Multiple sequence alignment - TraesCS6A01G138600

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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 TraesCS6A01G138600 chr6A 100.000 6859 0 0 1 6859 109982416 109989274 0.000000e+00 12667.0
1 TraesCS6A01G138600 chr6A 79.051 253 23 9 5890 6141 110331196 110331419 5.540000e-31 147.0
2 TraesCS6A01G138600 chr6B 94.381 6478 208 72 50 6464 175337280 175343664 0.000000e+00 9803.0
3 TraesCS6A01G138600 chr6B 91.071 392 18 7 6485 6859 175343745 175344136 1.320000e-141 514.0
4 TraesCS6A01G138600 chr6B 80.882 136 18 6 6007 6141 175709355 175709483 4.380000e-17 100.0
5 TraesCS6A01G138600 chr6D 94.176 6405 215 73 1 6337 91516258 91522572 0.000000e+00 9616.0
6 TraesCS6A01G138600 chr6D 90.706 538 33 6 6328 6859 91523935 91524461 0.000000e+00 701.0
7 TraesCS6A01G138600 chr7D 79.843 382 65 9 2867 3237 568952490 568952110 1.130000e-67 268.0
8 TraesCS6A01G138600 chr7D 85.938 64 6 3 300 360 568955287 568955224 1.600000e-06 65.8
9 TraesCS6A01G138600 chr7B 79.474 380 60 13 2866 3233 625299596 625299223 3.180000e-63 254.0
10 TraesCS6A01G138600 chr7B 100.000 32 0 0 329 360 625302380 625302349 7.430000e-05 60.2
11 TraesCS6A01G138600 chr7A 78.851 383 67 11 2866 3237 657719437 657719058 5.310000e-61 246.0
12 TraesCS6A01G138600 chr7A 100.000 32 0 0 329 360 657722291 657722260 7.430000e-05 60.2
13 TraesCS6A01G138600 chr4D 97.561 41 1 0 57 97 8394129 8394169 3.430000e-08 71.3


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 TraesCS6A01G138600 chr6A 109982416 109989274 6858 False 12667.0 12667 100.000 1 6859 1 chr6A.!!$F1 6858
1 TraesCS6A01G138600 chr6B 175337280 175344136 6856 False 5158.5 9803 92.726 50 6859 2 chr6B.!!$F2 6809
2 TraesCS6A01G138600 chr6D 91516258 91524461 8203 False 5158.5 9616 92.441 1 6859 2 chr6D.!!$F1 6858

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
108 113 0.034198 TGGCAAATCTTGACGTCCGA 59.966 50.0 14.12 10.09 43.38 4.55 F
1343 1412 0.259356 TTTTCCCCGGTGAAAGGTGT 59.741 50.0 12.00 0.00 35.77 4.16 F
1399 1471 0.035317 TCTGAACTTGGCATGCGTCT 59.965 50.0 12.44 0.00 0.00 4.18 F
1400 1472 0.167470 CTGAACTTGGCATGCGTCTG 59.833 55.0 12.44 4.38 0.00 3.51 F
1401 1473 0.250252 TGAACTTGGCATGCGTCTGA 60.250 50.0 12.44 0.00 0.00 3.27 F
1935 2016 0.435008 GTTCGGAGCAATATAGCGCG 59.565 55.0 0.00 0.00 40.15 6.86 F
3458 3563 0.521735 CCTGGCTCCGTTAAACTTGC 59.478 55.0 0.00 0.00 0.00 4.01 F
3854 3961 0.178990 GGCAACCAAGGGTGTCTCTT 60.179 55.0 5.96 0.00 35.34 2.85 F
4193 4300 0.333993 AGTCCTTGGATGCAGCCAAT 59.666 50.0 34.74 18.85 46.19 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1381 1453 0.167470 CAGACGCATGCCAAGTTCAG 59.833 55.000 13.15 0.00 0.00 3.02 R
2965 3069 0.605860 CAGCTGCAGCAAGAAGACCT 60.606 55.000 38.24 13.55 45.16 3.85 R
3091 3195 0.940126 CTTGCTCTGCAGAACACGTT 59.060 50.000 19.16 0.00 40.61 3.99 R
3117 3221 3.356290 AGCCAATGGTATGACAAACTCC 58.644 45.455 0.00 0.00 0.00 3.85 R
3440 3545 0.165944 CGCAAGTTTAACGGAGCCAG 59.834 55.000 4.51 0.00 0.00 4.85 R
3854 3961 1.556911 GTCAGAGGCTCAATCTCCCAA 59.443 52.381 18.26 0.00 31.96 4.12 R
4914 5021 0.465705 TAGAAGGCGCTGAATCCAGG 59.534 55.000 7.64 0.00 40.72 4.45 R
5694 5802 0.893447 ACCTCCTGTGGCGTAAGTAC 59.107 55.000 0.00 0.00 41.68 2.73 R
6102 6210 2.706890 ACATTAGGCAACACGGGTAAG 58.293 47.619 0.00 0.00 41.41 2.34 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
31 36 4.320023 TGCGGTAGAAACTAAATTCAGCA 58.680 39.130 0.00 0.00 0.00 4.41
34 39 6.072175 TGCGGTAGAAACTAAATTCAGCAAAT 60.072 34.615 0.00 0.00 30.72 2.32
103 108 6.761731 TTTTAAACATGGCAAATCTTGACG 57.238 33.333 0.00 0.00 43.38 4.35
104 109 5.446143 TTAAACATGGCAAATCTTGACGT 57.554 34.783 0.00 0.00 43.38 4.34
106 111 1.812571 ACATGGCAAATCTTGACGTCC 59.187 47.619 14.12 0.00 43.38 4.79
107 112 1.086696 ATGGCAAATCTTGACGTCCG 58.913 50.000 14.12 4.24 43.38 4.79
108 113 0.034198 TGGCAAATCTTGACGTCCGA 59.966 50.000 14.12 10.09 43.38 4.55
