Multiple sequence alignment - TraesCS4A01G017800

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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 TraesCS4A01G017800 chr4A 100.000 2318 0 0 543 2860 11771319 11773636 0.000000e+00 4281.0
1 TraesCS4A01G017800 chr4A 100.000 411 0 0 1 411 11770777 11771187 0.000000e+00 760.0
2 TraesCS4A01G017800 chr4B 86.590 1126 121 20 988 2100 569766447 569765339 0.000000e+00 1216.0
3 TraesCS4A01G017800 chr4B 85.106 517 47 10 2190 2705 569765081 569764594 4.250000e-138 501.0
4 TraesCS4A01G017800 chr4B 84.498 329 36 7 41 356 569767648 569767322 7.690000e-81 311.0
5 TraesCS4A01G017800 chr4B 79.675 123 12 5 2740 2860 569764588 569764477 3.060000e-10 76.8
6 TraesCS4A01G017800 chr4D 88.100 916 83 14 1426 2323 455763589 455762682 0.000000e+00 1064.0
7 TraesCS4A01G017800 chr4D 88.418 354 40 1 988 1341 455764055 455763703 2.630000e-115 425.0
8 TraesCS4A01G017800 chr4D 87.071 379 33 8 14 382 455765204 455764832 5.700000e-112 414.0
9 TraesCS4A01G017800 chr4D 85.567 388 25 5 2363 2748 455761483 455761125 7.480000e-101 377.0
10 TraesCS4A01G017800 chr4D 85.714 105 10 3 2756 2860 455759866 455759767 3.900000e-19 106.0


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 TraesCS4A01G017800 chr4A 11770777 11773636 2859 False 2520.5 4281 100.00000 1 2860 2 chr4A.!!$F1 2859
1 TraesCS4A01G017800 chr4B 569764477 569767648 3171 True 526.2 1216 83.96725 41 2860 4 chr4B.!!$R1 2819
2 TraesCS4A01G017800 chr4D 455759767 455765204 5437 True 477.2 1064 86.97400 14 2860 5 chr4D.!!$R1 2846

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
751 788 0.0293 CACTTTGGCCACTGAACGTG 59.971 55.0 3.88 0.17 43.41 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2323 3102 0.182061 ATTGGCTCGTGCATCAGGAT 59.818 50.0 12.07 0.0 41.91 3.24 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
24 25 2.563179 GGAGGGAAGGGAAAAGAAAAGC 59.437 50.000 0.00 0.00 0.00 3.51
48 49 4.468689 GGGACGGGCGGAGAAAGG 62.469 72.222 0.00 0.00 0.00 3.11
90 95 0.376152 GATGCAAGCATCGTCTGTGG 59.624 55.000 18.10 0.00 42.55 4.17
103 114 0.895530 TCTGTGGAGGTCAATCCGAC 59.104 55.000 0.00 0.00 42.77 4.79
147 158 2.125512 CTGCGGACGGGAGGAAAG 60.126 66.667 0.00 0.00 0.00 2.62
150 161 2.577593 CGGACGGGAGGAAAGGAC 59.422 66.667 0.00 0.00 0.00 3.85
163 174 0.246635 AAAGGACCAGGTGTCGATCG 59.753 55.000 9.36 9.36 45.46 3.69
181 195 2.815211 CTCATCGTGGCGGTGTGG 60.815 66.667 1.69 0.00 39.21 4.17
182 196 4.386951 TCATCGTGGCGGTGTGGG 62.387 66.667 1.69 0.00 39.21 4.61
189 203 1.152652 TGGCGGTGTGGGTGAAAAT 60.153 52.632 0.00 0.00 0.00 1.82
194 208 2.468831 CGGTGTGGGTGAAAATGTTTG 58.531 47.619 0.00 0.00 0.00 2.93
221 235 4.399004 TTTGTTGATGGGTGAAAGGTTG 57.601 40.909 0.00 0.00 0.00 3.77
242 265 1.083489 TAAATGAAAGTGGGAGCGCG 58.917 50.000 0.00 0.00 0.00 6.86
246 269 2.436646 AAAGTGGGAGCGCGGATG 60.437 61.111 8.83 0.00 0.00 3.51
317 340 0.110192 CTCCGACGAAAGCAAAAGGC 60.110 55.000 0.00 0.00 45.30 4.35
368 391 1.440938 TAGCGGCTTCTCTCTCTCGC 61.441 60.000 8.26 0.00 42.91 5.03
374 397 1.403679 GCTTCTCTCTCTCGCTTGCTA 59.596 52.381 0.00 0.00 0.00 3.49
559 582 3.656045 GGTCGTTGGTTGGGTGCG 61.656 66.667 0.00 0.00 0.00 5.34
560 583 2.589442 GTCGTTGGTTGGGTGCGA 60.589 61.111 0.00 0.00 0.00 5.10
561 584 2.181521 GTCGTTGGTTGGGTGCGAA 61.182 57.895 0.00 0.00 33.30 4.70
562 585 1.890041 TCGTTGGTTGGGTGCGAAG 60.890 57.895 0.00 0.00 0.00 3.79
597 626 0.041684 ATGGGCCTTTTCCTCCAAGG 59.958 55.000 4.53 0.00 43.47 3.61
600 629 4.442038 CCTTTTCCTCCAAGGCCC 57.558 61.111 0.00 0.00 34.59 5.80
601 630 1.776969 CCTTTTCCTCCAAGGCCCT 59.223 57.895 0.00 0.00 34.59 5.19
603 632 1.228862 TTTTCCTCCAAGGCCCTGC 60.229 57.895 0.00 0.00 34.61 4.85
642 679 3.617284 CCTAAACTTGGGCCTCGTAAAT 58.383 45.455 4.53 0.00 0.00 1.40
645 682 2.109425 ACTTGGGCCTCGTAAATGTC 57.891 50.000 4.53 0.00 0.00 3.06
646 683 1.628846 ACTTGGGCCTCGTAAATGTCT 59.371 47.619 4.53 0.00 0.00 3.41
650 687 1.679032 GGGCCTCGTAAATGTCTGCTT 60.679 52.381 0.84 0.00 0.00 3.91
651 688 1.398390 GGCCTCGTAAATGTCTGCTTG 59.602 52.381 0.00 0.00 0.00 4.01
652 689 1.202076 GCCTCGTAAATGTCTGCTTGC 60.202 52.381 0.00 0.00 0.00 4.01
656 693 3.920446 TCGTAAATGTCTGCTTGCTGTA 58.080 40.909 0.00 0.00 0.00 2.74
658 695 5.656480 TCGTAAATGTCTGCTTGCTGTATA 58.344 37.500 0.00 0.00 0.00 1.47
659 696 5.518847 TCGTAAATGTCTGCTTGCTGTATAC 59.481 40.000 0.00 0.00 0.00 1.47
661 698 6.291849 CGTAAATGTCTGCTTGCTGTATACTC 60.292 42.308 4.17 0.00 0.00 2.59
662 699 3.526931 TGTCTGCTTGCTGTATACTCC 57.473 47.619 4.17 0.00 0.00 3.85
663 700 2.168521 TGTCTGCTTGCTGTATACTCCC 59.831 50.000 4.17 0.00 0.00 4.30
668 705 2.170607 GCTTGCTGTATACTCCCCTCAA 59.829 50.000 4.17 0.00 0.00 3.02
