Multiple sequence alignment - TraesCS7A01G398200

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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 TraesCS7A01G398200 chr7A 100.000 4757 0 0 1 4757 577222067 577226823 0.000000e+00 8785
1 TraesCS7A01G398200 chr7A 93.103 522 29 6 1542 2057 93143659 93144179 0.000000e+00 758
2 TraesCS7A01G398200 chr7A 92.802 514 31 6 1549 2057 373293181 373292669 0.000000e+00 739
3 TraesCS7A01G398200 chr7A 88.095 294 29 5 1542 1830 94036007 94036299 1.270000e-90 344
4 TraesCS7A01G398200 chr7A 98.361 61 1 0 1997 2057 94036296 94036356 1.810000e-19 108
5 TraesCS7A01G398200 chr7B 93.490 4209 185 46 594 4757 535822170 535826334 0.000000e+00 6172
6 TraesCS7A01G398200 chr7D 94.104 3477 151 19 1309 4757 507420634 507424084 0.000000e+00 5236
7 TraesCS7A01G398200 chr7D 92.683 697 20 13 609 1289 507419901 507420582 0.000000e+00 976
8 TraesCS7A01G398200 chr7D 87.324 284 26 6 15 298 507419369 507419642 2.760000e-82 316
9 TraesCS7A01G398200 chr4A 92.692 520 32 5 1543 2057 535417223 535417741 0.000000e+00 745
10 TraesCS7A01G398200 chr4A 84.036 332 31 12 1187 1501 613941633 613941959 2.780000e-77 300
11 TraesCS7A01G398200 chr2A 92.514 521 33 5 1542 2057 736867100 736866581 0.000000e+00 741
12 TraesCS7A01G398200 chr1A 92.500 520 34 4 1542 2057 465397066 465396548 0.000000e+00 739
13 TraesCS7A01G398200 chr1A 91.747 521 34 6 1542 2057 5950451 5950967 0.000000e+00 715
14 TraesCS7A01G398200 chr1A 93.204 103 5 2 1187 1289 5950106 5950206 2.970000e-32 150
15 TraesCS7A01G398200 chr3D 84.337 166 25 1 1105 1270 593112148 593112312 1.370000e-35 161
16 TraesCS7A01G398200 chr3B 83.735 166 26 1 1105 1270 795377969 795378133 6.370000e-34 156
17 TraesCS7A01G398200 chr6A 79.255 188 34 4 1099 1282 506232464 506232650 5.000000e-25 126
18 TraesCS7A01G398200 chr6D 80.368 163 30 2 1099 1260 365275686 365275847 6.460000e-24 122
19 TraesCS7A01G398200 chr6B 80.368 163 30 2 1099 1260 550074337 550074498 6.460000e-24 122


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 TraesCS7A01G398200 chr7A 577222067 577226823 4756 False 8785.0 8785 100.000000 1 4757 1 chr7A.!!$F2 4756
1 TraesCS7A01G398200 chr7A 93143659 93144179 520 False 758.0 758 93.103000 1542 2057 1 chr7A.!!$F1 515
2 TraesCS7A01G398200 chr7A 373292669 373293181 512 True 739.0 739 92.802000 1549 2057 1 chr7A.!!$R1 508
3 TraesCS7A01G398200 chr7B 535822170 535826334 4164 False 6172.0 6172 93.490000 594 4757 1 chr7B.!!$F1 4163
4 TraesCS7A01G398200 chr7D 507419369 507424084 4715 False 2176.0 5236 91.370333 15 4757 3 chr7D.!!$F1 4742
5 TraesCS7A01G398200 chr4A 535417223 535417741 518 False 745.0 745 92.692000 1543 2057 1 chr4A.!!$F1 514
6 TraesCS7A01G398200 chr2A 736866581 736867100 519 True 741.0 741 92.514000 1542 2057 1 chr2A.!!$R1 515
7 TraesCS7A01G398200 chr1A 465396548 465397066 518 True 739.0 739 92.500000 1542 2057 1 chr1A.!!$R1 515
8 TraesCS7A01G398200 chr1A 5950106 5950967 861 False 432.5 715 92.475500 1187 2057 2 chr1A.!!$F1 870

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
416 417 0.103390 GGCTTCTTCTAGCTCCGACC 59.897 60.000 0.00 0.00 40.99 4.79 F
533 535 0.111354 GACGACGTCGGTATAGCTCG 60.111 60.000 37.89 13.34 44.95 5.03 F
558 619 0.323629 TTTACGCCTTGTCCTCCCTG 59.676 55.000 0.00 0.00 0.00 4.45 F
563 624 0.402121 GCCTTGTCCTCCCTGAGTTT 59.598 55.000 0.00 0.00 0.00 2.66 F
827 898 0.609662 TTTACTAACCGCTTCCGCCT 59.390 50.000 0.00 0.00 0.00 5.52 F
1503 1634 0.750546 GGGGCGGTAACAGGGAAATC 60.751 60.000 0.00 0.00 0.00 2.17 F
1521 1652 0.955428 TCATTTGACTCTGGCACGGC 60.955 55.000 0.00 0.00 32.53 5.68 F
1571 1705 0.991920 ACCTAGGGTGTCCATGTTGG 59.008 55.000 14.81 0.00 34.55 3.77 F
2087 2227 2.550639 GGGCATGCCTGTTTGTTTCAAT 60.551 45.455 34.70 0.00 36.10 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1330 1460 0.320050 ACAAATCGCCGGCCAAAAAT 59.680 45.000 23.46 3.85 0.00 1.82 R
1342 1472 0.466189 CCCCTGATCCCCACAAATCG 60.466 60.000 0.00 0.00 0.00 3.34 R
1359 1489 1.071542 CCCCAATTGAACCACAAACCC 59.928 52.381 7.12 0.00 42.03 4.11 R
1521 1652 1.203052 ACAAAGCCTGGCAATCAATCG 59.797 47.619 22.65 2.57 0.00 3.34 R
2061 2201 1.211457 ACAAACAGGCATGCCCAAAAA 59.789 42.857 33.14 0.00 36.58 1.94 R
2531 2687 4.765339 ACAACCTCCTATTGTAAAAGTGCC 59.235 41.667 0.00 0.00 38.51 5.01 R
2650 2807 6.405538 TCTCAACATAAAATTTGGCCATTCC 58.594 36.000 6.09 0.00 0.00 3.01 R
3199 3366 8.500753 AACAACGGATTATTATTTGCAGTAGA 57.499 30.769 0.00 0.00 0.00 2.59 R
3823 3990 0.829990 TGTCACAACAGCTGGACAGA 59.170 50.000 19.93 7.86 33.14 3.41 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
28 29 0.462047 GGTAGGCGTCTCATTGGTGG 60.462 60.000 0.00 0.00 0.00 4.61
32 33 2.690778 GCGTCTCATTGGTGGTGGC 61.691 63.158 0.00 0.00 0.00 5.01
61 62 0.609662 AAGGTGTGATTGGCATTGGC 59.390 50.000 2.73 2.73 40.13 4.52
62 63 1.153784 GGTGTGATTGGCATTGGCG 60.154 57.895 5.68 0.00 42.47 5.69
63 64 1.153784 GTGTGATTGGCATTGGCGG 60.154 57.895 5.68 0.00 42.47 6.13
