Multiple sequence alignment - TraesCS4A01G258300

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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 TraesCS4A01G258300 chr4A 100.000 2315 0 0 1 2315 571032596 571030282 0.000000e+00 4276
1 TraesCS4A01G258300 chr4A 94.118 170 10 0 1625 1794 6439273 6439104 2.280000e-65 259
2 TraesCS4A01G258300 chr4A 92.857 168 12 0 1625 1792 6464195 6464028 6.390000e-61 244
3 TraesCS4A01G258300 chr4A 84.000 150 20 3 1811 1957 117255765 117255617 8.620000e-30 141
4 TraesCS4A01G258300 chr4B 87.394 1650 122 34 1 1631 45205356 45206938 0.000000e+00 1816
5 TraesCS4A01G258300 chr4B 88.931 524 46 7 1800 2315 45207083 45207602 9.020000e-179 636
6 TraesCS4A01G258300 chr4D 86.727 1650 139 40 1 1631 31762083 31763671 0.000000e+00 1760
7 TraesCS4A01G258300 chr4D 82.667 150 22 3 1811 1957 509464521 509464373 1.870000e-26 130
8 TraesCS4A01G258300 chr4D 81.132 159 24 5 1822 1978 82727664 82727510 3.120000e-24 122
9 TraesCS4A01G258300 chr6A 80.876 1004 138 32 657 1634 535994404 535993429 0.000000e+00 741
10 TraesCS4A01G258300 chr6D 80.655 1008 138 39 657 1634 389607720 389606740 0.000000e+00 728
11 TraesCS4A01G258300 chr6D 90.476 168 16 0 1627 1794 293177237 293177404 2.990000e-54 222
12 TraesCS4A01G258300 chr6B 80.561 998 147 31 657 1634 583191052 583190082 0.000000e+00 725
13 TraesCS4A01G258300 chr6B 90.698 172 15 1 1627 1797 217931398 217931569 6.430000e-56 228
14 TraesCS4A01G258300 chr6B 83.333 144 20 3 1816 1957 233039235 233039376 1.870000e-26 130
15 TraesCS4A01G258300 chr1D 91.018 167 15 0 1628 1794 180851572 180851738 2.310000e-55 226
16 TraesCS4A01G258300 chr3B 89.385 179 17 2 1624 1801 8889164 8888987 8.320000e-55 224
17 TraesCS4A01G258300 chr3B 83.688 141 18 4 1804 1940 528176345 528176206 6.710000e-26 128
18 TraesCS4A01G258300 chr7B 90.964 166 13 2 1630 1794 595442058 595441894 2.990000e-54 222
19 TraesCS4A01G258300 chr1A 90.419 167 16 0 1628 1794 234232969 234233135 1.080000e-53 220
20 TraesCS4A01G258300 chr7D 89.143 175 18 1 1623 1797 525720958 525721131 1.390000e-52 217
21 TraesCS4A01G258300 chr7A 85.443 158 15 7 1804 1957 579808527 579808374 8.560000e-35 158
22 TraesCS4A01G258300 chr5A 84.892 139 17 3 1823 1958 556687518 556687381 1.120000e-28 137
23 TraesCS4A01G258300 chr2D 84.173 139 19 2 1821 1957 587101495 587101358 5.190000e-27 132


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 TraesCS4A01G258300 chr4A 571030282 571032596 2314 True 4276 4276 100.0000 1 2315 1 chr4A.!!$R4 2314
1 TraesCS4A01G258300 chr4B 45205356 45207602 2246 False 1226 1816 88.1625 1 2315 2 chr4B.!!$F1 2314
2 TraesCS4A01G258300 chr4D 31762083 31763671 1588 False 1760 1760 86.7270 1 1631 1 chr4D.!!$F1 1630
3 TraesCS4A01G258300 chr6A 535993429 535994404 975 True 741 741 80.8760 657 1634 1 chr6A.!!$R1 977
4 TraesCS4A01G258300 chr6D 389606740 389607720 980 True 728 728 80.6550 657 1634 1 chr6D.!!$R1 977
5 TraesCS4A01G258300 chr6B 583190082 583191052 970 True 725 725 80.5610 657 1634 1 chr6B.!!$R1 977

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
126 136 0.176449 TCAGCATCCATGTCCGACAG 59.824 55.0 7.41 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 2168 0.107459 AATCGGGCAGCTCTCTTTCC 60.107 55.0 0.0 0.0 0.0 3.13 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
50 52 8.743099 GTTTCTATTTTATATGAAAGGCGTTGC 58.257 33.333 0.00 0.00 0.00 4.17
63 66 1.503542 CGTTGCCCAGTTCTGCATC 59.496 57.895 0.00 0.00 37.33 3.91
66 69 1.340889 GTTGCCCAGTTCTGCATCAAA 59.659 47.619 0.00 0.00 37.33 2.69
67 70 1.250328 TGCCCAGTTCTGCATCAAAG 58.750 50.000 0.00 0.00 31.31 2.77
68 71 0.529378 GCCCAGTTCTGCATCAAAGG 59.471 55.000 0.00 0.00 0.00 3.11
76 79 7.198390 CCAGTTCTGCATCAAAGGTAAATATG 58.802 38.462 0.00 0.00 0.00 1.78
102 105 1.274728 CACTGGAGAGAGACTGGGTTG 59.725 57.143 0.00 0.00 0.00 3.77
104 107 1.548269 CTGGAGAGAGACTGGGTTGTC 59.452 57.143 0.00 0.00 37.23 3.18
126 136 0.176449 TCAGCATCCATGTCCGACAG 59.824 55.000 7.41 0.00 0.00 3.51
