Multiple sequence alignment - TraesCS1D01G389000

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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 TraesCS1D01G389000 chr1D 100.000 3646 0 0 1 3646 460869546 460865901 0.000000e+00 6734.0
1 TraesCS1D01G389000 chr1D 80.899 89 12 4 649 736 371198936 371198852 8.450000e-07 65.8
2 TraesCS1D01G389000 chr1A 90.769 2264 124 39 738 2963 551984437 551982221 0.000000e+00 2944.0
3 TraesCS1D01G389000 chr1A 94.545 605 24 5 3043 3646 551982224 551981628 0.000000e+00 926.0
4 TraesCS1D01G389000 chr1A 85.987 628 74 11 1 618 551985481 551984858 0.000000e+00 660.0
5 TraesCS1D01G389000 chr1A 95.960 99 4 0 2950 3048 575557261 575557359 1.050000e-35 161.0
6 TraesCS1D01G389000 chr1A 92.683 41 3 0 610 650 551984476 551984436 3.930000e-05 60.2
7 TraesCS1D01G389000 chr1B 92.569 1588 93 13 770 2340 633139469 633137890 0.000000e+00 2255.0
8 TraesCS1D01G389000 chr1B 94.581 609 25 8 3043 3646 633137357 633136752 0.000000e+00 935.0
9 TraesCS1D01G389000 chr1B 94.129 528 20 6 2447 2963 633137881 633137354 0.000000e+00 793.0
10 TraesCS1D01G389000 chr1B 87.468 391 47 2 1 390 633140367 633139978 2.000000e-122 449.0
11 TraesCS1D01G389000 chr1B 93.103 58 2 2 650 707 174339545 174339600 2.330000e-12 84.2
12 TraesCS1D01G389000 chr1B 85.333 75 9 2 646 720 470724729 470724657 3.900000e-10 76.8
13 TraesCS1D01G389000 chr1B 92.857 42 3 0 610 651 633139665 633139624 1.090000e-05 62.1
14 TraesCS1D01G389000 chr4B 90.984 122 7 4 2931 3049 166003038 166003158 1.050000e-35 161.0
15 TraesCS1D01G389000 chr7D 96.000 100 1 3 2952 3050 94261219 94261316 3.770000e-35 159.0
16 TraesCS1D01G389000 chr7D 97.802 91 2 0 2957 3047 104453475 104453565 1.360000e-34 158.0
17 TraesCS1D01G389000 chr7D 77.551 147 33 0 1 147 100989444 100989590 5.010000e-14 89.8
18 TraesCS1D01G389000 chr7D 80.952 105 14 5 650 752 365389938 365389838 1.090000e-10 78.7
19 TraesCS1D01G389000 chr6A 91.379 116 7 3 2945 3059 172113280 172113167 4.870000e-34 156.0
20 TraesCS1D01G389000 chr3B 94.118 102 3 3 2956 3054 101314949 101315050 6.310000e-33 152.0
21 TraesCS1D01G389000 chr3B 88.430 121 8 5 2958 3076 55098859 55098975 1.360000e-29 141.0
22 TraesCS1D01G389000 chr5D 93.269 104 4 3 2951 3052 223231462 223231360 2.270000e-32 150.0
23 TraesCS1D01G389000 chr5D 87.143 70 7 1 650 719 60145871 60145804 1.090000e-10 78.7
24 TraesCS1D01G389000 chr4D 83.636 165 22 5 451 612 487362345 487362507 2.270000e-32 150.0
25 TraesCS1D01G389000 chr4D 79.605 152 25 6 44 193 111946039 111945892 1.790000e-18 104.0
26 TraesCS1D01G389000 chr5A 91.150 113 5 5 2936 3044 428189464 428189353 8.160000e-32 148.0
27 TraesCS1D01G389000 chr6B 80.851 188 23 6 1976 2163 152654932 152654758 6.350000e-28 135.0
28 TraesCS1D01G389000 chr6B 76.522 230 49 5 3 230 680614067 680613841 1.780000e-23 121.0
29 TraesCS1D01G389000 chr6B 75.635 197 34 12 44 233 159706827 159706638 6.490000e-13 86.1
30 TraesCS1D01G389000 chr6B 81.633 98 13 4 649 745 509544416 509544323 3.900000e-10 76.8
31 TraesCS1D01G389000 chr6D 76.955 243 51 5 1 241 390160597 390160358 2.280000e-27 134.0
32 TraesCS1D01G389000 chr6D 87.356 87 8 2 650 736 20553753 20553670 3.000000e-16 97.1
33 TraesCS1D01G389000 chr6D 78.014 141 29 2 8 147 161915568 161915429 1.800000e-13 87.9
34 TraesCS1D01G389000 chr3A 74.107 224 53 5 1 222 58830781 58831001 1.800000e-13 87.9
35 TraesCS1D01G389000 chr3A 100.000 33 0 0 186 218 439464568 439464600 1.090000e-05 62.1
36 TraesCS1D01G389000 chr3D 85.714 70 8 1 650 719 474581800 474581733 5.050000e-09 73.1
37 TraesCS1D01G389000 chr5B 93.750 48 2 1 647 693 167283421 167283374 1.820000e-08 71.3


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 TraesCS1D01G389000 chr1D 460865901 460869546 3645 True 6734.00 6734 100.0000 1 3646 1 chr1D.!!$R2 3645
1 TraesCS1D01G389000 chr1A 551981628 551985481 3853 True 1147.55 2944 90.9960 1 3646 4 chr1A.!!$R1 3645
2 TraesCS1D01G389000 chr1B 633136752 633140367 3615 True 898.82 2255 92.3208 1 3646 5 chr1B.!!$R2 3645

