Multiple sequence alignment - TraesCS6D01G234500

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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 TraesCS6D01G234500 chr6D 100.000 3461 0 0 1 3461 328966191 328962731 0.000000e+00 6392.0
1 TraesCS6D01G234500 chr6B 92.605 2718 140 33 206 2878 493320110 493317409 0.000000e+00 3849.0
2 TraesCS6D01G234500 chr6B 86.058 416 41 12 2870 3271 493314146 493313734 6.860000e-117 431.0
3 TraesCS6D01G234500 chr6B 92.308 234 12 5 6 234 493320351 493320119 9.260000e-86 327.0
4 TraesCS6D01G234500 chr6B 86.070 201 27 1 3262 3461 493270258 493270058 7.520000e-52 215.0
5 TraesCS6D01G234500 chr6B 85.572 201 28 1 3262 3461 493272174 493271974 3.500000e-50 209.0
6 TraesCS6D01G234500 chr6B 84.337 166 25 1 3297 3461 493268295 493268130 9.940000e-36 161.0
7 TraesCS6D01G234500 chr6A 92.249 1316 50 21 1283 2550 468258034 468256723 0.000000e+00 1818.0
8 TraesCS6D01G234500 chr6A 89.298 1140 59 14 206 1316 468259145 468258040 0.000000e+00 1371.0
9 TraesCS6D01G234500 chr6A 90.792 543 30 5 2541 3073 468254736 468254204 0.000000e+00 708.0
10 TraesCS6D01G234500 chr1D 87.654 81 8 2 3054 3133 307342349 307342428 3.680000e-15 93.5
11 TraesCS6D01G234500 chr4B 85.185 81 10 2 3054 3133 564134496 564134575 7.960000e-12 82.4


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 TraesCS6D01G234500 chr6D 328962731 328966191 3460 True 6392.000000 6392 100.000000 1 3461 1 chr6D.!!$R1 3460
1 TraesCS6D01G234500 chr6B 493313734 493320351 6617 True 1535.666667 3849 90.323667 6 3271 3 chr6B.!!$R2 3265
2 TraesCS6D01G234500 chr6A 468254204 468259145 4941 True 1299.000000 1818 90.779667 206 3073 3 chr6A.!!$R1 2867

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
585 655 0.036671 AACTACAGTTACGCAGGCCC 60.037 55.0 0.0 0.0 36.32 5.80 F
976 1050 0.321122 CTGAACACAGAGTCCCAGGC 60.321 60.0 0.0 0.0 33.94 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2181 2343 0.679640 CGGGCTATTTGCACCAGGAA 60.680 55.0 0.00 0.0 43.53 3.36 R
2808 4979 0.246635 CCTCGAGAAAAAGGGAGCGA 59.753 55.0 15.71 0.0 0.00 4.93 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
86 87 8.667076 AAAGTTCATGAATTTGAAAAGAAGGG 57.333 30.769 15.98 0.00 37.36 3.95
90 91 5.070180 TCATGAATTTGAAAAGAAGGGCACA 59.930 36.000 0.00 0.00 0.00 4.57
187 191 7.951530 ATTGTTCATGAATTGGTGAAAAGTC 57.048 32.000 12.12 0.00 36.23 3.01
191 195 5.384336 TCATGAATTGGTGAAAAGTCCTCA 58.616 37.500 0.00 0.00 0.00 3.86
201 205 5.069119 GGTGAAAAGTCCTCAGGTTTGAAAT 59.931 40.000 0.00 0.00 31.69 2.17
202 206 6.264518 GGTGAAAAGTCCTCAGGTTTGAAATA 59.735 38.462 0.00 0.00 31.69 1.40
334 377 6.722301 AGAAGCTTTACAAAACCGACTAAAC 58.278 36.000 0.00 0.00 0.00 2.01
360 403 5.885912 AGCTTCTAGAAGTTTCACAAAACCA 59.114 36.000 28.72 0.00 44.87 3.67
416 462 2.518587 GGCCGGCCCATTTCCTAC 60.519 66.667 36.64 5.01 0.00 3.18
428 474 2.178912 TTTCCTACGTGCCCTTGAAG 57.821 50.000 0.00 0.00 0.00 3.02
429 475 1.053424 TTCCTACGTGCCCTTGAAGT 58.947 50.000 0.00 0.00 0.00 3.01
430 476 0.320374 TCCTACGTGCCCTTGAAGTG 59.680 55.000 0.00 0.00 0.00 3.16
431 477 1.298859 CCTACGTGCCCTTGAAGTGC 61.299 60.000 0.00 0.00 0.00 4.40
432 478 1.626654 CTACGTGCCCTTGAAGTGCG 61.627 60.000 0.00 0.00 0.00 5.34
433 479 4.389576 CGTGCCCTTGAAGTGCGC 62.390 66.667 0.00 0.00 0.00 6.09
434 480 4.043200 GTGCCCTTGAAGTGCGCC 62.043 66.667 4.18 0.00 0.00 6.53
435 481 4.577677 TGCCCTTGAAGTGCGCCA 62.578 61.111 4.18 0.00 0.00 5.69
436 482 3.064324 GCCCTTGAAGTGCGCCAT 61.064 61.111 4.18 0.00 0.00 4.40
437 483 2.639327 GCCCTTGAAGTGCGCCATT 61.639 57.895 4.18 0.00 0.00 3.16
438 484 1.966762 CCCTTGAAGTGCGCCATTT 59.033 52.632 4.18 0.00 0.00 2.32
439 485 0.109132 CCCTTGAAGTGCGCCATTTC 60.109 55.000 4.18 6.82 32.04 2.17
440 486 0.597568 CCTTGAAGTGCGCCATTTCA 59.402 50.000 4.18 9.60 38.09 2.69
441 487 1.401931 CCTTGAAGTGCGCCATTTCAG 60.402 52.381 4.18 6.54 40.21 3.02
442 488 1.536766 CTTGAAGTGCGCCATTTCAGA 59.463 47.619 4.18 3.30 40.21 3.27
443 489 1.159285 TGAAGTGCGCCATTTCAGAG 58.841 50.000 4.18 0.00 35.69 3.35
444 490 0.449388 GAAGTGCGCCATTTCAGAGG 59.551 55.000 4.18 0.00 31.78 3.69
445 491 0.250901 AAGTGCGCCATTTCAGAGGT 60.251 50.000 4.18 0.00 0.00 3.85
446 492 0.674895 AGTGCGCCATTTCAGAGGTC 60.675 55.000 4.18 0.00 0.00 3.85
473 519 2.730928 CCATTTGTAAAAACGCCTGCAG 59.269 45.455 6.78 6.78 0.00 4.41
554 624 1.083489 TGCTAAATCCGAACGCAAGG 58.917 50.000 0.00 0.00 46.39 3.61
563 633 4.544001 AACGCAAGGTCCAAACGA 57.456 50.000 4.67 0.00 46.39 3.85
566 636 0.390124 ACGCAAGGTCCAAACGAGTA 59.610 50.000 4.67 0.00 46.39 2.59
585 655 0.036671 AACTACAGTTACGCAGGCCC 60.037 55.000 0.00 0.00 36.32 5.80
639 709 1.672356 CTAAGCCGCACCAGCTGTT 60.672 57.895 13.81 0.00 40.49 3.16
747 818 8.476925 GTTTAACAACGATCTGGAACAAATTTC 58.523 33.333 0.00 0.00 38.70 2.17
853 927 7.074653 TGAAATTACAAGTAGACAACCCTCT 57.925 36.000 0.00 0.00 0.00 3.69
866 940 3.222603 CAACCCTCTAAAACACCAGCTT 58.777 45.455 0.00 0.00 0.00 3.74
915 989 1.564348 GGGTAAATTCTGCTCCCTGGA 59.436 52.381 0.00 0.00 35.63 3.86
976 1050 0.321122 CTGAACACAGAGTCCCAGGC 60.321 60.000 0.00 0.00 33.94 4.85
1027 1102 1.423845 CAAACCGCCTCATACGTGC 59.576 57.895 0.00 0.00 0.00 5.34
1030 1105 2.279517 CCGCCTCATACGTGCTCC 60.280 66.667 0.00 0.00 0.00 4.70
