Multiple sequence alignment - TraesCS4A01G006900

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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 TraesCS4A01G006900 chr4A 100.000 7300 0 0 1 7300 4595150 4587851 0.000000e+00 13481.0
1 TraesCS4A01G006900 chr4A 92.784 97 6 1 1383 1478 45361081 45361177 9.880000e-29 139.0
2 TraesCS4A01G006900 chr4D 94.062 3890 133 33 3468 7300 466018463 466022311 0.000000e+00 5814.0
3 TraesCS4A01G006900 chr4D 92.609 2706 108 40 736 3387 466015750 466018417 0.000000e+00 3805.0
4 TraesCS4A01G006900 chr4D 94.096 271 8 4 355 618 466015234 466015503 8.820000e-109 405.0
5 TraesCS4A01G006900 chr4D 85.634 355 19 17 1 333 466014817 466015161 1.950000e-90 344.0
6 TraesCS4A01G006900 chr4D 88.710 124 11 1 623 743 466015582 466015705 1.640000e-31 148.0
7 TraesCS4A01G006900 chr4B 94.748 3389 114 18 3841 7197 583478088 583481444 0.000000e+00 5214.0
8 TraesCS4A01G006900 chr4B 92.630 2836 104 48 630 3387 583474737 583477545 0.000000e+00 3982.0
9 TraesCS4A01G006900 chr4B 97.233 253 7 0 3504 3756 583477624 583477876 5.230000e-116 429.0
10 TraesCS4A01G006900 chr4B 90.511 274 16 5 355 626 583474013 583474278 3.240000e-93 353.0
11 TraesCS4A01G006900 chr4B 92.233 206 13 3 10 212 583473616 583473821 9.270000e-74 289.0
12 TraesCS4A01G006900 chr4B 93.421 76 2 1 7225 7300 583481443 583481515 7.740000e-20 110.0
13 TraesCS4A01G006900 chr4B 94.203 69 4 0 3756 3824 583477901 583477969 1.000000e-18 106.0
14 TraesCS4A01G006900 chr3D 91.463 164 12 1 1346 1507 330252908 330252745 2.650000e-54 224.0
15 TraesCS4A01G006900 chr5D 86.124 209 9 4 1346 1552 217742119 217742309 2.670000e-49 207.0
16 TraesCS4A01G006900 chr5D 100.000 29 0 0 1580 1608 524485159 524485187 4.000000e-03 54.7
17 TraesCS4A01G006900 chr6D 76.307 287 62 6 3848 4131 353350357 353350640 1.640000e-31 148.0
18 TraesCS4A01G006900 chr6B 76.307 287 62 6 3848 4131 525114066 525113783 1.640000e-31 148.0
19 TraesCS4A01G006900 chr1B 90.179 112 11 0 1914 2025 316642451 316642340 5.900000e-31 147.0
20 TraesCS4A01G006900 chr1A 93.258 89 5 1 1395 1482 314478186 314478274 5.940000e-26 130.0
21 TraesCS4A01G006900 chr6A 75.000 288 64 7 3848 4131 489228513 489228230 7.690000e-25 126.0
22 TraesCS4A01G006900 chr5B 89.888 89 8 1 1395 1482 498069660 498069572 5.990000e-21 113.0
23 TraesCS4A01G006900 chr7D 83.969 131 1 5 1492 1621 12550395 12550284 2.780000e-19 108.0
24 TraesCS4A01G006900 chr7D 96.970 33 1 0 1577 1609 12550017 12549985 1.000000e-03 56.5


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 TraesCS4A01G006900 chr4A 4587851 4595150 7299 True 13481.000000 13481 100.000000 1 7300 1 chr4A.!!$R1 7299
1 TraesCS4A01G006900 chr4D 466014817 466022311 7494 False 2103.200000 5814 91.022200 1 7300 5 chr4D.!!$F1 7299
2 TraesCS4A01G006900 chr4B 583473616 583481515 7899 False 1497.571429 5214 93.568429 10 7300 7 chr4B.!!$F1 7290

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
814 1423 0.636733 GTCAAATCGCAGCGCAAATG 59.363 50.0 10.87 6.65 0.00 2.32 F
2057 2696 0.109086 CACATCGTGCCTCTCGTTCT 60.109 55.0 0.00 0.00 0.00 3.01 F
2059 2698 0.171231 CATCGTGCCTCTCGTTCTGA 59.829 55.0 0.00 0.00 0.00 3.27 F
2066 2705 0.179089 CCTCTCGTTCTGAGCCATGG 60.179 60.0 7.63 7.63 44.86 3.66 F
3410 4080 0.327924 AATCACCATGGAACCGCTCA 59.672 50.0 21.47 0.00 0.00 4.26 F
4321 5146 0.178987 GCGATACAGGAGGAGGAGGA 60.179 60.0 0.00 0.00 0.00 3.71 F
4427 5252 0.609131 CGTTGCTCATCCTGGGGTTT 60.609 55.0 0.00 0.00 0.00 3.27 F
5720 6545 0.042708 CCGAAATCGAGAATGCTGCG 60.043 55.0 4.04 0.00 43.02 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2377 3019 0.036952 GCAGTTCAGGCAGAGTGCTA 60.037 55.000 8.48 0.00 44.28 3.49 R
3428 4098 0.036765 ATCGTACGTGCAACCATGGT 60.037 50.000 13.00 13.00 32.11 3.55 R
3431 4101 0.248012 TCCATCGTACGTGCAACCAT 59.752 50.000 16.05 0.00 0.00 3.55 R
3433 4103 0.650512 CATCCATCGTACGTGCAACC 59.349 55.000 16.05 0.00 0.00 3.77 R
4421 5246 0.033208 TGATGCCCATGAGAAACCCC 60.033 55.000 0.00 0.00 0.00 4.95 R
5720 6545 0.038166 TGTGGATGTTGGCCTCCTTC 59.962 55.000 3.32 1.91 31.66 3.46 R
5936 6762 2.038295 CCCAACCTGCCAAAAATAAGCA 59.962 45.455 0.00 0.00 34.79 3.91 R
6783 7614 0.107312 GATGTCTGTGGAGCTGGCAT 60.107 55.000 0.00 0.00 42.73 4.40 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
37 41 1.968540 GGCTTGACTGGGTGAGTGC 60.969 63.158 0.00 0.00 33.83 4.40
74 78 1.131315 GAAATCCACGAGCCTGCTTTC 59.869 52.381 0.00 0.00 0.00 2.62
76 80 1.557269 ATCCACGAGCCTGCTTTCCT 61.557 55.000 0.00 0.00 0.00 3.36
82 86 1.068954 CGAGCCTGCTTTCCTTTGAAC 60.069 52.381 0.00 0.00 0.00 3.18
84 88 2.560105 GAGCCTGCTTTCCTTTGAACAT 59.440 45.455 0.00 0.00 0.00 2.71
95 102 7.468631 GCTTTCCTTTGAACATGACACTTTCTA 60.469 37.037 0.00 0.00 0.00 2.10
203 210 1.714794 CAGCACTACCTGAAGAACCG 58.285 55.000 0.00 0.00 34.77 4.44
205 212 1.000955 AGCACTACCTGAAGAACCGTG 59.999 52.381 0.00 0.00 0.00 4.94
206 213 1.270147 GCACTACCTGAAGAACCGTGT 60.270 52.381 0.00 0.00 0.00 4.49
208 215 3.463944 CACTACCTGAAGAACCGTGTTT 58.536 45.455 0.00 0.00 0.00 2.83
236 243 5.845391 TTTTTGAGGAAATGAAGAACCGT 57.155 34.783 0.00 0.00 0.00 4.83
238 245 3.485463 TGAGGAAATGAAGAACCGTGT 57.515 42.857 0.00 0.00 0.00 4.49
