Multiple sequence alignment - TraesCS4A01G256800

Loading Multiple Alignment...

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 TraesCS4A01G256800 chr4A 100.000 4292 0 0 1 4292 569865440 569869731 0.000000e+00 7926.0
1 TraesCS4A01G256800 chr4A 82.031 768 126 11 2 762 577736134 577736896 1.010000e-180 643.0
2 TraesCS4A01G256800 chr4A 93.197 147 6 4 3914 4057 272955056 272954911 3.360000e-51 213.0
3 TraesCS4A01G256800 chr4A 88.636 88 10 0 2448 2535 569867971 569867884 1.630000e-19 108.0
4 TraesCS4A01G256800 chr4D 94.533 2945 133 15 907 3840 32770021 32767094 0.000000e+00 4521.0
5 TraesCS4A01G256800 chr4D 80.137 292 9 13 4042 4290 32766764 32766479 5.710000e-39 172.0
6 TraesCS4A01G256800 chr4D 92.857 70 5 0 832 901 32770119 32770050 7.590000e-18 102.0
7 TraesCS4A01G256800 chr4B 94.004 2485 108 25 1419 3881 47624501 47622036 0.000000e+00 3725.0
8 TraesCS4A01G256800 chr4B 91.344 439 19 2 937 1375 47624924 47624505 2.220000e-162 582.0
9 TraesCS4A01G256800 chr4B 86.184 152 5 9 4156 4292 47621933 47621783 2.670000e-32 150.0
10 TraesCS4A01G256800 chr6A 97.652 724 17 0 1 724 77979127 77979850 0.000000e+00 1243.0
11 TraesCS4A01G256800 chr6A 83.808 772 115 8 2 765 69924793 69924024 0.000000e+00 725.0
12 TraesCS4A01G256800 chr7B 93.709 763 46 2 1 762 732630561 732631322 0.000000e+00 1142.0
13 TraesCS4A01G256800 chr5B 92.126 762 56 2 1 762 26030944 26031701 0.000000e+00 1072.0
14 TraesCS4A01G256800 chr5B 90.576 764 68 4 1 762 701555395 701556156 0.000000e+00 1009.0
15 TraesCS4A01G256800 chr5B 83.943 766 115 8 1 762 576230205 576229444 0.000000e+00 726.0
16 TraesCS4A01G256800 chr5B 83.833 767 114 10 1 762 50280914 50280153 0.000000e+00 721.0
17 TraesCS4A01G256800 chr5B 83.572 767 116 10 1 762 115866533 115865772 0.000000e+00 710.0
18 TraesCS4A01G256800 chr3B 90.743 767 64 5 1 762 670305413 670304649 0.000000e+00 1016.0
19 TraesCS4A01G256800 chr3B 90.054 553 55 0 4 556 624879552 624879000 0.000000e+00 717.0
20 TraesCS4A01G256800 chr7D 83.333 768 115 10 2 762 593419026 593419787 0.000000e+00 697.0
21 TraesCS4A01G256800 chr2D 83.312 767 117 10 2 762 434695012 434695773 0.000000e+00 697.0
22 TraesCS4A01G256800 chr2D 86.957 92 11 1 2449 2540 75504894 75504984 7.590000e-18 102.0
23 TraesCS4A01G256800 chr1A 83.159 766 122 6 2 762 238698305 238699068 0.000000e+00 693.0
24 TraesCS4A01G256800 chr1A 94.521 146 4 3 3917 4059 346451342 346451486 5.590000e-54 222.0
25 TraesCS4A01G256800 chr1B 89.366 536 57 0 227 762 47199952 47200487 0.000000e+00 675.0
26 TraesCS4A01G256800 chr1B 87.685 203 22 3 2 203 47190978 47191178 2.580000e-57 233.0
27 TraesCS4A01G256800 chr1B 98.462 130 0 1 3917 4044 669017052 669017181 1.200000e-55 228.0
28 TraesCS4A01G256800 chr3A 80.940 766 120 10 2 762 411260745 411261489 2.220000e-162 582.0
29 TraesCS4A01G256800 chr2B 86.849 365 41 6 2 361 72987513 72987151 6.690000e-108 401.0
30 TraesCS4A01G256800 chr2B 89.655 87 7 2 2448 2533 232785730 232785815 4.540000e-20 110.0
31 TraesCS4A01G256800 chr2B 89.412 85 9 0 2448 2532 232785814 232785730 1.630000e-19 108.0
32 TraesCS4A01G256800 chr5A 97.710 131 1 1 3916 4044 645121665 645121795 1.550000e-54 224.0
33 TraesCS4A01G256800 chr5A 84.158 101 15 1 2433 2532 382114842 382114942 3.530000e-16 97.1
34 TraesCS4A01G256800 chr2A 95.745 141 2 3 3905 4041 43500208 43500348 1.550000e-54 224.0
35 TraesCS4A01G256800 chr2A 97.692 130 1 1 3917 4044 80886089 80885960 5.590000e-54 222.0
36 TraesCS4A01G256800 chrUn 95.714 140 2 3 3907 4042 183130869 183131008 5.590000e-54 222.0
37 TraesCS4A01G256800 chrUn 95.000 140 3 3 3907 4042 183183405 183183544 2.600000e-52 217.0
38 TraesCS4A01G256800 chrUn 95.000 140 3 3 3907 4042 254881168 254881307 2.600000e-52 217.0
39 TraesCS4A01G256800 chr5D 94.048 84 5 0 2448 2531 456063698 456063615 1.250000e-25 128.0
40 TraesCS4A01G256800 chr5D 92.045 88 6 1 2449 2536 456063615 456063701 5.830000e-24 122.0


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 TraesCS4A01G256800 chr4A 569865440 569869731 4291 False 7926.000000 7926 100.000000 1 4292 1 chr4A.!!$F1 4291
1 TraesCS4A01G256800 chr4A 577736134 577736896 762 False 643.000000 643 82.031000 2 762 1 chr4A.!!$F2 760
2 TraesCS4A01G256800 chr4D 32766479 32770119 3640 True 1598.333333 4521 89.175667 832 4290 3 chr4D.!!$R1 3458
3 TraesCS4A01G256800 chr4B 47621783 47624924 3141 True 1485.666667 3725 90.510667 937 4292 3 chr4B.!!$R1 3355
4 TraesCS4A01G256800 chr6A 77979127 77979850 723 False 1243.000000 1243 97.652000 1 724 1 chr6A.!!$F1 723
5 TraesCS4A01G256800 chr6A 69924024 69924793 769 True 725.000000 725 83.808000 2 765 1 chr6A.!!$R1 763
6 TraesCS4A01G256800 chr7B 732630561 732631322 761 False 1142.000000 1142 93.709000 1 762 1 chr7B.!!$F1 761
7 TraesCS4A01G256800 chr5B 26030944 26031701 757 False 1072.000000 1072 92.126000 1 762 1 chr5B.!!$F1 761