1542 1669 9.887406 ATTACGAATTAACTTTCATTTCAACGT 57.113 25.926 0.00 0.00 0.00 3.99
1543 1670 7.831750 ACGAATTAACTTTCATTTCAACGTC 57.168 32.000 0.00 0.00 0.00 4.34
1544 1671 7.411274 ACGAATTAACTTTCATTTCAACGTCA 58.589 30.769 0.00 0.00 0.00 4.35
1566 1700 4.471904 ACCGTATGACATGATGTGAACT 57.528 40.909 1.23 0.00 0.00 3.01
1585 1719 3.561143 ACTTTATGTGCAGGTTGGTGAA 58.439 40.909 0.00 0.00 0.00 3.18
1640 1774 0.944386 GACGGTTGTCAAGCACATGT 59.056 50.000 14.73 0.00 44.82 3.21
1648 1782 2.368548 TGTCAAGCACATGTACCAGAGT 59.631 45.455 0.00 0.00 0.00 3.24
1768 1902 0.846693 ACAGGAAGTTCTTGGCCAGT 59.153 50.000 18.18 0.00 0.00 4.00
1802 1936 5.363005 GCCTACAAGGACTATCTGAAGGTAA 59.637 44.000 0.00 0.00 37.67 2.85
1803 1937 6.042208 GCCTACAAGGACTATCTGAAGGTAAT 59.958 42.308 0.00 0.00 37.67 1.89
1804 1938 7.662897 CCTACAAGGACTATCTGAAGGTAATC 58.337 42.308 0.00 0.00 37.67 1.75
1805 1939 7.287927 CCTACAAGGACTATCTGAAGGTAATCA 59.712 40.741 0.00 0.00 37.67 2.57
1806 1940 7.496346 ACAAGGACTATCTGAAGGTAATCAA 57.504 36.000 0.00 0.00 0.00 2.57
1807 1941 8.095452 ACAAGGACTATCTGAAGGTAATCAAT 57.905 34.615 0.00 0.00 0.00 2.57
1808 1942 8.552296 ACAAGGACTATCTGAAGGTAATCAATT 58.448 33.333 0.00 0.00 0.00 2.32
1809 1943 9.050601 CAAGGACTATCTGAAGGTAATCAATTC 57.949 37.037 0.00 0.00 0.00 2.17
1869 2031 3.119531 CCACAAGAACTGCAAACTGAACA 60.120 43.478 0.00 0.00 0.00 3.18
1874 2036 6.039717 ACAAGAACTGCAAACTGAACATGTAT 59.960 34.615 0.00 0.00 0.00 2.29
2096 2258 3.335711 GGCATGGCCTACTCCCTT 58.664 61.111 8.35 0.00 46.69 3.95
2141 2303 2.317609 CGTCTTCGCCAACCCACAG 61.318 63.158 0.00 0.00 0.00 3.66
2162 2324 1.153549 GCCCGACTGGAGTAAGCAG 60.154 63.158 0.00 0.00 37.49 4.24
2180 2342 4.722700 ATCGCCTTGGCACGGCTT 62.723 61.111 29.30 15.95 45.37 4.35
2181 2343 4.947147 TCGCCTTGGCACGGCTTT 62.947 61.111 29.30 0.00 45.37 3.51
2183 2345 2.049156 GCCTTGGCACGGCTTTTC 60.049 61.111 26.16 0.00 44.17 2.29
2184 2346 2.650778 CCTTGGCACGGCTTTTCC 59.349 61.111 0.00 0.00 0.00 3.13
2185 2347 1.903404 CCTTGGCACGGCTTTTCCT 60.903 57.895 0.00 0.00 0.00 3.36
2186 2348 1.286880 CTTGGCACGGCTTTTCCTG 59.713 57.895 0.00 0.00 0.00 3.86
2713 4878 5.003692 TGGAAGAGTCTCTCAATCAATCG 57.996 43.478 1.96 0.00 32.06 3.34
2766 4937 4.862641 AAACTAAGCCACCTATGACCAT 57.137 40.909 0.00 0.00 0.00 3.55
2768 4939 3.384168 ACTAAGCCACCTATGACCATCA 58.616 45.455 0.00 0.00 0.00 3.07
2788 4959 2.512515 AGCGATTTGAGCTCGGCC 60.513 61.111 9.64 0.00 41.83 6.13
2808 4979 1.699634 CTGGATATTCGGTGGTCCCAT 59.300 52.381 0.00 0.00 0.00 4.00
2827 4998 0.246635 TCGCTCCCTTTTTCTCGAGG 59.753 55.000 13.56 0.00 0.00 4.63
2833 5004 2.152016 CCCTTTTTCTCGAGGGTTGAC 58.848 52.381 13.56 0.00 46.27 3.18
2850 5021 5.106830 GGGTTGACAACACCTTATTAACTCG 60.107 44.000 19.58 0.00 0.00 4.18
2853 5024 3.916761 ACAACACCTTATTAACTCGCGA 58.083 40.909 9.26 9.26 0.00 5.87
2958 8404 2.418197 GGTAATGTAGTCGCAGCCTTCA 60.418 50.000 0.00 0.00 0.00 3.02
2960 8406 0.108138 ATGTAGTCGCAGCCTTCACC 60.108 55.000 0.00 0.00 0.00 4.02
2963 8409 0.898326 TAGTCGCAGCCTTCACCAGA 60.898 55.000 0.00 0.00 0.00 3.86
3034 8480 6.041296 ACTGATGCAAAACCTTTCATCTTCTT 59.959 34.615 0.00 0.00 37.00 2.52
3100 8557 8.602472 AGTTTAGATCACTACTTTGAGGATCT 57.398 34.615 0.00 0.00 44.85 2.75
3105 8562 8.367660 AGATCACTACTTTGAGGATCTAAACA 57.632 34.615 0.00 0.00 41.99 2.83
3106 8563 8.254508 AGATCACTACTTTGAGGATCTAAACAC 58.745 37.037 0.00 0.00 41.99 3.32
3145 8602 6.774084 ACGAAGAGAGTAATCGTAGAAGTTC 58.226 40.000 0.00 0.00 46.86 3.01
3153 8610 6.861144 AGTAATCGTAGAAGTTCCAAGGTAC 58.139 40.000 0.00 0.00 43.58 3.34
3174 8631 3.094572 CTCACCCTTCAAATGGCTCATT 58.905 45.455 0.00 0.00 35.39 2.57
3183 8640 4.025360 TCAAATGGCTCATTGGTAGCAAT 58.975 39.130 14.31 14.31 41.93 3.56
3188 8645 3.947196 TGGCTCATTGGTAGCAATAACAG 59.053 43.478 19.18 15.34 41.93 3.16
3194 8651 7.698130 GCTCATTGGTAGCAATAACAGTTTTAG 59.302 37.037 19.18 4.21 39.83 1.85
3208 8665 4.820173 ACAGTTTTAGTACAAGCAAGGTCC 59.180 41.667 0.00 0.00 0.00 4.46
3209 8666 4.819630 CAGTTTTAGTACAAGCAAGGTCCA 59.180 41.667 0.00 0.00 0.00 4.02
3210 8667 4.820173 AGTTTTAGTACAAGCAAGGTCCAC 59.180 41.667 0.00 0.00 0.00 4.02
3220 8677 1.542375 AAGGTCCACAGCCAGGGAT 60.542 57.895 0.00 0.00 35.25 3.85
3241 8698 2.176889 AGAGCTTCATTGCTTGCCATT 58.823 42.857 0.00 0.00 44.17 3.16
3249 8706 1.588824 TTGCTTGCCATTGCCTCGAG 61.589 55.000 5.13 5.13 36.33 4.04
3258 8715 1.863454 CATTGCCTCGAGAATCTTCGG 59.137 52.381 15.71 0.00 40.83 4.30
3262 8719 1.281899 CCTCGAGAATCTTCGGCAAC 58.718 55.000 15.71 0.00 40.83 4.17
3271 8728 5.059833 AGAATCTTCGGCAACATTAGATCC 58.940 41.667 0.00 0.00 30.16 3.36
3272 8729 2.821546 TCTTCGGCAACATTAGATCCG 58.178 47.619 0.00 0.00 41.30 4.18
3273 8730 1.867233 CTTCGGCAACATTAGATCCGG 59.133 52.381 0.00 0.00 40.42 5.14
3274 8731 1.116308 TCGGCAACATTAGATCCGGA 58.884 50.000 6.61 6.61 40.42 5.14
3275 8732 1.202486 TCGGCAACATTAGATCCGGAC 60.202 52.381 6.12 0.11 40.42 4.79
3276 8733 1.202533 CGGCAACATTAGATCCGGACT 60.203 52.381 6.12 9.17 36.73 3.85
3277 8734 2.035449 CGGCAACATTAGATCCGGACTA 59.965 50.000 6.12 8.05 36.73 2.59
3278 8735 3.391049 GGCAACATTAGATCCGGACTAC 58.609 50.000 6.12 0.88 0.00 2.73
3279 8736 3.050619 GCAACATTAGATCCGGACTACG 58.949 50.000 6.12 7.14 43.80 3.51
