Multiple sequence alignment - TraesCS7B01G014700

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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 TraesCS7B01G014700 chr7B 100.000 4515 0 0 1 4515 11960926 11956412 0.000000e+00 8338
1 TraesCS7B01G014700 chr7B 86.743 958 105 17 1685 2636 11921892 11920951 0.000000e+00 1046
2 TraesCS7B01G014700 chr7B 85.075 1072 106 20 2038 3101 11926890 11925865 0.000000e+00 1044
3 TraesCS7B01G014700 chr7B 81.466 1214 134 45 3148 4316 11925870 11924703 0.000000e+00 911
4 TraesCS7B01G014700 chr7B 91.830 612 40 5 3912 4515 11918487 11917878 0.000000e+00 845
5 TraesCS7B01G014700 chr7B 79.162 979 124 42 3052 3972 11896168 11895212 5.000000e-169 604
6 TraesCS7B01G014700 chr7B 85.778 450 43 15 1156 1589 11929267 11928823 1.480000e-124 457
7 TraesCS7B01G014700 chr7B 88.398 362 35 5 1685 2044 11928497 11928141 3.230000e-116 429
8 TraesCS7B01G014700 chr7B 87.050 278 27 6 1412 1681 11922199 11921923 5.670000e-79 305
9 TraesCS7B01G014700 chr7A 85.079 1709 169 52 2823 4515 76119409 76117771 0.000000e+00 1664
10 TraesCS7B01G014700 chr7A 85.531 1244 128 26 394 1608 76122114 76120894 0.000000e+00 1253
11 TraesCS7B01G014700 chr7A 84.447 1003 115 24 2823 3812 75668473 75667499 0.000000e+00 950
12 TraesCS7B01G014700 chr7A 82.947 862 114 26 1771 2618 76120714 76119872 0.000000e+00 747
13 TraesCS7B01G014700 chr7A 76.662 1354 214 69 3028 4343 75572986 75571697 0.000000e+00 656
14 TraesCS7B01G014700 chr7A 79.817 981 118 40 3052 3972 75869055 75868095 3.810000e-180 641
15 TraesCS7B01G014700 chr7A 81.481 324 44 12 1 321 76122441 76122131 7.500000e-63 252
16 TraesCS7B01G014700 chr7D 88.134 1340 120 22 3101 4426 69590851 69589537 0.000000e+00 1557
17 TraesCS7B01G014700 chr7D 91.775 766 52 5 3153 3918 69532434 69531680 0.000000e+00 1055
18 TraesCS7B01G014700 chr7D 82.650 1268 132 48 1478 2696 69592663 69591435 0.000000e+00 1042
19 TraesCS7B01G014700 chr7D 85.700 1021 78 34 479 1481 69593793 69592823 0.000000e+00 1014
20 TraesCS7B01G014700 chr7D 88.787 767 69 14 1686 2444 69581112 69580355 0.000000e+00 924
21 TraesCS7B01G014700 chr7D 84.634 833 95 19 3076 3897 69487794 69486984 0.000000e+00 798
22 TraesCS7B01G014700 chr7D 76.497 1570 233 85 2823 4341 69484037 69482553 0.000000e+00 730
23 TraesCS7B01G014700 chr7D 89.817 383 33 3 4139 4515 69493240 69492858 1.890000e-133 486
24 TraesCS7B01G014700 chr7D 83.438 320 40 7 4 321 69594185 69593877 7.390000e-73 285


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 TraesCS7B01G014700 chr7B 11956412 11960926 4514 True 8338.000000 8338 100.0000 1 4515 1 chr7B.!!$R2 4514
1 TraesCS7B01G014700 chr7B 11917878 11929267 11389 True 719.571429 1046 86.6200 1156 4515 7 chr7B.!!$R3 3359
2 TraesCS7B01G014700 chr7B 11895212 11896168 956 True 604.000000 604 79.1620 3052 3972 1 chr7B.!!$R1 920
3 TraesCS7B01G014700 chr7A 76117771 76122441 4670 True 979.000000 1664 83.7595 1 4515 4 chr7A.!!$R4 4514
4 TraesCS7B01G014700 chr7A 75667499 75668473 974 True 950.000000 950 84.4470 2823 3812 1 chr7A.!!$R2 989
5 TraesCS7B01G014700 chr7A 75571697 75572986 1289 True 656.000000 656 76.6620 3028 4343 1 chr7A.!!$R1 1315
6 TraesCS7B01G014700 chr7A 75868095 75869055 960 True 641.000000 641 79.8170 3052 3972 1 chr7A.!!$R3 920
7 TraesCS7B01G014700 chr7D 69531680 69532434 754 True 1055.000000 1055 91.7750 3153 3918 1 chr7D.!!$R2 765
8 TraesCS7B01G014700 chr7D 69589537 69594185 4648 True 974.500000 1557 84.9805 4 4426 4 chr7D.!!$R5 4422
9 TraesCS7B01G014700 chr7D 69580355 69581112 757 True 924.000000 924 88.7870 1686 2444 1 chr7D.!!$R3 758
10 TraesCS7B01G014700 chr7D 69482553 69487794 5241 True 764.000000 798 80.5655 2823 4341 2 chr7D.!!$R4 1518

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
926 949 0.034059 GCTATCATCCCACGGACCAG 59.966 60.000 0.0 0.0 32.98 4.00 F
1166 1204 0.531200 GGTCGGTCAGGTACAAGGAG 59.469 60.000 0.0 0.0 0.00 3.69 F
2758 4805 1.078637 TGCATGTGAGCAGAGCCTC 60.079 57.895 0.0 0.0 40.11 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2781 4828 0.110056 GCACAATTGACGCACTGGAG 60.110 55.0 13.59 0.0 0.00 3.86 R
2842 4911 2.561733 TAGAGAATTCTGACCGCACG 57.438 50.0 14.00 0.0 34.79 5.34 R
4364 17176 0.541392 AGTGTGAGTCAACAGGTGCA 59.459 50.0 0.00 0.0 0.00 4.57 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
48 50 1.321074 ACCTACCAGTGGCTAGCGAC 61.321 60.000 21.02 21.02 0.00 5.19
50 52 2.337749 CTACCAGTGGCTAGCGACGG 62.338 65.000 26.59 26.59 0.00 4.79
53 55 1.805945 CAGTGGCTAGCGACGGAAC 60.806 63.158 22.06 7.50 0.00 3.62
57 59 0.389426 TGGCTAGCGACGGAACTTTC 60.389 55.000 9.00 0.00 0.00 2.62
71 74 0.744281 ACTTTCCAAAAGTGGCCACG 59.256 50.000 29.68 15.52 45.54 4.94
