Multiple sequence alignment - TraesCS2A01G582100

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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 TraesCS2A01G582100 chr2A 100.000 2733 0 0 1307 4039 774572217 774574949 0.000000e+00 5048
1 TraesCS2A01G582100 chr2A 100.000 1062 0 0 1 1062 774570911 774571972 0.000000e+00 1962
2 TraesCS2A01G582100 chr2D 87.344 2086 170 52 2005 4039 650323509 650321467 0.000000e+00 2303
3 TraesCS2A01G582100 chr2D 93.633 1068 50 13 1 1062 650325520 650324465 0.000000e+00 1580
4 TraesCS2A01G582100 chr2D 92.060 403 19 6 1307 1707 650324227 650323836 4.560000e-154 555
5 TraesCS2A01G582100 chr2B 86.327 2099 190 52 1979 4039 786227543 786225504 0.000000e+00 2196
6 TraesCS2A01G582100 chr2B 91.519 1073 76 11 1 1062 786229619 786228551 0.000000e+00 1463
7 TraesCS2A01G582100 chr2B 90.625 320 21 7 1390 1703 786228166 786227850 2.250000e-112 416
8 TraesCS2A01G582100 chrUn 87.705 366 31 9 3262 3618 96707544 96707904 8.080000e-112 414
9 TraesCS2A01G582100 chrUn 83.453 139 18 5 3127 3262 96702114 96702250 1.520000e-24 124
10 TraesCS2A01G582100 chr6B 86.792 371 38 11 3303 3673 47898731 47899090 1.750000e-108 403
11 TraesCS2A01G582100 chr6A 83.747 363 48 5 3687 4039 27197515 27197876 2.330000e-87 333


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 TraesCS2A01G582100 chr2A 774570911 774574949 4038 False 3505.000000 5048 100.000000 1 4039 2 chr2A.!!$F1 4038
1 TraesCS2A01G582100 chr2D 650321467 650325520 4053 True 1479.333333 2303 91.012333 1 4039 3 chr2D.!!$R1 4038
2 TraesCS2A01G582100 chr2B 786225504 786229619 4115 True 1358.333333 2196 89.490333 1 4039 3 chr2B.!!$R1 4038

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
945 954 0.390340 TCAGAGTGCTGCCGCTTAAG 60.390 55.0 0.7 0.0 42.01 1.85 F
1621 1696 0.395312 CCAACTACACGGAACTGGGT 59.605 55.0 0.0 0.0 0.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 2277 0.179936 ATGCTCTTGACCAGCTAGGC 59.820 55.0 2.5 0.0 43.14 3.93 R
3065 3259 0.245266 ACATACACATGACACGCCGA 59.755 50.0 0.0 0.0 35.96 5.54 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
97 98 2.870435 GCCAGTAAACTTCTTCAGGCGA 60.870 50.000 0.00 0.00 0.00 5.54
112 113 4.056125 CGACTGCCAGCGAGGACA 62.056 66.667 2.12 0.00 41.22 4.02
174 175 9.976511 CTTATCGTTGTAATCCCTAGAATTACA 57.023 33.333 18.90 18.90 38.52 2.41
209 210 1.020861 TAGCTCGACTCGCCGTGTTA 61.021 55.000 0.00 0.00 0.00 2.41
248 249 1.704070 GTTCAGGACTTCGAGTCTGC 58.296 55.000 12.62 1.09 44.46 4.26
286 287 2.158475 TGGATCCAGGGAATAATGTGCC 60.158 50.000 11.44 0.00 0.00 5.01
347 350 7.355017 TGCTGATCGTTTATGAAATATCTTGC 58.645 34.615 0.00 0.00 0.00 4.01
464 467 1.542492 AGTTTCTGCTGGGCTGATTG 58.458 50.000 0.40 0.00 36.48 2.67
480 483 3.791245 TGATTGTCCTTGGTTTTTGTGC 58.209 40.909 0.00 0.00 0.00 4.57
482 485 3.971245 TTGTCCTTGGTTTTTGTGCTT 57.029 38.095 0.00 0.00 0.00 3.91
561 564 8.450385 TGTTTTAACTTTTGTAACTGTTTCCG 57.550 30.769 0.00 0.00 0.00 4.30
616 619 1.880027 CACTGTTTTCTTCCCCTTCCG 59.120 52.381 0.00 0.00 0.00 4.30
694 699 5.326200 AGTCATTGTAGTAGCTGGTGTAC 57.674 43.478 0.00 0.00 0.00 2.90
780 786 7.951347 ATCAGGAATAGCCCATTCAAATATC 57.049 36.000 10.01 0.00 44.27 1.63
802 808 2.687700 TGCTTTGCAATTTGTGTGGT 57.312 40.000 0.00 0.00 34.76 4.16
806 812 3.126686 GCTTTGCAATTTGTGTGGTTGTT 59.873 39.130 0.00 0.00 0.00 2.83
824 830 6.878923 TGGTTGTTATTAGAATCTGTGGACAG 59.121 38.462 0.00 0.00 45.08 3.51
850 859 5.841957 ATGGACTGCAAATAATGAGGAAC 57.158 39.130 0.00 0.00 0.00 3.62
852 861 5.324409 TGGACTGCAAATAATGAGGAACTT 58.676 37.500 0.00 0.00 41.55 2.66
853 862 5.774690 TGGACTGCAAATAATGAGGAACTTT 59.225 36.000 0.00 0.00 41.55 2.66
895 904 6.317140 TCCTGAGATGCACAAATAAATCTCAC 59.683 38.462 8.02 0.00 46.22 3.51
945 954 0.390340 TCAGAGTGCTGCCGCTTAAG 60.390 55.000 0.70 0.00 42.01 1.85
946 955 1.078848 AGAGTGCTGCCGCTTAAGG 60.079 57.895 4.29 0.00 36.97 2.69
1365 1422 9.620660 AATTATTCAGTATGTCCGTTTGTTTTC 57.379 29.630 0.00 0.00 37.40 2.29
1374 1431 6.378710 TGTCCGTTTGTTTTCATTCATGTA 57.621 33.333 0.00 0.00 0.00 2.29
1375 1432 6.202937 TGTCCGTTTGTTTTCATTCATGTAC 58.797 36.000 0.00 0.00 0.00 2.90
1376 1433 6.183360 TGTCCGTTTGTTTTCATTCATGTACA 60.183 34.615 0.00 0.00 0.00 2.90
1377 1434 6.359617 GTCCGTTTGTTTTCATTCATGTACAG 59.640 38.462 0.33 0.00 0.00 2.74
1378 1435 6.038825 TCCGTTTGTTTTCATTCATGTACAGT 59.961 34.615 0.33 0.00 0.00 3.55
1379 1436 6.695278 CCGTTTGTTTTCATTCATGTACAGTT 59.305 34.615 0.33 0.00 0.00 3.16
