Multiple sequence alignment - TraesCS7D01G522000

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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 TraesCS7D01G522000 chr7D 100.000 4353 0 0 1 4353 619039900 619044252 0.000000e+00 8039.0
1 TraesCS7D01G522000 chr7D 100.000 28 0 0 1143 1170 263833021 263832994 8.000000e-03 52.8
2 TraesCS7D01G522000 chr7A 88.423 3602 239 74 453 3986 712769005 712772496 0.000000e+00 4178.0
3 TraesCS7D01G522000 chr7A 83.705 583 72 11 2287 2847 728248566 728247985 2.980000e-146 529.0
4 TraesCS7D01G522000 chr7A 88.949 371 15 10 1728 2098 728248941 728248597 6.690000e-118 435.0
5 TraesCS7D01G522000 chr7A 84.348 230 31 1 2337 2561 728247735 728247506 2.040000e-53 220.0
6 TraesCS7D01G522000 chr7A 88.024 167 19 1 3196 3362 712829791 712829956 3.430000e-46 196.0
7 TraesCS7D01G522000 chr7A 78.632 234 18 12 2607 2835 712979329 712979535 4.570000e-25 126.0
8 TraesCS7D01G522000 chr7A 100.000 30 0 0 1143 1172 286819164 286819135 6.080000e-04 56.5
9 TraesCS7D01G522000 chr7B 89.025 2852 187 41 1542 4342 713662621 713665397 0.000000e+00 3417.0
10 TraesCS7D01G522000 chr7B 82.511 1561 139 68 2 1497 713661119 713662610 0.000000e+00 1247.0
11 TraesCS7D01G522000 chr7B 82.638 887 100 28 856 1716 243783197 243782339 0.000000e+00 736.0
12 TraesCS7D01G522000 chr7B 77.365 296 47 15 3304 3590 713448453 713448737 1.620000e-34 158.0
13 TraesCS7D01G522000 chr7B 96.970 33 1 0 2398 2430 714464782 714464814 6.080000e-04 56.5
14 TraesCS7D01G522000 chr5B 80.536 560 71 19 1176 1716 91768755 91768215 3.150000e-106 396.0
15 TraesCS7D01G522000 chr5B 83.735 332 35 6 856 1178 91774283 91773962 3.290000e-76 296.0
16 TraesCS7D01G522000 chr5D 85.366 82 8 4 1125 1204 432533159 432533080 1.000000e-11 82.4


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 TraesCS7D01G522000 chr7D 619039900 619044252 4352 False 8039.000000 8039 100.000000 1 4353 1 chr7D.!!$F1 4352
1 TraesCS7D01G522000 chr7A 712769005 712772496 3491 False 4178.000000 4178 88.423000 453 3986 1 chr7A.!!$F1 3533
2 TraesCS7D01G522000 chr7A 728247506 728248941 1435 True 394.666667 529 85.667333 1728 2847 3 chr7A.!!$R2 1119
3 TraesCS7D01G522000 chr7B 713661119 713665397 4278 False 2332.000000 3417 85.768000 2 4342 2 chr7B.!!$F3 4340
4 TraesCS7D01G522000 chr7B 243782339 243783197 858 True 736.000000 736 82.638000 856 1716 1 chr7B.!!$R1 860
5 TraesCS7D01G522000 chr5B 91768215 91768755 540 True 396.000000 396 80.536000 1176 1716 1 chr5B.!!$R1 540

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
483 511 0.040157 CGATTAATGGCGGCATGTGG 60.040 55.0 26.50 11.93 0.0 4.17 F
831 887 0.179029 CGTCCCTCCCTCTCTCTCTC 60.179 65.0 0.00 0.00 0.0 3.20 F
1359 1473 0.030297 AGTCATGGGGATCCTGCTCT 60.030 55.0 12.58 2.00 0.0 4.09 F
1360 1474 0.108207 GTCATGGGGATCCTGCTCTG 59.892 60.0 12.58 3.11 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1352 1466 0.035881 ACACACATGACCAGAGCAGG 59.964 55.000 0.0 0.0 0.0 4.85 R
1928 2055 0.105593 CTCATATCTGGTGCTGGCGT 59.894 55.000 0.0 0.0 0.0 5.68 R
3205 3390 1.028905 AACCACCACCAACATGAACG 58.971 50.000 0.0 0.0 0.0 3.95 R
3399 3602 4.128925 TCCTAATAGCAGCAGACACAAG 57.871 45.455 0.0 0.0 0.0 3.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 6.609237 ATTGTAACATGTTCGATGATCCAG 57.391 37.500 15.85 0.00 0.00 3.86
43 44 6.533723 TGTAACATGTTCGATGATCCAGTAAC 59.466 38.462 15.85 2.92 0.00 2.50
49 50 2.766263 TCGATGATCCAGTAACAAGGCT 59.234 45.455 0.00 0.00 0.00 4.58
52 53 5.070446 TCGATGATCCAGTAACAAGGCTAAT 59.930 40.000 0.00 0.00 0.00 1.73
53 54 5.406780 CGATGATCCAGTAACAAGGCTAATC 59.593 44.000 0.00 0.00 0.00 1.75
57 58 2.169769 CCAGTAACAAGGCTAATCCGGA 59.830 50.000 6.61 6.61 40.77 5.14
59 60 2.835764 AGTAACAAGGCTAATCCGGACA 59.164 45.455 6.12 0.00 40.77 4.02
60 61 2.871096 AACAAGGCTAATCCGGACAA 57.129 45.000 6.12 0.00 40.77 3.18
61 62 2.403252 ACAAGGCTAATCCGGACAAG 57.597 50.000 6.12 8.62 40.77 3.16
63 64 2.280628 CAAGGCTAATCCGGACAAGAC 58.719 52.381 6.12 9.88 40.77 3.01
66 67 1.653151 GCTAATCCGGACAAGACCAC 58.347 55.000 6.12 0.00 0.00 4.16
80 81 3.498774 AGACCACTTGAATCTTGCACT 57.501 42.857 0.00 0.00 0.00 4.40
81 82 3.406764 AGACCACTTGAATCTTGCACTC 58.593 45.455 0.00 0.00 0.00 3.51
82 83 3.141398 GACCACTTGAATCTTGCACTCA 58.859 45.455 0.00 0.00 0.00 3.41
85 86 4.202050 ACCACTTGAATCTTGCACTCAAAC 60.202 41.667 0.00 0.00 0.00 2.93
86 87 4.037208 CCACTTGAATCTTGCACTCAAACT 59.963 41.667 0.00 0.00 0.00 2.66
87 88 5.450965 CCACTTGAATCTTGCACTCAAACTT 60.451 40.000 0.00 0.00 0.00 2.66
88 89 5.684626 CACTTGAATCTTGCACTCAAACTTC 59.315 40.000 0.00 0.00 0.00 3.01
95 96 4.102524 TCTTGCACTCAAACTTCCCTAAGA 59.897 41.667 0.00 0.00 36.50 2.10
103 104 4.528596 TCAAACTTCCCTAAGAGTGAGGAG 59.471 45.833 0.00 0.00 35.99 3.69
108 109 1.746220 CCCTAAGAGTGAGGAGTGACG 59.254 57.143 0.00 0.00 35.99 4.35
127 128 3.368822 CACCCCTGTGTTGCCATG 58.631 61.111 0.00 0.00 37.72 3.66
129 130 3.751246 CCCCTGTGTTGCCATGCG 61.751 66.667 0.00 0.00 0.00 4.73
131 132 2.985282 CCTGTGTTGCCATGCGGT 60.985 61.111 0.00 0.00 33.28 5.68
