Multiple sequence alignment - TraesCS5D01G105700

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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 TraesCS5D01G105700 chr5D 100.000 3208 0 0 1 3208 119613358 119610151 0.000000e+00 5925.0
1 TraesCS5D01G105700 chr5D 100.000 431 0 0 3563 3993 119609796 119609366 0.000000e+00 797.0
2 TraesCS5D01G105700 chr5D 87.963 432 45 4 3564 3993 291899940 291900366 1.660000e-138 503.0
3 TraesCS5D01G105700 chr5A 92.221 2404 103 31 576 2964 129720811 129718477 0.000000e+00 3326.0
4 TraesCS5D01G105700 chr5A 91.608 429 34 2 3564 3991 129717758 129717331 3.440000e-165 592.0
5 TraesCS5D01G105700 chr5A 90.708 452 21 6 98 549 129722164 129721734 2.070000e-162 582.0
6 TraesCS5D01G105700 chr5A 86.806 432 55 2 3564 3993 384217795 384218226 7.760000e-132 481.0
7 TraesCS5D01G105700 chr5A 88.696 115 12 1 3094 3208 681226377 681226264 5.380000e-29 139.0
8 TraesCS5D01G105700 chr5A 85.714 98 6 2 647 744 66819078 66818989 3.280000e-16 97.1
9 TraesCS5D01G105700 chr5B 94.361 1472 71 9 1622 3089 132539334 132537871 0.000000e+00 2248.0
10 TraesCS5D01G105700 chr5B 92.095 1050 36 13 574 1619 132540400 132539394 0.000000e+00 1435.0
11 TraesCS5D01G105700 chr5B 88.889 432 44 4 3564 3993 332439391 332439820 2.730000e-146 529.0
12 TraesCS5D01G105700 chr7D 86.745 513 49 13 25 533 65640055 65640552 1.620000e-153 553.0
13 TraesCS5D01G105700 chr7D 87.037 432 54 2 3564 3993 629822189 629821758 1.670000e-133 486.0
14 TraesCS5D01G105700 chr7D 84.034 119 19 0 41 159 616554324 616554442 9.070000e-22 115.0
15 TraesCS5D01G105700 chr7D 100.000 30 0 0 717 746 7708870 7708899 5.570000e-04 56.5
16 TraesCS5D01G105700 chr4D 87.731 432 51 2 3564 3993 113150970 113150539 1.660000e-138 503.0
17 TraesCS5D01G105700 chr4D 84.615 403 35 18 165 549 427896898 427897291 3.770000e-100 375.0
18 TraesCS5D01G105700 chr4D 86.957 115 15 0 3094 3208 253773879 253773993 3.240000e-26 130.0
19 TraesCS5D01G105700 chr4D 87.611 113 13 1 3096 3208 500408585 500408474 3.240000e-26 130.0
20 TraesCS5D01G105700 chr4D 85.965 114 13 1 38 151 198602993 198603103 7.010000e-23 119.0
21 TraesCS5D01G105700 chr4D 85.366 123 5 6 48 169 427884679 427884789 9.070000e-22 115.0
22 TraesCS5D01G105700 chr2A 87.529 433 50 4 3564 3993 595019206 595018775 7.710000e-137 497.0
23 TraesCS5D01G105700 chr2D 87.500 432 49 5 3564 3993 95279510 95279938 9.970000e-136 494.0
24 TraesCS5D01G105700 chr2D 87.719 114 12 2 3095 3208 293684861 293684972 9.000000e-27 132.0
25 TraesCS5D01G105700 chr7B 87.383 428 51 3 3563 3988 525888027 525888453 4.640000e-134 488.0
26 TraesCS5D01G105700 chr1B 79.857 561 64 24 27 548 32995451 32996001 8.160000e-97 364.0
27 TraesCS5D01G105700 chr4A 86.986 146 8 2 25 170 539991946 539992080 1.920000e-33 154.0
28 TraesCS5D01G105700 chr4A 93.443 61 3 1 178 237 539992386 539992446 5.500000e-14 89.8
29 TraesCS5D01G105700 chr3D 89.720 107 11 0 3102 3208 185251599 185251493 1.940000e-28 137.0
30 TraesCS5D01G105700 chr2B 87.611 113 14 0 3096 3208 582813177 582813065 9.000000e-27 132.0
31 TraesCS5D01G105700 chr2B 85.417 96 6 2 647 742 188817863 188817776 4.250000e-15 93.5
32 TraesCS5D01G105700 chr6D 86.842 114 15 0 3095 3208 65107592 65107705 1.160000e-25 128.0
33 TraesCS5D01G105700 chr6D 88.462 52 6 0 618 669 55078171 55078120 3.330000e-06 63.9
34 TraesCS5D01G105700 chr6A 86.842 114 15 0 3095 3208 132356162 132356275 1.160000e-25 128.0
35 TraesCS5D01G105700 chr1D 86.842 114 15 0 3095 3208 52738518 52738631 1.160000e-25 128.0
36 TraesCS5D01G105700 chr3A 84.158 101 8 3 647 747 25404912 25405004 1.530000e-14 91.6
37 TraesCS5D01G105700 chr1A 84.694 98 7 2 647 744 21253615 21253704 1.530000e-14 91.6
38 TraesCS5D01G105700 chr1A 96.970 33 1 0 710 742 461049401 461049369 5.570000e-04 56.5
39 TraesCS5D01G105700 chr3B 94.737 38 1 1 707 743 644300337 644300300 1.550000e-04 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 TraesCS5D01G105700 chr5D 119609366 119613358 3992 True 3361.0 5925 100.000000 1 3993 2 chr5D.!!$R1 3992
1 TraesCS5D01G105700 chr5A 129717331 129722164 4833 True 1500.0 3326 91.512333 98 3991 3 chr5A.!!$R3 3893
2 TraesCS5D01G105700 chr5B 132537871 132540400 2529 True 1841.5 2248 93.228000 574 3089 2 chr5B.!!$R1 2515