239 246 3.815809 TGAGGAAATGAAGAACCGTGTT 58.184 40.909 0.00 0.00 0.00 3.32
240 247 4.204012 TGAGGAAATGAAGAACCGTGTTT 58.796 39.130 0.00 0.00 0.00 2.83
241 248 4.642885 TGAGGAAATGAAGAACCGTGTTTT 59.357 37.500 0.00 0.00 0.00 2.43
242 249 4.932146 AGGAAATGAAGAACCGTGTTTTG 58.068 39.130 0.00 0.00 0.00 2.44
245 252 5.808030 GGAAATGAAGAACCGTGTTTTGAAA 59.192 36.000 0.00 0.00 0.00 2.69
247 254 3.749404 TGAAGAACCGTGTTTTGAAACG 58.251 40.909 2.53 0.00 41.74 3.60
248 255 3.436015 TGAAGAACCGTGTTTTGAAACGA 59.564 39.130 0.00 0.00 42.32 3.85
249 256 4.083431 TGAAGAACCGTGTTTTGAAACGAA 60.083 37.500 0.00 0.00 42.32 3.85
250 257 4.625972 AGAACCGTGTTTTGAAACGAAT 57.374 36.364 0.00 0.00 42.32 3.34
280 301 8.887717 ACAGCAGATAATCATACTGTTCTTTTC 58.112 33.333 0.00 0.00 34.89 2.29
287 308 9.774742 ATAATCATACTGTTCTTTTCTTTTCGC 57.225 29.630 0.00 0.00 0.00 4.70
288 309 6.861065 TCATACTGTTCTTTTCTTTTCGCT 57.139 33.333 0.00 0.00 0.00 4.93
289 310 7.259290 TCATACTGTTCTTTTCTTTTCGCTT 57.741 32.000 0.00 0.00 0.00 4.68
290 311 7.132213 TCATACTGTTCTTTTCTTTTCGCTTG 58.868 34.615 0.00 0.00 0.00 4.01
291 312 4.105486 ACTGTTCTTTTCTTTTCGCTTGC 58.895 39.130 0.00 0.00 0.00 4.01
292 313 4.142381 ACTGTTCTTTTCTTTTCGCTTGCT 60.142 37.500 0.00 0.00 0.00 3.91
313 334 5.693555 TGCTTTGCGAGTCAGATAATCATAG 59.306 40.000 0.00 0.00 0.00 2.23
335 356 4.217118 AGTGCTGCTTTCCAAATCTTACTG 59.783 41.667 0.00 0.00 0.00 2.74
337 358 3.057315 GCTGCTTTCCAAATCTTACTGCA 60.057 43.478 0.00 0.00 0.00 4.41
338 359 4.730657 CTGCTTTCCAAATCTTACTGCAG 58.269 43.478 13.48 13.48 39.16 4.41
341 362 5.767665 TGCTTTCCAAATCTTACTGCAGTAA 59.232 36.000 31.78 31.78 38.10 2.24
377 453 1.327690 TGTTCGTAGGCTAGCTGGGG 61.328 60.000 15.72 2.41 0.00 4.96
391 467 0.687354 CTGGGGATATTCTGGGACGG 59.313 60.000 0.00 0.00 0.00 4.79
517 594 1.077212 CTTGGTGGCAGGCTGCTAT 60.077 57.895 35.73 0.00 44.28 2.97
557 637 9.163899 TCTAGTACATATCCGAGTACATTCATC 57.836 37.037 0.00 0.00 42.26 2.92
565 645 7.730364 ATCCGAGTACATTCATCCATTAAAC 57.270 36.000 0.00 0.00 0.00 2.01
625 1169 6.384224 TGATCACATCAAAGAAACAAGCATC 58.616 36.000 0.00 0.00 36.11 3.91
628 1172 4.380678 CACATCAAAGAAACAAGCATCGTG 59.619 41.667 0.00 0.00 0.00 4.35
657 1201 1.134068 GGCAACAGGGTTCCTATCTCC 60.134 57.143 0.00 0.00 29.64 3.71
720 1264 2.699954 CACAGCTCGGACTTGGTAAAT 58.300 47.619 0.00 0.00 0.00 1.40
735 1279 8.644318 ACTTGGTAAATCATCAAGTACGTATC 57.356 34.615 0.00 0.00 46.12 2.24
803 1404 2.298300 GCACACGAAACAGTCAAATCG 58.702 47.619 0.00 0.00 40.90 3.34
807 1408 1.069906 ACGAAACAGTCAAATCGCAGC 60.070 47.619 0.00 0.00 38.80 5.25
814 1423 0.636733 GTCAAATCGCAGCGCAAATG 59.363 50.000 10.87 6.65 0.00 2.32
857 1469 1.168714 GCACCTGGCAGTAGAAAAGG 58.831 55.000 14.43 0.00 43.97 3.11
986 1598 4.717313 GGACCCAACGCCACCTCC 62.717 72.222 0.00 0.00 0.00 4.30
1560 2181 2.359169 GGACAGGGCGATGGTGAGA 61.359 63.158 0.00 0.00 0.00 3.27
1827 2466 0.736325 CCGGGCTGTTCAAGTACTCG 60.736 60.000 0.00 0.00 0.00 4.18
1965 2604 2.862536 CGACAAGTCGCAGATGATGAAT 59.137 45.455 9.85 0.00 46.50 2.57
1972 2611 1.524355 CGCAGATGATGAATGACGTCC 59.476 52.381 14.12 0.00 33.92 4.79
2042 2681 1.511305 CGTACCTCGGTGAGCACAT 59.489 57.895 2.75 0.00 35.71 3.21
2056 2695 2.363807 CACATCGTGCCTCTCGTTC 58.636 57.895 0.00 0.00 0.00 3.95
2057 2696 0.109086 CACATCGTGCCTCTCGTTCT 60.109 55.000 0.00 0.00 0.00 3.01
2058 2697 0.109086 ACATCGTGCCTCTCGTTCTG 60.109 55.000 0.00 0.00 0.00 3.02
2059 2698 0.171231 CATCGTGCCTCTCGTTCTGA 59.829 55.000 0.00 0.00 0.00 3.27
2060 2699 0.453793 ATCGTGCCTCTCGTTCTGAG 59.546 55.000 0.00 0.00 46.72 3.35
2061 2700 1.803519 CGTGCCTCTCGTTCTGAGC 60.804 63.158 0.00 0.00 44.86 4.26
2062 2701 1.446966 GTGCCTCTCGTTCTGAGCC 60.447 63.158 0.00 0.00 44.86 4.70
2063 2702 1.908299 TGCCTCTCGTTCTGAGCCA 60.908 57.895 0.00 0.00 44.86 4.75
2064 2703 1.260538 TGCCTCTCGTTCTGAGCCAT 61.261 55.000 0.00 0.00 44.86 4.40
2065 2704 0.809241 GCCTCTCGTTCTGAGCCATG 60.809 60.000 0.00 0.00 44.86 3.66
2066 2705 0.179089 CCTCTCGTTCTGAGCCATGG 60.179 60.000 7.63 7.63 44.86 3.66
2067 2706 0.809241 CTCTCGTTCTGAGCCATGGC 60.809 60.000 30.12 30.12 44.86 4.40
2068 2707 1.078918 CTCGTTCTGAGCCATGGCA 60.079 57.895 37.18 18.01 44.88 4.92
2069 2708 1.364626 CTCGTTCTGAGCCATGGCAC 61.365 60.000 37.18 31.28 44.88 5.01
2070 2709 3.966329 CTCGTTCTGAGCCATGGCACA 62.966 57.143 37.18 33.97 44.88 4.57
2085 2724 1.129251 GGCACACTGACATGTCATTCG 59.871 52.381 28.00 18.83 39.13 3.34
2095 2734 2.356695 ACATGTCATTCGTCATGCATGG 59.643 45.455 25.97 11.53 43.99 3.66
2105 2744 2.547430 CGTCATGCATGGATCTACTGCT 60.547 50.000 25.97 0.00 36.84 4.24
2333 2973 7.100458 GTAACCAAGATTACCAATTGCTGAT 57.900 36.000 0.00 0.00 0.00 2.90
2334 2974 5.587388 ACCAAGATTACCAATTGCTGATG 57.413 39.130 0.00 0.00 0.00 3.07
2361 3001 3.191669 TGTTCGTATCGATCGGCAAAAT 58.808 40.909 16.41 3.22 35.23 1.82
2363 3003 4.986034 TGTTCGTATCGATCGGCAAAATAT 59.014 37.500 16.41 1.66 35.23 1.28
2366 3006 7.008901 TGTTCGTATCGATCGGCAAAATATATC 59.991 37.037 16.41 0.00 35.23 1.63
2367 3007 6.792326 TCGTATCGATCGGCAAAATATATCT 58.208 36.000 16.41 0.00 0.00 1.98
2368 3008 6.691388 TCGTATCGATCGGCAAAATATATCTG 59.309 38.462 16.41 0.00 0.00 2.90
