Multiple sequence alignment - TraesCS6B01G444600

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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 TraesCS6B01G444600 chr6B 100.000 4476 0 0 1 4476 707006545 707011020 0.000000e+00 8266.0
1 TraesCS6B01G444600 chr6B 81.370 2759 434 57 882 3611 706972535 706975242 0.000000e+00 2174.0
2 TraesCS6B01G444600 chr6B 84.978 1125 163 6 2369 3492 707224962 707223843 0.000000e+00 1136.0
3 TraesCS6B01G444600 chr6B 97.561 41 0 1 657 697 707007143 707007182 8.030000e-08 69.4
4 TraesCS6B01G444600 chr6B 97.561 41 0 1 599 638 707007201 707007241 8.030000e-08 69.4
5 TraesCS6B01G444600 chr6A 91.670 2917 197 21 796 3681 610267976 610270877 0.000000e+00 3999.0
6 TraesCS6B01G444600 chr6A 79.963 2181 376 32 1324 3492 610274294 610276425 0.000000e+00 1550.0
7 TraesCS6B01G444600 chr6A 92.500 40 1 2 4407 4446 610065680 610065717 6.250000e-04 56.5
8 TraesCS6B01G444600 chr6D 85.484 3534 349 74 243 3662 463757712 463754229 0.000000e+00 3533.0
9 TraesCS6B01G444600 chr6D 78.369 2219 366 62 1332 3477 469603577 469605754 0.000000e+00 1334.0
10 TraesCS6B01G444600 chr6D 94.372 462 22 1 3781 4238 463754227 463753766 0.000000e+00 706.0
11 TraesCS6B01G444600 chr6D 91.765 85 4 1 1 82 463757794 463757710 1.020000e-21 115.0
12 TraesCS6B01G444600 chr6D 93.617 47 2 1 593 638 463757292 463757246 8.030000e-08 69.4
13 TraesCS6B01G444600 chrUn 80.572 2342 352 59 1324 3609 253311433 253313727 0.000000e+00 1709.0
14 TraesCS6B01G444600 chr2B 78.430 2216 407 48 1325 3484 402558016 402555816 0.000000e+00 1378.0
15 TraesCS6B01G444600 chr2D 77.847 2072 381 53 1469 3482 334265885 334263834 0.000000e+00 1212.0
16 TraesCS6B01G444600 chr2D 96.386 166 6 0 81 246 425287097 425286932 1.590000e-69 274.0
17 TraesCS6B01G444600 chr2A 75.885 1356 275 36 1325 2645 445034503 445033165 0.000000e+00 645.0
18 TraesCS6B01G444600 chr7D 94.505 182 8 2 68 248 205230659 205230479 3.410000e-71 279.0
19 TraesCS6B01G444600 chr7D 94.737 171 9 0 75 245 39001455 39001285 2.650000e-67 267.0
20 TraesCS6B01G444600 chr5D 95.322 171 8 0 75 245 25039974 25040144 5.710000e-69 272.0
21 TraesCS6B01G444600 chr1D 94.857 175 8 1 74 248 52360457 52360284 5.710000e-69 272.0
22 TraesCS6B01G444600 chr3B 94.350 177 8 2 69 245 54158612 54158786 2.050000e-68 270.0
23 TraesCS6B01G444600 chr3B 93.820 178 10 1 68 245 267227278 267227454 2.650000e-67 267.0
24 TraesCS6B01G444600 chr5A 91.979 187 13 2 62 247 555280750 555280935 1.230000e-65 261.0
25 TraesCS6B01G444600 chr7B 90.769 195 14 4 60 252 518023026 518022834 1.600000e-64 257.0


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 TraesCS6B01G444600 chr6B 707006545 707011020 4475 False 2801.60 8266 98.3740 1 4476 3 chr6B.!!$F2 4475
1 TraesCS6B01G444600 chr6B 706972535 706975242 2707 False 2174.00 2174 81.3700 882 3611 1 chr6B.!!$F1 2729
2 TraesCS6B01G444600 chr6B 707223843 707224962 1119 True 1136.00 1136 84.9780 2369 3492 1 chr6B.!!$R1 1123
3 TraesCS6B01G444600 chr6A 610267976 610276425 8449 False 2774.50 3999 85.8165 796 3681 2 chr6A.!!$F2 2885
4 TraesCS6B01G444600 chr6D 469603577 469605754 2177 False 1334.00 1334 78.3690 1332 3477 1 chr6D.!!$F1 2145
5 TraesCS6B01G444600 chr6D 463753766 463757794 4028 True 1105.85 3533 91.3095 1 4238 4 chr6D.!!$R1 4237
6 TraesCS6B01G444600 chrUn 253311433 253313727 2294 False 1709.00 1709 80.5720 1324 3609 1 chrUn.!!$F1 2285
7 TraesCS6B01G444600 chr2B 402555816 402558016 2200 True 1378.00 1378 78.4300 1325 3484 1 chr2B.!!$R1 2159
8 TraesCS6B01G444600 chr2D 334263834 334265885 2051 True 1212.00 1212 77.8470 1469 3482 1 chr2D.!!$R1 2013
9 TraesCS6B01G444600 chr2A 445033165 445034503 1338 True 645.00 645 75.8850 1325 2645 1 chr2A.!!$R1 1320

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
749 790 0.030638 TCAGGCAGCGAAACTTTTGC 59.969 50.0 5.68 5.68 35.87 3.68 F
948 1028 0.036483 TCGAGCTTGCTTACCATGCA 60.036 50.0 0.00 0.00 44.58 3.96 F
1721 1827 0.464452 CTTATCCTGGGTGTCCGTCC 59.536 60.0 0.00 0.00 35.24 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 1883 0.387878 CTGACTGCACAGAGACGGTC 60.388 60.0 4.31 0.0 41.62 4.79 R
1775 1884 0.823769 TCTGACTGCACAGAGACGGT 60.824 55.0 4.31 0.0 41.21 4.83 R
3659 3908 1.148310 ATCTTTTCTGGCACACGTCG 58.852 50.0 0.00 0.0 0.00 5.12 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
31 32 9.478238 AACCTTTTGAAAGTAACCCTTTAGTTA 57.522 29.630 3.09 0.00 43.47 2.24
88 92 9.440761 ACTAGAAATCTAATCATGTACTCCCTT 57.559 33.333 0.00 0.00 0.00 3.95
89 93 9.921637 CTAGAAATCTAATCATGTACTCCCTTC 57.078 37.037 0.00 0.00 0.00 3.46
90 94 7.437748 AGAAATCTAATCATGTACTCCCTTCG 58.562 38.462 0.00 0.00 0.00 3.79
91 95 6.732896 AATCTAATCATGTACTCCCTTCGT 57.267 37.500 0.00 0.00 0.00 3.85
92 96 6.732896 ATCTAATCATGTACTCCCTTCGTT 57.267 37.500 0.00 0.00 0.00 3.85
93 97 6.145338 TCTAATCATGTACTCCCTTCGTTC 57.855 41.667 0.00 0.00 0.00 3.95
94 98 3.821421 ATCATGTACTCCCTTCGTTCC 57.179 47.619 0.00 0.00 0.00 3.62
95 99 2.816411 TCATGTACTCCCTTCGTTCCT 58.184 47.619 0.00 0.00 0.00 3.36
96 100 3.972133 TCATGTACTCCCTTCGTTCCTA 58.028 45.455 0.00 0.00 0.00 2.94
97 101 4.346730 TCATGTACTCCCTTCGTTCCTAA 58.653 43.478 0.00 0.00 0.00 2.69
