Multiple sequence alignment - TraesCS5B01G494600

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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 TraesCS5B01G494600 chr5B 100.000 4574 0 0 1 4574 662460174 662455601 0.000000e+00 8447.0
1 TraesCS5B01G494600 chr5B 94.326 141 7 1 3770 3909 482995474 482995334 9.970000e-52 215.0
2 TraesCS5B01G494600 chr5D 93.599 3031 155 22 759 3777 526692564 526689561 0.000000e+00 4486.0
3 TraesCS5B01G494600 chr5D 93.883 703 17 3 3898 4574 526689564 526688862 0.000000e+00 1037.0
4 TraesCS5B01G494600 chr5D 94.830 619 32 0 1 619 526693867 526693249 0.000000e+00 966.0
5 TraesCS5B01G494600 chr5D 83.452 701 94 9 44 723 526719142 526718443 2.320000e-177 632.0
6 TraesCS5B01G494600 chr5D 94.326 141 7 1 3775 3914 211375623 211375763 9.970000e-52 215.0
7 TraesCS5B01G494600 chr5D 86.517 178 18 5 3005 3177 526752978 526752802 1.680000e-44 191.0
8 TraesCS5B01G494600 chr5A 91.985 1597 84 22 2197 3777 653851770 653850202 0.000000e+00 2200.0
9 TraesCS5B01G494600 chr5A 84.783 1426 132 38 725 2099 653853420 653852029 0.000000e+00 1352.0
10 TraesCS5B01G494600 chr5A 96.779 683 16 3 3898 4574 653850205 653849523 0.000000e+00 1134.0
11 TraesCS5B01G494600 chr5A 93.289 596 39 1 2 597 653854268 653853674 0.000000e+00 878.0
12 TraesCS5B01G494600 chr5A 86.239 545 70 3 1 541 653866609 653866066 1.830000e-163 586.0
13 TraesCS5B01G494600 chr5A 90.278 72 6 1 670 740 653853513 653853442 4.870000e-15 93.5
14 TraesCS5B01G494600 chr5A 85.000 60 9 0 1400 1459 653038829 653038888 1.370000e-05 62.1
15 TraesCS5B01G494600 chr7A 93.789 322 20 0 1156 1477 30405227 30405548 6.880000e-133 484.0
16 TraesCS5B01G494600 chr7A 86.117 461 51 8 1568 2016 30405610 30406069 6.880000e-133 484.0
17 TraesCS5B01G494600 chr2B 96.350 137 3 2 3775 3909 655599878 655599742 1.660000e-54 224.0
18 TraesCS5B01G494600 chr3D 94.521 146 5 3 3760 3904 614251078 614251221 5.960000e-54 222.0
19 TraesCS5B01G494600 chr1B 96.992 133 2 2 3769 3900 417425284 417425153 5.960000e-54 222.0
20 TraesCS5B01G494600 chr1B 96.296 135 3 2 3770 3903 623731981 623732114 2.140000e-53 220.0
21 TraesCS5B01G494600 chr4A 94.326 141 6 2 3762 3900 729151828 729151968 9.970000e-52 215.0
22 TraesCS5B01G494600 chr2D 94.326 141 6 2 3762 3901 536091165 536091026 9.970000e-52 215.0
23 TraesCS5B01G494600 chr7B 96.094 128 3 2 3774 3900 372835109 372834983 1.670000e-49 207.0


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 TraesCS5B01G494600 chr5B 662455601 662460174 4573 True 8447.0 8447 100.0000 1 4574 1 chr5B.!!$R2 4573
1 TraesCS5B01G494600 chr5D 526688862 526693867 5005 True 2163.0 4486 94.1040 1 4574 3 chr5D.!!$R3 4573
2 TraesCS5B01G494600 chr5D 526718443 526719142 699 True 632.0 632 83.4520 44 723 1 chr5D.!!$R1 679
3 TraesCS5B01G494600 chr5A 653849523 653854268 4745 True 1131.5 2200 91.4228 2 4574 5 chr5A.!!$R2 4572
4 TraesCS5B01G494600 chr5A 653866066 653866609 543 True 586.0 586 86.2390 1 541 1 chr5A.!!$R1 540
5 TraesCS5B01G494600 chr7A 30405227 30406069 842 False 484.0 484 89.9530 1156 2016 2 chr7A.!!$F1 860

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
123 124 0.462759 GCTCTCTGGTGAAATCCCGG 60.463 60.000 0.00 0.00 0.00 5.73 F
274 278 0.687920 TGTGGTCCGCCTGTATCAAA 59.312 50.000 0.00 0.00 35.27 2.69 F
1170 2002 1.062206 GGTCCTAACGCTCGTCGAG 59.938 63.158 18.08 18.08 41.67 4.04 F
1519 2351 1.070134 GAGTGTGCCGCTCCCATAATA 59.930 52.381 4.87 0.00 35.24 0.98 F
3090 4164 0.888619 TCCAGACTGACACTAAGGCG 59.111 55.000 3.32 0.00 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1170 2002 1.643832 GATTTGGCCTGCGATCGAC 59.356 57.895 21.57 10.98 0.00 4.20 R
1743 2608 2.032981 CTTCACACCGGCTGCTTTT 58.967 52.632 0.00 0.00 0.00 2.27 R
3090 4164 1.544314 GCCACATCAGCCCTAGGAATC 60.544 57.143 11.48 0.00 0.00 2.52 R
3204 4287 1.075374 TCATACTGCAGGGCCTGTTTT 59.925 47.619 32.80 19.48 33.43 2.43 R
3947 5038 0.615331 TGGGAGCAGAGTTGATGGAC 59.385 55.000 0.00 0.00 0.00 4.02 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
24 25 4.695217 TTGACAAACTTGAACCTGTCAC 57.305 40.909 3.36 0.00 45.78 3.67
71 72 1.755380 GTGACTATTGGGGAGCTACGT 59.245 52.381 0.00 0.00 0.00 3.57
75 76 0.906066 TATTGGGGAGCTACGTGCAA 59.094 50.000 0.00 0.00 45.94 4.08
79 80 1.819632 GGGAGCTACGTGCAATGGG 60.820 63.158 0.00 0.00 45.94 4.00
123 124 0.462759 GCTCTCTGGTGAAATCCCGG 60.463 60.000 0.00 0.00 0.00 5.73
164 165 3.569194 TCACTTGCCCACTTGAACTTA 57.431 42.857 0.00 0.00 0.00 2.24
165 166 3.211045 TCACTTGCCCACTTGAACTTAC 58.789 45.455 0.00 0.00 0.00 2.34
167 168 1.535462 CTTGCCCACTTGAACTTACCG 59.465 52.381 0.00 0.00 0.00 4.02
274 278 0.687920 TGTGGTCCGCCTGTATCAAA 59.312 50.000 0.00 0.00 35.27 2.69
557 561 1.679032 GGGTCTGTGGTCACAATAGCC 60.679 57.143 14.40 14.40 41.33 3.93
597 601 6.294508 GGCACAATATGATATGGGGTTGTAAC 60.295 42.308 0.00 0.00 0.00 2.50
620 732 4.965119 ATATTTCACCTTTCTTGTCCGC 57.035 40.909 0.00 0.00 0.00 5.54
624 736 1.689813 TCACCTTTCTTGTCCGCTGTA 59.310 47.619 0.00 0.00 0.00 2.74
