Multiple sequence alignment - TraesCS4D01G261800

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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 TraesCS4D01G261800 chr4D 100.000 5029 0 0 1 5029 432768178 432763150 0.000000e+00 9287
1 TraesCS4D01G261800 chr4B 88.074 2591 157 70 5 2480 530471502 530474055 0.000000e+00 2933
2 TraesCS4D01G261800 chr4B 84.330 1672 161 59 3003 4589 530474441 530476096 0.000000e+00 1543
3 TraesCS4D01G261800 chr4B 90.493 284 18 4 4702 4978 530476210 530476491 2.860000e-97 366
4 TraesCS4D01G261800 chr4B 89.781 274 18 5 2718 2981 530474182 530474455 4.820000e-90 342
5 TraesCS4D01G261800 chr4A 89.787 1410 56 22 1 1353 34048095 34046717 0.000000e+00 1725
6 TraesCS4D01G261800 chr4A 89.483 1179 81 15 1466 2612 34046630 34045463 0.000000e+00 1450
7 TraesCS4D01G261800 chr4A 88.982 1189 67 19 3810 4960 34043113 34041951 0.000000e+00 1411
8 TraesCS4D01G261800 chr4A 90.771 856 39 17 3003 3824 34045100 34044251 0.000000e+00 1107
9 TraesCS4D01G261800 chr4A 90.870 230 18 3 2754 2981 34045314 34045086 6.330000e-79 305
10 TraesCS4D01G261800 chr5D 89.524 105 9 2 2616 2719 521674821 521674718 1.140000e-26 132
11 TraesCS4D01G261800 chr7D 90.805 87 6 1 2635 2719 548805224 548805138 1.140000e-21 115
12 TraesCS4D01G261800 chrUn 90.588 85 8 0 2635 2719 84439838 84439922 4.110000e-21 113
13 TraesCS4D01G261800 chr7A 88.764 89 6 2 2635 2719 632908706 632908618 6.890000e-19 106
14 TraesCS4D01G261800 chr7A 88.764 89 6 2 2635 2719 632971259 632971171 6.890000e-19 106
15 TraesCS4D01G261800 chr7A 88.764 89 6 2 2635 2719 633037700 633037612 6.890000e-19 106
16 TraesCS4D01G261800 chr7A 89.286 84 7 1 2635 2716 631961254 631961171 2.480000e-18 104
17 TraesCS4D01G261800 chr7B 88.506 87 8 1 2635 2719 592361910 592361824 2.480000e-18 104
18 TraesCS4D01G261800 chr6B 88.372 86 10 0 2633 2718 59825855 59825770 2.480000e-18 104


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 TraesCS4D01G261800 chr4D 432763150 432768178 5028 True 9287.0 9287 100.0000 1 5029 1 chr4D.!!$R1 5028
1 TraesCS4D01G261800 chr4B 530471502 530476491 4989 False 1296.0 2933 88.1695 5 4978 4 chr4B.!!$F1 4973
2 TraesCS4D01G261800 chr4A 34041951 34048095 6144 True 1199.6 1725 89.9786 1 4960 5 chr4A.!!$R1 4959

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
279 284 0.171455 GTACACGAGGAGCACTCAGG 59.829 60.0 8.82 2.96 46.98 3.86 F
849 929 0.509499 CGTTTGCTTCGCTCCGTTTA 59.491 50.0 0.00 0.00 0.00 2.01 F
1796 1923 0.465824 AGATGAATGCAGGCCAGAGC 60.466 55.0 5.01 6.72 38.76 4.09 F
2925 3206 0.108992 CCATGAACCATGTGTGCTGC 60.109 55.0 0.00 0.00 39.94 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1443 1567 0.642291 CTGTCGTTGCTGCGTATGAG 59.358 55.000 0.00 0.00 0.00 2.90 R
2236 2403 2.124122 TCACGAACATGTGTGAAGTCG 58.876 47.619 14.72 13.62 41.82 4.18 R
2995 3276 0.399075 AACTACCAACAAGTCCCCCG 59.601 55.000 0.00 0.00 0.00 5.73 R
4327 5837 0.179200 CGTTAGTTGCCATTCCGTGC 60.179 55.000 0.00 0.00 0.00 5.34 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
198 203 6.422776 AGCATTTCTTTAGTGACAATACCG 57.577 37.500 0.00 0.00 0.00 4.02
276 281 1.135344 GGAAGTACACGAGGAGCACTC 60.135 57.143 0.00 0.00 43.02 3.51
279 284 0.171455 GTACACGAGGAGCACTCAGG 59.829 60.000 8.82 2.96 46.98 3.86
363 376 5.181245 AGTTACACATGCATTCAGTTGGTAC 59.819 40.000 0.00 0.00 0.00 3.34
365 378 2.083774 ACATGCATTCAGTTGGTACGG 58.916 47.619 0.00 0.00 0.00 4.02
396 414 4.759516 AGGGTTGCACGTTGTTTTATAG 57.240 40.909 0.00 0.00 0.00 1.31
397 415 3.057806 AGGGTTGCACGTTGTTTTATAGC 60.058 43.478 0.00 0.00 0.00 2.97
398 416 3.239254 GGTTGCACGTTGTTTTATAGCC 58.761 45.455 0.00 0.00 0.00 3.93
420 449 4.495184 CCCGTAGCACCGAATGTAAATTTC 60.495 45.833 0.00 0.00 0.00 2.17
616 657 2.670148 CCTCCTCCCCCTGAAACCG 61.670 68.421 0.00 0.00 0.00 4.44
849 929 0.509499 CGTTTGCTTCGCTCCGTTTA 59.491 50.000 0.00 0.00 0.00 2.01
902 994 0.843309 TGGTTTCTCTGGCAAGTGGA 59.157 50.000 0.00 0.00 0.00 4.02
951 1043 3.227276 CTACCCTGCGGCCGAGAT 61.227 66.667 33.48 16.11 0.00 2.75
952 1044 3.214250 CTACCCTGCGGCCGAGATC 62.214 68.421 33.48 12.13 0.00 2.75
978 1070 1.622499 CTCCCGACCCTAACCCCTA 59.378 63.158 0.00 0.00 0.00 3.53
1146 1238 2.514592 TCGGCGTACTACTCCCGG 60.515 66.667 6.85 0.00 41.02 5.73