132 133 2.256158 CTGTGTTGCCATGCGGTG 59.744 61.111 0.00 0.00 33.28 4.94
158 161 2.677971 CCTCTGGCAATTACGACCG 58.322 57.895 0.00 0.00 0.00 4.79
159 162 1.429148 CCTCTGGCAATTACGACCGC 61.429 60.000 0.00 0.00 0.00 5.68
188 191 2.094659 CGTCGAAAGCACGCCTCAT 61.095 57.895 0.00 0.00 0.00 2.90
193 196 2.809119 TCGAAAGCACGCCTCATAAAAA 59.191 40.909 0.00 0.00 0.00 1.94
213 216 0.896940 AGTCCTTAAGGCGACGGTCA 60.897 55.000 17.32 0.00 34.10 4.02
214 217 0.458025 GTCCTTAAGGCGACGGTCAG 60.458 60.000 17.32 2.49 34.44 3.51
215 218 1.153628 CCTTAAGGCGACGGTCAGG 60.154 63.158 9.00 2.33 0.00 3.86
219 222 2.776370 TAAGGCGACGGTCAGGGTCT 62.776 60.000 9.10 0.00 32.24 3.85
222 225 2.675423 CGACGGTCAGGGTCTCCA 60.675 66.667 9.10 0.00 34.83 3.86
223 226 2.971452 GACGGTCAGGGTCTCCAC 59.029 66.667 2.62 0.00 34.83 4.02
236 239 2.635427 GGTCTCCACCCTAGATCCATTC 59.365 54.545 0.00 0.00 36.54 2.67
239 242 4.039852 GTCTCCACCCTAGATCCATTCTTC 59.960 50.000 0.00 0.00 35.79 2.87
241 244 3.051032 TCCACCCTAGATCCATTCTTCCT 60.051 47.826 0.00 0.00 35.79 3.36
242 245 3.718956 CCACCCTAGATCCATTCTTCCTT 59.281 47.826 0.00 0.00 35.79 3.36
243 246 4.166919 CCACCCTAGATCCATTCTTCCTTT 59.833 45.833 0.00 0.00 35.79 3.11
244 247 5.372373 CACCCTAGATCCATTCTTCCTTTC 58.628 45.833 0.00 0.00 35.79 2.62
245 248 4.413851 ACCCTAGATCCATTCTTCCTTTCC 59.586 45.833 0.00 0.00 35.79 3.13
246 249 4.202514 CCCTAGATCCATTCTTCCTTTCCC 60.203 50.000 0.00 0.00 35.79 3.97
247 250 4.662650 CCTAGATCCATTCTTCCTTTCCCT 59.337 45.833 0.00 0.00 35.79 4.20
248 251 4.787135 AGATCCATTCTTCCTTTCCCTC 57.213 45.455 0.00 0.00 0.00 4.30
249 252 4.114597 AGATCCATTCTTCCTTTCCCTCA 58.885 43.478 0.00 0.00 0.00 3.86
250 253 4.541714 AGATCCATTCTTCCTTTCCCTCAA 59.458 41.667 0.00 0.00 0.00 3.02
251 254 4.740154 TCCATTCTTCCTTTCCCTCAAA 57.260 40.909 0.00 0.00 0.00 2.69
252 255 5.073437 TCCATTCTTCCTTTCCCTCAAAA 57.927 39.130 0.00 0.00 0.00 2.44
253 256 5.463154 TCCATTCTTCCTTTCCCTCAAAAA 58.537 37.500 0.00 0.00 0.00 1.94
278 281 2.131023 AGATCCATTCTTCCTCCACCC 58.869 52.381 0.00 0.00 0.00 4.61
282 285 0.548510 CATTCTTCCTCCACCCCCTC 59.451 60.000 0.00 0.00 0.00 4.30
285 288 4.364686 TTCCTCCACCCCCTCCCC 62.365 72.222 0.00 0.00 0.00 4.81
301 310 2.008723 CCCCAGTGGACCCCATGAT 61.009 63.158 11.95 0.00 35.28 2.45
306 315 2.616571 TGGACCCCATGATGGCCA 60.617 61.111 8.56 8.56 35.79 5.36
330 339 2.732597 CGTTCGCTCTCTAAGACCAAGG 60.733 54.545 0.00 0.00 0.00 3.61
331 340 2.492484 GTTCGCTCTCTAAGACCAAGGA 59.508 50.000 0.00 0.00 0.00 3.36
339 348 5.584913 TCTCTAAGACCAAGGAGAGAACAT 58.415 41.667 3.51 0.00 41.07 2.71
344 353 3.008485 AGACCAAGGAGAGAACATTCACC 59.992 47.826 0.00 0.00 0.00 4.02
347 356 3.693085 CCAAGGAGAGAACATTCACCATG 59.307 47.826 0.00 0.00 39.07 3.66
353 362 5.435291 GAGAGAACATTCACCATGGAGAAT 58.565 41.667 26.27 26.27 37.17 2.40
356 365 5.824421 AGAACATTCACCATGGAGAATTCT 58.176 37.500 28.52 25.98 37.17 2.40
389 399 8.523523 ACTAATTAACCAACCAATAAAAACGC 57.476 30.769 0.00 0.00 0.00 4.84
390 400 6.788684 AATTAACCAACCAATAAAAACGCC 57.211 33.333 0.00 0.00 0.00 5.68
391 401 2.823924 ACCAACCAATAAAAACGCCC 57.176 45.000 0.00 0.00 0.00 6.13
392 402 1.345089 ACCAACCAATAAAAACGCCCC 59.655 47.619 0.00 0.00 0.00 5.80
406 416 4.029809 CCCCCGTGACCTTCCCAC 62.030 72.222 0.00 0.00 0.00 4.61
415 443 0.250513 GACCTTCCCACTCTCGCAAT 59.749 55.000 0.00 0.00 0.00 3.56
437 465 7.661040 CAATAACAAACAAGACTCCCAAAGAT 58.339 34.615 0.00 0.00 0.00 2.40
446 474 8.107196 ACAAGACTCCCAAAGATATTAATCCT 57.893 34.615 0.00 0.00 31.98 3.24
447 475 8.214364 ACAAGACTCCCAAAGATATTAATCCTC 58.786 37.037 0.00 0.00 31.98 3.71
448 476 7.323052 AGACTCCCAAAGATATTAATCCTCC 57.677 40.000 0.00 0.00 31.98 4.30
449 477 6.851836 AGACTCCCAAAGATATTAATCCTCCA 59.148 38.462 0.00 0.00 31.98 3.86
451 479 6.183361 ACTCCCAAAGATATTAATCCTCCACC 60.183 42.308 0.00 0.00 31.98 4.61
453 481 5.162991 CCCAAAGATATTAATCCTCCACCCA 60.163 44.000 0.00 0.00 31.98 4.51
454 482 6.372931 CCAAAGATATTAATCCTCCACCCAA 58.627 40.000 0.00 0.00 31.98 4.12
455 483 6.265422 CCAAAGATATTAATCCTCCACCCAAC 59.735 42.308 0.00 0.00 31.98 3.77
456 484 5.584551 AGATATTAATCCTCCACCCAACC 57.415 43.478 0.00 0.00 31.98 3.77
467 495 2.291043 ACCCAACCGAAGCTCCGAT 61.291 57.895 0.00 0.00 0.00 4.18
469 497 0.177141 CCCAACCGAAGCTCCGATTA 59.823 55.000 0.00 0.00 0.00 1.75
483 511 0.040157 CGATTAATGGCGGCATGTGG 60.040 55.000 26.50 11.93 0.00 4.17
831 887 0.179029 CGTCCCTCCCTCTCTCTCTC 60.179 65.000 0.00 0.00 0.00 3.20
832 888 1.222567 GTCCCTCCCTCTCTCTCTCT 58.777 60.000 0.00 0.00 0.00 3.10
848 909 0.891373 CTCTTCCTGCTTCGTCCTCA 59.109 55.000 0.00 0.00 0.00 3.86
862 923 2.370445 CCTCATCGGTTGGCTCCCT 61.370 63.158 0.00 0.00 0.00 4.20
883 944 2.833582 TCGGATCCCTCGCCAGAC 60.834 66.667 6.06 0.00 0.00 3.51
884 945 3.917760 CGGATCCCTCGCCAGACC 61.918 72.222 6.06 0.00 0.00 3.85
933 994 4.555262 CTGTTGTTCTCTCTGTCTTCTCC 58.445 47.826 0.00 0.00 0.00 3.71
937 998 2.554893 GTTCTCTCTGTCTTCTCCGTGT 59.445 50.000 0.00 0.00 0.00 4.49
945 1008 1.961277 CTTCTCCGTGTGTGTGGGC 60.961 63.158 0.00 0.00 0.00 5.36
