Multiple sequence alignment - TraesCS4A01G319900

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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 TraesCS4A01G319900 chr4A 100.000 2881 0 0 1 2881 608611918 608609038 0.000000e+00 5321.0
1 TraesCS4A01G319900 chr5B 85.185 918 51 37 1312 2179 706304014 706304896 0.000000e+00 863.0
2 TraesCS4A01G319900 chr5B 90.308 650 39 6 2235 2881 706304878 706305506 0.000000e+00 830.0
3 TraesCS4A01G319900 chr5B 83.915 659 82 12 1 642 706301925 706302576 2.450000e-170 608.0
4 TraesCS4A01G319900 chr5B 77.376 526 35 31 669 1156 706303335 706303814 4.800000e-58 235.0
5 TraesCS4A01G319900 chr5B 81.776 214 20 8 2603 2815 706304907 706305102 8.260000e-36 161.0
6 TraesCS4A01G319900 chr5D 95.117 512 20 4 2375 2881 563853593 563854104 0.000000e+00 802.0
7 TraesCS4A01G319900 chr5D 84.968 632 80 7 1 624 563820006 563820630 6.780000e-176 627.0
8 TraesCS4A01G319900 chr5D 91.847 417 20 7 1738 2151 563853140 563853545 1.160000e-158 569.0
9 TraesCS4A01G319900 chr5D 79.110 517 38 34 670 1159 563852075 563852548 2.810000e-75 292.0
10 TraesCS4A01G319900 chr5D 88.889 225 13 4 1279 1499 563852713 563852929 1.700000e-67 267.0
11 TraesCS4A01G319900 chr5D 87.395 119 8 2 2734 2852 563853603 563853714 2.330000e-26 130.0
12 TraesCS4A01G319900 chr2B 91.761 352 28 1 2531 2881 248122614 248122965 3.340000e-134 488.0
13 TraesCS4A01G319900 chr2B 90.987 233 13 4 1952 2181 248106996 248107223 1.000000e-79 307.0
14 TraesCS4A01G319900 chr2B 89.032 155 11 5 2375 2525 248107316 248107468 1.360000e-43 187.0
15 TraesCS4A01G319900 chr7B 78.443 167 32 4 472 636 71834470 71834306 3.930000e-19 106.0
16 TraesCS4A01G319900 chr3D 80.952 126 22 2 443 567 399301862 399301738 6.570000e-17 99.0
17 TraesCS4A01G319900 chr7D 78.000 150 33 0 398 547 120326797 120326648 8.500000e-16 95.3
18 TraesCS4A01G319900 chr3A 96.875 32 1 0 855 886 15341208 15341239 1.000000e-03 54.7


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 TraesCS4A01G319900 chr4A 608609038 608611918 2880 True 5321.0 5321 100.0000 1 2881 1 chr4A.!!$R1 2880
1 TraesCS4A01G319900 chr5B 706301925 706305506 3581 False 539.4 863 83.7120 1 2881 5 chr5B.!!$F1 2880
2 TraesCS4A01G319900 chr5D 563820006 563820630 624 False 627.0 627 84.9680 1 624 1 chr5D.!!$F1 623
3 TraesCS4A01G319900 chr5D 563852075 563854104 2029 False 412.0 802 88.4716 670 2881 5 chr5D.!!$F2 2211

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
812 1574 0.033208 AACGGTGATCCCAATGCCAT 60.033 50.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 3052 0.320374 GTCGAGTGACACAATGGGGA 59.68 55.0 8.59 0.0 44.82 4.81 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
62 63 5.303259 TGCAGGCATCAAATATAGTACCA 57.697 39.130 0.00 0.00 0.00 3.25
67 68 6.712095 CAGGCATCAAATATAGTACCACATGT 59.288 38.462 0.00 0.00 0.00 3.21
109 110 3.474570 GCCATCGGCTGGGAGTCT 61.475 66.667 0.00 0.00 46.69 3.24
148 149 2.298610 TCTAGGTGTCGGACATAGCAG 58.701 52.381 14.78 9.38 38.58 4.24
207 216 7.857569 AGAATTGAACAAAAACAATGCATCTG 58.142 30.769 0.00 3.44 36.92 2.90
210 219 5.658468 TGAACAAAAACAATGCATCTGTCA 58.342 33.333 0.00 0.00 0.00 3.58
211 220 5.519566 TGAACAAAAACAATGCATCTGTCAC 59.480 36.000 0.00 0.00 0.00 3.67
226 235 3.883489 TCTGTCACGCTAGCATACTACAT 59.117 43.478 16.45 0.00 0.00 2.29
235 244 5.655488 GCTAGCATACTACATATGGACTGG 58.345 45.833 10.63 0.00 41.07 4.00
261 270 3.192001 CCAAGCTCAACACACAAGCATAT 59.808 43.478 0.00 0.00 38.51 1.78
271 280 2.684881 ACACAAGCATATGTAGCAAGCC 59.315 45.455 4.29 0.00 30.84 4.35
293 302 3.912496 TCATGGACCGATCATGAAGTT 57.088 42.857 0.00 0.00 45.30 2.66
294 303 3.797039 TCATGGACCGATCATGAAGTTC 58.203 45.455 0.00 0.00 45.30 3.01
295 304 3.197549 TCATGGACCGATCATGAAGTTCA 59.802 43.478 8.27 8.27 45.30 3.18
313 322 4.756642 AGTTCATCAACACACTACCACATG 59.243 41.667 0.00 0.00 34.60 3.21
318 327 2.734606 CAACACACTACCACATGTACCG 59.265 50.000 0.00 0.00 0.00 4.02
338 347 1.925415 TACGACACATGGACCGACCG 61.925 60.000 9.30 0.00 42.61 4.79
351 360 0.878523 CCGACCGTCAAGCTCAACAA 60.879 55.000 0.00 0.00 0.00 2.83
359 373 3.002656 CGTCAAGCTCAACAACACATCTT 59.997 43.478 0.00 0.00 0.00 2.40
374 388 6.239217 ACACATCTTCCATAGTAGCATTGA 57.761 37.500 0.00 0.00 0.00 2.57
387 401 1.812571 AGCATTGAAACCGACATGGAC 59.187 47.619 0.00 0.00 42.00 4.02
392 406 2.857483 TGAAACCGACATGGACAACAT 58.143 42.857 0.00 0.00 42.00 2.71
405 419 8.055279 ACATGGACAACATTTAAATCTACCAG 57.945 34.615 0.00 2.60 37.84 4.00
411 425 9.612620 GACAACATTTAAATCTACCAGAACAAG 57.387 33.333 0.00 0.00 0.00 3.16
412 426 8.576442 ACAACATTTAAATCTACCAGAACAAGG 58.424 33.333 0.00 0.00 0.00 3.61
413 427 7.158099 ACATTTAAATCTACCAGAACAAGGC 57.842 36.000 0.00 0.00 0.00 4.35
425 439 3.376234 CAGAACAAGGCGAACATCATCAT 59.624 43.478 0.00 0.00 0.00 2.45
447 462 0.604578 CCGAAACGGGAAGTCTACCA 59.395 55.000 2.00 0.00 44.15 3.25
449 464 2.268298 CGAAACGGGAAGTCTACCATG 58.732 52.381 0.00 0.00 0.00 3.66
