Multiple sequence alignment - TraesCS4A01G434500

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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 TraesCS4A01G434500 chr4A 100.000 2753 0 0 1 2753 705171420 705168668 0.000000e+00 5084.0
1 TraesCS4A01G434500 chr4A 91.275 1169 72 14 757 1918 705055328 705054183 0.000000e+00 1567.0
2 TraesCS4A01G434500 chr4A 87.733 1125 86 29 757 1866 704808055 704806968 0.000000e+00 1266.0
3 TraesCS4A01G434500 chr4A 96.629 534 9 6 2228 2753 705053779 705053247 0.000000e+00 878.0
4 TraesCS4A01G434500 chr4A 95.556 270 11 1 1919 2188 705054046 705053778 5.450000e-117 431.0
5 TraesCS4A01G434500 chr4A 91.743 109 8 1 2382 2490 704806448 704806341 1.710000e-32 150.0
6 TraesCS4A01G434500 chr7D 86.902 1504 127 36 604 2050 22523341 22521851 0.000000e+00 1622.0
7 TraesCS4A01G434500 chr7D 85.532 1175 79 45 755 1866 22270430 22269284 0.000000e+00 1144.0
8 TraesCS4A01G434500 chr7D 86.996 992 82 22 756 1725 22509997 22509031 0.000000e+00 1074.0
9 TraesCS4A01G434500 chr7D 84.021 388 49 8 1676 2053 22509039 22508655 7.250000e-96 361.0
10 TraesCS4A01G434500 chr7A 87.438 1202 102 28 529 1725 22916876 22915719 0.000000e+00 1338.0
11 TraesCS4A01G434500 chr7A 89.651 802 57 15 755 1542 22898544 22897755 0.000000e+00 998.0
12 TraesCS4A01G434500 chr7A 81.163 430 45 27 1603 2003 22897733 22897311 2.060000e-81 313.0
13 TraesCS4A01G434500 chr5B 90.377 478 41 1 975 1452 469337848 469338320 8.370000e-175 623.0
14 TraesCS4A01G434500 chr5B 87.500 80 9 1 2207 2286 671701035 671700957 1.050000e-14 91.6
15 TraesCS4A01G434500 chr1A 98.361 61 1 0 1464 1524 27383214 27383154 1.040000e-19 108.0
16 TraesCS4A01G434500 chr1A 96.721 61 2 0 1464 1524 442726932 442726872 4.850000e-18 102.0


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 TraesCS4A01G434500 chr4A 705168668 705171420 2752 True 5084.000000 5084 100.000000 1 2753 1 chr4A.!!$R1 2752
1 TraesCS4A01G434500 chr4A 705053247 705055328 2081 True 958.666667 1567 94.486667 757 2753 3 chr4A.!!$R3 1996
2 TraesCS4A01G434500 chr4A 704806341 704808055 1714 True 708.000000 1266 89.738000 757 2490 2 chr4A.!!$R2 1733
3 TraesCS4A01G434500 chr7D 22521851 22523341 1490 True 1622.000000 1622 86.902000 604 2050 1 chr7D.!!$R2 1446
4 TraesCS4A01G434500 chr7D 22269284 22270430 1146 True 1144.000000 1144 85.532000 755 1866 1 chr7D.!!$R1 1111
5 TraesCS4A01G434500 chr7D 22508655 22509997 1342 True 717.500000 1074 85.508500 756 2053 2 chr7D.!!$R3 1297
6 TraesCS4A01G434500 chr7A 22915719 22916876 1157 True 1338.000000 1338 87.438000 529 1725 1 chr7A.!!$R1 1196
7 TraesCS4A01G434500 chr7A 22897311 22898544 1233 True 655.500000 998 85.407000 755 2003 2 chr7A.!!$R2 1248

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
47 48 0.035439 AAAATGGAGCGTCGACCCAT 60.035 50.0 16.39 16.39 42.08 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1976 2354 0.770499 TCCAGACCATGCCTCAACAA 59.23 50.0 0.0 0.0 0.0 2.83 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
39 40 5.774498 AAAAAGAAGAGAAAATGGAGCGT 57.226 34.783 0.00 0.00 0.00 5.07
40 41 5.363979 AAAAGAAGAGAAAATGGAGCGTC 57.636 39.130 0.00 0.00 0.00 5.19
41 42 2.611518 AGAAGAGAAAATGGAGCGTCG 58.388 47.619 0.00 0.00 0.00 5.12
42 43 2.231478 AGAAGAGAAAATGGAGCGTCGA 59.769 45.455 0.00 0.00 0.00 4.20
43 44 1.997669 AGAGAAAATGGAGCGTCGAC 58.002 50.000 5.18 5.18 0.00 4.20
44 45 1.000145 GAGAAAATGGAGCGTCGACC 59.000 55.000 10.58 2.76 0.00 4.79
45 46 0.391263 AGAAAATGGAGCGTCGACCC 60.391 55.000 10.58 6.16 0.00 4.46
46 47 0.672401 GAAAATGGAGCGTCGACCCA 60.672 55.000 13.44 13.44 0.00 4.51
47 48 0.035439 AAAATGGAGCGTCGACCCAT 60.035 50.000 16.39 16.39 42.08 4.00
48 49 1.602237 AATGGAGCGTCGACCCATT 59.398 52.632 23.81 23.81 43.62 3.16
49 50 0.744414 AATGGAGCGTCGACCCATTG 60.744 55.000 26.83 9.36 45.82 2.82
50 51 2.511600 GGAGCGTCGACCCATTGG 60.512 66.667 10.58 0.00 37.80 3.16
51 52 3.195698 GAGCGTCGACCCATTGGC 61.196 66.667 10.58 6.36 33.59 4.52
52 53 3.665675 GAGCGTCGACCCATTGGCT 62.666 63.158 10.58 11.57 33.59 4.75
53 54 3.195698 GCGTCGACCCATTGGCTC 61.196 66.667 10.58 0.00 33.59 4.70
54 55 2.885644 CGTCGACCCATTGGCTCG 60.886 66.667 13.19 13.19 36.87 5.03
55 56 2.511600 GTCGACCCATTGGCTCGG 60.512 66.667 17.97 2.91 36.47 4.63
56 57 4.467084 TCGACCCATTGGCTCGGC 62.467 66.667 17.97 0.00 36.47 5.54
57 58 4.776322 CGACCCATTGGCTCGGCA 62.776 66.667 11.80 0.00 33.97 5.69
58 59 2.825836 GACCCATTGGCTCGGCAG 60.826 66.667 0.00 0.00 33.59 4.85
60 61 4.809496 CCCATTGGCTCGGCAGCT 62.809 66.667 0.00 0.00 46.03 4.24
61 62 3.515286 CCATTGGCTCGGCAGCTG 61.515 66.667 10.11 10.11 46.03 4.24
62 63 3.515286 CATTGGCTCGGCAGCTGG 61.515 66.667 17.12 0.00 46.03 4.85
63 64 4.809496 ATTGGCTCGGCAGCTGGG 62.809 66.667 17.12 0.00 46.03 4.45
