Multiple sequence alignment - TraesCS1B01G418600

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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 TraesCS1B01G418600 chr1B 100.000 4753 0 0 1 4753 642480312 642475560 0.000000e+00 8778.0
1 TraesCS1B01G418600 chr1D 92.907 3468 180 41 804 4250 465540340 465536918 0.000000e+00 4981.0
2 TraesCS1B01G418600 chr1D 88.000 525 41 7 4251 4753 465536813 465536289 6.810000e-168 601.0
3 TraesCS1B01G418600 chr1A 94.066 1601 76 11 2653 4250 557955022 557953438 0.000000e+00 2412.0
4 TraesCS1B01G418600 chr1A 87.611 678 66 11 851 1522 557957142 557956477 0.000000e+00 771.0
5 TraesCS1B01G418600 chr1A 92.966 526 26 4 1864 2381 557956124 557955602 0.000000e+00 756.0
6 TraesCS1B01G418600 chr1A 79.073 841 107 35 4 799 557958069 557957253 9.120000e-142 514.0
7 TraesCS1B01G418600 chr1A 84.082 534 49 13 4251 4753 557953324 557952796 2.570000e-132 483.0
8 TraesCS1B01G418600 chr1A 90.977 266 19 3 2378 2643 557955345 557955085 2.100000e-93 353.0
9 TraesCS1B01G418600 chr7A 83.735 166 24 3 1413 1576 717606501 717606665 2.290000e-33 154.0
10 TraesCS1B01G418600 chr3D 96.875 32 0 1 630 661 389203693 389203663 9.000000e-03 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 TraesCS1B01G418600 chr1B 642475560 642480312 4752 True 8778.0 8778 100.000000 1 4753 1 chr1B.!!$R1 4752
1 TraesCS1B01G418600 chr1D 465536289 465540340 4051 True 2791.0 4981 90.453500 804 4753 2 chr1D.!!$R1 3949
2 TraesCS1B01G418600 chr1A 557952796 557958069 5273 True 881.5 2412 88.129167 4 4753 6 chr1A.!!$R1 4749

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
263 278 0.036105 ATGTCGGAGCATGTGAAGCA 60.036 50.0 0.00 0.00 0.00 3.91 F
345 360 0.041312 CGTCAACTTTTGGTGCCGAG 60.041 55.0 0.00 0.00 36.98 4.63 F
1250 1366 0.166814 GTGGTTCTTTGCTAGCGCTG 59.833 55.0 22.90 11.45 36.97 5.18 F
3077 3579 0.036671 AGGTTCCGATGGTTCCGAAC 60.037 55.0 2.37 2.37 38.56 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 1764 0.096628 CAGAATCGCAGCTTCAGTGC 59.903 55.0 0.00 0.00 37.58 4.40 R
2292 2479 0.907704 TATGTTCCCAGCGGGTCAGT 60.908 55.0 12.46 2.81 44.74 3.41 R
3110 3612 0.178981 CCTCCCTTGGTGGCCATATG 60.179 60.0 9.72 3.71 31.53 1.78 R
4577 5226 0.110644 CGCAGAAGACGGAAAAGTGC 60.111 55.0 0.00 0.00 0.00 4.40 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
21 22 1.777272 TCCGAGGAGAGGATGATCTCA 59.223 52.381 6.12 0.00 46.31 3.27
25 26 3.191162 CGAGGAGAGGATGATCTCATGTC 59.809 52.174 6.12 0.00 46.31 3.06
27 28 5.569355 GAGGAGAGGATGATCTCATGTCTA 58.431 45.833 6.12 0.00 46.31 2.59
43 46 0.105658 TCTATCGGGGGTGAAGGAGG 60.106 60.000 0.00 0.00 0.00 4.30
52 55 1.767692 GTGAAGGAGGAAGGCCCAA 59.232 57.895 0.00 0.00 37.41 4.12
55 58 0.254462 GAAGGAGGAAGGCCCAAGAG 59.746 60.000 0.00 0.00 37.41 2.85
84 87 1.390565 GAAGGCATCAAGAGCTGCAT 58.609 50.000 1.02 0.00 38.59 3.96
91 94 0.107800 TCAAGAGCTGCATGGAGAGC 60.108 55.000 19.59 8.49 35.28 4.09
102 105 3.934962 GGAGAGCCGGATCCAGCC 61.935 72.222 17.84 12.15 35.54 4.85
109 112 4.570663 CGGATCCAGCCGTCGACC 62.571 72.222 13.41 0.00 46.07 4.79
121 124 4.460529 TCGACCCCGAAAACCAAC 57.539 55.556 0.00 0.00 42.51 3.77
122 125 1.227913 TCGACCCCGAAAACCAACC 60.228 57.895 0.00 0.00 42.51 3.77
126 129 1.302671 CCCCGAAAACCAACCGCTA 60.303 57.895 0.00 0.00 0.00 4.26
138 141 0.392998 AACCGCTATGGCCAGACTTG 60.393 55.000 13.05 1.79 43.94 3.16
147 150 2.825836 CCAGACTTGCCCATCGCC 60.826 66.667 0.00 0.00 36.24 5.54
148 151 2.046023 CAGACTTGCCCATCGCCA 60.046 61.111 0.00 0.00 36.24 5.69
149 152 2.045926 AGACTTGCCCATCGCCAC 60.046 61.111 0.00 0.00 36.24 5.01
166 181 1.906824 ACGGAGGTGACGATGGTGT 60.907 57.895 0.00 0.00 34.93 4.16
169 184 0.320374 GGAGGTGACGATGGTGTGAA 59.680 55.000 0.00 0.00 0.00 3.18
175 190 1.067565 TGACGATGGTGTGAAGAGAGC 60.068 52.381 0.00 0.00 0.00 4.09
192 207 2.048222 CAAAGGAGCGAGGCGACA 60.048 61.111 0.00 0.00 0.00 4.35
202 217 0.734253 CGAGGCGACAAAGAGGACAG 60.734 60.000 0.00 0.00 0.00 3.51
227 242 0.179129 GAGATGCATTTTGGGTGGCG 60.179 55.000 0.00 0.00 0.00 5.69
231 246 4.433877 CATTTTGGGTGGCGCCGG 62.434 66.667 23.90 0.00 38.44 6.13
232 247 4.986708 ATTTTGGGTGGCGCCGGT 62.987 61.111 23.90 0.00 38.44 5.28
248 263 1.398390 CCGGTGCTCTGCTTAAATGTC 59.602 52.381 0.00 0.00 0.00 3.06
257 272 2.679837 CTGCTTAAATGTCGGAGCATGT 59.320 45.455 0.00 0.00 43.44 3.21
259 274 2.677836 GCTTAAATGTCGGAGCATGTGA 59.322 45.455 0.00 0.00 35.29 3.58
263 278 0.036105 ATGTCGGAGCATGTGAAGCA 60.036 50.000 0.00 0.00 0.00 3.91
306 321 2.881827 GCGCGTATGTGGCACGTA 60.882 61.111 15.38 15.38 41.41 3.57
309 324 0.594028 CGCGTATGTGGCACGTATCT 60.594 55.000 21.50 2.66 41.41 1.98
318 333 1.146041 GCACGTATCTGGATGCCCA 59.854 57.895 0.00 0.00 40.95 5.36
328 343 1.303317 GGATGCCCACAAACCTCGT 60.303 57.895 0.00 0.00 0.00 4.18
336 351 2.425668 CCCACAAACCTCGTCAACTTTT 59.574 45.455 0.00 0.00 0.00 2.27
345 360 0.041312 CGTCAACTTTTGGTGCCGAG 60.041 55.000 0.00 0.00 36.98 4.63