64 65 1.303970 TGTGATTGGCATTGGCGGA 60.304 52.632 5.68 0.00 42.47 5.54
65 66 1.314534 TGTGATTGGCATTGGCGGAG 61.315 55.000 5.68 0.00 42.47 4.63
66 67 1.753848 TGATTGGCATTGGCGGAGG 60.754 57.895 5.68 0.00 42.47 4.30
81 82 2.281761 AGGGCGTGTGGAGCTTTG 60.282 61.111 0.00 0.00 34.52 2.77
86 87 1.444119 GCGTGTGGAGCTTTGGTCAA 61.444 55.000 0.00 0.00 0.00 3.18
88 89 0.954452 GTGTGGAGCTTTGGTCAAGG 59.046 55.000 0.00 0.00 32.37 3.61
99 100 1.002011 GGTCAAGGCTGAAGGGTCC 60.002 63.158 0.00 0.00 31.88 4.46
100 101 1.002011 GTCAAGGCTGAAGGGTCCC 60.002 63.158 0.00 0.00 31.88 4.46
101 102 2.045926 CAAGGCTGAAGGGTCCCG 60.046 66.667 0.99 0.00 0.00 5.14
102 103 4.035102 AAGGCTGAAGGGTCCCGC 62.035 66.667 0.99 0.00 0.00 6.13
113 114 1.078637 GGTCCCGCCTTTGTCTACC 60.079 63.158 0.00 0.00 0.00 3.18
132 133 6.436847 GTCTACCTTTAGTCTAGGTGGTCTTT 59.563 42.308 4.75 0.00 45.45 2.52
137 138 6.463897 CCTTTAGTCTAGGTGGTCTTTGACAA 60.464 42.308 0.07 0.00 33.68 3.18
146 147 4.099419 GGTGGTCTTTGACAACATCCTTTT 59.901 41.667 7.43 0.00 38.17 2.27
149 150 5.043248 GGTCTTTGACAACATCCTTTTGTG 58.957 41.667 0.07 0.00 37.31 3.33
160 161 6.403866 ACATCCTTTTGTGTTTTGCTCATA 57.596 33.333 0.00 0.00 0.00 2.15
181 182 1.686587 TGCCTTCTTCTCTGTTCGACA 59.313 47.619 0.00 0.00 0.00 4.35
231 232 3.611025 AGCTAGTGAGATTAGGCCTCT 57.389 47.619 9.68 0.00 0.00 3.69
232 233 4.733077 AGCTAGTGAGATTAGGCCTCTA 57.267 45.455 9.68 0.99 0.00 2.43
233 234 5.269554 AGCTAGTGAGATTAGGCCTCTAT 57.730 43.478 9.68 3.73 0.00 1.98
238 239 5.463154 AGTGAGATTAGGCCTCTATGTTCT 58.537 41.667 9.68 3.44 0.00 3.01
244 245 9.469097 GAGATTAGGCCTCTATGTTCTTATCTA 57.531 37.037 9.68 0.00 0.00 1.98
245 246 9.474313 AGATTAGGCCTCTATGTTCTTATCTAG 57.526 37.037 9.68 0.00 0.00 2.43
265 266 2.305927 AGACGAATCTGGGATGGTTGTT 59.694 45.455 0.00 0.00 32.29 2.83
266 267 2.420022 GACGAATCTGGGATGGTTGTTG 59.580 50.000 0.00 0.00 0.00 3.33
267 268 2.224769 ACGAATCTGGGATGGTTGTTGT 60.225 45.455 0.00 0.00 0.00 3.32
281 282 1.298014 GTTGTCCAGCCCTCCTCAG 59.702 63.158 0.00 0.00 0.00 3.35
298 299 3.057174 CCTCAGCTACTTTCTTCTCGTGT 60.057 47.826 0.00 0.00 0.00 4.49
299 300 3.902150 TCAGCTACTTTCTTCTCGTGTG 58.098 45.455 0.00 0.00 0.00 3.82
301 302 2.297597 AGCTACTTTCTTCTCGTGTGCT 59.702 45.455 0.00 0.00 0.00 4.40
303 304 3.854809 GCTACTTTCTTCTCGTGTGCTAG 59.145 47.826 0.00 0.00 0.00 3.42
304 305 2.678324 ACTTTCTTCTCGTGTGCTAGC 58.322 47.619 8.10 8.10 0.00 3.42
305 306 1.651138 CTTTCTTCTCGTGTGCTAGCG 59.349 52.381 10.77 0.00 0.00 4.26
306 307 0.879090 TTCTTCTCGTGTGCTAGCGA 59.121 50.000 10.77 0.00 35.70 4.93
307 308 0.879090 TCTTCTCGTGTGCTAGCGAA 59.121 50.000 10.77 5.32 36.65 4.70
308 309 0.985549 CTTCTCGTGTGCTAGCGAAC 59.014 55.000 10.77 9.78 36.65 3.95
309 310 0.728129 TTCTCGTGTGCTAGCGAACG 60.728 55.000 27.07 27.07 36.65 3.95
310 311 1.442184 CTCGTGTGCTAGCGAACGT 60.442 57.895 29.66 0.00 36.65 3.99
311 312 1.665544 CTCGTGTGCTAGCGAACGTG 61.666 60.000 29.66 25.62 36.65 4.49
312 313 2.014554 CGTGTGCTAGCGAACGTGT 61.015 57.895 25.54 0.00 0.00 4.49
313 314 1.545614 CGTGTGCTAGCGAACGTGTT 61.546 55.000 25.54 0.00 0.00 3.32
314 315 0.111266 GTGTGCTAGCGAACGTGTTG 60.111 55.000 10.77 0.00 0.00 3.33
315 316 1.154654 GTGCTAGCGAACGTGTTGC 60.155 57.895 10.77 0.00 0.00 4.17
316 317 1.592939 TGCTAGCGAACGTGTTGCA 60.593 52.632 10.77 2.95 0.00 4.08
317 318 1.154654 GCTAGCGAACGTGTTGCAC 60.155 57.895 0.00 0.00 0.00 4.57
327 328 2.755929 GTGTTGCACGATCCCTCTC 58.244 57.895 0.00 0.00 0.00 3.20
328 329 0.247736 GTGTTGCACGATCCCTCTCT 59.752 55.000 0.00 0.00 0.00 3.10
329 330 0.532573 TGTTGCACGATCCCTCTCTC 59.467 55.000 0.00 0.00 0.00 3.20
330 331 0.179097 GTTGCACGATCCCTCTCTCC 60.179 60.000 0.00 0.00 0.00 3.71
331 332 0.614697 TTGCACGATCCCTCTCTCCA 60.615 55.000 0.00 0.00 0.00 3.86
332 333 0.397675 TGCACGATCCCTCTCTCCAT 60.398 55.000 0.00 0.00 0.00 3.41
333 334 0.755686 GCACGATCCCTCTCTCCATT 59.244 55.000 0.00 0.00 0.00 3.16
334 335 1.270041 GCACGATCCCTCTCTCCATTC 60.270 57.143 0.00 0.00 0.00 2.67
335 336 1.342819 CACGATCCCTCTCTCCATTCC 59.657 57.143 0.00 0.00 0.00 3.01
336 337 0.972883 CGATCCCTCTCTCCATTCCC 59.027 60.000 0.00 0.00 0.00 3.97
337 338 1.482177 CGATCCCTCTCTCCATTCCCT 60.482 57.143 0.00 0.00 0.00 4.20
338 339 2.256306 GATCCCTCTCTCCATTCCCTC 58.744 57.143 0.00 0.00 0.00 4.30
339 340 0.105964 TCCCTCTCTCCATTCCCTCG 60.106 60.000 0.00 0.00 0.00 4.63
340 341 1.745264 CCTCTCTCCATTCCCTCGC 59.255 63.158 0.00 0.00 0.00 5.03
341 342 0.758685 CCTCTCTCCATTCCCTCGCT 60.759 60.000 0.00 0.00 0.00 4.93
342 343 0.673437 CTCTCTCCATTCCCTCGCTC 59.327 60.000 0.00 0.00 0.00 5.03
343 344 1.103987 TCTCTCCATTCCCTCGCTCG 61.104 60.000 0.00 0.00 0.00 5.03
344 345 1.076995 TCTCCATTCCCTCGCTCGA 60.077 57.895 0.00 0.00 0.00 4.04
345 346 1.103987 TCTCCATTCCCTCGCTCGAG 61.104 60.000 8.45 8.45 41.63 4.04
346 347 2.279784 CCATTCCCTCGCTCGAGC 60.280 66.667 27.64 27.64 40.69 5.03
347 348 2.790791 CCATTCCCTCGCTCGAGCT 61.791 63.158 32.88 11.58 40.69 4.09
