Multiple sequence alignment - TraesCS1A01G190900

Loading Multiple Alignment...

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 TraesCS1A01G190900 chr1A 100.000 5006 0 0 1 5006 345172186 345167181 0.000000e+00 9245.0
1 TraesCS1A01G190900 chr1A 100.000 131 0 0 3239 3369 35530966 35531096 5.010000e-60 243.0
2 TraesCS1A01G190900 chr1A 100.000 128 0 0 3242 3369 27289697 27289570 2.330000e-58 237.0
3 TraesCS1A01G190900 chr1B 93.027 3284 102 42 1 3244 372223828 372220632 0.000000e+00 4678.0
4 TraesCS1A01G190900 chr1B 95.660 1106 33 10 3367 4462 372220634 372219534 0.000000e+00 1762.0
5 TraesCS1A01G190900 chr1B 94.615 260 8 4 4545 4803 372219179 372218925 1.010000e-106 398.0
6 TraesCS1A01G190900 chr1B 89.071 183 13 3 4354 4530 372219425 372219244 2.350000e-53 220.0
7 TraesCS1A01G190900 chr1B 97.872 47 1 0 4495 4541 372219164 372219210 1.160000e-11 82.4
8 TraesCS1A01G190900 chr1D 95.476 2962 65 20 303 3244 272758262 272755350 0.000000e+00 4663.0
9 TraesCS1A01G190900 chr1D 96.778 1552 38 5 3367 4912 272755352 272753807 0.000000e+00 2579.0
10 TraesCS1A01G190900 chr1D 93.333 180 10 1 1 180 272758747 272758570 1.070000e-66 265.0
11 TraesCS1A01G190900 chr3A 100.000 131 0 0 3241 3371 158174828 158174958 5.010000e-60 243.0
12 TraesCS1A01G190900 chr5A 100.000 130 0 0 3241 3370 145678339 145678468 1.800000e-59 241.0
13 TraesCS1A01G190900 chr5A 98.507 134 2 0 3242 3375 688512219 688512352 2.330000e-58 237.0
14 TraesCS1A01G190900 chr5A 94.595 148 6 2 3235 3380 154345667 154345520 1.400000e-55 228.0
15 TraesCS1A01G190900 chr6A 99.237 131 1 0 3239 3369 617047908 617047778 2.330000e-58 237.0
16 TraesCS1A01G190900 chr5D 99.237 131 1 0 3240 3370 223020791 223020661 2.330000e-58 237.0
17 TraesCS1A01G190900 chr4A 98.496 133 2 0 3239 3371 112769476 112769344 8.380000e-58 235.0


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 TraesCS1A01G190900 chr1A 345167181 345172186 5005 True 9245.000000 9245 100.000000 1 5006 1 chr1A.!!$R2 5005
1 TraesCS1A01G190900 chr1B 372218925 372223828 4903 True 1764.500000 4678 93.093250 1 4803 4 chr1B.!!$R1 4802
2 TraesCS1A01G190900 chr1D 272753807 272758747 4940 True 2502.333333 4663 95.195667 1 4912 3 chr1D.!!$R1 4911

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
223 228 0.047176 AGAGAGAGGGGGAGAGGAGA 59.953 60.0 0.0 0.0 0.0 3.71 F
229 234 0.178861 AGGGGGAGAGGAGAAAAGCA 60.179 55.0 0.0 0.0 0.0 3.91 F
487 676 0.179015 CTCTGCCTCTACCTAGCCGA 60.179 60.0 0.0 0.0 0.0 5.54 F
488 677 0.179015 TCTGCCTCTACCTAGCCGAG 60.179 60.0 0.0 0.0 0.0 4.63 F
1741 1983 0.249398 GCCGCTTCTTCCAGGAGTAA 59.751 55.0 0.0 0.0 0.0 2.24 F
3257 3515 0.172803 CTTGTACTCCCTCCGTTCCG 59.827 60.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1990 2236 0.592754 GCTCCAACTACTCGCTAGCG 60.593 60.000 30.91 30.91 41.35 4.26 R
2165 2414 1.686052 TGTAGTTGCAAAAAGGCCAGG 59.314 47.619 5.01 0.00 0.00 4.45 R
2268 2517 5.339990 GGTGAATTTGATCCAACAATACCG 58.660 41.667 0.00 0.00 0.00 4.02 R
2652 2909 5.728351 AAGAAAAATCACAAACGACTCGA 57.272 34.783 5.20 0.00 0.00 4.04 R
3347 3605 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89 R
4937 5481 0.187361 AACTTTAACCCAGGCAGCCA 59.813 50.000 15.80 0.00 0.00 4.75 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
75 79 2.110901 TCTCGAGTAGAGTGGACCAC 57.889 55.000 17.43 17.43 46.86 4.16
88 92 3.003763 ACCACTCCCGCTTCTCCC 61.004 66.667 0.00 0.00 0.00 4.30
90 94 3.787001 CACTCCCGCTTCTCCCCC 61.787 72.222 0.00 0.00 0.00 5.40
143 147 5.013861 TGTTGCTATTTTTCTCGAACGAC 57.986 39.130 0.00 0.00 0.00 4.34
146 150 5.264060 TGCTATTTTTCTCGAACGACAAG 57.736 39.130 0.00 0.00 0.00 3.16
153 157 3.167921 TCTCGAACGACAAGGAAAACA 57.832 42.857 0.00 0.00 0.00 2.83
157 161 3.742369 TCGAACGACAAGGAAAACATACC 59.258 43.478 0.00 0.00 0.00 2.73
183 187 6.041523 CCAACCCAAGGTGAGAAAAATAAAGA 59.958 38.462 0.00 0.00 35.34 2.52
208 213 5.531122 TTTTCCGTTTGAAGAGAGAGAGA 57.469 39.130 0.00 0.00 33.63 3.10
210 215 4.022413 TCCGTTTGAAGAGAGAGAGAGA 57.978 45.455 0.00 0.00 0.00 3.10
213 218 3.128589 CGTTTGAAGAGAGAGAGAGAGGG 59.871 52.174 0.00 0.00 0.00 4.30
215 220 1.568597 TGAAGAGAGAGAGAGAGGGGG 59.431 57.143 0.00 0.00 0.00 5.40
217 222 1.522900 AGAGAGAGAGAGAGGGGGAG 58.477 60.000 0.00 0.00 0.00 4.30
220 225 0.478507 GAGAGAGAGAGGGGGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
223 228 0.047176 AGAGAGAGGGGGAGAGGAGA 59.953 60.000 0.00 0.00 0.00 3.71
224 229 0.930726 GAGAGAGGGGGAGAGGAGAA 59.069 60.000 0.00 0.00 0.00 2.87
225 230 1.289530 GAGAGAGGGGGAGAGGAGAAA 59.710 57.143 0.00 0.00 0.00 2.52
226 231 1.725182 AGAGAGGGGGAGAGGAGAAAA 59.275 52.381 0.00 0.00 0.00 2.29
227 232 2.115427 GAGAGGGGGAGAGGAGAAAAG 58.885 57.143 0.00 0.00 0.00 2.27
228 233 0.544223 GAGGGGGAGAGGAGAAAAGC 59.456 60.000 0.00 0.00 0.00 3.51
229 234 0.178861 AGGGGGAGAGGAGAAAAGCA 60.179 55.000 0.00 0.00 0.00 3.91
230 235 0.254462 GGGGGAGAGGAGAAAAGCAG 59.746 60.000 0.00 0.00 0.00 4.24
231 236 1.280457 GGGGAGAGGAGAAAAGCAGA 58.720 55.000 0.00 0.00 0.00 4.26
451 640 4.825679 CCACCCCTCCCTCCCTCC 62.826 77.778 0.00 0.00 0.00 4.30
452 641 4.825679 CACCCCTCCCTCCCTCCC 62.826 77.778 0.00 0.00 0.00 4.30
454 643 4.179599 CCCCTCCCTCCCTCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