88 91 4.145365 CCACGGGTGGTAATTATCTTGA 57.855 45.455 9.72 0.00 45.53 3.02
90 93 4.334481 CCACGGGTGGTAATTATCTTGAAC 59.666 45.833 9.72 0.00 45.53 3.18
109 112 2.253452 GCAAGAGTGCGTGCTTGG 59.747 61.111 12.29 0.00 44.57 3.61
114 117 0.393077 AGAGTGCGTGCTTGGTAGTT 59.607 50.000 0.00 0.00 0.00 2.24
165 168 7.014615 ACAATAAGAAATTTCTTGCTGTGAGGT 59.985 33.333 33.75 20.05 46.34 3.85
168 171 6.319141 AGAAATTTCTTGCTGTGAGGTTAC 57.681 37.500 15.11 0.00 32.55 2.50
173 176 0.400213 TTGCTGTGAGGTTACCAGGG 59.600 55.000 3.51 0.00 0.00 4.45
174 177 0.766674 TGCTGTGAGGTTACCAGGGT 60.767 55.000 3.51 0.00 0.00 4.34
175 178 1.272807 GCTGTGAGGTTACCAGGGTA 58.727 55.000 3.51 0.00 0.00 3.69
176 179 1.626825 GCTGTGAGGTTACCAGGGTAA 59.373 52.381 3.51 6.82 38.14 2.85
209 212 9.817365 CAGTGCAGTAATGCAGATTTATTATAC 57.183 33.333 19.62 1.89 46.32 1.47
210 213 9.784531 AGTGCAGTAATGCAGATTTATTATACT 57.215 29.630 19.62 4.39 46.32 2.12
255 262 3.260380 TCCCGCAAATTCATTCAACCAAT 59.740 39.130 0.00 0.00 0.00 3.16
287 294 4.910195 TCACATCATTGCTACCAAGAACT 58.090 39.130 0.00 0.00 33.80 3.01
305 313 9.546428 CCAAGAACTTGATAAAATGAAAACCTT 57.454 29.630 14.99 0.00 42.93 3.50
309 317 7.004555 ACTTGATAAAATGAAAACCTTCCCC 57.995 36.000 0.00 0.00 0.00 4.81
313 321 4.974645 AAAATGAAAACCTTCCCCTTCC 57.025 40.909 0.00 0.00 0.00 3.46
314 322 3.923273 AATGAAAACCTTCCCCTTCCT 57.077 42.857 0.00 0.00 0.00 3.36
315 323 2.971901 TGAAAACCTTCCCCTTCCTC 57.028 50.000 0.00 0.00 0.00 3.71
316 324 2.428901 TGAAAACCTTCCCCTTCCTCT 58.571 47.619 0.00 0.00 0.00 3.69
317 325 2.108250 TGAAAACCTTCCCCTTCCTCTG 59.892 50.000 0.00 0.00 0.00 3.35
320 328 2.133858 ACCTTCCCCTTCCTCTGAAA 57.866 50.000 0.00 0.00 0.00 2.69
321 329 2.428901 ACCTTCCCCTTCCTCTGAAAA 58.571 47.619 0.00 0.00 0.00 2.29
323 331 3.402708 ACCTTCCCCTTCCTCTGAAAATT 59.597 43.478 0.00 0.00 0.00 1.82
324 332 4.140686 ACCTTCCCCTTCCTCTGAAAATTT 60.141 41.667 0.00 0.00 0.00 1.82
325 333 4.840680 CCTTCCCCTTCCTCTGAAAATTTT 59.159 41.667 2.28 2.28 0.00 1.82
326 334 5.047021 CCTTCCCCTTCCTCTGAAAATTTTC 60.047 44.000 21.60 21.60 37.69 2.29
327 335 5.339423 TCCCCTTCCTCTGAAAATTTTCT 57.661 39.130 26.73 0.00 38.02 2.52
328 336 6.463053 TCCCCTTCCTCTGAAAATTTTCTA 57.537 37.500 26.73 16.19 38.02 2.10
329 337 6.246163 TCCCCTTCCTCTGAAAATTTTCTAC 58.754 40.000 26.73 6.79 38.02 2.59
330 338 5.419155 CCCCTTCCTCTGAAAATTTTCTACC 59.581 44.000 26.73 6.46 38.02 3.18
331 339 5.419155 CCCTTCCTCTGAAAATTTTCTACCC 59.581 44.000 26.73 6.12 38.02 3.69
332 340 6.249192 CCTTCCTCTGAAAATTTTCTACCCT 58.751 40.000 26.73 0.00 38.02 4.34
333 341 7.402862 CCTTCCTCTGAAAATTTTCTACCCTA 58.597 38.462 26.73 8.87 38.02 3.53
334 342 8.055790 CCTTCCTCTGAAAATTTTCTACCCTAT 58.944 37.037 26.73 0.00 38.02 2.57
335 343 9.467796 CTTCCTCTGAAAATTTTCTACCCTATT 57.532 33.333 26.73 0.00 38.02 1.73
336 344 9.462606 TTCCTCTGAAAATTTTCTACCCTATTC 57.537 33.333 26.73 2.84 38.02 1.75
337 345 8.053355 TCCTCTGAAAATTTTCTACCCTATTCC 58.947 37.037 26.73 2.36 38.02 3.01
338 346 8.055790 CCTCTGAAAATTTTCTACCCTATTCCT 58.944 37.037 26.73 0.00 38.02 3.36
368 376 3.899052 TTCTACCCTATGAACCAACGG 57.101 47.619 0.00 0.00 0.00 4.44
369 377 3.104519 TCTACCCTATGAACCAACGGA 57.895 47.619 0.00 0.00 0.00 4.69
370 378 3.028850 TCTACCCTATGAACCAACGGAG 58.971 50.000 0.00 0.00 0.00 4.63
371 379 0.909623 ACCCTATGAACCAACGGAGG 59.090 55.000 0.00 0.00 0.00 4.30
372 380 0.463833 CCCTATGAACCAACGGAGGC 60.464 60.000 0.00 0.00 0.00 4.70
373 381 0.541863 CCTATGAACCAACGGAGGCT 59.458 55.000 0.00 0.00 0.00 4.58
374 382 1.760613 CCTATGAACCAACGGAGGCTA 59.239 52.381 0.00 0.00 0.00 3.93
375 383 2.169769 CCTATGAACCAACGGAGGCTAA 59.830 50.000 0.00 0.00 0.00 3.09
376 384 2.109425 ATGAACCAACGGAGGCTAAC 57.891 50.000 0.00 0.00 0.00 2.34
377 385 0.759959 TGAACCAACGGAGGCTAACA 59.240 50.000 0.00 0.00 0.00 2.41
378 386 1.270625 TGAACCAACGGAGGCTAACAG 60.271 52.381 0.00 0.00 0.00 3.16
379 387 0.763035 AACCAACGGAGGCTAACAGT 59.237 50.000 0.00 0.00 0.00 3.55
380 388 0.763035 ACCAACGGAGGCTAACAGTT 59.237 50.000 0.00 0.00 0.00 3.16
381 389 1.270678 ACCAACGGAGGCTAACAGTTC 60.271 52.381 0.00 0.00 0.00 3.01
385 393 1.002087 ACGGAGGCTAACAGTTCCAAG 59.998 52.381 0.00 0.00 0.00 3.61
387 395 2.550208 CGGAGGCTAACAGTTCCAAGTT 60.550 50.000 0.00 0.00 0.00 2.66
389 397 2.737252 GAGGCTAACAGTTCCAAGTTCG 59.263 50.000 0.00 0.00 0.00 3.95
405 413 5.682862 CCAAGTTCGAGTTCAAGTTCAAATG 59.317 40.000 0.00 0.00 0.00 2.32
408 416 7.264373 AGTTCGAGTTCAAGTTCAAATGAAT 57.736 32.000 0.00 0.00 37.82 2.57
422 430 5.716094 TCAAATGAATCATTGAGCAACAGG 58.284 37.500 9.47 0.00 34.04 4.00
425 433 6.446781 AATGAATCATTGAGCAACAGGTAG 57.553 37.500 7.79 0.00 32.39 3.18
426 434 3.691118 TGAATCATTGAGCAACAGGTAGC 59.309 43.478 0.00 0.00 0.00 3.58