81 82 3.851128 GGAGCTCCCAGTACGCCC 61.851 72.222 23.19 0.00 34.14 6.13
82 83 4.208686 GAGCTCCCAGTACGCCCG 62.209 72.222 0.87 0.00 0.00 6.13
95 96 4.404654 GCCCGCGTTTGAGCCTTG 62.405 66.667 4.92 0.00 0.00 3.61
96 97 2.978010 CCCGCGTTTGAGCCTTGT 60.978 61.111 4.92 0.00 0.00 3.16
97 98 2.556287 CCGCGTTTGAGCCTTGTC 59.444 61.111 4.92 0.00 0.00 3.18
98 99 1.961277 CCGCGTTTGAGCCTTGTCT 60.961 57.895 4.92 0.00 0.00 3.41
99 100 1.493311 CGCGTTTGAGCCTTGTCTC 59.507 57.895 0.00 0.00 0.00 3.36
100 101 0.946221 CGCGTTTGAGCCTTGTCTCT 60.946 55.000 0.00 0.00 34.29 3.10
101 102 0.514691 GCGTTTGAGCCTTGTCTCTG 59.485 55.000 0.00 0.00 34.29 3.35
102 103 1.151668 CGTTTGAGCCTTGTCTCTGG 58.848 55.000 0.00 0.00 34.29 3.86
125 126 2.032681 GGCACTGGCGGAGTTTCT 59.967 61.111 0.00 0.00 42.47 2.52
126 127 2.035442 GGCACTGGCGGAGTTTCTC 61.035 63.158 0.00 0.00 42.47 2.87
127 128 2.035442 GCACTGGCGGAGTTTCTCC 61.035 63.158 0.00 5.79 46.44 3.71
156 157 5.453567 AAAAAGCCAATGAGTGTTAGTCC 57.546 39.130 0.00 0.00 0.00 3.85
157 158 4.373156 AAAGCCAATGAGTGTTAGTCCT 57.627 40.909 0.00 0.00 0.00 3.85
158 159 4.373156 AAGCCAATGAGTGTTAGTCCTT 57.627 40.909 0.00 0.00 0.00 3.36
159 160 3.679389 AGCCAATGAGTGTTAGTCCTTG 58.321 45.455 0.00 0.00 0.00 3.61
160 161 2.749621 GCCAATGAGTGTTAGTCCTTGG 59.250 50.000 13.23 13.23 42.58 3.61
161 162 3.559171 GCCAATGAGTGTTAGTCCTTGGA 60.559 47.826 18.77 0.00 42.42 3.53
162 163 4.848357 CCAATGAGTGTTAGTCCTTGGAT 58.152 43.478 12.57 0.00 42.42 3.41
163 164 5.629133 GCCAATGAGTGTTAGTCCTTGGATA 60.629 44.000 18.77 0.00 42.42 2.59
164 165 6.595682 CCAATGAGTGTTAGTCCTTGGATAT 58.404 40.000 12.57 0.00 42.42 1.63
165 166 7.056635 CCAATGAGTGTTAGTCCTTGGATATT 58.943 38.462 12.57 0.00 42.42 1.28
166 167 7.557719 CCAATGAGTGTTAGTCCTTGGATATTT 59.442 37.037 12.57 0.00 42.42 1.40
167 168 8.960591 CAATGAGTGTTAGTCCTTGGATATTTT 58.039 33.333 0.00 0.00 0.00 1.82
168 169 9.533831 AATGAGTGTTAGTCCTTGGATATTTTT 57.466 29.630 0.00 0.00 0.00 1.94
244 245 9.613428 TTGTAGGATATCAAAGTTGGTCTAATG 57.387 33.333 4.83 0.00 0.00 1.90
245 246 8.768397 TGTAGGATATCAAAGTTGGTCTAATGT 58.232 33.333 4.83 0.00 0.00 2.71
246 247 9.614792 GTAGGATATCAAAGTTGGTCTAATGTT 57.385 33.333 4.83 0.00 0.00 2.71
247 248 8.738645 AGGATATCAAAGTTGGTCTAATGTTC 57.261 34.615 4.83 0.00 0.00 3.18
248 249 8.552296 AGGATATCAAAGTTGGTCTAATGTTCT 58.448 33.333 4.83 0.00 0.00 3.01
249 250 9.832445 GGATATCAAAGTTGGTCTAATGTTCTA 57.168 33.333 4.83 0.00 0.00 2.10
252 253 8.779354 ATCAAAGTTGGTCTAATGTTCTACTC 57.221 34.615 0.00 0.00 0.00 2.59
253 254 7.732025 TCAAAGTTGGTCTAATGTTCTACTCA 58.268 34.615 0.00 0.00 0.00 3.41
254 255 7.656137 TCAAAGTTGGTCTAATGTTCTACTCAC 59.344 37.037 0.00 0.00 0.00 3.51
255 256 6.665992 AGTTGGTCTAATGTTCTACTCACA 57.334 37.500 0.00 0.00 0.00 3.58
256 257 7.246171 AGTTGGTCTAATGTTCTACTCACAT 57.754 36.000 0.00 0.00 36.36 3.21
257 258 7.099764 AGTTGGTCTAATGTTCTACTCACATG 58.900 38.462 0.00 0.00 34.97 3.21
258 259 6.605471 TGGTCTAATGTTCTACTCACATGT 57.395 37.500 0.00 0.00 34.97 3.21
259 260 6.398095 TGGTCTAATGTTCTACTCACATGTG 58.602 40.000 20.18 20.18 34.97 3.21
260 261 6.014584 TGGTCTAATGTTCTACTCACATGTGT 60.015 38.462 24.63 9.87 34.97 3.72
261 262 7.177744 TGGTCTAATGTTCTACTCACATGTGTA 59.822 37.037 24.63 10.51 34.97 2.90
262 263 8.033038 GGTCTAATGTTCTACTCACATGTGTAA 58.967 37.037 24.63 10.85 34.97 2.41
263 264 9.587772 GTCTAATGTTCTACTCACATGTGTAAT 57.412 33.333 24.63 13.80 34.97 1.89
267 268 8.846943 ATGTTCTACTCACATGTGTAATTTGA 57.153 30.769 24.63 13.49 33.42 2.69
268 269 8.310406 TGTTCTACTCACATGTGTAATTTGAG 57.690 34.615 24.63 15.07 39.72 3.02
269 270 8.147704 TGTTCTACTCACATGTGTAATTTGAGA 58.852 33.333 24.63 14.89 37.67 3.27
270 271 8.988934 GTTCTACTCACATGTGTAATTTGAGAA 58.011 33.333 24.63 18.83 37.67 2.87
271 272 9.554395 TTCTACTCACATGTGTAATTTGAGAAA 57.446 29.630 24.63 8.15 37.67 2.52
272 273 9.554395 TCTACTCACATGTGTAATTTGAGAAAA 57.446 29.630 24.63 0.42 37.67 2.29
299 300 8.918202 AAAAGACATTGTGGTATTCTTAGTGA 57.082 30.769 0.00 0.00 0.00 3.41
300 301 8.918202 AAAGACATTGTGGTATTCTTAGTGAA 57.082 30.769 0.00 0.00 39.24 3.18
301 302 8.553459 AAGACATTGTGGTATTCTTAGTGAAG 57.447 34.615 0.00 0.00 38.18 3.02
302 303 7.907389 AGACATTGTGGTATTCTTAGTGAAGA 58.093 34.615 0.00 0.00 40.04 2.87
313 314 6.462073 TTCTTAGTGAAGAACCGAAAATCG 57.538 37.500 0.00 0.00 44.94 3.34
314 315 5.775686 TCTTAGTGAAGAACCGAAAATCGA 58.224 37.500 0.58 0.00 39.41 3.59
315 316 6.218019 TCTTAGTGAAGAACCGAAAATCGAA 58.782 36.000 0.58 0.00 39.41 3.71
316 317 4.727235 AGTGAAGAACCGAAAATCGAAC 57.273 40.909 0.58 0.00 43.74 3.95
317 318 4.124238 AGTGAAGAACCGAAAATCGAACA 58.876 39.130 0.58 0.00 43.74 3.18
318 319 4.755123 AGTGAAGAACCGAAAATCGAACAT 59.245 37.500 0.58 0.00 43.74 2.71
