Multiple sequence alignment - TraesCS1D01G343100

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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 TraesCS1D01G343100 chr1D 100.000 2786 0 0 1 2786 432335220 432338005 0.000000e+00 5145.0
1 TraesCS1D01G343100 chr1D 95.652 161 7 0 2626 2786 472299044 472298884 2.750000e-65 259.0
2 TraesCS1D01G343100 chr1D 78.906 256 43 10 2218 2469 60323723 60323475 2.220000e-36 163.0
3 TraesCS1D01G343100 chr1B 88.379 2530 133 70 160 2625 583854505 583856937 0.000000e+00 2894.0
4 TraesCS1D01G343100 chr1B 90.503 179 16 1 1 178 583854317 583854495 4.640000e-58 235.0
5 TraesCS1D01G343100 chr1B 100.000 29 0 0 1815 1843 661627624 661627596 1.000000e-03 54.7
6 TraesCS1D01G343100 chr1A 87.726 1051 65 30 1 1034 530807770 530808773 0.000000e+00 1168.0
7 TraesCS1D01G343100 chr1A 87.781 712 52 26 1300 1983 530809013 530809717 0.000000e+00 800.0
8 TraesCS1D01G343100 chr1A 85.567 194 3 9 2003 2192 530809701 530809873 2.200000e-41 180.0
9 TraesCS1D01G343100 chr3B 93.785 177 8 2 2613 2786 23153997 23154173 2.130000e-66 263.0
10 TraesCS1D01G343100 chr3B 79.365 252 49 3 2212 2462 654346049 654346298 1.030000e-39 174.0
11 TraesCS1D01G343100 chr3B 78.968 252 50 3 2212 2462 654355443 654355692 4.770000e-38 169.0
12 TraesCS1D01G343100 chr6B 92.547 161 12 0 2626 2786 629122015 629122175 6.000000e-57 231.0
13 TraesCS1D01G343100 chr6D 80.882 272 43 8 2212 2480 304115559 304115824 3.640000e-49 206.0
14 TraesCS1D01G343100 chr2D 82.533 229 35 5 2227 2451 378360293 378360066 2.190000e-46 196.0
15 TraesCS1D01G343100 chr7D 81.405 242 41 4 2228 2467 246808005 246807766 7.870000e-46 195.0
16 TraesCS1D01G343100 chr5A 86.260 131 11 3 2657 2780 672414160 672414290 4.840000e-28 135.0
17 TraesCS1D01G343100 chr5B 74.319 257 57 9 2227 2479 108055938 108055687 1.770000e-17 100.0
18 TraesCS1D01G343100 chr7A 74.569 232 52 7 2228 2455 682889824 682889596 8.210000e-16 95.3


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 TraesCS1D01G343100 chr1D 432335220 432338005 2785 False 5145.0 5145 100.000000 1 2786 1 chr1D.!!$F1 2785
1 TraesCS1D01G343100 chr1B 583854317 583856937 2620 False 1564.5 2894 89.441000 1 2625 2 chr1B.!!$F1 2624
2 TraesCS1D01G343100 chr1A 530807770 530809873 2103 False 716.0 1168 87.024667 1 2192 3 chr1A.!!$F1 2191

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
20 21 0.600557 CTGACGAGCTTGACACCTCT 59.399 55.0 8.31 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1798 1946 0.248661 CGATCTGTAGTCGTGGCCTG 60.249 60.0 3.32 0.0 34.56 4.85 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
18 19 2.431023 ACTGACGAGCTTGACACCT 58.569 52.632 8.31 0.00 0.00 4.00
20 21 0.600557 CTGACGAGCTTGACACCTCT 59.399 55.000 8.31 0.00 0.00 3.69
38 39 2.886523 CTCTGCCCTGACATCACAAAAA 59.113 45.455 0.00 0.00 0.00 1.94
83 86 7.004691 CCTTCCTATTCCGGGATAAAAAGATT 58.995 38.462 19.02 0.00 32.41 2.40
85 88 7.144234 TCCTATTCCGGGATAAAAAGATTCA 57.856 36.000 3.46 0.00 0.00 2.57
99 102 5.536554 AAAGATTCAGACTAACGTGCATG 57.463 39.130 3.82 3.82 0.00 4.06
138 141 4.773323 ACCACTTGCTCTGAAAAATAGC 57.227 40.909 0.00 0.00 36.77 2.97
178 209 2.285083 TGAACACACCACTACTTGCAC 58.715 47.619 0.00 0.00 0.00 4.57
202 233 4.075682 GAGTGGATCGTCTCATGGATAGA 58.924 47.826 9.81 0.00 0.00 1.98
203 234 4.671831 AGTGGATCGTCTCATGGATAGAT 58.328 43.478 0.00 0.00 0.00 1.98
215 246 9.585099 GTCTCATGGATAGATAGATGAATGAAC 57.415 37.037 0.00 0.00 0.00 3.18
350 381 2.086054 ACAGTGCAGCAGCTAACTAC 57.914 50.000 9.15 0.58 42.74 2.73
367 399 3.956744 ACTACTCTGCCCATTTTTCTCC 58.043 45.455 0.00 0.00 0.00 3.71
373 405 4.222336 TCTGCCCATTTTTCTCCTTTTCA 58.778 39.130 0.00 0.00 0.00 2.69
374 406 4.840115 TCTGCCCATTTTTCTCCTTTTCAT 59.160 37.500 0.00 0.00 0.00 2.57
383 415 9.738832 CATTTTTCTCCTTTTCATTTTGCAAAT 57.261 25.926 13.65 0.39 0.00 2.32
387 419 6.590068 TCTCCTTTTCATTTTGCAAATCCAA 58.410 32.000 13.65 3.01 0.00 3.53
397 429 2.623535 TGCAAATCCAATCTGCAATGC 58.376 42.857 0.00 0.00 42.84 3.56
398 430 2.028020 TGCAAATCCAATCTGCAATGCA 60.028 40.909 7.99 7.99 42.84 3.96
399 431 2.350498 GCAAATCCAATCTGCAATGCAC 59.650 45.455 2.72 0.00 36.09 4.57
400 432 3.857052 CAAATCCAATCTGCAATGCACT 58.143 40.909 2.72 0.00 33.79 4.40
401 433 3.795623 AATCCAATCTGCAATGCACTC 57.204 42.857 2.72 0.00 33.79 3.51
402 434 2.203470 TCCAATCTGCAATGCACTCA 57.797 45.000 2.72 0.00 33.79 3.41
403 435 1.814394 TCCAATCTGCAATGCACTCAC 59.186 47.619 2.72 0.00 33.79 3.51
404 436 1.542472 CCAATCTGCAATGCACTCACA 59.458 47.619 2.72 0.00 33.79 3.58
405 437 2.415491 CCAATCTGCAATGCACTCACAG 60.415 50.000 2.72 0.00 33.79 3.66
406 438 2.484742 ATCTGCAATGCACTCACAGA 57.515 45.000 2.72 11.56 41.28 3.41
426 458 2.668457 GACTCACTGCACACCTTATTCG 59.332 50.000 0.00 0.00 0.00 3.34
709 752 2.272447 CCGCCGGAAAACCAACCAT 61.272 57.895 5.05 0.00 0.00 3.55
