Multiple sequence alignment - TraesCS1D01G266900

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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 TraesCS1D01G266900 chr1D 100.000 4630 0 0 1 4630 362778902 362783531 0.000000e+00 8551.0
1 TraesCS1D01G266900 chr1D 87.726 554 47 10 4083 4628 417248936 417249476 1.090000e-175 627.0
2 TraesCS1D01G266900 chr1A 89.420 3450 161 77 11 3328 462121416 462124793 0.000000e+00 4161.0
3 TraesCS1D01G266900 chr1A 89.759 166 4 3 3466 3618 462124790 462124955 2.830000e-47 200.0
4 TraesCS1D01G266900 chr1B 91.109 2092 105 40 1275 3328 485804039 485806087 0.000000e+00 2758.0
5 TraesCS1D01G266900 chr1B 88.676 1254 49 31 8 1208 485802320 485803533 0.000000e+00 1443.0
6 TraesCS1D01G266900 chr1B 87.755 98 8 4 3615 3709 485807528 485807624 1.360000e-20 111.0
7 TraesCS1D01G266900 chr2D 86.198 768 73 19 3874 4627 554073439 554074187 0.000000e+00 800.0
8 TraesCS1D01G266900 chr2D 84.367 774 98 16 3876 4630 69277480 69276711 0.000000e+00 737.0
9 TraesCS1D01G266900 chr2D 95.918 147 6 0 3325 3471 35309401 35309547 5.990000e-59 239.0
10 TraesCS1D01G266900 chr2D 94.872 39 0 1 3617 3655 440337403 440337367 5.000000e-05 60.2
11 TraesCS1D01G266900 chr2D 100.000 28 0 0 2659 2686 626911819 626911792 8.000000e-03 52.8
12 TraesCS1D01G266900 chr5A 83.312 779 93 29 3874 4630 595547227 595546464 0.000000e+00 684.0
13 TraesCS1D01G266900 chr5A 92.500 40 1 2 3666 3703 560729218 560729179 6.470000e-04 56.5
14 TraesCS1D01G266900 chr5B 83.182 773 99 23 3872 4630 56641782 56641027 0.000000e+00 678.0
15 TraesCS1D01G266900 chr5B 82.074 781 107 26 3872 4630 56954512 56953743 1.820000e-178 636.0
16 TraesCS1D01G266900 chr5B 81.461 178 25 6 3862 4034 591656913 591657087 6.250000e-29 139.0
17 TraesCS1D01G266900 chr3D 82.272 801 102 16 3868 4630 182326159 182326957 0.000000e+00 656.0
18 TraesCS1D01G266900 chr3D 91.781 146 10 1 3327 3472 591097168 591097025 7.860000e-48 202.0
19 TraesCS1D01G266900 chr3D 91.765 85 7 0 2542 2626 497373287 497373203 8.140000e-23 119.0
20 TraesCS1D01G266900 chr3D 100.000 28 0 0 2659 2686 538182667 538182640 8.000000e-03 52.8
21 TraesCS1D01G266900 chr6D 82.461 764 109 18 3881 4630 82471405 82470653 0.000000e+00 645.0
22 TraesCS1D01G266900 chr6D 95.105 143 6 1 3325 3466 132304713 132304855 1.680000e-54 224.0
23 TraesCS1D01G266900 chr6D 81.560 141 22 4 3876 4015 448632078 448632215 3.790000e-21 113.0
24 TraesCS1D01G266900 chr2B 82.194 775 108 19 3873 4630 90188422 90187661 1.400000e-179 640.0
25 TraesCS1D01G266900 chr2B 100.000 31 0 0 2590 2620 31730844 31730814 1.800000e-04 58.4
26 TraesCS1D01G266900 chr2B 90.476 42 2 1 3618 3657 738234097 738234056 2.000000e-03 54.7
27 TraesCS1D01G266900 chr4B 81.946 781 111 21 3876 4630 603038834 603039610 6.540000e-178 634.0
28 TraesCS1D01G266900 chr7B 89.506 486 46 3 4147 4630 599358985 599358503 1.100000e-170 610.0
29 TraesCS1D01G266900 chr7B 81.915 188 29 4 3871 4053 9000063 9000250 2.230000e-33 154.0
30 TraesCS1D01G266900 chr5D 81.078 798 103 17 3873 4630 105095781 105096570 1.110000e-165 593.0
31 TraesCS1D01G266900 chr5D 100.000 140 0 0 3327 3466 388099926 388099787 4.600000e-65 259.0
32 TraesCS1D01G266900 chr5D 95.862 145 6 0 3325 3469 10032320 10032464 7.740000e-58 235.0
33 TraesCS1D01G266900 chr5D 95.862 145 6 0 3325 3469 10033959 10034103 7.740000e-58 235.0
34 TraesCS1D01G266900 chr7A 80.740 784 110 31 3874 4630 441978438 441977669 1.450000e-159 573.0
35 TraesCS1D01G266900 chr6A 99.310 145 1 0 3327 3471 430744196 430744340 3.550000e-66 263.0
36 TraesCS1D01G266900 chr7D 99.301 143 1 0 3327 3469 21315984 21315842 4.600000e-65 259.0
37 TraesCS1D01G266900 chr4D 94.483 145 8 0 3325 3469 83289796 83289652 1.680000e-54 224.0
38 TraesCS1D01G266900 chr4D 93.289 149 10 0 3323 3471 46294807 46294659 2.170000e-53 220.0
39 TraesCS1D01G266900 chr4D 90.476 147 11 3 3328 3473 36439228 36439084 1.700000e-44 191.0
40 TraesCS1D01G266900 chr3A 91.765 85 7 0 2542 2626 637290458 637290542 8.140000e-23 119.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G266900 chr1D 362778902 362783531 4629 False 8551.000000 8551 100.0000 1 4630 1 chr1D.!!$F1 4629
1 TraesCS1D01G266900 chr1D 417248936 417249476 540 False 627.000000 627 87.7260 4083 4628 1 chr1D.!!$F2 545
2 TraesCS1D01G266900 chr1A 462121416 462124955 3539 False 2180.500000 4161 89.5895 11 3618 2 chr1A.!!$F1 3607
3 TraesCS1D01G266900 chr1B 485802320 485807624 5304 False 1437.333333 2758 89.1800 8 3709 3 chr1B.!!$F1 3701
4 TraesCS1D01G266900 chr2D 554073439 554074187 748 False 800.000000 800 86.1980 3874 4627 1 chr2D.!!$F2 753
5 TraesCS1D01G266900 chr2D 69276711 69277480 769 True 737.000000 737 84.3670 3876 4630 1 chr2D.!!$R1 754
6 TraesCS1D01G266900 chr5A 595546464 595547227 763 True 684.000000 684 83.3120 3874 4630 1 chr5A.!!$R2 756
7 TraesCS1D01G266900 chr5B 56641027 56641782 755 True 678.000000 678 83.1820 3872 4630 1 chr5B.!!$R1 758
8 TraesCS1D01G266900 chr5B 56953743 56954512 769 True 636.000000 636 82.0740 3872 4630 1 chr5B.!!$R2 758
9 TraesCS1D01G266900 chr3D 182326159 182326957 798 False 656.000000 656 82.2720 3868 4630 1 chr3D.!!$F1 762
