Multiple sequence alignment - TraesCS1D01G074400

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 TraesCS1D01G074400 chr1D 100.000 5069 0 0 1 5069 55673152 55668084 0.000000e+00 9361
1 TraesCS1D01G074400 chr1A 91.774 3647 150 56 942 4525 54078255 54074696 0.000000e+00 4935
2 TraesCS1D01G074400 chr1A 91.020 490 21 10 4603 5069 54074461 54073972 1.540000e-179 640
3 TraesCS1D01G074400 chr1A 83.582 536 30 30 1 488 54079163 54078638 2.780000e-122 449
4 TraesCS1D01G074400 chr1A 85.294 136 7 9 629 760 54078503 54078377 1.480000e-25 128
5 TraesCS1D01G074400 chr1B 88.642 3962 227 112 553 4409 90996276 90992433 0.000000e+00 4617
6 TraesCS1D01G074400 chr1B 90.214 327 25 2 4603 4922 90992154 90991828 2.180000e-113 420
7 TraesCS1D01G074400 chr1B 81.172 563 34 38 4 516 91001495 91000955 2.210000e-103 387
8 TraesCS1D01G074400 chr1B 95.402 87 4 0 4923 5009 90991540 90991454 6.840000e-29 139
9 TraesCS1D01G074400 chr4D 83.371 1317 155 27 2728 4035 484777484 484776223 0.000000e+00 1160
10 TraesCS1D01G074400 chr5A 81.839 1305 162 26 2739 4035 665823666 665822429 0.000000e+00 1027
11 TraesCS1D01G074400 chr4B 88.298 470 51 2 3569 4035 617857720 617857252 1.230000e-155 560


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 TraesCS1D01G074400 chr1D 55668084 55673152 5068 True 9361.000000 9361 100.000000 1 5069 1 chr1D.!!$R1 5068
1 TraesCS1D01G074400 chr1A 54073972 54079163 5191 True 1538.000000 4935 87.917500 1 5069 4 chr1A.!!$R1 5068
2 TraesCS1D01G074400 chr1B 90991454 90996276 4822 True 1725.333333 4617 91.419333 553 5009 3 chr1B.!!$R2 4456
3 TraesCS1D01G074400 chr1B 91000955 91001495 540 True 387.000000 387 81.172000 4 516 1 chr1B.!!$R1 512
4 TraesCS1D01G074400 chr4D 484776223 484777484 1261 True 1160.000000 1160 83.371000 2728 4035 1 chr4D.!!$R1 1307
5 TraesCS1D01G074400 chr5A 665822429 665823666 1237 True 1027.000000 1027 81.839000 2739 4035 1 chr5A.!!$R1 1296

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
456 519 0.030101 CCGTGCGAGATCCTCTTCTC 59.970 60.0 0.00 0.00 39.03 2.87 F
1387 1534 0.107361 GTTACCGGTGATTGGGGAGG 60.107 60.0 19.93 0.00 0.00 4.30 F
1396 1543 0.766288 GATTGGGGAGGGGAGAGGAG 60.766 65.0 0.00 0.00 0.00 3.69 F
3333 3574 0.950555 CACGGTGGACATGGACACAG 60.951 60.0 19.41 17.86 39.31 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 1896 0.110869 CGGGAGGCTAGGCTAGTAGT 59.889 60.000 20.27 7.67 0.00 2.73 R
3337 3578 0.335705 AATGTCCATGGCCATGACCA 59.664 50.000 41.32 34.00 45.82 4.02 R
3340 3581 1.005687 TGTGAATGTCCATGGCCATGA 59.994 47.619 41.32 25.40 41.20 3.07 R
4172 4439 0.167251 AATGGGCTAACGAAAACGCG 59.833 50.000 3.53 3.53 37.29 6.01 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
68 71 3.006728 GTCCACCCGACCCATCCA 61.007 66.667 0.00 0.00 35.23 3.41
129 169 2.586357 GTGAAGATCGCCCGCTCC 60.586 66.667 0.00 0.00 0.00 4.70
162 202 0.390860 GGCGTCCAGAGCAGATACAT 59.609 55.000 0.00 0.00 36.08 2.29
163 203 1.613925 GGCGTCCAGAGCAGATACATA 59.386 52.381 0.00 0.00 36.08 2.29
164 204 2.608261 GGCGTCCAGAGCAGATACATAC 60.608 54.545 0.00 0.00 36.08 2.39
165 205 2.034685 GCGTCCAGAGCAGATACATACA 59.965 50.000 0.00 0.00 34.19 2.29
187 227 2.553685 GGTAAACCAACCAATCTCCCGT 60.554 50.000 0.00 0.00 39.50 5.28
212 252 2.795329 AGCATCGACCCAACATTTCTT 58.205 42.857 0.00 0.00 0.00 2.52
243 294 3.243877 CGTAGATGCCGTTCAAGAGATTG 59.756 47.826 0.00 0.00 0.00 2.67
246 297 3.686726 AGATGCCGTTCAAGAGATTGTTC 59.313 43.478 0.00 0.00 0.00 3.18
247 298 1.798223 TGCCGTTCAAGAGATTGTTCG 59.202 47.619 0.00 0.00 0.00 3.95
248 299 1.798813 GCCGTTCAAGAGATTGTTCGT 59.201 47.619 0.00 0.00 0.00 3.85
249 300 2.159827 GCCGTTCAAGAGATTGTTCGTC 60.160 50.000 0.00 0.00 0.00 4.20
250 301 2.412089 CCGTTCAAGAGATTGTTCGTCC 59.588 50.000 0.00 0.00 0.00 4.79
251 302 3.057019 CGTTCAAGAGATTGTTCGTCCA 58.943 45.455 0.00 0.00 0.00 4.02
252 303 3.679980 CGTTCAAGAGATTGTTCGTCCAT 59.320 43.478 0.00 0.00 0.00 3.41
254 305 5.385617 GTTCAAGAGATTGTTCGTCCATTG 58.614 41.667 0.00 0.00 0.00 2.82
255 306 4.641396 TCAAGAGATTGTTCGTCCATTGT 58.359 39.130 0.00 0.00 0.00 2.71
257 308 5.049474 TCAAGAGATTGTTCGTCCATTGTTG 60.049 40.000 0.00 0.00 0.00 3.33