722 765 2.291365 CCAACCATGCATGATCTCGAA 58.709 47.619 28.31 0.00 0.00 3.71
726 769 2.224137 ACCATGCATGATCTCGAACGAT 60.224 45.455 28.31 0.00 0.00 3.73
752 795 3.234386 GCGTTTTTCTTGTGACCTATGC 58.766 45.455 0.00 0.00 0.00 3.14
753 796 3.821841 CGTTTTTCTTGTGACCTATGCC 58.178 45.455 0.00 0.00 0.00 4.40
755 798 3.410631 TTTTCTTGTGACCTATGCCGA 57.589 42.857 0.00 0.00 0.00 5.54
762 809 1.521681 GACCTATGCCGAGTGGTGC 60.522 63.158 0.00 0.00 37.67 5.01
764 811 0.686441 ACCTATGCCGAGTGGTGCTA 60.686 55.000 0.00 0.00 37.67 3.49
769 816 1.139947 GCCGAGTGGTGCTAGAGTC 59.860 63.158 0.00 0.00 37.67 3.36
839 892 4.610714 GCCGGCCTACAGCTAGCC 62.611 72.222 18.11 6.25 43.05 3.93
954 1017 2.543777 TCACAAGGAAGGAAGGTTCG 57.456 50.000 0.00 0.00 0.00 3.95
1059 1127 6.267699 TGATCAATTATCACTCATCGTACCCT 59.732 38.462 0.00 0.00 39.77 4.34
1060 1128 5.842907 TCAATTATCACTCATCGTACCCTG 58.157 41.667 0.00 0.00 0.00 4.45
1062 1130 0.753262 ATCACTCATCGTACCCTGGC 59.247 55.000 0.00 0.00 0.00 4.85
1117 1254 8.706521 TCTGTACTCTCTAGCTAGATTTACTGA 58.293 37.037 23.48 23.97 0.00 3.41
1125 1262 7.548097 TCTAGCTAGATTTACTGACAAACTGG 58.452 38.462 19.72 0.00 0.00 4.00
1177 1314 1.813513 ATCCTTGTGCTAGTGTGTGC 58.186 50.000 0.00 0.00 0.00 4.57
1288 1425 4.456253 CGCGTCCGCTCGTACTGT 62.456 66.667 10.21 0.00 39.32 3.55
1289 1426 2.787249 GCGTCCGCTCGTACTGTA 59.213 61.111 4.10 0.00 38.26 2.74
1290 1427 1.297451 GCGTCCGCTCGTACTGTAG 60.297 63.158 4.10 0.00 38.26 2.74
1291 1428 1.297451 CGTCCGCTCGTACTGTAGC 60.297 63.158 0.00 0.00 35.33 3.58
1292 1429 1.798735 GTCCGCTCGTACTGTAGCA 59.201 57.895 10.95 0.00 38.70 3.49
1293 1430 0.522915 GTCCGCTCGTACTGTAGCAC 60.523 60.000 10.95 1.36 38.70 4.40
1294 1431 0.956902 TCCGCTCGTACTGTAGCACA 60.957 55.000 10.95 0.00 38.70 4.57
1295 1432 0.109458 CCGCTCGTACTGTAGCACAA 60.109 55.000 10.95 0.00 38.70 3.33
1296 1433 0.982673 CGCTCGTACTGTAGCACAAC 59.017 55.000 10.95 0.00 38.70 3.32
1297 1434 1.664874 CGCTCGTACTGTAGCACAACA 60.665 52.381 10.95 0.00 38.70 3.33
1298 1435 1.719780 GCTCGTACTGTAGCACAACAC 59.280 52.381 6.80 0.00 38.63 3.32
1299 1436 2.860971 GCTCGTACTGTAGCACAACACA 60.861 50.000 6.80 0.00 38.63 3.72
1300 1437 2.724690 CTCGTACTGTAGCACAACACAC 59.275 50.000 0.00 0.00 0.00 3.82
1301 1438 2.359848 TCGTACTGTAGCACAACACACT 59.640 45.455 0.00 0.00 0.00 3.55
1302 1439 3.120792 CGTACTGTAGCACAACACACTT 58.879 45.455 0.00 0.00 0.00 3.16
1311 1448 5.679734 AGCACAACACACTTCTCTTTATG 57.320 39.130 0.00 0.00 0.00 1.90
1333 1470 1.524355 GCGAGTTCGATCATGACATGG 59.476 52.381 15.37 0.00 43.02 3.66
1356 1498 4.785658 GCGATATATACATCTGACCGACCG 60.786 50.000 0.00 0.00 0.00 4.79
1734 1882 0.179084 GGATCAATTCCTCCGACGCA 60.179 55.000 0.00 0.00 41.78 5.24
1798 1946 2.362668 CGTCTGACGTTCAACAAACC 57.637 50.000 21.30 0.00 36.74 3.27
1799 1947 1.661617 CGTCTGACGTTCAACAAACCA 59.338 47.619 21.30 0.00 36.74 3.67
1804 1952 0.681564 ACGTTCAACAAACCAGGCCA 60.682 50.000 5.01 0.00 34.11 5.36
1808 1970 1.098712 TCAACAAACCAGGCCACGAC 61.099 55.000 5.01 0.00 0.00 4.34
1821 1983 1.333931 GCCACGACTACAGATCGATCA 59.666 52.381 26.47 5.98 42.25 2.92
1822 1984 2.855187 GCCACGACTACAGATCGATCAC 60.855 54.545 26.47 1.76 42.25 3.06
1825 1990 3.971240 CACGACTACAGATCGATCACATG 59.029 47.826 26.47 18.05 42.25 3.21
1869 2037 0.953960 CGCCTGGGGTGTTAGTTGAC 60.954 60.000 1.98 0.00 0.00 3.18
1904 2086 9.863845 TCTTTGTGATGATACTATTAACGTGAA 57.136 29.630 0.00 0.00 0.00 3.18
1990 2172 4.434520 GCAGTGAGATGTAACCCTAACTC 58.565 47.826 0.00 0.00 0.00 3.01
2024 2207 4.256110 TGGCTGTGAGATGTAACTGAATG 58.744 43.478 0.00 0.00 0.00 2.67
2026 2209 5.046663 TGGCTGTGAGATGTAACTGAATGTA 60.047 40.000 0.00 0.00 0.00 2.29
2027 2210 5.292101 GGCTGTGAGATGTAACTGAATGTAC 59.708 44.000 0.00 0.00 0.00 2.90
2028 2211 5.004821 GCTGTGAGATGTAACTGAATGTACG 59.995 44.000 0.00 0.00 0.00 3.67
2029 2212 6.020971 TGTGAGATGTAACTGAATGTACGT 57.979 37.500 0.00 0.00 0.00 3.57
2114 2298 7.121315 TCGAGTAGAAAATGTCTTCAGATGAGA 59.879 37.037 0.00 0.00 37.84 3.27
2115 2299 7.219917 CGAGTAGAAAATGTCTTCAGATGAGAC 59.780 40.741 0.00 0.00 37.84 3.36
2116 2300 7.901029 AGTAGAAAATGTCTTCAGATGAGACA 58.099 34.615 7.30 7.30 45.07 3.41
2117 2301 8.034215 AGTAGAAAATGTCTTCAGATGAGACAG 58.966 37.037 10.16 0.00 44.35 3.51
2118 2302 6.171921 AGAAAATGTCTTCAGATGAGACAGG 58.828 40.000 10.16 0.00 44.35 4.00
2119 2303 5.752036 AAATGTCTTCAGATGAGACAGGA 57.248 39.130 10.16 0.00 44.35 3.86
2120 2304 5.341872 AATGTCTTCAGATGAGACAGGAG 57.658 43.478 10.16 0.00 44.35 3.69
2121 2305 4.039603 TGTCTTCAGATGAGACAGGAGA 57.960 45.455 1.33 0.00 37.61 3.71
2122 2306 4.608269 TGTCTTCAGATGAGACAGGAGAT 58.392 43.478 1.33 0.00 37.61 2.75
2123 2307 5.760131 TGTCTTCAGATGAGACAGGAGATA 58.240 41.667 1.33 0.00 37.61 1.98
2124 2308 6.372104 TGTCTTCAGATGAGACAGGAGATAT 58.628 40.000 1.33 0.00 37.61 1.63
