Multiple sequence alignment - TraesCS3D01G345500

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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 TraesCS3D01G345500 chr3D 100.000 7806 0 0 1 7806 457017710 457025515 0.000000e+00 14416.0
1 TraesCS3D01G345500 chr3B 91.365 3347 169 38 518 3813 603601110 603604387 0.000000e+00 4470.0
2 TraesCS3D01G345500 chr3B 95.775 781 31 2 5344 6123 603606343 603607122 0.000000e+00 1258.0
3 TraesCS3D01G345500 chr3B 95.903 781 25 4 6128 6905 603607190 603607966 0.000000e+00 1258.0
4 TraesCS3D01G345500 chr3B 95.052 667 29 3 4300 4964 603605098 603605762 0.000000e+00 1046.0
5 TraesCS3D01G345500 chr3B 91.568 676 31 15 6926 7582 603608257 603608925 0.000000e+00 909.0
6 TraesCS3D01G345500 chr3B 88.632 475 32 12 1 473 603600540 603600994 6.840000e-155 558.0
7 TraesCS3D01G345500 chr3B 90.640 203 18 1 4015 4216 603604877 603605079 1.290000e-67 268.0
8 TraesCS3D01G345500 chr3B 84.672 274 21 5 5049 5320 603605998 603606252 3.620000e-63 254.0
9 TraesCS3D01G345500 chr3B 82.745 255 13 17 7579 7804 603609230 603609482 1.720000e-46 198.0
10 TraesCS3D01G345500 chr3B 91.964 112 5 2 3810 3917 637088603 637088492 3.770000e-33 154.0
11 TraesCS3D01G345500 chr3B 85.455 110 12 3 3805 3911 259612823 259612931 2.300000e-20 111.0
12 TraesCS3D01G345500 chr3B 79.381 97 20 0 7098 7194 177888017 177888113 1.410000e-07 69.4
13 TraesCS3D01G345500 chr3B 93.023 43 3 0 5362 5404 603606341 603606299 6.540000e-06 63.9
14 TraesCS3D01G345500 chr3A 93.814 1843 66 19 825 2625 599860798 599862634 0.000000e+00 2728.0
15 TraesCS3D01G345500 chr3A 94.098 1203 58 4 2742 3936 599862625 599863822 0.000000e+00 1816.0
16 TraesCS3D01G345500 chr3A 95.685 927 30 5 6124 7041 599866129 599867054 0.000000e+00 1482.0
17 TraesCS3D01G345500 chr3A 91.231 1072 51 15 5045 6114 599865021 599866051 0.000000e+00 1419.0
18 TraesCS3D01G345500 chr3A 94.298 684 29 4 4321 5003 599864278 599864952 0.000000e+00 1038.0
19 TraesCS3D01G345500 chr3A 86.957 552 38 15 7280 7806 599867502 599868044 2.430000e-164 590.0
20 TraesCS3D01G345500 chr3A 83.699 638 52 16 122 739 599860158 599860763 8.850000e-154 555.0
21 TraesCS3D01G345500 chr3A 86.402 353 22 8 3949 4282 599863929 599864274 5.760000e-96 363.0
22 TraesCS3D01G345500 chr3A 100.000 33 0 0 3380 3412 599864986 599865018 2.350000e-05 62.1
23 TraesCS3D01G345500 chr2A 92.476 638 36 4 3949 4575 701775431 701776067 0.000000e+00 902.0
24 TraesCS3D01G345500 chr1B 87.135 754 59 22 950 1677 522061367 522060626 0.000000e+00 821.0
25 TraesCS3D01G345500 chr1D 86.853 753 63 17 950 1677 388651315 388650574 0.000000e+00 809.0
26 TraesCS3D01G345500 chr1A 86.430 759 61 23 950 1677 487741696 487740949 0.000000e+00 793.0
27 TraesCS3D01G345500 chr2D 84.592 331 47 3 1218 1546 161376682 161376354 7.550000e-85 326.0
28 TraesCS3D01G345500 chr2D 77.684 475 90 15 1210 1676 564095468 564095002 7.720000e-70 276.0
29 TraesCS3D01G345500 chr2B 84.290 331 48 3 1218 1546 217793140 217792812 3.510000e-83 320.0
30 TraesCS3D01G345500 chr2B 77.378 473 95 11 1210 1676 675356154 675355688 3.590000e-68 270.0
31 TraesCS3D01G345500 chr2B 86.598 97 13 0 7098 7194 63254819 63254915 2.980000e-19 108.0
32 TraesCS3D01G345500 chr2B 83.193 119 17 3 3804 3921 534281687 534281803 1.070000e-18 106.0
33 TraesCS3D01G345500 chr4B 89.565 115 8 3 3809 3920 450911683 450911796 8.160000e-30 143.0
34 TraesCS3D01G345500 chr5B 88.991 109 7 3 3810 3914 383528342 383528449 6.360000e-26 130.0
35 TraesCS3D01G345500 chr5B 82.353 119 18 3 3804 3921 512797927 512798043 4.980000e-17 100.0
36 TraesCS3D01G345500 chr5D 85.321 109 11 2 3810 3914 330709596 330709489 2.980000e-19 108.0
37 TraesCS3D01G345500 chr6D 85.437 103 11 4 3810 3911 129156610 129156511 3.850000e-18 104.0
38 TraesCS3D01G345500 chr7D 90.000 40 4 0 7098 7137 238300863 238300902 1.400000e-02 52.8


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 TraesCS3D01G345500 chr3D 457017710 457025515 7805 False 14416.000000 14416 100.000000 1 7806 1 chr3D.!!$F1 7805
1 TraesCS3D01G345500 chr3B 603600540 603609482 8942 False 1135.444444 4470 90.705778 1 7804 9 chr3B.!!$F3 7803
2 TraesCS3D01G345500 chr3A 599860158 599868044 7886 False 1117.011111 2728 91.798222 122 7806 9 chr3A.!!$F1 7684
3 TraesCS3D01G345500 chr2A 701775431 701776067 636 False 902.000000 902 92.476000 3949 4575 1 chr2A.!!$F1 626
4 TraesCS3D01G345500 chr1B 522060626 522061367 741 True 821.000000 821 87.135000 950 1677 1 chr1B.!!$R1 727
5 TraesCS3D01G345500 chr1D 388650574 388651315 741 True 809.000000 809 86.853000 950 1677 1 chr1D.!!$R1 727
6 TraesCS3D01G345500 chr1A 487740949 487741696 747 True 793.000000 793 86.430000 950 1677 1 chr1A.!!$R1 727

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
319 326 0.031178 GAAAAGCCCACTGCACTGTG 59.969 55.000 2.76 2.76 44.83 3.66 F
614 722 0.243907 CCTCTTTTCTCTCGCCGTGA 59.756 55.000 0.00 0.00 0.00 4.35 F
