Multiple sequence alignment - TraesCS5D01G506100

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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 TraesCS5D01G506100 chr5D 100.000 3045 0 0 1 3045 531973012 531969968 0.000000e+00 5624.0
1 TraesCS5D01G506100 chr5D 86.892 473 45 6 1300 1758 531901306 531900837 5.820000e-142 514.0
2 TraesCS5D01G506100 chr5D 80.916 131 14 9 2809 2938 353519774 353519894 3.230000e-15 93.5
3 TraesCS5D01G506100 chr5D 76.023 171 34 4 2202 2370 112344545 112344380 7.000000e-12 82.4
4 TraesCS5D01G506100 chr4A 91.436 1226 62 20 707 1919 640232029 640233224 0.000000e+00 1642.0
5 TraesCS5D01G506100 chr4A 76.538 520 72 41 2515 3010 675963663 675963170 3.920000e-59 239.0
6 TraesCS5D01G506100 chr5B 94.225 1039 42 7 755 1785 671188690 671187662 0.000000e+00 1570.0
7 TraesCS5D01G506100 chr5B 87.358 704 49 15 21 702 671189671 671188986 0.000000e+00 771.0
8 TraesCS5D01G506100 chr5B 85.099 557 60 12 1952 2503 671187569 671187031 5.740000e-152 547.0
9 TraesCS5D01G506100 chr5B 86.598 97 6 3 1826 1917 671187663 671187569 1.930000e-17 100.0
10 TraesCS5D01G506100 chr6B 86.251 1091 93 32 826 1898 415864618 415863567 0.000000e+00 1131.0
11 TraesCS5D01G506100 chr6B 92.547 483 33 2 1299 1781 415789552 415789073 0.000000e+00 689.0
12 TraesCS5D01G506100 chr6B 90.511 137 13 0 1098 1234 415789910 415789774 6.710000e-42 182.0
13 TraesCS5D01G506100 chr6B 92.473 93 2 2 738 829 415864744 415864656 8.860000e-26 128.0
14 TraesCS5D01G506100 chr6D 87.526 978 81 20 890 1850 267515604 267514651 0.000000e+00 1092.0
15 TraesCS5D01G506100 chr6D 92.798 486 32 2 1296 1781 267237317 267236835 0.000000e+00 701.0
16 TraesCS5D01G506100 chr6D 76.574 397 60 25 2637 3026 452847497 452847127 1.440000e-43 187.0
17 TraesCS5D01G506100 chr6D 90.511 137 13 0 1098 1234 267237713 267237577 6.710000e-42 182.0
18 TraesCS5D01G506100 chr6A 86.647 996 82 27 890 1856 381026551 381025578 0.000000e+00 1055.0
19 TraesCS5D01G506100 chr6A 92.857 476 31 2 1306 1781 380361707 380361235 0.000000e+00 688.0
20 TraesCS5D01G506100 chr6A 89.781 137 14 0 1098 1234 380362111 380361975 3.120000e-40 176.0
21 TraesCS5D01G506100 chr6A 76.071 397 62 25 2637 3026 598795689 598795319 3.120000e-40 176.0
22 TraesCS5D01G506100 chr7D 80.049 411 60 17 2637 3034 589506106 589505705 4.970000e-73 285.0
23 TraesCS5D01G506100 chr7D 76.705 176 34 7 2 173 564064042 564063870 1.160000e-14 91.6
24 TraesCS5D01G506100 chr1D 79.851 402 46 16 2634 3030 285612583 285612954 8.370000e-66 261.0
25 TraesCS5D01G506100 chr1D 75.862 551 86 29 2490 3028 427482419 427482934 1.410000e-58 237.0
26 TraesCS5D01G506100 chr7A 77.143 420 66 17 2637 3045 681026559 681026959 1.840000e-52 217.0
27 TraesCS5D01G506100 chr7A 83.544 79 7 5 2860 2936 89070907 89070833 5.450000e-08 69.4
28 TraesCS5D01G506100 chr7A 91.304 46 4 0 2325 2370 7381357 7381312 2.530000e-06 63.9
29 TraesCS5D01G506100 chr5A 75.862 435 76 19 1947 2373 115247316 115246903 8.610000e-46 195.0
30 TraesCS5D01G506100 chr1A 80.162 247 32 14 2788 3028 522556478 522556713 5.220000e-38 169.0
31 TraesCS5D01G506100 chr2D 97.222 36 1 0 138 173 524453956 524453921 9.120000e-06 62.1
32 TraesCS5D01G506100 chr3D 100.000 29 0 0 2901 2929 511530301 511530273 2.000000e-03 54.7
33 TraesCS5D01G506100 chr3A 85.455 55 4 4 2879 2931 696710031 696709979 2.000000e-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 TraesCS5D01G506100 chr5D 531969968 531973012 3044 True 5624.0 5624 100.0000 1 3045 1 chr5D.!!$R3 3044
1 TraesCS5D01G506100 chr4A 640232029 640233224 1195 False 1642.0 1642 91.4360 707 1919 1 chr4A.!!$F1 1212
2 TraesCS5D01G506100 chr5B 671187031 671189671 2640 True 747.0 1570 88.3200 21 2503 4 chr5B.!!$R1 2482
3 TraesCS5D01G506100 chr6B 415863567 415864744 1177 True 629.5 1131 89.3620 738 1898 2 chr6B.!!$R2 1160
4 TraesCS5D01G506100 chr6B 415789073 415789910 837 True 435.5 689 91.5290 1098 1781 2 chr6B.!!$R1 683
5 TraesCS5D01G506100 chr6D 267514651 267515604 953 True 1092.0 1092 87.5260 890 1850 1 chr6D.!!$R1 960
6 TraesCS5D01G506100 chr6D 267236835 267237713 878 True 441.5 701 91.6545 1098 1781 2 chr6D.!!$R3 683
7 TraesCS5D01G506100 chr6A 381025578 381026551 973 True 1055.0 1055 86.6470 890 1856 1 chr6A.!!$R1 966
8 TraesCS5D01G506100 chr6A 380361235 380362111 876 True 432.0 688 91.3190 1098 1781 2 chr6A.!!$R3 683
