Multiple sequence alignment - TraesCS2A01G378600

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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 TraesCS2A01G378600 chr2A 100.000 5868 0 0 1 5868 621476577 621482444 0.000000e+00 10837.0
1 TraesCS2A01G378600 chr2D 93.628 3327 119 40 1 3289 478708793 478705522 0.000000e+00 4883.0
2 TraesCS2A01G378600 chr2D 93.242 1746 69 11 3411 5150 478705525 478703823 0.000000e+00 2525.0
3 TraesCS2A01G378600 chr2D 94.522 712 36 3 5150 5861 478703784 478703076 0.000000e+00 1096.0
4 TraesCS2A01G378600 chr2B 93.818 3203 132 36 1 3185 561224070 561227224 0.000000e+00 4758.0
5 TraesCS2A01G378600 chr2B 93.581 2477 113 20 3411 5858 561227246 561229705 0.000000e+00 3651.0
6 TraesCS2A01G378600 chr2B 92.157 153 12 0 3274 3426 620596818 620596666 3.560000e-52 217.0
7 TraesCS2A01G378600 chr2B 100.000 28 0 0 3189 3216 561227217 561227244 1.100000e-02 52.8
8 TraesCS2A01G378600 chr7A 95.238 147 5 2 3273 3418 19936838 19936693 1.270000e-56 231.0
9 TraesCS2A01G378600 chr7A 99.194 124 1 0 3288 3411 38033235 38033358 2.130000e-54 224.0
10 TraesCS2A01G378600 chr3A 97.710 131 3 0 3284 3414 136477555 136477425 5.920000e-55 226.0
11 TraesCS2A01G378600 chr4A 95.683 139 5 1 3286 3424 637254104 637254241 7.650000e-54 222.0
12 TraesCS2A01G378600 chr4A 95.683 139 5 1 3286 3424 637324310 637324173 7.650000e-54 222.0
13 TraesCS2A01G378600 chr4A 95.000 140 6 1 3285 3424 637307155 637307293 9.900000e-53 219.0
14 TraesCS2A01G378600 chr4A 94.964 139 6 1 3286 3424 637364283 637364420 3.560000e-52 217.0
15 TraesCS2A01G378600 chr1B 95.620 137 6 0 3286 3422 476343233 476343369 2.750000e-53 220.0


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 TraesCS2A01G378600 chr2A 621476577 621482444 5867 False 10837.000000 10837 100.000000 1 5868 1 chr2A.!!$F1 5867
1 TraesCS2A01G378600 chr2D 478703076 478708793 5717 True 2834.666667 4883 93.797333 1 5861 3 chr2D.!!$R1 5860
2 TraesCS2A01G378600 chr2B 561224070 561229705 5635 False 2820.600000 4758 95.799667 1 5858 3 chr2B.!!$F1 5857

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
33 34 0.037326 TGTGCGCTTCTCTTGTAGGG 60.037 55.000 9.73 0.00 0.00 3.53 F
252 274 1.000896 CAGATTGGCCGGGTCCTTT 60.001 57.895 2.18 0.00 0.00 3.11 F
1221 1248 1.913778 ACATGGTTGCTGAATCTGCA 58.086 45.000 10.78 10.78 36.58 4.41 F
2178 2214 2.092753 TGATCCATCTCCTTGGCTCAAC 60.093 50.000 0.00 0.00 38.58 3.18 F
3302 3346 0.038744 AAAGTACTCCCTCCGTCCGA 59.961 55.000 0.00 0.00 0.00 4.55 F
3303 3347 0.038744 AAGTACTCCCTCCGTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1793 1827 1.137282 TCTTCGTGTACAGTTGCACCA 59.863 47.619 0.00 0.00 35.02 4.17 R
1833 1867 1.893137 TGAAACGAGCTGCTCTAGGAA 59.107 47.619 25.59 7.49 0.00 3.36 R
3138 3182 0.391966 GGTTGGTACGATCCTAGGGC 59.608 60.000 9.46 0.32 0.00 5.19 R
3391 3435 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12 R
4568 4625 0.179089 CTCCCAACTGAGGCATCTCG 60.179 60.000 0.00 0.00 42.79 4.04 R
4871 4929 0.820891 CTGTGACCTGCTTTGGCTGT 60.821 55.000 0.00 0.00 39.59 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
27 28 1.876156 CTTCCTTTGTGCGCTTCTCTT 59.124 47.619 9.73 0.00 0.00 2.85
33 34 0.037326 TGTGCGCTTCTCTTGTAGGG 60.037 55.000 9.73 0.00 0.00 3.53
36 37 1.346395 TGCGCTTCTCTTGTAGGGAAA 59.654 47.619 9.73 0.00 0.00 3.13
61 62 4.454504 ACGCACGTTTTCTGGATAAGATTT 59.545 37.500 0.00 0.00 33.93 2.17
62 63 5.048991 ACGCACGTTTTCTGGATAAGATTTT 60.049 36.000 0.00 0.00 33.93 1.82
70 71 6.395780 TTCTGGATAAGATTTTGGGGTACA 57.604 37.500 0.00 0.00 33.93 2.90
252 274 1.000896 CAGATTGGCCGGGTCCTTT 60.001 57.895 2.18 0.00 0.00 3.11
308 330 5.835113 TGGAGTTATTATTGGCTCTTTGC 57.165 39.130 0.00 0.00 41.94 3.68
325 347 6.091718 TCTTTGCTGTTTATGGGGTTTTAC 57.908 37.500 0.00 0.00 0.00 2.01
335 357 7.666804 TGTTTATGGGGTTTTACTTACTCTTCC 59.333 37.037 0.00 0.00 0.00 3.46
344 366 7.444487 GGTTTTACTTACTCTTCCTTCATGTGT 59.556 37.037 0.00 0.00 0.00 3.72
348 370 7.264373 ACTTACTCTTCCTTCATGTGTTTTG 57.736 36.000 0.00 0.00 0.00 2.44
349 371 4.574599 ACTCTTCCTTCATGTGTTTTGC 57.425 40.909 0.00 0.00 0.00 3.68
350 372 3.953612 ACTCTTCCTTCATGTGTTTTGCA 59.046 39.130 0.00 0.00 0.00 4.08
351 373 4.586001 ACTCTTCCTTCATGTGTTTTGCAT 59.414 37.500 0.00 0.00 0.00 3.96
352 374 4.873817 TCTTCCTTCATGTGTTTTGCATG 58.126 39.130 0.00 0.00 43.55 4.06
353 375 3.029320 TCCTTCATGTGTTTTGCATGC 57.971 42.857 11.82 11.82 42.34 4.06
354 376 2.364647 TCCTTCATGTGTTTTGCATGCA 59.635 40.909 18.46 18.46 42.34 3.96