451 466 1.276622 AACGGGAAGTCTACCATGCT 58.723 50.000 0.00 0.00 0.00 3.79
460 475 3.596214 AGTCTACCATGCTACCAAAACG 58.404 45.455 0.00 0.00 0.00 3.60
462 477 1.400494 CTACCATGCTACCAAAACGGC 59.600 52.381 0.00 0.00 39.03 5.68
466 481 1.582610 ATGCTACCAAAACGGCACCG 61.583 55.000 7.71 7.71 46.03 4.94
468 483 2.973316 CTACCAAAACGGCACCGCC 61.973 63.158 9.43 0.00 46.75 6.13
487 502 3.548745 CCAGCATCTGGTCTATCACAA 57.451 47.619 4.74 0.00 45.82 3.33
493 508 4.691175 CATCTGGTCTATCACAACCTCAG 58.309 47.826 0.00 0.00 36.47 3.35
532 547 6.970484 CAATACTTGCATAACCTACCATTCC 58.030 40.000 0.00 0.00 0.00 3.01
549 564 1.393603 TCCACCTGCAGATCTACTCG 58.606 55.000 17.39 0.00 0.00 4.18
550 565 1.107114 CCACCTGCAGATCTACTCGT 58.893 55.000 17.39 0.00 0.00 4.18
551 566 1.478510 CCACCTGCAGATCTACTCGTT 59.521 52.381 17.39 0.00 0.00 3.85
552 567 2.480416 CCACCTGCAGATCTACTCGTTC 60.480 54.545 17.39 0.00 0.00 3.95
553 568 1.402259 ACCTGCAGATCTACTCGTTCG 59.598 52.381 17.39 0.00 0.00 3.95
569 584 1.726791 GTTCGTACCACATGCTCACAG 59.273 52.381 0.00 0.00 0.00 3.66
572 587 1.929169 CGTACCACATGCTCACAGATG 59.071 52.381 0.00 0.00 0.00 2.90
575 590 3.920231 ACCACATGCTCACAGATGTAT 57.080 42.857 0.00 0.00 31.46 2.29
577 592 2.876550 CCACATGCTCACAGATGTATGG 59.123 50.000 0.00 0.00 31.46 2.74
594 612 2.798976 TGGTACAACGTGGTAGTGAC 57.201 50.000 2.12 0.00 31.92 3.67
602 620 3.093717 ACGTGGTAGTGACTGAACTTG 57.906 47.619 0.00 0.00 0.00 3.16
608 626 1.299541 AGTGACTGAACTTGCAACCG 58.700 50.000 0.00 0.00 0.00 4.44
611 629 0.586802 GACTGAACTTGCAACCGTCC 59.413 55.000 0.00 0.00 0.00 4.79
629 647 2.690510 AAGGAGCAGGGAGGAGGC 60.691 66.667 0.00 0.00 0.00 4.70
642 662 2.747686 GAGGCGGGGAACAACTCA 59.252 61.111 0.00 0.00 0.00 3.41
643 663 1.072505 GAGGCGGGGAACAACTCAA 59.927 57.895 0.00 0.00 0.00 3.02
644 664 1.228154 AGGCGGGGAACAACTCAAC 60.228 57.895 0.00 0.00 0.00 3.18
645 665 2.265904 GGCGGGGAACAACTCAACC 61.266 63.158 0.00 0.00 0.00 3.77
648 668 0.666374 CGGGGAACAACTCAACCAAC 59.334 55.000 0.00 0.00 0.00 3.77
649 669 1.037493 GGGGAACAACTCAACCAACC 58.963 55.000 0.00 0.00 0.00 3.77
650 670 1.686741 GGGGAACAACTCAACCAACCA 60.687 52.381 0.00 0.00 0.00 3.67
652 672 2.159156 GGGAACAACTCAACCAACCAAC 60.159 50.000 0.00 0.00 0.00 3.77
653 673 2.159156 GGAACAACTCAACCAACCAACC 60.159 50.000 0.00 0.00 0.00 3.77
655 675 1.099689 CAACTCAACCAACCAACCGT 58.900 50.000 0.00 0.00 0.00 4.83
656 676 1.099689 AACTCAACCAACCAACCGTG 58.900 50.000 0.00 0.00 0.00 4.94
657 677 1.358759 CTCAACCAACCAACCGTGC 59.641 57.895 0.00 0.00 0.00 5.34
658 678 2.025441 CAACCAACCAACCGTGCG 59.975 61.111 0.00 0.00 0.00 5.34
659 679 2.438795 AACCAACCAACCGTGCGT 60.439 55.556 0.00 0.00 0.00 5.24
661 681 4.622456 CCAACCAACCGTGCGTGC 62.622 66.667 0.00 0.00 0.00 5.34
662 682 4.954680 CAACCAACCGTGCGTGCG 62.955 66.667 0.00 0.00 0.00 5.34
699 1450 2.419297 CGGGAGGTCATGAAGAAGAAGG 60.419 54.545 0.00 0.00 0.00 3.46
731 1493 3.126879 GTGGCTGCGTGCATGCTA 61.127 61.111 29.83 16.05 45.15 3.49
734 1496 4.228097 GCTGCGTGCATGCTACGG 62.228 66.667 30.05 20.71 41.56 4.02
735 1497 4.228097 CTGCGTGCATGCTACGGC 62.228 66.667 30.05 24.33 41.56 5.68
761 1523 2.324860 GCCTTGTTTGGTAATCGCAAC 58.675 47.619 0.00 0.00 0.00 4.17
805 1567 2.949909 CGGTGGAACGGTGATCCCA 61.950 63.158 0.00 0.00 38.12 4.37
807 1569 0.034477 GGTGGAACGGTGATCCCAAT 60.034 55.000 0.00 0.00 38.12 3.16
812 1574 0.033208 AACGGTGATCCCAATGCCAT 60.033 50.000 0.00 0.00 0.00 4.40
814 1576 1.457823 CGGTGATCCCAATGCCATGG 61.458 60.000 7.63 7.63 40.35 3.66
816 1578 1.458020 TGATCCCAATGCCATGGCC 60.458 57.895 33.44 15.82 39.26 5.36
818 1580 4.837797 TCCCAATGCCATGGCCGG 62.838 66.667 33.44 27.85 39.26 6.13
821 1583 2.440796 CAATGCCATGGCCGGTCT 60.441 61.111 33.44 10.62 41.09 3.85
850 1621 1.227176 GGTCGATACAACCGAGGCC 60.227 63.158 0.00 0.00 36.66 5.19
946 1721 1.049289 ATTCCTCCCGTCACCTAGCC 61.049 60.000 0.00 0.00 0.00 3.93
947 1722 2.042843 CCTCCCGTCACCTAGCCT 60.043 66.667 0.00 0.00 0.00 4.58
948 1723 1.229359 CCTCCCGTCACCTAGCCTA 59.771 63.158 0.00 0.00 0.00 3.93
950 1725 1.455217 TCCCGTCACCTAGCCTAGC 60.455 63.158 0.00 0.00 0.00 3.42
955 1730 0.747852 GTCACCTAGCCTAGCTCCAC 59.252 60.000 0.00 0.00 40.44 4.02
966 1742 2.856039 TAGCTCCACCTCCACCTCCG 62.856 65.000 0.00 0.00 0.00 4.63
974 1750 4.988716 TCCACCTCCGTCGTGCCT 62.989 66.667 0.00 0.00 0.00 4.75
975 1751 4.436998 CCACCTCCGTCGTGCCTC 62.437 72.222 0.00 0.00 0.00 4.70
981 1757 4.849329 CCGTCGTGCCTCGGCTAC 62.849 72.222 9.65 5.16 42.47 3.58
985 1762 2.117156 TCGTGCCTCGGCTACCTAC 61.117 63.158 9.65 0.00 42.51 3.18
994 1771 2.029623 TCGGCTACCTACCTCATTCAC 58.970 52.381 0.00 0.00 0.00 3.18
1168 1996 1.676014 GCTCGGTACACTCCTGCATTT 60.676 52.381 0.00 0.00 0.00 2.32
1169 1997 2.271800 CTCGGTACACTCCTGCATTTC 58.728 52.381 0.00 0.00 0.00 2.17
1170 1998 1.621317 TCGGTACACTCCTGCATTTCA 59.379 47.619 0.00 0.00 0.00 2.69
1172 2000 2.778299 GGTACACTCCTGCATTTCACA 58.222 47.619 0.00 0.00 0.00 3.58