178 188 9.132521 CAGGAAACAAACTATGAACATGATTTC 57.867 33.333 0.00 0.00 0.00 2.17
190 200 2.158325 ACATGATTTCACCCAACACCCT 60.158 45.455 0.00 0.00 0.00 4.34
201 211 1.827969 CCAACACCCTCTACTCCTGAG 59.172 57.143 0.00 0.00 0.00 3.35
213 223 6.274157 TCTACTCCTGAGTCAACTTCATTC 57.726 41.667 2.48 0.00 42.54 2.67
238 248 2.770164 TCCAAGGCTACTTCTTGAGC 57.230 50.000 5.51 0.00 42.94 4.26
259 270 3.244596 GCTGACTATTAGTCCATTCCCCC 60.245 52.174 18.81 0.00 44.44 5.40
286 297 5.643379 TTCAATACCTCTTCCAATGTTGC 57.357 39.130 0.00 0.00 0.00 4.17
291 302 2.887152 ACCTCTTCCAATGTTGCAAGAC 59.113 45.455 0.00 0.00 0.00 3.01
292 303 2.886523 CCTCTTCCAATGTTGCAAGACA 59.113 45.455 0.00 0.00 0.00 3.41
296 307 4.159321 TCTTCCAATGTTGCAAGACACAAA 59.841 37.500 0.00 0.00 31.30 2.83
297 308 4.044336 TCCAATGTTGCAAGACACAAAG 57.956 40.909 0.00 0.00 31.30 2.77
298 309 2.540931 CCAATGTTGCAAGACACAAAGC 59.459 45.455 0.00 0.00 31.30 3.51
300 311 3.523606 ATGTTGCAAGACACAAAGCAA 57.476 38.095 0.00 0.00 43.90 3.91
304 315 4.389890 TTGCAAGACACAAAGCAATCTT 57.610 36.364 0.00 0.00 41.55 2.40
305 316 5.512753 TTGCAAGACACAAAGCAATCTTA 57.487 34.783 0.00 0.00 41.55 2.10
306 317 5.710513 TGCAAGACACAAAGCAATCTTAT 57.289 34.783 0.00 0.00 33.48 1.73
307 318 5.702865 TGCAAGACACAAAGCAATCTTATC 58.297 37.500 0.00 0.00 33.48 1.75
308 319 5.098211 GCAAGACACAAAGCAATCTTATCC 58.902 41.667 0.00 0.00 30.28 2.59
309 320 5.105997 GCAAGACACAAAGCAATCTTATCCT 60.106 40.000 0.00 0.00 30.28 3.24
310 321 6.571150 GCAAGACACAAAGCAATCTTATCCTT 60.571 38.462 0.00 0.00 30.28 3.36
311 322 7.362056 GCAAGACACAAAGCAATCTTATCCTTA 60.362 37.037 0.00 0.00 30.28 2.69
312 323 8.514594 CAAGACACAAAGCAATCTTATCCTTAA 58.485 33.333 0.00 0.00 30.28 1.85
313 324 8.814038 AGACACAAAGCAATCTTATCCTTAAT 57.186 30.769 0.00 0.00 31.02 1.40
314 325 9.247861 AGACACAAAGCAATCTTATCCTTAATT 57.752 29.630 0.00 0.00 31.02 1.40
315 326 9.508567 GACACAAAGCAATCTTATCCTTAATTC 57.491 33.333 0.00 0.00 31.02 2.17
335 346 9.531942 TTAATTCCTTATGCATAGCAACAATTG 57.468 29.630 6.50 3.24 43.62 2.32
341 352 4.112716 TGCATAGCAACAATTGGACATG 57.887 40.909 10.83 6.86 34.76 3.21
342 353 3.762823 TGCATAGCAACAATTGGACATGA 59.237 39.130 10.83 0.00 34.76 3.07
343 354 4.107622 GCATAGCAACAATTGGACATGAC 58.892 43.478 10.83 0.00 0.00 3.06
344 355 4.380761 GCATAGCAACAATTGGACATGACA 60.381 41.667 10.83 0.00 0.00 3.58
345 356 5.680408 GCATAGCAACAATTGGACATGACAT 60.680 40.000 10.83 0.00 0.00 3.06
346 357 4.445452 AGCAACAATTGGACATGACATC 57.555 40.909 10.83 0.00 0.00 3.06
347 358 3.827876 AGCAACAATTGGACATGACATCA 59.172 39.130 10.83 0.00 0.00 3.07
349 360 4.624024 GCAACAATTGGACATGACATCAAG 59.376 41.667 10.83 0.00 0.00 3.02
352 363 6.017400 ACAATTGGACATGACATCAAGTTC 57.983 37.500 10.83 0.00 0.00 3.01
353 364 5.047802 ACAATTGGACATGACATCAAGTTCC 60.048 40.000 10.83 0.00 0.00 3.62
383 394 8.190784 CAGTAAAATCTTGTTTTGAGTTGTCCT 58.809 33.333 0.00 0.00 0.00 3.85
393 406 2.115427 TGAGTTGTCCTGAGTCCAACA 58.885 47.619 12.14 0.27 40.64 3.33
398 411 1.134521 TGTCCTGAGTCCAACACACAC 60.135 52.381 0.00 0.00 0.00 3.82
407 420 2.098614 TCCAACACACACATGCAAACT 58.901 42.857 0.00 0.00 0.00 2.66
408 421 3.066064 GTCCAACACACACATGCAAACTA 59.934 43.478 0.00 0.00 0.00 2.24
415 428 5.049167 CACACACATGCAAACTAATTTGGT 58.951 37.500 0.00 0.00 44.64 3.67
416 429 5.523188 CACACACATGCAAACTAATTTGGTT 59.477 36.000 0.00 0.00 44.64 3.67
432 445 9.191995 CTAATTTGGTTTTCCTAAATCACACAC 57.808 33.333 0.00 0.00 38.11 3.82
464 477 6.160684 TCACAGAAAATTTGGCATCAAGATG 58.839 36.000 5.70 5.70 41.60 2.90
480 493 5.419542 TCAAGATGAGACCCAAATAGAACG 58.580 41.667 0.00 0.00 0.00 3.95
485 498 2.415512 GAGACCCAAATAGAACGTGTGC 59.584 50.000 0.00 0.00 0.00 4.57
496 509 0.599204 AACGTGTGCAGTACCTTCCG 60.599 55.000 0.00 0.00 0.00 4.30
502 515 0.320421 TGCAGTACCTTCCGCTGTTC 60.320 55.000 0.00 0.00 33.18 3.18
503 516 1.019805 GCAGTACCTTCCGCTGTTCC 61.020 60.000 0.00 0.00 33.18 3.62
509 522 1.338769 ACCTTCCGCTGTTCCACATAC 60.339 52.381 0.00 0.00 0.00 2.39
