Multiple sequence alignment - TraesCS2A01G134400

Loading Multiple Alignment...

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 TraesCS2A01G134400 chr2A 100.000 4774 0 0 1 4774 80842456 80847229 0.000000e+00 8817
1 TraesCS2A01G134400 chr2D 90.015 4587 233 83 1 4454 80102369 80106863 0.000000e+00 5725
2 TraesCS2A01G134400 chr2D 95.261 211 9 1 4460 4669 80107077 80107287 2.750000e-87 333
3 TraesCS2A01G134400 chr2B 87.988 4587 270 127 1 4442 131598344 131593894 0.000000e+00 5158
4 TraesCS2A01G134400 chr3A 84.158 101 16 0 4460 4560 717992797 717992897 1.090000e-16 99


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 TraesCS2A01G134400 chr2A 80842456 80847229 4773 False 8817 8817 100.000 1 4774 1 chr2A.!!$F1 4773
1 TraesCS2A01G134400 chr2D 80102369 80107287 4918 False 3029 5725 92.638 1 4669 2 chr2D.!!$F1 4668
2 TraesCS2A01G134400 chr2B 131593894 131598344 4450 True 5158 5158 87.988 1 4442 1 chr2B.!!$R1 4441

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
254 261 0.040058 ACCCATGCCATCTGAAGCAA 59.960 50.0 9.40 0.0 43.36 3.91 F
669 680 0.519961 AACGCCCGAAATACAACAGC 59.480 50.0 0.00 0.0 0.00 4.40 F
1389 1463 0.544595 AGACCCCACCACAGGTACTC 60.545 60.0 0.00 0.0 34.60 2.59 F
1888 1978 0.819582 ATTTGAAAGGCGGCTGATGG 59.180 50.0 14.21 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1539 1615 0.096454 CGACTGTCGATCGCACTACA 59.904 55.000 24.86 8.73 43.74 2.74 R
1982 2072 0.179092 GGATGGGCATTTGAGCTTGC 60.179 55.000 0.00 0.00 38.14 4.01 R
3324 3449 0.182061 ATCTGCGCCATGAGGTTCAT 59.818 50.000 4.18 0.00 37.65 2.57 R
3792 3931 1.464608 CATGTTCTTGCCTGTACACGG 59.535 52.381 0.00 0.00 0.00 4.94 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
51 55 2.949177 TCATTAGTTGCCCACACTGT 57.051 45.000 0.00 0.00 0.00 3.55
66 70 4.320494 CCACACTGTTTGCTACTCATTTCC 60.320 45.833 0.00 0.00 0.00 3.13
93 97 6.238759 GCAATATCCATTTTGTCCCTAGTGAC 60.239 42.308 0.00 0.00 35.77 3.67
112 116 4.011046 GCACCTGCAAAACAACGG 57.989 55.556 0.00 0.00 41.59 4.44
115 119 1.756561 ACCTGCAAAACAACGGGCT 60.757 52.632 0.00 0.00 35.58 5.19
191 198 1.906574 ACTACCTCGGGAAATTCAGCA 59.093 47.619 0.00 0.00 0.00 4.41
198 205 4.498682 CCTCGGGAAATTCAGCATCATTTC 60.499 45.833 0.00 6.13 38.27 2.17
219 226 9.094459 CATTTCGAAATGCAACAAAAGTATTTG 57.906 29.630 31.60 9.38 43.38 2.32
222 229 6.419413 TCGAAATGCAACAAAAGTATTTGGTC 59.581 34.615 0.00 0.00 42.59 4.02
225 232 2.403698 GCAACAAAAGTATTTGGTCGCG 59.596 45.455 0.00 0.00 42.59 5.87
228 235 4.141855 ACAAAAGTATTTGGTCGCGAAG 57.858 40.909 12.06 0.00 37.87 3.79
234 241 4.751060 AGTATTTGGTCGCGAAGTTATCA 58.249 39.130 12.06 0.00 0.00 2.15
247 254 3.959495 AGTTATCAACCCATGCCATCT 57.041 42.857 0.00 0.00 0.00 2.90
254 261 0.040058 ACCCATGCCATCTGAAGCAA 59.960 50.000 9.40 0.00 43.36 3.91
290 297 6.272792 TGGACTAGATACACCCAAAAAGGTAA 59.727 38.462 0.00 0.00 38.39 2.85
298 305 4.064388 CACCCAAAAAGGTAAATTGGCTG 58.936 43.478 0.00 0.00 41.80 4.85
308 315 4.021456 AGGTAAATTGGCTGTTTAGTTGGC 60.021 41.667 0.00 0.00 0.00 4.52
355 362 6.918067 TCAACAACTTCTCTCTCCTTCATA 57.082 37.500 0.00 0.00 0.00 2.15
391 398 8.808529 ACAAAATAGTCTCTCGATAATTTGTCG 58.191 33.333 9.02 9.02 40.30 4.35
428 435 6.037391 ACCGACAAAAATCTCGACTACAAAAA 59.963 34.615 0.00 0.00 31.24 1.94
493 500 0.889186 AGTGCCGATGGTTGGTTCAC 60.889 55.000 0.00 0.00 0.00 3.18
521 528 9.428097 GATGCACTAAATTCCTTTTCTCAAAAT 57.572 29.630 0.00 0.00 0.00 1.82
669 680 0.519961 AACGCCCGAAATACAACAGC 59.480 50.000 0.00 0.00 0.00 4.40
670 681 0.604243 ACGCCCGAAATACAACAGCA 60.604 50.000 0.00 0.00 0.00 4.41
847 862 1.083706 ACAGATTGGGCTCCCCTCT 59.916 57.895 1.89 2.14 45.70 3.69
850 865 2.041265 ATTGGGCTCCCCTCTCGT 59.959 61.111 1.89 0.00 45.70 4.18
859 874 1.820481 CCCCTCTCGTCGTCTCTCC 60.820 68.421 0.00 0.00 0.00 3.71
1037 1087 3.466879 CGCCGTACGTTTCTTCCC 58.533 61.111 15.21 0.00 36.87 3.97
1038 1088 2.096442 CGCCGTACGTTTCTTCCCC 61.096 63.158 15.21 0.00 36.87 4.81
1039 1089 2.096442 GCCGTACGTTTCTTCCCCG 61.096 63.158 15.21 0.00 0.00 5.73
1041 1091 2.096442 CGTACGTTTCTTCCCCGCC 61.096 63.158 7.22 0.00 0.00 6.13
1042 1092 1.004679 GTACGTTTCTTCCCCGCCA 60.005 57.895 0.00 0.00 0.00 5.69
1044 1094 1.474332 TACGTTTCTTCCCCGCCACT 61.474 55.000 0.00 0.00 0.00 4.00
1129 1196 1.360194 TTCCGTGTTGTTCGCGTGTT 61.360 50.000 5.77 0.00 46.91 3.32
1216 1287 1.004918 GAGGTGAAGGTGGTGGTCG 60.005 63.158 0.00 0.00 0.00 4.79
1223 1294 4.675029 GGTGGTGGTCGTGGACGG 62.675 72.222 0.00 0.00 40.29 4.79
1388 1462 0.836400 CAGACCCCACCACAGGTACT 60.836 60.000 0.00 0.00 43.88 2.73
1389 1463 0.544595 AGACCCCACCACAGGTACTC 60.545 60.000 0.00 0.00 34.60 2.59
