Multiple sequence alignment - TraesCS5B01G347200

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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 TraesCS5B01G347200 chr5B 100.000 2435 0 0 1 2435 528580525 528578091 0.000000e+00 4497
1 TraesCS5B01G347200 chr5B 88.324 1593 105 27 359 1941 528586999 528585478 0.000000e+00 1836
2 TraesCS5B01G347200 chr5B 88.889 504 44 6 1938 2435 528585451 528584954 5.760000e-171 610
3 TraesCS5B01G347200 chr5B 83.721 344 34 9 1 331 528587331 528586997 3.040000e-79 305
4 TraesCS5B01G347200 chr5B 74.023 435 99 9 1000 1424 528539299 528539729 5.390000e-37 165
5 TraesCS5B01G347200 chr5D 94.076 1958 80 18 1 1941 435269069 435267131 0.000000e+00 2940
6 TraesCS5B01G347200 chr5D 87.469 1604 108 31 359 1941 435274681 435273150 0.000000e+00 1762
7 TraesCS5B01G347200 chr5D 93.227 502 25 5 1938 2435 435267104 435266608 0.000000e+00 730
8 TraesCS5B01G347200 chr5D 88.515 505 46 8 1938 2435 435273123 435272624 3.460000e-168 601
9 TraesCS5B01G347200 chr5D 83.432 338 39 7 7 331 435275012 435274679 5.090000e-77 298
10 TraesCS5B01G347200 chr5A 94.219 1851 84 14 1 1837 549206484 549204643 0.000000e+00 2804
11 TraesCS5B01G347200 chr5A 93.714 1543 72 13 411 1941 549211302 549209773 0.000000e+00 2289
12 TraesCS5B01G347200 chr5A 88.680 1599 112 34 359 1941 549215691 549214146 0.000000e+00 1886
13 TraesCS5B01G347200 chr5A 90.278 504 35 9 1938 2435 549209746 549209251 0.000000e+00 647
14 TraesCS5B01G347200 chr5A 88.492 504 47 7 1938 2435 549214119 549213621 1.250000e-167 599
15 TraesCS5B01G347200 chr5A 77.880 651 91 31 1835 2435 549204336 549203689 2.980000e-94 355
16 TraesCS5B01G347200 chr5A 84.024 338 37 7 7 331 549216022 549215689 2.350000e-80 309


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 TraesCS5B01G347200 chr5B 528578091 528580525 2434 True 4497.000000 4497 100.000000 1 2435 1 chr5B.!!$R1 2434
1 TraesCS5B01G347200 chr5B 528584954 528587331 2377 True 917.000000 1836 86.978000 1 2435 3 chr5B.!!$R2 2434
2 TraesCS5B01G347200 chr5D 435266608 435275012 8404 True 1266.200000 2940 89.343800 1 2435 5 chr5D.!!$R1 2434
3 TraesCS5B01G347200 chr5A 549203689 549216022 12333 True 1269.857143 2804 88.183857 1 2435 7 chr5A.!!$R1 2434

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
419 438 0.320771 AAGCAGCGACGAAATGGAGT 60.321 50.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 1682 0.245266 TGCACAAATCAGCATGCCAG 59.755 50.0 15.66 7.84 37.26 4.85 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
54 55 7.375053 GCTAAATGTTCTAGATAGGACTCAGG 58.625 42.308 0.00 0.00 32.86 3.86
59 60 1.892474 CTAGATAGGACTCAGGCAGCC 59.108 57.143 1.84 1.84 0.00 4.85
66 67 0.459489 GACTCAGGCAGCCAGTAGAG 59.541 60.000 15.80 16.58 0.00 2.43
96 106 4.411327 TGAACTTTGAAAGACGTTTGCAG 58.589 39.130 12.53 0.00 0.00 4.41
97 107 4.155099 TGAACTTTGAAAGACGTTTGCAGA 59.845 37.500 12.53 0.00 0.00 4.26
102 112 4.273005 TGAAAGACGTTTGCAGAAGTTC 57.727 40.909 0.00 0.00 0.00 3.01
106 116 4.278678 AGACGTTTGCAGAAGTTCAAAG 57.721 40.909 5.50 0.00 33.43 2.77
114 124 7.417612 GTTTGCAGAAGTTCAAAGTTAGATGA 58.582 34.615 5.50 0.00 33.43 2.92
119 129 8.394121 GCAGAAGTTCAAAGTTAGATGATTAGG 58.606 37.037 5.50 0.00 0.00 2.69
134 144 6.604795 AGATGATTAGGCATTGTTAAGCAAGT 59.395 34.615 5.54 0.00 40.86 3.16
135 145 7.775093 AGATGATTAGGCATTGTTAAGCAAGTA 59.225 33.333 5.54 0.00 40.86 2.24
137 150 7.930217 TGATTAGGCATTGTTAAGCAAGTATC 58.070 34.615 0.00 0.00 40.86 2.24
147 160 7.672983 TGTTAAGCAAGTATCCAGAAAGAAG 57.327 36.000 0.00 0.00 0.00 2.85
150 163 8.657729 GTTAAGCAAGTATCCAGAAAGAAGTAC 58.342 37.037 0.00 0.00 0.00 2.73
152 165 4.567159 GCAAGTATCCAGAAAGAAGTACGG 59.433 45.833 0.00 0.00 0.00 4.02
161 174 2.197283 AAGAAGTACGGACCTCTCGT 57.803 50.000 0.00 0.00 43.64 4.18
162 180 1.736612 AGAAGTACGGACCTCTCGTC 58.263 55.000 0.00 0.00 41.38 4.20
165 183 1.736612 AGTACGGACCTCTCGTCTTC 58.263 55.000 0.00 0.00 41.64 2.87
171 189 2.288273 CGGACCTCTCGTCTTCTGTTTT 60.288 50.000 0.00 0.00 41.64 2.43
172 190 3.060602 GGACCTCTCGTCTTCTGTTTTG 58.939 50.000 0.00 0.00 41.64 2.44
