Multiple sequence alignment - TraesCS3D01G288700

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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 TraesCS3D01G288700 chr3D 100.000 5294 0 0 1 5294 397778389 397783682 0.000000e+00 9777.0
1 TraesCS3D01G288700 chr3D 94.624 93 5 0 3252 3344 397781608 397781700 1.540000e-30 145.0
2 TraesCS3D01G288700 chr3D 94.624 93 5 0 3220 3312 397781640 397781732 1.540000e-30 145.0
3 TraesCS3D01G288700 chr3A 91.279 3199 148 56 1 3165 517075402 517078503 0.000000e+00 4241.0
4 TraesCS3D01G288700 chr3A 90.448 1539 81 27 3356 4842 517078512 517080036 0.000000e+00 1967.0
5 TraesCS3D01G288700 chr3A 87.179 234 20 5 5064 5294 517080187 517080413 1.890000e-64 257.0
6 TraesCS3D01G288700 chr3A 98.148 108 2 0 3948 4055 368533783 368533890 7.000000e-44 189.0
7 TraesCS3D01G288700 chr3A 93.182 44 2 1 3240 3283 418753074 418753032 4.430000e-06 63.9
8 TraesCS3D01G288700 chr3B 92.234 1983 107 22 2 1947 523558981 523560953 0.000000e+00 2765.0
9 TraesCS3D01G288700 chr3B 93.046 1438 66 10 3432 4842 523562397 523563827 0.000000e+00 2071.0
10 TraesCS3D01G288700 chr3B 89.438 890 62 11 2114 2986 523561133 523562007 0.000000e+00 1094.0
11 TraesCS3D01G288700 chr3B 87.387 333 23 9 4946 5261 523568586 523568916 1.080000e-96 364.0
12 TraesCS3D01G288700 chr3B 92.021 188 13 2 2997 3183 523562119 523562305 4.070000e-66 263.0
13 TraesCS3D01G288700 chr3B 89.423 104 10 1 1983 2085 523560960 523561063 4.300000e-26 130.0
14 TraesCS3D01G288700 chr3B 95.000 60 3 0 4890 4949 523563840 523563899 1.570000e-15 95.3
15 TraesCS3D01G288700 chr3B 82.759 87 9 3 2572 2652 124387297 124387211 7.350000e-09 73.1
16 TraesCS3D01G288700 chr7B 93.145 496 26 7 65 554 304271730 304272223 0.000000e+00 721.0
17 TraesCS3D01G288700 chr7B 100.000 32 0 0 2581 2612 704263023 704262992 5.730000e-05 60.2
18 TraesCS3D01G288700 chr1B 89.286 112 8 2 3175 3283 3949965 3949855 2.570000e-28 137.0
19 TraesCS3D01G288700 chr1B 87.500 112 11 3 3172 3282 150361100 150361209 5.570000e-25 126.0
20 TraesCS3D01G288700 chr2D 93.506 77 4 1 3175 3251 88082887 88082812 4.330000e-21 113.0
21 TraesCS3D01G288700 chr4B 91.463 82 6 1 3170 3251 492223547 492223467 1.560000e-20 111.0
22 TraesCS3D01G288700 chr4A 91.463 82 6 1 3170 3251 56509431 56509351 1.560000e-20 111.0
23 TraesCS3D01G288700 chr1A 91.463 82 5 2 3170 3251 568391198 568391277 1.560000e-20 111.0
24 TraesCS3D01G288700 chr7D 89.535 86 8 1 3166 3251 151326435 151326519 2.020000e-19 108.0
25 TraesCS3D01G288700 chr6D 83.478 115 13 4 3173 3283 383757461 383757349 9.380000e-18 102.0
26 TraesCS3D01G288700 chr6B 83.193 119 12 4 3173 3283 574033743 574033625 9.380000e-18 102.0
27 TraesCS3D01G288700 chr6B 100.000 31 0 0 2582 2612 222858938 222858968 2.060000e-04 58.4
28 TraesCS3D01G288700 chr5D 92.308 65 5 0 3251 3315 11299596 11299532 5.650000e-15 93.5
29 TraesCS3D01G288700 chr5B 91.667 60 4 1 3225 3283 572602165 572602224 1.220000e-11 82.4
30 TraesCS3D01G288700 chr5A 100.000 28 0 0 3330 3357 6613073 6613100 1.000000e-02 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G288700 chr3D 397778389 397783682 5293 False 3355.666667 9777 96.416000 1 5294 3 chr3D.!!$F1 5293
1 TraesCS3D01G288700 chr3A 517075402 517080413 5011 False 2155.000000 4241 89.635333 1 5294 3 chr3A.!!$F2 5293
2 TraesCS3D01G288700 chr3B 523558981 523563899 4918 False 1069.716667 2765 91.860333 2 4949 6 chr3B.!!$F2 4947

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
253 257 0.033504 GTGTTGAGGGCTCGTTCTCA 59.966 55.0 0.00 0.00 38.14 3.27 F
793 809 1.289244 ACCATCCCATCCCCTTCACC 61.289 60.0 0.00 0.00 0.00 4.02 F
1257 1287 0.031043 TTGCTGCTCAACATGCACAC 59.969 50.0 0.00 0.00 36.37 3.82 F
1651 1682 0.250989 TCAGTGGTTTTAAGGCCGGG 60.251 55.0 2.18 0.00 0.00 5.73 F
2315 2405 0.963962 CCATGAACTGCAGCAGGTTT 59.036 50.0 26.38 12.56 35.51 3.27 F
2979 3087 0.966179 TAGGAGACTTGCTGCGACAA 59.034 50.0 0.00 0.00 43.67 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1189 1219 1.537135 GGCTGTTTGGTAGCGCAAAAA 60.537 47.619 11.47 1.03 42.03 1.94 R
2279 2369 0.396435 TGGCGTGGAAGTTCATGTCT 59.604 50.000 5.01 0.00 0.00 3.41 R
2548 2648 1.832883 TCCCATGCATACACCACAAC 58.167 50.000 0.00 0.00 0.00 3.32 R
3339 3549 0.115745 ACTACTCCCTCCGACCCAAA 59.884 55.000 0.00 0.00 0.00 3.28 R
3340 3550 0.115745 AACTACTCCCTCCGACCCAA 59.884 55.000 0.00 0.00 0.00 4.12 R
4856 5132 0.032912 TGACTATCCACGCACCCCTA 60.033 55.000 0.00 0.00 0.00 3.53 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
72 73 2.421424 GTGCTGTTCTGGCTAATCCAAG 59.579 50.000 0.00 0.00 46.01 3.61
88 91 0.524862 CAAGCTTCCATGACACTGGC 59.475 55.000 0.00 0.00 36.16 4.85
112 115 2.560105 ACTGCATTTTTCTTGCTCTCCC 59.440 45.455 0.00 0.00 40.77 4.30
116 119 3.758554 GCATTTTTCTTGCTCTCCCTGTA 59.241 43.478 0.00 0.00 37.14 2.74
149 152 2.171003 CCCCTGTTTTGGTTCCTCATC 58.829 52.381 0.00 0.00 0.00 2.92
172 175 3.228188 ACTCTCATTTGTGCCAAAGGA 57.772 42.857 12.32 12.32 0.00 3.36
247 251 1.157870 AACAACGTGTTGAGGGCTCG 61.158 55.000 18.87 0.00 39.45 5.03
253 257 0.033504 GTGTTGAGGGCTCGTTCTCA 59.966 55.000 0.00 0.00 38.14 3.27
310 321 9.668497 ATCACTGTTTTAGATAAGTTACCTTCC 57.332 33.333 0.00 0.00 31.89 3.46
313 324 7.038799 ACTGTTTTAGATAAGTTACCTTCCGGA 60.039 37.037 0.00 0.00 31.89 5.14
329 340 5.453480 CCTTCCGGAATCCTAGTTAAAGAGG 60.453 48.000 19.21 5.97 0.00 3.69