629 741 3.502211 CCTTTCTTGTCCGCTGTAAATGT 59.498 43.478 0.00 0.00 0.00 2.71
630 742 4.693566 CCTTTCTTGTCCGCTGTAAATGTA 59.306 41.667 0.00 0.00 0.00 2.29
631 743 5.180492 CCTTTCTTGTCCGCTGTAAATGTAA 59.820 40.000 0.00 0.00 0.00 2.41
633 745 5.794687 TCTTGTCCGCTGTAAATGTAATG 57.205 39.130 0.00 0.00 0.00 1.90
634 746 5.242434 TCTTGTCCGCTGTAAATGTAATGT 58.758 37.500 0.00 0.00 0.00 2.71
635 747 6.399743 TCTTGTCCGCTGTAAATGTAATGTA 58.600 36.000 0.00 0.00 0.00 2.29
637 749 7.551262 TCTTGTCCGCTGTAAATGTAATGTATT 59.449 33.333 0.00 0.00 0.00 1.89
638 750 7.010697 TGTCCGCTGTAAATGTAATGTATTG 57.989 36.000 0.00 0.00 0.00 1.90
639 751 5.907391 GTCCGCTGTAAATGTAATGTATTGC 59.093 40.000 0.00 0.00 0.00 3.56
640 752 5.820423 TCCGCTGTAAATGTAATGTATTGCT 59.180 36.000 0.00 0.00 0.00 3.91
641 753 6.018262 TCCGCTGTAAATGTAATGTATTGCTC 60.018 38.462 0.00 0.00 0.00 4.26
642 754 6.017934 CCGCTGTAAATGTAATGTATTGCTCT 60.018 38.462 0.00 0.00 0.00 4.09
643 755 7.409697 CGCTGTAAATGTAATGTATTGCTCTT 58.590 34.615 0.00 0.00 0.00 2.85
644 756 7.584123 CGCTGTAAATGTAATGTATTGCTCTTC 59.416 37.037 0.00 0.00 0.00 2.87
645 757 8.616076 GCTGTAAATGTAATGTATTGCTCTTCT 58.384 33.333 0.00 0.00 0.00 2.85
650 762 7.849804 ATGTAATGTATTGCTCTTCTTTCGT 57.150 32.000 0.00 0.00 0.00 3.85
651 763 7.060600 TGTAATGTATTGCTCTTCTTTCGTG 57.939 36.000 0.00 0.00 0.00 4.35
652 764 6.649141 TGTAATGTATTGCTCTTCTTTCGTGT 59.351 34.615 0.00 0.00 0.00 4.49
653 765 4.990543 TGTATTGCTCTTCTTTCGTGTG 57.009 40.909 0.00 0.00 0.00 3.82
654 766 2.977405 ATTGCTCTTCTTTCGTGTGC 57.023 45.000 0.00 0.00 0.00 4.57
655 767 1.662517 TTGCTCTTCTTTCGTGTGCA 58.337 45.000 0.00 0.00 0.00 4.57
656 768 1.662517 TGCTCTTCTTTCGTGTGCAA 58.337 45.000 0.00 0.00 0.00 4.08
657 769 1.599071 TGCTCTTCTTTCGTGTGCAAG 59.401 47.619 0.00 0.00 0.00 4.01
658 770 1.599542 GCTCTTCTTTCGTGTGCAAGT 59.400 47.619 0.00 0.00 0.00 3.16
659 771 2.348966 GCTCTTCTTTCGTGTGCAAGTC 60.349 50.000 0.00 0.00 0.00 3.01
660 772 2.866156 CTCTTCTTTCGTGTGCAAGTCA 59.134 45.455 0.00 0.00 0.00 3.41
661 773 2.607635 TCTTCTTTCGTGTGCAAGTCAC 59.392 45.455 0.00 0.00 45.82 3.67
667 779 2.690326 GTGTGCAAGTCACTCGGTT 58.310 52.632 0.00 0.00 45.81 4.44
677 789 4.877378 AGTCACTCGGTTTGTATGGTAA 57.123 40.909 0.00 0.00 0.00 2.85
678 790 5.217978 AGTCACTCGGTTTGTATGGTAAA 57.782 39.130 0.00 0.00 0.00 2.01
679 791 4.992951 AGTCACTCGGTTTGTATGGTAAAC 59.007 41.667 0.00 0.00 37.31 2.01
757 926 9.722184 AAAGATGTTGATCTCTATGGTATGATG 57.278 33.333 0.00 0.00 38.03 3.07
766 1573 3.958147 TCTATGGTATGATGACCGTGTGT 59.042 43.478 0.00 0.00 42.99 3.72
773 1580 1.535444 ATGACCGTGTGTGGGGAGA 60.535 57.895 0.00 0.00 0.00 3.71
803 1610 2.478894 CCTTGCTTCGAAGAAAGCGTAA 59.521 45.455 32.53 10.92 45.90 3.18
898 1708 3.452627 GGCCTTCTAGACAAATCCAGAGA 59.547 47.826 0.00 0.00 0.00 3.10
899 1709 4.442753 GGCCTTCTAGACAAATCCAGAGAG 60.443 50.000 0.00 0.00 0.00 3.20
900 1710 4.404073 GCCTTCTAGACAAATCCAGAGAGA 59.596 45.833 0.00 0.00 0.00 3.10
901 1711 5.451798 GCCTTCTAGACAAATCCAGAGAGAG 60.452 48.000 0.00 0.00 0.00 3.20
1001 1811 1.144936 CCAGCTAGCCTGCAGTACC 59.855 63.158 12.13 0.27 40.36 3.34
1088 1898 2.482494 CACAGATACCCTTTCCCTCCT 58.518 52.381 0.00 0.00 0.00 3.69
1089 1899 2.846827 CACAGATACCCTTTCCCTCCTT 59.153 50.000 0.00 0.00 0.00 3.36
1090 1900 3.116174 ACAGATACCCTTTCCCTCCTTC 58.884 50.000 0.00 0.00 0.00 3.46
1091 1901 2.439880 CAGATACCCTTTCCCTCCTTCC 59.560 54.545 0.00 0.00 0.00 3.46
1092 1902 2.322543 AGATACCCTTTCCCTCCTTCCT 59.677 50.000 0.00 0.00 0.00 3.36
1140 1950 4.812476 CGAATCCGCCTGCCACGA 62.812 66.667 0.00 0.00 0.00 4.35
1170 2002 1.062206 GGTCCTAACGCTCGTCGAG 59.938 63.158 18.08 18.08 41.67 4.04
1478 2310 4.282703 TGGGGTTTCTTCTCTGTACTGTAC 59.717 45.833 10.98 10.98 0.00 2.90
1480 2312 5.471257 GGGTTTCTTCTCTGTACTGTACTG 58.529 45.833 17.98 16.98 0.00 2.74
1482 2314 6.208204 GGGTTTCTTCTCTGTACTGTACTGTA 59.792 42.308 17.98 8.40 0.00 2.74
1519 2351 1.070134 GAGTGTGCCGCTCCCATAATA 59.930 52.381 4.87 0.00 35.24 0.98
1689 2552 5.072741 AGCTTCTTCTTGGTTCTGCATTTA 58.927 37.500 0.00 0.00 0.00 1.40
1691 2554 6.886459 AGCTTCTTCTTGGTTCTGCATTTATA 59.114 34.615 0.00 0.00 0.00 0.98
1694 2557 8.579850 TTCTTCTTGGTTCTGCATTTATATGT 57.420 30.769 0.00 0.00 34.12 2.29
1695 2558 7.988737 TCTTCTTGGTTCTGCATTTATATGTG 58.011 34.615 0.00 0.00 34.12 3.21
1699 2564 9.276590 TCTTGGTTCTGCATTTATATGTGATAG 57.723 33.333 0.00 0.00 34.12 2.08
1717 2582 9.685276 ATGTGATAGGTTTATCTGAATGTTTGA 57.315 29.630 0.00 0.00 37.23 2.69
1738 2603 1.492599 TGAGTGGGATTGTGTGTTGGA 59.507 47.619 0.00 0.00 0.00 3.53
1743 2608 1.317613 GGATTGTGTGTTGGACAGCA 58.682 50.000 0.00 0.00 34.28 4.41
1851 2716 9.640952 AATGGCAATATACTGGTAAGTAATTGT 57.359 29.630 0.00 0.00 42.17 2.71
1903 2775 3.206034 TCATTGCAGTTCATTTGCTCG 57.794 42.857 0.00 0.00 42.02 5.03
1904 2776 2.553602 TCATTGCAGTTCATTTGCTCGT 59.446 40.909 0.00 0.00 42.02 4.18
1909 2781 2.578495 CAGTTCATTTGCTCGTGCTTC 58.422 47.619 11.19 0.00 40.48 3.86
1934 2809 9.069082 TCCACGAAAAACTTTATTATCTGGAAA 57.931 29.630 0.00 0.00 0.00 3.13
