Multiple sequence alignment - TraesCS1A01G290800

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G290800 chr1A 100.000 5415 0 0 1 5415 487104420 487099006 0.000000e+00 10000.0
1 TraesCS1A01G290800 chr1D 90.206 2328 154 37 1 2277 387435234 387432930 0.000000e+00 2968.0
2 TraesCS1A01G290800 chr1D 90.457 1268 57 17 3039 4287 387432026 387430804 0.000000e+00 1613.0
3 TraesCS1A01G290800 chr1D 91.909 1100 55 12 4338 5414 387430810 387429722 0.000000e+00 1507.0
4 TraesCS1A01G290800 chr1B 89.355 1907 142 34 1092 2955 520815490 520813602 0.000000e+00 2340.0
5 TraesCS1A01G290800 chr1B 93.369 935 36 18 3026 3943 520813585 520812660 0.000000e+00 1360.0
6 TraesCS1A01G290800 chr1B 94.196 672 24 6 361 1031 520816268 520815611 0.000000e+00 1011.0
7 TraesCS1A01G290800 chr1B 86.176 340 44 3 4601 4937 629503709 629503370 1.110000e-96 364.0
8 TraesCS1A01G290800 chr1B 89.888 267 24 3 4338 4603 520810920 520810656 1.870000e-89 340.0
9 TraesCS1A01G290800 chr1B 86.404 228 15 7 4060 4287 520811125 520810914 9.070000e-58 235.0
10 TraesCS1A01G290800 chr1B 97.674 43 1 0 1037 1079 520815584 520815542 2.090000e-09 75.0
11 TraesCS1A01G290800 chr7B 86.589 343 38 6 4600 4937 382614266 382614605 6.620000e-99 372.0
12 TraesCS1A01G290800 chr3B 85.552 353 46 5 4600 4948 506120655 506120304 1.110000e-96 364.0
13 TraesCS1A01G290800 chr7D 86.503 326 41 2 4602 4924 405882965 405883290 6.670000e-94 355.0
14 TraesCS1A01G290800 chr7D 79.476 229 43 4 113 339 31396715 31396489 5.610000e-35 159.0
15 TraesCS1A01G290800 chr5D 86.503 326 41 2 4602 4924 231004546 231004871 6.670000e-94 355.0
16 TraesCS1A01G290800 chr5B 85.673 342 43 6 4601 4938 160193947 160194286 6.670000e-94 355.0
17 TraesCS1A01G290800 chr2A 86.503 326 41 3 4602 4924 12333361 12333686 6.670000e-94 355.0
18 TraesCS1A01G290800 chr4D 85.174 344 48 2 4599 4939 286103051 286102708 3.100000e-92 350.0
19 TraesCS1A01G290800 chr4D 86.667 75 10 0 1639 1713 498686114 498686040 3.480000e-12 84.2
20 TraesCS1A01G290800 chr4B 76.166 193 41 5 153 343 525171282 525171093 4.460000e-16 97.1
21 TraesCS1A01G290800 chr4B 86.667 75 10 0 1639 1713 640824013 640823939 3.480000e-12 84.2


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 TraesCS1A01G290800 chr1A 487099006 487104420 5414 True 10000.000000 10000 100.000000 1 5415 1 chr1A.!!$R1 5414
1 TraesCS1A01G290800 chr1D 387429722 387435234 5512 True 2029.333333 2968 90.857333 1 5414 3 chr1D.!!$R1 5413
2 TraesCS1A01G290800 chr1B 520810656 520816268 5612 True 893.500000 2340 91.814333 361 4603 6 chr1B.!!$R2 4242

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
251 253 0.097150 GCGGAAACTTGGCGATTCTC 59.903 55.0 0.0 0.0 0.00 2.87 F
1090 1119 0.383590 TGTTTGTTGGTCACCATGCG 59.616 50.0 0.0 0.0 31.53 4.73 F
2489 2577 0.620556 ACAAAGCCTCCGACCATGAT 59.379 50.0 0.0 0.0 0.00 2.45 F
2492 2580 0.911769 AAGCCTCCGACCATGATCAA 59.088 50.0 0.0 0.0 0.00 2.57 F
2542 2630 0.918258 TTGGAGCATGGGAGCACATA 59.082 50.0 0.0 0.0 36.85 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1186 1254 0.103208 GTAGTCCACCATCTCGGCTG 59.897 60.000 0.00 0.0 39.03 4.85 R
2796 2915 0.029567 GAGTGCCTATGTCTCCGTCG 59.970 60.000 0.00 0.0 0.00 5.12 R
3841 4304 1.835494 CACAAGTACTCGAGGGAGGA 58.165 55.000 18.41 0.0 44.93 3.71 R
4081 5970 3.408634 CAGGGACACCACGTTAAGAAAT 58.591 45.455 0.00 0.0 40.13 2.17 R
4455 6367 3.786635 AGCCATCAACTCTCGAATACAC 58.213 45.455 0.00 0.0 0.00 2.90 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
47 49 7.039784 TGTGGAAATATTCTGCTAAAAGTTGCT 60.040 33.333 0.00 0.00 0.00 3.91
88 90 0.177373 GACTTACATCCCGACCCCAC 59.823 60.000 0.00 0.00 0.00 4.61
109 111 1.987213 TGGGCGAGCTATGACCAAA 59.013 52.632 10.57 0.00 43.07 3.28
111 113 0.178068 GGGCGAGCTATGACCAAAGA 59.822 55.000 5.43 0.00 33.37 2.52
132 134 6.183309 AGACCAGTTCTTTTAATGCGATTC 57.817 37.500 0.00 0.00 0.00 2.52
137 139 6.744537 CCAGTTCTTTTAATGCGATTCTGAAG 59.255 38.462 0.00 0.00 0.00 3.02
160 162 7.543359 AGAATCATGGTCCAAAGAATCAAAA 57.457 32.000 12.67 0.00 0.00 2.44
162 164 8.255905 AGAATCATGGTCCAAAGAATCAAAATC 58.744 33.333 12.67 1.63 0.00 2.17
163 165 6.914654 TCATGGTCCAAAGAATCAAAATCA 57.085 33.333 0.00 0.00 0.00 2.57
164 166 7.484993 TCATGGTCCAAAGAATCAAAATCAT 57.515 32.000 0.00 0.00 0.00 2.45
169 171 9.709495 TGGTCCAAAGAATCAAAATCATAAAAG 57.291 29.630 0.00 0.00 0.00 2.27
187 189 8.206867 TCATAAAAGAAGTCATCTATGTCCCAG 58.793 37.037 0.00 0.00 37.42 4.45
194 196 0.759346 ATCTATGTCCCAGGAACCGC 59.241 55.000 0.00 0.00 0.00 5.68
206 208 2.933495 GGAACCGCCTAAAATCAACC 57.067 50.000 0.00 0.00 0.00 3.77
208 210 2.164338 GAACCGCCTAAAATCAACCCA 58.836 47.619 0.00 0.00 0.00 4.51
216 218 2.919666 AAAATCAACCCAGAATCGCG 57.080 45.000 0.00 0.00 0.00 5.87
232 234 0.504384 CGCGGTGCAATCTAGAATCG 59.496 55.000 0.00 0.00 0.00 3.34