348 349 1.299773 CATTCCCTCGCTCGAGCTC 60.300 63.158 32.88 2.73 40.69 4.09
349 350 1.454847 ATTCCCTCGCTCGAGCTCT 60.455 57.895 32.88 8.38 40.69 4.09
350 351 0.179015 ATTCCCTCGCTCGAGCTCTA 60.179 55.000 32.88 18.04 40.69 2.43
351 352 0.393944 TTCCCTCGCTCGAGCTCTAA 60.394 55.000 32.88 17.34 40.69 2.10
352 353 1.096386 TCCCTCGCTCGAGCTCTAAC 61.096 60.000 32.88 5.62 40.69 2.34
353 354 1.377366 CCCTCGCTCGAGCTCTAACA 61.377 60.000 32.88 10.27 40.69 2.41
354 355 0.665835 CCTCGCTCGAGCTCTAACAT 59.334 55.000 32.88 0.00 40.69 2.71
355 356 1.334599 CCTCGCTCGAGCTCTAACATC 60.335 57.143 32.88 3.35 40.69 3.06
356 357 1.332065 CTCGCTCGAGCTCTAACATCA 59.668 52.381 32.88 6.33 39.32 3.07
357 358 1.950216 TCGCTCGAGCTCTAACATCAT 59.050 47.619 32.88 0.00 39.32 2.45
358 359 2.049959 CGCTCGAGCTCTAACATCATG 58.950 52.381 32.88 10.73 39.32 3.07
359 360 2.402305 GCTCGAGCTCTAACATCATGG 58.598 52.381 29.88 0.00 38.21 3.66
360 361 2.035193 GCTCGAGCTCTAACATCATGGA 59.965 50.000 29.88 0.00 38.21 3.41
361 362 3.637432 CTCGAGCTCTAACATCATGGAC 58.363 50.000 12.85 0.00 0.00 4.02
362 363 2.033424 TCGAGCTCTAACATCATGGACG 59.967 50.000 12.85 0.00 0.00 4.79
363 364 2.748605 GAGCTCTAACATCATGGACGG 58.251 52.381 6.43 0.00 0.00 4.79
375 376 1.402896 ATGGACGGCGATGGTGATCT 61.403 55.000 16.62 0.00 0.00 2.75
377 378 1.592669 GACGGCGATGGTGATCTGG 60.593 63.158 16.62 0.00 0.00 3.86
381 382 0.179000 GGCGATGGTGATCTGGTTCT 59.821 55.000 0.00 0.00 0.00 3.01
385 386 2.167281 CGATGGTGATCTGGTTCTCAGT 59.833 50.000 0.00 0.00 43.76 3.41
387 388 4.583871 GATGGTGATCTGGTTCTCAGTTT 58.416 43.478 0.00 0.00 43.76 2.66
389 390 3.136443 TGGTGATCTGGTTCTCAGTTTGT 59.864 43.478 0.00 0.00 43.76 2.83
397 398 3.119531 TGGTTCTCAGTTTGTTGTTGCTG 60.120 43.478 0.00 0.00 0.00 4.41
406 407 2.057137 TGTTGTTGCTGGCTTCTTCT 57.943 45.000 0.00 0.00 0.00 2.85
411 412 2.006169 GTTGCTGGCTTCTTCTAGCTC 58.994 52.381 0.00 0.00 40.99 4.09
412 413 0.539051 TGCTGGCTTCTTCTAGCTCC 59.461 55.000 0.00 0.00 40.99 4.70
413 414 0.529555 GCTGGCTTCTTCTAGCTCCG 60.530 60.000 0.00 0.00 40.99 4.63
416 417 0.103390 GGCTTCTTCTAGCTCCGACC 59.897 60.000 0.00 0.00 40.99 4.79
417 418 0.818296 GCTTCTTCTAGCTCCGACCA 59.182 55.000 0.00 0.00 38.15 4.02
419 420 0.818296 TTCTTCTAGCTCCGACCAGC 59.182 55.000 0.00 0.00 39.99 4.85
430 431 4.821589 GACCAGCGGCTTCTCGGG 62.822 72.222 0.00 0.00 0.00 5.14
451 452 2.042831 GCGCTGGCTTCAAGGATGT 61.043 57.895 0.00 0.00 35.83 3.06
452 453 1.589716 GCGCTGGCTTCAAGGATGTT 61.590 55.000 0.00 0.00 35.83 2.71
453 454 0.449388 CGCTGGCTTCAAGGATGTTC 59.551 55.000 0.00 0.00 0.00 3.18
454 455 0.813821 GCTGGCTTCAAGGATGTTCC 59.186 55.000 0.00 0.00 36.58 3.62
456 457 0.690192 TGGCTTCAAGGATGTTCCGA 59.310 50.000 0.00 0.00 42.75 4.55
457 458 1.073125 TGGCTTCAAGGATGTTCCGAA 59.927 47.619 0.00 0.00 42.75 4.30
458 459 1.740025 GGCTTCAAGGATGTTCCGAAG 59.260 52.381 6.76 6.76 42.75 3.79
459 460 2.615493 GGCTTCAAGGATGTTCCGAAGA 60.615 50.000 12.57 0.37 42.75 2.87
460 461 3.274288 GCTTCAAGGATGTTCCGAAGAT 58.726 45.455 12.57 0.00 42.75 2.40
461 462 3.311048 GCTTCAAGGATGTTCCGAAGATC 59.689 47.826 9.31 9.31 42.75 2.75
462 463 4.507710 CTTCAAGGATGTTCCGAAGATCA 58.492 43.478 17.46 0.00 42.75 2.92
463 464 3.861840 TCAAGGATGTTCCGAAGATCAC 58.138 45.455 17.46 8.83 42.75 3.06
464 465 2.586258 AGGATGTTCCGAAGATCACG 57.414 50.000 17.46 0.00 42.75 4.35
470 471 3.294750 CCGAAGATCACGGGGTGA 58.705 61.111 19.11 0.38 46.90 4.02
497 499 1.566018 CTTTGCTCACGTTCGACCCC 61.566 60.000 0.00 0.00 0.00 4.95
518 520 1.587043 CGAGTGCAGGAGGAAGACGA 61.587 60.000 0.00 0.00 0.00 4.20
524 526 2.039405 AGGAGGAAGACGACGTCGG 61.039 63.158 37.89 21.83 44.95 4.79
527 529 1.012841 GAGGAAGACGACGTCGGTAT 58.987 55.000 37.89 24.26 44.95 2.73
529 531 2.208431 AGGAAGACGACGTCGGTATAG 58.792 52.381 37.89 13.31 44.95 1.31
531 533 1.596727 GAAGACGACGTCGGTATAGCT 59.403 52.381 37.89 22.02 44.95 3.32
532 534 1.216122 AGACGACGTCGGTATAGCTC 58.784 55.000 37.89 24.91 44.95 4.09
533 535 0.111354 GACGACGTCGGTATAGCTCG 60.111 60.000 37.89 13.34 44.95 5.03
534 536 0.807667 ACGACGTCGGTATAGCTCGT 60.808 55.000 37.89 14.02 44.95 4.18
536 538 0.654683 GACGTCGGTATAGCTCGTGT 59.345 55.000 20.41 6.31 34.93 4.49
538 540 0.654160 CGTCGGTATAGCTCGTGTCA 59.346 55.000 0.00 0.00 0.00 3.58
540 542 2.286831 CGTCGGTATAGCTCGTGTCATT 60.287 50.000 0.00 0.00 0.00 2.57
542 544 4.553351 CGTCGGTATAGCTCGTGTCATTTA 60.553 45.833 0.00 0.00 0.00 1.40
543 545 4.674211 GTCGGTATAGCTCGTGTCATTTAC 59.326 45.833 0.00 0.00 0.00 2.01
556 617 1.065709 TCATTTACGCCTTGTCCTCCC 60.066 52.381 0.00 0.00 0.00 4.30
557 618 1.065418 CATTTACGCCTTGTCCTCCCT 60.065 52.381 0.00 0.00 0.00 4.20
558 619 0.323629 TTTACGCCTTGTCCTCCCTG 59.676 55.000 0.00 0.00 0.00 4.45
559 620 0.543410 TTACGCCTTGTCCTCCCTGA 60.543 55.000 0.00 0.00 0.00 3.86
560 621 0.970937 TACGCCTTGTCCTCCCTGAG 60.971 60.000 0.00 0.00 0.00 3.35
561 622 2.286523 CGCCTTGTCCTCCCTGAGT 61.287 63.158 0.00 0.00 0.00 3.41