1319 1411 6.128282 ACGATGTGACACATTGGTTTAGATTC 60.128 38.462 30.62 12.37 42.87 2.52
1409 1533 2.158682 TGAAAAGGGTTGTGCTCTGCTA 60.159 45.455 0.00 0.00 0.00 3.49
1417 1541 2.299993 TGTGCTCTGCTAATTCCTCG 57.700 50.000 0.00 0.00 0.00 4.63
1427 1551 5.047590 TCTGCTAATTCCTCGTTAGTGACAA 60.048 40.000 0.00 0.00 32.90 3.18
1443 1567 5.831997 AGTGACAAGAACTTTACATTTGGC 58.168 37.500 0.00 0.00 0.00 4.52
1465 1589 2.159296 TCATACGCAGCAACGACAGTAT 60.159 45.455 5.33 0.00 36.70 2.12
1466 1590 3.065648 TCATACGCAGCAACGACAGTATA 59.934 43.478 5.33 0.00 36.70 1.47
1477 1601 7.950496 CAGCAACGACAGTATAAACTAGAAAAC 59.050 37.037 0.00 0.00 33.48 2.43
1525 1649 6.822667 AGAAATTTGGGATTGCCATTTTTC 57.177 33.333 17.42 17.42 35.15 2.29
1569 1694 7.620880 AGCTGTTATTAACATCTGGTGTCTTA 58.379 34.615 11.15 0.00 41.14 2.10
1629 1755 6.001449 CCAATTGGTAGAGAAATAGGGTGA 57.999 41.667 16.90 0.00 0.00 4.02
1630 1756 6.058183 CCAATTGGTAGAGAAATAGGGTGAG 58.942 44.000 16.90 0.00 0.00 3.51
1678 1805 3.451141 TGTTTGGATCTTTTGTGGTGC 57.549 42.857 0.00 0.00 0.00 5.01
1735 1862 2.408050 GCGCATAATTCACTCCTCGAT 58.592 47.619 0.30 0.00 0.00 3.59
1742 1869 2.672961 TTCACTCCTCGATGCGAAAT 57.327 45.000 0.00 0.00 34.74 2.17
1755 1882 7.153217 TCGATGCGAAATATCTACTGGAATA 57.847 36.000 0.00 0.00 31.06 1.75
1793 1920 0.822532 GGGAGATGAATGCAGGCCAG 60.823 60.000 5.01 0.00 0.00 4.85
1795 1922 1.595466 GAGATGAATGCAGGCCAGAG 58.405 55.000 5.01 0.00 0.00 3.35
1796 1923 0.465824 AGATGAATGCAGGCCAGAGC 60.466 55.000 5.01 6.72 38.76 4.09
1798 1925 0.465824 ATGAATGCAGGCCAGAGCTC 60.466 55.000 5.01 5.27 39.73 4.09
1903 2030 2.232298 CTCTTGGTCAGGACGAGGCC 62.232 65.000 0.00 0.00 0.00 5.19
1944 2071 8.576442 ACCAAAAATTGTATGAGTACTTCTTGG 58.424 33.333 0.00 0.00 0.00 3.61
1947 2081 6.743575 AATTGTATGAGTACTTCTTGGTGC 57.256 37.500 0.00 0.00 0.00 5.01
1948 2082 4.882842 TGTATGAGTACTTCTTGGTGCA 57.117 40.909 0.00 0.00 0.00 4.57
2026 2186 4.397417 GTCCAAAAGAGATCCAGTCCATTG 59.603 45.833 0.00 0.00 0.00 2.82
2035 2195 8.324191 AGAGATCCAGTCCATTGTTTAATAGA 57.676 34.615 0.00 0.00 0.00 1.98
2036 2196 8.428063 AGAGATCCAGTCCATTGTTTAATAGAG 58.572 37.037 0.00 0.00 0.00 2.43
2042 2202 7.711339 CCAGTCCATTGTTTAATAGAGTAGTCC 59.289 40.741 0.00 0.00 0.00 3.85
2081 2241 3.277715 GAGGCAGAAGGAGAATTTCAGG 58.722 50.000 0.00 0.00 0.00 3.86
2093 2253 7.569240 AGGAGAATTTCAGGGTAGACTTTATG 58.431 38.462 0.00 0.00 0.00 1.90
2179 2340 9.942850 TCATCTAATTTCATCTAAGTGAACACA 57.057 29.630 7.68 0.00 37.80 3.72
2186 2347 6.850752 TCATCTAAGTGAACACAGTCCATA 57.149 37.500 7.68 0.00 0.00 2.74
2192 2353 8.086522 TCTAAGTGAACACAGTCCATACTTAAC 58.913 37.037 7.68 0.00 31.97 2.01
2193 2354 5.227908 AGTGAACACAGTCCATACTTAACG 58.772 41.667 7.68 0.00 31.97 3.18
2196 2357 3.846360 ACACAGTCCATACTTAACGCTC 58.154 45.455 0.00 0.00 31.97 5.03
2197 2358 3.510360 ACACAGTCCATACTTAACGCTCT 59.490 43.478 0.00 0.00 31.97 4.09
2236 2403 6.763135 TGCTGATGATACATAAACTGAAGACC 59.237 38.462 0.00 0.00 0.00 3.85
2297 2465 9.553064 TGTGGAATGTAGCATAAAAATGTTTTT 57.447 25.926 8.36 8.36 42.51 1.94
2336 2504 2.098934 TGCTGTGCTTGTTAAGGTTGTG 59.901 45.455 0.00 0.00 0.00 3.33
2343 2511 3.443976 CTTGTTAAGGTTGTGTTGGCAC 58.556 45.455 0.00 0.00 45.44 5.01
2378 2546 7.865875 TTCGTTTATTTTGTGGATGATGTTG 57.134 32.000 0.00 0.00 0.00 3.33
2502 2670 5.041191 TCTTTCTTCTTCTTCTGCCAAGT 57.959 39.130 0.00 0.00 0.00 3.16
2507 2675 2.688507 TCTTCTTCTGCCAAGTAAGCG 58.311 47.619 0.00 0.00 0.00 4.68
2539 2707 1.150536 TCCGGGCTTATTGATGGCC 59.849 57.895 0.00 0.00 44.59 5.36
2562 2730 6.681777 CCAACTTTCCTGTATTTCTCCTTTG 58.318 40.000 0.00 0.00 0.00 2.77
2575 2743 9.191995 GTATTTCTCCTTTGTGTTTATTTGTGG 57.808 33.333 0.00 0.00 0.00 4.17
2585 2753 4.864247 GTGTTTATTTGTGGCATGCCTTAG 59.136 41.667 35.53 0.00 36.94 2.18
2648 2816 8.625786 TTTTAATTAACTACACCCTCTGTTCC 57.374 34.615 0.00 0.00 33.91 3.62
2649 2817 7.563724 TTAATTAACTACACCCTCTGTTCCT 57.436 36.000 0.00 0.00 33.91 3.36
2650 2818 8.669055 TTAATTAACTACACCCTCTGTTCCTA 57.331 34.615 0.00 0.00 33.91 2.94
2651 2819 7.563724 AATTAACTACACCCTCTGTTCCTAA 57.436 36.000 0.00 0.00 33.91 2.69
2652 2820 6.999705 TTAACTACACCCTCTGTTCCTAAA 57.000 37.500 0.00 0.00 33.91 1.85
2653 2821 7.563724 TTAACTACACCCTCTGTTCCTAAAT 57.436 36.000 0.00 0.00 33.91 1.40
2654 2822 5.422214 ACTACACCCTCTGTTCCTAAATG 57.578 43.478 0.00 0.00 33.91 2.32