438 446 2.504367 ACAGGTAGCCACACAATTGAC 58.496 47.619 13.59 0.00 0.00 3.18
444 452 4.083484 GGTAGCCACACAATTGACAAGTAC 60.083 45.833 13.59 6.31 0.00 2.73
452 460 7.255451 CCACACAATTGACAAGTACTGGTATTT 60.255 37.037 13.59 0.00 0.00 1.40
455 463 7.001674 ACAATTGACAAGTACTGGTATTTGGA 58.998 34.615 13.59 6.33 37.17 3.53
457 465 8.522830 CAATTGACAAGTACTGGTATTTGGAAT 58.477 33.333 1.89 12.00 37.17 3.01
458 466 7.681939 TTGACAAGTACTGGTATTTGGAATC 57.318 36.000 1.89 8.54 37.17 2.52
461 469 7.888021 TGACAAGTACTGGTATTTGGAATCAAT 59.112 33.333 1.89 0.00 37.17 2.57
465 473 8.281212 AGTACTGGTATTTGGAATCAATCAAC 57.719 34.615 0.00 0.00 32.28 3.18
466 474 8.109634 AGTACTGGTATTTGGAATCAATCAACT 58.890 33.333 0.00 0.00 32.28 3.16
470 478 6.038161 TGGTATTTGGAATCAATCAACTAGCG 59.962 38.462 0.00 0.00 32.75 4.26
473 481 2.938451 TGGAATCAATCAACTAGCGCTG 59.062 45.455 22.90 12.81 0.00 5.18
475 483 1.303309 ATCAATCAACTAGCGCTGGC 58.697 50.000 22.90 0.00 40.37 4.85
485 493 1.265635 CTAGCGCTGGCAGAGTAGTAG 59.734 57.143 22.90 13.31 43.41 2.57
714 723 2.650116 CGTCTGACTCTGGTGGGGG 61.650 68.421 6.21 0.00 0.00 5.40
732 741 1.511613 GGATCAGGGGAGGAACATCA 58.488 55.000 0.00 0.00 0.00 3.07
769 779 3.455469 GGCTGGAGCATGGGCAAC 61.455 66.667 0.20 0.00 44.61 4.17
770 780 2.362120 GCTGGAGCATGGGCAACT 60.362 61.111 0.00 0.00 44.61 3.16
771 781 2.707849 GCTGGAGCATGGGCAACTG 61.708 63.158 0.00 0.00 44.61 3.16
772 782 1.001764 CTGGAGCATGGGCAACTGA 60.002 57.895 0.00 0.00 44.61 3.41
773 783 1.303561 TGGAGCATGGGCAACTGAC 60.304 57.895 0.00 0.00 44.61 3.51
774 784 1.303561 GGAGCATGGGCAACTGACA 60.304 57.895 0.00 0.00 44.61 3.58
775 785 1.310933 GGAGCATGGGCAACTGACAG 61.311 60.000 0.00 0.00 44.61 3.51
776 786 0.321919 GAGCATGGGCAACTGACAGA 60.322 55.000 10.08 0.00 44.61 3.41
777 787 0.607489 AGCATGGGCAACTGACAGAC 60.607 55.000 10.08 0.00 44.61 3.51
778 788 0.890542 GCATGGGCAACTGACAGACA 60.891 55.000 10.08 0.59 40.72 3.41
779 789 1.830279 CATGGGCAACTGACAGACAT 58.170 50.000 10.08 2.92 0.00 3.06
780 790 2.165167 CATGGGCAACTGACAGACATT 58.835 47.619 10.08 0.00 0.00 2.71
781 791 1.896220 TGGGCAACTGACAGACATTC 58.104 50.000 10.08 0.00 0.00 2.67
782 792 1.142667 TGGGCAACTGACAGACATTCA 59.857 47.619 10.08 0.00 0.00 2.57
783 793 2.224843 TGGGCAACTGACAGACATTCAT 60.225 45.455 10.08 0.00 0.00 2.57
809 823 4.715523 GCACCCGCAGCCCAGTAA 62.716 66.667 0.00 0.00 38.36 2.24
821 835 0.822121 CCCAGTAATTTAGGCCCGGC 60.822 60.000 0.00 0.00 0.00 6.13
855 874 1.154221 GCCGATAGAGGAGAGGGGT 59.846 63.158 0.00 0.00 39.76 4.95
924 947 0.318762 GAGCTATCATCCCACGGACC 59.681 60.000 0.00 0.00 32.98 4.46
925 948 0.398522 AGCTATCATCCCACGGACCA 60.399 55.000 0.00 0.00 32.98 4.02
926 949 0.034059 GCTATCATCCCACGGACCAG 59.966 60.000 0.00 0.00 32.98 4.00
973 999 4.681978 GCCGCGGAGACCACAACT 62.682 66.667 33.48 0.00 0.00 3.16
984 1010 2.773458 CCACAACTGGTCCTAGGGT 58.227 57.895 9.46 0.00 32.03 4.34
993 1019 2.500098 CTGGTCCTAGGGTTTCGATTCA 59.500 50.000 9.46 0.00 0.00 2.57
996 1022 2.937149 GTCCTAGGGTTTCGATTCAAGC 59.063 50.000 9.46 0.00 0.00 4.01
1083 1111 2.569404 GACCATCAAGAAGTGAGTCCCT 59.431 50.000 0.00 0.00 40.43 4.20
1096 1124 0.767060 AGTCCCTCGTTCCCCTTTGT 60.767 55.000 0.00 0.00 0.00 2.83
1120 1151 2.973419 TTTTCGTGGTTTCGTATGGC 57.027 45.000 0.00 0.00 0.00 4.40
1136 1171 4.247380 GCCGGAGCCCTGAGATGG 62.247 72.222 5.05 0.00 0.00 3.51
1154 1189 3.861263 GATTTGCGCCGGTCGGTC 61.861 66.667 17.73 4.34 38.94 4.79
1166 1204 0.531200 GGTCGGTCAGGTACAAGGAG 59.469 60.000 0.00 0.00 0.00 3.69
1280 1332 4.352039 GTGCTCGTTCTTGATCTAATCGA 58.648 43.478 0.00 0.00 0.00 3.59
1284 1336 5.116377 GCTCGTTCTTGATCTAATCGATGTC 59.884 44.000 0.00 0.00 30.84 3.06
1409 1461 2.665185 AGAACAAGGTCCGTGCGC 60.665 61.111 0.00 0.00 0.00 6.09
1421 1473 1.590525 CGTGCGCCGAATTAGCCTA 60.591 57.895 4.18 0.00 39.56 3.93
1433 1485 5.856455 CCGAATTAGCCTACTTTGTTGTTTG 59.144 40.000 0.00 0.00 0.00 2.93
1441 1493 7.033185 AGCCTACTTTGTTGTTTGTTTACTTG 58.967 34.615 0.00 0.00 0.00 3.16
1456 1510 1.145571 ACTTGTTACTGGAAGCCCCA 58.854 50.000 0.00 0.00 44.25 4.96
1466 1520 1.992557 TGGAAGCCCCAGTGTAATCTT 59.007 47.619 0.00 0.00 40.82 2.40
1469 1523 4.200092 GGAAGCCCCAGTGTAATCTTAAG 58.800 47.826 0.00 0.00 34.14 1.85
1499 1717 6.475402 CAAAGTATTTTGTGTTCACCAGAACC 59.525 38.462 2.68 0.00 44.75 3.62
1513 1731 3.454812 ACCAGAACCTGTCTTACAACTGT 59.545 43.478 0.00 0.00 32.70 3.55
1605 2045 5.356882 TTCTTATCGGCAAGTTTGAGTTG 57.643 39.130 0.00 0.00 0.00 3.16
1623 2090 5.046231 TGAGTTGTACCATTAGGCATGTGTA 60.046 40.000 0.00 0.00 39.06 2.90
1655 2122 6.260870 TGTGCAACGGTTAATGTATTCATT 57.739 33.333 2.93 2.93 42.94 2.57
1681 2163 3.762823 TCATTTGCTTGTGTCATGGCATA 59.237 39.130 1.89 0.00 34.59 3.14
