Multiple sequence alignment - TraesCS6A01G088100

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 TraesCS6A01G088100 chr6A 100.000 3906 0 0 1 3906 56238806 56242711 0.000000e+00 7214.0
1 TraesCS6A01G088100 chr6A 83.432 338 44 3 47 380 56138574 56138903 1.760000e-78 303.0
2 TraesCS6A01G088100 chr6A 78.694 291 53 7 3390 3675 83042370 83042656 6.660000e-43 185.0
3 TraesCS6A01G088100 chrUn 93.894 1687 81 6 2220 3906 20117996 20116332 0.000000e+00 2525.0
4 TraesCS6A01G088100 chrUn 88.066 1324 68 32 1 1267 20120038 20118748 0.000000e+00 1487.0
5 TraesCS6A01G088100 chrUn 89.003 291 7 7 1727 2013 20118377 20118108 1.740000e-88 337.0
6 TraesCS6A01G088100 chrUn 82.143 280 38 5 105 380 20121463 20121192 3.040000e-56 230.0
7 TraesCS6A01G088100 chrUn 81.643 207 13 6 1386 1580 20118726 20118533 8.740000e-32 148.0
8 TraesCS6A01G088100 chrUn 85.000 80 11 1 302 380 87057085 87057164 3.240000e-11 80.5
9 TraesCS6A01G088100 chr6B 87.380 1672 102 50 2078 3696 92745509 92747124 0.000000e+00 1818.0
10 TraesCS6A01G088100 chr6B 87.748 808 39 22 701 1467 92744268 92745056 0.000000e+00 889.0
11 TraesCS6A01G088100 chr6B 90.909 297 25 2 1728 2022 92745213 92745509 7.860000e-107 398.0
12 TraesCS6A01G088100 chr6B 82.595 316 30 11 249 551 92743852 92744155 5.010000e-64 255.0
13 TraesCS6A01G088100 chr6B 90.566 53 5 0 3845 3897 92747468 92747520 1.950000e-08 71.3
14 TraesCS6A01G088100 chr4B 84.418 507 47 13 976 1466 217279723 217280213 1.640000e-128 470.0
15 TraesCS6A01G088100 chr4B 88.750 80 6 3 299 378 636462250 636462326 1.160000e-15 95.3
16 TraesCS6A01G088100 chr4B 78.289 152 17 10 414 551 664197455 664197306 2.500000e-12 84.2
17 TraesCS6A01G088100 chr7D 80.645 279 24 16 408 662 499064112 499063840 5.150000e-44 189.0
18 TraesCS6A01G088100 chr6D 80.357 280 28 20 408 663 87389257 87389533 1.850000e-43 187.0
19 TraesCS6A01G088100 chr6D 79.227 207 37 5 3375 3578 65624325 65624122 5.260000e-29 139.0
20 TraesCS6A01G088100 chr3D 80.435 276 27 17 403 657 416191852 416191583 6.660000e-43 185.0
21 TraesCS6A01G088100 chr7B 78.912 294 33 14 414 683 709355568 709355856 5.190000e-39 172.0
22 TraesCS6A01G088100 chr5B 78.671 286 36 16 399 662 62971012 62971294 2.410000e-37 167.0
23 TraesCS6A01G088100 chr5B 84.118 170 20 5 497 662 332409510 332409344 1.450000e-34 158.0
24 TraesCS6A01G088100 chr2A 78.125 288 37 17 399 662 32157013 32157298 4.040000e-35 159.0
25 TraesCS6A01G088100 chr5A 78.229 271 33 17 408 656 24192034 24192300 2.430000e-32 150.0
26 TraesCS6A01G088100 chr1A 78.261 253 33 13 430 662 459323569 459323319 4.070000e-30 143.0
27 TraesCS6A01G088100 chr1D 77.236 246 31 15 415 648 75928170 75927938 1.910000e-23 121.0
28 TraesCS6A01G088100 chr1D 89.041 73 8 0 308 380 393759968 393760040 1.490000e-14 91.6
29 TraesCS6A01G088100 chr3A 89.706 68 7 0 313 380 735612638 735612571 1.930000e-13 87.9
30 TraesCS6A01G088100 chr3A 85.915 71 10 0 314 384 647473051 647472981 4.190000e-10 76.8
31 TraesCS6A01G088100 chr5D 87.838 74 7 2 301 374 98814300 98814371 6.950000e-13 86.1
32 TraesCS6A01G088100 chr5D 86.076 79 8 3 301 378 509995017 509995093 9.000000e-12 82.4
33 TraesCS6A01G088100 chr2B 76.506 166 22 12 400 551 142749925 142750087 1.510000e-09 75.0


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 TraesCS6A01G088100 chr6A 56238806 56242711 3905 False 7214.00 7214 100.0000 1 3906 1 chr6A.!!$F2 3905
1 TraesCS6A01G088100 chrUn 20116332 20121463 5131 True 945.40 2525 86.9498 1 3906 5 chrUn.!!$R1 3905
2 TraesCS6A01G088100 chr6B 92743852 92747520 3668 False 686.26 1818 87.8396 249 3897 5 chr6B.!!$F1 3648

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
666 2116 0.041839 GCATCGCACGGACATGAATC 60.042 55.0 0.0 0.0 0.00 2.52 F
912 2395 0.456221 ACGACTCAAATCGATCCGCT 59.544 50.0 0.0 0.0 45.13 5.52 F
2156 3765 0.178068 ACTATTGCATTCCGGTCGCT 59.822 50.0 0.0 0.0 0.00 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1655 3196 0.392461 ACGTTGGACAGCTTGTGTGT 60.392 50.0 0.00 0.00 40.56 3.72 R
2869 4523 0.530744 CGATGTCCTTCCGGAAGACA 59.469 55.0 39.78 35.51 42.08 3.41 R
3834 5498 0.321298 TAGCACGCCCCAGAGAAAAC 60.321 55.0 0.00 0.00 0.00 2.43 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
43 1469 1.675219 GGTGTTACAAGGAGGGCGA 59.325 57.895 0.00 0.00 0.00 5.54
86 1512 3.602483 GGCATCAATTTGCAACTCCAAT 58.398 40.909 0.00 0.00 44.59 3.16
90 1516 2.633967 TCAATTTGCAACTCCAATGCCT 59.366 40.909 0.00 0.00 43.16 4.75
165 1592 2.408271 GATCACCACCAGATCTGCAA 57.592 50.000 17.76 0.00 39.01 4.08
168 1595 1.352017 TCACCACCAGATCTGCAACAT 59.648 47.619 17.76 0.00 0.00 2.71
181 1608 4.001248 AACATGCCATGGTGACGG 57.999 55.556 14.67 1.60 33.60 4.79
183 1610 0.960364 AACATGCCATGGTGACGGAC 60.960 55.000 14.67 0.00 33.60 4.79
251 1678 3.307339 GGAGAAGGAATGAGCTGTTGAGT 60.307 47.826 0.00 0.00 0.00 3.41
270 1697 3.551496 TTTGCAGGTGGGCGAGAGG 62.551 63.158 0.00 0.00 36.28 3.69
378 1805 1.931172 ACAAACGTAGTGAGCACACAC 59.069 47.619 16.79 10.98 45.00 3.82
380 1807 0.750850 AACGTAGTGAGCACACACCT 59.249 50.000 16.79 0.00 45.00 4.00
414 1841 8.580720 TGATGGATTTTATCTCTAGTCTAGCAC 58.419 37.037 1.60 0.00 0.00 4.40
415 1842 8.719645 ATGGATTTTATCTCTAGTCTAGCACT 57.280 34.615 1.60 0.00 39.41 4.40
