Multiple sequence alignment - TraesCS1D01G114200

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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 TraesCS1D01G114200 chr1D 100.000 5620 0 0 1 5620 110336286 110341905 0.000000e+00 10379
1 TraesCS1D01G114200 chr1D 91.439 549 35 7 3164 3710 488723193 488722655 0.000000e+00 743
2 TraesCS1D01G114200 chr1D 91.241 548 38 7 3164 3710 464158702 464158164 0.000000e+00 737
3 TraesCS1D01G114200 chr1D 90.698 129 9 3 2617 2743 48391337 48391464 9.680000e-38 169
4 TraesCS1D01G114200 chr1B 92.973 3259 177 22 2379 5614 167716724 167719953 0.000000e+00 4702
5 TraesCS1D01G114200 chr1B 92.333 1826 86 21 552 2349 167714922 167716721 0.000000e+00 2547
6 TraesCS1D01G114200 chr1B 95.631 206 7 1 3 208 167714366 167714569 4.200000e-86 329
7 TraesCS1D01G114200 chr1A 91.698 2096 136 15 2377 4466 114549390 114551453 0.000000e+00 2872
8 TraesCS1D01G114200 chr1A 93.087 1461 61 15 896 2348 114547960 114549388 0.000000e+00 2102
9 TraesCS1D01G114200 chr1A 95.415 1156 41 7 4467 5616 114551679 114552828 0.000000e+00 1831
10 TraesCS1D01G114200 chr1A 96.154 208 8 0 1 208 114546393 114546600 1.940000e-89 340
11 TraesCS1D01G114200 chr1A 90.854 164 4 4 565 720 114547311 114547471 5.710000e-50 209
12 TraesCS1D01G114200 chr1A 87.662 154 8 7 365 512 114547154 114547302 9.680000e-38 169
13 TraesCS1D01G114200 chr3D 89.610 1078 95 15 2719 3795 226022244 226023305 0.000000e+00 1354
14 TraesCS1D01G114200 chr3D 95.149 268 8 2 1603 1870 573314673 573314411 8.710000e-113 418
15 TraesCS1D01G114200 chr3D 94.776 268 9 2 1603 1870 474128909 474128647 4.050000e-111 412
16 TraesCS1D01G114200 chr3D 83.951 81 10 1 1058 1138 48452188 48452111 2.170000e-09 75
17 TraesCS1D01G114200 chr4D 91.985 786 51 7 3011 3795 12844366 12845140 0.000000e+00 1092
18 TraesCS1D01G114200 chr4D 92.760 221 14 1 3010 3230 197323870 197323652 9.090000e-83 318
19 TraesCS1D01G114200 chr4D 91.603 131 10 1 2616 2745 29833613 29833483 4.470000e-41 180
20 TraesCS1D01G114200 chr2D 91.349 786 57 8 3011 3795 467630531 467629756 0.000000e+00 1064
21 TraesCS1D01G114200 chr2D 94.776 268 9 2 1603 1870 573865164 573864902 4.050000e-111 412
22 TraesCS1D01G114200 chrUn 90.458 786 55 9 3011 3795 71029993 71029227 0.000000e+00 1018
23 TraesCS1D01G114200 chrUn 90.458 786 55 9 3011 3795 408524110 408524876 0.000000e+00 1018
24 TraesCS1D01G114200 chrUn 84.044 633 55 26 1262 1870 331637494 331638104 8.170000e-158 568
25 TraesCS1D01G114200 chr3B 90.351 570 48 5 3225 3794 254543124 254542562 0.000000e+00 741
26 TraesCS1D01G114200 chr3B 87.451 510 50 10 2719 3228 254606290 254605795 4.880000e-160 575
27 TraesCS1D01G114200 chr3B 94.574 129 5 2 2617 2743 42630945 42630817 1.240000e-46 198
28 TraesCS1D01G114200 chr3B 83.951 81 10 1 1058 1138 77006861 77006784 2.170000e-09 75
29 TraesCS1D01G114200 chr6D 91.257 549 36 7 3164 3710 123583530 123584068 0.000000e+00 737
30 TraesCS1D01G114200 chr6D 94.776 268 9 2 1603 1870 453201274 453201536 4.050000e-111 412
31 TraesCS1D01G114200 chr6D 88.152 211 23 2 2719 2929 453201529 453201737 3.360000e-62 250
32 TraesCS1D01G114200 chr4A 83.926 703 53 29 1180 1870 201150630 201149976 8.000000e-173 617
33 TraesCS1D01G114200 chr4A 83.880 701 55 27 1180 1870 211667994 211668646 2.880000e-172 616
34 TraesCS1D01G114200 chr4A 92.063 126 8 2 2616 2739 573322317 573322442 5.790000e-40 176
35 TraesCS1D01G114200 chr3A 82.656 738 71 31 1145 1870 530061630 530062322 8.060000e-168 601
36 TraesCS1D01G114200 chr3A 94.488 127 6 1 2617 2742 83748148 83748022 1.600000e-45 195
37 TraesCS1D01G114200 chr3A 93.798 129 6 2 2617 2743 34532576 34532448 5.750000e-45 193
38 TraesCS1D01G114200 chr5B 84.202 633 54 26 1262 1870 688472333 688471723 1.760000e-159 573
39 TraesCS1D01G114200 chr5B 83.730 504 39 23 1388 1870 688474941 688474460 2.400000e-118 436
40 TraesCS1D01G114200 chr6A 82.055 730 54 33 1151 1870 86629648 86628986 8.230000e-153 551
41 TraesCS1D01G114200 chr6A 94.776 268 9 3 1603 1870 33173287 33173025 4.050000e-111 412
42 TraesCS1D01G114200 chr6A 87.129 303 35 4 2719 3021 33173032 33172734 1.940000e-89 340
43 TraesCS1D01G114200 chr7D 95.522 268 7 3 1603 1870 177235493 177235231 1.870000e-114 424
44 TraesCS1D01G114200 chr2B 95.149 268 8 2 1603 1870 703576941 703577203 8.710000e-113 418
45 TraesCS1D01G114200 chr5A 90.076 131 11 2 2617 2745 82869920 82869790 9.680000e-38 169


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 TraesCS1D01G114200 chr1D 110336286 110341905 5619 False 10379.000000 10379 100.000000 1 5620 1 chr1D.!!$F2 5619
1 TraesCS1D01G114200 chr1D 488722655 488723193 538 True 743.000000 743 91.439000 3164 3710 1 chr1D.!!$R2 546
2 TraesCS1D01G114200 chr1D 464158164 464158702 538 True 737.000000 737 91.241000 3164 3710 1 chr1D.!!$R1 546
3 TraesCS1D01G114200 chr1B 167714366 167719953 5587 False 2526.000000 4702 93.645667 3 5614 3 chr1B.!!$F1 5611
4 TraesCS1D01G114200 chr1A 114546393 114552828 6435 False 1253.833333 2872 92.478333 1 5616 6 chr1A.!!$F1 5615
