Multiple sequence alignment - TraesCS7D01G276600

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 TraesCS7D01G276600 chr7D 100.000 7015 0 0 1 7015 264969767 264976781 0.000000e+00 12955.0
1 TraesCS7D01G276600 chr7D 97.315 745 14 5 1 742 112583091 112582350 0.000000e+00 1260.0
2 TraesCS7D01G276600 chr7D 96.467 736 21 4 1 735 162145827 162146558 0.000000e+00 1210.0
3 TraesCS7D01G276600 chr7D 95.788 736 23 5 1 735 488078085 488077357 0.000000e+00 1181.0
4 TraesCS7D01G276600 chr7A 96.004 2853 77 16 921 3752 289118702 289121538 0.000000e+00 4602.0
5 TraesCS7D01G276600 chr7A 95.725 2877 68 9 3749 6606 289128490 289131330 0.000000e+00 4580.0
6 TraesCS7D01G276600 chr7A 91.860 258 10 4 6767 7015 289131329 289131584 4.030000e-92 350.0
7 TraesCS7D01G276600 chr7A 96.203 79 3 0 2664 2742 538361847 538361769 5.710000e-26 130.0
8 TraesCS7D01G276600 chr7B 96.234 2151 54 11 4475 6606 245176240 245178382 0.000000e+00 3498.0
9 TraesCS7D01G276600 chr7B 96.367 2092 72 4 1233 3322 245172759 245174848 0.000000e+00 3439.0
10 TraesCS7D01G276600 chr7B 95.004 1181 24 14 3324 4485 245174893 245176057 0.000000e+00 1821.0
11 TraesCS7D01G276600 chr7B 95.468 331 13 1 859 1187 245171941 245172271 1.730000e-145 527.0
12 TraesCS7D01G276600 chr7B 93.411 258 6 4 6767 7015 245178381 245178636 8.590000e-99 372.0
13 TraesCS7D01G276600 chr5D 97.139 734 18 3 1 733 551062969 551063700 0.000000e+00 1236.0
14 TraesCS7D01G276600 chr5D 96.257 748 22 5 1 747 273275858 273276600 0.000000e+00 1221.0
15 TraesCS7D01G276600 chr3D 96.533 750 21 5 1 748 141481424 141482170 0.000000e+00 1236.0
16 TraesCS7D01G276600 chr3D 96.589 733 20 3 1 732 32167821 32168549 0.000000e+00 1210.0
17 TraesCS7D01G276600 chr4D 96.196 736 24 3 1 735 252181091 252181823 0.000000e+00 1201.0
18 TraesCS7D01G276600 chr4D 90.950 221 19 1 5323 5542 206060853 206061073 5.320000e-76 296.0
19 TraesCS7D01G276600 chr4D 96.089 179 6 1 6597 6774 93338034 93338212 2.480000e-74 291.0
20 TraesCS7D01G276600 chr4D 95.480 177 5 3 6601 6775 46028706 46028531 5.360000e-71 279.0
21 TraesCS7D01G276600 chr4D 89.593 221 22 1 5323 5542 281188407 281188627 5.360000e-71 279.0
22 TraesCS7D01G276600 chr4D 95.122 82 3 1 2664 2744 23322758 23322839 2.050000e-25 128.0
23 TraesCS7D01G276600 chr2B 94.173 738 30 6 1 729 46945517 46946250 0.000000e+00 1112.0
24 TraesCS7D01G276600 chr2A 90.283 741 30 13 12 738 470240149 470240861 0.000000e+00 931.0
25 TraesCS7D01G276600 chr2A 93.976 83 3 2 2667 2747 87880075 87879993 2.660000e-24 124.0
26 TraesCS7D01G276600 chr1D 91.071 224 19 1 5323 5545 268963493 268963270 1.140000e-77 302.0
27 TraesCS7D01G276600 chr1D 87.379 103 8 3 2640 2742 2223122 2223025 5.750000e-21 113.0
28 TraesCS7D01G276600 chr4B 90.625 224 20 1 5323 5545 258771564 258771341 5.320000e-76 296.0
29 TraesCS7D01G276600 chr4B 90.045 221 20 2 5326 5545 285608302 285608083 1.150000e-72 285.0
30 TraesCS7D01G276600 chr5A 96.610 177 5 1 6599 6774 694983848 694983672 6.880000e-75 292.0
31 TraesCS7D01G276600 chr5A 96.552 174 5 1 6599 6771 290391691 290391864 3.200000e-73 287.0
32 TraesCS7D01G276600 chr1A 97.661 171 3 1 6605 6774 233421342 233421512 6.880000e-75 292.0
33 TraesCS7D01G276600 chr6D 98.193 166 2 1 6604 6768 271602773 271602938 8.900000e-74 289.0
34 TraesCS7D01G276600 chr6D 90.045 221 21 1 5323 5542 365846886 365847106 1.150000e-72 285.0
35 TraesCS7D01G276600 chr6D 93.023 86 4 2 2664 2747 445729982 445729897 2.660000e-24 124.0
36 TraesCS7D01G276600 chr5B 90.179 224 19 2 5326 5547 192866767 192866545 8.900000e-74 289.0
37 TraesCS7D01G276600 chr5B 95.455 176 6 2 6605 6779 275370131 275369957 5.360000e-71 279.0
38 TraesCS7D01G276600 chr5B 88.119 101 11 1 2643 2742 650012449 650012549 1.240000e-22 119.0
39 TraesCS7D01G276600 chr3A 96.512 172 4 2 6601 6771 744921114 744920944 4.140000e-72 283.0
40 TraesCS7D01G276600 chr1B 95.480 177 6 2 6596 6771 486835802 486835627 1.490000e-71 281.0
41 TraesCS7D01G276600 chr6B 83.478 115 17 2 2635 2747 378286312 378286426 9.620000e-19 106.0
42 TraesCS7D01G276600 chr4A 97.059 34 1 0 825 858 739684127 739684094 2.730000e-04 58.4
43 TraesCS7D01G276600 chr4A 97.059 34 1 0 825 858 742078109 742078076 2.730000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G276600 chr7D 264969767 264976781 7014 False 12955.0 12955 100.0000 1 7015 1 chr7D.!!$F2 7014
1 TraesCS7D01G276600 chr7D 112582350 112583091 741 True 1260.0 1260 97.3150 1 742 1 chr7D.!!$R1 741
2 TraesCS7D01G276600 chr7D 162145827 162146558 731 False 1210.0 1210 96.4670 1 735 1 chr7D.!!$F1 734
3 TraesCS7D01G276600 chr7D 488077357 488078085 728 True 1181.0 1181 95.7880 1 735 1 chr7D.!!$R2 734
4 TraesCS7D01G276600 chr7A 289118702 289121538 2836 False 4602.0 4602 96.0040 921 3752 1 chr7A.!!$F1 2831
5 TraesCS7D01G276600 chr7A 289128490 289131584 3094 False 2465.0 4580 93.7925 3749 7015 2 chr7A.!!$F2 3266
6 TraesCS7D01G276600 chr7B 245171941 245178636 6695 False 1931.4 3498 95.2968 859 7015 5 chr7B.!!$F1 6156
