Multiple sequence alignment - TraesCS3D01G140800

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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 TraesCS3D01G140800 chr3D 100.000 2474 0 0 1 2474 102793178 102790705 0.000000e+00 4569.0
1 TraesCS3D01G140800 chr3D 90.323 93 9 0 1093 1185 340231019 340231111 3.340000e-24 122.0
2 TraesCS3D01G140800 chr3B 87.008 2132 164 53 1 2098 153669196 153667144 0.000000e+00 2298.0
3 TraesCS3D01G140800 chr3B 85.941 441 57 3 104 544 434651823 434652258 1.340000e-127 466.0
4 TraesCS3D01G140800 chr3B 84.361 454 66 2 105 556 730808197 730807747 8.120000e-120 440.0
5 TraesCS3D01G140800 chr3B 84.142 309 41 7 104 410 421093795 421093493 2.410000e-75 292.0
6 TraesCS3D01G140800 chr3A 90.014 1382 96 20 745 2108 552987525 552988882 0.000000e+00 1749.0
7 TraesCS3D01G140800 chr3A 80.928 194 15 9 2295 2468 552989355 552989546 1.540000e-27 134.0
8 TraesCS3D01G140800 chr2A 87.611 452 53 3 105 556 694326653 694326205 2.820000e-144 521.0
9 TraesCS3D01G140800 chr7D 85.526 456 57 7 104 556 634802866 634803315 3.730000e-128 468.0
10 TraesCS3D01G140800 chr7D 89.320 103 11 0 1082 1184 203955739 203955637 2.000000e-26 130.0
11 TraesCS3D01G140800 chr7D 84.259 108 11 4 1536 1637 187156817 187156924 1.570000e-17 100.0
12 TraesCS3D01G140800 chr5A 86.034 358 43 5 165 522 30150002 30150352 6.460000e-101 377.0
13 TraesCS3D01G140800 chr5A 88.350 103 12 0 1082 1184 328913037 328913139 9.290000e-25 124.0
14 TraesCS3D01G140800 chr1A 90.196 255 24 1 104 358 300578712 300578459 5.100000e-87 331.0
15 TraesCS3D01G140800 chr1A 100.000 55 0 0 2414 2468 129869993 129869939 4.350000e-18 102.0
16 TraesCS3D01G140800 chr1A 84.112 107 12 3 1536 1637 560495132 560495238 5.630000e-17 99.0
17 TraesCS3D01G140800 chr1B 88.168 262 30 1 104 365 330993339 330993079 6.640000e-81 311.0
18 TraesCS3D01G140800 chr1B 97.143 35 0 1 1534 1567 466105340 466105306 9.560000e-05 58.4
19 TraesCS3D01G140800 chr7B 80.310 452 52 16 107 556 486734530 486734946 8.590000e-80 307.0
20 TraesCS3D01G140800 chr2B 79.956 454 55 15 104 556 13430238 13429820 4.000000e-78 302.0
21 TraesCS3D01G140800 chr2B 94.595 37 2 0 1526 1562 706237142 706237178 9.560000e-05 58.4
22 TraesCS3D01G140800 chr4B 85.766 274 33 4 271 541 624396391 624396661 4.030000e-73 285.0
23 TraesCS3D01G140800 chr5D 91.346 104 9 0 1082 1185 439513289 439513392 2.560000e-30 143.0
24 TraesCS3D01G140800 chr6D 88.350 103 12 0 1082 1184 365351089 365350987 9.290000e-25 124.0
25 TraesCS3D01G140800 chr6D 87.500 104 13 0 1082 1185 47014665 47014562 1.200000e-23 121.0
26 TraesCS3D01G140800 chr6D 87.500 104 13 0 1082 1185 250496948 250497051 1.200000e-23 121.0
27 TraesCS3D01G140800 chr7A 86.869 99 8 3 1536 1629 391269817 391269915 3.360000e-19 106.0
28 TraesCS3D01G140800 chr4D 97.674 43 1 0 1263 1305 172979076 172979034 9.490000e-10 75.0
29 TraesCS3D01G140800 chrUn 97.059 34 1 0 1529 1562 155005400 155005367 9.560000e-05 58.4
30 TraesCS3D01G140800 chrUn 97.059 34 1 0 1529 1562 155087396 155087363 9.560000e-05 58.4


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 TraesCS3D01G140800 chr3D 102790705 102793178 2473 True 4569.0 4569 100.000 1 2474 1 chr3D.!!$R1 2473
1 TraesCS3D01G140800 chr3B 153667144 153669196 2052 True 2298.0 2298 87.008 1 2098 1 chr3B.!!$R1 2097
2 TraesCS3D01G140800 chr3A 552987525 552989546 2021 False 941.5 1749 85.471 745 2468 2 chr3A.!!$F1 1723

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
556 566 0.031994 GCAACGCCTGGACATGTTTT 59.968 50.0 0.0 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2303 2690 0.032678 CGAGTGGAGCAACAGACACT 59.967 55.0 0.0 0.0 45.99 3.55 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
49 50 4.435651 GCTGATACAAGCTTGACGTAAACC 60.436 45.833 32.50 12.05 40.20 3.27
118 119 6.612247 ATGATTTTACATTTGGCATGCATG 57.388 33.333 22.70 22.70 0.00 4.06
132 133 3.866910 GCATGCATGTCCTTACAAATTGG 59.133 43.478 26.79 0.00 39.58 3.16
163 164 7.284919 TCGATGGAGCTGTCTAATATGTTTA 57.715 36.000 0.00 0.00 0.00 2.01
305 306 4.867047 CGTAATGCAAATATTTGTTGGGCA 59.133 37.500 25.15 18.13 40.24 5.36
313 314 1.176527 ATTTGTTGGGCATCACCGAG 58.823 50.000 0.00 0.00 40.62 4.63
