Multiple sequence alignment - TraesCS7A01G129300

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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 TraesCS7A01G129300 chr7A 100.000 4444 0 0 1 4444 83284296 83288739 0.000000e+00 8207
1 TraesCS7A01G129300 chr7D 89.819 3919 232 69 477 4291 80505411 80509266 0.000000e+00 4872
2 TraesCS7A01G129300 chr7D 85.198 885 75 28 3432 4289 80709141 80709996 0.000000e+00 857
3 TraesCS7A01G129300 chr7D 92.683 328 19 4 3468 3792 80520254 80520579 6.730000e-128 468
4 TraesCS7A01G129300 chr7D 93.141 277 12 5 1 272 80503212 80503486 2.490000e-107 399
5 TraesCS7A01G129300 chr7B 89.313 3406 217 71 486 3803 27819594 27822940 0.000000e+00 4137
6 TraesCS7A01G129300 chr7B 87.413 429 32 8 3912 4331 28055722 28056137 1.450000e-129 473
7 TraesCS7A01G129300 chr6A 95.763 118 5 0 292 409 66266725 66266608 1.630000e-44 191
8 TraesCS7A01G129300 chr6A 93.220 118 8 0 292 409 66269542 66269659 1.640000e-39 174
9 TraesCS7A01G129300 chr3B 94.167 120 7 0 292 411 42176163 42176282 2.730000e-42 183
10 TraesCS7A01G129300 chr5B 94.068 118 7 0 292 409 663517377 663517260 3.530000e-41 180
11 TraesCS7A01G129300 chr3D 92.742 124 9 0 292 415 32390369 32390492 3.530000e-41 180
12 TraesCS7A01G129300 chr3D 91.870 123 9 1 292 414 231171631 231171510 2.130000e-38 171
13 TraesCS7A01G129300 chr4B 93.220 118 8 0 292 409 310957968 310957851 1.640000e-39 174
14 TraesCS7A01G129300 chr5D 91.803 122 9 1 292 412 387823807 387823928 7.640000e-38 169
15 TraesCS7A01G129300 chr5A 91.129 124 10 1 292 414 55273930 55274053 2.750000e-37 167


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 TraesCS7A01G129300 chr7A 83284296 83288739 4443 False 8207.0 8207 100.000 1 4444 1 chr7A.!!$F1 4443
1 TraesCS7A01G129300 chr7D 80503212 80509266 6054 False 2635.5 4872 91.480 1 4291 2 chr7D.!!$F3 4290
2 TraesCS7A01G129300 chr7D 80709141 80709996 855 False 857.0 857 85.198 3432 4289 1 chr7D.!!$F2 857
3 TraesCS7A01G129300 chr7B 27819594 27822940 3346 False 4137.0 4137 89.313 486 3803 1 chr7B.!!$F1 3317

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
874 2677 0.035820 GTCCACCACGCCATTCCTTA 60.036 55.0 0.0 0.0 0.00 2.69 F
1213 3037 0.452585 GAGTTCGCTCGCTCTAACCT 59.547 55.0 0.0 0.0 34.17 3.50 F
1472 3306 0.661020 ACGTGCTGTGTTAGTTTGGC 59.339 50.0 0.0 0.0 0.00 4.52 F
2912 4777 0.165944 CGGATTTCCAAGCACACGTC 59.834 55.0 0.0 0.0 35.14 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1708 3557 0.037232 GAGGTCCAAGTCAGTTCCCG 60.037 60.0 0.0 0.0 0.00 5.14 R
2559 4424 0.877071 CATCAGCACAATATCCCCGC 59.123 55.0 0.0 0.0 0.00 6.13 R
3287 5152 0.109342 CACCTTTCAGCAGGGACACT 59.891 55.0 0.0 0.0 38.42 3.55 R
4182 6073 0.108186 CCTCTGCGTGGTGCTTATCA 60.108 55.0 0.0 0.0 46.63 2.15 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
42 43 9.859427 TTGGATTCATGAACTATTTGTGATTTC 57.141 29.630 11.07 0.00 0.00 2.17
44 45 7.922811 GGATTCATGAACTATTTGTGATTTCCC 59.077 37.037 11.07 0.00 0.00 3.97
207 213 2.668632 GAAGGGGGTGCACATCGA 59.331 61.111 20.43 0.00 0.00 3.59
272 278 4.541973 ATTGGGGAGAAGAAATTGTTGC 57.458 40.909 0.00 0.00 0.00 4.17
275 281 1.202348 GGGAGAAGAAATTGTTGCGGG 59.798 52.381 0.00 0.00 0.00 6.13
299 305 4.911514 GTTTTCTGCAAAACTGGGACTA 57.088 40.909 6.73 0.00 45.53 2.59
300 306 5.257082 GTTTTCTGCAAAACTGGGACTAA 57.743 39.130 6.73 0.00 45.53 2.24
301 307 5.656480 GTTTTCTGCAAAACTGGGACTAAA 58.344 37.500 6.73 0.00 45.53 1.85
305 311 5.324409 TCTGCAAAACTGGGACTAAATCAT 58.676 37.500 0.00 0.00 0.00 2.45
306 312 5.415701 TCTGCAAAACTGGGACTAAATCATC 59.584 40.000 0.00 0.00 0.00 2.92
308 314 5.048083 TGCAAAACTGGGACTAAATCATCAC 60.048 40.000 0.00 0.00 0.00 3.06
311 317 6.764308 AAACTGGGACTAAATCATCACATG 57.236 37.500 0.00 0.00 0.00 3.21
312 318 5.698741 ACTGGGACTAAATCATCACATGA 57.301 39.130 0.00 0.00 44.55 3.07
313 319 5.678583 ACTGGGACTAAATCATCACATGAG 58.321 41.667 0.00 0.00 43.53 2.90
314 320 5.039920 TGGGACTAAATCATCACATGAGG 57.960 43.478 0.00 0.00 43.53 3.86
325 331 0.599558 CACATGAGGTGCAAGTTGGG 59.400 55.000 4.75 0.00 41.36 4.12
326 332 0.540365 ACATGAGGTGCAAGTTGGGG 60.540 55.000 4.75 0.00 0.00 4.96
329 335 1.072266 TGAGGTGCAAGTTGGGGTAT 58.928 50.000 4.75 0.00 0.00 2.73
330 336 1.271871 TGAGGTGCAAGTTGGGGTATG 60.272 52.381 4.75 0.00 0.00 2.39
335 341 1.967066 TGCAAGTTGGGGTATGGTTTG 59.033 47.619 4.75 0.00 0.00 2.93
336 342 1.275010 GCAAGTTGGGGTATGGTTTGG 59.725 52.381 4.75 0.00 0.00 3.28
338 344 2.560981 CAAGTTGGGGTATGGTTTGGTC 59.439 50.000 0.00 0.00 0.00 4.02
339 345 1.783979 AGTTGGGGTATGGTTTGGTCA 59.216 47.619 0.00 0.00 0.00 4.02
341 645 2.560981 GTTGGGGTATGGTTTGGTCAAG 59.439 50.000 0.00 0.00 0.00 3.02
346 650 4.502431 GGGGTATGGTTTGGTCAAGTTTTG 60.502 45.833 0.00 0.00 0.00 2.44
347 651 4.055360 GGTATGGTTTGGTCAAGTTTTGC 58.945 43.478 0.00 0.00 0.00 3.68
348 652 3.902881 ATGGTTTGGTCAAGTTTTGCA 57.097 38.095 0.00 0.00 0.00 4.08
350 654 3.330267 TGGTTTGGTCAAGTTTTGCAAC 58.670 40.909 0.00 0.00 0.00 4.17
352 656 2.990514 GTTTGGTCAAGTTTTGCAACGT 59.009 40.909 0.00 0.00 38.03 3.99
353 657 3.305398 TTGGTCAAGTTTTGCAACGTT 57.695 38.095 0.00 0.00 38.03 3.99
357 661 3.675698 GGTCAAGTTTTGCAACGTTGAAA 59.324 39.130 31.62 25.01 38.03 2.69
360 664 5.569823 GTCAAGTTTTGCAACGTTGAAACTA 59.430 36.000 31.71 21.75 38.03 2.24