1945 2820 9.274206 CTTTATTATCTGGAAAGCCTTAGTACC 57.726 37.037 0.00 0.00 34.31 3.34
1961 2836 6.037610 CCTTAGTACCATTCTCTGAACATTGC 59.962 42.308 0.00 0.00 0.00 3.56
1967 2842 2.275134 TCTCTGAACATTGCTTGGCA 57.725 45.000 0.00 0.00 36.47 4.92
1992 2872 4.134379 GATGAGCCATCTGTCTCAGAAA 57.866 45.455 3.58 0.00 44.04 2.52
2024 2904 7.065085 AGGATTGTTCGTCATAGAAATGTTCAG 59.935 37.037 0.00 0.00 34.50 3.02
2028 2908 6.704050 TGTTCGTCATAGAAATGTTCAGTTGA 59.296 34.615 0.00 0.00 34.50 3.18
2043 2923 8.450578 TGTTCAGTTGATAGATTTGTGAGTTT 57.549 30.769 0.00 0.00 0.00 2.66
2045 2925 9.173939 GTTCAGTTGATAGATTTGTGAGTTTTG 57.826 33.333 0.00 0.00 0.00 2.44
2067 2947 4.081365 TGACTATTGACAGGTTCGCCATAA 60.081 41.667 0.00 0.00 40.60 1.90
2175 3160 8.383175 ACCTTTCTGAATATTAAGTTCCTGTCA 58.617 33.333 0.00 0.00 0.00 3.58
2213 3284 6.239458 GGAAGTTCTGTATCCTCTCTATTGGG 60.239 46.154 2.25 0.00 0.00 4.12
2232 3303 3.091545 GGGCTGGAATGTTCATTTCAGA 58.908 45.455 27.90 1.99 39.04 3.27
2267 3338 6.567769 TTGTTTTGTTTTCATCGAAGCTTC 57.432 33.333 16.84 16.84 0.00 3.86
2289 3360 9.206870 GCTTCATTTTGTCTCATCCAAATAAAA 57.793 29.630 0.00 0.00 32.28 1.52
2360 3431 5.684626 GTCGTGGTACCGTTGATCTAATAAG 59.315 44.000 7.57 0.00 0.00 1.73
2398 3469 8.984891 ATTCATTTTGCAAATTCAGACGATTA 57.015 26.923 13.65 0.00 0.00 1.75
2520 3593 9.669353 CAATCATAAGGTACATAAAGAACATGC 57.331 33.333 0.00 0.00 0.00 4.06
2523 3596 5.897377 AAGGTACATAAAGAACATGCACC 57.103 39.130 0.00 0.00 39.29 5.01
2547 3620 6.101997 CAGTTTGGATAAAAAGGCATCCTTC 58.898 40.000 0.00 0.00 43.92 3.46
2576 3649 7.370383 TCAATTATTCTTGAAACAGAGTTGCC 58.630 34.615 0.00 0.00 32.35 4.52
2684 3757 9.662947 AATAGTTCCTTGTGTACCACTAAATAC 57.337 33.333 0.00 0.00 35.11 1.89
2693 3766 8.330466 TGTGTACCACTAAATACCTTTGAATG 57.670 34.615 0.00 0.00 35.11 2.67
2699 3772 6.152661 CCACTAAATACCTTTGAATGCCTCAA 59.847 38.462 0.00 0.00 42.48 3.02
2716 3789 3.507622 CCTCAAAGAAAAGGTGGATCCAC 59.492 47.826 33.14 33.14 45.49 4.02
2743 3816 7.167535 TCCACATTTAATGAGACAATGAGTGA 58.832 34.615 12.28 0.00 33.02 3.41
2770 3843 1.966451 GGGGTGAGGCAAACACTCG 60.966 63.158 0.00 0.00 39.36 4.18
2775 3848 2.954753 GAGGCAAACACTCGGTGCG 61.955 63.158 4.23 0.00 39.22 5.34
2791 3864 3.241995 CGGTGCGATCTAGTAGTTTTTGC 60.242 47.826 0.00 0.80 0.00 3.68
2883 3957 4.641989 ACTGCTGCAGTTAAATTGGATAGG 59.358 41.667 28.49 1.13 42.59 2.57
2970 4044 9.424319 AGGTTAACTATTCGCTGATACATAATG 57.576 33.333 5.42 0.00 0.00 1.90
2978 4052 5.095490 TCGCTGATACATAATGTGCTATCG 58.905 41.667 0.00 0.00 0.00 2.92
2987 4061 6.705782 ACATAATGTGCTATCGTTTTCTTCG 58.294 36.000 0.00 0.00 0.00 3.79
3090 4164 0.888619 TCCAGACTGACACTAAGGCG 59.111 55.000 3.32 0.00 0.00 5.52
3161 4240 3.492421 AATTGCTGCAACCGTATTCTG 57.508 42.857 18.51 0.00 0.00 3.02
3190 4272 4.136796 CACTTGAGGACAACCATTCTGAA 58.863 43.478 0.00 0.00 38.94 3.02
3194 4276 7.121759 CACTTGAGGACAACCATTCTGAATATT 59.878 37.037 1.98 0.00 38.94 1.28
3198 4280 7.556275 TGAGGACAACCATTCTGAATATTTACC 59.444 37.037 1.98 6.62 38.94 2.85
3204 4287 9.627123 CAACCATTCTGAATATTTACCCTCTTA 57.373 33.333 1.98 0.00 0.00 2.10
3337 4420 0.673644 AGCCCGGTTTTGAGTCATCG 60.674 55.000 0.00 0.00 0.00 3.84
3362 4451 7.280205 CGGTTAAGGAGCATAAGTACATTTCTT 59.720 37.037 0.00 0.00 0.00 2.52
3446 4536 6.318628 TGATGTAATTGCACAATCGGTTTAC 58.681 36.000 0.00 0.00 30.84 2.01
3479 4569 2.949451 AATAGCCTCCTATCGATGCG 57.051 50.000 8.54 0.00 37.22 4.73
3525 4615 6.906157 TGCATTTTCCTGAGATTTTTCTCT 57.094 33.333 4.76 0.00 37.62 3.10
3614 4705 4.527509 TTCACACTCTTGACTCAGATCC 57.472 45.455 0.00 0.00 0.00 3.36
3617 4708 2.490115 ACACTCTTGACTCAGATCCGAC 59.510 50.000 0.00 0.00 0.00 4.79
3634 4725 1.939934 CGACGCACACCAATAATCCAT 59.060 47.619 0.00 0.00 0.00 3.41
3698 4789 3.635373 CAGCTCATATGCACCTTCCATTT 59.365 43.478 0.00 0.00 34.99 2.32
3699 4790 4.098960 CAGCTCATATGCACCTTCCATTTT 59.901 41.667 0.00 0.00 34.99 1.82
3771 4862 6.807720 CAGTTTGCAATACACATGCTTCATTA 59.192 34.615 0.00 0.00 44.14 1.90
3777 4868 6.260936 GCAATACACATGCTTCATTAGGTACT 59.739 38.462 0.00 0.00 41.03 2.73
3778 4869 7.519008 GCAATACACATGCTTCATTAGGTACTC 60.519 40.741 0.00 0.00 39.44 2.59
3779 4870 4.770795 ACACATGCTTCATTAGGTACTCC 58.229 43.478 0.00 0.00 41.75 3.85
3780 4871 4.130118 CACATGCTTCATTAGGTACTCCC 58.870 47.826 0.00 0.00 41.75 4.30
3782 4873 4.101741 ACATGCTTCATTAGGTACTCCCTC 59.898 45.833 0.00 0.00 44.81 4.30
3783 4874 3.039011 TGCTTCATTAGGTACTCCCTCC 58.961 50.000 0.00 0.00 44.81 4.30
3784 4875 2.036089 GCTTCATTAGGTACTCCCTCCG 59.964 54.545 0.00 0.00 44.81 4.63
3785 4876 3.297736 CTTCATTAGGTACTCCCTCCGT 58.702 50.000 0.00 0.00 44.81 4.69
3786 4877 2.941480 TCATTAGGTACTCCCTCCGTC 58.059 52.381 0.00 0.00 44.81 4.79
3787 4878 2.512896 TCATTAGGTACTCCCTCCGTCT 59.487 50.000 0.00 0.00 44.81 4.18
3788 4879 2.725221 TTAGGTACTCCCTCCGTCTC 57.275 55.000 0.00 0.00 44.81 3.36
3789 4880 1.588239 TAGGTACTCCCTCCGTCTCA 58.412 55.000 0.00 0.00 44.81 3.27
3790 4881 0.702902 AGGTACTCCCTCCGTCTCAA 59.297 55.000 0.00 0.00 40.71 3.02
3791 4882 1.076677 AGGTACTCCCTCCGTCTCAAA 59.923 52.381 0.00 0.00 40.71 2.69
