Multiple sequence alignment - TraesCS7A01G532700

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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 TraesCS7A01G532700 chr7A 100.000 4131 0 0 1 4131 711368184 711372314 0.000000e+00 7629.0
1 TraesCS7A01G532700 chr7A 90.446 1884 143 9 715 2582 711258457 711260319 0.000000e+00 2447.0
2 TraesCS7A01G532700 chr7A 80.920 870 119 23 2610 3443 711278772 711279630 0.000000e+00 643.0
3 TraesCS7A01G532700 chr7A 75.372 942 182 35 2216 3124 709733273 709732349 3.840000e-110 409.0
4 TraesCS7A01G532700 chr7A 79.487 390 59 12 859 1236 711389580 711389960 1.470000e-64 257.0
5 TraesCS7A01G532700 chr7A 82.770 296 44 1 1650 1938 711390120 711390415 1.470000e-64 257.0
6 TraesCS7A01G532700 chr7A 97.059 34 0 1 3226 3258 709732271 709732238 5.770000e-04 56.5
7 TraesCS7A01G532700 chr7D 88.644 2721 185 49 1350 4020 617637356 617640002 0.000000e+00 3199.0
8 TraesCS7A01G532700 chr7D 94.792 1440 50 7 1493 2923 617625108 617626531 0.000000e+00 2220.0
9 TraesCS7A01G532700 chr7D 87.414 437 42 6 2915 3348 617634382 617634808 1.330000e-134 490.0
10 TraesCS7A01G532700 chr7D 79.568 602 77 21 708 1292 617636671 617637243 5.010000e-104 388.0
11 TraesCS7A01G532700 chr7D 77.473 546 92 20 1355 1891 617645295 617644772 8.680000e-77 298.0
12 TraesCS7A01G532700 chr7D 80.268 299 53 4 2746 3041 617641488 617641193 1.930000e-53 220.0
13 TraesCS7A01G532700 chr7B 87.111 1637 127 33 705 2281 711638233 711639845 0.000000e+00 1777.0
14 TraesCS7A01G532700 chr7B 87.286 991 82 18 2641 3621 711640621 711641577 0.000000e+00 1092.0
15 TraesCS7A01G532700 chr7B 77.716 893 128 40 1050 1891 711063165 711062293 8.030000e-132 481.0
16 TraesCS7A01G532700 chr7B 96.053 228 8 1 3905 4131 711642239 711642466 1.810000e-98 370.0
17 TraesCS7A01G532700 chr7B 89.931 288 25 3 372 657 706164946 706164661 6.520000e-98 368.0
18 TraesCS7A01G532700 chr7B 90.594 202 14 1 3632 3828 711641615 711641816 3.170000e-66 263.0
19 TraesCS7A01G532700 chr7B 100.000 33 0 0 3876 3908 711641817 711641849 1.240000e-05 62.1
20 TraesCS7A01G532700 chr1B 89.789 284 25 3 372 653 510295117 510294836 1.090000e-95 361.0
21 TraesCS7A01G532700 chr1B 89.531 277 25 3 374 648 3245508 3245234 8.500000e-92 348.0
22 TraesCS7A01G532700 chr1D 90.000 280 24 3 372 649 452997352 452997629 3.930000e-95 359.0
23 TraesCS7A01G532700 chr2B 88.396 293 27 6 361 650 339116339 339116051 3.060000e-91 346.0
24 TraesCS7A01G532700 chr2B 88.421 285 29 3 371 653 133122951 133123233 1.420000e-89 340.0
25 TraesCS7A01G532700 chr4A 88.968 281 27 3 372 650 201806778 201806500 1.100000e-90 344.0
26 TraesCS7A01G532700 chr3B 87.248 298 30 7 351 646 538630617 538630908 2.380000e-87 333.0
27 TraesCS7A01G532700 chr3B 87.986 283 28 5 371 650 34647709 34647430 3.080000e-86 329.0


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 TraesCS7A01G532700 chr7A 711368184 711372314 4130 False 7629.00 7629 100.000000 1 4131 1 chr7A.!!$F3 4130
1 TraesCS7A01G532700 chr7A 711258457 711260319 1862 False 2447.00 2447 90.446000 715 2582 1 chr7A.!!$F1 1867
2 TraesCS7A01G532700 chr7A 711278772 711279630 858 False 643.00 643 80.920000 2610 3443 1 chr7A.!!$F2 833
3 TraesCS7A01G532700 chr7A 711389580 711390415 835 False 257.00 257 81.128500 859 1938 2 chr7A.!!$F4 1079
4 TraesCS7A01G532700 chr7A 709732238 709733273 1035 True 232.75 409 86.215500 2216 3258 2 chr7A.!!$R1 1042
5 TraesCS7A01G532700 chr7D 617625108 617626531 1423 False 2220.00 2220 94.792000 1493 2923 1 chr7D.!!$F1 1430
6 TraesCS7A01G532700 chr7D 617634382 617640002 5620 False 1359.00 3199 85.208667 708 4020 3 chr7D.!!$F2 3312
7 TraesCS7A01G532700 chr7D 617641193 617645295 4102 True 259.00 298 78.870500 1355 3041 2 chr7D.!!$R1 1686
8 TraesCS7A01G532700 chr7B 711638233 711642466 4233 False 712.82 1777 92.208800 705 4131 5 chr7B.!!$F1 3426
9 TraesCS7A01G532700 chr7B 711062293 711063165 872 True 481.00 481 77.716000 1050 1891 1 chr7B.!!$R2 841

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
268 269 0.392998 CCGGTGCCTGCTGTCTTTAT 60.393 55.0 0.00 0.0 0.00 1.40 F
380 381 0.815734 AGCGTACACATTAGGCTCGT 59.184 50.0 0.00 0.0 34.00 4.18 F
1306 2988 0.956633 CAGTGTTGCTCAGTGCCAAT 59.043 50.0 4.84 0.0 40.06 3.16 F
2350 7129 0.409876 TCAGACCTAGCTGGACCACT 59.590 55.0 0.00 0.0 39.71 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1423 3154 0.033405 TTCGAGGCAGTACCCTAGCT 60.033 55.0 0.00 0.0 40.58 3.32 R
1634 3403 0.107312 ATGACAGTGGCTGGAGATGC 60.107 55.0 0.00 0.0 35.51 3.91 R
2969 7961 0.036765 GGCCGGACACTCATGTTACA 60.037 55.0 5.05 0.0 39.95 2.41 R
3158 8156 0.249955 TCATTGGATGAGCAGCGACA 59.750 50.0 0.00 0.0 33.59 4.35 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
25 26 8.570096 CAACATGAATGGACATATCATTGTTC 57.430 34.615 0.00 0.00 35.26 3.18
26 27 8.410912 CAACATGAATGGACATATCATTGTTCT 58.589 33.333 0.00 0.00 35.26 3.01
27 28 8.529424 ACATGAATGGACATATCATTGTTCTT 57.471 30.769 0.00 0.00 35.26 2.52
28 29 8.974238 ACATGAATGGACATATCATTGTTCTTT 58.026 29.630 0.00 0.00 35.26 2.52
32 33 9.956720 GAATGGACATATCATTGTTCTTTAAGG 57.043 33.333 0.00 0.00 35.26 2.69
35 36 6.239036 GGACATATCATTGTTCTTTAAGGGCC 60.239 42.308 0.00 0.00 0.00 5.80
