Multiple sequence alignment - TraesCS1B01G207800

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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 TraesCS1B01G207800 chr1B 100.000 6637 0 0 1 6637 375811184 375817820 0.000000e+00 12257.0
1 TraesCS1B01G207800 chr1B 79.952 828 140 20 3752 4571 375805049 375805858 2.670000e-163 586.0
2 TraesCS1B01G207800 chr1B 86.986 146 18 1 2034 2178 375813157 375813302 5.330000e-36 163.0
3 TraesCS1B01G207800 chr1B 86.986 146 18 1 1974 2119 375813217 375813361 5.330000e-36 163.0
4 TraesCS1B01G207800 chr1A 92.838 5571 248 58 1135 6637 348712151 348717638 0.000000e+00 7938.0
5 TraesCS1B01G207800 chr1A 89.474 494 41 3 1 494 348711004 348711486 1.220000e-171 614.0
6 TraesCS1B01G207800 chr1A 80.501 759 129 15 3821 4571 348693408 348694155 1.250000e-156 564.0
7 TraesCS1B01G207800 chr1A 92.193 269 7 7 508 763 348711471 348711738 1.050000e-97 368.0
8 TraesCS1B01G207800 chr1A 96.392 194 7 0 964 1157 348712061 348712254 2.990000e-83 320.0
9 TraesCS1B01G207800 chr1D 97.123 1703 26 5 3982 5666 276528971 276530668 0.000000e+00 2852.0
10 TraesCS1B01G207800 chr1D 92.018 2017 94 15 1994 3984 276526813 276528788 0.000000e+00 2771.0
11 TraesCS1B01G207800 chr1D 90.353 1078 71 14 1135 2190 276525883 276526949 0.000000e+00 1384.0
12 TraesCS1B01G207800 chr1D 91.498 494 41 1 1 494 276524647 276525139 0.000000e+00 678.0
13 TraesCS1B01G207800 chr1D 81.555 759 120 16 3821 4571 276502119 276502865 5.690000e-170 608.0
14 TraesCS1B01G207800 chr1D 91.587 416 9 4 508 920 276525124 276525516 9.730000e-153 551.0
15 TraesCS1B01G207800 chr1D 82.946 645 58 21 5715 6337 276530662 276531276 9.800000e-148 534.0
16 TraesCS1B01G207800 chr1D 91.954 348 15 7 6295 6637 276531279 276531618 6.020000e-130 475.0
17 TraesCS1B01G207800 chr1D 94.375 160 6 1 1001 1157 276525830 276525989 6.650000e-60 243.0
18 TraesCS1B01G207800 chr1D 81.500 200 27 4 160 349 116933379 116933578 8.910000e-34 156.0
19 TraesCS1B01G207800 chr1D 85.000 60 9 0 18 77 293340154 293340095 2.000000e-05 62.1
20 TraesCS1B01G207800 chr3B 80.983 1241 196 27 3617 4852 681954340 681955545 0.000000e+00 948.0
21 TraesCS1B01G207800 chr3B 80.526 760 104 23 2770 3524 681952997 681953717 1.630000e-150 544.0
22 TraesCS1B01G207800 chr3B 88.618 123 8 2 5180 5296 681955561 681955683 1.930000e-30 145.0
23 TraesCS1B01G207800 chr3B 76.923 195 19 12 6404 6593 681956688 681956861 3.300000e-13 87.9
24 TraesCS1B01G207800 chr7B 84.689 209 16 8 161 355 589403267 589403473 1.890000e-45 195.0
25 TraesCS1B01G207800 chr2D 82.353 204 25 4 163 355 446202149 446201946 4.120000e-37 167.0
26 TraesCS1B01G207800 chr5A 86.577 149 19 1 194 342 66194633 66194486 5.330000e-36 163.0
27 TraesCS1B01G207800 chr5A 88.679 53 5 1 18 69 671354100 671354152 5.560000e-06 63.9
28 TraesCS1B01G207800 chr6A 87.200 125 16 0 168 292 140728298 140728422 6.940000e-30 143.0
29 TraesCS1B01G207800 chr3A 78.138 247 36 10 120 351 9502482 9502239 2.500000e-29 141.0
30 TraesCS1B01G207800 chr6B 86.207 58 8 0 22 79 292954153 292954210 5.560000e-06 63.9
31 TraesCS1B01G207800 chr4D 100.000 28 0 0 18 45 238304355 238304382 1.200000e-02 52.8


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 TraesCS1B01G207800 chr1B 375811184 375817820 6636 False 12257.000 12257 100.00000 1 6637 1 chr1B.!!$F2 6636
1 TraesCS1B01G207800 chr1B 375805049 375805858 809 False 586.000 586 79.95200 3752 4571 1 chr1B.!!$F1 819
2 TraesCS1B01G207800 chr1A 348711004 348717638 6634 False 2310.000 7938 92.72425 1 6637 4 chr1A.!!$F2 6636
3 TraesCS1B01G207800 chr1A 348693408 348694155 747 False 564.000 564 80.50100 3821 4571 1 chr1A.!!$F1 750
4 TraesCS1B01G207800 chr1D 276524647 276531618 6971 False 1186.000 2852 91.48175 1 6637 8 chr1D.!!$F3 6636
5 TraesCS1B01G207800 chr1D 276502119 276502865 746 False 608.000 608 81.55500 3821 4571 1 chr1D.!!$F2 750
6 TraesCS1B01G207800 chr3B 681952997 681956861 3864 False 431.225 948 81.76250 2770 6593 4 chr3B.!!$F1 3823

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
475 476 0.178950 TGCTTGGTTGGTTGCCCATA 60.179 50.000 0.00 0.00 41.49 2.74 F
478 479 0.188587 TTGGTTGGTTGCCCATACCA 59.811 50.000 10.05 10.05 43.80 3.25 F
1843 2098 0.738389 CTTCGTTGTGGTTTGGTGCT 59.262 50.000 0.00 0.00 0.00 4.40 F
2554 2890 0.249398 ATAGGAGGTCGCGCTTTTGT 59.751 50.000 5.56 0.00 0.00 2.83 F
3089 3428 1.064952 CATCATGCTTGCGATGCTTCA 59.935 47.619 0.08 0.00 33.19 3.02 F