175 193 4.514401 ACCTCTCGTCTTCTGTTTTGTTT 58.486 39.130 0.00 0.00 0.00 2.83
176 194 4.332819 ACCTCTCGTCTTCTGTTTTGTTTG 59.667 41.667 0.00 0.00 0.00 2.93
177 195 4.332819 CCTCTCGTCTTCTGTTTTGTTTGT 59.667 41.667 0.00 0.00 0.00 2.83
179 197 6.249035 TCTCGTCTTCTGTTTTGTTTGTTT 57.751 33.333 0.00 0.00 0.00 2.83
180 198 6.674066 TCTCGTCTTCTGTTTTGTTTGTTTT 58.326 32.000 0.00 0.00 0.00 2.43
181 199 6.580791 TCTCGTCTTCTGTTTTGTTTGTTTTG 59.419 34.615 0.00 0.00 0.00 2.44
182 200 6.210078 TCGTCTTCTGTTTTGTTTGTTTTGT 58.790 32.000 0.00 0.00 0.00 2.83
183 201 6.361214 TCGTCTTCTGTTTTGTTTGTTTTGTC 59.639 34.615 0.00 0.00 0.00 3.18
184 202 6.362283 CGTCTTCTGTTTTGTTTGTTTTGTCT 59.638 34.615 0.00 0.00 0.00 3.41
185 203 7.096230 CGTCTTCTGTTTTGTTTGTTTTGTCTT 60.096 33.333 0.00 0.00 0.00 3.01
186 204 8.547894 GTCTTCTGTTTTGTTTGTTTTGTCTTT 58.452 29.630 0.00 0.00 0.00 2.52
187 205 8.760569 TCTTCTGTTTTGTTTGTTTTGTCTTTC 58.239 29.630 0.00 0.00 0.00 2.62
190 208 9.103861 TCTGTTTTGTTTGTTTTGTCTTTCTTT 57.896 25.926 0.00 0.00 0.00 2.52
192 210 9.495754 TGTTTTGTTTGTTTTGTCTTTCTTTTG 57.504 25.926 0.00 0.00 0.00 2.44
207 225 8.974408 GTCTTTCTTTTGTTGTTGTGTAAGTTT 58.026 29.630 0.00 0.00 0.00 2.66
211 229 6.584563 TCTTTTGTTGTTGTGTAAGTTTCTGC 59.415 34.615 0.00 0.00 0.00 4.26
261 280 8.723942 TCCTGCTATTTTTCAGAAAGAGATAC 57.276 34.615 0.00 0.00 32.26 2.24
264 283 8.186178 TGCTATTTTTCAGAAAGAGATACGAC 57.814 34.615 0.00 0.00 0.00 4.34
265 284 7.277981 TGCTATTTTTCAGAAAGAGATACGACC 59.722 37.037 0.00 0.00 0.00 4.79
266 285 7.277981 GCTATTTTTCAGAAAGAGATACGACCA 59.722 37.037 0.00 0.00 0.00 4.02
272 291 5.243060 TCAGAAAGAGATACGACCACTTCAA 59.757 40.000 0.00 0.00 0.00 2.69
277 296 4.396790 AGAGATACGACCACTTCAAGTCTC 59.603 45.833 0.00 0.00 0.00 3.36
278 297 2.983402 TACGACCACTTCAAGTCTCG 57.017 50.000 11.20 11.20 33.73 4.04
317 336 4.262463 CCAGTAGAACTGCTTACCACTCAA 60.262 45.833 1.43 0.00 44.63 3.02
318 337 5.482908 CAGTAGAACTGCTTACCACTCAAT 58.517 41.667 0.00 0.00 39.62 2.57
324 343 6.595716 AGAACTGCTTACCACTCAATAATGAC 59.404 38.462 0.00 0.00 0.00 3.06
331 350 8.893727 GCTTACCACTCAATAATGACAATAAGT 58.106 33.333 0.00 0.00 0.00 2.24
345 364 9.883142 AATGACAATAAGTTTTCAGTCCAAAAA 57.117 25.926 0.00 0.00 28.40 1.94
355 374 9.883142 AGTTTTCAGTCCAAAAATAAAATGACA 57.117 25.926 0.00 0.00 0.00 3.58
357 376 7.945033 TTCAGTCCAAAAATAAAATGACAGC 57.055 32.000 0.00 0.00 0.00 4.40
358 377 7.048629 TCAGTCCAAAAATAAAATGACAGCA 57.951 32.000 0.00 0.00 0.00 4.41
359 378 7.495901 TCAGTCCAAAAATAAAATGACAGCAA 58.504 30.769 0.00 0.00 0.00 3.91
360 379 7.652909 TCAGTCCAAAAATAAAATGACAGCAAG 59.347 33.333 0.00 0.00 0.00 4.01
361 380 7.439056 CAGTCCAAAAATAAAATGACAGCAAGT 59.561 33.333 0.00 0.00 0.00 3.16
374 393 4.100344 TGACAGCAAGTTAGTTGTAGTCCA 59.900 41.667 17.32 8.35 39.42 4.02
380 399 5.279356 GCAAGTTAGTTGTAGTCCAGTAGGT 60.279 44.000 1.55 0.00 38.55 3.08
382 401 5.890049 AGTTAGTTGTAGTCCAGTAGGTCT 58.110 41.667 0.00 0.00 37.12 3.85
390 409 6.312529 TGTAGTCCAGTAGGTCTATATTGGG 58.687 44.000 0.00 0.00 37.75 4.12
419 438 0.320771 AAGCAGCGACGAAATGGAGT 60.321 50.000 0.00 0.00 0.00 3.85
460 479 4.108699 TCAAACAGACAACCAGCAAAAG 57.891 40.909 0.00 0.00 0.00 2.27
477 496 7.094720 CCAGCAAAAGATTTTATGAAATTGCCA 60.095 33.333 12.68 0.00 37.57 4.92
503 522 5.722021 AAGTTGTTCACTTGTTTGGACTT 57.278 34.783 0.00 0.00 44.70 3.01
504 523 5.722021 AGTTGTTCACTTGTTTGGACTTT 57.278 34.783 0.00 0.00 27.32 2.66
505 524 5.469479 AGTTGTTCACTTGTTTGGACTTTG 58.531 37.500 0.00 0.00 27.32 2.77
506 525 4.448537 TGTTCACTTGTTTGGACTTTGG 57.551 40.909 0.00 0.00 0.00 3.28
523 542 6.293790 GGACTTTGGACCACTAAACACATTAC 60.294 42.308 0.00 0.00 0.00 1.89
530 549 5.442391 ACCACTAAACACATTACAACTGGT 58.558 37.500 0.00 0.00 0.00 4.00
577 596 6.525578 AAACCGTCAGACTATGTATCTCAA 57.474 37.500 0.00 0.00 0.00 3.02
581 600 6.205853 ACCGTCAGACTATGTATCTCAATCTC 59.794 42.308 0.00 0.00 0.00 2.75
585 604 6.208402 TCAGACTATGTATCTCAATCTCAGGC 59.792 42.308 0.00 0.00 0.00 4.85
590 609 6.788598 ATGTATCTCAATCTCAGGCGATAT 57.211 37.500 0.00 0.00 0.00 1.63
594 613 3.509184 TCTCAATCTCAGGCGATATCCAG 59.491 47.826 0.00 0.00 0.00 3.86