670 707 4.843728 CTTGCTGTATACTCCCCTCAAAA 58.156 43.478 4.17 0.00 0.00 2.44
673 710 4.042311 TGCTGTATACTCCCCTCAAAACAA 59.958 41.667 4.17 0.00 0.00 2.83
674 711 4.395231 GCTGTATACTCCCCTCAAAACAAC 59.605 45.833 4.17 0.00 0.00 3.32
678 715 1.524008 CTCCCCTCAAAACAACGGGC 61.524 60.000 0.00 0.00 35.29 6.13
679 716 2.570284 CCCCTCAAAACAACGGGCC 61.570 63.158 0.00 0.00 35.29 5.80
680 717 2.570284 CCCTCAAAACAACGGGCCC 61.570 63.158 13.57 13.57 0.00 5.80
681 718 2.570284 CCTCAAAACAACGGGCCCC 61.570 63.158 18.66 0.00 0.00 5.80
686 723 1.413077 CAAAACAACGGGCCCCTAAAA 59.587 47.619 18.66 0.00 0.00 1.52
687 724 1.790818 AAACAACGGGCCCCTAAAAA 58.209 45.000 18.66 0.00 0.00 1.94
704 741 1.981256 AAAAACGGCATCACCTGACT 58.019 45.000 0.00 0.00 35.61 3.41
705 742 1.981256 AAAACGGCATCACCTGACTT 58.019 45.000 0.00 0.00 35.61 3.01
706 743 1.523758 AAACGGCATCACCTGACTTC 58.476 50.000 0.00 0.00 35.61 3.01
707 744 0.670546 AACGGCATCACCTGACTTCG 60.671 55.000 0.00 0.00 35.61 3.79
708 745 1.811266 CGGCATCACCTGACTTCGG 60.811 63.158 0.00 0.00 35.61 4.30
709 746 2.109126 GGCATCACCTGACTTCGGC 61.109 63.158 0.00 0.00 34.51 5.54
710 747 2.109126 GCATCACCTGACTTCGGCC 61.109 63.158 0.00 0.00 0.00 6.13
711 748 1.811266 CATCACCTGACTTCGGCCG 60.811 63.158 22.12 22.12 0.00 6.13
712 749 3.665675 ATCACCTGACTTCGGCCGC 62.666 63.158 23.51 6.96 0.00 6.53
713 750 4.379243 CACCTGACTTCGGCCGCT 62.379 66.667 23.51 4.59 0.00 5.52
714 751 3.626924 ACCTGACTTCGGCCGCTT 61.627 61.111 23.51 6.45 0.00 4.68
715 752 2.358737 CCTGACTTCGGCCGCTTT 60.359 61.111 23.51 6.01 0.00 3.51
716 753 2.680913 CCTGACTTCGGCCGCTTTG 61.681 63.158 23.51 12.48 0.00 2.77
717 754 1.961277 CTGACTTCGGCCGCTTTGT 60.961 57.895 23.51 15.82 0.00 2.83
718 755 1.901650 CTGACTTCGGCCGCTTTGTC 61.902 60.000 23.51 23.12 0.00 3.18
719 756 1.668151 GACTTCGGCCGCTTTGTCT 60.668 57.895 23.51 0.00 0.00 3.41
745 782 3.525268 AAAAAGTCACTTTGGCCACTG 57.475 42.857 3.88 3.23 33.64 3.66
746 783 2.435372 AAAGTCACTTTGGCCACTGA 57.565 45.000 3.88 3.49 31.98 3.41
747 784 2.435372 AAGTCACTTTGGCCACTGAA 57.565 45.000 3.88 0.00 0.00 3.02
748 785 1.680338 AGTCACTTTGGCCACTGAAC 58.320 50.000 3.88 0.00 0.00 3.18
749 786 0.307760 GTCACTTTGGCCACTGAACG 59.692 55.000 3.88 0.00 0.00 3.95
751 788 0.029300 CACTTTGGCCACTGAACGTG 59.971 55.000 3.88 0.17 43.41 4.49
759 796 2.555123 CACTGAACGTGGGATTGGG 58.445 57.895 0.00 0.00 40.02 4.12
760 797 1.303317 ACTGAACGTGGGATTGGGC 60.303 57.895 0.00 0.00 0.00 5.36
764 801 2.515996 GAACGTGGGATTGGGCGAGA 62.516 60.000 0.00 0.00 0.00 4.04
767 804 3.781307 TGGGATTGGGCGAGACGG 61.781 66.667 0.00 0.00 0.00 4.79
809 854 4.389576 GACGGCACAAGCGGCAAG 62.390 66.667 1.45 0.00 44.14 4.01
839 884 2.724721 CGTGCGTCGTCGTGTTCT 60.725 61.111 3.66 0.00 39.49 3.01
841 886 1.198397 GTGCGTCGTCGTGTTCTTG 59.802 57.895 3.66 0.00 39.49 3.02
851 896 0.874175 CGTGTTCTTGCTGACGGTGA 60.874 55.000 0.00 0.00 0.00 4.02
858 903 4.357947 GCTGACGGTGACCTCGCA 62.358 66.667 0.00 0.00 0.00 5.10
950 1485 3.467119 CGCGGAACCTGTTCGACG 61.467 66.667 0.00 6.46 40.37 5.12
951 1486 2.355481 GCGGAACCTGTTCGACGT 60.355 61.111 4.09 0.00 40.37 4.34
959 1494 1.087771 CCTGTTCGACGTATTGCCCC 61.088 60.000 0.00 0.00 0.00 5.80
961 1496 2.509786 TTCGACGTATTGCCCCGC 60.510 61.111 0.00 0.00 0.00 6.13
964 1499 4.476752 GACGTATTGCCCCGCCCA 62.477 66.667 0.00 0.00 0.00 5.36
966 1501 3.514362 CGTATTGCCCCGCCCAAC 61.514 66.667 0.00 0.00 0.00 3.77
969 1504 2.001838 TATTGCCCCGCCCAACCTA 61.002 57.895 0.00 0.00 0.00 3.08
970 1505 2.273588 TATTGCCCCGCCCAACCTAC 62.274 60.000 0.00 0.00 0.00 3.18
975 1510 2.732619 CCCGCCCAACCTACTCTCC 61.733 68.421 0.00 0.00 0.00 3.71
976 1511 1.686110 CCGCCCAACCTACTCTCCT 60.686 63.158 0.00 0.00 0.00 3.69
977 1512 1.517832 CGCCCAACCTACTCTCCTG 59.482 63.158 0.00 0.00 0.00 3.86
978 1513 1.908483 GCCCAACCTACTCTCCTGG 59.092 63.158 0.00 0.00 0.00 4.45
979 1514 0.617820 GCCCAACCTACTCTCCTGGA 60.618 60.000 0.00 0.00 0.00 3.86
980 1515 1.196012 CCCAACCTACTCTCCTGGAC 58.804 60.000 0.00 0.00 0.00 4.02
981 1516 1.273324 CCCAACCTACTCTCCTGGACT 60.273 57.143 0.00 0.00 0.00 3.85
982 1517 2.104170 CCAACCTACTCTCCTGGACTC 58.896 57.143 0.00 0.00 0.00 3.36
983 1518 2.291930 CCAACCTACTCTCCTGGACTCT 60.292 54.545 0.00 0.00 0.00 3.24
984 1519 3.020984 CAACCTACTCTCCTGGACTCTC 58.979 54.545 0.00 0.00 0.00 3.20
985 1520 2.568979 ACCTACTCTCCTGGACTCTCT 58.431 52.381 0.00 0.00 0.00 3.10
986 1521 2.508300 ACCTACTCTCCTGGACTCTCTC 59.492 54.545 0.00 0.00 0.00 3.20
987 1522 2.777692 CCTACTCTCCTGGACTCTCTCT 59.222 54.545 0.00 0.00 0.00 3.10
988 1523 3.181454 CCTACTCTCCTGGACTCTCTCTC 60.181 56.522 0.00 0.00 0.00 3.20