3 TraesCS5D01G105700 chr1B 32995451 32996001 550 False 364.0 364 79.857000 27 548 1 chr1B.!!$F1 521

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
979 1921 0.175531 GTCTCTGCCTCTCTCTTGCC 59.824 60.0 0.00 0.00 0.00 4.52 F
1412 2357 0.107993 TCGCTCTTGAGCAAGGATGG 60.108 55.0 20.59 4.62 38.88 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2775 3793 0.035915 GACCAGAGGAAGCCAGGAAC 60.036 60.0 0.00 0.0 0.0 3.62 R
3179 4274 0.516877 CGACGCAAATGAGGCTCAAA 59.483 50.0 22.84 0.0 0.0 2.69 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
20 21 3.213206 TGCTTTGTGACATCCAACTCT 57.787 42.857 0.00 0.00 0.00 3.24
21 22 3.141398 TGCTTTGTGACATCCAACTCTC 58.859 45.455 0.00 0.00 0.00 3.20
22 23 3.181451 TGCTTTGTGACATCCAACTCTCT 60.181 43.478 0.00 0.00 0.00 3.10
23 24 4.040339 TGCTTTGTGACATCCAACTCTCTA 59.960 41.667 0.00 0.00 0.00 2.43
24 25 4.629200 GCTTTGTGACATCCAACTCTCTAG 59.371 45.833 0.00 0.00 0.00 2.43
25 26 3.876274 TGTGACATCCAACTCTCTAGC 57.124 47.619 0.00 0.00 0.00 3.42
26 27 3.165071 TGTGACATCCAACTCTCTAGCA 58.835 45.455 0.00 0.00 0.00 3.49
27 28 3.194329 TGTGACATCCAACTCTCTAGCAG 59.806 47.826 0.00 0.00 0.00 4.24
28 29 2.762887 TGACATCCAACTCTCTAGCAGG 59.237 50.000 0.00 0.00 0.00 4.85
29 30 2.102252 GACATCCAACTCTCTAGCAGGG 59.898 54.545 0.00 0.00 0.00 4.45
39 40 0.395862 TCTAGCAGGGAGAGTTCGGG 60.396 60.000 0.00 0.00 0.00 5.14
48 49 0.752376 GAGAGTTCGGGGAGATCGGT 60.752 60.000 0.00 0.00 0.00 4.69
49 50 0.324460 AGAGTTCGGGGAGATCGGTT 60.324 55.000 0.00 0.00 0.00 4.44
61 62 3.441011 ATCGGTTGGGATCCGTCGC 62.441 63.158 5.45 0.00 46.86 5.19
86 87 1.216710 CTCTGGTCTCGCCTCCAAC 59.783 63.158 0.00 0.00 38.35 3.77
87 88 2.232298 CTCTGGTCTCGCCTCCAACC 62.232 65.000 0.00 0.00 38.35 3.77
94 95 4.077184 CGCCTCCAACCGCCACTA 62.077 66.667 0.00 0.00 0.00 2.74
130 131 3.439540 AAATGACGCCGCCGCATT 61.440 55.556 3.34 3.34 40.36 3.56
157 158 3.515286 CCTCATGCCGCCTTGCTG 61.515 66.667 0.00 0.00 0.00 4.41
158 159 3.515286 CTCATGCCGCCTTGCTGG 61.515 66.667 0.00 0.00 39.35 4.85
224 236 1.383803 GGAGGGAGTGAGGGATGCT 60.384 63.158 0.00 0.00 0.00 3.79
226 238 0.689080 GAGGGAGTGAGGGATGCTGA 60.689 60.000 0.00 0.00 0.00 4.26
365 396 4.688879 GGTACCCAGCTTTTTATTGCAAAC 59.311 41.667 1.71 0.00 0.00 2.93
379 413 9.495754 TTTTATTGCAAACAAAAATGTGTTAGC 57.504 25.926 15.90 0.00 40.86 3.09
549 594 0.813184 ACGTAACGATGACGGACCAT 59.187 50.000 11.80 0.00 44.58 3.55
550 595 1.203052 ACGTAACGATGACGGACCATT 59.797 47.619 11.80 0.00 44.58 3.16
551 596 2.423185 ACGTAACGATGACGGACCATTA 59.577 45.455 11.80 0.00 44.58 1.90
555 600 5.116074 CGTAACGATGACGGACCATTATAAC 59.884 44.000 0.00 0.00 44.46 1.89
559 604 4.444388 CGATGACGGACCATTATAACACAG 59.556 45.833 0.00 0.00 35.72 3.66
560 605 4.131649 TGACGGACCATTATAACACAGG 57.868 45.455 0.00 0.00 0.00 4.00
561 606 2.870411 GACGGACCATTATAACACAGGC 59.130 50.000 0.00 0.00 0.00 4.85
562 607 2.237643 ACGGACCATTATAACACAGGCA 59.762 45.455 0.00 0.00 0.00 4.75
563 608 2.612212 CGGACCATTATAACACAGGCAC 59.388 50.000 0.00 0.00 0.00 5.01
565 610 4.013728 GGACCATTATAACACAGGCACAA 58.986 43.478 0.00 0.00 0.00 3.33
566 611 4.644685 GGACCATTATAACACAGGCACAAT 59.355 41.667 0.00 0.00 0.00 2.71
567 612 5.221048 GGACCATTATAACACAGGCACAATC 60.221 44.000 0.00 0.00 0.00 2.67
569 614 4.261155 CCATTATAACACAGGCACAATCGG 60.261 45.833 0.00 0.00 0.00 4.18
570 615 2.779755 ATAACACAGGCACAATCGGA 57.220 45.000 0.00 0.00 0.00 4.55
572 617 0.396435 AACACAGGCACAATCGGAGA 59.604 50.000 0.00 0.00 45.75 3.71
582 1523 4.438744 GGCACAATCGGAGACCTATTTTTG 60.439 45.833 0.00 0.00 42.51 2.44
703 1644 4.145052 GGATCAGAAATAATGGTGGGTCC 58.855 47.826 0.00 0.00 0.00 4.46
704 1645 4.141158 GGATCAGAAATAATGGTGGGTCCT 60.141 45.833 0.00 0.00 37.07 3.85
705 1646 4.946160 TCAGAAATAATGGTGGGTCCTT 57.054 40.909 0.00 0.00 37.07 3.36
706 1647 6.410388 GGATCAGAAATAATGGTGGGTCCTTA 60.410 42.308 0.00 0.00 37.07 2.69
707 1648 6.590656 TCAGAAATAATGGTGGGTCCTTAT 57.409 37.500 0.00 0.00 37.07 1.73
708 1649 6.980577 TCAGAAATAATGGTGGGTCCTTATT 58.019 36.000 0.00 0.00 34.34 1.40
709 1650 7.418378 TCAGAAATAATGGTGGGTCCTTATTT 58.582 34.615 5.80 5.80 39.38 1.40
710 1651 7.559897 TCAGAAATAATGGTGGGTCCTTATTTC 59.440 37.037 17.62 17.62 44.02 2.17
762 1703 5.049474 TGCCTTAATGTAATTGCTATGCTCG 60.049 40.000 0.00 0.00 36.99 5.03
810 1751 4.186077 TCCCACTCCGAGAGATAAGATT 57.814 45.455 1.33 0.00 33.32 2.40
