Multiple sequence alignment - TraesCS5A01G467200

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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 TraesCS5A01G467200 chr5A 100.000 2993 0 0 1 2993 645137439 645134447 0.000000e+00 5528.0
1 TraesCS5A01G467200 chr5A 100.000 257 0 0 3280 3536 645134160 645133904 3.190000e-130 475.0
2 TraesCS5A01G467200 chr5D 90.216 1390 62 38 58 1409 517763097 517761744 0.000000e+00 1746.0
3 TraesCS5A01G467200 chr5D 88.584 692 58 13 2304 2982 517761093 517760410 0.000000e+00 821.0
4 TraesCS5A01G467200 chr5D 90.104 192 18 1 3345 3536 517760399 517760209 7.580000e-62 248.0
5 TraesCS5A01G467200 chr5D 97.260 73 2 0 1 73 517763217 517763145 1.330000e-24 124.0
6 TraesCS5A01G467200 chr5B 89.510 734 54 12 2208 2934 650346712 650345995 0.000000e+00 907.0
7 TraesCS5A01G467200 chr5B 87.879 792 36 22 647 1409 650348518 650347758 0.000000e+00 876.0
8 TraesCS5A01G467200 chr5B 93.169 527 30 3 1407 1930 650347731 650347208 0.000000e+00 769.0
9 TraesCS5A01G467200 chr5B 89.438 445 32 9 148 585 650349680 650349244 6.670000e-152 547.0
10 TraesCS5A01G467200 chr5B 92.453 371 23 2 284 649 650348969 650348599 3.130000e-145 525.0
11 TraesCS5A01G467200 chr5B 94.857 175 8 1 3294 3467 650345994 650345820 4.500000e-69 272.0
12 TraesCS5A01G467200 chr5B 87.730 163 18 1 1944 2104 650346873 650346711 4.660000e-44 189.0
13 TraesCS5A01G467200 chr5B 93.651 126 6 2 2084 2208 187031784 187031908 1.680000e-43 187.0
14 TraesCS5A01G467200 chr7D 94.488 127 7 0 2086 2212 126669681 126669807 2.780000e-46 196.0
15 TraesCS5A01G467200 chr7A 96.581 117 4 0 2100 2216 689307109 689307225 1.000000e-45 195.0
16 TraesCS5A01G467200 chr7A 92.424 132 8 2 2085 2216 619039539 619039668 1.680000e-43 187.0
17 TraesCS5A01G467200 chr3B 96.610 118 3 1 2101 2217 70582214 70582097 1.000000e-45 195.0
18 TraesCS5A01G467200 chr3B 95.041 121 5 1 2099 2219 776360223 776360342 4.660000e-44 189.0
19 TraesCS5A01G467200 chr3A 97.368 114 2 1 2097 2210 583676702 583676590 3.600000e-45 193.0
20 TraesCS5A01G467200 chr7B 95.082 122 4 2 2093 2213 450588147 450588027 1.300000e-44 191.0
21 TraesCS5A01G467200 chr2A 90.714 140 8 5 2084 2220 655044720 655044857 7.800000e-42 182.0
22 TraesCS5A01G467200 chr2A 94.737 38 1 1 969 1006 410525346 410525382 1.370000e-04 58.4
23 TraesCS5A01G467200 chr6A 100.000 31 0 0 976 1006 470944200 470944170 1.370000e-04 58.4
24 TraesCS5A01G467200 chr4D 97.059 34 1 0 973 1006 126719793 126719826 1.370000e-04 58.4
25 TraesCS5A01G467200 chr4B 97.059 34 1 0 973 1006 279882272 279882305 1.370000e-04 58.4
26 TraesCS5A01G467200 chr4B 97.059 34 1 0 973 1006 348035885 348035918 1.370000e-04 58.4
27 TraesCS5A01G467200 chr2D 97.059 34 1 0 973 1006 219148229 219148262 1.370000e-04 58.4
28 TraesCS5A01G467200 chr1B 97.059 34 1 0 973 1006 250818289 250818322 1.370000e-04 58.4


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 TraesCS5A01G467200 chr5A 645133904 645137439 3535 True 3001.500000 5528 100.000000 1 3536 2 chr5A.!!$R1 3535
1 TraesCS5A01G467200 chr5D 517760209 517763217 3008 True 734.750000 1746 91.541000 1 3536 4 chr5D.!!$R1 3535
2 TraesCS5A01G467200 chr5B 650345820 650349680 3860 True 583.571429 907 90.719429 148 3467 7 chr5B.!!$R1 3319

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
335 979 0.750182 AACACCCAACTCCACGGTTG 60.750 55.0 0.00 0.00 44.17 3.77 F
2119 3444 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.0 14.79 0.04 33.41 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2257 3582 0.031585 TGACAGAAGTTCCACCGTCG 59.968 55.0 0.00 0.0 0.00 5.12 R
3361 4703 0.324285 GCCATGGCTAGATCTGGAGG 59.676 60.0 29.98 6.6 38.26 4.30 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
223 287 9.219603 GCACATATACATTACATCCTTATGTGT 57.780 33.333 16.83 0.00 45.99 3.72
328 972 1.328279 CCTCCAAAACACCCAACTCC 58.672 55.000 0.00 0.00 0.00 3.85
335 979 0.750182 AACACCCAACTCCACGGTTG 60.750 55.000 0.00 0.00 44.17 3.77
347 991 7.654116 CCAACTCCACGGTTGTTTAAAATTATT 59.346 33.333 6.60 0.00 43.36 1.40
644 1295 6.824305 AAAATGTAGAGGGTGAACTTCATG 57.176 37.500 0.00 0.00 0.00 3.07
