Multiple sequence alignment - TraesCS4A01G419600

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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 TraesCS4A01G419600 chr4A 100.000 6102 0 0 1 6102 690408648 690414749 0.000000e+00 11269.0
1 TraesCS4A01G419600 chr4A 94.014 3458 132 25 2695 6102 690621655 690618223 0.000000e+00 5169.0
2 TraesCS4A01G419600 chr4A 91.230 878 38 21 878 1742 690623586 690622735 0.000000e+00 1158.0
3 TraesCS4A01G419600 chr4A 93.320 509 32 2 2185 2692 690622257 690621750 0.000000e+00 750.0
4 TraesCS4A01G419600 chr4A 91.469 422 18 6 1742 2145 690622681 690622260 1.150000e-156 564.0
5 TraesCS4A01G419600 chr4A 91.795 195 16 0 1888 2082 690620232 690620038 7.790000e-69 272.0
6 TraesCS4A01G419600 chr4A 92.228 193 11 4 267 457 670838470 670838280 2.800000e-68 270.0
7 TraesCS4A01G419600 chr4A 75.207 242 56 4 3048 3288 294121064 294121302 1.800000e-20 111.0
8 TraesCS4A01G419600 chr4A 74.380 242 57 5 3048 3288 741112214 741112451 1.400000e-16 99.0
9 TraesCS4A01G419600 chr4A 97.059 34 1 0 183 216 123256706 123256739 2.380000e-04 58.4
10 TraesCS4A01G419600 chr7D 93.357 3869 182 26 1741 5553 34372401 34376250 0.000000e+00 5651.0
11 TraesCS4A01G419600 chr7D 90.251 1836 118 19 4166 5954 34471631 34473452 0.000000e+00 2342.0
12 TraesCS4A01G419600 chr7D 92.160 1620 80 22 913 2507 34758896 34757299 0.000000e+00 2244.0
13 TraesCS4A01G419600 chr7D 97.480 1230 22 3 2786 4006 34756490 34755261 0.000000e+00 2091.0
14 TraesCS4A01G419600 chr7D 92.889 1111 51 4 4046 5131 34755262 34754155 0.000000e+00 1589.0
15 TraesCS4A01G419600 chr7D 94.854 855 41 2 5129 5981 34754071 34753218 0.000000e+00 1332.0
16 TraesCS4A01G419600 chr7D 86.629 875 64 32 898 1742 34470486 34471337 0.000000e+00 918.0
17 TraesCS4A01G419600 chr7D 90.000 730 37 22 929 1637 34371596 34372310 0.000000e+00 911.0
18 TraesCS4A01G419600 chr7D 91.803 610 29 5 5481 6077 34376251 34376852 0.000000e+00 830.0
19 TraesCS4A01G419600 chr7D 96.694 242 7 1 2564 2804 34757097 34756856 9.530000e-108 401.0
20 TraesCS4A01G419600 chr7D 90.508 295 24 1 1784 2078 34471450 34471740 2.670000e-103 387.0
21 TraesCS4A01G419600 chr7D 92.857 196 13 1 1888 2082 34755200 34755005 3.600000e-72 283.0
22 TraesCS4A01G419600 chr7D 92.308 195 15 0 1888 2082 34374779 34374973 1.680000e-70 278.0
23 TraesCS4A01G419600 chr7D 89.781 137 6 5 5966 6102 34753129 34753001 1.050000e-37 169.0
24 TraesCS4A01G419600 chr7D 100.000 32 0 0 883 914 34470458 34470489 6.610000e-05 60.2
25 TraesCS4A01G419600 chr7A 91.996 2024 79 30 4090 6077 35001823 34999847 0.000000e+00 2763.0
26 TraesCS4A01G419600 chr7A 92.002 1813 103 24 4268 6077 34744682 34746455 0.000000e+00 2507.0
27 TraesCS4A01G419600 chr7A 89.419 860 46 15 5232 6077 34963750 34962922 0.000000e+00 1042.0
28 TraesCS4A01G419600 chr7A 89.034 766 57 14 884 1637 35003033 35002283 0.000000e+00 924.0
29 TraesCS4A01G419600 chr7A 86.220 820 65 22 879 1688 34743402 34744183 0.000000e+00 845.0
30 TraesCS4A01G419600 chr7A 87.458 295 30 4 1784 2078 34744376 34744663 3.520000e-87 333.0
31 TraesCS4A01G419600 chr7A 81.292 449 43 29 429 870 34742896 34743310 5.900000e-85 326.0
32 TraesCS4A01G419600 chr7A 92.308 195 15 0 1888 2082 35001806 35001612 1.680000e-70 278.0
33 TraesCS4A01G419600 chr7A 85.217 230 18 10 21 235 34742581 34742809 7.960000e-54 222.0
34 TraesCS4A01G419600 chr7A 84.358 179 12 6 1741 1903 35002019 35001841 1.760000e-35 161.0
35 TraesCS4A01G419600 chr7A 75.207 242 56 4 3048 3288 694787522 694787760 1.800000e-20 111.0
36 TraesCS4A01G419600 chr7A 74.486 243 56 6 3048 3288 605159971 605160209 3.890000e-17 100.0
37 TraesCS4A01G419600 chr2B 95.262 401 18 1 4268 4668 704812733 704813132 8.630000e-178 634.0
38 TraesCS4A01G419600 chr2B 86.765 272 27 4 1205 1469 704812365 704812634 1.660000e-75 294.0
39 TraesCS4A01G419600 chr2B 98.171 164 3 0 283 446 548626817 548626654 2.780000e-73 287.0
40 TraesCS4A01G419600 chr7B 96.067 178 7 0 280 457 705310600 705310777 2.150000e-74 291.0
41 TraesCS4A01G419600 chr6B 96.045 177 7 0 280 456 606434020 606433844 7.740000e-74 289.0
42 TraesCS4A01G419600 chr6B 96.045 177 6 1 275 451 160905311 160905136 2.780000e-73 287.0
43 TraesCS4A01G419600 chr6B 77.143 175 29 10 69 236 349466366 349466196 2.340000e-14 91.6
44 TraesCS4A01G419600 chr5B 97.041 169 5 0 278 446 497454794 497454962 1.000000e-72 285.0
45 TraesCS4A01G419600 chr5B 95.506 178 7 1 282 458 221204313 221204136 3.600000e-72 283.0
46 TraesCS4A01G419600 chr5A 95.000 180 6 3 276 453 290391868 290391690 4.660000e-71 279.0
47 TraesCS4A01G419600 chr6A 87.168 226 22 7 280 499 85270642 85270418 3.650000e-62 250.0
48 TraesCS4A01G419600 chr6A 97.059 34 0 1 186 218 15634282 15634315 8.540000e-04 56.5
49 TraesCS4A01G419600 chr4B 95.513 156 6 1 2642 2796 106227408 106227563 1.310000e-61 248.0
50 TraesCS4A01G419600 chr4B 93.711 159 9 1 2637 2794 438375175 438375333 2.840000e-58 237.0