342 353 2.286365 AAAGAGGGCATGTTCGGAAA 57.714 45.000 0.00 0.00 0.00 3.13
648 664 5.906073 CAATGTTTGGACAAGTTTCTTCCT 58.094 37.500 0.00 0.00 39.66 3.36
758 774 1.394917 ACGGTACTAGCTAACACGTCG 59.605 52.381 0.00 0.00 0.00 5.12
793 809 1.289244 ACCATCCCATCCCCTTCACC 61.289 60.000 0.00 0.00 0.00 4.02
990 1007 7.448469 AGTTTATTCTAGCTGTGATTGTTTGGT 59.552 33.333 0.00 0.00 0.00 3.67
992 1009 4.350368 TCTAGCTGTGATTGTTTGGTGA 57.650 40.909 0.00 0.00 0.00 4.02
1257 1287 0.031043 TTGCTGCTCAACATGCACAC 59.969 50.000 0.00 0.00 36.37 3.82
1263 1293 1.069296 GCTCAACATGCACACGCTAAA 60.069 47.619 0.00 0.00 39.64 1.85
1408 1438 3.258372 TGTCCTATTATCTCATGGGTCGC 59.742 47.826 0.00 0.00 0.00 5.19
1434 1465 7.545362 TTATTTTCTAAGATCTGCTCACAGC 57.455 36.000 0.00 0.00 44.10 4.40
1531 1562 3.848347 ATGCCGCATACGAGCTCCG 62.848 63.158 8.47 5.19 43.93 4.63
1651 1682 0.250989 TCAGTGGTTTTAAGGCCGGG 60.251 55.000 2.18 0.00 0.00 5.73
1686 1717 6.376864 TGATGATAAGTTTGTACATGGGGTTG 59.623 38.462 0.00 0.00 0.00 3.77
1703 1734 4.080526 GGGGTTGGATTAGAGCTTTGACTA 60.081 45.833 0.00 0.00 0.00 2.59
1776 1807 6.418101 AGTACCTGTTATGTGCTGATTCAAT 58.582 36.000 0.00 0.00 0.00 2.57
1779 1810 5.889853 ACCTGTTATGTGCTGATTCAATGAT 59.110 36.000 0.00 0.00 0.00 2.45
1890 1932 8.918202 TGGTCAACTCTTATTCTATTTGTTGT 57.082 30.769 0.00 0.00 35.98 3.32
1907 1949 8.851541 ATTTGTTGTTTATTTCTGGATGCATT 57.148 26.923 0.00 0.00 0.00 3.56
1962 2004 7.289310 AGGTTTTCCAATTTCCACAAATGATT 58.711 30.769 0.00 0.00 43.73 2.57
2057 2104 4.796606 AGCATGTTGGGAGCTGTAATATT 58.203 39.130 0.00 0.00 37.20 1.28
2061 2108 6.349611 GCATGTTGGGAGCTGTAATATTATGG 60.350 42.308 0.00 0.00 0.00 2.74
2091 2160 6.266330 TGTCAAACACCATCCACATATTGAAA 59.734 34.615 0.00 0.00 0.00 2.69
2134 2222 8.713271 GGTGCATCTCTTATACTTTGCTTATAC 58.287 37.037 0.00 0.00 0.00 1.47
2279 2369 9.778741 ATTCGATTAAAATTGATACTGCTAGGA 57.221 29.630 0.00 0.00 0.00 2.94
2315 2405 0.963962 CCATGAACTGCAGCAGGTTT 59.036 50.000 26.38 12.56 35.51 3.27
2316 2406 1.336517 CCATGAACTGCAGCAGGTTTG 60.337 52.381 26.38 19.73 35.51 2.93
2317 2407 1.338973 CATGAACTGCAGCAGGTTTGT 59.661 47.619 26.38 7.33 35.51 2.83
2318 2408 1.473258 TGAACTGCAGCAGGTTTGTT 58.527 45.000 26.38 11.87 35.51 2.83
2319 2409 1.824230 TGAACTGCAGCAGGTTTGTTT 59.176 42.857 26.38 10.28 35.51 2.83
2347 2437 9.320352 GTTTTGTTTTGTTTTGAGGTATACCAT 57.680 29.630 23.87 8.99 38.89 3.55
2373 2463 3.587797 TGCAACCCTCGTTACTCTTAG 57.412 47.619 0.00 0.00 0.00 2.18
2389 2479 4.769488 ACTCTTAGAGTCATGCTGAGTTGA 59.231 41.667 9.37 0.00 38.71 3.18
2395 2485 6.291648 AGAGTCATGCTGAGTTGATTCTTA 57.708 37.500 6.70 0.00 36.01 2.10
2396 2486 6.887013 AGAGTCATGCTGAGTTGATTCTTAT 58.113 36.000 6.70 0.00 36.01 1.73
2397 2487 6.985645 AGAGTCATGCTGAGTTGATTCTTATC 59.014 38.462 6.70 0.00 36.01 1.75
2398 2488 6.887013 AGTCATGCTGAGTTGATTCTTATCT 58.113 36.000 0.00 0.00 0.00 1.98
2399 2489 6.762187 AGTCATGCTGAGTTGATTCTTATCTG 59.238 38.462 0.00 0.00 0.00 2.90
2443 2535 2.024414 GTGGCACTGAACAAGAGGTTT 58.976 47.619 11.13 0.00 40.63 3.27
2468 2561 2.485426 ACTGAACCATGTCATTGCTTCG 59.515 45.455 0.00 0.00 0.00 3.79
2470 2563 2.226200 TGAACCATGTCATTGCTTCGTG 59.774 45.455 0.00 0.00 0.00 4.35
2472 2565 2.079158 ACCATGTCATTGCTTCGTGAG 58.921 47.619 0.00 0.00 0.00 3.51
2477 2570 3.575630 TGTCATTGCTTCGTGAGAGTAC 58.424 45.455 0.00 0.00 43.69 2.73
2493 2586 4.668636 AGAGTACTGCTTTCCTGTCTAGT 58.331 43.478 0.00 0.00 0.00 2.57
2498 2591 3.006323 ACTGCTTTCCTGTCTAGTGTCAG 59.994 47.826 0.00 0.00 0.00 3.51
2500 2593 3.005897 TGCTTTCCTGTCTAGTGTCAGTC 59.994 47.826 9.86 0.00 0.00 3.51
2501 2594 3.827625 CTTTCCTGTCTAGTGTCAGTCG 58.172 50.000 9.86 0.00 0.00 4.18
2502 2595 2.563261 TCCTGTCTAGTGTCAGTCGT 57.437 50.000 9.86 0.00 0.00 4.34
2510 2610 1.788258 AGTGTCAGTCGTGATGCTTG 58.212 50.000 0.00 0.00 34.36 4.01
2533 2633 2.304470 TGCTTATCTGTTGCCAGGTACA 59.696 45.455 0.00 0.00 33.99 2.90
2546 2646 3.192422 GCCAGGTACAACAAACATGCATA 59.808 43.478 0.00 0.00 0.00 3.14
2548 2648 5.401550 CCAGGTACAACAAACATGCATAAG 58.598 41.667 0.00 0.00 0.00 1.73
2549 2649 5.048083 CCAGGTACAACAAACATGCATAAGT 60.048 40.000 0.00 0.00 0.00 2.24
2621 2724 9.942850 TTTGATGATGATGTGAGTAAGAGTTTA 57.057 29.630 0.00 0.00 0.00 2.01
2667 2770 4.284829 TGATCAAGTTGTGGCAGTATGA 57.715 40.909 2.11 0.00 39.69 2.15
2706 2809 5.772825 TTTGTGATTCCAGGTCTCAAAAG 57.227 39.130 5.30 0.00 36.62 2.27
2754 2857 8.129211 GTGGAATATGTAGGTATGCAGTTTTTC 58.871 37.037 0.00 0.00 0.00 2.29
2796 2899 9.159254 AGTCTTGGAATTGTATGGATGTATCTA 57.841 33.333 0.00 0.00 0.00 1.98
2904 3012 1.807142 TCAAAATGCGGTAATGCGTCA 59.193 42.857 0.00 0.00 37.81 4.35
2966 3074 7.989170 TGTACTAGTACGATGTCATTTAGGAGA 59.011 37.037 24.36 1.80 38.85 3.71
2975 3083 2.349886 GTCATTTAGGAGACTTGCTGCG 59.650 50.000 0.00 0.00 43.67 5.18
2979 3087 0.966179 TAGGAGACTTGCTGCGACAA 59.034 50.000 0.00 0.00 43.67 3.18
2986 3094 2.193306 CTTGCTGCGACAAGTTTGTT 57.807 45.000 9.71 0.00 42.43 2.83
2989 3097 1.675483 TGCTGCGACAAGTTTGTTCAT 59.325 42.857 0.00 0.00 42.43 2.57
2991 3099 2.046313 CTGCGACAAGTTTGTTCATGC 58.954 47.619 0.00 3.02 42.43 4.06
2994 3102 3.052036 GCGACAAGTTTGTTCATGCATT 58.948 40.909 0.00 0.00 42.43 3.56
3037 3245 4.095782 AGTTACACAATGTTGCGTGACTTT 59.904 37.500 5.75 0.00 36.92 2.66