3792 4883 1.897802 GGTACTCCCTCCGTCTCAAAA 59.102 52.381 0.00 0.00 0.00 2.44
3793 4884 2.500504 GGTACTCCCTCCGTCTCAAAAT 59.499 50.000 0.00 0.00 0.00 1.82
3794 4885 3.055312 GGTACTCCCTCCGTCTCAAAATT 60.055 47.826 0.00 0.00 0.00 1.82
3795 4886 3.336138 ACTCCCTCCGTCTCAAAATTC 57.664 47.619 0.00 0.00 0.00 2.17
3796 4887 2.907042 ACTCCCTCCGTCTCAAAATTCT 59.093 45.455 0.00 0.00 0.00 2.40
3797 4888 3.328050 ACTCCCTCCGTCTCAAAATTCTT 59.672 43.478 0.00 0.00 0.00 2.52
3798 4889 3.674997 TCCCTCCGTCTCAAAATTCTTG 58.325 45.455 0.00 0.00 0.00 3.02
3799 4890 3.072476 TCCCTCCGTCTCAAAATTCTTGT 59.928 43.478 0.00 0.00 0.00 3.16
3800 4891 3.437049 CCCTCCGTCTCAAAATTCTTGTC 59.563 47.826 0.00 0.00 0.00 3.18
3801 4892 4.319177 CCTCCGTCTCAAAATTCTTGTCT 58.681 43.478 0.00 0.00 0.00 3.41
3802 4893 4.757149 CCTCCGTCTCAAAATTCTTGTCTT 59.243 41.667 0.00 0.00 0.00 3.01
3803 4894 5.932303 CCTCCGTCTCAAAATTCTTGTCTTA 59.068 40.000 0.00 0.00 0.00 2.10
3804 4895 6.091441 CCTCCGTCTCAAAATTCTTGTCTTAG 59.909 42.308 0.00 0.00 0.00 2.18
3805 4896 6.755206 TCCGTCTCAAAATTCTTGTCTTAGA 58.245 36.000 0.00 0.00 0.00 2.10
3806 4897 7.386851 TCCGTCTCAAAATTCTTGTCTTAGAT 58.613 34.615 0.00 0.00 0.00 1.98
3807 4898 7.878127 TCCGTCTCAAAATTCTTGTCTTAGATT 59.122 33.333 0.00 0.00 0.00 2.40
3808 4899 8.507249 CCGTCTCAAAATTCTTGTCTTAGATTT 58.493 33.333 0.00 0.00 0.00 2.17
3809 4900 9.322776 CGTCTCAAAATTCTTGTCTTAGATTTG 57.677 33.333 0.00 0.00 30.65 2.32
3820 4911 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
3821 4912 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
3822 4913 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
3823 4914 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
3824 4915 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
3825 4916 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
3826 4917 9.828852 CTTAGATTTGTCTAGATACGGATGTAC 57.171 37.037 0.00 0.00 32.26 2.90
3827 4918 7.216973 AGATTTGTCTAGATACGGATGTACC 57.783 40.000 0.00 0.00 32.26 3.34
3828 4919 7.005296 AGATTTGTCTAGATACGGATGTACCT 58.995 38.462 0.00 0.00 36.31 3.08
3829 4920 8.162085 AGATTTGTCTAGATACGGATGTACCTA 58.838 37.037 0.00 0.00 36.31 3.08
3830 4921 8.701908 ATTTGTCTAGATACGGATGTACCTAA 57.298 34.615 0.00 0.00 36.31 2.69
3831 4922 8.701908 TTTGTCTAGATACGGATGTACCTAAT 57.298 34.615 0.00 0.00 36.31 1.73
3832 4923 9.797642 TTTGTCTAGATACGGATGTACCTAATA 57.202 33.333 0.00 0.00 36.31 0.98
3833 4924 8.783833 TGTCTAGATACGGATGTACCTAATAC 57.216 38.462 0.00 0.00 36.31 1.89
3834 4925 8.600668 TGTCTAGATACGGATGTACCTAATACT 58.399 37.037 0.00 0.00 34.56 2.12
3840 4931 9.334693 GATACGGATGTACCTAATACTAAAACG 57.665 37.037 0.00 0.00 34.56 3.60
3841 4932 7.100458 ACGGATGTACCTAATACTAAAACGT 57.900 36.000 0.00 0.00 34.56 3.99
3842 4933 6.974622 ACGGATGTACCTAATACTAAAACGTG 59.025 38.462 0.00 0.00 34.56 4.49
3843 4934 7.148086 ACGGATGTACCTAATACTAAAACGTGA 60.148 37.037 0.00 0.00 34.56 4.35
3844 4935 7.166473 CGGATGTACCTAATACTAAAACGTGAC 59.834 40.741 0.00 0.00 34.56 3.67
3845 4936 8.193438 GGATGTACCTAATACTAAAACGTGACT 58.807 37.037 0.00 0.00 34.56 3.41
3846 4937 9.578439 GATGTACCTAATACTAAAACGTGACTT 57.422 33.333 0.00 0.00 34.56 3.01
3847 4938 8.746922 TGTACCTAATACTAAAACGTGACTTG 57.253 34.615 0.00 0.00 34.56 3.16
3848 4939 8.575589 TGTACCTAATACTAAAACGTGACTTGA 58.424 33.333 0.00 0.00 34.56 3.02
3849 4940 9.578439 GTACCTAATACTAAAACGTGACTTGAT 57.422 33.333 0.00 0.00 0.00 2.57
3851 4942 9.578439 ACCTAATACTAAAACGTGACTTGATAC 57.422 33.333 0.00 0.00 0.00 2.24
3852 4943 9.577110 CCTAATACTAAAACGTGACTTGATACA 57.423 33.333 0.00 0.00 0.00 2.29
3855 4946 6.963049 ACTAAAACGTGACTTGATACATCC 57.037 37.500 0.00 0.00 0.00 3.51
3856 4947 4.921470 AAAACGTGACTTGATACATCCG 57.079 40.909 0.00 0.00 0.00 4.18
3857 4948 3.587797 AACGTGACTTGATACATCCGT 57.412 42.857 0.00 0.00 0.00 4.69
3858 4949 4.707030 AACGTGACTTGATACATCCGTA 57.293 40.909 0.00 0.00 0.00 4.02
3859 4950 4.913335 ACGTGACTTGATACATCCGTAT 57.087 40.909 0.00 0.00 41.16 3.06
3860 4951 5.258456 ACGTGACTTGATACATCCGTATT 57.742 39.130 0.00 0.00 38.48 1.89
3861 4952 5.657474 ACGTGACTTGATACATCCGTATTT 58.343 37.500 0.00 0.00 38.48 1.40
3862 4953 5.518847 ACGTGACTTGATACATCCGTATTTG 59.481 40.000 0.00 0.00 38.48 2.32
3863 4954 5.051039 CGTGACTTGATACATCCGTATTTGG 60.051 44.000 0.00 0.00 38.48 3.28
3864 4955 6.046593 GTGACTTGATACATCCGTATTTGGA 58.953 40.000 0.00 0.00 43.58 3.53
3865 4956 6.018994 GTGACTTGATACATCCGTATTTGGAC 60.019 42.308 0.00 0.00 41.85 4.02
3866 4957 5.984725 ACTTGATACATCCGTATTTGGACA 58.015 37.500 0.00 0.00 41.85 4.02
3867 4958 6.411376 ACTTGATACATCCGTATTTGGACAA 58.589 36.000 0.00 0.00 41.85 3.18
3868 4959 6.882140 ACTTGATACATCCGTATTTGGACAAA 59.118 34.615 0.00 0.00 41.85 2.83
3869 4960 7.556275 ACTTGATACATCCGTATTTGGACAAAT 59.444 33.333 14.02 14.02 41.85 2.32
3870 4961 7.490962 TGATACATCCGTATTTGGACAAATC 57.509 36.000 13.07 5.63 41.85 2.17
3871 4962 7.279615 TGATACATCCGTATTTGGACAAATCT 58.720 34.615 13.07 0.00 41.85 2.40
3872 4963 8.425703 TGATACATCCGTATTTGGACAAATCTA 58.574 33.333 13.07 0.00 41.85 1.98