10 TraesCS1D01G266900 chr6D 82470653 82471405 752 True 645.000000 645 82.4610 3881 4630 1 chr6D.!!$R1 749
11 TraesCS1D01G266900 chr2B 90187661 90188422 761 True 640.000000 640 82.1940 3873 4630 1 chr2B.!!$R2 757
12 TraesCS1D01G266900 chr4B 603038834 603039610 776 False 634.000000 634 81.9460 3876 4630 1 chr4B.!!$F1 754
13 TraesCS1D01G266900 chr5D 105095781 105096570 789 False 593.000000 593 81.0780 3873 4630 1 chr5D.!!$F1 757
14 TraesCS1D01G266900 chr5D 10032320 10034103 1783 False 235.000000 235 95.8620 3325 3469 2 chr5D.!!$F2 144
15 TraesCS1D01G266900 chr7A 441977669 441978438 769 True 573.000000 573 80.7400 3874 4630 1 chr7A.!!$R1 756

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
386 409 0.111639 TGTTGGTTAGGAGTTGGGGC 59.888 55.0 0.00 0.00 0.00 5.80 F
814 906 0.262285 AGTAGAGCAGTAGGACCCCC 59.738 60.0 0.00 0.00 0.00 5.40 F
1047 1148 0.624795 ATCTCCTTGGTTCCCTCCCC 60.625 60.0 0.00 0.00 0.00 4.81 F
1528 2104 0.727970 CTCTTGCAGCAGTCTCATGC 59.272 55.0 0.00 0.00 46.88 4.06 F
3405 4049 0.039617 TTGAAATTTGTGGAGCGGCG 60.040 50.0 0.51 0.51 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2265 2887 0.541863 CCGTGCCCTTCCTTATCTGT 59.458 55.0 0.00 0.00 0.00 3.41 R
2578 3205 0.179000 ATGAGGAGGAACATGGCGAC 59.821 55.0 0.00 0.00 0.00 5.19 R
2797 3434 0.179009 AGAGCACAAGGAAAGCAGCA 60.179 50.0 0.00 0.00 0.00 4.41 R
3447 4091 0.554305 AAGGGGTTGTTCGGAAACCT 59.446 50.0 10.55 3.35 45.40 3.50 R
4390 6898 0.108329 AGGACGTCGCCGATGAAAAT 60.108 50.0 14.17 0.00 37.88 1.82 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
77 79 4.041762 ATGCGGAAAAGCGGGGGA 62.042 61.111 0.00 0.00 40.67 4.81
81 83 2.038837 CGGAAAAGCGGGGGAAGAC 61.039 63.158 0.00 0.00 0.00 3.01
82 84 2.038837 GGAAAAGCGGGGGAAGACG 61.039 63.158 0.00 0.00 0.00 4.18
194 197 2.194056 CGCATGGGCTCCAAGGAT 59.806 61.111 0.00 0.00 36.95 3.24
224 229 3.026630 TCTTACTGCACAGTTCTTCCG 57.973 47.619 8.86 0.00 42.54 4.30
386 409 0.111639 TGTTGGTTAGGAGTTGGGGC 59.888 55.000 0.00 0.00 0.00 5.80
388 411 0.774491 TTGGTTAGGAGTTGGGGCCT 60.774 55.000 0.84 0.00 38.31 5.19
389 412 1.303282 GGTTAGGAGTTGGGGCCTG 59.697 63.158 0.84 0.00 35.73 4.85
391 414 2.612493 TTAGGAGTTGGGGCCTGGC 61.612 63.158 11.05 11.05 35.73 4.85
537 562 3.131396 CCTATCTTGCGTTGTACCCATC 58.869 50.000 0.00 0.00 0.00 3.51
564 593 2.152016 CACTGATGCATCATGCTAGGG 58.848 52.381 28.81 17.49 45.31 3.53
591 620 1.466856 CAGTGGCATTGCACCATAGT 58.533 50.000 11.39 0.00 39.95 2.12
616 647 8.392612 GTGGCTTAAAACGCTCAATTAGTAATA 58.607 33.333 0.00 0.00 0.00 0.98
677 726 4.779696 TGATAATTAGACCATGCAGTGCA 58.220 39.130 22.22 22.22 44.86 4.57
744 806 0.321671 TGGAGAGCAGCCTGTACAAC 59.678 55.000 0.00 0.00 0.00 3.32
745 807 0.391793 GGAGAGCAGCCTGTACAACC 60.392 60.000 0.00 0.00 0.00 3.77
814 906 0.262285 AGTAGAGCAGTAGGACCCCC 59.738 60.000 0.00 0.00 0.00 5.40
882 979 3.503363 ACCACACATACATTCACTTGCAG 59.497 43.478 0.00 0.00 0.00 4.41
885 982 5.106038 CCACACATACATTCACTTGCAGAAT 60.106 40.000 0.00 0.00 36.19 2.40
886 983 6.093909 CCACACATACATTCACTTGCAGAATA 59.906 38.462 0.00 0.00 34.14 1.75
887 984 7.361971 CCACACATACATTCACTTGCAGAATAA 60.362 37.037 0.00 0.00 34.14 1.40
888 985 8.186163 CACACATACATTCACTTGCAGAATAAT 58.814 33.333 0.00 0.00 34.14 1.28
889 986 9.394767 ACACATACATTCACTTGCAGAATAATA 57.605 29.630 0.00 0.00 34.14 0.98
890 987 9.655769 CACATACATTCACTTGCAGAATAATAC 57.344 33.333 0.00 0.00 34.14 1.89
953 1050 2.137523 GCAACAAACAAATGCTCCCTG 58.862 47.619 0.00 0.00 37.12 4.45
961 1058 0.979187 AAATGCTCCCTGCCATTGGG 60.979 55.000 4.53 0.00 45.90 4.12
1041 1142 1.846439 TCATCCCATCTCCTTGGTTCC 59.154 52.381 0.00 0.00 34.77 3.62
1047 1148 0.624795 ATCTCCTTGGTTCCCTCCCC 60.625 60.000 0.00 0.00 0.00 4.81
1076 1177 2.036217 TGCCTTGCCAATTTCTGAACAG 59.964 45.455 0.00 0.00 0.00 3.16
1087 1188 1.428448 TCTGAACAGGCACGAAATCG 58.572 50.000 0.48 0.48 46.33 3.34
1255 1767 7.086376 CCCATTATTGACACTGACTTTCAAAG 58.914 38.462 0.00 0.00 33.13 2.77
1256 1768 7.040478 CCCATTATTGACACTGACTTTCAAAGA 60.040 37.037 3.49 0.00 33.13 2.52
1258 1770 5.757850 ATTGACACTGACTTTCAAAGACC 57.242 39.130 3.49 0.00 33.13 3.85
1259 1771 4.487714 TGACACTGACTTTCAAAGACCT 57.512 40.909 3.49 0.00 0.00 3.85
1264 1795 2.996621 CTGACTTTCAAAGACCTAGCCG 59.003 50.000 3.49 0.00 0.00 5.52
1266 1797 1.975680 ACTTTCAAAGACCTAGCCGGA 59.024 47.619 5.05 0.00 36.31 5.14
1337 1898 1.194121 CCTTTTCCTTGGCCCCCTTG 61.194 60.000 0.00 0.00 0.00 3.61
1521 2097 1.350351 ACCATTCTCTCTTGCAGCAGT 59.650 47.619 0.00 0.00 0.00 4.40
1524 2100 2.739885 TTCTCTCTTGCAGCAGTCTC 57.260 50.000 0.00 0.00 0.00 3.36
1525 2101 1.625511 TCTCTCTTGCAGCAGTCTCA 58.374 50.000 0.00 0.00 0.00 3.27
1526 2102 2.177734 TCTCTCTTGCAGCAGTCTCAT 58.822 47.619 0.00 0.00 0.00 2.90
1527 2103 2.094130 TCTCTCTTGCAGCAGTCTCATG 60.094 50.000 0.00 0.00 0.00 3.07
1528 2104 0.727970 CTCTTGCAGCAGTCTCATGC 59.272 55.000 0.00 0.00 46.88 4.06
1693 2290 5.894964 AGTGAGATCTCCTCCCTTTAAGTAC 59.105 44.000 20.03 6.58 41.25 2.73
1694 2291 5.657302 GTGAGATCTCCTCCCTTTAAGTACA 59.343 44.000 20.03 0.00 41.25 2.90
1695 2292 5.657302 TGAGATCTCCTCCCTTTAAGTACAC 59.343 44.000 20.03 0.00 41.25 2.90
1696 2293 5.590818 AGATCTCCTCCCTTTAAGTACACA 58.409 41.667 0.00 0.00 0.00 3.72