36 37 6.435164 ACATATCATTGTTCTTTAAGGGCCT 58.565 36.000 0.00 0.00 0.00 5.19
37 38 6.897413 ACATATCATTGTTCTTTAAGGGCCTT 59.103 34.615 24.44 24.44 0.00 4.35
38 39 7.400052 ACATATCATTGTTCTTTAAGGGCCTTT 59.600 33.333 26.29 5.08 0.00 3.11
39 40 6.686484 ATCATTGTTCTTTAAGGGCCTTTT 57.314 33.333 26.29 2.86 0.00 2.27
40 41 7.790782 ATCATTGTTCTTTAAGGGCCTTTTA 57.209 32.000 26.29 10.50 0.00 1.52
41 42 7.227049 TCATTGTTCTTTAAGGGCCTTTTAG 57.773 36.000 26.29 20.56 0.00 1.85
42 43 6.780522 TCATTGTTCTTTAAGGGCCTTTTAGT 59.219 34.615 26.29 1.03 0.00 2.24
43 44 7.289084 TCATTGTTCTTTAAGGGCCTTTTAGTT 59.711 33.333 26.29 0.13 0.00 2.24
45 46 8.536340 TTGTTCTTTAAGGGCCTTTTAGTTAA 57.464 30.769 26.29 8.58 0.00 2.01
46 47 8.173542 TGTTCTTTAAGGGCCTTTTAGTTAAG 57.826 34.615 26.29 16.62 0.00 1.85
47 48 7.781219 TGTTCTTTAAGGGCCTTTTAGTTAAGT 59.219 33.333 26.29 0.00 0.00 2.24
48 49 9.288576 GTTCTTTAAGGGCCTTTTAGTTAAGTA 57.711 33.333 26.29 9.45 0.00 2.24
49 50 9.865152 TTCTTTAAGGGCCTTTTAGTTAAGTAA 57.135 29.630 26.29 5.33 0.00 2.24
50 51 9.865152 TCTTTAAGGGCCTTTTAGTTAAGTAAA 57.135 29.630 26.29 13.08 0.00 2.01
70 71 9.959721 AAGTAAACTATATTGTTCCTGTCATGT 57.040 29.630 2.97 0.00 0.00 3.21
71 72 9.959721 AGTAAACTATATTGTTCCTGTCATGTT 57.040 29.630 2.97 0.00 0.00 2.71
81 82 7.624360 TGTTCCTGTCATGTTTATATGTTCC 57.376 36.000 0.00 0.00 0.00 3.62
82 83 7.171653 TGTTCCTGTCATGTTTATATGTTCCA 58.828 34.615 0.00 0.00 0.00 3.53
83 84 7.833682 TGTTCCTGTCATGTTTATATGTTCCAT 59.166 33.333 0.00 0.00 0.00 3.41
84 85 9.337396 GTTCCTGTCATGTTTATATGTTCCATA 57.663 33.333 0.00 0.00 0.00 2.74
86 87 9.506018 TCCTGTCATGTTTATATGTTCCATATG 57.494 33.333 6.93 0.00 0.00 1.78
87 88 8.239314 CCTGTCATGTTTATATGTTCCATATGC 58.761 37.037 6.93 0.00 0.00 3.14
89 90 7.659390 TGTCATGTTTATATGTTCCATATGCGA 59.341 33.333 6.93 0.00 0.00 5.10
90 91 8.503196 GTCATGTTTATATGTTCCATATGCGAA 58.497 33.333 6.93 0.00 0.00 4.70
91 92 9.230122 TCATGTTTATATGTTCCATATGCGAAT 57.770 29.630 9.07 0.00 0.00 3.34
105 106 9.890629 TCCATATGCGAATAAGAAATAATAGCT 57.109 29.630 0.00 0.00 0.00 3.32
132 133 9.816787 TTTTTGGGTAAATTAGGTGAGATTAGT 57.183 29.630 0.00 0.00 0.00 2.24
136 137 9.220906 TGGGTAAATTAGGTGAGATTAGTATGT 57.779 33.333 0.00 0.00 0.00 2.29
138 139 9.490379 GGTAAATTAGGTGAGATTAGTATGTGG 57.510 37.037 0.00 0.00 0.00 4.17
146 147 9.830186 AGGTGAGATTAGTATGTGGATAATACT 57.170 33.333 2.04 2.04 42.23 2.12
202 203 9.911138 TTGAACGAAATAATACTGTACTGTACA 57.089 29.630 18.77 18.77 37.13 2.90
230 231 9.435688 TGAATATAGAATAATGCTAATGCGTGT 57.564 29.630 0.00 0.00 43.34 4.49
234 235 6.486253 AGAATAATGCTAATGCGTGTATGG 57.514 37.500 0.00 0.00 43.34 2.74
235 236 5.997746 AGAATAATGCTAATGCGTGTATGGT 59.002 36.000 0.00 0.00 43.34 3.55
236 237 6.486657 AGAATAATGCTAATGCGTGTATGGTT 59.513 34.615 0.00 0.00 43.34 3.67
237 238 4.981806 AATGCTAATGCGTGTATGGTTT 57.018 36.364 0.00 0.00 43.34 3.27
238 239 4.981806 ATGCTAATGCGTGTATGGTTTT 57.018 36.364 0.00 0.00 43.34 2.43
239 240 4.349663 TGCTAATGCGTGTATGGTTTTC 57.650 40.909 0.00 0.00 43.34 2.29
240 241 4.006989 TGCTAATGCGTGTATGGTTTTCT 58.993 39.130 0.00 0.00 43.34 2.52
241 242 5.179533 TGCTAATGCGTGTATGGTTTTCTA 58.820 37.500 0.00 0.00 43.34 2.10
242 243 5.820423 TGCTAATGCGTGTATGGTTTTCTAT 59.180 36.000 0.00 0.00 43.34 1.98
243 244 6.018262 TGCTAATGCGTGTATGGTTTTCTATC 60.018 38.462 0.00 0.00 43.34 2.08
244 245 6.018262 GCTAATGCGTGTATGGTTTTCTATCA 60.018 38.462 0.00 0.00 0.00 2.15
245 246 5.734855 ATGCGTGTATGGTTTTCTATCAC 57.265 39.130 0.00 0.00 0.00 3.06
248 249 4.034048 GCGTGTATGGTTTTCTATCACCAG 59.966 45.833 0.00 0.00 46.38 4.00
249 250 4.034048 CGTGTATGGTTTTCTATCACCAGC 59.966 45.833 0.00 0.00 46.38 4.85
250 251 4.335594 GTGTATGGTTTTCTATCACCAGCC 59.664 45.833 0.00 0.00 46.38 4.85
251 252 2.107950 TGGTTTTCTATCACCAGCCG 57.892 50.000 0.00 0.00 38.20 5.52
252 253 1.339631 TGGTTTTCTATCACCAGCCGG 60.340 52.381 0.00 0.00 38.20 6.13
266 267 2.281761 CCGGTGCCTGCTGTCTTT 60.282 61.111 0.00 0.00 0.00 2.52
268 269 0.392998 CCGGTGCCTGCTGTCTTTAT 60.393 55.000 0.00 0.00 0.00 1.40
270 271 2.485479 CCGGTGCCTGCTGTCTTTATAT 60.485 50.000 0.00 0.00 0.00 0.86
271 272 3.244078 CCGGTGCCTGCTGTCTTTATATA 60.244 47.826 0.00 0.00 0.00 0.86
272 273 4.377021 CGGTGCCTGCTGTCTTTATATAA 58.623 43.478 0.00 0.00 0.00 0.98
273 274 4.449068 CGGTGCCTGCTGTCTTTATATAAG 59.551 45.833 0.00 0.00 0.00 1.73
274 275 5.368989 GGTGCCTGCTGTCTTTATATAAGT 58.631 41.667 0.00 0.00 0.00 2.24
275 276 6.522054 GGTGCCTGCTGTCTTTATATAAGTA 58.478 40.000 0.00 0.00 0.00 2.24
276 277 6.990349 GGTGCCTGCTGTCTTTATATAAGTAA 59.010 38.462 0.00 0.00 0.00 2.24
277 278 7.661847 GGTGCCTGCTGTCTTTATATAAGTAAT 59.338 37.037 0.00 0.00 0.00 1.89
278 279 9.706691 GTGCCTGCTGTCTTTATATAAGTAATA 57.293 33.333 0.00 0.00 0.00 0.98
304 305 9.942526 AATTAAATTTATCATCCCTCTTCCTGT 57.057 29.630 0.00 0.00 0.00 4.00
308 309 6.688073 TTTATCATCCCTCTTCCTGTATCC 57.312 41.667 0.00 0.00 0.00 2.59
309 310 3.706389 TCATCCCTCTTCCTGTATCCA 57.294 47.619 0.00 0.00 0.00 3.41
310 311 4.219392 TCATCCCTCTTCCTGTATCCAT 57.781 45.455 0.00 0.00 0.00 3.41
311 312 4.570926 TCATCCCTCTTCCTGTATCCATT 58.429 43.478 0.00 0.00 0.00 3.16
312 313 5.726560 TCATCCCTCTTCCTGTATCCATTA 58.273 41.667 0.00 0.00 0.00 1.90
313 314 6.150332 TCATCCCTCTTCCTGTATCCATTAA 58.850 40.000 0.00 0.00 0.00 1.40