1439 1513 1.794222 CCCAATTGACCGCTCGTTC 59.206 57.895 7.12 0.00 0.00 3.95
1452 1526 1.094785 CTCGTTCCGCCCATCAAATT 58.905 50.000 0.00 0.00 0.00 1.82
1493 1568 6.142817 GTCAAATTATCTCGCACAAACAGTT 58.857 36.000 0.00 0.00 0.00 3.16
1505 1580 8.352752 TCGCACAAACAGTTAATAGATAGATG 57.647 34.615 0.00 0.00 0.00 2.90
1507 1582 7.438160 CGCACAAACAGTTAATAGATAGATGGA 59.562 37.037 0.00 0.00 0.00 3.41
1541 1617 2.332514 GCATGTGCGCTTGTGTGT 59.667 55.556 9.73 0.00 0.00 3.72
1570 1646 3.374402 CAGTCGGTCGTCCCAGCT 61.374 66.667 0.00 0.00 0.00 4.24
1571 1647 2.044555 CAGTCGGTCGTCCCAGCTA 61.045 63.158 0.00 0.00 0.00 3.32
1572 1648 1.749638 AGTCGGTCGTCCCAGCTAG 60.750 63.158 0.00 0.00 0.00 3.42
1574 1650 4.208686 CGGTCGTCCCAGCTAGGC 62.209 72.222 0.00 0.00 35.39 3.93
1575 1651 3.851128 GGTCGTCCCAGCTAGGCC 61.851 72.222 0.00 0.00 35.39 5.19
1576 1652 3.851128 GTCGTCCCAGCTAGGCCC 61.851 72.222 0.00 0.00 35.39 5.80
1579 1655 2.285868 GTCCCAGCTAGGCCCCTA 59.714 66.667 0.00 0.00 35.39 3.53
1580 1656 1.839296 GTCCCAGCTAGGCCCCTAG 60.839 68.421 15.52 15.52 46.41 3.02
1581 1657 2.287251 CCCAGCTAGGCCCCTAGT 59.713 66.667 19.63 6.86 45.67 2.57
1582 1658 1.839296 CCCAGCTAGGCCCCTAGTC 60.839 68.421 19.63 13.09 45.67 2.59
1583 1659 1.839296 CCAGCTAGGCCCCTAGTCC 60.839 68.421 19.63 6.96 45.67 3.85
1584 1660 1.839296 CAGCTAGGCCCCTAGTCCC 60.839 68.421 19.63 6.35 45.67 4.46
1585 1661 2.285868 GCTAGGCCCCTAGTCCCA 59.714 66.667 19.63 0.00 45.67 4.37
1586 1662 1.384082 GCTAGGCCCCTAGTCCCAA 60.384 63.158 19.63 0.00 45.67 4.12
1587 1663 1.697082 GCTAGGCCCCTAGTCCCAAC 61.697 65.000 19.63 1.93 45.67 3.77
1588 1664 1.003835 TAGGCCCCTAGTCCCAACC 59.996 63.158 0.00 0.00 0.00 3.77
1716 1794 4.147306 TGACATTTTCGCGTAACAAATTGC 59.853 37.500 5.77 3.86 0.00 3.56
1743 1821 2.492881 TGGGTTGAATTATGCAGTGCTG 59.507 45.455 17.60 0.00 0.00 4.41
1791 1872 6.616947 TCCAAACAAAAGTCTTAGTTGTGTG 58.383 36.000 11.25 11.25 39.29 3.82
1795 1876 6.995511 ACAAAAGTCTTAGTTGTGTGCTTA 57.004 33.333 2.49 0.00 34.28 3.09
1807 1888 3.670625 TGTGTGCTTATGGTTGTACTCC 58.329 45.455 0.00 0.00 0.00 3.85
1851 1932 3.248363 CGACAGTTGCACTTGATTTCTCA 59.752 43.478 3.77 0.00 0.00 3.27
1888 1978 0.819582 ATTTGAAAGGCGGCTGATGG 59.180 50.000 14.21 0.00 0.00 3.51
1893 1983 3.650298 AAGGCGGCTGATGGCATGT 62.650 57.895 14.21 0.00 44.01 3.21
1896 1986 2.103538 CGGCTGATGGCATGTTGC 59.896 61.111 3.81 6.05 44.08 4.17
1927 2017 9.394477 TGAGATATTTCGATTAGTGTGTTATCG 57.606 33.333 0.00 0.00 41.75 2.92
1982 2072 2.095567 CACCGATTGGAGCAGTTCTTTG 60.096 50.000 5.81 0.00 39.21 2.77
2006 2098 1.688772 CTCAAATGCCCATCCTCCTG 58.311 55.000 0.00 0.00 0.00 3.86
2011 2103 1.132554 ATGCCCATCCTCCTGCCTAG 61.133 60.000 0.00 0.00 0.00 3.02
2012 2104 1.460305 GCCCATCCTCCTGCCTAGA 60.460 63.158 0.00 0.00 0.00 2.43
2013 2105 1.479368 GCCCATCCTCCTGCCTAGAG 61.479 65.000 0.00 0.00 0.00 2.43
2014 2106 1.479368 CCCATCCTCCTGCCTAGAGC 61.479 65.000 0.00 0.00 44.14 4.09
2041 2133 6.042552 AGTGAGTACAAGAGGATGGATAATGG 59.957 42.308 0.00 0.00 0.00 3.16
2042 2134 6.042093 GTGAGTACAAGAGGATGGATAATGGA 59.958 42.308 0.00 0.00 0.00 3.41
2043 2135 6.268617 TGAGTACAAGAGGATGGATAATGGAG 59.731 42.308 0.00 0.00 0.00 3.86
2092 2184 6.002911 CGATTTGTTTTTGCTAATCAAAGCG 58.997 36.000 22.38 22.38 45.67 4.68
2093 2185 5.649602 TTTGTTTTTGCTAATCAAAGCGG 57.350 34.783 7.32 0.00 45.85 5.52
2094 2186 4.314740 TGTTTTTGCTAATCAAAGCGGT 57.685 36.364 0.00 0.00 45.85 5.68
2098 2190 6.205076 TGTTTTTGCTAATCAAAGCGGTAGTA 59.795 34.615 0.00 0.00 45.85 1.82
2100 2192 4.730949 TGCTAATCAAAGCGGTAGTACT 57.269 40.909 0.00 0.00 45.85 2.73
2172 2264 6.451064 AAAAGGCCTCTTAAAATATCCACG 57.549 37.500 5.23 0.00 32.01 4.94
2173 2265 3.477530 AGGCCTCTTAAAATATCCACGC 58.522 45.455 0.00 0.00 0.00 5.34
2229 2321 8.100508 TCGAATCTTGGTAGTAGTATGATCTG 57.899 38.462 0.00 0.00 0.00 2.90
2303 2414 7.995488 AGCAGCTAATGACTTTACTAATCCAAT 59.005 33.333 0.00 0.00 0.00 3.16
2687 2798 3.329889 TTCTCCATGCCGGCCACT 61.330 61.111 26.77 5.57 33.14 4.00
2915 3026 1.370064 CGTCAACTTCCGGTTCCCT 59.630 57.895 0.00 0.00 35.74 4.20
2921 3032 3.327404 TTCCGGTTCCCTGGCCTC 61.327 66.667 3.32 0.00 0.00 4.70
3263 3386 2.672961 TCGTCCATGTAAGCCTTCAG 57.327 50.000 0.00 0.00 0.00 3.02
3280 3403 1.833630 TCAGTCCGCTTCCAATCATCT 59.166 47.619 0.00 0.00 0.00 2.90
3312 3437 3.802722 GCTGACAAGCTTAGTTGTGAG 57.197 47.619 0.00 0.00 46.60 3.51
3316 3441 5.773575 CTGACAAGCTTAGTTGTGAGACTA 58.226 41.667 0.00 0.00 42.38 2.59
3318 3443 5.983720 TGACAAGCTTAGTTGTGAGACTAAC 59.016 40.000 0.00 0.00 40.83 2.34
3323 3448 2.814280 AGTTGTGAGACTAACGGTGG 57.186 50.000 0.00 0.00 32.24 4.61