98 102 4.773674 TCATGTACTCCCTTCGTTCCTAAA 59.226 41.667 0.00 0.00 0.00 1.85
99 103 5.424252 TCATGTACTCCCTTCGTTCCTAAAT 59.576 40.000 0.00 0.00 0.00 1.40
100 104 6.608405 TCATGTACTCCCTTCGTTCCTAAATA 59.392 38.462 0.00 0.00 0.00 1.40
101 105 7.289317 TCATGTACTCCCTTCGTTCCTAAATAT 59.711 37.037 0.00 0.00 0.00 1.28
102 106 7.427989 TGTACTCCCTTCGTTCCTAAATATT 57.572 36.000 0.00 0.00 0.00 1.28
103 107 7.854337 TGTACTCCCTTCGTTCCTAAATATTT 58.146 34.615 5.89 5.89 0.00 1.40
104 108 7.767198 TGTACTCCCTTCGTTCCTAAATATTTG 59.233 37.037 11.05 1.40 0.00 2.32
105 109 6.718294 ACTCCCTTCGTTCCTAAATATTTGT 58.282 36.000 11.05 0.00 0.00 2.83
106 110 6.822170 ACTCCCTTCGTTCCTAAATATTTGTC 59.178 38.462 11.05 0.00 0.00 3.18
107 111 6.954232 TCCCTTCGTTCCTAAATATTTGTCT 58.046 36.000 11.05 0.00 0.00 3.41
108 112 7.399634 TCCCTTCGTTCCTAAATATTTGTCTT 58.600 34.615 11.05 0.00 0.00 3.01
109 113 7.886446 TCCCTTCGTTCCTAAATATTTGTCTTT 59.114 33.333 11.05 0.00 0.00 2.52
110 114 8.520351 CCCTTCGTTCCTAAATATTTGTCTTTT 58.480 33.333 11.05 0.00 0.00 2.27
111 115 9.908152 CCTTCGTTCCTAAATATTTGTCTTTTT 57.092 29.630 11.05 0.00 0.00 1.94
138 142 9.355215 AGAGATTTTAACAAGTGACTACATACG 57.645 33.333 0.00 0.00 0.00 3.06
139 143 9.350357 GAGATTTTAACAAGTGACTACATACGA 57.650 33.333 0.00 0.00 0.00 3.43
140 144 9.701098 AGATTTTAACAAGTGACTACATACGAA 57.299 29.630 0.00 0.00 0.00 3.85
141 145 9.953825 GATTTTAACAAGTGACTACATACGAAG 57.046 33.333 0.00 0.00 0.00 3.79
161 165 8.240883 ACGAAGTAAAATGAGTGAATCTACAC 57.759 34.615 0.00 0.00 41.94 2.90
204 208 7.991084 ACATCCATATGTGATAGTCCATTTG 57.009 36.000 1.24 0.00 44.79 2.32
205 209 7.748677 ACATCCATATGTGATAGTCCATTTGA 58.251 34.615 1.24 0.00 44.79 2.69
206 210 8.219868 ACATCCATATGTGATAGTCCATTTGAA 58.780 33.333 1.24 0.00 44.79 2.69
207 211 9.070179 CATCCATATGTGATAGTCCATTTGAAA 57.930 33.333 1.24 0.00 0.00 2.69
208 212 9.818270 ATCCATATGTGATAGTCCATTTGAAAT 57.182 29.630 1.24 0.00 0.00 2.17
209 213 9.288576 TCCATATGTGATAGTCCATTTGAAATC 57.711 33.333 1.24 0.00 0.00 2.17
210 214 9.293404 CCATATGTGATAGTCCATTTGAAATCT 57.707 33.333 1.24 0.00 0.00 2.40
239 243 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
240 244 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
241 245 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
242 246 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
243 247 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
244 248 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
245 249 6.667558 AATATTTAGGAACGGAGGGAGTAG 57.332 41.667 0.00 0.00 0.00 2.57
246 250 3.744940 TTTAGGAACGGAGGGAGTAGA 57.255 47.619 0.00 0.00 0.00 2.59
247 251 3.744940 TTAGGAACGGAGGGAGTAGAA 57.255 47.619 0.00 0.00 0.00 2.10
248 252 2.850695 AGGAACGGAGGGAGTAGAAT 57.149 50.000 0.00 0.00 0.00 2.40
249 253 3.117552 AGGAACGGAGGGAGTAGAATT 57.882 47.619 0.00 0.00 0.00 2.17
250 254 3.032459 AGGAACGGAGGGAGTAGAATTC 58.968 50.000 0.00 0.00 0.00 2.17
251 255 2.764572 GGAACGGAGGGAGTAGAATTCA 59.235 50.000 8.44 0.00 0.00 2.57
252 256 3.181474 GGAACGGAGGGAGTAGAATTCAG 60.181 52.174 8.44 0.00 0.00 3.02
257 261 2.103941 GAGGGAGTAGAATTCAGCCAGG 59.896 54.545 8.44 0.00 0.00 4.45
278 282 3.227614 GCTAGGCCTTCTTCTAGTAGCT 58.772 50.000 12.58 0.00 36.32 3.32
279 283 3.254903 GCTAGGCCTTCTTCTAGTAGCTC 59.745 52.174 12.58 0.00 36.32 4.09
293 297 2.610374 AGTAGCTCGAGATCACGAAGAC 59.390 50.000 18.75 13.04 41.67 3.01
308 315 6.873997 TCACGAAGACCACATTATCTTACAT 58.126 36.000 0.00 0.00 35.29 2.29
356 366 7.728148 AGAATGCAGATATATGCCTCTAGATG 58.272 38.462 19.14 0.00 45.91 2.90
359 369 5.049167 GCAGATATATGCCTCTAGATGCAC 58.951 45.833 22.77 11.22 40.88 4.57
362 372 7.273712 CAGATATATGCCTCTAGATGCACAAT 58.726 38.462 22.77 19.85 40.88 2.71
390 400 5.371526 TGTGGATGGCATTATTTCTCTCTC 58.628 41.667 0.00 0.00 0.00 3.20
391 401 4.759183 GTGGATGGCATTATTTCTCTCTCC 59.241 45.833 0.00 0.00 0.00 3.71
399 409 6.071952 GGCATTATTTCTCTCTCCAACACAAA 60.072 38.462 0.00 0.00 0.00 2.83
429 439 5.132144 ACATACTTCCTTGGTCCGGAATTAT 59.868 40.000 5.23 1.84 39.64 1.28
432 442 6.069705 ACTTCCTTGGTCCGGAATTATTTA 57.930 37.500 5.23 0.00 39.64 1.40
436 446 4.083484 CCTTGGTCCGGAATTATTTATCGC 60.083 45.833 5.23 0.00 0.00 4.58
451 471 9.988350 ATTATTTATCGCGAAAATGGATGTATC 57.012 29.630 25.70 0.00 0.00 2.24
461 481 7.306866 GCGAAAATGGATGTATCTAGAACTGAC 60.307 40.741 0.00 0.00 0.00 3.51
462 482 7.706607 CGAAAATGGATGTATCTAGAACTGACA 59.293 37.037 0.00 0.00 0.00 3.58
464 484 8.954950 AAATGGATGTATCTAGAACTGACAAG 57.045 34.615 0.00 0.00 0.00 3.16
466 486 8.768501 ATGGATGTATCTAGAACTGACAAGTA 57.231 34.615 0.00 0.00 34.77 2.24
467 487 8.589701 TGGATGTATCTAGAACTGACAAGTAA 57.410 34.615 0.00 0.00 34.77 2.24
468 488 9.201989 TGGATGTATCTAGAACTGACAAGTAAT 57.798 33.333 0.00 0.00 34.77 1.89
489 509 4.826274 TTCTGGATGGAAGGAGTAGTTG 57.174 45.455 0.00 0.00 0.00 3.16
491 511 4.624913 TCTGGATGGAAGGAGTAGTTGAT 58.375 43.478 0.00 0.00 0.00 2.57
502 522 3.446516 GGAGTAGTTGATTCTACGTGGGT 59.553 47.826 0.00 0.00 43.31 4.51
505 525 1.346395 AGTTGATTCTACGTGGGTGCA 59.654 47.619 0.00 0.00 0.00 4.57
512 532 0.865769 CTACGTGGGTGCACTTGAAC 59.134 55.000 17.98 8.98 0.00 3.18