946 1009 2.383245 CTTCTCCGTGTGTGTGGGCT 62.383 60.000 0.00 0.00 0.00 5.19
986 1055 3.403558 GGGAGTGGGGAGTGAGGC 61.404 72.222 0.00 0.00 0.00 4.70
1041 1110 3.805267 CGGAGCTCCAGCAATGTC 58.195 61.111 31.67 2.06 45.16 3.06
1091 1172 4.880537 CGGCAGCAGCGGGAGTAG 62.881 72.222 0.34 0.00 43.41 2.57
1092 1173 3.775654 GGCAGCAGCGGGAGTAGT 61.776 66.667 0.00 0.00 43.41 2.73
1250 1340 6.766944 AGCCAGTCTTGATTTCTTCAGATATG 59.233 38.462 0.00 0.00 35.27 1.78
1251 1341 6.765036 GCCAGTCTTGATTTCTTCAGATATGA 59.235 38.462 0.00 0.00 35.27 2.15
1252 1342 7.041916 GCCAGTCTTGATTTCTTCAGATATGAG 60.042 40.741 0.00 0.00 35.27 2.90
1335 1445 8.218423 AGGAAAACAAAGGGGATATTTTGATT 57.782 30.769 4.92 0.00 37.63 2.57
1350 1464 8.837099 ATATTTTGATTGTTTAGTCATGGGGA 57.163 30.769 0.00 0.00 0.00 4.81
1352 1466 6.773976 TTTGATTGTTTAGTCATGGGGATC 57.226 37.500 0.00 0.00 0.00 3.36
1354 1468 4.478317 TGATTGTTTAGTCATGGGGATCCT 59.522 41.667 12.58 0.00 0.00 3.24
1355 1469 3.931907 TGTTTAGTCATGGGGATCCTG 57.068 47.619 12.58 1.99 0.00 3.86
1356 1470 2.092429 TGTTTAGTCATGGGGATCCTGC 60.092 50.000 12.58 0.00 0.00 4.85
1357 1471 2.173569 GTTTAGTCATGGGGATCCTGCT 59.826 50.000 12.58 6.67 0.00 4.24
1358 1472 1.722034 TAGTCATGGGGATCCTGCTC 58.278 55.000 12.58 0.00 0.00 4.26
1359 1473 0.030297 AGTCATGGGGATCCTGCTCT 60.030 55.000 12.58 2.00 0.00 4.09
1360 1474 0.108207 GTCATGGGGATCCTGCTCTG 59.892 60.000 12.58 3.11 0.00 3.35
1361 1475 1.058428 TCATGGGGATCCTGCTCTGG 61.058 60.000 12.58 0.00 0.00 3.86
1373 1487 2.614779 CTGCTCTGGTCATGTGTGTAG 58.385 52.381 0.00 0.00 0.00 2.74
1376 1490 1.208052 CTCTGGTCATGTGTGTAGGGG 59.792 57.143 0.00 0.00 0.00 4.79
1429 1543 6.299141 TCTTGGCTCACAGTTTCTATTTCTT 58.701 36.000 0.00 0.00 0.00 2.52
1484 1599 5.441718 TTAGGGAGCAACAGATTCTTGAT 57.558 39.130 0.00 0.00 0.00 2.57
1490 1605 4.553323 AGCAACAGATTCTTGATTTGCAC 58.447 39.130 15.88 0.00 41.43 4.57
1494 1609 5.779529 ACAGATTCTTGATTTGCACAACT 57.220 34.783 0.00 0.00 0.00 3.16
1520 1635 4.162131 AGTTTGGTTTCCACTGCTGAAAAT 59.838 37.500 0.00 0.00 33.80 1.82
1521 1636 5.362430 AGTTTGGTTTCCACTGCTGAAAATA 59.638 36.000 0.00 0.00 33.80 1.40
1522 1637 5.860941 TTGGTTTCCACTGCTGAAAATAA 57.139 34.783 0.00 0.00 33.80 1.40
1523 1638 5.860941 TGGTTTCCACTGCTGAAAATAAA 57.139 34.783 0.00 0.00 33.80 1.40
1524 1639 6.227298 TGGTTTCCACTGCTGAAAATAAAA 57.773 33.333 0.00 0.00 33.80 1.52
1533 1649 7.588488 CCACTGCTGAAAATAAAAGCAAAATTG 59.412 33.333 0.00 0.00 45.72 2.32
1572 1694 1.968540 GGCCCTGTGCAGAGTGTTC 60.969 63.158 10.34 0.00 43.89 3.18
1667 1791 1.401552 TGCACACACTCTGCTTTTGAC 59.598 47.619 0.00 0.00 35.53 3.18
1698 1825 2.223611 ACAGACTACAGACTCGTGTTCG 59.776 50.000 0.00 0.00 38.55 3.95
1702 1829 2.225963 ACTACAGACTCGTGTTCGGAAG 59.774 50.000 0.00 0.00 37.69 3.46
1719 1846 7.604545 TGTTCGGAAGATTTGACATATGTGTAA 59.395 33.333 14.43 7.36 38.34 2.41
1721 1848 6.537301 TCGGAAGATTTGACATATGTGTAACC 59.463 38.462 14.43 0.00 34.77 2.85
1722 1849 6.538742 CGGAAGATTTGACATATGTGTAACCT 59.461 38.462 14.43 0.19 39.09 3.50
1723 1850 7.065803 CGGAAGATTTGACATATGTGTAACCTT 59.934 37.037 14.43 9.26 39.09 3.50
1726 1853 7.538575 AGATTTGACATATGTGTAACCTTTGC 58.461 34.615 14.43 0.00 39.09 3.68
1923 2050 2.348666 GCATCTTGTACGTGGTAAGCAG 59.651 50.000 0.00 0.00 0.00 4.24
1927 2054 0.669318 TGTACGTGGTAAGCAGCAGC 60.669 55.000 0.00 0.00 42.56 5.25
1928 2055 0.669318 GTACGTGGTAAGCAGCAGCA 60.669 55.000 3.17 0.00 45.49 4.41
1929 2056 0.669318 TACGTGGTAAGCAGCAGCAC 60.669 55.000 3.17 5.23 45.49 4.40
1930 2057 2.863153 GTGGTAAGCAGCAGCACG 59.137 61.111 3.17 0.00 45.49 5.34
1931 2058 3.049674 TGGTAAGCAGCAGCACGC 61.050 61.111 3.17 0.00 45.49 5.34
1932 2059 3.804193 GGTAAGCAGCAGCACGCC 61.804 66.667 3.17 0.00 45.49 5.68
1933 2060 3.049674 GTAAGCAGCAGCACGCCA 61.050 61.111 3.17 0.00 45.49 5.69
1934 2061 2.743538 TAAGCAGCAGCACGCCAG 60.744 61.111 3.17 0.00 45.49 4.85
1949 2076 1.871408 CGCCAGCACCAGATATGAGAC 60.871 57.143 0.00 0.00 0.00 3.36
2066 2197 7.047891 TGTTTGTCAATGTATCCTGACTATCC 58.952 38.462 4.07 0.00 42.06 2.59
2089 2220 5.317559 CGTGCGTGTTGCTTAATTTACATA 58.682 37.500 0.00 0.00 46.63 2.29
2152 2283 7.574779 CGTTGAATGTTCATCCCATAGTCAAAA 60.575 37.037 0.00 0.00 37.00 2.44
2171 2302 8.409371 AGTCAAAACATCTCTTTCTTCCTTTTC 58.591 33.333 0.00 0.00 0.00 2.29
2270 2407 7.223582 GTCCTCATCATCATGTTGTAGTTGTAG 59.776 40.741 3.76 0.00 0.00 2.74
2271 2408 7.044181 CCTCATCATCATGTTGTAGTTGTAGT 58.956 38.462 3.76 0.00 0.00 2.73
2272 2409 7.550551 CCTCATCATCATGTTGTAGTTGTAGTT 59.449 37.037 3.76 0.00 0.00 2.24
2274 2411 6.480524 TCATCATGTTGTAGTTGTAGTTGC 57.519 37.500 3.76 0.00 0.00 4.17
2275 2412 5.994668 TCATCATGTTGTAGTTGTAGTTGCA 59.005 36.000 3.76 0.00 0.00 4.08
2276 2413 5.666969 TCATGTTGTAGTTGTAGTTGCAC 57.333 39.130 0.00 0.00 0.00 4.57
2277 2414 5.119694 TCATGTTGTAGTTGTAGTTGCACA 58.880 37.500 0.00 0.00 0.00 4.57
2285 2422 4.207165 AGTTGTAGTTGCACACAATTCCT 58.793 39.130 10.04 2.35 38.27 3.36
2342 2479 7.615582 TCTGATGCTTCATAACTTTGGTTAG 57.384 36.000 2.33 0.00 40.65 2.34
2346 2483 7.609918 TGATGCTTCATAACTTTGGTTAGCTTA 59.390 33.333 0.00 0.00 40.65 3.09