51 TraesCS4A01G419600 chr4D 94.268 157 7 2 2642 2796 74079350 74079506 7.900000e-59 239.0
52 TraesCS4A01G419600 chr4D 76.871 147 24 9 136 276 1674533 1674675 2.360000e-09 75.0
53 TraesCS4A01G419600 chr6D 94.156 154 8 1 2643 2795 392273074 392273227 3.680000e-57 233.0
54 TraesCS4A01G419600 chr2A 93.168 161 8 3 2643 2801 141506470 141506311 3.680000e-57 233.0
55 TraesCS4A01G419600 chr2A 78.889 90 15 4 133 218 43498146 43498235 2.380000e-04 58.4
56 TraesCS4A01G419600 chr2A 89.362 47 1 4 186 228 496464891 496464845 8.540000e-04 56.5
57 TraesCS4A01G419600 chr1A 94.156 154 8 1 2642 2794 395177602 395177449 3.680000e-57 233.0
58 TraesCS4A01G419600 chr1A 74.525 263 62 5 3051 3312 265913116 265912858 6.470000e-20 110.0
59 TraesCS4A01G419600 chr1D 72.531 557 125 24 2878 3417 18932829 18933374 8.190000e-34 156.0
60 TraesCS4A01G419600 chr3D 76.033 242 54 4 3051 3291 312379609 312379371 8.310000e-24 122.0
61 TraesCS4A01G419600 chr3A 81.746 126 14 6 4169 4287 474433935 474433812 5.030000e-16 97.1
62 TraesCS4A01G419600 chr3A 96.970 33 0 1 186 217 590595731 590595763 3.000000e-03 54.7
63 TraesCS4A01G419600 chr3B 96.970 33 0 1 187 218 508469401 508469433 3.000000e-03 54.7


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 TraesCS4A01G419600 chr4A 690408648 690414749 6101 False 11269.000000 11269 100.000000 1 6102 1 chr4A.!!$F3 6101
1 TraesCS4A01G419600 chr4A 690618223 690623586 5363 True 1582.600000 5169 92.365600 878 6102 5 chr4A.!!$R2 5224
2 TraesCS4A01G419600 chr7D 34371596 34376852 5256 False 1917.500000 5651 91.867000 929 6077 4 chr7D.!!$F1 5148
3 TraesCS4A01G419600 chr7D 34753001 34758896 5895 True 1158.428571 2244 93.816429 913 6102 7 chr7D.!!$R1 5189
4 TraesCS4A01G419600 chr7D 34470458 34473452 2994 False 926.800000 2342 91.847000 883 5954 4 chr7D.!!$F2 5071
5 TraesCS4A01G419600 chr7A 34962922 34963750 828 True 1042.000000 1042 89.419000 5232 6077 1 chr7A.!!$R1 845
6 TraesCS4A01G419600 chr7A 34999847 35003033 3186 True 1031.500000 2763 89.424000 884 6077 4 chr7A.!!$R2 5193
7 TraesCS4A01G419600 chr7A 34742581 34746455 3874 False 846.600000 2507 86.437800 21 6077 5 chr7A.!!$F3 6056
8 TraesCS4A01G419600 chr2B 704812365 704813132 767 False 464.000000 634 91.013500 1205 4668 2 chr2B.!!$F1 3463

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
22 23 0.108992 GACCGTCCAGTATTGTCGCA 60.109 55.000 0.00 0.00 0.00 5.10 F
873 893 0.668535 CGTCTGGATGGCGTCATCTA 59.331 55.000 27.71 21.90 46.70 1.98 F
2316 2948 0.322098 TACGCAACCACCCTCCATTG 60.322 55.000 0.00 0.00 0.00 2.82 F
3621 4885 0.391597 TCCAGTTGACACCGGTTCTC 59.608 55.000 2.97 2.64 0.00 2.87 F
4208 5497 1.000607 TCAGTACACGTCTGGTTCTGC 60.001 52.381 6.35 0.00 34.15 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1389 1568 1.281960 CCCGTAGTCATACTCCGCG 59.718 63.158 0.00 0.00 0.00 6.46 R
2507 3140 1.199615 GGGAGAGGAGGGTGAAGAAG 58.800 60.000 0.00 0.00 0.00 2.85 R
4167 5432 0.179076 TCGTGCATCATGGGCTAGTG 60.179 55.000 10.83 0.62 0.00 2.74 R
4999 6315 1.041437 AGGATTGCGTACCTAGCCTC 58.959 55.000 0.00 0.00 28.72 4.70 R
5774 7294 0.332632 TTGCTTGGGAATGGCTAGCT 59.667 50.000 15.72 0.00 33.15 3.32 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
22 23 0.108992 GACCGTCCAGTATTGTCGCA 60.109 55.000 0.00 0.00 0.00 5.10
45 46 6.471839 CATGTCTTTTTCTGCTTTGTTTGTG 58.528 36.000 0.00 0.00 0.00 3.33
57 58 3.570926 TTGTTTGTGCCACACGTTTTA 57.429 38.095 0.00 0.00 37.14 1.52
60 61 4.106197 TGTTTGTGCCACACGTTTTATTC 58.894 39.130 0.00 0.00 37.14 1.75
69 70 7.593644 GTGCCACACGTTTTATTCTCTTTATTT 59.406 33.333 0.00 0.00 0.00 1.40
118 128 8.746052 TTGGTTTCTTTCTTCATTTCTCTACA 57.254 30.769 0.00 0.00 0.00 2.74
126 136 8.675705 TTTCTTCATTTCTCTACAACACATGA 57.324 30.769 0.00 0.00 0.00 3.07
137 147 6.437928 TCTACAACACATGACTGCATTTTTC 58.562 36.000 0.00 0.00 30.68 2.29
138 148 4.043750 ACAACACATGACTGCATTTTTCG 58.956 39.130 0.00 0.00 30.68 3.46
158 168 9.544314 TTTTTCGTACACATTATACAATTTCCG 57.456 29.630 0.00 0.00 0.00 4.30
161 171 8.923609 TCGTACACATTATACAATTTCCGTAA 57.076 30.769 0.00 0.00 0.00 3.18
162 172 8.806634 TCGTACACATTATACAATTTCCGTAAC 58.193 33.333 0.00 0.00 0.00 2.50
163 173 8.593842 CGTACACATTATACAATTTCCGTAACA 58.406 33.333 0.00 0.00 0.00 2.41
166 176 8.238631 ACACATTATACAATTTCCGTAACAACC 58.761 33.333 0.00 0.00 0.00 3.77
245 261 9.905713 AATATATGTTTTCATGTGTGTCTACCT 57.094 29.630 0.00 0.00 41.09 3.08
294 310 8.716674 TTTTGTATATATCTACTCCCTCCGTT 57.283 34.615 0.00 0.00 0.00 4.44
297 313 5.799978 ATATATCTACTCCCTCCGTTCCT 57.200 43.478 0.00 0.00 0.00 3.36
298 314 6.905067 ATATATCTACTCCCTCCGTTCCTA 57.095 41.667 0.00 0.00 0.00 2.94
301 317 3.359950 TCTACTCCCTCCGTTCCTAAAC 58.640 50.000 0.00 0.00 0.00 2.01
304 320 2.910977 ACTCCCTCCGTTCCTAAACATT 59.089 45.455 0.00 0.00 34.93 2.71
305 321 3.329814 ACTCCCTCCGTTCCTAAACATTT 59.670 43.478 0.00 0.00 34.93 2.32
307 323 3.073356 TCCCTCCGTTCCTAAACATTTGT 59.927 43.478 0.00 0.00 34.93 2.83