3165 3375 4.713792 ACTTTCAACTCCAAGATCCACT 57.286 40.909 0.00 0.00 0.00 4.00
3183 3393 8.661345 AGATCCACTATTTTTAATACTCCCTCC 58.339 37.037 0.00 0.00 0.00 4.30
3184 3394 6.823497 TCCACTATTTTTAATACTCCCTCCG 58.177 40.000 0.00 0.00 0.00 4.63
3185 3395 6.612456 TCCACTATTTTTAATACTCCCTCCGA 59.388 38.462 0.00 0.00 0.00 4.55
3186 3396 7.291651 TCCACTATTTTTAATACTCCCTCCGAT 59.708 37.037 0.00 0.00 0.00 4.18
3187 3397 7.603024 CCACTATTTTTAATACTCCCTCCGATC 59.397 40.741 0.00 0.00 0.00 3.69
3188 3398 7.603024 CACTATTTTTAATACTCCCTCCGATCC 59.397 40.741 0.00 0.00 0.00 3.36
3189 3399 5.961398 TTTTTAATACTCCCTCCGATCCA 57.039 39.130 0.00 0.00 0.00 3.41
3190 3400 6.509523 TTTTTAATACTCCCTCCGATCCAT 57.490 37.500 0.00 0.00 0.00 3.41
3191 3401 7.621006 TTTTTAATACTCCCTCCGATCCATA 57.379 36.000 0.00 0.00 0.00 2.74
3192 3402 7.808279 TTTTAATACTCCCTCCGATCCATAT 57.192 36.000 0.00 0.00 0.00 1.78
3193 3403 7.808279 TTTAATACTCCCTCCGATCCATATT 57.192 36.000 0.00 0.00 0.00 1.28
3194 3404 8.904648 TTTAATACTCCCTCCGATCCATATTA 57.095 34.615 0.00 0.00 0.00 0.98
3195 3405 8.904648 TTAATACTCCCTCCGATCCATATTAA 57.095 34.615 0.00 0.00 0.00 1.40
3196 3406 7.996758 AATACTCCCTCCGATCCATATTAAT 57.003 36.000 0.00 0.00 0.00 1.40
3197 3407 7.996758 ATACTCCCTCCGATCCATATTAATT 57.003 36.000 0.00 0.00 0.00 1.40
3198 3408 6.054860 ACTCCCTCCGATCCATATTAATTG 57.945 41.667 0.00 0.00 0.00 2.32
3199 3409 5.548056 ACTCCCTCCGATCCATATTAATTGT 59.452 40.000 0.00 0.00 0.00 2.71
3200 3410 6.049955 TCCCTCCGATCCATATTAATTGTC 57.950 41.667 0.00 0.00 0.00 3.18
3201 3411 4.870426 CCCTCCGATCCATATTAATTGTCG 59.130 45.833 0.00 0.00 0.00 4.35
3202 3412 4.330074 CCTCCGATCCATATTAATTGTCGC 59.670 45.833 0.00 0.00 0.00 5.19
3203 3413 5.147330 TCCGATCCATATTAATTGTCGCT 57.853 39.130 0.00 0.00 0.00 4.93
3204 3414 4.929211 TCCGATCCATATTAATTGTCGCTG 59.071 41.667 0.00 0.00 0.00 5.18
3205 3415 4.929211 CCGATCCATATTAATTGTCGCTGA 59.071 41.667 0.00 0.00 0.00 4.26
3206 3416 5.582269 CCGATCCATATTAATTGTCGCTGAT 59.418 40.000 0.00 0.00 0.00 2.90
3207 3417 6.092670 CCGATCCATATTAATTGTCGCTGATT 59.907 38.462 0.00 0.00 0.00 2.57
3208 3418 7.361201 CCGATCCATATTAATTGTCGCTGATTT 60.361 37.037 0.00 0.00 0.00 2.17
3209 3419 8.655970 CGATCCATATTAATTGTCGCTGATTTA 58.344 33.333 0.00 0.00 0.00 1.40
3210 3420 9.979270 GATCCATATTAATTGTCGCTGATTTAG 57.021 33.333 0.00 0.00 0.00 1.85
3211 3421 8.902540 TCCATATTAATTGTCGCTGATTTAGT 57.097 30.769 0.00 0.00 0.00 2.24
3212 3422 8.773645 TCCATATTAATTGTCGCTGATTTAGTG 58.226 33.333 0.00 0.00 38.28 2.74
3213 3423 7.535258 CCATATTAATTGTCGCTGATTTAGTGC 59.465 37.037 0.00 0.00 36.84 4.40
3214 3424 5.871465 TTAATTGTCGCTGATTTAGTGCA 57.129 34.783 0.00 0.00 36.84 4.57
3215 3425 4.764679 AATTGTCGCTGATTTAGTGCAA 57.235 36.364 0.00 0.00 37.35 4.08
3216 3426 4.764679 ATTGTCGCTGATTTAGTGCAAA 57.235 36.364 0.00 0.00 36.90 3.68
3217 3427 3.811722 TGTCGCTGATTTAGTGCAAAG 57.188 42.857 0.00 0.00 36.84 2.77
3218 3428 3.138304 TGTCGCTGATTTAGTGCAAAGT 58.862 40.909 0.00 0.00 36.84 2.66
3219 3429 3.563808 TGTCGCTGATTTAGTGCAAAGTT 59.436 39.130 0.00 0.00 36.84 2.66
3220 3430 4.036262 TGTCGCTGATTTAGTGCAAAGTTT 59.964 37.500 0.00 0.00 36.84 2.66
3221 3431 4.379793 GTCGCTGATTTAGTGCAAAGTTTG 59.620 41.667 11.41 11.41 36.84 2.93
3222 3432 4.036262 TCGCTGATTTAGTGCAAAGTTTGT 59.964 37.500 16.70 0.16 36.84 2.83
3223 3433 5.237561 TCGCTGATTTAGTGCAAAGTTTGTA 59.762 36.000 16.70 9.90 36.84 2.41
3224 3434 5.339611 CGCTGATTTAGTGCAAAGTTTGTAC 59.660 40.000 24.29 24.29 45.13 2.90
3233 3443 6.675515 GTGCAAAGTTTGTACTAAATCAGC 57.324 37.500 24.38 4.71 42.10 4.26
3234 3444 5.339611 GTGCAAAGTTTGTACTAAATCAGCG 59.660 40.000 24.38 0.00 42.10 5.18
3235 3445 5.237561 TGCAAAGTTTGTACTAAATCAGCGA 59.762 36.000 16.70 0.00 33.17 4.93
3236 3446 5.564127 GCAAAGTTTGTACTAAATCAGCGAC 59.436 40.000 16.70 0.00 33.17 5.19
3237 3447 6.655062 CAAAGTTTGTACTAAATCAGCGACA 58.345 36.000 7.48 0.00 33.17 4.35
3238 3448 6.854496 AAGTTTGTACTAAATCAGCGACAA 57.146 33.333 0.00 0.00 33.66 3.18
3239 3449 7.435068 AAGTTTGTACTAAATCAGCGACAAT 57.565 32.000 0.00 0.00 34.85 2.71
3240 3450 7.435068 AGTTTGTACTAAATCAGCGACAATT 57.565 32.000 0.00 0.00 34.85 2.32
3241 3451 8.542497 AGTTTGTACTAAATCAGCGACAATTA 57.458 30.769 0.00 0.00 34.85 1.40
3242 3452 8.656849 AGTTTGTACTAAATCAGCGACAATTAG 58.343 33.333 0.00 0.00 34.85 1.73
3243 3453 8.440833 GTTTGTACTAAATCAGCGACAATTAGT 58.559 33.333 0.00 0.00 39.43 2.24
3244 3454 9.642327 TTTGTACTAAATCAGCGACAATTAGTA 57.358 29.630 0.00 0.00 37.78 1.82
3245 3455 9.811995 TTGTACTAAATCAGCGACAATTAGTAT 57.188 29.630 12.16 0.00 39.72 2.12
3246 3456 9.244799 TGTACTAAATCAGCGACAATTAGTATG 57.755 33.333 12.16 0.00 39.72 2.39
3247 3457 7.715265 ACTAAATCAGCGACAATTAGTATGG 57.285 36.000 0.00 0.00 35.62 2.74
3248 3458 7.497595 ACTAAATCAGCGACAATTAGTATGGA 58.502 34.615 0.00 0.00 35.62 3.41
3249 3459 8.150945 ACTAAATCAGCGACAATTAGTATGGAT 58.849 33.333 0.00 0.00 35.62 3.41
3250 3460 7.426929 AAATCAGCGACAATTAGTATGGATC 57.573 36.000 0.00 0.00 0.00 3.36
3251 3461 5.791336 TCAGCGACAATTAGTATGGATCT 57.209 39.130 0.00 0.00 0.00 2.75
3252 3462 6.161855 TCAGCGACAATTAGTATGGATCTT 57.838 37.500 0.00 0.00 0.00 2.40
3253 3463 5.985530 TCAGCGACAATTAGTATGGATCTTG 59.014 40.000 0.00 0.00 0.00 3.02
3265 3475 9.982651 TTAGTATGGATCTTGTACTAAATCAGC 57.017 33.333 15.97 0.00 37.74 4.26
3271 3481 6.480320 GGATCTTGTACTAAATCAGCGACAAT 59.520 38.462 0.00 0.00 34.55 2.71