2655 2823 4.844655 ACTACACCCTCTGTTCCTAAATGT 59.155 41.667 0.00 0.00 33.91 2.71
2656 2824 6.021030 ACTACACCCTCTGTTCCTAAATGTA 58.979 40.000 0.00 0.00 33.91 2.29
2657 2825 5.836024 ACACCCTCTGTTCCTAAATGTAA 57.164 39.130 0.00 0.00 0.00 2.41
2658 2826 5.805728 ACACCCTCTGTTCCTAAATGTAAG 58.194 41.667 0.00 0.00 0.00 2.34
2659 2827 5.546499 ACACCCTCTGTTCCTAAATGTAAGA 59.454 40.000 0.00 0.00 0.00 2.10
2660 2828 6.215636 ACACCCTCTGTTCCTAAATGTAAGAT 59.784 38.462 0.00 0.00 0.00 2.40
2661 2829 6.540189 CACCCTCTGTTCCTAAATGTAAGATG 59.460 42.308 0.00 0.00 0.00 2.90
2662 2830 5.529060 CCCTCTGTTCCTAAATGTAAGATGC 59.471 44.000 0.00 0.00 0.00 3.91
2663 2831 6.352516 CCTCTGTTCCTAAATGTAAGATGCT 58.647 40.000 0.00 0.00 0.00 3.79
2664 2832 6.825721 CCTCTGTTCCTAAATGTAAGATGCTT 59.174 38.462 0.00 0.00 0.00 3.91
2665 2833 7.337942 CCTCTGTTCCTAAATGTAAGATGCTTT 59.662 37.037 0.00 0.00 0.00 3.51
2666 2834 8.044060 TCTGTTCCTAAATGTAAGATGCTTTG 57.956 34.615 0.00 0.00 0.00 2.77
2667 2835 7.121168 TCTGTTCCTAAATGTAAGATGCTTTGG 59.879 37.037 0.00 0.00 0.00 3.28
2668 2836 5.835113 TCCTAAATGTAAGATGCTTTGGC 57.165 39.130 0.00 0.00 39.26 4.52
2680 2848 3.815856 TGCTTTGGCAGTTCAATTTGA 57.184 38.095 0.00 0.00 44.28 2.69
2681 2849 4.134379 TGCTTTGGCAGTTCAATTTGAA 57.866 36.364 7.74 7.74 44.28 2.69
2682 2850 3.870419 TGCTTTGGCAGTTCAATTTGAAC 59.130 39.130 27.31 27.31 45.20 3.18
2693 2861 5.534207 TTCAATTTGAACTGCCAGAATGT 57.466 34.783 7.74 0.00 30.26 2.71
2694 2862 5.125100 TCAATTTGAACTGCCAGAATGTC 57.875 39.130 0.00 0.00 0.00 3.06
2695 2863 4.828939 TCAATTTGAACTGCCAGAATGTCT 59.171 37.500 0.00 0.00 0.00 3.41
2696 2864 5.302568 TCAATTTGAACTGCCAGAATGTCTT 59.697 36.000 0.00 0.00 0.00 3.01
2697 2865 6.489700 TCAATTTGAACTGCCAGAATGTCTTA 59.510 34.615 0.00 0.00 0.00 2.10
2698 2866 5.689383 TTTGAACTGCCAGAATGTCTTAC 57.311 39.130 0.00 0.00 0.00 2.34
2699 2867 4.350368 TGAACTGCCAGAATGTCTTACA 57.650 40.909 0.00 0.00 0.00 2.41
2700 2868 4.910195 TGAACTGCCAGAATGTCTTACAT 58.090 39.130 0.00 0.00 41.31 2.29
2734 2902 6.088541 AGGTAGTAGTTAACCTCTGGATCA 57.911 41.667 0.88 0.00 42.60 2.92
2779 3053 8.744652 ACAGCTATGTGATATCTGACCTATAAC 58.255 37.037 3.98 0.00 38.57 1.89
2794 3068 5.497474 ACCTATAACGCATGGTTCTTTTCT 58.503 37.500 0.00 0.00 40.09 2.52
2807 3081 8.887717 CATGGTTCTTTTCTTACTATTCCTGAG 58.112 37.037 0.00 0.00 0.00 3.35
2855 3129 9.920133 ATTTCTTATTTCTTGAAGCCTTCTTTC 57.080 29.630 5.96 0.00 31.48 2.62
2864 3145 8.668510 TCTTGAAGCCTTCTTTCATATGTATC 57.331 34.615 5.96 0.00 31.48 2.24
2867 3148 9.466497 TTGAAGCCTTCTTTCATATGTATCTTT 57.534 29.630 5.96 0.00 31.48 2.52
2868 3149 8.896744 TGAAGCCTTCTTTCATATGTATCTTTG 58.103 33.333 5.96 0.00 31.48 2.77
2886 3167 9.841295 GTATCTTTGGGTGTCCTATTATTTACA 57.159 33.333 0.00 0.00 0.00 2.41
2890 3171 6.243216 TGGGTGTCCTATTATTTACAGGTC 57.757 41.667 0.00 0.00 0.00 3.85
2925 3206 0.108992 CCATGAACCATGTGTGCTGC 60.109 55.000 0.00 0.00 39.94 5.25
2980 3261 4.338400 GGGGATATGCTTGTTGGTAGTTTC 59.662 45.833 0.00 0.00 0.00 2.78
2981 3262 5.193679 GGGATATGCTTGTTGGTAGTTTCT 58.806 41.667 0.00 0.00 0.00 2.52
2982 3263 5.652452 GGGATATGCTTGTTGGTAGTTTCTT 59.348 40.000 0.00 0.00 0.00 2.52
2983 3264 6.152831 GGGATATGCTTGTTGGTAGTTTCTTT 59.847 38.462 0.00 0.00 0.00 2.52
2984 3265 7.251281 GGATATGCTTGTTGGTAGTTTCTTTC 58.749 38.462 0.00 0.00 0.00 2.62
2985 3266 7.121315 GGATATGCTTGTTGGTAGTTTCTTTCT 59.879 37.037 0.00 0.00 0.00 2.52
2986 3267 6.715347 ATGCTTGTTGGTAGTTTCTTTCTT 57.285 33.333 0.00 0.00 0.00 2.52
2987 3268 6.524101 TGCTTGTTGGTAGTTTCTTTCTTT 57.476 33.333 0.00 0.00 0.00 2.52
2988 3269 6.930731 TGCTTGTTGGTAGTTTCTTTCTTTT 58.069 32.000 0.00 0.00 0.00 2.27
2989 3270 7.382898 TGCTTGTTGGTAGTTTCTTTCTTTTT 58.617 30.769 0.00 0.00 0.00 1.94
3006 3287 4.688770 TTTTTGCGGGGGACTTGT 57.311 50.000 0.00 0.00 0.00 3.16
3007 3288 2.903404 TTTTTGCGGGGGACTTGTT 58.097 47.368 0.00 0.00 0.00 2.83
3008 3289 0.461961 TTTTTGCGGGGGACTTGTTG 59.538 50.000 0.00 0.00 0.00 3.33
3009 3290 1.395826 TTTTGCGGGGGACTTGTTGG 61.396 55.000 0.00 0.00 0.00 3.77
3010 3291 2.575455 TTTGCGGGGGACTTGTTGGT 62.575 55.000 0.00 0.00 0.00 3.67
3011 3292 1.706995 TTGCGGGGGACTTGTTGGTA 61.707 55.000 0.00 0.00 0.00 3.25
3012 3293 1.376812 GCGGGGGACTTGTTGGTAG 60.377 63.158 0.00 0.00 0.00 3.18