1682 2164 3.853831 TTTGCTTGTGTCATGGCATAG 57.146 42.857 1.89 5.63 34.59 2.23
1683 2165 2.785540 TGCTTGTGTCATGGCATAGA 57.214 45.000 1.89 0.00 0.00 1.98
1688 2197 4.737054 CTTGTGTCATGGCATAGAAAACC 58.263 43.478 1.89 0.00 0.00 3.27
1760 2269 4.814224 ATGGCCAGGATAAAGTGGTTAT 57.186 40.909 13.05 0.00 36.10 1.89
1761 2270 5.922960 ATGGCCAGGATAAAGTGGTTATA 57.077 39.130 13.05 0.00 36.10 0.98
1762 2271 5.718801 TGGCCAGGATAAAGTGGTTATAA 57.281 39.130 0.00 0.00 36.10 0.98
1765 2274 7.228590 TGGCCAGGATAAAGTGGTTATAATAC 58.771 38.462 0.00 0.00 36.10 1.89
1769 2278 7.936847 CCAGGATAAAGTGGTTATAATACTGCA 59.063 37.037 6.22 0.00 32.26 4.41
1788 2297 9.765795 ATACTGCAATTAGATTTAGTCCACTAC 57.234 33.333 0.00 0.00 0.00 2.73
1825 2334 5.065731 GCTTTGCTAATGCTAGTGATGTTCT 59.934 40.000 0.00 0.00 40.48 3.01
1826 2335 6.426980 TTTGCTAATGCTAGTGATGTTCTG 57.573 37.500 0.00 0.00 40.48 3.02
1827 2336 4.445453 TGCTAATGCTAGTGATGTTCTGG 58.555 43.478 0.00 0.00 40.48 3.86
1829 2338 4.509600 GCTAATGCTAGTGATGTTCTGGTC 59.490 45.833 0.00 0.00 36.03 4.02
1830 2339 4.558226 AATGCTAGTGATGTTCTGGTCA 57.442 40.909 0.00 0.00 0.00 4.02
1831 2340 3.599730 TGCTAGTGATGTTCTGGTCAG 57.400 47.619 0.00 0.00 0.00 3.51
1832 2341 2.275318 GCTAGTGATGTTCTGGTCAGC 58.725 52.381 0.00 0.00 0.00 4.26
1833 2342 2.898705 CTAGTGATGTTCTGGTCAGCC 58.101 52.381 0.00 0.00 0.00 4.85
1984 2495 5.537188 TGTTTTGCTGTCAGTTGTCTTTTT 58.463 33.333 0.93 0.00 0.00 1.94
1993 2504 6.969366 TGTCAGTTGTCTTTTTGATATGTGG 58.031 36.000 0.00 0.00 0.00 4.17
2013 2524 8.725405 ATGTGGTATCGTTTTTCATGTGTATA 57.275 30.769 0.00 0.00 0.00 1.47
2044 2555 4.571984 GCACAATTCTTTGCTGAAAAACCT 59.428 37.500 0.00 0.00 36.22 3.50
2045 2556 5.752955 GCACAATTCTTTGCTGAAAAACCTA 59.247 36.000 0.00 0.00 36.22 3.08
2048 3815 5.789643 ATTCTTTGCTGAAAAACCTAGCA 57.210 34.783 0.00 0.00 44.92 3.49
2052 3820 3.302365 TGCTGAAAAACCTAGCATTGC 57.698 42.857 0.00 0.00 42.05 3.56
2091 3859 3.489738 GCATCACTGATTGTGTTATGGCC 60.490 47.826 0.00 0.00 46.27 5.36
2160 3929 2.230992 TCATGCCCAACAATTGCTGTAC 59.769 45.455 5.05 0.00 37.23 2.90
2170 3939 5.314923 ACAATTGCTGTACTATTTGCTGG 57.685 39.130 5.05 0.00 36.10 4.85
2172 3941 1.750193 TGCTGTACTATTTGCTGGGC 58.250 50.000 0.00 0.00 0.00 5.36
2178 3947 1.200519 ACTATTTGCTGGGCCGTCTA 58.799 50.000 0.00 0.00 0.00 2.59
2400 4178 3.526931 TCTGCCTCCTCGAATTACTTG 57.473 47.619 0.00 0.00 0.00 3.16
2562 4343 4.497006 GCAACTAGAATCAATTGCAGCGAT 60.497 41.667 0.00 0.00 45.38 4.58
2568 4349 8.408601 ACTAGAATCAATTGCAGCGATAATTTT 58.591 29.630 0.00 0.00 0.00 1.82
2587 4369 5.838531 TTTTGAAGTATGGGTTTGTTCGT 57.161 34.783 0.00 0.00 0.00 3.85
2601 4383 6.801862 GGGTTTGTTCGTTCATTAAAGATCAG 59.198 38.462 0.00 0.00 28.84 2.90
2665 4447 2.962859 AGTGGCACTCATTCCCTTTTT 58.037 42.857 15.88 0.00 0.00 1.94
2670 4452 2.162408 GCACTCATTCCCTTTTTCCGAG 59.838 50.000 0.00 0.00 0.00 4.63
2697 4489 5.356882 TGTTAGTTGATTTGCCTTCTTCG 57.643 39.130 0.00 0.00 0.00 3.79
2705 4497 1.757682 TTGCCTTCTTCGTTTGTGGT 58.242 45.000 0.00 0.00 0.00 4.16
2709 4501 2.093783 GCCTTCTTCGTTTGTGGTATCG 59.906 50.000 0.00 0.00 0.00 2.92
2739 4531 6.216662 TCCTTCCAAGGTGAATGAATAGGTAA 59.783 38.462 5.24 0.00 46.54 2.85
2741 4533 7.013655 CCTTCCAAGGTGAATGAATAGGTAATG 59.986 40.741 0.00 0.00 41.41 1.90
2758 4805 1.078637 TGCATGTGAGCAGAGCCTC 60.079 57.895 0.00 0.00 40.11 4.70
2790 4837 2.294512 TGCATATACTCTCTCCAGTGCG 59.705 50.000 0.00 0.00 34.28 5.34
2793 4840 2.130272 ATACTCTCTCCAGTGCGTCA 57.870 50.000 0.00 0.00 0.00 4.35
2802 4849 1.518056 CCAGTGCGTCAATTGTGCCT 61.518 55.000 18.23 13.30 0.00 4.75
2847 4916 1.429463 AGTTTCCTAGAAAGCGTGCG 58.571 50.000 0.00 0.00 0.00 5.34
2875 4944 5.888724 AGAATTCTCTATCTTCGACCACTGA 59.111 40.000 0.88 0.00 0.00 3.41
3014 5092 8.807667 AGAAAAACAAGTCAAATATGCTTCAG 57.192 30.769 0.00 0.00 0.00 3.02
3087 5167 3.118629 TCAGATGGCCAGTCAATAGTCAC 60.119 47.826 13.05 0.00 0.00 3.67
3092 5173 3.181445 TGGCCAGTCAATAGTCACTTTGT 60.181 43.478 0.00 0.00 0.00 2.83
3125 5206 9.984190 TTACCTTTTATGTTAAACATTGGGTTC 57.016 29.630 0.00 0.00 39.88 3.62
3130 5211 8.879342 TTTATGTTAAACATTGGGTTCAAGTG 57.121 30.769 0.00 0.00 39.88 3.16
3147 5228 9.705290 GGTTCAAGTGTAATAATTTGAAACCAT 57.295 29.630 3.18 0.00 39.91 3.55
3253 5346 0.807496 CTTAAAGCTCAGCACCAGGC 59.193 55.000 0.00 0.00 45.30 4.85
3257 5350 2.282745 GCTCAGCACCAGGCCTTT 60.283 61.111 0.00 0.00 46.50 3.11
3267 5360 1.145738 ACCAGGCCTTTGAAGTGATGT 59.854 47.619 0.00 0.00 0.00 3.06
3296 5394 5.582269 ACACTGATAATGTGTACATGCTGTC 59.418 40.000 0.00 0.00 45.49 3.51
3425 5532 2.939103 AGTGACAGTTTCTGTTCACTGC 59.061 45.455 21.53 5.96 45.44 4.40
3436 5543 4.960938 TCTGTTCACTGCTATGTTCTGTT 58.039 39.130 0.00 0.00 0.00 3.16
3437 5544 5.368145 TCTGTTCACTGCTATGTTCTGTTT 58.632 37.500 0.00 0.00 0.00 2.83
