Multiple sequence alignment - TraesCS3A01G248700

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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 TraesCS3A01G248700 chr3A 100.000 4313 0 0 1 4313 466643554 466647866 0.000000e+00 7965
1 TraesCS3A01G248700 chr3A 86.624 157 16 4 2 157 734150553 734150705 7.420000e-38 169
2 TraesCS3A01G248700 chr3A 89.916 119 11 1 4169 4286 374654639 374654757 7.470000e-33 152
3 TraesCS3A01G248700 chr3B 94.027 2277 105 11 2065 4313 447263313 447265586 0.000000e+00 3422
4 TraesCS3A01G248700 chr3B 88.206 1611 114 28 441 2018 447261740 447263307 0.000000e+00 1853
5 TraesCS3A01G248700 chr3B 88.235 119 13 1 4169 4286 399474897 399475015 1.620000e-29 141
6 TraesCS3A01G248700 chr3D 93.424 1399 66 6 2068 3440 347455883 347457281 0.000000e+00 2050
7 TraesCS3A01G248700 chr3D 86.211 1813 110 49 283 2018 347454126 347455875 0.000000e+00 1834
8 TraesCS3A01G248700 chr3D 94.785 882 43 3 3430 4310 347474821 347475700 0.000000e+00 1371
9 TraesCS3A01G248700 chr3D 90.909 121 10 1 4169 4288 350546365 350546245 1.240000e-35 161
10 TraesCS3A01G248700 chr3D 88.983 118 10 2 166 283 347453965 347454079 4.500000e-30 143
11 TraesCS3A01G248700 chr1B 89.041 146 16 0 1 146 101182168 101182023 9.530000e-42 182
12 TraesCS3A01G248700 chr6D 87.919 149 18 0 1 149 62131032 62131180 4.430000e-40 176
13 TraesCS3A01G248700 chr6D 88.525 122 13 1 4166 4286 187051703 187051824 3.480000e-31 147
14 TraesCS3A01G248700 chr5A 88.514 148 13 3 1 146 10207835 10207980 4.430000e-40 176
15 TraesCS3A01G248700 chr2A 87.097 155 18 2 1 154 20866348 20866195 1.590000e-39 174
16 TraesCS3A01G248700 chr2A 87.919 149 17 1 1 149 59564710 59564563 1.590000e-39 174
17 TraesCS3A01G248700 chr5B 86.335 161 14 5 1 158 706831565 706831720 7.420000e-38 169
18 TraesCS3A01G248700 chr7B 86.986 146 19 0 1 146 677773575 677773430 9.600000e-37 165
19 TraesCS3A01G248700 chr7D 85.093 161 21 2 1 158 390860978 390861138 1.240000e-35 161
20 TraesCS3A01G248700 chr6B 84.868 152 13 4 4169 4313 515412428 515412280 1.250000e-30 145
21 TraesCS3A01G248700 chr1D 84.314 153 14 6 4169 4313 450929643 450929493 1.620000e-29 141
22 TraesCS3A01G248700 chr2B 87.395 119 14 1 4169 4286 291879400 291879282 7.520000e-28 135


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 TraesCS3A01G248700 chr3A 466643554 466647866 4312 False 7965.000000 7965 100.000000 1 4313 1 chr3A.!!$F2 4312
1 TraesCS3A01G248700 chr3B 447261740 447265586 3846 False 2637.500000 3422 91.116500 441 4313 2 chr3B.!!$F2 3872
2 TraesCS3A01G248700 chr3D 347474821 347475700 879 False 1371.000000 1371 94.785000 3430 4310 1 chr3D.!!$F1 880
3 TraesCS3A01G248700 chr3D 347453965 347457281 3316 False 1342.333333 2050 89.539333 166 3440 3 chr3D.!!$F2 3274

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
35 36 0.108138 CGGAAGAGATGACCACCACC 60.108 60.0 0.0 0.0 0.0 4.61 F
36 37 0.108138 GGAAGAGATGACCACCACCG 60.108 60.0 0.0 0.0 0.0 4.94 F
236 237 0.394565 GCCACTTCTCACTCACACCT 59.605 55.0 0.0 0.0 0.0 4.00 F
2024 2168 0.038166 TGATGCTGGACCCAAGTTCC 59.962 55.0 0.0 0.0 0.0 3.62 F
2025 2169 0.329596 GATGCTGGACCCAAGTTCCT 59.670 55.0 0.0 0.0 0.0 3.36 F
2027 2171 0.555769 TGCTGGACCCAAGTTCCTTT 59.444 50.0 0.0 0.0 0.0 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 2046 0.100682 TCGTCCATCGACAAGCTAGC 59.899 55.000 6.62 6.62 44.01 3.42 R
2002 2146 0.994247 ACTTGGGTCCAGCATCATCA 59.006 50.000 0.00 0.00 0.00 3.07 R
2058 2202 0.395312 TCCCAAAACGACTCCCTGTC 59.605 55.000 0.00 0.00 42.06 3.51 R
3270 3462 1.523758 CAGTAACAAAGAAGCGGCCT 58.476 50.000 0.00 0.00 0.00 5.19 R
3273 3465 1.804748 GTCCCAGTAACAAAGAAGCGG 59.195 52.381 0.00 0.00 0.00 5.52 R
3915 4107 3.003480 CTCCGACCAAATGGAAAGAGTC 58.997 50.000 6.42 0.00 38.94 3.36 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
20 21 3.744719 CGACCAGCTCCGACGGAA 61.745 66.667 18.93 1.85 0.00 4.30
21 22 2.182030 GACCAGCTCCGACGGAAG 59.818 66.667 18.93 12.86 0.00 3.46
22 23 2.282958 ACCAGCTCCGACGGAAGA 60.283 61.111 18.93 0.00 0.00 2.87
23 24 2.272918 GACCAGCTCCGACGGAAGAG 62.273 65.000 18.93 7.68 0.00 2.85
24 25 2.046864 CCAGCTCCGACGGAAGAGA 61.047 63.158 18.93 0.00 31.43 3.10
25 26 1.388065 CCAGCTCCGACGGAAGAGAT 61.388 60.000 18.93 1.83 31.43 2.75
26 27 0.248825 CAGCTCCGACGGAAGAGATG 60.249 60.000 18.93 11.61 39.84 2.90
27 28 0.394488 AGCTCCGACGGAAGAGATGA 60.394 55.000 18.93 0.00 31.43 2.92
28 29 0.248702 GCTCCGACGGAAGAGATGAC 60.249 60.000 18.93 0.00 31.43 3.06
29 30 0.382515 CTCCGACGGAAGAGATGACC 59.617 60.000 18.93 0.00 31.43 4.02
30 31 0.323087 TCCGACGGAAGAGATGACCA 60.323 55.000 15.79 0.00 0.00 4.02
31 32 0.179134 CCGACGGAAGAGATGACCAC 60.179 60.000 8.64 0.00 0.00 4.16
32 33 0.179134 CGACGGAAGAGATGACCACC 60.179 60.000 0.00 0.00 0.00 4.61
33 34 0.895530 GACGGAAGAGATGACCACCA 59.104 55.000 0.00 0.00 0.00 4.17
34 35 0.608640 ACGGAAGAGATGACCACCAC 59.391 55.000 0.00 0.00 0.00 4.16
35 36 0.108138 CGGAAGAGATGACCACCACC 60.108 60.000 0.00 0.00 0.00 4.61
36 37 0.108138 GGAAGAGATGACCACCACCG 60.108 60.000 0.00 0.00 0.00 4.94
37 38 0.741221 GAAGAGATGACCACCACCGC 60.741 60.000 0.00 0.00 0.00 5.68
