Multiple sequence alignment - TraesCS5D01G497400

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 TraesCS5D01G497400 chr5D 100.000 7091 0 0 1 7091 527504673 527497583 0.000000e+00 13095.0
1 TraesCS5D01G497400 chr5D 94.186 86 5 0 2881 2966 282007096 282007011 1.610000e-26 132.0
2 TraesCS5D01G497400 chr5B 94.014 2957 114 20 843 3766 664027416 664024490 0.000000e+00 4421.0
3 TraesCS5D01G497400 chr5B 91.618 1706 74 31 5415 7090 664022875 664021209 0.000000e+00 2294.0
4 TraesCS5D01G497400 chr5B 95.099 1367 45 6 4034 5383 664024235 664022874 0.000000e+00 2134.0
5 TraesCS5D01G497400 chr5B 97.740 177 4 0 3859 4035 664024493 664024317 8.940000e-79 305.0
6 TraesCS5D01G497400 chr5A 93.880 2075 66 18 1707 3766 654622289 654620261 0.000000e+00 3072.0
7 TraesCS5D01G497400 chr5A 93.173 1787 85 12 5310 7091 654618518 654616764 0.000000e+00 2590.0
8 TraesCS5D01G497400 chr5A 95.192 832 15 7 3859 4682 654620264 654619450 0.000000e+00 1291.0
9 TraesCS5D01G497400 chr5A 91.470 762 50 6 956 1712 654623118 654622367 0.000000e+00 1033.0
10 TraesCS5D01G497400 chr5A 95.880 631 23 1 4684 5311 654619375 654618745 0.000000e+00 1018.0
11 TraesCS5D01G497400 chr5A 85.128 195 26 3 151 342 680470570 680470764 5.610000e-46 196.0
12 TraesCS5D01G497400 chr5A 82.587 201 32 3 138 336 680470612 680470811 2.630000e-39 174.0
13 TraesCS5D01G497400 chr7A 92.528 803 35 5 68 847 682078817 682078017 0.000000e+00 1127.0
14 TraesCS5D01G497400 chr7A 89.744 117 11 1 3754 3870 628008467 628008582 1.590000e-31 148.0
15 TraesCS5D01G497400 chr7D 87.402 889 66 19 1 857 470880382 470879508 0.000000e+00 979.0
16 TraesCS5D01G497400 chr7D 83.824 204 28 5 142 342 617978197 617978398 9.390000e-44 189.0
17 TraesCS5D01G497400 chr7D 88.991 109 7 5 2865 2968 310990197 310990305 5.770000e-26 130.0
18 TraesCS5D01G497400 chr7B 74.830 735 121 41 128 841 315605655 315606346 2.520000e-69 274.0
19 TraesCS5D01G497400 chr7B 90.435 115 10 1 3754 3868 589348426 589348313 4.430000e-32 150.0
20 TraesCS5D01G497400 chr7B 91.071 112 5 5 2865 2971 357651486 357651597 5.730000e-31 147.0
21 TraesCS5D01G497400 chr7B 83.125 160 23 4 156 313 437677440 437677283 7.410000e-30 143.0
22 TraesCS5D01G497400 chr3A 85.128 195 26 3 151 342 368656254 368656448 5.610000e-46 196.0
23 TraesCS5D01G497400 chr3A 83.582 201 30 3 138 336 368656296 368656495 1.210000e-42 185.0
24 TraesCS5D01G497400 chr2A 85.393 178 22 4 138 313 462569280 462569455 1.570000e-41 182.0
25 TraesCS5D01G497400 chr1A 91.589 107 8 1 3756 3862 351606753 351606858 5.730000e-31 147.0
26 TraesCS5D01G497400 chr1B 91.509 106 8 1 3758 3863 359902041 359902145 2.060000e-30 145.0
27 TraesCS5D01G497400 chr2D 92.929 99 6 1 3764 3862 24916170 24916073 7.410000e-30 143.0
28 TraesCS5D01G497400 chr2D 90.566 106 6 4 2865 2966 192181584 192181479 3.450000e-28 137.0
29 TraesCS5D01G497400 chr2D 90.476 105 5 5 2865 2965 351973352 351973455 4.460000e-27 134.0
30 TraesCS5D01G497400 chr2D 80.214 187 29 7 126 307 613449069 613449252 4.460000e-27 134.0
31 TraesCS5D01G497400 chr4D 90.090 111 8 3 3753 3863 323929563 323929670 2.670000e-29 141.0
32 TraesCS5D01G497400 chr4D 90.566 106 8 2 3758 3863 110081037 110080934 9.590000e-29 139.0
33 TraesCS5D01G497400 chr4D 89.815 108 10 1 3762 3869 494042369 494042475 3.450000e-28 137.0
34 TraesCS5D01G497400 chr6D 90.476 105 9 1 3758 3862 465968858 465968961 3.450000e-28 137.0
35 TraesCS5D01G497400 chr3B 89.908 109 6 5 2861 2965 672778077 672778184 1.240000e-27 135.0
36 TraesCS5D01G497400 chr3D 88.991 109 8 4 2862 2966 477910558 477910666 1.610000e-26 132.0
37 TraesCS5D01G497400 chr1D 100.000 29 0 0 813 841 70459429 70459401 4.000000e-03 54.7


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 TraesCS5D01G497400 chr5D 527497583 527504673 7090 True 13095.0 13095 100.00000 1 7091 1 chr5D.!!$R2 7090
1 TraesCS5D01G497400 chr5B 664021209 664027416 6207 True 2288.5 4421 94.61775 843 7090 4 chr5B.!!$R1 6247
2 TraesCS5D01G497400 chr5A 654616764 654623118 6354 True 1800.8 3072 93.91900 956 7091 5 chr5A.!!$R1 6135
3 TraesCS5D01G497400 chr7A 682078017 682078817 800 True 1127.0 1127 92.52800 68 847 1 chr7A.!!$R1 779
4 TraesCS5D01G497400 chr7D 470879508 470880382 874 True 979.0 979 87.40200 1 857 1 chr7D.!!$R1 856
5 TraesCS5D01G497400 chr7B 315605655 315606346 691 False 274.0 274 74.83000 128 841 1 chr7B.!!$F1 713

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
221 229 0.250901 AAGCTCCATTGCAACTCCGT 60.251 50.000 0.00 0.0 34.99 4.69 F
377 407 0.807667 CGAGATGAAGCGGGTGAAGG 60.808 60.000 0.00 0.0 0.00 3.46 F
1394 1476 0.873743 GAGAGCTCGCCATGTACAGC 60.874 60.000 8.37 0.0 0.00 4.40 F