650 1384 3.852578 AGAGGGTGAACTTCATGGGTATT 59.147 43.478 0.00 0.00 0.00 1.89
754 1490 4.097135 TGACATGGTTGCCCGTAATTTATG 59.903 41.667 0.00 0.00 0.00 1.90
789 1536 3.248024 ACTTCATGGTTGGGTGTCTAGA 58.752 45.455 0.00 0.00 0.00 2.43
790 1537 3.650942 ACTTCATGGTTGGGTGTCTAGAA 59.349 43.478 0.00 0.00 0.00 2.10
878 1634 4.008669 TAGTACCCACCCGGCCCA 62.009 66.667 0.00 0.00 33.26 5.36
879 1635 3.335410 TAGTACCCACCCGGCCCAT 62.335 63.158 0.00 0.00 33.26 4.00
880 1636 4.185286 GTACCCACCCGGCCCATC 62.185 72.222 0.00 0.00 33.26 3.51
881 1637 4.424867 TACCCACCCGGCCCATCT 62.425 66.667 0.00 0.00 33.26 2.90
882 1638 3.024337 TACCCACCCGGCCCATCTA 62.024 63.158 0.00 0.00 33.26 1.98
883 1639 3.873812 CCCACCCGGCCCATCTAC 61.874 72.222 0.00 0.00 0.00 2.59
884 1640 4.235762 CCACCCGGCCCATCTACG 62.236 72.222 0.00 0.00 0.00 3.51
885 1641 4.235762 CACCCGGCCCATCTACGG 62.236 72.222 0.00 0.00 46.79 4.02
937 1711 1.749638 GAAGGAGGACGAGGAGCGA 60.750 63.158 0.00 0.00 44.57 4.93
1198 1981 0.179108 CGAGTAAGAAGGCTTCCCCG 60.179 60.000 23.09 14.83 39.21 5.73
1199 1982 0.462225 GAGTAAGAAGGCTTCCCCGC 60.462 60.000 23.09 11.33 39.21 6.13
1292 2105 1.674611 GGTCGTGTGCTCGTGATTCG 61.675 60.000 0.00 0.00 41.41 3.34
1314 2127 4.201685 CGTAGGACAAATTAAGGTTGCGAG 60.202 45.833 0.00 0.00 0.00 5.03
1322 2135 3.955650 TTAAGGTTGCGAGTTAGAGCT 57.044 42.857 0.00 0.00 0.00 4.09
1331 2144 3.885901 TGCGAGTTAGAGCTAGTGATGAT 59.114 43.478 0.00 0.00 0.00 2.45
1332 2145 4.225984 GCGAGTTAGAGCTAGTGATGATG 58.774 47.826 0.00 0.00 0.00 3.07
1333 2146 4.793071 CGAGTTAGAGCTAGTGATGATGG 58.207 47.826 0.00 0.00 0.00 3.51
1345 2158 7.016957 AGCTAGTGATGATGGGATTGAATCTTA 59.983 37.037 5.03 0.00 0.00 2.10
1346 2159 7.828223 GCTAGTGATGATGGGATTGAATCTTAT 59.172 37.037 5.03 0.21 0.00 1.73
1347 2160 9.381033 CTAGTGATGATGGGATTGAATCTTATC 57.619 37.037 5.03 9.49 0.00 1.75
1366 2186 1.153349 CTGGTCCCTAAAGAGGCGC 60.153 63.158 0.00 0.00 42.21 6.53
1395 2218 4.641541 TGAGCATGTTTGATATCCAAGTGG 59.358 41.667 0.00 0.00 35.94 4.00
1396 2219 4.603131 AGCATGTTTGATATCCAAGTGGT 58.397 39.130 0.00 1.19 35.94 4.16
1397 2220 4.400251 AGCATGTTTGATATCCAAGTGGTG 59.600 41.667 0.00 0.00 35.94 4.17
1400 2223 5.957842 TGTTTGATATCCAAGTGGTGAAC 57.042 39.130 0.00 0.00 35.94 3.18
1401 2224 5.380900 TGTTTGATATCCAAGTGGTGAACA 58.619 37.500 0.00 0.00 35.94 3.18
1402 2225 5.830457 TGTTTGATATCCAAGTGGTGAACAA 59.170 36.000 0.00 0.00 35.94 2.83
1404 2227 7.015098 TGTTTGATATCCAAGTGGTGAACAATT 59.985 33.333 0.00 0.00 38.00 2.32
1405 2228 7.537596 TTGATATCCAAGTGGTGAACAATTT 57.462 32.000 0.00 0.00 34.73 1.82
1417 2271 3.996363 GTGAACAATTTTGGATCCAAGCC 59.004 43.478 25.69 11.16 37.24 4.35
1427 2281 6.371595 TTTGGATCCAAGCCAACAATTTAT 57.628 33.333 25.69 0.00 44.58 1.40
1447 2301 2.738013 ACTTACACAAGTACCGCCTC 57.262 50.000 0.00 0.00 43.33 4.70
1469 2323 8.088365 GCCTCACAAACCATTTCTAGTATTTTT 58.912 33.333 0.00 0.00 0.00 1.94
1546 2400 0.529378 CTCAGCCAATGGTTTCAGCC 59.471 55.000 0.00 0.00 0.00 4.85
1583 2569 6.635030 AACTTTTCCAACTTAGCCACTTAG 57.365 37.500 0.00 0.00 0.00 2.18
1762 2757 1.203038 TGTACCTGTACCCGTCCTTGA 60.203 52.381 5.07 0.00 35.26 3.02
1788 2788 9.616634 AGTGATAATTTTATGCTGCATTTATCG 57.383 29.630 24.96 0.00 29.54 2.92
1789 2789 9.398170 GTGATAATTTTATGCTGCATTTATCGT 57.602 29.630 24.96 11.98 29.54 3.73
1879 2881 2.223386 TGTCAAAACGTAACAGCTTGGC 60.223 45.455 0.00 0.00 0.00 4.52
1910 2912 0.678950 TGCCTTTGCCCTTTGCTAAC 59.321 50.000 0.00 0.00 42.00 2.34
1921 2923 5.538433 TGCCCTTTGCTAACAGTTTCTTTAT 59.462 36.000 0.00 0.00 42.00 1.40
1922 2924 6.717540 TGCCCTTTGCTAACAGTTTCTTTATA 59.282 34.615 0.00 0.00 42.00 0.98
1923 2925 7.094377 TGCCCTTTGCTAACAGTTTCTTTATAG 60.094 37.037 0.00 0.00 42.00 1.31
1924 2926 7.094334 GCCCTTTGCTAACAGTTTCTTTATAGT 60.094 37.037 0.00 0.00 36.87 2.12
1956 3279 3.681705 CTGCATGTGCTGTTAACCG 57.318 52.632 2.48 0.00 42.66 4.44
1969 3292 5.583061 TGCTGTTAACCGATTTACCTACATG 59.417 40.000 2.48 0.00 0.00 3.21
2007 3330 2.162681 CCTGTGGGCTTTCTTAAGTGG 58.837 52.381 1.63 0.00 33.74 4.00
2020 3343 7.803659 GCTTTCTTAAGTGGTTCTGATGTTAAC 59.196 37.037 1.63 0.00 33.74 2.01
2023 3346 8.603242 TCTTAAGTGGTTCTGATGTTAACTTC 57.397 34.615 13.22 13.22 0.00 3.01