319 320 5.238650 AGTGAAGAACCGAAAATCGAACATT 59.761 36.000 0.58 0.00 43.74 2.71
320 321 5.339611 GTGAAGAACCGAAAATCGAACATTG 59.660 40.000 0.58 0.00 43.74 2.82
321 322 5.237561 TGAAGAACCGAAAATCGAACATTGA 59.762 36.000 0.58 0.00 43.74 2.57
322 323 5.682943 AGAACCGAAAATCGAACATTGAA 57.317 34.783 0.58 0.00 43.74 2.69
323 324 6.254281 AGAACCGAAAATCGAACATTGAAT 57.746 33.333 0.58 0.00 43.74 2.57
324 325 7.372451 AGAACCGAAAATCGAACATTGAATA 57.628 32.000 0.58 0.00 43.74 1.75
325 326 7.241376 AGAACCGAAAATCGAACATTGAATAC 58.759 34.615 0.58 0.00 43.74 1.89
326 327 5.875930 ACCGAAAATCGAACATTGAATACC 58.124 37.500 0.58 0.00 43.74 2.73
327 328 5.413213 ACCGAAAATCGAACATTGAATACCA 59.587 36.000 0.58 0.00 43.74 3.25
328 329 5.737290 CCGAAAATCGAACATTGAATACCAC 59.263 40.000 0.58 0.00 43.74 4.16
329 330 6.403200 CCGAAAATCGAACATTGAATACCACT 60.403 38.462 0.58 0.00 43.74 4.00
330 331 6.465781 CGAAAATCGAACATTGAATACCACTG 59.534 38.462 0.00 0.00 43.74 3.66
331 332 7.447374 AAAATCGAACATTGAATACCACTGA 57.553 32.000 0.00 0.00 0.00 3.41
332 333 7.630242 AAATCGAACATTGAATACCACTGAT 57.370 32.000 0.00 0.00 0.00 2.90
333 334 8.731275 AAATCGAACATTGAATACCACTGATA 57.269 30.769 0.00 0.00 0.00 2.15
334 335 8.731275 AATCGAACATTGAATACCACTGATAA 57.269 30.769 0.00 0.00 0.00 1.75
335 336 8.908786 ATCGAACATTGAATACCACTGATAAT 57.091 30.769 0.00 0.00 0.00 1.28
336 337 8.731275 TCGAACATTGAATACCACTGATAATT 57.269 30.769 0.00 0.00 0.00 1.40
337 338 9.173021 TCGAACATTGAATACCACTGATAATTT 57.827 29.630 0.00 0.00 0.00 1.82
338 339 9.438291 CGAACATTGAATACCACTGATAATTTC 57.562 33.333 0.00 0.00 0.00 2.17
341 342 9.125026 ACATTGAATACCACTGATAATTTCTCC 57.875 33.333 0.00 0.00 0.00 3.71
342 343 9.123902 CATTGAATACCACTGATAATTTCTCCA 57.876 33.333 0.00 0.00 0.00 3.86
343 344 9.872684 ATTGAATACCACTGATAATTTCTCCAT 57.127 29.630 0.00 0.00 0.00 3.41
344 345 8.681486 TGAATACCACTGATAATTTCTCCATG 57.319 34.615 0.00 0.00 0.00 3.66
345 346 8.493607 TGAATACCACTGATAATTTCTCCATGA 58.506 33.333 0.00 0.00 0.00 3.07
346 347 9.342308 GAATACCACTGATAATTTCTCCATGAA 57.658 33.333 0.00 0.00 0.00 2.57
348 349 7.396540 ACCACTGATAATTTCTCCATGAAAC 57.603 36.000 0.00 0.00 46.08 2.78
349 350 7.177878 ACCACTGATAATTTCTCCATGAAACT 58.822 34.615 0.00 0.00 46.08 2.66
350 351 7.671398 ACCACTGATAATTTCTCCATGAAACTT 59.329 33.333 0.00 0.00 46.08 2.66
351 352 8.186821 CCACTGATAATTTCTCCATGAAACTTC 58.813 37.037 0.00 0.00 46.08 3.01
352 353 8.733458 CACTGATAATTTCTCCATGAAACTTCA 58.267 33.333 0.00 0.00 46.08 3.02
353 354 8.734386 ACTGATAATTTCTCCATGAAACTTCAC 58.266 33.333 0.00 0.00 46.08 3.18
354 355 8.634335 TGATAATTTCTCCATGAAACTTCACA 57.366 30.769 0.00 0.00 46.08 3.58
355 356 8.514594 TGATAATTTCTCCATGAAACTTCACAC 58.485 33.333 0.00 0.00 46.08 3.82
356 357 4.811555 TTTCTCCATGAAACTTCACACG 57.188 40.909 0.00 0.00 40.49 4.49
357 358 3.469008 TCTCCATGAAACTTCACACGT 57.531 42.857 0.00 0.00 40.49 4.49
358 359 4.594123 TCTCCATGAAACTTCACACGTA 57.406 40.909 0.00 0.00 40.49 3.57
359 360 4.951254 TCTCCATGAAACTTCACACGTAA 58.049 39.130 0.00 0.00 40.49 3.18
360 361 5.547465 TCTCCATGAAACTTCACACGTAAT 58.453 37.500 0.00 0.00 40.49 1.89
361 362 5.995282 TCTCCATGAAACTTCACACGTAATT 59.005 36.000 0.00 0.00 40.49 1.40
362 363 7.156000 TCTCCATGAAACTTCACACGTAATTA 58.844 34.615 0.00 0.00 40.49 1.40
363 364 7.330946 TCTCCATGAAACTTCACACGTAATTAG 59.669 37.037 0.00 0.00 40.49 1.73
364 365 7.156000 TCCATGAAACTTCACACGTAATTAGA 58.844 34.615 0.00 0.00 40.49 2.10
365 366 7.658167 TCCATGAAACTTCACACGTAATTAGAA 59.342 33.333 0.00 0.00 40.49 2.10
366 367 8.450964 CCATGAAACTTCACACGTAATTAGAAT 58.549 33.333 0.00 0.00 40.49 2.40
375 376 8.456904 TCACACGTAATTAGAATATATTCGGC 57.543 34.615 17.69 6.79 41.56 5.54
376 377 7.543172 TCACACGTAATTAGAATATATTCGGCC 59.457 37.037 17.69 0.00 41.56 6.13
377 378 7.329962 CACACGTAATTAGAATATATTCGGCCA 59.670 37.037 17.69 5.80 41.56 5.36
378 379 8.038944 ACACGTAATTAGAATATATTCGGCCAT 58.961 33.333 17.69 7.56 41.56 4.40
379 380 8.328146 CACGTAATTAGAATATATTCGGCCATG 58.672 37.037 17.69 11.64 41.56 3.66
380 381 8.038944 ACGTAATTAGAATATATTCGGCCATGT 58.961 33.333 17.69 12.13 41.56 3.21
381 382 9.524106 CGTAATTAGAATATATTCGGCCATGTA 57.476 33.333 17.69 2.77 41.56 2.29
384 385 8.908786 ATTAGAATATATTCGGCCATGTATGG 57.091 34.615 17.69 6.53 44.75 2.74
385 386 6.313519 AGAATATATTCGGCCATGTATGGT 57.686 37.500 17.69 0.00 44.29 3.55
386 387 7.432148 AGAATATATTCGGCCATGTATGGTA 57.568 36.000 17.69 0.00 44.29 3.25
387 388 8.034313 AGAATATATTCGGCCATGTATGGTAT 57.966 34.615 17.69 4.89 44.29 2.73
388 389 7.933577 AGAATATATTCGGCCATGTATGGTATG 59.066 37.037 17.69 3.42 44.29 2.39
399 400 7.444629 CCATGTATGGTATGGATCTTTTCAG 57.555 40.000 2.66 0.00 46.42 3.02
400 401 7.226441 CCATGTATGGTATGGATCTTTTCAGA 58.774 38.462 2.66 0.00 46.42 3.27
