Multiple sequence alignment - TraesCS3D01G378500

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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 TraesCS3D01G378500 chr3D 100.000 9897 0 0 1 9897 495568142 495578038 0.000000e+00 18277.0
1 TraesCS3D01G378500 chr3D 85.076 1052 123 22 7703 8743 576690823 576689795 0.000000e+00 1042.0
2 TraesCS3D01G378500 chr3D 92.908 141 10 0 6604 6744 576690961 576690821 1.300000e-48 206.0
3 TraesCS3D01G378500 chr3A 98.332 4376 69 2 4609 8980 635098975 635103350 0.000000e+00 7673.0
4 TraesCS3D01G378500 chr3A 94.909 4675 133 31 1 4611 635094282 635098915 0.000000e+00 7217.0
5 TraesCS3D01G378500 chr3B 97.281 4376 101 6 4609 8980 654478848 654483209 0.000000e+00 7406.0
6 TraesCS3D01G378500 chr3B 95.533 4589 135 29 57 4611 654474236 654478788 0.000000e+00 7275.0
7 TraesCS3D01G378500 chr3B 89.116 294 29 2 1 292 654473717 654474009 7.310000e-96 363.0
8 TraesCS3D01G378500 chr3B 84.466 309 47 1 3 310 654473122 654473430 4.490000e-78 303.0
9 TraesCS3D01G378500 chr3B 90.625 128 8 2 8977 9104 654483248 654483371 6.150000e-37 167.0
10 TraesCS3D01G378500 chr7D 86.548 1063 116 17 7690 8743 39315994 39317038 0.000000e+00 1146.0
11 TraesCS3D01G378500 chr7D 93.706 143 9 0 6603 6745 39315833 39315975 2.170000e-51 215.0
12 TraesCS3D01G378500 chr7D 88.889 144 11 4 6190 6333 5479345 5479207 1.320000e-38 172.0
13 TraesCS3D01G378500 chr7D 94.565 92 5 0 6603 6694 5479209 5479118 1.040000e-29 143.0
14 TraesCS3D01G378500 chr7D 80.000 150 25 4 4187 4335 638681497 638681352 1.360000e-18 106.0
15 TraesCS3D01G378500 chr2D 85.167 1045 109 20 7707 8739 4478918 4479928 0.000000e+00 1029.0
16 TraesCS3D01G378500 chr2D 91.892 111 9 0 6635 6745 4478777 4478887 1.330000e-33 156.0
17 TraesCS3D01G378500 chr2A 88.514 801 67 8 9122 9897 140430998 140430198 0.000000e+00 946.0
18 TraesCS3D01G378500 chr1D 82.771 563 70 10 9249 9784 376639260 376638698 2.500000e-130 477.0
19 TraesCS3D01G378500 chr6B 89.877 326 30 3 7766 8089 11168835 11168511 5.530000e-112 416.0
20 TraesCS3D01G378500 chr6B 95.105 143 7 0 6603 6745 11169786 11169644 1.000000e-54 226.0
21 TraesCS3D01G378500 chr5B 81.967 183 33 0 9167 9349 588392896 588393078 1.330000e-33 156.0
22 TraesCS3D01G378500 chr2B 96.875 32 1 0 8338 8369 94211050 94211081 5.000000e-03 54.7


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 TraesCS3D01G378500 chr3D 495568142 495578038 9896 False 18277.0 18277 100.0000 1 9897 1 chr3D.!!$F1 9896
1 TraesCS3D01G378500 chr3D 576689795 576690961 1166 True 624.0 1042 88.9920 6604 8743 2 chr3D.!!$R1 2139
2 TraesCS3D01G378500 chr3A 635094282 635103350 9068 False 7445.0 7673 96.6205 1 8980 2 chr3A.!!$F1 8979
3 TraesCS3D01G378500 chr3B 654473122 654483371 10249 False 3102.8 7406 91.4042 1 9104 5 chr3B.!!$F1 9103
4 TraesCS3D01G378500 chr7D 39315833 39317038 1205 False 680.5 1146 90.1270 6603 8743 2 chr7D.!!$F1 2140
5 TraesCS3D01G378500 chr2D 4478777 4479928 1151 False 592.5 1029 88.5295 6635 8739 2 chr2D.!!$F1 2104
6 TraesCS3D01G378500 chr2A 140430198 140430998 800 True 946.0 946 88.5140 9122 9897 1 chr2A.!!$R1 775
7 TraesCS3D01G378500 chr1D 376638698 376639260 562 True 477.0 477 82.7710 9249 9784 1 chr1D.!!$R1 535
8 TraesCS3D01G378500 chr6B 11168511 11169786 1275 True 321.0 416 92.4910 6603 8089 2 chr6B.!!$R1 1486

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
265 1327 0.100682 CGTGAGGGTGACGATACAGG 59.899 60.000 0.00 0.00 39.21 4.00 F
999 2123 0.041238 TCCCTGTCTGACGGATTCCT 59.959 55.000 18.02 0.00 0.00 3.36 F
1391 2521 0.395724 AGGGGCCGAACATTTGGATC 60.396 55.000 1.74 0.00 33.23 3.36 F
1873 3008 0.976641 TCTTGTAGTGCTGACCTGGG 59.023 55.000 0.00 0.00 0.00 4.45 F
2415 3557 1.249407 ACCGACTCTGAAGAGGACAC 58.751 55.000 11.87 0.51 46.13 3.67 F
3339 4481 1.004918 GCCAGCAGAGGTAACGTGT 60.005 57.895 0.00 0.00 46.39 4.49 F
3684 4826 1.517242 AGCGAGCAGTTGGAGAAAAG 58.483 50.000 0.00 0.00 0.00 2.27 F
4317 5473 4.161754 AGGGATACGTCTGGTCCTTTTTAG 59.838 45.833 0.00 0.00 37.60 1.85 F
4929 6149 0.099436 CGCAGCTACATTTTCCTGGC 59.901 55.000 0.00 0.00 0.00 4.85 F
5182 6402 0.670162 TGCTGCTGCTCCAGAAAAAC 59.330 50.000 17.00 0.00 40.48 2.43 F
5718 6938 0.886490 CTTCCTCTGCACGCAACCTT 60.886 55.000 0.00 0.00 0.00 3.50 F
