Multiple sequence alignment - TraesCS4A01G029500

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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 TraesCS4A01G029500 chr4A 100.000 2288 0 0 1 2288 21630963 21633250 0.000000e+00 4226.0
1 TraesCS4A01G029500 chr4A 80.469 128 23 2 1013 1139 596002422 596002296 1.870000e-16 97.1
2 TraesCS4A01G029500 chr4D 85.841 1582 99 62 277 1832 445497441 445495959 0.000000e+00 1565.0
3 TraesCS4A01G029500 chr4D 90.769 260 18 4 1889 2144 445495765 445495508 2.180000e-90 342.0
4 TraesCS4A01G029500 chr4D 92.000 75 2 2 89 163 445497597 445497527 4.020000e-18 102.0
5 TraesCS4A01G029500 chr4D 80.469 128 23 2 1013 1139 7587297 7587423 1.870000e-16 97.1
6 TraesCS4A01G029500 chr4B 86.282 1385 94 47 277 1632 556070525 556069208 0.000000e+00 1417.0
7 TraesCS4A01G029500 chr4B 93.774 257 13 3 1889 2144 556062943 556062689 1.280000e-102 383.0
8 TraesCS4A01G029500 chr4B 90.404 198 10 3 1641 1832 556063339 556063145 3.770000e-63 252.0
9 TraesCS4A01G029500 chr4B 87.671 146 6 3 2143 2288 556062650 556062517 2.350000e-35 159.0
10 TraesCS4A01G029500 chr4B 92.000 75 2 1 89 163 556070673 556070603 4.020000e-18 102.0


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 TraesCS4A01G029500 chr4A 21630963 21633250 2287 False 4226.000000 4226 100.000000 1 2288 1 chr4A.!!$F1 2287
1 TraesCS4A01G029500 chr4D 445495508 445497597 2089 True 669.666667 1565 89.536667 89 2144 3 chr4D.!!$R1 2055
2 TraesCS4A01G029500 chr4B 556069208 556070673 1465 True 759.500000 1417 89.141000 89 1632 2 chr4B.!!$R2 1543
3 TraesCS4A01G029500 chr4B 556062517 556063339 822 True 264.666667 383 90.616333 1641 2288 3 chr4B.!!$R1 647

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
964 997 0.098905 TTGAGCTCGGTCGATCGAAG 59.901 55.0 22.75 16.83 38.77 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2240 2513 0.389426 CGAACCGTGGTAGAACCTGG 60.389 60.0 0.0 0.0 39.58 4.45 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
25 26 8.518151 CTGCTAATAACTCATGATCAGTACAG 57.482 38.462 0.09 0.00 0.00 2.74
26 27 8.237811 TGCTAATAACTCATGATCAGTACAGA 57.762 34.615 0.09 0.00 0.00 3.41
27 28 8.355913 TGCTAATAACTCATGATCAGTACAGAG 58.644 37.037 0.09 6.03 0.00 3.35
28 29 7.328249 GCTAATAACTCATGATCAGTACAGAGC 59.672 40.741 0.09 0.00 0.00 4.09
29 30 6.721704 ATAACTCATGATCAGTACAGAGCA 57.278 37.500 8.73 8.73 38.41 4.26
30 31 4.383850 ACTCATGATCAGTACAGAGCAC 57.616 45.455 8.47 0.00 36.67 4.40
31 32 3.766051 ACTCATGATCAGTACAGAGCACA 59.234 43.478 8.47 2.24 36.67 4.57
32 33 4.111198 CTCATGATCAGTACAGAGCACAC 58.889 47.826 8.47 0.00 36.67 3.82
33 34 3.511146 TCATGATCAGTACAGAGCACACA 59.489 43.478 8.47 0.00 36.67 3.72
34 35 4.021192 TCATGATCAGTACAGAGCACACAA 60.021 41.667 8.47 0.00 36.67 3.33
35 36 3.917988 TGATCAGTACAGAGCACACAAG 58.082 45.455 1.67 0.00 0.00 3.16
36 37 2.154854 TCAGTACAGAGCACACAAGC 57.845 50.000 0.00 0.00 0.00 4.01
37 38 1.412343 TCAGTACAGAGCACACAAGCA 59.588 47.619 0.00 0.00 36.85 3.91
38 39 2.158971 TCAGTACAGAGCACACAAGCAA 60.159 45.455 0.00 0.00 36.85 3.91
39 40 2.222678 CAGTACAGAGCACACAAGCAAG 59.777 50.000 0.00 0.00 36.85 4.01
40 41 1.069636 GTACAGAGCACACAAGCAAGC 60.070 52.381 0.00 0.00 36.85 4.01
41 42 1.285023 CAGAGCACACAAGCAAGCC 59.715 57.895 0.00 0.00 36.85 4.35
42 43 1.900498 AGAGCACACAAGCAAGCCC 60.900 57.895 0.00 0.00 36.85 5.19
43 44 2.123769 AGCACACAAGCAAGCCCA 60.124 55.556 0.00 0.00 36.85 5.36
44 45 1.530013 GAGCACACAAGCAAGCCCAT 61.530 55.000 0.00 0.00 36.85 4.00
45 46 1.080298 GCACACAAGCAAGCCCATC 60.080 57.895 0.00 0.00 0.00 3.51
46 47 1.530013 GCACACAAGCAAGCCCATCT 61.530 55.000 0.00 0.00 0.00 2.90
47 48 0.242825 CACACAAGCAAGCCCATCTG 59.757 55.000 0.00 0.00 0.00 2.90
48 49 0.178981 ACACAAGCAAGCCCATCTGT 60.179 50.000 0.00 0.00 0.00 3.41
49 50 0.242825 CACAAGCAAGCCCATCTGTG 59.757 55.000 0.00 0.00 0.00 3.66
50 51 0.111061 ACAAGCAAGCCCATCTGTGA 59.889 50.000 0.00 0.00 0.00 3.58
51 52 1.272313 ACAAGCAAGCCCATCTGTGAT 60.272 47.619 0.00 0.00 0.00 3.06
52 53 2.025981 ACAAGCAAGCCCATCTGTGATA 60.026 45.455 0.00 0.00 0.00 2.15
53 54 2.338577 AGCAAGCCCATCTGTGATAC 57.661 50.000 0.00 0.00 0.00 2.24
54 55 1.133976 AGCAAGCCCATCTGTGATACC 60.134 52.381 0.00 0.00 0.00 2.73
55 56 1.408683 GCAAGCCCATCTGTGATACCA 60.409 52.381 0.00 0.00 0.00 3.25
56 57 2.292267 CAAGCCCATCTGTGATACCAC 58.708 52.381 0.00 0.00 43.46 4.16
67 68 2.556257 GTGATACCACACACACACACA 58.444 47.619 0.00 0.00 42.72 3.72
68 69 2.286833 GTGATACCACACACACACACAC 59.713 50.000 0.00 0.00 42.72 3.82
69 70 2.169561 TGATACCACACACACACACACT 59.830 45.455 0.00 0.00 0.00 3.55
70 71 2.772077 TACCACACACACACACACTT 57.228 45.000 0.00 0.00 0.00 3.16
71 72 1.164411 ACCACACACACACACACTTG 58.836 50.000 0.00 0.00 0.00 3.16
72 73 1.271108 ACCACACACACACACACTTGA 60.271 47.619 0.00 0.00 0.00 3.02
73 74 1.398041 CCACACACACACACACTTGAG 59.602 52.381 0.00 0.00 0.00 3.02