3438 5545 6.521162 TCTGTTCACTGCTATGTTCTGTTTA 58.479 36.000 0.00 0.00 0.00 2.01
3439 5546 7.161404 TCTGTTCACTGCTATGTTCTGTTTAT 58.839 34.615 0.00 0.00 0.00 1.40
3440 5547 7.331934 TCTGTTCACTGCTATGTTCTGTTTATC 59.668 37.037 0.00 0.00 0.00 1.75
3513 5621 5.357742 TCTTATGCAGCACCAAGAATCTA 57.642 39.130 15.77 0.00 0.00 1.98
3538 5646 0.376852 CCATGCGATGGTACCAAACG 59.623 55.000 28.46 28.46 45.54 3.60
3588 5697 7.455953 TGATTTAGGATGGATATGAGTACTGCT 59.544 37.037 0.00 0.00 0.00 4.24
3597 5706 5.866633 GGATATGAGTACTGCTATGCTGAAC 59.133 44.000 0.00 0.00 0.00 3.18
3599 5708 2.831526 TGAGTACTGCTATGCTGAACCA 59.168 45.455 0.00 0.00 0.00 3.67
3642 5753 4.467198 AATCGTGTACCAACCTCCTTAG 57.533 45.455 0.00 0.00 0.00 2.18
3700 5812 5.471257 AGAAGAAAGTGTATCGTTGTCCTC 58.529 41.667 0.00 0.00 0.00 3.71
3763 5894 4.275936 GGTGTTGTTAATGTTGCAGACTCT 59.724 41.667 0.00 0.00 0.00 3.24
3807 5938 7.615582 ATGTAAGTGTTGTCATATGGTTCAG 57.384 36.000 2.13 0.00 0.00 3.02
3857 5996 2.756760 CTCAGTTGCCAAGCCAACATAT 59.243 45.455 7.65 0.00 45.73 1.78
3861 6000 3.324556 AGTTGCCAAGCCAACATATTGTT 59.675 39.130 7.65 0.00 45.73 2.83
3868 10021 3.356290 AGCCAACATATTGTTCTGGGTC 58.644 45.455 0.00 0.00 38.77 4.46
3925 16726 0.248134 GCTCAGTGTACTCGTAGCCG 60.248 60.000 11.30 0.00 0.00 5.52
3964 16765 8.446599 TCATGTATGACTCTCGTAGTGATAAA 57.553 34.615 0.00 0.00 36.25 1.40
4026 16830 0.179054 GGAAGCTCCCCCGATACAAC 60.179 60.000 0.00 0.00 0.00 3.32
4116 16922 6.714278 TGAACCTTTATTTGGTACTACCTCC 58.286 40.000 6.79 0.00 39.58 4.30
4136 16942 7.332213 CCTCCTTAAGTTACAGAGGTAGTAC 57.668 44.000 15.18 0.00 39.45 2.73
4186 16997 6.235664 ACCGTATTATAAAAGGTGGCATAGG 58.764 40.000 8.50 0.00 33.37 2.57
4213 17024 8.520351 GCAAACCTACTACCACATAATTTTCTT 58.480 33.333 0.00 0.00 0.00 2.52
4239 17050 7.052873 CACTGAAAATAGAATGGAGGAGACAT 58.947 38.462 0.00 0.00 0.00 3.06
4241 17052 6.359804 TGAAAATAGAATGGAGGAGACATGG 58.640 40.000 0.00 0.00 0.00 3.66
4272 17083 3.118112 AGAGAGTTTATCACCATGCCCTG 60.118 47.826 0.00 0.00 0.00 4.45
4364 17176 1.678627 CCAGCTCGTAGTAGCATGACT 59.321 52.381 0.00 0.00 45.30 3.41
4382 17194 0.940126 CTGCACCTGTTGACTCACAC 59.060 55.000 0.00 0.00 0.00 3.82
4446 17258 2.033424 TGTGAGATAACGATCTGCCTCG 59.967 50.000 0.00 0.00 42.80 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.108776 CGCTAGCCACTGGTAGGTTA 58.891 55.000 9.66 0.00 41.79 2.85
29 30 1.000019 TCGCTAGCCACTGGTAGGT 60.000 57.895 9.66 0.00 41.79 3.08
71 74 4.947388 TGCTGTTCAAGATAATTACCACCC 59.053 41.667 0.00 0.00 0.00 4.61
88 91 1.097547 AAGCACGCACTCTTGCTGTT 61.098 50.000 0.00 0.00 45.57 3.16
90 93 1.082300 CAAGCACGCACTCTTGCTG 60.082 57.895 0.00 0.00 45.57 4.41
96 99 1.226746 AAACTACCAAGCACGCACTC 58.773 50.000 0.00 0.00 0.00 3.51
99 102 1.746220 ACAAAAACTACCAAGCACGCA 59.254 42.857 0.00 0.00 0.00 5.24
100 103 2.485266 ACAAAAACTACCAAGCACGC 57.515 45.000 0.00 0.00 0.00 5.34
101 104 2.533942 GCAACAAAAACTACCAAGCACG 59.466 45.455 0.00 0.00 0.00 5.34
109 112 5.971792 GTCTTCTCCTTGCAACAAAAACTAC 59.028 40.000 0.00 0.00 0.00 2.73
114 117 4.704540 TCAAGTCTTCTCCTTGCAACAAAA 59.295 37.500 0.00 0.00 39.30 2.44
165 168 5.131308 TGCACTGCTATTATTACCCTGGTAA 59.869 40.000 11.01 11.01 43.56 2.85
168 171 4.067896 CTGCACTGCTATTATTACCCTGG 58.932 47.826 1.98 0.00 0.00 4.45
210 213 9.398538 GGGACACCATTTTATACACAAATACTA 57.601 33.333 0.00 0.00 36.50 1.82
211 214 7.066525 CGGGACACCATTTTATACACAAATACT 59.933 37.037 0.00 0.00 36.13 2.12
212 215 7.190871 CGGGACACCATTTTATACACAAATAC 58.809 38.462 0.00 0.00 36.13 1.89
220 223 4.705337 TTTGCGGGACACCATTTTATAC 57.295 40.909 0.00 0.00 36.13 1.47
222 225 4.221703 TGAATTTGCGGGACACCATTTTAT 59.778 37.500 0.00 0.00 36.13 1.40
230 233 2.986479 GTTGAATGAATTTGCGGGACAC 59.014 45.455 0.00 0.00 0.00 3.67
255 262 4.795469 AGCAATGATGTGATATGGGTCAA 58.205 39.130 0.00 0.00 0.00 3.18
287 294 7.256511 GGAAGGGGAAGGTTTTCATTTTATCAA 60.257 37.037 0.00 0.00 34.90 2.57
305 313 5.339423 AGAAAATTTTCAGAGGAAGGGGA 57.661 39.130 28.00 0.00 39.61 4.81
309 317 9.467796 AATAGGGTAGAAAATTTTCAGAGGAAG 57.532 33.333 28.00 0.00 39.61 3.46
345 353 5.005094 CCGTTGGTTCATAGGGTAGAAAAA 58.995 41.667 0.00 0.00 0.00 1.94
346 354 4.286549 TCCGTTGGTTCATAGGGTAGAAAA 59.713 41.667 0.00 0.00 0.00 2.29
347 355 3.839490 TCCGTTGGTTCATAGGGTAGAAA 59.161 43.478 0.00 0.00 0.00 2.52
348 356 3.443052 TCCGTTGGTTCATAGGGTAGAA 58.557 45.455 0.00 0.00 0.00 2.10
349 357 3.028850 CTCCGTTGGTTCATAGGGTAGA 58.971 50.000 0.00 0.00 0.00 2.59
350 358 2.102588 CCTCCGTTGGTTCATAGGGTAG 59.897 54.545 0.00 0.00 0.00 3.18
351 359 2.112998 CCTCCGTTGGTTCATAGGGTA 58.887 52.381 0.00 0.00 0.00 3.69
352 360 0.909623 CCTCCGTTGGTTCATAGGGT 59.090 55.000 0.00 0.00 0.00 4.34