989 1524 2.562296 ACTCTCCTGGACTCTCTCTCT 58.438 52.381 0.00 0.00 0.00 3.10
990 1525 2.505819 ACTCTCCTGGACTCTCTCTCTC 59.494 54.545 0.00 0.00 0.00 3.20
991 1526 2.774234 CTCTCCTGGACTCTCTCTCTCT 59.226 54.545 0.00 0.00 0.00 3.10
999 1534 1.299541 CTCTCTCTCTCTCTCGTGCC 58.700 60.000 0.00 0.00 0.00 5.01
1007 1542 2.887568 CTCTCGTGCCATGGCGAC 60.888 66.667 30.87 25.83 45.51 5.19
1017 1552 2.751436 ATGGCGACGGCATTGCTT 60.751 55.556 29.04 9.89 46.61 3.91
1018 1553 2.764314 ATGGCGACGGCATTGCTTC 61.764 57.895 29.04 4.80 46.61 3.86
1019 1554 3.430862 GGCGACGGCATTGCTTCA 61.431 61.111 17.49 0.00 42.47 3.02
1103 1638 2.756283 CCGCTTCGAGGTCCCTCT 60.756 66.667 11.41 0.00 40.69 3.69
1104 1639 2.776913 CCGCTTCGAGGTCCCTCTC 61.777 68.421 11.41 0.00 40.69 3.20
1107 1642 1.000486 CTTCGAGGTCCCTCTCCCA 60.000 63.158 11.41 0.00 40.69 4.37
1108 1643 1.305046 TTCGAGGTCCCTCTCCCAC 60.305 63.158 11.41 0.00 40.69 4.61
1110 1645 2.760385 GAGGTCCCTCTCCCACGG 60.760 72.222 6.08 0.00 39.80 4.94
1164 1699 1.021920 GGCTTCTCTCCGTGCCTTTC 61.022 60.000 0.00 0.00 41.92 2.62
1198 1733 1.226686 CCTAGCTGCCGATGTCATGC 61.227 60.000 0.00 0.00 0.00 4.06
1343 1878 2.419667 GCTGCAGAAAAAGGTACGGTA 58.580 47.619 20.43 0.00 0.00 4.02
1358 1893 1.605058 CGGTACTGGTCACCTCAGGG 61.605 65.000 0.00 0.00 36.62 4.45
1369 1904 1.286305 ACCTCAGGGTTGGGTTGTGT 61.286 55.000 0.00 0.00 44.73 3.72
1397 1936 0.754957 TTCCAACCACCACCAGCAAG 60.755 55.000 0.00 0.00 0.00 4.01
1398 1937 2.202395 CCAACCACCACCAGCAAGG 61.202 63.158 0.00 0.00 45.67 3.61
1399 1938 2.521708 AACCACCACCAGCAAGGC 60.522 61.111 0.00 0.00 43.14 4.35
1400 1939 3.372422 AACCACCACCAGCAAGGCA 62.372 57.895 0.00 0.00 43.14 4.75
1401 1940 2.987547 CCACCACCAGCAAGGCAG 60.988 66.667 0.00 0.00 43.14 4.85
1402 1941 3.677648 CACCACCAGCAAGGCAGC 61.678 66.667 0.00 0.00 43.14 5.25
1422 1961 4.575645 CAGCAATCTGAAGGGAATTCTCTC 59.424 45.833 8.67 3.18 42.95 3.20
1443 2025 0.962356 GGCTGCAGTACAATGGCACT 60.962 55.000 16.64 0.00 33.34 4.40
1444 2026 1.678728 GGCTGCAGTACAATGGCACTA 60.679 52.381 16.64 0.00 33.34 2.74
1558 2140 0.394899 CACCCTGCAGGAGGAAATCC 60.395 60.000 34.91 0.00 46.33 3.01
1593 2175 0.958382 GCAGCACCGTGGTAATCCAA 60.958 55.000 2.23 0.00 46.15 3.53
1594 2176 1.750193 CAGCACCGTGGTAATCCAAT 58.250 50.000 2.23 0.00 46.15 3.16
1601 2183 1.749286 CGTGGTAATCCAATCCACCCC 60.749 57.143 7.78 0.00 46.15 4.95
1602 2184 0.930726 TGGTAATCCAATCCACCCCC 59.069 55.000 0.00 0.00 41.25 5.40
1617 2199 2.296920 CCCCCTTCCTTCATCGTCA 58.703 57.895 0.00 0.00 0.00 4.35
1630 2212 0.317160 ATCGTCAGTCCAACTCGCAA 59.683 50.000 0.00 0.00 0.00 4.85
1637 2219 1.470098 AGTCCAACTCGCAATGCATTC 59.530 47.619 9.53 3.97 0.00 2.67
1656 2239 4.377839 TTCGCATCTGAAACAAAAACCA 57.622 36.364 0.00 0.00 0.00 3.67
1657 2240 3.963665 TCGCATCTGAAACAAAAACCAG 58.036 40.909 0.00 0.00 0.00 4.00
1686 2269 3.393089 TCTCCTGAACTTGAGCTGTTC 57.607 47.619 8.16 8.16 42.77 3.18
1687 2270 2.968574 TCTCCTGAACTTGAGCTGTTCT 59.031 45.455 14.42 0.00 42.86 3.01
1689 2272 4.133078 CTCCTGAACTTGAGCTGTTCTTT 58.867 43.478 14.42 0.00 42.86 2.52
1698 2281 2.495270 TGAGCTGTTCTTTTTGTTGGCA 59.505 40.909 0.00 0.00 0.00 4.92
1700 2283 3.932089 GAGCTGTTCTTTTTGTTGGCAAA 59.068 39.130 0.00 0.00 42.25 3.68
1733 2316 4.467107 AGGGTCGGGGAGGAGCTC 62.467 72.222 4.71 4.71 34.90 4.09
1745 2328 2.049063 GAGCTCGTCAAGGCGTGT 60.049 61.111 0.00 0.00 0.00 4.49
1748 2331 1.065102 GAGCTCGTCAAGGCGTGTATA 59.935 52.381 0.00 0.00 0.00 1.47
1820 2403 1.408822 GGGGAGAAGATGATGGCGTTT 60.409 52.381 0.00 0.00 0.00 3.60
1864 2447 2.019984 GTTCCTGCCCAGATAGCAAAG 58.980 52.381 0.00 0.00 40.35 2.77
1867 2450 2.019984 CCTGCCCAGATAGCAAAGTTC 58.980 52.381 0.00 0.00 40.35 3.01
1942 2525 2.729194 AGAGTAGGAGTGTAGCCTGTG 58.271 52.381 0.00 0.00 36.96 3.66
1959 2542 3.476552 CTGTGGGAAGTTGTTTGCTCTA 58.523 45.455 0.00 0.00 0.00 2.43
1964 2547 4.518970 TGGGAAGTTGTTTGCTCTATGAAC 59.481 41.667 0.00 0.00 0.00 3.18
1980 2563 7.148606 GCTCTATGAACTGCTTGATGTATGATC 60.149 40.741 0.00 0.00 0.00 2.92
1981 2564 7.729116 TCTATGAACTGCTTGATGTATGATCA 58.271 34.615 0.00 0.00 0.00 2.92
1982 2565 6.862711 ATGAACTGCTTGATGTATGATCAG 57.137 37.500 0.09 0.00 0.00 2.90
1990 2587 6.155827 GCTTGATGTATGATCAGGAGTACTC 58.844 44.000 14.87 14.87 0.00 2.59
2029 2626 8.573885 CATGTTATTAAGCCAGACAATCATCAT 58.426 33.333 0.00 0.00 0.00 2.45
2035 2632 3.945921 AGCCAGACAATCATCATTGACAG 59.054 43.478 0.00 0.00 41.97 3.51
2046 2643 6.778834 TCATCATTGACAGCCATAAAATGT 57.221 33.333 0.00 0.00 31.63 2.71
2054 2651 5.716228 TGACAGCCATAAAATGTTTCTCCAT 59.284 36.000 0.00 0.00 0.00 3.41
2067 2664 7.951530 ATGTTTCTCCATTGTCATTTCAAAC 57.048 32.000 0.00 0.00 0.00 2.93