9 TraesCS5D01G506100 chr1D 427482419 427482934 515 False 237.0 237 75.8620 2490 3028 1 chr1D.!!$F2 538

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
990 1339 0.107361 CCAAACCCATCCGTACTCCC 60.107 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2208 2839 0.250513 AACTCTTCGATGGGTGCTCC 59.749 55.0 4.35 0.0 0.0 4.7 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
19 20 4.704833 CCGGGCGCCCCATATCAG 62.705 72.222 39.24 22.87 45.83 2.90
24 25 2.047844 CGCCCCATATCAGCCTCG 60.048 66.667 0.00 0.00 0.00 4.63
31 32 2.430465 CCATATCAGCCTCGGATTTGG 58.570 52.381 0.00 0.00 37.47 3.28
40 41 1.543429 CCTCGGATTTGGGCTGGATAC 60.543 57.143 0.00 0.00 0.00 2.24
45 46 0.474184 ATTTGGGCTGGATACGAGGG 59.526 55.000 0.00 0.00 42.51 4.30
46 47 0.912487 TTTGGGCTGGATACGAGGGT 60.912 55.000 0.00 0.00 42.51 4.34
53 54 1.227176 GGATACGAGGGTTGCGGTC 60.227 63.158 0.00 0.00 0.00 4.79
55 56 2.948840 GATACGAGGGTTGCGGTCGG 62.949 65.000 0.00 0.00 38.03 4.79
81 82 2.619646 GGTGTTTGAAGCCCGTTTAAGA 59.380 45.455 0.00 0.00 0.00 2.10
96 97 0.611618 TAAGACGCCTGTCCGGGTTA 60.612 55.000 0.00 0.00 46.74 2.85
104 105 3.322369 GCCTGTCCGGGTTAAATTTTTG 58.678 45.455 0.00 0.00 0.00 2.44
105 106 3.243941 GCCTGTCCGGGTTAAATTTTTGT 60.244 43.478 0.00 0.00 0.00 2.83
114 115 3.976306 GGTTAAATTTTTGTGACCGGTCG 59.024 43.478 28.70 0.00 0.00 4.79
119 120 1.155424 TTTTGTGACCGGTCGCTGAC 61.155 55.000 39.46 27.39 40.54 3.51
120 121 2.023414 TTTGTGACCGGTCGCTGACT 62.023 55.000 39.46 2.77 40.54 3.41
121 122 2.126424 GTGACCGGTCGCTGACTC 60.126 66.667 35.30 9.75 37.16 3.36
123 124 4.477975 GACCGGTCGCTGACTCGG 62.478 72.222 20.85 23.01 45.11 4.63
156 157 3.471354 GTATGAGACGGGTTTGGGG 57.529 57.895 0.00 0.00 0.00 4.96
212 216 3.318557 TGGGACGTACAAAATTTGAACCC 59.681 43.478 13.19 15.18 34.80 4.11
216 220 3.700038 ACGTACAAAATTTGAACCCCACA 59.300 39.130 13.19 0.00 0.00 4.17
255 275 2.699954 TGCCGACTCTCATTTTCCTTC 58.300 47.619 0.00 0.00 0.00 3.46
375 399 0.547712 AGCTTCTGCCCTCACCCTAA 60.548 55.000 0.00 0.00 40.80 2.69
380 404 1.992557 TCTGCCCTCACCCTAATTGTT 59.007 47.619 0.00 0.00 0.00 2.83
385 409 3.621558 CCCTCACCCTAATTGTTTCCTC 58.378 50.000 0.00 0.00 0.00 3.71
409 433 5.163764 CGTGAGCCAAGTCAAGCAAATAATA 60.164 40.000 0.00 0.00 0.00 0.98
541 565 0.752658 AGCTTTTTGGTTGCACTCCC 59.247 50.000 4.88 0.00 0.00 4.30
568 592 6.726035 CAATTTTGCAACAGCATTTTCTTG 57.274 33.333 0.00 0.00 38.23 3.02
574 598 5.042593 TGCAACAGCATTTTCTTGTACTTG 58.957 37.500 0.00 0.00 32.31 3.16
576 600 5.735922 GCAACAGCATTTTCTTGTACTTGGA 60.736 40.000 0.00 0.00 0.00 3.53
579 603 4.082125 AGCATTTTCTTGTACTTGGAGGG 58.918 43.478 0.00 0.00 0.00 4.30
581 605 4.706962 GCATTTTCTTGTACTTGGAGGGAT 59.293 41.667 0.00 0.00 0.00 3.85
584 608 7.093945 GCATTTTCTTGTACTTGGAGGGATAAA 60.094 37.037 0.00 0.00 0.00 1.40
593 617 5.793817 ACTTGGAGGGATAAAATTTGCAAC 58.206 37.500 0.00 0.00 0.00 4.17
607 631 0.533978 TGCAACAGCTGTTTAGGCGA 60.534 50.000 29.23 16.23 35.83 5.54
608 632 0.591170 GCAACAGCTGTTTAGGCGAA 59.409 50.000 29.23 0.00 35.83 4.70
609 633 1.663161 GCAACAGCTGTTTAGGCGAAC 60.663 52.381 29.23 7.90 35.83 3.95
610 634 1.601903 CAACAGCTGTTTAGGCGAACA 59.398 47.619 29.23 8.74 35.83 3.18
611 635 1.226746 ACAGCTGTTTAGGCGAACAC 58.773 50.000 15.25 4.23 35.76 3.32
612 636 0.517316 CAGCTGTTTAGGCGAACACC 59.483 55.000 5.25 0.91 35.76 4.16
613 637 0.396811 AGCTGTTTAGGCGAACACCT 59.603 50.000 5.55 2.95 44.31 4.00
614 638 1.202770 AGCTGTTTAGGCGAACACCTT 60.203 47.619 5.55 0.00 41.50 3.50
615 639 1.069227 GCTGTTTAGGCGAACACCTTG 60.069 52.381 5.55 0.00 41.50 3.61
616 640 0.948678 TGTTTAGGCGAACACCTTGC 59.051 50.000 5.55 0.00 41.50 4.01
617 641 0.948678 GTTTAGGCGAACACCTTGCA 59.051 50.000 0.00 0.00 41.50 4.08
623 647 1.539827 GGCGAACACCTTGCAACTAAT 59.460 47.619 0.00 0.00 0.00 1.73
625 649 2.979813 GCGAACACCTTGCAACTAATTG 59.020 45.455 0.00 0.00 38.99 2.32
641 665 8.741101 CAACTAATTGCAGCTGTAAATAAACA 57.259 30.769 21.35 1.60 0.00 2.83
651 675 8.168626 GCAGCTGTAAATAAACAAAAATAAGGC 58.831 33.333 16.64 0.00 0.00 4.35
652 676 9.423061 CAGCTGTAAATAAACAAAAATAAGGCT 57.577 29.630 5.25 0.00 0.00 4.58
660 684 9.705290 AATAAACAAAAATAAGGCTTGACGAAT 57.295 25.926 10.69 0.00 0.00 3.34
667 691 1.154225 GGCTTGACGAATGGTTGCG 60.154 57.895 0.00 0.00 0.00 4.85
