16
2009 2223 4.524802 ATTTCCCTGTGAGATGCCATTA 57.475 40.909 0.00 0.00 0.00 1.90
2041 2441 3.118811 GCAGGTTTAGAGAGAGCTCATGT 60.119 47.826 17.77 5.13 43.81 3.21
2071 2471 2.645192 CCCCGTGGGTTGCCATTTC 61.645 63.158 3.83 0.00 38.25 2.17
2101 2501 3.132646 CAGCAGGTTTAGAGAGAGCTCAT 59.867 47.826 17.77 3.42 43.81 2.90
2108 2508 6.490040 AGGTTTAGAGAGAGCTCATGAGTATC 59.510 42.308 23.38 20.05 43.81 2.24
2134 2534 2.566010 CCGTGGGTTGCCATTTCG 59.434 61.111 0.00 0.00 0.00 3.46
2140 2540 1.339631 TGGGTTGCCATTTCGGACTAG 60.340 52.381 0.00 0.00 36.56 2.57
2219 2619 2.492484 ACTAGCAGTGGTTTAGAGACCG 59.508 50.000 0.00 0.00 42.83 4.79
2238 2638 0.746923 GTGAGTACGGCATTTCCCCC 60.747 60.000 0.00 0.00 0.00 5.40
2239 2639 0.912487 TGAGTACGGCATTTCCCCCT 60.912 55.000 0.00 0.00 0.00 4.79
2247 2647 1.607801 GCATTTCCCCCTGAGTTGCC 61.608 60.000 0.00 0.00 30.53 4.52
2258 2658 3.152341 CCTGAGTTGCCATTTCTGACTT 58.848 45.455 0.00 0.00 0.00 3.01
2389 2790 4.477302 TTTACGTGCACCTTAGCTTTTC 57.523 40.909 12.15 0.00 34.99 2.29
2498 2899 7.318141 ACATTCTCCAAATGATGTTGACATTC 58.682 34.615 4.86 0.00 37.04 2.67
2523 2924 6.671190 TGAAGATGTCAATGCAACTTTACAG 58.329 36.000 0.00 0.00 31.51 2.74
2526 2927 4.829064 TGTCAATGCAACTTTACAGGAC 57.171 40.909 0.00 0.00 0.00 3.85
2539 2940 0.532862 ACAGGACTTGCTTGACCGTG 60.533 55.000 0.00 0.00 0.00 4.94
2616 3017 7.191593 ACAAAGTTCTATATTCCGGTAGGTT 57.808 36.000 0.00 0.00 39.05 3.50
2656 3057 4.019792 ACTGCTAATGATGTCACCACAA 57.980 40.909 0.00 0.00 35.64 3.33
2660 3061 3.002656 GCTAATGATGTCACCACAATCCG 59.997 47.826 0.00 0.00 35.64 4.18
2907 3308 5.650266 TCATGCCTTTTTATTATGTCCGTGT 59.350 36.000 0.00 0.00 0.00 4.49
2991 3392 6.694447 GTGTATCACACCTACCTGAGTTTAA 58.306 40.000 0.00 0.00 43.05 1.52
3003 3404 4.141018 ACCTGAGTTTAAACCCCTCAACAT 60.141 41.667 14.72 0.00 34.99 2.71
3072 3476 9.237187 TGTGCTAACATCATTAAATGGTTCTTA 57.763 29.630 0.00 0.00 0.00 2.10
3082 3486 8.832735 TCATTAAATGGTTCTTACCTTCTACCT 58.167 33.333 0.00 0.00 45.27 3.08
3156 3562 4.040445 ACTGTTGTACATTTGTGTTGCC 57.960 40.909 0.00 0.00 0.00 4.52
3190 3596 0.109723 TCACCCGTCTTTTCCTTGGG 59.890 55.000 0.00 0.00 45.70 4.12
3367 3773 2.223044 GGAAATAAGGCTTGCGAACTCG 60.223 50.000 10.69 0.00 43.27 4.18
3505 3911 0.835115 TGAAATGCATGCCCCCAACA 60.835 50.000 16.68 5.32 0.00 3.33
3511 3917 1.512230 CATGCCCCCAACATTGACG 59.488 57.895 0.00 0.00 0.00 4.35
3661 4067 0.764369 TCCTCAAGACACCACAGGCT 60.764 55.000 0.00 0.00 0.00 4.58
3776 4182 7.877612 TCAGCATTGTGAAATAGAGTCTTTACA 59.122 33.333 0.00 0.00 0.00 2.41
3842 4248 3.378742 TGCAAGTTAAAAGGCGAAGAACA 59.621 39.130 0.00 0.00 0.00 3.18
3955 4363 1.591059 CAGATGCTCTTCCGCCTCG 60.591 63.158 0.00 0.00 31.06 4.63
4004 4412 7.883391 TTGTACCCTTTGTGAAGTATTGAAA 57.117 32.000 0.00 0.00 0.00 2.69
4008 4416 5.539955 ACCCTTTGTGAAGTATTGAAATGCT 59.460 36.000 0.00 0.00 32.47 3.79
4063 4476 8.159447 AGAATTATCATCTAAGCTGTTGGCATA 58.841 33.333 0.00 0.00 44.79 3.14
4084 4497 7.918562 GGCATACCATAACACGTGAATAATTTT 59.081 33.333 25.01 6.55 35.26 1.82
4106 4519 6.471233 TTTACCATCAAACATTGTCAACCA 57.529 33.333 0.00 0.00 0.00 3.67
4129 4542 1.486211 TGCTCTACTGCCTTCCTACC 58.514 55.000 0.00 0.00 0.00 3.18
4131 4544 2.112190 GCTCTACTGCCTTCCTACCTT 58.888 52.381 0.00 0.00 0.00 3.50
4132 4545 2.502130 GCTCTACTGCCTTCCTACCTTT 59.498 50.000 0.00 0.00 0.00 3.11
4133 4546 3.680196 GCTCTACTGCCTTCCTACCTTTG 60.680 52.174 0.00 0.00 0.00 2.77
4136 4549 3.595190 ACTGCCTTCCTACCTTTGTTT 57.405 42.857 0.00 0.00 0.00 2.83
4137 4550 3.222603 ACTGCCTTCCTACCTTTGTTTG 58.777 45.455 0.00 0.00 0.00 2.93
4139 4552 1.272490 GCCTTCCTACCTTTGTTTGCC 59.728 52.381 0.00 0.00 0.00 4.52
4141 4554 2.820197 CCTTCCTACCTTTGTTTGCCTC 59.180 50.000 0.00 0.00 0.00 4.70
4142 4555 3.498661 CCTTCCTACCTTTGTTTGCCTCT 60.499 47.826 0.00 0.00 0.00 3.69
4143 4556 3.876309 TCCTACCTTTGTTTGCCTCTT 57.124 42.857 0.00 0.00 0.00 2.85
4144 4557 3.486383 TCCTACCTTTGTTTGCCTCTTG 58.514 45.455 0.00 0.00 0.00 3.02
4145 4558 3.137544 TCCTACCTTTGTTTGCCTCTTGA 59.862 43.478 0.00 0.00 0.00 3.02
4146 4559 3.888930 CCTACCTTTGTTTGCCTCTTGAA 59.111 43.478 0.00 0.00 0.00 2.69