38 39 2.125106 GAGATGACCACCACCGCC 60.125 66.667 0.00 0.00 0.00 6.13
39 40 4.082523 AGATGACCACCACCGCCG 62.083 66.667 0.00 0.00 0.00 6.46
40 41 4.077184 GATGACCACCACCGCCGA 62.077 66.667 0.00 0.00 0.00 5.54
41 42 4.388499 ATGACCACCACCGCCGAC 62.388 66.667 0.00 0.00 0.00 4.79
55 56 4.680237 CGACTGCACCGGCCAGAA 62.680 66.667 24.66 0.00 40.13 3.02
56 57 3.050275 GACTGCACCGGCCAGAAC 61.050 66.667 24.66 15.48 40.13 3.01
57 58 3.825160 GACTGCACCGGCCAGAACA 62.825 63.158 24.66 4.42 40.13 3.18
58 59 3.052082 CTGCACCGGCCAGAACAG 61.052 66.667 15.65 0.32 40.13 3.16
59 60 3.535629 CTGCACCGGCCAGAACAGA 62.536 63.158 15.65 0.00 40.13 3.41
60 61 2.045926 GCACCGGCCAGAACAGAT 60.046 61.111 0.00 0.00 0.00 2.90
61 62 2.109126 GCACCGGCCAGAACAGATC 61.109 63.158 0.00 0.00 0.00 2.75
62 63 1.450312 CACCGGCCAGAACAGATCC 60.450 63.158 0.00 0.00 0.00 3.36
63 64 2.202932 CCGGCCAGAACAGATCCG 60.203 66.667 2.24 0.00 39.79 4.18
64 65 2.721167 CCGGCCAGAACAGATCCGA 61.721 63.158 2.24 0.00 42.43 4.55
65 66 1.519455 CGGCCAGAACAGATCCGAC 60.519 63.158 2.24 0.00 42.43 4.79
66 67 1.153349 GGCCAGAACAGATCCGACC 60.153 63.158 0.00 0.00 0.00 4.79
67 68 1.519455 GCCAGAACAGATCCGACCG 60.519 63.158 0.00 0.00 0.00 4.79
68 69 1.141881 CCAGAACAGATCCGACCGG 59.858 63.158 0.00 0.00 0.00 5.28
140 141 4.465512 GCAGATTGCACGCCACCG 62.466 66.667 0.00 0.00 44.26 4.94
141 142 4.465512 CAGATTGCACGCCACCGC 62.466 66.667 0.00 0.00 38.22 5.68
143 144 4.465512 GATTGCACGCCACCGCAG 62.466 66.667 0.00 0.00 39.75 5.18
169 170 2.746277 GCCGCCCGAACAGAACAT 60.746 61.111 0.00 0.00 0.00 2.71
170 171 2.750888 GCCGCCCGAACAGAACATC 61.751 63.158 0.00 0.00 0.00 3.06
171 172 1.375396 CCGCCCGAACAGAACATCA 60.375 57.895 0.00 0.00 0.00 3.07
172 173 0.744414 CCGCCCGAACAGAACATCAT 60.744 55.000 0.00 0.00 0.00 2.45
173 174 1.472552 CCGCCCGAACAGAACATCATA 60.473 52.381 0.00 0.00 0.00 2.15
174 175 2.483876 CGCCCGAACAGAACATCATAT 58.516 47.619 0.00 0.00 0.00 1.78
175 176 3.554129 CCGCCCGAACAGAACATCATATA 60.554 47.826 0.00 0.00 0.00 0.86
201 202 4.458256 TTCCCGGTGTATATACAGGAGA 57.542 45.455 18.18 11.51 38.03 3.71
216 217 9.973450 ATATACAGGAGATATGATAAATGACGC 57.027 33.333 0.00 0.00 0.00 5.19
218 219 4.032217 CAGGAGATATGATAAATGACGCGC 59.968 45.833 5.73 0.00 0.00 6.86
223 224 1.732941 TGATAAATGACGCGCCACTT 58.267 45.000 5.73 0.00 0.00 3.16
235 236 0.946221 CGCCACTTCTCACTCACACC 60.946 60.000 0.00 0.00 0.00 4.16
236 237 0.394565 GCCACTTCTCACTCACACCT 59.605 55.000 0.00 0.00 0.00 4.00
268 269 2.961526 ACCTGTCGGTGACATATGAC 57.038 50.000 10.38 3.62 43.51 3.06
269 270 2.457598 ACCTGTCGGTGACATATGACT 58.542 47.619 10.38 0.00 43.51 3.41
297 345 0.886043 TATCTGCATGTGGCCATCGC 60.886 55.000 9.72 13.16 43.89 4.58
318 369 6.718388 TCGCAAAAGAATGCAAGTATAGATG 58.282 36.000 0.00 0.00 46.76 2.90
328 379 6.667007 TGCAAGTATAGATGACAACATGTG 57.333 37.500 0.00 0.00 36.82 3.21
336 387 7.783090 ATAGATGACAACATGTGAACATCTC 57.217 36.000 28.48 13.99 44.74 2.75
343 394 2.543578 TGTGAACATCTCGCAAGCC 58.456 52.632 0.00 0.00 41.63 4.35
355 406 3.313524 CAAGCCCAGGCCCCAAAC 61.314 66.667 4.70 0.00 43.17 2.93
364 415 1.913262 GGCCCCAAACCAAAGGAGG 60.913 63.158 0.00 0.00 0.00 4.30
365 416 1.152333 GCCCCAAACCAAAGGAGGT 60.152 57.895 0.00 0.00 45.91 3.85
382 433 4.230502 AGGAGGTGTGGGAATACATTCATT 59.769 41.667 4.45 0.00 38.53 2.57
395 446 4.210724 ACATTCATTGGCAAGAAATGGG 57.789 40.909 27.26 13.58 36.01 4.00
402 453 1.004745 TGGCAAGAAATGGGGAGAGAC 59.995 52.381 0.00 0.00 0.00 3.36
403 454 1.004745 GGCAAGAAATGGGGAGAGACA 59.995 52.381 0.00 0.00 0.00 3.41
404 455 2.555227 GGCAAGAAATGGGGAGAGACAA 60.555 50.000 0.00 0.00 0.00 3.18
405 456 2.489722 GCAAGAAATGGGGAGAGACAAC 59.510 50.000 0.00 0.00 0.00 3.32
406 457 3.754965 CAAGAAATGGGGAGAGACAACA 58.245 45.455 0.00 0.00 0.00 3.33
407 458 4.144297 CAAGAAATGGGGAGAGACAACAA 58.856 43.478 0.00 0.00 0.00 2.83
408 459 3.756117 AGAAATGGGGAGAGACAACAAC 58.244 45.455 0.00 0.00 0.00 3.32
409 460 3.395941 AGAAATGGGGAGAGACAACAACT 59.604 43.478 0.00 0.00 0.00 3.16
410 461 4.597507 AGAAATGGGGAGAGACAACAACTA 59.402 41.667 0.00 0.00 0.00 2.24
411 462 4.993705 AATGGGGAGAGACAACAACTAA 57.006 40.909 0.00 0.00 0.00 2.24
412 463 5.520748 AATGGGGAGAGACAACAACTAAT 57.479 39.130 0.00 0.00 0.00 1.73
413 464 6.636454 AATGGGGAGAGACAACAACTAATA 57.364 37.500 0.00 0.00 0.00 0.98
414 465 6.636454 ATGGGGAGAGACAACAACTAATAA 57.364 37.500 0.00 0.00 0.00 1.40
415 466 5.801380 TGGGGAGAGACAACAACTAATAAC 58.199 41.667 0.00 0.00 0.00 1.89
416 467 5.308497 TGGGGAGAGACAACAACTAATAACA 59.692 40.000 0.00 0.00 0.00 2.41
417 468 5.875359 GGGGAGAGACAACAACTAATAACAG 59.125 44.000 0.00 0.00 0.00 3.16
418 469 6.295688 GGGGAGAGACAACAACTAATAACAGA 60.296 42.308 0.00 0.00 0.00 3.41
419 470 7.331791 GGGAGAGACAACAACTAATAACAGAT 58.668 38.462 0.00 0.00 0.00 2.90
420 471 7.278868 GGGAGAGACAACAACTAATAACAGATG 59.721 40.741 0.00 0.00 0.00 2.90
421 472 7.278868 GGAGAGACAACAACTAATAACAGATGG 59.721 40.741 0.00 0.00 0.00 3.51
422 473 7.907389 AGAGACAACAACTAATAACAGATGGA 58.093 34.615 0.00 0.00 0.00 3.41
529 580 6.450545 AGGAAAATGAAAAGAGCAAACTAGC 58.549 36.000 0.00 0.00 0.00 3.42