355 377 3.007074 TCCTTCATGTGTTTTGCATGCAT 59.993 39.130 23.37 0.58 42.34 3.96
356 378 4.220163 TCCTTCATGTGTTTTGCATGCATA 59.780 37.500 23.37 14.80 42.34 3.14
357 379 4.565166 CCTTCATGTGTTTTGCATGCATAG 59.435 41.667 23.37 3.83 42.34 2.23
358 380 5.388408 TTCATGTGTTTTGCATGCATAGA 57.612 34.783 23.37 8.67 42.34 1.98
359 381 4.735985 TCATGTGTTTTGCATGCATAGAC 58.264 39.130 23.37 20.10 42.34 2.59
360 382 4.460034 TCATGTGTTTTGCATGCATAGACT 59.540 37.500 23.37 8.53 42.34 3.24
361 383 4.424061 TGTGTTTTGCATGCATAGACTC 57.576 40.909 23.37 19.14 0.00 3.36
362 384 4.074259 TGTGTTTTGCATGCATAGACTCT 58.926 39.130 23.37 0.00 0.00 3.24
363 385 4.083164 TGTGTTTTGCATGCATAGACTCTG 60.083 41.667 23.37 0.00 0.00 3.35
364 386 4.074259 TGTTTTGCATGCATAGACTCTGT 58.926 39.130 23.37 0.00 0.00 3.41
365 387 4.520111 TGTTTTGCATGCATAGACTCTGTT 59.480 37.500 23.37 0.00 0.00 3.16
366 388 5.009911 TGTTTTGCATGCATAGACTCTGTTT 59.990 36.000 23.37 0.00 0.00 2.83
367 389 6.206438 TGTTTTGCATGCATAGACTCTGTTTA 59.794 34.615 23.37 0.00 0.00 2.01
368 390 6.816134 TTTGCATGCATAGACTCTGTTTAA 57.184 33.333 23.37 4.76 0.00 1.52
369 391 5.801350 TGCATGCATAGACTCTGTTTAAC 57.199 39.130 18.46 0.00 0.00 2.01
370 392 5.244755 TGCATGCATAGACTCTGTTTAACA 58.755 37.500 18.46 0.00 0.00 2.41
371 393 5.882000 TGCATGCATAGACTCTGTTTAACAT 59.118 36.000 18.46 0.00 0.00 2.71
372 394 7.047271 TGCATGCATAGACTCTGTTTAACATA 58.953 34.615 18.46 0.00 0.00 2.29
373 395 7.716560 TGCATGCATAGACTCTGTTTAACATAT 59.283 33.333 18.46 0.00 0.00 1.78
376 398 9.836864 ATGCATAGACTCTGTTTAACATATGAA 57.163 29.630 10.38 8.57 0.00 2.57
410 432 8.964476 ACATATTGGGTCTGTAGATAAACTTG 57.036 34.615 0.00 0.00 0.00 3.16
471 493 4.645535 TGATTTCTGAACTCACCCAAGAG 58.354 43.478 6.37 0.00 41.44 2.85
618 640 4.449068 ACATTAGCGTCTTTGACAAGTGAG 59.551 41.667 0.00 0.00 32.09 3.51
641 664 6.685657 AGAGAAAATTCTGTTTCTGAATGGC 58.314 36.000 4.98 0.00 45.67 4.40
691 714 7.377766 TCTGTTCCACATATTACTCTTTTGC 57.622 36.000 0.00 0.00 0.00 3.68
733 758 6.605995 TCGAGTTCTTCCTGTATTGGATTCTA 59.394 38.462 0.00 0.00 35.83 2.10
734 759 7.287927 TCGAGTTCTTCCTGTATTGGATTCTAT 59.712 37.037 0.00 0.00 35.83 1.98
1221 1248 1.913778 ACATGGTTGCTGAATCTGCA 58.086 45.000 10.78 10.78 36.58 4.41
1327 1354 3.084786 GCTATTTCCACTTGTCTGGCTT 58.915 45.455 0.00 0.00 0.00 4.35
1426 1456 9.480053 CAGATTTTCTTGTCATGTTGGTTTATT 57.520 29.630 0.00 0.00 0.00 1.40
1713 1746 7.826252 AGTGCTACATCAGAAAATAGTTCATGT 59.174 33.333 0.00 0.00 0.00 3.21
1793 1827 6.757897 TCGACATATTTGGCAATTTCTTCT 57.242 33.333 0.00 0.00 0.00 2.85
1808 1842 2.833794 TCTTCTGGTGCAACTGTACAC 58.166 47.619 2.04 5.55 36.74 2.90
1878 1912 5.928264 AGGAACATGCTAAAATTTGTCTTGC 59.072 36.000 0.00 0.00 0.00 4.01
1929 1963 9.236006 AGGATTGGTGATAGATGCATTTATTAC 57.764 33.333 18.58 18.58 0.00 1.89
1936 1970 9.655769 GTGATAGATGCATTTATTACAAGTGTG 57.344 33.333 20.69 0.00 0.00 3.82
1979 2013 5.880332 TGGAAGGTACACTTATTCTCATTGC 59.120 40.000 0.00 0.00 40.21 3.56
2168 2204 9.902684 ATATTATTTCATCAGTGATCCATCTCC 57.097 33.333 1.56 0.00 33.56 3.71
2170 2206 5.705397 TTTCATCAGTGATCCATCTCCTT 57.295 39.130 1.56 0.00 33.56 3.36
2178 2214 2.092753 TGATCCATCTCCTTGGCTCAAC 60.093 50.000 0.00 0.00 38.58 3.18
2192 2228 9.120538 TCCTTGGCTCAACATATTTATTAGTTC 57.879 33.333 0.00 0.00 0.00 3.01
2207 2243 8.635765 TTTATTAGTTCCAACAGCTGAATTCT 57.364 30.769 23.35 12.46 0.00 2.40
2209 2245 6.959639 TTAGTTCCAACAGCTGAATTCTTT 57.040 33.333 23.35 0.00 0.00 2.52
2211 2247 6.959639 AGTTCCAACAGCTGAATTCTTTAA 57.040 33.333 23.35 0.56 0.00 1.52
2212 2248 7.530426 AGTTCCAACAGCTGAATTCTTTAAT 57.470 32.000 23.35 0.00 0.00 1.40
2213 2249 8.635765 AGTTCCAACAGCTGAATTCTTTAATA 57.364 30.769 23.35 0.00 0.00 0.98
2214 2250 9.077885 AGTTCCAACAGCTGAATTCTTTAATAA 57.922 29.630 23.35 0.00 0.00 1.40
2257 2293 4.887071 ACCAATAGTTCTGTGCTGTTGAAA 59.113 37.500 10.30 0.00 37.28 2.69
2274 2310 7.010460 GCTGTTGAAAATTAAAGCATGATACCC 59.990 37.037 0.00 0.00 0.00 3.69
2293 2329 5.010708 ACCCTTTTCACCTGGAATATTGT 57.989 39.130 0.00 0.00 34.91 2.71
2294 2330 5.402630 ACCCTTTTCACCTGGAATATTGTT 58.597 37.500 0.00 0.00 34.91 2.83
2321 2357 6.012658 TCATGAACCAAAATGTAGTGCTTC 57.987 37.500 0.00 0.00 0.00 3.86
2324 2360 5.771469 TGAACCAAAATGTAGTGCTTCATG 58.229 37.500 0.00 0.00 0.00 3.07
2329 2365 6.714810 ACCAAAATGTAGTGCTTCATGTTCTA 59.285 34.615 0.00 0.00 0.00 2.10
2332 2368 6.727824 AATGTAGTGCTTCATGTTCTACAC 57.272 37.500 14.62 8.62 41.95 2.90