3291 8748 1.221414 GGACTACGATTGCTGATGCC 58.779 55.000 0.00 0.00 38.71 4.40
3292 8749 1.221414 GACTACGATTGCTGATGCCC 58.779 55.000 0.00 0.00 38.71 5.36
3293 8750 0.179045 ACTACGATTGCTGATGCCCC 60.179 55.000 0.00 0.00 38.71 5.80
3294 8751 0.886490 CTACGATTGCTGATGCCCCC 60.886 60.000 0.00 0.00 38.71 5.40
3308 8765 4.872293 CCCCCAAATCAGCCAGTT 57.128 55.556 0.00 0.00 0.00 3.16
3309 8766 3.071671 CCCCCAAATCAGCCAGTTT 57.928 52.632 0.00 0.00 0.00 2.66
3310 8767 0.897621 CCCCCAAATCAGCCAGTTTC 59.102 55.000 0.00 0.00 0.00 2.78
3311 8768 0.527565 CCCCAAATCAGCCAGTTTCG 59.472 55.000 0.00 0.00 0.00 3.46
3312 8769 1.247567 CCCAAATCAGCCAGTTTCGT 58.752 50.000 0.00 0.00 0.00 3.85
3313 8770 1.200020 CCCAAATCAGCCAGTTTCGTC 59.800 52.381 0.00 0.00 0.00 4.20
3314 8771 2.154462 CCAAATCAGCCAGTTTCGTCT 58.846 47.619 0.00 0.00 0.00 4.18
3315 8772 2.160417 CCAAATCAGCCAGTTTCGTCTC 59.840 50.000 0.00 0.00 0.00 3.36
3316 8773 1.714794 AATCAGCCAGTTTCGTCTCG 58.285 50.000 0.00 0.00 0.00 4.04
3317 8774 0.108615 ATCAGCCAGTTTCGTCTCGG 60.109 55.000 0.00 0.00 0.00 4.63
3318 8775 1.006102 CAGCCAGTTTCGTCTCGGT 60.006 57.895 0.00 0.00 0.00 4.69
3319 8776 0.242825 CAGCCAGTTTCGTCTCGGTA 59.757 55.000 0.00 0.00 0.00 4.02
3320 8777 1.135083 CAGCCAGTTTCGTCTCGGTAT 60.135 52.381 0.00 0.00 0.00 2.73
3321 8778 2.098607 CAGCCAGTTTCGTCTCGGTATA 59.901 50.000 0.00 0.00 0.00 1.47
3322 8779 2.756760 AGCCAGTTTCGTCTCGGTATAA 59.243 45.455 0.00 0.00 0.00 0.98
3323 8780 2.856557 GCCAGTTTCGTCTCGGTATAAC 59.143 50.000 0.00 0.00 0.00 1.89
3324 8781 3.103738 CCAGTTTCGTCTCGGTATAACG 58.896 50.000 3.05 3.05 37.74 3.18
3325 8782 2.529090 CAGTTTCGTCTCGGTATAACGC 59.471 50.000 4.98 0.00 36.40 4.84
3326 8783 2.162208 AGTTTCGTCTCGGTATAACGCA 59.838 45.455 4.98 0.00 36.40 5.24
3327 8784 2.916716 GTTTCGTCTCGGTATAACGCAA 59.083 45.455 4.98 0.00 36.40 4.85
3328 8785 2.178474 TCGTCTCGGTATAACGCAAC 57.822 50.000 4.98 5.05 36.40 4.17
3329 8786 0.835740 CGTCTCGGTATAACGCAACG 59.164 55.000 18.19 18.19 36.05 4.10
3330 8787 1.529622 CGTCTCGGTATAACGCAACGA 60.530 52.381 23.90 8.65 40.98 3.85
3333 8790 2.463553 TCGGTATAACGCAACGAGAG 57.536 50.000 4.98 0.00 0.00 3.20
3334 8791 0.844503 CGGTATAACGCAACGAGAGC 59.155 55.000 0.00 0.00 0.00 4.09
3335 8792 1.796253 CGGTATAACGCAACGAGAGCA 60.796 52.381 0.00 0.00 0.00 4.26
3336 8793 1.587034 GGTATAACGCAACGAGAGCAC 59.413 52.381 0.00 0.00 0.00 4.40
3337 8794 1.587034 GTATAACGCAACGAGAGCACC 59.413 52.381 0.00 0.00 0.00 5.01
3338 8795 0.739813 ATAACGCAACGAGAGCACCC 60.740 55.000 0.00 0.00 0.00 4.61
3339 8796 2.089887 TAACGCAACGAGAGCACCCA 62.090 55.000 0.00 0.00 0.00 4.51
3340 8797 2.434884 CGCAACGAGAGCACCCAT 60.435 61.111 0.00 0.00 0.00 4.00
3341 8798 1.153647 CGCAACGAGAGCACCCATA 60.154 57.895 0.00 0.00 0.00 2.74
3342 8799 0.530650 CGCAACGAGAGCACCCATAT 60.531 55.000 0.00 0.00 0.00 1.78
3343 8800 1.221414 GCAACGAGAGCACCCATATC 58.779 55.000 0.00 0.00 0.00 1.63
3344 8801 1.202580 GCAACGAGAGCACCCATATCT 60.203 52.381 0.00 0.00 0.00 1.98
3345 8802 2.743183 GCAACGAGAGCACCCATATCTT 60.743 50.000 0.00 0.00 0.00 2.40
3346 8803 3.126831 CAACGAGAGCACCCATATCTTC 58.873 50.000 0.00 0.00 0.00 2.87
3347 8804 2.388735 ACGAGAGCACCCATATCTTCA 58.611 47.619 0.00 0.00 0.00 3.02
3348 8805 2.968574 ACGAGAGCACCCATATCTTCAT 59.031 45.455 0.00 0.00 0.00 2.57
3349 8806 3.244009 ACGAGAGCACCCATATCTTCATG 60.244 47.826 0.00 0.00 0.00 3.07
3350 8807 3.006217 CGAGAGCACCCATATCTTCATGA 59.994 47.826 0.00 0.00 0.00 3.07
3351 8808 4.314121 GAGAGCACCCATATCTTCATGAC 58.686 47.826 0.00 0.00 0.00 3.06
3352 8809 3.062763 GAGCACCCATATCTTCATGACG 58.937 50.000 0.00 0.00 0.00 4.35
3353 8810 2.146342 GCACCCATATCTTCATGACGG 58.854 52.381 0.00 0.00 0.00 4.79
3354 8811 2.146342 CACCCATATCTTCATGACGGC 58.854 52.381 0.00 0.00 0.00 5.68
3355 8812 1.072331 ACCCATATCTTCATGACGGCC 59.928 52.381 0.00 0.00 0.00 6.13
3356 8813 1.072173 CCCATATCTTCATGACGGCCA 59.928 52.381 2.24 0.00 0.00 5.36
3357 8814 2.487086 CCCATATCTTCATGACGGCCAA 60.487 50.000 2.24 0.00 0.00 4.52
3358 8815 3.415212 CCATATCTTCATGACGGCCAAT 58.585 45.455 2.24 0.00 0.00 3.16
3359 8816 4.565444 CCCATATCTTCATGACGGCCAATA 60.565 45.833 2.24 0.00 0.00 1.90
3360 8817 4.633126 CCATATCTTCATGACGGCCAATAG 59.367 45.833 2.24 0.00 0.00 1.73
3361 8818 1.953559 TCTTCATGACGGCCAATAGC 58.046 50.000 2.24 0.00 42.60 2.97
3362 8819 1.486310 TCTTCATGACGGCCAATAGCT 59.514 47.619 2.24 0.00 43.05 3.32
3368 8825 3.348236 CGGCCAATAGCTGCATCC 58.652 61.111 2.24 0.00 42.11 3.51
3369 8826 1.526686 CGGCCAATAGCTGCATCCA 60.527 57.895 2.24 0.00 42.11 3.41
3370 8827 1.789078 CGGCCAATAGCTGCATCCAC 61.789 60.000 2.24 0.00 42.11 4.02
3371 8828 0.752743 GGCCAATAGCTGCATCCACA 60.753 55.000 0.00 0.00 43.05 4.17
3372 8829 0.383231 GCCAATAGCTGCATCCACAC 59.617 55.000 1.02 0.00 38.99 3.82
3373 8830 0.659427 CCAATAGCTGCATCCACACG 59.341 55.000 1.02 0.00 0.00 4.49
3374 8831 1.372582 CAATAGCTGCATCCACACGT 58.627 50.000 1.02 0.00 0.00 4.49
3375 8832 2.549926 CAATAGCTGCATCCACACGTA 58.450 47.619 1.02 0.00 0.00 3.57
3376 8833 3.133691 CAATAGCTGCATCCACACGTAT 58.866 45.455 1.02 0.00 0.00 3.06
3377 8834 2.509052 TAGCTGCATCCACACGTATC 57.491 50.000 1.02 0.00 0.00 2.24