2071 2668 8.829612 GTTTCTCCATTGTCATTTCAAACAAAT 58.170 29.630 0.00 0.00 38.74 2.32
2121 2719 6.646240 CACACAAAGGTTTTGCAAGCTATATT 59.354 34.615 0.00 0.00 39.96 1.28
2122 2720 6.646240 ACACAAAGGTTTTGCAAGCTATATTG 59.354 34.615 0.00 5.45 39.96 1.90
2128 2726 7.707104 AGGTTTTGCAAGCTATATTGACATAC 58.293 34.615 0.00 0.00 39.04 2.39
2130 2728 7.416213 GGTTTTGCAAGCTATATTGACATACCA 60.416 37.037 0.00 0.00 31.32 3.25
2148 2746 8.331931 ACATACCAATTCTATTACAAGAGGGA 57.668 34.615 0.00 0.00 0.00 4.20
2169 2767 7.441836 AGGGAAAACAACAAATTCTACATTCC 58.558 34.615 0.00 0.00 33.52 3.01
2170 2768 7.070571 AGGGAAAACAACAAATTCTACATTCCA 59.929 33.333 0.00 0.00 35.45 3.53
2172 2770 8.925700 GGAAAACAACAAATTCTACATTCCATC 58.074 33.333 0.00 0.00 34.25 3.51
2173 2771 9.474920 GAAAACAACAAATTCTACATTCCATCA 57.525 29.630 0.00 0.00 0.00 3.07
2174 2772 9.829507 AAAACAACAAATTCTACATTCCATCAA 57.170 25.926 0.00 0.00 0.00 2.57
2185 2785 7.730084 TCTACATTCCATCAAGACTCCTTATG 58.270 38.462 0.00 0.00 0.00 1.90
2226 3005 3.582647 TCAGTGGCCTACATTCTTCAGAA 59.417 43.478 3.32 0.00 38.56 3.02
2243 3022 5.604758 TCAGAATAGTTCATCTGGTGGAG 57.395 43.478 3.23 0.00 42.62 3.86
2269 3048 8.462811 GCAGATAGCAGTTAAGATAGCATACTA 58.537 37.037 0.00 0.00 44.79 1.82
2287 3066 4.026356 ACTATGCTGAAGCTGTTCCTTT 57.974 40.909 3.61 0.00 42.66 3.11
2303 3082 5.300792 TGTTCCTTTTGTTCCCATCTTGTAC 59.699 40.000 0.00 0.00 0.00 2.90
2314 3093 4.040829 TCCCATCTTGTACATGAGCCATAG 59.959 45.833 15.72 0.00 0.00 2.23
2323 3102 3.378512 ACATGAGCCATAGACTCCTGAA 58.621 45.455 0.00 0.00 34.54 3.02
2324 3103 3.972638 ACATGAGCCATAGACTCCTGAAT 59.027 43.478 0.00 0.00 34.54 2.57
2343 4276 0.829990 TCCTGATGCACGAGCCAATA 59.170 50.000 1.39 0.00 41.13 1.90
2344 4277 1.202568 TCCTGATGCACGAGCCAATAG 60.203 52.381 1.39 0.00 41.13 1.73
2350 4283 2.778299 TGCACGAGCCAATAGAAGTTT 58.222 42.857 1.39 0.00 41.13 2.66
2360 4293 5.833131 AGCCAATAGAAGTTTGTTCAAGGAA 59.167 36.000 0.00 0.00 0.00 3.36
2400 4338 2.743664 GGCCAATTCTTTGCACCAATTC 59.256 45.455 0.00 0.00 31.32 2.17
2405 4343 5.163933 CCAATTCTTTGCACCAATTCATTCG 60.164 40.000 0.00 0.00 0.00 3.34
2406 4344 4.844998 TTCTTTGCACCAATTCATTCGA 57.155 36.364 0.00 0.00 0.00 3.71
2411 4349 4.359971 TGCACCAATTCATTCGATTCAG 57.640 40.909 0.00 0.00 0.00 3.02
2426 4364 0.750546 TTCAGCATGCTGGATCCTGC 60.751 55.000 39.72 30.90 43.75 4.85
2439 4377 3.730761 CCTGCACAAGCGCACCTC 61.731 66.667 11.47 0.00 46.23 3.85
2493 4433 8.393671 TGACATATGCAATGTATTAAGCATCA 57.606 30.769 12.51 0.00 43.67 3.07
2565 4505 2.489971 TGTTCATCGTCAGGTTTGTCC 58.510 47.619 0.00 0.00 0.00 4.02
2566 4506 1.804748 GTTCATCGTCAGGTTTGTCCC 59.195 52.381 0.00 0.00 36.75 4.46
2567 4507 1.052617 TCATCGTCAGGTTTGTCCCA 58.947 50.000 0.00 0.00 36.75 4.37
2568 4508 1.001974 TCATCGTCAGGTTTGTCCCAG 59.998 52.381 0.00 0.00 36.75 4.45
2569 4509 1.001974 CATCGTCAGGTTTGTCCCAGA 59.998 52.381 0.00 0.00 36.75 3.86
2570 4510 0.391597 TCGTCAGGTTTGTCCCAGAC 59.608 55.000 0.00 0.00 37.96 3.51
2571 4511 0.393077 CGTCAGGTTTGTCCCAGACT 59.607 55.000 0.00 0.00 38.67 3.24
2572 4512 1.605712 CGTCAGGTTTGTCCCAGACTC 60.606 57.143 0.00 0.00 38.67 3.36
2613 4553 1.858091 CTGTATGCGGTGATCAGTCC 58.142 55.000 0.00 0.00 0.00 3.85
2623 4563 3.739519 CGGTGATCAGTCCATCTTTCTCC 60.740 52.174 0.00 0.00 0.00 3.71
2648 4588 2.375014 TCCTCCAAAAACAACCCTCC 57.625 50.000 0.00 0.00 0.00 4.30
2650 4590 1.686587 CCTCCAAAAACAACCCTCCAC 59.313 52.381 0.00 0.00 0.00 4.02
2709 4649 9.685276 TCAATATGAAAAATCTACATCACTGGT 57.315 29.630 0.00 0.00 0.00 4.00
2718 4658 9.696572 AAAATCTACATCACTGGTAGTCTAGTA 57.303 33.333 0.00 0.00 39.36 1.82
2720 4660 7.191593 TCTACATCACTGGTAGTCTAGTACA 57.808 40.000 0.00 0.00 39.36 2.90
2722 4662 6.063496 ACATCACTGGTAGTCTAGTACAGA 57.937 41.667 11.24 0.00 33.69 3.41
2724 4664 6.600032 ACATCACTGGTAGTCTAGTACAGAAG 59.400 42.308 11.24 0.00 33.69 2.85
2729 4669 7.122948 CACTGGTAGTCTAGTACAGAAGGATTT 59.877 40.741 11.24 0.00 33.69 2.17
2737 4677 9.187996 GTCTAGTACAGAAGGATTTAGGTAACT 57.812 37.037 0.00 0.00 43.18 2.24
2789 5984 5.814188 TCAAACATGCAAAATGTTAAGCACA 59.186 32.000 4.67 0.00 40.94 4.57
2795 5990 4.337836 TGCAAAATGTTAAGCACACAGAGA 59.662 37.500 0.00 0.00 38.61 3.10
2796 5991 4.676924 GCAAAATGTTAAGCACACAGAGAC 59.323 41.667 0.00 0.00 38.61 3.36
2797 5992 5.215160 CAAAATGTTAAGCACACAGAGACC 58.785 41.667 0.00 0.00 38.61 3.85
2799 5994 3.111853 TGTTAAGCACACAGAGACCAG 57.888 47.619 0.00 0.00 0.00 4.00
2800 5995 2.698274 TGTTAAGCACACAGAGACCAGA 59.302 45.455 0.00 0.00 0.00 3.86
2801 5996 3.243873 TGTTAAGCACACAGAGACCAGAG 60.244 47.826 0.00 0.00 0.00 3.35
2802 5997 1.418334 AAGCACACAGAGACCAGAGT 58.582 50.000 0.00 0.00 0.00 3.24
2803 5998 0.678395 AGCACACAGAGACCAGAGTG 59.322 55.000 0.00 0.00 37.95 3.51
