Multiple sequence alignment - TraesCS6B01G158700

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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 TraesCS6B01G158700 chr6B 100.000 6093 0 0 1 6093 161354182 161348090 0.000000e+00 11252.0
1 TraesCS6B01G158700 chr6D 92.998 2942 128 30 1 2896 84686638 84683729 0.000000e+00 4220.0
2 TraesCS6B01G158700 chr6D 95.605 1843 69 4 3113 4943 84683661 84681819 0.000000e+00 2944.0
3 TraesCS6B01G158700 chr6D 94.825 1855 78 9 3104 4943 85543874 85545725 0.000000e+00 2878.0
4 TraesCS6B01G158700 chr6D 93.333 1830 86 17 1 1812 85503841 85505652 0.000000e+00 2671.0
5 TraesCS6B01G158700 chr6D 94.801 981 41 6 1917 2896 85506130 85507101 0.000000e+00 1520.0
6 TraesCS6B01G158700 chr6D 84.899 841 72 22 5287 6093 84681505 84680686 0.000000e+00 798.0
7 TraesCS6B01G158700 chr6D 85.549 692 59 14 5434 6093 85548922 85549604 0.000000e+00 686.0
8 TraesCS6B01G158700 chr6D 83.234 167 17 7 5287 5446 85546038 85546200 6.370000e-30 143.0
9 TraesCS6B01G158700 chr6A 92.558 2217 133 17 77 2278 101933561 101931362 0.000000e+00 3151.0
10 TraesCS6B01G158700 chr6A 88.354 2224 177 43 2281 4479 101931226 101929060 0.000000e+00 2597.0
11 TraesCS6B01G158700 chr6A 86.501 726 58 13 5391 6093 101911876 101911168 0.000000e+00 761.0
12 TraesCS6B01G158700 chr6A 93.487 476 28 2 4471 4943 101912752 101912277 0.000000e+00 704.0
13 TraesCS6B01G158700 chr6A 100.000 30 0 0 27 56 101933594 101933565 8.530000e-04 56.5
14 TraesCS6B01G158700 chr5B 80.170 822 128 27 760 1574 386558786 386557993 3.170000e-162 582.0
15 TraesCS6B01G158700 chr5B 87.574 169 16 4 2346 2510 386542215 386542048 2.240000e-44 191.0
16 TraesCS6B01G158700 chr5D 81.214 692 99 26 790 1472 330719187 330719856 4.180000e-146 529.0
17 TraesCS6B01G158700 chr5A 80.664 512 78 18 2346 2848 426347306 426347805 1.600000e-100 377.0
18 TraesCS6B01G158700 chr5A 86.508 252 34 0 4248 4499 426349653 426349904 1.670000e-70 278.0
19 TraesCS6B01G158700 chr1B 80.095 422 73 8 1211 1625 588644037 588644454 2.760000e-78 303.0
20 TraesCS6B01G158700 chr1B 76.354 554 100 22 1008 1556 588321942 588321415 1.010000e-67 268.0
21 TraesCS6B01G158700 chr1B 73.950 595 112 29 3931 4497 588486772 588486193 3.720000e-47 200.0
22 TraesCS6B01G158700 chr1B 94.118 85 5 0 2871 2955 22328136 22328220 4.960000e-26 130.0
23 TraesCS6B01G158700 chr1D 75.769 553 111 20 1008 1556 435154110 435153577 2.180000e-64 257.0
24 TraesCS6B01G158700 chr1D 75.094 534 97 26 1008 1523 424453092 424453607 3.700000e-52 217.0
25 TraesCS6B01G158700 chr1D 73.613 595 114 31 3931 4497 435151211 435150632 8.060000e-44 189.0
26 TraesCS6B01G158700 chr1D 86.022 93 12 1 3930 4022 13367732 13367641 1.400000e-16 99.0
27 TraesCS6B01G158700 chr4D 85.385 130 16 3 5287 5414 209215961 209216089 1.380000e-26 132.0
28 TraesCS6B01G158700 chr7D 92.208 77 6 0 2876 2952 75938526 75938602 6.460000e-20 110.0
29 TraesCS6B01G158700 chr7A 91.250 80 7 0 2876 2955 509222450 509222371 6.460000e-20 110.0
30 TraesCS6B01G158700 chr7A 88.764 89 9 1 2871 2958 643235705 643235617 2.320000e-19 108.0
31 TraesCS6B01G158700 chr4B 82.308 130 20 3 5287 5414 312160283 312160411 6.460000e-20 110.0
32 TraesCS6B01G158700 chr7B 88.764 89 9 1 2871 2958 638921267 638921355 2.320000e-19 108.0
33 TraesCS6B01G158700 chr7B 89.412 85 8 1 2876 2959 350972764 350972680 8.350000e-19 106.0
34 TraesCS6B01G158700 chr3B 91.139 79 7 0 2877 2955 692221742 692221820 2.320000e-19 108.0
35 TraesCS6B01G158700 chr3A 89.412 85 9 0 2871 2955 401201904 401201988 2.320000e-19 108.0


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 TraesCS6B01G158700 chr6B 161348090 161354182 6092 True 11252.000000 11252 100.000000 1 6093 1 chr6B.!!$R1 6092
1 TraesCS6B01G158700 chr6D 84680686 84686638 5952 True 2654.000000 4220 91.167333 1 6093 3 chr6D.!!$R1 6092
2 TraesCS6B01G158700 chr6D 85503841 85507101 3260 False 2095.500000 2671 94.067000 1 2896 2 chr6D.!!$F1 2895
3 TraesCS6B01G158700 chr6D 85543874 85549604 5730 False 1235.666667 2878 87.869333 3104 6093 3 chr6D.!!$F2 2989
4 TraesCS6B01G158700 chr6A 101929060 101933594 4534 True 1934.833333 3151 93.637333 27 4479 3 chr6A.!!$R2 4452
5 TraesCS6B01G158700 chr6A 101911168 101912752 1584 True 732.500000 761 89.994000 4471 6093 2 chr6A.!!$R1 1622
6 TraesCS6B01G158700 chr5B 386557993 386558786 793 True 582.000000 582 80.170000 760 1574 1 chr5B.!!$R2 814
7 TraesCS6B01G158700 chr5D 330719187 330719856 669 False 529.000000 529 81.214000 790 1472 1 chr5D.!!$F1 682
8 TraesCS6B01G158700 chr5A 426347306 426349904 2598 False 327.500000 377 83.586000 2346 4499 2 chr5A.!!$F1 2153
9 TraesCS6B01G158700 chr1B 588321415 588321942 527 True 268.000000 268 76.354000 1008 1556 1 chr1B.!!$R1 548
10 TraesCS6B01G158700 chr1D 435150632 435154110 3478 True 223.000000 257 74.691000 1008 4497 2 chr1D.!!$R2 3489
11 TraesCS6B01G158700 chr1D 424453092 424453607 515 False 217.000000 217 75.094000 1008 1523 1 chr1D.!!$F1 515