348 363 1.403679 TCAACTTTTGGTGCCGAGTTG 59.596 47.619 17.90 17.90 46.34 3.16
349 364 1.134175 CAACTTTTGGTGCCGAGTTGT 59.866 47.619 16.70 1.32 42.33 3.32
365 380 4.120589 GAGTTGTGAGAATTCGGATACCC 58.879 47.826 0.00 0.00 0.00 3.69
382 423 2.807895 CGGACGCGTCGTTGGATT 60.808 61.111 30.99 0.00 41.37 3.01
396 437 7.697291 GCGTCGTTGGATTATAAAATTGGTTTA 59.303 33.333 0.00 0.00 36.14 2.01
403 444 8.679100 TGGATTATAAAATTGGTTTAGACACCG 58.321 33.333 0.00 0.00 40.09 4.94
404 445 8.132995 GGATTATAAAATTGGTTTAGACACCGG 58.867 37.037 0.00 0.00 40.09 5.28
405 446 7.999450 TTATAAAATTGGTTTAGACACCGGT 57.001 32.000 0.00 0.00 40.09 5.28
407 448 5.771165 ATAAAATTGGTTTAGACACCGGTGT 59.229 36.000 39.49 39.49 40.09 4.16
419 460 1.132262 CACCGGTGTCCAAACATATGC 59.868 52.381 26.95 0.00 37.81 3.14
420 461 0.738389 CCGGTGTCCAAACATATGCC 59.262 55.000 1.58 0.00 37.81 4.40
421 462 0.738389 CGGTGTCCAAACATATGCCC 59.262 55.000 1.58 0.00 37.81 5.36
422 463 1.846007 GGTGTCCAAACATATGCCCA 58.154 50.000 1.58 0.00 37.81 5.36
423 464 1.476488 GGTGTCCAAACATATGCCCAC 59.524 52.381 1.58 1.15 37.81 4.61
425 466 1.271652 TGTCCAAACATATGCCCACGT 60.272 47.619 1.58 0.00 0.00 4.49
426 467 1.816224 GTCCAAACATATGCCCACGTT 59.184 47.619 1.58 0.00 0.00 3.99
427 468 2.230266 GTCCAAACATATGCCCACGTTT 59.770 45.455 1.58 0.00 31.96 3.60
428 469 2.894126 TCCAAACATATGCCCACGTTTT 59.106 40.909 1.58 0.00 29.40 2.43
429 470 4.079970 TCCAAACATATGCCCACGTTTTA 58.920 39.130 1.58 0.00 29.40 1.52
451 492 0.387239 GCAACGTGTTGAAGATGCCC 60.387 55.000 16.48 0.00 42.93 5.36
459 500 2.642311 TGTTGAAGATGCCCTTAGGTGA 59.358 45.455 0.00 0.00 34.68 4.02
515 558 9.793259 TCATTTAGTAGGAAGAAGTGTGAAATT 57.207 29.630 0.00 0.00 0.00 1.82
525 568 8.690840 GGAAGAAGTGTGAAATTTTATTTCGTG 58.309 33.333 7.43 0.00 0.00 4.35
528 571 7.591426 AGAAGTGTGAAATTTTATTTCGTGCTC 59.409 33.333 7.43 2.25 0.00 4.26
538 581 6.612247 TTTATTTCGTGCTCTTTCAGTTCA 57.388 33.333 0.00 0.00 0.00 3.18
540 583 1.865865 TCGTGCTCTTTCAGTTCACC 58.134 50.000 0.00 0.00 0.00 4.02
548 591 7.360861 CGTGCTCTTTCAGTTCACCATATAAAA 60.361 37.037 0.00 0.00 0.00 1.52
549 592 8.462016 GTGCTCTTTCAGTTCACCATATAAAAT 58.538 33.333 0.00 0.00 0.00 1.82
550 593 9.679661 TGCTCTTTCAGTTCACCATATAAAATA 57.320 29.630 0.00 0.00 0.00 1.40
551 594 9.937175 GCTCTTTCAGTTCACCATATAAAATAC 57.063 33.333 0.00 0.00 0.00 1.89
705 753 8.609478 TTTATTTCATATTTTTCGGCGAGTTC 57.391 30.769 10.46 0.00 0.00 3.01
706 754 5.614923 TTTCATATTTTTCGGCGAGTTCA 57.385 34.783 10.46 0.00 0.00 3.18
715 763 0.389817 CGGCGAGTTCATTCAGTGGA 60.390 55.000 0.00 0.00 0.00 4.02
743 791 8.358148 GGAAATATTCCTGTCGACTATAAGACA 58.642 37.037 17.92 0.00 46.57 3.41
781 829 7.979115 TGTTAATCTTAAAATGTTATGCCGC 57.021 32.000 0.00 0.00 0.00 6.53
782 830 7.767261 TGTTAATCTTAAAATGTTATGCCGCT 58.233 30.769 0.00 0.00 0.00 5.52
784 832 9.724839 GTTAATCTTAAAATGTTATGCCGCTTA 57.275 29.630 0.00 0.00 0.00 3.09
786 834 6.995511 TCTTAAAATGTTATGCCGCTTAGT 57.004 33.333 0.00 0.00 0.00 2.24
787 835 8.671384 ATCTTAAAATGTTATGCCGCTTAGTA 57.329 30.769 0.00 0.00 0.00 1.82
788 836 8.671384 TCTTAAAATGTTATGCCGCTTAGTAT 57.329 30.769 0.00 0.00 0.00 2.12
792 840 8.628882 AAAATGTTATGCCGCTTAGTATTTTC 57.371 30.769 12.12 0.00 0.00 2.29
793 841 5.744666 TGTTATGCCGCTTAGTATTTTCC 57.255 39.130 0.00 0.00 0.00 3.13
794 842 5.186942 TGTTATGCCGCTTAGTATTTTCCA 58.813 37.500 0.00 0.00 0.00 3.53
796 844 2.639065 TGCCGCTTAGTATTTTCCAGG 58.361 47.619 0.00 0.00 0.00 4.45
797 845 2.026636 TGCCGCTTAGTATTTTCCAGGT 60.027 45.455 0.00 0.00 0.00 4.00
799 847 2.354821 CCGCTTAGTATTTTCCAGGTGC 59.645 50.000 0.00 0.00 0.00 5.01
800 848 3.270877 CGCTTAGTATTTTCCAGGTGCT 58.729 45.455 0.00 0.00 0.00 4.40
801 849 3.309954 CGCTTAGTATTTTCCAGGTGCTC 59.690 47.826 0.00 0.00 0.00 4.26
802 850 3.628032 GCTTAGTATTTTCCAGGTGCTCC 59.372 47.826 0.00 0.00 0.00 4.70
823 900 6.127842 GCTCCATTCTTTTAACGGTGGAATTA 60.128 38.462 0.00 0.00 35.52 1.40
824 901 7.416326 GCTCCATTCTTTTAACGGTGGAATTAT 60.416 37.037 0.00 0.00 35.52 1.28
830 908 9.478768 TTCTTTTAACGGTGGAATTATTTTTCC 57.521 29.630 0.00 0.00 44.60 3.13
907 1018 3.158537 ATGTGCACCGTCCGACACA 62.159 57.895 15.69 10.82 46.16 3.72
930 1041 0.666577 AACGGCTGCGAGTGTACTTC 60.667 55.000 0.00 0.00 0.00 3.01
1093 1205 2.838693 GGCCCTCGTACCTCTCCC 60.839 72.222 0.00 0.00 0.00 4.30
1095 1207 2.518825 CCCTCGTACCTCTCCCCG 60.519 72.222 0.00 0.00 0.00 5.73
1144 1256 5.373812 TCTTCAACCTCCTATCCATTTCC 57.626 43.478 0.00 0.00 0.00 3.13
1156 1269 3.652057 TCCATTTCCATCCTCTGTTCC 57.348 47.619 0.00 0.00 0.00 3.62
1175 1288 2.922950 CGGTGGGGTTTCGACGAGA 61.923 63.158 0.00 0.00 0.00 4.04
1176 1289 1.080025 GGTGGGGTTTCGACGAGAG 60.080 63.158 0.00 0.00 0.00 3.20
1192 1308 3.187700 CGAGAGTTCCGGTTTAATCAGG 58.812 50.000 0.00 0.00 0.00 3.86
1193 1309 3.119245 CGAGAGTTCCGGTTTAATCAGGA 60.119 47.826 0.00 1.70 0.00 3.86
1229 1345 3.070748 GGTGCTCCTTTTGAGTTCTCTC 58.929 50.000 0.00 0.00 43.48 3.20
1230 1346 3.244387 GGTGCTCCTTTTGAGTTCTCTCT 60.244 47.826 0.00 0.00 43.48 3.10
