Multiple sequence alignment - TraesCS1B01G330600

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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 TraesCS1B01G330600 chr1B 100.000 3158 0 0 1 3158 556263818 556266975 0.000000e+00 5832.0
1 TraesCS1B01G330600 chr1B 96.947 1638 28 6 721 2357 556297063 556298679 0.000000e+00 2728.0
2 TraesCS1B01G330600 chr1B 95.189 1642 54 12 721 2356 556251143 556252765 0.000000e+00 2571.0
3 TraesCS1B01G330600 chr1B 91.461 1663 95 17 723 2356 556662838 556664482 0.000000e+00 2241.0
4 TraesCS1B01G330600 chr1B 98.118 744 12 2 2352 3094 556299738 556300480 0.000000e+00 1295.0
5 TraesCS1B01G330600 chr1B 87.872 470 45 8 2522 2987 556252507 556252968 2.770000e-150 542.0
6 TraesCS1B01G330600 chr1B 86.902 481 51 8 2522 2998 556835180 556835652 2.160000e-146 529.0
7 TraesCS1B01G330600 chr1B 86.902 481 51 8 2522 2998 556863601 556864073 2.160000e-146 529.0
8 TraesCS1B01G330600 chr1B 87.407 135 14 2 3024 3158 556252599 556252730 5.460000e-33 152.0
9 TraesCS1B01G330600 chr1B 84.672 137 16 3 3024 3158 556967737 556967870 7.110000e-27 132.0
10 TraesCS1B01G330600 chr1B 97.059 68 2 0 3091 3158 556306456 556306523 7.160000e-22 115.0
11 TraesCS1B01G330600 chr1B 93.333 60 4 0 288 347 317433913 317433972 4.340000e-14 89.8
12 TraesCS1B01G330600 chr1B 91.228 57 3 2 580 634 556964515 556964571 3.380000e-10 76.8
13 TraesCS1B01G330600 chr1A 94.046 1646 56 14 724 2356 509777035 509775419 0.000000e+00 2459.0
14 TraesCS1B01G330600 chr1A 93.486 1658 62 23 724 2356 509703806 509702170 0.000000e+00 2422.0
15 TraesCS1B01G330600 chr1A 91.471 1665 79 22 724 2357 509849715 509848083 0.000000e+00 2230.0
16 TraesCS1B01G330600 chr1A 91.662 1655 67 26 724 2344 509720190 509718573 0.000000e+00 2226.0
17 TraesCS1B01G330600 chr1A 91.541 1655 69 26 724 2344 509793570 509791953 0.000000e+00 2215.0
18 TraesCS1B01G330600 chr1A 86.074 517 49 13 2522 3026 509913701 509913196 4.640000e-148 534.0
19 TraesCS1B01G330600 chr1A 92.014 288 21 2 1 287 509849999 509849713 1.360000e-108 403.0
20 TraesCS1B01G330600 chr1A 91.667 288 22 2 1 287 509793854 509793568 6.350000e-107 398.0
21 TraesCS1B01G330600 chr1A 90.972 288 24 2 1 287 509720474 509720188 1.370000e-103 387.0
22 TraesCS1B01G330600 chr1A 88.000 125 10 3 596 715 509704021 509703897 3.280000e-30 143.0
23 TraesCS1B01G330600 chr1A 87.826 115 9 3 606 715 509777240 509777126 2.560000e-26 130.0
24 TraesCS1B01G330600 chr1A 97.059 34 0 1 602 635 509707658 509707690 4.400000e-04 56.5
25 TraesCS1B01G330600 chr1A 97.059 34 0 1 602 635 509780922 509780954 4.400000e-04 56.5
26 TraesCS1B01G330600 chr1D 91.711 1677 72 22 724 2357 412641923 412643575 0.000000e+00 2265.0
27 TraesCS1B01G330600 chr1D 93.186 1541 57 14 724 2227 412660187 412661716 0.000000e+00 2220.0
28 TraesCS1B01G330600 chr1D 91.280 1640 75 39 719 2324 412814141 412815746 0.000000e+00 2174.0
29 TraesCS1B01G330600 chr1D 92.679 1366 62 21 998 2356 412684071 412685405 0.000000e+00 1934.0
30 TraesCS1B01G330600 chr1D 92.533 1366 64 21 998 2356 412897765 412899099 0.000000e+00 1923.0
31 TraesCS1B01G330600 chr1D 87.379 515 43 14 2522 3026 412643315 412643817 3.530000e-159 571.0
32 TraesCS1B01G330600 chr1D 87.379 515 43 14 2522 3026 412747293 412747795 3.530000e-159 571.0
33 TraesCS1B01G330600 chr1D 87.379 515 43 14 2522 3026 412764456 412764958 3.530000e-159 571.0
34 TraesCS1B01G330600 chr1D 87.273 495 51 7 2522 3015 412789355 412789838 3.560000e-154 555.0
35 TraesCS1B01G330600 chr1D 91.696 289 14 6 719 1001 412897453 412897737 2.950000e-105 392.0
36 TraesCS1B01G330600 chr1D 93.281 253 16 1 36 287 412854429 412854681 3.850000e-99 372.0
37 TraesCS1B01G330600 chr1D 92.885 253 17 1 36 287 412659937 412660189 1.790000e-97 366.0
38 TraesCS1B01G330600 chr1D 92.885 253 17 1 36 287 412786320 412786572 1.790000e-97 366.0
39 TraesCS1B01G330600 chr1D 89.604 202 21 0 78 279 412641710 412641911 1.120000e-64 257.0
40 TraesCS1B01G330600 chr1D 89.604 202 21 0 78 279 412745688 412745889 1.120000e-64 257.0
41 TraesCS1B01G330600 chr1D 89.604 202 21 0 78 279 412762851 412763052 1.120000e-64 257.0
42 TraesCS1B01G330600 chr1D 86.667 135 14 3 3024 3158 412898941 412899071 2.540000e-31 147.0
43 TraesCS1B01G330600 chr1D 85.926 135 15 3 3024 3158 412815615 412815745 1.180000e-29 141.0
44 TraesCS1B01G330600 chr1D 81.600 125 19 3 2368 2490 256111861 256111739 2.000000e-17 100.0
45 TraesCS1B01G330600 chr1D 94.915 59 3 0 288 346 30673461 30673403 3.350000e-15 93.5
46 TraesCS1B01G330600 chr7D 92.424 66 3 2 288 351 1510177 1510242 3.350000e-15 93.5
47 TraesCS1B01G330600 chr7D 93.443 61 4 0 288 348 114820163 114820223 1.210000e-14 91.6
48 TraesCS1B01G330600 chr7D 93.443 61 2 2 288 347 84591499 84591440 4.340000e-14 89.8
49 TraesCS1B01G330600 chr7D 78.333 120 21 5 2397 2514 75261199 75261083 4.370000e-09 73.1
50 TraesCS1B01G330600 chr2D 90.278 72 5 2 288 359 30742950 30743019 3.350000e-15 93.5
51 TraesCS1B01G330600 chr7A 94.915 59 1 2 288 344 609507255 609507313 1.210000e-14 91.6
52 TraesCS1B01G330600 chr7A 81.818 88 15 1 2349 2435 516150476 516150563 4.370000e-09 73.1
53 TraesCS1B01G330600 chr7A 81.818 88 15 1 2349 2435 516150636 516150723 4.370000e-09 73.1
54 TraesCS1B01G330600 chr6B 93.548 62 2 2 289 348 662110352 662110291 1.210000e-14 91.6
55 TraesCS1B01G330600 chr6B 85.000 80 12 0 2361 2440 184144102 184144181 7.260000e-12 82.4
56 TraesCS1B01G330600 chr2A 94.828 58 3 0 289 346 701531202 701531145 1.210000e-14 91.6