5787 7007 2.936919 AGAAGCTGTCAACATGTGGA 57.063 45.000 0.00 0.00 0.00 4.02 F
6830 8051 3.177884 ACCCTGCACCAGCCAGAA 61.178 61.111 0.00 0.00 41.13 3.02 F
8311 10253 1.562008 TGGGACAAACAACTGGAGTCA 59.438 47.619 0.00 0.00 31.92 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1513 2648 1.202651 AGGTGTTCCTTGAAGGACACG 60.203 52.381 25.92 1.27 45.78 4.49 R
2212 3354 1.278127 CCTCTGCTAAAACGGGGAGAA 59.722 52.381 0.00 0.00 30.10 2.87 R
2613 3755 1.688197 CACAACTTTCCTTGGTGGCAT 59.312 47.619 0.00 0.00 35.26 4.40 R
3339 4481 2.100916 GCAGTACGAGGAGGAATGCTAA 59.899 50.000 0.00 0.00 0.00 3.09 R
4317 5473 0.686769 TCTACTCCCTCCTTTCCGGC 60.687 60.000 0.00 0.00 0.00 6.13 R
4911 6131 1.133790 CTGCCAGGAAAATGTAGCTGC 59.866 52.381 0.00 0.00 0.00 5.25 R
4929 6149 1.520494 ACTGCTCATCACAAGTGCTG 58.480 50.000 0.00 0.00 0.00 4.41 R
5787 7007 0.178981 AGTCCCTGTGCAGCAAATGT 60.179 50.000 0.00 0.00 0.00 2.71 R
6307 7527 3.251484 TGGGTCAGGAGAAGAATCAACT 58.749 45.455 0.00 0.00 0.00 3.16 R
6613 7834 4.162320 TCCACTCCAATATTCAGGACAGAC 59.838 45.833 0.00 0.00 0.00 3.51 R
6830 8051 5.424895 TGGCAATAGGGTAAATTTCATTGCT 59.575 36.000 21.06 0.00 44.70 3.91 R
6983 8204 7.854557 TGTTGATGAGATGGAACTTATTCAG 57.145 36.000 0.00 0.00 36.46 3.02 R
8437 10379 0.319211 ACAAACGATCACGCCTCGAA 60.319 50.000 8.60 0.00 43.96 3.71 R
9425 11413 0.666274 CGTCTGCGGCAAAGACAGTA 60.666 55.000 18.65 0.00 43.53 2.74 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
23 24 2.907897 CTTGTAGCCTTCCTCGCCGG 62.908 65.000 0.00 0.00 0.00 6.13
48 49 7.094634 GGACATTTGTTAGAACACATCTGTCAT 60.095 37.037 18.04 0.00 39.30 3.06
50 51 7.445096 ACATTTGTTAGAACACATCTGTCATGA 59.555 33.333 0.00 0.00 39.30 3.07
130 1192 1.154413 CATCACAAACGCGAGGCAC 60.154 57.895 15.93 0.00 0.00 5.01
200 1262 7.861372 CGATTACGTCTAAATAGAGGAACACAT 59.139 37.037 15.03 2.33 39.80 3.21
204 1266 6.379133 ACGTCTAAATAGAGGAACACATACCA 59.621 38.462 15.03 0.00 39.80 3.25
265 1327 0.100682 CGTGAGGGTGACGATACAGG 59.899 60.000 0.00 0.00 39.21 4.00
435 1524 1.067354 GGTACACGAAACCACCGAGAT 60.067 52.381 0.00 0.00 36.96 2.75
453 1542 1.841663 ATCGCTGCCAAACGTGTCAC 61.842 55.000 0.00 0.00 0.00 3.67
498 1587 0.464452 CTCCCGTCTACCCATCCAAC 59.536 60.000 0.00 0.00 0.00 3.77
512 1601 5.549619 ACCCATCCAACCCAATAATTCAAAA 59.450 36.000 0.00 0.00 0.00 2.44
539 1628 1.521681 GAAATCGCACGGCTAGGCT 60.522 57.895 15.11 0.00 0.00 4.58
753 1852 3.175710 ACCACCCAGTCCCACCAC 61.176 66.667 0.00 0.00 0.00 4.16
754 1853 3.966543 CCACCCAGTCCCACCACC 61.967 72.222 0.00 0.00 0.00 4.61
755 1854 3.966543 CACCCAGTCCCACCACCC 61.967 72.222 0.00 0.00 0.00 4.61
756 1855 4.202030 ACCCAGTCCCACCACCCT 62.202 66.667 0.00 0.00 0.00 4.34
757 1856 3.330720 CCCAGTCCCACCACCCTC 61.331 72.222 0.00 0.00 0.00 4.30
758 1857 3.330720 CCAGTCCCACCACCCTCC 61.331 72.222 0.00 0.00 0.00 4.30
759 1858 3.330720 CAGTCCCACCACCCTCCC 61.331 72.222 0.00 0.00 0.00 4.30
760 1859 3.542602 AGTCCCACCACCCTCCCT 61.543 66.667 0.00 0.00 0.00 4.20
761 1860 3.009714 GTCCCACCACCCTCCCTC 61.010 72.222 0.00 0.00 0.00 4.30
762 1861 4.348495 TCCCACCACCCTCCCTCC 62.348 72.222 0.00 0.00 0.00 4.30
764 1863 4.354943 CCACCACCCTCCCTCCCT 62.355 72.222 0.00 0.00 0.00 4.20
765 1864 2.689034 CACCACCCTCCCTCCCTC 60.689 72.222 0.00 0.00 0.00 4.30
766 1865 2.876858 ACCACCCTCCCTCCCTCT 60.877 66.667 0.00 0.00 0.00 3.69
886 2007 2.760385 CGTCCACCCCTCTCTCCC 60.760 72.222 0.00 0.00 0.00 4.30
999 2123 0.041238 TCCCTGTCTGACGGATTCCT 59.959 55.000 18.02 0.00 0.00 3.36
1142 2266 4.467084 GGCCCGTCGATTCCTGCA 62.467 66.667 0.00 0.00 0.00 4.41
1211 2338 2.023223 TTCGTTAGTTGCCGCCGTC 61.023 57.895 0.00 0.00 0.00 4.79
1391 2521 0.395724 AGGGGCCGAACATTTGGATC 60.396 55.000 1.74 0.00 33.23 3.36
1415 2547 5.450688 CCATCCGTAAGTCTGGTCTTAAGAG 60.451 48.000 5.12 0.00 33.52 2.85
1583 2718 6.385759 TGCCCATGTTCTTAGAATCCTAGTAA 59.614 38.462 0.00 0.00 0.00 2.24
1584 2719 7.092623 TGCCCATGTTCTTAGAATCCTAGTAAA 60.093 37.037 0.00 0.00 0.00 2.01
1590 2725 9.846248 TGTTCTTAGAATCCTAGTAAAACGTAC 57.154 33.333 0.00 0.00 0.00 3.67
1593 2728 9.236006 TCTTAGAATCCTAGTAAAACGTACTGT 57.764 33.333 0.00 0.00 0.00 3.55
1606 2741 6.667007 AAACGTACTGTATTATTTTCGGGG 57.333 37.500 0.00 0.00 0.00 5.73