2811 6006 4.928615 CACAGAGACCAGAGTGAAGAAATC 59.071 45.833 0.00 0.00 33.99 2.17
2822 6017 2.308866 GTGAAGAAATCCCCTTCCCAGA 59.691 50.000 0.00 0.00 39.30 3.86
2829 6024 0.991920 TCCCCTTCCCAGAACATGAC 59.008 55.000 0.00 0.00 0.00 3.06
2839 6034 3.325870 CCAGAACATGACGAGCTTGTAA 58.674 45.455 6.58 0.00 34.14 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.073098 TCTTTTCCCTTCCCTCCCAC 58.927 55.000 0.00 0.00 0.00 4.61
1 2 1.841334 TTCTTTTCCCTTCCCTCCCA 58.159 50.000 0.00 0.00 0.00 4.37
2 3 2.992847 TTTCTTTTCCCTTCCCTCCC 57.007 50.000 0.00 0.00 0.00 4.30
3 4 2.563179 GCTTTTCTTTTCCCTTCCCTCC 59.437 50.000 0.00 0.00 0.00 4.30
4 5 2.229062 CGCTTTTCTTTTCCCTTCCCTC 59.771 50.000 0.00 0.00 0.00 4.30
5 6 2.239400 CGCTTTTCTTTTCCCTTCCCT 58.761 47.619 0.00 0.00 0.00 4.20
6 7 1.272490 CCGCTTTTCTTTTCCCTTCCC 59.728 52.381 0.00 0.00 0.00 3.97
7 8 1.272490 CCCGCTTTTCTTTTCCCTTCC 59.728 52.381 0.00 0.00 0.00 3.46
8 9 2.229062 CTCCCGCTTTTCTTTTCCCTTC 59.771 50.000 0.00 0.00 0.00 3.46
9 10 2.158519 TCTCCCGCTTTTCTTTTCCCTT 60.159 45.455 0.00 0.00 0.00 3.95
10 11 1.423921 TCTCCCGCTTTTCTTTTCCCT 59.576 47.619 0.00 0.00 0.00 4.20
11 12 1.813178 CTCTCCCGCTTTTCTTTTCCC 59.187 52.381 0.00 0.00 0.00 3.97
12 13 1.813178 CCTCTCCCGCTTTTCTTTTCC 59.187 52.381 0.00 0.00 0.00 3.13
48 49 2.434359 CCGGTGCTCCTTTCGTCC 60.434 66.667 2.85 0.00 0.00 4.79
71 76 0.376152 CCACAGACGATGCTTGCATC 59.624 55.000 21.67 21.67 0.00 3.91
83 88 0.895530 TCGGATTGACCTCCACAGAC 59.104 55.000 0.00 0.00 34.78 3.51
84 89 0.895530 GTCGGATTGACCTCCACAGA 59.104 55.000 0.00 0.00 42.04 3.41
118 129 1.741401 TCCGCAGCATCACTTTCGG 60.741 57.895 0.00 0.00 41.17 4.30
147 158 2.202756 GCGATCGACACCTGGTCC 60.203 66.667 21.57 0.00 43.95 4.46
150 161 0.596083 GATGAGCGATCGACACCTGG 60.596 60.000 21.57 0.00 0.00 4.45
163 174 3.490759 CACACCGCCACGATGAGC 61.491 66.667 0.00 0.00 0.00 4.26
170 184 1.460273 ATTTTCACCCACACCGCCAC 61.460 55.000 0.00 0.00 0.00 5.01
172 186 1.288752 CATTTTCACCCACACCGCC 59.711 57.895 0.00 0.00 0.00 6.13
201 215 3.370104 ACAACCTTTCACCCATCAACAA 58.630 40.909 0.00 0.00 0.00 2.83
203 217 5.523438 TTAACAACCTTTCACCCATCAAC 57.477 39.130 0.00 0.00 0.00 3.18
210 224 6.478673 CCACTTTCATTTAACAACCTTTCACC 59.521 38.462 0.00 0.00 0.00 4.02
211 225 6.478673 CCCACTTTCATTTAACAACCTTTCAC 59.521 38.462 0.00 0.00 0.00 3.18
218 232 4.226761 CGCTCCCACTTTCATTTAACAAC 58.773 43.478 0.00 0.00 0.00 3.32
221 235 2.727916 CGCGCTCCCACTTTCATTTAAC 60.728 50.000 5.56 0.00 0.00 2.01
246 269 4.101119 TCTTATCTCGGAACCCTTGGATTC 59.899 45.833 0.00 0.00 0.00 2.52
259 282 1.688772 TTCCTCCGGTCTTATCTCGG 58.311 55.000 0.00 0.00 44.59 4.63
296 319 0.110192 CTTTTGCTTTCGTCGGAGCC 60.110 55.000 15.62 0.00 38.11 4.70
337 360 2.186903 CCGCTAATCACGCCACCT 59.813 61.111 0.00 0.00 0.00 4.00
389 412 3.782656 AGCGAGAGAAACCCCTAAAAA 57.217 42.857 0.00 0.00 0.00 1.94
542 565 3.656045 CGCACCCAACCAACGACC 61.656 66.667 0.00 0.00 0.00 4.79
543 566 2.113131 CTTCGCACCCAACCAACGAC 62.113 60.000 0.00 0.00 31.61 4.34
544 567 1.890041 CTTCGCACCCAACCAACGA 60.890 57.895 0.00 0.00 0.00 3.85
545 568 2.184167 ACTTCGCACCCAACCAACG 61.184 57.895 0.00 0.00 0.00 4.10
546 569 1.358759 CACTTCGCACCCAACCAAC 59.641 57.895 0.00 0.00 0.00 3.77
547 570 2.485795 GCACTTCGCACCCAACCAA 61.486 57.895 0.00 0.00 41.79 3.67
548 571 2.904866 GCACTTCGCACCCAACCA 60.905 61.111 0.00 0.00 41.79 3.67
621 650 2.773993 TTACGAGGCCCAAGTTTAGG 57.226 50.000 0.00 0.00 0.00 2.69
623 652 4.004982 GACATTTACGAGGCCCAAGTTTA 58.995 43.478 0.00 0.00 0.00 2.01
624 653 2.817844 GACATTTACGAGGCCCAAGTTT 59.182 45.455 0.00 0.00 0.00 2.66
625 654 2.039879 AGACATTTACGAGGCCCAAGTT 59.960 45.455 0.00 0.00 0.00 2.66
642 679 2.168521 GGGAGTATACAGCAAGCAGACA 59.831 50.000 5.50 0.00 0.00 3.41
645 682 1.765314 AGGGGAGTATACAGCAAGCAG 59.235 52.381 5.50 0.00 0.00 4.24
646 683 1.762957 GAGGGGAGTATACAGCAAGCA 59.237 52.381 5.50 0.00 0.00 3.91
650 687 3.585289 TGTTTTGAGGGGAGTATACAGCA 59.415 43.478 5.50 0.00 0.00 4.41
651 688 4.216411 TGTTTTGAGGGGAGTATACAGC 57.784 45.455 5.50 0.00 0.00 4.40
652 689 4.630069 CGTTGTTTTGAGGGGAGTATACAG 59.370 45.833 5.50 0.00 0.00 2.74
656 693 2.290705 CCCGTTGTTTTGAGGGGAGTAT 60.291 50.000 0.00 0.00 43.36 2.12
658 695 0.179001 CCCGTTGTTTTGAGGGGAGT 60.179 55.000 0.00 0.00 43.36 3.85
659 696 1.524008 GCCCGTTGTTTTGAGGGGAG 61.524 60.000 6.09 0.00 43.36 4.30
661 698 2.570284 GGCCCGTTGTTTTGAGGGG 61.570 63.158 0.00 0.00 43.95 4.79
662 699 2.570284 GGGCCCGTTGTTTTGAGGG 61.570 63.158 5.69 0.00 46.44 4.30
663 700 2.570284 GGGGCCCGTTGTTTTGAGG 61.570 63.158 17.79 0.00 0.00 3.86
668 705 1.790818 TTTTTAGGGGCCCGTTGTTT 58.209 45.000 24.63 0.00 0.00 2.83