363 667 7.329717 TCAAGTTTTGCAACGTTGAAACTAAAT 59.670 29.630 31.71 21.26 38.03 1.40
367 671 6.984740 TTGCAACGTTGAAACTAAATCATC 57.015 33.333 31.62 9.39 0.00 2.92
369 673 5.912396 TGCAACGTTGAAACTAAATCATCAC 59.088 36.000 31.62 8.32 0.00 3.06
371 675 6.582295 GCAACGTTGAAACTAAATCATCACAT 59.418 34.615 31.62 0.00 0.00 3.21
372 676 7.114811 GCAACGTTGAAACTAAATCATCACATT 59.885 33.333 31.62 0.00 0.00 2.71
386 690 9.590451 AAATCATCACATTAAATGCAAGTTAGG 57.410 29.630 0.00 0.00 0.00 2.69
387 691 7.099266 TCATCACATTAAATGCAAGTTAGGG 57.901 36.000 0.00 0.00 0.00 3.53
388 692 6.663093 TCATCACATTAAATGCAAGTTAGGGT 59.337 34.615 0.00 0.00 0.00 4.34
389 693 7.831690 TCATCACATTAAATGCAAGTTAGGGTA 59.168 33.333 0.00 0.00 0.00 3.69
390 694 7.385778 TCACATTAAATGCAAGTTAGGGTAC 57.614 36.000 0.00 0.00 0.00 3.34
407 711 3.248888 GGTACCTGGGATGCTATTACCT 58.751 50.000 4.06 0.00 0.00 3.08
409 713 3.060479 ACCTGGGATGCTATTACCTCA 57.940 47.619 0.00 0.00 0.00 3.86
410 714 3.602608 ACCTGGGATGCTATTACCTCAT 58.397 45.455 0.00 0.00 0.00 2.90
411 715 4.763355 ACCTGGGATGCTATTACCTCATA 58.237 43.478 0.00 0.00 0.00 2.15
412 716 5.162637 ACCTGGGATGCTATTACCTCATAA 58.837 41.667 0.00 0.00 0.00 1.90
413 717 5.610982 ACCTGGGATGCTATTACCTCATAAA 59.389 40.000 0.00 0.00 0.00 1.40
414 718 6.275618 ACCTGGGATGCTATTACCTCATAAAT 59.724 38.462 0.00 0.00 0.00 1.40
416 720 7.311549 CCTGGGATGCTATTACCTCATAAATCT 60.312 40.741 0.00 0.00 0.00 2.40
417 721 7.988937 TGGGATGCTATTACCTCATAAATCTT 58.011 34.615 0.00 0.00 0.00 2.40
418 722 8.103305 TGGGATGCTATTACCTCATAAATCTTC 58.897 37.037 0.00 0.00 0.00 2.87
420 724 8.103305 GGATGCTATTACCTCATAAATCTTCCA 58.897 37.037 0.00 0.00 0.00 3.53
437 2125 5.708948 TCTTCCAAAATAAACAAGCCATCG 58.291 37.500 0.00 0.00 0.00 3.84
438 2126 3.843999 TCCAAAATAAACAAGCCATCGC 58.156 40.909 0.00 0.00 0.00 4.58
439 2127 3.256879 TCCAAAATAAACAAGCCATCGCA 59.743 39.130 0.00 0.00 37.52 5.10
440 2128 3.613737 CCAAAATAAACAAGCCATCGCAG 59.386 43.478 0.00 0.00 37.52 5.18
441 2129 4.236935 CAAAATAAACAAGCCATCGCAGT 58.763 39.130 0.00 0.00 37.52 4.40
442 2130 4.519540 AAATAAACAAGCCATCGCAGTT 57.480 36.364 0.00 0.00 37.17 3.16
450 2138 2.174107 CATCGCAGTTGCACCGTG 59.826 61.111 4.84 0.00 42.21 4.94
461 2149 3.030652 CACCGTGCCAGTCCAAAC 58.969 61.111 0.00 0.00 0.00 2.93
469 2157 2.430694 GTGCCAGTCCAAACCTTCTTTT 59.569 45.455 0.00 0.00 0.00 2.27
470 2158 2.430332 TGCCAGTCCAAACCTTCTTTTG 59.570 45.455 0.00 0.00 36.40 2.44
474 2162 5.487433 CCAGTCCAAACCTTCTTTTGTTTT 58.513 37.500 0.00 0.00 35.09 2.43
477 2165 6.090763 CAGTCCAAACCTTCTTTTGTTTTGAC 59.909 38.462 9.86 9.86 42.70 3.18
479 2167 4.328712 CCAAACCTTCTTTTGTTTTGACGG 59.671 41.667 0.00 0.00 35.09 4.79
480 2168 3.793797 ACCTTCTTTTGTTTTGACGGG 57.206 42.857 0.00 0.00 0.00 5.28
585 2332 1.577328 CTGCCAGCCCAAACAGTACG 61.577 60.000 0.00 0.00 0.00 3.67
586 2333 1.599797 GCCAGCCCAAACAGTACGT 60.600 57.895 0.00 0.00 0.00 3.57
587 2334 0.320946 GCCAGCCCAAACAGTACGTA 60.321 55.000 0.00 0.00 0.00 3.57
588 2335 1.435577 CCAGCCCAAACAGTACGTAC 58.564 55.000 18.10 18.10 0.00 3.67
589 2336 1.001633 CCAGCCCAAACAGTACGTACT 59.998 52.381 22.45 22.45 36.90 2.73
590 2337 2.231964 CCAGCCCAAACAGTACGTACTA 59.768 50.000 26.95 0.00 34.13 1.82
591 2338 3.508762 CAGCCCAAACAGTACGTACTAG 58.491 50.000 26.95 21.60 34.13 2.57
691 2438 4.717629 CTCTCGACCGCACGGCAA 62.718 66.667 9.43 0.00 39.32 4.52
740 2502 3.256960 AAGAAAGCGGGCAGGGGA 61.257 61.111 0.00 0.00 0.00 4.81
741 2503 3.273788 AAGAAAGCGGGCAGGGGAG 62.274 63.158 0.00 0.00 0.00 4.30
774 2545 2.034879 CACCACACCAGATCACCGC 61.035 63.158 0.00 0.00 0.00 5.68
778 2549 0.603707 CACACCAGATCACCGCAAGT 60.604 55.000 0.00 0.00 0.00 3.16
811 2599 4.057428 GCGAGGCTGTCACGTCCT 62.057 66.667 0.00 0.00 0.00 3.85
835 2635 1.150135 TCTCCAACAAGTCCTCCTCCT 59.850 52.381 0.00 0.00 0.00 3.69
838 2638 0.615850 CAACAAGTCCTCCTCCTCCC 59.384 60.000 0.00 0.00 0.00 4.30
840 2640 1.394151 CAAGTCCTCCTCCTCCCCT 59.606 63.158 0.00 0.00 0.00 4.79
842 2642 2.123640 GTCCTCCTCCTCCCCTCG 60.124 72.222 0.00 0.00 0.00 4.63
843 2643 4.144727 TCCTCCTCCTCCCCTCGC 62.145 72.222 0.00 0.00 0.00 5.03
874 2677 0.035820 GTCCACCACGCCATTCCTTA 60.036 55.000 0.00 0.00 0.00 2.69
892 2711 1.592400 TACCCTCCAAGCGACGACTG 61.592 60.000 0.00 0.00 0.00 3.51
894 2713 2.259818 CTCCAAGCGACGACTGCT 59.740 61.111 0.00 0.00 46.68 4.24
895 2714 1.803519 CTCCAAGCGACGACTGCTC 60.804 63.158 0.00 0.00 43.14 4.26
898 2717 4.070552 AAGCGACGACTGCTCCCC 62.071 66.667 0.00 0.00 43.14 4.81
929 2750 2.560861 GCGCGCCAAATCTGTTCA 59.439 55.556 23.24 0.00 0.00 3.18
937 2758 1.072505 AAATCTGTTCACGCCGGGT 59.927 52.632 2.18 0.00 0.00 5.28
1090 2914 5.981088 TCTGTAAGTATACCGACACCAAA 57.019 39.130 0.00 0.00 33.76 3.28
1094 2918 3.521947 AGTATACCGACACCAAAGCTC 57.478 47.619 0.00 0.00 0.00 4.09
1121 2945 3.488090 CCCCGCTTTCGCTTCGAC 61.488 66.667 0.00 0.00 34.89 4.20
1193 3017 4.094684 CGTGAGCACCCTCGATTC 57.905 61.111 0.00 0.00 41.13 2.52
1213 3037 0.452585 GAGTTCGCTCGCTCTAACCT 59.547 55.000 0.00 0.00 34.17 3.50
1236 3060 4.829518 GGAATTTCGCCGTGCCGC 62.830 66.667 0.00 0.00 0.00 6.53
1309 3141 1.324736 CGAGTAATTCTGTTGAGGCGC 59.675 52.381 0.00 0.00 0.00 6.53
1324 3156 1.154150 GCGCTGCTCAATTTCGCTT 60.154 52.632 0.00 0.00 42.19 4.68