680 704 1.154413 GTTGCGCCATGTGAACTCG 60.154 57.895 4.18 0.00 0.00 4.18
702 726 0.249489 CGAAATGCCCTCCCTCGTAG 60.249 60.000 0.00 0.00 0.00 3.51
703 727 0.831307 GAAATGCCCTCCCTCGTAGT 59.169 55.000 0.00 0.00 0.00 2.73
704 728 0.831307 AAATGCCCTCCCTCGTAGTC 59.169 55.000 0.00 0.00 0.00 2.59
705 729 1.392710 AATGCCCTCCCTCGTAGTCG 61.393 60.000 0.00 0.00 38.55 4.18
706 730 3.217743 GCCCTCCCTCGTAGTCGG 61.218 72.222 0.00 0.00 37.69 4.79
707 731 3.217743 CCCTCCCTCGTAGTCGGC 61.218 72.222 0.00 0.00 37.69 5.54
708 732 2.124236 CCTCCCTCGTAGTCGGCT 60.124 66.667 0.00 0.00 37.69 5.52
709 733 2.188161 CCTCCCTCGTAGTCGGCTC 61.188 68.421 0.00 0.00 37.69 4.70
710 734 2.513204 TCCCTCGTAGTCGGCTCG 60.513 66.667 0.00 0.00 37.69 5.03
711 735 2.513204 CCCTCGTAGTCGGCTCGA 60.513 66.667 0.00 1.52 37.69 4.04
712 736 1.892862 CCCTCGTAGTCGGCTCGAT 60.893 63.158 11.02 0.00 38.42 3.59
726 750 2.095718 GGCTCGATGTCTTGTTTGGAAC 60.096 50.000 0.00 0.00 0.00 3.62
949 1298 0.733150 TCATCGTCAACGCTCTCGAT 59.267 50.000 0.00 0.00 42.44 3.59
950 1299 1.116436 CATCGTCAACGCTCTCGATC 58.884 55.000 0.00 0.00 40.29 3.69
951 1300 0.316278 ATCGTCAACGCTCTCGATCG 60.316 55.000 9.36 9.36 38.38 3.69
952 1301 1.060465 CGTCAACGCTCTCGATCGA 59.940 57.895 18.32 18.32 39.41 3.59
953 1302 0.921662 CGTCAACGCTCTCGATCGAG 60.922 60.000 34.20 34.20 43.21 4.04
990 1339 0.107361 CCAAACCCATCCGTACTCCC 60.107 60.000 0.00 0.00 0.00 4.30
1176 1543 1.192146 TGGCGTACCTCTCCAAGCTT 61.192 55.000 0.00 0.00 36.63 3.74
1196 1563 1.595993 CCTGTGACCCTCGACGTCAT 61.596 60.000 17.16 0.00 41.99 3.06
1304 1909 6.055231 TCTTTAACACTGACGACCAAATTG 57.945 37.500 0.00 0.00 0.00 2.32
1312 1917 3.996363 CTGACGACCAAATTGACTGATCA 59.004 43.478 0.00 0.00 0.00 2.92
1328 1933 3.033909 TGATCATCGACCAGTTCTCCAT 58.966 45.455 0.00 0.00 0.00 3.41
1349 1954 2.571757 GGCGAGGACGTGATCACA 59.428 61.111 24.93 0.00 41.98 3.58
1364 1969 3.626924 ACAGTGACGTGGGCCCTC 61.627 66.667 25.70 19.74 0.00 4.30
1484 2089 0.032952 CCCACGACGACCTCAAGAAA 59.967 55.000 0.00 0.00 0.00 2.52
1786 2391 4.330074 GCGCAAGAAGAATAACTAAGCTCA 59.670 41.667 0.30 0.00 43.02 4.26
1833 2447 0.667792 GTGCGCGACTTCTTCCTCTT 60.668 55.000 12.10 0.00 0.00 2.85
1856 2471 1.532090 CCTTTGCAACGTACGCACAAA 60.532 47.619 21.87 21.87 39.59 2.83
1919 2545 1.066430 GGGGAGCTCACGTGATTGTTA 60.066 52.381 20.40 0.00 0.00 2.41
1920 2546 2.000447 GGGAGCTCACGTGATTGTTAC 59.000 52.381 20.40 7.03 0.00 2.50
1921 2547 2.611971 GGGAGCTCACGTGATTGTTACA 60.612 50.000 20.40 0.00 0.00 2.41
1922 2548 2.412089 GGAGCTCACGTGATTGTTACAC 59.588 50.000 20.40 5.10 35.26 2.90
1923 2549 3.057019 GAGCTCACGTGATTGTTACACA 58.943 45.455 20.40 0.00 38.04 3.72
1924 2550 3.664107 AGCTCACGTGATTGTTACACAT 58.336 40.909 20.40 0.00 38.04 3.21
1925 2551 4.065088 AGCTCACGTGATTGTTACACATT 58.935 39.130 20.40 0.00 38.04 2.71
1926 2552 5.234752 AGCTCACGTGATTGTTACACATTA 58.765 37.500 20.40 0.00 38.04 1.90
1927 2553 5.120208 AGCTCACGTGATTGTTACACATTAC 59.880 40.000 20.40 0.00 38.04 1.89
1928 2554 5.670341 GCTCACGTGATTGTTACACATTACC 60.670 44.000 20.40 0.00 38.04 2.85
1929 2555 5.543714 TCACGTGATTGTTACACATTACCT 58.456 37.500 15.76 0.00 38.04 3.08
1930 2556 6.689554 TCACGTGATTGTTACACATTACCTA 58.310 36.000 15.76 0.00 38.04 3.08
1931 2557 7.324935 TCACGTGATTGTTACACATTACCTAT 58.675 34.615 15.76 0.00 38.04 2.57
1932 2558 8.468399 TCACGTGATTGTTACACATTACCTATA 58.532 33.333 15.76 0.00 38.04 1.31
1933 2559 9.256477 CACGTGATTGTTACACATTACCTATAT 57.744 33.333 10.90 0.00 38.04 0.86
1934 2560 9.256477 ACGTGATTGTTACACATTACCTATATG 57.744 33.333 0.00 0.00 38.04 1.78
1935 2561 9.256477 CGTGATTGTTACACATTACCTATATGT 57.744 33.333 0.00 0.00 38.04 2.29
1944 2570 8.988546 ACACATTACCTATATGTAAATGCCAA 57.011 30.769 4.93 0.00 34.59 4.52
1945 2571 9.415008 ACACATTACCTATATGTAAATGCCAAA 57.585 29.630 4.93 0.00 34.59 3.28
1946 2572 9.897744 CACATTACCTATATGTAAATGCCAAAG 57.102 33.333 4.93 0.00 34.59 2.77
1947 2573 9.640952 ACATTACCTATATGTAAATGCCAAAGT 57.359 29.630 4.93 0.00 34.59 2.66
1961 2587 0.593128 CAAAGTTTGGGACTGCTCCG 59.407 55.000 7.78 0.00 39.00 4.63
1967 2593 2.050836 TTGGGACTGCTCCGCTTCAA 62.051 55.000 0.00 0.00 37.46 2.69
1968 2594 1.302511 GGGACTGCTCCGCTTCAAA 60.303 57.895 0.00 0.00 37.46 2.69
2011 2641 1.202758 ACGTTGGAGCAGTTTCATCCA 60.203 47.619 0.00 0.00 41.33 3.41