686 723 1.880027 GAAGTCAGGTGATGCCGTTTT 59.120 47.619 0.00 0.00 43.70 2.43
687 724 1.523758 GAAGTCAGGTGATGCCGTTT 58.476 50.000 0.00 0.00 43.70 3.60
688 725 0.670546 CGAAGTCAGGTGATGCCGTT 60.671 55.000 0.00 0.00 43.70 4.44
689 726 1.079819 CGAAGTCAGGTGATGCCGT 60.080 57.895 0.00 0.00 43.70 5.68
690 727 1.811266 CCGAAGTCAGGTGATGCCG 60.811 63.158 0.00 0.00 43.70 5.69
691 728 2.109126 GCCGAAGTCAGGTGATGCC 61.109 63.158 0.00 0.00 37.58 4.40
692 729 2.109126 GGCCGAAGTCAGGTGATGC 61.109 63.158 0.00 0.00 0.00 3.91
693 730 1.811266 CGGCCGAAGTCAGGTGATG 60.811 63.158 24.07 0.00 0.00 3.07
694 731 2.579201 CGGCCGAAGTCAGGTGAT 59.421 61.111 24.07 0.00 0.00 3.06
695 732 4.373116 GCGGCCGAAGTCAGGTGA 62.373 66.667 33.48 0.00 0.00 4.02
696 733 3.883744 AAGCGGCCGAAGTCAGGTG 62.884 63.158 33.48 0.00 0.00 4.00
697 734 3.178540 AAAGCGGCCGAAGTCAGGT 62.179 57.895 33.48 0.00 0.00 4.00
698 735 2.358737 AAAGCGGCCGAAGTCAGG 60.359 61.111 33.48 0.00 0.00 3.86
699 736 1.901650 GACAAAGCGGCCGAAGTCAG 61.902 60.000 33.48 15.16 0.00 3.51
700 737 1.959226 GACAAAGCGGCCGAAGTCA 60.959 57.895 33.48 0.00 0.00 3.41
701 738 1.627550 GAGACAAAGCGGCCGAAGTC 61.628 60.000 33.48 26.99 0.00 3.01
702 739 1.668151 GAGACAAAGCGGCCGAAGT 60.668 57.895 33.48 20.50 0.00 3.01
703 740 1.227999 TTGAGACAAAGCGGCCGAAG 61.228 55.000 33.48 17.11 0.00 3.79
704 741 0.816018 TTTGAGACAAAGCGGCCGAA 60.816 50.000 33.48 7.84 0.00 4.30
705 742 0.816018 TTTTGAGACAAAGCGGCCGA 60.816 50.000 33.48 0.00 0.00 5.54
706 743 0.030101 TTTTTGAGACAAAGCGGCCG 59.970 50.000 24.05 24.05 0.00 6.13
707 744 3.957383 TTTTTGAGACAAAGCGGCC 57.043 47.368 0.00 0.00 0.00 6.13
729 766 1.680338 GTTCAGTGGCCAAAGTGACT 58.320 50.000 7.24 0.00 0.00 3.41
732 769 0.029300 CACGTTCAGTGGCCAAAGTG 59.971 55.000 7.24 6.96 46.77 3.16
743 780 2.398554 CGCCCAATCCCACGTTCAG 61.399 63.158 0.00 0.00 0.00 3.02
745 782 2.046700 TCGCCCAATCCCACGTTC 60.047 61.111 0.00 0.00 0.00 3.95
746 783 2.046314 CTCGCCCAATCCCACGTT 60.046 61.111 0.00 0.00 0.00 3.99
747 784 3.000819 TCTCGCCCAATCCCACGT 61.001 61.111 0.00 0.00 0.00 4.49
748 785 2.511600 GTCTCGCCCAATCCCACG 60.512 66.667 0.00 0.00 0.00 4.94
749 786 2.511600 CGTCTCGCCCAATCCCAC 60.512 66.667 0.00 0.00 0.00 4.61
751 788 4.547367 CCCGTCTCGCCCAATCCC 62.547 72.222 0.00 0.00 0.00 3.85
823 868 1.198397 CAAGAACACGACGACGCAC 59.802 57.895 7.30 0.00 43.96 5.34
824 869 2.582265 GCAAGAACACGACGACGCA 61.582 57.895 7.30 0.00 43.96 5.24
825 870 2.167918 GCAAGAACACGACGACGC 59.832 61.111 7.30 0.00 43.96 5.19
826 871 0.933047 TCAGCAAGAACACGACGACG 60.933 55.000 5.58 5.58 45.75 5.12
827 872 0.503117 GTCAGCAAGAACACGACGAC 59.497 55.000 0.00 0.00 0.00 4.34
828 873 2.881441 GTCAGCAAGAACACGACGA 58.119 52.632 0.00 0.00 0.00 4.20
829 874 1.482955 CGTCAGCAAGAACACGACG 59.517 57.895 0.00 0.00 42.79 5.12
830 875 0.874607 ACCGTCAGCAAGAACACGAC 60.875 55.000 0.00 0.00 34.06 4.34
831 876 0.874175 CACCGTCAGCAAGAACACGA 60.874 55.000 0.00 0.00 34.06 4.35
832 877 0.874175 TCACCGTCAGCAAGAACACG 60.874 55.000 0.00 0.00 0.00 4.49
833 878 0.582005 GTCACCGTCAGCAAGAACAC 59.418 55.000 0.00 0.00 0.00 3.32
834 879 0.531974 GGTCACCGTCAGCAAGAACA 60.532 55.000 0.00 0.00 0.00 3.18
835 880 0.249911 AGGTCACCGTCAGCAAGAAC 60.250 55.000 0.00 0.00 0.00 3.01
836 881 0.033504 GAGGTCACCGTCAGCAAGAA 59.966 55.000 0.00 0.00 0.00 2.52
837 882 1.666011 GAGGTCACCGTCAGCAAGA 59.334 57.895 0.00 0.00 0.00 3.02
839 884 2.338620 CGAGGTCACCGTCAGCAA 59.661 61.111 0.00 0.00 0.00 3.91
841 886 4.357947 TGCGAGGTCACCGTCAGC 62.358 66.667 0.00 0.00 0.00 4.26
937 1472 1.392510 GGCAATACGTCGAACAGGTTC 59.607 52.381 0.00 2.07 36.29 3.62
938 1473 1.435577 GGCAATACGTCGAACAGGTT 58.564 50.000 0.00 0.00 0.00 3.50
950 1485 2.273588 TAGGTTGGGCGGGGCAATAC 62.274 60.000 0.00 0.00 0.00 1.89
951 1486 2.001838 TAGGTTGGGCGGGGCAATA 61.002 57.895 0.00 0.00 0.00 1.90
959 1494 1.517832 CAGGAGAGTAGGTTGGGCG 59.482 63.158 0.00 0.00 0.00 6.13
961 1496 1.196012 GTCCAGGAGAGTAGGTTGGG 58.804 60.000 0.00 0.00 0.00 4.12
964 1499 2.923629 AGAGAGTCCAGGAGAGTAGGTT 59.076 50.000 0.00 0.00 0.00 3.50
966 1501 2.777692 AGAGAGAGTCCAGGAGAGTAGG 59.222 54.545 0.00 0.00 0.00 3.18
969 1504 2.505819 GAGAGAGAGAGTCCAGGAGAGT 59.494 54.545 0.00 0.00 0.00 3.24
970 1505 2.774234 AGAGAGAGAGAGTCCAGGAGAG 59.226 54.545 0.00 0.00 0.00 3.20
975 1510 2.168521 ACGAGAGAGAGAGAGAGTCCAG 59.831 54.545 0.00 0.00 0.00 3.86
976 1511 2.093711 CACGAGAGAGAGAGAGAGTCCA 60.094 54.545 0.00 0.00 0.00 4.02
977 1512 2.550978 CACGAGAGAGAGAGAGAGTCC 58.449 57.143 0.00 0.00 0.00 3.85
978 1513 1.933853 GCACGAGAGAGAGAGAGAGTC 59.066 57.143 0.00 0.00 0.00 3.36
979 1514 1.406887 GGCACGAGAGAGAGAGAGAGT 60.407 57.143 0.00 0.00 0.00 3.24