1173 2001 2.484264 GGTACACTCCTGCATTTCACAC 59.516 50.000 0.00 0.00 0.00 3.82
1175 2003 1.133823 ACACTCCTGCATTTCACACCA 60.134 47.619 0.00 0.00 0.00 4.17
1176 2004 2.165167 CACTCCTGCATTTCACACCAT 58.835 47.619 0.00 0.00 0.00 3.55
1177 2005 2.163010 CACTCCTGCATTTCACACCATC 59.837 50.000 0.00 0.00 0.00 3.51
1178 2006 2.040813 ACTCCTGCATTTCACACCATCT 59.959 45.455 0.00 0.00 0.00 2.90
1182 2010 3.508793 CCTGCATTTCACACCATCTTCTT 59.491 43.478 0.00 0.00 0.00 2.52
1190 2018 2.350804 CACACCATCTTCTTCATGCTCG 59.649 50.000 0.00 0.00 0.00 5.03
1198 2026 0.318120 TCTTCATGCTCGTGACTGCA 59.682 50.000 2.94 2.94 43.67 4.41
1199 2027 1.150827 CTTCATGCTCGTGACTGCAA 58.849 50.000 4.45 0.00 42.74 4.08
1200 2028 1.736126 CTTCATGCTCGTGACTGCAAT 59.264 47.619 4.45 0.00 42.74 3.56
1201 2029 1.081094 TCATGCTCGTGACTGCAATG 58.919 50.000 4.45 4.64 42.74 2.82
1202 2030 0.098200 CATGCTCGTGACTGCAATGG 59.902 55.000 4.45 0.00 42.74 3.16
1204 2032 3.044059 GCTCGTGACTGCAATGGCC 62.044 63.158 0.00 0.00 40.13 5.36
1205 2033 2.741985 TCGTGACTGCAATGGCCG 60.742 61.111 0.00 0.00 40.13 6.13
1207 2035 3.443045 GTGACTGCAATGGCCGGG 61.443 66.667 2.18 0.00 40.13 5.73
1238 2107 2.284190 GCTCCTACCAAACTCATGCTC 58.716 52.381 0.00 0.00 0.00 4.26
1240 2109 3.529533 CTCCTACCAAACTCATGCTCAG 58.470 50.000 0.00 0.00 0.00 3.35
1244 2113 0.524862 CCAAACTCATGCTCAGTGCC 59.475 55.000 0.00 0.00 42.00 5.01
1245 2114 1.531423 CAAACTCATGCTCAGTGCCT 58.469 50.000 0.00 0.00 42.00 4.75
1246 2115 1.467734 CAAACTCATGCTCAGTGCCTC 59.532 52.381 0.00 0.00 42.00 4.70
1247 2116 0.982704 AACTCATGCTCAGTGCCTCT 59.017 50.000 0.00 0.00 42.00 3.69
1248 2117 0.536260 ACTCATGCTCAGTGCCTCTC 59.464 55.000 0.00 0.00 42.00 3.20
1249 2118 0.535797 CTCATGCTCAGTGCCTCTCA 59.464 55.000 0.00 0.00 42.00 3.27
1250 2119 0.978907 TCATGCTCAGTGCCTCTCAA 59.021 50.000 0.00 0.00 42.00 3.02
1251 2120 1.085091 CATGCTCAGTGCCTCTCAAC 58.915 55.000 0.00 0.00 42.00 3.18
1252 2121 0.689055 ATGCTCAGTGCCTCTCAACA 59.311 50.000 0.00 0.00 42.00 3.33
1266 2135 5.620429 GCCTCTCAACACTGAACTAGTACTC 60.620 48.000 0.00 0.00 37.60 2.59
1267 2136 5.708230 CCTCTCAACACTGAACTAGTACTCT 59.292 44.000 0.00 0.00 37.60 3.24
1268 2137 6.348950 CCTCTCAACACTGAACTAGTACTCTG 60.349 46.154 0.00 0.00 37.60 3.35
1271 2140 7.068348 TCTCAACACTGAACTAGTACTCTGTTT 59.932 37.037 13.24 0.00 37.60 2.83
1272 2141 6.978659 TCAACACTGAACTAGTACTCTGTTTG 59.021 38.462 13.24 8.73 37.60 2.93
1273 2142 5.844004 ACACTGAACTAGTACTCTGTTTGG 58.156 41.667 13.24 11.54 37.60 3.28
1274 2143 4.686554 CACTGAACTAGTACTCTGTTTGGC 59.313 45.833 13.24 4.62 37.60 4.52
1277 2167 3.572604 ACTAGTACTCTGTTTGGCGAC 57.427 47.619 0.00 0.00 0.00 5.19
1293 2183 1.401670 GCGACGTGTCACTCAAGATCT 60.402 52.381 0.00 0.00 0.00 2.75
1304 2194 5.642919 GTCACTCAAGATCTGCTCTGAATTT 59.357 40.000 0.00 0.00 33.29 1.82
1305 2195 5.873712 TCACTCAAGATCTGCTCTGAATTTC 59.126 40.000 0.00 0.00 33.29 2.17
1306 2196 5.064962 CACTCAAGATCTGCTCTGAATTTCC 59.935 44.000 0.00 0.00 33.29 3.13
1307 2197 5.169992 TCAAGATCTGCTCTGAATTTCCA 57.830 39.130 0.00 0.00 33.29 3.53
1308 2198 5.563592 TCAAGATCTGCTCTGAATTTCCAA 58.436 37.500 0.00 0.00 33.29 3.53
1309 2199 6.005823 TCAAGATCTGCTCTGAATTTCCAAA 58.994 36.000 0.00 0.00 33.29 3.28
1310 2200 6.491062 TCAAGATCTGCTCTGAATTTCCAAAA 59.509 34.615 0.00 0.00 33.29 2.44
1456 2346 1.836383 GATTCGCTCGACACGGTAAT 58.164 50.000 3.50 0.00 0.00 1.89
1458 2348 1.621107 TTCGCTCGACACGGTAATTC 58.379 50.000 3.50 0.00 0.00 2.17
1459 2349 0.179156 TCGCTCGACACGGTAATTCC 60.179 55.000 3.50 0.00 0.00 3.01
1460 2350 1.143969 CGCTCGACACGGTAATTCCC 61.144 60.000 0.00 0.00 0.00 3.97
1511 2404 2.684881 CAACATGGATGGAGCTACAACC 59.315 50.000 18.25 18.25 34.21 3.77
1534 2427 5.362430 CCTCATCAGCCTACTCTAGAAAAGT 59.638 44.000 0.00 0.00 0.00 2.66
1580 2473 5.352284 TCTTAGCTTCAGTGAATTCGATCC 58.648 41.667 5.91 0.00 0.00 3.36
1584 2477 3.775202 CTTCAGTGAATTCGATCCGACT 58.225 45.455 5.91 0.00 34.89 4.18
1618 2514 9.654663 AGTCTTGTGTACTCTTCCAAAATATAC 57.345 33.333 0.00 0.00 0.00 1.47
1630 2526 9.921637 TCTTCCAAAATATACAACCAATTTCAC 57.078 29.630 0.00 0.00 0.00 3.18
1641 2537 6.924111 ACAACCAATTTCACATGTTATCCTC 58.076 36.000 0.00 0.00 0.00 3.71
1645 2541 4.882671 ATTTCACATGTTATCCTCGTGC 57.117 40.909 0.00 0.00 0.00 5.34
1648 2544 1.324435 CACATGTTATCCTCGTGCGTG 59.676 52.381 0.00 0.00 0.00 5.34
1679 2575 9.639563 TTCCATAATATAGAACCATTTTCTGCA 57.360 29.630 0.00 0.00 0.00 4.41
1686 2582 7.707624 ATAGAACCATTTTCTGCATTCTTCA 57.292 32.000 0.67 0.00 33.35 3.02
1687 2583 6.600882 AGAACCATTTTCTGCATTCTTCAT 57.399 33.333 0.00 0.00 29.22 2.57
1688 2584 7.707624 AGAACCATTTTCTGCATTCTTCATA 57.292 32.000 0.00 0.00 29.22 2.15
1689 2585 8.125978 AGAACCATTTTCTGCATTCTTCATAA 57.874 30.769 0.00 0.00 29.22 1.90
1690 2586 8.031277 AGAACCATTTTCTGCATTCTTCATAAC 58.969 33.333 0.00 0.00 29.22 1.89
1691 2587 7.230849 ACCATTTTCTGCATTCTTCATAACA 57.769 32.000 0.00 0.00 0.00 2.41