812 1753 3.891977 CCCACTCCGAGAGATAAGATTGA 59.108 47.826 1.33 0.00 33.32 2.57
813 1754 4.526262 CCCACTCCGAGAGATAAGATTGAT 59.474 45.833 1.33 0.00 33.32 2.57
814 1755 5.468592 CCACTCCGAGAGATAAGATTGATG 58.531 45.833 1.33 0.00 33.32 3.07
815 1756 5.468592 CACTCCGAGAGATAAGATTGATGG 58.531 45.833 1.33 0.00 33.32 3.51
816 1757 4.526262 ACTCCGAGAGATAAGATTGATGGG 59.474 45.833 1.33 0.00 33.32 4.00
817 1758 3.259374 TCCGAGAGATAAGATTGATGGGC 59.741 47.826 0.00 0.00 0.00 5.36
818 1759 3.007290 CCGAGAGATAAGATTGATGGGCA 59.993 47.826 0.00 0.00 0.00 5.36
819 1760 3.993081 CGAGAGATAAGATTGATGGGCAC 59.007 47.826 0.00 0.00 0.00 5.01
820 1761 4.502087 CGAGAGATAAGATTGATGGGCACA 60.502 45.833 0.00 0.00 0.00 4.57
821 1762 5.371526 GAGAGATAAGATTGATGGGCACAA 58.628 41.667 0.00 0.00 0.00 3.33
822 1763 5.950023 AGAGATAAGATTGATGGGCACAAT 58.050 37.500 0.00 0.00 40.08 2.71
823 1764 5.768662 AGAGATAAGATTGATGGGCACAATG 59.231 40.000 0.00 0.00 37.96 2.82
846 1787 2.215942 ATTTCCCCACCTTTCTTCCG 57.784 50.000 0.00 0.00 0.00 4.30
969 1911 1.613630 ATGGAACCCGTCTCTGCCT 60.614 57.895 0.00 0.00 0.00 4.75
971 1913 1.985116 GGAACCCGTCTCTGCCTCT 60.985 63.158 0.00 0.00 0.00 3.69
973 1915 0.968393 GAACCCGTCTCTGCCTCTCT 60.968 60.000 0.00 0.00 0.00 3.10
974 1916 0.968393 AACCCGTCTCTGCCTCTCTC 60.968 60.000 0.00 0.00 0.00 3.20
979 1921 0.175531 GTCTCTGCCTCTCTCTTGCC 59.824 60.000 0.00 0.00 0.00 4.52
981 1923 0.176219 CTCTGCCTCTCTCTTGCCTG 59.824 60.000 0.00 0.00 0.00 4.85
1139 2081 9.097257 CCATTTCTACTTGAGAAGAGAAGAATC 57.903 37.037 0.00 0.00 45.05 2.52
1140 2082 8.806634 CATTTCTACTTGAGAAGAGAAGAATCG 58.193 37.037 0.00 0.00 45.05 3.34
1141 2083 5.885881 TCTACTTGAGAAGAGAAGAATCGC 58.114 41.667 0.00 0.00 0.00 4.58
1142 2084 3.855858 ACTTGAGAAGAGAAGAATCGCC 58.144 45.455 0.00 0.00 0.00 5.54
1230 2172 1.003839 ATGCCGTCATGTCCACGTT 60.004 52.632 4.92 0.00 35.39 3.99
1247 2189 0.605589 GTTCACTACCACCTGCCACC 60.606 60.000 0.00 0.00 0.00 4.61
1248 2190 2.047274 CACTACCACCTGCCACCG 60.047 66.667 0.00 0.00 0.00 4.94
1249 2191 4.016706 ACTACCACCTGCCACCGC 62.017 66.667 0.00 0.00 0.00 5.68
1331 2276 0.179089 CTGATTCCTCCCGTGCTCTG 60.179 60.000 0.00 0.00 0.00 3.35
1412 2357 0.107993 TCGCTCTTGAGCAAGGATGG 60.108 55.000 20.59 4.62 38.88 3.51
1501 2449 1.065418 GGAATTCAGAGGCGAAAGGGA 60.065 52.381 7.93 0.00 0.00 4.20
1552 2500 0.175760 TGGTGATTCTGCTACGGCTC 59.824 55.000 0.00 0.00 39.59 4.70
1555 2503 1.929836 GTGATTCTGCTACGGCTCAAG 59.070 52.381 0.00 0.00 39.59 3.02
1556 2504 1.550524 TGATTCTGCTACGGCTCAAGT 59.449 47.619 0.00 0.00 39.59 3.16
1579 2527 5.821516 TTCTTTCAGGAGACTCGAGATAC 57.178 43.478 21.68 8.03 40.21 2.24
1609 2557 3.055891 TCGTGCTGATGGATTCTCTCAAA 60.056 43.478 0.00 0.00 0.00 2.69
1619 2567 6.338214 TGGATTCTCTCAAATATCTCGGAG 57.662 41.667 0.00 0.00 0.00 4.63
1627 2632 3.697542 TCAAATATCTCGGAGGAACGACA 59.302 43.478 4.96 0.00 38.06 4.35
1673 2678 1.677576 CTTTGAGACAAGCAGTGCCAA 59.322 47.619 12.58 4.74 0.00 4.52
1812 2820 4.987285 CCATCTCTGTATTCCACTGATTCG 59.013 45.833 0.00 0.00 34.91 3.34
1837 2845 5.075858 TGAAATTCATGATTTGCCTGACC 57.924 39.130 0.00 0.00 38.06 4.02
1847 2855 1.407656 TTGCCTGACCTGGACGAACT 61.408 55.000 0.00 0.00 0.00 3.01
1861 2869 2.428890 GACGAACTGAGAGGGATGTCAT 59.571 50.000 0.00 0.00 0.00 3.06
1940 2948 3.831715 TCATCATAGTATCAGCGACGG 57.168 47.619 0.00 0.00 0.00 4.79
1942 2950 3.188667 TCATCATAGTATCAGCGACGGAC 59.811 47.826 0.00 0.00 0.00 4.79
1984 2992 4.521256 ACGATAGGAAGGAGTTATCAGCTC 59.479 45.833 0.00 0.00 43.77 4.09
2038 3046 1.412710 AGCACGAAACAAGAGACCAGA 59.587 47.619 0.00 0.00 0.00 3.86
2195 3203 6.371809 TCGTGAAAAGCAAGAAGTACAAAT 57.628 33.333 0.00 0.00 31.94 2.32
2389 3397 3.064931 GACAAACAGGAAGAGGTTACCG 58.935 50.000 0.00 0.00 0.00 4.02
2477 3491 2.235898 AGACACCAAGAAGAGAGGCATC 59.764 50.000 0.00 0.00 0.00 3.91
2481 3495 2.235898 ACCAAGAAGAGAGGCATCTGAC 59.764 50.000 5.17 0.00 35.30 3.51
2487 3501 1.625818 AGAGAGGCATCTGACGGTTTT 59.374 47.619 5.17 0.00 35.30 2.43
2539 3553 2.031120 CACAGGAGAGTCTGGGAGATC 58.969 57.143 0.00 0.00 40.45 2.75
2548 3562 2.435069 AGTCTGGGAGATCAAGCTGATG 59.565 50.000 0.00 0.00 37.20 3.07
2651 3668 1.623163 TTTCCCGGGTTCATGTTTCC 58.377 50.000 22.86 0.00 0.00 3.13
2681 3698 2.045926 GGGAGCGCATTGTGGAGT 60.046 61.111 11.47 0.00 0.00 3.85