1608 2743 4.162131 ACGTACTGTATTATTTTCGGGGGT 59.838 41.667 0.00 0.00 0.00 4.95
1609 2744 4.508861 CGTACTGTATTATTTTCGGGGGTG 59.491 45.833 0.00 0.00 0.00 4.61
1610 2745 3.284617 ACTGTATTATTTTCGGGGGTGC 58.715 45.455 0.00 0.00 0.00 5.01
1611 2746 3.053917 ACTGTATTATTTTCGGGGGTGCT 60.054 43.478 0.00 0.00 0.00 4.40
1612 2747 3.951680 CTGTATTATTTTCGGGGGTGCTT 59.048 43.478 0.00 0.00 0.00 3.91
1613 2748 3.697045 TGTATTATTTTCGGGGGTGCTTG 59.303 43.478 0.00 0.00 0.00 4.01
1614 2749 2.588464 TTATTTTCGGGGGTGCTTGA 57.412 45.000 0.00 0.00 0.00 3.02
1615 2750 2.818751 TATTTTCGGGGGTGCTTGAT 57.181 45.000 0.00 0.00 0.00 2.57
1616 2751 1.937191 ATTTTCGGGGGTGCTTGATT 58.063 45.000 0.00 0.00 0.00 2.57
1645 2780 9.345517 CTGTACACCATTCAAATTTATTCTGTG 57.654 33.333 0.00 0.00 0.00 3.66
1647 2782 9.128107 GTACACCATTCAAATTTATTCTGTGTG 57.872 33.333 17.95 10.75 35.18 3.82
1648 2783 7.725251 ACACCATTCAAATTTATTCTGTGTGT 58.275 30.769 11.75 7.70 32.51 3.72
1649 2784 7.652909 ACACCATTCAAATTTATTCTGTGTGTG 59.347 33.333 11.75 0.00 32.51 3.82
1650 2785 7.116662 CACCATTCAAATTTATTCTGTGTGTGG 59.883 37.037 0.00 0.00 0.00 4.17
1651 2786 6.591062 CCATTCAAATTTATTCTGTGTGTGGG 59.409 38.462 0.00 0.00 0.00 4.61
1653 2788 7.825331 TTCAAATTTATTCTGTGTGTGGGTA 57.175 32.000 0.00 0.00 0.00 3.69
1655 2790 7.227873 TCAAATTTATTCTGTGTGTGGGTAGA 58.772 34.615 0.00 0.00 0.00 2.59
1656 2791 7.888021 TCAAATTTATTCTGTGTGTGGGTAGAT 59.112 33.333 0.00 0.00 0.00 1.98
1657 2792 8.522830 CAAATTTATTCTGTGTGTGGGTAGATT 58.477 33.333 0.00 0.00 0.00 2.40
1658 2793 8.650143 AATTTATTCTGTGTGTGGGTAGATTT 57.350 30.769 0.00 0.00 0.00 2.17
1659 2794 8.650143 ATTTATTCTGTGTGTGGGTAGATTTT 57.350 30.769 0.00 0.00 0.00 1.82
1660 2795 8.472007 TTTATTCTGTGTGTGGGTAGATTTTT 57.528 30.769 0.00 0.00 0.00 1.94
1661 2796 5.766150 TTCTGTGTGTGGGTAGATTTTTG 57.234 39.130 0.00 0.00 0.00 2.44
1662 2797 4.141287 TCTGTGTGTGGGTAGATTTTTGG 58.859 43.478 0.00 0.00 0.00 3.28
1663 2798 3.226777 TGTGTGTGGGTAGATTTTTGGG 58.773 45.455 0.00 0.00 0.00 4.12
1687 2822 2.479566 ACATGAGCTTAGTGGTGTGG 57.520 50.000 0.00 0.00 0.00 4.17
1688 2823 1.699634 ACATGAGCTTAGTGGTGTGGT 59.300 47.619 0.00 0.00 0.00 4.16
1791 2926 3.160269 ACTTCTGCTTCCAAATTCCCAG 58.840 45.455 0.00 0.00 0.00 4.45
1830 2965 9.120538 CTTATAAACCAATGTACAACTAGGCAT 57.879 33.333 0.00 0.00 0.00 4.40
1832 2967 4.301072 ACCAATGTACAACTAGGCATGT 57.699 40.909 0.00 0.00 0.00 3.21
1873 3008 0.976641 TCTTGTAGTGCTGACCTGGG 59.023 55.000 0.00 0.00 0.00 4.45
2212 3354 1.549170 CCTTACAGCACTCCTTACGGT 59.451 52.381 0.00 0.00 0.00 4.83
2413 3555 2.619646 GGATACCGACTCTGAAGAGGAC 59.380 54.545 11.87 4.86 46.13 3.85
2415 3557 1.249407 ACCGACTCTGAAGAGGACAC 58.751 55.000 11.87 0.51 46.13 3.67
2431 3573 3.461831 AGGACACTGAGCTCCTAGATACT 59.538 47.826 12.15 0.54 34.93 2.12
2631 3773 2.242043 AGATGCCACCAAGGAAAGTTG 58.758 47.619 0.00 0.00 41.22 3.16
2688 3830 3.564644 TCTTCGGAACCTGATCGAGATAC 59.435 47.826 0.00 0.00 34.33 2.24
2971 4113 3.117738 CAGACCCAGCAAATAAGGAGGAT 60.118 47.826 0.00 0.00 0.00 3.24
3121 4263 6.182627 AGCAATGTCAGAAGTTATGAATGGA 58.817 36.000 0.87 0.00 0.00 3.41
3339 4481 1.004918 GCCAGCAGAGGTAACGTGT 60.005 57.895 0.00 0.00 46.39 4.49
3344 4486 1.616865 AGCAGAGGTAACGTGTTAGCA 59.383 47.619 20.28 0.00 43.72 3.49
3684 4826 1.517242 AGCGAGCAGTTGGAGAAAAG 58.483 50.000 0.00 0.00 0.00 2.27
4180 5336 8.559536 CGCTAGATAATTTGACCAATGTAACAT 58.440 33.333 0.00 0.00 0.00 2.71
4317 5473 4.161754 AGGGATACGTCTGGTCCTTTTTAG 59.838 45.833 0.00 0.00 37.60 1.85
4348 5504 6.183347 AGGAGGGAGTAGACAATTCATTTTG 58.817 40.000 0.00 0.00 0.00 2.44
4439 5595 9.213799 CTCTCTATATATTGTCTCCTTTTTGGC 57.786 37.037 0.00 0.00 35.26 4.52
4545 5703 5.636123 TGACATACATTTAGGGGTGTGTTT 58.364 37.500 0.00 0.00 39.09 2.83
4911 6131 7.061752 AGAGGACTGTTTAAAAATCGATTCG 57.938 36.000 11.83 0.00 0.00 3.34
4929 6149 0.099436 CGCAGCTACATTTTCCTGGC 59.901 55.000 0.00 0.00 0.00 4.85
5182 6402 0.670162 TGCTGCTGCTCCAGAAAAAC 59.330 50.000 17.00 0.00 40.48 2.43
5186 6406 3.365767 GCTGCTGCTCCAGAAAAACTAAG 60.366 47.826 8.53 0.00 34.77 2.18
5188 6408 3.565482 TGCTGCTCCAGAAAAACTAAGTG 59.435 43.478 0.00 0.00 32.44 3.16
5559 6779 5.478679 AGAAGCTCACATGTACTCTTACACT 59.521 40.000 0.00 0.00 41.12 3.55