3324 3449 2.313317 AGTTGTGAGACTAACGGTGGA 58.687 47.619 0.00 0.00 32.24 4.02
3326 3451 2.993899 GTTGTGAGACTAACGGTGGATG 59.006 50.000 0.00 0.00 0.00 3.51
3327 3452 2.521126 TGTGAGACTAACGGTGGATGA 58.479 47.619 0.00 0.00 0.00 2.92
3328 3453 2.894765 TGTGAGACTAACGGTGGATGAA 59.105 45.455 0.00 0.00 0.00 2.57
3329 3454 3.251571 GTGAGACTAACGGTGGATGAAC 58.748 50.000 0.00 0.00 0.00 3.18
3330 3455 2.232941 TGAGACTAACGGTGGATGAACC 59.767 50.000 0.00 0.00 36.82 3.62
3331 3456 2.496470 GAGACTAACGGTGGATGAACCT 59.504 50.000 0.00 0.00 38.14 3.50
3332 3457 2.496470 AGACTAACGGTGGATGAACCTC 59.504 50.000 0.00 0.00 38.14 3.85
3333 3458 2.232941 GACTAACGGTGGATGAACCTCA 59.767 50.000 0.00 0.00 38.14 3.86
3335 3460 2.113860 AACGGTGGATGAACCTCATG 57.886 50.000 0.00 0.00 37.20 3.07
3337 3462 1.097547 CGGTGGATGAACCTCATGGC 61.098 60.000 0.00 0.00 37.20 4.40
3377 3510 4.681978 GGGTTCGTGCAGGCGTCT 62.682 66.667 0.35 0.00 0.00 4.18
3391 3524 2.179517 GTCTCGGAGCACGTGGAG 59.820 66.667 18.88 14.82 44.69 3.86
3392 3525 3.062466 TCTCGGAGCACGTGGAGG 61.062 66.667 18.88 0.00 44.69 4.30
3473 3606 3.296709 CTTCCTGACGGGGGTGACG 62.297 68.421 0.00 0.00 35.33 4.35
3711 3844 0.179000 CAAGATGAAGGAGGACGGGG 59.821 60.000 0.00 0.00 0.00 5.73
3815 3958 3.743911 CGTGTACAGGCAAGAACATGTTA 59.256 43.478 11.95 0.00 0.00 2.41
3849 3992 1.289276 TCGTGCGATGTCATTCCATG 58.711 50.000 0.00 0.00 0.00 3.66
3855 3998 0.672342 GATGTCATTCCATGGCTGCC 59.328 55.000 12.87 12.87 35.48 4.85
3918 4061 1.727022 CGCGTGAAAGCAAGGCAAG 60.727 57.895 0.00 0.00 36.85 4.01
3919 4062 1.360192 GCGTGAAAGCAAGGCAAGT 59.640 52.632 0.00 0.00 37.05 3.16
3965 4109 2.890474 GTACGACCCATGCAGCGG 60.890 66.667 0.00 0.00 0.00 5.52
4020 4180 4.263018 TGATGTTCTCCTCTTGTGTCTG 57.737 45.455 0.00 0.00 0.00 3.51
4032 4200 5.395768 CCTCTTGTGTCTGAAATAGTAGGGG 60.396 48.000 0.00 0.00 0.00 4.79
4034 4202 2.167693 TGTGTCTGAAATAGTAGGGGCG 59.832 50.000 0.00 0.00 0.00 6.13
4121 4295 1.004511 AGCAGAAGCCTGAGCATTTCT 59.995 47.619 0.00 0.00 43.02 2.52
4127 4301 4.831710 AGAAGCCTGAGCATTTCTTCTTTT 59.168 37.500 0.00 0.00 40.12 2.27
4132 4306 5.620879 GCCTGAGCATTTCTTCTTTTAGGTG 60.621 44.000 0.00 0.00 39.53 4.00
4168 4346 2.788786 GCAAAAACTGTCACCGTGATTG 59.211 45.455 4.13 5.32 0.00 2.67
4177 4357 1.003003 TCACCGTGATTGCAAGGATGA 59.997 47.619 4.94 4.75 45.22 2.92
4246 4431 3.215568 CAAGTGGCGGTGTTGGCA 61.216 61.111 0.00 0.00 42.76 4.92
4279 4485 7.173218 TGTTGTGAGTATCTGAAATTCTGAACC 59.827 37.037 6.66 1.34 34.92 3.62
4292 4498 4.535526 TTCTGAACCGAACATGATGAGA 57.464 40.909 0.00 0.00 0.00 3.27
4310 4516 3.294214 GAGAAACTGGACCGGGATAGTA 58.706 50.000 6.32 0.00 0.00 1.82
4312 4518 1.411041 AACTGGACCGGGATAGTAGC 58.589 55.000 6.32 0.00 0.00 3.58
4313 4519 0.556747 ACTGGACCGGGATAGTAGCT 59.443 55.000 6.32 0.00 0.00 3.32
4314 4520 0.962489 CTGGACCGGGATAGTAGCTG 59.038 60.000 6.32 0.00 0.00 4.24
4315 4521 0.554305 TGGACCGGGATAGTAGCTGA 59.446 55.000 6.32 0.00 0.00 4.26
4316 4522 1.249407 GGACCGGGATAGTAGCTGAG 58.751 60.000 6.32 0.00 0.00 3.35
4317 4523 0.599060 GACCGGGATAGTAGCTGAGC 59.401 60.000 6.32 0.00 0.00 4.26
4318 4524 0.828343 ACCGGGATAGTAGCTGAGCC 60.828 60.000 6.32 0.00 0.00 4.70
4361 4567 6.371548 GTGAAGTTATGAACAGAGCATGGTAA 59.628 38.462 0.00 0.00 0.00 2.85
4458 4665 3.803082 CCGAACACAGCGGCATGG 61.803 66.667 1.45 0.00 42.55 3.66
4494 4909 1.069636 CAACGTGCAGAGAGGAAAAGC 60.070 52.381 0.00 0.00 0.00 3.51
4527 4942 2.224159 GGCCTCCTTGTCACAGGGA 61.224 63.158 8.64 8.64 37.29 4.20
4528 4943 1.566298 GGCCTCCTTGTCACAGGGAT 61.566 60.000 9.50 0.00 38.90 3.85
4570 4985 8.514594 ACCAAATGTACAAGTCATCAAAGTATG 58.485 33.333 0.00 0.00 0.00 2.39
4584 4999 0.035439 AGTATGCCCCTGGTTTCACG 60.035 55.000 0.00 0.00 0.00 4.35
4592 5007 0.682852 CCTGGTTTCACGTAGGGTCA 59.317 55.000 0.00 0.00 0.00 4.02
4610 5025 0.376152 CAGAACACAGGCATCGCATC 59.624 55.000 0.00 0.00 0.00 3.91
4659 5074 3.755378 CCTGAAACCATCAACTTGAGGAG 59.245 47.826 4.98 0.00 37.67 3.69
4664 5079 4.647564 ACCATCAACTTGAGGAGATTGT 57.352 40.909 4.98 0.00 27.97 2.71
4665 5080 4.330250 ACCATCAACTTGAGGAGATTGTG 58.670 43.478 4.98 0.00 27.97 3.33
4666 5081 4.202503 ACCATCAACTTGAGGAGATTGTGT 60.203 41.667 4.98 0.00 27.97 3.72
4670 5085 7.040478 CCATCAACTTGAGGAGATTGTGTTTTA 60.040 37.037 4.98 0.00 27.97 1.52
4671 5086 7.873719 TCAACTTGAGGAGATTGTGTTTTAA 57.126 32.000 0.00 0.00 0.00 1.52
4672 5087 7.930217 TCAACTTGAGGAGATTGTGTTTTAAG 58.070 34.615 0.00 0.00 0.00 1.85
4673 5088 6.884280 ACTTGAGGAGATTGTGTTTTAAGG 57.116 37.500 0.00 0.00 0.00 2.69
4674 5089 6.365520 ACTTGAGGAGATTGTGTTTTAAGGT 58.634 36.000 0.00 0.00 0.00 3.50