3013 3294 2.063774 CGGGGGACTTGTTGGTAGT 58.936 57.895 0.00 0.00 0.00 2.73
3014 3295 0.399075 CGGGGGACTTGTTGGTAGTT 59.601 55.000 0.00 0.00 0.00 2.24
3015 3296 1.202842 CGGGGGACTTGTTGGTAGTTT 60.203 52.381 0.00 0.00 0.00 2.66
3057 3338 4.513442 TGGACTAAAACGGATCCATCTTG 58.487 43.478 13.41 0.00 36.30 3.02
3076 3365 8.180267 CCATCTTGTCTATTGTTGTCATCTTTC 58.820 37.037 0.00 0.00 0.00 2.62
3107 3396 5.947228 ATAATCCCATTTATGCACTGTCG 57.053 39.130 0.00 0.00 0.00 4.35
3112 3401 2.942376 CCATTTATGCACTGTCGGCTAA 59.058 45.455 0.00 0.00 0.00 3.09
3116 3405 1.021390 ATGCACTGTCGGCTAAGCAC 61.021 55.000 3.19 0.00 34.54 4.40
3365 3654 1.806542 GCTAATATCCATGTGCCACCG 59.193 52.381 0.00 0.00 0.00 4.94
3379 3679 2.160615 TGCCACCGTAACAATGATTTCG 59.839 45.455 0.00 0.00 0.00 3.46
3430 3746 3.760684 GCAATGTGGTCCTGAAAATCTCT 59.239 43.478 0.00 0.00 0.00 3.10
3492 3808 5.163612 CGATCTAGACTTGTTCCATCACAGA 60.164 44.000 0.00 0.00 0.00 3.41
3619 3935 9.923143 CGTGTACCCTGAAATTGATATATTCTA 57.077 33.333 0.00 0.00 0.00 2.10
3717 4034 0.390603 TTATGAGTGTTCCGGGTGCG 60.391 55.000 0.00 0.00 0.00 5.34
3836 5312 1.396648 TCCTGTCGTAAATGCAATGCG 59.603 47.619 0.00 6.96 0.00 4.73
3881 5360 5.523588 TGATTTATGCCCAATCCTTAACCA 58.476 37.500 0.00 0.00 30.64 3.67
3917 5396 7.937700 TCTTTCAGAATATATTCCTGGTCCT 57.062 36.000 19.67 0.00 37.51 3.85
3944 5423 3.347216 TCCAAGGTGCATAGAGCTTTTC 58.653 45.455 0.00 0.00 45.94 2.29
4008 5487 1.312815 GCTCCATTTCCAGGATTCCG 58.687 55.000 0.00 0.00 33.99 4.30
4009 5488 1.312815 CTCCATTTCCAGGATTCCGC 58.687 55.000 0.00 0.00 33.99 5.54
4010 5489 0.623194 TCCATTTCCAGGATTCCGCA 59.377 50.000 0.00 0.00 0.00 5.69
4065 5552 4.611310 CATGGTATGCAGAGTTGAACAG 57.389 45.455 0.00 0.00 0.00 3.16
4067 5554 3.664107 TGGTATGCAGAGTTGAACAGTC 58.336 45.455 0.00 0.00 0.00 3.51
4115 5603 1.978542 AGCGTTATGTCTCGTGTGTC 58.021 50.000 0.00 0.00 0.00 3.67
4171 5659 0.032678 ATTCCTAGTCATGCCTCGCG 59.967 55.000 0.00 0.00 0.00 5.87
4325 5835 7.201767 CCACTTACCACTAGTAGCTACGTAATT 60.202 40.741 17.99 10.81 30.92 1.40
4327 5837 5.511234 ACCACTAGTAGCTACGTAATTGG 57.489 43.478 17.99 19.99 0.00 3.16
4328 5838 4.202090 ACCACTAGTAGCTACGTAATTGGC 60.202 45.833 22.01 0.00 0.00 4.52
4331 5841 2.805845 AGTAGCTACGTAATTGGCACG 58.194 47.619 17.99 0.00 44.80 5.34
4334 5844 1.066716 AGCTACGTAATTGGCACGGAA 60.067 47.619 7.22 0.00 43.59 4.30
4350 5860 0.733150 GGAATGGCAACTAACGAGGC 59.267 55.000 0.00 0.00 37.61 4.70
4379 5889 3.207778 TGTCAAAAGTTGGTAGGTTCGG 58.792 45.455 0.00 0.00 0.00 4.30
4402 5915 5.407084 GGTTTGAACTCTCTAAGCTTGACTC 59.593 44.000 9.86 0.00 33.66 3.36
4433 5946 2.091541 CACATTACAATGCCGTTCCCT 58.908 47.619 1.84 0.00 40.04 4.20
4512 6040 5.452356 CCACCAAAAACTTGAATTGAGCTCT 60.452 40.000 16.19 0.00 0.00 4.09
4514 6042 7.373493 CACCAAAAACTTGAATTGAGCTCTAT 58.627 34.615 16.19 10.36 0.00 1.98
4515 6043 7.869429 CACCAAAAACTTGAATTGAGCTCTATT 59.131 33.333 21.07 21.07 0.00 1.73
4614 6161 2.501723 TCCCTGGTGCTGAAAGATACTC 59.498 50.000 0.00 0.00 34.07 2.59
4626 6173 2.898729 AGATACTCGGACCAATGCTG 57.101 50.000 0.00 0.00 0.00 4.41
4627 6174 1.202580 AGATACTCGGACCAATGCTGC 60.203 52.381 0.00 0.00 0.00 5.25
4745 6331 0.438445 CGACGAGAACCACGTACGTA 59.562 55.000 22.34 0.00 43.97 3.57
4816 6402 1.596934 GATGGTGGAAGCGACAGGA 59.403 57.895 0.00 0.00 36.92 3.86
4893 6485 3.391355 GCTTGCGCGTAACGGTAT 58.609 55.556 5.23 0.00 43.93 2.73
4904 6496 0.747644 TAACGGTATGAGGCGTCGGA 60.748 55.000 1.39 0.00 0.00 4.55
4971 6563 4.570663 CACCCGATCGCGACCTCC 62.571 72.222 12.93 0.00 40.82 4.30
4991 6583 4.992511 CCCGCCCCGAAACAACGA 62.993 66.667 0.00 0.00 35.09 3.85
4992 6584 3.419759 CCGCCCCGAAACAACGAG 61.420 66.667 0.00 0.00 35.09 4.18
4993 6585 4.084888 CGCCCCGAAACAACGAGC 62.085 66.667 0.00 0.00 35.09 5.03
4994 6586 2.975799 GCCCCGAAACAACGAGCA 60.976 61.111 0.00 0.00 34.40 4.26
4995 6587 2.943653 CCCCGAAACAACGAGCAC 59.056 61.111 0.00 0.00 35.09 4.40
4996 6588 1.890041 CCCCGAAACAACGAGCACA 60.890 57.895 0.00 0.00 35.09 4.57
4997 6589 1.440938 CCCCGAAACAACGAGCACAA 61.441 55.000 0.00 0.00 35.09 3.33
4998 6590 0.378962 CCCGAAACAACGAGCACAAA 59.621 50.000 0.00 0.00 35.09 2.83
4999 6591 1.462791 CCGAAACAACGAGCACAAAC 58.537 50.000 0.00 0.00 35.09 2.93
5000 6592 1.063469 CCGAAACAACGAGCACAAACT 59.937 47.619 0.00 0.00 35.09 2.66