7 TraesCS7D01G276600 chr5D 551062969 551063700 731 False 1236.0 1236 97.1390 1 733 1 chr5D.!!$F2 732
8 TraesCS7D01G276600 chr5D 273275858 273276600 742 False 1221.0 1221 96.2570 1 747 1 chr5D.!!$F1 746
9 TraesCS7D01G276600 chr3D 141481424 141482170 746 False 1236.0 1236 96.5330 1 748 1 chr3D.!!$F2 747
10 TraesCS7D01G276600 chr3D 32167821 32168549 728 False 1210.0 1210 96.5890 1 732 1 chr3D.!!$F1 731
11 TraesCS7D01G276600 chr4D 252181091 252181823 732 False 1201.0 1201 96.1960 1 735 1 chr4D.!!$F4 734
12 TraesCS7D01G276600 chr2B 46945517 46946250 733 False 1112.0 1112 94.1730 1 729 1 chr2B.!!$F1 728
13 TraesCS7D01G276600 chr2A 470240149 470240861 712 False 931.0 931 90.2830 12 738 1 chr2A.!!$F1 726

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
810 833 0.026544 TTCGTTCGTTCGGTTGTTGC 59.973 50.000 2.85 0.00 0.00 4.17 F
812 835 0.027063 CGTTCGTTCGGTTGTTGCTT 59.973 50.000 0.00 0.00 0.00 3.91 F
2244 2728 0.802494 CCGCCTTGGTGTGTATTGAC 59.198 55.000 0.00 0.00 0.00 3.18 F
2617 3101 0.943673 TTCAGTGTGTTGACATGGCG 59.056 50.000 0.00 0.00 33.63 5.69 F
2715 3199 1.555967 TTTGTATGCAGCCTTTCCCC 58.444 50.000 0.00 0.00 0.00 4.81 F
3409 3939 1.746615 CGACCACAATCCCAGGCTG 60.747 63.158 7.75 7.75 0.00 4.85 F
3731 4269 3.248266 ACGTGAAATACTTCCTGCGTAC 58.752 45.455 0.00 0.00 34.18 3.67 F
5515 6275 1.888512 CCTCCCATGTCAAGTTTGGTG 59.111 52.381 0.00 0.00 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2715 3199 1.138247 GGCCTCTTGCAGAAATGCG 59.862 57.895 0.00 0.00 43.89 4.73 R
2796 3280 4.452455 AGCTGGAAGTGAATTTGTAAGTCG 59.548 41.667 0.00 0.00 35.30 4.18 R
3097 3582 3.630312 CAGTTCCTTTTCCCTTTTCGACA 59.370 43.478 0.00 0.00 0.00 4.35 R
4304 4850 3.294214 GGAATCATGAGTGCCTTTGGAT 58.706 45.455 0.00 0.00 0.00 3.41 R
4570 5310 4.586235 ACACTTTGGGCCAGCGCT 62.586 61.111 2.64 2.64 34.44 5.92 R
5015 5775 5.575019 ACTTTGACCGTTATTTTGTGTGTC 58.425 37.500 0.00 0.00 0.00 3.67 R
5631 6391 2.297033 CTGTGGCTGCCAACTAAAACAT 59.703 45.455 25.23 0.00 34.18 2.71 R
6647 7413 0.321210 TGCCGGTATGTGGTCACTTG 60.321 55.000 1.90 0.00 0.00 3.16 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
338 339 4.084641 GCATTAGCATGTCGAGTGATCTTC 60.085 45.833 2.09 0.00 41.58 2.87
446 447 4.141228 TCTGAGTAATACCACCTCCGATCT 60.141 45.833 0.00 0.00 0.00 2.75
459 460 8.114102 ACCACCTCCGATCTATAATAAGTATCA 58.886 37.037 0.00 0.00 0.00 2.15
622 636 4.243270 CCAAACGAAAGATAAGTCGAGGT 58.757 43.478 0.00 0.00 39.64 3.85
714 737 7.714377 TCAAATTCATTTTGTACCTGTTGCAAT 59.286 29.630 0.59 0.00 44.25 3.56
721 744 0.250510 TACCTGTTGCAATGCACGGA 60.251 50.000 19.77 0.00 38.71 4.69
740 763 6.258068 GCACGGACTCTTTTGCTAGTAATAAT 59.742 38.462 0.00 0.00 32.00 1.28
778 801 8.792831 AAAATTATACGATACGATGAAGACGT 57.207 30.769 0.00 0.00 45.75 4.34
785 808 2.470196 ACGATGAAGACGTATCACCG 57.530 50.000 14.26 14.26 42.17 4.94
786 809 1.741706 ACGATGAAGACGTATCACCGT 59.258 47.619 15.43 15.43 42.06 4.83
787 810 2.938451 ACGATGAAGACGTATCACCGTA 59.062 45.455 18.66 0.00 44.88 4.02
788 811 3.562973 ACGATGAAGACGTATCACCGTAT 59.437 43.478 18.66 0.00 44.88 3.06
789 812 4.751600 ACGATGAAGACGTATCACCGTATA 59.248 41.667 18.66 0.00 44.88 1.47
790 813 5.078084 CGATGAAGACGTATCACCGTATAC 58.922 45.833 8.96 0.00 41.98 1.47
791 814 5.107182 CGATGAAGACGTATCACCGTATACT 60.107 44.000 8.96 0.00 41.98 2.12
792 815 6.565435 CGATGAAGACGTATCACCGTATACTT 60.565 42.308 8.96 0.00 41.98 2.24
793 816 6.052840 TGAAGACGTATCACCGTATACTTC 57.947 41.667 0.56 0.00 41.98 3.01
794 817 4.722203 AGACGTATCACCGTATACTTCG 57.278 45.455 0.56 0.00 41.98 3.79
795 818 4.122776 AGACGTATCACCGTATACTTCGT 58.877 43.478 0.56 0.00 41.98 3.85
796 819 4.572389 AGACGTATCACCGTATACTTCGTT 59.428 41.667 0.56 0.00 41.98 3.85
797 820 4.837567 ACGTATCACCGTATACTTCGTTC 58.162 43.478 0.56 0.00 39.73 3.95
798 821 3.896612 CGTATCACCGTATACTTCGTTCG 59.103 47.826 0.56 0.00 31.38 3.95
799 822 4.550831 CGTATCACCGTATACTTCGTTCGT 60.551 45.833 0.56 0.00 31.38 3.85
800 823 3.829886 TCACCGTATACTTCGTTCGTT 57.170 42.857 0.56 0.00 0.00 3.85
801 824 3.747193 TCACCGTATACTTCGTTCGTTC 58.253 45.455 0.56 0.00 0.00 3.95
802 825 2.523511 CACCGTATACTTCGTTCGTTCG 59.476 50.000 0.56 0.00 0.00 3.95
803 826 2.104144 CCGTATACTTCGTTCGTTCGG 58.896 52.381 0.56 0.00 0.00 4.30
804 827 2.476185 CCGTATACTTCGTTCGTTCGGT 60.476 50.000 0.56 0.00 0.00 4.69
805 828 3.163594 CGTATACTTCGTTCGTTCGGTT 58.836 45.455 0.56 0.00 0.00 4.44
806 829 3.002732 CGTATACTTCGTTCGTTCGGTTG 60.003 47.826 0.56 0.00 0.00 3.77
807 830 2.490328 TACTTCGTTCGTTCGGTTGT 57.510 45.000 2.85 0.00 0.00 3.32
808 831 1.643880 ACTTCGTTCGTTCGGTTGTT 58.356 45.000 2.85 0.00 0.00 2.83
809 832 1.325338 ACTTCGTTCGTTCGGTTGTTG 59.675 47.619 2.85 0.00 0.00 3.33
810 833 0.026544 TTCGTTCGTTCGGTTGTTGC 59.973 50.000 2.85 0.00 0.00 4.17
811 834 0.806884 TCGTTCGTTCGGTTGTTGCT 60.807 50.000 2.85 0.00 0.00 3.91
812 835 0.027063 CGTTCGTTCGGTTGTTGCTT 59.973 50.000 0.00 0.00 0.00 3.91
813 836 1.530236 CGTTCGTTCGGTTGTTGCTTT 60.530 47.619 0.00 0.00 0.00 3.51