2125 2309 6.838090 TGTCTTCAGATGAGACAGGAGATATT 59.162 38.462 1.33 0.00 37.61 1.28
2126 2310 7.344093 TGTCTTCAGATGAGACAGGAGATATTT 59.656 37.037 1.33 0.00 37.61 1.40
2127 2311 7.652909 GTCTTCAGATGAGACAGGAGATATTTG 59.347 40.741 0.00 0.00 33.20 2.32
2128 2312 7.562821 TCTTCAGATGAGACAGGAGATATTTGA 59.437 37.037 0.00 0.00 0.00 2.69
2129 2313 7.666063 TCAGATGAGACAGGAGATATTTGAA 57.334 36.000 0.00 0.00 0.00 2.69
2130 2314 8.082672 TCAGATGAGACAGGAGATATTTGAAA 57.917 34.615 0.00 0.00 0.00 2.69
2131 2315 8.712103 TCAGATGAGACAGGAGATATTTGAAAT 58.288 33.333 0.00 0.00 0.00 2.17
2132 2316 8.775527 CAGATGAGACAGGAGATATTTGAAATG 58.224 37.037 0.00 0.00 0.00 2.32
2133 2317 7.937942 AGATGAGACAGGAGATATTTGAAATGG 59.062 37.037 0.00 0.00 0.00 3.16
2134 2318 7.199167 TGAGACAGGAGATATTTGAAATGGA 57.801 36.000 0.00 0.00 0.00 3.41
2195 2379 2.763933 CTGAACTGTCAGTGCATCAGT 58.236 47.619 14.33 9.74 45.44 3.41
2196 2380 2.479275 CTGAACTGTCAGTGCATCAGTG 59.521 50.000 14.33 0.00 45.44 3.66
2197 2381 5.192844 CTGAACTGTCAGTGCATCAGTGC 62.193 52.174 14.33 13.23 45.79 4.40
2216 2400 6.051074 CAGTGCATGTGACAGGAGATATTTA 58.949 40.000 0.00 0.00 0.00 1.40
2217 2401 6.709397 CAGTGCATGTGACAGGAGATATTTAT 59.291 38.462 0.00 0.00 0.00 1.40
2248 2434 7.447374 TTTGAATATCCAACAAACGTCAGAT 57.553 32.000 0.00 0.00 0.00 2.90
2252 2438 8.356657 TGAATATCCAACAAACGTCAGATTTTT 58.643 29.630 0.00 0.00 0.00 1.94
2265 2451 5.422145 GTCAGATTTTTAGGCATGGCAAAT 58.578 37.500 22.64 17.51 0.00 2.32
2271 2457 2.418368 TAGGCATGGCAAATCGAACT 57.582 45.000 22.64 0.00 0.00 3.01
2334 2520 0.734889 AGGCGAGCATGAAAAATCCG 59.265 50.000 0.00 0.00 0.00 4.18
2345 2531 9.567848 GAGCATGAAAAATCCGTCTTAATTAAA 57.432 29.630 0.00 0.00 0.00 1.52
2378 2564 3.848272 AATTACCATGTTCGCCAACTG 57.152 42.857 0.00 0.00 33.17 3.16
2384 2570 2.988493 CCATGTTCGCCAACTGAATTTG 59.012 45.455 0.00 0.00 33.17 2.32
2402 2588 2.099141 TGCTATCCTCACAGCAACAC 57.901 50.000 0.00 0.00 44.49 3.32
2406 2592 3.441572 GCTATCCTCACAGCAACACAAAT 59.558 43.478 0.00 0.00 37.73 2.32
2453 2639 5.469421 GCCATTCCTAAGAATCTGATGTCAG 59.531 44.000 3.61 3.61 40.89 3.51
2506 2692 1.686052 AGCTGCTCTAGTCAGTATGCC 59.314 52.381 0.00 1.26 34.76 4.40
2545 2731 5.869344 TCATCACTTCTCGTCGAATCAAAAT 59.131 36.000 0.00 0.00 0.00 1.82
2546 2732 7.033185 TCATCACTTCTCGTCGAATCAAAATA 58.967 34.615 0.00 0.00 0.00 1.40
2550 2736 8.717821 TCACTTCTCGTCGAATCAAAATAAAAT 58.282 29.630 0.00 0.00 0.00 1.82
2551 2737 9.967245 CACTTCTCGTCGAATCAAAATAAAATA 57.033 29.630 0.00 0.00 0.00 1.40
2554 2740 9.982291 TTCTCGTCGAATCAAAATAAAATAAGG 57.018 29.630 0.00 0.00 0.00 2.69
2577 2765 2.146342 AGGTGCTCAGTTTTCGTGATG 58.854 47.619 0.00 0.00 0.00 3.07
2579 2767 2.290641 GGTGCTCAGTTTTCGTGATGTT 59.709 45.455 0.00 0.00 0.00 2.71
2625 2818 2.279741 TCAAGACACAGGCATTATCGC 58.720 47.619 0.00 0.00 0.00 4.58
2626 2819 2.009051 CAAGACACAGGCATTATCGCA 58.991 47.619 0.00 0.00 0.00 5.10
2627 2820 2.401583 AGACACAGGCATTATCGCAA 57.598 45.000 0.00 0.00 0.00 4.85
2628 2821 2.710377 AGACACAGGCATTATCGCAAA 58.290 42.857 0.00 0.00 0.00 3.68
2629 2822 3.081061 AGACACAGGCATTATCGCAAAA 58.919 40.909 0.00 0.00 0.00 2.44
2630 2823 3.505680 AGACACAGGCATTATCGCAAAAA 59.494 39.130 0.00 0.00 0.00 1.94
2631 2824 4.158394 AGACACAGGCATTATCGCAAAAAT 59.842 37.500 0.00 0.00 0.00 1.82
2632 2825 4.175516 ACACAGGCATTATCGCAAAAATG 58.824 39.130 0.00 0.00 36.40 2.32
2640 2833 6.722972 CATTATCGCAAAAATGCTAGACAC 57.277 37.500 0.00 0.00 0.00 3.67
2641 2834 5.871465 TTATCGCAAAAATGCTAGACACA 57.129 34.783 0.00 0.00 0.00 3.72
2642 2835 3.536158 TCGCAAAAATGCTAGACACAC 57.464 42.857 0.00 0.00 0.00 3.82
2643 2836 2.096466 TCGCAAAAATGCTAGACACACG 60.096 45.455 0.00 0.00 0.00 4.49
2644 2837 2.584791 GCAAAAATGCTAGACACACGG 58.415 47.619 0.00 0.00 0.00 4.94
2645 2838 2.668279 GCAAAAATGCTAGACACACGGG 60.668 50.000 0.00 0.00 0.00 5.28
2646 2839 1.165270 AAAATGCTAGACACACGGGC 58.835 50.000 0.00 0.00 0.00 6.13
2647 2840 0.676782 AAATGCTAGACACACGGGCC 60.677 55.000 0.00 0.00 0.00 5.80
2648 2841 2.852495 AATGCTAGACACACGGGCCG 62.852 60.000 27.06 27.06 0.00 6.13
2650 2843 4.063967 CTAGACACACGGGCCGCA 62.064 66.667 28.71 1.25 0.00 5.69
2651 2844 4.367023 TAGACACACGGGCCGCAC 62.367 66.667 28.71 12.81 0.00 5.34
2662 2855 4.250431 GCCGCACACGCACAAGTT 62.250 61.111 0.00 0.00 38.40 2.66
2663 2856 2.407210 CCGCACACGCACAAGTTT 59.593 55.556 0.00 0.00 38.40 2.66
2664 2857 1.226547 CCGCACACGCACAAGTTTT 60.227 52.632 0.00 0.00 38.40 2.43
2665 2858 0.028242 CCGCACACGCACAAGTTTTA 59.972 50.000 0.00 0.00 38.40 1.52
2666 2859 1.109296 CGCACACGCACAAGTTTTAC 58.891 50.000 0.00 0.00 38.40 2.01
2667 2860 1.109296 GCACACGCACAAGTTTTACG 58.891 50.000 0.00 0.00 38.36 3.18
2668 2861 1.737249 CACACGCACAAGTTTTACGG 58.263 50.000 0.00 0.00 0.00 4.02