5 TraesCS1D01G114200 chr3D 226022244 226023305 1061 False 1354.000000 1354 89.610000 2719 3795 1 chr3D.!!$F1 1076
6 TraesCS1D01G114200 chr4D 12844366 12845140 774 False 1092.000000 1092 91.985000 3011 3795 1 chr4D.!!$F1 784
7 TraesCS1D01G114200 chr2D 467629756 467630531 775 True 1064.000000 1064 91.349000 3011 3795 1 chr2D.!!$R1 784
8 TraesCS1D01G114200 chrUn 71029227 71029993 766 True 1018.000000 1018 90.458000 3011 3795 1 chrUn.!!$R1 784
9 TraesCS1D01G114200 chrUn 408524110 408524876 766 False 1018.000000 1018 90.458000 3011 3795 1 chrUn.!!$F2 784
10 TraesCS1D01G114200 chrUn 331637494 331638104 610 False 568.000000 568 84.044000 1262 1870 1 chrUn.!!$F1 608
11 TraesCS1D01G114200 chr3B 254542562 254543124 562 True 741.000000 741 90.351000 3225 3794 1 chr3B.!!$R3 569
12 TraesCS1D01G114200 chr6D 123583530 123584068 538 False 737.000000 737 91.257000 3164 3710 1 chr6D.!!$F1 546
13 TraesCS1D01G114200 chr4A 201149976 201150630 654 True 617.000000 617 83.926000 1180 1870 1 chr4A.!!$R1 690
14 TraesCS1D01G114200 chr4A 211667994 211668646 652 False 616.000000 616 83.880000 1180 1870 1 chr4A.!!$F1 690
15 TraesCS1D01G114200 chr3A 530061630 530062322 692 False 601.000000 601 82.656000 1145 1870 1 chr3A.!!$F1 725
16 TraesCS1D01G114200 chr5B 688471723 688474941 3218 True 504.500000 573 83.966000 1262 1870 2 chr5B.!!$R1 608
17 TraesCS1D01G114200 chr6A 86628986 86629648 662 True 551.000000 551 82.055000 1151 1870 1 chr6A.!!$R1 719
18 TraesCS1D01G114200 chr6A 33172734 33173287 553 True 376.000000 412 90.952500 1603 3021 2 chr6A.!!$R2 1418

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
880 1303 0.103337 AACCCCCTTCCTTCCTTCCT 60.103 55.0 0.00 0.0 0.00 3.36 F
2351 3733 0.252197 GACCATGCCTCCTTACGGTT 59.748 55.0 0.00 0.0 0.00 4.44 F
2426 3808 0.546122 TGGTGCCTCACTGAACTGTT 59.454 50.0 0.00 0.0 34.40 3.16 F
2568 3950 0.671781 CTGAGTGCCGCTAAAGCTGT 60.672 55.0 0.00 0.0 39.32 4.40 F
2649 4032 0.741221 GTGGGTTGATGCGACCTCTC 60.741 60.0 3.99 0.0 37.99 3.20 F
3432 5642 0.776810 TGAGGCCCTTGGTCATTTCA 59.223 50.0 0.00 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2796 4992 0.328450 ATGGAGTTATCCCTGGCCCA 60.328 55.000 0.0 0.0 46.04 5.36 R
3520 5741 0.102120 CAAGTGAAACGCAGGGCAAA 59.898 50.000 0.0 0.0 45.86 3.68 R
3693 5915 0.107752 TGAGCAGCACACACTTGACA 60.108 50.000 0.0 0.0 0.00 3.58 R
3895 6117 0.386476 ACAACGCACGGTACAGAAGA 59.614 50.000 0.0 0.0 0.00 2.87 R
4501 6953 1.019673 CTCCAACCTGCCATCATTCG 58.980 55.000 0.0 0.0 0.00 3.34 R
4707 7159 1.423921 GGAAAAGGACCTGGACTGGAA 59.576 52.381 0.0 0.0 0.00 3.53 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
25 26 6.238786 GCAGAAGAAGTCTATCCGTTCTATCA 60.239 42.308 0.00 0.00 33.56 2.15
26 27 7.359595 CAGAAGAAGTCTATCCGTTCTATCAG 58.640 42.308 0.00 0.00 33.56 2.90
154 155 8.902540 TTGTGATGATGGTACTAATATGAACC 57.097 34.615 0.00 0.00 0.00 3.62
172 173 0.179129 CCGCCTGTTGAATCATTGCC 60.179 55.000 0.00 0.00 0.00 4.52
208 209 4.869215 TGTCAATGTATTTTGCTGTGGTG 58.131 39.130 0.00 0.00 0.00 4.17
258 279 8.610248 TCAGGAAAATGTTATACGTTCTTTGA 57.390 30.769 0.00 0.00 0.00 2.69
260 281 9.672086 CAGGAAAATGTTATACGTTCTTTGAAA 57.328 29.630 0.00 0.00 0.00 2.69
261 282 9.673454 AGGAAAATGTTATACGTTCTTTGAAAC 57.327 29.630 0.00 0.00 0.00 2.78
285 341 3.196254 AGCAAAATTCTGGCCCAGTAATG 59.804 43.478 11.27 5.64 32.61 1.90
295 360 3.964031 TGGCCCAGTAATGTTTTTGAAGT 59.036 39.130 0.00 0.00 0.00 3.01
296 361 5.141182 TGGCCCAGTAATGTTTTTGAAGTA 58.859 37.500 0.00 0.00 0.00 2.24
297 362 5.010213 TGGCCCAGTAATGTTTTTGAAGTAC 59.990 40.000 0.00 0.00 0.00 2.73
321 386 6.325545 ACCAGTATACAATTTCCGGATGTCTA 59.674 38.462 12.37 5.22 0.00 2.59
322 387 7.147620 ACCAGTATACAATTTCCGGATGTCTAA 60.148 37.037 12.37 0.00 0.00 2.10
323 388 7.878127 CCAGTATACAATTTCCGGATGTCTAAT 59.122 37.037 12.37 2.41 0.00 1.73
324 389 9.273016 CAGTATACAATTTCCGGATGTCTAATT 57.727 33.333 12.37 8.67 0.00 1.40
339 404 7.169308 GGATGTCTAATTGGTTAGTGTATCGTG 59.831 40.741 0.00 0.00 38.72 4.35
366 431 2.986479 GTCAATTTTGCTGGCGTTTAGG 59.014 45.455 0.00 0.00 0.00 2.69
373 777 2.108168 TGCTGGCGTTTAGGAGAGTAT 58.892 47.619 0.00 0.00 0.00 2.12
376 780 4.049869 GCTGGCGTTTAGGAGAGTATTAC 58.950 47.826 0.00 0.00 0.00 1.89
512 921 2.329267 CTTTGCCTTCCTTTTTCCCCT 58.671 47.619 0.00 0.00 0.00 4.79
513 922 1.715785 TTGCCTTCCTTTTTCCCCTG 58.284 50.000 0.00 0.00 0.00 4.45
516 925 2.225017 TGCCTTCCTTTTTCCCCTGTAG 60.225 50.000 0.00 0.00 0.00 2.74
517 926 2.225041 GCCTTCCTTTTTCCCCTGTAGT 60.225 50.000 0.00 0.00 0.00 2.73
519 928 3.826729 CCTTCCTTTTTCCCCTGTAGTTG 59.173 47.826 0.00 0.00 0.00 3.16
520 929 4.447180 CCTTCCTTTTTCCCCTGTAGTTGA 60.447 45.833 0.00 0.00 0.00 3.18
521 930 5.325239 CTTCCTTTTTCCCCTGTAGTTGAT 58.675 41.667 0.00 0.00 0.00 2.57
523 932 5.321927 TCCTTTTTCCCCTGTAGTTGATTC 58.678 41.667 0.00 0.00 0.00 2.52
524 933 5.074515 TCCTTTTTCCCCTGTAGTTGATTCT 59.925 40.000 0.00 0.00 0.00 2.40
526 935 6.267699 CCTTTTTCCCCTGTAGTTGATTCTTT 59.732 38.462 0.00 0.00 0.00 2.52
528 937 7.669089 TTTTCCCCTGTAGTTGATTCTTTTT 57.331 32.000 0.00 0.00 0.00 1.94
546 955 4.327982 TTTTTCATCCGTGCCAAATTGA 57.672 36.364 0.00 0.00 0.00 2.57