2022 2652 3.567164 CAGTTTCATCCAAGAGTTGCAGT 59.433 43.478 0.00 0.00 0.00 4.40
2027 2657 2.957402 TCCAAGAGTTGCAGTTCCAT 57.043 45.000 0.00 0.00 0.00 3.41
2028 2658 4.019411 TCATCCAAGAGTTGCAGTTCCATA 60.019 41.667 0.00 0.00 0.00 2.74
2032 2662 5.241506 TCCAAGAGTTGCAGTTCCATAAAAG 59.758 40.000 0.00 0.00 0.00 2.27
2043 2673 8.313292 TGCAGTTCCATAAAAGAGCAATTTATT 58.687 29.630 0.00 0.00 32.15 1.40
2044 2674 8.598075 GCAGTTCCATAAAAGAGCAATTTATTG 58.402 33.333 0.00 0.00 40.66 1.90
2055 2685 6.991938 AGAGCAATTTATTGTGTTTGGCTTA 58.008 32.000 4.54 0.00 39.88 3.09
2059 2689 7.171337 AGCAATTTATTGTGTTTGGCTTACAAG 59.829 33.333 4.54 0.00 38.98 3.16
2117 2747 9.420118 TGTGAAATATTTATTTGGCTAGGTGAT 57.580 29.630 0.00 0.00 36.13 3.06
2174 2804 7.164230 GTGACATTATTGGGTAATTTCACCA 57.836 36.000 12.61 0.00 45.82 4.17
2175 2805 7.033185 GTGACATTATTGGGTAATTTCACCAC 58.967 38.462 12.61 0.00 45.82 4.16
2181 2811 4.171878 TGGGTAATTTCACCACAACTCA 57.828 40.909 0.00 0.00 40.65 3.41
2182 2812 4.735369 TGGGTAATTTCACCACAACTCAT 58.265 39.130 0.00 0.00 40.65 2.90
2207 2838 6.594159 TGAGAACTCTTCAAACTCGAGTTTTT 59.406 34.615 34.94 26.14 45.07 1.94
2208 2839 6.776094 AGAACTCTTCAAACTCGAGTTTTTG 58.224 36.000 34.94 26.88 45.07 2.44
2211 2842 5.294552 ACTCTTCAAACTCGAGTTTTTGGAG 59.705 40.000 33.51 33.51 45.07 3.86
2214 2845 3.064820 TCAAACTCGAGTTTTTGGAGCAC 59.935 43.478 34.94 0.00 45.07 4.40
2219 2850 1.200020 CGAGTTTTTGGAGCACCCATC 59.800 52.381 0.00 0.00 46.10 3.51
2244 2875 6.442513 AAGAGTTTCACCAAAGACAAGAAG 57.557 37.500 0.00 0.00 0.00 2.85
2304 2935 5.970023 AGACATCGTACAGCTATAACGTTTC 59.030 40.000 5.91 8.63 37.83 2.78
2306 2937 5.742453 ACATCGTACAGCTATAACGTTTCAG 59.258 40.000 5.91 5.24 37.83 3.02
2309 2940 5.570206 TCGTACAGCTATAACGTTTCAGTTG 59.430 40.000 5.91 14.17 37.83 3.16
2310 2941 4.663636 ACAGCTATAACGTTTCAGTTGC 57.336 40.909 18.90 11.10 35.70 4.17
2319 2950 9.910511 CTATAACGTTTCAGTTGCGTATTTTAT 57.089 29.630 5.91 0.00 37.92 1.40
2327 2958 5.234329 TCAGTTGCGTATTTTATAGCAGAGC 59.766 40.000 0.00 0.00 40.90 4.09
2343 2974 2.611292 CAGAGCTGAATTTTAGGGAGCG 59.389 50.000 0.00 0.00 34.75 5.03
2369 3000 3.885297 CAGTCCCAAATATGGCCTAAGTG 59.115 47.826 3.32 0.00 46.09 3.16
2372 3003 3.270960 TCCCAAATATGGCCTAAGTGGTT 59.729 43.478 3.32 0.00 46.09 3.67
2374 3005 5.044030 TCCCAAATATGGCCTAAGTGGTTTA 60.044 40.000 3.32 0.00 46.09 2.01
2382 3013 6.487299 TGGCCTAAGTGGTTTAAAAATTGT 57.513 33.333 3.32 0.00 38.35 2.71
2429 3060 7.385752 TGACCAATGATTTTTGCTTTGAGATTC 59.614 33.333 0.00 0.00 0.00 2.52
2431 3062 6.366877 CCAATGATTTTTGCTTTGAGATTCGT 59.633 34.615 0.00 0.00 0.00 3.85
2433 3064 4.681025 TGATTTTTGCTTTGAGATTCGTGC 59.319 37.500 0.00 0.00 0.00 5.34
2438 3069 4.305989 TGCTTTGAGATTCGTGCTTTTT 57.694 36.364 0.00 0.00 0.00 1.94
2472 3103 0.673985 GAGTTGTTTTGGGCTGGGTC 59.326 55.000 0.00 0.00 0.00 4.46
2499 3130 3.495434 ACTTACACGGATTTGGGTCAA 57.505 42.857 0.00 0.00 0.00 3.18
2507 3138 5.714806 ACACGGATTTGGGTCAATTAATTCT 59.285 36.000 0.00 0.00 0.00 2.40
2508 3139 6.210584 ACACGGATTTGGGTCAATTAATTCTT 59.789 34.615 0.00 0.00 0.00 2.52
2512 3143 9.816354 CGGATTTGGGTCAATTAATTCTTTAAT 57.184 29.630 0.00 0.00 39.23 1.40
2542 3173 2.779755 ACATTATCTGTGCGACCCAA 57.220 45.000 0.00 0.00 36.48 4.12
2567 3199 4.097418 CTCCCTCTCTCCCTTTGTTCTTA 58.903 47.826 0.00 0.00 0.00 2.10
2568 3200 3.838903 TCCCTCTCTCCCTTTGTTCTTAC 59.161 47.826 0.00 0.00 0.00 2.34
2569 3201 3.841255 CCCTCTCTCCCTTTGTTCTTACT 59.159 47.826 0.00 0.00 0.00 2.24
2575 3207 6.766467 TCTCTCCCTTTGTTCTTACTTGTTTC 59.234 38.462 0.00 0.00 0.00 2.78
2576 3208 6.419791 TCTCCCTTTGTTCTTACTTGTTTCA 58.580 36.000 0.00 0.00 0.00 2.69
2577 3209 7.060421 TCTCCCTTTGTTCTTACTTGTTTCAT 58.940 34.615 0.00 0.00 0.00 2.57
2581 3213 9.161629 CCCTTTGTTCTTACTTGTTTCATTTTT 57.838 29.630 0.00 0.00 0.00 1.94
2642 3274 8.485578 TTTTTATGAAAAAGGACTATGTGGGT 57.514 30.769 0.00 0.00 36.02 4.51
2643 3275 9.589461 TTTTTATGAAAAAGGACTATGTGGGTA 57.411 29.630 0.00 0.00 36.02 3.69
2645 3277 9.762381 TTTATGAAAAAGGACTATGTGGGTATT 57.238 29.630 0.00 0.00 0.00 1.89
2648 3280 8.485578 TGAAAAAGGACTATGTGGGTATTTTT 57.514 30.769 0.00 0.00 32.95 1.94
2654 3286 5.221244 GGACTATGTGGGTATTTTTGGATGC 60.221 44.000 0.00 0.00 0.00 3.91
2655 3287 4.649218 ACTATGTGGGTATTTTTGGATGCC 59.351 41.667 0.00 0.00 0.00 4.40