314 315 6.270927 TCATCCCTCTTCCTGTATCCATTAAG 59.729 42.308 0.00 0.00 0.00 1.85
316 317 6.689561 TCCCTCTTCCTGTATCCATTAAGTA 58.310 40.000 0.00 0.00 0.00 2.24
317 318 6.553852 TCCCTCTTCCTGTATCCATTAAGTAC 59.446 42.308 0.00 0.00 0.00 2.73
318 319 6.448006 CCTCTTCCTGTATCCATTAAGTACG 58.552 44.000 0.00 0.00 0.00 3.67
319 320 6.401047 TCTTCCTGTATCCATTAAGTACGG 57.599 41.667 0.00 0.00 0.00 4.02
320 321 6.131264 TCTTCCTGTATCCATTAAGTACGGA 58.869 40.000 0.00 0.00 0.00 4.69
321 322 5.779529 TCCTGTATCCATTAAGTACGGAC 57.220 43.478 0.00 0.00 0.00 4.79
322 323 4.586001 TCCTGTATCCATTAAGTACGGACC 59.414 45.833 0.00 0.00 0.00 4.46
323 324 4.342951 CCTGTATCCATTAAGTACGGACCA 59.657 45.833 0.00 0.00 0.00 4.02
324 325 5.509163 CCTGTATCCATTAAGTACGGACCAG 60.509 48.000 0.00 0.00 33.76 4.00
326 327 4.667519 ATCCATTAAGTACGGACCAGAC 57.332 45.455 0.00 0.00 0.00 3.51
328 329 3.833650 TCCATTAAGTACGGACCAGACAA 59.166 43.478 0.00 0.00 0.00 3.18
330 331 5.657745 TCCATTAAGTACGGACCAGACAATA 59.342 40.000 0.00 0.00 0.00 1.90
332 333 6.990349 CCATTAAGTACGGACCAGACAATAAT 59.010 38.462 0.00 0.00 0.00 1.28
333 334 7.170998 CCATTAAGTACGGACCAGACAATAATC 59.829 40.741 0.00 0.00 0.00 1.75
334 335 4.667519 AGTACGGACCAGACAATAATCC 57.332 45.455 0.00 0.00 0.00 3.01
335 336 4.028131 AGTACGGACCAGACAATAATCCA 58.972 43.478 0.00 0.00 0.00 3.41
336 337 3.992943 ACGGACCAGACAATAATCCAA 57.007 42.857 0.00 0.00 0.00 3.53
337 338 3.606687 ACGGACCAGACAATAATCCAAC 58.393 45.455 0.00 0.00 0.00 3.77
338 339 3.263425 ACGGACCAGACAATAATCCAACT 59.737 43.478 0.00 0.00 0.00 3.16
339 340 4.261801 CGGACCAGACAATAATCCAACTT 58.738 43.478 0.00 0.00 0.00 2.66
341 342 5.523916 CGGACCAGACAATAATCCAACTTAG 59.476 44.000 0.00 0.00 0.00 2.18
342 343 6.629515 CGGACCAGACAATAATCCAACTTAGA 60.630 42.308 0.00 0.00 0.00 2.10
343 344 7.283329 GGACCAGACAATAATCCAACTTAGAT 58.717 38.462 0.00 0.00 0.00 1.98
344 345 8.429641 GGACCAGACAATAATCCAACTTAGATA 58.570 37.037 0.00 0.00 0.00 1.98
356 357 8.924511 ATCCAACTTAGATATAACCCAACATG 57.075 34.615 0.00 0.00 0.00 3.21
357 358 7.287061 TCCAACTTAGATATAACCCAACATGG 58.713 38.462 0.00 0.00 37.25 3.66
369 370 1.735571 CCAACATGGGTTAGCGTACAC 59.264 52.381 0.00 0.00 34.87 2.90
372 373 3.343941 ACATGGGTTAGCGTACACATT 57.656 42.857 6.29 0.00 39.03 2.71
374 375 4.439057 ACATGGGTTAGCGTACACATTAG 58.561 43.478 6.29 0.61 39.03 1.73
375 376 3.530265 TGGGTTAGCGTACACATTAGG 57.470 47.619 0.00 0.00 0.00 2.69
376 377 2.207590 GGGTTAGCGTACACATTAGGC 58.792 52.381 0.00 0.00 0.00 3.93
377 378 2.159000 GGGTTAGCGTACACATTAGGCT 60.159 50.000 0.00 0.00 40.99 4.58
380 381 0.815734 AGCGTACACATTAGGCTCGT 59.184 50.000 0.00 0.00 34.00 4.18
383 384 2.223433 GCGTACACATTAGGCTCGTAGT 60.223 50.000 0.00 0.00 0.00 2.73
384 385 3.002656 GCGTACACATTAGGCTCGTAGTA 59.997 47.826 0.00 0.00 0.00 1.82
385 386 4.496341 GCGTACACATTAGGCTCGTAGTAA 60.496 45.833 0.00 0.00 0.00 2.24
386 387 5.755813 CGTACACATTAGGCTCGTAGTAAT 58.244 41.667 0.00 0.00 0.00 1.89
387 388 5.624081 CGTACACATTAGGCTCGTAGTAATG 59.376 44.000 0.00 0.00 39.20 1.90
390 391 5.595542 ACACATTAGGCTCGTAGTAATGGTA 59.404 40.000 9.52 0.00 38.12 3.25
391 392 6.150318 CACATTAGGCTCGTAGTAATGGTAG 58.850 44.000 9.52 0.00 38.12 3.18
393 394 7.000472 ACATTAGGCTCGTAGTAATGGTAGTA 59.000 38.462 9.52 0.00 38.12 1.82
394 395 7.668886 ACATTAGGCTCGTAGTAATGGTAGTAT 59.331 37.037 9.52 0.00 38.12 2.12
395 396 8.521176 CATTAGGCTCGTAGTAATGGTAGTATT 58.479 37.037 0.00 0.00 32.67 1.89
396 397 9.745018 ATTAGGCTCGTAGTAATGGTAGTATTA 57.255 33.333 0.00 0.00 0.00 0.98
397 398 9.745018 TTAGGCTCGTAGTAATGGTAGTATTAT 57.255 33.333 0.00 0.00 0.00 1.28
399 400 9.393512 AGGCTCGTAGTAATGGTAGTATTATAG 57.606 37.037 0.00 0.00 0.00 1.31
412 413 9.695155 TGGTAGTATTATAGCTAGTATCATGCA 57.305 33.333 0.00 0.00 0.00 3.96
416 417 8.147058 AGTATTATAGCTAGTATCATGCATGCC 58.853 37.037 22.25 11.72 0.00 4.40
417 418 4.831674 ATAGCTAGTATCATGCATGCCA 57.168 40.909 22.25 8.84 0.00 4.92
418 419 3.497103 AGCTAGTATCATGCATGCCAA 57.503 42.857 22.25 5.34 0.00 4.52
419 420 3.144506 AGCTAGTATCATGCATGCCAAC 58.855 45.455 22.25 17.59 0.00 3.77
420 421 3.144506 GCTAGTATCATGCATGCCAACT 58.855 45.455 22.25 22.78 0.00 3.16
422 423 4.391216 GCTAGTATCATGCATGCCAACTAG 59.609 45.833 32.38 32.38 37.27 2.57
439 440 6.332630 CCAACTAGGCAATTTTGATAAGGTG 58.667 40.000 0.00 0.00 0.00 4.00
440 441 6.071391 CCAACTAGGCAATTTTGATAAGGTGT 60.071 38.462 0.00 0.00 0.00 4.16
442 443 8.519526 CAACTAGGCAATTTTGATAAGGTGTTA 58.480 33.333 0.00 0.00 0.00 2.41
443 444 8.823220 ACTAGGCAATTTTGATAAGGTGTTAT 57.177 30.769 0.00 0.00 0.00 1.89
444 445 8.686334 ACTAGGCAATTTTGATAAGGTGTTATG 58.314 33.333 0.00 0.00 0.00 1.90
445 446 7.716799 AGGCAATTTTGATAAGGTGTTATGA 57.283 32.000 0.00 0.00 0.00 2.15
447 448 8.592809 AGGCAATTTTGATAAGGTGTTATGAAA 58.407 29.630 0.00 0.00 32.03 2.69
477 478 9.517868 AATGAAGAAAGAGAAAGTTGAGATCAT 57.482 29.630 0.00 0.00 0.00 2.45
644 645 9.823647 AGTATATGAAACTCTCCATTACAACAG 57.176 33.333 0.00 0.00 0.00 3.16
645 646 5.886960 ATGAAACTCTCCATTACAACAGC 57.113 39.130 0.00 0.00 0.00 4.40
646 647 4.072131 TGAAACTCTCCATTACAACAGCC 58.928 43.478 0.00 0.00 0.00 4.85
647 648 4.202461 TGAAACTCTCCATTACAACAGCCT 60.202 41.667 0.00 0.00 0.00 4.58