3283 3493 8.627208 AAATCAGCGACAATTAATATGGATCT 57.373 30.769 0.00 0.00 0.00 2.75
3284 3494 8.627208 AATCAGCGACAATTAATATGGATCTT 57.373 30.769 0.00 0.00 0.00 2.40
3285 3495 7.425577 TCAGCGACAATTAATATGGATCTTG 57.574 36.000 0.00 0.00 0.00 3.02
3286 3496 6.992123 TCAGCGACAATTAATATGGATCTTGT 59.008 34.615 0.00 0.00 0.00 3.16
3287 3497 8.147704 TCAGCGACAATTAATATGGATCTTGTA 58.852 33.333 0.00 0.00 0.00 2.41
3288 3498 8.223769 CAGCGACAATTAATATGGATCTTGTAC 58.776 37.037 0.00 0.00 0.00 2.90
3289 3499 8.150945 AGCGACAATTAATATGGATCTTGTACT 58.849 33.333 0.00 0.00 0.00 2.73
3290 3500 9.419297 GCGACAATTAATATGGATCTTGTACTA 57.581 33.333 0.00 0.00 0.00 1.82
3318 3528 9.857656 ATCAGTGACAATTAATATGGATCTTGT 57.142 29.630 0.00 0.00 0.00 3.16
3333 3543 5.425577 GATCTTGTACTAGATCAGCGACA 57.574 43.478 30.38 1.66 46.37 4.35
3334 3544 5.822278 GATCTTGTACTAGATCAGCGACAA 58.178 41.667 30.38 1.21 46.37 3.18
3335 3545 5.836821 TCTTGTACTAGATCAGCGACAAT 57.163 39.130 2.68 0.00 34.55 2.71
3336 3546 6.208988 TCTTGTACTAGATCAGCGACAATT 57.791 37.500 2.68 0.00 34.55 2.32
3337 3547 7.329588 TCTTGTACTAGATCAGCGACAATTA 57.670 36.000 2.68 0.00 34.55 1.40
3338 3548 7.768240 TCTTGTACTAGATCAGCGACAATTAA 58.232 34.615 2.68 0.00 34.55 1.40
3339 3549 8.414003 TCTTGTACTAGATCAGCGACAATTAAT 58.586 33.333 2.68 0.00 34.55 1.40
3340 3550 8.942338 TTGTACTAGATCAGCGACAATTAATT 57.058 30.769 0.00 0.00 31.65 1.40
3341 3551 8.942338 TGTACTAGATCAGCGACAATTAATTT 57.058 30.769 0.00 0.00 0.00 1.82
3342 3552 8.817100 TGTACTAGATCAGCGACAATTAATTTG 58.183 33.333 0.00 0.00 41.36 2.32
3343 3553 7.251704 ACTAGATCAGCGACAATTAATTTGG 57.748 36.000 0.00 0.00 39.80 3.28
3344 3554 5.505173 AGATCAGCGACAATTAATTTGGG 57.495 39.130 0.00 0.00 39.80 4.12
3345 3555 4.949856 AGATCAGCGACAATTAATTTGGGT 59.050 37.500 0.00 0.00 39.80 4.51
3346 3556 4.695217 TCAGCGACAATTAATTTGGGTC 57.305 40.909 0.00 2.80 39.80 4.46
3351 3561 3.064820 CGACAATTAATTTGGGTCGGAGG 59.935 47.826 22.37 3.47 45.36 4.30
3352 3562 3.361786 ACAATTAATTTGGGTCGGAGGG 58.638 45.455 0.00 0.00 39.80 4.30
3359 3569 0.115745 TTGGGTCGGAGGGAGTAGTT 59.884 55.000 0.00 0.00 0.00 2.24
3373 3583 6.712276 AGGGAGTAGTTTATTCCTCAAGTTG 58.288 40.000 0.00 0.00 35.15 3.16
3382 3592 9.057089 AGTTTATTCCTCAAGTTGTTTAGTCAG 57.943 33.333 2.11 0.00 0.00 3.51
3629 3852 3.240069 GTTGAAGAACAGTCATGCATGC 58.760 45.455 22.25 11.82 31.78 4.06
3723 3946 5.105269 TGCAGCATATTGTTTGATGAATGGT 60.105 36.000 0.00 0.00 32.33 3.55
3816 4048 2.560542 TGTTTTGCCATGTGGTCATACC 59.439 45.455 0.35 0.00 39.22 2.73
3864 4096 2.409948 AGGAGCATTGCCAGTAAGTC 57.590 50.000 4.70 0.00 0.00 3.01
3877 4109 4.652822 CCAGTAAGTCTAACTTGGCCTTT 58.347 43.478 3.32 0.00 39.11 3.11
3884 4116 9.609346 GTAAGTCTAACTTGGCCTTTGATATAA 57.391 33.333 3.32 0.00 39.11 0.98
3904 4136 6.867662 ATAAGCTGGTTTATCATGTGTAGC 57.132 37.500 0.00 0.00 0.00 3.58
3909 4141 5.760253 GCTGGTTTATCATGTGTAGCACTAT 59.240 40.000 0.00 0.00 35.11 2.12
3917 4149 4.588528 TCATGTGTAGCACTATGCCTATGA 59.411 41.667 0.00 0.00 46.52 2.15
4010 4242 1.302907 AGGCATGGGAAAGACTGGAT 58.697 50.000 0.00 0.00 0.00 3.41
4013 4245 1.956636 GCATGGGAAAGACTGGATGCA 60.957 52.381 0.00 0.00 36.91 3.96
4057 4289 7.787725 ACTCCTTCGATGATAAAATGGTAAC 57.212 36.000 0.00 0.00 0.00 2.50
4251 4483 3.243367 TGCAGTTCCACTTAATTGCACAC 60.243 43.478 3.08 0.00 44.19 3.82
4311 4543 2.551270 TGAAGTAGTGAAGCCCTGGAT 58.449 47.619 0.00 0.00 0.00 3.41
4424 4656 3.448686 AGACAATTTATCTGCGTCCTCG 58.551 45.455 0.00 0.00 40.37 4.63
4427 4659 0.753262 ATTTATCTGCGTCCTCGGCT 59.247 50.000 0.00 0.00 37.56 5.52
4631 4906 3.158676 GGTTGTGTGGCATAGGGTTTAA 58.841 45.455 0.00 0.00 0.00 1.52
4663 4938 4.899502 ACTGTCTTGATCGACAATTTCCT 58.100 39.130 5.18 0.00 42.80 3.36
4752 5028 1.237954 TGCATGCTTCGCCGGTTAAA 61.238 50.000 20.33 0.00 0.00 1.52
4836 5112 3.300013 GGCAACTCCTCGCTAGGT 58.700 61.111 3.89 0.00 44.09 3.08
4842 5118 0.033011 ACTCCTCGCTAGGTGTGGAT 60.033 55.000 10.89 0.00 45.69 3.41
4843 5119 1.214673 ACTCCTCGCTAGGTGTGGATA 59.785 52.381 10.89 0.00 45.69 2.59
4844 5120 1.883275 CTCCTCGCTAGGTGTGGATAG 59.117 57.143 3.89 0.00 44.09 2.08
4845 5121 1.214673 TCCTCGCTAGGTGTGGATAGT 59.785 52.381 3.89 0.00 44.09 2.12
4846 5122 1.609555 CCTCGCTAGGTGTGGATAGTC 59.390 57.143 0.00 0.00 38.19 2.59
4849 5125 3.296854 TCGCTAGGTGTGGATAGTCATT 58.703 45.455 0.00 0.00 0.00 2.57
4851 5127 4.161565 TCGCTAGGTGTGGATAGTCATTTT 59.838 41.667 0.00 0.00 0.00 1.82
4852 5128 4.876107 CGCTAGGTGTGGATAGTCATTTTT 59.124 41.667 0.00 0.00 0.00 1.94
4875 5151 0.032912 TAGGGGTGCGTGGATAGTCA 60.033 55.000 0.00 0.00 0.00 3.41
4888 5164 4.649674 GTGGATAGTCATGTAGGTTCCTCA 59.350 45.833 0.00 0.00 0.00 3.86
4940 5216 4.237724 GTTCTTGGGCTTTACAAAGATGC 58.762 43.478 5.89 0.00 38.28 3.91
4950 5226 5.622233 GCTTTACAAAGATGCCACTTTAGGG 60.622 44.000 5.89 0.00 37.91 3.53
4952 5228 8.508555 CTTTACAAAGATGCCACTTTAGGGCC 62.509 46.154 0.00 0.00 43.48 5.80
4957 5233 3.176728 GCCACTTTAGGGCCTCTTC 57.823 57.895 10.74 0.00 45.87 2.87
4958 5234 0.744771 GCCACTTTAGGGCCTCTTCG 60.745 60.000 10.74 0.00 45.87 3.79
4962 5238 3.198872 CACTTTAGGGCCTCTTCGATTC 58.801 50.000 10.74 0.00 0.00 2.52
4963 5239 2.838202 ACTTTAGGGCCTCTTCGATTCA 59.162 45.455 10.74 0.00 0.00 2.57
4964 5240 3.263425 ACTTTAGGGCCTCTTCGATTCAA 59.737 43.478 10.74 0.00 0.00 2.69