2669 2862 1.328069 CACACGCACAAGTTTTACGGA 59.672 47.619 0.00 0.00 0.00 4.69
2670 2863 1.328374 ACACGCACAAGTTTTACGGAC 59.672 47.619 0.00 0.00 0.00 4.79
2671 2864 0.578211 ACGCACAAGTTTTACGGACG 59.422 50.000 0.00 0.00 0.00 4.79
2672 2865 0.720173 CGCACAAGTTTTACGGACGC 60.720 55.000 0.00 0.00 0.00 5.19
2673 2866 0.720173 GCACAAGTTTTACGGACGCG 60.720 55.000 3.53 3.53 0.00 6.01
2674 2867 0.720173 CACAAGTTTTACGGACGCGC 60.720 55.000 5.73 0.00 0.00 6.86
2675 2868 0.877213 ACAAGTTTTACGGACGCGCT 60.877 50.000 5.73 0.00 0.00 5.92
2676 2869 0.450482 CAAGTTTTACGGACGCGCTG 60.450 55.000 5.73 6.95 0.00 5.18
2677 2870 0.598158 AAGTTTTACGGACGCGCTGA 60.598 50.000 5.73 0.00 0.00 4.26
2678 2871 1.129209 GTTTTACGGACGCGCTGAC 59.871 57.895 5.73 0.00 0.00 3.51
2679 2872 2.023223 TTTTACGGACGCGCTGACC 61.023 57.895 5.73 8.23 0.00 4.02
2680 2873 2.424705 TTTTACGGACGCGCTGACCT 62.425 55.000 5.73 2.57 0.00 3.85
2681 2874 2.424705 TTTACGGACGCGCTGACCTT 62.425 55.000 5.73 5.47 0.00 3.50
2682 2875 2.424705 TTACGGACGCGCTGACCTTT 62.425 55.000 5.73 1.98 0.00 3.11
2683 2876 2.807631 TACGGACGCGCTGACCTTTC 62.808 60.000 5.73 0.00 0.00 2.62
2684 2877 3.479269 GGACGCGCTGACCTTTCG 61.479 66.667 5.73 0.00 0.00 3.46
2685 2878 2.733593 GACGCGCTGACCTTTCGT 60.734 61.111 5.73 0.00 35.98 3.85
2686 2879 3.000080 GACGCGCTGACCTTTCGTG 62.000 63.158 5.73 0.00 39.33 4.35
2687 2880 3.036084 CGCGCTGACCTTTCGTGT 61.036 61.111 5.56 0.00 0.00 4.49
2688 2881 2.594962 CGCGCTGACCTTTCGTGTT 61.595 57.895 5.56 0.00 0.00 3.32
2689 2882 1.647084 GCGCTGACCTTTCGTGTTT 59.353 52.632 0.00 0.00 0.00 2.83
2690 2883 0.028902 GCGCTGACCTTTCGTGTTTT 59.971 50.000 0.00 0.00 0.00 2.43
2691 2884 1.262151 GCGCTGACCTTTCGTGTTTTA 59.738 47.619 0.00 0.00 0.00 1.52
2692 2885 2.286536 GCGCTGACCTTTCGTGTTTTAA 60.287 45.455 0.00 0.00 0.00 1.52
2693 2886 3.608474 GCGCTGACCTTTCGTGTTTTAAT 60.608 43.478 0.00 0.00 0.00 1.40
2694 2887 4.533222 CGCTGACCTTTCGTGTTTTAATT 58.467 39.130 0.00 0.00 0.00 1.40
2695 2888 4.378616 CGCTGACCTTTCGTGTTTTAATTG 59.621 41.667 0.00 0.00 0.00 2.32
2696 2889 4.679654 GCTGACCTTTCGTGTTTTAATTGG 59.320 41.667 0.00 0.00 0.00 3.16
2697 2890 4.612943 TGACCTTTCGTGTTTTAATTGGC 58.387 39.130 0.00 0.00 0.00 4.52
2698 2891 4.098044 TGACCTTTCGTGTTTTAATTGGCA 59.902 37.500 0.00 0.00 0.00 4.92
2699 2892 5.012328 ACCTTTCGTGTTTTAATTGGCAA 57.988 34.783 0.68 0.68 0.00 4.52
2700 2893 5.420409 ACCTTTCGTGTTTTAATTGGCAAA 58.580 33.333 3.01 0.00 0.00 3.68
2701 2894 5.875359 ACCTTTCGTGTTTTAATTGGCAAAA 59.125 32.000 3.01 0.00 0.00 2.44
2702 2895 6.036626 ACCTTTCGTGTTTTAATTGGCAAAAG 59.963 34.615 3.01 0.00 0.00 2.27
2703 2896 6.036626 CCTTTCGTGTTTTAATTGGCAAAAGT 59.963 34.615 3.01 0.00 0.00 2.66
2704 2897 7.222999 CCTTTCGTGTTTTAATTGGCAAAAGTA 59.777 33.333 3.01 0.00 0.00 2.24
2705 2898 8.475331 TTTCGTGTTTTAATTGGCAAAAGTAA 57.525 26.923 3.01 0.57 0.00 2.24
2706 2899 8.475331 TTCGTGTTTTAATTGGCAAAAGTAAA 57.525 26.923 3.01 6.99 0.00 2.01
2707 2900 7.896894 TCGTGTTTTAATTGGCAAAAGTAAAC 58.103 30.769 3.01 12.61 0.00 2.01
2708 2901 7.760340 TCGTGTTTTAATTGGCAAAAGTAAACT 59.240 29.630 20.70 0.00 0.00 2.66
2709 2902 8.384365 CGTGTTTTAATTGGCAAAAGTAAACTT 58.616 29.630 20.70 7.54 37.91 2.66
2710 2903 9.697250 GTGTTTTAATTGGCAAAAGTAAACTTC 57.303 29.630 20.70 14.37 34.61 3.01
2711 2904 9.660180 TGTTTTAATTGGCAAAAGTAAACTTCT 57.340 25.926 20.70 0.00 34.61 2.85
2713 2906 8.880878 TTTAATTGGCAAAAGTAAACTTCTCC 57.119 30.769 3.01 0.00 34.61 3.71
2714 2907 6.731292 AATTGGCAAAAGTAAACTTCTCCT 57.269 33.333 3.01 0.00 34.61 3.69
2715 2908 5.767816 TTGGCAAAAGTAAACTTCTCCTC 57.232 39.130 0.00 0.00 34.61 3.71
2716 2909 4.142038 TGGCAAAAGTAAACTTCTCCTCC 58.858 43.478 0.00 0.00 34.61 4.30
2717 2910 4.141251 TGGCAAAAGTAAACTTCTCCTCCT 60.141 41.667 0.00 0.00 34.61 3.69
2718 2911 5.072600 TGGCAAAAGTAAACTTCTCCTCCTA 59.927 40.000 0.00 0.00 34.61 2.94
2719 2912 5.411977 GGCAAAAGTAAACTTCTCCTCCTAC 59.588 44.000 0.00 0.00 34.61 3.18
2720 2913 6.231951 GCAAAAGTAAACTTCTCCTCCTACT 58.768 40.000 0.00 0.00 34.61 2.57
2721 2914 6.711194 GCAAAAGTAAACTTCTCCTCCTACTT 59.289 38.462 0.00 0.00 34.61 2.24
2722 2915 7.876582 GCAAAAGTAAACTTCTCCTCCTACTTA 59.123 37.037 0.00 0.00 34.61 2.24
2723 2916 9.774413 CAAAAGTAAACTTCTCCTCCTACTTAA 57.226 33.333 0.00 0.00 34.61 1.85
2724 2917 9.775854 AAAAGTAAACTTCTCCTCCTACTTAAC 57.224 33.333 0.00 0.00 34.61 2.01
2725 2918 7.479352 AGTAAACTTCTCCTCCTACTTAACC 57.521 40.000 0.00 0.00 0.00 2.85
2726 2919 5.402997 AAACTTCTCCTCCTACTTAACCG 57.597 43.478 0.00 0.00 0.00 4.44
2727 2920 2.759535 ACTTCTCCTCCTACTTAACCGC 59.240 50.000 0.00 0.00 0.00 5.68
2728 2921 1.772836 TCTCCTCCTACTTAACCGCC 58.227 55.000 0.00 0.00 0.00 6.13
2729 2922 0.751452 CTCCTCCTACTTAACCGCCC 59.249 60.000 0.00 0.00 0.00 6.13
2730 2923 0.688749 TCCTCCTACTTAACCGCCCC 60.689 60.000 0.00 0.00 0.00 5.80
