Multiple sequence alignment - TraesCS3A01G124500

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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 TraesCS3A01G124500 chr3A 100.000 4705 0 0 1 4705 100827282 100831986 0.000000e+00 8689.0
1 TraesCS3A01G124500 chr3B 92.557 2069 96 20 859 2918 132395895 132393876 0.000000e+00 2915.0
2 TraesCS3A01G124500 chr3B 95.691 673 26 3 2955 3627 132393881 132393212 0.000000e+00 1079.0
3 TraesCS3A01G124500 chr3B 91.350 474 20 8 4234 4705 132389498 132389044 3.090000e-176 628.0
4 TraesCS3A01G124500 chr3B 87.179 78 9 1 3774 3850 8721977 8721900 2.330000e-13 87.9
5 TraesCS3A01G124500 chr3B 88.889 72 4 3 3982 4051 132392768 132392699 8.390000e-13 86.1
6 TraesCS3A01G124500 chr3D 94.307 1739 78 11 1092 2819 84480600 84482328 0.000000e+00 2643.0
7 TraesCS3A01G124500 chr3D 92.896 732 49 3 2897 3627 84482328 84483057 0.000000e+00 1061.0
8 TraesCS3A01G124500 chr3D 89.844 512 22 10 4195 4705 84483918 84484400 8.590000e-177 630.0
9 TraesCS3A01G124500 chr3D 87.452 263 18 7 3620 3877 84483079 84483331 5.960000e-74 289.0
10 TraesCS3A01G124500 chr3D 92.913 127 9 0 3939 4065 84483325 84483451 8.040000e-43 185.0
11 TraesCS3A01G124500 chr3D 85.621 153 4 2 859 1011 84480303 84480437 1.360000e-30 145.0
12 TraesCS3A01G124500 chr2B 85.074 1829 173 44 976 2736 705354368 705352572 0.000000e+00 1773.0
13 TraesCS3A01G124500 chr2B 89.087 843 91 1 1 843 381523172 381522331 0.000000e+00 1046.0
14 TraesCS3A01G124500 chr2B 85.520 1029 115 22 2588 3594 705352151 705351135 0.000000e+00 1044.0
15 TraesCS3A01G124500 chr2B 83.908 87 13 1 3775 3860 390945153 390945239 1.090000e-11 82.4
16 TraesCS3A01G124500 chr2B 90.625 64 2 3 3797 3858 529265323 529265262 1.090000e-11 82.4
17 TraesCS3A01G124500 chr2B 90.909 55 3 1 2727 2781 705352300 705352248 6.530000e-09 73.1
18 TraesCS3A01G124500 chr2A 88.250 1217 106 19 976 2183 718973322 718972134 0.000000e+00 1421.0
19 TraesCS3A01G124500 chr2A 84.323 1027 123 23 2598 3600 718970924 718969912 0.000000e+00 970.0
20 TraesCS3A01G124500 chr2A 85.178 506 54 12 2245 2736 718971726 718971228 2.530000e-137 499.0
21 TraesCS3A01G124500 chr2A 90.625 64 2 3 3797 3858 593655888 593655827 1.090000e-11 82.4
22 TraesCS3A01G124500 chr1D 95.952 840 34 0 1 840 488960898 488961737 0.000000e+00 1363.0
23 TraesCS3A01G124500 chr6D 95.471 839 38 0 1 839 293326950 293327788 0.000000e+00 1339.0
24 TraesCS3A01G124500 chr2D 95.238 840 40 0 1 840 563418490 563419329 0.000000e+00 1330.0
25 TraesCS3A01G124500 chr2D 86.620 1136 97 25 1647 2736 584863814 584862688 0.000000e+00 1205.0
26 TraesCS3A01G124500 chr2D 85.659 1032 105 27 2586 3594 584862394 584861383 0.000000e+00 1046.0
27 TraesCS3A01G124500 chr2D 88.235 578 65 1 266 843 202435554 202434980 0.000000e+00 688.0
28 TraesCS3A01G124500 chr2D 85.827 635 58 20 976 1609 584864509 584863906 0.000000e+00 645.0
29 TraesCS3A01G124500 chr2D 98.113 53 1 0 4123 4175 417798823 417798771 5.010000e-15 93.5
30 TraesCS3A01G124500 chr2D 87.879 66 6 2 3797 3861 572703491 572703555 5.050000e-10 76.8
31 TraesCS3A01G124500 chr4D 94.624 837 45 0 1 837 263953257 263954093 0.000000e+00 1297.0
32 TraesCS3A01G124500 chr4D 84.063 822 119 7 28 840 98203441 98204259 0.000000e+00 782.0
33 TraesCS3A01G124500 chr4D 83.582 67 9 2 4121 4185 293136906 293136840 1.410000e-05 62.1
34 TraesCS3A01G124500 chr5A 90.357 840 81 0 1 840 386460798 386461637 0.000000e+00 1103.0
35 TraesCS3A01G124500 chr5A 87.179 78 8 2 3774 3850 375558943 375558867 2.330000e-13 87.9
36 TraesCS3A01G124500 chr7A 90.356 674 54 4 1 674 120570173 120570835 0.000000e+00 874.0
37 TraesCS3A01G124500 chr7B 84.340 811 120 7 36 843 452696484 452695678 0.000000e+00 787.0
38 TraesCS3A01G124500 chr1A 87.179 78 9 1 3774 3850 543475102 543475025 2.330000e-13 87.9
39 TraesCS3A01G124500 chr1A 89.091 55 6 0 4121 4175 495324195 495324249 8.450000e-08 69.4
40 TraesCS3A01G124500 chr5D 94.545 55 3 0 4121 4175 443651764 443651710 8.390000e-13 86.1
41 TraesCS3A01G124500 chr4A 86.667 75 9 1 3774 3847 181652562 181652488 1.090000e-11 82.4