2751 3768 1.337703 GTTGATGTGTTTGCTGGCTCA 59.662 47.619 0.00 0.00 0.00 4.26
2753 3770 1.202794 TGATGTGTTTGCTGGCTCAGA 60.203 47.619 6.40 0.00 32.44 3.27
2765 3783 5.945310 TGCTGGCTCAGAGGATTAAATAAT 58.055 37.500 0.00 0.00 32.44 1.28
2775 3793 7.446319 TCAGAGGATTAAATAATGGTGATGCTG 59.554 37.037 0.00 0.00 0.00 4.41
2779 3797 7.014615 AGGATTAAATAATGGTGATGCTGTTCC 59.985 37.037 0.00 0.00 0.00 3.62
2821 3839 1.002792 GTTTGTCAGGCTTCCGTGTTC 60.003 52.381 0.00 0.00 0.00 3.18
2828 3846 1.414919 AGGCTTCCGTGTTCTGTAACA 59.585 47.619 0.00 0.00 43.32 2.41
2900 3918 3.089573 AGCTGCAGTGCTTTTTCTTTC 57.910 42.857 17.60 0.00 40.93 2.62
2954 3972 8.836268 AGCAACAATTATTTTCATTGTGATGT 57.164 26.923 0.00 0.00 42.80 3.06
2956 3974 9.956797 GCAACAATTATTTTCATTGTGATGTAC 57.043 29.630 0.00 0.00 42.80 2.90
3017 4068 7.334858 TGTATGTGTGAATTGCTTGACCTATA 58.665 34.615 0.00 0.00 0.00 1.31
3018 4069 7.992608 TGTATGTGTGAATTGCTTGACCTATAT 59.007 33.333 0.00 0.00 0.00 0.86
3052 4103 4.996788 AACATATACTCCGTCCGTCTTT 57.003 40.909 0.00 0.00 0.00 2.52
3053 4104 4.564940 ACATATACTCCGTCCGTCTTTC 57.435 45.455 0.00 0.00 0.00 2.62
3061 4112 5.058490 ACTCCGTCCGTCTTTCAAAATAAA 58.942 37.500 0.00 0.00 0.00 1.40
3105 4200 4.091453 ACACTCAAAACGGACACAAAAG 57.909 40.909 0.00 0.00 0.00 2.27
3107 4202 4.022676 ACACTCAAAACGGACACAAAAGTT 60.023 37.500 0.00 0.00 0.00 2.66
3115 4210 1.416030 GGACACAAAAGTTGGCCCAAT 59.584 47.619 0.00 0.00 34.12 3.16
3116 4211 2.630580 GGACACAAAAGTTGGCCCAATA 59.369 45.455 0.00 0.00 34.12 1.90
3117 4212 3.070302 GGACACAAAAGTTGGCCCAATAA 59.930 43.478 0.00 0.00 34.12 1.40
3118 4213 4.306600 GACACAAAAGTTGGCCCAATAAG 58.693 43.478 0.00 0.00 34.12 1.73
3119 4214 3.066380 CACAAAAGTTGGCCCAATAAGC 58.934 45.455 0.00 0.00 34.12 3.09
3125 4220 4.081050 GGCCCAATAAGCCGATCC 57.919 61.111 0.00 0.00 41.41 3.36
3126 4221 1.150536 GGCCCAATAAGCCGATCCA 59.849 57.895 0.00 0.00 41.41 3.41
3127 4222 0.467290 GGCCCAATAAGCCGATCCAA 60.467 55.000 0.00 0.00 41.41 3.53
3128 4223 1.398692 GCCCAATAAGCCGATCCAAA 58.601 50.000 0.00 0.00 0.00 3.28
3129 4224 1.067060 GCCCAATAAGCCGATCCAAAC 59.933 52.381 0.00 0.00 0.00 2.93
3130 4225 1.333619 CCCAATAAGCCGATCCAAACG 59.666 52.381 0.00 0.00 0.00 3.60
3152 4247 2.935955 CGCGTCCGCTTTTTGTCT 59.064 55.556 10.21 0.00 39.32 3.41
3156 4251 1.285950 GTCCGCTTTTTGTCTGCCC 59.714 57.895 0.00 0.00 0.00 5.36
3162 4257 1.586154 CTTTTTGTCTGCCCGCCGAT 61.586 55.000 0.00 0.00 0.00 4.18
3163 4258 1.582610 TTTTTGTCTGCCCGCCGATC 61.583 55.000 0.00 0.00 0.00 3.69
3164 4259 3.969250 TTTGTCTGCCCGCCGATCC 62.969 63.158 0.00 0.00 0.00 3.36
3166 4261 4.241555 GTCTGCCCGCCGATCCAT 62.242 66.667 0.00 0.00 0.00 3.41
3167 4262 3.479203 TCTGCCCGCCGATCCATT 61.479 61.111 0.00 0.00 0.00 3.16
3168 4263 2.974698 CTGCCCGCCGATCCATTC 60.975 66.667 0.00 0.00 0.00 2.67
3169 4264 4.562425 TGCCCGCCGATCCATTCC 62.562 66.667 0.00 0.00 0.00 3.01
3171 4266 3.872603 CCCGCCGATCCATTCCCA 61.873 66.667 0.00 0.00 0.00 4.37
3172 4267 2.281070 CCGCCGATCCATTCCCAG 60.281 66.667 0.00 0.00 0.00 4.45
3173 4268 2.974698 CGCCGATCCATTCCCAGC 60.975 66.667 0.00 0.00 0.00 4.85
3174 4269 2.595754 GCCGATCCATTCCCAGCC 60.596 66.667 0.00 0.00 0.00 4.85
3175 4270 2.113986 CCGATCCATTCCCAGCCC 59.886 66.667 0.00 0.00 0.00 5.19
3176 4271 2.756042 CCGATCCATTCCCAGCCCA 61.756 63.158 0.00 0.00 0.00 5.36
3177 4272 1.227102 CGATCCATTCCCAGCCCAA 59.773 57.895 0.00 0.00 0.00 4.12
3178 4273 0.395586 CGATCCATTCCCAGCCCAAA 60.396 55.000 0.00 0.00 0.00 3.28
3179 4274 1.755265 CGATCCATTCCCAGCCCAAAT 60.755 52.381 0.00 0.00 0.00 2.32
3180 4275 2.401568 GATCCATTCCCAGCCCAAATT 58.598 47.619 0.00 0.00 0.00 1.82
3181 4276 2.340721 TCCATTCCCAGCCCAAATTT 57.659 45.000 0.00 0.00 0.00 1.82
3182 4277 1.907936 TCCATTCCCAGCCCAAATTTG 59.092 47.619 11.40 11.40 0.00 2.32
3183 4278 1.907936 CCATTCCCAGCCCAAATTTGA 59.092 47.619 19.86 0.00 0.00 2.69
3184 4279 2.093341 CCATTCCCAGCCCAAATTTGAG 60.093 50.000 19.86 7.62 0.00 3.02
3185 4280 0.975887 TTCCCAGCCCAAATTTGAGC 59.024 50.000 19.86 17.98 31.40 4.26
3186 4281 0.904394 TCCCAGCCCAAATTTGAGCC 60.904 55.000 19.72 7.63 31.63 4.70
3187 4282 0.906282 CCCAGCCCAAATTTGAGCCT 60.906 55.000 19.72 9.61 31.63 4.58
3188 4283 0.533951 CCAGCCCAAATTTGAGCCTC 59.466 55.000 19.72 4.48 31.63 4.70
3189 4284 1.259609 CAGCCCAAATTTGAGCCTCA 58.740 50.000 19.72 0.00 31.63 3.86