251 253 0.097150 GCGGAAACTTGGCGATTCTC 59.903 55.000 0.00 0.00 0.00 2.87
253 255 2.009774 CGGAAACTTGGCGATTCTCAT 58.990 47.619 0.00 0.00 0.00 2.90
254 256 3.194861 CGGAAACTTGGCGATTCTCATA 58.805 45.455 0.00 0.00 0.00 2.15
276 278 3.418684 TTCTAGCCAGTCCCTCAAAAC 57.581 47.619 0.00 0.00 0.00 2.43
281 283 3.103742 AGCCAGTCCCTCAAAACAAAAA 58.896 40.909 0.00 0.00 0.00 1.94
283 285 3.457234 CCAGTCCCTCAAAACAAAAAGC 58.543 45.455 0.00 0.00 0.00 3.51
307 309 6.707273 TTTGTTCCAAACTAGTACCCCTAT 57.293 37.500 0.00 0.00 0.00 2.57
318 320 6.659824 ACTAGTACCCCTATTGGACAATTTG 58.340 40.000 2.53 0.00 35.39 2.32
324 326 5.184287 ACCCCTATTGGACAATTTGTTTACG 59.816 40.000 3.08 0.00 35.39 3.18
358 360 4.162690 GGCCTTGCCGACCGAGAT 62.163 66.667 0.00 0.00 39.62 2.75
565 568 7.224557 CCACCCAAAAGAAAATAAAACAGTGAG 59.775 37.037 0.00 0.00 0.00 3.51
942 948 3.605612 CGTGTGATCGCAGATCGG 58.394 61.111 9.75 0.00 45.12 4.18
1021 1027 4.771577 TCATGGAAAAACAGGTACATGCAT 59.228 37.500 7.57 0.00 36.54 3.96
1028 1034 1.134431 ACAGGTACATGCATGCATCGA 60.134 47.619 30.07 17.71 33.90 3.59
1029 1035 2.148768 CAGGTACATGCATGCATCGAT 58.851 47.619 30.07 19.82 33.90 3.59
1030 1036 2.159037 CAGGTACATGCATGCATCGATC 59.841 50.000 30.07 19.94 33.90 3.69
1031 1037 2.145536 GGTACATGCATGCATCGATCA 58.854 47.619 30.07 10.71 33.90 2.92
1032 1038 2.096069 GGTACATGCATGCATCGATCAC 60.096 50.000 30.07 20.29 33.90 3.06
1033 1039 0.584876 ACATGCATGCATCGATCACG 59.415 50.000 30.07 18.76 41.26 4.35
1034 1040 0.724785 CATGCATGCATCGATCACGC 60.725 55.000 30.07 1.87 39.58 5.34
1035 1041 1.161563 ATGCATGCATCGATCACGCA 61.162 50.000 27.46 16.67 37.05 5.24
1079 1108 4.285807 TCAGTTTCGGATGTGTTTGTTG 57.714 40.909 0.00 0.00 0.00 3.33
1080 1109 3.066064 TCAGTTTCGGATGTGTTTGTTGG 59.934 43.478 0.00 0.00 0.00 3.77
1081 1110 3.020984 AGTTTCGGATGTGTTTGTTGGT 58.979 40.909 0.00 0.00 0.00 3.67
1082 1111 3.066203 AGTTTCGGATGTGTTTGTTGGTC 59.934 43.478 0.00 0.00 0.00 4.02
1083 1112 2.333688 TCGGATGTGTTTGTTGGTCA 57.666 45.000 0.00 0.00 0.00 4.02
1084 1113 1.944024 TCGGATGTGTTTGTTGGTCAC 59.056 47.619 0.00 0.00 0.00 3.67
1085 1114 1.001815 CGGATGTGTTTGTTGGTCACC 60.002 52.381 0.00 0.00 0.00 4.02
1086 1115 2.028130 GGATGTGTTTGTTGGTCACCA 58.972 47.619 0.00 0.00 0.00 4.17
1089 1118 1.135915 TGTGTTTGTTGGTCACCATGC 59.864 47.619 0.00 0.00 31.53 4.06
1090 1119 0.383590 TGTTTGTTGGTCACCATGCG 59.616 50.000 0.00 0.00 31.53 4.73
1556 1624 4.664677 GTGCAGCAGTCCGACGGT 62.665 66.667 14.79 0.00 0.00 4.83
1762 1834 4.549668 TCCTACGTCCAAAGGGTATATGT 58.450 43.478 0.00 0.00 33.40 2.29
1773 1845 6.127366 CCAAAGGGTATATGTTTGCACATCTT 60.127 38.462 0.00 0.00 43.06 2.40
1787 1859 3.246226 GCACATCTTACTCGCTACCATTG 59.754 47.826 0.00 0.00 0.00 2.82
1791 1863 3.259064 TCTTACTCGCTACCATTGCAAC 58.741 45.455 0.00 0.00 0.00 4.17
1962 2038 5.868258 GGTGCTATATGAGACATCACATGAG 59.132 44.000 0.00 0.00 38.57 2.90
1972 2048 1.478105 CATCACATGAGTCACGAGGGA 59.522 52.381 0.00 0.00 0.00 4.20
1975 2051 2.094026 TCACATGAGTCACGAGGGATTG 60.094 50.000 0.00 0.00 0.00 2.67
2008 2084 4.965119 ACATAAAAATTCCAGACCTCGC 57.035 40.909 0.00 0.00 0.00 5.03
2009 2085 3.374058 ACATAAAAATTCCAGACCTCGCG 59.626 43.478 0.00 0.00 0.00 5.87
2020 2096 3.193691 CCAGACCTCGCGGAAATATCTAT 59.806 47.826 6.13 0.00 0.00 1.98
2082 2159 8.729805 TTGCACTGATTTTAAAGAAATTTGGT 57.270 26.923 0.00 0.00 0.00 3.67
2083 2160 8.729805 TGCACTGATTTTAAAGAAATTTGGTT 57.270 26.923 0.00 0.00 0.00 3.67
2130 2207 6.581171 AGTTCAAATCTGGACAGGAATTTC 57.419 37.500 0.00 0.00 32.84 2.17
2168 2245 7.706281 AAATCTCGCTTAAGATATGTCAGTG 57.294 36.000 6.67 0.00 34.90 3.66
2171 2248 2.472861 CGCTTAAGATATGTCAGTGCGG 59.527 50.000 6.67 0.00 37.68 5.69
2185 2262 3.419759 GCGGTTTGCATCGGTCGT 61.420 61.111 0.00 0.00 45.45 4.34
2186 2263 2.776072 CGGTTTGCATCGGTCGTC 59.224 61.111 0.00 0.00 0.00 4.20
2187 2264 2.776072 GGTTTGCATCGGTCGTCG 59.224 61.111 0.00 0.00 40.90 5.12
2188 2265 2.025418 GGTTTGCATCGGTCGTCGT 61.025 57.895 0.00 0.00 40.32 4.34
2189 2266 1.129809 GTTTGCATCGGTCGTCGTG 59.870 57.895 0.00 0.00 40.32 4.35
2190 2267 1.300311 TTTGCATCGGTCGTCGTGT 60.300 52.632 0.00 0.00 40.32 4.49
2191 2268 0.876777 TTTGCATCGGTCGTCGTGTT 60.877 50.000 0.00 0.00 40.32 3.32
2225 2303 2.979678 TCCTCTACTTTGAAGCCAACCT 59.020 45.455 0.00 0.00 30.88 3.50
2227 2305 3.244561 CCTCTACTTTGAAGCCAACCTCA 60.245 47.826 0.00 0.00 30.88 3.86
2257 2335 4.571919 TGACGATGTTAGGGTTAACTTGG 58.428 43.478 5.42 0.00 39.90 3.61
2310 2396 1.734388 AAACAAAGGGTGGCAGACGC 61.734 55.000 0.00 0.00 37.80 5.19
2317 2403 3.117171 GTGGCAGACGCAGCAGAG 61.117 66.667 0.00 0.00 41.24 3.35
2324 2410 2.886081 CAGACGCAGCAGAGTAGAATT 58.114 47.619 0.00 0.00 0.00 2.17
2330 2416 3.986572 CGCAGCAGAGTAGAATTGGATAG 59.013 47.826 0.00 0.00 0.00 2.08