1405 1476 2.952310 GTTCCATGCCATCCTTCTAACC 59.048 50.000 0.00 0.00 0.00 2.85
1413 1484 3.007635 CCATCCTTCTAACCGAAACACC 58.992 50.000 0.00 0.00 0.00 4.16
1423 1495 0.891904 CCGAAACACCCGTGGGATTT 60.892 55.000 13.01 11.42 38.96 2.17
1437 1509 3.114606 TGGGATTTCTCTGCAGGATGTA 58.885 45.455 15.13 0.00 39.31 2.29
1452 1524 5.591877 GCAGGATGTAAGAGGAAATGATGTT 59.408 40.000 0.00 0.00 39.31 2.71
1516 1588 1.271446 CGCATCTCGATGGTAGCGTG 61.271 60.000 8.81 0.00 41.67 5.34
1561 1636 5.935945 TCCTCCTGTTTGAATCTGTGTTTA 58.064 37.500 0.00 0.00 0.00 2.01
1562 1637 5.763204 TCCTCCTGTTTGAATCTGTGTTTAC 59.237 40.000 0.00 0.00 0.00 2.01
1582 1657 2.505819 ACACCACCTGAGTTGATATCCC 59.494 50.000 0.00 0.00 0.00 3.85
1597 1672 4.729918 CCCTGCAGTGGTCTGGCC 62.730 72.222 13.81 0.00 41.57 5.36
1615 1690 2.156098 GCCAATTCCAACTACACGGAA 58.844 47.619 0.00 0.00 45.12 4.30
1621 1696 0.395312 CCAACTACACGGAACTGGGT 59.605 55.000 0.00 0.00 0.00 4.51
1624 1699 0.966920 ACTACACGGAACTGGGTCAG 59.033 55.000 0.00 0.00 37.52 3.51
1654 1729 5.189145 TGAGAAATACAGGGAGAAAGGTACC 59.811 44.000 2.73 2.73 0.00 3.34
1656 1731 6.509386 AGAAATACAGGGAGAAAGGTACCTA 58.491 40.000 16.67 0.00 0.00 3.08
1657 1732 6.383436 AGAAATACAGGGAGAAAGGTACCTAC 59.617 42.308 16.67 12.66 0.00 3.18
1690 1766 4.142315 GCTTTGCACATGTCATTCCACTAT 60.142 41.667 0.00 0.00 0.00 2.12
1691 1767 5.066375 GCTTTGCACATGTCATTCCACTATA 59.934 40.000 0.00 0.00 0.00 1.31
1723 1800 9.829507 AGCTCTATCTAATGCATTATATTCACC 57.170 33.333 19.17 7.02 0.00 4.02
1724 1801 9.050601 GCTCTATCTAATGCATTATATTCACCC 57.949 37.037 19.17 2.53 0.00 4.61
1725 1802 9.553064 CTCTATCTAATGCATTATATTCACCCC 57.447 37.037 19.17 0.00 0.00 4.95
1726 1803 9.056799 TCTATCTAATGCATTATATTCACCCCA 57.943 33.333 19.17 1.25 0.00 4.96
1727 1804 9.334947 CTATCTAATGCATTATATTCACCCCAG 57.665 37.037 19.17 5.45 0.00 4.45
1728 1805 5.945784 TCTAATGCATTATATTCACCCCAGC 59.054 40.000 19.17 0.00 0.00 4.85
1729 1806 2.875296 TGCATTATATTCACCCCAGCC 58.125 47.619 0.00 0.00 0.00 4.85
1730 1807 2.446666 TGCATTATATTCACCCCAGCCT 59.553 45.455 0.00 0.00 0.00 4.58
1731 1808 3.117169 TGCATTATATTCACCCCAGCCTT 60.117 43.478 0.00 0.00 0.00 4.35
1732 1809 4.105537 TGCATTATATTCACCCCAGCCTTA 59.894 41.667 0.00 0.00 0.00 2.69
1733 1810 5.222316 TGCATTATATTCACCCCAGCCTTAT 60.222 40.000 0.00 0.00 0.00 1.73
1734 1811 5.716703 GCATTATATTCACCCCAGCCTTATT 59.283 40.000 0.00 0.00 0.00 1.40
1735 1812 6.211384 GCATTATATTCACCCCAGCCTTATTT 59.789 38.462 0.00 0.00 0.00 1.40
1736 1813 7.396055 GCATTATATTCACCCCAGCCTTATTTA 59.604 37.037 0.00 0.00 0.00 1.40
1737 1814 8.960591 CATTATATTCACCCCAGCCTTATTTAG 58.039 37.037 0.00 0.00 0.00 1.85
1738 1815 4.881157 ATTCACCCCAGCCTTATTTAGT 57.119 40.909 0.00 0.00 0.00 2.24
1739 1816 5.987019 ATTCACCCCAGCCTTATTTAGTA 57.013 39.130 0.00 0.00 0.00 1.82
1740 1817 5.367945 TTCACCCCAGCCTTATTTAGTAG 57.632 43.478 0.00 0.00 0.00 2.57
1741 1818 4.368067 TCACCCCAGCCTTATTTAGTAGT 58.632 43.478 0.00 0.00 0.00 2.73
1742 1819 4.786454 TCACCCCAGCCTTATTTAGTAGTT 59.214 41.667 0.00 0.00 0.00 2.24
1743 1820 5.252164 TCACCCCAGCCTTATTTAGTAGTTT 59.748 40.000 0.00 0.00 0.00 2.66
1744 1821 6.444493 TCACCCCAGCCTTATTTAGTAGTTTA 59.556 38.462 0.00 0.00 0.00 2.01
1745 1822 6.766467 CACCCCAGCCTTATTTAGTAGTTTAG 59.234 42.308 0.00 0.00 0.00 1.85
1746 1823 5.763698 CCCCAGCCTTATTTAGTAGTTTAGC 59.236 44.000 0.00 0.00 0.00 3.09
1747 1824 6.354130 CCCAGCCTTATTTAGTAGTTTAGCA 58.646 40.000 0.00 0.00 0.00 3.49
1748 1825 6.483640 CCCAGCCTTATTTAGTAGTTTAGCAG 59.516 42.308 0.00 0.00 0.00 4.24
1749 1826 7.272978 CCAGCCTTATTTAGTAGTTTAGCAGA 58.727 38.462 0.00 0.00 0.00 4.26
1750 1827 7.934120 CCAGCCTTATTTAGTAGTTTAGCAGAT 59.066 37.037 0.00 0.00 0.00 2.90
1751 1828 9.331282 CAGCCTTATTTAGTAGTTTAGCAGATT 57.669 33.333 0.00 0.00 0.00 2.40
1764 1841 8.197988 AGTTTAGCAGATTCTAATTTGGTACG 57.802 34.615 5.04 0.00 34.52 3.67
1765 1842 7.822822 AGTTTAGCAGATTCTAATTTGGTACGT 59.177 33.333 5.04 0.00 34.52 3.57
1823 1905 8.942669 TGCTATTTGTATTAAAACTGAACACG 57.057 30.769 0.00 0.00 0.00 4.49
1863 1954 8.865420 TGCTTTGTACTTAAATGGTATGGTTA 57.135 30.769 0.00 0.00 0.00 2.85
1883 1976 6.126409 GGTTATATCTTGTTGTGGGGAATGA 58.874 40.000 0.00 0.00 0.00 2.57
1886 1979 9.349713 GTTATATCTTGTTGTGGGGAATGATTA 57.650 33.333 0.00 0.00 0.00 1.75
1889 1982 6.985653 TCTTGTTGTGGGGAATGATTAAAA 57.014 33.333 0.00 0.00 0.00 1.52
1910 2003 4.675190 ACTCTTCGATGCATCACTTTTG 57.325 40.909 25.70 12.90 0.00 2.44