814 837 2.285718 CGTTCGTTCGGTTGTTGCTTTA 60.286 45.455 0.00 0.00 0.00 1.85
815 838 3.605231 CGTTCGTTCGGTTGTTGCTTTAT 60.605 43.478 0.00 0.00 0.00 1.40
816 839 4.376210 CGTTCGTTCGGTTGTTGCTTTATA 60.376 41.667 0.00 0.00 0.00 0.98
817 840 4.650545 TCGTTCGGTTGTTGCTTTATAC 57.349 40.909 0.00 0.00 0.00 1.47
818 841 4.309099 TCGTTCGGTTGTTGCTTTATACT 58.691 39.130 0.00 0.00 0.00 2.12
819 842 4.751098 TCGTTCGGTTGTTGCTTTATACTT 59.249 37.500 0.00 0.00 0.00 2.24
820 843 5.077424 CGTTCGGTTGTTGCTTTATACTTC 58.923 41.667 0.00 0.00 0.00 3.01
821 844 5.107220 CGTTCGGTTGTTGCTTTATACTTCT 60.107 40.000 0.00 0.00 0.00 2.85
822 845 6.565247 CGTTCGGTTGTTGCTTTATACTTCTT 60.565 38.462 0.00 0.00 0.00 2.52
823 846 6.870971 TCGGTTGTTGCTTTATACTTCTTT 57.129 33.333 0.00 0.00 0.00 2.52
824 847 6.894828 TCGGTTGTTGCTTTATACTTCTTTC 58.105 36.000 0.00 0.00 0.00 2.62
825 848 5.788531 CGGTTGTTGCTTTATACTTCTTTCG 59.211 40.000 0.00 0.00 0.00 3.46
826 849 6.565247 CGGTTGTTGCTTTATACTTCTTTCGT 60.565 38.462 0.00 0.00 0.00 3.85
827 850 6.795593 GGTTGTTGCTTTATACTTCTTTCGTC 59.204 38.462 0.00 0.00 0.00 4.20
828 851 7.307811 GGTTGTTGCTTTATACTTCTTTCGTCT 60.308 37.037 0.00 0.00 0.00 4.18
829 852 7.347508 TGTTGCTTTATACTTCTTTCGTCTC 57.652 36.000 0.00 0.00 0.00 3.36
830 853 6.926826 TGTTGCTTTATACTTCTTTCGTCTCA 59.073 34.615 0.00 0.00 0.00 3.27
831 854 7.602644 TGTTGCTTTATACTTCTTTCGTCTCAT 59.397 33.333 0.00 0.00 0.00 2.90
832 855 9.084164 GTTGCTTTATACTTCTTTCGTCTCATA 57.916 33.333 0.00 0.00 0.00 2.15
833 856 9.647797 TTGCTTTATACTTCTTTCGTCTCATAA 57.352 29.630 0.00 0.00 0.00 1.90
834 857 9.817809 TGCTTTATACTTCTTTCGTCTCATAAT 57.182 29.630 0.00 0.00 0.00 1.28
901 924 9.053472 TCATTTGGTTATATAGGTGGTATAGGG 57.947 37.037 0.00 0.00 0.00 3.53
966 989 2.962421 TCCGTTTCTCATTTGGGCTTTT 59.038 40.909 0.00 0.00 0.00 2.27
1062 1085 1.840737 CATCCTCGTCCCGGATAGAT 58.159 55.000 0.73 0.00 39.20 1.98
1191 1223 3.137484 GCGCAAGGTCTCATACACA 57.863 52.632 0.30 0.00 38.28 3.72
1192 1224 1.438651 GCGCAAGGTCTCATACACAA 58.561 50.000 0.30 0.00 38.28 3.33
1193 1225 2.009774 GCGCAAGGTCTCATACACAAT 58.990 47.619 0.30 0.00 38.28 2.71
1254 1735 5.105023 CCTTCATCTCACTTCATCCTCTTCA 60.105 44.000 0.00 0.00 0.00 3.02
1382 1863 4.389374 CCAGTTGGTGTGACTTAGATGTT 58.611 43.478 0.00 0.00 0.00 2.71
1562 2043 4.267349 TGGGTACAGTTTTAGAGTCTGC 57.733 45.455 1.86 0.00 33.12 4.26
1564 2045 3.251571 GGTACAGTTTTAGAGTCTGCGG 58.748 50.000 1.86 0.00 33.12 5.69
1845 2328 7.599998 CAGGTTACTGCAGCAAAATTTTATCTT 59.400 33.333 15.27 0.00 38.01 2.40
1920 2403 5.047021 TGAGATACAACAGCTTAGCTTGTCT 60.047 40.000 13.95 8.45 36.40 3.41
1926 2409 4.181309 ACAGCTTAGCTTGTCTACTGAC 57.819 45.455 3.00 0.00 39.25 3.51
2090 2573 4.623932 ACATTCTCTCACCAAGCAGTAA 57.376 40.909 0.00 0.00 0.00 2.24
2092 2575 5.564550 ACATTCTCTCACCAAGCAGTAAAT 58.435 37.500 0.00 0.00 0.00 1.40
2132 2615 9.800433 AGTCAGAATTCTGCTATAATATCATCG 57.200 33.333 27.45 1.66 43.46 3.84
2244 2728 0.802494 CCGCCTTGGTGTGTATTGAC 59.198 55.000 0.00 0.00 0.00 3.18
2305 2789 8.982091 TTCATGGGTATAATATTTGACGGAAA 57.018 30.769 0.00 0.00 0.00 3.13
2617 3101 0.943673 TTCAGTGTGTTGACATGGCG 59.056 50.000 0.00 0.00 33.63 5.69
2715 3199 1.555967 TTTGTATGCAGCCTTTCCCC 58.444 50.000 0.00 0.00 0.00 4.81
2774 3258 5.643379 TGGAATCTAGGCAACAAATCAAC 57.357 39.130 0.00 0.00 41.41 3.18
2786 3270 6.844254 GCAACAAATCAACATTGCCATATTT 58.156 32.000 0.00 0.00 41.25 1.40
2796 3280 7.492020 TCAACATTGCCATATTTTGCAGAATAC 59.508 33.333 11.55 1.25 38.95 1.89
2907 3392 6.881602 ACTGTAGGTGATCCAGAATCTTTTTC 59.118 38.462 3.31 0.00 35.24 2.29
3048 3533 6.431198 TTGGTTGAGACAACAGTCTTTTAC 57.569 37.500 14.89 0.00 42.48 2.01
3170 3655 4.338118 ACACGTTTGATGAAAAGGATGTGT 59.662 37.500 0.00 0.00 37.15 3.72
3409 3939 1.746615 CGACCACAATCCCAGGCTG 60.747 63.158 7.75 7.75 0.00 4.85
3646 4183 7.493367 TCCCAACTTATCGTCAAACAAATTTT 58.507 30.769 0.00 0.00 0.00 1.82
3731 4269 3.248266 ACGTGAAATACTTCCTGCGTAC 58.752 45.455 0.00 0.00 34.18 3.67
3903 4441 5.008118 TGAATAGATCTGCTGAGTAGTCACG 59.992 44.000 5.18 0.00 0.00 4.35
3924 4462 8.636843 GTCACGTCTGTAGTTTCATTTAGTTAG 58.363 37.037 0.00 0.00 0.00 2.34
3950 4488 4.910195 TGGTCATTTCAGTGCAGAGTAAT 58.090 39.130 0.00 0.00 0.00 1.89
4120 4666 4.647611 TCCGCAAGTTAGGAAATGAAGAA 58.352 39.130 0.00 0.00 32.86 2.52
4512 5252 8.718656 AGAATAGTTTGAAGAGGCTACCATTAT 58.281 33.333 0.00 0.00 0.00 1.28
4550 5290 6.100404 AGTGAAAAATGCTTTGAATAGCCA 57.900 33.333 0.00 0.00 40.49 4.75
4570 5310 5.424895 AGCCAATCAGTTGCCCATTAATTTA 59.575 36.000 0.00 0.00 33.90 1.40
4608 5348 4.401202 TGTCGCAATTAGGATACACAGAGA 59.599 41.667 0.00 0.00 41.41 3.10
4799 5556 3.901222 TCTTCACAGACTGTATGGTTGGA 59.099 43.478 8.02 0.00 0.00 3.53
4800 5557 4.532126 TCTTCACAGACTGTATGGTTGGAT 59.468 41.667 8.02 0.00 0.00 3.41
4885 5644 7.335422 ACAGTTTCAGAAATAGATGATGGTGTC 59.665 37.037 0.00 0.00 0.00 3.67
5078 5838 2.684374 TGTGTGCTCATGTATGGAATGC 59.316 45.455 0.00 0.00 0.00 3.56
5082 5842 1.949525 GCTCATGTATGGAATGCCGTT 59.050 47.619 0.00 0.00 36.79 4.44