668 739 0.945099 TCGGCGAGCATCAGTAGTAG 59.055 55.000 4.99 0.00 33.17 2.57
669 740 0.663688 CGGCGAGCATCAGTAGTAGT 59.336 55.000 0.00 0.00 33.17 2.73
670 741 1.871676 CGGCGAGCATCAGTAGTAGTA 59.128 52.381 0.00 0.00 33.17 1.82
795 884 2.890474 CGGGTACTGCATGCGTCC 60.890 66.667 14.09 15.07 0.00 4.79
796 885 2.513897 GGGTACTGCATGCGTCCC 60.514 66.667 14.09 19.12 0.00 4.46
797 886 2.584608 GGTACTGCATGCGTCCCT 59.415 61.111 14.09 0.00 0.00 4.20
798 887 1.521681 GGTACTGCATGCGTCCCTC 60.522 63.158 14.09 1.20 0.00 4.30
799 888 1.878522 GTACTGCATGCGTCCCTCG 60.879 63.158 14.09 0.00 43.12 4.63
1185 1299 2.948720 GCAGGAGCTGGACGTCCTT 61.949 63.158 33.39 19.68 41.57 3.36
1309 1423 7.169982 CGAGGTGAGTTTATATGATTCAGTTCC 59.830 40.741 0.00 0.00 0.00 3.62
1317 1431 1.466856 TGATTCAGTTCCTGCATGCC 58.533 50.000 16.68 0.00 0.00 4.40
1323 1437 1.201647 CAGTTCCTGCATGCCAAGAAG 59.798 52.381 16.68 5.00 0.00 2.85
1324 1438 1.074405 AGTTCCTGCATGCCAAGAAGA 59.926 47.619 16.68 0.00 0.00 2.87
1325 1439 1.200948 GTTCCTGCATGCCAAGAAGAC 59.799 52.381 16.68 1.82 0.00 3.01
1361 1476 3.125658 TGTGATGTGAATCAAGTCGCATG 59.874 43.478 10.82 0.00 46.23 4.06
1397 1513 2.498167 AGAGCGTGCAAGTTTTGATCT 58.502 42.857 0.59 0.00 0.00 2.75
1479 1595 1.153823 CAAGATCGCGTTCCGGACT 60.154 57.895 1.83 0.00 37.59 3.85
1503 1619 1.850998 TCGGAGGAGGAGATACTGGAA 59.149 52.381 0.00 0.00 0.00 3.53
1506 1622 3.227614 GGAGGAGGAGATACTGGAAGAC 58.772 54.545 0.00 0.00 37.43 3.01
1566 1682 1.981259 ACAGCCCTAACCCAAGGTAT 58.019 50.000 0.00 0.00 33.12 2.73
1574 1690 3.692593 CCTAACCCAAGGTATCCAAAACG 59.307 47.826 0.00 0.00 33.12 3.60
1582 1698 5.335348 CCAAGGTATCCAAAACGAACGAATT 60.335 40.000 0.14 0.00 0.00 2.17
1583 1699 5.541098 AGGTATCCAAAACGAACGAATTC 57.459 39.130 0.14 0.00 0.00 2.17
1587 1703 6.468000 GGTATCCAAAACGAACGAATTCATTC 59.532 38.462 4.17 4.17 34.14 2.67
1588 1704 5.425577 TCCAAAACGAACGAATTCATTCA 57.574 34.783 14.08 0.00 36.61 2.57
1589 1705 5.209240 TCCAAAACGAACGAATTCATTCAC 58.791 37.500 14.08 0.00 36.61 3.18
1591 1707 5.685511 CCAAAACGAACGAATTCATTCACTT 59.314 36.000 14.08 3.99 36.61 3.16
1592 1708 6.198216 CCAAAACGAACGAATTCATTCACTTT 59.802 34.615 14.08 9.20 36.61 2.66
1593 1709 7.253950 CCAAAACGAACGAATTCATTCACTTTT 60.254 33.333 14.08 12.41 36.61 2.27
1594 1710 6.969669 AACGAACGAATTCATTCACTTTTC 57.030 33.333 14.08 0.00 36.61 2.29
1595 1711 6.300354 ACGAACGAATTCATTCACTTTTCT 57.700 33.333 14.08 0.00 36.61 2.52
1597 1713 8.029642 ACGAACGAATTCATTCACTTTTCTAT 57.970 30.769 14.08 0.00 36.61 1.98
1599 1715 9.625009 CGAACGAATTCATTCACTTTTCTATAG 57.375 33.333 14.08 0.00 36.61 1.31
1614 1745 9.790344 ACTTTTCTATAGATCATCAGATTTGGG 57.210 33.333 2.58 0.00 33.72 4.12
1627 1758 5.669477 TCAGATTTGGGTTGGAAAAGTTTG 58.331 37.500 0.00 0.00 0.00 2.93
1631 1762 2.192263 TGGGTTGGAAAAGTTTGGCTT 58.808 42.857 0.00 0.00 39.52 4.35
1632 1763 2.093235 TGGGTTGGAAAAGTTTGGCTTG 60.093 45.455 0.00 0.00 37.52 4.01
1633 1764 2.560504 GGTTGGAAAAGTTTGGCTTGG 58.439 47.619 0.00 0.00 37.52 3.61
1636 1767 1.128200 GGAAAAGTTTGGCTTGGGGT 58.872 50.000 0.00 0.00 37.52 4.95
1648 1779 2.080336 CTTGGGGTTGCAGGAAGGGA 62.080 60.000 0.00 0.00 0.00 4.20
1661 1792 3.962718 CAGGAAGGGATTAATTGGCATGT 59.037 43.478 0.00 0.00 0.00 3.21
1668 1799 9.686683 GAAGGGATTAATTGGCATGTACTATAT 57.313 33.333 0.00 0.00 0.00 0.86
1677 1808 5.832221 TGGCATGTACTATATAGCTCTCCT 58.168 41.667 9.78 0.00 0.00 3.69
1678 1809 5.888724 TGGCATGTACTATATAGCTCTCCTC 59.111 44.000 9.78 0.00 0.00 3.71
1679 1810 5.888724 GGCATGTACTATATAGCTCTCCTCA 59.111 44.000 9.78 0.37 0.00 3.86
1681 1812 7.069331 GGCATGTACTATATAGCTCTCCTCATT 59.931 40.741 9.78 0.00 0.00 2.57
1682 1813 8.474025 GCATGTACTATATAGCTCTCCTCATTT 58.526 37.037 9.78 0.00 0.00 2.32
1688 1819 9.815306 ACTATATAGCTCTCCTCATTTACTCAA 57.185 33.333 9.78 0.00 0.00 3.02
1697 1828 6.875726 TCTCCTCATTTACTCAAGTGTGATTG 59.124 38.462 0.00 0.00 31.85 2.67
1704 1835 8.729756 CATTTACTCAAGTGTGATTGACCATAA 58.270 33.333 0.00 0.00 35.40 1.90
1729 1861 6.777526 TTGGGTGAAATCGCTAAAATTTTG 57.222 33.333 13.76 5.05 0.00 2.44
1733 1865 6.811170 GGGTGAAATCGCTAAAATTTTGATGA 59.189 34.615 13.76 8.21 0.00 2.92
1738 1870 9.943465 GAAATCGCTAAAATTTTGATGAGTTTC 57.057 29.630 13.76 11.80 0.00 2.78
1750 1882 6.867662 TTGATGAGTTTCTTTCTCCAGTTC 57.132 37.500 0.00 0.00 0.00 3.01
1754 1886 5.848406 TGAGTTTCTTTCTCCAGTTCTCTC 58.152 41.667 0.00 0.00 0.00 3.20
1755 1887 5.221541 TGAGTTTCTTTCTCCAGTTCTCTCC 60.222 44.000 0.00 0.00 0.00 3.71
1756 1888 4.041075 AGTTTCTTTCTCCAGTTCTCTCCC 59.959 45.833 0.00 0.00 0.00 4.30
1757 1889 3.260269 TCTTTCTCCAGTTCTCTCCCA 57.740 47.619 0.00 0.00 0.00 4.37
1758 1890 3.796111 TCTTTCTCCAGTTCTCTCCCAT 58.204 45.455 0.00 0.00 0.00 4.00
1759 1891 3.772025 TCTTTCTCCAGTTCTCTCCCATC 59.228 47.826 0.00 0.00 0.00 3.51
1762 1894 0.687757 TCCAGTTCTCTCCCATCCCG 60.688 60.000 0.00 0.00 0.00 5.14
1777 1909 3.282021 CATCCCGTGGTTCATGATTTCT 58.718 45.455 0.00 0.00 0.00 2.52
1781 1913 3.535561 CCGTGGTTCATGATTTCTAGCT 58.464 45.455 0.00 0.00 0.00 3.32
1782 1914 3.310774 CCGTGGTTCATGATTTCTAGCTG 59.689 47.826 0.00 0.00 0.00 4.24