74 75 1.398041 CACACACACACACACTTGAGG 59.602 52.381 0.00 0.00 0.00 3.86
75 76 0.378257 CACACACACACACTTGAGGC 59.622 55.000 0.00 0.00 0.00 4.70
76 77 0.748005 ACACACACACACTTGAGGCC 60.748 55.000 0.00 0.00 0.00 5.19
77 78 0.747644 CACACACACACTTGAGGCCA 60.748 55.000 5.01 0.00 0.00 5.36
78 79 0.748005 ACACACACACTTGAGGCCAC 60.748 55.000 5.01 0.00 0.00 5.01
79 80 1.152963 ACACACACTTGAGGCCACC 60.153 57.895 5.01 0.00 0.00 4.61
80 81 1.149174 CACACACTTGAGGCCACCT 59.851 57.895 5.01 0.00 36.03 4.00
81 82 1.149174 ACACACTTGAGGCCACCTG 59.851 57.895 5.01 0.00 31.76 4.00
82 83 1.601759 CACACTTGAGGCCACCTGG 60.602 63.158 5.01 0.00 31.76 4.45
83 84 2.078665 ACACTTGAGGCCACCTGGT 61.079 57.895 5.01 0.00 37.57 4.00
84 85 1.601759 CACTTGAGGCCACCTGGTG 60.602 63.158 20.01 20.01 37.57 4.17
85 86 2.674380 CTTGAGGCCACCTGGTGC 60.674 66.667 21.47 15.71 37.57 5.01
86 87 3.496309 CTTGAGGCCACCTGGTGCA 62.496 63.158 21.47 10.82 37.57 4.57
87 88 3.496309 TTGAGGCCACCTGGTGCAG 62.496 63.158 21.47 9.89 37.57 4.41
139 140 3.420893 CATTAGTGCCACAAGGAAGGAA 58.579 45.455 0.00 0.00 36.89 3.36
163 164 1.537202 GGTGAGTTCATGCAGGTTCAC 59.463 52.381 18.17 18.17 35.42 3.18
164 165 2.498167 GTGAGTTCATGCAGGTTCACT 58.502 47.619 18.73 11.37 33.86 3.41
166 167 2.880268 TGAGTTCATGCAGGTTCACTTG 59.120 45.455 0.00 0.00 0.00 3.16
176 177 1.312815 GGTTCACTTGAAGCTGCACT 58.687 50.000 12.82 0.00 45.93 4.40
177 178 1.265365 GGTTCACTTGAAGCTGCACTC 59.735 52.381 12.82 0.00 45.93 3.51
179 180 1.875009 TCACTTGAAGCTGCACTCAG 58.125 50.000 0.00 0.00 43.16 3.35
181 182 2.158914 TCACTTGAAGCTGCACTCAGAA 60.159 45.455 0.00 0.00 42.95 3.02
182 183 2.032204 CACTTGAAGCTGCACTCAGAAC 60.032 50.000 0.00 0.00 42.95 3.01
183 184 2.158842 ACTTGAAGCTGCACTCAGAACT 60.159 45.455 0.00 0.00 42.95 3.01
184 185 2.627515 TGAAGCTGCACTCAGAACTT 57.372 45.000 1.02 0.00 42.95 2.66
185 186 2.487934 TGAAGCTGCACTCAGAACTTC 58.512 47.619 1.02 0.00 42.95 3.01
186 187 2.103771 TGAAGCTGCACTCAGAACTTCT 59.896 45.455 1.02 0.00 42.95 2.85
187 188 2.453983 AGCTGCACTCAGAACTTCTC 57.546 50.000 1.02 0.00 42.95 2.87
188 189 1.066914 GCTGCACTCAGAACTTCTCG 58.933 55.000 0.00 0.00 42.95 4.04
189 190 1.336332 GCTGCACTCAGAACTTCTCGA 60.336 52.381 0.00 0.00 42.95 4.04
190 191 2.594321 CTGCACTCAGAACTTCTCGAG 58.406 52.381 5.93 5.93 42.95 4.04
191 192 1.336332 TGCACTCAGAACTTCTCGAGC 60.336 52.381 7.81 8.25 30.22 5.03
192 193 1.067915 GCACTCAGAACTTCTCGAGCT 60.068 52.381 7.81 0.00 30.22 4.09
193 194 2.162608 GCACTCAGAACTTCTCGAGCTA 59.837 50.000 7.81 0.00 30.22 3.32
194 195 3.366476 GCACTCAGAACTTCTCGAGCTAA 60.366 47.826 7.81 0.00 30.22 3.09
195 196 4.411327 CACTCAGAACTTCTCGAGCTAAG 58.589 47.826 7.81 9.93 30.22 2.18
196 197 3.119637 ACTCAGAACTTCTCGAGCTAAGC 60.120 47.826 7.81 0.00 30.22 3.09
197 198 2.164624 TCAGAACTTCTCGAGCTAAGCC 59.835 50.000 7.81 3.51 0.00 4.35
198 199 1.133407 AGAACTTCTCGAGCTAAGCCG 59.867 52.381 7.81 0.00 0.00 5.52
199 200 0.173708 AACTTCTCGAGCTAAGCCGG 59.826 55.000 7.81 0.00 0.00 6.13
200 201 0.966370 ACTTCTCGAGCTAAGCCGGT 60.966 55.000 7.81 0.00 0.00 5.28
201 202 0.248702 CTTCTCGAGCTAAGCCGGTC 60.249 60.000 7.81 0.00 0.00 4.79
202 203 0.680280 TTCTCGAGCTAAGCCGGTCT 60.680 55.000 7.81 0.00 0.00 3.85
203 204 1.064946 CTCGAGCTAAGCCGGTCTG 59.935 63.158 1.90 0.00 0.00 3.51
204 205 2.583593 CGAGCTAAGCCGGTCTGC 60.584 66.667 1.90 2.82 0.00 4.26
205 206 2.202946 GAGCTAAGCCGGTCTGCC 60.203 66.667 1.90 0.00 0.00 4.85
206 207 3.741830 GAGCTAAGCCGGTCTGCCC 62.742 68.421 1.90 0.00 0.00 5.36
207 208 4.096003 GCTAAGCCGGTCTGCCCA 62.096 66.667 1.90 0.00 0.00 5.36
208 209 2.668632 CTAAGCCGGTCTGCCCAA 59.331 61.111 1.90 0.00 0.00 4.12
220 221 3.350833 GTCTGCCCAAGAACTGATGATT 58.649 45.455 0.00 0.00 36.40 2.57
226 227 6.115446 TGCCCAAGAACTGATGATTAGTTAG 58.885 40.000 2.36 0.00 38.42 2.34
227 228 6.116126 GCCCAAGAACTGATGATTAGTTAGT 58.884 40.000 2.36 0.00 38.42 2.24
228 229 6.599638 GCCCAAGAACTGATGATTAGTTAGTT 59.400 38.462 2.36 0.00 38.42 2.24
231 232 8.821894 CCAAGAACTGATGATTAGTTAGTTAGC 58.178 37.037 2.36 0.00 38.42 3.09
232 233 9.371136 CAAGAACTGATGATTAGTTAGTTAGCA 57.629 33.333 2.36 0.00 38.42 3.49
234 235 8.200792 AGAACTGATGATTAGTTAGTTAGCAGG 58.799 37.037 2.36 0.00 38.42 4.85
235 236 7.661536 ACTGATGATTAGTTAGTTAGCAGGA 57.338 36.000 0.00 0.00 0.00 3.86
237 238 8.147058 ACTGATGATTAGTTAGTTAGCAGGATG 58.853 37.037 0.00 0.00 40.87 3.51
238 239 7.445121 TGATGATTAGTTAGTTAGCAGGATGG 58.555 38.462 0.00 0.00 35.86 3.51
239 240 5.611374 TGATTAGTTAGTTAGCAGGATGGC 58.389 41.667 0.00 0.00 35.86 4.40
242 243 2.576191 AGTTAGTTAGCAGGATGGCCAA 59.424 45.455 10.96 0.00 35.86 4.52
243 244 3.203040 AGTTAGTTAGCAGGATGGCCAAT 59.797 43.478 10.96 0.00 35.86 3.16
246 247 1.410153 GTTAGCAGGATGGCCAATTGG 59.590 52.381 20.81 20.81 35.86 3.16
250 251 1.686800 AGGATGGCCAATTGGGTGC 60.687 57.895 25.73 11.38 39.65 5.01
252 253 0.396974 GGATGGCCAATTGGGTGCTA 60.397 55.000 25.73 9.98 39.65 3.49