4006 5079 2.492088 TCAGTATCGTCCTGACTTGGTG 59.508 50.000 0.00 0.00 34.12 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1544 1797 0.101219 GCGCAGGGAAGCAAAATAGG 59.899 55.0 0.30 0.00 0.00 2.57 R
2218 2547 0.385029 CTCTCATCTGCTCGACCCAG 59.615 60.0 2.63 2.63 0.00 4.45 R
3570 4178 0.596600 AGCTACACACGACCAACACG 60.597 55.0 0.00 0.00 0.00 4.49 R
3876 4761 0.616111 ATTCAGACCTGGGAGCGACT 60.616 55.0 0.00 0.00 0.00 4.18 R
4714 5803 0.540365 ACGTAGAGAACCACGGGGAA 60.540 55.0 12.96 0.00 42.35 3.97 R
5903 7099 0.036010 ATCAAGCTGTCACGAAGGGG 60.036 55.0 0.00 0.00 0.00 4.79 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
32 33 8.030692 CACAATGGAGATAAATTTTCTCTGCAA 58.969 33.333 20.59 10.31 40.13 4.08
213 214 2.009774 GAGCTAAAATTGAGCGAGCCA 58.990 47.619 0.00 0.00 44.98 4.75
241 242 2.999355 GCTCAAGATCAGCTCGTTTCTT 59.001 45.455 0.00 0.00 33.75 2.52
243 244 4.267452 GCTCAAGATCAGCTCGTTTCTTAG 59.733 45.833 0.00 0.00 33.75 2.18
260 261 7.253354 CGTTTCTTAGTCGAGCTACATAAAGTG 60.253 40.741 0.00 0.00 0.00 3.16
270 271 7.067129 TCGAGCTACATAAAGTGTTCATACTCT 59.933 37.037 0.00 0.00 42.29 3.24
271 272 7.166638 CGAGCTACATAAAGTGTTCATACTCTG 59.833 40.741 0.00 0.00 42.29 3.35
285 286 6.535963 TCATACTCTGCTCATTTCTTCTCA 57.464 37.500 0.00 0.00 0.00 3.27
402 403 1.303948 CCACCATCACCTCATGCCA 59.696 57.895 0.00 0.00 0.00 4.92
447 448 0.178967 TGGCAGCAGGATTTGTTGGA 60.179 50.000 0.00 0.00 38.34 3.53
453 454 4.521146 CAGCAGGATTTGTTGGATAGAGT 58.479 43.478 0.00 0.00 34.67 3.24
475 476 0.178950 TGCTTGGTTGGTTGCCCATA 60.179 50.000 0.00 0.00 41.49 2.74
478 479 0.188587 TTGGTTGGTTGCCCATACCA 59.811 50.000 10.05 10.05 43.80 3.25
484 485 2.741145 TGGTTGCCCATACCAAATACC 58.259 47.619 0.00 0.00 42.50 2.73
485 486 2.036387 GGTTGCCCATACCAAATACCC 58.964 52.381 0.00 0.00 35.67 3.69
486 487 2.624557 GGTTGCCCATACCAAATACCCA 60.625 50.000 0.00 0.00 35.67 4.51
487 488 3.304829 GTTGCCCATACCAAATACCCAT 58.695 45.455 0.00 0.00 0.00 4.00
488 489 3.697190 TGCCCATACCAAATACCCATT 57.303 42.857 0.00 0.00 0.00 3.16
489 490 3.303938 TGCCCATACCAAATACCCATTG 58.696 45.455 0.00 0.00 0.00 2.82
490 491 3.052566 TGCCCATACCAAATACCCATTGA 60.053 43.478 0.00 0.00 0.00 2.57
491 492 4.159557 GCCCATACCAAATACCCATTGAT 58.840 43.478 0.00 0.00 0.00 2.57
492 493 5.162936 TGCCCATACCAAATACCCATTGATA 60.163 40.000 0.00 0.00 0.00 2.15
493 494 5.418840 GCCCATACCAAATACCCATTGATAG 59.581 44.000 0.00 0.00 0.00 2.08
494 495 6.552008 CCCATACCAAATACCCATTGATAGT 58.448 40.000 0.00 0.00 0.00 2.12
495 496 6.659242 CCCATACCAAATACCCATTGATAGTC 59.341 42.308 0.00 0.00 0.00 2.59
496 497 6.659242 CCATACCAAATACCCATTGATAGTCC 59.341 42.308 0.00 0.00 0.00 3.85
497 498 5.061721 ACCAAATACCCATTGATAGTCCC 57.938 43.478 0.00 0.00 0.00 4.46
498 499 4.731929 ACCAAATACCCATTGATAGTCCCT 59.268 41.667 0.00 0.00 0.00 4.20
499 500 5.072741 CCAAATACCCATTGATAGTCCCTG 58.927 45.833 0.00 0.00 0.00 4.45
500 501 4.373156 AATACCCATTGATAGTCCCTGC 57.627 45.455 0.00 0.00 0.00 4.85
501 502 1.595311 ACCCATTGATAGTCCCTGCA 58.405 50.000 0.00 0.00 0.00 4.41
502 503 1.922447 ACCCATTGATAGTCCCTGCAA 59.078 47.619 0.00 0.00 0.00 4.08
503 504 2.311542 ACCCATTGATAGTCCCTGCAAA 59.688 45.455 0.00 0.00 0.00 3.68
504 505 3.245586 ACCCATTGATAGTCCCTGCAAAA 60.246 43.478 0.00 0.00 0.00 2.44
505 506 3.768757 CCCATTGATAGTCCCTGCAAAAA 59.231 43.478 0.00 0.00 0.00 1.94
602 604 9.712359 CATATTGGCAAATATCATGTTCGATAG 57.288 33.333 3.01 0.00 36.94 2.08
603 605 5.611796 TGGCAAATATCATGTTCGATAGC 57.388 39.130 0.00 0.00 31.56 2.97
604 606 5.062528 TGGCAAATATCATGTTCGATAGCA 58.937 37.500 0.00 0.00 31.56 3.49
605 607 5.530543 TGGCAAATATCATGTTCGATAGCAA 59.469 36.000 0.00 0.00 31.56 3.91
621 626 1.963515 AGCAAATTTCCGTGGCTCTTT 59.036 42.857 0.00 0.00 0.00 2.52
667 672 4.392138 ACGTTACTAAAAGCTCTTGCATCC 59.608 41.667 0.00 0.00 42.74 3.51
669 674 3.728385 ACTAAAAGCTCTTGCATCCCT 57.272 42.857 0.00 0.00 42.74 4.20
775 789 1.830847 ACCCAAAGGTCCCAAACGC 60.831 57.895 0.00 0.00 46.45 4.84
920 934 2.171725 CCGTTCCGATTTCCTCCGC 61.172 63.158 0.00 0.00 0.00 5.54
921 935 2.514013 CGTTCCGATTTCCTCCGCG 61.514 63.158 0.00 0.00 0.00 6.46
922 936 1.153706 GTTCCGATTTCCTCCGCGA 60.154 57.895 8.23 0.00 0.00 5.87
923 937 1.153706 TTCCGATTTCCTCCGCGAC 60.154 57.895 8.23 0.00 0.00 5.19
924 938 2.877360 TTCCGATTTCCTCCGCGACG 62.877 60.000 8.23 0.00 0.00 5.12
925 939 2.101575 CGATTTCCTCCGCGACGA 59.898 61.111 8.23 0.00 0.00 4.20
926 940 2.222217 CGATTTCCTCCGCGACGAC 61.222 63.158 8.23 0.00 0.00 4.34