8 TraesCS4A01G256800 chr5B 701555395 701556156 761 False 1009.000000 1009 90.576000 1 762 1 chr5B.!!$F2 761
9 TraesCS4A01G256800 chr5B 576229444 576230205 761 True 726.000000 726 83.943000 1 762 1 chr5B.!!$R3 761
10 TraesCS4A01G256800 chr5B 50280153 50280914 761 True 721.000000 721 83.833000 1 762 1 chr5B.!!$R1 761
11 TraesCS4A01G256800 chr5B 115865772 115866533 761 True 710.000000 710 83.572000 1 762 1 chr5B.!!$R2 761
12 TraesCS4A01G256800 chr3B 670304649 670305413 764 True 1016.000000 1016 90.743000 1 762 1 chr3B.!!$R2 761
13 TraesCS4A01G256800 chr3B 624879000 624879552 552 True 717.000000 717 90.054000 4 556 1 chr3B.!!$R1 552
14 TraesCS4A01G256800 chr7D 593419026 593419787 761 False 697.000000 697 83.333000 2 762 1 chr7D.!!$F1 760
15 TraesCS4A01G256800 chr2D 434695012 434695773 761 False 697.000000 697 83.312000 2 762 1 chr2D.!!$F2 760
16 TraesCS4A01G256800 chr1A 238698305 238699068 763 False 693.000000 693 83.159000 2 762 1 chr1A.!!$F1 760
17 TraesCS4A01G256800 chr1B 47199952 47200487 535 False 675.000000 675 89.366000 227 762 1 chr1B.!!$F2 535
18 TraesCS4A01G256800 chr3A 411260745 411261489 744 False 582.000000 582 80.940000 2 762 1 chr3A.!!$F1 760

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
790 803 0.251073 CCGAATCTAAACCCCCGTGT 59.749 55.0 0.0 0.0 0.0 4.49 F
797 810 0.397564 TAAACCCCCGTGTCAAGGTC 59.602 55.0 4.0 0.0 0.0 3.85 F
1490 1530 0.550638 AACCGAATTACCCCCTCCCA 60.551 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2780 2834 1.001633 TCTAAGACGGTTGCCAGGTTC 59.998 52.381 0.0 0.0 0.00 3.62 R
2918 2972 0.109132 GATGGGCAGAAAAGGTTGCG 60.109 55.000 0.0 0.0 41.17 4.85 R
3531 3586 0.032678 ATCATGACGACCGGCTCATC 59.967 55.000 0.0 0.0 0.00 2.92 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
109 110 5.011635 TCACGCTATGGTCAATATGGTATGT 59.988 40.000 0.00 0.00 0.00 2.29
247 251 1.379710 TTGCTGCACCACCACAACT 60.380 52.632 0.00 0.00 0.00 3.16
450 455 1.208614 CGTGAGGCTCTTGCTTTGC 59.791 57.895 16.72 0.00 39.59 3.68
493 499 2.796483 ATTTGCGTGGCAGCGGACTA 62.796 55.000 10.56 1.21 40.61 2.59
690 703 1.895131 GACATGTTTGGTTGGGCATCT 59.105 47.619 0.00 0.00 0.00 2.90
784 797 9.516546 AAAATAGGATATTCCGAATCTAAACCC 57.483 33.333 0.00 0.00 42.75 4.11
785 798 5.500546 AGGATATTCCGAATCTAAACCCC 57.499 43.478 0.00 0.00 42.75 4.95
786 799 4.288887 AGGATATTCCGAATCTAAACCCCC 59.711 45.833 0.00 0.00 42.75 5.40
787 800 2.632987 ATTCCGAATCTAAACCCCCG 57.367 50.000 0.00 0.00 0.00 5.73
788 801 1.278537 TTCCGAATCTAAACCCCCGT 58.721 50.000 0.00 0.00 0.00 5.28
789 802 0.538118 TCCGAATCTAAACCCCCGTG 59.462 55.000 0.00 0.00 0.00 4.94
790 803 0.251073 CCGAATCTAAACCCCCGTGT 59.749 55.000 0.00 0.00 0.00 4.49
791 804 1.648504 CGAATCTAAACCCCCGTGTC 58.351 55.000 0.00 0.00 0.00 3.67
792 805 1.066716 CGAATCTAAACCCCCGTGTCA 60.067 52.381 0.00 0.00 0.00 3.58
793 806 2.613474 CGAATCTAAACCCCCGTGTCAA 60.613 50.000 0.00 0.00 0.00 3.18
794 807 2.781681 ATCTAAACCCCCGTGTCAAG 57.218 50.000 0.00 0.00 0.00 3.02
795 808 0.688487 TCTAAACCCCCGTGTCAAGG 59.312 55.000 0.00 0.00 0.00 3.61
796 809 0.399075 CTAAACCCCCGTGTCAAGGT 59.601 55.000 4.00 0.00 0.00 3.50
797 810 0.397564 TAAACCCCCGTGTCAAGGTC 59.602 55.000 4.00 0.00 0.00 3.85
798 811 2.669777 AAACCCCCGTGTCAAGGTCG 62.670 60.000 4.00 0.00 0.00 4.79
799 812 4.388499 CCCCCGTGTCAAGGTCGG 62.388 72.222 4.00 0.00 43.30 4.79
810 823 3.706373 AGGTCGGCCTTCGTGCAT 61.706 61.111 0.35 0.00 44.18 3.96
811 824 3.499737 GGTCGGCCTTCGTGCATG 61.500 66.667 0.00 0.00 40.32 4.06
812 825 3.499737 GTCGGCCTTCGTGCATGG 61.500 66.667 5.98 0.00 40.32 3.66
813 826 4.776322 TCGGCCTTCGTGCATGGG 62.776 66.667 5.98 1.13 40.32 4.00
816 829 3.818787 GCCTTCGTGCATGGGCTG 61.819 66.667 16.44 1.14 41.20 4.85
817 830 2.360350 CCTTCGTGCATGGGCTGT 60.360 61.111 5.98 0.00 41.91 4.40
818 831 2.693762 CCTTCGTGCATGGGCTGTG 61.694 63.158 5.98 0.00 41.91 3.66
819 832 3.332493 CTTCGTGCATGGGCTGTGC 62.332 63.158 5.98 7.53 42.81 4.57
923 959 2.426752 CGTGCGTTCGCCCAAAAG 60.427 61.111 14.44 0.00 0.00 2.27
925 961 3.291383 TGCGTTCGCCCAAAAGGG 61.291 61.111 14.44 0.00 35.41 3.95
928 964 2.034607 CGTTCGCCCAAAAGGGAAA 58.965 52.632 4.37 0.00 39.99 3.13
1053 1093 4.687215 GCTCACTCGTGCCCTGCA 62.687 66.667 0.00 0.00 35.60 4.41
1131 1171 3.620300 CTCCGTGTTCGCGCAGGTA 62.620 63.158 8.75 0.00 35.54 3.08
1214 1254 2.991076 GCGAGTGGCGTGGTAGTCT 61.991 63.158 0.00 0.00 43.41 3.24
1241 1281 0.737019 GATCCCGCGTTACCGTTTCA 60.737 55.000 4.92 0.00 36.15 2.69
1347 1387 2.678336 GTGTAAGGGATTTCTCGCCTTG 59.322 50.000 0.00 0.00 35.20 3.61
1375 1415 2.539003 CGTTTCCGTGATGCCTGAA 58.461 52.632 0.00 0.00 0.00 3.02
1376 1416 1.086696 CGTTTCCGTGATGCCTGAAT 58.913 50.000 0.00 0.00 0.00 2.57
1380 1420 4.306600 GTTTCCGTGATGCCTGAATTTTT 58.693 39.130 0.00 0.00 0.00 1.94
1407 1447 5.710513 TTTGATGTTTTGATGGTCTGGAG 57.289 39.130 0.00 0.00 0.00 3.86