2657 3289 2.096248 GTGGGTATTTTTGGATGCCGA 58.904 47.619 0.00 0.00 33.11 5.54
2665 3297 0.396435 TTTGGATGCCGAGTGAGTGT 59.604 50.000 0.00 0.00 0.00 3.55
2668 3300 1.831106 TGGATGCCGAGTGAGTGTAAT 59.169 47.619 0.00 0.00 0.00 1.89
2676 3308 5.105675 TGCCGAGTGAGTGTAATTGTATACA 60.106 40.000 0.08 0.08 33.52 2.29
2699 3331 8.996024 ACACCCAAATACTTTAAAATATGTGC 57.004 30.769 1.94 0.00 0.00 4.57
2770 3402 4.084952 CCAATTTCAATGCGAAGTTGTGTG 60.085 41.667 8.59 0.00 45.26 3.82
2777 3409 1.201181 TGCGAAGTTGTGTGCAAGTTT 59.799 42.857 0.00 0.00 45.32 2.66
2778 3410 2.420372 TGCGAAGTTGTGTGCAAGTTTA 59.580 40.909 0.00 0.00 45.32 2.01
2779 3411 3.119814 TGCGAAGTTGTGTGCAAGTTTAA 60.120 39.130 0.00 0.00 45.32 1.52
2780 3412 3.854809 GCGAAGTTGTGTGCAAGTTTAAA 59.145 39.130 0.00 0.00 45.32 1.52
2781 3413 4.502645 GCGAAGTTGTGTGCAAGTTTAAAT 59.497 37.500 0.00 0.00 45.32 1.40
2782 3414 5.005299 GCGAAGTTGTGTGCAAGTTTAAATT 59.995 36.000 0.00 0.00 45.32 1.82
2783 3415 6.197468 GCGAAGTTGTGTGCAAGTTTAAATTA 59.803 34.615 0.00 0.00 45.32 1.40
2784 3416 7.096230 GCGAAGTTGTGTGCAAGTTTAAATTAT 60.096 33.333 0.00 0.00 45.32 1.28
2831 3463 9.967451 TTCAAAGGGTAATATCAATGTCACTAA 57.033 29.630 0.00 0.00 0.00 2.24
2917 3552 9.866655 TTATTCTTGAAGGGTAATATCAATGCT 57.133 29.630 0.00 0.00 33.03 3.79
2919 3554 8.677148 TTCTTGAAGGGTAATATCAATGCTAC 57.323 34.615 0.00 0.00 33.03 3.58
2934 3569 7.807977 TCAATGCTACTAATTCATTCCTTCC 57.192 36.000 0.00 0.00 0.00 3.46
2938 3573 7.067496 TGCTACTAATTCATTCCTTCCTAGG 57.933 40.000 0.82 0.82 43.46 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.909086 GAGGCTGATATGGGGCGCC 62.909 68.421 21.18 21.18 40.99 6.53
6 7 2.359230 GAGGCTGATATGGGGCGC 60.359 66.667 0.00 0.00 0.00 6.53
7 8 2.047844 CGAGGCTGATATGGGGCG 60.048 66.667 0.00 0.00 0.00 6.13
8 9 1.557269 ATCCGAGGCTGATATGGGGC 61.557 60.000 0.00 0.00 0.00 5.80
9 10 0.987294 AATCCGAGGCTGATATGGGG 59.013 55.000 0.00 0.00 0.00 4.96
10 11 2.430465 CAAATCCGAGGCTGATATGGG 58.570 52.381 0.00 0.00 0.00 4.00
11 12 2.430465 CCAAATCCGAGGCTGATATGG 58.570 52.381 0.00 0.00 0.00 2.74
12 13 2.430465 CCCAAATCCGAGGCTGATATG 58.570 52.381 0.00 0.00 0.00 1.78
13 14 1.271597 GCCCAAATCCGAGGCTGATAT 60.272 52.381 0.00 0.00 43.62 1.63
14 15 0.108585 GCCCAAATCCGAGGCTGATA 59.891 55.000 0.00 0.00 43.62 2.15
15 16 1.152881 GCCCAAATCCGAGGCTGAT 60.153 57.895 0.00 0.00 43.62 2.90
16 17 2.272146 GCCCAAATCCGAGGCTGA 59.728 61.111 0.00 0.00 43.62 4.26
24 25 1.543429 CCTCGTATCCAGCCCAAATCC 60.543 57.143 0.00 0.00 0.00 3.01
31 32 1.523938 GCAACCCTCGTATCCAGCC 60.524 63.158 0.00 0.00 0.00 4.85
53 54 4.383602 CTTCAAACACCCGCGCCG 62.384 66.667 0.00 0.00 0.00 6.46
55 56 4.700365 GGCTTCAAACACCCGCGC 62.700 66.667 0.00 0.00 0.00 6.86
62 63 3.974871 GTCTTAAACGGGCTTCAAACA 57.025 42.857 0.00 0.00 0.00 2.83
81 82 0.037160 AATTTAACCCGGACAGGCGT 59.963 50.000 0.73 0.00 39.21 5.68
84 85 4.038162 TCACAAAAATTTAACCCGGACAGG 59.962 41.667 0.73 0.00 40.63 4.00
86 87 4.202131 GGTCACAAAAATTTAACCCGGACA 60.202 41.667 0.73 0.00 0.00 4.02
88 89 3.004524 CGGTCACAAAAATTTAACCCGGA 59.995 43.478 0.73 0.00 0.00 5.14
90 91 3.243468 ACCGGTCACAAAAATTTAACCCG 60.243 43.478 0.00 0.00 0.00 5.28
96 97 1.679153 AGCGACCGGTCACAAAAATTT 59.321 42.857 32.80 3.87 0.00 1.82
104 105 2.126424 GAGTCAGCGACCGGTCAC 60.126 66.667 32.80 24.51 32.18 3.67
105 106 3.733960 CGAGTCAGCGACCGGTCA 61.734 66.667 32.80 12.00 32.18 4.02
123 124 1.808390 ATACGTTCAAGCGGACGGC 60.808 57.895 0.00 0.00 44.05 5.68
156 157 2.907897 CTACAGCTACAGCCGGGTGC 62.908 65.000 32.69 19.61 43.38 5.01
161 162 1.519455 GCACCTACAGCTACAGCCG 60.519 63.158 0.00 0.00 43.38 5.52
162 163 0.179097 GAGCACCTACAGCTACAGCC 60.179 60.000 0.00 0.00 43.58 4.85
163 164 0.820871 AGAGCACCTACAGCTACAGC 59.179 55.000 0.00 0.00 43.58 4.40
164 165 4.927978 ATAAGAGCACCTACAGCTACAG 57.072 45.455 0.00 0.00 43.58 2.74
165 166 6.978674 AATATAAGAGCACCTACAGCTACA 57.021 37.500 0.00 0.00 43.58 2.74
166 167 7.976734 CCATAATATAAGAGCACCTACAGCTAC 59.023 40.741 0.00 0.00 43.58 3.58
167 168 7.124298 CCCATAATATAAGAGCACCTACAGCTA 59.876 40.741 0.00 0.00 43.58 3.32
168 169 6.070538 CCCATAATATAAGAGCACCTACAGCT 60.071 42.308 0.00 0.00 46.82 4.24
212 216 2.436646 GGACGTCCTGGCATGTGG 60.437 66.667 27.64 0.00 0.00 4.17
230 234 2.859165 AAATGAGAGTCGGCAAAGGA 57.141 45.000 0.00 0.00 0.00 3.36
255 275 1.593469 TCGAGTTGAGCGATCGTAGAG 59.407 52.381 17.81 1.05 43.63 2.43