42 TraesCS3A01G124500 chr4A 92.308 52 4 0 4124 4175 607472025 607471974 1.820000e-09 75.0
43 TraesCS3A01G124500 chr6B 85.333 75 11 0 3774 3848 672922930 672923004 1.400000e-10 78.7
44 TraesCS3A01G124500 chr1B 91.228 57 3 2 4121 4175 361147740 361147796 5.050000e-10 76.8
45 TraesCS3A01G124500 chr1B 89.091 55 6 0 4121 4175 533803346 533803400 8.450000e-08 69.4
46 TraesCS3A01G124500 chr7D 89.286 56 5 1 4121 4175 634189956 634189901 8.450000e-08 69.4
47 TraesCS3A01G124500 chr6A 89.286 56 5 1 4120 4175 49711076 49711130 8.450000e-08 69.4


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 TraesCS3A01G124500 chr3A 100827282 100831986 4704 False 8689.000000 8689 100.000000 1 4705 1 chr3A.!!$F1 4704
1 TraesCS3A01G124500 chr3B 132389044 132395895 6851 True 1177.025000 2915 92.121750 859 4705 4 chr3B.!!$R2 3846
2 TraesCS3A01G124500 chr3D 84480303 84484400 4097 False 825.500000 2643 90.505500 859 4705 6 chr3D.!!$F1 3846
3 TraesCS3A01G124500 chr2B 381522331 381523172 841 True 1046.000000 1046 89.087000 1 843 1 chr2B.!!$R1 842
4 TraesCS3A01G124500 chr2B 705351135 705354368 3233 True 963.366667 1773 87.167667 976 3594 3 chr2B.!!$R3 2618
5 TraesCS3A01G124500 chr2A 718969912 718973322 3410 True 963.333333 1421 85.917000 976 3600 3 chr2A.!!$R2 2624
6 TraesCS3A01G124500 chr1D 488960898 488961737 839 False 1363.000000 1363 95.952000 1 840 1 chr1D.!!$F1 839
7 TraesCS3A01G124500 chr6D 293326950 293327788 838 False 1339.000000 1339 95.471000 1 839 1 chr6D.!!$F1 838
8 TraesCS3A01G124500 chr2D 563418490 563419329 839 False 1330.000000 1330 95.238000 1 840 1 chr2D.!!$F1 839
9 TraesCS3A01G124500 chr2D 584861383 584864509 3126 True 965.333333 1205 86.035333 976 3594 3 chr2D.!!$R3 2618
10 TraesCS3A01G124500 chr2D 202434980 202435554 574 True 688.000000 688 88.235000 266 843 1 chr2D.!!$R1 577
11 TraesCS3A01G124500 chr4D 263953257 263954093 836 False 1297.000000 1297 94.624000 1 837 1 chr4D.!!$F2 836
12 TraesCS3A01G124500 chr4D 98203441 98204259 818 False 782.000000 782 84.063000 28 840 1 chr4D.!!$F1 812
13 TraesCS3A01G124500 chr5A 386460798 386461637 839 False 1103.000000 1103 90.357000 1 840 1 chr5A.!!$F1 839
14 TraesCS3A01G124500 chr7A 120570173 120570835 662 False 874.000000 874 90.356000 1 674 1 chr7A.!!$F1 673
15 TraesCS3A01G124500 chr7B 452695678 452696484 806 True 787.000000 787 84.340000 36 843 1 chr7B.!!$R1 807

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
147 148 0.107703 CAGCTTATTCCCACCGAGCA 60.108 55.0 0.00 0.00 35.86 4.26 F
1062 1069 0.179045 AGCCACGCAGAAAACAGAGT 60.179 50.0 0.00 0.00 0.00 3.24 F
2838 4438 0.035176 AACATTGCATTGTGGGCCAC 59.965 50.0 29.75 29.75 34.56 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 2044 0.452987 CACAATCCATCGCAGTTGGG 59.547 55.0 6.02 0.0 34.85 4.12 R
2932 4536 0.393077 CTGTATCCAAGGGGTAGCGG 59.607 60.0 0.00 0.0 34.93 5.52 R
4595 9656 0.320697 GGGTCTGTACAAGGCGAAGT 59.679 55.0 0.00 0.0 0.00 3.01 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
34 35 2.019249 CGGACAGTGCATGATGGATTT 58.981 47.619 0.00 0.00 0.00 2.17
124 125 4.079787 AGCCTTTGGGAGATTGCTATTACA 60.080 41.667 0.00 0.00 33.58 2.41
147 148 0.107703 CAGCTTATTCCCACCGAGCA 60.108 55.000 0.00 0.00 35.86 4.26
179 180 1.360393 TTGGCCCTGGAACTCCAAGT 61.360 55.000 0.00 0.00 46.97 3.16
193 194 4.220724 ACTCCAAGTAGGTGTACACTTCA 58.779 43.478 24.55 8.14 42.12 3.02
204 205 2.486636 TACACTTCAGCCTCCGCGTG 62.487 60.000 4.92 0.00 41.18 5.34
410 411 6.015350 GGAGGAGGATAACGTTGATCATCTTA 60.015 42.308 20.84 0.00 35.10 2.10
430 431 5.835280 TCTTATGATCCAGTGCATCTACTCA 59.165 40.000 0.00 0.00 0.00 3.41
520 521 0.911525 CTCTGGAGTCATGGTGGGGT 60.912 60.000 0.00 0.00 0.00 4.95
556 557 8.605601 ATCGGCTTGATAAGGAGACACGTAAG 62.606 46.154 0.00 0.00 38.64 2.34
634 635 2.200337 GGTTTTCCGCTTGGTGGCT 61.200 57.895 0.00 0.00 32.51 4.75
750 751 3.884693 TGAGGAGTTAACGTAGTGTGTGA 59.115 43.478 0.00 0.00 45.00 3.58
761 768 3.245284 CGTAGTGTGTGAAGTTGGAGTTG 59.755 47.826 0.00 0.00 0.00 3.16
849 856 8.754991 TCTCTCTTCTATAAAGTTACTCTGGG 57.245 38.462 0.00 0.00 0.00 4.45