2028 3351 4.988540 TGGTTCTGATGTTAACTTCACTCG 59.011 41.667 17.62 10.32 0.00 4.18
2034 3357 4.754618 TGATGTTAACTTCACTCGTTGCAT 59.245 37.500 17.62 0.00 0.00 3.96
2064 3389 5.321102 TGGTTTTTGATATGTACCTGTGCT 58.679 37.500 0.00 0.00 0.00 4.40
2069 3394 4.817318 TGATATGTACCTGTGCTTGTCA 57.183 40.909 0.00 0.00 0.00 3.58
2076 3401 2.224606 ACCTGTGCTTGTCATTGAGTG 58.775 47.619 0.00 0.00 0.00 3.51
2084 3409 5.858581 GTGCTTGTCATTGAGTGGTATTTTC 59.141 40.000 0.00 0.00 0.00 2.29
2090 3415 9.513906 TTGTCATTGAGTGGTATTTTCATTCTA 57.486 29.630 0.00 0.00 0.00 2.10
2091 3416 8.946085 TGTCATTGAGTGGTATTTTCATTCTAC 58.054 33.333 0.00 0.00 0.00 2.59
2109 3434 9.710818 TCATTCTACATTTACTTAGTACTCCCT 57.289 33.333 0.00 0.00 0.00 4.20
2110 3435 9.968870 CATTCTACATTTACTTAGTACTCCCTC 57.031 37.037 0.00 0.00 0.00 4.30
2111 3436 8.530804 TTCTACATTTACTTAGTACTCCCTCC 57.469 38.462 0.00 0.00 0.00 4.30
2112 3437 5.848833 ACATTTACTTAGTACTCCCTCCG 57.151 43.478 0.00 0.00 0.00 4.63
2113 3438 5.267587 ACATTTACTTAGTACTCCCTCCGT 58.732 41.667 0.00 0.00 0.00 4.69
2114 3439 5.718607 ACATTTACTTAGTACTCCCTCCGTT 59.281 40.000 0.00 0.00 0.00 4.44
2115 3440 5.904362 TTTACTTAGTACTCCCTCCGTTC 57.096 43.478 0.00 0.00 0.00 3.95
2116 3441 2.363683 ACTTAGTACTCCCTCCGTTCG 58.636 52.381 0.00 0.00 0.00 3.95
2117 3442 1.674962 CTTAGTACTCCCTCCGTTCGG 59.325 57.143 0.00 4.74 0.00 4.30
2118 3443 0.911769 TAGTACTCCCTCCGTTCGGA 59.088 55.000 13.34 13.34 0.00 4.55
2119 3444 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
2120 3445 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
2121 3446 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
2122 3447 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2123 3448 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2124 3449 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2125 3450 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2126 3451 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2127 3452 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2128 3453 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2129 3454 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
2130 3455 2.030007 TCCGTTCGGAATTACTTGTCGT 60.030 45.455 11.66 0.00 0.00 4.34
2131 3456 3.190327 TCCGTTCGGAATTACTTGTCGTA 59.810 43.478 11.66 0.00 0.00 3.43
2132 3457 3.545078 CCGTTCGGAATTACTTGTCGTAG 59.455 47.826 5.19 0.00 0.00 3.51
2133 3458 4.406069 CGTTCGGAATTACTTGTCGTAGA 58.594 43.478 0.00 0.00 0.00 2.59
2134 3459 4.853196 CGTTCGGAATTACTTGTCGTAGAA 59.147 41.667 0.00 0.00 39.69 2.10
2135 3460 5.343058 CGTTCGGAATTACTTGTCGTAGAAA 59.657 40.000 0.00 0.00 39.69 2.52
2136 3461 6.034256 CGTTCGGAATTACTTGTCGTAGAAAT 59.966 38.462 0.00 0.00 39.69 2.17
2137 3462 6.880822 TCGGAATTACTTGTCGTAGAAATG 57.119 37.500 0.00 0.00 39.69 2.32
2138 3463 5.808540 TCGGAATTACTTGTCGTAGAAATGG 59.191 40.000 0.00 0.00 39.69 3.16
2139 3464 5.808540 CGGAATTACTTGTCGTAGAAATGGA 59.191 40.000 0.00 0.00 39.69 3.41
2140 3465 6.479001 CGGAATTACTTGTCGTAGAAATGGAT 59.521 38.462 0.00 0.00 39.69 3.41
2141 3466 7.516785 CGGAATTACTTGTCGTAGAAATGGATG 60.517 40.741 0.00 0.00 39.69 3.51
2142 3467 7.280205 GGAATTACTTGTCGTAGAAATGGATGT 59.720 37.037 0.00 0.00 39.69 3.06
2143 3468 9.309516 GAATTACTTGTCGTAGAAATGGATGTA 57.690 33.333 0.00 0.00 39.69 2.29
2144 3469 9.832445 AATTACTTGTCGTAGAAATGGATGTAT 57.168 29.630 0.00 0.00 39.69 2.29
2145 3470 8.867112 TTACTTGTCGTAGAAATGGATGTATC 57.133 34.615 0.00 0.00 39.69 2.24
2146 3471 7.113658 ACTTGTCGTAGAAATGGATGTATCT 57.886 36.000 0.00 0.00 39.69 1.98
2147 3472 8.234136 ACTTGTCGTAGAAATGGATGTATCTA 57.766 34.615 0.00 0.00 39.69 1.98
2148 3473 8.353684 ACTTGTCGTAGAAATGGATGTATCTAG 58.646 37.037 0.00 0.00 39.69 2.43
2149 3474 8.459911 TTGTCGTAGAAATGGATGTATCTAGA 57.540 34.615 0.00 0.00 39.69 2.43
2150 3475 7.872881 TGTCGTAGAAATGGATGTATCTAGAC 58.127 38.462 0.00 0.00 39.69 2.59
2151 3476 7.016466 GTCGTAGAAATGGATGTATCTAGACG 58.984 42.308 0.00 0.00 39.69 4.18
2152 3477 6.709397 TCGTAGAAATGGATGTATCTAGACGT 59.291 38.462 0.00 0.00 0.00 4.34
2153 3478 7.874528 TCGTAGAAATGGATGTATCTAGACGTA 59.125 37.037 0.00 0.00 0.00 3.57