980 1515 1.299541 GGCACGAGAGAGAGAGAGAG 58.700 60.000 0.00 0.00 0.00 3.20
981 1516 0.615850 TGGCACGAGAGAGAGAGAGA 59.384 55.000 0.00 0.00 0.00 3.10
982 1517 1.334556 CATGGCACGAGAGAGAGAGAG 59.665 57.143 0.00 0.00 0.00 3.20
983 1518 1.387539 CATGGCACGAGAGAGAGAGA 58.612 55.000 0.00 0.00 0.00 3.10
984 1519 0.385029 CCATGGCACGAGAGAGAGAG 59.615 60.000 0.00 0.00 0.00 3.20
985 1520 1.670949 GCCATGGCACGAGAGAGAGA 61.671 60.000 32.08 0.00 41.49 3.10
986 1521 1.227205 GCCATGGCACGAGAGAGAG 60.227 63.158 32.08 0.00 41.49 3.20
987 1522 2.895680 GCCATGGCACGAGAGAGA 59.104 61.111 32.08 0.00 41.49 3.10
988 1523 2.584418 CGCCATGGCACGAGAGAG 60.584 66.667 34.93 13.38 42.06 3.20
989 1524 3.068064 TCGCCATGGCACGAGAGA 61.068 61.111 34.93 20.36 42.06 3.10
990 1525 2.887568 GTCGCCATGGCACGAGAG 60.888 66.667 34.93 18.32 39.30 3.20
991 1526 4.794439 CGTCGCCATGGCACGAGA 62.794 66.667 36.96 25.33 43.07 4.04
999 1534 2.924922 GAAGCAATGCCGTCGCCATG 62.925 60.000 0.00 0.00 0.00 3.66
1049 1584 2.040278 AGCTGGAGGTGGAGGGAG 59.960 66.667 0.00 0.00 0.00 4.30
1087 1622 2.776913 GGAGAGGGACCTCGAAGCG 61.777 68.421 12.42 0.00 46.90 4.68
1096 1631 4.083862 GTGCCGTGGGAGAGGGAC 62.084 72.222 0.00 0.00 41.44 4.46
1110 1645 4.269523 TGTGGCTCACCTGGGTGC 62.270 66.667 14.35 4.39 45.04 5.01
1189 1724 1.094073 AGGAAGCAGCGCATGACATC 61.094 55.000 11.47 0.00 0.00 3.06
1190 1725 1.077930 AGGAAGCAGCGCATGACAT 60.078 52.632 11.47 0.00 0.00 3.06
1198 1733 0.246086 AAGACAGAGAGGAAGCAGCG 59.754 55.000 0.00 0.00 0.00 5.18
1358 1893 1.822371 ACTTGGAACACACAACCCAAC 59.178 47.619 0.00 0.00 39.29 3.77
1369 1904 1.006043 TGGTGGTTGGAACTTGGAACA 59.994 47.619 0.00 0.00 0.00 3.18
1397 1936 1.772836 ATTCCCTTCAGATTGCTGCC 58.227 50.000 0.00 0.00 42.01 4.85
1398 1937 3.022406 AGAATTCCCTTCAGATTGCTGC 58.978 45.455 0.65 0.00 42.01 5.25
1399 1938 4.525024 AGAGAATTCCCTTCAGATTGCTG 58.475 43.478 0.65 0.00 43.67 4.41
1400 1939 4.474287 AGAGAGAATTCCCTTCAGATTGCT 59.526 41.667 0.65 0.00 36.24 3.91
1401 1940 4.575645 CAGAGAGAATTCCCTTCAGATTGC 59.424 45.833 0.65 0.00 36.24 3.56
1402 1941 5.124645 CCAGAGAGAATTCCCTTCAGATTG 58.875 45.833 0.65 0.00 36.24 2.67
1422 1961 0.961857 TGCCATTGTACTGCAGCCAG 60.962 55.000 15.27 0.64 44.80 4.85
1464 2046 1.294659 GCCTGTTGGAGCAGAAGACG 61.295 60.000 0.00 0.00 38.70 4.18
1601 2183 1.134670 GGACTGACGATGAAGGAAGGG 60.135 57.143 0.00 0.00 0.00 3.95
1602 2184 1.550524 TGGACTGACGATGAAGGAAGG 59.449 52.381 0.00 0.00 0.00 3.46
1603 2185 2.996621 GTTGGACTGACGATGAAGGAAG 59.003 50.000 0.00 0.00 0.00 3.46
1604 2186 2.632996 AGTTGGACTGACGATGAAGGAA 59.367 45.455 0.00 0.00 0.00 3.36
1611 2193 0.317160 TTGCGAGTTGGACTGACGAT 59.683 50.000 0.00 0.00 0.00 3.73
1617 2199 1.470098 GAATGCATTGCGAGTTGGACT 59.530 47.619 18.59 0.00 0.00 3.85
1637 2219 3.730715 GTCTGGTTTTTGTTTCAGATGCG 59.269 43.478 0.00 0.00 38.34 4.73
1656 2239 0.247736 GTTCAGGAGATGCACCGTCT 59.752 55.000 0.00 0.00 31.77 4.18
1657 2240 0.247736 AGTTCAGGAGATGCACCGTC 59.752 55.000 0.00 0.00 0.00 4.79
1668 2251 3.845781 AAGAACAGCTCAAGTTCAGGA 57.154 42.857 15.47 0.00 45.93 3.86
1686 2269 3.197265 CCTCCTGTTTGCCAACAAAAAG 58.803 45.455 4.76 2.35 46.94 2.27
1687 2270 2.679349 GCCTCCTGTTTGCCAACAAAAA 60.679 45.455 4.76 0.00 46.94 1.94
1689 2272 0.463620 GCCTCCTGTTTGCCAACAAA 59.536 50.000 4.76 0.00 42.53 2.83
1698 2281 4.394712 CCGAGCGGCCTCCTGTTT 62.395 66.667 0.00 0.00 34.49 2.83
1733 2316 1.065701 AGCTCTATACACGCCTTGACG 59.934 52.381 0.00 0.00 39.50 4.35
1745 2328 3.560239 CCTCGGAGATGTCCAGCTCTATA 60.560 52.174 9.94 0.00 44.18 1.31
1748 2331 0.754957 CCTCGGAGATGTCCAGCTCT 60.755 60.000 9.94 0.00 44.18 4.09
1796 2379 0.683973 CCATCATCTTCTCCCCTCGG 59.316 60.000 0.00 0.00 0.00 4.63
1864 2447 1.134250 GCCTCCCAAGGATCTCAGAAC 60.134 57.143 0.00 0.00 46.67 3.01
1867 2450 1.134159 CAAGCCTCCCAAGGATCTCAG 60.134 57.143 0.00 0.00 41.63 3.35
1901 2484 3.093717 TCACTAAATAGCCTGCTACGC 57.906 47.619 0.04 0.00 0.00 4.42
1917 2500 3.010808 AGGCTACACTCCTACTCTTCACT 59.989 47.826 0.00 0.00 30.79 3.41
1942 2525 4.762251 AGTTCATAGAGCAAACAACTTCCC 59.238 41.667 0.00 0.00 0.00 3.97
1959 2542 5.763698 CCTGATCATACATCAAGCAGTTCAT 59.236 40.000 0.00 0.00 0.00 2.57
1964 2547 4.958509 ACTCCTGATCATACATCAAGCAG 58.041 43.478 0.00 0.00 0.00 4.24
1980 2563 4.979197 GCTGTGAAATATCGAGTACTCCTG 59.021 45.833 17.23 4.40 0.00 3.86
1981 2564 4.645136 TGCTGTGAAATATCGAGTACTCCT 59.355 41.667 17.23 7.50 0.00 3.69
1982 2565 4.933330 TGCTGTGAAATATCGAGTACTCC 58.067 43.478 17.23 1.87 0.00 3.85
1990 2587 7.535258 GGCTTAATAACATGCTGTGAAATATCG 59.465 37.037 0.00 0.00 0.00 2.92
2016 2613 3.692593 TGGCTGTCAATGATGATTGTCTG 59.307 43.478 4.76 4.97 40.09 3.51