2376 3018 5.869344 TCGGCAAAATATATCTGAATCCTCG 59.131 40.000 0.00 0.00 0.00 4.63
2377 3019 5.639506 CGGCAAAATATATCTGAATCCTCGT 59.360 40.000 0.00 0.00 0.00 4.18
2381 3023 7.331934 GCAAAATATATCTGAATCCTCGTAGCA 59.668 37.037 0.00 0.00 0.00 3.49
2410 3052 2.807967 TGAACTGCTGTACTTGTGCATC 59.192 45.455 0.00 0.00 36.07 3.91
2449 3091 1.946745 TTGTGCATCACGTCTTCACA 58.053 45.000 0.00 5.63 37.14 3.58
2470 3112 0.454600 TCATCTTCGGCTACGTGGTC 59.545 55.000 0.00 0.00 41.85 4.02
2591 3233 2.896168 CCGCCAACGAAGAGGTAATTA 58.104 47.619 0.00 0.00 43.93 1.40
2598 3240 5.577164 CCAACGAAGAGGTAATTAGTGTCTG 59.423 44.000 0.00 0.00 0.00 3.51
2599 3241 6.387465 CAACGAAGAGGTAATTAGTGTCTGA 58.613 40.000 0.00 0.00 0.00 3.27
2633 3282 3.181477 TGGAAAACAAACATGCAGTCTGG 60.181 43.478 1.14 0.00 0.00 3.86
2637 3286 2.936202 ACAAACATGCAGTCTGGACTT 58.064 42.857 1.14 0.00 40.20 3.01
2638 3287 2.620115 ACAAACATGCAGTCTGGACTTG 59.380 45.455 1.14 6.55 40.20 3.16
2639 3288 1.901591 AACATGCAGTCTGGACTTGG 58.098 50.000 1.14 0.00 40.20 3.61
2640 3289 0.767375 ACATGCAGTCTGGACTTGGT 59.233 50.000 1.14 0.00 40.20 3.67
2641 3290 1.143684 ACATGCAGTCTGGACTTGGTT 59.856 47.619 1.14 0.00 40.20 3.67
2642 3291 1.808945 CATGCAGTCTGGACTTGGTTC 59.191 52.381 1.14 0.00 40.20 3.62
2644 3293 1.202687 TGCAGTCTGGACTTGGTTCTG 60.203 52.381 1.14 0.00 40.20 3.02
2645 3294 1.070758 GCAGTCTGGACTTGGTTCTGA 59.929 52.381 1.14 0.00 40.20 3.27
2646 3295 2.485479 GCAGTCTGGACTTGGTTCTGAA 60.485 50.000 1.14 0.00 40.20 3.02
2659 3312 5.488262 TGGTTCTGAACTTCTGATCATCA 57.512 39.130 19.05 0.00 0.00 3.07
2660 3313 6.058553 TGGTTCTGAACTTCTGATCATCAT 57.941 37.500 19.05 0.00 0.00 2.45
2661 3314 5.878669 TGGTTCTGAACTTCTGATCATCATG 59.121 40.000 19.05 0.00 0.00 3.07
2662 3315 5.296283 GGTTCTGAACTTCTGATCATCATGG 59.704 44.000 19.05 0.00 0.00 3.66
2664 3317 6.496144 TCTGAACTTCTGATCATCATGGAT 57.504 37.500 0.00 0.00 0.00 3.41
2743 3396 2.645510 GACGGTGCTGTCGTTCGTG 61.646 63.158 0.00 0.00 41.22 4.35
2752 3405 0.526211 TGTCGTTCGTGATGGAGGAG 59.474 55.000 0.00 0.00 0.00 3.69
3011 3677 1.941209 GCGCCATCACTTTCTCTGTCA 60.941 52.381 0.00 0.00 0.00 3.58
3023 3689 3.944055 TCTCTGTCACTAGGCTTGTTC 57.056 47.619 0.00 0.00 0.00 3.18
3029 3695 1.376037 ACTAGGCTTGTTCGCTGGC 60.376 57.895 0.00 0.00 0.00 4.85
3049 3715 3.320826 GGCTGTAACTTTGGAAATGGTGT 59.679 43.478 0.00 0.00 0.00 4.16
3050 3716 4.298332 GCTGTAACTTTGGAAATGGTGTG 58.702 43.478 0.00 0.00 0.00 3.82
3053 3719 1.398692 ACTTTGGAAATGGTGTGCGT 58.601 45.000 0.00 0.00 0.00 5.24
3267 3937 2.725008 CCGGAGTCGCTCATCCTC 59.275 66.667 0.00 0.00 33.12 3.71
3378 4048 0.614134 AGAGGTTCTACGACCCCACC 60.614 60.000 0.00 0.00 40.73 4.61
3387 4057 3.455469 GACCCCACCCGAGGTACG 61.455 72.222 0.00 0.00 36.17 3.67
3389 4059 2.044053 CCCCACCCGAGGTACGTA 60.044 66.667 0.00 0.00 40.78 3.57
3390 4060 2.418083 CCCCACCCGAGGTACGTAC 61.418 68.421 17.56 17.56 40.78 3.67
3391 4061 1.678635 CCCACCCGAGGTACGTACA 60.679 63.158 26.02 0.00 40.78 2.90
3392 4062 1.250154 CCCACCCGAGGTACGTACAA 61.250 60.000 26.02 0.00 40.78 2.41
3393 4063 0.819582 CCACCCGAGGTACGTACAAT 59.180 55.000 26.02 14.56 40.78 2.71
3394 4064 1.202336 CCACCCGAGGTACGTACAATC 60.202 57.143 26.02 20.56 40.78 2.67
3395 4065 1.473677 CACCCGAGGTACGTACAATCA 59.526 52.381 26.02 0.00 40.78 2.57
3396 4066 1.474077 ACCCGAGGTACGTACAATCAC 59.526 52.381 26.02 9.22 40.78 3.06
3398 4068 1.473677 CCGAGGTACGTACAATCACCA 59.526 52.381 26.02 0.00 40.78 4.17
3399 4069 2.100252 CCGAGGTACGTACAATCACCAT 59.900 50.000 26.02 1.80 40.78 3.55
3400 4070 3.113322 CGAGGTACGTACAATCACCATG 58.887 50.000 26.02 7.59 37.22 3.66
3401 4071 3.454375 GAGGTACGTACAATCACCATGG 58.546 50.000 26.02 11.19 33.27 3.66
3402 4072 3.101437 AGGTACGTACAATCACCATGGA 58.899 45.455 26.02 0.00 33.27 3.41
3403 4073 3.516300 AGGTACGTACAATCACCATGGAA 59.484 43.478 26.02 6.38 33.27 3.53
3404 4074 3.619929 GGTACGTACAATCACCATGGAAC 59.380 47.826 26.02 3.75 0.00 3.62
3406 4076 1.663643 CGTACAATCACCATGGAACCG 59.336 52.381 21.47 5.06 0.00 4.44
3407 4077 1.400494 GTACAATCACCATGGAACCGC 59.600 52.381 21.47 0.00 0.00 5.68
3409 4079 0.734889 CAATCACCATGGAACCGCTC 59.265 55.000 21.47 0.00 0.00 5.03
3410 4080 0.327924 AATCACCATGGAACCGCTCA 59.672 50.000 21.47 0.00 0.00 4.26
3411 4081 0.548031 ATCACCATGGAACCGCTCAT 59.452 50.000 21.47 0.00 0.00 2.90
3412 4082 0.327924 TCACCATGGAACCGCTCATT 59.672 50.000 21.47 0.00 0.00 2.57
3413 4083 0.734889 CACCATGGAACCGCTCATTC 59.265 55.000 21.47 0.00 0.00 2.67
3414 4084 0.394352 ACCATGGAACCGCTCATTCC 60.394 55.000 21.47 4.07 45.13 3.01
3416 4086 1.153168 ATGGAACCGCTCATTCCCG 60.153 57.895 7.73 0.00 44.41 5.14
3417 4087 1.910580 ATGGAACCGCTCATTCCCGT 61.911 55.000 7.73 0.00 44.41 5.28
3418 4088 2.106683 GGAACCGCTCATTCCCGTG 61.107 63.158 0.21 0.00 39.91 4.94
3419 4089 2.746277 AACCGCTCATTCCCGTGC 60.746 61.111 0.00 0.00 0.00 5.34
3424 4094 3.499737 CTCATTCCCGTGCGCCAC 61.500 66.667 4.18 1.96 0.00 5.01
3433 4103 3.496131 GTGCGCCACCGTACCATG 61.496 66.667 4.18 0.00 43.05 3.66
3465 4135 2.125912 GGATGATCGATCGGCCGG 60.126 66.667 27.83 9.82 30.87 6.13
3466 4136 2.811317 GATGATCGATCGGCCGGC 60.811 66.667 27.83 21.18 0.00 6.13