309 325 4.324267 CCTCCGTTCCTAAACATTTGTCT 58.676 43.478 0.00 0.00 34.93 3.41
312 328 6.308371 TCCGTTCCTAAACATTTGTCTTTC 57.692 37.500 0.00 0.00 34.93 2.62
314 330 7.218614 TCCGTTCCTAAACATTTGTCTTTCTA 58.781 34.615 0.00 0.00 34.93 2.10
315 331 7.386848 TCCGTTCCTAAACATTTGTCTTTCTAG 59.613 37.037 0.00 0.00 34.93 2.43
316 332 7.386848 CCGTTCCTAAACATTTGTCTTTCTAGA 59.613 37.037 0.00 0.00 34.93 2.43
317 333 8.436200 CGTTCCTAAACATTTGTCTTTCTAGAG 58.564 37.037 0.00 0.00 34.93 2.43
329 345 9.573166 TTTGTCTTTCTAGAGATTTCAAATGGA 57.427 29.630 0.00 0.00 0.00 3.41
330 346 8.553459 TGTCTTTCTAGAGATTTCAAATGGAC 57.447 34.615 0.00 0.00 0.00 4.02
331 347 8.378565 TGTCTTTCTAGAGATTTCAAATGGACT 58.621 33.333 0.00 0.00 0.00 3.85
332 348 9.877178 GTCTTTCTAGAGATTTCAAATGGACTA 57.123 33.333 0.00 0.00 0.00 2.59
335 351 9.436957 TTTCTAGAGATTTCAAATGGACTACAC 57.563 33.333 0.00 0.00 0.00 2.90
337 353 8.762645 TCTAGAGATTTCAAATGGACTACACAT 58.237 33.333 0.00 0.00 0.00 3.21
339 355 8.723942 AGAGATTTCAAATGGACTACACATAC 57.276 34.615 0.00 0.00 0.00 2.39
340 356 8.321353 AGAGATTTCAAATGGACTACACATACA 58.679 33.333 0.00 0.00 0.00 2.29
341 357 8.498054 AGATTTCAAATGGACTACACATACAG 57.502 34.615 0.00 0.00 0.00 2.74
342 358 8.321353 AGATTTCAAATGGACTACACATACAGA 58.679 33.333 0.00 0.00 0.00 3.41
343 359 9.113838 GATTTCAAATGGACTACACATACAGAT 57.886 33.333 0.00 0.00 0.00 2.90
344 360 7.848223 TTCAAATGGACTACACATACAGATG 57.152 36.000 0.00 0.00 39.16 2.90
347 363 8.704668 TCAAATGGACTACACATACAGATGTAT 58.295 33.333 0.00 0.00 44.82 2.29
348 364 9.981114 CAAATGGACTACACATACAGATGTATA 57.019 33.333 5.21 0.00 44.82 1.47
387 403 9.323985 AGAGTATAGATTCACTCATTTTGCTTC 57.676 33.333 4.70 0.00 42.99 3.86
388 404 8.136057 AGTATAGATTCACTCATTTTGCTTCG 57.864 34.615 0.00 0.00 0.00 3.79
389 405 6.992063 ATAGATTCACTCATTTTGCTTCGT 57.008 33.333 0.00 0.00 0.00 3.85
390 406 9.031360 GTATAGATTCACTCATTTTGCTTCGTA 57.969 33.333 0.00 0.00 0.00 3.43
391 407 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
392 408 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
393 409 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
394 410 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
395 411 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
396 412 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
397 413 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
398 414 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
399 415 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
400 416 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
401 417 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
402 418 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
403 419 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
404 420 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
405 421 4.684242 TGCTTCGTATGTAGTCACTTGTTG 59.316 41.667 0.00 0.00 0.00 3.33
406 422 4.921515 GCTTCGTATGTAGTCACTTGTTGA 59.078 41.667 0.00 0.00 0.00 3.18
407 423 5.404366 GCTTCGTATGTAGTCACTTGTTGAA 59.596 40.000 0.00 0.00 35.39 2.69
408 424 6.073980 GCTTCGTATGTAGTCACTTGTTGAAA 60.074 38.462 0.00 0.00 35.39 2.69
409 425 7.360101 GCTTCGTATGTAGTCACTTGTTGAAAT 60.360 37.037 0.00 0.00 35.39 2.17
410 426 7.576750 TCGTATGTAGTCACTTGTTGAAATC 57.423 36.000 0.00 0.00 35.39 2.17
411 427 7.375834 TCGTATGTAGTCACTTGTTGAAATCT 58.624 34.615 0.00 0.00 35.39 2.40
412 428 7.541091 TCGTATGTAGTCACTTGTTGAAATCTC 59.459 37.037 0.00 0.00 35.39 2.75
413 429 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
414 430 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
415 431 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
416 432 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
417 433 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
418 434 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
419 435 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
420 436 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
421 437 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
422 438 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
423 439 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
424 440 9.050601 ACTTGTTGAAATCTCTAGAAAGACAAG 57.949 33.333 17.75 17.75 33.18 3.16
425 441 8.964476 TTGTTGAAATCTCTAGAAAGACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
446 462 5.139001 AGTATTTAGGAACGGAGGGAGTAG 58.861 45.833 0.00 0.00 0.00 2.57
447 463 3.463048 TTTAGGAACGGAGGGAGTAGT 57.537 47.619 0.00 0.00 0.00 2.73
448 464 4.591321 TTTAGGAACGGAGGGAGTAGTA 57.409 45.455 0.00 0.00 0.00 1.82
449 465 4.803329 TTAGGAACGGAGGGAGTAGTAT 57.197 45.455 0.00 0.00 0.00 2.12
450 466 5.912149 TTAGGAACGGAGGGAGTAGTATA 57.088 43.478 0.00 0.00 0.00 1.47
451 467 6.460103 TTAGGAACGGAGGGAGTAGTATAT 57.540 41.667 0.00 0.00 0.00 0.86
453 469 5.713807 AGGAACGGAGGGAGTAGTATATTT 58.286 41.667 0.00 0.00 0.00 1.40
