Multiple sequence alignment - TraesCS2D01G423000

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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 TraesCS2D01G423000 chr2D 100.000 3414 0 0 1 3414 536151403 536154816 0.000000e+00 6305.0
1 TraesCS2D01G423000 chr2D 88.298 94 5 2 2843 2936 382455938 382456025 1.300000e-19 108.0
2 TraesCS2D01G423000 chr2B 88.787 2613 122 63 418 2965 637575019 637577525 0.000000e+00 3044.0
3 TraesCS2D01G423000 chr2B 85.659 258 21 6 2961 3218 637582034 637582275 1.220000e-64 257.0
4 TraesCS2D01G423000 chr2B 95.349 129 6 0 68 196 637574515 637574643 4.470000e-49 206.0
5 TraesCS2D01G423000 chr2B 92.308 143 9 2 3272 3414 637582385 637582525 5.780000e-48 202.0
6 TraesCS2D01G423000 chr2B 91.429 105 5 1 321 425 637574856 637574956 1.280000e-29 141.0
7 TraesCS2D01G423000 chr2B 88.172 93 5 5 2843 2935 354879211 354879125 4.660000e-19 106.0
8 TraesCS2D01G423000 chr2A 84.872 2069 124 81 418 2416 678963826 678965775 0.000000e+00 1912.0
9 TraesCS2D01G423000 chr2A 92.270 608 23 9 2484 3081 678965795 678966388 0.000000e+00 841.0
10 TraesCS2D01G423000 chr2A 91.022 323 22 5 1 320 678963335 678963653 2.430000e-116 429.0
11 TraesCS2D01G423000 chr2A 88.942 208 13 6 3214 3414 678966418 678966622 7.320000e-62 248.0
12 TraesCS2D01G423000 chr2A 90.196 102 6 1 319 420 678963683 678963780 2.760000e-26 130.0
13 TraesCS2D01G423000 chr2A 100.000 28 0 0 2437 2464 678965772 678965799 6.000000e-03 52.8
14 TraesCS2D01G423000 chr5A 83.665 251 37 4 1998 2246 565395159 565395407 2.050000e-57 233.0
15 TraesCS2D01G423000 chr5A 97.059 34 1 0 2189 2222 702459801 702459834 1.320000e-04 58.4
16 TraesCS2D01G423000 chr5B 83.333 252 36 6 1998 2246 545405753 545406001 9.530000e-56 228.0
17 TraesCS2D01G423000 chr6A 88.542 96 5 3 2845 2940 584511362 584511451 1.000000e-20 111.0
18 TraesCS2D01G423000 chr4D 89.130 92 4 3 2844 2935 252173789 252173704 3.600000e-20 110.0
19 TraesCS2D01G423000 chr4D 87.719 57 7 0 2189 2245 506216839 506216783 2.200000e-07 67.6
20 TraesCS2D01G423000 chr1A 90.476 84 2 3 2845 2928 505489783 505489860 4.660000e-19 106.0
21 TraesCS2D01G423000 chr4A 86.139 101 7 6 2841 2941 743443040 743442947 6.030000e-18 102.0
22 TraesCS2D01G423000 chr4B 85.294 102 7 4 2834 2935 192792738 192792831 7.800000e-17 99.0
23 TraesCS2D01G423000 chr3D 81.188 101 16 2 2147 2244 414637651 414637551 1.020000e-10 78.7
24 TraesCS2D01G423000 chr3A 81.188 101 16 2 2147 2244 535727725 535727825 1.020000e-10 78.7
25 TraesCS2D01G423000 chr3B 79.310 116 19 4 2114 2225 540476583 540476469 3.650000e-10 76.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G423000 chr2D 536151403 536154816 3413 False 6305.000000 6305 100.000 1 3414 1 chr2D.!!$F2 3413
1 TraesCS2D01G423000 chr2B 637574515 637577525 3010 False 1130.333333 3044 91.855 68 2965 3 chr2B.!!$F1 2897
2 TraesCS2D01G423000 chr2A 678963335 678966622 3287 False 602.133333 1912 91.217 1 3414 6 chr2A.!!$F1 3413

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
978 1219 0.324738 TCCAGAGTACAGGGCAGAGG 60.325 60.0 0.0 0.0 0.0 3.69 F
1835 2132 0.041833 TGGTGGAGGAGAAGGAGGAG 59.958 60.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1939 2275 0.179048 AGATGATCGGCGGCATGAAA 60.179 50.0 18.11 0.0 0.00 2.69 R
3352 3750 0.030638 GCAGGTGCTCGCTTGAAAAA 59.969 50.0 0.00 0.0 38.21 1.94 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
84 85 2.998670 CTCATGTGTAGTTGGCTGAGTG 59.001 50.000 0.00 0.00 0.00 3.51
89 90 3.060602 GTGTAGTTGGCTGAGTGAACTC 58.939 50.000 3.41 3.41 43.15 3.01
109 110 2.143122 CGTGGCAGTACTGATGTTTGT 58.857 47.619 27.08 0.00 0.00 2.83
131 132 3.000041 GGCATGAACTGTAACGTGATGA 59.000 45.455 0.00 0.00 0.00 2.92
219 325 9.289303 GTATATCGATTTTGCAACTTGATGTTT 57.711 29.630 16.28 7.71 36.63 2.83
223 329 5.916883 CGATTTTGCAACTTGATGTTTCTCT 59.083 36.000 0.00 0.00 36.63 3.10
233 339 6.169094 ACTTGATGTTTCTCTGGTACTGATG 58.831 40.000 0.00 0.00 35.31 3.07
234 340 6.014242 ACTTGATGTTTCTCTGGTACTGATGA 60.014 38.462 0.00 0.00 35.31 2.92
235 341 6.550938 TGATGTTTCTCTGGTACTGATGAT 57.449 37.500 0.00 0.00 35.31 2.45
236 342 7.660030 TGATGTTTCTCTGGTACTGATGATA 57.340 36.000 0.00 0.00 35.31 2.15
237 343 7.492524 TGATGTTTCTCTGGTACTGATGATAC 58.507 38.462 0.00 0.00 35.31 2.24
241 347 9.862149 TGTTTCTCTGGTACTGATGATACTATA 57.138 33.333 0.00 0.00 35.31 1.31
259 365 9.841295 GATACTATAAATTCTGGGGTTGTTGTA 57.159 33.333 0.00 0.00 0.00 2.41
260 366 7.933215 ACTATAAATTCTGGGGTTGTTGTAC 57.067 36.000 0.00 0.00 0.00 2.90
261 367 5.890424 ATAAATTCTGGGGTTGTTGTACG 57.110 39.130 0.00 0.00 0.00 3.67
264 370 2.713863 TCTGGGGTTGTTGTACGTTT 57.286 45.000 0.00 0.00 0.00 3.60
305 414 5.539955 AGGTGAAAACAAAAGGCAGATACAT 59.460 36.000 0.00 0.00 0.00 2.29
344 484 1.136419 GCAAGCTGATGACATATCGCG 60.136 52.381 0.00 0.00 0.00 5.87
384 524 6.595326 CACATCCACTAATCAGAAGCAAAGTA 59.405 38.462 0.00 0.00 0.00 2.24
385 525 6.820656 ACATCCACTAATCAGAAGCAAAGTAG 59.179 38.462 0.00 0.00 0.00 2.57
386 526 6.605471 TCCACTAATCAGAAGCAAAGTAGA 57.395 37.500 0.00 0.00 0.00 2.59
387 527 6.634805 TCCACTAATCAGAAGCAAAGTAGAG 58.365 40.000 0.00 0.00 0.00 2.43
425 643 2.027385 AGAGAGCAGCGATGTCATGTA 58.973 47.619 1.22 0.00 0.00 2.29
449 669 0.716108 GACGATGAGAAACACTGCGG 59.284 55.000 0.00 0.00 0.00 5.69