2333 2419 3.326297 AGCAGAGTAGAATTGGATAGCCC 59.674 47.826 0.00 0.00 0.00 5.19
2343 2429 7.281366 AGAATTGGATAGCCCTGAATATCAT 57.719 36.000 0.00 0.00 35.38 2.45
2346 2432 5.169992 TGGATAGCCCTGAATATCATGTG 57.830 43.478 0.00 0.00 35.38 3.21
2355 2441 6.060136 CCCTGAATATCATGTGTTGAGACAT 58.940 40.000 0.00 0.00 37.89 3.06
2356 2442 7.219322 CCCTGAATATCATGTGTTGAGACATA 58.781 38.462 0.00 0.00 37.89 2.29
2401 2487 2.288518 GGCCGTTGGATCTCAGATCTAC 60.289 54.545 14.54 11.46 0.00 2.59
2412 2498 6.150976 GGATCTCAGATCTACTGGTCATAGTG 59.849 46.154 14.54 0.00 45.76 2.74
2416 2502 6.058833 TCAGATCTACTGGTCATAGTGAGAC 58.941 44.000 0.00 0.00 45.76 3.36
2421 2507 4.864483 ACTGGTCATAGTGAGACTCCTA 57.136 45.455 0.00 1.85 36.29 2.94
2423 2509 4.475381 ACTGGTCATAGTGAGACTCCTAGA 59.525 45.833 0.00 0.00 36.29 2.43
2454 2540 0.962489 AATATGGGACTCTCGAGGCG 59.038 55.000 13.56 6.84 37.31 5.52
2489 2577 0.620556 ACAAAGCCTCCGACCATGAT 59.379 50.000 0.00 0.00 0.00 2.45
2492 2580 0.911769 AAGCCTCCGACCATGATCAA 59.088 50.000 0.00 0.00 0.00 2.57
2539 2627 1.751927 CCTTGGAGCATGGGAGCAC 60.752 63.158 0.00 0.00 36.85 4.40
2540 2628 1.001764 CTTGGAGCATGGGAGCACA 60.002 57.895 0.00 0.00 36.85 4.57
2542 2630 0.918258 TTGGAGCATGGGAGCACATA 59.082 50.000 0.00 0.00 36.85 2.29
2543 2631 0.918258 TGGAGCATGGGAGCACATAA 59.082 50.000 0.00 0.00 36.85 1.90
2544 2632 1.496001 TGGAGCATGGGAGCACATAAT 59.504 47.619 0.00 0.00 36.85 1.28
2545 2633 2.710471 TGGAGCATGGGAGCACATAATA 59.290 45.455 0.00 0.00 36.85 0.98
2549 2637 5.251764 GAGCATGGGAGCACATAATATTCT 58.748 41.667 0.00 0.00 36.85 2.40
2550 2638 5.251764 AGCATGGGAGCACATAATATTCTC 58.748 41.667 0.00 0.00 36.85 2.87
2551 2639 4.397417 GCATGGGAGCACATAATATTCTCC 59.603 45.833 10.37 10.37 41.87 3.71
2558 2646 3.189287 GCACATAATATTCTCCCAAGCCG 59.811 47.826 0.00 0.00 0.00 5.52
2576 2682 5.662674 AGCCGAGAGTACTATTTTGTCTT 57.337 39.130 0.00 0.00 0.00 3.01
2583 2689 7.412020 CGAGAGTACTATTTTGTCTTCCAAAGC 60.412 40.741 0.00 0.00 43.63 3.51
2629 2735 2.992124 TTTTCAGTCAACACCGAGGA 57.008 45.000 0.00 0.00 0.00 3.71
2631 2737 1.410004 TTCAGTCAACACCGAGGACT 58.590 50.000 0.00 0.00 42.32 3.85
2652 2758 6.159299 ACTGTCGATCTTGATGATGAGATT 57.841 37.500 0.00 0.00 35.14 2.40
2661 2767 6.120220 TCTTGATGATGAGATTCATGCAAGT 58.880 36.000 16.71 0.00 37.20 3.16
2675 2781 5.332743 TCATGCAAGTTTTTATCTTCCCCT 58.667 37.500 0.00 0.00 0.00 4.79
2681 2787 6.418946 CAAGTTTTTATCTTCCCCTAGCTCT 58.581 40.000 0.00 0.00 0.00 4.09
2687 2793 6.831664 TTATCTTCCCCTAGCTCTGAAAAT 57.168 37.500 0.00 0.00 0.00 1.82
2688 2794 5.723860 ATCTTCCCCTAGCTCTGAAAATT 57.276 39.130 0.00 0.00 0.00 1.82
2690 2796 6.831664 TCTTCCCCTAGCTCTGAAAATTAT 57.168 37.500 0.00 0.00 0.00 1.28
2698 2804 6.931840 CCTAGCTCTGAAAATTATGACTACCC 59.068 42.308 0.00 0.00 0.00 3.69
2717 2835 8.166422 ACTACCCTTTTTACTGAATGAACAAG 57.834 34.615 0.00 0.00 0.00 3.16
2743 2861 4.953269 TCGTAGCACGATGAACATTTTTC 58.047 39.130 7.20 0.00 46.73 2.29
2796 2915 9.824534 CCACAATGAATTTGTTAATTTTTAGGC 57.175 29.630 0.00 0.00 46.51 3.93
2800 2919 7.555639 TGAATTTGTTAATTTTTAGGCGACG 57.444 32.000 0.00 0.00 34.16 5.12
2954 3080 4.212716 ACGAAGTGCCTGATATACCAGTA 58.787 43.478 0.00 0.00 42.51 2.74
2955 3081 4.278669 ACGAAGTGCCTGATATACCAGTAG 59.721 45.833 0.00 0.00 42.51 2.57
2956 3082 4.321304 CGAAGTGCCTGATATACCAGTAGG 60.321 50.000 0.00 0.00 42.21 3.18
2977 3103 4.900054 AGGTCCAGTACACCTAATCCATAC 59.100 45.833 1.58 0.00 42.91 2.39
2980 3106 6.183361 GGTCCAGTACACCTAATCCATACAAT 60.183 42.308 0.00 0.00 0.00 2.71
2981 3107 7.015877 GGTCCAGTACACCTAATCCATACAATA 59.984 40.741 0.00 0.00 0.00 1.90
2982 3108 8.594550 GTCCAGTACACCTAATCCATACAATAT 58.405 37.037 0.00 0.00 0.00 1.28
2983 3109 9.166222 TCCAGTACACCTAATCCATACAATATT 57.834 33.333 0.00 0.00 0.00 1.28
2984 3110 9.436957 CCAGTACACCTAATCCATACAATATTC 57.563 37.037 0.00 0.00 0.00 1.75
2985 3111 9.436957 CAGTACACCTAATCCATACAATATTCC 57.563 37.037 0.00 0.00 0.00 3.01
2986 3112 8.603304 AGTACACCTAATCCATACAATATTCCC 58.397 37.037 0.00 0.00 0.00 3.97
2987 3113 6.790319 ACACCTAATCCATACAATATTCCCC 58.210 40.000 0.00 0.00 0.00 4.81
2988 3114 6.566480 ACACCTAATCCATACAATATTCCCCT 59.434 38.462 0.00 0.00 0.00 4.79
2989 3115 7.742213 ACACCTAATCCATACAATATTCCCCTA 59.258 37.037 0.00 0.00 0.00 3.53
2990 3116 8.611257 CACCTAATCCATACAATATTCCCCTAA 58.389 37.037 0.00 0.00 0.00 2.69
2991 3117 9.189750 ACCTAATCCATACAATATTCCCCTAAA 57.810 33.333 0.00 0.00 0.00 1.85
3589 4027 1.967762 ACGCACGAGCATTCATTTTG 58.032 45.000 5.50 0.00 42.27 2.44
3603 4041 6.646240 GCATTCATTTTGTGTACCAACTGAAT 59.354 34.615 17.34 17.34 41.65 2.57
3745 4208 2.591148 CGTCAACTACACGTTATGACCG 59.409 50.000 9.16 0.00 33.63 4.79
3747 4210 3.605486 GTCAACTACACGTTATGACCGAC 59.395 47.826 0.00 0.00 33.63 4.79