2383 2520 4.154918 GGTCTGATTGAGCCTAACACAAAG 59.845 45.833 0.00 0.00 37.22 2.77
2396 2533 6.659776 CCTAACACAAAGCTTTCAACTACTC 58.340 40.000 9.23 0.00 0.00 2.59
2400 2537 2.808543 CAAAGCTTTCAACTACTCGGCT 59.191 45.455 9.23 0.00 0.00 5.52
2475 2612 4.819761 GATCCGGCAGTGCAGCGA 62.820 66.667 18.61 12.59 34.64 4.93
2565 2707 1.002033 GCTGTCTGAAACCAGTTGCTG 60.002 52.381 0.00 0.00 33.49 4.41
2600 2758 3.731652 TGTCATGCTTGTTTTTCTGGG 57.268 42.857 0.00 0.00 0.00 4.45
2816 2974 5.664908 ACATCATCTCTGAAACCCACTATCT 59.335 40.000 0.00 0.00 34.37 1.98
2835 2995 7.388224 CACTATCTCCTAATAGCACGAACTCTA 59.612 40.741 0.00 0.00 33.33 2.43
2903 3085 9.654663 TTCTGAATATCTGCTCATTCATCTATG 57.345 33.333 0.00 0.00 39.69 2.23
2962 3147 7.278646 AGTCTGAATTTCTTTTGTTCTTTTGGC 59.721 33.333 0.00 0.00 0.00 4.52
2964 3149 7.605691 TCTGAATTTCTTTTGTTCTTTTGGCAA 59.394 29.630 0.00 0.00 0.00 4.52
2967 3152 7.686438 ATTTCTTTTGTTCTTTTGGCAAGTT 57.314 28.000 0.00 0.00 0.00 2.66
3023 3208 8.777413 GTTGCTCATTCTGCTGTCATATAATTA 58.223 33.333 0.00 0.00 0.00 1.40
3045 3230 8.992835 ATTATCTTTTGATCTTTTTGGTCTGC 57.007 30.769 0.00 0.00 40.19 4.26
3072 3257 7.050377 TGAATTCAGAAATCCTCACATACCTC 58.950 38.462 3.38 0.00 0.00 3.85
3399 3602 1.000496 ACCGACGAGGAACTTCTGAAC 60.000 52.381 8.56 0.00 41.55 3.18
3402 3605 2.726760 CGACGAGGAACTTCTGAACTTG 59.273 50.000 0.00 0.00 41.55 3.16
3568 3773 4.856115 TTTGCCTTCTTTTCTTTTTGCG 57.144 36.364 0.00 0.00 0.00 4.85
3595 3800 9.790344 TTTTGATTTTTGATCTCTCTCTTCTCT 57.210 29.630 0.00 0.00 0.00 3.10
3618 3823 9.616156 CTCTCGGTGGATGTAATATAGTAGTAT 57.384 37.037 0.00 0.00 0.00 2.12
3695 3900 1.135915 CCGGACTGATGAACTCCTCAG 59.864 57.143 0.00 9.63 43.62 3.35
3742 3947 5.908341 TCACACCGCTATTGTACAATATCA 58.092 37.500 24.81 8.77 33.29 2.15
3762 3967 4.505217 CGTGCATGGTCTTCGCGC 62.505 66.667 0.00 0.00 0.00 6.86
3782 3988 3.243877 CGCAATGTTGATCTACTCGAAGG 59.756 47.826 8.74 0.00 0.00 3.46
3783 3989 3.001736 GCAATGTTGATCTACTCGAAGGC 59.998 47.826 8.74 1.26 0.00 4.35
3813 4019 0.603975 GGCAAAGTCGGTGAAGAGCT 60.604 55.000 0.00 0.00 0.00 4.09
3816 4022 2.483876 CAAAGTCGGTGAAGAGCTTCA 58.516 47.619 8.76 8.76 46.27 3.02
3852 4058 0.750249 GGAAGCCCAGCTCTCTAGTC 59.250 60.000 0.00 0.00 38.25 2.59
3863 4069 5.825679 CCAGCTCTCTAGTCAGTACTAACAT 59.174 44.000 0.00 0.00 37.75 2.71
3864 4070 6.320164 CCAGCTCTCTAGTCAGTACTAACATT 59.680 42.308 0.00 0.00 37.75 2.71
3909 4115 6.543465 TGCTATGGATACCAAAGTTCTTGATG 59.457 38.462 0.00 0.00 36.95 3.07
3911 4117 7.254932 GCTATGGATACCAAAGTTCTTGATGTC 60.255 40.741 0.00 0.00 36.95 3.06
3918 4124 5.066505 ACCAAAGTTCTTGATGTCAACTCAC 59.933 40.000 0.00 0.00 29.85 3.51
3923 4129 5.647658 AGTTCTTGATGTCAACTCACAACAA 59.352 36.000 0.00 0.00 36.88 2.83
3976 4186 3.565307 TGAGGGTGAAATCAACAGCTTT 58.435 40.909 0.26 0.00 34.61 3.51
3977 4187 3.318839 TGAGGGTGAAATCAACAGCTTTG 59.681 43.478 0.26 0.00 34.61 2.77
4034 4255 5.538118 TGTAATGAATTCGGACGAGCATAT 58.462 37.500 0.04 0.00 0.00 1.78
4041 4262 2.572290 TCGGACGAGCATATCTTGAGA 58.428 47.619 0.00 0.00 0.00 3.27
4062 4283 2.399916 GCTGAAGCTTCACATCTCCT 57.600 50.000 25.16 0.00 38.21 3.69
4066 4287 2.278854 GAAGCTTCACATCTCCTGCTC 58.721 52.381 21.67 0.00 0.00 4.26
4068 4289 1.838715 AGCTTCACATCTCCTGCTCAT 59.161 47.619 0.00 0.00 0.00 2.90
4112 4344 6.072175 GCAATGTATACCAAAGTTCAACCTGA 60.072 38.462 0.00 0.00 0.00 3.86
4121 4353 4.762289 AAGTTCAACCTGAGAGAACAGT 57.238 40.909 12.44 1.32 43.00 3.55
4122 4354 5.871396 AAGTTCAACCTGAGAGAACAGTA 57.129 39.130 12.44 0.00 43.00 2.74
4123 4355 6.426646 AAGTTCAACCTGAGAGAACAGTAT 57.573 37.500 12.44 0.00 43.00 2.12
4125 4357 5.777732 AGTTCAACCTGAGAGAACAGTATCT 59.222 40.000 12.44 0.00 43.00 1.98
4126 4358 6.948886 AGTTCAACCTGAGAGAACAGTATCTA 59.051 38.462 12.44 0.00 43.00 1.98
4127 4359 7.617723 AGTTCAACCTGAGAGAACAGTATCTAT 59.382 37.037 12.44 0.00 43.00 1.98
4128 4360 8.904834 GTTCAACCTGAGAGAACAGTATCTATA 58.095 37.037 0.00 0.00 40.89 1.31
4129 4361 8.684386 TCAACCTGAGAGAACAGTATCTATAG 57.316 38.462 0.00 0.00 36.30 1.31
4130 4362 8.275758 TCAACCTGAGAGAACAGTATCTATAGT 58.724 37.037 0.00 0.00 36.30 2.12
4131 4363 8.349245 CAACCTGAGAGAACAGTATCTATAGTG 58.651 40.741 0.00 3.72 39.14 2.74
4132 4364 6.488683 ACCTGAGAGAACAGTATCTATAGTGC 59.511 42.308 0.00 0.00 37.23 4.40
4133 4365 6.488344 CCTGAGAGAACAGTATCTATAGTGCA 59.512 42.308 0.00 0.00 37.23 4.57
4134 4366 7.176515 CCTGAGAGAACAGTATCTATAGTGCAT 59.823 40.741 0.00 0.00 37.23 3.96
4135 4367 9.225436 CTGAGAGAACAGTATCTATAGTGCATA 57.775 37.037 0.00 0.00 37.23 3.14
4136 4368 9.225436 TGAGAGAACAGTATCTATAGTGCATAG 57.775 37.037 0.00 0.00 37.23 2.23
4137 4369 9.226606 GAGAGAACAGTATCTATAGTGCATAGT 57.773 37.037 0.00 0.00 38.26 2.12
4140 4372 8.937884 AGAACAGTATCTATAGTGCATAGTACG 58.062 37.037 0.00 0.00 38.26 3.67
4160 4392 3.581332 ACGAGGGGAAGTCAACATCTTTA 59.419 43.478 0.00 0.00 0.00 1.85
4232 4464 3.633986 AGAAAACTTGCCTTCTGACTTGG 59.366 43.478 0.00 0.00 30.67 3.61
4242 4474 4.454948 TGACTTGGTCAGGCAACG 57.545 55.556 0.00 0.00 37.73 4.10