3481 4174 0.729140 CCGGCGAAGTTCATGCAAAC 60.729 55.000 9.30 0.00 0.00 2.93
3581 4274 4.899239 CAGATCGGGCTGGTCGGC 62.899 72.222 0.00 0.00 37.49 5.54
3653 4346 2.876645 GAGAACGCGACGAGGCAG 60.877 66.667 15.93 0.00 0.00 4.85
3752 4473 6.215636 AGGTGACTAGATCCATTAACCAAACT 59.784 38.462 0.00 0.00 40.61 2.66
3753 4474 6.316390 GGTGACTAGATCCATTAACCAAACTG 59.684 42.308 0.00 0.00 0.00 3.16
3754 4475 7.103641 GTGACTAGATCCATTAACCAAACTGA 58.896 38.462 0.00 0.00 0.00 3.41
3799 4520 2.422127 GCCTCACTAGTCTGTCTCTGTC 59.578 54.545 0.00 0.00 0.00 3.51
3807 4528 0.615331 TCTGTCTCTGTCAATGGGCC 59.385 55.000 0.00 0.00 0.00 5.80
3814 4535 4.424711 GTCAATGGGCCCGCCAGA 62.425 66.667 19.37 9.75 37.98 3.86
3824 4545 0.180406 GCCCGCCAGAATCTCCTAAA 59.820 55.000 0.00 0.00 0.00 1.85
3825 4546 1.954927 CCCGCCAGAATCTCCTAAAC 58.045 55.000 0.00 0.00 0.00 2.01
3828 4549 3.343617 CCGCCAGAATCTCCTAAACAAA 58.656 45.455 0.00 0.00 0.00 2.83
3829 4550 3.947834 CCGCCAGAATCTCCTAAACAAAT 59.052 43.478 0.00 0.00 0.00 2.32
3830 4551 4.399303 CCGCCAGAATCTCCTAAACAAATT 59.601 41.667 0.00 0.00 0.00 1.82
3831 4552 5.449177 CCGCCAGAATCTCCTAAACAAATTC 60.449 44.000 0.00 0.00 0.00 2.17
4173 4998 4.116328 TCAAGCTCGCCTCCGACG 62.116 66.667 0.00 0.00 38.82 5.12
4321 5146 0.178987 GCGATACAGGAGGAGGAGGA 60.179 60.000 0.00 0.00 0.00 3.71
4322 5147 1.904287 CGATACAGGAGGAGGAGGAG 58.096 60.000 0.00 0.00 0.00 3.69
4323 5148 1.546773 CGATACAGGAGGAGGAGGAGG 60.547 61.905 0.00 0.00 0.00 4.30
4328 5153 2.835895 GAGGAGGAGGAGGCGGAC 60.836 72.222 0.00 0.00 0.00 4.79
4415 5240 2.747855 CAGGAAGGGCCGTTGCTC 60.748 66.667 26.94 8.12 43.43 4.26
4421 5246 2.825836 GGGCCGTTGCTCATCCTG 60.826 66.667 0.00 0.00 38.13 3.86
4427 5252 0.609131 CGTTGCTCATCCTGGGGTTT 60.609 55.000 0.00 0.00 0.00 3.27
5219 6044 3.708631 TGTCCAAGATCTTCCTCATCCTC 59.291 47.826 4.57 0.00 0.00 3.71
5318 6143 0.824109 TACTGTCCATCCTGAAGCGG 59.176 55.000 0.00 0.00 0.00 5.52
5345 6170 1.519455 GATCAACGAGGAGGGCACG 60.519 63.158 0.00 0.00 0.00 5.34
5387 6212 1.079405 GAAGCCGATGGACGTGGAA 60.079 57.895 0.00 0.00 40.78 3.53
5663 6488 2.169352 CCTGTTCAGTGGGTCTATCAGG 59.831 54.545 0.00 0.00 34.23 3.86
5720 6545 0.042708 CCGAAATCGAGAATGCTGCG 60.043 55.000 4.04 0.00 43.02 5.18
5844 6669 5.012354 ACAAATCTCAACTTCCAATGCCAAT 59.988 36.000 0.00 0.00 0.00 3.16
5852 6677 5.391312 ACTTCCAATGCCAATCTTAACAC 57.609 39.130 0.00 0.00 0.00 3.32
5917 6742 7.604164 TGTTGTTTACATGGTTTTCACACATTT 59.396 29.630 0.00 0.00 0.00 2.32
5999 6825 1.134551 GGTGGTCAGAAGCAGAGGATC 60.135 57.143 0.00 0.00 32.53 3.36
6002 6828 0.529555 GTCAGAAGCAGAGGATCGCC 60.530 60.000 0.00 0.00 42.67 5.54
6164 6990 2.024871 CTCTCCACGATCCGCGAC 59.975 66.667 8.23 0.00 44.57 5.19
6302 7128 2.105128 CAGGCCTTCGCGTAGAGG 59.895 66.667 14.87 16.42 35.02 3.69
6423 7250 3.706600 TTCGGCAATGTTACCTTACCT 57.293 42.857 0.00 0.00 0.00 3.08
6425 7252 4.395959 TCGGCAATGTTACCTTACCTAG 57.604 45.455 0.00 0.00 0.00 3.02
6427 7254 4.117685 CGGCAATGTTACCTTACCTAGAC 58.882 47.826 0.00 0.00 0.00 2.59
6428 7255 4.449131 GGCAATGTTACCTTACCTAGACC 58.551 47.826 0.00 0.00 0.00 3.85
6429 7256 4.080751 GGCAATGTTACCTTACCTAGACCA 60.081 45.833 0.00 0.00 0.00 4.02
6430 7257 4.874396 GCAATGTTACCTTACCTAGACCAC 59.126 45.833 0.00 0.00 0.00 4.16
6431 7258 5.570034 GCAATGTTACCTTACCTAGACCACA 60.570 44.000 0.00 0.00 0.00 4.17
6432 7259 6.469410 CAATGTTACCTTACCTAGACCACAA 58.531 40.000 0.00 0.00 0.00 3.33
6433 7260 5.733620 TGTTACCTTACCTAGACCACAAG 57.266 43.478 0.00 0.00 0.00 3.16
6434 7261 5.396485 TGTTACCTTACCTAGACCACAAGA 58.604 41.667 0.00 0.00 0.00 3.02
6435 7262 6.021030 TGTTACCTTACCTAGACCACAAGAT 58.979 40.000 0.00 0.00 0.00 2.40
6448 7275 7.856145 AGACCACAAGATGATGAATAAACTC 57.144 36.000 0.00 0.00 0.00 3.01
6473 7300 6.450545 TGCGAGAATACAAGGATTAGATGAG 58.549 40.000 0.00 0.00 0.00 2.90
6475 7302 6.584563 GCGAGAATACAAGGATTAGATGAGAC 59.415 42.308 0.00 0.00 0.00 3.36
6502 7329 8.902806 GTCCATTTTCACAATATATGAACTCCA 58.097 33.333 2.55 0.00 35.82 3.86
6511 7338 1.672854 TATGAACTCCAGCCGGACGG 61.673 60.000 5.05 6.35 35.91 4.79
6630 7458 0.841961 TGCTCTTGGAGATGATGGGG 59.158 55.000 0.00 0.00 0.00 4.96
6735 7563 5.365403 TGAGCCGGTTATTTTACTTGTTG 57.635 39.130 1.90 0.00 0.00 3.33
6736 7564 4.822896 TGAGCCGGTTATTTTACTTGTTGT 59.177 37.500 1.90 0.00 0.00 3.32
6737 7565 5.049267 TGAGCCGGTTATTTTACTTGTTGTC 60.049 40.000 1.90 0.00 0.00 3.18
6763 7591 3.928375 GTGCTGGGCATTATTTGTGAAAG 59.072 43.478 0.00 0.00 41.91 2.62
6765 7593 4.467082 TGCTGGGCATTATTTGTGAAAGAT 59.533 37.500 0.00 0.00 31.71 2.40
6772 7603 7.276438 GGGCATTATTTGTGAAAGATGAAGAAC 59.724 37.037 0.00 0.00 0.00 3.01
6780 7611 6.255215 TGTGAAAGATGAAGAACGAAACAAC 58.745 36.000 0.00 0.00 0.00 3.32
6783 7614 5.811399 AAGATGAAGAACGAAACAACACA 57.189 34.783 0.00 0.00 0.00 3.72
6784 7615 6.377327 AAGATGAAGAACGAAACAACACAT 57.623 33.333 0.00 0.00 0.00 3.21
6799 7630 1.002868 ACATGCCAGCTCCACAGAC 60.003 57.895 0.00 0.00 0.00 3.51
6800 7631 1.002990 CATGCCAGCTCCACAGACA 60.003 57.895 0.00 0.00 0.00 3.41
6801 7632 0.393944 CATGCCAGCTCCACAGACAT 60.394 55.000 0.00 0.00 0.00 3.06
6802 7633 0.107312 ATGCCAGCTCCACAGACATC 60.107 55.000 0.00 0.00 0.00 3.06