3873 4964 9.268268 GATACATCCGTATTTGGACAAATCTAA 57.732 33.333 13.07 0.00 41.85 2.10
3874 4965 7.553881 ACATCCGTATTTGGACAAATCTAAG 57.446 36.000 13.07 1.07 41.85 2.18
3875 4966 7.335627 ACATCCGTATTTGGACAAATCTAAGA 58.664 34.615 13.07 7.57 41.85 2.10
3876 4967 7.280205 ACATCCGTATTTGGACAAATCTAAGAC 59.720 37.037 13.07 5.74 41.85 3.01
3877 4968 6.703319 TCCGTATTTGGACAAATCTAAGACA 58.297 36.000 13.07 0.00 40.99 3.41
3878 4969 7.162761 TCCGTATTTGGACAAATCTAAGACAA 58.837 34.615 13.07 0.00 40.99 3.18
3879 4970 7.333423 TCCGTATTTGGACAAATCTAAGACAAG 59.667 37.037 13.07 2.30 40.99 3.16
3880 4971 7.333423 CCGTATTTGGACAAATCTAAGACAAGA 59.667 37.037 13.07 0.00 40.99 3.02
3881 4972 8.717821 CGTATTTGGACAAATCTAAGACAAGAA 58.282 33.333 13.07 0.00 40.99 2.52
3886 4977 9.748708 TTGGACAAATCTAAGACAAGAATTTTG 57.251 29.630 0.00 0.00 34.13 2.44
3887 4978 8.359642 TGGACAAATCTAAGACAAGAATTTTGG 58.640 33.333 0.00 0.00 33.04 3.28
3888 4979 7.814587 GGACAAATCTAAGACAAGAATTTTGGG 59.185 37.037 0.00 0.00 33.04 4.12
3889 4980 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
3890 4981 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
3891 4982 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
3892 4983 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
3893 4984 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
3894 4985 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
3895 4986 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
3896 4987 2.107552 ACAAGAATTTTGGGACGGAGGA 59.892 45.455 0.00 0.00 0.00 3.71
3897 4988 2.749621 CAAGAATTTTGGGACGGAGGAG 59.250 50.000 0.00 0.00 0.00 3.69
3898 4989 1.985895 AGAATTTTGGGACGGAGGAGT 59.014 47.619 0.00 0.00 0.00 3.85
3899 4990 3.178865 AGAATTTTGGGACGGAGGAGTA 58.821 45.455 0.00 0.00 0.00 2.59
3900 4991 3.055312 AGAATTTTGGGACGGAGGAGTAC 60.055 47.826 0.00 0.00 0.00 2.73
3947 5038 7.195646 TGTTCTAGTCAAGTTCAGCAAAAATG 58.804 34.615 0.00 0.00 0.00 2.32
4021 5115 8.697960 CATCAGAATATCAGATACAACAGAACG 58.302 37.037 0.00 0.00 0.00 3.95
4054 5174 5.356751 GTGATGAAATGTACCAGGCAACATA 59.643 40.000 8.18 0.00 35.30 2.29
4189 5309 5.008118 GCTCTTGATTACCTTGTATCTTGCC 59.992 44.000 0.00 0.00 0.00 4.52
4317 5437 1.300697 AGGCGACCACGTTGAGAAC 60.301 57.895 0.00 0.00 41.98 3.01
4324 5444 2.027625 CACGTTGAGAACCTCCCGC 61.028 63.158 0.00 0.00 30.60 6.13
4364 5484 3.200593 GCTGCCTGTGCTCATCCG 61.201 66.667 0.00 0.00 38.71 4.18
4519 5639 2.743636 TCCTGATCGTGTTCAAGACC 57.256 50.000 0.00 0.00 0.00 3.85
4537 5657 2.802106 GTCTTCCTCGGGCTCTCG 59.198 66.667 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.009829 GTGCTGCTAAGGTGATTCCG 58.990 55.000 0.00 0.00 41.99 4.30
71 72 1.358787 AGGTCCAAAGATCCCATTGCA 59.641 47.619 0.00 0.00 0.00 4.08
75 76 2.507471 GTGAGAGGTCCAAAGATCCCAT 59.493 50.000 0.00 0.00 0.00 4.00
79 80 3.685139 TGTGTGAGAGGTCCAAAGATC 57.315 47.619 0.00 0.00 0.00 2.75
123 124 3.651803 AGTTAGATCTGCCATACTCGC 57.348 47.619 5.18 0.00 0.00 5.03
164 165 2.631062 TCCTGTCAGATTGTTGTACGGT 59.369 45.455 0.00 0.00 0.00 4.83
165 166 3.313012 TCCTGTCAGATTGTTGTACGG 57.687 47.619 0.00 0.00 0.00 4.02
167 168 4.385825 TGGTTCCTGTCAGATTGTTGTAC 58.614 43.478 0.00 0.00 0.00 2.90
274 278 0.323629 TTCCGTTCCCGAGCAATTCT 59.676 50.000 0.00 0.00 35.63 2.40
336 340 4.275936 GCCGAGGTATAATGACAATGCTTT 59.724 41.667 0.00 0.00 0.00 3.51
338 342 3.181455 TGCCGAGGTATAATGACAATGCT 60.181 43.478 0.00 0.00 0.00 3.79
486 490 1.005097 TGTGAATGAAGCCCAGCTCAT 59.995 47.619 0.00 0.00 38.25 2.90
557 561 1.745115 TGCCGAAATGGAAGCTCCG 60.745 57.895 0.00 0.00 40.17 4.63
570 574 2.642311 ACCCCATATCATATTGTGCCGA 59.358 45.455 0.00 0.00 0.00 5.54
597 601 5.095490 GCGGACAAGAAAGGTGAAATATTG 58.905 41.667 0.00 0.00 0.00 1.90
624 736 8.730680 ACGAAAGAAGAGCAATACATTACATTT 58.269 29.630 0.00 0.00 0.00 2.32
629 741 6.402118 GCACACGAAAGAAGAGCAATACATTA 60.402 38.462 0.00 0.00 0.00 1.90
630 742 5.617751 GCACACGAAAGAAGAGCAATACATT 60.618 40.000 0.00 0.00 0.00 2.71
631 743 4.142816 GCACACGAAAGAAGAGCAATACAT 60.143 41.667 0.00 0.00 0.00 2.29
633 745 3.186409 TGCACACGAAAGAAGAGCAATAC 59.814 43.478 0.00 0.00 34.85 1.89
634 746 3.398406 TGCACACGAAAGAAGAGCAATA 58.602 40.909 0.00 0.00 34.85 1.90
635 747 2.221169 TGCACACGAAAGAAGAGCAAT 58.779 42.857 0.00 0.00 34.85 3.56
637 749 1.599071 CTTGCACACGAAAGAAGAGCA 59.401 47.619 0.00 0.00 35.55 4.26
638 750 1.599542 ACTTGCACACGAAAGAAGAGC 59.400 47.619 0.00 0.00 0.00 4.09
639 751 2.866156 TGACTTGCACACGAAAGAAGAG 59.134 45.455 0.00 0.00 0.00 2.85
640 752 2.607635 GTGACTTGCACACGAAAGAAGA 59.392 45.455 0.00 0.00 46.91 2.87
641 753 2.974165 GTGACTTGCACACGAAAGAAG 58.026 47.619 0.00 0.00 46.91 2.85
652 764 2.605837 TACAAACCGAGTGACTTGCA 57.394 45.000 0.00 0.00 0.00 4.08
653 765 2.159627 CCATACAAACCGAGTGACTTGC 59.840 50.000 0.00 0.00 0.00 4.01
654 766 3.399330 ACCATACAAACCGAGTGACTTG 58.601 45.455 0.00 0.00 0.00 3.16
655 767 3.764237 ACCATACAAACCGAGTGACTT 57.236 42.857 0.00 0.00 0.00 3.01
656 768 4.877378 TTACCATACAAACCGAGTGACT 57.123 40.909 0.00 0.00 0.00 3.41