488 713 1.302511 GCGGAGAAAGGGCAGACAA 60.303 57.895 0.00 0.00 0.00 3.18
563 798 6.049955 AGCTAAGCACAGATACCAAAACTA 57.950 37.500 0.00 0.00 0.00 2.24
598 833 2.354259 CAGAAGAGCATCAGTTCACCC 58.646 52.381 0.00 0.00 37.82 4.61
601 836 0.534412 AGAGCATCAGTTCACCCTCG 59.466 55.000 0.00 0.00 37.82 4.63
642 877 0.721718 GTGCTACGATGCAAGTGACC 59.278 55.000 8.44 0.00 45.12 4.02
722 957 0.388649 CACGCCACTACACCTCACTC 60.389 60.000 0.00 0.00 0.00 3.51
731 966 4.459337 CACTACACCTCACTCACATCTACA 59.541 45.833 0.00 0.00 0.00 2.74
794 1031 2.223805 CGGCTTTTCCACTGCTTTCTTT 60.224 45.455 0.00 0.00 34.01 2.52
795 1032 3.384668 GGCTTTTCCACTGCTTTCTTTC 58.615 45.455 0.00 0.00 34.01 2.62
796 1033 3.068732 GGCTTTTCCACTGCTTTCTTTCT 59.931 43.478 0.00 0.00 34.01 2.52
797 1034 4.442052 GGCTTTTCCACTGCTTTCTTTCTT 60.442 41.667 0.00 0.00 34.01 2.52
841 1082 1.178276 TCCACGCTTCCTCTTCTCTC 58.822 55.000 0.00 0.00 0.00 3.20
850 1091 1.621672 CCTCTTCTCTCCAGTGGCCC 61.622 65.000 3.51 0.00 0.00 5.80
917 1158 1.927174 GCGGTGCAGTAGACAATACTG 59.073 52.381 10.06 10.06 45.62 2.74
961 1202 1.970114 TCCGAGTGTCCGACTGTCC 60.970 63.158 1.55 0.00 33.83 4.02
962 1203 2.265904 CCGAGTGTCCGACTGTCCA 61.266 63.158 1.55 0.00 33.83 4.02
963 1204 1.210413 CGAGTGTCCGACTGTCCAG 59.790 63.158 1.55 0.00 33.83 3.86
968 1209 1.199558 GTGTCCGACTGTCCAGAGTAC 59.800 57.143 1.55 0.00 0.00 2.73
978 1219 0.324738 TCCAGAGTACAGGGCAGAGG 60.325 60.000 0.00 0.00 0.00 3.69
1005 1253 0.463204 CGACAGTGGAGATCATGGCT 59.537 55.000 0.00 0.00 0.00 4.75
1059 1313 0.673022 CGCTGCTCTTCTTCCTGCTT 60.673 55.000 0.00 0.00 0.00 3.91
1060 1314 1.404717 CGCTGCTCTTCTTCCTGCTTA 60.405 52.381 0.00 0.00 0.00 3.09
1070 1324 4.333913 TCTTCCTGCTTATCATGCTCTC 57.666 45.455 0.00 0.00 0.00 3.20
1128 1391 7.399191 TCCAGTGAACCAAGATACTATAACAGT 59.601 37.037 0.00 0.00 41.62 3.55
1179 1442 1.138069 TCTGTTCTGCGTTTGAGTGGA 59.862 47.619 0.00 0.00 0.00 4.02
1182 1445 1.261619 GTTCTGCGTTTGAGTGGAGTG 59.738 52.381 0.00 0.00 0.00 3.51
1183 1446 0.249868 TCTGCGTTTGAGTGGAGTGG 60.250 55.000 0.00 0.00 0.00 4.00
1203 1466 2.614057 GGAGTGGAGTGAAAACAGTGTG 59.386 50.000 0.00 0.00 0.00 3.82
1206 1469 2.614057 GTGGAGTGAAAACAGTGTGGAG 59.386 50.000 0.00 0.00 0.00 3.86
1210 1473 3.798202 AGTGAAAACAGTGTGGAGTCTC 58.202 45.455 0.00 0.00 0.00 3.36
1211 1474 3.197766 AGTGAAAACAGTGTGGAGTCTCA 59.802 43.478 0.00 0.00 0.00 3.27
1270 1533 5.123820 TGCATTGTGCTAACTAATTGGAGTC 59.876 40.000 3.41 0.00 45.31 3.36
1360 1624 0.392706 TCAAGCTCAACTTCGCCAGA 59.607 50.000 0.00 0.00 36.04 3.86
1387 1651 3.109547 CCGACGCAAGCGCAACTA 61.110 61.111 15.09 0.00 44.19 2.24
1489 1759 4.698625 AACCCTCCCGACGCTCCT 62.699 66.667 0.00 0.00 0.00 3.69
1734 2031 2.084101 CGATCGTCGTTGTGCCGAA 61.084 57.895 7.03 0.00 38.80 4.30
1783 2080 4.779733 GGCGGAGGACCAGGAGGA 62.780 72.222 0.00 0.00 38.69 3.71
1784 2081 3.151022 GCGGAGGACCAGGAGGAG 61.151 72.222 0.00 0.00 38.69 3.69
1785 2082 2.443016 CGGAGGACCAGGAGGAGG 60.443 72.222 0.00 0.00 38.69 4.30
1786 2083 2.997584 CGGAGGACCAGGAGGAGGA 61.998 68.421 0.00 0.00 38.69 3.71
1828 2125 3.319198 GGCGGTGGTGGAGGAGAA 61.319 66.667 0.00 0.00 0.00 2.87
1831 2128 1.609501 CGGTGGTGGAGGAGAAGGA 60.610 63.158 0.00 0.00 0.00 3.36
1832 2129 1.608717 CGGTGGTGGAGGAGAAGGAG 61.609 65.000 0.00 0.00 0.00 3.69
1833 2130 1.268283 GGTGGTGGAGGAGAAGGAGG 61.268 65.000 0.00 0.00 0.00 4.30
1834 2131 0.252284 GTGGTGGAGGAGAAGGAGGA 60.252 60.000 0.00 0.00 0.00 3.71
1835 2132 0.041833 TGGTGGAGGAGAAGGAGGAG 59.958 60.000 0.00 0.00 0.00 3.69
1836 2133 0.689412 GGTGGAGGAGAAGGAGGAGG 60.689 65.000 0.00 0.00 0.00 4.30
1837 2134 1.002274 TGGAGGAGAAGGAGGAGGC 59.998 63.158 0.00 0.00 0.00 4.70
1838 2135 2.131067 GGAGGAGAAGGAGGAGGCG 61.131 68.421 0.00 0.00 0.00 5.52
1839 2136 2.042435 AGGAGAAGGAGGAGGCGG 60.042 66.667 0.00 0.00 0.00 6.13
1840 2137 2.042843 GGAGAAGGAGGAGGCGGA 60.043 66.667 0.00 0.00 0.00 5.54
1841 2138 2.131067 GGAGAAGGAGGAGGCGGAG 61.131 68.421 0.00 0.00 0.00 4.63
1842 2139 2.042435 AGAAGGAGGAGGCGGAGG 60.042 66.667 0.00 0.00 0.00 4.30
1879 2191 1.002274 TGGAGGAGGAGAAGGAGGC 59.998 63.158 0.00 0.00 0.00 4.70
1901 2228 3.145551 GCGGAGGCGTAGGAGGAA 61.146 66.667 0.00 0.00 0.00 3.36
1924 2251 1.002274 TGGAGGAGAAGGAGGAGGC 59.998 63.158 0.00 0.00 0.00 4.70
1963 2299 2.574955 GCCGCCGATCATCTACCCT 61.575 63.158 0.00 0.00 0.00 4.34
2246 2582 0.673644 CACCAGCGACCCAAGTAAGG 60.674 60.000 0.00 0.00 0.00 2.69
2262 2598 1.640917 AAGGCCTCAAACCTCGAGTA 58.359 50.000 5.23 0.00 36.14 2.59
2264 2600 1.550976 AGGCCTCAAACCTCGAGTAAG 59.449 52.381 12.31 0.00 28.76 2.34
2266 2602 1.066787 GCCTCAAACCTCGAGTAAGCT 60.067 52.381 12.31 0.00 0.00 3.74
2267 2603 2.613223 GCCTCAAACCTCGAGTAAGCTT 60.613 50.000 12.31 3.48 0.00 3.74
2268 2604 3.254892 CCTCAAACCTCGAGTAAGCTTC 58.745 50.000 12.31 0.00 0.00 3.86
2269 2605 2.917971 CTCAAACCTCGAGTAAGCTTCG 59.082 50.000 12.31 0.00 0.00 3.79
2270 2606 1.390463 CAAACCTCGAGTAAGCTTCGC 59.610 52.381 12.31 0.00 0.00 4.70
2271 2607 0.456312 AACCTCGAGTAAGCTTCGCG 60.456 55.000 12.31 8.90 0.00 5.87
2272 2608 1.136984 CCTCGAGTAAGCTTCGCGT 59.863 57.895 12.31 0.00 0.00 6.01
2273 2609 1.134530 CCTCGAGTAAGCTTCGCGTG 61.135 60.000 12.31 9.29 0.00 5.34
2274 2610 0.454620 CTCGAGTAAGCTTCGCGTGT 60.455 55.000 0.00 0.00 0.00 4.49
2275 2611 0.453950 TCGAGTAAGCTTCGCGTGTC 60.454 55.000 0.00 0.00 0.00 3.67