1913 2006 5.120830 ACTCTTCGATGCATCACTTTTGTAC 59.879 40.000 25.70 0.00 0.00 2.90
1914 2007 4.994217 TCTTCGATGCATCACTTTTGTACA 59.006 37.500 25.70 0.00 0.00 2.90
1917 2010 4.032786 TCGATGCATCACTTTTGTACATCG 59.967 41.667 25.70 14.39 43.88 3.84
1918 2011 3.469899 TGCATCACTTTTGTACATCGC 57.530 42.857 0.00 0.00 0.00 4.58
1965 2059 6.226052 AGAAAAATCCATTGTCTTTGCCTTC 58.774 36.000 0.00 0.00 0.00 3.46
1970 2064 4.326826 TCCATTGTCTTTGCCTTCACTAG 58.673 43.478 0.00 0.00 0.00 2.57
1974 2068 4.527509 TGTCTTTGCCTTCACTAGAGAG 57.472 45.455 0.00 0.00 0.00 3.20
1975 2069 3.898123 TGTCTTTGCCTTCACTAGAGAGT 59.102 43.478 0.00 0.00 35.80 3.24
1976 2070 5.077564 TGTCTTTGCCTTCACTAGAGAGTA 58.922 41.667 0.00 0.00 33.32 2.59
1977 2071 5.184096 TGTCTTTGCCTTCACTAGAGAGTAG 59.816 44.000 0.00 0.00 33.32 2.57
2016 2181 4.421058 CAATCCAATCAGCACAACAGATG 58.579 43.478 0.00 0.00 0.00 2.90
2029 2194 2.398252 ACAGATGTGGCATCTGAGTG 57.602 50.000 32.84 16.31 46.25 3.51
2082 2249 7.819900 AGAATACACTTCACCTGCTTACTAAAG 59.180 37.037 0.00 0.00 35.68 1.85
2100 2269 0.689623 AGCAGCAGCAGAACTTACCT 59.310 50.000 3.17 0.00 45.49 3.08
2108 2277 3.681897 CAGCAGAACTTACCTGTAGCTTG 59.318 47.826 0.00 0.00 34.29 4.01
2176 2345 6.698008 ATGACTGAATGTGTTTTGAAGTCA 57.302 33.333 5.20 5.20 44.60 3.41
2181 2350 9.121517 GACTGAATGTGTTTTGAAGTCATATTG 57.878 33.333 0.00 0.00 34.19 1.90
2182 2351 7.596248 ACTGAATGTGTTTTGAAGTCATATTGC 59.404 33.333 0.00 0.00 0.00 3.56
2183 2352 7.660112 TGAATGTGTTTTGAAGTCATATTGCT 58.340 30.769 0.00 0.00 0.00 3.91
2188 2362 9.243637 TGTGTTTTGAAGTCATATTGCTTTTAC 57.756 29.630 0.00 0.00 0.00 2.01
2196 2370 9.974750 GAAGTCATATTGCTTTTACAAGACTAC 57.025 33.333 0.00 0.00 33.77 2.73
2205 2379 5.050295 GCTTTTACAAGACTACAGTGGTGTC 60.050 44.000 0.00 9.00 33.20 3.67
2206 2380 5.601583 TTTACAAGACTACAGTGGTGTCA 57.398 39.130 16.45 0.00 38.19 3.58
2208 2382 4.481368 ACAAGACTACAGTGGTGTCAAA 57.519 40.909 16.45 0.00 38.19 2.69
2222 2403 5.007724 GTGGTGTCAAAAAGTCCTAGAAGTG 59.992 44.000 0.00 0.00 0.00 3.16
2224 2405 4.515567 GTGTCAAAAAGTCCTAGAAGTGGG 59.484 45.833 0.00 0.00 0.00 4.61
2230 2411 2.233305 GTCCTAGAAGTGGGACCTGA 57.767 55.000 0.00 0.00 46.38 3.86
2270 2451 6.769822 CCCATCAAACAGATATTACAGAAGCT 59.230 38.462 0.00 0.00 34.43 3.74
2276 2457 9.481340 CAAACAGATATTACAGAAGCTATGCTA 57.519 33.333 0.00 0.00 38.25 3.49
2329 2510 9.399403 GTTAGTTTTCAGATTTGAGATTGGAAC 57.601 33.333 0.00 0.00 34.15 3.62
2353 2535 7.219484 CCAACCTTGGGCTAAATAATGATAG 57.781 40.000 0.00 0.00 44.70 2.08
2354 2536 7.004086 CCAACCTTGGGCTAAATAATGATAGA 58.996 38.462 0.00 0.00 44.70 1.98
2355 2537 7.505585 CCAACCTTGGGCTAAATAATGATAGAA 59.494 37.037 0.00 0.00 44.70 2.10
2356 2538 8.571336 CAACCTTGGGCTAAATAATGATAGAAG 58.429 37.037 0.00 0.00 0.00 2.85
2357 2539 8.045720 ACCTTGGGCTAAATAATGATAGAAGA 57.954 34.615 0.00 0.00 0.00 2.87
2358 2540 7.939588 ACCTTGGGCTAAATAATGATAGAAGAC 59.060 37.037 0.00 0.00 0.00 3.01
2359 2541 7.391833 CCTTGGGCTAAATAATGATAGAAGACC 59.608 40.741 0.00 0.00 0.00 3.85
2360 2542 7.633018 TGGGCTAAATAATGATAGAAGACCT 57.367 36.000 0.00 0.00 0.00 3.85
2361 2543 8.045720 TGGGCTAAATAATGATAGAAGACCTT 57.954 34.615 0.00 0.00 0.00 3.50
2362 2544 9.166222 TGGGCTAAATAATGATAGAAGACCTTA 57.834 33.333 0.00 0.00 0.00 2.69
2422 2607 5.415415 GGCTGCAAGTCTTTAGTATGATG 57.585 43.478 0.50 0.00 34.11 3.07
2423 2608 5.118990 GGCTGCAAGTCTTTAGTATGATGA 58.881 41.667 0.50 0.00 34.11 2.92
2424 2609 5.236047 GGCTGCAAGTCTTTAGTATGATGAG 59.764 44.000 0.50 0.00 34.11 2.90
2465 2650 0.251474 AGATGTGCCATTGTGCAGGT 60.251 50.000 0.00 0.00 43.02 4.00
2510 2696 7.899974 ACTTCGTCTTCAATCTTCATTTATCG 58.100 34.615 0.00 0.00 0.00 2.92
2515 2702 6.409185 GTCTTCAATCTTCATTTATCGTTGCG 59.591 38.462 0.00 0.00 0.00 4.85
2566 2753 1.976474 GGCGTTCCCCTGCAATCAA 60.976 57.895 0.00 0.00 0.00 2.57
2660 2847 7.393515 AGTTTCCTATTTTTCGCAAGGTCTATT 59.606 33.333 0.00 0.00 38.47 1.73
2662 2849 5.820947 TCCTATTTTTCGCAAGGTCTATTCC 59.179 40.000 0.00 0.00 38.47 3.01
2663 2850 5.588648 CCTATTTTTCGCAAGGTCTATTCCA 59.411 40.000 0.00 0.00 38.47 3.53
2664 2851 5.567138 ATTTTTCGCAAGGTCTATTCCAG 57.433 39.130 0.00 0.00 38.47 3.86
2665 2852 2.024176 TTCGCAAGGTCTATTCCAGC 57.976 50.000 0.00 0.00 38.47 4.85
2671 2858 3.378427 GCAAGGTCTATTCCAGCGAAAAT 59.622 43.478 0.00 0.00 0.00 1.82
2672 2859 4.496507 GCAAGGTCTATTCCAGCGAAAATC 60.497 45.833 0.00 0.00 0.00 2.17
2674 2861 5.104259 AGGTCTATTCCAGCGAAAATCTT 57.896 39.130 0.00 0.00 0.00 2.40
2675 2862 5.501156 AGGTCTATTCCAGCGAAAATCTTT 58.499 37.500 0.00 0.00 0.00 2.52