5188 5948 5.739161 GTGTTGCAGGATTCAATTAATCGAC 59.261 40.000 0.00 0.00 44.32 4.20
5466 6226 5.653255 ATGGCTAGTCCTTGGTGATATTT 57.347 39.130 0.00 0.00 35.26 1.40
5515 6275 1.888512 CCTCCCATGTCAAGTTTGGTG 59.111 52.381 0.00 0.00 0.00 4.17
5547 6307 9.166173 CAACCTCTCTTGACATTATCAACATTA 57.834 33.333 0.00 0.00 42.62 1.90
5886 6650 0.600255 ACGCAAAGACCTGGAAGTCG 60.600 55.000 0.00 0.00 41.83 4.18
5933 6697 2.037251 AGTGTACATTGAGCGAGTGGTT 59.963 45.455 0.00 0.00 0.00 3.67
6131 6896 9.846248 GAATCTATTGTTTTGCTGTTATTCTGT 57.154 29.630 0.00 0.00 0.00 3.41
6300 7065 8.576442 ACCAAGACATAACCAAAGAATGTTTAG 58.424 33.333 0.00 0.00 34.09 1.85
6614 7380 9.463902 TCTTCTATTTATTATCTACTCCCTCCG 57.536 37.037 0.00 0.00 0.00 4.63
6615 7381 9.245481 CTTCTATTTATTATCTACTCCCTCCGT 57.755 37.037 0.00 0.00 0.00 4.69
6616 7382 9.597681 TTCTATTTATTATCTACTCCCTCCGTT 57.402 33.333 0.00 0.00 0.00 4.44
6617 7383 9.240734 TCTATTTATTATCTACTCCCTCCGTTC 57.759 37.037 0.00 0.00 0.00 3.95
6618 7384 6.661304 TTTATTATCTACTCCCTCCGTTCC 57.339 41.667 0.00 0.00 0.00 3.62
6619 7385 3.967467 TTATCTACTCCCTCCGTTCCT 57.033 47.619 0.00 0.00 0.00 3.36
6620 7386 5.595814 ATTATCTACTCCCTCCGTTCCTA 57.404 43.478 0.00 0.00 0.00 2.94
6621 7387 3.967467 ATCTACTCCCTCCGTTCCTAA 57.033 47.619 0.00 0.00 0.00 2.69
6622 7388 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
6623 7389 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
6624 7390 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
6625 7391 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
6626 7392 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
6627 7393 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
6628 7394 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
6629 7395 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
6630 7396 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
6631 7397 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
6632 7398 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
6633 7399 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
6634 7400 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
6635 7401 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
6636 7402 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
6637 7403 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
6638 7404 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
6651 7417 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
6652 7418 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
6653 7419 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
6654 7420 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
6655 7421 7.657761 TCTTTCTAGAGATTTCAACAAGTGACC 59.342 37.037 0.00 0.00 35.39 4.02
6656 7422 6.419484 TCTAGAGATTTCAACAAGTGACCA 57.581 37.500 0.00 0.00 35.39 4.02
6657 7423 6.223852 TCTAGAGATTTCAACAAGTGACCAC 58.776 40.000 0.00 0.00 35.39 4.16
6658 7424 4.780815 AGAGATTTCAACAAGTGACCACA 58.219 39.130 2.78 0.00 35.39 4.17
6659 7425 5.380043 AGAGATTTCAACAAGTGACCACAT 58.620 37.500 2.78 0.00 35.39 3.21
6660 7426 6.533730 AGAGATTTCAACAAGTGACCACATA 58.466 36.000 2.78 0.00 35.39 2.29
6661 7427 6.428159 AGAGATTTCAACAAGTGACCACATAC 59.572 38.462 2.78 0.00 35.39 2.39
6662 7428 5.473504 AGATTTCAACAAGTGACCACATACC 59.526 40.000 2.78 0.00 35.39 2.73
6663 7429 2.761559 TCAACAAGTGACCACATACCG 58.238 47.619 2.78 0.00 0.00 4.02
6664 7430 1.804151 CAACAAGTGACCACATACCGG 59.196 52.381 0.00 0.00 0.00 5.28
6665 7431 0.321298 ACAAGTGACCACATACCGGC 60.321 55.000 0.00 0.00 0.00 6.13
6666 7432 0.321210 CAAGTGACCACATACCGGCA 60.321 55.000 0.00 0.00 0.00 5.69
6667 7433 0.398696 AAGTGACCACATACCGGCAA 59.601 50.000 0.00 0.00 0.00 4.52
6668 7434 0.398696 AGTGACCACATACCGGCAAA 59.601 50.000 0.00 0.00 0.00 3.68
6669 7435 1.202830 AGTGACCACATACCGGCAAAA 60.203 47.619 0.00 0.00 0.00 2.44
6670 7436 1.816224 GTGACCACATACCGGCAAAAT 59.184 47.619 0.00 0.00 0.00 1.82
6671 7437 1.815613 TGACCACATACCGGCAAAATG 59.184 47.619 0.00 3.00 0.00 2.32
6672 7438 2.088423 GACCACATACCGGCAAAATGA 58.912 47.619 0.00 0.00 0.00 2.57
6673 7439 2.091541 ACCACATACCGGCAAAATGAG 58.908 47.619 0.00 0.00 0.00 2.90
6674 7440 2.091541 CCACATACCGGCAAAATGAGT 58.908 47.619 0.00 0.00 0.00 3.41
6675 7441 2.159393 CCACATACCGGCAAAATGAGTG 60.159 50.000 0.00 0.00 0.00 3.51
6676 7442 2.746904 CACATACCGGCAAAATGAGTGA 59.253 45.455 0.00 0.00 0.00 3.41
6677 7443 3.190327 CACATACCGGCAAAATGAGTGAA 59.810 43.478 0.00 0.00 0.00 3.18
6678 7444 4.016444 ACATACCGGCAAAATGAGTGAAT 58.984 39.130 0.00 0.00 0.00 2.57
6679 7445 4.096382 ACATACCGGCAAAATGAGTGAATC 59.904 41.667 0.00 0.00 0.00 2.52
6680 7446 2.795329 ACCGGCAAAATGAGTGAATCT 58.205 42.857 0.00 0.00 0.00 2.40
6681 7447 3.950397 ACCGGCAAAATGAGTGAATCTA 58.050 40.909 0.00 0.00 0.00 1.98
6682 7448 3.689649 ACCGGCAAAATGAGTGAATCTAC 59.310 43.478 0.00 0.00 0.00 2.59
6683 7449 3.689161 CCGGCAAAATGAGTGAATCTACA 59.311 43.478 0.00 0.00 0.00 2.74
6684 7450 4.437390 CCGGCAAAATGAGTGAATCTACAC 60.437 45.833 0.00 0.00 40.60 2.90