6941 7803 2.744202 ACAATCAGCGCTCTACCTTTTG 59.256 45.455 7.13 6.43 0.00 2.44
6970 7832 2.029623 GCTATGGAGTACCGACCTTCA 58.970 52.381 0.00 0.00 39.42 3.02
7012 7900 9.048446 TGGTAAATTATTATCTACCGAACTTGC 57.952 33.333 1.39 0.00 37.25 4.01
7072 7960 0.744771 GGCCGAGGAGCGAAAAGATT 60.745 55.000 0.00 0.00 44.57 2.40
7073 7961 1.472728 GGCCGAGGAGCGAAAAGATTA 60.473 52.381 0.00 0.00 44.57 1.75
7197 8085 4.816385 TCGCCTTATCTTGATGTCCAATTC 59.184 41.667 0.00 0.00 33.68 2.17
7198 8086 4.818546 CGCCTTATCTTGATGTCCAATTCT 59.181 41.667 0.00 0.00 33.68 2.40
7257 8145 9.991906 TGGTAGTACATTTATTAGGAGCATAAC 57.008 33.333 2.06 0.00 0.00 1.89
7258 8146 9.991906 GGTAGTACATTTATTAGGAGCATAACA 57.008 33.333 2.06 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 41 7.467267 CGTGGATTTCATCTATTTGGTTAGGTG 60.467 40.741 0.00 0.00 32.56 4.00
74 78 5.765182 ACCTAGAAAGTGTCATGTTCAAAGG 59.235 40.000 13.10 13.10 34.92 3.11
76 80 7.041372 GCTTACCTAGAAAGTGTCATGTTCAAA 60.041 37.037 0.00 0.00 0.00 2.69
82 86 4.331168 GCTGCTTACCTAGAAAGTGTCATG 59.669 45.833 0.00 0.00 0.00 3.07
84 88 3.614150 CGCTGCTTACCTAGAAAGTGTCA 60.614 47.826 0.00 0.00 0.00 3.58
95 102 0.613260 TTCATCACCGCTGCTTACCT 59.387 50.000 0.00 0.00 0.00 3.08
214 221 5.126384 ACACGGTTCTTCATTTCCTCAAAAA 59.874 36.000 0.00 0.00 0.00 1.94
215 222 4.642885 ACACGGTTCTTCATTTCCTCAAAA 59.357 37.500 0.00 0.00 0.00 2.44
217 224 3.815809 ACACGGTTCTTCATTTCCTCAA 58.184 40.909 0.00 0.00 0.00 3.02
218 225 3.485463 ACACGGTTCTTCATTTCCTCA 57.515 42.857 0.00 0.00 0.00 3.86
219 226 4.830826 AAACACGGTTCTTCATTTCCTC 57.169 40.909 0.00 0.00 0.00 3.71
220 227 4.642885 TCAAAACACGGTTCTTCATTTCCT 59.357 37.500 0.00 0.00 0.00 3.36
221 228 4.927422 TCAAAACACGGTTCTTCATTTCC 58.073 39.130 0.00 0.00 0.00 3.13
224 231 4.796312 CGTTTCAAAACACGGTTCTTCATT 59.204 37.500 6.45 0.00 38.81 2.57
225 232 4.095185 TCGTTTCAAAACACGGTTCTTCAT 59.905 37.500 6.45 0.00 38.81 2.57
230 237 6.139638 GTCTTATTCGTTTCAAAACACGGTTC 59.860 38.462 6.45 0.00 38.81 3.62
231 238 5.967088 GTCTTATTCGTTTCAAAACACGGTT 59.033 36.000 6.45 0.00 38.81 4.44
232 239 5.064962 TGTCTTATTCGTTTCAAAACACGGT 59.935 36.000 6.45 0.00 38.81 4.83
233 240 5.503498 TGTCTTATTCGTTTCAAAACACGG 58.497 37.500 6.45 0.00 38.81 4.94
234 241 5.113529 GCTGTCTTATTCGTTTCAAAACACG 59.886 40.000 6.45 0.00 38.81 4.49
235 242 5.968848 TGCTGTCTTATTCGTTTCAAAACAC 59.031 36.000 6.45 0.00 38.81 3.32
236 243 6.037720 TCTGCTGTCTTATTCGTTTCAAAACA 59.962 34.615 6.45 0.00 38.81 2.83
238 245 6.612247 TCTGCTGTCTTATTCGTTTCAAAA 57.388 33.333 0.00 0.00 0.00 2.44
239 246 6.801539 ATCTGCTGTCTTATTCGTTTCAAA 57.198 33.333 0.00 0.00 0.00 2.69
240 247 7.899178 TTATCTGCTGTCTTATTCGTTTCAA 57.101 32.000 0.00 0.00 0.00 2.69
241 248 7.763985 TGATTATCTGCTGTCTTATTCGTTTCA 59.236 33.333 0.00 0.00 0.00 2.69
242 249 8.131455 TGATTATCTGCTGTCTTATTCGTTTC 57.869 34.615 0.00 0.00 0.00 2.78
245 252 8.580720 AGTATGATTATCTGCTGTCTTATTCGT 58.419 33.333 0.00 0.00 0.00 3.85
247 254 9.703892 ACAGTATGATTATCTGCTGTCTTATTC 57.296 33.333 9.61 0.00 39.69 1.75
249 256 9.703892 GAACAGTATGATTATCTGCTGTCTTAT 57.296 33.333 13.56 3.35 39.69 1.73
250 257 8.918116 AGAACAGTATGATTATCTGCTGTCTTA 58.082 33.333 13.56 0.00 39.69 2.10
286 307 0.801251 ATCTGACTCGCAAAGCAAGC 59.199 50.000 0.00 0.00 0.00 4.01
287 308 4.330894 TGATTATCTGACTCGCAAAGCAAG 59.669 41.667 0.00 0.00 0.00 4.01
288 309 4.252878 TGATTATCTGACTCGCAAAGCAA 58.747 39.130 0.00 0.00 0.00 3.91
289 310 3.860641 TGATTATCTGACTCGCAAAGCA 58.139 40.909 0.00 0.00 0.00 3.91
290 311 5.694006 ACTATGATTATCTGACTCGCAAAGC 59.306 40.000 0.00 0.00 0.00 3.51
291 312 6.346439 GCACTATGATTATCTGACTCGCAAAG 60.346 42.308 0.00 0.00 0.00 2.77
292 313 5.463392 GCACTATGATTATCTGACTCGCAAA 59.537 40.000 0.00 0.00 0.00 3.68
299 320 6.073331 GGAAAGCAGCACTATGATTATCTGAC 60.073 42.308 0.00 0.00 0.00 3.51
313 334 4.479619 CAGTAAGATTTGGAAAGCAGCAC 58.520 43.478 0.00 0.00 0.00 4.40
335 356 4.344390 AGCCCCTTGTATACTACTTACTGC 59.656 45.833 4.17 0.00 0.00 4.40
337 358 5.526434 ACAGCCCCTTGTATACTACTTACT 58.474 41.667 4.17 0.00 0.00 2.24
338 359 5.866159 ACAGCCCCTTGTATACTACTTAC 57.134 43.478 4.17 0.00 0.00 2.34
341 362 3.383825 CGAACAGCCCCTTGTATACTACT 59.616 47.826 4.17 0.00 0.00 2.57
342 363 3.131755 ACGAACAGCCCCTTGTATACTAC 59.868 47.826 4.17 0.00 0.00 2.73
343 364 3.368248 ACGAACAGCCCCTTGTATACTA 58.632 45.455 4.17 0.00 0.00 1.82
344 365 2.185387 ACGAACAGCCCCTTGTATACT 58.815 47.619 4.17 0.00 0.00 2.12
345 366 2.685850 ACGAACAGCCCCTTGTATAC 57.314 50.000 0.00 0.00 0.00 1.47
346 367 2.696707 CCTACGAACAGCCCCTTGTATA 59.303 50.000 0.00 0.00 0.00 1.47
348 369 0.899720 CCTACGAACAGCCCCTTGTA 59.100 55.000 0.00 0.00 0.00 2.41
349 370 1.677552 CCTACGAACAGCCCCTTGT 59.322 57.895 0.00 0.00 0.00 3.16
350 371 1.745489 GCCTACGAACAGCCCCTTG 60.745 63.158 0.00 0.00 0.00 3.61
351 372 0.616679 TAGCCTACGAACAGCCCCTT 60.617 55.000 0.00 0.00 0.00 3.95
353 374 1.442148 CTAGCCTACGAACAGCCCC 59.558 63.158 0.00 0.00 0.00 5.80
377 453 3.553828 TGAAACCCGTCCCAGAATATC 57.446 47.619 0.00 0.00 0.00 1.63
391 467 2.359478 ACGACGCCCCATGAAACC 60.359 61.111 0.00 0.00 0.00 3.27
425 502 2.813908 GCGCGAGACGGTCCAAAT 60.814 61.111 12.10 0.00 43.93 2.32
517 594 3.334581 TGTACTAGACAGGGTTGGGAGTA 59.665 47.826 0.00 0.00 32.86 2.59