2676 2863 5.355350 AGGTCTATTCCAGCGAAAATCTTTG 59.645 40.000 0.00 0.00 0.00 2.77
2681 2868 4.237349 TCCAGCGAAAATCTTTGTTTCC 57.763 40.909 0.00 0.00 32.40 3.13
2693 2883 4.681744 TCTTTGTTTCCATTTCTGTGTGC 58.318 39.130 0.00 0.00 0.00 4.57
2727 2917 7.856145 TCCAAACACAAATGCACTTATTTTT 57.144 28.000 0.00 0.00 0.00 1.94
2758 2948 4.949856 ACATTTCTGAGTTGACAACAGGTT 59.050 37.500 20.08 0.00 33.19 3.50
2767 2957 2.004017 TGACAACAGGTTGACGTGAAC 58.996 47.619 18.28 9.59 42.93 3.18
2812 3002 4.954875 ACAAGTTCTTGAAGTCAGAGAGG 58.045 43.478 17.75 0.00 0.00 3.69
2830 3020 0.544697 GGGGCGGTCTATTTGGAGAA 59.455 55.000 0.00 0.00 0.00 2.87
2839 3029 6.830114 GGTCTATTTGGAGAACGTATCAAG 57.170 41.667 0.00 0.00 0.00 3.02
2949 3139 7.119846 GGTGATGCTCTAACTCAACAGTTTATT 59.880 37.037 0.00 0.00 40.16 1.40
2953 3143 8.677148 TGCTCTAACTCAACAGTTTATTTTCT 57.323 30.769 0.00 0.00 40.16 2.52
2954 3144 8.559536 TGCTCTAACTCAACAGTTTATTTTCTG 58.440 33.333 0.00 0.00 40.16 3.02
2970 3160 5.477607 TTTTCTGTATTCCTCGTCTCCAA 57.522 39.130 0.00 0.00 0.00 3.53
2974 3164 3.427573 TGTATTCCTCGTCTCCAACAGA 58.572 45.455 0.00 0.00 0.00 3.41
2976 3166 2.814280 TTCCTCGTCTCCAACAGAAC 57.186 50.000 0.00 0.00 30.72 3.01
2986 3176 4.151867 GTCTCCAACAGAACGGTAATTCAC 59.848 45.833 0.00 0.00 30.72 3.18
2987 3177 4.039973 TCTCCAACAGAACGGTAATTCACT 59.960 41.667 0.00 0.00 0.00 3.41
3044 3238 3.844211 AGCTGTTGGAGGTTTGAGGTATA 59.156 43.478 0.00 0.00 0.00 1.47
3045 3239 4.475016 AGCTGTTGGAGGTTTGAGGTATAT 59.525 41.667 0.00 0.00 0.00 0.86
3065 3259 0.467384 CTCCAGGGAAGATCATGCGT 59.533 55.000 0.00 0.00 0.00 5.24
3099 3297 6.785488 TGTGTATGTGTCATCTGTTCTTTC 57.215 37.500 0.00 0.00 0.00 2.62
3100 3298 6.524734 TGTGTATGTGTCATCTGTTCTTTCT 58.475 36.000 0.00 0.00 0.00 2.52
3183 3381 4.809426 ACTCTGTTTTCTACACGGTGAAAG 59.191 41.667 16.29 11.52 34.29 2.62
3188 3386 5.591067 TGTTTTCTACACGGTGAAAGGAAAT 59.409 36.000 16.29 0.00 34.29 2.17
3189 3387 6.766944 TGTTTTCTACACGGTGAAAGGAAATA 59.233 34.615 16.29 13.14 34.29 1.40
3191 3389 6.790285 TTCTACACGGTGAAAGGAAATAAC 57.210 37.500 16.29 0.00 0.00 1.89
3199 3399 5.619086 CGGTGAAAGGAAATAACATTTCGCT 60.619 40.000 15.12 2.57 44.64 4.93
3287 3489 4.398044 TCTCAAAAACCGAATGGGCTATTC 59.602 41.667 13.07 13.07 41.46 1.75
3333 3535 7.341769 TCTTTTTGGGAACAGAAAAATCTCTCA 59.658 33.333 0.00 0.00 43.00 3.27
3400 3602 6.655003 AGTTGATATCAATGTTGGAACTTCGT 59.345 34.615 20.65 0.00 38.24 3.85
3491 3693 3.695606 GTCCTGAGCTGGGCGACA 61.696 66.667 0.00 0.00 0.00 4.35
3496 3698 4.314440 GAGCTGGGCGACACCACA 62.314 66.667 0.00 0.00 42.05 4.17
3571 3773 5.279657 GGCTTTCTTGGACTTTGATTTGGAT 60.280 40.000 0.00 0.00 0.00 3.41
3631 3833 6.670695 ATGCCAAACAGGATTAGAAACTTT 57.329 33.333 0.00 0.00 41.22 2.66
3636 3838 8.088365 GCCAAACAGGATTAGAAACTTTTATGT 58.912 33.333 0.00 0.00 41.22 2.29
3656 3858 9.665719 TTTATGTTGTATGTCTGAATCTTAGCA 57.334 29.630 0.00 0.00 0.00 3.49
3657 3859 9.665719 TTATGTTGTATGTCTGAATCTTAGCAA 57.334 29.630 0.00 0.00 0.00 3.91
3658 3860 7.977789 TGTTGTATGTCTGAATCTTAGCAAA 57.022 32.000 0.00 0.00 0.00 3.68
3659 3861 8.565896 TGTTGTATGTCTGAATCTTAGCAAAT 57.434 30.769 0.00 0.00 0.00 2.32
3660 3862 8.453320 TGTTGTATGTCTGAATCTTAGCAAATG 58.547 33.333 0.00 0.00 0.00 2.32
3661 3863 8.668353 GTTGTATGTCTGAATCTTAGCAAATGA 58.332 33.333 0.00 0.00 0.00 2.57
3662 3864 8.429493 TGTATGTCTGAATCTTAGCAAATGAG 57.571 34.615 0.00 0.00 0.00 2.90
3664 3866 5.809001 TGTCTGAATCTTAGCAAATGAGGT 58.191 37.500 0.00 0.00 0.00 3.85
3665 3867 6.240894 TGTCTGAATCTTAGCAAATGAGGTT 58.759 36.000 0.00 0.00 0.00 3.50
3666 3868 6.149973 TGTCTGAATCTTAGCAAATGAGGTTG 59.850 38.462 0.00 0.00 0.00 3.77
3667 3869 6.372659 GTCTGAATCTTAGCAAATGAGGTTGA 59.627 38.462 0.00 0.00 0.00 3.18
3668 3870 7.066766 GTCTGAATCTTAGCAAATGAGGTTGAT 59.933 37.037 0.00 0.00 0.00 2.57
3669 3871 7.281774 TCTGAATCTTAGCAAATGAGGTTGATC 59.718 37.037 0.00 0.00 0.00 2.92
3670 3872 7.114754 TGAATCTTAGCAAATGAGGTTGATCT 58.885 34.615 0.00 0.00 0.00 2.75
3671 3873 6.939132 ATCTTAGCAAATGAGGTTGATCTG 57.061 37.500 0.00 0.00 0.00 2.90
3704 3914 4.943705 GCTTGGTTCCATGTCTGAATCTTA 59.056 41.667 6.60 0.00 0.00 2.10
3705 3915 5.065731 GCTTGGTTCCATGTCTGAATCTTAG 59.934 44.000 6.60 0.00 0.00 2.18
3709 3919 5.423015 GTTCCATGTCTGAATCTTAGCAGA 58.577 41.667 0.00 0.00 38.72 4.26
3715 3925 4.057432 GTCTGAATCTTAGCAGATGAGGC 58.943 47.826 0.00 0.00 42.51 4.70
3716 3926 3.966006 TCTGAATCTTAGCAGATGAGGCT 59.034 43.478 0.00 0.00 39.00 4.58