823 931 1.302913 CCATACCGTTGCACACCCA 60.303 57.895 0.00 0.00 0.00 4.51 F
1826 2034 0.105039 GGACATCCCGGTAGCTGAAG 59.895 60.000 0.00 0.00 0.00 3.02 F
1983 2191 1.003118 TGCATCACCTTTACTCCGCTT 59.997 47.619 0.00 0.00 0.00 4.68 F
2732 2948 0.026674 CATCATACGTTGTGCTGCCG 59.973 55.000 0.00 0.00 0.00 5.69 F
2767 2983 0.867746 GATGTGCTTTGCTGACGTCA 59.132 50.000 18.88 18.88 0.00 4.35 F
4010 4328 1.135139 TCTGCCTATCTGAAGCACGAC 59.865 52.381 0.00 0.00 32.06 4.34 F
5140 6018 0.038166 TGGTGAAGGGTTCATCTGCC 59.962 55.000 1.83 0.00 41.40 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 1951 0.033894 TAAACCCAGAAATCCCGCCC 60.034 55.000 0.00 0.00 0.00 6.13 R
1787 1995 0.035056 ATTGCCAGCACTCCACCTAC 60.035 55.000 0.00 0.00 0.00 3.18 R
2654 2870 0.179078 TACCGTTCGCACTGGTGTTT 60.179 50.000 10.74 0.00 37.20 2.83 R
2659 2875 0.320073 TTTCCTACCGTTCGCACTGG 60.320 55.000 0.00 0.00 0.00 4.00 R
3646 3870 0.322322 CACATGGGCCATGCTGTTTT 59.678 50.000 39.55 20.99 44.80 2.43 R
3818 4042 1.734163 AAGACAAGTAATTCGGGGCG 58.266 50.000 0.00 0.00 0.00 6.13 R
4372 5084 2.876581 ACCAGGGGAAAACAGATGAAC 58.123 47.619 0.00 0.00 0.00 3.18 R
5301 6180 0.116342 TAGAGGGCAAGGACACCTGA 59.884 55.000 0.00 0.00 34.02 3.86 R
6984 8282 1.373570 GCACTGCTCTTGGTACATCC 58.626 55.000 0.00 0.00 39.30 3.51 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
25 26 0.956633 CTCAATGCAGCCACACAGTT 59.043 50.000 0.00 0.00 0.00 3.16
67 68 7.013942 TCGTAGCCTAACTTAATGATAAGCTGA 59.986 37.037 0.00 0.00 41.92 4.26
81 82 9.696917 AATGATAAGCTGATTTTTCTTTTCGTT 57.303 25.926 0.00 0.00 0.00 3.85
82 83 9.696917 ATGATAAGCTGATTTTTCTTTTCGTTT 57.303 25.926 0.00 0.00 0.00 3.60
148 149 4.946784 ATGGTAAGCTGATTTCACGAAC 57.053 40.909 0.00 0.00 0.00 3.95
190 196 4.847365 AATGACACGATGATTTCACGAG 57.153 40.909 0.00 0.00 0.00 4.18
202 208 9.066939 CGATGATTTCACGAGTTAATATCTAGG 57.933 37.037 0.00 0.00 0.00 3.02
204 210 9.915629 ATGATTTCACGAGTTAATATCTAGGTC 57.084 33.333 0.00 0.00 0.00 3.85
205 211 9.132923 TGATTTCACGAGTTAATATCTAGGTCT 57.867 33.333 0.00 0.00 0.00 3.85
208 214 8.969260 TTCACGAGTTAATATCTAGGTCTACA 57.031 34.615 0.00 0.00 0.00 2.74
278 285 1.719600 GCAGTCGCTTTCTCATGTCT 58.280 50.000 0.00 0.00 34.30 3.41
298 305 4.932200 GTCTCGTTCAATCCAACAATCTCT 59.068 41.667 0.00 0.00 0.00 3.10
299 306 5.409826 GTCTCGTTCAATCCAACAATCTCTT 59.590 40.000 0.00 0.00 0.00 2.85
317 324 0.746063 TTGAAAAGCCCACTGCACTG 59.254 50.000 0.00 0.00 44.83 3.66
318 325 0.395586 TGAAAAGCCCACTGCACTGT 60.396 50.000 0.00 0.00 44.83 3.55
319 326 0.031178 GAAAAGCCCACTGCACTGTG 59.969 55.000 2.76 2.76 44.83 3.66
355 363 2.422597 TGTTTCAGTTCCTGCCATACG 58.577 47.619 0.00 0.00 0.00 3.06
378 386 2.369394 CTTGGAAAGCCATGGTCCTAC 58.631 52.381 18.17 6.26 45.46 3.18
379 387 1.668826 TGGAAAGCCATGGTCCTACT 58.331 50.000 18.17 2.51 39.92 2.57
380 388 2.840511 TGGAAAGCCATGGTCCTACTA 58.159 47.619 18.17 0.00 39.92 1.82
414 422 5.270083 TCGAAAGCTTTACACACACAAATG 58.730 37.500 12.68 0.00 0.00 2.32
439 447 8.038944 TGTGTAGTTCCAATTACAGGTAAGATC 58.961 37.037 0.00 0.00 32.73 2.75
448 456 5.514500 TTACAGGTAAGATCCCAAAGCTT 57.486 39.130 0.00 0.00 0.00 3.74
450 458 4.336280 ACAGGTAAGATCCCAAAGCTTTC 58.664 43.478 9.23 0.00 0.00 2.62
451 459 3.696548 CAGGTAAGATCCCAAAGCTTTCC 59.303 47.826 9.23 4.17 31.56 3.13
453 461 4.086457 GGTAAGATCCCAAAGCTTTCCAA 58.914 43.478 9.23 0.00 31.70 3.53
463 471 4.050553 CAAAGCTTTCCAAGAATTCGCAA 58.949 39.130 9.23 0.00 0.00 4.85
611 719 1.153549 CCCCTCTTTTCTCTCGCCG 60.154 63.158 0.00 0.00 0.00 6.46
612 720 1.592223 CCCTCTTTTCTCTCGCCGT 59.408 57.895 0.00 0.00 0.00 5.68
613 721 0.737715 CCCTCTTTTCTCTCGCCGTG 60.738 60.000 0.00 0.00 0.00 4.94
614 722 0.243907 CCTCTTTTCTCTCGCCGTGA 59.756 55.000 0.00 0.00 0.00 4.35
696 804 2.747855 GGACCCAGAAGCGCCAAG 60.748 66.667 2.29 0.00 0.00 3.61
817 925 4.787286 CCCCGCCATACCGTTGCA 62.787 66.667 0.00 0.00 0.00 4.08
818 926 3.505184 CCCGCCATACCGTTGCAC 61.505 66.667 0.00 0.00 0.00 4.57
821 929 2.874751 GCCATACCGTTGCACACC 59.125 61.111 0.00 0.00 0.00 4.16
822 930 2.696759 GCCATACCGTTGCACACCC 61.697 63.158 0.00 0.00 0.00 4.61
823 931 1.302913 CCATACCGTTGCACACCCA 60.303 57.895 0.00 0.00 0.00 4.51
827 946 1.404479 TACCGTTGCACACCCAGACT 61.404 55.000 0.00 0.00 0.00 3.24
1735 1935 5.848833 ATTTGGGAGAATCTGCATTTCTC 57.151 39.130 22.36 22.36 45.42 2.87
1740 1940 4.897025 GAGAATCTGCATTTCTCAAGGG 57.103 45.455 24.19 0.00 45.46 3.95
1742 1942 4.927049 AGAATCTGCATTTCTCAAGGGAA 58.073 39.130 6.29 0.00 0.00 3.97
1762 1968 2.760634 AAAAACATGGGCGGGATTTC 57.239 45.000 0.00 0.00 0.00 2.17
1775 1983 2.693074 CGGGATTTCTGGGTTTAATGGG 59.307 50.000 0.00 0.00 0.00 4.00
1778 1986 3.774766 GGATTTCTGGGTTTAATGGGCTT 59.225 43.478 0.00 0.00 0.00 4.35
1787 1995 4.095932 GGGTTTAATGGGCTTTCTTAGTCG 59.904 45.833 0.00 0.00 0.00 4.18
1826 2034 0.105039 GGACATCCCGGTAGCTGAAG 59.895 60.000 0.00 0.00 0.00 3.02