1409 1449 4.728772 TGATGTTTTGATGGTCTGGAGTT 58.271 39.130 0.00 0.00 0.00 3.01
1434 1474 5.790593 AGTATTGTTGTTCGGTGACACTAT 58.209 37.500 5.39 0.00 0.00 2.12
1474 1514 1.263217 CCTGTGCACGAACAACTAACC 59.737 52.381 13.13 0.00 0.00 2.85
1483 1523 3.996363 ACGAACAACTAACCGAATTACCC 59.004 43.478 0.00 0.00 0.00 3.69
1484 1524 3.371898 CGAACAACTAACCGAATTACCCC 59.628 47.826 0.00 0.00 0.00 4.95
1485 1525 3.354948 ACAACTAACCGAATTACCCCC 57.645 47.619 0.00 0.00 0.00 5.40
1486 1526 2.914941 ACAACTAACCGAATTACCCCCT 59.085 45.455 0.00 0.00 0.00 4.79
1487 1527 3.054875 ACAACTAACCGAATTACCCCCTC 60.055 47.826 0.00 0.00 0.00 4.30
1488 1528 2.121948 ACTAACCGAATTACCCCCTCC 58.878 52.381 0.00 0.00 0.00 4.30
1489 1529 1.419012 CTAACCGAATTACCCCCTCCC 59.581 57.143 0.00 0.00 0.00 4.30
1490 1530 0.550638 AACCGAATTACCCCCTCCCA 60.551 55.000 0.00 0.00 0.00 4.37
1840 1887 6.852853 CCGTATTGTGCAATGTCAGATATTTC 59.147 38.462 7.60 0.00 32.50 2.17
1865 1912 4.013267 AGGATCACACAAGCTATATGGC 57.987 45.455 2.23 2.23 0.00 4.40
1923 1970 4.749245 ATTACAGTGGTCAAAAAGCTCG 57.251 40.909 0.00 0.00 0.00 5.03
1955 2002 0.877743 GTTCTCTGCCAGTTCCAAGC 59.122 55.000 0.00 0.00 0.00 4.01
1975 2022 4.652822 AGCGGTTGGGGAGATATTATTTC 58.347 43.478 0.00 0.00 0.00 2.17
2028 2075 2.038164 TCCACCTCATGAGCTGCATATC 59.962 50.000 17.76 0.00 34.82 1.63
2421 2468 3.191371 CAGGTTTCCTGCATTAAGTGACC 59.809 47.826 2.77 0.00 45.13 4.02
2423 2470 3.191371 GGTTTCCTGCATTAAGTGACCTG 59.809 47.826 0.00 0.00 0.00 4.00
2492 2540 6.720012 AAGACGTTTTTGCAGTTCAATTTT 57.280 29.167 0.00 0.00 34.12 1.82
2526 2575 6.651975 ACGTCTTATATTTAGGGACAGAGG 57.348 41.667 0.00 0.00 0.00 3.69
2544 2594 9.245481 GGACAGAGGTAGTACTATTATTGCTAT 57.755 37.037 5.75 0.00 0.00 2.97
2642 2693 5.012239 TCTTTTCTGAAATCCCCATGAGTG 58.988 41.667 3.31 0.00 0.00 3.51
2717 2769 7.476540 TTTCTCTAGTGTTACATTAGAGGCA 57.523 36.000 30.81 20.91 45.03 4.75
2718 2770 7.661536 TTCTCTAGTGTTACATTAGAGGCAT 57.338 36.000 30.81 0.00 45.03 4.40
2719 2771 7.043961 TCTCTAGTGTTACATTAGAGGCATG 57.956 40.000 30.81 15.67 45.03 4.06
2720 2772 5.601662 TCTAGTGTTACATTAGAGGCATGC 58.398 41.667 9.90 9.90 29.86 4.06
2721 2773 3.198068 AGTGTTACATTAGAGGCATGCG 58.802 45.455 12.44 0.00 0.00 4.73
2722 2774 3.118775 AGTGTTACATTAGAGGCATGCGA 60.119 43.478 12.44 0.00 0.00 5.10
2736 2790 2.263077 CATGCGAGAGGTGTTACAGAC 58.737 52.381 0.00 0.00 0.00 3.51
2766 2820 0.945099 TGATACTAGGAGCGCTGACG 59.055 55.000 18.48 2.34 44.07 4.35
2873 2927 3.127589 TGATTGTGGGATATGTTACGCG 58.872 45.455 3.53 3.53 0.00 6.01
2909 2963 2.760374 GGTGAGCCAATCTCTATTCCG 58.240 52.381 0.00 0.00 42.38 4.30
2918 2972 1.693627 TCTCTATTCCGCCTCTGGTC 58.306 55.000 0.00 0.00 0.00 4.02
2935 2989 1.152860 TCGCAACCTTTTCTGCCCA 60.153 52.632 0.00 0.00 35.01 5.36
2946 3000 4.463891 CCTTTTCTGCCCATCATGTAGTTT 59.536 41.667 0.00 0.00 0.00 2.66
2959 3013 8.156820 CCATCATGTAGTTTCCTGACCATAATA 58.843 37.037 0.00 0.00 0.00 0.98
2999 3053 3.056821 TGAATGAAGATGACGAACTCGGT 60.057 43.478 3.88 0.00 44.95 4.69
3065 3119 1.447489 CAGCAGAGCCTTCCACTCG 60.447 63.158 0.00 0.00 39.23 4.18
3116 3170 2.426522 ACTACGACAAGGCAGTACGTA 58.573 47.619 0.00 0.00 38.18 3.57
3142 3196 8.319146 AGAAACGATGAAACCCTAAAGAGATTA 58.681 33.333 0.00 0.00 0.00 1.75
3147 3201 7.715249 CGATGAAACCCTAAAGAGATTATTCCA 59.285 37.037 0.00 0.00 0.00 3.53
3194 3248 5.121811 GTGCAATGTACTCCATCTCTGATT 58.878 41.667 0.00 0.00 31.75 2.57
3196 3250 4.024218 GCAATGTACTCCATCTCTGATTGC 60.024 45.833 0.00 0.00 38.12 3.56
3206 3260 4.512198 CCATCTCTGATTGCTCTTGTCATC 59.488 45.833 0.00 0.00 0.00 2.92
3287 3341 1.079819 CCGTGAAGAGCACCGACAT 60.080 57.895 0.00 0.00 44.85 3.06
3321 3375 4.857871 TCTTCGCATTTACAAATCGAGG 57.142 40.909 0.00 9.90 33.22 4.63
3430 3485 1.896660 TTTCCACCTTCCAGCGTGC 60.897 57.895 0.00 0.00 0.00 5.34
3474 3529 0.179029 AGGTGTGGTTCCAGGTTTCG 60.179 55.000 0.00 0.00 0.00 3.46
3508 3563 7.068226 CAGTAAAAAGGAAGAGGGAAGAAAACA 59.932 37.037 0.00 0.00 0.00 2.83
3509 3564 6.867519 AAAAAGGAAGAGGGAAGAAAACAA 57.132 33.333 0.00 0.00 0.00 2.83
3510 3565 6.471233 AAAAGGAAGAGGGAAGAAAACAAG 57.529 37.500 0.00 0.00 0.00 3.16
3525 3580 4.810191 AAACAAGAAGATCTAGGTCGCT 57.190 40.909 0.00 0.00 0.00 4.93
3526 3581 5.916661 AAACAAGAAGATCTAGGTCGCTA 57.083 39.130 0.00 0.00 0.00 4.26
3527 3582 4.904253 ACAAGAAGATCTAGGTCGCTAC 57.096 45.455 0.00 0.00 0.00 3.58
3528 3583 3.312973 ACAAGAAGATCTAGGTCGCTACG 59.687 47.826 0.00 0.00 0.00 3.51
3531 3586 1.595466 AGATCTAGGTCGCTACGTGG 58.405 55.000 0.00 0.00 0.00 4.94
3533 3588 2.152830 GATCTAGGTCGCTACGTGGAT 58.847 52.381 9.21 9.21 42.29 3.41
3534 3589 1.306148 TCTAGGTCGCTACGTGGATG 58.694 55.000 1.81 0.00 0.00 3.51
3535 3590 1.134310 TCTAGGTCGCTACGTGGATGA 60.134 52.381 1.81 0.00 0.00 2.92
3594 3649 1.627864 AGGGGTCAAAATTCCCGTTG 58.372 50.000 0.00 0.00 45.13 4.10