4675 5090 6.486993 ACTTGAGGAGATTGTGTTTTAAGGTC 59.513 38.462 0.00 0.00 0.00 3.85
4676 5091 5.313712 TGAGGAGATTGTGTTTTAAGGTCC 58.686 41.667 0.00 0.00 0.00 4.46
4677 5092 4.324267 AGGAGATTGTGTTTTAAGGTCCG 58.676 43.478 0.00 0.00 0.00 4.79
4678 5093 3.439129 GGAGATTGTGTTTTAAGGTCCGG 59.561 47.826 0.00 0.00 0.00 5.14
4679 5094 4.070009 GAGATTGTGTTTTAAGGTCCGGT 58.930 43.478 0.00 0.00 0.00 5.28
4680 5095 4.070009 AGATTGTGTTTTAAGGTCCGGTC 58.930 43.478 0.00 0.00 0.00 4.79
4681 5096 3.564053 TTGTGTTTTAAGGTCCGGTCT 57.436 42.857 0.00 0.00 0.00 3.85
4682 5097 4.686191 TTGTGTTTTAAGGTCCGGTCTA 57.314 40.909 0.00 0.00 0.00 2.59
4683 5098 4.895668 TGTGTTTTAAGGTCCGGTCTAT 57.104 40.909 0.00 0.00 0.00 1.98
4684 5099 4.824289 TGTGTTTTAAGGTCCGGTCTATC 58.176 43.478 0.00 0.00 0.00 2.08
4685 5100 4.283978 TGTGTTTTAAGGTCCGGTCTATCA 59.716 41.667 0.00 0.00 0.00 2.15
4686 5101 5.221682 TGTGTTTTAAGGTCCGGTCTATCAA 60.222 40.000 0.00 0.00 0.00 2.57
4687 5102 5.878669 GTGTTTTAAGGTCCGGTCTATCAAT 59.121 40.000 0.00 0.00 0.00 2.57
4688 5103 7.043565 GTGTTTTAAGGTCCGGTCTATCAATA 58.956 38.462 0.00 0.00 0.00 1.90
4689 5104 7.010830 GTGTTTTAAGGTCCGGTCTATCAATAC 59.989 40.741 0.00 3.22 0.00 1.89
4690 5105 6.795144 TTTAAGGTCCGGTCTATCAATACA 57.205 37.500 0.00 0.00 0.00 2.29
4691 5106 6.795144 TTAAGGTCCGGTCTATCAATACAA 57.205 37.500 0.00 0.00 0.00 2.41
4692 5107 4.939052 AGGTCCGGTCTATCAATACAAG 57.061 45.455 0.00 0.00 0.00 3.16
4693 5108 3.069729 AGGTCCGGTCTATCAATACAAGC 59.930 47.826 0.00 0.00 0.00 4.01
4694 5109 3.069729 GGTCCGGTCTATCAATACAAGCT 59.930 47.826 0.00 0.00 0.00 3.74
4695 5110 4.051922 GTCCGGTCTATCAATACAAGCTG 58.948 47.826 0.00 0.00 0.00 4.24
4696 5111 3.704566 TCCGGTCTATCAATACAAGCTGT 59.295 43.478 0.00 0.00 0.00 4.40
4697 5112 4.161565 TCCGGTCTATCAATACAAGCTGTT 59.838 41.667 0.00 0.00 0.00 3.16
4698 5113 4.271049 CCGGTCTATCAATACAAGCTGTTG 59.729 45.833 0.00 0.00 39.82 3.33
4699 5114 4.271049 CGGTCTATCAATACAAGCTGTTGG 59.729 45.833 0.00 0.00 38.07 3.77
4700 5115 5.186198 GGTCTATCAATACAAGCTGTTGGT 58.814 41.667 0.00 0.00 38.07 3.67
4701 5116 5.648092 GGTCTATCAATACAAGCTGTTGGTT 59.352 40.000 0.00 0.00 38.07 3.67
4708 5123 2.298411 CAAGCTGTTGGTTGCTGTTT 57.702 45.000 0.00 0.00 43.34 2.83
4709 5124 1.928503 CAAGCTGTTGGTTGCTGTTTG 59.071 47.619 0.00 0.00 43.34 2.93
4710 5125 1.473258 AGCTGTTGGTTGCTGTTTGA 58.527 45.000 0.00 0.00 38.21 2.69
4711 5126 1.134946 AGCTGTTGGTTGCTGTTTGAC 59.865 47.619 0.00 0.00 38.21 3.18
4712 5127 1.826327 CTGTTGGTTGCTGTTTGACG 58.174 50.000 0.00 0.00 0.00 4.35
4713 5128 0.179150 TGTTGGTTGCTGTTTGACGC 60.179 50.000 0.00 0.00 0.00 5.19
4714 5129 1.063327 TTGGTTGCTGTTTGACGCG 59.937 52.632 3.53 3.53 0.00 6.01
4715 5130 1.369839 TTGGTTGCTGTTTGACGCGA 61.370 50.000 15.93 0.00 0.00 5.87
4716 5131 1.368850 GGTTGCTGTTTGACGCGAC 60.369 57.895 15.93 7.62 39.31 5.19
4717 5132 1.717728 GTTGCTGTTTGACGCGACG 60.718 57.895 15.93 0.00 31.54 5.12
4718 5133 1.878975 TTGCTGTTTGACGCGACGA 60.879 52.632 15.93 2.77 0.00 4.20
4719 5134 1.218875 TTGCTGTTTGACGCGACGAT 61.219 50.000 15.93 0.00 0.00 3.73
4720 5135 1.225475 GCTGTTTGACGCGACGATG 60.225 57.895 15.93 1.30 0.00 3.84
4721 5136 1.416049 CTGTTTGACGCGACGATGG 59.584 57.895 15.93 0.00 0.00 3.51
4722 5137 2.095843 GTTTGACGCGACGATGGC 59.904 61.111 15.93 0.00 0.00 4.40
4723 5138 3.115892 TTTGACGCGACGATGGCC 61.116 61.111 15.93 0.00 0.00 5.36
4724 5139 3.583276 TTTGACGCGACGATGGCCT 62.583 57.895 15.93 0.00 0.00 5.19
4725 5140 3.982372 TTGACGCGACGATGGCCTC 62.982 63.158 15.93 0.00 0.00 4.70
4726 5141 4.194720 GACGCGACGATGGCCTCT 62.195 66.667 15.93 0.00 0.00 3.69
4727 5142 2.827190 ACGCGACGATGGCCTCTA 60.827 61.111 15.93 0.00 0.00 2.43
4728 5143 2.353607 CGCGACGATGGCCTCTAC 60.354 66.667 0.00 0.00 0.00 2.59
4729 5144 2.835705 CGCGACGATGGCCTCTACT 61.836 63.158 0.00 0.00 0.00 2.57
4730 5145 1.008309 GCGACGATGGCCTCTACTC 60.008 63.158 3.32 0.00 0.00 2.59
4731 5146 1.448922 GCGACGATGGCCTCTACTCT 61.449 60.000 3.32 0.00 0.00 3.24
4732 5147 1.880271 CGACGATGGCCTCTACTCTA 58.120 55.000 3.32 0.00 0.00 2.43
4733 5148 2.428491 CGACGATGGCCTCTACTCTAT 58.572 52.381 3.32 0.00 0.00 1.98
4734 5149 2.814919 CGACGATGGCCTCTACTCTATT 59.185 50.000 3.32 0.00 0.00 1.73
4735 5150 4.001652 CGACGATGGCCTCTACTCTATTA 58.998 47.826 3.32 0.00 0.00 0.98
4736 5151 4.093703 CGACGATGGCCTCTACTCTATTAG 59.906 50.000 3.32 0.00 0.00 1.73
4737 5152 5.244189 ACGATGGCCTCTACTCTATTAGA 57.756 43.478 3.32 0.00 0.00 2.10
4739 5154 5.013287 ACGATGGCCTCTACTCTATTAGAGA 59.987 44.000 24.24 9.40 45.07 3.10
4740 5155 5.353123 CGATGGCCTCTACTCTATTAGAGAC 59.647 48.000 24.24 1.45 45.07 3.36