3190 4285 1.829222 CAGCCCAAATTTGAGCCTCAT 59.171 47.619 19.72 0.00 31.63 2.90
3191 4286 2.235402 CAGCCCAAATTTGAGCCTCATT 59.765 45.455 19.72 0.00 31.63 2.57
3192 4287 2.908351 AGCCCAAATTTGAGCCTCATTT 59.092 40.909 19.72 0.00 31.63 2.32
3193 4288 3.004862 GCCCAAATTTGAGCCTCATTTG 58.995 45.455 19.86 11.98 30.31 2.32
3194 4289 3.004862 CCCAAATTTGAGCCTCATTTGC 58.995 45.455 19.86 0.00 29.56 3.68
3195 4290 2.669434 CCAAATTTGAGCCTCATTTGCG 59.331 45.455 19.86 5.53 29.56 4.85
3196 4291 3.319755 CAAATTTGAGCCTCATTTGCGT 58.680 40.909 13.08 0.00 0.00 5.24
3197 4292 2.927553 ATTTGAGCCTCATTTGCGTC 57.072 45.000 0.00 0.00 0.00 5.19
3198 4293 0.516877 TTTGAGCCTCATTTGCGTCG 59.483 50.000 0.00 0.00 0.00 5.12
3199 4294 1.298157 TTGAGCCTCATTTGCGTCGG 61.298 55.000 0.00 0.00 0.00 4.79
3200 4295 3.100862 GAGCCTCATTTGCGTCGGC 62.101 63.158 0.00 0.00 40.99 5.54
3201 4296 4.520846 GCCTCATTTGCGTCGGCG 62.521 66.667 4.29 4.29 44.10 6.46
3584 4746 1.589196 GTCTGATACCGCCACGCTC 60.589 63.158 0.00 0.00 0.00 5.03
3657 4820 1.372997 GCCTGCTTCTTCGACGACA 60.373 57.895 0.00 0.00 0.00 4.35
3662 4825 2.049802 TTCTTCGACGACACCCGC 60.050 61.111 0.00 0.00 43.32 6.13
3671 4834 1.027792 ACGACACCCGCAAGTTGTTT 61.028 50.000 4.48 0.00 43.32 2.83
3676 4839 0.745128 ACCCGCAAGTTGTTTGACGA 60.745 50.000 4.48 0.00 39.21 4.20
3683 4846 2.793278 AGTTGTTTGACGATTTGCCC 57.207 45.000 0.00 0.00 0.00 5.36
3703 4866 1.737793 CGCAAGGTACAAATGGACTCC 59.262 52.381 0.00 0.00 0.00 3.85
3706 4869 0.108329 AGGTACAAATGGACTCCGCG 60.108 55.000 0.00 0.00 0.00 6.46
3716 4879 2.672307 ACTCCGCGGACGAGTTCT 60.672 61.111 27.28 1.26 43.93 3.01
3724 4887 1.070108 GCGGACGAGTTCTTTTTCCAC 60.070 52.381 0.00 0.00 0.00 4.02
3731 4894 6.198403 GGACGAGTTCTTTTTCCACAATTTTC 59.802 38.462 0.00 0.00 0.00 2.29
3780 4943 0.534652 GATGAGGAGATGGTGGCTGC 60.535 60.000 0.00 0.00 0.00 5.25
3787 4950 0.892358 AGATGGTGGCTGCTGTGTTG 60.892 55.000 0.00 0.00 0.00 3.33
3821 4984 1.222115 CCTTAGTAATCAGCGGCCGC 61.222 60.000 42.34 42.34 42.33 6.53
3864 5027 1.608025 GCACACTCCGGAGTTGAATCA 60.608 52.381 34.54 0.00 40.20 2.57
3917 5080 1.255667 GGACTACTTCGAGCCACCCA 61.256 60.000 0.00 0.00 0.00 4.51
3948 5111 0.525761 AAACATCACCAATTCCGGCG 59.474 50.000 0.00 0.00 0.00 6.46
3967 5130 2.180204 CCGTTTCCGCATGGCTAGG 61.180 63.158 0.00 0.00 34.14 3.02
3968 5131 1.449601 CGTTTCCGCATGGCTAGGT 60.450 57.895 0.00 0.00 34.14 3.08
3991 5154 6.198591 GGTATCTTTTCAACCGTATTCGAGAG 59.801 42.308 0.00 0.00 39.71 3.20
3992 5155 4.491676 TCTTTTCAACCGTATTCGAGAGG 58.508 43.478 0.00 0.00 39.71 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.141398 GAGAGTTGGATGTCACAAAGCA 58.859 45.455 0.00 0.00 0.00 3.91
2 3 4.629200 GCTAGAGAGTTGGATGTCACAAAG 59.371 45.833 0.00 0.00 0.00 2.77
3 4 4.040339 TGCTAGAGAGTTGGATGTCACAAA 59.960 41.667 0.00 0.00 0.00 2.83
4 5 3.578282 TGCTAGAGAGTTGGATGTCACAA 59.422 43.478 0.00 0.00 0.00 3.33
5 6 3.165071 TGCTAGAGAGTTGGATGTCACA 58.835 45.455 0.00 0.00 0.00 3.58
6 7 3.430098 CCTGCTAGAGAGTTGGATGTCAC 60.430 52.174 0.00 0.00 0.00 3.67
7 8 2.762887 CCTGCTAGAGAGTTGGATGTCA 59.237 50.000 0.00 0.00 0.00 3.58
8 9 2.102252 CCCTGCTAGAGAGTTGGATGTC 59.898 54.545 0.00 0.00 0.00 3.06
9 10 2.114616 CCCTGCTAGAGAGTTGGATGT 58.885 52.381 0.00 0.00 0.00 3.06
10 11 2.364970 CTCCCTGCTAGAGAGTTGGATG 59.635 54.545 0.00 0.00 32.86 3.51
11 12 2.246067 TCTCCCTGCTAGAGAGTTGGAT 59.754 50.000 0.00 0.00 35.46 3.41
12 13 1.641192 TCTCCCTGCTAGAGAGTTGGA 59.359 52.381 0.00 0.00 35.46 3.53
13 14 2.151502 TCTCCCTGCTAGAGAGTTGG 57.848 55.000 0.00 0.00 35.46 3.77
18 19 1.408961 CCGAACTCTCCCTGCTAGAGA 60.409 57.143 7.09 6.80 42.63 3.10
19 20 1.028905 CCGAACTCTCCCTGCTAGAG 58.971 60.000 0.00 0.00 44.99 2.43
20 21 0.395862 CCCGAACTCTCCCTGCTAGA 60.396 60.000 0.00 0.00 0.00 2.43
21 22 1.395826 CCCCGAACTCTCCCTGCTAG 61.396 65.000 0.00 0.00 0.00 3.42
22 23 1.381327 CCCCGAACTCTCCCTGCTA 60.381 63.158 0.00 0.00 0.00 3.49
23 24 2.685380 CCCCGAACTCTCCCTGCT 60.685 66.667 0.00 0.00 0.00 4.24
24 25 2.683933 TCCCCGAACTCTCCCTGC 60.684 66.667 0.00 0.00 0.00 4.85
25 26 0.397816 ATCTCCCCGAACTCTCCCTG 60.398 60.000 0.00 0.00 0.00 4.45
26 27 0.105913 GATCTCCCCGAACTCTCCCT 60.106 60.000 0.00 0.00 0.00 4.20
27 28 1.457009 CGATCTCCCCGAACTCTCCC 61.457 65.000 0.00 0.00 0.00 4.30
28 29 1.457009 CCGATCTCCCCGAACTCTCC 61.457 65.000 0.00 0.00 0.00 3.71