517 537 2.539476 GTGGGTGCACTTGAACTTTTG 58.461 47.619 17.98 0.00 0.00 2.44
518 538 1.134848 TGGGTGCACTTGAACTTTTGC 60.135 47.619 17.98 0.00 35.45 3.68
519 539 1.199624 GGTGCACTTGAACTTTTGCG 58.800 50.000 17.98 0.00 37.82 4.85
520 540 1.202245 GGTGCACTTGAACTTTTGCGA 60.202 47.619 17.98 0.00 37.82 5.10
554 595 2.069273 GTCACGTTCAACAGGGATGAG 58.931 52.381 0.00 0.00 0.00 2.90
572 613 2.028130 GCTGCAGCTGACACTTGTT 58.972 52.632 31.33 0.00 38.21 2.83
573 614 0.317603 GCTGCAGCTGACACTTGTTG 60.318 55.000 31.33 3.43 38.21 3.33
574 615 1.302366 CTGCAGCTGACACTTGTTGA 58.698 50.000 20.43 0.00 0.00 3.18
575 616 1.003116 CTGCAGCTGACACTTGTTGAC 60.003 52.381 20.43 0.00 0.00 3.18
576 617 0.041839 GCAGCTGACACTTGTTGACG 60.042 55.000 20.43 0.00 0.00 4.35
577 618 0.041839 CAGCTGACACTTGTTGACGC 60.042 55.000 8.42 0.00 0.00 5.19
578 619 0.461870 AGCTGACACTTGTTGACGCA 60.462 50.000 0.00 0.00 0.00 5.24
579 620 0.316196 GCTGACACTTGTTGACGCAC 60.316 55.000 0.00 0.00 0.00 5.34
580 621 1.006086 CTGACACTTGTTGACGCACA 58.994 50.000 0.00 0.00 0.00 4.57
581 622 1.004610 CTGACACTTGTTGACGCACAG 60.005 52.381 0.00 0.00 0.00 3.66
582 623 1.006832 GACACTTGTTGACGCACAGT 58.993 50.000 0.00 0.00 0.00 3.55
598 639 0.604780 CAGTCCCACAGTTCAGCAGG 60.605 60.000 0.00 0.00 0.00 4.85
619 660 6.813152 GCAGGTAGCATGTAAACAAATGAAAT 59.187 34.615 0.00 0.00 44.79 2.17
650 691 1.893808 CACAAGCGGTCCAGCAACT 60.894 57.895 8.15 0.00 40.15 3.16
651 692 0.602638 CACAAGCGGTCCAGCAACTA 60.603 55.000 8.15 0.00 40.15 2.24
652 693 0.320771 ACAAGCGGTCCAGCAACTAG 60.321 55.000 8.15 0.00 40.15 2.57
653 694 0.037326 CAAGCGGTCCAGCAACTAGA 60.037 55.000 0.00 0.00 40.15 2.43
654 695 0.247736 AAGCGGTCCAGCAACTAGAG 59.752 55.000 0.00 0.00 40.15 2.43
655 696 0.612174 AGCGGTCCAGCAACTAGAGA 60.612 55.000 0.00 0.00 40.15 3.10
656 697 0.179124 GCGGTCCAGCAACTAGAGAG 60.179 60.000 0.00 0.00 37.05 3.20
691 732 2.828549 AAATAGCTTGGGCCGGCG 60.829 61.111 22.54 7.65 39.73 6.46
707 748 4.988598 CGACAAGGCCGGCACAGT 62.989 66.667 30.85 22.33 0.00 3.55
727 768 3.133721 AGTGACAGTGAAGCTTCTGAACT 59.866 43.478 26.09 18.28 35.84 3.01
742 783 1.343142 TGAACTAGTCAGGCAGCGAAA 59.657 47.619 0.00 0.00 0.00 3.46
749 790 0.030638 TCAGGCAGCGAAACTTTTGC 59.969 50.000 5.68 5.68 35.87 3.68
758 799 4.975502 CAGCGAAACTTTTGCACTAATCAA 59.024 37.500 14.92 0.00 0.00 2.57
759 800 5.458452 CAGCGAAACTTTTGCACTAATCAAA 59.542 36.000 14.92 0.00 0.00 2.69
762 803 6.336392 CGAAACTTTTGCACTAATCAAAACG 58.664 36.000 0.00 0.00 38.17 3.60
763 804 6.020995 CGAAACTTTTGCACTAATCAAAACGT 60.021 34.615 0.00 0.00 38.17 3.99
789 856 6.616237 AAAAAGAGCAATCCATCTTTCCAT 57.384 33.333 1.05 0.00 43.25 3.41
818 885 3.194542 AGAACTGGAGAAGAGAACGGATG 59.805 47.826 0.00 0.00 0.00 3.51
820 887 2.757868 ACTGGAGAAGAGAACGGATGAG 59.242 50.000 0.00 0.00 0.00 2.90
835 902 3.119173 CGGATGAGCAGAAAGAGAGTTCT 60.119 47.826 0.00 0.00 38.41 3.01
844 911 5.982890 AGAAAGAGAGTTCTGGAGAAGAG 57.017 43.478 0.00 0.00 36.48 2.85
845 912 5.640147 AGAAAGAGAGTTCTGGAGAAGAGA 58.360 41.667 0.00 0.00 36.48 3.10
878 952 2.027073 CTTCTACACAGCGGCGCAA 61.027 57.895 35.02 16.31 0.00 4.85
908 982 2.555757 AGACCTTGTGATCTTTGCTTGC 59.444 45.455 0.00 0.00 0.00 4.01
948 1028 0.036483 TCGAGCTTGCTTACCATGCA 60.036 50.000 0.00 0.00 44.58 3.96
949 1029 1.019673 CGAGCTTGCTTACCATGCAT 58.980 50.000 0.00 0.00 44.58 3.96
1186 1275 4.673968 TCTAGGACCAGAAACTCAAGCTA 58.326 43.478 0.00 0.00 0.00 3.32
1231 1320 1.577328 CGCAGGGTTCACATGTGTCC 61.577 60.000 24.63 24.29 0.00 4.02
1276 1365 2.151202 TCCTCTTTGCGGTGTTCATTC 58.849 47.619 0.00 0.00 0.00 2.67
1317 1406 6.998074 TCAACCCTAATAATGCCATAACTCAG 59.002 38.462 0.00 0.00 0.00 3.35
1386 1484 4.469657 AGAATGCAACCCTTGAGTTTACA 58.530 39.130 0.00 0.00 0.00 2.41
1461 1559 1.079266 CAGCTCAGGCCAGTCTGTC 60.079 63.158 5.01 0.00 39.73 3.51
1523 1621 2.674852 TCGATCAGAGAAATGCAACAGC 59.325 45.455 0.00 0.00 0.00 4.40
1533 1631 4.374702 GCAACAGCGTGGCAGTCG 62.375 66.667 3.60 0.00 31.84 4.18
1666 1769 2.224378 ACTCCCAGATGGATTACATGCG 60.224 50.000 0.00 0.00 44.07 4.73
1702 1805 2.167075 ACCACCACAACTATACTACCGC 59.833 50.000 0.00 0.00 0.00 5.68
1718 1824 1.227263 CGCTTATCCTGGGTGTCCG 60.227 63.158 0.00 0.00 35.24 4.79
1721 1827 0.464452 CTTATCCTGGGTGTCCGTCC 59.536 60.000 0.00 0.00 35.24 4.79
1774 1883 4.627611 ATTCGTGAATGAAAGCCTCATG 57.372 40.909 0.00 0.00 44.43 3.07
1775 1884 3.333029 TCGTGAATGAAAGCCTCATGA 57.667 42.857 0.00 0.00 44.43 3.07
1819 1943 2.816204 ATCATCAGATCTCACTGCCG 57.184 50.000 0.00 0.00 37.75 5.69
1821 1945 0.179092 CATCAGATCTCACTGCCGCA 60.179 55.000 0.00 0.00 37.75 5.69
1872 1999 1.734477 CAGACGGACACTTGAGGCG 60.734 63.158 0.00 0.00 0.00 5.52
1922 2055 5.296780 ACCGTGGAGTATGATTTAATGCAAG 59.703 40.000 0.00 0.00 0.00 4.01
2096 2238 8.413309 TCCAATCTCTTGTCAAGAAATTCAAT 57.587 30.769 15.97 1.76 37.02 2.57
2110 2252 9.918630 CAAGAAATTCAATACCATCAACTCTTT 57.081 29.630 0.00 0.00 0.00 2.52
2297 2457 5.744171 TCTCTTTGCAATCAATACAGCCTA 58.256 37.500 0.00 0.00 31.33 3.93
2608 2816 3.196901 GGTTTGGGTCAGTTTTTGAAGGT 59.803 43.478 0.00 0.00 37.61 3.50
3118 3327 3.728845 TGTCTACAGCTTTGGAGTTGTC 58.271 45.455 0.00 0.00 42.80 3.18