1692 2588 7.844009 ACCATTTTCTGCATTCTTCATAACAT 58.156 30.769 0.00 0.00 0.00 2.71
1694 2590 8.814235 CCATTTTCTGCATTCTTCATAACATTC 58.186 33.333 0.00 0.00 0.00 2.67
1725 2627 8.537728 AATATAGAACCATTTTCTGCATTCCA 57.462 30.769 0.00 0.00 0.00 3.53
1727 2629 9.812347 ATATAGAACCATTTTCTGCATTCCATA 57.188 29.630 0.00 0.00 0.00 2.74
1728 2630 6.855763 AGAACCATTTTCTGCATTCCATAA 57.144 33.333 0.00 0.00 0.00 1.90
1730 2632 8.537728 AGAACCATTTTCTGCATTCCATAATA 57.462 30.769 0.00 0.00 0.00 0.98
1731 2633 9.151177 AGAACCATTTTCTGCATTCCATAATAT 57.849 29.630 0.00 0.00 0.00 1.28
1734 2636 9.812347 ACCATTTTCTGCATTCCATAATATAGA 57.188 29.630 0.00 0.00 0.00 1.98
1926 2869 3.760684 CTGAATAGCTTTTTGGGTGCTCT 59.239 43.478 0.00 0.00 38.15 4.09
1929 2872 0.480252 AGCTTTTTGGGTGCTCTCCT 59.520 50.000 0.00 0.00 30.41 3.69
1930 2873 1.133356 AGCTTTTTGGGTGCTCTCCTT 60.133 47.619 0.00 0.00 30.41 3.36
1931 2874 1.000171 GCTTTTTGGGTGCTCTCCTTG 60.000 52.381 0.00 0.00 0.00 3.61
2004 2947 1.574263 AGTTAGCCAGGAAGAGGGTC 58.426 55.000 0.00 0.00 38.04 4.46
2052 2995 5.509832 TGCTATGCTATCCCAGATTGAAT 57.490 39.130 0.00 0.00 0.00 2.57
2053 2996 6.625532 TGCTATGCTATCCCAGATTGAATA 57.374 37.500 0.00 0.00 0.00 1.75
2054 2997 7.019656 TGCTATGCTATCCCAGATTGAATAA 57.980 36.000 0.00 0.00 0.00 1.40
2055 2998 7.108194 TGCTATGCTATCCCAGATTGAATAAG 58.892 38.462 0.00 0.00 0.00 1.73
2112 3055 6.498304 CAAAGATTGCTGTTATATGTGTCCC 58.502 40.000 0.00 0.00 0.00 4.46
2116 3059 4.518278 TGCTGTTATATGTGTCCCCATT 57.482 40.909 0.00 0.00 0.00 3.16
2126 3069 0.034756 TGTCCCCATTGTGTCACTCG 59.965 55.000 4.27 0.00 0.00 4.18
2153 3096 6.751425 CACTGCTGAGATGTTTACTCTAAGAG 59.249 42.308 0.00 0.00 35.66 2.85
2154 3097 6.661377 ACTGCTGAGATGTTTACTCTAAGAGA 59.339 38.462 0.00 0.00 35.66 3.10
2156 3099 6.887002 TGCTGAGATGTTTACTCTAAGAGAGA 59.113 38.462 11.37 0.00 45.07 3.10
2185 3128 9.678260 AGAAAATAGAATGCTGAGATGTTTACT 57.322 29.630 0.00 0.00 0.00 2.24
2187 3130 8.443953 AAATAGAATGCTGAGATGTTTACTCC 57.556 34.615 0.00 0.00 33.95 3.85
2188 3131 5.426689 AGAATGCTGAGATGTTTACTCCA 57.573 39.130 0.00 0.00 33.95 3.86
2189 3132 5.809001 AGAATGCTGAGATGTTTACTCCAA 58.191 37.500 0.00 0.00 33.95 3.53
2190 3133 5.879223 AGAATGCTGAGATGTTTACTCCAAG 59.121 40.000 0.00 0.00 33.95 3.61
2191 3134 4.890158 TGCTGAGATGTTTACTCCAAGA 57.110 40.909 0.00 0.00 33.95 3.02
2192 3135 5.426689 TGCTGAGATGTTTACTCCAAGAT 57.573 39.130 0.00 0.00 33.95 2.40
2193 3136 6.544928 TGCTGAGATGTTTACTCCAAGATA 57.455 37.500 0.00 0.00 33.95 1.98
2194 3137 6.946340 TGCTGAGATGTTTACTCCAAGATAA 58.054 36.000 0.00 0.00 33.95 1.75
2195 3138 7.044181 TGCTGAGATGTTTACTCCAAGATAAG 58.956 38.462 0.00 0.00 33.95 1.73
2196 3139 7.093333 TGCTGAGATGTTTACTCCAAGATAAGA 60.093 37.037 0.00 0.00 33.95 2.10
2198 3141 9.658799 CTGAGATGTTTACTCCAAGATAAGAAA 57.341 33.333 0.00 0.00 33.95 2.52
2209 3152 9.118300 ACTCCAAGATAAGAAAATAGAATGCTG 57.882 33.333 0.00 0.00 0.00 4.41
2210 3153 9.334947 CTCCAAGATAAGAAAATAGAATGCTGA 57.665 33.333 0.00 0.00 0.00 4.26
2211 3154 9.334947 TCCAAGATAAGAAAATAGAATGCTGAG 57.665 33.333 0.00 0.00 0.00 3.35
2212 3155 9.334947 CCAAGATAAGAAAATAGAATGCTGAGA 57.665 33.333 0.00 0.00 0.00 3.27
2217 3160 7.934855 AAGAAAATAGAATGCTGAGATGTGT 57.065 32.000 0.00 0.00 0.00 3.72
2218 3161 7.551035 AGAAAATAGAATGCTGAGATGTGTC 57.449 36.000 0.00 0.00 0.00 3.67
2219 3162 7.337167 AGAAAATAGAATGCTGAGATGTGTCT 58.663 34.615 0.00 0.00 37.42 3.41
2220 3163 7.828223 AGAAAATAGAATGCTGAGATGTGTCTT 59.172 33.333 0.00 0.00 33.97 3.01
2221 3164 6.922247 AATAGAATGCTGAGATGTGTCTTG 57.078 37.500 0.00 0.00 33.97 3.02
2222 3165 3.607741 AGAATGCTGAGATGTGTCTTGG 58.392 45.455 0.00 0.00 33.97 3.61
2223 3166 2.414994 ATGCTGAGATGTGTCTTGGG 57.585 50.000 0.00 0.00 33.97 4.12
2224 3167 1.351076 TGCTGAGATGTGTCTTGGGA 58.649 50.000 0.00 0.00 33.97 4.37
2225 3168 1.699083 TGCTGAGATGTGTCTTGGGAA 59.301 47.619 0.00 0.00 33.97 3.97
2226 3169 2.306805 TGCTGAGATGTGTCTTGGGAAT 59.693 45.455 0.00 0.00 33.97 3.01
2227 3170 3.245016 TGCTGAGATGTGTCTTGGGAATT 60.245 43.478 0.00 0.00 33.97 2.17
2228 3171 4.019411 TGCTGAGATGTGTCTTGGGAATTA 60.019 41.667 0.00 0.00 33.97 1.40
2229 3172 4.333926 GCTGAGATGTGTCTTGGGAATTAC 59.666 45.833 0.00 0.00 33.97 1.89
2230 3173 5.738909 CTGAGATGTGTCTTGGGAATTACT 58.261 41.667 0.00 0.00 33.97 2.24
2231 3174 5.734720 TGAGATGTGTCTTGGGAATTACTC 58.265 41.667 0.00 0.00 33.97 2.59
2232 3175 5.104259 AGATGTGTCTTGGGAATTACTCC 57.896 43.478 0.00 0.00 44.54 3.85
2233 3176 4.785376 AGATGTGTCTTGGGAATTACTCCT 59.215 41.667 0.00 0.00 44.68 3.69
2234 3177 5.964477 AGATGTGTCTTGGGAATTACTCCTA 59.036 40.000 0.00 0.00 44.68 2.94
2235 3178 5.416271 TGTGTCTTGGGAATTACTCCTAC 57.584 43.478 0.00 0.00 44.68 3.18
2236 3179 4.841813 TGTGTCTTGGGAATTACTCCTACA 59.158 41.667 0.00 0.00 44.68 2.74
2237 3180 5.308497 TGTGTCTTGGGAATTACTCCTACAA 59.692 40.000 0.00 0.00 44.68 2.41
2238 3181 6.183361 TGTGTCTTGGGAATTACTCCTACAAA 60.183 38.462 0.00 0.00 44.68 2.83