361 385 2.514458 AACAATTAGGGTGAGGGCAG 57.486 50.000 0.00 0.00 0.00 4.85
375 399 2.154462 CTTGGCTCACGAGGAAACAAT 58.846 47.619 0.00 0.00 0.00 2.71
380 404 0.756294 TTGACTTGGCTCACGAGGAA 59.244 50.000 0.00 0.00 34.66 3.36
385 409 0.662619 TTTGCTTGACTTGGCTCACG 59.337 50.000 0.00 0.00 0.00 4.35
409 433 0.181824 ACCAAAGGTTACACGGCTGT 59.818 50.000 0.00 0.00 27.29 4.40
518 542 2.860136 GAGTGCAACCAAAAAGCTCAAC 59.140 45.455 0.00 0.00 37.80 3.18
560 584 8.950007 TTTTATCCCTCCAAGTACAAGAAAAT 57.050 30.769 0.00 0.00 0.00 1.82
568 592 6.524101 TGCAAATTTTATCCCTCCAAGTAC 57.476 37.500 0.00 0.00 0.00 2.73
574 598 4.081476 AGCTGTTGCAAATTTTATCCCTCC 60.081 41.667 0.00 0.00 42.74 4.30
576 600 4.284234 ACAGCTGTTGCAAATTTTATCCCT 59.716 37.500 15.25 0.00 42.74 4.20
579 603 7.622048 GCCTAAACAGCTGTTGCAAATTTTATC 60.622 37.037 31.73 9.34 42.74 1.75
581 605 5.465056 GCCTAAACAGCTGTTGCAAATTTTA 59.535 36.000 31.73 16.40 42.74 1.52
584 608 3.392882 GCCTAAACAGCTGTTGCAAATT 58.607 40.909 31.73 17.59 42.74 1.82
616 640 8.741101 TGTTTATTTACAGCTGCAATTAGTTG 57.259 30.769 15.27 0.00 38.39 3.16
617 641 9.757227 TTTGTTTATTTACAGCTGCAATTAGTT 57.243 25.926 15.27 0.00 0.00 2.24
625 649 8.168626 GCCTTATTTTTGTTTATTTACAGCTGC 58.831 33.333 15.27 0.00 0.00 5.25
641 665 5.722021 ACCATTCGTCAAGCCTTATTTTT 57.278 34.783 0.00 0.00 0.00 1.94
646 670 1.810151 GCAACCATTCGTCAAGCCTTA 59.190 47.619 0.00 0.00 0.00 2.69
647 671 0.598065 GCAACCATTCGTCAAGCCTT 59.402 50.000 0.00 0.00 0.00 4.35
649 673 1.154225 CGCAACCATTCGTCAAGCC 60.154 57.895 0.00 0.00 0.00 4.35
651 675 1.154225 GGCGCAACCATTCGTCAAG 60.154 57.895 10.83 0.00 38.86 3.02
652 676 1.894282 TGGCGCAACCATTCGTCAA 60.894 52.632 10.83 0.00 46.36 3.18
667 691 3.499737 CGGCCGAGTTCACATGGC 61.500 66.667 24.07 4.34 46.82 4.40
702 726 1.126846 CAAACAAGACATCGAGCCGAC 59.873 52.381 0.00 0.00 39.18 4.79
703 727 1.428448 CAAACAAGACATCGAGCCGA 58.572 50.000 0.00 0.00 41.13 5.54
704 728 0.443869 CCAAACAAGACATCGAGCCG 59.556 55.000 0.00 0.00 0.00 5.52
705 729 1.808411 TCCAAACAAGACATCGAGCC 58.192 50.000 0.00 0.00 0.00 4.70
706 730 2.411547 CGTTCCAAACAAGACATCGAGC 60.412 50.000 0.00 0.00 0.00 5.03
707 731 2.157668 CCGTTCCAAACAAGACATCGAG 59.842 50.000 0.00 0.00 0.00 4.04
708 732 2.139917 CCGTTCCAAACAAGACATCGA 58.860 47.619 0.00 0.00 0.00 3.59
709 733 2.139917 TCCGTTCCAAACAAGACATCG 58.860 47.619 0.00 0.00 0.00 3.84
710 734 3.609409 GCTTCCGTTCCAAACAAGACATC 60.609 47.826 0.00 0.00 0.00 3.06
711 735 2.293399 GCTTCCGTTCCAAACAAGACAT 59.707 45.455 0.00 0.00 0.00 3.06
712 736 1.673920 GCTTCCGTTCCAAACAAGACA 59.326 47.619 0.00 0.00 0.00 3.41
726 750 2.408050 AGCTAATTCTATGCGCTTCCG 58.592 47.619 9.73 0.00 37.57 4.30
934 1283 0.921662 CTCGATCGAGAGCGTTGACG 60.922 60.000 36.13 9.20 44.53 4.35
949 1298 2.225727 CGTGTATATGTAGGCAGCTCGA 59.774 50.000 0.00 0.00 0.00 4.04
950 1299 2.585845 CGTGTATATGTAGGCAGCTCG 58.414 52.381 0.00 0.00 0.00 5.03
951 1300 2.329379 GCGTGTATATGTAGGCAGCTC 58.671 52.381 0.00 0.00 0.00 4.09
952 1301 1.000955 GGCGTGTATATGTAGGCAGCT 59.999 52.381 0.00 0.00 0.00 4.24
953 1302 1.270094 TGGCGTGTATATGTAGGCAGC 60.270 52.381 7.65 0.00 33.47 5.25
990 1339 3.174265 GGGGCTGGGAGAGATGGG 61.174 72.222 0.00 0.00 0.00 4.00
1088 1455 1.078848 GCCATGACCAGCTTCGACT 60.079 57.895 0.00 0.00 0.00 4.18
1093 1460 2.629656 GCAACGCCATGACCAGCTT 61.630 57.895 0.00 0.00 0.00 3.74
1176 1543 1.970114 GACGTCGAGGGTCACAGGA 60.970 63.158 10.27 0.00 34.56 3.86
1312 1917 0.179000 GGCATGGAGAACTGGTCGAT 59.821 55.000 0.00 0.00 0.00 3.59
1349 1954 2.847234 TTGAGGGCCCACGTCACT 60.847 61.111 27.56 0.00 43.10 3.41
1484 2089 1.131638 TGAACTGGCAGGTCTTGTCT 58.868 50.000 30.91 0.00 31.84 3.41
1786 2391 1.005394 CCTTGCCACGTACGGTTCT 60.005 57.895 21.06 0.00 0.00 3.01
1833 2447 0.810426 TGCGTACGTTGCAAAGGACA 60.810 50.000 24.58 10.70 39.87 4.02
1856 2471 8.035394 CACTCTCTTACATTACATGTACACCTT 58.965 37.037 4.68 0.00 44.79 3.50
1919 2545 8.988546 TTGGCATTTACATATAGGTAATGTGT 57.011 30.769 10.54 0.00 42.09 3.72
1920 2546 9.897744 CTTTGGCATTTACATATAGGTAATGTG 57.102 33.333 10.54 12.71 38.05 3.21
1921 2547 9.640952 ACTTTGGCATTTACATATAGGTAATGT 57.359 29.630 10.54 1.21 40.57 2.71
1925 2551 8.908903 CCAAACTTTGGCATTTACATATAGGTA 58.091 33.333 7.63 0.00 45.17 3.08
1926 2552 7.781056 CCAAACTTTGGCATTTACATATAGGT 58.219 34.615 7.63 0.00 45.17 3.08