4965 5241 3.992943 TTAGGGCCTCTTCGATTCAAA 57.007 42.857 10.74 0.00 0.00 2.69
4966 5242 2.115343 AGGGCCTCTTCGATTCAAAC 57.885 50.000 0.00 0.00 0.00 2.93
4967 5243 1.630878 AGGGCCTCTTCGATTCAAACT 59.369 47.619 0.00 0.00 0.00 2.66
4968 5244 2.040412 AGGGCCTCTTCGATTCAAACTT 59.960 45.455 0.00 0.00 0.00 2.66
4969 5245 3.263425 AGGGCCTCTTCGATTCAAACTTA 59.737 43.478 0.00 0.00 0.00 2.24
4970 5246 4.080299 AGGGCCTCTTCGATTCAAACTTAT 60.080 41.667 0.00 0.00 0.00 1.73
4971 5247 4.640647 GGGCCTCTTCGATTCAAACTTATT 59.359 41.667 0.84 0.00 0.00 1.40
4972 5248 5.125578 GGGCCTCTTCGATTCAAACTTATTT 59.874 40.000 0.84 0.00 0.00 1.40
4973 5249 6.350194 GGGCCTCTTCGATTCAAACTTATTTT 60.350 38.462 0.84 0.00 0.00 1.82
4974 5250 7.090808 GGCCTCTTCGATTCAAACTTATTTTT 58.909 34.615 0.00 0.00 0.00 1.94
4996 5272 6.528014 TTTTTCGTATGCAACTCTTTCGTA 57.472 33.333 0.00 0.00 0.00 3.43
5046 5323 8.950210 TCAGCTGAGTTAAAATTATGAGAAAGG 58.050 33.333 13.74 0.00 0.00 3.11
5047 5324 8.734386 CAGCTGAGTTAAAATTATGAGAAAGGT 58.266 33.333 8.42 0.00 0.00 3.50
5048 5325 9.301897 AGCTGAGTTAAAATTATGAGAAAGGTT 57.698 29.630 0.00 0.00 0.00 3.50
5049 5326 9.914131 GCTGAGTTAAAATTATGAGAAAGGTTT 57.086 29.630 0.00 0.00 0.00 3.27
5056 5333 5.921962 ATTATGAGAAAGGTTTTCCCTGC 57.078 39.130 0.00 0.00 45.47 4.85
5057 5334 2.746279 TGAGAAAGGTTTTCCCTGCA 57.254 45.000 0.00 0.00 45.47 4.41
5058 5335 3.025322 TGAGAAAGGTTTTCCCTGCAA 57.975 42.857 0.00 0.00 45.47 4.08
5059 5336 3.370104 TGAGAAAGGTTTTCCCTGCAAA 58.630 40.909 0.00 0.00 45.47 3.68
5060 5337 3.772025 TGAGAAAGGTTTTCCCTGCAAAA 59.228 39.130 0.00 0.00 45.47 2.44
5061 5338 4.223923 TGAGAAAGGTTTTCCCTGCAAAAA 59.776 37.500 0.00 0.00 45.47 1.94
5091 5368 1.694150 TGAGAAAGATATCCCCCGCAG 59.306 52.381 0.00 0.00 0.00 5.18
5095 5372 3.202151 AGAAAGATATCCCCCGCAGAAAA 59.798 43.478 0.00 0.00 0.00 2.29
5125 5403 6.544564 GGTTACGGGGAAGATTCAATTATTCA 59.455 38.462 0.00 0.00 0.00 2.57
5260 5539 9.844790 CAACACACATGTTCATGTCTTTTATAT 57.155 29.630 14.43 0.00 46.46 0.86
5262 5541 7.970061 ACACACATGTTCATGTCTTTTATATGC 59.030 33.333 14.43 0.00 34.46 3.14
5263 5542 7.969508 CACACATGTTCATGTCTTTTATATGCA 59.030 33.333 14.43 0.00 31.37 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 0.890542 TGTGCCAGTGTCATGGAAGC 60.891 55.000 0.00 0.00 43.57 3.86
88 91 3.973657 AGAGCAAGAAAAATGCAGTGTG 58.026 40.909 0.00 0.00 46.22 3.82
101 104 1.077169 TCAGGTACAGGGAGAGCAAGA 59.923 52.381 0.00 0.00 0.00 3.02
105 108 1.404315 CGTTTCAGGTACAGGGAGAGC 60.404 57.143 0.00 0.00 0.00 4.09
112 115 0.953960 GGGCACCGTTTCAGGTACAG 60.954 60.000 0.00 0.00 43.89 2.74
266 277 4.141158 AGTGATGGTTTCTCCTCAACCTTT 60.141 41.667 3.60 0.00 43.75 3.11
310 321 3.134081 TGCCCTCTTTAACTAGGATTCCG 59.866 47.826 4.18 0.00 34.58 4.30
313 324 5.717119 ACATGCCCTCTTTAACTAGGATT 57.283 39.130 4.18 0.00 34.58 3.01
329 340 1.153958 GCTGCTTTCCGAACATGCC 60.154 57.895 0.00 0.00 0.00 4.40
342 353 1.071385 AGTAGTCTGCAAGTTGCTGCT 59.929 47.619 27.17 25.16 45.31 4.24
648 664 1.533625 CCACCGGCTTCATCTTCAAA 58.466 50.000 0.00 0.00 0.00 2.69
758 774 5.656416 TGGGATGGTTTCATGATAAGGTTTC 59.344 40.000 0.00 0.00 32.98 2.78
990 1007 6.489700 TCAGCAAAAACCTCATAGTTTGATCA 59.510 34.615 0.00 0.00 39.83 2.92
992 1009 6.899393 TCAGCAAAAACCTCATAGTTTGAT 57.101 33.333 0.00 0.00 39.83 2.57
1189 1219 1.537135 GGCTGTTTGGTAGCGCAAAAA 60.537 47.619 11.47 1.03 42.03 1.94
1257 1287 6.422776 AGTGAATCCACATTTAGTTTAGCG 57.577 37.500 0.00 0.00 45.54 4.26
1263 1293 6.126863 TGAGGAAGTGAATCCACATTTAGT 57.873 37.500 0.00 0.00 45.54 2.24
1408 1438 8.121708 GCTGTGAGCAGATCTTAGAAAATAAAG 58.878 37.037 0.00 0.00 45.28 1.85
1434 1465 9.994432 GACAATAATTTATCAAGGAACTCACTG 57.006 33.333 0.00 0.00 38.49 3.66
1436 1467 8.665685 ACGACAATAATTTATCAAGGAACTCAC 58.334 33.333 0.00 0.00 38.49 3.51
1531 1562 5.670341 GCAATCAAAAATCTCATTGCAGCAC 60.670 40.000 9.96 0.00 46.87 4.40
1728 1759 9.675464 ACTAAATCAGATTATTTTTCCACCGTA 57.325 29.630 0.00 0.00 31.63 4.02
1779 1810 9.545105 CCCAACACACCGTTAATATTAATAGTA 57.455 33.333 11.00 0.00 35.52 1.82
1798 1831 7.161404 TCACATGATATTATAGCTCCCAACAC 58.839 38.462 0.00 0.00 0.00 3.32
1886 1928 9.369904 ACATAAATGCATCCAGAAATAAACAAC 57.630 29.630 0.00 0.00 0.00 3.32
1890 1932 9.420118 AGGTACATAAATGCATCCAGAAATAAA 57.580 29.630 0.00 0.00 0.00 1.40
1893 1935 7.293073 AGAGGTACATAAATGCATCCAGAAAT 58.707 34.615 0.00 0.00 0.00 2.17
1932 1974 6.155475 TGTGGAAATTGGAAAACCTTACAG 57.845 37.500 0.00 0.00 0.00 2.74
2057 2104 5.133491 TGGATGGTGTTTGACATATCCCATA 59.867 40.000 17.26 4.55 40.74 2.74
2061 2108 4.269183 TGTGGATGGTGTTTGACATATCC 58.731 43.478 14.95 14.95 41.29 2.59
2075 2122 7.549839 AGAACAACATTTCAATATGTGGATGG 58.450 34.615 0.00 0.00 38.69 3.51
2091 2160 6.435277 AGATGCACCAAGAAATAGAACAACAT 59.565 34.615 0.00 0.00 0.00 2.71
2153 2243 3.061403 CCGTAACAGAACGCATAATCGTC 60.061 47.826 0.00 0.00 42.46 4.20
2219 2309 9.959721 ATACATAGTACATTATTTCCCCACATC 57.040 33.333 0.00 0.00 0.00 3.06
2273 2363 3.526534 GTGGAAGTTCATGTCTCCTAGC 58.473 50.000 5.01 0.00 0.00 3.42
2279 2369 0.396435 TGGCGTGGAAGTTCATGTCT 59.604 50.000 5.01 0.00 0.00 3.41
2315 2405 7.762382 ACCTCAAAACAAAACAAAACAAAACA 58.238 26.923 0.00 0.00 0.00 2.83
2316 2406 9.885934 ATACCTCAAAACAAAACAAAACAAAAC 57.114 25.926 0.00 0.00 0.00 2.43
2319 2409 9.152595 GGTATACCTCAAAACAAAACAAAACAA 57.847 29.630 15.09 0.00 0.00 2.83