597 616 4.159321 TCAATCTCAGGCGATATCCAGATC 59.841 45.833 0.00 0.00 0.00 2.75
609 628 9.994432 GGCGATATCCAGATCTTTAAATAATTG 57.006 33.333 0.00 0.00 0.00 2.32
633 652 2.783135 TCTCATTTCCCACAGAACTGC 58.217 47.619 1.46 0.00 35.62 4.40
634 653 1.815003 CTCATTTCCCACAGAACTGCC 59.185 52.381 1.46 0.00 35.62 4.85
635 654 1.425066 TCATTTCCCACAGAACTGCCT 59.575 47.619 1.46 0.00 35.62 4.75
693 718 1.076559 TCATGAAGCATGCCCCTGG 60.077 57.895 15.66 1.67 41.18 4.45
700 725 2.428925 GCATGCCCCTGGTCCATTG 61.429 63.158 6.36 0.00 0.00 2.82
737 762 3.610114 GCGGCACATTGTGATATCCAATC 60.610 47.826 20.77 0.00 35.23 2.67
738 763 3.565063 CGGCACATTGTGATATCCAATCA 59.435 43.478 20.77 1.31 35.23 2.57
755 780 4.505918 CCAATCACCCAAACACTACCACTA 60.506 45.833 0.00 0.00 0.00 2.74
759 784 2.370849 ACCCAAACACTACCACTACTGG 59.629 50.000 0.00 0.00 44.26 4.00
762 787 3.326747 CAAACACTACCACTACTGGCTC 58.673 50.000 0.00 0.00 42.08 4.70
763 788 1.558233 ACACTACCACTACTGGCTCC 58.442 55.000 0.00 0.00 42.08 4.70
768 793 0.687354 ACCACTACTGGCTCCAACAG 59.313 55.000 0.00 0.00 42.08 3.16
792 817 1.304134 AAAGGGCAAAGGGGTAGCG 60.304 57.895 0.00 0.00 0.00 4.26
804 829 2.093128 AGGGGTAGCGTCTAAACATTGG 60.093 50.000 0.00 0.00 0.00 3.16
840 865 1.676967 CCTTGTCCCTTGCCAGCTC 60.677 63.158 0.00 0.00 0.00 4.09
896 921 6.569127 TCTTCAGCCCACCTATAAATACAA 57.431 37.500 0.00 0.00 0.00 2.41
909 934 6.201044 CCTATAAATACAACAGCTCTGAACCG 59.799 42.308 3.60 0.00 0.00 4.44
934 959 1.250328 TCCATCCACAAGCAAAGCAG 58.750 50.000 0.00 0.00 0.00 4.24
936 961 1.336517 CCATCCACAAGCAAAGCAGTG 60.337 52.381 7.37 7.37 36.87 3.66
953 978 3.070018 CAGTGCTGCTAGCTTAACACTT 58.930 45.455 21.64 10.60 42.97 3.16
1003 1028 6.627087 AGAAAGAAGGAGATACAACCATGA 57.373 37.500 0.00 0.00 0.00 3.07
1026 1051 3.065655 CAGTGCCAAGAGACTTTCTCAG 58.934 50.000 5.99 0.00 45.73 3.35
1034 1059 6.820656 GCCAAGAGACTTTCTCAGATGATAAA 59.179 38.462 5.99 0.00 45.73 1.40
1059 1084 1.969862 GCAAAGAGTGGCAGCCATT 59.030 52.632 19.75 14.72 35.28 3.16
1113 1138 0.033920 AAGTCGATGAGTGCTGCACA 59.966 50.000 31.90 15.06 36.74 4.57
1155 1180 1.970917 GCGCCATGTACACTGCTGAC 61.971 60.000 14.46 3.18 0.00 3.51
1371 1396 0.604780 CTGTGGTGAGACCTTGCCAG 60.605 60.000 0.00 0.00 39.58 4.85
1376 1401 1.373570 GTGAGACCTTGCCAGTATGC 58.626 55.000 0.00 0.00 31.97 3.14
1458 1483 5.238650 AGGATTCAGTTGTTCGTTTTACCTG 59.761 40.000 0.00 0.00 0.00 4.00
1520 1545 9.921637 GTTCTATGTAGGAGATAGGAAATGAAG 57.078 37.037 0.00 0.00 0.00 3.02
1579 1604 2.563179 GACTCCTGACTGCTTAGTTCCA 59.437 50.000 0.00 0.00 0.00 3.53
1580 1605 3.177228 ACTCCTGACTGCTTAGTTCCAT 58.823 45.455 0.00 0.00 0.00 3.41
1588 1613 6.398918 TGACTGCTTAGTTCCATAACTCTTC 58.601 40.000 0.00 0.00 42.42 2.87
1591 1616 7.454225 ACTGCTTAGTTCCATAACTCTTCTTT 58.546 34.615 0.00 0.00 42.42 2.52
1592 1617 7.604545 ACTGCTTAGTTCCATAACTCTTCTTTC 59.395 37.037 0.00 0.00 42.42 2.62
1593 1618 7.680730 TGCTTAGTTCCATAACTCTTCTTTCT 58.319 34.615 0.00 0.00 42.42 2.52
1594 1619 7.604164 TGCTTAGTTCCATAACTCTTCTTTCTG 59.396 37.037 0.00 0.00 42.42 3.02
1595 1620 7.413548 GCTTAGTTCCATAACTCTTCTTTCTGC 60.414 40.741 0.00 0.00 42.42 4.26
1599 1624 4.021456 TCCATAACTCTTCTTTCTGCGACA 60.021 41.667 0.00 0.00 0.00 4.35
1607 1632 5.689819 TCTTCTTTCTGCGACAAATTAAGC 58.310 37.500 0.00 0.00 0.00 3.09
1631 1656 6.256757 GCTAAGGCTCTATTGTGTTAGACAAG 59.743 42.308 0.81 0.00 40.60 3.16
1632 1657 8.585055 GCTAAGGCTCTATTGTGTTAGACAAGG 61.585 44.444 0.81 0.00 40.60 3.61
1644 1669 8.044908 TTGTGTTAGACAAGGAAGTTAAGACTT 58.955 33.333 0.00 0.00 42.98 3.01
1652 1677 9.274206 GACAAGGAAGTTAAGACTTAAGTTGAT 57.726 33.333 25.75 14.57 45.88 2.57
1653 1678 9.057089 ACAAGGAAGTTAAGACTTAAGTTGATG 57.943 33.333 25.75 21.69 45.88 3.07
1654 1679 9.273016 CAAGGAAGTTAAGACTTAAGTTGATGA 57.727 33.333 25.75 0.00 45.88 2.92
1655 1680 9.495572 AAGGAAGTTAAGACTTAAGTTGATGAG 57.504 33.333 25.75 0.00 45.88 2.90
1656 1681 8.652290 AGGAAGTTAAGACTTAAGTTGATGAGT 58.348 33.333 25.75 6.67 45.88 3.41
1657 1682 8.927721 GGAAGTTAAGACTTAAGTTGATGAGTC 58.072 37.037 25.75 13.46 45.88 3.36
1659 1684 9.482627 AAGTTAAGACTTAAGTTGATGAGTCTG 57.517 33.333 21.86 0.00 45.88 3.51