2832 3014 1.073923 GGTGATTGGTGAAGACCCACT 59.926 52.381 0.00 0.0 42.34 4.00 F
3786 3991 0.257616 TCCCTCCGCCCCAAAATAAG 59.742 55.000 0.00 0.0 0.00 1.73 F
3787 3992 0.033503 CCCTCCGCCCCAAAATAAGT 60.034 55.000 0.00 0.0 0.00 2.24 F
4835 5204 0.175073 GGTGTCGGGCTAGGTTAGTG 59.825 60.000 0.00 0.0 0.00 2.74 F
5621 6223 1.399440 CATTGTGCGGTGAGATCCTTG 59.601 52.381 0.00 0.0 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 2034 1.359833 ACGCGGACAGTAACGTCAA 59.640 52.632 12.47 0.00 37.66 3.18 R
2274 2446 0.675837 CCCTGATCACACTGTGCCAG 60.676 60.000 17.54 17.54 35.45 4.85 R
2955 3141 2.642171 TCCCATGTTGTACTCCCTCT 57.358 50.000 0.00 0.00 0.00 3.69 R
3768 3973 0.033503 ACTTATTTTGGGGCGGAGGG 60.034 55.000 0.00 0.00 0.00 4.30 R
4736 5105 0.107456 AATAGCTGCATGGGGAGACG 59.893 55.000 1.02 0.00 33.71 4.18 R
5144 5516 0.879765 CAGGTTTGCAGCTCCTTCTG 59.120 55.000 0.00 0.00 37.15 3.02 R
5853 6455 0.321298 GGAAAACGCTACCAGCTCCA 60.321 55.000 0.00 0.00 39.60 3.86 R
6713 7348 1.202903 AGGAATCCAGGCTGATGATGC 60.203 52.381 17.94 9.58 0.00 3.91 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
40 41 3.000819 ATCCGGGGTCGCAACTCA 61.001 61.111 0.00 0.00 34.56 3.41
103 104 3.069946 ACGGGATGGCGTTCGGTA 61.070 61.111 0.00 0.00 0.00 4.02
191 199 0.391661 AGCTCCAACGCAACATCGAT 60.392 50.000 0.00 0.00 0.00 3.59
221 229 0.250901 AAGCTCCATTGCAACTCCGT 60.251 50.000 0.00 0.00 34.99 4.69
326 356 2.657372 CGAAGCTCGTTGTAACTCTGAC 59.343 50.000 0.00 0.00 34.72 3.51
372 402 2.490217 CGTCGAGATGAAGCGGGT 59.510 61.111 0.00 0.00 0.00 5.28
377 407 0.807667 CGAGATGAAGCGGGTGAAGG 60.808 60.000 0.00 0.00 0.00 3.46
841 919 5.296035 CAGTCGGTTTACAGGAAGAGTTTTT 59.704 40.000 0.00 0.00 0.00 1.94
948 1027 1.439679 CCGTAACTTTCCTCTGCACC 58.560 55.000 0.00 0.00 0.00 5.01
1045 1124 2.522193 CCCTAGAGCTCCGTCCCC 60.522 72.222 10.93 0.00 0.00 4.81
1076 1155 4.781959 TAGCGTACGCACCACCGC 62.782 66.667 38.58 12.51 46.07 5.68
1113 1192 4.446413 CGGCCGGCGACCTACTTT 62.446 66.667 22.54 0.00 0.00 2.66
1121 1203 1.080093 CGACCTACTTTGGAGCGCA 60.080 57.895 11.47 0.00 0.00 6.09
1203 1285 1.462731 CCATCTCTCTCAGCTCCGGG 61.463 65.000 0.00 0.00 0.00 5.73
1315 1397 1.340600 CCCTAACCAATTTCGGCTCCA 60.341 52.381 0.00 0.00 0.00 3.86
1394 1476 0.873743 GAGAGCTCGCCATGTACAGC 60.874 60.000 8.37 0.00 0.00 4.40
1404 1486 2.341257 CCATGTACAGCGAGATATGGC 58.659 52.381 0.33 0.00 0.00 4.40
1417 1499 7.174772 CAGCGAGATATGGCTAGAGATATATGT 59.825 40.741 0.00 0.00 37.41 2.29
1518 1600 8.225777 ACCAAACGACTAACTTCGAATATTTTC 58.774 33.333 0.00 0.00 41.78 2.29
1522 1604 8.395940 ACGACTAACTTCGAATATTTTCTCAG 57.604 34.615 0.00 0.00 41.78 3.35
1593 1682 9.541143 TTTCTTCGTATTTCATATGCTGTATCA 57.459 29.630 0.00 0.00 0.00 2.15
1628 1717 2.362077 GCATGTATAGTGGCCCTTTTGG 59.638 50.000 0.00 0.00 39.97 3.28
1769 1941 7.698163 ATCCATCTCCTAAGGTTTCTACATT 57.302 36.000 0.00 0.00 32.30 2.71
1782 1954 2.722094 TCTACATTTTCCATGGCGCTT 58.278 42.857 6.96 0.00 0.00 4.68
1862 2034 2.676822 TCTTCGCTCCTCCGTGCT 60.677 61.111 0.00 0.00 0.00 4.40
1935 2107 6.622896 GCGATGAAAGCTACAAAGGTATTGTT 60.623 38.462 0.00 0.00 34.11 2.83
1965 2137 7.849804 TTAGTCTTCATGTTTTCTCTATGCC 57.150 36.000 0.00 0.00 0.00 4.40
2312 2484 6.508777 TCAGGGGAAAAACTTAACAAAATCG 58.491 36.000 0.00 0.00 0.00 3.34
2339 2511 2.369394 CTCCCTGTGCTATGGTTTTCC 58.631 52.381 0.00 0.00 41.14 3.13
2456 2629 6.605849 TGAGCAGTTACTACGTAAACTGTAG 58.394 40.000 28.13 13.38 43.87 2.74
2505 2678 3.762288 TGTACTCTGTTAGAGGCGTGATT 59.238 43.478 10.31 0.00 46.45 2.57
2578 2751 3.368236 GCGTGCTTCGGGAATAAGATATC 59.632 47.826 0.00 0.00 40.26 1.63
2620 2794 7.433708 TGTCCTGTTTATTGACTGTACATTG 57.566 36.000 0.00 0.00 0.00 2.82
2731 2905 9.595823 GTTGTTGGTTAGATAGCAATAGAAGTA 57.404 33.333 0.00 0.00 45.20 2.24
2774 2948 9.017509 ACCAGATAATCATAAATGCCACATAAG 57.982 33.333 0.00 0.00 0.00 1.73
2832 3014 1.073923 GGTGATTGGTGAAGACCCACT 59.926 52.381 0.00 0.00 42.34 4.00
2936 3122 9.698309 AAATACGTCTAGATACATCCATTTGAG 57.302 33.333 0.00 0.00 0.00 3.02
2955 3141 7.841915 TTTGAGCGACAAGTAATATGAATCA 57.158 32.000 0.00 0.00 39.77 2.57
2988 3174 2.111613 ACATGGGAAATTGGAGGGACAA 59.888 45.455 0.00 0.00 34.41 3.18
3008 3194 7.860872 GGGACAAACCTTAATAAATAAGATGCG 59.139 37.037 0.00 0.00 43.16 4.73
3026 3212 5.581085 AGATGCGTTACCAAAGTGATCTTAC 59.419 40.000 0.00 0.00 33.09 2.34
3027 3213 4.890088 TGCGTTACCAAAGTGATCTTACT 58.110 39.130 0.00 0.00 33.09 2.24
3028 3214 6.028146 TGCGTTACCAAAGTGATCTTACTA 57.972 37.500 0.00 0.00 33.09 1.82
3029 3215 6.457355 TGCGTTACCAAAGTGATCTTACTAA 58.543 36.000 0.00 0.00 33.09 2.24