471 660 2.978278 CCCTCTGGATTGGAATAGCTCT 59.022 50.000 0.00 0.00 0.00 4.09
476 665 2.105477 TGGATTGGAATAGCTCTGCCTC 59.895 50.000 0.00 0.00 0.00 4.70
477 666 2.371510 GGATTGGAATAGCTCTGCCTCT 59.628 50.000 0.00 0.00 0.00 3.69
478 667 3.580458 GGATTGGAATAGCTCTGCCTCTA 59.420 47.826 0.00 0.00 0.00 2.43
480 669 2.320781 TGGAATAGCTCTGCCTCTACC 58.679 52.381 0.00 0.00 0.00 3.18
481 670 2.091055 TGGAATAGCTCTGCCTCTACCT 60.091 50.000 0.00 0.00 0.00 3.08
482 671 3.140332 TGGAATAGCTCTGCCTCTACCTA 59.860 47.826 0.00 0.00 0.00 3.08
483 672 3.761752 GGAATAGCTCTGCCTCTACCTAG 59.238 52.174 0.00 0.00 0.00 3.02
484 673 2.279935 TAGCTCTGCCTCTACCTAGC 57.720 55.000 0.00 0.00 0.00 3.42
485 674 0.469144 AGCTCTGCCTCTACCTAGCC 60.469 60.000 0.00 0.00 0.00 3.93
486 675 1.801309 GCTCTGCCTCTACCTAGCCG 61.801 65.000 0.00 0.00 0.00 5.52
487 676 0.179015 CTCTGCCTCTACCTAGCCGA 60.179 60.000 0.00 0.00 0.00 5.54
488 677 0.179015 TCTGCCTCTACCTAGCCGAG 60.179 60.000 0.00 0.00 0.00 4.63
489 678 0.466555 CTGCCTCTACCTAGCCGAGT 60.467 60.000 0.00 0.00 0.00 4.18
490 679 0.465824 TGCCTCTACCTAGCCGAGTC 60.466 60.000 0.00 0.00 0.00 3.36
491 680 1.174078 GCCTCTACCTAGCCGAGTCC 61.174 65.000 0.00 0.00 0.00 3.85
506 699 3.364062 CGAGTCCGCATTAGAACTACTG 58.636 50.000 0.00 0.00 0.00 2.74
549 742 1.069090 GAGTGGCGTCTGGTGTTCA 59.931 57.895 0.00 0.00 0.00 3.18
600 796 1.445066 CGGCGATCTCATCCATCCG 60.445 63.158 0.00 0.00 0.00 4.18
601 797 1.668294 GGCGATCTCATCCATCCGT 59.332 57.895 0.00 0.00 0.00 4.69
602 798 0.389166 GGCGATCTCATCCATCCGTC 60.389 60.000 0.00 0.00 0.00 4.79
603 799 0.389166 GCGATCTCATCCATCCGTCC 60.389 60.000 0.00 0.00 0.00 4.79
658 854 1.497161 AACCCCCACCTAATCTCTCG 58.503 55.000 0.00 0.00 0.00 4.04
672 868 1.002087 TCTCTCGCTCCCTTTTGTTCC 59.998 52.381 0.00 0.00 0.00 3.62
683 879 2.762327 CCTTTTGTTCCCATCCTCCATG 59.238 50.000 0.00 0.00 0.00 3.66
684 880 1.851304 TTTGTTCCCATCCTCCATGC 58.149 50.000 0.00 0.00 0.00 4.06
687 883 1.358787 TGTTCCCATCCTCCATGCTTT 59.641 47.619 0.00 0.00 0.00 3.51
688 884 2.580322 TGTTCCCATCCTCCATGCTTTA 59.420 45.455 0.00 0.00 0.00 1.85
689 885 3.217626 GTTCCCATCCTCCATGCTTTAG 58.782 50.000 0.00 0.00 0.00 1.85
690 886 1.143684 TCCCATCCTCCATGCTTTAGC 59.856 52.381 0.00 0.00 42.50 3.09
783 979 1.946768 TCTCCAGCCTTTTTGTTCGTG 59.053 47.619 0.00 0.00 0.00 4.35
784 980 1.946768 CTCCAGCCTTTTTGTTCGTGA 59.053 47.619 0.00 0.00 0.00 4.35
787 983 2.099098 CCAGCCTTTTTGTTCGTGAGTT 59.901 45.455 0.00 0.00 0.00 3.01
788 984 3.428862 CCAGCCTTTTTGTTCGTGAGTTT 60.429 43.478 0.00 0.00 0.00 2.66
791 987 3.303229 GCCTTTTTGTTCGTGAGTTTGTG 59.697 43.478 0.00 0.00 0.00 3.33
792 988 4.728534 CCTTTTTGTTCGTGAGTTTGTGA 58.271 39.130 0.00 0.00 0.00 3.58
918 1127 1.939934 TGTTTGTTGGCTTCAGACTCG 59.060 47.619 0.00 0.00 0.00 4.18
919 1128 2.210116 GTTTGTTGGCTTCAGACTCGA 58.790 47.619 0.00 0.00 0.00 4.04
943 1152 0.884704 TGAAACTCAAGCTCACGGCC 60.885 55.000 0.00 0.00 43.05 6.13
1203 1433 1.973281 CCATCAGCACCACCACCAC 60.973 63.158 0.00 0.00 0.00 4.16
1212 1448 2.115910 CACCACCACCACCAGCAT 59.884 61.111 0.00 0.00 0.00 3.79
1221 1457 2.407428 CCACCAGCATCAGCAGCAG 61.407 63.158 0.00 0.00 45.49 4.24
1222 1458 2.750637 ACCAGCATCAGCAGCAGC 60.751 61.111 0.00 0.00 45.49 5.25
1223 1459 2.750237 CCAGCATCAGCAGCAGCA 60.750 61.111 3.17 0.00 45.49 4.41
1224 1460 2.765356 CCAGCATCAGCAGCAGCAG 61.765 63.158 3.17 0.00 45.49 4.24
1557 1799 3.151022 CCACTCTCCTCCGCCTCC 61.151 72.222 0.00 0.00 0.00 4.30
1732 1974 1.261619 CATAATCACCGCCGCTTCTTC 59.738 52.381 0.00 0.00 0.00 2.87
1735 1977 2.859273 ATCACCGCCGCTTCTTCCAG 62.859 60.000 0.00 0.00 0.00 3.86
1736 1978 4.394712 ACCGCCGCTTCTTCCAGG 62.395 66.667 0.00 0.00 0.00 4.45
1738 1980 2.510238 CGCCGCTTCTTCCAGGAG 60.510 66.667 0.00 0.00 0.00 3.69
1740 1982 1.898154 GCCGCTTCTTCCAGGAGTA 59.102 57.895 0.00 0.00 0.00 2.59
1741 1983 0.249398 GCCGCTTCTTCCAGGAGTAA 59.751 55.000 0.00 0.00 0.00 2.24
1742 1984 1.338769 GCCGCTTCTTCCAGGAGTAAA 60.339 52.381 0.00 0.00 0.00 2.01
1743 1985 2.681097 GCCGCTTCTTCCAGGAGTAAAT 60.681 50.000 0.00 0.00 0.00 1.40
1744 1986 3.198872 CCGCTTCTTCCAGGAGTAAATC 58.801 50.000 0.00 0.00 0.00 2.17
1745 1987 3.118592 CCGCTTCTTCCAGGAGTAAATCT 60.119 47.826 0.00 0.00 0.00 2.40
1895 2141 5.487433 TCGCATTCTTTTCCTGATCTTACA 58.513 37.500 0.00 0.00 0.00 2.41
1910 2156 9.401058 CCTGATCTTACATTGTTTATTCCTTCT 57.599 33.333 0.00 0.00 0.00 2.85
1990 2236 0.793250 GACTTGCGAGCCTTTGACTC 59.207 55.000 0.00 0.00 0.00 3.36
2188 2437 2.697751 TGGCCTTTTTGCAACTACACAT 59.302 40.909 3.32 0.00 0.00 3.21
2268 2517 4.566987 AGGGACTAGTTGAAACGATTGAC 58.433 43.478 0.00 0.00 36.02 3.18
2716 2973 6.830114 ATAGCGAGCTTTAGATGTTTGTAC 57.170 37.500 1.86 0.00 0.00 2.90
2775 3032 2.168936 TCCTCAATGCCATGCAATTTCC 59.831 45.455 0.00 0.00 43.62 3.13
3045 3302 7.120923 AGGTACGTAATTATCTTGTGTGGAT 57.879 36.000 0.00 0.00 0.00 3.41
3047 3304 8.698210 AGGTACGTAATTATCTTGTGTGGATTA 58.302 33.333 0.00 0.00 0.00 1.75
3074 3331 3.004106 GGATACTGATGCTTGCACATTCC 59.996 47.826 0.00 2.98 0.00 3.01
3083 3340 2.728846 GCTTGCACATTCCACATGTACG 60.729 50.000 0.00 0.00 0.00 3.67
3244 3502 4.517453 TGATTGCACACCTTTACCTTGTAC 59.483 41.667 0.00 0.00 0.00 2.90
3245 3503 3.849563 TGCACACCTTTACCTTGTACT 57.150 42.857 0.00 0.00 0.00 2.73