5600 6820 3.065371 ACTGTTCTTGTGAAAAGCCTTCG 59.935 43.478 0.00 0.00 40.36 3.79
5718 6938 0.886490 CTTCCTCTGCACGCAACCTT 60.886 55.000 0.00 0.00 0.00 3.50
5751 6971 5.485662 AGTTTTTGGAACTCAGTTTCTCG 57.514 39.130 0.00 0.00 0.00 4.04
5787 7007 2.936919 AGAAGCTGTCAACATGTGGA 57.063 45.000 0.00 0.00 0.00 4.02
6053 7273 8.349983 AGAGTGTGCGTTTCTACAAATATTTTT 58.650 29.630 0.00 0.00 0.00 1.94
6062 7282 6.832520 TCTACAAATATTTTTCTGCAGCCA 57.167 33.333 9.47 0.00 0.00 4.75
6069 7289 8.545420 CAAATATTTTTCTGCAGCCATACATTC 58.455 33.333 9.47 0.00 0.00 2.67
6225 7445 3.354397 GAAGAACACAAACAGTTCAGCG 58.646 45.455 8.54 0.00 45.93 5.18
6830 8051 3.177884 ACCCTGCACCAGCCAGAA 61.178 61.111 0.00 0.00 41.13 3.02
6983 8204 5.703876 AGAAAGAAATTGAAACTGGCGATC 58.296 37.500 0.00 0.00 0.00 3.69
8311 10253 1.562008 TGGGACAAACAACTGGAGTCA 59.438 47.619 0.00 0.00 31.92 3.41
8437 10379 1.980765 TCAGTTCCAGATGGTTGAGCT 59.019 47.619 0.00 0.00 36.34 4.09
8521 10463 1.310933 GCTGCCATGGTCCTTGTCTG 61.311 60.000 14.67 0.00 0.00 3.51
8802 10747 4.890088 AGACGCTGGTAATAAAACTGTCA 58.110 39.130 0.00 0.00 0.00 3.58
8821 10766 6.769822 ACTGTCAAAAATGACTCTCAGAATGT 59.230 34.615 10.03 0.00 39.41 2.71
8828 10773 1.552337 GACTCTCAGAATGTGCAGGGA 59.448 52.381 0.00 0.00 37.40 4.20
8844 10789 2.109126 GGAAGCCGCGCATCTTTCT 61.109 57.895 8.75 0.00 0.00 2.52
8850 10795 2.557056 AGCCGCGCATCTTTCTATAGTA 59.443 45.455 8.75 0.00 0.00 1.82
8853 10798 3.859961 CCGCGCATCTTTCTATAGTATGG 59.140 47.826 8.75 0.00 0.00 2.74
8869 10814 4.583871 AGTATGGAAGTTTGAGGCTTCTG 58.416 43.478 0.00 0.00 41.36 3.02
8912 10857 5.789643 AGCAATGACTGGTAATTTGTGTT 57.210 34.783 0.00 0.00 32.70 3.32
9032 11019 5.045505 TGGTTATTAGATGTGTGTAGCCCAA 60.046 40.000 0.00 0.00 0.00 4.12
9040 11027 4.027674 TGTGTGTAGCCCAAATGTACAT 57.972 40.909 1.41 1.41 0.00 2.29
9045 11032 4.332819 GTGTAGCCCAAATGTACATGAGAC 59.667 45.833 9.63 2.27 0.00 3.36
9061 11048 7.246171 ACATGAGACTGTTTCTATTAGGTGT 57.754 36.000 0.00 0.00 33.22 4.16
9064 11051 7.770366 TGAGACTGTTTCTATTAGGTGTACA 57.230 36.000 0.00 0.00 33.22 2.90
9065 11052 8.362464 TGAGACTGTTTCTATTAGGTGTACAT 57.638 34.615 0.00 0.00 33.22 2.29
9066 11053 8.251026 TGAGACTGTTTCTATTAGGTGTACATG 58.749 37.037 0.00 0.00 33.22 3.21
9067 11054 8.362464 AGACTGTTTCTATTAGGTGTACATGA 57.638 34.615 0.00 0.00 30.17 3.07
9068 11055 8.470805 AGACTGTTTCTATTAGGTGTACATGAG 58.529 37.037 0.00 0.00 30.17 2.90
9073 11060 7.914427 TTCTATTAGGTGTACATGAGATGGT 57.086 36.000 0.00 0.00 33.60 3.55
9089 11076 2.550487 GGTGTGCATTAGCGAACCA 58.450 52.632 0.00 0.00 44.19 3.67
9104 11091 4.039124 AGCGAACCAGAACCATTTCAATTT 59.961 37.500 0.00 0.00 33.72 1.82
9105 11092 4.150451 GCGAACCAGAACCATTTCAATTTG 59.850 41.667 0.00 0.00 33.72 2.32
9106 11093 5.527951 CGAACCAGAACCATTTCAATTTGA 58.472 37.500 0.00 0.00 33.72 2.69
9107 11094 5.630680 CGAACCAGAACCATTTCAATTTGAG 59.369 40.000 0.00 0.00 33.72 3.02
9108 11095 6.514870 CGAACCAGAACCATTTCAATTTGAGA 60.515 38.462 0.00 0.00 33.72 3.27
9109 11096 6.923199 ACCAGAACCATTTCAATTTGAGAT 57.077 33.333 0.00 0.00 33.72 2.75
9110 11097 7.307131 ACCAGAACCATTTCAATTTGAGATT 57.693 32.000 0.00 0.00 33.72 2.40
9111 11098 7.156673 ACCAGAACCATTTCAATTTGAGATTG 58.843 34.615 0.00 0.47 33.72 2.67
9112 11099 7.156673 CCAGAACCATTTCAATTTGAGATTGT 58.843 34.615 0.00 1.05 33.72 2.71
9113 11100 7.658575 CCAGAACCATTTCAATTTGAGATTGTT 59.341 33.333 15.15 15.15 32.20 2.83
9114 11101 9.048446 CAGAACCATTTCAATTTGAGATTGTTT 57.952 29.630 15.90 5.01 30.53 2.83
9115 11102 9.264719 AGAACCATTTCAATTTGAGATTGTTTC 57.735 29.630 15.90 11.33 30.53 2.78
9116 11103 9.264719 GAACCATTTCAATTTGAGATTGTTTCT 57.735 29.630 15.90 0.88 30.53 2.52
9133 11120 4.522789 TGTTTCTATTTGGCCAAGGAAGTC 59.477 41.667 19.48 17.83 0.00 3.01
9172 11159 2.563427 GCGCTTCCTTGCTTCACC 59.437 61.111 0.00 0.00 0.00 4.02
9190 11177 1.048724 CCATGGGCGTCTTCCTCCTA 61.049 60.000 2.85 0.00 0.00 2.94
9199 11186 2.766828 CGTCTTCCTCCTATCCAAAGGT 59.233 50.000 0.00 0.00 37.91 3.50
9208 11195 5.339530 CCTCCTATCCAAAGGTTTCTGTGAT 60.340 44.000 0.00 0.00 37.91 3.06
9221 11208 9.965902 AAGGTTTCTGTGATAAGTATGAGAAAT 57.034 29.630 0.00 0.00 33.35 2.17
9226 11213 8.722480 TCTGTGATAAGTATGAGAAATTGGTG 57.278 34.615 0.00 0.00 0.00 4.17