2276 2612 0.728129 CGAGTAAGCTTCGCGTGTCA 60.728 55.000 0.00 0.00 0.00 3.58
2277 2613 1.415374 GAGTAAGCTTCGCGTGTCAA 58.585 50.000 0.00 0.00 0.00 3.18
2278 2614 1.993370 GAGTAAGCTTCGCGTGTCAAT 59.007 47.619 0.00 0.00 0.00 2.57
2279 2615 1.726791 AGTAAGCTTCGCGTGTCAATG 59.273 47.619 0.00 0.00 0.00 2.82
2280 2616 0.442310 TAAGCTTCGCGTGTCAATGC 59.558 50.000 0.00 0.00 34.77 3.56
2281 2617 1.506309 AAGCTTCGCGTGTCAATGCA 61.506 50.000 5.77 0.00 38.30 3.96
2282 2618 1.135315 GCTTCGCGTGTCAATGCAT 59.865 52.632 5.77 0.00 38.30 3.96
2283 2619 0.454957 GCTTCGCGTGTCAATGCATT 60.455 50.000 5.99 5.99 38.30 3.56
2284 2620 1.202020 GCTTCGCGTGTCAATGCATTA 60.202 47.619 12.53 0.00 38.30 1.90
2285 2621 2.727607 GCTTCGCGTGTCAATGCATTAA 60.728 45.455 12.53 0.00 38.30 1.40
2286 2622 2.804421 TCGCGTGTCAATGCATTAAG 57.196 45.000 12.53 0.46 38.30 1.85
2287 2623 1.182673 CGCGTGTCAATGCATTAAGC 58.817 50.000 12.53 9.87 45.96 3.09
2299 2635 1.336125 GCATTAAGCAGCTCCATCCAC 59.664 52.381 0.00 0.00 44.79 4.02
2302 2638 0.621571 TAAGCAGCTCCATCCACCCT 60.622 55.000 0.00 0.00 0.00 4.34
2329 2682 2.035449 CCATGAACCATCATCCATGCAC 59.965 50.000 0.00 0.00 44.53 4.57
2365 2731 7.270779 TCATGATCGATCTTGATTTTCTGTCT 58.729 34.615 29.96 0.00 36.45 3.41
2416 2782 1.737793 GCGTTCAACCTTGTATGAGGG 59.262 52.381 0.00 0.00 41.31 4.30
2417 2783 2.356135 CGTTCAACCTTGTATGAGGGG 58.644 52.381 0.00 0.00 41.31 4.79
2418 2784 2.290071 CGTTCAACCTTGTATGAGGGGT 60.290 50.000 0.00 0.00 41.31 4.95
2419 2785 3.344515 GTTCAACCTTGTATGAGGGGTC 58.655 50.000 0.00 0.00 41.31 4.46
2420 2786 2.915869 TCAACCTTGTATGAGGGGTCT 58.084 47.619 0.00 0.00 41.31 3.85
2421 2787 2.571653 TCAACCTTGTATGAGGGGTCTG 59.428 50.000 0.00 0.00 41.31 3.51
2422 2788 2.571653 CAACCTTGTATGAGGGGTCTGA 59.428 50.000 0.00 0.00 41.31 3.27
2423 2789 3.136641 ACCTTGTATGAGGGGTCTGAT 57.863 47.619 0.00 0.00 41.31 2.90
2424 2790 3.464828 ACCTTGTATGAGGGGTCTGATT 58.535 45.455 0.00 0.00 41.31 2.57
2425 2791 3.200825 ACCTTGTATGAGGGGTCTGATTG 59.799 47.826 0.00 0.00 41.31 2.67
2426 2792 3.455910 CCTTGTATGAGGGGTCTGATTGA 59.544 47.826 0.00 0.00 32.94 2.57
2427 2793 4.444022 CCTTGTATGAGGGGTCTGATTGAG 60.444 50.000 0.00 0.00 32.94 3.02
2428 2794 3.041211 TGTATGAGGGGTCTGATTGAGG 58.959 50.000 0.00 0.00 0.00 3.86
2429 2795 1.516110 ATGAGGGGTCTGATTGAGGG 58.484 55.000 0.00 0.00 0.00 4.30
2430 2796 0.119155 TGAGGGGTCTGATTGAGGGT 59.881 55.000 0.00 0.00 0.00 4.34
2431 2797 1.364678 TGAGGGGTCTGATTGAGGGTA 59.635 52.381 0.00 0.00 0.00 3.69
2432 2798 1.763545 GAGGGGTCTGATTGAGGGTAC 59.236 57.143 0.00 0.00 0.00 3.34
2433 2799 0.464452 GGGGTCTGATTGAGGGTACG 59.536 60.000 0.00 0.00 0.00 3.67
2434 2800 0.179081 GGGTCTGATTGAGGGTACGC 60.179 60.000 0.77 0.77 0.00 4.42
2435 2801 0.535335 GGTCTGATTGAGGGTACGCA 59.465 55.000 12.95 0.00 0.00 5.24
2436 2802 1.471676 GGTCTGATTGAGGGTACGCAG 60.472 57.143 12.95 0.00 0.00 5.18
2437 2803 1.476891 GTCTGATTGAGGGTACGCAGA 59.523 52.381 12.95 2.12 0.00 4.26
2438 2804 1.751351 TCTGATTGAGGGTACGCAGAG 59.249 52.381 12.95 0.00 0.00 3.35
2439 2805 0.824109 TGATTGAGGGTACGCAGAGG 59.176 55.000 12.95 0.00 0.00 3.69
2479 2845 5.241064 CCAATTTTCAGCTATCATGAGGAGG 59.759 44.000 0.09 0.00 0.00 4.30
2512 2878 1.339610 CCATTTGTTTCGAGGCCACAA 59.660 47.619 5.01 2.97 0.00 3.33
2618 2987 8.613060 ATTCCTTGACATGTGCATTATACTAG 57.387 34.615 1.15 0.00 0.00 2.57
2619 2988 7.124573 TCCTTGACATGTGCATTATACTAGT 57.875 36.000 1.15 0.00 0.00 2.57
2620 2989 8.245195 TCCTTGACATGTGCATTATACTAGTA 57.755 34.615 1.15 4.77 0.00 1.82
2621 2990 8.141909 TCCTTGACATGTGCATTATACTAGTAC 58.858 37.037 1.15 0.00 0.00 2.73
2637 3006 1.621814 AGTACGTAGCTTCTTGGGCAA 59.378 47.619 0.00 0.00 0.00 4.52
2697 3070 8.762481 AACCTTCTTGACCAAATTAGTTTAGT 57.238 30.769 0.00 0.00 0.00 2.24
2698 3071 8.762481 ACCTTCTTGACCAAATTAGTTTAGTT 57.238 30.769 0.00 0.00 0.00 2.24
2699 3072 9.197306 ACCTTCTTGACCAAATTAGTTTAGTTT 57.803 29.630 0.00 0.00 0.00 2.66
2847 3220 6.998802 AGCATCTCCAGATAAACATAGTACC 58.001 40.000 0.00 0.00 32.63 3.34
2861 3234 2.629017 AGTACCCCCTCCGTAAAGAA 57.371 50.000 0.00 0.00 0.00 2.52
2894 3279 6.256686 AGCGTTTAGATCACTAAAGTAGTCG 58.743 40.000 0.00 0.00 45.42 4.18
2905 3290 5.566774 CACTAAAGTAGTCGTCTAAACACGG 59.433 44.000 0.00 0.00 40.35 4.94
2928 3313 8.925338 ACGGGACTCTTATATTTCTTTACAGAT 58.075 33.333 0.00 0.00 0.00 2.90
2949 3336 7.226325 ACAGATGTAGTACGTGATAACTAGGAC 59.774 40.741 0.00 0.00 0.00 3.85
2983 3374 3.545703 AGACACAAGAACCCAGTGAAAG 58.454 45.455 0.00 0.00 37.05 2.62
2989 3380 2.334023 AGAACCCAGTGAAAGAGCTCT 58.666 47.619 11.45 11.45 0.00 4.09
2998 3389 5.689514 CCAGTGAAAGAGCTCTATATTGACG 59.310 44.000 18.59 8.47 0.00 4.35
3049 3440 1.714794 CTACCGGAGCACTGACAAAG 58.285 55.000 9.46 0.00 0.00 2.77
3050 3441 0.320421 TACCGGAGCACTGACAAAGC 60.320 55.000 9.46 0.00 0.00 3.51
3081 3472 1.018226 AGAACACGATGCAGCAGAGC 61.018 55.000 1.53 0.00 0.00 4.09
3083 3474 0.604780 AACACGATGCAGCAGAGCTT 60.605 50.000 1.53 0.00 36.40 3.74
3085 3476 1.134580 ACACGATGCAGCAGAGCTTAT 60.135 47.619 1.53 0.00 36.40 1.73
3086 3477 1.526041 CACGATGCAGCAGAGCTTATC 59.474 52.381 1.53 0.00 36.40 1.75
3087 3478 1.137675 ACGATGCAGCAGAGCTTATCA 59.862 47.619 1.53 2.35 36.40 2.15
3088 3479 2.207590 CGATGCAGCAGAGCTTATCAA 58.792 47.619 1.53 0.00 36.40 2.57