3595 3650 0.037697 GGGGTCAAAATTCCCGTTGC 60.038 55.000 0.00 0.00 44.27 4.17
3719 3774 5.692115 TGAGGAATTGCTGACTGGTATAA 57.308 39.130 3.35 0.00 0.00 0.98
3720 3775 6.252599 TGAGGAATTGCTGACTGGTATAAT 57.747 37.500 3.35 0.00 0.00 1.28
3830 3898 0.184451 ATTCCAAGCCGCCTGATGAT 59.816 50.000 0.00 0.00 0.00 2.45
3873 4189 1.441732 AAACGGTCAGTCAAACGGCC 61.442 55.000 0.00 0.00 0.00 6.13
3887 4203 3.131478 GGCCCAAATCCACGACGG 61.131 66.667 0.00 0.00 0.00 4.79
3910 4226 5.421203 GCAAACGAACGACTATACTATTGC 58.579 41.667 0.14 0.00 33.62 3.56
3916 4232 6.205076 ACGAACGACTATACTATTGCAGATCT 59.795 38.462 0.14 0.00 0.00 2.75
3921 4237 7.334921 ACGACTATACTATTGCAGATCTACTCC 59.665 40.741 0.00 0.00 0.00 3.85
3922 4238 7.201661 CGACTATACTATTGCAGATCTACTCCC 60.202 44.444 0.00 0.00 0.00 4.30
3923 4239 7.704727 ACTATACTATTGCAGATCTACTCCCT 58.295 38.462 0.00 0.00 0.00 4.20
3924 4240 6.849085 ATACTATTGCAGATCTACTCCCTG 57.151 41.667 0.00 0.00 0.00 4.45
3925 4241 4.551671 ACTATTGCAGATCTACTCCCTGT 58.448 43.478 0.00 0.00 0.00 4.00
3926 4242 4.965532 ACTATTGCAGATCTACTCCCTGTT 59.034 41.667 0.00 0.00 0.00 3.16
3927 4243 3.895232 TTGCAGATCTACTCCCTGTTC 57.105 47.619 0.00 0.00 0.00 3.18
3928 4244 2.111384 TGCAGATCTACTCCCTGTTCC 58.889 52.381 0.00 0.00 0.00 3.62
3929 4245 1.067821 GCAGATCTACTCCCTGTTCCG 59.932 57.143 0.00 0.00 0.00 4.30
3930 4246 2.656002 CAGATCTACTCCCTGTTCCGA 58.344 52.381 0.00 0.00 0.00 4.55
3931 4247 3.024547 CAGATCTACTCCCTGTTCCGAA 58.975 50.000 0.00 0.00 0.00 4.30
3932 4248 3.639094 CAGATCTACTCCCTGTTCCGAAT 59.361 47.826 0.00 0.00 0.00 3.34
3933 4249 4.100189 CAGATCTACTCCCTGTTCCGAATT 59.900 45.833 0.00 0.00 0.00 2.17
3934 4250 5.302059 CAGATCTACTCCCTGTTCCGAATTA 59.698 44.000 0.00 0.00 0.00 1.40
3935 4251 4.996788 TCTACTCCCTGTTCCGAATTAC 57.003 45.455 0.00 0.00 0.00 1.89
3936 4252 4.607239 TCTACTCCCTGTTCCGAATTACT 58.393 43.478 0.00 0.00 0.00 2.24
3937 4253 5.021458 TCTACTCCCTGTTCCGAATTACTT 58.979 41.667 0.00 0.00 0.00 2.24
3938 4254 3.939066 ACTCCCTGTTCCGAATTACTTG 58.061 45.455 0.00 0.00 0.00 3.16
3939 4255 3.326880 ACTCCCTGTTCCGAATTACTTGT 59.673 43.478 0.00 0.00 0.00 3.16
3940 4256 3.933332 CTCCCTGTTCCGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
3941 4257 3.581332 TCCCTGTTCCGAATTACTTGTCT 59.419 43.478 0.00 0.00 0.00 3.41
3942 4258 4.041198 TCCCTGTTCCGAATTACTTGTCTT 59.959 41.667 0.00 0.00 0.00 3.01
3943 4259 4.154195 CCCTGTTCCGAATTACTTGTCTTG 59.846 45.833 0.00 0.00 0.00 3.02
3944 4260 4.154195 CCTGTTCCGAATTACTTGTCTTGG 59.846 45.833 0.00 0.00 0.00 3.61
3945 4261 4.963373 TGTTCCGAATTACTTGTCTTGGA 58.037 39.130 0.00 0.00 0.00 3.53
3946 4262 5.556915 TGTTCCGAATTACTTGTCTTGGAT 58.443 37.500 0.00 0.00 0.00 3.41
3947 4263 6.001460 TGTTCCGAATTACTTGTCTTGGATT 58.999 36.000 0.00 0.00 0.00 3.01
3948 4264 6.488683 TGTTCCGAATTACTTGTCTTGGATTT 59.511 34.615 0.00 0.00 0.00 2.17
3949 4265 6.494893 TCCGAATTACTTGTCTTGGATTTG 57.505 37.500 0.00 0.00 0.00 2.32
3950 4266 6.001460 TCCGAATTACTTGTCTTGGATTTGT 58.999 36.000 0.00 0.00 0.00 2.83
3951 4267 6.148811 TCCGAATTACTTGTCTTGGATTTGTC 59.851 38.462 0.00 0.00 0.00 3.18
3952 4268 6.149474 CCGAATTACTTGTCTTGGATTTGTCT 59.851 38.462 0.00 0.00 0.00 3.41
3953 4269 7.333423 CCGAATTACTTGTCTTGGATTTGTCTA 59.667 37.037 0.00 0.00 0.00 2.59
3954 4270 8.383619 CGAATTACTTGTCTTGGATTTGTCTAG 58.616 37.037 0.00 0.00 0.00 2.43
3955 4271 9.436957 GAATTACTTGTCTTGGATTTGTCTAGA 57.563 33.333 0.00 0.00 0.00 2.43
3956 4272 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
3958 4274 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
3959 4275 7.036220 ACTTGTCTTGGATTTGTCTAGATACG 58.964 38.462 0.00 0.00 0.00 3.06
3960 4276 5.902681 TGTCTTGGATTTGTCTAGATACGG 58.097 41.667 0.00 0.00 0.00 4.02
3961 4277 5.655090 TGTCTTGGATTTGTCTAGATACGGA 59.345 40.000 0.00 0.00 0.00 4.69
3962 4278 6.323996 TGTCTTGGATTTGTCTAGATACGGAT 59.676 38.462 0.00 0.00 0.00 4.18
3963 4279 6.642950 GTCTTGGATTTGTCTAGATACGGATG 59.357 42.308 0.00 0.00 0.00 3.51
3964 4280 6.323996 TCTTGGATTTGTCTAGATACGGATGT 59.676 38.462 0.00 0.00 0.00 3.06
3965 4281 7.504574 TCTTGGATTTGTCTAGATACGGATGTA 59.495 37.037 0.00 0.00 34.45 2.29
3966 4282 7.776618 TGGATTTGTCTAGATACGGATGTAT 57.223 36.000 0.00 0.00 43.97 2.29
3982 4298 8.466617 ACGGATGTATCTAGACTCATTTTAGT 57.533 34.615 11.25 7.70 0.00 2.24
3983 4299 8.353684 ACGGATGTATCTAGACTCATTTTAGTG 58.646 37.037 11.25 3.85 0.00 2.74
3984 4300 7.327275 CGGATGTATCTAGACTCATTTTAGTGC 59.673 40.741 11.25 0.00 0.00 4.40
3985 4301 8.364142 GGATGTATCTAGACTCATTTTAGTGCT 58.636 37.037 11.25 0.00 0.00 4.40
3988 4304 9.628500 TGTATCTAGACTCATTTTAGTGCTAGA 57.372 33.333 0.00 0.00 38.76 2.43
3992 4308 9.069082 TCTAGACTCATTTTAGTGCTAGATACC 57.931 37.037 0.00 0.00 34.69 2.73
3993 4309 7.906199 AGACTCATTTTAGTGCTAGATACCT 57.094 36.000 0.00 0.00 0.00 3.08
3994 4310 7.947282 AGACTCATTTTAGTGCTAGATACCTC 58.053 38.462 0.00 0.00 0.00 3.85