258 309 4.641396 AGAGATTGTTCGTCCATTGTTGA 58.359 39.130 0.00 0.00 0.00 3.18
259 310 5.248640 AGAGATTGTTCGTCCATTGTTGAT 58.751 37.500 0.00 0.00 0.00 2.57
290 346 3.242641 GCGTTTCCTTCTTTTCTGTCGTT 60.243 43.478 0.00 0.00 0.00 3.85
291 347 4.515432 CGTTTCCTTCTTTTCTGTCGTTC 58.485 43.478 0.00 0.00 0.00 3.95
292 348 4.270325 CGTTTCCTTCTTTTCTGTCGTTCT 59.730 41.667 0.00 0.00 0.00 3.01
311 367 1.514443 GGACGTTCTCGCTCCTTCG 60.514 63.158 0.00 0.00 41.18 3.79
322 378 1.874345 GCTCCTTCGACCTCGTTCCA 61.874 60.000 0.00 0.00 40.80 3.53
323 379 0.601558 CTCCTTCGACCTCGTTCCAA 59.398 55.000 0.00 0.00 40.80 3.53
325 381 1.203994 TCCTTCGACCTCGTTCCAATC 59.796 52.381 0.00 0.00 40.80 2.67
326 382 1.641577 CTTCGACCTCGTTCCAATCC 58.358 55.000 0.00 0.00 40.80 3.01
327 383 0.248289 TTCGACCTCGTTCCAATCCC 59.752 55.000 0.00 0.00 40.80 3.85
330 386 1.896122 GACCTCGTTCCAATCCCCGT 61.896 60.000 0.00 0.00 0.00 5.28
332 388 1.518572 CTCGTTCCAATCCCCGTCG 60.519 63.158 0.00 0.00 0.00 5.12
375 432 3.359002 GTGTCCACGTCGTAGGGT 58.641 61.111 0.00 0.00 0.00 4.34
455 518 2.010582 GCCGTGCGAGATCCTCTTCT 62.011 60.000 0.00 0.00 0.00 2.85
456 519 0.030101 CCGTGCGAGATCCTCTTCTC 59.970 60.000 0.00 0.00 39.03 2.87
457 520 1.021202 CGTGCGAGATCCTCTTCTCT 58.979 55.000 0.00 0.00 40.03 3.10
458 521 1.403679 CGTGCGAGATCCTCTTCTCTT 59.596 52.381 0.00 0.00 40.03 2.85
459 522 2.540769 CGTGCGAGATCCTCTTCTCTTC 60.541 54.545 0.00 0.00 40.03 2.87
464 527 4.207165 CGAGATCCTCTTCTCTTCCTTCT 58.793 47.826 0.00 0.00 40.03 2.85
468 531 4.412060 TCCTCTTCTCTTCCTTCTTCCT 57.588 45.455 0.00 0.00 0.00 3.36
509 601 0.819582 TCATCATCTCTGACGCTGCA 59.180 50.000 0.00 0.00 33.22 4.41
518 610 2.676839 CTCTGACGCTGCATTCTTTGAT 59.323 45.455 0.00 0.00 0.00 2.57
520 612 1.394572 TGACGCTGCATTCTTTGATCG 59.605 47.619 0.00 0.00 0.00 3.69
521 613 1.660607 GACGCTGCATTCTTTGATCGA 59.339 47.619 0.00 0.00 0.00 3.59
525 622 3.425359 CGCTGCATTCTTTGATCGAACTT 60.425 43.478 0.00 0.00 0.00 2.66
530 627 5.063944 TGCATTCTTTGATCGAACTTCTAGC 59.936 40.000 0.00 0.00 0.00 3.42
532 629 6.402550 GCATTCTTTGATCGAACTTCTAGCAA 60.403 38.462 0.00 0.00 0.00 3.91
544 641 1.152881 CTAGCAATCCCACCTGCCC 60.153 63.158 0.00 0.00 39.47 5.36
545 642 2.631012 CTAGCAATCCCACCTGCCCC 62.631 65.000 0.00 0.00 39.47 5.80
546 643 4.066139 GCAATCCCACCTGCCCCT 62.066 66.667 0.00 0.00 32.18 4.79
547 644 2.772924 CAATCCCACCTGCCCCTT 59.227 61.111 0.00 0.00 0.00 3.95
548 645 1.079073 CAATCCCACCTGCCCCTTT 59.921 57.895 0.00 0.00 0.00 3.11
549 646 0.972471 CAATCCCACCTGCCCCTTTC 60.972 60.000 0.00 0.00 0.00 2.62
550 647 1.149133 AATCCCACCTGCCCCTTTCT 61.149 55.000 0.00 0.00 0.00 2.52
551 648 1.149133 ATCCCACCTGCCCCTTTCTT 61.149 55.000 0.00 0.00 0.00 2.52
559 656 3.117284 ACCTGCCCCTTTCTTCTTGTTTA 60.117 43.478 0.00 0.00 0.00 2.01
560 657 3.255888 CCTGCCCCTTTCTTCTTGTTTAC 59.744 47.826 0.00 0.00 0.00 2.01
592 689 2.080693 TGCTACGTTGGCGAATTTCAT 58.919 42.857 0.00 0.00 42.00 2.57
597 694 3.305110 ACGTTGGCGAATTTCATGTTTC 58.695 40.909 0.00 0.00 42.00 2.78
600 697 1.201181 TGGCGAATTTCATGTTTCCCG 59.799 47.619 0.00 0.00 0.00 5.14
601 698 1.201414 GGCGAATTTCATGTTTCCCGT 59.799 47.619 0.00 0.00 0.00 5.28
602 699 2.515912 GCGAATTTCATGTTTCCCGTC 58.484 47.619 0.00 0.00 0.00 4.79
603 700 2.731027 GCGAATTTCATGTTTCCCGTCC 60.731 50.000 0.00 0.00 0.00 4.79
604 701 2.475519 CGAATTTCATGTTTCCCGTCCG 60.476 50.000 0.00 0.00 0.00 4.79
605 702 1.459450 ATTTCATGTTTCCCGTCCGG 58.541 50.000 0.00 0.00 0.00 5.14
606 703 0.108963 TTTCATGTTTCCCGTCCGGT 59.891 50.000 0.00 0.00 0.00 5.28
607 704 0.320946 TTCATGTTTCCCGTCCGGTC 60.321 55.000 0.00 0.00 0.00 4.79
608 705 1.189524 TCATGTTTCCCGTCCGGTCT 61.190 55.000 0.00 0.00 0.00 3.85
609 706 0.321298 CATGTTTCCCGTCCGGTCTT 60.321 55.000 0.00 0.00 0.00 3.01
624 721 2.956333 CGGTCTTTCTTTGTTTTCCCCT 59.044 45.455 0.00 0.00 0.00 4.79
625 722 4.139038 CGGTCTTTCTTTGTTTTCCCCTA 58.861 43.478 0.00 0.00 0.00 3.53
626 723 4.023450 CGGTCTTTCTTTGTTTTCCCCTAC 60.023 45.833 0.00 0.00 0.00 3.18
640 739 1.417890 CCCCTACTAGCATTGACTGGG 59.582 57.143 0.00 0.00 0.00 4.45