562 623 1.831652 CGCCTTGTCCTCCCTGAGTT 61.832 60.000 0.00 0.00 0.00 3.01
563 624 0.402121 GCCTTGTCCTCCCTGAGTTT 59.598 55.000 0.00 0.00 0.00 2.66
564 625 1.202940 GCCTTGTCCTCCCTGAGTTTT 60.203 52.381 0.00 0.00 0.00 2.43
565 626 2.753168 GCCTTGTCCTCCCTGAGTTTTT 60.753 50.000 0.00 0.00 0.00 1.94
612 673 6.895782 TGAAGGGTTCTTTTCTTCTTGTAGA 58.104 36.000 0.00 0.00 38.10 2.59
698 760 2.845345 CCCCAGTTGGCCTTGTCCT 61.845 63.158 3.32 0.00 0.00 3.85
720 782 3.893763 CTCTCGGCGCGTGATCCT 61.894 66.667 8.43 0.00 0.00 3.24
733 796 3.153270 GATCCTCCCCGCTTCGTCC 62.153 68.421 0.00 0.00 0.00 4.79
745 808 1.841663 CTTCGTCCCGCACCAACTTG 61.842 60.000 0.00 0.00 0.00 3.16
774 845 2.216782 CTTGGCTTCTCCCTTCCCCC 62.217 65.000 0.00 0.00 0.00 5.40
789 860 4.548513 CCCCCTCTCCCTCTCCCG 62.549 77.778 0.00 0.00 0.00 5.14
821 892 2.676342 CGCCTGATTTTACTAACCGCTT 59.324 45.455 0.00 0.00 0.00 4.68
822 893 3.242316 CGCCTGATTTTACTAACCGCTTC 60.242 47.826 0.00 0.00 0.00 3.86
823 894 3.064958 GCCTGATTTTACTAACCGCTTCC 59.935 47.826 0.00 0.00 0.00 3.46
824 895 3.308866 CCTGATTTTACTAACCGCTTCCG 59.691 47.826 0.00 0.00 0.00 4.30
825 896 2.674357 TGATTTTACTAACCGCTTCCGC 59.326 45.455 0.00 0.00 0.00 5.54
826 897 1.441738 TTTTACTAACCGCTTCCGCC 58.558 50.000 0.00 0.00 0.00 6.13
827 898 0.609662 TTTACTAACCGCTTCCGCCT 59.390 50.000 0.00 0.00 0.00 5.52
959 1030 3.397613 CTACCAGCTCAGCCCAGCC 62.398 68.421 0.00 0.00 40.65 4.85
1275 1364 4.683432 GTGAGCACGCCTTCTTCT 57.317 55.556 0.00 0.00 0.00 2.85
1286 1375 1.209261 GCCTTCTTCTTCCTCCCTCTG 59.791 57.143 0.00 0.00 0.00 3.35
1288 1377 2.909662 CCTTCTTCTTCCTCCCTCTGTT 59.090 50.000 0.00 0.00 0.00 3.16
1292 1381 2.239681 TCTTCCTCCCTCTGTTCTCC 57.760 55.000 0.00 0.00 0.00 3.71
1294 1383 1.258445 TTCCTCCCTCTGTTCTCCGC 61.258 60.000 0.00 0.00 0.00 5.54
1330 1460 5.989168 TCATTTTCGAGCTAGAGTTTGTGAA 59.011 36.000 0.00 0.00 0.00 3.18
1342 1472 1.262950 GTTTGTGAATTTTTGGCCGGC 59.737 47.619 21.18 21.18 0.00 6.13
1359 1489 1.103398 GGCGATTTGTGGGGATCAGG 61.103 60.000 0.00 0.00 0.00 3.86
1366 1497 1.071314 TGTGGGGATCAGGGGTTTGT 61.071 55.000 0.00 0.00 0.00 2.83
1382 1513 0.755686 TTGTGGTTCAATTGGGGTGC 59.244 50.000 5.42 0.00 0.00 5.01
1411 1542 3.124921 CAACGGTGGTGATCGGCC 61.125 66.667 0.00 0.00 0.00 6.13
1463 1594 7.944061 TGCGGTACTAATAATAGTAGAGCAAA 58.056 34.615 17.91 4.03 45.31 3.68
1466 1597 9.962783 CGGTACTAATAATAGTAGAGCAAACTT 57.037 33.333 1.47 0.00 43.53 2.66
1503 1634 0.750546 GGGGCGGTAACAGGGAAATC 60.751 60.000 0.00 0.00 0.00 2.17
1521 1652 0.955428 TCATTTGACTCTGGCACGGC 60.955 55.000 0.00 0.00 32.53 5.68
1571 1705 0.991920 ACCTAGGGTGTCCATGTTGG 59.008 55.000 14.81 0.00 34.55 3.77
1606 1742 3.650461 TGCTTGGGAAATTTTTAGGCCTT 59.350 39.130 12.58 0.00 0.00 4.35
1626 1762 9.938280 AGGCCTTTAAATTGGACTAAAATTTAC 57.062 29.630 0.00 0.00 40.51 2.01
1627 1763 9.938280 GGCCTTTAAATTGGACTAAAATTTACT 57.062 29.630 0.00 0.00 38.53 2.24
1656 1792 6.728200 TCATCATGAATTGCGGAACTATTTC 58.272 36.000 0.00 0.00 0.00 2.17
1667 1803 5.106712 TGCGGAACTATTTCAAGTGAATGTC 60.107 40.000 0.00 0.00 33.54 3.06
1678 1814 5.830912 TCAAGTGAATGTCGAAGCAATTTT 58.169 33.333 0.00 0.00 0.00 1.82
1682 1819 5.687285 AGTGAATGTCGAAGCAATTTTGTTC 59.313 36.000 0.00 0.00 0.00 3.18
1749 1888 5.068329 TGTCTTAATTTTGTGTGGACATGCA 59.932 36.000 0.00 0.00 30.13 3.96
1936 2075 9.606631 AATTACAACTTTTTGAACTGCCAAATA 57.393 25.926 0.00 0.00 36.12 1.40
1971 2110 7.701539 TCTTTCCTGCAGCTTAATATTTTGA 57.298 32.000 8.66 0.00 0.00 2.69
2024 2164 3.520290 TCCAGTGTATTAGAGTTGCCG 57.480 47.619 0.00 0.00 0.00 5.69
2087 2227 2.550639 GGGCATGCCTGTTTGTTTCAAT 60.551 45.455 34.70 0.00 36.10 2.57
2123 2263 9.583765 GTAACTCACGGTAGAAGAGAATAAAAT 57.416 33.333 0.00 0.00 33.69 1.82
2126 2266 7.760340 ACTCACGGTAGAAGAGAATAAAATGAC 59.240 37.037 0.00 0.00 33.69 3.06
2186 2326 3.569701 GCCCAATTCTTCAGTGTCAGAAA 59.430 43.478 10.35 0.00 32.76 2.52
2505 2661 6.370166 CACAAACACAAACAGTTTACCCAAAT 59.630 34.615 0.00 0.00 37.10 2.32
2507 2663 5.669164 ACACAAACAGTTTACCCAAATGT 57.331 34.783 0.00 0.00 0.00 2.71
2531 2687 6.452494 AAGATCTTTGCTTCTGATGGAATG 57.548 37.500 0.88 2.22 33.01 2.67
2650 2807 2.797156 GCAGACTAGTACGCATCCAATG 59.203 50.000 10.38 0.00 0.00 2.82
2845 3012 8.662781 TTAGGCTCTTGTGTGTATATTCAATC 57.337 34.615 0.00 0.00 0.00 2.67
3199 3366 5.567423 GCTTATTTCCAATTGAACAGCCTGT 60.567 40.000 7.12 0.00 31.05 4.00
3435 3602 4.354162 GGGCCAGCGGTTTACCCA 62.354 66.667 4.39 0.00 40.52 4.51
3587 3754 4.844085 TCCTCCAGGTAAGAAATCAGTTGA 59.156 41.667 0.00 0.00 36.34 3.18
3610 3777 5.940192 TGATGGTTGACAATGTCTTGTAC 57.060 39.130 14.97 7.31 45.57 2.90
3611 3778 5.372373 TGATGGTTGACAATGTCTTGTACA 58.628 37.500 14.97 7.04 45.57 2.90
3612 3779 5.469760 TGATGGTTGACAATGTCTTGTACAG 59.530 40.000 14.97 0.00 45.57 2.74
3659 3826 4.022849 AGTTCTAACACATGCCTCTTTTGC 60.023 41.667 0.00 0.00 0.00 3.68
3829 3996 4.280174 TGTAACTACAGTTCCTGTCTGTCC 59.720 45.833 0.00 0.00 41.21 4.02