4147 4560 4.340950 CCTACCTTTGTTTGCCTCTTGAAA 59.659 41.667 0.00 0.00 0.00 2.69
4148 4561 5.011023 CCTACCTTTGTTTGCCTCTTGAAAT 59.989 40.000 0.00 0.00 0.00 2.17
4150 4563 6.670695 ACCTTTGTTTGCCTCTTGAAATAT 57.329 33.333 0.00 0.00 0.00 1.28
4152 4565 8.189119 ACCTTTGTTTGCCTCTTGAAATATTA 57.811 30.769 0.00 0.00 0.00 0.98
4187 4600 9.846248 GTTTGAAATTATAAGATGAAGTGCAGT 57.154 29.630 0.00 0.00 0.00 4.40
4190 4603 8.668353 TGAAATTATAAGATGAAGTGCAGTGTC 58.332 33.333 0.00 0.00 0.00 3.67
4191 4604 8.565896 AAATTATAAGATGAAGTGCAGTGTCA 57.434 30.769 0.00 1.81 0.00 3.58
4192 4605 8.743085 AATTATAAGATGAAGTGCAGTGTCAT 57.257 30.769 14.95 14.95 34.71 3.06
4193 4606 9.836864 AATTATAAGATGAAGTGCAGTGTCATA 57.163 29.630 14.98 4.91 32.18 2.15
4194 4607 9.836864 ATTATAAGATGAAGTGCAGTGTCATAA 57.163 29.630 14.98 8.89 32.18 1.90
4195 4608 7.783090 ATAAGATGAAGTGCAGTGTCATAAG 57.217 36.000 14.98 0.00 32.18 1.73
4206 4620 5.622378 GCAGTGTCATAAGTCTGCTTAAAC 58.378 41.667 8.46 0.00 46.35 2.01
4217 4631 7.256286 TAAGTCTGCTTAAACGAGAGTTATCC 58.744 38.462 0.00 0.00 43.90 2.59
4227 4641 3.182967 CGAGAGTTATCCTTGAGTGCAC 58.817 50.000 9.40 9.40 0.00 4.57
4228 4642 3.367395 CGAGAGTTATCCTTGAGTGCACA 60.367 47.826 21.04 0.00 0.00 4.57
4229 4643 4.679106 CGAGAGTTATCCTTGAGTGCACAT 60.679 45.833 21.04 4.90 0.00 3.21
4234 4648 2.831685 TCCTTGAGTGCACATTACGT 57.168 45.000 21.04 0.00 0.00 3.57
4235 4649 3.120321 TCCTTGAGTGCACATTACGTT 57.880 42.857 21.04 0.00 0.00 3.99
4292 4706 6.681865 GCAAGGCTTTAAAGTGAAACCTGTTA 60.682 38.462 16.38 0.00 37.80 2.41
4293 4707 6.387041 AGGCTTTAAAGTGAAACCTGTTAC 57.613 37.500 16.38 0.00 37.80 2.50
4294 4708 6.127101 AGGCTTTAAAGTGAAACCTGTTACT 58.873 36.000 16.38 0.00 37.80 2.24
4315 4729 2.649331 AAAGACATGCTTCATGCTGC 57.351 45.000 6.71 0.00 44.80 5.25
4348 4762 2.909006 TCCAGGCTCAAGTTTCTCATCT 59.091 45.455 0.00 0.00 0.00 2.90
4357 4771 7.984617 GGCTCAAGTTTCTCATCTAAGTATCTT 59.015 37.037 0.00 0.00 0.00 2.40
4358 4772 8.816144 GCTCAAGTTTCTCATCTAAGTATCTTG 58.184 37.037 0.00 0.00 0.00 3.02
4396 4810 6.669125 ATCATGGTTCATGTTCCTTTTCAA 57.331 33.333 7.63 0.00 41.98 2.69
4397 4811 6.477053 TCATGGTTCATGTTCCTTTTCAAA 57.523 33.333 7.63 0.00 41.98 2.69
4403 4817 8.482128 TGGTTCATGTTCCTTTTCAAATAAAGT 58.518 29.630 9.49 0.00 34.11 2.66
4439 4853 7.759489 AGACAAAAAGCAATACTCCACATAA 57.241 32.000 0.00 0.00 0.00 1.90
4451 4865 8.355169 CAATACTCCACATAATTGAAATCCTGG 58.645 37.037 0.00 0.00 32.29 4.45
4456 4870 6.159575 TCCACATAATTGAAATCCTGGGAGTA 59.840 38.462 0.00 0.00 0.00 2.59
4462 4876 5.693769 TTGAAATCCTGGGAGTAGGTTAG 57.306 43.478 0.00 0.00 38.99 2.34
4479 4893 9.125026 AGTAGGTTAGCAATAATCAAATGAAGG 57.875 33.333 0.00 0.00 0.00 3.46
4487 4901 9.643693 AGCAATAATCAAATGAAGGTGTTAAAG 57.356 29.630 0.00 0.00 0.00 1.85
4490 4930 9.995003 AATAATCAAATGAAGGTGTTAAAGCAA 57.005 25.926 0.00 0.00 0.00 3.91
4508 4948 6.899393 AAGCAACATTAAACATTCCTCTGA 57.101 33.333 0.00 0.00 0.00 3.27
4522 4962 2.558795 TCCTCTGAAAGAACACTCTCCG 59.441 50.000 0.00 0.00 46.34 4.63
4526 4966 1.686587 TGAAAGAACACTCTCCGCAGA 59.313 47.619 0.00 0.00 0.00 4.26
4527 4967 2.062519 GAAAGAACACTCTCCGCAGAC 58.937 52.381 0.00 0.00 0.00 3.51
4528 4968 0.318762 AAGAACACTCTCCGCAGACC 59.681 55.000 0.00 0.00 0.00 3.85
4529 4969 0.827925 AGAACACTCTCCGCAGACCA 60.828 55.000 0.00 0.00 0.00 4.02
4532 4972 1.080230 CACTCTCCGCAGACCACAG 60.080 63.158 0.00 0.00 0.00 3.66
4533 4973 1.531840 ACTCTCCGCAGACCACAGT 60.532 57.895 0.00 0.00 0.00 3.55
4534 4974 0.251209 ACTCTCCGCAGACCACAGTA 60.251 55.000 0.00 0.00 0.00 2.74
4535 4975 0.888619 CTCTCCGCAGACCACAGTAA 59.111 55.000 0.00 0.00 0.00 2.24
4538 4978 0.172578 TCCGCAGACCACAGTAATCG 59.827 55.000 0.00 0.00 0.00 3.34
4539 4979 0.172578 CCGCAGACCACAGTAATCGA 59.827 55.000 0.00 0.00 0.00 3.59
4540 4980 1.403647 CCGCAGACCACAGTAATCGAA 60.404 52.381 0.00 0.00 0.00 3.71
4541 4981 1.654105 CGCAGACCACAGTAATCGAAC 59.346 52.381 0.00 0.00 0.00 3.95
4542 4982 2.671351 CGCAGACCACAGTAATCGAACT 60.671 50.000 0.00 0.00 0.00 3.01
4543 4983 3.326747 GCAGACCACAGTAATCGAACTT 58.673 45.455 0.00 0.00 0.00 2.66
4571 5011 3.760580 AGCTGCAGTTGTCTTCTTAGT 57.239 42.857 16.64 0.00 0.00 2.24