2347 2437 4.060205 GAGTAACGAGGGTTGCAAAGTAA 58.940 43.478 0.00 0.00 40.72 2.24
2373 2463 6.985645 AGATAAGAATCAACTCAGCATGACTC 59.014 38.462 0.00 0.00 35.63 3.36
2443 2535 2.553602 GCAATGACATGGTTCAGTCACA 59.446 45.455 0.00 0.00 46.38 3.58
2468 2561 3.257127 AGACAGGAAAGCAGTACTCTCAC 59.743 47.826 0.00 0.00 0.00 3.51
2470 2563 4.703093 ACTAGACAGGAAAGCAGTACTCTC 59.297 45.833 0.00 0.00 0.00 3.20
2472 2565 4.218852 ACACTAGACAGGAAAGCAGTACTC 59.781 45.833 0.00 0.00 0.00 2.59
2477 2570 3.006323 ACTGACACTAGACAGGAAAGCAG 59.994 47.826 15.92 0.00 41.01 4.24
2493 2586 1.866601 CAACAAGCATCACGACTGACA 59.133 47.619 0.00 0.00 0.00 3.58
2533 2633 5.049167 CACCACAACTTATGCATGTTTGTT 58.951 37.500 10.16 6.08 0.00 2.83
2539 2639 4.353737 GCATACACCACAACTTATGCATG 58.646 43.478 10.16 0.00 44.14 4.06
2546 2646 2.170166 CCCATGCATACACCACAACTT 58.830 47.619 0.00 0.00 0.00 2.66
2548 2648 1.832883 TCCCATGCATACACCACAAC 58.167 50.000 0.00 0.00 0.00 3.32
2549 2649 2.593925 TTCCCATGCATACACCACAA 57.406 45.000 0.00 0.00 0.00 3.33
2621 2724 5.014202 AGTAGACAAAACACCCAAAACTGT 58.986 37.500 0.00 0.00 0.00 3.55
2667 2770 9.846248 GAATCACAAAATTAAGTCTTAGCATGT 57.154 29.630 0.00 0.00 0.00 3.21
2725 2828 5.130311 ACTGCATACCTACATATTCCACACA 59.870 40.000 0.00 0.00 0.00 3.72
2754 2857 4.641989 CCAAGACTGGAAATTATCACAGGG 59.358 45.833 0.00 0.00 46.92 4.45
2904 3012 9.199982 CAAGAATGCAATTTTAGACACAAGAAT 57.800 29.630 0.00 0.00 36.07 2.40
2950 3058 4.269603 CAGCAAGTCTCCTAAATGACATCG 59.730 45.833 0.00 0.00 35.81 3.84
2998 3106 8.439993 TTGTGTAACTGCATAAGTCTACAAAA 57.560 30.769 0.00 0.00 38.56 2.44
3037 3245 8.417106 TGTTATTTTCTGGCACAAATCAACTAA 58.583 29.630 11.11 0.00 38.70 2.24
3126 3335 9.556030 GTTGAAAGTTGAAAATACTATACAGCC 57.444 33.333 0.00 0.00 0.00 4.85
3158 3368 7.603024 CGGAGGGAGTATTAAAAATAGTGGATC 59.397 40.741 0.00 0.00 0.00 3.36
3165 3375 7.621006 TGGATCGGAGGGAGTATTAAAAATA 57.379 36.000 0.00 0.00 0.00 1.40
3183 3393 6.653273 ATCAGCGACAATTAATATGGATCG 57.347 37.500 0.00 0.00 0.00 3.69
3184 3394 9.979270 CTAAATCAGCGACAATTAATATGGATC 57.021 33.333 0.00 0.00 0.00 3.36
3185 3395 9.507329 ACTAAATCAGCGACAATTAATATGGAT 57.493 29.630 0.00 0.00 0.00 3.41
3186 3396 8.773645 CACTAAATCAGCGACAATTAATATGGA 58.226 33.333 0.00 0.00 0.00 3.41
3187 3397 7.535258 GCACTAAATCAGCGACAATTAATATGG 59.465 37.037 0.00 0.00 0.00 2.74
3188 3398 8.069574 TGCACTAAATCAGCGACAATTAATATG 58.930 33.333 0.00 0.00 0.00 1.78
3189 3399 8.153479 TGCACTAAATCAGCGACAATTAATAT 57.847 30.769 0.00 0.00 0.00 1.28
3190 3400 7.546778 TGCACTAAATCAGCGACAATTAATA 57.453 32.000 0.00 0.00 0.00 0.98
3191 3401 6.435430 TGCACTAAATCAGCGACAATTAAT 57.565 33.333 0.00 0.00 0.00 1.40
3192 3402 5.871465 TGCACTAAATCAGCGACAATTAA 57.129 34.783 0.00 0.00 0.00 1.40
3193 3403 5.871465 TTGCACTAAATCAGCGACAATTA 57.129 34.783 0.00 0.00 0.00 1.40
3194 3404 4.764679 TTGCACTAAATCAGCGACAATT 57.235 36.364 0.00 0.00 0.00 2.32
3195 3405 4.216257 ACTTTGCACTAAATCAGCGACAAT 59.784 37.500 0.00 0.00 0.00 2.71
3196 3406 3.563808 ACTTTGCACTAAATCAGCGACAA 59.436 39.130 0.00 0.00 0.00 3.18
3197 3407 3.138304 ACTTTGCACTAAATCAGCGACA 58.862 40.909 0.00 0.00 0.00 4.35
3198 3408 3.813529 ACTTTGCACTAAATCAGCGAC 57.186 42.857 0.00 0.00 0.00 5.19
3199 3409 4.036262 ACAAACTTTGCACTAAATCAGCGA 59.964 37.500 1.14 0.00 0.00 4.93
3200 3410 4.290155 ACAAACTTTGCACTAAATCAGCG 58.710 39.130 1.14 0.00 0.00 5.18
3201 3411 6.438763 AGTACAAACTTTGCACTAAATCAGC 58.561 36.000 5.69 0.00 35.56 4.26
3202 3412 9.944663 TTTAGTACAAACTTTGCACTAAATCAG 57.055 29.630 24.23 0.00 46.58 2.90
3207 3417 8.073768 GCTGATTTAGTACAAACTTTGCACTAA 58.926 33.333 17.90 17.90 43.93 2.24
3208 3418 7.570507 CGCTGATTTAGTACAAACTTTGCACTA 60.571 37.037 9.65 9.65 38.24 2.74
3209 3419 6.438763 GCTGATTTAGTACAAACTTTGCACT 58.561 36.000 11.37 11.37 40.29 4.40
3210 3420 5.339611 CGCTGATTTAGTACAAACTTTGCAC 59.660 40.000 1.14 0.00 37.15 4.57
3211 3421 5.237561 TCGCTGATTTAGTACAAACTTTGCA 59.762 36.000 1.14 0.00 37.15 4.08
3212 3422 5.564127 GTCGCTGATTTAGTACAAACTTTGC 59.436 40.000 1.14 0.00 37.15 3.68
3213 3423 6.655062 TGTCGCTGATTTAGTACAAACTTTG 58.345 36.000 0.00 0.00 37.15 2.77
3214 3424 6.854496 TGTCGCTGATTTAGTACAAACTTT 57.146 33.333 0.00 0.00 37.15 2.66
3215 3425 6.854496 TTGTCGCTGATTTAGTACAAACTT 57.146 33.333 0.00 0.00 37.15 2.66
3216 3426 7.435068 AATTGTCGCTGATTTAGTACAAACT 57.565 32.000 0.00 0.00 37.68 2.66
3217 3427 8.440833 ACTAATTGTCGCTGATTTAGTACAAAC 58.559 33.333 0.00 0.00 37.68 2.93
3218 3428 8.542497 ACTAATTGTCGCTGATTTAGTACAAA 57.458 30.769 0.00 0.00 37.68 2.83
3219 3429 9.811995 ATACTAATTGTCGCTGATTTAGTACAA 57.188 29.630 0.00 0.00 38.16 2.41
3220 3430 9.244799 CATACTAATTGTCGCTGATTTAGTACA 57.755 33.333 0.00 0.00 0.00 2.90
3221 3431 8.700644 CCATACTAATTGTCGCTGATTTAGTAC 58.299 37.037 0.00 0.00 0.00 2.73
3222 3432 8.635328 TCCATACTAATTGTCGCTGATTTAGTA 58.365 33.333 0.00 0.00 0.00 1.82
3223 3433 7.497595 TCCATACTAATTGTCGCTGATTTAGT 58.502 34.615 0.00 0.00 0.00 2.24
3224 3434 7.946655 TCCATACTAATTGTCGCTGATTTAG 57.053 36.000 0.00 0.00 0.00 1.85
3225 3435 8.367911 AGATCCATACTAATTGTCGCTGATTTA 58.632 33.333 0.00 0.00 0.00 1.40
3226 3436 7.220030 AGATCCATACTAATTGTCGCTGATTT 58.780 34.615 0.00 0.00 0.00 2.17
3227 3437 6.763355 AGATCCATACTAATTGTCGCTGATT 58.237 36.000 0.00 0.00 0.00 2.57
3228 3438 6.352016 AGATCCATACTAATTGTCGCTGAT 57.648 37.500 0.00 0.00 0.00 2.90