109 114 0.721718 GGCAAATCTTGACGTCCGAG 59.278 55.000 14.12 11.22 0.00 4.63
110 115 1.671850 GGCAAATCTTGACGTCCGAGA 60.672 52.381 14.12 16.26 39.53 4.04
111 116 1.390463 GCAAATCTTGACGTCCGAGAC 59.610 52.381 17.70 5.20 38.09 3.36
155 160 7.498900 CCTGCATGATAATTTACTTCAGTGGTA 59.501 37.037 0.00 0.00 0.00 3.25
156 161 8.208718 TGCATGATAATTTACTTCAGTGGTAC 57.791 34.615 0.00 0.00 0.00 3.34
232 274 1.235281 GGGTGCGGTGGAGAAGAAAC 61.235 60.000 0.00 0.00 0.00 2.78
280 322 4.729458 GCACGTTGCACAGAGAAAAAGTTA 60.729 41.667 5.30 0.00 44.26 2.24
418 463 2.156343 AGAAGAACAGCACCGAGAAC 57.844 50.000 0.00 0.00 0.00 3.01
438 484 4.724262 GAAGTGCACTTCCCCTCC 57.276 61.111 38.44 20.34 44.93 4.30
448 494 0.467290 CTTCCCCTCCCTCTCTCTCG 60.467 65.000 0.00 0.00 0.00 4.04
455 501 2.218603 CTCCCTCTCTCTCGCTTCTAC 58.781 57.143 0.00 0.00 0.00 2.59
456 502 1.841277 TCCCTCTCTCTCGCTTCTACT 59.159 52.381 0.00 0.00 0.00 2.57
457 503 2.158871 TCCCTCTCTCTCGCTTCTACTC 60.159 54.545 0.00 0.00 0.00 2.59
458 504 2.218603 CCTCTCTCTCGCTTCTACTCC 58.781 57.143 0.00 0.00 0.00 3.85
459 505 2.218603 CTCTCTCTCGCTTCTACTCCC 58.781 57.143 0.00 0.00 0.00 4.30
506 563 2.126424 GCAAGAAGCAGCAGCAGC 60.126 61.111 3.17 0.46 45.49 5.25
629 686 3.910490 GAGATCTGAGGCGCCGCT 61.910 66.667 30.49 16.83 0.00 5.52
989 1055 1.277557 CCTGTGTTGCCTTCTAGCTCT 59.722 52.381 0.00 0.00 0.00 4.09
1100 1169 1.748493 TCAGTTGGCAGTTTTCGCTTT 59.252 42.857 0.00 0.00 0.00 3.51
1101 1170 1.854126 CAGTTGGCAGTTTTCGCTTTG 59.146 47.619 0.00 0.00 0.00 2.77
1233 1302 7.598869 TCACTAATACACTTGATGACACTGTTC 59.401 37.037 0.00 0.00 0.00 3.18
1247 1316 4.451900 ACACTGTTCCTGGTTCTTTACAG 58.548 43.478 0.00 0.00 39.03 2.74
1252 1321 3.402628 TCCTGGTTCTTTACAGTCTGC 57.597 47.619 0.00 0.00 32.90 4.26
1273 1342 9.313118 GTCTGCCCATTTAAATGTTTATAAAGG 57.687 33.333 23.24 16.16 34.60 3.11
1312 1381 9.651718 CTTGTATTTAATAGTGCGGATTTTCTC 57.348 33.333 0.00 0.00 0.00 2.87
1343 1412 0.259356 TTTTCCCCGGTGAAAGGTGT 59.741 50.000 12.00 0.00 35.77 4.16
1345 1414 0.688487 TTCCCCGGTGAAAGGTGTAG 59.312 55.000 0.00 0.00 0.00 2.74
1351 1423 3.368116 CCCGGTGAAAGGTGTAGAAGTAG 60.368 52.174 0.00 0.00 0.00 2.57
1355 1427 6.264088 CGGTGAAAGGTGTAGAAGTAGTATC 58.736 44.000 0.00 0.00 0.00 2.24
1381 1453 4.016444 TGTAGGATGCAGGAACCATTTTC 58.984 43.478 0.00 0.00 0.00 2.29
1382 1454 3.463048 AGGATGCAGGAACCATTTTCT 57.537 42.857 0.00 0.00 0.00 2.52
1383 1455 3.094572 AGGATGCAGGAACCATTTTCTG 58.905 45.455 0.00 0.00 0.00 3.02
1384 1456 3.091545 GGATGCAGGAACCATTTTCTGA 58.908 45.455 0.00 0.00 0.00 3.27
1386 1458 4.488879 GATGCAGGAACCATTTTCTGAAC 58.511 43.478 0.00 0.00 0.00 3.18
1387 1459 3.565307 TGCAGGAACCATTTTCTGAACT 58.435 40.909 0.00 0.00 0.00 3.01
1389 1461 4.202141 TGCAGGAACCATTTTCTGAACTTG 60.202 41.667 0.00 0.00 0.00 3.16
1391 1463 3.321968 AGGAACCATTTTCTGAACTTGGC 59.678 43.478 14.58 3.54 0.00 4.52
1396 1468 2.420628 TTTTCTGAACTTGGCATGCG 57.579 45.000 12.44 0.00 0.00 4.73
1397 1469 1.317613 TTTCTGAACTTGGCATGCGT 58.682 45.000 12.44 0.52 0.00 5.24
1398 1470 0.874390 TTCTGAACTTGGCATGCGTC 59.126 50.000 12.44 4.44 0.00 5.19
1399 1471 0.035317 TCTGAACTTGGCATGCGTCT 59.965 50.000 12.44 0.00 0.00 4.18
1400 1472 0.167470 CTGAACTTGGCATGCGTCTG 59.833 55.000 12.44 4.38 0.00 3.51
1401 1473 0.250252 TGAACTTGGCATGCGTCTGA 60.250 50.000 12.44 0.00 0.00 3.27
1402 1474 0.874390 GAACTTGGCATGCGTCTGAA 59.126 50.000 12.44 0.00 0.00 3.02
1403 1475 1.266718 GAACTTGGCATGCGTCTGAAA 59.733 47.619 12.44 0.00 0.00 2.69
1404 1476 1.538047 ACTTGGCATGCGTCTGAAAT 58.462 45.000 12.44 0.00 0.00 2.17
1405 1477 2.710377 ACTTGGCATGCGTCTGAAATA 58.290 42.857 12.44 0.00 0.00 1.40
1406 1478 3.282021 ACTTGGCATGCGTCTGAAATAT 58.718 40.909 12.44 0.00 0.00 1.28
1407 1479 3.065786 ACTTGGCATGCGTCTGAAATATG 59.934 43.478 12.44 0.00 0.00 1.78
1408 1480 1.334556 TGGCATGCGTCTGAAATATGC 59.665 47.619 12.44 10.85 42.43 3.14
1409 1481 1.605710 GGCATGCGTCTGAAATATGCT 59.394 47.619 12.44 0.00 42.68 3.79