1660 1685 8.091449 AGTTAAGACTTAAGTTGATGAGTCTGG 58.909 37.037 10.02 0.00 45.88 3.86
1661 1686 4.826556 AGACTTAAGTTGATGAGTCTGGC 58.173 43.478 10.02 0.00 45.14 4.85
1662 1687 4.284490 AGACTTAAGTTGATGAGTCTGGCA 59.716 41.667 10.02 0.00 45.14 4.92
1663 1688 5.046014 AGACTTAAGTTGATGAGTCTGGCAT 60.046 40.000 10.02 0.00 45.14 4.40
1664 1689 4.940046 ACTTAAGTTGATGAGTCTGGCATG 59.060 41.667 1.12 0.00 0.00 4.06
1665 1690 1.747709 AGTTGATGAGTCTGGCATGC 58.252 50.000 9.90 9.90 0.00 4.06
1666 1691 1.281287 AGTTGATGAGTCTGGCATGCT 59.719 47.619 18.92 0.00 0.00 3.79
1667 1692 1.400846 GTTGATGAGTCTGGCATGCTG 59.599 52.381 18.92 11.12 0.00 4.41
1668 1693 0.906775 TGATGAGTCTGGCATGCTGA 59.093 50.000 18.92 13.37 0.00 4.26
1669 1694 1.489230 TGATGAGTCTGGCATGCTGAT 59.511 47.619 18.92 0.00 0.00 2.90
1670 1695 2.092592 TGATGAGTCTGGCATGCTGATT 60.093 45.455 18.92 12.71 0.00 2.57
1671 1696 2.502142 TGAGTCTGGCATGCTGATTT 57.498 45.000 18.92 8.86 0.00 2.17
1672 1697 2.089201 TGAGTCTGGCATGCTGATTTG 58.911 47.619 18.92 2.03 0.00 2.32
1727 1753 7.554835 TGGTACTAGTTTAGCAAAATGGTATGG 59.445 37.037 0.00 0.00 35.47 2.74
1771 1797 9.974750 GTTATCTTCTGCAATAACTGTTAGAAC 57.025 33.333 10.45 0.00 36.09 3.01
1772 1798 7.617041 ATCTTCTGCAATAACTGTTAGAACC 57.383 36.000 6.40 0.00 31.42 3.62
1774 1800 6.874134 TCTTCTGCAATAACTGTTAGAACCTC 59.126 38.462 6.40 0.00 31.42 3.85
1775 1801 6.360370 TCTGCAATAACTGTTAGAACCTCT 57.640 37.500 6.40 0.00 0.00 3.69
1776 1802 6.769512 TCTGCAATAACTGTTAGAACCTCTT 58.230 36.000 6.40 0.00 0.00 2.85
1777 1803 6.650807 TCTGCAATAACTGTTAGAACCTCTTG 59.349 38.462 6.40 5.20 0.00 3.02
1779 1805 5.181245 GCAATAACTGTTAGAACCTCTTGCA 59.819 40.000 19.73 0.00 36.27 4.08
1789 1819 2.191128 ACCTCTTGCAGATCACCAAC 57.809 50.000 0.00 0.00 0.00 3.77
1798 1828 4.264253 TGCAGATCACCAACCTTATTCTG 58.736 43.478 0.00 0.00 33.86 3.02
1801 1831 3.852578 AGATCACCAACCTTATTCTGGGT 59.147 43.478 0.00 0.00 37.44 4.51
1810 1840 5.010708 ACCTTATTCTGGGTGGTCAAAAT 57.989 39.130 0.00 0.00 34.16 1.82
1811 1841 6.147437 ACCTTATTCTGGGTGGTCAAAATA 57.853 37.500 0.00 0.00 34.16 1.40
1867 1897 5.500645 AGGAAACTGTAAGAACAACAAGC 57.499 39.130 0.00 0.00 41.13 4.01
1871 1901 4.531659 ACTGTAAGAACAACAAGCGAAC 57.468 40.909 0.00 0.00 37.43 3.95
1906 1936 7.283807 ACATATGAGATGCTGCTAATCAAACAA 59.716 33.333 10.38 0.00 0.00 2.83
1926 1960 4.827284 ACAAACCATCAACTAAAGAGGTGG 59.173 41.667 0.00 0.00 41.16 4.61
1983 2047 1.068610 CGTTGTGGGCATAACCAACTG 60.069 52.381 0.00 0.00 43.76 3.16
1985 2049 1.904287 TGTGGGCATAACCAACTGTC 58.096 50.000 0.00 0.00 43.76 3.51
1995 2059 8.100791 GGGCATAACCAACTGTCAGATTATATA 58.899 37.037 6.91 0.00 42.05 0.86
2002 2066 9.331466 ACCAACTGTCAGATTATATATCTCCAT 57.669 33.333 6.91 0.00 0.00 3.41
2010 2074 8.573097 TCAGATTATATATCTCCATCTGAGGGT 58.427 37.037 15.50 0.00 43.11 4.34
2035 2099 7.607991 GTCCACCCTATGTATTTTATCAGGATG 59.392 40.741 0.00 0.00 37.54 3.51
2038 2102 9.436957 CACCCTATGTATTTTATCAGGATGTAC 57.563 37.037 0.00 0.00 37.40 2.90
2039 2103 9.393786 ACCCTATGTATTTTATCAGGATGTACT 57.606 33.333 0.00 0.00 37.40 2.73
2046 2110 6.985188 TTTTATCAGGATGTACTCAAGCAC 57.015 37.500 0.00 0.00 37.40 4.40
2143 2207 6.421801 GCACAAACTGAATGCAAACTAAGAAT 59.578 34.615 0.00 0.00 39.23 2.40
2145 2209 9.462174 CACAAACTGAATGCAAACTAAGAATTA 57.538 29.630 0.00 0.00 0.00 1.40
2149 2213 9.846248 AACTGAATGCAAACTAAGAATTATGAC 57.154 29.630 0.00 0.00 0.00 3.06
2150 2214 8.462016 ACTGAATGCAAACTAAGAATTATGACC 58.538 33.333 0.00 0.00 0.00 4.02
2151 2215 8.347004 TGAATGCAAACTAAGAATTATGACCA 57.653 30.769 0.00 0.00 0.00 4.02
2152 2216 8.461222 TGAATGCAAACTAAGAATTATGACCAG 58.539 33.333 0.00 0.00 0.00 4.00
2203 2270 3.706086 GCAGGTTATTTGACATGGGGATT 59.294 43.478 0.00 0.00 32.32 3.01
2205 2272 4.036734 CAGGTTATTTGACATGGGGATTCG 59.963 45.833 0.00 0.00 0.00 3.34
2213 2280 0.311790 CATGGGGATTCGGCATTTCG 59.688 55.000 0.00 0.00 0.00 3.46
2214 2281 0.106719 ATGGGGATTCGGCATTTCGT 60.107 50.000 0.00 0.00 0.00 3.85
2224 2291 1.557443 GGCATTTCGTAGATCCGCCG 61.557 60.000 0.00 0.00 35.20 6.46
2277 2344 1.336125 GCTGCCATTACCTCTGAATGC 59.664 52.381 0.00 0.00 33.70 3.56