850 857 8.558312 TCTCTCTTCTATAAAGTTACTCTGGGA 58.442 37.037 0.00 0.00 0.00 4.37
851 858 9.191479 CTCTCTTCTATAAAGTTACTCTGGGAA 57.809 37.037 0.00 0.00 0.00 3.97
852 859 9.543231 TCTCTTCTATAAAGTTACTCTGGGAAA 57.457 33.333 0.00 0.00 0.00 3.13
956 963 4.828939 TGGTCTACGTAGGTTTTCTCTTCA 59.171 41.667 22.01 0.00 0.00 3.02
1062 1069 0.179045 AGCCACGCAGAAAACAGAGT 60.179 50.000 0.00 0.00 0.00 3.24
1320 1409 2.435372 TGATTTCTGGTACCATGCCC 57.565 50.000 16.75 4.87 0.00 5.36
1322 1411 0.623723 ATTTCTGGTACCATGCCCGT 59.376 50.000 16.75 0.00 0.00 5.28
1377 1466 1.418342 CGTTTATCCCGGACACTGCG 61.418 60.000 0.73 0.00 0.00 5.18
1582 1671 6.483640 AGAATGCGATTATAAAGAGGTTCACC 59.516 38.462 0.00 0.00 0.00 4.02
1603 1692 2.496899 ACATTCCATTCGAGGTTGCT 57.503 45.000 0.00 0.00 0.00 3.91
1604 1693 2.086869 ACATTCCATTCGAGGTTGCTG 58.913 47.619 0.00 0.00 0.00 4.41
1605 1694 1.098050 ATTCCATTCGAGGTTGCTGC 58.902 50.000 0.00 0.00 0.00 5.25
1606 1695 0.960364 TTCCATTCGAGGTTGCTGCC 60.960 55.000 0.00 0.00 0.00 4.85
1607 1696 1.675310 CCATTCGAGGTTGCTGCCA 60.675 57.895 0.00 0.00 0.00 4.92
1608 1697 1.503542 CATTCGAGGTTGCTGCCAC 59.496 57.895 0.00 0.00 0.00 5.01
1609 1698 0.957395 CATTCGAGGTTGCTGCCACT 60.957 55.000 3.76 0.00 0.00 4.00
1610 1699 0.957395 ATTCGAGGTTGCTGCCACTG 60.957 55.000 3.76 0.00 0.00 3.66
1640 1786 9.559958 CACAATTTTTCTACCTTGTGCTATTAG 57.440 33.333 1.81 0.00 41.18 1.73
1887 2044 2.409948 AGAGCAGGAAGTACATTGGC 57.590 50.000 0.00 0.00 0.00 4.52
1890 2047 0.323360 GCAGGAAGTACATTGGCCCA 60.323 55.000 0.00 0.00 0.00 5.36
2185 2342 5.917462 AGCAACTTTGAGCAGGTAATTTTT 58.083 33.333 0.00 0.00 0.00 1.94
2439 2953 7.331440 CCTGCATTTTCTGTTGTTTATGCAATA 59.669 33.333 0.00 0.00 45.16 1.90
2485 2999 4.599047 TTGGAATTGTTCATTGGTGACC 57.401 40.909 0.00 0.00 33.11 4.02
2517 3033 7.750229 AATGAAGAAAAGTATCAGCAACTGA 57.250 32.000 0.00 0.00 44.99 3.41
2527 3043 4.633980 GCAACTGACCCTTTTGCG 57.366 55.556 0.00 0.00 36.57 4.85
2565 3097 5.270083 CGAATGTTGTAGTTGTGCTTGAAA 58.730 37.500 0.00 0.00 0.00 2.69
2596 3134 2.463876 ACGCACATGACATGATACTCG 58.536 47.619 22.19 16.71 0.00 4.18
2616 3732 3.684305 TCGGTCACATAGTTGAATGCTTG 59.316 43.478 0.00 0.00 0.00 4.01
2679 4255 8.182881 ACAAATTCACCATGAAATGTTTGTTTG 58.817 29.630 12.61 10.67 40.91 2.93
2838 4438 0.035176 AACATTGCATTGTGGGCCAC 59.965 50.000 29.75 29.75 34.56 5.01
2839 4439 1.446445 CATTGCATTGTGGGCCACG 60.446 57.895 30.14 17.93 37.14 4.94
2845 4445 3.298958 TTGTGGGCCACGCAAAAA 58.701 50.000 30.14 16.53 45.89 1.94
2846 4446 1.826024 TTGTGGGCCACGCAAAAAT 59.174 47.368 30.14 0.00 45.89 1.82
2924 4528 7.631717 ATTTTTAGGAGGTTATCTTCTGTGC 57.368 36.000 0.00 0.00 32.44 4.57
2928 4532 3.584848 AGGAGGTTATCTTCTGTGCAAGT 59.415 43.478 0.00 0.00 27.80 3.16
2932 4536 3.366374 GGTTATCTTCTGTGCAAGTTGCC 60.366 47.826 24.59 15.94 44.23 4.52
2933 4537 1.251251 ATCTTCTGTGCAAGTTGCCC 58.749 50.000 24.59 14.56 44.23 5.36
3186 4795 1.148310 CAGAATGCGTTCACGACCTT 58.852 50.000 20.45 0.00 43.02 3.50
3198 4807 0.832135 ACGACCTTCTCCTCCTTGCA 60.832 55.000 0.00 0.00 0.00 4.08
3243 4852 2.955660 CAGGCTCGTCTTCTTCTATCCT 59.044 50.000 0.00 0.00 0.00 3.24
3307 4916 1.228367 CACCCCTGCTTCAAGCTGT 60.228 57.895 11.57 0.00 42.97 4.40
3375 4984 1.810030 GACGATGGTGAAGGTCGGC 60.810 63.158 0.00 0.00 39.53 5.54
3435 5044 1.277557 CACCAGGAGTTCAGGGAGAAG 59.722 57.143 0.00 0.00 36.78 2.85
3486 5095 4.329545 TCTGCCGTGTTCAGCCCC 62.330 66.667 0.00 0.00 0.00 5.80
3575 5185 2.162681 GTGATGAAAACACTCTGGGGG 58.837 52.381 0.00 0.00 36.60 5.40
3597 5213 7.441836 GGGGTGACAATTTTGTTATCTTTTCT 58.558 34.615 0.00 0.00 42.43 2.52
3724 5503 6.072893 TCACTTATTTTTCCTACCTTGCGTTC 60.073 38.462 0.00 0.00 0.00 3.95
3726 5505 1.515081 TTTTCCTACCTTGCGTTCCG 58.485 50.000 0.00 0.00 0.00 4.30
3728 5507 2.791501 TTCCTACCTTGCGTTCCGGC 62.792 60.000 0.00 0.00 0.00 6.13
3729 5508 2.264794 CTACCTTGCGTTCCGGCT 59.735 61.111 0.00 0.00 0.00 5.52
3730 5509 2.047655 TACCTTGCGTTCCGGCTG 60.048 61.111 0.00 0.00 0.00 4.85
3795 5575 6.886178 AATACTCCCCTGTACACTATTGTT 57.114 37.500 0.00 0.00 37.15 2.83
3808 5588 6.366315 ACACTATTGTTAGACGTTTTTGCA 57.634 33.333 0.00 0.00 28.43 4.08