3830 3997 2.958818 ACTACAGTTCCTGTCTGTCCA 58.041 47.619 0.00 0.00 41.21 4.02
3940 4108 4.627035 GTGCTTCTTTTCTTGCAAACTGTT 59.373 37.500 0.00 0.00 37.17 3.16
3988 4156 9.460019 TGGTCATTACATTGATCTTAACATTGA 57.540 29.630 0.00 0.00 0.00 2.57
4036 4204 3.330405 TGCTGCCTGGGCTGAATTATATA 59.670 43.478 20.01 0.00 41.63 0.86
4037 4205 3.944015 GCTGCCTGGGCTGAATTATATAG 59.056 47.826 20.01 3.78 41.63 1.31
4176 4348 2.411904 CCACTCTTGCTCTGTTCAGTC 58.588 52.381 0.00 0.00 0.00 3.51
4177 4349 2.224137 CCACTCTTGCTCTGTTCAGTCA 60.224 50.000 0.00 0.00 0.00 3.41
4178 4350 3.058450 CACTCTTGCTCTGTTCAGTCAG 58.942 50.000 0.00 0.00 36.85 3.51
4179 4351 2.697751 ACTCTTGCTCTGTTCAGTCAGT 59.302 45.455 0.00 0.00 36.85 3.41
4193 4365 4.883083 TCAGTCAGTGTCTTGTACATTCC 58.117 43.478 0.00 0.00 41.10 3.01
4307 4479 5.649970 AGTAGTAGTAGCTCATGTAGGGT 57.350 43.478 0.00 0.00 0.00 4.34
4410 4584 4.189231 GTGTGAATGTGGTGTATAGGTCC 58.811 47.826 0.00 0.00 0.00 4.46
4415 4589 5.249622 TGAATGTGGTGTATAGGTCCTTCAA 59.750 40.000 0.00 0.00 0.00 2.69
4440 4615 5.011635 TGTCATAGTGTCTTTCTGTTGGCTA 59.988 40.000 0.00 0.00 0.00 3.93
4611 4786 5.368256 AATGCTCTCAACAAACAGCTTAG 57.632 39.130 0.00 0.00 32.76 2.18
4612 4787 2.549754 TGCTCTCAACAAACAGCTTAGC 59.450 45.455 0.00 0.00 32.76 3.09
4613 4788 2.095516 GCTCTCAACAAACAGCTTAGCC 60.096 50.000 0.00 0.00 0.00 3.93
4614 4789 3.406764 CTCTCAACAAACAGCTTAGCCT 58.593 45.455 0.00 0.00 0.00 4.58
4615 4790 3.403038 TCTCAACAAACAGCTTAGCCTC 58.597 45.455 0.00 0.00 0.00 4.70
4616 4791 3.141398 CTCAACAAACAGCTTAGCCTCA 58.859 45.455 0.00 0.00 0.00 3.86
4626 4801 1.134551 GCTTAGCCTCACCTCCTGAAG 60.135 57.143 0.00 0.00 0.00 3.02
4681 4858 6.717289 TGGTTTACTTGCACCTTATATCACT 58.283 36.000 0.00 0.00 33.76 3.41
4684 4861 7.335924 GGTTTACTTGCACCTTATATCACTCAA 59.664 37.037 0.00 0.00 0.00 3.02
4689 4866 8.462016 ACTTGCACCTTATATCACTCAATTTTC 58.538 33.333 0.00 0.00 0.00 2.29
4699 4876 3.059166 CACTCAATTTTCGCCCAAAAGG 58.941 45.455 0.00 0.00 37.40 3.11
4712 4889 1.620524 CCAAAAGGGCATCCAGGTGAT 60.621 52.381 0.00 0.00 34.83 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.341531 CCAATGAGACGCCTACCTAGG 59.658 57.143 7.41 7.41 46.42 3.02
6 7 2.032620 ACCAATGAGACGCCTACCTAG 58.967 52.381 0.00 0.00 0.00 3.02
8 9 0.537188 CACCAATGAGACGCCTACCT 59.463 55.000 0.00 0.00 0.00 3.08
9 10 0.462047 CCACCAATGAGACGCCTACC 60.462 60.000 0.00 0.00 0.00 3.18
10 11 0.249398 ACCACCAATGAGACGCCTAC 59.751 55.000 0.00 0.00 0.00 3.18
11 12 0.249120 CACCACCAATGAGACGCCTA 59.751 55.000 0.00 0.00 0.00 3.93
12 13 1.003355 CACCACCAATGAGACGCCT 60.003 57.895 0.00 0.00 0.00 5.52
13 14 2.040544 CCACCACCAATGAGACGCC 61.041 63.158 0.00 0.00 0.00 5.68
32 33 3.726517 CACACCTTTGGCGCCTCG 61.727 66.667 29.70 15.30 0.00 4.63
62 63 3.553095 AAAGCTCCACACGCCCTCC 62.553 63.158 0.00 0.00 0.00 4.30
63 64 2.032681 AAAGCTCCACACGCCCTC 59.967 61.111 0.00 0.00 0.00 4.30
64 65 2.281761 CAAAGCTCCACACGCCCT 60.282 61.111 0.00 0.00 0.00 5.19
65 66 3.365265 CCAAAGCTCCACACGCCC 61.365 66.667 0.00 0.00 0.00 6.13
66 67 2.594592 ACCAAAGCTCCACACGCC 60.595 61.111 0.00 0.00 0.00 5.68
81 82 1.002011 GGACCCTTCAGCCTTGACC 60.002 63.158 0.00 0.00 31.71 4.02
88 89 3.569200 AAAGGCGGGACCCTTCAGC 62.569 63.158 9.41 4.08 44.28 4.26
91 92 1.674651 GACAAAGGCGGGACCCTTC 60.675 63.158 9.41 0.00 44.28 3.46
94 95 1.078637 GTAGACAAAGGCGGGACCC 60.079 63.158 0.00 0.00 40.58 4.46
99 100 3.056035 AGACTAAAGGTAGACAAAGGCGG 60.056 47.826 0.00 0.00 0.00 6.13
100 101 4.189639 AGACTAAAGGTAGACAAAGGCG 57.810 45.455 0.00 0.00 0.00 5.52
101 102 5.187381 ACCTAGACTAAAGGTAGACAAAGGC 59.813 44.000 0.00 0.00 45.69 4.35
102 103 6.351117 CCACCTAGACTAAAGGTAGACAAAGG 60.351 46.154 0.00 0.00 45.78 3.11
113 114 6.097915 TGTCAAAGACCACCTAGACTAAAG 57.902 41.667 0.00 0.00 33.64 1.85
132 133 4.629200 GCAAAACACAAAAGGATGTTGTCA 59.371 37.500 0.00 0.00 45.13 3.58
137 138 4.734398 TGAGCAAAACACAAAAGGATGT 57.266 36.364 0.00 0.00 0.00 3.06
146 147 4.081406 AGAAGGCATATGAGCAAAACACA 58.919 39.130 6.97 0.00 35.83 3.72
149 150 5.356470 AGAGAAGAAGGCATATGAGCAAAAC 59.644 40.000 6.97 0.00 35.83 2.43
160 161 2.300152 TGTCGAACAGAGAAGAAGGCAT 59.700 45.455 0.00 0.00 0.00 4.40
181 182 4.675146 CGAAATCGGAATTGATGGTGCTTT 60.675 41.667 0.00 0.00 35.37 3.51
231 232 7.942894 TCCCAGATTCGTCTAGATAAGAACATA 59.057 37.037 0.00 0.00 35.47 2.29
232 233 6.778069 TCCCAGATTCGTCTAGATAAGAACAT 59.222 38.462 0.00 0.00 35.47 2.71
233 234 6.127101 TCCCAGATTCGTCTAGATAAGAACA 58.873 40.000 0.00 0.00 35.47 3.18
238 239 5.394738 ACCATCCCAGATTCGTCTAGATAA 58.605 41.667 0.00 0.00 0.00 1.75
244 245 1.909302 ACAACCATCCCAGATTCGTCT 59.091 47.619 0.00 0.00 0.00 4.18
245 246 2.403252 ACAACCATCCCAGATTCGTC 57.597 50.000 0.00 0.00 0.00 4.20
265 266 2.168272 TAGCTGAGGAGGGCTGGACA 62.168 60.000 0.00 0.00 39.31 4.02
266 267 1.381872 TAGCTGAGGAGGGCTGGAC 60.382 63.158 0.00 0.00 39.31 4.02
267 268 1.381872 GTAGCTGAGGAGGGCTGGA 60.382 63.158 0.00 0.00 39.31 3.86