9235 11222 6.830838 AGTATGAGAAATTGGTGAGGGATTTC 59.169 38.462 0.00 0.00 39.10 2.17
9244 11231 1.214305 TGAGGGATTTCTGGTGGGGG 61.214 60.000 0.00 0.00 0.00 5.40
9316 11303 4.024545 CCTAAACGGGCGGGTGGT 62.025 66.667 0.00 0.00 0.00 4.16
9352 11339 5.997746 GGATATGCACCTGTTTAATCTAGCA 59.002 40.000 0.00 0.00 35.03 3.49
9391 11378 0.389948 GGAGACTGCTACAACACCCG 60.390 60.000 0.00 0.00 0.00 5.28
9424 11412 7.596494 TCTTTGCAAGAGTTATGAAATCCAAG 58.404 34.615 0.00 0.00 32.71 3.61
9425 11413 6.899393 TTGCAAGAGTTATGAAATCCAAGT 57.101 33.333 0.00 0.00 0.00 3.16
9434 11447 9.220767 GAGTTATGAAATCCAAGTACTGTCTTT 57.779 33.333 0.00 0.00 0.00 2.52
9438 11451 2.163818 TCCAAGTACTGTCTTTGCCG 57.836 50.000 0.00 0.00 0.00 5.69
9440 11453 1.225855 CAAGTACTGTCTTTGCCGCA 58.774 50.000 0.00 0.00 0.00 5.69
9464 11477 0.394899 CATCCCCAGTTTGGAGAGGC 60.395 60.000 0.00 0.00 40.96 4.70
9485 11498 3.274288 CATAGAAGCAGGGTTGGAACTC 58.726 50.000 0.00 0.00 0.00 3.01
9506 11519 8.950007 AACTCCTCAAAAAGGGTATAATTTGA 57.050 30.769 0.00 0.00 46.23 2.69
9520 11533 8.871125 GGGTATAATTTGAAGACTAGGAGATGA 58.129 37.037 0.00 0.00 0.00 2.92
9536 11549 7.951347 AGGAGATGAAAAGAGCATACAAATT 57.049 32.000 0.00 0.00 0.00 1.82
9539 11552 8.246180 GGAGATGAAAAGAGCATACAAATTCAA 58.754 33.333 0.00 0.00 0.00 2.69
9548 11561 4.704540 AGCATACAAATTCAACGGGATCAA 59.295 37.500 0.00 0.00 0.00 2.57
9581 11594 4.373116 GAGGGTCTTCGCACGGCA 62.373 66.667 0.00 0.00 0.00 5.69
9631 11644 2.497273 GGGTGAACCAGCTAATGCATTT 59.503 45.455 18.75 0.00 42.74 2.32
9652 11665 2.711009 TGGACAGGAAAGAGTGGAACAT 59.289 45.455 0.00 0.00 44.52 2.71
9665 11678 6.815089 AGAGTGGAACATAGAGCTGATTAAG 58.185 40.000 0.00 0.00 44.52 1.85
9688 11701 2.927553 ATCTTCCATGCTTTTGACGC 57.072 45.000 0.00 0.00 0.00 5.19
9705 11718 3.063452 TGACGCGGAAGAAATTATCAAGC 59.937 43.478 12.47 0.00 0.00 4.01
9728 11741 1.202698 GCTATCCCTCAAGCGGATGTT 60.203 52.381 9.16 0.00 40.44 2.71
9761 11774 2.711711 ATGGCATCATGAACGGAGC 58.288 52.632 0.00 0.00 31.34 4.70
9791 11804 5.944049 TTTCAGTAAGAAGCGCGTATAAG 57.056 39.130 8.43 0.00 37.57 1.73
9803 11816 1.121240 CGTATAAGCTTGCCGAGTCG 58.879 55.000 9.86 5.29 0.00 4.18
9804 11817 0.853419 GTATAAGCTTGCCGAGTCGC 59.147 55.000 9.86 3.40 0.00 5.19
9885 11898 9.388506 GAAGTATATGGGATGTCATATGGAAAG 57.611 37.037 2.13 0.00 39.73 2.62
9891 11904 4.498009 GGGATGTCATATGGAAAGCAAACG 60.498 45.833 2.13 0.00 0.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 7.189693 TGACAGATGTGTTCTAACAAATGTC 57.810 36.000 3.23 11.63 43.24 3.06
48 49 1.972198 CCAGCGGTGAGGTAGTTCA 59.028 57.895 17.83 0.00 0.00 3.18
50 51 1.553690 ATGCCAGCGGTGAGGTAGTT 61.554 55.000 17.83 0.00 0.00 2.24
157 1219 7.731720 ACGTAATCGATAATTTTTCACGTCAA 58.268 30.769 0.00 0.00 35.40 3.18
173 1235 7.066163 TGTGTTCCTCTATTTAGACGTAATCGA 59.934 37.037 0.00 0.00 40.62 3.59
188 1250 3.638860 ACGGATGGTATGTGTTCCTCTA 58.361 45.455 0.00 0.00 0.00 2.43
200 1262 0.034863 GGCCCAAAGAACGGATGGTA 60.035 55.000 0.00 0.00 32.13 3.25
204 1266 2.045340 CGGGCCCAAAGAACGGAT 60.045 61.111 24.92 0.00 0.00 4.18
226 1288 7.011109 CCTCACGATTTCCTAATTTATTGTCGT 59.989 37.037 0.00 0.00 39.98 4.34
321 1395 2.233922 GGGAGAACGAATCCTTCACAGA 59.766 50.000 0.00 0.00 37.01 3.41
435 1524 2.202946 TGACACGTTTGGCAGCGA 60.203 55.556 17.87 0.00 34.98 4.93
453 1542 1.447314 GGGTCGCTCAAGTTACCGG 60.447 63.158 0.00 0.00 32.53 5.28
498 1587 3.795877 AGCGCCATTTTGAATTATTGGG 58.204 40.909 2.29 0.00 0.00 4.12
626 1721 1.481871 ACGTATGAACTGGATCCGGT 58.518 50.000 21.21 21.21 37.08 5.28
627 1722 2.607282 GCTACGTATGAACTGGATCCGG 60.607 54.545 19.66 19.66 0.00 5.14
628 1723 2.034179 TGCTACGTATGAACTGGATCCG 59.966 50.000 7.39 4.62 0.00 4.18
629 1724 3.381949 GTGCTACGTATGAACTGGATCC 58.618 50.000 4.20 4.20 0.00 3.36
630 1725 3.381949 GGTGCTACGTATGAACTGGATC 58.618 50.000 0.00 0.00 0.00 3.36
631 1726 2.223735 CGGTGCTACGTATGAACTGGAT 60.224 50.000 0.00 0.00 0.00 3.41
753 1852 3.039526 AGGGAGAGGGAGGGAGGG 61.040 72.222 0.00 0.00 0.00 4.30
754 1853 2.188215 AACAGGGAGAGGGAGGGAGG 62.188 65.000 0.00 0.00 0.00 4.30
755 1854 0.252927 AAACAGGGAGAGGGAGGGAG 60.253 60.000 0.00 0.00 0.00 4.30
756 1855 0.252742 GAAACAGGGAGAGGGAGGGA 60.253 60.000 0.00 0.00 0.00 4.20