3089 3480 2.033065 CGATGCAGCAGAGCTTATCAAC 60.033 50.000 1.53 0.88 36.40 3.18
3091 3482 2.625737 TGCAGCAGAGCTTATCAACTC 58.374 47.619 0.00 0.00 36.40 3.01
3092 3483 2.235650 TGCAGCAGAGCTTATCAACTCT 59.764 45.455 0.00 0.00 44.06 3.24
3093 3484 3.448660 TGCAGCAGAGCTTATCAACTCTA 59.551 43.478 0.00 0.00 41.31 2.43
3094 3485 4.081476 TGCAGCAGAGCTTATCAACTCTAA 60.081 41.667 0.00 0.00 41.31 2.10
3095 3486 4.507388 GCAGCAGAGCTTATCAACTCTAAG 59.493 45.833 0.00 0.00 41.31 2.18
3097 3488 5.519566 CAGCAGAGCTTATCAACTCTAAGTG 59.480 44.000 0.00 0.00 41.31 3.16
3098 3489 5.420421 AGCAGAGCTTATCAACTCTAAGTGA 59.580 40.000 0.00 0.00 41.31 3.41
3099 3490 6.098124 AGCAGAGCTTATCAACTCTAAGTGAT 59.902 38.462 0.00 0.00 41.31 3.06
3100 3491 7.286546 AGCAGAGCTTATCAACTCTAAGTGATA 59.713 37.037 0.00 0.00 41.31 2.15
3101 3492 7.594758 GCAGAGCTTATCAACTCTAAGTGATAG 59.405 40.741 0.00 0.00 41.31 2.08
3104 3495 7.432869 AGCTTATCAACTCTAAGTGATAGCAG 58.567 38.462 0.00 4.24 0.00 4.24
3105 3496 7.286546 AGCTTATCAACTCTAAGTGATAGCAGA 59.713 37.037 0.00 0.00 0.00 4.26
3106 3497 7.923344 GCTTATCAACTCTAAGTGATAGCAGAA 59.077 37.037 0.00 0.00 0.00 3.02
3107 3498 9.979578 CTTATCAACTCTAAGTGATAGCAGAAT 57.020 33.333 0.00 0.00 0.00 2.40
3111 3502 9.587772 TCAACTCTAAGTGATAGCAGAATAAAC 57.412 33.333 0.00 0.00 0.00 2.01
3112 3503 9.371136 CAACTCTAAGTGATAGCAGAATAAACA 57.629 33.333 0.00 0.00 0.00 2.83
3113 3504 9.593134 AACTCTAAGTGATAGCAGAATAAACAG 57.407 33.333 0.00 0.00 0.00 3.16
3114 3505 8.972127 ACTCTAAGTGATAGCAGAATAAACAGA 58.028 33.333 0.00 0.00 0.00 3.41
3115 3506 9.243637 CTCTAAGTGATAGCAGAATAAACAGAC 57.756 37.037 0.00 0.00 0.00 3.51
3116 3507 8.198109 TCTAAGTGATAGCAGAATAAACAGACC 58.802 37.037 0.00 0.00 0.00 3.85
3117 3508 6.552445 AGTGATAGCAGAATAAACAGACCT 57.448 37.500 0.00 0.00 0.00 3.85
3118 3509 6.344500 AGTGATAGCAGAATAAACAGACCTG 58.656 40.000 0.00 0.00 0.00 4.00
3123 3514 5.665381 GCAGAATAAACAGACCTGCTATC 57.335 43.478 0.00 0.00 44.75 2.08
3124 3515 5.363939 GCAGAATAAACAGACCTGCTATCT 58.636 41.667 0.00 0.00 44.75 1.98
3125 3516 5.819901 GCAGAATAAACAGACCTGCTATCTT 59.180 40.000 0.00 0.00 44.75 2.40
3126 3517 6.317391 GCAGAATAAACAGACCTGCTATCTTT 59.683 38.462 0.00 0.00 44.75 2.52
3127 3518 7.148171 GCAGAATAAACAGACCTGCTATCTTTT 60.148 37.037 0.00 0.00 44.75 2.27
3128 3519 9.383519 CAGAATAAACAGACCTGCTATCTTTTA 57.616 33.333 0.00 0.00 0.00 1.52
3129 3520 9.384764 AGAATAAACAGACCTGCTATCTTTTAC 57.615 33.333 0.00 0.00 0.00 2.01
3130 3521 9.162764 GAATAAACAGACCTGCTATCTTTTACA 57.837 33.333 0.00 0.00 0.00 2.41
3131 3522 8.723942 ATAAACAGACCTGCTATCTTTTACAG 57.276 34.615 0.00 0.00 0.00 2.74
3132 3523 6.360370 AACAGACCTGCTATCTTTTACAGA 57.640 37.500 0.00 0.00 35.33 3.41
3133 3524 6.360370 ACAGACCTGCTATCTTTTACAGAA 57.640 37.500 0.00 0.00 34.16 3.02
3134 3525 6.166982 ACAGACCTGCTATCTTTTACAGAAC 58.833 40.000 0.00 0.00 34.16 3.01
3135 3526 6.166279 CAGACCTGCTATCTTTTACAGAACA 58.834 40.000 0.00 0.00 34.16 3.18
3136 3527 6.820656 CAGACCTGCTATCTTTTACAGAACAT 59.179 38.462 0.00 0.00 34.16 2.71
3137 3528 6.820656 AGACCTGCTATCTTTTACAGAACATG 59.179 38.462 0.00 0.00 34.16 3.21
3138 3529 5.355350 ACCTGCTATCTTTTACAGAACATGC 59.645 40.000 0.00 0.00 34.16 4.06
3139 3530 5.469373 TGCTATCTTTTACAGAACATGCG 57.531 39.130 0.00 0.00 34.16 4.73
3140 3531 4.332543 TGCTATCTTTTACAGAACATGCGG 59.667 41.667 0.00 0.00 34.16 5.69
3141 3532 3.764885 ATCTTTTACAGAACATGCGGC 57.235 42.857 0.00 0.00 34.16 6.53
3142 3533 1.810151 TCTTTTACAGAACATGCGGCC 59.190 47.619 0.00 0.00 0.00 6.13
3143 3534 1.539388 CTTTTACAGAACATGCGGCCA 59.461 47.619 2.24 0.00 0.00 5.36
3144 3535 1.610363 TTTACAGAACATGCGGCCAA 58.390 45.000 2.24 0.00 0.00 4.52
3145 3536 0.878416 TTACAGAACATGCGGCCAAC 59.122 50.000 2.24 0.00 0.00 3.77
3146 3537 0.250510 TACAGAACATGCGGCCAACA 60.251 50.000 2.24 0.00 0.00 3.33
3147 3538 1.081242 CAGAACATGCGGCCAACAC 60.081 57.895 2.24 0.00 0.00 3.32
3148 3539 1.528076 AGAACATGCGGCCAACACA 60.528 52.632 2.24 0.00 0.00 3.72
3149 3540 1.106351 AGAACATGCGGCCAACACAA 61.106 50.000 2.24 0.00 0.00 3.33
3150 3541 0.038343 GAACATGCGGCCAACACAAT 60.038 50.000 2.24 0.00 0.00 2.71
3151 3542 1.201181 GAACATGCGGCCAACACAATA 59.799 47.619 2.24 0.00 0.00 1.90
3152 3543 0.525761 ACATGCGGCCAACACAATAC 59.474 50.000 2.24 0.00 0.00 1.89
3153 3544 0.810648 CATGCGGCCAACACAATACT 59.189 50.000 2.24 0.00 0.00 2.12
3154 3545 1.202114 CATGCGGCCAACACAATACTT 59.798 47.619 2.24 0.00 0.00 2.24
3155 3546 0.595588 TGCGGCCAACACAATACTTG 59.404 50.000 2.24 0.00 0.00 3.16
3156 3547 0.732538 GCGGCCAACACAATACTTGC 60.733 55.000 2.24 0.00 0.00 4.01
3157 3548 0.595588 CGGCCAACACAATACTTGCA 59.404 50.000 2.24 0.00 0.00 4.08
3158 3549 1.202114 CGGCCAACACAATACTTGCAT 59.798 47.619 2.24 0.00 0.00 3.96
3159 3550 2.731968 CGGCCAACACAATACTTGCATC 60.732 50.000 2.24 0.00 0.00 3.91
3160 3551 2.230992 GGCCAACACAATACTTGCATCA 59.769 45.455 0.00 0.00 0.00 3.07
3161 3552 3.305950 GGCCAACACAATACTTGCATCAA 60.306 43.478 0.00 0.00 0.00 2.57
3162 3553 3.922240 GCCAACACAATACTTGCATCAAG 59.078 43.478 5.13 5.13 45.85 3.02
3163 3554 4.321156 GCCAACACAATACTTGCATCAAGA 60.321 41.667 12.89 0.00 43.42 3.02
3164 3555 5.622914 GCCAACACAATACTTGCATCAAGAT 60.623 40.000 12.89 0.93 43.42 2.40
3165 3556 5.803461 CCAACACAATACTTGCATCAAGATG 59.197 40.000 12.89 5.70 43.42 2.90