401 402 7.720957 CCATGTATGGTATGGATCTTTTCAGAA 59.279 37.037 2.66 0.00 46.42 3.02
402 403 9.293404 CATGTATGGTATGGATCTTTTCAGAAT 57.707 33.333 0.00 0.00 30.76 2.40
403 404 9.872684 ATGTATGGTATGGATCTTTTCAGAATT 57.127 29.630 0.00 0.00 30.76 2.17
418 419 9.298774 CTTTTCAGAATTATTTGATCTTCCAGC 57.701 33.333 0.00 0.00 0.00 4.85
419 420 6.949352 TCAGAATTATTTGATCTTCCAGCC 57.051 37.500 0.00 0.00 0.00 4.85
420 421 6.666678 TCAGAATTATTTGATCTTCCAGCCT 58.333 36.000 0.00 0.00 0.00 4.58
421 422 7.121382 TCAGAATTATTTGATCTTCCAGCCTT 58.879 34.615 0.00 0.00 0.00 4.35
422 423 7.616935 TCAGAATTATTTGATCTTCCAGCCTTT 59.383 33.333 0.00 0.00 0.00 3.11
423 424 8.255905 CAGAATTATTTGATCTTCCAGCCTTTT 58.744 33.333 0.00 0.00 0.00 2.27
424 425 8.819845 AGAATTATTTGATCTTCCAGCCTTTTT 58.180 29.630 0.00 0.00 0.00 1.94
461 462 9.800433 TTTATAATTTATAATGGATGCGCATGG 57.200 29.630 30.76 0.00 31.27 3.66
462 463 5.981088 AATTTATAATGGATGCGCATGGA 57.019 34.783 30.76 14.35 0.00 3.41
463 464 5.981088 ATTTATAATGGATGCGCATGGAA 57.019 34.783 30.76 13.31 0.00 3.53
464 465 4.764679 TTATAATGGATGCGCATGGAAC 57.235 40.909 30.76 13.34 0.00 3.62
465 466 1.317613 TAATGGATGCGCATGGAACC 58.682 50.000 30.76 22.62 0.00 3.62
466 467 0.683828 AATGGATGCGCATGGAACCA 60.684 50.000 30.76 27.56 42.42 3.67
467 468 1.105167 ATGGATGCGCATGGAACCAG 61.105 55.000 30.76 0.00 41.55 4.00
468 469 2.484062 GGATGCGCATGGAACCAGG 61.484 63.158 30.76 0.88 0.00 4.45
469 470 1.750399 GATGCGCATGGAACCAGGT 60.750 57.895 30.76 0.00 0.00 4.00
470 471 1.304381 ATGCGCATGGAACCAGGTT 60.304 52.632 24.69 3.79 0.00 3.50
471 472 1.315257 ATGCGCATGGAACCAGGTTC 61.315 55.000 24.69 22.73 41.32 3.62
500 501 8.541899 AAAAAGACCATTGTCCCTAAAACTAA 57.458 30.769 0.00 0.00 42.81 2.24
501 502 7.520451 AAAGACCATTGTCCCTAAAACTAAC 57.480 36.000 0.00 0.00 42.81 2.34
502 503 5.567430 AGACCATTGTCCCTAAAACTAACC 58.433 41.667 0.00 0.00 42.81 2.85
503 504 4.669700 ACCATTGTCCCTAAAACTAACCC 58.330 43.478 0.00 0.00 0.00 4.11
504 505 4.106663 ACCATTGTCCCTAAAACTAACCCA 59.893 41.667 0.00 0.00 0.00 4.51
505 506 5.222463 ACCATTGTCCCTAAAACTAACCCAT 60.222 40.000 0.00 0.00 0.00 4.00
506 507 5.719563 CCATTGTCCCTAAAACTAACCCATT 59.280 40.000 0.00 0.00 0.00 3.16
507 508 6.212589 CCATTGTCCCTAAAACTAACCCATTT 59.787 38.462 0.00 0.00 0.00 2.32
508 509 7.256511 CCATTGTCCCTAAAACTAACCCATTTT 60.257 37.037 0.00 0.00 32.85 1.82
509 510 7.678207 TTGTCCCTAAAACTAACCCATTTTT 57.322 32.000 0.00 0.00 30.80 1.94
558 559 4.521130 ATGACACAGACGACTTGTGTAT 57.479 40.909 18.82 12.33 45.43 2.29
562 563 3.168963 CACAGACGACTTGTGTATACCG 58.831 50.000 0.00 0.00 0.00 4.02
568 569 3.058293 ACGACTTGTGTATACCGAACGAA 60.058 43.478 0.00 0.00 0.00 3.85
570 571 3.841643 ACTTGTGTATACCGAACGAAGG 58.158 45.455 0.00 0.00 0.00 3.46
571 572 2.282701 TGTGTATACCGAACGAAGGC 57.717 50.000 0.00 0.00 0.00 4.35
575 576 1.525619 GTATACCGAACGAAGGCATGC 59.474 52.381 9.90 9.90 0.00 4.06
576 577 0.814010 ATACCGAACGAAGGCATGCC 60.814 55.000 30.12 30.12 0.00 4.40
577 578 2.173758 TACCGAACGAAGGCATGCCA 62.174 55.000 37.18 10.88 38.92 4.92
578 579 2.114670 CCGAACGAAGGCATGCCAT 61.115 57.895 37.18 27.80 38.92 4.40
601 602 2.262915 CCCACCGCACAGAGAGAC 59.737 66.667 0.00 0.00 0.00 3.36
607 608 2.871099 GCACAGAGAGACGCGAGA 59.129 61.111 15.93 0.00 0.00 4.04
609 610 0.796491 GCACAGAGAGACGCGAGAAG 60.796 60.000 15.93 0.00 0.00 2.85
610 611 0.796491 CACAGAGAGACGCGAGAAGC 60.796 60.000 15.93 0.00 43.95 3.86
653 656 3.382832 CGAGGAGCGGGAACAGGT 61.383 66.667 0.00 0.00 36.03 4.00
694 697 0.687757 AGGCGCATAGACAGAAGGGA 60.688 55.000 10.83 0.00 0.00 4.20
765 778 4.162690 ATCCTCCCGCGCCAAGTC 62.163 66.667 0.00 0.00 0.00 3.01
847 870 2.964803 GCCTCCCTCCCACCTATAAACT 60.965 54.545 0.00 0.00 0.00 2.66
904 932 4.776322 CACCGCCGCAATCCTCCA 62.776 66.667 0.00 0.00 0.00 3.86
912 940 1.138859 CCGCAATCCTCCATACTCACA 59.861 52.381 0.00 0.00 0.00 3.58
932 960 4.035814 ACATTCATCCAGATCCACAGAGA 58.964 43.478 0.00 0.00 0.00 3.10
934 962 2.037901 TCATCCAGATCCACAGAGAGC 58.962 52.381 0.00 0.00 0.00 4.09
937 965 0.102120 CCAGATCCACAGAGAGCGAC 59.898 60.000 0.00 0.00 0.00 5.19
973 1004 2.886081 TCAAGAGATCAAGAAGCTCGC 58.114 47.619 0.00 0.00 33.98 5.03
976 1015 0.873743 GAGATCAAGAAGCTCGCCCG 60.874 60.000 0.00 0.00 0.00 6.13
1266 1344 4.003788 AGGTCCAAGGTCCGTGCG 62.004 66.667 0.00 0.00 0.00 5.34
1323 1401 4.225340 CTCGGCTCCGACGACGAG 62.225 72.222 13.38 13.38 38.55 4.18
1329 1410 1.740664 CTCCGACGACGAGGACTCA 60.741 63.158 9.28 0.00 42.66 3.41
1401 1482 2.028130 GTGGATGATGACGAGGACTCT 58.972 52.381 0.00 0.00 0.00 3.24
1452 1533 4.498520 CTCGTCACCATCGCCGCT 62.499 66.667 0.00 0.00 0.00 5.52
1583 1664 2.665603 GCCGCTGAGGAAGAAGGT 59.334 61.111 0.09 0.00 45.00 3.50
1589 1670 2.289072 CGCTGAGGAAGAAGGTTTCTGA 60.289 50.000 0.00 0.00 40.59 3.27