4581 5021 7.698970 GCAGTTGTCTTCTTAGTATAGTCAGTC 59.301 40.741 0.00 0.00 0.00 3.51
4624 5065 0.321122 GCCTCCTGGAGCCAATATCG 60.321 60.000 18.51 3.20 34.57 2.92
4632 5073 2.644299 TGGAGCCAATATCGGGAATGAT 59.356 45.455 0.00 0.00 0.00 2.45
4654 5095 2.031769 GCAAAGGCATTTTTGAACAGCC 60.032 45.455 10.58 0.00 45.54 4.85
4663 5104 4.497473 TTTTTGAACAGCCGTCATAAGG 57.503 40.909 0.00 0.00 0.00 2.69
4674 5115 3.792401 CCGTCATAAGGTATGCAGTCAA 58.208 45.455 0.00 0.00 36.14 3.18
4678 5119 6.481976 CCGTCATAAGGTATGCAGTCAAATAA 59.518 38.462 0.00 0.00 36.14 1.40
4679 5120 7.345192 CGTCATAAGGTATGCAGTCAAATAAC 58.655 38.462 0.00 0.00 36.14 1.89
4680 5121 7.011016 CGTCATAAGGTATGCAGTCAAATAACA 59.989 37.037 0.00 0.00 36.14 2.41
4681 5122 8.122952 GTCATAAGGTATGCAGTCAAATAACAC 58.877 37.037 0.00 0.00 36.14 3.32
4682 5123 5.545658 AAGGTATGCAGTCAAATAACACG 57.454 39.130 0.00 0.00 0.00 4.49
4683 5124 3.374058 AGGTATGCAGTCAAATAACACGC 59.626 43.478 0.00 0.00 0.00 5.34
4684 5125 2.919666 ATGCAGTCAAATAACACGCC 57.080 45.000 0.00 0.00 0.00 5.68
4685 5126 0.515127 TGCAGTCAAATAACACGCCG 59.485 50.000 0.00 0.00 0.00 6.46
4686 5127 0.179200 GCAGTCAAATAACACGCCGG 60.179 55.000 0.00 0.00 0.00 6.13
4687 5128 1.153353 CAGTCAAATAACACGCCGGT 58.847 50.000 1.90 0.00 0.00 5.28
4688 5129 2.339418 CAGTCAAATAACACGCCGGTA 58.661 47.619 1.90 0.00 0.00 4.02
4689 5130 2.933906 CAGTCAAATAACACGCCGGTAT 59.066 45.455 1.90 0.00 0.00 2.73
4690 5131 2.933906 AGTCAAATAACACGCCGGTATG 59.066 45.455 1.90 4.17 0.00 2.39
4691 5132 2.031191 GTCAAATAACACGCCGGTATGG 59.969 50.000 1.90 0.00 42.50 2.74
4692 5133 2.093606 TCAAATAACACGCCGGTATGGA 60.094 45.455 1.90 0.00 42.00 3.41
4693 5134 2.234300 AATAACACGCCGGTATGGAG 57.766 50.000 1.90 0.00 44.31 3.86
4694 5135 1.405872 ATAACACGCCGGTATGGAGA 58.594 50.000 1.90 0.00 40.56 3.71
4695 5136 0.457035 TAACACGCCGGTATGGAGAC 59.543 55.000 1.90 0.00 40.56 3.36
4696 5137 1.255667 AACACGCCGGTATGGAGACT 61.256 55.000 1.90 0.00 40.56 3.24
4697 5138 1.255667 ACACGCCGGTATGGAGACTT 61.256 55.000 1.90 0.00 40.56 3.01
4698 5139 0.527817 CACGCCGGTATGGAGACTTC 60.528 60.000 1.90 0.00 40.56 3.01
4699 5140 0.968901 ACGCCGGTATGGAGACTTCA 60.969 55.000 1.90 0.00 40.56 3.02
4700 5141 0.389391 CGCCGGTATGGAGACTTCAT 59.611 55.000 1.90 0.88 40.56 2.57
4701 5142 1.202533 CGCCGGTATGGAGACTTCATT 60.203 52.381 0.36 0.00 40.56 2.57
4702 5143 2.741878 CGCCGGTATGGAGACTTCATTT 60.742 50.000 0.36 0.00 40.56 2.32
4703 5144 2.614057 GCCGGTATGGAGACTTCATTTG 59.386 50.000 0.36 0.00 42.00 2.32
4704 5145 3.873910 CCGGTATGGAGACTTCATTTGT 58.126 45.455 0.36 0.00 42.00 2.83
4705 5146 4.682320 GCCGGTATGGAGACTTCATTTGTA 60.682 45.833 0.36 0.00 42.00 2.41
4706 5147 5.424757 CCGGTATGGAGACTTCATTTGTAA 58.575 41.667 0.36 0.00 42.00 2.41
4707 5148 6.055588 CCGGTATGGAGACTTCATTTGTAAT 58.944 40.000 0.36 0.00 42.00 1.89
4708 5149 6.202954 CCGGTATGGAGACTTCATTTGTAATC 59.797 42.308 0.36 0.00 42.00 1.75
4709 5150 6.074302 CGGTATGGAGACTTCATTTGTAATCG 60.074 42.308 0.36 0.00 0.00 3.34
4710 5151 6.761714 GGTATGGAGACTTCATTTGTAATCGT 59.238 38.462 0.36 0.00 0.00 3.73
4711 5152 6.910536 ATGGAGACTTCATTTGTAATCGTC 57.089 37.500 0.00 0.00 0.00 4.20
4712 5153 5.789521 TGGAGACTTCATTTGTAATCGTCA 58.210 37.500 0.00 0.00 0.00 4.35
4713 5154 6.227522 TGGAGACTTCATTTGTAATCGTCAA 58.772 36.000 0.00 0.00 0.00 3.18
4714 5155 6.147164 TGGAGACTTCATTTGTAATCGTCAAC 59.853 38.462 0.00 0.00 0.00 3.18
4715 5156 6.402226 GGAGACTTCATTTGTAATCGTCAACC 60.402 42.308 0.00 0.00 0.00 3.77
4716 5157 5.411669 AGACTTCATTTGTAATCGTCAACCC 59.588 40.000 0.00 0.00 0.00 4.11
4717 5158 5.313712 ACTTCATTTGTAATCGTCAACCCT 58.686 37.500 0.00 0.00 0.00 4.34
4718 5159 5.768164 ACTTCATTTGTAATCGTCAACCCTT 59.232 36.000 0.00 0.00 0.00 3.95
4719 5160 6.938030 ACTTCATTTGTAATCGTCAACCCTTA 59.062 34.615 0.00 0.00 0.00 2.69
4720 5161 7.610305 ACTTCATTTGTAATCGTCAACCCTTAT 59.390 33.333 0.00 0.00 0.00 1.73
4721 5162 7.931578 TCATTTGTAATCGTCAACCCTTATT 57.068 32.000 0.00 0.00 0.00 1.40
4722 5163 7.757526 TCATTTGTAATCGTCAACCCTTATTG 58.242 34.615 0.00 0.00 0.00 1.90
4723 5164 7.392113 TCATTTGTAATCGTCAACCCTTATTGT 59.608 33.333 0.00 0.00 0.00 2.71