1235 1351 3.711704 TCCTTTTGAGTTCTCTCTGTGGT 59.288 43.478 1.53 0.00 40.98 4.16
1237 1353 4.513318 CCTTTTGAGTTCTCTCTGTGGTTC 59.487 45.833 1.53 0.00 40.98 3.62
1241 1357 4.697514 TGAGTTCTCTCTGTGGTTCTTTG 58.302 43.478 1.53 0.00 40.98 2.77
1250 1366 0.166814 GTGGTTCTTTGCTAGCGCTG 59.833 55.000 22.90 11.45 36.97 5.18
1258 1374 3.198489 GCTAGCGCTGCTGGTTCC 61.198 66.667 22.90 0.00 40.10 3.62
1270 1386 0.610232 CTGGTTCCTGGGCCTGAAAG 60.610 60.000 12.58 3.24 0.00 2.62
1280 1396 1.581447 GCCTGAAAGCGTTCTTGGG 59.419 57.895 19.57 16.00 34.60 4.12
1304 1422 7.262772 GGTTTTAATTAACCTTGGGTAGATGC 58.737 38.462 0.00 0.00 43.44 3.91
1320 1438 4.289238 AGATGCAGGGATGATCTGAATC 57.711 45.455 4.35 4.35 44.06 2.52
1330 1448 0.598680 GATCTGAATCGAGGTGCCGG 60.599 60.000 0.00 0.00 0.00 6.13
1333 1451 4.162690 GAATCGAGGTGCCGGGCT 62.163 66.667 21.46 0.00 0.00 5.19
1335 1453 2.973180 GAATCGAGGTGCCGGGCTAC 62.973 65.000 21.46 15.75 0.00 3.58
1339 1457 3.682292 GAGGTGCCGGGCTACCTTG 62.682 68.421 30.63 0.00 46.92 3.61
1346 1464 1.449601 CGGGCTACCTTGCGATTGT 60.450 57.895 0.00 0.00 33.28 2.71
1347 1465 1.024579 CGGGCTACCTTGCGATTGTT 61.025 55.000 0.00 0.00 33.28 2.83
1348 1466 1.173913 GGGCTACCTTGCGATTGTTT 58.826 50.000 0.00 0.00 0.00 2.83
1349 1467 1.132453 GGGCTACCTTGCGATTGTTTC 59.868 52.381 0.00 0.00 0.00 2.78
1350 1468 1.132453 GGCTACCTTGCGATTGTTTCC 59.868 52.381 0.00 0.00 0.00 3.13
1351 1469 1.132453 GCTACCTTGCGATTGTTTCCC 59.868 52.381 0.00 0.00 0.00 3.97
1352 1470 2.711542 CTACCTTGCGATTGTTTCCCT 58.288 47.619 0.00 0.00 0.00 4.20
1355 1473 2.296190 ACCTTGCGATTGTTTCCCTTTC 59.704 45.455 0.00 0.00 0.00 2.62
1359 1477 1.891011 GCGATTGTTTCCCTTTCCCCT 60.891 52.381 0.00 0.00 0.00 4.79
1364 1482 2.673258 TGTTTCCCTTTCCCCTTTGTC 58.327 47.619 0.00 0.00 0.00 3.18
1365 1483 1.611977 GTTTCCCTTTCCCCTTTGTCG 59.388 52.381 0.00 0.00 0.00 4.35
1388 1506 3.562182 GGGAGGAGTTTGGTTCTTGAAA 58.438 45.455 0.00 0.00 0.00 2.69
1396 1514 8.704668 AGGAGTTTGGTTCTTGAAATTTGTTAT 58.295 29.630 0.00 0.00 0.00 1.89
1397 1515 8.764287 GGAGTTTGGTTCTTGAAATTTGTTATG 58.236 33.333 0.00 0.00 0.00 1.90
1398 1516 8.141835 AGTTTGGTTCTTGAAATTTGTTATGC 57.858 30.769 0.00 0.00 0.00 3.14
1399 1517 7.226523 AGTTTGGTTCTTGAAATTTGTTATGCC 59.773 33.333 0.00 0.00 0.00 4.40
1401 1519 6.222389 TGGTTCTTGAAATTTGTTATGCCTG 58.778 36.000 0.00 0.00 0.00 4.85
1443 1561 2.618241 GCGATTGGTTCAGATATGCCAA 59.382 45.455 2.47 2.47 43.95 4.52
1465 1583 0.912486 GGCCCAATACTCCAGTCACT 59.088 55.000 0.00 0.00 0.00 3.41
1506 1624 4.770010 TGGAAATTTTACTGCCCAAGTAGG 59.230 41.667 0.00 0.00 42.38 3.18
1562 1680 9.241919 CCTGAACTGATAGAGTCATAGATATGT 57.758 37.037 0.00 0.00 35.97 2.29
1584 1702 3.633525 TGGAACGGTCGCTATACATTACT 59.366 43.478 0.00 0.00 0.00 2.24
1590 1708 5.528690 ACGGTCGCTATACATTACTTGACTA 59.471 40.000 0.00 0.00 0.00 2.59
1591 1709 6.206243 ACGGTCGCTATACATTACTTGACTAT 59.794 38.462 0.00 0.00 0.00 2.12
1592 1710 6.741811 CGGTCGCTATACATTACTTGACTATC 59.258 42.308 0.00 0.00 0.00 2.08
1593 1711 7.361031 CGGTCGCTATACATTACTTGACTATCT 60.361 40.741 0.00 0.00 0.00 1.98
1594 1712 8.298140 GGTCGCTATACATTACTTGACTATCTT 58.702 37.037 0.00 0.00 0.00 2.40
1611 1729 9.731819 TGACTATCTTATCTAATCGTGTGAAAC 57.268 33.333 0.00 0.00 37.35 2.78
1612 1730 9.953697 GACTATCTTATCTAATCGTGTGAAACT 57.046 33.333 0.00 0.00 38.04 2.66
1613 1731 9.737427 ACTATCTTATCTAATCGTGTGAAACTG 57.263 33.333 0.00 0.00 38.04 3.16
1614 1732 9.186323 CTATCTTATCTAATCGTGTGAAACTGG 57.814 37.037 0.00 0.00 38.04 4.00
1615 1733 6.931838 TCTTATCTAATCGTGTGAAACTGGT 58.068 36.000 0.00 0.00 38.04 4.00
1616 1734 7.033791 TCTTATCTAATCGTGTGAAACTGGTC 58.966 38.462 0.00 0.00 38.04 4.02
1619 1737 4.988540 TCTAATCGTGTGAAACTGGTCTTG 59.011 41.667 0.00 0.00 38.04 3.02
1637 1755 5.502606 GTCTTGCTCTGTAGTTTTTGTGAC 58.497 41.667 0.00 0.00 0.00 3.67
1644 1762 6.622896 GCTCTGTAGTTTTTGTGACACAGTTT 60.623 38.462 8.55 0.00 35.88 2.66
1646 1764 5.623335 TGTAGTTTTTGTGACACAGTTTCG 58.377 37.500 8.55 0.00 0.00 3.46
1754 1882 2.435805 AGTTCTGCACTCTCCAACTCAA 59.564 45.455 0.00 0.00 0.00 3.02
1844 1978 1.401539 GCAAAGGCTGGTGATTTCGTC 60.402 52.381 2.77 0.00 36.96 4.20
1854 1988 3.317711 TGGTGATTTCGTCTGTTGCAAAT 59.682 39.130 0.00 0.00 0.00 2.32
1855 1989 3.670055 GGTGATTTCGTCTGTTGCAAATG 59.330 43.478 0.00 0.00 0.00 2.32
1937 2122 2.292126 TGGCAAGAGAATTTGGGGCATA 60.292 45.455 0.00 0.00 0.00 3.14
2055 2242 5.675684 TGTGATCACAGCCTTATCAACTA 57.324 39.130 24.56 0.00 36.21 2.24
2059 2246 7.874528 TGTGATCACAGCCTTATCAACTATATG 59.125 37.037 24.56 0.00 36.21 1.78
2085 2272 3.054728 TGCAGGGAAATATCTTGAACCGA 60.055 43.478 0.00 0.00 0.00 4.69
2292 2479 6.591935 ACTGTCTATTCAAAGGAAAGACACA 58.408 36.000 13.41 2.37 41.18 3.72
2409 2856 3.587923 CTCTCAGCCTCTGAAGAGTTTG 58.412 50.000 6.59 4.69 40.18 2.93
2425 2872 4.114794 GAGTTTGATGTTGCTGCTTTTGT 58.885 39.130 0.00 0.00 0.00 2.83
2428 2875 5.063817 AGTTTGATGTTGCTGCTTTTGTTTC 59.936 36.000 0.00 0.00 0.00 2.78