757 1856 1.275421 GGAAACAGGGAGAGGGAGGG 61.275 65.000 0.00 0.00 0.00 4.30
758 1857 0.252927 AGGAAACAGGGAGAGGGAGG 60.253 60.000 0.00 0.00 0.00 4.30
759 1858 1.199615 GAGGAAACAGGGAGAGGGAG 58.800 60.000 0.00 0.00 0.00 4.30
760 1859 0.252742 GGAGGAAACAGGGAGAGGGA 60.253 60.000 0.00 0.00 0.00 4.20
761 1860 0.252927 AGGAGGAAACAGGGAGAGGG 60.253 60.000 0.00 0.00 0.00 4.30
762 1861 1.199615 GAGGAGGAAACAGGGAGAGG 58.800 60.000 0.00 0.00 0.00 3.69
763 1862 1.199615 GGAGGAGGAAACAGGGAGAG 58.800 60.000 0.00 0.00 0.00 3.20
764 1863 0.252742 GGGAGGAGGAAACAGGGAGA 60.253 60.000 0.00 0.00 0.00 3.71
765 1864 1.275421 GGGGAGGAGGAAACAGGGAG 61.275 65.000 0.00 0.00 0.00 4.30
766 1865 1.229853 GGGGAGGAGGAAACAGGGA 60.230 63.158 0.00 0.00 0.00 4.20
874 1995 2.947785 ACGGAGGGAGAGAGGGGT 60.948 66.667 0.00 0.00 0.00 4.95
875 1996 2.123640 GACGGAGGGAGAGAGGGG 60.124 72.222 0.00 0.00 0.00 4.79
1074 2198 1.409101 CCCGATAAAACCCACCCGATT 60.409 52.381 0.00 0.00 0.00 3.34
1391 2521 4.401519 TCTTAAGACCAGACTTACGGATGG 59.598 45.833 0.00 0.00 38.83 3.51
1429 2564 6.070251 TCCACATGTAGTTCACCTATCATGTT 60.070 38.462 0.00 0.00 41.36 2.71
1513 2648 1.202651 AGGTGTTCCTTGAAGGACACG 60.203 52.381 25.92 1.27 45.78 4.49
1583 2718 5.585844 CCCCCGAAAATAATACAGTACGTTT 59.414 40.000 0.00 0.00 0.00 3.60
1584 2719 5.118286 CCCCCGAAAATAATACAGTACGTT 58.882 41.667 0.00 0.00 0.00 3.99
1590 2725 3.551846 AGCACCCCCGAAAATAATACAG 58.448 45.455 0.00 0.00 0.00 2.74
1591 2726 3.655615 AGCACCCCCGAAAATAATACA 57.344 42.857 0.00 0.00 0.00 2.29
1592 2727 3.949113 TCAAGCACCCCCGAAAATAATAC 59.051 43.478 0.00 0.00 0.00 1.89
1593 2728 4.237976 TCAAGCACCCCCGAAAATAATA 57.762 40.909 0.00 0.00 0.00 0.98
1594 2729 3.094484 TCAAGCACCCCCGAAAATAAT 57.906 42.857 0.00 0.00 0.00 1.28
1606 2741 4.069304 TGGTGTACAGTAAATCAAGCACC 58.931 43.478 0.00 7.14 43.70 5.01
1608 2743 6.000840 TGAATGGTGTACAGTAAATCAAGCA 58.999 36.000 0.00 0.00 0.00 3.91
1609 2744 6.494893 TGAATGGTGTACAGTAAATCAAGC 57.505 37.500 0.00 0.00 0.00 4.01
1610 2745 9.912634 AATTTGAATGGTGTACAGTAAATCAAG 57.087 29.630 0.00 0.00 0.00 3.02
1645 2780 3.227614 ACACCCAAAAATCTACCCACAC 58.772 45.455 0.00 0.00 0.00 3.82
1647 2782 4.828387 TGTAACACCCAAAAATCTACCCAC 59.172 41.667 0.00 0.00 0.00 4.61
1648 2783 5.063017 TGTAACACCCAAAAATCTACCCA 57.937 39.130 0.00 0.00 0.00 4.51
1649 2784 5.712917 TCATGTAACACCCAAAAATCTACCC 59.287 40.000 0.00 0.00 0.00 3.69
1650 2785 6.625081 GCTCATGTAACACCCAAAAATCTACC 60.625 42.308 0.00 0.00 0.00 3.18
1651 2786 6.151144 AGCTCATGTAACACCCAAAAATCTAC 59.849 38.462 0.00 0.00 0.00 2.59
1653 2788 5.079643 AGCTCATGTAACACCCAAAAATCT 58.920 37.500 0.00 0.00 0.00 2.40
1655 2790 5.806654 AAGCTCATGTAACACCCAAAAAT 57.193 34.783 0.00 0.00 0.00 1.82
1656 2791 5.830991 ACTAAGCTCATGTAACACCCAAAAA 59.169 36.000 0.00 0.00 0.00 1.94
1657 2792 5.240623 CACTAAGCTCATGTAACACCCAAAA 59.759 40.000 0.00 0.00 0.00 2.44
1658 2793 4.759693 CACTAAGCTCATGTAACACCCAAA 59.240 41.667 0.00 0.00 0.00 3.28
1659 2794 4.323417 CACTAAGCTCATGTAACACCCAA 58.677 43.478 0.00 0.00 0.00 4.12
1660 2795 3.307410 CCACTAAGCTCATGTAACACCCA 60.307 47.826 0.00 0.00 0.00 4.51
1661 2796 3.270877 CCACTAAGCTCATGTAACACCC 58.729 50.000 0.00 0.00 0.00 4.61
1662 2797 3.684788 CACCACTAAGCTCATGTAACACC 59.315 47.826 0.00 0.00 0.00 4.16
1663 2798 4.152402 CACACCACTAAGCTCATGTAACAC 59.848 45.833 0.00 0.00 0.00 3.32
1687 2822 5.767816 ACAACCAGTGGATTCTACAAAAC 57.232 39.130 18.40 0.00 0.00 2.43
1688 2823 8.472007 AATAACAACCAGTGGATTCTACAAAA 57.528 30.769 18.40 0.00 0.00 2.44
1721 2856 8.195436 AGAGATAGCGCAAAATAAGTTACTGTA 58.805 33.333 11.47 0.00 0.00 2.74
1739 2874 5.665459 ACACACCAGAATTACAGAGATAGC 58.335 41.667 0.00 0.00 0.00 2.97
1791 2926 6.484818 TGGTTTATAAGTTCCAGCGTAAAC 57.515 37.500 0.00 0.00 33.53 2.01
1827 2962 3.792956 CCAGTTATTCGCATTGAACATGC 59.207 43.478 0.00 0.00 40.00 4.06
1830 2965 4.574892 TCTCCAGTTATTCGCATTGAACA 58.425 39.130 0.00 0.00 40.00 3.18
1832 2967 6.115446 AGAATCTCCAGTTATTCGCATTGAA 58.885 36.000 0.00 0.00 41.81 2.69
1873 3008 7.765307 TCCATCACAGCAATCTAAGAATTTTC 58.235 34.615 0.00 0.00 0.00 2.29
2078 3220 4.398673 AGAATCACTACAGGTAAGGACGTC 59.601 45.833 7.13 7.13 0.00 4.34
2212 3354 1.278127 CCTCTGCTAAAACGGGGAGAA 59.722 52.381 0.00 0.00 30.10 2.87