4724 5165 6.489127 TTGTAATCGTCAACCCTTATTGTG 57.511 37.500 0.00 0.00 0.00 3.33
4725 5166 5.553123 TGTAATCGTCAACCCTTATTGTGT 58.447 37.500 0.00 0.00 0.00 3.72
4726 5167 5.640357 TGTAATCGTCAACCCTTATTGTGTC 59.360 40.000 0.00 0.00 0.00 3.67
4727 5168 4.553330 ATCGTCAACCCTTATTGTGTCT 57.447 40.909 0.00 0.00 0.00 3.41
4728 5169 4.345859 TCGTCAACCCTTATTGTGTCTT 57.654 40.909 0.00 0.00 0.00 3.01
4729 5170 4.710324 TCGTCAACCCTTATTGTGTCTTT 58.290 39.130 0.00 0.00 0.00 2.52
4730 5171 5.856156 TCGTCAACCCTTATTGTGTCTTTA 58.144 37.500 0.00 0.00 0.00 1.85
4731 5172 6.289834 TCGTCAACCCTTATTGTGTCTTTAA 58.710 36.000 0.00 0.00 0.00 1.52
4732 5173 6.766944 TCGTCAACCCTTATTGTGTCTTTAAA 59.233 34.615 0.00 0.00 0.00 1.52
4733 5174 7.446013 TCGTCAACCCTTATTGTGTCTTTAAAT 59.554 33.333 0.00 0.00 0.00 1.40
4734 5175 8.079809 CGTCAACCCTTATTGTGTCTTTAAATT 58.920 33.333 0.00 0.00 0.00 1.82
4735 5176 9.758651 GTCAACCCTTATTGTGTCTTTAAATTT 57.241 29.630 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.486123 AGATATGTACAGCTGTATTATCCATCT 57.514 33.333 31.54 25.98 33.56 2.90
2 3 9.881649 CAAGATATGTACAGCTGTATTATCCAT 57.118 33.333 31.54 27.71 33.56 3.41
3 4 8.870116 ACAAGATATGTACAGCTGTATTATCCA 58.130 33.333 31.54 24.78 41.63 3.41
4 5 9.712305 AACAAGATATGTACAGCTGTATTATCC 57.288 33.333 31.54 21.48 42.99 2.59
7 8 9.884636 AACAACAAGATATGTACAGCTGTATTA 57.115 29.630 28.37 21.79 42.99 0.98
8 9 8.792830 AACAACAAGATATGTACAGCTGTATT 57.207 30.769 28.37 20.49 42.99 1.89
9 10 8.260818 AGAACAACAAGATATGTACAGCTGTAT 58.739 33.333 28.37 17.58 42.99 2.29
10 11 7.611770 AGAACAACAAGATATGTACAGCTGTA 58.388 34.615 22.67 22.67 42.99 2.74
11 12 6.467677 AGAACAACAAGATATGTACAGCTGT 58.532 36.000 25.12 25.12 42.99 4.40
12 13 6.591448 TGAGAACAACAAGATATGTACAGCTG 59.409 38.462 13.48 13.48 42.99 4.24
13 14 6.701340 TGAGAACAACAAGATATGTACAGCT 58.299 36.000 0.33 0.00 42.99 4.24
14 15 6.456181 GCTGAGAACAACAAGATATGTACAGC 60.456 42.308 0.33 0.00 42.99 4.40
15 16 6.815641 AGCTGAGAACAACAAGATATGTACAG 59.184 38.462 0.33 0.00 42.99 2.74
16 17 6.591448 CAGCTGAGAACAACAAGATATGTACA 59.409 38.462 8.42 0.00 42.99 2.90
17 18 6.813649 TCAGCTGAGAACAACAAGATATGTAC 59.186 38.462 13.74 0.00 42.99 2.90
27 28 3.515630 GATCGATCAGCTGAGAACAACA 58.484 45.455 22.96 1.83 0.00 3.33
82 83 0.869730 CGTATAAAAATCCCCGCCCG 59.130 55.000 0.00 0.00 0.00 6.13
85 86 1.002142 GGCACGTATAAAAATCCCCGC 60.002 52.381 0.00 0.00 0.00 6.13
88 89 3.949113 TGGAAGGCACGTATAAAAATCCC 59.051 43.478 0.00 0.00 0.00 3.85
131 132 2.092968 TCAGGTTCAGCAACTCTGTTGT 60.093 45.455 11.35 0.00 43.32 3.32
136 137 2.787994 CCAATCAGGTTCAGCAACTCT 58.212 47.619 0.00 0.00 32.50 3.24
139 140 0.961019 TGCCAATCAGGTTCAGCAAC 59.039 50.000 0.00 0.00 40.61 4.17
145 146 5.360714 TCCATTTTCTATGCCAATCAGGTTC 59.639 40.000 0.00 0.00 40.61 3.62
147 148 4.870636 TCCATTTTCTATGCCAATCAGGT 58.129 39.130 0.00 0.00 40.61 4.00
151 152 4.022503 GCCTCTCCATTTTCTATGCCAATC 60.023 45.833 0.00 0.00 0.00 2.67
155 157 3.220674 AGCCTCTCCATTTTCTATGCC 57.779 47.619 0.00 0.00 0.00 4.40
166 168 2.667470 GTGGTAGTCATAGCCTCTCCA 58.333 52.381 0.00 0.00 0.00 3.86
168 170 1.609555 CGGTGGTAGTCATAGCCTCTC 59.390 57.143 0.00 0.00 0.00 3.20
169 171 1.214673 TCGGTGGTAGTCATAGCCTCT 59.785 52.381 0.00 0.00 0.00 3.69
177 179 1.067974 CTGTTGTGTCGGTGGTAGTCA 59.932 52.381 0.00 0.00 0.00 3.41
183 185 0.319900 CTCCTCTGTTGTGTCGGTGG 60.320 60.000 0.00 0.00 0.00 4.61
210 216 3.474920 ACAATAGGTCTTCCCCCTTCAT 58.525 45.455 0.00 0.00 33.35 2.57
211 217 2.929301 ACAATAGGTCTTCCCCCTTCA 58.071 47.619 0.00 0.00 33.35 3.02
234 240 9.294030 GCACTTCTTTATGGAAATCTTTATGTG 57.706 33.333 0.00 0.00 0.00 3.21
235 241 9.247861 AGCACTTCTTTATGGAAATCTTTATGT 57.752 29.630 0.00 0.00 0.00 2.29
238 244 9.077885 ACAAGCACTTCTTTATGGAAATCTTTA 57.922 29.630 0.00 0.00 31.27 1.85
241 247 6.571150 GCACAAGCACTTCTTTATGGAAATCT 60.571 38.462 0.00 0.00 41.58 2.40
242 248 5.574443 GCACAAGCACTTCTTTATGGAAATC 59.426 40.000 0.00 0.00 41.58 2.17
243 249 5.244626 AGCACAAGCACTTCTTTATGGAAAT 59.755 36.000 0.00 0.00 45.49 2.17
264 271 4.168291 TGCGTGTGTGTCCCAGCA 62.168 61.111 0.00 0.00 0.00 4.41
295 302 1.148310 CATCGGTTCACGTGAAAGCT 58.852 50.000 31.20 17.18 44.69 3.74
