Multiple sequence alignment - TraesCS3B01G121000

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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 TraesCS3B01G121000 chr3B 100.000 4311 0 0 1 4311 91430362 91426052 0.000000e+00 7962.0
1 TraesCS3B01G121000 chr3B 89.286 84 6 3 3772 3854 740052715 740052796 7.630000e-18 102.0
2 TraesCS3B01G121000 chr3D 93.692 2473 121 27 1331 3797 58113454 58111011 0.000000e+00 3670.0
3 TraesCS3B01G121000 chr3D 91.846 1300 64 15 1 1279 58114748 58113470 0.000000e+00 1775.0
4 TraesCS3B01G121000 chr3D 94.643 336 18 0 3967 4302 58111008 58110673 4.940000e-144 521.0
5 TraesCS3B01G121000 chr3D 95.798 119 4 1 3854 3972 536894846 536894963 1.580000e-44 191.0
6 TraesCS3B01G121000 chr3D 93.496 123 6 2 3854 3975 283321137 283321258 9.520000e-42 182.0
7 TraesCS3B01G121000 chr3A 91.715 1376 73 18 1 1355 67152710 67151355 0.000000e+00 1871.0
8 TraesCS3B01G121000 chr3A 95.042 1190 55 4 2524 3709 67150121 67148932 0.000000e+00 1868.0
9 TraesCS3B01G121000 chr3A 92.851 1091 56 14 1444 2525 67151321 67150244 0.000000e+00 1563.0
10 TraesCS3B01G121000 chr3A 97.297 37 1 0 3967 4003 67125635 67125599 3.600000e-06 63.9
11 TraesCS3B01G121000 chrUn 88.764 178 17 3 3794 3969 128516228 128516404 9.390000e-52 215.0
12 TraesCS3B01G121000 chr7B 87.500 176 19 2 3794 3969 392820019 392819847 2.630000e-47 200.0
13 TraesCS3B01G121000 chr7B 95.690 116 4 1 3854 3969 678632472 678632358 7.360000e-43 185.0
14 TraesCS3B01G121000 chr7B 87.500 96 7 3 3792 3887 593417957 593418047 5.900000e-19 106.0
15 TraesCS3B01G121000 chr1A 86.517 178 16 7 3794 3969 276575262 276575091 5.690000e-44 189.0
16 TraesCS3B01G121000 chr1A 85.000 80 9 2 4151 4228 53444421 53444343 1.290000e-10 78.7
17 TraesCS3B01G121000 chr5D 94.958 119 5 1 3854 3972 361648056 361647939 7.360000e-43 185.0
18 TraesCS3B01G121000 chr5D 97.059 68 2 0 3787 3854 480703723 480703656 9.800000e-22 115.0
19 TraesCS3B01G121000 chr2D 95.690 116 4 1 3854 3969 591951794 591951908 7.360000e-43 185.0
20 TraesCS3B01G121000 chr2D 91.089 101 4 2 3794 3894 189528069 189527974 9.730000e-27 132.0
21 TraesCS3B01G121000 chr4D 94.167 120 6 1 3854 3973 108872407 108872525 9.520000e-42 182.0
22 TraesCS3B01G121000 chr4D 83.740 123 19 1 3969 4090 455620394 455620516 9.800000e-22 115.0
23 TraesCS3B01G121000 chr5B 92.742 124 7 2 3854 3976 125257088 125256966 1.230000e-40 178.0
24 TraesCS3B01G121000 chr1B 82.584 178 18 8 3794 3969 14866946 14866780 1.250000e-30 145.0
25 TraesCS3B01G121000 chr2B 89.583 96 6 2 3794 3889 101490639 101490548 7.570000e-23 119.0
26 TraesCS3B01G121000 chr4B 94.521 73 3 1 3781 3853 625981897 625981826 1.270000e-20 111.0


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 TraesCS3B01G121000 chr3B 91426052 91430362 4310 True 7962.000000 7962 100.000000 1 4311 1 chr3B.!!$R1 4310
1 TraesCS3B01G121000 chr3D 58110673 58114748 4075 True 1988.666667 3670 93.393667 1 4302 3 chr3D.!!$R1 4301
2 TraesCS3B01G121000 chr3A 67148932 67152710 3778 True 1767.333333 1871 93.202667 1 3709 3 chr3A.!!$R2 3708

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
792 803 0.101579 GGGTAGAGTGCTCGAGCTTC 59.898 60.0 35.27 29.64 42.66 3.86 F
813 824 0.468648 GCCCTGGTAGGCGTATTTCT 59.531 55.0 0.00 0.00 44.57 2.52 F
1619 1661 0.603707 CTGCGCCAGAGGTGAAGAAA 60.604 55.0 4.18 0.00 41.22 2.52 F
2225 2273 0.451792 CTGAAGAGCGCTCGTTTTGC 60.452 55.0 30.39 16.18 34.09 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 1849 0.171455 GTCTCAGCGTCGTCAGGAAT 59.829 55.000 0.0 0.0 0.0 3.01 R
2215 2263 0.249031 AACAGGCAAGCAAAACGAGC 60.249 50.000 0.0 0.0 0.0 5.03 R
2818 2992 1.256376 GATGCTCGATTGTACACTGCG 59.744 52.381 0.0 0.0 0.0 5.18 R
3957 4134 0.175989 GTTGCTCTTACTCCCCTCCG 59.824 60.000 0.0 0.0 0.0 4.63 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
41 42 3.512033 ACAGAGATGCTAACGAGAACC 57.488 47.619 0.00 0.00 0.00 3.62
101 102 2.159254 TGAAAGCCTGAAACACAACAGC 60.159 45.455 0.00 0.00 33.40 4.40
134 139 3.422796 AGAGAAGGAGCTACGAAGAACA 58.577 45.455 0.00 0.00 0.00 3.18