686 786 6.292919 GGTTTTAATTAATGCGGCACAAAACA 60.293 34.615 22.04 7.51 36.71 2.83
690 790 0.529555 AATGCGGCACAAAACACCAC 60.530 50.000 4.03 0.00 0.00 4.16
717 817 1.911464 CGTAGTCGTAGTCGTCACGTA 59.089 52.381 0.00 0.00 40.27 3.57
722 822 4.787598 AGTCGTAGTCGTCACGTATTTTT 58.212 39.130 0.00 0.00 40.27 1.94
808 915 1.994779 ACCGCGAAGTAAAATACACGG 59.005 47.619 8.23 0.00 44.70 4.94
861 973 3.695606 GTGCCTGTGCGGGAGAGA 61.696 66.667 0.39 0.00 41.78 3.10
879 991 1.141858 AGAATCCAAAGGATCGGAGCC 59.858 52.381 3.56 3.56 42.27 4.70
1133 1261 1.140852 CCATCGCCATCCAGGTTAGAA 59.859 52.381 0.00 0.00 40.61 2.10
1179 1317 0.324738 TCTCTCTCTGATTGCCCCGT 60.325 55.000 0.00 0.00 0.00 5.28
1228 1374 1.364626 TTCTACTCCGCTCCGTCGTC 61.365 60.000 0.00 0.00 0.00 4.20
1259 1405 1.832219 CCATCCATGGCGAGAGGAA 59.168 57.895 6.96 0.00 41.75 3.36
1334 1480 4.363990 CCGTGGCGTCTCTGCTGT 62.364 66.667 0.00 0.00 34.52 4.40
1382 1529 2.486592 GGTTTCAGTTACCGGTGATTGG 59.513 50.000 19.93 2.78 0.00 3.16
1383 1530 2.483014 TTCAGTTACCGGTGATTGGG 57.517 50.000 19.93 1.64 0.00 4.12
1384 1531 0.616371 TCAGTTACCGGTGATTGGGG 59.384 55.000 19.93 0.00 0.00 4.96
1385 1532 0.616371 CAGTTACCGGTGATTGGGGA 59.384 55.000 19.93 0.00 0.00 4.81
1386 1533 0.909623 AGTTACCGGTGATTGGGGAG 59.090 55.000 19.93 0.00 0.00 4.30
1387 1534 0.107361 GTTACCGGTGATTGGGGAGG 60.107 60.000 19.93 0.00 0.00 4.30
1388 1535 1.276140 TTACCGGTGATTGGGGAGGG 61.276 60.000 19.93 0.00 0.00 4.30
1389 1536 3.809013 CCGGTGATTGGGGAGGGG 61.809 72.222 0.00 0.00 0.00 4.79
1390 1537 2.690881 CGGTGATTGGGGAGGGGA 60.691 66.667 0.00 0.00 0.00 4.81
1391 1538 2.746375 CGGTGATTGGGGAGGGGAG 61.746 68.421 0.00 0.00 0.00 4.30
1392 1539 1.307866 GGTGATTGGGGAGGGGAGA 60.308 63.158 0.00 0.00 0.00 3.71
1393 1540 1.348775 GGTGATTGGGGAGGGGAGAG 61.349 65.000 0.00 0.00 0.00 3.20
1394 1541 1.004758 TGATTGGGGAGGGGAGAGG 59.995 63.158 0.00 0.00 0.00 3.69
1395 1542 1.318380 GATTGGGGAGGGGAGAGGA 59.682 63.158 0.00 0.00 0.00 3.71
1396 1543 0.766288 GATTGGGGAGGGGAGAGGAG 60.766 65.000 0.00 0.00 0.00 3.69
1397 1544 2.277126 ATTGGGGAGGGGAGAGGAGG 62.277 65.000 0.00 0.00 0.00 4.30
1398 1545 4.179599 GGGGAGGGGAGAGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
1399 1546 4.179599 GGGAGGGGAGAGGAGGGG 62.180 77.778 0.00 0.00 0.00 4.79
1400 1547 3.036959 GGAGGGGAGAGGAGGGGA 61.037 72.222 0.00 0.00 0.00 4.81
1401 1548 2.612251 GAGGGGAGAGGAGGGGAG 59.388 72.222 0.00 0.00 0.00 4.30
1402 1549 3.039526 AGGGGAGAGGAGGGGAGG 61.040 72.222 0.00 0.00 0.00 4.30
1403 1550 3.369388 GGGGAGAGGAGGGGAGGT 61.369 72.222 0.00 0.00 0.00 3.85
1404 1551 2.019272 GGGGAGAGGAGGGGAGGTA 61.019 68.421 0.00 0.00 0.00 3.08
1485 1635 2.938838 AGGGTGCTACTGCTAGTCTAG 58.061 52.381 2.18 2.18 40.48 2.43
1486 1636 2.242708 AGGGTGCTACTGCTAGTCTAGT 59.757 50.000 8.68 0.00 40.48 2.57
1487 1637 3.458857 AGGGTGCTACTGCTAGTCTAGTA 59.541 47.826 8.68 3.15 40.48 1.82
1488 1638 3.816523 GGGTGCTACTGCTAGTCTAGTAG 59.183 52.174 19.99 19.99 45.75 2.57
1687 1853 1.066858 TCAATCACTCCGGCTCTGTTC 60.067 52.381 0.00 0.00 0.00 3.18
1706 1872 1.737008 GTTGGTCTCCTTCGCGTCC 60.737 63.158 5.77 0.00 0.00 4.79
1727 1893 3.255888 CCAGTACTTATCCATCGCAGCTA 59.744 47.826 0.00 0.00 0.00 3.32
1730 1896 2.039418 ACTTATCCATCGCAGCTACCA 58.961 47.619 0.00 0.00 0.00 3.25
1760 1926 3.953775 CCTCCCGTGGTGCCAAGT 61.954 66.667 3.68 0.00 0.00 3.16
1781 1947 4.803613 AGTTCCAATTTGTGTTCGCTTTTC 59.196 37.500 0.00 0.00 0.00 2.29
1784 1951 2.799978 CAATTTGTGTTCGCTTTTCCCC 59.200 45.455 0.00 0.00 0.00 4.81
1791 1958 2.224769 TGTTCGCTTTTCCCCTCATTCT 60.225 45.455 0.00 0.00 0.00 2.40
1793 1960 1.351017 TCGCTTTTCCCCTCATTCTGT 59.649 47.619 0.00 0.00 0.00 3.41
1885 2052 5.041191 TGGGATAGAAGAGGCATCTTTTC 57.959 43.478 15.77 12.08 45.98 2.29
1886 2053 4.141390 TGGGATAGAAGAGGCATCTTTTCC 60.141 45.833 15.77 19.20 45.98 3.13
1922 2090 2.600731 CGCGTATCTGATTGATCTCCC 58.399 52.381 0.00 0.00 36.65 4.30
1944 2129 5.243207 CCGTAATTTGGTAGGTGGATATCC 58.757 45.833 15.39 15.39 0.00 2.59
1979 2164 7.414436 TGTTTGTTTGCAGATTAGTAGTGTTC 58.586 34.615 0.00 0.00 0.00 3.18
1990 2175 8.244113 CAGATTAGTAGTGTTCATGTCTGTGTA 58.756 37.037 0.00 0.00 0.00 2.90