513 526 1.277842 TCCGCTGTTCCACATACACAT 59.722 47.619 0.00 0.00 0.00 3.21
525 538 7.209471 TCCACATACACATAAACTTTGTTCC 57.791 36.000 0.00 0.00 0.00 3.62
526 539 6.773200 TCCACATACACATAAACTTTGTTCCA 59.227 34.615 0.00 0.00 0.00 3.53
534 547 1.341080 AACTTTGTTCCATGGCCAGG 58.659 50.000 13.05 12.17 0.00 4.45
591 610 5.063880 CACCCTGTAAGACTTGCTACTTTT 58.936 41.667 4.86 0.00 34.07 2.27
595 614 6.708949 CCCTGTAAGACTTGCTACTTTTTGTA 59.291 38.462 4.86 0.00 34.07 2.41
602 621 8.324163 AGACTTGCTACTTTTTGTATAACCTG 57.676 34.615 0.00 0.00 0.00 4.00
607 626 9.742144 TTGCTACTTTTTGTATAACCTGGAATA 57.258 29.630 0.00 0.00 0.00 1.75
628 647 4.722361 ATTCCCTGTTTAGAGACTCGAC 57.278 45.455 0.00 0.00 0.00 4.20
646 665 1.526887 GACATATGCCATCGTGAACCG 59.473 52.381 1.58 0.00 38.13 4.44
651 670 1.522806 GCCATCGTGAACCGCCATA 60.523 57.895 0.00 0.00 36.19 2.74
663 682 3.040147 ACCGCCATATTCAATAGTCGG 57.960 47.619 11.20 11.20 41.18 4.79
695 714 7.064847 CGAGTAGAGCTTCAGAGTTTAGAGTTA 59.935 40.741 0.00 0.00 0.00 2.24
697 716 5.961272 AGAGCTTCAGAGTTTAGAGTTAGC 58.039 41.667 0.00 0.00 0.00 3.09
698 717 5.478679 AGAGCTTCAGAGTTTAGAGTTAGCA 59.521 40.000 0.00 0.00 0.00 3.49
709 728 8.499403 AGTTTAGAGTTAGCATTTTCATCCTC 57.501 34.615 0.00 0.00 0.00 3.71
746 767 5.418310 AGAGTTGTTTATTTGTGACCGTG 57.582 39.130 0.00 0.00 0.00 4.94
755 776 1.686355 TTGTGACCGTGCATCCTTTT 58.314 45.000 0.00 0.00 0.00 2.27
821 850 8.137437 TGAATTTCTTGTCTTGGTCTGAAAATC 58.863 33.333 0.00 0.00 0.00 2.17
884 914 2.416747 TGTCAGTACTTGCAGCATGAC 58.583 47.619 16.17 16.17 39.69 3.06
937 969 6.152661 TCAGTTTTGTGATGAACCTTTTGTCT 59.847 34.615 0.00 0.00 0.00 3.41
999 1033 2.689983 CAGACAAACTTCCCTTGTTGCT 59.310 45.455 0.00 0.00 37.14 3.91
1019 1053 5.569355 TGCTATGGAATCCAAGTTCTTTCA 58.431 37.500 5.89 0.00 36.95 2.69
1095 1129 3.808174 GCGAGTTGTTTCTGAAACTAGGT 59.192 43.478 27.75 14.41 41.90 3.08
1119 1153 0.607489 GCCATGAGGTGCAGTTCACT 60.607 55.000 0.00 0.00 44.98 3.41
1215 1249 3.864686 CATTTCGCCGGAGCCGTG 61.865 66.667 5.05 0.00 37.81 4.94
1367 1404 3.416382 GTTGTTAAGGCGCCGCGA 61.416 61.111 23.20 7.42 0.00 5.87
1415 1454 2.079925 GTTTTCTCTGTGCTGGGCTAG 58.920 52.381 0.00 0.00 0.00 3.42
1446 1485 1.677552 CGGTACCAGGCTGGACTTT 59.322 57.895 38.99 19.67 40.96 2.66
1498 1537 5.993441 TGAATCGTCTGATGAACATGCATAT 59.007 36.000 0.00 0.00 34.24 1.78
1623 1680 6.931281 CACAACTCTCCATCTTTTCTCTACAA 59.069 38.462 0.00 0.00 0.00 2.41
1641 1705 7.343833 TCTCTACAAAATATTACTCCCTCCGTT 59.656 37.037 0.00 0.00 0.00 4.44
1643 1707 5.434408 ACAAAATATTACTCCCTCCGTTCC 58.566 41.667 0.00 0.00 0.00 3.62
1644 1708 5.191124 ACAAAATATTACTCCCTCCGTTCCT 59.809 40.000 0.00 0.00 0.00 3.36
1648 1712 7.628501 AATATTACTCCCTCCGTTCCTAAAT 57.371 36.000 0.00 0.00 0.00 1.40
1649 1713 8.731591 AATATTACTCCCTCCGTTCCTAAATA 57.268 34.615 0.00 0.00 0.00 1.40
1650 1714 8.912614 ATATTACTCCCTCCGTTCCTAAATAT 57.087 34.615 0.00 0.00 0.00 1.28
1652 1716 8.731591 ATTACTCCCTCCGTTCCTAAATATAA 57.268 34.615 0.00 0.00 0.00 0.98
1653 1717 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
1654 1718 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
1656 1720 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
1657 1721 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
1658 1722 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
1659 1723 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
1660 1724 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
1662 1726 9.090692 TCCGTTCCTAAATATAAGTCTTTTTCG 57.909 33.333 0.00 0.00 0.00 3.46
1677 1741 8.788409 AGTCTTTTTCGAGATTTCAAATGAAC 57.212 30.769 0.00 0.00 33.13 3.18
1678 1742 8.624776 AGTCTTTTTCGAGATTTCAAATGAACT 58.375 29.630 0.00 0.00 33.13 3.01
1680 1744 9.878599 TCTTTTTCGAGATTTCAAATGAACTAC 57.121 29.630 0.00 0.00 33.13 2.73
1681 1745 9.118236 CTTTTTCGAGATTTCAAATGAACTACC 57.882 33.333 0.00 0.00 33.13 3.18
1683 1747 7.921786 TTCGAGATTTCAAATGAACTACCAT 57.078 32.000 0.00 0.00 33.13 3.55