2284 2351 4.201851 CCATTACCTCTGAATGCTTTCGTG 60.202 45.833 7.73 3.90 33.70 4.35
2288 2355 3.251004 ACCTCTGAATGCTTTCGTGTTTC 59.749 43.478 7.73 0.00 34.39 2.78
2289 2356 3.499918 CCTCTGAATGCTTTCGTGTTTCT 59.500 43.478 7.73 0.00 34.39 2.52
2295 2362 5.238432 TGAATGCTTTCGTGTTTCTACATGT 59.762 36.000 2.69 2.69 41.20 3.21
2298 2365 6.403333 TGCTTTCGTGTTTCTACATGTATC 57.597 37.500 5.91 0.00 41.20 2.24
2304 2371 6.452242 TCGTGTTTCTACATGTATCAGTTGT 58.548 36.000 5.91 0.00 41.20 3.32
2313 2380 6.560253 ACATGTATCAGTTGTTTTCAGACC 57.440 37.500 0.00 0.00 0.00 3.85
2328 2396 7.447238 TGTTTTCAGACCCTGTTTTTCTATAGG 59.553 37.037 0.00 0.00 32.61 2.57
2339 2407 9.566432 CCTGTTTTTCTATAGGCTATTCTGAAT 57.434 33.333 13.08 8.14 0.00 2.57
2392 2462 4.704540 TGCGTTTTGATATGGATTGTCCTT 59.295 37.500 0.00 0.00 37.46 3.36
2417 2487 3.056821 TGTGTACTGTTTCAGAGGATCCG 60.057 47.826 5.98 0.00 35.18 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 1.012841 GCAATCACTCTACTGGCTGC 58.987 55.000 0.00 0.00 0.00 5.25
59 60 5.698089 TCAAAGTTCAGCAATCACTCTACTG 59.302 40.000 0.00 0.00 0.00 2.74
66 67 4.672413 CGTCTTTCAAAGTTCAGCAATCAC 59.328 41.667 0.00 0.00 0.00 3.06
96 106 8.268850 TGCCTAATCATCTAACTTTGAACTTC 57.731 34.615 0.00 0.00 0.00 3.01
97 107 8.814038 ATGCCTAATCATCTAACTTTGAACTT 57.186 30.769 0.00 0.00 0.00 2.66
106 116 7.930217 TGCTTAACAATGCCTAATCATCTAAC 58.070 34.615 0.00 0.00 0.00 2.34
114 124 6.833416 TGGATACTTGCTTAACAATGCCTAAT 59.167 34.615 0.00 0.00 37.72 1.73
119 129 5.818136 TCTGGATACTTGCTTAACAATGC 57.182 39.130 0.00 0.00 37.72 3.56
134 144 4.607239 AGGTCCGTACTTCTTTCTGGATA 58.393 43.478 0.00 0.00 0.00 2.59
135 145 3.442076 AGGTCCGTACTTCTTTCTGGAT 58.558 45.455 0.00 0.00 0.00 3.41
137 150 2.826725 AGAGGTCCGTACTTCTTTCTGG 59.173 50.000 0.00 0.00 38.84 3.86
152 165 3.718815 ACAAAACAGAAGACGAGAGGTC 58.281 45.455 0.00 0.00 46.45 3.85
161 174 8.655651 AAAGACAAAACAAACAAAACAGAAGA 57.344 26.923 0.00 0.00 0.00 2.87
162 180 8.764287 AGAAAGACAAAACAAACAAAACAGAAG 58.236 29.630 0.00 0.00 0.00 2.85
165 183 9.715123 AAAAGAAAGACAAAACAAACAAAACAG 57.285 25.926 0.00 0.00 0.00 3.16
171 189 8.202745 ACAACAAAAGAAAGACAAAACAAACA 57.797 26.923 0.00 0.00 0.00 2.83
172 190 8.942924 CAACAACAAAAGAAAGACAAAACAAAC 58.057 29.630 0.00 0.00 0.00 2.93
175 193 7.278868 ACACAACAACAAAAGAAAGACAAAACA 59.721 29.630 0.00 0.00 0.00 2.83
176 194 7.626446 ACACAACAACAAAAGAAAGACAAAAC 58.374 30.769 0.00 0.00 0.00 2.43
177 195 7.778470 ACACAACAACAAAAGAAAGACAAAA 57.222 28.000 0.00 0.00 0.00 2.44
179 197 8.138712 ACTTACACAACAACAAAAGAAAGACAA 58.861 29.630 0.00 0.00 0.00 3.18
180 198 7.653647 ACTTACACAACAACAAAAGAAAGACA 58.346 30.769 0.00 0.00 0.00 3.41
181 199 8.515473 AACTTACACAACAACAAAAGAAAGAC 57.485 30.769 0.00 0.00 0.00 3.01
182 200 9.187455 GAAACTTACACAACAACAAAAGAAAGA 57.813 29.630 0.00 0.00 0.00 2.52
183 201 9.191995 AGAAACTTACACAACAACAAAAGAAAG 57.808 29.630 0.00 0.00 0.00 2.62
184 202 8.973378 CAGAAACTTACACAACAACAAAAGAAA 58.027 29.630 0.00 0.00 0.00 2.52
185 203 7.115663 GCAGAAACTTACACAACAACAAAAGAA 59.884 33.333 0.00 0.00 0.00 2.52
186 204 6.584563 GCAGAAACTTACACAACAACAAAAGA 59.415 34.615 0.00 0.00 0.00 2.52
187 205 6.586082 AGCAGAAACTTACACAACAACAAAAG 59.414 34.615 0.00 0.00 0.00 2.27
190 208 5.637006 AGCAGAAACTTACACAACAACAA 57.363 34.783 0.00 0.00 0.00 2.83
192 210 6.090129 TCAAAGCAGAAACTTACACAACAAC 58.910 36.000 0.00 0.00 0.00 3.32
207 225 7.160547 TGCTAAATTCATTGATCAAAGCAGA 57.839 32.000 19.69 10.58 32.88 4.26
211 229 8.475331 AAAGCTGCTAAATTCATTGATCAAAG 57.525 30.769 13.09 8.43 0.00 2.77
248 266 4.765339 TGAAGTGGTCGTATCTCTTTCTGA 59.235 41.667 0.00 0.00 0.00 3.27
251 269 5.471257 ACTTGAAGTGGTCGTATCTCTTTC 58.529 41.667 0.00 0.00 0.00 2.62
261 280 1.267261 AGTCGAGACTTGAAGTGGTCG 59.733 52.381 16.52 16.52 38.83 4.79
264 283 2.554462 TCTCAGTCGAGACTTGAAGTGG 59.446 50.000 0.90 0.00 43.55 4.00
265 284 3.906014 TCTCAGTCGAGACTTGAAGTG 57.094 47.619 0.90 0.00 43.55 3.16
277 296 6.796426 TCTACTGGACAATATTTCTCAGTCG 58.204 40.000 14.06 10.27 36.87 4.18
278 297 8.254508 AGTTCTACTGGACAATATTTCTCAGTC 58.745 37.037 14.06 6.12 36.87 3.51