1942 2568 0.593128 CGGAGCAGTCCCAAACTTTG 59.407 55.000 0.00 0.00 40.20 2.77
1943 2569 3.021451 CGGAGCAGTCCCAAACTTT 57.979 52.632 0.00 0.00 40.20 2.66
1944 2570 4.800554 CGGAGCAGTCCCAAACTT 57.199 55.556 0.00 0.00 40.20 2.66
1961 2587 7.878477 TGATGAAATTGAACTGATTTGAAGC 57.122 32.000 0.00 0.00 0.00 3.86
1967 2593 9.778993 CGTAGATTTGATGAAATTGAACTGATT 57.221 29.630 0.00 0.00 31.58 2.57
1968 2594 8.950210 ACGTAGATTTGATGAAATTGAACTGAT 58.050 29.630 0.00 0.00 31.58 2.90
2011 2641 5.048434 GCTCTTTTATGGAACTGCAACTCTT 60.048 40.000 0.00 0.00 0.00 2.85
2022 2652 9.995003 AACACAATAAATTGCTCTTTTATGGAA 57.005 25.926 2.60 0.00 41.38 3.53
2027 2657 7.930865 AGCCAAACACAATAAATTGCTCTTTTA 59.069 29.630 2.60 0.00 41.38 1.52
2028 2658 6.767423 AGCCAAACACAATAAATTGCTCTTTT 59.233 30.769 2.60 0.00 41.38 2.27
2032 2662 6.644592 TGTAAGCCAAACACAATAAATTGCTC 59.355 34.615 2.60 0.00 41.38 4.26
2043 2673 3.813166 GAGCTACTTGTAAGCCAAACACA 59.187 43.478 0.00 0.00 41.02 3.72
2044 2674 3.188667 GGAGCTACTTGTAAGCCAAACAC 59.811 47.826 0.00 0.00 41.02 3.32
2130 2760 4.003648 CACTGTTGACTTGATACCCCTTC 58.996 47.826 0.00 0.00 0.00 3.46
2133 2763 3.695830 TCACTGTTGACTTGATACCCC 57.304 47.619 0.00 0.00 0.00 4.95
2154 2784 7.610865 AGTTGTGGTGAAATTACCCAATAATG 58.389 34.615 0.00 0.00 40.09 1.90
2157 2787 6.307776 TGAGTTGTGGTGAAATTACCCAATA 58.692 36.000 0.00 0.00 40.09 1.90
2164 2794 6.998074 AGTTCTCATGAGTTGTGGTGAAATTA 59.002 34.615 21.92 0.00 0.00 1.40
2174 2804 6.352516 AGTTTGAAGAGTTCTCATGAGTTGT 58.647 36.000 21.92 7.79 0.00 3.32
2175 2805 6.346439 CGAGTTTGAAGAGTTCTCATGAGTTG 60.346 42.308 21.92 0.00 0.00 3.16
2181 2811 5.461032 ACTCGAGTTTGAAGAGTTCTCAT 57.539 39.130 13.58 0.00 41.93 2.90
2182 2812 4.920640 ACTCGAGTTTGAAGAGTTCTCA 57.079 40.909 13.58 0.00 41.93 3.27
2208 2839 0.250513 AACTCTTCGATGGGTGCTCC 59.749 55.000 4.35 0.00 0.00 4.70
2211 2842 1.464997 GTGAAACTCTTCGATGGGTGC 59.535 52.381 4.35 1.44 33.94 5.01
2214 2845 2.472695 TGGTGAAACTCTTCGATGGG 57.527 50.000 0.00 0.00 36.74 4.00
2219 2850 4.570772 TCTTGTCTTTGGTGAAACTCTTCG 59.429 41.667 0.00 0.00 36.74 3.79
2272 2903 4.177026 AGCTGTACGATGTCTCATTTCAC 58.823 43.478 0.00 0.00 0.00 3.18
2273 2904 4.456280 AGCTGTACGATGTCTCATTTCA 57.544 40.909 0.00 0.00 0.00 2.69
2274 2905 7.149112 CGTTATAGCTGTACGATGTCTCATTTC 60.149 40.741 10.41 0.00 37.47 2.17
2275 2906 6.637254 CGTTATAGCTGTACGATGTCTCATTT 59.363 38.462 10.41 0.00 37.47 2.32
2278 2909 4.573607 ACGTTATAGCTGTACGATGTCTCA 59.426 41.667 19.43 0.00 38.56 3.27
2279 2910 5.093169 ACGTTATAGCTGTACGATGTCTC 57.907 43.478 19.43 0.00 38.56 3.36
2280 2911 5.496133 AACGTTATAGCTGTACGATGTCT 57.504 39.130 19.43 0.00 38.56 3.41
2281 2912 5.740569 TGAAACGTTATAGCTGTACGATGTC 59.259 40.000 19.43 13.88 38.56 3.06
2282 2913 5.643664 TGAAACGTTATAGCTGTACGATGT 58.356 37.500 19.43 3.30 38.56 3.06
2283 2914 5.742453 ACTGAAACGTTATAGCTGTACGATG 59.258 40.000 19.43 2.74 38.56 3.84
2284 2915 5.888105 ACTGAAACGTTATAGCTGTACGAT 58.112 37.500 19.43 8.52 38.56 3.73
2285 2916 5.300969 ACTGAAACGTTATAGCTGTACGA 57.699 39.130 19.43 1.64 38.56 3.43
2286 2917 5.720433 GCAACTGAAACGTTATAGCTGTACG 60.720 44.000 0.00 13.32 40.85 3.67
2287 2918 5.548250 GCAACTGAAACGTTATAGCTGTAC 58.452 41.667 0.00 0.00 0.00 2.90
2288 2919 4.325204 CGCAACTGAAACGTTATAGCTGTA 59.675 41.667 0.00 0.00 0.00 2.74
2289 2920 3.122948 CGCAACTGAAACGTTATAGCTGT 59.877 43.478 0.00 0.00 0.00 4.40
2290 2921 3.122948 ACGCAACTGAAACGTTATAGCTG 59.877 43.478 0.00 6.02 36.46 4.24
2304 2935 5.235186 AGCTCTGCTATAAAATACGCAACTG 59.765 40.000 0.00 0.00 36.99 3.16
2306 2937 5.234329 TCAGCTCTGCTATAAAATACGCAAC 59.766 40.000 0.00 0.00 36.40 4.17
2309 2940 5.907197 TTCAGCTCTGCTATAAAATACGC 57.093 39.130 0.00 0.00 36.40 4.42
2319 2950 4.684485 GCTCCCTAAAATTCAGCTCTGCTA 60.684 45.833 0.00 0.00 36.40 3.49
2327 2958 1.943340 GCTCCGCTCCCTAAAATTCAG 59.057 52.381 0.00 0.00 0.00 3.02
2343 2974 1.322442 GCCATATTTGGGACTGCTCC 58.678 55.000 4.23 0.00 43.84 4.70
2357 2988 8.196378 ACAATTTTTAAACCACTTAGGCCATA 57.804 30.769 5.01 0.00 43.14 2.74
2405 3036 6.366877 CGAATCTCAAAGCAAAAATCATTGGT 59.633 34.615 0.00 0.00 42.43 3.67
2408 3039 6.128742 GCACGAATCTCAAAGCAAAAATCATT 60.129 34.615 0.00 0.00 0.00 2.57
2409 3040 5.346822 GCACGAATCTCAAAGCAAAAATCAT 59.653 36.000 0.00 0.00 0.00 2.45