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
64 65 0.106519 GTCCTTAGGGGCATGTGCAT 60.107 55.0 7.36 0.0 44.36 3.96 F
152 153 0.179145 CGACGGCTCGTTCTATTGGT 60.179 55.0 1.80 0.0 41.37 3.67 F
173 174 0.250727 CTGGTGATTGTCCGGTGGTT 60.251 55.0 0.00 0.0 0.00 3.67 F
1265 2039 0.798776 CTGGTCGCTGGATGTTTCAC 59.201 55.0 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1050 1823 0.034059 CGTTGCTGGTGAGGTTCTCT 59.966 55.000 0.0 0.0 0.00 3.10 R
1388 2179 0.178975 CCACCACCCAGCTACCAAAA 60.179 55.000 0.0 0.0 0.00 2.44 R
1463 2254 1.538876 CCCCCAGTCCAGACTCCAA 60.539 63.158 0.0 0.0 40.20 3.53 R
3201 4043 1.199789 TGATTCAACAGCATGAACGGC 59.800 47.619 0.0 0.0 41.78 5.68 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
30 31 2.616842 GGGTTCAACGCCGATGAATATT 59.383 45.455 12.94 0.00 38.89 1.28
38 39 1.442769 CCGATGAATATTGCTCCCGG 58.557 55.000 0.00 0.00 0.00 5.73
59 60 1.696063 CAATGGTCCTTAGGGGCATG 58.304 55.000 0.00 0.00 39.39 4.06
64 65 0.106519 GTCCTTAGGGGCATGTGCAT 60.107 55.000 7.36 0.00 44.36 3.96
72 73 0.737219 GGGCATGTGCATGAAGACTC 59.263 55.000 15.53 0.00 44.36 3.36
148 149 0.317938 GCATCGACGGCTCGTTCTAT 60.318 55.000 3.77 0.00 41.37 1.98
150 151 1.781429 CATCGACGGCTCGTTCTATTG 59.219 52.381 0.00 0.00 41.37 1.90
152 153 0.179145 CGACGGCTCGTTCTATTGGT 60.179 55.000 1.80 0.00 41.37 3.67
154 155 2.457970 GACGGCTCGTTCTATTGGTAC 58.542 52.381 1.80 0.00 41.37 3.34
160 161 3.119245 GCTCGTTCTATTGGTACTGGTGA 60.119 47.826 0.00 0.00 0.00 4.02
173 174 0.250727 CTGGTGATTGTCCGGTGGTT 60.251 55.000 0.00 0.00 0.00 3.67
183 184 3.170717 TGTCCGGTGGTTTAGAGATCTT 58.829 45.455 0.00 0.00 0.00 2.40
193 194 9.832445 GGTGGTTTAGAGATCTTGATGTAATTA 57.168 33.333 0.00 0.00 0.00 1.40
226 230 6.978343 TTAAGGTGATTTGTACTTCCGATG 57.022 37.500 0.00 0.00 0.00 3.84
230 234 4.693566 GGTGATTTGTACTTCCGATGAACA 59.306 41.667 0.00 0.00 0.00 3.18
232 236 6.537301 GGTGATTTGTACTTCCGATGAACATA 59.463 38.462 0.00 0.00 0.00 2.29
235 239 9.256477 TGATTTGTACTTCCGATGAACATATAC 57.744 33.333 0.00 0.00 0.00 1.47
328 332 9.743057 CTTAAACAGTGAACCATTGATACAAAA 57.257 29.630 0.00 0.00 0.00 2.44
363 370 4.367166 TCTGTAGGACAATAATGTGGGGA 58.633 43.478 0.00 0.00 40.74 4.81
384 391 6.350103 GGGAGGAGGTAGTAGAAAATTCTTG 58.650 44.000 0.29 0.00 38.70 3.02
420 674 4.396478 GCTAAACAGATTTCTCCCCTCAAC 59.604 45.833 0.00 0.00 0.00 3.18
466 720 6.500336 ACAGACTTGAACCTAGGGATAGTTA 58.500 40.000 14.81 0.00 0.00 2.24
469 723 9.144298 CAGACTTGAACCTAGGGATAGTTATAA 57.856 37.037 14.81 0.00 0.00 0.98
494 748 8.869986 AAATTTCCTATTTTTAGGGGCCTATT 57.130 30.769 0.84 0.00 37.81 1.73
500 754 5.974156 ATTTTTAGGGGCCTATTTGCAAT 57.026 34.783 0.84 0.00 0.00 3.56
508 762 4.322567 GGGCCTATTTGCAATGTTTTCAA 58.677 39.130 0.84 0.00 0.00 2.69
509 763 4.943093 GGGCCTATTTGCAATGTTTTCAAT 59.057 37.500 0.84 0.00 0.00 2.57
511 765 6.037062 GGGCCTATTTGCAATGTTTTCAATAC 59.963 38.462 0.84 0.00 0.00 1.89
513 767 7.201548 GGCCTATTTGCAATGTTTTCAATACAG 60.202 37.037 0.00 0.00 0.00 2.74
530 786 2.550978 ACAGTCGTGTTTTCTGGTCAG 58.449 47.619 0.00 0.00 30.30 3.51
534 790 2.795470 GTCGTGTTTTCTGGTCAGTCTC 59.205 50.000 0.00 0.00 0.00 3.36
538 795 4.261656 CGTGTTTTCTGGTCAGTCTCTAGT 60.262 45.833 0.00 0.00 0.00 2.57
542 799 6.098409 TGTTTTCTGGTCAGTCTCTAGTTTCT 59.902 38.462 0.00 0.00 0.00 2.52
543 800 5.968528 TTCTGGTCAGTCTCTAGTTTCTC 57.031 43.478 0.00 0.00 0.00 2.87
544 801 4.986783 TCTGGTCAGTCTCTAGTTTCTCA 58.013 43.478 0.00 0.00 0.00 3.27
552 809 4.023878 AGTCTCTAGTTTCTCACGTGTGTC 60.024 45.833 16.51 8.45 0.00 3.67
555 812 3.881089 TCTAGTTTCTCACGTGTGTCTGA 59.119 43.478 16.51 4.83 0.00 3.27
563 820 4.758165 TCTCACGTGTGTCTGACTATGTAA 59.242 41.667 16.51 0.00 0.00 2.41
615 872 7.772332 ATATGGTTGCTCTAAAAGAACGTAG 57.228 36.000 0.00 0.00 0.00 3.51
651 1298 7.755373 GTCCAAACTCCTTTTGCTCATATTTAC 59.245 37.037 0.00 0.00 43.03 2.01
652 1299 7.669722 TCCAAACTCCTTTTGCTCATATTTACT 59.330 33.333 0.00 0.00 43.03 2.24