416 1843 8.540507 TGGATTTTATCTCTAGTCTAGCACTT 57.459 34.615 1.60 0.00 36.43 3.16
472 1900 4.766891 TCCATCATCTTTTGTCCAACCTTC 59.233 41.667 0.00 0.00 0.00 3.46
476 1904 5.147032 TCATCTTTTGTCCAACCTTCCATT 58.853 37.500 0.00 0.00 0.00 3.16
477 1905 6.310941 TCATCTTTTGTCCAACCTTCCATTA 58.689 36.000 0.00 0.00 0.00 1.90
478 1906 6.208599 TCATCTTTTGTCCAACCTTCCATTAC 59.791 38.462 0.00 0.00 0.00 1.89
479 1907 4.830600 TCTTTTGTCCAACCTTCCATTACC 59.169 41.667 0.00 0.00 0.00 2.85
491 1922 9.573166 CAACCTTCCATTACCTGATAATCAATA 57.427 33.333 0.00 0.00 30.54 1.90
495 1926 9.573166 CTTCCATTACCTGATAATCAATAACCA 57.427 33.333 0.00 0.00 30.54 3.67
524 1960 8.936864 CGTATCTTCTGAACCAATTCTACTTTT 58.063 33.333 0.00 0.00 35.69 2.27
603 2053 6.146601 ACACAATCACATCATTGTTGACAA 57.853 33.333 0.00 0.00 43.17 3.18
653 2103 5.734855 ATATTTATATCCCGTTGCATCGC 57.265 39.130 11.68 0.00 0.00 4.58
654 2104 2.535012 TTATATCCCGTTGCATCGCA 57.465 45.000 11.68 0.83 36.47 5.10
655 2105 1.790755 TATATCCCGTTGCATCGCAC 58.209 50.000 11.68 0.00 38.71 5.34
656 2106 1.221466 ATATCCCGTTGCATCGCACG 61.221 55.000 11.68 6.67 38.71 5.34
660 2110 3.410516 CGTTGCATCGCACGGACA 61.411 61.111 3.94 0.00 38.71 4.02
661 2111 2.739704 CGTTGCATCGCACGGACAT 61.740 57.895 3.94 0.00 38.71 3.06
662 2112 1.226101 GTTGCATCGCACGGACATG 60.226 57.895 0.00 0.00 38.71 3.21
663 2113 1.375268 TTGCATCGCACGGACATGA 60.375 52.632 0.00 0.00 38.71 3.07
664 2114 0.952984 TTGCATCGCACGGACATGAA 60.953 50.000 0.00 0.00 38.71 2.57
666 2116 0.041839 GCATCGCACGGACATGAATC 60.042 55.000 0.00 0.00 0.00 2.52
669 2119 2.022764 TCGCACGGACATGAATCAAT 57.977 45.000 0.00 0.00 0.00 2.57
671 2121 2.746904 TCGCACGGACATGAATCAATTT 59.253 40.909 0.00 0.00 0.00 1.82
672 2122 3.935828 TCGCACGGACATGAATCAATTTA 59.064 39.130 0.00 0.00 0.00 1.40
673 2123 4.393371 TCGCACGGACATGAATCAATTTAA 59.607 37.500 0.00 0.00 0.00 1.52
674 2124 4.495472 CGCACGGACATGAATCAATTTAAC 59.505 41.667 0.00 0.00 0.00 2.01
675 2125 5.640732 GCACGGACATGAATCAATTTAACT 58.359 37.500 0.00 0.00 0.00 2.24
907 2390 1.137086 CTCCCCACGACTCAAATCGAT 59.863 52.381 1.63 0.00 45.13 3.59
908 2391 1.136305 TCCCCACGACTCAAATCGATC 59.864 52.381 0.00 0.00 45.13 3.69
909 2392 1.571919 CCCACGACTCAAATCGATCC 58.428 55.000 0.00 0.00 45.13 3.36
910 2393 1.200483 CCACGACTCAAATCGATCCG 58.800 55.000 0.00 0.00 45.13 4.18
911 2394 0.572590 CACGACTCAAATCGATCCGC 59.427 55.000 0.00 0.00 45.13 5.54
912 2395 0.456221 ACGACTCAAATCGATCCGCT 59.544 50.000 0.00 0.00 45.13 5.52
920 2403 0.546598 AATCGATCCGCTTCCCCTTT 59.453 50.000 0.00 0.00 0.00 3.11
972 2467 1.022982 CGTAAAAACCCTCTCCCCGC 61.023 60.000 0.00 0.00 0.00 6.13
973 2468 0.679002 GTAAAAACCCTCTCCCCGCC 60.679 60.000 0.00 0.00 0.00 6.13
974 2469 0.843343 TAAAAACCCTCTCCCCGCCT 60.843 55.000 0.00 0.00 0.00 5.52
975 2470 2.138453 AAAAACCCTCTCCCCGCCTC 62.138 60.000 0.00 0.00 0.00 4.70
980 2475 4.896829 CTCTCCCCGCCTCCGCTA 62.897 72.222 0.00 0.00 0.00 4.26
981 2476 4.452251 TCTCCCCGCCTCCGCTAA 62.452 66.667 0.00 0.00 0.00 3.09
982 2477 4.222847 CTCCCCGCCTCCGCTAAC 62.223 72.222 0.00 0.00 0.00 2.34
1020 2515 1.448540 GGTGCTGTGGGAGATCACG 60.449 63.158 0.00 0.00 40.31 4.35
1167 2662 4.189188 CACCCCCGCTCGTACTCG 62.189 72.222 0.00 0.00 38.55 4.18
1168 2663 4.729918 ACCCCCGCTCGTACTCGT 62.730 66.667 0.00 0.00 38.33 4.18
1267 2792 1.730902 CTGACTGGTCGTGCTGTCG 60.731 63.158 0.00 0.00 32.64 4.35
1268 2793 3.106407 GACTGGTCGTGCTGTCGC 61.106 66.667 0.00 0.00 0.00 5.19
1311 2837 0.541296 ACCAATGCTTTGCTCCTGCT 60.541 50.000 6.81 0.00 40.48 4.24
1319 2845 1.577328 TTTGCTCCTGCTTAGCGTGC 61.577 55.000 0.00 1.84 43.11 5.34
1359 2885 2.014594 GTAGCAATGGGTACAGCGC 58.985 57.895 0.00 0.00 45.18 5.92
1371 2897 1.871039 GTACAGCGCCAGAACAAAGAA 59.129 47.619 2.29 0.00 0.00 2.52
1380 2906 3.568538 CCAGAACAAAGAATTGGCTTCG 58.431 45.455 0.00 0.00 41.01 3.79
1420 2949 4.202050 GGCTGAATGAAATCTGCGGTAAAT 60.202 41.667 0.00 0.00 43.01 1.40
1471 3000 2.896685 ACTAGCCTCATAGGATGTGCTC 59.103 50.000 0.00 0.00 37.67 4.26
1481 3010 1.710816 GGATGTGCTCCTAGCTACCT 58.289 55.000 0.03 0.00 42.97 3.08
1485 3026 2.656002 TGTGCTCCTAGCTACCTGTAG 58.344 52.381 0.03 0.00 42.97 2.74
1522 3063 1.287041 GGTGTCTTCGGTAACACGGC 61.287 60.000 8.36 0.00 45.31 5.68
1523 3064 1.005867 TGTCTTCGGTAACACGGCC 60.006 57.895 0.00 0.00 0.00 6.13
1525 3066 3.484547 CTTCGGTAACACGGCCGC 61.485 66.667 28.58 8.35 46.79 6.53
1526 3067 4.296593 TTCGGTAACACGGCCGCA 62.297 61.111 28.58 4.92 46.79 5.69
1527 3068 4.728102 TCGGTAACACGGCCGCAG 62.728 66.667 28.58 21.36 46.79 5.18
1542 3083 3.580193 CAGCTGCGCAGGCCATAC 61.580 66.667 36.47 19.77 38.85 2.39
1574 3115 3.297134 TTCTGCTTTGTCTGTCCCTTT 57.703 42.857 0.00 0.00 0.00 3.11
1575 3116 4.431416 TTCTGCTTTGTCTGTCCCTTTA 57.569 40.909 0.00 0.00 0.00 1.85
1576 3117 4.431416 TCTGCTTTGTCTGTCCCTTTAA 57.569 40.909 0.00 0.00 0.00 1.52
1577 3118 4.985538 TCTGCTTTGTCTGTCCCTTTAAT 58.014 39.130 0.00 0.00 0.00 1.40
1578 3119 5.003804 TCTGCTTTGTCTGTCCCTTTAATC 58.996 41.667 0.00 0.00 0.00 1.75
1579 3120 4.079253 TGCTTTGTCTGTCCCTTTAATCC 58.921 43.478 0.00 0.00 0.00 3.01
1580 3121 4.202567 TGCTTTGTCTGTCCCTTTAATCCT 60.203 41.667 0.00 0.00 0.00 3.24
1581 3122 4.396478 GCTTTGTCTGTCCCTTTAATCCTC 59.604 45.833 0.00 0.00 0.00 3.71