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
23 24 0.382158 CCTCGCGCTGACAGAAGATA 59.618 55.000 6.65 0.00 0.00 1.98 F
56 57 1.075601 ATCAAAAGCCAGGGGACTCA 58.924 50.000 0.00 0.00 40.21 3.41 F
736 743 1.119684 TATGTCGCCCAGCATGTACT 58.880 50.000 0.00 0.00 0.00 2.73 F
2223 2880 1.080569 CAATGCCGCCGAGCTTTTT 60.081 52.632 0.00 0.00 0.00 1.94 F
3924 5181 0.746063 TGGCTCAGGCACAAAACTTG 59.254 50.000 0.00 0.00 40.87 3.16 F
4681 6140 0.838554 TGGAGGTGATCACGGGGAAA 60.839 55.000 19.33 0.47 0.00 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1113 1158 0.168788 CGGCCGAGACGTTGTAGTTA 59.831 55.0 24.07 0.00 0.00 2.24 R
1245 1290 0.683412 GGACCAGGTACTTGGACGTT 59.317 55.0 29.18 7.81 34.60 3.99 R
2515 3315 0.314935 ACGCCTGCCAGAAAAACATG 59.685 50.0 0.00 0.00 0.00 3.21 R
4100 5380 0.615331 TCTCCCTGCAGAACATGGTC 59.385 55.0 17.39 1.26 35.65 4.02 R
4928 6387 0.108804 CTACCGGTGTTGACGATGCT 60.109 55.0 19.93 0.00 0.00 3.79 R
5675 9941 0.319555 TAGAACAGACTGCACGGTGC 60.320 55.0 25.55 25.55 45.29 5.01 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
23 24 0.382158 CCTCGCGCTGACAGAAGATA 59.618 55.000 6.65 0.00 0.00 1.98
56 57 1.075601 ATCAAAAGCCAGGGGACTCA 58.924 50.000 0.00 0.00 40.21 3.41
73 74 4.201930 GGACTCATCGTACAAGGTCAGTAG 60.202 50.000 0.00 0.00 0.00 2.57
156 157 3.605664 GCCACAAAACTGCCGCCT 61.606 61.111 0.00 0.00 0.00 5.52
184 185 2.660552 CCACCACACGACCACGAC 60.661 66.667 0.00 0.00 42.66 4.34
189 190 3.533105 ACACGACCACGACTGCCA 61.533 61.111 0.00 0.00 42.66 4.92
250 254 5.394005 CCTCCAGAGTGAAACATACAGAGAG 60.394 48.000 0.00 0.00 41.43 3.20
252 256 5.954752 TCCAGAGTGAAACATACAGAGAGAT 59.045 40.000 0.00 0.00 41.43 2.75
253 257 7.119387 TCCAGAGTGAAACATACAGAGAGATA 58.881 38.462 0.00 0.00 41.43 1.98
254 258 7.615757 TCCAGAGTGAAACATACAGAGAGATAA 59.384 37.037 0.00 0.00 41.43 1.75
255 259 8.420222 CCAGAGTGAAACATACAGAGAGATAAT 58.580 37.037 0.00 0.00 41.43 1.28
302 306 1.408969 TGCTTTGGTTGGGAGGAAAC 58.591 50.000 0.00 0.00 0.00 2.78
396 400 1.717038 TTCCCTGGTTGGCCGGTTTA 61.717 55.000 1.90 0.00 39.55 2.01
471 475 4.516698 ACCAATCTGCTTACTTGTTCTGTG 59.483 41.667 0.00 0.00 0.00 3.66
506 510 4.075682 TGACCTTGACGCCAATAATTTGA 58.924 39.130 0.00 0.00 34.60 2.69
652 659 4.934001 TGCATGACTCTTTGATCTTGAGAC 59.066 41.667 14.04 9.88 0.00 3.36
726 733 2.826725 AGGCTCTACTTATATGTCGCCC 59.173 50.000 16.40 7.09 37.00 6.13
728 735 3.367498 GGCTCTACTTATATGTCGCCCAG 60.367 52.174 12.12 0.00 0.00 4.45
736 743 1.119684 TATGTCGCCCAGCATGTACT 58.880 50.000 0.00 0.00 0.00 2.73
740 747 1.539827 GTCGCCCAGCATGTACTTTTT 59.460 47.619 0.00 0.00 0.00 1.94
771 778 2.737830 CTAGCCCCTCTAAGCGCC 59.262 66.667 2.29 0.00 0.00 6.53
781 788 4.627801 TAAGCGCCGGGTGCACAA 62.628 61.111 32.04 15.32 42.00 3.33
785 792 4.690719 CGCCGGGTGCACAAGGTA 62.691 66.667 24.56 0.00 41.33 3.08
786 793 2.746277 GCCGGGTGCACAAGGTAG 60.746 66.667 24.56 7.67 40.77 3.18
787 794 2.746277 CCGGGTGCACAAGGTAGC 60.746 66.667 20.43 0.00 0.00 3.58
788 795 2.031919 CGGGTGCACAAGGTAGCA 59.968 61.111 20.43 0.00 38.65 3.49
829 850 1.469767 CGTGAACTGGAGCGATCATCA 60.470 52.381 1.84 0.00 0.00 3.07
943 973 2.093973 CGGTACTGAGCTCCAACATCTT 60.094 50.000 12.15 0.00 0.00 2.40
949 979 1.661112 GAGCTCCAACATCTTGTACGC 59.339 52.381 0.87 0.00 0.00 4.42
957 987 4.991056 CCAACATCTTGTACGCTATGCTAT 59.009 41.667 2.14 0.00 0.00 2.97
958 988 5.119279 CCAACATCTTGTACGCTATGCTATC 59.881 44.000 2.14 0.00 0.00 2.08
959 989 4.810790 ACATCTTGTACGCTATGCTATCC 58.189 43.478 2.14 0.00 0.00 2.59
960 990 4.524714 ACATCTTGTACGCTATGCTATCCT 59.475 41.667 2.14 0.00 0.00 3.24
1038 1080 2.441164 ATCGACTGCGGCCTCTCT 60.441 61.111 0.00 0.00 38.28 3.10
1440 1491 1.148273 GGTCTGCCTGGTGAACACA 59.852 57.895 7.25 0.00 0.00 3.72
1477 1528 3.423162 ATCTCGTCGCTGGAGCTGC 62.423 63.158 0.00 0.00 39.32 5.25
1829 2093 2.761767 CACATGATCCAGCCAAAATCCA 59.238 45.455 0.00 0.00 0.00 3.41
1879 2396 6.170675 ACTATGAATTGCGACTTCAAGTTC 57.829 37.500 0.00 0.00 36.30 3.01
1887 2404 2.154462 CGACTTCAAGTTCCAGCCAAT 58.846 47.619 0.00 0.00 0.00 3.16
1897 2414 3.887716 AGTTCCAGCCAATATCTTGCATC 59.112 43.478 0.00 0.00 0.00 3.91
1921 2512 4.817464 TGAGTAAGTGGTAATTTGCACGTT 59.183 37.500 0.00 0.00 0.00 3.99
2034 2652 1.377856 GCCCAACTCCTCTGCTTCC 60.378 63.158 0.00 0.00 0.00 3.46
2208 2865 3.746045 ATACTACCGCCGTTCATCAAT 57.254 42.857 0.00 0.00 0.00 2.57
2223 2880 1.080569 CAATGCCGCCGAGCTTTTT 60.081 52.632 0.00 0.00 0.00 1.94
2275 2932 2.771943 GACCCTCAGGATGGTGAATACA 59.228 50.000 0.00 0.00 34.20 2.29
2407 3207 4.273148 AGGCTAAGTACCAGTTGAACAG 57.727 45.455 0.00 0.00 0.00 3.16
2456 3256 2.344093 AGAACCTAGTGTGGGATGGT 57.656 50.000 0.00 0.00 0.00 3.55
2515 3315 3.120792 TCACAAGCGTGTAAGTCTGAAC 58.879 45.455 4.57 0.00 44.02 3.18
2572 3372 7.105588 TGTCACACAATGAGAGTTAAGCATAT 58.894 34.615 0.00 0.00 38.28 1.78
2626 3426 1.067635 AGAAACATGTCATTTGGCGGC 60.068 47.619 0.00 0.00 0.00 6.53