2239 3182 6.884836 GTGTCTTGGGAATTACTCCTACAAAT 59.115 38.462 0.00 0.00 44.68 2.32
2240 3183 7.393515 GTGTCTTGGGAATTACTCCTACAAATT 59.606 37.037 0.00 0.00 44.68 1.82
2241 3184 8.607713 TGTCTTGGGAATTACTCCTACAAATTA 58.392 33.333 0.00 0.00 44.68 1.40
2242 3185 9.110502 GTCTTGGGAATTACTCCTACAAATTAG 57.889 37.037 0.00 0.00 44.68 1.73
2243 3186 9.053472 TCTTGGGAATTACTCCTACAAATTAGA 57.947 33.333 0.00 0.00 44.68 2.10
2244 3187 9.681062 CTTGGGAATTACTCCTACAAATTAGAA 57.319 33.333 0.00 0.00 44.68 2.10
2246 3189 9.627123 TGGGAATTACTCCTACAAATTAGAATG 57.373 33.333 0.00 0.00 44.68 2.67
2247 3190 8.568794 GGGAATTACTCCTACAAATTAGAATGC 58.431 37.037 0.00 0.00 44.68 3.56
2248 3191 8.568794 GGAATTACTCCTACAAATTAGAATGCC 58.431 37.037 0.00 0.00 41.61 4.40
2249 3192 7.730364 ATTACTCCTACAAATTAGAATGCCG 57.270 36.000 0.00 0.00 0.00 5.69
2250 3193 5.353394 ACTCCTACAAATTAGAATGCCGA 57.647 39.130 0.00 0.00 0.00 5.54
2251 3194 5.360591 ACTCCTACAAATTAGAATGCCGAG 58.639 41.667 0.00 0.00 0.00 4.63
2252 3195 5.128827 ACTCCTACAAATTAGAATGCCGAGA 59.871 40.000 0.00 0.00 0.00 4.04
2253 3196 6.174720 TCCTACAAATTAGAATGCCGAGAT 57.825 37.500 0.00 0.00 0.00 2.75
2314 3257 5.652518 TCACGACGGTCATGAATTTACATA 58.347 37.500 4.17 0.00 0.00 2.29
2334 3277 1.055040 CATGCTGGGGGTTCCAAAAA 58.945 50.000 0.00 0.00 46.51 1.94
2358 3301 3.118775 AGTGCTTAGATGATGGCGTGTTA 60.119 43.478 0.00 0.00 0.00 2.41
2362 3305 4.682787 CTTAGATGATGGCGTGTTAGTCA 58.317 43.478 0.00 0.00 0.00 3.41
2381 3324 6.884280 AGTCACGACTCATGTGATCATATA 57.116 37.500 4.46 0.00 46.98 0.86
2529 3476 2.494471 CTGAAATTTGATCCTGGCAGCA 59.506 45.455 9.56 0.00 0.00 4.41
2557 3504 7.344134 AGAAAATGGTATTTAGGACAGGTACC 58.656 38.462 2.73 2.73 36.26 3.34
2560 3507 5.216665 TGGTATTTAGGACAGGTACCTCT 57.783 43.478 12.84 9.24 38.76 3.69
2690 3640 8.914011 TCTAAAACAGTAGCTTAGATGATAGCA 58.086 33.333 0.00 0.00 39.85 3.49
2860 3811 6.472887 ACTCAGAGGATATTTCGGTTTTCAA 58.527 36.000 1.53 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 4.825546 CAAAAGTGCTTGAGAGACATGT 57.174 40.909 0.00 0.00 0.00 3.21
148 149 5.331876 ACTGAAGACCATAGTCAAGCTAC 57.668 43.478 0.00 0.00 46.15 3.58
207 216 5.096169 CCATATGTAGTATGCTAGCGTGAC 58.904 45.833 19.93 14.15 39.10 3.67
210 219 5.010933 AGTCCATATGTAGTATGCTAGCGT 58.989 41.667 15.08 15.08 39.10 5.07
211 220 5.335935 CAGTCCATATGTAGTATGCTAGCG 58.664 45.833 10.77 0.00 39.10 4.26
226 235 1.555075 GAGCTTGGTGACCAGTCCATA 59.445 52.381 3.77 0.00 33.81 2.74
235 244 1.378531 TGTGTGTTGAGCTTGGTGAC 58.621 50.000 0.00 0.00 0.00 3.67
261 270 1.408683 GGTCCATGATGGCTTGCTACA 60.409 52.381 6.59 0.00 37.47 2.74
271 280 3.736720 ACTTCATGATCGGTCCATGATG 58.263 45.455 17.81 17.81 46.57 3.07
293 302 4.350368 ACATGTGGTAGTGTGTTGATGA 57.650 40.909 0.00 0.00 0.00 2.92
294 303 4.391830 GGTACATGTGGTAGTGTGTTGATG 59.608 45.833 9.11 0.00 31.13 3.07
295 304 4.575885 GGTACATGTGGTAGTGTGTTGAT 58.424 43.478 9.11 0.00 31.13 2.57
313 322 1.468054 GGTCCATGTGTCGTACGGTAC 60.468 57.143 16.52 14.71 0.00 3.34
318 327 0.457337 GGTCGGTCCATGTGTCGTAC 60.457 60.000 0.00 0.00 35.97 3.67
338 347 4.531332 GAAGATGTGTTGTTGAGCTTGAC 58.469 43.478 0.00 0.00 0.00 3.18
351 360 6.239217 TCAATGCTACTATGGAAGATGTGT 57.761 37.500 0.00 0.00 0.00 3.72
359 373 4.081365 TGTCGGTTTCAATGCTACTATGGA 60.081 41.667 0.00 0.00 0.00 3.41
374 388 5.776173 TTAAATGTTGTCCATGTCGGTTT 57.224 34.783 0.00 0.00 32.82 3.27
387 401 7.542130 GCCTTGTTCTGGTAGATTTAAATGTTG 59.458 37.037 5.17 0.00 0.00 3.33
392 406 5.553123 TCGCCTTGTTCTGGTAGATTTAAA 58.447 37.500 0.00 0.00 0.00 1.52
405 419 3.544834 CGATGATGATGTTCGCCTTGTTC 60.545 47.826 0.00 0.00 0.00 3.18
413 427 1.208259 TTCGGCGATGATGATGTTCG 58.792 50.000 11.76 0.00 36.02 3.95
425 439 1.243342 TAGACTTCCCGTTTCGGCGA 61.243 55.000 4.99 4.99 46.86 5.54
437 452 4.092968 CGTTTTGGTAGCATGGTAGACTTC 59.907 45.833 4.51 0.00 0.00 3.01
449 464 2.559330 CGGTGCCGTTTTGGTAGC 59.441 61.111 1.93 0.00 46.17 3.58
451 466 2.979120 GGCGGTGCCGTTTTGGTA 60.979 61.111 12.46 0.00 39.62 3.25
468 483 3.118482 AGGTTGTGATAGACCAGATGCTG 60.118 47.826 0.00 0.00 38.42 4.41
470 485 3.118629 TGAGGTTGTGATAGACCAGATGC 60.119 47.826 0.00 0.00 38.42 3.91
477 492 4.883083 TGTTGTCTGAGGTTGTGATAGAC 58.117 43.478 0.00 0.00 38.52 2.59
482 497 3.836365 TGATGTTGTCTGAGGTTGTGA 57.164 42.857 0.00 0.00 0.00 3.58
483 498 4.067192 TCATGATGTTGTCTGAGGTTGTG 58.933 43.478 0.00 0.00 0.00 3.33
487 502 3.244665 TGCTTCATGATGTTGTCTGAGGT 60.245 43.478 10.05 0.00 0.00 3.85
525 540 1.293062 AGATCTGCAGGTGGAATGGT 58.707 50.000 15.13 0.00 0.00 3.55
530 545 1.341089 ACGAGTAGATCTGCAGGTGGA 60.341 52.381 15.13 0.00 0.00 4.02
532 547 2.792890 CGAACGAGTAGATCTGCAGGTG 60.793 54.545 15.13 0.00 0.00 4.00
549 564 1.726791 CTGTGAGCATGTGGTACGAAC 59.273 52.381 0.00 0.00 0.00 3.95
550 565 1.616374 TCTGTGAGCATGTGGTACGAA 59.384 47.619 0.00 0.00 0.00 3.85
551 566 1.253100 TCTGTGAGCATGTGGTACGA 58.747 50.000 0.00 0.00 0.00 3.43