3995 4311 7.014808 AGACTCATTTTAGTGCTAGATACCTCC 59.985 40.741 0.00 0.00 0.00 4.30
3996 4312 6.085555 TCATTTTAGTGCTAGATACCTCCG 57.914 41.667 0.00 0.00 0.00 4.63
3997 4313 5.597182 TCATTTTAGTGCTAGATACCTCCGT 59.403 40.000 0.00 0.00 0.00 4.69
3998 4314 6.774170 TCATTTTAGTGCTAGATACCTCCGTA 59.226 38.462 0.00 0.00 0.00 4.02
3999 4315 7.450634 TCATTTTAGTGCTAGATACCTCCGTAT 59.549 37.037 0.00 0.00 37.92 3.06
4011 4327 6.837471 ATACCTCCGTATCTAGACAAATCC 57.163 41.667 0.00 0.00 28.45 3.01
4012 4328 4.543689 ACCTCCGTATCTAGACAAATCCA 58.456 43.478 0.00 0.00 0.00 3.41
4013 4329 4.960469 ACCTCCGTATCTAGACAAATCCAA 59.040 41.667 0.00 0.00 0.00 3.53
4014 4330 5.069251 ACCTCCGTATCTAGACAAATCCAAG 59.931 44.000 0.00 0.00 0.00 3.61
4015 4331 5.302059 CCTCCGTATCTAGACAAATCCAAGA 59.698 44.000 0.00 0.00 0.00 3.02
4016 4332 6.145338 TCCGTATCTAGACAAATCCAAGAC 57.855 41.667 0.00 0.00 0.00 3.01
4017 4333 5.655090 TCCGTATCTAGACAAATCCAAGACA 59.345 40.000 0.00 0.00 0.00 3.41
4018 4334 6.153851 TCCGTATCTAGACAAATCCAAGACAA 59.846 38.462 0.00 0.00 0.00 3.18
4019 4335 6.477033 CCGTATCTAGACAAATCCAAGACAAG 59.523 42.308 0.00 0.00 0.00 3.16
4020 4336 7.036220 CGTATCTAGACAAATCCAAGACAAGT 58.964 38.462 0.00 0.00 0.00 3.16
4021 4337 8.188799 CGTATCTAGACAAATCCAAGACAAGTA 58.811 37.037 0.00 0.00 0.00 2.24
4022 4338 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
4024 4340 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
4025 4341 9.436957 TCTAGACAAATCCAAGACAAGTAATTC 57.563 33.333 0.00 0.00 0.00 2.17
4026 4342 9.219603 CTAGACAAATCCAAGACAAGTAATTCA 57.780 33.333 0.00 0.00 0.00 2.57
4027 4343 8.103948 AGACAAATCCAAGACAAGTAATTCAG 57.896 34.615 0.00 0.00 0.00 3.02
4028 4344 7.939039 AGACAAATCCAAGACAAGTAATTCAGA 59.061 33.333 0.00 0.00 0.00 3.27
4029 4345 8.463930 ACAAATCCAAGACAAGTAATTCAGAA 57.536 30.769 0.00 0.00 0.00 3.02
4030 4346 8.352942 ACAAATCCAAGACAAGTAATTCAGAAC 58.647 33.333 0.00 0.00 0.00 3.01
4031 4347 6.727824 ATCCAAGACAAGTAATTCAGAACG 57.272 37.500 0.00 0.00 0.00 3.95
4032 4348 4.994852 TCCAAGACAAGTAATTCAGAACGG 59.005 41.667 0.00 0.00 0.00 4.44
4033 4349 4.994852 CCAAGACAAGTAATTCAGAACGGA 59.005 41.667 0.00 0.00 0.00 4.69
4034 4350 5.120830 CCAAGACAAGTAATTCAGAACGGAG 59.879 44.000 0.00 0.00 0.00 4.63
4035 4351 4.822026 AGACAAGTAATTCAGAACGGAGG 58.178 43.478 0.00 0.00 0.00 4.30
4036 4352 3.933332 GACAAGTAATTCAGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
4037 4353 3.581332 ACAAGTAATTCAGAACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
4038 4354 4.184629 CAAGTAATTCAGAACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
4039 4355 3.442076 AGTAATTCAGAACGGAGGGAGT 58.558 45.455 0.00 0.00 0.00 3.85
4040 4356 4.607239 AGTAATTCAGAACGGAGGGAGTA 58.393 43.478 0.00 0.00 0.00 2.59
4061 4377 6.779860 AGTAGTAGAGAAGGAAAAATTGCCA 58.220 36.000 0.00 0.00 0.00 4.92
4073 4389 7.175104 AGGAAAAATTGCCATCTAGACTTGTA 58.825 34.615 0.00 0.00 0.00 2.41
4074 4390 7.337942 AGGAAAAATTGCCATCTAGACTTGTAG 59.662 37.037 0.00 0.00 0.00 2.74
4075 4391 7.121315 GGAAAAATTGCCATCTAGACTTGTAGT 59.879 37.037 0.00 0.00 0.00 2.73
4076 4392 8.409358 AAAAATTGCCATCTAGACTTGTAGTT 57.591 30.769 0.00 0.00 0.00 2.24
4077 4393 6.992063 AATTGCCATCTAGACTTGTAGTTG 57.008 37.500 0.00 0.00 0.00 3.16
4078 4394 5.483685 TTGCCATCTAGACTTGTAGTTGT 57.516 39.130 0.00 0.00 0.00 3.32
4109 4425 6.579865 TCTTAGAACAGTCCGATTTTATCCC 58.420 40.000 0.00 0.00 0.00 3.85
4122 4438 1.875420 TTATCCCGACACGGCGAACA 61.875 55.000 16.62 0.00 46.86 3.18
4213 4578 1.995066 ATCGCACCAGATCCACCCA 60.995 57.895 0.00 0.00 0.00 4.51
4214 4579 1.348008 ATCGCACCAGATCCACCCAT 61.348 55.000 0.00 0.00 0.00 4.00
4215 4580 1.820906 CGCACCAGATCCACCCATG 60.821 63.158 0.00 0.00 0.00 3.66
4216 4581 1.304282 GCACCAGATCCACCCATGT 59.696 57.895 0.00 0.00 0.00 3.21
4282 4653 3.093172 GGAGGGCAGGAGAAGGGG 61.093 72.222 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 8.723365 TGGATTCATAAATAGCCTTTCTCCTAA 58.277 33.333 0.00 0.00 0.00 2.69
247 251 1.059584 TGGAGGAAGCCACCTGTTCA 61.060 55.000 3.95 0.00 40.73 3.18
450 455 1.078426 GTTGTCCCAGGTCATCCGG 60.078 63.158 0.00 0.00 39.05 5.14
493 499 4.102524 TGATATCATTAACCGCCTCTTGGT 59.897 41.667 0.00 0.00 42.98 3.67
584 590 4.087085 CGCTCGAAAATAAAAGTGCAAGTG 59.913 41.667 0.00 0.00 0.00 3.16
597 603 6.980051 ATTAAAGTTCCTACGCTCGAAAAT 57.020 33.333 0.00 0.00 0.00 1.82
690 703 1.381867 ACAAGATTGGGGTCATGGGA 58.618 50.000 0.00 0.00 0.00 4.37
762 775 5.486419 GGGGGTTTAGATTCGGAATATCCTA 59.514 44.000 2.65 0.00 33.30 2.94
763 776 4.288887 GGGGGTTTAGATTCGGAATATCCT 59.711 45.833 2.65 0.00 33.30 3.24
764 777 4.586884 GGGGGTTTAGATTCGGAATATCC 58.413 47.826 2.65 0.00 0.00 2.59
766 779 3.649502 ACGGGGGTTTAGATTCGGAATAT 59.350 43.478 2.65 2.90 0.00 1.28
767 780 3.040477 ACGGGGGTTTAGATTCGGAATA 58.960 45.455 2.65 0.00 0.00 1.75