2430 2877 1.276415 TGTTGCTGCTTTTGTTTCGC 58.724 45.000 0.00 0.00 0.00 4.70
2451 2898 6.837992 TCGCTTCCAATGTTTTTCTGTATAC 58.162 36.000 0.00 0.00 0.00 1.47
2466 2913 6.730960 TCTGTATACGTTTCCAACATTTCC 57.269 37.500 0.00 0.00 0.00 3.13
2476 2923 5.584253 TTCCAACATTTCCGAAAACAGAA 57.416 34.783 0.00 0.00 0.00 3.02
2477 2924 5.181690 TCCAACATTTCCGAAAACAGAAG 57.818 39.130 0.00 0.00 0.00 2.85
2587 3034 4.861102 AAGTGAGGCTGAAATCCAAAAG 57.139 40.909 0.00 0.00 0.00 2.27
2596 3043 5.011023 GGCTGAAATCCAAAAGAAGAAAGGA 59.989 40.000 0.00 0.00 0.00 3.36
2615 3062 4.093011 AGGATATCACCAGAGGTCTATGC 58.907 47.826 4.83 0.00 31.02 3.14
2758 3259 4.161001 GGATTCTCTTCCATGTTTGCCATT 59.839 41.667 0.00 0.00 35.72 3.16
2826 3328 4.034510 GGCTGTCAGATTTAACTGAATCCG 59.965 45.833 3.32 0.00 46.34 4.18
2831 3333 8.786826 TGTCAGATTTAACTGAATCCGTTAAT 57.213 30.769 10.07 2.73 46.34 1.40
2847 3349 3.188460 CGTTAATGTAGCTGGTGCAGTTT 59.812 43.478 2.93 0.00 42.74 2.66
2851 3353 2.374184 TGTAGCTGGTGCAGTTTTTGT 58.626 42.857 0.00 0.00 42.74 2.83
2869 3371 8.082242 AGTTTTTGTATTCCTGACATAGCAAAC 58.918 33.333 0.00 0.00 0.00 2.93
2873 3375 6.413892 TGTATTCCTGACATAGCAAACATCA 58.586 36.000 0.00 0.00 0.00 3.07
2888 3390 6.647895 AGCAAACATCATCAACCTGATTTTTC 59.352 34.615 0.00 0.00 34.77 2.29
2893 3395 6.642131 ACATCATCAACCTGATTTTTCGTTTG 59.358 34.615 0.00 0.00 34.28 2.93
2966 3468 8.357402 AGTATTTTGTCTGGAACCATTACAAAC 58.643 33.333 22.46 16.48 39.33 2.93
3077 3579 0.036671 AGGTTCCGATGGTTCCGAAC 60.037 55.000 2.37 2.37 38.56 3.95
3245 3747 1.428448 TCAATCGCTCAACACTTCGG 58.572 50.000 0.00 0.00 0.00 4.30
3265 3767 3.119849 CGGGTCAAAAGACTGCAATTAGG 60.120 47.826 0.00 0.00 0.00 2.69
3284 3786 2.294791 AGGTCGGATCTATTCTGCTTCG 59.705 50.000 0.00 0.00 0.00 3.79
3343 3845 1.405526 GCATCGCTTGGACCTGACTTA 60.406 52.381 0.00 0.00 0.00 2.24
3353 3855 0.824759 ACCTGACTTATGCTCGGTCC 59.175 55.000 0.00 0.00 0.00 4.46
3492 3994 3.092301 TCTGTCGTTGATCCTCATGACT 58.908 45.455 0.00 0.00 34.90 3.41
3498 4000 3.620374 CGTTGATCCTCATGACTTGAAGG 59.380 47.826 0.00 0.00 32.78 3.46
3515 4017 3.245586 TGAAGGGTTACATGATGGGCTTT 60.246 43.478 0.00 0.00 0.00 3.51
3575 4077 5.003804 ACAAACGAGGCTTGTAATCTCATT 58.996 37.500 8.05 0.00 35.26 2.57
3659 4161 1.048601 TACTTGATCCGGCATCCCTC 58.951 55.000 0.00 0.00 0.00 4.30
3665 4167 0.106519 ATCCGGCATCCCTCAAAAGG 60.107 55.000 0.00 0.00 42.95 3.11
3710 4212 3.265489 TGGTTCCTTCCTTTGGGATACT 58.735 45.455 0.00 0.00 41.87 2.12
3785 4287 3.008330 CAGAAGATTCCTGAAGCACTGG 58.992 50.000 11.59 0.00 38.68 4.00
3829 4331 3.683802 AGAGTTTGCAGAAGATTCCTGG 58.316 45.455 0.00 0.00 32.51 4.45
3843 4345 6.936968 AGATTCCTGGGACCTTGTATATAC 57.063 41.667 5.89 5.89 0.00 1.47
3853 4355 9.060137 TGGGACCTTGTATATACTTTAGGAAAA 57.940 33.333 24.00 6.92 0.00 2.29
3952 4455 2.887152 AGAACCTTGCAGGCACTAAAAG 59.113 45.455 0.00 0.00 39.63 2.27
4016 4520 5.972107 AGCATATGTCCATTTAGGCATTC 57.028 39.130 4.29 0.00 36.18 2.67
4019 4523 2.418368 TGTCCATTTAGGCATTCGCT 57.582 45.000 0.00 0.00 38.60 4.93
4024 4528 2.223876 CCATTTAGGCATTCGCTTGCAT 60.224 45.455 10.84 6.75 44.59 3.96
4094 4600 9.552114 CAGATGCAAGAAGATTTTGTTAAGTAG 57.448 33.333 0.00 0.00 0.00 2.57
4115 4624 5.520376 AGAAAGTGTCAAAGTCCATTTGG 57.480 39.130 0.90 0.00 46.93 3.28
4172 4681 2.286294 CAGACAGATGGAGCAATAACGC 59.714 50.000 0.00 0.00 0.00 4.84
4190 4699 2.936032 AAGGGGAGGAGCCACACC 60.936 66.667 0.00 0.00 45.20 4.16
4191 4700 3.810687 AAGGGGAGGAGCCACACCA 62.811 63.158 7.99 0.00 45.20 4.17
4192 4701 3.256960 GGGGAGGAGCCACACCAA 61.257 66.667 0.00 0.00 41.00 3.67
4193 4702 2.034221 GGGAGGAGCCACACCAAC 59.966 66.667 0.00 0.00 38.95 3.77
4195 4704 1.380302 GGAGGAGCCACACCAACAT 59.620 57.895 0.00 0.00 36.34 2.71
4203 4712 4.485163 GAGCCACACCAACATAAACATTC 58.515 43.478 0.00 0.00 0.00 2.67
4217 4726 4.096003 ATTCGTGCCCCTCACCCG 62.096 66.667 0.00 0.00 42.69 5.28
4259 4881 1.306654 ACCCTAACCAGGATGCCGA 60.307 57.895 0.00 0.00 45.91 5.54
4262 4884 1.276421 CCCTAACCAGGATGCCGATAG 59.724 57.143 0.00 0.00 45.91 2.08
4264 4886 0.685097 TAACCAGGATGCCGATAGCC 59.315 55.000 0.00 0.00 42.71 3.93
4282 4904 0.385751 CCGCCATGATCGTCTACACT 59.614 55.000 0.00 0.00 0.00 3.55
4322 4944 2.759795 GAGCAGGCAAGGGACCTT 59.240 61.111 0.00 0.00 34.42 3.50
4345 4967 0.974010 TCGACTCCGGTAATGGCCTT 60.974 55.000 3.32 0.00 36.24 4.35
4363 4985 2.447047 CCTTACCCATTGCCCCTAAGAT 59.553 50.000 0.00 0.00 0.00 2.40
4373 4995 2.237143 TGCCCCTAAGATCTCAACACTG 59.763 50.000 0.00 0.00 0.00 3.66
4412 5036 5.297569 AGGTGCTCCAATTCTAGGATTAC 57.702 43.478 7.70 0.00 33.99 1.89
4413 5037 4.721776 AGGTGCTCCAATTCTAGGATTACA 59.278 41.667 7.70 0.00 33.99 2.41
4503 5151 4.818534 TGAATTTCAGTTGTGTCTCAGC 57.181 40.909 0.00 0.00 0.00 4.26
4577 5226 6.403200 CGAACCTGACTTAAATGGTTACATGG 60.403 42.308 0.00 0.00 42.15 3.66
4578 5227 4.705023 ACCTGACTTAAATGGTTACATGGC 59.295 41.667 0.00 0.00 37.40 4.40
4588 5237 1.883926 GGTTACATGGCACTTTTCCGT 59.116 47.619 0.00 0.00 0.00 4.69