154 159 0.334676 CCATGGCCTAACCTGGGAAA 59.665 55.000 3.32 0.00 40.22 3.13
456 461 2.973710 ACCAGGATTACTAGGGCTACC 58.026 52.381 0.00 0.00 0.00 3.18
463 468 3.951563 TTACTAGGGCTACCGTTAGGA 57.048 47.619 0.00 0.00 43.47 2.94
519 524 2.042843 CGGTAGGAGCTGGGGTCT 60.043 66.667 0.00 0.00 0.00 3.85
642 649 4.151582 GGGGGTTCGATTCGGCGA 62.152 66.667 4.99 4.99 38.72 5.54
643 650 2.585247 GGGGTTCGATTCGGCGAG 60.585 66.667 10.46 0.00 41.79 5.03
644 651 3.262686 GGGTTCGATTCGGCGAGC 61.263 66.667 10.46 5.69 41.79 5.03
645 652 3.617538 GGTTCGATTCGGCGAGCG 61.618 66.667 22.48 22.48 41.53 5.03
646 653 2.578713 GTTCGATTCGGCGAGCGA 60.579 61.111 25.56 25.56 41.79 4.93
647 654 2.277949 TTCGATTCGGCGAGCGAG 60.278 61.111 26.90 14.53 41.79 5.03
648 655 3.751401 TTCGATTCGGCGAGCGAGG 62.751 63.158 26.90 11.52 41.79 4.63
649 656 4.554363 CGATTCGGCGAGCGAGGT 62.554 66.667 23.60 3.09 0.00 3.85
650 657 2.202756 GATTCGGCGAGCGAGGTT 60.203 61.111 10.46 0.00 0.00 3.50
651 658 1.810030 GATTCGGCGAGCGAGGTTT 60.810 57.895 10.46 0.00 0.00 3.27
652 659 1.753468 GATTCGGCGAGCGAGGTTTC 61.753 60.000 10.46 0.00 0.00 2.78
653 660 2.227089 ATTCGGCGAGCGAGGTTTCT 62.227 55.000 10.46 0.00 0.00 2.52
669 676 2.937149 GTTTCTGGCCGAGGAATTCTAC 59.063 50.000 5.23 0.00 0.00 2.59
687 694 4.641396 TCTACAAGAAGCAAGCAAAGCTA 58.359 39.130 0.00 0.00 42.53 3.32
731 741 3.125146 CGATTCGAATTGGAAGTGAAGCA 59.875 43.478 16.45 0.00 0.00 3.91
781 792 2.355986 TGCGGCATTCGGGTAGAGT 61.356 57.895 0.00 0.00 39.69 3.24
782 793 1.883084 GCGGCATTCGGGTAGAGTG 60.883 63.158 0.00 0.00 39.31 3.51
789 800 1.654954 TTCGGGTAGAGTGCTCGAGC 61.655 60.000 30.42 30.42 42.50 5.03
792 803 0.101579 GGGTAGAGTGCTCGAGCTTC 59.898 60.000 35.27 29.64 42.66 3.86
794 805 1.202245 GGTAGAGTGCTCGAGCTTCTG 60.202 57.143 34.87 8.63 42.66 3.02
799 810 2.511145 GCTCGAGCTTCTGCCCTG 60.511 66.667 29.88 0.00 40.80 4.45
813 824 0.468648 GCCCTGGTAGGCGTATTTCT 59.531 55.000 0.00 0.00 44.57 2.52
816 827 2.224066 CCCTGGTAGGCGTATTTCTCAG 60.224 54.545 0.00 0.00 32.73 3.35
817 828 2.224066 CCTGGTAGGCGTATTTCTCAGG 60.224 54.545 0.00 0.00 35.27 3.86
823 834 5.221382 GGTAGGCGTATTTCTCAGGAATACA 60.221 44.000 15.11 0.00 0.00 2.29
832 843 2.496070 TCTCAGGAATACACAACCCGAG 59.504 50.000 0.00 0.00 0.00 4.63
847 858 3.999046 ACCCGAGTTATGAAACGTCTTT 58.001 40.909 0.00 0.00 40.73 2.52
860 871 3.928727 ACGTCTTTCCATGTCTAACGA 57.071 42.857 10.53 0.00 33.25 3.85
862 873 4.817517 ACGTCTTTCCATGTCTAACGAAT 58.182 39.130 10.53 0.00 33.25 3.34
881 892 0.878416 TGCGTAAACTGGCAATGACC 59.122 50.000 0.00 0.00 35.98 4.02
984 1004 3.120385 TCGACGGCGCGAGAGTTA 61.120 61.111 12.10 0.00 35.01 2.24
986 1006 1.585521 CGACGGCGCGAGAGTTATT 60.586 57.895 12.10 0.00 0.00 1.40
987 1007 1.798368 CGACGGCGCGAGAGTTATTG 61.798 60.000 12.10 0.00 0.00 1.90
989 1009 2.871427 CGGCGCGAGAGTTATTGCC 61.871 63.158 12.10 0.00 39.10 4.52
990 1010 1.521681 GGCGCGAGAGTTATTGCCT 60.522 57.895 12.10 0.00 39.38 4.75
991 1011 1.638467 GCGCGAGAGTTATTGCCTG 59.362 57.895 12.10 0.00 0.00 4.85
994 1017 1.766143 GCGAGAGTTATTGCCTGCGG 61.766 60.000 0.00 0.00 0.00 5.69
1118 1147 2.282180 GCCCAAGCCGTCAAAGGA 60.282 61.111 0.00 0.00 0.00 3.36
1122 1151 1.028905 CCAAGCCGTCAAAGGACAAA 58.971 50.000 0.00 0.00 44.54 2.83
1131 1160 1.118838 CAAAGGACAAACCCAAGCCA 58.881 50.000 0.00 0.00 40.05 4.75
1285 1314 2.007608 GCCATTTCCTCCACGTTCTAC 58.992 52.381 0.00 0.00 0.00 2.59
1286 1315 2.629051 CCATTTCCTCCACGTTCTACC 58.371 52.381 0.00 0.00 0.00 3.18
1386 1421 7.599998 ACTTTAAAAGCAAGTGCAATAGAATGG 59.400 33.333 6.00 0.00 45.16 3.16
1480 1522 4.149598 TGCTCTAGTGTTCAGTGTTAGGA 58.850 43.478 0.00 0.00 0.00 2.94
1517 1559 8.376270 ACTACACTATTTAGGCAGAGAAGTTTT 58.624 33.333 0.00 0.00 0.00 2.43
1547 1589 5.738909 TGTCAATTGATTGTTGGTTGGTTT 58.261 33.333 12.12 0.00 38.84 3.27
1619 1661 0.603707 CTGCGCCAGAGGTGAAGAAA 60.604 55.000 4.18 0.00 41.22 2.52
1684 1726 5.698545 GGGACTGCATATATGAAGTGAGAAC 59.301 44.000 27.98 14.33 46.59 3.01
1724 1766 6.312399 TGGTCTTTATGCACTTTACAGTTG 57.688 37.500 0.00 0.00 0.00 3.16