3809 5589 6.427150 ACACTATTGTTAGACGTTTTTGCAG 58.573 36.000 0.00 0.00 28.43 4.41
3810 5590 6.037830 ACACTATTGTTAGACGTTTTTGCAGT 59.962 34.615 0.00 0.00 28.43 4.40
3811 5591 6.910433 CACTATTGTTAGACGTTTTTGCAGTT 59.090 34.615 0.00 0.00 0.00 3.16
3812 5592 7.431084 CACTATTGTTAGACGTTTTTGCAGTTT 59.569 33.333 0.00 0.00 0.00 2.66
3813 5593 8.614346 ACTATTGTTAGACGTTTTTGCAGTTTA 58.386 29.630 0.00 0.00 0.00 2.01
3814 5594 9.440784 CTATTGTTAGACGTTTTTGCAGTTTAA 57.559 29.630 0.00 0.00 0.00 1.52
3815 5595 8.690680 ATTGTTAGACGTTTTTGCAGTTTAAA 57.309 26.923 0.00 0.00 0.00 1.52
3816 5596 8.690680 TTGTTAGACGTTTTTGCAGTTTAAAT 57.309 26.923 0.00 0.00 0.00 1.40
3817 5597 8.690680 TGTTAGACGTTTTTGCAGTTTAAATT 57.309 26.923 0.00 0.00 0.00 1.82
3818 5598 8.587950 TGTTAGACGTTTTTGCAGTTTAAATTG 58.412 29.630 6.35 6.35 0.00 2.32
3821 5601 7.671827 AGACGTTTTTGCAGTTTAAATTGAAC 58.328 30.769 14.30 8.43 0.00 3.18
3831 5611 6.855996 CAGTTTAAATTGAACTGCAAGAACG 58.144 36.000 15.89 0.00 45.02 3.95
3832 5612 5.458779 AGTTTAAATTGAACTGCAAGAACGC 59.541 36.000 2.22 0.00 40.42 4.84
3850 5630 6.746120 AGAACGCCTTATATTAGTGTACAGG 58.254 40.000 0.00 0.00 0.00 4.00
3859 5639 9.804977 CTTATATTAGTGTACAGGGGTAGTACT 57.195 37.037 0.00 0.00 41.76 2.73
3871 5651 4.856182 AGGGGTAGTACTTCCCAAGAAAAT 59.144 41.667 31.84 10.63 45.06 1.82
3881 5661 6.010850 ACTTCCCAAGAAAATCTTTACTCCC 58.989 40.000 0.00 0.00 33.78 4.30
3882 5662 5.592587 TCCCAAGAAAATCTTTACTCCCA 57.407 39.130 0.00 0.00 33.78 4.37
3890 5670 7.066781 AGAAAATCTTTACTCCCAGAAAACCA 58.933 34.615 0.00 0.00 0.00 3.67
3891 5671 7.563556 AGAAAATCTTTACTCCCAGAAAACCAA 59.436 33.333 0.00 0.00 0.00 3.67
3893 5673 6.840780 ATCTTTACTCCCAGAAAACCAATG 57.159 37.500 0.00 0.00 0.00 2.82
3895 5675 6.133356 TCTTTACTCCCAGAAAACCAATGTT 58.867 36.000 0.00 0.00 35.82 2.71
3926 5706 1.338107 ACAGTGAATCACTCCGACCA 58.662 50.000 13.72 0.00 43.43 4.02
3931 5711 2.093447 GTGAATCACTCCGACCAATCCT 60.093 50.000 6.07 0.00 0.00 3.24
3932 5712 2.571653 TGAATCACTCCGACCAATCCTT 59.428 45.455 0.00 0.00 0.00 3.36
3943 5726 4.386711 CGACCAATCCTTAATACCCCTTC 58.613 47.826 0.00 0.00 0.00 3.46
4009 5807 6.241207 TGATTCAACTAGTTAAGTGCTTGC 57.759 37.500 8.04 0.00 38.88 4.01
4010 5808 5.181245 TGATTCAACTAGTTAAGTGCTTGCC 59.819 40.000 8.04 0.00 38.88 4.52
4065 5863 7.552687 TGGTTCAATATCAATCAGGTCTAACAC 59.447 37.037 0.00 0.00 0.00 3.32
4067 5865 7.107639 TCAATATCAATCAGGTCTAACACGA 57.892 36.000 0.00 0.00 0.00 4.35
4070 5868 4.594123 TCAATCAGGTCTAACACGAACA 57.406 40.909 0.00 0.00 0.00 3.18
4071 5869 5.147330 TCAATCAGGTCTAACACGAACAT 57.853 39.130 0.00 0.00 0.00 2.71
4072 5870 5.547465 TCAATCAGGTCTAACACGAACATT 58.453 37.500 0.00 0.00 0.00 2.71
4099 8490 6.138761 GCTACTTTCCTCAATCAATTATGCG 58.861 40.000 0.00 0.00 0.00 4.73
4100 8491 6.017934 GCTACTTTCCTCAATCAATTATGCGA 60.018 38.462 0.00 0.00 0.00 5.10
4102 8493 5.882557 ACTTTCCTCAATCAATTATGCGACT 59.117 36.000 0.00 0.00 0.00 4.18
4105 8496 3.499918 CCTCAATCAATTATGCGACTCCC 59.500 47.826 0.00 0.00 0.00 4.30
4107 8498 2.554032 CAATCAATTATGCGACTCCCCC 59.446 50.000 0.00 0.00 0.00 5.40
4108 8499 1.208706 TCAATTATGCGACTCCCCCA 58.791 50.000 0.00 0.00 0.00 4.96
4109 8500 1.134220 TCAATTATGCGACTCCCCCAC 60.134 52.381 0.00 0.00 0.00 4.61
4110 8501 0.182775 AATTATGCGACTCCCCCACC 59.817 55.000 0.00 0.00 0.00 4.61
4115 8506 4.029809 CGACTCCCCCACCCCAAC 62.030 72.222 0.00 0.00 0.00 3.77
4116 8507 2.856988 GACTCCCCCACCCCAACA 60.857 66.667 0.00 0.00 0.00 3.33
4117 8508 3.182996 ACTCCCCCACCCCAACAC 61.183 66.667 0.00 0.00 0.00 3.32
4119 8510 3.503839 TCCCCCACCCCAACACAC 61.504 66.667 0.00 0.00 0.00 3.82
4120 8511 3.826822 CCCCCACCCCAACACACA 61.827 66.667 0.00 0.00 0.00 3.72
4121 8512 2.520741 CCCCACCCCAACACACAC 60.521 66.667 0.00 0.00 0.00 3.82
4123 8514 1.380515 CCCACCCCAACACACACAA 60.381 57.895 0.00 0.00 0.00 3.33
4124 8515 1.391157 CCCACCCCAACACACACAAG 61.391 60.000 0.00 0.00 0.00 3.16
4125 8516 0.682855 CCACCCCAACACACACAAGT 60.683 55.000 0.00 0.00 0.00 3.16
4126 8517 1.181786 CACCCCAACACACACAAGTT 58.818 50.000 0.00 0.00 0.00 2.66