649 650 5.499004 AACTCTCCATTACAACAGCCTTA 57.501 39.130 0.00 0.00 0.00 2.69
650 651 5.091261 ACTCTCCATTACAACAGCCTTAG 57.909 43.478 0.00 0.00 0.00 2.18
651 652 3.873910 TCTCCATTACAACAGCCTTAGC 58.126 45.455 0.00 0.00 40.32 3.09
652 653 3.263170 TCTCCATTACAACAGCCTTAGCA 59.737 43.478 0.00 0.00 43.56 3.49
653 654 4.009675 CTCCATTACAACAGCCTTAGCAA 58.990 43.478 0.00 0.00 43.56 3.91
654 655 4.599041 TCCATTACAACAGCCTTAGCAAT 58.401 39.130 0.00 0.00 43.56 3.56
655 656 4.398988 TCCATTACAACAGCCTTAGCAATG 59.601 41.667 0.00 0.00 43.56 2.82
656 657 4.158394 CCATTACAACAGCCTTAGCAATGT 59.842 41.667 0.00 0.00 43.56 2.71
659 660 7.416664 CCATTACAACAGCCTTAGCAATGTTAT 60.417 37.037 0.00 0.00 43.56 1.89
660 661 8.620416 CATTACAACAGCCTTAGCAATGTTATA 58.380 33.333 0.00 0.00 43.56 0.98
661 662 6.436843 ACAACAGCCTTAGCAATGTTATAC 57.563 37.500 0.00 0.00 43.56 1.47
662 663 5.064707 ACAACAGCCTTAGCAATGTTATACG 59.935 40.000 0.00 0.00 43.56 3.06
663 664 4.127171 ACAGCCTTAGCAATGTTATACGG 58.873 43.478 0.00 0.00 43.56 4.02
664 665 3.498397 CAGCCTTAGCAATGTTATACGGG 59.502 47.826 0.00 0.00 43.56 5.28
665 666 2.812011 GCCTTAGCAATGTTATACGGGG 59.188 50.000 0.00 0.00 39.53 5.73
667 668 4.806286 GCCTTAGCAATGTTATACGGGGAT 60.806 45.833 0.00 0.00 39.53 3.85
670 671 6.594159 CCTTAGCAATGTTATACGGGGATTAG 59.406 42.308 0.00 0.00 0.00 1.73
671 672 5.818678 AGCAATGTTATACGGGGATTAGA 57.181 39.130 0.00 0.00 0.00 2.10
672 673 5.548406 AGCAATGTTATACGGGGATTAGAC 58.452 41.667 0.00 0.00 0.00 2.59
673 674 5.307196 AGCAATGTTATACGGGGATTAGACT 59.693 40.000 0.00 0.00 0.00 3.24
674 675 6.495872 AGCAATGTTATACGGGGATTAGACTA 59.504 38.462 0.00 0.00 0.00 2.59
675 676 6.812160 GCAATGTTATACGGGGATTAGACTAG 59.188 42.308 0.00 0.00 0.00 2.57
676 677 7.309621 GCAATGTTATACGGGGATTAGACTAGA 60.310 40.741 0.00 0.00 0.00 2.43
677 678 7.700022 ATGTTATACGGGGATTAGACTAGAC 57.300 40.000 0.00 0.00 0.00 2.59
678 679 6.604171 TGTTATACGGGGATTAGACTAGACA 58.396 40.000 0.00 0.00 0.00 3.41
679 680 6.713903 TGTTATACGGGGATTAGACTAGACAG 59.286 42.308 0.00 0.00 0.00 3.51
680 681 2.308690 ACGGGGATTAGACTAGACAGC 58.691 52.381 0.00 0.00 0.00 4.40
682 683 2.554893 CGGGGATTAGACTAGACAGCTC 59.445 54.545 0.00 0.00 0.00 4.09
683 684 3.567397 GGGGATTAGACTAGACAGCTCA 58.433 50.000 0.00 0.00 0.00 4.26
684 685 4.156477 GGGGATTAGACTAGACAGCTCAT 58.844 47.826 0.00 0.00 0.00 2.90
685 686 4.219725 GGGGATTAGACTAGACAGCTCATC 59.780 50.000 0.00 0.00 0.00 2.92
686 687 4.219725 GGGATTAGACTAGACAGCTCATCC 59.780 50.000 0.00 4.40 33.00 3.51
687 688 4.219725 GGATTAGACTAGACAGCTCATCCC 59.780 50.000 0.00 0.00 30.45 3.85
688 689 4.528076 TTAGACTAGACAGCTCATCCCT 57.472 45.455 0.00 0.00 0.00 4.20
690 691 3.827722 AGACTAGACAGCTCATCCCTAC 58.172 50.000 0.00 0.00 0.00 3.18
691 692 3.461831 AGACTAGACAGCTCATCCCTACT 59.538 47.826 0.00 0.00 0.00 2.57
692 693 3.818773 GACTAGACAGCTCATCCCTACTC 59.181 52.174 0.00 0.00 0.00 2.59
693 694 2.080654 AGACAGCTCATCCCTACTCC 57.919 55.000 0.00 0.00 0.00 3.85
694 695 1.573376 AGACAGCTCATCCCTACTCCT 59.427 52.381 0.00 0.00 0.00 3.69
697 698 2.023501 ACAGCTCATCCCTACTCCTCTT 60.024 50.000 0.00 0.00 0.00 2.85
698 699 3.037549 CAGCTCATCCCTACTCCTCTTT 58.962 50.000 0.00 0.00 0.00 2.52
699 700 3.037549 AGCTCATCCCTACTCCTCTTTG 58.962 50.000 0.00 0.00 0.00 2.77
700 701 2.769095 GCTCATCCCTACTCCTCTTTGT 59.231 50.000 0.00 0.00 0.00 2.83
703 704 4.026744 TCATCCCTACTCCTCTTTGTCTG 58.973 47.826 0.00 0.00 0.00 3.51
704 705 3.544698 TCCCTACTCCTCTTTGTCTGT 57.455 47.619 0.00 0.00 0.00 3.41
705 706 4.669866 TCCCTACTCCTCTTTGTCTGTA 57.330 45.455 0.00 0.00 0.00 2.74
706 707 4.342359 TCCCTACTCCTCTTTGTCTGTAC 58.658 47.826 0.00 0.00 0.00 2.90
707 708 4.087182 CCCTACTCCTCTTTGTCTGTACA 58.913 47.826 0.00 0.00 0.00 2.90
708 709 4.158764 CCCTACTCCTCTTTGTCTGTACAG 59.841 50.000 17.17 17.17 36.83 2.74
711 712 3.322254 ACTCCTCTTTGTCTGTACAGTGG 59.678 47.826 21.99 13.04 36.83 4.00
712 713 3.305720 TCCTCTTTGTCTGTACAGTGGT 58.694 45.455 21.99 0.00 36.83 4.16
713 714 4.476297 TCCTCTTTGTCTGTACAGTGGTA 58.524 43.478 21.99 0.00 36.83 3.25
726 2308 3.473625 ACAGTGGTAAGTTGTTGTAGCC 58.526 45.455 0.00 0.00 0.00 3.93
878 2474 7.700234 GTCTACTCAGTAGTCAATCATCACTTG 59.300 40.741 11.77 0.00 37.41 3.16
993 2612 8.558700 TGGTTTGATTTGATACATCATACATCG 58.441 33.333 6.04 0.00 35.46 3.84
1071 2690 1.787057 GCGACGACGAGATCCTCCAT 61.787 60.000 12.29 0.00 42.66 3.41
1141 2760 2.306255 GAACTTCCGGCCGGATAGCA 62.306 60.000 45.44 30.17 44.74 3.49
1306 2988 0.956633 CAGTGTTGCTCAGTGCCAAT 59.043 50.000 4.84 0.00 40.06 3.16
1307 2989 2.153645 CAGTGTTGCTCAGTGCCAATA 58.846 47.619 4.84 0.00 40.06 1.90
1309 2993 2.554032 AGTGTTGCTCAGTGCCAATAAC 59.446 45.455 0.00 0.00 42.00 1.89
1418 3149 1.195442 TGTCGCACCCCAATCTGGTA 61.195 55.000 0.00 0.00 35.17 3.25
1423 3154 1.890573 GCACCCCAATCTGGTAAAGCA 60.891 52.381 0.00 0.00 35.17 3.91
1457 3191 2.091112 CGAAGACGAGCAGCACCTG 61.091 63.158 0.00 0.00 42.66 4.00
1495 3229 1.818642 CCACAAGGAAGCTTGGAGAG 58.181 55.000 2.10 0.00 38.55 3.20
1634 3403 0.979665 ATGATGATGTAGGGGCCTCG 59.020 55.000 0.84 0.00 0.00 4.63
1944 3726 6.523840 GGGCTTTTATATTGATGAATTGCCA 58.476 36.000 0.00 0.00 34.78 4.92
2151 6569 9.860898 CTAAAAAGGCTATGAAGTTTAAGCATT 57.139 29.630 0.00 4.06 40.34 3.56