1866 2074 7.155328 GGTGTCTCTTTCATTCAGAACTTAGA 58.845 38.462 0.00 0.00 35.56 2.10
1892 2100 1.064685 CGGAAGGAATTTGGGTAGGCT 60.065 52.381 0.00 0.00 0.00 4.58
1983 2191 1.003118 TGCATCACCTTTACTCCGCTT 59.997 47.619 0.00 0.00 0.00 4.68
2091 2299 1.067060 GGGTTCTGTGTTTGGTGCTTC 59.933 52.381 0.00 0.00 0.00 3.86
2099 2307 1.133513 TGTTTGGTGCTTCAGGTCCAT 60.134 47.619 0.00 0.00 0.00 3.41
2109 2317 3.582208 GCTTCAGGTCCATGATCTAGGAT 59.418 47.826 9.45 0.00 36.11 3.24
2119 2327 7.398829 GTCCATGATCTAGGATGTCTCTAGTA 58.601 42.308 9.45 0.00 36.11 1.82
2133 2341 7.852550 TGTCTCTAGTATCAGCCTACTACTA 57.147 40.000 0.00 0.00 33.96 1.82
2231 2439 5.244851 AGTTCTTCAGTGTGAGATGAGCTTA 59.755 40.000 0.00 0.00 30.36 3.09
2391 2599 1.656652 GATGGATGGTGTGTCTTCCG 58.343 55.000 0.00 0.00 34.72 4.30
2406 2615 8.124199 GTGTGTCTTCCGTTTTACTTAATTTGA 58.876 33.333 0.00 0.00 0.00 2.69
2443 2658 4.404394 TCCTTTATGTAGAGAATGCGTGGA 59.596 41.667 0.00 0.00 0.00 4.02
2478 2693 7.661847 CCTATGAGATAATGTAAGGAACCAACC 59.338 40.741 0.00 0.00 0.00 3.77
2541 2757 3.436496 GAAGTACTATCCACGTGAGCAC 58.564 50.000 19.30 7.57 0.00 4.40
2605 2821 5.059833 AGCTTATCAAGTATGCTTACTGGC 58.940 41.667 12.62 10.08 39.91 4.85
2626 2842 4.161102 GCTGGGACTTAGGGTGTAGATAT 58.839 47.826 0.00 0.00 0.00 1.63
2660 2876 8.896320 AAACCATAAAATAACAAGGAAACACC 57.104 30.769 0.00 0.00 39.35 4.16
2670 2886 1.157870 AGGAAACACCAGTGCGAACG 61.158 55.000 0.00 0.00 42.04 3.95
2671 2887 1.278637 GAAACACCAGTGCGAACGG 59.721 57.895 0.00 3.23 0.00 4.44
2688 2904 2.547990 ACGGTAGGAAAATGGTCTCCT 58.452 47.619 0.00 0.00 44.49 3.69
2689 2905 2.910977 ACGGTAGGAAAATGGTCTCCTT 59.089 45.455 0.00 0.00 42.29 3.36
2691 2907 3.532542 GGTAGGAAAATGGTCTCCTTCG 58.467 50.000 0.00 0.00 42.29 3.79
2723 2939 4.081142 TCCCACATTGTCTCATCATACGTT 60.081 41.667 0.00 0.00 0.00 3.99
2732 2948 0.026674 CATCATACGTTGTGCTGCCG 59.973 55.000 0.00 0.00 0.00 5.69
2767 2983 0.867746 GATGTGCTTTGCTGACGTCA 59.132 50.000 18.88 18.88 0.00 4.35
2800 3021 3.044305 GGTTTGCGCGCTCTGTCT 61.044 61.111 33.29 0.00 0.00 3.41
2821 3042 2.900273 GTGCCATAGTCCGCTCCA 59.100 61.111 0.00 0.00 0.00 3.86
3359 3583 3.221771 TGGCACACTGTTATGCTTCTTT 58.778 40.909 12.18 0.00 41.74 2.52
3361 3585 3.503748 GGCACACTGTTATGCTTCTTTCT 59.496 43.478 12.18 0.00 41.74 2.52
3369 3593 7.173218 CACTGTTATGCTTCTTTCTTACTTCCA 59.827 37.037 0.00 0.00 0.00 3.53
3515 3739 5.241064 GCCACTAGTCTCGTCTGGAATTATA 59.759 44.000 0.00 0.00 0.00 0.98
3519 3743 3.253677 AGTCTCGTCTGGAATTATAGCCG 59.746 47.826 0.00 0.00 0.00 5.52
3534 3758 4.682778 ATAGCCGTGCCATTACTTTCTA 57.317 40.909 0.00 0.00 0.00 2.10
3732 3956 8.965986 AGTAACTGTGAAGTTTCAAGTTTTTC 57.034 30.769 18.44 13.06 39.21 2.29
3738 3962 6.589523 TGTGAAGTTTCAAGTTTTTCCATGTG 59.410 34.615 0.00 0.00 39.21 3.21
3739 3963 6.811170 GTGAAGTTTCAAGTTTTTCCATGTGA 59.189 34.615 0.00 0.00 39.21 3.58
3820 4044 4.765856 TCTGATATAAAGTACTCCCTCCGC 59.234 45.833 0.00 0.00 0.00 5.54
3832 4056 1.525442 CCTCCGCCCCGAATTACTT 59.475 57.895 0.00 0.00 0.00 2.24
3891 4115 9.132923 ACATCCGTATCTAGACAAATCTAAGAA 57.867 33.333 0.00 0.00 36.98 2.52
3918 4142 7.580007 AGTAATTTGGGACGGAGGTAATATTT 58.420 34.615 0.00 0.00 0.00 1.40
3921 4145 4.411256 TGGGACGGAGGTAATATTTGAC 57.589 45.455 0.00 0.00 0.00 3.18
4009 4327 1.474330 TCTGCCTATCTGAAGCACGA 58.526 50.000 0.00 0.00 32.06 4.35
4010 4328 1.135139 TCTGCCTATCTGAAGCACGAC 59.865 52.381 0.00 0.00 32.06 4.34
4013 4342 2.028112 TGCCTATCTGAAGCACGACTTT 60.028 45.455 0.00 0.00 39.29 2.66
4042 4742 4.081406 TGTGCCAGATAGTTTTCTGCATT 58.919 39.130 0.00 0.00 41.50 3.56
4105 4806 8.031277 CCTGAAATTCTCCATCTTAAAACTTGG 58.969 37.037 0.00 0.00 0.00 3.61
4107 4808 7.728083 TGAAATTCTCCATCTTAAAACTTGGGA 59.272 33.333 0.00 0.00 0.00 4.37
4116 4817 8.971073 CCATCTTAAAACTTGGGATTAATCAGT 58.029 33.333 17.07 9.12 0.00 3.41
4236 4948 5.751028 GCGCTTGGGCATTTTATTATTTGTA 59.249 36.000 0.00 0.00 38.60 2.41
4260 4972 7.676683 ACTACAGCCTGAAAGAATATTAGGA 57.323 36.000 0.00 0.00 34.07 2.94
4264 4976 7.222872 ACAGCCTGAAAGAATATTAGGATCAG 58.777 38.462 0.00 8.54 34.07 2.90
4282 4994 2.886523 TCAGAATTGTGGTCTGCTTTGG 59.113 45.455 2.33 0.00 41.94 3.28
4298 5010 4.034742 TGCTTTGGAACTTGAAGTTACGTC 59.965 41.667 15.02 1.21 41.99 4.34
4300 5012 5.728351 TTTGGAACTTGAAGTTACGTCAG 57.272 39.130 15.02 0.00 41.99 3.51
4326 5038 7.414540 GCTCATATTCTTTTCGAGTGTGGAAAT 60.415 37.037 0.00 0.00 33.74 2.17
4493 5205 1.203287 GCTCCAAATGTTCCTCTTGGC 59.797 52.381 0.00 0.00 39.61 4.52
4663 5376 6.033196 GTCGTGTGACATATATGGCGTATAAC 59.967 42.308 16.96 8.17 44.82 1.89
4694 5407 2.938451 GGTCATCGCTGATCATTTGTCA 59.062 45.455 0.00 0.00 32.39 3.58
4712 5425 2.235898 GTCAGCTGAGGAAGTTGAGGAT 59.764 50.000 18.89 0.00 45.62 3.24
4727 5440 9.620259 GAAGTTGAGGATATAAAGGAGATGTTT 57.380 33.333 0.00 0.00 0.00 2.83
4858 5571 6.875948 TGAAGCTGTAAGTATTGCAAAGAA 57.124 33.333 1.71 0.00 41.07 2.52
4938 5651 9.401058 CTATTTTCCTAGAAGATCAATTGGTGT 57.599 33.333 5.42 0.00 0.00 4.16