1653 1737 1.188219 AGTCGCTGAAGAGGAAGGCA 61.188 55.000 0.00 0.00 0.00 4.75
1763 1898 3.087031 CCAAGCACTGATGGATTTCTGT 58.913 45.455 0.00 0.00 39.12 3.41
1779 1955 7.122650 TGGATTTCTGTTCTTTTTGTCAGTTCT 59.877 33.333 0.00 0.00 0.00 3.01
1782 1958 6.422776 TCTGTTCTTTTTGTCAGTTCTGTC 57.577 37.500 0.00 0.00 0.00 3.51
2071 2786 7.009179 TGAATCTTCCTGTACTGTGATCTTT 57.991 36.000 0.00 0.00 0.00 2.52
2084 2799 9.344309 GTACTGTGATCTTTAGTAGAAACACTC 57.656 37.037 0.00 0.00 41.03 3.51
2114 2829 2.530701 AGTAGTTCCTGTACTGCTGCT 58.469 47.619 0.00 0.00 39.25 4.24
2171 2886 3.938963 AGAGGTTGCGTGTAATTGGTATG 59.061 43.478 0.00 0.00 0.00 2.39
2176 2891 3.327626 TGCGTGTAATTGGTATGTTCGT 58.672 40.909 0.00 0.00 0.00 3.85
2179 2894 4.143073 GCGTGTAATTGGTATGTTCGTGAA 60.143 41.667 0.00 0.00 0.00 3.18
2180 2895 5.446741 GCGTGTAATTGGTATGTTCGTGAAT 60.447 40.000 0.00 0.00 0.00 2.57
2183 2898 7.535940 CGTGTAATTGGTATGTTCGTGAATTTT 59.464 33.333 0.00 0.00 0.00 1.82
2219 2934 9.934190 TTTTTACCGAAAAAGTAGTTCATGTAC 57.066 29.630 0.00 0.00 39.16 2.90
2220 2935 8.891671 TTTACCGAAAAAGTAGTTCATGTACT 57.108 30.769 10.07 10.07 31.80 2.73
2221 2936 6.780706 ACCGAAAAAGTAGTTCATGTACTG 57.219 37.500 14.64 0.00 30.90 2.74
2222 2937 6.285990 ACCGAAAAAGTAGTTCATGTACTGT 58.714 36.000 14.64 0.00 30.90 3.55
2223 2938 6.202188 ACCGAAAAAGTAGTTCATGTACTGTG 59.798 38.462 14.64 0.00 30.90 3.66
2224 2939 6.422701 CCGAAAAAGTAGTTCATGTACTGTGA 59.577 38.462 14.64 0.00 30.90 3.58
2225 2940 7.117812 CCGAAAAAGTAGTTCATGTACTGTGAT 59.882 37.037 14.64 0.00 30.90 3.06
2226 2941 8.162880 CGAAAAAGTAGTTCATGTACTGTGATC 58.837 37.037 14.64 5.38 30.90 2.92
2283 2998 8.615211 TGTTTATCAAGCTCAGTTAATGCTATG 58.385 33.333 0.00 0.00 35.85 2.23
2338 3053 4.081087 TCCTTATCTGTCCTTGTTGCTACC 60.081 45.833 0.00 0.00 0.00 3.18
2386 3102 9.195411 TCTTGCTTATTTTTATGCTTCTTTGTG 57.805 29.630 0.00 0.00 0.00 3.33
2423 3139 7.878477 TGAAAAATCATGTCATGCTTCTTTC 57.122 32.000 8.03 14.96 0.00 2.62
2710 3433 4.447342 CCATCCCTGCCACCACCC 62.447 72.222 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.560953 CGACGCTCCATTTTCTCTTCTTTTT 60.561 40.000 0.00 0.00 0.00 1.94
18 19 4.083802 CGACGCTCCATTTTCTCTTCTTTT 60.084 41.667 0.00 0.00 0.00 2.27
19 20 3.433615 CGACGCTCCATTTTCTCTTCTTT 59.566 43.478 0.00 0.00 0.00 2.52
20 21 2.996621 CGACGCTCCATTTTCTCTTCTT 59.003 45.455 0.00 0.00 0.00 2.52
21 22 2.231478 TCGACGCTCCATTTTCTCTTCT 59.769 45.455 0.00 0.00 0.00 2.85
22 23 2.345942 GTCGACGCTCCATTTTCTCTTC 59.654 50.000 0.00 0.00 0.00 2.87
23 24 2.338500 GTCGACGCTCCATTTTCTCTT 58.662 47.619 0.00 0.00 0.00 2.85
24 25 1.404315 GGTCGACGCTCCATTTTCTCT 60.404 52.381 9.92 0.00 0.00 3.10
25 26 1.000145 GGTCGACGCTCCATTTTCTC 59.000 55.000 9.92 0.00 0.00 2.87
26 27 0.391263 GGGTCGACGCTCCATTTTCT 60.391 55.000 23.96 0.00 0.00 2.52
27 28 0.672401 TGGGTCGACGCTCCATTTTC 60.672 55.000 29.62 3.53 0.00 2.29
28 29 0.035439 ATGGGTCGACGCTCCATTTT 60.035 50.000 29.62 6.19 38.00 1.82
29 30 0.035439 AATGGGTCGACGCTCCATTT 60.035 50.000 29.62 14.61 45.78 2.32
30 31 1.602237 AATGGGTCGACGCTCCATT 59.398 52.632 29.62 26.43 43.93 3.16
31 32 1.153369 CAATGGGTCGACGCTCCAT 60.153 57.895 29.62 22.82 42.52 3.41
32 33 2.264480 CAATGGGTCGACGCTCCA 59.736 61.111 29.62 21.69 34.79 3.86
33 34 2.511600 CCAATGGGTCGACGCTCC 60.512 66.667 29.62 16.92 0.00 4.70
34 35 3.195698 GCCAATGGGTCGACGCTC 61.196 66.667 29.62 13.54 36.17 5.03
35 36 3.665675 GAGCCAATGGGTCGACGCT 62.666 63.158 29.62 21.19 40.45 5.07
36 37 3.195698 GAGCCAATGGGTCGACGC 61.196 66.667 24.41 24.41 40.45 5.19
41 42 2.825836 CTGCCGAGCCAATGGGTC 60.826 66.667 20.67 20.67 45.64 4.46
64 65 3.851128 GGGCGTACTGGGAGCTCC 61.851 72.222 25.59 25.59 0.00 4.70
65 66 4.208686 CGGGCGTACTGGGAGCTC 62.209 72.222 4.71 4.71 0.00 4.09
78 79 4.404654 CAAGGCTCAAACGCGGGC 62.405 66.667 12.47 4.07 0.00 6.13
79 80 2.966309 GACAAGGCTCAAACGCGGG 61.966 63.158 12.47 0.00 0.00 6.13
80 81 1.901650 GAGACAAGGCTCAAACGCGG 61.902 60.000 12.47 0.00 35.01 6.46
81 82 0.946221 AGAGACAAGGCTCAAACGCG 60.946 55.000 3.53 3.53 37.37 6.01
82 83 0.514691 CAGAGACAAGGCTCAAACGC 59.485 55.000 5.61 0.00 37.37 4.84
83 84 1.151668 CCAGAGACAAGGCTCAAACG 58.848 55.000 5.61 0.00 37.37 3.60
107 108 3.423154 GAAACTCCGCCAGTGCCG 61.423 66.667 0.00 0.00 34.56 5.69
108 109 2.032681 AGAAACTCCGCCAGTGCC 59.967 61.111 0.00 0.00 34.56 5.01
109 110 2.035442 GGAGAAACTCCGCCAGTGC 61.035 63.158 1.97 0.00 41.08 4.40
110 111 4.285851 GGAGAAACTCCGCCAGTG 57.714 61.111 1.97 0.00 41.08 3.66
134 135 5.140454 AGGACTAACACTCATTGGCTTTTT 58.860 37.500 0.00 0.00 0.00 1.94
135 136 4.729868 AGGACTAACACTCATTGGCTTTT 58.270 39.130 0.00 0.00 0.00 2.27
136 137 4.373156 AGGACTAACACTCATTGGCTTT 57.627 40.909 0.00 0.00 0.00 3.51
137 138 4.074970 CAAGGACTAACACTCATTGGCTT 58.925 43.478 0.00 0.00 0.00 4.35