3166 3557 6.384224 CAACACAATACTTGCATCAAGATGT 58.616 36.000 12.89 10.95 43.42 3.06
3167 3558 7.361971 CCAACACAATACTTGCATCAAGATGTA 60.362 37.037 12.89 4.42 43.42 2.29
3168 3559 7.870509 ACACAATACTTGCATCAAGATGTAT 57.129 32.000 12.89 2.79 43.42 2.29
3169 3560 8.962884 ACACAATACTTGCATCAAGATGTATA 57.037 30.769 12.89 0.00 43.42 1.47
3170 3561 9.394767 ACACAATACTTGCATCAAGATGTATAA 57.605 29.630 12.89 4.71 43.42 0.98
3174 3565 9.903682 AATACTTGCATCAAGATGTATAAATGC 57.096 29.630 12.89 0.00 43.42 3.56
3175 3566 7.337480 ACTTGCATCAAGATGTATAAATGCA 57.663 32.000 12.89 3.87 45.44 3.96
3176 3567 7.198390 ACTTGCATCAAGATGTATAAATGCAC 58.802 34.615 12.89 0.00 46.39 4.57
3177 3568 6.075762 TGCATCAAGATGTATAAATGCACC 57.924 37.500 11.35 0.00 43.12 5.01
3178 3569 5.593502 TGCATCAAGATGTATAAATGCACCA 59.406 36.000 11.35 0.00 43.12 4.17
3179 3570 6.265876 TGCATCAAGATGTATAAATGCACCAT 59.734 34.615 11.35 0.00 43.12 3.55
3180 3571 6.805271 GCATCAAGATGTATAAATGCACCATC 59.195 38.462 11.35 0.00 40.80 3.51
3181 3572 7.309012 GCATCAAGATGTATAAATGCACCATCT 60.309 37.037 11.35 0.00 42.94 2.90
3182 3573 7.500720 TCAAGATGTATAAATGCACCATCTG 57.499 36.000 9.94 6.55 40.89 2.90
3199 3590 3.266964 GCAAGTGCAATGCCGAGA 58.733 55.556 13.39 0.00 41.59 4.04
3200 3591 1.154150 GCAAGTGCAATGCCGAGAC 60.154 57.895 13.39 0.00 41.59 3.36
3201 3592 1.855213 GCAAGTGCAATGCCGAGACA 61.855 55.000 13.39 0.00 41.59 3.41
3202 3593 0.167470 CAAGTGCAATGCCGAGACAG 59.833 55.000 1.53 0.00 0.00 3.51
3203 3594 1.580845 AAGTGCAATGCCGAGACAGC 61.581 55.000 1.53 0.00 0.00 4.40
3204 3595 2.037136 GTGCAATGCCGAGACAGCT 61.037 57.895 1.53 0.00 0.00 4.24
3205 3596 0.740868 GTGCAATGCCGAGACAGCTA 60.741 55.000 1.53 0.00 0.00 3.32
3206 3597 0.740868 TGCAATGCCGAGACAGCTAC 60.741 55.000 1.53 0.00 0.00 3.58
3207 3598 0.740868 GCAATGCCGAGACAGCTACA 60.741 55.000 0.00 0.00 0.00 2.74
3208 3599 1.725641 CAATGCCGAGACAGCTACAA 58.274 50.000 0.00 0.00 0.00 2.41
3209 3600 1.662629 CAATGCCGAGACAGCTACAAG 59.337 52.381 0.00 0.00 0.00 3.16
3210 3601 0.176680 ATGCCGAGACAGCTACAAGG 59.823 55.000 0.00 0.00 0.00 3.61
3211 3602 1.185618 TGCCGAGACAGCTACAAGGT 61.186 55.000 0.00 0.00 0.00 3.50
3212 3603 0.037232 GCCGAGACAGCTACAAGGTT 60.037 55.000 0.00 0.00 0.00 3.50
3242 3633 7.169813 CAGCAGATACGAAGCTTAATTCACATA 59.830 37.037 0.00 0.00 36.26 2.29
3246 3637 9.601217 AGATACGAAGCTTAATTCACATAAACT 57.399 29.630 0.00 0.00 0.00 2.66
3339 3737 0.034059 CTGTATCCGTCCCATCAGCC 59.966 60.000 0.00 0.00 0.00 4.85
3340 3738 0.398522 TGTATCCGTCCCATCAGCCT 60.399 55.000 0.00 0.00 0.00 4.58
3342 3740 1.141053 GTATCCGTCCCATCAGCCTTT 59.859 52.381 0.00 0.00 0.00 3.11
3343 3741 0.625849 ATCCGTCCCATCAGCCTTTT 59.374 50.000 0.00 0.00 0.00 2.27
3344 3742 0.035439 TCCGTCCCATCAGCCTTTTC 60.035 55.000 0.00 0.00 0.00 2.29
3352 3750 4.901250 TCCCATCAGCCTTTTCTTTTTCTT 59.099 37.500 0.00 0.00 0.00 2.52
3371 3769 0.030638 TTTTTCAAGCGAGCACCTGC 59.969 50.000 0.00 0.00 42.49 4.85
3372 3770 1.795170 TTTTCAAGCGAGCACCTGCC 61.795 55.000 0.00 0.00 43.38 4.85
3379 3777 1.377725 CGAGCACCTGCCTGGAAAT 60.378 57.895 0.00 0.00 43.38 2.17
3405 3803 3.985019 ATTTTTCTGATTGCATGGCCA 57.015 38.095 8.56 8.56 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.627123 CCTTCACAGTTCACATTCACACA 59.373 43.478 0.00 0.00 0.00 3.72
84 85 2.263077 CATCAGTACTGCCACGAGTTC 58.737 52.381 18.45 0.00 0.00 3.01
89 90 2.096268 CACAAACATCAGTACTGCCACG 60.096 50.000 18.45 8.33 0.00 4.94
109 110 2.535012 TCACGTTACAGTTCATGCCA 57.465 45.000 0.00 0.00 0.00 4.92
131 132 6.404403 CGCATACTCAAGACCGTACCATATAT 60.404 42.308 0.00 0.00 0.00 0.86
233 339 8.747538 ACAACAACCCCAGAATTTATAGTATC 57.252 34.615 0.00 0.00 0.00 2.24
234 340 9.623000 GTACAACAACCCCAGAATTTATAGTAT 57.377 33.333 0.00 0.00 0.00 2.12
235 341 7.765360 CGTACAACAACCCCAGAATTTATAGTA 59.235 37.037 0.00 0.00 0.00 1.82
236 342 6.596497 CGTACAACAACCCCAGAATTTATAGT 59.404 38.462 0.00 0.00 0.00 2.12
237 343 6.596497 ACGTACAACAACCCCAGAATTTATAG 59.404 38.462 0.00 0.00 0.00 1.31
241 347 3.558033 ACGTACAACAACCCCAGAATTT 58.442 40.909 0.00 0.00 0.00 1.82
247 353 0.739561 GCAAACGTACAACAACCCCA 59.260 50.000 0.00 0.00 0.00 4.96
259 365 3.119193 CAGGCCAACAGCAAACGT 58.881 55.556 5.01 0.00 46.50 3.99
260 366 2.355009 GCAGGCCAACAGCAAACG 60.355 61.111 5.01 0.00 46.50 3.60
261 367 1.300388 CAGCAGGCCAACAGCAAAC 60.300 57.895 5.01 0.00 46.50 2.93
264 370 1.302752 CTACAGCAGGCCAACAGCA 60.303 57.895 5.01 0.00 46.50 4.41
305 414 3.536917 CGCCTGGCTGATACCGGA 61.537 66.667 17.92 0.00 38.48 5.14
329 469 2.162408 TCCTAGCGCGATATGTCATCAG 59.838 50.000 12.10 0.00 0.00 2.90
344 484 4.001618 GGATGTGATCCTCTTTCCTAGC 57.998 50.000 0.00 0.00 46.19 3.42
369 509 6.437162 ACTCTCTCTCTACTTTGCTTCTGATT 59.563 38.462 0.00 0.00 0.00 2.57
384 524 3.985019 TTCACGTCCTACTCTCTCTCT 57.015 47.619 0.00 0.00 0.00 3.10
385 525 4.255301 TCTTTCACGTCCTACTCTCTCTC 58.745 47.826 0.00 0.00 0.00 3.20
386 526 4.020039 TCTCTTTCACGTCCTACTCTCTCT 60.020 45.833 0.00 0.00 0.00 3.10
387 527 4.255301 TCTCTTTCACGTCCTACTCTCTC 58.745 47.826 0.00 0.00 0.00 3.20
425 643 1.000163 AGTGTTTCTCATCGTCAGCGT 60.000 47.619 0.00 0.00 39.49 5.07
449 669 1.620822 TGCTCAAGGAAAGGAAAGCC 58.379 50.000 0.00 0.00 0.00 4.35
488 713 1.525995 CCACCGCAAGACACAAGGT 60.526 57.895 0.00 0.00 43.02 3.50
563 798 0.823356 TTCTGCCTTTCTTGCCGCTT 60.823 50.000 0.00 0.00 0.00 4.68