353 361 0.463833 GCCTCCGTTGGTTCATAGGG 60.464 60.000 0.00 0.00 0.00 3.53
354 362 0.541863 AGCCTCCGTTGGTTCATAGG 59.458 55.000 0.00 0.00 0.00 2.57
355 363 3.195661 GTTAGCCTCCGTTGGTTCATAG 58.804 50.000 0.00 0.00 0.00 2.23
356 364 2.568062 TGTTAGCCTCCGTTGGTTCATA 59.432 45.455 0.00 0.00 0.00 2.15
357 365 1.349688 TGTTAGCCTCCGTTGGTTCAT 59.650 47.619 0.00 0.00 0.00 2.57
358 366 0.759959 TGTTAGCCTCCGTTGGTTCA 59.240 50.000 0.00 0.00 0.00 3.18
359 367 1.270678 ACTGTTAGCCTCCGTTGGTTC 60.271 52.381 0.00 0.00 0.00 3.62
360 368 0.763035 ACTGTTAGCCTCCGTTGGTT 59.237 50.000 0.00 0.00 0.00 3.67
361 369 0.763035 AACTGTTAGCCTCCGTTGGT 59.237 50.000 0.00 0.00 0.00 3.67
362 370 1.439679 GAACTGTTAGCCTCCGTTGG 58.560 55.000 0.00 0.00 0.00 3.77
363 371 1.270625 TGGAACTGTTAGCCTCCGTTG 60.271 52.381 0.00 0.00 0.00 4.10
364 372 1.053424 TGGAACTGTTAGCCTCCGTT 58.947 50.000 0.00 0.00 0.00 4.44
365 373 1.002087 CTTGGAACTGTTAGCCTCCGT 59.998 52.381 0.00 0.00 0.00 4.69
366 374 1.002087 ACTTGGAACTGTTAGCCTCCG 59.998 52.381 0.00 0.00 0.00 4.63
367 375 2.861147 ACTTGGAACTGTTAGCCTCC 57.139 50.000 0.00 0.00 0.00 4.30
368 376 2.737252 CGAACTTGGAACTGTTAGCCTC 59.263 50.000 0.00 0.00 0.00 4.70
369 377 2.367567 TCGAACTTGGAACTGTTAGCCT 59.632 45.455 0.00 0.00 0.00 4.58
370 378 2.737252 CTCGAACTTGGAACTGTTAGCC 59.263 50.000 0.00 0.00 0.00 3.93
371 379 3.391049 ACTCGAACTTGGAACTGTTAGC 58.609 45.455 0.00 0.00 0.00 3.09
372 380 5.047847 TGAACTCGAACTTGGAACTGTTAG 58.952 41.667 0.00 0.00 0.00 2.34
373 381 5.013568 TGAACTCGAACTTGGAACTGTTA 57.986 39.130 0.00 0.00 0.00 2.41
374 382 3.869065 TGAACTCGAACTTGGAACTGTT 58.131 40.909 0.00 0.00 0.00 3.16
375 383 3.536956 TGAACTCGAACTTGGAACTGT 57.463 42.857 0.00 0.00 0.00 3.55
376 384 3.871594 ACTTGAACTCGAACTTGGAACTG 59.128 43.478 0.00 0.00 0.00 3.16
377 385 4.138487 ACTTGAACTCGAACTTGGAACT 57.862 40.909 0.00 0.00 0.00 3.01
378 386 4.331717 TGAACTTGAACTCGAACTTGGAAC 59.668 41.667 0.00 0.00 0.00 3.62
379 387 4.509616 TGAACTTGAACTCGAACTTGGAA 58.490 39.130 0.00 0.00 0.00 3.53
380 388 4.131649 TGAACTTGAACTCGAACTTGGA 57.868 40.909 0.00 0.00 0.00 3.53
381 389 4.875544 TTGAACTTGAACTCGAACTTGG 57.124 40.909 0.00 0.00 0.00 3.61
385 393 7.132213 TGATTCATTTGAACTTGAACTCGAAC 58.868 34.615 0.00 0.00 36.80 3.95
387 395 6.859420 TGATTCATTTGAACTTGAACTCGA 57.141 33.333 0.00 0.00 36.80 4.04
389 397 9.125906 CTCAATGATTCATTTGAACTTGAACTC 57.874 33.333 9.19 1.04 36.80 3.01
405 413 3.065925 GGCTACCTGTTGCTCAATGATTC 59.934 47.826 3.88 0.00 0.00 2.52
408 416 1.350684 TGGCTACCTGTTGCTCAATGA 59.649 47.619 3.88 0.00 0.00 2.57
422 430 4.755123 AGTACTTGTCAATTGTGTGGCTAC 59.245 41.667 5.13 0.00 0.00 3.58
425 433 3.304659 CCAGTACTTGTCAATTGTGTGGC 60.305 47.826 5.13 0.45 0.00 5.01
426 434 3.882888 ACCAGTACTTGTCAATTGTGTGG 59.117 43.478 5.13 4.84 0.00 4.17
438 446 8.279970 TGATTGATTCCAAATACCAGTACTTG 57.720 34.615 0.00 0.00 35.67 3.16
444 452 7.420800 GCTAGTTGATTGATTCCAAATACCAG 58.579 38.462 0.00 0.00 35.67 4.00
452 460 2.938451 CAGCGCTAGTTGATTGATTCCA 59.062 45.455 10.99 0.00 0.00 3.53
455 463 1.672881 GCCAGCGCTAGTTGATTGATT 59.327 47.619 10.99 0.00 0.00 2.57
457 465 0.036483 TGCCAGCGCTAGTTGATTGA 60.036 50.000 10.99 0.00 35.36 2.57
458 466 0.376152 CTGCCAGCGCTAGTTGATTG 59.624 55.000 10.99 0.00 35.36 2.67
461 469 1.216444 CTCTGCCAGCGCTAGTTGA 59.784 57.895 10.99 5.87 35.36 3.18
465 473 1.265635 CTACTACTCTGCCAGCGCTAG 59.734 57.143 10.99 3.03 35.36 3.42
466 474 1.309950 CTACTACTCTGCCAGCGCTA 58.690 55.000 10.99 0.00 35.36 4.26
470 478 3.444388 AGTTGTACTACTACTCTGCCAGC 59.556 47.826 8.27 0.00 28.27 4.85
473 481 5.640189 TTCAGTTGTACTACTACTCTGCC 57.360 43.478 9.68 0.00 32.07 4.85
475 483 7.251994 GTCCATTCAGTTGTACTACTACTCTG 58.748 42.308 9.68 5.80 32.07 3.35
485 493 1.990563 CGTCGGTCCATTCAGTTGTAC 59.009 52.381 0.00 0.00 0.00 2.90
559 567 2.640302 GGCTGCTCTGACGGTCTCA 61.640 63.158 9.88 1.92 0.00 3.27
616 624 2.202610 CGCAATCTCCGTCGAGCA 60.203 61.111 0.00 0.00 35.94 4.26
706 714 3.632049 TCCCCTGATCCCCCACCA 61.632 66.667 0.00 0.00 0.00 4.17
714 723 1.202580 CGTGATGTTCCTCCCCTGATC 60.203 57.143 0.00 0.00 0.00 2.92
769 779 4.634883 CCCTTTCTGATGAATGTCTGTCAG 59.365 45.833 0.00 0.00 39.47 3.51
770 780 4.582869 CCCTTTCTGATGAATGTCTGTCA 58.417 43.478 0.00 0.00 31.56 3.58
771 781 3.376546 GCCCTTTCTGATGAATGTCTGTC 59.623 47.826 0.00 0.00 31.56 3.51
772 782 3.245016 TGCCCTTTCTGATGAATGTCTGT 60.245 43.478 0.00 0.00 31.56 3.41
773 783 3.128242 GTGCCCTTTCTGATGAATGTCTG 59.872 47.826 0.00 0.00 31.56 3.51
774 784 3.350833 GTGCCCTTTCTGATGAATGTCT 58.649 45.455 0.00 0.00 31.56 3.41
775 785 2.424956 GGTGCCCTTTCTGATGAATGTC 59.575 50.000 0.00 0.00 31.56 3.06
776 786 2.450476 GGTGCCCTTTCTGATGAATGT 58.550 47.619 0.00 0.00 31.56 2.71