2644 3444 3.245797 CGGCTTGAGTGGTGATATATCG 58.754 50.000 8.19 0.00 0.00 2.92
2689 3489 4.280425 GCTATCCAGTACCTGTAAGTACCC 59.720 50.000 0.00 0.00 43.02 3.69
2690 3490 3.105959 TCCAGTACCTGTAAGTACCCC 57.894 52.381 0.00 0.00 43.02 4.95
2691 3491 2.656432 TCCAGTACCTGTAAGTACCCCT 59.344 50.000 0.00 0.00 43.02 4.79
2696 3496 6.013466 CCAGTACCTGTAAGTACCCCTTTTTA 60.013 42.308 0.00 0.00 43.02 1.52
2697 3497 7.452562 CAGTACCTGTAAGTACCCCTTTTTAA 58.547 38.462 0.00 0.00 43.02 1.52
2712 3512 9.076781 ACCCCTTTTTAAAAATCCATTTTCATG 57.923 29.630 13.55 0.00 41.42 3.07
2743 3543 3.767131 TGGCAGTACAGCTCACTATTACA 59.233 43.478 10.30 0.00 34.17 2.41
2786 3591 9.747898 TTAGGGATTTGTCACATAATAACTTGT 57.252 29.630 0.00 0.00 0.00 3.16
2896 3914 4.929781 ACCTCCGTATCGAAATGTAAGAC 58.070 43.478 0.00 0.00 0.00 3.01
2906 3924 9.962759 GTATCGAAATGTAAGACGTTTTTGTAT 57.037 29.630 0.00 0.00 37.43 2.29
2907 3925 8.874745 ATCGAAATGTAAGACGTTTTTGTATG 57.125 30.769 0.00 0.00 37.43 2.39
2908 3926 6.793203 TCGAAATGTAAGACGTTTTTGTATGC 59.207 34.615 0.00 0.00 37.43 3.14
2909 3927 6.795114 CGAAATGTAAGACGTTTTTGTATGCT 59.205 34.615 0.00 0.00 37.43 3.79
2911 3929 9.262472 GAAATGTAAGACGTTTTTGTATGCTAG 57.738 33.333 0.00 0.00 37.43 3.42
2912 3930 7.900782 ATGTAAGACGTTTTTGTATGCTAGT 57.099 32.000 0.00 0.00 0.00 2.57
2915 3933 9.258826 TGTAAGACGTTTTTGTATGCTAGTTTA 57.741 29.630 0.00 0.00 0.00 2.01
2916 3934 9.737025 GTAAGACGTTTTTGTATGCTAGTTTAG 57.263 33.333 0.00 0.00 0.00 1.85
2942 3960 9.869757 GCCTACAAAAACATCTTATATTTTGGT 57.130 29.630 12.68 3.79 43.54 3.67
2965 3983 7.834181 TGGTACGGAGGTAGTAGTATTTTAGTT 59.166 37.037 0.00 0.00 0.00 2.24
2966 3984 9.338622 GGTACGGAGGTAGTAGTATTTTAGTTA 57.661 37.037 0.00 0.00 0.00 2.24
3002 4020 2.787473 TTGATCTGGCTACAACCCTG 57.213 50.000 0.00 0.00 0.00 4.45
3025 4047 5.870433 TGCTATCCATTTTTGCAATTGACTG 59.130 36.000 10.34 0.00 0.00 3.51
3028 4050 7.009540 GCTATCCATTTTTGCAATTGACTGTAC 59.990 37.037 10.34 0.00 0.00 2.90
3029 4051 5.537188 TCCATTTTTGCAATTGACTGTACC 58.463 37.500 10.34 0.00 0.00 3.34
3041 4063 7.578571 GCAATTGACTGTACCAAAATAATCCCA 60.579 37.037 10.34 0.00 0.00 4.37
3110 4140 7.642586 GTCCTTTCAATGTTGTTAGTGTGTTAC 59.357 37.037 0.00 0.00 0.00 2.50
3141 4171 8.762426 GTTGATACTTACGACACTTTTCTTCTT 58.238 33.333 0.00 0.00 0.00 2.52
3180 4210 3.988976 TCCTTCAGAGATTTGACAGGG 57.011 47.619 0.00 0.00 31.72 4.45
3191 4221 4.762251 AGATTTGACAGGGAACAAGCTTAC 59.238 41.667 0.00 0.00 0.00 2.34
3284 4322 0.819259 TGCCTCTGCCGCCATTTATC 60.819 55.000 0.00 0.00 36.33 1.75
3292 4330 2.811431 TGCCGCCATTTATCTTATTCCG 59.189 45.455 0.00 0.00 0.00 4.30
3295 4333 4.062293 CCGCCATTTATCTTATTCCGACA 58.938 43.478 0.00 0.00 0.00 4.35
3445 4642 1.287425 GCATCCGTGGTTGTAGTAGC 58.713 55.000 0.00 0.00 0.00 3.58
3561 4788 4.081406 TCCATCTGTAACTGCAAGCAATT 58.919 39.130 0.00 0.00 37.60 2.32
3568 4795 2.736144 ACTGCAAGCAATTGTGATGG 57.264 45.000 7.40 0.00 37.60 3.51
3600 4827 8.194769 CAGTGGGTAATACTTGTTTTGTTCTTT 58.805 33.333 0.00 0.00 0.00 2.52
3635 4862 8.094798 TGAAGAACCGGCAAATATACATAATC 57.905 34.615 0.00 0.00 0.00 1.75
3924 5181 0.746063 TGGCTCAGGCACAAAACTTG 59.254 50.000 0.00 0.00 40.87 3.16
4100 5380 2.795329 AGTTCCCCAATGCTAACACTG 58.205 47.619 0.00 0.00 0.00 3.66
4508 5965 1.115467 CCCGAGTATGTCTCCTTGCT 58.885 55.000 0.00 0.00 39.84 3.91
4606 6064 0.875908 ATATGCACTGCAGGTACGCG 60.876 55.000 19.93 3.53 43.65 6.01
4643 6102 2.987149 ACTGAAAAGAGCGATGTGTACG 59.013 45.455 0.00 0.00 0.00 3.67
4681 6140 0.838554 TGGAGGTGATCACGGGGAAA 60.839 55.000 19.33 0.47 0.00 3.13
4771 6230 3.782443 GGGGACATCGAGGGCGTT 61.782 66.667 0.69 0.00 38.98 4.84
4810 6269 1.470979 GGCGACTATGATGTCAACGGT 60.471 52.381 0.00 0.00 36.82 4.83
4883 6342 4.124351 GACCGACGATGACCCGCA 62.124 66.667 0.00 0.00 0.00 5.69
4944 6439 3.027170 GCAGCATCGTCAACACCGG 62.027 63.158 0.00 0.00 0.00 5.28
4949 6444 1.153901 ATCGTCAACACCGGTAGCG 60.154 57.895 6.87 7.49 0.00 4.26
4953 6448 2.666862 CAACACCGGTAGCGCCAA 60.667 61.111 6.87 0.00 36.97 4.52
4954 6449 2.038269 CAACACCGGTAGCGCCAAT 61.038 57.895 6.87 0.00 36.97 3.16
4956 6451 3.202001 CACCGGTAGCGCCAATGG 61.202 66.667 6.87 3.95 36.97 3.16
4984 6479 6.136857 TCCCAGCTCAAGTTCTAGTATGTAT 58.863 40.000 0.00 0.00 0.00 2.29
5000 6498 2.542851 TATGCCACCAACCAGCCCA 61.543 57.895 0.00 0.00 0.00 5.36
5040 6538 2.434884 CGCAACGCTCAGGATGGT 60.435 61.111 0.00 0.00 36.16 3.55
5041 6539 1.153647 CGCAACGCTCAGGATGGTA 60.154 57.895 0.00 0.00 36.16 3.25
5055 6553 4.038162 CAGGATGGTACCTAACTCTAGCAC 59.962 50.000 14.36 0.00 38.32 4.40
5096 6594 3.200593 CAGCAGCACGATGAGGCC 61.201 66.667 0.00 0.00 30.38 5.19
5099 6597 4.147449 CAGCACGATGAGGCCGGA 62.147 66.667 5.05 0.00 0.00 5.14
5100 6598 3.157252 AGCACGATGAGGCCGGAT 61.157 61.111 5.05 0.00 0.00 4.18
5102 6600 1.373497 GCACGATGAGGCCGGATAG 60.373 63.158 5.05 0.00 0.00 2.08
5103 6601 1.290324 CACGATGAGGCCGGATAGG 59.710 63.158 5.05 0.00 44.97 2.57