4984 5697 6.992715 GGAGCATTGCTATCTAAAGGAGTAAA 59.007 38.462 11.96 0.00 39.88 2.01
5020 5733 6.870971 AACTACGCTTTTATGGAGTTTTCA 57.129 33.333 0.00 0.00 0.00 2.69
5026 5739 6.206634 ACGCTTTTATGGAGTTTTCATGAGAA 59.793 34.615 0.00 0.00 0.00 2.87
5027 5740 7.094205 ACGCTTTTATGGAGTTTTCATGAGAAT 60.094 33.333 1.53 0.00 32.89 2.40
5029 5742 9.428097 GCTTTTATGGAGTTTTCATGAGAATTT 57.572 29.630 1.53 0.00 32.89 1.82
5059 5936 6.726490 ACTTTACATCCGTGATAGGTATGT 57.274 37.500 0.00 0.00 36.61 2.29
5063 5940 5.808366 ACATCCGTGATAGGTATGTCAAT 57.192 39.130 0.00 0.00 31.28 2.57
5066 5943 7.378966 ACATCCGTGATAGGTATGTCAATAAG 58.621 38.462 0.00 0.00 31.28 1.73
5075 5952 4.127171 GGTATGTCAATAAGTGCGGTCAT 58.873 43.478 0.00 0.00 0.00 3.06
5098 5975 2.733956 GGCCCACTGGACATTCAATTA 58.266 47.619 0.00 0.00 40.65 1.40
5111 5988 7.119407 TGGACATTCAATTATGTGCCAAAATTG 59.881 33.333 9.54 0.00 43.68 2.32
5117 5995 7.613585 TCAATTATGTGCCAAAATTGTCTCAT 58.386 30.769 6.84 0.00 40.10 2.90
5128 6006 7.864379 GCCAAAATTGTCTCATATATGGTGAAG 59.136 37.037 12.78 3.12 0.00 3.02
5140 6018 0.038166 TGGTGAAGGGTTCATCTGCC 59.962 55.000 1.83 0.00 41.40 4.85
5143 6021 0.770499 TGAAGGGTTCATCTGCCACA 59.230 50.000 0.00 0.00 34.08 4.17
5148 6026 3.242011 AGGGTTCATCTGCCACAAAATT 58.758 40.909 0.00 0.00 0.00 1.82
5194 6072 4.757657 TGTACGAAATAAACAGCCATGTGT 59.242 37.500 0.00 0.00 40.39 3.72
5215 6093 9.877178 ATGTGTTTTTGTGATAGTTTTGGTTAA 57.123 25.926 0.00 0.00 0.00 2.01
5216 6094 9.706691 TGTGTTTTTGTGATAGTTTTGGTTAAA 57.293 25.926 0.00 0.00 0.00 1.52
5217 6095 9.961266 GTGTTTTTGTGATAGTTTTGGTTAAAC 57.039 29.630 0.00 0.00 45.26 2.01
5262 6140 9.330063 TGTAGCTCCAAAAGATTTGATATACAG 57.670 33.333 4.47 0.00 0.00 2.74
5278 6156 7.712797 TGATATACAGCAAAGAATCACGTAGA 58.287 34.615 0.00 0.00 0.00 2.59
5282 6160 6.560253 ACAGCAAAGAATCACGTAGAAAAT 57.440 33.333 0.00 0.00 0.00 1.82
5301 6180 8.474710 AGAAAATGCAATATCATCTTAAGCCT 57.525 30.769 0.00 0.00 0.00 4.58
5398 6344 4.098914 TCCCACAGCTAACAAATGTTCT 57.901 40.909 1.37 0.00 39.31 3.01
5449 6396 4.322198 GCATCCATTGGTAGGCCATTTATG 60.322 45.833 5.01 1.55 45.56 1.90
5454 6401 7.072562 TCCATTGGTAGGCCATTTATGTATTT 58.927 34.615 5.01 0.00 45.56 1.40
5501 6448 8.990163 AGGGTAAATAAATGTGGTCGAATTAT 57.010 30.769 0.00 0.00 0.00 1.28
5643 6591 0.469705 TGCTGTTTGGGCTGTCCATT 60.470 50.000 0.00 0.00 46.52 3.16
5660 6608 2.028748 CCATTTTCCTTCTGCCAGTTGG 60.029 50.000 0.00 0.00 38.53 3.77
5684 6632 8.250332 TGGTTTTTAGATGCTATTCCATTGTTC 58.750 33.333 0.00 0.00 0.00 3.18
5700 6648 7.776107 TCCATTGTTCAACATGTCAAACTTTA 58.224 30.769 18.65 8.98 0.00 1.85
5718 6666 6.699575 ACTTTATATCTGGTGGTGATTTGC 57.300 37.500 0.00 0.00 0.00 3.68
5724 6672 1.068895 CTGGTGGTGATTTGCTGCAAA 59.931 47.619 27.78 27.78 37.75 3.68
5745 6693 6.735968 GCAAATATTTGACTTAGCCCCTTAGC 60.736 42.308 28.33 6.35 40.55 3.09
5822 6770 6.097412 GCCAGACTAGAAATGAAAATTCCCAT 59.903 38.462 0.00 0.00 0.00 4.00
5883 6831 4.610333 TGTGACTCATTCCCTTCTAGCTA 58.390 43.478 0.00 0.00 0.00 3.32
6051 6999 3.961182 GACAGTGTGTCGACTCACTTTA 58.039 45.455 37.46 10.01 45.16 1.85
6057 7005 4.263209 GTGTGTCGACTCACTTTATCATCG 59.737 45.833 32.67 0.00 38.90 3.84
6212 7228 5.389859 TTGAGTTGATGGTTGCAATTAGG 57.610 39.130 0.59 0.00 0.00 2.69
6249 7265 1.901085 CACAGGGAGGGCAGTAGAC 59.099 63.158 0.00 0.00 0.00 2.59
6253 7269 1.351017 CAGGGAGGGCAGTAGACAAAA 59.649 52.381 0.00 0.00 0.00 2.44
6267 7283 7.628580 GCAGTAGACAAAACTGGGATAAATTCC 60.629 40.741 5.47 0.00 43.71 3.01
6640 7661 7.383102 TGACTAAAAGATCATCTGCTTTTCC 57.617 36.000 0.00 0.00 41.80 3.13
6808 7829 3.254657 TCAAATTGGGCGTGGAGTAAAAG 59.745 43.478 0.00 0.00 0.00 2.27
6809 7830 1.173913 ATTGGGCGTGGAGTAAAAGC 58.826 50.000 0.00 0.00 0.00 3.51
6931 8222 0.106967 GAACCCCCTCTGATTGGCTC 60.107 60.000 0.00 0.00 0.00 4.70
7049 8454 9.295214 TGATGTTAAGTGTTGTACAATGTTTTG 57.705 29.630 12.26 0.00 38.86 2.44
7116 8521 1.242076 AAGATGTTGTGCTGGCTCAC 58.758 50.000 3.99 3.99 37.48 3.51
7132 8537 2.031508 GCTCACTATCTCGTAGGTGCTC 60.032 54.545 0.00 0.00 34.56 4.26
7147 8552 4.965352 AGGTGCTCATAGGGATATGGTAT 58.035 43.478 0.00 0.00 0.00 2.73
7150 8555 3.132824 TGCTCATAGGGATATGGTATGCG 59.867 47.826 0.00 0.00 0.00 4.73
7151 8556 3.133003 GCTCATAGGGATATGGTATGCGT 59.867 47.826 0.00 0.00 0.00 5.24
7152 8557 4.686972 CTCATAGGGATATGGTATGCGTG 58.313 47.826 0.00 0.00 0.00 5.34
7153 8558 3.118775 TCATAGGGATATGGTATGCGTGC 60.119 47.826 0.00 0.00 0.00 5.34
7164 8569 2.019708 TATGCGTGCGTGCGTTCATC 62.020 55.000 0.00 0.00 37.81 2.92
7195 8600 4.450757 GTGTATGTGTGTGTATGTGAGCAA 59.549 41.667 0.00 0.00 0.00 3.91
7196 8601 5.122239 GTGTATGTGTGTGTATGTGAGCAAT 59.878 40.000 0.00 0.00 0.00 3.56
7199 8604 2.094258 GTGTGTGTATGTGAGCAATCGG 59.906 50.000 0.00 0.00 0.00 4.18
7230 8635 7.717875 TGTACTGTGTTAAAAAGAAGGTGCTAT 59.282 33.333 0.00 0.00 0.00 2.97
7245 8651 4.213482 AGGTGCTATCGTGTTCTTGAAAAC 59.787 41.667 0.00 0.00 0.00 2.43