6720 7486 9.901172 TGTCTATATACATCCGTATGTGATAGT 57.099 33.333 17.08 3.55 45.99 2.12
6722 7488 9.557061 TCTATATACATCCGTATGTGATAGTCC 57.443 37.037 17.08 0.00 45.99 3.85
6723 7489 9.338622 CTATATACATCCGTATGTGATAGTCCA 57.661 37.037 3.56 0.00 45.99 4.02
6724 7490 8.768501 ATATACATCCGTATGTGATAGTCCAT 57.231 34.615 3.56 0.00 45.99 3.41
6725 7491 5.808366 ACATCCGTATGTGATAGTCCATT 57.192 39.130 0.00 0.00 44.79 3.16
6726 7492 6.174720 ACATCCGTATGTGATAGTCCATTT 57.825 37.500 0.00 0.00 44.79 2.32
6727 7493 5.991606 ACATCCGTATGTGATAGTCCATTTG 59.008 40.000 0.00 0.00 44.79 2.32
6728 7494 5.862678 TCCGTATGTGATAGTCCATTTGA 57.137 39.130 0.00 0.00 0.00 2.69
6729 7495 6.228616 TCCGTATGTGATAGTCCATTTGAA 57.771 37.500 0.00 0.00 0.00 2.69
6730 7496 6.645306 TCCGTATGTGATAGTCCATTTGAAA 58.355 36.000 0.00 0.00 0.00 2.69
6731 7497 7.279615 TCCGTATGTGATAGTCCATTTGAAAT 58.720 34.615 0.00 0.00 0.00 2.17
6732 7498 7.441157 TCCGTATGTGATAGTCCATTTGAAATC 59.559 37.037 0.00 0.00 0.00 2.17
6733 7499 7.442364 CCGTATGTGATAGTCCATTTGAAATCT 59.558 37.037 0.00 0.00 0.00 2.40
6734 7500 8.491152 CGTATGTGATAGTCCATTTGAAATCTC 58.509 37.037 0.00 0.00 0.00 2.75
6735 7501 9.553064 GTATGTGATAGTCCATTTGAAATCTCT 57.447 33.333 0.00 0.00 0.00 3.10
6738 7504 9.958180 TGTGATAGTCCATTTGAAATCTCTAAA 57.042 29.630 0.00 0.00 0.00 1.85
6744 7510 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
6745 7511 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
6762 7528 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
6763 7529 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
6764 7530 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
6765 7531 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
6766 7532 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
6767 7533 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
6768 7534 6.667558 AATATTTAGGAACGGAGGGAGTAG 57.332 41.667 0.00 0.00 0.00 2.57
6769 7535 3.744940 TTTAGGAACGGAGGGAGTAGA 57.255 47.619 0.00 0.00 0.00 2.59
6770 7536 3.967467 TTAGGAACGGAGGGAGTAGAT 57.033 47.619 0.00 0.00 0.00 1.98
6771 7537 2.074729 AGGAACGGAGGGAGTAGATG 57.925 55.000 0.00 0.00 0.00 2.90
6772 7538 0.389757 GGAACGGAGGGAGTAGATGC 59.610 60.000 0.00 0.00 0.00 3.91
6773 7539 1.404843 GAACGGAGGGAGTAGATGCT 58.595 55.000 0.00 0.00 0.00 3.79
6774 7540 1.338655 GAACGGAGGGAGTAGATGCTC 59.661 57.143 0.00 0.00 34.89 4.26
6775 7541 0.553819 ACGGAGGGAGTAGATGCTCT 59.446 55.000 0.00 0.00 35.89 4.09
6776 7542 1.775459 ACGGAGGGAGTAGATGCTCTA 59.225 52.381 0.00 0.00 35.89 2.43
6813 7579 3.369576 GCTTCTTACTCCTGTACCCTTGG 60.370 52.174 0.00 0.00 0.00 3.61
6825 7591 5.496556 CTGTACCCTTGGTGTCATATTCAA 58.503 41.667 0.00 0.00 36.19 2.69
6827 7593 5.943416 TGTACCCTTGGTGTCATATTCAAAG 59.057 40.000 0.00 0.00 36.19 2.77
6863 7630 3.014623 GCCGTATCTGCTTTAAAAGGGT 58.985 45.455 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 6.003950 AGTCATGGTATAAATACATGCCACC 58.996 40.000 0.00 0.00 42.52 4.61
338 339 4.160439 TGCAGGAGGAACATTAGTCTACTG 59.840 45.833 0.00 0.00 40.26 2.74
459 460 4.772886 ACTGGGTTTAGTTCAAGACTGT 57.227 40.909 0.00 0.00 39.48 3.55
622 636 1.207089 CACCCAATCAGTCGGCTTCTA 59.793 52.381 0.00 0.00 0.00 2.10
714 737 1.070134 ACTAGCAAAAGAGTCCGTGCA 59.930 47.619 11.57 0.00 39.50 4.57
752 775 9.241317 ACGTCTTCATCGTATCGTATAATTTTT 57.759 29.630 0.00 0.00 39.78 1.94
753 776 8.792831 ACGTCTTCATCGTATCGTATAATTTT 57.207 30.769 0.00 0.00 39.78 1.82
765 788 3.597377 CGGTGATACGTCTTCATCGTA 57.403 47.619 20.14 0.00 41.59 3.43
766 789 2.470196 CGGTGATACGTCTTCATCGT 57.530 50.000 20.14 0.00 41.59 3.73
768 791 6.238610 AGTATACGGTGATACGTCTTCATC 57.761 41.667 0.00 0.00 45.08 2.92
769 792 6.565435 CGAAGTATACGGTGATACGTCTTCAT 60.565 42.308 14.54 0.00 45.08 2.57
770 793 5.277011 CGAAGTATACGGTGATACGTCTTCA 60.277 44.000 14.54 0.00 45.08 3.02
771 794 5.136020 CGAAGTATACGGTGATACGTCTTC 58.864 45.833 0.00 0.00 45.08 2.87
772 795 4.572389 ACGAAGTATACGGTGATACGTCTT 59.428 41.667 0.00 6.30 43.66 3.01
773 796 4.122776 ACGAAGTATACGGTGATACGTCT 58.877 43.478 0.00 0.00 43.66 4.18
774 797 4.458951 ACGAAGTATACGGTGATACGTC 57.541 45.455 0.00 8.97 43.66 4.34
775 798 4.550831 CGAACGAAGTATACGGTGATACGT 60.551 45.833 0.00 0.00 45.00 3.57
776 799 3.896612 CGAACGAAGTATACGGTGATACG 59.103 47.826 0.00 0.00 45.00 3.06
777 800 4.837567 ACGAACGAAGTATACGGTGATAC 58.162 43.478 0.14 0.00 45.00 2.24
778 801 5.484173 AACGAACGAAGTATACGGTGATA 57.516 39.130 0.14 0.00 45.00 2.15
779 802 4.346129 GAACGAACGAAGTATACGGTGAT 58.654 43.478 0.14 0.00 45.00 3.06
780 803 3.724716 CGAACGAACGAAGTATACGGTGA 60.725 47.826 0.14 0.00 45.00 4.02
781 804 2.523511 CGAACGAACGAAGTATACGGTG 59.476 50.000 0.14 0.00 45.00 4.94
782 805 2.476185 CCGAACGAACGAAGTATACGGT 60.476 50.000 0.14 0.00 45.00 4.83
783 806 2.104144 CCGAACGAACGAAGTATACGG 58.896 52.381 0.14 0.00 45.00 4.02
784 807 2.774007 ACCGAACGAACGAAGTATACG 58.226 47.619 0.14 0.00 45.00 3.06
785 808 3.914364 ACAACCGAACGAACGAAGTATAC 59.086 43.478 0.14 0.00 45.00 1.47