3378 8835 0.826715 AGCTGCATCCACACGTATCT 59.173 50.000 1.02 0.00 0.00 1.98
3379 8836 1.208052 AGCTGCATCCACACGTATCTT 59.792 47.619 1.02 0.00 0.00 2.40
3380 8837 2.430694 AGCTGCATCCACACGTATCTTA 59.569 45.455 1.02 0.00 0.00 2.10
3381 8838 3.118775 AGCTGCATCCACACGTATCTTAA 60.119 43.478 1.02 0.00 0.00 1.85
3382 8839 3.809832 GCTGCATCCACACGTATCTTAAT 59.190 43.478 0.00 0.00 0.00 1.40
3383 8840 4.273480 GCTGCATCCACACGTATCTTAATT 59.727 41.667 0.00 0.00 0.00 1.40
3384 8841 5.733226 TGCATCCACACGTATCTTAATTG 57.267 39.130 0.00 0.00 0.00 2.32
3385 8842 5.182487 TGCATCCACACGTATCTTAATTGT 58.818 37.500 0.00 0.00 0.00 2.71
3386 8843 6.342111 TGCATCCACACGTATCTTAATTGTA 58.658 36.000 0.00 0.00 0.00 2.41
3387 8844 6.819146 TGCATCCACACGTATCTTAATTGTAA 59.181 34.615 0.00 0.00 0.00 2.41
3388 8845 7.497579 TGCATCCACACGTATCTTAATTGTAAT 59.502 33.333 0.00 0.00 0.00 1.89
3389 8846 8.342634 GCATCCACACGTATCTTAATTGTAATT 58.657 33.333 0.00 0.00 0.00 1.40
3390 8847 9.650371 CATCCACACGTATCTTAATTGTAATTG 57.350 33.333 0.00 0.00 0.00 2.32
3391 8848 9.607988 ATCCACACGTATCTTAATTGTAATTGA 57.392 29.630 0.00 0.00 0.00 2.57
3392 8849 9.093970 TCCACACGTATCTTAATTGTAATTGAG 57.906 33.333 0.00 3.49 34.39 3.02
3393 8850 8.335356 CCACACGTATCTTAATTGTAATTGAGG 58.665 37.037 8.64 0.00 34.02 3.86
3394 8851 8.335356 CACACGTATCTTAATTGTAATTGAGGG 58.665 37.037 8.64 1.50 34.02 4.30
3395 8852 8.044908 ACACGTATCTTAATTGTAATTGAGGGT 58.955 33.333 8.64 2.87 34.02 4.34
3396 8853 8.335356 CACGTATCTTAATTGTAATTGAGGGTG 58.665 37.037 8.64 8.24 34.02 4.61
3397 8854 7.497909 ACGTATCTTAATTGTAATTGAGGGTGG 59.502 37.037 8.64 1.76 34.02 4.61
3398 8855 6.715347 ATCTTAATTGTAATTGAGGGTGGC 57.285 37.500 8.64 0.00 34.02 5.01
3399 8856 4.638421 TCTTAATTGTAATTGAGGGTGGCG 59.362 41.667 8.64 0.00 34.02 5.69
3400 8857 1.102978 ATTGTAATTGAGGGTGGCGC 58.897 50.000 0.00 0.00 0.00 6.53
3401 8858 0.250945 TTGTAATTGAGGGTGGCGCA 60.251 50.000 10.83 0.00 0.00 6.09
3402 8859 0.250945 TGTAATTGAGGGTGGCGCAA 60.251 50.000 10.83 0.00 0.00 4.85
3403 8860 1.102978 GTAATTGAGGGTGGCGCAAT 58.897 50.000 10.83 0.00 33.96 3.56
3404 8861 1.065551 GTAATTGAGGGTGGCGCAATC 59.934 52.381 10.83 0.00 31.52 2.67
3405 8862 1.322538 AATTGAGGGTGGCGCAATCC 61.323 55.000 5.72 5.72 31.52 3.01
3406 8863 2.497792 ATTGAGGGTGGCGCAATCCA 62.498 55.000 18.56 0.00 0.00 3.41
3412 8869 2.359850 TGGCGCAATCCACTCCAC 60.360 61.111 10.83 0.00 0.00 4.02
3413 8870 2.045926 GGCGCAATCCACTCCACT 60.046 61.111 10.83 0.00 0.00 4.00
3414 8871 1.675641 GGCGCAATCCACTCCACTT 60.676 57.895 10.83 0.00 0.00 3.16
3415 8872 1.648467 GGCGCAATCCACTCCACTTC 61.648 60.000 10.83 0.00 0.00 3.01
3416 8873 0.955428 GCGCAATCCACTCCACTTCA 60.955 55.000 0.30 0.00 0.00 3.02
3417 8874 1.081892 CGCAATCCACTCCACTTCAG 58.918 55.000 0.00 0.00 0.00 3.02
3418 8875 1.609061 CGCAATCCACTCCACTTCAGT 60.609 52.381 0.00 0.00 0.00 3.41
3419 8876 2.508526 GCAATCCACTCCACTTCAGTT 58.491 47.619 0.00 0.00 0.00 3.16
3420 8877 2.887152 GCAATCCACTCCACTTCAGTTT 59.113 45.455 0.00 0.00 0.00 2.66
3421 8878 3.304928 GCAATCCACTCCACTTCAGTTTG 60.305 47.826 0.00 0.00 0.00 2.93
3422 8879 4.136796 CAATCCACTCCACTTCAGTTTGA 58.863 43.478 0.00 0.00 0.00 2.69
3423 8880 3.475566 TCCACTCCACTTCAGTTTGAG 57.524 47.619 2.90 2.90 33.14 3.02
3424 8881 2.104792 TCCACTCCACTTCAGTTTGAGG 59.895 50.000 7.74 0.00 31.90 3.86
3425 8882 2.104792 CCACTCCACTTCAGTTTGAGGA 59.895 50.000 7.74 0.00 31.90 3.71
3426 8883 3.433598 CCACTCCACTTCAGTTTGAGGAA 60.434 47.826 7.74 0.00 31.90 3.36
3427 8884 4.392940 CACTCCACTTCAGTTTGAGGAAT 58.607 43.478 7.74 0.00 31.90 3.01
3428 8885 4.823989 CACTCCACTTCAGTTTGAGGAATT 59.176 41.667 7.74 0.00 31.90 2.17
3429 8886 5.300286 CACTCCACTTCAGTTTGAGGAATTT 59.700 40.000 7.74 0.00 31.90 1.82
3430 8887 5.300286 ACTCCACTTCAGTTTGAGGAATTTG 59.700 40.000 7.74 0.00 31.90 2.32
3431 8888 5.445069 TCCACTTCAGTTTGAGGAATTTGA 58.555 37.500 0.00 0.00 0.00 2.69
3432 8889 5.890985 TCCACTTCAGTTTGAGGAATTTGAA 59.109 36.000 0.00 0.00 0.00 2.69
3433 8890 6.039717 TCCACTTCAGTTTGAGGAATTTGAAG 59.960 38.462 9.60 9.60 42.01 3.02
3434 8891 6.183360 CCACTTCAGTTTGAGGAATTTGAAGT 60.183 38.462 10.62 10.62 45.60 3.01
3435 8892 6.914757 CACTTCAGTTTGAGGAATTTGAAGTC 59.085 38.462 12.66 0.00 44.41 3.01
3436 8893 6.830838 ACTTCAGTTTGAGGAATTTGAAGTCT 59.169 34.615 10.62 0.00 43.70 3.24
3437 8894 6.867662 TCAGTTTGAGGAATTTGAAGTCTC 57.132 37.500 0.00 0.00 0.00 3.36
3438 8895 6.356556 TCAGTTTGAGGAATTTGAAGTCTCA 58.643 36.000 0.00 0.00 0.00 3.27
3439 8896 6.260936 TCAGTTTGAGGAATTTGAAGTCTCAC 59.739 38.462 0.00 0.00 0.00 3.51
3440 8897 6.261826 CAGTTTGAGGAATTTGAAGTCTCACT 59.738 38.462 0.00 0.00 0.00 3.41
3441 8898 6.830838 AGTTTGAGGAATTTGAAGTCTCACTT 59.169 34.615 0.00 0.00 41.95 3.16
3442 8899 6.624352 TTGAGGAATTTGAAGTCTCACTTG 57.376 37.500 0.00 0.00 38.80 3.16
3443 8900 5.684704 TGAGGAATTTGAAGTCTCACTTGT 58.315 37.500 0.00 0.00 38.80 3.16
3444 8901 5.528690 TGAGGAATTTGAAGTCTCACTTGTG 59.471 40.000 0.00 0.00 38.80 3.33
3445 8902 4.276926 AGGAATTTGAAGTCTCACTTGTGC 59.723 41.667 0.00 0.00 38.80 4.57
3446 8903 4.540824 GAATTTGAAGTCTCACTTGTGCC 58.459 43.478 0.00 0.00 38.80 5.01
3447 8904 1.967319 TTGAAGTCTCACTTGTGCCC 58.033 50.000 0.00 0.00 38.80 5.36