4128 8519 2.755655 CACCCCAACACACACAAGTTTA 59.244 45.455 0.00 0.00 0.00 2.01
4130 8521 4.580995 CACCCCAACACACACAAGTTTATA 59.419 41.667 0.00 0.00 0.00 0.98
4131 8522 4.825085 ACCCCAACACACACAAGTTTATAG 59.175 41.667 0.00 0.00 0.00 1.31
4132 8523 5.067273 CCCCAACACACACAAGTTTATAGA 58.933 41.667 0.00 0.00 0.00 1.98
4133 8524 5.048991 CCCCAACACACACAAGTTTATAGAC 60.049 44.000 0.00 0.00 0.00 2.59
4136 8527 7.415765 CCCAACACACACAAGTTTATAGACAAA 60.416 37.037 0.00 0.00 0.00 2.83
4175 9217 6.440010 ACACCATCAAATCAATACCATTGGAA 59.560 34.615 10.37 0.00 0.00 3.53
4176 9218 7.038445 ACACCATCAAATCAATACCATTGGAAA 60.038 33.333 10.37 0.00 0.00 3.13
4177 9219 7.988599 CACCATCAAATCAATACCATTGGAAAT 59.011 33.333 10.37 0.00 0.00 2.17
4179 9221 9.480053 CCATCAAATCAATACCATTGGAAATAC 57.520 33.333 10.37 0.00 0.00 1.89
4214 9272 9.715123 TCATCATGTTATTATAAAACGCAACAG 57.285 29.630 0.00 0.00 30.23 3.16
4215 9273 9.715123 CATCATGTTATTATAAAACGCAACAGA 57.285 29.630 0.00 0.00 30.23 3.41
4248 9306 1.638133 CGCTCCAAGATGTCAGACAG 58.362 55.000 9.64 0.00 0.00 3.51
4258 9316 5.275067 AGATGTCAGACAGAATTAGCTCC 57.725 43.478 9.64 0.00 0.00 4.70
4274 9333 9.507329 GAATTAGCTCCAAGATTATGATAACCA 57.493 33.333 0.00 0.00 0.00 3.67
4427 9488 5.880054 TTGATCCAATTCCTTCTCGAAAC 57.120 39.130 0.00 0.00 0.00 2.78
4442 9503 7.044052 CCTTCTCGAAACAAAAGTCAATTCAAC 60.044 37.037 0.00 0.00 0.00 3.18
4448 9509 8.638565 CGAAACAAAAGTCAATTCAACCATATC 58.361 33.333 0.00 0.00 0.00 1.63
4481 9542 2.673368 GCAAGAGGTACATCTTCAACCG 59.327 50.000 19.37 9.59 37.43 4.44
4522 9583 6.260936 ACAAAATCTCTCACTACACAAACCTG 59.739 38.462 0.00 0.00 0.00 4.00
4590 9651 3.393687 AGGGGATAGATAACACAAGGCA 58.606 45.455 0.00 0.00 0.00 4.75
4592 9653 3.883489 GGGGATAGATAACACAAGGCAAC 59.117 47.826 0.00 0.00 0.00 4.17
4606 9667 1.235724 GGCAACTAACTTCGCCTTGT 58.764 50.000 0.00 0.00 41.50 3.16
4607 9668 2.419667 GGCAACTAACTTCGCCTTGTA 58.580 47.619 0.00 0.00 41.50 2.41
4608 9669 2.159037 GGCAACTAACTTCGCCTTGTAC 59.841 50.000 0.00 0.00 41.50 2.90
4609 9670 2.803956 GCAACTAACTTCGCCTTGTACA 59.196 45.455 0.00 0.00 0.00 2.90
4610 9671 3.120649 GCAACTAACTTCGCCTTGTACAG 60.121 47.826 0.00 0.00 0.00 2.74
4611 9672 4.304110 CAACTAACTTCGCCTTGTACAGA 58.696 43.478 0.00 0.00 0.00 3.41
4612 9673 3.910648 ACTAACTTCGCCTTGTACAGAC 58.089 45.455 0.00 0.00 0.00 3.51
4613 9674 2.165319 AACTTCGCCTTGTACAGACC 57.835 50.000 0.00 0.00 0.00 3.85
4614 9675 0.320697 ACTTCGCCTTGTACAGACCC 59.679 55.000 0.00 0.00 0.00 4.46
4615 9676 0.320374 CTTCGCCTTGTACAGACCCA 59.680 55.000 0.00 0.00 0.00 4.51
4616 9677 0.981183 TTCGCCTTGTACAGACCCAT 59.019 50.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.329545 GCCCAGCGGTGGTTGAGA 62.330 66.667 30.39 0.00 43.23 3.27
124 125 1.024579 CGGTGGGAATAAGCTGCGTT 61.025 55.000 0.00 0.00 0.00 4.84
147 148 4.751431 GCCAAACAGCCTCATCCT 57.249 55.556 0.00 0.00 0.00 3.24
179 180 2.176889 GGAGGCTGAAGTGTACACCTA 58.823 52.381 22.28 8.18 0.00 3.08
193 194 2.034879 CATTTGACACGCGGAGGCT 61.035 57.895 12.47 0.00 36.88 4.58
204 205 2.352127 GCACCCTTGAAGAGCATTTGAC 60.352 50.000 0.00 0.00 0.00 3.18
279 280 2.095059 GCGAGCCACATGAAAATCTTGT 60.095 45.455 0.00 0.00 35.47 3.16
410 411 3.243670 CGTGAGTAGATGCACTGGATCAT 60.244 47.826 12.58 0.00 32.98 2.45
430 431 2.248280 TGTTGTGCCATACTTGACGT 57.752 45.000 0.00 0.00 0.00 4.34
520 521 6.462487 CCTTATCAAGCCGATTTCTGGTACTA 60.462 42.308 0.00 0.00 35.39 1.82
556 557 3.736126 GCATCACCAAGCTATCAAAAGCC 60.736 47.826 0.00 0.00 43.86 4.35
701 702 1.305297 TGTCGACTCCATGCCCTCT 60.305 57.895 17.92 0.00 0.00 3.69
750 751 1.944709 GCCACGTTACAACTCCAACTT 59.055 47.619 0.00 0.00 0.00 2.66
761 768 2.505557 CGACCGAGGCCACGTTAC 60.506 66.667 21.30 10.65 0.00 2.50
853 860 1.767681 TGCCAACAGCCCAGAATTTTT 59.232 42.857 0.00 0.00 42.71 1.94
854 861 1.345415 CTGCCAACAGCCCAGAATTTT 59.655 47.619 0.00 0.00 42.71 1.82
855 862 0.971386 CTGCCAACAGCCCAGAATTT 59.029 50.000 0.00 0.00 42.71 1.82
856 863 2.662309 CTGCCAACAGCCCAGAATT 58.338 52.632 0.00 0.00 42.71 2.17
857 864 4.428845 CTGCCAACAGCCCAGAAT 57.571 55.556 0.00 0.00 42.71 2.40