3030 3216 6.930164 TGCGTTACCAAAGTGATCTTACTAAA 59.070 34.615 0.00 0.00 33.09 1.85
3031 3217 7.117236 TGCGTTACCAAAGTGATCTTACTAAAG 59.883 37.037 0.00 0.00 33.09 1.85
3032 3218 7.117379 GCGTTACCAAAGTGATCTTACTAAAGT 59.883 37.037 0.00 0.00 34.13 2.66
3084 3274 8.768397 TGATTATGTCCTACACAAAGTATCCTT 58.232 33.333 0.00 0.00 38.97 3.36
3092 3282 8.383175 TCCTACACAAAGTATCCTTTTGAAGAT 58.617 33.333 4.87 0.00 38.87 2.40
3335 3525 5.219633 GTCGACCTGTTTGCAAAATGTAAT 58.780 37.500 14.67 0.00 0.00 1.89
3336 3526 6.017026 TGTCGACCTGTTTGCAAAATGTAATA 60.017 34.615 14.67 0.00 0.00 0.98
3337 3527 6.304683 GTCGACCTGTTTGCAAAATGTAATAC 59.695 38.462 14.67 4.69 0.00 1.89
3338 3528 6.205853 TCGACCTGTTTGCAAAATGTAATACT 59.794 34.615 14.67 0.00 0.00 2.12
3339 3529 6.523201 CGACCTGTTTGCAAAATGTAATACTC 59.477 38.462 14.67 0.00 0.00 2.59
3340 3530 6.687604 ACCTGTTTGCAAAATGTAATACTCC 58.312 36.000 14.67 0.00 0.00 3.85
3350 3540 9.780186 GCAAAATGTAATACTCCTACCTCTTAT 57.220 33.333 0.00 0.00 0.00 1.73
3395 3585 8.902806 ACAGTTACTTTGTTTGATCTGATTTCA 58.097 29.630 0.00 0.00 0.00 2.69
3408 3598 9.524106 TTGATCTGATTTCAAATTCATGTATGC 57.476 29.630 0.00 0.00 30.44 3.14
3627 3832 1.756950 TCGTAGCCGCTGGGATTCT 60.757 57.895 2.16 0.00 31.59 2.40
3673 3878 9.344772 CATCTAGAGGTAGTCAAATACAGTAGT 57.655 37.037 0.00 0.00 0.00 2.73
3773 3978 9.984190 CTAATCTTTGTAATTAGTACTCCCTCC 57.016 37.037 0.00 0.00 33.77 4.30
3774 3979 6.461110 TCTTTGTAATTAGTACTCCCTCCG 57.539 41.667 0.00 0.00 33.46 4.63
3775 3980 4.660789 TTGTAATTAGTACTCCCTCCGC 57.339 45.455 0.00 0.00 33.46 5.54
3776 3981 2.961062 TGTAATTAGTACTCCCTCCGCC 59.039 50.000 0.00 0.00 33.46 6.13
3777 3982 1.421480 AATTAGTACTCCCTCCGCCC 58.579 55.000 0.00 0.00 0.00 6.13
3778 3983 0.471401 ATTAGTACTCCCTCCGCCCC 60.471 60.000 0.00 0.00 0.00 5.80
3779 3984 1.877672 TTAGTACTCCCTCCGCCCCA 61.878 60.000 0.00 0.00 0.00 4.96
3780 3985 1.877672 TAGTACTCCCTCCGCCCCAA 61.878 60.000 0.00 0.00 0.00 4.12
3781 3986 2.123180 TACTCCCTCCGCCCCAAA 59.877 61.111 0.00 0.00 0.00 3.28
3782 3987 1.539372 TACTCCCTCCGCCCCAAAA 60.539 57.895 0.00 0.00 0.00 2.44
3783 3988 0.917333 TACTCCCTCCGCCCCAAAAT 60.917 55.000 0.00 0.00 0.00 1.82
3784 3989 0.917333 ACTCCCTCCGCCCCAAAATA 60.917 55.000 0.00 0.00 0.00 1.40
3785 3990 0.257616 CTCCCTCCGCCCCAAAATAA 59.742 55.000 0.00 0.00 0.00 1.40
3786 3991 0.257616 TCCCTCCGCCCCAAAATAAG 59.742 55.000 0.00 0.00 0.00 1.73
3787 3992 0.033503 CCCTCCGCCCCAAAATAAGT 60.034 55.000 0.00 0.00 0.00 2.24
3788 3993 1.102978 CCTCCGCCCCAAAATAAGTG 58.897 55.000 0.00 0.00 0.00 3.16
3789 3994 1.615919 CCTCCGCCCCAAAATAAGTGT 60.616 52.381 0.00 0.00 0.00 3.55
3790 3995 1.743394 CTCCGCCCCAAAATAAGTGTC 59.257 52.381 0.00 0.00 0.00 3.67
3791 3996 1.353022 TCCGCCCCAAAATAAGTGTCT 59.647 47.619 0.00 0.00 0.00 3.41
3792 3997 1.743394 CCGCCCCAAAATAAGTGTCTC 59.257 52.381 0.00 0.00 0.00 3.36
3793 3998 2.432444 CGCCCCAAAATAAGTGTCTCA 58.568 47.619 0.00 0.00 0.00 3.27
3794 3999 2.817258 CGCCCCAAAATAAGTGTCTCAA 59.183 45.455 0.00 0.00 0.00 3.02
3795 4000 3.119849 CGCCCCAAAATAAGTGTCTCAAG 60.120 47.826 0.00 0.00 0.00 3.02
3796 4001 3.367395 GCCCCAAAATAAGTGTCTCAAGC 60.367 47.826 0.00 0.00 0.00 4.01
3797 4002 4.082125 CCCCAAAATAAGTGTCTCAAGCT 58.918 43.478 0.00 0.00 0.00 3.74
3798 4003 4.524328 CCCCAAAATAAGTGTCTCAAGCTT 59.476 41.667 0.00 0.00 0.00 3.74
3799 4004 5.710099 CCCCAAAATAAGTGTCTCAAGCTTA 59.290 40.000 0.00 0.00 0.00 3.09
3800 4005 6.127897 CCCCAAAATAAGTGTCTCAAGCTTAG 60.128 42.308 0.00 0.00 0.00 2.18
3801 4006 6.431234 CCCAAAATAAGTGTCTCAAGCTTAGT 59.569 38.462 0.00 0.00 0.00 2.24
3802 4007 7.606456 CCCAAAATAAGTGTCTCAAGCTTAGTA 59.394 37.037 0.00 0.00 0.00 1.82
3803 4008 8.443937 CCAAAATAAGTGTCTCAAGCTTAGTAC 58.556 37.037 0.00 0.00 0.00 2.73
3804 4009 8.988934 CAAAATAAGTGTCTCAAGCTTAGTACA 58.011 33.333 0.00 0.36 0.00 2.90
3805 4010 9.555727 AAAATAAGTGTCTCAAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
3806 4011 8.535690 AATAAGTGTCTCAAGCTTAGTACAAC 57.464 34.615 0.00 0.00 0.00 3.32
3807 4012 5.793030 AGTGTCTCAAGCTTAGTACAACT 57.207 39.130 0.00 0.00 0.00 3.16
3808 4013 6.163135 AGTGTCTCAAGCTTAGTACAACTT 57.837 37.500 0.00 0.00 0.00 2.66
3809 4014 6.583562 AGTGTCTCAAGCTTAGTACAACTTT 58.416 36.000 0.00 0.00 0.00 2.66
3810 4015 6.480320 AGTGTCTCAAGCTTAGTACAACTTTG 59.520 38.462 0.00 0.00 0.00 2.77
3811 4016 6.258068 GTGTCTCAAGCTTAGTACAACTTTGT 59.742 38.462 0.00 0.00 44.86 2.83
3812 4017 7.437267 GTGTCTCAAGCTTAGTACAACTTTGTA 59.563 37.037 0.00 0.00 42.35 2.41
3826 4031 6.277605 ACAACTTTGTACTAATGTTTTGGGC 58.722 36.000 0.00 0.00 40.16 5.36
3827 4032 6.127310 ACAACTTTGTACTAATGTTTTGGGCA 60.127 34.615 0.00 0.00 40.16 5.36