2014 2199 2.039818 TGCCGGTTTACTGTTGTGAA 57.960 45.000 1.90 0.00 0.00 3.18
2020 2205 4.286910 CGGTTTACTGTTGTGAATTGTGG 58.713 43.478 0.00 0.00 0.00 4.17
2021 2206 4.048504 GGTTTACTGTTGTGAATTGTGGC 58.951 43.478 0.00 0.00 0.00 5.01
2147 2332 3.486875 CCAGACCGTCAGTGTTTTTGTTC 60.487 47.826 0.40 0.00 0.00 3.18
2171 2356 3.990469 AGTTGTGCGTCTCTGTTTCATAG 59.010 43.478 0.00 0.00 0.00 2.23
2175 2360 5.720202 TGTGCGTCTCTGTTTCATAGTATT 58.280 37.500 0.00 0.00 0.00 1.89
2177 2362 7.489160 TGTGCGTCTCTGTTTCATAGTATTAT 58.511 34.615 0.00 0.00 0.00 1.28
2178 2363 8.626526 TGTGCGTCTCTGTTTCATAGTATTATA 58.373 33.333 0.00 0.00 0.00 0.98
2179 2364 9.459640 GTGCGTCTCTGTTTCATAGTATTATAA 57.540 33.333 0.00 0.00 0.00 0.98
2203 2388 4.814771 ACTTAAGTAGCGCACTTTCTGTTT 59.185 37.500 23.58 6.85 45.54 2.83
2206 2391 5.532025 AAGTAGCGCACTTTCTGTTTATC 57.468 39.130 11.47 0.00 45.54 1.75
2212 2397 4.617223 GCGCACTTTCTGTTTATCCTTTTC 59.383 41.667 0.30 0.00 0.00 2.29
2218 2403 9.617975 CACTTTCTGTTTATCCTTTTCTGAATC 57.382 33.333 0.00 0.00 0.00 2.52
2225 2410 7.554118 TGTTTATCCTTTTCTGAATCTGCTAGG 59.446 37.037 0.00 0.00 0.00 3.02
2227 2412 4.836825 TCCTTTTCTGAATCTGCTAGGTG 58.163 43.478 0.00 0.00 0.00 4.00
2339 2526 0.955428 TTGTTTGGCTAGCAGGCTCG 60.955 55.000 18.24 0.00 41.96 5.03
2372 2559 4.744631 CCATGTTTTGCAAACCTACTGAAC 59.255 41.667 12.39 5.40 0.00 3.18
2538 2752 3.023119 GTCATGTGTGCAAATATCCCCA 58.977 45.455 0.00 0.00 0.00 4.96
2640 2875 2.363306 TTTCACATGTGGGCACTTCT 57.637 45.000 25.16 0.00 0.00 2.85
2847 3085 1.583477 GAGCAGCTGGGAACAAAGC 59.417 57.895 17.12 0.00 42.06 3.51
3124 3362 3.316308 AGCAGTCATATGGATTTTTCCGC 59.684 43.478 2.13 0.00 0.00 5.54
3328 3569 4.028490 GGGCACGGTGGACATGGA 62.028 66.667 10.60 0.00 0.00 3.41
3333 3574 0.950555 CACGGTGGACATGGACACAG 60.951 60.000 19.41 17.86 39.31 3.66
3334 3575 2.034879 CGGTGGACATGGACACAGC 61.035 63.158 19.41 10.85 39.31 4.40
3335 3576 1.675641 GGTGGACATGGACACAGCC 60.676 63.158 19.41 3.64 39.31 4.85
3336 3577 1.073025 GTGGACATGGACACAGCCA 59.927 57.895 14.76 0.00 43.23 4.75
3342 3583 2.077579 ATGGACACAGCCATGGTCA 58.922 52.632 14.67 1.57 46.62 4.02
3343 3584 0.627451 ATGGACACAGCCATGGTCAT 59.373 50.000 14.67 3.80 46.62 3.06
3344 3585 0.322726 TGGACACAGCCATGGTCATG 60.323 55.000 14.67 12.44 38.51 3.07
3421 3680 1.065647 ATGGAGATCATGAGCAGGGG 58.934 55.000 14.38 0.00 34.22 4.79
3478 3737 9.578439 ACTTCTATTACCGTTACAACTAATCAC 57.422 33.333 0.00 0.00 0.00 3.06
4077 4342 0.865769 GTGTGCCTGTTAACGGTCTG 59.134 55.000 13.35 0.00 0.00 3.51
4089 4354 5.350365 TGTTAACGGTCTGTCATCTTAATGC 59.650 40.000 0.26 0.00 32.58 3.56
4090 4355 3.610040 ACGGTCTGTCATCTTAATGCA 57.390 42.857 0.00 0.00 32.58 3.96
4172 4439 9.502091 TTGGTGCTGGAGAAATATTATATGTAC 57.498 33.333 0.00 0.00 0.00 2.90
4219 4486 6.053005 TGAATGAACTATTAATCGGGTGGTC 58.947 40.000 0.00 0.00 0.00 4.02
4259 4526 4.283978 ACATGGATGCAATTTCCAGACAAA 59.716 37.500 12.81 0.00 46.06 2.83
4305 4572 3.492102 ACCTGCATGTGTAGTTTCAGT 57.508 42.857 0.00 0.00 0.00 3.41
4325 4601 3.067833 GTGACACCCTTTCTTAGCACTC 58.932 50.000 0.00 0.00 0.00 3.51
4343 4619 6.744112 AGCACTCTATGTAAAGATCTGCTAC 58.256 40.000 0.00 2.05 37.51 3.58
4348 4624 7.666388 ACTCTATGTAAAGATCTGCTACGGTAT 59.334 37.037 0.00 0.00 0.00 2.73
4349 4625 7.817641 TCTATGTAAAGATCTGCTACGGTATG 58.182 38.462 0.00 0.00 0.00 2.39
4351 4627 4.891168 TGTAAAGATCTGCTACGGTATGGA 59.109 41.667 0.00 0.00 0.00 3.41
4352 4628 4.323553 AAAGATCTGCTACGGTATGGAC 57.676 45.455 0.00 0.00 0.00 4.02
4353 4629 2.945456 AGATCTGCTACGGTATGGACA 58.055 47.619 0.00 0.00 0.00 4.02
4354 4630 2.887783 AGATCTGCTACGGTATGGACAG 59.112 50.000 0.00 0.00 0.00 3.51
4355 4631 2.139323 TCTGCTACGGTATGGACAGT 57.861 50.000 0.00 0.00 37.73 3.55
4356 4632 3.286329 TCTGCTACGGTATGGACAGTA 57.714 47.619 0.00 0.00 35.46 2.74
4357 4633 2.947652 TCTGCTACGGTATGGACAGTAC 59.052 50.000 0.00 0.00 35.46 2.73
4370 4646 3.039011 GGACAGTACTGGGTATGGATGT 58.961 50.000 26.12 2.22 34.19 3.06
4375 4651 7.208064 ACAGTACTGGGTATGGATGTTTATT 57.792 36.000 26.12 0.00 34.19 1.40
4423 4732 2.989166 GCTTCCAGCAGTTTTTATGTGC 59.011 45.455 0.00 0.00 41.89 4.57