253 254 1.484038 GATGGCCAATTGGGTGCTAA 58.516 50.000 25.73 5.30 39.65 3.09
255 256 1.949799 TGGCCAATTGGGTGCTAATT 58.050 45.000 25.73 0.00 39.65 1.40
256 257 1.830477 TGGCCAATTGGGTGCTAATTC 59.170 47.619 25.73 5.55 39.65 2.17
257 258 1.830477 GGCCAATTGGGTGCTAATTCA 59.170 47.619 25.73 0.00 39.65 2.57
263 264 5.069383 CCAATTGGGTGCTAATTCATCATCA 59.931 40.000 17.36 0.00 0.00 3.07
269 270 5.479375 GGGTGCTAATTCATCATCATGGATT 59.521 40.000 0.00 0.00 40.78 3.01
271 272 7.362401 GGGTGCTAATTCATCATCATGGATTAC 60.362 40.741 0.00 0.00 38.87 1.89
273 274 6.372381 TGCTAATTCATCATCATGGATTACGG 59.628 38.462 0.00 0.00 38.87 4.02
274 275 6.183360 GCTAATTCATCATCATGGATTACGGG 60.183 42.308 0.00 0.00 38.87 5.28
275 276 3.057969 TCATCATCATGGATTACGGGC 57.942 47.619 0.00 0.00 0.00 6.13
352 353 2.084681 CGTACCACGAACAGCGACC 61.085 63.158 0.00 0.00 46.05 4.79
380 381 2.555664 AGCAGAAGGGATGAGGAGAAA 58.444 47.619 0.00 0.00 0.00 2.52
403 404 2.201022 CCGGGTGGTCCTAGATCCG 61.201 68.421 0.00 0.00 37.50 4.18
452 453 2.421424 GTGTCTGCTCAAGCTTTATGGG 59.579 50.000 0.00 0.00 42.66 4.00
453 454 2.019984 GTCTGCTCAAGCTTTATGGGG 58.980 52.381 0.00 0.00 42.66 4.96
476 477 2.038269 GCCGGGAACAAGAATCGCA 61.038 57.895 2.18 0.00 0.00 5.10
478 479 1.369091 CCGGGAACAAGAATCGCAGG 61.369 60.000 0.00 0.00 0.00 4.85
502 517 1.959985 CGATCCTGTCTGCCTACTCAT 59.040 52.381 0.00 0.00 0.00 2.90
521 536 2.045561 TTTTTGCGGTCAAGAGGTCA 57.954 45.000 0.00 0.00 33.12 4.02
523 538 2.270352 TTTGCGGTCAAGAGGTCATT 57.730 45.000 0.00 0.00 33.12 2.57
525 540 0.955428 TGCGGTCAAGAGGTCATTGC 60.955 55.000 0.00 0.00 0.00 3.56
535 550 5.105392 TCAAGAGGTCATTGCACAACTTTTT 60.105 36.000 0.00 0.00 0.00 1.94
573 588 7.732222 AGGCATTCAGGGTAAAAATTTATCA 57.268 32.000 0.00 0.00 0.00 2.15
577 592 9.696917 GCATTCAGGGTAAAAATTTATCATAGG 57.303 33.333 0.00 0.00 0.00 2.57
593 608 8.718102 TTATCATAGGAAGTAAAGTGAGCAAC 57.282 34.615 0.00 0.00 0.00 4.17
621 637 1.205893 TGAACCAAGGTGTTTGTTGGC 59.794 47.619 0.94 0.00 46.25 4.52
622 638 0.174617 AACCAAGGTGTTTGTTGGCG 59.825 50.000 0.94 0.00 46.25 5.69
646 662 6.035435 CGAGGAGATGAAAAATGTCAGTGTAG 59.965 42.308 0.00 0.00 0.00 2.74
661 677 4.526650 TCAGTGTAGTGTTCATTAGGAGCA 59.473 41.667 0.00 0.00 34.02 4.26
664 680 5.877012 AGTGTAGTGTTCATTAGGAGCAATG 59.123 40.000 0.00 0.00 38.54 2.82
666 682 3.689347 AGTGTTCATTAGGAGCAATGCA 58.311 40.909 8.35 0.00 38.54 3.96
667 683 4.275810 AGTGTTCATTAGGAGCAATGCAT 58.724 39.130 8.35 0.00 38.54 3.96
668 684 4.337555 AGTGTTCATTAGGAGCAATGCATC 59.662 41.667 8.35 1.97 38.54 3.91
669 685 4.337555 GTGTTCATTAGGAGCAATGCATCT 59.662 41.667 8.35 6.79 38.54 2.90
670 686 4.577693 TGTTCATTAGGAGCAATGCATCTC 59.422 41.667 8.35 2.92 36.13 2.75
671 687 4.426736 TCATTAGGAGCAATGCATCTCA 57.573 40.909 8.35 0.00 36.13 3.27
672 688 4.386711 TCATTAGGAGCAATGCATCTCAG 58.613 43.478 8.35 1.77 36.13 3.35
673 689 3.920231 TTAGGAGCAATGCATCTCAGT 57.080 42.857 8.35 6.33 0.00 3.41
674 690 2.039818 AGGAGCAATGCATCTCAGTG 57.960 50.000 8.35 4.60 43.15 3.66
689 711 1.742268 TCAGTGATCTCACAGAGAGCG 59.258 52.381 12.54 0.00 46.57 5.03
702 724 0.873054 GAGAGCGCATTATGCTGCAT 59.127 50.000 25.90 20.18 44.18 3.96
703 725 0.591659 AGAGCGCATTATGCTGCATG 59.408 50.000 24.59 11.24 44.18 4.06
704 726 1.002250 GAGCGCATTATGCTGCATGC 61.002 55.000 24.59 19.39 44.18 4.06
735 757 2.298163 CTGTGAGGCTGCAGGAATTTTT 59.702 45.455 17.12 0.00 0.00 1.94
779 801 1.065701 GCTGCTCAGATGCCAAATCAG 59.934 52.381 0.29 0.00 0.00 2.90
814 836 1.656441 GGCACAGTGGCACAGAAAG 59.344 57.895 21.89 8.71 41.80 2.62
815 837 1.008079 GCACAGTGGCACAGAAAGC 60.008 57.895 21.41 14.46 41.80 3.51
819 841 1.694150 ACAGTGGCACAGAAAGCTAGA 59.306 47.619 21.41 0.00 41.80 2.43
899 926 2.988549 GCGTGCGTTCTCACAGTCG 61.989 63.158 0.00 0.00 36.80 4.18
902 929 3.150895 GCGTTCTCACAGTCGCAG 58.849 61.111 0.00 0.00 46.40 5.18
909 936 1.287730 CTCACAGTCGCAGTTGCTCC 61.288 60.000 2.29 0.00 39.32 4.70
923 950 4.479993 CTCCCTGCCTTGCTCCCG 62.480 72.222 0.00 0.00 0.00 5.14
937 970 3.751246 CCCGCACCACCATTGCAG 61.751 66.667 0.00 0.00 40.20 4.41
942 975 1.604308 CACCACCATTGCAGGCTGA 60.604 57.895 20.86 0.00 0.00 4.26
943 976 1.303888 ACCACCATTGCAGGCTGAG 60.304 57.895 20.86 4.17 0.00 3.35
964 997 0.098905 TTGAGCTCGGTCGATCGAAG 59.901 55.000 22.75 16.83 38.77 3.79
965 998 1.009449 GAGCTCGGTCGATCGAAGG 60.009 63.158 22.75 12.54 38.77 3.46
967 1000 1.298488 GCTCGGTCGATCGAAGGAC 60.298 63.158 22.75 7.82 38.77 3.85
1288 1321 2.104451 CCCATCTCCATCTCCAAGTGAG 59.896 54.545 0.00 0.00 42.90 3.51
1309 1342 4.699522 AAGCCAAGCGACCCGTCC 62.700 66.667 0.00 0.00 0.00 4.79
1315 1374 0.744414 CAAGCGACCCGTCCATCATT 60.744 55.000 0.00 0.00 0.00 2.57
1319 1378 1.145759 CGACCCGTCCATCATTCACG 61.146 60.000 0.00 0.00 0.00 4.35
1360 1424 3.353836 CCGGCGGTGACAACAAGG 61.354 66.667 19.97 0.00 0.00 3.61
1361 1425 2.280524 CGGCGGTGACAACAAGGA 60.281 61.111 0.00 0.00 0.00 3.36