1826 1960 1.071385 GGTCAGCTGGTATGGATCAGG 59.929 57.143 15.13 0.00 0.00 3.86
1828 1962 0.471191 CAGCTGGTATGGATCAGGCA 59.529 55.000 5.57 0.00 0.00 4.75
1832 1966 2.224719 GCTGGTATGGATCAGGCAGATT 60.225 50.000 0.00 0.00 37.00 2.40
1834 1968 3.321039 TGGTATGGATCAGGCAGATTCT 58.679 45.455 0.00 0.00 37.00 2.40
1842 1976 1.483827 TCAGGCAGATTCTGTAGCTGG 59.516 52.381 14.90 0.72 33.43 4.85
1847 1981 2.898705 CAGATTCTGTAGCTGGTGGAC 58.101 52.381 5.46 0.00 0.00 4.02
1882 2016 1.774110 TTGCTTGGTTCTTGCTTGGA 58.226 45.000 0.00 0.00 0.00 3.53
1886 2020 3.894427 TGCTTGGTTCTTGCTTGGATAAA 59.106 39.130 0.00 0.00 0.00 1.40
1888 2022 4.021981 GCTTGGTTCTTGCTTGGATAAACT 60.022 41.667 0.00 0.00 0.00 2.66
1890 2024 5.705609 TGGTTCTTGCTTGGATAAACTTC 57.294 39.130 0.00 0.00 0.00 3.01
1896 2030 7.687941 TCTTGCTTGGATAAACTTCCTTAAG 57.312 36.000 0.00 0.00 36.68 1.85
1921 2057 4.013050 AGGAAAATCTTGGCTAGCTTGTC 58.987 43.478 15.72 5.01 0.00 3.18
1929 2065 0.872021 GGCTAGCTTGTCGATGGACG 60.872 60.000 15.72 0.00 46.49 4.79
1940 2076 3.614159 TCGATGGACGACCGTTTATAG 57.386 47.619 0.00 0.00 46.45 1.31
1941 2077 2.291465 TCGATGGACGACCGTTTATAGG 59.709 50.000 0.00 0.00 46.45 2.57
1942 2078 2.033801 CGATGGACGACCGTTTATAGGT 59.966 50.000 0.00 0.00 46.16 3.08
1943 2079 3.489738 CGATGGACGACCGTTTATAGGTT 60.490 47.826 0.00 0.00 43.01 3.50
2002 2146 7.704789 ACGTTTAGATTCGTGACTTTAGTTT 57.295 32.000 0.00 0.00 38.85 2.66
2010 2154 5.530519 TCGTGACTTTAGTTTGATGATGC 57.469 39.130 0.00 0.00 0.00 3.91
2018 2162 1.355381 AGTTTGATGATGCTGGACCCA 59.645 47.619 0.00 0.00 0.00 4.51
2020 2164 2.133281 TTGATGATGCTGGACCCAAG 57.867 50.000 0.00 0.00 0.00 3.61
2023 2167 2.019984 GATGATGCTGGACCCAAGTTC 58.980 52.381 0.00 0.00 0.00 3.01
2024 2168 0.038166 TGATGCTGGACCCAAGTTCC 59.962 55.000 0.00 0.00 0.00 3.62
2025 2169 0.329596 GATGCTGGACCCAAGTTCCT 59.670 55.000 0.00 0.00 0.00 3.36
2026 2170 0.779997 ATGCTGGACCCAAGTTCCTT 59.220 50.000 0.00 0.00 0.00 3.36
2027 2171 0.555769 TGCTGGACCCAAGTTCCTTT 59.444 50.000 0.00 0.00 0.00 3.11
2028 2172 1.063266 TGCTGGACCCAAGTTCCTTTT 60.063 47.619 0.00 0.00 0.00 2.27
2029 2173 2.039418 GCTGGACCCAAGTTCCTTTTT 58.961 47.619 0.00 0.00 0.00 1.94
2030 2174 3.227614 GCTGGACCCAAGTTCCTTTTTA 58.772 45.455 0.00 0.00 0.00 1.52
2031 2175 3.639561 GCTGGACCCAAGTTCCTTTTTAA 59.360 43.478 0.00 0.00 0.00 1.52
2032 2176 4.500887 GCTGGACCCAAGTTCCTTTTTAAC 60.501 45.833 0.00 0.00 0.00 2.01
2033 2177 4.611367 TGGACCCAAGTTCCTTTTTAACA 58.389 39.130 0.00 0.00 0.00 2.41
2034 2178 4.647399 TGGACCCAAGTTCCTTTTTAACAG 59.353 41.667 0.00 0.00 0.00 3.16
2035 2179 4.038763 GGACCCAAGTTCCTTTTTAACAGG 59.961 45.833 0.00 0.00 0.00 4.00
2036 2180 3.964688 ACCCAAGTTCCTTTTTAACAGGG 59.035 43.478 12.28 12.28 44.06 4.45
2037 2181 4.219919 CCCAAGTTCCTTTTTAACAGGGA 58.780 43.478 9.58 0.00 42.50 4.20
2038 2182 4.280929 CCCAAGTTCCTTTTTAACAGGGAG 59.719 45.833 9.58 0.00 42.50 4.30
2039 2183 4.893524 CCAAGTTCCTTTTTAACAGGGAGT 59.106 41.667 0.00 0.00 31.50 3.85
2040 2184 5.009710 CCAAGTTCCTTTTTAACAGGGAGTC 59.990 44.000 0.00 0.00 31.50 3.36
2041 2185 4.386711 AGTTCCTTTTTAACAGGGAGTCG 58.613 43.478 0.00 0.00 31.50 4.18
2042 2186 4.132336 GTTCCTTTTTAACAGGGAGTCGT 58.868 43.478 0.00 0.00 31.50 4.34
2043 2187 4.426736 TCCTTTTTAACAGGGAGTCGTT 57.573 40.909 0.00 0.00 31.50 3.85
2044 2188 4.784177 TCCTTTTTAACAGGGAGTCGTTT 58.216 39.130 0.00 0.00 31.50 3.60
2045 2189 5.195185 TCCTTTTTAACAGGGAGTCGTTTT 58.805 37.500 0.00 0.00 31.50 2.43
2046 2190 5.653330 TCCTTTTTAACAGGGAGTCGTTTTT 59.347 36.000 0.00 0.00 31.50 1.94
2093 2237 5.736951 TTTGGGATGTGACCAATTAAAGG 57.263 39.130 0.00 0.00 46.55 3.11
2100 2244 4.208746 TGTGACCAATTAAAGGGAAACGT 58.791 39.130 3.02 0.00 0.00 3.99
2271 2416 9.571810 GATGTACAATCAAATGTAAATTGCTCA 57.428 29.630 0.00 0.00 34.56 4.26
2289 2434 3.496507 GCTCAAGAAATCCTTATCCTCGC 59.503 47.826 0.00 0.00 32.86 5.03
2294 2439 1.333177 AATCCTTATCCTCGCTCGCT 58.667 50.000 0.00 0.00 0.00 4.93
2310 2455 4.032900 CGCTCGCTTGAGTTGTACAATATT 59.967 41.667 12.26 0.65 42.01 1.28
2395 2540 6.198687 TGCGAAATTAGACTTTTTGAGTGTG 58.801 36.000 0.00 0.00 39.19 3.82
2396 2541 5.625311 GCGAAATTAGACTTTTTGAGTGTGG 59.375 40.000 0.00 0.00 39.19 4.17
2456 2642 9.173021 CACATACTTTCAATTGGTAACCATCTA 57.827 33.333 5.42 0.00 31.53 1.98
2471 2658 9.411189 GGTAACCATCTAATTATTGTTGGGTTA 57.589 33.333 0.00 0.00 0.00 2.85
2498 2685 4.591498 TCCTAAAGCTTGTAGAGTTGACCA 59.409 41.667 0.00 0.00 0.00 4.02
2538 2725 3.577389 GGCATAGCCTTTGGACACT 57.423 52.632 0.00 0.00 46.69 3.55
2557 2744 8.286191 GGACACTTCCATAGAAATCTCAATTT 57.714 34.615 0.00 0.00 42.30 1.82
2571 2758 9.269415 GAAATCTCAATTTGTGCAAATTATTGC 57.731 29.630 18.75 12.04 46.01 3.56
2597 2784 6.040504 TGTCTAACATATGCGTCTAGTTCCAT 59.959 38.462 1.58 0.00 0.00 3.41
2609 2796 9.781834 TGCGTCTAGTTCCATAATTTTATTTTG 57.218 29.630 0.00 0.00 0.00 2.44
2678 2867 9.766277 GCAGTTTTATGTTTTGTGAAATTTTCA 57.234 25.926 7.74 7.74 37.33 2.69
2725 2915 6.809196 GGTTTCCGTTGCATTTTTATGATGTA 59.191 34.615 0.00 0.00 0.00 2.29
2732 2922 7.306167 CGTTGCATTTTTATGATGTAATGAGCC 60.306 37.037 0.00 0.00 37.93 4.70