3717 3927 4.059511 CTGAATCTTAGCAGATGAGGCTG 58.940 47.826 0.00 0.00 42.62 4.85
3718 3928 3.708121 TGAATCTTAGCAGATGAGGCTGA 59.292 43.478 0.00 0.00 42.62 4.26
3722 3932 4.734266 TCTTAGCAGATGAGGCTGATCTA 58.266 43.478 16.25 0.00 42.62 1.98
3756 3966 2.032528 TGCACAGTACTGGCAGCC 59.967 61.111 25.71 3.66 33.85 4.85
3774 3984 1.679977 CACCAATGCTCCACCCAGG 60.680 63.158 0.00 0.00 39.47 4.45
3788 3998 0.035056 CCCAGGACACCTCCAATGAC 60.035 60.000 0.00 0.00 39.39 3.06
3904 4117 8.695456 GGATTTCATACAATCCCTACAAACATT 58.305 33.333 1.52 0.00 44.71 2.71
3923 4136 3.719268 TTCACATCATGCAGGGTTACT 57.281 42.857 0.00 0.00 0.00 2.24
3926 4139 5.372343 TCACATCATGCAGGGTTACTTAT 57.628 39.130 0.00 0.00 0.00 1.73
3944 4157 5.665459 ACTTATAAGTCTCAGGTGCATCAC 58.335 41.667 12.50 0.00 32.86 3.06
3946 4159 2.758736 AAGTCTCAGGTGCATCACTC 57.241 50.000 0.00 0.00 34.40 3.51
3954 4167 3.519107 TCAGGTGCATCACTCCTTTGATA 59.481 43.478 0.00 0.00 40.37 2.15
3973 4197 4.651045 TGATATGCATATAGGATGGTCGCT 59.349 41.667 19.12 0.00 0.00 4.93
3992 4216 2.561569 CTTACCTCGTAAATGGCAGGG 58.438 52.381 0.00 0.00 0.00 4.45
3995 4219 1.910671 ACCTCGTAAATGGCAGGGTTA 59.089 47.619 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 4.385825 TGAAGAAGTTTACTGGCGTTGAT 58.614 39.130 0.00 0.00 0.00 2.57
97 98 2.601666 TCTGTCCTCGCTGGCAGT 60.602 61.111 17.16 0.00 39.41 4.40
174 175 0.108615 GCTACAGCGACAGACATGGT 60.109 55.000 0.00 0.00 0.00 3.55
248 249 4.142138 GGATCCAGCACCTAATACGATAGG 60.142 50.000 6.95 10.68 46.62 2.57
286 287 2.286294 GGCAAGTCATGATAAGCTGTCG 59.714 50.000 0.00 0.00 0.00 4.35
415 418 6.028368 CAGAAATGCTTGTAGAAAGATGCAG 58.972 40.000 0.00 0.00 33.40 4.41
464 467 4.744631 CACATAAGCACAAAAACCAAGGAC 59.255 41.667 0.00 0.00 0.00 3.85
512 515 2.936202 TCCTTCCAATCAAGGCATAGC 58.064 47.619 0.00 0.00 42.63 2.97
513 516 5.704515 CAGTATCCTTCCAATCAAGGCATAG 59.295 44.000 0.00 0.00 42.63 2.23
542 545 7.281549 AGTCATACGGAAACAGTTACAAAAGTT 59.718 33.333 0.00 0.00 0.00 2.66
561 564 5.163652 GGTTTGGCCAAATGTAGAGTCATAC 60.164 44.000 32.52 15.88 37.17 2.39
586 589 5.123936 GGAAGAAAACAGTGTTACTCCACT 58.876 41.667 9.37 0.52 46.40 4.00
643 648 7.504924 TTTGGACATTCTTTAAACGATGAGT 57.495 32.000 11.20 2.12 0.00 3.41
780 786 3.312973 ACCACACAAATTGCAAAGCATTG 59.687 39.130 1.71 9.41 38.76 2.82
802 808 6.472016 TGCTGTCCACAGATTCTAATAACAA 58.528 36.000 11.04 0.00 46.59 2.83
806 812 7.235399 TCCATATGCTGTCCACAGATTCTAATA 59.765 37.037 11.04 0.00 46.59 0.98
824 830 5.474532 TCCTCATTATTTGCAGTCCATATGC 59.525 40.000 0.00 0.00 44.11 3.14
850 859 9.364989 CTCAGGAAGTCTTAGAATGTCTTAAAG 57.635 37.037 0.00 0.00 0.00 1.85
852 861 8.651589 TCTCAGGAAGTCTTAGAATGTCTTAA 57.348 34.615 0.00 0.00 0.00 1.85
853 862 8.690884 CATCTCAGGAAGTCTTAGAATGTCTTA 58.309 37.037 0.00 0.00 30.39 2.10
895 904 1.893808 AAGTGGCAAGCACCTGTCG 60.894 57.895 0.00 0.00 0.00 4.35
945 954 2.503356 TGAGAAGGATTGGAGAAGAGCC 59.497 50.000 0.00 0.00 0.00 4.70
946 955 3.902881 TGAGAAGGATTGGAGAAGAGC 57.097 47.619 0.00 0.00 0.00 4.09
1340 1397 8.788806 TGAAAACAAACGGACATACTGAATAAT 58.211 29.630 0.00 0.00 0.00 1.28
1350 1407 5.841810 ACATGAATGAAAACAAACGGACAT 58.158 33.333 0.00 0.00 0.00 3.06
1355 1412 7.430793 TGAACTGTACATGAATGAAAACAAACG 59.569 33.333 0.00 0.00 0.00 3.60
1365 1422 5.469760 TGGAACTGTGAACTGTACATGAATG 59.530 40.000 0.00 0.00 0.00 2.67
1374 1431 1.133823 TGGCATGGAACTGTGAACTGT 60.134 47.619 0.00 0.00 0.00 3.55
1375 1432 1.608055 TGGCATGGAACTGTGAACTG 58.392 50.000 0.00 0.00 0.00 3.16
1376 1433 2.440409 GATGGCATGGAACTGTGAACT 58.560 47.619 3.81 0.00 0.00 3.01
1377 1434 1.474077 GGATGGCATGGAACTGTGAAC 59.526 52.381 3.81 0.00 0.00 3.18
1378 1435 1.355381 AGGATGGCATGGAACTGTGAA 59.645 47.619 3.81 0.00 0.00 3.18
1379 1436 0.994247 AGGATGGCATGGAACTGTGA 59.006 50.000 3.81 0.00 0.00 3.58
1405 1476 0.519961 GAAATCCCACGGGTGTTTCG 59.480 55.000 15.13 0.00 34.33 3.46
1413 1484 0.745845 CCTGCAGAGAAATCCCACGG 60.746 60.000 17.39 0.00 0.00 4.94
1423 1495 3.388552 TCCTCTTACATCCTGCAGAGA 57.611 47.619 17.39 11.43 32.56 3.10
1437 1509 4.914983 TGAGCTCAACATCATTTCCTCTT 58.085 39.130 15.67 0.00 0.00 2.85
1452 1524 1.483827 CCCTTGTATCTGCTGAGCTCA 59.516 52.381 17.19 17.19 0.00 4.26
1516 1588 8.196802 AGGATTTCAAACTAAAACTGCAAAAC 57.803 30.769 0.00 0.00 0.00 2.43
1561 1636 2.505819 GGGATATCAACTCAGGTGGTGT 59.494 50.000 4.83 0.00 0.00 4.16
1562 1637 2.774234 AGGGATATCAACTCAGGTGGTG 59.226 50.000 4.83 0.00 0.00 4.17