326 333 3.352447 CAGGTACGATGCCTGTCTG 57.648 57.895 13.62 0.00 46.22 3.51
421 437 2.166459 TCCGTTCTCACATTCTGCCTAG 59.834 50.000 0.00 0.00 0.00 3.02
422 438 2.176045 TCCGTTCTCACATTCTGCCTA 58.824 47.619 0.00 0.00 0.00 3.93
427 443 2.808543 GCAGTTTCCGTTCTCACATTCT 59.191 45.455 0.00 0.00 0.00 2.40
428 444 2.548057 TGCAGTTTCCGTTCTCACATTC 59.452 45.455 0.00 0.00 0.00 2.67
453 469 2.644992 GACTTGCCTGGGTTTGCG 59.355 61.111 0.00 0.00 0.00 4.85
456 472 0.110486 ATCACGACTTGCCTGGGTTT 59.890 50.000 0.00 0.00 0.00 3.27
462 478 0.898320 AGCTGTATCACGACTTGCCT 59.102 50.000 0.00 0.00 0.00 4.75
463 479 2.159226 AGTAGCTGTATCACGACTTGCC 60.159 50.000 0.00 0.00 0.00 4.52
465 481 5.487153 AGTAGTAGCTGTATCACGACTTG 57.513 43.478 0.00 0.00 0.00 3.16
466 482 6.347696 AGTAGTAGTAGCTGTATCACGACTT 58.652 40.000 4.92 0.00 31.75 3.01
467 483 5.916318 AGTAGTAGTAGCTGTATCACGACT 58.084 41.667 0.00 0.04 33.54 4.18
468 484 6.479660 AGAAGTAGTAGTAGCTGTATCACGAC 59.520 42.308 0.00 0.00 0.00 4.34
469 485 6.580788 AGAAGTAGTAGTAGCTGTATCACGA 58.419 40.000 0.00 0.00 0.00 4.35
470 486 6.847956 AGAAGTAGTAGTAGCTGTATCACG 57.152 41.667 0.00 0.00 0.00 4.35
471 487 8.891671 ACTAGAAGTAGTAGTAGCTGTATCAC 57.108 38.462 0.00 0.00 37.76 3.06
472 488 9.979578 GTACTAGAAGTAGTAGTAGCTGTATCA 57.020 37.037 0.00 0.00 41.53 2.15
473 489 9.423061 GGTACTAGAAGTAGTAGTAGCTGTATC 57.577 40.741 0.00 0.00 43.51 2.24
474 490 8.932610 TGGTACTAGAAGTAGTAGTAGCTGTAT 58.067 37.037 16.31 0.00 45.53 2.29
475 491 8.200792 GTGGTACTAGAAGTAGTAGTAGCTGTA 58.799 40.741 16.31 0.00 45.53 2.74
476 492 7.047271 GTGGTACTAGAAGTAGTAGTAGCTGT 58.953 42.308 16.31 0.00 45.53 4.40
477 493 6.482973 GGTGGTACTAGAAGTAGTAGTAGCTG 59.517 46.154 16.31 0.00 45.53 4.24
478 494 6.157645 TGGTGGTACTAGAAGTAGTAGTAGCT 59.842 42.308 16.31 0.00 45.53 3.32
479 495 6.259829 GTGGTGGTACTAGAAGTAGTAGTAGC 59.740 46.154 10.97 10.97 45.53 3.58
480 496 6.765512 GGTGGTGGTACTAGAAGTAGTAGTAG 59.234 46.154 0.00 0.00 41.53 2.57
481 497 6.215431 TGGTGGTGGTACTAGAAGTAGTAGTA 59.785 42.308 0.00 0.00 41.53 1.82
482 498 5.014544 TGGTGGTGGTACTAGAAGTAGTAGT 59.985 44.000 0.00 0.00 41.53 2.73
483 499 5.356470 GTGGTGGTGGTACTAGAAGTAGTAG 59.644 48.000 0.00 0.00 41.53 2.57
484 500 5.256474 GTGGTGGTGGTACTAGAAGTAGTA 58.744 45.833 0.00 0.00 40.23 1.82
489 505 2.028385 GTGGTGGTGGTGGTACTAGAAG 60.028 54.545 0.00 0.00 0.00 2.85
491 507 1.636148 GTGGTGGTGGTGGTACTAGA 58.364 55.000 0.00 0.00 0.00 2.43
516 573 2.032722 TCGTCGTTCAAATTCAAACCCG 60.033 45.455 0.00 2.18 0.00 5.28
567 640 1.378778 ACGGTCCCTCTTCTCTCGG 60.379 63.158 0.00 0.00 0.00 4.63
639 735 1.900486 GAGGGAGGAAGGAAAAGACGA 59.100 52.381 0.00 0.00 0.00 4.20
698 794 0.922626 AAGCAAGGGGAGGAAGGATC 59.077 55.000 0.00 0.00 0.00 3.36
708 809 1.911471 GGGAGAGAGAAGCAAGGGG 59.089 63.158 0.00 0.00 0.00 4.79
711 812 1.135333 GGTACGGGAGAGAGAAGCAAG 59.865 57.143 0.00 0.00 0.00 4.01
712 813 1.183549 GGTACGGGAGAGAGAAGCAA 58.816 55.000 0.00 0.00 0.00 3.91
713 814 0.039180 TGGTACGGGAGAGAGAAGCA 59.961 55.000 0.00 0.00 0.00 3.91
714 815 0.741915 CTGGTACGGGAGAGAGAAGC 59.258 60.000 0.00 0.00 0.00 3.86
715 816 2.018515 GTCTGGTACGGGAGAGAGAAG 58.981 57.143 0.00 0.00 33.92 2.85
718 819 1.096386 CGGTCTGGTACGGGAGAGAG 61.096 65.000 0.00 0.00 33.92 3.20
719 820 1.077930 CGGTCTGGTACGGGAGAGA 60.078 63.158 0.00 0.00 33.92 3.10
721 822 2.753043 GCGGTCTGGTACGGGAGA 60.753 66.667 0.00 0.00 33.92 3.71
722 823 3.066190 TGCGGTCTGGTACGGGAG 61.066 66.667 0.00 0.00 33.92 4.30
724 825 4.446413 GGTGCGGTCTGGTACGGG 62.446 72.222 0.00 0.00 33.92 5.28
727 828 2.431942 CGTGGTGCGGTCTGGTAC 60.432 66.667 0.00 0.00 36.85 3.34
763 877 2.339769 GATTGGTAGGGTGGCTATCCT 58.660 52.381 7.22 7.22 41.47 3.24
839 958 0.856982 AATGGGGCCGGATTGGATTA 59.143 50.000 5.05 0.00 42.00 1.75
894 1013 4.637489 CCTCGATCGGAGCTGGCG 62.637 72.222 16.41 0.00 41.71 5.69
906 1025 3.154473 CGAATCCCCCTGCCTCGA 61.154 66.667 0.00 0.00 0.00 4.04
908 1027 3.764160 CTGCGAATCCCCCTGCCTC 62.764 68.421 0.00 0.00 0.00 4.70
909 1028 3.801997 CTGCGAATCCCCCTGCCT 61.802 66.667 0.00 0.00 0.00 4.75
910 1029 3.125376 ATCTGCGAATCCCCCTGCC 62.125 63.158 0.00 0.00 0.00 4.85