927 941 2.202570 ATTTCCTCCGCGACGACG 60.203 61.111 8.23 2.12 42.93 5.12
1090 1337 4.473520 CTTCCCATGCCGCGGACT 62.474 66.667 33.48 12.49 0.00 3.85
1140 1390 3.847602 CCGCTGCTGGAGGAGGAG 61.848 72.222 4.82 0.00 43.00 3.69
1141 1391 3.847602 CGCTGCTGGAGGAGGAGG 61.848 72.222 0.00 0.00 40.48 4.30
1142 1392 2.364842 GCTGCTGGAGGAGGAGGA 60.365 66.667 0.00 0.00 40.48 3.71
1143 1393 2.433994 GCTGCTGGAGGAGGAGGAG 61.434 68.421 0.00 0.00 40.48 3.69
1144 1394 2.364842 TGCTGGAGGAGGAGGAGC 60.365 66.667 0.00 0.00 0.00 4.70
1145 1395 2.364842 GCTGGAGGAGGAGGAGCA 60.365 66.667 0.00 0.00 0.00 4.26
1146 1396 2.433994 GCTGGAGGAGGAGGAGCAG 61.434 68.421 0.00 0.00 0.00 4.24
1147 1397 2.364842 TGGAGGAGGAGGAGCAGC 60.365 66.667 0.00 0.00 0.00 5.25
1148 1398 2.364842 GGAGGAGGAGGAGCAGCA 60.365 66.667 0.00 0.00 0.00 4.41
1149 1399 2.433994 GGAGGAGGAGGAGCAGCAG 61.434 68.421 0.00 0.00 0.00 4.24
1150 1400 3.082701 AGGAGGAGGAGCAGCAGC 61.083 66.667 0.00 0.00 42.56 5.25
1151 1401 3.397439 GGAGGAGGAGCAGCAGCA 61.397 66.667 3.17 0.00 45.49 4.41
1152 1402 2.187424 GAGGAGGAGCAGCAGCAG 59.813 66.667 3.17 0.00 45.49 4.24
1153 1403 4.098722 AGGAGGAGCAGCAGCAGC 62.099 66.667 3.17 0.46 45.49 5.25
1154 1404 4.405671 GGAGGAGCAGCAGCAGCA 62.406 66.667 12.92 0.00 45.49 4.41
1155 1405 2.820479 GAGGAGCAGCAGCAGCAG 60.820 66.667 12.92 0.00 45.49 4.24
1164 1414 4.124943 CAGCAGCAGCCTCCCCAT 62.125 66.667 0.00 0.00 43.56 4.00
1165 1415 4.124943 AGCAGCAGCCTCCCCATG 62.125 66.667 0.00 0.00 43.56 3.66
1187 1437 4.222847 GGATGCCCGAGTCGACCC 62.223 72.222 15.64 0.00 0.00 4.46
1188 1438 4.570663 GATGCCCGAGTCGACCCG 62.571 72.222 15.64 13.02 0.00 5.28
1191 1441 4.570663 GCCCGAGTCGACCCGATG 62.571 72.222 21.79 12.35 38.42 3.84
1192 1442 2.827190 CCCGAGTCGACCCGATGA 60.827 66.667 21.79 0.00 38.42 2.92
1193 1443 2.408022 CCGAGTCGACCCGATGAC 59.592 66.667 21.79 0.00 38.42 3.06
1194 1444 2.022902 CGAGTCGACCCGATGACG 59.977 66.667 14.93 4.36 40.05 4.35
1195 1445 2.278013 GAGTCGACCCGATGACGC 60.278 66.667 13.01 0.00 40.05 5.19
1196 1446 3.753070 GAGTCGACCCGATGACGCC 62.753 68.421 13.01 0.00 40.05 5.68
1457 1710 5.187186 TGTCTGTTTAGTCCTGTTCTATCCC 59.813 44.000 0.00 0.00 0.00 3.85
1508 1761 2.862674 TTACCTGCGGCGGGCTTAAG 62.863 60.000 27.45 3.28 44.05 1.85
1541 1794 7.440523 AATTAATCCGCTGGAATATCTTGTC 57.559 36.000 1.44 0.00 34.34 3.18
1542 1795 2.910688 TCCGCTGGAATATCTTGTCC 57.089 50.000 0.00 0.00 0.00 4.02
1543 1796 2.398588 TCCGCTGGAATATCTTGTCCT 58.601 47.619 0.00 0.00 34.77 3.85
1544 1797 2.365617 TCCGCTGGAATATCTTGTCCTC 59.634 50.000 0.00 0.00 34.77 3.71
1719 1972 6.966461 CCCTTTGATTACCCCTAGATAGGTAT 59.034 42.308 5.21 0.00 42.03 2.73
1720 1973 8.127038 CCCTTTGATTACCCCTAGATAGGTATA 58.873 40.741 5.21 0.00 42.03 1.47
1739 1993 5.177696 GGTATAGCTACTTTTGCGATTCCAG 59.822 44.000 0.00 0.00 34.78 3.86
1740 1994 2.359900 AGCTACTTTTGCGATTCCAGG 58.640 47.619 0.00 0.00 35.28 4.45
1797 2052 4.446371 CCCTTGATTTGGCACTAGACTAG 58.554 47.826 8.00 8.00 0.00 2.57
1843 2098 0.738389 CTTCGTTGTGGTTTGGTGCT 59.262 50.000 0.00 0.00 0.00 4.40
1893 2148 2.360801 TGGTTAGTTTGGTTTGCTGCTC 59.639 45.455 0.00 0.00 0.00 4.26
1894 2149 2.288213 GGTTAGTTTGGTTTGCTGCTCC 60.288 50.000 0.00 1.75 0.00 4.70
1895 2150 1.234821 TAGTTTGGTTTGCTGCTCCG 58.765 50.000 0.00 0.00 0.00 4.63
1896 2151 1.661509 GTTTGGTTTGCTGCTCCGC 60.662 57.895 0.00 0.00 0.00 5.54
1897 2152 2.124060 TTTGGTTTGCTGCTCCGCA 61.124 52.632 0.00 0.00 38.31 5.69
1987 2250 2.424842 ATTGCAGGGTCCGGCTTCAA 62.425 55.000 12.86 0.00 37.97 2.69
2002 2265 0.761323 TTCAACCGAGGAGGGACACA 60.761 55.000 0.00 0.00 46.96 3.72
2013 2276 1.902508 GAGGGACACAAGGAGACATCA 59.097 52.381 0.00 0.00 0.00 3.07
2014 2277 1.905215 AGGGACACAAGGAGACATCAG 59.095 52.381 0.00 0.00 0.00 2.90
2027 2290 9.393512 CAAGGAGACATCAGAAGATAAAAATCT 57.606 33.333 0.00 0.00 31.88 2.40
2084 2350 4.697352 CGAGGAGACATCAAAGGACAAAAT 59.303 41.667 0.00 0.00 0.00 1.82
2102 2368 2.907458 ATTCCCTTCAAGGTTCCAGG 57.093 50.000 1.78 0.00 31.93 4.45
2105 2371 1.068121 CCCTTCAAGGTTCCAGGTCT 58.932 55.000 1.78 0.00 31.93 3.85
2106 2372 1.271597 CCCTTCAAGGTTCCAGGTCTG 60.272 57.143 1.78 0.00 31.93 3.51
2115 2381 3.234349 CCAGGTCTGGCCGATGAT 58.766 61.111 3.86 0.00 44.73 2.45
2151 2480 7.010160 AGACATCAAAGGACAAAAATCCCTTA 58.990 34.615 0.00 0.00 39.21 2.69
2177 2506 0.979709 CCAGGTCTGGCAGATGAGGA 60.980 60.000 21.84 0.00 44.73 3.71
2283 2612 1.947456 CGACGTCCTGAGGATGATGTA 59.053 52.381 26.63 0.00 40.94 2.29