1362 1426 2.317609 CGGCGGTGACAACAAGGAG 61.318 63.158 0.00 0.00 0.00 3.69
1363 1427 1.070786 GGCGGTGACAACAAGGAGA 59.929 57.895 0.00 0.00 0.00 3.71
1364 1428 0.951040 GGCGGTGACAACAAGGAGAG 60.951 60.000 0.00 0.00 0.00 3.20
1365 1429 1.569479 GCGGTGACAACAAGGAGAGC 61.569 60.000 0.00 0.00 0.00 4.09
1366 1430 0.249868 CGGTGACAACAAGGAGAGCA 60.250 55.000 0.00 0.00 0.00 4.26
1367 1431 1.230324 GGTGACAACAAGGAGAGCAC 58.770 55.000 0.00 0.00 0.00 4.40
1368 1432 1.230324 GTGACAACAAGGAGAGCACC 58.770 55.000 0.00 0.00 0.00 5.01
1369 1433 0.249868 TGACAACAAGGAGAGCACCG 60.250 55.000 0.00 0.00 34.73 4.94
1393 1457 2.742372 GCATCCGGCGAGTGTTGT 60.742 61.111 9.30 0.00 0.00 3.32
1394 1458 1.447140 GCATCCGGCGAGTGTTGTA 60.447 57.895 9.30 0.00 0.00 2.41
1395 1459 1.693083 GCATCCGGCGAGTGTTGTAC 61.693 60.000 9.30 0.00 0.00 2.90
1396 1460 1.153901 ATCCGGCGAGTGTTGTACG 60.154 57.895 9.30 0.00 0.00 3.67
1397 1461 1.588824 ATCCGGCGAGTGTTGTACGA 61.589 55.000 9.30 0.00 0.00 3.43
1398 1462 1.800315 CCGGCGAGTGTTGTACGAG 60.800 63.158 9.30 0.00 0.00 4.18
1399 1463 2.434134 CGGCGAGTGTTGTACGAGC 61.434 63.158 0.00 0.00 36.37 5.03
1400 1464 2.092882 GGCGAGTGTTGTACGAGCC 61.093 63.158 0.00 0.00 44.74 4.70
1401 1465 2.092882 GCGAGTGTTGTACGAGCCC 61.093 63.158 0.00 0.00 32.84 5.19
1402 1466 1.445582 CGAGTGTTGTACGAGCCCC 60.446 63.158 0.00 0.00 0.00 5.80
1403 1467 1.445582 GAGTGTTGTACGAGCCCCG 60.446 63.158 0.00 0.00 45.44 5.73
1404 1468 2.433664 GTGTTGTACGAGCCCCGG 60.434 66.667 0.00 0.00 43.93 5.73
1405 1469 2.918802 TGTTGTACGAGCCCCGGT 60.919 61.111 0.00 0.00 43.93 5.28
1406 1470 2.125793 GTTGTACGAGCCCCGGTC 60.126 66.667 0.00 0.00 43.93 4.79
1445 1512 7.606456 CGTAATAAGCCAAGGGTTCATATGTAT 59.394 37.037 6.84 0.00 37.08 2.29
1446 1513 9.297037 GTAATAAGCCAAGGGTTCATATGTATT 57.703 33.333 6.84 2.99 37.08 1.89
1447 1514 8.782137 AATAAGCCAAGGGTTCATATGTATTT 57.218 30.769 6.84 0.00 37.08 1.40
1448 1515 6.469782 AAGCCAAGGGTTCATATGTATTTG 57.530 37.500 1.90 2.70 0.00 2.32
1449 1516 5.518865 AGCCAAGGGTTCATATGTATTTGT 58.481 37.500 1.90 0.00 0.00 2.83
1450 1517 5.360714 AGCCAAGGGTTCATATGTATTTGTG 59.639 40.000 1.90 0.00 0.00 3.33
1451 1518 5.591099 CCAAGGGTTCATATGTATTTGTGC 58.409 41.667 1.90 0.00 0.00 4.57
1452 1519 5.360714 CCAAGGGTTCATATGTATTTGTGCT 59.639 40.000 1.90 0.00 0.00 4.40
1488 1558 9.239551 ACGGAGTATGTATGTATGTATGTATGT 57.760 33.333 0.00 0.00 41.94 2.29
1522 1595 7.893658 TGTGGTAGTAATAATCTTAGCTAGGC 58.106 38.462 0.00 0.00 0.00 3.93
1523 1596 7.728981 TGTGGTAGTAATAATCTTAGCTAGGCT 59.271 37.037 0.00 0.00 43.41 4.58
1524 1597 9.240734 GTGGTAGTAATAATCTTAGCTAGGCTA 57.759 37.037 0.00 0.00 40.44 3.93
1525 1598 9.463902 TGGTAGTAATAATCTTAGCTAGGCTAG 57.536 37.037 17.33 17.33 42.34 3.42
1547 1620 0.316204 AGGTTGAAGCTGCATTGCAC 59.684 50.000 7.38 5.24 33.79 4.57
1607 1680 2.670251 CCGGCCGGCTGTACAAAA 60.670 61.111 34.96 0.00 0.00 2.44
1608 1681 2.686816 CCGGCCGGCTGTACAAAAG 61.687 63.158 34.96 12.67 0.00 2.27
1609 1682 2.686816 CGGCCGGCTGTACAAAAGG 61.687 63.158 27.83 1.33 0.00 3.11
1610 1683 2.340328 GGCCGGCTGTACAAAAGGG 61.340 63.158 28.56 0.00 0.00 3.95
1739 1822 3.493334 TCCATCATTAGGTATCCGTCGT 58.507 45.455 0.00 0.00 0.00 4.34
1741 1824 3.489444 CATCATTAGGTATCCGTCGTCG 58.511 50.000 0.00 0.00 0.00 5.12
1743 1826 2.545526 TCATTAGGTATCCGTCGTCGAC 59.454 50.000 15.51 15.51 39.71 4.20
1745 1828 3.452755 TTAGGTATCCGTCGTCGACTA 57.547 47.619 22.18 11.25 39.71 2.59
1746 1829 1.863267 AGGTATCCGTCGTCGACTAG 58.137 55.000 22.18 13.75 39.71 2.57
1747 1830 1.137872 AGGTATCCGTCGTCGACTAGT 59.862 52.381 22.18 10.42 39.71 2.57
1748 1831 1.260033 GGTATCCGTCGTCGACTAGTG 59.740 57.143 22.18 7.35 39.71 2.74
1816 1900 7.848223 TGTGTCTGATTAACAATACCATGAG 57.152 36.000 0.00 0.00 0.00 2.90
1821 1905 7.439655 GTCTGATTAACAATACCATGAGGACTC 59.560 40.741 0.00 0.00 38.69 3.36
1822 1906 6.280643 TGATTAACAATACCATGAGGACTCG 58.719 40.000 0.00 0.00 38.69 4.18
1832 1916 5.556915 ACCATGAGGACTCGTAATTGAAAA 58.443 37.500 0.00 0.00 38.69 2.29
1834 1918 6.072673 ACCATGAGGACTCGTAATTGAAAAAC 60.073 38.462 0.00 0.00 38.69 2.43
1835 1919 6.072728 CCATGAGGACTCGTAATTGAAAAACA 60.073 38.462 0.00 0.00 36.89 2.83
1837 1921 6.954944 TGAGGACTCGTAATTGAAAAACAAG 58.045 36.000 0.00 0.00 42.02 3.16
1838 1922 6.017440 TGAGGACTCGTAATTGAAAAACAAGG 60.017 38.462 0.00 0.00 42.02 3.61
1839 1923 4.915667 GGACTCGTAATTGAAAAACAAGGC 59.084 41.667 0.00 0.00 42.02 4.35
1840 1924 5.506649 GGACTCGTAATTGAAAAACAAGGCA 60.507 40.000 0.00 0.00 42.02 4.75
1841 1925 6.084326 ACTCGTAATTGAAAAACAAGGCAT 57.916 33.333 0.00 0.00 42.02 4.40
1843 1927 7.653647 ACTCGTAATTGAAAAACAAGGCATTA 58.346 30.769 0.00 0.00 42.02 1.90
1844 1928 8.303876 ACTCGTAATTGAAAAACAAGGCATTAT 58.696 29.630 0.00 0.00 42.02 1.28
1846 1930 8.300286 TCGTAATTGAAAAACAAGGCATTATGA 58.700 29.630 0.00 0.00 42.02 2.15