911 1030 1.599240 GATCTGCGAATCCCCCTGC 60.599 63.158 0.00 0.00 0.00 4.85
913 1032 2.511452 CGGATCTGCGAATCCCCCT 61.511 63.158 10.65 0.00 41.98 4.79
914 1033 2.031163 CGGATCTGCGAATCCCCC 59.969 66.667 10.65 0.00 41.98 5.40
917 1036 2.666526 GCCCGGATCTGCGAATCC 60.667 66.667 0.73 7.03 41.63 3.01
941 1077 2.895680 GCATCACAGGGAGAGCGA 59.104 61.111 0.00 0.00 0.00 4.93
994 1135 3.869272 GACGCTCGGCATGGCTTG 61.869 66.667 18.09 10.54 0.00 4.01
1209 1356 2.100631 CGAGTTGGGGTCGATGTGC 61.101 63.158 0.00 0.00 39.92 4.57
1674 1821 3.576356 GCCGGATCACCATGTGCG 61.576 66.667 5.05 0.00 35.59 5.34
1677 1824 1.077501 CCTTGCCGGATCACCATGT 60.078 57.895 5.05 0.00 35.59 3.21
1715 1862 7.820648 AGAAATGCAATTACAAACGAGAGATT 58.179 30.769 0.00 0.00 33.67 2.40
1745 1895 3.939592 AGGCCATTTAGTAAAGTCGAAGC 59.060 43.478 5.01 0.00 0.00 3.86
1750 1902 6.412214 TGTTCCTAGGCCATTTAGTAAAGTC 58.588 40.000 5.01 0.00 0.00 3.01
1767 1919 6.538945 TCACACTGCAGTATTATGTTCCTA 57.461 37.500 21.20 0.00 0.00 2.94
1798 1950 1.373371 CTTGGCTTGCCGGCTTTTC 60.373 57.895 29.70 15.14 39.32 2.29
1805 1957 2.049802 CTGTTGCTTGGCTTGCCG 60.050 61.111 7.18 0.00 0.00 5.69
1812 1964 5.353678 TGAAACAAAAATTCCTGTTGCTTGG 59.646 36.000 10.45 0.00 35.95 3.61
1818 1970 9.447157 TGAAGAAATGAAACAAAAATTCCTGTT 57.553 25.926 0.44 0.44 37.36 3.16
1863 2015 7.274904 CAGTTTCTGAAATAATGCTGGTGAATG 59.725 37.037 6.06 0.00 32.44 2.67
1891 2043 8.871629 TCACTTAATTAGGGCAATTCTTGTTA 57.128 30.769 0.00 0.00 37.93 2.41
1895 2047 7.775053 TGTTCACTTAATTAGGGCAATTCTT 57.225 32.000 0.00 0.00 37.93 2.52
1904 2056 8.286800 TCGTTTTGACATGTTCACTTAATTAGG 58.713 33.333 0.00 0.00 32.26 2.69
1984 2137 3.266772 TGGCATCTCACAGGGAAATTACT 59.733 43.478 0.00 0.00 0.00 2.24
2009 2223 4.026744 TCTCTAAACCTGCTGCTAGTCAT 58.973 43.478 0.00 0.00 0.00 3.06
2041 2441 2.411628 CCACGGGGAAATGACATACA 57.588 50.000 0.00 0.00 35.59 2.29
2071 2471 1.476891 TCTAAACCTGCTGCTAGTCCG 59.523 52.381 0.00 0.00 0.00 4.79
2101 2501 2.434336 CCACGGGGAAATGAGATACTCA 59.566 50.000 0.00 3.95 39.89 3.41
2134 2534 2.761208 TCTCTAAACCTGCTGCTAGTCC 59.239 50.000 0.00 0.00 0.00 3.85
2140 2540 1.206849 AGCTCTCTCTAAACCTGCTGC 59.793 52.381 0.00 0.00 0.00 5.25
2219 2619 0.746923 GGGGGAAATGCCGTACTCAC 60.747 60.000 0.00 0.00 37.63 3.51
2228 2628 1.607801 GGCAACTCAGGGGGAAATGC 61.608 60.000 0.00 0.00 36.77 3.56
2238 2638 3.611057 GCAAGTCAGAAATGGCAACTCAG 60.611 47.826 0.00 0.00 37.61 3.35
2239 2639 2.294233 GCAAGTCAGAAATGGCAACTCA 59.706 45.455 0.00 0.00 37.61 3.41
2247 2647 1.884579 ACCTGCTGCAAGTCAGAAATG 59.115 47.619 3.02 0.00 45.72 2.32
2258 2658 0.686789 TGAGCTCTAAACCTGCTGCA 59.313 50.000 16.19 0.88 37.16 4.41
2371 2772 0.865769 CGAAAAGCTAAGGTGCACGT 59.134 50.000 11.45 8.83 34.99 4.49
2389 2790 1.139734 CCCGATCAGAGTCCACACG 59.860 63.158 0.00 0.00 0.00 4.49
2498 2899 6.671190 TGTAAAGTTGCATTGACATCTTCAG 58.329 36.000 0.00 0.00 34.94 3.02
2523 2924 1.966451 CCCACGGTCAAGCAAGTCC 60.966 63.158 0.00 0.00 0.00 3.85
2526 2927 1.973281 ATGCCCACGGTCAAGCAAG 60.973 57.895 0.99 0.00 38.99 4.01
2539 2940 2.736670 AAAGGTCTATCCACATGCCC 57.263 50.000 0.00 0.00 39.02 5.36
2607 3008 5.272283 ACTCAACATATACAACCTACCGG 57.728 43.478 0.00 0.00 0.00 5.28
2656 3057 5.421056 TCACTAGTGTTCAAGGTTATCGGAT 59.579 40.000 21.99 0.00 0.00 4.18
2660 3061 5.351740 GCCTTCACTAGTGTTCAAGGTTATC 59.648 44.000 28.95 16.63 36.71 1.75
2991 3392 1.341976 GGGCACATATGTTGAGGGGTT 60.342 52.381 5.37 0.00 0.00 4.11
3003 3404 7.901029 TCAAATTAAATTGAAGTGGGCACATA 58.099 30.769 3.42 0.00 36.42 2.29
3072 3476 8.896722 TCTTTTGTCTCTTATAGGTAGAAGGT 57.103 34.615 0.00 0.00 0.00 3.50
3156 3562 1.676014 GGGTGATCTGGTCAAACTCCG 60.676 57.143 0.00 0.00 38.90 4.63
3190 3596 2.234908 ACCAAGTAGGACACATCTGCTC 59.765 50.000 0.00 0.00 41.22 4.26
3367 3773 5.220416 GCATGTGGATTTGTCGTAGAAGTAC 60.220 44.000 0.00 0.00 39.69 2.73
3478 3884 1.259840 GCATGCATTTCAGTGGGGGT 61.260 55.000 14.21 0.00 0.00 4.95
3505 3911 0.719465 GTTCCGCAACGATCGTCAAT 59.281 50.000 22.98 2.55 0.00 2.57
3511 3917 1.007336 AGTCGTGTTCCGCAACGATC 61.007 55.000 0.91 0.00 34.95 3.69
3755 4161 9.442047 CTTCCTGTAAAGACTCTATTTCACAAT 57.558 33.333 0.00 0.00 0.00 2.71