547 956 4.327982 TTTTCATCCGTGCCAAATTGAA 57.672 36.364 0.00 0.00 0.00 2.69
548 957 4.533919 TTTCATCCGTGCCAAATTGAAT 57.466 36.364 0.00 0.00 0.00 2.57
550 959 4.898829 TCATCCGTGCCAAATTGAATAG 57.101 40.909 0.00 0.00 0.00 1.73
555 964 2.543641 GTGCCAAATTGAATAGCCTGC 58.456 47.619 0.00 0.00 0.00 4.85
587 996 5.758784 GGTTCGAAATCCCTAGAATTACCAG 59.241 44.000 0.00 0.00 0.00 4.00
588 997 4.957296 TCGAAATCCCTAGAATTACCAGC 58.043 43.478 0.00 0.00 0.00 4.85
589 998 3.741344 CGAAATCCCTAGAATTACCAGCG 59.259 47.826 0.00 0.00 0.00 5.18
612 1021 4.325030 GGTAGGGTGATCTGAATTTGGGAA 60.325 45.833 0.00 0.00 0.00 3.97
622 1031 5.841810 TCTGAATTTGGGAACACAATTGAC 58.158 37.500 13.59 0.62 42.67 3.18
777 1194 0.605319 AAAATCCGAACGCAGGAGCA 60.605 50.000 0.81 0.00 41.66 4.26
787 1204 2.513204 CAGGAGCATCGCCCACAG 60.513 66.667 0.00 0.00 34.37 3.66
793 1210 2.047274 CATCGCCCACAGGAACGT 60.047 61.111 0.00 0.00 33.47 3.99
794 1211 1.671054 CATCGCCCACAGGAACGTT 60.671 57.895 0.00 0.00 33.47 3.99
841 1264 1.864082 GTTGCCCACAAAATCCAAACG 59.136 47.619 0.00 0.00 37.58 3.60
877 1300 3.001086 ACATAAACCCCCTTCCTTCCTT 58.999 45.455 0.00 0.00 0.00 3.36
880 1303 0.103337 AACCCCCTTCCTTCCTTCCT 60.103 55.000 0.00 0.00 0.00 3.36
1481 2838 1.151899 TGCACCACCTACCCCTTCT 60.152 57.895 0.00 0.00 0.00 2.85
1483 2840 1.911702 GCACCACCTACCCCTTCTCC 61.912 65.000 0.00 0.00 0.00 3.71
1510 2868 2.047655 TAGCGTGAGGGTTTGCCG 60.048 61.111 0.00 0.00 34.97 5.69
1585 2944 3.648982 TTGTGCGCCTGCTTCACG 61.649 61.111 4.18 0.00 43.34 4.35
1737 3106 1.141053 AGACCGCTCTCAAGGTTTGTT 59.859 47.619 0.00 0.00 41.51 2.83
1753 3125 9.039870 CAAGGTTTGTTTGTGCTTCATAATAAA 57.960 29.630 0.00 0.00 0.00 1.40
1863 3243 4.202040 TGTGCATCAACTTTCTTGTTCTGG 60.202 41.667 0.00 0.00 0.00 3.86
1871 3251 6.538742 TCAACTTTCTTGTTCTGGTTCTAGTG 59.461 38.462 0.00 0.00 0.00 2.74
1873 3253 6.049790 ACTTTCTTGTTCTGGTTCTAGTGTC 58.950 40.000 0.00 0.00 0.00 3.67
1877 3257 2.557056 TGTTCTGGTTCTAGTGTCGAGG 59.443 50.000 0.00 0.00 0.00 4.63
1885 3265 4.868734 GGTTCTAGTGTCGAGGTTAATTGG 59.131 45.833 0.00 0.00 0.00 3.16
1887 3267 6.350445 GGTTCTAGTGTCGAGGTTAATTGGTA 60.350 42.308 0.00 0.00 0.00 3.25
1902 3282 7.556635 GGTTAATTGGTATGCTTCTAGAGGTTT 59.443 37.037 3.55 0.00 0.00 3.27
1903 3283 8.398665 GTTAATTGGTATGCTTCTAGAGGTTTG 58.601 37.037 3.55 0.00 0.00 2.93
1921 3301 6.924111 AGGTTTGTTTGGATGTCATATTGTC 58.076 36.000 0.00 0.00 0.00 3.18
1939 3319 5.681337 TTGTCGATCATGTTAGTTTTGCA 57.319 34.783 0.00 0.00 0.00 4.08
1973 3355 6.428799 GCAGCAGAAATGTGAATATCTTCTC 58.571 40.000 0.00 0.00 32.29 2.87
1974 3356 6.647569 CAGCAGAAATGTGAATATCTTCTCG 58.352 40.000 0.00 0.00 32.29 4.04
1986 3368 6.806739 TGAATATCTTCTCGCCATATGTAACG 59.193 38.462 1.24 2.99 32.29 3.18
2041 3423 2.825861 AAATGCAAACCCTTCTGCTG 57.174 45.000 0.00 0.00 39.38 4.41
2044 3426 0.756442 TGCAAACCCTTCTGCTGCTT 60.756 50.000 0.00 0.00 39.38 3.91
2089 3471 5.104485 GGTTTGGGTCAGGATGTAAGTAGAT 60.104 44.000 0.00 0.00 37.40 1.98
2097 3479 7.095607 GGTCAGGATGTAAGTAGATAAATTGCG 60.096 40.741 0.00 0.00 37.40 4.85
2108 3490 1.643868 TAAATTGCGAGCTGGCCACG 61.644 55.000 18.69 5.39 0.00 4.94
2150 3532 2.159393 CGTCTGCCCATGTAACATTTGG 60.159 50.000 0.00 0.00 0.00 3.28
2152 3534 1.549620 CTGCCCATGTAACATTTGGCA 59.450 47.619 13.36 13.36 45.96 4.92
2153 3535 1.973515 TGCCCATGTAACATTTGGCAA 59.026 42.857 12.04 0.00 45.23 4.52
2154 3536 2.289320 TGCCCATGTAACATTTGGCAAC 60.289 45.455 12.04 0.00 45.23 4.17
2155 3537 2.605030 CCCATGTAACATTTGGCAACG 58.395 47.619 0.00 0.00 42.51 4.10
2156 3538 1.991965 CCATGTAACATTTGGCAACGC 59.008 47.619 0.00 0.00 42.51 4.84
2181 3563 1.070038 CCGCCAAAAATGCACATCAC 58.930 50.000 0.00 0.00 0.00 3.06
2183 3565 2.406130 CGCCAAAAATGCACATCACTT 58.594 42.857 0.00 0.00 0.00 3.16
2186 3568 4.266029 CGCCAAAAATGCACATCACTTATC 59.734 41.667 0.00 0.00 0.00 1.75
2231 3613 2.965147 AGGGTTTGGTTGTCCTTTCATG 59.035 45.455 0.00 0.00 34.23 3.07
2235 3617 4.382577 GGTTTGGTTGTCCTTTCATGTGTT 60.383 41.667 0.00 0.00 34.23 3.32
2244 3626 4.280677 GTCCTTTCATGTGTTGGGAAATGA 59.719 41.667 0.00 0.00 30.88 2.57
2260 3642 5.066505 GGGAAATGAATGTGTACAGCTAAGG 59.933 44.000 0.00 0.00 0.00 2.69
2262 3644 2.985896 TGAATGTGTACAGCTAAGGGC 58.014 47.619 0.00 0.00 42.19 5.19
2275 3657 2.287608 GCTAAGGGCAATTGATAACGCC 60.288 50.000 10.34 1.08 44.10 5.68
2278 3660 1.476488 AGGGCAATTGATAACGCCAAC 59.524 47.619 10.34 0.00 46.75 3.77
2303 3685 6.557110 GGATGTCTAAGCCTATAAGACGATC 58.443 44.000 0.00 0.00 42.05 3.69
2349 3731 0.469917 ATGACCATGCCTCCTTACGG 59.530 55.000 0.00 0.00 0.00 4.02
2351 3733 0.252197 GACCATGCCTCCTTACGGTT 59.748 55.000 0.00 0.00 0.00 4.44
2352 3734 1.483415 GACCATGCCTCCTTACGGTTA 59.517 52.381 0.00 0.00 0.00 2.85
2353 3735 1.208776 ACCATGCCTCCTTACGGTTAC 59.791 52.381 0.00 0.00 0.00 2.50
2354 3736 1.485066 CCATGCCTCCTTACGGTTACT 59.515 52.381 0.00 0.00 0.00 2.24
2355 3737 2.093128 CCATGCCTCCTTACGGTTACTT 60.093 50.000 0.00 0.00 0.00 2.24
2356 3738 2.754946 TGCCTCCTTACGGTTACTTG 57.245 50.000 0.00 0.00 0.00 3.16
2357 3739 2.250031 TGCCTCCTTACGGTTACTTGA 58.750 47.619 0.00 0.00 0.00 3.02