1597 1672 3.188460 CCAGTTCCGTGTAGTTGGAATTG 59.812 47.826 8.90 8.90 46.04 2.32
1615 1690 2.836636 TCTCATAGAGCTGACCCAGT 57.163 50.000 0.00 0.00 33.43 4.00
1621 1696 5.458595 TCCCTGTATTTCTCATAGAGCTGA 58.541 41.667 0.00 0.00 0.00 4.26
1624 1699 6.412362 TTCTCCCTGTATTTCTCATAGAGC 57.588 41.667 0.00 0.00 0.00 4.09
1654 1729 7.978982 ACATGTGCAAAGCTATAGAAAAGTAG 58.021 34.615 3.21 0.00 0.00 2.57
1656 1731 6.430925 TGACATGTGCAAAGCTATAGAAAAGT 59.569 34.615 1.15 0.00 0.00 2.66
1657 1732 6.845302 TGACATGTGCAAAGCTATAGAAAAG 58.155 36.000 1.15 0.00 0.00 2.27
1704 1781 5.945784 GCTGGGGTGAATATAATGCATTAGA 59.054 40.000 22.76 19.35 0.00 2.10
1705 1782 5.126061 GGCTGGGGTGAATATAATGCATTAG 59.874 44.000 22.76 8.82 0.00 1.73
1706 1783 5.016173 GGCTGGGGTGAATATAATGCATTA 58.984 41.667 20.95 20.95 0.00 1.90
1707 1784 3.834231 GGCTGGGGTGAATATAATGCATT 59.166 43.478 17.56 17.56 0.00 3.56
1708 1785 3.076484 AGGCTGGGGTGAATATAATGCAT 59.924 43.478 0.00 0.00 0.00 3.96
1709 1786 2.446666 AGGCTGGGGTGAATATAATGCA 59.553 45.455 0.00 0.00 0.00 3.96
1710 1787 3.160679 AGGCTGGGGTGAATATAATGC 57.839 47.619 0.00 0.00 0.00 3.56
1711 1788 7.781324 AAATAAGGCTGGGGTGAATATAATG 57.219 36.000 0.00 0.00 0.00 1.90
1712 1789 8.678798 ACTAAATAAGGCTGGGGTGAATATAAT 58.321 33.333 0.00 0.00 0.00 1.28
1713 1790 8.052621 ACTAAATAAGGCTGGGGTGAATATAA 57.947 34.615 0.00 0.00 0.00 0.98
1714 1791 7.642094 ACTAAATAAGGCTGGGGTGAATATA 57.358 36.000 0.00 0.00 0.00 0.86
1715 1792 6.530601 ACTAAATAAGGCTGGGGTGAATAT 57.469 37.500 0.00 0.00 0.00 1.28
1716 1793 5.987019 ACTAAATAAGGCTGGGGTGAATA 57.013 39.130 0.00 0.00 0.00 1.75
1717 1794 4.881157 ACTAAATAAGGCTGGGGTGAAT 57.119 40.909 0.00 0.00 0.00 2.57
1718 1795 4.786454 ACTACTAAATAAGGCTGGGGTGAA 59.214 41.667 0.00 0.00 0.00 3.18
1719 1796 4.368067 ACTACTAAATAAGGCTGGGGTGA 58.632 43.478 0.00 0.00 0.00 4.02
1720 1797 4.772886 ACTACTAAATAAGGCTGGGGTG 57.227 45.455 0.00 0.00 0.00 4.61
1721 1798 5.791303 AAACTACTAAATAAGGCTGGGGT 57.209 39.130 0.00 0.00 0.00 4.95
1722 1799 5.763698 GCTAAACTACTAAATAAGGCTGGGG 59.236 44.000 0.00 0.00 0.00 4.96
1723 1800 6.354130 TGCTAAACTACTAAATAAGGCTGGG 58.646 40.000 0.00 0.00 0.00 4.45
1724 1801 7.272978 TCTGCTAAACTACTAAATAAGGCTGG 58.727 38.462 0.00 0.00 0.00 4.85
1725 1802 8.894768 ATCTGCTAAACTACTAAATAAGGCTG 57.105 34.615 0.00 0.00 0.00 4.85
1726 1803 9.549078 GAATCTGCTAAACTACTAAATAAGGCT 57.451 33.333 0.00 0.00 0.00 4.58
1727 1804 9.549078 AGAATCTGCTAAACTACTAAATAAGGC 57.451 33.333 0.00 0.00 0.00 4.35
1738 1815 9.309516 CGTACCAAATTAGAATCTGCTAAACTA 57.690 33.333 0.00 0.00 34.33 2.24
1739 1816 7.822822 ACGTACCAAATTAGAATCTGCTAAACT 59.177 33.333 0.00 0.00 34.33 2.66
1740 1817 7.971455 ACGTACCAAATTAGAATCTGCTAAAC 58.029 34.615 0.00 0.00 34.33 2.01
1741 1818 8.447833 CAACGTACCAAATTAGAATCTGCTAAA 58.552 33.333 0.00 0.00 34.33 1.85
1742 1819 7.604927 ACAACGTACCAAATTAGAATCTGCTAA 59.395 33.333 0.00 0.00 35.06 3.09
1743 1820 7.101054 ACAACGTACCAAATTAGAATCTGCTA 58.899 34.615 0.00 0.00 0.00 3.49
1744 1821 5.938125 ACAACGTACCAAATTAGAATCTGCT 59.062 36.000 0.00 0.00 0.00 4.24
1745 1822 6.178239 ACAACGTACCAAATTAGAATCTGC 57.822 37.500 0.00 0.00 0.00 4.26
1746 1823 7.388712 CGTACAACGTACCAAATTAGAATCTG 58.611 38.462 0.00 0.00 36.74 2.90
1747 1824 6.532657 CCGTACAACGTACCAAATTAGAATCT 59.467 38.462 0.00 0.00 40.58 2.40
1748 1825 6.311200 ACCGTACAACGTACCAAATTAGAATC 59.689 38.462 0.00 0.00 40.58 2.52
1749 1826 6.165577 ACCGTACAACGTACCAAATTAGAAT 58.834 36.000 0.00 0.00 40.58 2.40
1750 1827 5.537188 ACCGTACAACGTACCAAATTAGAA 58.463 37.500 0.00 0.00 40.58 2.10
1751 1828 5.132897 ACCGTACAACGTACCAAATTAGA 57.867 39.130 0.00 0.00 40.58 2.10
1754 1831 4.379652 AGAACCGTACAACGTACCAAATT 58.620 39.130 0.00 0.00 40.58 1.82
1758 1835 4.295051 GTTAAGAACCGTACAACGTACCA 58.705 43.478 0.00 0.00 40.58 3.25
1797 1874 9.388346 CGTGTTCAGTTTTAATACAAATAGCAA 57.612 29.630 0.00 0.00 0.00 3.91
1798 1875 8.775527 TCGTGTTCAGTTTTAATACAAATAGCA 58.224 29.630 0.00 0.00 0.00 3.49
1857 1948 5.725551 TCCCCACAACAAGATATAACCAT 57.274 39.130 0.00 0.00 0.00 3.55
1863 1954 8.837099 TTTAATCATTCCCCACAACAAGATAT 57.163 30.769 0.00 0.00 0.00 1.63
1867 1958 6.758254 AGTTTTAATCATTCCCCACAACAAG 58.242 36.000 0.00 0.00 0.00 3.16
1869 1960 6.074648 AGAGTTTTAATCATTCCCCACAACA 58.925 36.000 0.00 0.00 0.00 3.33
1870 1961 6.590234 AGAGTTTTAATCATTCCCCACAAC 57.410 37.500 0.00 0.00 0.00 3.32
1883 1976 6.992063 AGTGATGCATCGAAGAGTTTTAAT 57.008 33.333 21.34 0.00 43.63 1.40