2731 2924 1.693152 CCTCCTACTTAACCGCCCCC 61.693 65.000 0.00 0.00 0.00 5.40
2749 2942 2.456577 CCCCCTGATTTTAACTGGTGG 58.543 52.381 0.00 0.00 0.00 4.61
2750 2943 2.456577 CCCCTGATTTTAACTGGTGGG 58.543 52.381 0.00 0.00 0.00 4.61
2751 2944 2.456577 CCCTGATTTTAACTGGTGGGG 58.543 52.381 0.00 0.00 0.00 4.96
2752 2945 2.225267 CCCTGATTTTAACTGGTGGGGT 60.225 50.000 0.00 0.00 0.00 4.95
2753 2946 2.825532 CCTGATTTTAACTGGTGGGGTG 59.174 50.000 0.00 0.00 0.00 4.61
2754 2947 2.825532 CTGATTTTAACTGGTGGGGTGG 59.174 50.000 0.00 0.00 0.00 4.61
2755 2948 2.176045 GATTTTAACTGGTGGGGTGGG 58.824 52.381 0.00 0.00 0.00 4.61
2756 2949 0.470268 TTTTAACTGGTGGGGTGGGC 60.470 55.000 0.00 0.00 0.00 5.36
2757 2950 2.700407 TTTAACTGGTGGGGTGGGCG 62.700 60.000 0.00 0.00 0.00 6.13
2772 2965 2.358984 GCGTCCAGGCCCGTAAAA 60.359 61.111 0.00 0.00 0.00 1.52
2773 2966 2.683859 GCGTCCAGGCCCGTAAAAC 61.684 63.158 0.00 0.00 0.00 2.43
2774 2967 1.004200 CGTCCAGGCCCGTAAAACT 60.004 57.895 0.00 0.00 0.00 2.66
2775 2968 1.017701 CGTCCAGGCCCGTAAAACTC 61.018 60.000 0.00 0.00 0.00 3.01
2776 2969 0.675837 GTCCAGGCCCGTAAAACTCC 60.676 60.000 0.00 0.00 0.00 3.85
2777 2970 1.743995 CCAGGCCCGTAAAACTCCG 60.744 63.158 0.00 0.00 0.00 4.63
2778 2971 1.004200 CAGGCCCGTAAAACTCCGT 60.004 57.895 0.00 0.00 0.00 4.69
2779 2972 0.247185 CAGGCCCGTAAAACTCCGTA 59.753 55.000 0.00 0.00 0.00 4.02
2780 2973 1.134610 CAGGCCCGTAAAACTCCGTAT 60.135 52.381 0.00 0.00 0.00 3.06
2781 2974 1.556451 AGGCCCGTAAAACTCCGTATT 59.444 47.619 0.00 0.00 0.00 1.89
2782 2975 2.765699 AGGCCCGTAAAACTCCGTATTA 59.234 45.455 0.00 0.00 0.00 0.98
2783 2976 3.389002 AGGCCCGTAAAACTCCGTATTAT 59.611 43.478 0.00 0.00 0.00 1.28
2784 2977 4.129380 GGCCCGTAAAACTCCGTATTATT 58.871 43.478 0.00 0.00 0.00 1.40
2785 2978 4.212004 GGCCCGTAAAACTCCGTATTATTC 59.788 45.833 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.673665 CAGGGCAGAGGTGTCAAGC 60.674 63.158 0.00 0.00 0.00 4.01
18 19 2.655090 TTTTGTGATGTCAGGGCAGA 57.345 45.000 0.00 0.00 0.00 4.26
20 21 4.832266 ACTAATTTTTGTGATGTCAGGGCA 59.168 37.500 0.00 0.00 0.00 5.36
38 39 6.603599 GGAAGGTTGCCTGAATCTTTACTAAT 59.396 38.462 0.00 0.00 34.95 1.73
83 86 2.030628 TCGAACATGCACGTTAGTCTGA 60.031 45.455 0.00 0.00 0.00 3.27
85 88 2.717580 TCGAACATGCACGTTAGTCT 57.282 45.000 0.00 0.00 0.00 3.24
99 102 0.452784 GTTGCAAGGCGACATCGAAC 60.453 55.000 0.00 0.00 42.10 3.95
134 137 1.211457 AGCAGCTGCAAGGTTAGCTAT 59.789 47.619 38.24 12.19 46.63 2.97
137 140 1.012841 CTAGCAGCTGCAAGGTTAGC 58.987 55.000 38.24 10.26 46.63 3.09
138 141 1.012841 GCTAGCAGCTGCAAGGTTAG 58.987 55.000 38.24 28.89 46.63 2.34
178 209 0.031314 CCATGAGACGATCCACTCCG 59.969 60.000 0.00 0.00 32.84 4.63
202 233 4.021981 TCGATCGCCTGTTCATTCATCTAT 60.022 41.667 11.09 0.00 0.00 1.98
203 234 3.317993 TCGATCGCCTGTTCATTCATCTA 59.682 43.478 11.09 0.00 0.00 1.98
215 246 2.278206 CTCCGTGTCGATCGCCTG 60.278 66.667 11.09 0.00 0.00 4.85
341 372 4.576330 AAAATGGGCAGAGTAGTTAGCT 57.424 40.909 0.00 0.00 0.00 3.32
350 381 4.281688 TGAAAAGGAGAAAAATGGGCAGAG 59.718 41.667 0.00 0.00 0.00 3.35
367 399 6.799925 GCAGATTGGATTTGCAAAATGAAAAG 59.200 34.615 17.19 4.68 37.75 2.27
383 415 1.814394 GTGAGTGCATTGCAGATTGGA 59.186 47.619 12.53 0.00 40.08 3.53
387 419 2.082231 GTCTGTGAGTGCATTGCAGAT 58.918 47.619 12.53 3.55 40.08 2.90
394 426 1.607509 GCAGTGAGTCTGTGAGTGCAT 60.608 52.381 0.00 0.00 45.23 3.96
397 429 1.202452 TGTGCAGTGAGTCTGTGAGTG 60.202 52.381 0.00 0.00 45.23 3.51
398 430 1.114627 TGTGCAGTGAGTCTGTGAGT 58.885 50.000 0.00 0.00 45.23 3.41
399 431 1.495878 GTGTGCAGTGAGTCTGTGAG 58.504 55.000 0.00 0.00 45.23 3.51
400 432 0.104855 GGTGTGCAGTGAGTCTGTGA 59.895 55.000 0.00 0.00 45.23 3.58
401 433 0.105593 AGGTGTGCAGTGAGTCTGTG 59.894 55.000 0.00 0.00 45.23 3.66
402 434 0.833287 AAGGTGTGCAGTGAGTCTGT 59.167 50.000 0.00 0.00 45.23 3.41
403 435 2.820059 TAAGGTGTGCAGTGAGTCTG 57.180 50.000 0.00 0.00 46.12 3.51
404 436 3.615110 CGAATAAGGTGTGCAGTGAGTCT 60.615 47.826 0.00 0.00 0.00 3.24
405 437 2.668457 CGAATAAGGTGTGCAGTGAGTC 59.332 50.000 0.00 0.00 0.00 3.36
406 438 2.612972 CCGAATAAGGTGTGCAGTGAGT 60.613 50.000 0.00 0.00 0.00 3.41
426 458 1.134946 ACTGTTGCAGCACTGTTTTCC 59.865 47.619 0.00 0.00 34.37 3.13
659 702 4.814294 CCGAAGAGGGCGAACCGG 62.814 72.222 0.00 0.00 46.96 5.28
668 711 4.410400 AAAGGCCGGCCGAAGAGG 62.410 66.667 38.88 10.90 41.95 3.69
669 712 3.127533 CAAAGGCCGGCCGAAGAG 61.128 66.667 38.88 23.71 41.95 2.85
670 713 4.715523 CCAAAGGCCGGCCGAAGA 62.716 66.667 38.88 0.00 41.95 2.87
709 752 1.856802 CCATCGTTCGAGATCATGCA 58.143 50.000 0.00 0.00 0.00 3.96
722 765 1.512156 AAGAAAAACGCCGCCATCGT 61.512 50.000 0.00 0.00 42.54 3.73
726 769 1.064946 CACAAGAAAAACGCCGCCA 59.935 52.632 0.00 0.00 0.00 5.69
752 795 1.306642 ACGACTCTAGCACCACTCGG 61.307 60.000 0.00 0.00 38.77 4.63