2358 3740 2.232941 TGCCTCCTTACGGTTACTTGAG 59.767 50.000 0.00 0.00 0.00 3.02
2359 3741 2.233186 GCCTCCTTACGGTTACTTGAGT 59.767 50.000 0.00 0.00 0.00 3.41
2360 3742 3.445096 GCCTCCTTACGGTTACTTGAGTA 59.555 47.826 0.00 0.00 0.00 2.59
2361 3743 4.439837 GCCTCCTTACGGTTACTTGAGTAG 60.440 50.000 0.00 0.00 0.00 2.57
2362 3744 4.097589 CCTCCTTACGGTTACTTGAGTAGG 59.902 50.000 0.00 0.00 0.00 3.18
2363 3745 4.666512 TCCTTACGGTTACTTGAGTAGGT 58.333 43.478 0.00 0.00 0.00 3.08
2364 3746 5.815581 TCCTTACGGTTACTTGAGTAGGTA 58.184 41.667 0.00 0.00 0.00 3.08
2365 3747 6.426587 TCCTTACGGTTACTTGAGTAGGTAT 58.573 40.000 0.00 0.00 0.00 2.73
2366 3748 6.891908 TCCTTACGGTTACTTGAGTAGGTATT 59.108 38.462 0.00 0.00 0.00 1.89
2367 3749 8.052748 TCCTTACGGTTACTTGAGTAGGTATTA 58.947 37.037 0.00 0.00 0.00 0.98
2368 3750 8.854117 CCTTACGGTTACTTGAGTAGGTATTAT 58.146 37.037 0.00 0.00 0.00 1.28
2369 3751 9.890352 CTTACGGTTACTTGAGTAGGTATTATC 57.110 37.037 0.00 0.00 0.00 1.75
2370 3752 7.886629 ACGGTTACTTGAGTAGGTATTATCA 57.113 36.000 0.00 0.00 0.00 2.15
2371 3753 8.297470 ACGGTTACTTGAGTAGGTATTATCAA 57.703 34.615 0.00 0.00 0.00 2.57
2372 3754 8.752187 ACGGTTACTTGAGTAGGTATTATCAAA 58.248 33.333 0.00 0.00 31.70 2.69
2373 3755 9.590451 CGGTTACTTGAGTAGGTATTATCAAAA 57.410 33.333 0.00 0.00 31.70 2.44
2377 3759 8.451908 ACTTGAGTAGGTATTATCAAAATGGC 57.548 34.615 0.00 0.00 31.70 4.40
2394 3776 1.889170 TGGCACACAAAGAACAACACA 59.111 42.857 0.00 0.00 0.00 3.72
2401 3783 6.728200 CACACAAAGAACAACACATAGATGT 58.272 36.000 0.00 0.00 42.84 3.06
2424 3806 1.901591 ATTGGTGCCTCACTGAACTG 58.098 50.000 0.00 0.00 34.40 3.16
2426 3808 0.546122 TGGTGCCTCACTGAACTGTT 59.454 50.000 0.00 0.00 34.40 3.16
2437 3819 3.629398 CACTGAACTGTTGAAGCCTCTTT 59.371 43.478 0.00 0.00 0.00 2.52
2438 3820 3.629398 ACTGAACTGTTGAAGCCTCTTTG 59.371 43.478 0.00 0.00 0.00 2.77
2452 3834 2.203337 TTTGGCCTGACTTGCGCT 60.203 55.556 9.73 0.00 0.00 5.92
2460 3842 2.021964 CTGACTTGCGCTCATGCTCG 62.022 60.000 9.73 2.66 36.97 5.03
2479 3861 3.423154 GCGCCAGGAAAGGTGACG 61.423 66.667 0.00 0.00 41.75 4.35
2491 3873 4.571176 GGAAAGGTGACGCTCTTAATTAGG 59.429 45.833 0.00 0.00 0.00 2.69
2492 3874 3.180891 AGGTGACGCTCTTAATTAGGC 57.819 47.619 0.00 0.00 0.00 3.93
2496 3878 4.686554 GGTGACGCTCTTAATTAGGCATAG 59.313 45.833 0.00 0.00 0.00 2.23
2500 3882 4.833380 ACGCTCTTAATTAGGCATAGGAGA 59.167 41.667 0.00 0.00 29.39 3.71
2510 3892 1.403687 GCATAGGAGAGTCGGGGCTT 61.404 60.000 0.00 0.00 0.00 4.35
2511 3893 1.996798 CATAGGAGAGTCGGGGCTTA 58.003 55.000 0.00 0.00 0.00 3.09
2533 3915 3.656559 GCTGTTGCTGATGAAACCAATT 58.343 40.909 0.00 0.00 36.03 2.32
2548 3930 1.540797 CCAATTGCTGGTGTTTGTGGG 60.541 52.381 0.00 0.00 40.78 4.61
2568 3950 0.671781 CTGAGTGCCGCTAAAGCTGT 60.672 55.000 0.00 0.00 39.32 4.40
2590 3972 2.292267 CGGTGAGCCTCATAGCAATTT 58.708 47.619 0.00 0.00 34.23 1.82
2591 3973 2.289002 CGGTGAGCCTCATAGCAATTTC 59.711 50.000 0.00 0.00 34.23 2.17
2611 3993 3.320823 TGCGTCATTGAGGAAGCAA 57.679 47.368 10.43 0.00 46.57 3.91
2630 4012 2.320587 GCTGTGTGCCAAGAGGTCG 61.321 63.158 0.00 0.00 37.19 4.79
2642 4025 2.047274 AGGTCGTGGGTTGATGCG 60.047 61.111 0.00 0.00 0.00 4.73
2643 4026 2.047655 GGTCGTGGGTTGATGCGA 60.048 61.111 0.00 0.00 0.00 5.10
2649 4032 0.741221 GTGGGTTGATGCGACCTCTC 60.741 60.000 3.99 0.00 37.99 3.20
2656 4039 3.076104 ATGCGACCTCTCTGCATTG 57.924 52.632 0.00 0.00 46.55 2.82
2698 4081 3.127250 TGCCTTGTATAATCCTTCCCCA 58.873 45.455 0.00 0.00 0.00 4.96
2699 4082 3.138283 TGCCTTGTATAATCCTTCCCCAG 59.862 47.826 0.00 0.00 0.00 4.45
2704 4087 2.918774 ATAATCCTTCCCCAGACCCT 57.081 50.000 0.00 0.00 0.00 4.34
2739 4935 2.175202 CTTCTAGCACTGGGTCTGTCT 58.825 52.381 0.00 0.00 0.00 3.41
2740 4936 2.310779 TCTAGCACTGGGTCTGTCTT 57.689 50.000 0.00 0.00 0.00 3.01
2756 4952 5.062809 GTCTGTCTTTTCTATTGAGGAAGCG 59.937 44.000 0.00 0.00 0.00 4.68
2780 4976 4.948257 CAGACTGCTGCAGCCATA 57.052 55.556 34.64 16.55 41.18 2.74
2788 4984 1.701292 TGCTGCAGCCATATACATCCT 59.299 47.619 34.64 0.00 41.18 3.24
2793 4989 5.303259 TGCAGCCATATACATCCTTAACA 57.697 39.130 0.00 0.00 0.00 2.41
2794 4990 5.689835 TGCAGCCATATACATCCTTAACAA 58.310 37.500 0.00 0.00 0.00 2.83
2796 4992 6.777091 TGCAGCCATATACATCCTTAACAATT 59.223 34.615 0.00 0.00 0.00 2.32
2802 4998 3.182887 ACATCCTTAACAATTGGGCCA 57.817 42.857 10.83 0.00 0.00 5.36
2804 5000 2.230130 TCCTTAACAATTGGGCCAGG 57.770 50.000 6.23 9.30 0.00 4.45
2806 5002 1.272985 CCTTAACAATTGGGCCAGGGA 60.273 52.381 6.23 0.00 0.00 4.20
2901 5097 5.717178 AGAAGAGCTGGAAACACTGTAGATA 59.283 40.000 0.00 0.00 35.60 1.98
2915 5111 8.908786 ACACTGTAGATATTTTGGTATGGATG 57.091 34.615 0.00 0.00 0.00 3.51
2935 5131 6.379988 TGGATGTGTGCTCTAGAATGTAACTA 59.620 38.462 0.00 0.00 0.00 2.24
2949 5145 7.556844 AGAATGTAACTATCATGTCGTTTCCT 58.443 34.615 0.00 0.00 0.00 3.36
2967 5163 6.312487 GTTTCCTCTTTAAGTTAATGCGGTC 58.688 40.000 14.05 6.17 0.00 4.79
3066 5262 4.556699 GCCAATGCTTATCGGGATTGTAAC 60.557 45.833 7.64 0.00 41.36 2.50
3196 5393 6.486248 TGCTATATTTTTCATCGCTGTGAAC 58.514 36.000 0.00 0.00 37.80 3.18