4596 5245 0.110644 GCACTTTTCCGTCTTCTGCG 60.111 55.000 0.00 0.00 0.00 5.18
4614 5263 1.737029 GCGCATCTGCTTAGACTGTCA 60.737 52.381 10.88 0.00 39.32 3.58
4628 5277 7.928706 GCTTAGACTGTCAATAGATACACCAAT 59.071 37.037 10.88 0.00 0.00 3.16
4629 5278 9.254133 CTTAGACTGTCAATAGATACACCAATG 57.746 37.037 10.88 0.00 0.00 2.82
4699 5348 0.184692 TTCACCACAGGCATGTCCAA 59.815 50.000 0.00 0.00 37.65 3.53
4701 5350 0.822944 CACCACAGGCATGTCCAACA 60.823 55.000 0.00 0.00 37.65 3.33
4705 5354 1.200716 CACAGGCATGTCCAACACATC 59.799 52.381 0.00 0.00 44.60 3.06
4706 5355 0.448990 CAGGCATGTCCAACACATCG 59.551 55.000 8.58 0.00 44.60 3.84
4714 5363 4.271696 TGTCCAACACATCGATTCTCTT 57.728 40.909 0.00 0.00 0.00 2.85
4718 5368 3.254060 CAACACATCGATTCTCTTCGGT 58.746 45.455 0.00 0.00 39.56 4.69
4730 5380 7.710907 TCGATTCTCTTCGGTGATTTGAATAAT 59.289 33.333 0.00 0.00 39.56 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.159382 GAGATCATCCTCTCCTCGGAC 58.841 57.143 0.00 0.00 36.47 4.79
1 2 1.777272 TGAGATCATCCTCTCCTCGGA 59.223 52.381 0.00 0.00 40.85 4.55
2 3 2.284754 TGAGATCATCCTCTCCTCGG 57.715 55.000 0.00 0.00 40.85 4.63
21 22 1.062428 TCCTTCACCCCCGATAGACAT 60.062 52.381 0.00 0.00 39.76 3.06
25 26 0.105658 TCCTCCTTCACCCCCGATAG 60.106 60.000 0.00 0.00 0.00 2.08
27 28 0.983378 CTTCCTCCTTCACCCCCGAT 60.983 60.000 0.00 0.00 0.00 4.18
43 46 2.924421 CCTATGTTCTCTTGGGCCTTC 58.076 52.381 4.53 0.00 0.00 3.46
52 55 1.195115 TGCCTTCGCCTATGTTCTCT 58.805 50.000 0.00 0.00 0.00 3.10
55 58 1.953559 TGATGCCTTCGCCTATGTTC 58.046 50.000 0.00 0.00 0.00 3.18
75 78 2.909577 GGCTCTCCATGCAGCTCT 59.090 61.111 8.82 0.00 35.82 4.09
78 81 3.472943 ATCCGGCTCTCCATGCAGC 62.473 63.158 0.00 1.82 34.65 5.25
84 87 3.157252 GCTGGATCCGGCTCTCCA 61.157 66.667 34.25 16.39 44.39 3.86
102 105 1.594836 TTGGTTTTCGGGGTCGACG 60.595 57.895 9.92 0.00 45.92 5.12
105 108 2.609759 CGGTTGGTTTTCGGGGTCG 61.610 63.158 0.00 0.00 37.82 4.79
109 112 0.450184 CATAGCGGTTGGTTTTCGGG 59.550 55.000 0.00 0.00 0.00 5.14
112 115 0.172578 GGCCATAGCGGTTGGTTTTC 59.827 55.000 14.41 1.99 41.24 2.29
120 123 1.221840 CAAGTCTGGCCATAGCGGT 59.778 57.895 5.51 0.00 41.24 5.68
121 124 2.182842 GCAAGTCTGGCCATAGCGG 61.183 63.158 5.51 0.00 41.24 5.52
122 125 3.414272 GCAAGTCTGGCCATAGCG 58.586 61.111 5.51 0.00 41.24 4.26
147 150 1.446099 CACCATCGTCACCTCCGTG 60.446 63.158 0.00 0.00 41.72 4.94
148 151 1.906824 ACACCATCGTCACCTCCGT 60.907 57.895 0.00 0.00 0.00 4.69
149 152 1.446099 CACACCATCGTCACCTCCG 60.446 63.158 0.00 0.00 0.00 4.63
159 162 2.746362 CCTTTGCTCTCTTCACACCATC 59.254 50.000 0.00 0.00 0.00 3.51
160 163 2.373169 TCCTTTGCTCTCTTCACACCAT 59.627 45.455 0.00 0.00 0.00 3.55
163 178 1.803555 GCTCCTTTGCTCTCTTCACAC 59.196 52.381 0.00 0.00 0.00 3.82
166 181 0.969149 TCGCTCCTTTGCTCTCTTCA 59.031 50.000 0.00 0.00 0.00 3.02
169 184 1.896694 CCTCGCTCCTTTGCTCTCT 59.103 57.895 0.00 0.00 0.00 3.10
175 190 1.227999 TTTGTCGCCTCGCTCCTTTG 61.228 55.000 0.00 0.00 0.00 2.77
192 207 3.134442 GCATCTCATCTCCTGTCCTCTTT 59.866 47.826 0.00 0.00 0.00 2.52
202 217 3.067742 CACCCAAAATGCATCTCATCTCC 59.932 47.826 0.00 0.00 33.40 3.71
227 242 0.099436 CATTTAAGCAGAGCACCGGC 59.901 55.000 0.00 0.00 41.61 6.13
230 245 1.398390 CCGACATTTAAGCAGAGCACC 59.602 52.381 0.00 0.00 0.00 5.01
231 246 2.346803 TCCGACATTTAAGCAGAGCAC 58.653 47.619 0.00 0.00 0.00 4.40
232 247 2.621338 CTCCGACATTTAAGCAGAGCA 58.379 47.619 0.00 0.00 0.00 4.26
233 248 1.328986 GCTCCGACATTTAAGCAGAGC 59.671 52.381 0.00 0.00 38.56 4.09
248 263 0.524816 GCATTGCTTCACATGCTCCG 60.525 55.000 0.16 0.00 37.10 4.63
263 278 0.108992 CACCGCATTGAAGCAGCATT 60.109 50.000 0.00 0.00 0.00 3.56
301 316 0.177836 TGTGGGCATCCAGATACGTG 59.822 55.000 0.00 0.00 45.05 4.49
302 317 0.908910 TTGTGGGCATCCAGATACGT 59.091 50.000 0.00 0.00 45.05 3.57
305 320 1.922447 AGGTTTGTGGGCATCCAGATA 59.078 47.619 0.00 0.00 45.05 1.98
306 321 0.706433 AGGTTTGTGGGCATCCAGAT 59.294 50.000 0.00 0.00 45.05 2.90
309 324 1.303236 CGAGGTTTGTGGGCATCCA 60.303 57.895 0.00 0.00 41.58 3.41
318 333 3.086282 ACCAAAAGTTGACGAGGTTTGT 58.914 40.909 0.00 0.00 0.00 2.83
328 343 1.757682 AACTCGGCACCAAAAGTTGA 58.242 45.000 0.00 0.00 31.05 3.18
336 351 0.396435 ATTCTCACAACTCGGCACCA 59.604 50.000 0.00 0.00 0.00 4.17
361 376 4.403137 CAACGACGCGTCCGGGTA 62.403 66.667 31.84 0.00 39.99 3.69
365 380 0.868602 ATAATCCAACGACGCGTCCG 60.869 55.000 31.84 26.84 39.99 4.79
370 385 5.575019 ACCAATTTTATAATCCAACGACGC 58.425 37.500 0.00 0.00 0.00 5.19
371 386 9.217223 CTAAACCAATTTTATAATCCAACGACG 57.783 33.333 0.00 0.00 0.00 5.12
382 423 6.941436 ACACCGGTGTCTAAACCAATTTTATA 59.059 34.615 34.41 0.00 40.24 0.98
402 443 0.738389 GGGCATATGTTTGGACACCG 59.262 55.000 4.29 0.00 38.91 4.94
403 444 1.476488 GTGGGCATATGTTTGGACACC 59.524 52.381 4.29 0.00 38.91 4.16
404 445 1.132262 CGTGGGCATATGTTTGGACAC 59.868 52.381 4.29 4.49 38.91 3.67
405 446 1.271652 ACGTGGGCATATGTTTGGACA 60.272 47.619 4.29 0.00 40.71 4.02