29 30 0.752376 ACCGATCTCCCCGAACTCTC 60.752 60.000 0.00 0.00 0.00 3.20
36 37 2.100879 GATCCCAACCGATCTCCCCG 62.101 65.000 0.00 0.00 36.51 5.73
65 66 4.200283 GAGGCGAGACCAGAGGCG 62.200 72.222 0.00 0.00 43.14 5.52
87 88 1.069378 GAAGACGACCGTTAGTGGCG 61.069 60.000 0.00 0.00 35.56 5.69
91 92 1.811359 CAGAGGAAGACGACCGTTAGT 59.189 52.381 0.00 0.00 0.00 2.24
93 94 0.524862 GCAGAGGAAGACGACCGTTA 59.475 55.000 0.00 0.00 0.00 3.18
94 95 1.289380 GCAGAGGAAGACGACCGTT 59.711 57.895 0.00 0.00 0.00 4.44
157 158 4.814294 CTGTCCTACACGGCGGCC 62.814 72.222 13.24 9.54 0.00 6.13
158 159 4.065281 ACTGTCCTACACGGCGGC 62.065 66.667 13.24 0.00 34.19 6.53
159 160 2.126071 CACTGTCCTACACGGCGG 60.126 66.667 13.24 2.35 34.19 6.13
160 161 1.154016 CTCACTGTCCTACACGGCG 60.154 63.158 4.80 4.80 34.19 6.46
161 162 0.171455 CTCTCACTGTCCTACACGGC 59.829 60.000 0.00 0.00 34.19 5.68
224 236 3.570540 CCCACTCTCTCCATAGTCATCA 58.429 50.000 0.00 0.00 0.00 3.07
226 238 2.427002 CCCCCACTCTCTCCATAGTCAT 60.427 54.545 0.00 0.00 0.00 3.06
365 396 7.538303 AAAAAGTGAGGCTAACACATTTTTG 57.462 32.000 13.32 0.00 42.33 2.44
509 554 4.208666 CGTCAGTGCTTATGTGAGATGATG 59.791 45.833 0.00 0.00 0.00 3.07
549 594 4.081365 TCTCCGATTGTGCCTGTGTTATAA 60.081 41.667 0.00 0.00 0.00 0.98
550 595 3.449377 TCTCCGATTGTGCCTGTGTTATA 59.551 43.478 0.00 0.00 0.00 0.98
551 596 2.236146 TCTCCGATTGTGCCTGTGTTAT 59.764 45.455 0.00 0.00 0.00 1.89
555 600 1.021390 GGTCTCCGATTGTGCCTGTG 61.021 60.000 0.00 0.00 0.00 3.66
559 604 2.622064 AATAGGTCTCCGATTGTGCC 57.378 50.000 0.00 0.00 28.10 5.01
560 605 4.156008 ACAAAAATAGGTCTCCGATTGTGC 59.844 41.667 0.00 0.00 29.66 4.57
561 606 5.880054 ACAAAAATAGGTCTCCGATTGTG 57.120 39.130 0.00 0.00 29.66 3.33
562 607 7.989416 TTTACAAAAATAGGTCTCCGATTGT 57.011 32.000 0.00 0.00 29.66 2.71
563 608 8.512138 AGTTTTACAAAAATAGGTCTCCGATTG 58.488 33.333 0.00 0.00 29.66 2.67
565 610 8.512138 CAAGTTTTACAAAAATAGGTCTCCGAT 58.488 33.333 0.00 0.00 0.00 4.18
566 611 7.520937 GCAAGTTTTACAAAAATAGGTCTCCGA 60.521 37.037 0.00 0.00 0.00 4.55
567 612 6.581166 GCAAGTTTTACAAAAATAGGTCTCCG 59.419 38.462 0.00 0.00 0.00 4.63
569 614 7.430441 TGGCAAGTTTTACAAAAATAGGTCTC 58.570 34.615 0.00 0.00 0.00 3.36
570 615 7.354751 TGGCAAGTTTTACAAAAATAGGTCT 57.645 32.000 0.00 0.00 0.00 3.85
572 617 8.972458 ATTTGGCAAGTTTTACAAAAATAGGT 57.028 26.923 0.00 0.00 36.53 3.08
582 1523 8.442384 CCAACATTCATATTTGGCAAGTTTTAC 58.558 33.333 0.00 0.00 33.72 2.01
703 1644 8.996651 ATGGTCCCAACTATTAAGGAAATAAG 57.003 34.615 0.00 0.00 29.59 1.73
704 1645 8.787818 AGATGGTCCCAACTATTAAGGAAATAA 58.212 33.333 0.00 0.00 29.59 1.40
705 1646 8.344939 AGATGGTCCCAACTATTAAGGAAATA 57.655 34.615 0.00 0.00 0.00 1.40
706 1647 7.226059 AGATGGTCCCAACTATTAAGGAAAT 57.774 36.000 0.00 0.00 0.00 2.17
707 1648 6.652205 AGATGGTCCCAACTATTAAGGAAA 57.348 37.500 0.00 0.00 0.00 3.13
708 1649 6.652205 AAGATGGTCCCAACTATTAAGGAA 57.348 37.500 0.00 0.00 0.00 3.36
709 1650 7.758820 TTAAGATGGTCCCAACTATTAAGGA 57.241 36.000 0.00 0.00 0.00 3.36
710 1651 8.817092 TTTTAAGATGGTCCCAACTATTAAGG 57.183 34.615 0.00 0.00 0.00 2.69
762 1703 2.034687 ACTGTCATGCTGGCCACC 59.965 61.111 0.00 0.00 0.00 4.61
810 1751 3.055963 GGAAATTGACATTGTGCCCATCA 60.056 43.478 0.00 0.00 0.00 3.07
812 1753 2.236893 GGGAAATTGACATTGTGCCCAT 59.763 45.455 0.00 0.00 32.76 4.00
813 1754 1.622811 GGGAAATTGACATTGTGCCCA 59.377 47.619 0.00 0.00 32.76 5.36
814 1755 1.066215 GGGGAAATTGACATTGTGCCC 60.066 52.381 1.68 1.68 32.16 5.36
815 1756 1.622811 TGGGGAAATTGACATTGTGCC 59.377 47.619 0.00 0.00 0.00 5.01
816 1757 2.612721 GGTGGGGAAATTGACATTGTGC 60.613 50.000 0.00 0.00 0.00 4.57
817 1758 2.899256 AGGTGGGGAAATTGACATTGTG 59.101 45.455 0.00 0.00 0.00 3.33
818 1759 3.258722 AGGTGGGGAAATTGACATTGT 57.741 42.857 0.00 0.00 0.00 2.71
819 1760 4.284234 AGAAAGGTGGGGAAATTGACATTG 59.716 41.667 0.00 0.00 0.00 2.82
820 1761 4.492646 AGAAAGGTGGGGAAATTGACATT 58.507 39.130 0.00 0.00 0.00 2.71
821 1762 4.132122 AGAAAGGTGGGGAAATTGACAT 57.868 40.909 0.00 0.00 0.00 3.06
822 1763 3.611025 AGAAAGGTGGGGAAATTGACA 57.389 42.857 0.00 0.00 0.00 3.58
823 1764 3.258372 GGAAGAAAGGTGGGGAAATTGAC 59.742 47.826 0.00 0.00 0.00 3.18
846 1787 4.032703 AGTGTGTTCACAAAGATTGCAC 57.967 40.909 7.22 0.00 46.01 4.57