1410 1482 2.033801 GGCATGCGTCTGAAATATGCTT 59.966 45.455 12.44 0.00 42.68 3.91
1411 1483 3.294943 GCATGCGTCTGAAATATGCTTC 58.705 45.455 0.00 0.00 40.58 3.86
1412 1484 3.851105 GCATGCGTCTGAAATATGCTTCC 60.851 47.826 0.00 0.00 40.58 3.46
1413 1485 3.266510 TGCGTCTGAAATATGCTTCCT 57.733 42.857 0.00 0.00 0.00 3.36
1414 1486 4.400529 TGCGTCTGAAATATGCTTCCTA 57.599 40.909 0.00 0.00 0.00 2.94
1415 1487 4.371786 TGCGTCTGAAATATGCTTCCTAG 58.628 43.478 0.00 0.00 0.00 3.02
1416 1488 4.099419 TGCGTCTGAAATATGCTTCCTAGA 59.901 41.667 0.00 0.00 0.00 2.43
1439 1511 6.702282 AGAGCTAGTGTTGTTAACTGAACTTC 59.298 38.462 7.22 3.08 38.98 3.01
1441 1513 6.821665 AGCTAGTGTTGTTAACTGAACTTCAA 59.178 34.615 7.22 0.00 38.98 2.69
1442 1514 7.499232 AGCTAGTGTTGTTAACTGAACTTCAAT 59.501 33.333 7.22 0.00 38.98 2.57
1452 1526 9.974750 GTTAACTGAACTTCAATTATCTGCTAC 57.025 33.333 0.00 0.00 34.96 3.58
1453 1527 7.617041 AACTGAACTTCAATTATCTGCTACC 57.383 36.000 0.00 0.00 0.00 3.18
1457 1531 5.297569 ACTTCAATTATCTGCTACCCCTC 57.702 43.478 0.00 0.00 0.00 4.30
1460 1534 3.648067 TCAATTATCTGCTACCCCTCCTG 59.352 47.826 0.00 0.00 0.00 3.86
1483 1559 4.716943 CTCAGACGATTTTCCTTTTCAGC 58.283 43.478 0.00 0.00 0.00 4.26
1498 1574 2.381725 TCAGCATCAGAAGAGCACAG 57.618 50.000 0.00 0.00 0.00 3.66
1556 1632 1.172180 CCCTCGTTTCTTTGCCTGCA 61.172 55.000 0.00 0.00 0.00 4.41
1606 1682 1.620819 AGGTCACAGTGAGCAGGTTAG 59.379 52.381 29.78 0.00 46.52 2.34
1607 1683 1.338200 GGTCACAGTGAGCAGGTTAGG 60.338 57.143 24.90 0.00 43.79 2.69
1639 1718 7.670140 TCCTCTCAGTACAGAGATTTAACTGAA 59.330 37.037 17.28 0.00 44.22 3.02
1668 1748 9.727627 GTTGTAGATACATACAAGTACCAGTAC 57.272 37.037 0.00 0.00 44.18 2.73
1669 1749 9.465199 TTGTAGATACATACAAGTACCAGTACA 57.535 33.333 10.41 0.00 39.98 2.90
1671 1751 9.118300 GTAGATACATACAAGTACCAGTACAGT 57.882 37.037 10.41 10.09 38.48 3.55
1681 1761 7.283580 ACAAGTACCAGTACAGTTTGCAAAATA 59.716 33.333 14.67 4.25 38.48 1.40
1694 1774 8.866956 CAGTTTGCAAAATAGATTTCATTCTCC 58.133 33.333 14.67 0.00 0.00 3.71
1696 1776 6.469782 TGCAAAATAGATTTCATTCTCCCC 57.530 37.500 0.00 0.00 0.00 4.81
1697 1777 5.363580 TGCAAAATAGATTTCATTCTCCCCC 59.636 40.000 0.00 0.00 0.00 5.40
1698 1778 5.600069 GCAAAATAGATTTCATTCTCCCCCT 59.400 40.000 0.00 0.00 0.00 4.79
1699 1779 6.239148 GCAAAATAGATTTCATTCTCCCCCTC 60.239 42.308 0.00 0.00 0.00 4.30
1700 1780 5.590976 AATAGATTTCATTCTCCCCCTCC 57.409 43.478 0.00 0.00 0.00 4.30
1701 1781 3.157556 AGATTTCATTCTCCCCCTCCT 57.842 47.619 0.00 0.00 0.00 3.69
1702 1782 4.302004 AGATTTCATTCTCCCCCTCCTA 57.698 45.455 0.00 0.00 0.00 2.94
1703 1783 4.849129 AGATTTCATTCTCCCCCTCCTAT 58.151 43.478 0.00 0.00 0.00 2.57
1704 1784 5.238736 AGATTTCATTCTCCCCCTCCTATT 58.761 41.667 0.00 0.00 0.00 1.73
1705 1785 4.796110 TTTCATTCTCCCCCTCCTATTG 57.204 45.455 0.00 0.00 0.00 1.90
1706 1786 3.438131 TCATTCTCCCCCTCCTATTGT 57.562 47.619 0.00 0.00 0.00 2.71
1707 1787 3.048600 TCATTCTCCCCCTCCTATTGTG 58.951 50.000 0.00 0.00 0.00 3.33
1712 1792 2.846827 CTCCCCCTCCTATTGTGAGTTT 59.153 50.000 0.00 0.00 0.00 2.66
1721 1801 6.150140 CCTCCTATTGTGAGTTTCCTTTTGAG 59.850 42.308 0.00 0.00 0.00 3.02
1740 1820 1.072806 AGTTCCATGTCTTGCAGCAGA 59.927 47.619 0.00 0.00 0.00 4.26
1745 1825 2.753452 CCATGTCTTGCAGCAGATCTTT 59.247 45.455 0.00 0.00 0.00 2.52
1746 1826 3.943381 CCATGTCTTGCAGCAGATCTTTA 59.057 43.478 0.00 0.00 0.00 1.85
1845 1926 4.036262 TCAACAAACAAGGAAATGGAGTCG 59.964 41.667 0.00 0.00 0.00 4.18
1866 1947 2.039084 GCAGATCCCCAACTATCCGAAT 59.961 50.000 0.00 0.00 0.00 3.34
1873 1954 2.548920 CCCAACTATCCGAATCTGCCTC 60.549 54.545 0.00 0.00 0.00 4.70
1934 2015 1.784525 AGTTCGGAGCAATATAGCGC 58.215 50.000 0.00 0.00 40.15 5.92
1935 2016 0.435008 GTTCGGAGCAATATAGCGCG 59.565 55.000 0.00 0.00 40.15 6.86
1943 2024 2.936498 AGCAATATAGCGCGTCTGTTTT 59.064 40.909 8.43 2.78 40.15 2.43
1944 2025 3.029074 GCAATATAGCGCGTCTGTTTTG 58.971 45.455 8.43 15.01 31.49 2.44