2348 7127 1.623811 GTTTCAGACCTAGCTGGACCA 59.376 52.381 0.00 0.00 39.71 4.02
2350 7129 0.409876 TCAGACCTAGCTGGACCACT 59.590 55.000 0.00 0.00 39.71 4.00
2352 7131 1.066573 CAGACCTAGCTGGACCACTTG 60.067 57.143 0.00 0.00 39.71 3.16
2354 7133 1.205893 GACCTAGCTGGACCACTTGAG 59.794 57.143 0.00 0.00 39.71 3.02
2472 7282 8.844812 GCACAATCTTGCAGCTAGATAAGCAC 62.845 46.154 18.25 7.66 45.51 4.40
2491 7301 3.055385 GCACCCATGTACTTTCTACCAGA 60.055 47.826 0.00 0.00 0.00 3.86
2493 7303 3.518303 ACCCATGTACTTTCTACCAGACC 59.482 47.826 0.00 0.00 0.00 3.85
2562 7494 3.699038 TGCTAATGTGTTGCCCTTTATCC 59.301 43.478 0.00 0.00 0.00 2.59
2670 7654 4.768130 TGAACTAGTAGCAGTGACACTC 57.232 45.455 4.74 1.09 0.00 3.51
2777 7761 2.147387 AGTTTCGGGGTGGTGCTCT 61.147 57.895 0.00 0.00 0.00 4.09
2795 7779 0.543277 CTTGGAGATACTGGCAGGCA 59.457 55.000 20.34 6.48 0.00 4.75
2887 7879 1.078214 CAAGCGCCAGATCTCCCAA 60.078 57.895 2.29 0.00 0.00 4.12
2969 7961 1.375268 GCGCTCAAGTGCCTCTCTT 60.375 57.895 0.00 0.00 45.15 2.85
2975 7967 3.803715 GCTCAAGTGCCTCTCTTGTAACA 60.804 47.826 8.03 0.00 41.78 2.41
3170 8168 4.101448 GGGGGTGTCGCTGCTCAT 62.101 66.667 0.00 0.00 0.00 2.90
3303 8320 7.682787 ACAGAAGGGATATGATTAGTGAAGT 57.317 36.000 0.00 0.00 0.00 3.01
3326 8343 2.727123 TTGTTTTGAGGACTCTGCCA 57.273 45.000 0.56 0.00 0.00 4.92
3432 8456 3.244911 ACTGAACTGGTTGGTTATCCTGG 60.245 47.826 0.00 0.00 34.23 4.45
3433 8457 2.983192 TGAACTGGTTGGTTATCCTGGA 59.017 45.455 0.00 0.00 34.23 3.86
3530 8577 5.419788 CACTCCATTCCAAATTGATTGAGGA 59.580 40.000 0.00 0.00 41.85 3.71
3537 8584 8.910944 CATTCCAAATTGATTGAGGATAACTCT 58.089 33.333 0.00 0.00 46.72 3.24
3686 8760 7.229506 ACTTTGTCAAAGCTTAGCACTAGAATT 59.770 33.333 22.58 0.00 42.27 2.17
3779 8858 1.147191 AGAATCCATGATGGCCTGCAT 59.853 47.619 6.59 4.50 37.47 3.96
3806 8885 2.961062 AGCTCCACTTGCATTGAAAAGT 59.039 40.909 0.00 0.70 37.09 2.66
3841 8920 1.340017 TGATAAAGGGCAGTCTGGTGC 60.340 52.381 1.14 0.00 43.19 5.01
3922 9394 7.344134 TCCTATACTAAGTTCTGTGCTACTCA 58.656 38.462 0.00 0.00 0.00 3.41
4044 9516 4.299586 TGTAAGATGATTGGCTGGTTGA 57.700 40.909 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.410912 AGAACAATGATATGTCCATTCATGTTG 58.589 33.333 0.00 0.00 32.40 3.33
6 7 9.956720 CCTTAAAGAACAATGATATGTCCATTC 57.043 33.333 0.00 0.00 32.40 2.67
7 8 8.917088 CCCTTAAAGAACAATGATATGTCCATT 58.083 33.333 0.00 0.00 34.83 3.16
8 9 7.014615 GCCCTTAAAGAACAATGATATGTCCAT 59.985 37.037 0.00 0.00 31.81 3.41
9 10 6.321181 GCCCTTAAAGAACAATGATATGTCCA 59.679 38.462 0.00 0.00 31.81 4.02
10 11 6.239036 GGCCCTTAAAGAACAATGATATGTCC 60.239 42.308 0.00 0.00 31.81 4.02
11 12 6.547510 AGGCCCTTAAAGAACAATGATATGTC 59.452 38.462 0.00 0.00 31.81 3.06
12 13 6.435164 AGGCCCTTAAAGAACAATGATATGT 58.565 36.000 0.00 0.00 34.24 2.29
13 14 6.966534 AGGCCCTTAAAGAACAATGATATG 57.033 37.500 0.00 0.00 0.00 1.78
14 15 7.978099 AAAGGCCCTTAAAGAACAATGATAT 57.022 32.000 0.00 0.00 0.00 1.63
15 16 7.790782 AAAAGGCCCTTAAAGAACAATGATA 57.209 32.000 0.00 0.00 0.00 2.15
16 17 6.686484 AAAAGGCCCTTAAAGAACAATGAT 57.314 33.333 0.00 0.00 0.00 2.45
17 18 6.780522 ACTAAAAGGCCCTTAAAGAACAATGA 59.219 34.615 11.00 0.00 0.00 2.57
18 19 6.993079 ACTAAAAGGCCCTTAAAGAACAATG 58.007 36.000 11.00 0.00 0.00 2.82
19 20 7.612065 AACTAAAAGGCCCTTAAAGAACAAT 57.388 32.000 11.00 0.00 0.00 2.71
20 21 8.536340 TTAACTAAAAGGCCCTTAAAGAACAA 57.464 30.769 11.00 1.35 0.00 2.83
21 22 7.781219 ACTTAACTAAAAGGCCCTTAAAGAACA 59.219 33.333 11.00 0.00 0.00 3.18
22 23 8.174733 ACTTAACTAAAAGGCCCTTAAAGAAC 57.825 34.615 11.00 0.00 0.00 3.01
23 24 9.865152 TTACTTAACTAAAAGGCCCTTAAAGAA 57.135 29.630 11.00 0.00 0.00 2.52
24 25 9.865152 TTTACTTAACTAAAAGGCCCTTAAAGA 57.135 29.630 11.00 0.00 0.00 2.52
25 26 9.903682 GTTTACTTAACTAAAAGGCCCTTAAAG 57.096 33.333 0.00 0.00 33.79 1.85
26 27 9.645128 AGTTTACTTAACTAAAAGGCCCTTAAA 57.355 29.630 0.00 0.00 45.22 1.52
45 46 9.959721 AACATGACAGGAACAATATAGTTTACT 57.040 29.630 0.00 0.00 0.00 2.24
55 56 8.686334 GGAACATATAAACATGACAGGAACAAT 58.314 33.333 0.00 0.00 0.00 2.71
56 57 7.667635 TGGAACATATAAACATGACAGGAACAA 59.332 33.333 0.00 0.00 0.00 2.83
58 59 7.624360 TGGAACATATAAACATGACAGGAAC 57.376 36.000 0.00 0.00 0.00 3.62
79 80 9.890629 AGCTATTATTTCTTATTCGCATATGGA 57.109 29.630 4.56 0.00 0.00 3.41
106 107 9.816787 ACTAATCTCACCTAATTTACCCAAAAA 57.183 29.630 0.00 0.00 0.00 1.94
111 112 9.490379 CACATACTAATCTCACCTAATTTACCC 57.510 37.037 0.00 0.00 0.00 3.69
112 113 9.490379 CCACATACTAATCTCACCTAATTTACC 57.510 37.037 0.00 0.00 0.00 2.85
120 121 9.830186 AGTATTATCCACATACTAATCTCACCT 57.170 33.333 0.00 0.00 35.97 4.00
204 205 9.435688 ACACGCATTAGCATTATTCTATATTCA 57.564 29.630 0.00 0.00 42.27 2.57
208 209 9.313118 CCATACACGCATTAGCATTATTCTATA 57.687 33.333 0.00 0.00 42.27 1.31
210 211 7.158697 ACCATACACGCATTAGCATTATTCTA 58.841 34.615 0.00 0.00 42.27 2.10
211 212 5.997746 ACCATACACGCATTAGCATTATTCT 59.002 36.000 0.00 0.00 42.27 2.40
212 213 6.241207 ACCATACACGCATTAGCATTATTC 57.759 37.500 0.00 0.00 42.27 1.75
213 214 6.633500 AACCATACACGCATTAGCATTATT 57.367 33.333 0.00 0.00 42.27 1.40
214 215 6.633500 AAACCATACACGCATTAGCATTAT 57.367 33.333 0.00 0.00 42.27 1.28
215 216 6.317642 AGAAAACCATACACGCATTAGCATTA 59.682 34.615 0.00 0.00 42.27 1.90