1582 3123 3.887621 TGTCTGTCCCTTTAATCCTCG 57.112 47.619 0.00 0.00 0.00 4.63
1583 3124 2.093658 TGTCTGTCCCTTTAATCCTCGC 60.094 50.000 0.00 0.00 0.00 5.03
1584 3125 1.485066 TCTGTCCCTTTAATCCTCGCC 59.515 52.381 0.00 0.00 0.00 5.54
1585 3126 1.209504 CTGTCCCTTTAATCCTCGCCA 59.790 52.381 0.00 0.00 0.00 5.69
1586 3127 1.209504 TGTCCCTTTAATCCTCGCCAG 59.790 52.381 0.00 0.00 0.00 4.85
1587 3128 0.837272 TCCCTTTAATCCTCGCCAGG 59.163 55.000 0.00 0.00 42.01 4.45
1613 3154 1.135960 TCCAATGTGACCACACCTCA 58.864 50.000 4.83 0.00 45.05 3.86
1618 3159 0.916086 TGTGACCACACCTCAGGTTT 59.084 50.000 0.00 0.00 45.40 3.27
1619 3160 1.134220 TGTGACCACACCTCAGGTTTC 60.134 52.381 0.00 0.00 45.40 2.78
1621 3162 1.843851 TGACCACACCTCAGGTTTCTT 59.156 47.619 0.00 0.00 38.50 2.52
1622 3163 2.158813 TGACCACACCTCAGGTTTCTTC 60.159 50.000 0.00 0.00 38.50 2.87
1623 3164 2.104963 GACCACACCTCAGGTTTCTTCT 59.895 50.000 0.00 0.00 38.50 2.85
1624 3165 3.314693 ACCACACCTCAGGTTTCTTCTA 58.685 45.455 0.00 0.00 33.39 2.10
1625 3166 3.325135 ACCACACCTCAGGTTTCTTCTAG 59.675 47.826 0.00 0.00 33.39 2.43
1626 3167 3.325135 CCACACCTCAGGTTTCTTCTAGT 59.675 47.826 0.00 0.00 31.02 2.57
1627 3168 4.310769 CACACCTCAGGTTTCTTCTAGTG 58.689 47.826 0.00 0.00 31.02 2.74
1628 3169 3.325135 ACACCTCAGGTTTCTTCTAGTGG 59.675 47.826 0.00 0.00 31.02 4.00
1629 3170 2.303311 ACCTCAGGTTTCTTCTAGTGGC 59.697 50.000 0.00 0.00 27.29 5.01
1630 3171 2.303022 CCTCAGGTTTCTTCTAGTGGCA 59.697 50.000 0.00 0.00 0.00 4.92
1631 3172 3.244561 CCTCAGGTTTCTTCTAGTGGCAA 60.245 47.826 0.00 0.00 0.00 4.52
1632 3173 4.389374 CTCAGGTTTCTTCTAGTGGCAAA 58.611 43.478 0.00 0.00 0.00 3.68
1633 3174 4.787551 TCAGGTTTCTTCTAGTGGCAAAA 58.212 39.130 0.00 0.00 0.00 2.44
1634 3175 5.197451 TCAGGTTTCTTCTAGTGGCAAAAA 58.803 37.500 0.00 0.00 0.00 1.94
1635 3176 5.067283 TCAGGTTTCTTCTAGTGGCAAAAAC 59.933 40.000 0.00 0.00 0.00 2.43
1636 3177 4.953579 AGGTTTCTTCTAGTGGCAAAAACA 59.046 37.500 0.00 0.00 0.00 2.83
1637 3178 5.067805 AGGTTTCTTCTAGTGGCAAAAACAG 59.932 40.000 0.00 0.00 0.00 3.16
1638 3179 5.067283 GGTTTCTTCTAGTGGCAAAAACAGA 59.933 40.000 0.00 0.00 0.00 3.41
1639 3180 5.751243 TTCTTCTAGTGGCAAAAACAGAC 57.249 39.130 0.00 0.00 0.00 3.51
1640 3181 4.134563 TCTTCTAGTGGCAAAAACAGACC 58.865 43.478 0.00 0.00 0.00 3.85
1641 3182 3.569194 TCTAGTGGCAAAAACAGACCA 57.431 42.857 0.00 0.00 0.00 4.02
1642 3183 3.476552 TCTAGTGGCAAAAACAGACCAG 58.523 45.455 0.00 0.00 31.46 4.00
1643 3184 2.143876 AGTGGCAAAAACAGACCAGT 57.856 45.000 0.00 0.00 31.46 4.00
1644 3185 3.290948 AGTGGCAAAAACAGACCAGTA 57.709 42.857 0.00 0.00 34.05 2.74
1645 3186 3.214328 AGTGGCAAAAACAGACCAGTAG 58.786 45.455 0.00 0.00 34.05 2.57
1646 3187 2.949644 GTGGCAAAAACAGACCAGTAGT 59.050 45.455 0.00 0.00 31.46 2.73
1647 3188 3.003378 GTGGCAAAAACAGACCAGTAGTC 59.997 47.826 0.00 0.00 46.71 2.59
1658 3199 4.275838 GACCAGTAGTCGAGTGATACAC 57.724 50.000 2.10 0.00 35.30 2.90
1659 3200 3.682696 ACCAGTAGTCGAGTGATACACA 58.317 45.455 2.10 0.00 36.74 3.72
1673 3214 1.577468 TACACACAAGCTGTCCAACG 58.423 50.000 0.00 0.00 0.00 4.10
1683 3224 1.000506 GCTGTCCAACGTAAGGTCTCA 59.999 52.381 6.83 5.05 46.39 3.27
1692 3233 6.203338 TCCAACGTAAGGTCTCAACATAAAAC 59.797 38.462 6.83 0.00 46.39 2.43
1722 3263 4.950050 AGGCGTTCCTGTTATCTCATTAG 58.050 43.478 0.00 0.00 42.34 1.73
1723 3264 4.649674 AGGCGTTCCTGTTATCTCATTAGA 59.350 41.667 0.00 0.00 42.34 2.10
1724 3265 4.985409 GGCGTTCCTGTTATCTCATTAGAG 59.015 45.833 0.00 0.00 43.48 2.43
1769 3373 3.685550 GCCCAGCATTTCTAGCTTTAGGA 60.686 47.826 0.00 0.00 41.14 2.94
1778 3382 6.721571 TTTCTAGCTTTAGGACGACATTTG 57.278 37.500 0.00 0.00 0.00 2.32
1781 3385 6.228258 TCTAGCTTTAGGACGACATTTGTTT 58.772 36.000 0.00 0.00 0.00 2.83
1782 3386 5.767816 AGCTTTAGGACGACATTTGTTTT 57.232 34.783 0.00 0.00 0.00 2.43
1821 3425 6.986817 TCTGTAGGAGCATTATACTTTTGAGC 59.013 38.462 0.00 0.00 0.00 4.26
1823 3427 6.986817 TGTAGGAGCATTATACTTTTGAGCTC 59.013 38.462 6.82 6.82 44.51 4.09
1897 3502 7.605691 CAGTCTTGAGTTCATTTCTCTGGTTAT 59.394 37.037 0.00 0.00 33.59 1.89
1912 3517 4.646945 TCTGGTTATTTTGTGCTGTTTGGA 59.353 37.500 0.00 0.00 0.00 3.53
2013 3621 3.755378 GCATGAGACTCATTTCACCTTGT 59.245 43.478 15.50 0.00 34.28 3.16
2016 3624 4.780815 TGAGACTCATTTCACCTTGTTGT 58.219 39.130 0.00 0.00 0.00 3.32
2021 3629 8.918202 AGACTCATTTCACCTTGTTGTAAATA 57.082 30.769 0.00 0.00 0.00 1.40
2022 3630 9.349713 AGACTCATTTCACCTTGTTGTAAATAA 57.650 29.630 0.00 0.00 0.00 1.40
2025 3633 9.573133 CTCATTTCACCTTGTTGTAAATAATCC 57.427 33.333 0.00 0.00 0.00 3.01
2026 3634 8.527810 TCATTTCACCTTGTTGTAAATAATCCC 58.472 33.333 0.00 0.00 0.00 3.85
2027 3635 8.531146 CATTTCACCTTGTTGTAAATAATCCCT 58.469 33.333 0.00 0.00 0.00 4.20
2028 3636 7.696992 TTCACCTTGTTGTAAATAATCCCTC 57.303 36.000 0.00 0.00 0.00 4.30
2029 3637 6.184789 TCACCTTGTTGTAAATAATCCCTCC 58.815 40.000 0.00 0.00 0.00 4.30
2030 3638 5.065988 CACCTTGTTGTAAATAATCCCTCCG 59.934 44.000 0.00 0.00 0.00 4.63
2031 3639 5.190677 CCTTGTTGTAAATAATCCCTCCGT 58.809 41.667 0.00 0.00 0.00 4.69
2032 3640 5.296035 CCTTGTTGTAAATAATCCCTCCGTC 59.704 44.000 0.00 0.00 0.00 4.79
2033 3641 4.773013 TGTTGTAAATAATCCCTCCGTCC 58.227 43.478 0.00 0.00 0.00 4.79