653 1300 7.970614 CCAAACTCCTTTTGCTCATATTTACTC 59.029 37.037 0.00 0.00 43.03 2.59
654 1301 7.631717 AACTCCTTTTGCTCATATTTACTCC 57.368 36.000 0.00 0.00 0.00 3.85
655 1302 6.122964 ACTCCTTTTGCTCATATTTACTCCC 58.877 40.000 0.00 0.00 0.00 4.30
656 1303 6.069381 ACTCCTTTTGCTCATATTTACTCCCT 60.069 38.462 0.00 0.00 0.00 4.20
657 1304 6.357367 TCCTTTTGCTCATATTTACTCCCTC 58.643 40.000 0.00 0.00 0.00 4.30
658 1305 5.532779 CCTTTTGCTCATATTTACTCCCTCC 59.467 44.000 0.00 0.00 0.00 4.30
659 1306 4.336889 TTGCTCATATTTACTCCCTCCG 57.663 45.455 0.00 0.00 0.00 4.63
660 1307 3.305720 TGCTCATATTTACTCCCTCCGT 58.694 45.455 0.00 0.00 0.00 4.69
661 1308 4.476297 TGCTCATATTTACTCCCTCCGTA 58.524 43.478 0.00 0.00 0.00 4.02
662 1309 4.897076 TGCTCATATTTACTCCCTCCGTAA 59.103 41.667 0.00 0.00 0.00 3.18
663 1310 5.364446 TGCTCATATTTACTCCCTCCGTAAA 59.636 40.000 0.00 0.00 40.07 2.01
664 1311 6.126997 TGCTCATATTTACTCCCTCCGTAAAA 60.127 38.462 0.00 0.00 39.45 1.52
665 1312 6.935208 GCTCATATTTACTCCCTCCGTAAAAT 59.065 38.462 0.00 0.00 39.45 1.82
666 1313 8.092687 GCTCATATTTACTCCCTCCGTAAAATA 58.907 37.037 0.00 0.00 39.45 1.40
667 1314 9.991906 CTCATATTTACTCCCTCCGTAAAATAA 57.008 33.333 0.00 0.00 39.45 1.40
676 1323 8.312564 ACTCCCTCCGTAAAATAATATAAGAGC 58.687 37.037 0.00 0.00 0.00 4.09
677 1324 8.431910 TCCCTCCGTAAAATAATATAAGAGCT 57.568 34.615 0.00 0.00 0.00 4.09
678 1325 8.877195 TCCCTCCGTAAAATAATATAAGAGCTT 58.123 33.333 0.00 0.00 0.00 3.74
679 1326 9.503399 CCCTCCGTAAAATAATATAAGAGCTTT 57.497 33.333 0.00 0.00 0.00 3.51
711 1358 9.530633 CACTACTTTATAGTGATCTAAACACCC 57.469 37.037 8.13 0.00 45.69 4.61
712 1359 9.490083 ACTACTTTATAGTGATCTAAACACCCT 57.510 33.333 0.00 0.00 38.82 4.34
779 1544 6.494666 AATCAAGTATACGAGGATTTCCCA 57.505 37.500 11.48 0.00 37.41 4.37
782 1548 6.713276 TCAAGTATACGAGGATTTCCCAAAA 58.287 36.000 0.00 0.00 37.41 2.44
812 1585 6.449698 AGTAGACGGTAGAATTCGTGAAAAA 58.550 36.000 0.00 0.00 39.88 1.94
842 1615 1.627550 GAGGACGAGCAGGCGAAAAC 61.628 60.000 0.00 0.00 34.83 2.43
844 1617 1.298859 GGACGAGCAGGCGAAAACAT 61.299 55.000 0.00 0.00 34.83 2.71
853 1626 3.545703 CAGGCGAAAACATCCCTAAGAT 58.454 45.455 0.00 0.00 34.66 2.40
895 1668 2.682494 TAGACCAGGTCCACCGCC 60.682 66.667 16.72 0.00 42.08 6.13
946 1719 4.498520 CGTCCAGATCGCTGCCGT 62.499 66.667 0.00 0.00 40.91 5.68
1050 1823 3.399181 GTCCCCGTCATCCAGGCA 61.399 66.667 0.00 0.00 0.00 4.75
1186 1959 2.906389 TCTGGAGGTGTGCTCAGTTTAT 59.094 45.455 0.00 0.00 0.00 1.40
1243 2017 4.224715 TCTCGTGGATCATTAGCGTAAG 57.775 45.455 0.00 0.00 43.44 2.34
1250 2024 3.458189 GATCATTAGCGTAAGTGCTGGT 58.542 45.455 0.00 0.00 46.70 4.00
1262 2036 1.073025 TGCTGGTCGCTGGATGTTT 59.927 52.632 0.00 0.00 40.11 2.83
1265 2039 0.798776 CTGGTCGCTGGATGTTTCAC 59.201 55.000 0.00 0.00 0.00 3.18
1282 2056 4.730949 TTCACTACAAGTATTCGAGGGG 57.269 45.455 0.00 0.00 0.00 4.79
1285 2059 3.700038 CACTACAAGTATTCGAGGGGAGT 59.300 47.826 0.00 0.00 0.00 3.85
1294 2080 4.855298 ATTCGAGGGGAGTGGATTTTTA 57.145 40.909 0.00 0.00 0.00 1.52
1370 2161 5.470845 AACTATGATGCGCTAACAACTTC 57.529 39.130 9.73 0.00 0.00 3.01
1409 2200 0.844661 TTGGTAGCTGGGTGGTGGAT 60.845 55.000 0.00 0.00 0.00 3.41
1420 2211 5.338300 GCTGGGTGGTGGATTGATTTAAAAT 60.338 40.000 0.00 0.00 0.00 1.82
1421 2212 6.127196 GCTGGGTGGTGGATTGATTTAAAATA 60.127 38.462 0.00 0.00 0.00 1.40
1425 2216 9.325198 GGGTGGTGGATTGATTTAAAATAATTC 57.675 33.333 0.00 0.00 0.00 2.17
1462 2253 3.246226 GCTAGGTTGAGATGCATTGTACG 59.754 47.826 0.00 0.00 0.00 3.67
1463 2254 3.334583 AGGTTGAGATGCATTGTACGT 57.665 42.857 0.00 0.00 0.00 3.57
1464 2255 3.674997 AGGTTGAGATGCATTGTACGTT 58.325 40.909 0.00 0.00 0.00 3.99
1520 2346 3.628646 AACGGTGGGCATGCCTCTC 62.629 63.158 34.70 23.43 36.10 3.20
1557 2383 6.095160 CCACTAGGTGTATCTAGTTTTCGAGT 59.905 42.308 2.12 0.00 45.32 4.18
1558 2384 6.967767 CACTAGGTGTATCTAGTTTTCGAGTG 59.032 42.308 2.12 0.00 45.32 3.51
1592 2418 2.508526 AGTGATGCTCTTGTTGGTTCC 58.491 47.619 0.00 0.00 0.00 3.62
1597 2423 4.473196 TGATGCTCTTGTTGGTTCCCTATA 59.527 41.667 0.00 0.00 0.00 1.31