552 567 1.929169 CATCTGTGAGCATGTGGTACG 59.071 52.381 0.00 0.00 0.00 3.67
553 568 2.977914 ACATCTGTGAGCATGTGGTAC 58.022 47.619 0.00 0.00 31.80 3.34
569 584 4.802039 CACTACCACGTTGTACCATACATC 59.198 45.833 0.00 0.00 38.68 3.06
572 587 4.082571 AGTCACTACCACGTTGTACCATAC 60.083 45.833 0.00 0.00 0.00 2.39
575 590 2.034939 CAGTCACTACCACGTTGTACCA 59.965 50.000 0.00 0.00 0.00 3.25
577 592 3.631145 TCAGTCACTACCACGTTGTAC 57.369 47.619 0.00 0.00 0.00 2.90
588 605 2.159014 ACGGTTGCAAGTTCAGTCACTA 60.159 45.455 0.00 0.00 0.00 2.74
594 612 1.002468 CTTGGACGGTTGCAAGTTCAG 60.002 52.381 0.00 0.00 44.14 3.02
602 620 2.281484 TGCTCCTTGGACGGTTGC 60.281 61.111 0.00 0.00 0.00 4.17
608 626 1.613630 TCCTCCCTGCTCCTTGGAC 60.614 63.158 0.00 0.00 0.00 4.02
611 629 3.041469 GCCTCCTCCCTGCTCCTTG 62.041 68.421 0.00 0.00 0.00 3.61
629 647 0.666374 GTTGGTTGAGTTGTTCCCCG 59.334 55.000 0.00 0.00 0.00 5.73
632 652 2.159156 GGTTGGTTGGTTGAGTTGTTCC 60.159 50.000 0.00 0.00 0.00 3.62
642 662 2.438795 ACGCACGGTTGGTTGGTT 60.439 55.556 0.00 0.00 0.00 3.67
643 663 3.206246 CACGCACGGTTGGTTGGT 61.206 61.111 0.00 0.00 0.00 3.67
644 664 4.622456 GCACGCACGGTTGGTTGG 62.622 66.667 0.00 0.00 0.00 3.77
645 665 4.954680 CGCACGCACGGTTGGTTG 62.955 66.667 0.00 0.00 0.00 3.77
710 1461 4.666253 ATGCACGCAGCCACCCTT 62.666 61.111 0.00 0.00 44.83 3.95
714 1465 3.126879 TAGCATGCACGCAGCCAC 61.127 61.111 21.98 0.00 44.83 5.01
715 1466 3.126879 GTAGCATGCACGCAGCCA 61.127 61.111 21.98 0.00 44.83 4.75
718 1469 4.228097 GCCGTAGCATGCACGCAG 62.228 66.667 26.66 18.86 38.07 5.18
721 1472 2.106131 TAGGCCGTAGCATGCACG 59.894 61.111 25.71 25.71 42.56 5.34
743 1505 3.980775 CCTTGTTGCGATTACCAAACAAG 59.019 43.478 16.42 16.42 34.65 3.16
761 1523 1.865788 TACGTCCGTCCCGTTCCTTG 61.866 60.000 0.00 0.00 39.60 3.61
778 1540 2.739671 GTTCCACCGCCACCGTAC 60.740 66.667 0.00 0.00 0.00 3.67
779 1541 4.360964 CGTTCCACCGCCACCGTA 62.361 66.667 0.00 0.00 0.00 4.02
789 1551 1.094785 CATTGGGATCACCGTTCCAC 58.905 55.000 0.00 0.00 44.64 4.02
805 1567 1.754234 GAAGACCGGCCATGGCATT 60.754 57.895 36.56 21.74 44.11 3.56
807 1569 3.329889 AGAAGACCGGCCATGGCA 61.330 61.111 36.56 0.00 44.11 4.92
812 1574 2.425592 CACACAGAAGACCGGCCA 59.574 61.111 0.00 0.00 0.00 5.36
814 1576 1.961277 CCACACACAGAAGACCGGC 60.961 63.158 0.00 0.00 0.00 6.13
816 1578 0.600255 GACCCACACACAGAAGACCG 60.600 60.000 0.00 0.00 0.00 4.79
818 1580 0.387929 TCGACCCACACACAGAAGAC 59.612 55.000 0.00 0.00 0.00 3.01
819 1581 1.338107 ATCGACCCACACACAGAAGA 58.662 50.000 0.00 0.00 0.00 2.87
821 1583 1.964933 TGTATCGACCCACACACAGAA 59.035 47.619 0.00 0.00 0.00 3.02
946 1721 1.045911 GGAGGTGGAGGTGGAGCTAG 61.046 65.000 0.00 0.00 0.00 3.42
947 1722 1.001760 GGAGGTGGAGGTGGAGCTA 59.998 63.158 0.00 0.00 0.00 3.32
948 1723 2.284995 GGAGGTGGAGGTGGAGCT 60.285 66.667 0.00 0.00 0.00 4.09
950 1725 2.283966 ACGGAGGTGGAGGTGGAG 60.284 66.667 0.00 0.00 0.00 3.86
955 1730 4.436998 GCACGACGGAGGTGGAGG 62.437 72.222 0.00 0.00 35.94 4.30
966 1742 2.117156 TAGGTAGCCGAGGCACGAC 61.117 63.158 17.18 10.57 45.77 4.34
974 1750 2.029623 GTGAATGAGGTAGGTAGCCGA 58.970 52.381 0.00 0.00 0.00 5.54
975 1751 1.068741 GGTGAATGAGGTAGGTAGCCG 59.931 57.143 0.00 0.00 0.00 5.52
977 1753 1.068741 CGGGTGAATGAGGTAGGTAGC 59.931 57.143 0.00 0.00 0.00 3.58
980 1756 1.623542 GGCGGGTGAATGAGGTAGGT 61.624 60.000 0.00 0.00 0.00 3.08
981 1757 1.146263 GGCGGGTGAATGAGGTAGG 59.854 63.158 0.00 0.00 0.00 3.18
985 1762 1.825191 CCATGGCGGGTGAATGAGG 60.825 63.158 0.00 0.00 0.00 3.86
1035 1824 2.512515 CTGCTTACCTGGAGCCGC 60.513 66.667 0.00 0.00 39.38 6.53
1119 1929 1.301677 GGAGGAAGCGCTTCTTGGTG 61.302 60.000 40.11 0.00 39.45 4.17
1122 1932 1.301677 GGTGGAGGAAGCGCTTCTTG 61.302 60.000 40.11 0.00 39.45 3.02
1168 1996 3.603532 GAGCATGAAGAAGATGGTGTGA 58.396 45.455 0.00 0.00 31.75 3.58
1169 1997 2.350804 CGAGCATGAAGAAGATGGTGTG 59.649 50.000 0.00 0.00 31.75 3.82
1170 1998 2.027745 ACGAGCATGAAGAAGATGGTGT 60.028 45.455 0.00 0.00 31.75 4.16
1172 2000 2.234661 TCACGAGCATGAAGAAGATGGT 59.765 45.455 0.00 0.00 34.27 3.55
1173 2001 2.606725 GTCACGAGCATGAAGAAGATGG 59.393 50.000 0.00 0.00 0.00 3.51
1175 2003 3.519579 CAGTCACGAGCATGAAGAAGAT 58.480 45.455 0.00 0.00 0.00 2.40
1176 2004 2.928301 GCAGTCACGAGCATGAAGAAGA 60.928 50.000 0.00 0.00 0.00 2.87
1177 2005 1.392853 GCAGTCACGAGCATGAAGAAG 59.607 52.381 0.00 0.00 0.00 2.85
1178 2006 1.270252 TGCAGTCACGAGCATGAAGAA 60.270 47.619 0.00 0.00 35.51 2.52
1182 2010 1.081094 CATTGCAGTCACGAGCATGA 58.919 50.000 0.00 0.00 40.94 3.07
1190 2018 3.443045 CCCGGCCATTGCAGTCAC 61.443 66.667 2.24 0.00 40.13 3.67
1198 2026 0.904394 ATTTTGCTGTCCCGGCCATT 60.904 50.000 2.24 0.00 34.37 3.16
1199 2027 1.305213 ATTTTGCTGTCCCGGCCAT 60.305 52.632 2.24 0.00 34.37 4.40
1200 2028 2.117206 ATTTTGCTGTCCCGGCCA 59.883 55.556 2.24 0.00 34.37 5.36
1201 2029 2.573340 CATTTTGCTGTCCCGGCC 59.427 61.111 0.00 0.00 34.37 6.13
1202 2030 2.125952 GCATTTTGCTGTCCCGGC 60.126 61.111 0.00 0.00 40.96 6.13