2034 3642 4.472108 TGTTGTAAATAATCCCTCCGTCCT 59.528 41.667 0.00 0.00 0.00 3.85
2035 3643 5.662208 TGTTGTAAATAATCCCTCCGTCCTA 59.338 40.000 0.00 0.00 0.00 2.94
2036 3644 6.156602 TGTTGTAAATAATCCCTCCGTCCTAA 59.843 38.462 0.00 0.00 0.00 2.69
2037 3645 6.811634 TGTAAATAATCCCTCCGTCCTAAA 57.188 37.500 0.00 0.00 0.00 1.85
2038 3646 6.823497 TGTAAATAATCCCTCCGTCCTAAAG 58.177 40.000 0.00 0.00 0.00 1.85
2039 3647 5.970501 AAATAATCCCTCCGTCCTAAAGT 57.029 39.130 0.00 0.00 0.00 2.66
2040 3648 5.970501 AATAATCCCTCCGTCCTAAAGTT 57.029 39.130 0.00 0.00 0.00 2.66
2041 3649 3.629142 AATCCCTCCGTCCTAAAGTTG 57.371 47.619 0.00 0.00 0.00 3.16
2042 3650 2.019807 TCCCTCCGTCCTAAAGTTGT 57.980 50.000 0.00 0.00 0.00 3.32
2043 3651 1.621814 TCCCTCCGTCCTAAAGTTGTG 59.378 52.381 0.00 0.00 0.00 3.33
2044 3652 1.439679 CCTCCGTCCTAAAGTTGTGC 58.560 55.000 0.00 0.00 0.00 4.57
2045 3653 1.002087 CCTCCGTCCTAAAGTTGTGCT 59.998 52.381 0.00 0.00 0.00 4.40
2046 3654 2.232941 CCTCCGTCCTAAAGTTGTGCTA 59.767 50.000 0.00 0.00 0.00 3.49
2047 3655 3.306502 CCTCCGTCCTAAAGTTGTGCTAA 60.307 47.826 0.00 0.00 0.00 3.09
2048 3656 4.312443 CTCCGTCCTAAAGTTGTGCTAAA 58.688 43.478 0.00 0.00 0.00 1.85
2049 3657 4.901868 TCCGTCCTAAAGTTGTGCTAAAT 58.098 39.130 0.00 0.00 0.00 1.40
2050 3658 4.933400 TCCGTCCTAAAGTTGTGCTAAATC 59.067 41.667 0.00 0.00 0.00 2.17
2051 3659 4.693566 CCGTCCTAAAGTTGTGCTAAATCA 59.306 41.667 0.00 0.00 0.00 2.57
2052 3660 5.180492 CCGTCCTAAAGTTGTGCTAAATCAA 59.820 40.000 0.00 0.00 0.00 2.57
2053 3661 6.293735 CCGTCCTAAAGTTGTGCTAAATCAAA 60.294 38.462 0.00 0.00 0.00 2.69
2054 3662 6.797033 CGTCCTAAAGTTGTGCTAAATCAAAG 59.203 38.462 0.00 0.00 0.00 2.77
2055 3663 7.307751 CGTCCTAAAGTTGTGCTAAATCAAAGA 60.308 37.037 0.00 0.00 0.00 2.52
2056 3664 7.803659 GTCCTAAAGTTGTGCTAAATCAAAGAC 59.196 37.037 0.00 0.00 0.00 3.01
2057 3665 7.500892 TCCTAAAGTTGTGCTAAATCAAAGACA 59.499 33.333 0.00 0.00 0.00 3.41
2058 3666 7.591426 CCTAAAGTTGTGCTAAATCAAAGACAC 59.409 37.037 0.00 0.00 0.00 3.67
2059 3667 6.699575 AAGTTGTGCTAAATCAAAGACACT 57.300 33.333 0.00 0.00 0.00 3.55
2060 3668 6.699575 AGTTGTGCTAAATCAAAGACACTT 57.300 33.333 0.00 0.00 0.00 3.16
2061 3669 7.801716 AGTTGTGCTAAATCAAAGACACTTA 57.198 32.000 0.00 0.00 0.00 2.24
2062 3670 8.396272 AGTTGTGCTAAATCAAAGACACTTAT 57.604 30.769 0.00 0.00 0.00 1.73
2063 3671 8.850156 AGTTGTGCTAAATCAAAGACACTTATT 58.150 29.630 0.00 0.00 0.00 1.40
2064 3672 9.463443 GTTGTGCTAAATCAAAGACACTTATTT 57.537 29.630 0.00 0.00 0.00 1.40
2066 3674 9.462174 TGTGCTAAATCAAAGACACTTATTTTG 57.538 29.630 0.00 0.00 34.07 2.44
2067 3675 8.915654 GTGCTAAATCAAAGACACTTATTTTGG 58.084 33.333 0.00 0.00 33.70 3.28
2068 3676 8.637986 TGCTAAATCAAAGACACTTATTTTGGT 58.362 29.630 0.00 0.00 33.70 3.67
2072 3680 9.965824 AAATCAAAGACACTTATTTTGGTACTG 57.034 29.630 0.00 0.00 33.70 2.74
2073 3681 8.918202 ATCAAAGACACTTATTTTGGTACTGA 57.082 30.769 0.00 0.00 33.70 3.41
2074 3682 8.378172 TCAAAGACACTTATTTTGGTACTGAG 57.622 34.615 0.00 0.00 33.70 3.35
2075 3683 7.444183 TCAAAGACACTTATTTTGGTACTGAGG 59.556 37.037 0.00 0.00 33.70 3.86
2076 3684 5.805728 AGACACTTATTTTGGTACTGAGGG 58.194 41.667 0.00 0.00 0.00 4.30
2080 3688 6.499350 ACACTTATTTTGGTACTGAGGGAGTA 59.501 38.462 0.00 0.00 35.96 2.59
2092 3700 6.875972 ACTGAGGGAGTAGATATTGTTTGT 57.124 37.500 0.00 0.00 30.86 2.83
2123 3731 9.429359 AGTGTACTTTGTTCTCTCTGAATATTG 57.571 33.333 0.00 0.00 36.99 1.90
2124 3732 8.171840 GTGTACTTTGTTCTCTCTGAATATTGC 58.828 37.037 0.00 0.00 36.99 3.56
2126 3734 6.240894 ACTTTGTTCTCTCTGAATATTGCCA 58.759 36.000 0.00 0.00 36.99 4.92
2127 3735 6.373774 ACTTTGTTCTCTCTGAATATTGCCAG 59.626 38.462 0.00 0.00 36.99 4.85
2133 3742 5.541484 TCTCTCTGAATATTGCCAGCAGATA 59.459 40.000 0.00 0.00 35.32 1.98
2134 3743 6.042437 TCTCTCTGAATATTGCCAGCAGATAA 59.958 38.462 0.00 0.00 35.32 1.75
2138 3747 8.327941 TCTGAATATTGCCAGCAGATAAATAC 57.672 34.615 0.00 0.00 31.24 1.89
2140 3749 9.440773 CTGAATATTGCCAGCAGATAAATACTA 57.559 33.333 0.00 0.00 0.00 1.82
2150 3759 7.239271 CAGCAGATAAATACTATTGCATTCCG 58.761 38.462 0.00 0.00 34.17 4.30
2151 3760 6.372659 AGCAGATAAATACTATTGCATTCCGG 59.627 38.462 0.00 0.00 34.17 5.14
2154 3763 6.590292 AGATAAATACTATTGCATTCCGGTCG 59.410 38.462 0.00 0.00 0.00 4.79
2155 3764 1.860676 TACTATTGCATTCCGGTCGC 58.139 50.000 0.00 3.15 0.00 5.19
2156 3765 0.178068 ACTATTGCATTCCGGTCGCT 59.822 50.000 0.00 0.00 0.00 4.93
2157 3766 1.299541 CTATTGCATTCCGGTCGCTT 58.700 50.000 0.00 0.00 0.00 4.68
2175 3785 6.043411 GTCGCTTATACCATCCATTATCCTC 58.957 44.000 0.00 0.00 0.00 3.71
2181 3791 9.261035 CTTATACCATCCATTATCCTCTGTAGT 57.739 37.037 0.00 0.00 0.00 2.73
2215 3832 8.514330 TGAAACCTTAATTTCAGTAGTGTTGT 57.486 30.769 1.00 0.00 42.32 3.32
2216 3833 8.402472 TGAAACCTTAATTTCAGTAGTGTTGTG 58.598 33.333 1.00 0.00 42.32 3.33
2218 3835 7.259290 ACCTTAATTTCAGTAGTGTTGTGTG 57.741 36.000 0.00 0.00 0.00 3.82
2300 3924 2.232696 TGCTGTGCTAAATCTGGTCGTA 59.767 45.455 0.00 0.00 0.00 3.43
2301 3925 2.603560 GCTGTGCTAAATCTGGTCGTAC 59.396 50.000 0.00 0.00 0.00 3.67
2370 4024 8.284693 GCTTATTGAAATTGTCACTGCATTTTT 58.715 29.630 0.00 0.00 35.39 1.94
2661 4315 0.828022 TCGACCATGAATAAGGCCGT 59.172 50.000 0.00 0.00 32.33 5.68