286 305 7.048512 GGTAAGCAGTTCTACTGGACAATATT 58.951 38.462 8.73 0.00 46.01 1.28
291 310 3.006537 GTGGTAAGCAGTTCTACTGGACA 59.993 47.826 8.73 0.00 46.01 4.02
331 350 8.825745 GCTGTCATTTTATTTTTGGACTGAAAA 58.174 29.630 0.00 0.00 0.00 2.29
332 351 7.984050 TGCTGTCATTTTATTTTTGGACTGAAA 59.016 29.630 0.00 0.00 0.00 2.69
333 352 7.495901 TGCTGTCATTTTATTTTTGGACTGAA 58.504 30.769 0.00 0.00 0.00 3.02
334 353 7.048629 TGCTGTCATTTTATTTTTGGACTGA 57.951 32.000 0.00 0.00 0.00 3.41
335 354 7.439056 ACTTGCTGTCATTTTATTTTTGGACTG 59.561 33.333 0.00 0.00 0.00 3.51
336 355 7.500141 ACTTGCTGTCATTTTATTTTTGGACT 58.500 30.769 0.00 0.00 0.00 3.85
337 356 7.713764 ACTTGCTGTCATTTTATTTTTGGAC 57.286 32.000 0.00 0.00 0.00 4.02
338 357 9.474920 CTAACTTGCTGTCATTTTATTTTTGGA 57.525 29.630 0.00 0.00 0.00 3.53
339 358 9.260002 ACTAACTTGCTGTCATTTTATTTTTGG 57.740 29.630 0.00 0.00 0.00 3.28
342 361 9.816354 ACAACTAACTTGCTGTCATTTTATTTT 57.184 25.926 0.00 0.00 32.41 1.82
345 364 9.284968 ACTACAACTAACTTGCTGTCATTTTAT 57.715 29.630 0.00 0.00 32.41 1.40
346 365 8.671384 ACTACAACTAACTTGCTGTCATTTTA 57.329 30.769 0.00 0.00 32.41 1.52
347 366 7.255139 GGACTACAACTAACTTGCTGTCATTTT 60.255 37.037 0.00 0.00 37.24 1.82
348 367 6.204882 GGACTACAACTAACTTGCTGTCATTT 59.795 38.462 0.00 0.00 37.24 2.32
349 368 5.701290 GGACTACAACTAACTTGCTGTCATT 59.299 40.000 0.00 0.00 37.24 2.57
350 369 5.221641 TGGACTACAACTAACTTGCTGTCAT 60.222 40.000 0.00 0.00 37.24 3.06
351 370 4.100344 TGGACTACAACTAACTTGCTGTCA 59.900 41.667 0.00 0.00 37.24 3.58
352 371 4.628074 TGGACTACAACTAACTTGCTGTC 58.372 43.478 0.00 0.00 35.92 3.51
353 372 4.101119 ACTGGACTACAACTAACTTGCTGT 59.899 41.667 0.00 0.00 32.41 4.40
354 373 4.632153 ACTGGACTACAACTAACTTGCTG 58.368 43.478 0.00 0.00 32.41 4.41
355 374 4.957684 ACTGGACTACAACTAACTTGCT 57.042 40.909 0.00 0.00 32.41 3.91
356 375 5.169295 CCTACTGGACTACAACTAACTTGC 58.831 45.833 0.00 0.00 31.65 4.01
357 376 6.208994 AGACCTACTGGACTACAACTAACTTG 59.791 42.308 0.00 0.00 36.63 3.16
358 377 6.313324 AGACCTACTGGACTACAACTAACTT 58.687 40.000 0.00 0.00 36.63 2.66
359 378 5.890049 AGACCTACTGGACTACAACTAACT 58.110 41.667 0.00 0.00 36.63 2.24
360 379 7.878547 ATAGACCTACTGGACTACAACTAAC 57.121 40.000 0.00 0.00 41.80 2.34
374 393 5.420215 ACACTCCCCAATATAGACCTACT 57.580 43.478 0.00 0.00 0.00 2.57
380 399 5.903010 TGCTTCTTACACTCCCCAATATAGA 59.097 40.000 0.00 0.00 0.00 1.98
382 401 5.454755 GCTGCTTCTTACACTCCCCAATATA 60.455 44.000 0.00 0.00 0.00 0.86
387 406 0.324943 GCTGCTTCTTACACTCCCCA 59.675 55.000 0.00 0.00 0.00 4.96
390 409 1.351153 GTCGCTGCTTCTTACACTCC 58.649 55.000 0.00 0.00 0.00 3.85
419 438 7.823799 TGTTTGATTAGTAGCATCTCATGTGAA 59.176 33.333 0.90 0.00 0.00 3.18
484 503 4.524714 TCCAAAGTCCAAACAAGTGAACAA 59.475 37.500 0.00 0.00 0.00 2.83
494 513 4.399934 TGTTTAGTGGTCCAAAGTCCAAAC 59.600 41.667 0.00 0.00 32.72 2.93
499 518 5.767816 AATGTGTTTAGTGGTCCAAAGTC 57.232 39.130 0.00 0.00 0.00 3.01
500 519 6.123651 TGTAATGTGTTTAGTGGTCCAAAGT 58.876 36.000 0.00 0.00 0.00 2.66
501 520 6.627395 TGTAATGTGTTTAGTGGTCCAAAG 57.373 37.500 0.00 0.00 0.00 2.77
502 521 6.603997 AGTTGTAATGTGTTTAGTGGTCCAAA 59.396 34.615 0.00 0.00 0.00 3.28
503 522 6.038825 CAGTTGTAATGTGTTTAGTGGTCCAA 59.961 38.462 0.00 0.00 0.00 3.53
504 523 5.529430 CAGTTGTAATGTGTTTAGTGGTCCA 59.471 40.000 0.00 0.00 0.00 4.02
505 524 5.048991 CCAGTTGTAATGTGTTTAGTGGTCC 60.049 44.000 0.00 0.00 0.00 4.46
506 525 5.529800 ACCAGTTGTAATGTGTTTAGTGGTC 59.470 40.000 0.00 0.00 28.20 4.02
549 568 3.660865 ACATAGTCTGACGGTTTTCCAC 58.339 45.455 1.52 0.00 40.70 4.02
577 596 3.979911 AGATCTGGATATCGCCTGAGAT 58.020 45.455 0.00 0.00 38.95 2.75
581 600 8.777865 TTATTTAAAGATCTGGATATCGCCTG 57.222 34.615 0.00 0.00 0.00 4.85
619 638 0.687354 GAGAGGCAGTTCTGTGGGAA 59.313 55.000 1.78 0.00 0.00 3.97
633 652 2.810274 CCAACATGTGAACAGTGAGAGG 59.190 50.000 0.00 0.00 0.00 3.69
634 653 3.496130 GTCCAACATGTGAACAGTGAGAG 59.504 47.826 0.00 0.00 0.00 3.20
635 654 3.466836 GTCCAACATGTGAACAGTGAGA 58.533 45.455 0.00 0.00 0.00 3.27
693 718 0.253044 TACTGGCCTGCTCAATGGAC 59.747 55.000 9.95 0.00 0.00 4.02