1945 2026 3.485216 GCAATATAGCGCGTCTGTTTTGT 60.485 43.478 20.54 0.00 31.17 2.83
1946 2027 4.260051 GCAATATAGCGCGTCTGTTTTGTA 60.260 41.667 20.54 2.60 31.17 2.41
1948 2029 6.418956 CAATATAGCGCGTCTGTTTTGTAAT 58.581 36.000 8.43 0.00 0.00 1.89
1949 2030 4.939509 ATAGCGCGTCTGTTTTGTAATT 57.060 36.364 8.43 0.00 0.00 1.40
1950 2031 7.703298 ATATAGCGCGTCTGTTTTGTAATTA 57.297 32.000 8.43 0.00 0.00 1.40
1952 2033 4.460505 AGCGCGTCTGTTTTGTAATTAAC 58.539 39.130 8.43 0.00 0.00 2.01
2201 2301 6.763303 AGCAAACAACCAACGAATTATTTC 57.237 33.333 0.00 0.00 0.00 2.17
2291 2391 1.966451 GGTGTTTCCTCCGCTGGTG 60.966 63.158 0.00 0.00 0.00 4.17
2332 2432 7.574592 GCAATTCTCTGCTGTATCTTTTGAACT 60.575 37.037 0.00 0.00 39.34 3.01
2342 2442 7.746475 GCTGTATCTTTTGAACTGTCATGTTAC 59.254 37.037 0.00 0.00 32.48 2.50
2524 2624 5.238650 TGCAGCTACTTTTCTTGGTTCTTAC 59.761 40.000 0.00 0.00 0.00 2.34
2580 2680 9.128404 CGTATAGCCTTGTATATACCCTCATTA 57.872 37.037 10.38 0.00 33.25 1.90
2596 2696 4.445453 CTCATTACATACAGCCTTGCTCA 58.555 43.478 0.00 0.00 36.40 4.26
2731 2831 3.512033 ATAAGTGCGAAGAGACTGGTC 57.488 47.619 0.00 0.00 0.00 4.02
2779 2879 5.324409 TGGTACATCTGCTCTTCCAATTTT 58.676 37.500 0.00 0.00 0.00 1.82
2781 2881 6.945435 TGGTACATCTGCTCTTCCAATTTTTA 59.055 34.615 0.00 0.00 0.00 1.52
2783 2883 8.470002 GGTACATCTGCTCTTCCAATTTTTATT 58.530 33.333 0.00 0.00 0.00 1.40
2881 2985 5.078949 TGGTTGATCAGGAATGACAACAAT 58.921 37.500 17.33 0.00 41.37 2.71
3091 3195 6.190587 TCCTCTCAGATACTCAGATTTGTCA 58.809 40.000 0.00 0.00 0.00 3.58
3117 3221 2.359107 TGCAGAGCAAGCCCTTCG 60.359 61.111 0.00 0.00 34.76 3.79
3372 3477 8.177119 TGCCTTTTATATCTTGTTCTTTGTGT 57.823 30.769 0.00 0.00 0.00 3.72
3373 3478 8.637986 TGCCTTTTATATCTTGTTCTTTGTGTT 58.362 29.630 0.00 0.00 0.00 3.32
3379 3484 7.986085 ATATCTTGTTCTTTGTGTTAGTGCT 57.014 32.000 0.00 0.00 0.00 4.40
3380 3485 6.699575 ATCTTGTTCTTTGTGTTAGTGCTT 57.300 33.333 0.00 0.00 0.00 3.91
3381 3486 6.509418 TCTTGTTCTTTGTGTTAGTGCTTT 57.491 33.333 0.00 0.00 0.00 3.51
3382 3487 6.321717 TCTTGTTCTTTGTGTTAGTGCTTTG 58.678 36.000 0.00 0.00 0.00 2.77
3383 3488 5.637006 TGTTCTTTGTGTTAGTGCTTTGT 57.363 34.783 0.00 0.00 0.00 2.83
3384 3489 6.745159 TGTTCTTTGTGTTAGTGCTTTGTA 57.255 33.333 0.00 0.00 0.00 2.41
3440 3545 6.318900 CCCTAAATTATCACCACTTCTTCACC 59.681 42.308 0.00 0.00 0.00 4.02
3458 3563 0.521735 CCTGGCTCCGTTAAACTTGC 59.478 55.000 0.00 0.00 0.00 4.01
3500 3605 8.830201 ATATCTATCTAGCTTGTTTTCTGCTG 57.170 34.615 0.00 0.00 37.62 4.41
3502 3607 6.102663 TCTATCTAGCTTGTTTTCTGCTGTC 58.897 40.000 0.00 0.00 37.62 3.51
3679 3786 9.859427 TTGAAATAAGAATTATCTGTTTGCCAG 57.141 29.630 0.00 0.00 41.21 4.85
3701 3808 4.716003 GGCGGACCTTTACTTGCT 57.284 55.556 0.00 0.00 0.00 3.91
3854 3961 0.178990 GGCAACCAAGGGTGTCTCTT 60.179 55.000 5.96 0.00 35.34 2.85
3911 4018 1.694150 TCATCTCCTTTCCCTATGCGG 59.306 52.381 0.00 0.00 0.00 5.69
3957 4064 5.940470 GGATTGCCTTCCTTATATGGTACAG 59.060 44.000 4.67 0.90 35.41 2.74
4012 4119 8.729756 TCAAACGATATCAGTGAACAATCAATT 58.270 29.630 3.12 0.00 37.30 2.32
4143 4250 1.970640 GATGGAGCAAACCCAGGTTTT 59.029 47.619 12.13 0.00 44.84 2.43
4154 4261 3.490348 ACCCAGGTTTTCAGTCATTCAG 58.510 45.455 0.00 0.00 0.00 3.02
4193 4300 0.333993 AGTCCTTGGATGCAGCCAAT 59.666 50.000 34.74 18.85 46.19 3.16
4900 5007 4.294416 TCTAGCTCTCATGTTAACTCGC 57.706 45.455 7.22 0.94 0.00 5.03
4914 5021 1.567504 ACTCGCCGCATATACAACAC 58.432 50.000 0.00 0.00 0.00 3.32
4915 5022 0.859232 CTCGCCGCATATACAACACC 59.141 55.000 0.00 0.00 0.00 4.16
5235 5342 4.934602 GGCTGCTTAGATGAATCAGGATAC 59.065 45.833 0.00 0.00 32.82 2.24
5322 5429 5.667466 GAATTGACTTACCCACCTAATCGA 58.333 41.667 0.00 0.00 0.00 3.59
5324 5431 5.687166 TTGACTTACCCACCTAATCGAAT 57.313 39.130 0.00 0.00 0.00 3.34
5596 5704 5.069781 TGGCAGTAAGTTTTTAGGCAACAAT 59.930 36.000 0.00 0.00 41.41 2.71
5672 5780 3.531538 TGTAATCTGCAGGGAATTCGTC 58.468 45.455 15.13 2.47 0.00 4.20