454 470 5.774184 AGGAACGGAGGGAGTAGTATATTTC 59.226 44.000 0.00 0.00 0.00 2.17
455 471 5.537674 GGAACGGAGGGAGTAGTATATTTCA 59.462 44.000 0.00 0.00 0.00 2.69
456 472 6.210984 GGAACGGAGGGAGTAGTATATTTCAT 59.789 42.308 0.00 0.00 0.00 2.57
457 473 7.395489 GGAACGGAGGGAGTAGTATATTTCATA 59.605 40.741 0.00 0.00 0.00 2.15
458 474 8.896722 AACGGAGGGAGTAGTATATTTCATAT 57.103 34.615 0.00 0.00 0.00 1.78
459 475 8.294954 ACGGAGGGAGTAGTATATTTCATATG 57.705 38.462 0.00 0.00 0.00 1.78
460 476 8.114102 ACGGAGGGAGTAGTATATTTCATATGA 58.886 37.037 0.00 0.00 0.00 2.15
461 477 8.967918 CGGAGGGAGTAGTATATTTCATATGAA 58.032 37.037 14.23 14.23 0.00 2.57
577 594 9.603921 ATTGAAAGAATGTCACAGAAATTTTGT 57.396 25.926 0.00 0.00 27.02 2.83
578 595 9.434420 TTGAAAGAATGTCACAGAAATTTTGTT 57.566 25.926 0.00 0.00 27.02 2.83
579 596 9.434420 TGAAAGAATGTCACAGAAATTTTGTTT 57.566 25.926 0.00 0.00 0.00 2.83
580 597 9.906111 GAAAGAATGTCACAGAAATTTTGTTTC 57.094 29.630 0.00 1.15 0.00 2.78
581 598 9.657419 AAAGAATGTCACAGAAATTTTGTTTCT 57.343 25.926 0.00 3.14 39.16 2.52
594 611 9.929722 GAAATTTTGTTTCTGACCCATTAAAAC 57.070 29.630 0.00 0.00 0.00 2.43
719 737 7.076842 TGAACATCTATTAAAAGCAGAGCAC 57.923 36.000 0.00 0.00 0.00 4.40
722 740 7.636150 ACATCTATTAAAAGCAGAGCACATT 57.364 32.000 0.00 0.00 0.00 2.71
723 741 8.059798 ACATCTATTAAAAGCAGAGCACATTT 57.940 30.769 0.00 0.00 0.00 2.32
732 752 4.641396 AGCAGAGCACATTTTAGTACACA 58.359 39.130 0.00 0.00 0.00 3.72
747 767 9.534565 TTTTAGTACACAGCATTTGCATTTTTA 57.465 25.926 5.20 0.00 45.16 1.52
751 771 9.054922 AGTACACAGCATTTGCATTTTTAAAAT 57.945 25.926 0.55 0.00 45.16 1.82
755 775 7.006387 CACAGCATTTGCATTTTTAAAATACGC 59.994 33.333 0.55 4.47 45.16 4.42
764 784 8.219769 TGCATTTTTAAAATACGCAATGAACAG 58.780 29.630 11.35 0.00 0.00 3.16
776 796 7.216920 ACGCAATGAACAGTTTTTAGAAAAC 57.783 32.000 7.93 7.93 0.00 2.43
778 798 7.544217 ACGCAATGAACAGTTTTTAGAAAACTT 59.456 29.630 14.27 3.76 38.32 2.66
830 850 9.582431 TGTATCTGGTATTTTCGAAAGTAGAAG 57.418 33.333 12.80 12.64 0.00 2.85
831 851 9.798994 GTATCTGGTATTTTCGAAAGTAGAAGA 57.201 33.333 18.97 18.97 0.00 2.87
870 890 2.202932 GCGTCTGGATGGCGTCAT 60.203 61.111 0.00 0.00 46.81 3.06
873 893 0.668535 CGTCTGGATGGCGTCATCTA 59.331 55.000 27.71 21.90 46.70 1.98
874 894 1.270826 CGTCTGGATGGCGTCATCTAT 59.729 52.381 27.71 0.00 46.70 1.98
875 895 2.488153 CGTCTGGATGGCGTCATCTATA 59.512 50.000 27.71 13.40 46.70 1.31
876 896 3.426829 CGTCTGGATGGCGTCATCTATAG 60.427 52.174 27.71 21.72 46.70 1.31
1161 1297 4.189539 CCCCCTCTCCTCTCATCG 57.810 66.667 0.00 0.00 0.00 3.84
1171 1312 1.178534 CCTCTCATCGCCTCTCCTCC 61.179 65.000 0.00 0.00 0.00 4.30
1172 1313 1.514678 CTCTCATCGCCTCTCCTCCG 61.515 65.000 0.00 0.00 0.00 4.63
1174 1315 3.531207 CATCGCCTCTCCTCCGCA 61.531 66.667 0.00 0.00 0.00 5.69
1179 1320 4.504916 CCTCTCCTCCGCACGCTG 62.505 72.222 0.00 0.00 0.00 5.18
1180 1321 4.504916 CTCTCCTCCGCACGCTGG 62.505 72.222 0.00 0.00 0.00 4.85
1389 1568 0.593128 ATTGACCGTTGCAGCTGTTC 59.407 50.000 16.64 5.29 0.00 3.18
1398 1577 1.519455 GCAGCTGTTCGCGGAGTAT 60.519 57.895 16.64 0.00 45.59 2.12
1577 1757 4.174762 CCTACTAGGTTCTCTTTGTTCGC 58.825 47.826 0.00 0.00 0.00 4.70
1599 1779 2.094894 CCTTGCTTCGTAATGCTGTCAG 59.905 50.000 0.00 0.00 0.00 3.51
1615 1795 4.036567 TGTCAGTTGATATCGTAACCCG 57.963 45.455 0.00 0.00 38.13 5.28
1619 1799 6.035843 GTCAGTTGATATCGTAACCCGTTAA 58.964 40.000 0.00 0.00 37.94 2.01
1625 1805 7.467557 TGATATCGTAACCCGTTAAACATTC 57.532 36.000 0.00 0.00 37.94 2.67
1702 1882 5.565592 TCTAGTGAATCGTTAGGCGTTTA 57.434 39.130 0.00 0.00 42.13 2.01
1804 2361 5.351465 ACATCGTGTTCAGCTCGAAATTTAT 59.649 36.000 0.00 0.00 44.57 1.40
1899 2524 6.360329 GTCGGACTTTTGTGTTAAGTGTATG 58.640 40.000 0.00 0.00 36.04 2.39
2065 2696 4.521639 TCTGCTGAACTTCAATGAAAGCAT 59.478 37.500 17.19 0.00 38.41 3.79
2161 2793 4.383552 GCACCTAGATCTCTTCCATGTGTT 60.384 45.833 0.00 0.00 0.00 3.32
2164 2796 6.093219 CACCTAGATCTCTTCCATGTGTTTTG 59.907 42.308 0.00 0.00 0.00 2.44
2168 2800 9.388506 CTAGATCTCTTCCATGTGTTTTGTTAT 57.611 33.333 0.00 0.00 0.00 1.89
2216 2848 1.133915 GGTGTTTGGACTTGGACTCCA 60.134 52.381 0.00 0.00 35.91 3.86
2222 2854 1.255667 GGACTTGGACTCCAGCCGTA 61.256 60.000 0.00 0.00 33.81 4.02
2283 2915 0.610687 CCTTTCTCCTCTCGCCACTT 59.389 55.000 0.00 0.00 0.00 3.16
2298 2930 2.868839 GCCACTTCCACTACAACGCTTA 60.869 50.000 0.00 0.00 0.00 3.09
2316 2948 0.322098 TACGCAACCACCCTCCATTG 60.322 55.000 0.00 0.00 0.00 2.82
2360 2993 5.565637 CGACCAACATATATCTCCTCACCTG 60.566 48.000 0.00 0.00 0.00 4.00
2362 2995 4.285517 CCAACATATATCTCCTCACCTGCT 59.714 45.833 0.00 0.00 0.00 4.24
2363 2996 5.221803 CCAACATATATCTCCTCACCTGCTT 60.222 44.000 0.00 0.00 0.00 3.91
2384 3017 5.811100 GCTTCTTATCTACACTACACAACCC 59.189 44.000 0.00 0.00 0.00 4.11
2416 3049 7.123247 CACCTATTTCTTCACCTCAAAATCCAT 59.877 37.037 0.00 0.00 0.00 3.41
2438 3071 6.409695 CCATCTACACCTATTTCTCCACCATT 60.410 42.308 0.00 0.00 0.00 3.16