890 897 2.032620 CTCTACGGCCCAGACTGTAAT 58.967 52.381 0.00 0.00 31.14 1.89
956 963 1.305930 GCGTGCGGGAAGGAAAGATT 61.306 55.000 0.00 0.00 0.00 2.40
1045 1052 0.588252 CCACTCTGTTTTCTGCGTGG 59.412 55.000 0.00 0.00 43.97 4.94
1062 1069 2.571653 CAAAGGTACCACATCTCTCCCA 59.428 50.000 15.94 0.00 0.00 4.37
1468 1557 2.391389 CGGCAGCTTCCTTTCGTCC 61.391 63.158 0.00 0.00 0.00 4.79
1582 1671 3.310774 CAGCAACCTCGAATGGAATGTAG 59.689 47.826 0.00 0.00 0.00 2.74
1604 1693 1.866601 GAAAAATTGTGGCACAGTGGC 59.133 47.619 20.97 20.17 41.80 5.01
1605 1694 3.457610 AGAAAAATTGTGGCACAGTGG 57.542 42.857 20.97 0.00 41.80 4.00
1606 1695 4.037923 AGGTAGAAAAATTGTGGCACAGTG 59.962 41.667 20.97 0.00 41.80 3.66
1607 1696 4.215109 AGGTAGAAAAATTGTGGCACAGT 58.785 39.130 20.97 15.68 41.80 3.55
1608 1697 4.853924 AGGTAGAAAAATTGTGGCACAG 57.146 40.909 20.97 0.00 41.80 3.66
1609 1698 4.404073 ACAAGGTAGAAAAATTGTGGCACA 59.596 37.500 17.96 17.96 34.71 4.57
1610 1699 4.744631 CACAAGGTAGAAAAATTGTGGCAC 59.255 41.667 11.55 11.55 45.49 5.01
1670 1821 8.691661 AACAGCACCGATTATATAAAGGAAAT 57.308 30.769 20.63 7.99 0.00 2.17
1887 2044 0.452987 CACAATCCATCGCAGTTGGG 59.547 55.000 6.02 0.00 34.85 4.12
1890 2047 3.119388 CCATTTCACAATCCATCGCAGTT 60.119 43.478 0.00 0.00 0.00 3.16
2185 2342 3.198409 TGCAAGAAGCTTCTCTGAACA 57.802 42.857 28.58 18.23 45.94 3.18
2439 2953 4.024556 GCTGCGATAGTAATGCACTGAAAT 60.025 41.667 0.00 0.00 38.24 2.17
2451 2965 4.513442 ACAATTCCAAAGCTGCGATAGTA 58.487 39.130 0.00 0.00 39.35 1.82
2485 2999 7.430502 GCTGATACTTTTCTTCATTTCCAATCG 59.569 37.037 0.00 0.00 0.00 3.34
2517 3033 2.741517 GCATTAATTTGCGCAAAAGGGT 59.258 40.909 36.42 23.59 33.56 4.34
2527 3043 3.520569 ACATTCGGTGGCATTAATTTGC 58.479 40.909 0.00 0.00 42.01 3.68
2596 3134 6.316140 TCATACAAGCATTCAACTATGTGACC 59.684 38.462 0.00 0.00 0.00 4.02
2616 3732 3.686016 ACCAACCACATGAAGGTCATAC 58.314 45.455 13.55 0.00 38.76 2.39
2648 4224 7.718272 ACATTTCATGGTGAATTTGTTTCAG 57.282 32.000 0.00 0.00 44.89 3.02
2679 4255 9.956720 CATGAATTATTTTCTCATGGGACTAAC 57.043 33.333 0.00 0.00 41.73 2.34
2702 4278 8.798859 AGGAGTATTAAGCAAATATAGCCATG 57.201 34.615 0.00 0.00 32.70 3.66
2838 4438 7.357368 CCACAATGCAATGTTTTTATTTTTGCG 60.357 33.333 4.20 0.00 44.23 4.85
2839 4439 7.434602 ACCACAATGCAATGTTTTTATTTTTGC 59.565 29.630 4.20 0.00 42.23 3.68
2843 4443 8.987890 GTAGACCACAATGCAATGTTTTTATTT 58.012 29.630 4.20 0.00 0.00 1.40
2845 4445 7.665690 TGTAGACCACAATGCAATGTTTTTAT 58.334 30.769 4.20 0.00 32.95 1.40
2846 4446 7.043961 TGTAGACCACAATGCAATGTTTTTA 57.956 32.000 4.20 0.00 32.95 1.52
2903 4507 5.755409 TGCACAGAAGATAACCTCCTAAA 57.245 39.130 0.00 0.00 0.00 1.85
2924 4528 2.750237 GGGGTAGCGGGCAACTTG 60.750 66.667 0.00 0.00 0.00 3.16
2928 4532 4.041762 CCAAGGGGTAGCGGGCAA 62.042 66.667 0.00 0.00 0.00 4.52
2932 4536 0.393077 CTGTATCCAAGGGGTAGCGG 59.607 60.000 0.00 0.00 34.93 5.52
2933 4537 1.068741 GACTGTATCCAAGGGGTAGCG 59.931 57.143 0.00 0.00 34.93 4.26
2990 4598 1.735360 TGGTGACAAAAGCAGCAGC 59.265 52.632 0.00 0.00 38.67 5.25
3186 4795 0.900182 TTCTCGCTGCAAGGAGGAGA 60.900 55.000 12.32 0.00 38.04 3.71
3198 4807 1.376543 CAATCACCAGCATTCTCGCT 58.623 50.000 0.00 0.00 45.21 4.93
3243 4852 0.178767 CATCATCCTCCCGCAAGACA 59.821 55.000 0.00 0.00 43.02 3.41
3375 4984 1.654954 CGACCTCGTCTGTGTAGGGG 61.655 65.000 0.00 0.00 34.52 4.79
3435 5044 1.064463 TCCTCCATCCATTTCTGGTGC 60.064 52.381 0.00 0.00 43.61 5.01
3486 5095 2.203056 TTCCCATCATGCTCCGCG 60.203 61.111 0.00 0.00 0.00 6.46
3574 5184 8.871686 ACAGAAAAGATAACAAAATTGTCACC 57.128 30.769 0.00 0.00 41.31 4.02
3597 5213 0.250727 GCCACACAAGAGCCCTTACA 60.251 55.000 0.00 0.00 0.00 2.41
3726 5505 1.506718 GGAAACTAAAGCGGCAGCC 59.493 57.895 4.82 0.00 46.67 4.85
3728 5507 1.463674 ATGGGAAACTAAAGCGGCAG 58.536 50.000 1.45 0.00 0.00 4.85
3729 5508 1.917872 AATGGGAAACTAAAGCGGCA 58.082 45.000 1.45 0.00 0.00 5.69
3730 5509 3.313012 AAAATGGGAAACTAAAGCGGC 57.687 42.857 0.00 0.00 0.00 6.53
3757 5537 4.650131 GGGAGTATTAGAGTTGCCTGTAGT 59.350 45.833 0.00 0.00 0.00 2.73
3761 5541 3.041946 AGGGGAGTATTAGAGTTGCCTG 58.958 50.000 0.00 0.00 0.00 4.85