565 645 6.324819 GCCGATGTCCAATGGATTATTATTG 58.675 40.000 4.81 0.26 32.73 1.90
586 670 0.371645 GATCAAAGCTCTCAACGCCG 59.628 55.000 0.00 0.00 0.00 6.46
621 710 2.821366 CCAGGCTCCACACGATGC 60.821 66.667 0.00 0.00 0.00 3.91
625 1169 3.357079 GTTGCCAGGCTCCACACG 61.357 66.667 14.15 0.00 0.00 4.49
657 1201 0.721718 GGCTTCGACAAATGGAGACG 59.278 55.000 0.00 0.00 0.00 4.18
720 1264 6.389906 CCTGCATATGATACGTACTTGATGA 58.610 40.000 6.97 0.00 0.00 2.92
729 1273 3.751479 TTCTGCCTGCATATGATACGT 57.249 42.857 6.97 0.00 0.00 3.57
730 1274 4.248058 TGATTCTGCCTGCATATGATACG 58.752 43.478 6.97 0.00 0.00 3.06
731 1275 5.646793 ACATGATTCTGCCTGCATATGATAC 59.353 40.000 6.97 0.00 0.00 2.24
734 1278 4.070009 GACATGATTCTGCCTGCATATGA 58.930 43.478 6.97 0.00 0.00 2.15
735 1279 3.818773 TGACATGATTCTGCCTGCATATG 59.181 43.478 0.00 0.00 0.00 1.78
738 1282 2.430248 TGACATGATTCTGCCTGCAT 57.570 45.000 0.00 0.00 0.00 3.96
803 1404 1.065031 CAACGGTACATTTGCGCTGC 61.065 55.000 9.73 0.00 0.00 5.25
814 1423 1.090052 GCCAGGATCAGCAACGGTAC 61.090 60.000 0.00 0.00 0.00 3.34
846 1455 2.069273 CGCTGTGTCCCTTTTCTACTG 58.931 52.381 0.00 0.00 0.00 2.74
851 1460 2.556287 CGCGCTGTGTCCCTTTTC 59.444 61.111 5.56 0.00 0.00 2.29
986 1598 2.513204 CCATGGTCGCAGCTCCAG 60.513 66.667 2.57 4.89 35.22 3.86
1330 1951 2.665185 GTCCCTGTGTGTCCGTGC 60.665 66.667 0.00 0.00 0.00 5.34
1332 1953 3.612681 CGGTCCCTGTGTGTCCGT 61.613 66.667 0.00 0.00 36.99 4.69
1338 1959 3.681835 GACGAGCGGTCCCTGTGT 61.682 66.667 9.39 0.00 39.90 3.72
1344 1965 3.823330 ATGGACGACGAGCGGTCC 61.823 66.667 9.39 10.20 46.49 4.46
1689 2316 1.446272 GCTGTAGGACGTGGCACTC 60.446 63.158 16.72 11.73 0.00 3.51
1692 2319 2.920384 TGGCTGTAGGACGTGGCA 60.920 61.111 0.00 0.00 0.00 4.92
1951 2590 2.463876 GACGTCATTCATCATCTGCGA 58.536 47.619 11.55 0.00 0.00 5.10
1965 2604 2.885113 CTGATCTGCCGGACGTCA 59.115 61.111 18.91 2.01 0.00 4.35
1972 2611 0.528466 ATGTACACGCTGATCTGCCG 60.528 55.000 17.78 14.73 0.00 5.69
2042 2681 1.876664 CTCAGAACGAGAGGCACGA 59.123 57.895 0.00 0.00 45.45 4.35
2044 2683 4.177229 GCTCAGAACGAGAGGCAC 57.823 61.111 0.00 0.00 45.45 5.01
2047 2686 0.179089 CCATGGCTCAGAACGAGAGG 60.179 60.000 0.00 0.00 45.45 3.69
2048 2687 0.809241 GCCATGGCTCAGAACGAGAG 60.809 60.000 29.98 0.00 45.45 3.20
2049 2688 1.219124 GCCATGGCTCAGAACGAGA 59.781 57.895 29.98 0.00 45.45 4.04
2050 2689 1.078918 TGCCATGGCTCAGAACGAG 60.079 57.895 35.53 0.00 45.37 4.18
2051 2690 1.375908 GTGCCATGGCTCAGAACGA 60.376 57.895 35.53 11.81 42.51 3.85
2052 2691 1.672030 TGTGCCATGGCTCAGAACG 60.672 57.895 35.53 0.00 39.30 3.95
2053 2692 0.607489 AGTGTGCCATGGCTCAGAAC 60.607 55.000 35.41 25.49 43.78 3.01
2054 2693 0.607217 CAGTGTGCCATGGCTCAGAA 60.607 55.000 35.41 15.45 43.78 3.02
2056 2695 1.002990 TCAGTGTGCCATGGCTCAG 60.003 57.895 35.41 25.94 43.78 3.35
2057 2696 1.302752 GTCAGTGTGCCATGGCTCA 60.303 57.895 35.53 33.80 41.45 4.26
2058 2697 0.679002 ATGTCAGTGTGCCATGGCTC 60.679 55.000 35.53 31.63 42.51 4.70
2059 2698 0.963856 CATGTCAGTGTGCCATGGCT 60.964 55.000 35.53 14.65 42.51 4.75
2060 2699 1.246056 ACATGTCAGTGTGCCATGGC 61.246 55.000 30.54 30.54 40.16 4.40
2061 2700 0.806868 GACATGTCAGTGTGCCATGG 59.193 55.000 21.07 7.63 40.16 3.66
2062 2701 1.525941 TGACATGTCAGTGTGCCATG 58.474 50.000 24.56 14.40 41.31 3.66
2063 2702 2.502142 ATGACATGTCAGTGTGCCAT 57.498 45.000 30.63 11.23 43.61 4.40
2064 2703 2.153645 GAATGACATGTCAGTGTGCCA 58.846 47.619 31.49 7.80 43.61 4.92
2065 2704 1.129251 CGAATGACATGTCAGTGTGCC 59.871 52.381 31.49 16.53 43.61 5.01
2066 2705 1.800586 ACGAATGACATGTCAGTGTGC 59.199 47.619 31.49 16.87 43.61 4.57
2067 2706 3.059166 TGACGAATGACATGTCAGTGTG 58.941 45.455 31.49 24.00 43.61 3.82
2068 2707 3.385193 TGACGAATGACATGTCAGTGT 57.615 42.857 31.49 26.51 43.61 3.55
2069 2708 3.484721 GCATGACGAATGACATGTCAGTG 60.485 47.826 31.49 23.82 45.87 3.66
2070 2709 2.674852 GCATGACGAATGACATGTCAGT 59.325 45.455 30.63 29.12 45.87 3.41
2085 2724 3.123157 AGCAGTAGATCCATGCATGAC 57.877 47.619 28.31 16.92 42.45 3.06
2095 2734 5.390461 CGCTCATCAGTACTAGCAGTAGATC 60.390 48.000 14.19 0.00 34.60 2.75
2105 2744 3.368013 CCAACCAACGCTCATCAGTACTA 60.368 47.826 0.00 0.00 0.00 1.82
2281 2920 1.476471 CCCATGACTTCCTGGATCTGC 60.476 57.143 0.00 0.00 34.24 4.26
2342 2982 7.220108 CAGATATATTTTGCCGATCGATACGAA 59.780 37.037 18.66 8.88 39.99 3.85
2343 2983 6.691388 CAGATATATTTTGCCGATCGATACGA 59.309 38.462 18.66 2.48 41.13 3.43
2350 2990 7.254252 CGAGGATTCAGATATATTTTGCCGATC 60.254 40.741 0.00 0.00 0.00 3.69
2353 2993 5.639506 ACGAGGATTCAGATATATTTTGCCG 59.360 40.000 0.00 0.00 0.00 5.69
2355 2995 7.331934 TGCTACGAGGATTCAGATATATTTTGC 59.668 37.037 0.00 0.00 0.00 3.68
2361 3001 6.372937 CAGAGTGCTACGAGGATTCAGATATA 59.627 42.308 0.00 0.00 0.00 0.86
2363 3003 4.517075 CAGAGTGCTACGAGGATTCAGATA 59.483 45.833 0.00 0.00 0.00 1.98
2366 3006 2.797792 GCAGAGTGCTACGAGGATTCAG 60.798 54.545 0.00 0.00 40.96 3.02
2367 3007 1.135139 GCAGAGTGCTACGAGGATTCA 59.865 52.381 0.00 0.00 40.96 2.57
2368 3008 1.537135 GGCAGAGTGCTACGAGGATTC 60.537 57.143 0.00 0.00 44.28 2.52
2376 3018 1.719600 CAGTTCAGGCAGAGTGCTAC 58.280 55.000 0.00 0.00 44.28 3.58