657 769 4.152938 GGTTTACCATACAAACCGAGTGAC 59.847 45.833 1.54 0.00 43.94 3.67
658 770 4.317488 GGTTTACCATACAAACCGAGTGA 58.683 43.478 1.54 0.00 43.94 3.41
659 771 4.673534 GGTTTACCATACAAACCGAGTG 57.326 45.455 1.54 0.00 43.94 3.51
749 904 1.651987 CCACACACGGTCATCATACC 58.348 55.000 0.00 0.00 36.08 2.73
757 926 1.469335 TTCTCTCCCCACACACGGTC 61.469 60.000 0.00 0.00 0.00 4.79
766 1573 3.717294 GGCGCCTTTCTCTCCCCA 61.717 66.667 22.15 0.00 0.00 4.96
773 1580 2.328099 CGAAGCAAGGCGCCTTTCT 61.328 57.895 38.60 35.11 44.04 2.52
898 1708 0.461516 TGAGACGACGCCGATACTCT 60.462 55.000 0.00 0.00 39.50 3.24
899 1709 0.587285 ATGAGACGACGCCGATACTC 59.413 55.000 0.00 4.53 39.50 2.59
900 1710 0.587285 GATGAGACGACGCCGATACT 59.413 55.000 0.00 0.00 39.50 2.12
901 1711 0.385723 GGATGAGACGACGCCGATAC 60.386 60.000 0.00 0.00 39.50 2.24
962 1772 3.485431 CGAACTGCAGAGCGCCTG 61.485 66.667 23.35 18.16 45.67 4.85
982 1792 1.522580 GTACTGCAGGCTAGCTGGC 60.523 63.158 19.93 14.65 37.72 4.85
1073 1883 2.993604 AGGAAGGAGGGAAAGGGTAT 57.006 50.000 0.00 0.00 0.00 2.73
1088 1898 3.556298 GAAACGGGCGGGGAAGGAA 62.556 63.158 0.00 0.00 0.00 3.36
1089 1899 4.024545 GAAACGGGCGGGGAAGGA 62.025 66.667 0.00 0.00 0.00 3.36
1090 1900 3.971109 GAGAAACGGGCGGGGAAGG 62.971 68.421 0.00 0.00 0.00 3.46
1091 1901 2.436115 GAGAAACGGGCGGGGAAG 60.436 66.667 0.00 0.00 0.00 3.46
1092 1902 4.024545 GGAGAAACGGGCGGGGAA 62.025 66.667 0.00 0.00 0.00 3.97
1170 2002 1.643832 GATTTGGCCTGCGATCGAC 59.356 57.895 21.57 10.98 0.00 4.20
1459 2291 7.083230 GGTACAGTACAGTACAGAGAAGAAAC 58.917 42.308 24.58 5.09 44.76 2.78
1519 2351 5.511545 GGAGACACATCCTGAAACTGTACTT 60.512 44.000 0.00 0.00 36.35 2.24
1672 2535 7.936496 TCACATATAAATGCAGAACCAAGAA 57.064 32.000 0.00 0.00 36.50 2.52
1691 2554 9.685276 TCAAACATTCAGATAAACCTATCACAT 57.315 29.630 0.00 0.00 37.05 3.21
1694 2557 9.904198 TCATCAAACATTCAGATAAACCTATCA 57.096 29.630 0.00 0.00 37.05 2.15
1699 2564 7.253422 CCACTCATCAAACATTCAGATAAACC 58.747 38.462 0.00 0.00 0.00 3.27
1709 2574 4.834496 ACACAATCCCACTCATCAAACATT 59.166 37.500 0.00 0.00 0.00 2.71
1717 2582 2.108075 TCCAACACACAATCCCACTCAT 59.892 45.455 0.00 0.00 0.00 2.90
1743 2608 2.032981 CTTCACACCGGCTGCTTTT 58.967 52.632 0.00 0.00 0.00 2.27
1851 2716 6.930164 GGTGAAGAGACATATAGACTCGTCTA 59.070 42.308 9.04 9.04 43.60 2.59
1903 2775 8.021396 AGATAATAAAGTTTTTCGTGGAAGCAC 58.979 33.333 0.00 0.00 0.00 4.40
1904 2776 8.020819 CAGATAATAAAGTTTTTCGTGGAAGCA 58.979 33.333 0.00 0.00 0.00 3.91
1909 2781 9.341899 CTTTCCAGATAATAAAGTTTTTCGTGG 57.658 33.333 0.00 0.00 0.00 4.94
1913 2785 9.929180 AAGGCTTTCCAGATAATAAAGTTTTTC 57.071 29.630 0.00 0.00 33.67 2.29
1934 2809 4.777896 TGTTCAGAGAATGGTACTAAGGCT 59.222 41.667 0.00 0.00 0.00 4.58
1945 2820 3.057104 TGCCAAGCAATGTTCAGAGAATG 60.057 43.478 0.00 0.00 34.76 2.67
1961 2836 3.510846 GGCTCATCTGCTGCCAAG 58.489 61.111 0.00 0.00 45.46 3.61
1992 2872 6.471233 TCTATGACGAACAATCCTTCAGAT 57.529 37.500 0.00 0.00 36.48 2.90
2036 2916 6.564125 CGAACCTGTCAATAGTCAAAACTCAC 60.564 42.308 0.00 0.00 36.92 3.51
2038 2918 5.614887 GCGAACCTGTCAATAGTCAAAACTC 60.615 44.000 0.00 0.00 36.92 3.01
2043 2923 2.037902 TGGCGAACCTGTCAATAGTCAA 59.962 45.455 0.00 0.00 36.63 3.18
2045 2925 2.380084 TGGCGAACCTGTCAATAGTC 57.620 50.000 0.00 0.00 36.63 2.59
2050 2930 4.279671 ACATTTTTATGGCGAACCTGTCAA 59.720 37.500 0.00 0.00 36.63 3.18
2090 2970 9.613428 TTTCCTGTATTATGGATCTAACTGTTG 57.387 33.333 2.69 0.00 31.76 3.33
2148 3133 8.794335 ACAGGAACTTAATATTCAGAAAGGTC 57.206 34.615 3.65 4.69 34.60 3.85
2213 3284 5.776744 ACTTTCTGAAATGAACATTCCAGC 58.223 37.500 8.51 0.00 33.80 4.85
2325 3396 2.354199 GGTACCACGACTAGCTGAGTAC 59.646 54.545 7.15 1.32 39.06 2.73
2360 3431 5.834239 CAAAATGAATTTGTCTCAGTGGC 57.166 39.130 0.00 0.00 42.84 5.01
2520 3593 4.599047 TGCCTTTTTATCCAAACTGGTG 57.401 40.909 0.00 0.00 39.03 4.17
2523 3596 5.665916 AGGATGCCTTTTTATCCAAACTG 57.334 39.130 0.00 0.00 44.26 3.16
2671 3744 6.602009 AGGCATTCAAAGGTATTTAGTGGTAC 59.398 38.462 0.00 0.00 0.00 3.34
2693 3766 2.493675 GGATCCACCTTTTCTTTGAGGC 59.506 50.000 6.95 0.00 36.48 4.70
2716 3789 6.600822 ACTCATTGTCTCATTAAATGTGGAGG 59.399 38.462 0.00 0.00 33.84 4.30
2743 3816 4.264172 TGTTTGCCTCACCCCTTTATATGT 60.264 41.667 0.00 0.00 0.00 2.29
2770 3843 3.933332 AGCAAAAACTACTAGATCGCACC 59.067 43.478 0.00 0.00 0.00 5.01
2853 3927 1.882912 TAACTGCAGCAGTCCAACTG 58.117 50.000 28.38 0.00 44.62 3.16
2854 3928 2.638480 TTAACTGCAGCAGTCCAACT 57.362 45.000 28.38 14.80 44.62 3.16
2970 4044 4.151867 AGGAAACGAAGAAAACGATAGCAC 59.848 41.667 0.00 0.00 42.67 4.40
2978 4052 7.096189 GCCTAAATTGAAGGAAACGAAGAAAAC 60.096 37.037 10.60 0.00 36.08 2.43
2987 4061 3.832490 ACCAGGCCTAAATTGAAGGAAAC 59.168 43.478 3.98 1.53 36.08 2.78
3090 4164 1.544314 GCCACATCAGCCCTAGGAATC 60.544 57.143 11.48 0.00 0.00 2.52
3161 4240 1.940613 GTTGTCCTCAAGTGTGTCCAC 59.059 52.381 0.00 0.00 42.17 4.02
3190 4272 6.068438 AGGGCCTGTTTTAAGAGGGTAAATAT 60.068 38.462 4.50 0.00 39.72 1.28
3194 4276 2.990998 AGGGCCTGTTTTAAGAGGGTAA 59.009 45.455 4.50 0.00 39.72 2.85