768 781 1.841919 ACGGGGGTTTAGATTCGGAAT 59.158 47.619 2.19 2.19 0.00 3.01
769 782 1.065998 CACGGGGGTTTAGATTCGGAA 60.066 52.381 0.00 0.00 0.00 4.30
770 783 0.538118 CACGGGGGTTTAGATTCGGA 59.462 55.000 0.00 0.00 0.00 4.55
771 784 0.251073 ACACGGGGGTTTAGATTCGG 59.749 55.000 0.00 0.00 0.00 4.30
772 785 1.066716 TGACACGGGGGTTTAGATTCG 60.067 52.381 0.00 0.00 0.00 3.34
773 786 2.773993 TGACACGGGGGTTTAGATTC 57.226 50.000 0.00 0.00 0.00 2.52
774 787 2.290705 CCTTGACACGGGGGTTTAGATT 60.291 50.000 0.00 0.00 0.00 2.40
775 788 1.280998 CCTTGACACGGGGGTTTAGAT 59.719 52.381 0.00 0.00 0.00 1.98
776 789 0.688487 CCTTGACACGGGGGTTTAGA 59.312 55.000 0.00 0.00 0.00 2.10
777 790 0.399075 ACCTTGACACGGGGGTTTAG 59.601 55.000 2.65 0.00 0.00 1.85
778 791 0.397564 GACCTTGACACGGGGGTTTA 59.602 55.000 2.65 0.00 31.60 2.01
779 792 1.149854 GACCTTGACACGGGGGTTT 59.850 57.895 2.65 0.00 31.60 3.27
780 793 2.833957 GACCTTGACACGGGGGTT 59.166 61.111 2.65 0.00 31.60 4.11
781 794 3.622826 CGACCTTGACACGGGGGT 61.623 66.667 2.65 0.00 34.45 4.95
782 795 4.388499 CCGACCTTGACACGGGGG 62.388 72.222 2.65 0.00 42.48 5.40
794 807 3.499737 CATGCACGAAGGCCGACC 61.500 66.667 0.00 0.00 41.76 4.79
795 808 3.499737 CCATGCACGAAGGCCGAC 61.500 66.667 0.00 0.00 41.76 4.79
796 809 4.776322 CCCATGCACGAAGGCCGA 62.776 66.667 0.00 0.00 41.76 5.54
799 812 3.818787 CAGCCCATGCACGAAGGC 61.819 66.667 9.50 9.50 46.13 4.35
800 813 2.360350 ACAGCCCATGCACGAAGG 60.360 61.111 0.00 0.00 41.13 3.46
801 814 2.872557 CACAGCCCATGCACGAAG 59.127 61.111 0.00 0.00 41.13 3.79
802 815 3.364441 GCACAGCCCATGCACGAA 61.364 61.111 0.00 0.00 42.88 3.85
852 865 1.322538 GGCCCAGTATTGCCTTGGTG 61.323 60.000 0.00 0.00 44.46 4.17
934 970 1.426041 CGTTTATGCTAGCCGCGGTT 61.426 55.000 28.70 24.92 43.27 4.44
935 971 1.881252 CGTTTATGCTAGCCGCGGT 60.881 57.895 28.70 16.08 43.27 5.68
943 983 1.816259 GCGCCCACCGTTTATGCTA 60.816 57.895 0.00 0.00 39.71 3.49
1033 1073 2.283532 AGGGCACGAGTGAGCTCT 60.284 61.111 16.19 0.00 37.72 4.09
1214 1254 0.683828 TAACGCGGGATCACCTACCA 60.684 55.000 12.47 0.00 36.97 3.25
1311 1351 1.588824 TACACGACGCGGAAGGTGAT 61.589 55.000 21.85 11.94 34.59 3.06
1380 1420 5.697178 CAGACCATCAAAACATCAAATGCAA 59.303 36.000 0.00 0.00 0.00 4.08
1407 1447 6.018507 AGTGTCACCGAACAACAATACTTAAC 60.019 38.462 0.00 0.00 0.00 2.01
1409 1449 5.603596 AGTGTCACCGAACAACAATACTTA 58.396 37.500 0.00 0.00 0.00 2.24
1434 1474 2.481969 GGTGCGCTAAGTCTGATGATCA 60.482 50.000 9.73 0.00 0.00 2.92
1474 1514 2.517998 TTTTGGGAGGGGGTAATTCG 57.482 50.000 0.00 0.00 0.00 3.34
1799 1846 5.236478 ACAATACGGTGAAAACAGTTCTGAG 59.764 40.000 6.83 0.00 0.00 3.35
1840 1887 2.672961 TAGCTTGTGTGATCCTTCCG 57.327 50.000 0.00 0.00 0.00 4.30
1865 1912 6.334202 GGAACATCCTGTAAGAAGTAGACAG 58.666 44.000 0.00 0.00 40.26 3.51
1923 1970 3.520569 GCAGAGAACATCCTTCAGTCTC 58.479 50.000 0.00 0.00 0.00 3.36
1955 2002 4.332828 GGGAAATAATATCTCCCCAACCG 58.667 47.826 0.00 0.00 42.77 4.44
2717 2769 1.893137 TGTCTGTAACACCTCTCGCAT 59.107 47.619 0.00 0.00 31.20 4.73
2718 2770 1.324383 TGTCTGTAACACCTCTCGCA 58.676 50.000 0.00 0.00 31.20 5.10
2719 2771 2.094700 TGATGTCTGTAACACCTCTCGC 60.095 50.000 0.00 0.00 41.75 5.03
2720 2772 3.850122 TGATGTCTGTAACACCTCTCG 57.150 47.619 0.00 0.00 41.75 4.04
2721 2773 7.389053 AGAAAAATGATGTCTGTAACACCTCTC 59.611 37.037 0.00 0.00 41.75 3.20
2722 2774 7.173907 CAGAAAAATGATGTCTGTAACACCTCT 59.826 37.037 0.00 0.00 41.75 3.69
2736 2790 6.347240 GCGCTCCTAGTATCAGAAAAATGATG 60.347 42.308 0.00 0.00 40.16 3.07
2780 2834 1.001633 TCTAAGACGGTTGCCAGGTTC 59.998 52.381 0.00 0.00 0.00 3.62
2918 2972 0.109132 GATGGGCAGAAAAGGTTGCG 60.109 55.000 0.00 0.00 41.17 4.85
2935 2989 9.950496 GATATTATGGTCAGGAAACTACATGAT 57.050 33.333 0.00 0.00 40.21 2.45
2946 3000 4.588951 AGACGCAAGATATTATGGTCAGGA 59.411 41.667 0.00 0.00 43.62 3.86
2959 3013 1.002430 TCAGGAGCAAAGACGCAAGAT 59.998 47.619 0.00 0.00 43.62 2.40
3065 3119 1.294780 CCAGTCTCTCAGGCACACC 59.705 63.158 0.00 0.00 0.00 4.16
3116 3170 6.110411 TCTCTTTAGGGTTTCATCGTTTCT 57.890 37.500 0.00 0.00 0.00 2.52
3126 3180 6.011096 TGGGTGGAATAATCTCTTTAGGGTTT 60.011 38.462 0.00 0.00 0.00 3.27
3137 3191 3.496160 GCGTATGGTGGGTGGAATAATCT 60.496 47.826 0.00 0.00 0.00 2.40
3142 3196 0.550914 ATGCGTATGGTGGGTGGAAT 59.449 50.000 0.00 0.00 0.00 3.01
3147 3201 0.550914 ATCCAATGCGTATGGTGGGT 59.449 50.000 4.62 0.00 39.09 4.51
3194 3248 3.863780 GCAGAGAACAGATGACAAGAGCA 60.864 47.826 0.00 0.00 0.00 4.26
3196 3250 3.922910 TGCAGAGAACAGATGACAAGAG 58.077 45.455 0.00 0.00 0.00 2.85
3206 3260 1.423395 GAACGACCTGCAGAGAACAG 58.577 55.000 17.39 0.00 34.82 3.16
3249 3303 1.518133 GACAGGCTCGCTGCAGTAG 60.518 63.158 16.64 14.14 45.15 2.57
3258 3312 4.717629 TTCACGGCGACAGGCTCG 62.718 66.667 16.62 0.00 45.97 5.03
3287 3341 0.320771 GCGAAGAAGGCAGGTTCAGA 60.321 55.000 0.00 0.00 0.00 3.27
3321 3375 3.253188 TCACATTAAGCCAACTTCAGCAC 59.747 43.478 0.00 0.00 37.33 4.40