625 860 1.421410 CCGGTCACTTGCATCGTAGC 61.421 60.000 0.00 0.00 0.00 3.58
642 877 2.209064 TTTCTCGAGGAAGCGTCCCG 62.209 60.000 15.64 17.34 46.30 5.14
655 890 3.045688 GCCAACTCTTTTTGCTTTCTCG 58.954 45.455 0.00 0.00 0.00 4.04
685 920 1.663074 GGCGACGATGATCCTGCTC 60.663 63.158 0.00 0.00 0.00 4.26
722 957 6.624423 TCGATGATCCATGTATGTAGATGTG 58.376 40.000 0.00 0.00 0.00 3.21
731 966 5.022122 AGGACAGATCGATGATCCATGTAT 58.978 41.667 17.28 0.00 39.66 2.29
794 1031 1.412710 AGCGGCCATCGATAAGAAAGA 59.587 47.619 2.24 0.00 42.43 2.52
795 1032 1.795286 GAGCGGCCATCGATAAGAAAG 59.205 52.381 2.24 0.00 42.43 2.62
796 1033 1.540363 GGAGCGGCCATCGATAAGAAA 60.540 52.381 2.24 0.00 42.43 2.52
797 1034 0.033504 GGAGCGGCCATCGATAAGAA 59.966 55.000 2.24 0.00 42.43 2.52
917 1158 2.264794 CACCGGTAGCCTGACACC 59.735 66.667 6.87 0.00 0.00 4.16
961 1202 1.480137 CTTCCTCTGCCCTGTACTCTG 59.520 57.143 0.00 0.00 0.00 3.35
962 1203 1.859302 CTTCCTCTGCCCTGTACTCT 58.141 55.000 0.00 0.00 0.00 3.24
963 1204 0.176910 GCTTCCTCTGCCCTGTACTC 59.823 60.000 0.00 0.00 0.00 2.59
968 1209 1.676967 GGTTGCTTCCTCTGCCCTG 60.677 63.158 0.00 0.00 0.00 4.45
978 1219 0.033504 TCTCCACTGTCGGTTGCTTC 59.966 55.000 0.00 0.00 0.00 3.86
1005 1253 0.603439 TGCTGATTCTGCAGTTGCGA 60.603 50.000 14.67 0.00 45.83 5.10
1059 1313 2.623416 CGTGGTGGTAGAGAGCATGATA 59.377 50.000 0.00 0.00 35.06 2.15
1060 1314 1.410517 CGTGGTGGTAGAGAGCATGAT 59.589 52.381 0.00 0.00 35.06 2.45
1157 1420 2.354510 CCACTCAAACGCAGAACAGAAA 59.645 45.455 0.00 0.00 0.00 2.52
1179 1442 2.505819 ACTGTTTTCACTCCACTCCACT 59.494 45.455 0.00 0.00 0.00 4.00
1182 1445 2.614057 CACACTGTTTTCACTCCACTCC 59.386 50.000 0.00 0.00 0.00 3.85
1183 1446 2.614057 CCACACTGTTTTCACTCCACTC 59.386 50.000 0.00 0.00 0.00 3.51
1203 1466 0.037790 GCTGGTCACTGTGAGACTCC 60.038 60.000 11.41 9.36 36.29 3.85
1206 1469 0.965439 AGAGCTGGTCACTGTGAGAC 59.035 55.000 11.41 8.04 35.29 3.36
1210 1473 4.567435 CGAGAGCTGGTCACTGTG 57.433 61.111 9.78 0.17 0.00 3.66
1270 1533 0.670162 CTGCTCCACCAACACAAAGG 59.330 55.000 0.00 0.00 0.00 3.11
1378 1642 3.400054 GGAGGGGGTAGTTGCGCT 61.400 66.667 9.73 0.00 0.00 5.92
1379 1643 4.484872 GGGAGGGGGTAGTTGCGC 62.485 72.222 0.00 0.00 0.00 6.09
1383 1647 1.001376 GACGAGGGAGGGGGTAGTT 59.999 63.158 0.00 0.00 0.00 2.24
1384 1648 2.688538 GACGAGGGAGGGGGTAGT 59.311 66.667 0.00 0.00 0.00 2.73
1385 1649 2.518825 CGACGAGGGAGGGGGTAG 60.519 72.222 0.00 0.00 0.00 3.18
1386 1650 4.828296 GCGACGAGGGAGGGGGTA 62.828 72.222 0.00 0.00 0.00 3.69
1585 1858 2.514824 GGGCTGGGCTCGAATGAC 60.515 66.667 0.00 0.00 0.00 3.06
1734 2031 4.807039 CGAATTCGTCGGGCGGGT 62.807 66.667 19.67 0.00 46.45 5.28
1775 2072 1.382420 CTCCCTGTCCTCCTCCTGG 60.382 68.421 0.00 0.00 0.00 4.45
1776 2073 1.382420 CCTCCCTGTCCTCCTCCTG 60.382 68.421 0.00 0.00 0.00 3.86
1777 2074 1.547755 TCCTCCCTGTCCTCCTCCT 60.548 63.158 0.00 0.00 0.00 3.69
1778 2075 1.075600 CTCCTCCCTGTCCTCCTCC 60.076 68.421 0.00 0.00 0.00 4.30
1779 2076 1.075600 CCTCCTCCCTGTCCTCCTC 60.076 68.421 0.00 0.00 0.00 3.71
1780 2077 3.114390 CCTCCTCCCTGTCCTCCT 58.886 66.667 0.00 0.00 0.00 3.69
1781 2078 2.766229 GCCTCCTCCCTGTCCTCC 60.766 72.222 0.00 0.00 0.00 4.30
1782 2079 2.569218 TACGCCTCCTCCCTGTCCTC 62.569 65.000 0.00 0.00 0.00 3.71
1783 2080 2.575455 CTACGCCTCCTCCCTGTCCT 62.575 65.000 0.00 0.00 0.00 3.85
1784 2081 2.043248 TACGCCTCCTCCCTGTCC 60.043 66.667 0.00 0.00 0.00 4.02
1785 2082 2.128507 CCTACGCCTCCTCCCTGTC 61.129 68.421 0.00 0.00 0.00 3.51
1786 2083 2.042843 CCTACGCCTCCTCCCTGT 60.043 66.667 0.00 0.00 0.00 4.00
1839 2136 4.154347 CACCTCCTCCTGCGCCTC 62.154 72.222 4.18 0.00 0.00 4.70
1842 2139 4.767255 CACCACCTCCTCCTGCGC 62.767 72.222 0.00 0.00 0.00 6.09
1843 2140 4.087892 CCACCACCTCCTCCTGCG 62.088 72.222 0.00 0.00 0.00 5.18
1844 2141 2.930562 ACCACCACCTCCTCCTGC 60.931 66.667 0.00 0.00 0.00 4.85
1845 2142 2.596851 CCACCACCACCTCCTCCTG 61.597 68.421 0.00 0.00 0.00 3.86
1852 2149 2.203998 CCTCCTCCACCACCACCT 60.204 66.667 0.00 0.00 0.00 4.00
1901 2228 1.684049 CTCCTTCTCCTCCACCGCT 60.684 63.158 0.00 0.00 0.00 5.52
1939 2275 0.179048 AGATGATCGGCGGCATGAAA 60.179 50.000 18.11 0.00 0.00 2.69
2246 2582 1.066787 AGCTTACTCGAGGTTTGAGGC 60.067 52.381 18.41 10.44 37.79 4.70
2266 2602 2.727607 GCTTAATGCATTGACACGCGAA 60.728 45.455 22.27 4.60 42.31 4.70
2267 2603 1.202020 GCTTAATGCATTGACACGCGA 60.202 47.619 22.27 0.00 42.31 5.87
2268 2604 1.182673 GCTTAATGCATTGACACGCG 58.817 50.000 22.27 3.53 42.31 6.01
2279 2615 1.336125 GTGGATGGAGCTGCTTAATGC 59.664 52.381 6.82 6.83 43.25 3.56
2280 2616 1.952296 GGTGGATGGAGCTGCTTAATG 59.048 52.381 6.82 0.00 0.00 1.90
2281 2617 1.133668 GGGTGGATGGAGCTGCTTAAT 60.134 52.381 6.82 0.06 0.00 1.40
2282 2618 0.255890 GGGTGGATGGAGCTGCTTAA 59.744 55.000 6.82 0.00 0.00 1.85
2283 2619 0.621571 AGGGTGGATGGAGCTGCTTA 60.622 55.000 6.82 0.00 0.00 3.09
2284 2620 1.919600 GAGGGTGGATGGAGCTGCTT 61.920 60.000 6.82 0.00 0.00 3.91
2285 2621 2.285969 AGGGTGGATGGAGCTGCT 60.286 61.111 6.82 0.00 0.00 4.24
2286 2622 2.191641 GAGGGTGGATGGAGCTGC 59.808 66.667 0.00 0.00 0.00 5.25
2287 2623 2.750657 GGGAGGGTGGATGGAGCTG 61.751 68.421 0.00 0.00 0.00 4.24
2288 2624 2.367512 GGGAGGGTGGATGGAGCT 60.368 66.667 0.00 0.00 0.00 4.09
2289 2625 2.692368 TGGGAGGGTGGATGGAGC 60.692 66.667 0.00 0.00 0.00 4.70