3229 3439 5.791336 AGATCCATACTAATTGTCGCTGA 57.209 39.130 0.00 0.00 0.00 4.26
3230 3440 5.755375 ACAAGATCCATACTAATTGTCGCTG 59.245 40.000 0.00 0.00 0.00 5.18
3231 3441 5.918608 ACAAGATCCATACTAATTGTCGCT 58.081 37.500 0.00 0.00 0.00 4.93
3232 3442 6.924060 AGTACAAGATCCATACTAATTGTCGC 59.076 38.462 0.00 0.00 33.31 5.19
3233 3443 9.961265 TTAGTACAAGATCCATACTAATTGTCG 57.039 33.333 13.30 0.00 36.79 4.35
3239 3449 9.982651 GCTGATTTAGTACAAGATCCATACTAA 57.017 33.333 13.30 13.30 38.83 2.24
3240 3450 8.297426 CGCTGATTTAGTACAAGATCCATACTA 58.703 37.037 0.00 4.88 31.65 1.82
3241 3451 7.014326 TCGCTGATTTAGTACAAGATCCATACT 59.986 37.037 0.00 6.43 33.73 2.12
3242 3452 7.115095 GTCGCTGATTTAGTACAAGATCCATAC 59.885 40.741 0.00 0.00 0.00 2.39
3243 3453 7.145985 GTCGCTGATTTAGTACAAGATCCATA 58.854 38.462 0.00 0.00 0.00 2.74
3244 3454 5.986135 GTCGCTGATTTAGTACAAGATCCAT 59.014 40.000 0.00 0.00 0.00 3.41
3245 3455 5.105513 TGTCGCTGATTTAGTACAAGATCCA 60.106 40.000 0.00 0.00 0.00 3.41
3246 3456 5.348986 TGTCGCTGATTTAGTACAAGATCC 58.651 41.667 0.00 0.00 0.00 3.36
3247 3457 6.887376 TTGTCGCTGATTTAGTACAAGATC 57.113 37.500 0.00 0.00 32.84 2.75
3248 3458 7.849804 AATTGTCGCTGATTTAGTACAAGAT 57.150 32.000 0.00 0.00 37.62 2.40
3249 3459 8.766000 TTAATTGTCGCTGATTTAGTACAAGA 57.234 30.769 0.00 0.00 37.62 3.02
3292 3502 9.857656 ACAAGATCCATATTAATTGTCACTGAT 57.142 29.630 0.00 0.00 0.00 2.90
3312 3522 5.836821 TTGTCGCTGATCTAGTACAAGAT 57.163 39.130 0.00 0.00 38.95 2.40
3313 3523 5.836821 ATTGTCGCTGATCTAGTACAAGA 57.163 39.130 0.00 0.00 37.62 3.02
3314 3524 7.987268 TTAATTGTCGCTGATCTAGTACAAG 57.013 36.000 0.00 0.00 37.62 3.16
3315 3525 8.942338 AATTAATTGTCGCTGATCTAGTACAA 57.058 30.769 0.00 6.11 38.16 2.41
3316 3526 8.817100 CAAATTAATTGTCGCTGATCTAGTACA 58.183 33.333 0.39 0.00 34.16 2.90
3317 3527 8.276325 CCAAATTAATTGTCGCTGATCTAGTAC 58.724 37.037 0.39 0.00 37.32 2.73
3318 3528 7.441157 CCCAAATTAATTGTCGCTGATCTAGTA 59.559 37.037 0.39 0.00 37.32 1.82
3319 3529 6.260936 CCCAAATTAATTGTCGCTGATCTAGT 59.739 38.462 0.39 0.00 37.32 2.57
3320 3530 6.260936 ACCCAAATTAATTGTCGCTGATCTAG 59.739 38.462 0.39 0.00 37.32 2.43
3321 3531 6.119536 ACCCAAATTAATTGTCGCTGATCTA 58.880 36.000 0.39 0.00 37.32 1.98
3322 3532 4.949856 ACCCAAATTAATTGTCGCTGATCT 59.050 37.500 0.39 0.00 37.32 2.75
3323 3533 5.248870 ACCCAAATTAATTGTCGCTGATC 57.751 39.130 0.39 0.00 37.32 2.92
3324 3534 4.201910 CGACCCAAATTAATTGTCGCTGAT 60.202 41.667 19.99 1.69 37.32 2.90
3325 3535 3.126171 CGACCCAAATTAATTGTCGCTGA 59.874 43.478 19.99 0.00 37.32 4.26
3326 3536 3.425404 CGACCCAAATTAATTGTCGCTG 58.575 45.455 19.99 7.85 37.32 5.18
3327 3537 2.422127 CCGACCCAAATTAATTGTCGCT 59.578 45.455 23.73 0.00 36.64 4.93
3328 3538 2.420722 TCCGACCCAAATTAATTGTCGC 59.579 45.455 23.73 6.28 36.64 5.19
3329 3539 3.064820 CCTCCGACCCAAATTAATTGTCG 59.935 47.826 22.83 22.83 37.31 4.35
3330 3540 3.380320 CCCTCCGACCCAAATTAATTGTC 59.620 47.826 0.39 4.47 37.32 3.18
3331 3541 3.010808 TCCCTCCGACCCAAATTAATTGT 59.989 43.478 0.39 0.00 37.32 2.71
3332 3542 3.626930 TCCCTCCGACCCAAATTAATTG 58.373 45.455 0.39 0.00 38.84 2.32
3333 3543 3.268595 ACTCCCTCCGACCCAAATTAATT 59.731 43.478 0.00 0.00 0.00 1.40
3334 3544 2.850568 ACTCCCTCCGACCCAAATTAAT 59.149 45.455 0.00 0.00 0.00 1.40
3335 3545 2.271777 ACTCCCTCCGACCCAAATTAA 58.728 47.619 0.00 0.00 0.00 1.40
3336 3546 1.961133 ACTCCCTCCGACCCAAATTA 58.039 50.000 0.00 0.00 0.00 1.40
3337 3547 1.838077 CTACTCCCTCCGACCCAAATT 59.162 52.381 0.00 0.00 0.00 1.82
3338 3548 1.273666 ACTACTCCCTCCGACCCAAAT 60.274 52.381 0.00 0.00 0.00 2.32
3339 3549 0.115745 ACTACTCCCTCCGACCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
3340 3550 0.115745 AACTACTCCCTCCGACCCAA 59.884 55.000 0.00 0.00 0.00 4.12
3341 3551 0.115745 AAACTACTCCCTCCGACCCA 59.884 55.000 0.00 0.00 0.00 4.51
3342 3552 2.149973 TAAACTACTCCCTCCGACCC 57.850 55.000 0.00 0.00 0.00 4.46
3343 3553 3.069300 GGAATAAACTACTCCCTCCGACC 59.931 52.174 0.00 0.00 0.00 4.79
3344 3554 3.959449 AGGAATAAACTACTCCCTCCGAC 59.041 47.826 0.00 0.00 0.00 4.79
3345 3555 4.213513 GAGGAATAAACTACTCCCTCCGA 58.786 47.826 0.00 0.00 35.39 4.55
3346 3556 3.958798 TGAGGAATAAACTACTCCCTCCG 59.041 47.826 0.00 0.00 39.42 4.63
3347 3557 5.425862 ACTTGAGGAATAAACTACTCCCTCC 59.574 44.000 0.00 0.00 39.42 4.30
3351 3561 7.981102 AACAACTTGAGGAATAAACTACTCC 57.019 36.000 0.00 0.00 0.00 3.85
3359 3569 8.429641 AGACTGACTAAACAACTTGAGGAATAA 58.570 33.333 0.00 0.00 0.00 1.40
3424 3647 8.080363 AGTAAAATGTACACCCCTTTCAAAAA 57.920 30.769 0.00 0.00 0.00 1.94
3425 3648 7.663043 AGTAAAATGTACACCCCTTTCAAAA 57.337 32.000 0.00 0.00 0.00 2.44
3426 3649 8.943594 ATAGTAAAATGTACACCCCTTTCAAA 57.056 30.769 0.00 0.00 0.00 2.69
3427 3650 8.798402 CAATAGTAAAATGTACACCCCTTTCAA 58.202 33.333 0.00 0.00 0.00 2.69
3428 3651 7.094118 GCAATAGTAAAATGTACACCCCTTTCA 60.094 37.037 0.00 0.00 0.00 2.69
3429 3652 7.122204 AGCAATAGTAAAATGTACACCCCTTTC 59.878 37.037 0.00 0.00 0.00 2.62
3430 3653 6.951778 AGCAATAGTAAAATGTACACCCCTTT 59.048 34.615 0.00 0.00 0.00 3.11
3431 3654 6.490492 AGCAATAGTAAAATGTACACCCCTT 58.510 36.000 0.00 0.00 0.00 3.95
3432 3655 6.074698 AGCAATAGTAAAATGTACACCCCT 57.925 37.500 0.00 0.00 0.00 4.79
3433 3656 7.052248 AGTAGCAATAGTAAAATGTACACCCC 58.948 38.462 0.00 0.00 0.00 4.95