3139 3348 5.820423 TGTCGTGATGGAAATATTAAGTGGG 59.180 40.000 0.00 0.00 0.00 4.61
3465 3692 6.038382 CCATCTCAAGCATCCATATTATCAGC 59.962 42.308 0.00 0.00 0.00 4.26
3625 3870 4.854291 GTGAAGTATCTCACTGTTGACTCG 59.146 45.833 0.00 0.00 42.11 4.18
3665 3914 2.452813 GGTAGTGCCATGCGACGTG 61.453 63.158 0.00 0.00 37.17 4.49
3681 3930 3.326747 GACGTGTGCCAGAAAAGATACT 58.673 45.455 0.00 0.00 0.00 2.12
3685 3938 4.620803 CGTGTGCCAGAAAAGATACTAGGT 60.621 45.833 0.00 0.00 0.00 3.08
3687 3940 4.192317 GTGCCAGAAAAGATACTAGGTGG 58.808 47.826 0.00 0.00 0.00 4.61
3691 3944 4.192317 CAGAAAAGATACTAGGTGGTGGC 58.808 47.826 0.00 0.00 0.00 5.01
3702 3955 0.110486 GGTGGTGGCTTGAAGGAAGA 59.890 55.000 0.00 0.00 32.82 2.87
3704 3957 1.609072 GTGGTGGCTTGAAGGAAGAAC 59.391 52.381 0.00 0.00 32.82 3.01
3708 3961 3.057245 GGTGGCTTGAAGGAAGAACAATC 60.057 47.826 0.00 0.00 32.82 2.67
3711 3964 4.042809 TGGCTTGAAGGAAGAACAATCCTA 59.957 41.667 0.00 0.00 46.65 2.94
3712 3965 4.396478 GGCTTGAAGGAAGAACAATCCTAC 59.604 45.833 0.00 0.00 46.65 3.18
3713 3966 4.396478 GCTTGAAGGAAGAACAATCCTACC 59.604 45.833 0.00 0.00 46.65 3.18
3714 3967 5.804771 GCTTGAAGGAAGAACAATCCTACCT 60.805 44.000 0.00 0.00 46.65 3.08
3715 3968 5.422214 TGAAGGAAGAACAATCCTACCTC 57.578 43.478 0.00 0.00 46.65 3.85
3716 3969 5.094387 TGAAGGAAGAACAATCCTACCTCT 58.906 41.667 0.00 0.00 46.65 3.69
3717 3970 5.046304 TGAAGGAAGAACAATCCTACCTCTG 60.046 44.000 0.00 0.00 46.65 3.35
3718 3971 4.430441 AGGAAGAACAATCCTACCTCTGT 58.570 43.478 0.00 0.00 45.51 3.41
3719 3972 4.468153 AGGAAGAACAATCCTACCTCTGTC 59.532 45.833 0.00 0.00 45.51 3.51
3720 3973 4.383226 GGAAGAACAATCCTACCTCTGTCC 60.383 50.000 0.00 0.00 33.98 4.02
3721 3974 3.108376 AGAACAATCCTACCTCTGTCCC 58.892 50.000 0.00 0.00 0.00 4.46
3722 3975 2.642171 ACAATCCTACCTCTGTCCCA 57.358 50.000 0.00 0.00 0.00 4.37
3723 3976 2.915869 ACAATCCTACCTCTGTCCCAA 58.084 47.619 0.00 0.00 0.00 4.12
3724 3977 3.256704 ACAATCCTACCTCTGTCCCAAA 58.743 45.455 0.00 0.00 0.00 3.28
3725 3978 3.852578 ACAATCCTACCTCTGTCCCAAAT 59.147 43.478 0.00 0.00 0.00 2.32
3726 3979 4.292306 ACAATCCTACCTCTGTCCCAAATT 59.708 41.667 0.00 0.00 0.00 1.82
3727 3980 5.222337 ACAATCCTACCTCTGTCCCAAATTT 60.222 40.000 0.00 0.00 0.00 1.82
3728 3981 4.301072 TCCTACCTCTGTCCCAAATTTG 57.699 45.455 11.40 11.40 0.00 2.32
3740 3993 3.255969 CCAAATTTGGGGCAGATGAAG 57.744 47.619 26.87 0.00 44.70 3.02
3741 3994 2.568509 CCAAATTTGGGGCAGATGAAGT 59.431 45.455 26.87 0.00 44.70 3.01
3742 3995 3.768757 CCAAATTTGGGGCAGATGAAGTA 59.231 43.478 26.87 0.00 44.70 2.24
3743 3996 4.381932 CCAAATTTGGGGCAGATGAAGTAC 60.382 45.833 26.87 0.00 44.70 2.73
3744 3997 4.322057 AATTTGGGGCAGATGAAGTACT 57.678 40.909 0.00 0.00 0.00 2.73
3745 3998 3.806949 TTTGGGGCAGATGAAGTACTT 57.193 42.857 8.13 8.13 0.00 2.24
3746 3999 4.919774 TTTGGGGCAGATGAAGTACTTA 57.080 40.909 8.42 0.00 0.00 2.24
3747 4000 5.450818 TTTGGGGCAGATGAAGTACTTAT 57.549 39.130 8.42 2.87 0.00 1.73
3748 4001 6.569127 TTTGGGGCAGATGAAGTACTTATA 57.431 37.500 8.42 1.04 0.00 0.98
3749 4002 6.569127 TTGGGGCAGATGAAGTACTTATAA 57.431 37.500 8.42 0.00 0.00 0.98
3750 4003 6.569127 TGGGGCAGATGAAGTACTTATAAA 57.431 37.500 8.42 0.00 0.00 1.40
3751 4004 6.354130 TGGGGCAGATGAAGTACTTATAAAC 58.646 40.000 8.42 0.00 0.00 2.01
3752 4005 6.157994 TGGGGCAGATGAAGTACTTATAAACT 59.842 38.462 8.42 1.71 0.00 2.66
3766 4019 9.075678 GTACTTATAAACTGGAGATAGTGCCTA 57.924 37.037 0.00 0.00 0.00 3.93
3791 4044 6.183361 ACTGTGGTAGGGAGAAACTACATTTT 60.183 38.462 0.00 0.00 41.95 1.82
3893 4146 5.130705 AGATAGGTGGTCACTGAGTATGA 57.869 43.478 0.93 0.00 0.00 2.15
3982 4235 0.451783 CGCATTTCTACACTTGGGGC 59.548 55.000 0.00 0.00 0.00 5.80
3997 4250 8.449423 ACACTTGGGGCTATATCTGAAATATA 57.551 34.615 0.00 0.00 0.00 0.86
4045 4298 1.344438 GACACCACACTCCACATCTGA 59.656 52.381 0.00 0.00 0.00 3.27
4048 4301 1.271054 ACCACACTCCACATCTGAAGC 60.271 52.381 0.00 0.00 0.00 3.86
4052 4305 0.617413 ACTCCACATCTGAAGCTGGG 59.383 55.000 0.00 0.00 0.00 4.45
4081 4338 8.732531 GTGGTACTACATAACATTTGGCTTTTA 58.267 33.333 4.23 0.00 31.51 1.52
4116 4373 8.770438 ACAATTGAAGTAAAAACAGCTGAAAA 57.230 26.923 23.35 0.00 0.00 2.29
4122 4421 8.131100 TGAAGTAAAAACAGCTGAAAATCTGAG 58.869 33.333 23.35 0.00 34.57 3.35
4125 4424 8.686334 AGTAAAAACAGCTGAAAATCTGAGAAA 58.314 29.630 23.35 0.00 34.57 2.52
4165 4478 6.183360 GGTTCTGTTAAACCAAACTGAATGGA 60.183 38.462 10.77 0.00 46.62 3.41
4180 4493 0.324943 ATGGAAGGTACGCTGCAACT 59.675 50.000 0.00 0.00 0.00 3.16
4184 4556 2.076863 GAAGGTACGCTGCAACTCAAT 58.923 47.619 0.00 0.00 0.00 2.57
4189 4561 0.588252 ACGCTGCAACTCAATGTGTC 59.412 50.000 0.00 0.00 0.00 3.67
4194 4566 3.937706 GCTGCAACTCAATGTGTCTCTAT 59.062 43.478 0.00 0.00 0.00 1.98
4238 4610 9.231297 CTCCAATCTTTCCAACTAGTGAAAATA 57.769 33.333 9.06 2.81 30.65 1.40
4242 4614 7.979444 TCTTTCCAACTAGTGAAAATACAGG 57.021 36.000 9.06 0.00 30.65 4.00
4243 4615 6.430000 TCTTTCCAACTAGTGAAAATACAGGC 59.570 38.462 9.06 0.00 30.65 4.85
4249 4621 7.370383 CAACTAGTGAAAATACAGGCACAATT 58.630 34.615 0.00 0.00 33.85 2.32
4251 4623 7.951591 ACTAGTGAAAATACAGGCACAATTTT 58.048 30.769 0.00 4.13 35.95 1.82