1870 1916 2.301346 AGCTTGTTTGTTGTGAGAGGG 58.699 47.619 0.00 0.00 0.00 4.30
2026 2072 6.344500 TCTTTATCCTCTGATCAAACAGCTC 58.656 40.000 0.00 0.00 37.75 4.09
2047 2093 5.277250 GCTCACATAGACTAAATGCTTCAGC 60.277 44.000 0.00 0.00 42.50 4.26
2124 2172 8.797350 TCCATTGTATCATAGCCTTCATATTG 57.203 34.615 0.00 0.00 0.00 1.90
2165 2213 8.738645 ATCAATAGGTTTTGTCTCCTAATGTC 57.261 34.615 0.00 0.00 39.36 3.06
2186 2234 9.691362 AATGTCGTTTCAATTACTGCTATTTTT 57.309 25.926 0.00 0.00 0.00 1.94
2215 2263 5.845985 TGTAGTTCAATTTCTGAAGAGCG 57.154 39.130 0.00 0.00 44.83 5.03
2225 2273 0.451792 CTGAAGAGCGCTCGTTTTGC 60.452 55.000 30.39 16.18 34.09 3.68
2232 2280 1.727022 CGCTCGTTTTGCTTGCCTG 60.727 57.895 0.00 0.00 0.00 4.85
2303 2351 2.358582 TGCCAGGCATATTTTCACATCG 59.641 45.455 11.22 0.00 31.71 3.84
2412 2461 5.880901 AGTTAATCTGCCTTTCTTCTTCCA 58.119 37.500 0.00 0.00 0.00 3.53
2415 2464 1.774254 TCTGCCTTTCTTCTTCCACCA 59.226 47.619 0.00 0.00 0.00 4.17
2480 2530 1.808945 AGCTTTCTTGCATGTTCTCGG 59.191 47.619 0.00 0.00 34.99 4.63
2482 2532 2.226437 GCTTTCTTGCATGTTCTCGGAA 59.774 45.455 0.00 0.00 0.00 4.30
2604 2778 4.920340 GCATCAGTATTCAGGACGTATGAG 59.080 45.833 3.45 0.00 0.00 2.90
2818 2992 1.886542 ACAAGAAAACGGGCAGGAATC 59.113 47.619 0.00 0.00 0.00 2.52
2867 3041 5.811399 TGAAACACTGGTTTGTTCTACAG 57.189 39.130 0.00 0.00 46.84 2.74
2871 3045 5.228945 ACACTGGTTTGTTCTACAGCTAT 57.771 39.130 0.00 0.00 34.40 2.97
2933 3107 9.695526 TCACATTTTAAAAATTGTGGATCTCTG 57.304 29.630 24.27 9.96 44.31 3.35
2943 3117 8.503458 AAATTGTGGATCTCTGTCTTCTATTG 57.497 34.615 0.00 0.00 0.00 1.90
3212 3387 7.141758 ACATCCTTTATTTATGCTCCTCTGA 57.858 36.000 0.00 0.00 0.00 3.27
3219 3394 2.381752 TATGCTCCTCTGATTCCGGA 57.618 50.000 0.00 0.00 0.00 5.14
3237 3412 3.875134 CCGGATTTTAATCTACGGCTGTT 59.125 43.478 1.99 0.00 34.88 3.16
3356 3531 3.485463 ACCGGAGTTTCTTTGATGACA 57.515 42.857 9.46 0.00 0.00 3.58
3357 3532 3.403038 ACCGGAGTTTCTTTGATGACAG 58.597 45.455 9.46 0.00 0.00 3.51
3380 3555 1.009078 GACTGATACAAGCATGCGCA 58.991 50.000 14.96 14.96 42.27 6.09
3419 3595 8.588789 CGTGTTCCAAAAGTTAAACTTAAAAGG 58.411 33.333 0.00 0.00 37.47 3.11
3498 3674 1.613925 GATCGTGCATACTAGAGGCCA 59.386 52.381 5.01 0.00 32.41 5.36
3561 3738 4.021632 TCGAGGTCATGATGATTCTGATCC 60.022 45.833 0.00 0.00 0.00 3.36
3611 3788 3.255642 GCACAATTGAGACCCAAGCTTTA 59.744 43.478 13.59 0.00 38.31 1.85
3634 3811 3.007506 TGTGGATTCCGTGTAAGATGTGT 59.992 43.478 0.00 0.00 0.00 3.72
3797 3974 2.034812 CCGGATTGCCTAGTGACTACTC 59.965 54.545 0.00 0.00 38.36 2.59
3798 3975 2.034812 CGGATTGCCTAGTGACTACTCC 59.965 54.545 0.00 0.00 38.36 3.85
3799 3976 2.365941 GGATTGCCTAGTGACTACTCCC 59.634 54.545 0.00 0.00 38.36 4.30
3800 3977 2.921834 TTGCCTAGTGACTACTCCCT 57.078 50.000 0.00 0.00 38.36 4.20
3801 3978 2.438800 TGCCTAGTGACTACTCCCTC 57.561 55.000 0.00 0.00 38.36 4.30
3802 3979 1.063867 TGCCTAGTGACTACTCCCTCC 60.064 57.143 0.00 0.00 38.36 4.30
3803 3980 1.970092 CCTAGTGACTACTCCCTCCG 58.030 60.000 0.00 0.00 38.36 4.63
3804 3981 1.212441 CCTAGTGACTACTCCCTCCGT 59.788 57.143 0.00 0.00 38.36 4.69
3805 3982 2.356947 CCTAGTGACTACTCCCTCCGTT 60.357 54.545 0.00 0.00 38.36 4.44
3806 3983 1.836802 AGTGACTACTCCCTCCGTTC 58.163 55.000 0.00 0.00 28.79 3.95
3807 3984 0.816373 GTGACTACTCCCTCCGTTCC 59.184 60.000 0.00 0.00 0.00 3.62
3808 3985 0.406750 TGACTACTCCCTCCGTTCCA 59.593 55.000 0.00 0.00 0.00 3.53
3809 3986 1.203087 TGACTACTCCCTCCGTTCCAA 60.203 52.381 0.00 0.00 0.00 3.53
3810 3987 1.897802 GACTACTCCCTCCGTTCCAAA 59.102 52.381 0.00 0.00 0.00 3.28
3811 3988 2.301009 GACTACTCCCTCCGTTCCAAAA 59.699 50.000 0.00 0.00 0.00 2.44
3812 3989 2.910977 ACTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
3813 3990 2.971901 ACTCCCTCCGTTCCAAAATT 57.028 45.000 0.00 0.00 0.00 1.82
3814 3991 2.791655 ACTCCCTCCGTTCCAAAATTC 58.208 47.619 0.00 0.00 0.00 2.17
3815 3992 2.375509 ACTCCCTCCGTTCCAAAATTCT 59.624 45.455 0.00 0.00 0.00 2.40
3816 3993 3.181433 ACTCCCTCCGTTCCAAAATTCTT 60.181 43.478 0.00 0.00 0.00 2.52
3817 3994 3.153919 TCCCTCCGTTCCAAAATTCTTG 58.846 45.455 0.00 0.00 0.00 3.02