3201 5398 1.705256 TTCATCGCTGTGAACGGTAC 58.295 50.000 0.00 0.00 33.41 3.34
3210 5407 3.429207 GCTGTGAACGGTACTCTCTTTTC 59.571 47.826 0.00 0.00 0.00 2.29
3211 5408 3.986277 TGTGAACGGTACTCTCTTTTCC 58.014 45.455 0.00 0.00 0.00 3.13
3223 5420 2.149578 CTCTTTTCCCTCACACAGCAG 58.850 52.381 0.00 0.00 0.00 4.24
3232 5430 2.027377 CCTCACACAGCAGGATTTCTCT 60.027 50.000 0.00 0.00 30.32 3.10
3320 5529 5.885230 TGGTTTTCTATGATGCACTCAAG 57.115 39.130 0.00 0.00 37.44 3.02
3337 5547 5.006455 CACTCAAGACATCCTTTCGATCATG 59.994 44.000 0.00 0.00 31.42 3.07
3342 5552 5.248640 AGACATCCTTTCGATCATGTTGTT 58.751 37.500 0.00 0.00 29.43 2.83
3391 5601 7.246027 ACCCAATGGTTTTCCTATTTAAGAGT 58.754 34.615 0.00 0.00 44.75 3.24
3432 5642 0.776810 TGAGGCCCTTGGTCATTTCA 59.223 50.000 0.00 0.00 0.00 2.69
3446 5661 4.574013 GGTCATTTCATGAACTAGGCTCAG 59.426 45.833 7.89 0.00 43.61 3.35
3475 5691 8.695456 AGTAACTCATTTGTGGAAAAACTTGAT 58.305 29.630 0.00 0.00 0.00 2.57
3486 5707 7.014134 TGTGGAAAAACTTGATGATGTGTGTAT 59.986 33.333 0.00 0.00 0.00 2.29
3520 5741 5.897050 TGTTTTGTTTTGAAGCGGATAACT 58.103 33.333 0.00 0.00 0.00 2.24
3584 5805 8.849168 TGAATAGTAGGAATTTATGCACCATTG 58.151 33.333 0.00 0.00 0.00 2.82
3617 5839 5.005779 CCATAACTCTTAAACTAGCACTGCG 59.994 44.000 0.00 0.00 0.00 5.18
3693 5915 1.750399 CCGGCAAGCTGCTATGGTT 60.750 57.895 0.90 0.00 44.28 3.67
3714 5936 2.224257 TGTCAAGTGTGTGCTGCTCATA 60.224 45.455 7.73 2.20 0.00 2.15
3832 6054 1.484240 GGAGAGATGTACAGCCAAGCT 59.516 52.381 7.66 0.19 40.77 3.74
3865 6087 7.133133 TGTAACTCAACTTTCTCTTTAGGGT 57.867 36.000 0.00 0.00 0.00 4.34
4097 6320 2.787994 AGCTGACATTACTGCTGCTTT 58.212 42.857 0.00 0.00 41.92 3.51
4110 6333 1.608283 GCTGCTTTCTACCAGGTTCGT 60.608 52.381 0.00 0.00 0.00 3.85
4432 6659 6.584471 TGGTATATCCCATACACCTTTGTT 57.416 37.500 0.00 0.00 34.52 2.83
4498 6950 4.082571 CCAAATTGGAACTTCTCATCGCTT 60.083 41.667 6.04 0.00 40.96 4.68
4501 6953 0.729690 GGAACTTCTCATCGCTTGCC 59.270 55.000 0.00 0.00 0.00 4.52
4571 7023 1.077429 GGTGAAGCCAGGGGACATC 60.077 63.158 0.00 0.00 37.17 3.06
4706 7158 0.038251 CTGCCGTGTGCTGAGACTTA 60.038 55.000 0.00 0.00 41.11 2.24
4707 7159 0.608130 TGCCGTGTGCTGAGACTTAT 59.392 50.000 0.00 0.00 42.00 1.73
4803 7255 1.590932 CTTGCGGGATTCTCCATCAG 58.409 55.000 0.00 0.00 38.64 2.90
4868 7324 4.114794 GTGAATTTCCATTAGCATGTGGC 58.885 43.478 0.00 0.00 45.30 5.01
4988 7444 8.078596 GCTTGTAAAATGAGATGAACATATCCC 58.921 37.037 6.91 0.00 0.00 3.85
5017 7473 1.458445 CTGCTTGTGTCACATGAGTCG 59.542 52.381 20.02 2.99 0.00 4.18
5050 7506 7.391148 TTCTTGCCACCTAAAATATGTCTTC 57.609 36.000 0.00 0.00 0.00 2.87
5091 7548 6.617371 AGGAGTTGGGTCTGATTTGATATAGT 59.383 38.462 0.00 0.00 0.00 2.12
5093 7550 7.419057 GGAGTTGGGTCTGATTTGATATAGTGA 60.419 40.741 0.00 0.00 0.00 3.41
5208 7667 4.074970 AGCCTGTTTGTCATAACCAGAAG 58.925 43.478 0.00 0.00 0.00 2.85
5370 7839 4.543590 AGAATATCCTGTTATGCCGGAG 57.456 45.455 5.05 0.00 0.00 4.63
5425 7894 0.232303 CGAACGTTGCCTGAACTGAC 59.768 55.000 5.00 0.00 31.70 3.51
5426 7895 1.583054 GAACGTTGCCTGAACTGACT 58.417 50.000 5.00 0.00 31.70 3.41
5427 7896 1.261619 GAACGTTGCCTGAACTGACTG 59.738 52.381 5.00 0.00 31.70 3.51
5428 7897 0.464036 ACGTTGCCTGAACTGACTGA 59.536 50.000 0.00 0.00 31.70 3.41
5458 7927 9.013229 AGATGAGCTCTATAGTAGAAGTTGATG 57.987 37.037 16.19 0.00 33.75 3.07
5542 8013 9.148879 AGCTAGTACAATGGATAGACAATAAGT 57.851 33.333 0.00 0.00 0.00 2.24
5603 8074 4.461781 CCATGCTGATTGTCTTCTTCCTTT 59.538 41.667 0.00 0.00 0.00 3.11
5616 8087 6.150140 GTCTTCTTCCTTTGATTGTATGCTGT 59.850 38.462 0.00 0.00 0.00 4.40
5617 8088 6.372659 TCTTCTTCCTTTGATTGTATGCTGTC 59.627 38.462 0.00 0.00 0.00 3.51
5618 8089 5.809001 TCTTCCTTTGATTGTATGCTGTCT 58.191 37.500 0.00 0.00 0.00 3.41
5619 8090 5.645067 TCTTCCTTTGATTGTATGCTGTCTG 59.355 40.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 8.747538 AAGTTCCACACAGTAAAATAAGTTCT 57.252 30.769 0.00 0.00 0.00 3.01
153 154 0.179129 GGCAATGATTCAACAGGCGG 60.179 55.000 0.00 0.00 0.00 6.13
154 155 0.523968 CGGCAATGATTCAACAGGCG 60.524 55.000 14.40 14.40 38.61 5.52
172 173 3.974401 ACATTGACAAACGAATTCAAGCG 59.026 39.130 6.22 0.00 32.91 4.68
234 255 9.672086 TTTCAAAGAACGTATAACATTTTCCTG 57.328 29.630 0.00 0.00 0.00 3.86
258 279 2.172293 TGGGCCAGAATTTTGCTTGTTT 59.828 40.909 0.00 0.00 0.00 2.83
260 281 1.345415 CTGGGCCAGAATTTTGCTTGT 59.655 47.619 29.96 0.00 32.44 3.16
261 282 1.345415 ACTGGGCCAGAATTTTGCTTG 59.655 47.619 38.99 10.09 35.18 4.01
295 360 6.325545 AGACATCCGGAAATTGTATACTGGTA 59.674 38.462 9.01 0.00 0.00 3.25
296 361 5.130477 AGACATCCGGAAATTGTATACTGGT 59.870 40.000 9.01 0.00 0.00 4.00
297 362 5.611374 AGACATCCGGAAATTGTATACTGG 58.389 41.667 9.01 0.00 0.00 4.00
321 386 4.391830 CAGCACACGATACACTAACCAATT 59.608 41.667 0.00 0.00 0.00 2.32
322 387 3.932710 CAGCACACGATACACTAACCAAT 59.067 43.478 0.00 0.00 0.00 3.16
323 388 3.322369 CAGCACACGATACACTAACCAA 58.678 45.455 0.00 0.00 0.00 3.67
324 389 2.353307 CCAGCACACGATACACTAACCA 60.353 50.000 0.00 0.00 0.00 3.67
339 404 1.787012 CCAGCAAAATTGACCAGCAC 58.213 50.000 0.00 0.00 0.00 4.40
366 431 5.231568 CGTCCGGAAATTGTGTAATACTCTC 59.768 44.000 5.23 0.00 0.00 3.20