4244 4476 0.531974 TGACTTGGTCAGGCAACGTC 60.532 55.000 0.00 0.00 37.73 4.34
4271 4503 1.423845 CGCGTCATTACCCTGTTGC 59.576 57.895 0.00 0.00 0.00 4.17
4288 4520 0.675083 TGCAGGTGCTGGTTCAAATG 59.325 50.000 3.18 0.00 42.66 2.32
4297 4529 0.950836 TGGTTCAAATGTCAGCGTGG 59.049 50.000 0.00 0.00 0.00 4.94
4305 4537 0.973632 ATGTCAGCGTGGTTGGACTA 59.026 50.000 0.00 0.00 0.00 2.59
4306 4538 0.973632 TGTCAGCGTGGTTGGACTAT 59.026 50.000 0.00 0.00 0.00 2.12
4312 4544 1.657094 GCGTGGTTGGACTATACAACG 59.343 52.381 0.00 0.00 46.89 4.10
4342 4574 2.358247 GCGCCGGTTCCTTCTTCA 60.358 61.111 1.90 0.00 0.00 3.02
4343 4575 1.964373 GCGCCGGTTCCTTCTTCAA 60.964 57.895 1.90 0.00 0.00 2.69
4344 4576 1.912371 GCGCCGGTTCCTTCTTCAAG 61.912 60.000 1.90 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 6.599244 ACTGGATCATCGAACATGTTACAATT 59.401 34.615 11.95 0.00 0.00 2.32
19 20 6.533723 TGTTACTGGATCATCGAACATGTTAC 59.466 38.462 11.95 4.61 0.00 2.50
22 23 5.084818 TGTTACTGGATCATCGAACATGT 57.915 39.130 0.00 0.00 0.00 3.21
25 26 4.503910 CCTTGTTACTGGATCATCGAACA 58.496 43.478 0.00 0.00 0.00 3.18
31 32 5.625150 GGATTAGCCTTGTTACTGGATCAT 58.375 41.667 0.00 0.00 0.00 2.45
34 35 3.181454 CCGGATTAGCCTTGTTACTGGAT 60.181 47.826 0.00 0.00 0.00 3.41
39 40 3.255969 TGTCCGGATTAGCCTTGTTAC 57.744 47.619 7.81 0.00 0.00 2.50
43 44 2.280628 GTCTTGTCCGGATTAGCCTTG 58.719 52.381 7.81 0.00 0.00 3.61
49 50 3.328382 CAAGTGGTCTTGTCCGGATTA 57.672 47.619 7.81 0.00 44.09 1.75
57 58 3.316308 GTGCAAGATTCAAGTGGTCTTGT 59.684 43.478 19.32 0.00 46.51 3.16
59 60 3.817647 GAGTGCAAGATTCAAGTGGTCTT 59.182 43.478 0.00 0.00 32.70 3.01
60 61 3.181451 TGAGTGCAAGATTCAAGTGGTCT 60.181 43.478 0.00 0.00 0.00 3.85
61 62 3.141398 TGAGTGCAAGATTCAAGTGGTC 58.859 45.455 0.00 0.00 0.00 4.02
63 64 4.037208 AGTTTGAGTGCAAGATTCAAGTGG 59.963 41.667 0.00 0.00 35.04 4.00
66 67 5.218139 GGAAGTTTGAGTGCAAGATTCAAG 58.782 41.667 0.00 0.00 34.53 3.02
78 79 4.284746 CCTCACTCTTAGGGAAGTTTGAGT 59.715 45.833 12.85 0.00 39.03 3.41
79 80 4.528596 TCCTCACTCTTAGGGAAGTTTGAG 59.471 45.833 0.00 9.48 39.66 3.02
80 81 4.489737 TCCTCACTCTTAGGGAAGTTTGA 58.510 43.478 0.00 0.00 34.66 2.69
81 82 4.284746 ACTCCTCACTCTTAGGGAAGTTTG 59.715 45.833 0.00 0.00 34.66 2.93
82 83 4.284746 CACTCCTCACTCTTAGGGAAGTTT 59.715 45.833 0.00 0.00 34.66 2.66
85 86 3.445805 GTCACTCCTCACTCTTAGGGAAG 59.554 52.174 0.00 0.00 34.66 3.46
86 87 3.432378 GTCACTCCTCACTCTTAGGGAA 58.568 50.000 0.00 0.00 34.66 3.97
87 88 2.618302 CGTCACTCCTCACTCTTAGGGA 60.618 54.545 0.00 0.00 34.66 4.20
88 89 1.746220 CGTCACTCCTCACTCTTAGGG 59.254 57.143 0.00 0.00 34.66 3.53
95 96 1.179814 GGGTGTCGTCACTCCTCACT 61.180 60.000 12.42 0.00 43.41 3.41
143 146 3.098555 GGCGGTCGTAATTGCCAG 58.901 61.111 0.00 0.00 46.76 4.85
172 175 2.087501 TTTATGAGGCGTGCTTTCGA 57.912 45.000 0.00 0.00 0.00 3.71
193 196 0.245813 GACCGTCGCCTTAAGGACTT 59.754 55.000 26.21 5.01 37.39 3.01
194 197 0.896940 TGACCGTCGCCTTAAGGACT 60.897 55.000 26.21 0.25 37.39 3.85
195 198 0.458025 CTGACCGTCGCCTTAAGGAC 60.458 60.000 26.21 14.05 37.39 3.85
196 199 1.601419 CCTGACCGTCGCCTTAAGGA 61.601 60.000 26.21 1.67 37.39 3.36
202 205 4.680537 AGACCCTGACCGTCGCCT 62.681 66.667 0.00 0.00 35.33 5.52
215 218 2.407340 ATGGATCTAGGGTGGAGACC 57.593 55.000 0.00 0.00 42.27 3.85
219 222 3.051032 AGGAAGAATGGATCTAGGGTGGA 60.051 47.826 0.00 0.00 37.42 4.02
222 225 4.413851 GGAAAGGAAGAATGGATCTAGGGT 59.586 45.833 0.00 0.00 37.42 4.34
223 226 4.202514 GGGAAAGGAAGAATGGATCTAGGG 60.203 50.000 0.00 0.00 37.42 3.53
226 229 5.288687 TGAGGGAAAGGAAGAATGGATCTA 58.711 41.667 0.00 0.00 37.42 1.98
230 233 4.740154 TTTGAGGGAAAGGAAGAATGGA 57.260 40.909 0.00 0.00 0.00 3.41
258 261 2.131023 GGGTGGAGGAAGAATGGATCT 58.869 52.381 0.00 0.00 41.32 2.75
259 262 1.143889 GGGGTGGAGGAAGAATGGATC 59.856 57.143 0.00 0.00 0.00 3.36
260 263 1.226311 GGGGTGGAGGAAGAATGGAT 58.774 55.000 0.00 0.00 0.00 3.41
261 264 0.919289 GGGGGTGGAGGAAGAATGGA 60.919 60.000 0.00 0.00 0.00 3.41
262 265 0.921256 AGGGGGTGGAGGAAGAATGG 60.921 60.000 0.00 0.00 0.00 3.16
263 266 0.548510 GAGGGGGTGGAGGAAGAATG 59.451 60.000 0.00 0.00 0.00 2.67
264 267 0.624795 GGAGGGGGTGGAGGAAGAAT 60.625 60.000 0.00 0.00 0.00 2.40
265 268 1.229853 GGAGGGGGTGGAGGAAGAA 60.230 63.158 0.00 0.00 0.00 2.52
266 269 2.454941 GGAGGGGGTGGAGGAAGA 59.545 66.667 0.00 0.00 0.00 2.87
282 285 3.743017 CATGGGGTCCACTGGGGG 61.743 72.222 0.00 0.00 35.80 5.40
285 288 1.228228 CCATCATGGGGTCCACTGG 59.772 63.158 0.00 0.00 35.80 4.00
287 290 2.693871 GGCCATCATGGGGTCCACT 61.694 63.158 5.62 0.00 38.19 4.00
288 291 2.123726 GGCCATCATGGGGTCCAC 60.124 66.667 5.62 0.00 38.19 4.02
289 292 2.244633 TTGGCCATCATGGGGTCCA 61.245 57.895 6.09 1.06 38.19 4.02
290 293 1.758122 GTTGGCCATCATGGGGTCC 60.758 63.158 6.09 0.00 38.19 4.46
301 310 3.876589 GAGAGCGAACGGTTGGCCA 62.877 63.158 21.77 0.00 34.67 5.36
306 315 1.201880 GGTCTTAGAGAGCGAACGGTT 59.798 52.381 0.00 0.00 32.69 4.44
330 339 4.478206 TCTCCATGGTGAATGTTCTCTC 57.522 45.455 14.08 0.00 34.11 3.20