3837 4243 4.890088 TCACATTACGCCTAACTTGTTCT 58.110 39.130 0.00 0.00 0.00 3.01
3842 4248 3.000727 GCACTCACATTACGCCTAACTT 58.999 45.455 0.00 0.00 0.00 2.66
3955 4363 7.622893 AAGGAATGAAAGAATTGAGCTCTAC 57.377 36.000 16.19 3.77 0.00 2.59
4004 4412 1.407437 GGTGATTTCGAGACCCAGCAT 60.407 52.381 5.03 0.00 0.00 3.79
4008 4416 3.433306 AAATGGTGATTTCGAGACCCA 57.567 42.857 0.00 0.00 0.00 4.51
4063 4476 8.794553 TGGTAAAAATTATTCACGTGTTATGGT 58.205 29.630 16.51 1.79 0.00 3.55
4084 4497 6.041409 ACATGGTTGACAATGTTTGATGGTAA 59.959 34.615 0.00 0.00 0.00 2.85
4092 4505 4.099881 AGAGCAACATGGTTGACAATGTTT 59.900 37.500 12.96 2.01 35.33 2.83
4106 4519 1.912043 AGGAAGGCAGTAGAGCAACAT 59.088 47.619 0.00 0.00 35.83 2.71
4167 4580 8.743085 ATGACACTGCACTTCATCTTATAATT 57.257 30.769 0.00 0.00 0.00 1.40
4168 4581 9.836864 TTATGACACTGCACTTCATCTTATAAT 57.163 29.630 3.73 0.00 32.24 1.28
4175 4588 5.063186 CAGACTTATGACACTGCACTTCATC 59.937 44.000 3.73 0.00 32.24 2.92
4178 4591 4.917887 CAGACTTATGACACTGCACTTC 57.082 45.455 0.00 0.00 0.00 3.01
4185 4598 5.779922 TCGTTTAAGCAGACTTATGACACT 58.220 37.500 0.00 0.00 38.18 3.55
4187 4600 6.020971 TCTCGTTTAAGCAGACTTATGACA 57.979 37.500 0.00 0.00 38.18 3.58
4190 4603 6.952935 AACTCTCGTTTAAGCAGACTTATG 57.047 37.500 0.00 0.00 38.18 1.90
4191 4604 7.921745 GGATAACTCTCGTTTAAGCAGACTTAT 59.078 37.037 0.00 0.00 38.18 1.73
4192 4605 7.122353 AGGATAACTCTCGTTTAAGCAGACTTA 59.878 37.037 0.00 0.00 36.57 2.24
4193 4606 6.071278 AGGATAACTCTCGTTTAAGCAGACTT 60.071 38.462 0.00 0.00 35.92 3.01
4194 4607 5.419471 AGGATAACTCTCGTTTAAGCAGACT 59.581 40.000 0.00 0.00 34.59 3.24
4195 4608 5.652518 AGGATAACTCTCGTTTAAGCAGAC 58.347 41.667 0.00 0.00 34.59 3.51
4200 4614 6.035112 GCACTCAAGGATAACTCTCGTTTAAG 59.965 42.308 0.00 0.00 34.59 1.85
4206 4620 3.182967 GTGCACTCAAGGATAACTCTCG 58.817 50.000 10.32 0.00 0.00 4.04
4235 4649 4.408596 AGTTGATGCTTTGAAGGGGAAAAA 59.591 37.500 0.00 0.00 0.00 1.94
4239 4653 2.978156 AGTTGATGCTTTGAAGGGGA 57.022 45.000 0.00 0.00 0.00 4.81
4315 4729 4.422073 TGAGCCTGGAATATGTTAGTGG 57.578 45.455 0.00 0.00 0.00 4.00
4357 4771 9.072375 TGAACCATGATTGAACAATAAGTTACA 57.928 29.630 0.00 0.00 41.51 2.41
4378 4792 8.887036 ACTTTATTTGAAAAGGAACATGAACC 57.113 30.769 0.00 1.92 40.16 3.62
4408 4822 9.679661 TGGAGTATTGCTTTTTGTCTATCATAA 57.320 29.630 0.00 0.00 0.00 1.90
4409 4823 9.109393 GTGGAGTATTGCTTTTTGTCTATCATA 57.891 33.333 0.00 0.00 0.00 2.15
4410 4824 7.611467 TGTGGAGTATTGCTTTTTGTCTATCAT 59.389 33.333 0.00 0.00 0.00 2.45
4417 4831 8.584157 TCAATTATGTGGAGTATTGCTTTTTGT 58.416 29.630 0.00 0.00 0.00 2.83
4418 4832 8.984891 TCAATTATGTGGAGTATTGCTTTTTG 57.015 30.769 0.00 0.00 0.00 2.44
4431 4845 5.044179 ACTCCCAGGATTTCAATTATGTGGA 60.044 40.000 0.00 0.00 0.00 4.02
4439 4853 5.398012 GCTAACCTACTCCCAGGATTTCAAT 60.398 44.000 0.00 0.00 39.18 2.57
4451 4865 8.677148 TCATTTGATTATTGCTAACCTACTCC 57.323 34.615 0.00 0.00 0.00 3.85
4456 4870 7.397192 ACACCTTCATTTGATTATTGCTAACCT 59.603 33.333 0.00 0.00 0.00 3.50
4462 4876 8.382875 GCTTTAACACCTTCATTTGATTATTGC 58.617 33.333 0.00 0.00 0.00 3.56
4487 4901 7.370383 TCTTTCAGAGGAATGTTTAATGTTGC 58.630 34.615 0.00 0.00 31.93 4.17
4490 4930 8.352942 GTGTTCTTTCAGAGGAATGTTTAATGT 58.647 33.333 0.00 0.00 31.93 2.71
4494 4934 7.509546 AGAGTGTTCTTTCAGAGGAATGTTTA 58.490 34.615 0.00 0.00 31.93 2.01
4497 4937 5.512232 GGAGAGTGTTCTTTCAGAGGAATGT 60.512 44.000 0.00 0.00 32.53 2.71
4498 4938 4.934602 GGAGAGTGTTCTTTCAGAGGAATG 59.065 45.833 0.00 0.00 32.53 2.67
4499 4939 4.322349 CGGAGAGTGTTCTTTCAGAGGAAT 60.322 45.833 0.00 0.00 32.53 3.01
4502 4942 2.928731 GCGGAGAGTGTTCTTTCAGAGG 60.929 54.545 0.00 0.00 32.53 3.69
4508 4948 1.270358 GGTCTGCGGAGAGTGTTCTTT 60.270 52.381 6.98 0.00 32.53 2.52
4522 4962 2.960819 AGTTCGATTACTGTGGTCTGC 58.039 47.619 0.00 0.00 0.00 4.26
4526 4966 4.766375 CCCATAAGTTCGATTACTGTGGT 58.234 43.478 15.41 0.00 34.97 4.16
4527 4967 3.560068 GCCCATAAGTTCGATTACTGTGG 59.440 47.826 12.01 12.01 35.82 4.17
4528 4968 4.442706 AGCCCATAAGTTCGATTACTGTG 58.557 43.478 0.00 0.00 0.00 3.66
4529 4969 4.755266 AGCCCATAAGTTCGATTACTGT 57.245 40.909 0.00 0.00 0.00 3.55