1325 3157 0.730494 GCGCTGCTCAATTTCGCTTT 60.730 50.000 0.00 0.00 42.19 3.51
1340 3172 3.131396 TCGCTTTGAAAGAGTCTTGGTC 58.869 45.455 9.48 1.73 0.00 4.02
1363 3195 1.886542 GCCTGGTTTGGTTTGTAGGAG 59.113 52.381 0.00 0.00 0.00 3.69
1411 3243 1.137086 ACTGGGCAAGTAGATGCTACG 59.863 52.381 0.00 0.00 45.68 3.51
1458 3291 1.281656 CGGAAGGTCCAAAACGTGC 59.718 57.895 0.00 0.00 35.91 5.34
1472 3306 0.661020 ACGTGCTGTGTTAGTTTGGC 59.339 50.000 0.00 0.00 0.00 4.52
1491 3325 1.078759 CGTTGGAGGACGCATCTGTC 61.079 60.000 0.00 0.00 36.12 3.51
1519 3353 1.902938 AAGCCCTCTTGTCTCTTTGC 58.097 50.000 0.00 0.00 0.00 3.68
1524 3358 1.396301 CCTCTTGTCTCTTTGCGATGC 59.604 52.381 0.00 0.00 0.00 3.91
1549 3383 2.028130 AGTTTCGCAATTGTTGTCCCA 58.972 42.857 7.40 0.00 0.00 4.37
1555 3389 1.890876 CAATTGTTGTCCCAGACCGA 58.109 50.000 0.00 0.00 0.00 4.69
1564 3401 1.672356 CCCAGACCGAAGCCAAGTG 60.672 63.158 0.00 0.00 0.00 3.16
1575 3412 3.871006 CGAAGCCAAGTGTATTATGCTCA 59.129 43.478 0.00 0.00 0.00 4.26
1578 3415 4.588899 AGCCAAGTGTATTATGCTCACAA 58.411 39.130 0.00 0.00 34.94 3.33
1590 3429 9.056005 GTATTATGCTCACAAATGGACATAGAA 57.944 33.333 0.00 0.00 30.57 2.10
1594 3433 4.572389 GCTCACAAATGGACATAGAACGAT 59.428 41.667 0.00 0.00 0.00 3.73
1606 3445 5.560724 ACATAGAACGATAATTGGGATGGG 58.439 41.667 0.00 0.00 0.00 4.00
1609 3448 4.655963 AGAACGATAATTGGGATGGGATG 58.344 43.478 0.00 0.00 0.00 3.51
1613 3452 5.313712 ACGATAATTGGGATGGGATGTTAC 58.686 41.667 0.00 0.00 0.00 2.50
1619 3458 3.045634 TGGGATGGGATGTTACTTCGAT 58.954 45.455 0.00 0.00 0.00 3.59
1620 3459 3.181455 TGGGATGGGATGTTACTTCGATG 60.181 47.826 0.00 0.00 0.00 3.84
1622 3471 4.039973 GGGATGGGATGTTACTTCGATGTA 59.960 45.833 7.05 7.05 0.00 2.29
1624 3473 4.054780 TGGGATGTTACTTCGATGTAGC 57.945 45.455 15.51 15.51 0.00 3.58
1631 3480 2.563471 ACTTCGATGTAGCGTTCCTC 57.437 50.000 1.47 0.00 0.00 3.71
1640 3489 4.537135 TGTAGCGTTCCTCTGATTTTCT 57.463 40.909 0.00 0.00 0.00 2.52
1641 3490 4.245660 TGTAGCGTTCCTCTGATTTTCTG 58.754 43.478 0.00 0.00 0.00 3.02
1649 3498 4.655963 TCCTCTGATTTTCTGTTCTTGGG 58.344 43.478 0.00 0.00 0.00 4.12
1650 3499 4.350816 TCCTCTGATTTTCTGTTCTTGGGA 59.649 41.667 0.00 0.00 0.00 4.37
1651 3500 4.699257 CCTCTGATTTTCTGTTCTTGGGAG 59.301 45.833 0.00 0.00 0.00 4.30
1653 3502 5.694995 TCTGATTTTCTGTTCTTGGGAGTT 58.305 37.500 0.00 0.00 0.00 3.01
1654 3503 6.837312 TCTGATTTTCTGTTCTTGGGAGTTA 58.163 36.000 0.00 0.00 0.00 2.24
1655 3504 6.936900 TCTGATTTTCTGTTCTTGGGAGTTAG 59.063 38.462 0.00 0.00 0.00 2.34
1659 3508 2.303022 TCTGTTCTTGGGAGTTAGGCAG 59.697 50.000 0.00 0.00 0.00 4.85
1673 3522 1.302907 AGGCAGGATTGGTTCAGGAT 58.697 50.000 0.00 0.00 0.00 3.24
1684 3533 2.280628 GGTTCAGGATTTAGGAGCACG 58.719 52.381 0.00 0.00 0.00 5.34
1695 3544 2.086054 AGGAGCACGAGTGAATTGTC 57.914 50.000 7.50 0.00 0.00 3.18
1698 3547 2.744202 GGAGCACGAGTGAATTGTCATT 59.256 45.455 7.50 0.00 35.80 2.57
1702 3551 3.304659 GCACGAGTGAATTGTCATTGGTT 60.305 43.478 7.50 0.00 31.45 3.67
1704 3553 4.024133 CACGAGTGAATTGTCATTGGTTGA 60.024 41.667 0.00 0.00 31.45 3.18
1708 3557 6.074888 CGAGTGAATTGTCATTGGTTGAAAAC 60.075 38.462 0.00 0.00 40.49 2.43
1740 3589 3.184382 TGGACCTCTGATTCTGTACCA 57.816 47.619 0.00 0.00 0.00 3.25
1826 3675 1.021390 CATCAGGTGGGTGTTCTCGC 61.021 60.000 0.00 0.00 0.00 5.03
1942 3791 1.136110 GGCTCTCAGGTTACTGCTCTC 59.864 57.143 0.00 0.00 44.54 3.20
1944 3793 2.099098 GCTCTCAGGTTACTGCTCTCTC 59.901 54.545 0.00 0.00 44.54 3.20
1949 3798 1.484240 AGGTTACTGCTCTCTCCATGC 59.516 52.381 0.00 0.00 0.00 4.06
1959 3808 3.666274 CTCTCTCCATGCTGATCCATTC 58.334 50.000 0.00 0.00 0.00 2.67
2052 3909 4.440387 GCTGTCTAGTTGGGCTAGTAGTTC 60.440 50.000 0.00 0.00 45.65 3.01
2069 3926 4.916983 AGTTCATTGCTTTACTTGCACA 57.083 36.364 0.00 0.00 40.40 4.57
2112 3969 4.830826 AGCTGCCTAACTAAACAACAAC 57.169 40.909 0.00 0.00 0.00 3.32
2122 3979 6.524101 AACTAAACAACAACCAACTGTCAT 57.476 33.333 0.00 0.00 0.00 3.06
2168 4025 3.426695 GGAACACTGATCTTTGATTGCGG 60.427 47.826 0.00 0.00 0.00 5.69
2197 4054 4.829968 TCGTTAGGTAGGATATCCTCTCG 58.170 47.826 27.86 20.65 44.77 4.04
2389 4254 2.616510 GCACCAGTTCTGCTCTTACCAT 60.617 50.000 0.00 0.00 0.00 3.55
2408 4273 3.370978 CCATGTTAACTCTGCTTACACCG 59.629 47.826 7.22 0.00 0.00 4.94
2509 4374 2.893489 GGGACAGAAATGGAGTTTGCTT 59.107 45.455 0.00 0.00 0.00 3.91
2517 4382 5.240403 AGAAATGGAGTTTGCTTCAGAAGTC 59.760 40.000 11.94 5.03 32.93 3.01
2559 4424 3.447742 GCACAAAAACCTCCTGAGTTTG 58.552 45.455 7.01 7.01 35.72 2.93
2562 4427 1.318576 AAAACCTCCTGAGTTTGCGG 58.681 50.000 0.00 0.00 0.00 5.69
2580 4445 1.883638 CGGGGATATTGTGCTGATGGG 60.884 57.143 0.00 0.00 0.00 4.00
2739 4604 4.260091 GCGTGAGTAAACGTCTTCTTTGTT 60.260 41.667 0.00 0.00 45.32 2.83
2769 4634 9.416794 AGTAGCATGACATAGATAATTCTTTCG 57.583 33.333 0.00 0.00 33.17 3.46
2797 4662 3.008049 ACTTCCGGTAAGCAGTTTGAGAT 59.992 43.478 0.00 0.00 38.93 2.75
2846 4711 1.349026 CTTCACCACCATGAGACACCT 59.651 52.381 0.00 0.00 0.00 4.00
2903 4768 5.765677 TGTGTTACTTGATTCGGATTTCCAA 59.234 36.000 0.00 0.00 35.14 3.53
2912 4777 0.165944 CGGATTTCCAAGCACACGTC 59.834 55.000 0.00 0.00 35.14 4.34
3144 5009 2.464459 CGAAACTGGATGCTCCCGC 61.464 63.158 0.50 0.00 35.03 6.13
3194 5059 2.416547 CGCGGACTCAAAACTCAATGAT 59.583 45.455 0.00 0.00 0.00 2.45
3233 5098 2.644798 ACTAAAGAGGGTGGTGCTGATT 59.355 45.455 0.00 0.00 0.00 2.57