2284 2613 2.554462 CGACGTCCTGAGGATGATGTAT 59.446 50.000 26.63 3.99 40.94 2.29
2285 2614 3.610349 CGACGTCCTGAGGATGATGTATG 60.610 52.174 26.63 6.06 40.94 2.39
2286 2615 2.036475 ACGTCCTGAGGATGATGTATGC 59.964 50.000 26.63 0.00 40.94 3.14
2287 2616 2.036346 CGTCCTGAGGATGATGTATGCA 59.964 50.000 15.69 0.00 40.94 3.96
2288 2617 3.306571 CGTCCTGAGGATGATGTATGCAT 60.307 47.826 15.69 3.79 40.94 3.96
2289 2618 4.649692 GTCCTGAGGATGATGTATGCATT 58.350 43.478 3.65 0.00 32.34 3.56
2290 2619 5.068636 GTCCTGAGGATGATGTATGCATTT 58.931 41.667 3.65 0.00 32.34 2.32
2291 2620 5.180868 GTCCTGAGGATGATGTATGCATTTC 59.819 44.000 3.65 0.48 32.34 2.17
2292 2621 5.067954 CCTGAGGATGATGTATGCATTTCA 58.932 41.667 3.54 6.82 35.07 2.69
2293 2622 5.710567 CCTGAGGATGATGTATGCATTTCAT 59.289 40.000 3.54 11.55 39.17 2.57
2294 2623 6.882678 CCTGAGGATGATGTATGCATTTCATA 59.117 38.462 3.54 1.34 36.63 2.15
2295 2624 7.392393 CCTGAGGATGATGTATGCATTTCATAA 59.608 37.037 3.54 4.31 39.22 1.90
2296 2625 8.873186 TGAGGATGATGTATGCATTTCATAAT 57.127 30.769 3.54 9.13 39.22 1.28
2297 2626 9.304335 TGAGGATGATGTATGCATTTCATAATT 57.696 29.630 3.54 1.66 39.22 1.40
2298 2627 9.569167 GAGGATGATGTATGCATTTCATAATTG 57.431 33.333 3.54 0.00 39.22 2.32
2390 2719 6.493458 AGTTATCACTAAATGCCACTTTGGTT 59.507 34.615 0.00 0.00 40.46 3.67
2411 2740 8.343168 TGGTTTACCAATTTTATCTAGTGTGG 57.657 34.615 0.00 0.00 44.35 4.17
2432 2763 3.161067 GCATGCACTCTCCCTCTATCTA 58.839 50.000 14.21 0.00 0.00 1.98
2436 2767 4.211125 TGCACTCTCCCTCTATCTAACAG 58.789 47.826 0.00 0.00 0.00 3.16
2508 2844 5.300286 CAGTTCTGTTTGTTCTCCAGGATTT 59.700 40.000 0.00 0.00 0.00 2.17
2547 2883 0.536687 TCCCACTATAGGAGGTCGCG 60.537 60.000 0.00 0.00 0.00 5.87
2554 2890 0.249398 ATAGGAGGTCGCGCTTTTGT 59.751 50.000 5.56 0.00 0.00 2.83
2597 2933 9.944663 GAGATCCTAGATATTACGATCATGAAC 57.055 37.037 0.00 0.00 33.33 3.18
2628 2964 2.598589 CGGATTTCGTCGGAACTGTTA 58.401 47.619 0.00 0.00 0.00 2.41
2675 3014 5.124036 TCTTGGAAATGGTTATCCCGATT 57.876 39.130 0.00 0.00 34.68 3.34
2762 3101 3.990092 TGTATGGATCTGTACAATCCGC 58.010 45.455 21.72 17.07 44.81 5.54
2914 3253 7.924947 TCATTGTTTGCACTTGTGATATTTTGA 59.075 29.630 4.79 0.00 0.00 2.69
2915 3254 8.714179 CATTGTTTGCACTTGTGATATTTTGAT 58.286 29.630 4.79 0.00 0.00 2.57
2916 3255 9.926158 ATTGTTTGCACTTGTGATATTTTGATA 57.074 25.926 4.79 0.00 0.00 2.15
3011 3350 6.314896 GCTTGTAGATACTCAATGCTGTTCTT 59.685 38.462 0.00 0.00 0.00 2.52
3037 3376 4.451900 ACAAACTGACTCGTGGAAAGAAT 58.548 39.130 0.00 0.00 0.00 2.40
3062 3401 3.116096 TCCCTGTGGTAAGCTAGACAT 57.884 47.619 0.00 0.00 0.00 3.06
3089 3428 1.064952 CATCATGCTTGCGATGCTTCA 59.935 47.619 0.08 0.00 33.19 3.02
3132 3473 7.426929 AAATGTGTTTGTTTTACTGTTTGCA 57.573 28.000 0.00 0.00 0.00 4.08
3570 4178 3.350219 TCAGTGGTTCCTTTGCCTATC 57.650 47.619 0.00 0.00 0.00 2.08
3661 4533 3.370978 CGTTGGCCGCTTATATTATCAGG 59.629 47.826 0.00 0.00 0.00 3.86
3691 4563 8.718102 TTCAAGTCTTGTTTAGCTATATGTCC 57.282 34.615 12.30 0.00 0.00 4.02
3692 4564 7.847096 TCAAGTCTTGTTTAGCTATATGTCCA 58.153 34.615 12.30 0.00 0.00 4.02
3876 4761 9.679661 TTGCTTGATAAATTAGATGAGGTAACA 57.320 29.630 0.00 0.00 41.41 2.41
3906 4794 2.568956 CAGGTCTGAATCTGAGGAACCA 59.431 50.000 3.95 0.00 33.11 3.67
3995 5068 6.037940 TCACTACCAGTTACATCAGTATCGTC 59.962 42.308 0.00 0.00 0.00 4.20
4006 5079 2.492088 TCAGTATCGTCCTGACTTGGTG 59.508 50.000 0.00 0.00 34.12 4.17
4371 5451 2.512515 GCTCCCCTGATGACGTGC 60.513 66.667 0.00 0.00 0.00 5.34
4526 5614 4.207841 GGTCACTACGTTTGTTATATCCGC 59.792 45.833 0.00 0.00 0.00 5.54
4714 5803 7.067496 TCTGTTCTATGTCAAGAAAGGTTCT 57.933 36.000 0.00 0.00 43.15 3.01
4732 5821 0.172803 CTTCCCCGTGGTTCTCTACG 59.827 60.000 0.00 0.00 45.64 3.51
4740 5829 3.058016 CCGTGGTTCTCTACGTTACTTGA 60.058 47.826 0.00 0.00 44.84 3.02
4741 5830 4.156915 CGTGGTTCTCTACGTTACTTGAG 58.843 47.826 0.00 0.00 42.17 3.02
4742 5831 4.083643 CGTGGTTCTCTACGTTACTTGAGA 60.084 45.833 0.00 0.00 42.17 3.27
4811 5903 3.582208 AGGATTAGATGAGGATGGTGCTC 59.418 47.826 0.00 0.00 35.21 4.26
4857 5949 3.641436 AGTGGTAGTGACAGTGACAATGA 59.359 43.478 10.34 0.00 0.00 2.57
5022 6114 2.153401 TGGGTTGCAGCCTAGGTGT 61.153 57.895 19.84 0.00 36.53 4.16
5311 6409 5.526115 CACGGTAAGTGTGTTCTTTCTCTA 58.474 41.667 0.00 0.00 45.51 2.43
5400 6558 8.315391 TCCTTCTATATCAATGAAATGCGAAG 57.685 34.615 0.00 0.00 0.00 3.79
5423 6583 6.166982 AGAAGAAACAGCACAGTAATAGTCC 58.833 40.000 0.00 0.00 0.00 3.85