2442 3075 5.501156 ACACCTATTTCTCCACCATTTCTC 58.499 41.667 0.00 0.00 0.00 2.87
2485 3118 5.832595 TCTGAATCTACATCCTCTCCTTCTG 59.167 44.000 0.00 0.00 0.00 3.02
2486 3119 5.523588 TGAATCTACATCCTCTCCTTCTGT 58.476 41.667 0.00 0.00 0.00 3.41
2507 3140 8.008513 TCTGTAACATCCTCCACTAGTTATTC 57.991 38.462 0.00 0.00 0.00 1.75
2582 3360 1.329256 ACCATCCCGTCTAATCCTCG 58.671 55.000 0.00 0.00 0.00 4.63
2589 3367 1.663445 CCGTCTAATCCTCGTCGCATC 60.663 57.143 0.00 0.00 0.00 3.91
3531 4795 4.805609 GCAGATCCACTTCTGGTCTCTTTT 60.806 45.833 3.85 0.00 42.78 2.27
3621 4885 0.391597 TCCAGTTGACACCGGTTCTC 59.608 55.000 2.97 2.64 0.00 2.87
3666 4930 5.278957 CCTGTTTCTGACCCAACCTTTTATG 60.279 44.000 0.00 0.00 0.00 1.90
3826 5091 4.225942 TCTTAACCTTGGTCTGCATCTCAT 59.774 41.667 0.00 0.00 0.00 2.90
3980 5245 2.880890 GCACACTGTTTCCTGTTCATCT 59.119 45.455 0.00 0.00 0.00 2.90
4006 5271 5.982356 TGAAGCAGAATACTGAGCTATTGT 58.018 37.500 0.00 0.00 46.03 2.71
4072 5337 5.302823 AGTTTTTCAGGAATTTCACTCCAGG 59.697 40.000 0.00 0.00 35.20 4.45
4118 5383 1.749063 GCAGGGGGCTGTTAATTGTAC 59.251 52.381 0.00 0.00 40.25 2.90
4167 5432 7.133891 ACATTAGCTTGTCATGTTCAGTTAC 57.866 36.000 0.00 0.00 0.00 2.50
4208 5497 1.000607 TCAGTACACGTCTGGTTCTGC 60.001 52.381 6.35 0.00 34.15 4.26
4239 5528 4.223923 ACAAGCAGAGCTATATGTATCCCC 59.776 45.833 0.00 0.00 38.25 4.81
4470 5785 4.518590 TCCATTCTTTTCTCGTTGCATTCA 59.481 37.500 0.00 0.00 0.00 2.57
4572 5888 1.067295 TTGATGACCTTGAGTGGCCT 58.933 50.000 3.32 0.00 0.00 5.19
4602 5918 5.685954 CAGCATTCAGATTCATTTTCATCCG 59.314 40.000 0.00 0.00 0.00 4.18
4821 6137 4.393990 ACAGGTAAAACTATTGCGCCTAAC 59.606 41.667 4.18 0.00 0.00 2.34
4835 6151 2.804572 CGCCTAACATCTACAGCATGCT 60.805 50.000 16.30 16.30 42.53 3.79
4858 6174 3.441572 GCTTCTTTGTGCTGACCATACAT 59.558 43.478 0.00 0.00 0.00 2.29
4999 6315 1.008538 GCACCTGGTTTCAGTTGCG 60.009 57.895 0.00 0.00 46.53 4.85
5047 6363 1.792757 TTGCTGGAGGGGCTCAACAT 61.793 55.000 0.00 0.00 31.08 2.71
5053 6369 0.329596 GAGGGGCTCAACATCCAAGT 59.670 55.000 0.00 0.00 0.00 3.16
5248 6655 4.691860 TGACTTGTCGTAACCTACTAGC 57.308 45.455 0.00 0.00 0.00 3.42
5509 6921 9.388506 CTAGATATTTATCCATGGCTGGTTTAG 57.611 37.037 6.96 0.00 43.61 1.85
5572 7063 3.119319 TGGACTATGTGGGCATTAAGGA 58.881 45.455 0.00 0.00 36.58 3.36
5573 7064 3.118038 TGGACTATGTGGGCATTAAGGAC 60.118 47.826 0.00 0.00 36.58 3.85
5574 7065 3.136626 GGACTATGTGGGCATTAAGGACT 59.863 47.826 0.00 0.00 36.58 3.85
5666 7160 2.550830 CCAGAGTTGGTACTGCAAGT 57.449 50.000 0.00 0.00 43.21 3.16
5721 7215 0.038801 CTCGCACTGCTCTCAACAGA 60.039 55.000 0.00 0.00 38.55 3.41
5774 7294 1.360852 ACCAGGGCCCATTGTTCAATA 59.639 47.619 27.56 0.00 0.00 1.90
5957 7477 3.728845 ACGTGTGGATTGGCTATACATC 58.271 45.455 0.00 0.00 27.31 3.06
5981 7605 2.698855 TTGAGAGGAATGCCAGCTAC 57.301 50.000 0.00 0.00 36.29 3.58
6089 7713 7.873505 AGTAAAAAGTACAGTCAGTCAAGATCC 59.126 37.037 0.00 0.00 0.00 3.36
6094 7718 6.010850 AGTACAGTCAGTCAAGATCCTAACA 58.989 40.000 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.734707 CGACAATACTGGACGGTCCAC 60.735 57.143 25.53 12.96 42.67 4.02
1 2 0.528924 CGACAATACTGGACGGTCCA 59.471 55.000 27.17 27.17 45.98 4.02
2 3 0.804933 GCGACAATACTGGACGGTCC 60.805 60.000 20.36 20.36 36.96 4.46
3 4 0.108992 TGCGACAATACTGGACGGTC 60.109 55.000 0.00 0.00 0.00 4.79
4 5 0.535335 ATGCGACAATACTGGACGGT 59.465 50.000 0.00 0.00 0.00 4.83
5 6 0.930310 CATGCGACAATACTGGACGG 59.070 55.000 0.00 0.00 0.00 4.79
6 7 1.588404 GACATGCGACAATACTGGACG 59.412 52.381 0.00 0.00 0.00 4.79
7 8 2.893637 AGACATGCGACAATACTGGAC 58.106 47.619 0.00 0.00 0.00 4.02
8 9 3.610040 AAGACATGCGACAATACTGGA 57.390 42.857 0.00 0.00 0.00 3.86
9 10 4.685169 AAAAGACATGCGACAATACTGG 57.315 40.909 0.00 0.00 0.00 4.00
10 11 5.791974 CAGAAAAAGACATGCGACAATACTG 59.208 40.000 0.00 0.00 0.00 2.74
11 12 5.617751 GCAGAAAAAGACATGCGACAATACT 60.618 40.000 0.00 0.00 0.00 2.12
12 13 4.554973 GCAGAAAAAGACATGCGACAATAC 59.445 41.667 0.00 0.00 0.00 1.89
13 14 4.455533 AGCAGAAAAAGACATGCGACAATA 59.544 37.500 0.00 0.00 43.41 1.90
14 15 3.254166 AGCAGAAAAAGACATGCGACAAT 59.746 39.130 0.00 0.00 43.41 2.71
15 16 2.618241 AGCAGAAAAAGACATGCGACAA 59.382 40.909 0.00 0.00 43.41 3.18
16 17 2.221169 AGCAGAAAAAGACATGCGACA 58.779 42.857 0.00 0.00 43.41 4.35
17 18 2.977405 AGCAGAAAAAGACATGCGAC 57.023 45.000 0.00 0.00 43.41 5.19
18 19 3.066621 ACAAAGCAGAAAAAGACATGCGA 59.933 39.130 0.00 0.00 43.41 5.10
19 20 3.374745 ACAAAGCAGAAAAAGACATGCG 58.625 40.909 0.00 0.00 43.41 4.73
22 23 5.063817 GCACAAACAAAGCAGAAAAAGACAT 59.936 36.000 0.00 0.00 0.00 3.06
45 46 8.515473 AAAATAAAGAGAATAAAACGTGTGGC 57.485 30.769 0.00 0.00 0.00 5.01
92 93 9.184523 TGTAGAGAAATGAAGAAAGAAACCAAA 57.815 29.630 0.00 0.00 0.00 3.28
95 96 8.621286 TGTTGTAGAGAAATGAAGAAAGAAACC 58.379 33.333 0.00 0.00 0.00 3.27
97 98 9.173021 TGTGTTGTAGAGAAATGAAGAAAGAAA 57.827 29.630 0.00 0.00 0.00 2.52
116 126 4.043750 CGAAAAATGCAGTCATGTGTTGT 58.956 39.130 0.00 0.00 32.23 3.32