326 327 2.584608 CCGAGGAGGAACGGCAAT 59.415 61.111 0.00 0.00 45.00 3.56
332 333 3.279434 GAGGAGGAACGGCAATAAATGT 58.721 45.455 0.00 0.00 0.00 2.71
334 335 2.752903 GGAGGAACGGCAATAAATGTGT 59.247 45.455 0.00 0.00 0.00 3.72
346 347 7.519970 CGGCAATAAATGTGTAAAGAGATACCC 60.520 40.741 0.00 0.00 0.00 3.69
352 353 1.202371 TGTAAAGAGATACCCGCAGCG 60.202 52.381 8.18 8.18 0.00 5.18
365 366 2.329379 CCGCAGCGAGGTAGATATTTC 58.671 52.381 18.75 0.00 0.00 2.17
366 367 2.329379 CGCAGCGAGGTAGATATTTCC 58.671 52.381 9.98 0.00 0.00 3.13
403 404 9.705290 AAATTCAAAACAACTTGAGTACACTTT 57.295 25.926 0.00 0.00 36.69 2.66
433 434 7.609760 TTATCACATCTCTATGTTTTTGCGT 57.390 32.000 0.00 0.00 44.07 5.24
466 476 3.379240 TCATGTTGTTTTTCATGTGGCG 58.621 40.909 0.00 0.00 41.22 5.69
493 503 9.161629 TCGTGCAAGATTTCAAGAGATTTATTA 57.838 29.630 0.00 0.00 0.00 0.98
516 526 3.010420 TGTCTCGAGAGTGTGTATGAGG 58.990 50.000 17.22 0.00 0.00 3.86
522 532 3.637229 CGAGAGTGTGTATGAGGGGTAAT 59.363 47.826 0.00 0.00 0.00 1.89
550 560 3.276091 CGTTGCAACGCCTGGACA 61.276 61.111 35.89 0.00 46.06 4.02
551 561 2.616330 CGTTGCAACGCCTGGACAT 61.616 57.895 35.89 0.00 46.06 3.06
552 562 1.081242 GTTGCAACGCCTGGACATG 60.081 57.895 14.90 0.00 0.00 3.21
553 563 1.528076 TTGCAACGCCTGGACATGT 60.528 52.632 0.00 0.00 0.00 3.21
554 564 1.106351 TTGCAACGCCTGGACATGTT 61.106 50.000 0.00 0.00 0.00 2.71
555 565 1.106351 TGCAACGCCTGGACATGTTT 61.106 50.000 0.00 0.00 0.00 2.83
556 566 0.031994 GCAACGCCTGGACATGTTTT 59.968 50.000 0.00 0.00 0.00 2.43
557 567 1.537990 GCAACGCCTGGACATGTTTTT 60.538 47.619 0.00 0.00 0.00 1.94
590 600 8.458843 GTGTGGTTGATGTTTGCTAGTAATTAT 58.541 33.333 0.00 0.00 0.00 1.28
642 652 4.554036 CCCCGCCTTGGCTAGAGC 62.554 72.222 10.12 0.00 41.14 4.09
643 653 3.474570 CCCGCCTTGGCTAGAGCT 61.475 66.667 10.12 0.00 41.70 4.09
645 655 1.686325 CCCGCCTTGGCTAGAGCTAA 61.686 60.000 10.12 0.45 41.70 3.09
647 657 1.406887 CCGCCTTGGCTAGAGCTAAAA 60.407 52.381 10.12 0.00 40.95 1.52
648 658 1.936547 CGCCTTGGCTAGAGCTAAAAG 59.063 52.381 10.12 4.08 40.95 2.27
649 659 2.293170 GCCTTGGCTAGAGCTAAAAGG 58.707 52.381 18.76 18.76 40.95 3.11
650 660 2.092914 GCCTTGGCTAGAGCTAAAAGGA 60.093 50.000 23.56 0.00 42.82 3.36
651 661 3.622455 GCCTTGGCTAGAGCTAAAAGGAA 60.622 47.826 23.56 0.00 42.82 3.36
653 663 4.080863 CCTTGGCTAGAGCTAAAAGGAAGA 60.081 45.833 18.48 0.00 42.82 2.87
654 664 5.491982 CTTGGCTAGAGCTAAAAGGAAGAA 58.508 41.667 1.81 0.00 40.95 2.52
655 665 5.091261 TGGCTAGAGCTAAAAGGAAGAAG 57.909 43.478 0.81 0.00 41.70 2.85
656 666 4.080863 TGGCTAGAGCTAAAAGGAAGAAGG 60.081 45.833 0.81 0.00 41.70 3.46
657 667 4.447290 GCTAGAGCTAAAAGGAAGAAGGG 58.553 47.826 0.00 0.00 38.21 3.95
660 670 3.332187 AGAGCTAAAAGGAAGAAGGGCTT 59.668 43.478 0.00 0.00 40.25 4.35
675 715 2.203126 CTTCCGGCCAGCAGATCC 60.203 66.667 2.24 0.00 0.00 3.36
676 716 3.008517 TTCCGGCCAGCAGATCCA 61.009 61.111 2.24 0.00 0.00 3.41
682 722 0.106819 GGCCAGCAGATCCACATTCT 60.107 55.000 0.00 0.00 0.00 2.40
683 723 1.307097 GCCAGCAGATCCACATTCTC 58.693 55.000 0.00 0.00 0.00 2.87
684 724 1.964552 CCAGCAGATCCACATTCTCC 58.035 55.000 0.00 0.00 0.00 3.71
685 725 1.489649 CCAGCAGATCCACATTCTCCT 59.510 52.381 0.00 0.00 0.00 3.69
686 726 2.485124 CCAGCAGATCCACATTCTCCTC 60.485 54.545 0.00 0.00 0.00 3.71
687 727 2.169978 CAGCAGATCCACATTCTCCTCA 59.830 50.000 0.00 0.00 0.00 3.86
689 729 3.118334 AGCAGATCCACATTCTCCTCAAG 60.118 47.826 0.00 0.00 0.00 3.02
690 730 3.118482 GCAGATCCACATTCTCCTCAAGA 60.118 47.826 0.00 0.00 0.00 3.02
691 731 4.440880 CAGATCCACATTCTCCTCAAGAC 58.559 47.826 0.00 0.00 32.27 3.01
692 732 4.081254 CAGATCCACATTCTCCTCAAGACA 60.081 45.833 0.00 0.00 32.27 3.41
693 733 4.533707 AGATCCACATTCTCCTCAAGACAA 59.466 41.667 0.00 0.00 32.27 3.18
694 734 4.705110 TCCACATTCTCCTCAAGACAAA 57.295 40.909 0.00 0.00 32.27 2.83
695 735 4.389374 TCCACATTCTCCTCAAGACAAAC 58.611 43.478 0.00 0.00 32.27 2.93
696 736 3.503748 CCACATTCTCCTCAAGACAAACC 59.496 47.826 0.00 0.00 32.27 3.27
697 737 4.136796 CACATTCTCCTCAAGACAAACCA 58.863 43.478 0.00 0.00 32.27 3.67
698 738 4.023707 CACATTCTCCTCAAGACAAACCAC 60.024 45.833 0.00 0.00 32.27 4.16
699 739 4.141390 ACATTCTCCTCAAGACAAACCACT 60.141 41.667 0.00 0.00 32.27 4.00