57 TraesCS1B01G330600 chrUn 78.788 132 24 4 2395 2524 229275815 229275944 5.610000e-13 86.1
58 TraesCS1B01G330600 chrUn 78.788 132 24 4 2395 2524 299750957 299750828 5.610000e-13 86.1
59 TraesCS1B01G330600 chr3B 81.731 104 17 2 2369 2471 771189144 771189042 5.610000e-13 86.1
60 TraesCS1B01G330600 chr3B 84.286 70 10 1 2358 2427 707418845 707418913 2.030000e-07 67.6


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 TraesCS1B01G330600 chr1B 556263818 556266975 3157 False 5832.000000 5832 100.000000 1 3158 1 chr1B.!!$F2 3157
1 TraesCS1B01G330600 chr1B 556662838 556664482 1644 False 2241.000000 2241 91.461000 723 2356 1 chr1B.!!$F4 1633
2 TraesCS1B01G330600 chr1B 556297063 556300480 3417 False 2011.500000 2728 97.532500 721 3094 2 chr1B.!!$F8 2373
3 TraesCS1B01G330600 chr1B 556251143 556252968 1825 False 1088.333333 2571 90.156000 721 3158 3 chr1B.!!$F7 2437
4 TraesCS1B01G330600 chr1A 509848083 509849999 1916 True 1316.500000 2230 91.742500 1 2357 2 chr1A.!!$R6 2356
5 TraesCS1B01G330600 chr1A 509718573 509720474 1901 True 1306.500000 2226 91.317000 1 2344 2 chr1A.!!$R3 2343
6 TraesCS1B01G330600 chr1A 509791953 509793854 1901 True 1306.500000 2215 91.604000 1 2344 2 chr1A.!!$R5 2343
7 TraesCS1B01G330600 chr1A 509775419 509777240 1821 True 1294.500000 2459 90.936000 606 2356 2 chr1A.!!$R4 1750
8 TraesCS1B01G330600 chr1A 509702170 509704021 1851 True 1282.500000 2422 90.743000 596 2356 2 chr1A.!!$R2 1760
9 TraesCS1B01G330600 chr1A 509913196 509913701 505 True 534.000000 534 86.074000 2522 3026 1 chr1A.!!$R1 504
10 TraesCS1B01G330600 chr1D 412684071 412685405 1334 False 1934.000000 1934 92.679000 998 2356 1 chr1D.!!$F1 1358
11 TraesCS1B01G330600 chr1D 412659937 412661716 1779 False 1293.000000 2220 93.035500 36 2227 2 chr1D.!!$F4 2191
12 TraesCS1B01G330600 chr1D 412814141 412815746 1605 False 1157.500000 2174 88.603000 719 3158 2 chr1D.!!$F8 2439
13 TraesCS1B01G330600 chr1D 412641710 412643817 2107 False 1031.000000 2265 89.564667 78 3026 3 chr1D.!!$F3 2948
14 TraesCS1B01G330600 chr1D 412897453 412899099 1646 False 820.666667 1923 90.298667 719 3158 3 chr1D.!!$F9 2439
15 TraesCS1B01G330600 chr1D 412786320 412789838 3518 False 460.500000 555 90.079000 36 3015 2 chr1D.!!$F7 2979
16 TraesCS1B01G330600 chr1D 412745688 412747795 2107 False 414.000000 571 88.491500 78 3026 2 chr1D.!!$F5 2948
17 TraesCS1B01G330600 chr1D 412762851 412764958 2107 False 414.000000 571 88.491500 78 3026 2 chr1D.!!$F6 2948

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
532 533 0.034896 CGGACACAGCAGGGTAAGTT 59.965 55.0 0.0 0.0 0.00 2.66 F
537 538 0.107831 ACAGCAGGGTAAGTTTGCGA 59.892 50.0 0.0 0.0 42.47 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2332 2515 1.202065 CGTCGGATGTGGCAATTTCAG 60.202 52.381 0.0 0.0 0.0 3.02 R
2991 5679 2.799126 ATTGGTAAGGCGGTTGATGA 57.201 45.000 0.0 0.0 0.0 2.92 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
51 52 7.438160 TCTTCACGCAAGATCAAACGAATATAT 59.562 33.333 8.06 0.00 36.08 0.86
54 55 6.787515 CACGCAAGATCAAACGAATATATCAC 59.212 38.462 8.06 0.00 43.62 3.06
65 66 4.820173 ACGAATATATCACCGACTGAGACA 59.180 41.667 8.48 0.00 30.20 3.41
68 69 7.174426 ACGAATATATCACCGACTGAGACATAA 59.826 37.037 8.48 0.00 30.20 1.90
116 117 8.390143 TGTGGTGCCAGTATAAATATATGGATT 58.610 33.333 7.87 0.00 32.55 3.01
161 162 0.744414 CCAGTAGGTGGTGGCATTCG 60.744 60.000 0.00 0.00 42.17 3.34
175 176 1.969256 GCATTCGTTTGTTGCACGTAG 59.031 47.619 0.00 0.00 38.81 3.51
240 241 8.978472 TGATGGCTAATTAGTAAGTTAGTGAGT 58.022 33.333 13.91 0.00 31.98 3.41
243 244 9.690913 TGGCTAATTAGTAAGTTAGTGAGTAGA 57.309 33.333 16.73 0.01 31.98 2.59
252 253 9.080097 AGTAAGTTAGTGAGTAGATTGTTGTCT 57.920 33.333 0.00 0.00 0.00 3.41
255 256 8.865420 AGTTAGTGAGTAGATTGTTGTCTAGA 57.135 34.615 0.00 0.00 31.66 2.43
256 257 8.952278 AGTTAGTGAGTAGATTGTTGTCTAGAG 58.048 37.037 0.00 0.00 31.66 2.43
257 258 8.948145 GTTAGTGAGTAGATTGTTGTCTAGAGA 58.052 37.037 0.00 0.00 31.66 3.10
258 259 9.516546 TTAGTGAGTAGATTGTTGTCTAGAGAA 57.483 33.333 0.00 0.00 31.66 2.87
259 260 8.410673 AGTGAGTAGATTGTTGTCTAGAGAAA 57.589 34.615 3.51 0.00 31.66 2.52
260 261 8.861086 AGTGAGTAGATTGTTGTCTAGAGAAAA 58.139 33.333 3.51 0.00 31.66 2.29
261 262 9.646427 GTGAGTAGATTGTTGTCTAGAGAAAAT 57.354 33.333 3.51 6.78 31.66 1.82
284 285 7.992754 ATTAGTGAATTCATCTAATGAGGGC 57.007 36.000 25.79 8.50 40.94 5.19
285 286 5.643421 AGTGAATTCATCTAATGAGGGCT 57.357 39.130 12.12 0.00 40.94 5.19
286 287 6.011122 AGTGAATTCATCTAATGAGGGCTT 57.989 37.500 12.12 0.00 40.94 4.35
287 288 5.826737 AGTGAATTCATCTAATGAGGGCTTG 59.173 40.000 12.12 0.00 40.94 4.01
288 289 5.591877 GTGAATTCATCTAATGAGGGCTTGT 59.408 40.000 12.12 0.00 40.94 3.16
289 290 5.591472 TGAATTCATCTAATGAGGGCTTGTG 59.409 40.000 3.38 0.00 40.94 3.33
290 291 3.565764 TCATCTAATGAGGGCTTGTGG 57.434 47.619 0.00 0.00 33.59 4.17
291 292 1.952296 CATCTAATGAGGGCTTGTGGC 59.048 52.381 0.00 0.00 40.90 5.01
292 293 1.289160 TCTAATGAGGGCTTGTGGCT 58.711 50.000 0.00 0.00 41.46 4.75
293 294 1.065199 TCTAATGAGGGCTTGTGGCTG 60.065 52.381 0.00 0.00 41.46 4.85
294 295 0.680921 TAATGAGGGCTTGTGGCTGC 60.681 55.000 0.00 0.00 41.46 5.25
295 296 2.718487 AATGAGGGCTTGTGGCTGCA 62.718 55.000 0.50 0.00 41.46 4.41
296 297 2.362120 GAGGGCTTGTGGCTGCAT 60.362 61.111 0.50 0.00 41.46 3.96
297 298 2.678934 AGGGCTTGTGGCTGCATG 60.679 61.111 0.50 0.00 41.46 4.06
298 299 4.446413 GGGCTTGTGGCTGCATGC 62.446 66.667 11.82 11.82 41.46 4.06
299 300 3.687102 GGCTTGTGGCTGCATGCA 61.687 61.111 21.29 21.29 45.15 3.96