407 448 2.208132 AACGTGGGCATATGTTTGGA 57.792 45.000 4.29 0.00 0.00 3.53
408 449 3.311486 AAAACGTGGGCATATGTTTGG 57.689 42.857 4.29 0.00 39.15 3.28
409 450 4.803088 CCATAAAACGTGGGCATATGTTTG 59.197 41.667 4.29 2.31 39.15 2.93
411 452 3.181480 GCCATAAAACGTGGGCATATGTT 60.181 43.478 4.29 0.00 45.70 2.71
413 454 3.011949 GCCATAAAACGTGGGCATATG 57.988 47.619 0.00 0.00 45.70 1.78
419 460 3.393112 CGTTGCCATAAAACGTGGG 57.607 52.632 0.00 0.00 44.07 4.61
425 466 4.902443 TCTTCAACACGTTGCCATAAAA 57.098 36.364 5.01 0.00 40.24 1.52
426 467 4.793071 CATCTTCAACACGTTGCCATAAA 58.207 39.130 5.01 0.00 40.24 1.40
427 468 3.365868 GCATCTTCAACACGTTGCCATAA 60.366 43.478 5.01 0.00 40.24 1.90
428 469 2.161410 GCATCTTCAACACGTTGCCATA 59.839 45.455 5.01 0.00 40.24 2.74
429 470 1.068333 GCATCTTCAACACGTTGCCAT 60.068 47.619 5.01 0.00 40.24 4.40
435 476 2.615493 CCTAAGGGCATCTTCAACACGT 60.615 50.000 0.00 0.00 36.93 4.49
482 525 9.284968 CACTTCTTCCTACTAAATGAAGGAAAA 57.715 33.333 4.72 2.59 46.13 2.29
483 526 8.437575 ACACTTCTTCCTACTAAATGAAGGAAA 58.562 33.333 4.72 0.00 46.13 3.13
489 532 9.793259 AATTTCACACTTCTTCCTACTAAATGA 57.207 29.630 0.00 0.00 0.00 2.57
515 558 6.427150 GTGAACTGAAAGAGCACGAAATAAA 58.573 36.000 0.00 0.00 37.43 1.40
525 568 9.937175 GTATTTTATATGGTGAACTGAAAGAGC 57.063 33.333 0.00 0.00 37.43 4.09
619 662 9.713713 TTGGATATTTCAATGAATTGCATATGG 57.286 29.630 4.56 0.00 35.78 2.74
678 726 9.581099 AACTCGCCGAAAAATATGAAATAAATT 57.419 25.926 0.00 0.00 29.06 1.82
689 737 4.693566 ACTGAATGAACTCGCCGAAAAATA 59.306 37.500 0.00 0.00 0.00 1.40
693 741 1.798223 CACTGAATGAACTCGCCGAAA 59.202 47.619 0.00 0.00 0.00 3.46
694 742 1.428448 CACTGAATGAACTCGCCGAA 58.572 50.000 0.00 0.00 0.00 4.30
695 743 0.389817 CCACTGAATGAACTCGCCGA 60.390 55.000 0.00 0.00 0.00 5.54
699 747 3.319137 TCCTTCCACTGAATGAACTCG 57.681 47.619 0.00 0.00 0.00 4.18
720 768 8.466617 AGTGTCTTATAGTCGACAGGAATATT 57.533 34.615 19.50 0.00 40.48 1.28
723 771 6.153000 ACAAGTGTCTTATAGTCGACAGGAAT 59.847 38.462 19.50 8.02 40.48 3.01
729 777 6.469595 GTCATCACAAGTGTCTTATAGTCGAC 59.530 42.308 7.70 7.70 0.00 4.20
737 785 8.725405 TTAACAAAGTCATCACAAGTGTCTTA 57.275 30.769 0.00 0.00 0.00 2.10
780 828 3.628032 GGAGCACCTGGAAAATACTAAGC 59.372 47.826 0.00 0.00 0.00 3.09
781 829 4.843728 TGGAGCACCTGGAAAATACTAAG 58.156 43.478 0.00 0.00 37.04 2.18
782 830 4.919774 TGGAGCACCTGGAAAATACTAA 57.080 40.909 0.00 0.00 37.04 2.24
784 832 4.018050 AGAATGGAGCACCTGGAAAATACT 60.018 41.667 0.00 0.00 37.04 2.12
786 834 4.591321 AGAATGGAGCACCTGGAAAATA 57.409 40.909 0.00 0.00 37.04 1.40
787 835 3.463048 AGAATGGAGCACCTGGAAAAT 57.537 42.857 0.00 0.00 37.04 1.82
788 836 2.978156 AGAATGGAGCACCTGGAAAA 57.022 45.000 0.00 0.00 37.04 2.29
792 840 3.119849 CGTTAAAAGAATGGAGCACCTGG 60.120 47.826 0.71 0.00 37.04 4.45
793 841 3.119849 CCGTTAAAAGAATGGAGCACCTG 60.120 47.826 0.71 0.00 37.04 4.00
794 842 3.081804 CCGTTAAAAGAATGGAGCACCT 58.918 45.455 0.71 0.00 37.04 4.00
796 844 3.365969 CCACCGTTAAAAGAATGGAGCAC 60.366 47.826 2.58 0.00 0.00 4.40
797 845 2.817258 CCACCGTTAAAAGAATGGAGCA 59.183 45.455 2.58 0.00 0.00 4.26
799 847 5.897377 ATTCCACCGTTAAAAGAATGGAG 57.103 39.130 2.58 0.00 37.52 3.86
800 848 7.948034 ATAATTCCACCGTTAAAAGAATGGA 57.052 32.000 2.58 0.00 34.44 3.41
801 849 8.996024 AAATAATTCCACCGTTAAAAGAATGG 57.004 30.769 0.00 0.00 0.00 3.16
862 940 5.301805 GTCCTCAAGATTTCACCCTCAAAAA 59.698 40.000 0.00 0.00 0.00 1.94
865 943 3.244911 GGTCCTCAAGATTTCACCCTCAA 60.245 47.826 0.00 0.00 0.00 3.02
874 985 2.290260 TGCACATCGGTCCTCAAGATTT 60.290 45.455 0.00 0.00 0.00 2.17
878 989 1.021390 GGTGCACATCGGTCCTCAAG 61.021 60.000 20.43 0.00 0.00 3.02
907 1018 0.037697 TACACTCGCAGCCGTTCAAT 60.038 50.000 0.00 0.00 35.54 2.57
936 1047 1.693083 GATAACGCCGTGTGCAGTCC 61.693 60.000 0.00 0.00 41.33 3.85
1137 1249 2.659428 GGGAACAGAGGATGGAAATGG 58.341 52.381 0.00 0.00 0.00 3.16
1144 1256 1.221840 CCACCGGGAACAGAGGATG 59.778 63.158 6.32 0.00 35.59 3.51
1156 1269 3.927163 CTCGTCGAAACCCCACCGG 62.927 68.421 0.00 0.00 37.81 5.28
1170 1283 3.368116 CCTGATTAAACCGGAACTCTCGT 60.368 47.826 9.46 0.00 0.00 4.18
1171 1284 3.119245 TCCTGATTAAACCGGAACTCTCG 60.119 47.826 9.46 0.00 0.00 4.04
1175 1288 4.903045 TTCTCCTGATTAAACCGGAACT 57.097 40.909 9.46 0.00 0.00 3.01
1176 1289 5.001874 AGTTTCTCCTGATTAAACCGGAAC 58.998 41.667 9.46 0.00 34.39 3.62
1177 1290 5.001232 CAGTTTCTCCTGATTAAACCGGAA 58.999 41.667 9.46 0.00 34.39 4.30
1178 1291 4.285003 TCAGTTTCTCCTGATTAAACCGGA 59.715 41.667 9.46 0.00 36.57 5.14
1179 1292 4.575885 TCAGTTTCTCCTGATTAAACCGG 58.424 43.478 0.00 0.00 36.57 5.28
1192 1308 4.142513 GGAGCACCAATCAATCAGTTTCTC 60.143 45.833 0.00 0.00 35.97 2.87
1193 1309 3.760684 GGAGCACCAATCAATCAGTTTCT 59.239 43.478 0.00 0.00 35.97 2.52
1229 1345 0.166814 GCGCTAGCAAAGAACCACAG 59.833 55.000 16.45 0.00 44.35 3.66
1230 1346 2.244000 GCGCTAGCAAAGAACCACA 58.756 52.632 16.45 0.00 44.35 4.17
1241 1357 3.198489 GGAACCAGCAGCGCTAGC 61.198 66.667 10.99 16.77 45.58 3.42