700 740 3.475566 TCTCCTCAAGACAAACCACTG 57.524 47.619 0.00 0.00 0.00 3.66
701 741 2.104792 TCTCCTCAAGACAAACCACTGG 59.895 50.000 0.00 0.00 0.00 4.00
702 742 1.843851 TCCTCAAGACAAACCACTGGT 59.156 47.619 0.00 0.00 37.65 4.00
703 743 2.158813 TCCTCAAGACAAACCACTGGTC 60.159 50.000 0.00 0.00 33.12 4.02
704 744 1.867233 CTCAAGACAAACCACTGGTCG 59.133 52.381 0.00 0.00 33.12 4.79
705 745 0.944386 CAAGACAAACCACTGGTCGG 59.056 55.000 0.00 0.00 33.12 4.79
706 746 0.818040 AAGACAAACCACTGGTCGGC 60.818 55.000 0.00 0.00 33.12 5.54
707 747 2.203294 ACAAACCACTGGTCGGCC 60.203 61.111 0.00 0.00 33.12 6.13
708 748 2.983592 CAAACCACTGGTCGGCCC 60.984 66.667 2.12 0.00 33.12 5.80
709 749 4.636435 AAACCACTGGTCGGCCCG 62.636 66.667 2.12 0.00 33.12 6.13
719 759 3.739167 TCGGCCCGACTTGTTTTG 58.261 55.556 0.00 0.00 0.00 2.44
731 771 4.134563 GACTTGTTTTGTAAGCCCAGAGA 58.865 43.478 0.00 0.00 0.00 3.10
735 775 3.075148 GTTTTGTAAGCCCAGAGAGGTC 58.925 50.000 0.00 0.00 34.66 3.85
950 991 4.176752 CCGCCCCAGAACCCTAGC 62.177 72.222 0.00 0.00 0.00 3.42
951 992 4.176752 CGCCCCAGAACCCTAGCC 62.177 72.222 0.00 0.00 0.00 3.93
952 993 4.176752 GCCCCAGAACCCTAGCCG 62.177 72.222 0.00 0.00 0.00 5.52
1125 1166 0.532862 CCGAGCTCCGCCACAAATAT 60.533 55.000 8.47 0.00 36.84 1.28
1128 1169 2.221055 CGAGCTCCGCCACAAATATAAC 59.779 50.000 8.47 0.00 0.00 1.89
1143 1184 2.083835 ATAACGTCCGCTCCATCCCG 62.084 60.000 0.00 0.00 0.00 5.14
1395 1436 2.416107 CTGCTGACAAGGCCAAGGGA 62.416 60.000 5.01 0.00 0.00 4.20
1552 1595 6.554982 TCACCAGTTCTGTTAGGATATGCTAT 59.445 38.462 4.64 0.00 0.00 2.97
1558 1601 8.584157 AGTTCTGTTAGGATATGCTATCTGAAG 58.416 37.037 23.09 10.93 0.00 3.02
1559 1602 8.580720 GTTCTGTTAGGATATGCTATCTGAAGA 58.419 37.037 23.09 12.44 0.00 2.87
1562 1608 7.890515 TGTTAGGATATGCTATCTGAAGACTG 58.109 38.462 4.64 0.00 0.00 3.51
1569 1615 9.434420 GATATGCTATCTGAAGACTGCTTTATT 57.566 33.333 7.56 0.00 33.61 1.40
1577 1623 9.988815 ATCTGAAGACTGCTTTATTATTCGTAT 57.011 29.630 0.00 0.00 33.61 3.06
1584 1630 8.007821 ACTGCTTTATTATTCGTATGATGTCG 57.992 34.615 0.00 0.00 0.00 4.35
1593 1640 2.054363 CGTATGATGTCGTGGATGAGC 58.946 52.381 0.00 0.00 0.00 4.26
1598 1645 1.732259 GATGTCGTGGATGAGCGTTTT 59.268 47.619 0.00 0.00 0.00 2.43
1599 1646 1.144969 TGTCGTGGATGAGCGTTTTC 58.855 50.000 0.00 0.00 0.00 2.29
1602 1649 2.032377 GTCGTGGATGAGCGTTTTCAAA 60.032 45.455 0.00 0.00 0.00 2.69
1604 1655 2.661594 GTGGATGAGCGTTTTCAAACC 58.338 47.619 0.00 0.00 35.51 3.27
1607 1658 3.383185 TGGATGAGCGTTTTCAAACCTTT 59.617 39.130 0.00 0.00 35.51 3.11
1608 1659 4.580995 TGGATGAGCGTTTTCAAACCTTTA 59.419 37.500 0.00 0.00 35.51 1.85
1619 1670 7.042791 CGTTTTCAAACCTTTAATGTGCATCTT 60.043 33.333 0.00 0.00 35.51 2.40
1621 1672 9.823647 TTTTCAAACCTTTAATGTGCATCTTTA 57.176 25.926 0.00 0.00 0.00 1.85
1622 1673 9.995003 TTTCAAACCTTTAATGTGCATCTTTAT 57.005 25.926 0.00 0.00 0.00 1.40
1623 1674 8.984891 TCAAACCTTTAATGTGCATCTTTATG 57.015 30.769 0.00 0.00 36.09 1.90
1626 1677 5.957774 ACCTTTAATGTGCATCTTTATGGGT 59.042 36.000 0.00 2.65 33.38 4.51
1627 1678 6.096846 ACCTTTAATGTGCATCTTTATGGGTC 59.903 38.462 0.00 0.00 33.38 4.46
1628 1679 6.322201 CCTTTAATGTGCATCTTTATGGGTCT 59.678 38.462 0.00 0.00 33.38 3.85
1629 1680 6.698008 TTAATGTGCATCTTTATGGGTCTG 57.302 37.500 0.00 0.00 33.38 3.51
1733 1791 6.743575 ATTAAGTTTATCTGTGTGCACCTC 57.256 37.500 15.69 8.29 0.00 3.85
1754 1812 7.130681 CCTCTAGAGGTTAAATTGACCATCT 57.869 40.000 28.12 10.71 43.61 2.90
1775 1833 7.339721 CCATCTGTTAGTTCTCAGGTTAGACTA 59.660 40.741 0.00 0.00 33.13 2.59
1783 1841 5.599999 TCTCAGGTTAGACTAATCCTTGC 57.400 43.478 11.48 0.00 0.00 4.01
1785 1843 3.132289 TCAGGTTAGACTAATCCTTGCCG 59.868 47.826 11.48 4.31 0.00 5.69
1831 1889 6.141560 TGCTGTTTTGTGATGTTTATGTGA 57.858 33.333 0.00 0.00 0.00 3.58
1846 1904 6.868339 TGTTTATGTGATATGCTCTGTATCGG 59.132 38.462 0.00 0.00 32.46 4.18
1868 1926 6.490381 TCGGTTTGCTAGATCATACTAGATGT 59.510 38.462 0.00 0.00 41.42 3.06
1924 1982 6.670695 ATCTGCAAGGGAAATGTTAAACTT 57.329 33.333 0.00 0.00 0.00 2.66
1971 2029 6.028146 TGGTGAATTCATCCTGTTTTCATG 57.972 37.500 16.06 0.00 0.00 3.07
1993 2052 1.734707 GCAGTTGCAATGCACCATCTC 60.735 52.381 21.39 0.00 43.31 2.75