1223 2071 2.426522 GCACTGAGCATGAGTTTGGTA 58.573 47.619 0.00 0.00 44.79 3.25
1240 2109 2.246719 AGTTCAGTGTTGAGAGGCAC 57.753 50.000 0.00 0.00 34.15 5.01
1244 2113 6.205853 ACAGAGTACTAGTTCAGTGTTGAGAG 59.794 42.308 0.00 0.00 38.24 3.20
1245 2114 6.062749 ACAGAGTACTAGTTCAGTGTTGAGA 58.937 40.000 0.00 0.00 38.24 3.27
1246 2115 6.320494 ACAGAGTACTAGTTCAGTGTTGAG 57.680 41.667 0.00 0.00 38.24 3.02
1247 2116 6.710597 AACAGAGTACTAGTTCAGTGTTGA 57.289 37.500 14.61 0.00 38.24 3.18
1248 2117 6.201044 CCAAACAGAGTACTAGTTCAGTGTTG 59.799 42.308 15.54 11.03 38.24 3.33
1249 2118 6.281405 CCAAACAGAGTACTAGTTCAGTGTT 58.719 40.000 0.00 7.14 38.24 3.32
1250 2119 5.739358 GCCAAACAGAGTACTAGTTCAGTGT 60.739 44.000 0.00 0.69 38.24 3.55
1251 2120 4.686554 GCCAAACAGAGTACTAGTTCAGTG 59.313 45.833 0.00 8.13 38.24 3.66
1252 2121 4.558898 CGCCAAACAGAGTACTAGTTCAGT 60.559 45.833 0.00 0.00 41.62 3.41
1255 2124 3.919197 GTCGCCAAACAGAGTACTAGTTC 59.081 47.826 0.00 0.00 0.00 3.01
1266 2135 1.151777 AGTGACACGTCGCCAAACAG 61.152 55.000 7.11 0.00 40.77 3.16
1267 2136 1.149361 GAGTGACACGTCGCCAAACA 61.149 55.000 7.11 0.00 40.77 2.83
1268 2137 1.149361 TGAGTGACACGTCGCCAAAC 61.149 55.000 7.11 0.00 40.77 2.93
1271 2140 1.299850 CTTGAGTGACACGTCGCCA 60.300 57.895 7.11 3.05 40.77 5.69
1272 2141 0.388649 ATCTTGAGTGACACGTCGCC 60.389 55.000 7.11 0.60 40.77 5.54
1273 2142 0.985549 GATCTTGAGTGACACGTCGC 59.014 55.000 2.47 2.47 40.22 5.19
1274 2143 2.245942 CAGATCTTGAGTGACACGTCG 58.754 52.381 0.00 0.00 0.00 5.12
1277 2167 2.094803 AGAGCAGATCTTGAGTGACACG 60.095 50.000 0.00 0.00 32.99 4.49
1293 2183 5.804944 TTGGATTTTGGAAATTCAGAGCA 57.195 34.783 0.00 0.00 0.00 4.26
1403 2293 0.734253 CGAACTTGGTCTCTCCGCTG 60.734 60.000 0.00 0.00 39.52 5.18
1409 2299 1.289380 GTCGGCGAACTTGGTCTCT 59.711 57.895 12.92 0.00 0.00 3.10
1476 2369 1.135603 CATGTTGAGCAATCACCGGTG 60.136 52.381 29.26 29.26 0.00 4.94
1511 2404 6.463995 ACTTTTCTAGAGTAGGCTGATGAG 57.536 41.667 0.00 0.00 0.00 2.90
1534 2427 8.415950 AGATGTATTTATGGTGTTGTTTCCAA 57.584 30.769 0.00 0.00 37.27 3.53
1551 2444 7.981789 TCGAATTCACTGAAGCTAAGATGTATT 59.018 33.333 6.22 4.33 0.00 1.89
1552 2445 7.492524 TCGAATTCACTGAAGCTAAGATGTAT 58.507 34.615 6.22 0.00 0.00 2.29
1553 2446 6.863275 TCGAATTCACTGAAGCTAAGATGTA 58.137 36.000 6.22 0.00 0.00 2.29
1554 2447 5.724328 TCGAATTCACTGAAGCTAAGATGT 58.276 37.500 6.22 0.00 0.00 3.06
1558 2451 4.208047 CGGATCGAATTCACTGAAGCTAAG 59.792 45.833 6.22 0.00 0.00 2.18
1618 2514 6.029607 CGAGGATAACATGTGAAATTGGTTG 58.970 40.000 0.00 0.00 0.00 3.77
1627 2523 1.203758 ACGCACGAGGATAACATGTGA 59.796 47.619 0.00 0.00 32.39 3.58
1630 2526 1.921243 TCACGCACGAGGATAACATG 58.079 50.000 0.00 0.00 0.00 3.21
1638 2534 1.934589 TGGAATAATCACGCACGAGG 58.065 50.000 0.00 0.00 0.00 4.63
1641 2537 8.628882 TCTATATTATGGAATAATCACGCACG 57.371 34.615 0.00 0.00 46.08 5.34
1671 2567 9.630098 GAAGAATGTTATGAAGAATGCAGAAAA 57.370 29.630 0.00 0.00 0.00 2.29
1674 2570 7.926674 TGAAGAATGTTATGAAGAATGCAGA 57.073 32.000 0.00 0.00 0.00 4.26
1717 2619 8.759481 TGTTTGGTTCTATATTATGGAATGCA 57.241 30.769 5.85 0.00 32.27 3.96
1723 2625 9.248291 GCAACATTGTTTGGTTCTATATTATGG 57.752 33.333 0.00 0.00 0.00 2.74
1724 2626 9.800433 TGCAACATTGTTTGGTTCTATATTATG 57.200 29.630 0.00 0.00 0.00 1.90
1727 2629 7.039082 ACCTGCAACATTGTTTGGTTCTATATT 60.039 33.333 0.00 0.00 0.00 1.28
1728 2630 6.437162 ACCTGCAACATTGTTTGGTTCTATAT 59.563 34.615 0.00 0.00 0.00 0.86
1730 2632 4.588528 ACCTGCAACATTGTTTGGTTCTAT 59.411 37.500 0.00 0.00 0.00 1.98
1731 2633 3.957497 ACCTGCAACATTGTTTGGTTCTA 59.043 39.130 0.00 0.00 0.00 2.10
1732 2634 2.765699 ACCTGCAACATTGTTTGGTTCT 59.234 40.909 0.00 0.00 0.00 3.01
1733 2635 3.177997 ACCTGCAACATTGTTTGGTTC 57.822 42.857 0.00 0.00 0.00 3.62
1734 2636 3.055530 TCAACCTGCAACATTGTTTGGTT 60.056 39.130 18.17 18.17 37.49 3.67
1735 2637 2.499289 TCAACCTGCAACATTGTTTGGT 59.501 40.909 0.00 6.12 0.00 3.67
1736 2638 3.125316 CTCAACCTGCAACATTGTTTGG 58.875 45.455 0.00 5.51 0.00 3.28
1894 2837 1.825622 GCTATTCAGGCAGGGGCAC 60.826 63.158 0.00 0.00 43.71 5.01
1926 2869 5.250200 AGAGTACAACAACAACAACAAGGA 58.750 37.500 0.00 0.00 0.00 3.36
1929 2872 9.991388 GTATTTAGAGTACAACAACAACAACAA 57.009 29.630 0.00 0.00 0.00 2.83
1930 2873 9.163899 TGTATTTAGAGTACAACAACAACAACA 57.836 29.630 0.00 0.00 0.00 3.33
1957 2900 8.623903 GTTTCAGCCAGTTCATCATTTGATATA 58.376 33.333 0.00 0.00 33.34 0.86
1962 2905 5.130292 AGTTTCAGCCAGTTCATCATTTG 57.870 39.130 0.00 0.00 0.00 2.32
2016 2959 7.432252 GGATAGCATAGCATACACAAAAACAAC 59.568 37.037 0.00 0.00 0.00 3.32
2109 3052 0.320374 GTCGAGTGACACAATGGGGA 59.680 55.000 8.59 0.00 44.82 4.81
2110 3053 2.840974 GTCGAGTGACACAATGGGG 58.159 57.895 8.59 0.00 44.82 4.96
2126 3069 4.815269 AGAGTAAACATCTCAGCAGTGTC 58.185 43.478 0.00 0.00 34.73 3.67
2183 3126 9.118300 CAGCATTCTATTTTCTTATCTTGGAGT 57.882 33.333 0.00 0.00 0.00 3.85