1250 1366 2.713531 TTTCAGGCCCAGGAACCAGC 62.714 60.000 0.00 0.00 0.00 4.85
1258 1374 0.890996 AAGAACGCTTTCAGGCCCAG 60.891 55.000 0.00 0.00 33.72 4.45
1263 1379 1.318576 AACCCAAGAACGCTTTCAGG 58.681 50.000 5.66 6.59 33.72 3.86
1280 1396 7.832769 TGCATCTACCCAAGGTTAATTAAAAC 58.167 34.615 0.00 0.00 37.09 2.43
1304 1422 2.632028 ACCTCGATTCAGATCATCCCTG 59.368 50.000 0.00 0.00 32.33 4.45
1330 1448 1.132453 GGAAACAATCGCAAGGTAGCC 59.868 52.381 0.00 0.00 38.47 3.93
1333 1451 2.871096 AGGGAAACAATCGCAAGGTA 57.129 45.000 0.00 0.00 43.19 3.08
1335 1453 2.352715 GGAAAGGGAAACAATCGCAAGG 60.353 50.000 0.00 0.00 43.19 3.61
1339 1457 0.530744 GGGGAAAGGGAAACAATCGC 59.469 55.000 0.00 0.00 41.15 4.58
1341 1459 3.646162 ACAAAGGGGAAAGGGAAACAATC 59.354 43.478 0.00 0.00 0.00 2.67
1346 1464 1.479757 CCGACAAAGGGGAAAGGGAAA 60.480 52.381 0.00 0.00 0.00 3.13
1347 1465 0.111639 CCGACAAAGGGGAAAGGGAA 59.888 55.000 0.00 0.00 0.00 3.97
1348 1466 1.765074 CCGACAAAGGGGAAAGGGA 59.235 57.895 0.00 0.00 0.00 4.20
1349 1467 4.415783 CCGACAAAGGGGAAAGGG 57.584 61.111 0.00 0.00 0.00 3.95
1359 1477 0.109723 CAAACTCCTCCCCCGACAAA 59.890 55.000 0.00 0.00 0.00 2.83
1364 1482 1.002502 GAACCAAACTCCTCCCCCG 60.003 63.158 0.00 0.00 0.00 5.73
1365 1483 0.778083 AAGAACCAAACTCCTCCCCC 59.222 55.000 0.00 0.00 0.00 5.40
1388 1506 2.071778 ATCGGCCAGGCATAACAAAT 57.928 45.000 15.19 0.00 0.00 2.32
1396 1514 2.046023 CAGTGAATCGGCCAGGCA 60.046 61.111 15.19 0.00 0.00 4.75
1397 1515 2.825836 CCAGTGAATCGGCCAGGC 60.826 66.667 1.26 1.26 0.00 4.85
1398 1516 2.124570 CCCAGTGAATCGGCCAGG 60.125 66.667 2.24 0.00 0.00 4.45
1399 1517 1.002134 AACCCAGTGAATCGGCCAG 60.002 57.895 2.24 0.00 0.00 4.85
1401 1519 0.322546 AAGAACCCAGTGAATCGGCC 60.323 55.000 0.00 0.00 0.00 6.13
1443 1561 2.706190 GTGACTGGAGTATTGGGCCTAT 59.294 50.000 4.53 5.15 0.00 2.57
1456 1574 1.460504 CCGCTGTACTAGTGACTGGA 58.539 55.000 5.39 0.00 39.30 3.86
1506 1624 4.119442 TCGTAGTCTATTTCAAGTGGGC 57.881 45.455 0.00 0.00 0.00 5.36
1562 1680 3.633525 AGTAATGTATAGCGACCGTTCCA 59.366 43.478 0.00 0.00 0.00 3.53
1563 1681 4.234530 AGTAATGTATAGCGACCGTTCC 57.765 45.455 0.00 0.00 0.00 3.62
1590 1708 7.556844 ACCAGTTTCACACGATTAGATAAGAT 58.443 34.615 0.00 0.00 0.00 2.40
1591 1709 6.931838 ACCAGTTTCACACGATTAGATAAGA 58.068 36.000 0.00 0.00 0.00 2.10
1592 1710 7.036220 AGACCAGTTTCACACGATTAGATAAG 58.964 38.462 0.00 0.00 0.00 1.73
1593 1711 6.931838 AGACCAGTTTCACACGATTAGATAA 58.068 36.000 0.00 0.00 0.00 1.75
1594 1712 6.525578 AGACCAGTTTCACACGATTAGATA 57.474 37.500 0.00 0.00 0.00 1.98
1610 1728 4.423625 AAAACTACAGAGCAAGACCAGT 57.576 40.909 0.00 0.00 0.00 4.00
1611 1729 4.576463 ACAAAAACTACAGAGCAAGACCAG 59.424 41.667 0.00 0.00 0.00 4.00
1612 1730 4.335315 CACAAAAACTACAGAGCAAGACCA 59.665 41.667 0.00 0.00 0.00 4.02
1613 1731 4.574828 TCACAAAAACTACAGAGCAAGACC 59.425 41.667 0.00 0.00 0.00 3.85
1614 1732 5.064707 TGTCACAAAAACTACAGAGCAAGAC 59.935 40.000 0.00 0.00 0.00 3.01
1615 1733 5.064707 GTGTCACAAAAACTACAGAGCAAGA 59.935 40.000 0.00 0.00 0.00 3.02
1616 1734 5.163764 TGTGTCACAAAAACTACAGAGCAAG 60.164 40.000 2.31 0.00 0.00 4.01
1619 1737 4.332819 ACTGTGTCACAAAAACTACAGAGC 59.667 41.667 7.18 0.00 36.88 4.09
1646 1764 0.096628 CAGAATCGCAGCTTCAGTGC 59.903 55.000 0.00 0.00 37.58 4.40
1819 1952 1.422531 ATCACCAGCCTTTGCCAAAA 58.577 45.000 0.00 0.00 38.69 2.44
1830 1963 1.400242 GCAACAGACGAAATCACCAGC 60.400 52.381 0.00 0.00 0.00 4.85
1854 1988 2.584835 GCCCATAGGATATGGCAACA 57.415 50.000 9.86 0.00 45.53 3.33
1859 1993 4.305539 TGACAATGCCCATAGGATATGG 57.694 45.455 8.58 8.58 38.88 2.74
1861 1995 5.015497 TGGATTGACAATGCCCATAGGATAT 59.985 40.000 16.07 0.00 33.47 1.63
2029 2215 4.910195 TGATAAGGCTGTGATCACAACTT 58.090 39.130 31.49 31.49 41.33 2.66
2055 2242 8.945195 TCAAGATATTTCCCTGCAATTCATAT 57.055 30.769 0.00 0.00 0.00 1.78
2059 2246 6.276091 GGTTCAAGATATTTCCCTGCAATTC 58.724 40.000 0.00 0.00 0.00 2.17
2085 2272 6.418057 TTTCTGGTAGTGCATTTGGATTTT 57.582 33.333 0.00 0.00 0.00 1.82
2292 2479 0.907704 TATGTTCCCAGCGGGTCAGT 60.908 55.000 12.46 2.81 44.74 3.41
2353 2540 3.362040 TCCAAAATGGACAGGCAGG 57.638 52.632 0.00 0.00 42.67 4.85
2409 2856 2.097250 GCGAAACAAAAGCAGCAACATC 60.097 45.455 0.00 0.00 0.00 3.06
2425 2872 5.004922 ACAGAAAAACATTGGAAGCGAAA 57.995 34.783 0.00 0.00 0.00 3.46
2428 2875 5.732647 CGTATACAGAAAAACATTGGAAGCG 59.267 40.000 3.32 0.00 0.00 4.68
2430 2877 9.113876 GAAACGTATACAGAAAAACATTGGAAG 57.886 33.333 3.32 0.00 0.00 3.46
2451 2898 5.957366 TCTGTTTTCGGAAATGTTGGAAACG 60.957 40.000 3.67 0.00 40.20 3.60
2466 2913 4.033358 AGAGCGCATTATCTTCTGTTTTCG 59.967 41.667 11.47 0.00 0.00 3.46
2476 2923 8.090831 TCATTCTTATACAAGAGCGCATTATCT 58.909 33.333 11.47 0.00 41.75 1.98
2477 2924 8.165428 GTCATTCTTATACAAGAGCGCATTATC 58.835 37.037 11.47 0.00 41.75 1.75
2587 3034 5.365314 AGACCTCTGGTGATATCCTTTCTTC 59.635 44.000 0.00 0.00 35.25 2.87
2596 3043 3.837146 CCAGCATAGACCTCTGGTGATAT 59.163 47.826 13.75 0.00 42.07 1.63