2154 3479 8.666573 CGTAGAAATGGATGTATCTAGACGTAT 58.333 37.037 0.00 0.00 0.00 3.06
2180 3505 9.542462 TTTTACTTCTAGATACATCCATTTCCG 57.458 33.333 0.00 0.00 0.00 4.30
2181 3506 6.978674 ACTTCTAGATACATCCATTTCCGA 57.021 37.500 0.00 0.00 0.00 4.55
2182 3507 6.987386 ACTTCTAGATACATCCATTTCCGAG 58.013 40.000 0.00 0.00 0.00 4.63
2183 3508 6.778069 ACTTCTAGATACATCCATTTCCGAGA 59.222 38.462 0.00 0.00 0.00 4.04
2184 3509 6.576662 TCTAGATACATCCATTTCCGAGAC 57.423 41.667 0.00 0.00 0.00 3.36
2185 3510 6.068670 TCTAGATACATCCATTTCCGAGACA 58.931 40.000 0.00 0.00 0.00 3.41
2186 3511 5.614324 AGATACATCCATTTCCGAGACAA 57.386 39.130 0.00 0.00 0.00 3.18
2187 3512 5.605534 AGATACATCCATTTCCGAGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
2188 3513 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
2189 3514 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
2190 3515 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
2191 3516 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
2192 3517 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
2193 3518 6.316390 ACATCCATTTCCGAGACAAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
2194 3519 5.183228 TCCATTTCCGAGACAAGTAATTCC 58.817 41.667 0.00 0.00 0.00 3.01
2195 3520 4.034048 CCATTTCCGAGACAAGTAATTCCG 59.966 45.833 0.00 0.00 0.00 4.30
2196 3521 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
2197 3522 4.524316 TTCCGAGACAAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
2198 3523 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
2199 3524 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
2200 3525 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
2201 3526 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
2202 3527 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
2203 3528 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2204 3529 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2205 3530 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
2206 3531 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2207 3532 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
2208 3533 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
2209 3534 2.083628 ATTCCGAACGGAGGGAGTAT 57.916 50.000 15.34 3.38 46.06 2.12
2210 3535 1.108776 TTCCGAACGGAGGGAGTATG 58.891 55.000 15.34 0.00 46.06 2.39
2213 3538 0.815734 CGAACGGAGGGAGTATGTGT 59.184 55.000 0.00 0.00 0.00 3.72
2219 3544 3.383825 ACGGAGGGAGTATGTGTTATGAC 59.616 47.826 0.00 0.00 0.00 3.06
2257 3582 6.639563 AGTTGAAATATTAACATGGGCCAAC 58.360 36.000 11.89 0.00 0.00 3.77
2262 3587 0.956410 TTAACATGGGCCAACGACGG 60.956 55.000 11.89 0.00 0.00 4.79
2283 3608 4.513692 CGGTGGAACTTCTGTCAAAACATA 59.486 41.667 0.00 0.00 36.74 2.29
2284 3609 5.008217 CGGTGGAACTTCTGTCAAAACATAA 59.992 40.000 0.00 0.00 36.74 1.90
2285 3610 6.206498 GGTGGAACTTCTGTCAAAACATAAC 58.794 40.000 0.00 0.00 36.74 1.89
2286 3611 5.907391 GTGGAACTTCTGTCAAAACATAACG 59.093 40.000 0.00 0.00 34.13 3.18
2287 3612 5.008217 TGGAACTTCTGTCAAAACATAACGG 59.992 40.000 0.00 0.00 34.13 4.44
2288 3613 5.008316 GGAACTTCTGTCAAAACATAACGGT 59.992 40.000 0.00 0.00 34.13 4.83
2289 3614 6.445357 AACTTCTGTCAAAACATAACGGTT 57.555 33.333 0.00 0.00 34.13 4.44
2290 3615 5.816919 ACTTCTGTCAAAACATAACGGTTG 58.183 37.500 3.07 0.00 34.13 3.77
2291 3616 4.217754 TCTGTCAAAACATAACGGTTGC 57.782 40.909 3.07 0.00 34.13 4.17
2292 3617 3.880490 TCTGTCAAAACATAACGGTTGCT 59.120 39.130 3.07 0.00 34.13 3.91
2293 3618 5.057819 TCTGTCAAAACATAACGGTTGCTA 58.942 37.500 3.07 0.00 34.13 3.49
2347 3676 6.992063 AAATACTGCAATACACTTCTCCTG 57.008 37.500 0.00 0.00 0.00 3.86
2466 3803 4.660938 GCTTCCAAGGTGGCCCGT 62.661 66.667 0.00 0.00 37.47 5.28
2512 3849 4.880537 CGCTGGGTCTAGCTGCCG 62.881 72.222 0.00 0.00 41.51 5.69
2560 3897 8.876303 ATCAGATGATGAATACTAGCTAGTCA 57.124 34.615 29.28 20.91 42.53 3.41
2611 3949 8.846211 CCAGTTGAGTAATTCCTGTAAGAAAAA 58.154 33.333 0.00 0.00 34.07 1.94
2636 3974 5.674525 AGAACATCATTGTGTATCCGATGT 58.325 37.500 0.00 0.00 46.46 3.06
2724 4064 8.830201 TGTTTTATTCATACAATGCTGCTTTT 57.170 26.923 0.00 0.00 0.00 2.27