3248 5113 0.320050 TGATTGGACTAGCGTGCACA 59.680 50.000 18.64 0.00 41.42 4.57
3281 5146 2.287069 CGATAAGAGACCGACGATGCTT 60.287 50.000 0.00 0.00 0.00 3.91
3287 5152 0.454600 GACCGACGATGCTTGAGGTA 59.545 55.000 0.00 0.00 31.35 3.08
3453 5321 1.229177 GGGGCTTGATGGGTTGGTT 60.229 57.895 0.00 0.00 0.00 3.67
3454 5322 1.543944 GGGGCTTGATGGGTTGGTTG 61.544 60.000 0.00 0.00 0.00 3.77
3455 5323 1.543944 GGGCTTGATGGGTTGGTTGG 61.544 60.000 0.00 0.00 0.00 3.77
3456 5324 0.831711 GGCTTGATGGGTTGGTTGGT 60.832 55.000 0.00 0.00 0.00 3.67
3458 5326 1.544246 GCTTGATGGGTTGGTTGGTAC 59.456 52.381 0.00 0.00 0.00 3.34
3459 5327 2.167662 CTTGATGGGTTGGTTGGTACC 58.832 52.381 4.43 4.43 45.26 3.34
3463 5331 4.834911 GGTTGGTTGGTACCCTGG 57.165 61.111 10.07 0.00 44.35 4.45
3464 5332 2.156920 GGTTGGTTGGTACCCTGGA 58.843 57.895 10.07 0.00 44.35 3.86
3465 5333 0.251033 GGTTGGTTGGTACCCTGGAC 60.251 60.000 10.07 2.93 44.35 4.02
3466 5334 0.769247 GTTGGTTGGTACCCTGGACT 59.231 55.000 10.07 0.00 44.35 3.85
3658 5526 1.898574 GTGTGCACTGGGTGGAAGG 60.899 63.158 19.41 0.00 35.32 3.46
3669 5537 0.391966 GGTGGAAGGCCCGTATACTC 59.608 60.000 0.00 0.00 37.93 2.59
3704 5572 2.229543 GCATGCTTCATCCTGTTGTCAA 59.770 45.455 11.37 0.00 0.00 3.18
3719 5587 4.155099 TGTTGTCAACTGTGTTGGTTACTG 59.845 41.667 16.45 0.00 0.00 2.74
3737 5605 7.916450 TGGTTACTGTAAACAAAATTTCCTTCG 59.084 33.333 15.50 0.00 31.29 3.79
3738 5606 7.096353 GGTTACTGTAAACAAAATTTCCTTCGC 60.096 37.037 10.62 0.00 0.00 4.70
3739 5607 5.897050 ACTGTAAACAAAATTTCCTTCGCA 58.103 33.333 0.00 0.00 0.00 5.10
3740 5608 6.512297 ACTGTAAACAAAATTTCCTTCGCAT 58.488 32.000 0.00 0.00 0.00 4.73
3760 5631 5.178067 CGCATATACAACTGAATGCAGATGA 59.822 40.000 17.43 2.26 44.90 2.92
3793 5664 2.909006 TGCTCTCTCCTTCCTGACAATT 59.091 45.455 0.00 0.00 0.00 2.32
3815 5686 1.246737 CCCTCTGCAGGCCAGTTTTC 61.247 60.000 15.13 0.00 42.38 2.29
3831 5702 4.033243 CAGTTTTCCTGTCTTTGCTTTTGC 59.967 41.667 0.00 0.00 40.18 3.68
3949 5829 1.903183 AGCTCCGCCTATCCTATTTCC 59.097 52.381 0.00 0.00 0.00 3.13
4000 5880 1.202510 GCCCTAGCTCATGAGACAGTG 60.203 57.143 27.04 13.43 35.50 3.66
4003 5883 2.757314 CCTAGCTCATGAGACAGTGACA 59.243 50.000 27.04 0.53 0.00 3.58
4030 5917 4.457603 TGATCACAGGGTCCATTTTAAACG 59.542 41.667 0.00 0.00 0.00 3.60
4032 5919 3.816523 TCACAGGGTCCATTTTAAACGAC 59.183 43.478 0.00 0.00 0.00 4.34
4048 5935 2.199236 ACGACTTTCACCGAAACAGTC 58.801 47.619 0.00 0.00 0.00 3.51
4053 5940 2.702592 TTCACCGAAACAGTCCAACT 57.297 45.000 0.00 0.00 0.00 3.16
4063 5950 2.047061 ACAGTCCAACTTAGGCAGTGA 58.953 47.619 0.00 0.00 35.12 3.41
4090 5980 7.784633 AAAGAAAAAGGAAATCATCGCAAAA 57.215 28.000 0.00 0.00 0.00 2.44
4095 5985 1.478105 GGAAATCATCGCAAAAGGGCT 59.522 47.619 0.00 0.00 0.00 5.19
4113 6003 3.367703 GGGCTAAAACACTAGCACGTAGA 60.368 47.826 5.10 0.00 45.17 2.59
4139 6029 0.822164 GGCGTGCTAGAGTCCCTAAA 59.178 55.000 0.00 0.00 0.00 1.85
4217 6108 1.676678 GAGGGTGCGGCTATGTCTCA 61.677 60.000 0.00 0.00 0.00 3.27
4229 6120 1.668419 ATGTCTCACTATTTGCCGGC 58.332 50.000 22.73 22.73 0.00 6.13
4234 6125 1.137404 CACTATTTGCCGGCAGTGC 59.863 57.895 30.75 6.55 32.72 4.40
4247 6138 1.153628 CAGTGCACCGGCCTAGTAC 60.154 63.158 14.63 0.00 40.13 2.73
4248 6139 1.305046 AGTGCACCGGCCTAGTACT 60.305 57.895 14.63 0.00 40.13 2.73
4255 6146 0.249489 CCGGCCTAGTACTCACATGC 60.249 60.000 0.00 0.00 0.00 4.06
4257 6148 1.269309 CGGCCTAGTACTCACATGCTC 60.269 57.143 0.00 0.00 0.00 4.26
4350 6245 9.820229 TTACTTAATTATTTCAAAGTGCTCACG 57.180 29.630 2.81 0.00 34.23 4.35
4351 6246 8.094798 ACTTAATTATTTCAAAGTGCTCACGA 57.905 30.769 0.00 0.00 36.20 4.35
4352 6247 8.730680 ACTTAATTATTTCAAAGTGCTCACGAT 58.269 29.630 0.00 0.00 36.20 3.73
4354 6249 9.982291 TTAATTATTTCAAAGTGCTCACGATAC 57.018 29.630 0.00 0.00 36.20 2.24
4355 6250 7.609760 ATTATTTCAAAGTGCTCACGATACA 57.390 32.000 0.00 0.00 36.20 2.29
4356 6251 4.725556 TTTCAAAGTGCTCACGATACAC 57.274 40.909 0.00 0.00 36.20 2.90
4357 6252 3.660501 TCAAAGTGCTCACGATACACT 57.339 42.857 0.00 0.00 46.27 3.55
4365 6260 6.831769 AGTGCTCACGATACACTTAAAAATG 58.168 36.000 0.00 0.00 41.78 2.32
4366 6261 6.426937 AGTGCTCACGATACACTTAAAAATGT 59.573 34.615 0.00 0.00 41.78 2.71
4367 6262 7.041372 AGTGCTCACGATACACTTAAAAATGTT 60.041 33.333 0.00 0.00 41.78 2.71
4368 6263 7.268447 GTGCTCACGATACACTTAAAAATGTTC 59.732 37.037 0.00 0.00 0.00 3.18
4369 6264 7.041712 TGCTCACGATACACTTAAAAATGTTCA 60.042 33.333 0.00 0.00 0.00 3.18
4370 6265 7.962918 GCTCACGATACACTTAAAAATGTTCAT 59.037 33.333 0.00 0.00 0.00 2.57
4371 6266 9.265938 CTCACGATACACTTAAAAATGTTCATG 57.734 33.333 0.00 0.00 0.00 3.07
4372 6267 7.748683 TCACGATACACTTAAAAATGTTCATGC 59.251 33.333 0.00 0.00 0.00 4.06
4373 6268 7.536964 CACGATACACTTAAAAATGTTCATGCA 59.463 33.333 0.00 0.00 0.00 3.96
4374 6269 7.750458 ACGATACACTTAAAAATGTTCATGCAG 59.250 33.333 0.00 0.00 0.00 4.41
4375 6270 7.750458 CGATACACTTAAAAATGTTCATGCAGT 59.250 33.333 0.00 0.00 0.00 4.40
4376 6271 9.410556 GATACACTTAAAAATGTTCATGCAGTT 57.589 29.630 0.00 0.00 0.00 3.16
4377 6272 9.762933 ATACACTTAAAAATGTTCATGCAGTTT 57.237 25.926 0.00 0.00 38.12 2.66
4379 6274 9.593134 ACACTTAAAAATGTTCATGCAGTTTAA 57.407 25.926 0.00 3.37 35.92 1.52
4405 6300 8.710835 AAAAATCTTCGCCAAACTTTTAGAAA 57.289 26.923 0.00 0.00 0.00 2.52