753 796 0.522180 AACGACTCTAGCACCACTCG 59.478 55.000 0.00 0.00 0.00 4.18
755 798 2.488545 CAGTAACGACTCTAGCACCACT 59.511 50.000 0.00 0.00 31.73 4.00
762 809 2.506865 CGCACACAGTAACGACTCTAG 58.493 52.381 0.00 0.00 31.73 2.43
764 811 0.663568 GCGCACACAGTAACGACTCT 60.664 55.000 0.30 0.00 31.73 3.24
769 816 3.773630 CCCGCGCACACAGTAACG 61.774 66.667 8.75 0.00 0.00 3.18
792 844 2.703798 GCACGGGGTGTACGCTAGA 61.704 63.158 6.35 0.00 35.75 2.43
932 991 3.744530 CGAACCTTCCTTCCTTGTGAACT 60.745 47.826 0.00 0.00 0.00 3.01
989 1052 1.343821 CAAGGCATCGCGTTACGTC 59.656 57.895 5.77 0.00 44.19 4.34
993 1056 3.192230 CGCCAAGGCATCGCGTTA 61.192 61.111 12.19 0.00 40.99 3.18
1053 1121 2.171568 AGTAACTAGGGCCAGGGTAC 57.828 55.000 6.18 11.04 0.00 3.34
1059 1127 1.488390 CCGGTAAGTAACTAGGGCCA 58.512 55.000 6.18 0.00 0.00 5.36
1060 1128 0.755079 CCCGGTAAGTAACTAGGGCC 59.245 60.000 0.00 0.00 38.52 5.80
1062 1130 1.758862 CACCCCGGTAAGTAACTAGGG 59.241 57.143 0.00 0.00 42.75 3.53
1117 1254 3.056322 GTGATCTACCGTACCCAGTTTGT 60.056 47.826 0.00 0.00 0.00 2.83
1177 1314 1.927174 GTCCATGGAAGATCGAACGTG 59.073 52.381 18.20 0.00 0.00 4.49
1223 1360 0.956633 ATGCATGCATGGATCGGAAC 59.043 50.000 31.74 8.62 33.26 3.62
1224 1361 3.425122 ATGCATGCATGGATCGGAA 57.575 47.368 31.74 0.21 33.26 4.30
1284 1421 3.133003 AGAGAAGTGTGTTGTGCTACAGT 59.867 43.478 0.00 0.00 32.09 3.55
1285 1422 3.722147 AGAGAAGTGTGTTGTGCTACAG 58.278 45.455 0.00 0.00 0.00 2.74
1286 1423 3.819564 AGAGAAGTGTGTTGTGCTACA 57.180 42.857 0.00 0.00 0.00 2.74
1287 1424 6.593978 CATAAAGAGAAGTGTGTTGTGCTAC 58.406 40.000 0.00 0.00 0.00 3.58
1288 1425 5.179368 GCATAAAGAGAAGTGTGTTGTGCTA 59.821 40.000 0.00 0.00 34.60 3.49
1289 1426 4.023707 GCATAAAGAGAAGTGTGTTGTGCT 60.024 41.667 0.00 0.00 34.60 4.40
1290 1427 4.222114 GCATAAAGAGAAGTGTGTTGTGC 58.778 43.478 0.00 0.00 0.00 4.57
1291 1428 4.457810 CGCATAAAGAGAAGTGTGTTGTG 58.542 43.478 0.00 0.00 0.00 3.33
1292 1429 3.058914 GCGCATAAAGAGAAGTGTGTTGT 60.059 43.478 0.30 0.00 0.00 3.32
1293 1430 3.482786 GCGCATAAAGAGAAGTGTGTTG 58.517 45.455 0.30 0.00 0.00 3.33
1294 1431 2.157668 CGCGCATAAAGAGAAGTGTGTT 59.842 45.455 8.75 0.00 0.00 3.32
1295 1432 1.726791 CGCGCATAAAGAGAAGTGTGT 59.273 47.619 8.75 0.00 0.00 3.72
1296 1433 1.992667 TCGCGCATAAAGAGAAGTGTG 59.007 47.619 8.75 0.00 0.00 3.82
1297 1434 2.263077 CTCGCGCATAAAGAGAAGTGT 58.737 47.619 8.75 0.00 34.13 3.55
1298 1435 2.263077 ACTCGCGCATAAAGAGAAGTG 58.737 47.619 14.93 0.00 36.03 3.16
1299 1436 2.656560 ACTCGCGCATAAAGAGAAGT 57.343 45.000 14.93 0.00 36.03 3.01
1300 1437 2.035342 CGAACTCGCGCATAAAGAGAAG 60.035 50.000 14.93 0.00 36.03 2.85
1301 1438 1.917955 CGAACTCGCGCATAAAGAGAA 59.082 47.619 14.93 0.00 36.03 2.87
1302 1439 1.131693 TCGAACTCGCGCATAAAGAGA 59.868 47.619 14.93 0.00 39.60 3.10
1311 1448 1.139816 TGTCATGATCGAACTCGCGC 61.140 55.000 0.00 0.00 39.60 6.86
1333 1470 4.599047 GGTCGGTCAGATGTATATATCGC 58.401 47.826 4.05 0.09 32.33 4.58
1356 1498 1.924524 ACATCACATAAGCGTACGTGC 59.075 47.619 17.90 0.18 0.00 5.34
1788 1936 0.394488 TCGTGGCCTGGTTTGTTGAA 60.394 50.000 3.32 0.00 0.00 2.69
1798 1946 0.248661 CGATCTGTAGTCGTGGCCTG 60.249 60.000 3.32 0.00 34.56 4.85
1799 1947 0.393944 TCGATCTGTAGTCGTGGCCT 60.394 55.000 3.32 0.00 39.91 5.19
1804 1952 3.549019 GCATGTGATCGATCTGTAGTCGT 60.549 47.826 25.02 8.13 39.91 4.34
1808 1970 3.123116 GCATGCATGTGATCGATCTGTAG 59.877 47.826 26.79 13.89 0.00 2.74
1856 2023 1.975660 TGCAAGGTCAACTAACACCC 58.024 50.000 0.00 0.00 32.45 4.61
1857 2024 2.884639 ACATGCAAGGTCAACTAACACC 59.115 45.455 0.00 0.00 0.00 4.16
1869 2037 4.713824 ATCATCACAAAGACATGCAAGG 57.286 40.909 0.00 0.00 0.00 3.61
1926 2108 9.541143 CATACGGTGCATGGATAATATAACATA 57.459 33.333 0.00 0.00 0.00 2.29
1927 2109 8.437360 CATACGGTGCATGGATAATATAACAT 57.563 34.615 0.00 0.00 0.00 2.71
1928 2110 7.841915 CATACGGTGCATGGATAATATAACA 57.158 36.000 0.00 0.00 0.00 2.41
1962 2144 1.734465 GTTACATCTCACTGCCAGCAC 59.266 52.381 0.00 0.00 0.00 4.40
2006 2189 5.861787 CACGTACATTCAGTTACATCTCACA 59.138 40.000 0.00 0.00 0.00 3.58
2024 2207 4.303993 ACCCGGCCACACACGTAC 62.304 66.667 2.24 0.00 0.00 3.67
2027 2210 3.687102 TAGACCCGGCCACACACG 61.687 66.667 2.24 0.00 0.00 4.49
2028 2211 2.047560 GTAGACCCGGCCACACAC 60.048 66.667 2.24 0.00 0.00 3.82
2029 2212 3.315949 GGTAGACCCGGCCACACA 61.316 66.667 2.24 0.00 0.00 3.72
2086 2270 7.918033 TCATCTGAAGACATTTTCTACTCGATC 59.082 37.037 0.00 0.00 32.51 3.69
2114 2298 9.347240 CAGTAATCCATTTCAAATATCTCCTGT 57.653 33.333 0.00 0.00 0.00 4.00
2115 2299 9.565090 TCAGTAATCCATTTCAAATATCTCCTG 57.435 33.333 0.00 0.00 0.00 3.86
2129 2313 9.911788 AGACATACAAATCTTCAGTAATCCATT 57.088 29.630 0.00 0.00 0.00 3.16
2130 2314 9.553064 GAGACATACAAATCTTCAGTAATCCAT 57.447 33.333 0.00 0.00 0.00 3.41
2131 2315 8.539544 TGAGACATACAAATCTTCAGTAATCCA 58.460 33.333 0.00 0.00 0.00 3.41