2760 4100 2.030805 GCCATCTTGCCGAATATGTTCC 60.031 50.000 0.00 0.00 0.00 3.62
2761 4101 3.213506 CCATCTTGCCGAATATGTTCCA 58.786 45.455 0.00 0.00 0.00 3.53
2776 4116 3.832276 TGTTCCATTGTATTTTCGCTGC 58.168 40.909 0.00 0.00 0.00 5.25
2881 4221 6.983890 ACTCTGTTGTTTCTTTCTCTCTCTTC 59.016 38.462 0.00 0.00 0.00 2.87
2965 4305 2.171659 TGGCACAAACTGTAGTTCCTGA 59.828 45.455 0.00 0.00 37.25 3.86
2979 4320 8.941995 TGTAGTTCCTGACATATATCTAGCTT 57.058 34.615 0.00 0.00 0.00 3.74
2982 4323 6.496565 AGTTCCTGACATATATCTAGCTTGCT 59.503 38.462 0.00 0.00 0.00 3.91
2984 4325 7.637631 TCCTGACATATATCTAGCTTGCTAG 57.362 40.000 20.18 20.18 0.00 3.42
3350 4692 4.632153 ACTTGAGCACGTTTCTTCATACT 58.368 39.130 0.00 0.00 0.00 2.12
3427 4769 3.391296 GGCATATCTCCACCCTAACTCAA 59.609 47.826 0.00 0.00 0.00 3.02
3432 4774 7.635089 GCATATCTCCACCCTAACTCAAGTTAA 60.635 40.741 4.32 0.00 39.70 2.01
3461 4803 6.478512 TGCCACAGGAAATTTAGAACTTTT 57.521 33.333 0.00 0.00 0.00 2.27
3504 4846 9.697990 ATGAAATTTACCAAATAAATGCCCATT 57.302 25.926 0.00 0.00 41.73 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
283 347 5.817816 CGAGCTACATGGAGTCCTTTTATTT 59.182 40.000 11.33 0.00 0.00 1.40
450 1099 1.066656 CAACAACGCATGGTGCATCG 61.067 55.000 2.63 0.00 45.36 3.84
644 1295 1.904287 TGGGCGATTGCATAATACCC 58.096 50.000 7.38 5.59 45.35 3.69
650 1384 1.404748 CATGTGTTGGGCGATTGCATA 59.595 47.619 7.38 0.00 45.35 3.14
708 1444 9.740239 GTCACATCATCAATTTATGCAAGTTAT 57.260 29.630 0.00 0.00 0.00 1.89
863 1619 4.185286 GATGGGCCGGGTGGGTAC 62.185 72.222 2.18 0.00 38.44 3.34
878 1634 0.666913 CGTTCCGTGGATCCGTAGAT 59.333 55.000 7.39 0.00 34.57 1.98
879 1635 1.996786 GCGTTCCGTGGATCCGTAGA 61.997 60.000 7.39 0.00 0.00 2.59
880 1636 1.588139 GCGTTCCGTGGATCCGTAG 60.588 63.158 7.39 0.33 0.00 3.51
881 1637 1.875420 TTGCGTTCCGTGGATCCGTA 61.875 55.000 7.39 3.60 0.00 4.02
882 1638 3.229156 TTGCGTTCCGTGGATCCGT 62.229 57.895 7.39 0.00 0.00 4.69
883 1639 2.433491 TTGCGTTCCGTGGATCCG 60.433 61.111 7.39 0.00 0.00 4.18
884 1640 2.396157 GGTTGCGTTCCGTGGATCC 61.396 63.158 4.20 4.20 0.00 3.36
885 1641 2.396157 GGGTTGCGTTCCGTGGATC 61.396 63.158 0.00 0.00 0.00 3.36
898 1666 3.119388 TCTCGTATTCGTGGTTAGGGTTG 60.119 47.826 0.00 0.00 38.33 3.77
937 1711 0.886490 CCAAGCAGAGGAAGCGTGTT 60.886 55.000 0.00 0.00 39.36 3.32
1035 1815 1.251251 GCTTCACCACCTTGCAGAAT 58.749 50.000 0.00 0.00 0.00 2.40
1201 1984 3.522731 CGTGGAGCGAGAGAGGGG 61.523 72.222 0.00 0.00 44.77 4.79
1213 1996 2.356075 CAAACCGTACCGCGTGGA 60.356 61.111 24.59 2.03 39.21 4.02
1216 1999 0.530431 AAAGACAAACCGTACCGCGT 60.530 50.000 4.92 0.00 39.32 6.01
1236 2019 1.601162 GCTTCGCGGGTACGATTGATA 60.601 52.381 6.13 0.00 42.54 2.15
1237 2020 0.874607 GCTTCGCGGGTACGATTGAT 60.875 55.000 6.13 0.00 42.54 2.57
1239 2022 1.752501 CTGCTTCGCGGGTACGATTG 61.753 60.000 6.13 0.00 42.54 2.67
1292 2105 4.694037 ACTCGCAACCTTAATTTGTCCTAC 59.306 41.667 0.00 0.00 0.00 3.18
1314 2127 5.736951 ATCCCATCATCACTAGCTCTAAC 57.263 43.478 0.00 0.00 0.00 2.34
1322 2135 8.324306 GGATAAGATTCAATCCCATCATCACTA 58.676 37.037 9.82 0.00 36.44 2.74
1331 2144 4.104738 GGACCAGGATAAGATTCAATCCCA 59.895 45.833 12.19 0.00 42.32 4.37
1332 2145 4.507512 GGGACCAGGATAAGATTCAATCCC 60.508 50.000 12.19 0.00 42.32 3.85
1333 2146 4.352298 AGGGACCAGGATAAGATTCAATCC 59.648 45.833 0.00 9.10 41.77 3.01
1345 2158 1.512735 GCCTCTTTAGGGACCAGGAT 58.487 55.000 0.00 0.00 43.87 3.24
1346 2159 0.976073 CGCCTCTTTAGGGACCAGGA 60.976 60.000 0.00 0.00 43.87 3.86
1347 2160 1.522569 CGCCTCTTTAGGGACCAGG 59.477 63.158 0.00 0.00 43.87 4.45
1366 2186 5.007921 TGGATATCAAACATGCTCACAATCG 59.992 40.000 4.83 0.00 0.00 3.34
1395 2218 3.996363 GGCTTGGATCCAAAATTGTTCAC 59.004 43.478 26.87 8.61 35.33 3.18
1396 2219 3.645212 TGGCTTGGATCCAAAATTGTTCA 59.355 39.130 26.87 14.49 35.33 3.18
1397 2220 4.270245 TGGCTTGGATCCAAAATTGTTC 57.730 40.909 26.87 12.45 35.33 3.18
1400 2223 4.005487 TGTTGGCTTGGATCCAAAATTG 57.995 40.909 26.87 16.54 44.36 2.32
1401 2224 4.703379 TTGTTGGCTTGGATCCAAAATT 57.297 36.364 26.87 0.00 44.36 1.82
1402 2225 4.914177 ATTGTTGGCTTGGATCCAAAAT 57.086 36.364 26.87 18.81 44.36 1.82