969 1911 0.837691 TCAAGCCCAGGCAAGAGAGA 60.838 55.000 12.03 0.00 44.88 3.10
971 1913 0.478072 TTTCAAGCCCAGGCAAGAGA 59.522 50.000 12.03 0.54 44.88 3.10
973 1915 1.039856 GTTTTCAAGCCCAGGCAAGA 58.960 50.000 12.03 5.20 44.88 3.02
974 1916 1.043022 AGTTTTCAAGCCCAGGCAAG 58.957 50.000 12.03 2.61 44.88 4.01
979 1921 2.546584 GCCAAGAAGTTTTCAAGCCCAG 60.547 50.000 0.00 0.00 0.00 4.45
981 1923 1.602920 CGCCAAGAAGTTTTCAAGCCC 60.603 52.381 0.00 0.00 0.00 5.19
1141 2083 2.110967 CCATGTCAGCCGCAAGAGG 61.111 63.158 0.00 0.00 43.02 3.69
1142 2084 2.758089 GCCATGTCAGCCGCAAGAG 61.758 63.158 0.00 0.00 43.02 2.85
1218 2160 1.964933 TGGTAGTGAACGTGGACATGA 59.035 47.619 0.00 0.00 0.00 3.07
1230 2172 2.579657 CGGTGGCAGGTGGTAGTGA 61.580 63.158 0.00 0.00 0.00 3.41
1338 2283 1.300388 CACCACAAAGGCAAGCAGC 60.300 57.895 0.00 0.00 43.14 5.25
1412 2357 2.540515 TCTTGACGGATTCGAGATTGC 58.459 47.619 0.00 0.00 39.55 3.56
1473 2421 1.283321 GCCTCTGAATTCCCCTCTTGT 59.717 52.381 2.27 0.00 0.00 3.16
1501 2449 2.338015 CCGCATGCCTCACAGCTTT 61.338 57.895 13.15 0.00 0.00 3.51
1552 2500 4.621991 TCGAGTCTCCTGAAAGAAACTTG 58.378 43.478 0.00 0.00 34.07 3.16
1555 2503 4.506886 TCTCGAGTCTCCTGAAAGAAAC 57.493 45.455 13.13 0.00 34.07 2.78
1556 2504 5.710567 TGTATCTCGAGTCTCCTGAAAGAAA 59.289 40.000 13.13 0.00 34.07 2.52
1579 2527 1.081892 CCATCAGCACGAACCTCTTG 58.918 55.000 0.00 0.00 0.00 3.02
1609 2557 3.021695 TGTTGTCGTTCCTCCGAGATAT 58.978 45.455 0.00 0.00 37.56 1.63
1619 2567 1.004292 CGACCAGTTTGTTGTCGTTCC 60.004 52.381 0.00 0.00 44.96 3.62
1627 2632 3.804036 TCACATCTTCGACCAGTTTGTT 58.196 40.909 0.00 0.00 0.00 2.83
1673 2678 4.276642 GGAAAATTCCTCTGAATCAGCCT 58.723 43.478 5.18 0.00 44.11 4.58
1727 2735 3.791973 TGTGTTCATCCACAAACCAAC 57.208 42.857 0.00 0.00 42.13 3.77
1812 2820 3.869246 CAGGCAAATCATGAATTTCAGCC 59.131 43.478 13.08 13.08 42.60 4.85
1837 2845 1.135915 CATCCCTCTCAGTTCGTCCAG 59.864 57.143 0.00 0.00 0.00 3.86
1847 2855 1.063642 AGTCCGATGACATCCCTCTCA 60.064 52.381 9.87 0.00 44.33 3.27
1916 2924 5.393962 CGTCGCTGATACTATGATGATGAA 58.606 41.667 0.00 0.00 0.00 2.57
1940 2948 5.580691 TCGTCACAATATTCTTCACCATGTC 59.419 40.000 0.00 0.00 0.00 3.06
1942 2950 6.609237 ATCGTCACAATATTCTTCACCATG 57.391 37.500 0.00 0.00 0.00 3.66
2389 3397 1.849976 GCCTCTGCTGTGCTGTGTTC 61.850 60.000 0.00 0.00 33.53 3.18
2477 3491 3.057019 TCGTCATTCTCAAAACCGTCAG 58.943 45.455 0.00 0.00 0.00 3.51
2481 3495 2.055838 TCGTCGTCATTCTCAAAACCG 58.944 47.619 0.00 0.00 0.00 4.44
2487 3501 0.601057 TGGCTTCGTCGTCATTCTCA 59.399 50.000 0.00 0.00 0.00 3.27
2539 3553 6.779117 AGTCATCGTTAATTTCATCAGCTTG 58.221 36.000 0.00 0.00 0.00 4.01
2548 3562 4.026475 CGAGGCAGAGTCATCGTTAATTTC 60.026 45.833 0.00 0.00 35.79 2.17
2651 3668 0.447801 CGCTCCCTTCAAATCCAACG 59.552 55.000 0.00 0.00 0.00 4.10
2681 3698 1.194781 GGACCTCCTGAGAAGTGGCA 61.195 60.000 0.00 0.00 0.00 4.92
2751 3768 7.293073 ACAGCATCACCATTATTTAATCCTCT 58.707 34.615 0.00 0.00 0.00 3.69
2753 3770 7.014615 GGAACAGCATCACCATTATTTAATCCT 59.985 37.037 0.00 0.00 0.00 3.24
2765 3783 1.303561 GCCAGGAACAGCATCACCA 60.304 57.895 0.00 0.00 0.00 4.17
2775 3793 0.035915 GACCAGAGGAAGCCAGGAAC 60.036 60.000 0.00 0.00 0.00 3.62
2779 3797 1.197430 AGTGGACCAGAGGAAGCCAG 61.197 60.000 0.00 0.00 0.00 4.85
2821 3839 9.398170 CAAGGAAAACACTTTATGATGTTACAG 57.602 33.333 0.00 0.00 38.08 2.74
2828 3846 7.687941 ATCGACAAGGAAAACACTTTATGAT 57.312 32.000 0.00 0.00 0.00 2.45
2897 3915 8.746052 TCCTAGTTTCAGACATTTCTTTGAAA 57.254 30.769 0.00 0.00 37.25 2.69
2954 3972 6.039159 TGACAATTCACAATGCAAAGACAGTA 59.961 34.615 0.00 0.00 0.00 2.74
2956 3974 5.283294 TGACAATTCACAATGCAAAGACAG 58.717 37.500 0.00 0.00 0.00 3.51
2961 4012 5.692654 CAGTCATGACAATTCACAATGCAAA 59.307 36.000 27.02 0.00 33.38 3.68
3018 4069 9.275398 ACGGAGTATATGTTTGTTTTAAGTGAA 57.725 29.630 0.00 0.00 41.94 3.18
3073 4124 5.468746 TCCGTTTTGAGTGTCCTTGATTTAG 59.531 40.000 0.00 0.00 0.00 1.85
3074 4125 5.237779 GTCCGTTTTGAGTGTCCTTGATTTA 59.762 40.000 0.00 0.00 0.00 1.40
3075 4126 4.036380 GTCCGTTTTGAGTGTCCTTGATTT 59.964 41.667 0.00 0.00 0.00 2.17
3076 4127 3.564225 GTCCGTTTTGAGTGTCCTTGATT 59.436 43.478 0.00 0.00 0.00 2.57
3078 4129 2.093394 TGTCCGTTTTGAGTGTCCTTGA 60.093 45.455 0.00 0.00 0.00 3.02
3079 4130 2.031683 GTGTCCGTTTTGAGTGTCCTTG 59.968 50.000 0.00 0.00 0.00 3.61