1697 2294 5.422650 AGATCTCCTCCCTTTAAGTACACAC 59.577 44.000 0.00 0.00 0.00 3.82
1701 2298 4.527038 TCCTCCCTTTAAGTACACACAGAG 59.473 45.833 0.00 0.00 0.00 3.35
1740 2343 3.667497 TCCAAGCTATATTGCTCCTCG 57.333 47.619 12.14 2.25 43.24 4.63
1902 2517 4.327680 GGGTTCAAGAATGAGTACTTGCT 58.672 43.478 0.00 0.00 41.91 3.91
1903 2518 4.762251 GGGTTCAAGAATGAGTACTTGCTT 59.238 41.667 0.00 0.00 41.91 3.91
1906 2521 6.348050 GGTTCAAGAATGAGTACTTGCTTCTG 60.348 42.308 13.20 9.36 41.91 3.02
1908 2523 6.993079 TCAAGAATGAGTACTTGCTTCTGTA 58.007 36.000 13.20 5.50 41.91 2.74
1931 2552 1.971695 GGGTTTCAGCCCGTCCTTG 60.972 63.158 0.00 0.00 39.17 3.61
1947 2568 1.613836 CTTGTGCTTCCCTGCTCTTT 58.386 50.000 0.00 0.00 0.00 2.52
1968 2589 9.317936 CTCTTTTCCTTTTTCTGTATGCTTTTT 57.682 29.630 0.00 0.00 0.00 1.94
2004 2625 5.987953 TGACTTGATGAGAGACAGAAACAAG 59.012 40.000 0.00 0.00 36.50 3.16
2006 2627 4.613925 TGATGAGAGACAGAAACAAGCT 57.386 40.909 0.00 0.00 0.00 3.74
2007 2628 5.728637 TGATGAGAGACAGAAACAAGCTA 57.271 39.130 0.00 0.00 0.00 3.32
2008 2629 5.473931 TGATGAGAGACAGAAACAAGCTAC 58.526 41.667 0.00 0.00 0.00 3.58
2015 2637 6.019779 AGACAGAAACAAGCTACTACTCTG 57.980 41.667 9.84 9.84 35.92 3.35
2032 2654 5.613358 ACTCTGCATTTTAGTTTCTTCCG 57.387 39.130 0.00 0.00 0.00 4.30
2121 2743 1.021390 CGGATTGCCACACCAGAGTC 61.021 60.000 0.00 0.00 0.00 3.36
2134 2756 2.840651 ACCAGAGTCCTTATCCAACCAG 59.159 50.000 0.00 0.00 0.00 4.00
2202 2824 3.068560 ACGTGCCGCAAGTTTCTTATAA 58.931 40.909 6.09 0.00 0.00 0.98
2246 2868 1.450312 GTGATGCGTCTTCAGGGGG 60.450 63.158 7.58 0.00 0.00 5.40
2298 2925 2.029073 ACGGTGAACTCAGCCGTG 59.971 61.111 18.94 4.00 45.12 4.94
2450 3077 3.050275 GCAGTCAAGGCCGTGGAC 61.050 66.667 19.08 16.39 0.00 4.02
2523 3150 1.690219 CCTCCATGAAGGACCTCGGG 61.690 65.000 0.00 0.00 43.07 5.14
2550 3177 4.393155 AACGCCAGCGCCATCTCA 62.393 61.111 12.72 0.00 44.19 3.27
2796 3433 3.315142 ATTCTGGCTTCCGCGAGCA 62.315 57.895 19.83 6.88 44.49 4.26
2797 3434 2.599645 ATTCTGGCTTCCGCGAGCAT 62.600 55.000 19.83 3.72 44.49 3.79
2826 3463 2.579241 CTTGTGCTCTGCTCATGCGC 62.579 60.000 0.00 0.00 43.34 6.09
2928 3569 3.081133 CATGACTACGTGCCGTGC 58.919 61.111 10.01 1.68 41.39 5.34
3149 3790 3.785859 ACCATGACCATCGCCGCT 61.786 61.111 0.00 0.00 0.00 5.52
3177 3818 2.456119 CGCCATGACTGTCTTCGGC 61.456 63.158 19.23 19.23 36.16 5.54
3256 3897 3.119096 GGTGAGAAACGCCGGAGC 61.119 66.667 5.05 0.00 39.46 4.70
3274 3915 1.884464 CTGCTGGTATGTGCGCGAT 60.884 57.895 12.10 0.00 0.00 4.58
3320 3964 5.826208 AGATGAGCAGCATTCAATTCATGTA 59.174 36.000 0.00 0.00 37.34 2.29
3405 4049 0.039617 TTGAAATTTGTGGAGCGGCG 60.040 50.000 0.51 0.51 0.00 6.46
3419 4063 2.349755 GGCGGTTTACCAGCTCCA 59.650 61.111 12.87 0.00 36.36 3.86
3447 4091 2.023015 TCAGGATTTCTAGGAGCTGGGA 60.023 50.000 0.00 0.00 0.00 4.37
3455 4099 0.976073 TAGGAGCTGGGAGGTTTCCG 60.976 60.000 0.00 0.00 45.04 4.30
3542 4195 5.682234 TGAGTGGCATTCTTCTAATCTGA 57.318 39.130 11.47 0.00 0.00 3.27
3609 4276 6.851836 AGGTTCCTCCTCAAATATCAGGAATA 59.148 38.462 2.17 0.00 44.42 1.75
3613 4280 8.980481 TCCTCCTCAAATATCAGGAATAAAAC 57.020 34.615 0.00 0.00 38.39 2.43
3647 5586 2.285977 CGGGGTATTCCTTCTTTTCGG 58.714 52.381 0.00 0.00 35.33 4.30
3649 5588 3.620472 CGGGGTATTCCTTCTTTTCGGAA 60.620 47.826 0.00 0.00 42.96 4.30
3650 5589 4.338012 GGGGTATTCCTTCTTTTCGGAAA 58.662 43.478 0.00 0.00 42.16 3.13
3651 5590 4.768448 GGGGTATTCCTTCTTTTCGGAAAA 59.232 41.667 14.64 14.64 42.16 2.29
3652 5591 5.244402 GGGGTATTCCTTCTTTTCGGAAAAA 59.756 40.000 15.99 2.86 42.16 1.94
3672 5611 4.718940 AAAACTCCCAAAATATGCGGAG 57.281 40.909 0.00 0.00 45.10 4.63
3673 5612 2.348411 ACTCCCAAAATATGCGGAGG 57.652 50.000 6.88 0.00 44.46 4.30
3674 5613 0.954452 CTCCCAAAATATGCGGAGGC 59.046 55.000 0.00 0.00 40.26 4.70
3675 5614 0.467290 TCCCAAAATATGCGGAGGCC 60.467 55.000 0.00 0.00 38.85 5.19
3685 5624 2.735237 CGGAGGCCGGGAGTATTC 59.265 66.667 2.18 0.00 44.15 1.75
3686 5625 2.868986 CGGAGGCCGGGAGTATTCC 61.869 68.421 2.18 0.00 44.15 3.01
3687 5626 1.459730 GGAGGCCGGGAGTATTCCT 60.460 63.158 2.18 0.00 43.49 3.36
3688 5627 1.473497 GGAGGCCGGGAGTATTCCTC 61.473 65.000 12.24 12.24 43.49 3.71
3721 5660 6.432403 AAAAACTCCCCAAAATATGCAGAA 57.568 33.333 0.00 0.00 0.00 3.02
3726 5665 1.067516 CCCAAAATATGCAGAAGCCGG 59.932 52.381 0.00 0.00 41.13 6.13
3734 5673 0.108585 TGCAGAAGCCGGGGATATTC 59.891 55.000 2.18 0.00 41.13 1.75
3737 5676 1.421646 CAGAAGCCGGGGATATTCCTT 59.578 52.381 2.18 0.00 36.57 3.36
3742 5681 2.514160 AGCCGGGGATATTCCTTCTTTT 59.486 45.455 2.18 0.00 36.57 2.27
3743 5682 3.052869 AGCCGGGGATATTCCTTCTTTTT 60.053 43.478 2.18 0.00 36.57 1.94
3747 5686 5.420739 CCGGGGATATTCCTTCTTTTTGAAA 59.579 40.000 0.00 0.00 36.57 2.69
3748 5687 6.071051 CCGGGGATATTCCTTCTTTTTGAAAA 60.071 38.462 0.00 0.00 36.57 2.29
3749 5688 7.382898 CGGGGATATTCCTTCTTTTTGAAAAA 58.617 34.615 0.00 2.83 36.57 1.94
3772 5711 7.719778 AAACTCCTCAAAATCAAAATTCTGC 57.280 32.000 0.00 0.00 0.00 4.26
3773 5712 6.409524 ACTCCTCAAAATCAAAATTCTGCA 57.590 33.333 0.00 0.00 0.00 4.41
3774 5713 6.819284 ACTCCTCAAAATCAAAATTCTGCAA 58.181 32.000 0.00 0.00 0.00 4.08
3775 5714 7.274447 ACTCCTCAAAATCAAAATTCTGCAAA 58.726 30.769 0.00 0.00 0.00 3.68