4252 4624 8.421002 ACTAGTGAAAATACAGGCACAATTTTT 58.579 29.630 0.00 0.00 33.99 1.94
4301 4673 8.347004 ACACATTGTATAAACATTCATGGACA 57.653 30.769 0.00 0.00 34.97 4.02
4302 4674 8.970020 ACACATTGTATAAACATTCATGGACAT 58.030 29.630 0.00 0.00 34.97 3.06
4303 4675 9.806203 CACATTGTATAAACATTCATGGACATT 57.194 29.630 0.00 0.00 34.97 2.71
4329 4701 9.442047 TTTTTGAAACAAGTGGACATTGTATTT 57.558 25.926 0.00 0.00 39.91 1.40
4330 4702 8.417780 TTTGAAACAAGTGGACATTGTATTTG 57.582 30.769 0.00 0.00 39.91 2.32
4331 4703 7.340122 TGAAACAAGTGGACATTGTATTTGA 57.660 32.000 2.84 0.00 39.91 2.69
4332 4704 7.776107 TGAAACAAGTGGACATTGTATTTGAA 58.224 30.769 2.84 0.00 39.91 2.69
4334 4706 9.260002 GAAACAAGTGGACATTGTATTTGAAAT 57.740 29.630 0.00 0.00 39.91 2.17
4335 4707 8.592105 AACAAGTGGACATTGTATTTGAAATG 57.408 30.769 0.00 0.00 39.91 2.32
4336 4708 7.725251 ACAAGTGGACATTGTATTTGAAATGT 58.275 30.769 0.00 0.89 46.87 2.71
4450 5911 8.763356 TGAACATTTTTATTGAAACATGTGAGC 58.237 29.630 0.00 0.00 33.40 4.26
4456 5917 8.659925 TTTTATTGAAACATGTGAGCATTTGT 57.340 26.923 0.00 0.00 31.99 2.83
4457 5918 9.755804 TTTTATTGAAACATGTGAGCATTTGTA 57.244 25.926 0.00 0.00 31.99 2.41
4461 5922 6.979465 TGAAACATGTGAGCATTTGTATTGA 58.021 32.000 0.00 0.00 31.99 2.57
4465 5926 8.836268 AACATGTGAGCATTTGTATTGAATTT 57.164 26.923 0.00 0.00 31.99 1.82
4466 5927 8.836268 ACATGTGAGCATTTGTATTGAATTTT 57.164 26.923 0.00 0.00 31.99 1.82
4467 5928 8.928733 ACATGTGAGCATTTGTATTGAATTTTC 58.071 29.630 0.00 0.00 31.99 2.29
4468 5929 8.927721 CATGTGAGCATTTGTATTGAATTTTCA 58.072 29.630 0.00 0.00 31.99 2.69
4469 5930 8.296799 TGTGAGCATTTGTATTGAATTTTCAC 57.703 30.769 0.00 0.00 36.83 3.18
4471 5932 7.599998 GTGAGCATTTGTATTGAATTTTCACCT 59.400 33.333 0.00 0.00 36.83 4.00
4473 5934 6.369615 AGCATTTGTATTGAATTTTCACCTGC 59.630 34.615 0.00 0.00 36.83 4.85
4474 5935 6.147492 GCATTTGTATTGAATTTTCACCTGCA 59.853 34.615 0.00 0.00 36.83 4.41
4475 5936 7.148373 GCATTTGTATTGAATTTTCACCTGCAT 60.148 33.333 0.00 0.00 36.83 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.165372 TGCACCCTAGGAATAACTAAAGGG 59.835 45.833 11.48 3.66 35.55 3.95
31 32 2.381911 CAATGCTTGCACCCTAGGAAT 58.618 47.619 11.48 0.00 0.00 3.01
71 75 5.069251 AGGAACGAAGGGAGTACATGATTAG 59.931 44.000 0.00 0.00 0.00 1.73
76 80 4.730949 TTAGGAACGAAGGGAGTACATG 57.269 45.455 0.00 0.00 0.00 3.21
82 86 7.048512 AGACAAATATTTAGGAACGAAGGGAG 58.951 38.462 0.00 0.00 0.00 4.30
83 87 6.954232 AGACAAATATTTAGGAACGAAGGGA 58.046 36.000 0.00 0.00 0.00 4.20
84 88 7.625828 AAGACAAATATTTAGGAACGAAGGG 57.374 36.000 0.00 0.00 0.00 3.95
85 89 9.908152 AAAAAGACAAATATTTAGGAACGAAGG 57.092 29.630 0.00 0.00 0.00 3.46
112 116 9.355215 CGTATGTAGTCACTTGTTAAAATCTCT 57.645 33.333 0.00 0.00 0.00 3.10
113 117 9.350357 TCGTATGTAGTCACTTGTTAAAATCTC 57.650 33.333 0.00 0.00 0.00 2.75
114 118 9.701098 TTCGTATGTAGTCACTTGTTAAAATCT 57.299 29.630 0.00 0.00 0.00 2.40
115 119 9.953825 CTTCGTATGTAGTCACTTGTTAAAATC 57.046 33.333 0.00 0.00 0.00 2.17
116 120 9.485206 ACTTCGTATGTAGTCACTTGTTAAAAT 57.515 29.630 0.00 0.00 0.00 1.82
117 121 8.876275 ACTTCGTATGTAGTCACTTGTTAAAA 57.124 30.769 0.00 0.00 0.00 1.52
118 122 9.964303 TTACTTCGTATGTAGTCACTTGTTAAA 57.036 29.630 0.00 0.00 0.00 1.52
119 123 9.964303 TTTACTTCGTATGTAGTCACTTGTTAA 57.036 29.630 0.00 0.00 0.00 2.01
120 124 9.964303 TTTTACTTCGTATGTAGTCACTTGTTA 57.036 29.630 0.00 0.00 0.00 2.41
121 125 8.876275 TTTTACTTCGTATGTAGTCACTTGTT 57.124 30.769 0.00 0.00 0.00 2.83
122 126 8.922676 CATTTTACTTCGTATGTAGTCACTTGT 58.077 33.333 0.00 0.00 0.00 3.16
123 127 9.135843 TCATTTTACTTCGTATGTAGTCACTTG 57.864 33.333 0.00 0.00 0.00 3.16
124 128 9.355215 CTCATTTTACTTCGTATGTAGTCACTT 57.645 33.333 0.00 0.00 0.00 3.16
125 129 8.521176 ACTCATTTTACTTCGTATGTAGTCACT 58.479 33.333 0.00 0.00 0.00 3.41
126 130 8.584600 CACTCATTTTACTTCGTATGTAGTCAC 58.415 37.037 0.00 0.00 0.00 3.67
127 131 8.517056 TCACTCATTTTACTTCGTATGTAGTCA 58.483 33.333 0.00 0.00 0.00 3.41
128 132 8.906636 TCACTCATTTTACTTCGTATGTAGTC 57.093 34.615 0.00 0.00 0.00 2.59
129 133 9.871238 ATTCACTCATTTTACTTCGTATGTAGT 57.129 29.630 0.00 0.00 0.00 2.73
135 139 9.350357 GTGTAGATTCACTCATTTTACTTCGTA 57.650 33.333 0.00 0.00 35.68 3.43
136 140 8.088981 AGTGTAGATTCACTCATTTTACTTCGT 58.911 33.333 0.00 0.00 44.07 3.85
137 141 8.467402 AGTGTAGATTCACTCATTTTACTTCG 57.533 34.615 0.00 0.00 44.07 3.79
178 182 9.676861 CAAATGGACTATCACATATGGATGTAT 57.323 33.333 7.80 0.00 44.82 2.29
179 183 8.879227 TCAAATGGACTATCACATATGGATGTA 58.121 33.333 7.80 0.00 44.82 2.29
181 185 8.625786 TTCAAATGGACTATCACATATGGATG 57.374 34.615 7.80 0.00 39.16 3.51
182 186 9.818270 ATTTCAAATGGACTATCACATATGGAT 57.182 29.630 7.80 9.38 0.00 3.41
183 187 9.288576 GATTTCAAATGGACTATCACATATGGA 57.711 33.333 7.80 2.05 0.00 3.41
184 188 9.293404 AGATTTCAAATGGACTATCACATATGG 57.707 33.333 7.80 0.00 0.00 2.74
213 217 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
214 218 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
215 219 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
216 220 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
217 221 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
218 222 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