3080 4131 2.285977 GTGTCCGTTTTGAGTGTCCTT 58.714 47.619 0.00 0.00 0.00 3.36
3082 4133 1.658994 TGTGTCCGTTTTGAGTGTCC 58.341 50.000 0.00 0.00 0.00 4.02
3083 4134 3.750639 TTTGTGTCCGTTTTGAGTGTC 57.249 42.857 0.00 0.00 0.00 3.67
3084 4135 3.504520 ACTTTTGTGTCCGTTTTGAGTGT 59.495 39.130 0.00 0.00 0.00 3.55
3085 4136 4.091453 ACTTTTGTGTCCGTTTTGAGTG 57.909 40.909 0.00 0.00 0.00 3.51
3086 4137 4.481463 CAACTTTTGTGTCCGTTTTGAGT 58.519 39.130 0.00 0.00 0.00 3.41
3087 4138 3.857093 CCAACTTTTGTGTCCGTTTTGAG 59.143 43.478 0.00 0.00 0.00 3.02
3151 4246 2.974698 GAATGGATCGGCGGGCAG 60.975 66.667 7.21 0.00 0.00 4.85
3152 4247 4.562425 GGAATGGATCGGCGGGCA 62.562 66.667 7.21 0.00 0.00 5.36
3156 4251 2.974698 GCTGGGAATGGATCGGCG 60.975 66.667 0.00 0.00 0.00 6.46
3162 4257 1.907936 CAAATTTGGGCTGGGAATGGA 59.092 47.619 10.49 0.00 0.00 3.41
3163 4258 1.907936 TCAAATTTGGGCTGGGAATGG 59.092 47.619 17.90 0.00 0.00 3.16
3164 4259 3.255969 CTCAAATTTGGGCTGGGAATG 57.744 47.619 17.90 0.00 0.00 2.67
3173 4268 3.004862 GCAAATGAGGCTCAAATTTGGG 58.995 45.455 30.22 16.04 40.20 4.12
3174 4269 2.669434 CGCAAATGAGGCTCAAATTTGG 59.331 45.455 30.22 21.44 40.20 3.28
3175 4270 3.319755 ACGCAAATGAGGCTCAAATTTG 58.680 40.909 27.49 27.49 41.88 2.32
3176 4271 3.578688 GACGCAAATGAGGCTCAAATTT 58.421 40.909 22.84 15.38 0.00 1.82
3177 4272 2.414559 CGACGCAAATGAGGCTCAAATT 60.415 45.455 22.84 16.39 0.00 1.82
3178 4273 1.131126 CGACGCAAATGAGGCTCAAAT 59.869 47.619 22.84 10.89 0.00 2.32
3179 4274 0.516877 CGACGCAAATGAGGCTCAAA 59.483 50.000 22.84 0.00 0.00 2.69
3180 4275 1.298157 CCGACGCAAATGAGGCTCAA 61.298 55.000 22.84 5.13 0.00 3.02
3181 4276 1.741401 CCGACGCAAATGAGGCTCA 60.741 57.895 21.19 21.19 0.00 4.26
3182 4277 3.093278 CCGACGCAAATGAGGCTC 58.907 61.111 7.79 7.79 0.00 4.70
3183 4278 3.127533 GCCGACGCAAATGAGGCT 61.128 61.111 0.00 0.00 44.06 4.58
3184 4279 4.520846 CGCCGACGCAAATGAGGC 62.521 66.667 0.00 0.00 44.00 4.70
3562 4657 1.807886 GTGGCGGTATCAGACGAGT 59.192 57.895 0.00 0.00 0.00 4.18
3563 4658 1.298413 CGTGGCGGTATCAGACGAG 60.298 63.158 0.00 0.00 31.71 4.18
3564 4659 2.795973 CGTGGCGGTATCAGACGA 59.204 61.111 0.00 0.00 31.71 4.20
3565 4660 2.954868 GCGTGGCGGTATCAGACG 60.955 66.667 0.00 0.00 0.00 4.18
3566 4661 1.589196 GAGCGTGGCGGTATCAGAC 60.589 63.158 0.00 0.00 37.83 3.51
3567 4662 2.805546 GAGCGTGGCGGTATCAGA 59.194 61.111 0.00 0.00 37.83 3.27
3568 4663 2.655364 CGAGCGTGGCGGTATCAG 60.655 66.667 0.00 0.00 37.83 2.90
3569 4664 4.865761 GCGAGCGTGGCGGTATCA 62.866 66.667 0.00 0.00 37.83 2.15
3635 4798 1.664965 GTCGAAGAAGCAGGCACGT 60.665 57.895 0.00 0.00 39.69 4.49
3638 4801 1.372997 GTCGTCGAAGAAGCAGGCA 60.373 57.895 1.62 0.00 39.69 4.75
3657 4820 0.745128 TCGTCAAACAACTTGCGGGT 60.745 50.000 0.00 0.00 36.12 5.28
3662 4825 2.794350 GGGCAAATCGTCAAACAACTTG 59.206 45.455 0.00 0.00 36.25 3.16
3671 4834 2.331893 CCTTGCGGGCAAATCGTCA 61.332 57.895 7.57 0.00 35.33 4.35
3676 4839 1.333177 TTTGTACCTTGCGGGCAAAT 58.667 45.000 7.57 1.71 35.69 2.32
3683 4846 1.737793 GGAGTCCATTTGTACCTTGCG 59.262 52.381 3.60 0.00 0.00 4.85
3703 4866 0.163146 GGAAAAAGAACTCGTCCGCG 59.837 55.000 0.00 0.00 39.92 6.46
3706 4869 4.830826 ATTGTGGAAAAAGAACTCGTCC 57.169 40.909 0.00 0.00 0.00 4.79
3716 4879 5.872070 AGTCGCAAAGAAAATTGTGGAAAAA 59.128 32.000 1.30 0.00 40.38 1.94
3724 4887 3.536158 TCCGAGTCGCAAAGAAAATTG 57.464 42.857 7.12 0.00 0.00 2.32
3731 4894 2.544685 AGAATCATCCGAGTCGCAAAG 58.455 47.619 7.12 0.00 41.15 2.77
3757 4920 1.945387 CCACCATCTCCTCATCGTTG 58.055 55.000 0.00 0.00 0.00 4.10
3758 4921 0.179000 GCCACCATCTCCTCATCGTT 59.821 55.000 0.00 0.00 0.00 3.85
3821 4984 1.144936 GGATCGAGCCCCAGAACAG 59.855 63.158 9.02 0.00 0.00 3.16
3864 5027 2.032681 GGCCGCTCTCTTGGTTGT 59.967 61.111 0.00 0.00 0.00 3.32
3870 5033 0.329596 AAGGAAATGGCCGCTCTCTT 59.670 50.000 0.00 0.00 0.00 2.85
3911 5074 2.359975 GAAGAGCGGGTTGGGTGG 60.360 66.667 0.00 0.00 0.00 4.61
3917 5080 1.880027 GTGATGTTTGAAGAGCGGGTT 59.120 47.619 0.00 0.00 0.00 4.11
3951 5114 2.143925 GATACCTAGCCATGCGGAAAC 58.856 52.381 0.00 0.00 0.00 2.78
3967 5130 6.198591 CCTCTCGAATACGGTTGAAAAGATAC 59.801 42.308 0.00 0.00 40.21 2.24
3968 5131 6.270815 CCTCTCGAATACGGTTGAAAAGATA 58.729 40.000 0.00 0.00 40.21 1.98


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

AutoCloner maintained by Alex Coulton.