4491 4802 4.096984 GGTCATCTGGTGCCTAAAATGAAG 59.903 45.833 0.00 0.00 0.00 3.02
4503 4814 0.316204 AAATGAAGTGCACTGCTGCC 59.684 50.000 25.34 10.71 43.51 4.85
4529 4908 8.199449 CAGTTTTAATGCATCCATTCCACTATT 58.801 33.333 0.00 0.00 41.68 1.73
4550 4929 3.754965 TGCACATAGAAAGGAGCAAAGT 58.245 40.909 0.00 0.00 0.00 2.66
4557 4936 6.944862 ACATAGAAAGGAGCAAAGTGAATTCT 59.055 34.615 7.05 0.00 0.00 2.40
4581 4960 9.832445 TCTTTCATAGTTTTCTCACTACTTTGT 57.168 29.630 0.00 0.00 31.92 2.83
4589 4968 8.451748 AGTTTTCTCACTACTTTGTCTTTCAAC 58.548 33.333 0.00 0.00 35.61 3.18
4592 4971 9.661563 TTTCTCACTACTTTGTCTTTCAACTTA 57.338 29.630 0.00 0.00 35.61 2.24
4617 5089 3.710209 ATTTCTTCTCACACTGGAGGG 57.290 47.619 0.00 0.00 35.58 4.30
4682 5155 4.638421 CAGTTTGGTCCTACAGTCACAAAA 59.362 41.667 0.00 0.00 30.73 2.44
4819 5298 0.804364 TGCACATGAGTTCGATTGGC 59.196 50.000 0.00 0.00 0.00 4.52
4902 5381 2.036992 CTGATCTGTAGCCCCACATCTC 59.963 54.545 0.00 0.00 0.00 2.75
4999 5768 9.258826 TCATTTTGTATATGGCATTTAATGTGC 57.741 29.630 4.78 5.11 41.78 4.57
5040 5809 0.798776 CTTTGAGCGCAATTCGACCT 59.201 50.000 11.47 0.00 41.67 3.85
5053 5822 2.768253 TCGACCTGATTTCACTGCAT 57.232 45.000 0.00 0.00 0.00 3.96
5058 5827 4.679106 CGACCTGATTTCACTGCATACTCT 60.679 45.833 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 71 1.457831 GGCGGACTGGTAGGAGGAT 60.458 63.158 0.00 0.00 0.00 3.24
162 202 4.263594 GGGAGATTGGTTGGTTTACCTGTA 60.264 45.833 0.00 0.00 39.04 2.74
163 203 3.499745 GGGAGATTGGTTGGTTTACCTGT 60.500 47.826 0.00 0.00 39.04 4.00
164 204 3.089284 GGGAGATTGGTTGGTTTACCTG 58.911 50.000 0.00 0.00 39.04 4.00
165 205 2.290705 CGGGAGATTGGTTGGTTTACCT 60.291 50.000 0.00 0.00 39.04 3.08
187 227 0.109532 TGTTGGGTCGATGCTTGGAA 59.890 50.000 0.00 0.00 0.00 3.53
212 252 1.672854 CGGCATCTACGGAACTGGGA 61.673 60.000 0.00 0.00 0.00 4.37
250 301 1.705256 GCACAGTGCCATCAACAATG 58.295 50.000 15.27 0.00 37.42 2.82
251 302 0.241749 CGCACAGTGCCATCAACAAT 59.758 50.000 20.16 0.00 41.12 2.71
252 303 1.100463 ACGCACAGTGCCATCAACAA 61.100 50.000 20.16 0.00 41.12 2.83
254 305 0.030638 AAACGCACAGTGCCATCAAC 59.969 50.000 20.16 0.00 41.12 3.18
255 306 0.310543 GAAACGCACAGTGCCATCAA 59.689 50.000 20.16 0.00 41.12 2.57
257 308 1.210155 GGAAACGCACAGTGCCATC 59.790 57.895 20.16 14.38 41.12 3.51
258 309 0.823356 AAGGAAACGCACAGTGCCAT 60.823 50.000 20.16 5.50 41.12 4.40
259 310 1.444119 GAAGGAAACGCACAGTGCCA 61.444 55.000 20.16 0.00 41.12 4.92
262 315 3.065371 AGAAAAGAAGGAAACGCACAGTG 59.935 43.478 0.00 0.00 0.00 3.66
290 346 0.894184 AAGGAGCGAGAACGTCCAGA 60.894 55.000 0.00 0.00 39.90 3.86
291 347 0.456995 GAAGGAGCGAGAACGTCCAG 60.457 60.000 0.00 0.00 39.90 3.86
292 348 1.585006 GAAGGAGCGAGAACGTCCA 59.415 57.895 0.00 0.00 39.90 4.02
311 367 1.153429 CGGGGATTGGAACGAGGTC 60.153 63.158 0.00 0.00 0.00 3.85
322 378 2.496291 GGATCGACCGACGGGGATT 61.496 63.158 20.00 0.00 42.82 3.01
323 379 2.910994 GGATCGACCGACGGGGAT 60.911 66.667 20.00 19.39 42.82 3.85
327 383 3.593794 GAGGGGATCGACCGACGG 61.594 72.222 13.61 13.61 42.82 4.79
330 386 2.195139 GAGGAGGGGATCGACCGA 59.805 66.667 0.00 0.00 40.11 4.69
332 388 2.524640 GGGAGGAGGGGATCGACC 60.525 72.222 0.00 0.00 38.08 4.79
455 518 1.194781 AGCGGCAGGAAGAAGGAAGA 61.195 55.000 1.45 0.00 0.00 2.87
456 519 0.322008 AAGCGGCAGGAAGAAGGAAG 60.322 55.000 1.45 0.00 0.00 3.46
457 520 0.110486 AAAGCGGCAGGAAGAAGGAA 59.890 50.000 1.45 0.00 0.00 3.36
458 521 0.606401 CAAAGCGGCAGGAAGAAGGA 60.606 55.000 1.45 0.00 0.00 3.36
459 522 1.589716 CCAAAGCGGCAGGAAGAAGG 61.590 60.000 1.45 0.00 0.00 3.46
464 527 2.668212 CGACCAAAGCGGCAGGAA 60.668 61.111 12.16 0.00 39.03 3.36
509 601 7.011857 GGATTGCTAGAAGTTCGATCAAAGAAT 59.988 37.037 6.39 0.00 0.00 2.40
518 610 2.093658 GGTGGGATTGCTAGAAGTTCGA 60.094 50.000 0.00 0.00 0.00 3.71
520 612 3.274288 CAGGTGGGATTGCTAGAAGTTC 58.726 50.000 0.00 0.00 0.00 3.01
521 613 2.619074 GCAGGTGGGATTGCTAGAAGTT 60.619 50.000 0.00 0.00 37.35 2.66
525 622 1.635817 GGGCAGGTGGGATTGCTAGA 61.636 60.000 0.00 0.00 40.15 2.43
530 627 0.972471 GAAAGGGGCAGGTGGGATTG 60.972 60.000 0.00 0.00 0.00 2.67