3448 8905 1.131638 TGAAGTCTCACTTGTGCCCT 58.868 50.000 0.00 0.00 38.80 5.19
3449 8906 1.490490 TGAAGTCTCACTTGTGCCCTT 59.510 47.619 0.00 0.00 38.80 3.95
3450 8907 2.147150 GAAGTCTCACTTGTGCCCTTC 58.853 52.381 0.00 4.15 38.80 3.46
3451 8908 0.398318 AGTCTCACTTGTGCCCTTCC 59.602 55.000 0.00 0.00 0.00 3.46
3452 8909 0.398318 GTCTCACTTGTGCCCTTCCT 59.602 55.000 0.00 0.00 0.00 3.36
3453 8910 0.397941 TCTCACTTGTGCCCTTCCTG 59.602 55.000 0.00 0.00 0.00 3.86
3454 8911 0.397941 CTCACTTGTGCCCTTCCTGA 59.602 55.000 0.00 0.00 0.00 3.86
3455 8912 0.843309 TCACTTGTGCCCTTCCTGAA 59.157 50.000 0.00 0.00 0.00 3.02
3456 8913 1.214175 TCACTTGTGCCCTTCCTGAAA 59.786 47.619 0.00 0.00 0.00 2.69
3457 8914 1.338020 CACTTGTGCCCTTCCTGAAAC 59.662 52.381 0.00 0.00 0.00 2.78
3458 8915 1.215423 ACTTGTGCCCTTCCTGAAACT 59.785 47.619 0.00 0.00 0.00 2.66
3459 8916 2.310538 CTTGTGCCCTTCCTGAAACTT 58.689 47.619 0.00 0.00 0.00 2.66
3460 8917 1.981256 TGTGCCCTTCCTGAAACTTC 58.019 50.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 5.867166 TGCAAACTTCTTTCAAATTTGTGC 58.133 33.333 17.47 15.64 33.70 4.57
161 162 8.735692 ACTTTTCACCAATTCATGAACAATTT 57.264 26.923 11.07 0.00 34.61 1.82
171 175 4.144297 CCTGAGGACTTTTCACCAATTCA 58.856 43.478 0.00 0.00 0.00 2.57
187 191 7.786178 TCGTGAATATATTTCAAACCTGAGG 57.214 36.000 0.00 0.00 31.69 3.86
306 349 3.749609 TCGGTTTTGTAAAGCTTCTAGCC 59.250 43.478 0.00 0.00 43.77 3.93
334 377 6.693113 GGTTTTGTGAAACTTCTAGAAGCTTG 59.307 38.462 28.64 9.84 43.68 4.01
384 430 0.894835 CGGCCCATTTAGTTTGCCTT 59.105 50.000 0.00 0.00 39.97 4.35
385 431 0.970427 CCGGCCCATTTAGTTTGCCT 60.970 55.000 0.00 0.00 39.97 4.75
428 474 1.796796 GACCTCTGAAATGGCGCAC 59.203 57.895 10.83 0.00 0.00 5.34
429 475 1.741401 CGACCTCTGAAATGGCGCA 60.741 57.895 10.83 0.00 0.00 6.09
430 476 1.741770 ACGACCTCTGAAATGGCGC 60.742 57.895 0.00 0.00 0.00 6.53
431 477 1.970917 GCACGACCTCTGAAATGGCG 61.971 60.000 0.00 0.00 0.00 5.69
432 478 1.796796 GCACGACCTCTGAAATGGC 59.203 57.895 0.00 0.00 0.00 4.40
433 479 1.970917 GCGCACGACCTCTGAAATGG 61.971 60.000 0.30 0.00 0.00 3.16
434 480 1.421485 GCGCACGACCTCTGAAATG 59.579 57.895 0.30 0.00 0.00 2.32
435 481 1.741770 GGCGCACGACCTCTGAAAT 60.742 57.895 10.83 0.00 0.00 2.17
436 482 2.357034 GGCGCACGACCTCTGAAA 60.357 61.111 10.83 0.00 0.00 2.69
437 483 2.449031 AATGGCGCACGACCTCTGAA 62.449 55.000 10.83 0.00 0.00 3.02
438 484 2.449031 AAATGGCGCACGACCTCTGA 62.449 55.000 10.83 0.00 0.00 3.27
439 485 2.034879 AAATGGCGCACGACCTCTG 61.035 57.895 10.83 0.00 0.00 3.35
440 486 2.034879 CAAATGGCGCACGACCTCT 61.035 57.895 10.83 0.00 0.00 3.69
441 487 1.017177 TACAAATGGCGCACGACCTC 61.017 55.000 10.83 0.00 0.00 3.85
442 488 0.604243 TTACAAATGGCGCACGACCT 60.604 50.000 10.83 0.00 0.00 3.85
443 489 0.238817 TTTACAAATGGCGCACGACC 59.761 50.000 10.83 0.00 0.00 4.79
444 490 2.039327 TTTTACAAATGGCGCACGAC 57.961 45.000 10.83 0.00 0.00 4.34
445 491 2.386249 GTTTTTACAAATGGCGCACGA 58.614 42.857 10.83 0.00 0.00 4.35
446 492 1.121611 CGTTTTTACAAATGGCGCACG 59.878 47.619 10.83 1.24 0.00 5.34
566 636 0.036671 GGGCCTGCGTAACTGTAGTT 60.037 55.000 0.84 2.51 41.73 2.24
639 709 4.015406 CCCGGCAGCCACACACTA 62.015 66.667 13.30 0.00 0.00 2.74
706 776 2.757980 TAAACAAGTCCGGGCCTGCC 62.758 60.000 5.85 0.00 0.00 4.85
747 818 6.413818 GGCCGTATATTCAAACGAAATCAAAG 59.586 38.462 0.00 0.00 41.55 2.77
853 927 1.801309 GCCCGCAAGCTGGTGTTTTA 61.801 55.000 0.00 0.00 0.00 1.52
887 961 3.084786 AGCAGAATTTACCCAGCAGTTC 58.915 45.455 0.00 0.00 0.00 3.01
915 989 8.111545 TGGTACGTCATGAGGTATATATAGGTT 58.888 37.037 26.14 2.45 34.69 3.50
976 1050 4.099170 GCTCCGCTGCTTGCTGTG 62.099 66.667 0.00 6.15 40.11 3.66
1268 1343 1.020437 TCGAACAACTGCAATGCACA 58.980 45.000 2.72 0.00 33.79 4.57
1541 1668 4.180817 TCACATCATGTCATACGGTTGAC 58.819 43.478 11.74 11.74 45.05 3.18
1542 1669 4.464069 TCACATCATGTCATACGGTTGA 57.536 40.909 0.00 0.00 0.00 3.18
1543 1670 4.631377 AGTTCACATCATGTCATACGGTTG 59.369 41.667 0.00 0.00 0.00 3.77
1544 1671 4.832248 AGTTCACATCATGTCATACGGTT 58.168 39.130 0.00 0.00 0.00 4.44
1566 1700 3.561143 ACTTCACCAACCTGCACATAAA 58.439 40.909 0.00 0.00 0.00 1.40
1640 1774 1.464734 CTCGAGCCTGAACTCTGGTA 58.535 55.000 0.00 0.00 37.30 3.25
1648 1782 1.595993 CCGTTCTCCTCGAGCCTGAA 61.596 60.000 6.99 7.81 0.00 3.02
1802 1936 3.141398 ACACAACTGCAGACGAATTGAT 58.859 40.909 23.35 5.34 0.00 2.57
1803 1937 2.560504 ACACAACTGCAGACGAATTGA 58.439 42.857 23.35 0.00 0.00 2.57
1804 1938 3.242706 TGAACACAACTGCAGACGAATTG 60.243 43.478 23.35 16.20 0.00 2.32
1805 1939 2.942376 TGAACACAACTGCAGACGAATT 59.058 40.909 23.35 8.83 0.00 2.17
1806 1940 2.560504 TGAACACAACTGCAGACGAAT 58.439 42.857 23.35 1.20 0.00 3.34
1807 1941 2.017138 TGAACACAACTGCAGACGAA 57.983 45.000 23.35 0.00 0.00 3.85
1808 1942 2.135139 GATGAACACAACTGCAGACGA 58.865 47.619 23.35 0.00 0.00 4.20
1809 1943 2.138320 AGATGAACACAACTGCAGACG 58.862 47.619 23.35 13.16 0.00 4.18
1892 2054 2.279517 CTCGCGCCCAGATGGTAC 60.280 66.667 0.00 0.00 36.04 3.34
2141 2303 1.139095 CTTACTCCAGTCGGGCGTC 59.861 63.158 0.00 0.00 35.77 5.19
2180 2342 1.555967 GGGCTATTTGCACCAGGAAA 58.444 50.000 0.00 0.00 45.15 3.13
2181 2343 0.679640 CGGGCTATTTGCACCAGGAA 60.680 55.000 0.00 0.00 43.53 3.36