3762 5542 3.041946 CAGGGGAGTATTAGAGTTGCCT 58.958 50.000 0.00 0.00 0.00 4.75
3795 5575 8.800031 GTTCAATTTAAACTGCAAAAACGTCTA 58.200 29.630 0.00 0.00 0.00 2.59
3808 5588 5.458779 GCGTTCTTGCAGTTCAATTTAAACT 59.541 36.000 0.00 0.00 37.44 2.66
3809 5589 5.332280 GGCGTTCTTGCAGTTCAATTTAAAC 60.332 40.000 0.00 0.00 36.28 2.01
3810 5590 4.742659 GGCGTTCTTGCAGTTCAATTTAAA 59.257 37.500 0.00 0.00 36.28 1.52
3811 5591 4.037446 AGGCGTTCTTGCAGTTCAATTTAA 59.963 37.500 0.00 0.00 36.28 1.52
3812 5592 3.568007 AGGCGTTCTTGCAGTTCAATTTA 59.432 39.130 0.00 0.00 36.28 1.40
3813 5593 2.362077 AGGCGTTCTTGCAGTTCAATTT 59.638 40.909 0.00 0.00 36.28 1.82
3814 5594 1.956477 AGGCGTTCTTGCAGTTCAATT 59.044 42.857 0.00 0.00 36.28 2.32
3815 5595 1.609208 AGGCGTTCTTGCAGTTCAAT 58.391 45.000 0.00 0.00 36.28 2.57
3816 5596 1.388547 AAGGCGTTCTTGCAGTTCAA 58.611 45.000 0.00 0.00 36.28 2.69
3817 5597 2.248280 TAAGGCGTTCTTGCAGTTCA 57.752 45.000 0.00 0.00 36.93 3.18
3818 5598 5.485662 AATATAAGGCGTTCTTGCAGTTC 57.514 39.130 0.00 0.00 36.93 3.01
3821 5601 5.523916 ACACTAATATAAGGCGTTCTTGCAG 59.476 40.000 0.00 0.00 36.93 4.41
3824 5604 7.169308 CCTGTACACTAATATAAGGCGTTCTTG 59.831 40.741 0.00 0.00 36.93 3.02
3825 5605 7.208080 CCTGTACACTAATATAAGGCGTTCTT 58.792 38.462 0.00 0.00 39.40 2.52
3826 5606 6.239232 CCCTGTACACTAATATAAGGCGTTCT 60.239 42.308 0.00 0.00 0.00 3.01
3827 5607 5.924825 CCCTGTACACTAATATAAGGCGTTC 59.075 44.000 0.00 0.00 0.00 3.95
3828 5608 5.221581 CCCCTGTACACTAATATAAGGCGTT 60.222 44.000 0.00 0.00 0.00 4.84
3829 5609 4.282703 CCCCTGTACACTAATATAAGGCGT 59.717 45.833 0.00 0.00 0.00 5.68
3830 5610 4.282703 ACCCCTGTACACTAATATAAGGCG 59.717 45.833 0.00 0.00 0.00 5.52
3831 5611 5.820404 ACCCCTGTACACTAATATAAGGC 57.180 43.478 0.00 0.00 0.00 4.35
3832 5612 9.018582 GTACTACCCCTGTACACTAATATAAGG 57.981 40.741 0.00 0.00 39.79 2.69
3850 5630 6.063496 AGATTTTCTTGGGAAGTACTACCC 57.937 41.667 12.56 9.29 45.74 3.69
3859 5639 5.959512 TGGGAGTAAAGATTTTCTTGGGAA 58.040 37.500 0.00 0.00 36.71 3.97
3871 5651 5.701224 ACATTGGTTTTCTGGGAGTAAAGA 58.299 37.500 0.00 0.00 0.00 2.52
3897 5677 9.878667 TCGGAGTGATTCACTGTATAAAATTAA 57.121 29.630 23.57 0.00 45.44 1.40
3898 5678 9.309516 GTCGGAGTGATTCACTGTATAAAATTA 57.690 33.333 23.57 0.00 45.44 1.40
3900 5680 6.761714 GGTCGGAGTGATTCACTGTATAAAAT 59.238 38.462 23.57 0.00 45.44 1.82
3903 5683 4.707934 TGGTCGGAGTGATTCACTGTATAA 59.292 41.667 23.57 2.77 45.44 0.98
3904 5684 4.274978 TGGTCGGAGTGATTCACTGTATA 58.725 43.478 23.57 4.12 45.44 1.47
3905 5685 3.096852 TGGTCGGAGTGATTCACTGTAT 58.903 45.455 23.57 0.00 45.44 2.29
3906 5686 2.521126 TGGTCGGAGTGATTCACTGTA 58.479 47.619 23.57 6.19 45.44 2.74
3907 5687 1.338107 TGGTCGGAGTGATTCACTGT 58.662 50.000 23.57 0.77 45.44 3.55
3908 5688 2.455674 TTGGTCGGAGTGATTCACTG 57.544 50.000 23.57 10.55 45.44 3.66
3910 5690 2.093447 AGGATTGGTCGGAGTGATTCAC 60.093 50.000 8.82 8.82 34.10 3.18
3911 5691 2.187958 AGGATTGGTCGGAGTGATTCA 58.812 47.619 0.00 0.00 0.00 2.57
3912 5692 2.990066 AGGATTGGTCGGAGTGATTC 57.010 50.000 0.00 0.00 0.00 2.52
3913 5693 4.837093 TTAAGGATTGGTCGGAGTGATT 57.163 40.909 0.00 0.00 0.00 2.57
3914 5694 5.221661 GGTATTAAGGATTGGTCGGAGTGAT 60.222 44.000 0.00 0.00 0.00 3.06
3915 5695 4.100498 GGTATTAAGGATTGGTCGGAGTGA 59.900 45.833 0.00 0.00 0.00 3.41
3921 5701 4.141574 TGAAGGGGTATTAAGGATTGGTCG 60.142 45.833 0.00 0.00 0.00 4.79
3922 5702 5.382664 TGAAGGGGTATTAAGGATTGGTC 57.617 43.478 0.00 0.00 0.00 4.02
3926 5706 6.067901 TGGGATTTGAAGGGGTATTAAGGATT 60.068 38.462 0.00 0.00 0.00 3.01
3931 5711 7.873699 TTTTTGGGATTTGAAGGGGTATTAA 57.126 32.000 0.00 0.00 0.00 1.40
3932 5712 8.325046 CAATTTTTGGGATTTGAAGGGGTATTA 58.675 33.333 0.00 0.00 0.00 0.98
3943 5726 5.533482 TGTACCGACAATTTTTGGGATTTG 58.467 37.500 2.91 0.00 30.68 2.32
3988 5786 5.182001 CAGGCAAGCACTTAACTAGTTGAAT 59.818 40.000 18.56 0.00 33.85 2.57
4009 5807 0.676466 TATGCCTCCGTTGCAACAGG 60.676 55.000 28.01 26.23 42.92 4.00
4010 5808 0.447801 GTATGCCTCCGTTGCAACAG 59.552 55.000 28.01 18.12 42.92 3.16
4021 5819 6.291377 TGAACCATCAGAATAAGTATGCCTC 58.709 40.000 0.00 0.00 0.00 4.70