3434 3657 8.502105 AAGTAGCAATAGTAAAATGTACACCC 57.498 34.615 0.00 0.00 0.00 4.61
3538 3761 8.140628 GGGTTAAACCAACTTTACGGAATAAAA 58.859 33.333 4.11 0.00 41.02 1.52
3547 3770 7.104043 ACAAGAAGGGTTAAACCAACTTTAC 57.896 36.000 13.24 0.00 41.02 2.01
3549 3772 6.614694 AACAAGAAGGGTTAAACCAACTTT 57.385 33.333 13.24 0.00 41.02 2.66
3550 3773 6.614694 AAACAAGAAGGGTTAAACCAACTT 57.385 33.333 13.24 13.20 41.02 2.66
3629 3852 0.379669 GATGCATGGCTCCTTCAACG 59.620 55.000 2.46 0.00 0.00 4.10
3816 4048 8.528917 TCTCTTTCAAGCATTTTTCATGAATG 57.471 30.769 9.40 6.07 37.51 2.67
3864 4096 6.016777 CCAGCTTATATCAAAGGCCAAGTTAG 60.017 42.308 5.01 0.00 0.00 2.34
3877 4109 9.710900 CTACACATGATAAACCAGCTTATATCA 57.289 33.333 0.00 8.93 38.66 2.15
3884 4116 3.941483 GTGCTACACATGATAAACCAGCT 59.059 43.478 0.00 0.00 34.08 4.24
3904 4136 3.181472 TGTCAGCTGTCATAGGCATAGTG 60.181 47.826 14.67 0.00 0.00 2.74
3909 4141 1.556451 ACATGTCAGCTGTCATAGGCA 59.444 47.619 23.14 0.95 0.00 4.75
3917 4149 4.085357 TGGTTTTAGACATGTCAGCTGT 57.915 40.909 27.02 9.10 0.00 4.40
4010 4242 1.200252 GACAGAGTCGCTAGTTCTGCA 59.800 52.381 12.51 0.00 41.52 4.41
4013 4245 3.570550 AGTTTGACAGAGTCGCTAGTTCT 59.429 43.478 0.00 0.00 34.95 3.01
4212 4444 1.443407 CACCTCTGATACTGCCCCG 59.557 63.158 0.00 0.00 0.00 5.73
4251 4483 3.173599 CGACTTGCAATTATGGCACTTG 58.826 45.455 0.00 0.00 41.75 3.16
4311 4543 5.488919 ACTTCCAGGAAGAATGTAGAATCCA 59.511 40.000 32.59 0.00 41.71 3.41
4427 4659 1.450134 CGATGCAGGGCAGCTAACA 60.450 57.895 4.89 0.00 43.23 2.41
4470 4723 1.559149 GGACGCGCGGAAACTGTTAA 61.559 55.000 35.22 0.00 0.00 2.01
4524 4780 4.826183 GGTGATACCAATCGAGTACTACCT 59.174 45.833 0.00 0.00 38.42 3.08
4612 4886 3.766591 CCATTAAACCCTATGCCACACAA 59.233 43.478 0.00 0.00 0.00 3.33
4631 4906 3.058016 CGATCAAGACAGTTTGCAACCAT 60.058 43.478 0.00 0.00 0.00 3.55
4653 4928 6.152379 GGTGATCACTGAAAAGGAAATTGTC 58.848 40.000 24.50 0.00 0.00 3.18
4663 4938 3.636300 CCCAACTTGGTGATCACTGAAAA 59.364 43.478 24.50 13.05 35.17 2.29
4752 5028 1.548582 CCAAAGAGGTGCCAGGAACAT 60.549 52.381 0.00 0.00 0.00 2.71
4852 5128 2.306512 ACTATCCACGCACCCCTAAAAA 59.693 45.455 0.00 0.00 0.00 1.94
4853 5129 1.910671 ACTATCCACGCACCCCTAAAA 59.089 47.619 0.00 0.00 0.00 1.52
4854 5130 1.483415 GACTATCCACGCACCCCTAAA 59.517 52.381 0.00 0.00 0.00 1.85
4855 5131 1.117150 GACTATCCACGCACCCCTAA 58.883 55.000 0.00 0.00 0.00 2.69
4856 5132 0.032912 TGACTATCCACGCACCCCTA 60.033 55.000 0.00 0.00 0.00 3.53
4857 5133 0.691078 ATGACTATCCACGCACCCCT 60.691 55.000 0.00 0.00 0.00 4.79
4858 5134 0.532862 CATGACTATCCACGCACCCC 60.533 60.000 0.00 0.00 0.00 4.95
4859 5135 0.178068 ACATGACTATCCACGCACCC 59.822 55.000 0.00 0.00 0.00 4.61
4860 5136 2.545952 CCTACATGACTATCCACGCACC 60.546 54.545 0.00 0.00 0.00 5.01
4861 5137 2.100916 ACCTACATGACTATCCACGCAC 59.899 50.000 0.00 0.00 0.00 5.34
4862 5138 2.384828 ACCTACATGACTATCCACGCA 58.615 47.619 0.00 0.00 0.00 5.24
4863 5139 3.381949 GAACCTACATGACTATCCACGC 58.618 50.000 0.00 0.00 0.00 5.34
4864 5140 3.637229 AGGAACCTACATGACTATCCACG 59.363 47.826 0.00 0.00 0.00 4.94
4865 5141 4.649674 TGAGGAACCTACATGACTATCCAC 59.350 45.833 0.00 0.14 0.00 4.02
4866 5142 4.878968 TGAGGAACCTACATGACTATCCA 58.121 43.478 0.00 0.00 0.00 3.41
4867 5143 5.871396 TTGAGGAACCTACATGACTATCC 57.129 43.478 0.00 0.35 0.00 2.59
4868 5144 6.708054 CCATTTGAGGAACCTACATGACTATC 59.292 42.308 0.00 0.00 0.00 2.08
4869 5145 6.595682 CCATTTGAGGAACCTACATGACTAT 58.404 40.000 0.00 0.00 0.00 2.12
4870 5146 5.629133 GCCATTTGAGGAACCTACATGACTA 60.629 44.000 0.00 0.00 0.00 2.59
4875 5151 2.643551 CGCCATTTGAGGAACCTACAT 58.356 47.619 0.00 0.00 0.00 2.29
4905 5181 3.344515 CCCAAGAACCCTAACTTAGCAC 58.655 50.000 0.00 0.00 0.00 4.40
4940 5216 0.902531 TCGAAGAGGCCCTAAAGTGG 59.097 55.000 0.00 0.00 0.00 4.00
4973 5249 5.412526 ACGAAAGAGTTGCATACGAAAAA 57.587 34.783 0.00 0.00 0.00 1.94
4974 5250 6.347079 CCTTACGAAAGAGTTGCATACGAAAA 60.347 38.462 0.00 0.00 34.37 2.29
4975 5251 5.119588 CCTTACGAAAGAGTTGCATACGAAA 59.880 40.000 0.00 0.00 34.37 3.46
4976 5252 4.624024 CCTTACGAAAGAGTTGCATACGAA 59.376 41.667 0.00 0.00 34.37 3.85
5060 5337 9.579932 GGGGATATCTTTCTCATAACTTCATTT 57.420 33.333 2.05 0.00 0.00 2.32
5061 5338 8.166726 GGGGGATATCTTTCTCATAACTTCATT 58.833 37.037 2.05 0.00 0.00 2.57
5062 5339 7.527868 CGGGGGATATCTTTCTCATAACTTCAT 60.528 40.741 2.05 0.00 0.00 2.57
5063 5340 6.239600 CGGGGGATATCTTTCTCATAACTTCA 60.240 42.308 2.05 0.00 0.00 3.02
5067 5344 4.254492 GCGGGGGATATCTTTCTCATAAC 58.746 47.826 2.05 0.00 0.00 1.89
5076 5353 3.662759 TTTTTCTGCGGGGGATATCTT 57.337 42.857 2.05 0.00 0.00 2.40
5095 5372 4.732065 TGAATCTTCCCCGTAACCTTTTT 58.268 39.130 0.00 0.00 0.00 1.94
5099 5376 4.586306 AATTGAATCTTCCCCGTAACCT 57.414 40.909 0.00 0.00 0.00 3.50
5100 5377 6.544564 TGAATAATTGAATCTTCCCCGTAACC 59.455 38.462 0.00 0.00 0.00 2.85
5105 5383 8.796475 ACATATTGAATAATTGAATCTTCCCCG 58.204 33.333 0.00 0.00 0.00 5.73
5145 5424 6.699895 TGTGTACAGTATGATTGAAACGAC 57.300 37.500 0.00 0.00 39.69 4.34
5147 5426 7.346208 TCTTGTGTACAGTATGATTGAAACG 57.654 36.000 0.00 0.00 39.69 3.60
5148 5427 7.148407 CCCTCTTGTGTACAGTATGATTGAAAC 60.148 40.741 0.00 0.00 39.69 2.78
5160 5439 4.201950 GCATAATTGCCCTCTTGTGTACAG 60.202 45.833 0.00 0.00 43.38 2.74


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

AutoCloner maintained by Alex Coulton.