2683 4337 2.667418 GCTCAGAAGCCTGCCTCA 59.333 61.111 0.00 0.00 43.10 3.86
2782 4436 1.091771 CCACGATGATGCAGTCCACC 61.092 60.000 0.00 0.00 0.00 4.61
2869 4523 1.216990 GGAAGGACATGATGGAGGGT 58.783 55.000 0.00 0.00 0.00 4.34
2987 4641 0.250901 TTTGGCCTGGAGCAGAACTC 60.251 55.000 3.32 0.00 46.50 3.01
3011 4665 5.290493 TCACTAGCCCTGTAATAATGGTG 57.710 43.478 0.00 0.00 0.00 4.17
3049 4703 0.318107 CTGTTGCTCCGCCTGTTTTG 60.318 55.000 0.00 0.00 0.00 2.44
3214 4874 5.543714 TGTGTCGTAGTATGAAACAACCAT 58.456 37.500 12.22 0.00 28.84 3.55
3230 4890 0.105593 CCATAGATGCTGCTGGTCGT 59.894 55.000 0.00 0.00 0.00 4.34
3262 4922 1.135575 CGAATGAAAACAGCAGAGGGC 60.136 52.381 0.00 0.00 45.30 5.19
3328 4992 5.554636 CGATCAGAAATCACTTGCACTAAC 58.445 41.667 0.00 0.00 0.00 2.34
3340 5004 3.120321 TGCACTAACGTGTTTCCTCAT 57.880 42.857 0.00 0.00 43.16 2.90
3341 5005 4.260139 TGCACTAACGTGTTTCCTCATA 57.740 40.909 0.00 0.00 43.16 2.15
3363 5027 1.760086 CATCCTCCTCCTCTGCCGT 60.760 63.158 0.00 0.00 0.00 5.68
3451 5115 1.982958 ACCGGTGGGAGTCATAGTTTT 59.017 47.619 6.12 0.00 36.97 2.43
3483 5147 4.219725 GGAGCAGTAGATAGGTCTCCATTC 59.780 50.000 0.00 0.00 39.75 2.67
3508 5172 1.319614 TGGCGAGATGATGGTGTCGA 61.320 55.000 0.00 0.00 37.08 4.20
3518 5182 0.605319 ATGGTGTCGACGTTGGCATT 60.605 50.000 14.28 0.00 0.00 3.56
3533 5197 6.643360 ACGTTGGCATTTAATAAGTTTTGTCC 59.357 34.615 0.00 0.00 0.00 4.02
3566 5230 0.250684 TTTCGGAGCAGGCAACATGA 60.251 50.000 0.00 0.00 41.41 3.07
3596 5260 2.544844 TGATCCCCCGACTCTAGTTT 57.455 50.000 0.00 0.00 0.00 2.66
3631 5295 2.031516 GTCGGTCTCGGTCTCGTCA 61.032 63.158 0.00 0.00 37.69 4.35
3678 5342 1.757699 GACTCCGCCTAGTTGGATCTT 59.242 52.381 0.00 0.00 38.35 2.40
3679 5343 2.957006 GACTCCGCCTAGTTGGATCTTA 59.043 50.000 0.00 0.00 38.35 2.10
3699 5363 3.409804 AGGGATTTGGATCATTTGCCT 57.590 42.857 0.00 0.00 33.77 4.75
3707 5371 2.682856 TGGATCATTTGCCTCGCTTTAC 59.317 45.455 0.00 0.00 0.00 2.01
3729 5393 4.535692 ACATGGGGTTTAATGATTTGCCTT 59.464 37.500 0.00 0.00 0.00 4.35
3731 5395 5.930837 TGGGGTTTAATGATTTGCCTTAG 57.069 39.130 0.00 0.00 0.00 2.18
3733 5397 4.959839 GGGGTTTAATGATTTGCCTTAGGA 59.040 41.667 0.69 0.00 0.00 2.94
3753 5417 2.787473 TTGTCTCAATGGCTAGTGGG 57.213 50.000 0.00 0.00 0.00 4.61
3754 5418 1.656587 TGTCTCAATGGCTAGTGGGT 58.343 50.000 0.00 0.00 0.00 4.51
3776 5440 3.334891 CCCCACCCGTCAATCCCA 61.335 66.667 0.00 0.00 0.00 4.37
3805 5469 3.517500 GGGGTGGAGGCAAATAATCAAAA 59.482 43.478 0.00 0.00 0.00 2.44
3864 5752 0.528470 GGCGTGCTATAGCTCCCTAG 59.472 60.000 24.61 10.04 42.66 3.02
3899 5787 0.751643 GGGGTGGCAATTCGCTATGT 60.752 55.000 0.00 0.00 41.91 2.29
3903 5791 2.544267 GGTGGCAATTCGCTATGTAGAC 59.456 50.000 0.00 0.00 41.91 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.514781 TGTCGTCATGCTACAGTAAACT 57.485 40.909 0.00 0.00 0.00 2.66
2 3 4.091509 CCTTGTCGTCATGCTACAGTAAAC 59.908 45.833 0.00 0.00 0.00 2.01
3 4 4.242475 CCTTGTCGTCATGCTACAGTAAA 58.758 43.478 0.00 0.00 0.00 2.01
4 5 3.368013 CCCTTGTCGTCATGCTACAGTAA 60.368 47.826 0.00 0.00 0.00 2.24
19 1445 2.552373 CCCTCCTTGTAACACCCTTGTC 60.552 54.545 0.00 0.00 33.55 3.18
120 1546 2.038952 AGCTCATAGTGGTTCAACAGCA 59.961 45.455 0.00 0.00 0.00 4.41
165 1592 1.377202 GTCCGTCACCATGGCATGT 60.377 57.895 24.80 11.18 0.00 3.21
181 1608 2.946762 GTTCACGCCTTGCAGGTC 59.053 61.111 0.00 0.00 37.80 3.85
183 1610 3.726517 CCGTTCACGCCTTGCAGG 61.727 66.667 0.00 0.00 38.80 4.85
193 1620 1.446272 CTTCTCCCGCTCCGTTCAC 60.446 63.158 0.00 0.00 0.00 3.18
251 1678 1.600636 CTCTCGCCCACCTGCAAAA 60.601 57.895 0.00 0.00 0.00 2.44
270 1697 3.379865 TTCCACATACCGAGCGGGC 62.380 63.158 14.07 0.00 40.62 6.13
439 1866 8.960591 GGACAAAAGATGATGGAAAGAAAGATA 58.039 33.333 0.00 0.00 0.00 1.98
445 1872 5.243730 GGTTGGACAAAAGATGATGGAAAGA 59.756 40.000 0.00 0.00 0.00 2.52
456 1883 4.830600 GGTAATGGAAGGTTGGACAAAAGA 59.169 41.667 0.00 0.00 0.00 2.52
477 1905 9.871238 GATACGTATGGTTATTGATTATCAGGT 57.129 33.333 13.97 0.00 0.00 4.00
491 1922 5.670792 TGGTTCAGAAGATACGTATGGTT 57.329 39.130 13.97 6.13 0.00 3.67
495 1926 8.915036 AGTAGAATTGGTTCAGAAGATACGTAT 58.085 33.333 8.05 8.05 36.79 3.06
502 1938 9.847224 AAGTAAAAGTAGAATTGGTTCAGAAGA 57.153 29.630 0.00 0.00 36.79 2.87
592 2042 8.301730 AGCTTGTGATTTATTTGTCAACAATG 57.698 30.769 0.00 0.00 35.55 2.82
596 2046 9.410556 ACATTAGCTTGTGATTTATTTGTCAAC 57.589 29.630 0.00 0.00 0.00 3.18
627 2077 7.223971 GCGATGCAACGGGATATAAATATTCTA 59.776 37.037 18.44 0.00 0.00 2.10
628 2078 6.037172 GCGATGCAACGGGATATAAATATTCT 59.963 38.462 18.44 0.00 0.00 2.40
629 2079 6.183360 TGCGATGCAACGGGATATAAATATTC 60.183 38.462 18.44 0.00 34.76 1.75
650 2100 2.022764 ATTGATTCATGTCCGTGCGA 57.977 45.000 0.00 0.00 0.00 5.10
651 2101 2.830772 AATTGATTCATGTCCGTGCG 57.169 45.000 0.00 0.00 0.00 5.34
653 2103 9.619316 TTTTAGTTAAATTGATTCATGTCCGTG 57.381 29.630 0.00 0.00 0.00 4.94
907 2390 3.712907 CGGGAAAGGGGAAGCGGA 61.713 66.667 0.00 0.00 0.00 5.54
908 2391 2.552231 ATTCGGGAAAGGGGAAGCGG 62.552 60.000 0.00 0.00 0.00 5.52
909 2392 1.077716 ATTCGGGAAAGGGGAAGCG 60.078 57.895 0.00 0.00 0.00 4.68
910 2393 1.095807 CGATTCGGGAAAGGGGAAGC 61.096 60.000 0.00 0.00 0.00 3.86
911 2394 1.095807 GCGATTCGGGAAAGGGGAAG 61.096 60.000 8.34 0.00 0.00 3.46