2746 2936 9.241317 GATGTAATGAGCCTTGATTTTACAATG 57.759 33.333 0.00 0.00 34.39 2.82
2753 2943 9.206870 TGAGCCTTGATTTTACAATGAATTTTC 57.793 29.630 0.00 0.00 0.00 2.29
3008 3198 4.725790 ATGGACTAGCAAATTTCTTGCC 57.274 40.909 5.87 0.00 45.98 4.52
3009 3199 2.825532 TGGACTAGCAAATTTCTTGCCC 59.174 45.455 5.87 1.46 45.98 5.36
3032 3222 2.750657 GGCCCCTCAGGTCCTCATG 61.751 68.421 0.00 0.00 38.26 3.07
3061 3251 3.067320 GGCCTCATGACAAAATCTTAGGC 59.933 47.826 0.00 6.72 45.98 3.93
3064 3254 2.682856 TCATGACAAAATCTTAGGCGCC 59.317 45.455 21.89 21.89 0.00 6.53
3065 3255 1.083489 TGACAAAATCTTAGGCGCCG 58.917 50.000 23.20 7.22 0.00 6.46
3080 3272 1.605712 GCGCCGTCAATAGCCTAAGAT 60.606 52.381 0.00 0.00 0.00 2.40
3241 3433 4.349503 ATGCGAGCCCTGGCACAA 62.350 61.111 11.38 0.00 46.56 3.33
3270 3462 1.678123 GCTGCTCAAGATCCTGCTTCA 60.678 52.381 0.00 0.00 0.00 3.02
3300 3492 2.552599 TTGTTACTGGGACGCATCAA 57.447 45.000 0.00 0.00 0.00 2.57
3338 3530 2.487762 ACACTGGATAACATTTGGCGTG 59.512 45.455 0.00 0.00 0.00 5.34
3524 3716 6.114767 AGACGGTTGGTTCACTAAACTAAAA 58.885 36.000 0.00 0.00 39.67 1.52
3561 3753 8.882736 AGCGAAACTTGATTTTCTTCAAATTTT 58.117 25.926 0.00 0.00 35.77 1.82
3633 3825 9.268268 TGATAAATCGTGAGTTGAAAGTTAACT 57.732 29.630 1.12 1.12 40.84 2.24
3641 3833 7.355778 GTGAGTTGAAAGTTAACTTCCATGAG 58.644 38.462 20.78 0.00 38.42 2.90
3733 3925 9.995003 TCACATTTCCTAAAATATTGCTTTTGT 57.005 25.926 0.00 0.00 33.27 2.83
3883 4075 9.042632 CATGAATTTGAAATTTAACATGTTGCG 57.957 29.630 21.42 0.00 32.26 4.85
4167 4359 4.248859 TCTGCTAAGTCACTTGAAGCATC 58.751 43.478 14.17 0.00 41.93 3.91
4181 4374 9.844790 CACTTGAAGCATCTAAAAATGTATGAA 57.155 29.630 0.00 0.00 0.00 2.57
4215 4408 0.893270 TCATCAAAAGGTGGGCACGG 60.893 55.000 0.00 0.00 0.00 4.94
4239 4432 7.768807 GATAGCTAATCCACTCTTTCTCCTA 57.231 40.000 0.00 0.00 0.00 2.94
4255 4448 4.947883 TCTCCTATTGTTCTTCCCTCTCA 58.052 43.478 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.685214 CTTCCGTCGGAGCTGGTCG 62.685 68.421 14.79 0.00 31.21 4.79
4 5 2.182030 CTTCCGTCGGAGCTGGTC 59.818 66.667 14.79 0.00 31.21 4.02
5 6 2.282958 TCTTCCGTCGGAGCTGGT 60.283 61.111 14.79 0.00 31.21 4.00
6 7 1.388065 ATCTCTTCCGTCGGAGCTGG 61.388 60.000 14.79 6.67 31.21 4.85
7 8 0.248825 CATCTCTTCCGTCGGAGCTG 60.249 60.000 14.79 9.12 31.21 4.24
8 9 0.394488 TCATCTCTTCCGTCGGAGCT 60.394 55.000 14.79 0.00 31.21 4.09
9 10 0.248702 GTCATCTCTTCCGTCGGAGC 60.249 60.000 14.79 0.00 31.21 4.70
10 11 0.382515 GGTCATCTCTTCCGTCGGAG 59.617 60.000 14.79 9.05 31.21 4.63
11 12 0.323087 TGGTCATCTCTTCCGTCGGA 60.323 55.000 10.71 10.71 0.00 4.55
12 13 0.179134 GTGGTCATCTCTTCCGTCGG 60.179 60.000 4.39 4.39 0.00 4.79
13 14 0.179134 GGTGGTCATCTCTTCCGTCG 60.179 60.000 0.00 0.00 0.00 5.12
14 15 0.895530 TGGTGGTCATCTCTTCCGTC 59.104 55.000 0.00 0.00 0.00 4.79
15 16 0.608640 GTGGTGGTCATCTCTTCCGT 59.391 55.000 0.00 0.00 0.00 4.69
16 17 0.108138 GGTGGTGGTCATCTCTTCCG 60.108 60.000 0.00 0.00 0.00 4.30
17 18 0.108138 CGGTGGTGGTCATCTCTTCC 60.108 60.000 0.00 0.00 0.00 3.46
18 19 0.741221 GCGGTGGTGGTCATCTCTTC 60.741 60.000 0.00 0.00 0.00 2.87
19 20 1.296715 GCGGTGGTGGTCATCTCTT 59.703 57.895 0.00 0.00 0.00 2.85
20 21 2.660064 GGCGGTGGTGGTCATCTCT 61.660 63.158 0.00 0.00 0.00 3.10
21 22 2.125106 GGCGGTGGTGGTCATCTC 60.125 66.667 0.00 0.00 0.00 2.75
22 23 4.082523 CGGCGGTGGTGGTCATCT 62.083 66.667 0.00 0.00 0.00 2.90
23 24 4.077184 TCGGCGGTGGTGGTCATC 62.077 66.667 7.21 0.00 0.00 2.92
24 25 4.388499 GTCGGCGGTGGTGGTCAT 62.388 66.667 7.21 0.00 0.00 3.06
38 39 4.680237 TTCTGGCCGGTGCAGTCG 62.680 66.667 12.43 0.00 40.13 4.18
39 40 3.050275 GTTCTGGCCGGTGCAGTC 61.050 66.667 12.43 0.00 40.13 3.51
40 41 3.832237 CTGTTCTGGCCGGTGCAGT 62.832 63.158 21.76 0.00 40.13 4.40
41 42 2.809861 ATCTGTTCTGGCCGGTGCAG 62.810 60.000 23.14 23.14 40.13 4.41
42 43 2.803155 GATCTGTTCTGGCCGGTGCA 62.803 60.000 12.43 10.78 40.13 4.57
43 44 2.045926 ATCTGTTCTGGCCGGTGC 60.046 61.111 12.43 6.33 0.00 5.01
44 45 1.450312 GGATCTGTTCTGGCCGGTG 60.450 63.158 12.43 0.00 0.00 4.94
45 46 2.990479 GGATCTGTTCTGGCCGGT 59.010 61.111 12.43 0.00 0.00 5.28
46 47 2.202932 CGGATCTGTTCTGGCCGG 60.203 66.667 4.71 4.71 38.40 6.13
47 48 1.519455 GTCGGATCTGTTCTGGCCG 60.519 63.158 0.00 0.00 43.11 6.13
48 49 4.522971 GTCGGATCTGTTCTGGCC 57.477 61.111 0.00 0.00 28.26 5.36
49 50 1.519455 CGGTCGGATCTGTTCTGGC 60.519 63.158 0.42 0.00 34.35 4.85
50 51 1.141881 CCGGTCGGATCTGTTCTGG 59.858 63.158 2.83 7.13 37.50 3.86
51 52 0.101399 CTCCGGTCGGATCTGTTCTG 59.899 60.000 12.79 1.88 44.24 3.02
52 53 1.038130 CCTCCGGTCGGATCTGTTCT 61.038 60.000 12.79 0.00 44.24 3.01
53 54 1.321074 ACCTCCGGTCGGATCTGTTC 61.321 60.000 17.46 0.00 44.24 3.18
54 55 1.305046 ACCTCCGGTCGGATCTGTT 60.305 57.895 17.46 0.00 44.24 3.16
55 56 2.052690 CACCTCCGGTCGGATCTGT 61.053 63.158 17.46 7.86 44.24 3.41
56 57 2.808315 CACCTCCGGTCGGATCTG 59.192 66.667 17.46 7.22 44.24 2.90
57 58 3.148279 GCACCTCCGGTCGGATCT 61.148 66.667 17.46 0.00 44.24 2.75
58 59 4.222847 GGCACCTCCGGTCGGATC 62.223 72.222 17.46 9.04 44.24 3.36
117 118 1.136147 GCGTGCAATCTGCCTTCAG 59.864 57.895 0.00 0.00 44.23 3.02
118 119 2.334946 GGCGTGCAATCTGCCTTCA 61.335 57.895 11.95 0.00 44.23 3.02