331 340 4.916041 TTCTCCATGGTGAATGTTCTCT 57.084 40.909 22.34 0.00 34.11 3.10
353 362 7.726291 TGGTTGGTTAATTAGTTGATTGGAGAA 59.274 33.333 0.00 0.00 0.00 2.87
356 365 7.841282 TTGGTTGGTTAATTAGTTGATTGGA 57.159 32.000 0.00 0.00 0.00 3.53
364 373 7.599621 GGCGTTTTTATTGGTTGGTTAATTAGT 59.400 33.333 0.00 0.00 0.00 2.24
366 375 6.872547 GGGCGTTTTTATTGGTTGGTTAATTA 59.127 34.615 0.00 0.00 0.00 1.40
369 378 4.502777 GGGGCGTTTTTATTGGTTGGTTAA 60.503 41.667 0.00 0.00 0.00 2.01
389 399 4.029809 GTGGGAAGGTCACGGGGG 62.030 72.222 0.00 0.00 0.00 5.40
390 400 2.928396 AGTGGGAAGGTCACGGGG 60.928 66.667 0.00 0.00 39.86 5.73
391 401 1.889530 GAGAGTGGGAAGGTCACGGG 61.890 65.000 0.00 0.00 39.86 5.28
392 402 1.592223 GAGAGTGGGAAGGTCACGG 59.408 63.158 0.00 0.00 39.86 4.94
396 406 0.250513 ATTGCGAGAGTGGGAAGGTC 59.749 55.000 0.00 0.00 0.00 3.85
400 410 3.410631 TTGTTATTGCGAGAGTGGGAA 57.589 42.857 0.00 0.00 0.00 3.97
401 411 3.071479 GTTTGTTATTGCGAGAGTGGGA 58.929 45.455 0.00 0.00 0.00 4.37
402 412 2.811431 TGTTTGTTATTGCGAGAGTGGG 59.189 45.455 0.00 0.00 0.00 4.61
403 413 4.213270 TCTTGTTTGTTATTGCGAGAGTGG 59.787 41.667 0.00 0.00 0.00 4.00
405 415 5.057149 AGTCTTGTTTGTTATTGCGAGAGT 58.943 37.500 0.00 0.00 0.00 3.24
406 416 5.389935 GGAGTCTTGTTTGTTATTGCGAGAG 60.390 44.000 0.00 0.00 0.00 3.20
415 443 8.934023 AATATCTTTGGGAGTCTTGTTTGTTA 57.066 30.769 0.00 0.00 0.00 2.41
437 465 3.386063 TCGGTTGGGTGGAGGATTAATA 58.614 45.455 0.00 0.00 0.00 0.98
446 474 2.747686 GAGCTTCGGTTGGGTGGA 59.252 61.111 0.00 0.00 0.00 4.02
447 475 2.359975 GGAGCTTCGGTTGGGTGG 60.360 66.667 0.00 0.00 0.00 4.61
448 476 2.521958 ATCGGAGCTTCGGTTGGGTG 62.522 60.000 15.94 0.00 0.00 4.61
449 477 1.838073 AATCGGAGCTTCGGTTGGGT 61.838 55.000 13.33 0.00 31.72 4.51
451 479 2.018542 TTAATCGGAGCTTCGGTTGG 57.981 50.000 23.36 0.00 35.01 3.77
453 481 2.561569 CCATTAATCGGAGCTTCGGTT 58.438 47.619 18.65 18.65 37.27 4.44
454 482 1.810412 GCCATTAATCGGAGCTTCGGT 60.810 52.381 15.94 3.64 0.00 4.69
455 483 0.868406 GCCATTAATCGGAGCTTCGG 59.132 55.000 15.94 0.00 0.00 4.30
456 484 0.508641 CGCCATTAATCGGAGCTTCG 59.491 55.000 8.54 8.54 0.00 3.79
467 495 1.383456 GCTCCACATGCCGCCATTAA 61.383 55.000 0.00 0.00 0.00 1.40
469 497 3.142838 GCTCCACATGCCGCCATT 61.143 61.111 0.00 0.00 0.00 3.16
483 511 4.222847 CTCCCGGGTAAGCCGCTC 62.223 72.222 22.86 0.00 34.97 5.03
611 645 3.807538 CGTGGTCATGGCTGCTGC 61.808 66.667 7.10 7.10 38.76 5.25
613 647 3.640407 ACCGTGGTCATGGCTGCT 61.640 61.111 8.99 0.00 41.20 4.24
614 648 3.434319 CACCGTGGTCATGGCTGC 61.434 66.667 8.99 0.00 41.20 5.25
615 649 2.747460 CCACCGTGGTCATGGCTG 60.747 66.667 9.64 6.89 41.20 4.85
616 650 4.033776 CCCACCGTGGTCATGGCT 62.034 66.667 16.55 0.00 41.20 4.75
639 673 1.443702 CTGACGTGAACGCCATCGA 60.444 57.895 2.11 0.00 44.43 3.59
675 713 3.085533 GCCCTCCTTTCTTTTCTTCCTC 58.914 50.000 0.00 0.00 0.00 3.71
677 715 1.813178 CGCCCTCCTTTCTTTTCTTCC 59.187 52.381 0.00 0.00 0.00 3.46
831 887 1.800655 CGATGAGGACGAAGCAGGAAG 60.801 57.143 0.00 0.00 0.00 3.46
832 888 0.173481 CGATGAGGACGAAGCAGGAA 59.827 55.000 0.00 0.00 0.00 3.36
848 909 1.616628 AGGAAGGGAGCCAACCGAT 60.617 57.895 0.00 0.00 0.00 4.18
862 923 2.838225 GGCGAGGGATCCGAGGAA 60.838 66.667 5.45 0.00 0.00 3.36
933 994 3.279116 CACCAGCCCACACACACG 61.279 66.667 0.00 0.00 0.00 4.49
937 998 2.152729 TGGATCACCAGCCCACACA 61.153 57.895 0.00 0.00 41.77 3.72
946 1009 2.237965 CCACCCCCTTGGATCACCA 61.238 63.158 0.00 0.00 45.34 4.17
967 1030 2.122729 CTCACTCCCCACTCCCCA 59.877 66.667 0.00 0.00 0.00 4.96
1081 1162 2.760385 GCTCCCACTACTCCCGCT 60.760 66.667 0.00 0.00 0.00 5.52
1082 1163 3.075005 TGCTCCCACTACTCCCGC 61.075 66.667 0.00 0.00 0.00 6.13
1083 1164 3.082579 GCTGCTCCCACTACTCCCG 62.083 68.421 0.00 0.00 0.00 5.14
1084 1165 2.736826 GGCTGCTCCCACTACTCCC 61.737 68.421 0.00 0.00 0.00 4.30
1085 1166 2.904131 GGCTGCTCCCACTACTCC 59.096 66.667 0.00 0.00 0.00 3.85
1086 1167 2.496817 CGGCTGCTCCCACTACTC 59.503 66.667 0.00 0.00 0.00 2.59
1087 1168 3.775654 GCGGCTGCTCCCACTACT 61.776 66.667 11.21 0.00 38.39 2.57
1250 1340 4.044426 GGTGCACTTGACAACAAAATCTC 58.956 43.478 17.98 0.00 35.49 2.75
1251 1341 3.181476 GGGTGCACTTGACAACAAAATCT 60.181 43.478 17.98 0.00 35.49 2.40
1252 1342 3.123050 GGGTGCACTTGACAACAAAATC 58.877 45.455 17.98 0.00 35.49 2.17
1258 1362 0.875059 GCTAGGGTGCACTTGACAAC 59.125 55.000 17.98 0.00 0.00 3.32
1335 1445 2.092429 GCAGGATCCCCATGACTAAACA 60.092 50.000 8.55 0.00 33.88 2.83
1350 1464 1.065636 CACACATGACCAGAGCAGGAT 60.066 52.381 0.00 0.00 0.00 3.24
1352 1466 0.035881 ACACACATGACCAGAGCAGG 59.964 55.000 0.00 0.00 0.00 4.85
1354 1468 1.276138 CCTACACACATGACCAGAGCA 59.724 52.381 0.00 0.00 0.00 4.26
1355 1469 1.406069 CCCTACACACATGACCAGAGC 60.406 57.143 0.00 0.00 0.00 4.09
1356 1470 1.208052 CCCCTACACACATGACCAGAG 59.792 57.143 0.00 0.00 0.00 3.35
1357 1471 1.275666 CCCCTACACACATGACCAGA 58.724 55.000 0.00 0.00 0.00 3.86
1358 1472 0.253044 CCCCCTACACACATGACCAG 59.747 60.000 0.00 0.00 0.00 4.00
1359 1473 0.178888 TCCCCCTACACACATGACCA 60.179 55.000 0.00 0.00 0.00 4.02