777 787 1.753073 GGGTGCCCTTTCTGATGAATG 59.247 52.381 0.00 0.00 31.56 2.67
778 788 1.683011 CGGGTGCCCTTTCTGATGAAT 60.683 52.381 5.64 0.00 31.56 2.57
779 789 0.322456 CGGGTGCCCTTTCTGATGAA 60.322 55.000 5.64 0.00 0.00 2.57
780 790 1.299648 CGGGTGCCCTTTCTGATGA 59.700 57.895 5.64 0.00 0.00 2.92
781 791 2.409870 GCGGGTGCCCTTTCTGATG 61.410 63.158 5.64 0.00 33.98 3.07
782 792 2.044946 GCGGGTGCCCTTTCTGAT 60.045 61.111 5.64 0.00 33.98 2.90
783 793 3.551496 CTGCGGGTGCCCTTTCTGA 62.551 63.158 5.64 0.00 41.78 3.27
800 814 0.182775 CGGGCCTAAATTACTGGGCT 59.817 55.000 0.84 0.00 44.54 5.19
833 847 1.238625 CCTCTCCTCTATCGGCGTCC 61.239 65.000 6.85 0.00 0.00 4.79
855 874 1.912220 CGGTATCTCCTGGGCCAAA 59.088 57.895 8.04 0.00 0.00 3.28
958 981 2.738521 CCAGTTGTGGTCTCCGCG 60.739 66.667 0.00 0.00 39.30 6.46
971 997 2.249309 ATCGAAACCCTAGGACCAGT 57.751 50.000 11.48 0.00 0.00 4.00
973 999 2.542550 TGAATCGAAACCCTAGGACCA 58.457 47.619 11.48 0.00 0.00 4.02
977 1003 2.939103 CTGCTTGAATCGAAACCCTAGG 59.061 50.000 0.06 0.06 0.00 3.02
984 1010 2.368439 CCCATCCTGCTTGAATCGAAA 58.632 47.619 0.00 0.00 0.00 3.46
993 1019 0.909610 TCGACTTCCCCATCCTGCTT 60.910 55.000 0.00 0.00 0.00 3.91
996 1022 1.137872 CTCTTCGACTTCCCCATCCTG 59.862 57.143 0.00 0.00 0.00 3.86
1120 1151 3.554342 CCCATCTCAGGGCTCCGG 61.554 72.222 0.00 0.00 43.10 5.14
1153 1188 1.938585 CACCTCCTCCTTGTACCTGA 58.061 55.000 0.00 0.00 0.00 3.86
1154 1189 0.250513 GCACCTCCTCCTTGTACCTG 59.749 60.000 0.00 0.00 0.00 4.00
1181 1219 1.215647 CTCGGTGTCCTTCTTCCGG 59.784 63.158 0.00 0.00 42.71 5.14
1250 1302 0.537371 AAGAACGAGCACCCCCAAAG 60.537 55.000 0.00 0.00 0.00 2.77
1280 1332 4.827087 CGGCCTGCGAGCAGACAT 62.827 66.667 24.93 0.00 46.30 3.06
1363 1415 5.241506 GGAGAAATTGATGAAGTTGGTGTCA 59.758 40.000 0.00 0.00 0.00 3.58
1409 1461 5.622770 AACAACAAAGTAGGCTAATTCGG 57.377 39.130 7.77 6.28 0.00 4.30
1421 1473 9.187455 CAGTAACAAGTAAACAAACAACAAAGT 57.813 29.630 0.00 0.00 0.00 2.66
1433 1485 3.504906 GGGGCTTCCAGTAACAAGTAAAC 59.495 47.826 0.00 0.00 35.00 2.01
1499 1717 4.209288 CCAAACGAGACAGTTGTAAGACAG 59.791 45.833 0.00 0.00 34.14 3.51
1513 1731 0.750249 TGTCTGCTGTCCAAACGAGA 59.250 50.000 0.00 0.00 0.00 4.04
1590 2030 1.944024 TGGTACAACTCAAACTTGCCG 59.056 47.619 0.00 0.00 31.92 5.69
1605 2045 6.158023 ACTAGTACACATGCCTAATGGTAC 57.842 41.667 0.00 0.00 40.94 3.34
1623 2090 2.543777 ACCGTTGCACATGAACTAGT 57.456 45.000 0.00 0.00 0.00 2.57
1655 2122 5.170021 GCCATGACACAAGCAAATGAAATA 58.830 37.500 0.00 0.00 0.00 1.40
1681 2163 9.322773 GGTAATAATTAGTAGCTTCGGTTTTCT 57.677 33.333 13.37 0.00 0.00 2.52
1682 2164 9.101655 TGGTAATAATTAGTAGCTTCGGTTTTC 57.898 33.333 19.35 0.00 0.00 2.29
1683 2165 9.106070 CTGGTAATAATTAGTAGCTTCGGTTTT 57.894 33.333 19.35 0.00 0.00 2.43
1762 2271 9.765795 GTAGTGGACTAAATCTAATTGCAGTAT 57.234 33.333 0.00 0.00 0.00 2.12
1765 2274 6.483640 GGGTAGTGGACTAAATCTAATTGCAG 59.516 42.308 0.00 0.00 0.00 4.41
1769 2278 7.184022 ACCAAGGGTAGTGGACTAAATCTAATT 59.816 37.037 0.00 0.00 39.62 1.40
1788 2297 2.381911 AGCAAAGCATATGACCAAGGG 58.618 47.619 6.97 0.00 0.00 3.95
1825 2334 1.367471 CAAGTCTGACGGCTGACCA 59.633 57.895 23.14 0.00 42.12 4.02
1826 2335 0.667792 GACAAGTCTGACGGCTGACC 60.668 60.000 23.14 5.66 42.12 4.02
1827 2336 0.315568 AGACAAGTCTGACGGCTGAC 59.684 55.000 19.79 19.79 41.65 3.51
1829 2338 1.269778 TGAAGACAAGTCTGACGGCTG 60.270 52.381 3.08 4.33 40.36 4.85
1830 2339 1.040646 TGAAGACAAGTCTGACGGCT 58.959 50.000 3.08 0.00 40.36 5.52
1831 2340 1.728971 CATGAAGACAAGTCTGACGGC 59.271 52.381 3.08 0.00 40.36 5.68
1832 2341 1.728971 GCATGAAGACAAGTCTGACGG 59.271 52.381 3.08 1.66 40.36 4.79
1833 2342 2.407090 TGCATGAAGACAAGTCTGACG 58.593 47.619 3.08 0.00 40.36 4.35
1893 2402 4.491676 CTTTCTCCAAATCCAACTGCATG 58.508 43.478 0.00 0.00 0.00 4.06
1984 2495 7.335673 ACACATGAAAAACGATACCACATATCA 59.664 33.333 0.00 0.00 39.94 2.15
2019 2530 5.163774 GGTTTTTCAGCAAAGAATTGTGCAA 60.164 36.000 7.80 0.00 43.42 4.08
2038 2549 5.264395 ACCTTCATAGCAATGCTAGGTTTT 58.736 37.500 23.53 3.25 44.66 2.43
2091 3859 5.418310 TTTGTCCTAACTTTTCAAGCTCG 57.582 39.130 0.00 0.00 0.00 5.03
2160 3929 2.037772 AGATAGACGGCCCAGCAAATAG 59.962 50.000 0.00 0.00 0.00 1.73
2170 3939 4.822026 AGCACAATTATAGATAGACGGCC 58.178 43.478 0.00 0.00 0.00 6.13
2172 3941 8.383619 GCAATTAGCACAATTATAGATAGACGG 58.616 37.037 0.00 0.00 44.79 4.79
2267 4043 4.024556 GCAATTCTGTGATACAGGGAATCG 60.025 45.833 8.91 0.00 45.94 3.34
2297 4073 3.306902 CAGCCTCTGGAACCTAGGA 57.693 57.895 17.98 0.00 31.64 2.94
2390 4168 8.425491 CACTCTAAGTACACAACAAGTAATTCG 58.575 37.037 0.00 0.00 32.73 3.34
2400 4178 4.868314 ACCTCCACTCTAAGTACACAAC 57.132 45.455 0.00 0.00 0.00 3.32