219 223 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
220 224 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
221 225 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
222 226 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
223 227 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
224 228 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
225 229 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
226 230 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
227 231 3.744940 TTCTACTCCCTCCGTTCCTAA 57.255 47.619 0.00 0.00 0.00 2.69
228 232 3.967467 ATTCTACTCCCTCCGTTCCTA 57.033 47.619 0.00 0.00 0.00 2.94
229 233 2.850695 ATTCTACTCCCTCCGTTCCT 57.149 50.000 0.00 0.00 0.00 3.36
230 234 2.764572 TGAATTCTACTCCCTCCGTTCC 59.235 50.000 7.05 0.00 0.00 3.62
231 235 3.738590 GCTGAATTCTACTCCCTCCGTTC 60.739 52.174 7.05 0.00 0.00 3.95
232 236 2.168728 GCTGAATTCTACTCCCTCCGTT 59.831 50.000 7.05 0.00 0.00 4.44
233 237 1.757699 GCTGAATTCTACTCCCTCCGT 59.242 52.381 7.05 0.00 0.00 4.69
234 238 1.069358 GGCTGAATTCTACTCCCTCCG 59.931 57.143 7.05 0.00 0.00 4.63
235 239 2.103941 CTGGCTGAATTCTACTCCCTCC 59.896 54.545 7.05 0.00 0.00 4.30
236 240 2.103941 CCTGGCTGAATTCTACTCCCTC 59.896 54.545 7.05 0.00 0.00 4.30
237 241 2.122768 CCTGGCTGAATTCTACTCCCT 58.877 52.381 7.05 0.00 0.00 4.20
238 242 1.475930 GCCTGGCTGAATTCTACTCCC 60.476 57.143 12.43 0.90 0.00 4.30
239 243 1.488393 AGCCTGGCTGAATTCTACTCC 59.512 52.381 22.71 3.35 37.57 3.85
240 244 2.998316 AGCCTGGCTGAATTCTACTC 57.002 50.000 22.71 0.00 37.57 2.59
241 245 2.703007 CCTAGCCTGGCTGAATTCTACT 59.297 50.000 30.83 3.04 40.10 2.57
242 246 3.118905 CCTAGCCTGGCTGAATTCTAC 57.881 52.381 30.83 0.00 40.10 2.59
257 261 3.227614 AGCTACTAGAAGAAGGCCTAGC 58.772 50.000 5.16 8.16 36.67 3.42
270 274 4.052608 TCTTCGTGATCTCGAGCTACTAG 58.947 47.826 18.16 12.45 40.86 2.57
278 282 1.530323 TGTGGTCTTCGTGATCTCGA 58.470 50.000 15.41 15.41 38.08 4.04
279 283 2.568696 ATGTGGTCTTCGTGATCTCG 57.431 50.000 10.84 10.84 0.00 4.04
308 315 7.660112 TCTTTCGCCGGAGTATAAAATATACA 58.340 34.615 5.05 0.00 0.00 2.29
359 369 7.767198 AGAAATAATGCCATCCACAAAGAATTG 59.233 33.333 0.00 0.00 42.46 2.32
362 372 6.664816 AGAGAAATAATGCCATCCACAAAGAA 59.335 34.615 0.00 0.00 0.00 2.52
374 384 4.943705 TGTGTTGGAGAGAGAAATAATGCC 59.056 41.667 0.00 0.00 0.00 4.40
399 409 7.186972 TCCGGACCAAGGAAGTATGTATATAT 58.813 38.462 0.00 0.00 34.33 0.86
402 412 4.806892 TCCGGACCAAGGAAGTATGTATA 58.193 43.478 0.00 0.00 34.33 1.47
417 427 3.319755 TCGCGATAAATAATTCCGGACC 58.680 45.455 1.83 0.00 0.00 4.46
429 439 8.085909 TCTAGATACATCCATTTTCGCGATAAA 58.914 33.333 15.79 15.53 0.00 1.40
432 442 6.025749 TCTAGATACATCCATTTTCGCGAT 57.974 37.500 10.88 0.00 0.00 4.58
436 446 7.706607 TGTCAGTTCTAGATACATCCATTTTCG 59.293 37.037 0.00 0.00 0.00 3.46
451 471 7.493971 CCATCCAGAATTACTTGTCAGTTCTAG 59.506 40.741 0.00 0.00 34.06 2.43
461 481 5.749462 ACTCCTTCCATCCAGAATTACTTG 58.251 41.667 0.00 0.00 0.00 3.16
462 482 6.674419 ACTACTCCTTCCATCCAGAATTACTT 59.326 38.462 0.00 0.00 0.00 2.24
464 484 6.487299 ACTACTCCTTCCATCCAGAATTAC 57.513 41.667 0.00 0.00 0.00 1.89
466 486 5.488919 TCAACTACTCCTTCCATCCAGAATT 59.511 40.000 0.00 0.00 0.00 2.17
467 487 5.032846 TCAACTACTCCTTCCATCCAGAAT 58.967 41.667 0.00 0.00 0.00 2.40
468 488 4.425772 TCAACTACTCCTTCCATCCAGAA 58.574 43.478 0.00 0.00 0.00 3.02
469 489 4.061131 TCAACTACTCCTTCCATCCAGA 57.939 45.455 0.00 0.00 0.00 3.86
470 490 5.130145 AGAATCAACTACTCCTTCCATCCAG 59.870 44.000 0.00 0.00 0.00 3.86
471 491 5.032846 AGAATCAACTACTCCTTCCATCCA 58.967 41.667 0.00 0.00 0.00 3.41
489 509 1.732259 CAAGTGCACCCACGTAGAATC 59.268 52.381 14.63 0.00 46.62 2.52
491 511 0.753867 TCAAGTGCACCCACGTAGAA 59.246 50.000 14.63 0.00 46.62 2.10
502 522 1.065401 CCTCGCAAAAGTTCAAGTGCA 59.935 47.619 0.00 0.00 36.80 4.57
505 525 1.318576 CCCCTCGCAAAAGTTCAAGT 58.681 50.000 0.00 0.00 0.00 3.16
512 532 0.895559 AGAAAGCCCCCTCGCAAAAG 60.896 55.000 0.00 0.00 0.00 2.27
517 537 2.751837 CCAAGAAAGCCCCCTCGC 60.752 66.667 0.00 0.00 0.00 5.03
518 538 1.377333 GACCAAGAAAGCCCCCTCG 60.377 63.158 0.00 0.00 0.00 4.63
519 539 0.609406 GTGACCAAGAAAGCCCCCTC 60.609 60.000 0.00 0.00 0.00 4.30
520 540 1.460699 GTGACCAAGAAAGCCCCCT 59.539 57.895 0.00 0.00 0.00 4.79
554 595 0.317603 CAACAAGTGTCAGCTGCAGC 60.318 55.000 31.53 31.53 42.49 5.25
572 613 1.966901 AACTGTGGGACTGTGCGTCA 61.967 55.000 0.00 0.00 44.68 4.35
573 614 1.222115 GAACTGTGGGACTGTGCGTC 61.222 60.000 0.00 0.00 42.07 5.19
574 615 1.227556 GAACTGTGGGACTGTGCGT 60.228 57.895 0.00 0.00 30.49 5.24
575 616 1.224069 CTGAACTGTGGGACTGTGCG 61.224 60.000 0.00 0.00 29.03 5.34
576 617 1.510480 GCTGAACTGTGGGACTGTGC 61.510 60.000 0.00 0.00 30.49 4.57
577 618 0.179048 TGCTGAACTGTGGGACTGTG 60.179 55.000 0.00 0.00 30.49 3.66
578 619 0.107456 CTGCTGAACTGTGGGACTGT 59.893 55.000 0.00 0.00 0.00 3.55
579 620 0.604780 CCTGCTGAACTGTGGGACTG 60.605 60.000 0.00 0.00 0.00 3.51
580 621 1.056700 ACCTGCTGAACTGTGGGACT 61.057 55.000 0.00 0.00 0.00 3.85
581 622 0.685097 TACCTGCTGAACTGTGGGAC 59.315 55.000 0.00 0.00 0.00 4.46