1404 2227 4.703379 AAATTGTTGGCTTGGATCCAAA 57.297 36.364 26.87 10.88 44.36 3.28
1405 2228 6.667414 AGTATAAATTGTTGGCTTGGATCCAA 59.333 34.615 25.53 25.53 40.98 3.53
1427 2281 3.057315 GTGAGGCGGTACTTGTGTAAGTA 60.057 47.826 0.00 0.00 45.07 2.24
1447 2301 9.965824 AGTGAAAAATACTAGAAATGGTTTGTG 57.034 29.630 0.00 0.00 0.00 3.33
1469 2323 5.575157 AGAGGTCAGTCATTCTTCTAGTGA 58.425 41.667 0.00 0.00 0.00 3.41
1530 2384 0.901580 CCAGGCTGAAACCATTGGCT 60.902 55.000 17.94 0.00 35.69 4.75
1546 2400 5.253330 TGGAAAAGTTAGCTTACCATCCAG 58.747 41.667 14.36 0.00 36.83 3.86
1604 2590 4.795278 GTGAACATCGCAAATGGAGATTTC 59.205 41.667 1.58 0.00 33.37 2.17
1718 2713 1.542915 CAGAAACCATGCCAACTGGAG 59.457 52.381 0.00 0.00 37.22 3.86
1720 2715 1.331214 ACAGAAACCATGCCAACTGG 58.669 50.000 0.00 0.00 39.80 4.00
1762 2757 9.616634 CGATAAATGCAGCATAAAATTATCACT 57.383 29.630 24.51 4.25 31.72 3.41
1831 2833 2.043939 TCTACTCTCCTGCCCCTTGTTA 59.956 50.000 0.00 0.00 0.00 2.41
1838 2840 0.750249 GAAGCTCTACTCTCCTGCCC 59.250 60.000 0.00 0.00 0.00 5.36
1840 2842 2.099098 GACAGAAGCTCTACTCTCCTGC 59.901 54.545 0.00 0.00 0.00 4.85
1879 2881 1.228367 AAAGGCAGCCTGTGGTGAG 60.228 57.895 17.05 0.00 42.66 3.51
1921 2923 7.438160 GCACATGCAGTATTATTCTACACACTA 59.562 37.037 0.00 0.00 41.59 2.74
1922 2924 6.258727 GCACATGCAGTATTATTCTACACACT 59.741 38.462 0.00 0.00 41.59 3.55
1923 2925 6.258727 AGCACATGCAGTATTATTCTACACAC 59.741 38.462 6.64 0.00 45.16 3.82
1924 2926 6.258507 CAGCACATGCAGTATTATTCTACACA 59.741 38.462 6.64 0.00 45.16 3.72
1939 2941 1.819928 ATCGGTTAACAGCACATGCA 58.180 45.000 8.10 0.00 45.16 3.96
1940 2942 2.919666 AATCGGTTAACAGCACATGC 57.080 45.000 8.10 0.00 42.49 4.06
1942 2944 4.585879 AGGTAAATCGGTTAACAGCACAT 58.414 39.130 8.10 0.00 31.10 3.21
1951 3274 6.778834 TGAGACATGTAGGTAAATCGGTTA 57.221 37.500 0.00 0.00 0.00 2.85
1956 3279 6.925610 TGCAATGAGACATGTAGGTAAATC 57.074 37.500 0.00 0.00 0.00 2.17
1999 3322 8.283291 GTGAAGTTAACATCAGAACCACTTAAG 58.717 37.037 13.52 0.00 0.00 1.85
2007 3330 6.355638 CAACGAGTGAAGTTAACATCAGAAC 58.644 40.000 13.52 7.52 0.00 3.01
2034 3357 8.465999 CAGGTACATATCAAAAACCATGCTAAA 58.534 33.333 0.00 0.00 32.43 1.85
2050 3373 5.744171 TCAATGACAAGCACAGGTACATAT 58.256 37.500 0.00 0.00 0.00 1.78
2064 3389 8.408043 AGAATGAAAATACCACTCAATGACAA 57.592 30.769 0.00 0.00 0.00 3.18
2084 3409 9.968870 GAGGGAGTACTAAGTAAATGTAGAATG 57.031 37.037 0.00 0.00 0.00 2.67
2090 3415 5.267587 ACGGAGGGAGTACTAAGTAAATGT 58.732 41.667 0.00 0.00 0.00 2.71
2091 3416 5.848833 ACGGAGGGAGTACTAAGTAAATG 57.151 43.478 0.00 0.00 0.00 2.32
2098 3423 1.281867 TCCGAACGGAGGGAGTACTAA 59.718 52.381 12.04 0.00 39.76 2.24
2101 3426 1.109609 ATTCCGAACGGAGGGAGTAC 58.890 55.000 15.34 0.00 46.06 2.73
2104 3429 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2105 3430 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
2106 3431 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2107 3432 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2108 3433 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
2109 3434 2.030007 ACGACAAGTAATTCCGAACGGA 60.030 45.455 12.04 12.04 43.52 4.69
2110 3435 2.331194 ACGACAAGTAATTCCGAACGG 58.669 47.619 6.94 6.94 0.00 4.44
2111 3436 4.406069 TCTACGACAAGTAATTCCGAACG 58.594 43.478 0.00 0.00 34.45 3.95
2112 3437 6.695292 TTTCTACGACAAGTAATTCCGAAC 57.305 37.500 0.00 0.00 34.45 3.95
2113 3438 6.311935 CCATTTCTACGACAAGTAATTCCGAA 59.688 38.462 0.00 0.00 34.45 4.30
2114 3439 5.808540 CCATTTCTACGACAAGTAATTCCGA 59.191 40.000 0.00 0.00 34.45 4.55
2115 3440 5.808540 TCCATTTCTACGACAAGTAATTCCG 59.191 40.000 0.00 0.00 34.45 4.30
2116 3441 7.280205 ACATCCATTTCTACGACAAGTAATTCC 59.720 37.037 0.00 0.00 34.45 3.01
2117 3442 8.197988 ACATCCATTTCTACGACAAGTAATTC 57.802 34.615 0.00 0.00 34.45 2.17
2118 3443 9.832445 ATACATCCATTTCTACGACAAGTAATT 57.168 29.630 0.00 0.00 34.45 1.40
2119 3444 9.477484 GATACATCCATTTCTACGACAAGTAAT 57.523 33.333 0.00 0.00 34.45 1.89
2120 3445 8.692710 AGATACATCCATTTCTACGACAAGTAA 58.307 33.333 0.00 0.00 34.45 2.24
2121 3446 8.234136 AGATACATCCATTTCTACGACAAGTA 57.766 34.615 0.00 0.00 0.00 2.24