2413 3555 3.561143 ACCAGTATCTAGGAGCTCAGTG 58.439 50.000 17.19 6.69 0.00 3.66
2415 3557 3.826524 TGACCAGTATCTAGGAGCTCAG 58.173 50.000 17.19 5.30 0.00 3.35
2613 3755 1.688197 CACAACTTTCCTTGGTGGCAT 59.312 47.619 0.00 0.00 35.26 4.40
2631 3773 2.838736 AGATGACATTACCGGCATCAC 58.161 47.619 16.60 0.33 39.57 3.06
2663 3805 4.204799 TCTCGATCAGGTTCCGAAGATAA 58.795 43.478 0.00 0.00 31.59 1.75
2688 3830 4.588899 TGTAAGTTGATCATTGGTCAGGG 58.411 43.478 0.00 0.00 0.00 4.45
2971 4113 6.291377 GGGATTAGCAAGAGTATCAACATCA 58.709 40.000 0.00 0.00 37.82 3.07
3121 4263 6.231211 ACGACTAACAAGGATCTTGAATTGT 58.769 36.000 13.74 8.96 37.47 2.71
3339 4481 2.100916 GCAGTACGAGGAGGAATGCTAA 59.899 50.000 0.00 0.00 0.00 3.09
3344 4486 2.145397 TGAGCAGTACGAGGAGGAAT 57.855 50.000 0.00 0.00 0.00 3.01
3527 4669 4.908601 ATTCATTGATGATAGCCCGGTA 57.091 40.909 0.00 0.00 36.56 4.02
3641 4783 3.266513 TCCTGGTCAATGATGGTGAATGA 59.733 43.478 0.00 0.00 0.00 2.57
3684 4826 3.857549 TGCCTATCATATCGCTGAGAC 57.142 47.619 0.00 0.00 0.00 3.36
4286 5442 4.543689 ACCAGACGTATCCCTAGATCAAA 58.456 43.478 0.00 0.00 33.67 2.69
4317 5473 0.686769 TCTACTCCCTCCTTTCCGGC 60.687 60.000 0.00 0.00 0.00 6.13
4348 5504 5.753438 TCAACGCAGTCCTAATAATGATCAC 59.247 40.000 0.00 0.00 45.00 3.06
4545 5703 5.918608 AGCAACTCAGTACTTTCTTTCTCA 58.081 37.500 0.00 0.00 0.00 3.27
4911 6131 1.133790 CTGCCAGGAAAATGTAGCTGC 59.866 52.381 0.00 0.00 0.00 5.25
4929 6149 1.520494 ACTGCTCATCACAAGTGCTG 58.480 50.000 0.00 0.00 0.00 4.41
5412 6632 8.425577 AACAAGAATTAAGATGTATGACCTCG 57.574 34.615 0.00 0.00 0.00 4.63
5685 6905 7.454225 GTGCAGAGGAAGATATTATAACCCTT 58.546 38.462 0.00 0.00 0.00 3.95
5787 7007 0.178981 AGTCCCTGTGCAGCAAATGT 60.179 50.000 0.00 0.00 0.00 2.71
6053 7273 6.205464 GCTAAATAAGAATGTATGGCTGCAGA 59.795 38.462 20.43 0.00 0.00 4.26
6095 7315 7.439655 GGACCTTCAAGCATAGAAGTATGTTAG 59.560 40.741 10.57 0.00 40.62 2.34
6225 7445 8.519799 TGACTTCCAAAAATATTCCCTCATAC 57.480 34.615 0.00 0.00 0.00 2.39
6298 7518 8.091449 TCAGGAGAAGAATCAACTTAGAGAAAC 58.909 37.037 0.00 0.00 0.00 2.78
6307 7527 3.251484 TGGGTCAGGAGAAGAATCAACT 58.749 45.455 0.00 0.00 0.00 3.16
6613 7834 4.162320 TCCACTCCAATATTCAGGACAGAC 59.838 45.833 0.00 0.00 0.00 3.51
6830 8051 5.424895 TGGCAATAGGGTAAATTTCATTGCT 59.575 36.000 21.06 0.00 44.70 3.91
6983 8204 7.854557 TGTTGATGAGATGGAACTTATTCAG 57.145 36.000 0.00 0.00 36.46 3.02
8174 10116 5.184864 TGTTCTGGAAACACAAGAAACACAT 59.815 36.000 0.00 0.00 35.60 3.21
8311 10253 1.003580 ACAAGCGATGTCTTCACCCAT 59.996 47.619 0.00 0.00 37.96 4.00
8437 10379 0.319211 ACAAACGATCACGCCTCGAA 60.319 50.000 8.60 0.00 43.96 3.71
8521 10463 5.253330 TGGACTCAACCATATTTTCCAGTC 58.747 41.667 0.00 0.00 34.77 3.51
8783 10728 7.593273 TCATTTTTGACAGTTTTATTACCAGCG 59.407 33.333 0.00 0.00 0.00 5.18
8802 10747 5.048224 CCTGCACATTCTGAGAGTCATTTTT 60.048 40.000 0.00 0.00 0.00 1.94
8828 10773 2.224066 ACTATAGAAAGATGCGCGGCTT 60.224 45.455 8.83 5.75 0.00 4.35
8844 10789 7.125811 ACAGAAGCCTCAAACTTCCATACTATA 59.874 37.037 0.00 0.00 43.75 1.31
8850 10795 3.152341 CACAGAAGCCTCAAACTTCCAT 58.848 45.455 0.00 0.00 43.75 3.41
8853 10798 4.639135 AAACACAGAAGCCTCAAACTTC 57.361 40.909 0.00 0.00 43.16 3.01
8980 10925 7.155328 CCATCTTCTAGCAATTAACGGACTAT 58.845 38.462 0.00 0.00 0.00 2.12
8981 10926 6.097839 ACCATCTTCTAGCAATTAACGGACTA 59.902 38.462 0.00 0.00 0.00 2.59
8982 10927 5.104900 ACCATCTTCTAGCAATTAACGGACT 60.105 40.000 0.00 0.00 0.00 3.85
8983 10928 5.116882 ACCATCTTCTAGCAATTAACGGAC 58.883 41.667 0.00 0.00 0.00 4.79
9032 11019 9.823647 CCTAATAGAAACAGTCTCATGTACATT 57.176 33.333 5.37 0.00 37.84 2.71
9040 11027 7.770366 TGTACACCTAATAGAAACAGTCTCA 57.230 36.000 0.00 0.00 37.84 3.27
9045 11032 9.254133 CATCTCATGTACACCTAATAGAAACAG 57.746 37.037 0.00 0.00 0.00 3.16
9061 11048 4.129380 GCTAATGCACACCATCTCATGTA 58.871 43.478 0.00 0.00 39.41 2.29
9064 11051 2.158914 TCGCTAATGCACACCATCTCAT 60.159 45.455 0.00 0.00 39.64 2.90
9065 11052 1.206849 TCGCTAATGCACACCATCTCA 59.793 47.619 0.00 0.00 39.64 3.27
9066 11053 1.939974 TCGCTAATGCACACCATCTC 58.060 50.000 0.00 0.00 39.64 2.75
9067 11054 2.009774 GTTCGCTAATGCACACCATCT 58.990 47.619 0.00 0.00 39.64 2.90