2011 2070 6.382570 ACCATCTCTGTTTCTAATAGCAGTCT 59.617 38.462 0.00 0.00 0.00 3.24
2026 2085 0.108615 AGTCTGGATCCTGCGTTTCG 60.109 55.000 14.23 0.00 0.00 3.46
2072 2131 8.650714 CATTAGTTTTAGCAAGAAATTTCAGGC 58.349 33.333 19.99 20.13 0.00 4.85
2075 2134 4.685169 TTAGCAAGAAATTTCAGGCTCG 57.315 40.909 28.72 10.50 38.90 5.03
2099 2158 8.630917 TCGTTGAAAAGAAATTTATAACCACCA 58.369 29.630 0.00 0.00 30.34 4.17
2127 2221 7.491048 AGTTTTTCAGATAATTTTGCGTGTGTT 59.509 29.630 0.00 0.00 0.00 3.32
2136 2230 1.106351 TTGCGTGTGTTGCCCTTGAT 61.106 50.000 0.00 0.00 0.00 2.57
2141 2235 3.564511 CGTGTGTTGCCCTTGATTTTAG 58.435 45.455 0.00 0.00 0.00 1.85
2142 2236 3.611530 CGTGTGTTGCCCTTGATTTTAGG 60.612 47.826 0.00 0.00 0.00 2.69
2156 2250 7.394359 CCTTGATTTTAGGAGGACATTCAAAGA 59.606 37.037 0.00 0.00 34.56 2.52
2157 2251 8.884124 TTGATTTTAGGAGGACATTCAAAGAT 57.116 30.769 0.00 0.00 0.00 2.40
2165 2259 5.529060 GGAGGACATTCAAAGATACATGGTC 59.471 44.000 0.00 0.00 0.00 4.02
2170 2264 3.992943 TCAAAGATACATGGTCGGGTT 57.007 42.857 0.00 0.00 0.00 4.11
2202 2296 3.980646 TTTCGGTTTTGTCTGTGATGG 57.019 42.857 0.00 0.00 0.00 3.51
2203 2297 2.631160 TCGGTTTTGTCTGTGATGGT 57.369 45.000 0.00 0.00 0.00 3.55
2204 2298 3.755112 TCGGTTTTGTCTGTGATGGTA 57.245 42.857 0.00 0.00 0.00 3.25
2205 2299 3.659786 TCGGTTTTGTCTGTGATGGTAG 58.340 45.455 0.00 0.00 0.00 3.18
2213 2335 4.883083 TGTCTGTGATGGTAGTTTCTGTC 58.117 43.478 0.00 0.00 0.00 3.51
2214 2336 3.921021 GTCTGTGATGGTAGTTTCTGTCG 59.079 47.826 0.00 0.00 0.00 4.35
2221 2343 2.490903 TGGTAGTTTCTGTCGCTCTACC 59.509 50.000 11.32 11.32 46.09 3.18
2225 2347 1.544691 GTTTCTGTCGCTCTACCTGGA 59.455 52.381 0.00 0.00 0.00 3.86
2236 2358 3.096092 CTCTACCTGGAGCTTCTTCTGT 58.904 50.000 0.00 0.00 0.00 3.41
2246 2368 6.061441 TGGAGCTTCTTCTGTTGAAATGTTA 58.939 36.000 0.00 0.00 0.00 2.41
2247 2369 6.716628 TGGAGCTTCTTCTGTTGAAATGTTAT 59.283 34.615 0.00 0.00 0.00 1.89
2248 2370 7.882791 TGGAGCTTCTTCTGTTGAAATGTTATA 59.117 33.333 0.00 0.00 0.00 0.98
2249 2371 8.178313 GGAGCTTCTTCTGTTGAAATGTTATAC 58.822 37.037 0.00 0.00 0.00 1.47
2250 2372 8.621532 AGCTTCTTCTGTTGAAATGTTATACA 57.378 30.769 0.00 0.00 0.00 2.29
2251 2373 9.066892 AGCTTCTTCTGTTGAAATGTTATACAA 57.933 29.630 0.00 0.00 0.00 2.41
2252 2374 9.846248 GCTTCTTCTGTTGAAATGTTATACAAT 57.154 29.630 0.00 0.00 0.00 2.71
2262 2649 9.949174 TTGAAATGTTATACAATGATGAATCGG 57.051 29.630 0.00 0.00 0.00 4.18
2264 2651 9.385902 GAAATGTTATACAATGATGAATCGGTG 57.614 33.333 0.00 0.00 0.00 4.94
2271 2658 4.154737 ACAATGATGAATCGGTGTCTGTTG 59.845 41.667 0.00 0.00 0.00 3.33
2278 2665 0.601558 TCGGTGTCTGTTGCTCTACC 59.398 55.000 0.00 0.00 0.00 3.18
2279 2666 0.389948 CGGTGTCTGTTGCTCTACCC 60.390 60.000 0.00 0.00 0.00 3.69
2280 2667 0.036294 GGTGTCTGTTGCTCTACCCC 60.036 60.000 0.00 0.00 0.00 4.95
2293 2680 2.595009 CTACCCCGGGCTTCTTCTGC 62.595 65.000 17.73 0.00 0.00 4.26
2304 2691 4.030134 GCTTCTTCTGCCAATGAATGAG 57.970 45.455 0.00 0.00 0.00 2.90
2305 2692 3.442977 GCTTCTTCTGCCAATGAATGAGT 59.557 43.478 0.00 0.00 0.00 3.41
2306 2693 4.674623 GCTTCTTCTGCCAATGAATGAGTG 60.675 45.833 0.00 0.00 0.00 3.51
2307 2694 4.025040 TCTTCTGCCAATGAATGAGTGT 57.975 40.909 0.00 0.00 0.00 3.55
2308 2695 4.005650 TCTTCTGCCAATGAATGAGTGTC 58.994 43.478 0.00 0.00 0.00 3.67
2309 2696 3.708403 TCTGCCAATGAATGAGTGTCT 57.292 42.857 0.00 0.00 0.00 3.41
2310 2697 3.340928 TCTGCCAATGAATGAGTGTCTG 58.659 45.455 0.00 0.00 0.00 3.51
2311 2698 3.079578 CTGCCAATGAATGAGTGTCTGT 58.920 45.455 0.00 0.00 0.00 3.41
2312 2699 3.489355 TGCCAATGAATGAGTGTCTGTT 58.511 40.909 0.00 0.00 0.00 3.16
2313 2700 3.253921 TGCCAATGAATGAGTGTCTGTTG 59.746 43.478 0.00 0.00 0.00 3.33
2314 2701 3.829948 CCAATGAATGAGTGTCTGTTGC 58.170 45.455 0.00 0.00 0.00 4.17
2315 2702 3.504906 CCAATGAATGAGTGTCTGTTGCT 59.495 43.478 0.00 0.00 0.00 3.91
2316 2703 4.379186 CCAATGAATGAGTGTCTGTTGCTC 60.379 45.833 0.00 0.00 0.00 4.26
2317 2704 2.771089 TGAATGAGTGTCTGTTGCTCC 58.229 47.619 0.00 0.00 0.00 4.70
2318 2705 2.104622 TGAATGAGTGTCTGTTGCTCCA 59.895 45.455 0.00 0.00 0.00 3.86
2319 2706 2.175878 ATGAGTGTCTGTTGCTCCAC 57.824 50.000 0.00 0.00 0.00 4.02
2320 2707 1.123077 TGAGTGTCTGTTGCTCCACT 58.877 50.000 0.00 0.00 40.67 4.00