118 128 4.305989 ACGAAAAATGCAGTCATGTGTT 57.694 36.364 0.00 0.00 32.23 3.32
126 136 8.035165 TGTATAATGTGTACGAAAAATGCAGT 57.965 30.769 0.00 0.00 0.00 4.40
137 147 8.593842 TGTTACGGAAATTGTATAATGTGTACG 58.406 33.333 0.00 0.00 0.00 3.67
158 168 4.026393 GCAACAAAATGTTCCGGTTGTTAC 60.026 41.667 15.70 8.82 41.10 2.50
161 171 2.093973 TGCAACAAAATGTTCCGGTTGT 60.094 40.909 0.00 0.00 38.77 3.32
162 172 2.283884 GTGCAACAAAATGTTCCGGTTG 59.716 45.455 0.00 0.00 38.77 3.77
163 173 2.167487 AGTGCAACAAAATGTTCCGGTT 59.833 40.909 0.00 0.00 38.77 4.44
165 175 2.223688 TGAGTGCAACAAAATGTTCCGG 60.224 45.455 0.00 0.00 38.77 5.14
166 176 3.077229 TGAGTGCAACAAAATGTTCCG 57.923 42.857 0.00 0.00 38.77 4.30
227 243 7.397892 TGAAAAAGGTAGACACACATGAAAA 57.602 32.000 0.00 0.00 0.00 2.29
228 244 7.424803 CATGAAAAAGGTAGACACACATGAAA 58.575 34.615 0.00 0.00 35.95 2.69
229 245 6.514870 GCATGAAAAAGGTAGACACACATGAA 60.515 38.462 0.00 0.00 35.95 2.57
230 246 5.048782 GCATGAAAAAGGTAGACACACATGA 60.049 40.000 0.00 0.00 35.95 3.07
231 247 5.156355 GCATGAAAAAGGTAGACACACATG 58.844 41.667 0.00 0.00 36.65 3.21
232 248 4.826733 TGCATGAAAAAGGTAGACACACAT 59.173 37.500 0.00 0.00 0.00 3.21
233 249 4.203226 TGCATGAAAAAGGTAGACACACA 58.797 39.130 0.00 0.00 0.00 3.72
234 250 4.829064 TGCATGAAAAAGGTAGACACAC 57.171 40.909 0.00 0.00 0.00 3.82
235 251 7.176515 ACAATATGCATGAAAAAGGTAGACACA 59.823 33.333 10.16 0.00 0.00 3.72
236 252 7.538575 ACAATATGCATGAAAAAGGTAGACAC 58.461 34.615 10.16 0.00 0.00 3.67
237 253 7.701539 ACAATATGCATGAAAAAGGTAGACA 57.298 32.000 10.16 0.00 0.00 3.41
238 254 8.673711 TGTACAATATGCATGAAAAAGGTAGAC 58.326 33.333 10.16 0.00 0.00 2.59
239 255 8.800370 TGTACAATATGCATGAAAAAGGTAGA 57.200 30.769 10.16 0.00 0.00 2.59
242 258 9.189156 ACTATGTACAATATGCATGAAAAAGGT 57.811 29.630 10.16 0.66 35.03 3.50
266 282 8.804204 CGGAGGGAGTAGATATATACAAAAACT 58.196 37.037 10.03 1.19 0.00 2.66
272 288 6.217074 AGGAACGGAGGGAGTAGATATATACA 59.783 42.308 10.03 0.00 0.00 2.29
273 289 6.661777 AGGAACGGAGGGAGTAGATATATAC 58.338 44.000 0.00 0.00 0.00 1.47
274 290 6.905067 AGGAACGGAGGGAGTAGATATATA 57.095 41.667 0.00 0.00 0.00 0.86
275 291 5.799978 AGGAACGGAGGGAGTAGATATAT 57.200 43.478 0.00 0.00 0.00 0.86
276 292 6.708885 TTAGGAACGGAGGGAGTAGATATA 57.291 41.667 0.00 0.00 0.00 0.86
277 293 5.595814 TTAGGAACGGAGGGAGTAGATAT 57.404 43.478 0.00 0.00 0.00 1.63
278 294 5.136105 GTTTAGGAACGGAGGGAGTAGATA 58.864 45.833 0.00 0.00 0.00 1.98
279 295 3.959449 GTTTAGGAACGGAGGGAGTAGAT 59.041 47.826 0.00 0.00 0.00 1.98
280 296 3.245371 TGTTTAGGAACGGAGGGAGTAGA 60.245 47.826 0.00 0.00 38.65 2.59
281 297 3.094572 TGTTTAGGAACGGAGGGAGTAG 58.905 50.000 0.00 0.00 38.65 2.57
304 320 9.003658 GTCCATTTGAAATCTCTAGAAAGACAA 57.996 33.333 0.00 0.00 0.00 3.18
305 321 8.378565 AGTCCATTTGAAATCTCTAGAAAGACA 58.621 33.333 0.00 0.00 0.00 3.41
307 323 9.877178 GTAGTCCATTTGAAATCTCTAGAAAGA 57.123 33.333 0.00 0.00 0.00 2.52
309 325 9.436957 GTGTAGTCCATTTGAAATCTCTAGAAA 57.563 33.333 0.00 0.00 0.00 2.52
312 328 8.954950 ATGTGTAGTCCATTTGAAATCTCTAG 57.045 34.615 0.00 0.00 0.00 2.43
314 330 8.321353 TGTATGTGTAGTCCATTTGAAATCTCT 58.679 33.333 0.00 0.00 0.00 3.10
315 331 8.492673 TGTATGTGTAGTCCATTTGAAATCTC 57.507 34.615 0.00 0.00 0.00 2.75
316 332 8.321353 TCTGTATGTGTAGTCCATTTGAAATCT 58.679 33.333 0.00 0.00 0.00 2.40
317 333 8.492673 TCTGTATGTGTAGTCCATTTGAAATC 57.507 34.615 0.00 0.00 0.00 2.17
319 335 7.882791 ACATCTGTATGTGTAGTCCATTTGAAA 59.117 33.333 0.00 0.00 44.79 2.69
321 337 6.946340 ACATCTGTATGTGTAGTCCATTTGA 58.054 36.000 0.00 0.00 44.79 2.69
322 338 8.893219 ATACATCTGTATGTGTAGTCCATTTG 57.107 34.615 2.10 0.00 45.99 2.32
361 377 9.323985 GAAGCAAAATGAGTGAATCTATACTCT 57.676 33.333 0.00 0.00 42.86 3.24
362 378 8.272176 CGAAGCAAAATGAGTGAATCTATACTC 58.728 37.037 0.00 0.00 42.77 2.59
363 379 7.766278 ACGAAGCAAAATGAGTGAATCTATACT 59.234 33.333 0.00 0.00 0.00 2.12
364 380 7.910304 ACGAAGCAAAATGAGTGAATCTATAC 58.090 34.615 0.00 0.00 0.00 1.47
365 381 9.764363 ATACGAAGCAAAATGAGTGAATCTATA 57.236 29.630 0.00 0.00 0.00 1.31
366 382 6.992063 ACGAAGCAAAATGAGTGAATCTAT 57.008 33.333 0.00 0.00 0.00 1.98
367 383 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
368 384 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
369 385 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
370 386 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
371 387 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
372 388 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
373 389 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
374 390 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
375 391 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
376 392 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
377 393 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
378 394 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