2183 2345 1.378514 ACGGGCTATTTGCACCAGG 60.379 57.895 0.00 0.00 43.53 4.45
2184 2346 1.656818 CCACGGGCTATTTGCACCAG 61.657 60.000 0.00 0.00 43.53 4.00
2185 2347 1.677300 CCACGGGCTATTTGCACCA 60.677 57.895 0.00 0.00 43.53 4.17
2186 2348 0.751643 ATCCACGGGCTATTTGCACC 60.752 55.000 0.00 0.00 43.53 5.01
2414 2577 1.296056 GATGGGGTTGACGAACGTGG 61.296 60.000 4.19 0.00 32.28 4.94
2519 2688 6.827251 CGGTAGCCCTATATTATCTGACTACA 59.173 42.308 0.00 0.00 31.34 2.74
2642 4807 5.465532 TTGCAGCACAAATTCTAAATCCA 57.534 34.783 0.00 0.00 34.56 3.41
2713 4878 3.653344 TGTATAGCAAGGCATGTCGATC 58.347 45.455 0.00 0.00 0.00 3.69
2750 4921 2.308570 TGTTGATGGTCATAGGTGGCTT 59.691 45.455 0.00 0.00 0.00 4.35
2766 4937 1.070821 CGAGCTCAAATCGCTGTTGA 58.929 50.000 15.40 0.00 37.96 3.18
2768 4939 1.639298 GCCGAGCTCAAATCGCTGTT 61.639 55.000 15.40 0.00 37.96 3.16
2788 4959 1.128200 TGGGACCACCGAATATCCAG 58.872 55.000 0.00 0.00 44.64 3.86
2808 4979 0.246635 CCTCGAGAAAAAGGGAGCGA 59.753 55.000 15.71 0.00 0.00 4.93
2827 4998 5.616204 GCGAGTTAATAAGGTGTTGTCAACC 60.616 44.000 13.13 0.00 30.37 3.77
2833 5004 4.914312 TTCGCGAGTTAATAAGGTGTTG 57.086 40.909 9.59 0.00 0.00 3.33
2885 8330 7.912778 AGGCCAGAGATTATCTATATTCCTC 57.087 40.000 5.01 0.00 36.10 3.71
2958 8404 3.235200 ACTTAGAAGCTCACAGTCTGGT 58.765 45.455 4.53 0.00 0.00 4.00
2960 8406 4.876125 TGAACTTAGAAGCTCACAGTCTG 58.124 43.478 0.00 0.00 0.00 3.51
2963 8409 3.999663 GCATGAACTTAGAAGCTCACAGT 59.000 43.478 0.00 0.00 34.31 3.55
3034 8480 6.498651 AGGGAGTCTCATTCAAGAAGTAAAGA 59.501 38.462 1.47 0.00 0.00 2.52
3113 8570 9.719279 CTACGATTACTCTCTTCGTAAAAGAAT 57.281 33.333 5.98 0.00 44.78 2.40
3116 8573 9.212687 CTTCTACGATTACTCTCTTCGTAAAAG 57.787 37.037 5.98 5.02 44.78 2.27
3120 8577 7.010923 GGAACTTCTACGATTACTCTCTTCGTA 59.989 40.741 4.59 4.59 43.66 3.43
3121 8578 6.183360 GGAACTTCTACGATTACTCTCTTCGT 60.183 42.308 2.63 2.63 46.72 3.85
3122 8579 6.183360 TGGAACTTCTACGATTACTCTCTTCG 60.183 42.308 0.00 0.00 38.76 3.79
3125 8582 6.095720 CCTTGGAACTTCTACGATTACTCTCT 59.904 42.308 0.00 0.00 0.00 3.10
3127 8584 5.715753 ACCTTGGAACTTCTACGATTACTCT 59.284 40.000 0.00 0.00 0.00 3.24
3128 8585 5.963594 ACCTTGGAACTTCTACGATTACTC 58.036 41.667 0.00 0.00 0.00 2.59
3129 8586 5.997384 ACCTTGGAACTTCTACGATTACT 57.003 39.130 0.00 0.00 0.00 2.24
3133 8590 5.014858 TGAGTACCTTGGAACTTCTACGAT 58.985 41.667 0.00 0.00 0.00 3.73
3137 8594 3.836562 GGGTGAGTACCTTGGAACTTCTA 59.163 47.826 0.00 0.00 46.66 2.10
3141 8598 2.417719 AGGGTGAGTACCTTGGAACT 57.582 50.000 0.00 0.00 46.66 3.01
3153 8610 2.205022 TGAGCCATTTGAAGGGTGAG 57.795 50.000 0.00 0.00 36.91 3.51
3162 8619 3.872511 TTGCTACCAATGAGCCATTTG 57.127 42.857 0.00 0.00 39.30 2.32
3174 8631 8.905660 TTGTACTAAAACTGTTATTGCTACCA 57.094 30.769 0.00 0.00 0.00 3.25
3183 8640 6.484308 GGACCTTGCTTGTACTAAAACTGTTA 59.516 38.462 0.00 0.00 0.00 2.41
3188 8645 4.577283 TGTGGACCTTGCTTGTACTAAAAC 59.423 41.667 0.00 0.00 0.00 2.43
3194 8651 0.875059 GCTGTGGACCTTGCTTGTAC 59.125 55.000 0.00 0.00 0.00 2.90
3208 8665 0.835941 AAGCTCTATCCCTGGCTGTG 59.164 55.000 0.00 0.00 35.08 3.66
3209 8666 1.127343 GAAGCTCTATCCCTGGCTGT 58.873 55.000 0.00 0.00 35.08 4.40
3210 8667 1.126488 TGAAGCTCTATCCCTGGCTG 58.874 55.000 0.00 0.00 35.08 4.85
3220 8677 2.495155 TGGCAAGCAATGAAGCTCTA 57.505 45.000 0.00 0.00 45.89 2.43
3241 8698 1.141881 GCCGAAGATTCTCGAGGCA 59.858 57.895 13.56 0.00 43.65 4.75
3249 8706 4.084328 CGGATCTAATGTTGCCGAAGATTC 60.084 45.833 0.00 0.00 44.43 2.52
3258 8715 3.050619 CGTAGTCCGGATCTAATGTTGC 58.949 50.000 7.81 0.00 0.00 4.17
3262 8719 3.921021 GCAATCGTAGTCCGGATCTAATG 59.079 47.826 7.81 7.66 37.11 1.90
3271 8728 0.855349 GCATCAGCAATCGTAGTCCG 59.145 55.000 0.00 0.00 41.58 4.79
3272 8729 1.221414 GGCATCAGCAATCGTAGTCC 58.779 55.000 0.00 0.00 44.61 3.85
3273 8730 1.221414 GGGCATCAGCAATCGTAGTC 58.779 55.000 0.00 0.00 44.61 2.59
3274 8731 0.179045 GGGGCATCAGCAATCGTAGT 60.179 55.000 0.00 0.00 44.61 2.73
3275 8732 0.886490 GGGGGCATCAGCAATCGTAG 60.886 60.000 0.00 0.00 44.61 3.51
3276 8733 1.148273 GGGGGCATCAGCAATCGTA 59.852 57.895 0.00 0.00 44.61 3.43
3277 8734 2.124151 GGGGGCATCAGCAATCGT 60.124 61.111 0.00 0.00 44.61 3.73
3291 8748 0.897621 GAAACTGGCTGATTTGGGGG 59.102 55.000 0.00 0.00 0.00 5.40
3292 8749 0.527565 CGAAACTGGCTGATTTGGGG 59.472 55.000 0.00 0.00 0.00 4.96
3293 8750 1.200020 GACGAAACTGGCTGATTTGGG 59.800 52.381 0.00 0.00 0.00 4.12
3294 8751 2.154462 AGACGAAACTGGCTGATTTGG 58.846 47.619 0.00 0.10 0.00 3.28
3295 8752 2.159787 CGAGACGAAACTGGCTGATTTG 60.160 50.000 0.00 0.00 0.00 2.32
3296 8753 2.069273 CGAGACGAAACTGGCTGATTT 58.931 47.619 0.00 0.00 0.00 2.17
3297 8754 1.673033 CCGAGACGAAACTGGCTGATT 60.673 52.381 0.00 0.00 0.00 2.57
3298 8755 0.108615 CCGAGACGAAACTGGCTGAT 60.109 55.000 0.00 0.00 0.00 2.90
3299 8756 1.289066 CCGAGACGAAACTGGCTGA 59.711 57.895 0.00 0.00 0.00 4.26
3300 8757 0.242825 TACCGAGACGAAACTGGCTG 59.757 55.000 0.00 0.00 0.00 4.85
3301 8758 1.183549 ATACCGAGACGAAACTGGCT 58.816 50.000 0.00 0.00 0.00 4.75
3302 8759 2.856557 GTTATACCGAGACGAAACTGGC 59.143 50.000 0.00 0.00 0.00 4.85
3303 8760 3.103738 CGTTATACCGAGACGAAACTGG 58.896 50.000 0.00 0.00 38.99 4.00
3304 8761 2.529090 GCGTTATACCGAGACGAAACTG 59.471 50.000 0.00 0.00 38.99 3.16