2132 2316 8.948631 TGAGACATACAAATCTTCAGTAATCC 57.051 34.615 0.00 0.00 0.00 3.01
2134 2318 9.334947 CCATGAGACATACAAATCTTCAGTAAT 57.665 33.333 0.00 0.00 0.00 1.89
2192 2376 2.398252 ATCTCCTGTCACATGCACTG 57.602 50.000 0.00 0.00 0.00 3.66
2193 2377 4.767578 AATATCTCCTGTCACATGCACT 57.232 40.909 0.00 0.00 0.00 4.40
2194 2378 8.607441 TTATAAATATCTCCTGTCACATGCAC 57.393 34.615 0.00 0.00 0.00 4.57
2195 2379 9.223099 CATTATAAATATCTCCTGTCACATGCA 57.777 33.333 0.00 0.00 0.00 3.96
2196 2380 8.671921 CCATTATAAATATCTCCTGTCACATGC 58.328 37.037 0.00 0.00 0.00 4.06
2197 2381 9.948964 TCCATTATAAATATCTCCTGTCACATG 57.051 33.333 0.00 0.00 0.00 3.21
2238 2422 4.618227 GCCATGCCTAAAAATCTGACGTTT 60.618 41.667 0.00 0.00 0.00 3.60
2239 2423 3.119495 GCCATGCCTAAAAATCTGACGTT 60.119 43.478 0.00 0.00 0.00 3.99
2241 2425 2.423185 TGCCATGCCTAAAAATCTGACG 59.577 45.455 0.00 0.00 0.00 4.35
2248 2434 4.021544 AGTTCGATTTGCCATGCCTAAAAA 60.022 37.500 0.00 0.00 0.00 1.94
2252 2438 2.418368 AGTTCGATTTGCCATGCCTA 57.582 45.000 0.00 0.00 0.00 3.93
2302 2488 4.893424 TGCTCGCCTATAAATTTTCCAC 57.107 40.909 0.00 0.00 0.00 4.02
2345 2531 9.139174 CGAACATGGTAATTTTCTAGCAAAAAT 57.861 29.630 0.00 0.00 39.83 1.82
2384 2570 2.099141 TGTGTTGCTGTGAGGATAGC 57.901 50.000 0.00 0.00 40.29 2.97
2406 2592 7.120285 TGGCAAATCAAAAGTTTTTCATGACAA 59.880 29.630 0.00 0.00 0.00 3.18
2506 2692 0.877071 GATGAACACTGTGGGCTGTG 59.123 55.000 13.09 3.65 46.00 3.66
2545 2731 7.833285 AAACTGAGCACCTTTCCTTATTTTA 57.167 32.000 0.00 0.00 0.00 1.52
2546 2732 6.731292 AAACTGAGCACCTTTCCTTATTTT 57.269 33.333 0.00 0.00 0.00 1.82
2550 2736 3.813166 CGAAAACTGAGCACCTTTCCTTA 59.187 43.478 0.00 0.00 0.00 2.69
2551 2737 2.618709 CGAAAACTGAGCACCTTTCCTT 59.381 45.455 0.00 0.00 0.00 3.36
2553 2739 1.947456 ACGAAAACTGAGCACCTTTCC 59.053 47.619 0.00 0.00 0.00 3.13
2554 2740 2.612212 TCACGAAAACTGAGCACCTTTC 59.388 45.455 0.00 0.00 0.00 2.62
2589 2780 0.662619 TTGAAGTCGCACAAGCCTTG 59.337 50.000 2.11 2.11 37.52 3.61
2625 2818 2.668279 GCCCGTGTGTCTAGCATTTTTG 60.668 50.000 0.00 0.00 0.00 2.44
2626 2819 1.539827 GCCCGTGTGTCTAGCATTTTT 59.460 47.619 0.00 0.00 0.00 1.94
2627 2820 1.165270 GCCCGTGTGTCTAGCATTTT 58.835 50.000 0.00 0.00 0.00 1.82
2628 2821 0.676782 GGCCCGTGTGTCTAGCATTT 60.677 55.000 0.00 0.00 0.00 2.32
2629 2822 1.078426 GGCCCGTGTGTCTAGCATT 60.078 57.895 0.00 0.00 0.00 3.56
2630 2823 2.584608 GGCCCGTGTGTCTAGCAT 59.415 61.111 0.00 0.00 0.00 3.79
2631 2824 4.063967 CGGCCCGTGTGTCTAGCA 62.064 66.667 0.00 0.00 0.00 3.49
2633 2826 4.063967 TGCGGCCCGTGTGTCTAG 62.064 66.667 4.45 0.00 0.00 2.43
2634 2827 4.367023 GTGCGGCCCGTGTGTCTA 62.367 66.667 4.45 0.00 0.00 2.59
2648 2841 1.109296 CGTAAAACTTGTGCGTGTGC 58.891 50.000 0.00 0.00 43.20 4.57
2649 2842 1.328069 TCCGTAAAACTTGTGCGTGTG 59.672 47.619 0.00 0.00 0.00 3.82
2650 2843 1.328374 GTCCGTAAAACTTGTGCGTGT 59.672 47.619 0.00 0.00 0.00 4.49
2651 2844 1.655325 CGTCCGTAAAACTTGTGCGTG 60.655 52.381 0.00 0.00 0.00 5.34
2652 2845 0.578211 CGTCCGTAAAACTTGTGCGT 59.422 50.000 0.00 0.00 0.00 5.24
2653 2846 0.720173 GCGTCCGTAAAACTTGTGCG 60.720 55.000 0.00 0.00 0.00 5.34
2654 2847 0.720173 CGCGTCCGTAAAACTTGTGC 60.720 55.000 0.00 0.00 0.00 4.57
2655 2848 0.720173 GCGCGTCCGTAAAACTTGTG 60.720 55.000 8.43 0.00 36.67 3.33
2656 2849 0.877213 AGCGCGTCCGTAAAACTTGT 60.877 50.000 8.43 0.00 36.67 3.16
2657 2850 0.450482 CAGCGCGTCCGTAAAACTTG 60.450 55.000 8.43 0.00 36.67 3.16
2658 2851 0.598158 TCAGCGCGTCCGTAAAACTT 60.598 50.000 8.43 0.00 36.67 2.66
2659 2852 1.007038 TCAGCGCGTCCGTAAAACT 60.007 52.632 8.43 0.00 36.67 2.66
2660 2853 1.129209 GTCAGCGCGTCCGTAAAAC 59.871 57.895 8.43 0.00 36.67 2.43
2661 2854 2.023223 GGTCAGCGCGTCCGTAAAA 61.023 57.895 8.43 0.00 36.67 1.52
2662 2855 2.424705 AAGGTCAGCGCGTCCGTAAA 62.425 55.000 8.43 0.00 36.67 2.01
2663 2856 2.424705 AAAGGTCAGCGCGTCCGTAA 62.425 55.000 8.43 0.00 36.67 3.18
2664 2857 2.807631 GAAAGGTCAGCGCGTCCGTA 62.808 60.000 8.43 0.00 36.67 4.02
2665 2858 4.295119 AAAGGTCAGCGCGTCCGT 62.295 61.111 8.43 1.12 36.67 4.69
2666 2859 3.479269 GAAAGGTCAGCGCGTCCG 61.479 66.667 8.43 0.00 37.57 4.79
2667 2860 3.479269 CGAAAGGTCAGCGCGTCC 61.479 66.667 8.43 6.07 0.00 4.79
2668 2861 2.733593 ACGAAAGGTCAGCGCGTC 60.734 61.111 8.43 0.00 0.00 5.19
2669 2862 3.036084 CACGAAAGGTCAGCGCGT 61.036 61.111 8.43 0.00 35.33 6.01
2670 2863 2.101209 AAACACGAAAGGTCAGCGCG 62.101 55.000 0.00 0.00 0.00 6.86
2671 2864 0.028902 AAAACACGAAAGGTCAGCGC 59.971 50.000 0.00 0.00 0.00 5.92
2672 2865 3.595709 TTAAAACACGAAAGGTCAGCG 57.404 42.857 0.00 0.00 0.00 5.18
2673 2866 4.679654 CCAATTAAAACACGAAAGGTCAGC 59.320 41.667 0.00 0.00 0.00 4.26
2674 2867 4.679654 GCCAATTAAAACACGAAAGGTCAG 59.320 41.667 0.00 0.00 0.00 3.51
2675 2868 4.098044 TGCCAATTAAAACACGAAAGGTCA 59.902 37.500 0.00 0.00 0.00 4.02