379 395 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
380 396 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
381 397 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
382 398 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
383 399 4.921515 TCAACAAGTGACTACATACGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
384 400 7.402811 TTTCAACAAGTGACTACATACGAAG 57.597 36.000 0.00 0.00 35.39 3.79
385 401 7.870954 AGATTTCAACAAGTGACTACATACGAA 59.129 33.333 0.00 0.00 35.39 3.85
386 402 7.375834 AGATTTCAACAAGTGACTACATACGA 58.624 34.615 0.00 0.00 35.39 3.43
387 403 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
388 404 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
390 406 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
391 407 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
392 408 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
393 409 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
394 410 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
395 411 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
396 412 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
397 413 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
398 414 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
399 415 9.050601 ACTTGTCTTTCTAGAGATTTCAACAAG 57.949 33.333 18.42 18.42 32.73 3.16
400 416 8.964476 ACTTGTCTTTCTAGAGATTTCAACAA 57.036 30.769 0.00 0.00 0.00 2.83
410 426 9.291664 CGTTCCTAAATACTTGTCTTTCTAGAG 57.708 37.037 0.00 0.00 0.00 2.43
411 427 8.248945 CCGTTCCTAAATACTTGTCTTTCTAGA 58.751 37.037 0.00 0.00 0.00 2.43
412 428 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
413 429 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
414 430 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
415 431 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
416 432 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
417 433 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
418 434 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
419 435 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
420 436 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
421 437 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
422 438 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
423 439 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
424 440 4.892345 ACTACTCCCTCCGTTCCTAAATAC 59.108 45.833 0.00 0.00 0.00 1.89
425 441 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
429 445 6.460103 AATATACTACTCCCTCCGTTCCTA 57.540 41.667 0.00 0.00 0.00 2.94
430 446 5.336491 AATATACTACTCCCTCCGTTCCT 57.664 43.478 0.00 0.00 0.00 3.36
433 449 8.750298 CATATGAAATATACTACTCCCTCCGTT 58.250 37.037 0.00 0.00 37.44 4.44
493 509 9.607988 AGTCCAAAAATTACATCGTATCATACA 57.392 29.630 0.00 0.00 0.00 2.29
497 513 8.556194 GCATAGTCCAAAAATTACATCGTATCA 58.444 33.333 0.00 0.00 0.00 2.15
498 514 8.556194 TGCATAGTCCAAAAATTACATCGTATC 58.444 33.333 0.00 0.00 0.00 2.24
499 515 8.445275 TGCATAGTCCAAAAATTACATCGTAT 57.555 30.769 0.00 0.00 0.00 3.06
500 516 7.851387 TGCATAGTCCAAAAATTACATCGTA 57.149 32.000 0.00 0.00 0.00 3.43
501 517 6.751514 TGCATAGTCCAAAAATTACATCGT 57.248 33.333 0.00 0.00 0.00 3.73
502 518 7.540400 TGTTTGCATAGTCCAAAAATTACATCG 59.460 33.333 0.00 0.00 34.33 3.84
503 519 8.755696 TGTTTGCATAGTCCAAAAATTACATC 57.244 30.769 0.00 0.00 34.33 3.06
504 520 9.153721 CATGTTTGCATAGTCCAAAAATTACAT 57.846 29.630 0.00 0.00 34.33 2.29
505 521 8.147058 ACATGTTTGCATAGTCCAAAAATTACA 58.853 29.630 0.00 0.00 34.33 2.41
506 522 8.532977 ACATGTTTGCATAGTCCAAAAATTAC 57.467 30.769 0.00 0.00 34.33 1.89
507 523 9.553064 AAACATGTTTGCATAGTCCAAAAATTA 57.447 25.926 22.71 0.00 34.33 1.40
508 524 8.449251 AAACATGTTTGCATAGTCCAAAAATT 57.551 26.923 22.71 0.00 34.33 1.82
509 525 8.449251 AAAACATGTTTGCATAGTCCAAAAAT 57.551 26.923 23.93 0.04 34.33 1.82
510 526 7.856145 AAAACATGTTTGCATAGTCCAAAAA 57.144 28.000 23.93 0.00 34.33 1.94
551 567 9.603921 ACAAAATTTCTGTGACATTCTTTCAAT 57.396 25.926 0.00 0.00 0.00 2.57
579 596 9.816787 AGGTTTATAAAGTTTTAATGGGTCAGA 57.183 29.630 0.00 0.00 0.00 3.27
665 682 9.744468 GTTTCAAAAATATGTAGGTGACACTTT 57.256 29.630 5.39 0.00 42.17 2.66
668 685 9.691362 AATGTTTCAAAAATATGTAGGTGACAC 57.309 29.630 0.00 0.00 42.17 3.67
712 730 4.452114 TGCTGTGTACTAAAATGTGCTCTG 59.548 41.667 0.00 0.00 0.00 3.35
714 732 5.551760 ATGCTGTGTACTAAAATGTGCTC 57.448 39.130 0.00 0.00 0.00 4.26
716 734 5.164061 GCAAATGCTGTGTACTAAAATGTGC 60.164 40.000 0.00 0.00 38.21 4.57
719 737 7.585286 AATGCAAATGCTGTGTACTAAAATG 57.415 32.000 6.97 0.00 42.66 2.32
722 740 9.534565 TTAAAAATGCAAATGCTGTGTACTAAA 57.465 25.926 6.97 0.00 42.66 1.85
723 741 9.534565 TTTAAAAATGCAAATGCTGTGTACTAA 57.465 25.926 6.97 0.00 42.66 2.24
725 743 8.430801 TTTTAAAAATGCAAATGCTGTGTACT 57.569 26.923 6.97 0.00 42.66 2.73
732 752 7.126726 TGCGTATTTTAAAAATGCAAATGCT 57.873 28.000 18.99 0.19 42.66 3.79