3828 4033 6.472686 ACTTTGTACTAATGTTTTGGGCAA 57.527 33.333 0.00 0.00 0.00 4.52
3829 4034 6.879400 ACTTTGTACTAATGTTTTGGGCAAA 58.121 32.000 0.00 0.00 0.00 3.68
3830 4035 6.983890 ACTTTGTACTAATGTTTTGGGCAAAG 59.016 34.615 0.00 0.00 41.04 2.77
3831 4036 6.472686 TTGTACTAATGTTTTGGGCAAAGT 57.527 33.333 0.00 0.00 0.00 2.66
3832 4037 6.472686 TGTACTAATGTTTTGGGCAAAGTT 57.527 33.333 0.00 0.00 0.00 2.66
3833 4038 6.276847 TGTACTAATGTTTTGGGCAAAGTTG 58.723 36.000 0.00 0.00 0.00 3.16
3834 4039 5.606348 ACTAATGTTTTGGGCAAAGTTGA 57.394 34.783 0.00 0.00 0.00 3.18
3835 4040 5.600696 ACTAATGTTTTGGGCAAAGTTGAG 58.399 37.500 0.00 0.00 0.00 3.02
3836 4041 4.751767 AATGTTTTGGGCAAAGTTGAGA 57.248 36.364 0.00 0.00 0.00 3.27
3837 4042 3.518634 TGTTTTGGGCAAAGTTGAGAC 57.481 42.857 0.00 0.00 0.00 3.36
3838 4043 2.828520 TGTTTTGGGCAAAGTTGAGACA 59.171 40.909 0.00 0.00 0.00 3.41
3839 4044 3.186909 GTTTTGGGCAAAGTTGAGACAC 58.813 45.455 0.00 0.00 0.00 3.67
3840 4045 2.435372 TTGGGCAAAGTTGAGACACT 57.565 45.000 0.00 0.00 0.00 3.55
3841 4046 2.435372 TGGGCAAAGTTGAGACACTT 57.565 45.000 0.00 0.00 38.74 3.16
3842 4047 3.569194 TGGGCAAAGTTGAGACACTTA 57.431 42.857 0.00 0.00 35.87 2.24
3843 4048 4.098914 TGGGCAAAGTTGAGACACTTAT 57.901 40.909 0.00 0.00 35.87 1.73
3844 4049 4.469657 TGGGCAAAGTTGAGACACTTATT 58.530 39.130 0.00 0.00 35.87 1.40
3845 4050 4.892934 TGGGCAAAGTTGAGACACTTATTT 59.107 37.500 0.00 0.00 35.87 1.40
3846 4051 5.362430 TGGGCAAAGTTGAGACACTTATTTT 59.638 36.000 0.00 0.00 35.87 1.82
3847 4052 5.691754 GGGCAAAGTTGAGACACTTATTTTG 59.308 40.000 0.00 0.00 35.87 2.44
3848 4053 5.691754 GGCAAAGTTGAGACACTTATTTTGG 59.308 40.000 0.00 0.00 35.87 3.28
3849 4054 5.691754 GCAAAGTTGAGACACTTATTTTGGG 59.308 40.000 0.00 0.00 35.87 4.12
3850 4055 5.453567 AAGTTGAGACACTTATTTTGGGC 57.546 39.130 0.00 0.00 35.10 5.36
3851 4056 3.826729 AGTTGAGACACTTATTTTGGGCC 59.173 43.478 0.00 0.00 0.00 5.80
3852 4057 2.432444 TGAGACACTTATTTTGGGCCG 58.568 47.619 0.00 0.00 0.00 6.13
3853 4058 1.743394 GAGACACTTATTTTGGGCCGG 59.257 52.381 0.00 0.00 0.00 6.13
3854 4059 1.353022 AGACACTTATTTTGGGCCGGA 59.647 47.619 5.05 0.00 0.00 5.14
3855 4060 1.743394 GACACTTATTTTGGGCCGGAG 59.257 52.381 5.05 0.00 0.00 4.63
3948 4153 2.644151 AGTCCCTATTGGTTGAACCCT 58.356 47.619 12.53 1.68 37.50 4.34
4006 4211 5.250982 AGAAACTCATGCTCATGTGATTGA 58.749 37.500 16.04 0.08 39.72 2.57
4204 4500 5.565592 TCCCATTTGATCGATCTGTTTTG 57.434 39.130 25.02 14.68 0.00 2.44
4678 4974 8.443937 GTTATGTTTTCCTAGACAAGCACTAAG 58.556 37.037 0.00 0.00 0.00 2.18
4736 5105 1.493311 CACGAAAGCGAGCTGGTTC 59.507 57.895 0.00 0.00 41.64 3.62
4754 5123 0.760567 TCGTCTCCCCATGCAGCTAT 60.761 55.000 0.00 0.00 0.00 2.97
4820 5189 1.238439 CTCCAAATGCAGAACGGTGT 58.762 50.000 0.00 0.00 0.00 4.16
4830 5199 2.602568 AACGGTGTCGGGCTAGGT 60.603 61.111 0.00 0.00 41.39 3.08
4835 5204 0.175073 GGTGTCGGGCTAGGTTAGTG 59.825 60.000 0.00 0.00 0.00 2.74
4899 5271 9.696917 AACAAATTCTGTCAAAATCTGAATACC 57.303 29.630 0.00 0.00 37.23 2.73
4957 5329 7.984391 TCCTAATATTGTGCAAATACTGTGTG 58.016 34.615 0.00 0.00 0.00 3.82
4986 5358 2.744202 CCTGCAGTACTGTTCCATTCAC 59.256 50.000 23.44 4.72 0.00 3.18
5059 5431 3.705051 ACGGACTACTGAGGGTAATTCA 58.295 45.455 0.00 0.00 0.00 2.57
5144 5516 5.010617 TCCCAGGAAATGTAGCAACTTTTTC 59.989 40.000 0.00 0.00 34.21 2.29
5382 5984 3.941483 AGGCTATGTTCTGTATGCACAAC 59.059 43.478 0.00 0.00 33.22 3.32
5391 5993 6.014925 TGTTCTGTATGCACAACTTCCTAGTA 60.015 38.462 3.84 0.00 33.22 1.82
5392 5994 6.599356 TCTGTATGCACAACTTCCTAGTAA 57.401 37.500 0.00 0.00 33.22 2.24
5404 6006 9.722184 ACAACTTCCTAGTAAAGAATAACCTTC 57.278 33.333 8.64 0.00 33.17 3.46
5436 6038 2.420628 TGCCATGCGTTCTTTTTCAG 57.579 45.000 0.00 0.00 0.00 3.02
5460 6062 7.010738 CAGACTTGCAAATGACTTTTCAAACAT 59.989 33.333 0.00 0.00 34.61 2.71
5576 6178 8.806429 TTTGCCATAAGATAATCAAGTGAAGA 57.194 30.769 0.00 0.00 0.00 2.87
5588 6190 5.930837 TCAAGTGAAGAAAACCACCATTT 57.069 34.783 0.00 0.00 34.00 2.32
5621 6223 1.399440 CATTGTGCGGTGAGATCCTTG 59.601 52.381 0.00 0.00 0.00 3.61
5649 6251 9.959775 CTGACTTTTACATTAATCTTCGAAGAC 57.040 33.333 29.24 12.08 37.98 3.01
5714 6316 3.072476 CTGGCAGGGCAGTACAGT 58.928 61.111 14.11 0.00 0.00 3.55
5741 6343 2.032071 CGACCCCCACCAACAGAC 59.968 66.667 0.00 0.00 0.00 3.51
5853 6455 0.486879 TTCCCAGGGGACAAAATGCT 59.513 50.000 6.55 0.00 45.11 3.79
5856 6458 0.251742 CCAGGGGACAAAATGCTGGA 60.252 55.000 0.00 0.00 29.02 3.86
5882 6484 2.275380 GCGTTTTCCCCTGCCATGT 61.275 57.895 0.00 0.00 0.00 3.21
5940 6542 0.961019 TTTTGCCTCGCATGAGCTTT 59.039 45.000 0.00 0.00 41.13 3.51
6084 6686 0.240945 ATGTAACGGCTGCAACTTGC 59.759 50.000 6.82 6.82 45.29 4.01