5509 6682 3.574354 AGAAGAAGAAGATGGGATGGC 57.426 47.619 0.00 0.00 0.00 4.40
5574 6747 2.684843 GCTGGCACTTCAAGGCTCG 61.685 63.158 0.00 0.00 0.00 5.03
5678 6854 1.338105 GGTTTCATGCCAGCCCTTTTC 60.338 52.381 0.00 0.00 0.00 2.29
5689 6865 3.119708 CCAGCCCTTTTCGATTTTCTCTG 60.120 47.826 0.00 0.00 0.00 3.35
5784 6977 6.597672 AGCAACGGAAACATCAGATATAAACA 59.402 34.615 0.00 0.00 0.00 2.83
5785 6978 7.120579 AGCAACGGAAACATCAGATATAAACAA 59.879 33.333 0.00 0.00 0.00 2.83
5786 6979 7.915397 GCAACGGAAACATCAGATATAAACAAT 59.085 33.333 0.00 0.00 0.00 2.71
5838 7033 6.801575 ACTGGAAATTCGCTCTTGTTTTAAA 58.198 32.000 0.00 0.00 0.00 1.52
5839 7034 6.918022 ACTGGAAATTCGCTCTTGTTTTAAAG 59.082 34.615 0.00 0.00 0.00 1.85
5843 7038 8.600625 GGAAATTCGCTCTTGTTTTAAAGTTTT 58.399 29.630 0.00 0.00 0.00 2.43
5844 7039 9.967245 GAAATTCGCTCTTGTTTTAAAGTTTTT 57.033 25.926 0.00 0.00 0.00 1.94
5886 7082 5.008316 AGGAAAAGGTTGATGAAACGTGTAC 59.992 40.000 0.00 0.00 39.91 2.90
5892 7088 4.510340 GGTTGATGAAACGTGTACTGTCTT 59.490 41.667 0.00 0.00 39.91 3.01
5893 7089 5.693104 GGTTGATGAAACGTGTACTGTCTTA 59.307 40.000 0.00 0.00 39.91 2.10
5896 7092 6.274579 TGATGAAACGTGTACTGTCTTAACA 58.725 36.000 0.00 0.00 0.00 2.41
5897 7093 6.926826 TGATGAAACGTGTACTGTCTTAACAT 59.073 34.615 0.00 0.00 34.13 2.71
5898 7094 7.439955 TGATGAAACGTGTACTGTCTTAACATT 59.560 33.333 0.00 0.00 34.13 2.71
5899 7095 7.542534 TGAAACGTGTACTGTCTTAACATTT 57.457 32.000 0.00 0.00 34.13 2.32
5901 7097 8.452534 TGAAACGTGTACTGTCTTAACATTTTT 58.547 29.630 0.00 0.00 34.13 1.94
5917 7113 1.314730 TTTTTCCCCTTCGTGACAGC 58.685 50.000 0.00 0.00 0.00 4.40
5922 7118 0.036010 CCCCTTCGTGACAGCTTGAT 60.036 55.000 0.00 0.00 0.00 2.57
5926 7149 3.557595 CCCTTCGTGACAGCTTGATATTC 59.442 47.826 0.00 0.00 0.00 1.75
6034 7269 4.479993 CCAGAGCAGGGAAGCGGG 62.480 72.222 0.00 0.00 40.15 6.13
6038 7273 3.249189 AGCAGGGAAGCGGGTGAA 61.249 61.111 0.00 0.00 40.15 3.18
6039 7274 2.044946 GCAGGGAAGCGGGTGAAT 60.045 61.111 0.00 0.00 0.00 2.57
6077 7312 1.059369 CAATGACGGCGAAGAAGCG 59.941 57.895 16.62 0.00 38.18 4.68
6124 7359 5.367302 ACTATCTACAGAAGACGAGGGTAC 58.633 45.833 0.00 0.00 36.93 3.34
6128 7363 6.043135 ATCTACAGAAGACGAGGGTACCAAA 61.043 44.000 15.35 0.00 45.80 3.28
6137 7372 4.757773 GGTACCAAAAGGGAGGGC 57.242 61.111 7.15 0.00 41.15 5.19
6138 7373 1.000019 GGTACCAAAAGGGAGGGCC 60.000 63.158 7.15 0.00 41.15 5.80
6139 7374 1.771646 GTACCAAAAGGGAGGGCCA 59.228 57.895 6.18 0.00 41.15 5.36
6140 7375 0.323451 GTACCAAAAGGGAGGGCCAG 60.323 60.000 6.18 0.00 41.15 4.85
6141 7376 1.506028 TACCAAAAGGGAGGGCCAGG 61.506 60.000 6.18 0.00 41.15 4.45
6142 7377 2.547595 CCAAAAGGGAGGGCCAGGA 61.548 63.158 6.18 0.00 40.01 3.86
6143 7378 1.000396 CAAAAGGGAGGGCCAGGAG 60.000 63.158 6.18 0.00 35.15 3.69
6144 7379 1.151587 AAAAGGGAGGGCCAGGAGA 60.152 57.895 6.18 0.00 35.15 3.71
6176 7411 1.497161 CGGAGGTAGAAGGGGACATT 58.503 55.000 0.00 0.00 0.00 2.71
6190 7436 7.939588 AGAAGGGGACATTTATATAAACTGCTC 59.060 37.037 10.07 4.40 0.00 4.26
6229 7475 1.134037 ACCGTTAGCACAAGGGTTTCA 60.134 47.619 9.03 0.00 35.08 2.69
6235 7481 0.249031 GCACAAGGGTTTCACAGTGC 60.249 55.000 0.00 0.00 44.31 4.40
6266 7512 4.044426 GACCAGTGACACTGCAATTTTTC 58.956 43.478 27.09 11.42 44.63 2.29
6267 7513 3.446873 ACCAGTGACACTGCAATTTTTCA 59.553 39.130 27.09 0.00 44.63 2.69
6312 7561 4.759782 TGAGCTTTGCTGAACTATACTCC 58.240 43.478 0.00 0.00 39.88 3.85
6316 7608 4.938226 GCTTTGCTGAACTATACTCCAGTT 59.062 41.667 0.00 0.00 38.92 3.16
6317 7609 5.412904 GCTTTGCTGAACTATACTCCAGTTT 59.587 40.000 0.00 0.00 36.38 2.66
6318 7610 6.402658 GCTTTGCTGAACTATACTCCAGTTTC 60.403 42.308 0.00 0.00 36.38 2.78
6319 7611 5.086104 TGCTGAACTATACTCCAGTTTCC 57.914 43.478 0.00 0.00 36.38 3.13
6320 7612 4.081087 TGCTGAACTATACTCCAGTTTCCC 60.081 45.833 0.00 0.00 36.38 3.97
6391 7691 3.420893 CTTTTCATAGGGCAAGGACACA 58.579 45.455 0.00 0.00 0.00 3.72
6596 7909 2.700371 CTCATATACAGAGCCACCACCA 59.300 50.000 0.00 0.00 0.00 4.17
6597 7910 2.434336 TCATATACAGAGCCACCACCAC 59.566 50.000 0.00 0.00 0.00 4.16
6598 7911 1.945580 TATACAGAGCCACCACCACA 58.054 50.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
213 214 3.492309 CGAGCTGATCTTGAGCCAATACT 60.492 47.826 0.00 0.00 37.12 2.12
241 242 6.505044 TGAACACTTTATGTAGCTCGACTA 57.495 37.500 0.00 0.00 42.31 2.59
243 244 6.973474 AGTATGAACACTTTATGTAGCTCGAC 59.027 38.462 0.00 0.00 42.31 4.20
260 261 6.815641 TGAGAAGAAATGAGCAGAGTATGAAC 59.184 38.462 0.00 0.00 0.00 3.18