4406 6301 8.710835 AAAATCTTCGCCAAACTTTTAGAAAA 57.289 26.923 0.00 0.00 0.00 2.29
4407 6302 8.887036 AAATCTTCGCCAAACTTTTAGAAAAT 57.113 26.923 0.00 0.00 0.00 1.82
4408 6303 7.873739 ATCTTCGCCAAACTTTTAGAAAATG 57.126 32.000 0.00 0.00 0.00 2.32
4409 6304 6.801575 TCTTCGCCAAACTTTTAGAAAATGT 58.198 32.000 0.00 0.00 0.00 2.71
4410 6305 7.262048 TCTTCGCCAAACTTTTAGAAAATGTT 58.738 30.769 0.00 0.00 0.00 2.71
4411 6306 7.762159 TCTTCGCCAAACTTTTAGAAAATGTTT 59.238 29.630 9.37 9.37 33.60 2.83
4412 6307 7.227992 TCGCCAAACTTTTAGAAAATGTTTG 57.772 32.000 23.44 23.44 40.96 2.93
4413 6308 6.814146 TCGCCAAACTTTTAGAAAATGTTTGT 59.186 30.769 25.72 6.06 40.46 2.83
4414 6309 7.974501 TCGCCAAACTTTTAGAAAATGTTTGTA 59.025 29.630 25.72 16.29 40.46 2.41
4415 6310 8.053653 CGCCAAACTTTTAGAAAATGTTTGTAC 58.946 33.333 25.72 20.34 40.46 2.90
4416 6311 8.874816 GCCAAACTTTTAGAAAATGTTTGTACA 58.125 29.630 25.72 0.00 40.46 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 8.469200 TGGGAAATCACAAATAGTTCATGAATC 58.531 33.333 12.12 5.72 0.00 2.52
22 23 7.773489 TTGGGAAATCACAAATAGTTCATGA 57.227 32.000 0.00 0.00 36.13 3.07
280 286 5.596361 TGATTTAGTCCCAGTTTTGCAGAAA 59.404 36.000 0.00 0.00 0.00 2.52
281 287 5.136828 TGATTTAGTCCCAGTTTTGCAGAA 58.863 37.500 0.00 0.00 0.00 3.02
283 289 5.183713 TGATGATTTAGTCCCAGTTTTGCAG 59.816 40.000 0.00 0.00 0.00 4.41
284 290 5.048083 GTGATGATTTAGTCCCAGTTTTGCA 60.048 40.000 0.00 0.00 0.00 4.08
285 291 5.048083 TGTGATGATTTAGTCCCAGTTTTGC 60.048 40.000 0.00 0.00 0.00 3.68
286 292 6.573664 TGTGATGATTTAGTCCCAGTTTTG 57.426 37.500 0.00 0.00 0.00 2.44
287 293 6.947733 TCATGTGATGATTTAGTCCCAGTTTT 59.052 34.615 0.00 0.00 33.59 2.43
290 296 5.397221 CCTCATGTGATGATTTAGTCCCAGT 60.397 44.000 0.00 0.00 38.85 4.00
292 298 4.474651 ACCTCATGTGATGATTTAGTCCCA 59.525 41.667 0.00 0.00 38.85 4.37
293 299 5.041191 ACCTCATGTGATGATTTAGTCCC 57.959 43.478 0.00 0.00 38.85 4.46
308 314 0.540365 ACCCCAACTTGCACCTCATG 60.540 55.000 0.00 0.00 0.00 3.07
311 317 1.463674 CATACCCCAACTTGCACCTC 58.536 55.000 0.00 0.00 0.00 3.85
312 318 0.039618 CCATACCCCAACTTGCACCT 59.960 55.000 0.00 0.00 0.00 4.00
313 319 0.251608 ACCATACCCCAACTTGCACC 60.252 55.000 0.00 0.00 0.00 5.01
314 320 1.627864 AACCATACCCCAACTTGCAC 58.372 50.000 0.00 0.00 0.00 4.57
316 322 1.275010 CCAAACCATACCCCAACTTGC 59.725 52.381 0.00 0.00 0.00 4.01
320 326 2.296073 TGACCAAACCATACCCCAAC 57.704 50.000 0.00 0.00 0.00 3.77
321 327 2.178106 ACTTGACCAAACCATACCCCAA 59.822 45.455 0.00 0.00 0.00 4.12
322 328 1.783979 ACTTGACCAAACCATACCCCA 59.216 47.619 0.00 0.00 0.00 4.96
323 329 2.597578 ACTTGACCAAACCATACCCC 57.402 50.000 0.00 0.00 0.00 4.95
324 330 4.627058 CAAAACTTGACCAAACCATACCC 58.373 43.478 0.00 0.00 0.00 3.69
325 331 4.055360 GCAAAACTTGACCAAACCATACC 58.945 43.478 0.00 0.00 0.00 2.73
326 332 4.688021 TGCAAAACTTGACCAAACCATAC 58.312 39.130 0.00 0.00 0.00 2.39
329 335 3.330267 GTTGCAAAACTTGACCAAACCA 58.670 40.909 0.00 0.00 0.00 3.67
330 336 2.347150 CGTTGCAAAACTTGACCAAACC 59.653 45.455 0.00 0.00 0.00 3.27
335 341 2.869897 TCAACGTTGCAAAACTTGACC 58.130 42.857 23.47 0.00 0.00 4.02
336 342 4.384547 AGTTTCAACGTTGCAAAACTTGAC 59.615 37.500 28.67 13.08 0.00 3.18
338 344 4.901866 AGTTTCAACGTTGCAAAACTTG 57.098 36.364 28.67 6.95 0.00 3.16
339 345 7.329717 TGATTTAGTTTCAACGTTGCAAAACTT 59.670 29.630 34.18 24.23 0.00 2.66
341 645 6.983910 TGATTTAGTTTCAACGTTGCAAAAC 58.016 32.000 26.19 26.19 0.00 2.43
346 650 5.912396 TGTGATGATTTAGTTTCAACGTTGC 59.088 36.000 23.47 9.76 0.00 4.17
347 651 8.506140 AATGTGATGATTTAGTTTCAACGTTG 57.494 30.769 22.35 22.35 0.00 4.10
360 664 9.590451 CCTAACTTGCATTTAATGTGATGATTT 57.410 29.630 6.81 0.00 0.00 2.17
363 667 6.663093 ACCCTAACTTGCATTTAATGTGATGA 59.337 34.615 6.81 0.00 0.00 2.92
367 671 6.377146 AGGTACCCTAACTTGCATTTAATGTG 59.623 38.462 8.74 0.86 28.47 3.21
369 673 6.183360 CCAGGTACCCTAACTTGCATTTAATG 60.183 42.308 8.74 0.00 29.64 1.90
371 675 5.258051 CCAGGTACCCTAACTTGCATTTAA 58.742 41.667 8.74 0.00 29.64 1.52
372 676 4.324719 CCCAGGTACCCTAACTTGCATTTA 60.325 45.833 8.74 0.00 29.64 1.40
374 678 2.025321 CCCAGGTACCCTAACTTGCATT 60.025 50.000 8.74 0.00 29.64 3.56
375 679 1.564348 CCCAGGTACCCTAACTTGCAT 59.436 52.381 8.74 0.00 29.64 3.96
380 684 1.009675 AGCATCCCAGGTACCCTAACT 59.990 52.381 8.74 0.00 29.64 2.24
381 685 1.508256 AGCATCCCAGGTACCCTAAC 58.492 55.000 8.74 0.00 29.64 2.34
382 686 3.648683 ATAGCATCCCAGGTACCCTAA 57.351 47.619 8.74 0.00 29.64 2.69
383 687 3.648683 AATAGCATCCCAGGTACCCTA 57.351 47.619 8.74 1.02 29.64 3.53
384 688 2.514726 AATAGCATCCCAGGTACCCT 57.485 50.000 8.74 0.00 0.00 4.34
385 689 2.305052 GGTAATAGCATCCCAGGTACCC 59.695 54.545 8.74 0.00 0.00 3.69
386 690 3.248888 AGGTAATAGCATCCCAGGTACC 58.751 50.000 2.73 2.73 0.00 3.34
387 691 3.901844 TGAGGTAATAGCATCCCAGGTAC 59.098 47.826 0.00 0.00 0.00 3.34
388 692 4.207698 TGAGGTAATAGCATCCCAGGTA 57.792 45.455 0.00 0.00 0.00 3.08
389 693 3.060479 TGAGGTAATAGCATCCCAGGT 57.940 47.619 0.00 0.00 0.00 4.00
390 694 5.762179 TTATGAGGTAATAGCATCCCAGG 57.238 43.478 0.00 0.00 0.00 4.45
391 695 7.628234 AGATTTATGAGGTAATAGCATCCCAG 58.372 38.462 0.00 0.00 0.00 4.45
393 697 7.554476 GGAAGATTTATGAGGTAATAGCATCCC 59.446 40.741 0.00 0.00 0.00 3.85
394 698 8.103305 TGGAAGATTTATGAGGTAATAGCATCC 58.897 37.037 0.00 0.00 0.00 3.51