2357 2393 6.825610 AGTCTTGCTGAAAATATAGCTAGCT 58.174 36.000 23.12 23.12 40.80 3.32
2358 2394 7.957002 AGTCTTGCTGAAAATATAGCTAGCTA 58.043 34.615 26.09 26.09 40.80 3.32
2359 2395 7.870445 AGTCTTGCTGAAAATATAGCTAGCTAC 59.130 37.037 26.41 13.06 40.80 3.58
2360 2396 7.653713 GTCTTGCTGAAAATATAGCTAGCTACA 59.346 37.037 26.41 16.56 40.80 2.74
2361 2397 8.204160 TCTTGCTGAAAATATAGCTAGCTACAA 58.796 33.333 26.41 19.11 40.80 2.41
2362 2398 8.731275 TTGCTGAAAATATAGCTAGCTACAAA 57.269 30.769 26.41 15.08 40.52 2.83
2363 2399 8.731275 TGCTGAAAATATAGCTAGCTACAAAA 57.269 30.769 26.41 12.66 40.52 2.44
2364 2400 9.342308 TGCTGAAAATATAGCTAGCTACAAAAT 57.658 29.630 26.41 13.92 40.52 1.82
2702 2745 8.147244 ACTATTATCAGTTCCTTACACAGGTT 57.853 34.615 0.00 0.00 44.37 3.50
2703 2746 9.263446 ACTATTATCAGTTCCTTACACAGGTTA 57.737 33.333 0.00 0.00 44.37 2.85
2713 2756 7.311092 TCCTTACACAGGTTATCTTGAAAGA 57.689 36.000 0.00 0.00 44.37 2.52
2998 3042 8.531146 ACAATTTACCAGGTCCAATTGATTTAG 58.469 33.333 28.80 12.65 38.41 1.85
3008 3052 7.614192 AGGTCCAATTGATTTAGTCCGTAATTT 59.386 33.333 7.12 0.00 0.00 1.82
3065 3109 9.474920 TGCTATGATGTTTTTACAAAGAAAAGG 57.525 29.630 0.00 0.00 30.30 3.11
3070 3114 6.959671 TGTTTTTACAAAGAAAAGGCAGTG 57.040 33.333 0.00 0.00 30.30 3.66
3138 3182 4.746115 CAGTTGGTGTTGATGGTTCATTTG 59.254 41.667 0.00 0.00 0.00 2.32
3174 3218 4.142403 ACCAACCGTATGATTTGCAATCAG 60.142 41.667 0.00 0.00 0.00 2.90
3285 3329 5.591472 CAGAGCATCATCTCAACCCAATAAA 59.409 40.000 0.00 0.00 37.82 1.40
3286 3330 5.826737 AGAGCATCATCTCAACCCAATAAAG 59.173 40.000 0.00 0.00 37.82 1.85
3287 3331 5.513233 AGCATCATCTCAACCCAATAAAGT 58.487 37.500 0.00 0.00 0.00 2.66
3288 3332 6.662755 AGCATCATCTCAACCCAATAAAGTA 58.337 36.000 0.00 0.00 0.00 2.24
3289 3333 6.543831 AGCATCATCTCAACCCAATAAAGTAC 59.456 38.462 0.00 0.00 0.00 2.73
3290 3334 6.543831 GCATCATCTCAACCCAATAAAGTACT 59.456 38.462 0.00 0.00 0.00 2.73
3291 3335 7.254932 GCATCATCTCAACCCAATAAAGTACTC 60.255 40.741 0.00 0.00 0.00 2.59
3292 3336 6.650120 TCATCTCAACCCAATAAAGTACTCC 58.350 40.000 0.00 0.00 0.00 3.85
3293 3337 5.431179 TCTCAACCCAATAAAGTACTCCC 57.569 43.478 0.00 0.00 0.00 4.30
3294 3338 5.098663 TCTCAACCCAATAAAGTACTCCCT 58.901 41.667 0.00 0.00 0.00 4.20
3295 3339 5.189145 TCTCAACCCAATAAAGTACTCCCTC 59.811 44.000 0.00 0.00 0.00 4.30
3296 3340 4.226620 TCAACCCAATAAAGTACTCCCTCC 59.773 45.833 0.00 0.00 0.00 4.30
3297 3341 2.770232 ACCCAATAAAGTACTCCCTCCG 59.230 50.000 0.00 0.00 0.00 4.63
3298 3342 2.770232 CCCAATAAAGTACTCCCTCCGT 59.230 50.000 0.00 0.00 0.00 4.69
3299 3343 3.181468 CCCAATAAAGTACTCCCTCCGTC 60.181 52.174 0.00 0.00 0.00 4.79
3300 3344 3.181468 CCAATAAAGTACTCCCTCCGTCC 60.181 52.174 0.00 0.00 0.00 4.79
3301 3345 1.755179 TAAAGTACTCCCTCCGTCCG 58.245 55.000 0.00 0.00 0.00 4.79
3302 3346 0.038744 AAAGTACTCCCTCCGTCCGA 59.961 55.000 0.00 0.00 0.00 4.55
3303 3347 0.038744 AAGTACTCCCTCCGTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
3304 3348 0.038744 AGTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.00 0.00 3.46
3305 3349 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
3306 3350 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
3307 3351 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
3308 3352 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
3309 3353 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
3310 3354 1.753073 TCCCTCCGTCCGAAAATACTC 59.247 52.381 0.00 0.00 0.00 2.59
3311 3355 1.535437 CCCTCCGTCCGAAAATACTCG 60.535 57.143 0.00 0.00 38.58 4.18
3312 3356 1.133790 CCTCCGTCCGAAAATACTCGT 59.866 52.381 0.00 0.00 37.11 4.18
3313 3357 2.448219 CTCCGTCCGAAAATACTCGTC 58.552 52.381 0.00 0.00 37.11 4.20
3314 3358 1.811965 TCCGTCCGAAAATACTCGTCA 59.188 47.619 0.00 0.00 37.11 4.35
3315 3359 2.424601 TCCGTCCGAAAATACTCGTCAT 59.575 45.455 0.00 0.00 37.11 3.06
3316 3360 2.787680 CCGTCCGAAAATACTCGTCATC 59.212 50.000 0.00 0.00 37.11 2.92
3317 3361 3.431856 CGTCCGAAAATACTCGTCATCA 58.568 45.455 0.00 0.00 37.11 3.07
3318 3362 3.855379 CGTCCGAAAATACTCGTCATCAA 59.145 43.478 0.00 0.00 37.11 2.57
3319 3363 4.325204 CGTCCGAAAATACTCGTCATCAAA 59.675 41.667 0.00 0.00 37.11 2.69
3320 3364 5.164031 CGTCCGAAAATACTCGTCATCAAAA 60.164 40.000 0.00 0.00 37.11 2.44
3321 3365 6.455113 CGTCCGAAAATACTCGTCATCAAAAT 60.455 38.462 0.00 0.00 37.11 1.82
3322 3366 7.253850 CGTCCGAAAATACTCGTCATCAAAATA 60.254 37.037 0.00 0.00 37.11 1.40
3323 3367 8.056571 GTCCGAAAATACTCGTCATCAAAATAG 58.943 37.037 0.00 0.00 37.11 1.73