119 120 2.486966 GGCGTGCAATCTGCCTTC 59.513 61.111 11.95 0.00 44.23 3.46
123 124 4.465512 CGGTGGCGTGCAATCTGC 62.466 66.667 0.00 0.00 45.29 4.26
124 125 4.465512 GCGGTGGCGTGCAATCTG 62.466 66.667 0.00 0.00 0.00 2.90
126 127 4.465512 CTGCGGTGGCGTGCAATC 62.466 66.667 0.00 0.00 44.10 2.67
152 153 2.746277 ATGTTCTGTTCGGGCGGC 60.746 61.111 0.00 0.00 0.00 6.53
153 154 0.744414 ATGATGTTCTGTTCGGGCGG 60.744 55.000 0.00 0.00 0.00 6.13
154 155 1.934589 TATGATGTTCTGTTCGGGCG 58.065 50.000 0.00 0.00 0.00 6.13
155 156 6.560253 AAATATATGATGTTCTGTTCGGGC 57.440 37.500 0.00 0.00 0.00 6.13
183 184 7.825331 ATCATATCTCCTGTATATACACCGG 57.175 40.000 11.62 12.32 31.93 5.28
201 202 3.664107 AGTGGCGCGTCATTTATCATAT 58.336 40.909 19.85 0.00 0.00 1.78
215 216 1.300931 TGTGAGTGAGAAGTGGCGC 60.301 57.895 0.00 0.00 0.00 6.53
216 217 0.946221 GGTGTGAGTGAGAAGTGGCG 60.946 60.000 0.00 0.00 0.00 5.69
218 219 1.414181 ACAGGTGTGAGTGAGAAGTGG 59.586 52.381 0.00 0.00 0.00 4.00
223 224 2.419990 CAAACCACAGGTGTGAGTGAGA 60.420 50.000 11.80 0.00 43.28 3.27
268 269 4.738541 GCCACATGCAGATAAAATTCCCAG 60.739 45.833 0.00 0.00 40.77 4.45
269 270 3.132646 GCCACATGCAGATAAAATTCCCA 59.867 43.478 0.00 0.00 40.77 4.37
297 345 9.282247 GTTGTCATCTATACTTGCATTCTTTTG 57.718 33.333 0.00 0.00 0.00 2.44
318 369 2.480037 TGCGAGATGTTCACATGTTGTC 59.520 45.455 0.00 0.00 36.57 3.18
328 379 1.372087 CCTGGGCTTGCGAGATGTTC 61.372 60.000 4.70 0.00 0.00 3.18
343 394 2.216331 CCTTTGGTTTGGGGCCTGG 61.216 63.158 0.84 0.00 0.00 4.45
355 406 2.041081 TGTATTCCCACACCTCCTTTGG 59.959 50.000 0.00 0.00 0.00 3.28
364 415 3.446873 TGCCAATGAATGTATTCCCACAC 59.553 43.478 2.41 0.00 35.97 3.82
365 416 3.706183 TGCCAATGAATGTATTCCCACA 58.294 40.909 2.41 0.00 35.97 4.17
382 433 1.004745 GTCTCTCCCCATTTCTTGCCA 59.995 52.381 0.00 0.00 0.00 4.92
395 446 7.278868 CCATCTGTTATTAGTTGTTGTCTCTCC 59.721 40.741 0.00 0.00 0.00 3.71
403 454 9.959721 ACTGTTATCCATCTGTTATTAGTTGTT 57.040 29.630 0.00 0.00 0.00 2.83
410 461 7.928706 GCTCTGTACTGTTATCCATCTGTTATT 59.071 37.037 0.00 0.00 0.00 1.40
411 462 7.288852 AGCTCTGTACTGTTATCCATCTGTTAT 59.711 37.037 0.00 0.00 0.00 1.89
412 463 6.607600 AGCTCTGTACTGTTATCCATCTGTTA 59.392 38.462 0.00 0.00 0.00 2.41
413 464 5.423610 AGCTCTGTACTGTTATCCATCTGTT 59.576 40.000 0.00 0.00 0.00 3.16
414 465 4.959210 AGCTCTGTACTGTTATCCATCTGT 59.041 41.667 0.00 0.00 0.00 3.41
415 466 5.528043 AGCTCTGTACTGTTATCCATCTG 57.472 43.478 0.00 0.00 0.00 2.90
416 467 7.847711 AATAGCTCTGTACTGTTATCCATCT 57.152 36.000 0.00 0.00 0.00 2.90
417 468 9.015367 TCTAATAGCTCTGTACTGTTATCCATC 57.985 37.037 0.00 0.00 0.00 3.51
418 469 8.941995 TCTAATAGCTCTGTACTGTTATCCAT 57.058 34.615 0.00 0.00 0.00 3.41
419 470 7.999545 ACTCTAATAGCTCTGTACTGTTATCCA 59.000 37.037 0.00 0.00 0.00 3.41
420 471 8.398878 ACTCTAATAGCTCTGTACTGTTATCC 57.601 38.462 0.00 0.00 0.00 2.59
430 481 5.491982 CCACCAAAACTCTAATAGCTCTGT 58.508 41.667 0.00 0.00 0.00 3.41
529 580 6.452611 GCGAGTCTTTGAAACGTCAACTATAG 60.453 42.308 0.00 0.00 43.52 1.31
575 626 4.318593 CAGCGACGACGAATATATGAGTTC 59.681 45.833 12.29 0.00 42.66 3.01
576 627 4.219802 CAGCGACGACGAATATATGAGTT 58.780 43.478 12.29 0.00 42.66 3.01
668 739 0.096976 TACACGTACGCTTCGCCTAC 59.903 55.000 16.72 0.00 0.00 3.18
669 740 0.801872 TTACACGTACGCTTCGCCTA 59.198 50.000 16.72 0.00 0.00 3.93
670 741 0.730494 GTTACACGTACGCTTCGCCT 60.730 55.000 16.72 0.00 0.00 5.52
791 880 2.259875 GACAGTGAGAGCGAGGGACG 62.260 65.000 0.00 0.00 45.66 4.79
792 881 1.509004 GACAGTGAGAGCGAGGGAC 59.491 63.158 0.00 0.00 0.00 4.46
793 882 2.041115 CGACAGTGAGAGCGAGGGA 61.041 63.158 0.00 0.00 0.00 4.20
794 883 2.487428 CGACAGTGAGAGCGAGGG 59.513 66.667 0.00 0.00 0.00 4.30
795 884 2.202544 GCGACAGTGAGAGCGAGG 60.203 66.667 0.00 0.00 0.00 4.63
796 885 1.799519 GTGCGACAGTGAGAGCGAG 60.800 63.158 0.00 0.00 0.00 5.03
797 886 1.866853 ATGTGCGACAGTGAGAGCGA 61.867 55.000 0.00 0.00 0.00 4.93
798 887 0.179163 TATGTGCGACAGTGAGAGCG 60.179 55.000 0.00 0.00 0.00 5.03
799 888 1.135257 AGTATGTGCGACAGTGAGAGC 60.135 52.381 0.00 0.00 0.00 4.09
800 889 2.524034 CAGTATGTGCGACAGTGAGAG 58.476 52.381 0.00 0.00 0.00 3.20
801 890 1.402852 GCAGTATGTGCGACAGTGAGA 60.403 52.381 0.00 0.00 43.99 3.27
802 891 0.994995 GCAGTATGTGCGACAGTGAG 59.005 55.000 0.00 0.00 43.99 3.51
803 892 3.122150 GCAGTATGTGCGACAGTGA 57.878 52.632 0.00 0.00 43.99 3.41
924 1032 1.515631 CGTATATTTATAGCGGCGCGG 59.484 52.381 27.59 11.08 0.00 6.46
1117 1231 4.742201 GGCGGCAGAGCTCAACGA 62.742 66.667 23.01 0.00 37.29 3.85
1171 1285 1.135344 GTAGTCAAGGACGTCCAGCTC 60.135 57.143 35.00 21.36 37.67 4.09
1309 1423 0.609957 TGGGTCTTCTTGGCATGCAG 60.610 55.000 21.36 9.52 0.00 4.41
1317 1431 5.707298 ACAATGTGTATCTTGGGTCTTCTTG 59.293 40.000 0.00 0.00 0.00 3.02
1323 1437 4.943705 ACATCACAATGTGTATCTTGGGTC 59.056 41.667 13.55 0.00 44.51 4.46
1324 1438 4.922206 ACATCACAATGTGTATCTTGGGT 58.078 39.130 13.55 0.00 44.51 4.51
1361 1476 3.744426 ACGCTCTTGGTGTTTGTGTATAC 59.256 43.478 0.00 0.00 34.69 1.47
1397 1513 2.041081 AGAACAATCCCCAAACCGATCA 59.959 45.455 0.00 0.00 0.00 2.92