2453 4232 5.104900 AGGTAGTCCGCTAAATGAACAATCT 60.105 40.000 0.00 0.00 39.05 2.40
2552 4333 6.919662 CCATACTTCAAAATTATCGCTGCAAT 59.080 34.615 0.00 0.00 0.00 3.56
2562 4343 7.942990 ACGAACAAACCCATACTTCAAAATTA 58.057 30.769 0.00 0.00 0.00 1.40
2568 4349 4.452825 TGAACGAACAAACCCATACTTCA 58.547 39.130 0.00 0.00 0.00 3.02
2641 4423 0.244721 GGGAATGAGTGCCACTTTGC 59.755 55.000 0.00 0.00 37.76 3.68
2665 4447 4.884668 AATCAACTAACAACTCCTCGGA 57.115 40.909 0.00 0.00 0.00 4.55
2670 4452 5.241728 AGAAGGCAAATCAACTAACAACTCC 59.758 40.000 0.00 0.00 0.00 3.85
2697 4489 5.182380 TGGAAGGAATTTCGATACCACAAAC 59.818 40.000 0.00 0.00 36.62 2.93
2739 4531 0.464013 GAGGCTCTGCTCACATGCAT 60.464 55.000 7.40 0.00 42.48 3.96
2741 4533 0.392729 AAGAGGCTCTGCTCACATGC 60.393 55.000 19.53 0.00 0.00 4.06
2779 4826 1.462283 CACAATTGACGCACTGGAGAG 59.538 52.381 13.59 0.00 0.00 3.20
2781 4828 0.110056 GCACAATTGACGCACTGGAG 60.110 55.000 13.59 0.00 0.00 3.86
2818 4865 8.038944 ACGCTTTCTAGGAAACTTGTATTGATA 58.961 33.333 0.00 0.00 43.67 2.15
2821 4868 6.307155 CACGCTTTCTAGGAAACTTGTATTG 58.693 40.000 0.00 0.00 43.67 1.90
2842 4911 2.561733 TAGAGAATTCTGACCGCACG 57.438 50.000 14.00 0.00 34.79 5.34
2847 4916 5.067936 TGGTCGAAGATAGAGAATTCTGACC 59.932 44.000 21.74 21.74 41.56 4.02
2988 5064 9.897744 CTGAAGCATATTTGACTTGTTTTTCTA 57.102 29.630 0.00 0.00 0.00 2.10
2990 5066 8.579682 ACTGAAGCATATTTGACTTGTTTTTC 57.420 30.769 0.00 0.00 0.00 2.29
2994 5071 6.421801 GCAAACTGAAGCATATTTGACTTGTT 59.578 34.615 0.00 0.00 34.62 2.83
2996 5073 6.154445 AGCAAACTGAAGCATATTTGACTTG 58.846 36.000 0.00 0.00 34.62 3.16
3008 5086 4.985044 TTACTTACGAGCAAACTGAAGC 57.015 40.909 0.00 0.00 0.00 3.86
3014 5092 7.592439 AAGAAGGTATTACTTACGAGCAAAC 57.408 36.000 0.00 0.00 0.00 2.93
3066 5146 3.118482 AGTGACTATTGACTGGCCATCTG 60.118 47.826 5.51 0.00 0.00 2.90
3074 5154 8.539770 ACATAGAACAAAGTGACTATTGACTG 57.460 34.615 12.25 6.40 0.00 3.51
3151 5232 4.863491 AGCATTTGTGCTGTTACAGAAAG 58.137 39.130 17.40 0.00 44.44 2.62
3253 5346 5.180117 CAGTGTAAGGACATCACTTCAAAGG 59.820 44.000 0.00 0.00 39.89 3.11
3257 5350 5.745312 ATCAGTGTAAGGACATCACTTCA 57.255 39.130 0.00 0.00 39.89 3.02
3296 5394 0.609131 ACCAGGAACCTGCCAAATCG 60.609 55.000 14.66 2.97 42.35 3.34
3436 5543 7.731054 ACCACAGCCAAAACAAAATAAGATAA 58.269 30.769 0.00 0.00 0.00 1.75
3437 5544 7.296628 ACCACAGCCAAAACAAAATAAGATA 57.703 32.000 0.00 0.00 0.00 1.98
3438 5545 6.173427 ACCACAGCCAAAACAAAATAAGAT 57.827 33.333 0.00 0.00 0.00 2.40
3439 5546 5.606348 ACCACAGCCAAAACAAAATAAGA 57.394 34.783 0.00 0.00 0.00 2.10
3440 5547 7.778470 TTTACCACAGCCAAAACAAAATAAG 57.222 32.000 0.00 0.00 0.00 1.73
3469 5576 0.176680 CCAGCGCATGAGTTAGGTCT 59.823 55.000 11.47 0.00 0.00 3.85
3538 5646 2.345760 CCTGGGCAAGTGTGATGGC 61.346 63.158 0.00 0.00 42.20 4.40
3588 5697 3.689347 ACAATCAGCTTGGTTCAGCATA 58.311 40.909 0.00 0.00 42.84 3.14
3597 5706 3.820467 TGAAGTGGTTACAATCAGCTTGG 59.180 43.478 0.00 0.00 39.30 3.61
3599 5708 6.463995 TTTTGAAGTGGTTACAATCAGCTT 57.536 33.333 0.00 0.00 0.00 3.74
3642 5753 5.064579 CCAAAATTTATGAAAACGATGCCCC 59.935 40.000 0.00 0.00 0.00 5.80
3700 5812 4.335315 TGGCTACAGTTCAGTTCAAAACAG 59.665 41.667 0.00 0.00 0.00 3.16
3857 5996 4.285863 ACAAAATCCAAGACCCAGAACAA 58.714 39.130 0.00 0.00 0.00 2.83
3861 6000 5.701224 AGTTTACAAAATCCAAGACCCAGA 58.299 37.500 0.00 0.00 0.00 3.86
3868 10021 9.831737 CAGAACAGATAGTTTACAAAATCCAAG 57.168 33.333 0.00 0.00 41.51 3.61
3975 16779 7.770366 TCAACTCCAGTTATCACTACAGTAA 57.230 36.000 0.00 0.00 36.32 2.24
3992 16796 1.202545 GCTTCCCCGTAGATCAACTCC 60.203 57.143 0.00 0.00 0.00 3.85
3993 16797 1.757699 AGCTTCCCCGTAGATCAACTC 59.242 52.381 0.00 0.00 0.00 3.01
4116 16922 9.355215 CATGTTGTACTACCTCTGTAACTTAAG 57.645 37.037 0.00 0.00 0.00 1.85
4136 16942 5.048154 TGGTTGGATGTGAATGTACATGTTG 60.048 40.000 9.63 0.00 41.15 3.33
4186 16997 6.769134 AAATTATGTGGTAGTAGGTTTGCC 57.231 37.500 0.00 0.00 0.00 4.52
4213 17024 6.213397 TGTCTCCTCCATTCTATTTTCAGTGA 59.787 38.462 0.00 0.00 0.00 3.41
4214 17025 6.409704 TGTCTCCTCCATTCTATTTTCAGTG 58.590 40.000 0.00 0.00 0.00 3.66
4239 17050 2.704190 AAACTCTCTGTCTCCCTCCA 57.296 50.000 0.00 0.00 0.00 3.86
4241 17052 4.098807 GGTGATAAACTCTCTGTCTCCCTC 59.901 50.000 0.00 0.00 0.00 4.30
4345 17157 2.725490 CAGTCATGCTACTACGAGCTG 58.275 52.381 0.00 0.00 43.27 4.24
4364 17176 0.541392 AGTGTGAGTCAACAGGTGCA 59.459 50.000 0.00 0.00 0.00 4.57
4368 17180 2.213499 GTTCCAGTGTGAGTCAACAGG 58.787 52.381 0.00 2.72 0.00 4.00
4382 17194 9.277783 CTCCTAAATTATTCTATGTGGTTCCAG 57.722 37.037 0.00 0.00 0.00 3.86
4446 17258 2.952310 ACAACAACAAGAGGGCTCTTTC 59.048 45.455 0.00 0.00 46.95 2.62


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

AutoCloner maintained by Alex Coulton.