4067 5865 3.695830 TGAGGAAAGTAGCCGAATGTT 57.304 42.857 0.00 0.00 0.00 2.71
4070 5868 4.487714 TGATTGAGGAAAGTAGCCGAAT 57.512 40.909 0.00 0.00 0.00 3.34
4071 5869 3.973206 TGATTGAGGAAAGTAGCCGAA 57.027 42.857 0.00 0.00 0.00 4.30
4072 5870 3.973206 TTGATTGAGGAAAGTAGCCGA 57.027 42.857 0.00 0.00 0.00 5.54
4074 5872 6.442112 GCATAATTGATTGAGGAAAGTAGCC 58.558 40.000 0.00 0.00 0.00 3.93
4075 5873 6.017934 TCGCATAATTGATTGAGGAAAGTAGC 60.018 38.462 0.00 0.00 0.00 3.58
4077 5875 7.047891 AGTCGCATAATTGATTGAGGAAAGTA 58.952 34.615 0.00 0.00 0.00 2.24
4080 5878 5.296780 GGAGTCGCATAATTGATTGAGGAAA 59.703 40.000 0.00 0.00 0.00 3.13
4081 5879 4.816385 GGAGTCGCATAATTGATTGAGGAA 59.184 41.667 0.00 0.00 0.00 3.36
4082 5880 4.380531 GGAGTCGCATAATTGATTGAGGA 58.619 43.478 0.00 0.00 0.00 3.71
4099 8490 2.856988 TGTTGGGGTGGGGGAGTC 60.857 66.667 0.00 0.00 0.00 3.36
4100 8491 3.182996 GTGTTGGGGTGGGGGAGT 61.183 66.667 0.00 0.00 0.00 3.85
4102 8493 3.503839 GTGTGTTGGGGTGGGGGA 61.504 66.667 0.00 0.00 0.00 4.81
4105 8496 1.380515 TTGTGTGTGTTGGGGTGGG 60.381 57.895 0.00 0.00 0.00 4.61
4107 8498 1.181786 AACTTGTGTGTGTTGGGGTG 58.818 50.000 0.00 0.00 0.00 4.61
4108 8499 1.931635 AAACTTGTGTGTGTTGGGGT 58.068 45.000 0.00 0.00 0.00 4.95
4109 8500 5.048991 GTCTATAAACTTGTGTGTGTTGGGG 60.049 44.000 0.00 0.00 0.00 4.96
4110 8501 5.529430 TGTCTATAAACTTGTGTGTGTTGGG 59.471 40.000 0.00 0.00 0.00 4.12
4156 9198 8.601047 TGGTATTTCCAATGGTATTGATTTGA 57.399 30.769 0.00 0.00 44.12 2.69
4183 9225 9.891828 GCGTTTTATAATAACATGATGAATCCA 57.108 29.630 0.00 0.00 0.00 3.41
4188 9230 9.715123 CTGTTGCGTTTTATAATAACATGATGA 57.285 29.630 0.00 0.00 0.00 2.92
4189 9231 9.715123 TCTGTTGCGTTTTATAATAACATGATG 57.285 29.630 0.00 0.00 0.00 3.07
4192 9234 7.965655 TGGTCTGTTGCGTTTTATAATAACATG 59.034 33.333 0.00 0.00 0.00 3.21
4193 9235 8.046294 TGGTCTGTTGCGTTTTATAATAACAT 57.954 30.769 0.00 0.00 0.00 2.71
4207 9265 3.357079 GTGGGCTGGTCTGTTGCG 61.357 66.667 0.00 0.00 0.00 4.85
4248 9306 9.507329 TGGTTATCATAATCTTGGAGCTAATTC 57.493 33.333 0.00 0.00 0.00 2.17
4258 9316 9.459640 CAATTCTTGCTGGTTATCATAATCTTG 57.540 33.333 0.00 0.00 0.00 3.02
4274 9333 9.399797 TGATATTTGAGTATGTCAATTCTTGCT 57.600 29.630 0.00 0.00 44.89 3.91
4284 9343 7.954788 GGAGACCTTGATATTTGAGTATGTC 57.045 40.000 0.00 0.00 0.00 3.06
4403 9464 6.434028 TGTTTCGAGAAGGAATTGGATCAATT 59.566 34.615 5.67 5.67 45.25 2.32
4423 9484 9.474920 TGATATGGTTGAATTGACTTTTGTTTC 57.525 29.630 0.00 0.00 0.00 2.78
4427 9488 9.778993 CTAGTGATATGGTTGAATTGACTTTTG 57.221 33.333 0.00 0.00 0.00 2.44
4442 9503 5.674525 TCTTGCTGGTTTCTAGTGATATGG 58.325 41.667 0.00 0.00 0.00 2.74
4448 9509 3.409026 ACCTCTTGCTGGTTTCTAGTG 57.591 47.619 0.00 0.00 33.34 2.74
4493 9554 7.857734 TTGTGTAGTGAGAGATTTTGTTTGA 57.142 32.000 0.00 0.00 0.00 2.69
4522 9583 5.637387 GTGTTCAGAGATTGAGAGAAGTTCC 59.363 44.000 0.00 0.00 37.07 3.62
4590 9651 4.304939 GTCTGTACAAGGCGAAGTTAGTT 58.695 43.478 0.00 0.00 0.00 2.24
4592 9653 3.251571 GGTCTGTACAAGGCGAAGTTAG 58.748 50.000 0.00 0.00 0.00 2.34
4593 9654 2.028748 GGGTCTGTACAAGGCGAAGTTA 60.029 50.000 0.00 0.00 0.00 2.24
4594 9655 1.270678 GGGTCTGTACAAGGCGAAGTT 60.271 52.381 0.00 0.00 0.00 2.66
4595 9656 0.320697 GGGTCTGTACAAGGCGAAGT 59.679 55.000 0.00 0.00 0.00 3.01
4597 9658 0.981183 ATGGGTCTGTACAAGGCGAA 59.019 50.000 0.00 0.00 0.00 4.70
4598 9659 1.479323 GTATGGGTCTGTACAAGGCGA 59.521 52.381 0.00 0.00 0.00 5.54
4599 9660 1.206132 TGTATGGGTCTGTACAAGGCG 59.794 52.381 0.00 0.00 0.00 5.52
4600 9661 3.560636 ATGTATGGGTCTGTACAAGGC 57.439 47.619 0.00 0.00 34.77 4.35
4601 9662 4.640201 CCAAATGTATGGGTCTGTACAAGG 59.360 45.833 0.00 0.00 36.79 3.61
4602 9663 5.818136 CCAAATGTATGGGTCTGTACAAG 57.182 43.478 0.00 0.00 36.79 3.16
4613 9674 3.206150 CTTCGTCCTCCCAAATGTATGG 58.794 50.000 0.00 0.00 40.35 2.74
4614 9675 3.206150 CCTTCGTCCTCCCAAATGTATG 58.794 50.000 0.00 0.00 0.00 2.39
4615 9676 2.421529 GCCTTCGTCCTCCCAAATGTAT 60.422 50.000 0.00 0.00 0.00 2.29
4616 9677 1.065709 GCCTTCGTCCTCCCAAATGTA 60.066 52.381 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.