4532 4972 4.686554 CAGCTAGCCCATAAGTTCGATTAC 59.313 45.833 12.13 0.00 0.00 1.89
4533 4973 4.799586 GCAGCTAGCCCATAAGTTCGATTA 60.800 45.833 12.13 0.00 37.23 1.75
4534 4974 3.733337 CAGCTAGCCCATAAGTTCGATT 58.267 45.455 12.13 0.00 0.00 3.34
4535 4975 2.548920 GCAGCTAGCCCATAAGTTCGAT 60.549 50.000 12.13 0.00 37.23 3.59
4538 4978 2.216898 CTGCAGCTAGCCCATAAGTTC 58.783 52.381 12.13 0.00 44.83 3.01
4539 4979 1.561542 ACTGCAGCTAGCCCATAAGTT 59.438 47.619 15.27 0.00 44.83 2.66
4540 4980 1.207791 ACTGCAGCTAGCCCATAAGT 58.792 50.000 15.27 5.74 44.83 2.24
4541 4981 1.945394 CAACTGCAGCTAGCCCATAAG 59.055 52.381 15.27 5.08 44.83 1.73
4542 4982 1.281867 ACAACTGCAGCTAGCCCATAA 59.718 47.619 15.27 0.00 44.83 1.90
4543 4983 0.911769 ACAACTGCAGCTAGCCCATA 59.088 50.000 15.27 0.00 44.83 2.74
4571 5011 7.521669 TCCTCTTGAGATCATGACTGACTATA 58.478 38.462 0.00 0.00 33.22 1.31
4581 5021 6.403418 GCTCAAAAGTTCCTCTTGAGATCATG 60.403 42.308 15.94 0.00 45.86 3.07
4607 5048 0.322975 CCCGATATTGGCTCCAGGAG 59.677 60.000 12.81 12.81 0.00 3.69
4644 5085 3.134574 ACCTTATGACGGCTGTTCAAA 57.865 42.857 0.00 0.00 0.00 2.69
4647 5088 2.544267 GCATACCTTATGACGGCTGTTC 59.456 50.000 0.00 0.00 38.45 3.18
4654 5095 5.991328 ATTTGACTGCATACCTTATGACG 57.009 39.130 0.00 0.00 38.45 4.35
4663 5104 3.680789 GGCGTGTTATTTGACTGCATAC 58.319 45.455 0.00 0.00 0.00 2.39
4674 5115 1.758280 TCTCCATACCGGCGTGTTATT 59.242 47.619 6.01 0.00 33.14 1.40
4678 5119 1.255667 AAGTCTCCATACCGGCGTGT 61.256 55.000 6.01 6.18 33.14 4.49
4679 5120 0.527817 GAAGTCTCCATACCGGCGTG 60.528 60.000 6.01 0.00 33.14 5.34
4680 5121 0.968901 TGAAGTCTCCATACCGGCGT 60.969 55.000 6.01 0.00 33.14 5.68
4681 5122 0.389391 ATGAAGTCTCCATACCGGCG 59.611 55.000 0.00 0.00 33.14 6.46
4682 5123 2.614057 CAAATGAAGTCTCCATACCGGC 59.386 50.000 0.00 0.00 33.14 6.13
4683 5124 3.873910 ACAAATGAAGTCTCCATACCGG 58.126 45.455 0.00 0.00 0.00 5.28
4684 5125 6.074302 CGATTACAAATGAAGTCTCCATACCG 60.074 42.308 0.00 0.00 0.00 4.02
4685 5126 6.761714 ACGATTACAAATGAAGTCTCCATACC 59.238 38.462 0.00 0.00 0.00 2.73
4686 5127 7.491372 TGACGATTACAAATGAAGTCTCCATAC 59.509 37.037 0.00 0.00 0.00 2.39
4687 5128 7.552459 TGACGATTACAAATGAAGTCTCCATA 58.448 34.615 0.00 0.00 0.00 2.74
4688 5129 6.406370 TGACGATTACAAATGAAGTCTCCAT 58.594 36.000 0.00 0.00 0.00 3.41
4689 5130 5.789521 TGACGATTACAAATGAAGTCTCCA 58.210 37.500 0.00 0.00 0.00 3.86
4690 5131 6.402226 GGTTGACGATTACAAATGAAGTCTCC 60.402 42.308 0.00 0.00 0.00 3.71
4691 5132 6.402226 GGGTTGACGATTACAAATGAAGTCTC 60.402 42.308 0.00 0.00 0.00 3.36
4692 5133 5.411669 GGGTTGACGATTACAAATGAAGTCT 59.588 40.000 0.00 0.00 0.00 3.24
4693 5134 5.411669 AGGGTTGACGATTACAAATGAAGTC 59.588 40.000 0.00 0.00 0.00 3.01
4694 5135 5.313712 AGGGTTGACGATTACAAATGAAGT 58.686 37.500 0.00 0.00 0.00 3.01
4695 5136 5.880054 AGGGTTGACGATTACAAATGAAG 57.120 39.130 0.00 0.00 0.00 3.02
4696 5137 7.931578 ATAAGGGTTGACGATTACAAATGAA 57.068 32.000 0.00 0.00 0.00 2.57
4697 5138 7.392113 ACAATAAGGGTTGACGATTACAAATGA 59.608 33.333 0.00 0.00 33.37 2.57
4698 5139 7.484641 CACAATAAGGGTTGACGATTACAAATG 59.515 37.037 0.00 0.00 33.37 2.32
4699 5140 7.175990 ACACAATAAGGGTTGACGATTACAAAT 59.824 33.333 0.00 0.00 33.37 2.32
4700 5141 6.487331 ACACAATAAGGGTTGACGATTACAAA 59.513 34.615 0.00 0.00 33.37 2.83
4701 5142 5.998981 ACACAATAAGGGTTGACGATTACAA 59.001 36.000 0.00 0.00 33.37 2.41
4702 5143 5.553123 ACACAATAAGGGTTGACGATTACA 58.447 37.500 0.00 0.00 33.37 2.41
4703 5144 5.873164 AGACACAATAAGGGTTGACGATTAC 59.127 40.000 0.00 0.00 30.42 1.89
4704 5145 6.045072 AGACACAATAAGGGTTGACGATTA 57.955 37.500 0.00 0.00 30.42 1.75
4705 5146 4.906618 AGACACAATAAGGGTTGACGATT 58.093 39.130 0.00 0.00 30.42 3.34
4706 5147 4.553330 AGACACAATAAGGGTTGACGAT 57.447 40.909 0.00 0.00 30.42 3.73
4707 5148 4.345859 AAGACACAATAAGGGTTGACGA 57.654 40.909 0.00 0.00 30.42 4.20
4708 5149 6.548441 TTAAAGACACAATAAGGGTTGACG 57.452 37.500 0.00 0.00 30.42 4.35
4709 5150 9.758651 AAATTTAAAGACACAATAAGGGTTGAC 57.241 29.630 0.00 0.00 30.42 3.18


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

AutoCloner maintained by Alex Coulton.