1479 1595 2.372504 CAGTATCTCCTCCTCCGACCTA 59.627 54.545 0.00 0.00 0.00 3.08
1503 1619 0.251653 TCCTCCACTTGTAGCCGTCT 60.252 55.000 0.00 0.00 0.00 4.18
1506 1622 0.608640 ACTTCCTCCACTTGTAGCCG 59.391 55.000 0.00 0.00 0.00 5.52
1566 1682 5.008217 AGTGAATGAATTCGTTCGTTTTGGA 59.992 36.000 27.22 11.53 43.07 3.53
1588 1704 9.790344 CCCAAATCTGATGATCTATAGAAAAGT 57.210 33.333 6.52 0.00 31.51 2.66
1589 1705 9.790344 ACCCAAATCTGATGATCTATAGAAAAG 57.210 33.333 6.52 0.98 31.51 2.27
1591 1707 9.565090 CAACCCAAATCTGATGATCTATAGAAA 57.435 33.333 6.52 0.00 31.51 2.52
1592 1708 8.159447 CCAACCCAAATCTGATGATCTATAGAA 58.841 37.037 6.52 0.00 31.51 2.10
1593 1709 7.513781 TCCAACCCAAATCTGATGATCTATAGA 59.486 37.037 4.57 4.57 31.51 1.98
1594 1710 7.683578 TCCAACCCAAATCTGATGATCTATAG 58.316 38.462 0.00 0.00 31.51 1.31
1595 1711 7.631510 TCCAACCCAAATCTGATGATCTATA 57.368 36.000 0.00 0.00 31.51 1.31
1597 1713 5.974156 TCCAACCCAAATCTGATGATCTA 57.026 39.130 0.00 0.00 31.51 1.98
1599 1715 5.920193 TTTCCAACCCAAATCTGATGATC 57.080 39.130 0.00 0.00 31.51 2.92
1601 1717 5.147032 ACTTTTCCAACCCAAATCTGATGA 58.853 37.500 0.00 0.00 0.00 2.92
1602 1718 5.473066 ACTTTTCCAACCCAAATCTGATG 57.527 39.130 0.00 0.00 0.00 3.07
1604 1720 5.396213 CCAAACTTTTCCAACCCAAATCTGA 60.396 40.000 0.00 0.00 0.00 3.27
1606 1722 4.685848 GCCAAACTTTTCCAACCCAAATCT 60.686 41.667 0.00 0.00 0.00 2.40
1607 1723 3.563808 GCCAAACTTTTCCAACCCAAATC 59.436 43.478 0.00 0.00 0.00 2.17
1613 1744 2.560504 CCAAGCCAAACTTTTCCAACC 58.439 47.619 0.00 0.00 36.04 3.77
1614 1745 2.560504 CCCAAGCCAAACTTTTCCAAC 58.439 47.619 0.00 0.00 36.04 3.77
1627 1758 2.203625 TTCCTGCAACCCCAAGCC 60.204 61.111 0.00 0.00 0.00 4.35
1631 1762 1.442886 AATCCCTTCCTGCAACCCCA 61.443 55.000 0.00 0.00 0.00 4.96
1632 1763 0.629058 TAATCCCTTCCTGCAACCCC 59.371 55.000 0.00 0.00 0.00 4.95
1633 1764 2.525105 TTAATCCCTTCCTGCAACCC 57.475 50.000 0.00 0.00 0.00 4.11
1636 1767 2.765699 GCCAATTAATCCCTTCCTGCAA 59.234 45.455 0.00 0.00 0.00 4.08
1668 1799 5.717178 ACACTTGAGTAAATGAGGAGAGCTA 59.283 40.000 0.00 0.00 0.00 3.32
1669 1800 4.530161 ACACTTGAGTAAATGAGGAGAGCT 59.470 41.667 0.00 0.00 0.00 4.09
1670 1801 4.629200 CACACTTGAGTAAATGAGGAGAGC 59.371 45.833 0.00 0.00 0.00 4.09
1673 1804 6.875726 TCAATCACACTTGAGTAAATGAGGAG 59.124 38.462 0.00 0.00 34.35 3.69
1674 1805 6.650807 GTCAATCACACTTGAGTAAATGAGGA 59.349 38.462 0.00 0.00 35.88 3.71
1677 1808 6.295249 TGGTCAATCACACTTGAGTAAATGA 58.705 36.000 0.00 0.00 35.88 2.57
1678 1809 6.558771 TGGTCAATCACACTTGAGTAAATG 57.441 37.500 0.00 0.00 35.88 2.32
1679 1810 8.862325 TTATGGTCAATCACACTTGAGTAAAT 57.138 30.769 0.00 0.00 35.88 1.40
1681 1812 8.862325 AATTATGGTCAATCACACTTGAGTAA 57.138 30.769 0.00 0.00 35.88 2.24
1682 1813 8.729756 CAAATTATGGTCAATCACACTTGAGTA 58.270 33.333 0.00 0.00 35.88 2.59
1683 1814 7.309377 CCAAATTATGGTCAATCACACTTGAGT 60.309 37.037 0.00 0.00 44.85 3.41
1684 1815 7.031372 CCAAATTATGGTCAATCACACTTGAG 58.969 38.462 0.00 0.00 44.85 3.02
1685 1816 6.923012 CCAAATTATGGTCAATCACACTTGA 58.077 36.000 0.00 0.00 44.85 3.02
1704 1835 7.659390 TCAAAATTTTAGCGATTTCACCCAAAT 59.341 29.630 2.44 0.00 37.41 2.32
1717 1849 9.185192 AGAAAGAAACTCATCAAAATTTTAGCG 57.815 29.630 2.44 0.00 0.00 4.26
1729 1861 6.463360 AGAGAACTGGAGAAAGAAACTCATC 58.537 40.000 0.00 0.00 36.26 2.92
1733 1865 4.041075 GGGAGAGAACTGGAGAAAGAAACT 59.959 45.833 0.00 0.00 0.00 2.66
1738 1870 3.118445 GGATGGGAGAGAACTGGAGAAAG 60.118 52.174 0.00 0.00 0.00 2.62
1756 1888 3.282021 AGAAATCATGAACCACGGGATG 58.718 45.455 0.00 0.00 0.00 3.51
1757 1889 3.652057 AGAAATCATGAACCACGGGAT 57.348 42.857 0.00 0.00 0.00 3.85
1758 1890 3.681594 GCTAGAAATCATGAACCACGGGA 60.682 47.826 0.00 0.00 0.00 5.14
1759 1891 2.614057 GCTAGAAATCATGAACCACGGG 59.386 50.000 0.00 0.00 0.00 5.28
1762 1894 4.265073 ACCAGCTAGAAATCATGAACCAC 58.735 43.478 0.00 0.00 0.00 4.16
1777 1909 2.196595 AGGCCATGAAACTACCAGCTA 58.803 47.619 5.01 0.00 0.00 3.32
1781 1913 4.288626 AGAAACTAGGCCATGAAACTACCA 59.711 41.667 5.01 0.00 0.00 3.25
1782 1914 4.844884 AGAAACTAGGCCATGAAACTACC 58.155 43.478 5.01 0.00 0.00 3.18
1826 1960 1.208052 TCCACCAGCTACAGAATCTGC 59.792 52.381 10.62 0.00 34.37 4.26
1828 1962 1.834263 GGTCCACCAGCTACAGAATCT 59.166 52.381 0.00 0.00 35.64 2.40
1832 1966 4.966247 TGGTCCACCAGCTACAGA 57.034 55.556 0.00 0.00 42.01 3.41
1842 1976 3.665745 AATGCAACAGAATTGGTCCAC 57.334 42.857 0.00 0.00 0.00 4.02
1896 2030 5.047731 ACAAGCTAGCCAAGATTTTCCTTTC 60.048 40.000 12.13 0.00 29.18 2.62
1906 2041 1.134699 CCATCGACAAGCTAGCCAAGA 60.135 52.381 12.13 4.78 0.00 3.02
1907 2042 1.134699 TCCATCGACAAGCTAGCCAAG 60.135 52.381 12.13 3.96 0.00 3.61
1908 2043 0.901827 TCCATCGACAAGCTAGCCAA 59.098 50.000 12.13 0.00 0.00 4.52
1909 2044 0.175760 GTCCATCGACAAGCTAGCCA 59.824 55.000 12.13 0.00 38.99 4.75
1910 2045 0.872021 CGTCCATCGACAAGCTAGCC 60.872 60.000 12.13 0.00 42.86 3.93
1911 2046 0.100682 TCGTCCATCGACAAGCTAGC 59.899 55.000 6.62 6.62 44.01 3.42
1921 2057 2.033801 ACCTATAAACGGTCGTCCATCG 59.966 50.000 0.00 0.00 41.41 3.84
1977 2121 8.693504 CAAACTAAAGTCACGAATCTAAACGTA 58.306 33.333 0.00 0.00 40.76 3.57