3776 5715 7.769970 ACTCCTCAAAATCAAAATTCTGCAAAA 59.230 29.630 0.00 0.00 0.00 2.44
3777 5716 8.145316 TCCTCAAAATCAAAATTCTGCAAAAG 57.855 30.769 0.00 0.00 0.00 2.27
3778 5717 6.854381 CCTCAAAATCAAAATTCTGCAAAAGC 59.146 34.615 0.00 0.00 0.00 3.51
3779 5718 7.317842 TCAAAATCAAAATTCTGCAAAAGCA 57.682 28.000 0.00 0.00 0.00 3.91
3780 5719 7.759465 TCAAAATCAAAATTCTGCAAAAGCAA 58.241 26.923 0.00 0.00 0.00 3.91
3781 5720 8.242053 TCAAAATCAAAATTCTGCAAAAGCAAA 58.758 25.926 0.00 0.00 0.00 3.68
3782 5721 9.026074 CAAAATCAAAATTCTGCAAAAGCAAAT 57.974 25.926 0.00 0.00 0.00 2.32
3783 5722 8.791355 AAATCAAAATTCTGCAAAAGCAAATC 57.209 26.923 0.00 0.00 0.00 2.17
3784 5723 6.922247 TCAAAATTCTGCAAAAGCAAATCA 57.078 29.167 0.00 0.00 0.00 2.57
3785 5724 7.499321 TCAAAATTCTGCAAAAGCAAATCAT 57.501 28.000 0.00 0.00 0.00 2.45
3786 5725 7.932335 TCAAAATTCTGCAAAAGCAAATCATT 58.068 26.923 0.00 0.00 0.00 2.57
3787 5726 8.407064 TCAAAATTCTGCAAAAGCAAATCATTT 58.593 25.926 0.00 0.00 0.00 2.32
3788 5727 8.687301 CAAAATTCTGCAAAAGCAAATCATTTC 58.313 29.630 0.00 0.00 0.00 2.17
3789 5728 7.499321 AATTCTGCAAAAGCAAATCATTTCA 57.501 28.000 0.00 0.00 0.00 2.69
3790 5729 6.922247 TTCTGCAAAAGCAAATCATTTCAA 57.078 29.167 0.00 0.00 0.00 2.69
3791 5730 6.922247 TCTGCAAAAGCAAATCATTTCAAA 57.078 29.167 0.00 0.00 0.00 2.69
3792 5731 6.717413 TCTGCAAAAGCAAATCATTTCAAAC 58.283 32.000 0.00 0.00 0.00 2.93
3793 5732 6.539464 TCTGCAAAAGCAAATCATTTCAAACT 59.461 30.769 0.00 0.00 0.00 2.66
3794 5733 6.487960 TGCAAAAGCAAATCATTTCAAACTG 58.512 32.000 0.00 0.00 0.00 3.16
3795 5734 6.315642 TGCAAAAGCAAATCATTTCAAACTGA 59.684 30.769 0.00 0.00 0.00 3.41
3796 5735 7.148289 TGCAAAAGCAAATCATTTCAAACTGAA 60.148 29.630 0.00 0.00 34.03 3.02
3813 5752 9.912634 TCAAACTGAAATTGGAATTCATTAGAC 57.087 29.630 7.93 0.00 36.30 2.59
3814 5753 8.853345 CAAACTGAAATTGGAATTCATTAGACG 58.147 33.333 7.93 0.00 36.30 4.18
3815 5754 7.921786 ACTGAAATTGGAATTCATTAGACGA 57.078 32.000 7.93 0.00 36.30 4.20
3816 5755 7.752695 ACTGAAATTGGAATTCATTAGACGAC 58.247 34.615 7.93 0.00 36.30 4.34
3817 5756 7.390440 ACTGAAATTGGAATTCATTAGACGACA 59.610 33.333 7.93 0.00 36.30 4.35
3818 5757 8.279970 TGAAATTGGAATTCATTAGACGACAT 57.720 30.769 7.93 0.00 32.10 3.06
3819 5758 8.183536 TGAAATTGGAATTCATTAGACGACATG 58.816 33.333 7.93 0.00 32.10 3.21
3820 5759 5.484173 TTGGAATTCATTAGACGACATGC 57.516 39.130 7.93 0.00 0.00 4.06
3821 5760 4.769688 TGGAATTCATTAGACGACATGCT 58.230 39.130 7.93 0.00 0.00 3.79
3822 5761 4.571984 TGGAATTCATTAGACGACATGCTG 59.428 41.667 7.93 0.00 0.00 4.41
3823 5762 4.521943 GAATTCATTAGACGACATGCTGC 58.478 43.478 0.00 0.00 0.00 5.25
3824 5763 1.559831 TCATTAGACGACATGCTGCG 58.440 50.000 0.00 0.00 0.00 5.18
3825 5764 1.135112 TCATTAGACGACATGCTGCGT 60.135 47.619 8.35 8.35 44.33 5.24
3826 5765 2.098443 TCATTAGACGACATGCTGCGTA 59.902 45.455 8.55 0.00 41.34 4.42
3827 5766 2.188837 TTAGACGACATGCTGCGTAG 57.811 50.000 8.55 0.00 41.34 3.51
3828 5767 1.092348 TAGACGACATGCTGCGTAGT 58.908 50.000 8.55 0.00 41.34 2.73
3829 5768 0.243907 AGACGACATGCTGCGTAGTT 59.756 50.000 8.55 0.00 41.34 2.24
3830 5769 1.471287 AGACGACATGCTGCGTAGTTA 59.529 47.619 8.55 0.00 41.34 2.24
3831 5770 2.099263 AGACGACATGCTGCGTAGTTAT 59.901 45.455 8.55 0.00 41.34 1.89
3832 5771 3.314357 AGACGACATGCTGCGTAGTTATA 59.686 43.478 8.55 0.00 41.34 0.98
3833 5772 3.369385 ACGACATGCTGCGTAGTTATAC 58.631 45.455 1.53 0.00 39.21 1.47
3834 5773 3.181494 ACGACATGCTGCGTAGTTATACA 60.181 43.478 1.53 0.00 39.21 2.29
3835 5774 3.981416 CGACATGCTGCGTAGTTATACAT 59.019 43.478 1.53 0.00 31.76 2.29
3836 5775 4.444388 CGACATGCTGCGTAGTTATACATT 59.556 41.667 1.53 0.00 31.76 2.71
3837 5776 5.051039 CGACATGCTGCGTAGTTATACATTT 60.051 40.000 1.53 0.00 31.76 2.32
3838 5777 6.143278 CGACATGCTGCGTAGTTATACATTTA 59.857 38.462 1.53 0.00 31.76 1.40
3839 5778 7.408132 ACATGCTGCGTAGTTATACATTTAG 57.592 36.000 1.53 0.00 31.76 1.85
3840 5779 7.207383 ACATGCTGCGTAGTTATACATTTAGA 58.793 34.615 1.53 0.00 31.76 2.10
3841 5780 7.872993 ACATGCTGCGTAGTTATACATTTAGAT 59.127 33.333 1.53 0.00 31.76 1.98
3842 5781 9.353999 CATGCTGCGTAGTTATACATTTAGATA 57.646 33.333 1.53 0.00 31.76 1.98
3843 5782 8.738199 TGCTGCGTAGTTATACATTTAGATAC 57.262 34.615 1.53 0.00 31.76 2.24
3844 5783 8.354426 TGCTGCGTAGTTATACATTTAGATACA 58.646 33.333 1.53 0.00 31.76 2.29
3845 5784 9.188588 GCTGCGTAGTTATACATTTAGATACAA 57.811 33.333 1.53 0.00 31.76 2.41
3858 5797 8.888716 ACATTTAGATACAATCATAAACACGCA 58.111 29.630 0.00 0.00 0.00 5.24
3859 5798 9.882996 CATTTAGATACAATCATAAACACGCAT 57.117 29.630 0.00 0.00 0.00 4.73
3861 5800 8.887036 TTAGATACAATCATAAACACGCATCT 57.113 30.769 0.00 0.00 0.00 2.90
3862 5801 7.792374 AGATACAATCATAAACACGCATCTT 57.208 32.000 0.00 0.00 0.00 2.40
3863 5802 8.213518 AGATACAATCATAAACACGCATCTTT 57.786 30.769 0.00 0.00 0.00 2.52
3864 5803 8.338259 AGATACAATCATAAACACGCATCTTTC 58.662 33.333 0.00 0.00 0.00 2.62
3865 5804 6.500684 ACAATCATAAACACGCATCTTTCT 57.499 33.333 0.00 0.00 0.00 2.52
3866 5805 6.913170 ACAATCATAAACACGCATCTTTCTT 58.087 32.000 0.00 0.00 0.00 2.52
3867 5806 6.803320 ACAATCATAAACACGCATCTTTCTTG 59.197 34.615 0.00 0.00 0.00 3.02
3868 5807 4.722194 TCATAAACACGCATCTTTCTTGC 58.278 39.130 0.00 0.00 36.74 4.01