373 777 1.158434 GGCGTCCGGAAATTGTGTAA 58.842 50.000 5.23 0.00 0.00 2.41
376 780 1.006832 CTAGGCGTCCGGAAATTGTG 58.993 55.000 5.23 0.00 0.00 3.33
492 901 2.037641 CAGGGGAAAAAGGAAGGCAAAG 59.962 50.000 0.00 0.00 0.00 2.77
526 935 4.327982 TTCAATTTGGCACGGATGAAAA 57.672 36.364 0.00 0.00 0.00 2.29
528 937 4.439974 GCTATTCAATTTGGCACGGATGAA 60.440 41.667 6.64 6.64 0.00 2.57
529 938 3.066621 GCTATTCAATTTGGCACGGATGA 59.933 43.478 0.00 0.00 0.00 2.92
530 939 3.374745 GCTATTCAATTTGGCACGGATG 58.625 45.455 0.00 0.00 0.00 3.51
531 940 2.362077 GGCTATTCAATTTGGCACGGAT 59.638 45.455 0.00 0.00 0.00 4.18
532 941 1.748493 GGCTATTCAATTTGGCACGGA 59.252 47.619 0.00 0.00 0.00 4.69
533 942 1.750778 AGGCTATTCAATTTGGCACGG 59.249 47.619 0.00 0.00 0.00 4.94
534 943 2.801063 CAGGCTATTCAATTTGGCACG 58.199 47.619 0.00 0.00 0.00 5.34
535 944 2.094078 TGCAGGCTATTCAATTTGGCAC 60.094 45.455 0.00 0.00 0.00 5.01
536 945 2.166870 CTGCAGGCTATTCAATTTGGCA 59.833 45.455 5.57 0.00 0.00 4.92
537 946 2.167075 ACTGCAGGCTATTCAATTTGGC 59.833 45.455 19.93 0.00 0.00 4.52
538 947 4.082081 TCAACTGCAGGCTATTCAATTTGG 60.082 41.667 19.93 0.00 0.00 3.28
540 949 5.394883 CCATCAACTGCAGGCTATTCAATTT 60.395 40.000 19.93 0.00 0.00 1.82
541 950 4.098960 CCATCAACTGCAGGCTATTCAATT 59.901 41.667 19.93 0.00 0.00 2.32
544 953 2.025981 ACCATCAACTGCAGGCTATTCA 60.026 45.455 19.93 0.00 0.00 2.57
545 954 2.648059 ACCATCAACTGCAGGCTATTC 58.352 47.619 19.93 0.00 0.00 1.75
546 955 2.814805 ACCATCAACTGCAGGCTATT 57.185 45.000 19.93 0.00 0.00 1.73
547 956 2.648059 GAACCATCAACTGCAGGCTAT 58.352 47.619 19.93 4.87 0.00 2.97
548 957 1.675714 CGAACCATCAACTGCAGGCTA 60.676 52.381 19.93 2.32 0.00 3.93
550 959 0.955428 TCGAACCATCAACTGCAGGC 60.955 55.000 19.93 0.00 0.00 4.85
555 964 3.347216 AGGGATTTCGAACCATCAACTG 58.653 45.455 11.04 0.00 0.00 3.16
587 996 2.614057 CAAATTCAGATCACCCTACCGC 59.386 50.000 0.00 0.00 0.00 5.68
588 997 3.206150 CCAAATTCAGATCACCCTACCG 58.794 50.000 0.00 0.00 0.00 4.02
589 998 3.202151 TCCCAAATTCAGATCACCCTACC 59.798 47.826 0.00 0.00 0.00 3.18
612 1021 4.158394 GGATAGCATGTTGGTCAATTGTGT 59.842 41.667 5.13 0.00 0.00 3.72
622 1031 0.846015 TCCCTGGGATAGCATGTTGG 59.154 55.000 12.53 0.00 0.00 3.77
748 1165 2.470140 CGTTCGGATTTTGTTCGTCTCG 60.470 50.000 0.00 0.00 0.00 4.04
777 1194 1.375523 GAACGTTCCTGTGGGCGAT 60.376 57.895 17.68 0.00 0.00 4.58
841 1264 0.100682 TATGTCCTCGTCGCTCTTGC 59.899 55.000 0.00 0.00 0.00 4.01
877 1300 0.849540 GGGGGAAAGGGGAAGAAGGA 60.850 60.000 0.00 0.00 0.00 3.36
1467 2824 1.132500 GATGGAGAAGGGGTAGGTGG 58.868 60.000 0.00 0.00 0.00 4.61
1481 2838 3.149981 CCTCACGCTACATAGAGATGGA 58.850 50.000 0.00 0.00 37.39 3.41
1483 2840 2.887783 ACCCTCACGCTACATAGAGATG 59.112 50.000 0.00 0.00 39.16 2.90
1591 2950 1.202604 TCTTCTGACCGGCGACTTTTT 60.203 47.619 9.30 0.00 0.00 1.94
1601 2960 0.103026 TCGCCATCATCTTCTGACCG 59.897 55.000 0.00 0.00 36.48 4.79
1753 3125 5.470098 AGAACAAGCACGTTGATAAGACAAT 59.530 36.000 0.00 0.00 38.60 2.71
1863 3243 5.476614 ACCAATTAACCTCGACACTAGAAC 58.523 41.667 0.00 0.00 0.00 3.01
1871 3251 5.116882 AGAAGCATACCAATTAACCTCGAC 58.883 41.667 0.00 0.00 0.00 4.20
1873 3253 6.513180 TCTAGAAGCATACCAATTAACCTCG 58.487 40.000 0.00 0.00 0.00 4.63
1877 3257 8.398665 CAAACCTCTAGAAGCATACCAATTAAC 58.601 37.037 0.00 0.00 0.00 2.01
1885 3265 5.938125 TCCAAACAAACCTCTAGAAGCATAC 59.062 40.000 0.00 0.00 0.00 2.39
1887 3267 4.985538 TCCAAACAAACCTCTAGAAGCAT 58.014 39.130 0.00 0.00 0.00 3.79
1902 3282 6.112058 TGATCGACAATATGACATCCAAACA 58.888 36.000 0.00 0.00 0.00 2.83
1903 3283 6.603237 TGATCGACAATATGACATCCAAAC 57.397 37.500 0.00 0.00 0.00 2.93
1921 3301 3.848019 GCTGTGCAAAACTAACATGATCG 59.152 43.478 0.00 0.00 0.00 3.69
1939 3319 0.752743 TTTCTGCTGCCAGTTGCTGT 60.753 50.000 0.00 0.00 42.00 4.40
1946 3326 4.579340 AGATATTCACATTTCTGCTGCCAG 59.421 41.667 0.00 0.00 40.54 4.85
1949 3329 6.374565 AGAAGATATTCACATTTCTGCTGC 57.625 37.500 2.42 0.00 27.79 5.25
1955 3335 5.991328 TGGCGAGAAGATATTCACATTTC 57.009 39.130 2.42 0.00 0.00 2.17
1973 3355 3.423515 GCATCATGACGTTACATATGGCG 60.424 47.826 7.80 10.80 0.00 5.69
1974 3356 3.498018 TGCATCATGACGTTACATATGGC 59.502 43.478 7.80 0.00 0.00 4.40
2044 3426 2.796483 AATGTAGCCGTGCCGCTGAA 62.796 55.000 0.61 0.00 40.08 3.02
2055 3437 1.182667 GACCCAAACCCAATGTAGCC 58.817 55.000 0.00 0.00 0.00 3.93
2089 3471 1.643868 CGTGGCCAGCTCGCAATTTA 61.644 55.000 5.11 0.00 0.00 1.40
2156 3538 1.732683 GCATTTTTGGCGGACACGG 60.733 57.895 0.00 0.00 41.36 4.94
2157 3539 1.007964 TGCATTTTTGGCGGACACG 60.008 52.632 0.00 0.00 44.63 4.49
2194 3576 8.206126 ACCAAACCCTTCATATTTCTTTTCAT 57.794 30.769 0.00 0.00 0.00 2.57
2205 3587 4.463050 AAGGACAACCAAACCCTTCATA 57.537 40.909 0.00 0.00 34.11 2.15
2231 3613 5.446143 TGTACACATTCATTTCCCAACAC 57.554 39.130 0.00 0.00 0.00 3.32
2235 3617 4.032960 AGCTGTACACATTCATTTCCCA 57.967 40.909 0.00 0.00 0.00 4.37
2244 3626 3.433306 TTGCCCTTAGCTGTACACATT 57.567 42.857 0.00 0.00 44.23 2.71
2262 3644 3.181501 ACATCCGTTGGCGTTATCAATTG 60.182 43.478 0.00 0.00 36.15 2.32