2377 3019 0.036952 GCAGTTCAGGCAGAGTGCTA 60.037 55.000 8.48 0.00 44.28 3.49
2381 3023 1.001406 GTACAGCAGTTCAGGCAGAGT 59.999 52.381 0.00 0.00 0.00 3.24
2410 3052 6.540189 GCACAAACCCTGCCATCTATATATAG 59.460 42.308 12.84 12.84 0.00 1.31
2449 3091 1.480954 ACCACGTAGCCGAAGATGAAT 59.519 47.619 0.00 0.00 37.88 2.57
2470 3112 0.804989 GCCATGAAGTTCTGAACCCG 59.195 55.000 16.48 1.83 0.00 5.28
2591 3233 5.019470 TCCATCAGTCTATGTTCAGACACT 58.981 41.667 6.08 0.00 46.15 3.55
2598 3240 7.648142 TGTTTGTTTTCCATCAGTCTATGTTC 58.352 34.615 0.00 0.00 0.00 3.18
2599 3241 7.581213 TGTTTGTTTTCCATCAGTCTATGTT 57.419 32.000 0.00 0.00 0.00 2.71
2611 3260 3.181477 CCAGACTGCATGTTTGTTTTCCA 60.181 43.478 0.00 0.00 0.00 3.53
2633 3282 5.300752 TGATCAGAAGTTCAGAACCAAGTC 58.699 41.667 9.85 3.16 0.00 3.01
2637 3286 5.488262 TGATGATCAGAAGTTCAGAACCA 57.512 39.130 9.85 6.00 0.00 3.67
2638 3287 5.296283 CCATGATGATCAGAAGTTCAGAACC 59.704 44.000 9.85 0.46 0.00 3.62
2639 3288 6.111382 TCCATGATGATCAGAAGTTCAGAAC 58.889 40.000 5.00 5.00 0.00 3.01
2640 3289 6.303903 TCCATGATGATCAGAAGTTCAGAA 57.696 37.500 5.50 0.00 0.00 3.02
2641 3290 5.945144 TCCATGATGATCAGAAGTTCAGA 57.055 39.130 5.50 2.64 0.00 3.27
2642 3291 6.289064 TGATCCATGATGATCAGAAGTTCAG 58.711 40.000 9.75 0.00 44.65 3.02
2659 3312 1.112113 ACGACGCCTAGTTGATCCAT 58.888 50.000 0.00 0.00 37.67 3.41
2660 3313 1.402968 GTACGACGCCTAGTTGATCCA 59.597 52.381 0.00 0.00 37.67 3.41
2661 3314 1.268948 GGTACGACGCCTAGTTGATCC 60.269 57.143 0.00 0.00 37.67 3.36
2662 3315 1.402968 TGGTACGACGCCTAGTTGATC 59.597 52.381 0.00 0.00 37.67 2.92
2664 3317 1.068333 GTTGGTACGACGCCTAGTTGA 60.068 52.381 0.00 0.00 37.67 3.18
2743 3396 4.925861 GCCAGCCGCTCCTCCATC 62.926 72.222 0.00 0.00 0.00 3.51
2909 3562 2.203126 GCCGCCCTTGATCTCCTG 60.203 66.667 0.00 0.00 0.00 3.86
2910 3563 3.854669 CGCCGCCCTTGATCTCCT 61.855 66.667 0.00 0.00 0.00 3.69
3011 3677 1.376037 GCCAGCGAACAAGCCTAGT 60.376 57.895 0.00 0.00 38.01 2.57
3023 3689 1.234821 TTCCAAAGTTACAGCCAGCG 58.765 50.000 0.00 0.00 0.00 5.18
3029 3695 4.298332 GCACACCATTTCCAAAGTTACAG 58.702 43.478 0.00 0.00 0.00 2.74
3267 3937 3.512680 GACGATCAGGTTCAGGTTGTAG 58.487 50.000 0.00 0.00 0.00 2.74
3378 4048 1.473677 TGGTGATTGTACGTACCTCGG 59.526 52.381 22.43 0.00 44.69 4.63
3387 4057 1.400494 GCGGTTCCATGGTGATTGTAC 59.600 52.381 12.58 0.24 0.00 2.90
3389 4059 0.038166 AGCGGTTCCATGGTGATTGT 59.962 50.000 12.58 0.00 0.00 2.71
3390 4060 0.734889 GAGCGGTTCCATGGTGATTG 59.265 55.000 12.58 0.52 0.00 2.67
3391 4061 0.327924 TGAGCGGTTCCATGGTGATT 59.672 50.000 12.58 0.00 0.00 2.57
3392 4062 0.548031 ATGAGCGGTTCCATGGTGAT 59.452 50.000 12.58 0.00 0.00 3.06
3393 4063 0.327924 AATGAGCGGTTCCATGGTGA 59.672 50.000 12.58 0.00 0.00 4.02
3394 4064 0.734889 GAATGAGCGGTTCCATGGTG 59.265 55.000 12.58 1.65 0.00 4.17
3395 4065 0.394352 GGAATGAGCGGTTCCATGGT 60.394 55.000 12.58 0.00 43.67 3.55
3396 4066 1.103398 GGGAATGAGCGGTTCCATGG 61.103 60.000 4.97 4.97 45.56 3.66
3398 4068 1.153168 CGGGAATGAGCGGTTCCAT 60.153 57.895 16.19 0.00 45.56 3.41
3399 4069 2.267642 CGGGAATGAGCGGTTCCA 59.732 61.111 16.19 0.00 45.56 3.53
3400 4070 2.106683 CACGGGAATGAGCGGTTCC 61.107 63.158 8.69 8.69 43.52 3.62
3401 4071 2.750888 GCACGGGAATGAGCGGTTC 61.751 63.158 0.00 0.00 0.00 3.62
3402 4072 2.746277 GCACGGGAATGAGCGGTT 60.746 61.111 0.00 0.00 0.00 4.44
3407 4077 3.499737 GTGGCGCACGGGAATGAG 61.500 66.667 10.83 0.00 0.00 2.90
3416 4086 3.496131 CATGGTACGGTGGCGCAC 61.496 66.667 10.83 5.50 0.00 5.34
3417 4087 4.769063 CCATGGTACGGTGGCGCA 62.769 66.667 10.83 0.00 30.40 6.09
3418 4088 4.770874 ACCATGGTACGGTGGCGC 62.771 66.667 18.10 0.00 39.84 6.53
3419 4089 2.046700 AACCATGGTACGGTGGCG 60.047 61.111 20.12 0.00 39.84 5.69
3420 4090 2.696759 GCAACCATGGTACGGTGGC 61.697 63.158 20.12 11.38 45.98 5.01
3421 4091 1.302913 TGCAACCATGGTACGGTGG 60.303 57.895 20.12 12.22 41.59 4.61
3422 4092 1.873165 GTGCAACCATGGTACGGTG 59.127 57.895 20.12 14.03 36.67 4.94
3423 4093 1.669760 CGTGCAACCATGGTACGGT 60.670 57.895 24.73 5.91 40.05 4.83
3424 4094 0.390078 TACGTGCAACCATGGTACGG 60.390 55.000 31.64 20.44 46.41 4.02
3426 4096 0.717224 CGTACGTGCAACCATGGTAC 59.283 55.000 20.12 14.37 33.76 3.34
3427 4097 0.602060 TCGTACGTGCAACCATGGTA 59.398 50.000 20.12 0.00 32.11 3.25
3428 4098 0.036765 ATCGTACGTGCAACCATGGT 60.037 50.000 13.00 13.00 32.11 3.55
3429 4099 0.373370 CATCGTACGTGCAACCATGG 59.627 55.000 16.05 11.19 32.11 3.66
3430 4100 0.373370 CCATCGTACGTGCAACCATG 59.627 55.000 16.05 9.33 0.00 3.66
3431 4101 0.248012 TCCATCGTACGTGCAACCAT 59.752 50.000 16.05 0.00 0.00 3.55
3432 4102 0.248012 ATCCATCGTACGTGCAACCA 59.752 50.000 16.05 0.00 0.00 3.67
3433 4103 0.650512 CATCCATCGTACGTGCAACC 59.349 55.000 16.05 0.00 0.00 3.77
3465 4135 2.405892 ACAGTTTGCATGAACTTCGC 57.594 45.000 0.90 0.00 37.76 4.70
3466 4136 4.143115 ACGATACAGTTTGCATGAACTTCG 60.143 41.667 16.60 16.60 40.51 3.79
3481 4174 2.349438 GCACACAACCAACACGATACAG 60.349 50.000 0.00 0.00 0.00 2.74
3736 4429 7.572523 TCATCATCAGTTTGGTTAATGGATC 57.427 36.000 0.00 0.00 0.00 3.36
3752 4473 1.071071 TCAGCATCGGCATCATCATCA 59.929 47.619 0.00 0.00 44.61 3.07
3753 4474 1.804601 TCAGCATCGGCATCATCATC 58.195 50.000 0.00 0.00 44.61 2.92