395 699 9.507329 TTGGAAGATTTATGAGGTAATAGCATC 57.493 33.333 0.00 0.00 0.00 3.91
397 701 9.693739 TTTTGGAAGATTTATGAGGTAATAGCA 57.306 29.630 0.00 0.00 0.00 3.49
407 711 9.651913 GGCTTGTTTATTTTGGAAGATTTATGA 57.348 29.630 0.00 0.00 0.00 2.15
410 714 9.651913 GATGGCTTGTTTATTTTGGAAGATTTA 57.348 29.630 0.00 0.00 0.00 1.40
411 715 7.331687 CGATGGCTTGTTTATTTTGGAAGATTT 59.668 33.333 0.00 0.00 0.00 2.17
412 716 6.813152 CGATGGCTTGTTTATTTTGGAAGATT 59.187 34.615 0.00 0.00 0.00 2.40
413 717 6.332630 CGATGGCTTGTTTATTTTGGAAGAT 58.667 36.000 0.00 0.00 0.00 2.40
414 718 5.708948 CGATGGCTTGTTTATTTTGGAAGA 58.291 37.500 0.00 0.00 0.00 2.87
416 720 4.241681 GCGATGGCTTGTTTATTTTGGAA 58.758 39.130 0.00 0.00 35.83 3.53
417 721 3.256879 TGCGATGGCTTGTTTATTTTGGA 59.743 39.130 0.15 0.00 40.82 3.53
418 722 3.583806 TGCGATGGCTTGTTTATTTTGG 58.416 40.909 0.15 0.00 40.82 3.28
420 724 4.519540 ACTGCGATGGCTTGTTTATTTT 57.480 36.364 0.15 0.00 40.82 1.82
424 2112 1.068610 GCAACTGCGATGGCTTGTTTA 60.069 47.619 0.15 0.00 40.82 2.01
450 2138 2.430694 ACAAAAGAAGGTTTGGACTGGC 59.569 45.455 3.02 0.00 41.82 4.85
461 2149 3.443976 CACCCGTCAAAACAAAAGAAGG 58.556 45.455 0.00 0.00 0.00 3.46
469 2157 2.902846 CCCGCACCCGTCAAAACA 60.903 61.111 0.00 0.00 0.00 2.83
470 2158 3.666253 CCCCGCACCCGTCAAAAC 61.666 66.667 0.00 0.00 0.00 2.43
503 2235 3.792047 GGGTTCGGTTTACGGCGC 61.792 66.667 6.90 0.00 44.45 6.53
539 2271 2.418976 GCACTTTCCATTCTAACCGGAC 59.581 50.000 9.46 0.00 0.00 4.79
613 2360 3.842923 CTCCGCTGACAGCCCGAT 61.843 66.667 21.55 0.00 38.18 4.18
710 2472 0.949105 CTTTCTTGACCCGTCGGTGG 60.949 60.000 11.06 0.00 44.88 4.61
740 2502 4.223125 TGGGCTGGTGGCTTTGCT 62.223 61.111 0.00 0.00 41.46 3.91
741 2503 3.994853 GTGGGCTGGTGGCTTTGC 61.995 66.667 0.00 0.00 41.46 3.68
742 2504 3.305516 GGTGGGCTGGTGGCTTTG 61.306 66.667 0.00 0.00 41.46 2.77
743 2505 3.831637 TGGTGGGCTGGTGGCTTT 61.832 61.111 0.00 0.00 41.46 3.51
774 2545 1.197430 AGCCTGGAGTCCTGGACTTG 61.197 60.000 33.21 20.48 43.53 3.16
778 2549 3.005539 GCAGCCTGGAGTCCTGGA 61.006 66.667 33.21 3.30 44.09 3.86
811 2599 0.687354 GAGGACTTGTTGGAGAGCCA 59.313 55.000 0.00 0.00 44.17 4.75
843 2643 4.394712 GTGGACTGGTGGGCGAGG 62.395 72.222 0.00 0.00 0.00 4.63
874 2677 2.600769 AGTCGTCGCTTGGAGGGT 60.601 61.111 0.00 0.00 0.00 4.34
1079 2903 1.371558 GGAGAGCTTTGGTGTCGGT 59.628 57.895 0.00 0.00 0.00 4.69
1213 3037 2.360600 CGGCGAAATTCCCACCCA 60.361 61.111 0.00 0.00 0.00 4.51
1236 3060 1.813513 CACAACCTAGCCAGACAAGG 58.186 55.000 0.00 0.00 36.42 3.61
1290 3122 2.349886 CAGCGCCTCAACAGAATTACTC 59.650 50.000 2.29 0.00 0.00 2.59
1309 3141 4.539870 TCTTTCAAAGCGAAATTGAGCAG 58.460 39.130 7.93 0.00 42.69 4.24
1324 3156 1.542547 GCCGGACCAAGACTCTTTCAA 60.543 52.381 5.05 0.00 0.00 2.69
1325 3157 0.034896 GCCGGACCAAGACTCTTTCA 59.965 55.000 5.05 0.00 0.00 2.69
1340 3172 0.824182 TACAAACCAAACCAGGCCGG 60.824 55.000 11.48 11.48 42.50 6.13
1377 3209 3.062466 CAGTCCCGACGAGCCTCA 61.062 66.667 0.00 0.00 36.20 3.86
1425 3257 0.389391 TTCCGGAGATGAGATTCGCC 59.611 55.000 3.34 0.00 32.74 5.54
1458 3291 1.944024 TCCAACGCCAAACTAACACAG 59.056 47.619 0.00 0.00 0.00 3.66
1472 3306 1.078759 GACAGATGCGTCCTCCAACG 61.079 60.000 1.23 0.00 45.31 4.10
1491 3325 2.820197 GACAAGAGGGCTTAAACAAGGG 59.180 50.000 0.00 0.00 31.81 3.95
1492 3326 3.753797 GAGACAAGAGGGCTTAAACAAGG 59.246 47.826 0.00 0.00 31.81 3.61
1519 3353 2.873170 TTGCGAAACTGTTAGCATCG 57.127 45.000 19.38 13.93 43.67 3.84
1524 3358 4.675114 GGACAACAATTGCGAAACTGTTAG 59.325 41.667 2.01 1.02 31.00 2.34
1549 3383 4.442706 CATAATACACTTGGCTTCGGTCT 58.557 43.478 0.00 0.00 0.00 3.85
1555 3389 4.588899 TGTGAGCATAATACACTTGGCTT 58.411 39.130 0.00 0.00 0.00 4.35
1564 3401 8.607441 TCTATGTCCATTTGTGAGCATAATAC 57.393 34.615 0.00 0.00 0.00 1.89
1575 3412 7.013274 CCCAATTATCGTTCTATGTCCATTTGT 59.987 37.037 0.00 0.00 0.00 2.83
1578 3415 6.837312 TCCCAATTATCGTTCTATGTCCATT 58.163 36.000 0.00 0.00 0.00 3.16
1590 3429 4.453480 AACATCCCATCCCAATTATCGT 57.547 40.909 0.00 0.00 0.00 3.73
1594 3433 5.131308 TCGAAGTAACATCCCATCCCAATTA 59.869 40.000 0.00 0.00 0.00 1.40
1606 3445 4.206609 GGAACGCTACATCGAAGTAACATC 59.793 45.833 1.76 0.00 0.00 3.06
1609 3448 3.767278 AGGAACGCTACATCGAAGTAAC 58.233 45.455 1.76 0.00 0.00 2.50
1613 3452 2.097629 TCAGAGGAACGCTACATCGAAG 59.902 50.000 0.00 0.00 35.27 3.79
1619 3458 4.245660 CAGAAAATCAGAGGAACGCTACA 58.754 43.478 0.00 0.00 35.27 2.74
1620 3459 4.246458 ACAGAAAATCAGAGGAACGCTAC 58.754 43.478 0.00 0.00 35.27 3.58
1622 3471 3.409026 ACAGAAAATCAGAGGAACGCT 57.591 42.857 0.00 0.00 40.82 5.07
1624 3473 5.334414 CCAAGAACAGAAAATCAGAGGAACG 60.334 44.000 0.00 0.00 0.00 3.95
1631 3480 6.150140 CCTAACTCCCAAGAACAGAAAATCAG 59.850 42.308 0.00 0.00 0.00 2.90
1640 3489 1.351017 CCTGCCTAACTCCCAAGAACA 59.649 52.381 0.00 0.00 0.00 3.18
1641 3490 1.628846 TCCTGCCTAACTCCCAAGAAC 59.371 52.381 0.00 0.00 0.00 3.01
1649 3498 3.274288 CTGAACCAATCCTGCCTAACTC 58.726 50.000 0.00 0.00 0.00 3.01
1650 3499 2.025887 CCTGAACCAATCCTGCCTAACT 60.026 50.000 0.00 0.00 0.00 2.24
1651 3500 2.026262 TCCTGAACCAATCCTGCCTAAC 60.026 50.000 0.00 0.00 0.00 2.34
1653 3502 1.965414 TCCTGAACCAATCCTGCCTA 58.035 50.000 0.00 0.00 0.00 3.93