138 139 3.560025 CCAAGGACTAACACTCATTGGCT 60.560 47.826 0.00 0.00 41.33 4.75
139 140 2.749621 CCAAGGACTAACACTCATTGGC 59.250 50.000 0.00 0.00 41.33 4.52
140 141 4.286297 TCCAAGGACTAACACTCATTGG 57.714 45.455 5.65 5.65 46.47 3.16
141 142 8.511604 AAATATCCAAGGACTAACACTCATTG 57.488 34.615 0.00 0.00 0.00 2.82
142 143 9.533831 AAAAATATCCAAGGACTAACACTCATT 57.466 29.630 0.00 0.00 0.00 2.57
218 219 9.613428 CATTAGACCAACTTTGATATCCTACAA 57.387 33.333 0.00 0.00 0.00 2.41
219 220 8.768397 ACATTAGACCAACTTTGATATCCTACA 58.232 33.333 0.00 0.00 0.00 2.74
220 221 9.614792 AACATTAGACCAACTTTGATATCCTAC 57.385 33.333 0.00 0.00 0.00 3.18
221 222 9.832445 GAACATTAGACCAACTTTGATATCCTA 57.168 33.333 0.00 0.00 0.00 2.94
222 223 8.552296 AGAACATTAGACCAACTTTGATATCCT 58.448 33.333 0.00 0.00 0.00 3.24
223 224 8.738645 AGAACATTAGACCAACTTTGATATCC 57.261 34.615 0.00 0.00 0.00 2.59
226 227 9.871238 GAGTAGAACATTAGACCAACTTTGATA 57.129 33.333 0.00 0.00 0.00 2.15
227 228 8.375506 TGAGTAGAACATTAGACCAACTTTGAT 58.624 33.333 0.00 0.00 0.00 2.57
228 229 7.656137 GTGAGTAGAACATTAGACCAACTTTGA 59.344 37.037 0.00 0.00 0.00 2.69
229 230 7.441157 TGTGAGTAGAACATTAGACCAACTTTG 59.559 37.037 0.00 0.00 0.00 2.77
230 231 7.506114 TGTGAGTAGAACATTAGACCAACTTT 58.494 34.615 0.00 0.00 0.00 2.66
231 232 7.062749 TGTGAGTAGAACATTAGACCAACTT 57.937 36.000 0.00 0.00 0.00 2.66
232 233 6.665992 TGTGAGTAGAACATTAGACCAACT 57.334 37.500 0.00 0.00 0.00 3.16
233 234 6.874134 ACATGTGAGTAGAACATTAGACCAAC 59.126 38.462 0.00 0.00 36.10 3.77
234 235 6.873605 CACATGTGAGTAGAACATTAGACCAA 59.126 38.462 21.64 0.00 36.10 3.67
235 236 6.014584 ACACATGTGAGTAGAACATTAGACCA 60.015 38.462 31.94 0.00 36.10 4.02
236 237 6.398918 ACACATGTGAGTAGAACATTAGACC 58.601 40.000 31.94 0.00 36.10 3.85
237 238 8.981724 TTACACATGTGAGTAGAACATTAGAC 57.018 34.615 31.94 0.00 36.10 2.59
241 242 9.283768 TCAAATTACACATGTGAGTAGAACATT 57.716 29.630 31.94 13.30 36.10 2.71
242 243 8.846943 TCAAATTACACATGTGAGTAGAACAT 57.153 30.769 31.94 8.87 38.81 2.71
243 244 8.147704 TCTCAAATTACACATGTGAGTAGAACA 58.852 33.333 31.94 8.38 37.55 3.18
244 245 8.534333 TCTCAAATTACACATGTGAGTAGAAC 57.466 34.615 31.94 0.00 37.55 3.01
245 246 9.554395 TTTCTCAAATTACACATGTGAGTAGAA 57.446 29.630 31.94 22.22 37.55 2.10
246 247 9.554395 TTTTCTCAAATTACACATGTGAGTAGA 57.446 29.630 31.94 18.52 37.55 2.59
273 274 9.349713 TCACTAAGAATACCACAATGTCTTTTT 57.650 29.630 0.00 0.00 31.28 1.94
274 275 8.918202 TCACTAAGAATACCACAATGTCTTTT 57.082 30.769 0.00 0.00 31.28 2.27
275 276 8.918202 TTCACTAAGAATACCACAATGTCTTT 57.082 30.769 0.00 0.00 31.28 2.52
276 277 8.375506 TCTTCACTAAGAATACCACAATGTCTT 58.624 33.333 0.00 0.00 38.81 3.01
277 278 7.907389 TCTTCACTAAGAATACCACAATGTCT 58.093 34.615 0.00 0.00 38.81 3.41
278 279 8.547967 TTCTTCACTAAGAATACCACAATGTC 57.452 34.615 0.00 0.00 44.85 3.06
288 289 8.030692 TCGATTTTCGGTTCTTCACTAAGAATA 58.969 33.333 4.06 0.00 44.33 1.75
289 290 6.872020 TCGATTTTCGGTTCTTCACTAAGAAT 59.128 34.615 4.06 0.00 44.33 2.40
290 291 6.218019 TCGATTTTCGGTTCTTCACTAAGAA 58.782 36.000 0.00 0.00 43.21 2.52
291 292 5.775686 TCGATTTTCGGTTCTTCACTAAGA 58.224 37.500 0.00 0.00 40.88 2.10
292 293 6.073980 TGTTCGATTTTCGGTTCTTCACTAAG 60.074 38.462 0.00 0.00 40.88 2.18
293 294 5.754406 TGTTCGATTTTCGGTTCTTCACTAA 59.246 36.000 0.00 0.00 40.88 2.24
294 295 5.291178 TGTTCGATTTTCGGTTCTTCACTA 58.709 37.500 0.00 0.00 40.88 2.74
295 296 4.124238 TGTTCGATTTTCGGTTCTTCACT 58.876 39.130 0.00 0.00 40.88 3.41
296 297 4.461992 TGTTCGATTTTCGGTTCTTCAC 57.538 40.909 0.00 0.00 40.88 3.18
297 298 5.237561 TCAATGTTCGATTTTCGGTTCTTCA 59.762 36.000 0.00 0.00 40.88 3.02
298 299 5.685841 TCAATGTTCGATTTTCGGTTCTTC 58.314 37.500 0.00 0.00 40.88 2.87
299 300 5.682943 TCAATGTTCGATTTTCGGTTCTT 57.317 34.783 0.00 0.00 40.88 2.52
300 301 5.682943 TTCAATGTTCGATTTTCGGTTCT 57.317 34.783 0.00 0.00 40.88 3.01
301 302 6.468000 GGTATTCAATGTTCGATTTTCGGTTC 59.532 38.462 0.00 0.00 40.88 3.62
302 303 6.072397 TGGTATTCAATGTTCGATTTTCGGTT 60.072 34.615 0.00 0.00 40.88 4.44
303 304 5.413213 TGGTATTCAATGTTCGATTTTCGGT 59.587 36.000 0.00 0.00 40.88 4.69
304 305 5.737290 GTGGTATTCAATGTTCGATTTTCGG 59.263 40.000 0.00 0.00 40.88 4.30
305 306 6.465781 CAGTGGTATTCAATGTTCGATTTTCG 59.534 38.462 0.00 0.00 37.67 3.46
306 307 7.526608 TCAGTGGTATTCAATGTTCGATTTTC 58.473 34.615 0.00 0.00 41.68 2.29
307 308 7.447374 TCAGTGGTATTCAATGTTCGATTTT 57.553 32.000 0.00 0.00 41.68 1.82
308 309 7.630242 ATCAGTGGTATTCAATGTTCGATTT 57.370 32.000 0.00 0.00 41.68 2.17
309 310 8.731275 TTATCAGTGGTATTCAATGTTCGATT 57.269 30.769 0.00 0.00 41.68 3.34
310 311 8.908786 ATTATCAGTGGTATTCAATGTTCGAT 57.091 30.769 0.00 0.00 41.68 3.59
311 312 8.731275 AATTATCAGTGGTATTCAATGTTCGA 57.269 30.769 0.00 0.00 41.68 3.71