5001 6593 2.363220 CGAAACAACGAGCACAAACTC 58.637 47.619 0.00 0.00 35.09 3.01
5002 6594 2.716398 GAAACAACGAGCACAAACTCC 58.284 47.619 0.00 0.00 32.79 3.85
5003 6595 0.655733 AACAACGAGCACAAACTCCG 59.344 50.000 0.00 0.00 32.79 4.63
5004 6596 0.461339 ACAACGAGCACAAACTCCGT 60.461 50.000 0.00 0.00 32.79 4.69
5005 6597 0.042188 CAACGAGCACAAACTCCGTG 60.042 55.000 0.00 0.00 37.43 4.94
5006 6598 1.157870 AACGAGCACAAACTCCGTGG 61.158 55.000 0.00 0.00 34.85 4.94
5007 6599 2.946762 GAGCACAAACTCCGTGGC 59.053 61.111 0.00 0.00 34.85 5.01
5008 6600 2.594592 AGCACAAACTCCGTGGCC 60.595 61.111 0.00 0.00 34.85 5.36
5009 6601 4.025401 GCACAAACTCCGTGGCCG 62.025 66.667 0.00 0.00 34.85 6.13
5010 6602 4.025401 CACAAACTCCGTGGCCGC 62.025 66.667 6.11 6.11 0.00 6.53
5013 6605 3.993584 AAACTCCGTGGCCGCGTA 61.994 61.111 34.58 21.16 0.00 4.42
5014 6606 3.518419 AAACTCCGTGGCCGCGTAA 62.518 57.895 34.58 22.07 0.00 3.18
5015 6607 4.729856 ACTCCGTGGCCGCGTAAC 62.730 66.667 34.58 9.13 0.00 2.50
5025 6617 2.507769 CGCGTAACGGACCCTTCC 60.508 66.667 0.00 0.00 38.44 3.46
5026 6618 2.976356 GCGTAACGGACCCTTCCT 59.024 61.111 0.00 0.00 40.23 3.36
5027 6619 1.294459 GCGTAACGGACCCTTCCTT 59.706 57.895 0.00 0.00 40.23 3.36
5028 6620 0.321034 GCGTAACGGACCCTTCCTTT 60.321 55.000 0.00 0.00 40.23 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 84 6.239217 TGCAGGTGATTACTGATAGTGATT 57.761 37.500 0.00 0.00 38.20 2.57
276 281 2.988493 CAATGCACAAACCGATTTCCTG 59.012 45.455 0.00 0.00 0.00 3.86
279 284 3.900941 AGTCAATGCACAAACCGATTTC 58.099 40.909 0.00 0.00 0.00 2.17
363 376 0.875059 GCAACCCTTTCAGAGTTCCG 59.125 55.000 0.00 0.00 0.00 4.30
365 378 1.264288 CGTGCAACCCTTTCAGAGTTC 59.736 52.381 0.00 0.00 0.00 3.01
379 392 2.095668 CGGGCTATAAAACAACGTGCAA 60.096 45.455 0.00 0.00 0.00 4.08
385 403 3.064408 GGTGCTACGGGCTATAAAACAAC 59.936 47.826 4.43 0.00 42.39 3.32
396 414 0.460635 TTACATTCGGTGCTACGGGC 60.461 55.000 1.05 0.00 42.22 6.13
397 415 2.012937 TTTACATTCGGTGCTACGGG 57.987 50.000 1.05 0.00 0.00 5.28
398 416 4.584394 GAAATTTACATTCGGTGCTACGG 58.416 43.478 0.00 0.00 0.00 4.02
420 449 3.201290 ACATCTAAGCTCAATTCCAGCG 58.799 45.455 0.00 0.00 42.14 5.18
849 929 2.048222 CAGTGTCGCCGTCCACAT 60.048 61.111 11.07 0.00 33.99 3.21
902 994 2.351276 CAGCTTAGCCCGTGGGTT 59.649 61.111 6.82 2.67 37.65 4.11
949 1041 3.846254 TCGGGAGGGGAGGGGATC 61.846 72.222 0.00 0.00 0.00 3.36
950 1042 4.173701 GTCGGGAGGGGAGGGGAT 62.174 72.222 0.00 0.00 0.00 3.85
954 1046 3.017896 TTAGGGTCGGGAGGGGAGG 62.018 68.421 0.00 0.00 0.00 4.30
955 1047 1.761271 GTTAGGGTCGGGAGGGGAG 60.761 68.421 0.00 0.00 0.00 4.30
956 1048 2.365764 GTTAGGGTCGGGAGGGGA 59.634 66.667 0.00 0.00 0.00 4.81
957 1049 2.767073 GGTTAGGGTCGGGAGGGG 60.767 72.222 0.00 0.00 0.00 4.79
1237 1329 3.703127 GAGTTCCCGGGCCTTCGT 61.703 66.667 18.49 0.00 0.00 3.85
1319 1411 9.103048 GTAAACATCAGTAAATGAGAAAACACG 57.897 33.333 0.00 0.00 42.53 4.49
1354 1478 9.737844 AGCTCTTACCTAATACTACCATACTAC 57.262 37.037 0.00 0.00 0.00 2.73
1357 1481 8.632906 TCAGCTCTTACCTAATACTACCATAC 57.367 38.462 0.00 0.00 0.00 2.39
1358 1482 9.824216 ATTCAGCTCTTACCTAATACTACCATA 57.176 33.333 0.00 0.00 0.00 2.74
1359 1483 8.728596 ATTCAGCTCTTACCTAATACTACCAT 57.271 34.615 0.00 0.00 0.00 3.55
1360 1484 7.783119 TGATTCAGCTCTTACCTAATACTACCA 59.217 37.037 0.00 0.00 0.00 3.25
1361 1485 8.179509 TGATTCAGCTCTTACCTAATACTACC 57.820 38.462 0.00 0.00 0.00 3.18
1364 1488 8.928448 TCATTGATTCAGCTCTTACCTAATACT 58.072 33.333 0.00 0.00 0.00 2.12
1372 1496 6.151817 ACCCTTTTCATTGATTCAGCTCTTAC 59.848 38.462 0.00 0.00 0.00 2.34
1409 1533 5.855045 AGTTCTTGTCACTAACGAGGAATT 58.145 37.500 0.00 0.00 39.56 2.17
1417 1541 7.378728 GCCAAATGTAAAGTTCTTGTCACTAAC 59.621 37.037 0.00 0.00 0.00 2.34
1427 1551 5.163754 GCGTATGAGCCAAATGTAAAGTTCT 60.164 40.000 0.00 0.00 0.00 3.01
1443 1567 0.642291 CTGTCGTTGCTGCGTATGAG 59.358 55.000 0.00 0.00 0.00 2.90
1477 1601 6.598525 TGTTTGCTCATGACAGTATTAAACG 58.401 36.000 0.00 0.00 0.00 3.60
1493 1617 5.334337 GCAATCCCAAATTTCTTGTTTGCTC 60.334 40.000 14.04 0.00 35.71 4.26
1569 1694 3.134574 TGTTTCACGAACAGCCCTAAT 57.865 42.857 0.00 0.00 43.13 1.73
1623 1749 3.181420 ACCTGTAGAACACTACTCACCCT 60.181 47.826 0.00 0.00 37.81 4.34
1624 1750 3.163467 ACCTGTAGAACACTACTCACCC 58.837 50.000 0.00 0.00 37.81 4.61