3324 3368 7.977293 TCCGAAAATACTCGTCATCAAAATAGA 59.023 33.333 0.00 0.00 37.11 1.98
3325 3369 8.765219 CCGAAAATACTCGTCATCAAAATAGAT 58.235 33.333 0.00 0.00 37.11 1.98
3333 3377 8.893727 ACTCGTCATCAAAATAGATAAAAAGGG 58.106 33.333 0.00 0.00 0.00 3.95
3334 3378 9.109393 CTCGTCATCAAAATAGATAAAAAGGGA 57.891 33.333 0.00 0.00 0.00 4.20
3335 3379 9.627123 TCGTCATCAAAATAGATAAAAAGGGAT 57.373 29.630 0.00 0.00 0.00 3.85
3336 3380 9.669353 CGTCATCAAAATAGATAAAAAGGGATG 57.331 33.333 0.00 0.00 0.00 3.51
3379 3423 9.170890 ACATCTAGATACATCCCCTTTTATTCA 57.829 33.333 4.54 0.00 0.00 2.57
3385 3429 8.927411 AGATACATCCCCTTTTATTCATTTTGG 58.073 33.333 0.00 0.00 0.00 3.28
3386 3430 6.950860 ACATCCCCTTTTATTCATTTTGGT 57.049 33.333 0.00 0.00 0.00 3.67
3387 3431 6.710278 ACATCCCCTTTTATTCATTTTGGTG 58.290 36.000 0.00 0.00 0.00 4.17
3388 3432 6.500049 ACATCCCCTTTTATTCATTTTGGTGA 59.500 34.615 0.00 0.00 0.00 4.02
3389 3433 6.353404 TCCCCTTTTATTCATTTTGGTGAC 57.647 37.500 0.00 0.00 0.00 3.67
3390 3434 5.841237 TCCCCTTTTATTCATTTTGGTGACA 59.159 36.000 0.00 0.00 39.83 3.58
3403 3447 3.048337 TGGTGACAAGTATTTCCGGAC 57.952 47.619 1.83 0.00 37.44 4.79
3404 3448 1.997606 GGTGACAAGTATTTCCGGACG 59.002 52.381 1.83 0.00 0.00 4.79
3405 3449 1.997606 GTGACAAGTATTTCCGGACGG 59.002 52.381 1.83 3.96 0.00 4.79
3406 3450 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
3407 3451 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
3408 3452 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3409 3453 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3488 3533 3.127425 AGCACTGGTTTCTTGGTAGTC 57.873 47.619 0.00 0.00 0.00 2.59
3521 3566 5.163693 ACACAAAGTGTTAGTTAACTGGCAC 60.164 40.000 24.58 24.58 45.08 5.01
3654 3699 5.664457 TGATGTAGATCTGATGGTTCACAC 58.336 41.667 5.18 0.00 0.00 3.82
3888 3935 8.877779 CAAGAAATGATTAAGAGAGTCGTCATT 58.122 33.333 0.00 0.00 37.76 2.57
3900 3947 6.748198 AGAGAGTCGTCATTTTAGAAATCGAC 59.252 38.462 14.55 14.55 43.82 4.20
3907 3962 6.020281 CGTCATTTTAGAAATCGACCTCTGAG 60.020 42.308 8.09 0.00 0.00 3.35
3941 3996 4.647611 TGTGGATATGTCGAACCTGTTTT 58.352 39.130 0.00 0.00 0.00 2.43
3943 3998 4.454504 GTGGATATGTCGAACCTGTTTTGT 59.545 41.667 0.00 0.00 0.00 2.83
3962 4017 8.578151 TGTTTTGTCAAACTTGGGGTTATATAC 58.422 33.333 0.00 0.00 42.61 1.47
4017 4072 6.145534 TGAAACTTACTGTAAGATCACAAGCG 59.854 38.462 28.96 4.88 39.09 4.68
4072 4127 3.018423 TCAGAGATCCTGATGGTCGAA 57.982 47.619 9.14 0.00 46.38 3.71
4106 4161 6.183360 GCTAATGCTTTCCTTTTGTTTCGATG 60.183 38.462 0.00 0.00 36.03 3.84
4193 4248 6.879458 AGCTTGTACTGGAAGAAAATAATCGT 59.121 34.615 0.00 0.00 37.43 3.73
4242 4297 6.377327 TTCAAACATTTCAGGTCAGTCTTC 57.623 37.500 0.00 0.00 0.00 2.87
4263 4318 6.489700 TCTTCCTTTTCATGTGCAATTACTCA 59.510 34.615 0.00 0.00 0.00 3.41
4379 4434 5.705609 TTCTTCCAGGCTCAAAATAACAC 57.294 39.130 0.00 0.00 0.00 3.32
4535 4592 6.228995 TGCCTCTAATGATGCTTCTTCTATG 58.771 40.000 0.88 0.00 35.35 2.23
4568 4625 3.004862 CCAAATGCCTGGAAAAATGAGC 58.995 45.455 0.00 0.00 38.96 4.26
4569 4626 2.660189 AATGCCTGGAAAAATGAGCG 57.340 45.000 0.00 0.00 0.00 5.03
4610 4667 1.000274 GCGGTGAATGAAAACCTTGCT 60.000 47.619 0.00 0.00 34.06 3.91
4785 4843 9.390795 CAATTTTGTGTTTCTCTTGATCTAGTG 57.609 33.333 4.06 2.20 0.00 2.74
4814 4872 6.111669 ACTTACCAAGTAACCTTTCTCTCC 57.888 41.667 0.00 0.00 40.69 3.71
4871 4929 0.615331 GCCAAGAGGATGGTGAGTCA 59.385 55.000 0.00 0.00 42.75 3.41
4929 4987 0.527113 TTCATCGGTAGTTCGGCGAA 59.473 50.000 19.83 19.83 0.00 4.70
4947 5005 9.582431 TTCGGCGAATTATAGGAAGATAAATAG 57.418 33.333 19.83 0.00 0.00 1.73
5096 5155 4.644234 TGTATATTGGTGGCTGAACATTGG 59.356 41.667 0.00 0.00 0.00 3.16
5150 5209 3.231889 CTCGTCCTGCTGCACCTGT 62.232 63.158 0.00 0.00 0.00 4.00
5152 5211 1.446792 CGTCCTGCTGCACCTGTAG 60.447 63.158 0.00 0.00 0.00 2.74
5154 5213 0.108424 GTCCTGCTGCACCTGTAGAG 60.108 60.000 0.00 0.00 0.00 2.43
5155 5214 0.542938 TCCTGCTGCACCTGTAGAGT 60.543 55.000 0.00 0.00 0.00 3.24
5156 5215 1.186200 CCTGCTGCACCTGTAGAGTA 58.814 55.000 0.00 0.00 0.00 2.59
5157 5216 1.550524 CCTGCTGCACCTGTAGAGTAA 59.449 52.381 0.00 0.00 0.00 2.24
5158 5217 2.028112 CCTGCTGCACCTGTAGAGTAAA 60.028 50.000 0.00 0.00 0.00 2.01
5159 5218 3.369892 CCTGCTGCACCTGTAGAGTAAAT 60.370 47.826 0.00 0.00 0.00 1.40
5161 5220 4.755411 TGCTGCACCTGTAGAGTAAATAC 58.245 43.478 0.00 0.00 0.00 1.89
5162 5221 4.466370 TGCTGCACCTGTAGAGTAAATACT 59.534 41.667 0.00 0.00 39.71 2.12
5163 5222 5.655090 TGCTGCACCTGTAGAGTAAATACTA 59.345 40.000 0.00 0.00 36.50 1.82