2676 2869 4.612943 TGCCAATTAAAACACGAAAGGTC 58.387 39.130 0.00 0.00 0.00 3.85
2677 2870 4.657436 TGCCAATTAAAACACGAAAGGT 57.343 36.364 0.00 0.00 0.00 3.50
2678 2871 5.975410 TTTGCCAATTAAAACACGAAAGG 57.025 34.783 0.00 0.00 0.00 3.11
2679 2872 6.999456 ACTTTTGCCAATTAAAACACGAAAG 58.001 32.000 0.00 0.00 35.55 2.62
2680 2873 6.969828 ACTTTTGCCAATTAAAACACGAAA 57.030 29.167 0.00 0.00 0.00 3.46
2681 2874 8.381387 GTTTACTTTTGCCAATTAAAACACGAA 58.619 29.630 0.00 0.00 0.00 3.85
2682 2875 7.760340 AGTTTACTTTTGCCAATTAAAACACGA 59.240 29.630 0.00 0.00 0.00 4.35
2683 2876 7.901002 AGTTTACTTTTGCCAATTAAAACACG 58.099 30.769 0.00 0.00 0.00 4.49
2684 2877 9.697250 GAAGTTTACTTTTGCCAATTAAAACAC 57.303 29.630 0.00 0.00 36.11 3.32
2685 2878 9.660180 AGAAGTTTACTTTTGCCAATTAAAACA 57.340 25.926 0.00 0.00 36.11 2.83
2687 2880 9.320352 GGAGAAGTTTACTTTTGCCAATTAAAA 57.680 29.630 0.00 0.00 36.11 1.52
2688 2881 8.700973 AGGAGAAGTTTACTTTTGCCAATTAAA 58.299 29.630 0.00 0.00 36.11 1.52
2689 2882 8.245195 AGGAGAAGTTTACTTTTGCCAATTAA 57.755 30.769 0.00 0.00 36.11 1.40
2690 2883 7.039993 GGAGGAGAAGTTTACTTTTGCCAATTA 60.040 37.037 0.00 0.00 36.11 1.40
2691 2884 6.239317 GGAGGAGAAGTTTACTTTTGCCAATT 60.239 38.462 0.00 0.00 36.11 2.32
2692 2885 5.243954 GGAGGAGAAGTTTACTTTTGCCAAT 59.756 40.000 0.00 0.00 36.11 3.16
2693 2886 4.583073 GGAGGAGAAGTTTACTTTTGCCAA 59.417 41.667 0.00 0.00 36.11 4.52
2694 2887 4.141251 AGGAGGAGAAGTTTACTTTTGCCA 60.141 41.667 0.00 0.00 36.11 4.92
2695 2888 4.399219 AGGAGGAGAAGTTTACTTTTGCC 58.601 43.478 0.00 0.03 36.11 4.52
2696 2889 6.231951 AGTAGGAGGAGAAGTTTACTTTTGC 58.768 40.000 0.00 0.00 36.11 3.68
2697 2890 9.774413 TTAAGTAGGAGGAGAAGTTTACTTTTG 57.226 33.333 0.00 0.00 36.11 2.44
2698 2891 9.775854 GTTAAGTAGGAGGAGAAGTTTACTTTT 57.224 33.333 0.00 0.00 36.11 2.27
2699 2892 8.373981 GGTTAAGTAGGAGGAGAAGTTTACTTT 58.626 37.037 0.00 0.00 36.11 2.66
2700 2893 7.309683 CGGTTAAGTAGGAGGAGAAGTTTACTT 60.310 40.741 0.00 0.00 39.23 2.24
2701 2894 6.152492 CGGTTAAGTAGGAGGAGAAGTTTACT 59.848 42.308 0.00 0.00 0.00 2.24
2702 2895 6.328714 CGGTTAAGTAGGAGGAGAAGTTTAC 58.671 44.000 0.00 0.00 0.00 2.01
2703 2896 5.105595 GCGGTTAAGTAGGAGGAGAAGTTTA 60.106 44.000 0.00 0.00 0.00 2.01
2704 2897 4.322574 GCGGTTAAGTAGGAGGAGAAGTTT 60.323 45.833 0.00 0.00 0.00 2.66
2705 2898 3.195182 GCGGTTAAGTAGGAGGAGAAGTT 59.805 47.826 0.00 0.00 0.00 2.66
2706 2899 2.759535 GCGGTTAAGTAGGAGGAGAAGT 59.240 50.000 0.00 0.00 0.00 3.01
2707 2900 2.101082 GGCGGTTAAGTAGGAGGAGAAG 59.899 54.545 0.00 0.00 0.00 2.85
2708 2901 2.105766 GGCGGTTAAGTAGGAGGAGAA 58.894 52.381 0.00 0.00 0.00 2.87
2709 2902 1.687368 GGGCGGTTAAGTAGGAGGAGA 60.687 57.143 0.00 0.00 0.00 3.71
2710 2903 0.751452 GGGCGGTTAAGTAGGAGGAG 59.249 60.000 0.00 0.00 0.00 3.69
2711 2904 0.688749 GGGGCGGTTAAGTAGGAGGA 60.689 60.000 0.00 0.00 0.00 3.71
2712 2905 1.693152 GGGGGCGGTTAAGTAGGAGG 61.693 65.000 0.00 0.00 0.00 4.30
2713 2906 1.828081 GGGGGCGGTTAAGTAGGAG 59.172 63.158 0.00 0.00 0.00 3.69
2714 2907 4.055178 GGGGGCGGTTAAGTAGGA 57.945 61.111 0.00 0.00 0.00 2.94
2729 2922 2.456577 CCACCAGTTAAAATCAGGGGG 58.543 52.381 0.00 0.00 36.42 5.40
2730 2923 2.456577 CCCACCAGTTAAAATCAGGGG 58.543 52.381 0.00 0.00 0.00 4.79
2731 2924 2.225267 ACCCCACCAGTTAAAATCAGGG 60.225 50.000 0.00 0.00 38.04 4.45
2732 2925 2.825532 CACCCCACCAGTTAAAATCAGG 59.174 50.000 0.00 0.00 0.00 3.86
2733 2926 2.825532 CCACCCCACCAGTTAAAATCAG 59.174 50.000 0.00 0.00 0.00 2.90
2734 2927 2.491825 CCCACCCCACCAGTTAAAATCA 60.492 50.000 0.00 0.00 0.00 2.57
2735 2928 2.176045 CCCACCCCACCAGTTAAAATC 58.824 52.381 0.00 0.00 0.00 2.17
2736 2929 1.829666 GCCCACCCCACCAGTTAAAAT 60.830 52.381 0.00 0.00 0.00 1.82
2737 2930 0.470268 GCCCACCCCACCAGTTAAAA 60.470 55.000 0.00 0.00 0.00 1.52
2738 2931 1.154221 GCCCACCCCACCAGTTAAA 59.846 57.895 0.00 0.00 0.00 1.52
2739 2932 2.848032 GCCCACCCCACCAGTTAA 59.152 61.111 0.00 0.00 0.00 2.01
2740 2933 3.642503 CGCCCACCCCACCAGTTA 61.643 66.667 0.00 0.00 0.00 2.24
2755 2948 2.358984 TTTTACGGGCCTGGACGC 60.359 61.111 18.00 3.63 0.00 5.19
2756 2949 1.004200 AGTTTTACGGGCCTGGACG 60.004 57.895 18.00 7.10 0.00 4.79
2757 2950 0.675837 GGAGTTTTACGGGCCTGGAC 60.676 60.000 18.00 8.92 0.00 4.02
2758 2951 1.681076 GGAGTTTTACGGGCCTGGA 59.319 57.895 18.00 3.57 0.00 3.86
2759 2952 1.743995 CGGAGTTTTACGGGCCTGG 60.744 63.158 18.00 4.46 0.00 4.45
2760 2953 0.247185 TACGGAGTTTTACGGGCCTG 59.753 55.000 11.02 11.02 37.78 4.85
2761 2954 1.197812 ATACGGAGTTTTACGGGCCT 58.802 50.000 0.84 0.00 37.78 5.19
2762 2955 2.028420 AATACGGAGTTTTACGGGCC 57.972 50.000 0.00 0.00 37.78 5.80
2763 2956 5.334435 GAATAATACGGAGTTTTACGGGC 57.666 43.478 0.00 0.00 37.78 6.13


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

AutoCloner maintained by Alex Coulton.