1598 2424 5.132648 TGATGCTCTTGTTGGTTCCCTATAT 59.867 40.000 0.00 0.00 0.00 0.86
1623 2449 2.166459 TGAGACTCGTATGGAAAGCTGG 59.834 50.000 0.00 0.00 0.00 4.85
1646 2474 8.246908 TGGTTAGACAATGTAATTACAGTTCG 57.753 34.615 22.03 12.03 39.92 3.95
1766 2595 6.337356 TCAAGTTTCCTGTTTCCATTTTGTC 58.663 36.000 0.00 0.00 0.00 3.18
1804 2633 7.753630 TCGACTATAAGGAATTACCCTAGACT 58.246 38.462 0.00 0.00 40.05 3.24
1833 2662 7.761409 TGCTTATCTGCTATTTAACCAAACAG 58.239 34.615 0.00 0.00 0.00 3.16
1871 2700 6.452872 GCATGATGATTTGTTCGTTTTACAGC 60.453 38.462 0.00 0.00 0.00 4.40
1925 2754 1.285280 CTGGTATCTGGGGGTTCACA 58.715 55.000 0.00 0.00 0.00 3.58
1962 2791 7.489757 GCTTCGTCTTCTACTTTCTGATAATGT 59.510 37.037 0.00 0.00 0.00 2.71
1970 2799 8.079211 TCTACTTTCTGATAATGTTGGTAGCT 57.921 34.615 0.00 0.00 0.00 3.32
1994 2823 1.172180 TTGGGCTCTTGGCAAAGTCG 61.172 55.000 0.00 0.00 44.01 4.18
2042 2871 6.721318 TGATAGTTGGAGCAGGATTTTAGTT 58.279 36.000 0.00 0.00 0.00 2.24
2121 2950 6.152154 GTGGTTTACACCCTAACTGCATAAAT 59.848 38.462 0.00 0.00 43.49 1.40
2271 3100 3.592059 TCTTATTTGGTACGGCTGTCAC 58.408 45.455 0.00 0.00 0.00 3.67
2305 3134 3.906720 TGGACCAGGAGTTATACAAGC 57.093 47.619 0.00 0.00 0.00 4.01
2334 3163 7.145932 ACAACTCTAATTTGCCACTATGTTC 57.854 36.000 0.00 0.00 0.00 3.18
2344 3173 5.818136 TGCCACTATGTTCAAAGATTAGC 57.182 39.130 0.00 0.00 0.00 3.09
2351 3180 7.278646 CACTATGTTCAAAGATTAGCTGTAGCA 59.721 37.037 6.65 0.00 45.16 3.49
2373 3202 5.339530 GCATTAGATAATCCAGTAGGGCCAT 60.340 44.000 6.18 0.00 36.21 4.40
2376 3205 5.763876 AGATAATCCAGTAGGGCCATAAC 57.236 43.478 6.18 0.12 36.21 1.89
2386 3215 6.068010 CAGTAGGGCCATAACCATGAATAAA 58.932 40.000 6.18 0.00 33.67 1.40
2403 3233 5.768164 TGAATAAAAGTGAACTTGGGAGGAC 59.232 40.000 0.00 0.00 36.12 3.85
2414 3244 8.652290 GTGAACTTGGGAGGACTATTATCTATT 58.348 37.037 0.00 0.00 0.00 1.73
2415 3245 9.892444 TGAACTTGGGAGGACTATTATCTATTA 57.108 33.333 0.00 0.00 0.00 0.98
2482 3312 6.289834 AGATGTTGCAAAATGATCCAAACAA 58.710 32.000 6.90 0.00 0.00 2.83
2483 3313 5.987777 TGTTGCAAAATGATCCAAACAAG 57.012 34.783 0.00 0.00 0.00 3.16
2518 3350 7.436933 TCTACTCAGTTGCCATATGTATTCTG 58.563 38.462 1.24 5.60 0.00 3.02
2801 3635 3.833442 TGCGTATGATATCGTCCACATC 58.167 45.455 0.00 0.00 0.00 3.06
2881 3722 5.055812 GGAAGGAGCTAATGTCAGATGAAG 58.944 45.833 0.00 0.00 0.00 3.02
2964 3805 9.659830 CACATTTTTGTTGTTAGTTACTACTCC 57.340 33.333 0.00 0.00 35.78 3.85
2965 3806 8.843262 ACATTTTTGTTGTTAGTTACTACTCCC 58.157 33.333 0.00 0.00 35.78 4.30
2966 3807 9.063615 CATTTTTGTTGTTAGTTACTACTCCCT 57.936 33.333 0.00 0.00 35.78 4.20
2967 3808 8.667076 TTTTTGTTGTTAGTTACTACTCCCTC 57.333 34.615 0.00 0.00 35.78 4.30
2968 3809 5.990120 TGTTGTTAGTTACTACTCCCTCC 57.010 43.478 0.00 0.00 35.78 4.30
2969 3810 4.460382 TGTTGTTAGTTACTACTCCCTCCG 59.540 45.833 0.00 0.00 35.78 4.63
2970 3811 4.307032 TGTTAGTTACTACTCCCTCCGT 57.693 45.455 0.00 0.00 35.78 4.69
2971 3812 5.435686 TGTTAGTTACTACTCCCTCCGTA 57.564 43.478 0.00 0.00 35.78 4.02
2972 3813 5.815581 TGTTAGTTACTACTCCCTCCGTAA 58.184 41.667 0.00 0.00 35.78 3.18
2973 3814 6.245408 TGTTAGTTACTACTCCCTCCGTAAA 58.755 40.000 0.00 0.00 35.78 2.01
2974 3815 6.151144 TGTTAGTTACTACTCCCTCCGTAAAC 59.849 42.308 0.00 0.00 35.78 2.01
2975 3816 4.928263 AGTTACTACTCCCTCCGTAAACT 58.072 43.478 0.00 0.00 0.00 2.66
2976 3817 6.067217 AGTTACTACTCCCTCCGTAAACTA 57.933 41.667 0.00 0.00 0.00 2.24
2977 3818 6.485171 AGTTACTACTCCCTCCGTAAACTAA 58.515 40.000 0.00 0.00 0.00 2.24
2978 3819 7.122048 AGTTACTACTCCCTCCGTAAACTAAT 58.878 38.462 0.00 0.00 0.00 1.73
2979 3820 8.275040 AGTTACTACTCCCTCCGTAAACTAATA 58.725 37.037 0.00 0.00 0.00 0.98
2980 3821 9.072375 GTTACTACTCCCTCCGTAAACTAATAT 57.928 37.037 0.00 0.00 0.00 1.28
2983 3824 9.294614 ACTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
2984 3825 9.512588 CTACTCCCTCCGTAAACTAATATAAGA 57.487 37.037 0.00 0.00 0.00 2.10
2985 3826 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2986 3827 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