3763 4226 1.139058 CCGACCCATCCCTTTACTCAG 59.861 57.143 0.00 0.00 0.00 3.35
3953 4416 9.588096 TGTACAATGAGTGACTCCATATATACT 57.412 33.333 10.52 0.00 0.00 2.12
3955 4418 8.948401 ACAATGAGTGACTCCATATATACTCT 57.052 34.615 10.52 0.00 36.43 3.24
4045 5934 2.540931 TCGTTTGCGACCAAGAACTAAC 59.459 45.455 0.00 0.00 42.81 2.34
4050 5939 3.472652 TGCGACCAAGAACTAACATGTT 58.527 40.909 16.68 16.68 0.00 2.71
4134 6023 3.628008 TGGTGAGCCTACTCGAAAGATA 58.372 45.455 0.00 0.00 46.69 1.98
4135 6024 3.632604 TGGTGAGCCTACTCGAAAGATAG 59.367 47.826 0.00 0.00 46.69 2.08
4145 6056 6.970043 CCTACTCGAAAGATAGTCAACTCAAG 59.030 42.308 0.00 0.00 40.84 3.02
4186 6097 4.265856 AGGGAAGGGATTTGGGAATAAC 57.734 45.455 0.00 0.00 0.00 1.89
4283 6195 6.814954 AGTAGACATAATTCATGGACTGGT 57.185 37.500 0.00 0.00 39.13 4.00
4284 6196 7.914427 AGTAGACATAATTCATGGACTGGTA 57.086 36.000 0.00 0.00 39.13 3.25
4285 6197 8.497910 AGTAGACATAATTCATGGACTGGTAT 57.502 34.615 0.00 0.00 39.13 2.73
4286 6198 8.938883 AGTAGACATAATTCATGGACTGGTATT 58.061 33.333 0.00 0.00 39.13 1.89
4287 6199 9.561069 GTAGACATAATTCATGGACTGGTATTT 57.439 33.333 0.00 0.00 39.13 1.40
4289 6201 9.479549 AGACATAATTCATGGACTGGTATTTTT 57.520 29.630 0.00 0.00 39.13 1.94
4350 6262 7.774625 TCATCTTCAATCATGGTATTAACTGCA 59.225 33.333 0.00 0.00 0.00 4.41
4543 6455 5.313712 TCTTAAACCTGCTTTCCTAGTTGG 58.686 41.667 0.00 0.00 37.10 3.77
4581 6493 4.406326 TGTGGCTATGAATCTTTACCCGTA 59.594 41.667 0.00 0.00 0.00 4.02
4588 6500 5.168647 TGAATCTTTACCCGTATTGGTGT 57.831 39.130 0.00 0.00 39.53 4.16
4670 6582 8.851541 AAATTCCACAATGTAAGATGCATTTT 57.148 26.923 7.70 7.70 34.68 1.82
4722 6634 8.537858 TGACCCTCTAGGAAAAGAAAAGTATAC 58.462 37.037 0.00 0.00 39.89 1.47
4806 6721 5.105310 TGTGTGTATCTCTTCCTTTCCTAGC 60.105 44.000 0.00 0.00 0.00 3.42
4822 6737 8.624776 CCTTTCCTAGCCTAAATGATTTACTTG 58.375 37.037 0.00 0.00 0.00 3.16
4824 6739 6.900194 TCCTAGCCTAAATGATTTACTTGCT 58.100 36.000 13.16 13.16 0.00 3.91
4955 6871 7.013464 AGAGTATAATTTAGAGACAGGACACGG 59.987 40.741 0.00 0.00 0.00 4.94
4968 6884 3.871594 CAGGACACGGAAGGAATGATAAC 59.128 47.826 0.00 0.00 0.00 1.89
4984 6900 7.306866 GGAATGATAACTTTGACGCTAGATGAC 60.307 40.741 0.00 0.00 0.00 3.06
4992 6908 2.098607 TGACGCTAGATGACCCTTTACG 59.901 50.000 0.00 0.00 0.00 3.18
4995 6911 3.114065 CGCTAGATGACCCTTTACGTTC 58.886 50.000 0.00 0.00 0.00 3.95
4996 6912 3.114065 GCTAGATGACCCTTTACGTTCG 58.886 50.000 0.00 0.00 0.00 3.95
5002 6918 1.659098 GACCCTTTACGTTCGATGCTG 59.341 52.381 0.00 0.00 0.00 4.41
5060 6976 5.232463 GGTCGATGGTATAATTCGGCTAAA 58.768 41.667 0.00 0.00 37.61 1.85
5061 6977 5.347907 GGTCGATGGTATAATTCGGCTAAAG 59.652 44.000 0.00 0.00 37.61 1.85
5104 7020 6.276847 ACGAGAAGTTGGATCATATCTTGAC 58.723 40.000 0.00 0.00 37.11 3.18
5153 7088 5.119694 CACTTTAGAGGAGTATTTCTGGCC 58.880 45.833 0.00 0.00 0.00 5.36
5167 7102 0.695347 CTGGCCAGAAACTTCCTCCT 59.305 55.000 29.88 0.00 0.00 3.69
5170 7105 0.988063 GCCAGAAACTTCCTCCTCCT 59.012 55.000 0.00 0.00 0.00 3.69
5171 7106 1.065782 GCCAGAAACTTCCTCCTCCTC 60.066 57.143 0.00 0.00 0.00 3.71
5173 7108 1.557371 CAGAAACTTCCTCCTCCTCCC 59.443 57.143 0.00 0.00 0.00 4.30
5174 7109 0.913205 GAAACTTCCTCCTCCTCCCC 59.087 60.000 0.00 0.00 0.00 4.81
5175 7110 0.550393 AAACTTCCTCCTCCTCCCCC 60.550 60.000 0.00 0.00 0.00 5.40
5176 7111 1.465189 AACTTCCTCCTCCTCCCCCT 61.465 60.000 0.00 0.00 0.00 4.79
5177 7112 1.074850 CTTCCTCCTCCTCCCCCTC 60.075 68.421 0.00 0.00 0.00 4.30
5178 7113 2.613576 CTTCCTCCTCCTCCCCCTCC 62.614 70.000 0.00 0.00 0.00 4.30
5179 7114 4.179599 CCTCCTCCTCCCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
5180 7115 4.179599 CTCCTCCTCCCCCTCCCC 62.180 77.778 0.00 0.00 0.00 4.81
5202 7137 2.216898 CTCTTGGATTTCGATGAGGCC 58.783 52.381 0.00 0.00 0.00 5.19
5204 7139 0.251916 TTGGATTTCGATGAGGCCGT 59.748 50.000 0.00 0.00 0.00 5.68
5206 7141 0.657840 GGATTTCGATGAGGCCGTTG 59.342 55.000 0.00 0.00 0.00 4.10
5207 7142 1.651987 GATTTCGATGAGGCCGTTGA 58.348 50.000 0.00 0.00 0.00 3.18
5224 7159 0.036164 TGATGTGGGGAACAAGACCG 59.964 55.000 0.00 0.00 43.61 4.79
5225 7160 1.303317 ATGTGGGGAACAAGACCGC 60.303 57.895 0.00 0.00 43.61 5.68
5256 7191 1.600957 GAGTTGTCATGCATGATCCGG 59.399 52.381 30.89 2.63 39.30 5.14
5279 7214 1.850345 AGGAAGGACACCAAGGTTGAA 59.150 47.619 0.00 0.00 0.00 2.69
5284 7219 1.133915 GGACACCAAGGTTGAAGTGGA 60.134 52.381 0.00 0.00 36.23 4.02
5294 7229 7.290014 ACCAAGGTTGAAGTGGAAATTTAAGAT 59.710 33.333 0.00 0.00 36.23 2.40
5296 7231 7.468141 AGGTTGAAGTGGAAATTTAAGATCC 57.532 36.000 0.00 0.00 0.00 3.36
5304 7239 6.540189 AGTGGAAATTTAAGATCCGACATCTG 59.460 38.462 0.00 0.00 35.96 2.90
5319 7254 8.201554 TCCGACATCTGAGAAAATTATTTCAG 57.798 34.615 4.34 6.65 46.03 3.02
5321 7256 7.412853 CGACATCTGAGAAAATTATTTCAGGG 58.587 38.462 11.05 7.85 46.03 4.45