312 313 9.438291 GAAATTATCAGTGGTATTCAATGTTCG 57.562 33.333 0.00 0.00 41.68 3.95
315 316 9.125026 GGAGAAATTATCAGTGGTATTCAATGT 57.875 33.333 0.77 0.00 41.68 2.71
316 317 9.123902 TGGAGAAATTATCAGTGGTATTCAATG 57.876 33.333 0.77 0.00 42.27 2.82
317 318 9.872684 ATGGAGAAATTATCAGTGGTATTCAAT 57.127 29.630 0.77 0.00 0.00 2.57
318 319 9.123902 CATGGAGAAATTATCAGTGGTATTCAA 57.876 33.333 0.77 0.00 0.00 2.69
319 320 8.493607 TCATGGAGAAATTATCAGTGGTATTCA 58.506 33.333 0.00 0.00 0.00 2.57
320 321 8.908786 TCATGGAGAAATTATCAGTGGTATTC 57.091 34.615 0.00 0.00 0.00 1.75
321 322 9.699410 TTTCATGGAGAAATTATCAGTGGTATT 57.301 29.630 0.00 0.00 41.17 1.89
335 336 4.196193 ACGTGTGAAGTTTCATGGAGAAA 58.804 39.130 0.00 0.00 43.71 2.52
336 337 3.804036 ACGTGTGAAGTTTCATGGAGAA 58.196 40.909 0.00 0.00 39.73 2.87
337 338 3.469008 ACGTGTGAAGTTTCATGGAGA 57.531 42.857 0.00 0.00 39.73 3.71
338 339 5.862924 ATTACGTGTGAAGTTTCATGGAG 57.137 39.130 0.00 0.00 39.73 3.86
339 340 7.156000 TCTAATTACGTGTGAAGTTTCATGGA 58.844 34.615 0.00 0.00 39.73 3.41
340 341 7.359262 TCTAATTACGTGTGAAGTTTCATGG 57.641 36.000 0.00 0.00 39.73 3.66
349 350 8.918658 GCCGAATATATTCTAATTACGTGTGAA 58.081 33.333 20.47 0.00 34.69 3.18
350 351 7.543172 GGCCGAATATATTCTAATTACGTGTGA 59.457 37.037 20.47 0.00 34.69 3.58
351 352 7.329962 TGGCCGAATATATTCTAATTACGTGTG 59.670 37.037 20.47 3.52 34.69 3.82
352 353 7.380536 TGGCCGAATATATTCTAATTACGTGT 58.619 34.615 20.47 0.00 34.69 4.49
353 354 7.821595 TGGCCGAATATATTCTAATTACGTG 57.178 36.000 20.47 4.56 34.69 4.49
354 355 8.038944 ACATGGCCGAATATATTCTAATTACGT 58.961 33.333 20.47 8.84 34.69 3.57
355 356 8.420374 ACATGGCCGAATATATTCTAATTACG 57.580 34.615 20.47 8.30 34.69 3.18
358 359 9.342308 CCATACATGGCCGAATATATTCTAATT 57.658 33.333 20.47 2.47 41.75 1.40
359 360 8.908786 CCATACATGGCCGAATATATTCTAAT 57.091 34.615 20.47 8.07 41.75 1.73
376 377 8.681486 TTCTGAAAAGATCCATACCATACATG 57.319 34.615 0.00 0.00 0.00 3.21
377 378 9.872684 AATTCTGAAAAGATCCATACCATACAT 57.127 29.630 0.00 0.00 0.00 2.29
392 393 9.298774 GCTGGAAGATCAAATAATTCTGAAAAG 57.701 33.333 0.00 0.00 34.07 2.27
393 394 8.253113 GGCTGGAAGATCAAATAATTCTGAAAA 58.747 33.333 0.00 0.00 34.07 2.29
394 395 7.616935 AGGCTGGAAGATCAAATAATTCTGAAA 59.383 33.333 0.00 0.00 34.07 2.69
395 396 7.121382 AGGCTGGAAGATCAAATAATTCTGAA 58.879 34.615 0.00 0.00 34.07 3.02
396 397 6.666678 AGGCTGGAAGATCAAATAATTCTGA 58.333 36.000 0.00 0.00 34.07 3.27
397 398 6.956202 AGGCTGGAAGATCAAATAATTCTG 57.044 37.500 0.00 0.00 34.07 3.02
398 399 7.968014 AAAGGCTGGAAGATCAAATAATTCT 57.032 32.000 0.00 0.00 34.07 2.40
435 436 9.800433 CCATGCGCATCCATTATAAATTATAAA 57.200 29.630 22.51 0.00 34.59 1.40
436 437 9.183368 TCCATGCGCATCCATTATAAATTATAA 57.817 29.630 22.51 7.78 35.32 0.98
437 438 8.744568 TCCATGCGCATCCATTATAAATTATA 57.255 30.769 22.51 0.00 0.00 0.98
438 439 7.643569 TCCATGCGCATCCATTATAAATTAT 57.356 32.000 22.51 0.00 0.00 1.28
439 440 7.312154 GTTCCATGCGCATCCATTATAAATTA 58.688 34.615 22.51 0.00 0.00 1.40
440 441 5.981088 TCCATGCGCATCCATTATAAATT 57.019 34.783 22.51 0.00 0.00 1.82
441 442 5.336690 GGTTCCATGCGCATCCATTATAAAT 60.337 40.000 22.51 0.00 0.00 1.40
442 443 4.022416 GGTTCCATGCGCATCCATTATAAA 60.022 41.667 22.51 3.24 0.00 1.40
443 444 3.505680 GGTTCCATGCGCATCCATTATAA 59.494 43.478 22.51 4.29 0.00 0.98
444 445 3.081061 GGTTCCATGCGCATCCATTATA 58.919 45.455 22.51 0.00 0.00 0.98
445 446 1.888512 GGTTCCATGCGCATCCATTAT 59.111 47.619 22.51 0.00 0.00 1.28
446 447 1.317613 GGTTCCATGCGCATCCATTA 58.682 50.000 22.51 0.90 0.00 1.90
447 448 0.683828 TGGTTCCATGCGCATCCATT 60.684 50.000 22.51 0.00 0.00 3.16
448 449 1.076850 TGGTTCCATGCGCATCCAT 60.077 52.632 22.51 0.00 0.00 3.41
449 450 1.750018 CTGGTTCCATGCGCATCCA 60.750 57.895 22.51 22.70 0.00 3.41
450 451 2.484062 CCTGGTTCCATGCGCATCC 61.484 63.158 22.51 19.11 0.00 3.51
451 452 1.315257 AACCTGGTTCCATGCGCATC 61.315 55.000 22.51 9.29 0.00 3.91
452 453 1.304381 AACCTGGTTCCATGCGCAT 60.304 52.632 19.28 19.28 0.00 4.73
453 454 1.971167 GAACCTGGTTCCATGCGCA 60.971 57.895 25.74 14.96 36.65 6.09
454 455 2.877691 GAACCTGGTTCCATGCGC 59.122 61.111 25.74 0.00 36.65 6.09
475 476 8.418662 GTTAGTTTTAGGGACAATGGTCTTTTT 58.581 33.333 0.00 0.00 43.77 1.94
476 477 7.014905 GGTTAGTTTTAGGGACAATGGTCTTTT 59.985 37.037 0.00 0.00 43.77 2.27
477 478 6.492429 GGTTAGTTTTAGGGACAATGGTCTTT 59.508 38.462 0.00 0.00 43.77 2.52
478 479 6.008331 GGTTAGTTTTAGGGACAATGGTCTT 58.992 40.000 0.00 0.00 43.77 3.01
479 480 5.516062 GGGTTAGTTTTAGGGACAATGGTCT 60.516 44.000 0.00 0.00 43.77 3.85
480 481 4.703575 GGGTTAGTTTTAGGGACAATGGTC 59.296 45.833 0.00 0.00 43.55 4.02
481 482 4.106663 TGGGTTAGTTTTAGGGACAATGGT 59.893 41.667 0.00 0.00 0.00 3.55