1627 1753 8.185506 TCAAAATACCTGTAGAACACTACTCA 57.814 34.615 0.00 0.00 37.81 3.41
1628 1754 9.088512 CATCAAAATACCTGTAGAACACTACTC 57.911 37.037 0.00 0.00 37.81 2.59
1629 1755 8.594550 ACATCAAAATACCTGTAGAACACTACT 58.405 33.333 0.00 0.00 37.81 2.57
1630 1756 8.773404 ACATCAAAATACCTGTAGAACACTAC 57.227 34.615 0.00 0.00 37.56 2.73
1735 1862 6.665992 AGGTATTCCAGTAGATATTTCGCA 57.334 37.500 0.00 0.00 35.89 5.10
1765 1892 5.514310 CCTGCATTCATCTCCCTTGATCATA 60.514 44.000 0.00 0.00 0.00 2.15
1793 1920 4.688511 TCTCAGAACTAGTTTCGAGCTC 57.311 45.455 21.72 2.73 39.47 4.09
1795 1922 4.547532 TGTTCTCAGAACTAGTTTCGAGC 58.452 43.478 18.49 13.74 39.47 5.03
1796 1923 7.644986 AATTGTTCTCAGAACTAGTTTCGAG 57.355 36.000 18.49 20.99 39.47 4.04
1798 1925 8.122952 ACAAAATTGTTCTCAGAACTAGTTTCG 58.877 33.333 19.88 17.28 38.47 3.46
1931 2058 5.675684 TCATATGCACCAAGAAGTACTCA 57.324 39.130 0.00 0.00 0.00 3.41
1978 2138 6.436738 TCACAGGTACCTAAAACATGGTAA 57.563 37.500 15.80 0.00 40.09 2.85
2026 2186 8.025445 TCTTCAACACGGACTACTCTATTAAAC 58.975 37.037 0.00 0.00 0.00 2.01
2035 2195 3.800506 CGTTTTCTTCAACACGGACTACT 59.199 43.478 0.00 0.00 0.00 2.57
2036 2196 4.111489 CGTTTTCTTCAACACGGACTAC 57.889 45.455 0.00 0.00 0.00 2.73
2042 2202 2.286184 CCTCACCGTTTTCTTCAACACG 60.286 50.000 0.00 0.00 0.00 4.49
2058 2218 3.679389 TGAAATTCTCCTTCTGCCTCAC 58.321 45.455 0.00 0.00 0.00 3.51
2081 2241 9.070179 TCCTTTTGGTAAAACATAAAGTCTACC 57.930 33.333 0.00 0.00 41.38 3.18
2093 2253 6.103330 TGAAGCAACTTCCTTTTGGTAAAAC 58.897 36.000 4.96 0.00 39.51 2.43
2178 2339 6.481954 AAAAAGAGCGTTAAGTATGGACTG 57.518 37.500 0.00 0.00 35.52 3.51
2236 2403 2.124122 TCACGAACATGTGTGAAGTCG 58.876 47.619 14.72 13.62 41.82 4.18
2297 2465 8.588472 AGCACAGCAAGATCTATAACACATATA 58.412 33.333 0.00 0.00 0.00 0.86
2305 2473 7.280876 CCTTAACAAGCACAGCAAGATCTATAA 59.719 37.037 0.00 0.00 0.00 0.98
2336 2504 5.291293 ACGAATTAAGTACATGTGCCAAC 57.709 39.130 9.11 0.00 0.00 3.77
2377 2545 9.434275 TGTATTAGGATTATCTGGAGAAAGACA 57.566 33.333 0.00 0.00 0.00 3.41
2378 2546 9.921637 CTGTATTAGGATTATCTGGAGAAAGAC 57.078 37.037 0.00 0.00 0.00 3.01
2402 2570 7.713942 GGTCAATAACTATAAGGTTGTACCCTG 59.286 40.741 0.00 0.00 39.75 4.45
2502 2670 4.628333 CCGGACAATCTAAAGTTTCGCTTA 59.372 41.667 0.00 0.00 36.17 3.09
2507 2675 3.344515 AGCCCGGACAATCTAAAGTTTC 58.655 45.455 0.73 0.00 0.00 2.78
2539 2707 7.141363 CACAAAGGAGAAATACAGGAAAGTTG 58.859 38.462 0.00 0.00 0.00 3.16
2540 2708 6.833933 ACACAAAGGAGAAATACAGGAAAGTT 59.166 34.615 0.00 0.00 0.00 2.66
2562 2730 3.317603 AGGCATGCCACAAATAAACAC 57.682 42.857 37.18 6.57 38.92 3.32
2575 2743 5.642063 TCAGTGTAGTTTAACTAAGGCATGC 59.358 40.000 9.90 9.90 31.62 4.06
2628 2796 7.563724 TTTAGGAACAGAGGGTGTAGTTAAT 57.436 36.000 0.00 0.00 39.03 1.40
2630 2798 6.499350 ACATTTAGGAACAGAGGGTGTAGTTA 59.501 38.462 0.00 0.00 39.03 2.24
2631 2799 5.309806 ACATTTAGGAACAGAGGGTGTAGTT 59.690 40.000 0.00 0.00 39.03 2.24
2632 2800 4.844655 ACATTTAGGAACAGAGGGTGTAGT 59.155 41.667 0.00 0.00 39.03 2.73
2633 2801 5.422214 ACATTTAGGAACAGAGGGTGTAG 57.578 43.478 0.00 0.00 39.03 2.74
2634 2802 6.727231 TCTTACATTTAGGAACAGAGGGTGTA 59.273 38.462 0.00 0.00 39.03 2.90
2635 2803 5.546499 TCTTACATTTAGGAACAGAGGGTGT 59.454 40.000 0.00 0.00 43.24 4.16
2636 2804 6.049955 TCTTACATTTAGGAACAGAGGGTG 57.950 41.667 0.00 0.00 0.00 4.61
2637 2805 6.653989 CATCTTACATTTAGGAACAGAGGGT 58.346 40.000 0.00 0.00 0.00 4.34
2638 2806 5.529060 GCATCTTACATTTAGGAACAGAGGG 59.471 44.000 0.00 0.00 0.00 4.30
2639 2807 6.352516 AGCATCTTACATTTAGGAACAGAGG 58.647 40.000 0.00 0.00 0.00 3.69
2640 2808 7.856145 AAGCATCTTACATTTAGGAACAGAG 57.144 36.000 0.00 0.00 0.00 3.35
2641 2809 7.121168 CCAAAGCATCTTACATTTAGGAACAGA 59.879 37.037 0.00 0.00 0.00 3.41
2642 2810 7.253422 CCAAAGCATCTTACATTTAGGAACAG 58.747 38.462 0.00 0.00 0.00 3.16
2643 2811 6.350110 GCCAAAGCATCTTACATTTAGGAACA 60.350 38.462 0.00 0.00 39.53 3.18
2644 2812 6.036470 GCCAAAGCATCTTACATTTAGGAAC 58.964 40.000 0.00 0.00 39.53 3.62
2645 2813 5.714333 TGCCAAAGCATCTTACATTTAGGAA 59.286 36.000 0.00 0.00 46.52 3.36
2646 2814 5.260424 TGCCAAAGCATCTTACATTTAGGA 58.740 37.500 0.00 0.00 46.52 2.94
2647 2815 5.581126 TGCCAAAGCATCTTACATTTAGG 57.419 39.130 0.00 0.00 46.52 2.69
2655 2823 7.686371 TTCAAATTGAACTGCCAAAGCATCTTA 60.686 33.333 4.03 0.00 38.89 2.10