582 623 0.976641 CTACCTGCTGAACTGTGGGA 59.023 55.000 0.00 0.00 0.00 4.37
588 629 3.981071 TTACATGCTACCTGCTGAACT 57.019 42.857 0.00 0.00 43.37 3.01
598 639 9.573133 AAGCTATTTCATTTGTTTACATGCTAC 57.427 29.630 0.00 0.00 0.00 3.58
619 660 3.918253 CTTGTGCCGGCCCAAGCTA 62.918 63.158 33.65 9.74 39.73 3.32
650 691 9.719355 TTTCATTTGTTTACATGCTACTCTCTA 57.281 29.630 0.00 0.00 0.00 2.43
651 692 8.621532 TTTCATTTGTTTACATGCTACTCTCT 57.378 30.769 0.00 0.00 0.00 3.10
654 695 9.226345 GCTATTTCATTTGTTTACATGCTACTC 57.774 33.333 0.00 0.00 0.00 2.59
655 696 8.960591 AGCTATTTCATTTGTTTACATGCTACT 58.039 29.630 0.00 0.00 0.00 2.57
656 697 9.573133 AAGCTATTTCATTTGTTTACATGCTAC 57.427 29.630 0.00 0.00 0.00 3.58
691 732 3.357079 CACTGTGCCGGCCTTGTC 61.357 66.667 26.77 9.75 0.00 3.18
707 748 3.827008 AGTTCAGAAGCTTCACTGTCA 57.173 42.857 27.57 7.56 35.84 3.58
727 768 2.543777 AAAGTTTCGCTGCCTGACTA 57.456 45.000 0.00 0.00 0.00 2.59
738 779 6.020995 ACGTTTTGATTAGTGCAAAAGTTTCG 60.021 34.615 0.00 0.00 43.48 3.46
739 780 7.216920 ACGTTTTGATTAGTGCAAAAGTTTC 57.783 32.000 0.00 0.00 43.48 2.78
742 783 8.690680 TTTTACGTTTTGATTAGTGCAAAAGT 57.309 26.923 0.00 0.00 43.48 2.66
835 902 4.202577 TGGTCTAGTCAGTTCTCTTCTCCA 60.203 45.833 0.00 0.00 0.00 3.86
838 905 5.826643 AGATGGTCTAGTCAGTTCTCTTCT 58.173 41.667 0.00 0.00 0.00 2.85
839 906 6.377146 AGAAGATGGTCTAGTCAGTTCTCTTC 59.623 42.308 14.64 14.64 37.45 2.87
841 908 5.826643 AGAAGATGGTCTAGTCAGTTCTCT 58.173 41.667 0.00 0.00 0.00 3.10
842 909 6.600032 TGTAGAAGATGGTCTAGTCAGTTCTC 59.400 42.308 13.81 9.73 30.70 2.87
843 910 6.376018 GTGTAGAAGATGGTCTAGTCAGTTCT 59.624 42.308 14.36 14.36 30.70 3.01
844 911 6.151312 TGTGTAGAAGATGGTCTAGTCAGTTC 59.849 42.308 0.00 0.00 30.70 3.01
845 912 6.010850 TGTGTAGAAGATGGTCTAGTCAGTT 58.989 40.000 0.00 0.00 30.70 3.16
850 924 3.378742 CGCTGTGTAGAAGATGGTCTAGT 59.621 47.826 0.00 0.00 30.70 2.57
908 982 1.929836 GATGAGCTTTGCGGAGTAGTG 59.070 52.381 0.00 0.00 0.00 2.74
948 1028 3.123273 ACCAGTCAGTTATTGGCCCTAT 58.877 45.455 0.00 0.00 38.54 2.57
949 1029 2.557869 ACCAGTCAGTTATTGGCCCTA 58.442 47.619 0.00 0.00 38.54 3.53
1012 1098 0.246086 AGCACGAGGAAGAAGAGCAG 59.754 55.000 0.00 0.00 0.00 4.24
1014 1100 1.074752 CAAGCACGAGGAAGAAGAGC 58.925 55.000 0.00 0.00 0.00 4.09
1059 1145 1.405105 GAATAATTCAAGGCCTGCGCA 59.595 47.619 10.98 10.98 36.38 6.09
1142 1231 4.388499 GGGTGACGATGGTGCGGT 62.388 66.667 0.00 0.00 35.12 5.68
1186 1275 0.832135 TCAAGTTCGGAGTCAGGGCT 60.832 55.000 0.00 0.00 0.00 5.19
1231 1320 2.436646 GCATGGTGACTGACGGGG 60.437 66.667 0.00 0.00 0.00 5.73
1276 1365 2.726633 GTTGAACCCAACGTTGATGTG 58.273 47.619 29.35 15.95 42.60 3.21
1298 1387 5.106396 GGCTGCTGAGTTATGGCATTATTAG 60.106 44.000 4.78 0.00 35.37 1.73
1310 1399 1.254975 TACCTGCGGCTGCTGAGTTA 61.255 55.000 24.51 10.36 42.14 2.24
1317 1406 2.182842 CCAGATTACCTGCGGCTGC 61.183 63.158 11.65 11.65 41.57 5.25
1352 1450 1.059098 TGCATTCTCTGTGACAGGGT 58.941 50.000 12.89 0.00 33.01 4.34
1386 1484 0.546598 GGACCAAGTTCCCATCCGAT 59.453 55.000 0.00 0.00 0.00 4.18
1461 1559 0.374758 CGGTGATCAACATTCCAGCG 59.625 55.000 12.13 0.00 42.56 5.18
1523 1621 1.061131 GATGATCAAACGACTGCCACG 59.939 52.381 0.00 0.00 0.00 4.94
1533 1631 6.183360 CCAATGTGTCAGTAGGATGATCAAAC 60.183 42.308 0.00 0.00 0.00 2.93
1666 1769 2.017049 GGTGGTGTGGATTCAGCATAC 58.983 52.381 2.16 0.00 45.28 2.39
1702 1805 0.464452 GGACGGACACCCAGGATAAG 59.536 60.000 0.00 0.00 0.00 1.73
1718 1824 4.766891 TGGATCATTTCCTTTCTTGTGGAC 59.233 41.667 0.00 0.00 45.68 4.02
1721 1827 8.526147 AGTTATTGGATCATTTCCTTTCTTGTG 58.474 33.333 0.00 0.00 45.68 3.33
1773 1882 1.660355 GACTGCACAGAGACGGTCA 59.340 57.895 11.27 0.00 41.05 4.02
1774 1883 0.387878 CTGACTGCACAGAGACGGTC 60.388 60.000 4.31 0.00 41.62 4.79
1775 1884 0.823769 TCTGACTGCACAGAGACGGT 60.824 55.000 4.31 0.00 41.21 4.83
1819 1943 1.173913 ACCGGGTAGATTTTGCTTGC 58.826 50.000 6.32 0.00 0.00 4.01
1821 1945 3.706600 TGTACCGGGTAGATTTTGCTT 57.293 42.857 7.25 0.00 0.00 3.91
1872 1999 3.635373 TGATAGACCAGACCGTTCATACC 59.365 47.826 0.00 0.00 0.00 2.73
1922 2055 6.598064 ACTGTTGGGTAAGCACAATAATCTAC 59.402 38.462 0.00 0.00 40.52 2.59
2143 2285 1.617850 GTTGCATTCACAACCATGGGA 59.382 47.619 18.09 0.00 43.34 4.37
2297 2457 5.010012 CAGAGGAGTTGTAACCAAATGCTTT 59.990 40.000 0.00 0.00 45.46 3.51
2881 3089 5.164620 TGCACTCCTCATGAAGATAACAA 57.835 39.130 0.00 0.00 0.00 2.83
3003 3212 4.081087 TCACTACCTTGCTTTGATCCCTAC 60.081 45.833 0.00 0.00 0.00 3.18
3118 3327 6.288294 TCTCCCACTTAATATTTCCATCACG 58.712 40.000 0.00 0.00 0.00 4.35
3164 3373 2.175202 GAGCTGAACTTCCTCCTCAGA 58.825 52.381 0.00 0.00 39.15 3.27
3465 3692 1.901464 CACCCGTTTCACCTTGGGG 60.901 63.158 0.65 0.00 46.38 4.96
3659 3908 1.148310 ATCTTTTCTGGCACACGTCG 58.852 50.000 0.00 0.00 0.00 5.12
3665 3914 4.192317 CCACCTAGTATCTTTTCTGGCAC 58.808 47.826 0.00 0.00 0.00 5.01
3681 3930 1.351017 CTTCCTTCAAGCCACCACCTA 59.649 52.381 0.00 0.00 0.00 3.08
3685 3938 1.214175 TGTTCTTCCTTCAAGCCACCA 59.786 47.619 0.00 0.00 31.26 4.17
3687 3940 3.057245 GGATTGTTCTTCCTTCAAGCCAC 60.057 47.826 6.55 0.00 44.02 5.01
3691 3944 5.810095 AGGTAGGATTGTTCTTCCTTCAAG 58.190 41.667 0.00 0.00 40.84 3.02