7258 8667 4.502962 TCTTGAAAACAAAAGCAAGGTGG 58.497 39.130 0.00 0.00 38.53 4.61
7285 8742 2.360553 AGAGACGAGACAATGTGCAG 57.639 50.000 0.00 0.00 0.00 4.41
7312 8834 4.695217 ACACAAGGTACAAATAATGGCG 57.305 40.909 0.00 0.00 0.00 5.69
7376 8898 3.616219 TGCTTTCGTAACCCATAAGCAT 58.384 40.909 0.00 0.00 44.30 3.79
7460 8991 4.133078 CTGGATAATCAGAACCCAGAAGC 58.867 47.826 0.00 0.00 45.35 3.86
7514 9048 0.837272 GGGGTACTTGCAGCAGGATA 59.163 55.000 12.26 0.00 0.00 2.59
7516 9050 2.289565 GGGTACTTGCAGCAGGATAAC 58.710 52.381 12.26 6.24 0.00 1.89
7549 9083 1.134521 TGAATTCGGGGGACAAGATCG 60.135 52.381 0.04 0.00 0.00 3.69
7612 9454 3.807631 GCGCATGCATCCGGAGGTA 62.808 63.158 18.73 14.56 46.17 3.08
7643 9490 4.091800 GCGACAGCAAACAAAATGCATATT 59.908 37.500 0.00 0.00 46.22 1.28
7651 9498 6.305639 CAAACAAAATGCATATTTCCCAACG 58.694 36.000 0.00 0.00 35.50 4.10
7653 9500 4.221703 ACAAAATGCATATTTCCCAACGGA 59.778 37.500 0.00 0.00 35.50 4.69
7654 9501 5.174395 CAAAATGCATATTTCCCAACGGAA 58.826 37.500 0.00 0.00 46.91 4.30
7678 9539 2.438614 TCTGTCGCCCCTCTCTCG 60.439 66.667 0.00 0.00 0.00 4.04
7751 9622 3.426159 CGCCACGGCATCATATAAAATCC 60.426 47.826 9.11 0.00 42.06 3.01
7755 9626 5.447683 CCACGGCATCATATAAAATCCATCG 60.448 44.000 0.00 0.00 0.00 3.84
7758 9629 5.582269 CGGCATCATATAAAATCCATCGTCT 59.418 40.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.811307 ACAACTGTGTGGCTGCATT 58.189 47.368 0.50 0.00 36.31 3.56
25 26 1.311859 ACGAGTTCGAGTGTACCACA 58.688 50.000 8.72 0.00 43.02 4.17
37 38 9.182933 CTTATCATTAAGTTAGGCTACGAGTTC 57.817 37.037 0.00 0.00 31.85 3.01
38 39 7.652507 GCTTATCATTAAGTTAGGCTACGAGTT 59.347 37.037 0.00 0.00 37.68 3.01
40 41 7.327275 CAGCTTATCATTAAGTTAGGCTACGAG 59.673 40.741 0.00 0.00 37.68 4.18
41 42 7.013942 TCAGCTTATCATTAAGTTAGGCTACGA 59.986 37.037 0.00 0.00 37.68 3.43
43 44 9.495572 AATCAGCTTATCATTAAGTTAGGCTAC 57.504 33.333 0.00 0.00 37.68 3.58
124 125 6.128117 GGTTCGTGAAATCAGCTTACCATTAA 60.128 38.462 0.00 0.00 0.00 1.40
130 131 4.742438 TTGGTTCGTGAAATCAGCTTAC 57.258 40.909 0.00 0.00 0.00 2.34
202 208 9.382244 GCACGGAAATATTTTTGATATGTAGAC 57.618 33.333 1.43 0.00 0.00 2.59
204 210 9.169468 GTGCACGGAAATATTTTTGATATGTAG 57.831 33.333 0.00 0.00 0.00 2.74
205 211 8.898761 AGTGCACGGAAATATTTTTGATATGTA 58.101 29.630 12.01 0.00 0.00 2.29
206 212 7.701924 CAGTGCACGGAAATATTTTTGATATGT 59.298 33.333 11.96 0.00 0.00 2.29
207 213 7.167968 CCAGTGCACGGAAATATTTTTGATATG 59.832 37.037 19.14 0.87 0.00 1.78
208 214 7.147915 ACCAGTGCACGGAAATATTTTTGATAT 60.148 33.333 27.07 3.53 0.00 1.63
210 216 5.047377 ACCAGTGCACGGAAATATTTTTGAT 60.047 36.000 27.07 4.41 0.00 2.57
212 218 4.555262 ACCAGTGCACGGAAATATTTTTG 58.445 39.130 27.07 10.25 0.00 2.44
216 222 3.350219 AGACCAGTGCACGGAAATATT 57.650 42.857 27.07 9.52 0.00 1.28
219 225 1.202758 TGAAGACCAGTGCACGGAAAT 60.203 47.619 27.07 15.25 0.00 2.17
278 285 5.304778 TCAAGAGATTGTTGGATTGAACGA 58.695 37.500 0.00 0.00 0.00 3.85
298 305 0.746063 CAGTGCAGTGGGCTTTTCAA 59.254 50.000 14.08 0.00 45.15 2.69
299 306 0.395586 ACAGTGCAGTGGGCTTTTCA 60.396 50.000 24.91 0.00 45.15 2.69
317 324 5.529800 TGAAACAAGAAAGCTAAGGTACCAC 59.470 40.000 15.94 0.01 0.00 4.16
318 325 5.686753 TGAAACAAGAAAGCTAAGGTACCA 58.313 37.500 15.94 0.00 0.00 3.25
319 326 5.763698 ACTGAAACAAGAAAGCTAAGGTACC 59.236 40.000 2.73 2.73 0.00 3.34
373 381 4.574674 TCGAAGTTGGGTAGTAGTAGGA 57.425 45.455 0.00 0.00 0.00 2.94
378 386 4.189639 AGCTTTCGAAGTTGGGTAGTAG 57.810 45.455 0.00 0.00 0.00 2.57
379 387 4.612264 AAGCTTTCGAAGTTGGGTAGTA 57.388 40.909 0.00 0.00 0.00 1.82
380 388 3.487120 AAGCTTTCGAAGTTGGGTAGT 57.513 42.857 0.00 0.00 0.00 2.73
414 422 7.494952 GGATCTTACCTGTAATTGGAACTACAC 59.505 40.741 0.00 0.00 0.00 2.90
439 447 3.578688 CGAATTCTTGGAAAGCTTTGGG 58.421 45.455 18.30 3.85 45.70 4.12
448 456 9.337396 ACTATTATGTATTGCGAATTCTTGGAA 57.663 29.630 3.52 0.00 0.00 3.53
507 602 4.280174 GCAATGGAGTGGCATATCAGAAAT 59.720 41.667 0.00 0.00 0.00 2.17
516 612 3.594568 CACGCAATGGAGTGGCAT 58.405 55.556 0.00 0.00 40.63 4.40
612 720 4.617520 TTTGACTGCGCCCGCTCA 62.618 61.111 14.13 7.32 42.51 4.26
613 721 4.090057 GTTTGACTGCGCCCGCTC 62.090 66.667 14.13 4.70 42.51 5.03
768 876 4.864334 GATGGGGTCGGCAGGCAG 62.864 72.222 0.00 0.00 0.00 4.85
771 879 3.482232 GATGGATGGGGTCGGCAGG 62.482 68.421 0.00 0.00 0.00 4.85
772 880 2.111878 GATGGATGGGGTCGGCAG 59.888 66.667 0.00 0.00 0.00 4.85
773 881 3.860605 CGATGGATGGGGTCGGCA 61.861 66.667 0.00 0.00 0.00 5.69
775 883 2.207229 TAGCGATGGATGGGGTCGG 61.207 63.158 0.00 0.00 36.00 4.79
776 884 1.006102 GTAGCGATGGATGGGGTCG 60.006 63.158 0.00 0.00 38.34 4.79
777 885 1.006102 CGTAGCGATGGATGGGGTC 60.006 63.158 0.00 0.00 0.00 4.46
778 886 3.138625 CGTAGCGATGGATGGGGT 58.861 61.111 0.00 0.00 0.00 4.95
817 925 1.344763 GCAGTAACTGAGTCTGGGTGT 59.655 52.381 3.85 0.00 32.44 4.16
818 926 1.620819 AGCAGTAACTGAGTCTGGGTG 59.379 52.381 3.85 0.00 32.44 4.61