5164 5223 6.183360 TGCTGCACCTGTAGAGTAAATACTAG 60.183 42.308 0.00 0.00 36.50 2.57
5166 5225 7.013083 GCTGCACCTGTAGAGTAAATACTAGTA 59.987 40.741 4.77 4.77 36.50 1.82
5167 5226 8.447924 TGCACCTGTAGAGTAAATACTAGTAG 57.552 38.462 8.85 0.00 36.50 2.57
5168 5227 8.270030 TGCACCTGTAGAGTAAATACTAGTAGA 58.730 37.037 8.85 0.00 36.50 2.59
5169 5228 9.118300 GCACCTGTAGAGTAAATACTAGTAGAA 57.882 37.037 8.85 0.00 36.50 2.10
5249 5347 6.531503 TTTTGCCGGTCCATATTTATTTGA 57.468 33.333 1.90 0.00 0.00 2.69
5270 5368 4.154015 TGATTCTCCTTGTATGCAAACGTG 59.846 41.667 0.00 0.00 33.73 4.49
5328 5426 1.661617 CTATCCTAGACGATCGAGCCG 59.338 57.143 24.34 7.16 0.00 5.52
5347 5445 3.758300 CCGGTGCAAAAACTACATGATC 58.242 45.455 0.00 0.00 0.00 2.92
5383 5481 0.529833 CAATGGCGGCCACAATGTTA 59.470 50.000 26.48 0.00 35.80 2.41
5425 5523 0.540923 GCTCATCCTTGTCTCTGGCT 59.459 55.000 0.00 0.00 0.00 4.75
5443 5541 2.512286 GCATAGTCCAGCTGCGCA 60.512 61.111 10.98 10.98 0.00 6.09
5467 5565 0.323957 AGAGCAGAGCAATGTCAGCA 59.676 50.000 0.00 0.00 31.61 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.390124 AACGTGCGTCTTTCCCTACA 59.610 50.000 0.00 0.00 0.00 2.74
33 34 1.595794 TCCAGAAAACGTGCGTCTTTC 59.404 47.619 16.61 16.61 0.00 2.62
36 37 2.736144 TATCCAGAAAACGTGCGTCT 57.264 45.000 0.00 0.00 0.00 4.18
61 62 0.770557 AGACCTGGCTTGTACCCCAA 60.771 55.000 0.00 0.00 0.00 4.12
62 63 1.151899 AGACCTGGCTTGTACCCCA 60.152 57.895 0.00 0.00 0.00 4.96
70 71 4.339335 AGGGAACAGACCTGGCTT 57.661 55.556 0.00 0.00 36.85 4.35
126 147 1.948834 CAATCAACACACAGTGAGGCA 59.051 47.619 7.81 0.00 36.96 4.75
241 263 2.675423 GGTGGAAAAGGACCCGGC 60.675 66.667 0.00 0.00 0.00 6.13
252 274 4.884668 ATCGAGAAAGTAACAGGTGGAA 57.115 40.909 0.00 0.00 0.00 3.53
308 330 8.631480 AAGAGTAAGTAAAACCCCATAAACAG 57.369 34.615 0.00 0.00 0.00 3.16
325 347 6.145535 GCAAAACACATGAAGGAAGAGTAAG 58.854 40.000 0.00 0.00 0.00 2.34
335 357 5.287752 GTCTATGCATGCAAAACACATGAAG 59.712 40.000 26.68 9.08 46.33 3.02
344 366 5.710513 AAACAGAGTCTATGCATGCAAAA 57.289 34.783 26.68 15.04 0.00 2.44
348 370 5.801350 TGTTAAACAGAGTCTATGCATGC 57.199 39.130 11.82 11.82 0.00 4.06
349 371 9.264719 TCATATGTTAAACAGAGTCTATGCATG 57.735 33.333 10.16 0.00 0.00 4.06
350 372 9.836864 TTCATATGTTAAACAGAGTCTATGCAT 57.163 29.630 3.79 3.79 0.00 3.96
351 373 9.836864 ATTCATATGTTAAACAGAGTCTATGCA 57.163 29.630 1.90 0.00 0.00 3.96
373 395 9.308000 ACAGACCCAATATGTTAAAGAAATTCA 57.692 29.630 0.00 0.00 23.55 2.57
394 416 5.181245 TGGCAAAGCAAGTTTATCTACAGAC 59.819 40.000 0.00 0.00 0.00 3.51
395 417 5.312895 TGGCAAAGCAAGTTTATCTACAGA 58.687 37.500 0.00 0.00 0.00 3.41
397 419 5.070001 ACTGGCAAAGCAAGTTTATCTACA 58.930 37.500 0.00 0.00 40.28 2.74
398 420 5.629079 ACTGGCAAAGCAAGTTTATCTAC 57.371 39.130 0.00 0.00 40.28 2.59
408 430 1.952990 TCAATTCGACTGGCAAAGCAA 59.047 42.857 0.00 0.00 0.00 3.91
410 432 2.790387 GATCAATTCGACTGGCAAAGC 58.210 47.619 0.00 0.00 0.00 3.51
471 493 6.073222 TCAGATTCTTTCTTTTCCTACGCAAC 60.073 38.462 0.00 0.00 29.93 4.17
545 567 1.728971 CTCTTCTCAACCGCATGACAC 59.271 52.381 0.00 0.00 0.00 3.67
618 640 6.364435 GTGCCATTCAGAAACAGAATTTTCTC 59.636 38.462 0.00 0.00 42.74 2.87
691 714 4.446371 ACTCGAAATTTCCTATGCCTCAG 58.554 43.478 12.54 0.00 0.00 3.35
1353 1380 2.544685 CTGAACGATGGAGACCACATC 58.455 52.381 0.00 0.00 40.95 3.06
1426 1456 9.676129 AGGATAGAAGGAAAGATTTATGGTAGA 57.324 33.333 0.00 0.00 0.00 2.59
1443 1474 5.734498 CGAACGCAAAAATCAAGGATAGAAG 59.266 40.000 0.00 0.00 0.00 2.85
1633 1665 6.925165 CCATGTAAGCAGAAAAACAAGAACAT 59.075 34.615 0.00 0.00 0.00 2.71
1713 1746 4.993705 ATAAGTGTTGTCCCTTCTTGGA 57.006 40.909 0.00 0.00 38.35 3.53
1730 1763 7.448420 TCCATTCAGGCTCAGATCTAAATAAG 58.552 38.462 0.00 0.00 37.29 1.73
1772 1806 6.532657 CACCAGAAGAAATTGCCAAATATGTC 59.467 38.462 0.00 0.00 0.00 3.06
1793 1827 1.137282 TCTTCGTGTACAGTTGCACCA 59.863 47.619 0.00 0.00 35.02 4.17
1833 1867 1.893137 TGAAACGAGCTGCTCTAGGAA 59.107 47.619 25.59 7.49 0.00 3.36
1928 1962 5.753438 CGTCCTAATATATGCACACACTTGT 59.247 40.000 0.00 0.00 35.84 3.16
1929 1963 5.983118 TCGTCCTAATATATGCACACACTTG 59.017 40.000 0.00 0.00 0.00 3.16
1932 1966 5.402568 CACTCGTCCTAATATATGCACACAC 59.597 44.000 0.00 0.00 0.00 3.82
1936 1970 5.386958 TCCACTCGTCCTAATATATGCAC 57.613 43.478 0.00 0.00 0.00 4.57
1979 2013 9.077885 AGGCCCAAAATGTAGTATTTGTATATG 57.922 33.333 0.00 0.00 35.30 1.78
2002 2036 5.746990 ACTCATGTCCCACTATATAAGGC 57.253 43.478 0.00 0.00 0.00 4.35