2987 3828 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
2988 3829 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
2989 3830 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
2990 3831 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
3018 3859 9.733219 GATAACTACTTTAGTGATCTAAACGCT 57.267 33.333 4.09 0.00 41.55 5.07
3019 3860 9.733219 ATAACTACTTTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 40.05 5.03
3020 3861 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
3021 3862 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
3022 3863 8.954350 ACTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
3023 3864 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
3035 3876 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
3036 3877 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
3037 3878 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
3038 3879 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
3039 3880 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
3040 3881 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
3041 3882 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
3120 3962 3.966665 TGGCCAGTGTATCAGATATCACA 59.033 43.478 0.00 0.00 33.84 3.58
3122 3964 4.562347 GGCCAGTGTATCAGATATCACAGG 60.562 50.000 19.43 19.43 39.38 4.00
3123 3965 4.039730 GCCAGTGTATCAGATATCACAGGT 59.960 45.833 21.89 0.00 38.88 4.00
3124 3966 5.536260 CCAGTGTATCAGATATCACAGGTG 58.464 45.833 17.99 11.34 34.38 4.00
3125 3967 5.069648 CCAGTGTATCAGATATCACAGGTGT 59.930 44.000 17.99 0.00 34.38 4.16
3201 4043 7.044771 CGAAACAATTACATCACATCATTTCCG 60.045 37.037 0.00 0.00 0.00 4.30
3202 4044 5.581605 ACAATTACATCACATCATTTCCGC 58.418 37.500 0.00 0.00 0.00 5.54
3389 4231 6.817641 TGTGTTTTTCAGCTGATTTTGATTGT 59.182 30.769 19.04 0.00 0.00 2.71
3393 4235 9.558648 GTTTTTCAGCTGATTTTGATTGTTTTT 57.441 25.926 19.04 0.00 0.00 1.94
3595 4438 1.623542 CCCCAGAACCCTAACCTCCG 61.624 65.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.424711 GACCATTGCCCGGGAGCA 62.425 66.667 29.31 14.10 42.17 4.26
38 39 1.455773 GCCCCTAAGGACCATTGCC 60.456 63.158 0.00 0.00 38.24 4.52
42 43 0.552848 CACATGCCCCTAAGGACCAT 59.447 55.000 0.00 0.00 38.24 3.55
59 60 1.211457 AGATGGGGAGTCTTCATGCAC 59.789 52.381 0.00 0.00 0.00 4.57
64 65 2.325661 TGACAGATGGGGAGTCTTCA 57.674 50.000 0.00 0.00 0.00 3.02
72 73 2.304092 CCATGTTGATGACAGATGGGG 58.696 52.381 0.00 0.00 42.62 4.96
148 149 1.002659 CCGGACAATCACCAGTACCAA 59.997 52.381 0.00 0.00 0.00 3.67
150 151 0.611714 ACCGGACAATCACCAGTACC 59.388 55.000 9.46 0.00 0.00 3.34
152 153 0.611200 CCACCGGACAATCACCAGTA 59.389 55.000 9.46 0.00 0.00 2.74
154 155 0.250727 AACCACCGGACAATCACCAG 60.251 55.000 9.46 0.00 0.00 4.00
160 161 3.775316 AGATCTCTAAACCACCGGACAAT 59.225 43.478 9.46 0.00 0.00 2.71
211 213 9.607988 TTGTATATGTTCATCGGAAGTACAAAT 57.392 29.630 0.00 0.00 31.80 2.32
466 720 8.869986 AGGCCCCTAAAAATAGGAAATTTTAT 57.130 30.769 0.00 0.00 39.60 1.40
469 723 8.869986 AATAGGCCCCTAAAAATAGGAAATTT 57.130 30.769 0.00 0.00 39.60 1.82
471 725 7.202093 GCAAATAGGCCCCTAAAAATAGGAAAT 60.202 37.037 0.00 0.00 39.60 2.17
475 729 4.898861 TGCAAATAGGCCCCTAAAAATAGG 59.101 41.667 0.00 0.00 36.98 2.57
476 730 6.478512 TTGCAAATAGGCCCCTAAAAATAG 57.521 37.500 0.00 0.00 31.73 1.73
477 731 6.385467 ACATTGCAAATAGGCCCCTAAAAATA 59.615 34.615 1.71 0.00 31.73 1.40
478 732 5.191522 ACATTGCAAATAGGCCCCTAAAAAT 59.808 36.000 1.71 0.00 31.73 1.82
479 733 4.534103 ACATTGCAAATAGGCCCCTAAAAA 59.466 37.500 1.71 0.00 31.73 1.94
489 743 8.761575 ACTGTATTGAAAACATTGCAAATAGG 57.238 30.769 1.71 0.00 0.00 2.57
494 748 5.685068 CACGACTGTATTGAAAACATTGCAA 59.315 36.000 0.00 0.00 0.00 4.08
500 754 6.964370 CAGAAAACACGACTGTATTGAAAACA 59.036 34.615 0.00 0.00 0.00 2.83
508 762 4.202223 ACTGACCAGAAAACACGACTGTAT 60.202 41.667 3.76 0.00 0.00 2.29
509 763 3.131577 ACTGACCAGAAAACACGACTGTA 59.868 43.478 3.76 0.00 0.00 2.74