2122 3447 7.113658 AGATACATCCATTTCTACGACAAGT 57.886 36.000 0.00 0.00 0.00 3.16
2123 3448 8.568794 TCTAGATACATCCATTTCTACGACAAG 58.431 37.037 0.00 0.00 0.00 3.16
2124 3449 8.350722 GTCTAGATACATCCATTTCTACGACAA 58.649 37.037 0.00 0.00 0.00 3.18
2125 3450 7.307811 CGTCTAGATACATCCATTTCTACGACA 60.308 40.741 0.00 0.00 0.00 4.35
2126 3451 7.016466 CGTCTAGATACATCCATTTCTACGAC 58.984 42.308 0.00 0.00 0.00 4.34
2127 3452 6.709397 ACGTCTAGATACATCCATTTCTACGA 59.291 38.462 0.00 0.00 29.41 3.43
2128 3453 6.900189 ACGTCTAGATACATCCATTTCTACG 58.100 40.000 0.00 0.00 0.00 3.51
2154 3479 9.542462 CGGAAATGGATGTATCTAGAAGTAAAA 57.458 33.333 0.00 0.00 0.00 1.52
2155 3480 8.920174 TCGGAAATGGATGTATCTAGAAGTAAA 58.080 33.333 0.00 0.00 0.00 2.01
2156 3481 8.473358 TCGGAAATGGATGTATCTAGAAGTAA 57.527 34.615 0.00 0.00 0.00 2.24
2157 3482 7.942894 TCTCGGAAATGGATGTATCTAGAAGTA 59.057 37.037 0.00 0.00 0.00 2.24
2158 3483 6.778069 TCTCGGAAATGGATGTATCTAGAAGT 59.222 38.462 0.00 0.00 0.00 3.01
2159 3484 7.087639 GTCTCGGAAATGGATGTATCTAGAAG 58.912 42.308 0.00 0.00 0.00 2.85
2160 3485 6.549736 TGTCTCGGAAATGGATGTATCTAGAA 59.450 38.462 0.00 0.00 0.00 2.10
2161 3486 6.068670 TGTCTCGGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
2162 3487 6.332735 TGTCTCGGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
2163 3488 6.323996 ACTTGTCTCGGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
2164 3489 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
2165 3490 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
2166 3491 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
2167 3492 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
2168 3493 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
2169 3494 6.238484 GGAATTACTTGTCTCGGAAATGGATG 60.238 42.308 0.00 0.00 0.00 3.51
2170 3495 5.823045 GGAATTACTTGTCTCGGAAATGGAT 59.177 40.000 0.00 0.00 0.00 3.41
2171 3496 5.183228 GGAATTACTTGTCTCGGAAATGGA 58.817 41.667 0.00 0.00 0.00 3.41
2172 3497 4.034048 CGGAATTACTTGTCTCGGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
2173 3498 4.868171 TCGGAATTACTTGTCTCGGAAATG 59.132 41.667 0.00 0.00 0.00 2.32
2174 3499 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
2175 3500 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
2176 3501 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
2177 3502 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
2178 3503 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
2179 3504 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
2180 3505 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
2181 3506 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
2182 3507 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2183 3508 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2184 3509 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2185 3510 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2186 3511 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2187 3512 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2188 3513 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2189 3514 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
2190 3515 1.687123 CATACTCCCTCCGTTCGGAAT 59.313 52.381 14.79 2.14 33.41 3.01
2191 3516 1.108776 CATACTCCCTCCGTTCGGAA 58.891 55.000 14.79 0.00 33.41 4.30
2192 3517 0.033796 ACATACTCCCTCCGTTCGGA 60.034 55.000 13.34 13.34 0.00 4.55
2193 3518 0.102481 CACATACTCCCTCCGTTCGG 59.898 60.000 4.74 4.74 0.00 4.30
2194 3519 0.815734 ACACATACTCCCTCCGTTCG 59.184 55.000 0.00 0.00 0.00 3.95
2195 3520 4.098960 TCATAACACATACTCCCTCCGTTC 59.901 45.833 0.00 0.00 0.00 3.95
2196 3521 4.028131 TCATAACACATACTCCCTCCGTT 58.972 43.478 0.00 0.00 0.00 4.44
2197 3522 3.383825 GTCATAACACATACTCCCTCCGT 59.616 47.826 0.00 0.00 0.00 4.69
2198 3523 3.550233 CGTCATAACACATACTCCCTCCG 60.550 52.174 0.00 0.00 0.00 4.63
2199 3524 3.635373 TCGTCATAACACATACTCCCTCC 59.365 47.826 0.00 0.00 0.00 4.30
2200 3525 4.913335 TCGTCATAACACATACTCCCTC 57.087 45.455 0.00 0.00 0.00 4.30
2201 3526 5.141182 AGATCGTCATAACACATACTCCCT 58.859 41.667 0.00 0.00 0.00 4.20
2202 3527 5.455056 AGATCGTCATAACACATACTCCC 57.545 43.478 0.00 0.00 0.00 4.30