5694 5802 4.332543 TCAACAGCGTATCTTGCATAAAGG 59.667 41.667 0.00 0.00 36.46 3.11
6102 6210 6.254522 TGTAGGGCCTCTAATATTAGACTCC 58.745 44.000 19.23 19.83 34.99 3.85
6136 6246 5.295950 TGCCTAATGTTTGTTTTGGTCATG 58.704 37.500 0.00 0.00 0.00 3.07
6223 6333 4.380550 GCCTTTATGCTGTGGTAAAACTCC 60.381 45.833 0.00 0.00 0.00 3.85
6286 6396 5.534654 AGTGACTAGTGAGCTAATCCTGATC 59.465 44.000 0.00 0.00 0.00 2.92
6297 6407 5.190528 AGCTAATCCTGATCAACTCTCCAAA 59.809 40.000 0.00 0.00 0.00 3.28
6343 7825 3.066342 TGAGCTAATCCTTCTACGTTCGG 59.934 47.826 0.00 0.00 0.00 4.30
6357 7839 9.188588 CTTCTACGTTCGGCTTGAAATATATAA 57.811 33.333 0.00 0.00 38.60 0.98
6468 7954 8.607459 CATTTAGCAGTGTTCTCAGTAATAAGG 58.393 37.037 0.00 0.00 0.00 2.69
6631 8194 9.815936 CATTGAATTAATGGCTGAAAGAAAAAC 57.184 29.630 0.00 0.00 41.99 2.43
6658 8222 1.483595 TTCTCCTGAGGCCAGTGGTG 61.484 60.000 11.74 4.56 38.74 4.17
6710 8278 6.586344 TCTCCCAATCACATATCAGTTTCTC 58.414 40.000 0.00 0.00 0.00 2.87
6713 8281 6.066690 CCCAATCACATATCAGTTTCTCCAT 58.933 40.000 0.00 0.00 0.00 3.41
6714 8282 6.548622 CCCAATCACATATCAGTTTCTCCATT 59.451 38.462 0.00 0.00 0.00 3.16
6733 8301 0.036732 TCCCTCATGCCTGTTGTGAC 59.963 55.000 0.00 0.00 0.00 3.67
6745 8313 0.249489 GTTGTGACCTCAGTGCTCGT 60.249 55.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 7.602753 ACCATTTGCTGAATTTAGTTTCTACC 58.397 34.615 0.00 0.00 0.00 3.18
106 111 3.416277 CACAACATAATTTGCCGTCTCG 58.584 45.455 0.00 0.00 0.00 4.04
107 112 3.758300 CCACAACATAATTTGCCGTCTC 58.242 45.455 0.00 0.00 0.00 3.36
108 113 2.094752 GCCACAACATAATTTGCCGTCT 60.095 45.455 0.00 0.00 0.00 4.18
109 114 2.258755 GCCACAACATAATTTGCCGTC 58.741 47.619 0.00 0.00 0.00 4.79
110 115 1.067213 GGCCACAACATAATTTGCCGT 60.067 47.619 0.00 0.00 0.00 5.68
111 116 1.204467 AGGCCACAACATAATTTGCCG 59.796 47.619 5.01 0.00 42.16 5.69
117 122 2.737544 TCATGCAGGCCACAACATAAT 58.262 42.857 5.01 0.00 0.00 1.28
123 128 4.955450 AGTAAATTATCATGCAGGCCACAA 59.045 37.500 5.01 0.00 0.00 3.33
155 160 5.306394 GGCTGAAAAAGGTACACTTCTAGT 58.694 41.667 0.00 0.00 38.85 2.57
156 161 4.389077 CGGCTGAAAAAGGTACACTTCTAG 59.611 45.833 0.00 0.00 38.85 2.43
280 322 9.507329 TCTTCTCTATCATGCACTTTAAAAACT 57.493 29.630 0.00 0.00 0.00 2.66
438 484 2.218603 GGAGTAGAAGCGAGAGAGAGG 58.781 57.143 0.00 0.00 0.00 3.69
455 501 0.665835 CTGCTCGTGCTACTAGGGAG 59.334 60.000 11.19 0.00 40.48 4.30
456 502 1.384989 GCTGCTCGTGCTACTAGGGA 61.385 60.000 11.19 0.00 40.48 4.20
457 503 1.066587 GCTGCTCGTGCTACTAGGG 59.933 63.158 11.19 0.00 40.48 3.53
458 504 1.066587 GGCTGCTCGTGCTACTAGG 59.933 63.158 11.19 0.00 40.48 3.02
459 505 0.248825 CTGGCTGCTCGTGCTACTAG 60.249 60.000 11.19 6.20 40.48 2.57
506 563 2.360100 AGCAAGCTGCCTCTGCTG 60.360 61.111 17.46 0.00 46.52 4.41
629 686 2.125147 CCCGATTGCGAGAAGGCA 60.125 61.111 0.00 0.00 42.12 4.75
747 811 4.748409 GAGCCTCTCGATCCAAGC 57.252 61.111 0.00 0.00 0.00 4.01
779 843 1.520787 CGGTCCTTTTCGATCCGGG 60.521 63.158 0.00 0.00 37.92 5.73
818 883 4.521062 CCTCTTGCCTCCGCTCCG 62.521 72.222 0.00 0.00 35.36 4.63
819 884 2.470938 AAACCTCTTGCCTCCGCTCC 62.471 60.000 0.00 0.00 35.36 4.70
820 885 1.003233 AAACCTCTTGCCTCCGCTC 60.003 57.895 0.00 0.00 35.36 5.03
821 886 1.302832 CAAACCTCTTGCCTCCGCT 60.303 57.895 0.00 0.00 35.36 5.52
989 1055 3.488216 CGAGAGATTCATGCTTGACGAGA 60.488 47.826 1.02 0.00 0.00 4.04
1047 1116 1.386525 TAATACCTTCGGGCGACGCT 61.387 55.000 20.77 0.00 43.86 5.07
1056 1125 6.422776 AATGCAAAGACAGTAATACCTTCG 57.577 37.500 0.00 0.00 0.00 3.79
1100 1169 4.319139 TTGCACAGATTTAAAGCAAGCA 57.681 36.364 6.19 9.44 39.95 3.91
1101 1170 4.925054 TGATTGCACAGATTTAAAGCAAGC 59.075 37.500 16.13 16.13 46.73 4.01
1233 1302 2.427506 GGCAGACTGTAAAGAACCAGG 58.572 52.381 3.99 0.00 32.90 4.45
1247 1316 9.313118 CCTTTATAAACATTTAAATGGGCAGAC 57.687 33.333 27.43 0.00 40.70 3.51
1285 1354 9.391006 AGAAAATCCGCACTATTAAATACAAGA 57.609 29.630 0.00 0.00 0.00 3.02