3198 4280 1.177401 GCAGGGCCTGTTTTAAGAGG 58.823 55.000 32.80 5.59 42.11 3.69
3204 4287 1.075374 TCATACTGCAGGGCCTGTTTT 59.925 47.619 32.80 19.48 33.43 2.43
3231 4314 4.559153 CCAAATCGAATGCCTTGAACTTT 58.441 39.130 0.00 0.00 0.00 2.66
3337 4420 8.507524 AAGAAATGTACTTATGCTCCTTAACC 57.492 34.615 0.00 0.00 0.00 2.85
3362 4451 9.516546 TCGAGACATTAAGATCCTTATAAGCTA 57.483 33.333 6.99 0.00 0.00 3.32
3386 4475 2.078849 TGCACAAGGATACACACTCG 57.921 50.000 0.00 0.00 41.41 4.18
3446 4536 5.537674 AGGAGGCTATTTTCAGCATTATTGG 59.462 40.000 0.00 0.00 43.67 3.16
3479 4569 6.501781 CATAAATTGCTTCTCCAATCTCCAC 58.498 40.000 0.00 0.00 34.50 4.02
3525 4615 2.015456 TTGCTGACTCCTTCTCCTCA 57.985 50.000 0.00 0.00 0.00 3.86
3535 4625 6.902341 TGTATTCTCAATTGTTTGCTGACTC 58.098 36.000 5.13 0.00 32.61 3.36
3614 4705 1.364721 TGGATTATTGGTGTGCGTCG 58.635 50.000 0.00 0.00 0.00 5.12
3617 4708 3.127589 TCGTATGGATTATTGGTGTGCG 58.872 45.455 0.00 0.00 0.00 5.34
3634 4725 7.427030 GCTGTTGCGTAAATGATAAAATTCGTA 59.573 33.333 0.00 0.00 0.00 3.43
3698 4789 5.390885 GCGCTGATGTTTCATTTCTCAGTAA 60.391 40.000 0.00 0.00 36.55 2.24
3699 4790 4.093408 GCGCTGATGTTTCATTTCTCAGTA 59.907 41.667 0.00 0.00 36.55 2.74
3777 4868 3.072476 ACAAGAATTTTGAGACGGAGGGA 59.928 43.478 7.18 0.00 0.00 4.20
3778 4869 3.412386 ACAAGAATTTTGAGACGGAGGG 58.588 45.455 7.18 0.00 0.00 4.30
3779 4870 4.319177 AGACAAGAATTTTGAGACGGAGG 58.681 43.478 7.18 0.00 0.00 4.30
3780 4871 5.931441 AAGACAAGAATTTTGAGACGGAG 57.069 39.130 7.18 0.00 0.00 4.63
3781 4872 6.755206 TCTAAGACAAGAATTTTGAGACGGA 58.245 36.000 7.18 0.00 0.00 4.69
3782 4873 7.602517 ATCTAAGACAAGAATTTTGAGACGG 57.397 36.000 7.18 0.00 0.00 4.79
3783 4874 9.322776 CAAATCTAAGACAAGAATTTTGAGACG 57.677 33.333 7.18 0.00 31.51 4.18
3794 4885 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
3795 4886 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
3796 4887 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
3797 4888 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
3798 4889 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
3799 4890 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
3800 4891 9.828852 GTACATCCGTATCTAGACAAATCTAAG 57.171 37.037 0.00 0.00 36.98 2.18
3801 4892 8.790718 GGTACATCCGTATCTAGACAAATCTAA 58.209 37.037 0.00 0.00 36.98 2.10
3802 4893 8.162085 AGGTACATCCGTATCTAGACAAATCTA 58.838 37.037 0.00 0.00 37.29 1.98
3803 4894 7.005296 AGGTACATCCGTATCTAGACAAATCT 58.995 38.462 0.00 0.00 37.29 2.40
3804 4895 7.216973 AGGTACATCCGTATCTAGACAAATC 57.783 40.000 0.00 0.00 37.29 2.17
3805 4896 8.701908 TTAGGTACATCCGTATCTAGACAAAT 57.298 34.615 0.00 0.00 41.33 2.32
3806 4897 8.701908 ATTAGGTACATCCGTATCTAGACAAA 57.298 34.615 0.00 0.00 41.33 2.83
3807 4898 9.224267 GTATTAGGTACATCCGTATCTAGACAA 57.776 37.037 0.00 0.00 41.33 3.18
3808 4899 8.600668 AGTATTAGGTACATCCGTATCTAGACA 58.399 37.037 0.00 0.00 41.33 3.41
3814 4905 9.334693 CGTTTTAGTATTAGGTACATCCGTATC 57.665 37.037 0.00 0.00 41.99 2.24
3815 4906 8.850156 ACGTTTTAGTATTAGGTACATCCGTAT 58.150 33.333 0.00 0.00 41.99 3.06
3816 4907 8.128582 CACGTTTTAGTATTAGGTACATCCGTA 58.871 37.037 0.00 0.00 41.99 4.02
3817 4908 6.974622 CACGTTTTAGTATTAGGTACATCCGT 59.025 38.462 0.00 0.00 41.99 4.69
3818 4909 7.166473 GTCACGTTTTAGTATTAGGTACATCCG 59.834 40.741 0.00 0.00 41.99 4.18
3819 4910 8.193438 AGTCACGTTTTAGTATTAGGTACATCC 58.807 37.037 0.00 0.00 35.67 3.51
3820 4911 9.578439 AAGTCACGTTTTAGTATTAGGTACATC 57.422 33.333 0.00 0.00 35.67 3.06
3821 4912 9.362539 CAAGTCACGTTTTAGTATTAGGTACAT 57.637 33.333 0.00 0.00 35.67 2.29
3822 4913 8.575589 TCAAGTCACGTTTTAGTATTAGGTACA 58.424 33.333 0.00 0.00 35.67 2.90
3823 4914 8.970691 TCAAGTCACGTTTTAGTATTAGGTAC 57.029 34.615 0.00 0.00 0.00 3.34
3825 4916 9.578439 GTATCAAGTCACGTTTTAGTATTAGGT 57.422 33.333 0.00 0.00 0.00 3.08
3826 4917 9.577110 TGTATCAAGTCACGTTTTAGTATTAGG 57.423 33.333 0.00 0.00 0.00 2.69
3829 4920 9.095065 GGATGTATCAAGTCACGTTTTAGTATT 57.905 33.333 0.00 0.00 0.00 1.89
3830 4921 7.434307 CGGATGTATCAAGTCACGTTTTAGTAT 59.566 37.037 0.00 0.00 0.00 2.12
3831 4922 6.748658 CGGATGTATCAAGTCACGTTTTAGTA 59.251 38.462 0.00 0.00 0.00 1.82
3832 4923 5.575606 CGGATGTATCAAGTCACGTTTTAGT 59.424 40.000 0.00 0.00 0.00 2.24
3833 4924 5.575606 ACGGATGTATCAAGTCACGTTTTAG 59.424 40.000 0.00 0.00 0.00 1.85
3834 4925 5.472148 ACGGATGTATCAAGTCACGTTTTA 58.528 37.500 0.00 0.00 0.00 1.52
3835 4926 4.312443 ACGGATGTATCAAGTCACGTTTT 58.688 39.130 0.00 0.00 0.00 2.43
3836 4927 3.921677 ACGGATGTATCAAGTCACGTTT 58.078 40.909 0.00 0.00 0.00 3.60
3837 4928 3.587797 ACGGATGTATCAAGTCACGTT 57.412 42.857 0.00 0.00 0.00 3.99
3838 4929 4.913335 ATACGGATGTATCAAGTCACGT 57.087 40.909 0.00 0.00 36.56 4.49
3839 4930 5.051039 CCAAATACGGATGTATCAAGTCACG 60.051 44.000 0.00 0.00 40.42 4.35
3840 4931 6.018994 GTCCAAATACGGATGTATCAAGTCAC 60.019 42.308 0.00 0.00 40.42 3.67
3841 4932 6.046593 GTCCAAATACGGATGTATCAAGTCA 58.953 40.000 0.00 0.00 40.42 3.41
3842 4933 6.046593 TGTCCAAATACGGATGTATCAAGTC 58.953 40.000 0.00 0.00 40.42 3.01