1847 1931 9.086336 CGTAATTGAAAAACAAGGCATTATGAT 57.914 29.630 0.00 0.00 42.02 2.45
1852 1936 6.149142 TGAAAAACAAGGCATTATGATTTGGC 59.851 34.615 11.67 0.00 38.60 4.52
1874 2056 7.839907 TGGCTAAACAAATATCTCAAGCATTT 58.160 30.769 0.00 0.00 0.00 2.32
1875 2057 7.760794 TGGCTAAACAAATATCTCAAGCATTTG 59.239 33.333 11.92 11.92 42.61 2.32
1876 2058 7.254218 GGCTAAACAAATATCTCAAGCATTTGC 60.254 37.037 12.81 0.00 41.31 3.68
1904 2133 4.550422 GAGGAAGATGAAGTTTGTTTGGC 58.450 43.478 0.00 0.00 0.00 4.52
1906 2135 5.385198 AGGAAGATGAAGTTTGTTTGGCTA 58.615 37.500 0.00 0.00 0.00 3.93
1937 2166 2.648059 GAGGATTGGGAGTGTTGGATG 58.352 52.381 0.00 0.00 0.00 3.51
1939 2168 2.025887 AGGATTGGGAGTGTTGGATGTC 60.026 50.000 0.00 0.00 0.00 3.06
1950 2179 2.202756 GGATGTCGGGACTCGCAC 60.203 66.667 0.00 0.00 39.05 5.34
1970 2199 3.937706 CACCAAGGCATTGTTGTTGAAAA 59.062 39.130 10.60 0.00 34.39 2.29
2056 2289 2.324541 GATGAGCCTAGACCACCTCAT 58.675 52.381 1.97 1.97 45.04 2.90
2090 2323 1.433534 GTCTTTCTGGTGGAAGAGCG 58.566 55.000 0.00 0.00 35.16 5.03
2100 2333 2.427506 GTGGAAGAGCGTCCTCAAATT 58.572 47.619 4.19 0.00 40.68 1.82
2208 2481 6.428159 AGTCAGTGATACAACTTCCATCAAAC 59.572 38.462 0.00 0.00 30.85 2.93
2222 2495 4.103153 TCCATCAAACAGGTTGTTCTCTCT 59.897 41.667 0.00 0.00 40.14 3.10
2236 2509 2.544721 TCTCTCTGCAAATCTGGAGGT 58.455 47.619 0.00 0.00 41.18 3.85
2237 2510 2.909006 TCTCTCTGCAAATCTGGAGGTT 59.091 45.455 0.00 0.00 41.18 3.50
2238 2511 3.055530 TCTCTCTGCAAATCTGGAGGTTC 60.056 47.826 0.00 0.00 41.18 3.62
2239 2512 2.639347 TCTCTGCAAATCTGGAGGTTCA 59.361 45.455 0.00 0.00 41.18 3.18
2240 2513 2.746362 CTCTGCAAATCTGGAGGTTCAC 59.254 50.000 0.00 0.00 41.18 3.18
2241 2514 1.815003 CTGCAAATCTGGAGGTTCACC 59.185 52.381 0.00 0.00 37.36 4.02
2242 2515 1.144708 TGCAAATCTGGAGGTTCACCA 59.855 47.619 0.00 0.00 38.89 4.17
2249 2522 2.409064 TGGAGGTTCACCAGGTTCTA 57.591 50.000 0.00 0.00 38.89 2.10
2254 2527 1.607251 GGTTCACCAGGTTCTACCACG 60.607 57.143 8.94 0.00 41.95 4.94
2265 2538 3.240011 TACCACGGTTCGGCCCAA 61.240 61.111 0.00 0.00 0.00 4.12
2266 2539 2.530958 CTACCACGGTTCGGCCCAAT 62.531 60.000 0.00 0.00 0.00 3.16
2267 2540 2.524951 TACCACGGTTCGGCCCAATC 62.525 60.000 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.355913 TCTGTACTGATCATGAGTTATTAGCAG 58.644 37.037 0.09 0.00 0.00 4.24
1 2 8.237811 TCTGTACTGATCATGAGTTATTAGCA 57.762 34.615 0.09 0.00 0.00 3.49
2 3 7.328249 GCTCTGTACTGATCATGAGTTATTAGC 59.672 40.741 0.09 0.00 0.00 3.09
3 4 8.355913 TGCTCTGTACTGATCATGAGTTATTAG 58.644 37.037 0.09 0.00 0.00 1.73
4 5 8.138074 GTGCTCTGTACTGATCATGAGTTATTA 58.862 37.037 9.15 0.00 0.00 0.98
5 6 6.983307 GTGCTCTGTACTGATCATGAGTTATT 59.017 38.462 9.15 0.00 0.00 1.40
6 7 6.097412 TGTGCTCTGTACTGATCATGAGTTAT 59.903 38.462 9.15 0.00 0.00 1.89
7 8 5.418840 TGTGCTCTGTACTGATCATGAGTTA 59.581 40.000 9.15 0.00 0.00 2.24
8 9 4.221482 TGTGCTCTGTACTGATCATGAGTT 59.779 41.667 9.15 0.00 0.00 3.01
9 10 3.766051 TGTGCTCTGTACTGATCATGAGT 59.234 43.478 9.15 0.00 0.00 3.41
10 11 4.111198 GTGTGCTCTGTACTGATCATGAG 58.889 47.826 9.15 1.11 0.00 2.90
11 12 3.511146 TGTGTGCTCTGTACTGATCATGA 59.489 43.478 9.15 0.00 0.00 3.07
12 13 3.853475 TGTGTGCTCTGTACTGATCATG 58.147 45.455 9.15 0.00 0.00 3.07
13 14 4.502016 CTTGTGTGCTCTGTACTGATCAT 58.498 43.478 9.15 0.00 0.00 2.45
14 15 3.862264 GCTTGTGTGCTCTGTACTGATCA 60.862 47.826 2.62 2.58 0.00 2.92
15 16 2.670414 GCTTGTGTGCTCTGTACTGATC 59.330 50.000 2.62 0.00 0.00 2.92
16 17 2.037641 TGCTTGTGTGCTCTGTACTGAT 59.962 45.455 2.62 0.00 0.00 2.90
17 18 1.412343 TGCTTGTGTGCTCTGTACTGA 59.588 47.619 2.21 2.21 0.00 3.41
18 19 1.869774 TGCTTGTGTGCTCTGTACTG 58.130 50.000 0.00 0.00 0.00 2.74
19 20 2.487934 CTTGCTTGTGTGCTCTGTACT 58.512 47.619 0.00 0.00 0.00 2.73
20 21 1.069636 GCTTGCTTGTGTGCTCTGTAC 60.070 52.381 0.00 0.00 0.00 2.90
21 22 1.229428 GCTTGCTTGTGTGCTCTGTA 58.771 50.000 0.00 0.00 0.00 2.74
22 23 1.450531 GGCTTGCTTGTGTGCTCTGT 61.451 55.000 0.00 0.00 0.00 3.41
23 24 1.285023 GGCTTGCTTGTGTGCTCTG 59.715 57.895 0.00 0.00 0.00 3.35
24 25 1.900498 GGGCTTGCTTGTGTGCTCT 60.900 57.895 0.00 0.00 0.00 4.09
25 26 1.530013 ATGGGCTTGCTTGTGTGCTC 61.530 55.000 0.00 0.00 0.00 4.26
26 27 1.530013 GATGGGCTTGCTTGTGTGCT 61.530 55.000 0.00 0.00 0.00 4.40
27 28 1.080298 GATGGGCTTGCTTGTGTGC 60.080 57.895 0.00 0.00 0.00 4.57
28 29 0.242825 CAGATGGGCTTGCTTGTGTG 59.757 55.000 0.00 0.00 0.00 3.82
29 30 0.178981 ACAGATGGGCTTGCTTGTGT 60.179 50.000 0.00 0.00 0.00 3.72
30 31 0.242825 CACAGATGGGCTTGCTTGTG 59.757 55.000 0.00 0.00 0.00 3.33
31 32 0.111061 TCACAGATGGGCTTGCTTGT 59.889 50.000 0.00 0.00 0.00 3.16
32 33 1.471119 ATCACAGATGGGCTTGCTTG 58.529 50.000 0.00 0.00 0.00 4.01
33 34 2.648059 GTATCACAGATGGGCTTGCTT 58.352 47.619 0.00 0.00 0.00 3.91
34 35 1.133976 GGTATCACAGATGGGCTTGCT 60.134 52.381 0.00 0.00 0.00 3.91
35 36 1.312815 GGTATCACAGATGGGCTTGC 58.687 55.000 0.00 0.00 0.00 4.01