2290 2626 2.378634 GGTGGGAGGGTGGATGGAG 61.379 68.421 0.00 0.00 0.00 3.86
2291 2627 2.286121 GGTGGGAGGGTGGATGGA 60.286 66.667 0.00 0.00 0.00 3.41
2292 2628 3.420482 GGGTGGGAGGGTGGATGG 61.420 72.222 0.00 0.00 0.00 3.51
2293 2629 2.008723 ATGGGTGGGAGGGTGGATG 61.009 63.158 0.00 0.00 0.00 3.51
2294 2630 2.008723 CATGGGTGGGAGGGTGGAT 61.009 63.158 0.00 0.00 0.00 3.41
2299 2635 1.583784 ATGGTTCATGGGTGGGAGGG 61.584 60.000 0.00 0.00 0.00 4.30
2302 2638 1.215173 GATGATGGTTCATGGGTGGGA 59.785 52.381 0.00 0.00 42.73 4.37
2338 2691 7.046652 ACAGAAAATCAAGATCGATCATGAGT 58.953 34.615 30.14 26.90 37.85 3.41
2365 2731 1.201424 AGCCTGCAGAGATCATGACA 58.799 50.000 17.39 0.00 0.00 3.58
2416 2782 0.535335 TGCGTACCCTCAATCAGACC 59.465 55.000 0.00 0.00 0.00 3.85
2417 2783 1.476891 TCTGCGTACCCTCAATCAGAC 59.523 52.381 0.00 0.00 0.00 3.51
2418 2784 1.751351 CTCTGCGTACCCTCAATCAGA 59.249 52.381 0.00 0.00 0.00 3.27
2419 2785 1.202463 CCTCTGCGTACCCTCAATCAG 60.202 57.143 0.00 0.00 0.00 2.90
2420 2786 0.824109 CCTCTGCGTACCCTCAATCA 59.176 55.000 0.00 0.00 0.00 2.57
2421 2787 0.530870 GCCTCTGCGTACCCTCAATC 60.531 60.000 0.00 0.00 0.00 2.67
2422 2788 0.978146 AGCCTCTGCGTACCCTCAAT 60.978 55.000 0.00 0.00 44.33 2.57
2423 2789 1.609501 AGCCTCTGCGTACCCTCAA 60.610 57.895 0.00 0.00 44.33 3.02
2424 2790 2.037367 AGCCTCTGCGTACCCTCA 59.963 61.111 0.00 0.00 44.33 3.86
2425 2791 2.496817 CAGCCTCTGCGTACCCTC 59.503 66.667 0.00 0.00 44.33 4.30
2434 2800 0.388294 TCATCGATCTGCAGCCTCTG 59.612 55.000 9.47 4.20 34.12 3.35
2435 2801 0.675083 CTCATCGATCTGCAGCCTCT 59.325 55.000 9.47 0.00 0.00 3.69
2436 2802 0.945265 GCTCATCGATCTGCAGCCTC 60.945 60.000 9.47 7.44 0.00 4.70
2437 2803 1.069427 GCTCATCGATCTGCAGCCT 59.931 57.895 9.47 0.00 0.00 4.58
2438 2804 1.960250 GGCTCATCGATCTGCAGCC 60.960 63.158 9.47 16.26 42.87 4.85
2439 2805 0.812811 TTGGCTCATCGATCTGCAGC 60.813 55.000 9.47 12.15 0.00 5.25
2618 2987 2.000447 CTTGCCCAAGAAGCTACGTAC 59.000 52.381 1.83 0.00 40.79 3.67
2619 2988 1.897133 TCTTGCCCAAGAAGCTACGTA 59.103 47.619 8.19 0.00 43.79 3.57
2620 2989 0.685097 TCTTGCCCAAGAAGCTACGT 59.315 50.000 8.19 0.00 43.79 3.57
2621 2990 3.532896 TCTTGCCCAAGAAGCTACG 57.467 52.632 8.19 0.00 43.79 3.51
2637 3006 2.565841 GGGCACGATTAAGCATCTTCT 58.434 47.619 0.00 0.00 0.00 2.85
2710 3083 4.827284 AACACCAAGTTAGGCATATATGGC 59.173 41.667 27.29 27.29 42.33 4.40
2847 3220 6.427242 GCTCTTATATTTTCTTTACGGAGGGG 59.573 42.308 0.00 0.00 0.00 4.79
2894 3279 8.196103 AGAAATATAAGAGTCCCGTGTTTAGAC 58.804 37.037 0.00 0.00 0.00 2.59
2928 3313 6.643388 TCAGTCCTAGTTATCACGTACTACA 58.357 40.000 0.00 0.00 0.00 2.74
2949 3336 7.206687 GGTTCTTGTGTCTATATCCTTCTCAG 58.793 42.308 0.00 0.00 0.00 3.35
2983 3374 4.585955 TTGTCCCGTCAATATAGAGCTC 57.414 45.455 5.27 5.27 0.00 4.09
2989 3380 4.578516 CCTGCATTTTGTCCCGTCAATATA 59.421 41.667 0.00 0.00 0.00 0.86
3049 3440 1.559831 GTGTTCTTGGCTGTTTGTGC 58.440 50.000 0.00 0.00 0.00 4.57
3050 3441 1.400142 TCGTGTTCTTGGCTGTTTGTG 59.600 47.619 0.00 0.00 0.00 3.33
3081 3472 9.979578 ATTCTGCTATCACTTAGAGTTGATAAG 57.020 33.333 0.00 0.00 36.51 1.73
3085 3476 9.587772 GTTTATTCTGCTATCACTTAGAGTTGA 57.412 33.333 0.00 0.00 0.00 3.18
3086 3477 9.371136 TGTTTATTCTGCTATCACTTAGAGTTG 57.629 33.333 0.00 0.00 0.00 3.16
3087 3478 9.593134 CTGTTTATTCTGCTATCACTTAGAGTT 57.407 33.333 0.00 0.00 0.00 3.01
3088 3479 8.972127 TCTGTTTATTCTGCTATCACTTAGAGT 58.028 33.333 0.00 0.00 0.00 3.24
3089 3480 9.243637 GTCTGTTTATTCTGCTATCACTTAGAG 57.756 37.037 0.00 0.00 0.00 2.43
3091 3482 8.200792 AGGTCTGTTTATTCTGCTATCACTTAG 58.799 37.037 0.00 0.00 0.00 2.18
3092 3483 7.981789 CAGGTCTGTTTATTCTGCTATCACTTA 59.018 37.037 0.00 0.00 0.00 2.24
3093 3484 6.820656 CAGGTCTGTTTATTCTGCTATCACTT 59.179 38.462 0.00 0.00 0.00 3.16
3094 3485 6.344500 CAGGTCTGTTTATTCTGCTATCACT 58.656 40.000 0.00 0.00 0.00 3.41
3095 3486 5.007136 GCAGGTCTGTTTATTCTGCTATCAC 59.993 44.000 0.00 0.00 45.03 3.06
3097 3488 5.665381 GCAGGTCTGTTTATTCTGCTATC 57.335 43.478 0.00 0.00 45.03 2.08
3104 3495 9.162764 TGTAAAAGATAGCAGGTCTGTTTATTC 57.837 33.333 0.00 0.00 0.00 1.75
3105 3496 9.167311 CTGTAAAAGATAGCAGGTCTGTTTATT 57.833 33.333 0.00 0.00 0.00 1.40
3106 3497 8.540388 TCTGTAAAAGATAGCAGGTCTGTTTAT 58.460 33.333 0.00 0.00 0.00 1.40
3107 3498 7.903145 TCTGTAAAAGATAGCAGGTCTGTTTA 58.097 34.615 0.00 0.00 0.00 2.01
3108 3499 6.769512 TCTGTAAAAGATAGCAGGTCTGTTT 58.230 36.000 0.00 0.00 0.00 2.83
3109 3500 6.360370 TCTGTAAAAGATAGCAGGTCTGTT 57.640 37.500 0.00 0.00 0.00 3.16
3110 3501 6.166982 GTTCTGTAAAAGATAGCAGGTCTGT 58.833 40.000 0.00 0.00 33.93 3.41
3111 3502 6.166279 TGTTCTGTAAAAGATAGCAGGTCTG 58.834 40.000 0.00 0.00 33.93 3.51
3112 3503 6.360370 TGTTCTGTAAAAGATAGCAGGTCT 57.640 37.500 0.00 0.00 33.93 3.85
3113 3504 6.457528 GCATGTTCTGTAAAAGATAGCAGGTC 60.458 42.308 0.00 0.00 33.93 3.85
3114 3505 5.355350 GCATGTTCTGTAAAAGATAGCAGGT 59.645 40.000 0.00 0.00 33.93 4.00
3115 3506 5.503031 CGCATGTTCTGTAAAAGATAGCAGG 60.503 44.000 0.00 0.00 33.93 4.85
3116 3507 5.496387 CGCATGTTCTGTAAAAGATAGCAG 58.504 41.667 0.00 0.00 33.93 4.24
3117 3508 4.332543 CCGCATGTTCTGTAAAAGATAGCA 59.667 41.667 0.00 0.00 33.93 3.49
3118 3509 4.786609 GCCGCATGTTCTGTAAAAGATAGC 60.787 45.833 0.00 0.00 33.93 2.97
3119 3510 4.260784 GGCCGCATGTTCTGTAAAAGATAG 60.261 45.833 0.00 0.00 33.93 2.08