300 301 2.577059 GCTTGTGGCTGCATGCAT 59.423 55.556 22.97 0.00 45.15 3.96
301 302 1.518572 GCTTGTGGCTGCATGCATC 60.519 57.895 22.97 17.75 45.15 3.91
302 303 1.226575 CTTGTGGCTGCATGCATCG 60.227 57.895 22.97 12.00 45.15 3.84
303 304 1.929806 CTTGTGGCTGCATGCATCGT 61.930 55.000 22.97 0.00 45.15 3.73
304 305 1.925415 TTGTGGCTGCATGCATCGTC 61.925 55.000 22.97 13.00 45.15 4.20
305 306 2.110967 GTGGCTGCATGCATCGTCT 61.111 57.895 22.97 0.00 45.15 4.18
306 307 0.811219 GTGGCTGCATGCATCGTCTA 60.811 55.000 22.97 6.11 45.15 2.59
307 308 0.531311 TGGCTGCATGCATCGTCTAG 60.531 55.000 22.97 8.76 45.15 2.43
308 309 0.249615 GGCTGCATGCATCGTCTAGA 60.250 55.000 22.97 0.00 45.15 2.43
309 310 1.607509 GGCTGCATGCATCGTCTAGAT 60.608 52.381 22.97 0.00 45.15 1.98
318 319 0.965439 ATCGTCTAGATGCAGAGGCC 59.035 55.000 7.11 0.00 38.36 5.19
319 320 1.007964 CGTCTAGATGCAGAGGCCG 60.008 63.158 0.00 0.00 40.13 6.13
320 321 1.365633 GTCTAGATGCAGAGGCCGG 59.634 63.158 0.00 0.00 40.13 6.13
321 322 1.834378 TCTAGATGCAGAGGCCGGG 60.834 63.158 2.18 0.00 40.13 5.73
322 323 2.844362 TAGATGCAGAGGCCGGGG 60.844 66.667 2.18 0.00 40.13 5.73
373 374 2.877691 GGCGACCAAATGAGGTGC 59.122 61.111 0.00 0.00 43.38 5.01
374 375 1.971167 GGCGACCAAATGAGGTGCA 60.971 57.895 0.00 0.00 43.38 4.57
375 376 1.503542 GCGACCAAATGAGGTGCAG 59.496 57.895 0.00 0.00 43.38 4.41
376 377 0.955428 GCGACCAAATGAGGTGCAGA 60.955 55.000 0.00 0.00 43.38 4.26
377 378 1.742761 CGACCAAATGAGGTGCAGAT 58.257 50.000 0.00 0.00 43.38 2.90
378 379 1.399440 CGACCAAATGAGGTGCAGATG 59.601 52.381 0.00 0.00 43.38 2.90
379 380 2.440409 GACCAAATGAGGTGCAGATGT 58.560 47.619 0.00 0.00 43.38 3.06
380 381 3.609853 GACCAAATGAGGTGCAGATGTA 58.390 45.455 0.00 0.00 43.38 2.29
381 382 3.614092 ACCAAATGAGGTGCAGATGTAG 58.386 45.455 0.00 0.00 41.30 2.74
382 383 3.009473 ACCAAATGAGGTGCAGATGTAGT 59.991 43.478 0.00 0.00 41.30 2.73
383 384 4.012374 CCAAATGAGGTGCAGATGTAGTT 58.988 43.478 0.00 0.00 0.00 2.24
384 385 4.460382 CCAAATGAGGTGCAGATGTAGTTT 59.540 41.667 0.00 0.00 0.00 2.66
385 386 5.047802 CCAAATGAGGTGCAGATGTAGTTTT 60.048 40.000 0.00 0.00 0.00 2.43
386 387 6.449698 CAAATGAGGTGCAGATGTAGTTTTT 58.550 36.000 0.00 0.00 0.00 1.94
407 408 3.839051 TTTTTGTTTGCCTGTTTTGCC 57.161 38.095 0.00 0.00 0.00 4.52
408 409 2.777832 TTTGTTTGCCTGTTTTGCCT 57.222 40.000 0.00 0.00 0.00 4.75
409 410 2.777832 TTGTTTGCCTGTTTTGCCTT 57.222 40.000 0.00 0.00 0.00 4.35
410 411 3.895232 TTGTTTGCCTGTTTTGCCTTA 57.105 38.095 0.00 0.00 0.00 2.69
411 412 3.451141 TGTTTGCCTGTTTTGCCTTAG 57.549 42.857 0.00 0.00 0.00 2.18
412 413 2.135139 GTTTGCCTGTTTTGCCTTAGC 58.865 47.619 0.00 0.00 40.48 3.09
413 414 0.678950 TTGCCTGTTTTGCCTTAGCC 59.321 50.000 0.00 0.00 38.69 3.93
414 415 0.468958 TGCCTGTTTTGCCTTAGCCA 60.469 50.000 0.00 0.00 38.69 4.75
415 416 0.244721 GCCTGTTTTGCCTTAGCCAG 59.755 55.000 0.00 0.00 38.69 4.85
416 417 1.909700 CCTGTTTTGCCTTAGCCAGA 58.090 50.000 0.00 0.00 38.69 3.86
417 418 2.450476 CCTGTTTTGCCTTAGCCAGAT 58.550 47.619 0.00 0.00 38.69 2.90
418 419 2.424956 CCTGTTTTGCCTTAGCCAGATC 59.575 50.000 0.00 0.00 38.69 2.75
419 420 2.424956 CTGTTTTGCCTTAGCCAGATCC 59.575 50.000 0.00 0.00 38.69 3.36
420 421 2.224992 TGTTTTGCCTTAGCCAGATCCA 60.225 45.455 0.00 0.00 38.69 3.41
421 422 2.825532 GTTTTGCCTTAGCCAGATCCAA 59.174 45.455 0.00 0.00 38.69 3.53
422 423 2.128771 TTGCCTTAGCCAGATCCAAC 57.871 50.000 0.00 0.00 38.69 3.77
423 424 1.289160 TGCCTTAGCCAGATCCAACT 58.711 50.000 0.00 0.00 38.69 3.16
424 425 2.477245 TGCCTTAGCCAGATCCAACTA 58.523 47.619 0.00 0.00 38.69 2.24
425 426 2.435805 TGCCTTAGCCAGATCCAACTAG 59.564 50.000 0.00 0.00 38.69 2.57
426 427 2.224402 GCCTTAGCCAGATCCAACTAGG 60.224 54.545 0.00 0.00 39.47 3.02
427 428 6.974431 TGCCTTAGCCAGATCCAACTAGGA 62.974 50.000 0.00 0.00 45.46 2.94
438 439 4.835284 TCCAACTAGGACATGTATGCAA 57.165 40.909 0.00 0.00 43.07 4.08
439 440 5.372343 TCCAACTAGGACATGTATGCAAT 57.628 39.130 0.00 0.00 43.07 3.56
440 441 5.125356 TCCAACTAGGACATGTATGCAATG 58.875 41.667 0.00 0.00 43.07 2.82
441 442 4.261322 CCAACTAGGACATGTATGCAATGC 60.261 45.833 0.00 0.00 41.22 3.56
442 443 4.155063 ACTAGGACATGTATGCAATGCA 57.845 40.909 11.44 11.44 44.90 3.96
443 444 4.132336 ACTAGGACATGTATGCAATGCAG 58.868 43.478 14.98 1.59 43.77 4.41
444 445 3.286329 AGGACATGTATGCAATGCAGA 57.714 42.857 14.98 6.18 43.77 4.26
453 454 2.747396 TGCAATGCAGACAAATTCCC 57.253 45.000 2.72 0.00 33.32 3.97
454 455 1.969208 TGCAATGCAGACAAATTCCCA 59.031 42.857 2.72 0.00 33.32 4.37
455 456 2.288948 TGCAATGCAGACAAATTCCCAC 60.289 45.455 2.72 0.00 33.32 4.61
456 457 2.288948 GCAATGCAGACAAATTCCCACA 60.289 45.455 0.00 0.00 0.00 4.17
457 458 3.618019 GCAATGCAGACAAATTCCCACAT 60.618 43.478 0.00 0.00 0.00 3.21
458 459 3.880047 ATGCAGACAAATTCCCACATG 57.120 42.857 0.00 0.00 0.00 3.21
459 460 2.874014 TGCAGACAAATTCCCACATGA 58.126 42.857 0.00 0.00 0.00 3.07
460 461 2.557924 TGCAGACAAATTCCCACATGAC 59.442 45.455 0.00 0.00 0.00 3.06
461 462 2.557924 GCAGACAAATTCCCACATGACA 59.442 45.455 0.00 0.00 0.00 3.58
462 463 3.005684 GCAGACAAATTCCCACATGACAA 59.994 43.478 0.00 0.00 0.00 3.18
463 464 4.549458 CAGACAAATTCCCACATGACAAC 58.451 43.478 0.00 0.00 0.00 3.32
464 465 3.573967 AGACAAATTCCCACATGACAACC 59.426 43.478 0.00 0.00 0.00 3.77
465 466 3.303938 ACAAATTCCCACATGACAACCA 58.696 40.909 0.00 0.00 0.00 3.67
466 467 3.708631 ACAAATTCCCACATGACAACCAA 59.291 39.130 0.00 0.00 0.00 3.67
467 468 4.163078 ACAAATTCCCACATGACAACCAAA 59.837 37.500 0.00 0.00 0.00 3.28
468 469 4.335400 AATTCCCACATGACAACCAAAC 57.665 40.909 0.00 0.00 0.00 2.93