3702 3955 2.915869 TGGGACAGAGGTAGGATTGTT 58.084 47.619 0.00 0.00 0.00 2.83
3704 3957 4.510167 ATTTGGGACAGAGGTAGGATTG 57.490 45.455 0.00 0.00 42.39 2.67
3708 3961 3.356290 CCAAATTTGGGACAGAGGTAGG 58.644 50.000 26.87 0.00 44.70 3.18
3721 3974 3.967332 ACTTCATCTGCCCCAAATTTG 57.033 42.857 11.40 11.40 0.00 2.32
3722 3975 4.677182 AGTACTTCATCTGCCCCAAATTT 58.323 39.130 0.00 0.00 0.00 1.82
3723 3976 4.322057 AGTACTTCATCTGCCCCAAATT 57.678 40.909 0.00 0.00 0.00 1.82
3724 3977 4.322057 AAGTACTTCATCTGCCCCAAAT 57.678 40.909 1.12 0.00 0.00 2.32
3725 3978 3.806949 AAGTACTTCATCTGCCCCAAA 57.193 42.857 1.12 0.00 0.00 3.28
3726 3979 6.569127 TTATAAGTACTTCATCTGCCCCAA 57.431 37.500 12.39 0.00 0.00 4.12
3727 3980 6.157994 AGTTTATAAGTACTTCATCTGCCCCA 59.842 38.462 12.39 0.00 0.00 4.96
3728 3981 6.483640 CAGTTTATAAGTACTTCATCTGCCCC 59.516 42.308 12.39 0.00 0.00 5.80
3729 3982 6.483640 CCAGTTTATAAGTACTTCATCTGCCC 59.516 42.308 12.39 0.00 0.00 5.36
3730 3983 7.272978 TCCAGTTTATAAGTACTTCATCTGCC 58.727 38.462 12.39 0.00 0.00 4.85
3731 3984 8.198109 TCTCCAGTTTATAAGTACTTCATCTGC 58.802 37.037 12.39 0.00 0.00 4.26
3737 3990 9.465985 GCACTATCTCCAGTTTATAAGTACTTC 57.534 37.037 12.39 0.00 0.00 3.01
3738 3991 8.422566 GGCACTATCTCCAGTTTATAAGTACTT 58.577 37.037 13.68 13.68 0.00 2.24
3739 3992 7.785506 AGGCACTATCTCCAGTTTATAAGTACT 59.214 37.037 0.00 0.00 36.02 2.73
3740 3993 7.953752 AGGCACTATCTCCAGTTTATAAGTAC 58.046 38.462 0.00 0.00 36.02 2.73
3741 3994 9.075678 GTAGGCACTATCTCCAGTTTATAAGTA 57.924 37.037 0.00 0.00 45.60 2.24
3742 3995 7.785506 AGTAGGCACTATCTCCAGTTTATAAGT 59.214 37.037 0.00 0.00 45.60 2.24
3743 3996 8.085296 CAGTAGGCACTATCTCCAGTTTATAAG 58.915 40.741 0.00 0.00 45.60 1.73
3744 3997 7.563924 ACAGTAGGCACTATCTCCAGTTTATAA 59.436 37.037 0.00 0.00 45.60 0.98
3745 3998 7.014326 CACAGTAGGCACTATCTCCAGTTTATA 59.986 40.741 0.00 0.00 45.60 0.98
3746 3999 5.900123 ACAGTAGGCACTATCTCCAGTTTAT 59.100 40.000 0.00 0.00 45.60 1.40
3747 4000 5.127194 CACAGTAGGCACTATCTCCAGTTTA 59.873 44.000 0.00 0.00 45.60 2.01
3748 4001 4.081420 CACAGTAGGCACTATCTCCAGTTT 60.081 45.833 0.00 0.00 45.60 2.66
3749 4002 3.449018 CACAGTAGGCACTATCTCCAGTT 59.551 47.826 0.00 0.00 45.60 3.16
3750 4003 3.027412 CACAGTAGGCACTATCTCCAGT 58.973 50.000 0.00 0.00 45.60 4.00
3751 4004 2.363680 CCACAGTAGGCACTATCTCCAG 59.636 54.545 0.00 0.00 45.60 3.86
3752 4005 2.292257 ACCACAGTAGGCACTATCTCCA 60.292 50.000 0.00 0.00 45.60 3.86
3766 4019 3.853207 TGTAGTTTCTCCCTACCACAGT 58.147 45.455 0.00 0.00 35.06 3.55
3910 4163 7.725251 AGCATACCATCTTTGTGAAAAGAAAA 58.275 30.769 5.11 0.00 41.57 2.29
4045 4298 2.616524 TGTAGTACCACTTCCCAGCTT 58.383 47.619 0.00 0.00 0.00 3.74
4048 4301 5.670792 TGTTATGTAGTACCACTTCCCAG 57.329 43.478 0.00 0.00 0.00 4.45
4052 4305 6.598064 AGCCAAATGTTATGTAGTACCACTTC 59.402 38.462 0.00 0.00 0.00 3.01
4102 4359 7.380602 CGATTTCTCAGATTTTCAGCTGTTTTT 59.619 33.333 14.67 0.00 33.90 1.94
4106 4363 5.240891 TCGATTTCTCAGATTTTCAGCTGT 58.759 37.500 14.67 0.00 33.90 4.40
4116 4373 5.533903 CCAATTCCCAATCGATTTCTCAGAT 59.466 40.000 8.21 0.00 0.00 2.90
4122 4421 4.402474 AGAACCCAATTCCCAATCGATTTC 59.598 41.667 8.21 0.00 38.16 2.17
4125 4424 3.290710 CAGAACCCAATTCCCAATCGAT 58.709 45.455 0.00 0.00 38.16 3.59
4165 4478 1.806542 CATTGAGTTGCAGCGTACCTT 59.193 47.619 0.00 0.00 0.00 3.50
4220 4592 6.016610 GTGCCTGTATTTTCACTAGTTGGAAA 60.017 38.462 4.67 4.67 37.09 3.13
4275 4647 9.454859 TGTCCATGAATGTTTATACAATGTGTA 57.545 29.630 0.00 0.00 37.91 2.90
4276 4648 8.347004 TGTCCATGAATGTTTATACAATGTGT 57.653 30.769 0.00 0.00 37.91 3.72
4277 4649 9.806203 AATGTCCATGAATGTTTATACAATGTG 57.194 29.630 0.00 0.00 37.91 3.21
4303 4675 9.442047 AAATACAATGTCCACTTGTTTCAAAAA 57.558 25.926 0.00 0.00 37.89 1.94
4305 4677 8.253810 TCAAATACAATGTCCACTTGTTTCAAA 58.746 29.630 0.00 0.00 37.89 2.69
4306 4678 7.776107 TCAAATACAATGTCCACTTGTTTCAA 58.224 30.769 0.00 0.00 37.89 2.69
4307 4679 7.340122 TCAAATACAATGTCCACTTGTTTCA 57.660 32.000 0.00 0.00 37.89 2.69
4308 4680 8.641499 TTTCAAATACAATGTCCACTTGTTTC 57.359 30.769 0.00 0.00 37.89 2.78
4309 4681 9.044150 CATTTCAAATACAATGTCCACTTGTTT 57.956 29.630 0.00 0.00 37.89 2.83
4310 4682 8.203485 ACATTTCAAATACAATGTCCACTTGTT 58.797 29.630 0.00 0.00 38.97 2.83
4311 4683 7.725251 ACATTTCAAATACAATGTCCACTTGT 58.275 30.769 0.00 0.00 38.97 3.16
4430 5686 9.107177 ACAAATGCTCACATGTTTCAATAAAAA 57.893 25.926 0.00 0.00 36.36 1.94
4432 5688 9.926158 ATACAAATGCTCACATGTTTCAATAAA 57.074 25.926 0.00 0.00 36.36 1.40
4435 5896 8.089597 TCAATACAAATGCTCACATGTTTCAAT 58.910 29.630 0.00 0.00 36.36 2.57
4436 5897 7.432059 TCAATACAAATGCTCACATGTTTCAA 58.568 30.769 0.00 0.00 36.36 2.69
4438 5899 7.872163 TTCAATACAAATGCTCACATGTTTC 57.128 32.000 0.00 0.00 36.36 2.78
4445 5906 7.599998 AGGTGAAAATTCAATACAAATGCTCAC 59.400 33.333 0.00 0.00 39.21 3.51
4448 5909 6.369615 GCAGGTGAAAATTCAATACAAATGCT 59.630 34.615 0.00 0.00 39.21 3.79
4449 5910 6.147492 TGCAGGTGAAAATTCAATACAAATGC 59.853 34.615 0.00 0.00 39.21 3.56
4450 5911 7.655236 TGCAGGTGAAAATTCAATACAAATG 57.345 32.000 0.00 0.00 39.21 2.32


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

AutoCloner maintained by Alex Coulton.