6100 6702 7.377398 TGCAACTTGCTACAACATATTTGAAT 58.623 30.769 14.78 0.00 45.31 2.57
6125 6727 5.248477 ACTGGCTCCAGATTAGTGTTCTTTA 59.752 40.000 21.75 0.00 46.30 1.85
6155 6757 7.496263 TGCTATAATATCCTCAGCTACTAGTCG 59.504 40.741 0.00 0.00 33.38 4.18
6160 6762 3.952931 TCCTCAGCTACTAGTCGAACTT 58.047 45.455 0.00 0.00 0.00 2.66
6244 6852 7.998212 GTCATGCAGAAAAGATAAAACAAAACG 59.002 33.333 0.00 0.00 0.00 3.60
6268 6876 1.542915 ACAAAGCTGCTGCATACTTGG 59.457 47.619 18.42 15.40 42.74 3.61
6313 6921 5.701290 GGTTTTAGAATATCCATGACCGGAG 59.299 44.000 9.46 0.00 38.83 4.63
6323 6931 2.028112 CCATGACCGGAGAAAGACAGAA 60.028 50.000 9.46 0.00 0.00 3.02
6324 6932 3.557054 CCATGACCGGAGAAAGACAGAAA 60.557 47.826 9.46 0.00 0.00 2.52
6365 6973 5.862924 AATACCTCAATCACAAAGACACG 57.137 39.130 0.00 0.00 0.00 4.49
6366 6974 3.469008 ACCTCAATCACAAAGACACGA 57.531 42.857 0.00 0.00 0.00 4.35
6367 6975 3.393800 ACCTCAATCACAAAGACACGAG 58.606 45.455 0.00 0.00 0.00 4.18
6368 6976 3.069586 ACCTCAATCACAAAGACACGAGA 59.930 43.478 0.00 0.00 0.00 4.04
6369 6977 4.058124 CCTCAATCACAAAGACACGAGAA 58.942 43.478 0.00 0.00 0.00 2.87
6370 6978 4.511454 CCTCAATCACAAAGACACGAGAAA 59.489 41.667 0.00 0.00 0.00 2.52
6371 6979 5.180117 CCTCAATCACAAAGACACGAGAAAT 59.820 40.000 0.00 0.00 0.00 2.17
6372 6980 6.368791 CCTCAATCACAAAGACACGAGAAATA 59.631 38.462 0.00 0.00 0.00 1.40
6373 6981 7.117241 TCAATCACAAAGACACGAGAAATAC 57.883 36.000 0.00 0.00 0.00 1.89
6374 6982 6.704050 TCAATCACAAAGACACGAGAAATACA 59.296 34.615 0.00 0.00 0.00 2.29
6375 6983 5.900339 TCACAAAGACACGAGAAATACAC 57.100 39.130 0.00 0.00 0.00 2.90
6429 7037 8.974060 TTAAAGTCTAAACCACAGAACAAGAT 57.026 30.769 0.00 0.00 0.00 2.40
6452 7087 5.090845 TGCACCTATATCCCTTGTATGCTA 58.909 41.667 0.00 0.00 0.00 3.49
6604 7239 8.035394 AGATAACTGCTACATGGAAATATACCG 58.965 37.037 0.00 0.00 0.00 4.02
6635 7270 8.462016 CAATTCCCTTCTACTTCCATTAGTTTG 58.538 37.037 0.00 0.00 0.00 2.93
6662 7297 5.354513 GGTTTATCCAAGTTAGAGCCAACTC 59.645 44.000 0.00 0.00 37.78 3.01
6675 7310 0.179056 CCAACTCGTTCACCCACAGT 60.179 55.000 0.00 0.00 0.00 3.55
6677 7312 0.249322 AACTCGTTCACCCACAGTCG 60.249 55.000 0.00 0.00 0.00 4.18
6713 7348 5.297527 TCATCATTGGAATCATCTTTGTCGG 59.702 40.000 0.00 0.00 0.00 4.79
6721 7356 3.264998 TCATCTTTGTCGGCATCATCA 57.735 42.857 0.00 0.00 0.00 3.07
6788 7425 5.524646 ACTCCTGCAAACAAATTTTCATGTG 59.475 36.000 0.00 0.00 0.00 3.21
6845 7483 4.816925 GCAAGGAGGATATGTACCTTCAAC 59.183 45.833 0.00 0.00 40.21 3.18
6846 7484 5.629133 GCAAGGAGGATATGTACCTTCAACA 60.629 44.000 0.00 0.00 40.21 3.33
6864 7502 5.304778 TCAACAAAGGACTCGAATTCATCA 58.695 37.500 6.22 0.00 0.00 3.07
6894 7532 1.826385 CTGATGGGGTCCAGTTGAAC 58.174 55.000 0.00 0.00 36.75 3.18
7009 7647 6.240549 AGTCTACCGAGATTGGATCAAATT 57.759 37.500 0.00 0.00 33.14 1.82
7029 7667 3.134574 TCCTTCGCCTTGTATTGTTGT 57.865 42.857 0.00 0.00 0.00 3.32
7030 7668 3.482436 TCCTTCGCCTTGTATTGTTGTT 58.518 40.909 0.00 0.00 0.00 2.83
7031 7669 3.252215 TCCTTCGCCTTGTATTGTTGTTG 59.748 43.478 0.00 0.00 0.00 3.33
7040 7678 6.627953 GCCTTGTATTGTTGTTGCCTATGAAT 60.628 38.462 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 0.041839 CTGCTGTTGTGAGTTGCGAC 60.042 55.000 0.00 0.00 0.00 5.19
40 41 2.906897 CAACGCCCCTGCTGTTGT 60.907 61.111 11.38 0.00 42.08 3.32
221 229 1.971695 TGCTGAGTTCGAGCTCCGA 60.972 57.895 24.21 7.86 46.94 4.55
230 238 3.112709 GCCGTCGGTGCTGAGTTC 61.113 66.667 13.94 0.00 0.00 3.01
326 356 0.042708 CGAATTGCGATGGAGCTTCG 60.043 55.000 1.88 1.88 44.57 3.79
372 402 2.343758 GACGCCACTGCTCCTTCA 59.656 61.111 0.00 0.00 34.43 3.02
846 924 3.228188 TCCCAGTCACATGCTCTTTTT 57.772 42.857 0.00 0.00 0.00 1.94
847 925 2.957402 TCCCAGTCACATGCTCTTTT 57.043 45.000 0.00 0.00 0.00 2.27
848 926 2.957402 TTCCCAGTCACATGCTCTTT 57.043 45.000 0.00 0.00 0.00 2.52
849 927 2.719739 CATTCCCAGTCACATGCTCTT 58.280 47.619 0.00 0.00 0.00 2.85
850 928 1.681166 GCATTCCCAGTCACATGCTCT 60.681 52.381 0.00 0.00 39.20 4.09
851 929 0.737219 GCATTCCCAGTCACATGCTC 59.263 55.000 0.00 0.00 39.20 4.26
923 1002 2.437180 GGAAAGTTACGGGCCGGG 60.437 66.667 31.78 3.37 0.00 5.73
1113 1192 4.069232 CCTTCCGTCTGCGCTCCA 62.069 66.667 9.73 0.00 36.67 3.86
1121 1203 3.003763 GGGGCTCACCTTCCGTCT 61.004 66.667 0.00 0.00 40.03 4.18
1315 1397 2.237392 GAGAATTGCCTCCCACTGTAGT 59.763 50.000 0.00 0.00 0.00 2.73
1394 1476 9.061435 TGAACATATATCTCTAGCCATATCTCG 57.939 37.037 0.00 0.00 0.00 4.04
1571 1660 7.931407 AGGTTGATACAGCATATGAAATACGAA 59.069 33.333 6.97 0.00 0.00 3.85
1593 1682 6.650807 CACTATACATGCCATTTATCGAGGTT 59.349 38.462 0.00 0.00 0.00 3.50