707 732 1.031571 ACAATGTGCCGCCATACTGG 61.032 55.000 0.00 0.00 41.55 4.00
737 762 3.399330 CAGTAGTGGTAGTGTTTGGGTG 58.601 50.000 0.00 0.00 0.00 4.61
738 763 2.370849 CCAGTAGTGGTAGTGTTTGGGT 59.629 50.000 8.59 0.00 39.30 4.51
755 780 2.113986 GCACCTGTTGGAGCCAGT 59.886 61.111 0.00 0.00 42.88 4.00
759 784 1.662044 CTTTGGCACCTGTTGGAGC 59.338 57.895 0.00 0.00 46.98 4.70
762 787 3.458653 CCCTTTGGCACCTGTTGG 58.541 61.111 0.00 0.00 39.83 3.77
780 805 3.048337 TGTTTAGACGCTACCCCTTTG 57.952 47.619 0.00 0.00 0.00 2.77
781 806 3.994931 ATGTTTAGACGCTACCCCTTT 57.005 42.857 0.00 0.00 0.00 3.11
782 807 3.606687 CAATGTTTAGACGCTACCCCTT 58.393 45.455 0.00 0.00 0.00 3.95
783 808 2.093128 CCAATGTTTAGACGCTACCCCT 60.093 50.000 0.00 0.00 0.00 4.79
784 809 2.093341 TCCAATGTTTAGACGCTACCCC 60.093 50.000 0.00 0.00 0.00 4.95
785 810 3.255969 TCCAATGTTTAGACGCTACCC 57.744 47.619 0.00 0.00 0.00 3.69
786 811 4.189231 ACATCCAATGTTTAGACGCTACC 58.811 43.478 0.00 0.00 41.63 3.18
804 829 0.659957 GGCCATGAGCTTCGAACATC 59.340 55.000 0.00 0.00 43.05 3.06
810 835 1.372087 GGACAAGGCCATGAGCTTCG 61.372 60.000 16.33 0.00 43.05 3.79
853 878 1.382522 TAGGCATGCAGCTTAAGTGC 58.617 50.000 21.36 17.75 44.79 4.40
896 921 4.379243 CCGGCGGTTCAGAGCTGT 62.379 66.667 19.97 0.00 38.02 4.40
909 934 2.700773 GCTTGTGGATGGAACCGGC 61.701 63.158 0.00 0.00 0.00 6.13
934 959 3.067106 TCAAGTGTTAAGCTAGCAGCAC 58.933 45.455 18.83 15.02 45.56 4.40
936 961 3.067106 TGTCAAGTGTTAAGCTAGCAGC 58.933 45.455 18.83 0.00 42.84 5.25
938 963 4.066646 TGTGTCAAGTGTTAAGCTAGCA 57.933 40.909 18.83 0.00 0.00 3.49
939 964 5.418310 TTTGTGTCAAGTGTTAAGCTAGC 57.582 39.130 6.62 6.62 0.00 3.42
948 973 3.375299 GCTCAGAGTTTTGTGTCAAGTGT 59.625 43.478 0.00 0.00 0.00 3.55
953 978 4.333649 CAGAAAGCTCAGAGTTTTGTGTCA 59.666 41.667 21.89 0.00 35.82 3.58
990 1015 3.200605 TGGCACTGATCATGGTTGTATCT 59.799 43.478 0.00 0.00 0.00 1.98
1003 1028 3.326006 TGAGAAAGTCTCTTGGCACTGAT 59.674 43.478 6.80 0.00 43.73 2.90
1026 1051 6.404074 CCACTCTTTGCCACTTCTTTATCATC 60.404 42.308 0.00 0.00 0.00 2.92
1034 1059 0.183492 TGCCACTCTTTGCCACTTCT 59.817 50.000 0.00 0.00 0.00 2.85
1059 1084 0.252881 ACATGAGCCTCTTCCTCCCA 60.253 55.000 0.00 0.00 0.00 4.37
1113 1138 1.001641 GCCCTTCACTGCCACTGAT 60.002 57.895 0.00 0.00 0.00 2.90
1155 1180 4.016706 ACCTCAAACCGCCTCCCG 62.017 66.667 0.00 0.00 0.00 5.14
1371 1396 1.202348 GGCTCCAAACCACTTGCATAC 59.798 52.381 0.00 0.00 33.27 2.39
1376 1401 1.915141 AGATGGCTCCAAACCACTTG 58.085 50.000 0.00 0.00 40.82 3.16
1379 1404 2.301346 CCATAGATGGCTCCAAACCAC 58.699 52.381 0.00 0.00 41.75 4.16
1520 1545 5.581126 TGGTCAACTTGCAATATGATTCC 57.419 39.130 14.98 13.01 0.00 3.01
1579 1604 7.440523 AATTTGTCGCAGAAAGAAGAGTTAT 57.559 32.000 0.00 0.00 39.69 1.89
1580 1605 6.861065 AATTTGTCGCAGAAAGAAGAGTTA 57.139 33.333 0.00 0.00 39.69 2.24
1588 1613 6.024049 CCTTAGCTTAATTTGTCGCAGAAAG 58.976 40.000 0.00 0.00 39.69 2.62
1591 1616 3.374058 GCCTTAGCTTAATTTGTCGCAGA 59.626 43.478 0.00 0.00 35.50 4.26
1592 1617 3.685058 GCCTTAGCTTAATTTGTCGCAG 58.315 45.455 0.00 0.00 35.50 5.18
1593 1618 3.757745 GCCTTAGCTTAATTTGTCGCA 57.242 42.857 0.00 0.00 35.50 5.10
1607 1632 6.758886 CCTTGTCTAACACAATAGAGCCTTAG 59.241 42.308 0.00 0.00 44.32 2.18
1621 1646 9.760077 CTTAAGTCTTAACTTCCTTGTCTAACA 57.240 33.333 0.65 0.00 44.64 2.41
1624 1649 9.760077 CAACTTAAGTCTTAACTTCCTTGTCTA 57.240 33.333 8.95 0.00 44.64 2.59
1627 1652 9.057089 CATCAACTTAAGTCTTAACTTCCTTGT 57.943 33.333 8.95 0.00 44.64 3.16
1631 1656 8.834749 ACTCATCAACTTAAGTCTTAACTTCC 57.165 34.615 8.95 0.00 44.64 3.46
1632 1657 9.699703 AGACTCATCAACTTAAGTCTTAACTTC 57.300 33.333 8.95 2.01 44.57 3.01
1638 1663 5.221722 TGCCAGACTCATCAACTTAAGTCTT 60.222 40.000 8.95 0.00 44.57 3.01
1644 1669 3.054875 AGCATGCCAGACTCATCAACTTA 60.055 43.478 15.66 0.00 0.00 2.24
1652 1677 2.089201 CAAATCAGCATGCCAGACTCA 58.911 47.619 15.66 0.00 34.76 3.41
1653 1678 2.089980 ACAAATCAGCATGCCAGACTC 58.910 47.619 15.66 0.00 34.76 3.36
1654 1679 1.816835 CACAAATCAGCATGCCAGACT 59.183 47.619 15.66 0.00 34.76 3.24
1655 1680 1.734707 GCACAAATCAGCATGCCAGAC 60.735 52.381 15.66 0.00 34.76 3.51