469 470 2.443958 TCCCACATGACAACCAAACA 57.556 45.000 0.00 0.00 0.00 2.83
470 471 2.028130 TCCCACATGACAACCAAACAC 58.972 47.619 0.00 0.00 0.00 3.32
471 472 1.268999 CCCACATGACAACCAAACACG 60.269 52.381 0.00 0.00 0.00 4.49
472 473 1.673400 CCACATGACAACCAAACACGA 59.327 47.619 0.00 0.00 0.00 4.35
473 474 2.540769 CCACATGACAACCAAACACGAC 60.541 50.000 0.00 0.00 0.00 4.34
474 475 1.673920 ACATGACAACCAAACACGACC 59.326 47.619 0.00 0.00 0.00 4.79
475 476 1.001815 CATGACAACCAAACACGACCC 60.002 52.381 0.00 0.00 0.00 4.46
476 477 0.253610 TGACAACCAAACACGACCCT 59.746 50.000 0.00 0.00 0.00 4.34
477 478 1.485480 TGACAACCAAACACGACCCTA 59.515 47.619 0.00 0.00 0.00 3.53
478 479 2.140717 GACAACCAAACACGACCCTAG 58.859 52.381 0.00 0.00 0.00 3.02
479 480 1.487558 ACAACCAAACACGACCCTAGT 59.512 47.619 0.00 0.00 0.00 2.57
480 481 1.871039 CAACCAAACACGACCCTAGTG 59.129 52.381 0.00 0.00 44.57 2.74
481 482 0.395312 ACCAAACACGACCCTAGTGG 59.605 55.000 0.00 0.00 43.41 4.00
491 492 4.368003 CCTAGTGGGCGAAGGGTA 57.632 61.111 0.00 0.00 0.00 3.69
492 493 2.599216 CCTAGTGGGCGAAGGGTAA 58.401 57.895 0.00 0.00 0.00 2.85
493 494 0.464452 CCTAGTGGGCGAAGGGTAAG 59.536 60.000 0.00 0.00 0.00 2.34
494 495 0.179081 CTAGTGGGCGAAGGGTAAGC 60.179 60.000 0.00 0.00 0.00 3.09
495 496 0.616679 TAGTGGGCGAAGGGTAAGCT 60.617 55.000 0.00 0.00 0.00 3.74
496 497 1.002502 GTGGGCGAAGGGTAAGCTT 60.003 57.895 3.48 3.48 0.00 3.74
497 498 0.608308 GTGGGCGAAGGGTAAGCTTT 60.608 55.000 3.20 0.00 0.00 3.51
498 499 0.111639 TGGGCGAAGGGTAAGCTTTT 59.888 50.000 3.20 0.00 0.00 2.27
499 500 1.254026 GGGCGAAGGGTAAGCTTTTT 58.746 50.000 3.20 0.00 0.00 1.94
523 524 2.184323 TTTTTGCACGGACACAGCA 58.816 47.368 0.00 0.00 36.32 4.41
524 525 0.100325 TTTTTGCACGGACACAGCAG 59.900 50.000 0.00 0.00 39.72 4.24
525 526 1.723608 TTTTGCACGGACACAGCAGG 61.724 55.000 0.00 0.00 39.72 4.85
526 527 4.624364 TGCACGGACACAGCAGGG 62.624 66.667 0.00 0.00 33.75 4.45
527 528 4.626081 GCACGGACACAGCAGGGT 62.626 66.667 0.00 0.00 0.00 4.34
528 529 3.056458 CACGGACACAGCAGGGTA 58.944 61.111 0.00 0.00 0.00 3.69
529 530 1.369692 CACGGACACAGCAGGGTAA 59.630 57.895 0.00 0.00 0.00 2.85
530 531 0.670546 CACGGACACAGCAGGGTAAG 60.671 60.000 0.00 0.00 0.00 2.34
531 532 1.119574 ACGGACACAGCAGGGTAAGT 61.120 55.000 0.00 0.00 0.00 2.24
532 533 0.034896 CGGACACAGCAGGGTAAGTT 59.965 55.000 0.00 0.00 0.00 2.66
533 534 1.542547 CGGACACAGCAGGGTAAGTTT 60.543 52.381 0.00 0.00 0.00 2.66
534 535 1.880027 GGACACAGCAGGGTAAGTTTG 59.120 52.381 0.00 0.00 0.00 2.93
535 536 1.266989 GACACAGCAGGGTAAGTTTGC 59.733 52.381 0.00 0.00 38.09 3.68
536 537 0.238289 CACAGCAGGGTAAGTTTGCG 59.762 55.000 0.00 0.00 42.47 4.85
537 538 0.107831 ACAGCAGGGTAAGTTTGCGA 59.892 50.000 0.00 0.00 42.47 5.10
538 539 0.798776 CAGCAGGGTAAGTTTGCGAG 59.201 55.000 0.00 0.00 42.47 5.03
539 540 0.321653 AGCAGGGTAAGTTTGCGAGG 60.322 55.000 0.00 0.00 42.47 4.63
540 541 0.605589 GCAGGGTAAGTTTGCGAGGT 60.606 55.000 0.00 0.00 0.00 3.85
541 542 1.338389 GCAGGGTAAGTTTGCGAGGTA 60.338 52.381 0.00 0.00 0.00 3.08
542 543 2.344025 CAGGGTAAGTTTGCGAGGTAC 58.656 52.381 0.00 0.00 0.00 3.34
543 544 1.277273 AGGGTAAGTTTGCGAGGTACC 59.723 52.381 2.73 2.73 34.63 3.34
544 545 1.676916 GGGTAAGTTTGCGAGGTACCC 60.677 57.143 8.74 11.24 45.33 3.69
545 546 1.676916 GGTAAGTTTGCGAGGTACCCC 60.677 57.143 8.74 0.00 0.00 4.95
546 547 1.277273 GTAAGTTTGCGAGGTACCCCT 59.723 52.381 8.74 0.00 46.66 4.79
547 548 1.648116 AAGTTTGCGAGGTACCCCTA 58.352 50.000 8.74 0.00 42.86 3.53
548 549 1.648116 AGTTTGCGAGGTACCCCTAA 58.352 50.000 8.74 0.00 42.86 2.69
549 550 2.193993 AGTTTGCGAGGTACCCCTAAT 58.806 47.619 8.74 0.00 42.86 1.73
550 551 2.574824 AGTTTGCGAGGTACCCCTAATT 59.425 45.455 8.74 0.00 42.86 1.40
551 552 2.941064 GTTTGCGAGGTACCCCTAATTC 59.059 50.000 8.74 0.00 42.86 2.17
552 553 2.170012 TGCGAGGTACCCCTAATTCT 57.830 50.000 8.74 0.00 42.86 2.40
553 554 1.760613 TGCGAGGTACCCCTAATTCTG 59.239 52.381 8.74 0.00 42.86 3.02
554 555 1.761198 GCGAGGTACCCCTAATTCTGT 59.239 52.381 8.74 0.00 42.86 3.41
555 556 2.169978 GCGAGGTACCCCTAATTCTGTT 59.830 50.000 8.74 0.00 42.86 3.16
556 557 3.370209 GCGAGGTACCCCTAATTCTGTTT 60.370 47.826 8.74 0.00 42.86 2.83
557 558 4.189231 CGAGGTACCCCTAATTCTGTTTG 58.811 47.826 8.74 0.00 42.86 2.93
558 559 4.323257 CGAGGTACCCCTAATTCTGTTTGT 60.323 45.833 8.74 0.00 42.86 2.83
559 560 4.918588 AGGTACCCCTAATTCTGTTTGTG 58.081 43.478 8.74 0.00 40.19 3.33
560 561 4.352893 AGGTACCCCTAATTCTGTTTGTGT 59.647 41.667 8.74 0.00 40.19 3.72
561 562 5.548836 AGGTACCCCTAATTCTGTTTGTGTA 59.451 40.000 8.74 0.00 40.19 2.90
562 563 6.044637 AGGTACCCCTAATTCTGTTTGTGTAA 59.955 38.462 8.74 0.00 40.19 2.41
563 564 6.373495 GGTACCCCTAATTCTGTTTGTGTAAG 59.627 42.308 0.00 0.00 0.00 2.34
564 565 4.765339 ACCCCTAATTCTGTTTGTGTAAGC 59.235 41.667 0.00 0.00 0.00 3.09
565 566 4.764823 CCCCTAATTCTGTTTGTGTAAGCA 59.235 41.667 0.00 0.00 0.00 3.91
566 567 5.335661 CCCCTAATTCTGTTTGTGTAAGCAC 60.336 44.000 0.00 0.00 45.44 4.40
586 587 5.738370 GCACGTATATTGCTCGAAAAATCT 58.262 37.500 0.00 0.00 37.00 2.40
587 588 5.841296 GCACGTATATTGCTCGAAAAATCTC 59.159 40.000 0.00 0.00 37.00 2.75
588 589 6.509517 GCACGTATATTGCTCGAAAAATCTCA 60.510 38.462 0.00 0.00 37.00 3.27
589 590 7.398746 CACGTATATTGCTCGAAAAATCTCAA 58.601 34.615 0.00 0.00 0.00 3.02
590 591 7.580523 CACGTATATTGCTCGAAAAATCTCAAG 59.419 37.037 0.00 0.00 0.00 3.02
591 592 7.277981 ACGTATATTGCTCGAAAAATCTCAAGT 59.722 33.333 0.00 0.00 0.00 3.16
592 593 8.752254 CGTATATTGCTCGAAAAATCTCAAGTA 58.248 33.333 0.00 0.00 0.00 2.24
636 637 3.058501 GGCACCGGTACAAATATATGCAC 60.059 47.826 6.87 0.00 33.48 4.57