3818 3995 2.890945 CCCTCCGTTCCAAAATTCTTGT 59.109 45.455 0.00 0.00 0.00 3.16
3819 3996 3.057526 CCCTCCGTTCCAAAATTCTTGTC 60.058 47.826 0.00 0.00 0.00 3.18
3820 3997 3.821033 CCTCCGTTCCAAAATTCTTGTCT 59.179 43.478 0.00 0.00 0.00 3.41
3821 3998 4.278419 CCTCCGTTCCAAAATTCTTGTCTT 59.722 41.667 0.00 0.00 0.00 3.01
3822 3999 5.472137 CCTCCGTTCCAAAATTCTTGTCTTA 59.528 40.000 0.00 0.00 0.00 2.10
3823 4000 6.348540 CCTCCGTTCCAAAATTCTTGTCTTAG 60.349 42.308 0.00 0.00 0.00 2.18
3824 4001 6.292923 TCCGTTCCAAAATTCTTGTCTTAGA 58.707 36.000 0.00 0.00 0.00 2.10
3825 4002 6.940298 TCCGTTCCAAAATTCTTGTCTTAGAT 59.060 34.615 0.00 0.00 0.00 1.98
3826 4003 7.447238 TCCGTTCCAAAATTCTTGTCTTAGATT 59.553 33.333 0.00 0.00 0.00 2.40
3827 4004 8.082242 CCGTTCCAAAATTCTTGTCTTAGATTT 58.918 33.333 0.00 0.00 0.00 2.17
3828 4005 8.905702 CGTTCCAAAATTCTTGTCTTAGATTTG 58.094 33.333 0.00 0.00 29.84 2.32
3829 4006 9.750125 GTTCCAAAATTCTTGTCTTAGATTTGT 57.250 29.630 0.00 0.00 28.79 2.83
3830 4007 9.965824 TTCCAAAATTCTTGTCTTAGATTTGTC 57.034 29.630 0.00 0.00 28.79 3.18
3831 4008 9.354673 TCCAAAATTCTTGTCTTAGATTTGTCT 57.645 29.630 0.00 0.00 28.79 3.41
3839 4016 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
3840 4017 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
3842 4019 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
3843 4020 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
3850 4027 9.832445 ATTTGTCTAAATACGGATGTATCAAGT 57.168 29.630 0.00 0.00 40.42 3.16
3851 4028 8.867112 TTGTCTAAATACGGATGTATCAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
3852 4029 8.002984 TGTCTAAATACGGATGTATCAAGTCA 57.997 34.615 0.00 0.00 40.42 3.41
3853 4030 7.919091 TGTCTAAATACGGATGTATCAAGTCAC 59.081 37.037 0.00 0.00 40.42 3.67
3854 4031 7.381678 GTCTAAATACGGATGTATCAAGTCACC 59.618 40.741 0.00 0.00 40.42 4.02
3855 4032 2.981859 ACGGATGTATCAAGTCACCC 57.018 50.000 0.00 0.00 0.00 4.61
3856 4033 2.184533 ACGGATGTATCAAGTCACCCA 58.815 47.619 0.00 0.00 0.00 4.51
3857 4034 2.569853 ACGGATGTATCAAGTCACCCAA 59.430 45.455 0.00 0.00 0.00 4.12
3858 4035 3.008594 ACGGATGTATCAAGTCACCCAAA 59.991 43.478 0.00 0.00 0.00 3.28
3859 4036 4.006989 CGGATGTATCAAGTCACCCAAAA 58.993 43.478 0.00 0.00 0.00 2.44
3860 4037 4.640201 CGGATGTATCAAGTCACCCAAAAT 59.360 41.667 0.00 0.00 0.00 1.82
3861 4038 5.125417 CGGATGTATCAAGTCACCCAAAATT 59.875 40.000 0.00 0.00 0.00 1.82
3862 4039 6.564328 GGATGTATCAAGTCACCCAAAATTC 58.436 40.000 0.00 0.00 0.00 2.17
3863 4040 6.378280 GGATGTATCAAGTCACCCAAAATTCT 59.622 38.462 0.00 0.00 0.00 2.40
3864 4041 7.093771 GGATGTATCAAGTCACCCAAAATTCTT 60.094 37.037 0.00 0.00 0.00 2.52
3865 4042 6.980593 TGTATCAAGTCACCCAAAATTCTTG 58.019 36.000 0.00 0.00 35.21 3.02
3866 4043 6.549364 TGTATCAAGTCACCCAAAATTCTTGT 59.451 34.615 0.00 0.00 35.35 3.16
3867 4044 5.514274 TCAAGTCACCCAAAATTCTTGTC 57.486 39.130 0.00 0.00 35.35 3.18
3868 4045 5.200483 TCAAGTCACCCAAAATTCTTGTCT 58.800 37.500 0.00 0.00 35.35 3.41
3869 4046 5.656416 TCAAGTCACCCAAAATTCTTGTCTT 59.344 36.000 0.00 0.00 35.35 3.01
3870 4047 6.831353 TCAAGTCACCCAAAATTCTTGTCTTA 59.169 34.615 0.00 0.00 35.35 2.10
3871 4048 6.884280 AGTCACCCAAAATTCTTGTCTTAG 57.116 37.500 0.00 0.00 0.00 2.18
3872 4049 6.601332 AGTCACCCAAAATTCTTGTCTTAGA 58.399 36.000 0.00 0.00 0.00 2.10
3873 4050 7.234355 AGTCACCCAAAATTCTTGTCTTAGAT 58.766 34.615 0.00 0.00 0.00 1.98
3874 4051 7.725844 AGTCACCCAAAATTCTTGTCTTAGATT 59.274 33.333 0.00 0.00 0.00 2.40
3875 4052 8.360390 GTCACCCAAAATTCTTGTCTTAGATTT 58.640 33.333 0.00 0.00 0.00 2.17
3876 4053 8.359642 TCACCCAAAATTCTTGTCTTAGATTTG 58.640 33.333 0.00 0.00 29.84 2.32
3877 4054 8.143835 CACCCAAAATTCTTGTCTTAGATTTGT 58.856 33.333 0.00 0.00 28.79 2.83
3878 4055 8.360390 ACCCAAAATTCTTGTCTTAGATTTGTC 58.640 33.333 0.00 0.00 28.79 3.18
3879 4056 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
3887 4064 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
3888 4065 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
3958 4135 5.682943 TGTAAGACAAGAATTTTGGGACG 57.317 39.130 5.68 0.00 0.00 4.79