2321 2708 1.789506 GAGTGTCTGTTGCTCCACTC 58.210 55.000 0.00 0.00 44.75 3.51
2322 2709 0.032678 AGTGTCTGTTGCTCCACTCG 59.967 55.000 0.00 0.00 32.97 4.18
2323 2710 0.946221 GTGTCTGTTGCTCCACTCGG 60.946 60.000 0.00 0.00 0.00 4.63
2324 2711 1.374758 GTCTGTTGCTCCACTCGGG 60.375 63.158 0.00 0.00 38.37 5.14
2325 2712 2.046892 CTGTTGCTCCACTCGGGG 60.047 66.667 0.00 0.00 37.22 5.73
2342 2729 2.033801 CGGGGCTTATTCTGCTGAAATG 59.966 50.000 10.27 4.96 35.63 2.32
2363 2750 8.619146 AAATGTTATACAATCAATTGAGTGCG 57.381 30.769 30.14 12.79 43.21 5.34
2365 2752 5.353956 TGTTATACAATCAATTGAGTGCGCT 59.646 36.000 30.14 19.01 43.21 5.92
2366 2753 2.907910 ACAATCAATTGAGTGCGCTC 57.092 45.000 30.14 20.51 43.21 5.03
2367 2754 1.129251 ACAATCAATTGAGTGCGCTCG 59.871 47.619 30.14 10.78 43.21 5.03
2376 2763 4.404654 GTGCGCTCGGGCTTTTGG 62.405 66.667 9.73 0.00 36.09 3.28
2394 2781 5.486735 TTTGGTGCATTCTTTTCCATGAT 57.513 34.783 0.00 0.00 0.00 2.45
2400 2787 5.068723 GTGCATTCTTTTCCATGATCATCCT 59.931 40.000 4.86 0.00 0.00 3.24
2408 2795 5.658198 TTCCATGATCATCCTTCCAAGAT 57.342 39.130 4.86 0.00 0.00 2.40
2446 2850 5.937540 TCCATTCGTCAAATTCTCTGCTTAA 59.062 36.000 0.00 0.00 0.00 1.85
2468 2872 4.922206 ACATCAAACAGAAGCATCCCTTA 58.078 39.130 0.00 0.00 32.78 2.69
2469 2873 4.702131 ACATCAAACAGAAGCATCCCTTAC 59.298 41.667 0.00 0.00 32.78 2.34
2470 2874 3.686016 TCAAACAGAAGCATCCCTTACC 58.314 45.455 0.00 0.00 32.78 2.85
2471 2875 2.403252 AACAGAAGCATCCCTTACCG 57.597 50.000 0.00 0.00 32.78 4.02
2472 2876 1.276622 ACAGAAGCATCCCTTACCGT 58.723 50.000 0.00 0.00 32.78 4.83
2473 2877 1.628846 ACAGAAGCATCCCTTACCGTT 59.371 47.619 0.00 0.00 32.78 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.338249 ACGTCAAGCTTGTATCAGCATT 58.662 40.909 25.19 0.00 42.84 3.56
24 25 2.977914 ACGTCAAGCTTGTATCAGCAT 58.022 42.857 25.19 2.19 42.84 3.79
92 93 8.779303 CATGCATGCCAAATGTAAAATCATTAT 58.221 29.630 14.93 0.00 37.09 1.28
100 101 3.514706 AGGACATGCATGCCAAATGTAAA 59.485 39.130 29.62 0.00 34.74 2.01
103 104 1.563924 AGGACATGCATGCCAAATGT 58.436 45.000 29.62 18.94 37.24 2.71
111 112 5.075858 ACCAATTTGTAAGGACATGCATG 57.924 39.130 25.09 25.09 34.86 4.06
132 133 2.808543 AGACAGCTCCATCGAAAACAAC 59.191 45.455 0.00 0.00 0.00 3.32
140 141 6.923508 TGTAAACATATTAGACAGCTCCATCG 59.076 38.462 0.00 0.00 0.00 3.84
163 164 6.605594 TCCAAGTGAAGTCTTAATTTGGTTGT 59.394 34.615 19.08 0.00 36.05 3.32
213 214 8.905850 TGCATAAGAGCATCATTTTTATCTTGA 58.094 29.630 0.00 0.00 40.11 3.02
263 264 7.908082 GCATTACGATGAAAATAGCAAAGTACA 59.092 33.333 0.00 0.00 35.16 2.90
280 281 5.752955 GCCCAACAAATATTTGCATTACGAT 59.247 36.000 24.82 3.32 41.79 3.73
305 306 3.617368 CCGTTCCTCCTCGGTGAT 58.383 61.111 0.00 0.00 41.58 3.06
313 314 2.752903 ACACATTTATTGCCGTTCCTCC 59.247 45.455 0.00 0.00 0.00 4.30
322 323 7.352739 CGGGTATCTCTTTACACATTTATTGC 58.647 38.462 0.00 0.00 0.00 3.56
326 327 5.979993 TGCGGGTATCTCTTTACACATTTA 58.020 37.500 0.00 0.00 0.00 1.40
332 333 1.202371 CGCTGCGGGTATCTCTTTACA 60.202 52.381 15.40 0.00 0.00 2.41
334 335 1.337071 CTCGCTGCGGGTATCTCTTTA 59.663 52.381 23.03 0.00 0.00 1.85
346 347 2.288213 TGGAAATATCTACCTCGCTGCG 60.288 50.000 17.25 17.25 0.00 5.18
466 476 4.935885 ATCTCTTGAAATCTTGCACGAC 57.064 40.909 0.00 0.00 0.00 4.34
479 489 9.958234 CTCTCGAGACATTAATAAATCTCTTGA 57.042 33.333 12.08 13.18 32.59 3.02
493 503 4.097135 CCTCATACACACTCTCGAGACATT 59.903 45.833 12.08 0.00 0.00 2.71
534 544 1.081242 CATGTCCAGGCGTTGCAAC 60.081 57.895 19.89 19.89 0.00 4.17
537 547 0.031994 AAAACATGTCCAGGCGTTGC 59.968 50.000 0.00 0.00 0.00 4.17
555 565 4.527509 ACATCAACCACACACACAAAAA 57.472 36.364 0.00 0.00 0.00 1.94
556 566 4.527509 AACATCAACCACACACACAAAA 57.472 36.364 0.00 0.00 0.00 2.44
557 567 4.240888 CAAACATCAACCACACACACAAA 58.759 39.130 0.00 0.00 0.00 2.83
558 568 3.842820 CAAACATCAACCACACACACAA 58.157 40.909 0.00 0.00 0.00 3.33
559 569 2.416566 GCAAACATCAACCACACACACA 60.417 45.455 0.00 0.00 0.00 3.72
560 570 2.159254 AGCAAACATCAACCACACACAC 60.159 45.455 0.00 0.00 0.00 3.82
561 571 2.098614 AGCAAACATCAACCACACACA 58.901 42.857 0.00 0.00 0.00 3.72
562 572 2.869233 AGCAAACATCAACCACACAC 57.131 45.000 0.00 0.00 0.00 3.82