2167 2203 8.352942 GGAACTAATAAATATGTTGAGCCAAGG 58.647 37.037 0.00 0.00 0.00 3.61
2168 2204 8.902806 TGGAACTAATAAATATGTTGAGCCAAG 58.097 33.333 0.00 0.00 0.00 3.61
2170 2206 8.682710 GTTGGAACTAATAAATATGTTGAGCCA 58.317 33.333 0.00 0.00 0.00 4.75
2192 2228 8.598075 GCAATTATTAAAGAATTCAGCTGTTGG 58.402 33.333 14.67 0.00 0.00 3.77
2206 2242 8.937634 ATCAAAAGCTCAGGCAATTATTAAAG 57.062 30.769 0.00 0.00 41.70 1.85
2207 2243 9.153721 CAATCAAAAGCTCAGGCAATTATTAAA 57.846 29.630 0.00 0.00 41.70 1.52
2209 2245 7.975616 GTCAATCAAAAGCTCAGGCAATTATTA 59.024 33.333 0.00 0.00 41.70 0.98
2211 2247 6.335777 GTCAATCAAAAGCTCAGGCAATTAT 58.664 36.000 0.00 0.00 41.70 1.28
2212 2248 5.336690 GGTCAATCAAAAGCTCAGGCAATTA 60.337 40.000 0.00 0.00 41.70 1.40
2213 2249 4.562143 GGTCAATCAAAAGCTCAGGCAATT 60.562 41.667 0.00 0.00 41.70 2.32
2214 2250 3.056322 GGTCAATCAAAAGCTCAGGCAAT 60.056 43.478 0.00 0.00 41.70 3.56
2257 2293 7.400052 AGGTGAAAAGGGTATCATGCTTTAATT 59.600 33.333 0.00 0.00 0.00 1.40
2274 2310 8.359642 TGAGAAAACAATATTCCAGGTGAAAAG 58.640 33.333 0.00 0.00 36.33 2.27
2293 2329 6.922957 GCACTACATTTTGGTTCATGAGAAAA 59.077 34.615 10.18 10.18 35.08 2.29
2294 2330 6.265196 AGCACTACATTTTGGTTCATGAGAAA 59.735 34.615 0.00 0.00 35.08 2.52
2321 2357 4.658713 CAGCAAGACTGTGTAGAACATG 57.341 45.455 0.00 0.00 41.86 3.21
2351 2387 4.498177 GCCAGCCTTTATTTTGTAGCTAGC 60.498 45.833 6.62 6.62 0.00 3.42
2352 2388 4.640201 TGCCAGCCTTTATTTTGTAGCTAG 59.360 41.667 0.00 0.00 0.00 3.42
2353 2389 4.594970 TGCCAGCCTTTATTTTGTAGCTA 58.405 39.130 0.00 0.00 0.00 3.32
2354 2390 3.430453 TGCCAGCCTTTATTTTGTAGCT 58.570 40.909 0.00 0.00 0.00 3.32
2355 2391 3.866883 TGCCAGCCTTTATTTTGTAGC 57.133 42.857 0.00 0.00 0.00 3.58
2356 2392 6.165577 ACAAATGCCAGCCTTTATTTTGTAG 58.834 36.000 0.00 0.00 0.00 2.74
2357 2393 6.107901 ACAAATGCCAGCCTTTATTTTGTA 57.892 33.333 0.00 0.00 0.00 2.41
2358 2394 4.971939 ACAAATGCCAGCCTTTATTTTGT 58.028 34.783 0.00 0.00 0.00 2.83
2359 2395 5.945466 AACAAATGCCAGCCTTTATTTTG 57.055 34.783 0.00 0.00 0.00 2.44
2360 2396 6.298361 AGAAACAAATGCCAGCCTTTATTTT 58.702 32.000 0.00 0.56 0.00 1.82
2361 2397 5.868454 AGAAACAAATGCCAGCCTTTATTT 58.132 33.333 0.00 0.00 0.00 1.40
2362 2398 5.488262 AGAAACAAATGCCAGCCTTTATT 57.512 34.783 0.00 0.00 0.00 1.40
2363 2399 5.951747 TCTAGAAACAAATGCCAGCCTTTAT 59.048 36.000 0.00 0.00 0.00 1.40
2364 2400 5.321102 TCTAGAAACAAATGCCAGCCTTTA 58.679 37.500 0.00 0.00 0.00 1.85
2365 2401 4.151883 TCTAGAAACAAATGCCAGCCTTT 58.848 39.130 0.00 0.00 0.00 3.11
2366 2402 3.766545 TCTAGAAACAAATGCCAGCCTT 58.233 40.909 0.00 0.00 0.00 4.35
2627 2663 8.552083 AACAATTTTGACTGAAAGCTTTCTTT 57.448 26.923 33.03 22.39 44.67 2.52
2702 2745 8.374743 CCCCCTCAAAATTTTTCTTTCAAGATA 58.625 33.333 0.00 0.00 34.49 1.98
2703 2746 7.226441 CCCCCTCAAAATTTTTCTTTCAAGAT 58.774 34.615 0.00 0.00 34.49 2.40
2705 2748 5.239306 GCCCCCTCAAAATTTTTCTTTCAAG 59.761 40.000 0.00 0.00 0.00 3.02
2713 2756 4.865905 ACTTTTGCCCCCTCAAAATTTTT 58.134 34.783 0.00 0.00 42.77 1.94
2964 3008 8.485578 TTGGACCTGGTAAATTGTAAAGAAAT 57.514 30.769 0.00 0.00 0.00 2.17
3008 3052 8.846211 GCTATAAGCAAAATAGGTTGGTAATGA 58.154 33.333 0.00 0.00 41.89 2.57
3065 3109 2.215907 AGATGATACTGTCGCACTGC 57.784 50.000 0.00 0.00 0.00 4.40
3070 3114 4.340894 TTTTGCAAGATGATACTGTCGC 57.659 40.909 0.00 0.00 0.00 5.19
3138 3182 0.391966 GGTTGGTACGATCCTAGGGC 59.608 60.000 9.46 0.32 0.00 5.19
3174 3218 6.402222 AGTATCTCAACTCAATCTCAACCAC 58.598 40.000 0.00 0.00 0.00 4.16
3285 3329 0.038744 TTTCGGACGGAGGGAGTACT 59.961 55.000 0.00 0.00 0.00 2.73
3286 3330 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
3287 3331 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
3288 3332 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
3289 3333 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
3290 3334 1.753073 GAGTATTTTCGGACGGAGGGA 59.247 52.381 0.00 0.00 0.00 4.20
3291 3335 1.535437 CGAGTATTTTCGGACGGAGGG 60.535 57.143 0.00 0.00 36.95 4.30
3292 3336 1.133790 ACGAGTATTTTCGGACGGAGG 59.866 52.381 0.00 0.00 44.57 4.30
3293 3337 2.159476 TGACGAGTATTTTCGGACGGAG 60.159 50.000 0.00 0.00 44.57 4.63
3294 3338 1.811965 TGACGAGTATTTTCGGACGGA 59.188 47.619 0.00 0.00 44.57 4.69
3295 3339 2.267188 TGACGAGTATTTTCGGACGG 57.733 50.000 0.00 0.00 44.57 4.79
3296 3340 3.431856 TGATGACGAGTATTTTCGGACG 58.568 45.455 0.00 0.00 44.57 4.79
3297 3341 5.773239 TTTGATGACGAGTATTTTCGGAC 57.227 39.130 0.00 0.00 44.57 4.79
3298 3342 6.978343 ATTTTGATGACGAGTATTTTCGGA 57.022 33.333 0.00 0.00 44.57 4.55