1685 1749 9.613428 TTCGAGATTTCAAATGAACTACCATAT 57.387 29.630 0.00 0.00 33.13 1.78
1735 1799 9.323985 AGAGTCTAGATTCACTTATTTTGCATC 57.676 33.333 16.67 0.00 0.00 3.91
1736 1800 8.136057 AGTCTAGATTCACTTATTTTGCATCG 57.864 34.615 0.00 0.00 0.00 3.84
1737 1801 6.848296 GTCTAGATTCACTTATTTTGCATCGC 59.152 38.462 0.00 0.00 0.00 4.58
1738 1802 5.565592 AGATTCACTTATTTTGCATCGCA 57.434 34.783 0.00 0.00 36.47 5.10
1740 1804 5.975344 AGATTCACTTATTTTGCATCGCATG 59.025 36.000 0.00 0.00 38.76 4.06
1741 1805 4.700268 TCACTTATTTTGCATCGCATGT 57.300 36.364 0.00 0.00 38.76 3.21
1742 1806 5.809719 TCACTTATTTTGCATCGCATGTA 57.190 34.783 0.00 0.00 38.76 2.29
1743 1807 5.809464 TCACTTATTTTGCATCGCATGTAG 58.191 37.500 0.00 0.00 38.76 2.74
1744 1808 5.353956 TCACTTATTTTGCATCGCATGTAGT 59.646 36.000 0.00 0.00 38.76 2.73
1745 1809 5.678483 CACTTATTTTGCATCGCATGTAGTC 59.322 40.000 0.00 0.00 38.76 2.59
1746 1810 5.353956 ACTTATTTTGCATCGCATGTAGTCA 59.646 36.000 0.00 0.00 38.76 3.41
1747 1811 4.906065 ATTTTGCATCGCATGTAGTCAT 57.094 36.364 0.00 0.00 38.76 3.06
1748 1812 3.950087 TTTGCATCGCATGTAGTCATC 57.050 42.857 0.00 0.00 38.76 2.92
1749 1813 2.896745 TGCATCGCATGTAGTCATCT 57.103 45.000 0.00 0.00 31.71 2.90
1750 1814 2.476821 TGCATCGCATGTAGTCATCTG 58.523 47.619 0.00 0.00 31.71 2.90
1751 1815 2.159057 TGCATCGCATGTAGTCATCTGT 60.159 45.455 0.00 0.00 31.71 3.41
1752 1816 2.868583 GCATCGCATGTAGTCATCTGTT 59.131 45.455 0.00 0.00 31.15 3.16
1753 1817 3.302935 GCATCGCATGTAGTCATCTGTTG 60.303 47.826 0.00 0.00 31.15 3.33
1754 1818 3.866883 TCGCATGTAGTCATCTGTTGA 57.133 42.857 0.00 0.00 31.15 3.18
1755 1819 4.186856 TCGCATGTAGTCATCTGTTGAA 57.813 40.909 0.00 0.00 35.70 2.69
1756 1820 4.565022 TCGCATGTAGTCATCTGTTGAAA 58.435 39.130 0.00 0.00 35.70 2.69
1757 1821 5.178061 TCGCATGTAGTCATCTGTTGAAAT 58.822 37.500 0.00 0.00 35.70 2.17
1758 1822 5.291858 TCGCATGTAGTCATCTGTTGAAATC 59.708 40.000 0.00 0.00 35.70 2.17
1759 1823 5.292834 CGCATGTAGTCATCTGTTGAAATCT 59.707 40.000 0.00 0.00 35.70 2.40
1760 1824 6.509199 CGCATGTAGTCATCTGTTGAAATCTC 60.509 42.308 0.00 0.00 35.70 2.75
1761 1825 6.538021 GCATGTAGTCATCTGTTGAAATCTCT 59.462 38.462 0.00 0.00 35.70 3.10
1762 1826 7.708322 GCATGTAGTCATCTGTTGAAATCTCTA 59.292 37.037 0.00 0.00 35.70 2.43
1763 1827 9.247126 CATGTAGTCATCTGTTGAAATCTCTAG 57.753 37.037 0.00 0.00 35.70 2.43
1766 1830 9.862371 GTAGTCATCTGTTGAAATCTCTAGAAA 57.138 33.333 0.00 0.00 35.70 2.52
1770 1834 8.037758 TCATCTGTTGAAATCTCTAGAAAGACC 58.962 37.037 0.00 0.00 0.00 3.85
1771 1835 7.546250 TCTGTTGAAATCTCTAGAAAGACCT 57.454 36.000 0.00 0.00 0.00 3.85
1772 1836 8.651589 TCTGTTGAAATCTCTAGAAAGACCTA 57.348 34.615 0.00 0.00 0.00 3.08
1799 1863 7.691993 TTTAGGAATGGAGGAAGTAATAGCT 57.308 36.000 0.00 0.00 0.00 3.32
1800 1864 8.792830 TTTAGGAATGGAGGAAGTAATAGCTA 57.207 34.615 0.00 0.00 0.00 3.32
1813 1877 7.612633 GGAAGTAATAGCTAGCTACTATCACCT 59.387 40.741 26.41 10.48 30.00 4.00
1886 1950 5.107453 GGACTGAAATGAGTGAACAAGTACG 60.107 44.000 0.00 0.00 0.00 3.67
1916 1980 4.022676 TGCGTCTATACATGCGATTTAGGA 60.023 41.667 0.00 0.00 0.00 2.94
2018 2083 6.017605 GGTTCTGGATGTATGCTTTGTGATAG 60.018 42.308 0.00 0.00 0.00 2.08
2025 2090 8.028938 GGATGTATGCTTTGTGATAGTGTTTTT 58.971 33.333 0.00 0.00 0.00 1.94
2047 2112 1.000396 GAATCTGCTGCTTGGGGGT 60.000 57.895 0.00 0.00 0.00 4.95
2048 2113 1.304713 AATCTGCTGCTTGGGGGTG 60.305 57.895 0.00 0.00 0.00 4.61
2049 2114 1.792757 AATCTGCTGCTTGGGGGTGA 61.793 55.000 0.00 0.00 0.00 4.02
2059 2129 3.457749 TGCTTGGGGGTGATTTTCTTTTT 59.542 39.130 0.00 0.00 0.00 1.94
2061 2131 5.309282 TGCTTGGGGGTGATTTTCTTTTTAT 59.691 36.000 0.00 0.00 0.00 1.40
2065 2135 5.047660 TGGGGGTGATTTTCTTTTTATGTCG 60.048 40.000 0.00 0.00 0.00 4.35
2072 2142 5.776173 TTTTCTTTTTATGTCGGCCTTGA 57.224 34.783 0.00 0.00 0.00 3.02
2087 2157 4.823989 CGGCCTTGAAGGATCTTGATTAAT 59.176 41.667 16.93 0.00 37.67 1.40
2088 2158 5.300286 CGGCCTTGAAGGATCTTGATTAATT 59.700 40.000 16.93 0.00 37.67 1.40