1628 1717 2.098117 GCAGGGATATTGTTGTCTGTGC 59.902 50.000 0.00 0.00 0.00 4.57
1769 1941 1.530419 ACCACAAGCGCCATGGAAA 60.530 52.632 24.47 0.00 36.94 3.13
1782 1954 4.262089 TGCCCGCACATCACCACA 62.262 61.111 0.00 0.00 0.00 4.17
1862 2034 1.359833 ACGCGGACAGTAACGTCAA 59.640 52.632 12.47 0.00 37.66 3.18
1869 2041 3.411808 GTCAATGACGCGGACAGTA 57.588 52.632 12.47 0.00 0.00 2.74
1912 2084 7.029563 CCAACAATACCTTTGTAGCTTTCATC 58.970 38.462 0.00 0.00 31.50 2.92
1935 2107 8.519799 AGAGAAAACATGAAGACTAAAAACCA 57.480 30.769 0.00 0.00 0.00 3.67
1987 2159 7.479980 CAGAAATAAGCGGATGGTAAATGAAA 58.520 34.615 0.00 0.00 0.00 2.69
1991 2163 4.278419 GGCAGAAATAAGCGGATGGTAAAT 59.722 41.667 0.00 0.00 0.00 1.40
2255 2427 7.996066 TGTGCCAGGTACAACAATATAACATAT 59.004 33.333 8.12 0.00 0.00 1.78
2262 2434 4.009675 CACTGTGCCAGGTACAACAATAT 58.990 43.478 12.00 0.00 35.51 1.28
2263 2435 3.181449 ACACTGTGCCAGGTACAACAATA 60.181 43.478 12.00 0.00 35.51 1.90
2274 2446 0.675837 CCCTGATCACACTGTGCCAG 60.676 60.000 17.54 17.54 35.45 4.85
2340 2512 5.659079 TGTAATTCCCAAACTTGAGTGGTTT 59.341 36.000 0.00 0.00 37.37 3.27
2397 2569 9.630098 CAACAAAAACTGAGCTATATTGACATT 57.370 29.630 0.00 0.00 0.00 2.71
2731 2905 6.936968 ATCTGGTTGTCTCTTTACTACCTT 57.063 37.500 8.63 0.00 43.20 3.50
2936 3122 5.406780 CCCTCTGATTCATATTACTTGTCGC 59.593 44.000 0.00 0.00 0.00 5.19
2955 3141 2.642171 TCCCATGTTGTACTCCCTCT 57.358 50.000 0.00 0.00 0.00 3.69
2988 3174 9.398538 TGGTAACGCATCTTATTTATTAAGGTT 57.601 29.630 0.00 0.00 37.73 3.50
3084 3274 9.890629 ATAGTTTCTACATGCACTATCTTCAAA 57.109 29.630 0.00 0.00 28.10 2.69
3092 3282 5.123227 GGCCAATAGTTTCTACATGCACTA 58.877 41.667 0.00 0.00 0.00 2.74
3339 3529 9.979578 GCATATATCTCATTCATAAGAGGTAGG 57.020 37.037 0.00 0.00 31.51 3.18
3350 3540 5.861727 ACTGTGCAGCATATATCTCATTCA 58.138 37.500 0.00 0.00 0.00 2.57
3539 3742 6.889301 AACAGAAGAAATCATGAGAGCAAA 57.111 33.333 0.09 0.00 0.00 3.68
3701 3906 1.362768 TTCAGATCACGCATGCTGTC 58.637 50.000 17.13 12.08 0.00 3.51
3766 3971 0.257616 TTATTTTGGGGCGGAGGGAG 59.742 55.000 0.00 0.00 0.00 4.30
3767 3972 0.257616 CTTATTTTGGGGCGGAGGGA 59.742 55.000 0.00 0.00 0.00 4.20
3768 3973 0.033503 ACTTATTTTGGGGCGGAGGG 60.034 55.000 0.00 0.00 0.00 4.30
3769 3974 1.102978 CACTTATTTTGGGGCGGAGG 58.897 55.000 0.00 0.00 0.00 4.30
3770 3975 1.743394 GACACTTATTTTGGGGCGGAG 59.257 52.381 0.00 0.00 0.00 4.63
3771 3976 1.353022 AGACACTTATTTTGGGGCGGA 59.647 47.619 0.00 0.00 0.00 5.54
3772 3977 1.743394 GAGACACTTATTTTGGGGCGG 59.257 52.381 0.00 0.00 0.00 6.13
3773 3978 2.432444 TGAGACACTTATTTTGGGGCG 58.568 47.619 0.00 0.00 0.00 6.13
3774 3979 3.367395 GCTTGAGACACTTATTTTGGGGC 60.367 47.826 0.00 0.00 0.00 5.80
3775 3980 4.082125 AGCTTGAGACACTTATTTTGGGG 58.918 43.478 0.00 0.00 0.00 4.96
3776 3981 5.712152 AAGCTTGAGACACTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
3777 3982 7.440523 ACTAAGCTTGAGACACTTATTTTGG 57.559 36.000 9.86 0.00 0.00 3.28
3778 3983 8.988934 TGTACTAAGCTTGAGACACTTATTTTG 58.011 33.333 9.86 0.00 0.00 2.44
3779 3984 9.555727 TTGTACTAAGCTTGAGACACTTATTTT 57.444 29.630 9.86 0.00 0.00 1.82
3780 3985 8.989980 GTTGTACTAAGCTTGAGACACTTATTT 58.010 33.333 9.86 0.00 0.00 1.40
3781 3986 8.368668 AGTTGTACTAAGCTTGAGACACTTATT 58.631 33.333 9.86 0.00 0.00 1.40
3782 3987 7.897864 AGTTGTACTAAGCTTGAGACACTTAT 58.102 34.615 9.86 0.00 0.00 1.73
3783 3988 7.286215 AGTTGTACTAAGCTTGAGACACTTA 57.714 36.000 9.86 0.00 0.00 2.24
3784 3989 6.163135 AGTTGTACTAAGCTTGAGACACTT 57.837 37.500 9.86 0.00 0.00 3.16
3785 3990 5.793030 AGTTGTACTAAGCTTGAGACACT 57.207 39.130 9.86 7.29 0.00 3.55
3786 3991 6.258068 ACAAAGTTGTACTAAGCTTGAGACAC 59.742 38.462 9.86 7.18 40.16 3.67
3787 3992 6.346096 ACAAAGTTGTACTAAGCTTGAGACA 58.654 36.000 9.86 7.12 40.16 3.41
3788 3993 6.846325 ACAAAGTTGTACTAAGCTTGAGAC 57.154 37.500 9.86 4.39 40.16 3.36
3801 4006 7.068348 TGCCCAAAACATTAGTACAAAGTTGTA 59.932 33.333 0.00 0.00 42.35 2.41
3802 4007 6.127310 TGCCCAAAACATTAGTACAAAGTTGT 60.127 34.615 1.75 1.75 44.86 3.32
3803 4008 6.276847 TGCCCAAAACATTAGTACAAAGTTG 58.723 36.000 0.00 0.00 0.00 3.16
3804 4009 6.472686 TGCCCAAAACATTAGTACAAAGTT 57.527 33.333 0.00 0.00 0.00 2.66
3805 4010 6.472686 TTGCCCAAAACATTAGTACAAAGT 57.527 33.333 0.00 0.00 0.00 2.66
3806 4011 6.983890 ACTTTGCCCAAAACATTAGTACAAAG 59.016 34.615 9.42 9.42 44.24 2.77
3807 4012 6.879400 ACTTTGCCCAAAACATTAGTACAAA 58.121 32.000 0.00 0.00 0.00 2.83
3808 4013 6.472686 ACTTTGCCCAAAACATTAGTACAA 57.527 33.333 0.00 0.00 0.00 2.41
3809 4014 6.096987 TCAACTTTGCCCAAAACATTAGTACA 59.903 34.615 0.00 0.00 0.00 2.90
3810 4015 6.508777 TCAACTTTGCCCAAAACATTAGTAC 58.491 36.000 0.00 0.00 0.00 2.73