647 648 9.410556 GTACAAATATATGCACCATGAAATTCC 57.589 33.333 0.00 0.00 0.00 3.01
655 656 2.752354 CACCATGAAATTCCCACGCTTA 59.248 45.455 0.00 0.00 0.00 3.09
683 684 3.845781 CCAGTAGGTGGCATTCACTAT 57.154 47.619 0.00 0.00 45.38 2.12
685 686 3.879295 CCAGTAGGTGGCATTCACTATTG 59.121 47.826 0.00 0.00 45.38 1.90
686 687 3.313526 CAGTAGGTGGCATTCACTATTGC 59.686 47.826 0.00 0.00 45.38 3.56
702 708 6.070251 TCACTATTGCCCTCTCTGTTGATTAA 60.070 38.462 0.00 0.00 0.00 1.40
706 712 4.724399 TGCCCTCTCTGTTGATTAAAACA 58.276 39.130 0.00 0.00 37.71 2.83
712 718 6.258230 TCTCTGTTGATTAAAACATGGCAG 57.742 37.500 0.00 0.00 39.25 4.85
715 721 3.254411 TGTTGATTAAAACATGGCAGCGA 59.746 39.130 0.00 0.00 35.16 4.93
717 723 4.717233 TGATTAAAACATGGCAGCGAAT 57.283 36.364 0.00 0.00 0.00 3.34
720 726 5.576384 TGATTAAAACATGGCAGCGAATTTC 59.424 36.000 0.00 0.00 0.00 2.17
918 1021 0.109723 TATATTTCCCCGGTGCCAGC 59.890 55.000 0.00 0.00 0.00 4.85
2153 2336 0.658897 AAGTGCAACGTGGTTAACCG 59.341 50.000 19.65 11.07 45.86 4.44
2188 2371 5.695851 AGAAGTACAAGGCTGTTTTGATG 57.304 39.130 0.00 0.00 36.96 3.07
2228 2411 6.092122 CCTGTAAATTGCTGTAAGATTGTCGA 59.908 38.462 0.00 0.00 34.07 4.20
2229 2412 7.360861 CCTGTAAATTGCTGTAAGATTGTCGAA 60.361 37.037 0.00 0.00 34.07 3.71
2230 2413 8.039603 TGTAAATTGCTGTAAGATTGTCGAAT 57.960 30.769 0.00 0.00 34.07 3.34
2231 2414 8.511321 TGTAAATTGCTGTAAGATTGTCGAATT 58.489 29.630 0.00 0.00 34.07 2.17
2232 2415 7.801547 AAATTGCTGTAAGATTGTCGAATTG 57.198 32.000 0.00 0.00 34.07 2.32
2233 2416 4.340894 TGCTGTAAGATTGTCGAATTGC 57.659 40.909 0.00 0.00 34.07 3.56
2234 2417 4.002982 TGCTGTAAGATTGTCGAATTGCT 58.997 39.130 0.00 0.00 34.07 3.91
2235 2418 4.142838 TGCTGTAAGATTGTCGAATTGCTG 60.143 41.667 0.00 0.00 34.07 4.41
2236 2419 4.142816 GCTGTAAGATTGTCGAATTGCTGT 60.143 41.667 0.00 0.00 34.07 4.40
2237 2420 5.063438 GCTGTAAGATTGTCGAATTGCTGTA 59.937 40.000 0.00 0.00 34.07 2.74
2238 2421 6.402118 GCTGTAAGATTGTCGAATTGCTGTAA 60.402 38.462 0.00 0.00 34.07 2.41
2239 2422 7.060600 TGTAAGATTGTCGAATTGCTGTAAG 57.939 36.000 0.00 0.00 0.00 2.34
2240 2423 6.871492 TGTAAGATTGTCGAATTGCTGTAAGA 59.129 34.615 0.00 0.00 34.07 2.10
2241 2424 6.992063 AAGATTGTCGAATTGCTGTAAGAT 57.008 33.333 0.00 0.00 34.07 2.40
2242 2425 6.992063 AGATTGTCGAATTGCTGTAAGATT 57.008 33.333 0.00 0.00 34.07 2.40
2243 2426 6.779117 AGATTGTCGAATTGCTGTAAGATTG 58.221 36.000 0.00 0.00 34.07 2.67
2244 2427 5.940192 TTGTCGAATTGCTGTAAGATTGT 57.060 34.783 0.00 0.00 34.07 2.71
2245 2428 5.530519 TGTCGAATTGCTGTAAGATTGTC 57.469 39.130 0.00 0.00 34.07 3.18
2246 2429 4.091365 TGTCGAATTGCTGTAAGATTGTCG 59.909 41.667 0.00 0.00 34.07 4.35
2349 2532 1.541147 ACACTGAAATTGCCACATCCG 59.459 47.619 0.00 0.00 0.00 4.18
2410 3657 2.283298 TCATTGCCGATGAAGAGAAGC 58.717 47.619 0.00 0.00 41.73 3.86
2991 5679 1.847798 TTGGCCGGTTGGATAGCAGT 61.848 55.000 1.90 0.00 37.49 4.40
3094 5785 5.753721 AGATTGTTGTAGCTCCTTTCTCT 57.246 39.130 0.00 0.00 0.00 3.10
3095 5786 5.729510 AGATTGTTGTAGCTCCTTTCTCTC 58.270 41.667 0.00 0.00 0.00 3.20
3096 5787 5.483583 AGATTGTTGTAGCTCCTTTCTCTCT 59.516 40.000 0.00 0.00 0.00 3.10
3097 5788 4.792521 TGTTGTAGCTCCTTTCTCTCTC 57.207 45.455 0.00 0.00 0.00 3.20
3098 5789 4.152647 TGTTGTAGCTCCTTTCTCTCTCA 58.847 43.478 0.00 0.00 0.00 3.27
3099 5790 4.588951 TGTTGTAGCTCCTTTCTCTCTCAA 59.411 41.667 0.00 0.00 0.00 3.02
3100 5791 5.070446 TGTTGTAGCTCCTTTCTCTCTCAAA 59.930 40.000 0.00 0.00 0.00 2.69
3101 5792 6.169800 GTTGTAGCTCCTTTCTCTCTCAAAT 58.830 40.000 0.00 0.00 0.00 2.32
3102 5793 5.971763 TGTAGCTCCTTTCTCTCTCAAATC 58.028 41.667 0.00 0.00 0.00 2.17
3103 5794 5.719085 TGTAGCTCCTTTCTCTCTCAAATCT 59.281 40.000 0.00 0.00 0.00 2.40
3104 5795 5.760484 AGCTCCTTTCTCTCTCAAATCTT 57.240 39.130 0.00 0.00 0.00 2.40
3105 5796 6.125589 AGCTCCTTTCTCTCTCAAATCTTT 57.874 37.500 0.00 0.00 0.00 2.52
3106 5797 6.541907 AGCTCCTTTCTCTCTCAAATCTTTT 58.458 36.000 0.00 0.00 0.00 2.27
3107 5798 7.003482 AGCTCCTTTCTCTCTCAAATCTTTTT 58.997 34.615 0.00 0.00 0.00 1.94
3108 5799 7.174772 AGCTCCTTTCTCTCTCAAATCTTTTTC 59.825 37.037 0.00 0.00 0.00 2.29
3109 5800 7.174772 GCTCCTTTCTCTCTCAAATCTTTTTCT 59.825 37.037 0.00 0.00 0.00 2.52
3110 5801 8.986929 TCCTTTCTCTCTCAAATCTTTTTCTT 57.013 30.769 0.00 0.00 0.00 2.52
3111 5802 9.413734 TCCTTTCTCTCTCAAATCTTTTTCTTT 57.586 29.630 0.00 0.00 0.00 2.52
3112 5803 9.676195 CCTTTCTCTCTCAAATCTTTTTCTTTC 57.324 33.333 0.00 0.00 0.00 2.62
3157 5848 8.402798 ACAACCAATTGAATATCTTGTACACA 57.597 30.769 7.12 0.00 39.30 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.928375 GCGTGAAGATCCATGCAAATTTT 59.072 39.130 10.29 0.00 45.68 1.82
17 18 2.681682 ATCTTGCGTGAAGATCCATGCA 60.682 45.455 13.03 13.03 46.84 3.96
51 52 4.594123 TTTGTTATGTCTCAGTCGGTGA 57.406 40.909 0.00 0.00 0.00 4.02
54 55 4.988540 TCAGTTTTGTTATGTCTCAGTCGG 59.011 41.667 0.00 0.00 0.00 4.79
65 66 6.119536 TGCTATCCCGAATCAGTTTTGTTAT 58.880 36.000 0.00 0.00 0.00 1.89
68 69 3.950397 TGCTATCCCGAATCAGTTTTGT 58.050 40.909 0.00 0.00 0.00 2.83
111 112 9.865152 TTGAAGACATGGAAATATCATAATCCA 57.135 29.630 5.30 5.30 45.42 3.41
161 162 2.116366 CAAAGGCTACGTGCAACAAAC 58.884 47.619 0.00 0.00 45.15 2.93
175 176 4.237724 GCCAAGTTCTAATCAACAAAGGC 58.762 43.478 0.00 0.00 34.63 4.35
258 259 8.854117 GCCCTCATTAGATGAATTCACTAATTT 58.146 33.333 24.96 13.92 39.11 1.82
259 260 8.223330 AGCCCTCATTAGATGAATTCACTAATT 58.777 33.333 24.96 15.30 39.11 1.40
260 261 7.753630 AGCCCTCATTAGATGAATTCACTAAT 58.246 34.615 23.38 23.38 39.11 1.73