532 629 1.149133 AAGAAAGGGGCAGGTGGGAT 61.149 55.000 0.00 0.00 0.00 3.85
544 641 7.360946 CGGTGGATTAGTAAACAAGAAGAAAGG 60.361 40.741 0.00 0.00 0.00 3.11
545 642 7.519002 CGGTGGATTAGTAAACAAGAAGAAAG 58.481 38.462 0.00 0.00 0.00 2.62
546 643 6.072893 GCGGTGGATTAGTAAACAAGAAGAAA 60.073 38.462 0.00 0.00 0.00 2.52
547 644 5.410439 GCGGTGGATTAGTAAACAAGAAGAA 59.590 40.000 0.00 0.00 0.00 2.52
548 645 4.933400 GCGGTGGATTAGTAAACAAGAAGA 59.067 41.667 0.00 0.00 0.00 2.87
549 646 4.935808 AGCGGTGGATTAGTAAACAAGAAG 59.064 41.667 0.00 0.00 0.00 2.85
550 647 4.693566 CAGCGGTGGATTAGTAAACAAGAA 59.306 41.667 6.74 0.00 0.00 2.52
551 648 4.250464 CAGCGGTGGATTAGTAAACAAGA 58.750 43.478 6.74 0.00 0.00 3.02
559 656 0.102481 CGTAGCAGCGGTGGATTAGT 59.898 55.000 17.54 0.00 0.00 2.24
560 657 0.102481 ACGTAGCAGCGGTGGATTAG 59.898 55.000 17.54 0.00 35.98 1.73
592 689 0.249996 GAAAGACCGGACGGGAAACA 60.250 55.000 9.46 0.00 39.97 2.83
597 694 0.250166 ACAAAGAAAGACCGGACGGG 60.250 55.000 9.46 6.67 43.62 5.28
600 697 3.243301 GGGAAAACAAAGAAAGACCGGAC 60.243 47.826 9.46 0.10 0.00 4.79
601 698 2.953648 GGGAAAACAAAGAAAGACCGGA 59.046 45.455 9.46 0.00 0.00 5.14
602 699 2.035449 GGGGAAAACAAAGAAAGACCGG 59.965 50.000 0.00 0.00 0.00 5.28
603 700 2.956333 AGGGGAAAACAAAGAAAGACCG 59.044 45.455 0.00 0.00 0.00 4.79
604 701 5.138276 AGTAGGGGAAAACAAAGAAAGACC 58.862 41.667 0.00 0.00 0.00 3.85
605 702 6.072618 GCTAGTAGGGGAAAACAAAGAAAGAC 60.073 42.308 0.00 0.00 0.00 3.01
606 703 6.002082 GCTAGTAGGGGAAAACAAAGAAAGA 58.998 40.000 0.00 0.00 0.00 2.52
607 704 5.768164 TGCTAGTAGGGGAAAACAAAGAAAG 59.232 40.000 0.00 0.00 0.00 2.62
608 705 5.697067 TGCTAGTAGGGGAAAACAAAGAAA 58.303 37.500 0.00 0.00 0.00 2.52
609 706 5.313280 TGCTAGTAGGGGAAAACAAAGAA 57.687 39.130 0.00 0.00 0.00 2.52
624 721 4.832248 CTGAAACCCAGTCAATGCTAGTA 58.168 43.478 0.00 0.00 38.10 1.82
625 722 3.679389 CTGAAACCCAGTCAATGCTAGT 58.321 45.455 0.00 0.00 38.10 2.57
626 723 2.421424 GCTGAAACCCAGTCAATGCTAG 59.579 50.000 0.00 0.00 44.71 3.42
686 786 1.659335 CGACTACGCACGTTGTGGT 60.659 57.895 14.57 6.43 34.54 4.16
690 790 1.245224 GACTACGACTACGCACGTTG 58.755 55.000 0.00 1.43 43.96 4.10
722 822 3.742433 ACGGGCATGTTTTTCATTCAA 57.258 38.095 0.00 0.00 34.09 2.69
723 823 3.742433 AACGGGCATGTTTTTCATTCA 57.258 38.095 0.00 0.00 34.09 2.57
724 824 3.121113 CGAAACGGGCATGTTTTTCATTC 59.879 43.478 8.25 0.00 41.89 2.67
725 825 3.056304 CGAAACGGGCATGTTTTTCATT 58.944 40.909 8.25 0.00 41.89 2.57
726 826 2.035321 ACGAAACGGGCATGTTTTTCAT 59.965 40.909 8.25 0.00 41.89 2.57
727 827 1.405821 ACGAAACGGGCATGTTTTTCA 59.594 42.857 8.25 0.00 41.89 2.69
728 828 2.128367 ACGAAACGGGCATGTTTTTC 57.872 45.000 8.25 0.00 41.89 2.29
729 829 2.197577 CAACGAAACGGGCATGTTTTT 58.802 42.857 8.25 0.00 41.89 1.94
770 872 3.731717 GCGGTTAAAAAGATGCAACGAAA 59.268 39.130 0.00 0.00 0.00 3.46
781 885 7.201091 CGTGTATTTTACTTCGCGGTTAAAAAG 60.201 37.037 18.00 11.41 0.00 2.27
808 915 6.019559 GTCAATCAACCAAAAGAAAACAGCTC 60.020 38.462 0.00 0.00 0.00 4.09
848 960 0.250234 TTGGATTCTCTCCCGCACAG 59.750 55.000 0.00 0.00 44.23 3.66
860 972 1.598882 GGCTCCGATCCTTTGGATTC 58.401 55.000 0.26 0.00 43.27 2.52
861 973 0.183731 GGGCTCCGATCCTTTGGATT 59.816 55.000 0.26 0.00 43.27 3.01
917 1029 3.369576 CGGTAAAGGAAAAGGAGGAGAGG 60.370 52.174 0.00 0.00 0.00 3.69
918 1030 3.514309 TCGGTAAAGGAAAAGGAGGAGAG 59.486 47.826 0.00 0.00 0.00 3.20
921 1033 2.974099 TGTCGGTAAAGGAAAAGGAGGA 59.026 45.455 0.00 0.00 0.00 3.71
922 1034 3.072211 GTGTCGGTAAAGGAAAAGGAGG 58.928 50.000 0.00 0.00 0.00 4.30
924 1036 3.842007 TGTGTCGGTAAAGGAAAAGGA 57.158 42.857 0.00 0.00 0.00 3.36
925 1037 4.904253 TTTGTGTCGGTAAAGGAAAAGG 57.096 40.909 0.00 0.00 0.00 3.11
926 1038 7.380333 GGTAATTTTGTGTCGGTAAAGGAAAAG 59.620 37.037 0.00 0.00 0.00 2.27
927 1039 7.201835 GGTAATTTTGTGTCGGTAAAGGAAAA 58.798 34.615 0.00 0.00 0.00 2.29
1059 1184 2.359975 CGCCAGGGAGTTTGGGAC 60.360 66.667 0.00 0.00 36.19 4.46
1152 1289 3.567164 GCAATCAGAGAGAGAGAGAGAGG 59.433 52.174 0.00 0.00 0.00 3.69
1153 1290 3.567164 GGCAATCAGAGAGAGAGAGAGAG 59.433 52.174 0.00 0.00 0.00 3.20
1154 1291 3.554934 GGCAATCAGAGAGAGAGAGAGA 58.445 50.000 0.00 0.00 0.00 3.10