821 929 2.165437 GAGGAGCAGTAACTGAGTCTGG 59.835 54.545 3.85 0.00 32.44 3.86
822 930 3.088532 AGAGGAGCAGTAACTGAGTCTG 58.911 50.000 0.00 0.00 32.44 3.51
823 931 3.449746 AGAGGAGCAGTAACTGAGTCT 57.550 47.619 0.00 0.00 32.44 3.24
827 946 3.622630 GGAGTAGAGGAGCAGTAACTGA 58.377 50.000 0.00 0.00 32.44 3.41
900 1035 1.525197 CGCTCGCTCTACTCTACTCTG 59.475 57.143 0.00 0.00 0.00 3.35
1081 1243 0.618458 TGGTGCGGCTTATTCTTCCT 59.382 50.000 0.00 0.00 0.00 3.36
1082 1244 1.017387 CTGGTGCGGCTTATTCTTCC 58.983 55.000 0.00 0.00 0.00 3.46
1233 1431 1.213799 GTACGTCACCCCGAACTCC 59.786 63.158 0.00 0.00 0.00 3.85
1748 1948 1.829533 CCCAGAAATCCCGCCCATG 60.830 63.158 0.00 0.00 0.00 3.66
1750 1950 2.087857 AAACCCAGAAATCCCGCCCA 62.088 55.000 0.00 0.00 0.00 5.36
1751 1951 0.033894 TAAACCCAGAAATCCCGCCC 60.034 55.000 0.00 0.00 0.00 6.13
1762 1968 5.016831 ACTAAGAAAGCCCATTAAACCCAG 58.983 41.667 0.00 0.00 0.00 4.45
1775 1983 3.193056 ACTCCACCTACGACTAAGAAAGC 59.807 47.826 0.00 0.00 0.00 3.51
1778 1986 2.490903 GCACTCCACCTACGACTAAGAA 59.509 50.000 0.00 0.00 0.00 2.52
1787 1995 0.035056 ATTGCCAGCACTCCACCTAC 60.035 55.000 0.00 0.00 0.00 3.18
1826 2034 3.223589 ACCAACCAAGCAACGGCC 61.224 61.111 0.00 0.00 42.56 6.13
1866 2074 6.068670 CCTACCCAAATTCCTTCCGATAATT 58.931 40.000 0.00 0.00 0.00 1.40
1892 2100 0.738975 AGCTACAGTCGCATTCGCTA 59.261 50.000 0.00 0.00 35.30 4.26
1983 2191 8.303780 TGAACTAATGCCATATCAATCCAAAA 57.696 30.769 0.00 0.00 0.00 2.44
2091 2299 4.158786 AGACATCCTAGATCATGGACCTG 58.841 47.826 8.58 7.26 34.90 4.00
2099 2307 7.109501 GCTGATACTAGAGACATCCTAGATCA 58.890 42.308 0.00 0.00 37.59 2.92
2109 2317 6.750660 AGTAGTAGGCTGATACTAGAGACA 57.249 41.667 10.65 0.00 38.58 3.41
2119 2327 6.174760 CGATTCCTAGTAGTAGTAGGCTGAT 58.825 44.000 22.00 16.01 40.39 2.90
2133 2341 3.515901 ACTTGCTTCTTCCGATTCCTAGT 59.484 43.478 0.00 0.00 0.00 2.57
2231 2439 6.576778 ATTTATCCTAAAGTACAGCCCACT 57.423 37.500 0.00 0.00 0.00 4.00
2263 2471 9.681062 CCCTTCCTAAACTGTAATAATTTCAGA 57.319 33.333 6.61 0.00 33.93 3.27
2406 2615 6.248569 ACATAAAGGACGGGATTGTATCTT 57.751 37.500 0.00 0.00 0.00 2.40
2518 2734 2.426024 GCTCACGTGGATAGTACTTCCA 59.574 50.000 17.00 17.63 40.96 3.53
2541 2757 1.338337 AGTGTCACTGTCAGGACGAAG 59.662 52.381 4.21 0.00 36.83 3.79
2605 2821 5.148502 ACATATCTACACCCTAAGTCCCAG 58.851 45.833 0.00 0.00 0.00 4.45
2649 2865 1.021202 TTCGCACTGGTGTTTCCTTG 58.979 50.000 2.64 0.00 37.07 3.61
2650 2866 1.021968 GTTCGCACTGGTGTTTCCTT 58.978 50.000 2.64 0.00 37.07 3.36
2651 2867 1.157870 CGTTCGCACTGGTGTTTCCT 61.158 55.000 2.64 0.00 37.07 3.36
2652 2868 1.278637 CGTTCGCACTGGTGTTTCC 59.721 57.895 2.64 0.00 0.00 3.13
2653 2869 1.278637 CCGTTCGCACTGGTGTTTC 59.721 57.895 2.64 0.00 0.00 2.78
2654 2870 0.179078 TACCGTTCGCACTGGTGTTT 60.179 50.000 10.74 0.00 37.20 2.83
2655 2871 0.599204 CTACCGTTCGCACTGGTGTT 60.599 55.000 10.74 0.00 37.20 3.32
2656 2872 1.006571 CTACCGTTCGCACTGGTGT 60.007 57.895 10.74 0.00 37.20 4.16
2657 2873 1.736645 CCTACCGTTCGCACTGGTG 60.737 63.158 10.74 0.00 37.20 4.17
2658 2874 1.466025 TTCCTACCGTTCGCACTGGT 61.466 55.000 6.88 6.88 39.80 4.00
2659 2875 0.320073 TTTCCTACCGTTCGCACTGG 60.320 55.000 0.00 0.00 0.00 4.00
2660 2876 1.504359 TTTTCCTACCGTTCGCACTG 58.496 50.000 0.00 0.00 0.00 3.66
2670 2886 3.532542 CGAAGGAGACCATTTTCCTACC 58.467 50.000 0.00 0.00 42.95 3.18
2671 2887 2.937149 GCGAAGGAGACCATTTTCCTAC 59.063 50.000 0.00 0.00 42.95 3.18
2707 2923 3.679502 CAGCACAACGTATGATGAGACAA 59.320 43.478 11.46 0.00 35.45 3.18
2708 2924 3.253230 CAGCACAACGTATGATGAGACA 58.747 45.455 11.46 0.00 35.45 3.41
2732 2948 0.796312 CATCAACACCCGTAGCACAC 59.204 55.000 0.00 0.00 0.00 3.82
2744 2960 1.002576 CGTCAGCAAAGCACATCAACA 60.003 47.619 0.00 0.00 0.00 3.33
2767 2983 2.035626 CCGCCCAGTGGTCCATTT 59.964 61.111 8.74 0.00 0.00 2.32
2800 3021 2.183300 GCGGACTATGGCACGACA 59.817 61.111 0.00 0.00 0.00 4.35
2821 3042 4.612033 GCGACGCTACAAGGTTGTATTTTT 60.612 41.667 13.73 0.00 42.26 1.94
2888 3109 9.307121 AGATGAAAATAGATCACTTTCTGTACG 57.693 33.333 12.57 0.00 31.67 3.67
3076 3300 1.292085 AGGTAGTACCGGCCCAAAAT 58.708 50.000 13.76 0.00 44.90 1.82
3359 3583 7.394016 TGAATAGTTTCTGCATGGAAGTAAGA 58.606 34.615 0.00 0.00 32.78 2.10
3361 3585 7.168219 ACTGAATAGTTTCTGCATGGAAGTAA 58.832 34.615 0.00 0.00 34.99 2.24
3369 3593 5.413833 CCACTGAACTGAATAGTTTCTGCAT 59.586 40.000 0.00 0.00 46.79 3.96
3515 3739 3.560636 ATAGAAAGTAATGGCACGGCT 57.439 42.857 0.00 0.00 0.00 5.52
3646 3870 0.322322 CACATGGGCCATGCTGTTTT 59.678 50.000 39.55 20.99 44.80 2.43
3655 3879 2.364970 GCTAATTAATGCACATGGGCCA 59.635 45.455 19.33 9.61 0.00 5.36
3732 3956 8.127150 TCCAGAGTTATAGATGTATCACATGG 57.873 38.462 10.09 10.09 39.27 3.66
3805 4029 1.993948 GGGGCGGAGGGAGTACTTT 60.994 63.158 0.00 0.00 0.00 2.66
3818 4042 1.734163 AAGACAAGTAATTCGGGGCG 58.266 50.000 0.00 0.00 0.00 6.13
3820 4044 6.598064 ACAAATCTAAGACAAGTAATTCGGGG 59.402 38.462 0.00 0.00 0.00 5.73