1654 3503 1.302907 ATCCTGAACCAATCCTGCCT 58.697 50.000 0.00 0.00 0.00 4.75
1655 3504 2.149973 AATCCTGAACCAATCCTGCC 57.850 50.000 0.00 0.00 0.00 4.85
1659 3508 3.885901 GCTCCTAAATCCTGAACCAATCC 59.114 47.826 0.00 0.00 0.00 3.01
1673 3522 3.994392 GACAATTCACTCGTGCTCCTAAA 59.006 43.478 0.00 0.00 0.00 1.85
1684 3533 6.074888 CGTTTTCAACCAATGACAATTCACTC 60.075 38.462 0.00 0.00 37.92 3.51
1695 3544 3.067461 TCAGTTCCCGTTTTCAACCAATG 59.933 43.478 0.00 0.00 0.00 2.82
1698 3547 2.018515 GTCAGTTCCCGTTTTCAACCA 58.981 47.619 0.00 0.00 0.00 3.67
1702 3551 2.092861 TCCAAGTCAGTTCCCGTTTTCA 60.093 45.455 0.00 0.00 0.00 2.69
1704 3553 2.294979 GTCCAAGTCAGTTCCCGTTTT 58.705 47.619 0.00 0.00 0.00 2.43
1708 3557 0.037232 GAGGTCCAAGTCAGTTCCCG 60.037 60.000 0.00 0.00 0.00 5.14
1716 3565 3.971245 ACAGAATCAGAGGTCCAAGTC 57.029 47.619 0.00 0.00 0.00 3.01
1740 3589 1.649321 TGGTGAGCATGAACTCTCCT 58.351 50.000 17.14 0.00 46.12 3.69
1826 3675 2.422231 CCGACTGGAGCTCCCTCAG 61.422 68.421 29.95 22.05 39.96 3.35
1942 3791 6.046290 TGTATAGAATGGATCAGCATGGAG 57.954 41.667 0.00 0.00 36.16 3.86
1944 3793 7.148120 GGAAATGTATAGAATGGATCAGCATGG 60.148 40.741 0.00 0.00 36.16 3.66
1949 3798 8.874744 ATTGGGAAATGTATAGAATGGATCAG 57.125 34.615 0.00 0.00 0.00 2.90
1959 3808 6.267699 GGGAAAGGGAATTGGGAAATGTATAG 59.732 42.308 0.00 0.00 0.00 1.31
1992 3849 4.787882 GCGATAAAGCTGGCATTCTTCTTC 60.788 45.833 0.00 3.46 0.00 2.87
1993 3850 3.065925 GCGATAAAGCTGGCATTCTTCTT 59.934 43.478 0.00 0.00 0.00 2.52
1994 3851 2.615912 GCGATAAAGCTGGCATTCTTCT 59.384 45.455 0.00 0.00 0.00 2.85
2052 3909 3.737266 CCAACTGTGCAAGTAAAGCAATG 59.263 43.478 0.00 0.00 44.64 2.82
2069 3926 2.722094 TCGAATAGCATTTGCCCAACT 58.278 42.857 0.00 0.00 43.38 3.16
2104 3961 8.691797 AGTTATAAATGACAGTTGGTTGTTGTT 58.308 29.630 0.00 0.00 0.00 2.83
2122 3979 9.251440 TCCAGAGCAGACTAAAGTAGTTATAAA 57.749 33.333 0.00 0.00 39.59 1.40
2168 4025 6.377712 AGGATATCCTACCTAACGAATGCTAC 59.622 42.308 23.34 0.00 46.48 3.58
2197 4054 3.955650 TGTCTAAGTTGACCTGCCTAC 57.044 47.619 0.00 0.00 36.21 3.18
2389 4254 4.530710 ATCGGTGTAAGCAGAGTTAACA 57.469 40.909 8.61 0.00 0.00 2.41
2502 4367 4.999751 AGATTCGACTTCTGAAGCAAAC 57.000 40.909 17.00 6.85 34.31 2.93
2509 4374 4.283467 TCTTCCCAAAGATTCGACTTCTGA 59.717 41.667 0.00 0.00 36.59 3.27
2517 4382 3.623510 GCCTTACTCTTCCCAAAGATTCG 59.376 47.826 0.00 0.00 40.68 3.34
2559 4424 0.877071 CATCAGCACAATATCCCCGC 59.123 55.000 0.00 0.00 0.00 6.13
2562 4427 1.251251 GCCCATCAGCACAATATCCC 58.749 55.000 0.00 0.00 0.00 3.85
2580 4445 1.237285 ACACCAGAATGCGTTCAGGC 61.237 55.000 25.43 0.00 42.92 4.85
2739 4604 9.232473 AGAATTATCTATGTCATGCTACTACGA 57.768 33.333 0.00 0.00 32.88 3.43
2769 4634 5.428496 AACTGCTTACCGGAAGTAAAAAC 57.572 39.130 9.46 0.00 40.43 2.43
2846 4711 3.327464 TGATGCTTCCATGGATTATCGGA 59.673 43.478 17.06 3.83 0.00 4.55
2903 4768 1.143183 AAAGTCACCGACGTGTGCT 59.857 52.632 0.00 8.66 41.09 4.40
2912 4777 3.125316 GCTTCATAAGACCAAAGTCACCG 59.875 47.826 0.00 0.00 46.15 4.94
3144 5009 2.287668 CGTATCTACCCTCTTTCGCCAG 60.288 54.545 0.00 0.00 0.00 4.85
3203 5068 3.578716 CCACCCTCTTTAGTTCAGACTCA 59.421 47.826 0.00 0.00 37.33 3.41
3218 5083 0.678048 GTCCAATCAGCACCACCCTC 60.678 60.000 0.00 0.00 0.00 4.30
3233 5098 1.300620 GTGTGTGCACGCTAGTCCA 60.301 57.895 29.04 6.85 38.69 4.02
3248 5113 3.444388 GTCTCTTATCGGGTTCTCTGTGT 59.556 47.826 0.00 0.00 0.00 3.72
3281 5146 0.114364 TCAGCAGGGACACTACCTCA 59.886 55.000 0.00 0.00 35.78 3.86
3287 5152 0.109342 CACCTTTCAGCAGGGACACT 59.891 55.000 0.00 0.00 38.42 3.55
3454 5322 4.756203 CTAGGGGCTAGTCCAGGGTACC 62.756 63.636 16.93 2.17 37.82 3.34
3455 5323 0.559699 TAGGGGCTAGTCCAGGGTAC 59.440 60.000 16.93 0.00 36.21 3.34
3456 5324 0.858369 CTAGGGGCTAGTCCAGGGTA 59.142 60.000 16.93 0.00 36.21 3.69
3458 5326 1.152226 CCTAGGGGCTAGTCCAGGG 60.152 68.421 16.93 9.80 36.21 4.45
3459 5327 0.858369 TACCTAGGGGCTAGTCCAGG 59.142 60.000 16.93 16.65 36.21 4.45
3460 5328 2.900546 CAATACCTAGGGGCTAGTCCAG 59.099 54.545 16.93 4.57 36.21 3.86
3461 5329 2.427297 CCAATACCTAGGGGCTAGTCCA 60.427 54.545 16.93 0.00 36.21 4.02
3462 5330 2.258109 CCAATACCTAGGGGCTAGTCC 58.742 57.143 14.81 4.21 32.62 3.85
3463 5331 2.973710 ACCAATACCTAGGGGCTAGTC 58.026 52.381 14.81 0.00 32.62 2.59
3464 5332 3.731130 TCTACCAATACCTAGGGGCTAGT 59.269 47.826 14.81 7.45 32.62 2.57
3465 5333 4.202695 ACTCTACCAATACCTAGGGGCTAG 60.203 50.000 14.81 8.81 35.63 3.42
3466 5334 3.731130 ACTCTACCAATACCTAGGGGCTA 59.269 47.826 14.81 0.00 35.63 3.93
3658 5526 0.608640 CATCTGGGGAGTATACGGGC 59.391 60.000 0.00 0.00 0.00 6.13
3704 5572 6.821031 TTTGTTTACAGTAACCAACACAGT 57.179 33.333 2.89 0.00 0.00 3.55
3719 5587 9.562583 TGTATATGCGAAGGAAATTTTGTTTAC 57.437 29.630 0.00 0.00 0.00 2.01
3737 5605 6.204301 AGTCATCTGCATTCAGTTGTATATGC 59.796 38.462 3.80 0.00 42.75 3.14
3738 5606 7.307811 CCAGTCATCTGCATTCAGTTGTATATG 60.308 40.741 3.80 0.00 39.72 1.78
3739 5607 6.709397 CCAGTCATCTGCATTCAGTTGTATAT 59.291 38.462 3.80 0.00 39.72 0.86
3740 5608 6.051074 CCAGTCATCTGCATTCAGTTGTATA 58.949 40.000 3.80 0.00 39.72 1.47
3760 5631 2.633967 GGAGAGAGCATGATCATCCAGT 59.366 50.000 23.09 0.00 31.16 4.00
3815 5686 2.144482 CCTGCAAAAGCAAAGACAGG 57.856 50.000 0.00 0.00 38.81 4.00
3831 5702 4.796038 ATCCTGCAAAATGAAGAACCTG 57.204 40.909 0.00 0.00 0.00 4.00