563 573 3.550820 ACTAGCAAACATCAACCACACA 58.449 40.909 0.00 0.00 0.00 3.72
564 574 5.682943 TTACTAGCAAACATCAACCACAC 57.317 39.130 0.00 0.00 0.00 3.82
565 575 6.892658 AATTACTAGCAAACATCAACCACA 57.107 33.333 0.00 0.00 0.00 4.17
657 667 2.899339 GATCTGCTGGCCGGAAGC 60.899 66.667 18.31 19.66 41.22 3.86
660 670 3.785859 GTGGATCTGCTGGCCGGA 61.786 66.667 18.31 1.55 0.00 5.14
661 671 2.898920 AATGTGGATCTGCTGGCCGG 62.899 60.000 7.41 7.41 0.00 6.13
662 672 1.442526 GAATGTGGATCTGCTGGCCG 61.443 60.000 0.00 0.00 0.00 6.13
675 715 4.023707 GTGGTTTGTCTTGAGGAGAATGTG 60.024 45.833 0.00 0.00 35.79 3.21
676 716 4.137543 GTGGTTTGTCTTGAGGAGAATGT 58.862 43.478 0.00 0.00 35.79 2.71
682 722 1.843851 ACCAGTGGTTTGTCTTGAGGA 59.156 47.619 9.70 0.00 27.29 3.71
683 723 2.222027 GACCAGTGGTTTGTCTTGAGG 58.778 52.381 17.93 0.00 35.25 3.86
684 724 1.867233 CGACCAGTGGTTTGTCTTGAG 59.133 52.381 17.93 0.00 35.25 3.02
685 725 1.474320 CCGACCAGTGGTTTGTCTTGA 60.474 52.381 17.93 0.00 35.25 3.02
686 726 0.944386 CCGACCAGTGGTTTGTCTTG 59.056 55.000 17.93 0.00 35.25 3.02
687 727 0.818040 GCCGACCAGTGGTTTGTCTT 60.818 55.000 17.93 0.00 35.25 3.01
689 729 2.258726 GGCCGACCAGTGGTTTGTC 61.259 63.158 17.93 8.60 35.25 3.18
690 730 2.203294 GGCCGACCAGTGGTTTGT 60.203 61.111 17.93 0.00 35.25 2.83
691 731 2.983592 GGGCCGACCAGTGGTTTG 60.984 66.667 17.93 12.25 35.25 2.93
692 732 4.636435 CGGGCCGACCAGTGGTTT 62.636 66.667 24.41 0.00 40.22 3.27
702 742 0.106335 TACAAAACAAGTCGGGCCGA 59.894 50.000 27.46 27.46 0.00 5.54
703 743 0.945813 TTACAAAACAAGTCGGGCCG 59.054 50.000 22.51 22.51 0.00 6.13
704 744 1.335597 GCTTACAAAACAAGTCGGGCC 60.336 52.381 0.00 0.00 0.00 5.80
705 745 1.335597 GGCTTACAAAACAAGTCGGGC 60.336 52.381 0.00 0.00 0.00 6.13
706 746 1.268625 GGGCTTACAAAACAAGTCGGG 59.731 52.381 0.00 0.00 0.00 5.14
707 747 1.950909 TGGGCTTACAAAACAAGTCGG 59.049 47.619 0.00 0.00 0.00 4.79
708 748 2.875933 TCTGGGCTTACAAAACAAGTCG 59.124 45.455 0.00 0.00 0.00 4.18
709 749 4.134563 TCTCTGGGCTTACAAAACAAGTC 58.865 43.478 0.00 0.00 0.00 3.01
710 750 4.137543 CTCTCTGGGCTTACAAAACAAGT 58.862 43.478 0.00 0.00 0.00 3.16
719 759 1.116308 GAGGACCTCTCTGGGCTTAC 58.884 60.000 14.72 0.00 45.52 2.34
731 771 4.689062 TCTCTGGACTAATTTGAGGACCT 58.311 43.478 0.00 0.00 0.00 3.85
735 775 6.712547 ACTTGTTTCTCTGGACTAATTTGAGG 59.287 38.462 0.00 0.00 0.00 3.86
1125 1166 2.777972 CGGGATGGAGCGGACGTTA 61.778 63.158 0.00 0.00 0.00 3.18
1128 1169 3.559657 GATCGGGATGGAGCGGACG 62.560 68.421 0.00 0.00 0.00 4.79
1143 1184 1.586564 CTCGTCGTCCTTGCGGATC 60.587 63.158 0.00 0.00 42.43 3.36
1395 1436 1.301479 GTCCTCCGCCGTGAACTTT 60.301 57.895 0.00 0.00 0.00 2.66
1552 1595 9.249457 CATACGAATAATAAAGCAGTCTTCAGA 57.751 33.333 0.00 0.00 0.00 3.27
1558 1601 8.156553 CGACATCATACGAATAATAAAGCAGTC 58.843 37.037 0.00 0.00 0.00 3.51
1559 1602 7.652105 ACGACATCATACGAATAATAAAGCAGT 59.348 33.333 0.00 0.00 0.00 4.40
1562 1608 7.115805 TCCACGACATCATACGAATAATAAAGC 59.884 37.037 0.00 0.00 0.00 3.51
1569 1615 5.699097 TCATCCACGACATCATACGAATA 57.301 39.130 0.00 0.00 0.00 1.75
1577 1623 0.246360 AACGCTCATCCACGACATCA 59.754 50.000 0.00 0.00 0.00 3.07
1584 1630 2.293399 AGGTTTGAAAACGCTCATCCAC 59.707 45.455 0.11 0.00 39.77 4.02
1593 1640 5.957910 TGCACATTAAAGGTTTGAAAACG 57.042 34.783 0.11 0.00 39.77 3.60
1598 1645 8.034215 CCATAAAGATGCACATTAAAGGTTTGA 58.966 33.333 0.00 0.00 0.00 2.69
1599 1646 7.278424 CCCATAAAGATGCACATTAAAGGTTTG 59.722 37.037 0.00 0.00 0.00 2.93
1602 1649 5.957774 ACCCATAAAGATGCACATTAAAGGT 59.042 36.000 0.00 0.00 0.00 3.50
1604 1655 7.148018 ACAGACCCATAAAGATGCACATTAAAG 60.148 37.037 0.00 0.00 0.00 1.85
1607 1658 5.589855 CACAGACCCATAAAGATGCACATTA 59.410 40.000 0.00 0.00 0.00 1.90
1608 1659 4.400251 CACAGACCCATAAAGATGCACATT 59.600 41.667 0.00 0.00 0.00 2.71
1619 1670 1.367346 TCCAAGGCACAGACCCATAA 58.633 50.000 0.00 0.00 0.00 1.90
1621 1672 0.706433 AATCCAAGGCACAGACCCAT 59.294 50.000 0.00 0.00 0.00 4.00
1622 1673 0.482446 AAATCCAAGGCACAGACCCA 59.518 50.000 0.00 0.00 0.00 4.51
1623 1674 1.273327 CAAAATCCAAGGCACAGACCC 59.727 52.381 0.00 0.00 0.00 4.46
1626 1677 5.508567 TCATATCAAAATCCAAGGCACAGA 58.491 37.500 0.00 0.00 0.00 3.41