285 286 5.396484 TCGACTCGTATTTTGTCTCGATTT 58.604 37.500 0.00 0.00 0.00 2.17
432 433 4.225942 TGACTCTATCCAACAAATCCTGCT 59.774 41.667 0.00 0.00 0.00 4.24
447 448 4.012374 CAACCAACCAAGCATGACTCTAT 58.988 43.478 0.00 0.00 0.00 1.98
453 454 2.048601 GGCAACCAACCAAGCATGA 58.951 52.632 0.00 0.00 0.00 3.07
475 476 4.731929 AGGGACTATCAATGGGTATTTGGT 59.268 41.667 0.00 0.00 36.02 3.67
478 479 4.167892 TGCAGGGACTATCAATGGGTATTT 59.832 41.667 0.00 0.00 36.02 1.40
479 480 3.721575 TGCAGGGACTATCAATGGGTATT 59.278 43.478 0.00 0.00 36.02 1.89
480 481 3.326521 TGCAGGGACTATCAATGGGTAT 58.673 45.455 0.00 0.00 36.02 2.73
481 482 2.770447 TGCAGGGACTATCAATGGGTA 58.230 47.619 0.00 0.00 36.02 3.69
482 483 1.595311 TGCAGGGACTATCAATGGGT 58.405 50.000 0.00 0.00 36.02 4.51
483 484 2.734755 TTGCAGGGACTATCAATGGG 57.265 50.000 0.00 0.00 36.02 4.00
519 520 3.182152 AGGCCGGCAAGATATAACCTAT 58.818 45.455 30.85 0.00 0.00 2.57
602 604 2.438868 AAAGAGCCACGGAAATTTGC 57.561 45.000 0.00 0.00 0.00 3.68
603 605 3.716601 ACAAAAGAGCCACGGAAATTTG 58.283 40.909 0.00 0.00 33.68 2.32
604 606 4.400529 AACAAAAGAGCCACGGAAATTT 57.599 36.364 0.00 0.00 0.00 1.82
605 607 4.558697 GCTAACAAAAGAGCCACGGAAATT 60.559 41.667 0.00 0.00 32.25 1.82
775 789 3.249080 GTCCTCTTCGTCCTTATCTCTCG 59.751 52.174 0.00 0.00 0.00 4.04
839 853 4.753662 CGGTCGGAGTCCTCCCCA 62.754 72.222 7.77 0.00 46.96 4.96
859 873 1.721926 GCGGCGAGAGACTTTATATGC 59.278 52.381 12.98 0.00 36.51 3.14
1090 1337 3.395702 CATTGGGTCGACGGGGGA 61.396 66.667 9.92 0.00 0.00 4.81
1127 1377 2.364842 GCTCCTCCTCCTCCAGCA 60.365 66.667 0.00 0.00 0.00 4.41
1131 1381 2.364842 TGCTGCTCCTCCTCCTCC 60.365 66.667 0.00 0.00 0.00 4.30
1132 1382 3.092780 GCTGCTGCTCCTCCTCCTC 62.093 68.421 8.53 0.00 36.03 3.71
1133 1383 3.082701 GCTGCTGCTCCTCCTCCT 61.083 66.667 8.53 0.00 36.03 3.69
1134 1384 3.388703 CTGCTGCTGCTCCTCCTCC 62.389 68.421 17.00 0.00 40.48 4.30
1135 1385 2.187424 CTGCTGCTGCTCCTCCTC 59.813 66.667 17.00 0.00 40.48 3.71
1136 1386 4.098722 GCTGCTGCTGCTCCTCCT 62.099 66.667 22.10 0.00 40.48 3.69
1137 1387 4.405671 TGCTGCTGCTGCTCCTCC 62.406 66.667 27.67 3.30 40.48 4.30
1138 1388 2.820479 CTGCTGCTGCTGCTCCTC 60.820 66.667 27.67 3.96 40.48 3.71
1147 1397 4.124943 ATGGGGAGGCTGCTGCTG 62.125 66.667 15.64 0.77 39.59 4.41
1148 1398 4.124943 CATGGGGAGGCTGCTGCT 62.125 66.667 15.64 1.41 39.59 4.24
1170 1420 4.222847 GGGTCGACTCGGGCATCC 62.223 72.222 16.46 1.15 0.00 3.51
1171 1421 4.570663 CGGGTCGACTCGGGCATC 62.571 72.222 29.91 2.56 0.00 3.91
1174 1424 4.570663 CATCGGGTCGACTCGGGC 62.571 72.222 35.31 9.14 39.18 6.13
1175 1425 2.827190 TCATCGGGTCGACTCGGG 60.827 66.667 35.31 26.89 39.18 5.14
1176 1426 2.408022 GTCATCGGGTCGACTCGG 59.592 66.667 35.31 21.55 39.18 4.63
1177 1427 2.022902 CGTCATCGGGTCGACTCG 59.977 66.667 31.54 31.54 39.18 4.18
1178 1428 2.278013 GCGTCATCGGGTCGACTC 60.278 66.667 16.46 11.18 39.18 3.36
1179 1429 3.823330 GGCGTCATCGGGTCGACT 61.823 66.667 16.46 0.00 39.18 4.18
1201 1451 2.837291 CTCCTCCTCCTCCAGCGG 60.837 72.222 0.00 0.00 0.00 5.52
1202 1452 2.837291 CCTCCTCCTCCTCCAGCG 60.837 72.222 0.00 0.00 0.00 5.18
1203 1453 1.457455 CTCCTCCTCCTCCTCCAGC 60.457 68.421 0.00 0.00 0.00 4.85
1204 1454 1.232792 CCTCCTCCTCCTCCTCCAG 59.767 68.421 0.00 0.00 0.00 3.86
1205 1455 1.230650 TCCTCCTCCTCCTCCTCCA 60.231 63.158 0.00 0.00 0.00 3.86
1300 1550 2.650116 GCTTCTCCTCCGGCTGTGA 61.650 63.158 0.00 0.00 0.00 3.58
1302 1552 2.604686 TGCTTCTCCTCCGGCTGT 60.605 61.111 0.00 0.00 0.00 4.40
1423 1676 7.661847 ACAGGACTAAACAGACAAAATAGAAGG 59.338 37.037 0.00 0.00 0.00 3.46
1457 1710 0.598680 GGAACTGCCCGATGATCGAG 60.599 60.000 17.52 3.71 43.74 4.04
1508 1761 1.495951 CGGATTAATTAGCGCCCGC 59.504 57.895 2.29 4.20 42.33 6.13
1511 1764 0.517316 CCAGCGGATTAATTAGCGCC 59.483 55.000 2.29 0.00 34.34 6.53
1541 1794 2.027385 GCAGGGAAGCAAAATAGGAGG 58.973 52.381 0.00 0.00 0.00 4.30
1542 1795 1.672881 CGCAGGGAAGCAAAATAGGAG 59.327 52.381 0.00 0.00 0.00 3.69
1543 1796 1.750193 CGCAGGGAAGCAAAATAGGA 58.250 50.000 0.00 0.00 0.00 2.94
1544 1797 0.101219 GCGCAGGGAAGCAAAATAGG 59.899 55.000 0.30 0.00 0.00 2.57
1613 1866 2.355126 CGACGCCATCCCGATCAG 60.355 66.667 0.00 0.00 0.00 2.90
1719 1972 3.531538 CCTGGAATCGCAAAAGTAGCTA 58.468 45.455 0.00 0.00 0.00 3.32
1720 1973 2.359900 CCTGGAATCGCAAAAGTAGCT 58.640 47.619 0.00 0.00 0.00 3.32
1922 2185 6.095440 GGCACCAGATTAGTGATGTTAATGTT 59.905 38.462 0.00 0.00 37.42 2.71
1987 2250 1.913762 CCTTGTGTCCCTCCTCGGT 60.914 63.158 0.00 0.00 0.00 4.69