1286 1355 9.651718 GAGAAAATCCGCACTATTAAATACAAG 57.348 33.333 0.00 0.00 0.00 3.16
1287 1356 8.332464 CGAGAAAATCCGCACTATTAAATACAA 58.668 33.333 0.00 0.00 0.00 2.41
1288 1357 7.847487 CGAGAAAATCCGCACTATTAAATACA 58.153 34.615 0.00 0.00 0.00 2.29
1322 1391 1.272212 CACCTTTCACCGGGGAAAATG 59.728 52.381 30.68 25.95 36.42 2.32
1323 1392 1.133294 ACACCTTTCACCGGGGAAAAT 60.133 47.619 30.68 19.79 36.42 1.82
1324 1393 0.259356 ACACCTTTCACCGGGGAAAA 59.741 50.000 30.68 15.77 36.42 2.29
1332 1401 7.034397 GTGATACTACTTCTACACCTTTCACC 58.966 42.308 0.00 0.00 0.00 4.02
1343 1412 7.778382 TGCATCCTACAAGTGATACTACTTCTA 59.222 37.037 0.00 0.00 38.78 2.10
1345 1414 6.806751 TGCATCCTACAAGTGATACTACTTC 58.193 40.000 0.00 0.00 38.78 3.01
1351 1423 4.672587 TCCTGCATCCTACAAGTGATAC 57.327 45.455 0.00 0.00 0.00 2.24
1355 1427 2.290260 TGGTTCCTGCATCCTACAAGTG 60.290 50.000 0.00 0.00 0.00 3.16
1381 1453 0.167470 CAGACGCATGCCAAGTTCAG 59.833 55.000 13.15 0.00 0.00 3.02
1382 1454 0.250252 TCAGACGCATGCCAAGTTCA 60.250 50.000 13.15 0.00 0.00 3.18
1383 1455 0.874390 TTCAGACGCATGCCAAGTTC 59.126 50.000 13.15 0.99 0.00 3.01
1384 1456 1.317613 TTTCAGACGCATGCCAAGTT 58.682 45.000 13.15 0.00 0.00 2.66
1386 1458 3.624900 CATATTTCAGACGCATGCCAAG 58.375 45.455 13.15 0.00 0.00 3.61
1387 1459 2.223548 GCATATTTCAGACGCATGCCAA 60.224 45.455 13.15 0.00 36.78 4.52
1389 1461 1.605710 AGCATATTTCAGACGCATGCC 59.394 47.619 13.15 0.00 42.30 4.40
1391 1463 3.562973 AGGAAGCATATTTCAGACGCATG 59.437 43.478 0.00 0.00 0.00 4.06
1396 1468 5.852827 AGCTCTAGGAAGCATATTTCAGAC 58.147 41.667 6.24 0.00 45.00 3.51
1397 1469 6.780031 ACTAGCTCTAGGAAGCATATTTCAGA 59.220 38.462 6.24 0.00 45.00 3.27
1398 1470 6.867816 CACTAGCTCTAGGAAGCATATTTCAG 59.132 42.308 6.24 0.00 45.00 3.02
1399 1471 6.325028 ACACTAGCTCTAGGAAGCATATTTCA 59.675 38.462 6.24 0.00 45.00 2.69
1400 1472 6.754193 ACACTAGCTCTAGGAAGCATATTTC 58.246 40.000 6.24 0.00 45.00 2.17
1401 1473 6.739331 ACACTAGCTCTAGGAAGCATATTT 57.261 37.500 6.24 0.00 45.00 1.40
1402 1474 6.098982 ACAACACTAGCTCTAGGAAGCATATT 59.901 38.462 6.24 0.00 45.00 1.28
1403 1475 5.600484 ACAACACTAGCTCTAGGAAGCATAT 59.400 40.000 6.24 0.00 45.00 1.78
1404 1476 4.956700 ACAACACTAGCTCTAGGAAGCATA 59.043 41.667 6.24 0.00 45.00 3.14
1405 1477 3.772025 ACAACACTAGCTCTAGGAAGCAT 59.228 43.478 6.24 0.00 45.00 3.79
1406 1478 3.165875 ACAACACTAGCTCTAGGAAGCA 58.834 45.455 6.24 0.00 45.00 3.91
1407 1479 3.878160 ACAACACTAGCTCTAGGAAGC 57.122 47.619 8.60 0.00 42.82 3.86
1408 1480 6.809196 CAGTTAACAACACTAGCTCTAGGAAG 59.191 42.308 8.61 1.54 37.49 3.46
1409 1481 6.492429 TCAGTTAACAACACTAGCTCTAGGAA 59.508 38.462 8.61 0.00 37.49 3.36
1410 1482 6.008331 TCAGTTAACAACACTAGCTCTAGGA 58.992 40.000 8.61 0.00 37.49 2.94
1411 1483 6.268825 TCAGTTAACAACACTAGCTCTAGG 57.731 41.667 8.61 1.13 37.49 3.02
1412 1484 7.371936 AGTTCAGTTAACAACACTAGCTCTAG 58.628 38.462 8.61 2.55 40.83 2.43
1413 1485 7.286215 AGTTCAGTTAACAACACTAGCTCTA 57.714 36.000 8.61 0.00 40.83 2.43
1414 1486 6.163135 AGTTCAGTTAACAACACTAGCTCT 57.837 37.500 8.61 0.00 40.83 4.09
1415 1487 6.479001 TGAAGTTCAGTTAACAACACTAGCTC 59.521 38.462 8.61 2.28 40.83 4.09
1416 1488 6.346096 TGAAGTTCAGTTAACAACACTAGCT 58.654 36.000 8.61 0.00 40.83 3.32
1439 1511 3.808618 GCAGGAGGGGTAGCAGATAATTG 60.809 52.174 0.00 0.00 0.00 2.32
1441 1513 1.981495 GCAGGAGGGGTAGCAGATAAT 59.019 52.381 0.00 0.00 0.00 1.28
1442 1514 1.062121 AGCAGGAGGGGTAGCAGATAA 60.062 52.381 0.00 0.00 0.00 1.75
1448 1522 1.381872 TCTGAGCAGGAGGGGTAGC 60.382 63.158 0.00 0.00 0.00 3.58
1452 1526 1.333636 AATCGTCTGAGCAGGAGGGG 61.334 60.000 0.00 0.00 0.00 4.79
1453 1527 0.539051 AAATCGTCTGAGCAGGAGGG 59.461 55.000 0.00 0.00 0.00 4.30
1457 1531 2.393271 AGGAAAATCGTCTGAGCAGG 57.607 50.000 0.00 0.00 0.00 4.85
1460 1534 4.716943 CTGAAAAGGAAAATCGTCTGAGC 58.283 43.478 0.00 0.00 0.00 4.26
1498 1574 3.191371 CCACAACTCTGAATTTAGGCACC 59.809 47.826 0.00 0.00 0.00 5.01
1508 1584 1.891919 GGCGTGCCACAACTCTGAA 60.892 57.895 5.89 0.00 35.81 3.02