912 2395 1.078001 GCGATTCGGGAAAGGGGAA 60.078 57.895 8.34 0.00 0.00 3.97
920 2403 1.522806 CGGATTTGGCGATTCGGGA 60.523 57.895 8.34 0.00 0.00 5.14
949 2438 0.037046 GGAGAGGGTTTTTACGGCGA 60.037 55.000 16.62 0.00 0.00 5.54
972 2467 4.157120 CGGTGGGGTTAGCGGAGG 62.157 72.222 0.00 0.00 37.86 4.30
973 2468 4.832608 GCGGTGGGGTTAGCGGAG 62.833 72.222 0.00 0.00 41.47 4.63
1167 2662 3.186047 CCGTCGTGAATCGGGCAC 61.186 66.667 0.00 0.00 42.61 5.01
1359 2885 3.568538 CGAAGCCAATTCTTTGTTCTGG 58.431 45.455 0.00 0.00 35.61 3.86
1371 2897 1.518367 TCCCCTAATCCGAAGCCAAT 58.482 50.000 0.00 0.00 0.00 3.16
1380 2906 0.468214 GCCCAAGCTTCCCCTAATCC 60.468 60.000 0.00 0.00 35.50 3.01
1493 3034 1.581934 CGAAGACACCTGACAAAGCA 58.418 50.000 0.00 0.00 0.00 3.91
1501 3042 1.415374 CGTGTTACCGAAGACACCTG 58.585 55.000 8.76 0.00 42.35 4.00
1528 3069 0.877649 CTACAGTATGGCCTGCGCAG 60.878 60.000 30.52 30.52 43.62 5.18
1529 3070 1.143838 CTACAGTATGGCCTGCGCA 59.856 57.895 10.98 10.98 43.62 6.09
1530 3071 2.247437 GCTACAGTATGGCCTGCGC 61.247 63.158 3.32 0.00 43.62 6.09
1531 3072 0.877649 CTGCTACAGTATGGCCTGCG 60.878 60.000 3.32 0.00 43.62 5.18
1562 3103 2.093658 GCGAGGATTAAAGGGACAGACA 60.094 50.000 0.00 0.00 0.00 3.41
1565 3106 1.209504 TGGCGAGGATTAAAGGGACAG 59.790 52.381 0.00 0.00 0.00 3.51
1578 3119 2.494530 GGACTAGCTCCTGGCGAGG 61.495 68.421 8.78 8.78 45.82 4.63
1579 3120 1.323271 TTGGACTAGCTCCTGGCGAG 61.323 60.000 11.21 0.00 46.71 5.03
1582 3123 0.543749 ACATTGGACTAGCTCCTGGC 59.456 55.000 11.21 0.00 40.26 4.85
1583 3124 1.833630 TCACATTGGACTAGCTCCTGG 59.166 52.381 11.21 0.00 40.26 4.45
1584 3125 2.419297 GGTCACATTGGACTAGCTCCTG 60.419 54.545 11.21 6.18 40.26 3.86
1585 3126 1.834263 GGTCACATTGGACTAGCTCCT 59.166 52.381 11.21 0.00 40.26 3.69
1586 3127 1.555075 TGGTCACATTGGACTAGCTCC 59.445 52.381 0.00 4.84 39.97 4.70
1587 3128 2.028112 TGTGGTCACATTGGACTAGCTC 60.028 50.000 0.00 0.00 37.91 4.09
1588 3129 1.977854 TGTGGTCACATTGGACTAGCT 59.022 47.619 0.00 0.00 37.91 3.32
1589 3130 2.076863 GTGTGGTCACATTGGACTAGC 58.923 52.381 7.08 0.00 43.97 3.42
1590 3131 2.303022 AGGTGTGGTCACATTGGACTAG 59.697 50.000 7.08 0.00 45.45 2.57
1591 3132 2.301870 GAGGTGTGGTCACATTGGACTA 59.698 50.000 7.08 0.00 45.45 2.59
1598 3139 1.140312 AACCTGAGGTGTGGTCACAT 58.860 50.000 4.15 0.00 45.45 3.21
1602 3143 2.104963 AGAAGAAACCTGAGGTGTGGTC 59.895 50.000 4.15 0.00 35.34 4.02
1613 3154 4.953579 TGTTTTTGCCACTAGAAGAAACCT 59.046 37.500 0.00 0.00 0.00 3.50
1618 3159 4.134563 GGTCTGTTTTTGCCACTAGAAGA 58.865 43.478 0.00 0.00 0.00 2.87
1619 3160 3.882888 TGGTCTGTTTTTGCCACTAGAAG 59.117 43.478 0.00 0.00 0.00 2.85
1621 3162 3.118038 ACTGGTCTGTTTTTGCCACTAGA 60.118 43.478 0.00 0.00 0.00 2.43
1622 3163 3.214328 ACTGGTCTGTTTTTGCCACTAG 58.786 45.455 0.00 0.00 0.00 2.57
1623 3164 3.290948 ACTGGTCTGTTTTTGCCACTA 57.709 42.857 0.00 0.00 0.00 2.74
1624 3165 2.143876 ACTGGTCTGTTTTTGCCACT 57.856 45.000 0.00 0.00 0.00 4.00
1625 3166 2.949644 ACTACTGGTCTGTTTTTGCCAC 59.050 45.455 0.00 0.00 0.00 5.01
1626 3167 3.211045 GACTACTGGTCTGTTTTTGCCA 58.789 45.455 0.00 0.00 41.46 4.92
1627 3168 2.223377 CGACTACTGGTCTGTTTTTGCC 59.777 50.000 0.00 0.00 42.44 4.52
1628 3169 3.128349 TCGACTACTGGTCTGTTTTTGC 58.872 45.455 0.00 0.00 42.44 3.68
1629 3170 4.209288 CACTCGACTACTGGTCTGTTTTTG 59.791 45.833 0.00 0.00 42.44 2.44
1630 3171 4.098960 TCACTCGACTACTGGTCTGTTTTT 59.901 41.667 0.00 0.00 42.44 1.94
1631 3172 3.635373 TCACTCGACTACTGGTCTGTTTT 59.365 43.478 0.00 0.00 42.44 2.43
1632 3173 3.220110 TCACTCGACTACTGGTCTGTTT 58.780 45.455 0.00 0.00 42.44 2.83
1633 3174 2.860009 TCACTCGACTACTGGTCTGTT 58.140 47.619 0.00 0.00 42.44 3.16
1634 3175 2.563261 TCACTCGACTACTGGTCTGT 57.437 50.000 0.00 0.00 42.44 3.41
1635 3176 3.939592 TGTATCACTCGACTACTGGTCTG 59.060 47.826 0.00 0.00 42.44 3.51
1636 3177 3.940221 GTGTATCACTCGACTACTGGTCT 59.060 47.826 0.00 0.00 42.44 3.85
1637 3178 3.688185 TGTGTATCACTCGACTACTGGTC 59.312 47.826 1.72 0.00 37.14 4.02
1638 3179 3.439476 GTGTGTATCACTCGACTACTGGT 59.561 47.826 1.72 0.00 43.13 4.00
1639 3180 3.439129 TGTGTGTATCACTCGACTACTGG 59.561 47.826 1.72 0.00 46.27 4.00
1640 3181 4.680171 TGTGTGTATCACTCGACTACTG 57.320 45.455 1.72 0.00 46.27 2.74
1641 3182 4.379603 GCTTGTGTGTATCACTCGACTACT 60.380 45.833 1.72 0.00 46.27 2.57
1642 3183 3.852536 GCTTGTGTGTATCACTCGACTAC 59.147 47.826 1.72 0.00 46.27 2.73
1643 3184 3.756963 AGCTTGTGTGTATCACTCGACTA 59.243 43.478 1.72 0.00 46.27 2.59
1644 3185 2.558795 AGCTTGTGTGTATCACTCGACT 59.441 45.455 1.72 0.00 46.27 4.18
1645 3186 2.663602 CAGCTTGTGTGTATCACTCGAC 59.336 50.000 1.72 0.00 46.27 4.20
1646 3187 2.296190 ACAGCTTGTGTGTATCACTCGA 59.704 45.455 1.72 0.00 46.27 4.04
1647 3188 2.663602 GACAGCTTGTGTGTATCACTCG 59.336 50.000 1.72 0.00 46.27 4.18
1648 3189 2.996621 GGACAGCTTGTGTGTATCACTC 59.003 50.000 1.72 0.00 46.27 3.51
1649 3190 2.368548 TGGACAGCTTGTGTGTATCACT 59.631 45.455 1.72 0.00 46.27 3.41
1650 3191 2.766313 TGGACAGCTTGTGTGTATCAC 58.234 47.619 0.00 0.00 46.31 3.06
1651 3192 3.138304 GTTGGACAGCTTGTGTGTATCA 58.862 45.455 0.00 0.00 40.56 2.15
1652 3193 2.157668 CGTTGGACAGCTTGTGTGTATC 59.842 50.000 0.00 0.00 40.56 2.24
1653 3194 2.143122 CGTTGGACAGCTTGTGTGTAT 58.857 47.619 0.00 0.00 40.56 2.29