2002 2265 9.612066 GAGATTTTTATCTTCTGATGTCTCCTT 57.388 33.333 0.00 0.00 34.32 3.36
2027 2290 1.699634 CTGGACCTGGAACCTTGAAGA 59.300 52.381 0.00 0.00 0.00 2.87
2084 2350 1.423921 GACCTGGAACCTTGAAGGGAA 59.576 52.381 16.78 0.00 40.58 3.97
2102 2368 0.811616 GTGTCCATCATCGGCCAGAC 60.812 60.000 2.24 0.00 0.00 3.51
2105 2371 2.186644 CGTGTCCATCATCGGCCA 59.813 61.111 2.24 0.00 0.00 5.36
2106 2372 1.592669 CTCGTGTCCATCATCGGCC 60.593 63.158 0.00 0.00 0.00 6.13
2115 2381 1.627864 TTGATGTCTCCTCGTGTCCA 58.372 50.000 0.00 0.00 0.00 4.02
2215 2544 0.820226 TCATCTGCTCGACCCAGAAG 59.180 55.000 13.29 10.05 42.12 2.85
2218 2547 0.385029 CTCTCATCTGCTCGACCCAG 59.615 60.000 2.63 2.63 0.00 4.45
2285 2614 6.954944 AGCAAATGCATCAATTATGAAATGC 58.045 32.000 8.28 0.00 45.16 3.56
2292 2621 9.826574 ACAGAAATTAGCAAATGCATCAATTAT 57.173 25.926 8.28 1.59 45.16 1.28
2293 2622 9.304731 GACAGAAATTAGCAAATGCATCAATTA 57.695 29.630 8.28 0.00 45.16 1.40
2294 2623 7.820386 TGACAGAAATTAGCAAATGCATCAATT 59.180 29.630 8.28 7.34 45.16 2.32
2295 2624 7.324935 TGACAGAAATTAGCAAATGCATCAAT 58.675 30.769 8.28 1.64 45.16 2.57
2296 2625 6.689554 TGACAGAAATTAGCAAATGCATCAA 58.310 32.000 8.28 0.00 45.16 2.57
2297 2626 6.270156 TGACAGAAATTAGCAAATGCATCA 57.730 33.333 8.28 0.00 45.16 3.07
2298 2627 7.766219 ATTGACAGAAATTAGCAAATGCATC 57.234 32.000 8.28 0.00 45.16 3.91
2390 2719 7.416213 GCATGCCACACTAGATAAAATTGGTAA 60.416 37.037 6.36 0.00 0.00 2.85
2411 2740 1.969923 AGATAGAGGGAGAGTGCATGC 59.030 52.381 11.82 11.82 0.00 4.06
2432 2763 2.555757 GCATGAGCTTCCAGTTTCTGTT 59.444 45.455 0.00 0.00 37.91 3.16
2436 2767 2.157738 AGTGCATGAGCTTCCAGTTTC 58.842 47.619 0.00 0.00 42.74 2.78
2508 2844 3.486383 GAACAACCACAAGAATCCTCCA 58.514 45.455 0.00 0.00 0.00 3.86
2547 2883 4.217754 TGTTCATGACGGTAACAAAAGC 57.782 40.909 0.00 0.00 30.54 3.51
2554 2890 5.046591 AGGATCTCTTTGTTCATGACGGTAA 60.047 40.000 0.00 0.00 0.00 2.85
2587 2923 3.688272 GCCACAATGAAGTTCATGATCG 58.312 45.455 18.94 10.41 37.15 3.69
2597 2933 1.468520 ACGAAATCCGCCACAATGAAG 59.531 47.619 0.00 0.00 43.32 3.02
2619 2955 3.013921 TGCCAATTCGGATAACAGTTCC 58.986 45.455 0.00 0.00 36.56 3.62
2628 2964 2.816087 GCACTATGATGCCAATTCGGAT 59.184 45.455 0.00 0.00 39.86 4.18
2710 3049 1.956629 ATCGTCCAACTGGGTAGCCG 61.957 60.000 6.45 3.90 38.11 5.52
2762 3101 1.359848 GTTGTGCCTACCATCAGACG 58.640 55.000 0.00 0.00 0.00 4.18
2861 3200 5.887035 TGTCATGAATGTTTGGATGATAGCA 59.113 36.000 0.00 0.00 0.00 3.49
3011 3350 2.033372 TCCACGAGTCAGTTTGTACCA 58.967 47.619 0.00 0.00 0.00 3.25
3037 3376 4.081087 GTCTAGCTTACCACAGGGAAATCA 60.081 45.833 0.00 0.00 38.05 2.57
3062 3401 3.500455 GCAAGCATGATGTTGCACA 57.500 47.368 20.10 0.00 46.83 4.57
3089 3428 8.105829 ACACATTTACTTGATCTGAGAGGAAAT 58.894 33.333 0.00 0.00 0.00 2.17
3132 3473 2.292569 CGATGCAGCCTATGAAAGCAAT 59.707 45.455 0.00 0.00 38.85 3.56
3223 3564 2.154854 TTCAGAAGCTTCGACACCAG 57.845 50.000 20.43 6.41 0.00 4.00
3225 3566 2.755650 TCTTTCAGAAGCTTCGACACC 58.244 47.619 20.43 0.00 32.75 4.16
3380 3721 2.414481 CAGCAGAATTCGTCAGAACCAG 59.586 50.000 0.00 0.00 39.48 4.00
3570 4178 0.596600 AGCTACACACGACCAACACG 60.597 55.000 0.00 0.00 0.00 4.49
3640 4512 3.689649 CCCTGATAATATAAGCGGCCAAC 59.310 47.826 2.24 0.00 0.00 3.77
3661 4533 9.771534 ATATAGCTAAACAAGACTTGAATCTCC 57.228 33.333 21.95 5.51 0.00 3.71
3737 4613 5.987953 CAGTACATAATCACAGGGATGACTG 59.012 44.000 0.00 0.00 44.03 3.51
3876 4761 0.616111 ATTCAGACCTGGGAGCGACT 60.616 55.000 0.00 0.00 0.00 4.18
3936 4824 0.746659 ACACCTGGCTTTTCAGTTGC 59.253 50.000 0.00 0.00 31.50 4.17
3995 5068 8.455903 AATTATCAATCATACACCAAGTCAGG 57.544 34.615 0.00 0.00 0.00 3.86
4371 5451 7.364522 TGATCAAATTAGAAGAAAGTGGACG 57.635 36.000 0.00 0.00 0.00 4.79
4714 5803 0.540365 ACGTAGAGAACCACGGGGAA 60.540 55.000 12.96 0.00 42.35 3.97
4732 5821 6.858478 GCAACATTTCCTTCTTCTCAAGTAAC 59.142 38.462 0.00 0.00 0.00 2.50
4740 5829 3.499918 CGACAGCAACATTTCCTTCTTCT 59.500 43.478 0.00 0.00 0.00 2.85
4741 5830 3.365364 CCGACAGCAACATTTCCTTCTTC 60.365 47.826 0.00 0.00 0.00 2.87
4742 5831 2.554032 CCGACAGCAACATTTCCTTCTT 59.446 45.455 0.00 0.00 0.00 2.52
4857 5949 3.309682 CGTGACATCTTGTTCAACACTGT 59.690 43.478 0.00 0.00 0.00 3.55
4891 5983 0.843309 TTTTCTCTGCTGGTCCACCA 59.157 50.000 0.00 0.00 45.30 4.17
4892 5984 1.981256 TTTTTCTCTGCTGGTCCACC 58.019 50.000 0.00 0.00 0.00 4.61
4893 5985 3.149196 TCATTTTTCTCTGCTGGTCCAC 58.851 45.455 0.00 0.00 0.00 4.02