5112 6610 3.719214 CCGGATAGGCTTTGTCGC 58.281 61.111 0.00 0.00 0.00 5.19
5119 6617 3.365535 GGCTTTGTCGCCCATTGT 58.634 55.556 0.00 0.00 44.41 2.71
5120 6618 2.562125 GGCTTTGTCGCCCATTGTA 58.438 52.632 0.00 0.00 44.41 2.41
5121 6619 0.451783 GGCTTTGTCGCCCATTGTAG 59.548 55.000 0.00 0.00 44.41 2.74
5122 6620 1.448985 GCTTTGTCGCCCATTGTAGA 58.551 50.000 0.00 0.00 0.00 2.59
5146 6644 1.106351 TGCCTTTGTGCATCAACGGT 61.106 50.000 18.70 0.00 44.24 4.83
5147 6645 0.878416 GCCTTTGTGCATCAACGGTA 59.122 50.000 18.70 1.03 44.24 4.02
5148 6646 1.472480 GCCTTTGTGCATCAACGGTAT 59.528 47.619 18.70 0.00 44.24 2.73
5160 6658 1.396996 CAACGGTATTCGGAGGCTTTG 59.603 52.381 0.00 0.00 44.45 2.77
5171 6669 4.448210 TCGGAGGCTTTGATTATGTAACC 58.552 43.478 0.00 0.00 0.00 2.85
5172 6670 4.163458 TCGGAGGCTTTGATTATGTAACCT 59.837 41.667 0.00 0.00 0.00 3.50
5173 6671 4.881850 CGGAGGCTTTGATTATGTAACCTT 59.118 41.667 0.00 0.00 0.00 3.50
5229 6727 2.629051 GGTACCCAACTGATGTGTAGC 58.371 52.381 0.00 0.00 0.00 3.58
5230 6728 2.236395 GGTACCCAACTGATGTGTAGCT 59.764 50.000 0.00 0.00 0.00 3.32
5231 6729 2.479566 ACCCAACTGATGTGTAGCTG 57.520 50.000 0.00 0.00 0.00 4.24
5232 6730 1.699634 ACCCAACTGATGTGTAGCTGT 59.300 47.619 0.00 0.00 0.00 4.40
5233 6731 2.106511 ACCCAACTGATGTGTAGCTGTT 59.893 45.455 0.00 0.00 35.20 3.16
5234 6732 3.149196 CCCAACTGATGTGTAGCTGTTT 58.851 45.455 0.00 0.00 33.01 2.83
5235 6733 3.058016 CCCAACTGATGTGTAGCTGTTTG 60.058 47.826 0.00 0.00 33.01 2.93
5236 6734 3.565482 CCAACTGATGTGTAGCTGTTTGT 59.435 43.478 0.00 0.00 33.01 2.83
5237 6735 4.754618 CCAACTGATGTGTAGCTGTTTGTA 59.245 41.667 0.00 0.00 33.01 2.41
5238 6736 5.106948 CCAACTGATGTGTAGCTGTTTGTAG 60.107 44.000 0.00 0.00 33.01 2.74
5239 6737 3.997021 ACTGATGTGTAGCTGTTTGTAGC 59.003 43.478 0.00 0.00 44.01 3.58
5251 6749 6.502195 GCTGTTTGTAGCTCTTTTTCTTTG 57.498 37.500 0.00 0.00 40.52 2.77
5252 6750 6.036470 GCTGTTTGTAGCTCTTTTTCTTTGT 58.964 36.000 0.00 0.00 40.52 2.83
5253 6751 6.020360 GCTGTTTGTAGCTCTTTTTCTTTGTG 60.020 38.462 0.00 0.00 40.52 3.33
5254 6752 5.804979 TGTTTGTAGCTCTTTTTCTTTGTGC 59.195 36.000 0.00 0.00 0.00 4.57
5255 6753 5.835113 TTGTAGCTCTTTTTCTTTGTGCT 57.165 34.783 0.00 0.00 35.26 4.40
5256 6754 5.173774 TGTAGCTCTTTTTCTTTGTGCTG 57.826 39.130 0.00 0.00 33.49 4.41
5257 6755 4.640201 TGTAGCTCTTTTTCTTTGTGCTGT 59.360 37.500 0.00 0.00 33.49 4.40
5258 6756 4.298744 AGCTCTTTTTCTTTGTGCTGTC 57.701 40.909 0.00 0.00 0.00 3.51
5259 6757 3.038710 GCTCTTTTTCTTTGTGCTGTCG 58.961 45.455 0.00 0.00 0.00 4.35
5260 6758 3.487544 GCTCTTTTTCTTTGTGCTGTCGT 60.488 43.478 0.00 0.00 0.00 4.34
5261 6759 4.273005 TCTTTTTCTTTGTGCTGTCGTC 57.727 40.909 0.00 0.00 0.00 4.20
5262 6760 3.687212 TCTTTTTCTTTGTGCTGTCGTCA 59.313 39.130 0.00 0.00 0.00 4.35
5263 6761 3.398954 TTTTCTTTGTGCTGTCGTCAC 57.601 42.857 0.00 0.00 35.14 3.67
5264 6762 2.309528 TTCTTTGTGCTGTCGTCACT 57.690 45.000 0.00 0.00 35.58 3.41
5265 6763 2.309528 TCTTTGTGCTGTCGTCACTT 57.690 45.000 0.00 0.00 35.58 3.16
5266 6764 1.933181 TCTTTGTGCTGTCGTCACTTG 59.067 47.619 0.00 0.00 35.58 3.16
5267 6765 1.933181 CTTTGTGCTGTCGTCACTTGA 59.067 47.619 0.00 0.00 35.58 3.02
5268 6766 1.570813 TTGTGCTGTCGTCACTTGAG 58.429 50.000 0.00 0.00 35.58 3.02
5269 6767 0.744281 TGTGCTGTCGTCACTTGAGA 59.256 50.000 0.00 0.00 35.58 3.27
5270 6768 1.132588 GTGCTGTCGTCACTTGAGAC 58.867 55.000 0.00 0.00 35.61 3.36
5271 6769 0.744281 TGCTGTCGTCACTTGAGACA 59.256 50.000 9.63 9.63 41.90 3.41
5274 6772 2.492019 TGTCGTCACTTGAGACAGTG 57.508 50.000 7.17 0.00 44.96 3.66
5275 6773 1.749063 TGTCGTCACTTGAGACAGTGT 59.251 47.619 0.00 0.00 44.10 3.55
5276 6774 2.946990 TGTCGTCACTTGAGACAGTGTA 59.053 45.455 0.00 0.00 44.10 2.90
5277 6775 3.379057 TGTCGTCACTTGAGACAGTGTAA 59.621 43.478 0.00 0.00 44.10 2.41
5278 6776 3.975670 GTCGTCACTTGAGACAGTGTAAG 59.024 47.826 0.00 0.00 44.10 2.34
5279 6777 2.726760 CGTCACTTGAGACAGTGTAAGC 59.273 50.000 0.00 0.00 44.10 3.09
5280 6778 3.717707 GTCACTTGAGACAGTGTAAGCA 58.282 45.455 0.00 0.00 44.10 3.91
5281 6779 4.310769 GTCACTTGAGACAGTGTAAGCAT 58.689 43.478 0.00 0.00 44.10 3.79
5282 6780 4.387256 GTCACTTGAGACAGTGTAAGCATC 59.613 45.833 0.00 0.00 44.10 3.91
5283 6781 3.366121 CACTTGAGACAGTGTAAGCATCG 59.634 47.826 0.00 0.00 39.59 3.84
5285 6783 3.660501 TGAGACAGTGTAAGCATCGTT 57.339 42.857 0.00 0.00 0.00 3.85
5294 6792 6.649141 ACAGTGTAAGCATCGTTATTTTCTCA 59.351 34.615 0.00 0.00 0.00 3.27
5302 6800 7.029563 AGCATCGTTATTTTCTCAATTCCAAC 58.970 34.615 0.00 0.00 0.00 3.77
5321 6820 1.078759 CTCTACTGAGTTTGCCGGCG 61.079 60.000 23.90 7.94 35.67 6.46
5322 6821 2.047655 TACTGAGTTTGCCGGCGG 60.048 61.111 24.35 24.35 0.00 6.13
5323 6822 2.501223 CTACTGAGTTTGCCGGCGGA 62.501 60.000 33.44 12.50 0.00 5.54
5324 6823 2.102109 TACTGAGTTTGCCGGCGGAA 62.102 55.000 33.44 19.61 0.00 4.30
5326 6825 3.431725 GAGTTTGCCGGCGGAAGG 61.432 66.667 33.44 2.59 0.00 3.46
5332 6831 3.777910 GCCGGCGGAAGGTTCCTA 61.778 66.667 33.44 0.00 45.33 2.94