3246 3504 3.735591 TGCACACCTTTACCTTGTACTC 58.264 45.455 0.00 0.00 0.00 2.59
3247 3505 3.072211 GCACACCTTTACCTTGTACTCC 58.928 50.000 0.00 0.00 0.00 3.85
3248 3506 3.671716 CACACCTTTACCTTGTACTCCC 58.328 50.000 0.00 0.00 0.00 4.30
3249 3507 3.326880 CACACCTTTACCTTGTACTCCCT 59.673 47.826 0.00 0.00 0.00 4.20
3250 3508 3.581770 ACACCTTTACCTTGTACTCCCTC 59.418 47.826 0.00 0.00 0.00 4.30
3251 3509 3.055312 CACCTTTACCTTGTACTCCCTCC 60.055 52.174 0.00 0.00 0.00 4.30
3252 3510 2.167900 CCTTTACCTTGTACTCCCTCCG 59.832 54.545 0.00 0.00 0.00 4.63
3253 3511 2.610438 TTACCTTGTACTCCCTCCGT 57.390 50.000 0.00 0.00 0.00 4.69
3254 3512 2.610438 TACCTTGTACTCCCTCCGTT 57.390 50.000 0.00 0.00 0.00 4.44
3255 3513 1.264295 ACCTTGTACTCCCTCCGTTC 58.736 55.000 0.00 0.00 0.00 3.95
3256 3514 0.535797 CCTTGTACTCCCTCCGTTCC 59.464 60.000 0.00 0.00 0.00 3.62
3257 3515 0.172803 CTTGTACTCCCTCCGTTCCG 59.827 60.000 0.00 0.00 0.00 4.30
3258 3516 0.251297 TTGTACTCCCTCCGTTCCGA 60.251 55.000 0.00 0.00 0.00 4.55
3259 3517 0.251297 TGTACTCCCTCCGTTCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
3260 3518 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
3261 3519 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
3262 3520 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
3263 3521 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
3264 3522 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
3265 3523 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
3266 3524 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
3267 3525 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
3268 3526 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
3269 3527 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
3270 3528 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
3271 3529 3.991773 TCCGTTCCGAATTACTTGTCTTG 59.008 43.478 0.00 0.00 0.00 3.02
3272 3530 3.124636 CCGTTCCGAATTACTTGTCTTGG 59.875 47.826 0.00 0.00 0.00 3.61
3273 3531 3.991773 CGTTCCGAATTACTTGTCTTGGA 59.008 43.478 0.00 0.00 0.00 3.53
3274 3532 4.630069 CGTTCCGAATTACTTGTCTTGGAT 59.370 41.667 0.00 0.00 0.00 3.41
3275 3533 5.121768 CGTTCCGAATTACTTGTCTTGGATT 59.878 40.000 0.00 0.00 0.00 3.01
3276 3534 6.348213 CGTTCCGAATTACTTGTCTTGGATTT 60.348 38.462 0.00 0.00 0.00 2.17
3277 3535 6.494893 TCCGAATTACTTGTCTTGGATTTG 57.505 37.500 0.00 0.00 0.00 2.32
3278 3536 6.001460 TCCGAATTACTTGTCTTGGATTTGT 58.999 36.000 0.00 0.00 0.00 2.83
3279 3537 6.148811 TCCGAATTACTTGTCTTGGATTTGTC 59.851 38.462 0.00 0.00 0.00 3.18
3280 3538 6.149474 CCGAATTACTTGTCTTGGATTTGTCT 59.851 38.462 0.00 0.00 0.00 3.41
3281 3539 7.333423 CCGAATTACTTGTCTTGGATTTGTCTA 59.667 37.037 0.00 0.00 0.00 2.59
3282 3540 8.383619 CGAATTACTTGTCTTGGATTTGTCTAG 58.616 37.037 0.00 0.00 0.00 2.43
3283 3541 9.436957 GAATTACTTGTCTTGGATTTGTCTAGA 57.563 33.333 0.00 0.00 0.00 2.43
3284 3542 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
3286 3544 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
3287 3545 7.036220 ACTTGTCTTGGATTTGTCTAGATACG 58.964 38.462 0.00 0.00 0.00 3.06
3288 3546 5.902681 TGTCTTGGATTTGTCTAGATACGG 58.097 41.667 0.00 0.00 0.00 4.02
3289 3547 5.655090 TGTCTTGGATTTGTCTAGATACGGA 59.345 40.000 0.00 0.00 0.00 4.69
3290 3548 6.183360 TGTCTTGGATTTGTCTAGATACGGAG 60.183 42.308 0.00 0.00 0.00 4.63
3291 3549 5.302059 TCTTGGATTTGTCTAGATACGGAGG 59.698 44.000 0.00 0.00 0.00 4.30
3292 3550 4.543689 TGGATTTGTCTAGATACGGAGGT 58.456 43.478 0.00 0.00 0.00 3.85
3293 3551 5.698104 TGGATTTGTCTAGATACGGAGGTA 58.302 41.667 0.00 0.00 0.00 3.08
3294 3552 6.312529 TGGATTTGTCTAGATACGGAGGTAT 58.687 40.000 0.00 0.00 42.01 2.73
3307 3565 7.778185 ATACGGAGGTATCTAGCACTAAAAT 57.222 36.000 0.00 0.00 34.18 1.82
3308 3566 5.844004 ACGGAGGTATCTAGCACTAAAATG 58.156 41.667 0.00 0.00 0.00 2.32
3309 3567 5.597182 ACGGAGGTATCTAGCACTAAAATGA 59.403 40.000 0.00 0.00 0.00 2.57
3310 3568 6.153067 CGGAGGTATCTAGCACTAAAATGAG 58.847 44.000 0.00 0.00 0.00 2.90
3311 3569 6.239064 CGGAGGTATCTAGCACTAAAATGAGT 60.239 42.308 0.00 0.00 0.00 3.41
3312 3570 7.149307 GGAGGTATCTAGCACTAAAATGAGTC 58.851 42.308 0.00 0.00 0.00 3.36
3313 3571 7.014808 GGAGGTATCTAGCACTAAAATGAGTCT 59.985 40.741 0.00 0.00 0.00 3.24
3314 3572 8.998277 AGGTATCTAGCACTAAAATGAGTCTA 57.002 34.615 0.00 0.00 0.00 2.59
3315 3573 9.073475 AGGTATCTAGCACTAAAATGAGTCTAG 57.927 37.037 0.00 0.00 33.29 2.43
3316 3574 9.069082 GGTATCTAGCACTAAAATGAGTCTAGA 57.931 37.037 11.59 11.59 38.76 2.43
3320 3578 9.628500 TCTAGCACTAAAATGAGTCTAGATACA 57.372 33.333 0.00 0.00 34.65 2.29
3323 3581 8.364142 AGCACTAAAATGAGTCTAGATACATCC 58.636 37.037 12.66 0.00 0.00 3.51
3324 3582 7.327275 GCACTAAAATGAGTCTAGATACATCCG 59.673 40.741 12.66 6.68 0.00 4.18
3325 3583 8.353684 CACTAAAATGAGTCTAGATACATCCGT 58.646 37.037 12.66 7.10 0.00 4.69
3326 3584 9.570468 ACTAAAATGAGTCTAGATACATCCGTA 57.430 33.333 12.66 6.93 0.00 4.02
3340 3598 7.776618 ATACATCCGTATCTAGACAAATCCA 57.223 36.000 0.00 0.00 32.66 3.41
3341 3599 6.479972 ACATCCGTATCTAGACAAATCCAA 57.520 37.500 0.00 0.00 0.00 3.53
3342 3600 6.516718 ACATCCGTATCTAGACAAATCCAAG 58.483 40.000 0.00 0.00 0.00 3.61
3343 3601 6.323996 ACATCCGTATCTAGACAAATCCAAGA 59.676 38.462 0.00 0.00 0.00 3.02