261 262 7.141758 AGCCCTCATTAGATGAATTCACTAA 57.858 36.000 21.87 21.87 39.11 2.24
262 263 6.753913 AGCCCTCATTAGATGAATTCACTA 57.246 37.500 11.07 11.29 39.11 2.74
263 264 5.643421 AGCCCTCATTAGATGAATTCACT 57.357 39.130 11.07 12.25 39.11 3.41
264 265 5.591877 ACAAGCCCTCATTAGATGAATTCAC 59.408 40.000 11.07 5.15 39.11 3.18
265 266 5.591472 CACAAGCCCTCATTAGATGAATTCA 59.409 40.000 11.26 11.26 39.11 2.57
266 267 5.009410 CCACAAGCCCTCATTAGATGAATTC 59.991 44.000 0.00 0.00 39.11 2.17
267 268 4.891756 CCACAAGCCCTCATTAGATGAATT 59.108 41.667 0.00 0.00 39.11 2.17
268 269 4.467769 CCACAAGCCCTCATTAGATGAAT 58.532 43.478 0.00 0.00 39.11 2.57
269 270 3.889815 CCACAAGCCCTCATTAGATGAA 58.110 45.455 0.00 0.00 39.11 2.57
270 271 2.421952 GCCACAAGCCCTCATTAGATGA 60.422 50.000 0.00 0.00 34.78 2.92
271 272 1.952296 GCCACAAGCCCTCATTAGATG 59.048 52.381 0.00 0.00 34.35 2.90
272 273 1.849039 AGCCACAAGCCCTCATTAGAT 59.151 47.619 0.00 0.00 45.47 1.98
273 274 1.065199 CAGCCACAAGCCCTCATTAGA 60.065 52.381 0.00 0.00 45.47 2.10
274 275 1.386533 CAGCCACAAGCCCTCATTAG 58.613 55.000 0.00 0.00 45.47 1.73
275 276 0.680921 GCAGCCACAAGCCCTCATTA 60.681 55.000 0.00 0.00 45.47 1.90
276 277 1.980772 GCAGCCACAAGCCCTCATT 60.981 57.895 0.00 0.00 45.47 2.57
277 278 2.362120 GCAGCCACAAGCCCTCAT 60.362 61.111 0.00 0.00 45.47 2.90
278 279 3.214190 ATGCAGCCACAAGCCCTCA 62.214 57.895 0.00 0.00 45.47 3.86
279 280 2.362120 ATGCAGCCACAAGCCCTC 60.362 61.111 0.00 0.00 45.47 4.30
280 281 2.678934 CATGCAGCCACAAGCCCT 60.679 61.111 0.00 0.00 45.47 5.19
281 282 4.446413 GCATGCAGCCACAAGCCC 62.446 66.667 14.21 0.00 45.47 5.19
282 283 2.901051 GATGCATGCAGCCACAAGCC 62.901 60.000 25.21 1.89 45.47 4.35
283 284 1.518572 GATGCATGCAGCCACAAGC 60.519 57.895 25.21 0.00 44.83 4.01
284 285 1.226575 CGATGCATGCAGCCACAAG 60.227 57.895 28.76 11.68 44.83 3.16
285 286 1.925415 GACGATGCATGCAGCCACAA 61.925 55.000 28.76 1.75 44.83 3.33
286 287 2.360225 ACGATGCATGCAGCCACA 60.360 55.556 28.76 2.58 44.83 4.17
287 288 0.811219 TAGACGATGCATGCAGCCAC 60.811 55.000 28.76 21.61 44.83 5.01
288 289 0.531311 CTAGACGATGCATGCAGCCA 60.531 55.000 28.76 11.54 44.83 4.75
289 290 0.249615 TCTAGACGATGCATGCAGCC 60.250 55.000 28.76 19.54 44.83 4.85
290 291 1.459975 CATCTAGACGATGCATGCAGC 59.540 52.381 25.69 25.69 42.75 5.25
299 300 0.965439 GGCCTCTGCATCTAGACGAT 59.035 55.000 0.00 0.00 40.13 3.73
300 301 1.448119 CGGCCTCTGCATCTAGACGA 61.448 60.000 0.00 0.00 40.13 4.20
301 302 1.007964 CGGCCTCTGCATCTAGACG 60.008 63.158 0.00 0.00 40.13 4.18
302 303 1.365633 CCGGCCTCTGCATCTAGAC 59.634 63.158 0.00 0.00 40.13 2.59
303 304 1.834378 CCCGGCCTCTGCATCTAGA 60.834 63.158 0.00 0.00 40.13 2.43
304 305 2.739784 CCCGGCCTCTGCATCTAG 59.260 66.667 0.00 0.00 40.13 2.43
305 306 2.844362 CCCCGGCCTCTGCATCTA 60.844 66.667 0.00 0.00 40.13 1.98
342 343 3.963129 TGGTCGCCCTCATTAGATTTTT 58.037 40.909 0.00 0.00 0.00 1.94
343 344 3.644966 TGGTCGCCCTCATTAGATTTT 57.355 42.857 0.00 0.00 0.00 1.82
344 345 3.644966 TTGGTCGCCCTCATTAGATTT 57.355 42.857 0.00 0.00 0.00 2.17
345 346 3.644966 TTTGGTCGCCCTCATTAGATT 57.355 42.857 0.00 0.00 0.00 2.40
346 347 3.136443 TCATTTGGTCGCCCTCATTAGAT 59.864 43.478 0.00 0.00 0.00 1.98
347 348 2.503765 TCATTTGGTCGCCCTCATTAGA 59.496 45.455 0.00 0.00 0.00 2.10
348 349 2.874701 CTCATTTGGTCGCCCTCATTAG 59.125 50.000 0.00 0.00 0.00 1.73
349 350 2.421388 CCTCATTTGGTCGCCCTCATTA 60.421 50.000 0.00 0.00 0.00 1.90
350 351 1.683011 CCTCATTTGGTCGCCCTCATT 60.683 52.381 0.00 0.00 0.00 2.57
351 352 0.107017 CCTCATTTGGTCGCCCTCAT 60.107 55.000 0.00 0.00 0.00 2.90
352 353 1.299648 CCTCATTTGGTCGCCCTCA 59.700 57.895 0.00 0.00 0.00 3.86
353 354 1.026718 CACCTCATTTGGTCGCCCTC 61.027 60.000 0.00 0.00 38.45 4.30
354 355 1.002134 CACCTCATTTGGTCGCCCT 60.002 57.895 0.00 0.00 38.45 5.19
355 356 2.700773 GCACCTCATTTGGTCGCCC 61.701 63.158 0.00 0.00 38.45 6.13
356 357 1.926511 CTGCACCTCATTTGGTCGCC 61.927 60.000 0.00 0.00 38.45 5.54
357 358 0.955428 TCTGCACCTCATTTGGTCGC 60.955 55.000 0.00 0.00 38.45 5.19
358 359 1.399440 CATCTGCACCTCATTTGGTCG 59.601 52.381 0.00 0.00 38.45 4.79
359 360 2.440409 ACATCTGCACCTCATTTGGTC 58.560 47.619 0.00 0.00 38.45 4.02
360 361 2.592102 ACATCTGCACCTCATTTGGT 57.408 45.000 0.00 0.00 41.77 3.67
361 362 3.614092 ACTACATCTGCACCTCATTTGG 58.386 45.455 0.00 0.00 0.00 3.28
362 363 5.633830 AAACTACATCTGCACCTCATTTG 57.366 39.130 0.00 0.00 0.00 2.32
363 364 6.655078 AAAAACTACATCTGCACCTCATTT 57.345 33.333 0.00 0.00 0.00 2.32
387 388 3.416156 AGGCAAAACAGGCAAACAAAAA 58.584 36.364 0.00 0.00 36.37 1.94
388 389 3.064900 AGGCAAAACAGGCAAACAAAA 57.935 38.095 0.00 0.00 36.37 2.44
389 390 2.777832 AGGCAAAACAGGCAAACAAA 57.222 40.000 0.00 0.00 36.37 2.83
390 391 2.777832 AAGGCAAAACAGGCAAACAA 57.222 40.000 0.00 0.00 36.37 2.83
391 392 2.482839 GCTAAGGCAAAACAGGCAAACA 60.483 45.455 0.00 0.00 38.54 2.83
392 393 2.135139 GCTAAGGCAAAACAGGCAAAC 58.865 47.619 0.00 0.00 38.54 2.93
393 394 1.069978 GGCTAAGGCAAAACAGGCAAA 59.930 47.619 0.00 0.00 40.87 3.68
394 395 0.678950 GGCTAAGGCAAAACAGGCAA 59.321 50.000 0.00 0.00 40.87 4.52
395 396 0.468958 TGGCTAAGGCAAAACAGGCA 60.469 50.000 0.00 0.00 40.80 4.75
396 397 0.244721 CTGGCTAAGGCAAAACAGGC 59.755 55.000 0.00 0.00 37.73 4.85
397 398 1.909700 TCTGGCTAAGGCAAAACAGG 58.090 50.000 0.00 0.00 37.73 4.00
398 399 2.424956 GGATCTGGCTAAGGCAAAACAG 59.575 50.000 0.00 0.00 37.73 3.16
399 400 2.224992 TGGATCTGGCTAAGGCAAAACA 60.225 45.455 0.00 0.00 37.73 2.83
400 401 2.446435 TGGATCTGGCTAAGGCAAAAC 58.554 47.619 0.00 0.00 37.73 2.43
401 402 2.825532 GTTGGATCTGGCTAAGGCAAAA 59.174 45.455 0.00 0.00 37.73 2.44