482 483 4.668636 TGGGTTAGTTTTAGGGACAATGG 58.331 43.478 0.00 0.00 0.00 3.16
483 484 6.850752 AATGGGTTAGTTTTAGGGACAATG 57.149 37.500 0.00 0.00 0.00 2.82
484 485 7.865530 AAAATGGGTTAGTTTTAGGGACAAT 57.134 32.000 0.00 0.00 0.00 2.71
485 486 7.678207 AAAAATGGGTTAGTTTTAGGGACAA 57.322 32.000 0.00 0.00 35.05 3.18
525 526 9.701098 AGTCGTCTGTGTCATTTAAACTTATTA 57.299 29.630 0.00 0.00 0.00 0.98
526 527 8.603242 AGTCGTCTGTGTCATTTAAACTTATT 57.397 30.769 0.00 0.00 0.00 1.40
527 528 8.495949 CAAGTCGTCTGTGTCATTTAAACTTAT 58.504 33.333 0.00 0.00 0.00 1.73
535 536 3.531538 ACACAAGTCGTCTGTGTCATTT 58.468 40.909 12.12 0.00 42.32 2.32
538 539 4.320714 GGTATACACAAGTCGTCTGTGTCA 60.321 45.833 18.43 9.15 44.45 3.58
539 540 4.164294 GGTATACACAAGTCGTCTGTGTC 58.836 47.826 18.43 8.66 44.45 3.67
540 541 3.365666 CGGTATACACAAGTCGTCTGTGT 60.366 47.826 18.74 18.74 46.76 3.72
541 542 3.120095 TCGGTATACACAAGTCGTCTGTG 60.120 47.826 5.01 11.09 39.26 3.66
545 546 2.842485 CGTTCGGTATACACAAGTCGTC 59.158 50.000 5.01 0.00 0.00 4.20
558 559 1.448893 GGCATGCCTTCGTTCGGTA 60.449 57.895 29.98 0.00 0.00 4.02
632 635 2.104530 GTTCCCGCTCCTCGCTAC 59.895 66.667 0.00 0.00 36.73 3.58
636 639 3.382832 ACCTGTTCCCGCTCCTCG 61.383 66.667 0.00 0.00 38.08 4.63
671 674 2.590007 CTGTCTATGCGCCTGGGC 60.590 66.667 4.18 0.00 37.85 5.36
765 778 5.529014 CCAAGAAAATGGCGGTAAAAATG 57.471 39.130 0.00 0.00 32.78 2.32
862 889 0.975887 GGGGATGGATGAGAGAGAGC 59.024 60.000 0.00 0.00 0.00 4.09
904 932 5.367644 TGTGGATCTGGATGAATGTGAGTAT 59.632 40.000 0.00 0.00 0.00 2.12
912 940 3.071312 GCTCTCTGTGGATCTGGATGAAT 59.929 47.826 0.00 0.00 0.00 2.57
932 960 2.405594 GACGATCTCGCTGTCGCT 59.594 61.111 0.00 0.00 44.43 4.93
937 965 0.029433 TTGATCCGACGATCTCGCTG 59.971 55.000 0.00 0.00 44.61 5.18
1238 1277 3.190738 TTGGACCTGGCGGACTTGG 62.191 63.158 0.00 0.00 0.00 3.61
1239 1278 1.672356 CTTGGACCTGGCGGACTTG 60.672 63.158 0.00 0.00 0.00 3.16
1240 1279 2.750350 CTTGGACCTGGCGGACTT 59.250 61.111 0.00 0.00 0.00 3.01
1241 1280 3.322466 CCTTGGACCTGGCGGACT 61.322 66.667 0.00 0.00 0.00 3.85
1242 1281 3.607370 GACCTTGGACCTGGCGGAC 62.607 68.421 0.00 0.00 0.00 4.79
1323 1401 2.766400 CGCCTCGTCCTCTGAGTCC 61.766 68.421 3.66 0.00 0.00 3.85
1329 1410 3.999297 GACCTCCGCCTCGTCCTCT 62.999 68.421 0.00 0.00 0.00 3.69
1380 1461 1.751351 GAGTCCTCGTCATCATCCACA 59.249 52.381 0.00 0.00 0.00 4.17
1455 1536 4.314440 ACGCGCTTCCTCTTGGCA 62.314 61.111 5.73 0.00 0.00 4.92
1583 1664 3.126879 CCGCCGCAGCATCAGAAA 61.127 61.111 0.00 0.00 39.83 2.52
1763 1898 3.938963 AGCGACAGAACTGACAAAAAGAA 59.061 39.130 8.87 0.00 0.00 2.52
1940 2314 8.785329 ATTTTAGGAAGACTTTCAGATCTCAC 57.215 34.615 0.00 0.00 34.90 3.51
1976 2354 0.770499 TCCAGACCATGCCTCAACAA 59.230 50.000 0.00 0.00 0.00 2.83
2084 2799 8.391106 GCAGTACAGGAACTACTAAATCATTTG 58.609 37.037 0.00 0.00 36.02 2.32
2154 2869 3.747010 ACGAACATACCAATTACACGCAA 59.253 39.130 0.00 0.00 0.00 4.85
2193 2908 9.934190 GTACATGAACTACTTTTTCGGTAAAAA 57.066 29.630 0.00 0.00 41.21 1.94
2194 2909 9.328845 AGTACATGAACTACTTTTTCGGTAAAA 57.671 29.630 0.00 0.00 34.64 1.52
2195 2910 8.767085 CAGTACATGAACTACTTTTTCGGTAAA 58.233 33.333 0.00 0.00 0.00 2.01
2196 2911 7.927629 ACAGTACATGAACTACTTTTTCGGTAA 59.072 33.333 0.00 0.00 0.00 2.85
2197 2912 7.383029 CACAGTACATGAACTACTTTTTCGGTA 59.617 37.037 0.00 0.00 0.00 4.02
2198 2913 6.202188 CACAGTACATGAACTACTTTTTCGGT 59.798 38.462 0.00 0.00 0.00 4.69
2199 2914 6.422701 TCACAGTACATGAACTACTTTTTCGG 59.577 38.462 0.00 0.00 0.00 4.30
2200 2915 7.402811 TCACAGTACATGAACTACTTTTTCG 57.597 36.000 0.00 0.00 0.00 3.46
2201 2916 9.209175 AGATCACAGTACATGAACTACTTTTTC 57.791 33.333 0.00 0.00 28.32 2.29
2209 2924 9.507329 ACATTTTTAGATCACAGTACATGAACT 57.493 29.630 0.00 12.51 34.07 3.01
2218 2933 9.850628 CATCATCAAACATTTTTAGATCACAGT 57.149 29.630 0.00 0.00 0.00 3.55
2219 2934 9.850628 ACATCATCAAACATTTTTAGATCACAG 57.149 29.630 0.00 0.00 0.00 3.66
2226 2941 9.801714 GCAAGAAACATCATCAAACATTTTTAG 57.198 29.630 0.00 0.00 0.00 1.85
2283 2998 7.170320 ACTTGAATTCACTTTGCAATTCACATC 59.830 33.333 7.89 1.25 44.77 3.06
2386 3102 6.596497 ACATGATTTTTCATTCCAGCATTTCC 59.404 34.615 0.00 0.00 0.00 3.13
2517 3235 7.797121 TGATTAAGATATAGGAGCATGGACA 57.203 36.000 0.00 0.00 0.00 4.02
2518 3236 9.678260 ATTTGATTAAGATATAGGAGCATGGAC 57.322 33.333 0.00 0.00 0.00 4.02
2519 3237 9.896645 GATTTGATTAAGATATAGGAGCATGGA 57.103 33.333 0.00 0.00 0.00 3.41
2520 3238 9.118300 GGATTTGATTAAGATATAGGAGCATGG 57.882 37.037 0.00 0.00 0.00 3.66
2522 3240 9.066842 AGGGATTTGATTAAGATATAGGAGCAT 57.933 33.333 0.00 0.00 0.00 3.79
2523 3241 8.454859 AGGGATTTGATTAAGATATAGGAGCA 57.545 34.615 0.00 0.00 0.00 4.26
2524 3242 8.543774 TGAGGGATTTGATTAAGATATAGGAGC 58.456 37.037 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.