1535 1611 0.537371 CAGGCAAAGAAACGAGGGGT 60.537 55.000 0.00 0.00 0.00 4.95
1565 1641 2.785562 TGAGGAAAATACAACACCCGG 58.214 47.619 0.00 0.00 0.00 5.73
1606 1682 5.197451 TCTCTGTACTGAGAGGAAGAATCC 58.803 45.833 23.99 0.00 40.10 3.01
1607 1683 6.959639 ATCTCTGTACTGAGAGGAAGAATC 57.040 41.667 29.03 0.00 44.98 2.52
1639 1718 9.817809 CTGGTACTTGTATGTATCTACAACATT 57.182 33.333 0.00 0.00 39.99 2.71
1650 1729 6.869913 GCAAACTGTACTGGTACTTGTATGTA 59.130 38.462 11.44 0.00 37.00 2.29
1651 1730 5.699458 GCAAACTGTACTGGTACTTGTATGT 59.301 40.000 11.44 0.00 37.00 2.29
1652 1731 5.699001 TGCAAACTGTACTGGTACTTGTATG 59.301 40.000 11.44 6.31 37.00 2.39
1653 1732 5.860611 TGCAAACTGTACTGGTACTTGTAT 58.139 37.500 11.44 1.85 37.00 2.29
1668 1748 8.866956 GGAGAATGAAATCTATTTTGCAAACTG 58.133 33.333 12.39 5.19 0.00 3.16
1669 1749 8.037166 GGGAGAATGAAATCTATTTTGCAAACT 58.963 33.333 12.39 9.52 0.00 2.66
1671 1751 7.330262 GGGGAGAATGAAATCTATTTTGCAAA 58.670 34.615 8.05 8.05 0.00 3.68
1681 1761 3.157556 AGGAGGGGGAGAATGAAATCT 57.842 47.619 0.00 0.00 0.00 2.40
1691 1771 2.182516 ACTCACAATAGGAGGGGGAG 57.817 55.000 0.00 0.00 36.70 4.30
1694 1774 2.846827 AGGAAACTCACAATAGGAGGGG 59.153 50.000 0.00 0.00 32.90 4.79
1696 1776 6.003950 TCAAAAGGAAACTCACAATAGGAGG 58.996 40.000 0.00 0.00 42.68 4.30
1697 1777 6.712547 ACTCAAAAGGAAACTCACAATAGGAG 59.287 38.462 0.00 0.00 42.68 3.69
1698 1778 6.601332 ACTCAAAAGGAAACTCACAATAGGA 58.399 36.000 0.00 0.00 42.68 2.94
1699 1779 6.884280 ACTCAAAAGGAAACTCACAATAGG 57.116 37.500 0.00 0.00 42.68 2.57
1700 1780 7.013274 TGGAACTCAAAAGGAAACTCACAATAG 59.987 37.037 0.00 0.00 42.68 1.73
1701 1781 6.831353 TGGAACTCAAAAGGAAACTCACAATA 59.169 34.615 0.00 0.00 42.68 1.90
1702 1782 5.656416 TGGAACTCAAAAGGAAACTCACAAT 59.344 36.000 0.00 0.00 42.68 2.71
1703 1783 5.013547 TGGAACTCAAAAGGAAACTCACAA 58.986 37.500 0.00 0.00 42.68 3.33
1704 1784 4.594970 TGGAACTCAAAAGGAAACTCACA 58.405 39.130 0.00 0.00 42.68 3.58
1705 1785 5.067805 ACATGGAACTCAAAAGGAAACTCAC 59.932 40.000 0.00 0.00 42.68 3.51
1706 1786 5.200483 ACATGGAACTCAAAAGGAAACTCA 58.800 37.500 0.00 0.00 42.68 3.41
1707 1787 5.532779 AGACATGGAACTCAAAAGGAAACTC 59.467 40.000 0.00 0.00 42.68 3.01
1712 1792 3.569701 GCAAGACATGGAACTCAAAAGGA 59.430 43.478 0.00 0.00 0.00 3.36
1721 1801 1.527034 TCTGCTGCAAGACATGGAAC 58.473 50.000 3.02 0.00 34.07 3.62
1773 1853 7.179516 TCACTATGTAAGTCCATTGGTGTCTAA 59.820 37.037 1.86 0.00 35.76 2.10
1774 1854 6.666113 TCACTATGTAAGTCCATTGGTGTCTA 59.334 38.462 1.86 0.00 35.76 2.59
1781 1861 9.088512 GTAGAAACTCACTATGTAAGTCCATTG 57.911 37.037 0.00 0.00 35.76 2.82
1795 1875 5.535406 CCGATACCTATGGTAGAAACTCACT 59.465 44.000 2.82 0.00 41.83 3.41
1845 1926 1.048601 TCGGATAGTTGGGGATCTGC 58.951 55.000 0.00 0.00 0.00 4.26
1866 1947 2.224378 GCATATAAGCTGTGGAGGCAGA 60.224 50.000 0.00 0.00 38.70 4.26
1873 1954 2.033801 GCAGTTGGCATATAAGCTGTGG 59.966 50.000 0.00 0.00 43.97 4.17
1923 2004 3.029074 CAAAACAGACGCGCTATATTGC 58.971 45.455 5.73 0.00 0.00 3.56
1925 2006 6.598753 ATTACAAAACAGACGCGCTATATT 57.401 33.333 5.73 0.00 0.00 1.28
1931 2012 4.317291 CAGTTAATTACAAAACAGACGCGC 59.683 41.667 5.73 0.00 0.00 6.86
1934 2015 7.847487 TGAGACAGTTAATTACAAAACAGACG 58.153 34.615 0.00 0.00 0.00 4.18
1946 2027 7.809806 GCAGCAAAGTTTATGAGACAGTTAATT 59.190 33.333 4.58 0.00 0.00 1.40
1948 2029 6.486657 AGCAGCAAAGTTTATGAGACAGTTAA 59.513 34.615 0.00 0.00 0.00 2.01
1949 2030 5.997746 AGCAGCAAAGTTTATGAGACAGTTA 59.002 36.000 0.00 0.00 0.00 2.24
1950 2031 4.823989 AGCAGCAAAGTTTATGAGACAGTT 59.176 37.500 0.00 0.00 0.00 3.16
1952 2033 5.368256 AAGCAGCAAAGTTTATGAGACAG 57.632 39.130 0.00 0.00 0.00 3.51
2201 2301 5.042593 TCACTTGCAGTTAATGTTTTGCAG 58.957 37.500 0.00 0.00 46.02 4.41
2225 2325 2.579624 ATCCACCATGGGTACTGGTA 57.420 50.000 18.09 5.35 45.23 3.25
2332 2432 8.291740 CAGTTGATCTGAAAATGTAACATGACA 58.708 33.333 0.00 0.00 46.27 3.58