786 809 4.159377 ACAACCGAACGAACGAAGTATA 57.841 40.909 0.14 0.00 45.00 1.47
787 810 3.017265 ACAACCGAACGAACGAAGTAT 57.983 42.857 0.14 0.00 45.00 2.12
788 811 2.490328 ACAACCGAACGAACGAAGTA 57.510 45.000 0.14 0.00 45.00 2.24
790 813 1.914257 GCAACAACCGAACGAACGAAG 60.914 52.381 0.14 0.99 35.09 3.79
791 814 0.026544 GCAACAACCGAACGAACGAA 59.973 50.000 0.14 0.00 35.09 3.85
792 815 0.806884 AGCAACAACCGAACGAACGA 60.807 50.000 0.14 0.00 35.09 3.85
793 816 0.027063 AAGCAACAACCGAACGAACG 59.973 50.000 0.00 0.00 0.00 3.95
794 817 2.182904 AAAGCAACAACCGAACGAAC 57.817 45.000 0.00 0.00 0.00 3.95
795 818 4.751098 AGTATAAAGCAACAACCGAACGAA 59.249 37.500 0.00 0.00 0.00 3.85
796 819 4.309099 AGTATAAAGCAACAACCGAACGA 58.691 39.130 0.00 0.00 0.00 3.85
797 820 4.657075 AGTATAAAGCAACAACCGAACG 57.343 40.909 0.00 0.00 0.00 3.95
798 821 6.237313 AGAAGTATAAAGCAACAACCGAAC 57.763 37.500 0.00 0.00 0.00 3.95
799 822 6.870971 AAGAAGTATAAAGCAACAACCGAA 57.129 33.333 0.00 0.00 0.00 4.30
800 823 6.347079 CGAAAGAAGTATAAAGCAACAACCGA 60.347 38.462 0.00 0.00 0.00 4.69
801 824 5.788531 CGAAAGAAGTATAAAGCAACAACCG 59.211 40.000 0.00 0.00 0.00 4.44
802 825 6.665465 ACGAAAGAAGTATAAAGCAACAACC 58.335 36.000 0.00 0.00 0.00 3.77
803 826 7.573627 AGACGAAAGAAGTATAAAGCAACAAC 58.426 34.615 0.00 0.00 0.00 3.32
804 827 7.439955 TGAGACGAAAGAAGTATAAAGCAACAA 59.560 33.333 0.00 0.00 0.00 2.83
805 828 6.926826 TGAGACGAAAGAAGTATAAAGCAACA 59.073 34.615 0.00 0.00 0.00 3.33
806 829 7.347508 TGAGACGAAAGAAGTATAAAGCAAC 57.652 36.000 0.00 0.00 0.00 4.17
807 830 9.647797 TTATGAGACGAAAGAAGTATAAAGCAA 57.352 29.630 0.00 0.00 0.00 3.91
808 831 9.817809 ATTATGAGACGAAAGAAGTATAAAGCA 57.182 29.630 0.00 0.00 0.00 3.91
838 861 9.445786 CAAGTGTTGTCAAAAACGTTCTTATAT 57.554 29.630 0.00 0.00 32.47 0.86
839 862 8.452534 ACAAGTGTTGTCAAAAACGTTCTTATA 58.547 29.630 0.00 0.00 40.56 0.98
840 863 7.309920 ACAAGTGTTGTCAAAAACGTTCTTAT 58.690 30.769 0.00 0.00 40.56 1.73
841 864 6.670233 ACAAGTGTTGTCAAAAACGTTCTTA 58.330 32.000 0.00 0.00 40.56 2.10
842 865 5.525199 ACAAGTGTTGTCAAAAACGTTCTT 58.475 33.333 0.00 0.00 40.56 2.52
843 866 5.116069 ACAAGTGTTGTCAAAAACGTTCT 57.884 34.783 0.00 0.00 40.56 3.01
844 867 7.380320 CAATACAAGTGTTGTCAAAAACGTTC 58.620 34.615 0.00 0.00 44.12 3.95
845 868 6.309251 CCAATACAAGTGTTGTCAAAAACGTT 59.691 34.615 0.00 0.00 44.12 3.99
846 869 5.802956 CCAATACAAGTGTTGTCAAAAACGT 59.197 36.000 8.53 0.00 44.12 3.99
847 870 5.231147 CCCAATACAAGTGTTGTCAAAAACG 59.769 40.000 8.53 0.00 44.12 3.60
848 871 6.334202 TCCCAATACAAGTGTTGTCAAAAAC 58.666 36.000 8.53 0.00 44.12 2.43
849 872 6.153680 ACTCCCAATACAAGTGTTGTCAAAAA 59.846 34.615 8.53 0.00 44.12 1.94
850 873 5.654650 ACTCCCAATACAAGTGTTGTCAAAA 59.345 36.000 8.53 0.00 44.12 2.44
851 874 5.197451 ACTCCCAATACAAGTGTTGTCAAA 58.803 37.500 8.53 0.00 44.12 2.69
852 875 4.787551 ACTCCCAATACAAGTGTTGTCAA 58.212 39.130 8.53 0.00 44.12 3.18
853 876 4.431416 ACTCCCAATACAAGTGTTGTCA 57.569 40.909 8.53 0.00 44.12 3.58
854 877 4.819630 TGAACTCCCAATACAAGTGTTGTC 59.180 41.667 8.53 1.15 44.12 3.18
856 879 5.964958 ATGAACTCCCAATACAAGTGTTG 57.035 39.130 3.08 3.08 0.00 3.33
857 880 6.239289 CCAAATGAACTCCCAATACAAGTGTT 60.239 38.462 0.00 0.00 0.00 3.32
858 881 5.243730 CCAAATGAACTCCCAATACAAGTGT 59.756 40.000 0.00 0.00 0.00 3.55
859 882 5.243730 ACCAAATGAACTCCCAATACAAGTG 59.756 40.000 0.00 0.00 0.00 3.16
860 883 5.393866 ACCAAATGAACTCCCAATACAAGT 58.606 37.500 0.00 0.00 0.00 3.16
861 884 5.982890 ACCAAATGAACTCCCAATACAAG 57.017 39.130 0.00 0.00 0.00 3.16
862 885 9.707957 ATATAACCAAATGAACTCCCAATACAA 57.292 29.630 0.00 0.00 0.00 2.41
913 936 5.440610 AGAGGGCAATCTGAAATTCGTAAT 58.559 37.500 0.00 0.00 0.00 1.89
917 940 3.539604 AGAGAGGGCAATCTGAAATTCG 58.460 45.455 0.00 0.00 0.00 3.34
918 941 4.704057 ACAAGAGAGGGCAATCTGAAATTC 59.296 41.667 0.00 0.00 0.00 2.17
926 949 1.742268 GAAGCACAAGAGAGGGCAATC 59.258 52.381 0.00 0.00 0.00 2.67
966 989 1.381056 GAGCAGGAGGGAGAGAGCA 60.381 63.158 0.00 0.00 0.00 4.26
1062 1085 2.819595 GCCTTCAGCGATGGCGAA 60.820 61.111 15.70 0.80 46.35 4.70
1200 1232 1.069775 GGTTTGTGGTAAGGAGGGGA 58.930 55.000 0.00 0.00 0.00 4.81
1201 1233 1.004394 GAGGTTTGTGGTAAGGAGGGG 59.996 57.143 0.00 0.00 0.00 4.79
1205 1237 5.311121 TGGAATTAGAGGTTTGTGGTAAGGA 59.689 40.000 0.00 0.00 0.00 3.36
1206 1238 5.414765 GTGGAATTAGAGGTTTGTGGTAAGG 59.585 44.000 0.00 0.00 0.00 2.69
1209 1241 4.600111 AGGTGGAATTAGAGGTTTGTGGTA 59.400 41.667 0.00 0.00 0.00 3.25
1254 1735 1.686110 CTCCTTAGCCTGGGTCGGT 60.686 63.158 0.00 0.00 0.00 4.69
1382 1863 1.678728 GCACCCCATCTGATCGACAAA 60.679 52.381 0.00 0.00 0.00 2.83
1562 2043 4.527564 GCCAATTAATTTCATCTCGACCG 58.472 43.478 0.00 0.00 0.00 4.79
1564 2045 5.066505 AGTGGCCAATTAATTTCATCTCGAC 59.933 40.000 7.24 0.00 0.00 4.20
1845 2328 8.625651 TCAAATGATTCAAACGAAGGTTTAAGA 58.374 29.630 0.00 0.00 44.32 2.10
1920 2403 1.203187 AGCTCCACCAGGAAGTCAGTA 60.203 52.381 0.00 0.00 45.19 2.74
1926 2409 2.392662 TCTGATAGCTCCACCAGGAAG 58.607 52.381 0.00 0.00 45.19 3.46