3869 5808 2.422276 AAACACGCATCTTTCTTGCC 57.578 45.000 0.00 0.00 36.75 4.52
3870 5809 0.598065 AACACGCATCTTTCTTGCCC 59.402 50.000 0.00 0.00 36.75 5.36
3879 5818 4.625083 GCATCTTTCTTGCCCTCTTAGAGT 60.625 45.833 8.55 0.00 33.95 3.24
3932 5872 1.577328 AAAAGCGTATGCAGCGTGCT 61.577 50.000 10.11 7.39 45.31 4.40
3992 5933 1.450025 GGCCGCTGTAAACTTTAGCT 58.550 50.000 0.00 0.00 35.36 3.32
4001 5944 1.429463 AAACTTTAGCTCGCGTGAGG 58.571 50.000 26.24 12.26 42.79 3.86
4016 5959 3.388703 GAGGAGCTCCAGCAGGCAG 62.389 68.421 33.90 0.00 45.16 4.85
4034 5983 1.369930 GTGCAAACTTTAGCGCGCA 60.370 52.632 35.10 16.82 35.03 6.09
4053 6045 2.222931 GCACGCGCTCAAACAACATATA 60.223 45.455 5.73 0.00 34.30 0.86
4054 6046 3.546020 GCACGCGCTCAAACAACATATAT 60.546 43.478 5.73 0.00 34.30 0.86
4057 6049 4.085261 ACGCGCTCAAACAACATATATACG 60.085 41.667 5.73 0.00 0.00 3.06
4068 6065 8.422973 AACAACATATATACGCCGAACTAAAA 57.577 30.769 0.00 0.00 0.00 1.52
4069 6066 8.597662 ACAACATATATACGCCGAACTAAAAT 57.402 30.769 0.00 0.00 0.00 1.82
4131 6284 6.546972 TTTCACAATGCGTACATAGTTCAA 57.453 33.333 0.00 0.00 34.62 2.69
4138 6294 7.012327 ACAATGCGTACATAGTTCAAAGCATAT 59.988 33.333 0.00 0.00 42.34 1.78
4142 6298 9.869757 TGCGTACATAGTTCAAAGCATATATAT 57.130 29.630 0.00 0.00 0.00 0.86
4156 6315 7.640597 AGCATATATATAGAACTACGGTGCA 57.359 36.000 10.29 0.00 0.00 4.57
4158 6317 7.974501 AGCATATATATAGAACTACGGTGCAAC 59.025 37.037 10.29 0.00 0.00 4.17
4159 6318 7.974501 GCATATATATAGAACTACGGTGCAACT 59.025 37.037 0.00 0.00 36.74 3.16
4160 6319 9.856488 CATATATATAGAACTACGGTGCAACTT 57.144 33.333 0.00 0.00 36.74 2.66
4161 6320 9.856488 ATATATATAGAACTACGGTGCAACTTG 57.144 33.333 0.00 0.00 36.74 3.16
4163 6322 3.402628 AGAACTACGGTGCAACTTGAT 57.597 42.857 0.00 0.00 36.74 2.57
4164 6323 4.530710 AGAACTACGGTGCAACTTGATA 57.469 40.909 0.00 0.00 36.74 2.15
4169 6375 5.754778 ACTACGGTGCAACTTGATAAAAAC 58.245 37.500 0.00 0.00 36.74 2.43
4170 6376 4.911514 ACGGTGCAACTTGATAAAAACT 57.088 36.364 0.00 0.00 36.74 2.66
4340 6848 4.681978 GTGCCTTCCACCGACGCT 62.682 66.667 0.00 0.00 38.55 5.07
4343 6851 2.342279 CCTTCCACCGACGCTTGA 59.658 61.111 0.00 0.00 0.00 3.02
4523 7073 4.381612 CCTGTTCTGTTATAAGACGAGGCA 60.382 45.833 0.00 0.00 0.00 4.75
4531 7081 2.798445 TAAGACGAGGCAGAGGGGCA 62.798 60.000 0.00 0.00 46.44 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.761504 GTCATCAGTGTATCTGTAGTAGTACTA 57.238 37.037 5.90 5.90 43.97 1.82
2 3 8.265764 TGTCATCAGTGTATCTGTAGTAGTACT 58.734 37.037 8.14 8.14 43.97 2.73
3 4 8.336806 GTGTCATCAGTGTATCTGTAGTAGTAC 58.663 40.741 0.37 0.37 43.97 2.73
6 7 6.511929 CGGTGTCATCAGTGTATCTGTAGTAG 60.512 46.154 0.00 0.00 43.97 2.57
9 10 4.602006 CGGTGTCATCAGTGTATCTGTAG 58.398 47.826 0.00 0.00 43.97 2.74
77 79 0.460311 CGGCTGAATCTACCCGTCTT 59.540 55.000 0.00 0.00 36.18 3.01
81 83 1.300233 GAGCGGCTGAATCTACCCG 60.300 63.158 7.50 0.00 43.38 5.28
82 84 1.069935 GGAGCGGCTGAATCTACCC 59.930 63.158 7.50 0.00 0.00 3.69
159 161 1.577328 CGTTCAGGTGCGCCAAATCT 61.577 55.000 20.59 0.00 37.19 2.40
224 229 2.814336 ACTCCAAATTCTTCAGTTCCGC 59.186 45.455 0.00 0.00 0.00 5.54
330 349 6.126863 TGGATAACATGTAGGGAATCCATC 57.873 41.667 16.59 0.00 38.31 3.51
331 350 6.529084 TTGGATAACATGTAGGGAATCCAT 57.471 37.500 19.21 0.00 41.73 3.41
332 351 5.985175 TTGGATAACATGTAGGGAATCCA 57.015 39.130 16.59 16.59 40.75 3.41
393 416 3.264964 GGAAGTAATTGTCTGGTACCCCA 59.735 47.826 10.07 0.21 38.87 4.96
587 616 5.897377 AATTGAGCGTTTTAAGCCACTAT 57.103 34.783 0.00 0.00 34.64 2.12
591 620 6.804770 TTACTAATTGAGCGTTTTAAGCCA 57.195 33.333 0.00 0.00 34.64 4.75
630 661 9.918630 CATCATCAGTGTGTGTCTATGATAATA 57.081 33.333 0.00 0.00 33.49 0.98
631 662 8.645110 TCATCATCAGTGTGTGTCTATGATAAT 58.355 33.333 0.00 0.00 33.49 1.28
632 663 8.010733 TCATCATCAGTGTGTGTCTATGATAA 57.989 34.615 0.00 0.00 33.49 1.75
633 664 7.587037 TCATCATCAGTGTGTGTCTATGATA 57.413 36.000 0.00 0.00 33.49 2.15
634 665 6.475596 TCATCATCAGTGTGTGTCTATGAT 57.524 37.500 0.00 0.00 35.11 2.45
635 666 5.920193 TCATCATCAGTGTGTGTCTATGA 57.080 39.130 0.00 0.00 0.00 2.15
636 667 8.828688 ATTATCATCATCAGTGTGTGTCTATG 57.171 34.615 0.00 0.00 0.00 2.23
638 669 9.971922 CTAATTATCATCATCAGTGTGTGTCTA 57.028 33.333 0.00 0.00 0.00 2.59
639 670 8.699130 TCTAATTATCATCATCAGTGTGTGTCT 58.301 33.333 0.00 0.00 0.00 3.41
640 671 8.759641 GTCTAATTATCATCATCAGTGTGTGTC 58.240 37.037 0.00 0.00 0.00 3.67
641 672 7.712639 GGTCTAATTATCATCATCAGTGTGTGT 59.287 37.037 0.00 0.00 0.00 3.72
642 673 7.712205 TGGTCTAATTATCATCATCAGTGTGTG 59.288 37.037 0.00 0.00 0.00 3.82
677 726 7.016153 TGGTGTACTGATTTCCAAGATAAGT 57.984 36.000 0.00 0.00 0.00 2.24
744 806 3.426159 GCATTGAACCATTGTACACTCGG 60.426 47.826 0.00 0.00 0.00 4.63
745 807 3.188254 TGCATTGAACCATTGTACACTCG 59.812 43.478 0.00 0.00 0.00 4.18
814 906 3.907260 TTGAGGCTCCAAGGCAGCG 62.907 63.158 12.86 0.00 44.19 5.18
887 984 9.160496 CGTCCCTCGTAGAAGTATTATTAGTAT 57.840 37.037 0.00 0.00 34.09 2.12
888 985 7.118390 GCGTCCCTCGTAGAAGTATTATTAGTA 59.882 40.741 0.00 0.00 42.13 1.82
889 986 6.072783 GCGTCCCTCGTAGAAGTATTATTAGT 60.073 42.308 0.00 0.00 42.13 2.24
890 987 6.072838 TGCGTCCCTCGTAGAAGTATTATTAG 60.073 42.308 0.00 0.00 42.13 1.73