273 274 3.181491 CGAGAAGAAAGTAGCTGAGGAGG 60.181 52.174 0.00 0.00 0.00 4.30
281 282 2.678324 AGCACACGAGAAGAAAGTAGC 58.322 47.619 0.00 0.00 0.00 3.58
298 299 1.592939 TGCAACACGTTCGCTAGCA 60.593 52.632 16.45 0.00 0.00 3.49
299 300 1.154654 GTGCAACACGTTCGCTAGC 60.155 57.895 4.06 4.06 36.32 3.42
309 310 0.247736 AGAGAGGGATCGTGCAACAC 59.752 55.000 0.00 0.00 35.74 3.32
310 311 0.532573 GAGAGAGGGATCGTGCAACA 59.467 55.000 0.00 0.00 35.74 3.33
311 312 0.179097 GGAGAGAGGGATCGTGCAAC 60.179 60.000 0.00 0.00 0.00 4.17
312 313 0.614697 TGGAGAGAGGGATCGTGCAA 60.615 55.000 0.00 0.00 0.00 4.08
313 314 0.397675 ATGGAGAGAGGGATCGTGCA 60.398 55.000 0.00 0.00 0.00 4.57
314 315 0.755686 AATGGAGAGAGGGATCGTGC 59.244 55.000 0.00 0.00 0.00 5.34
315 316 1.342819 GGAATGGAGAGAGGGATCGTG 59.657 57.143 0.00 0.00 0.00 4.35
316 317 1.710816 GGAATGGAGAGAGGGATCGT 58.289 55.000 0.00 0.00 0.00 3.73
317 318 0.972883 GGGAATGGAGAGAGGGATCG 59.027 60.000 0.00 0.00 0.00 3.69
318 319 2.256306 GAGGGAATGGAGAGAGGGATC 58.744 57.143 0.00 0.00 0.00 3.36
319 320 1.482177 CGAGGGAATGGAGAGAGGGAT 60.482 57.143 0.00 0.00 0.00 3.85
320 321 0.105964 CGAGGGAATGGAGAGAGGGA 60.106 60.000 0.00 0.00 0.00 4.20
321 322 1.753368 GCGAGGGAATGGAGAGAGGG 61.753 65.000 0.00 0.00 0.00 4.30
322 323 0.758685 AGCGAGGGAATGGAGAGAGG 60.759 60.000 0.00 0.00 0.00 3.69
323 324 0.673437 GAGCGAGGGAATGGAGAGAG 59.327 60.000 0.00 0.00 0.00 3.20
324 325 1.103987 CGAGCGAGGGAATGGAGAGA 61.104 60.000 0.00 0.00 0.00 3.10
325 326 1.103987 TCGAGCGAGGGAATGGAGAG 61.104 60.000 0.00 0.00 0.00 3.20
326 327 1.076995 TCGAGCGAGGGAATGGAGA 60.077 57.895 0.00 0.00 0.00 3.71
327 328 1.361993 CTCGAGCGAGGGAATGGAG 59.638 63.158 11.83 0.00 38.51 3.86
328 329 2.786495 GCTCGAGCGAGGGAATGGA 61.786 63.158 23.61 0.00 42.19 3.41
329 330 2.279784 GCTCGAGCGAGGGAATGG 60.280 66.667 23.61 0.00 42.19 3.16
339 340 2.035193 TCCATGATGTTAGAGCTCGAGC 59.965 50.000 30.01 30.01 42.49 5.03
340 341 3.637432 GTCCATGATGTTAGAGCTCGAG 58.363 50.000 8.45 8.45 0.00 4.04
341 342 2.033424 CGTCCATGATGTTAGAGCTCGA 59.967 50.000 8.37 0.00 0.00 4.04
342 343 2.389059 CGTCCATGATGTTAGAGCTCG 58.611 52.381 8.37 0.00 0.00 5.03
343 344 2.748605 CCGTCCATGATGTTAGAGCTC 58.251 52.381 5.27 5.27 0.00 4.09
344 345 1.202580 GCCGTCCATGATGTTAGAGCT 60.203 52.381 0.00 0.00 0.00 4.09
345 346 1.221414 GCCGTCCATGATGTTAGAGC 58.779 55.000 0.00 0.00 0.00 4.09
346 347 1.067060 TCGCCGTCCATGATGTTAGAG 59.933 52.381 0.00 0.00 0.00 2.43
347 348 1.107945 TCGCCGTCCATGATGTTAGA 58.892 50.000 0.00 0.00 0.00 2.10
348 349 1.794701 CATCGCCGTCCATGATGTTAG 59.205 52.381 0.00 0.00 35.81 2.34
349 350 1.540146 CCATCGCCGTCCATGATGTTA 60.540 52.381 0.00 0.00 38.22 2.41
350 351 0.815213 CCATCGCCGTCCATGATGTT 60.815 55.000 0.00 0.00 38.22 2.71
351 352 1.227645 CCATCGCCGTCCATGATGT 60.228 57.895 0.00 0.00 38.22 3.06
352 353 1.227645 ACCATCGCCGTCCATGATG 60.228 57.895 0.00 0.00 39.32 3.07
353 354 1.227645 CACCATCGCCGTCCATGAT 60.228 57.895 0.00 0.00 0.00 2.45
354 355 1.685355 ATCACCATCGCCGTCCATGA 61.685 55.000 0.00 0.00 0.00 3.07
355 356 1.224069 GATCACCATCGCCGTCCATG 61.224 60.000 0.00 0.00 0.00 3.66
356 357 1.069765 GATCACCATCGCCGTCCAT 59.930 57.895 0.00 0.00 0.00 3.41
357 358 2.058001 AGATCACCATCGCCGTCCA 61.058 57.895 0.00 0.00 33.75 4.02
358 359 1.592669 CAGATCACCATCGCCGTCC 60.593 63.158 0.00 0.00 33.75 4.79
359 360 1.592669 CCAGATCACCATCGCCGTC 60.593 63.158 0.00 0.00 33.75 4.79
360 361 1.899437 AACCAGATCACCATCGCCGT 61.899 55.000 0.00 0.00 33.75 5.68
361 362 1.153369 AACCAGATCACCATCGCCG 60.153 57.895 0.00 0.00 33.75 6.46
362 363 0.179000 AGAACCAGATCACCATCGCC 59.821 55.000 0.00 0.00 33.75 5.54
363 364 1.134699 TGAGAACCAGATCACCATCGC 60.135 52.381 0.00 0.00 33.75 4.58
375 376 3.088532 AGCAACAACAAACTGAGAACCA 58.911 40.909 0.00 0.00 0.00 3.67
377 378 3.438360 CCAGCAACAACAAACTGAGAAC 58.562 45.455 0.00 0.00 31.67 3.01
381 382 1.473258 AGCCAGCAACAACAAACTGA 58.527 45.000 0.00 0.00 31.67 3.41
385 386 2.760092 AGAAGAAGCCAGCAACAACAAA 59.240 40.909 0.00 0.00 0.00 2.83
387 388 2.057137 AGAAGAAGCCAGCAACAACA 57.943 45.000 0.00 0.00 0.00 3.33
389 390 2.154462 GCTAGAAGAAGCCAGCAACAA 58.846 47.619 0.00 0.00 36.45 2.83
397 398 0.103390 GGTCGGAGCTAGAAGAAGCC 59.897 60.000 0.00 0.00 43.86 4.35
413 414 4.821589 CCCGAGAAGCCGCTGGTC 62.822 72.222 0.00 0.00 0.00 4.02
433 434 1.589716 AACATCCTTGAAGCCAGCGC 61.590 55.000 0.00 0.00 0.00 5.92
434 435 0.449388 GAACATCCTTGAAGCCAGCG 59.551 55.000 0.00 0.00 0.00 5.18
436 437 1.089920 CGGAACATCCTTGAAGCCAG 58.910 55.000 0.00 0.00 33.30 4.85
437 438 0.690192 TCGGAACATCCTTGAAGCCA 59.310 50.000 0.00 0.00 33.30 4.75
438 439 1.740025 CTTCGGAACATCCTTGAAGCC 59.260 52.381 2.47 0.00 30.86 4.35
439 440 2.699954 TCTTCGGAACATCCTTGAAGC 58.300 47.619 8.38 0.00 35.38 3.86
440 441 4.331168 GTGATCTTCGGAACATCCTTGAAG 59.669 45.833 3.94 7.38 36.17 3.02
441 442 4.253685 GTGATCTTCGGAACATCCTTGAA 58.746 43.478 3.94 0.00 33.30 2.69
442 443 3.676049 CGTGATCTTCGGAACATCCTTGA 60.676 47.826 3.94 0.00 33.30 3.02