1656 1681 0.528924 GCACAAATCAGCATGCCAGA 59.471 50.000 15.66 13.69 34.76 3.86
1657 1682 0.245266 TGCACAAATCAGCATGCCAG 59.755 50.000 15.66 7.84 37.26 4.85
1658 1683 0.680061 TTGCACAAATCAGCATGCCA 59.320 45.000 15.66 0.78 40.94 4.92
1659 1684 1.355971 CTTGCACAAATCAGCATGCC 58.644 50.000 15.66 0.00 40.94 4.40
1661 1686 1.724623 GTGCTTGCACAAATCAGCATG 59.275 47.619 19.36 0.00 40.94 4.06
1662 1687 1.341852 TGTGCTTGCACAAATCAGCAT 59.658 42.857 23.78 0.00 40.94 3.79
1663 1688 0.745468 TGTGCTTGCACAAATCAGCA 59.255 45.000 23.78 4.41 39.32 4.41
1664 1689 1.134226 GTGTGCTTGCACAAATCAGC 58.866 50.000 26.86 12.00 39.07 4.26
1665 1690 2.495409 TGTGTGCTTGCACAAATCAG 57.505 45.000 26.86 0.00 45.17 2.90
1671 1696 3.593096 TCAATTTTTGTGTGCTTGCACA 58.407 36.364 22.47 22.47 46.30 4.57
1672 1697 4.142945 TGTTCAATTTTTGTGTGCTTGCAC 60.143 37.500 17.73 17.73 39.65 4.57
1684 1709 9.185680 ACTAGTACCAAGTTCTGTTCAATTTTT 57.814 29.630 0.00 0.00 0.00 1.94
1753 1779 6.621596 GCAAGAGGTTCTAACAGTTATTGCAG 60.622 42.308 15.83 0.00 35.52 4.41
1774 1800 4.946157 AGAATAAGGTTGGTGATCTGCAAG 59.054 41.667 0.00 0.00 0.00 4.01
1775 1801 4.701651 CAGAATAAGGTTGGTGATCTGCAA 59.298 41.667 0.00 0.00 0.00 4.08
1776 1802 4.264253 CAGAATAAGGTTGGTGATCTGCA 58.736 43.478 0.00 0.00 0.00 4.41
1777 1803 3.629398 CCAGAATAAGGTTGGTGATCTGC 59.371 47.826 0.00 0.00 33.28 4.26
1779 1805 3.852578 ACCCAGAATAAGGTTGGTGATCT 59.147 43.478 0.00 0.00 29.94 2.75
1789 1819 7.475137 TTTATTTTGACCACCCAGAATAAGG 57.525 36.000 0.00 0.00 35.74 2.69
1844 1874 5.273944 GCTTGTTGTTCTTACAGTTTCCTG 58.726 41.667 0.00 0.00 44.68 3.86
1871 1901 4.750598 CAGCATCTCATATGTGAACTCCAG 59.249 45.833 11.26 0.00 33.05 3.86
1906 1936 4.141251 ACACCACCTCTTTAGTTGATGGTT 60.141 41.667 0.00 0.00 36.85 3.67
1967 2031 1.812571 CTGACAGTTGGTTATGCCCAC 59.187 52.381 0.00 0.00 33.14 4.61
1976 2040 8.727100 TGGAGATATATAATCTGACAGTTGGT 57.273 34.615 1.59 0.00 0.00 3.67
1983 2047 8.859090 CCCTCAGATGGAGATATATAATCTGAC 58.141 40.741 15.50 4.47 45.06 3.51
2010 2074 7.294720 ACATCCTGATAAAATACATAGGGTGGA 59.705 37.037 0.00 0.00 40.01 4.02
2020 2084 8.552034 GTGCTTGAGTACATCCTGATAAAATAC 58.448 37.037 0.00 0.00 0.00 1.89
2026 2090 4.956075 TGAGTGCTTGAGTACATCCTGATA 59.044 41.667 0.00 0.00 32.87 2.15
2028 2092 3.165071 TGAGTGCTTGAGTACATCCTGA 58.835 45.455 0.00 0.00 32.87 3.86
2062 2126 5.737860 ACTCTCTTGTGATTGTGCATCATA 58.262 37.500 0.00 0.00 44.11 2.15
2143 2207 6.662755 ACAAGATTTAGCCATCTGGTCATAA 58.337 36.000 0.00 0.00 32.66 1.90
2145 2209 5.121380 ACAAGATTTAGCCATCTGGTCAT 57.879 39.130 0.00 0.00 32.66 3.06
2146 2210 4.574674 ACAAGATTTAGCCATCTGGTCA 57.425 40.909 0.00 0.00 32.66 4.02
2147 2211 7.934120 AGTTATACAAGATTTAGCCATCTGGTC 59.066 37.037 2.17 0.00 38.29 4.02
2148 2212 7.806180 AGTTATACAAGATTTAGCCATCTGGT 58.194 34.615 4.13 4.13 40.16 4.00
2149 2213 9.950496 ATAGTTATACAAGATTTAGCCATCTGG 57.050 33.333 0.00 0.00 33.52 3.86
2203 2270 0.596600 GCGGATCTACGAAATGCCGA 60.597 55.000 13.13 0.00 41.11 5.54
2205 2272 1.557443 CGGCGGATCTACGAAATGCC 61.557 60.000 0.00 0.00 37.66 4.40
2224 2291 1.135333 CGAGAGTAACTTCTGGCCCTC 59.865 57.143 0.00 0.00 0.00 4.30
2277 2344 7.582435 ACTGATACATGTAGAAACACGAAAG 57.418 36.000 11.91 0.06 38.78 2.62
2284 2351 9.599322 CTGAAAACAACTGATACATGTAGAAAC 57.401 33.333 11.91 3.87 0.00 2.78
2288 2355 7.148407 GGGTCTGAAAACAACTGATACATGTAG 60.148 40.741 11.91 1.97 0.00 2.74
2289 2356 6.653320 GGGTCTGAAAACAACTGATACATGTA 59.347 38.462 8.27 8.27 0.00 2.29
2295 2362 5.304686 ACAGGGTCTGAAAACAACTGATA 57.695 39.130 1.59 0.00 35.18 2.15
2298 2365 4.718940 AAACAGGGTCTGAAAACAACTG 57.281 40.909 1.59 0.00 35.18 3.16
2304 2371 6.433093 GCCTATAGAAAAACAGGGTCTGAAAA 59.567 38.462 0.00 0.00 35.18 2.29
2313 2380 8.964476 TTCAGAATAGCCTATAGAAAAACAGG 57.036 34.615 0.00 0.00 0.00 4.00
2339 2407 8.372459 ACAACTACATCCTACTTTGACATTGTA 58.628 33.333 0.00 0.00 0.00 2.41
2392 2462 5.279506 GGATCCTCTGAAACAGTACACAAGA 60.280 44.000 3.84 0.00 32.61 3.02
2417 2487 2.435586 AGCTGTGCGTGCAGGATC 60.436 61.111 11.29 2.53 37.00 3.36


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

AutoCloner maintained by Alex Coulton.