4741 5156 5.915744 TGGCCTCTACTCTATTAGAGACT 57.084 43.478 24.24 8.12 45.07 3.24
4742 5157 7.576978 ATGGCCTCTACTCTATTAGAGACTA 57.423 40.000 24.24 8.77 45.07 2.59
4743 5158 7.390013 TGGCCTCTACTCTATTAGAGACTAA 57.610 40.000 24.24 8.17 45.07 2.24
4744 5159 7.225725 TGGCCTCTACTCTATTAGAGACTAAC 58.774 42.308 24.24 10.42 45.07 2.34
4745 5160 7.072708 TGGCCTCTACTCTATTAGAGACTAACT 59.927 40.741 24.24 6.18 45.07 2.24
4746 5161 8.596293 GGCCTCTACTCTATTAGAGACTAACTA 58.404 40.741 24.24 6.92 45.07 2.24
4760 5175 8.638629 AGAGACTAACTAATTGTACTCAGTGT 57.361 34.615 0.00 0.00 0.00 3.55
4761 5176 9.736414 AGAGACTAACTAATTGTACTCAGTGTA 57.264 33.333 0.00 0.00 0.00 2.90
4762 5177 9.991388 GAGACTAACTAATTGTACTCAGTGTAG 57.009 37.037 0.00 0.00 0.00 2.74
4763 5178 8.958506 AGACTAACTAATTGTACTCAGTGTAGG 58.041 37.037 0.00 0.00 0.00 3.18
4764 5179 7.545489 ACTAACTAATTGTACTCAGTGTAGGC 58.455 38.462 0.00 0.00 0.00 3.93
4765 5180 6.607004 AACTAATTGTACTCAGTGTAGGCT 57.393 37.500 0.00 0.00 0.00 4.58
4766 5181 5.967088 ACTAATTGTACTCAGTGTAGGCTG 58.033 41.667 0.00 0.00 37.81 4.85
4767 5182 2.743636 TTGTACTCAGTGTAGGCTGC 57.256 50.000 0.00 0.00 36.49 5.25
4768 5183 1.924731 TGTACTCAGTGTAGGCTGCT 58.075 50.000 3.77 0.00 36.49 4.24
4769 5184 3.081710 TGTACTCAGTGTAGGCTGCTA 57.918 47.619 3.77 0.00 36.49 3.49
4770 5185 3.632333 TGTACTCAGTGTAGGCTGCTAT 58.368 45.455 3.77 0.00 36.49 2.97
4771 5186 4.788679 TGTACTCAGTGTAGGCTGCTATA 58.211 43.478 3.77 0.00 36.49 1.31
4772 5187 5.386060 TGTACTCAGTGTAGGCTGCTATAT 58.614 41.667 3.77 0.00 36.49 0.86
4773 5188 4.862902 ACTCAGTGTAGGCTGCTATATG 57.137 45.455 3.77 0.00 36.49 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.883142 AATGAAGAGGAAAATTTAAACAACACA 57.117 25.926 0.00 0.00 0.00 3.72
38 42 1.028905 TAGCAAACAGTGTGGGCAAC 58.971 50.000 18.36 0.00 0.00 4.17
51 55 6.039717 GGATATTGCAGGAAATGAGTAGCAAA 59.960 38.462 0.00 0.00 43.97 3.68
66 70 5.829924 ACTAGGGACAAAATGGATATTGCAG 59.170 40.000 0.00 0.00 0.00 4.41
162 169 7.126115 TGAATTTCCCGAGGTAGTTATTAAGGA 59.874 37.037 0.00 0.00 0.00 3.36
167 174 5.123936 GCTGAATTTCCCGAGGTAGTTATT 58.876 41.667 0.00 0.00 0.00 1.40
191 198 8.761575 ATACTTTTGTTGCATTTCGAAATGAT 57.238 26.923 41.10 24.34 46.72 2.45
198 205 6.523676 ACCAAATACTTTTGTTGCATTTCG 57.476 33.333 0.00 0.00 40.55 3.46
219 226 1.004595 GGGTTGATAACTTCGCGACC 58.995 55.000 9.15 3.32 0.00 4.79
222 229 1.268032 GCATGGGTTGATAACTTCGCG 60.268 52.381 0.00 0.00 0.00 5.87
225 232 4.037208 CAGATGGCATGGGTTGATAACTTC 59.963 45.833 3.81 0.00 0.00 3.01
228 235 3.554934 TCAGATGGCATGGGTTGATAAC 58.445 45.455 3.81 0.00 0.00 1.89
234 241 0.040058 TGCTTCAGATGGCATGGGTT 59.960 50.000 3.81 0.00 33.23 4.11
247 254 4.402155 AGTCCAAGAAACAATGTTGCTTCA 59.598 37.500 16.06 3.90 36.11 3.02
254 261 6.879458 GGTGTATCTAGTCCAAGAAACAATGT 59.121 38.462 0.00 0.00 0.00 2.71
290 297 4.379652 CAAAGCCAACTAAACAGCCAATT 58.620 39.130 0.00 0.00 0.00 2.32
308 315 0.445436 CGACAAGCAGGCTAGCAAAG 59.555 55.000 18.24 6.49 36.85 2.77
428 435 5.585390 CAAGACTGCAAAGTCAATCTTGTT 58.415 37.500 8.62 0.00 42.21 2.83
429 436 5.179045 CAAGACTGCAAAGTCAATCTTGT 57.821 39.130 8.62 0.00 42.21 3.16
450 457 1.205893 GCATTTTTGCCCCGGAATACA 59.794 47.619 0.73 0.00 0.00 2.29
451 458 1.934589 GCATTTTTGCCCCGGAATAC 58.065 50.000 0.73 0.00 0.00 1.89
475 482 1.169661 TGTGAACCAACCATCGGCAC 61.170 55.000 0.00 0.00 0.00 5.01
478 485 1.739466 CATCTGTGAACCAACCATCGG 59.261 52.381 0.00 0.00 0.00 4.18
493 500 7.149569 TGAGAAAAGGAATTTAGTGCATCTG 57.850 36.000 0.00 0.00 0.00 2.90
763 774 2.332362 CTGCCTACGTATCGCCGTGT 62.332 60.000 11.12 0.00 41.92 4.49
766 777 2.050351 CCTGCCTACGTATCGCCG 60.050 66.667 11.12 5.96 0.00 6.46
847 862 1.153608 CGAGAGGGAGAGACGACGA 60.154 63.158 0.00 0.00 0.00 4.20
850 865 2.124653 GGCGAGAGGGAGAGACGA 60.125 66.667 0.00 0.00 0.00 4.20
919 952 2.885644 CGTGATGGGGAAGCGACG 60.886 66.667 0.00 0.00 0.00 5.12
920 953 3.195698 GCGTGATGGGGAAGCGAC 61.196 66.667 0.00 0.00 0.00 5.19
921 954 4.467084 GGCGTGATGGGGAAGCGA 62.467 66.667 0.00 0.00 0.00 4.93
928 978 4.100084 TGGAGCAGGCGTGATGGG 62.100 66.667 11.29 0.00 0.00 4.00
1037 1087 2.434359 GTCTTTCCGGAGTGGCGG 60.434 66.667 3.34 0.00 37.80 6.13
1038 1088 2.434359 GGTCTTTCCGGAGTGGCG 60.434 66.667 3.34 0.00 37.80 5.69
1410 1484 3.675775 CGGTCAATTGGGCATTTTAGTGG 60.676 47.826 5.42 0.00 0.00 4.00
1439 1513 2.985957 ATTGGAAATTTGATGGGCGG 57.014 45.000 0.00 0.00 0.00 6.13
1481 1555 7.438160 TCCATCTATCTATTAACTGTTTGTGCG 59.562 37.037 0.00 0.00 0.00 5.34
1493 1568 6.390048 AGACCGGAGTCCATCTATCTATTA 57.610 41.667 9.46 0.00 44.72 0.98