2390 2490 7.712639 GCTGAGTGAAATCCTACAGAATTATCA 59.287 37.037 0.00 0.00 0.00 2.15
2437 2537 1.337167 GCCATGAAGGTCTTTTGCCAC 60.337 52.381 0.00 0.00 40.61 5.01
2475 2575 9.197694 CAAGATAACTAACCTCGAAAGATATGG 57.802 37.037 0.00 0.00 40.84 2.74
2580 2680 1.747355 GCATTGAGCAAGGCTGTATGT 59.253 47.619 12.07 0.00 43.87 2.29
2596 2696 3.599343 TGAATCTTACACGAGCTGCATT 58.401 40.909 1.02 0.00 0.00 3.56
2731 2831 1.686355 ATAGGACAGAGTCTCCAGCG 58.314 55.000 0.00 0.00 32.47 5.18
2798 2898 1.338337 CAGTAGGGTATGGAGAGCACG 59.662 57.143 0.00 0.00 0.00 5.34
2881 2985 1.134699 CGTATTCCCAGAAGCAGCTGA 60.135 52.381 20.43 0.00 38.14 4.26
2965 3069 0.605860 CAGCTGCAGCAAGAAGACCT 60.606 55.000 38.24 13.55 45.16 3.85
3091 3195 0.940126 CTTGCTCTGCAGAACACGTT 59.060 50.000 19.16 0.00 40.61 3.99
3117 3221 3.356290 AGCCAATGGTATGACAAACTCC 58.644 45.455 0.00 0.00 0.00 3.85
3440 3545 0.165944 CGCAAGTTTAACGGAGCCAG 59.834 55.000 4.51 0.00 0.00 4.85
3485 3590 1.668419 ACGACAGCAGAAAACAAGCT 58.332 45.000 0.00 0.00 39.63 3.74
3500 3605 2.656560 AACATGGAGCTCACTACGAC 57.343 50.000 17.19 0.00 0.00 4.34
3502 3607 3.325870 TGAAAACATGGAGCTCACTACG 58.674 45.455 17.19 1.14 0.00 3.51
3701 3808 7.876068 ACCATCAACTCGAAATCAAACTAGTAA 59.124 33.333 0.00 0.00 0.00 2.24
3854 3961 1.556911 GTCAGAGGCTCAATCTCCCAA 59.443 52.381 18.26 0.00 31.96 4.12
4074 4181 0.329261 CATCCTCCTTTCCACCTGCA 59.671 55.000 0.00 0.00 0.00 4.41
4143 4250 3.882888 GTCCACCAAAACTGAATGACTGA 59.117 43.478 0.00 0.00 0.00 3.41
4154 4261 4.142038 ACTCATACCAAGTCCACCAAAAC 58.858 43.478 0.00 0.00 0.00 2.43
4900 5007 2.613026 TCCAGGTGTTGTATATGCGG 57.387 50.000 0.00 0.00 0.00 5.69
4914 5021 0.465705 TAGAAGGCGCTGAATCCAGG 59.534 55.000 7.64 0.00 40.72 4.45
4915 5022 2.315925 TTAGAAGGCGCTGAATCCAG 57.684 50.000 7.64 0.00 43.22 3.86
5235 5342 3.297979 CAGAATTTTCCGAAAATGACGCG 59.702 43.478 17.79 3.53 40.05 6.01
5484 5592 4.410400 GGGTCCTCCAACTGGCCG 62.410 72.222 0.00 0.00 35.00 6.13
5596 5704 3.966665 AGTGGCAAAAGAATCTTGGGAAA 59.033 39.130 0.00 0.00 0.00 3.13
5672 5780 4.094887 ACCTTTATGCAAGATACGCTGTTG 59.905 41.667 0.00 0.00 33.80 3.33
5694 5802 0.893447 ACCTCCTGTGGCGTAAGTAC 59.107 55.000 0.00 0.00 41.68 2.73
6102 6210 2.706890 ACATTAGGCAACACGGGTAAG 58.293 47.619 0.00 0.00 41.41 2.34
6223 6333 6.093633 GCAATAAACTCCTACTAAACTGTGGG 59.906 42.308 0.00 0.00 39.55 4.61
6297 6407 8.867097 TCACTAGTCACTAACTCCAACTAAAAT 58.133 33.333 0.00 0.00 39.55 1.82
6423 7909 8.602328 GCTAAATGCTATATCTGTCATGATCAC 58.398 37.037 0.00 0.00 38.95 3.06
6425 7911 8.713737 TGCTAAATGCTATATCTGTCATGATC 57.286 34.615 0.00 0.00 43.37 2.92
6468 7954 6.525629 ACATGGGCTACTTGTAATGATACTC 58.474 40.000 0.00 0.00 35.87 2.59
6477 7963 6.663953 GGATCTATCTACATGGGCTACTTGTA 59.336 42.308 0.00 7.21 38.33 2.41
6479 7965 5.481824 TGGATCTATCTACATGGGCTACTTG 59.518 44.000 0.00 0.00 0.00 3.16
6480 7966 5.655394 TGGATCTATCTACATGGGCTACTT 58.345 41.667 0.00 0.00 0.00 2.24
6481 7967 5.276694 TGGATCTATCTACATGGGCTACT 57.723 43.478 0.00 0.00 0.00 2.57
6482 7968 5.717178 TCTTGGATCTATCTACATGGGCTAC 59.283 44.000 0.00 0.00 0.00 3.58
6483 7969 5.903923 TCTTGGATCTATCTACATGGGCTA 58.096 41.667 0.00 0.00 0.00 3.93
6487 8033 4.469227 CCCCTCTTGGATCTATCTACATGG 59.531 50.000 0.00 0.00 35.39 3.66
6553 8115 1.616994 GGACCCAAAAGGCACATAGCT 60.617 52.381 0.00 0.00 44.79 3.32
6556 8118 1.080638 AGGGACCCAAAAGGCACATA 58.919 50.000 14.60 0.00 40.58 2.29
6631 8194 1.474143 GGCCTCAGGAGAAGGAAATCG 60.474 57.143 0.00 0.00 0.00 3.34
6658 8222 3.738281 CGTCACATTCACCCTCCAGATAC 60.738 52.174 0.00 0.00 0.00 2.24
6710 8278 1.108776 CAACAGGCATGAGGGAATGG 58.891 55.000 4.84 0.00 0.00 3.16
6713 8281 0.770499 TCACAACAGGCATGAGGGAA 59.230 50.000 4.84 0.00 0.00 3.97
6714 8282 0.036732 GTCACAACAGGCATGAGGGA 59.963 55.000 4.84 0.07 0.00 4.20
6745 8313 3.095278 GACGTCGAAGCGTTGCGA 61.095 61.111 0.00 0.00 45.79 5.10


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

AutoCloner maintained by Alex Coulton.