3305 8762 2.162208 TGCGTTATACCGAGACGAAACT 59.838 45.455 0.00 0.00 38.99 2.66
3306 8763 2.518949 TGCGTTATACCGAGACGAAAC 58.481 47.619 0.00 0.00 38.99 2.78
3307 8764 2.916716 GTTGCGTTATACCGAGACGAAA 59.083 45.455 0.00 0.00 38.99 3.46
3308 8765 2.518949 GTTGCGTTATACCGAGACGAA 58.481 47.619 0.00 0.00 38.99 3.85
3309 8766 1.529622 CGTTGCGTTATACCGAGACGA 60.530 52.381 11.00 0.00 38.82 4.20
3310 8767 0.835740 CGTTGCGTTATACCGAGACG 59.164 55.000 0.00 0.00 39.61 4.18
3311 8768 2.107178 CTCGTTGCGTTATACCGAGAC 58.893 52.381 0.00 0.00 45.81 3.36
3312 8769 2.463553 CTCGTTGCGTTATACCGAGA 57.536 50.000 0.00 0.00 45.81 4.04
3313 8770 2.373269 CTCTCGTTGCGTTATACCGAG 58.627 52.381 0.00 0.00 44.67 4.63
3314 8771 1.532505 GCTCTCGTTGCGTTATACCGA 60.533 52.381 0.00 0.00 0.00 4.69
3315 8772 0.844503 GCTCTCGTTGCGTTATACCG 59.155 55.000 0.00 0.00 0.00 4.02
3316 8773 1.587034 GTGCTCTCGTTGCGTTATACC 59.413 52.381 0.00 0.00 0.00 2.73
3317 8774 1.587034 GGTGCTCTCGTTGCGTTATAC 59.413 52.381 0.00 0.00 0.00 1.47
3318 8775 1.470285 GGGTGCTCTCGTTGCGTTATA 60.470 52.381 0.00 0.00 0.00 0.98
3319 8776 0.739813 GGGTGCTCTCGTTGCGTTAT 60.740 55.000 0.00 0.00 0.00 1.89
3320 8777 1.373748 GGGTGCTCTCGTTGCGTTA 60.374 57.895 0.00 0.00 0.00 3.18
3321 8778 2.665185 GGGTGCTCTCGTTGCGTT 60.665 61.111 0.00 0.00 0.00 4.84
3322 8779 1.884075 TATGGGTGCTCTCGTTGCGT 61.884 55.000 0.00 0.00 0.00 5.24
3323 8780 0.530650 ATATGGGTGCTCTCGTTGCG 60.531 55.000 0.00 0.00 0.00 4.85
3324 8781 1.202580 AGATATGGGTGCTCTCGTTGC 60.203 52.381 0.00 0.00 0.00 4.17
3325 8782 2.898729 AGATATGGGTGCTCTCGTTG 57.101 50.000 0.00 0.00 0.00 4.10
3326 8783 2.766263 TGAAGATATGGGTGCTCTCGTT 59.234 45.455 0.00 0.00 0.00 3.85
3327 8784 2.388735 TGAAGATATGGGTGCTCTCGT 58.611 47.619 0.00 0.00 0.00 4.18
3328 8785 3.006217 TCATGAAGATATGGGTGCTCTCG 59.994 47.826 0.00 0.00 0.00 4.04
3329 8786 4.314121 GTCATGAAGATATGGGTGCTCTC 58.686 47.826 0.00 0.00 0.00 3.20
3330 8787 3.244009 CGTCATGAAGATATGGGTGCTCT 60.244 47.826 2.01 0.00 0.00 4.09
3331 8788 3.062763 CGTCATGAAGATATGGGTGCTC 58.937 50.000 2.01 0.00 0.00 4.26
3332 8789 2.224378 CCGTCATGAAGATATGGGTGCT 60.224 50.000 10.47 0.00 0.00 4.40
3333 8790 2.146342 CCGTCATGAAGATATGGGTGC 58.854 52.381 10.47 0.00 0.00 5.01
3334 8791 2.146342 GCCGTCATGAAGATATGGGTG 58.854 52.381 10.47 0.00 0.00 4.61
3335 8792 1.072331 GGCCGTCATGAAGATATGGGT 59.928 52.381 10.47 0.00 0.00 4.51
3336 8793 1.072173 TGGCCGTCATGAAGATATGGG 59.928 52.381 10.47 0.00 0.00 4.00
3337 8794 2.549064 TGGCCGTCATGAAGATATGG 57.451 50.000 10.47 0.00 0.00 2.74
3338 8795 4.093998 GCTATTGGCCGTCATGAAGATATG 59.906 45.833 10.47 0.00 34.27 1.78
3339 8796 4.019860 AGCTATTGGCCGTCATGAAGATAT 60.020 41.667 10.47 1.08 43.05 1.63
3340 8797 3.324846 AGCTATTGGCCGTCATGAAGATA 59.675 43.478 10.47 0.00 43.05 1.98
3341 8798 2.105477 AGCTATTGGCCGTCATGAAGAT 59.895 45.455 10.47 0.00 43.05 2.40
3342 8799 1.486310 AGCTATTGGCCGTCATGAAGA 59.514 47.619 10.47 0.00 43.05 2.87
3343 8800 1.600957 CAGCTATTGGCCGTCATGAAG 59.399 52.381 0.00 0.00 43.05 3.02
3344 8801 1.667236 CAGCTATTGGCCGTCATGAA 58.333 50.000 0.00 0.00 43.05 2.57
3345 8802 0.815213 GCAGCTATTGGCCGTCATGA 60.815 55.000 0.00 0.00 43.05 3.07
3346 8803 1.096967 TGCAGCTATTGGCCGTCATG 61.097 55.000 0.00 0.00 43.05 3.07
3347 8804 0.179009 ATGCAGCTATTGGCCGTCAT 60.179 50.000 0.00 0.00 43.05 3.06
3348 8805 0.815213 GATGCAGCTATTGGCCGTCA 60.815 55.000 0.00 0.00 43.05 4.35
3349 8806 1.510480 GGATGCAGCTATTGGCCGTC 61.510 60.000 0.22 0.00 43.05 4.79
3350 8807 1.526917 GGATGCAGCTATTGGCCGT 60.527 57.895 0.22 0.00 43.05 5.68
3351 8808 1.526686 TGGATGCAGCTATTGGCCG 60.527 57.895 0.22 0.00 43.05 6.13
3352 8809 0.752743 TGTGGATGCAGCTATTGGCC 60.753 55.000 0.22 0.00 43.05 5.36
3353 8810 0.383231 GTGTGGATGCAGCTATTGGC 59.617 55.000 0.22 0.00 42.19 4.52
3354 8811 0.659427 CGTGTGGATGCAGCTATTGG 59.341 55.000 0.22 0.00 0.00 3.16
3355 8812 1.372582 ACGTGTGGATGCAGCTATTG 58.627 50.000 0.22 0.00 0.00 1.90
3356 8813 2.979814 TACGTGTGGATGCAGCTATT 57.020 45.000 0.22 0.00 0.00 1.73
3357 8814 2.630098 AGATACGTGTGGATGCAGCTAT 59.370 45.455 0.22 0.00 0.00 2.97
3358 8815 2.031870 AGATACGTGTGGATGCAGCTA 58.968 47.619 0.22 0.00 0.00 3.32
3359 8816 0.826715 AGATACGTGTGGATGCAGCT 59.173 50.000 0.22 0.00 0.00 4.24
3360 8817 1.656652 AAGATACGTGTGGATGCAGC 58.343 50.000 0.00 0.00 0.00 5.25
3361 8818 5.294306 ACAATTAAGATACGTGTGGATGCAG 59.706 40.000 0.00 0.00 0.00 4.41
3362 8819 5.182487 ACAATTAAGATACGTGTGGATGCA 58.818 37.500 0.00 0.00 0.00 3.96
3363 8820 5.734855 ACAATTAAGATACGTGTGGATGC 57.265 39.130 0.00 0.00 0.00 3.91
3364 8821 9.650371 CAATTACAATTAAGATACGTGTGGATG 57.350 33.333 0.00 0.00 0.00 3.51
3365 8822 9.607988 TCAATTACAATTAAGATACGTGTGGAT 57.392 29.630 0.00 0.00 0.00 3.41
3366 8823 9.093970 CTCAATTACAATTAAGATACGTGTGGA 57.906 33.333 0.00 0.00 0.00 4.02
3367 8824 8.335356 CCTCAATTACAATTAAGATACGTGTGG 58.665 37.037 0.00 0.00 0.00 4.17
3368 8825 8.335356 CCCTCAATTACAATTAAGATACGTGTG 58.665 37.037 0.00 0.00 0.00 3.82
3369 8826 8.044908 ACCCTCAATTACAATTAAGATACGTGT 58.955 33.333 0.00 0.00 0.00 4.49
3370 8827 8.335356 CACCCTCAATTACAATTAAGATACGTG 58.665 37.037 0.00 0.00 0.00 4.49