3843 4934 5.984725 TGTCCAAATACGGATGTATCAAGT 58.015 37.500 0.00 0.00 40.42 3.16
3844 4935 6.918892 TTGTCCAAATACGGATGTATCAAG 57.081 37.500 0.00 0.00 40.42 3.02
3845 4936 7.773224 AGATTTGTCCAAATACGGATGTATCAA 59.227 33.333 5.29 0.00 40.42 2.57
3846 4937 7.279615 AGATTTGTCCAAATACGGATGTATCA 58.720 34.615 5.29 0.00 40.42 2.15
3847 4938 7.730364 AGATTTGTCCAAATACGGATGTATC 57.270 36.000 5.29 0.00 40.42 2.24
3848 4939 9.273016 CTTAGATTTGTCCAAATACGGATGTAT 57.727 33.333 5.29 0.00 43.14 2.29
3849 4940 8.479689 TCTTAGATTTGTCCAAATACGGATGTA 58.520 33.333 5.29 0.00 40.77 2.29
3850 4941 7.280205 GTCTTAGATTTGTCCAAATACGGATGT 59.720 37.037 5.29 0.00 40.77 3.06
3851 4942 7.279981 TGTCTTAGATTTGTCCAAATACGGATG 59.720 37.037 5.29 0.00 40.77 3.51
3852 4943 7.335627 TGTCTTAGATTTGTCCAAATACGGAT 58.664 34.615 5.29 0.00 40.77 4.18
3853 4944 6.703319 TGTCTTAGATTTGTCCAAATACGGA 58.297 36.000 5.29 0.82 40.77 4.69
3854 4945 6.978343 TGTCTTAGATTTGTCCAAATACGG 57.022 37.500 5.29 0.00 40.77 4.02
3855 4946 8.251750 TCTTGTCTTAGATTTGTCCAAATACG 57.748 34.615 5.29 0.00 40.77 3.06
3860 4951 9.748708 CAAAATTCTTGTCTTAGATTTGTCCAA 57.251 29.630 0.00 0.00 0.00 3.53
3861 4952 8.359642 CCAAAATTCTTGTCTTAGATTTGTCCA 58.640 33.333 0.00 0.00 28.79 4.02
3862 4953 7.814587 CCCAAAATTCTTGTCTTAGATTTGTCC 59.185 37.037 0.00 0.00 28.79 4.02
3863 4954 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
3864 4955 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
3865 4956 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
3866 4957 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
3867 4958 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
3868 4959 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
3869 4960 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
3870 4961 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
3871 4962 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
3872 4963 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
3873 4964 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
3874 4965 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3875 4966 2.107552 TCCTCCGTCCCAAAATTCTTGT 59.892 45.455 0.00 0.00 0.00 3.16
3876 4967 2.749621 CTCCTCCGTCCCAAAATTCTTG 59.250 50.000 0.00 0.00 0.00 3.02
3877 4968 2.375509 ACTCCTCCGTCCCAAAATTCTT 59.624 45.455 0.00 0.00 0.00 2.52
3878 4969 1.985895 ACTCCTCCGTCCCAAAATTCT 59.014 47.619 0.00 0.00 0.00 2.40
3879 4970 2.491675 ACTCCTCCGTCCCAAAATTC 57.508 50.000 0.00 0.00 0.00 2.17
3880 4971 2.640826 TGTACTCCTCCGTCCCAAAATT 59.359 45.455 0.00 0.00 0.00 1.82
3881 4972 2.262637 TGTACTCCTCCGTCCCAAAAT 58.737 47.619 0.00 0.00 0.00 1.82
3882 4973 1.719529 TGTACTCCTCCGTCCCAAAA 58.280 50.000 0.00 0.00 0.00 2.44
3883 4974 1.719529 TTGTACTCCTCCGTCCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
3884 4975 1.719529 TTTGTACTCCTCCGTCCCAA 58.280 50.000 0.00 0.00 0.00 4.12
3885 4976 1.345415 GTTTTGTACTCCTCCGTCCCA 59.655 52.381 0.00 0.00 0.00 4.37
3886 4977 1.345415 TGTTTTGTACTCCTCCGTCCC 59.655 52.381 0.00 0.00 0.00 4.46
3887 4978 2.825861 TGTTTTGTACTCCTCCGTCC 57.174 50.000 0.00 0.00 0.00 4.79
3888 4979 4.270325 GCATATGTTTTGTACTCCTCCGTC 59.730 45.833 4.29 0.00 0.00 4.79
3889 4980 4.189231 GCATATGTTTTGTACTCCTCCGT 58.811 43.478 4.29 0.00 0.00 4.69
3890 4981 4.188462 TGCATATGTTTTGTACTCCTCCG 58.812 43.478 4.29 0.00 0.00 4.63
3891 4982 5.880332 TCTTGCATATGTTTTGTACTCCTCC 59.120 40.000 4.29 0.00 0.00 4.30
3892 4983 6.985188 TCTTGCATATGTTTTGTACTCCTC 57.015 37.500 4.29 0.00 0.00 3.71
3893 4984 6.127897 GCTTCTTGCATATGTTTTGTACTCCT 60.128 38.462 4.29 0.00 42.31 3.69
3894 4985 6.030228 GCTTCTTGCATATGTTTTGTACTCC 58.970 40.000 4.29 0.00 42.31 3.85
3895 4986 6.846350 AGCTTCTTGCATATGTTTTGTACTC 58.154 36.000 4.29 0.00 45.94 2.59
3896 4987 6.824305 AGCTTCTTGCATATGTTTTGTACT 57.176 33.333 4.29 0.00 45.94 2.73
3897 4988 7.272084 CAGAAGCTTCTTGCATATGTTTTGTAC 59.728 37.037 26.44 0.00 45.94 2.90
3898 4989 7.040478 ACAGAAGCTTCTTGCATATGTTTTGTA 60.040 33.333 26.44 0.00 41.18 2.41
3899 4990 6.154445 CAGAAGCTTCTTGCATATGTTTTGT 58.846 36.000 26.44 0.00 45.94 2.83
3900 4991 6.154445 ACAGAAGCTTCTTGCATATGTTTTG 58.846 36.000 26.44 13.24 41.18 2.44
3947 5038 0.615331 TGGGAGCAGAGTTGATGGAC 59.385 55.000 0.00 0.00 0.00 4.02
4021 5115 7.809806 CCTGGTACATTTCATCACTTCTTTTTC 59.190 37.037 0.00 0.00 38.20 2.29
4027 5147 4.009675 TGCCTGGTACATTTCATCACTTC 58.990 43.478 0.00 0.00 38.20 3.01
4054 5174 7.620094 TGGAAACCTAGCTAGAACTTTAGAGAT 59.380 37.037 22.70 0.00 0.00 2.75
4189 5309 3.312421 TGCTTCAAGAGTCGGTGAAAAAG 59.688 43.478 11.82 4.16 33.52 2.27
4300 5420 2.315386 GGTTCTCAACGTGGTCGCC 61.315 63.158 0.00 0.00 41.18 5.54
4317 5437 1.069258 GAATACTTCGGGCGGGAGG 59.931 63.158 5.26 0.00 0.00 4.30
4324 5444 2.973694 TCGAAAGGGAATACTTCGGG 57.026 50.000 3.88 0.00 0.00 5.14
4462 5582 1.206578 CATCCACGCGGTTGTCAAC 59.793 57.895 12.47 7.20 0.00 3.18
4519 5639 2.802106 GAGAGCCCGAGGAAGACG 59.198 66.667 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.