1627 1678 5.840243 TCATATCAAAATCCAAGGCACAG 57.160 39.130 0.00 0.00 0.00 3.66
1628 1679 5.951148 TCTTCATATCAAAATCCAAGGCACA 59.049 36.000 0.00 0.00 0.00 4.57
1629 1680 6.096001 AGTCTTCATATCAAAATCCAAGGCAC 59.904 38.462 0.00 0.00 0.00 5.01
1714 1767 4.772624 TCTAGAGGTGCACACAGATAAACT 59.227 41.667 20.43 2.34 0.00 2.66
1733 1791 9.319143 CTAACAGATGGTCAATTTAACCTCTAG 57.681 37.037 7.99 0.00 37.69 2.43
1745 1803 4.593206 ACCTGAGAACTAACAGATGGTCAA 59.407 41.667 0.00 0.00 36.38 3.18
1747 1805 4.810191 ACCTGAGAACTAACAGATGGTC 57.190 45.455 0.00 0.00 36.38 4.02
1754 1812 7.894364 AGGATTAGTCTAACCTGAGAACTAACA 59.106 37.037 10.98 0.00 29.69 2.41
1775 1833 3.244422 TGAACTAACACTCGGCAAGGATT 60.244 43.478 0.00 0.00 0.00 3.01
1783 1841 3.841643 ACGGTAATGAACTAACACTCGG 58.158 45.455 0.00 0.00 0.00 4.63
1785 1843 6.183360 GCAACTACGGTAATGAACTAACACTC 60.183 42.308 5.15 0.00 0.00 3.51
1831 1889 4.342862 AGCAAACCGATACAGAGCATAT 57.657 40.909 0.00 0.00 0.00 1.78
1846 1904 9.190858 CAGAACATCTAGTATGATCTAGCAAAC 57.809 37.037 11.70 0.00 37.78 2.93
1868 1926 3.630312 GGCTGACCAAAAACTACACAGAA 59.370 43.478 0.00 0.00 35.26 3.02
1921 1979 3.616219 TGTGCAAGTAACTTCCACAAGT 58.384 40.909 0.00 0.00 38.91 3.16
1924 1982 3.317711 CCATTGTGCAAGTAACTTCCACA 59.682 43.478 0.00 0.00 39.92 4.17
1971 2029 2.047939 GGTGCATTGCAACTGCCC 60.048 61.111 19.36 19.55 43.73 5.36
1993 2052 5.988561 GGATCCAGACTGCTATTAGAAACAG 59.011 44.000 6.95 0.00 36.22 3.16
2011 2070 1.079405 GGACGAAACGCAGGATCCA 60.079 57.895 15.82 0.00 0.00 3.41
2020 2079 1.000607 TGACCAGAGAAGGACGAAACG 60.001 52.381 0.00 0.00 0.00 3.60
2026 2085 2.147150 GCAAACTGACCAGAGAAGGAC 58.853 52.381 3.76 0.00 0.00 3.85
2072 2131 9.124807 GGTGGTTATAAATTTCTTTTCAACGAG 57.875 33.333 0.00 0.00 0.00 4.18
2099 2158 9.128107 CACACGCAAAATTATCTGAAAAACTAT 57.872 29.630 0.00 0.00 0.00 2.12
2104 2163 6.292061 GCAACACACGCAAAATTATCTGAAAA 60.292 34.615 0.00 0.00 0.00 2.29
2115 2209 0.459237 CAAGGGCAACACACGCAAAA 60.459 50.000 0.00 0.00 39.74 2.44
2117 2211 1.106351 ATCAAGGGCAACACACGCAA 61.106 50.000 0.00 0.00 39.74 4.85
2127 2221 2.647299 TGTCCTCCTAAAATCAAGGGCA 59.353 45.455 0.00 0.00 41.07 5.36
2136 2230 9.177608 CATGTATCTTTGAATGTCCTCCTAAAA 57.822 33.333 0.00 0.00 0.00 1.52
2141 2235 5.440610 ACCATGTATCTTTGAATGTCCTCC 58.559 41.667 0.00 0.00 0.00 4.30
2142 2236 5.235186 CGACCATGTATCTTTGAATGTCCTC 59.765 44.000 0.00 0.00 0.00 3.71
2156 2250 2.507407 AGCAAAACCCGACCATGTAT 57.493 45.000 0.00 0.00 0.00 2.29
2157 2251 2.279935 AAGCAAAACCCGACCATGTA 57.720 45.000 0.00 0.00 0.00 2.29
2185 2279 3.399330 ACTACCATCACAGACAAAACCG 58.601 45.455 0.00 0.00 0.00 4.44
2188 2282 6.119536 ACAGAAACTACCATCACAGACAAAA 58.880 36.000 0.00 0.00 0.00 2.44
2189 2283 5.680619 ACAGAAACTACCATCACAGACAAA 58.319 37.500 0.00 0.00 0.00 2.83
2190 2284 5.290493 ACAGAAACTACCATCACAGACAA 57.710 39.130 0.00 0.00 0.00 3.18
2194 2288 2.668457 GCGACAGAAACTACCATCACAG 59.332 50.000 0.00 0.00 0.00 3.66
2197 2291 2.826128 AGAGCGACAGAAACTACCATCA 59.174 45.455 0.00 0.00 0.00 3.07
2198 2292 3.512033 AGAGCGACAGAAACTACCATC 57.488 47.619 0.00 0.00 0.00 3.51
2199 2293 3.130693 GGTAGAGCGACAGAAACTACCAT 59.869 47.826 14.26 0.00 46.87 3.55
2200 2294 2.490903 GGTAGAGCGACAGAAACTACCA 59.509 50.000 14.26 0.00 46.87 3.25
2201 2295 3.148026 GGTAGAGCGACAGAAACTACC 57.852 52.381 0.00 0.00 43.60 3.18
2202 2296 3.427773 CCAGGTAGAGCGACAGAAACTAC 60.428 52.174 0.00 0.00 34.55 2.73
2203 2297 2.753452 CCAGGTAGAGCGACAGAAACTA 59.247 50.000 0.00 0.00 0.00 2.24
2204 2298 1.546476 CCAGGTAGAGCGACAGAAACT 59.454 52.381 0.00 0.00 0.00 2.66
2205 2299 1.544691 TCCAGGTAGAGCGACAGAAAC 59.455 52.381 0.00 0.00 0.00 2.78
2221 2343 4.518211 ACATTTCAACAGAAGAAGCTCCAG 59.482 41.667 0.00 0.00 0.00 3.86
2225 2347 8.621532 TGTATAACATTTCAACAGAAGAAGCT 57.378 30.769 0.00 0.00 0.00 3.74
2236 2358 9.949174 CCGATTCATCATTGTATAACATTTCAA 57.051 29.630 0.00 0.00 0.00 2.69
2246 2368 5.674525 ACAGACACCGATTCATCATTGTAT 58.325 37.500 0.00 0.00 0.00 2.29
2247 2369 5.084818 ACAGACACCGATTCATCATTGTA 57.915 39.130 0.00 0.00 0.00 2.41
2248 2370 3.942829 ACAGACACCGATTCATCATTGT 58.057 40.909 0.00 0.00 0.00 2.71
2249 2371 4.655027 CAACAGACACCGATTCATCATTG 58.345 43.478 0.00 0.00 0.00 2.82