3344 3602 6.145338 TCCGTATCTAGACAAATCCAAGAC 57.855 41.667 0.00 0.00 0.00 3.01
3345 3603 5.655090 TCCGTATCTAGACAAATCCAAGACA 59.345 40.000 0.00 0.00 0.00 3.41
3346 3604 6.153851 TCCGTATCTAGACAAATCCAAGACAA 59.846 38.462 0.00 0.00 0.00 3.18
3347 3605 6.477033 CCGTATCTAGACAAATCCAAGACAAG 59.523 42.308 0.00 0.00 0.00 3.16
3348 3606 7.036220 CGTATCTAGACAAATCCAAGACAAGT 58.964 38.462 0.00 0.00 0.00 3.16
3349 3607 8.188799 CGTATCTAGACAAATCCAAGACAAGTA 58.811 37.037 0.00 0.00 0.00 2.24
3350 3608 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
3352 3610 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
3353 3611 9.436957 TCTAGACAAATCCAAGACAAGTAATTC 57.563 33.333 0.00 0.00 0.00 2.17
3354 3612 7.133891 AGACAAATCCAAGACAAGTAATTCG 57.866 36.000 0.00 0.00 0.00 3.34
3355 3613 6.149474 AGACAAATCCAAGACAAGTAATTCGG 59.851 38.462 0.00 0.00 0.00 4.30
3356 3614 6.001460 ACAAATCCAAGACAAGTAATTCGGA 58.999 36.000 0.00 0.00 0.00 4.55
3357 3615 6.488683 ACAAATCCAAGACAAGTAATTCGGAA 59.511 34.615 0.00 0.00 0.00 4.30
3358 3616 6.496338 AATCCAAGACAAGTAATTCGGAAC 57.504 37.500 0.00 0.00 0.00 3.62
3389 3647 9.771534 GGAGTATTACATTCATAGAGCTTTCTT 57.228 33.333 0.00 0.00 0.00 2.52
3600 3860 1.000506 GCGACACCTGTTCAGGTTCTA 59.999 52.381 20.24 0.00 40.85 2.10
3981 4242 0.819259 ACAACAACAGGCATGACGCT 60.819 50.000 4.84 0.00 41.91 5.07
4350 4612 4.284746 AGAACTCTAGCTTGTTTACCTGCT 59.715 41.667 0.00 0.00 39.30 4.24
4378 4860 0.317603 CTGCTGCTTGAGTGTGTTGC 60.318 55.000 0.00 0.00 0.00 4.17
4417 4905 3.878086 TCTGATTGTGTTTTCAGACGC 57.122 42.857 0.00 0.00 42.52 5.19
4437 4925 1.635487 CGGTATGGGAATGGGATGGAT 59.365 52.381 0.00 0.00 0.00 3.41
4462 4950 2.507407 TTATTGGGTTGAGCTGGGTC 57.493 50.000 0.00 0.00 0.00 4.46
4463 4951 1.668826 TATTGGGTTGAGCTGGGTCT 58.331 50.000 0.00 0.00 0.00 3.85
4543 5081 9.107177 AGCATGAACTAGTTGATCATCTTTAAG 57.893 33.333 14.14 6.14 36.26 1.85
4688 5226 7.439955 ACCGGATTTGAAATTGTTTAAAACCTC 59.560 33.333 9.46 0.00 0.00 3.85
4706 5244 2.293122 CCTCGTGACTTCCAAAAATGCA 59.707 45.455 0.00 0.00 0.00 3.96
4870 5414 8.848474 TTTTTGTGGAATTTTGTTGGTTAGAA 57.152 26.923 0.00 0.00 0.00 2.10
4880 5424 4.223556 TGTTGGTTAGAAACACCAGTCA 57.776 40.909 0.00 0.00 45.27 3.41
4894 5438 4.345257 ACACCAGTCACTCTAACTTCATGT 59.655 41.667 0.00 0.00 0.00 3.21
4895 5439 5.538813 ACACCAGTCACTCTAACTTCATGTA 59.461 40.000 0.00 0.00 0.00 2.29
4935 5479 5.098218 TGCTTTGAAATGCAAAAATGAGC 57.902 34.783 0.00 0.00 45.26 4.26
4936 5480 4.023878 TGCTTTGAAATGCAAAAATGAGCC 60.024 37.500 0.00 0.00 45.26 4.70
4937 5481 4.214758 GCTTTGAAATGCAAAAATGAGCCT 59.785 37.500 0.00 0.00 45.26 4.58
4938 5482 5.676532 TTTGAAATGCAAAAATGAGCCTG 57.323 34.783 0.00 0.00 43.18 4.85
4939 5483 3.666274 TGAAATGCAAAAATGAGCCTGG 58.334 40.909 0.00 0.00 0.00 4.45
4940 5484 2.103537 AATGCAAAAATGAGCCTGGC 57.896 45.000 11.65 11.65 0.00 4.85
4941 5485 1.272807 ATGCAAAAATGAGCCTGGCT 58.727 45.000 23.64 23.64 43.88 4.75
4942 5486 0.319083 TGCAAAAATGAGCCTGGCTG 59.681 50.000 28.82 11.87 39.88 4.85
4943 5487 1.017701 GCAAAAATGAGCCTGGCTGC 61.018 55.000 28.82 18.32 39.88 5.25
4944 5488 0.390735 CAAAAATGAGCCTGGCTGCC 60.391 55.000 28.82 13.54 39.88 4.85
4945 5489 0.543646 AAAAATGAGCCTGGCTGCCT 60.544 50.000 28.82 7.21 39.88 4.75
4946 5490 1.255667 AAAATGAGCCTGGCTGCCTG 61.256 55.000 28.82 19.25 39.88 4.85
4947 5491 3.657038 AATGAGCCTGGCTGCCTGG 62.657 63.158 33.15 33.15 44.16 4.45
4951 5495 4.047125 GCCTGGCTGCCTGGGTTA 62.047 66.667 36.07 10.08 42.02 2.85
4952 5496 2.763215 CCTGGCTGCCTGGGTTAA 59.237 61.111 30.82 4.62 38.71 2.01
4953 5497 1.076549 CCTGGCTGCCTGGGTTAAA 59.923 57.895 30.82 3.87 38.71 1.52
4954 5498 0.967380 CCTGGCTGCCTGGGTTAAAG 60.967 60.000 30.82 13.12 38.71 1.85
4955 5499 0.251341 CTGGCTGCCTGGGTTAAAGT 60.251 55.000 21.03 0.00 0.00 2.66
4956 5500 0.187361 TGGCTGCCTGGGTTAAAGTT 59.813 50.000 21.03 0.00 0.00 2.66
4957 5501 1.425831 TGGCTGCCTGGGTTAAAGTTA 59.574 47.619 21.03 0.00 0.00 2.24
4958 5502 1.816835 GGCTGCCTGGGTTAAAGTTAC 59.183 52.381 12.43 0.00 0.00 2.50
4959 5503 2.510613 GCTGCCTGGGTTAAAGTTACA 58.489 47.619 0.00 0.00 0.00 2.41
4960 5504 3.089284 GCTGCCTGGGTTAAAGTTACAT 58.911 45.455 0.00 0.00 0.00 2.29
4961 5505 3.119495 GCTGCCTGGGTTAAAGTTACATG 60.119 47.826 0.00 0.00 0.00 3.21
4962 5506 3.426615 TGCCTGGGTTAAAGTTACATGG 58.573 45.455 0.00 0.00 0.00 3.66
4963 5507 3.181427 TGCCTGGGTTAAAGTTACATGGT 60.181 43.478 0.00 0.00 0.00 3.55
4964 5508 3.830178 GCCTGGGTTAAAGTTACATGGTT 59.170 43.478 0.00 0.00 0.00 3.67
4965 5509 4.282449 GCCTGGGTTAAAGTTACATGGTTT 59.718 41.667 0.00 0.00 0.00 3.27
4966 5510 5.778862 CCTGGGTTAAAGTTACATGGTTTG 58.221 41.667 0.00 0.00 0.00 2.93
4967 5511 5.279256 CCTGGGTTAAAGTTACATGGTTTGG 60.279 44.000 0.00 0.00 0.00 3.28
4968 5512 4.589374 TGGGTTAAAGTTACATGGTTTGGG 59.411 41.667 0.00 0.00 0.00 4.12
4969 5513 4.833938 GGGTTAAAGTTACATGGTTTGGGA 59.166 41.667 0.00 0.00 0.00 4.37
4970 5514 5.304871 GGGTTAAAGTTACATGGTTTGGGAA 59.695 40.000 0.00 0.00 0.00 3.97
4971 5515 6.183360 GGGTTAAAGTTACATGGTTTGGGAAA 60.183 38.462 0.00 0.00 0.00 3.13
4972 5516 7.446769 GGTTAAAGTTACATGGTTTGGGAAAT 58.553 34.615 0.00 0.00 0.00 2.17
4973 5517 7.934665 GGTTAAAGTTACATGGTTTGGGAAATT 59.065 33.333 0.00 0.00 0.00 1.82
4974 5518 8.984764 GTTAAAGTTACATGGTTTGGGAAATTC 58.015 33.333 0.00 0.00 0.00 2.17