3299 3343 8.126871 TCTATTTTGATGACGAGTATTTTCGG 57.873 34.615 0.00 0.00 44.57 4.30
3307 3351 8.893727 CCCTTTTTATCTATTTTGATGACGAGT 58.106 33.333 0.00 0.00 0.00 4.18
3308 3352 9.109393 TCCCTTTTTATCTATTTTGATGACGAG 57.891 33.333 0.00 0.00 0.00 4.18
3309 3353 9.627123 ATCCCTTTTTATCTATTTTGATGACGA 57.373 29.630 0.00 0.00 0.00 4.20
3310 3354 9.669353 CATCCCTTTTTATCTATTTTGATGACG 57.331 33.333 0.00 0.00 0.00 4.35
3353 3397 9.170890 TGAATAAAAGGGGATGTATCTAGATGT 57.829 33.333 15.79 1.25 0.00 3.06
3359 3403 8.927411 CCAAAATGAATAAAAGGGGATGTATCT 58.073 33.333 0.00 0.00 0.00 1.98
3360 3404 8.704668 ACCAAAATGAATAAAAGGGGATGTATC 58.295 33.333 0.00 0.00 0.00 2.24
3361 3405 8.485392 CACCAAAATGAATAAAAGGGGATGTAT 58.515 33.333 0.00 0.00 0.00 2.29
3362 3406 7.676043 TCACCAAAATGAATAAAAGGGGATGTA 59.324 33.333 0.00 0.00 0.00 2.29
3363 3407 6.500049 TCACCAAAATGAATAAAAGGGGATGT 59.500 34.615 0.00 0.00 0.00 3.06
3364 3408 6.818142 GTCACCAAAATGAATAAAAGGGGATG 59.182 38.462 0.00 0.00 28.65 3.51
3365 3409 6.500049 TGTCACCAAAATGAATAAAAGGGGAT 59.500 34.615 0.00 0.00 28.65 3.85
3366 3410 5.841237 TGTCACCAAAATGAATAAAAGGGGA 59.159 36.000 0.00 0.00 0.00 4.81
3367 3411 6.107901 TGTCACCAAAATGAATAAAAGGGG 57.892 37.500 0.00 0.00 0.00 4.79
3368 3412 7.216494 ACTTGTCACCAAAATGAATAAAAGGG 58.784 34.615 0.00 0.00 0.00 3.95
3369 3413 9.927668 ATACTTGTCACCAAAATGAATAAAAGG 57.072 29.630 0.00 0.00 0.00 3.11
3373 3417 9.921637 GGAAATACTTGTCACCAAAATGAATAA 57.078 29.630 0.00 0.00 0.00 1.40
3374 3418 8.240682 CGGAAATACTTGTCACCAAAATGAATA 58.759 33.333 0.00 0.00 0.00 1.75
3375 3419 7.090173 CGGAAATACTTGTCACCAAAATGAAT 58.910 34.615 0.00 0.00 0.00 2.57
3376 3420 6.442952 CGGAAATACTTGTCACCAAAATGAA 58.557 36.000 0.00 0.00 0.00 2.57
3377 3421 5.048364 CCGGAAATACTTGTCACCAAAATGA 60.048 40.000 0.00 0.00 0.00 2.57
3378 3422 5.048364 TCCGGAAATACTTGTCACCAAAATG 60.048 40.000 0.00 0.00 0.00 2.32
3379 3423 5.048294 GTCCGGAAATACTTGTCACCAAAAT 60.048 40.000 5.23 0.00 0.00 1.82
3380 3424 4.276431 GTCCGGAAATACTTGTCACCAAAA 59.724 41.667 5.23 0.00 0.00 2.44
3381 3425 3.816523 GTCCGGAAATACTTGTCACCAAA 59.183 43.478 5.23 0.00 0.00 3.28
3382 3426 3.404899 GTCCGGAAATACTTGTCACCAA 58.595 45.455 5.23 0.00 0.00 3.67
3383 3427 2.610976 CGTCCGGAAATACTTGTCACCA 60.611 50.000 5.23 0.00 0.00 4.17
3384 3428 1.997606 CGTCCGGAAATACTTGTCACC 59.002 52.381 5.23 0.00 0.00 4.02
3385 3429 1.997606 CCGTCCGGAAATACTTGTCAC 59.002 52.381 5.23 0.00 37.50 3.67
3386 3430 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
3387 3431 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3388 3432 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3389 3433 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3390 3434 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
3391 3435 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
3392 3436 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3393 3437 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3394 3438 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3395 3439 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
3396 3440 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
3397 3441 2.593978 CTACTCCCTCCGTCCGGA 59.406 66.667 0.00 0.00 42.90 5.14
3398 3442 3.217743 GCTACTCCCTCCGTCCGG 61.218 72.222 0.00 0.00 0.00 5.14
3399 3443 2.050350 TTGCTACTCCCTCCGTCCG 61.050 63.158 0.00 0.00 0.00 4.79
3400 3444 0.971447 AGTTGCTACTCCCTCCGTCC 60.971 60.000 0.00 0.00 0.00 4.79
3401 3445 1.760192 TAGTTGCTACTCCCTCCGTC 58.240 55.000 3.45 0.00 35.78 4.79
3402 3446 2.226962 TTAGTTGCTACTCCCTCCGT 57.773 50.000 3.45 0.00 35.78 4.69
3403 3447 4.341520 ACTTATTAGTTGCTACTCCCTCCG 59.658 45.833 3.45 0.00 35.78 4.63
3404 3448 5.599242 AGACTTATTAGTTGCTACTCCCTCC 59.401 44.000 3.45 0.00 35.78 4.30
3405 3449 6.718522 AGACTTATTAGTTGCTACTCCCTC 57.281 41.667 3.45 0.00 35.78 4.30
3406 3450 6.630638 GCAAGACTTATTAGTTGCTACTCCCT 60.631 42.308 3.45 0.00 35.94 4.20
3407 3451 5.524281 GCAAGACTTATTAGTTGCTACTCCC 59.476 44.000 3.45 0.00 35.94 4.30
3408 3452 5.232414 CGCAAGACTTATTAGTTGCTACTCC 59.768 44.000 3.45 0.00 36.44 3.85
3409 3453 6.034591 TCGCAAGACTTATTAGTTGCTACTC 58.965 40.000 3.45 0.00 45.01 2.59
3460 3505 2.930950 AGAAACCAGTGCTTTGCTACA 58.069 42.857 0.00 0.00 0.00 2.74
3507 3552 5.860611 ACATACACTGTGCCAGTTAACTAA 58.139 37.500 8.04 0.00 42.59 2.24
3527 3572 7.534282 TCGCATTATTTTGTATCAACACACAT 58.466 30.769 0.00 0.00 34.61 3.21
3654 3699 1.066002 GGTCCATGCACAATTGGATCG 59.934 52.381 9.89 0.00 43.61 3.69