2416 3047 3.988379 AAAGCACGAATCTCAAAGCAA 57.012 38.095 0.00 0.00 0.00 3.91
2438 3069 7.308229 CCAAAACAACTCACAAAATTGACCAAA 60.308 33.333 0.00 0.00 0.00 3.28
2439 3070 6.148480 CCAAAACAACTCACAAAATTGACCAA 59.852 34.615 0.00 0.00 0.00 3.67
2440 3071 5.641209 CCAAAACAACTCACAAAATTGACCA 59.359 36.000 0.00 0.00 0.00 4.02
2442 3073 5.447144 GCCCAAAACAACTCACAAAATTGAC 60.447 40.000 0.00 0.00 0.00 3.18
2443 3074 4.633565 GCCCAAAACAACTCACAAAATTGA 59.366 37.500 0.00 0.00 0.00 2.57
2444 3075 4.635324 AGCCCAAAACAACTCACAAAATTG 59.365 37.500 0.00 0.00 0.00 2.32
2445 3076 4.635324 CAGCCCAAAACAACTCACAAAATT 59.365 37.500 0.00 0.00 0.00 1.82
2446 3077 4.190772 CAGCCCAAAACAACTCACAAAAT 58.809 39.130 0.00 0.00 0.00 1.82
2448 3079 2.093764 CCAGCCCAAAACAACTCACAAA 60.094 45.455 0.00 0.00 0.00 2.83
2449 3080 1.480137 CCAGCCCAAAACAACTCACAA 59.520 47.619 0.00 0.00 0.00 3.33
2450 3081 1.110442 CCAGCCCAAAACAACTCACA 58.890 50.000 0.00 0.00 0.00 3.58
2451 3082 0.389025 CCCAGCCCAAAACAACTCAC 59.611 55.000 0.00 0.00 0.00 3.51
2478 3109 4.620589 TTGACCCAAATCCGTGTAAGTA 57.379 40.909 0.00 0.00 0.00 2.24
2523 3154 2.356135 GTTGGGTCGCACAGATAATGT 58.644 47.619 0.00 0.00 45.43 2.71
2529 3160 2.847234 AGGGTTGGGTCGCACAGA 60.847 61.111 0.00 0.00 0.00 3.41
2532 3163 4.717313 GGGAGGGTTGGGTCGCAC 62.717 72.222 0.00 0.00 0.00 5.34
2536 3167 0.978667 GAGAGAGGGAGGGTTGGGTC 60.979 65.000 0.00 0.00 0.00 4.46
2540 3171 0.252927 AAGGGAGAGAGGGAGGGTTG 60.253 60.000 0.00 0.00 0.00 3.77
2542 3173 0.252927 CAAAGGGAGAGAGGGAGGGT 60.253 60.000 0.00 0.00 0.00 4.34
2618 3250 9.762381 ATACCCACATAGTCCTTTTTCATAAAA 57.238 29.630 0.00 0.00 0.00 1.52
2619 3251 9.762381 AATACCCACATAGTCCTTTTTCATAAA 57.238 29.630 0.00 0.00 0.00 1.40
2622 3254 8.664669 AAAATACCCACATAGTCCTTTTTCAT 57.335 30.769 0.00 0.00 0.00 2.57
2624 3256 7.817478 CCAAAAATACCCACATAGTCCTTTTTC 59.183 37.037 0.00 0.00 0.00 2.29
2625 3257 7.511028 TCCAAAAATACCCACATAGTCCTTTTT 59.489 33.333 0.00 0.00 0.00 1.94
2626 3258 7.013834 TCCAAAAATACCCACATAGTCCTTTT 58.986 34.615 0.00 0.00 0.00 2.27
2627 3259 6.557568 TCCAAAAATACCCACATAGTCCTTT 58.442 36.000 0.00 0.00 0.00 3.11
2628 3260 6.147437 TCCAAAAATACCCACATAGTCCTT 57.853 37.500 0.00 0.00 0.00 3.36
2629 3261 5.789574 TCCAAAAATACCCACATAGTCCT 57.210 39.130 0.00 0.00 0.00 3.85
2630 3262 5.221244 GCATCCAAAAATACCCACATAGTCC 60.221 44.000 0.00 0.00 0.00 3.85
2632 3264 4.649218 GGCATCCAAAAATACCCACATAGT 59.351 41.667 0.00 0.00 0.00 2.12
2633 3265 4.261572 CGGCATCCAAAAATACCCACATAG 60.262 45.833 0.00 0.00 0.00 2.23
2637 3269 2.096248 TCGGCATCCAAAAATACCCAC 58.904 47.619 0.00 0.00 0.00 4.61
2638 3270 2.291282 ACTCGGCATCCAAAAATACCCA 60.291 45.455 0.00 0.00 0.00 4.51
2639 3271 2.099098 CACTCGGCATCCAAAAATACCC 59.901 50.000 0.00 0.00 0.00 3.69
2640 3272 3.013921 TCACTCGGCATCCAAAAATACC 58.986 45.455 0.00 0.00 0.00 2.73
2641 3273 3.689649 ACTCACTCGGCATCCAAAAATAC 59.310 43.478 0.00 0.00 0.00 1.89
2642 3274 3.689161 CACTCACTCGGCATCCAAAAATA 59.311 43.478 0.00 0.00 0.00 1.40
2643 3275 2.489329 CACTCACTCGGCATCCAAAAAT 59.511 45.455 0.00 0.00 0.00 1.82
2645 3277 1.202758 ACACTCACTCGGCATCCAAAA 60.203 47.619 0.00 0.00 0.00 2.44
2648 3280 1.262417 TTACACTCACTCGGCATCCA 58.738 50.000 0.00 0.00 0.00 3.41
2654 3286 6.807708 GTGTATACAATTACACTCACTCGG 57.192 41.667 7.25 0.00 45.48 4.63
2745 3377 4.148696 CACAACTTCGCATTGAAATTGGAC 59.851 41.667 4.22 0.00 45.61 4.02
2746 3378 4.202101 ACACAACTTCGCATTGAAATTGGA 60.202 37.500 4.22 0.00 45.61 3.53
2747 3379 4.050553 ACACAACTTCGCATTGAAATTGG 58.949 39.130 4.22 0.00 45.61 3.16
2756 3388 1.024271 ACTTGCACACAACTTCGCAT 58.976 45.000 0.00 0.00 33.71 4.73
2759 3391 6.567769 AATTTAAACTTGCACACAACTTCG 57.432 33.333 0.00 0.00 0.00 3.79
2788 3420 9.739276 ACCCTTTGAAAAAGAAAGAAAGAAATT 57.261 25.926 1.31 0.00 33.01 1.82
2802 3434 9.921637 GTGACATTGATATTACCCTTTGAAAAA 57.078 29.630 0.00 0.00 0.00 1.94
2805 3437 9.967451 TTAGTGACATTGATATTACCCTTTGAA 57.033 29.630 0.00 0.00 0.00 2.69
2891 3524 9.866655 AGCATTGATATTACCCTTCAAGAATAA 57.133 29.630 0.00 0.00 33.26 1.40
2893 3526 9.289782 GTAGCATTGATATTACCCTTCAAGAAT 57.710 33.333 0.00 0.00 33.26 2.40
2910 3545 7.577303 AGGAAGGAATGAATTAGTAGCATTGA 58.423 34.615 0.00 0.00 32.80 2.57


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

AutoCloner maintained by Alex Coulton.