511 765 2.540101 GACTGACCAGAAAACACGACTG 59.460 50.000 3.76 0.00 0.00 3.51
513 767 2.795470 GAGACTGACCAGAAAACACGAC 59.205 50.000 3.76 0.00 0.00 4.34
530 786 4.023878 AGACACACGTGAGAAACTAGAGAC 60.024 45.833 25.01 0.00 0.00 3.36
534 790 3.975670 GTCAGACACACGTGAGAAACTAG 59.024 47.826 25.01 10.96 0.00 2.57
538 795 4.037565 ACATAGTCAGACACACGTGAGAAA 59.962 41.667 25.01 0.00 0.00 2.52
542 799 4.517832 AGTTACATAGTCAGACACACGTGA 59.482 41.667 25.01 0.00 0.00 4.35
543 800 4.795268 AGTTACATAGTCAGACACACGTG 58.205 43.478 15.48 15.48 0.00 4.49
544 801 5.449107 AAGTTACATAGTCAGACACACGT 57.551 39.130 2.66 0.00 0.00 4.49
592 849 6.694447 ACTACGTTCTTTTAGAGCAACCATA 58.306 36.000 0.00 0.00 0.00 2.74
593 850 5.548406 ACTACGTTCTTTTAGAGCAACCAT 58.452 37.500 0.00 0.00 0.00 3.55
607 864 7.858583 GTTTGGACTTTATCAAACTACGTTCT 58.141 34.615 0.00 0.00 45.28 3.01
651 1298 8.532819 AGCTCTTATATTATTTTACGGAGGGAG 58.467 37.037 0.00 0.00 0.00 4.30
652 1299 8.431910 AGCTCTTATATTATTTTACGGAGGGA 57.568 34.615 0.00 0.00 0.00 4.20
653 1300 9.503399 AAAGCTCTTATATTATTTTACGGAGGG 57.497 33.333 0.00 0.00 0.00 4.30
685 1332 9.530633 GGGTGTTTAGATCACTATAAAGTAGTG 57.469 37.037 8.53 8.53 44.56 2.74
686 1333 9.490083 AGGGTGTTTAGATCACTATAAAGTAGT 57.510 33.333 0.00 0.00 36.25 2.73
720 1367 6.512342 TGAAAAACACTCCTTCCGTAAAAA 57.488 33.333 0.00 0.00 0.00 1.94
721 1368 6.512342 TTGAAAAACACTCCTTCCGTAAAA 57.488 33.333 0.00 0.00 0.00 1.52
722 1369 5.449451 GCTTGAAAAACACTCCTTCCGTAAA 60.449 40.000 0.00 0.00 0.00 2.01
723 1370 4.035909 GCTTGAAAAACACTCCTTCCGTAA 59.964 41.667 0.00 0.00 0.00 3.18
724 1371 3.562557 GCTTGAAAAACACTCCTTCCGTA 59.437 43.478 0.00 0.00 0.00 4.02
725 1372 2.357952 GCTTGAAAAACACTCCTTCCGT 59.642 45.455 0.00 0.00 0.00 4.69
726 1373 2.357637 TGCTTGAAAAACACTCCTTCCG 59.642 45.455 0.00 0.00 0.00 4.30
727 1374 4.112634 GTTGCTTGAAAAACACTCCTTCC 58.887 43.478 0.00 0.00 0.00 3.46
728 1375 4.998788 AGTTGCTTGAAAAACACTCCTTC 58.001 39.130 0.00 0.00 0.00 3.46
729 1376 4.706962 AGAGTTGCTTGAAAAACACTCCTT 59.293 37.500 0.00 0.00 30.42 3.36
730 1377 4.096984 CAGAGTTGCTTGAAAAACACTCCT 59.903 41.667 0.00 0.00 30.42 3.69
731 1378 4.354587 CAGAGTTGCTTGAAAAACACTCC 58.645 43.478 0.00 0.00 30.42 3.85
732 1379 3.793492 GCAGAGTTGCTTGAAAAACACTC 59.207 43.478 0.00 0.00 46.95 3.51
733 1380 3.774066 GCAGAGTTGCTTGAAAAACACT 58.226 40.909 0.00 0.00 46.95 3.55
758 1405 5.943349 TTGGGAAATCCTCGTATACTTGA 57.057 39.130 0.56 0.00 36.20 3.02
782 1548 6.585322 CACGAATTCTACCGTCTACTCTTTTT 59.415 38.462 3.52 0.00 36.83 1.94
787 1553 4.871993 TCACGAATTCTACCGTCTACTC 57.128 45.455 3.52 0.00 36.83 2.59
812 1585 1.609320 GCTCGTCCTCAGCCTTTTCTT 60.609 52.381 0.00 0.00 0.00 2.52
822 1595 2.094757 TTTTCGCCTGCTCGTCCTCA 62.095 55.000 0.00 0.00 0.00 3.86
842 1615 4.125124 TCTGAGGGAGATCTTAGGGATG 57.875 50.000 0.00 0.00 34.33 3.51
844 1617 4.626942 TTTCTGAGGGAGATCTTAGGGA 57.373 45.455 0.00 0.00 0.00 4.20
872 1645 2.612221 CGGTGGACCTGGTCTAGTTTTC 60.612 54.545 25.01 7.88 32.47 2.29
873 1646 1.346722 CGGTGGACCTGGTCTAGTTTT 59.653 52.381 25.01 0.00 32.47 2.43
874 1647 0.974383 CGGTGGACCTGGTCTAGTTT 59.026 55.000 25.01 0.00 32.47 2.66
895 1668 4.596585 ACGGGGTTGGGTGGCTTG 62.597 66.667 0.00 0.00 0.00 4.01
946 1719 4.779733 GGGGCGGAGAGTCTGGGA 62.780 72.222 0.00 0.00 0.00 4.37
1050 1823 0.034059 CGTTGCTGGTGAGGTTCTCT 59.966 55.000 0.00 0.00 0.00 3.10
1131 1904 1.885163 GAGTCCACCGTCGAACCCAT 61.885 60.000 0.00 0.00 0.00 4.00
1250 2024 3.244078 ACTTGTAGTGAAACATCCAGCGA 60.244 43.478 0.00 0.00 41.43 4.93
1262 2036 3.952323 CTCCCCTCGAATACTTGTAGTGA 59.048 47.826 0.00 0.00 0.00 3.41
1265 2039 3.068307 CCACTCCCCTCGAATACTTGTAG 59.932 52.174 0.00 0.00 0.00 2.74
1285 2059 8.883731 TGCTCAAAAACGAAAAATAAAAATCCA 58.116 25.926 0.00 0.00 0.00 3.41
1294 2080 4.126437 CCCCTTGCTCAAAAACGAAAAAT 58.874 39.130 0.00 0.00 0.00 1.82
1370 2161 4.805192 CCAAAAGTTCCAATTCACTGTGTG 59.195 41.667 7.79 0.00 34.45 3.82
1388 2179 0.178975 CCACCACCCAGCTACCAAAA 60.179 55.000 0.00 0.00 0.00 2.44