1654 3195 1.134640 ACGTTGGACAGCTTGTGTGTA 60.135 47.619 0.00 0.00 40.56 2.90
1655 3196 0.392461 ACGTTGGACAGCTTGTGTGT 60.392 50.000 0.00 0.00 40.56 3.72
1656 3197 1.577468 TACGTTGGACAGCTTGTGTG 58.423 50.000 0.00 0.00 40.56 3.82
1657 3198 2.210116 CTTACGTTGGACAGCTTGTGT 58.790 47.619 0.00 0.00 44.49 3.72
1658 3199 1.531149 CCTTACGTTGGACAGCTTGTG 59.469 52.381 0.00 0.00 0.00 3.33
1659 3200 1.140252 ACCTTACGTTGGACAGCTTGT 59.860 47.619 13.21 0.00 0.00 3.16
1673 3214 7.254353 GCCTATCGTTTTATGTTGAGACCTTAC 60.254 40.741 0.00 0.00 0.00 2.34
1683 3224 2.612212 CGCCTGCCTATCGTTTTATGTT 59.388 45.455 0.00 0.00 0.00 2.71
1692 3233 2.815308 AGGAACGCCTGCCTATCG 59.185 61.111 0.00 0.00 44.90 2.92
1717 3258 5.896073 AGATAAACCTCCCACCTCTAATG 57.104 43.478 0.00 0.00 0.00 1.90
1722 3263 5.880887 CAGTAAAAGATAAACCTCCCACCTC 59.119 44.000 0.00 0.00 0.00 3.85
1723 3264 5.281037 CCAGTAAAAGATAAACCTCCCACCT 60.281 44.000 0.00 0.00 0.00 4.00
1724 3265 4.948004 CCAGTAAAAGATAAACCTCCCACC 59.052 45.833 0.00 0.00 0.00 4.61
1769 3373 8.635877 TGCTTTACATTTAAAACAAATGTCGT 57.364 26.923 16.30 0.00 44.83 4.34
1823 3427 1.089920 CTCAACTCCAAATGAGCGGG 58.910 55.000 0.00 0.00 45.61 6.13
1897 3502 5.830991 AGTAGGTAATCCAAACAGCACAAAA 59.169 36.000 0.00 0.00 35.89 2.44
2013 3621 6.811634 TTAGGACGGAGGGATTATTTACAA 57.188 37.500 0.00 0.00 0.00 2.41
2016 3624 7.092757 ACAACTTTAGGACGGAGGGATTATTTA 60.093 37.037 0.00 0.00 0.00 1.40
2021 3629 2.910977 ACAACTTTAGGACGGAGGGATT 59.089 45.455 0.00 0.00 0.00 3.01
2022 3630 2.236395 CACAACTTTAGGACGGAGGGAT 59.764 50.000 0.00 0.00 0.00 3.85
2023 3631 1.621814 CACAACTTTAGGACGGAGGGA 59.378 52.381 0.00 0.00 0.00 4.20
2024 3632 1.944430 GCACAACTTTAGGACGGAGGG 60.944 57.143 0.00 0.00 0.00 4.30
2025 3633 1.002087 AGCACAACTTTAGGACGGAGG 59.998 52.381 0.00 0.00 0.00 4.30
2026 3634 2.457366 AGCACAACTTTAGGACGGAG 57.543 50.000 0.00 0.00 0.00 4.63
2027 3635 4.339872 TTTAGCACAACTTTAGGACGGA 57.660 40.909 0.00 0.00 0.00 4.69
2028 3636 4.693566 TGATTTAGCACAACTTTAGGACGG 59.306 41.667 0.00 0.00 0.00 4.79
2029 3637 5.856126 TGATTTAGCACAACTTTAGGACG 57.144 39.130 0.00 0.00 0.00 4.79
2030 3638 7.803659 GTCTTTGATTTAGCACAACTTTAGGAC 59.196 37.037 0.00 0.00 0.00 3.85
2031 3639 7.500892 TGTCTTTGATTTAGCACAACTTTAGGA 59.499 33.333 0.00 0.00 0.00 2.94
2032 3640 7.591426 GTGTCTTTGATTTAGCACAACTTTAGG 59.409 37.037 0.00 0.00 0.00 2.69
2033 3641 8.345565 AGTGTCTTTGATTTAGCACAACTTTAG 58.654 33.333 0.00 0.00 0.00 1.85
2034 3642 8.220755 AGTGTCTTTGATTTAGCACAACTTTA 57.779 30.769 0.00 0.00 0.00 1.85
2035 3643 7.100458 AGTGTCTTTGATTTAGCACAACTTT 57.900 32.000 0.00 0.00 0.00 2.66
2036 3644 6.699575 AGTGTCTTTGATTTAGCACAACTT 57.300 33.333 0.00 0.00 0.00 2.66
2037 3645 6.699575 AAGTGTCTTTGATTTAGCACAACT 57.300 33.333 0.00 0.00 0.00 3.16
2038 3646 9.463443 AAATAAGTGTCTTTGATTTAGCACAAC 57.537 29.630 0.00 0.00 0.00 3.32
2040 3648 9.462174 CAAAATAAGTGTCTTTGATTTAGCACA 57.538 29.630 0.00 0.00 32.87 4.57
2041 3649 8.915654 CCAAAATAAGTGTCTTTGATTTAGCAC 58.084 33.333 0.00 0.00 32.87 4.40
2042 3650 8.637986 ACCAAAATAAGTGTCTTTGATTTAGCA 58.362 29.630 0.00 0.00 32.87 3.49
2046 3654 9.965824 CAGTACCAAAATAAGTGTCTTTGATTT 57.034 29.630 0.00 0.00 32.87 2.17
2047 3655 9.349713 TCAGTACCAAAATAAGTGTCTTTGATT 57.650 29.630 0.00 0.00 32.87 2.57
2048 3656 8.918202 TCAGTACCAAAATAAGTGTCTTTGAT 57.082 30.769 0.00 0.00 32.87 2.57
2049 3657 7.444183 CCTCAGTACCAAAATAAGTGTCTTTGA 59.556 37.037 0.00 0.00 32.87 2.69
2050 3658 7.308589 CCCTCAGTACCAAAATAAGTGTCTTTG 60.309 40.741 0.00 0.00 0.00 2.77
2051 3659 6.715264 CCCTCAGTACCAAAATAAGTGTCTTT 59.285 38.462 0.00 0.00 0.00 2.52
2052 3660 6.043938 TCCCTCAGTACCAAAATAAGTGTCTT 59.956 38.462 0.00 0.00 0.00 3.01
2053 3661 5.546499 TCCCTCAGTACCAAAATAAGTGTCT 59.454 40.000 0.00 0.00 0.00 3.41
2054 3662 5.801380 TCCCTCAGTACCAAAATAAGTGTC 58.199 41.667 0.00 0.00 0.00 3.67
2055 3663 5.309806 ACTCCCTCAGTACCAAAATAAGTGT 59.690 40.000 0.00 0.00 31.37 3.55
2056 3664 5.805728 ACTCCCTCAGTACCAAAATAAGTG 58.194 41.667 0.00 0.00 31.37 3.16
2057 3665 6.958192 TCTACTCCCTCAGTACCAAAATAAGT 59.042 38.462 0.00 0.00 36.43 2.24
2058 3666 7.419711 TCTACTCCCTCAGTACCAAAATAAG 57.580 40.000 0.00 0.00 36.43 1.73
2059 3667 7.989947 ATCTACTCCCTCAGTACCAAAATAA 57.010 36.000 0.00 0.00 36.43 1.40
2060 3668 9.670442 AATATCTACTCCCTCAGTACCAAAATA 57.330 33.333 0.00 0.00 36.43 1.40
2061 3669 8.432805 CAATATCTACTCCCTCAGTACCAAAAT 58.567 37.037 0.00 0.00 36.43 1.82
2062 3670 7.402071 ACAATATCTACTCCCTCAGTACCAAAA 59.598 37.037 0.00 0.00 36.43 2.44
2063 3671 6.901300 ACAATATCTACTCCCTCAGTACCAAA 59.099 38.462 0.00 0.00 36.43 3.28
2064 3672 6.441222 ACAATATCTACTCCCTCAGTACCAA 58.559 40.000 0.00 0.00 36.43 3.67
2065 3673 6.027025 ACAATATCTACTCCCTCAGTACCA 57.973 41.667 0.00 0.00 36.43 3.25
2066 3674 6.980416 AACAATATCTACTCCCTCAGTACC 57.020 41.667 0.00 0.00 36.43 3.34
2067 3675 7.707035 CACAAACAATATCTACTCCCTCAGTAC 59.293 40.741 0.00 0.00 36.43 2.73
2068 3676 7.399191 ACACAAACAATATCTACTCCCTCAGTA 59.601 37.037 0.00 0.00 36.43 2.74
2069 3677 6.213600 ACACAAACAATATCTACTCCCTCAGT 59.786 38.462 0.00 0.00 39.41 3.41
2070 3678 6.644347 ACACAAACAATATCTACTCCCTCAG 58.356 40.000 0.00 0.00 0.00 3.35