1886 1979 5.695851 AAAGTGATGCATCGAAGAGTTTT 57.304 34.783 21.34 10.50 43.63 2.43
1889 1982 4.067896 ACAAAAGTGATGCATCGAAGAGT 58.932 39.130 21.34 12.38 43.63 3.24
1910 2003 0.935196 GAACATTCCCCGCGATGTAC 59.065 55.000 8.23 0.00 0.00 2.90
1913 2006 3.420943 GGAACATTCCCCGCGATG 58.579 61.111 8.23 5.70 41.62 3.84
1945 2039 4.590222 AGTGAAGGCAAAGACAATGGATTT 59.410 37.500 0.00 0.00 0.00 2.17
1948 2042 3.228188 AGTGAAGGCAAAGACAATGGA 57.772 42.857 0.00 0.00 0.00 3.41
1955 2049 5.571285 TCTACTCTCTAGTGAAGGCAAAGA 58.429 41.667 0.00 0.00 36.36 2.52
1974 2068 8.677300 TGGATTGCATTTCTTATGAGTTTCTAC 58.323 33.333 0.00 0.00 0.00 2.59
1975 2069 8.806429 TGGATTGCATTTCTTATGAGTTTCTA 57.194 30.769 0.00 0.00 0.00 2.10
1976 2070 7.707624 TGGATTGCATTTCTTATGAGTTTCT 57.292 32.000 0.00 0.00 0.00 2.52
1977 2071 8.937634 ATTGGATTGCATTTCTTATGAGTTTC 57.062 30.769 0.00 0.00 0.00 2.78
1988 2147 3.852286 TGTGCTGATTGGATTGCATTTC 58.148 40.909 0.00 0.00 37.76 2.17
1990 2149 3.007074 TGTTGTGCTGATTGGATTGCATT 59.993 39.130 0.00 0.00 37.76 3.56
2016 2181 2.079925 GAGAAACCACTCAGATGCCAC 58.920 52.381 0.00 0.00 36.95 5.01
2022 2187 1.699730 TGACCGAGAAACCACTCAGA 58.300 50.000 0.00 0.00 36.80 3.27
2029 2194 3.181510 GCACACATTATGACCGAGAAACC 60.182 47.826 0.00 0.00 0.00 3.27
2082 2249 0.801251 CAGGTAAGTTCTGCTGCTGC 59.199 55.000 8.89 8.89 40.20 5.25
2083 2250 2.175878 ACAGGTAAGTTCTGCTGCTG 57.824 50.000 0.00 0.00 35.78 4.41
2087 2254 3.866449 GCAAGCTACAGGTAAGTTCTGCT 60.866 47.826 0.00 0.00 35.78 4.24
2089 2256 3.003480 GGCAAGCTACAGGTAAGTTCTG 58.997 50.000 0.00 0.00 38.16 3.02
2090 2257 2.907042 AGGCAAGCTACAGGTAAGTTCT 59.093 45.455 0.00 0.00 0.00 3.01
2108 2277 0.179936 ATGCTCTTGACCAGCTAGGC 59.820 55.000 2.50 0.00 43.14 3.93
2117 2286 2.008329 CTGAGAAGCCATGCTCTTGAC 58.992 52.381 3.58 0.00 38.25 3.18
2176 2345 7.883311 ACCACTGTAGTCTTGTAAAAGCAATAT 59.117 33.333 0.00 0.00 0.00 1.28
2181 2350 4.814771 ACACCACTGTAGTCTTGTAAAAGC 59.185 41.667 0.00 0.00 0.00 3.51
2182 2351 6.046593 TGACACCACTGTAGTCTTGTAAAAG 58.953 40.000 8.15 0.00 33.56 2.27
2183 2352 5.979993 TGACACCACTGTAGTCTTGTAAAA 58.020 37.500 8.15 0.00 33.56 1.52
2188 2362 5.354234 ACTTTTTGACACCACTGTAGTCTTG 59.646 40.000 8.15 0.00 33.56 3.02
2196 2370 4.703897 TCTAGGACTTTTTGACACCACTG 58.296 43.478 0.00 0.00 0.00 3.66
2222 2403 1.541588 GCAAACTGTTGATCAGGTCCC 59.458 52.381 0.00 0.00 44.18 4.46
2224 2405 3.057946 GGAAGCAAACTGTTGATCAGGTC 60.058 47.826 0.00 0.00 44.18 3.85
2230 2411 3.499338 TGATGGGAAGCAAACTGTTGAT 58.501 40.909 0.00 0.00 36.83 2.57
2270 2451 8.217111 TGAATAGTTGGATCCAAACATAGCATA 58.783 33.333 28.64 11.36 37.70 3.14
2276 2457 7.781324 AACTTGAATAGTTGGATCCAAACAT 57.219 32.000 28.64 20.18 45.33 2.71
2318 2499 2.875296 CCAAGGTTGGTTCCAATCTCA 58.125 47.619 16.38 0.00 43.43 3.27
2385 2567 5.643777 ACTTGCAGCCTAACATAAACTGTAG 59.356 40.000 0.00 0.00 36.98 2.74
2510 2696 0.525242 TGCAGCAGAAAACACGCAAC 60.525 50.000 0.00 0.00 0.00 4.17
2515 2702 4.503741 TCCTAATTGCAGCAGAAAACAC 57.496 40.909 0.00 0.00 0.00 3.32
2566 2753 1.915141 CTGGTTCCTGTCCAGCAAAT 58.085 50.000 0.00 0.00 44.46 2.32
2572 2759 0.824109 CGCTATCTGGTTCCTGTCCA 59.176 55.000 0.00 0.00 0.00 4.02
2575 2762 2.363680 CTCATCGCTATCTGGTTCCTGT 59.636 50.000 0.00 0.00 0.00 4.00
2660 2847 3.634448 TGGAAACAAAGATTTTCGCTGGA 59.366 39.130 0.00 0.00 37.44 3.86
2676 2863 2.384382 CACGCACACAGAAATGGAAAC 58.616 47.619 0.00 0.00 0.00 2.78
2681 2868 1.464687 GCTAGCACGCACACAGAAATG 60.465 52.381 10.63 0.00 0.00 2.32
2693 2883 1.225855 TGTGTTTGGAAGCTAGCACG 58.774 50.000 18.83 0.00 0.00 5.34
2728 2918 9.554395 TGTTGTCAACTCAGAAATGTTTAGATA 57.446 29.630 16.45 0.00 0.00 1.98
2749 2939 1.003851 CGTTCACGTCAACCTGTTGT 58.996 50.000 9.65 0.00 41.16 3.32
2758 2948 0.306228 CATTGTTGCCGTTCACGTCA 59.694 50.000 0.00 0.00 37.74 4.35
2785 2975 6.096987 TCTCTGACTTCAAGAACTTGTACAGT 59.903 38.462 13.15 12.86 41.16 3.55
2812 3002 1.664873 GTTCTCCAAATAGACCGCCC 58.335 55.000 0.00 0.00 0.00 6.13
2830 3020 3.070446 TGGTGAAGTTCCACTTGATACGT 59.930 43.478 0.00 0.00 38.80 3.57
2949 3139 4.282449 TGTTGGAGACGAGGAATACAGAAA 59.718 41.667 0.00 0.00 0.00 2.52
2953 3143 3.427573 TCTGTTGGAGACGAGGAATACA 58.572 45.455 0.00 0.00 0.00 2.29
2954 3144 4.174762 GTTCTGTTGGAGACGAGGAATAC 58.825 47.826 0.00 0.00 0.00 1.89
2959 3149 0.388649 CCGTTCTGTTGGAGACGAGG 60.389 60.000 0.00 0.00 31.01 4.63
2960 3150 0.314302 ACCGTTCTGTTGGAGACGAG 59.686 55.000 0.00 0.00 31.01 4.18
2970 3160 3.813166 CACCAAGTGAATTACCGTTCTGT 59.187 43.478 0.00 0.00 35.23 3.41