1980 2124 9.530129 CATCAAACTAAAGTCACGAATCTAAAC 57.470 33.333 0.00 0.00 0.00 2.01
1988 2132 5.120674 CAGCATCATCAAACTAAAGTCACGA 59.879 40.000 0.00 0.00 0.00 4.35
2002 2146 0.994247 ACTTGGGTCCAGCATCATCA 59.006 50.000 0.00 0.00 0.00 3.07
2020 2164 4.132336 ACGACTCCCTGTTAAAAAGGAAC 58.868 43.478 6.97 0.00 36.91 3.62
2023 2167 5.509716 AAAACGACTCCCTGTTAAAAAGG 57.490 39.130 0.00 0.00 34.31 3.11
2046 2190 5.070847 ACGACTCCCTGTCCTAGTTTAAAAA 59.929 40.000 0.00 0.00 42.49 1.94
2047 2191 4.590222 ACGACTCCCTGTCCTAGTTTAAAA 59.410 41.667 0.00 0.00 42.49 1.52
2048 2192 4.154942 ACGACTCCCTGTCCTAGTTTAAA 58.845 43.478 0.00 0.00 42.49 1.52
2049 2193 3.771216 ACGACTCCCTGTCCTAGTTTAA 58.229 45.455 0.00 0.00 42.49 1.52
2050 2194 3.446442 ACGACTCCCTGTCCTAGTTTA 57.554 47.619 0.00 0.00 42.49 2.01
2051 2195 2.305858 ACGACTCCCTGTCCTAGTTT 57.694 50.000 0.00 0.00 42.49 2.66
2052 2196 2.305858 AACGACTCCCTGTCCTAGTT 57.694 50.000 0.00 0.00 42.49 2.24
2053 2197 2.299297 CAAAACGACTCCCTGTCCTAGT 59.701 50.000 0.00 0.00 42.49 2.57
2054 2198 2.353803 CCAAAACGACTCCCTGTCCTAG 60.354 54.545 0.00 0.00 42.49 3.02
2055 2199 1.621814 CCAAAACGACTCCCTGTCCTA 59.378 52.381 0.00 0.00 42.49 2.94
2056 2200 0.396811 CCAAAACGACTCCCTGTCCT 59.603 55.000 0.00 0.00 42.49 3.85
2057 2201 0.605589 CCCAAAACGACTCCCTGTCC 60.606 60.000 0.00 0.00 42.49 4.02
2058 2202 0.395312 TCCCAAAACGACTCCCTGTC 59.605 55.000 0.00 0.00 42.06 3.51
2059 2203 1.064825 ATCCCAAAACGACTCCCTGT 58.935 50.000 0.00 0.00 0.00 4.00
2060 2204 1.271379 ACATCCCAAAACGACTCCCTG 60.271 52.381 0.00 0.00 0.00 4.45
2061 2205 1.064825 ACATCCCAAAACGACTCCCT 58.935 50.000 0.00 0.00 0.00 4.20
2062 2206 1.165270 CACATCCCAAAACGACTCCC 58.835 55.000 0.00 0.00 0.00 4.30
2063 2207 1.804748 GTCACATCCCAAAACGACTCC 59.195 52.381 0.00 0.00 0.00 3.85
2071 2215 4.530161 CCCTTTAATTGGTCACATCCCAAA 59.470 41.667 0.00 0.00 44.70 3.28
2074 2218 3.976015 TCCCTTTAATTGGTCACATCCC 58.024 45.455 0.00 0.00 0.00 3.85
2093 2237 8.021973 AGATCTCATCGTATACAATACGTTTCC 58.978 37.037 16.46 4.55 41.25 3.13
2185 2330 6.944862 ACAGAAGAATAGCAAATTGAGACCTT 59.055 34.615 0.00 0.00 0.00 3.50
2271 2416 3.800604 GCGAGCGAGGATAAGGATTTCTT 60.801 47.826 0.00 0.00 39.40 2.52
2289 2434 9.425893 CATTAAATATTGTACAACTCAAGCGAG 57.574 33.333 11.22 0.00 45.49 5.03
2471 2658 7.044798 GTCAACTCTACAAGCTTTAGGATCAT 58.955 38.462 0.00 0.00 0.00 2.45
2498 2685 7.057894 TGCCGGTCAAGATTTATTTATACCTT 58.942 34.615 1.90 0.00 0.00 3.50
2537 2724 7.541162 TGCACAAATTGAGATTTCTATGGAAG 58.459 34.615 0.00 0.00 33.25 3.46
2538 2725 7.465353 TGCACAAATTGAGATTTCTATGGAA 57.535 32.000 0.00 0.00 33.25 3.53
2571 2758 5.915758 GGAACTAGACGCATATGTTAGACAG 59.084 44.000 4.29 0.00 0.00 3.51
2597 2784 9.907229 ACACTTCCCCAAAACAAAATAAAATTA 57.093 25.926 0.00 0.00 0.00 1.40
2609 2796 4.715713 AGAACTAGACACTTCCCCAAAAC 58.284 43.478 0.00 0.00 0.00 2.43
2615 2802 6.038997 ACAATGTAGAACTAGACACTTCCC 57.961 41.667 0.00 0.00 0.00 3.97
2725 2915 9.729281 AAATTCATTGTAAAATCAAGGCTCATT 57.271 25.926 0.00 0.00 0.00 2.57
2732 2922 8.863049 CCCTCGAAAATTCATTGTAAAATCAAG 58.137 33.333 0.00 0.00 0.00 3.02
2746 2936 3.146847 AGTGTTCACCCCTCGAAAATTC 58.853 45.455 0.00 0.00 0.00 2.17
2753 2943 3.939066 AGATTTTAGTGTTCACCCCTCG 58.061 45.455 0.00 0.00 0.00 4.63
2870 3060 5.230182 GGGAAATTTAAGACTTGCCAACAG 58.770 41.667 0.00 0.00 31.35 3.16
3008 3198 2.042930 ACCTGAGGGGCCTAAGGG 59.957 66.667 19.34 12.60 46.83 3.95
3061 3251 2.440539 ATCTTAGGCTATTGACGGCG 57.559 50.000 4.80 4.80 0.00 6.46
3241 3433 5.996513 CAGGATCTTGAGCAGCATAGTAAAT 59.003 40.000 0.00 0.00 0.00 1.40
3270 3462 1.523758 CAGTAACAAAGAAGCGGCCT 58.476 50.000 0.00 0.00 0.00 5.19
3273 3465 1.804748 GTCCCAGTAACAAAGAAGCGG 59.195 52.381 0.00 0.00 0.00 5.52
3300 3492 4.564406 CCAGTGTTTGATCAAGGAGCTAGT 60.564 45.833 8.41 0.00 0.00 2.57
3338 3530 6.881602 AGTTTCATTCTAGGAAGACCAATCAC 59.118 38.462 0.00 0.00 38.94 3.06
3498 3690 4.520179 AGTTTAGTGAACCAACCGTCTTT 58.480 39.130 0.00 0.00 39.13 2.52
3500 3692 3.832615 AGTTTAGTGAACCAACCGTCT 57.167 42.857 0.00 0.00 39.13 4.18
3524 3716 7.923414 AATCAAGTTTCGCTTCCTAGTAAAT 57.077 32.000 0.00 0.00 34.69 1.40
3561 3753 7.148255 CCACTTTCAACCGAAATCTCATCATAA 60.148 37.037 0.00 0.00 40.32 1.90
3641 3833 7.841915 TTGAAAAAGAAATGAGGTTTCAACC 57.158 32.000 0.00 0.00 46.97 3.77
3733 3925 4.574892 TCATGAACATCGGCTTTCAACTA 58.425 39.130 0.00 0.00 35.42 2.24
3817 4009 9.547279 ACTCATTTTAATTAGGAAATGGGAAGT 57.453 29.630 21.45 14.53 43.26 3.01
3907 4099 4.377431 CCAAATGGAAAGAGTCGAACTTCG 60.377 45.833 4.72 4.72 38.24 3.79
3915 4107 3.003480 CTCCGACCAAATGGAAAGAGTC 58.997 50.000 6.42 0.00 38.94 3.36
4146 4338 4.252073 AGATGCTTCAAGTGACTTAGCAG 58.748 43.478 22.54 10.04 38.10 4.24
4148 4340 6.727824 TTTAGATGCTTCAAGTGACTTAGC 57.272 37.500 12.05 12.05 0.00 3.09
4215 4408 6.664428 AGGAGAAAGAGTGGATTAGCTATC 57.336 41.667 0.00 0.00 0.00 2.08
4239 4432 4.107072 TGAGGATGAGAGGGAAGAACAAT 58.893 43.478 0.00 0.00 0.00 2.71
4255 4448 8.219178 AGCTCATTAGATGAAAAAGATGAGGAT 58.781 33.333 11.69 0.00 40.31 3.24


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

AutoCloner maintained by Alex Coulton.