2092 2575 9.734620 CAGAATTCTGACTTACACAAAATGAAA 57.265 29.630 28.13 0.00 46.59 2.69
2132 2615 6.926272 AGCTTAGATTATCGGTCAGATTCAAC 59.074 38.462 0.00 0.00 40.66 3.18
2244 2728 7.548075 ACTTGACTGTACAGTAATTATTTCGGG 59.452 37.037 27.98 11.54 42.66 5.14
2652 3136 4.508128 CGGACCCGCTACGTGCAT 62.508 66.667 0.00 0.00 43.06 3.96
2715 3199 1.138247 GGCCTCTTGCAGAAATGCG 59.862 57.895 0.00 0.00 43.89 4.73
2774 3258 6.142798 GTCGTATTCTGCAAAATATGGCAATG 59.857 38.462 10.97 0.00 39.93 2.82
2786 3270 7.172532 AGTGAATTTGTAAGTCGTATTCTGCAA 59.827 33.333 0.00 0.00 0.00 4.08
2796 3280 4.452455 AGCTGGAAGTGAATTTGTAAGTCG 59.548 41.667 0.00 0.00 35.30 4.18
2907 3392 6.091305 TCTGACATTGCAGATTTAAGAACTCG 59.909 38.462 6.68 0.00 39.84 4.18
3097 3582 3.630312 CAGTTCCTTTTCCCTTTTCGACA 59.370 43.478 0.00 0.00 0.00 4.35
3170 3655 4.046286 ACCAGCATTTTCAGGAATGGTA 57.954 40.909 3.13 0.00 43.63 3.25
3315 3800 4.711399 CATGCCAGAAATCTGTATCAGGA 58.289 43.478 9.43 0.00 42.27 3.86
3409 3939 8.854979 TGTGCTATATTGATGTATTGCAAAAC 57.145 30.769 1.71 0.00 41.82 2.43
3579 4116 9.417561 AGAATGCTACCTAGTGTACTGTAAATA 57.582 33.333 0.00 0.00 0.00 1.40
3580 4117 8.307582 AGAATGCTACCTAGTGTACTGTAAAT 57.692 34.615 0.00 0.00 0.00 1.40
3646 4183 8.328758 ACATTTGTTATCTCTAGTTGGGATTGA 58.671 33.333 0.00 0.00 0.00 2.57
3697 4234 6.905578 AGTATTTCACGTTATTTTGTGGACC 58.094 36.000 0.00 0.00 36.74 4.46
3731 4269 6.631238 CACACGTACTACAAGTTCAATTTTGG 59.369 38.462 0.00 0.00 0.00 3.28
3897 4435 6.746120 ACTAAATGAAACTACAGACGTGACT 58.254 36.000 0.00 0.00 0.00 3.41
3924 4462 4.202050 ACTCTGCACTGAAATGACCAAAAC 60.202 41.667 0.00 0.00 0.00 2.43
3950 4488 9.288124 CAAAATTCATAGTTTATGTCATTGCGA 57.712 29.630 0.00 0.00 37.45 5.10
4120 4666 4.074970 GGATTATCCGCTGACCAATGAAT 58.925 43.478 0.00 0.00 0.00 2.57
4304 4850 3.294214 GGAATCATGAGTGCCTTTGGAT 58.706 45.455 0.00 0.00 0.00 3.41
4512 5252 8.450964 GCATTTTTCACTATACTGCTAAAGTGA 58.549 33.333 0.10 0.10 44.86 3.41
4550 5290 5.591099 CGCTAAATTAATGGGCAACTGATT 58.409 37.500 0.00 0.00 0.00 2.57
4570 5310 4.586235 ACACTTTGGGCCAGCGCT 62.586 61.111 2.64 2.64 34.44 5.92
4608 5348 5.766174 TGAAAGCTCAAACCCGTTAACTAAT 59.234 36.000 3.71 0.00 0.00 1.73
5015 5775 5.575019 ACTTTGACCGTTATTTTGTGTGTC 58.425 37.500 0.00 0.00 0.00 3.67
5078 5838 8.798748 AAATCTCATACGAACTATAGAAACGG 57.201 34.615 6.78 0.00 0.00 4.44
5466 6226 6.071108 CCATAAAGAGAGACCTGAAGAACTGA 60.071 42.308 0.00 0.00 0.00 3.41
5515 6275 3.944055 TGTCAAGAGAGGTTGAGCTAC 57.056 47.619 0.00 0.00 37.12 3.58
5631 6391 2.297033 CTGTGGCTGCCAACTAAAACAT 59.703 45.455 25.23 0.00 34.18 2.71
5886 6650 7.996385 ACATACAGCCCATTTATGTTTTCTAC 58.004 34.615 0.00 0.00 33.54 2.59
5933 6697 2.528127 TCCCTCGCCAACCTTCCA 60.528 61.111 0.00 0.00 0.00 3.53
6476 7242 3.199677 CAACGGTGTGAAGTGAAAGGTA 58.800 45.455 0.00 0.00 0.00 3.08
6589 7355 9.245481 ACGGAGGGAGTAGATAATAAATAGAAG 57.755 37.037 0.00 0.00 0.00 2.85
6606 7372 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
6607 7373 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
6609 7375 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
6625 7391 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
6626 7392 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
6627 7393 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
6628 7394 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
6629 7395 7.657761 GGTCACTTGTTGAAATCTCTAGAAAGA 59.342 37.037 0.00 0.00 35.39 2.52
6630 7396 7.442364 TGGTCACTTGTTGAAATCTCTAGAAAG 59.558 37.037 0.00 0.00 35.39 2.62
6631 7397 7.226720 GTGGTCACTTGTTGAAATCTCTAGAAA 59.773 37.037 0.00 0.00 35.39 2.52
6632 7398 6.706270 GTGGTCACTTGTTGAAATCTCTAGAA 59.294 38.462 0.00 0.00 35.39 2.10
6633 7399 6.183360 TGTGGTCACTTGTTGAAATCTCTAGA 60.183 38.462 2.66 0.00 35.39 2.43
6634 7400 5.991606 TGTGGTCACTTGTTGAAATCTCTAG 59.008 40.000 2.66 0.00 35.39 2.43
6635 7401 5.924356 TGTGGTCACTTGTTGAAATCTCTA 58.076 37.500 2.66 0.00 35.39 2.43
6636 7402 4.780815 TGTGGTCACTTGTTGAAATCTCT 58.219 39.130 2.66 0.00 35.39 3.10
6637 7403 5.695851 ATGTGGTCACTTGTTGAAATCTC 57.304 39.130 2.66 0.00 35.39 2.75
6638 7404 5.473504 GGTATGTGGTCACTTGTTGAAATCT 59.526 40.000 2.66 0.00 35.39 2.40
6639 7405 5.616866 CGGTATGTGGTCACTTGTTGAAATC 60.617 44.000 2.66 0.00 35.39 2.17
6640 7406 4.215399 CGGTATGTGGTCACTTGTTGAAAT 59.785 41.667 2.66 0.00 35.39 2.17
6641 7407 3.562141 CGGTATGTGGTCACTTGTTGAAA 59.438 43.478 2.66 0.00 35.39 2.69
6642 7408 3.135225 CGGTATGTGGTCACTTGTTGAA 58.865 45.455 2.66 0.00 35.39 2.69
6643 7409 2.549134 CCGGTATGTGGTCACTTGTTGA 60.549 50.000 0.00 0.00 0.00 3.18
6644 7410 1.804151 CCGGTATGTGGTCACTTGTTG 59.196 52.381 0.00 0.00 0.00 3.33
6645 7411 1.880646 GCCGGTATGTGGTCACTTGTT 60.881 52.381 1.90 0.00 0.00 2.83
6646 7412 0.321298 GCCGGTATGTGGTCACTTGT 60.321 55.000 1.90 0.00 0.00 3.16
6647 7413 0.321210 TGCCGGTATGTGGTCACTTG 60.321 55.000 1.90 0.00 0.00 3.16
6648 7414 0.398696 TTGCCGGTATGTGGTCACTT 59.601 50.000 1.90 0.00 0.00 3.16
6649 7415 0.398696 TTTGCCGGTATGTGGTCACT 59.601 50.000 1.90 0.00 0.00 3.41