4975 5519 5.738619 AGTTACATGGTTTGGGAAATTCC 57.261 39.130 2.79 2.79 35.23 3.01
4976 5520 5.151454 AGTTACATGGTTTGGGAAATTCCA 58.849 37.500 14.68 0.00 38.64 3.53
4977 5521 5.604650 AGTTACATGGTTTGGGAAATTCCAA 59.395 36.000 14.68 0.00 44.29 3.53
4978 5522 4.622260 ACATGGTTTGGGAAATTCCAAG 57.378 40.909 14.68 0.00 46.19 3.61
4979 5523 3.973305 ACATGGTTTGGGAAATTCCAAGT 59.027 39.130 14.68 0.00 46.19 3.16
4980 5524 4.411869 ACATGGTTTGGGAAATTCCAAGTT 59.588 37.500 14.68 0.00 46.19 2.66
4981 5525 5.104151 ACATGGTTTGGGAAATTCCAAGTTT 60.104 36.000 14.68 0.00 46.19 2.66
4982 5526 6.100424 ACATGGTTTGGGAAATTCCAAGTTTA 59.900 34.615 14.68 0.00 46.19 2.01
4983 5527 6.561519 TGGTTTGGGAAATTCCAAGTTTAA 57.438 33.333 14.68 0.00 46.19 1.52
4984 5528 7.142995 TGGTTTGGGAAATTCCAAGTTTAAT 57.857 32.000 14.68 0.00 46.19 1.40
4985 5529 8.263854 TGGTTTGGGAAATTCCAAGTTTAATA 57.736 30.769 14.68 0.00 46.19 0.98
4986 5530 8.151596 TGGTTTGGGAAATTCCAAGTTTAATAC 58.848 33.333 14.68 0.00 46.19 1.89
4987 5531 8.372459 GGTTTGGGAAATTCCAAGTTTAATACT 58.628 33.333 14.68 0.00 46.19 2.12
4988 5532 9.419297 GTTTGGGAAATTCCAAGTTTAATACTC 57.581 33.333 14.68 0.00 46.19 2.59
4989 5533 8.950007 TTGGGAAATTCCAAGTTTAATACTCT 57.050 30.769 14.68 0.00 41.44 3.24
4990 5534 8.950007 TGGGAAATTCCAAGTTTAATACTCTT 57.050 30.769 14.68 0.00 38.64 2.85
4991 5535 9.374711 TGGGAAATTCCAAGTTTAATACTCTTT 57.625 29.630 14.68 0.00 38.64 2.52
4997 5541 8.754991 TTCCAAGTTTAATACTCTTTTCCACA 57.245 30.769 0.00 0.00 35.54 4.17
4998 5542 8.934023 TCCAAGTTTAATACTCTTTTCCACAT 57.066 30.769 0.00 0.00 35.54 3.21
4999 5543 8.792633 TCCAAGTTTAATACTCTTTTCCACATG 58.207 33.333 0.00 0.00 35.54 3.21
5000 5544 8.792633 CCAAGTTTAATACTCTTTTCCACATGA 58.207 33.333 0.00 0.00 35.54 3.07
5001 5545 9.612620 CAAGTTTAATACTCTTTTCCACATGAC 57.387 33.333 0.00 0.00 35.54 3.06
5002 5546 8.336801 AGTTTAATACTCTTTTCCACATGACC 57.663 34.615 0.00 0.00 28.23 4.02
5003 5547 7.942341 AGTTTAATACTCTTTTCCACATGACCA 59.058 33.333 0.00 0.00 28.23 4.02
5004 5548 8.739972 GTTTAATACTCTTTTCCACATGACCAT 58.260 33.333 0.00 0.00 0.00 3.55
5005 5549 9.967451 TTTAATACTCTTTTCCACATGACCATA 57.033 29.630 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 92 1.456705 CGGGGAAGAGAGAGAGGGG 60.457 68.421 0.00 0.00 0.00 4.79
90 94 2.131067 GGCGGGGAAGAGAGAGAGG 61.131 68.421 0.00 0.00 0.00 3.69
100 104 2.441532 CTCTACTCGGGCGGGGAA 60.442 66.667 0.00 0.00 0.00 3.97
118 122 4.840772 CGTTCGAGAAAAATAGCAACAGTG 59.159 41.667 0.00 0.00 0.00 3.66
143 147 2.565391 GGGTTGGGGTATGTTTTCCTTG 59.435 50.000 0.00 0.00 0.00 3.61
146 150 2.312424 TGGGTTGGGGTATGTTTTCC 57.688 50.000 0.00 0.00 0.00 3.13
153 157 0.999712 CTCACCTTGGGTTGGGGTAT 59.000 55.000 0.00 0.00 31.02 2.73
157 161 2.080654 TTTTCTCACCTTGGGTTGGG 57.919 50.000 0.00 0.00 31.02 4.12
190 195 3.128589 CCTCTCTCTCTCTCTTCAAACGG 59.871 52.174 0.00 0.00 0.00 4.44
208 213 1.903955 GCTTTTCTCCTCTCCCCCTCT 60.904 57.143 0.00 0.00 0.00 3.69
210 215 0.178861 TGCTTTTCTCCTCTCCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
213 218 1.209261 CCTCTGCTTTTCTCCTCTCCC 59.791 57.143 0.00 0.00 0.00 4.30
215 220 3.430236 GCTACCTCTGCTTTTCTCCTCTC 60.430 52.174 0.00 0.00 0.00 3.20
217 222 2.499693 AGCTACCTCTGCTTTTCTCCTC 59.500 50.000 0.00 0.00 37.52 3.71
220 225 2.419436 GGGAGCTACCTCTGCTTTTCTC 60.419 54.545 8.12 0.00 41.30 2.87
223 228 0.621082 GGGGAGCTACCTCTGCTTTT 59.379 55.000 16.60 0.00 41.30 2.27
224 229 0.547712 TGGGGAGCTACCTCTGCTTT 60.548 55.000 16.60 0.00 41.30 3.51
225 230 0.547712 TTGGGGAGCTACCTCTGCTT 60.548 55.000 16.60 0.00 41.30 3.91
226 231 1.081092 TTGGGGAGCTACCTCTGCT 59.919 57.895 16.60 0.00 44.24 4.24
227 232 1.222113 GTTGGGGAGCTACCTCTGC 59.778 63.158 16.60 0.00 40.48 4.26
228 233 1.757699 GTAGTTGGGGAGCTACCTCTG 59.242 57.143 16.60 0.00 40.48 3.35
229 234 1.685491 CGTAGTTGGGGAGCTACCTCT 60.685 57.143 16.60 13.35 40.48 3.69
230 235 0.745468 CGTAGTTGGGGAGCTACCTC 59.255 60.000 16.60 5.65 40.19 3.85
231 236 1.328430 GCGTAGTTGGGGAGCTACCT 61.328 60.000 16.60 0.00 38.98 3.08
390 579 1.021968 GCAGCGAAATTACGGGGAAT 58.978 50.000 0.00 0.00 0.00 3.01
451 640 3.806507 GCAGAGCTATTCCAATCCAGAGG 60.807 52.174 0.00 0.00 0.00 3.69
452 641 3.401182 GCAGAGCTATTCCAATCCAGAG 58.599 50.000 0.00 0.00 0.00 3.35
453 642 2.105477 GGCAGAGCTATTCCAATCCAGA 59.895 50.000 0.00 0.00 0.00 3.86
454 643 2.106166 AGGCAGAGCTATTCCAATCCAG 59.894 50.000 0.00 0.00 0.00 3.86
471 660 0.465824 GACTCGGCTAGGTAGAGGCA 60.466 60.000 0.00 0.00 42.01 4.75
476 665 1.173444 ATGCGGACTCGGCTAGGTAG 61.173 60.000 9.73 0.00 36.79 3.18
477 666 0.754217 AATGCGGACTCGGCTAGGTA 60.754 55.000 9.73 0.00 36.79 3.08
478 667 0.754217 TAATGCGGACTCGGCTAGGT 60.754 55.000 9.73 0.00 36.79 3.08
480 669 0.952280 TCTAATGCGGACTCGGCTAG 59.048 55.000 9.73 4.80 36.79 3.42
481 670 1.066605 GTTCTAATGCGGACTCGGCTA 59.933 52.381 9.73 0.00 36.79 3.93
482 671 0.179108 GTTCTAATGCGGACTCGGCT 60.179 55.000 9.73 0.00 36.79 5.52
483 672 0.179108 AGTTCTAATGCGGACTCGGC 60.179 55.000 1.67 1.67 36.79 5.54
484 673 2.358267 AGTAGTTCTAATGCGGACTCGG 59.642 50.000 0.00 0.00 36.79 4.63
485 674 3.064958 TCAGTAGTTCTAATGCGGACTCG 59.935 47.826 2.91 0.00 39.81 4.18
486 675 4.602995 CTCAGTAGTTCTAATGCGGACTC 58.397 47.826 2.91 0.00 0.00 3.36