2029 2626 5.538053 TGGAGAAACATTTTATGGCTGTCAA 59.462 36.000 0.00 0.00 33.60 3.18
2035 2632 6.397272 TGACAATGGAGAAACATTTTATGGC 58.603 36.000 0.00 0.00 38.94 4.40
2046 2643 8.961294 ATTTGTTTGAAATGACAATGGAGAAA 57.039 26.923 0.00 0.00 35.85 2.52
2106 2704 7.637631 TGGTATGTCAATATAGCTTGCAAAA 57.362 32.000 0.00 0.00 33.38 2.44
2121 2719 8.210946 CCCTCTTGTAATAGAATTGGTATGTCA 58.789 37.037 0.00 0.00 0.00 3.58
2122 2720 8.429641 TCCCTCTTGTAATAGAATTGGTATGTC 58.570 37.037 0.00 0.00 0.00 3.06
2128 2726 8.348285 TGTTTTCCCTCTTGTAATAGAATTGG 57.652 34.615 0.00 0.00 0.00 3.16
2130 2728 9.362151 TGTTGTTTTCCCTCTTGTAATAGAATT 57.638 29.630 0.00 0.00 0.00 2.17
2140 2738 7.488322 TGTAGAATTTGTTGTTTTCCCTCTTG 58.512 34.615 0.00 0.00 0.00 3.02
2141 2739 7.654022 TGTAGAATTTGTTGTTTTCCCTCTT 57.346 32.000 0.00 0.00 0.00 2.85
2148 2746 9.829507 TTGATGGAATGTAGAATTTGTTGTTTT 57.170 25.926 0.00 0.00 0.00 2.43
2169 2767 6.983307 CCTCTGTAACATAAGGAGTCTTGATG 59.017 42.308 0.00 0.00 34.59 3.07
2170 2768 6.407525 GCCTCTGTAACATAAGGAGTCTTGAT 60.408 42.308 1.95 0.00 34.59 2.57
2172 2770 5.105146 AGCCTCTGTAACATAAGGAGTCTTG 60.105 44.000 1.95 0.00 34.59 3.02
2173 2771 5.026790 AGCCTCTGTAACATAAGGAGTCTT 58.973 41.667 1.95 0.00 37.03 3.01
2174 2772 4.615513 AGCCTCTGTAACATAAGGAGTCT 58.384 43.478 1.95 0.00 0.00 3.24
2185 2785 6.145535 CACTGAAAAATTGAGCCTCTGTAAC 58.854 40.000 0.00 0.00 0.00 2.50
2226 3005 3.378512 TCTGCTCCACCAGATGAACTAT 58.621 45.455 0.00 0.00 36.96 2.12
2243 3022 7.319646 AGTATGCTATCTTAACTGCTATCTGC 58.680 38.462 0.00 0.00 43.25 4.26
2269 3048 2.961062 ACAAAAGGAACAGCTTCAGCAT 59.039 40.909 0.75 0.00 45.16 3.79
2303 3082 4.563168 GGATTCAGGAGTCTATGGCTCATG 60.563 50.000 7.40 7.40 43.56 3.07
2314 3093 2.559440 GTGCATCAGGATTCAGGAGTC 58.441 52.381 0.00 0.00 0.00 3.36
2323 3102 0.182061 ATTGGCTCGTGCATCAGGAT 59.818 50.000 12.07 0.00 41.91 3.24
2324 3103 0.829990 TATTGGCTCGTGCATCAGGA 59.170 50.000 12.07 0.00 41.91 3.86
2343 4276 5.827797 TGCACTATTCCTTGAACAAACTTCT 59.172 36.000 0.00 0.00 0.00 2.85
2344 4277 6.072112 TGCACTATTCCTTGAACAAACTTC 57.928 37.500 0.00 0.00 0.00 3.01
2350 4283 6.296026 ACTAAGTTGCACTATTCCTTGAACA 58.704 36.000 0.00 0.00 0.00 3.18
2360 4293 3.600388 GCCAGTGACTAAGTTGCACTAT 58.400 45.455 0.00 0.00 40.63 2.12
2378 4316 1.126488 TTGGTGCAAAGAATTGGCCA 58.874 45.000 0.00 0.00 37.02 5.36
2400 4338 1.944709 TCCAGCATGCTGAATCGAATG 59.055 47.619 42.21 25.31 46.30 2.67
2405 4343 2.273538 AGGATCCAGCATGCTGAATC 57.726 50.000 42.21 37.16 46.30 2.52
2411 4349 1.317431 TTGTGCAGGATCCAGCATGC 61.317 55.000 31.54 23.13 45.06 4.06
2426 4364 0.671472 TCATGAGAGGTGCGCTTGTG 60.671 55.000 9.73 0.00 0.00 3.33
2469 4407 9.681692 TTTGATGCTTAATACATTGCATATGTC 57.318 29.630 14.94 0.00 44.80 3.06
2491 4431 7.156000 TGACTGTAAGGTTATTCATCGTTTGA 58.844 34.615 0.00 0.00 39.30 2.69
2493 4433 7.119262 CCTTGACTGTAAGGTTATTCATCGTTT 59.881 37.037 0.00 0.00 41.85 3.60
2524 4464 5.931532 ACATCACTATTTTTCTGAGTTGCG 58.068 37.500 0.00 0.00 0.00 4.85
2565 4505 1.302832 GGCACAACTGGGAGTCTGG 60.303 63.158 0.00 0.00 0.00 3.86
2566 4506 0.886490 GTGGCACAACTGGGAGTCTG 60.886 60.000 13.86 0.00 44.16 3.51
2567 4507 1.451936 GTGGCACAACTGGGAGTCT 59.548 57.895 13.86 0.00 44.16 3.24
2568 4508 1.600916 GGTGGCACAACTGGGAGTC 60.601 63.158 20.82 0.00 46.61 3.36
2569 4509 2.515901 GGTGGCACAACTGGGAGT 59.484 61.111 20.82 0.00 46.61 3.85
2613 4553 4.029520 TGGAGGAAGAGAGGAGAAAGATG 58.970 47.826 0.00 0.00 0.00 2.90
2623 4563 3.570125 GGGTTGTTTTTGGAGGAAGAGAG 59.430 47.826 0.00 0.00 0.00 3.20
2749 4689 6.318648 GCATGTTTGATGGATGTTTACTCCTA 59.681 38.462 0.00 0.00 33.69 2.94
2789 5984 4.020662 GGATTTCTTCACTCTGGTCTCTGT 60.021 45.833 0.00 0.00 0.00 3.41
2795 5990 2.637165 AGGGGATTTCTTCACTCTGGT 58.363 47.619 0.00 0.00 0.00 4.00
2796 5991 3.615155 GAAGGGGATTTCTTCACTCTGG 58.385 50.000 0.00 0.00 40.08 3.86
2797 5992 3.615155 GGAAGGGGATTTCTTCACTCTG 58.385 50.000 6.24 0.00 41.59 3.35
2799 5994 2.308866 TGGGAAGGGGATTTCTTCACTC 59.691 50.000 7.46 0.00 43.14 3.51
2800 5995 2.310052 CTGGGAAGGGGATTTCTTCACT 59.690 50.000 7.46 0.00 43.14 3.41
2801 5996 2.308866 TCTGGGAAGGGGATTTCTTCAC 59.691 50.000 6.24 3.11 43.06 3.18
2802 5997 2.642982 TCTGGGAAGGGGATTTCTTCA 58.357 47.619 6.24 0.00 41.59 3.02
2803 5998 3.245264 TGTTCTGGGAAGGGGATTTCTTC 60.245 47.826 0.00 0.00 39.73 2.87
2811 6006 0.392998 CGTCATGTTCTGGGAAGGGG 60.393 60.000 0.00 0.00 0.00 4.79
2822 6017 5.493133 TTGTTTTACAAGCTCGTCATGTT 57.507 34.783 0.00 0.00 32.34 2.71
2829 6024 3.599514 CGCATCTTTGTTTTACAAGCTCG 59.400 43.478 0.00 0.00 39.53 5.03


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

AutoCloner maintained by Alex Coulton.