5334 6833 2.186125 CGGCGGAAGGTTCCTACC 59.814 66.667 0.00 7.28 45.33 3.18
5355 6854 4.124351 TAGCGACCGGCCAACTCG 62.124 66.667 0.00 3.73 45.17 4.18
5368 6867 0.806868 CAACTCGTGCCGTCCTACTA 59.193 55.000 0.00 0.00 0.00 1.82
5369 6868 0.807496 AACTCGTGCCGTCCTACTAC 59.193 55.000 0.00 0.00 0.00 2.73
5377 6876 1.640604 CGTCCTACTACGGTCGCTC 59.359 63.158 0.00 0.00 39.19 5.03
5399 6901 2.626840 CTTCACTGCTTCTTCCTAGCC 58.373 52.381 0.00 0.00 37.85 3.93
5402 6904 2.111384 CACTGCTTCTTCCTAGCCCTA 58.889 52.381 0.00 0.00 37.85 3.53
5446 9685 3.773667 TGGATGCTCATGAGTCTTCTTCT 59.226 43.478 23.38 0.63 0.00 2.85
5452 9691 4.562347 GCTCATGAGTCTTCTTCTGGTTCA 60.562 45.833 23.38 0.00 0.00 3.18
5453 9692 5.545588 CTCATGAGTCTTCTTCTGGTTCAA 58.454 41.667 14.95 0.00 0.00 2.69
5455 9694 6.356556 TCATGAGTCTTCTTCTGGTTCAAAA 58.643 36.000 0.00 0.00 0.00 2.44
5461 9702 5.299279 GTCTTCTTCTGGTTCAAAATGTGGA 59.701 40.000 0.00 0.00 0.00 4.02
5462 9703 5.532406 TCTTCTTCTGGTTCAAAATGTGGAG 59.468 40.000 0.00 0.00 0.00 3.86
5468 9709 3.450457 TGGTTCAAAATGTGGAGTTTGCT 59.550 39.130 0.00 0.00 37.13 3.91
5475 9720 4.674306 TGGAGTTTGCTGCCACAA 57.326 50.000 0.00 0.00 31.52 3.33
5486 9731 2.126888 GCCACAATGGTCGTTGCG 60.127 61.111 3.10 0.00 40.46 4.85
5495 9740 4.373116 GTCGTTGCGGCCCTCTGA 62.373 66.667 0.00 0.00 0.00 3.27
5496 9741 3.390521 TCGTTGCGGCCCTCTGAT 61.391 61.111 0.00 0.00 0.00 2.90
5497 9742 2.892425 CGTTGCGGCCCTCTGATC 60.892 66.667 0.00 0.00 0.00 2.92
5501 9748 3.157252 GCGGCCCTCTGATCTCCA 61.157 66.667 0.00 0.00 0.00 3.86
5503 9750 2.049627 GCGGCCCTCTGATCTCCAAT 62.050 60.000 0.00 0.00 0.00 3.16
5510 9757 4.577875 CCCTCTGATCTCCAATAAGATGC 58.422 47.826 0.00 0.00 36.13 3.91
5512 9759 3.657634 TCTGATCTCCAATAAGATGCGC 58.342 45.455 0.00 0.00 36.13 6.09
5528 9775 1.498865 GCGCCATTCGTACTGATGGG 61.499 60.000 19.81 13.40 41.07 4.00
5529 9776 1.498865 CGCCATTCGTACTGATGGGC 61.499 60.000 19.81 16.91 40.78 5.36
5530 9777 0.463654 GCCATTCGTACTGATGGGCA 60.464 55.000 19.81 0.00 42.63 5.36
5675 9941 1.531149 CGGCATAGAATTAAGGGTGCG 59.469 52.381 0.00 0.00 33.62 5.34
5695 9962 1.872237 GCACCGTGCAGTCTGTTCTAA 60.872 52.381 18.79 0.00 44.26 2.10
5696 9963 2.688507 CACCGTGCAGTCTGTTCTAAT 58.311 47.619 0.93 0.00 0.00 1.73
5697 9964 3.067106 CACCGTGCAGTCTGTTCTAATT 58.933 45.455 0.93 0.00 0.00 1.40
5699 9966 3.498397 ACCGTGCAGTCTGTTCTAATTTG 59.502 43.478 0.93 0.00 0.00 2.32
5700 9967 3.482786 CGTGCAGTCTGTTCTAATTTGC 58.517 45.455 0.93 0.00 0.00 3.68
5702 9969 4.470462 GTGCAGTCTGTTCTAATTTGCTG 58.530 43.478 0.93 0.00 0.00 4.41
5703 9970 3.058016 TGCAGTCTGTTCTAATTTGCTGC 60.058 43.478 0.93 0.00 45.58 5.25
5704 9971 3.671702 GCAGTCTGTTCTAATTTGCTGCC 60.672 47.826 0.93 0.00 41.29 4.85
5705 9972 2.744202 AGTCTGTTCTAATTTGCTGCCG 59.256 45.455 0.00 0.00 0.00 5.69
5706 9973 2.083774 TCTGTTCTAATTTGCTGCCGG 58.916 47.619 0.00 0.00 0.00 6.13
5707 9974 0.525761 TGTTCTAATTTGCTGCCGGC 59.474 50.000 22.73 22.73 42.22 6.13
5708 9975 0.523335 GTTCTAATTTGCTGCCGGCG 60.523 55.000 23.90 17.75 45.43 6.46
5709 9976 1.653094 TTCTAATTTGCTGCCGGCGG 61.653 55.000 31.57 31.57 45.43 6.13
5738 10005 4.373116 GGAACGGCGGAGACTGCA 62.373 66.667 13.24 0.00 0.00 4.41
5820 10087 0.035458 GACGGGGATTCTGGCATAGG 59.965 60.000 0.00 0.00 0.00 2.57
5879 10146 1.143183 GCGCCTTCCGAGTAATGGA 59.857 57.895 0.00 0.00 40.02 3.41
5889 10157 4.517815 GTAATGGACGCGGCGGGA 62.518 66.667 31.03 8.78 0.00 5.14
5971 10239 4.759205 AGCCCATTTGACCCCCGC 62.759 66.667 0.00 0.00 0.00 6.13
6011 10279 3.057337 CCAACGTCGAGTCCCCTT 58.943 61.111 0.00 0.00 0.00 3.95
6063 10343 4.373116 GCCGGACAGGAGCGACAA 62.373 66.667 5.05 0.00 45.00 3.18
6067 10348 1.374758 GGACAGGAGCGACAACAGG 60.375 63.158 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.850377 CTGGCTATCTTCTGTCAGCG 58.150 55.000 0.00 0.00 34.80 5.18
23 24 0.251474 TTTGATGGCTTGAGCTGGCT 60.251 50.000 0.00 0.00 41.70 4.75
90 91 0.250338 GGCAGTGGATCCGTATTCCC 60.250 60.000 7.39 0.00 31.87 3.97
96 97 4.082523 CACCGGCAGTGGATCCGT 62.083 66.667 7.39 0.00 43.26 4.69
140 141 1.856265 GAGAGGCGGCAGTTTTGTGG 61.856 60.000 13.08 0.00 0.00 4.17
156 157 3.311110 GTGGTGGAGGCGGTGAGA 61.311 66.667 0.00 0.00 0.00 3.27
169 170 2.415843 CAGTCGTGGTCGTGTGGT 59.584 61.111 0.00 0.00 38.33 4.16
176 177 1.227556 AACAGTGGCAGTCGTGGTC 60.228 57.895 0.00 0.00 0.00 4.02
184 185 1.364626 GCGGAGATCAACAGTGGCAG 61.365 60.000 0.00 0.00 0.00 4.85
250 254 9.922305 GAAGCACACAAGTCTACAATAATTATC 57.078 33.333 0.00 0.00 0.00 1.75
252 256 8.840833 TGAAGCACACAAGTCTACAATAATTA 57.159 30.769 0.00 0.00 0.00 1.40
253 257 7.744087 TGAAGCACACAAGTCTACAATAATT 57.256 32.000 0.00 0.00 0.00 1.40
254 258 7.607607 TCATGAAGCACACAAGTCTACAATAAT 59.392 33.333 0.00 0.00 0.00 1.28
255 259 6.934083 TCATGAAGCACACAAGTCTACAATAA 59.066 34.615 0.00 0.00 0.00 1.40
257 261 5.308014 TCATGAAGCACACAAGTCTACAAT 58.692 37.500 0.00 0.00 0.00 2.71
260 264 4.310769 ACTCATGAAGCACACAAGTCTAC 58.689 43.478 0.00 0.00 0.00 2.59