2089 2159 6.514048 CGGCCTTGAAGGATCTTGATTAATTC 60.514 42.308 16.93 0.00 37.67 2.17
2091 2161 7.424001 GCCTTGAAGGATCTTGATTAATTCAG 58.576 38.462 16.93 0.00 37.67 3.02
2099 2169 8.975295 AGGATCTTGATTAATTCAGAAAAAGGG 58.025 33.333 0.00 0.00 35.27 3.95
2100 2170 8.971073 GGATCTTGATTAATTCAGAAAAAGGGA 58.029 33.333 0.00 0.00 35.27 4.20
2110 2180 4.392940 TCAGAAAAAGGGAAAGAGAGCTG 58.607 43.478 0.00 0.00 0.00 4.24
2172 2242 2.185310 ATCCACGGAGGGCAACACTC 62.185 60.000 0.00 0.00 38.24 3.51
2192 2262 1.260544 GCTGACCAAAAGGCCATCTT 58.739 50.000 5.01 0.00 37.28 2.40
2198 2268 1.067635 CCAAAAGGCCATCTTCAACGG 60.068 52.381 5.01 0.00 33.94 4.44
2204 2274 1.079127 CCATCTTCAACGGCGACCT 60.079 57.895 16.62 0.00 0.00 3.85
2213 2283 2.663852 CGGCGACCTTCAAACCGT 60.664 61.111 0.00 0.00 39.05 4.83
2222 2292 4.678574 CGACCTTCAAACCGTCCATGTATA 60.679 45.833 0.00 0.00 0.00 1.47
2226 2296 5.360649 TTCAAACCGTCCATGTATATCCA 57.639 39.130 0.00 0.00 0.00 3.41
2227 2297 5.360649 TCAAACCGTCCATGTATATCCAA 57.639 39.130 0.00 0.00 0.00 3.53
2229 2299 5.587043 TCAAACCGTCCATGTATATCCAAAC 59.413 40.000 0.00 0.00 0.00 2.93
2231 2301 3.064207 CCGTCCATGTATATCCAAACCG 58.936 50.000 0.00 0.00 0.00 4.44
2232 2302 2.478894 CGTCCATGTATATCCAAACCGC 59.521 50.000 0.00 0.00 0.00 5.68
2238 2308 2.931325 TGTATATCCAAACCGCGTTGTC 59.069 45.455 4.92 0.00 0.00 3.18
2239 2309 2.396590 ATATCCAAACCGCGTTGTCT 57.603 45.000 4.92 0.00 0.00 3.41
2242 2312 1.890041 CCAAACCGCGTTGTCTGGA 60.890 57.895 4.92 0.00 0.00 3.86
2243 2313 1.234615 CCAAACCGCGTTGTCTGGAT 61.235 55.000 4.92 0.00 0.00 3.41
2247 2317 2.230940 CCGCGTTGTCTGGATAGCG 61.231 63.158 4.92 0.36 46.07 4.26
2264 2334 1.061887 CGGAAGCCATTTAACGCGG 59.938 57.895 12.47 0.00 0.00 6.46
2269 2339 1.516169 GCCATTTAACGCGGGCTTG 60.516 57.895 12.47 0.87 43.09 4.01
2275 2345 1.283613 TTAACGCGGGCTTGTACACG 61.284 55.000 12.47 0.00 0.00 4.49
2301 2372 2.210116 TCTTCTGCAAACGGAGACAAC 58.790 47.619 0.00 0.00 31.21 3.32
2303 2374 0.179234 TCTGCAAACGGAGACAACCA 59.821 50.000 0.00 0.00 0.00 3.67
2305 2376 0.950836 TGCAAACGGAGACAACCATG 59.049 50.000 0.00 0.00 0.00 3.66
2309 2380 0.324943 AACGGAGACAACCATGAGGG 59.675 55.000 0.00 0.00 44.81 4.30
2311 2382 1.077429 GGAGACAACCATGAGGGGC 60.077 63.158 0.00 0.00 42.91 5.80
2312 2383 1.566298 GGAGACAACCATGAGGGGCT 61.566 60.000 0.00 0.00 42.91 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.653344 GCCAATGGGTTTCTCTTTCAAC 58.347 45.455 0.00 0.00 36.17 3.18
15 16 7.881142 TCATATAAAATAGAAACGCCAATGGG 58.119 34.615 0.00 0.00 37.18 4.00
50 52 1.915141 ACCTTTGATGCAGAACTGGG 58.085 50.000 3.99 0.00 0.00 4.45
51 53 5.649782 ATTTACCTTTGATGCAGAACTGG 57.350 39.130 3.99 0.00 0.00 4.00
55 57 7.716799 AACCATATTTACCTTTGATGCAGAA 57.283 32.000 0.00 0.00 0.00 3.02
57 59 8.849168 TGATAACCATATTTACCTTTGATGCAG 58.151 33.333 0.00 0.00 0.00 4.41
63 66 8.746052 TCCAGTGATAACCATATTTACCTTTG 57.254 34.615 0.00 0.00 0.00 2.77
66 69 7.789831 TCTCTCCAGTGATAACCATATTTACCT 59.210 37.037 0.00 0.00 0.00 3.08
67 70 7.963532 TCTCTCCAGTGATAACCATATTTACC 58.036 38.462 0.00 0.00 0.00 2.85
68 71 8.861086 TCTCTCTCCAGTGATAACCATATTTAC 58.139 37.037 0.00 0.00 0.00 2.01
76 79 3.383185 CCAGTCTCTCTCCAGTGATAACC 59.617 52.174 0.00 0.00 0.00 2.85
102 105 1.661341 GGACATGGATGCTGAGTGAC 58.339 55.000 0.00 0.00 0.00 3.67
104 107 0.176449 TCGGACATGGATGCTGAGTG 59.824 55.000 0.00 0.00 0.00 3.51
126 136 6.151691 TGTATTTCATTTCTTTGCTGCTCAC 58.848 36.000 0.00 0.00 0.00 3.51
178 188 0.613777 GGAGTAGAGGGTGTTGGGTG 59.386 60.000 0.00 0.00 0.00 4.61
190 200 5.106118 CGAATGAAGTTGACTCAGGAGTAGA 60.106 44.000 1.20 0.00 42.66 2.59
201 211 1.468914 GGAAGGCCGAATGAAGTTGAC 59.531 52.381 0.00 0.00 0.00 3.18
225 235 6.801575 ACTAATAGTCAGCTCAAGAAGTAGC 58.198 40.000 0.00 0.00 39.08 3.58
232 242 5.988561 GGAATGGACTAATAGTCAGCTCAAG 59.011 44.000 20.57 0.00 46.79 3.02
238 248 4.625607 GGGGGAATGGACTAATAGTCAG 57.374 50.000 20.57 0.00 46.79 3.51
259 270 4.316025 TTGGAAGAGGTATTGAAAGGGG 57.684 45.455 0.00 0.00 0.00 4.79