1360 1474 0.541863 CTCCCCCTACACACATGACC 59.458 60.000 0.00 0.00 0.00 4.02
1361 1475 0.107654 GCTCCCCCTACACACATGAC 60.108 60.000 0.00 0.00 0.00 3.06
1373 1487 3.237741 CTCGGATCCTGCTCCCCC 61.238 72.222 10.75 0.00 31.04 5.40
1376 1490 4.292178 CCGCTCGGATCCTGCTCC 62.292 72.222 19.69 1.16 37.50 4.70
1429 1543 5.391310 GCGAGCAAAGATTGAGAAATGAAGA 60.391 40.000 0.00 0.00 0.00 2.87
1465 1580 4.741342 CAAATCAAGAATCTGTTGCTCCC 58.259 43.478 0.00 0.00 0.00 4.30
1470 1585 5.981315 AGTTGTGCAAATCAAGAATCTGTTG 59.019 36.000 0.00 0.00 0.00 3.33
1484 1599 5.393678 GGAAACCAAACTCTAGTTGTGCAAA 60.394 40.000 0.00 0.00 38.44 3.68
1490 1605 4.261197 GCAGTGGAAACCAAACTCTAGTTG 60.261 45.833 0.00 0.00 38.44 3.16
1494 1609 3.135712 TCAGCAGTGGAAACCAAACTCTA 59.864 43.478 0.00 0.00 34.18 2.43
1572 1694 2.943033 CCACACGCTTAATTTAGGGGAG 59.057 50.000 12.41 7.37 32.78 4.30
1626 1748 4.083802 GCATAGGAATAAGATTGCACGGTC 60.084 45.833 0.00 0.00 0.00 4.79
1692 1819 6.128282 ACACATATGTCAAATCTTCCGAACAC 60.128 38.462 5.07 0.00 31.55 3.32
1698 1825 7.865706 AGGTTACACATATGTCAAATCTTCC 57.134 36.000 5.07 1.43 40.48 3.46
1702 1829 7.538575 AGCAAAGGTTACACATATGTCAAATC 58.461 34.615 5.07 3.72 40.48 2.17
1719 1846 1.458639 GGCTGCACAAGAGCAAAGGT 61.459 55.000 0.50 0.00 45.13 3.50
1721 1848 1.081641 CGGCTGCACAAGAGCAAAG 60.082 57.895 0.50 0.00 45.13 2.77
1722 1849 2.554636 CCGGCTGCACAAGAGCAAA 61.555 57.895 0.50 0.00 45.13 3.68
1723 1850 2.979676 CCGGCTGCACAAGAGCAA 60.980 61.111 0.50 0.00 45.13 3.91
1726 1853 4.711949 AGCCCGGCTGCACAAGAG 62.712 66.667 12.38 0.00 37.57 2.85
1927 2054 0.179076 TCATATCTGGTGCTGGCGTG 60.179 55.000 0.00 0.00 0.00 5.34
1928 2055 0.105593 CTCATATCTGGTGCTGGCGT 59.894 55.000 0.00 0.00 0.00 5.68
1929 2056 0.390492 TCTCATATCTGGTGCTGGCG 59.610 55.000 0.00 0.00 0.00 5.69
1930 2057 1.871408 CGTCTCATATCTGGTGCTGGC 60.871 57.143 0.00 0.00 0.00 4.85
1931 2058 1.871408 GCGTCTCATATCTGGTGCTGG 60.871 57.143 0.00 0.00 0.00 4.85
1932 2059 1.068281 AGCGTCTCATATCTGGTGCTG 59.932 52.381 0.00 0.00 0.00 4.41
1933 2060 1.407936 AGCGTCTCATATCTGGTGCT 58.592 50.000 0.00 0.00 0.00 4.40
1934 2061 1.863454 CAAGCGTCTCATATCTGGTGC 59.137 52.381 0.00 0.00 0.00 5.01
1935 2062 3.443099 TCAAGCGTCTCATATCTGGTG 57.557 47.619 0.00 0.00 0.00 4.17
1936 2063 4.100035 TGAATCAAGCGTCTCATATCTGGT 59.900 41.667 0.00 0.00 0.00 4.00
1937 2064 4.625028 TGAATCAAGCGTCTCATATCTGG 58.375 43.478 0.00 0.00 0.00 3.86
1938 2065 5.288015 ACTGAATCAAGCGTCTCATATCTG 58.712 41.667 0.00 0.00 0.00 2.90
1939 2066 5.508825 GGACTGAATCAAGCGTCTCATATCT 60.509 44.000 1.99 0.00 0.00 1.98
1940 2067 4.683781 GGACTGAATCAAGCGTCTCATATC 59.316 45.833 1.99 0.00 0.00 1.63
1949 2076 1.813513 ACCAAGGACTGAATCAAGCG 58.186 50.000 0.00 0.00 0.00 4.68
2066 2197 3.546617 TGTAAATTAAGCAACACGCACG 58.453 40.909 0.00 0.00 46.13 5.34
2089 2220 1.338769 GGTGTGGGCGACAATTAGTCT 60.339 52.381 3.20 0.00 45.32 3.24
2126 2257 4.875536 TGACTATGGGATGAACATTCAACG 59.124 41.667 0.00 0.00 41.13 4.10
2152 2283 7.995488 TCAGAAAGAAAAGGAAGAAAGAGATGT 59.005 33.333 0.00 0.00 0.00 3.06
2192 2323 9.826574 ACCTCAAGTCGCTTGTAAATTATAATA 57.173 29.630 15.83 0.00 41.66 0.98
2208 2339 2.888513 CAAGAATGCACCTCAAGTCG 57.111 50.000 0.00 0.00 0.00 4.18
2234 2368 3.068732 TGATGATGAGGACGACAAGGATC 59.931 47.826 0.00 0.00 0.00 3.36
2270 2407 3.141398 TCTCAGAGGAATTGTGTGCAAC 58.859 45.455 0.00 0.00 37.44 4.17
2271 2408 3.490439 TCTCAGAGGAATTGTGTGCAA 57.510 42.857 0.00 0.00 39.16 4.08
2272 2409 3.708403 ATCTCAGAGGAATTGTGTGCA 57.292 42.857 0.00 0.00 0.00 4.57
2274 2411 3.754850 TGCAATCTCAGAGGAATTGTGTG 59.245 43.478 11.61 0.00 0.00 3.82
2275 2412 4.025040 TGCAATCTCAGAGGAATTGTGT 57.975 40.909 11.61 0.00 0.00 3.72
2276 2413 4.380233 GGTTGCAATCTCAGAGGAATTGTG 60.380 45.833 0.59 0.00 0.00 3.33
2277 2414 3.760684 GGTTGCAATCTCAGAGGAATTGT 59.239 43.478 0.59 0.00 0.00 2.71
2285 2422 6.417258 TCATTATTCAGGTTGCAATCTCAGA 58.583 36.000 9.91 2.00 0.00 3.27
2316 2453 7.472334 AACCAAAGTTATGAAGCATCAGAAT 57.528 32.000 1.98 0.00 38.87 2.40
2342 2479 3.565902 AGACCACAAAGTTTCAGCTAAGC 59.434 43.478 0.00 0.00 0.00 3.09
2346 2483 3.281727 TCAGACCACAAAGTTTCAGCT 57.718 42.857 0.00 0.00 0.00 4.24
2383 2520 2.285488 GCATAGCCGAGTAGTTGAAAGC 59.715 50.000 0.00 0.00 0.00 3.51
2400 2537 5.698089 GCTGTAGATCACATTAAGCTGCATA 59.302 40.000 1.02 0.00 36.29 3.14
2565 2707 7.543172 ACAAGCATGACATTGTCAACAATATTC 59.457 33.333 22.44 8.37 45.96 1.75
2600 2758 3.003068 GTCCACTGCATTCATCTGTATGC 59.997 47.826 13.05 13.05 45.32 3.14
2816 2974 7.870509 TTAAGTAGAGTTCGTGCTATTAGGA 57.129 36.000 0.00 0.00 0.00 2.94
2835 2995 6.606796 TGCAATGATATGGTGACCAATTAAGT 59.393 34.615 9.06 0.00 36.95 2.24
2885 3067 5.820404 TGACCATAGATGAATGAGCAGAT 57.180 39.130 0.00 0.00 0.00 2.90
2953 3137 4.799564 ACAGACAAACTTGCCAAAAGAA 57.200 36.364 0.00 0.00 0.00 2.52
2962 3147 9.520204 AATTCAGAATGTTTACAGACAAACTTG 57.480 29.630 0.00 0.00 38.85 3.16
2964 3149 9.736023 GAAATTCAGAATGTTTACAGACAAACT 57.264 29.630 0.00 0.00 38.85 2.66
2967 3152 7.862372 GCAGAAATTCAGAATGTTTACAGACAA 59.138 33.333 0.00 0.00 37.40 3.18