3832 4056 9.692749 CACTAAAGTGTAGACAAATCTAAGACA 57.307 33.333 1.81 0.00 39.20 3.41
3851 4075 7.649973 AGATACGGATGTAGCTAACACTAAAG 58.350 38.462 0.00 0.00 45.09 1.85
3891 4115 3.801307 ACCTCCGTCCCAAATTACTTT 57.199 42.857 0.00 0.00 0.00 2.66
3918 4142 5.888982 AAGTAGGAGGAACTTCAAAGTCA 57.111 39.130 0.00 0.00 41.55 3.41
4024 4724 4.707030 TGCAATGCAGAAAACTATCTGG 57.293 40.909 2.72 0.00 45.60 3.86
4042 4742 8.962884 TCAAGTTTATGCTTATAGATTCTGCA 57.037 30.769 0.00 0.00 38.05 4.41
4105 4806 8.099364 TCTGAAACAACAGAACTGATTAATCC 57.901 34.615 12.90 0.00 42.79 3.01
4236 4948 7.676683 TCCTAATATTCTTTCAGGCTGTAGT 57.323 36.000 15.27 0.00 0.00 2.73
4242 4954 8.860780 ATTCTGATCCTAATATTCTTTCAGGC 57.139 34.615 13.36 0.00 32.10 4.85
4254 4966 5.104193 AGCAGACCACAATTCTGATCCTAAT 60.104 40.000 3.53 0.00 42.81 1.73
4260 4972 3.508793 CCAAAGCAGACCACAATTCTGAT 59.491 43.478 3.53 0.00 42.81 2.90
4264 4976 3.319122 AGTTCCAAAGCAGACCACAATTC 59.681 43.478 0.00 0.00 0.00 2.17
4282 4994 4.049186 TGAGCTGACGTAACTTCAAGTTC 58.951 43.478 5.92 0.00 39.51 3.01
4298 5010 5.220548 CCACACTCGAAAAGAATATGAGCTG 60.221 44.000 0.00 0.00 0.00 4.24
4300 5012 4.870426 TCCACACTCGAAAAGAATATGAGC 59.130 41.667 0.00 0.00 0.00 4.26
4372 5084 2.876581 ACCAGGGGAAAACAGATGAAC 58.123 47.619 0.00 0.00 0.00 3.18
4493 5205 6.662414 TTAAGCCTTGACTTGACAATATCG 57.338 37.500 0.00 0.00 0.00 2.92
4663 5376 3.334691 TCAGCGATGACCTGGTAAAAAG 58.665 45.455 0.00 0.00 0.00 2.27
4694 5407 6.183361 CCTTTATATCCTCAACTTCCTCAGCT 60.183 42.308 0.00 0.00 0.00 4.24
4712 5425 8.278639 TCCATTGCCTTAAACATCTCCTTTATA 58.721 33.333 0.00 0.00 0.00 0.98
4727 5440 6.000246 TCATTGTCAGTATCCATTGCCTTA 58.000 37.500 0.00 0.00 0.00 2.69
4919 5632 7.331026 TGTTAGACACCAATTGATCTTCTAGG 58.669 38.462 7.12 0.00 0.00 3.02
4921 5634 8.999431 GTTTGTTAGACACCAATTGATCTTCTA 58.001 33.333 7.12 4.70 0.00 2.10
4926 5639 6.149633 GTGGTTTGTTAGACACCAATTGATC 58.850 40.000 7.12 1.63 27.82 2.92
4938 5651 5.893500 TCCCCAAATATGTGGTTTGTTAGA 58.106 37.500 11.17 0.00 36.90 2.10
5029 5742 7.879160 ACCTATCACGGATGTAAAGTTTTAACA 59.121 33.333 0.00 0.00 0.00 2.41
5034 5747 7.562135 ACATACCTATCACGGATGTAAAGTTT 58.438 34.615 0.00 0.00 0.00 2.66
5035 5748 7.120923 ACATACCTATCACGGATGTAAAGTT 57.879 36.000 0.00 0.00 0.00 2.66
5036 5749 6.322969 TGACATACCTATCACGGATGTAAAGT 59.677 38.462 0.00 0.00 31.03 2.66
5038 5751 6.718522 TGACATACCTATCACGGATGTAAA 57.281 37.500 0.00 0.00 31.03 2.01
5039 5752 6.718522 TTGACATACCTATCACGGATGTAA 57.281 37.500 0.00 0.00 31.03 2.41
5040 5753 6.911250 ATTGACATACCTATCACGGATGTA 57.089 37.500 0.00 0.00 31.03 2.29
5041 5754 5.808366 ATTGACATACCTATCACGGATGT 57.192 39.130 0.00 0.00 33.52 3.06
5042 5755 7.329471 CACTTATTGACATACCTATCACGGATG 59.671 40.741 0.00 0.00 0.00 3.51
5043 5756 7.378966 CACTTATTGACATACCTATCACGGAT 58.621 38.462 0.00 0.00 0.00 4.18
5045 5758 5.405571 GCACTTATTGACATACCTATCACGG 59.594 44.000 0.00 0.00 0.00 4.94
5059 5936 2.905075 CCAGATGACCGCACTTATTGA 58.095 47.619 0.00 0.00 0.00 2.57
5063 5940 1.220749 GGCCAGATGACCGCACTTA 59.779 57.895 0.00 0.00 0.00 2.24
5066 5943 4.408821 TGGGCCAGATGACCGCAC 62.409 66.667 0.00 0.00 0.00 5.34
5075 5952 1.133181 TGAATGTCCAGTGGGCCAGA 61.133 55.000 12.24 0.00 0.00 3.86
5098 5975 7.288389 ACCATATATGAGACAATTTTGGCACAT 59.712 33.333 14.54 12.64 46.80 3.21
5111 5988 6.174720 TGAACCCTTCACCATATATGAGAC 57.825 41.667 14.54 0.63 34.08 3.36
5117 5995 4.202461 GGCAGATGAACCCTTCACCATATA 60.202 45.833 0.00 0.00 43.48 0.86
5128 6006 3.683365 AATTTTGTGGCAGATGAACCC 57.317 42.857 0.00 0.00 0.00 4.11
5143 6021 7.428282 AAAAGTTCGGTTTGACACAAATTTT 57.572 28.000 0.00 0.00 0.00 1.82
5148 6026 6.087522 CACTTAAAAGTTCGGTTTGACACAA 58.912 36.000 0.00 0.00 37.08 3.33
5215 6093 8.136165 GCTACACATAGTTAGCTACACATAGTT 58.864 37.037 0.00 0.00 33.15 2.24
5216 6094 7.502895 AGCTACACATAGTTAGCTACACATAGT 59.497 37.037 1.25 0.00 43.30 2.12
5217 6095 7.877003 AGCTACACATAGTTAGCTACACATAG 58.123 38.462 1.25 0.00 43.30 2.23
5218 6096 7.040617 GGAGCTACACATAGTTAGCTACACATA 60.041 40.741 7.79 0.00 44.89 2.29
5219 6097 6.239064 GGAGCTACACATAGTTAGCTACACAT 60.239 42.308 7.79 0.00 44.89 3.21
5220 6098 5.067413 GGAGCTACACATAGTTAGCTACACA 59.933 44.000 7.79 0.00 44.89 3.72
5221 6099 5.521544 GGAGCTACACATAGTTAGCTACAC 58.478 45.833 7.79 0.00 44.89 2.90
5222 6100 5.769484 GGAGCTACACATAGTTAGCTACA 57.231 43.478 7.79 0.00 44.89 2.74
5223 6101 5.769484 TGGAGCTACACATAGTTAGCTAC 57.231 43.478 0.00 5.97 44.89 3.58
5224 6102 6.785337 TTTGGAGCTACACATAGTTAGCTA 57.215 37.500 0.00 0.00 44.89 3.32
5226 6104 6.106673 TCTTTTGGAGCTACACATAGTTAGC 58.893 40.000 0.00 0.00 35.91 3.09
5227 6105 8.723942 AATCTTTTGGAGCTACACATAGTTAG 57.276 34.615 0.00 0.00 0.00 2.34
5228 6106 8.946085 CAAATCTTTTGGAGCTACACATAGTTA 58.054 33.333 0.00 0.00 0.00 2.24
5262 6140 5.153513 TGCATTTTCTACGTGATTCTTTGC 58.846 37.500 0.00 0.08 0.00 3.68