260 271 5.264395 ACATTGGAAGAGGTATTGAAAGGG 58.736 41.667 0.00 0.00 0.00 3.95
286 297 6.506500 AGGATAAGATTGCTTTGTGTCTTG 57.493 37.500 0.00 0.00 35.56 3.02
291 302 8.689972 AGGAATTAAGGATAAGATTGCTTTGTG 58.310 33.333 0.00 0.00 35.56 3.33
292 303 8.829373 AGGAATTAAGGATAAGATTGCTTTGT 57.171 30.769 0.00 0.00 35.56 2.83
296 307 9.018582 GCATAAGGAATTAAGGATAAGATTGCT 57.981 33.333 0.00 0.00 32.56 3.91
297 308 8.796475 TGCATAAGGAATTAAGGATAAGATTGC 58.204 33.333 0.00 0.00 0.00 3.56
302 313 9.453572 TGCTATGCATAAGGAATTAAGGATAAG 57.546 33.333 8.00 0.00 31.71 1.73
303 314 9.806448 TTGCTATGCATAAGGAATTAAGGATAA 57.194 29.630 8.00 0.00 38.76 1.75
304 315 9.231297 GTTGCTATGCATAAGGAATTAAGGATA 57.769 33.333 8.00 0.00 38.76 2.59
305 316 7.725397 TGTTGCTATGCATAAGGAATTAAGGAT 59.275 33.333 8.00 0.00 38.76 3.24
306 317 7.059788 TGTTGCTATGCATAAGGAATTAAGGA 58.940 34.615 8.00 0.00 38.76 3.36
307 318 7.275888 TGTTGCTATGCATAAGGAATTAAGG 57.724 36.000 8.00 0.00 38.76 2.69
308 319 9.754382 AATTGTTGCTATGCATAAGGAATTAAG 57.246 29.630 8.00 0.00 38.76 1.85
309 320 9.531942 CAATTGTTGCTATGCATAAGGAATTAA 57.468 29.630 8.00 9.16 38.76 1.40
310 321 8.143193 CCAATTGTTGCTATGCATAAGGAATTA 58.857 33.333 8.00 3.37 38.76 1.40
311 322 6.987992 CCAATTGTTGCTATGCATAAGGAATT 59.012 34.615 8.00 5.67 38.76 2.17
312 323 6.324512 TCCAATTGTTGCTATGCATAAGGAAT 59.675 34.615 8.00 0.00 38.76 3.01
313 324 5.655974 TCCAATTGTTGCTATGCATAAGGAA 59.344 36.000 8.00 6.90 38.76 3.36
314 325 5.067674 GTCCAATTGTTGCTATGCATAAGGA 59.932 40.000 8.00 0.85 38.76 3.36
315 326 5.163530 TGTCCAATTGTTGCTATGCATAAGG 60.164 40.000 8.00 0.00 38.76 2.69
349 360 9.581099 TCAAAACAAGATTTTACTGAAAGGAAC 57.419 29.630 0.00 0.00 35.67 3.62
352 363 9.586435 AACTCAAAACAAGATTTTACTGAAAGG 57.414 29.630 0.00 0.00 39.30 3.11
383 394 1.308047 GCATGTGTGTGTTGGACTCA 58.692 50.000 0.00 0.00 0.00 3.41
393 406 5.275067 ACCAAATTAGTTTGCATGTGTGT 57.725 34.783 5.23 0.00 42.66 3.72
398 411 8.600449 TTAGGAAAACCAAATTAGTTTGCATG 57.400 30.769 12.00 0.00 42.66 4.06
407 420 8.919145 AGTGTGTGATTTAGGAAAACCAAATTA 58.081 29.630 0.00 0.00 0.00 1.40
408 421 7.791029 AGTGTGTGATTTAGGAAAACCAAATT 58.209 30.769 0.00 0.00 0.00 1.82
429 442 9.423061 GCCAAATTTTCTGTGAAATTATAGTGT 57.577 29.630 0.00 0.00 38.04 3.55
459 472 5.178797 CACGTTCTATTTGGGTCTCATCTT 58.821 41.667 0.00 0.00 0.00 2.40
464 477 2.415512 GCACACGTTCTATTTGGGTCTC 59.584 50.000 0.00 0.00 0.00 3.36
480 493 1.004918 AGCGGAAGGTACTGCACAC 60.005 57.895 0.00 0.00 43.72 3.82
485 498 0.320374 TGGAACAGCGGAAGGTACTG 59.680 55.000 0.00 0.00 40.86 2.74
502 515 6.976088 TGGAACAAAGTTTATGTGTATGTGG 58.024 36.000 0.00 0.00 31.92 4.17
525 538 1.273327 GGTTGAAAAGACCTGGCCATG 59.727 52.381 5.51 6.06 34.27 3.66
526 539 1.632589 GGTTGAAAAGACCTGGCCAT 58.367 50.000 5.51 0.00 34.27 4.40
534 547 3.568430 AGGGAACAATCGGTTGAAAAGAC 59.432 43.478 16.93 0.13 40.63 3.01
602 621 6.040616 TCGAGTCTCTAAACAGGGAATATTCC 59.959 42.308 24.14 24.14 46.82 3.01
607 626 4.087182 TGTCGAGTCTCTAAACAGGGAAT 58.913 43.478 0.00 0.00 0.00 3.01
646 665 3.695830 TCCCCGACTATTGAATATGGC 57.304 47.619 0.00 0.00 0.00 4.40
663 682 1.135333 CTGAAGCTCTACTCGGTTCCC 59.865 57.143 0.00 0.00 37.91 3.97
676 695 5.730296 TGCTAACTCTAAACTCTGAAGCT 57.270 39.130 0.00 0.00 0.00 3.74
695 714 6.664816 TGAAATAACTGGAGGATGAAAATGCT 59.335 34.615 0.00 0.00 0.00 3.79
697 716 8.059798 ACTGAAATAACTGGAGGATGAAAATG 57.940 34.615 0.00 0.00 0.00 2.32
698 717 9.753674 TTACTGAAATAACTGGAGGATGAAAAT 57.246 29.630 0.00 0.00 0.00 1.82
735 756 1.686355 AAAGGATGCACGGTCACAAA 58.314 45.000 0.00 0.00 0.00 2.83
790 819 6.931281 CAGACCAAGACAAGAAATTCAGTAGA 59.069 38.462 0.00 0.00 0.00 2.59
857 887 4.222114 GCTGCAAGTACTGACAATTTGAC 58.778 43.478 2.79 0.00 35.30 3.18
937 969 4.952335 TCCGGGTTACCTTAACAAAACAAA 59.048 37.500 0.00 0.00 40.39 2.83
955 989 3.701040 AGGATGAAATGTTTGATTCCGGG 59.299 43.478 0.00 0.00 0.00 5.73
999 1033 6.659242 GGAACTGAAAGAACTTGGATTCCATA 59.341 38.462 6.15 0.00 37.43 2.74