5325 7260 7.865706 TCTGAGAAAATTATTTCAGGGCTAC 57.134 36.000 11.05 0.00 46.03 3.58
5337 7272 2.094182 TCAGGGCTACGCTAAGAGTTTG 60.094 50.000 0.00 0.00 0.00 2.93
5378 7313 8.913487 AAAGAAAAGGATCAATTGATTGCTTT 57.087 26.923 21.57 21.07 37.68 3.51
5414 7349 5.506317 CCGACATTAAAGCAGAATCATTCCC 60.506 44.000 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.542525 TCCACATATTTGGTTACCCCTTCT 59.457 41.667 7.77 0.00 37.93 2.85
10 12 9.463443 GCAGAATATTTCCACATATTTGGTTAC 57.537 33.333 7.77 0.00 37.93 2.50
21 23 7.039784 AGCAACTTTTAGCAGAATATTTCCACA 60.040 33.333 0.00 0.00 0.00 4.17
47 49 3.128764 CACTTACATCCTGACTGTAGCGA 59.871 47.826 0.00 0.00 31.17 4.93
74 76 2.203938 ACTGTGGGGTCGGGATGT 60.204 61.111 0.00 0.00 0.00 3.06
88 90 1.227380 GGTCATAGCTCGCCCACTG 60.227 63.158 0.00 0.00 0.00 3.66
95 97 2.093973 ACTGGTCTTTGGTCATAGCTCG 60.094 50.000 0.00 0.00 0.00 5.03
109 111 5.940470 AGAATCGCATTAAAAGAACTGGTCT 59.060 36.000 0.00 0.00 38.69 3.85
111 113 5.705441 TCAGAATCGCATTAAAAGAACTGGT 59.295 36.000 0.00 0.00 0.00 4.00
132 134 6.376299 TGATTCTTTGGACCATGATTCTTCAG 59.624 38.462 0.00 0.00 34.73 3.02
137 139 8.036575 TGATTTTGATTCTTTGGACCATGATTC 58.963 33.333 0.00 4.28 0.00 2.52
143 145 9.709495 CTTTTATGATTTTGATTCTTTGGACCA 57.291 29.630 0.00 0.00 0.00 4.02
160 162 8.717717 TGGGACATAGATGACTTCTTTTATGAT 58.282 33.333 8.72 0.00 35.79 2.45
162 164 7.443575 CCTGGGACATAGATGACTTCTTTTATG 59.556 40.741 0.00 0.00 38.20 1.90
163 165 7.348274 TCCTGGGACATAGATGACTTCTTTTAT 59.652 37.037 0.00 0.00 38.20 1.40
164 166 6.672218 TCCTGGGACATAGATGACTTCTTTTA 59.328 38.462 0.00 0.00 38.20 1.52
169 171 4.443598 GGTTCCTGGGACATAGATGACTTC 60.444 50.000 7.57 0.00 38.20 3.01
172 174 2.224066 CGGTTCCTGGGACATAGATGAC 60.224 54.545 7.57 0.00 38.20 3.06
179 181 0.912487 TTAGGCGGTTCCTGGGACAT 60.912 55.000 7.57 0.00 46.98 3.06
187 189 1.475280 GGGTTGATTTTAGGCGGTTCC 59.525 52.381 0.00 0.00 0.00 3.62
194 196 3.242739 CGCGATTCTGGGTTGATTTTAGG 60.243 47.826 0.00 0.00 0.00 2.69
198 200 1.094785 CCGCGATTCTGGGTTGATTT 58.905 50.000 8.23 0.00 0.00 2.17
206 208 1.091771 AGATTGCACCGCGATTCTGG 61.092 55.000 8.23 0.00 32.11 3.86
208 210 1.409064 TCTAGATTGCACCGCGATTCT 59.591 47.619 8.23 1.13 32.11 2.40
216 218 0.861837 CCGCGATTCTAGATTGCACC 59.138 55.000 8.23 0.00 0.00 5.01
232 234 0.097150 GAGAATCGCCAAGTTTCCGC 59.903 55.000 0.00 0.00 30.73 5.54
251 253 4.963318 TGAGGGACTGGCTAGAATTATG 57.037 45.455 3.17 0.00 41.55 1.90
253 255 5.013704 TGTTTTGAGGGACTGGCTAGAATTA 59.986 40.000 3.17 0.00 41.55 1.40
254 256 4.202567 TGTTTTGAGGGACTGGCTAGAATT 60.203 41.667 3.17 0.00 41.55 2.17
281 283 8.905245 ATAGGGGTACTAGTTTGGAACAAAGCT 61.905 40.741 0.00 0.00 38.35 3.74
283 285 6.718294 ATAGGGGTACTAGTTTGGAACAAAG 58.282 40.000 0.00 0.00 38.35 2.77
307 309 2.693591 TGGCCGTAAACAAATTGTCCAA 59.306 40.909 0.00 0.00 0.00 3.53
350 352 1.664873 GTTTTGGGCCTATCTCGGTC 58.335 55.000 4.53 0.00 0.00 4.79
358 360 0.475044 AACCAGTCGTTTTGGGCCTA 59.525 50.000 4.53 0.00 40.11 3.93
454 456 1.623311 CCCGAGGGGCAAAATCTTTTT 59.377 47.619 0.00 0.00 35.35 1.94
470 472 0.178767 CATGATTGTCTGAGGCCCGA 59.821 55.000 0.00 0.00 0.00 5.14
471 473 0.107508 ACATGATTGTCTGAGGCCCG 60.108 55.000 0.00 0.00 0.00 6.13
472 474 2.134789 AACATGATTGTCTGAGGCCC 57.865 50.000 0.00 0.00 34.06 5.80
475 477 5.835257 ACACAAAAACATGATTGTCTGAGG 58.165 37.500 0.00 0.00 37.66 3.86
477 479 6.698008 AGACACAAAAACATGATTGTCTGA 57.302 33.333 0.00 0.00 41.59 3.27
478 480 6.291955 GCAAGACACAAAAACATGATTGTCTG 60.292 38.462 8.33 5.33 42.17 3.51
479 481 5.750067 GCAAGACACAAAAACATGATTGTCT 59.250 36.000 0.00 0.57 44.29 3.41
565 568 0.103937 CACGGGGCTCAAGAGATCTC 59.896 60.000 15.29 15.29 0.00 2.75
799 802 3.898509 TGGGCGTTTGTGCACTGC 61.899 61.111 19.41 15.71 39.64 4.40
800 803 2.026014 GTGGGCGTTTGTGCACTG 59.974 61.111 19.41 6.50 39.64 3.66
801 804 1.599606 TTTGTGGGCGTTTGTGCACT 61.600 50.000 19.41 0.00 39.64 4.40
802 805 0.529555 ATTTGTGGGCGTTTGTGCAC 60.530 50.000 10.75 10.75 39.27 4.57
803 806 0.176680 AATTTGTGGGCGTTTGTGCA 59.823 45.000 0.00 0.00 36.28 4.57
942 948 2.833582 ATGCATGCAGCTGGCTCC 60.834 61.111 26.69 0.00 45.94 4.70
967 973 2.858344 CGTAGCTTTGATAACCTCACGG 59.142 50.000 0.00 0.00 32.17 4.94
1021 1027 2.885164 CGGTGCGTGATCGATGCA 60.885 61.111 0.54 3.22 44.73 3.96
1069 1098 1.135915 GCATGGTGACCAACAAACACA 59.864 47.619 9.06 0.00 36.95 3.72
1089 1118 2.505777 CTGCTCAGAGCGACCACG 60.506 66.667 17.81 0.00 46.26 4.94
1090 1119 2.125753 CCTGCTCAGAGCGACCAC 60.126 66.667 17.81 0.00 46.26 4.16
1186 1254 0.103208 GTAGTCCACCATCTCGGCTG 59.897 60.000 0.00 0.00 39.03 4.85
1190 1258 1.410517 AGCATGTAGTCCACCATCTCG 59.589 52.381 0.00 0.00 0.00 4.04
1595 1663 4.735132 TTCCGTCGCCCGCTCTTG 62.735 66.667 0.00 0.00 34.38 3.02
1628 1696 1.216710 CACCTCCTCGCTGGTCTTC 59.783 63.158 0.00 0.00 33.75 2.87