3430 3485 4.857871 TGAAGGTCATTATCGAAAAGCG 57.142 40.909 0.00 0.00 42.69 4.68
3474 3529 0.037160 TCCTTTTTACTGGTCCGCCC 59.963 55.000 0.00 0.00 0.00 6.13
3508 3563 3.312973 CACGTAGCGACCTAGATCTTCTT 59.687 47.826 0.00 0.00 0.00 2.52
3509 3564 2.873472 CACGTAGCGACCTAGATCTTCT 59.127 50.000 0.00 0.00 0.00 2.85
3510 3565 2.031857 CCACGTAGCGACCTAGATCTTC 60.032 54.545 0.00 0.00 0.00 2.87
3525 3580 2.767445 CGACCGGCTCATCCACGTA 61.767 63.158 0.00 0.00 34.01 3.57
3526 3581 4.129737 CGACCGGCTCATCCACGT 62.130 66.667 0.00 0.00 34.01 4.49
3527 3582 4.129737 ACGACCGGCTCATCCACG 62.130 66.667 0.00 0.00 34.01 4.94
3528 3583 2.202756 GACGACCGGCTCATCCAC 60.203 66.667 0.00 0.00 34.01 4.02
3531 3586 0.032678 ATCATGACGACCGGCTCATC 59.967 55.000 0.00 0.00 0.00 2.92
3533 3588 1.037579 AGATCATGACGACCGGCTCA 61.038 55.000 0.00 0.00 0.00 4.26
3534 3589 0.952280 TAGATCATGACGACCGGCTC 59.048 55.000 0.00 0.00 0.00 4.70
3535 3590 0.955178 CTAGATCATGACGACCGGCT 59.045 55.000 0.00 0.00 0.00 5.52
3594 3649 2.475685 GGACGCCAATTTCGTAGAAAGC 60.476 50.000 2.86 0.00 45.90 3.51
3595 3650 2.739913 TGGACGCCAATTTCGTAGAAAG 59.260 45.455 2.86 0.00 45.90 2.62
3719 3774 5.762179 TCAGAGATCCAAACCACTGTAAT 57.238 39.130 0.00 0.00 0.00 1.89
3720 3775 5.560722 TTCAGAGATCCAAACCACTGTAA 57.439 39.130 0.00 0.00 0.00 2.41
3786 3848 6.753107 ATTGGTAAACTAATTCAAGGGTCG 57.247 37.500 0.00 0.00 0.00 4.79
3873 4189 0.386731 GTTTGCCGTCGTGGATTTGG 60.387 55.000 0.51 0.00 42.00 3.28
3887 4203 5.005012 TGCAATAGTATAGTCGTTCGTTTGC 59.995 40.000 0.00 0.00 37.00 3.68
3893 4209 8.723311 AGTAGATCTGCAATAGTATAGTCGTTC 58.277 37.037 13.64 0.00 0.00 3.95
3910 4226 2.656002 TCGGAACAGGGAGTAGATCTG 58.344 52.381 5.18 0.00 34.91 2.90
3916 4232 4.529377 ACAAGTAATTCGGAACAGGGAGTA 59.471 41.667 0.00 0.00 0.00 2.59
3921 4237 4.154195 CCAAGACAAGTAATTCGGAACAGG 59.846 45.833 0.00 0.00 0.00 4.00
3922 4238 4.994852 TCCAAGACAAGTAATTCGGAACAG 59.005 41.667 0.00 0.00 0.00 3.16
3923 4239 4.963373 TCCAAGACAAGTAATTCGGAACA 58.037 39.130 0.00 0.00 0.00 3.18
3924 4240 6.496338 AATCCAAGACAAGTAATTCGGAAC 57.504 37.500 0.00 0.00 0.00 3.62
3925 4241 6.488683 ACAAATCCAAGACAAGTAATTCGGAA 59.511 34.615 0.00 0.00 0.00 4.30
3926 4242 6.001460 ACAAATCCAAGACAAGTAATTCGGA 58.999 36.000 0.00 0.00 0.00 4.55
3927 4243 6.149474 AGACAAATCCAAGACAAGTAATTCGG 59.851 38.462 0.00 0.00 0.00 4.30
3928 4244 7.133891 AGACAAATCCAAGACAAGTAATTCG 57.866 36.000 0.00 0.00 0.00 3.34
3929 4245 9.436957 TCTAGACAAATCCAAGACAAGTAATTC 57.563 33.333 0.00 0.00 0.00 2.17
3930 4246 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
3932 4248 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
3933 4249 8.188799 CGTATCTAGACAAATCCAAGACAAGTA 58.811 37.037 0.00 0.00 0.00 2.24
3934 4250 7.036220 CGTATCTAGACAAATCCAAGACAAGT 58.964 38.462 0.00 0.00 0.00 3.16
3935 4251 6.477033 CCGTATCTAGACAAATCCAAGACAAG 59.523 42.308 0.00 0.00 0.00 3.16
3936 4252 6.153851 TCCGTATCTAGACAAATCCAAGACAA 59.846 38.462 0.00 0.00 0.00 3.18
3937 4253 5.655090 TCCGTATCTAGACAAATCCAAGACA 59.345 40.000 0.00 0.00 0.00 3.41
3938 4254 6.145338 TCCGTATCTAGACAAATCCAAGAC 57.855 41.667 0.00 0.00 0.00 3.01
3939 4255 6.323996 ACATCCGTATCTAGACAAATCCAAGA 59.676 38.462 0.00 0.00 0.00 3.02
3940 4256 6.516718 ACATCCGTATCTAGACAAATCCAAG 58.483 40.000 0.00 0.00 0.00 3.61
3941 4257 6.479972 ACATCCGTATCTAGACAAATCCAA 57.520 37.500 0.00 0.00 0.00 3.53
3942 4258 7.776618 ATACATCCGTATCTAGACAAATCCA 57.223 36.000 0.00 0.00 32.66 3.41
3956 4272 9.570468 ACTAAAATGAGTCTAGATACATCCGTA 57.430 33.333 12.66 6.93 0.00 4.02
3957 4273 8.353684 CACTAAAATGAGTCTAGATACATCCGT 58.646 37.037 12.66 7.10 0.00 4.69
3958 4274 7.327275 GCACTAAAATGAGTCTAGATACATCCG 59.673 40.741 12.66 6.68 0.00 4.18
3959 4275 8.364142 AGCACTAAAATGAGTCTAGATACATCC 58.636 37.037 12.66 0.00 0.00 3.51
3962 4278 9.628500 TCTAGCACTAAAATGAGTCTAGATACA 57.372 33.333 0.00 0.00 34.65 2.29
3966 4282 9.069082 GGTATCTAGCACTAAAATGAGTCTAGA 57.931 37.037 11.59 11.59 38.76 2.43
3967 4283 9.073475 AGGTATCTAGCACTAAAATGAGTCTAG 57.927 37.037 0.00 0.00 33.29 2.43
3968 4284 8.998277 AGGTATCTAGCACTAAAATGAGTCTA 57.002 34.615 0.00 0.00 0.00 2.59
3969 4285 7.014808 GGAGGTATCTAGCACTAAAATGAGTCT 59.985 40.741 0.00 0.00 0.00 3.24
3970 4286 7.149307 GGAGGTATCTAGCACTAAAATGAGTC 58.851 42.308 0.00 0.00 0.00 3.36
3971 4287 6.239064 CGGAGGTATCTAGCACTAAAATGAGT 60.239 42.308 0.00 0.00 0.00 3.41
3972 4288 6.153067 CGGAGGTATCTAGCACTAAAATGAG 58.847 44.000 0.00 0.00 0.00 2.90
3973 4289 5.597182 ACGGAGGTATCTAGCACTAAAATGA 59.403 40.000 0.00 0.00 0.00 2.57
3974 4290 5.844004 ACGGAGGTATCTAGCACTAAAATG 58.156 41.667 0.00 0.00 0.00 2.32
3975 4291 7.778185 ATACGGAGGTATCTAGCACTAAAAT 57.222 36.000 0.00 0.00 34.18 1.82
3988 4304 6.312529 TGGATTTGTCTAGATACGGAGGTAT 58.687 40.000 0.00 0.00 42.01 2.73