302 306 3.066342 CACACCGTACCAGGTATACTCTG 59.934 52.174 1.54 12.08 43.89 3.35
396 400 6.985188 AACACGTAATGTAATGCTCAAGAT 57.015 33.333 0.00 0.00 42.31 2.40
740 747 2.770232 GGGGCTAGCTAACTAGGACAAA 59.230 50.000 15.72 0.00 45.25 2.83
771 778 2.031919 TGCTACCTTGTGCACCCG 59.968 61.111 15.69 4.86 33.94 5.28
922 946 1.478510 AGATGTTGGAGCTCAGTACCG 59.521 52.381 17.19 0.00 0.00 4.02
957 987 2.302199 CTGCCTGCATGCGAGTAGGA 62.302 60.000 22.47 9.08 43.25 2.94
958 988 1.886313 CTGCCTGCATGCGAGTAGG 60.886 63.158 15.72 15.72 43.41 3.18
959 989 1.886313 CCTGCCTGCATGCGAGTAG 60.886 63.158 14.09 14.72 0.00 2.57
960 990 2.187685 CCTGCCTGCATGCGAGTA 59.812 61.111 14.09 5.27 0.00 2.59
1038 1080 1.213799 CACGTAGCTGCTCTGCTCA 59.786 57.895 4.91 0.00 42.97 4.26
1103 1148 0.461516 GTTGTAGTTAGAGCCGGGGC 60.462 60.000 2.18 0.18 42.33 5.80
1105 1150 0.529378 ACGTTGTAGTTAGAGCCGGG 59.471 55.000 2.18 0.00 0.00 5.73
1113 1158 0.168788 CGGCCGAGACGTTGTAGTTA 59.831 55.000 24.07 0.00 0.00 2.24
1245 1290 0.683412 GGACCAGGTACTTGGACGTT 59.317 55.000 29.18 7.81 34.60 3.99
1386 1437 2.750637 ACGACGGCGATGACCTCT 60.751 61.111 22.49 0.00 41.64 3.69
1477 1528 4.760047 CGTGTCCTTGAGGGGCCG 62.760 72.222 0.00 0.00 39.39 6.13
1598 1809 1.765255 TTGGTGTACGGGACCCACA 60.765 57.895 12.15 5.35 30.67 4.17
1829 2093 7.721286 GCTGTGAAGTACTGCTAATATGAAT 57.279 36.000 1.64 0.00 46.92 2.57
1879 2396 3.483421 TCAGATGCAAGATATTGGCTGG 58.517 45.455 1.67 0.00 0.00 4.85
1887 2404 5.939764 ACCACTTACTCAGATGCAAGATA 57.060 39.130 0.00 0.00 0.00 1.98
1897 2414 4.451096 ACGTGCAAATTACCACTTACTCAG 59.549 41.667 0.00 0.00 0.00 3.35
1921 2512 2.679092 CAGGAGCCTGCAATGGGA 59.321 61.111 3.18 0.00 37.24 4.37
2034 2652 1.134699 TCAAAGTCGCCTATGAGCCAG 60.135 52.381 0.00 0.00 0.00 4.85
2208 2865 2.329614 GGTAAAAAGCTCGGCGGCA 61.330 57.895 19.61 0.00 34.17 5.69
2223 2880 1.688269 CGGCGGTGGAAATAGGGGTA 61.688 60.000 0.00 0.00 0.00 3.69
2305 3098 5.178061 CAAGTTAGTCAGACCATGTGCATA 58.822 41.667 0.00 0.00 0.00 3.14
2316 3109 2.526304 AACAGCGCAAGTTAGTCAGA 57.474 45.000 11.47 0.00 41.68 3.27
2407 3207 2.434774 GGTCACCCACCCAGTTCC 59.565 66.667 0.00 0.00 39.69 3.62
2456 3256 4.809193 AGATGGGATAGCTACAGTTCAGA 58.191 43.478 0.00 0.00 0.00 3.27
2515 3315 0.314935 ACGCCTGCCAGAAAAACATG 59.685 50.000 0.00 0.00 0.00 3.21
2572 3372 5.696270 CACAGTAGTTCAGACAGCACATTTA 59.304 40.000 0.00 0.00 0.00 1.40
2626 3426 7.821652 AGTATGACGATATATCACCACTCAAG 58.178 38.462 13.11 0.00 0.00 3.02
2644 3444 4.494855 GCTTTGAGATTGGCGAAGTATGAC 60.495 45.833 0.00 0.00 0.00 3.06
2711 3511 4.081406 AGCTGTACTGCCAAAATTCATCA 58.919 39.130 19.81 0.00 0.00 3.07
2712 3512 4.156556 TGAGCTGTACTGCCAAAATTCATC 59.843 41.667 19.81 9.00 0.00 2.92
2885 3761 9.262472 CTAGCATACAAAAACGTCTTACATTTC 57.738 33.333 0.00 0.00 0.00 2.17
2916 3934 9.869757 ACCAAAATATAAGATGTTTTTGTAGGC 57.130 29.630 0.00 0.00 37.36 3.93
2920 3938 9.849166 CCGTACCAAAATATAAGATGTTTTTGT 57.151 29.630 0.00 4.41 37.36 2.83
2928 3946 8.488308 ACTACCTCCGTACCAAAATATAAGAT 57.512 34.615 0.00 0.00 0.00 2.40
2930 3948 8.854117 ACTACTACCTCCGTACCAAAATATAAG 58.146 37.037 0.00 0.00 0.00 1.73
2943 3961 8.854117 CCATAACTAAAATACTACTACCTCCGT 58.146 37.037 0.00 0.00 0.00 4.69
2966 3984 9.240734 GCCAGATCAATCTTAATATTCTTCCAT 57.759 33.333 0.00 0.00 34.22 3.41
2988 4006 1.202698 GGATAGCAGGGTTGTAGCCAG 60.203 57.143 0.00 0.00 38.48 4.85
3002 4020 5.870978 ACAGTCAATTGCAAAAATGGATAGC 59.129 36.000 1.71 0.00 0.00 2.97
3110 4140 9.953825 GAAAAGTGTCGTAAGTATCAACAATAG 57.046 33.333 0.00 0.00 39.48 1.73
3141 4171 6.378564 TGAAGGAACCAAACAGTTTTGACATA 59.621 34.615 4.15 0.00 44.38 2.29
3180 4210 4.959149 GAATCGTTCCAGTAAGCTTGTTC 58.041 43.478 9.86 0.00 0.00 3.18
3205 4235 2.802787 ATTCGTATCAGAAGGCCGAG 57.197 50.000 0.00 0.00 33.19 4.63
3284 4322 3.489785 GCGATTAGTGGTGTCGGAATAAG 59.510 47.826 0.00 0.00 36.00 1.73
3292 4330 2.166664 AGAGGAAGCGATTAGTGGTGTC 59.833 50.000 0.00 0.00 0.00 3.67
3295 4333 3.983044 AAAGAGGAAGCGATTAGTGGT 57.017 42.857 0.00 0.00 0.00 4.16
3461 4658 9.659830 TGTTTTCTTCTTATTACGAAAAAGAGC 57.340 29.630 0.00 0.00 37.18 4.09
3561 4788 1.228215 CCACTGTGGCACCATCACA 60.228 57.895 14.87 0.00 42.11 3.58
3568 4795 2.747446 CAAGTATTACCCACTGTGGCAC 59.253 50.000 21.47 11.55 35.79 5.01
3600 4827 5.029807 TGCCGGTTCTTCATATGACAATA 57.970 39.130 4.48 0.00 0.00 1.90
3635 4862 1.354040 GATTGCACGTCACTCTCCTG 58.646 55.000 0.00 0.00 0.00 3.86
3924 5181 3.634397 TTCCTGTGATGAATCCCTGTC 57.366 47.619 0.00 0.00 0.00 3.51
4100 5380 0.615331 TCTCCCTGCAGAACATGGTC 59.385 55.000 17.39 1.26 35.65 4.02
4282 5723 0.589708 CCTGCATGCACATCATACCG 59.410 55.000 18.46 3.31 33.19 4.02
4540 5998 0.859374 CAGTCGTCTCAGTCGCATCG 60.859 60.000 0.00 0.00 0.00 3.84
4606 6064 2.717390 TCAGTGAGCTCTAGGACTGTC 58.283 52.381 23.69 0.00 37.63 3.51
4643 6102 1.299089 GCAACACGACACCAAAGCC 60.299 57.895 0.00 0.00 0.00 4.35
4681 6140 0.953960 GGATTTGCACGAACGGAGGT 60.954 55.000 0.00 0.00 0.00 3.85