2656 2824 6.908969 TTCAAATTGAACTGCCAAAGCATCTT 60.909 34.615 4.03 0.00 38.89 2.40
2657 2825 5.453621 TTCAAATTGAACTGCCAAAGCATCT 60.454 36.000 4.03 0.00 38.89 2.90
2658 2826 4.751098 TTCAAATTGAACTGCCAAAGCATC 59.249 37.500 4.03 0.00 38.89 3.91
2659 2827 4.706035 TTCAAATTGAACTGCCAAAGCAT 58.294 34.783 4.03 0.00 38.89 3.79
2660 2828 4.134379 TTCAAATTGAACTGCCAAAGCA 57.866 36.364 4.03 0.00 37.88 3.91
2671 2839 5.302568 AGACATTCTGGCAGTTCAAATTGAA 59.697 36.000 15.27 4.03 33.32 2.69
2672 2840 4.828939 AGACATTCTGGCAGTTCAAATTGA 59.171 37.500 15.27 0.00 0.00 2.57
2673 2841 5.130292 AGACATTCTGGCAGTTCAAATTG 57.870 39.130 15.27 4.14 0.00 2.32
2674 2842 5.796424 AAGACATTCTGGCAGTTCAAATT 57.204 34.783 15.27 1.90 0.00 1.82
2675 2843 5.769662 TGTAAGACATTCTGGCAGTTCAAAT 59.230 36.000 15.27 3.78 0.00 2.32
2676 2844 5.129634 TGTAAGACATTCTGGCAGTTCAAA 58.870 37.500 15.27 1.14 0.00 2.69
2677 2845 4.713553 TGTAAGACATTCTGGCAGTTCAA 58.286 39.130 15.27 1.54 0.00 2.69
2678 2846 4.350368 TGTAAGACATTCTGGCAGTTCA 57.650 40.909 15.27 0.03 0.00 3.18
2679 2847 5.886960 AATGTAAGACATTCTGGCAGTTC 57.113 39.130 15.27 7.17 44.91 3.01
2691 2859 9.256228 ACTACCTCTGATTCTAAATGTAAGACA 57.744 33.333 0.00 0.00 0.00 3.41
2700 2868 9.765295 AGGTTAACTACTACCTCTGATTCTAAA 57.235 33.333 5.42 0.00 40.78 1.85
2712 2880 5.892686 AGTGATCCAGAGGTTAACTACTACC 59.107 44.000 5.42 0.00 34.54 3.18
2713 2881 8.569641 CATAGTGATCCAGAGGTTAACTACTAC 58.430 40.741 5.42 1.13 0.00 2.73
2714 2882 7.230913 GCATAGTGATCCAGAGGTTAACTACTA 59.769 40.741 5.42 0.00 0.00 1.82
2716 2884 6.041069 AGCATAGTGATCCAGAGGTTAACTAC 59.959 42.308 5.42 0.26 0.00 2.73
2724 2892 4.412796 TTCAAGCATAGTGATCCAGAGG 57.587 45.455 0.00 0.00 0.00 3.69
2779 3053 6.316390 AGGAATAGTAAGAAAAGAACCATGCG 59.684 38.462 0.00 0.00 0.00 4.73
2864 3145 7.116736 ACCTGTAAATAATAGGACACCCAAAG 58.883 38.462 0.00 0.00 35.55 2.77
2867 3148 5.968167 AGACCTGTAAATAATAGGACACCCA 59.032 40.000 0.00 0.00 35.55 4.51
2868 3149 6.496144 AGACCTGTAAATAATAGGACACCC 57.504 41.667 0.00 0.00 35.55 4.61
2886 3167 6.384015 TCATGGTCAGTGTATCATAAAGACCT 59.616 38.462 0.00 0.00 43.31 3.85
2890 3171 6.823182 TGGTTCATGGTCAGTGTATCATAAAG 59.177 38.462 0.00 0.00 0.00 1.85
2925 3206 9.057089 GGGTTTTATTACAGGAGAACATGATAG 57.943 37.037 0.00 0.00 0.00 2.08
2989 3270 0.461961 CAACAAGTCCCCCGCAAAAA 59.538 50.000 0.00 0.00 0.00 1.94
2990 3271 1.395826 CCAACAAGTCCCCCGCAAAA 61.396 55.000 0.00 0.00 0.00 2.44
2991 3272 1.830408 CCAACAAGTCCCCCGCAAA 60.830 57.895 0.00 0.00 0.00 3.68
2992 3273 1.706995 TACCAACAAGTCCCCCGCAA 61.707 55.000 0.00 0.00 0.00 4.85
2993 3274 2.119484 CTACCAACAAGTCCCCCGCA 62.119 60.000 0.00 0.00 0.00 5.69
2994 3275 1.376812 CTACCAACAAGTCCCCCGC 60.377 63.158 0.00 0.00 0.00 6.13
2995 3276 0.399075 AACTACCAACAAGTCCCCCG 59.601 55.000 0.00 0.00 0.00 5.73
2996 3277 2.158579 TGAAACTACCAACAAGTCCCCC 60.159 50.000 0.00 0.00 0.00 5.40
2997 3278 3.217681 TGAAACTACCAACAAGTCCCC 57.782 47.619 0.00 0.00 0.00 4.81
2998 3279 4.394729 TCATGAAACTACCAACAAGTCCC 58.605 43.478 0.00 0.00 0.00 4.46
2999 3280 6.385649 TTTCATGAAACTACCAACAAGTCC 57.614 37.500 16.91 0.00 0.00 3.85
3000 3281 7.679659 GTTTTCATGAAACTACCAACAAGTC 57.320 36.000 20.35 0.00 43.44 3.01
3012 3293 9.528018 TCCAAGAACATTTAGTTTTCATGAAAC 57.472 29.630 20.35 14.74 46.42 2.78
3013 3294 9.528018 GTCCAAGAACATTTAGTTTTCATGAAA 57.472 29.630 16.91 16.91 41.51 2.69
3014 3295 8.912988 AGTCCAAGAACATTTAGTTTTCATGAA 58.087 29.630 3.38 3.38 41.51 2.57
3015 3296 8.463930 AGTCCAAGAACATTTAGTTTTCATGA 57.536 30.769 0.00 0.00 41.51 3.07
3082 3371 7.121168 CCGACAGTGCATAAATGGGATTATTAT 59.879 37.037 0.00 0.00 0.00 1.28
3102 3391 3.932710 TCATAAAAGTGCTTAGCCGACAG 59.067 43.478 0.29 0.00 0.00 3.51
3107 3396 5.410067 TGCAATTCATAAAAGTGCTTAGCC 58.590 37.500 10.91 0.00 36.18 3.93
3112 3401 6.088016 TGAACTGCAATTCATAAAAGTGCT 57.912 33.333 6.47 0.00 33.62 4.40
3142 3431 6.922540 AGGATACCTAGGGCATAAATTGTTT 58.077 36.000 14.81 0.00 28.47 2.83
3316 3605 3.506067 CCTTCAGCCAATAAAACTCCGTT 59.494 43.478 0.00 0.00 0.00 4.44
3365 3654 9.051027 CATTGTAGTCAACGAAATCATTGTTAC 57.949 33.333 0.00 0.00 36.33 2.50
3379 3679 7.435068 AACTAATGACACCATTGTAGTCAAC 57.565 36.000 11.03 0.00 44.47 3.18
3430 3746 3.322541 TCCGACTTCACCTGTCATTTGTA 59.677 43.478 0.00 0.00 34.37 2.41