1762 1834 3.259064 GGTAGCGAGTAAGATGTGCAAA 58.741 45.455 0.00 0.00 0.00 3.68
1773 1845 2.753055 TGTTGCAATGGTAGCGAGTA 57.247 45.000 0.59 0.00 33.85 2.59
1787 1859 4.214437 GCAAGCGATGAACTATATGTTGC 58.786 43.478 0.00 0.00 39.30 4.17
1791 1863 4.746611 TCACTGCAAGCGATGAACTATATG 59.253 41.667 0.00 0.00 37.60 1.78
1874 1948 8.400184 ACTACCATAAGTTTAAGTTTGGGTTC 57.600 34.615 11.25 0.00 0.00 3.62
1908 1983 9.825109 GACTTAGACATAAGAAAATCTTAGGCT 57.175 33.333 10.67 10.79 42.57 4.58
1921 1996 4.938080 AGCACCATCGACTTAGACATAAG 58.062 43.478 0.00 0.00 43.50 1.73
1962 2038 3.058224 CCAAAAGTTCAATCCCTCGTGAC 60.058 47.826 0.00 0.00 0.00 3.67
2026 2102 3.735591 TCGAAACCCGAAAGAACTTCAT 58.264 40.909 0.00 0.00 45.43 2.57
2038 2114 4.035091 TGCAATTTGATAGATCGAAACCCG 59.965 41.667 0.00 0.00 34.10 5.28
2041 2117 6.775088 TCAGTGCAATTTGATAGATCGAAAC 58.225 36.000 0.00 0.00 34.10 2.78
2168 2245 3.362851 GACGACCGATGCAAACCGC 62.363 63.158 0.00 0.00 42.89 5.68
2171 2248 1.129809 CACGACGACCGATGCAAAC 59.870 57.895 0.00 0.00 41.76 2.93
2199 2277 3.650942 TGGCTTCAAAGTAGAGGAAGGAA 59.349 43.478 0.00 0.00 38.71 3.36
2225 2303 6.469410 ACCCTAACATCGTCAAAGTAATTGA 58.531 36.000 0.00 0.00 45.71 2.57
2227 2305 8.724229 GTTAACCCTAACATCGTCAAAGTAATT 58.276 33.333 0.00 0.00 37.85 1.40
2257 2335 4.280929 AGAAAACCTTGAGCATGTAAACCC 59.719 41.667 0.00 0.00 0.00 4.11
2310 2396 4.314121 GGCTATCCAATTCTACTCTGCTG 58.686 47.826 0.00 0.00 0.00 4.41
2317 2403 7.624549 TGATATTCAGGGCTATCCAATTCTAC 58.375 38.462 0.00 0.00 38.24 2.59
2324 2410 4.598807 ACACATGATATTCAGGGCTATCCA 59.401 41.667 0.00 0.00 38.24 3.41
2330 2416 4.274459 GTCTCAACACATGATATTCAGGGC 59.726 45.833 0.00 0.00 37.44 5.19
2333 2419 8.883954 AGTATGTCTCAACACATGATATTCAG 57.116 34.615 0.00 0.00 38.48 3.02
2343 2429 3.619733 GCATGGGAGTATGTCTCAACACA 60.620 47.826 0.00 0.00 39.90 3.72
2346 2432 3.462021 GAGCATGGGAGTATGTCTCAAC 58.538 50.000 0.00 0.00 39.90 3.18
2355 2441 3.094062 GCGCTGGAGCATGGGAGTA 62.094 63.158 0.00 0.00 42.21 2.59
2356 2442 4.479993 GCGCTGGAGCATGGGAGT 62.480 66.667 0.00 0.00 42.21 3.85
2401 2487 5.042463 TCTAGGAGTCTCACTATGACCAG 57.958 47.826 1.47 0.00 35.21 4.00
2412 2498 3.056536 TGTGTGCATGTTCTAGGAGTCTC 60.057 47.826 0.00 0.00 0.00 3.36
2416 2502 6.238566 CCATATTTGTGTGCATGTTCTAGGAG 60.239 42.308 0.00 0.00 0.00 3.69
2421 2507 4.158394 GTCCCATATTTGTGTGCATGTTCT 59.842 41.667 0.00 0.00 0.00 3.01
2423 2509 4.088634 AGTCCCATATTTGTGTGCATGTT 58.911 39.130 0.00 0.00 0.00 2.71
2473 2561 0.911769 TTGATCATGGTCGGAGGCTT 59.088 50.000 0.59 0.00 0.00 4.35
2489 2577 4.803924 GCCATTGGATACGAGATCCATTGA 60.804 45.833 28.19 16.08 46.51 2.57
2492 2580 2.026822 GGCCATTGGATACGAGATCCAT 60.027 50.000 19.78 10.53 46.51 3.41
2539 2627 5.152623 TCTCGGCTTGGGAGAATATTATG 57.847 43.478 0.00 0.00 37.59 1.90
2540 2628 4.841246 ACTCTCGGCTTGGGAGAATATTAT 59.159 41.667 12.45 0.00 39.86 1.28
2542 2630 3.041946 ACTCTCGGCTTGGGAGAATATT 58.958 45.455 12.45 0.00 39.86 1.28
2543 2631 2.683768 ACTCTCGGCTTGGGAGAATAT 58.316 47.619 12.45 0.00 39.86 1.28
2544 2632 2.160721 ACTCTCGGCTTGGGAGAATA 57.839 50.000 12.45 0.00 39.86 1.75
2545 2633 1.757699 GTACTCTCGGCTTGGGAGAAT 59.242 52.381 12.45 0.00 39.86 2.40
2549 2637 2.750141 ATAGTACTCTCGGCTTGGGA 57.250 50.000 0.00 0.00 0.00 4.37
2550 2638 3.821421 AAATAGTACTCTCGGCTTGGG 57.179 47.619 0.00 0.00 0.00 4.12
2551 2639 4.504858 ACAAAATAGTACTCTCGGCTTGG 58.495 43.478 0.00 0.00 0.00 3.61
2552 2640 5.411781 AGACAAAATAGTACTCTCGGCTTG 58.588 41.667 0.00 0.00 0.00 4.01
2553 2641 5.662674 AGACAAAATAGTACTCTCGGCTT 57.337 39.130 0.00 0.00 0.00 4.35
2554 2642 5.394333 GGAAGACAAAATAGTACTCTCGGCT 60.394 44.000 0.00 0.00 0.00 5.52
2555 2643 4.804665 GGAAGACAAAATAGTACTCTCGGC 59.195 45.833 0.00 0.00 0.00 5.54
2599 2705 6.366061 GGTGTTGACTGAAAATTAGCAAATCC 59.634 38.462 0.00 0.00 0.00 3.01
2605 2711 4.378459 CCTCGGTGTTGACTGAAAATTAGC 60.378 45.833 0.00 0.00 37.02 3.09
2629 2735 5.787953 ATCTCATCATCAAGATCGACAGT 57.212 39.130 0.00 0.00 33.72 3.55
2631 2737 6.152932 TGAATCTCATCATCAAGATCGACA 57.847 37.500 0.00 0.00 33.72 4.35
2632 2738 6.401260 GCATGAATCTCATCATCAAGATCGAC 60.401 42.308 0.00 0.00 37.96 4.20
2652 2758 5.332743 AGGGGAAGATAAAAACTTGCATGA 58.667 37.500 6.60 0.00 37.42 3.07
2661 2767 6.636454 TTCAGAGCTAGGGGAAGATAAAAA 57.364 37.500 0.00 0.00 0.00 1.94
2675 2781 7.676683 AGGGTAGTCATAATTTTCAGAGCTA 57.323 36.000 0.00 0.00 0.00 3.32
2688 2794 9.444600 GTTCATTCAGTAAAAAGGGTAGTCATA 57.555 33.333 0.00 0.00 0.00 2.15
2690 2796 7.284074 TGTTCATTCAGTAAAAAGGGTAGTCA 58.716 34.615 0.00 0.00 0.00 3.41
2698 2804 9.072294 ACGAAAACTTGTTCATTCAGTAAAAAG 57.928 29.630 0.00 0.00 0.00 2.27
2707 2825 4.607235 CGTGCTACGAAAACTTGTTCATTC 59.393 41.667 3.04 0.00 46.05 2.67
2708 2826 4.523813 CGTGCTACGAAAACTTGTTCATT 58.476 39.130 3.04 0.00 46.05 2.57