2203 3528 5.009710 TGGAGATCGTCATAACACATACTCC 59.990 44.000 0.00 0.00 40.06 3.85
2204 3529 6.073327 TGGAGATCGTCATAACACATACTC 57.927 41.667 0.00 0.00 0.00 2.59
2205 3530 6.656632 ATGGAGATCGTCATAACACATACT 57.343 37.500 2.66 0.00 0.00 2.12
2206 3531 7.594714 ACTATGGAGATCGTCATAACACATAC 58.405 38.462 10.66 0.00 0.00 2.39
2207 3532 7.761038 ACTATGGAGATCGTCATAACACATA 57.239 36.000 10.66 0.00 0.00 2.29
2208 3533 6.656632 ACTATGGAGATCGTCATAACACAT 57.343 37.500 10.66 0.00 0.00 3.21
2209 3534 7.284716 ACTTACTATGGAGATCGTCATAACACA 59.715 37.037 10.66 0.00 0.00 3.72
2210 3535 7.649973 ACTTACTATGGAGATCGTCATAACAC 58.350 38.462 10.66 0.00 0.00 3.32
2213 3538 8.459911 TCAACTTACTATGGAGATCGTCATAA 57.540 34.615 10.66 1.10 0.00 1.90
2257 3582 0.031585 TGACAGAAGTTCCACCGTCG 59.968 55.000 0.00 0.00 0.00 5.12
2262 3587 5.907391 CGTTATGTTTTGACAGAAGTTCCAC 59.093 40.000 0.00 0.00 0.00 4.02
2323 3648 6.942576 ACAGGAGAAGTGTATTGCAGTATTTT 59.057 34.615 0.00 0.00 0.00 1.82
2347 3676 2.514458 ATTCAGGACATGGACCCAAC 57.486 50.000 0.00 0.00 0.00 3.77
2466 3803 3.320826 TGAACTTCGTTGACATCTCCTGA 59.679 43.478 0.00 0.00 0.00 3.86
2512 3849 3.988379 TTTGTCACCATTCTTGAGCAC 57.012 42.857 0.00 0.00 0.00 4.40
2560 3897 7.040409 GGAAACTCCACTTGATATCAAAACAGT 60.040 37.037 18.47 14.04 36.28 3.55
2573 3910 3.545703 ACTCAACTGGAAACTCCACTTG 58.454 45.455 8.12 8.12 42.67 3.16
2611 3949 7.445121 ACATCGGATACACAATGATGTTCTAT 58.555 34.615 0.61 0.00 45.28 1.98
2617 3955 6.368213 CAATGACATCGGATACACAATGATG 58.632 40.000 0.00 0.00 41.60 3.07
2620 3958 4.576053 ACCAATGACATCGGATACACAATG 59.424 41.667 0.00 0.00 0.00 2.82
2623 3961 3.904800 ACCAATGACATCGGATACACA 57.095 42.857 0.00 0.00 0.00 3.72
2710 4050 7.119262 GGAGAGTTAAGTAAAAGCAGCATTGTA 59.881 37.037 0.00 0.00 0.00 2.41
2714 4054 5.645497 CAGGAGAGTTAAGTAAAAGCAGCAT 59.355 40.000 0.00 0.00 0.00 3.79
2715 4055 4.997395 CAGGAGAGTTAAGTAAAAGCAGCA 59.003 41.667 0.00 0.00 0.00 4.41
2718 4058 4.324267 GCCAGGAGAGTTAAGTAAAAGCA 58.676 43.478 0.00 0.00 0.00 3.91
2724 4064 3.995636 AGATGGCCAGGAGAGTTAAGTA 58.004 45.455 13.05 0.00 0.00 2.24
2730 4070 1.606531 GCAAGATGGCCAGGAGAGT 59.393 57.895 13.05 0.00 0.00 3.24
2760 4100 3.861113 AGCAATGCAGCGAAAATACAATG 59.139 39.130 8.35 0.00 40.15 2.82
2761 4101 4.114058 AGCAATGCAGCGAAAATACAAT 57.886 36.364 8.35 0.00 40.15 2.71
2776 4116 5.278463 GCACACCCTGGTATTATTAGCAATG 60.278 44.000 0.00 1.32 35.52 2.82
2824 4164 7.194607 TCTGCAAGTTCTTTAGATTTCAGTG 57.805 36.000 0.00 0.00 33.76 3.66
2832 4172 7.179338 AGTCCTCTTATCTGCAAGTTCTTTAGA 59.821 37.037 0.00 0.00 33.76 2.10
2881 4221 5.452078 TTAACCAGAACTGCTTGATTTGG 57.548 39.130 0.00 0.00 0.00 3.28
3281 4622 3.438183 TCAGAGTCTTTGTACTACCCCC 58.562 50.000 0.00 0.00 0.00 5.40
3282 4623 4.621038 GCTTCAGAGTCTTTGTACTACCCC 60.621 50.000 0.00 0.00 0.00 4.95
3283 4624 4.021368 TGCTTCAGAGTCTTTGTACTACCC 60.021 45.833 0.00 0.00 0.00 3.69
3284 4625 5.135508 TGCTTCAGAGTCTTTGTACTACC 57.864 43.478 0.00 0.00 0.00 3.18
3285 4626 6.529829 CAGATGCTTCAGAGTCTTTGTACTAC 59.470 42.308 2.07 0.00 0.00 2.73
3286 4627 6.350528 CCAGATGCTTCAGAGTCTTTGTACTA 60.351 42.308 2.07 0.00 0.00 1.82
3287 4628 5.477510 CAGATGCTTCAGAGTCTTTGTACT 58.522 41.667 2.07 0.00 0.00 2.73
3288 4629 4.629200 CCAGATGCTTCAGAGTCTTTGTAC 59.371 45.833 2.07 0.00 0.00 2.90
3289 4630 4.284490 ACCAGATGCTTCAGAGTCTTTGTA 59.716 41.667 2.07 0.00 0.00 2.41
3290 4631 3.072184 ACCAGATGCTTCAGAGTCTTTGT 59.928 43.478 2.07 0.00 0.00 2.83
3291 4632 3.436015 CACCAGATGCTTCAGAGTCTTTG 59.564 47.826 2.07 0.00 0.00 2.77
3292 4633 3.326006 TCACCAGATGCTTCAGAGTCTTT 59.674 43.478 2.07 0.00 0.00 2.52
3350 4692 8.621073 TGGCTAGATCTGGAGGTATTAGTAATA 58.379 37.037 10.75 0.00 0.00 0.98
3361 4703 0.324285 GCCATGGCTAGATCTGGAGG 59.676 60.000 29.98 6.60 38.26 4.30
3427 4769 1.144913 TCCTGTGGCAAAGGCTTAACT 59.855 47.619 19.53 0.00 40.87 2.24
3432 4774 1.720781 AATTTCCTGTGGCAAAGGCT 58.279 45.000 19.53 3.16 40.87 4.58
3478 4820 9.697990 AATGGGCATTTATTTGGTAAATTTCAT 57.302 25.926 0.00 0.00 40.23 2.57


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

AutoCloner maintained by Alex Coulton.