2275 3657 5.921408 GTCTTATAGGCTTAGACATCCGTTG 59.079 44.000 15.14 0.00 38.49 4.10
2278 3660 4.454847 TCGTCTTATAGGCTTAGACATCCG 59.545 45.833 18.18 8.90 38.52 4.18
2303 3685 6.647067 GTGGATTATTCTCGGAGTTGGAATAG 59.353 42.308 4.69 0.00 34.70 1.73
2351 3733 9.555727 GCCATTTTGATAATACCTACTCAAGTA 57.444 33.333 0.00 0.00 0.00 2.24
2352 3734 8.052748 TGCCATTTTGATAATACCTACTCAAGT 58.947 33.333 0.00 0.00 0.00 3.16
2353 3735 8.345565 GTGCCATTTTGATAATACCTACTCAAG 58.654 37.037 0.00 0.00 0.00 3.02
2354 3736 7.831690 TGTGCCATTTTGATAATACCTACTCAA 59.168 33.333 0.00 0.00 0.00 3.02
2355 3737 7.282224 GTGTGCCATTTTGATAATACCTACTCA 59.718 37.037 0.00 0.00 0.00 3.41
2356 3738 7.282224 TGTGTGCCATTTTGATAATACCTACTC 59.718 37.037 0.00 0.00 0.00 2.59
2357 3739 7.116075 TGTGTGCCATTTTGATAATACCTACT 58.884 34.615 0.00 0.00 0.00 2.57
2358 3740 7.328277 TGTGTGCCATTTTGATAATACCTAC 57.672 36.000 0.00 0.00 0.00 3.18
2359 3741 7.946381 TTGTGTGCCATTTTGATAATACCTA 57.054 32.000 0.00 0.00 0.00 3.08
2360 3742 6.849085 TTGTGTGCCATTTTGATAATACCT 57.151 33.333 0.00 0.00 0.00 3.08
2361 3743 7.319646 TCTTTGTGTGCCATTTTGATAATACC 58.680 34.615 0.00 0.00 0.00 2.73
2362 3744 8.647226 GTTCTTTGTGTGCCATTTTGATAATAC 58.353 33.333 0.00 0.00 0.00 1.89
2363 3745 8.363390 TGTTCTTTGTGTGCCATTTTGATAATA 58.637 29.630 0.00 0.00 0.00 0.98
2364 3746 7.215789 TGTTCTTTGTGTGCCATTTTGATAAT 58.784 30.769 0.00 0.00 0.00 1.28
2365 3747 6.577103 TGTTCTTTGTGTGCCATTTTGATAA 58.423 32.000 0.00 0.00 0.00 1.75
2366 3748 6.154203 TGTTCTTTGTGTGCCATTTTGATA 57.846 33.333 0.00 0.00 0.00 2.15
2367 3749 5.021033 TGTTCTTTGTGTGCCATTTTGAT 57.979 34.783 0.00 0.00 0.00 2.57
2368 3750 4.462508 TGTTCTTTGTGTGCCATTTTGA 57.537 36.364 0.00 0.00 0.00 2.69
2369 3751 4.391216 TGTTGTTCTTTGTGTGCCATTTTG 59.609 37.500 0.00 0.00 0.00 2.44
2370 3752 4.391523 GTGTTGTTCTTTGTGTGCCATTTT 59.608 37.500 0.00 0.00 0.00 1.82
2371 3753 3.932089 GTGTTGTTCTTTGTGTGCCATTT 59.068 39.130 0.00 0.00 0.00 2.32
2372 3754 3.056250 TGTGTTGTTCTTTGTGTGCCATT 60.056 39.130 0.00 0.00 0.00 3.16
2373 3755 2.495270 TGTGTTGTTCTTTGTGTGCCAT 59.505 40.909 0.00 0.00 0.00 4.40
2374 3756 1.889170 TGTGTTGTTCTTTGTGTGCCA 59.111 42.857 0.00 0.00 0.00 4.92
2375 3757 2.645730 TGTGTTGTTCTTTGTGTGCC 57.354 45.000 0.00 0.00 0.00 5.01
2376 3758 5.168526 TCTATGTGTTGTTCTTTGTGTGC 57.831 39.130 0.00 0.00 0.00 4.57
2377 3759 6.728200 ACATCTATGTGTTGTTCTTTGTGTG 58.272 36.000 0.00 0.00 40.03 3.82
2394 3776 5.104360 AGTGAGGCACCAATTACACATCTAT 60.104 40.000 0.00 0.00 34.49 1.98
2401 3783 3.146066 GTTCAGTGAGGCACCAATTACA 58.854 45.455 0.00 0.00 34.49 2.41
2402 3784 3.189287 CAGTTCAGTGAGGCACCAATTAC 59.811 47.826 0.00 0.00 34.49 1.89
2410 3792 2.564771 CTTCAACAGTTCAGTGAGGCA 58.435 47.619 0.00 0.00 0.00 4.75
2437 3819 3.258228 ATGAGCGCAAGTCAGGCCA 62.258 57.895 11.47 0.00 41.68 5.36
2438 3820 2.437359 ATGAGCGCAAGTCAGGCC 60.437 61.111 11.47 0.00 41.68 5.19
2460 3842 4.344865 TCACCTTTCCTGGCGCCC 62.345 66.667 26.77 6.44 0.00 6.13
2475 3857 4.587262 TCCTATGCCTAATTAAGAGCGTCA 59.413 41.667 1.04 0.00 0.00 4.35
2479 3861 6.353404 ACTCTCCTATGCCTAATTAAGAGC 57.647 41.667 6.50 1.90 33.87 4.09
2491 3873 1.403687 AAGCCCCGACTCTCCTATGC 61.404 60.000 0.00 0.00 0.00 3.14
2492 3874 1.889829 CTAAGCCCCGACTCTCCTATG 59.110 57.143 0.00 0.00 0.00 2.23
2496 3878 1.758906 AGCTAAGCCCCGACTCTCC 60.759 63.158 0.00 0.00 0.00 3.71
2500 3882 1.296715 CAACAGCTAAGCCCCGACT 59.703 57.895 0.00 0.00 0.00 4.18
2510 3892 3.138884 TGGTTTCATCAGCAACAGCTA 57.861 42.857 0.00 0.00 36.70 3.32
2511 3893 1.985473 TGGTTTCATCAGCAACAGCT 58.015 45.000 0.00 0.00 39.75 4.24
2533 3915 2.126596 CAGCCCACAAACACCAGCA 61.127 57.895 0.00 0.00 0.00 4.41
2548 3930 2.787915 GCTTTAGCGGCACTCAGC 59.212 61.111 1.45 0.00 44.65 4.26
2564 3946 4.687215 TGAGGCTCACCGCACAGC 62.687 66.667 14.43 0.00 41.32 4.40
2571 3953 3.282021 TGAAATTGCTATGAGGCTCACC 58.718 45.455 21.37 11.74 0.00 4.02
2590 3972 1.338960 TGCTTCCTCAATGACGCATGA 60.339 47.619 0.00 0.00 34.95 3.07
2591 3973 1.089112 TGCTTCCTCAATGACGCATG 58.911 50.000 0.00 0.00 34.95 4.06
2597 3979 2.156917 CACAGCTTGCTTCCTCAATGA 58.843 47.619 0.00 0.00 0.00 2.57
2602 3984 1.578423 GCACACAGCTTGCTTCCTC 59.422 57.895 1.51 0.00 41.15 3.71
2611 3993 1.072159 GACCTCTTGGCACACAGCT 59.928 57.895 0.00 0.00 44.79 4.24
2630 4012 0.741221 GAGAGGTCGCATCAACCCAC 60.741 60.000 0.00 0.00 37.52 4.61
2642 4025 1.085091 CAGTGCAATGCAGAGAGGTC 58.915 55.000 8.73 0.00 40.08 3.85
2643 4026 0.399454 ACAGTGCAATGCAGAGAGGT 59.601 50.000 15.18 0.00 40.08 3.85
2656 4039 1.856265 GCCTTACACCTGCACAGTGC 61.856 60.000 19.37 19.37 45.29 4.40
2698 4081 2.683933 CCACGCCAGGTAGGGTCT 60.684 66.667 0.00 0.00 38.09 3.85
2699 4082 3.782443 CCCACGCCAGGTAGGGTC 61.782 72.222 5.13 0.00 38.09 4.46
2704 4087 2.606519 AAGCTCCCACGCCAGGTA 60.607 61.111 0.00 0.00 0.00 3.08
2711 4094 0.459237 CAGTGCTAGAAGCTCCCACG 60.459 60.000 0.00 0.00 42.97 4.94
2739 4935 2.026262 AGCCCGCTTCCTCAATAGAAAA 60.026 45.455 0.00 0.00 0.00 2.29
2740 4936 1.559682 AGCCCGCTTCCTCAATAGAAA 59.440 47.619 0.00 0.00 0.00 2.52
2774 4970 6.721208 CCCAATTGTTAAGGATGTATATGGCT 59.279 38.462 4.43 0.00 0.00 4.75