747 767 9.522804 TTCTAAAAACTGTTCATTGCGTATTTT 57.477 25.926 0.00 0.00 0.00 1.82
751 771 8.185505 AGTTTTCTAAAAACTGTTCATTGCGTA 58.814 29.630 15.06 0.00 38.88 4.42
853 873 2.202932 ATGACGCCATCCAGACGC 60.203 61.111 0.00 0.00 0.00 5.19
870 890 3.039011 GGTTCAGGCCTTGGACTATAGA 58.961 50.000 0.00 0.00 35.46 1.98
873 893 0.541863 CGGTTCAGGCCTTGGACTAT 59.458 55.000 0.00 0.00 35.46 2.12
874 894 1.980052 CGGTTCAGGCCTTGGACTA 59.020 57.895 0.00 0.00 35.46 2.59
875 895 2.750350 CGGTTCAGGCCTTGGACT 59.250 61.111 0.00 0.00 35.46 3.85
876 896 2.180159 TAGCGGTTCAGGCCTTGGAC 62.180 60.000 0.00 3.48 34.24 4.02
1158 1294 3.532155 GTGCGGAGGAGAGGCGAT 61.532 66.667 0.00 0.00 0.00 4.58
1185 1326 2.814919 CGAGACCTTAGATGGAGCGTAT 59.185 50.000 0.00 0.00 0.00 3.06
1389 1568 1.281960 CCCGTAGTCATACTCCGCG 59.718 63.158 0.00 0.00 0.00 6.46
1577 1757 1.398390 GACAGCATTACGAAGCAAGGG 59.602 52.381 0.00 0.00 0.00 3.95
1615 1795 4.436523 GCCACGATTATGCGAATGTTTAAC 59.563 41.667 0.00 0.00 34.83 2.01
1619 1799 2.755836 GCCACGATTATGCGAATGTT 57.244 45.000 0.00 0.00 34.83 2.71
1691 1871 5.515626 CAGTCACAGTATCTAAACGCCTAAC 59.484 44.000 0.00 0.00 0.00 2.34
1692 1872 5.184479 ACAGTCACAGTATCTAAACGCCTAA 59.816 40.000 0.00 0.00 0.00 2.69
1702 1882 2.889512 TCCACCACAGTCACAGTATCT 58.110 47.619 0.00 0.00 0.00 1.98
1804 2361 7.861629 AGTTACATCCATCTCCAGAATTAACA 58.138 34.615 0.00 0.00 0.00 2.41
1899 2524 3.438087 ACAGTACAGCACTCAATCAATGC 59.562 43.478 0.00 0.00 39.74 3.56
2065 2696 4.391830 GTCGTAGGAGCAAAATGATTGACA 59.608 41.667 0.00 0.00 0.00 3.58
2164 2796 9.376075 CCATAGTGTTCATCTGGATATCATAAC 57.624 37.037 4.83 0.58 0.00 1.89
2168 2800 7.803487 ATCCATAGTGTTCATCTGGATATCA 57.197 36.000 4.83 0.00 43.24 2.15
2222 2854 7.333528 AGACAACATGGCGTGAAATAATTAT 57.666 32.000 14.82 0.00 0.00 1.28
2298 2930 1.603455 CAATGGAGGGTGGTTGCGT 60.603 57.895 0.00 0.00 0.00 5.24
2316 2948 2.544694 CGTGATGAGGATGTACAGGAGC 60.545 54.545 0.33 0.00 0.00 4.70
2360 2993 5.811100 GGGTTGTGTAGTGTAGATAAGAAGC 59.189 44.000 0.00 0.00 0.00 3.86
2362 2995 7.892241 AGTAGGGTTGTGTAGTGTAGATAAGAA 59.108 37.037 0.00 0.00 0.00 2.52
2363 2996 7.408543 AGTAGGGTTGTGTAGTGTAGATAAGA 58.591 38.462 0.00 0.00 0.00 2.10
2384 3017 7.406031 TGAGGTGAAGAAATAGGTGTAGTAG 57.594 40.000 0.00 0.00 0.00 2.57
2416 3049 6.443849 AGAAATGGTGGAGAAATAGGTGTAGA 59.556 38.462 0.00 0.00 0.00 2.59
2438 3071 2.171448 GCTGAAGCTGATAAGGGGAGAA 59.829 50.000 0.00 0.00 38.21 2.87
2442 3075 2.106166 AGATGCTGAAGCTGATAAGGGG 59.894 50.000 3.61 0.00 42.66 4.79
2485 3118 8.697292 AGAAGAATAACTAGTGGAGGATGTTAC 58.303 37.037 0.00 0.00 0.00 2.50
2486 3119 8.840200 AGAAGAATAACTAGTGGAGGATGTTA 57.160 34.615 0.00 0.00 0.00 2.41
2507 3140 1.199615 GGGAGAGGAGGGTGAAGAAG 58.800 60.000 0.00 0.00 0.00 2.85
2582 3360 2.161486 GCTCGAGTGGTGATGCGAC 61.161 63.158 15.13 0.00 0.00 5.19
2589 3367 1.376424 ATGCTTGGCTCGAGTGGTG 60.376 57.895 15.13 3.93 0.00 4.17
2711 3582 6.266168 ACTGAAATGAGTGAACAAACACAA 57.734 33.333 0.00 0.00 42.45 3.33
3621 4885 2.468831 GGAGCGACTAGAATCAAGCTG 58.531 52.381 0.00 0.00 34.85 4.24
3826 5091 2.650322 AGAGAGGTAGGAGTGGAAGTGA 59.350 50.000 0.00 0.00 0.00 3.41
4118 5383 2.228103 AGTGCAGCACTGAATCAATGTG 59.772 45.455 27.73 0.00 43.63 3.21
4167 5432 0.179076 TCGTGCATCATGGGCTAGTG 60.179 55.000 10.83 0.62 0.00 2.74
4239 5528 3.312421 TGCTTTCGTTGAAGTTCAGAAGG 59.688 43.478 5.56 8.76 0.00 3.46
4396 5711 1.374758 GACTGGAGTGTTCCCTGCG 60.375 63.158 0.00 0.00 43.33 5.18
4470 5785 3.754188 AACGTTAGAACTCGTAGCGAT 57.246 42.857 0.00 0.00 39.39 4.58
4572 5888 1.282738 TGAATCTGAATGCTGGAGCCA 59.717 47.619 0.00 0.00 41.18 4.75
4810 6126 2.213499 GCTGTAGATGTTAGGCGCAAT 58.787 47.619 10.83 0.00 0.00 3.56
4835 6151 1.985473 ATGGTCAGCACAAAGAAGCA 58.015 45.000 0.00 0.00 0.00 3.91
4836 6152 2.813754 TGTATGGTCAGCACAAAGAAGC 59.186 45.455 0.00 0.00 0.00 3.86
4837 6153 5.633830 AATGTATGGTCAGCACAAAGAAG 57.366 39.130 0.00 0.00 0.00 2.85
4858 6174 7.676947 ACTTGTACTTATACCTTGCAGAGAAA 58.323 34.615 0.00 0.00 0.00 2.52
4999 6315 1.041437 AGGATTGCGTACCTAGCCTC 58.959 55.000 0.00 0.00 28.72 4.70
5053 6369 6.677781 AAGAATTCGATAAAAGCAATCCGA 57.322 33.333 0.00 0.00 0.00 4.55
5248 6655 3.910568 AAGAAAGATCCAGAGCTGAGG 57.089 47.619 0.00 0.00 0.00 3.86
5371 6781 3.286353 TGAATGTCCTTGACACTTTGCA 58.714 40.909 0.00 0.00 45.65 4.08
5380 6790 9.241919 TCTAATTATTGCTTTGAATGTCCTTGA 57.758 29.630 0.00 0.00 0.00 3.02
5605 7099 3.422603 CGATGTAGTTGCGGTGTAACAAC 60.423 47.826 0.00 0.00 45.15 3.32
5666 7160 7.123397 AGACAGAGACATAATGAGCTCAACTAA 59.877 37.037 22.50 6.81 0.00 2.24
5721 7215 5.690364 GCACTAAGCTAGATTAATTGGGGGT 60.690 44.000 1.54 0.00 41.15 4.95
5774 7294 0.332632 TTGCTTGGGAATGGCTAGCT 59.667 50.000 15.72 0.00 33.15 3.32
5957 7477 2.094854 GCTGGCATTCCTCTCAAAGTTG 60.095 50.000 0.00 0.00 0.00 3.16
5981 7605 5.785599 CGTTGCAGATAAAAAGAACTTCTCG 59.214 40.000 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.