3811 4016 6.547880 TCTCAACTTTGCCCAAAACATTAGTA 59.452 34.615 0.00 0.00 0.00 1.82
3812 4017 5.362430 TCTCAACTTTGCCCAAAACATTAGT 59.638 36.000 0.00 0.00 0.00 2.24
3813 4018 5.691754 GTCTCAACTTTGCCCAAAACATTAG 59.308 40.000 0.00 0.00 0.00 1.73
3814 4019 5.127845 TGTCTCAACTTTGCCCAAAACATTA 59.872 36.000 0.00 0.00 0.00 1.90
3815 4020 4.081198 TGTCTCAACTTTGCCCAAAACATT 60.081 37.500 0.00 0.00 0.00 2.71
3816 4021 3.450457 TGTCTCAACTTTGCCCAAAACAT 59.550 39.130 0.00 0.00 0.00 2.71
3817 4022 2.828520 TGTCTCAACTTTGCCCAAAACA 59.171 40.909 0.00 0.00 0.00 2.83
3818 4023 3.119137 AGTGTCTCAACTTTGCCCAAAAC 60.119 43.478 0.00 0.00 0.00 2.43
3819 4024 3.096092 AGTGTCTCAACTTTGCCCAAAA 58.904 40.909 0.00 0.00 0.00 2.44
3820 4025 2.733956 AGTGTCTCAACTTTGCCCAAA 58.266 42.857 0.00 0.00 0.00 3.28
3821 4026 2.435372 AGTGTCTCAACTTTGCCCAA 57.565 45.000 0.00 0.00 0.00 4.12
3822 4027 2.435372 AAGTGTCTCAACTTTGCCCA 57.565 45.000 0.00 0.00 37.05 5.36
3823 4028 5.453567 AAATAAGTGTCTCAACTTTGCCC 57.546 39.130 0.00 0.00 40.77 5.36
3824 4029 5.691754 CCAAAATAAGTGTCTCAACTTTGCC 59.308 40.000 0.00 0.00 40.77 4.52
3825 4030 5.691754 CCCAAAATAAGTGTCTCAACTTTGC 59.308 40.000 0.00 0.00 40.77 3.68
3826 4031 5.691754 GCCCAAAATAAGTGTCTCAACTTTG 59.308 40.000 0.00 0.00 40.77 2.77
3827 4032 5.221441 GGCCCAAAATAAGTGTCTCAACTTT 60.221 40.000 0.00 0.00 40.77 2.66
3828 4033 4.280929 GGCCCAAAATAAGTGTCTCAACTT 59.719 41.667 0.00 0.00 42.89 2.66
3829 4034 3.826729 GGCCCAAAATAAGTGTCTCAACT 59.173 43.478 0.00 0.00 0.00 3.16
3830 4035 3.365969 CGGCCCAAAATAAGTGTCTCAAC 60.366 47.826 0.00 0.00 0.00 3.18
3831 4036 2.817258 CGGCCCAAAATAAGTGTCTCAA 59.183 45.455 0.00 0.00 0.00 3.02
3832 4037 2.432444 CGGCCCAAAATAAGTGTCTCA 58.568 47.619 0.00 0.00 0.00 3.27
3833 4038 1.743394 CCGGCCCAAAATAAGTGTCTC 59.257 52.381 0.00 0.00 0.00 3.36
3834 4039 1.353022 TCCGGCCCAAAATAAGTGTCT 59.647 47.619 0.00 0.00 0.00 3.41
3835 4040 1.743394 CTCCGGCCCAAAATAAGTGTC 59.257 52.381 0.00 0.00 0.00 3.67
3836 4041 1.615919 CCTCCGGCCCAAAATAAGTGT 60.616 52.381 0.00 0.00 0.00 3.55
3837 4042 1.102978 CCTCCGGCCCAAAATAAGTG 58.897 55.000 0.00 0.00 0.00 3.16
3838 4043 0.033503 CCCTCCGGCCCAAAATAAGT 60.034 55.000 0.00 0.00 0.00 2.24
3839 4044 0.257616 TCCCTCCGGCCCAAAATAAG 59.742 55.000 0.00 0.00 0.00 1.73
3840 4045 0.257616 CTCCCTCCGGCCCAAAATAA 59.742 55.000 0.00 0.00 0.00 1.40
3841 4046 0.917333 ACTCCCTCCGGCCCAAAATA 60.917 55.000 0.00 0.00 0.00 1.40
3842 4047 0.917333 TACTCCCTCCGGCCCAAAAT 60.917 55.000 0.00 0.00 0.00 1.82
3843 4048 0.917333 ATACTCCCTCCGGCCCAAAA 60.917 55.000 0.00 0.00 0.00 2.44
3844 4049 1.307517 ATACTCCCTCCGGCCCAAA 60.308 57.895 0.00 0.00 0.00 3.28
3845 4050 1.764854 GATACTCCCTCCGGCCCAA 60.765 63.158 0.00 0.00 0.00 4.12
3846 4051 2.122989 GATACTCCCTCCGGCCCA 60.123 66.667 0.00 0.00 0.00 5.36
3847 4052 2.122989 TGATACTCCCTCCGGCCC 60.123 66.667 0.00 0.00 0.00 5.80
3848 4053 1.122019 ATGTGATACTCCCTCCGGCC 61.122 60.000 0.00 0.00 0.00 6.13
3849 4054 1.629043 TATGTGATACTCCCTCCGGC 58.371 55.000 0.00 0.00 0.00 6.13
3850 4055 3.165875 ACATATGTGATACTCCCTCCGG 58.834 50.000 7.78 0.00 0.00 5.14
3851 4056 4.082845 AGACATATGTGATACTCCCTCCG 58.917 47.826 14.43 0.00 0.00 4.63
3852 4057 6.249951 ACTAGACATATGTGATACTCCCTCC 58.750 44.000 14.43 0.00 0.00 4.30
3853 4058 7.337436 GGTACTAGACATATGTGATACTCCCTC 59.663 44.444 14.43 0.00 0.00 4.30
3854 4059 7.018751 AGGTACTAGACATATGTGATACTCCCT 59.981 40.741 14.43 7.29 36.02 4.20
3855 4060 7.176490 AGGTACTAGACATATGTGATACTCCC 58.824 42.308 14.43 5.09 36.02 4.30
3856 4061 8.638629 AAGGTACTAGACATATGTGATACTCC 57.361 38.462 14.43 8.99 38.49 3.85
3859 4064 9.790389 GCATAAGGTACTAGACATATGTGATAC 57.210 37.037 14.43 9.48 38.49 2.24
3860 4065 9.528489 TGCATAAGGTACTAGACATATGTGATA 57.472 33.333 14.43 5.20 38.49 2.15
3861 4066 8.422577 TGCATAAGGTACTAGACATATGTGAT 57.577 34.615 14.43 4.19 38.49 3.06
4385 4681 4.502016 AGATCATGCAGTTGTAGTCAGTG 58.498 43.478 0.00 0.00 0.00 3.66
4553 4849 5.452078 TTAGCAAGAACCAAATTCACCAG 57.548 39.130 0.00 0.00 40.09 4.00
4554 4850 4.261994 GCTTAGCAAGAACCAAATTCACCA 60.262 41.667 0.00 0.00 40.09 4.17
4594 4890 3.309954 GCTAAGCCAACACTAGCACATAC 59.690 47.826 0.00 0.00 34.22 2.39
4595 4891 3.197766 AGCTAAGCCAACACTAGCACATA 59.802 43.478 3.41 0.00 36.33 2.29
4678 4974 4.863131 ACAGCACTTTCGTTACTACATAGC 59.137 41.667 0.00 0.00 0.00 2.97
4682 5051 3.732219 CGAACAGCACTTTCGTTACTACA 59.268 43.478 6.28 0.00 40.77 2.74
4692 5061 3.206150 AGAATCACACGAACAGCACTTT 58.794 40.909 0.00 0.00 0.00 2.66
4736 5105 0.107456 AATAGCTGCATGGGGAGACG 59.893 55.000 1.02 0.00 33.71 4.18
4754 5123 4.444306 CGTAGCCTGGGATGGATAGAAAAA 60.444 45.833 0.00 0.00 0.00 1.94