443 444 2.604914 CGTGATCTTCGGAACATCCTTG 59.395 50.000 3.94 0.00 33.30 3.61
445 446 2.586258 CGTGATCTTCGGAACATCCT 57.414 50.000 3.94 0.00 33.30 3.24
453 454 1.153628 GTCACCCCGTGATCTTCGG 60.154 63.158 18.26 18.26 44.63 4.30
454 455 0.175760 ATGTCACCCCGTGATCTTCG 59.824 55.000 0.00 0.00 44.63 3.79
456 457 0.175760 CGATGTCACCCCGTGATCTT 59.824 55.000 0.00 0.00 44.63 2.40
457 458 0.683179 TCGATGTCACCCCGTGATCT 60.683 55.000 0.00 0.00 44.63 2.75
458 459 0.249073 CTCGATGTCACCCCGTGATC 60.249 60.000 0.00 0.00 44.63 2.92
459 460 1.816537 CTCGATGTCACCCCGTGAT 59.183 57.895 0.00 0.00 44.63 3.06
460 461 3.001902 GCTCGATGTCACCCCGTGA 62.002 63.158 0.00 0.00 40.50 4.35
461 462 2.507110 AAGCTCGATGTCACCCCGTG 62.507 60.000 0.00 0.00 34.45 4.94
462 463 1.827399 AAAGCTCGATGTCACCCCGT 61.827 55.000 0.00 0.00 0.00 5.28
463 464 1.079127 AAAGCTCGATGTCACCCCG 60.079 57.895 0.00 0.00 0.00 5.73
464 465 1.648467 GCAAAGCTCGATGTCACCCC 61.648 60.000 0.00 0.00 0.00 4.95
465 466 0.674895 AGCAAAGCTCGATGTCACCC 60.675 55.000 0.00 0.00 30.62 4.61
497 499 2.507992 CTTCCTCCTGCACTCGCG 60.508 66.667 0.00 0.00 42.97 5.87
506 508 2.039405 CCGACGTCGTCTTCCTCCT 61.039 63.158 33.49 0.00 37.74 3.69
511 513 1.596727 AGCTATACCGACGTCGTCTTC 59.403 52.381 33.49 17.92 37.74 2.87
518 520 0.654683 GACACGAGCTATACCGACGT 59.345 55.000 0.00 0.00 37.68 4.34
524 526 3.424529 GGCGTAAATGACACGAGCTATAC 59.575 47.826 0.00 0.00 41.91 1.47
527 529 1.475280 AGGCGTAAATGACACGAGCTA 59.525 47.619 0.00 0.00 41.91 3.32
529 531 1.076332 AAGGCGTAAATGACACGAGC 58.924 50.000 0.00 0.00 41.91 5.03
531 533 2.063266 GACAAGGCGTAAATGACACGA 58.937 47.619 0.00 0.00 41.91 4.35
532 534 1.127951 GGACAAGGCGTAAATGACACG 59.872 52.381 0.00 0.00 42.24 4.49
533 535 2.415512 GAGGACAAGGCGTAAATGACAC 59.584 50.000 0.00 0.00 0.00 3.67
534 536 2.614481 GGAGGACAAGGCGTAAATGACA 60.614 50.000 0.00 0.00 0.00 3.58
536 538 1.065709 GGGAGGACAAGGCGTAAATGA 60.066 52.381 0.00 0.00 0.00 2.57
538 540 1.065418 CAGGGAGGACAAGGCGTAAAT 60.065 52.381 0.00 0.00 0.00 1.40
540 542 0.543410 TCAGGGAGGACAAGGCGTAA 60.543 55.000 0.00 0.00 0.00 3.18
542 544 2.203788 TCAGGGAGGACAAGGCGT 60.204 61.111 0.00 0.00 0.00 5.68
543 545 1.831652 AACTCAGGGAGGACAAGGCG 61.832 60.000 0.00 0.00 33.35 5.52
584 645 7.676004 ACAAGAAGAAAAGAACCCTTCAAAAA 58.324 30.769 0.00 0.00 38.89 1.94
585 646 7.239763 ACAAGAAGAAAAGAACCCTTCAAAA 57.760 32.000 0.00 0.00 38.89 2.44
586 647 6.850752 ACAAGAAGAAAAGAACCCTTCAAA 57.149 33.333 0.00 0.00 38.89 2.69
587 648 7.282450 GTCTACAAGAAGAAAAGAACCCTTCAA 59.718 37.037 0.00 0.00 38.89 2.69
588 649 6.766467 GTCTACAAGAAGAAAAGAACCCTTCA 59.234 38.462 0.00 0.00 38.89 3.02
589 650 6.766467 TGTCTACAAGAAGAAAAGAACCCTTC 59.234 38.462 0.00 0.00 37.23 3.46
590 651 6.659824 TGTCTACAAGAAGAAAAGAACCCTT 58.340 36.000 0.00 0.00 0.00 3.95
591 652 6.248569 TGTCTACAAGAAGAAAAGAACCCT 57.751 37.500 0.00 0.00 0.00 4.34
592 653 6.937436 TTGTCTACAAGAAGAAAAGAACCC 57.063 37.500 0.00 0.00 0.00 4.11
593 654 6.905609 CGTTTGTCTACAAGAAGAAAAGAACC 59.094 38.462 0.00 0.00 37.15 3.62
594 655 7.461918 ACGTTTGTCTACAAGAAGAAAAGAAC 58.538 34.615 0.00 0.00 37.15 3.01
595 656 7.605410 ACGTTTGTCTACAAGAAGAAAAGAA 57.395 32.000 0.00 0.00 37.15 2.52
596 657 8.882415 ATACGTTTGTCTACAAGAAGAAAAGA 57.118 30.769 0.00 0.00 37.15 2.52
597 658 9.370126 CAATACGTTTGTCTACAAGAAGAAAAG 57.630 33.333 0.00 0.00 37.15 2.27
603 664 4.150980 CCGCAATACGTTTGTCTACAAGAA 59.849 41.667 0.00 0.00 41.42 2.52
605 666 3.181524 CCCGCAATACGTTTGTCTACAAG 60.182 47.826 0.00 0.00 41.42 3.16
607 668 2.288948 ACCCGCAATACGTTTGTCTACA 60.289 45.455 0.00 0.00 41.42 2.74
612 673 0.250381 TCCACCCGCAATACGTTTGT 60.250 50.000 0.00 0.00 41.42 2.83
733 796 3.977244 GTGGGCAAGTTGGTGCGG 61.977 66.667 4.75 0.00 45.91 5.69
755 818 1.304617 GGGGAAGGGAGAAGCCAAG 59.695 63.158 0.00 0.00 38.95 3.61
774 845 4.150454 AGCGGGAGAGGGAGAGGG 62.150 72.222 0.00 0.00 0.00 4.30
776 847 2.520741 GGAGCGGGAGAGGGAGAG 60.521 72.222 0.00 0.00 0.00 3.20
777 848 4.144727 GGGAGCGGGAGAGGGAGA 62.145 72.222 0.00 0.00 0.00 3.71
826 897 1.068474 CGCGCTAATAATCCCGGAAG 58.932 55.000 0.73 0.00 0.00 3.46
827 898 0.947180 GCGCGCTAATAATCCCGGAA 60.947 55.000 26.67 0.00 0.00 4.30
945 1016 2.750637 CTTGGCTGGGCTGAGCTG 60.751 66.667 3.72 0.00 39.11 4.24
954 1025 0.181350 CCTAACCCTAGCTTGGCTGG 59.819 60.000 8.91 3.97 40.10 4.85
959 1030 2.092323 GCAAACCCTAACCCTAGCTTG 58.908 52.381 0.00 0.00 0.00 4.01
960 1031 1.339727 CGCAAACCCTAACCCTAGCTT 60.340 52.381 0.00 0.00 0.00 3.74
1268 1357 3.837731 AGAACAGAGGGAGGAAGAAGAAG 59.162 47.826 0.00 0.00 0.00 2.85
1270 1359 3.436243 GAGAACAGAGGGAGGAAGAAGA 58.564 50.000 0.00 0.00 0.00 2.87
1275 1364 1.258445 GCGGAGAACAGAGGGAGGAA 61.258 60.000 0.00 0.00 0.00 3.36
1307 1436 5.845985 TCACAAACTCTAGCTCGAAAATG 57.154 39.130 0.00 0.00 0.00 2.32
1330 1460 0.320050 ACAAATCGCCGGCCAAAAAT 59.680 45.000 23.46 3.85 0.00 1.82