216 217 4.981806 AAACCATACACGCATTAGCATT 57.018 36.364 0.00 0.00 42.27 3.56
217 218 4.640201 AGAAAACCATACACGCATTAGCAT 59.360 37.500 0.00 0.00 42.27 3.79
220 221 7.345192 GTGATAGAAAACCATACACGCATTAG 58.655 38.462 0.00 0.00 0.00 1.73
221 222 6.259167 GGTGATAGAAAACCATACACGCATTA 59.741 38.462 0.00 0.00 36.41 1.90
224 225 3.936453 GGTGATAGAAAACCATACACGCA 59.064 43.478 0.00 0.00 36.41 5.24
226 227 4.034048 GCTGGTGATAGAAAACCATACACG 59.966 45.833 0.00 0.00 45.24 4.49
228 229 4.523083 GGCTGGTGATAGAAAACCATACA 58.477 43.478 0.00 0.00 45.24 2.29
229 230 3.560068 CGGCTGGTGATAGAAAACCATAC 59.440 47.826 0.00 0.00 45.24 2.39
230 231 3.433031 CCGGCTGGTGATAGAAAACCATA 60.433 47.826 2.29 0.00 45.24 2.74
231 232 2.643551 CGGCTGGTGATAGAAAACCAT 58.356 47.619 0.00 0.00 45.24 3.55
232 233 1.339631 CCGGCTGGTGATAGAAAACCA 60.340 52.381 2.29 0.00 44.20 3.67
233 234 1.379527 CCGGCTGGTGATAGAAAACC 58.620 55.000 2.29 0.00 36.96 3.27
248 249 4.945367 TATAAAGACAGCAGGCACCGGC 62.945 54.545 0.00 3.37 40.13 6.13
249 250 0.392998 ATAAAGACAGCAGGCACCGG 60.393 55.000 0.00 0.00 0.00 5.28
250 251 2.309528 TATAAAGACAGCAGGCACCG 57.690 50.000 0.00 0.00 0.00 4.94
251 252 5.368989 ACTTATATAAAGACAGCAGGCACC 58.631 41.667 0.00 0.00 0.00 5.01
252 253 8.608844 ATTACTTATATAAAGACAGCAGGCAC 57.391 34.615 0.00 0.00 0.00 5.01
278 279 9.942526 ACAGGAAGAGGGATGATAAATTTAATT 57.057 29.630 1.21 0.00 0.00 1.40
282 283 8.166726 GGATACAGGAAGAGGGATGATAAATTT 58.833 37.037 0.00 0.00 0.00 1.82
283 284 7.295672 TGGATACAGGAAGAGGGATGATAAATT 59.704 37.037 0.00 0.00 46.17 1.82
288 289 4.219392 TGGATACAGGAAGAGGGATGAT 57.781 45.455 0.00 0.00 46.17 2.45
289 290 3.706389 TGGATACAGGAAGAGGGATGA 57.294 47.619 0.00 0.00 46.17 2.92
303 304 5.068198 TGTCTGGTCCGTACTTAATGGATAC 59.932 44.000 0.00 0.00 45.27 2.24
304 305 5.202765 TGTCTGGTCCGTACTTAATGGATA 58.797 41.667 0.00 0.00 45.27 2.59
305 306 4.028131 TGTCTGGTCCGTACTTAATGGAT 58.972 43.478 0.00 0.00 45.27 3.41
307 308 3.880047 TGTCTGGTCCGTACTTAATGG 57.120 47.619 0.00 0.00 35.30 3.16
308 309 7.170998 GGATTATTGTCTGGTCCGTACTTAATG 59.829 40.741 0.00 0.00 0.00 1.90
309 310 7.147620 TGGATTATTGTCTGGTCCGTACTTAAT 60.148 37.037 0.00 0.00 0.00 1.40
310 311 6.154877 TGGATTATTGTCTGGTCCGTACTTAA 59.845 38.462 0.00 0.00 0.00 1.85
311 312 5.657745 TGGATTATTGTCTGGTCCGTACTTA 59.342 40.000 0.00 0.00 0.00 2.24
312 313 4.468510 TGGATTATTGTCTGGTCCGTACTT 59.531 41.667 0.00 0.00 0.00 2.24
313 314 4.028131 TGGATTATTGTCTGGTCCGTACT 58.972 43.478 0.00 0.00 0.00 2.73
314 315 4.395959 TGGATTATTGTCTGGTCCGTAC 57.604 45.455 0.00 0.00 0.00 3.67
316 317 3.263425 AGTTGGATTATTGTCTGGTCCGT 59.737 43.478 0.00 0.00 0.00 4.69
317 318 3.873910 AGTTGGATTATTGTCTGGTCCG 58.126 45.455 0.00 0.00 0.00 4.79
318 319 6.650120 TCTAAGTTGGATTATTGTCTGGTCC 58.350 40.000 0.00 0.00 0.00 4.46
330 331 9.354673 CATGTTGGGTTATATCTAAGTTGGATT 57.645 33.333 7.07 0.00 0.00 3.01
332 333 7.287061 CCATGTTGGGTTATATCTAAGTTGGA 58.713 38.462 0.00 0.00 32.67 3.53
333 334 7.510549 CCATGTTGGGTTATATCTAAGTTGG 57.489 40.000 0.00 0.00 32.67 3.77
350 351 2.418692 TGTGTACGCTAACCCATGTTG 58.581 47.619 8.10 0.00 35.87 3.33
351 352 2.843401 TGTGTACGCTAACCCATGTT 57.157 45.000 8.10 0.00 38.52 2.71
352 353 3.343941 AATGTGTACGCTAACCCATGT 57.656 42.857 8.10 0.00 0.00 3.21
353 354 3.807622 CCTAATGTGTACGCTAACCCATG 59.192 47.826 8.10 0.00 0.00 3.66
354 355 3.743269 GCCTAATGTGTACGCTAACCCAT 60.743 47.826 8.10 0.00 0.00 4.00
356 357 2.159000 AGCCTAATGTGTACGCTAACCC 60.159 50.000 8.10 0.00 0.00 4.11
357 358 3.121544 GAGCCTAATGTGTACGCTAACC 58.878 50.000 8.10 0.00 0.00 2.85
358 359 2.787680 CGAGCCTAATGTGTACGCTAAC 59.212 50.000 8.10 0.00 0.00 2.34
359 360 2.424601 ACGAGCCTAATGTGTACGCTAA 59.575 45.455 8.10 0.00 0.00 3.09
360 361 2.019249 ACGAGCCTAATGTGTACGCTA 58.981 47.619 8.10 0.00 0.00 4.26
362 363 2.223433 ACTACGAGCCTAATGTGTACGC 60.223 50.000 0.00 0.00 0.00 4.42
363 364 3.687572 ACTACGAGCCTAATGTGTACG 57.312 47.619 0.00 0.00 0.00 3.67
365 366 5.595542 ACCATTACTACGAGCCTAATGTGTA 59.404 40.000 0.00 0.00 0.00 2.90
367 368 4.945246 ACCATTACTACGAGCCTAATGTG 58.055 43.478 0.00 0.00 0.00 3.21
369 370 6.328641 ACTACCATTACTACGAGCCTAATG 57.671 41.667 0.00 0.00 0.00 1.90
374 375 8.127954 GCTATAATACTACCATTACTACGAGCC 58.872 40.741 0.00 0.00 0.00 4.70
375 376 8.891720 AGCTATAATACTACCATTACTACGAGC 58.108 37.037 0.00 0.00 0.00 5.03
386 387 9.695155 TGCATGATACTAGCTATAATACTACCA 57.305 33.333 0.00 0.00 0.00 3.25
390 391 8.147058 GGCATGCATGATACTAGCTATAATACT 58.853 37.037 30.64 0.00 0.00 2.12
391 392 7.928167 TGGCATGCATGATACTAGCTATAATAC 59.072 37.037 30.64 5.71 0.00 1.89
393 394 6.892485 TGGCATGCATGATACTAGCTATAAT 58.108 36.000 30.64 0.00 0.00 1.28
394 395 6.298441 TGGCATGCATGATACTAGCTATAA 57.702 37.500 30.64 0.00 0.00 0.98
395 396 5.937975 TGGCATGCATGATACTAGCTATA 57.062 39.130 30.64 1.53 0.00 1.31
396 397 4.831674 TGGCATGCATGATACTAGCTAT 57.168 40.909 30.64 0.00 0.00 2.97
397 398 4.040829 AGTTGGCATGCATGATACTAGCTA 59.959 41.667 30.64 7.90 0.00 3.32
398 399 3.144506 GTTGGCATGCATGATACTAGCT 58.855 45.455 30.64 0.00 0.00 3.32
399 400 3.144506 AGTTGGCATGCATGATACTAGC 58.855 45.455 30.64 12.56 0.00 3.42
402 403 3.748083 CCTAGTTGGCATGCATGATACT 58.252 45.455 30.64 26.11 0.00 2.12