1019 1053 1.001406 CTCCGACAAGCTTCAGGAACT 59.999 52.381 13.19 0.00 43.88 3.01
1095 1129 0.692476 ACTGCACCTCATGGCTGTAA 59.308 50.000 3.08 0.00 39.87 2.41
1215 1249 2.079049 CGGAGGTTTACTGCTTCGC 58.921 57.895 0.00 0.00 35.02 4.70
1386 1425 4.022589 CAGCACAGAGAAAACCACATGAAT 60.023 41.667 0.00 0.00 0.00 2.57
1415 1454 1.670015 GTACCGGGGCTAGCCATAC 59.330 63.158 34.09 23.81 37.98 2.39
1498 1537 4.902258 TCCACCCCCACCCAACGA 62.902 66.667 0.00 0.00 0.00 3.85
1623 1680 7.441903 TTTAGGAACGGAGGGAGTAATATTT 57.558 36.000 0.00 0.00 0.00 1.40
1651 1715 9.237846 GTTCATTTGAAATCTCGAAAAAGACTT 57.762 29.630 0.00 0.00 35.58 3.01
1652 1716 8.624776 AGTTCATTTGAAATCTCGAAAAAGACT 58.375 29.630 0.00 0.00 35.58 3.24
1653 1717 8.788409 AGTTCATTTGAAATCTCGAAAAAGAC 57.212 30.769 0.00 0.00 35.58 3.01
1654 1718 9.878599 GTAGTTCATTTGAAATCTCGAAAAAGA 57.121 29.630 0.00 0.00 35.58 2.52
1656 1720 8.625651 TGGTAGTTCATTTGAAATCTCGAAAAA 58.374 29.630 0.00 0.00 35.58 1.94
1657 1721 8.160521 TGGTAGTTCATTTGAAATCTCGAAAA 57.839 30.769 0.00 0.00 35.58 2.29
1658 1722 7.737972 TGGTAGTTCATTTGAAATCTCGAAA 57.262 32.000 0.00 0.00 35.58 3.46
1659 1723 7.921786 ATGGTAGTTCATTTGAAATCTCGAA 57.078 32.000 0.00 0.00 35.58 3.71
1711 1775 7.254590 GCGATGCAAAATAAGTGAATCTAGACT 60.255 37.037 0.00 0.00 29.84 3.24
1712 1776 6.848296 GCGATGCAAAATAAGTGAATCTAGAC 59.152 38.462 0.00 0.00 29.84 2.59
1713 1777 6.538381 TGCGATGCAAAATAAGTGAATCTAGA 59.462 34.615 0.00 0.00 34.76 2.43
1714 1778 6.718388 TGCGATGCAAAATAAGTGAATCTAG 58.282 36.000 0.00 0.00 34.76 2.43
1715 1779 6.676237 TGCGATGCAAAATAAGTGAATCTA 57.324 33.333 0.00 0.00 34.76 1.98
1716 1780 5.565592 TGCGATGCAAAATAAGTGAATCT 57.434 34.783 0.00 0.00 34.76 2.40
1717 1781 5.745294 ACATGCGATGCAAAATAAGTGAATC 59.255 36.000 0.00 0.00 43.62 2.52
1718 1782 5.653507 ACATGCGATGCAAAATAAGTGAAT 58.346 33.333 0.00 0.00 43.62 2.57
1719 1783 5.058149 ACATGCGATGCAAAATAAGTGAA 57.942 34.783 0.00 0.00 43.62 3.18
1721 1785 5.572211 ACTACATGCGATGCAAAATAAGTG 58.428 37.500 0.00 0.00 43.62 3.16
1722 1786 5.353956 TGACTACATGCGATGCAAAATAAGT 59.646 36.000 0.00 0.00 43.62 2.24
1723 1787 5.809464 TGACTACATGCGATGCAAAATAAG 58.191 37.500 0.00 0.00 43.62 1.73
1724 1788 5.809719 TGACTACATGCGATGCAAAATAA 57.190 34.783 0.00 0.00 43.62 1.40
1726 1790 4.577693 AGATGACTACATGCGATGCAAAAT 59.422 37.500 0.00 0.00 43.62 1.82
1732 1796 4.114794 TCAACAGATGACTACATGCGATG 58.885 43.478 0.00 0.00 36.82 3.84
1733 1797 4.391405 TCAACAGATGACTACATGCGAT 57.609 40.909 0.00 0.00 36.82 4.58
1734 1798 3.866883 TCAACAGATGACTACATGCGA 57.133 42.857 0.00 0.00 36.82 5.10
1735 1799 4.926860 TTTCAACAGATGACTACATGCG 57.073 40.909 0.00 0.00 37.92 4.73
1736 1800 6.538021 AGAGATTTCAACAGATGACTACATGC 59.462 38.462 0.00 0.00 37.92 4.06
1737 1801 9.247126 CTAGAGATTTCAACAGATGACTACATG 57.753 37.037 0.00 0.00 37.92 3.21
1738 1802 9.194972 TCTAGAGATTTCAACAGATGACTACAT 57.805 33.333 0.00 0.00 37.92 2.29
1740 1804 9.862371 TTTCTAGAGATTTCAACAGATGACTAC 57.138 33.333 0.00 0.00 37.92 2.73
1742 1806 8.811017 TCTTTCTAGAGATTTCAACAGATGACT 58.189 33.333 0.00 0.00 37.92 3.41
1743 1807 8.868916 GTCTTTCTAGAGATTTCAACAGATGAC 58.131 37.037 0.00 0.00 37.92 3.06
1744 1808 8.037758 GGTCTTTCTAGAGATTTCAACAGATGA 58.962 37.037 0.00 0.00 35.85 2.92
1745 1809 8.040132 AGGTCTTTCTAGAGATTTCAACAGATG 58.960 37.037 0.00 0.00 0.00 2.90
1746 1810 8.144862 AGGTCTTTCTAGAGATTTCAACAGAT 57.855 34.615 0.00 0.00 0.00 2.90
1747 1811 7.546250 AGGTCTTTCTAGAGATTTCAACAGA 57.454 36.000 0.00 0.00 0.00 3.41
1778 1842 5.247337 GCTAGCTATTACTTCCTCCATTCCT 59.753 44.000 7.70 0.00 0.00 3.36
1779 1843 5.247337 AGCTAGCTATTACTTCCTCCATTCC 59.753 44.000 17.69 0.00 0.00 3.01
1781 1845 7.013834 AGTAGCTAGCTATTACTTCCTCCATT 58.986 38.462 26.59 0.00 0.00 3.16
1783 1847 5.954757 AGTAGCTAGCTATTACTTCCTCCA 58.045 41.667 26.59 0.00 0.00 3.86
1789 1853 8.798402 CAAGGTGATAGTAGCTAGCTATTACTT 58.202 37.037 26.59 20.15 36.38 2.24
1794 1858 6.209788 GGAACAAGGTGATAGTAGCTAGCTAT 59.790 42.308 26.59 12.91 32.38 2.97