3120 3511 3.625764 GGCCGCATGTTCTGTAAAAGATA 59.374 43.478 0.00 0.00 33.93 1.98
3121 3512 2.423538 GGCCGCATGTTCTGTAAAAGAT 59.576 45.455 0.00 0.00 33.93 2.40
3122 3513 1.810151 GGCCGCATGTTCTGTAAAAGA 59.190 47.619 0.00 0.00 0.00 2.52
3123 3514 1.539388 TGGCCGCATGTTCTGTAAAAG 59.461 47.619 0.00 0.00 0.00 2.27
3124 3515 1.610363 TGGCCGCATGTTCTGTAAAA 58.390 45.000 0.00 0.00 0.00 1.52
3125 3516 1.268352 GTTGGCCGCATGTTCTGTAAA 59.732 47.619 0.00 0.00 0.00 2.01
3126 3517 0.878416 GTTGGCCGCATGTTCTGTAA 59.122 50.000 0.00 0.00 0.00 2.41
3127 3518 0.250510 TGTTGGCCGCATGTTCTGTA 60.251 50.000 0.00 0.00 0.00 2.74
3128 3519 1.528076 TGTTGGCCGCATGTTCTGT 60.528 52.632 0.00 0.00 0.00 3.41
3129 3520 1.081242 GTGTTGGCCGCATGTTCTG 60.081 57.895 0.00 0.00 0.00 3.02
3130 3521 1.106351 TTGTGTTGGCCGCATGTTCT 61.106 50.000 0.00 0.00 32.58 3.01
3131 3522 0.038343 ATTGTGTTGGCCGCATGTTC 60.038 50.000 0.00 0.00 32.58 3.18
3132 3523 1.067915 GTATTGTGTTGGCCGCATGTT 60.068 47.619 0.00 0.00 32.58 2.71
3133 3524 0.525761 GTATTGTGTTGGCCGCATGT 59.474 50.000 0.00 0.00 32.58 3.21
3134 3525 0.810648 AGTATTGTGTTGGCCGCATG 59.189 50.000 0.00 0.00 32.58 4.06
3135 3526 1.202114 CAAGTATTGTGTTGGCCGCAT 59.798 47.619 0.00 0.00 42.34 4.73
3136 3527 0.595588 CAAGTATTGTGTTGGCCGCA 59.404 50.000 0.00 0.00 42.34 5.69
3137 3528 3.399879 CAAGTATTGTGTTGGCCGC 57.600 52.632 0.00 0.00 42.34 6.53
3148 3539 9.903682 GCATTTATACATCTTGATGCAAGTATT 57.096 29.630 10.20 0.00 41.66 1.89
3149 3540 9.070179 TGCATTTATACATCTTGATGCAAGTAT 57.930 29.630 10.20 4.25 44.60 2.12
3150 3541 8.449251 TGCATTTATACATCTTGATGCAAGTA 57.551 30.769 10.20 0.00 44.60 2.24
3151 3542 7.337480 TGCATTTATACATCTTGATGCAAGT 57.663 32.000 10.20 0.00 44.60 3.16
3154 3545 5.593502 TGGTGCATTTATACATCTTGATGCA 59.406 36.000 10.20 4.85 45.15 3.96
3155 3546 6.075762 TGGTGCATTTATACATCTTGATGC 57.924 37.500 10.20 0.00 40.07 3.91
3156 3547 8.021396 CAGATGGTGCATTTATACATCTTGATG 58.979 37.037 8.87 8.87 44.08 3.07
3157 3548 8.107399 CAGATGGTGCATTTATACATCTTGAT 57.893 34.615 11.58 0.00 44.08 2.57
3158 3549 7.500720 CAGATGGTGCATTTATACATCTTGA 57.499 36.000 11.58 0.00 44.08 3.02
3182 3573 1.154150 GTCTCGGCATTGCACTTGC 60.154 57.895 11.39 11.51 42.50 4.01
3183 3574 0.167470 CTGTCTCGGCATTGCACTTG 59.833 55.000 11.39 0.00 0.00 3.16
3184 3575 1.580845 GCTGTCTCGGCATTGCACTT 61.581 55.000 11.39 0.00 35.55 3.16
3185 3576 2.037136 GCTGTCTCGGCATTGCACT 61.037 57.895 11.39 0.00 35.55 4.40
3186 3577 0.740868 TAGCTGTCTCGGCATTGCAC 60.741 55.000 11.39 0.25 38.37 4.57
3187 3578 0.740868 GTAGCTGTCTCGGCATTGCA 60.741 55.000 11.39 0.00 38.37 4.08
3188 3579 0.740868 TGTAGCTGTCTCGGCATTGC 60.741 55.000 0.00 0.00 38.37 3.56
3189 3580 1.662629 CTTGTAGCTGTCTCGGCATTG 59.337 52.381 0.00 0.00 38.37 2.82
3190 3581 1.406069 CCTTGTAGCTGTCTCGGCATT 60.406 52.381 0.00 0.00 38.37 3.56
3191 3582 0.176680 CCTTGTAGCTGTCTCGGCAT 59.823 55.000 0.00 0.00 38.37 4.40
3192 3583 1.185618 ACCTTGTAGCTGTCTCGGCA 61.186 55.000 0.00 0.00 38.37 5.69
3193 3584 0.037232 AACCTTGTAGCTGTCTCGGC 60.037 55.000 0.00 0.00 35.73 5.54
3194 3585 2.457366 AAACCTTGTAGCTGTCTCGG 57.543 50.000 0.00 0.00 0.00 4.63
3195 3586 4.304110 TGTAAAACCTTGTAGCTGTCTCG 58.696 43.478 0.00 0.00 0.00 4.04
3196 3587 4.152580 GCTGTAAAACCTTGTAGCTGTCTC 59.847 45.833 0.00 0.00 0.00 3.36
3197 3588 4.065789 GCTGTAAAACCTTGTAGCTGTCT 58.934 43.478 0.00 0.00 0.00 3.41
3198 3589 3.813166 TGCTGTAAAACCTTGTAGCTGTC 59.187 43.478 0.00 0.00 32.66 3.51
3199 3590 3.815401 CTGCTGTAAAACCTTGTAGCTGT 59.185 43.478 0.00 0.00 32.66 4.40
3200 3591 4.065088 TCTGCTGTAAAACCTTGTAGCTG 58.935 43.478 0.00 0.00 32.66 4.24
3201 3592 4.351874 TCTGCTGTAAAACCTTGTAGCT 57.648 40.909 0.00 0.00 32.66 3.32
3202 3593 5.220416 CGTATCTGCTGTAAAACCTTGTAGC 60.220 44.000 0.00 0.00 0.00 3.58
3203 3594 6.097356 TCGTATCTGCTGTAAAACCTTGTAG 58.903 40.000 0.00 0.00 0.00 2.74
3204 3595 6.028146 TCGTATCTGCTGTAAAACCTTGTA 57.972 37.500 0.00 0.00 0.00 2.41
3205 3596 4.890088 TCGTATCTGCTGTAAAACCTTGT 58.110 39.130 0.00 0.00 0.00 3.16
3206 3597 5.671329 GCTTCGTATCTGCTGTAAAACCTTG 60.671 44.000 0.00 0.00 0.00 3.61
3207 3598 4.392138 GCTTCGTATCTGCTGTAAAACCTT 59.608 41.667 0.00 0.00 0.00 3.50
3208 3599 3.933332 GCTTCGTATCTGCTGTAAAACCT 59.067 43.478 0.00 0.00 0.00 3.50
3209 3600 3.933332 AGCTTCGTATCTGCTGTAAAACC 59.067 43.478 0.00 0.00 35.54 3.27
3210 3601 5.532025 AAGCTTCGTATCTGCTGTAAAAC 57.468 39.130 0.00 0.00 37.11 2.43
3211 3602 7.843490 ATTAAGCTTCGTATCTGCTGTAAAA 57.157 32.000 0.00 0.00 37.11 1.52
3212 3603 7.547722 TGAATTAAGCTTCGTATCTGCTGTAAA 59.452 33.333 0.00 0.00 37.11 2.01
3246 3637 9.275398 ACCACTACTTATTTGATTTTTGACGTA 57.725 29.630 0.00 0.00 0.00 3.57
3247 3638 8.161699 ACCACTACTTATTTGATTTTTGACGT 57.838 30.769 0.00 0.00 0.00 4.34
3308 3706 1.533469 GGATACAGCCGGCGGTAGAT 61.533 60.000 36.19 25.94 30.89 1.98
3352 3750 0.030638 GCAGGTGCTCGCTTGAAAAA 59.969 50.000 0.00 0.00 38.21 1.94
3361 3759 1.372087 GATTTCCAGGCAGGTGCTCG 61.372 60.000 1.26 0.00 41.70 5.03
3371 3769 9.374838 CAATCAGAAAAATTAAGGATTTCCAGG 57.625 33.333 0.00 0.00 36.96 4.45
3372 3770 8.876790 GCAATCAGAAAAATTAAGGATTTCCAG 58.123 33.333 0.00 2.57 36.96 3.86
3379 3777 6.108015 GCCATGCAATCAGAAAAATTAAGGA 58.892 36.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.