415 416 6.071391 ACACCTTATCAAAATTGCCTAGTTGG 60.071 38.462 0.00 0.00 39.35 3.77
416 417 6.924111 ACACCTTATCAAAATTGCCTAGTTG 58.076 36.000 0.00 0.00 0.00 3.16
417 418 7.539034 AACACCTTATCAAAATTGCCTAGTT 57.461 32.000 0.00 0.00 0.00 2.24
418 419 8.686334 CATAACACCTTATCAAAATTGCCTAGT 58.314 33.333 0.00 0.00 0.00 2.57
419 420 8.902806 TCATAACACCTTATCAAAATTGCCTAG 58.097 33.333 0.00 0.00 0.00 3.02
420 421 8.815565 TCATAACACCTTATCAAAATTGCCTA 57.184 30.769 0.00 0.00 0.00 3.93
422 423 8.770438 TTTCATAACACCTTATCAAAATTGCC 57.230 30.769 0.00 0.00 0.00 4.52
502 503 9.515226 TCATGTATGACACATAGTAGCATAGTA 57.485 33.333 0.00 0.00 46.47 1.82
503 504 8.409358 TCATGTATGACACATAGTAGCATAGT 57.591 34.615 0.00 0.00 46.47 2.12
620 621 7.715249 GGCTGTTGTAATGGAGAGTTTCATATA 59.285 37.037 0.00 0.00 0.00 0.86
621 622 6.543831 GGCTGTTGTAATGGAGAGTTTCATAT 59.456 38.462 0.00 0.00 0.00 1.78
623 624 4.702131 GGCTGTTGTAATGGAGAGTTTCAT 59.298 41.667 0.00 0.00 0.00 2.57
625 626 4.327680 AGGCTGTTGTAATGGAGAGTTTC 58.672 43.478 0.00 0.00 0.00 2.78
626 627 4.373156 AGGCTGTTGTAATGGAGAGTTT 57.627 40.909 0.00 0.00 0.00 2.66
627 628 4.373156 AAGGCTGTTGTAATGGAGAGTT 57.627 40.909 0.00 0.00 0.00 3.01
630 631 3.263170 TGCTAAGGCTGTTGTAATGGAGA 59.737 43.478 0.00 0.00 39.59 3.71
631 632 3.609853 TGCTAAGGCTGTTGTAATGGAG 58.390 45.455 0.00 0.00 39.59 3.86
632 633 3.712016 TGCTAAGGCTGTTGTAATGGA 57.288 42.857 0.00 0.00 39.59 3.41
633 634 4.158394 ACATTGCTAAGGCTGTTGTAATGG 59.842 41.667 20.23 9.62 39.59 3.16
634 635 5.314923 ACATTGCTAAGGCTGTTGTAATG 57.685 39.130 17.08 17.08 39.59 1.90
636 637 7.201574 CGTATAACATTGCTAAGGCTGTTGTAA 60.202 37.037 0.00 0.00 37.40 2.41
637 638 6.256975 CGTATAACATTGCTAAGGCTGTTGTA 59.743 38.462 0.00 2.40 37.40 2.41
638 639 5.064707 CGTATAACATTGCTAAGGCTGTTGT 59.935 40.000 0.00 3.13 37.40 3.32
639 640 5.501715 CGTATAACATTGCTAAGGCTGTTG 58.498 41.667 0.00 0.00 37.40 3.33
640 641 4.574828 CCGTATAACATTGCTAAGGCTGTT 59.425 41.667 0.00 0.00 39.23 3.16
641 642 4.127171 CCGTATAACATTGCTAAGGCTGT 58.873 43.478 0.00 0.00 39.59 4.40
642 643 3.498397 CCCGTATAACATTGCTAAGGCTG 59.502 47.826 0.00 0.00 39.59 4.85
643 644 3.496160 CCCCGTATAACATTGCTAAGGCT 60.496 47.826 0.00 0.00 39.59 4.58
644 645 2.812011 CCCCGTATAACATTGCTAAGGC 59.188 50.000 0.00 0.00 39.26 4.35
645 646 4.345859 TCCCCGTATAACATTGCTAAGG 57.654 45.455 0.00 0.00 0.00 2.69
646 647 7.331193 GTCTAATCCCCGTATAACATTGCTAAG 59.669 40.741 0.00 0.00 0.00 2.18
647 648 7.015877 AGTCTAATCCCCGTATAACATTGCTAA 59.984 37.037 0.00 0.00 0.00 3.09
649 650 5.307196 AGTCTAATCCCCGTATAACATTGCT 59.693 40.000 0.00 0.00 0.00 3.91
650 651 5.548406 AGTCTAATCCCCGTATAACATTGC 58.452 41.667 0.00 0.00 0.00 3.56
651 652 8.027771 GTCTAGTCTAATCCCCGTATAACATTG 58.972 40.741 0.00 0.00 0.00 2.82
652 653 7.727186 TGTCTAGTCTAATCCCCGTATAACATT 59.273 37.037 0.00 0.00 0.00 2.71
653 654 7.236529 TGTCTAGTCTAATCCCCGTATAACAT 58.763 38.462 0.00 0.00 0.00 2.71
654 655 6.604171 TGTCTAGTCTAATCCCCGTATAACA 58.396 40.000 0.00 0.00 0.00 2.41
655 656 6.349197 GCTGTCTAGTCTAATCCCCGTATAAC 60.349 46.154 0.00 0.00 0.00 1.89
656 657 5.709164 GCTGTCTAGTCTAATCCCCGTATAA 59.291 44.000 0.00 0.00 0.00 0.98
659 660 3.137913 AGCTGTCTAGTCTAATCCCCGTA 59.862 47.826 0.00 0.00 0.00 4.02
660 661 2.091775 AGCTGTCTAGTCTAATCCCCGT 60.092 50.000 0.00 0.00 0.00 5.28
661 662 2.554893 GAGCTGTCTAGTCTAATCCCCG 59.445 54.545 0.00 0.00 0.00 5.73
662 663 3.567397 TGAGCTGTCTAGTCTAATCCCC 58.433 50.000 0.00 0.00 0.00 4.81
663 664 4.219725 GGATGAGCTGTCTAGTCTAATCCC 59.780 50.000 0.00 0.00 34.86 3.85
664 665 4.219725 GGGATGAGCTGTCTAGTCTAATCC 59.780 50.000 0.00 9.82 37.36 3.01
665 666 5.076873 AGGGATGAGCTGTCTAGTCTAATC 58.923 45.833 0.00 0.00 0.00 1.75
667 668 4.528076 AGGGATGAGCTGTCTAGTCTAA 57.472 45.455 0.00 0.00 0.00 2.10
670 671 3.818773 GAGTAGGGATGAGCTGTCTAGTC 59.181 52.174 0.00 0.00 0.00 2.59
671 672 3.435890 GGAGTAGGGATGAGCTGTCTAGT 60.436 52.174 0.00 0.00 0.00 2.57
672 673 3.153919 GGAGTAGGGATGAGCTGTCTAG 58.846 54.545 0.00 0.00 0.00 2.43
673 674 2.786445 AGGAGTAGGGATGAGCTGTCTA 59.214 50.000 0.00 0.00 0.00 2.59
674 675 1.573376 AGGAGTAGGGATGAGCTGTCT 59.427 52.381 0.00 0.00 0.00 3.41
675 676 1.960689 GAGGAGTAGGGATGAGCTGTC 59.039 57.143 0.00 0.00 0.00 3.51
676 677 1.573376 AGAGGAGTAGGGATGAGCTGT 59.427 52.381 0.00 0.00 0.00 4.40
677 678 2.380064 AGAGGAGTAGGGATGAGCTG 57.620 55.000 0.00 0.00 0.00 4.24
678 679 3.037549 CAAAGAGGAGTAGGGATGAGCT 58.962 50.000 0.00 0.00 0.00 4.09
679 680 2.769095 ACAAAGAGGAGTAGGGATGAGC 59.231 50.000 0.00 0.00 0.00 4.26
680 681 4.099266 CAGACAAAGAGGAGTAGGGATGAG 59.901 50.000 0.00 0.00 0.00 2.90
682 683 3.772025 ACAGACAAAGAGGAGTAGGGATG 59.228 47.826 0.00 0.00 0.00 3.51
683 684 4.067944 ACAGACAAAGAGGAGTAGGGAT 57.932 45.455 0.00 0.00 0.00 3.85
684 685 3.544698 ACAGACAAAGAGGAGTAGGGA 57.455 47.619 0.00 0.00 0.00 4.20
685 686 4.087182 TGTACAGACAAAGAGGAGTAGGG 58.913 47.826 0.00 0.00 30.68 3.53
686 687 4.767928 ACTGTACAGACAAAGAGGAGTAGG 59.232 45.833 29.30 0.00 34.35 3.18
687 688 5.336055 CCACTGTACAGACAAAGAGGAGTAG 60.336 48.000 29.30 0.00 34.35 2.57
688 689 4.523173 CCACTGTACAGACAAAGAGGAGTA 59.477 45.833 29.30 0.00 34.35 2.59
690 691 3.322254 ACCACTGTACAGACAAAGAGGAG 59.678 47.826 29.30 7.19 34.35 3.69