3713 3758 7.803189 CCACTAAGTACTGCAATTTTGTTGTAG 59.197 37.037 0.00 4.66 37.98 2.74
3888 3935 4.801330 TGCTCAGAGGTCGATTTCTAAA 57.199 40.909 0.00 0.00 0.00 1.85
3900 3947 4.370049 CACAGATACTCAATGCTCAGAGG 58.630 47.826 0.00 0.00 36.20 3.69
3907 3962 5.347093 CGACATATCCACAGATACTCAATGC 59.653 44.000 0.00 0.00 37.80 3.56
3941 3996 6.181908 GGTGTATATAACCCCAAGTTTGACA 58.818 40.000 0.00 0.00 40.05 3.58
3943 3998 6.390048 TGGTGTATATAACCCCAAGTTTGA 57.610 37.500 9.99 0.00 40.05 2.69
3962 4017 2.107950 ATACCACACGGTTGATGGTG 57.892 50.000 15.42 4.17 46.31 4.17
3967 4022 4.938832 CCTCATTAAATACCACACGGTTGA 59.061 41.667 0.00 0.00 46.31 3.18
3986 4041 6.269077 TGATCTTACAGTAAGTTTCACCCTCA 59.731 38.462 18.16 8.15 37.10 3.86
3988 4043 6.042781 TGTGATCTTACAGTAAGTTTCACCCT 59.957 38.462 30.73 10.86 42.45 4.34
4045 4100 3.359194 CAGGATCTCTGAACCTGCG 57.641 57.895 10.20 0.00 43.58 5.18
4094 4149 4.377839 TGGAACAAGCATCGAAACAAAA 57.622 36.364 0.00 0.00 31.92 2.44
4242 4297 7.537715 TGTATGAGTAATTGCACATGAAAAGG 58.462 34.615 14.85 0.00 0.00 3.11
4263 4318 3.539604 GAACTCCTGCATTCTGCTGTAT 58.460 45.455 0.34 0.00 45.31 2.29
4351 4406 5.982890 TTTTGAGCCTGGAAGAAATAAGG 57.017 39.130 0.00 0.00 34.07 2.69
4379 4434 0.848942 CACGCGATTGAAGAGATCGG 59.151 55.000 15.93 2.20 44.80 4.18
4449 4504 4.224433 GCAACTGAATTATGCATGGATCG 58.776 43.478 10.16 4.13 39.81 3.69
4535 4592 1.636988 GCATTTGGCTCATGCTGTTC 58.363 50.000 12.51 0.00 43.26 3.18
4556 4613 1.745087 GGCATCTCGCTCATTTTTCCA 59.255 47.619 0.00 0.00 41.91 3.53
4568 4625 0.179089 CTCCCAACTGAGGCATCTCG 60.179 60.000 0.00 0.00 42.79 4.04
4569 4626 0.908198 ACTCCCAACTGAGGCATCTC 59.092 55.000 0.00 0.00 40.36 2.75
4610 4667 5.955959 TGTAAGATCTGGGAGCAAGTAACTA 59.044 40.000 0.00 0.00 0.00 2.24
4771 4829 6.672266 AAGTTGGTTCACTAGATCAAGAGA 57.328 37.500 0.00 0.00 0.00 3.10
4772 4830 6.814146 GGTAAGTTGGTTCACTAGATCAAGAG 59.186 42.308 0.00 0.00 0.00 2.85
4785 4843 6.544931 AGAAAGGTTACTTGGTAAGTTGGTTC 59.455 38.462 0.00 0.00 42.81 3.62
4814 4872 4.616835 GCTATTTCCAAGAACTTGTGCCTG 60.617 45.833 12.54 0.00 38.85 4.85
4871 4929 0.820891 CTGTGACCTGCTTTGGCTGT 60.821 55.000 0.00 0.00 39.59 4.40
5096 5155 1.728971 CTGAAACCATCACTGCTCGAC 59.271 52.381 0.00 0.00 33.47 4.20
5157 5216 9.804758 GTTGTTGCTACATCTTCTACTAGTATT 57.195 33.333 2.33 0.00 33.44 1.89
5158 5217 8.967918 TGTTGTTGCTACATCTTCTACTAGTAT 58.032 33.333 2.33 0.00 33.44 2.12
5159 5218 8.344446 TGTTGTTGCTACATCTTCTACTAGTA 57.656 34.615 0.81 1.89 33.44 1.82
5161 5220 8.029522 TCTTGTTGTTGCTACATCTTCTACTAG 58.970 37.037 0.81 3.19 33.44 2.57
5162 5221 7.892609 TCTTGTTGTTGCTACATCTTCTACTA 58.107 34.615 0.81 0.00 33.44 1.82
5163 5222 6.759272 TCTTGTTGTTGCTACATCTTCTACT 58.241 36.000 0.81 0.00 33.44 2.57
5164 5223 7.421530 TTCTTGTTGTTGCTACATCTTCTAC 57.578 36.000 0.81 0.00 33.44 2.59
5166 5225 5.049129 GCTTCTTGTTGTTGCTACATCTTCT 60.049 40.000 0.81 0.00 33.44 2.85
5167 5226 5.049129 AGCTTCTTGTTGTTGCTACATCTTC 60.049 40.000 0.81 0.00 33.44 2.87
5168 5227 4.823989 AGCTTCTTGTTGTTGCTACATCTT 59.176 37.500 0.81 0.00 33.44 2.40
5169 5228 4.392940 AGCTTCTTGTTGTTGCTACATCT 58.607 39.130 0.81 0.00 33.44 2.90
5171 5230 6.824305 ATTAGCTTCTTGTTGTTGCTACAT 57.176 33.333 0.81 0.00 36.19 2.29
5172 5231 7.659799 TCTTATTAGCTTCTTGTTGTTGCTACA 59.340 33.333 0.00 0.00 36.19 2.74
5173 5232 8.029642 TCTTATTAGCTTCTTGTTGTTGCTAC 57.970 34.615 0.00 0.00 36.19 3.58
5175 5234 7.229506 AGTTCTTATTAGCTTCTTGTTGTTGCT 59.770 33.333 0.00 0.00 37.72 3.91
5176 5235 7.363431 AGTTCTTATTAGCTTCTTGTTGTTGC 58.637 34.615 0.00 0.00 0.00 4.17
5178 5237 8.722394 GCTAGTTCTTATTAGCTTCTTGTTGTT 58.278 33.333 0.00 0.00 39.30 2.83
5179 5238 8.257830 GCTAGTTCTTATTAGCTTCTTGTTGT 57.742 34.615 0.00 0.00 39.30 3.32
5249 5347 4.323417 TCACGTTTGCATACAAGGAGAAT 58.677 39.130 8.06 0.00 37.04 2.40
5270 5368 5.012328 AGACAAACTAGACATCCGGATTC 57.988 43.478 16.19 15.41 0.00 2.52
5328 5426 4.380867 CCAGGATCATGTAGTTTTTGCACC 60.381 45.833 6.62 0.00 0.00 5.01
5347 5445 3.592059 CATTGACCAGATTTTTGCCAGG 58.408 45.455 0.00 0.00 0.00 4.45
5383 5481 0.324943 AAGTGCAGGAATGCTACGGT 59.675 50.000 1.53 0.00 35.49 4.83
5405 5503 0.463474 GCCAGAGACAAGGATGAGCC 60.463 60.000 0.00 0.00 0.00 4.70
5443 5541 2.149578 GACATTGCTCTGCTCTTGTGT 58.850 47.619 0.00 0.00 0.00 3.72
5467 5565 0.036105 TCTGACATTGCTCATGGCGT 60.036 50.000 0.00 0.00 45.35 5.68


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

AutoCloner maintained by Alex Coulton.