953 1050 6.094742 TGAAAAAGAAAGAAAAACCCAATGGC 59.905 34.615 0.00 0.00 33.59 4.40
961 1058 7.127917 TGCAAGGTGAAAAAGAAAGAAAAAC 57.872 32.000 0.00 0.00 0.00 2.43
1041 1142 0.041684 AAGGCATTTGGAAGGGGAGG 59.958 55.000 0.00 0.00 0.00 4.30
1047 1148 2.773993 ATTGGCAAGGCATTTGGAAG 57.226 45.000 5.96 0.00 37.26 3.46
1076 1177 0.237235 TCACAAAGCGATTTCGTGCC 59.763 50.000 17.86 0.00 42.22 5.01
1087 1188 2.163211 GAGGAGGAGCAATTCACAAAGC 59.837 50.000 0.00 0.00 0.00 3.51
1255 1767 1.457831 ATGGAGGTCCGGCTAGGTC 60.458 63.158 0.00 0.00 41.99 3.85
1256 1768 1.457831 GATGGAGGTCCGGCTAGGT 60.458 63.158 0.00 0.00 41.99 3.08
1258 1770 2.223803 ATAGATGGAGGTCCGGCTAG 57.776 55.000 0.00 0.00 39.43 3.42
1259 1771 2.110188 AGAATAGATGGAGGTCCGGCTA 59.890 50.000 0.00 0.00 39.43 3.93
1264 1795 5.240403 GCATGAAAAGAATAGATGGAGGTCC 59.760 44.000 0.00 0.00 0.00 4.46
1266 1797 4.818546 CGCATGAAAAGAATAGATGGAGGT 59.181 41.667 0.00 0.00 0.00 3.85
1337 1898 7.012799 GGAAGAAAGGAGATGGAAATGATACAC 59.987 40.741 0.00 0.00 0.00 2.90
1521 2097 0.883370 GCCTGATGATGCGCATGAGA 60.883 55.000 30.76 11.91 40.22 3.27
1524 2100 1.282875 CAGCCTGATGATGCGCATG 59.717 57.895 30.76 13.49 37.34 4.06
1525 2101 0.750546 AACAGCCTGATGATGCGCAT 60.751 50.000 25.66 25.66 40.77 4.73
1526 2102 1.377594 AACAGCCTGATGATGCGCA 60.378 52.632 14.96 14.96 0.00 6.09
1527 2103 1.063649 CAACAGCCTGATGATGCGC 59.936 57.895 0.00 0.00 0.00 6.09
1528 2104 1.089112 TTCAACAGCCTGATGATGCG 58.911 50.000 5.44 0.00 29.25 4.73
1693 2290 2.422597 ACGTCTCTCTCTCTCTGTGTG 58.577 52.381 0.00 0.00 0.00 3.82
1694 2291 2.851263 ACGTCTCTCTCTCTCTGTGT 57.149 50.000 0.00 0.00 0.00 3.72
1695 2292 3.857052 AGTACGTCTCTCTCTCTCTGTG 58.143 50.000 0.00 0.00 0.00 3.66
1696 2293 5.864418 ATAGTACGTCTCTCTCTCTCTGT 57.136 43.478 0.00 0.00 0.00 3.41
1697 2294 7.033791 GGATATAGTACGTCTCTCTCTCTCTG 58.966 46.154 0.00 0.00 0.00 3.35
1701 2298 6.091713 GCTTGGATATAGTACGTCTCTCTCTC 59.908 46.154 0.00 0.00 0.00 3.20
1740 2343 3.146847 CAAGAACCAACCCTACAAGACC 58.853 50.000 0.00 0.00 0.00 3.85
1902 2517 3.219281 GGCTGAAACCCAAGTTACAGAA 58.781 45.455 0.00 0.00 34.19 3.02
1903 2518 2.858745 GGCTGAAACCCAAGTTACAGA 58.141 47.619 0.00 0.00 34.19 3.41
1931 2552 0.884514 GGAAAAGAGCAGGGAAGCAC 59.115 55.000 0.00 0.00 36.85 4.40
1947 2568 7.951591 AGCTAAAAAGCATACAGAAAAAGGAA 58.048 30.769 0.00 0.00 37.25 3.36
1968 2589 8.753133 TCTCTCATCAAGTCAAGAATAAAGCTA 58.247 33.333 0.00 0.00 0.00 3.32
2004 2625 7.835634 AGAAACTAAAATGCAGAGTAGTAGC 57.164 36.000 6.44 3.30 0.00 3.58
2006 2627 7.544566 CGGAAGAAACTAAAATGCAGAGTAGTA 59.455 37.037 6.44 0.00 0.00 1.82
2007 2628 6.369065 CGGAAGAAACTAAAATGCAGAGTAGT 59.631 38.462 0.00 0.00 0.00 2.73
2008 2629 6.369065 ACGGAAGAAACTAAAATGCAGAGTAG 59.631 38.462 0.00 0.00 0.00 2.57
2015 2637 5.106673 ACTGCTACGGAAGAAACTAAAATGC 60.107 40.000 0.00 0.00 0.00 3.56
2032 2654 4.207224 CACGCATACTAATCACACTGCTAC 59.793 45.833 0.00 0.00 0.00 3.58
2121 2743 4.162040 AGCAAGATCTGGTTGGATAAGG 57.838 45.455 0.00 0.00 28.96 2.69
2265 2887 0.541863 CCGTGCCCTTCCTTATCTGT 59.458 55.000 0.00 0.00 0.00 3.41
2523 3150 2.358737 CTGGCGTTGGTGGAGGAC 60.359 66.667 0.00 0.00 0.00 3.85
2578 3205 0.179000 ATGAGGAGGAACATGGCGAC 59.821 55.000 0.00 0.00 0.00 5.19
2796 3433 0.886563 GAGCACAAGGAAAGCAGCAT 59.113 50.000 0.00 0.00 0.00 3.79
2797 3434 0.179009 AGAGCACAAGGAAAGCAGCA 60.179 50.000 0.00 0.00 0.00 4.41
2806 3443 1.801332 GCATGAGCAGAGCACAAGG 59.199 57.895 0.00 0.00 41.58 3.61
2940 3581 0.683973 AGGTTCAGGTGAGACAGCAG 59.316 55.000 0.00 0.00 33.95 4.24
3149 3790 1.377202 GTCATGGCGGCAGAAAGGA 60.377 57.895 19.29 6.88 0.00 3.36
3193 3834 5.824624 ACAGATTACAGGCAAACATGATAGG 59.175 40.000 0.00 0.00 0.00 2.57
3196 3837 8.432013 TCTATACAGATTACAGGCAAACATGAT 58.568 33.333 0.00 0.00 0.00 2.45
3234 3875 1.087771 CCGGCGTTTCTCACCATACC 61.088 60.000 6.01 0.00 0.00 2.73
3256 3897 1.884464 ATCGCGCACATACCAGCAG 60.884 57.895 8.75 0.00 0.00 4.24
3274 3915 2.225091 ACCATCAGTCCAGCATTTTCCA 60.225 45.455 0.00 0.00 0.00 3.53
3320 3964 2.040178 CTCCGAACAGGGCCTAACTAT 58.960 52.381 5.28 0.00 41.52 2.12
3364 4008 2.680352 GACTCCACCTGCTCCGGA 60.680 66.667 2.93 2.93 0.00 5.14
3405 4049 2.152016 GAGTTGTGGAGCTGGTAAACC 58.848 52.381 0.00 0.00 0.00 3.27
3419 4063 4.161377 GCTCCTAGAAATCCTGAGAGTTGT 59.839 45.833 0.00 0.00 28.55 3.32
3447 4091 0.554305 AAGGGGTTGTTCGGAAACCT 59.446 50.000 10.55 3.35 45.40 3.50
3455 4099 1.675116 GGCGAGACTAAGGGGTTGTTC 60.675 57.143 0.00 0.00 0.00 3.18
3609 4276 1.270252 CCGGCCTCTGCATTTTGTTTT 60.270 47.619 0.00 0.00 40.13 2.43
3613 4280 2.713967 CCCCGGCCTCTGCATTTTG 61.714 63.158 0.00 0.00 40.13 2.44
3650 5589 4.081697 CCTCCGCATATTTTGGGAGTTTTT 60.082 41.667 5.33 0.00 39.40 1.94
3651 5590 3.447229 CCTCCGCATATTTTGGGAGTTTT 59.553 43.478 5.33 0.00 39.40 2.43
3652 5591 3.023832 CCTCCGCATATTTTGGGAGTTT 58.976 45.455 5.33 0.00 39.40 2.66
3653 5592 2.654863 CCTCCGCATATTTTGGGAGTT 58.345 47.619 5.33 0.00 39.40 3.01
3654 5593 1.750682 GCCTCCGCATATTTTGGGAGT 60.751 52.381 5.33 0.00 39.40 3.85
3655 5594 0.954452 GCCTCCGCATATTTTGGGAG 59.046 55.000 0.00 0.00 40.62 4.30
3656 5595 0.467290 GGCCTCCGCATATTTTGGGA 60.467 55.000 0.00 0.00 40.62 4.37