3959 4136 4.517453 TGTAAGACAAGAATTTTGGGACGG 59.483 41.667 0.00 0.00 0.00 4.79
3960 4137 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
3961 4138 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
3962 4139 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
3963 4140 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
3964 4141 0.331616 AGAATTTTGGGACGGAGGGG 59.668 55.000 0.00 0.00 0.00 4.79
3965 4142 0.330267 GAATTTTGGGACGGAGGGGA 59.670 55.000 0.00 0.00 0.00 4.81
4037 4214 8.753497 ATAACTATCATATAGATCACGGAGCA 57.247 34.615 0.00 0.00 38.19 4.26
4042 4219 5.912892 TCATATAGATCACGGAGCACAAAA 58.087 37.500 0.00 0.00 0.00 2.44
4071 4248 5.680151 GCTCTAGTAGAGTTGTCATTCACCC 60.680 48.000 24.74 3.52 44.12 4.61
4113 4290 6.543430 TTCAAAATATTTGGAGACCATGGG 57.457 37.500 18.09 0.00 31.53 4.00
4118 4295 1.455822 TTTGGAGACCATGGGGACTT 58.544 50.000 18.09 0.00 39.36 3.01
4129 4306 0.110486 TGGGGACTTGTTTGGAGCTC 59.890 55.000 4.71 4.71 0.00 4.09
4148 4325 2.328099 GCTCTGAACCCAACTGCCG 61.328 63.158 0.00 0.00 0.00 5.69
4149 4326 1.371183 CTCTGAACCCAACTGCCGA 59.629 57.895 0.00 0.00 0.00 5.54
4165 4342 0.250166 CCGACGTGGGAGGAAAGTTT 60.250 55.000 11.78 0.00 0.00 2.66
4189 4366 2.125912 CTTCCTCCTCGTGCCACG 60.126 66.667 11.80 11.80 44.19 4.94
4241 4418 1.153046 CACCGGCGATGGGGTAAAT 60.153 57.895 9.30 0.00 33.95 1.40
4243 4420 1.153046 CCGGCGATGGGGTAAATGT 60.153 57.895 9.30 0.00 0.00 2.71
4253 4430 3.850752 TGGGGTAAATGTGGTTGTCAAT 58.149 40.909 0.00 0.00 0.00 2.57
4273 4450 3.951775 TCATTTGGCCATTAACACCAC 57.048 42.857 6.09 0.00 31.83 4.16
4298 4475 2.158900 CGCTCACTCCAATTCCTATGGT 60.159 50.000 0.00 0.00 39.09 3.55
4302 4479 3.199946 TCACTCCAATTCCTATGGTGACC 59.800 47.826 0.00 0.00 39.09 4.02
4303 4480 2.509964 ACTCCAATTCCTATGGTGACCC 59.490 50.000 0.00 0.00 39.09 4.46
4305 4482 2.922955 TCCAATTCCTATGGTGACCCAA 59.077 45.455 0.00 0.00 46.04 4.12
4306 4483 3.023832 CCAATTCCTATGGTGACCCAAC 58.976 50.000 0.00 0.00 46.04 3.77
4307 4484 3.023832 CAATTCCTATGGTGACCCAACC 58.976 50.000 0.00 0.00 46.04 3.77
4308 4485 2.053747 TTCCTATGGTGACCCAACCT 57.946 50.000 0.00 0.00 46.04 3.50
4309 4486 1.285280 TCCTATGGTGACCCAACCTG 58.715 55.000 0.00 0.00 46.04 4.00
4310 4487 1.203376 TCCTATGGTGACCCAACCTGA 60.203 52.381 0.00 0.00 46.04 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.521256 AGGATAGGTTCTCGTTAGCATCTC 59.479 45.833 0.00 0.00 0.00 2.75
41 42 4.415596 AGAATCAGCAGGGAGTAGGATAG 58.584 47.826 0.00 0.00 0.00 2.08
101 102 3.997064 CTTCTCTCCCCGTGCGCTG 62.997 68.421 9.73 0.08 0.00 5.18
134 139 0.849094 TTCCCAGGTTAGGCCATGGT 60.849 55.000 14.67 0.00 40.61 3.55
235 240 2.683933 ATGACGGCGGAGGAGGTT 60.684 61.111 13.24 0.00 0.00 3.50
388 393 3.357079 CGTGTTGGCAGTGAGGGC 61.357 66.667 0.00 0.00 0.00 5.19
416 421 2.564504 GTTCTAGGTCCGGTTGGTTACT 59.435 50.000 0.00 0.00 36.30 2.24
456 461 3.203716 GCTCCAAACCCTAATCCTAACG 58.796 50.000 0.00 0.00 0.00 3.18
463 468 0.107165 GCTCCGCTCCAAACCCTAAT 60.107 55.000 0.00 0.00 0.00 1.73
626 633 2.585247 CTCGCCGAATCGAACCCC 60.585 66.667 3.36 0.00 38.08 4.95
641 648 2.815647 CGGCCAGAAACCTCGCTC 60.816 66.667 2.24 0.00 0.00 5.03
642 649 3.302347 CTCGGCCAGAAACCTCGCT 62.302 63.158 2.24 0.00 0.00 4.93
643 650 2.815647 CTCGGCCAGAAACCTCGC 60.816 66.667 2.24 0.00 0.00 5.03
644 651 2.125512 CCTCGGCCAGAAACCTCG 60.126 66.667 2.24 0.00 0.00 4.63
645 652 0.253327 ATTCCTCGGCCAGAAACCTC 59.747 55.000 2.24 0.00 0.00 3.85
646 653 0.698818 AATTCCTCGGCCAGAAACCT 59.301 50.000 2.24 0.00 0.00 3.50
647 654 1.095600 GAATTCCTCGGCCAGAAACC 58.904 55.000 2.24 0.00 0.00 3.27
648 655 2.115343 AGAATTCCTCGGCCAGAAAC 57.885 50.000 2.24 2.05 0.00 2.78
649 656 2.569853 TGTAGAATTCCTCGGCCAGAAA 59.430 45.455 2.24 0.00 0.00 2.52
650 657 2.184533 TGTAGAATTCCTCGGCCAGAA 58.815 47.619 2.24 2.46 0.00 3.02
651 658 1.860641 TGTAGAATTCCTCGGCCAGA 58.139 50.000 2.24 0.00 0.00 3.86
652 659 2.168521 TCTTGTAGAATTCCTCGGCCAG 59.831 50.000 2.24 0.00 0.00 4.85
653 660 2.184533 TCTTGTAGAATTCCTCGGCCA 58.815 47.619 2.24 0.00 0.00 5.36