487 676 3.181485 GCTCAGTAGTTCTAATGCGGACT 60.181 47.826 2.91 0.00 0.00 3.85
488 677 3.117046 GCTCAGTAGTTCTAATGCGGAC 58.883 50.000 2.91 0.00 0.00 4.79
489 678 3.024547 AGCTCAGTAGTTCTAATGCGGA 58.975 45.455 2.91 0.00 0.00 5.54
490 679 3.119291 CAGCTCAGTAGTTCTAATGCGG 58.881 50.000 2.91 0.92 0.00 5.69
491 680 4.033990 TCAGCTCAGTAGTTCTAATGCG 57.966 45.455 2.91 0.00 0.00 4.73
506 699 0.173255 GCTCACTCCTCACTCAGCTC 59.827 60.000 0.00 0.00 0.00 4.09
549 742 1.864669 CTCCTCCTCCTCTCTTGCTT 58.135 55.000 0.00 0.00 0.00 3.91
600 796 1.299541 CACGCACCTAATGGATGGAC 58.700 55.000 0.00 0.00 37.04 4.02
601 797 0.463654 GCACGCACCTAATGGATGGA 60.464 55.000 0.00 0.00 37.04 3.41
602 798 0.747644 TGCACGCACCTAATGGATGG 60.748 55.000 0.00 0.00 37.04 3.51
603 799 0.378257 GTGCACGCACCTAATGGATG 59.622 55.000 11.13 0.00 40.79 3.51
630 826 3.417779 GTGGGGGTTAGGAGGGGC 61.418 72.222 0.00 0.00 0.00 5.80
690 886 7.284034 ACCTCCAGAATATTATCAGCAGTTTTG 59.716 37.037 0.00 0.00 0.00 2.44
691 887 7.349598 ACCTCCAGAATATTATCAGCAGTTTT 58.650 34.615 0.00 0.00 0.00 2.43
692 888 6.904626 ACCTCCAGAATATTATCAGCAGTTT 58.095 36.000 0.00 0.00 0.00 2.66
693 889 6.506538 ACCTCCAGAATATTATCAGCAGTT 57.493 37.500 0.00 0.00 0.00 3.16
694 890 6.126652 ACAACCTCCAGAATATTATCAGCAGT 60.127 38.462 0.00 0.00 0.00 4.40
695 891 6.294473 ACAACCTCCAGAATATTATCAGCAG 58.706 40.000 0.00 0.00 0.00 4.24
696 892 6.252599 ACAACCTCCAGAATATTATCAGCA 57.747 37.500 0.00 0.00 0.00 4.41
697 893 7.420800 CAAACAACCTCCAGAATATTATCAGC 58.579 38.462 0.00 0.00 0.00 4.26
783 979 4.781071 CTGCATCTCAAACTCACAAACTC 58.219 43.478 0.00 0.00 0.00 3.01
784 980 3.004106 GCTGCATCTCAAACTCACAAACT 59.996 43.478 0.00 0.00 0.00 2.66
787 983 2.854963 AGCTGCATCTCAAACTCACAA 58.145 42.857 1.02 0.00 0.00 3.33
788 984 2.556144 AGCTGCATCTCAAACTCACA 57.444 45.000 1.02 0.00 0.00 3.58
791 987 1.396301 CGGAAGCTGCATCTCAAACTC 59.604 52.381 1.02 0.00 0.00 3.01
792 988 1.002430 TCGGAAGCTGCATCTCAAACT 59.998 47.619 1.02 0.00 0.00 2.66
879 1088 8.503458 ACAAACAAAACCAATCAATCAATCAA 57.497 26.923 0.00 0.00 0.00 2.57
918 1127 2.736192 GTGAGCTTGAGTTTCAGCTCTC 59.264 50.000 19.16 13.31 42.58 3.20
919 1128 2.765122 GTGAGCTTGAGTTTCAGCTCT 58.235 47.619 19.16 0.00 42.58 4.09
943 1152 2.476051 CGTTACCGCAGCTGCTTG 59.524 61.111 34.22 26.50 39.32 4.01
1203 1433 2.360726 TGCTGCTGATGCTGGTGG 60.361 61.111 0.00 0.00 40.48 4.61
1542 1784 4.824515 CCGGAGGCGGAGGAGAGT 62.825 72.222 0.00 0.00 46.14 3.24
1732 1974 7.065923 GGCAAGTTAGTTAAGATTTACTCCTGG 59.934 40.741 0.00 0.00 0.00 4.45
1735 1977 7.916914 TGGCAAGTTAGTTAAGATTTACTCC 57.083 36.000 0.00 0.00 0.00 3.85
1736 1978 8.947115 ACATGGCAAGTTAGTTAAGATTTACTC 58.053 33.333 0.00 0.00 0.00 2.59
1738 1980 8.947115 AGACATGGCAAGTTAGTTAAGATTTAC 58.053 33.333 0.00 0.00 0.00 2.01
1740 1982 7.575720 GCAGACATGGCAAGTTAGTTAAGATTT 60.576 37.037 0.00 0.00 0.00 2.17
1741 1983 6.127897 GCAGACATGGCAAGTTAGTTAAGATT 60.128 38.462 0.00 0.00 0.00 2.40
1742 1984 5.355350 GCAGACATGGCAAGTTAGTTAAGAT 59.645 40.000 0.00 0.00 0.00 2.40
1743 1985 4.695455 GCAGACATGGCAAGTTAGTTAAGA 59.305 41.667 0.00 0.00 0.00 2.10
1744 1986 4.974591 GCAGACATGGCAAGTTAGTTAAG 58.025 43.478 0.00 0.00 0.00 1.85
1895 2141 7.840716 TGAATGGATGGAGAAGGAATAAACAAT 59.159 33.333 0.00 0.00 0.00 2.71
1910 2156 3.058341 ACTGGATGGATGAATGGATGGA 58.942 45.455 0.00 0.00 0.00 3.41
1990 2236 0.592754 GCTCCAACTACTCGCTAGCG 60.593 60.000 30.91 30.91 41.35 4.26
2165 2414 1.686052 TGTAGTTGCAAAAAGGCCAGG 59.314 47.619 5.01 0.00 0.00 4.45
2268 2517 5.339990 GGTGAATTTGATCCAACAATACCG 58.660 41.667 0.00 0.00 0.00 4.02
2652 2909 5.728351 AAGAAAAATCACAAACGACTCGA 57.272 34.783 5.20 0.00 0.00 4.04
2716 2973 6.030228 GTGACTCCTCAAAAGAAACAACAAG 58.970 40.000 0.00 0.00 0.00 3.16
2775 3032 3.859961 ACGACAGAATTAGATTGCAGACG 59.140 43.478 0.00 0.00 0.00 4.18
3045 3302 7.053498 TGTGCAAGCATCAGTATCCTATTTAA 58.947 34.615 0.00 0.00 0.00 1.52
3047 3304 5.439721 TGTGCAAGCATCAGTATCCTATTT 58.560 37.500 0.00 0.00 0.00 1.40
3252 3510 6.496338 AATCCAAGACAAGTAATTCGGAAC 57.504 37.500 0.00 0.00 0.00 3.62
3253 3511 6.488683 ACAAATCCAAGACAAGTAATTCGGAA 59.511 34.615 0.00 0.00 0.00 4.30
3254 3512 6.001460 ACAAATCCAAGACAAGTAATTCGGA 58.999 36.000 0.00 0.00 0.00 4.55
3255 3513 6.149474 AGACAAATCCAAGACAAGTAATTCGG 59.851 38.462 0.00 0.00 0.00 4.30
3256 3514 7.133891 AGACAAATCCAAGACAAGTAATTCG 57.866 36.000 0.00 0.00 0.00 3.34
3257 3515 9.436957 TCTAGACAAATCCAAGACAAGTAATTC 57.563 33.333 0.00 0.00 0.00 2.17
3258 3516 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
3260 3518 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
3261 3519 8.188799 CGTATCTAGACAAATCCAAGACAAGTA 58.811 37.037 0.00 0.00 0.00 2.24
3262 3520 7.036220 CGTATCTAGACAAATCCAAGACAAGT 58.964 38.462 0.00 0.00 0.00 3.16
3263 3521 6.477033 CCGTATCTAGACAAATCCAAGACAAG 59.523 42.308 0.00 0.00 0.00 3.16
3264 3522 6.153851 TCCGTATCTAGACAAATCCAAGACAA 59.846 38.462 0.00 0.00 0.00 3.18
3265 3523 5.655090 TCCGTATCTAGACAAATCCAAGACA 59.345 40.000 0.00 0.00 0.00 3.41
3266 3524 6.145338 TCCGTATCTAGACAAATCCAAGAC 57.855 41.667 0.00 0.00 0.00 3.01
3267 3525 5.302059 CCTCCGTATCTAGACAAATCCAAGA 59.698 44.000 0.00 0.00 0.00 3.02
3268 3526 5.069251 ACCTCCGTATCTAGACAAATCCAAG 59.931 44.000 0.00 0.00 0.00 3.61