5270 6148 8.437360 AAGATGATATTGCATTTTCTACGTGA 57.563 30.769 0.00 0.00 0.00 4.35
5278 6156 8.241497 TGAGGCTTAAGATGATATTGCATTTT 57.759 30.769 6.67 0.00 0.00 1.82
5282 6160 5.163163 ACCTGAGGCTTAAGATGATATTGCA 60.163 40.000 6.67 0.00 0.00 4.08
5301 6180 0.116342 TAGAGGGCAAGGACACCTGA 59.884 55.000 0.00 0.00 34.02 3.86
5398 6344 8.771920 AAATGAAACAGTCATCGTAGTGATTA 57.228 30.769 0.00 0.00 46.80 1.75
5454 6401 7.189794 CCCTACTATGGAATATAAGAGGGACA 58.810 42.308 0.00 0.00 33.81 4.02
5542 6490 3.330701 TCACAAGTTTGAGCCCTCCTATT 59.669 43.478 0.00 0.00 0.00 1.73
5643 6591 2.452600 AACCAACTGGCAGAAGGAAA 57.547 45.000 27.81 0.00 39.32 3.13
5660 6608 9.638239 TTGAACAATGGAATAGCATCTAAAAAC 57.362 29.630 0.00 0.00 0.00 2.43
5684 6632 7.970061 CCACCAGATATAAAGTTTGACATGTTG 59.030 37.037 0.00 0.00 0.00 3.33
5700 6648 2.954318 GCAGCAAATCACCACCAGATAT 59.046 45.455 0.00 0.00 0.00 1.63
5718 6666 4.646492 AGGGGCTAAGTCAAATATTTGCAG 59.354 41.667 21.15 15.45 38.05 4.41
5724 6672 5.625150 CAGCTAAGGGGCTAAGTCAAATAT 58.375 41.667 0.00 0.00 41.00 1.28
5822 6770 5.932303 GTGGCGAGCTAGAATAAATATCCAA 59.068 40.000 0.00 0.00 0.00 3.53
6051 6999 7.645340 GCAATAAGTTATTTCAAGCACGATGAT 59.355 33.333 5.34 0.00 0.00 2.45
6057 7005 6.856895 AGAGGCAATAAGTTATTTCAAGCAC 58.143 36.000 14.24 9.34 0.00 4.40
6123 7075 5.888161 ACAATCTCAATCCACCCAAGATAAC 59.112 40.000 0.00 0.00 0.00 1.89
6125 7077 5.191522 TGACAATCTCAATCCACCCAAGATA 59.808 40.000 0.00 0.00 0.00 1.98
6126 7078 4.018141 TGACAATCTCAATCCACCCAAGAT 60.018 41.667 0.00 0.00 0.00 2.40
6212 7228 5.237344 CCTGTGCCAAATAGTTATACTGCTC 59.763 44.000 0.00 0.00 0.00 4.26
6267 7283 3.181774 CGAACTAATGCGAGTAAATCCGG 59.818 47.826 0.00 0.00 0.00 5.14
6640 7661 2.569059 CCATCCTACAGTTGATGCCAG 58.431 52.381 7.08 0.00 37.61 4.85
6808 7829 3.037431 TGCACAAATAAACACCATGGC 57.963 42.857 13.04 0.00 0.00 4.40
6809 7830 4.567971 ACATGCACAAATAAACACCATGG 58.432 39.130 11.19 11.19 34.48 3.66
6920 7941 2.865119 ACACATGTGAGCCAATCAGA 57.135 45.000 31.94 0.00 39.07 3.27
6931 8222 6.406370 TCCAGGAGAACTAATTACACATGTG 58.594 40.000 24.25 24.25 0.00 3.21
6983 8281 1.645034 CACTGCTCTTGGTACATCCG 58.355 55.000 0.00 0.00 39.30 4.18
6984 8282 1.373570 GCACTGCTCTTGGTACATCC 58.626 55.000 0.00 0.00 39.30 3.51
7012 8310 5.680619 ACACTTAACATCAGTGGTTCAGAA 58.319 37.500 5.14 0.00 45.20 3.02
7049 8454 5.865552 TCTAGAAACTGTATTTGTGTACGGC 59.134 40.000 0.00 0.00 34.91 5.68
7116 8521 3.692101 CCCTATGAGCACCTACGAGATAG 59.308 52.174 0.00 0.00 0.00 2.08
7132 8537 3.198068 GCACGCATACCATATCCCTATG 58.802 50.000 0.00 0.00 35.47 2.23
7147 8552 4.070818 GATGAACGCACGCACGCA 62.071 61.111 0.00 0.00 36.19 5.24
7150 8555 4.147322 CCCGATGAACGCACGCAC 62.147 66.667 0.00 0.00 41.07 5.34
7151 8556 2.766875 TAACCCGATGAACGCACGCA 62.767 55.000 0.00 0.00 41.07 5.24
7152 8557 1.628447 TTAACCCGATGAACGCACGC 61.628 55.000 0.00 0.00 41.07 5.34
7153 8558 0.368907 CTTAACCCGATGAACGCACG 59.631 55.000 0.00 0.00 41.07 5.34
7164 8569 3.395639 ACACACACATACACTTAACCCG 58.604 45.455 0.00 0.00 0.00 5.28
7195 8600 7.442969 TCTTTTTAACACAGTACAATCACCGAT 59.557 33.333 0.00 0.00 0.00 4.18
7196 8601 6.762187 TCTTTTTAACACAGTACAATCACCGA 59.238 34.615 0.00 0.00 0.00 4.69
7199 8604 8.403236 ACCTTCTTTTTAACACAGTACAATCAC 58.597 33.333 0.00 0.00 0.00 3.06
7230 8635 4.799678 TGCTTTTGTTTTCAAGAACACGA 58.200 34.783 0.00 0.00 39.11 4.35
7245 8651 1.600023 TCGGTACCACCTTGCTTTTG 58.400 50.000 13.54 0.00 35.66 2.44
7258 8667 3.549299 TTGTCTCGTCTCTTTCGGTAC 57.451 47.619 0.00 0.00 0.00 3.34
7312 8834 1.135112 GGTGAAAATGGAACGGCATCC 60.135 52.381 0.00 0.00 40.10 3.51
7376 8898 4.504596 GGCATGGCATCGGTCCCA 62.505 66.667 15.47 0.00 35.21 4.37
7444 8968 2.617532 GCTCAGCTTCTGGGTTCTGATT 60.618 50.000 0.00 0.00 33.88 2.57
7460 8991 1.433053 GCTCTGCTGCTGATGCTCAG 61.433 60.000 9.72 8.34 46.90 3.35
7475 9006 3.521727 CCCACCCTACCTATTATGCTCT 58.478 50.000 0.00 0.00 0.00 4.09
7514 9048 3.120546 CGAATTCAACTGCATCACTCGTT 60.121 43.478 6.22 0.00 0.00 3.85
7516 9050 2.222886 CCGAATTCAACTGCATCACTCG 60.223 50.000 6.22 0.00 0.00 4.18
7571 9105 7.252768 GCGCTTACTAAAAACGCTTAACATAAC 60.253 37.037 0.00 0.00 45.71 1.89
7612 9454 2.766313 TGTTTGCTGTCGCTGTATCTT 58.234 42.857 0.00 0.00 36.97 2.40
7614 9456 3.536158 TTTGTTTGCTGTCGCTGTATC 57.464 42.857 0.00 0.00 36.97 2.24
7616 9458 3.626977 CATTTTGTTTGCTGTCGCTGTA 58.373 40.909 0.00 0.00 36.97 2.74
7622 9469 6.402442 GGGAAATATGCATTTTGTTTGCTGTC 60.402 38.462 3.54 0.00 40.77 3.51
7660 9507 2.477176 CGAGAGAGGGGCGACAGAG 61.477 68.421 0.00 0.00 0.00 3.35
7661 9508 2.438614 CGAGAGAGGGGCGACAGA 60.439 66.667 0.00 0.00 0.00 3.41
7691 9552 2.540769 CCGCCGCACTGGTTTATTATTG 60.541 50.000 0.00 0.00 41.21 1.90
7751 9622 2.050691 CGCCAAACCAAAAAGACGATG 58.949 47.619 0.00 0.00 0.00 3.84
7755 9626 2.403259 CCATCGCCAAACCAAAAAGAC 58.597 47.619 0.00 0.00 0.00 3.01
7758 9629 0.465705 TGCCATCGCCAAACCAAAAA 59.534 45.000 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.