3754 4475 2.084546 CATCAGCATCGGCATCATCAT 58.915 47.619 0.00 0.00 44.61 2.45
3799 4520 2.442643 ATTCTGGCGGGCCCATTG 60.443 61.111 24.92 6.71 44.33 2.82
3807 4528 2.691409 TGTTTAGGAGATTCTGGCGG 57.309 50.000 0.00 0.00 0.00 6.13
3814 4535 9.147732 ACCAAGAAAGAATTTGTTTAGGAGATT 57.852 29.630 9.93 0.00 38.53 2.40
3828 4549 9.154632 ACCAACCTAAATAAACCAAGAAAGAAT 57.845 29.630 0.00 0.00 0.00 2.40
3829 4550 8.417884 CACCAACCTAAATAAACCAAGAAAGAA 58.582 33.333 0.00 0.00 0.00 2.52
3830 4551 7.780745 TCACCAACCTAAATAAACCAAGAAAGA 59.219 33.333 0.00 0.00 0.00 2.52
3831 4552 7.865889 GTCACCAACCTAAATAAACCAAGAAAG 59.134 37.037 0.00 0.00 0.00 2.62
4379 5204 1.964891 CCGCTGCAGCTCCCATATG 60.965 63.158 34.22 17.01 39.32 1.78
4415 5240 1.410648 CCCATGAGAAACCCCAGGATG 60.411 57.143 0.00 0.00 0.00 3.51
4421 5246 0.033208 TGATGCCCATGAGAAACCCC 60.033 55.000 0.00 0.00 0.00 4.95
4427 5252 4.223800 GCGTTGATGCCCATGAGA 57.776 55.556 0.00 0.00 0.00 3.27
4580 5405 3.687321 CTGCCCCGTCATGGTGAGG 62.687 68.421 0.00 0.00 35.15 3.86
4868 5693 1.079543 GAGCGTGAGTGGAGTGCAT 60.080 57.895 0.00 0.00 0.00 3.96
5132 5957 1.443872 CCAGAGCGTCACCGTGTAC 60.444 63.158 0.00 0.00 36.15 2.90
5219 6044 1.813192 GGAGAAGGAGCTGAGGACG 59.187 63.158 0.00 0.00 0.00 4.79
5345 6170 2.508439 TTGATCGTCCGCCGCTTC 60.508 61.111 0.00 0.00 36.19 3.86
5387 6212 1.205893 GCGAAGATCACCTTCCTCAGT 59.794 52.381 0.00 0.00 46.65 3.41
5663 6488 0.676736 TGCCGAACCCAATGTTTTCC 59.323 50.000 0.00 0.00 37.29 3.13
5720 6545 0.038166 TGTGGATGTTGGCCTCCTTC 59.962 55.000 3.32 1.91 31.66 3.46
5781 6606 2.884639 ACAATTTGTGAGCAGTGGTACC 59.115 45.455 4.43 4.43 0.00 3.34
5936 6762 2.038295 CCCAACCTGCCAAAAATAAGCA 59.962 45.455 0.00 0.00 34.79 3.91
6002 6828 4.862092 AGGACTGCTCGCGCGATG 62.862 66.667 34.86 26.17 39.65 3.84
6008 6834 2.047844 TGCTTCAGGACTGCTCGC 60.048 61.111 0.00 0.00 0.00 5.03
6302 7128 5.448904 GGGATCAGTTCGTAGTTCTGTACTC 60.449 48.000 0.00 0.00 38.33 2.59
6419 7246 8.547481 TTATTCATCATCTTGTGGTCTAGGTA 57.453 34.615 0.00 0.00 0.00 3.08
6420 7247 5.965033 ATTCATCATCTTGTGGTCTAGGT 57.035 39.130 0.00 0.00 0.00 3.08
6421 7248 7.989741 AGTTTATTCATCATCTTGTGGTCTAGG 59.010 37.037 0.00 0.00 0.00 3.02
6423 7250 8.762645 AGAGTTTATTCATCATCTTGTGGTCTA 58.237 33.333 0.00 0.00 0.00 2.59
6425 7252 7.678218 GCAGAGTTTATTCATCATCTTGTGGTC 60.678 40.741 0.00 0.00 0.00 4.02
6427 7254 6.493116 GCAGAGTTTATTCATCATCTTGTGG 58.507 40.000 0.00 0.00 0.00 4.17
6428 7255 6.036408 TCGCAGAGTTTATTCATCATCTTGTG 59.964 38.462 0.00 0.00 0.00 3.33
6429 7256 6.108687 TCGCAGAGTTTATTCATCATCTTGT 58.891 36.000 0.00 0.00 0.00 3.16
6430 7257 6.594284 TCGCAGAGTTTATTCATCATCTTG 57.406 37.500 0.00 0.00 0.00 3.02
6448 7275 6.450545 TCATCTAATCCTTGTATTCTCGCAG 58.549 40.000 0.00 0.00 0.00 5.18
6473 7300 8.612619 AGTTCATATATTGTGAAAATGGACGTC 58.387 33.333 7.13 7.13 37.34 4.34
6475 7302 8.070171 GGAGTTCATATATTGTGAAAATGGACG 58.930 37.037 5.18 0.00 37.34 4.79
6511 7338 0.867746 TTCGCGGCATCATTATCAGC 59.132 50.000 6.13 0.00 0.00 4.26
6630 7458 4.976116 GCCACATCAATCCGCTTAATTAAC 59.024 41.667 0.00 0.00 0.00 2.01
6735 7563 0.810031 ATAATGCCCAGCACGACGAC 60.810 55.000 0.00 0.00 43.04 4.34
6736 7564 0.107897 AATAATGCCCAGCACGACGA 60.108 50.000 0.00 0.00 43.04 4.20
6737 7565 0.732571 AAATAATGCCCAGCACGACG 59.267 50.000 0.00 0.00 43.04 5.12
6763 7591 4.379793 GCATGTGTTGTTTCGTTCTTCATC 59.620 41.667 0.00 0.00 0.00 2.92
6765 7593 3.488384 GGCATGTGTTGTTTCGTTCTTCA 60.488 43.478 0.00 0.00 0.00 3.02
6772 7603 0.311790 AGCTGGCATGTGTTGTTTCG 59.688 50.000 0.00 0.00 0.00 3.46
6780 7611 1.002990 TCTGTGGAGCTGGCATGTG 60.003 57.895 0.00 0.00 0.00 3.21
6783 7614 0.107312 GATGTCTGTGGAGCTGGCAT 60.107 55.000 0.00 0.00 42.73 4.40
6784 7615 1.297689 GATGTCTGTGGAGCTGGCA 59.702 57.895 0.00 0.00 35.19 4.92
6799 7630 2.354503 CCTCCCTTATGCGAGATGGATG 60.355 54.545 0.00 0.00 0.00 3.51
6800 7631 1.905215 CCTCCCTTATGCGAGATGGAT 59.095 52.381 0.00 0.00 0.00 3.41
6801 7632 1.342074 CCTCCCTTATGCGAGATGGA 58.658 55.000 0.00 0.00 0.00 3.41
6802 7633 0.322975 CCCTCCCTTATGCGAGATGG 59.677 60.000 0.00 0.00 0.00 3.51
6843 7674 7.094805 GCACCAGAATCTTCACTACACAATTTA 60.095 37.037 0.00 0.00 0.00 1.40
6844 7675 6.294176 GCACCAGAATCTTCACTACACAATTT 60.294 38.462 0.00 0.00 0.00 1.82
6867 7698 0.178967 TGGCCAGTTCCAAATGAGCA 60.179 50.000 0.00 0.00 32.18 4.26
6902 7733 4.440826 TTGTCTGGGCCTTAACAACTAA 57.559 40.909 4.53 0.00 0.00 2.24
6903 7734 4.042311 TGATTGTCTGGGCCTTAACAACTA 59.958 41.667 17.14 9.34 34.71 2.24
6941 7803 4.219944 TCGGTACTCCATAGCATCATAACC 59.780 45.833 0.00 0.00 0.00 2.85
7121 8009 1.824230 ACCAAGCTTGAAACAGCAACA 59.176 42.857 28.05 0.00 42.84 3.33
7197 8085 1.271163 TGTTCAGGGTAAGGCGGAAAG 60.271 52.381 0.00 0.00 0.00 2.62
7198 8086 0.766131 TGTTCAGGGTAAGGCGGAAA 59.234 50.000 0.00 0.00 0.00 3.13
7257 8145 5.352569 CCTATAAGAACACTTCAGCAAGGTG 59.647 44.000 0.65 0.65 33.37 4.00
7258 8146 5.013183 ACCTATAAGAACACTTCAGCAAGGT 59.987 40.000 0.00 0.00 33.37 3.50
7259 8147 5.491982 ACCTATAAGAACACTTCAGCAAGG 58.508 41.667 0.00 0.00 33.37 3.61


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

AutoCloner maintained by Alex Coulton.