1505 1580 1.112950 CCCTAGAAAGACCGGAGTCC 58.887 60.000 9.46 0.00 44.72 3.85
1507 1582 0.252103 TGCCCTAGAAAGACCGGAGT 60.252 55.000 9.46 0.00 0.00 3.85
1534 1610 1.001158 TGTCGATCGCACTACACACAA 60.001 47.619 11.09 0.00 0.00 3.33
1539 1615 0.096454 CGACTGTCGATCGCACTACA 59.904 55.000 24.86 8.73 43.74 2.74
1541 1617 1.022982 ACCGACTGTCGATCGCACTA 61.023 55.000 29.93 0.00 43.74 2.74
1570 1646 1.003835 GGTTGGGACTAGGGGCCTA 59.996 63.158 0.84 0.00 0.00 3.93
1571 1647 2.286197 GGTTGGGACTAGGGGCCT 60.286 66.667 0.84 0.00 0.00 5.19
1572 1648 3.417779 GGGTTGGGACTAGGGGCC 61.418 72.222 0.00 0.00 0.00 5.80
1574 1650 2.680370 GCTGGGTTGGGACTAGGGG 61.680 68.421 0.00 0.00 0.00 4.79
1575 1651 1.915078 CTGCTGGGTTGGGACTAGGG 61.915 65.000 0.00 0.00 0.00 3.53
1576 1652 1.201429 ACTGCTGGGTTGGGACTAGG 61.201 60.000 0.00 0.00 0.00 3.02
1577 1653 0.250513 GACTGCTGGGTTGGGACTAG 59.749 60.000 0.00 0.00 0.00 2.57
1578 1654 1.198759 GGACTGCTGGGTTGGGACTA 61.199 60.000 0.00 0.00 0.00 2.59
1579 1655 2.529744 GGACTGCTGGGTTGGGACT 61.530 63.158 0.00 0.00 0.00 3.85
1580 1656 2.034221 GGACTGCTGGGTTGGGAC 59.966 66.667 0.00 0.00 0.00 4.46
1581 1657 3.636231 CGGACTGCTGGGTTGGGA 61.636 66.667 0.00 0.00 0.00 4.37
1582 1658 4.722700 CCGGACTGCTGGGTTGGG 62.723 72.222 0.00 0.00 36.87 4.12
1583 1659 3.491598 AACCGGACTGCTGGGTTGG 62.492 63.158 9.46 0.00 37.05 3.77
1584 1660 2.113139 AACCGGACTGCTGGGTTG 59.887 61.111 9.46 0.00 37.05 3.77
1585 1661 2.113139 CAACCGGACTGCTGGGTT 59.887 61.111 9.46 0.00 37.05 4.11
1586 1662 3.953775 CCAACCGGACTGCTGGGT 61.954 66.667 9.46 0.00 45.41 4.51
1587 1663 2.589157 TACCAACCGGACTGCTGGG 61.589 63.158 9.46 0.00 45.41 4.45
1588 1664 1.375523 GTACCAACCGGACTGCTGG 60.376 63.158 9.46 9.08 46.62 4.85
1716 1794 3.519579 TGCATAATTCAACCCAAATGCG 58.480 40.909 0.00 0.00 41.96 4.73
1783 1864 4.714632 AGTACAACCATAAGCACACAACT 58.285 39.130 0.00 0.00 0.00 3.16
1791 1872 9.420551 GTGTATTATAGGAGTACAACCATAAGC 57.579 37.037 10.84 9.54 30.87 3.09
1795 1876 7.567622 ACTGGTGTATTATAGGAGTACAACCAT 59.432 37.037 10.84 5.89 35.66 3.55
1807 1888 8.139350 TGTCGGTATCAAACTGGTGTATTATAG 58.861 37.037 0.00 0.00 34.96 1.31
1880 1970 1.141019 CTGCAACATGCCATCAGCC 59.859 57.895 0.00 0.00 44.23 4.85
1882 1972 0.892755 AACCTGCAACATGCCATCAG 59.107 50.000 0.00 0.00 44.23 2.90
1888 1978 4.644103 AATATCTCAACCTGCAACATGC 57.356 40.909 0.00 0.00 45.29 4.06
1893 1983 7.011389 CACTAATCGAAATATCTCAACCTGCAA 59.989 37.037 0.00 0.00 0.00 4.08
1896 1986 7.492669 ACACACTAATCGAAATATCTCAACCTG 59.507 37.037 0.00 0.00 0.00 4.00
1982 2072 0.179092 GGATGGGCATTTGAGCTTGC 60.179 55.000 0.00 0.00 38.14 4.01
2006 2098 1.380524 TGTACTCACTCGCTCTAGGC 58.619 55.000 0.00 0.00 37.64 3.93
2011 2103 2.085320 TCCTCTTGTACTCACTCGCTC 58.915 52.381 0.00 0.00 0.00 5.03
2012 2104 2.201921 TCCTCTTGTACTCACTCGCT 57.798 50.000 0.00 0.00 0.00 4.93
2013 2105 2.480416 CCATCCTCTTGTACTCACTCGC 60.480 54.545 0.00 0.00 0.00 5.03
2014 2106 3.017442 TCCATCCTCTTGTACTCACTCG 58.983 50.000 0.00 0.00 0.00 4.18
2041 2133 1.196012 CACTACAACCCCCTCTCCTC 58.804 60.000 0.00 0.00 0.00 3.71
2042 2134 0.492276 ACACTACAACCCCCTCTCCT 59.508 55.000 0.00 0.00 0.00 3.69
2043 2135 1.359168 AACACTACAACCCCCTCTCC 58.641 55.000 0.00 0.00 0.00 3.71
2092 2184 4.578105 AGTGATACGTTAGGCAGTACTACC 59.422 45.833 3.67 3.67 0.00 3.18
2093 2185 5.747951 AGTGATACGTTAGGCAGTACTAC 57.252 43.478 0.00 0.00 0.00 2.73
2094 2186 6.764308 AAAGTGATACGTTAGGCAGTACTA 57.236 37.500 0.00 0.00 0.00 1.82
2098 2190 5.656213 ACTAAAGTGATACGTTAGGCAGT 57.344 39.130 15.49 0.00 42.05 4.40
2100 2192 8.472413 AGATTAACTAAAGTGATACGTTAGGCA 58.528 33.333 15.49 4.10 42.05 4.75
2110 2202 7.123847 ACCCGTGAGTAGATTAACTAAAGTGAT 59.876 37.037 0.00 0.00 32.49 3.06
2172 2264 2.536365 TCGATTCGTGGTACATTCTGC 58.464 47.619 5.89 0.00 44.52 4.26
2173 2265 4.085568 CGATTCGATTCGTGGTACATTCTG 60.086 45.833 18.87 0.00 44.52 3.02
2206 2298 8.410673 TCCAGATCATACTACTACCAAGATTC 57.589 38.462 0.00 0.00 0.00 2.52
2207 2299 8.964533 ATCCAGATCATACTACTACCAAGATT 57.035 34.615 0.00 0.00 0.00 2.40
2208 2300 8.964533 AATCCAGATCATACTACTACCAAGAT 57.035 34.615 0.00 0.00 0.00 2.40
2209 2301 9.877222 TTAATCCAGATCATACTACTACCAAGA 57.123 33.333 0.00 0.00 0.00 3.02
2234 2326 7.415206 GGCGCCTATGGAATATTCGATATTTTT 60.415 37.037 22.15 0.00 35.68 1.94
2303 2414 3.133362 ACAACCAGTTAACTCGAGACCAA 59.867 43.478 21.68 6.72 0.00 3.67
2885 2996 2.047655 TTGACGGCACCGATGACC 60.048 61.111 17.40 0.18 42.83 4.02
3263 3386 2.632377 TGAAGATGATTGGAAGCGGAC 58.368 47.619 0.00 0.00 0.00 4.79
3280 3403 2.873245 GCTTGTCAGCACAGAGGATGAA 60.873 50.000 0.00 0.00 46.49 2.57