4820 5189 3.775261 AAAAACACTAACCTAGCCCGA 57.225 42.857 0.00 0.00 0.00 5.14
4986 5358 8.335532 TGTTTAAATCTACAGGAAATCCAGTG 57.664 34.615 7.67 0.00 36.37 3.66
5144 5516 0.879765 CAGGTTTGCAGCTCCTTCTG 59.120 55.000 0.00 0.00 37.15 3.02
5392 5994 9.698309 CATGTACGATATCAGAAGGTTATTCTT 57.302 33.333 3.12 0.00 0.00 2.52
5404 6006 2.346545 CGCATGGCATGTACGATATCAG 59.653 50.000 26.94 0.00 0.00 2.90
5412 6014 2.919666 AAAGAACGCATGGCATGTAC 57.080 45.000 26.94 15.73 0.00 2.90
5436 6038 6.645700 TGTTTGAAAAGTCATTTGCAAGTC 57.354 33.333 0.00 0.00 43.36 3.01
5460 6062 8.394971 TCAGAATTTTTAGTCTGCTTGATTGA 57.605 30.769 0.00 0.00 40.93 2.57
5550 6152 8.896744 TCTTCACTTGATTATCTTATGGCAAAG 58.103 33.333 0.00 0.00 0.00 2.77
5588 6190 5.008514 CACCGCACAATGATAATATCCAACA 59.991 40.000 0.00 0.00 0.00 3.33
5621 6223 9.959775 CTTCGAAGATTAATGTAAAAGTCAGTC 57.040 33.333 20.74 0.00 35.04 3.51
5853 6455 0.321298 GGAAAACGCTACCAGCTCCA 60.321 55.000 0.00 0.00 39.60 3.86
5856 6458 1.002502 GGGGAAAACGCTACCAGCT 60.003 57.895 0.00 0.00 39.60 4.24
5882 6484 2.355108 CCGAAAGAAGCCAGATGAGGAA 60.355 50.000 0.00 0.00 0.00 3.36
6084 6686 7.498900 TGGAGCCAGTATTCAAATATGTTGTAG 59.501 37.037 0.00 0.00 0.00 2.74
6100 6702 4.353777 AGAACACTAATCTGGAGCCAGTA 58.646 43.478 15.67 4.11 43.96 2.74
6125 6727 8.837099 AGTAGCTGAGGATATTATAGCAGAAT 57.163 34.615 0.00 0.00 36.87 2.40
6155 6757 7.148171 CCCATTATCAACAGAAGAAGGAAGTTC 60.148 40.741 0.00 0.00 35.08 3.01
6160 6762 5.104360 CCTCCCATTATCAACAGAAGAAGGA 60.104 44.000 0.00 0.00 0.00 3.36
6202 6807 6.600427 TCTGCATGACATAATCAACAATCAGT 59.400 34.615 0.00 0.00 41.93 3.41
6203 6808 7.023197 TCTGCATGACATAATCAACAATCAG 57.977 36.000 0.00 0.00 41.93 2.90
6204 6809 7.393841 TTCTGCATGACATAATCAACAATCA 57.606 32.000 0.00 0.00 41.93 2.57
6205 6810 8.692110 TTTTCTGCATGACATAATCAACAATC 57.308 30.769 0.00 0.00 41.93 2.67
6206 6811 8.525316 TCTTTTCTGCATGACATAATCAACAAT 58.475 29.630 0.00 0.00 41.93 2.71
6207 6812 7.884257 TCTTTTCTGCATGACATAATCAACAA 58.116 30.769 0.00 0.00 41.93 2.83
6221 6829 8.641499 TTCGTTTTGTTTTATCTTTTCTGCAT 57.359 26.923 0.00 0.00 0.00 3.96
6244 6852 3.905784 AGTATGCAGCAGCTTTGTTTTC 58.094 40.909 0.00 0.00 42.74 2.29
6268 6876 4.283212 ACCAGAGCTTCTCCTAATATGCTC 59.717 45.833 0.00 0.00 44.85 4.26
6336 6944 8.874816 GTCTTTGTGATTGAGGTATTTAGAGAC 58.125 37.037 0.00 0.00 0.00 3.36
6365 6973 7.275779 TGCTTGAGATAGTTTCGTGTATTTCTC 59.724 37.037 0.00 0.00 0.00 2.87
6366 6974 7.063544 GTGCTTGAGATAGTTTCGTGTATTTCT 59.936 37.037 0.00 0.00 0.00 2.52
6367 6975 7.063544 AGTGCTTGAGATAGTTTCGTGTATTTC 59.936 37.037 0.00 0.00 0.00 2.17
6368 6976 6.874134 AGTGCTTGAGATAGTTTCGTGTATTT 59.126 34.615 0.00 0.00 0.00 1.40
6369 6977 6.311445 CAGTGCTTGAGATAGTTTCGTGTATT 59.689 38.462 0.00 0.00 0.00 1.89
6370 6978 5.807520 CAGTGCTTGAGATAGTTTCGTGTAT 59.192 40.000 0.00 0.00 0.00 2.29
6371 6979 5.048294 TCAGTGCTTGAGATAGTTTCGTGTA 60.048 40.000 0.00 0.00 0.00 2.90
6372 6980 3.990469 CAGTGCTTGAGATAGTTTCGTGT 59.010 43.478 0.00 0.00 0.00 4.49
6373 6981 4.237724 TCAGTGCTTGAGATAGTTTCGTG 58.762 43.478 0.00 0.00 0.00 4.35
6374 6982 4.521130 TCAGTGCTTGAGATAGTTTCGT 57.479 40.909 0.00 0.00 0.00 3.85
6375 6983 5.635280 TCTTTCAGTGCTTGAGATAGTTTCG 59.365 40.000 0.00 0.00 37.07 3.46
6429 7037 3.909995 AGCATACAAGGGATATAGGTGCA 59.090 43.478 0.00 0.00 32.82 4.57
6475 7110 5.807011 CGATGCTTGTGATATATTCGATGGA 59.193 40.000 0.00 0.00 0.00 3.41
6519 7154 7.731054 AGGATATAGGTCTTTCTTGTGTGATC 58.269 38.462 0.00 0.00 0.00 2.92
6533 7168 6.746120 TCGAGTAGCAAAAAGGATATAGGTC 58.254 40.000 0.00 0.00 0.00 3.85
6604 7239 3.129462 GGAAGTAGAAGGGAATTGCTTGC 59.871 47.826 0.00 0.00 0.00 4.01
6635 7270 3.628032 GGCTCTAACTTGGATAAACCTGC 59.372 47.826 0.00 0.00 39.86 4.85
6662 7297 2.357034 CCCGACTGTGGGTGAACG 60.357 66.667 8.09 0.00 44.76 3.95
6675 7310 4.009675 CAATGATGAAGAGAAAACCCCGA 58.990 43.478 0.00 0.00 0.00 5.14
6677 7312 4.344104 TCCAATGATGAAGAGAAAACCCC 58.656 43.478 0.00 0.00 0.00 4.95
6713 7348 1.202903 AGGAATCCAGGCTGATGATGC 60.203 52.381 17.94 9.58 0.00 3.91
6721 7356 1.306997 TTCCCGAGGAATCCAGGCT 60.307 57.895 0.61 0.00 36.71 4.58
6788 7425 3.004862 CGTGGGTAATGTTGAGGGTTAC 58.995 50.000 0.00 0.00 0.00 2.50
6845 7483 3.375299 GGGTGATGAATTCGAGTCCTTTG 59.625 47.826 0.04 0.00 0.00 2.77
6846 7484 3.610911 GGGTGATGAATTCGAGTCCTTT 58.389 45.455 0.04 0.00 0.00 3.11
6864 7502 3.402681 CCATCAGCAGGACCGGGT 61.403 66.667 6.32 0.00 0.00 5.28
6894 7532 3.133003 ACTGGATGGAGATTAGTCAACCG 59.867 47.826 0.00 0.00 0.00 4.44
7009 7647 3.134574 ACAACAATACAAGGCGAAGGA 57.865 42.857 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.