3840 5720 4.094294 CAGCCATGAAAATCCTGCAAAATG 59.906 41.667 0.00 0.00 0.00 2.32
3841 5721 4.020039 TCAGCCATGAAAATCCTGCAAAAT 60.020 37.500 0.00 0.00 30.61 1.82
3934 5814 4.160439 TGATAGCAGGAAATAGGATAGGCG 59.840 45.833 0.00 0.00 0.00 5.52
3949 5829 4.701765 AGCTTAGGACAACATGATAGCAG 58.298 43.478 0.00 0.00 0.00 4.24
3984 5864 5.196695 AGTATGTCACTGTCTCATGAGCTA 58.803 41.667 18.36 8.09 35.62 3.32
4000 5880 2.766263 TGGACCCTGTGATCAGTATGTC 59.234 50.000 0.00 1.18 39.82 3.06
4003 5883 5.456921 AAAATGGACCCTGTGATCAGTAT 57.543 39.130 0.00 0.00 39.82 2.12
4030 5917 2.557317 TGGACTGTTTCGGTGAAAGTC 58.443 47.619 3.79 3.79 31.87 3.01
4032 5919 2.943033 AGTTGGACTGTTTCGGTGAAAG 59.057 45.455 0.00 0.00 31.87 2.62
4090 5980 1.346722 ACGTGCTAGTGTTTTAGCCCT 59.653 47.619 0.00 0.00 44.29 5.19
4095 5985 5.694231 TGTCTCTACGTGCTAGTGTTTTA 57.306 39.130 0.00 0.00 0.00 1.52
4113 6003 1.950909 GACTCTAGCACGCCTATGTCT 59.049 52.381 0.00 0.00 31.92 3.41
4139 6029 8.667463 CAATGATTTGAAGTTGGAAACAAACTT 58.333 29.630 4.24 4.24 43.17 2.66
4175 6066 3.314913 TGCGTGGTGCTTATCATATTTGG 59.685 43.478 0.00 0.00 46.63 3.28
4176 6067 4.273235 TCTGCGTGGTGCTTATCATATTTG 59.727 41.667 0.00 0.00 46.63 2.32
4179 6070 3.555795 CCTCTGCGTGGTGCTTATCATAT 60.556 47.826 0.00 0.00 46.63 1.78
4180 6071 2.224042 CCTCTGCGTGGTGCTTATCATA 60.224 50.000 0.00 0.00 46.63 2.15
4181 6072 1.473965 CCTCTGCGTGGTGCTTATCAT 60.474 52.381 0.00 0.00 46.63 2.45
4182 6073 0.108186 CCTCTGCGTGGTGCTTATCA 60.108 55.000 0.00 0.00 46.63 2.15
4183 6074 0.811616 CCCTCTGCGTGGTGCTTATC 60.812 60.000 0.00 0.00 46.63 1.75
4184 6075 1.221840 CCCTCTGCGTGGTGCTTAT 59.778 57.895 0.00 0.00 46.63 1.73
4185 6076 2.214216 ACCCTCTGCGTGGTGCTTA 61.214 57.895 0.00 0.00 46.63 3.09
4186 6077 3.560251 ACCCTCTGCGTGGTGCTT 61.560 61.111 0.00 0.00 46.63 3.91
4187 6078 4.320456 CACCCTCTGCGTGGTGCT 62.320 66.667 0.00 0.00 44.98 4.40
4217 6108 1.303236 TGCACTGCCGGCAAATAGT 60.303 52.632 32.09 21.96 38.54 2.12
4229 6120 1.153628 GTACTAGGCCGGTGCACTG 60.154 63.158 19.25 19.25 40.13 3.66
4234 6125 1.112113 ATGTGAGTACTAGGCCGGTG 58.888 55.000 13.41 3.22 0.00 4.94
4238 6129 2.035632 AGAGCATGTGAGTACTAGGCC 58.964 52.381 0.00 0.00 0.00 5.19
4324 6219 9.820229 CGTGAGCACTTTGAAATAATTAAGTAA 57.180 29.630 0.00 0.00 30.19 2.24
4325 6220 9.210329 TCGTGAGCACTTTGAAATAATTAAGTA 57.790 29.630 0.00 0.00 30.19 2.24
4326 6221 8.094798 TCGTGAGCACTTTGAAATAATTAAGT 57.905 30.769 0.00 0.00 0.00 2.24
4328 6223 9.982291 GTATCGTGAGCACTTTGAAATAATTAA 57.018 29.630 0.00 0.00 0.00 1.40
4329 6224 9.157104 TGTATCGTGAGCACTTTGAAATAATTA 57.843 29.630 0.00 0.00 0.00 1.40
4330 6225 7.962918 GTGTATCGTGAGCACTTTGAAATAATT 59.037 33.333 0.00 0.00 0.00 1.40
4331 6226 7.334421 AGTGTATCGTGAGCACTTTGAAATAAT 59.666 33.333 0.00 0.00 40.13 1.28
4332 6227 6.649141 AGTGTATCGTGAGCACTTTGAAATAA 59.351 34.615 0.00 0.00 40.13 1.40
4333 6228 6.163476 AGTGTATCGTGAGCACTTTGAAATA 58.837 36.000 0.00 0.00 40.13 1.40
4334 6229 4.997395 AGTGTATCGTGAGCACTTTGAAAT 59.003 37.500 0.00 0.00 40.13 2.17
4335 6230 4.377021 AGTGTATCGTGAGCACTTTGAAA 58.623 39.130 0.00 0.00 40.13 2.69
4336 6231 3.990092 AGTGTATCGTGAGCACTTTGAA 58.010 40.909 0.00 0.00 40.13 2.69
4337 6232 3.660501 AGTGTATCGTGAGCACTTTGA 57.339 42.857 0.00 0.00 40.13 2.69
4341 6236 6.426937 ACATTTTTAAGTGTATCGTGAGCACT 59.573 34.615 0.00 4.65 44.31 4.40
4342 6237 6.599437 ACATTTTTAAGTGTATCGTGAGCAC 58.401 36.000 0.00 0.00 0.00 4.40
4343 6238 6.795098 ACATTTTTAAGTGTATCGTGAGCA 57.205 33.333 0.00 0.00 0.00 4.26
4344 6239 7.295201 TGAACATTTTTAAGTGTATCGTGAGC 58.705 34.615 0.00 0.00 0.00 4.26
4345 6240 9.265938 CATGAACATTTTTAAGTGTATCGTGAG 57.734 33.333 12.01 0.00 31.54 3.51
4346 6241 7.748683 GCATGAACATTTTTAAGTGTATCGTGA 59.251 33.333 16.74 0.00 31.54 4.35
4347 6242 7.536964 TGCATGAACATTTTTAAGTGTATCGTG 59.463 33.333 0.00 12.53 32.22 4.35
4348 6243 7.589395 TGCATGAACATTTTTAAGTGTATCGT 58.411 30.769 0.00 0.00 0.00 3.73
4349 6244 7.750458 ACTGCATGAACATTTTTAAGTGTATCG 59.250 33.333 0.00 0.00 0.00 2.92
4350 6245 8.970691 ACTGCATGAACATTTTTAAGTGTATC 57.029 30.769 0.00 0.00 0.00 2.24
4351 6246 9.762933 AAACTGCATGAACATTTTTAAGTGTAT 57.237 25.926 0.00 0.00 0.00 2.29
4353 6248 9.593134 TTAAACTGCATGAACATTTTTAAGTGT 57.407 25.926 0.00 0.00 0.00 3.55
4380 6275 8.710835 TTTCTAAAAGTTTGGCGAAGATTTTT 57.289 26.923 12.93 10.60 0.00 1.94
4381 6276 8.710835 TTTTCTAAAAGTTTGGCGAAGATTTT 57.289 26.923 12.51 12.51 0.00 1.82
4382 6277 8.764287 CATTTTCTAAAAGTTTGGCGAAGATTT 58.236 29.630 0.00 0.00 0.00 2.17
4383 6278 7.926018 ACATTTTCTAAAAGTTTGGCGAAGATT 59.074 29.630 0.00 0.00 0.00 2.40
4384 6279 7.433680 ACATTTTCTAAAAGTTTGGCGAAGAT 58.566 30.769 0.00 0.00 0.00 2.40
4385 6280 6.801575 ACATTTTCTAAAAGTTTGGCGAAGA 58.198 32.000 0.00 0.00 0.00 2.87
4386 6281 7.463469 AACATTTTCTAAAAGTTTGGCGAAG 57.537 32.000 0.00 0.00 0.00 3.79
4387 6282 7.332182 ACAAACATTTTCTAAAAGTTTGGCGAA 59.668 29.630 24.51 0.00 42.72 4.70
4388 6283 6.814146 ACAAACATTTTCTAAAAGTTTGGCGA 59.186 30.769 24.51 0.00 42.72 5.54
4389 6284 6.999456 ACAAACATTTTCTAAAAGTTTGGCG 58.001 32.000 24.51 10.31 42.72 5.69
4390 6285 8.874816 TGTACAAACATTTTCTAAAAGTTTGGC 58.125 29.630 24.51 19.43 42.72 4.52


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

AutoCloner maintained by Alex Coulton.