6650 7416 1.240256 TTTTGCCGGTATGTGGTCAC 58.760 50.000 1.90 0.00 0.00 3.67
6651 7417 1.815613 CATTTTGCCGGTATGTGGTCA 59.184 47.619 1.90 0.00 0.00 4.02
6652 7418 2.088423 TCATTTTGCCGGTATGTGGTC 58.912 47.619 1.90 0.00 0.00 4.02
6653 7419 2.091541 CTCATTTTGCCGGTATGTGGT 58.908 47.619 1.90 0.00 0.00 4.16
6654 7420 2.091541 ACTCATTTTGCCGGTATGTGG 58.908 47.619 1.90 3.50 0.00 4.17
6655 7421 2.746904 TCACTCATTTTGCCGGTATGTG 59.253 45.455 1.90 5.99 0.00 3.21
6656 7422 3.066291 TCACTCATTTTGCCGGTATGT 57.934 42.857 1.90 0.00 0.00 2.29
6657 7423 4.336433 AGATTCACTCATTTTGCCGGTATG 59.664 41.667 1.90 2.46 0.00 2.39
6658 7424 4.526970 AGATTCACTCATTTTGCCGGTAT 58.473 39.130 1.90 0.00 0.00 2.73
6659 7425 3.950397 AGATTCACTCATTTTGCCGGTA 58.050 40.909 1.90 0.00 0.00 4.02
6660 7426 2.795329 AGATTCACTCATTTTGCCGGT 58.205 42.857 1.90 0.00 0.00 5.28
6661 7427 3.689161 TGTAGATTCACTCATTTTGCCGG 59.311 43.478 0.00 0.00 0.00 6.13
6662 7428 4.393062 AGTGTAGATTCACTCATTTTGCCG 59.607 41.667 0.00 0.00 44.07 5.69
6663 7429 5.886960 AGTGTAGATTCACTCATTTTGCC 57.113 39.130 0.00 0.00 44.07 4.52
6694 7460 9.901172 ACTATCACATACGGATGTATATAGACA 57.099 33.333 30.73 11.02 44.82 3.41
6696 7462 9.557061 GGACTATCACATACGGATGTATATAGA 57.443 37.037 30.73 19.35 44.82 1.98
6697 7463 9.338622 TGGACTATCACATACGGATGTATATAG 57.661 37.037 26.27 26.27 44.82 1.31
6698 7464 9.862149 ATGGACTATCACATACGGATGTATATA 57.138 33.333 14.23 12.96 44.82 0.86
6699 7465 8.768501 ATGGACTATCACATACGGATGTATAT 57.231 34.615 14.23 12.50 44.82 0.86
6700 7466 8.589701 AATGGACTATCACATACGGATGTATA 57.410 34.615 14.23 10.59 44.82 1.47
6701 7467 7.482169 AATGGACTATCACATACGGATGTAT 57.518 36.000 14.23 10.02 44.82 2.29
6702 7468 6.911250 AATGGACTATCACATACGGATGTA 57.089 37.500 14.23 2.61 44.82 2.29
6704 7470 6.223120 TCAAATGGACTATCACATACGGATG 58.777 40.000 5.94 5.94 39.16 3.51
6705 7471 6.419484 TCAAATGGACTATCACATACGGAT 57.581 37.500 0.00 0.00 0.00 4.18
6706 7472 5.862678 TCAAATGGACTATCACATACGGA 57.137 39.130 0.00 0.00 0.00 4.69
6707 7473 6.918892 TTTCAAATGGACTATCACATACGG 57.081 37.500 0.00 0.00 0.00 4.02
6708 7474 8.370493 AGATTTCAAATGGACTATCACATACG 57.630 34.615 0.00 0.00 0.00 3.06
6709 7475 9.553064 AGAGATTTCAAATGGACTATCACATAC 57.447 33.333 0.00 0.00 0.00 2.39
6712 7478 9.958180 TTTAGAGATTTCAAATGGACTATCACA 57.042 29.630 0.00 0.00 0.00 3.58
6718 7484 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
6719 7485 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
6736 7502 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
6737 7503 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
6738 7504 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
6739 7505 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
6740 7506 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
6741 7507 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
6742 7508 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
6743 7509 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
6744 7510 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
6745 7511 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
6746 7512 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
6747 7513 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
6748 7514 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
6749 7515 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
6750 7516 3.563223 CATCTACTCCCTCCGTTCCTAA 58.437 50.000 0.00 0.00 0.00 2.69
6751 7517 2.752154 GCATCTACTCCCTCCGTTCCTA 60.752 54.545 0.00 0.00 0.00 2.94
6752 7518 2.030045 GCATCTACTCCCTCCGTTCCT 61.030 57.143 0.00 0.00 0.00 3.36
6753 7519 0.389757 GCATCTACTCCCTCCGTTCC 59.610 60.000 0.00 0.00 0.00 3.62
6754 7520 1.338655 GAGCATCTACTCCCTCCGTTC 59.661 57.143 0.00 0.00 0.00 3.95
6755 7521 1.404843 GAGCATCTACTCCCTCCGTT 58.595 55.000 0.00 0.00 0.00 4.44
6756 7522 3.119225 GAGCATCTACTCCCTCCGT 57.881 57.895 0.00 0.00 0.00 4.69
6768 7534 5.376854 TTTGCCTCTTTTTGTAGAGCATC 57.623 39.130 0.00 0.00 40.28 3.91
6769 7535 4.321527 GCTTTGCCTCTTTTTGTAGAGCAT 60.322 41.667 0.00 0.00 40.28 3.79
6770 7536 3.004734 GCTTTGCCTCTTTTTGTAGAGCA 59.995 43.478 0.00 0.00 40.28 4.26
6771 7537 3.254411 AGCTTTGCCTCTTTTTGTAGAGC 59.746 43.478 0.00 0.00 40.28 4.09
6772 7538 5.240403 AGAAGCTTTGCCTCTTTTTGTAGAG 59.760 40.000 0.00 0.00 41.10 2.43
6773 7539 5.133221 AGAAGCTTTGCCTCTTTTTGTAGA 58.867 37.500 0.00 0.00 0.00 2.59
6774 7540 5.444663 AGAAGCTTTGCCTCTTTTTGTAG 57.555 39.130 0.00 0.00 0.00 2.74
6775 7541 5.852282 AAGAAGCTTTGCCTCTTTTTGTA 57.148 34.783 0.00 0.00 36.09 2.41
6776 7542 4.743057 AAGAAGCTTTGCCTCTTTTTGT 57.257 36.364 0.00 0.00 36.09 2.83
6777 7543 5.836347 AGTAAGAAGCTTTGCCTCTTTTTG 58.164 37.500 0.00 0.00 39.60 2.44
6825 7591 4.689612 ACGGCATGATCTTGTATACCTT 57.310 40.909 10.05 0.00 0.00 3.50
6827 7593 5.807520 CAGATACGGCATGATCTTGTATACC 59.192 44.000 10.05 2.47 29.73 2.73


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

AutoCloner maintained by Alex Coulton.