402 403 2.041620 AGTTGGATCTGGCTAAGGCAAA 59.958 45.455 0.00 0.00 37.73 3.68
403 404 1.635487 AGTTGGATCTGGCTAAGGCAA 59.365 47.619 0.00 0.00 37.73 4.52
404 405 1.289160 AGTTGGATCTGGCTAAGGCA 58.711 50.000 0.00 0.00 40.87 4.75
405 406 2.224402 CCTAGTTGGATCTGGCTAAGGC 60.224 54.545 0.00 0.00 38.35 4.35
406 407 3.309296 TCCTAGTTGGATCTGGCTAAGG 58.691 50.000 0.00 0.00 40.56 2.69
416 417 9.966356 TGCATTGCATACATGTCCTAGTTGGAT 62.966 40.741 7.38 0.00 39.58 3.41
417 418 4.835284 TTGCATACATGTCCTAGTTGGA 57.165 40.909 0.00 0.00 43.86 3.53
418 419 4.261322 GCATTGCATACATGTCCTAGTTGG 60.261 45.833 0.00 0.00 37.10 3.77
419 420 4.336153 TGCATTGCATACATGTCCTAGTTG 59.664 41.667 7.38 0.00 31.71 3.16
420 421 4.525996 TGCATTGCATACATGTCCTAGTT 58.474 39.130 7.38 0.00 31.71 2.24
421 422 4.132336 CTGCATTGCATACATGTCCTAGT 58.868 43.478 12.53 0.00 38.13 2.57
422 423 4.212847 GTCTGCATTGCATACATGTCCTAG 59.787 45.833 18.98 1.77 38.13 3.02
423 424 4.129380 GTCTGCATTGCATACATGTCCTA 58.871 43.478 18.98 0.00 38.13 2.94
424 425 2.947652 GTCTGCATTGCATACATGTCCT 59.052 45.455 18.98 0.00 38.13 3.85
425 426 2.684374 TGTCTGCATTGCATACATGTCC 59.316 45.455 21.72 0.53 39.92 4.02
426 427 4.359971 TTGTCTGCATTGCATACATGTC 57.640 40.909 24.82 7.64 43.18 3.06
427 428 4.787260 TTTGTCTGCATTGCATACATGT 57.213 36.364 24.82 2.69 43.18 3.21
428 429 5.233476 GGAATTTGTCTGCATTGCATACATG 59.767 40.000 24.82 9.17 43.18 3.21
429 430 5.353938 GGAATTTGTCTGCATTGCATACAT 58.646 37.500 24.82 13.95 43.18 2.29
430 431 4.381825 GGGAATTTGTCTGCATTGCATACA 60.382 41.667 21.72 21.72 42.31 2.29
431 432 4.114794 GGGAATTTGTCTGCATTGCATAC 58.885 43.478 17.54 17.54 38.13 2.39
432 433 3.768215 TGGGAATTTGTCTGCATTGCATA 59.232 39.130 12.53 1.58 38.13 3.14
433 434 2.568062 TGGGAATTTGTCTGCATTGCAT 59.432 40.909 12.53 0.00 38.13 3.96
434 435 1.969208 TGGGAATTTGTCTGCATTGCA 59.031 42.857 11.50 11.50 36.92 4.08
435 436 2.288948 TGTGGGAATTTGTCTGCATTGC 60.289 45.455 0.46 0.46 0.00 3.56
436 437 3.663995 TGTGGGAATTTGTCTGCATTG 57.336 42.857 0.00 0.00 0.00 2.82
437 438 3.833650 TCATGTGGGAATTTGTCTGCATT 59.166 39.130 0.00 0.00 0.00 3.56
438 439 3.194116 GTCATGTGGGAATTTGTCTGCAT 59.806 43.478 0.00 0.00 0.00 3.96
439 440 2.557924 GTCATGTGGGAATTTGTCTGCA 59.442 45.455 0.00 0.00 0.00 4.41
440 441 2.557924 TGTCATGTGGGAATTTGTCTGC 59.442 45.455 0.00 0.00 0.00 4.26
441 442 4.549458 GTTGTCATGTGGGAATTTGTCTG 58.451 43.478 0.00 0.00 0.00 3.51
442 443 3.573967 GGTTGTCATGTGGGAATTTGTCT 59.426 43.478 0.00 0.00 0.00 3.41
443 444 3.320541 TGGTTGTCATGTGGGAATTTGTC 59.679 43.478 0.00 0.00 0.00 3.18
444 445 3.303938 TGGTTGTCATGTGGGAATTTGT 58.696 40.909 0.00 0.00 0.00 2.83
445 446 4.333913 TTGGTTGTCATGTGGGAATTTG 57.666 40.909 0.00 0.00 0.00 2.32
446 447 4.163078 TGTTTGGTTGTCATGTGGGAATTT 59.837 37.500 0.00 0.00 0.00 1.82
447 448 3.708631 TGTTTGGTTGTCATGTGGGAATT 59.291 39.130 0.00 0.00 0.00 2.17
448 449 3.069443 GTGTTTGGTTGTCATGTGGGAAT 59.931 43.478 0.00 0.00 0.00 3.01
449 450 2.428890 GTGTTTGGTTGTCATGTGGGAA 59.571 45.455 0.00 0.00 0.00 3.97
450 451 2.028130 GTGTTTGGTTGTCATGTGGGA 58.972 47.619 0.00 0.00 0.00 4.37
451 452 1.268999 CGTGTTTGGTTGTCATGTGGG 60.269 52.381 0.00 0.00 0.00 4.61
452 453 1.673400 TCGTGTTTGGTTGTCATGTGG 59.327 47.619 0.00 0.00 0.00 4.17
453 454 2.540769 GGTCGTGTTTGGTTGTCATGTG 60.541 50.000 0.00 0.00 0.00 3.21
454 455 1.673920 GGTCGTGTTTGGTTGTCATGT 59.326 47.619 0.00 0.00 0.00 3.21
455 456 1.001815 GGGTCGTGTTTGGTTGTCATG 60.002 52.381 0.00 0.00 0.00 3.07
456 457 1.133915 AGGGTCGTGTTTGGTTGTCAT 60.134 47.619 0.00 0.00 0.00 3.06
457 458 0.253610 AGGGTCGTGTTTGGTTGTCA 59.746 50.000 0.00 0.00 0.00 3.58
458 459 2.140717 CTAGGGTCGTGTTTGGTTGTC 58.859 52.381 0.00 0.00 0.00 3.18
459 460 1.487558 ACTAGGGTCGTGTTTGGTTGT 59.512 47.619 0.00 0.00 0.00 3.32
460 461 1.871039 CACTAGGGTCGTGTTTGGTTG 59.129 52.381 0.00 0.00 0.00 3.77
461 462 1.202722 CCACTAGGGTCGTGTTTGGTT 60.203 52.381 0.00 0.00 0.00 3.67
462 463 0.395312 CCACTAGGGTCGTGTTTGGT 59.605 55.000 0.00 0.00 0.00 3.67
463 464 3.226884 CCACTAGGGTCGTGTTTGG 57.773 57.895 0.00 0.00 0.00 3.28
474 475 0.464452 CTTACCCTTCGCCCACTAGG 59.536 60.000 0.00 0.00 39.47 3.02
475 476 0.179081 GCTTACCCTTCGCCCACTAG 60.179 60.000 0.00 0.00 0.00 2.57
476 477 0.616679 AGCTTACCCTTCGCCCACTA 60.617 55.000 0.00 0.00 0.00 2.74
477 478 1.489560 AAGCTTACCCTTCGCCCACT 61.490 55.000 0.00 0.00 0.00 4.00
478 479 0.608308 AAAGCTTACCCTTCGCCCAC 60.608 55.000 0.00 0.00 0.00 4.61
479 480 0.111639 AAAAGCTTACCCTTCGCCCA 59.888 50.000 0.00 0.00 0.00 5.36
480 481 1.254026 AAAAAGCTTACCCTTCGCCC 58.746 50.000 0.00 0.00 0.00 6.13
505 506 0.100325 CTGCTGTGTCCGTGCAAAAA 59.900 50.000 0.00 0.00 36.22 1.94
506 507 1.723608 CCTGCTGTGTCCGTGCAAAA 61.724 55.000 0.00 0.00 36.22 2.44
507 508 2.186160 CCTGCTGTGTCCGTGCAAA 61.186 57.895 0.00 0.00 36.22 3.68
508 509 2.591429 CCTGCTGTGTCCGTGCAA 60.591 61.111 0.00 0.00 36.22 4.08
509 510 4.624364 CCCTGCTGTGTCCGTGCA 62.624 66.667 0.00 0.00 35.30 4.57
510 511 2.725203 TTACCCTGCTGTGTCCGTGC 62.725 60.000 0.00 0.00 0.00 5.34
511 512 0.670546 CTTACCCTGCTGTGTCCGTG 60.671 60.000 0.00 0.00 0.00 4.94
512 513 1.119574 ACTTACCCTGCTGTGTCCGT 61.120 55.000 0.00 0.00 0.00 4.69
513 514 0.034896 AACTTACCCTGCTGTGTCCG 59.965 55.000 0.00 0.00 0.00 4.79
514 515 1.880027 CAAACTTACCCTGCTGTGTCC 59.120 52.381 0.00 0.00 0.00 4.02
515 516 1.266989 GCAAACTTACCCTGCTGTGTC 59.733 52.381 0.00 0.00 33.20 3.67
516 517 1.318576 GCAAACTTACCCTGCTGTGT 58.681 50.000 0.00 0.00 33.20 3.72