3023 3208 5.541484 AGGCAGACCAAAAAGATCAAAAGAT 59.459 36.000 0.00 0.00 39.06 2.40
3045 3230 6.261826 GGTATGTGAGGATTTCTGAATTCAGG 59.738 42.308 30.33 15.13 43.91 3.86
3072 3257 3.189287 AGAGCTGAGCGGTTTATGTTTTG 59.811 43.478 0.00 0.00 0.00 2.44
3125 3310 4.521130 ACAATGAGCTCGAGAGTGTAAA 57.479 40.909 18.75 0.00 0.00 2.01
3201 3386 1.885887 CACCACCAACATGAACGGAAT 59.114 47.619 0.00 0.00 0.00 3.01
3205 3390 1.028905 AACCACCACCAACATGAACG 58.971 50.000 0.00 0.00 0.00 3.95
3399 3602 4.128925 TCCTAATAGCAGCAGACACAAG 57.871 45.455 0.00 0.00 0.00 3.16
3402 3605 3.133003 TCCTTCCTAATAGCAGCAGACAC 59.867 47.826 0.00 0.00 0.00 3.67
3568 3773 9.824534 GAGAAGAGAGAGATCAAAAATCAAAAC 57.175 33.333 0.00 0.00 0.00 2.43
3725 3930 5.308147 CACGCATGATATTGTACAATAGCG 58.692 41.667 34.61 34.61 43.55 4.26
3742 3947 2.753966 GCGAAGACCATGCACGCAT 61.754 57.895 10.30 0.00 46.75 4.73
3754 3959 1.725641 AGATCAACATTGCGCGAAGA 58.274 45.000 12.10 0.94 0.00 2.87
3762 3967 3.557595 GGCCTTCGAGTAGATCAACATTG 59.442 47.826 0.00 0.00 0.00 2.82
3782 3988 1.132453 GACTTTGCCCTACAAATCGGC 59.868 52.381 0.00 0.00 46.90 5.54
3783 3989 1.396996 CGACTTTGCCCTACAAATCGG 59.603 52.381 11.58 0.00 46.90 4.18
3816 4022 8.551682 TGGGCTTCCAAATTTTCAAGATATAT 57.448 30.769 9.25 0.00 37.67 0.86
3817 4023 7.417797 GCTGGGCTTCCAAATTTTCAAGATATA 60.418 37.037 9.25 0.00 40.58 0.86
3818 4024 6.631088 GCTGGGCTTCCAAATTTTCAAGATAT 60.631 38.462 9.25 0.00 40.58 1.63
3829 4035 0.998145 AGAGAGCTGGGCTTCCAAAT 59.002 50.000 0.00 0.00 39.88 2.32
3837 4043 1.679153 GTACTGACTAGAGAGCTGGGC 59.321 57.143 0.00 0.00 0.00 5.36
3852 4058 8.015658 GCTAACCACTTCAAAATGTTAGTACTG 58.984 37.037 5.39 0.00 40.14 2.74
3884 4090 6.061022 TCAAGAACTTTGGTATCCATAGCA 57.939 37.500 6.24 0.00 36.31 3.49
3887 4093 7.629157 TGACATCAAGAACTTTGGTATCCATA 58.371 34.615 0.00 0.00 31.53 2.74
3909 4115 5.701290 AGGTAAGCTATTGTTGTGAGTTGAC 59.299 40.000 0.00 0.00 0.00 3.18
3911 4117 6.204688 TCAAGGTAAGCTATTGTTGTGAGTTG 59.795 38.462 0.00 0.00 0.00 3.16
3918 4124 7.202016 TGTTTCTCAAGGTAAGCTATTGTTG 57.798 36.000 0.00 0.00 0.00 3.33
3976 4186 6.667558 TTAATGGCCATCATATGCATTTCA 57.332 33.333 21.08 0.00 34.44 2.69
3977 4187 6.089820 CGTTTAATGGCCATCATATGCATTTC 59.910 38.462 21.08 0.00 34.44 2.17
4019 4229 3.570125 TCTCAAGATATGCTCGTCCGAAT 59.430 43.478 0.00 0.00 0.00 3.34
4026 4236 3.974912 TCAGCTTCTCAAGATATGCTCG 58.025 45.455 0.00 0.00 0.00 5.03
4053 4274 5.695363 CACTACAATATGAGCAGGAGATGTG 59.305 44.000 0.00 0.00 0.00 3.21
4062 4283 7.471721 CGGAATTTTTCACTACAATATGAGCA 58.528 34.615 0.00 0.00 0.00 4.26
4066 4287 8.533965 CATTGCGGAATTTTTCACTACAATATG 58.466 33.333 0.00 0.00 0.00 1.78
4068 4289 7.598278 ACATTGCGGAATTTTTCACTACAATA 58.402 30.769 0.00 0.00 0.00 1.90
4121 4353 6.157471 TCCCCTCGTACTATGCACTATAGATA 59.843 42.308 6.78 0.00 41.10 1.98
4122 4354 5.045066 TCCCCTCGTACTATGCACTATAGAT 60.045 44.000 6.78 0.00 41.10 1.98
4123 4355 4.287845 TCCCCTCGTACTATGCACTATAGA 59.712 45.833 6.78 0.00 41.10 1.98
4125 4357 4.645863 TCCCCTCGTACTATGCACTATA 57.354 45.455 0.00 0.00 0.00 1.31
4126 4358 3.520691 TCCCCTCGTACTATGCACTAT 57.479 47.619 0.00 0.00 0.00 2.12
4127 4359 3.220110 CTTCCCCTCGTACTATGCACTA 58.780 50.000 0.00 0.00 0.00 2.74
4128 4360 2.032620 CTTCCCCTCGTACTATGCACT 58.967 52.381 0.00 0.00 0.00 4.40
4129 4361 1.755380 ACTTCCCCTCGTACTATGCAC 59.245 52.381 0.00 0.00 0.00 4.57
4130 4362 2.029623 GACTTCCCCTCGTACTATGCA 58.970 52.381 0.00 0.00 0.00 3.96
4131 4363 2.029623 TGACTTCCCCTCGTACTATGC 58.970 52.381 0.00 0.00 0.00 3.14
4132 4364 3.446161 TGTTGACTTCCCCTCGTACTATG 59.554 47.826 0.00 0.00 0.00 2.23
4133 4365 3.705051 TGTTGACTTCCCCTCGTACTAT 58.295 45.455 0.00 0.00 0.00 2.12
4134 4366 3.159213 TGTTGACTTCCCCTCGTACTA 57.841 47.619 0.00 0.00 0.00 1.82
4135 4367 2.005370 TGTTGACTTCCCCTCGTACT 57.995 50.000 0.00 0.00 0.00 2.73
4136 4368 2.496470 AGATGTTGACTTCCCCTCGTAC 59.504 50.000 0.00 0.00 0.00 3.67
4137 4369 2.816411 AGATGTTGACTTCCCCTCGTA 58.184 47.619 0.00 0.00 0.00 3.43
4138 4370 1.645710 AGATGTTGACTTCCCCTCGT 58.354 50.000 0.00 0.00 0.00 4.18
4139 4371 2.770164 AAGATGTTGACTTCCCCTCG 57.230 50.000 0.00 0.00 0.00 4.63
4140 4372 8.047310 TCTTTATAAAGATGTTGACTTCCCCTC 58.953 37.037 21.46 0.00 39.95 4.30
4182 4414 8.873215 AATTGATAGGACGACTTTACATAGTG 57.127 34.615 0.00 0.00 0.00 2.74
4183 4415 9.530633 GAAATTGATAGGACGACTTTACATAGT 57.469 33.333 0.00 0.00 0.00 2.12
4184 4416 9.529325 TGAAATTGATAGGACGACTTTACATAG 57.471 33.333 0.00 0.00 0.00 2.23
4227 4459 1.594293 CGACGTTGCCTGACCAAGT 60.594 57.895 0.00 0.00 0.00 3.16
4271 4503 1.955778 TGACATTTGAACCAGCACCTG 59.044 47.619 0.00 0.00 0.00 4.00
4288 4520 2.094390 TGTATAGTCCAACCACGCTGAC 60.094 50.000 0.00 0.00 0.00 3.51
4297 4529 3.127548 TCTCCGACGTTGTATAGTCCAAC 59.872 47.826 1.30 0.00 39.01 3.77
4305 4537 2.415625 GCTCAAGTCTCCGACGTTGTAT 60.416 50.000 1.30 0.00 37.67 2.29
4306 4538 1.068748 GCTCAAGTCTCCGACGTTGTA 60.069 52.381 1.30 0.00 37.67 2.41
4312 4544 2.507324 GGCGCTCAAGTCTCCGAC 60.507 66.667 7.64 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.