36 37 2.292267 GTGGTATCACAGATGGGCTTG 58.708 52.381 0.00 0.00 43.13 4.01
37 38 2.717639 GTGGTATCACAGATGGGCTT 57.282 50.000 0.00 0.00 43.13 4.35
47 48 2.286833 GTGTGTGTGTGTGTGGTATCAC 59.713 50.000 0.00 0.00 43.87 3.06
48 49 2.169561 AGTGTGTGTGTGTGTGGTATCA 59.830 45.455 0.00 0.00 0.00 2.15
49 50 2.833794 AGTGTGTGTGTGTGTGGTATC 58.166 47.619 0.00 0.00 0.00 2.24
50 51 2.942376 CAAGTGTGTGTGTGTGTGGTAT 59.058 45.455 0.00 0.00 0.00 2.73
51 52 2.028020 TCAAGTGTGTGTGTGTGTGGTA 60.028 45.455 0.00 0.00 0.00 3.25
52 53 1.164411 CAAGTGTGTGTGTGTGTGGT 58.836 50.000 0.00 0.00 0.00 4.16
53 54 1.398041 CTCAAGTGTGTGTGTGTGTGG 59.602 52.381 0.00 0.00 0.00 4.17
54 55 1.398041 CCTCAAGTGTGTGTGTGTGTG 59.602 52.381 0.00 0.00 0.00 3.82
55 56 1.737838 CCTCAAGTGTGTGTGTGTGT 58.262 50.000 0.00 0.00 0.00 3.72
56 57 0.378257 GCCTCAAGTGTGTGTGTGTG 59.622 55.000 0.00 0.00 0.00 3.82
57 58 0.748005 GGCCTCAAGTGTGTGTGTGT 60.748 55.000 0.00 0.00 0.00 3.72
58 59 0.747644 TGGCCTCAAGTGTGTGTGTG 60.748 55.000 3.32 0.00 0.00 3.82
59 60 0.748005 GTGGCCTCAAGTGTGTGTGT 60.748 55.000 3.32 0.00 0.00 3.72
60 61 1.447317 GGTGGCCTCAAGTGTGTGTG 61.447 60.000 3.32 0.00 0.00 3.82
61 62 1.152963 GGTGGCCTCAAGTGTGTGT 60.153 57.895 3.32 0.00 0.00 3.72
62 63 1.149174 AGGTGGCCTCAAGTGTGTG 59.851 57.895 3.32 0.00 0.00 3.82
63 64 1.149174 CAGGTGGCCTCAAGTGTGT 59.851 57.895 3.32 0.00 0.00 3.72
64 65 1.601759 CCAGGTGGCCTCAAGTGTG 60.602 63.158 3.32 0.00 0.00 3.82
65 66 2.078665 ACCAGGTGGCCTCAAGTGT 61.079 57.895 3.32 0.00 39.32 3.55
66 67 1.601759 CACCAGGTGGCCTCAAGTG 60.602 63.158 12.40 5.51 39.32 3.16
67 68 2.839098 CACCAGGTGGCCTCAAGT 59.161 61.111 12.40 0.00 39.32 3.16
68 69 2.674380 GCACCAGGTGGCCTCAAG 60.674 66.667 21.77 0.00 39.32 3.02
69 70 3.496309 CTGCACCAGGTGGCCTCAA 62.496 63.158 21.77 0.00 39.32 3.02
70 71 3.957586 CTGCACCAGGTGGCCTCA 61.958 66.667 21.77 9.41 39.32 3.86
71 72 3.958860 ACTGCACCAGGTGGCCTC 61.959 66.667 21.77 4.84 39.32 4.70
72 73 4.275508 CACTGCACCAGGTGGCCT 62.276 66.667 21.77 0.00 39.32 5.19
75 76 4.584518 TGCCACTGCACCAGGTGG 62.585 66.667 21.77 16.49 44.23 4.61
84 85 1.815421 CTACCATCCGTGCCACTGC 60.815 63.158 0.00 0.00 38.26 4.40
85 86 1.153369 CCTACCATCCGTGCCACTG 60.153 63.158 0.00 0.00 0.00 3.66
86 87 2.367202 CCCTACCATCCGTGCCACT 61.367 63.158 0.00 0.00 0.00 4.00
87 88 2.189521 CCCTACCATCCGTGCCAC 59.810 66.667 0.00 0.00 0.00 5.01
126 127 0.111253 ACCTGCTTCCTTCCTTGTGG 59.889 55.000 0.00 0.00 0.00 4.17
130 131 1.439543 ACTCACCTGCTTCCTTCCTT 58.560 50.000 0.00 0.00 0.00 3.36
131 132 1.349357 GAACTCACCTGCTTCCTTCCT 59.651 52.381 0.00 0.00 0.00 3.36
132 133 1.072331 TGAACTCACCTGCTTCCTTCC 59.928 52.381 0.00 0.00 0.00 3.46
133 134 2.550830 TGAACTCACCTGCTTCCTTC 57.449 50.000 0.00 0.00 0.00 3.46
139 140 0.322277 CCTGCATGAACTCACCTGCT 60.322 55.000 0.00 0.00 34.08 4.24
163 164 2.492012 AGTTCTGAGTGCAGCTTCAAG 58.508 47.619 0.00 0.00 42.01 3.02
164 165 2.627515 AGTTCTGAGTGCAGCTTCAA 57.372 45.000 0.00 0.00 42.01 2.69
166 167 2.736192 GAGAAGTTCTGAGTGCAGCTTC 59.264 50.000 10.90 0.00 42.01 3.86
170 171 2.594321 CTCGAGAAGTTCTGAGTGCAG 58.406 52.381 10.90 0.00 43.67 4.41
174 175 3.119637 GCTTAGCTCGAGAAGTTCTGAGT 60.120 47.826 18.75 15.76 32.58 3.41
176 177 2.164624 GGCTTAGCTCGAGAAGTTCTGA 59.835 50.000 18.75 7.40 0.00 3.27
177 178 2.535331 GGCTTAGCTCGAGAAGTTCTG 58.465 52.381 18.75 3.14 0.00 3.02
179 180 1.551145 CGGCTTAGCTCGAGAAGTTC 58.449 55.000 18.75 7.74 0.00 3.01
181 182 0.966370 ACCGGCTTAGCTCGAGAAGT 60.966 55.000 18.75 1.72 0.00 3.01
182 183 0.248702 GACCGGCTTAGCTCGAGAAG 60.249 60.000 18.75 13.00 0.00 2.85
183 184 0.680280 AGACCGGCTTAGCTCGAGAA 60.680 55.000 18.75 0.83 0.00 2.87
184 185 1.077644 AGACCGGCTTAGCTCGAGA 60.078 57.895 18.75 0.00 0.00 4.04
185 186 1.064946 CAGACCGGCTTAGCTCGAG 59.935 63.158 8.45 8.45 0.00 4.04
186 187 3.064987 GCAGACCGGCTTAGCTCGA 62.065 63.158 14.67 0.00 0.00 4.04
187 188 2.583593 GCAGACCGGCTTAGCTCG 60.584 66.667 0.00 6.15 0.00 5.03
188 189 2.202946 GGCAGACCGGCTTAGCTC 60.203 66.667 0.00 0.00 37.17 4.09
189 190 3.787001 GGGCAGACCGGCTTAGCT 61.787 66.667 0.00 0.00 40.90 3.32
190 191 3.622060 TTGGGCAGACCGGCTTAGC 62.622 63.158 0.00 0.00 44.64 3.09
191 192 1.450312 CTTGGGCAGACCGGCTTAG 60.450 63.158 0.00 0.00 44.64 2.18
192 193 1.485294 TTCTTGGGCAGACCGGCTTA 61.485 55.000 0.00 0.00 44.64 3.09
193 194 2.829384 TTCTTGGGCAGACCGGCTT 61.829 57.895 0.00 0.00 44.64 4.35
194 195 3.249189 TTCTTGGGCAGACCGGCT 61.249 61.111 0.00 0.00 44.64 5.52
195 196 3.056328 GTTCTTGGGCAGACCGGC 61.056 66.667 0.00 0.00 44.64 6.13
196 197 1.672356 CAGTTCTTGGGCAGACCGG 60.672 63.158 0.00 0.00 44.64 5.28
197 198 0.036010 ATCAGTTCTTGGGCAGACCG 60.036 55.000 0.00 0.00 44.64 4.79
198 199 1.003580 TCATCAGTTCTTGGGCAGACC 59.996 52.381 0.00 0.00 40.81 3.85
199 200 2.479566 TCATCAGTTCTTGGGCAGAC 57.520 50.000 0.00 0.00 0.00 3.51
200 201 3.726557 AATCATCAGTTCTTGGGCAGA 57.273 42.857 0.00 0.00 0.00 4.26