2071 3679 6.440647 AGACACAAACAATATCTACTCCCTCA 59.559 38.462 0.00 0.00 0.00 3.86
2072 3680 6.879400 AGACACAAACAATATCTACTCCCTC 58.121 40.000 0.00 0.00 0.00 4.30
2073 3681 6.875972 AGACACAAACAATATCTACTCCCT 57.124 37.500 0.00 0.00 0.00 4.20
2074 3682 7.707035 CACTAGACACAAACAATATCTACTCCC 59.293 40.741 0.00 0.00 0.00 4.30
2075 3683 8.251721 ACACTAGACACAAACAATATCTACTCC 58.748 37.037 0.00 0.00 0.00 3.85
2080 3688 9.998106 AAAGTACACTAGACACAAACAATATCT 57.002 29.630 0.00 0.00 0.00 1.98
2092 3700 6.771267 TCAGAGAGAACAAAGTACACTAGACA 59.229 38.462 0.00 0.00 0.00 3.41
2123 3731 5.947228 TGCAATAGTATTTATCTGCTGGC 57.053 39.130 5.58 0.00 0.00 4.85
2124 3732 7.533426 GGAATGCAATAGTATTTATCTGCTGG 58.467 38.462 0.00 0.00 29.73 4.85
2126 3734 6.372659 CCGGAATGCAATAGTATTTATCTGCT 59.627 38.462 0.00 0.00 29.73 4.24
2127 3735 6.149474 ACCGGAATGCAATAGTATTTATCTGC 59.851 38.462 9.46 0.00 29.73 4.26
2133 3742 3.250040 GCGACCGGAATGCAATAGTATTT 59.750 43.478 9.46 0.00 29.73 1.40
2134 3743 2.806244 GCGACCGGAATGCAATAGTATT 59.194 45.455 9.46 0.00 32.43 1.89
2138 3747 1.299541 AAGCGACCGGAATGCAATAG 58.700 50.000 9.46 0.00 0.00 1.73
2140 3749 1.967319 ATAAGCGACCGGAATGCAAT 58.033 45.000 9.46 4.02 0.00 3.56
2142 3751 1.539496 GGTATAAGCGACCGGAATGCA 60.539 52.381 9.46 0.00 0.00 3.96
2150 3759 5.104900 AGGATAATGGATGGTATAAGCGACC 60.105 44.000 0.00 0.00 37.49 4.79
2151 3760 5.978814 AGGATAATGGATGGTATAAGCGAC 58.021 41.667 0.00 0.00 0.00 5.19
2154 3763 6.951971 ACAGAGGATAATGGATGGTATAAGC 58.048 40.000 0.00 0.00 0.00 3.09
2155 3764 9.261035 ACTACAGAGGATAATGGATGGTATAAG 57.739 37.037 0.00 0.00 0.00 1.73
2175 3785 5.091261 AGGTTTCAGGCTGAATACTACAG 57.909 43.478 28.98 0.00 36.11 2.74
2300 3924 3.919216 GACAAGCAGTCATCACTAGTGT 58.081 45.455 21.99 7.40 46.77 3.55
2357 4010 1.686052 TGGTCCCAAAAATGCAGTGAC 59.314 47.619 0.00 0.00 0.00 3.67
2683 4337 3.036577 TCGTGCGTCGAGGTCTTT 58.963 55.556 7.01 0.00 44.01 2.52
2782 4436 2.510012 TTGCTCGCGCTGATCCTG 60.510 61.111 5.56 0.00 36.97 3.86
2869 4523 0.530744 CGATGTCCTTCCGGAAGACA 59.469 55.000 39.78 35.51 42.08 3.41
2987 4641 5.702670 CACCATTATTACAGGGCTAGTGATG 59.297 44.000 0.00 0.00 0.00 3.07
3011 4665 2.286294 CAGCGATTATGTTCAGCACTCC 59.714 50.000 0.00 0.00 0.00 3.85
3049 4703 9.816354 ATTTGTTAGAAAATGTATATTGGCCAC 57.184 29.630 3.88 0.00 0.00 5.01
3096 4750 5.527582 AGTTGGAAGAAATCATGCGGTATAC 59.472 40.000 0.00 0.00 0.00 1.47
3214 4874 1.257750 ACCACGACCAGCAGCATCTA 61.258 55.000 0.00 0.00 0.00 1.98
3230 4890 4.720649 TTTTCATTCGAAAACACCACCA 57.279 36.364 0.00 0.00 44.32 4.17
3262 4922 3.937706 AGCTTCACAAGGATGAAAGATCG 59.062 43.478 0.00 0.00 38.12 3.69
3328 4992 2.858344 GGATGACGTATGAGGAAACACG 59.142 50.000 0.00 0.00 40.15 4.49
3340 5004 1.751032 GCAGAGGAGGAGGATGACGTA 60.751 57.143 0.00 0.00 0.00 3.57
3341 5005 1.040339 GCAGAGGAGGAGGATGACGT 61.040 60.000 0.00 0.00 0.00 4.34
3363 5027 0.539901 GGAGGCAGGCTATCTACCGA 60.540 60.000 0.00 0.00 34.02 4.69
3401 5065 2.124085 CCCCCTCACACCCCTACA 59.876 66.667 0.00 0.00 0.00 2.74
3427 5091 1.955080 CTATGACTCCCACCGGTAGAC 59.045 57.143 6.87 2.05 0.00 2.59
3466 5130 2.095161 CGCCGAATGGAGACCTATCTAC 60.095 54.545 0.00 0.00 37.19 2.59
3483 5147 4.592192 ATCATCTCGCCACCGCCG 62.592 66.667 0.00 0.00 0.00 6.46
3497 5161 1.666553 GCCAACGTCGACACCATCA 60.667 57.895 17.16 0.00 0.00 3.07
3508 5172 6.643360 GGACAAAACTTATTAAATGCCAACGT 59.357 34.615 0.00 0.00 0.00 3.99
3518 5182 7.931578 ACATGATCGGGACAAAACTTATTAA 57.068 32.000 0.00 0.00 0.00 1.40
3566 5230 1.138266 CGGGGGATCAAGACGTACAAT 59.862 52.381 0.00 0.00 0.00 2.71
3596 5260 1.202256 CGACCAACCTTCATCGATCGA 60.202 52.381 21.86 21.86 36.70 3.59
3631 5295 1.071471 CAAACCTCACACGCTCCCT 59.929 57.895 0.00 0.00 0.00 4.20
3678 5342 4.473444 GAGGCAAATGATCCAAATCCCTA 58.527 43.478 0.00 0.00 0.00 3.53
3679 5343 3.303049 GAGGCAAATGATCCAAATCCCT 58.697 45.455 0.00 0.00 0.00 4.20
3699 5363 4.590918 TCATTAAACCCCATGTAAAGCGA 58.409 39.130 0.00 0.00 0.00 4.93
3707 5371 4.758773 AGGCAAATCATTAAACCCCATG 57.241 40.909 0.00 0.00 0.00 3.66
3729 5393 4.101585 CCACTAGCCATTGAGACAATCCTA 59.898 45.833 0.00 0.00 0.00 2.94
3731 5395 3.209410 CCACTAGCCATTGAGACAATCC 58.791 50.000 0.00 0.00 0.00 3.01
3733 5397 2.578021 ACCCACTAGCCATTGAGACAAT 59.422 45.455 0.00 0.00 0.00 2.71
3781 5445 1.217942 GATTATTTGCCTCCACCCCCT 59.782 52.381 0.00 0.00 0.00 4.79
3782 5446 1.063266 TGATTATTTGCCTCCACCCCC 60.063 52.381 0.00 0.00 0.00 5.40
3783 5447 2.452600 TGATTATTTGCCTCCACCCC 57.547 50.000 0.00 0.00 0.00 4.95
3784 5448 4.817318 TTTTGATTATTTGCCTCCACCC 57.183 40.909 0.00 0.00 0.00 4.61
3785 5449 7.781056 TCTAATTTTGATTATTTGCCTCCACC 58.219 34.615 0.00 0.00 0.00 4.61
3786 5450 9.252962 CATCTAATTTTGATTATTTGCCTCCAC 57.747 33.333 0.00 0.00 0.00 4.02
3787 5451 8.980596 ACATCTAATTTTGATTATTTGCCTCCA 58.019 29.630 0.00 0.00 0.00 3.86
3805 5469 4.278310 GGTTGCCCCAGTTTACATCTAAT 58.722 43.478 0.00 0.00 0.00 1.73
3833 5497 1.896660 GCACGCCCCAGAGAAAACA 60.897 57.895 0.00 0.00 0.00 2.83
3834 5498 0.321298 TAGCACGCCCCAGAGAAAAC 60.321 55.000 0.00 0.00 0.00 2.43
3835 5499 0.618458 ATAGCACGCCCCAGAGAAAA 59.382 50.000 0.00 0.00 0.00 2.29
3864 5752 0.672711 CCCCGGAGAAGAAAACGACC 60.673 60.000 0.73 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.