3269 3527 4.960469 ACCTCCGTATCTAGACAAATCCAA 59.040 41.667 0.00 0.00 0.00 3.53
3270 3528 4.543689 ACCTCCGTATCTAGACAAATCCA 58.456 43.478 0.00 0.00 0.00 3.41
3271 3529 6.837471 ATACCTCCGTATCTAGACAAATCC 57.163 41.667 0.00 0.00 28.45 3.01
3283 3541 7.450634 TCATTTTAGTGCTAGATACCTCCGTAT 59.549 37.037 0.00 0.00 37.92 3.06
3284 3542 6.774170 TCATTTTAGTGCTAGATACCTCCGTA 59.226 38.462 0.00 0.00 0.00 4.02
3285 3543 5.597182 TCATTTTAGTGCTAGATACCTCCGT 59.403 40.000 0.00 0.00 0.00 4.69
3286 3544 6.085555 TCATTTTAGTGCTAGATACCTCCG 57.914 41.667 0.00 0.00 0.00 4.63
3287 3545 7.014808 AGACTCATTTTAGTGCTAGATACCTCC 59.985 40.741 0.00 0.00 0.00 4.30
3288 3546 7.947282 AGACTCATTTTAGTGCTAGATACCTC 58.053 38.462 0.00 0.00 0.00 3.85
3289 3547 7.906199 AGACTCATTTTAGTGCTAGATACCT 57.094 36.000 0.00 0.00 0.00 3.08
3290 3548 9.069082 TCTAGACTCATTTTAGTGCTAGATACC 57.931 37.037 0.00 0.00 34.69 2.73
3294 3552 9.628500 TGTATCTAGACTCATTTTAGTGCTAGA 57.372 33.333 0.00 0.00 38.76 2.43
3297 3555 8.364142 GGATGTATCTAGACTCATTTTAGTGCT 58.636 37.037 11.25 0.00 0.00 4.40
3298 3556 7.327275 CGGATGTATCTAGACTCATTTTAGTGC 59.673 40.741 11.25 0.00 0.00 4.40
3299 3557 8.353684 ACGGATGTATCTAGACTCATTTTAGTG 58.646 37.037 11.25 3.85 0.00 2.74
3300 3558 8.466617 ACGGATGTATCTAGACTCATTTTAGT 57.533 34.615 11.25 7.70 0.00 2.24
3316 3574 7.776618 TGGATTTGTCTAGATACGGATGTAT 57.223 36.000 0.00 0.00 43.97 2.29
3317 3575 7.504574 TCTTGGATTTGTCTAGATACGGATGTA 59.495 37.037 0.00 0.00 34.45 2.29
3318 3576 6.323996 TCTTGGATTTGTCTAGATACGGATGT 59.676 38.462 0.00 0.00 0.00 3.06
3319 3577 6.642950 GTCTTGGATTTGTCTAGATACGGATG 59.357 42.308 0.00 0.00 0.00 3.51
3320 3578 6.323996 TGTCTTGGATTTGTCTAGATACGGAT 59.676 38.462 0.00 0.00 0.00 4.18
3321 3579 5.655090 TGTCTTGGATTTGTCTAGATACGGA 59.345 40.000 0.00 0.00 0.00 4.69
3322 3580 5.902681 TGTCTTGGATTTGTCTAGATACGG 58.097 41.667 0.00 0.00 0.00 4.02
3323 3581 7.036220 ACTTGTCTTGGATTTGTCTAGATACG 58.964 38.462 0.00 0.00 0.00 3.06
3324 3582 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
3326 3584 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
3327 3585 9.436957 GAATTACTTGTCTTGGATTTGTCTAGA 57.563 33.333 0.00 0.00 0.00 2.43
3328 3586 8.383619 CGAATTACTTGTCTTGGATTTGTCTAG 58.616 37.037 0.00 0.00 0.00 2.43
3329 3587 7.333423 CCGAATTACTTGTCTTGGATTTGTCTA 59.667 37.037 0.00 0.00 0.00 2.59
3330 3588 6.149474 CCGAATTACTTGTCTTGGATTTGTCT 59.851 38.462 0.00 0.00 0.00 3.41
3331 3589 6.148811 TCCGAATTACTTGTCTTGGATTTGTC 59.851 38.462 0.00 0.00 0.00 3.18
3332 3590 6.001460 TCCGAATTACTTGTCTTGGATTTGT 58.999 36.000 0.00 0.00 0.00 2.83
3333 3591 6.494893 TCCGAATTACTTGTCTTGGATTTG 57.505 37.500 0.00 0.00 0.00 2.32
3334 3592 6.348213 CGTTCCGAATTACTTGTCTTGGATTT 60.348 38.462 0.00 0.00 0.00 2.17
3335 3593 5.121768 CGTTCCGAATTACTTGTCTTGGATT 59.878 40.000 0.00 0.00 0.00 3.01
3336 3594 4.630069 CGTTCCGAATTACTTGTCTTGGAT 59.370 41.667 0.00 0.00 0.00 3.41
3337 3595 3.991773 CGTTCCGAATTACTTGTCTTGGA 59.008 43.478 0.00 0.00 0.00 3.53
3338 3596 3.124636 CCGTTCCGAATTACTTGTCTTGG 59.875 47.826 0.00 0.00 0.00 3.61
3339 3597 3.991773 TCCGTTCCGAATTACTTGTCTTG 59.008 43.478 0.00 0.00 0.00 3.02
3340 3598 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
3341 3599 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
3342 3600 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
3343 3601 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
3344 3602 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
3345 3603 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
3346 3604 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
3347 3605 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
3348 3606 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
3349 3607 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
3350 3608 2.083628 ATACTCCCTCCGTTCCGAAT 57.916 50.000 0.00 0.00 0.00 3.34
3351 3609 1.856629 AATACTCCCTCCGTTCCGAA 58.143 50.000 0.00 0.00 0.00 4.30
3352 3610 2.301346 GTAATACTCCCTCCGTTCCGA 58.699 52.381 0.00 0.00 0.00 4.55
3353 3611 2.026641 TGTAATACTCCCTCCGTTCCG 58.973 52.381 0.00 0.00 0.00 4.30
3354 3612 4.100498 TGAATGTAATACTCCCTCCGTTCC 59.900 45.833 0.00 0.00 0.00 3.62
3355 3613 5.272283 TGAATGTAATACTCCCTCCGTTC 57.728 43.478 0.00 0.00 0.00 3.95
3356 3614 5.888982 ATGAATGTAATACTCCCTCCGTT 57.111 39.130 0.00 0.00 0.00 4.44
3357 3615 6.312529 TCTATGAATGTAATACTCCCTCCGT 58.687 40.000 0.00 0.00 0.00 4.69
3358 3616 6.626181 GCTCTATGAATGTAATACTCCCTCCG 60.626 46.154 0.00 0.00 0.00 4.63
3359 3617 6.439058 AGCTCTATGAATGTAATACTCCCTCC 59.561 42.308 0.00 0.00 0.00 4.30
3360 3618 7.475137 AGCTCTATGAATGTAATACTCCCTC 57.525 40.000 0.00 0.00 0.00 4.30
3361 3619 7.863901 AAGCTCTATGAATGTAATACTCCCT 57.136 36.000 0.00 0.00 0.00 4.20
3362 3620 8.371699 AGAAAGCTCTATGAATGTAATACTCCC 58.628 37.037 0.00 0.00 0.00 4.30
3363 3621 9.771534 AAGAAAGCTCTATGAATGTAATACTCC 57.228 33.333 0.00 0.00 0.00 3.85
3365 3623 9.771534 GGAAGAAAGCTCTATGAATGTAATACT 57.228 33.333 0.00 0.00 0.00 2.12
3366 3624 9.771534 AGGAAGAAAGCTCTATGAATGTAATAC 57.228 33.333 0.00 0.00 0.00 1.89
3600 3860 5.163519 CGGCAGAGACAATTCCCAAATTAAT 60.164 40.000 0.00 0.00 33.27 1.40