201 202 4.521146 ACTAATCATCAGTTCTTGGGCAG 58.479 43.478 0.00 0.00 0.00 4.85
202 203 4.574674 ACTAATCATCAGTTCTTGGGCA 57.425 40.909 0.00 0.00 0.00 5.36
203 204 6.116126 ACTAACTAATCATCAGTTCTTGGGC 58.884 40.000 0.00 0.00 37.42 5.36
204 205 9.319143 CTAACTAACTAATCATCAGTTCTTGGG 57.681 37.037 0.00 0.00 37.42 4.12
205 206 8.821894 GCTAACTAACTAATCATCAGTTCTTGG 58.178 37.037 0.00 0.00 37.42 3.61
206 207 9.371136 TGCTAACTAACTAATCATCAGTTCTTG 57.629 33.333 0.00 0.00 37.42 3.02
207 208 9.593134 CTGCTAACTAACTAATCATCAGTTCTT 57.407 33.333 0.00 0.00 37.42 2.52
208 209 8.200792 CCTGCTAACTAACTAATCATCAGTTCT 58.799 37.037 0.00 0.00 37.42 3.01
220 221 3.380393 TGGCCATCCTGCTAACTAACTA 58.620 45.455 0.00 0.00 0.00 2.24
226 227 1.410153 CCAATTGGCCATCCTGCTAAC 59.590 52.381 12.53 0.00 34.39 2.34
227 228 1.688942 CCCAATTGGCCATCCTGCTAA 60.689 52.381 19.75 0.00 36.11 3.09
228 229 0.106066 CCCAATTGGCCATCCTGCTA 60.106 55.000 19.75 0.00 0.00 3.49
231 232 1.963464 GCACCCAATTGGCCATCCTG 61.963 60.000 19.75 4.04 37.83 3.86
232 233 1.686800 GCACCCAATTGGCCATCCT 60.687 57.895 19.75 0.00 37.83 3.24
234 235 1.484038 TTAGCACCCAATTGGCCATC 58.516 50.000 19.75 7.47 37.83 3.51
235 236 2.179377 ATTAGCACCCAATTGGCCAT 57.821 45.000 19.75 6.93 37.83 4.40
237 238 1.830477 TGAATTAGCACCCAATTGGCC 59.170 47.619 19.75 9.23 37.83 5.36
238 239 3.132646 TGATGAATTAGCACCCAATTGGC 59.867 43.478 19.75 8.02 37.83 4.52
239 240 5.069383 TGATGATGAATTAGCACCCAATTGG 59.931 40.000 18.21 18.21 41.37 3.16
242 243 5.245301 CCATGATGATGAATTAGCACCCAAT 59.755 40.000 0.00 0.00 0.00 3.16
243 244 4.585581 CCATGATGATGAATTAGCACCCAA 59.414 41.667 0.00 0.00 0.00 4.12
246 247 6.585695 AATCCATGATGATGAATTAGCACC 57.414 37.500 0.00 0.00 0.00 5.01
250 251 6.183360 GCCCGTAATCCATGATGATGAATTAG 60.183 42.308 0.00 0.00 0.00 1.73
252 253 4.460382 GCCCGTAATCCATGATGATGAATT 59.540 41.667 0.00 0.00 0.00 2.17
253 254 4.012374 GCCCGTAATCCATGATGATGAAT 58.988 43.478 0.00 0.00 0.00 2.57
255 256 2.612721 CGCCCGTAATCCATGATGATGA 60.613 50.000 0.00 0.00 0.00 2.92
256 257 1.733912 CGCCCGTAATCCATGATGATG 59.266 52.381 0.00 0.00 0.00 3.07
257 258 1.339055 CCGCCCGTAATCCATGATGAT 60.339 52.381 0.00 0.00 0.00 2.45
263 264 4.619227 CCGCCGCCCGTAATCCAT 62.619 66.667 0.00 0.00 34.38 3.41
352 353 4.305769 CTCATCCCTTCTGCTAGATTTCG 58.694 47.826 0.00 0.00 0.00 3.46
380 381 2.364579 TAGGACCACCCGGCGAAT 60.365 61.111 9.30 0.00 40.87 3.34
403 404 1.160329 ACAACTTGCTCGCTGTCCAC 61.160 55.000 0.00 0.00 0.00 4.02
428 429 1.889545 AAAGCTTGAGCAGACACCTC 58.110 50.000 0.00 0.00 45.16 3.85
460 461 1.369091 CCCTGCGATTCTTGTTCCCG 61.369 60.000 0.00 0.00 0.00 5.14
493 506 1.810151 TGACCGCAAAAATGAGTAGGC 59.190 47.619 0.00 0.00 0.00 3.93
502 517 2.045561 TGACCTCTTGACCGCAAAAA 57.954 45.000 0.00 0.00 32.73 1.94
535 550 6.287525 CCTGAATGCCTTTTCTTTTGGTAAA 58.712 36.000 0.00 0.00 0.00 2.01
536 551 5.221621 CCCTGAATGCCTTTTCTTTTGGTAA 60.222 40.000 0.00 0.00 0.00 2.85
537 552 4.283212 CCCTGAATGCCTTTTCTTTTGGTA 59.717 41.667 0.00 0.00 0.00 3.25
545 560 7.744087 AAATTTTTACCCTGAATGCCTTTTC 57.256 32.000 0.00 0.00 0.00 2.29
550 565 9.696917 CTATGATAAATTTTTACCCTGAATGCC 57.303 33.333 0.00 0.00 0.00 4.40
573 588 5.248477 TCTGGTTGCTCACTTTACTTCCTAT 59.752 40.000 0.00 0.00 0.00 2.57
577 592 5.297029 AGTTTCTGGTTGCTCACTTTACTTC 59.703 40.000 0.00 0.00 0.00 3.01
587 602 2.297701 TGGTTCAGTTTCTGGTTGCTC 58.702 47.619 0.00 0.00 31.51 4.26
589 604 2.223805 CCTTGGTTCAGTTTCTGGTTGC 60.224 50.000 0.00 0.00 31.51 4.17
593 608 2.654863 ACACCTTGGTTCAGTTTCTGG 58.345 47.619 0.00 0.00 31.51 3.86
621 637 4.692625 ACACTGACATTTTTCATCTCCTCG 59.307 41.667 0.00 0.00 0.00 4.63
622 638 6.876257 ACTACACTGACATTTTTCATCTCCTC 59.124 38.462 0.00 0.00 0.00 3.71
646 662 4.337555 AGATGCATTGCTCCTAATGAACAC 59.662 41.667 10.49 0.00 39.79 3.32
661 677 4.161754 TCTGTGAGATCACTGAGATGCATT 59.838 41.667 15.90 0.00 45.59 3.56
664 680 3.797451 TCTGTGAGATCACTGAGATGC 57.203 47.619 15.90 0.00 45.59 3.91
670 686 1.798446 GCGCTCTCTGTGAGATCACTG 60.798 57.143 13.74 12.94 46.55 3.66
671 687 0.455410 GCGCTCTCTGTGAGATCACT 59.545 55.000 13.74 0.00 46.55 3.41
672 688 0.172127 TGCGCTCTCTGTGAGATCAC 59.828 55.000 9.73 6.01 45.39 3.06
673 689 1.109609 ATGCGCTCTCTGTGAGATCA 58.890 50.000 9.73 7.22 45.39 2.92
674 690 2.222007 AATGCGCTCTCTGTGAGATC 57.778 50.000 9.73 2.17 45.39 2.75
703 725 2.614446 CCTCACAGTGTGCAGCAGC 61.614 63.158 18.80 0.00 42.57 5.25
704 726 2.614446 GCCTCACAGTGTGCAGCAG 61.614 63.158 24.16 14.90 33.62 4.24
779 801 2.602257 GCCATTGGCCTAATTTGTCC 57.398 50.000 17.28 0.00 44.06 4.02
805 827 2.495669 AGAGAGGTCTAGCTTTCTGTGC 59.504 50.000 0.00 0.00 0.00 4.57
812 834 6.462347 GCTGCTTAATTAGAGAGGTCTAGCTT 60.462 42.308 0.00 0.00 36.61 3.74
814 836 5.010617 AGCTGCTTAATTAGAGAGGTCTAGC 59.989 44.000 0.00 0.00 36.61 3.42
815 837 6.294508 GGAGCTGCTTAATTAGAGAGGTCTAG 60.295 46.154 2.53 0.00 36.61 2.43