3371 8828 7.497909 CCACCCTCAATTACAATTAAGATACGT 59.502 37.037 0.00 0.00 0.00 3.57
3372 8829 7.519970 GCCACCCTCAATTACAATTAAGATACG 60.520 40.741 0.00 0.00 0.00 3.06
3373 8830 7.519970 CGCCACCCTCAATTACAATTAAGATAC 60.520 40.741 0.00 0.00 0.00 2.24
3374 8831 6.485313 CGCCACCCTCAATTACAATTAAGATA 59.515 38.462 0.00 0.00 0.00 1.98
3375 8832 5.299279 CGCCACCCTCAATTACAATTAAGAT 59.701 40.000 0.00 0.00 0.00 2.40
3376 8833 4.638421 CGCCACCCTCAATTACAATTAAGA 59.362 41.667 0.00 0.00 0.00 2.10
3377 8834 4.733523 GCGCCACCCTCAATTACAATTAAG 60.734 45.833 0.00 0.00 0.00 1.85
3378 8835 3.129638 GCGCCACCCTCAATTACAATTAA 59.870 43.478 0.00 0.00 0.00 1.40
3379 8836 2.685897 GCGCCACCCTCAATTACAATTA 59.314 45.455 0.00 0.00 0.00 1.40
3380 8837 1.476488 GCGCCACCCTCAATTACAATT 59.524 47.619 0.00 0.00 0.00 2.32
3381 8838 1.102978 GCGCCACCCTCAATTACAAT 58.897 50.000 0.00 0.00 0.00 2.71
3382 8839 0.250945 TGCGCCACCCTCAATTACAA 60.251 50.000 4.18 0.00 0.00 2.41
3383 8840 0.250945 TTGCGCCACCCTCAATTACA 60.251 50.000 4.18 0.00 0.00 2.41
3384 8841 1.065551 GATTGCGCCACCCTCAATTAC 59.934 52.381 4.18 0.00 31.30 1.89
3385 8842 1.388547 GATTGCGCCACCCTCAATTA 58.611 50.000 4.18 0.00 31.30 1.40
3386 8843 1.322538 GGATTGCGCCACCCTCAATT 61.323 55.000 4.18 0.00 31.30 2.32
3387 8844 1.754234 GGATTGCGCCACCCTCAAT 60.754 57.895 4.18 0.00 33.57 2.57
3388 8845 2.361104 GGATTGCGCCACCCTCAA 60.361 61.111 4.18 0.00 0.00 3.02
3389 8846 3.645660 TGGATTGCGCCACCCTCA 61.646 61.111 4.18 0.00 31.66 3.86
3395 8852 2.359850 GTGGAGTGGATTGCGCCA 60.360 61.111 4.18 0.00 33.51 5.69
3396 8853 1.648467 GAAGTGGAGTGGATTGCGCC 61.648 60.000 4.18 0.00 0.00 6.53
3397 8854 0.955428 TGAAGTGGAGTGGATTGCGC 60.955 55.000 0.00 0.00 0.00 6.09
3398 8855 1.081892 CTGAAGTGGAGTGGATTGCG 58.918 55.000 0.00 0.00 0.00 4.85
3399 8856 2.191128 ACTGAAGTGGAGTGGATTGC 57.809 50.000 0.00 0.00 0.00 3.56
3400 8857 4.136796 TCAAACTGAAGTGGAGTGGATTG 58.863 43.478 0.00 0.00 0.00 2.67
3401 8858 4.392940 CTCAAACTGAAGTGGAGTGGATT 58.607 43.478 4.88 0.00 0.00 3.01
3402 8859 3.244700 CCTCAAACTGAAGTGGAGTGGAT 60.245 47.826 10.00 0.00 31.95 3.41
3403 8860 2.104792 CCTCAAACTGAAGTGGAGTGGA 59.895 50.000 10.00 0.00 31.95 4.02
3404 8861 2.104792 TCCTCAAACTGAAGTGGAGTGG 59.895 50.000 10.00 3.22 31.95 4.00
3405 8862 3.475566 TCCTCAAACTGAAGTGGAGTG 57.524 47.619 10.00 4.36 31.95 3.51
3406 8863 4.713792 ATTCCTCAAACTGAAGTGGAGT 57.286 40.909 10.00 0.00 31.95 3.85
3407 8864 5.532406 TCAAATTCCTCAAACTGAAGTGGAG 59.468 40.000 5.74 5.74 32.99 3.86
3408 8865 5.445069 TCAAATTCCTCAAACTGAAGTGGA 58.555 37.500 0.00 0.00 0.00 4.02
3409 8866 5.772825 TCAAATTCCTCAAACTGAAGTGG 57.227 39.130 0.00 0.00 0.00 4.00
3410 8867 6.799512 ACTTCAAATTCCTCAAACTGAAGTG 58.200 36.000 14.14 0.00 44.22 3.16
3411 8868 6.830838 AGACTTCAAATTCCTCAAACTGAAGT 59.169 34.615 14.60 14.60 46.28 3.01
3412 8869 7.012704 TGAGACTTCAAATTCCTCAAACTGAAG 59.987 37.037 9.60 9.60 41.58 3.02
3413 8870 6.828273 TGAGACTTCAAATTCCTCAAACTGAA 59.172 34.615 0.00 0.00 31.72 3.02
3414 8871 6.260936 GTGAGACTTCAAATTCCTCAAACTGA 59.739 38.462 0.00 0.00 35.89 3.41
3415 8872 6.261826 AGTGAGACTTCAAATTCCTCAAACTG 59.738 38.462 0.00 0.00 35.89 3.16
3416 8873 6.360618 AGTGAGACTTCAAATTCCTCAAACT 58.639 36.000 0.00 0.00 35.89 2.66
3417 8874 6.625873 AGTGAGACTTCAAATTCCTCAAAC 57.374 37.500 0.00 0.00 35.89 2.93
3418 8875 6.603201 ACAAGTGAGACTTCAAATTCCTCAAA 59.397 34.615 0.00 0.00 36.03 2.69
3419 8876 6.038603 CACAAGTGAGACTTCAAATTCCTCAA 59.961 38.462 0.00 0.00 36.03 3.02
3420 8877 5.528690 CACAAGTGAGACTTCAAATTCCTCA 59.471 40.000 0.00 0.00 36.03 3.86
3421 8878 5.561725 GCACAAGTGAGACTTCAAATTCCTC 60.562 44.000 4.04 0.00 36.03 3.71
3422 8879 4.276926 GCACAAGTGAGACTTCAAATTCCT 59.723 41.667 4.04 0.00 36.03 3.36
3423 8880 4.540824 GCACAAGTGAGACTTCAAATTCC 58.459 43.478 4.04 0.00 36.03 3.01
3424 8881 4.540824 GGCACAAGTGAGACTTCAAATTC 58.459 43.478 4.04 0.00 36.03 2.17
3425 8882 3.319122 GGGCACAAGTGAGACTTCAAATT 59.681 43.478 4.04 0.00 36.03 1.82
3426 8883 2.887152 GGGCACAAGTGAGACTTCAAAT 59.113 45.455 4.04 0.00 36.03 2.32
3427 8884 2.092429 AGGGCACAAGTGAGACTTCAAA 60.092 45.455 4.04 0.00 36.03 2.69
3428 8885 1.490490 AGGGCACAAGTGAGACTTCAA 59.510 47.619 4.04 0.00 36.03 2.69
3429 8886 1.131638 AGGGCACAAGTGAGACTTCA 58.868 50.000 4.04 0.00 36.03 3.02
3430 8887 2.147150 GAAGGGCACAAGTGAGACTTC 58.853 52.381 4.04 9.61 36.03 3.01
3431 8888 1.202818 GGAAGGGCACAAGTGAGACTT 60.203 52.381 4.04 4.52 39.39 3.01
3432 8889 0.398318 GGAAGGGCACAAGTGAGACT 59.602 55.000 4.04 0.00 0.00 3.24
3433 8890 0.398318 AGGAAGGGCACAAGTGAGAC 59.602 55.000 4.04 0.00 0.00 3.36
3434 8891 0.397941 CAGGAAGGGCACAAGTGAGA 59.602 55.000 4.04 0.00 0.00 3.27
3435 8892 0.397941 TCAGGAAGGGCACAAGTGAG 59.602 55.000 4.04 0.00 0.00 3.51
3436 8893 0.843309 TTCAGGAAGGGCACAAGTGA 59.157 50.000 4.04 0.00 0.00 3.41
3437 8894 1.338020 GTTTCAGGAAGGGCACAAGTG 59.662 52.381 0.00 0.00 0.00 3.16
3438 8895 1.215423 AGTTTCAGGAAGGGCACAAGT 59.785 47.619 0.00 0.00 0.00 3.16
3439 8896 1.986882 AGTTTCAGGAAGGGCACAAG 58.013 50.000 0.00 0.00 0.00 3.16
3440 8897 2.306847 GAAGTTTCAGGAAGGGCACAA 58.693 47.619 0.00 0.00 0.00 3.33
3441 8898 1.981256 GAAGTTTCAGGAAGGGCACA 58.019 50.000 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.