2774 2893 8.643752 CGTCGCCTAAAAATTAACAAATTCATT 58.356 29.630 0.00 0.00 0.00 2.57
2776 2895 6.583050 CCGTCGCCTAAAAATTAACAAATTCA 59.417 34.615 0.00 0.00 0.00 2.57
2783 2902 4.389687 TGTCTCCGTCGCCTAAAAATTAAC 59.610 41.667 0.00 0.00 0.00 2.01
2796 2915 0.029567 GAGTGCCTATGTCTCCGTCG 59.970 60.000 0.00 0.00 0.00 5.12
2800 2919 1.501582 AAGGGAGTGCCTATGTCTCC 58.498 55.000 2.47 0.00 44.78 3.71
2891 3017 6.803154 ACACAAATAAACTCTAAGGCAGAC 57.197 37.500 0.00 0.00 0.00 3.51
2923 3049 2.037251 TCAGGCACTTCGTTAGCTTCTT 59.963 45.455 0.00 0.00 34.60 2.52
2927 3053 4.262079 GGTATATCAGGCACTTCGTTAGCT 60.262 45.833 0.00 0.00 34.60 3.32
2954 3080 3.484953 TGGATTAGGTGTACTGGACCT 57.515 47.619 8.33 8.33 46.10 3.85
2955 3081 4.652421 TGTATGGATTAGGTGTACTGGACC 59.348 45.833 0.00 0.00 0.00 4.46
2956 3082 5.864418 TGTATGGATTAGGTGTACTGGAC 57.136 43.478 0.00 0.00 0.00 4.02
2957 3083 8.736097 ATATTGTATGGATTAGGTGTACTGGA 57.264 34.615 0.00 0.00 0.00 3.86
2958 3084 9.436957 GAATATTGTATGGATTAGGTGTACTGG 57.563 37.037 0.00 0.00 0.00 4.00
2959 3085 9.436957 GGAATATTGTATGGATTAGGTGTACTG 57.563 37.037 0.00 0.00 0.00 2.74
2960 3086 8.603304 GGGAATATTGTATGGATTAGGTGTACT 58.397 37.037 0.00 0.00 0.00 2.73
2961 3087 7.827729 GGGGAATATTGTATGGATTAGGTGTAC 59.172 40.741 0.00 0.00 0.00 2.90
2962 3088 7.742213 AGGGGAATATTGTATGGATTAGGTGTA 59.258 37.037 0.00 0.00 0.00 2.90
2990 3116 8.887264 TTGTATGGTGTATGGATTAGGTTTTT 57.113 30.769 0.00 0.00 0.00 1.94
2992 3118 9.569122 GTATTGTATGGTGTATGGATTAGGTTT 57.431 33.333 0.00 0.00 0.00 3.27
2993 3119 8.719596 TGTATTGTATGGTGTATGGATTAGGTT 58.280 33.333 0.00 0.00 0.00 3.50
2994 3120 8.270137 TGTATTGTATGGTGTATGGATTAGGT 57.730 34.615 0.00 0.00 0.00 3.08
2995 3121 9.166173 CATGTATTGTATGGTGTATGGATTAGG 57.834 37.037 0.00 0.00 0.00 2.69
2996 3122 9.942850 TCATGTATTGTATGGTGTATGGATTAG 57.057 33.333 0.00 0.00 0.00 1.73
2997 3123 9.719355 GTCATGTATTGTATGGTGTATGGATTA 57.281 33.333 0.00 0.00 0.00 1.75
2998 3124 7.665559 GGTCATGTATTGTATGGTGTATGGATT 59.334 37.037 0.00 0.00 0.00 3.01
2999 3125 7.168219 GGTCATGTATTGTATGGTGTATGGAT 58.832 38.462 0.00 0.00 0.00 3.41
3000 3126 6.465178 GGGTCATGTATTGTATGGTGTATGGA 60.465 42.308 0.00 0.00 0.00 3.41
3001 3127 5.705441 GGGTCATGTATTGTATGGTGTATGG 59.295 44.000 0.00 0.00 0.00 2.74
3002 3128 5.705441 GGGGTCATGTATTGTATGGTGTATG 59.295 44.000 0.00 0.00 0.00 2.39
3003 3129 5.222048 GGGGGTCATGTATTGTATGGTGTAT 60.222 44.000 0.00 0.00 0.00 2.29
3004 3130 4.103469 GGGGGTCATGTATTGTATGGTGTA 59.897 45.833 0.00 0.00 0.00 2.90
3005 3131 3.117663 GGGGGTCATGTATTGTATGGTGT 60.118 47.826 0.00 0.00 0.00 4.16
3006 3132 3.138283 AGGGGGTCATGTATTGTATGGTG 59.862 47.826 0.00 0.00 0.00 4.17
3007 3133 3.403322 AGGGGGTCATGTATTGTATGGT 58.597 45.455 0.00 0.00 0.00 3.55
3008 3134 5.779241 ATAGGGGGTCATGTATTGTATGG 57.221 43.478 0.00 0.00 0.00 2.74
3013 3139 6.490040 CCAAAGTTATAGGGGGTCATGTATTG 59.510 42.308 0.00 0.00 0.00 1.90
3589 4027 4.002982 TGATCTGCATTCAGTTGGTACAC 58.997 43.478 0.00 0.00 41.10 2.90
3603 4041 2.608016 GCGGTCGATAATCTGATCTGCA 60.608 50.000 0.00 0.00 0.00 4.41
3745 4208 2.478292 TCCTGAGTAAAGGGATGGGTC 58.522 52.381 0.00 0.00 37.96 4.46
3747 4210 3.459598 TCAATCCTGAGTAAAGGGATGGG 59.540 47.826 0.00 0.00 39.49 4.00
3763 4226 2.688507 TCGACAACAGAAGCTCAATCC 58.311 47.619 0.00 0.00 0.00 3.01
3841 4304 1.835494 CACAAGTACTCGAGGGAGGA 58.165 55.000 18.41 0.00 44.93 3.71
4080 5969 3.818773 CAGGGACACCACGTTAAGAAATT 59.181 43.478 0.00 0.00 40.13 1.82
4081 5970 3.408634 CAGGGACACCACGTTAAGAAAT 58.591 45.455 0.00 0.00 40.13 2.17
4134 6023 4.752101 GTGTGCTAATCACTTGAGTTGACT 59.248 41.667 0.00 0.00 45.81 3.41
4135 6024 4.511454 TGTGTGCTAATCACTTGAGTTGAC 59.489 41.667 0.00 0.00 45.81 3.18
4171 6082 8.630037 CAATAGTAGTTGTTATTCCCAAATCCC 58.370 37.037 0.00 0.00 0.00 3.85
4176 6087 9.967451 TGAATCAATAGTAGTTGTTATTCCCAA 57.033 29.630 0.00 0.00 28.69 4.12
4313 6225 8.683615 CCATGATTGAAGATGAAGAGATCAAAA 58.316 33.333 0.00 0.00 42.54 2.44
4314 6226 7.832685 ACCATGATTGAAGATGAAGAGATCAAA 59.167 33.333 0.00 0.00 42.54 2.69
4315 6227 7.344134 ACCATGATTGAAGATGAAGAGATCAA 58.656 34.615 0.00 0.00 42.54 2.57
4316 6228 6.896883 ACCATGATTGAAGATGAAGAGATCA 58.103 36.000 0.00 0.00 43.67 2.92
4317 6229 9.504708 AATACCATGATTGAAGATGAAGAGATC 57.495 33.333 0.00 0.00 0.00 2.75
4323 6235 8.623903 GCAGTTAATACCATGATTGAAGATGAA 58.376 33.333 0.00 0.00 0.00 2.57
4324 6236 7.774625 TGCAGTTAATACCATGATTGAAGATGA 59.225 33.333 0.00 0.00 0.00 2.92
4325 6237 7.933396 TGCAGTTAATACCATGATTGAAGATG 58.067 34.615 0.00 0.00 0.00 2.90
4326 6238 8.523915 TTGCAGTTAATACCATGATTGAAGAT 57.476 30.769 0.00 0.00 0.00 2.40
4327 6239 7.828717 TCTTGCAGTTAATACCATGATTGAAGA 59.171 33.333 0.00 0.00 0.00 2.87
4328 6240 7.988737 TCTTGCAGTTAATACCATGATTGAAG 58.011 34.615 0.00 0.00 0.00 3.02