1160 1297 0.324738 ACGGGGCAATCAGAGAGAGA 60.325 55.000 0.00 0.00 0.00 3.10
1228 1374 1.076044 GGATGGTCCATTGGTGGGG 60.076 63.158 5.65 0.00 46.06 4.96
1344 1490 2.557920 ACCCAGAGCAGAAACTGAAG 57.442 50.000 2.81 0.00 36.38 3.02
1382 1529 4.179599 CCCCTCCTCTCCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
1383 1530 3.036959 TCCCCTCCTCTCCCCTCC 61.037 72.222 0.00 0.00 0.00 4.30
1384 1531 2.612251 CTCCCCTCCTCTCCCCTC 59.388 72.222 0.00 0.00 0.00 4.30
1385 1532 2.541709 TACCTCCCCTCCTCTCCCCT 62.542 65.000 0.00 0.00 0.00 4.79
1386 1533 2.019272 TACCTCCCCTCCTCTCCCC 61.019 68.421 0.00 0.00 0.00 4.81
1387 1534 1.544703 CTACCTCCCCTCCTCTCCC 59.455 68.421 0.00 0.00 0.00 4.30
1388 1535 1.000041 TCCTACCTCCCCTCCTCTCC 61.000 65.000 0.00 0.00 0.00 3.71
1389 1536 0.186630 GTCCTACCTCCCCTCCTCTC 59.813 65.000 0.00 0.00 0.00 3.20
1390 1537 1.647334 CGTCCTACCTCCCCTCCTCT 61.647 65.000 0.00 0.00 0.00 3.69
1391 1538 1.152715 CGTCCTACCTCCCCTCCTC 60.153 68.421 0.00 0.00 0.00 3.71
1392 1539 3.017139 CGTCCTACCTCCCCTCCT 58.983 66.667 0.00 0.00 0.00 3.69
1393 1540 2.838693 GCGTCCTACCTCCCCTCC 60.839 72.222 0.00 0.00 0.00 4.30
1394 1541 3.217743 CGCGTCCTACCTCCCCTC 61.218 72.222 0.00 0.00 0.00 4.30
1395 1542 4.835891 CCGCGTCCTACCTCCCCT 62.836 72.222 4.92 0.00 0.00 4.79
1531 1681 3.063485 ACCAACAAAATAAACATGCGCC 58.937 40.909 4.18 0.00 0.00 6.53
1687 1853 2.049433 ACGCGAAGGAGACCAACG 60.049 61.111 15.93 0.00 0.00 4.10
1706 1872 3.377346 AGCTGCGATGGATAAGTACTG 57.623 47.619 0.00 0.00 0.00 2.74
1727 1893 1.133419 GGAGGCTAGGCTAGTAGTGGT 60.133 57.143 20.27 0.00 0.00 4.16
1730 1896 0.110869 CGGGAGGCTAGGCTAGTAGT 59.889 60.000 20.27 7.67 0.00 2.73
1759 1925 4.026062 GGAAAAGCGAACACAAATTGGAAC 60.026 41.667 0.00 0.00 0.00 3.62
1760 1926 4.116238 GGAAAAGCGAACACAAATTGGAA 58.884 39.130 0.00 0.00 0.00 3.53
1781 1947 0.395311 ATGCTGCACAGAATGAGGGG 60.395 55.000 3.57 0.00 39.69 4.79
1784 1951 2.747989 ACAAGATGCTGCACAGAATGAG 59.252 45.455 3.57 0.00 39.69 2.90
1791 1958 0.890542 GGGTCACAAGATGCTGCACA 60.891 55.000 3.57 0.00 0.00 4.57
1793 1960 1.672030 CGGGTCACAAGATGCTGCA 60.672 57.895 4.13 4.13 0.00 4.41
1830 1997 5.838531 ATCTGGTAGTAGACACAGCTAAC 57.161 43.478 0.00 0.00 0.00 2.34
1864 2031 4.103943 AGGAAAAGATGCCTCTTCTATCCC 59.896 45.833 18.85 10.93 40.93 3.85
1867 2034 5.359292 GCAAAGGAAAAGATGCCTCTTCTAT 59.641 40.000 4.61 0.00 40.93 1.98
1885 2052 1.135315 CGGCATTCAGTCGCAAAGG 59.865 57.895 0.00 0.00 39.16 3.11
1886 2053 4.751539 CGGCATTCAGTCGCAAAG 57.248 55.556 0.00 0.00 39.16 2.77
1904 2072 3.924918 ACGGGAGATCAATCAGATACG 57.075 47.619 0.00 0.00 37.00 3.06
1922 2090 4.927425 CGGATATCCACCTACCAAATTACG 59.073 45.833 21.70 0.00 35.14 3.18
1944 2129 5.270083 TCTGCAAACAAACATAAGAACACG 58.730 37.500 0.00 0.00 0.00 4.49
1979 2164 1.995484 CGGCAAGACTACACAGACATG 59.005 52.381 0.00 0.00 0.00 3.21
1990 2175 2.218603 CAACAGTAAACCGGCAAGACT 58.781 47.619 0.00 0.00 0.00 3.24
2014 2199 2.146342 CTGAACGAGAAGTGCCACAAT 58.854 47.619 0.00 0.00 0.00 2.71
2020 2205 3.692791 AAAAACCTGAACGAGAAGTGC 57.307 42.857 0.00 0.00 0.00 4.40
2044 2229 0.806102 CCGCGAATTCGATCACACCT 60.806 55.000 31.01 0.00 43.02 4.00
2147 2332 2.351418 TGAAACAGAGACGCACAACTTG 59.649 45.455 0.00 0.00 0.00 3.16
2185 2370 3.933332 GGATAAACAGAAAGTGCGCTACT 59.067 43.478 9.73 7.89 42.89 2.57
2186 2371 3.933332 AGGATAAACAGAAAGTGCGCTAC 59.067 43.478 9.73 5.32 0.00 3.58
2187 2372 4.202245 AGGATAAACAGAAAGTGCGCTA 57.798 40.909 9.73 0.00 0.00 4.26
2188 2373 3.059352 AGGATAAACAGAAAGTGCGCT 57.941 42.857 9.73 0.00 0.00 5.92
2191 2376 6.970484 TCAGAAAAGGATAAACAGAAAGTGC 58.030 36.000 0.00 0.00 0.00 4.40
2192 2377 9.617975 GATTCAGAAAAGGATAAACAGAAAGTG 57.382 33.333 0.00 0.00 0.00 3.16
2203 2388 6.156949 ACACCTAGCAGATTCAGAAAAGGATA 59.843 38.462 0.00 0.00 0.00 2.59
2206 2391 4.394300 CACACCTAGCAGATTCAGAAAAGG 59.606 45.833 0.00 0.00 0.00 3.11
2212 2397 1.661341 GCCACACCTAGCAGATTCAG 58.339 55.000 0.00 0.00 0.00 3.02
2225 2410 2.224305 AGAGTAACTCAAGTGGCCACAC 60.224 50.000 36.39 23.27 39.30 3.82
2227 2412 2.417719 CAGAGTAACTCAAGTGGCCAC 58.582 52.381 29.22 29.22 32.06 5.01