669 676 3.924686 CCATTAGCTTTGCTTGCTTCTTG 59.075 43.478 0.00 1.71 40.44 3.02
731 741 2.048127 GTTGAACTCGCCGCCTCT 60.048 61.111 0.00 0.00 0.00 3.69
799 810 3.814005 TTCCTGAGAAATACGCCTACC 57.186 47.619 0.00 0.00 0.00 3.18
813 824 2.253610 ACTCGGGTTGTGTATTCCTGA 58.746 47.619 0.00 0.00 35.62 3.86
816 827 4.761975 TCATAACTCGGGTTGTGTATTCC 58.238 43.478 22.27 0.00 42.54 3.01
817 828 6.540205 GTTTCATAACTCGGGTTGTGTATTC 58.460 40.000 22.27 9.65 42.54 1.75
823 834 3.062042 GACGTTTCATAACTCGGGTTGT 58.938 45.455 11.94 0.00 36.92 3.32
832 843 6.481954 AGACATGGAAAGACGTTTCATAAC 57.518 37.500 0.00 0.00 43.52 1.89
860 871 2.094752 GGTCATTGCCAGTTTACGCATT 60.095 45.455 0.00 0.00 34.35 3.56
862 873 0.878416 GGTCATTGCCAGTTTACGCA 59.122 50.000 0.00 0.00 0.00 5.24
874 885 2.693762 CCTGGCAGTGCGGTCATTG 61.694 63.158 14.43 0.00 33.59 2.82
1118 1147 2.524148 GGGCTGGCTTGGGTTTGT 60.524 61.111 0.00 0.00 0.00 2.83
1272 1301 3.306379 GGGGGTAGAACGTGGAGG 58.694 66.667 0.00 0.00 0.00 4.30
1286 1315 3.933048 CTGCCACAGCTTCAGGGGG 62.933 68.421 0.00 0.00 40.80 5.40
1298 1327 1.970114 ACTGACAGCATGCTGCCAC 60.970 57.895 40.65 31.17 46.52 5.01
1326 1357 5.461032 TGTAATTGCCTTCGACCAATTTT 57.539 34.783 17.66 4.42 40.81 1.82
1328 1359 6.959639 ATATGTAATTGCCTTCGACCAATT 57.040 33.333 17.00 17.00 42.46 2.32
1329 1360 7.450074 TCTATATGTAATTGCCTTCGACCAAT 58.550 34.615 0.00 0.00 33.35 3.16
1335 1369 9.599322 GTCAAAATCTATATGTAATTGCCTTCG 57.401 33.333 0.00 0.00 0.00 3.79
1372 1407 4.397420 TGACACAACCATTCTATTGCACT 58.603 39.130 0.00 0.00 0.00 4.40
1386 1421 4.686091 TGTTCTCATTCTCGATGACACAAC 59.314 41.667 0.00 0.00 39.83 3.32
1517 1559 9.258826 CAACCAACAATCAATTGACAGAATAAA 57.741 29.630 11.07 0.00 40.14 1.40
1519 1561 7.015098 ACCAACCAACAATCAATTGACAGAATA 59.985 33.333 11.07 0.00 40.14 1.75
1547 1589 4.566004 ACGTGCTCTTCTTTGCTAATACA 58.434 39.130 0.00 0.00 0.00 2.29
1601 1643 0.884704 GTTTCTTCACCTCTGGCGCA 60.885 55.000 10.83 0.00 0.00 6.09
1619 1661 0.316204 CGTTGTAGAGTGAACGGGGT 59.684 55.000 0.00 0.00 40.96 4.95
1766 1811 3.985925 CAGAGCAAATGAAGGTCAAAAGC 59.014 43.478 0.00 0.00 36.03 3.51
1804 1849 0.171455 GTCTCAGCGTCGTCAGGAAT 59.829 55.000 0.00 0.00 0.00 3.01
1815 1860 4.098055 ACTAGTACACATTGTCTCAGCG 57.902 45.455 0.00 0.00 0.00 5.18
1870 1916 5.876612 ATCACAAAGAGCAAGAATCAGAC 57.123 39.130 0.00 0.00 0.00 3.51
1996 2042 6.550938 TTGATCAGAGGATAAAGAAGAGCA 57.449 37.500 0.00 0.00 32.67 4.26
2047 2093 5.544136 TCACAATCAACGAACATACCATG 57.456 39.130 0.00 0.00 0.00 3.66
2186 2234 9.567776 TCTTCAGAAATTGAACTACAACCATTA 57.432 29.630 0.00 0.00 40.82 1.90
2215 2263 0.249031 AACAGGCAAGCAAAACGAGC 60.249 50.000 0.00 0.00 0.00 5.03
2225 2273 2.787994 ACAGAATGGAGAACAGGCAAG 58.212 47.619 0.00 0.00 43.62 4.01
2232 2280 2.294233 TGCAGCAAACAGAATGGAGAAC 59.706 45.455 0.00 0.00 43.62 3.01
2284 2332 4.142403 ACAACGATGTGAAAATATGCCTGG 60.142 41.667 0.00 0.00 38.69 4.45
2303 2351 5.901552 TGAAGGAAGGAAACAAATGACAAC 58.098 37.500 0.00 0.00 0.00 3.32
2488 2538 4.763073 ACGCTAGAAACATAGGTTTACCC 58.237 43.478 5.33 0.00 46.84 3.69
2509 2559 6.228995 AGTGTTTCCTAGTAGGCAGTAAAAC 58.771 40.000 17.57 17.57 34.61 2.43
2686 2860 6.339730 ACTAGACAGATGAGAAAGCATCAAG 58.660 40.000 0.00 0.00 45.52 3.02
2818 2992 1.256376 GATGCTCGATTGTACACTGCG 59.744 52.381 0.00 0.00 0.00 5.18
2867 3041 7.756722 GGATATTTGGTGCACATAATTGATAGC 59.243 37.037 20.43 10.16 0.00 2.97
2871 3045 6.832900 TCAGGATATTTGGTGCACATAATTGA 59.167 34.615 20.43 13.38 0.00 2.57
2912 3086 9.965824 GAAGACAGAGATCCACAATTTTTAAAA 57.034 29.630 0.00 0.00 0.00 1.52
2913 3087 9.354673 AGAAGACAGAGATCCACAATTTTTAAA 57.645 29.630 0.00 0.00 0.00 1.52
2918 3092 8.105829 ACAATAGAAGACAGAGATCCACAATTT 58.894 33.333 0.00 0.00 0.00 1.82
2933 3107 9.463443 AAAACATTGCAACTTACAATAGAAGAC 57.537 29.630 0.00 0.00 36.00 3.01
3171 3346 4.287067 AGGATGTTTACTGGAAGCTTGAGA 59.713 41.667 2.10 0.00 37.60 3.27
3212 3387 4.755123 CAGCCGTAGATTAAAATCCGGAAT 59.245 41.667 9.01 0.00 40.45 3.01
3219 3394 9.880157 TTAGTAAGAACAGCCGTAGATTAAAAT 57.120 29.630 0.00 0.00 0.00 1.82