1342 1472 0.466189 CCCCTGATCCCCACAAATCG 60.466 60.000 0.00 0.00 0.00 3.34
1359 1489 1.071542 CCCCAATTGAACCACAAACCC 59.928 52.381 7.12 0.00 42.03 4.11
1366 1497 1.415659 CAAAGCACCCCAATTGAACCA 59.584 47.619 7.12 0.00 0.00 3.67
1382 1513 1.528309 ACCGTTGGAGGCCACAAAG 60.528 57.895 13.64 14.77 30.78 2.77
1411 1542 1.470098 CCGAATTCACAAGCCTTCCAG 59.530 52.381 6.22 0.00 0.00 3.86
1429 1560 2.083167 TTAGTACCGCAAAACTCCCG 57.917 50.000 0.00 0.00 0.00 5.14
1463 1594 2.116125 GCAACCAGCTCCCCAAGT 59.884 61.111 0.00 0.00 41.15 3.16
1503 1634 1.503542 GCCGTGCCAGAGTCAAATG 59.496 57.895 0.00 0.00 0.00 2.32
1521 1652 1.203052 ACAAAGCCTGGCAATCAATCG 59.797 47.619 22.65 2.57 0.00 3.34
1534 1665 2.357952 AGGTCTCACGAAAAACAAAGCC 59.642 45.455 0.00 0.00 0.00 4.35
1571 1705 4.519540 TCCCAAGCAGCTAAAAATGTTC 57.480 40.909 0.00 0.00 0.00 3.18
1626 1762 4.735985 TCCGCAATTCATGATGAAACAAG 58.264 39.130 12.36 4.78 40.12 3.16
1627 1763 4.780275 TCCGCAATTCATGATGAAACAA 57.220 36.364 12.36 0.00 40.12 2.83
1656 1792 5.459762 ACAAAATTGCTTCGACATTCACTTG 59.540 36.000 0.00 0.00 0.00 3.16
1667 1803 2.295909 TCCCCAGAACAAAATTGCTTCG 59.704 45.455 0.00 0.00 0.00 3.79
1678 1814 3.238597 CCAAATTTCCTTCCCCAGAACA 58.761 45.455 0.00 0.00 0.00 3.18
1682 1819 1.571955 CCCCAAATTTCCTTCCCCAG 58.428 55.000 0.00 0.00 0.00 4.45
1703 1840 9.630098 AGACAAATTAACATCATGAAACACATC 57.370 29.630 0.00 0.00 37.07 3.06
1936 2075 4.070716 CTGCAGGAAAGAACTCAACAGAT 58.929 43.478 5.57 0.00 0.00 2.90
2060 2200 2.158638 ACAAACAGGCATGCCCAAAAAT 60.159 40.909 33.14 10.96 36.58 1.82
2061 2201 1.211457 ACAAACAGGCATGCCCAAAAA 59.789 42.857 33.14 0.00 36.58 1.94
2087 2227 1.225855 CGTGAGTTACAAGGCAGCAA 58.774 50.000 0.00 0.00 0.00 3.91
2123 2263 6.582636 ACTTCATGAGTAGTGACAAAAGTCA 58.417 36.000 0.00 0.00 36.65 3.41
2126 2266 9.817365 CATTAACTTCATGAGTAGTGACAAAAG 57.183 33.333 0.79 0.00 37.72 2.27
2186 2326 6.165577 CCATAACCATTTTTGCAGTTTAGCT 58.834 36.000 0.00 0.00 34.99 3.32
2454 2598 9.844790 GTTTGTGATCATGAACATCTTTTATCA 57.155 29.630 9.06 0.00 0.00 2.15
2458 2602 7.490840 TGTGTTTGTGATCATGAACATCTTTT 58.509 30.769 21.95 0.00 34.86 2.27
2505 2661 6.053632 TCCATCAGAAGCAAAGATCTTACA 57.946 37.500 8.75 0.00 0.00 2.41
2507 2663 6.544931 CCATTCCATCAGAAGCAAAGATCTTA 59.455 38.462 8.75 0.00 38.07 2.10
2531 2687 4.765339 ACAACCTCCTATTGTAAAAGTGCC 59.235 41.667 0.00 0.00 38.51 5.01
2650 2807 6.405538 TCTCAACATAAAATTTGGCCATTCC 58.594 36.000 6.09 0.00 0.00 3.01
2818 2985 9.632638 ATTGAATATACACACAAGAGCCTAAAT 57.367 29.630 0.00 0.00 0.00 1.40
3199 3366 8.500753 AACAACGGATTATTATTTGCAGTAGA 57.499 30.769 0.00 0.00 0.00 2.59
3587 3754 6.003326 TGTACAAGACATTGTCAACCATCAT 58.997 36.000 18.57 0.00 46.90 2.45
3823 3990 0.829990 TGTCACAACAGCTGGACAGA 59.170 50.000 19.93 7.86 33.14 3.41
3940 4108 9.594478 GACCAACCTTTAAGAATGAAAAAGAAA 57.406 29.630 0.00 0.00 0.00 2.52
3988 4156 6.062258 TCAAGTAAAAGGGCTAGCTAATGT 57.938 37.500 15.72 0.33 0.00 2.71
4036 4204 6.831976 ACAACCTGAAATAGAGTGAGAAACT 58.168 36.000 0.00 0.00 43.85 2.66
4037 4205 6.147985 GGACAACCTGAAATAGAGTGAGAAAC 59.852 42.308 0.00 0.00 0.00 2.78
4149 4317 1.738350 CAGAGCAAGAGTGGCTTCATG 59.262 52.381 0.00 0.00 42.78 3.07
4176 4348 3.417069 TGGGGAATGTACAAGACACTG 57.583 47.619 0.00 0.00 42.17 3.66
4177 4349 3.054361 GGATGGGGAATGTACAAGACACT 60.054 47.826 0.00 0.00 42.17 3.55
4178 4350 3.279434 GGATGGGGAATGTACAAGACAC 58.721 50.000 0.00 0.00 42.17 3.67
4179 4351 2.241176 GGGATGGGGAATGTACAAGACA 59.759 50.000 0.00 0.00 43.97 3.41
4193 4365 0.468771 GAATTCCTGCAGGGGATGGG 60.469 60.000 32.23 6.20 32.49 4.00
4410 4584 7.664082 ACAGAAAGACACTATGACATTGAAG 57.336 36.000 3.80 0.00 0.00 3.02
4415 4589 4.697352 GCCAACAGAAAGACACTATGACAT 59.303 41.667 0.00 0.00 0.00 3.06
4465 4640 5.983720 ACGGTGATGTAACTGATATACAAGC 59.016 40.000 0.00 0.00 36.88 4.01
4474 4649 8.780846 ATTTAATTACACGGTGATGTAACTGA 57.219 30.769 16.29 0.00 45.39 3.41
4574 4749 7.465353 TGAGAGCATTTGAATTTGAACCATA 57.535 32.000 0.00 0.00 0.00 2.74
4611 4786 0.980423 ACTTCTTCAGGAGGTGAGGC 59.020 55.000 0.00 0.00 36.21 4.70
4612 4787 4.467795 TCAATACTTCTTCAGGAGGTGAGG 59.532 45.833 0.00 0.00 36.21 3.86
4613 4788 5.667539 TCAATACTTCTTCAGGAGGTGAG 57.332 43.478 0.00 0.00 36.21 3.51
4614 4789 6.433847 TTTCAATACTTCTTCAGGAGGTGA 57.566 37.500 0.00 0.00 35.78 4.02
4615 4790 8.792830 TTATTTCAATACTTCTTCAGGAGGTG 57.207 34.615 0.00 0.00 35.78 4.00
4616 4791 9.807921 TTTTATTTCAATACTTCTTCAGGAGGT 57.192 29.630 0.00 0.00 37.94 3.85
4653 4828 8.052748 TGATATAAGGTGCAAGTAAACCAGAAT 58.947 33.333 0.00 0.00 39.05 2.40
4654 4829 7.335924 GTGATATAAGGTGCAAGTAAACCAGAA 59.664 37.037 0.00 0.00 39.05 3.02
4655 4830 6.821665 GTGATATAAGGTGCAAGTAAACCAGA 59.178 38.462 0.00 0.00 39.05 3.86
4699 4876 2.555757 GCAGATAAATCACCTGGATGCC 59.444 50.000 0.00 0.00 36.02 4.40
4712 4889 6.179756 TGAGGATGCAAGTAAAGCAGATAAA 58.820 36.000 0.00 0.00 46.36 1.40


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

AutoCloner maintained by Alex Coulton.