3312 3437 2.232941 TGAGGTTCATCCACCGTTAGTC 59.767 50.000 0.00 0.00 42.33 2.59
3316 3441 1.340017 CCATGAGGTTCATCCACCGTT 60.340 52.381 0.00 0.00 42.33 4.44
3318 3443 1.097547 GCCATGAGGTTCATCCACCG 61.098 60.000 0.00 0.00 42.33 4.94
3323 3448 0.462581 TCTGCGCCATGAGGTTCATC 60.463 55.000 4.18 0.00 34.28 2.92
3324 3449 0.182061 ATCTGCGCCATGAGGTTCAT 59.818 50.000 4.18 0.00 37.65 2.57
3326 3451 1.493950 CGATCTGCGCCATGAGGTTC 61.494 60.000 4.18 0.00 37.19 3.62
3327 3452 1.522355 CGATCTGCGCCATGAGGTT 60.522 57.895 4.18 0.00 37.19 3.50
3328 3453 2.107750 CGATCTGCGCCATGAGGT 59.892 61.111 4.18 0.00 37.19 3.85
3350 3483 2.062177 CACGAACCCCCTCCCGTAT 61.062 63.158 0.00 0.00 33.62 3.06
3792 3931 1.464608 CATGTTCTTGCCTGTACACGG 59.535 52.381 0.00 0.00 0.00 4.94
3793 3932 2.143122 ACATGTTCTTGCCTGTACACG 58.857 47.619 0.00 0.00 0.00 4.49
3794 3933 4.378459 GCTAACATGTTCTTGCCTGTACAC 60.378 45.833 15.85 0.00 0.00 2.90
3815 3958 2.291043 ACGATCCGGTTCTTGGGCT 61.291 57.895 10.71 0.00 0.00 5.19
3918 4061 0.394565 CTCCGATCATCCTTCCCCAC 59.605 60.000 0.00 0.00 0.00 4.61
3919 4062 0.264657 TCTCCGATCATCCTTCCCCA 59.735 55.000 0.00 0.00 0.00 4.96
3951 4095 2.969238 GATCCGCTGCATGGGTCG 60.969 66.667 2.89 0.00 0.00 4.79
3965 4109 2.597040 CGACAGCGTGAGTACTACGATC 60.597 54.545 21.31 15.32 43.82 3.69
4020 4180 4.403585 AAAGAGTCGCCCCTACTATTTC 57.596 45.455 0.00 0.00 34.23 2.17
4032 4200 3.242316 ACAGAAACGTCAAAAAGAGTCGC 60.242 43.478 0.00 0.00 0.00 5.19
4034 4202 8.836959 AATTTACAGAAACGTCAAAAAGAGTC 57.163 30.769 0.00 0.00 0.00 3.36
4086 4260 1.274167 TCTGCTACCACTAACAACGGG 59.726 52.381 0.00 0.00 0.00 5.28
4088 4262 2.412089 GCTTCTGCTACCACTAACAACG 59.588 50.000 0.00 0.00 36.03 4.10
4092 4266 2.233922 TCAGGCTTCTGCTACCACTAAC 59.766 50.000 0.00 0.00 38.36 2.34
4127 4301 9.656040 TTTTTGCTAGACGAATAAATACACCTA 57.344 29.630 0.00 0.00 0.00 3.08
4132 4306 9.474249 GACAGTTTTTGCTAGACGAATAAATAC 57.526 33.333 0.00 0.00 0.00 1.89
4168 4346 7.486647 AGAAAATATTCACATGTCATCCTTGC 58.513 34.615 0.00 0.00 38.06 4.01
4199 4379 7.008440 TGATGAAAACGCTAGAAAGATGATG 57.992 36.000 0.00 0.00 0.00 3.07
4209 4389 2.938451 TGCCATCTGATGAAAACGCTAG 59.062 45.455 18.92 0.26 0.00 3.42
4213 4393 3.495193 CACTTGCCATCTGATGAAAACG 58.505 45.455 18.92 3.07 0.00 3.60
4246 4431 9.512588 AATTTCAGATACTCACAACAAAGATCT 57.487 29.630 0.00 0.00 0.00 2.75
4279 4485 3.372206 GGTCCAGTTTCTCATCATGTTCG 59.628 47.826 0.00 0.00 0.00 3.95
4292 4498 1.761198 GCTACTATCCCGGTCCAGTTT 59.239 52.381 0.00 0.00 0.00 2.66
4317 4523 2.136878 ATGCTCTACGCCCCTCAGG 61.137 63.158 0.00 0.00 38.05 3.86
4318 4524 1.068753 CATGCTCTACGCCCCTCAG 59.931 63.158 0.00 0.00 38.05 3.35
4336 4542 4.697352 ACCATGCTCTGTTCATAACTTCAC 59.303 41.667 0.00 0.00 0.00 3.18
4454 4661 1.402968 GCAACATGCCTCTGTACCATG 59.597 52.381 7.31 7.31 41.49 3.66
4456 4663 0.399833 TGCAACATGCCTCTGTACCA 59.600 50.000 0.00 0.00 44.23 3.25
4458 4665 1.135972 CGTTGCAACATGCCTCTGTAC 60.136 52.381 28.01 0.00 44.23 2.90
4478 4893 1.916697 GCGGCTTTTCCTCTCTGCAC 61.917 60.000 0.00 0.00 0.00 4.57
4494 4909 4.821589 GCCGTCTCCTCTTGGCGG 62.822 72.222 2.18 2.18 44.60 6.13
4527 4942 1.271871 TGGTCACATCGGCTTTCCAAT 60.272 47.619 0.00 0.00 0.00 3.16
4528 4943 0.109532 TGGTCACATCGGCTTTCCAA 59.890 50.000 0.00 0.00 0.00 3.53
4570 4985 1.376812 CCTACGTGAAACCAGGGGC 60.377 63.158 0.00 0.00 33.15 5.80
4584 4999 0.685097 TGCCTGTGTTCTGACCCTAC 59.315 55.000 0.00 0.00 0.00 3.18
4592 5007 1.086067 CGATGCGATGCCTGTGTTCT 61.086 55.000 0.00 0.00 0.00 3.01
4659 5074 4.070009 AGACCGGACCTTAAAACACAATC 58.930 43.478 9.46 0.00 0.00 2.67
4664 5079 5.486735 TTGATAGACCGGACCTTAAAACA 57.513 39.130 9.46 0.00 0.00 2.83
4665 5080 7.043565 TGTATTGATAGACCGGACCTTAAAAC 58.956 38.462 9.46 0.00 0.00 2.43
4666 5081 7.185318 TGTATTGATAGACCGGACCTTAAAA 57.815 36.000 9.46 0.71 0.00 1.52
4670 5085 4.443034 GCTTGTATTGATAGACCGGACCTT 60.443 45.833 9.46 0.00 0.00 3.50
4671 5086 3.069729 GCTTGTATTGATAGACCGGACCT 59.930 47.826 9.46 7.49 0.00 3.85
4672 5087 3.069729 AGCTTGTATTGATAGACCGGACC 59.930 47.826 9.46 0.00 0.00 4.46
4673 5088 4.051922 CAGCTTGTATTGATAGACCGGAC 58.948 47.826 9.46 0.10 0.00 4.79
4674 5089 3.704566 ACAGCTTGTATTGATAGACCGGA 59.295 43.478 9.46 0.00 0.00 5.14
4675 5090 4.060038 ACAGCTTGTATTGATAGACCGG 57.940 45.455 0.00 0.00 0.00 5.28
4676 5091 4.271049 CCAACAGCTTGTATTGATAGACCG 59.729 45.833 0.00 0.00 0.00 4.79
4677 5092 5.186198 ACCAACAGCTTGTATTGATAGACC 58.814 41.667 0.00 0.00 0.00 3.85
4678 5093 6.546395 CAACCAACAGCTTGTATTGATAGAC 58.454 40.000 0.00 0.00 0.00 2.59
4679 5094 5.123820 GCAACCAACAGCTTGTATTGATAGA 59.876 40.000 0.00 0.00 0.00 1.98