2615 3062 3.347216 CTGTCCAGGTTTATGTTCCCAG 58.653 50.000 0.00 0.00 0.00 4.45
2758 3259 9.898152 TGACATATGTAGGTCATGAATAAACAA 57.102 29.630 8.71 0.00 41.42 2.83
2797 3298 6.398918 TCAGTTAAATCTGACAGCCTCTAAC 58.601 40.000 0.00 3.56 39.20 2.34
2804 3306 4.631813 ACGGATTCAGTTAAATCTGACAGC 59.368 41.667 11.37 0.00 42.30 4.40
2826 3328 4.766404 AAACTGCACCAGCTACATTAAC 57.234 40.909 0.00 0.00 42.74 2.01
2831 3333 2.374184 ACAAAAACTGCACCAGCTACA 58.626 42.857 0.00 0.00 42.74 2.74
2847 3349 7.392953 TGATGTTTGCTATGTCAGGAATACAAA 59.607 33.333 0.00 0.00 34.18 2.83
2851 3353 7.281841 TGATGATGTTTGCTATGTCAGGAATA 58.718 34.615 0.00 0.00 34.18 1.75
2869 3371 6.089820 CCAAACGAAAAATCAGGTTGATGATG 59.910 38.462 0.00 0.00 39.84 3.07
2873 3375 5.529581 ACCAAACGAAAAATCAGGTTGAT 57.470 34.783 0.00 0.00 39.09 2.57
2888 3390 6.460664 AACAAAAGTGAAAAGAACCAAACG 57.539 33.333 0.00 0.00 0.00 3.60
2893 3395 9.797556 AATACAGTAACAAAAGTGAAAAGAACC 57.202 29.630 0.00 0.00 0.00 3.62
2927 3429 8.265055 CCAGACAAAATACTTAGTTATCCAGGA 58.735 37.037 0.00 0.00 0.00 3.86
2945 3447 5.068460 CCTGTTTGTAATGGTTCCAGACAAA 59.932 40.000 20.85 20.85 35.38 2.83
2966 3468 4.703575 TCCTTCATTTCAGCAATTCTCCTG 59.296 41.667 0.00 0.00 0.00 3.86
3110 3612 0.178981 CCTCCCTTGGTGGCCATATG 60.179 60.000 9.72 3.71 31.53 1.78
3265 3767 3.627732 TCGAAGCAGAATAGATCCGAC 57.372 47.619 0.00 0.00 0.00 4.79
3284 3786 9.220767 GATTTGAGGAAGTACCCATACATTATC 57.779 37.037 0.00 0.00 40.05 1.75
3343 3845 2.403252 AAATTCTTCGGACCGAGCAT 57.597 45.000 17.51 7.64 37.14 3.79
3353 3855 6.183360 GCTGAATTGGCTGTAAAAATTCTTCG 60.183 38.462 8.36 0.00 39.79 3.79
3492 3994 2.311542 AGCCCATCATGTAACCCTTCAA 59.688 45.455 0.00 0.00 0.00 2.69
3498 4000 2.427095 GGTCAAAGCCCATCATGTAACC 59.573 50.000 0.00 0.00 0.00 2.85
3575 4077 2.033141 GCCCAGCTGTGCTTCTCA 59.967 61.111 14.44 0.00 36.40 3.27
3659 4161 1.779569 CTTCAAGCAGCAGCCTTTTG 58.220 50.000 0.00 0.00 43.56 2.44
3665 4167 0.736325 CAATGGCTTCAAGCAGCAGC 60.736 55.000 12.53 0.00 44.75 5.25
3785 4287 1.167155 TCCAGCGAGCTCCGTATCTC 61.167 60.000 8.47 0.00 41.15 2.75
3843 4345 9.078990 ACAGAAGAAAAGGGTATTTTCCTAAAG 57.921 33.333 8.95 1.05 38.74 1.85
3853 4355 4.666512 ACATGCACAGAAGAAAAGGGTAT 58.333 39.130 0.00 0.00 0.00 2.73
3855 4357 2.949447 ACATGCACAGAAGAAAAGGGT 58.051 42.857 0.00 0.00 0.00 4.34
3863 4366 5.413833 AGGTCAAGATTTACATGCACAGAAG 59.586 40.000 0.00 0.00 0.00 2.85
4016 4520 5.469373 TTACAGATTACAGAATGCAAGCG 57.531 39.130 0.00 0.00 42.53 4.68
4094 4600 4.051237 GCCAAATGGACTTTGACACTTTC 58.949 43.478 2.98 0.00 45.96 2.62
4115 4624 4.577693 TCAATCATAGCTTTGAGTCATGGC 59.422 41.667 12.51 9.07 0.00 4.40
4158 4667 1.392589 CCCTTGCGTTATTGCTCCAT 58.607 50.000 0.00 0.00 35.36 3.41
4159 4668 0.679640 CCCCTTGCGTTATTGCTCCA 60.680 55.000 0.00 0.00 35.36 3.86
4172 4681 2.352805 GTGTGGCTCCTCCCCTTG 59.647 66.667 0.00 0.00 0.00 3.61
4190 4699 2.491693 AGGGGCACGAATGTTTATGTTG 59.508 45.455 0.00 0.00 0.00 3.33
4191 4700 2.752903 GAGGGGCACGAATGTTTATGTT 59.247 45.455 0.00 0.00 0.00 2.71
4192 4701 2.290641 TGAGGGGCACGAATGTTTATGT 60.291 45.455 0.00 0.00 0.00 2.29
4193 4702 2.097466 GTGAGGGGCACGAATGTTTATG 59.903 50.000 0.00 0.00 37.83 1.90
4195 4704 1.816074 GTGAGGGGCACGAATGTTTA 58.184 50.000 0.00 0.00 37.83 2.01
4217 4726 1.506493 CTGATCAGGGCGCATTAGTC 58.494 55.000 15.38 1.71 0.00 2.59
4259 4881 1.545841 TAGACGATCATGGCGGCTAT 58.454 50.000 16.96 0.00 46.97 2.97
4262 4884 1.067416 TGTAGACGATCATGGCGGC 59.933 57.895 0.00 0.00 36.94 6.53
4264 4886 1.065551 TCAGTGTAGACGATCATGGCG 59.934 52.381 7.23 7.23 0.00 5.69
4282 4904 1.296392 CAGGCGTGATGAAGGGTCA 59.704 57.895 0.00 0.00 38.41 4.02
4322 4944 0.174845 CCATTACCGGAGTCGAAGCA 59.825 55.000 9.46 0.00 39.00 3.91
4345 4967 2.979678 GAGATCTTAGGGGCAATGGGTA 59.020 50.000 0.00 0.00 0.00 3.69
4373 4995 3.125316 GCACCTAACTGCACATAACAGAC 59.875 47.826 0.00 0.00 38.55 3.51
4503 5151 7.770897 AGCAGTTAACTGGAGTTTATGGAATAG 59.229 37.037 31.42 5.65 43.94 1.73
4551 5200 5.856156 TGTAACCATTTAAGTCAGGTTCGA 58.144 37.500 0.00 0.00 42.95 3.71
4561 5210 6.589907 GGAAAAGTGCCATGTAACCATTTAAG 59.410 38.462 0.00 0.00 0.00 1.85
4577 5226 0.110644 CGCAGAAGACGGAAAAGTGC 60.111 55.000 0.00 0.00 0.00 4.40
4578 5227 0.110644 GCGCAGAAGACGGAAAAGTG 60.111 55.000 0.30 0.00 0.00 3.16
4596 5245 5.595885 TCTATTGACAGTCTAAGCAGATGC 58.404 41.667 1.31 0.00 42.49 3.91
4614 5263 7.112122 TGAGTTTCTGCATTGGTGTATCTATT 58.888 34.615 0.00 0.00 0.00 1.73
4628 5277 6.691754 TTTCAACTGTATTGAGTTTCTGCA 57.308 33.333 0.00 0.00 33.75 4.41
4629 5278 8.579682 AATTTTCAACTGTATTGAGTTTCTGC 57.420 30.769 0.00 0.00 33.75 4.26
4699 5348 2.492088 TCACCGAAGAGAATCGATGTGT 59.508 45.455 0.00 0.00 45.48 3.72
4701 5350 4.392921 AATCACCGAAGAGAATCGATGT 57.607 40.909 0.00 0.00 45.48 3.06
4705 5354 5.725110 ATTCAAATCACCGAAGAGAATCG 57.275 39.130 0.00 0.00 42.67 3.34
4714 5363 9.884636 TCTTCTCTTTATTATTCAAATCACCGA 57.115 29.630 0.00 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.