3237 3412 7.180229 TCCTGACAGAAACATCCATTAGTAAGA 59.820 37.037 3.32 0.00 0.00 2.10
3356 3531 2.819115 CATGCTTGTATCAGTCGCTCT 58.181 47.619 0.00 0.00 0.00 4.09
3357 3532 1.260033 GCATGCTTGTATCAGTCGCTC 59.740 52.381 11.37 0.00 0.00 5.03
3380 3555 2.317685 GAACACGTGTGCCGCAAGTT 62.318 55.000 24.16 2.05 37.70 2.66
3419 3595 7.063308 ACACACAAACAACATTCACTCATTTTC 59.937 33.333 0.00 0.00 0.00 2.29
3498 3674 5.553123 GATCAGAATCATCAGCCTCTTGAT 58.447 41.667 0.00 0.00 38.30 2.57
3561 3738 3.440173 ACCTTAATGTGCCACAATCTTCG 59.560 43.478 0.00 0.00 0.00 3.79
3611 3788 4.191544 CACATCTTACACGGAATCCACAT 58.808 43.478 0.00 0.00 0.00 3.21
3634 3811 8.983702 TCAACATCAATTCATTCCATAGATCA 57.016 30.769 0.00 0.00 0.00 2.92
3706 3883 9.423061 GCAACATAAATTTGACTCACCTTTAAT 57.577 29.630 0.00 0.00 0.00 1.40
3714 3891 7.222417 CACACAAAGCAACATAAATTTGACTCA 59.778 33.333 0.00 0.00 36.41 3.41
3726 3903 2.099592 CAGGACACACACAAAGCAACAT 59.900 45.455 0.00 0.00 0.00 2.71
3771 3948 1.040646 CACTAGGCAATCCGGAGCTA 58.959 55.000 11.34 2.89 37.47 3.32
3797 3974 2.890945 ACAAGAATTTTGGAACGGAGGG 59.109 45.455 0.00 0.00 0.00 4.30
3798 3975 3.821033 AGACAAGAATTTTGGAACGGAGG 59.179 43.478 0.00 0.00 0.00 4.30
3799 3976 5.438761 AAGACAAGAATTTTGGAACGGAG 57.561 39.130 0.00 0.00 0.00 4.63
3800 3977 6.292923 TCTAAGACAAGAATTTTGGAACGGA 58.707 36.000 0.00 0.00 0.00 4.69
3801 3978 6.554334 TCTAAGACAAGAATTTTGGAACGG 57.446 37.500 0.00 0.00 0.00 4.44
3802 3979 8.905702 CAAATCTAAGACAAGAATTTTGGAACG 58.094 33.333 5.68 0.00 28.49 3.95
3803 3980 9.750125 ACAAATCTAAGACAAGAATTTTGGAAC 57.250 29.630 0.00 0.00 33.04 3.62
3804 3981 9.965824 GACAAATCTAAGACAAGAATTTTGGAA 57.034 29.630 0.00 0.00 33.04 3.53
3805 3982 9.354673 AGACAAATCTAAGACAAGAATTTTGGA 57.645 29.630 0.00 0.00 33.04 3.53
3813 3990 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
3814 3991 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
3816 3993 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
3817 3994 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
3824 4001 9.832445 ACTTGATACATCCGTATTTAGACAAAT 57.168 29.630 0.00 0.00 38.48 2.32
3825 4002 9.309516 GACTTGATACATCCGTATTTAGACAAA 57.690 33.333 0.00 0.00 38.48 2.83
3826 4003 8.471609 TGACTTGATACATCCGTATTTAGACAA 58.528 33.333 0.00 0.00 38.48 3.18
3827 4004 7.919091 GTGACTTGATACATCCGTATTTAGACA 59.081 37.037 0.00 0.00 38.48 3.41
3828 4005 7.381678 GGTGACTTGATACATCCGTATTTAGAC 59.618 40.741 0.00 0.00 38.48 2.59
3829 4006 7.431249 GGTGACTTGATACATCCGTATTTAGA 58.569 38.462 0.00 0.00 38.48 2.10
3830 4007 6.645415 GGGTGACTTGATACATCCGTATTTAG 59.355 42.308 0.00 0.00 38.48 1.85
3831 4008 6.098552 TGGGTGACTTGATACATCCGTATTTA 59.901 38.462 0.00 0.00 39.86 1.40
3832 4009 5.104693 TGGGTGACTTGATACATCCGTATTT 60.105 40.000 0.00 0.00 39.86 1.40
3833 4010 4.407621 TGGGTGACTTGATACATCCGTATT 59.592 41.667 0.00 0.00 39.86 1.89
3834 4011 3.964688 TGGGTGACTTGATACATCCGTAT 59.035 43.478 0.00 0.00 39.86 3.06
3835 4012 3.367321 TGGGTGACTTGATACATCCGTA 58.633 45.455 0.00 0.00 39.86 4.02
3836 4013 2.184533 TGGGTGACTTGATACATCCGT 58.815 47.619 0.00 0.00 39.86 4.69
3837 4014 2.979814 TGGGTGACTTGATACATCCG 57.020 50.000 0.00 0.00 39.86 4.18
3838 4015 6.378280 AGAATTTTGGGTGACTTGATACATCC 59.622 38.462 0.00 0.00 37.75 3.51
3839 4016 7.396540 AGAATTTTGGGTGACTTGATACATC 57.603 36.000 0.00 0.00 0.00 3.06
3840 4017 7.233348 ACAAGAATTTTGGGTGACTTGATACAT 59.767 33.333 0.00 0.00 38.30 2.29
3841 4018 6.549364 ACAAGAATTTTGGGTGACTTGATACA 59.451 34.615 0.00 0.00 38.30 2.29
3842 4019 6.981722 ACAAGAATTTTGGGTGACTTGATAC 58.018 36.000 0.00 0.00 38.30 2.24
3843 4020 7.004086 AGACAAGAATTTTGGGTGACTTGATA 58.996 34.615 0.00 0.00 38.30 2.15
3844 4021 5.835280 AGACAAGAATTTTGGGTGACTTGAT 59.165 36.000 0.00 0.00 38.30 2.57
3845 4022 5.200483 AGACAAGAATTTTGGGTGACTTGA 58.800 37.500 0.00 0.00 38.30 3.02
3846 4023 5.520376 AGACAAGAATTTTGGGTGACTTG 57.480 39.130 0.00 0.00 39.98 3.16
3847 4024 7.060421 TCTAAGACAAGAATTTTGGGTGACTT 58.940 34.615 0.00 0.00 0.00 3.01
3848 4025 6.601332 TCTAAGACAAGAATTTTGGGTGACT 58.399 36.000 5.68 0.00 0.00 3.41