4708 6167 5.185635 CCACTTGACAATATGAATGGGTTGT 59.814 40.000 1.99 0.00 37.49 3.32
4810 6269 3.228017 TCGGCGACCTTCCACACA 61.228 61.111 4.99 0.00 0.00 3.72
4928 6387 0.108804 CTACCGGTGTTGACGATGCT 60.109 55.000 19.93 0.00 0.00 3.79
4944 6439 1.166531 GGGATCACCATTGGCGCTAC 61.167 60.000 7.64 0.00 39.85 3.58
4956 6451 2.777832 AGAACTTGAGCTGGGATCAC 57.222 50.000 0.00 0.00 0.00 3.06
4984 6479 4.912395 GTGGGCTGGTTGGTGGCA 62.912 66.667 0.00 0.00 0.00 4.92
5000 6498 1.305297 TCTGGGCGACATCAGAGGT 60.305 57.895 0.00 0.00 35.37 3.85
5027 6525 1.755380 GTTAGGTACCATCCTGAGCGT 59.245 52.381 15.94 0.00 38.41 5.07
5040 6538 1.019673 CGCCGTGCTAGAGTTAGGTA 58.980 55.000 0.00 0.00 0.00 3.08
5041 6539 0.964358 ACGCCGTGCTAGAGTTAGGT 60.964 55.000 0.00 0.00 0.00 3.08
5080 6578 4.827087 CGGCCTCATCGTGCTGCT 62.827 66.667 0.00 0.00 0.00 4.24
5103 6601 1.130561 GTCTACAATGGGCGACAAAGC 59.869 52.381 0.00 0.00 0.00 3.51
5112 6610 0.552848 AGGCATGGGTCTACAATGGG 59.447 55.000 0.00 0.00 0.00 4.00
5113 6611 2.428171 CAAAGGCATGGGTCTACAATGG 59.572 50.000 0.00 0.00 0.00 3.16
5114 6612 3.091545 ACAAAGGCATGGGTCTACAATG 58.908 45.455 0.00 0.00 0.00 2.82
5115 6613 3.091545 CACAAAGGCATGGGTCTACAAT 58.908 45.455 0.00 0.00 0.00 2.71
5116 6614 2.513753 CACAAAGGCATGGGTCTACAA 58.486 47.619 0.00 0.00 0.00 2.41
5117 6615 1.886222 GCACAAAGGCATGGGTCTACA 60.886 52.381 0.00 0.00 0.00 2.74
5118 6616 0.811281 GCACAAAGGCATGGGTCTAC 59.189 55.000 0.00 0.00 0.00 2.59
5119 6617 0.403655 TGCACAAAGGCATGGGTCTA 59.596 50.000 0.00 0.00 39.25 2.59
5120 6618 1.153524 TGCACAAAGGCATGGGTCT 59.846 52.632 0.00 0.00 39.25 3.85
5121 6619 3.776158 TGCACAAAGGCATGGGTC 58.224 55.556 0.00 0.00 39.25 4.46
5143 6641 2.240493 ATCAAAGCCTCCGAATACCG 57.760 50.000 0.00 0.00 38.18 4.02
5144 6642 5.063880 ACATAATCAAAGCCTCCGAATACC 58.936 41.667 0.00 0.00 0.00 2.73
5146 6644 6.708949 GGTTACATAATCAAAGCCTCCGAATA 59.291 38.462 0.00 0.00 0.00 1.75
5147 6645 5.531287 GGTTACATAATCAAAGCCTCCGAAT 59.469 40.000 0.00 0.00 0.00 3.34
5148 6646 4.879545 GGTTACATAATCAAAGCCTCCGAA 59.120 41.667 0.00 0.00 0.00 4.30
5171 6669 8.677300 TGATCAATCCCTCGAAAATAGAAAAAG 58.323 33.333 0.00 0.00 0.00 2.27
5172 6670 8.574251 TGATCAATCCCTCGAAAATAGAAAAA 57.426 30.769 0.00 0.00 0.00 1.94
5173 6671 8.623903 CATGATCAATCCCTCGAAAATAGAAAA 58.376 33.333 0.00 0.00 0.00 2.29
5184 6682 3.198409 TGTTCCATGATCAATCCCTCG 57.802 47.619 0.00 0.00 0.00 4.63
5210 6708 3.262420 CAGCTACACATCAGTTGGGTAC 58.738 50.000 0.00 0.00 41.33 3.34
5211 6709 2.903784 ACAGCTACACATCAGTTGGGTA 59.096 45.455 0.00 0.00 41.33 3.69
5212 6710 1.699634 ACAGCTACACATCAGTTGGGT 59.300 47.619 0.00 0.00 46.23 4.51
5213 6711 2.479566 ACAGCTACACATCAGTTGGG 57.520 50.000 0.00 0.00 33.70 4.12
5214 6712 3.565482 ACAAACAGCTACACATCAGTTGG 59.435 43.478 0.00 0.00 0.00 3.77
5215 6713 4.818534 ACAAACAGCTACACATCAGTTG 57.181 40.909 0.00 0.00 0.00 3.16
5216 6714 4.452455 GCTACAAACAGCTACACATCAGTT 59.548 41.667 0.00 0.00 38.57 3.16
5217 6715 3.997021 GCTACAAACAGCTACACATCAGT 59.003 43.478 0.00 0.00 38.57 3.41
5218 6716 4.590400 GCTACAAACAGCTACACATCAG 57.410 45.455 0.00 0.00 38.57 2.90
5228 6726 6.020360 CACAAAGAAAAAGAGCTACAAACAGC 60.020 38.462 0.00 0.00 42.12 4.40
5229 6727 6.020360 GCACAAAGAAAAAGAGCTACAAACAG 60.020 38.462 0.00 0.00 0.00 3.16
5230 6728 5.804979 GCACAAAGAAAAAGAGCTACAAACA 59.195 36.000 0.00 0.00 0.00 2.83
5231 6729 6.020360 CAGCACAAAGAAAAAGAGCTACAAAC 60.020 38.462 0.00 0.00 0.00 2.93
5232 6730 6.035843 CAGCACAAAGAAAAAGAGCTACAAA 58.964 36.000 0.00 0.00 0.00 2.83
5233 6731 5.125417 ACAGCACAAAGAAAAAGAGCTACAA 59.875 36.000 0.00 0.00 0.00 2.41
5234 6732 4.640201 ACAGCACAAAGAAAAAGAGCTACA 59.360 37.500 0.00 0.00 0.00 2.74
5235 6733 5.175090 ACAGCACAAAGAAAAAGAGCTAC 57.825 39.130 0.00 0.00 0.00 3.58
5236 6734 4.024893 CGACAGCACAAAGAAAAAGAGCTA 60.025 41.667 0.00 0.00 0.00 3.32
5237 6735 3.242870 CGACAGCACAAAGAAAAAGAGCT 60.243 43.478 0.00 0.00 0.00 4.09
5238 6736 3.038710 CGACAGCACAAAGAAAAAGAGC 58.961 45.455 0.00 0.00 0.00 4.09
5239 6737 4.201812 TGACGACAGCACAAAGAAAAAGAG 60.202 41.667 0.00 0.00 0.00 2.85
5240 6738 3.687212 TGACGACAGCACAAAGAAAAAGA 59.313 39.130 0.00 0.00 0.00 2.52
5241 6739 3.786048 GTGACGACAGCACAAAGAAAAAG 59.214 43.478 0.00 0.00 36.31 2.27
5242 6740 3.438781 AGTGACGACAGCACAAAGAAAAA 59.561 39.130 0.00 0.00 38.70 1.94
5243 6741 3.006940 AGTGACGACAGCACAAAGAAAA 58.993 40.909 0.00 0.00 38.70 2.29
5244 6742 2.627945 AGTGACGACAGCACAAAGAAA 58.372 42.857 0.00 0.00 38.70 2.52
5245 6743 2.309528 AGTGACGACAGCACAAAGAA 57.690 45.000 0.00 0.00 38.70 2.52
5246 6744 1.933181 CAAGTGACGACAGCACAAAGA 59.067 47.619 0.00 0.00 38.70 2.52
5247 6745 1.933181 TCAAGTGACGACAGCACAAAG 59.067 47.619 0.00 0.00 38.70 2.77
5248 6746 1.933181 CTCAAGTGACGACAGCACAAA 59.067 47.619 0.00 0.00 38.70 2.83
5249 6747 1.136110 TCTCAAGTGACGACAGCACAA 59.864 47.619 0.00 0.00 38.70 3.33