9068 11055 1.064060 GGTTCGCTAATGCACACCATC 59.936 52.381 0.00 0.00 39.49 3.51
9073 11060 1.804151 GTTCTGGTTCGCTAATGCACA 59.196 47.619 0.00 0.00 39.64 4.57
9089 11076 9.264719 GAAACAATCTCAAATTGAAATGGTTCT 57.735 29.630 18.03 5.48 32.84 3.01
9104 11091 5.185635 CCTTGGCCAAATAGAAACAATCTCA 59.814 40.000 20.91 0.00 39.71 3.27
9105 11092 5.418840 TCCTTGGCCAAATAGAAACAATCTC 59.581 40.000 20.91 0.00 39.71 2.75
9106 11093 5.332743 TCCTTGGCCAAATAGAAACAATCT 58.667 37.500 20.91 0.00 42.48 2.40
9107 11094 5.659440 TCCTTGGCCAAATAGAAACAATC 57.341 39.130 20.91 0.00 0.00 2.67
9108 11095 5.543790 ACTTCCTTGGCCAAATAGAAACAAT 59.456 36.000 20.91 6.16 0.00 2.71
9109 11096 4.898861 ACTTCCTTGGCCAAATAGAAACAA 59.101 37.500 20.91 1.20 0.00 2.83
9110 11097 4.479158 ACTTCCTTGGCCAAATAGAAACA 58.521 39.130 20.91 1.54 0.00 2.83
9111 11098 4.082190 GGACTTCCTTGGCCAAATAGAAAC 60.082 45.833 20.91 16.46 0.00 2.78
9112 11099 4.086457 GGACTTCCTTGGCCAAATAGAAA 58.914 43.478 20.91 8.34 0.00 2.52
9113 11100 3.075283 TGGACTTCCTTGGCCAAATAGAA 59.925 43.478 20.91 19.71 36.82 2.10
9114 11101 2.647299 TGGACTTCCTTGGCCAAATAGA 59.353 45.455 20.91 13.67 36.82 1.98
9115 11102 2.755103 GTGGACTTCCTTGGCCAAATAG 59.245 50.000 20.91 17.82 36.82 1.73
9116 11103 2.802719 GTGGACTTCCTTGGCCAAATA 58.197 47.619 20.91 7.53 36.82 1.40
9117 11104 1.632589 GTGGACTTCCTTGGCCAAAT 58.367 50.000 20.91 2.47 36.82 2.32
9118 11105 0.821711 CGTGGACTTCCTTGGCCAAA 60.822 55.000 20.91 1.92 36.82 3.28
9119 11106 1.228124 CGTGGACTTCCTTGGCCAA 60.228 57.895 19.25 19.25 36.82 4.52
9120 11107 2.391724 GACGTGGACTTCCTTGGCCA 62.392 60.000 0.00 0.00 36.82 5.36
9172 11159 1.001406 GATAGGAGGAAGACGCCCATG 59.999 57.143 0.00 0.00 40.38 3.66
9190 11177 8.328758 TCATACTTATCACAGAAACCTTTGGAT 58.671 33.333 0.00 0.00 0.00 3.41
9199 11186 9.739276 ACCAATTTCTCATACTTATCACAGAAA 57.261 29.630 0.00 0.00 35.07 2.52
9208 11195 6.884472 TCCCTCACCAATTTCTCATACTTA 57.116 37.500 0.00 0.00 0.00 2.24
9221 11208 1.075374 CCACCAGAAATCCCTCACCAA 59.925 52.381 0.00 0.00 0.00 3.67
9226 11213 1.615262 CCCCCACCAGAAATCCCTC 59.385 63.158 0.00 0.00 0.00 4.30
9244 11231 3.604582 CTTCCTGTGACCTTCTTCATCC 58.395 50.000 0.00 0.00 0.00 3.51
9316 11303 3.181434 GGTGCATATCCCTGAACCCAATA 60.181 47.826 0.00 0.00 38.74 1.90
9418 11406 2.699954 CGGCAAAGACAGTACTTGGAT 58.300 47.619 0.00 0.00 0.00 3.41
9419 11407 1.876416 GCGGCAAAGACAGTACTTGGA 60.876 52.381 0.00 0.00 0.00 3.53
9421 11409 1.195448 CTGCGGCAAAGACAGTACTTG 59.805 52.381 3.44 0.00 0.00 3.16
9424 11412 0.790814 GTCTGCGGCAAAGACAGTAC 59.209 55.000 15.14 0.00 42.98 2.73
9425 11413 0.666274 CGTCTGCGGCAAAGACAGTA 60.666 55.000 18.65 0.00 43.53 2.74
9438 11451 1.675641 AAACTGGGGATGCGTCTGC 60.676 57.895 5.77 0.00 43.20 4.26
9440 11453 1.002134 CCAAACTGGGGATGCGTCT 60.002 57.895 5.77 0.00 32.67 4.18
9464 11477 3.274288 GAGTTCCAACCCTGCTTCTATG 58.726 50.000 0.00 0.00 0.00 2.23
9485 11498 9.025041 AGTCTTCAAATTATACCCTTTTTGAGG 57.975 33.333 0.00 0.00 45.86 3.86
9506 11519 6.558488 ATGCTCTTTTCATCTCCTAGTCTT 57.442 37.500 0.00 0.00 0.00 3.01
9520 11533 5.242838 TCCCGTTGAATTTGTATGCTCTTTT 59.757 36.000 0.00 0.00 0.00 2.27
9521 11534 4.764823 TCCCGTTGAATTTGTATGCTCTTT 59.235 37.500 0.00 0.00 0.00 2.52
9581 11594 2.685388 TCTCGAGCGTCTGATGAAAGAT 59.315 45.455 7.81 0.00 0.00 2.40
9631 11644 2.123589 TGTTCCACTCTTTCCTGTCCA 58.876 47.619 0.00 0.00 0.00 4.02
9665 11678 3.365820 CGTCAAAAGCATGGAAGATTTGC 59.634 43.478 0.00 0.00 36.63 3.68
9688 11701 3.629398 AGCCAGCTTGATAATTTCTTCCG 59.371 43.478 0.00 0.00 0.00 4.30
9705 11718 1.070445 CCGCTTGAGGGATAGCCAG 59.930 63.158 0.00 0.00 33.86 4.85
9728 11741 0.679505 GCCATGCTATCTGGTCCGTA 59.320 55.000 0.00 0.00 36.10 4.02
9755 11768 2.737376 GAAAACGCTCCGCTCCGT 60.737 61.111 0.00 0.00 39.70 4.69
9761 11774 2.159827 GCTTCTTACTGAAAACGCTCCG 60.160 50.000 0.00 0.00 33.79 4.63
9767 11780 2.943843 ACGCGCTTCTTACTGAAAAC 57.056 45.000 5.73 0.00 33.79 2.43
9825 11838 3.562635 CGAAGAACTCGTTGGGGC 58.437 61.111 0.00 0.00 42.89 5.80
9852 11865 1.624336 TCCCATATACTTCGGTCCCG 58.376 55.000 0.00 0.00 41.35 5.14
9863 11876 7.269522 TGCTTTCCATATGACATCCCATATA 57.730 36.000 3.65 0.00 37.57 0.86


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

AutoCloner maintained by Alex Coulton.