3492 3808 4.223923 CCAAGAAGGAGACACTCATAAGGT 59.776 45.833 0.00 0.00 41.22 3.50
3565 3881 7.033791 CCAGATCAAATGTTGAATTCCAGAAG 58.966 38.462 2.27 0.00 43.95 2.85
3580 3896 2.093128 GGGTACACGGTCCAGATCAAAT 60.093 50.000 0.00 0.00 0.00 2.32
3619 3935 1.627834 CAGGAAGAAAGCCAGGAGACT 59.372 52.381 0.00 0.00 46.44 3.24
3788 4112 6.338214 TGCTTCATTGCAAATGGTTAACTA 57.662 33.333 1.71 0.00 40.29 2.24
3795 4119 4.748102 GGACATATGCTTCATTGCAAATGG 59.252 41.667 1.71 0.00 46.61 3.16
3836 5312 7.553881 TCATACTGCAACTATAAAAAGAGCC 57.446 36.000 0.00 0.00 0.00 4.70
3867 5346 3.831911 TCTTTTGCTGGTTAAGGATTGGG 59.168 43.478 0.00 0.00 0.00 4.12
3944 5423 0.447801 CGGAACCCAATTCTCTTGCG 59.552 55.000 0.00 0.00 37.48 4.85
3980 5459 1.706287 GGAAATGGAGCGGCTCGTTC 61.706 60.000 22.63 22.12 36.42 3.95
4055 5542 2.594654 CGATACAGCGACTGTTCAACTC 59.405 50.000 15.81 6.85 42.59 3.01
4067 5554 1.755161 AGCATTACGTCGATACAGCG 58.245 50.000 0.00 0.00 0.00 5.18
4115 5603 8.119226 CCGAAAGAAATGAGCTATTTACAGAAG 58.881 37.037 0.00 0.00 39.06 2.85
4171 5659 9.974750 GAGAATCTAAATACAGCAGTGTAAAAC 57.025 33.333 0.00 0.00 42.54 2.43
4325 5835 0.250945 TTAGTTGCCATTCCGTGCCA 60.251 50.000 0.00 0.00 0.00 4.92
4327 5837 0.179200 CGTTAGTTGCCATTCCGTGC 60.179 55.000 0.00 0.00 0.00 5.34
4328 5838 1.393539 CTCGTTAGTTGCCATTCCGTG 59.606 52.381 0.00 0.00 0.00 4.94
4331 5841 0.733150 GCCTCGTTAGTTGCCATTCC 59.267 55.000 0.00 0.00 0.00 3.01
4334 5844 2.106683 GCGCCTCGTTAGTTGCCAT 61.107 57.895 0.00 0.00 0.00 4.40
4350 5860 3.249917 ACCAACTTTTGACAAAACTGCG 58.750 40.909 9.30 3.04 0.00 5.18
4379 5889 5.986135 TGAGTCAAGCTTAGAGAGTTCAAAC 59.014 40.000 0.00 0.00 0.00 2.93
4402 5915 4.496341 GCATTGTAATGTGGATCGTCCTTG 60.496 45.833 6.48 0.00 38.65 3.61
4443 5956 0.677098 ACAGAAGCAGCAGCAGGATG 60.677 55.000 3.17 0.00 45.49 3.51
4512 6040 7.072328 TGGACCAGGATTCATGTTAGATCAATA 59.928 37.037 0.00 0.00 0.00 1.90
4514 6042 5.191522 TGGACCAGGATTCATGTTAGATCAA 59.808 40.000 0.00 0.00 0.00 2.57
4515 6043 4.721274 TGGACCAGGATTCATGTTAGATCA 59.279 41.667 0.00 0.00 0.00 2.92
4529 6076 1.635487 CCCTTCAAGAATGGACCAGGA 59.365 52.381 0.00 0.00 0.00 3.86
4614 6161 3.818787 GGCAGCAGCATTGGTCCG 61.819 66.667 2.65 0.00 44.61 4.79
4627 6174 1.973281 AACACAAGGATGCGGGCAG 60.973 57.895 0.00 0.00 0.00 4.85
4695 6242 4.537135 ACGGCTTCTTCTACTCAAATCA 57.463 40.909 0.00 0.00 0.00 2.57
4696 6243 4.691216 ACAACGGCTTCTTCTACTCAAATC 59.309 41.667 0.00 0.00 0.00 2.17
4697 6244 4.642429 ACAACGGCTTCTTCTACTCAAAT 58.358 39.130 0.00 0.00 0.00 2.32
4700 6247 2.351447 CGACAACGGCTTCTTCTACTCA 60.351 50.000 0.00 0.00 35.72 3.41
4816 6402 2.365237 GTAGCCGGACCTCCCCTT 60.365 66.667 5.05 0.00 0.00 3.95
4904 6496 2.919328 GGTGGCTTTGGCTTGGCT 60.919 61.111 0.00 0.00 38.73 4.75
4978 6570 1.440938 TTGTGCTCGTTGTTTCGGGG 61.441 55.000 0.00 0.00 0.00 5.73
4979 6571 0.378962 TTTGTGCTCGTTGTTTCGGG 59.621 50.000 0.00 0.00 0.00 5.14
4980 6572 1.063469 AGTTTGTGCTCGTTGTTTCGG 59.937 47.619 0.00 0.00 0.00 4.30
4981 6573 2.363220 GAGTTTGTGCTCGTTGTTTCG 58.637 47.619 0.00 0.00 0.00 3.46
4982 6574 2.716398 GGAGTTTGTGCTCGTTGTTTC 58.284 47.619 0.00 0.00 36.41 2.78
4983 6575 1.063469 CGGAGTTTGTGCTCGTTGTTT 59.937 47.619 0.00 0.00 36.41 2.83
4984 6576 0.655733 CGGAGTTTGTGCTCGTTGTT 59.344 50.000 0.00 0.00 36.41 2.83
4985 6577 0.461339 ACGGAGTTTGTGCTCGTTGT 60.461 50.000 0.00 0.00 37.78 3.32
4986 6578 0.042188 CACGGAGTTTGTGCTCGTTG 60.042 55.000 0.00 0.00 41.61 4.10
4987 6579 1.157870 CCACGGAGTTTGTGCTCGTT 61.158 55.000 0.00 0.00 41.61 3.85
4988 6580 1.594293 CCACGGAGTTTGTGCTCGT 60.594 57.895 0.00 0.00 41.61 4.18
4989 6581 2.954753 GCCACGGAGTTTGTGCTCG 61.955 63.158 0.00 0.00 41.61 5.03
4990 6582 2.617274 GGCCACGGAGTTTGTGCTC 61.617 63.158 0.00 0.00 41.61 4.26
4991 6583 2.594592 GGCCACGGAGTTTGTGCT 60.595 61.111 0.00 0.00 41.61 4.40
4992 6584 4.025401 CGGCCACGGAGTTTGTGC 62.025 66.667 2.24 0.00 41.61 4.57
4993 6585 4.025401 GCGGCCACGGAGTTTGTG 62.025 66.667 2.24 0.00 41.61 3.33
4996 6588 3.518419 TTACGCGGCCACGGAGTTT 62.518 57.895 18.84 0.00 41.61 2.66
4997 6589 3.993584 TTACGCGGCCACGGAGTT 61.994 61.111 18.84 0.00 41.61 3.01
5008 6600 2.507769 GGAAGGGTCCGTTACGCG 60.508 66.667 3.53 3.53 45.40 6.01


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

AutoCloner maintained by Alex Coulton.