1420 2211 6.706270 CCTAGCAGGAAAATCTAAGCGAATTA 59.294 38.462 0.00 0.00 37.67 1.40
1421 2212 5.529060 CCTAGCAGGAAAATCTAAGCGAATT 59.471 40.000 0.00 0.00 37.67 2.17
1425 2216 3.798202 ACCTAGCAGGAAAATCTAAGCG 58.202 45.455 8.91 0.00 37.67 4.68
1462 2253 1.679898 CCCCAGTCCAGACTCCAAC 59.320 63.158 0.00 0.00 40.20 3.77
1463 2254 1.538876 CCCCCAGTCCAGACTCCAA 60.539 63.158 0.00 0.00 40.20 3.53
1464 2255 2.122729 CCCCCAGTCCAGACTCCA 59.877 66.667 0.00 0.00 40.20 3.86
1520 2346 5.860941 ACACCTAGTGGATCTAACATCTG 57.139 43.478 0.00 0.00 37.94 2.90
1557 2383 3.391296 GCATCACTTCTATACCCCTTCCA 59.609 47.826 0.00 0.00 0.00 3.53
1558 2384 3.648545 AGCATCACTTCTATACCCCTTCC 59.351 47.826 0.00 0.00 0.00 3.46
1592 2418 5.416013 TCCATACGAGTCTCAAGCATATAGG 59.584 44.000 0.00 0.00 0.00 2.57
1597 2423 4.437239 CTTTCCATACGAGTCTCAAGCAT 58.563 43.478 0.00 0.00 0.00 3.79
1598 2424 3.849911 CTTTCCATACGAGTCTCAAGCA 58.150 45.455 0.00 0.00 0.00 3.91
1623 2449 8.248117 ACCGAACTGTAATTACATTGTCTAAC 57.752 34.615 18.35 6.58 35.36 2.34
1646 2474 9.251792 CCAACCAAACAAGTTAAAATAGTTACC 57.748 33.333 0.00 0.00 0.00 2.85
1766 2595 7.198390 TCCTTATAGTCGAAAAGGTGTTATCG 58.802 38.462 13.66 0.00 40.58 2.92
1804 2633 9.988815 TTTGGTTAAATAGCAGATAAGCAAAAA 57.011 25.926 18.18 5.68 45.92 1.94
1808 2637 7.148086 CCTGTTTGGTTAAATAGCAGATAAGCA 60.148 37.037 0.00 0.00 34.70 3.91
1833 2662 1.747355 CATCATGCTCAGGACAAACCC 59.253 52.381 0.00 0.00 40.05 4.11
1846 2675 6.452872 GCTGTAAAACGAACAAATCATCATGC 60.453 38.462 0.00 0.00 0.00 4.06
1962 2791 3.115390 AGAGCCCAATAGAAGCTACCAA 58.885 45.455 0.00 0.00 36.87 3.67
1970 2799 2.897271 TTGCCAAGAGCCCAATAGAA 57.103 45.000 0.00 0.00 42.71 2.10
1994 2823 2.510768 ACGTGTGGACTGAGAACTTC 57.489 50.000 0.00 0.00 0.00 3.01
2042 2871 1.901464 GCCGGCCAAAACTCCTTCA 60.901 57.895 18.11 0.00 0.00 3.02
2121 2950 7.732222 AAAATAGCATCCAAGGGTCAAAATA 57.268 32.000 0.00 0.00 0.00 1.40
2183 3012 9.558396 TTAATTTAGACTAAAACCAAAGACGGA 57.442 29.630 11.57 0.00 0.00 4.69
2271 3100 3.181476 CCTGGTCCAAACTTCAGGTTTTG 60.181 47.826 0.00 0.00 44.77 2.44
2285 3114 3.178046 TGCTTGTATAACTCCTGGTCCA 58.822 45.455 0.00 0.00 0.00 4.02
2290 3119 9.197694 GAGTTGTATATGCTTGTATAACTCCTG 57.802 37.037 23.05 0.00 39.55 3.86
2343 3172 7.038659 CCTACTGGATTATCTAATGCTACAGC 58.961 42.308 3.59 0.00 35.39 4.40
2344 3173 7.551585 CCCTACTGGATTATCTAATGCTACAG 58.448 42.308 3.59 0.00 35.39 2.74
2351 3180 7.092399 GGTTATGGCCCTACTGGATTATCTAAT 60.092 40.741 0.00 0.00 35.39 1.73
2361 3190 1.774254 TCATGGTTATGGCCCTACTGG 59.226 52.381 0.00 0.00 34.97 4.00
2373 3202 7.726291 TCCCAAGTTCACTTTTATTCATGGTTA 59.274 33.333 0.00 0.00 33.11 2.85
2376 3205 6.350445 CCTCCCAAGTTCACTTTTATTCATGG 60.350 42.308 0.00 0.00 33.11 3.66
2386 3215 6.674419 AGATAATAGTCCTCCCAAGTTCACTT 59.326 38.462 0.00 0.00 36.45 3.16
2415 3245 9.649167 GGCCATTAACTATAACATAGATACGTT 57.351 33.333 0.00 0.00 0.00 3.99
2416 3246 8.809066 TGGCCATTAACTATAACATAGATACGT 58.191 33.333 0.00 0.00 0.00 3.57
2417 3247 9.084164 GTGGCCATTAACTATAACATAGATACG 57.916 37.037 9.72 0.00 0.00 3.06
2482 3312 6.166982 GGCAACTGAGTAGAATAAACAGTCT 58.833 40.000 0.00 0.00 37.92 3.24
2483 3313 5.932303 TGGCAACTGAGTAGAATAAACAGTC 59.068 40.000 0.00 0.00 37.92 3.51
2501 3333 8.383318 AGAACATACAGAATACATATGGCAAC 57.617 34.615 7.80 0.00 31.75 4.17
2801 3635 4.465660 TCTCCTTCCATCAGAACTCAGAAG 59.534 45.833 0.00 0.00 0.00 2.85
2881 3722 3.387397 GGGAAATCTTGCATATGCTTGC 58.613 45.455 27.13 17.31 42.66 4.01
2959 3800 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
2960 3801 8.003629 ACTCTTATATTAGTTTACGGAGGGAGT 58.996 37.037 0.00 0.00 0.00 3.85
2961 3802 8.298140 CACTCTTATATTAGTTTACGGAGGGAG 58.702 40.741 0.00 0.00 0.00 4.30
2962 3803 7.781693 ACACTCTTATATTAGTTTACGGAGGGA 59.218 37.037 0.00 0.00 0.00 4.20
2963 3804 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
2964 3805 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
2991 3832 9.733219 GCGTTTAGATCACTAAAGTAGTTATCT 57.267 33.333 13.75 13.75 46.18 1.98