5250 6748 0.744281 TCTCAAGTGACGACAGCACA 59.256 50.000 0.00 0.00 38.70 4.57
5251 6749 1.132588 GTCTCAAGTGACGACAGCAC 58.867 55.000 0.00 0.00 36.53 4.40
5252 6750 0.744281 TGTCTCAAGTGACGACAGCA 59.256 50.000 0.00 0.00 39.64 4.41
5253 6751 1.413382 CTGTCTCAAGTGACGACAGC 58.587 55.000 19.01 0.00 45.37 4.40
5262 6760 3.005897 ACGATGCTTACACTGTCTCAAGT 59.994 43.478 0.00 0.00 0.00 3.16
5263 6761 3.579709 ACGATGCTTACACTGTCTCAAG 58.420 45.455 0.00 0.00 0.00 3.02
5264 6762 3.660501 ACGATGCTTACACTGTCTCAA 57.339 42.857 0.00 0.00 0.00 3.02
5265 6763 3.660501 AACGATGCTTACACTGTCTCA 57.339 42.857 0.00 0.00 0.00 3.27
5266 6764 6.648725 AAATAACGATGCTTACACTGTCTC 57.351 37.500 0.00 0.00 0.00 3.36
5267 6765 6.874134 AGAAAATAACGATGCTTACACTGTCT 59.126 34.615 0.00 0.00 0.00 3.41
5268 6766 7.061752 AGAAAATAACGATGCTTACACTGTC 57.938 36.000 0.00 0.00 0.00 3.51
5269 6767 6.649141 TGAGAAAATAACGATGCTTACACTGT 59.351 34.615 0.00 0.00 0.00 3.55
5270 6768 7.060600 TGAGAAAATAACGATGCTTACACTG 57.939 36.000 0.00 0.00 0.00 3.66
5271 6769 7.667043 TTGAGAAAATAACGATGCTTACACT 57.333 32.000 0.00 0.00 0.00 3.55
5272 6770 8.895932 AATTGAGAAAATAACGATGCTTACAC 57.104 30.769 0.00 0.00 0.00 2.90
5273 6771 8.181573 GGAATTGAGAAAATAACGATGCTTACA 58.818 33.333 0.00 0.00 0.00 2.41
5274 6772 8.181573 TGGAATTGAGAAAATAACGATGCTTAC 58.818 33.333 0.00 0.00 0.00 2.34
5275 6773 8.275015 TGGAATTGAGAAAATAACGATGCTTA 57.725 30.769 0.00 0.00 0.00 3.09
5276 6774 7.156876 TGGAATTGAGAAAATAACGATGCTT 57.843 32.000 0.00 0.00 0.00 3.91
5277 6775 6.757897 TGGAATTGAGAAAATAACGATGCT 57.242 33.333 0.00 0.00 0.00 3.79
5278 6776 7.029563 AGTTGGAATTGAGAAAATAACGATGC 58.970 34.615 0.00 0.00 0.00 3.91
5279 6777 8.454106 AGAGTTGGAATTGAGAAAATAACGATG 58.546 33.333 0.00 0.00 0.00 3.84
5280 6778 8.567285 AGAGTTGGAATTGAGAAAATAACGAT 57.433 30.769 0.00 0.00 0.00 3.73
5281 6779 7.979444 AGAGTTGGAATTGAGAAAATAACGA 57.021 32.000 0.00 0.00 0.00 3.85
5282 6780 8.936864 AGTAGAGTTGGAATTGAGAAAATAACG 58.063 33.333 0.00 0.00 0.00 3.18
5285 6783 9.658799 CTCAGTAGAGTTGGAATTGAGAAAATA 57.341 33.333 0.00 0.00 37.11 1.40
5326 6825 0.459078 GGTCGCTACCAGGTAGGAAC 59.541 60.000 25.56 19.28 45.98 3.62
5336 6835 4.078516 AGTTGGCCGGTCGCTACC 62.079 66.667 0.00 0.00 42.95 3.18
5360 6859 1.443322 GGGAGCGACCGTAGTAGGAC 61.443 65.000 0.00 0.00 40.11 3.85
5368 6867 2.600769 AGTGAAGGGAGCGACCGT 60.601 61.111 0.00 0.00 40.11 4.83
5369 6868 2.125912 CAGTGAAGGGAGCGACCG 60.126 66.667 0.00 0.00 40.11 4.79
5377 6876 2.679349 GCTAGGAAGAAGCAGTGAAGGG 60.679 54.545 0.00 0.00 39.83 3.95
5399 6901 4.098501 GGCCATTTTCTCTGTGGATTTAGG 59.901 45.833 0.00 0.00 34.94 2.69
5402 6904 3.509442 TGGCCATTTTCTCTGTGGATTT 58.491 40.909 0.00 0.00 34.94 2.17
5446 9685 3.450457 AGCAAACTCCACATTTTGAACCA 59.550 39.130 0.00 0.00 35.13 3.67
5452 9691 1.761784 TGGCAGCAAACTCCACATTTT 59.238 42.857 0.00 0.00 0.00 1.82
5453 9692 1.412079 TGGCAGCAAACTCCACATTT 58.588 45.000 0.00 0.00 0.00 2.32
5455 9694 4.927557 TGGCAGCAAACTCCACAT 57.072 50.000 0.00 0.00 0.00 3.21
5461 9702 0.675633 GACCATTGTGGCAGCAAACT 59.324 50.000 0.00 0.00 42.67 2.66
5462 9703 0.664166 CGACCATTGTGGCAGCAAAC 60.664 55.000 0.00 0.00 42.67 2.93
5468 9709 2.902419 CGCAACGACCATTGTGGCA 61.902 57.895 0.00 0.00 42.67 4.92
5474 9719 4.344865 AGGGCCGCAACGACCATT 62.345 61.111 0.00 0.00 28.98 3.16
5475 9720 4.778143 GAGGGCCGCAACGACCAT 62.778 66.667 1.02 0.00 28.98 3.55
5486 9731 2.975489 TCTTATTGGAGATCAGAGGGCC 59.025 50.000 0.00 0.00 0.00 5.80
5495 9740 2.936919 TGGCGCATCTTATTGGAGAT 57.063 45.000 10.83 0.00 36.84 2.75
5496 9741 2.936919 ATGGCGCATCTTATTGGAGA 57.063 45.000 10.83 0.00 0.00 3.71
5497 9742 2.096069 CGAATGGCGCATCTTATTGGAG 60.096 50.000 10.83 0.00 0.00 3.86
5501 9748 3.494626 CAGTACGAATGGCGCATCTTATT 59.505 43.478 10.83 0.99 46.04 1.40
5503 9750 2.100087 TCAGTACGAATGGCGCATCTTA 59.900 45.455 10.83 0.00 46.04 2.10
5512 9759 1.299541 GTGCCCATCAGTACGAATGG 58.700 55.000 17.87 17.87 0.00 3.16
5675 9941 0.319555 TAGAACAGACTGCACGGTGC 60.320 55.000 25.55 25.55 45.29 5.01
5685 9952 2.159517 CCGGCAGCAAATTAGAACAGAC 60.160 50.000 0.00 0.00 0.00 3.51
5798 10065 1.734655 ATGCCAGAATCCCCGTCTAT 58.265 50.000 0.00 0.00 0.00 1.98
5820 10087 4.617959 TGATCCCGTCGATGATTTTCTAC 58.382 43.478 6.11 0.00 0.00 2.59
5873 10140 3.509137 GATCCCGCCGCGTCCATTA 62.509 63.158 12.58 0.00 0.00 1.90
5889 10157 2.125106 GCCTTGGCGGAGTTCGAT 60.125 61.111 0.00 0.00 42.43 3.59
5959 10227 4.733542 CGGTGGCGGGGGTCAAAT 62.734 66.667 0.00 0.00 0.00 2.32
5985 10253 3.645975 CGACGTTGGCGCCAAGTT 61.646 61.111 40.97 29.84 42.83 2.66
6050 10330 1.374758 CCCTGTTGTCGCTCCTGTC 60.375 63.158 0.00 0.00 0.00 3.51
6062 10342 1.492993 GGCTTGAGTCCCTCCCTGTT 61.493 60.000 0.00 0.00 0.00 3.16
6063 10343 1.920835 GGCTTGAGTCCCTCCCTGT 60.921 63.158 0.00 0.00 0.00 4.00
6067 10348 2.896443 CGAGGCTTGAGTCCCTCC 59.104 66.667 7.99 0.00 43.78 4.30


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

AutoCloner maintained by Alex Coulton.