4933 6025 0.606673 GGACTCCTTGTGACAAGCCC 60.607 60.000 19.45 12.73 0.00 5.19
5022 6114 4.023980 CTGTGTTCCTCCAGATGGTACTA 58.976 47.826 0.00 0.00 36.34 1.82
5400 6558 5.351740 GGGACTATTACTGTGCTGTTTCTTC 59.648 44.000 0.00 0.00 0.00 2.87
5423 6583 1.668751 AGCACAACGTACAAACACAGG 59.331 47.619 0.00 0.00 0.00 4.00
5509 6682 2.630158 CAGGAGAATCACAAGAGCCTG 58.370 52.381 0.00 0.00 36.25 4.85
5574 6747 1.066071 GGAGTTGGAGCCTACTGTTCC 60.066 57.143 8.32 0.97 32.61 3.62
5678 6854 5.931441 AAAAGGTGTCTCAGAGAAAATCG 57.069 39.130 0.20 0.00 0.00 3.34
5689 6865 2.092375 CCCCATCCCTAAAAGGTGTCTC 60.092 54.545 0.00 0.00 31.93 3.36
5853 7048 9.460019 TTTCATCAACCTTTTCCTTTCAAAATT 57.540 25.926 0.00 0.00 0.00 1.82
5871 7067 6.757478 TGTTAAGACAGTACACGTTTCATCAA 59.243 34.615 0.00 0.00 0.00 2.57
5898 7094 1.133915 AGCTGTCACGAAGGGGAAAAA 60.134 47.619 0.00 0.00 0.00 1.94
5899 7095 0.472471 AGCTGTCACGAAGGGGAAAA 59.528 50.000 0.00 0.00 0.00 2.29
5901 7097 0.250295 CAAGCTGTCACGAAGGGGAA 60.250 55.000 0.00 0.00 0.00 3.97
5902 7098 1.118965 TCAAGCTGTCACGAAGGGGA 61.119 55.000 0.00 0.00 0.00 4.81
5903 7099 0.036010 ATCAAGCTGTCACGAAGGGG 60.036 55.000 0.00 0.00 0.00 4.79
5904 7100 2.672961 TATCAAGCTGTCACGAAGGG 57.327 50.000 0.00 0.00 0.00 3.95
5905 7101 4.269603 CAGAATATCAAGCTGTCACGAAGG 59.730 45.833 0.00 0.00 0.00 3.46
5906 7102 4.867047 ACAGAATATCAAGCTGTCACGAAG 59.133 41.667 0.00 0.00 38.41 3.79
5910 7106 4.436584 GCACACAGAATATCAAGCTGTCAC 60.437 45.833 0.00 0.00 40.63 3.67
5912 7108 3.242220 CGCACACAGAATATCAAGCTGTC 60.242 47.826 0.00 0.00 40.63 3.51
5914 7110 2.674852 ACGCACACAGAATATCAAGCTG 59.325 45.455 0.00 0.00 35.81 4.24
5915 7111 2.932614 GACGCACACAGAATATCAAGCT 59.067 45.455 0.00 0.00 0.00 3.74
5916 7112 2.932614 AGACGCACACAGAATATCAAGC 59.067 45.455 0.00 0.00 0.00 4.01
5917 7113 5.536554 AAAGACGCACACAGAATATCAAG 57.463 39.130 0.00 0.00 0.00 3.02
5922 7118 7.197071 ACAAAATAAAGACGCACACAGAATA 57.803 32.000 0.00 0.00 0.00 1.75
5926 7149 8.012809 TGTATAACAAAATAAAGACGCACACAG 58.987 33.333 0.00 0.00 0.00 3.66
5985 7220 1.073025 ATCTGCAAGCGGGACACAA 59.927 52.632 0.37 0.00 0.00 3.33
6034 7269 1.379642 GCTGCAGCCTGGGTATTCAC 61.380 60.000 28.76 0.00 34.31 3.18
6038 7273 2.593978 CTGCTGCAGCCTGGGTAT 59.406 61.111 34.64 0.00 41.18 2.73
6077 7312 0.459585 TACGCTGCCATTCGTCTTCC 60.460 55.000 0.00 0.00 39.79 3.46
6091 7326 7.474190 GTCTTCTGTAGATAGTTCTTTACGCT 58.526 38.462 0.00 0.00 34.79 5.07
6124 7359 2.037847 CCTGGCCCTCCCTTTTGG 59.962 66.667 0.00 0.00 39.97 3.28
6128 7363 2.041928 CTCTCCTGGCCCTCCCTT 59.958 66.667 0.00 0.00 0.00 3.95
6137 7372 1.202746 GCTTATTCCTGCCTCTCCTGG 60.203 57.143 0.00 0.00 0.00 4.45
6138 7373 1.539929 CGCTTATTCCTGCCTCTCCTG 60.540 57.143 0.00 0.00 0.00 3.86
6139 7374 0.755686 CGCTTATTCCTGCCTCTCCT 59.244 55.000 0.00 0.00 0.00 3.69
6140 7375 0.250081 CCGCTTATTCCTGCCTCTCC 60.250 60.000 0.00 0.00 0.00 3.71
6141 7376 0.753262 TCCGCTTATTCCTGCCTCTC 59.247 55.000 0.00 0.00 0.00 3.20
6142 7377 0.755686 CTCCGCTTATTCCTGCCTCT 59.244 55.000 0.00 0.00 0.00 3.69
6143 7378 0.250081 CCTCCGCTTATTCCTGCCTC 60.250 60.000 0.00 0.00 0.00 4.70
6144 7379 0.983378 ACCTCCGCTTATTCCTGCCT 60.983 55.000 0.00 0.00 0.00 4.75
6152 7387 1.219724 TCCCCTTCTACCTCCGCTTAT 59.780 52.381 0.00 0.00 0.00 1.73
6153 7388 0.632835 TCCCCTTCTACCTCCGCTTA 59.367 55.000 0.00 0.00 0.00 3.09
6176 7411 4.026062 CGCGCACTTGAGCAGTTTATATAA 60.026 41.667 8.75 0.00 41.01 0.98
6190 7436 2.034001 GGTAATTAGCTACGCGCACTTG 60.034 50.000 5.73 0.00 42.61 3.16
6229 7475 2.700897 ACTGGTCTACTTTCTGCACTGT 59.299 45.455 0.00 0.00 0.00 3.55
6235 7481 4.302455 CAGTGTCACTGGTCTACTTTCTG 58.698 47.826 23.09 0.00 42.35 3.02
6266 7512 2.884012 TGGCCATCTGTTACAAGTGTTG 59.116 45.455 0.00 0.00 0.00 3.33
6267 7513 2.884639 GTGGCCATCTGTTACAAGTGTT 59.115 45.455 9.72 0.00 0.00 3.32
6319 7611 1.672898 CAAACCATGCAACAGGGGG 59.327 57.895 3.08 0.00 39.88 5.40
6320 7612 0.831288 TCCAAACCATGCAACAGGGG 60.831 55.000 3.08 0.08 39.88 4.79
6374 7674 0.618458 GGTGTGTCCTTGCCCTATGA 59.382 55.000 0.00 0.00 0.00 2.15
6578 7891 2.477245 TGTGGTGGTGGCTCTGTATAT 58.523 47.619 0.00 0.00 0.00 0.86
6596 7909 5.299028 TGTTACTGCATGACAACAGATTTGT 59.701 36.000 14.01 0.00 39.87 2.83
6597 7910 5.761003 TGTTACTGCATGACAACAGATTTG 58.239 37.500 14.01 0.00 37.35 2.32
6598 7911 6.389830 TTGTTACTGCATGACAACAGATTT 57.610 33.333 14.01 0.00 37.35 2.17


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

AutoCloner maintained by Alex Coulton.