2986 3176 2.223688 TGCGGAAACAACATTCACCAAG 60.224 45.455 0.00 0.00 0.00 3.61
2987 3177 1.751351 TGCGGAAACAACATTCACCAA 59.249 42.857 0.00 0.00 0.00 3.67
2999 3189 3.436704 TCTTGATGTCATTCTGCGGAAAC 59.563 43.478 12.96 7.62 34.90 2.78
3001 3191 3.333029 TCTTGATGTCATTCTGCGGAA 57.667 42.857 11.11 11.11 35.78 4.30
3002 3192 3.264947 CTTCTTGATGTCATTCTGCGGA 58.735 45.455 0.00 0.00 0.00 5.54
3044 3238 1.347050 CGCATGATCTTCCCTGGAGAT 59.653 52.381 0.00 0.00 0.00 2.75
3045 3239 0.755079 CGCATGATCTTCCCTGGAGA 59.245 55.000 0.00 0.00 0.00 3.71
3065 3259 0.245266 ACATACACATGACACGCCGA 59.755 50.000 0.00 0.00 35.96 5.54
3221 3421 1.130955 GGCTGTGTTTTGTTGCATCG 58.869 50.000 0.00 0.00 0.00 3.84
3333 3535 4.336889 TTTGTCGACACTTCCATCTCTT 57.663 40.909 19.90 0.00 0.00 2.85
3400 3602 4.101585 CCTAGCTCTGGGATATTTGACACA 59.898 45.833 0.00 0.00 32.26 3.72
3491 3693 4.415150 CGCTGGGCCAGATGTGGT 62.415 66.667 37.07 0.00 46.96 4.16
3571 3773 1.478654 GGGACTTTTGTGCAAGGAGGA 60.479 52.381 0.00 0.00 42.95 3.71
3631 3833 9.665719 TTGCTAAGATTCAGACATACAACATAA 57.334 29.630 0.00 0.00 0.00 1.90
3636 3838 8.791327 TCATTTGCTAAGATTCAGACATACAA 57.209 30.769 0.00 0.00 0.00 2.41
3643 3845 6.475504 TCAACCTCATTTGCTAAGATTCAGA 58.524 36.000 0.00 0.00 0.00 3.27
3644 3846 6.748333 TCAACCTCATTTGCTAAGATTCAG 57.252 37.500 0.00 0.00 0.00 3.02
3645 3847 7.066645 CAGATCAACCTCATTTGCTAAGATTCA 59.933 37.037 0.00 0.00 0.00 2.57
3646 3848 7.416022 CAGATCAACCTCATTTGCTAAGATTC 58.584 38.462 0.00 0.00 0.00 2.52
3647 3849 6.320672 CCAGATCAACCTCATTTGCTAAGATT 59.679 38.462 0.00 0.00 0.00 2.40
3648 3850 5.826737 CCAGATCAACCTCATTTGCTAAGAT 59.173 40.000 0.00 0.00 0.00 2.40
3650 3852 5.188434 TCCAGATCAACCTCATTTGCTAAG 58.812 41.667 0.00 0.00 0.00 2.18
3653 3855 3.726557 TCCAGATCAACCTCATTTGCT 57.273 42.857 0.00 0.00 0.00 3.91
3654 3856 3.490419 GCATCCAGATCAACCTCATTTGC 60.490 47.826 0.00 0.00 0.00 3.68
3655 3857 3.697542 TGCATCCAGATCAACCTCATTTG 59.302 43.478 0.00 0.00 0.00 2.32
3656 3858 3.952323 CTGCATCCAGATCAACCTCATTT 59.048 43.478 0.00 0.00 41.77 2.32
3657 3859 3.552875 CTGCATCCAGATCAACCTCATT 58.447 45.455 0.00 0.00 41.77 2.57
3658 3860 2.158652 CCTGCATCCAGATCAACCTCAT 60.159 50.000 0.00 0.00 41.77 2.90
3659 3861 1.211212 CCTGCATCCAGATCAACCTCA 59.789 52.381 0.00 0.00 41.77 3.86
3660 3862 1.487976 TCCTGCATCCAGATCAACCTC 59.512 52.381 0.00 0.00 41.77 3.85
3661 3863 1.489649 CTCCTGCATCCAGATCAACCT 59.510 52.381 0.00 0.00 41.77 3.50
3662 3864 1.964552 CTCCTGCATCCAGATCAACC 58.035 55.000 0.00 0.00 41.77 3.77
3664 3866 1.210538 AGCTCCTGCATCCAGATCAA 58.789 50.000 0.00 0.00 41.77 2.57
3665 3867 1.134189 CAAGCTCCTGCATCCAGATCA 60.134 52.381 0.00 0.00 41.77 2.92
3666 3868 1.595466 CAAGCTCCTGCATCCAGATC 58.405 55.000 0.00 0.00 41.77 2.75
3667 3869 0.183014 CCAAGCTCCTGCATCCAGAT 59.817 55.000 0.00 0.00 41.77 2.90
3668 3870 1.203441 ACCAAGCTCCTGCATCCAGA 61.203 55.000 0.00 0.00 41.77 3.86
3669 3871 0.323178 AACCAAGCTCCTGCATCCAG 60.323 55.000 0.00 0.00 42.74 3.86
3670 3872 0.322816 GAACCAAGCTCCTGCATCCA 60.323 55.000 0.00 0.00 42.74 3.41
3671 3873 1.034292 GGAACCAAGCTCCTGCATCC 61.034 60.000 0.00 0.00 42.74 3.51
3704 3914 2.961510 ACTAGATCAGCCTCATCTGCT 58.038 47.619 0.00 0.00 40.41 4.24
3705 3915 4.078537 TCTACTAGATCAGCCTCATCTGC 58.921 47.826 0.00 0.00 32.61 4.26
3709 3919 5.047164 CAGCAATCTACTAGATCAGCCTCAT 60.047 44.000 15.03 1.13 36.75 2.90
3715 3925 7.144661 CAGGTAACAGCAATCTACTAGATCAG 58.855 42.308 0.00 0.00 33.74 2.90
3716 3926 7.043961 CAGGTAACAGCAATCTACTAGATCA 57.956 40.000 0.00 0.00 33.74 2.92
3756 3966 1.679977 CCTGGGTGGAGCATTGGTG 60.680 63.158 0.00 0.00 38.35 4.17
3774 3984 1.098050 GGCATGTCATTGGAGGTGTC 58.902 55.000 0.00 0.00 0.00 3.67
3904 4117 3.719268 AAGTAACCCTGCATGATGTGA 57.281 42.857 0.00 0.00 0.00 3.58
3923 4136 5.163405 GGAGTGATGCACCTGAGACTTATAA 60.163 44.000 0.00 0.00 34.49 0.98
3926 4139 2.497675 GGAGTGATGCACCTGAGACTTA 59.502 50.000 0.00 0.00 34.49 2.24
3944 4157 7.571919 ACCATCCTATATGCATATCAAAGGAG 58.428 38.462 28.36 21.77 36.35 3.69
3946 4159 6.481313 CGACCATCCTATATGCATATCAAAGG 59.519 42.308 22.33 21.64 0.00 3.11
3954 4167 3.988976 AAGCGACCATCCTATATGCAT 57.011 42.857 3.79 3.79 0.00 3.96
3973 4197 1.910671 ACCCTGCCATTTACGAGGTAA 59.089 47.619 0.00 0.00 0.00 2.85
3992 4216 7.158021 CAGATCATCCTCCTTCCTACAATAAC 58.842 42.308 0.00 0.00 0.00 1.89
3995 4219 4.041444 GCAGATCATCCTCCTTCCTACAAT 59.959 45.833 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.