1795 1859 5.535406 GGAACAAGGTGATAGTAGCTAGCTA 59.465 44.000 20.67 20.67 0.00 3.32
1796 1860 4.342665 GGAACAAGGTGATAGTAGCTAGCT 59.657 45.833 23.12 23.12 0.00 3.32
1797 1861 4.099573 TGGAACAAGGTGATAGTAGCTAGC 59.900 45.833 6.62 6.62 31.92 3.42
1798 1862 5.854010 TGGAACAAGGTGATAGTAGCTAG 57.146 43.478 0.00 0.00 31.92 3.42
1864 1928 4.211374 GCGTACTTGTTCACTCATTTCAGT 59.789 41.667 0.00 0.00 0.00 3.41
1886 1950 4.149922 TCGCATGTATAGACGCATTTTAGC 59.850 41.667 0.00 0.00 0.00 3.09
1946 2011 7.931015 ATATCATAACAAGGTACTCCCTCAA 57.069 36.000 0.00 0.00 45.47 3.02
1992 2057 3.009723 ACAAAGCATACATCCAGAACCG 58.990 45.455 0.00 0.00 0.00 4.44
2018 2083 4.114794 AGCAGCAGATTCAACAAAAACAC 58.885 39.130 0.00 0.00 0.00 3.32
2025 2090 1.250328 CCCAAGCAGCAGATTCAACA 58.750 50.000 0.00 0.00 0.00 3.33
2047 2112 5.975693 AGGCCGACATAAAAAGAAAATCA 57.024 34.783 0.00 0.00 0.00 2.57
2048 2113 6.386654 TCAAGGCCGACATAAAAAGAAAATC 58.613 36.000 0.00 0.00 0.00 2.17
2049 2114 6.339587 TCAAGGCCGACATAAAAAGAAAAT 57.660 33.333 0.00 0.00 0.00 1.82
2059 2129 2.398588 AGATCCTTCAAGGCCGACATA 58.601 47.619 0.00 0.00 34.61 2.29
2061 2131 0.984230 AAGATCCTTCAAGGCCGACA 59.016 50.000 0.00 0.00 34.61 4.35
2065 2135 6.322201 TGAATTAATCAAGATCCTTCAAGGCC 59.678 38.462 0.00 0.00 32.75 5.19
2087 2157 4.823989 CAGCTCTCTTTCCCTTTTTCTGAA 59.176 41.667 0.00 0.00 0.00 3.02
2088 2158 4.392940 CAGCTCTCTTTCCCTTTTTCTGA 58.607 43.478 0.00 0.00 0.00 3.27
2089 2159 3.057666 GCAGCTCTCTTTCCCTTTTTCTG 60.058 47.826 0.00 0.00 0.00 3.02
2091 2161 2.230025 GGCAGCTCTCTTTCCCTTTTTC 59.770 50.000 0.00 0.00 0.00 2.29
2095 2165 1.688211 GGGCAGCTCTCTTTCCCTT 59.312 57.895 0.00 0.00 32.53 3.95
2096 2166 2.664081 CGGGCAGCTCTCTTTCCCT 61.664 63.158 0.00 0.00 32.89 4.20
2097 2167 1.977293 ATCGGGCAGCTCTCTTTCCC 61.977 60.000 0.00 0.00 32.14 3.97
2098 2168 0.107459 AATCGGGCAGCTCTCTTTCC 60.107 55.000 0.00 0.00 0.00 3.13
2099 2169 2.604046 TAATCGGGCAGCTCTCTTTC 57.396 50.000 0.00 0.00 0.00 2.62
2100 2170 3.567478 ATTAATCGGGCAGCTCTCTTT 57.433 42.857 0.00 0.00 0.00 2.52
2143 2213 2.093181 CCCTCCGTGGATAATTGTGACA 60.093 50.000 0.00 0.00 38.35 3.58
2150 2220 0.916086 TGTTGCCCTCCGTGGATAAT 59.084 50.000 0.00 0.00 38.35 1.28
2192 2262 1.161563 GGTTTGAAGGTCGCCGTTGA 61.162 55.000 0.00 0.00 0.00 3.18
2198 2268 0.953960 ATGGACGGTTTGAAGGTCGC 60.954 55.000 0.00 0.00 0.00 5.19
2204 2274 5.360649 TGGATATACATGGACGGTTTGAA 57.639 39.130 0.00 0.00 0.00 2.69
2213 2283 2.103432 ACGCGGTTTGGATATACATGGA 59.897 45.455 12.47 0.00 0.00 3.41
2222 2292 1.234615 CCAGACAACGCGGTTTGGAT 61.235 55.000 16.72 1.93 43.75 3.41
2226 2296 1.722011 CTATCCAGACAACGCGGTTT 58.278 50.000 12.47 0.00 0.00 3.27
2227 2297 0.739813 GCTATCCAGACAACGCGGTT 60.740 55.000 12.47 0.00 0.00 4.44
2229 2299 2.230940 CGCTATCCAGACAACGCGG 61.231 63.158 12.47 0.00 37.25 6.46
2231 2301 0.459585 TTCCGCTATCCAGACAACGC 60.460 55.000 0.00 0.00 0.00 4.84
2232 2302 1.560923 CTTCCGCTATCCAGACAACG 58.439 55.000 0.00 0.00 0.00 4.10
2238 2308 1.972872 AAATGGCTTCCGCTATCCAG 58.027 50.000 0.00 0.00 36.20 3.86
2239 2309 3.211045 GTTAAATGGCTTCCGCTATCCA 58.789 45.455 0.00 0.00 36.20 3.41
2242 2312 1.602377 GCGTTAAATGGCTTCCGCTAT 59.398 47.619 0.00 0.00 39.21 2.97
2243 2313 1.011333 GCGTTAAATGGCTTCCGCTA 58.989 50.000 0.00 0.00 35.64 4.26
2247 2317 1.431845 CCCGCGTTAAATGGCTTCC 59.568 57.895 4.92 0.00 0.00 3.46
2256 2326 1.283613 CGTGTACAAGCCCGCGTTAA 61.284 55.000 4.92 0.00 0.00 2.01
2257 2327 1.733758 CGTGTACAAGCCCGCGTTA 60.734 57.895 4.92 0.00 0.00 3.18
2261 2331 2.195123 AAATGCGTGTACAAGCCCGC 62.195 55.000 27.33 22.78 45.92 6.13
2264 2334 2.989422 AGAAAATGCGTGTACAAGCC 57.011 45.000 27.33 13.72 34.90 4.35
2267 2337 3.313803 TGCAGAAGAAAATGCGTGTACAA 59.686 39.130 0.00 0.00 45.54 2.41
2269 2339 3.536158 TGCAGAAGAAAATGCGTGTAC 57.464 42.857 0.00 0.00 45.54 2.90
2275 2345 2.982470 CTCCGTTTGCAGAAGAAAATGC 59.018 45.455 0.00 0.00 42.86 3.56


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

AutoCloner maintained by Alex Coulton.