691 692 3.305720 ACCACTGTACAGACAAAGAGGA 58.694 45.455 29.30 0.00 34.35 3.71
692 693 3.753294 ACCACTGTACAGACAAAGAGG 57.247 47.619 29.30 18.09 34.35 3.69
693 694 5.844004 ACTTACCACTGTACAGACAAAGAG 58.156 41.667 29.30 18.80 34.35 2.85
694 695 5.864418 ACTTACCACTGTACAGACAAAGA 57.136 39.130 29.30 9.20 34.35 2.52
697 698 5.347620 ACAACTTACCACTGTACAGACAA 57.652 39.130 29.30 14.48 34.35 3.18
698 699 5.113383 CAACAACTTACCACTGTACAGACA 58.887 41.667 29.30 7.99 0.00 3.41
699 700 5.114081 ACAACAACTTACCACTGTACAGAC 58.886 41.667 29.30 0.00 0.00 3.51
700 701 5.347620 ACAACAACTTACCACTGTACAGA 57.652 39.130 29.30 3.66 0.00 3.41
703 704 4.450080 GGCTACAACAACTTACCACTGTAC 59.550 45.833 0.00 0.00 0.00 2.90
704 705 4.634199 GGCTACAACAACTTACCACTGTA 58.366 43.478 0.00 0.00 0.00 2.74
705 706 3.473625 GGCTACAACAACTTACCACTGT 58.526 45.455 0.00 0.00 0.00 3.55
706 707 2.478894 CGGCTACAACAACTTACCACTG 59.521 50.000 0.00 0.00 0.00 3.66
707 708 2.366266 TCGGCTACAACAACTTACCACT 59.634 45.455 0.00 0.00 0.00 4.00
708 709 2.735134 CTCGGCTACAACAACTTACCAC 59.265 50.000 0.00 0.00 0.00 4.16
711 712 2.991866 GTCCTCGGCTACAACAACTTAC 59.008 50.000 0.00 0.00 0.00 2.34
712 713 2.028748 GGTCCTCGGCTACAACAACTTA 60.029 50.000 0.00 0.00 0.00 2.24
713 714 1.270678 GGTCCTCGGCTACAACAACTT 60.271 52.381 0.00 0.00 0.00 2.66
726 2308 6.420008 CACTTAATTATTTACTCCGGTCCTCG 59.580 42.308 0.00 0.00 38.88 4.63
852 2448 7.328277 AGTGATGATTGACTACTGAGTAGAC 57.672 40.000 25.21 19.23 38.29 2.59
878 2474 8.787852 AGCAAGCTTGATATAGCCTTAAATTAC 58.212 33.333 30.39 5.34 42.20 1.89
1005 2624 2.436824 GGCCTCCGGAAGCAGTTC 60.437 66.667 25.85 5.34 0.00 3.01
1044 2663 1.521010 CTCGTCGTCGCTCCTAGGA 60.521 63.158 11.98 11.98 36.96 2.94
1056 2675 0.595588 CTGGATGGAGGATCTCGTCG 59.404 60.000 0.00 0.00 33.73 5.12
1071 2690 0.768221 AACTCCTGAGGTTGGCTGGA 60.768 55.000 0.00 0.00 33.17 3.86
1119 2738 2.926242 TCCGGCCGGAAGTTCCTT 60.926 61.111 43.93 0.00 42.05 3.36
1306 2988 6.859420 GGTTGGTACCGAGTTAAAAAGTTA 57.141 37.500 7.57 0.00 34.01 2.24
1307 2989 5.756195 GGTTGGTACCGAGTTAAAAAGTT 57.244 39.130 7.57 0.00 34.01 2.66
1339 3023 8.997621 AGATTCAGAAACAAATTCATGAATGG 57.002 30.769 21.39 17.85 41.14 3.16
1423 3154 0.033405 TTCGAGGCAGTACCCTAGCT 60.033 55.000 0.00 0.00 40.58 3.32
1457 3191 2.131183 GGCATGAACTCATAGACGAGC 58.869 52.381 0.00 0.00 36.42 5.03
1495 3229 7.553044 ACTGTTAATTACTCCTGTAAAGATGGC 59.447 37.037 0.00 0.00 41.36 4.40
1504 3238 7.511268 TGTGGTAAACTGTTAATTACTCCTGT 58.489 34.615 0.00 0.00 33.53 4.00
1634 3403 0.107312 ATGACAGTGGCTGGAGATGC 60.107 55.000 0.00 0.00 35.51 3.91
1697 3466 2.109126 GTCGCTGTGGAGGAATGCC 61.109 63.158 0.00 0.00 0.00 4.40
1944 3726 4.082125 ACAGCCTTTTTGCATAGTAGCTT 58.918 39.130 0.00 0.00 34.99 3.74
2151 6569 5.755409 TCAACCCTGAGAAGCAAACTATA 57.245 39.130 0.00 0.00 0.00 1.31
2348 7127 0.768221 TGAAGGGGTCCAGCTCAAGT 60.768 55.000 0.00 0.00 0.00 3.16
2350 7129 1.761174 GTGAAGGGGTCCAGCTCAA 59.239 57.895 0.00 0.00 0.00 3.02
2352 7131 1.566298 ATGGTGAAGGGGTCCAGCTC 61.566 60.000 0.00 0.00 0.00 4.09
2354 7133 0.846693 ATATGGTGAAGGGGTCCAGC 59.153 55.000 0.00 0.00 0.00 4.85
2472 7282 3.430374 CGGTCTGGTAGAAAGTACATGGG 60.430 52.174 0.00 0.00 0.00 4.00
2493 7303 3.496131 CATTCCCCGCCGTTGACG 61.496 66.667 0.00 0.00 39.44 4.35
2777 7761 0.543277 CTGCCTGCCAGTATCTCCAA 59.457 55.000 0.00 0.00 36.79 3.53
2911 7903 1.076923 GCCGGAGAGGGAGTACTGA 60.077 63.158 5.05 0.00 41.48 3.41
2969 7961 0.036765 GGCCGGACACTCATGTTACA 60.037 55.000 5.05 0.00 39.95 2.41
2975 7967 4.148825 GCTCGGCCGGACACTCAT 62.149 66.667 27.83 0.00 0.00 2.90
3092 8084 2.427506 GCTACCACCAAACTTCCTGAG 58.572 52.381 0.00 0.00 0.00 3.35
3158 8156 0.249955 TCATTGGATGAGCAGCGACA 59.750 50.000 0.00 0.00 33.59 4.35
3170 8168 5.250543 TCCCTCTTTACACTTCATCATTGGA 59.749 40.000 0.00 0.00 0.00 3.53
3326 8343 2.636830 CTCATTTCCAATCAGCGAGGT 58.363 47.619 0.00 0.00 0.00 3.85
3432 8456 2.017049 ACTGAGCAAACAACCTGTGTC 58.983 47.619 0.00 0.00 40.60 3.67
3433 8457 2.017049 GACTGAGCAAACAACCTGTGT 58.983 47.619 0.00 0.00 44.64 3.72
3530 8577 9.877178 CTGTAGACTTTGTCCAAATAGAGTTAT 57.123 33.333 0.00 0.00 32.18 1.89
3654 8728 6.918022 GTGCTAAGCTTTGACAAAGTTTACAT 59.082 34.615 24.83 11.03 41.32 2.29
3656 8730 6.495706 AGTGCTAAGCTTTGACAAAGTTTAC 58.504 36.000 24.83 20.01 41.32 2.01
3671 8745 7.980099 TCACTACCTTTAATTCTAGTGCTAAGC 59.020 37.037 8.22 0.00 37.21 3.09
3686 8760 5.594725 TGTGCAAACCAAATCACTACCTTTA 59.405 36.000 0.00 0.00 0.00 1.85
3806 8885 7.784073 TGCCCTTTATCAATTTGGAATGATAGA 59.216 33.333 0.00 0.00 39.12 1.98
3828 8907 1.181098 AACAATGCACCAGACTGCCC 61.181 55.000 0.00 0.00 36.21 5.36
3841 8920 5.633830 ACATCCTGAAGCAAGTAACAATG 57.366 39.130 0.00 0.00 0.00 2.82
3922 9394 6.723298 AGCTCAAGTGCTCAACTAGTATAT 57.277 37.500 0.00 0.00 39.34 0.86
3965 9437 1.375908 CCTGCTGCTTTCACGGCTA 60.376 57.895 0.00 0.00 42.69 3.93
4000 9472 4.319177 ACACAAGTGAGCTGGATAAGAAC 58.681 43.478 7.28 0.00 0.00 3.01
4044 9516 5.185454 TGACGAAACATCTCATATTTGGCT 58.815 37.500 0.00 0.00 0.00 4.75
4079 9552 4.782691 TCATGATTCAGTAGAGGTTCCCAA 59.217 41.667 0.00 0.00 0.00 4.12
4102 9575 5.923204 ACATTTCTTCAGAGTTCAGACACT 58.077 37.500 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.