2992 3833 9.733219 AGCGTTTAGATCACTAAAGTAGTTATC 57.267 33.333 0.00 2.65 45.42 1.75
2993 3834 9.733219 GAGCGTTTAGATCACTAAAGTAGTTAT 57.267 33.333 0.00 0.00 45.42 1.89
2994 3835 8.954350 AGAGCGTTTAGATCACTAAAGTAGTTA 58.046 33.333 0.00 0.00 45.42 2.24
2995 3836 7.828712 AGAGCGTTTAGATCACTAAAGTAGTT 58.171 34.615 0.00 0.00 45.42 2.24
2996 3837 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
2997 3838 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
3009 3850 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
3010 3851 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
3011 3852 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
3012 3853 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
3013 3854 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
3014 3855 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
3015 3856 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
3016 3857 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
3017 3858 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
3018 3859 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
3019 3860 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
3022 3863 9.819754 AATAGTACTCCCTCCGTAAACTAATAT 57.180 33.333 0.00 0.00 0.00 1.28
3024 3865 9.072375 GTAATAGTACTCCCTCCGTAAACTAAT 57.928 37.037 0.00 0.00 0.00 1.73
3025 3866 8.275040 AGTAATAGTACTCCCTCCGTAAACTAA 58.725 37.037 0.00 0.00 35.55 2.24
3026 3867 7.716998 CAGTAATAGTACTCCCTCCGTAAACTA 59.283 40.741 0.00 0.00 38.58 2.24
3027 3868 6.545298 CAGTAATAGTACTCCCTCCGTAAACT 59.455 42.308 0.00 0.00 38.58 2.66
3028 3869 6.319911 ACAGTAATAGTACTCCCTCCGTAAAC 59.680 42.308 0.00 0.00 38.58 2.01
3029 3870 6.426587 ACAGTAATAGTACTCCCTCCGTAAA 58.573 40.000 0.00 0.00 38.58 2.01
3030 3871 6.006275 ACAGTAATAGTACTCCCTCCGTAA 57.994 41.667 0.00 0.00 38.58 3.18
3031 3872 5.367937 AGACAGTAATAGTACTCCCTCCGTA 59.632 44.000 0.00 0.00 38.58 4.02
3032 3873 4.165758 AGACAGTAATAGTACTCCCTCCGT 59.834 45.833 0.00 0.00 38.58 4.69
3033 3874 4.716794 AGACAGTAATAGTACTCCCTCCG 58.283 47.826 0.00 0.00 38.58 4.63
3034 3875 6.840527 ACTAGACAGTAATAGTACTCCCTCC 58.159 44.000 0.00 0.00 38.58 4.30
3035 3876 8.623030 CAAACTAGACAGTAATAGTACTCCCTC 58.377 40.741 0.00 0.00 38.58 4.30
3036 3877 7.560626 CCAAACTAGACAGTAATAGTACTCCCT 59.439 40.741 0.00 3.45 38.58 4.20
3037 3878 7.341512 ACCAAACTAGACAGTAATAGTACTCCC 59.658 40.741 0.00 0.00 38.58 4.30
3038 3879 8.189460 CACCAAACTAGACAGTAATAGTACTCC 58.811 40.741 0.00 0.00 38.58 3.85
3039 3880 8.954350 TCACCAAACTAGACAGTAATAGTACTC 58.046 37.037 0.00 0.00 38.58 2.59
3040 3881 8.874744 TCACCAAACTAGACAGTAATAGTACT 57.125 34.615 0.00 0.00 41.49 2.73
3041 3882 9.351570 GTTCACCAAACTAGACAGTAATAGTAC 57.648 37.037 0.00 0.00 33.48 2.73
3122 3964 7.958112 AACGAATTTAAGTGTTGTGTTACAC 57.042 32.000 8.76 8.76 46.86 2.90
3123 3965 9.488124 GTAAACGAATTTAAGTGTTGTGTTACA 57.512 29.630 0.00 0.00 32.04 2.41
3124 3966 8.946935 GGTAAACGAATTTAAGTGTTGTGTTAC 58.053 33.333 0.00 0.00 32.04 2.50
3125 3967 8.127954 GGGTAAACGAATTTAAGTGTTGTGTTA 58.872 33.333 0.00 0.00 32.04 2.41
3144 3986 3.681417 GGTGAACTACGACATGGGTAAAC 59.319 47.826 0.00 0.00 0.00 2.01
3201 4043 1.199789 TGATTCAACAGCATGAACGGC 59.800 47.619 0.00 0.00 41.78 5.68
3202 4044 2.485426 AGTGATTCAACAGCATGAACGG 59.515 45.455 0.00 0.00 41.78 4.44
3360 4202 6.090628 TCAAAATCAGCTGAAAAACACACAAC 59.909 34.615 22.50 0.00 0.00 3.32
3362 4204 5.718146 TCAAAATCAGCTGAAAAACACACA 58.282 33.333 22.50 0.00 0.00 3.72
3363 4205 6.833342 ATCAAAATCAGCTGAAAAACACAC 57.167 33.333 22.50 0.00 0.00 3.82
3433 4276 4.322567 AGGTCATGCTTCTCTCTCAAAAC 58.677 43.478 0.00 0.00 0.00 2.43
3462 4305 0.465460 GCCCAATGAGCCCATTACGA 60.465 55.000 0.00 0.00 40.81 3.43
3464 4307 1.035139 CAGCCCAATGAGCCCATTAC 58.965 55.000 0.00 0.00 40.81 1.89
3595 4438 1.977293 GAGGAGGCCATGGTGGAGAC 61.977 65.000 14.67 0.00 40.96 3.36


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

AutoCloner maintained by Alex Coulton.