3989 4305 5.698104 TGGATTTGTCTAGATACGGAGGTA 58.302 41.667 0.00 0.00 0.00 3.08
3990 4306 4.543689 TGGATTTGTCTAGATACGGAGGT 58.456 43.478 0.00 0.00 0.00 3.85
3991 4307 5.302059 TCTTGGATTTGTCTAGATACGGAGG 59.698 44.000 0.00 0.00 0.00 4.30
3992 4308 6.183360 TGTCTTGGATTTGTCTAGATACGGAG 60.183 42.308 0.00 0.00 0.00 4.63
3993 4309 5.655090 TGTCTTGGATTTGTCTAGATACGGA 59.345 40.000 0.00 0.00 0.00 4.69
3994 4310 5.902681 TGTCTTGGATTTGTCTAGATACGG 58.097 41.667 0.00 0.00 0.00 4.02
3995 4311 7.036220 ACTTGTCTTGGATTTGTCTAGATACG 58.964 38.462 0.00 0.00 0.00 3.06
3996 4312 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
3998 4314 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
3999 4315 9.436957 GAATTACTTGTCTTGGATTTGTCTAGA 57.563 33.333 0.00 0.00 0.00 2.43
4000 4316 9.219603 TGAATTACTTGTCTTGGATTTGTCTAG 57.780 33.333 0.00 0.00 0.00 2.43
4001 4317 9.219603 CTGAATTACTTGTCTTGGATTTGTCTA 57.780 33.333 0.00 0.00 0.00 2.59
4002 4318 7.939039 TCTGAATTACTTGTCTTGGATTTGTCT 59.061 33.333 0.00 0.00 0.00 3.41
4003 4319 8.099364 TCTGAATTACTTGTCTTGGATTTGTC 57.901 34.615 0.00 0.00 0.00 3.18
4004 4320 8.352942 GTTCTGAATTACTTGTCTTGGATTTGT 58.647 33.333 0.00 0.00 0.00 2.83
4005 4321 7.535258 CGTTCTGAATTACTTGTCTTGGATTTG 59.465 37.037 0.00 0.00 0.00 2.32
4006 4322 7.308589 CCGTTCTGAATTACTTGTCTTGGATTT 60.309 37.037 0.00 0.00 0.00 2.17
4007 4323 6.149474 CCGTTCTGAATTACTTGTCTTGGATT 59.851 38.462 0.00 0.00 0.00 3.01
4008 4324 5.643777 CCGTTCTGAATTACTTGTCTTGGAT 59.356 40.000 0.00 0.00 0.00 3.41
4009 4325 4.994852 CCGTTCTGAATTACTTGTCTTGGA 59.005 41.667 0.00 0.00 0.00 3.53
4010 4326 4.994852 TCCGTTCTGAATTACTTGTCTTGG 59.005 41.667 0.00 0.00 0.00 3.61
4011 4327 5.120830 CCTCCGTTCTGAATTACTTGTCTTG 59.879 44.000 0.00 0.00 0.00 3.02
4012 4328 5.238583 CCTCCGTTCTGAATTACTTGTCTT 58.761 41.667 0.00 0.00 0.00 3.01
4013 4329 4.322801 CCCTCCGTTCTGAATTACTTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
4014 4330 3.933332 CCCTCCGTTCTGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
4015 4331 3.581332 TCCCTCCGTTCTGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
4016 4332 4.184629 CTCCCTCCGTTCTGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
4017 4333 3.838903 ACTCCCTCCGTTCTGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
4018 4334 3.442076 ACTCCCTCCGTTCTGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
4019 4335 3.889520 ACTCCCTCCGTTCTGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
4020 4336 4.607239 ACTACTCCCTCCGTTCTGAATTA 58.393 43.478 0.00 0.00 0.00 1.40
4021 4337 3.442076 ACTACTCCCTCCGTTCTGAATT 58.558 45.455 0.00 0.00 0.00 2.17
4022 4338 3.103080 ACTACTCCCTCCGTTCTGAAT 57.897 47.619 0.00 0.00 0.00 2.57
4023 4339 2.599408 ACTACTCCCTCCGTTCTGAA 57.401 50.000 0.00 0.00 0.00 3.02
4024 4340 2.842496 TCTACTACTCCCTCCGTTCTGA 59.158 50.000 0.00 0.00 0.00 3.27
4025 4341 3.118334 TCTCTACTACTCCCTCCGTTCTG 60.118 52.174 0.00 0.00 0.00 3.02
4026 4342 3.113824 TCTCTACTACTCCCTCCGTTCT 58.886 50.000 0.00 0.00 0.00 3.01
4027 4343 3.557228 TCTCTACTACTCCCTCCGTTC 57.443 52.381 0.00 0.00 0.00 3.95
4028 4344 3.371810 CCTTCTCTACTACTCCCTCCGTT 60.372 52.174 0.00 0.00 0.00 4.44
4029 4345 2.173143 CCTTCTCTACTACTCCCTCCGT 59.827 54.545 0.00 0.00 0.00 4.69
4030 4346 2.438763 TCCTTCTCTACTACTCCCTCCG 59.561 54.545 0.00 0.00 0.00 4.63
4031 4347 4.523168 TTCCTTCTCTACTACTCCCTCC 57.477 50.000 0.00 0.00 0.00 4.30
4032 4348 6.854091 TTTTTCCTTCTCTACTACTCCCTC 57.146 41.667 0.00 0.00 0.00 4.30
4033 4349 7.625469 CAATTTTTCCTTCTCTACTACTCCCT 58.375 38.462 0.00 0.00 0.00 4.20
4034 4350 6.316640 GCAATTTTTCCTTCTCTACTACTCCC 59.683 42.308 0.00 0.00 0.00 4.30
4035 4351 6.316640 GGCAATTTTTCCTTCTCTACTACTCC 59.683 42.308 0.00 0.00 0.00 3.85
4036 4352 6.879458 TGGCAATTTTTCCTTCTCTACTACTC 59.121 38.462 0.00 0.00 0.00 2.59
4037 4353 6.779860 TGGCAATTTTTCCTTCTCTACTACT 58.220 36.000 0.00 0.00 0.00 2.57
4038 4354 7.554476 AGATGGCAATTTTTCCTTCTCTACTAC 59.446 37.037 0.00 0.00 33.21 2.73
4039 4355 7.633789 AGATGGCAATTTTTCCTTCTCTACTA 58.366 34.615 0.00 0.00 33.21 1.82
4040 4356 6.488715 AGATGGCAATTTTTCCTTCTCTACT 58.511 36.000 0.00 0.00 33.21 2.57
4061 4377 4.949121 AGGGGACAACTACAAGTCTAGAT 58.051 43.478 0.00 0.00 35.18 1.98
4073 4389 3.835395 CTGTTCTAAGAGAGGGGACAACT 59.165 47.826 0.00 0.00 0.00 3.16
4074 4390 3.579151 ACTGTTCTAAGAGAGGGGACAAC 59.421 47.826 0.00 0.00 0.00 3.32
4075 4391 3.833070 GACTGTTCTAAGAGAGGGGACAA 59.167 47.826 0.00 0.00 0.00 3.18
4076 4392 3.432378 GACTGTTCTAAGAGAGGGGACA 58.568 50.000 0.00 0.00 0.00 4.02
4077 4393 2.761767 GGACTGTTCTAAGAGAGGGGAC 59.238 54.545 0.00 0.00 0.00 4.46
4078 4394 2.620886 CGGACTGTTCTAAGAGAGGGGA 60.621 54.545 0.00 0.00 0.00 4.81
4109 4425 1.186408 CGTTATATGTTCGCCGTGTCG 59.814 52.381 0.00 0.00 0.00 4.35
4122 4438 4.588951 TCCTGTCTCTGCAATCCGTTATAT 59.411 41.667 0.00 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.