4282 4543 7.666063 TCTAGAATTCATGATCCACAGAAGA 57.334 36.000 8.44 0.00 0.00 2.87
4417 4905 1.064003 TCCATCCCATTCCCATACCG 58.936 55.000 0.00 0.00 0.00 4.02
4437 4925 4.385199 CCCAGCTCAACCCAATAATACTGA 60.385 45.833 0.00 0.00 0.00 3.41
4543 5081 3.040409 GCCTGCAGCAGTTTATTGC 57.960 52.632 21.26 12.08 44.41 3.56
4578 5116 1.340991 ACCAAGATGTCCCATTTCCCG 60.341 52.381 0.00 0.00 0.00 5.14
4580 5118 4.164221 TCTCTACCAAGATGTCCCATTTCC 59.836 45.833 0.00 0.00 0.00 3.13
4688 5226 3.077229 TGTGCATTTTTGGAAGTCACG 57.923 42.857 0.00 0.00 0.00 4.35
4706 5244 7.043565 GCATTTCCTATGACCATGAATTTTGT 58.956 34.615 0.00 0.00 0.00 2.83
4870 5414 5.163301 ACATGAAGTTAGAGTGACTGGTGTT 60.163 40.000 0.00 0.00 0.00 3.32
4913 5457 4.023878 GGCTCATTTTTGCATTTCAAAGCA 60.024 37.500 9.76 0.00 44.62 3.91
4914 5458 4.214758 AGGCTCATTTTTGCATTTCAAAGC 59.785 37.500 0.00 0.00 44.62 3.51
4915 5459 5.334569 CCAGGCTCATTTTTGCATTTCAAAG 60.335 40.000 0.00 0.00 44.62 2.77
4916 5460 4.515944 CCAGGCTCATTTTTGCATTTCAAA 59.484 37.500 0.00 0.00 42.50 2.69
4917 5461 4.066490 CCAGGCTCATTTTTGCATTTCAA 58.934 39.130 0.00 0.00 0.00 2.69
4918 5462 3.666274 CCAGGCTCATTTTTGCATTTCA 58.334 40.909 0.00 0.00 0.00 2.69
4919 5463 2.417586 GCCAGGCTCATTTTTGCATTTC 59.582 45.455 3.29 0.00 0.00 2.17
4920 5464 2.039348 AGCCAGGCTCATTTTTGCATTT 59.961 40.909 8.70 0.00 30.62 2.32
4921 5465 1.626825 AGCCAGGCTCATTTTTGCATT 59.373 42.857 8.70 0.00 30.62 3.56
4922 5466 1.066430 CAGCCAGGCTCATTTTTGCAT 60.066 47.619 12.53 0.00 36.40 3.96
4923 5467 0.319083 CAGCCAGGCTCATTTTTGCA 59.681 50.000 12.53 0.00 36.40 4.08
4924 5468 1.017701 GCAGCCAGGCTCATTTTTGC 61.018 55.000 12.53 7.49 36.40 3.68
4925 5469 0.390735 GGCAGCCAGGCTCATTTTTG 60.391 55.000 12.53 0.00 36.40 2.44
4926 5470 1.977685 GGCAGCCAGGCTCATTTTT 59.022 52.632 12.53 0.00 36.40 1.94
4927 5471 3.704151 GGCAGCCAGGCTCATTTT 58.296 55.556 12.53 0.00 36.40 1.82
4934 5478 3.583882 TTAACCCAGGCAGCCAGGC 62.584 63.158 17.79 1.84 44.61 4.85
4935 5479 0.967380 CTTTAACCCAGGCAGCCAGG 60.967 60.000 16.28 16.28 0.00 4.45
4936 5480 0.251341 ACTTTAACCCAGGCAGCCAG 60.251 55.000 15.80 5.28 0.00 4.85
4937 5481 0.187361 AACTTTAACCCAGGCAGCCA 59.813 50.000 15.80 0.00 0.00 4.75
4938 5482 1.816835 GTAACTTTAACCCAGGCAGCC 59.183 52.381 1.84 1.84 0.00 4.85
4939 5483 2.510613 TGTAACTTTAACCCAGGCAGC 58.489 47.619 0.00 0.00 0.00 5.25
4940 5484 3.443681 CCATGTAACTTTAACCCAGGCAG 59.556 47.826 0.00 0.00 0.00 4.85
4941 5485 3.181427 ACCATGTAACTTTAACCCAGGCA 60.181 43.478 0.00 0.00 0.00 4.75
4942 5486 3.427573 ACCATGTAACTTTAACCCAGGC 58.572 45.455 0.00 0.00 0.00 4.85
4943 5487 5.279256 CCAAACCATGTAACTTTAACCCAGG 60.279 44.000 0.00 0.00 0.00 4.45
4944 5488 5.279256 CCCAAACCATGTAACTTTAACCCAG 60.279 44.000 0.00 0.00 0.00 4.45
4945 5489 4.589374 CCCAAACCATGTAACTTTAACCCA 59.411 41.667 0.00 0.00 0.00 4.51
4946 5490 4.833938 TCCCAAACCATGTAACTTTAACCC 59.166 41.667 0.00 0.00 0.00 4.11
4947 5491 6.408107 TTCCCAAACCATGTAACTTTAACC 57.592 37.500 0.00 0.00 0.00 2.85
4948 5492 8.896320 AATTTCCCAAACCATGTAACTTTAAC 57.104 30.769 0.00 0.00 0.00 2.01
4949 5493 8.151596 GGAATTTCCCAAACCATGTAACTTTAA 58.848 33.333 3.89 0.00 0.00 1.52
4950 5494 7.290248 TGGAATTTCCCAAACCATGTAACTTTA 59.710 33.333 12.90 0.00 35.03 1.85
4951 5495 6.100424 TGGAATTTCCCAAACCATGTAACTTT 59.900 34.615 12.90 0.00 35.03 2.66
4952 5496 5.604650 TGGAATTTCCCAAACCATGTAACTT 59.395 36.000 12.90 0.00 35.03 2.66
4953 5497 5.151454 TGGAATTTCCCAAACCATGTAACT 58.849 37.500 12.90 0.00 35.03 2.24
4954 5498 5.476091 TGGAATTTCCCAAACCATGTAAC 57.524 39.130 12.90 0.00 35.03 2.50
4955 5499 5.604650 ACTTGGAATTTCCCAAACCATGTAA 59.395 36.000 12.90 0.00 44.78 2.41
4956 5500 5.151454 ACTTGGAATTTCCCAAACCATGTA 58.849 37.500 12.90 0.00 44.78 2.29
4957 5501 3.973305 ACTTGGAATTTCCCAAACCATGT 59.027 39.130 12.90 0.00 44.78 3.21
4958 5502 4.622260 ACTTGGAATTTCCCAAACCATG 57.378 40.909 12.90 0.00 44.78 3.66
4959 5503 5.645056 AAACTTGGAATTTCCCAAACCAT 57.355 34.783 12.90 0.00 44.78 3.55
4960 5504 6.561519 TTAAACTTGGAATTTCCCAAACCA 57.438 33.333 12.90 0.00 44.78 3.67
4961 5505 8.372459 AGTATTAAACTTGGAATTTCCCAAACC 58.628 33.333 12.90 0.00 44.78 3.27
4962 5506 9.419297 GAGTATTAAACTTGGAATTTCCCAAAC 57.581 33.333 12.90 2.02 44.78 2.93
4963 5507 9.374711 AGAGTATTAAACTTGGAATTTCCCAAA 57.625 29.630 12.90 0.85 44.78 3.28
4964 5508 8.950007 AGAGTATTAAACTTGGAATTTCCCAA 57.050 30.769 12.90 6.57 43.42 4.12
4965 5509 8.950007 AAGAGTATTAAACTTGGAATTTCCCA 57.050 30.769 12.90 0.83 39.07 4.37
4971 5515 9.362151 TGTGGAAAAGAGTATTAAACTTGGAAT 57.638 29.630 0.00 0.00 39.07 3.01
4972 5516 8.754991 TGTGGAAAAGAGTATTAAACTTGGAA 57.245 30.769 0.00 0.00 39.07 3.53
4973 5517 8.792633 CATGTGGAAAAGAGTATTAAACTTGGA 58.207 33.333 0.00 0.00 39.07 3.53
4974 5518 8.792633 TCATGTGGAAAAGAGTATTAAACTTGG 58.207 33.333 0.00 0.00 39.07 3.61
4975 5519 9.612620 GTCATGTGGAAAAGAGTATTAAACTTG 57.387 33.333 0.00 0.00 39.07 3.16
4976 5520 8.793592 GGTCATGTGGAAAAGAGTATTAAACTT 58.206 33.333 0.00 0.00 39.07 2.66
4977 5521 7.942341 TGGTCATGTGGAAAAGAGTATTAAACT 59.058 33.333 0.00 0.00 42.80 2.66
4978 5522 8.106247 TGGTCATGTGGAAAAGAGTATTAAAC 57.894 34.615 0.00 0.00 0.00 2.01
4979 5523 8.877864 ATGGTCATGTGGAAAAGAGTATTAAA 57.122 30.769 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.