3657 5596 1.795170 CGGCCTCCGCATATTTTGGG 61.795 60.000 0.00 0.00 41.17 4.12
3658 5597 1.654220 CGGCCTCCGCATATTTTGG 59.346 57.895 0.00 0.00 41.17 3.28
3659 5598 1.654220 CCGGCCTCCGCATATTTTG 59.346 57.895 0.00 0.00 46.86 2.44
3660 5599 1.528309 CCCGGCCTCCGCATATTTT 60.528 57.895 0.00 0.00 46.86 1.82
3661 5600 2.113139 CCCGGCCTCCGCATATTT 59.887 61.111 0.00 0.00 46.86 1.40
3662 5601 2.847234 TCCCGGCCTCCGCATATT 60.847 61.111 0.00 0.00 46.86 1.28
3663 5602 2.725127 TACTCCCGGCCTCCGCATAT 62.725 60.000 0.00 0.00 46.86 1.78
3664 5603 2.725127 ATACTCCCGGCCTCCGCATA 62.725 60.000 0.00 0.00 46.86 3.14
3665 5604 4.853142 TACTCCCGGCCTCCGCAT 62.853 66.667 0.00 0.00 46.86 4.73
3666 5605 4.853142 ATACTCCCGGCCTCCGCA 62.853 66.667 0.00 0.00 46.86 5.69
3667 5606 3.516866 GAATACTCCCGGCCTCCGC 62.517 68.421 0.00 0.00 46.86 5.54
3669 5608 1.459730 AGGAATACTCCCGGCCTCC 60.460 63.158 0.00 0.00 43.64 4.30
3670 5609 2.051105 GAGGAATACTCCCGGCCTC 58.949 63.158 0.00 6.31 43.64 4.70
3671 5610 4.297207 GAGGAATACTCCCGGCCT 57.703 61.111 0.00 0.00 43.64 5.19
3718 5657 1.700186 GAAGGAATATCCCCGGCTTCT 59.300 52.381 0.00 0.00 37.19 2.85
3719 5658 1.700186 AGAAGGAATATCCCCGGCTTC 59.300 52.381 0.00 0.44 37.19 3.86
3721 5660 1.821088 AAGAAGGAATATCCCCGGCT 58.179 50.000 0.00 0.00 37.19 5.52
3747 5686 7.769970 TGCAGAATTTTGATTTTGAGGAGTTTT 59.230 29.630 0.00 0.00 0.00 2.43
3748 5687 7.274447 TGCAGAATTTTGATTTTGAGGAGTTT 58.726 30.769 0.00 0.00 0.00 2.66
3749 5688 6.819284 TGCAGAATTTTGATTTTGAGGAGTT 58.181 32.000 0.00 0.00 0.00 3.01
3750 5689 6.409524 TGCAGAATTTTGATTTTGAGGAGT 57.590 33.333 0.00 0.00 0.00 3.85
3751 5690 7.718272 TTTGCAGAATTTTGATTTTGAGGAG 57.282 32.000 0.00 0.00 0.00 3.69
3752 5691 7.254863 GCTTTTGCAGAATTTTGATTTTGAGGA 60.255 33.333 0.00 0.00 46.58 3.71
3753 5692 6.854381 GCTTTTGCAGAATTTTGATTTTGAGG 59.146 34.615 0.00 0.00 46.58 3.86
3754 5693 7.831750 GCTTTTGCAGAATTTTGATTTTGAG 57.168 32.000 0.00 0.00 46.58 3.02
3770 5709 7.148289 TTCAGTTTGAAATGATTTGCTTTTGCA 60.148 29.630 0.00 0.00 43.05 4.08
3771 5710 7.188157 TTCAGTTTGAAATGATTTGCTTTTGC 58.812 30.769 0.00 0.00 38.60 3.68
3787 5726 9.912634 GTCTAATGAATTCCAATTTCAGTTTGA 57.087 29.630 2.27 0.00 0.00 2.69
3788 5727 8.853345 CGTCTAATGAATTCCAATTTCAGTTTG 58.147 33.333 2.27 0.00 0.00 2.93
3789 5728 8.792633 TCGTCTAATGAATTCCAATTTCAGTTT 58.207 29.630 2.27 0.00 0.00 2.66
3790 5729 8.237267 GTCGTCTAATGAATTCCAATTTCAGTT 58.763 33.333 2.27 0.00 0.00 3.16
3791 5730 7.390440 TGTCGTCTAATGAATTCCAATTTCAGT 59.610 33.333 2.27 0.00 0.00 3.41
3792 5731 7.751732 TGTCGTCTAATGAATTCCAATTTCAG 58.248 34.615 2.27 0.00 0.00 3.02
3793 5732 7.680442 TGTCGTCTAATGAATTCCAATTTCA 57.320 32.000 2.27 0.00 0.00 2.69
3794 5733 7.166473 GCATGTCGTCTAATGAATTCCAATTTC 59.834 37.037 2.27 0.00 0.00 2.17
3795 5734 6.974622 GCATGTCGTCTAATGAATTCCAATTT 59.025 34.615 2.27 0.00 0.00 1.82
3796 5735 6.319658 AGCATGTCGTCTAATGAATTCCAATT 59.680 34.615 2.27 0.00 0.00 2.32
3797 5736 5.824624 AGCATGTCGTCTAATGAATTCCAAT 59.175 36.000 2.27 0.00 0.00 3.16
3798 5737 5.065090 CAGCATGTCGTCTAATGAATTCCAA 59.935 40.000 2.27 0.00 0.00 3.53
3799 5738 4.571984 CAGCATGTCGTCTAATGAATTCCA 59.428 41.667 2.27 0.00 0.00 3.53
3800 5739 4.553547 GCAGCATGTCGTCTAATGAATTCC 60.554 45.833 2.27 0.00 39.31 3.01
3801 5740 4.521943 GCAGCATGTCGTCTAATGAATTC 58.478 43.478 0.00 0.00 39.31 2.17
3802 5741 3.001634 CGCAGCATGTCGTCTAATGAATT 59.998 43.478 0.00 0.00 39.31 2.17
3803 5742 2.541346 CGCAGCATGTCGTCTAATGAAT 59.459 45.455 0.00 0.00 39.31 2.57
3804 5743 1.926510 CGCAGCATGTCGTCTAATGAA 59.073 47.619 0.00 0.00 39.31 2.57
3805 5744 1.135112 ACGCAGCATGTCGTCTAATGA 60.135 47.619 0.00 0.00 43.20 2.57
3806 5745 1.280982 ACGCAGCATGTCGTCTAATG 58.719 50.000 0.00 0.00 43.20 1.90
3807 5746 2.099263 ACTACGCAGCATGTCGTCTAAT 59.901 45.455 11.77 0.00 43.20 1.73
3808 5747 1.471287 ACTACGCAGCATGTCGTCTAA 59.529 47.619 11.77 0.00 43.20 2.10
3809 5748 1.092348 ACTACGCAGCATGTCGTCTA 58.908 50.000 11.77 0.00 43.20 2.59
3810 5749 0.243907 AACTACGCAGCATGTCGTCT 59.756 50.000 11.77 0.00 43.20 4.18
3811 5750 1.904144 TAACTACGCAGCATGTCGTC 58.096 50.000 11.77 0.00 43.20 4.20
3812 5751 2.579207 ATAACTACGCAGCATGTCGT 57.421 45.000 12.72 12.72 46.84 4.34
3813 5752 3.368495 TGTATAACTACGCAGCATGTCG 58.632 45.455 0.00 0.00 40.48 4.35
3814 5753 5.907197 AATGTATAACTACGCAGCATGTC 57.093 39.130 0.00 0.00 39.31 3.06
3815 5754 7.207383 TCTAAATGTATAACTACGCAGCATGT 58.793 34.615 0.00 0.00 39.31 3.21
3816 5755 7.637709 TCTAAATGTATAACTACGCAGCATG 57.362 36.000 0.00 0.00 40.87 4.06
3817 5756 9.355215 GTATCTAAATGTATAACTACGCAGCAT 57.645 33.333 0.00 0.00 0.00 3.79
3818 5757 8.354426 TGTATCTAAATGTATAACTACGCAGCA 58.646 33.333 0.00 0.00 0.00 4.41
3819 5758 8.738199 TGTATCTAAATGTATAACTACGCAGC 57.262 34.615 0.00 0.00 0.00 5.25
3832 5771 8.888716 TGCGTGTTTATGATTGTATCTAAATGT 58.111 29.630 0.00 0.00 0.00 2.71
3833 5772 9.882996 ATGCGTGTTTATGATTGTATCTAAATG 57.117 29.630 0.00 0.00 0.00 2.32
3835 5774 9.325198 AGATGCGTGTTTATGATTGTATCTAAA 57.675 29.630 0.00 0.00 0.00 1.85
3836 5775 8.887036 AGATGCGTGTTTATGATTGTATCTAA 57.113 30.769 0.00 0.00 0.00 2.10
3837 5776 8.887036 AAGATGCGTGTTTATGATTGTATCTA 57.113 30.769 0.00 0.00 0.00 1.98
3838 5777 7.792374 AAGATGCGTGTTTATGATTGTATCT 57.208 32.000 0.00 0.00 0.00 1.98