2250 2372 3.127548 GCAACAGACACCGATTCATCATT 59.872 43.478 0.00 0.00 0.00 2.57
2251 2373 2.679837 GCAACAGACACCGATTCATCAT 59.320 45.455 0.00 0.00 0.00 2.45
2252 2374 2.076100 GCAACAGACACCGATTCATCA 58.924 47.619 0.00 0.00 0.00 3.07
2253 2375 2.349886 GAGCAACAGACACCGATTCATC 59.650 50.000 0.00 0.00 0.00 2.92
2261 2648 0.036294 GGGGTAGAGCAACAGACACC 60.036 60.000 0.00 0.00 0.00 4.16
2262 2649 0.389948 CGGGGTAGAGCAACAGACAC 60.390 60.000 0.00 0.00 0.00 3.67
2264 2651 1.218316 CCGGGGTAGAGCAACAGAC 59.782 63.158 0.00 0.00 0.00 3.51
2271 2658 2.313051 GAAGAAGCCCGGGGTAGAGC 62.313 65.000 28.74 15.71 0.00 4.09
2293 2680 3.504906 AGCAACAGACACTCATTCATTGG 59.495 43.478 0.00 0.00 0.00 3.16
2294 2681 4.379186 GGAGCAACAGACACTCATTCATTG 60.379 45.833 0.00 0.00 31.88 2.82
2295 2682 3.755378 GGAGCAACAGACACTCATTCATT 59.245 43.478 0.00 0.00 31.88 2.57
2296 2683 3.244665 TGGAGCAACAGACACTCATTCAT 60.245 43.478 0.00 0.00 31.88 2.57
2297 2684 2.104622 TGGAGCAACAGACACTCATTCA 59.895 45.455 0.00 0.00 31.88 2.57
2298 2685 2.481952 GTGGAGCAACAGACACTCATTC 59.518 50.000 0.00 0.00 31.88 2.67
2299 2686 2.105477 AGTGGAGCAACAGACACTCATT 59.895 45.455 0.00 0.00 39.84 2.57
2300 2687 1.696336 AGTGGAGCAACAGACACTCAT 59.304 47.619 0.00 0.00 39.84 2.90
2301 2688 1.123077 AGTGGAGCAACAGACACTCA 58.877 50.000 0.00 0.00 39.84 3.41
2302 2689 3.997672 AGTGGAGCAACAGACACTC 57.002 52.632 0.00 0.00 39.84 3.51
2303 2690 0.032678 CGAGTGGAGCAACAGACACT 59.967 55.000 0.00 0.00 45.99 3.55
2304 2691 0.946221 CCGAGTGGAGCAACAGACAC 60.946 60.000 0.00 0.00 37.49 3.67
2305 2692 1.367471 CCGAGTGGAGCAACAGACA 59.633 57.895 0.00 0.00 37.49 3.41
2306 2693 1.374758 CCCGAGTGGAGCAACAGAC 60.375 63.158 0.00 0.00 37.49 3.51
2307 2694 2.583441 CCCCGAGTGGAGCAACAGA 61.583 63.158 0.00 0.00 37.49 3.41
2308 2695 2.046892 CCCCGAGTGGAGCAACAG 60.047 66.667 0.00 0.00 37.49 3.16
2309 2696 4.329545 GCCCCGAGTGGAGCAACA 62.330 66.667 0.00 0.00 37.49 3.33
2310 2697 2.180159 TAAGCCCCGAGTGGAGCAAC 62.180 60.000 0.00 0.00 37.49 4.17
2311 2698 1.271840 ATAAGCCCCGAGTGGAGCAA 61.272 55.000 0.00 0.00 37.49 3.91
2312 2699 1.271840 AATAAGCCCCGAGTGGAGCA 61.272 55.000 0.00 0.00 37.49 4.26
2313 2700 0.533085 GAATAAGCCCCGAGTGGAGC 60.533 60.000 0.00 0.00 37.49 4.70
2314 2701 1.123928 AGAATAAGCCCCGAGTGGAG 58.876 55.000 0.00 0.00 37.49 3.86
2315 2702 0.830648 CAGAATAAGCCCCGAGTGGA 59.169 55.000 0.00 0.00 37.49 4.02
2316 2703 0.815615 GCAGAATAAGCCCCGAGTGG 60.816 60.000 0.00 0.00 0.00 4.00
2317 2704 0.179000 AGCAGAATAAGCCCCGAGTG 59.821 55.000 0.00 0.00 0.00 3.51
2318 2705 0.179000 CAGCAGAATAAGCCCCGAGT 59.821 55.000 0.00 0.00 0.00 4.18
2319 2706 0.465705 TCAGCAGAATAAGCCCCGAG 59.534 55.000 0.00 0.00 0.00 4.63
2320 2707 0.908910 TTCAGCAGAATAAGCCCCGA 59.091 50.000 0.00 0.00 0.00 5.14
2321 2708 1.750193 TTTCAGCAGAATAAGCCCCG 58.250 50.000 0.00 0.00 32.89 5.73
2322 2709 3.026694 ACATTTCAGCAGAATAAGCCCC 58.973 45.455 0.00 0.00 32.89 5.80
2323 2710 4.725790 AACATTTCAGCAGAATAAGCCC 57.274 40.909 0.00 0.00 32.89 5.19
2324 2711 7.930217 TGTATAACATTTCAGCAGAATAAGCC 58.070 34.615 0.00 0.00 32.89 4.35
2325 2712 9.956720 ATTGTATAACATTTCAGCAGAATAAGC 57.043 29.630 0.00 0.00 32.89 3.09
2331 2718 9.791820 CAATTGATTGTATAACATTTCAGCAGA 57.208 29.630 0.00 0.00 33.22 4.26
2342 2729 5.810525 AGCGCACTCAATTGATTGTATAAC 58.189 37.500 22.36 8.40 38.84 1.89
2352 2739 2.787249 CCCGAGCGCACTCAATTG 59.213 61.111 11.47 0.00 43.66 2.32
2363 2750 2.158561 AATGCACCAAAAGCCCGAGC 62.159 55.000 0.00 0.00 40.32 5.03
2365 2752 0.539438 AGAATGCACCAAAAGCCCGA 60.539 50.000 0.00 0.00 0.00 5.14
2366 2753 0.318120 AAGAATGCACCAAAAGCCCG 59.682 50.000 0.00 0.00 0.00 6.13
2367 2754 2.549064 AAAGAATGCACCAAAAGCCC 57.451 45.000 0.00 0.00 0.00 5.19
2376 2763 5.068723 AGGATGATCATGGAAAAGAATGCAC 59.931 40.000 14.30 0.00 0.00 4.57
2394 2781 5.503634 TTCAGACAATCTTGGAAGGATGA 57.496 39.130 0.00 0.00 0.00 2.92
2400 2787 6.323482 TGGACAAAATTCAGACAATCTTGGAA 59.677 34.615 0.00 0.00 0.00 3.53
2408 2795 5.298026 TGACGAATGGACAAAATTCAGACAA 59.702 36.000 0.00 0.00 34.34 3.18
2446 2850 3.446442 AGGGATGCTTCTGTTTGATGT 57.554 42.857 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.