4329 6241 7.828717 TCTCTTGCAGTTAATACCATGATTGAA 59.171 33.333 0.00 0.00 0.00 2.69
4330 6242 7.337938 TCTCTTGCAGTTAATACCATGATTGA 58.662 34.615 0.00 0.00 0.00 2.57
4331 6243 7.558161 TCTCTTGCAGTTAATACCATGATTG 57.442 36.000 0.00 0.00 0.00 2.67
4332 6244 8.627403 CATTCTCTTGCAGTTAATACCATGATT 58.373 33.333 0.00 0.00 0.00 2.57
4333 6245 7.994911 TCATTCTCTTGCAGTTAATACCATGAT 59.005 33.333 0.00 0.00 0.00 2.45
4334 6246 7.337938 TCATTCTCTTGCAGTTAATACCATGA 58.662 34.615 0.00 0.00 0.00 3.07
4335 6247 7.558161 TCATTCTCTTGCAGTTAATACCATG 57.442 36.000 0.00 0.00 0.00 3.66
4336 6248 8.462016 GTTTCATTCTCTTGCAGTTAATACCAT 58.538 33.333 0.00 0.00 0.00 3.55
4350 6262 6.150140 CCGGATCTCTTTTGTTTCATTCTCTT 59.850 38.462 0.00 0.00 0.00 2.85
4455 6367 3.786635 AGCCATCAACTCTCGAATACAC 58.213 45.455 0.00 0.00 0.00 2.90
4459 6371 7.253422 CAAAATAAAGCCATCAACTCTCGAAT 58.747 34.615 0.00 0.00 0.00 3.34
4543 6455 2.362077 AGCCACAAATCACAACTCAACC 59.638 45.455 0.00 0.00 0.00 3.77
4581 6493 6.884836 GGAGTATTAAAGTCTCCAACACCAAT 59.115 38.462 14.79 0.00 44.85 3.16
4588 6500 4.404715 CGGAGGGAGTATTAAAGTCTCCAA 59.595 45.833 18.78 0.00 46.61 3.53
4680 6592 3.749609 AGGGTCAAAAACGGAATTACGAG 59.250 43.478 18.96 1.12 37.61 4.18
4722 6634 1.825191 CACATGCAATCGGGGGAGG 60.825 63.158 0.00 0.00 0.00 4.30
4763 6677 3.071602 CACAATCGGGAGAGGGATACATT 59.928 47.826 0.00 0.00 45.48 2.71
4765 6679 2.039418 CACAATCGGGAGAGGGATACA 58.961 52.381 0.00 0.00 45.48 2.29
4766 6680 2.040178 ACACAATCGGGAGAGGGATAC 58.960 52.381 0.00 0.00 45.48 2.24
4806 6721 8.623903 TGATTAGCAGCAAGTAAATCATTTAGG 58.376 33.333 0.00 0.00 32.99 2.69
4822 6737 5.718649 TGTCTAATTCGTTGATTAGCAGC 57.281 39.130 9.52 0.00 38.76 5.25
4824 6739 7.097192 ACTCTTGTCTAATTCGTTGATTAGCA 58.903 34.615 9.52 8.61 38.76 3.49
4890 6806 7.801104 TCTAAGGTGTATTATTTCTGGCATGA 58.199 34.615 0.00 0.00 0.00 3.07
4929 6845 7.013464 CCGTGTCCTGTCTCTAAATTATACTCT 59.987 40.741 0.00 0.00 0.00 3.24
4932 6848 7.035840 TCCGTGTCCTGTCTCTAAATTATAC 57.964 40.000 0.00 0.00 0.00 1.47
4942 6858 0.966920 TTCCTTCCGTGTCCTGTCTC 59.033 55.000 0.00 0.00 0.00 3.36
4955 6871 5.803020 AGCGTCAAAGTTATCATTCCTTC 57.197 39.130 0.00 0.00 0.00 3.46
4968 6884 2.969628 AGGGTCATCTAGCGTCAAAG 57.030 50.000 0.00 0.00 0.00 2.77
4984 6900 1.722011 ACAGCATCGAACGTAAAGGG 58.278 50.000 0.00 0.00 0.00 3.95
4992 6908 5.699839 AGGTTTTCAATAACAGCATCGAAC 58.300 37.500 0.00 0.00 0.00 3.95
4995 6911 6.662414 TCTAGGTTTTCAATAACAGCATCG 57.338 37.500 0.00 0.00 0.00 3.84
4996 6912 9.294030 CAAATCTAGGTTTTCAATAACAGCATC 57.706 33.333 0.00 0.00 0.00 3.91
5060 6976 2.994186 ACGTTGGTGTTTACAGACCT 57.006 45.000 0.00 0.00 32.98 3.85
5061 6977 2.472488 CGTACGTTGGTGTTTACAGACC 59.528 50.000 7.22 0.00 0.00 3.85
5153 7088 1.557371 GGGAGGAGGAGGAAGTTTCTG 59.443 57.143 0.00 0.00 0.00 3.02
5178 7113 1.490490 TCATCGAAATCCAAGAGGGGG 59.510 52.381 0.00 0.00 37.22 5.40
5179 7114 2.486191 CCTCATCGAAATCCAAGAGGGG 60.486 54.545 0.00 0.00 39.12 4.79
5180 7115 2.843701 CCTCATCGAAATCCAAGAGGG 58.156 52.381 0.00 0.00 39.12 4.30
5181 7116 2.216898 GCCTCATCGAAATCCAAGAGG 58.783 52.381 0.00 0.00 44.19 3.69
5182 7117 2.216898 GGCCTCATCGAAATCCAAGAG 58.783 52.381 0.00 0.00 0.00 2.85
5183 7118 1.473257 CGGCCTCATCGAAATCCAAGA 60.473 52.381 0.00 0.00 0.00 3.02
5184 7119 0.940126 CGGCCTCATCGAAATCCAAG 59.060 55.000 0.00 0.00 0.00 3.61
5194 7129 1.097547 CCCACATCAACGGCCTCATC 61.098 60.000 0.00 0.00 0.00 2.92
5202 7137 1.535462 GTCTTGTTCCCCACATCAACG 59.465 52.381 0.00 0.00 34.43 4.10
5204 7139 1.544537 CGGTCTTGTTCCCCACATCAA 60.545 52.381 0.00 0.00 34.43 2.57
5206 7141 1.305930 GCGGTCTTGTTCCCCACATC 61.306 60.000 0.00 0.00 34.43 3.06
5207 7142 1.303317 GCGGTCTTGTTCCCCACAT 60.303 57.895 0.00 0.00 34.43 3.21
5224 7159 4.149396 GCATGACAACTCAAATGACAAAGC 59.851 41.667 0.00 0.00 0.00 3.51
5225 7160 5.283294 TGCATGACAACTCAAATGACAAAG 58.717 37.500 0.00 0.00 0.00 2.77
5256 7191 1.303643 CCTTGGTGTCCTTCCTGCC 60.304 63.158 0.00 0.00 0.00 4.85
5279 7214 6.540189 CAGATGTCGGATCTTAAATTTCCACT 59.460 38.462 0.00 0.00 0.00 4.00
5284 7219 8.792830 TTTCTCAGATGTCGGATCTTAAATTT 57.207 30.769 0.00 0.00 0.00 1.82
5294 7229 7.280876 CCTGAAATAATTTTCTCAGATGTCGGA 59.719 37.037 1.24 0.00 41.54 4.55
5296 7231 7.412853 CCCTGAAATAATTTTCTCAGATGTCG 58.587 38.462 1.24 0.00 41.54 4.35
5325 7260 2.755650 ACACCACTCAAACTCTTAGCG 58.244 47.619 0.00 0.00 0.00 4.26
5337 7272 9.063615 TCCTTTTCTTTCTTATAAACACCACTC 57.936 33.333 0.00 0.00 0.00 3.51
5378 7313 2.163818 AATGTCGGAAGCTTCAACGA 57.836 45.000 27.02 23.00 0.00 3.85
5390 7325 5.506317 GGGAATGATTCTGCTTTAATGTCGG 60.506 44.000 5.03 0.00 0.00 4.79
5391 7326 5.514279 GGGAATGATTCTGCTTTAATGTCG 58.486 41.667 5.03 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.