3839 5778 8.338259 AGAAAGATGCGTGTTTATGATTGTATC 58.662 33.333 0.29 0.00 0.00 2.24
3840 5779 8.213518 AGAAAGATGCGTGTTTATGATTGTAT 57.786 30.769 0.29 0.00 0.00 2.29
3841 5780 7.609760 AGAAAGATGCGTGTTTATGATTGTA 57.390 32.000 0.29 0.00 0.00 2.41
3842 5781 6.500684 AGAAAGATGCGTGTTTATGATTGT 57.499 33.333 0.29 0.00 0.00 2.71
3843 5782 6.237384 GCAAGAAAGATGCGTGTTTATGATTG 60.237 38.462 14.41 11.67 33.57 2.67
3844 5783 5.801947 GCAAGAAAGATGCGTGTTTATGATT 59.198 36.000 14.41 1.74 33.57 2.57
3845 5784 5.335127 GCAAGAAAGATGCGTGTTTATGAT 58.665 37.500 14.41 0.00 33.57 2.45
3846 5785 4.379394 GGCAAGAAAGATGCGTGTTTATGA 60.379 41.667 14.41 0.00 44.75 2.15
3847 5786 3.853671 GGCAAGAAAGATGCGTGTTTATG 59.146 43.478 0.29 5.42 44.75 1.90
3848 5787 3.119495 GGGCAAGAAAGATGCGTGTTTAT 60.119 43.478 0.29 0.00 44.75 1.40
3849 5788 2.227865 GGGCAAGAAAGATGCGTGTTTA 59.772 45.455 0.29 0.00 44.75 2.01
3850 5789 1.000274 GGGCAAGAAAGATGCGTGTTT 60.000 47.619 0.00 0.00 44.75 2.83
3851 5790 0.598065 GGGCAAGAAAGATGCGTGTT 59.402 50.000 0.00 0.00 44.75 3.32
3852 5791 0.250901 AGGGCAAGAAAGATGCGTGT 60.251 50.000 0.00 0.00 44.75 4.49
3853 5792 0.449388 GAGGGCAAGAAAGATGCGTG 59.551 55.000 0.00 0.00 44.75 5.34
3854 5793 0.326264 AGAGGGCAAGAAAGATGCGT 59.674 50.000 0.00 0.00 44.75 5.24
3855 5794 1.457346 AAGAGGGCAAGAAAGATGCG 58.543 50.000 0.00 0.00 44.75 4.73
3856 5795 3.876320 CTCTAAGAGGGCAAGAAAGATGC 59.124 47.826 0.00 0.00 43.08 3.91
3857 5796 5.096443 ACTCTAAGAGGGCAAGAAAGATG 57.904 43.478 0.00 0.00 33.35 2.90
3858 5797 6.843861 AGATACTCTAAGAGGGCAAGAAAGAT 59.156 38.462 0.00 0.00 33.35 2.40
3859 5798 6.198639 AGATACTCTAAGAGGGCAAGAAAGA 58.801 40.000 0.00 0.00 33.35 2.52
3860 5799 6.462347 GGAGATACTCTAAGAGGGCAAGAAAG 60.462 46.154 0.00 0.00 33.35 2.62
3861 5800 5.364157 GGAGATACTCTAAGAGGGCAAGAAA 59.636 44.000 0.00 0.00 33.35 2.52
3862 5801 4.896482 GGAGATACTCTAAGAGGGCAAGAA 59.104 45.833 0.00 0.00 33.35 2.52
3863 5802 4.079154 TGGAGATACTCTAAGAGGGCAAGA 60.079 45.833 0.00 0.00 33.35 3.02
3864 5803 4.219115 TGGAGATACTCTAAGAGGGCAAG 58.781 47.826 0.00 0.00 33.35 4.01
3865 5804 4.265856 TGGAGATACTCTAAGAGGGCAA 57.734 45.455 0.00 0.00 33.35 4.52
3866 5805 3.961408 GTTGGAGATACTCTAAGAGGGCA 59.039 47.826 0.00 0.00 31.92 5.36
3867 5806 3.961408 TGTTGGAGATACTCTAAGAGGGC 59.039 47.826 0.00 0.00 31.92 5.19
3868 5807 4.038642 GCTGTTGGAGATACTCTAAGAGGG 59.961 50.000 17.98 0.00 40.70 4.30
3869 5808 4.038642 GGCTGTTGGAGATACTCTAAGAGG 59.961 50.000 17.98 5.98 40.70 3.69
3870 5809 4.261405 CGGCTGTTGGAGATACTCTAAGAG 60.261 50.000 14.24 14.24 42.30 2.85
3879 5818 1.558167 TTGGGCGGCTGTTGGAGATA 61.558 55.000 9.56 0.00 0.00 1.98
3932 5872 0.040514 CGTGCAAAATCAGGCGTTCA 60.041 50.000 0.00 0.00 0.00 3.18
3942 5882 4.101790 CTCCGCGCCGTGCAAAAT 62.102 61.111 0.00 0.00 46.97 1.82
3992 5933 3.443925 CTGGAGCTCCTCACGCGA 61.444 66.667 32.28 10.39 36.82 5.87
4001 5944 2.436292 CACTGCCTGCTGGAGCTC 60.436 66.667 14.77 4.71 42.66 4.09
4016 5959 1.369930 TGCGCGCTAAAGTTTGCAC 60.370 52.632 33.29 0.00 0.00 4.57
4034 5983 4.085261 CGTATATATGTTGTTTGAGCGCGT 60.085 41.667 8.43 0.00 0.00 6.01
4040 5990 6.044046 AGTTCGGCGTATATATGTTGTTTGA 58.956 36.000 6.85 0.00 0.00 2.69
4054 6046 9.705471 CATATGTTTTTATTTTAGTTCGGCGTA 57.295 29.630 6.85 0.00 0.00 4.42
4057 6049 8.401046 TGCATATGTTTTTATTTTAGTTCGGC 57.599 30.769 4.29 0.00 0.00 5.54
4098 6203 8.072238 TGTACGCATTGTGAAATATCTATGTC 57.928 34.615 3.82 0.00 0.00 3.06
4131 6284 8.063200 TGCACCGTAGTTCTATATATATGCTT 57.937 34.615 5.44 0.00 0.00 3.91
4138 6294 7.337480 TCAAGTTGCACCGTAGTTCTATATA 57.663 36.000 0.00 0.00 0.00 0.86
4142 6298 4.530710 ATCAAGTTGCACCGTAGTTCTA 57.469 40.909 0.00 0.00 0.00 2.10
4144 6300 5.600908 TTTATCAAGTTGCACCGTAGTTC 57.399 39.130 0.00 0.00 0.00 3.01
4147 6303 5.997385 AGTTTTTATCAAGTTGCACCGTAG 58.003 37.500 0.00 0.00 0.00 3.51
4148 6304 6.707161 AGTAGTTTTTATCAAGTTGCACCGTA 59.293 34.615 0.00 0.00 0.00 4.02
4152 6311 7.013529 CCGTAGTAGTTTTTATCAAGTTGCAC 58.986 38.462 0.00 0.00 0.00 4.57
4153 6312 6.707161 ACCGTAGTAGTTTTTATCAAGTTGCA 59.293 34.615 0.00 0.00 0.00 4.08
4154 6313 7.013529 CACCGTAGTAGTTTTTATCAAGTTGC 58.986 38.462 0.00 0.00 0.00 4.17
4156 6315 6.707161 TGCACCGTAGTAGTTTTTATCAAGTT 59.293 34.615 0.00 0.00 0.00 2.66
4158 6317 6.715344 TGCACCGTAGTAGTTTTTATCAAG 57.285 37.500 0.00 0.00 0.00 3.02
4159 6318 6.707161 AGTTGCACCGTAGTAGTTTTTATCAA 59.293 34.615 0.00 0.00 0.00 2.57
4160 6319 6.225318 AGTTGCACCGTAGTAGTTTTTATCA 58.775 36.000 0.00 0.00 0.00 2.15
4161 6320 6.716898 AGTTGCACCGTAGTAGTTTTTATC 57.283 37.500 0.00 0.00 0.00 1.75
4163 6322 6.980593 TCTAGTTGCACCGTAGTAGTTTTTA 58.019 36.000 0.00 0.00 0.00 1.52
4164 6323 5.846203 TCTAGTTGCACCGTAGTAGTTTTT 58.154 37.500 0.00 0.00 0.00 1.94
4169 6375 3.442977 AGGTTCTAGTTGCACCGTAGTAG 59.557 47.826 0.00 0.00 37.05 2.57
4170 6376 3.424703 AGGTTCTAGTTGCACCGTAGTA 58.575 45.455 0.00 0.00 37.05 1.82
4276 6745 2.430367 GCAGGTGGGGAGTCGTTT 59.570 61.111 0.00 0.00 0.00 3.60
4390 6898 0.108329 AGGACGTCGCCGATGAAAAT 60.108 50.000 14.17 0.00 37.88 1.82
4552 7485 0.742505 ACTTCCACGACGTCTTCACA 59.257 50.000 14.70 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.