517 518 0.238289 CGCAAACTTACCCTGCTGTG 59.762 55.000 0.00 0.00 33.82 3.66
518 519 0.107831 TCGCAAACTTACCCTGCTGT 59.892 50.000 0.00 0.00 33.82 4.40
519 520 0.798776 CTCGCAAACTTACCCTGCTG 59.201 55.000 0.00 0.00 33.82 4.41
520 521 0.321653 CCTCGCAAACTTACCCTGCT 60.322 55.000 0.00 0.00 33.82 4.24
521 522 0.605589 ACCTCGCAAACTTACCCTGC 60.606 55.000 0.00 0.00 0.00 4.85
522 523 2.344025 GTACCTCGCAAACTTACCCTG 58.656 52.381 0.00 0.00 0.00 4.45
523 524 1.277273 GGTACCTCGCAAACTTACCCT 59.723 52.381 4.06 0.00 0.00 4.34
524 525 1.730501 GGTACCTCGCAAACTTACCC 58.269 55.000 4.06 0.00 0.00 3.69
539 540 6.128090 GCTTACACAAACAGAATTAGGGGTAC 60.128 42.308 0.00 0.00 0.00 3.34
540 541 5.941647 GCTTACACAAACAGAATTAGGGGTA 59.058 40.000 0.00 0.00 0.00 3.69
541 542 4.765339 GCTTACACAAACAGAATTAGGGGT 59.235 41.667 0.00 0.00 0.00 4.95
542 543 4.764823 TGCTTACACAAACAGAATTAGGGG 59.235 41.667 0.00 0.00 0.00 4.79
543 544 5.699839 GTGCTTACACAAACAGAATTAGGG 58.300 41.667 0.00 0.00 46.61 3.53
563 564 5.738370 AGATTTTTCGAGCAATATACGTGC 58.262 37.500 0.00 2.60 42.55 5.34
564 565 6.933130 TGAGATTTTTCGAGCAATATACGTG 58.067 36.000 0.00 0.00 0.00 4.49
565 566 7.277981 ACTTGAGATTTTTCGAGCAATATACGT 59.722 33.333 0.00 0.00 32.72 3.57
566 567 7.621991 ACTTGAGATTTTTCGAGCAATATACG 58.378 34.615 0.00 0.00 32.72 3.06
592 593 9.770097 GTGCCACATGCTATACTGAATATATAT 57.230 33.333 0.00 0.00 42.00 0.86
593 594 8.204160 GGTGCCACATGCTATACTGAATATATA 58.796 37.037 0.00 0.00 42.00 0.86
594 595 7.050377 GGTGCCACATGCTATACTGAATATAT 58.950 38.462 0.00 0.00 42.00 0.86
595 596 6.406370 GGTGCCACATGCTATACTGAATATA 58.594 40.000 0.00 0.00 42.00 0.86
596 597 5.248640 GGTGCCACATGCTATACTGAATAT 58.751 41.667 0.00 0.00 42.00 1.28
597 598 4.641396 GGTGCCACATGCTATACTGAATA 58.359 43.478 0.00 0.00 42.00 1.75
598 599 3.480470 GGTGCCACATGCTATACTGAAT 58.520 45.455 0.00 0.00 42.00 2.57
599 600 2.741553 CGGTGCCACATGCTATACTGAA 60.742 50.000 0.00 0.00 42.00 3.02
600 601 1.202521 CGGTGCCACATGCTATACTGA 60.203 52.381 0.00 0.00 42.00 3.41
601 602 1.220529 CGGTGCCACATGCTATACTG 58.779 55.000 0.00 0.00 42.00 2.74
602 603 0.106708 CCGGTGCCACATGCTATACT 59.893 55.000 0.00 0.00 42.00 2.12
603 604 0.179056 ACCGGTGCCACATGCTATAC 60.179 55.000 6.12 0.00 42.00 1.47
604 605 1.069513 GTACCGGTGCCACATGCTATA 59.930 52.381 19.93 0.00 42.00 1.31
636 637 2.752354 TGTAAGCGTGGGAATTTCATGG 59.248 45.455 0.00 0.00 0.00 3.66
647 648 2.762745 ACTGGTAGTTTGTAAGCGTGG 58.237 47.619 0.00 0.00 0.00 4.94
655 656 2.051692 TGCCACCTACTGGTAGTTTGT 58.948 47.619 6.96 0.00 46.60 2.83
682 683 5.774690 TGTTTTAATCAACAGAGAGGGCAAT 59.225 36.000 0.00 0.00 32.70 3.56
683 684 5.136828 TGTTTTAATCAACAGAGAGGGCAA 58.863 37.500 0.00 0.00 32.70 4.52
685 686 5.393461 CCATGTTTTAATCAACAGAGAGGGC 60.393 44.000 0.00 0.00 40.01 5.19
686 687 5.393461 GCCATGTTTTAATCAACAGAGAGGG 60.393 44.000 0.00 0.00 40.01 4.30
689 690 5.335897 GCTGCCATGTTTTAATCAACAGAGA 60.336 40.000 0.00 0.00 40.01 3.10
692 698 3.609373 CGCTGCCATGTTTTAATCAACAG 59.391 43.478 0.00 0.00 40.01 3.16
702 708 1.269448 ACGAAATTCGCTGCCATGTTT 59.731 42.857 15.90 0.00 45.12 2.83
706 712 1.398390 GAAGACGAAATTCGCTGCCAT 59.602 47.619 15.90 0.00 45.12 4.40
799 894 3.763897 AGTTGTTCCTTGTTTGCACTCTT 59.236 39.130 0.00 0.00 0.00 2.85
918 1021 3.518998 GCTGCTGCTGCTGATGGG 61.519 66.667 23.39 5.95 40.01 4.00
2031 2214 4.388499 TCCTTGAAGGCGCCGGTC 62.388 66.667 23.20 22.57 34.61 4.79
2153 2336 3.656559 TGTACTTCTTCGGTGGCTTAAC 58.343 45.455 0.00 0.00 0.00 2.01
2201 2384 6.245408 ACAATCTTACAGCAATTTACAGGGA 58.755 36.000 0.00 0.00 0.00 4.20
2228 2411 5.178797 AGCTACGACAATCTTACAGCAATT 58.821 37.500 0.00 0.00 0.00 2.32
2229 2412 4.759782 AGCTACGACAATCTTACAGCAAT 58.240 39.130 0.00 0.00 0.00 3.56
2230 2413 4.174009 GAGCTACGACAATCTTACAGCAA 58.826 43.478 0.00 0.00 0.00 3.91
2231 2414 3.428999 GGAGCTACGACAATCTTACAGCA 60.429 47.826 0.00 0.00 0.00 4.41
2232 2415 3.117046 GGAGCTACGACAATCTTACAGC 58.883 50.000 0.00 0.00 0.00 4.40
2233 2416 4.640789 AGGAGCTACGACAATCTTACAG 57.359 45.455 0.00 0.00 0.00 2.74
2234 2417 5.185249 AGAAAGGAGCTACGACAATCTTACA 59.815 40.000 0.00 0.00 0.00 2.41
2235 2418 5.652518 AGAAAGGAGCTACGACAATCTTAC 58.347 41.667 0.00 0.00 0.00 2.34
2236 2419 5.652891 AGAGAAAGGAGCTACGACAATCTTA 59.347 40.000 0.00 0.00 0.00 2.10
2237 2420 4.464597 AGAGAAAGGAGCTACGACAATCTT 59.535 41.667 0.00 0.00 0.00 2.40
2238 2421 4.020543 AGAGAAAGGAGCTACGACAATCT 58.979 43.478 0.00 0.00 0.00 2.40
2239 2422 4.097286 AGAGAGAAAGGAGCTACGACAATC 59.903 45.833 0.00 0.00 0.00 2.67
2240 2423 4.020543 AGAGAGAAAGGAGCTACGACAAT 58.979 43.478 0.00 0.00 0.00 2.71
2241 2424 3.422796 AGAGAGAAAGGAGCTACGACAA 58.577 45.455 0.00 0.00 0.00 3.18
2242 2425 3.011119 GAGAGAGAAAGGAGCTACGACA 58.989 50.000 0.00 0.00 0.00 4.35
2243 2426 3.011119 TGAGAGAGAAAGGAGCTACGAC 58.989 50.000 0.00 0.00 0.00 4.34
2244 2427 3.351794 TGAGAGAGAAAGGAGCTACGA 57.648 47.619 0.00 0.00 0.00 3.43
2245 2428 3.442273 AGTTGAGAGAGAAAGGAGCTACG 59.558 47.826 0.00 0.00 0.00 3.51
2246 2429 5.185056 AGAAGTTGAGAGAGAAAGGAGCTAC 59.815 44.000 0.00 0.00 0.00 3.58
2332 2515 1.202065 CGTCGGATGTGGCAATTTCAG 60.202 52.381 0.00 0.00 0.00 3.02
2991 5679 2.799126 ATTGGTAAGGCGGTTGATGA 57.201 45.000 0.00 0.00 0.00 2.92
3079 5770 5.719085 AGATTTGAGAGAGAAAGGAGCTACA 59.281 40.000 0.00 0.00 0.00 2.74
3131 5822 9.508642 TGTGTACAAGATATTCAATTGGTTGTA 57.491 29.630 5.42 7.68 36.69 2.41
3132 5823 8.402798 TGTGTACAAGATATTCAATTGGTTGT 57.597 30.769 5.42 8.52 36.69 3.32


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

AutoCloner maintained by Alex Coulton.