2298 2483 6.860023 ACAATATATGCCTACGAACTAACGAC 59.140 38.462 0.00 0.00 37.03 4.34
2339 2526 2.231964 TGCAAAACATGGCAGGAATCTC 59.768 45.455 5.99 0.00 34.58 2.75
2372 2559 1.614903 TCAGCCAAGGCAAAGTCAATG 59.385 47.619 14.40 0.05 44.88 2.82
2493 2707 8.408043 ACAGTCATTAAGATTGAAATCCACAA 57.592 30.769 0.00 0.00 37.41 3.33
2538 2752 9.784531 AATAGTCAATTAAGATCACGATCCAAT 57.215 29.630 3.39 1.87 38.58 3.16
2592 2811 6.919775 ACTATCACAAGTAGAAGTGGAAGT 57.080 37.500 0.00 0.00 36.43 3.01
2726 2964 7.224753 ACAACTGAGTCAATACACAAGTACAAG 59.775 37.037 0.00 0.00 31.96 3.16
2782 3020 1.002624 TTCAGGAACATGGGGCGAC 60.003 57.895 0.00 0.00 0.00 5.19
2783 3021 1.299648 CTTCAGGAACATGGGGCGA 59.700 57.895 0.00 0.00 0.00 5.54
3124 3362 3.474600 CAGTGCCCCAAGAATCTCTATG 58.525 50.000 0.00 0.00 0.00 2.23
3337 3578 0.335705 AATGTCCATGGCCATGACCA 59.664 50.000 41.32 34.00 45.82 4.02
3338 3579 1.035139 GAATGTCCATGGCCATGACC 58.965 55.000 41.32 30.28 41.20 4.02
3339 3580 1.406539 GTGAATGTCCATGGCCATGAC 59.593 52.381 41.32 33.36 41.20 3.06
3340 3581 1.005687 TGTGAATGTCCATGGCCATGA 59.994 47.619 41.32 25.40 41.20 3.07
3341 3582 1.476477 TGTGAATGTCCATGGCCATG 58.524 50.000 34.82 34.82 38.51 3.66
3342 3583 2.036387 CATGTGAATGTCCATGGCCAT 58.964 47.619 14.09 14.09 35.82 4.40
3343 3584 1.005687 TCATGTGAATGTCCATGGCCA 59.994 47.619 8.56 8.56 39.12 5.36
3344 3585 1.406539 GTCATGTGAATGTCCATGGCC 59.593 52.381 6.96 0.00 37.64 5.36
3421 3680 2.032550 GTGCTCATGGTGATGTACATGC 59.967 50.000 14.43 8.29 43.11 4.06
3478 3737 1.638133 CAGTGCTCGAATGAGAGTGG 58.362 55.000 0.00 0.00 45.57 4.00
3826 4091 0.898320 CCATCTCACGGAGACCACTT 59.102 55.000 5.85 0.00 41.76 3.16
3937 4202 5.900865 TGTCAAGCATTTTATCAGCATCA 57.099 34.783 0.00 0.00 0.00 3.07
4077 4342 9.922305 GTCTAACATTAACTGCATTAAGATGAC 57.078 33.333 0.00 0.00 36.20 3.06
4089 4354 5.853282 GCAAGTGCAAGTCTAACATTAACTG 59.147 40.000 0.00 0.00 41.59 3.16
4090 4355 6.002062 GCAAGTGCAAGTCTAACATTAACT 57.998 37.500 0.00 0.00 41.59 2.24
4172 4439 0.167251 AATGGGCTAACGAAAACGCG 59.833 50.000 3.53 3.53 37.29 6.01
4219 4486 5.416083 TCCATGTGAATACAAACGACTAGG 58.584 41.667 0.00 0.00 40.84 3.02
4259 4526 2.683211 ACTCACAAGGGGCTCAAAAT 57.317 45.000 0.00 0.00 0.00 1.82
4305 4572 2.972713 AGAGTGCTAAGAAAGGGTGTCA 59.027 45.455 0.00 0.00 0.00 3.58
4325 4601 7.030165 CCATACCGTAGCAGATCTTTACATAG 58.970 42.308 12.36 5.30 0.00 2.23
4343 4619 1.481871 ACCCAGTACTGTCCATACCG 58.518 55.000 21.18 3.53 0.00 4.02
4348 4624 2.932184 TCCATACCCAGTACTGTCCA 57.068 50.000 21.18 6.10 0.00 4.02
4349 4625 3.039011 ACATCCATACCCAGTACTGTCC 58.961 50.000 21.18 0.00 0.00 4.02
4351 4627 6.824958 ATAAACATCCATACCCAGTACTGT 57.175 37.500 21.18 6.67 0.00 3.55
4352 4628 7.279615 TGAATAAACATCCATACCCAGTACTG 58.720 38.462 16.34 16.34 0.00 2.74
4353 4629 7.127339 ACTGAATAAACATCCATACCCAGTACT 59.873 37.037 0.00 0.00 30.48 2.73
4354 4630 7.280356 ACTGAATAAACATCCATACCCAGTAC 58.720 38.462 0.00 0.00 30.48 2.73
4355 4631 7.446106 ACTGAATAAACATCCATACCCAGTA 57.554 36.000 0.00 0.00 30.48 2.74
4356 4632 6.327386 ACTGAATAAACATCCATACCCAGT 57.673 37.500 0.00 0.00 0.00 4.00
4357 4633 7.557719 AGAAACTGAATAAACATCCATACCCAG 59.442 37.037 0.00 0.00 0.00 4.45
4503 4814 5.969423 AGTGGAATGGATGCATTAAAACTG 58.031 37.500 12.89 0.00 0.00 3.16
4529 4908 3.503363 CACTTTGCTCCTTTCTATGTGCA 59.497 43.478 0.00 0.00 0.00 4.57
4557 4936 9.832445 AGACAAAGTAGTGAGAAAACTATGAAA 57.168 29.630 0.00 0.00 35.20 2.69
4592 4971 6.660949 CCCTCCAGTGTGAGAAGAAATAAAAT 59.339 38.462 9.46 0.00 34.11 1.82
4617 5089 6.416161 GCAGAGTAAAAATATTTAGCAGCTGC 59.584 38.462 31.53 31.53 42.49 5.25
4682 5155 0.806241 AACGTTTGTGCCGTGAAAGT 59.194 45.000 0.00 0.00 38.77 2.66
4725 5198 5.922544 GCAAGCTAAAAATGCATATACAGGG 59.077 40.000 0.00 0.00 39.81 4.45
4819 5298 0.954449 CTGCAGCTTGGACAGTCTGG 60.954 60.000 0.00 0.00 31.08 3.86
4902 5381 6.271396 TCAATGTTGCTCAAAATTTGAACG 57.729 33.333 9.85 0.53 39.58 3.95
4999 5768 3.004106 GCTATACCAAAGATGCAAGGCTG 59.996 47.826 0.00 0.00 0.00 4.85
5040 5809 4.558226 ACCAGAGTATGCAGTGAAATCA 57.442 40.909 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.