2776 4972 6.071391 GGCCCAATTGTTAAGGATGTATATGG 60.071 42.308 4.43 0.00 0.00 2.74
2779 4975 6.019656 TGGCCCAATTGTTAAGGATGTATA 57.980 37.500 0.00 0.00 0.00 1.47
2780 4976 4.877773 TGGCCCAATTGTTAAGGATGTAT 58.122 39.130 0.00 0.00 0.00 2.29
2788 4984 2.938428 ATCCCTGGCCCAATTGTTAA 57.062 45.000 0.00 0.00 0.00 2.01
2793 4989 1.217942 GGAGTTATCCCTGGCCCAATT 59.782 52.381 0.00 0.00 40.03 2.32
2794 4990 0.853530 GGAGTTATCCCTGGCCCAAT 59.146 55.000 0.00 0.00 40.03 3.16
2796 4992 0.328450 ATGGAGTTATCCCTGGCCCA 60.328 55.000 0.00 0.00 46.04 5.36
2802 4998 6.078456 TGACAATCAAATGGAGTTATCCCT 57.922 37.500 0.00 0.00 46.04 4.20
2832 5028 8.206867 TGAGGACAATCAAATGGAGTTATCTAG 58.793 37.037 0.00 0.00 0.00 2.43
2901 5097 4.603131 AGAGCACACATCCATACCAAAAT 58.397 39.130 0.00 0.00 0.00 1.82
2915 5111 7.923344 ACATGATAGTTACATTCTAGAGCACAC 59.077 37.037 0.00 0.00 0.00 3.82
2935 5131 8.842358 TTAACTTAAAGAGGAAACGACATGAT 57.158 30.769 0.00 0.00 0.00 2.45
2949 5145 6.428465 TGATGTTGACCGCATTAACTTAAAGA 59.572 34.615 0.00 0.00 0.00 2.52
2967 5163 8.857216 GCTGAAGATCTTGTTTAATTGATGTTG 58.143 33.333 14.00 0.00 0.00 3.33
3066 5262 5.146460 CAAACACGTGAATGGTGAATACTG 58.854 41.667 25.01 0.00 38.73 2.74
3196 5393 2.561419 TGTGAGGGAAAAGAGAGTACCG 59.439 50.000 0.00 0.00 0.00 4.02
3201 5398 2.224378 TGCTGTGTGAGGGAAAAGAGAG 60.224 50.000 0.00 0.00 0.00 3.20
3210 5407 1.004044 AGAAATCCTGCTGTGTGAGGG 59.996 52.381 0.00 0.00 0.00 4.30
3211 5408 2.027377 AGAGAAATCCTGCTGTGTGAGG 60.027 50.000 0.00 0.00 0.00 3.86
3223 5420 1.186200 GGCCCCAAACAGAGAAATCC 58.814 55.000 0.00 0.00 0.00 3.01
3232 5430 1.719063 AAGCAGAGAGGCCCCAAACA 61.719 55.000 0.00 0.00 0.00 2.83
3320 5529 5.551760 AACAACATGATCGAAAGGATGTC 57.448 39.130 0.00 0.00 34.82 3.06
3337 5547 3.057946 GTCATGCCCTCTCTTGAAACAAC 60.058 47.826 0.00 0.00 0.00 3.32
3342 5552 3.349927 CAATGTCATGCCCTCTCTTGAA 58.650 45.455 0.00 0.00 0.00 2.69
3411 5621 2.027385 GAAATGACCAAGGGCCTCATC 58.973 52.381 6.46 5.54 0.00 2.92
3432 5642 5.020132 AGTTACTGACTGAGCCTAGTTCAT 58.980 41.667 0.00 0.00 37.17 2.57
3437 5647 5.590530 AATGAGTTACTGACTGAGCCTAG 57.409 43.478 0.00 0.00 39.19 3.02
3438 5648 5.246203 ACAAATGAGTTACTGACTGAGCCTA 59.754 40.000 0.00 0.00 39.19 3.93
3439 5649 4.040952 ACAAATGAGTTACTGACTGAGCCT 59.959 41.667 0.00 0.00 39.19 4.58
3440 5650 4.153117 CACAAATGAGTTACTGACTGAGCC 59.847 45.833 0.00 0.00 39.19 4.70
3441 5651 4.153117 CCACAAATGAGTTACTGACTGAGC 59.847 45.833 0.00 0.00 39.19 4.26
3446 5661 7.480810 AGTTTTTCCACAAATGAGTTACTGAC 58.519 34.615 0.00 0.00 0.00 3.51
3475 5691 4.990426 CAGAACACACAGATACACACATCA 59.010 41.667 0.00 0.00 0.00 3.07
3486 5707 6.078202 TCAAAACAAAACAGAACACACAGA 57.922 33.333 0.00 0.00 0.00 3.41
3520 5741 0.102120 CAAGTGAAACGCAGGGCAAA 59.898 50.000 0.00 0.00 45.86 3.68
3584 5805 9.685828 CTAGTTTAAGAGTTATGGACAGATAGC 57.314 37.037 0.00 0.00 0.00 2.97
3593 5814 5.005779 CGCAGTGCTAGTTTAAGAGTTATGG 59.994 44.000 14.33 0.00 0.00 2.74
3617 5839 8.462016 TCAGCCTGATTAGAAATTTTAAAGAGC 58.538 33.333 0.00 0.00 0.00 4.09
3621 5843 8.028938 GCAGTCAGCCTGATTAGAAATTTTAAA 58.971 33.333 0.00 0.00 44.49 1.52
3693 5915 0.107752 TGAGCAGCACACACTTGACA 60.108 50.000 0.00 0.00 0.00 3.58
3714 5936 5.529800 ACGACCTTTGCTGTTTTTGTAGTAT 59.470 36.000 0.00 0.00 0.00 2.12
3795 6017 8.478877 ACATCTCTCCATCGAAACTAGTAAAAT 58.521 33.333 0.00 0.00 0.00 1.82
3802 6024 5.221067 GCTGTACATCTCTCCATCGAAACTA 60.221 44.000 0.00 0.00 0.00 2.24
3808 6030 1.683385 TGGCTGTACATCTCTCCATCG 59.317 52.381 0.00 0.00 0.00 3.84
3812 6034 1.484240 AGCTTGGCTGTACATCTCTCC 59.516 52.381 0.00 0.00 37.57 3.71
3865 6087 5.850557 ATTCCACAACTGTCAACATTTGA 57.149 34.783 17.02 0.00 38.35 2.69
3895 6117 0.386476 ACAACGCACGGTACAGAAGA 59.614 50.000 0.00 0.00 0.00 2.87
4097 6320 4.124238 CAAAAGTGAACGAACCTGGTAGA 58.876 43.478 0.00 0.00 0.00 2.59
4432 6659 2.294233 GCAAAGCATCAAGAACCAGACA 59.706 45.455 0.00 0.00 0.00 3.41
4501 6953 1.019673 CTCCAACCTGCCATCATTCG 58.980 55.000 0.00 0.00 0.00 3.34
4571 7023 2.885644 CCGTCGCTGAATGACCGG 60.886 66.667 0.00 0.00 32.68 5.28
4706 7158 2.041755 GGAAAAGGACCTGGACTGGAAT 59.958 50.000 0.00 0.00 0.00 3.01
4707 7159 1.423921 GGAAAAGGACCTGGACTGGAA 59.576 52.381 0.00 0.00 0.00 3.53
4965 7421 9.699410 AAAGGGATATGTTCATCTCATTTTACA 57.301 29.630 1.78 0.00 0.00 2.41
4988 7444 5.437289 TGTGACACAAGCAGGAAATAAAG 57.563 39.130 5.62 0.00 0.00 1.85
4992 7448 3.489355 TCATGTGACACAAGCAGGAAAT 58.511 40.909 13.23 0.00 0.00 2.17
5017 7473 2.029623 AGGTGGCAAGAATGATGATGC 58.970 47.619 0.00 0.00 38.06 3.91
5050 7506 4.043037 ACTCCTTCGCCGAAATTACTAG 57.957 45.455 0.00 0.00 0.00 2.57
5091 7548 2.819608 GGAGCAAGCAAAACATACCTCA 59.180 45.455 0.00 0.00 0.00 3.86
5093 7550 2.821969 CTGGAGCAAGCAAAACATACCT 59.178 45.455 0.00 0.00 0.00 3.08
5208 7667 5.738619 ACCCAAAATCAATTCTACCAACC 57.261 39.130 0.00 0.00 0.00 3.77
5218 7677 2.818921 TGCCTGCTACCCAAAATCAAT 58.181 42.857 0.00 0.00 0.00 2.57
5370 7839 2.606587 TTCTCCCCTTGCCCTCTGC 61.607 63.158 0.00 0.00 41.77 4.26


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

AutoCloner maintained by Alex Coulton.