3849 4026 6.877611 TCTAAGACAAGAATTTTGGGTGAC 57.122 37.500 5.68 0.00 0.00 3.67
3850 4027 8.359642 CAAATCTAAGACAAGAATTTTGGGTGA 58.640 33.333 5.68 0.00 28.49 4.02
3851 4028 8.143835 ACAAATCTAAGACAAGAATTTTGGGTG 58.856 33.333 0.00 0.00 33.04 4.61
3852 4029 8.250143 ACAAATCTAAGACAAGAATTTTGGGT 57.750 30.769 0.00 0.00 33.04 4.51
3853 4030 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
3861 4038 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
3862 4039 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
3932 4109 8.293867 CGTCCCAAAATTCTTGTCTTACATTTA 58.706 33.333 0.00 0.00 0.00 1.40
3933 4110 7.145323 CGTCCCAAAATTCTTGTCTTACATTT 58.855 34.615 0.00 0.00 0.00 2.32
3934 4111 6.294508 CCGTCCCAAAATTCTTGTCTTACATT 60.295 38.462 0.00 0.00 0.00 2.71
3935 4112 5.183140 CCGTCCCAAAATTCTTGTCTTACAT 59.817 40.000 0.00 0.00 0.00 2.29
3936 4113 4.517453 CCGTCCCAAAATTCTTGTCTTACA 59.483 41.667 0.00 0.00 0.00 2.41
3937 4114 4.758165 TCCGTCCCAAAATTCTTGTCTTAC 59.242 41.667 0.00 0.00 0.00 2.34
3938 4115 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
3939 4116 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
3940 4117 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
3941 4118 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3942 4119 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
3943 4120 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
3944 4121 1.272480 CCCCTCCGTCCCAAAATTCTT 60.272 52.381 0.00 0.00 0.00 2.52
3945 4122 0.331616 CCCCTCCGTCCCAAAATTCT 59.668 55.000 0.00 0.00 0.00 2.40
3946 4123 0.330267 TCCCCTCCGTCCCAAAATTC 59.670 55.000 0.00 0.00 0.00 2.17
3947 4124 0.331616 CTCCCCTCCGTCCCAAAATT 59.668 55.000 0.00 0.00 0.00 1.82
3948 4125 0.845102 ACTCCCCTCCGTCCCAAAAT 60.845 55.000 0.00 0.00 0.00 1.82
3949 4126 0.178897 TACTCCCCTCCGTCCCAAAA 60.179 55.000 0.00 0.00 0.00 2.44
3950 4127 0.178897 TTACTCCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
3951 4128 0.616679 CTTACTCCCCTCCGTCCCAA 60.617 60.000 0.00 0.00 0.00 4.12
3952 4129 1.001248 CTTACTCCCCTCCGTCCCA 59.999 63.158 0.00 0.00 0.00 4.37
3953 4130 0.756070 CTCTTACTCCCCTCCGTCCC 60.756 65.000 0.00 0.00 0.00 4.46
3954 4131 1.393487 GCTCTTACTCCCCTCCGTCC 61.393 65.000 0.00 0.00 0.00 4.79
3955 4132 0.683504 TGCTCTTACTCCCCTCCGTC 60.684 60.000 0.00 0.00 0.00 4.79
3956 4133 0.252103 TTGCTCTTACTCCCCTCCGT 60.252 55.000 0.00 0.00 0.00 4.69
3957 4134 0.175989 GTTGCTCTTACTCCCCTCCG 59.824 60.000 0.00 0.00 0.00 4.63
3958 4135 1.483004 GAGTTGCTCTTACTCCCCTCC 59.517 57.143 0.00 0.00 36.79 4.30
3959 4136 2.462723 AGAGTTGCTCTTACTCCCCTC 58.537 52.381 0.00 0.00 42.35 4.30
3960 4137 2.632763 AGAGTTGCTCTTACTCCCCT 57.367 50.000 0.00 0.00 42.35 4.79
3961 4138 5.834204 TCTAATAGAGTTGCTCTTACTCCCC 59.166 44.000 3.87 0.00 42.35 4.81
3962 4139 6.963083 TCTAATAGAGTTGCTCTTACTCCC 57.037 41.667 3.87 0.00 42.35 4.30
4053 4230 3.983044 AGGGGTGAATGACAACTCTAC 57.017 47.619 0.00 0.00 46.38 2.59
4096 4273 3.407209 AGTCCCCATGGTCTCCAAATAT 58.593 45.455 11.73 0.00 36.95 1.28
4113 4290 0.603975 AGCGAGCTCCAAACAAGTCC 60.604 55.000 8.47 0.00 0.00 3.85
4118 4295 0.392706 TTCAGAGCGAGCTCCAAACA 59.607 50.000 20.15 0.00 43.70 2.83
4129 4306 2.328099 GGCAGTTGGGTTCAGAGCG 61.328 63.158 0.00 0.00 0.00 5.03
4148 4325 2.143925 CTGAAACTTTCCTCCCACGTC 58.856 52.381 0.00 0.00 0.00 4.34
4149 4326 1.814248 GCTGAAACTTTCCTCCCACGT 60.814 52.381 0.00 0.00 0.00 4.49
4165 4342 0.891373 CACGAGGAGGAAGAAGCTGA 59.109 55.000 0.00 0.00 0.00 4.26
4189 4366 0.541764 TGCCACTTCAAATCCCACCC 60.542 55.000 0.00 0.00 0.00 4.61
4237 4414 5.931146 GCCAAATGATTGACAACCACATTTA 59.069 36.000 19.66 0.00 38.52 1.40
4241 4418 2.036992 GGCCAAATGATTGACAACCACA 59.963 45.455 0.00 0.00 38.94 4.17
4243 4420 2.323599 TGGCCAAATGATTGACAACCA 58.676 42.857 0.61 0.00 38.94 3.67
4253 4430 2.230025 CGTGGTGTTAATGGCCAAATGA 59.770 45.455 10.96 0.00 33.66 2.57
4273 4450 2.436646 AATTGGAGTGAGCGGCCG 60.437 61.111 24.05 24.05 0.00 6.13


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

AutoCloner maintained by Alex Coulton.