2184 3127 9.334947 TCAGCATTCTATTTTCTTATCTTGGAG 57.665 33.333 0.00 0.00 0.00 3.86
2185 3128 9.334947 CTCAGCATTCTATTTTCTTATCTTGGA 57.665 33.333 0.00 0.00 0.00 3.53
2191 3134 9.624373 ACACATCTCAGCATTCTATTTTCTTAT 57.376 29.630 0.00 0.00 0.00 1.73
2192 3135 9.102757 GACACATCTCAGCATTCTATTTTCTTA 57.897 33.333 0.00 0.00 0.00 2.10
2193 3136 7.828223 AGACACATCTCAGCATTCTATTTTCTT 59.172 33.333 0.00 0.00 0.00 2.52
2194 3137 7.337167 AGACACATCTCAGCATTCTATTTTCT 58.663 34.615 0.00 0.00 0.00 2.52
2195 3138 7.551035 AGACACATCTCAGCATTCTATTTTC 57.449 36.000 0.00 0.00 0.00 2.29
2196 3139 7.148120 CCAAGACACATCTCAGCATTCTATTTT 60.148 37.037 0.00 0.00 32.34 1.82
2198 3141 5.821470 CCAAGACACATCTCAGCATTCTATT 59.179 40.000 0.00 0.00 32.34 1.73
2200 3143 4.383444 CCCAAGACACATCTCAGCATTCTA 60.383 45.833 0.00 0.00 32.34 2.10
2201 3144 3.607741 CCAAGACACATCTCAGCATTCT 58.392 45.455 0.00 0.00 32.34 2.40
2202 3145 2.681848 CCCAAGACACATCTCAGCATTC 59.318 50.000 0.00 0.00 32.34 2.67
2203 3146 2.306805 TCCCAAGACACATCTCAGCATT 59.693 45.455 0.00 0.00 32.34 3.56
2204 3147 1.911357 TCCCAAGACACATCTCAGCAT 59.089 47.619 0.00 0.00 32.34 3.79
2205 3148 1.351076 TCCCAAGACACATCTCAGCA 58.649 50.000 0.00 0.00 32.34 4.41
2206 3149 2.479566 TTCCCAAGACACATCTCAGC 57.520 50.000 0.00 0.00 32.34 4.26
2207 3150 5.738909 AGTAATTCCCAAGACACATCTCAG 58.261 41.667 0.00 0.00 32.34 3.35
2208 3151 5.338381 GGAGTAATTCCCAAGACACATCTCA 60.338 44.000 0.00 0.00 40.37 3.27
2209 3152 5.119694 GGAGTAATTCCCAAGACACATCTC 58.880 45.833 0.00 0.00 40.37 2.75
2210 3153 5.104259 GGAGTAATTCCCAAGACACATCT 57.896 43.478 0.00 0.00 40.37 2.90
2223 3166 8.283291 CGGCATTCTAATTTGTAGGAGTAATTC 58.717 37.037 0.00 0.00 0.00 2.17
2224 3167 7.990886 TCGGCATTCTAATTTGTAGGAGTAATT 59.009 33.333 0.00 0.00 0.00 1.40
2225 3168 7.506114 TCGGCATTCTAATTTGTAGGAGTAAT 58.494 34.615 0.00 0.00 0.00 1.89
2226 3169 6.880484 TCGGCATTCTAATTTGTAGGAGTAA 58.120 36.000 0.00 0.00 0.00 2.24
2227 3170 6.322969 TCTCGGCATTCTAATTTGTAGGAGTA 59.677 38.462 0.00 0.00 0.00 2.59
2228 3171 5.128827 TCTCGGCATTCTAATTTGTAGGAGT 59.871 40.000 0.00 0.00 0.00 3.85
2229 3172 5.601662 TCTCGGCATTCTAATTTGTAGGAG 58.398 41.667 0.00 0.00 0.00 3.69
2230 3173 5.607939 TCTCGGCATTCTAATTTGTAGGA 57.392 39.130 0.00 0.00 0.00 2.94
2231 3174 6.867662 AATCTCGGCATTCTAATTTGTAGG 57.132 37.500 0.00 0.00 0.00 3.18
2232 3175 8.818141 TCTAATCTCGGCATTCTAATTTGTAG 57.182 34.615 0.00 0.00 0.00 2.74
2233 3176 9.778741 AATCTAATCTCGGCATTCTAATTTGTA 57.221 29.630 0.00 0.00 0.00 2.41
2234 3177 8.562892 CAATCTAATCTCGGCATTCTAATTTGT 58.437 33.333 0.00 0.00 0.00 2.83
2235 3178 7.536622 GCAATCTAATCTCGGCATTCTAATTTG 59.463 37.037 0.00 0.00 0.00 2.32
2236 3179 7.308830 GGCAATCTAATCTCGGCATTCTAATTT 60.309 37.037 0.00 0.00 0.00 1.82
2237 3180 6.150140 GGCAATCTAATCTCGGCATTCTAATT 59.850 38.462 0.00 0.00 0.00 1.40
2238 3181 5.645497 GGCAATCTAATCTCGGCATTCTAAT 59.355 40.000 0.00 0.00 0.00 1.73
2239 3182 4.997395 GGCAATCTAATCTCGGCATTCTAA 59.003 41.667 0.00 0.00 0.00 2.10
2240 3183 4.563580 GGGCAATCTAATCTCGGCATTCTA 60.564 45.833 0.00 0.00 0.00 2.10
2241 3184 3.406764 GGCAATCTAATCTCGGCATTCT 58.593 45.455 0.00 0.00 0.00 2.40
2242 3185 2.485814 GGGCAATCTAATCTCGGCATTC 59.514 50.000 0.00 0.00 0.00 2.67
2243 3186 2.107204 AGGGCAATCTAATCTCGGCATT 59.893 45.455 0.00 0.00 0.00 3.56
2244 3187 1.701847 AGGGCAATCTAATCTCGGCAT 59.298 47.619 0.00 0.00 0.00 4.40
2245 3188 1.131638 AGGGCAATCTAATCTCGGCA 58.868 50.000 0.00 0.00 0.00 5.69
2246 3189 2.147150 GAAGGGCAATCTAATCTCGGC 58.853 52.381 0.00 0.00 0.00 5.54
2247 3190 3.760580 AGAAGGGCAATCTAATCTCGG 57.239 47.619 0.00 0.00 0.00 4.63
2248 3191 7.095017 GGAATTTAGAAGGGCAATCTAATCTCG 60.095 40.741 10.74 0.00 38.72 4.04
2249 3192 7.721399 TGGAATTTAGAAGGGCAATCTAATCTC 59.279 37.037 10.74 10.03 38.72 2.75
2250 3193 7.503902 GTGGAATTTAGAAGGGCAATCTAATCT 59.496 37.037 10.74 3.54 38.72 2.40
2251 3194 7.503902 AGTGGAATTTAGAAGGGCAATCTAATC 59.496 37.037 10.74 7.45 38.72 1.75
2252 3195 7.357471 AGTGGAATTTAGAAGGGCAATCTAAT 58.643 34.615 10.74 0.06 38.72 1.73
2253 3196 6.731467 AGTGGAATTTAGAAGGGCAATCTAA 58.269 36.000 7.03 7.03 37.55 2.10
2334 3277 2.679837 CACGCCATCATCTAAGCACTTT 59.320 45.455 0.00 0.00 0.00 2.66
2336 3279 1.208052 ACACGCCATCATCTAAGCACT 59.792 47.619 0.00 0.00 0.00 4.40
2337 3280 1.656652 ACACGCCATCATCTAAGCAC 58.343 50.000 0.00 0.00 0.00 4.40
2338 3281 2.401583 AACACGCCATCATCTAAGCA 57.598 45.000 0.00 0.00 0.00 3.91
2343 3286 2.893637 GTGACTAACACGCCATCATCT 58.106 47.619 0.00 0.00 39.78 2.90
2358 3301 5.781210 ATATGATCACATGAGTCGTGACT 57.219 39.130 19.28 1.35 45.64 3.41
2381 3324 8.049117 TGTTCTTAAGCTTGGTCATGATATCTT 58.951 33.333 9.86 1.71 0.00 2.40
2468 3415 5.366477 TGAAATATCCTCACAGTAGCATGGA 59.634 40.000 0.00 0.00 0.00 3.41
2529 3476 8.721133 ACCTGTCCTAAATACCATTTTCTTTT 57.279 30.769 0.00 0.00 0.00 2.27
2690 3640 2.485426 CCACAGAAGTTGCGATGAACAT 59.515 45.455 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.