4680 5095 5.124457 AGCAACCAACAGCTTGTATTGATAG 59.876 40.000 0.00 0.00 38.01 2.08
4681 5096 5.009631 AGCAACCAACAGCTTGTATTGATA 58.990 37.500 0.00 0.00 38.01 2.15
4682 5097 3.828451 AGCAACCAACAGCTTGTATTGAT 59.172 39.130 0.00 0.00 38.01 2.57
4683 5098 3.004629 CAGCAACCAACAGCTTGTATTGA 59.995 43.478 0.00 0.00 39.50 2.57
4684 5099 3.243501 ACAGCAACCAACAGCTTGTATTG 60.244 43.478 0.00 0.00 39.50 1.90
4685 5100 2.958355 ACAGCAACCAACAGCTTGTATT 59.042 40.909 0.00 0.00 39.50 1.89
4686 5101 2.586425 ACAGCAACCAACAGCTTGTAT 58.414 42.857 0.00 0.00 39.50 2.29
4687 5102 2.051334 ACAGCAACCAACAGCTTGTA 57.949 45.000 0.00 0.00 39.50 2.41
4688 5103 1.185315 AACAGCAACCAACAGCTTGT 58.815 45.000 0.00 0.00 39.50 3.16
4689 5104 1.928503 CAAACAGCAACCAACAGCTTG 59.071 47.619 0.00 0.00 39.50 4.01
4690 5105 1.824230 TCAAACAGCAACCAACAGCTT 59.176 42.857 0.00 0.00 39.50 3.74
4691 5106 1.134946 GTCAAACAGCAACCAACAGCT 59.865 47.619 0.00 0.00 42.94 4.24
4692 5107 1.559831 GTCAAACAGCAACCAACAGC 58.440 50.000 0.00 0.00 0.00 4.40
4693 5108 1.826327 CGTCAAACAGCAACCAACAG 58.174 50.000 0.00 0.00 0.00 3.16
4694 5109 0.179150 GCGTCAAACAGCAACCAACA 60.179 50.000 0.00 0.00 0.00 3.33
4695 5110 1.199852 CGCGTCAAACAGCAACCAAC 61.200 55.000 0.00 0.00 0.00 3.77
4696 5111 1.063327 CGCGTCAAACAGCAACCAA 59.937 52.632 0.00 0.00 0.00 3.67
4697 5112 1.815840 TCGCGTCAAACAGCAACCA 60.816 52.632 5.77 0.00 0.00 3.67
4698 5113 1.368850 GTCGCGTCAAACAGCAACC 60.369 57.895 5.77 0.00 0.00 3.77
4699 5114 1.717728 CGTCGCGTCAAACAGCAAC 60.718 57.895 5.77 0.00 0.00 4.17
4700 5115 1.218875 ATCGTCGCGTCAAACAGCAA 61.219 50.000 5.77 0.00 0.00 3.91
4701 5116 1.663388 ATCGTCGCGTCAAACAGCA 60.663 52.632 5.77 0.00 0.00 4.41
4702 5117 1.225475 CATCGTCGCGTCAAACAGC 60.225 57.895 5.77 0.00 0.00 4.40
4703 5118 1.416049 CCATCGTCGCGTCAAACAG 59.584 57.895 5.77 0.00 0.00 3.16
4704 5119 2.663478 GCCATCGTCGCGTCAAACA 61.663 57.895 5.77 0.00 0.00 2.83
4705 5120 2.095843 GCCATCGTCGCGTCAAAC 59.904 61.111 5.77 0.00 0.00 2.93
4706 5121 3.115892 GGCCATCGTCGCGTCAAA 61.116 61.111 5.77 0.00 0.00 2.69
4707 5122 3.982372 GAGGCCATCGTCGCGTCAA 62.982 63.158 5.01 0.00 40.11 3.18
4708 5123 4.492160 GAGGCCATCGTCGCGTCA 62.492 66.667 5.01 0.00 40.11 4.35
4709 5124 2.831366 TAGAGGCCATCGTCGCGTC 61.831 63.158 5.01 0.00 40.55 5.19
4710 5125 2.827190 TAGAGGCCATCGTCGCGT 60.827 61.111 5.01 0.00 32.68 6.01
4711 5126 2.353607 GTAGAGGCCATCGTCGCG 60.354 66.667 5.01 0.00 32.68 5.87
4712 5127 1.008309 GAGTAGAGGCCATCGTCGC 60.008 63.158 5.01 0.00 32.68 5.19
4713 5128 1.880271 TAGAGTAGAGGCCATCGTCG 58.120 55.000 5.01 0.00 32.68 5.12
4714 5129 5.247084 TCTAATAGAGTAGAGGCCATCGTC 58.753 45.833 5.01 0.00 0.00 4.20
4715 5130 5.013287 TCTCTAATAGAGTAGAGGCCATCGT 59.987 44.000 16.09 0.00 44.93 3.73
4716 5131 5.353123 GTCTCTAATAGAGTAGAGGCCATCG 59.647 48.000 16.09 0.00 43.96 3.84
4717 5132 6.753107 GTCTCTAATAGAGTAGAGGCCATC 57.247 45.833 16.09 0.00 43.96 3.51
4734 5149 9.736414 ACACTGAGTACAATTAGTTAGTCTCTA 57.264 33.333 0.00 0.00 27.44 2.43
4735 5150 8.638629 ACACTGAGTACAATTAGTTAGTCTCT 57.361 34.615 0.00 0.00 27.44 3.10
4736 5151 9.991388 CTACACTGAGTACAATTAGTTAGTCTC 57.009 37.037 0.00 0.00 27.44 3.36
4737 5152 8.958506 CCTACACTGAGTACAATTAGTTAGTCT 58.041 37.037 0.00 0.00 27.44 3.24
4738 5153 7.701501 GCCTACACTGAGTACAATTAGTTAGTC 59.298 40.741 0.00 0.00 27.44 2.59
4739 5154 7.396623 AGCCTACACTGAGTACAATTAGTTAGT 59.603 37.037 0.00 0.00 29.53 2.24
4740 5155 7.702772 CAGCCTACACTGAGTACAATTAGTTAG 59.297 40.741 0.00 0.34 40.25 2.34
4741 5156 7.544622 CAGCCTACACTGAGTACAATTAGTTA 58.455 38.462 0.00 0.00 40.25 2.24
4742 5157 6.398918 CAGCCTACACTGAGTACAATTAGTT 58.601 40.000 0.00 0.00 40.25 2.24
4743 5158 5.624738 GCAGCCTACACTGAGTACAATTAGT 60.625 44.000 0.00 0.00 40.25 2.24
4744 5159 4.806247 GCAGCCTACACTGAGTACAATTAG 59.194 45.833 0.00 0.00 40.25 1.73
4745 5160 4.466370 AGCAGCCTACACTGAGTACAATTA 59.534 41.667 0.00 0.00 40.25 1.40
4746 5161 3.261897 AGCAGCCTACACTGAGTACAATT 59.738 43.478 0.00 0.00 40.25 2.32
4747 5162 2.834549 AGCAGCCTACACTGAGTACAAT 59.165 45.455 0.00 0.00 40.25 2.71
4748 5163 2.248248 AGCAGCCTACACTGAGTACAA 58.752 47.619 0.00 0.00 40.25 2.41
4749 5164 1.924731 AGCAGCCTACACTGAGTACA 58.075 50.000 0.00 0.00 40.25 2.90
4750 5165 5.704888 CATATAGCAGCCTACACTGAGTAC 58.295 45.833 0.00 0.00 40.25 2.73
4751 5166 5.966742 CATATAGCAGCCTACACTGAGTA 57.033 43.478 0.00 0.00 40.25 2.59
4752 5167 4.862902 CATATAGCAGCCTACACTGAGT 57.137 45.455 0.00 0.00 40.25 3.41


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

AutoCloner maintained by Alex Coulton.