819 841 3.068873 CGGAGCTGCTTAATTAGAGAGGT 59.931 47.826 2.53 0.00 0.00 3.85
856 883 3.498397 GCTCCGTGTGTATTTATGGATGG 59.502 47.826 0.00 0.00 31.89 3.51
857 884 3.184379 CGCTCCGTGTGTATTTATGGATG 59.816 47.826 0.00 0.00 31.89 3.51
858 885 3.390135 CGCTCCGTGTGTATTTATGGAT 58.610 45.455 0.00 0.00 31.89 3.41
859 886 2.816689 CGCTCCGTGTGTATTTATGGA 58.183 47.619 0.00 0.00 0.00 3.41
889 916 4.343581 GCAACTGCGACTGTGAGA 57.656 55.556 0.00 0.00 0.00 3.27
923 950 2.993264 AGCCTGCAATGGTGGTGC 60.993 61.111 0.00 0.00 42.55 5.01
943 976 1.941734 CGATCGACCGAGCTCAAGC 60.942 63.158 15.40 0.37 42.49 4.01
1056 1089 4.540735 CCCACGATGTACCCCCGC 62.541 72.222 0.00 0.00 0.00 6.13
1266 1299 1.142465 CACTTGGAGATGGAGATGGGG 59.858 57.143 0.00 0.00 0.00 4.96
1296 1329 0.744414 AATGATGGACGGGTCGCTTG 60.744 55.000 0.00 0.00 0.00 4.01
1306 1339 2.709475 GCGCCGTGAATGATGGAC 59.291 61.111 0.00 0.00 31.27 4.02
1309 1342 3.940640 CCGGCGCCGTGAATGATG 61.941 66.667 43.12 24.12 37.81 3.07
1379 1443 2.191354 CTCGTACAACACTCGCCGGA 62.191 60.000 5.05 0.00 0.00 5.14
1380 1444 1.800315 CTCGTACAACACTCGCCGG 60.800 63.158 0.00 0.00 0.00 6.13
1381 1445 2.434134 GCTCGTACAACACTCGCCG 61.434 63.158 0.00 0.00 0.00 6.46
1382 1446 2.092882 GGCTCGTACAACACTCGCC 61.093 63.158 0.00 0.00 34.38 5.54
1383 1447 2.092882 GGGCTCGTACAACACTCGC 61.093 63.158 0.00 0.00 0.00 5.03
1384 1448 1.445582 GGGGCTCGTACAACACTCG 60.446 63.158 0.00 0.00 0.00 4.18
1385 1449 1.445582 CGGGGCTCGTACAACACTC 60.446 63.158 0.00 0.00 0.00 3.51
1386 1450 2.654877 CGGGGCTCGTACAACACT 59.345 61.111 0.00 0.00 0.00 3.55
1387 1451 2.433664 CCGGGGCTCGTACAACAC 60.434 66.667 5.83 0.00 37.11 3.32
1388 1452 2.918802 ACCGGGGCTCGTACAACA 60.919 61.111 5.83 0.00 37.11 3.33
1389 1453 2.125793 GACCGGGGCTCGTACAAC 60.126 66.667 5.83 0.00 37.11 3.32
1390 1454 3.751246 CGACCGGGGCTCGTACAA 61.751 66.667 5.83 0.00 37.11 2.41
1391 1455 4.720902 TCGACCGGGGCTCGTACA 62.721 66.667 5.83 0.00 37.11 2.90
1392 1456 3.443045 TTCGACCGGGGCTCGTAC 61.443 66.667 5.83 0.00 37.11 3.67
1393 1457 3.443045 GTTCGACCGGGGCTCGTA 61.443 66.667 5.83 0.00 37.11 3.43
1395 1459 4.367023 TTGTTCGACCGGGGCTCG 62.367 66.667 6.32 6.49 38.88 5.03
1396 1460 2.240162 ATCTTGTTCGACCGGGGCTC 62.240 60.000 6.32 0.00 0.00 4.70
1397 1461 2.240162 GATCTTGTTCGACCGGGGCT 62.240 60.000 6.32 0.00 0.00 5.19
1398 1462 1.814169 GATCTTGTTCGACCGGGGC 60.814 63.158 6.32 0.00 0.00 5.80
1399 1463 1.518572 CGATCTTGTTCGACCGGGG 60.519 63.158 6.32 0.00 41.62 5.73
1400 1464 1.509463 TCGATCTTGTTCGACCGGG 59.491 57.895 6.32 0.00 42.81 5.73
1405 1469 4.731961 GCTTATTACGTCGATCTTGTTCGA 59.268 41.667 0.00 0.36 45.27 3.71
1406 1470 4.085721 GGCTTATTACGTCGATCTTGTTCG 60.086 45.833 0.00 0.00 40.46 3.95
1407 1471 4.802039 TGGCTTATTACGTCGATCTTGTTC 59.198 41.667 0.00 0.00 0.00 3.18
1445 1512 6.764308 ACTCCGTATTACTACTAGCACAAA 57.236 37.500 0.00 0.00 0.00 2.83
1446 1513 7.500227 ACATACTCCGTATTACTACTAGCACAA 59.500 37.037 0.00 0.00 0.00 3.33
1447 1514 6.994496 ACATACTCCGTATTACTACTAGCACA 59.006 38.462 0.00 0.00 0.00 4.57
1448 1515 7.432350 ACATACTCCGTATTACTACTAGCAC 57.568 40.000 0.00 0.00 0.00 4.40
1449 1516 9.159364 CATACATACTCCGTATTACTACTAGCA 57.841 37.037 0.00 0.00 0.00 3.49
1450 1517 9.160496 ACATACATACTCCGTATTACTACTAGC 57.840 37.037 0.00 0.00 0.00 3.42
1482 1552 6.173427 ACTACCACATCATGCATACATACA 57.827 37.500 0.00 0.00 33.67 2.29
1483 1553 8.777865 ATTACTACCACATCATGCATACATAC 57.222 34.615 0.00 0.00 33.67 2.39
1485 1555 9.964354 ATTATTACTACCACATCATGCATACAT 57.036 29.630 0.00 0.00 36.79 2.29
1486 1556 9.435688 GATTATTACTACCACATCATGCATACA 57.564 33.333 0.00 0.00 0.00 2.29
1487 1557 9.658799 AGATTATTACTACCACATCATGCATAC 57.341 33.333 0.00 0.00 0.00 2.39
1490 1560 9.710900 CTAAGATTATTACTACCACATCATGCA 57.289 33.333 0.00 0.00 0.00 3.96
1491 1561 8.660373 GCTAAGATTATTACTACCACATCATGC 58.340 37.037 0.00 0.00 0.00 4.06
1492 1562 9.935241 AGCTAAGATTATTACTACCACATCATG 57.065 33.333 0.00 0.00 0.00 3.07
1521 1594 1.294857 GCAGCTTCAACCTAGCTAGC 58.705 55.000 15.74 6.62 46.80 3.42
1522 1595 2.680312 TGCAGCTTCAACCTAGCTAG 57.320 50.000 14.20 14.20 46.80 3.42
1523 1596 3.273434 CAATGCAGCTTCAACCTAGCTA 58.727 45.455 0.00 0.00 46.80 3.32
1525 1598 1.468736 GCAATGCAGCTTCAACCTAGC 60.469 52.381 0.00 0.00 38.93 3.42
1547 1620 1.315690 CATCAGCTACCTGCCAATGG 58.684 55.000 0.00 0.00 44.23 3.16
1609 1682 2.777692 TCTCATGTTATTGGGTCCCTCC 59.222 50.000 10.00 0.00 0.00 4.30
1610 1683 3.181450 CCTCTCATGTTATTGGGTCCCTC 60.181 52.174 10.00 0.00 0.00 4.30
1748 1831 0.450184 ACGTACGCAATGGCAAATCC 59.550 50.000 16.72 0.00 41.24 3.01
1816 1900 4.915667 GCCTTGTTTTTCAATTACGAGTCC 59.084 41.667 0.00 0.00 35.35 3.85
1821 1905 8.459521 TCATAATGCCTTGTTTTTCAATTACG 57.540 30.769 0.00 0.00 35.35 3.18
1832 1916 6.543430 TTAGCCAAATCATAATGCCTTGTT 57.457 33.333 0.00 0.00 0.00 2.83
1834 1918 6.339730 TGTTTAGCCAAATCATAATGCCTTG 58.660 36.000 0.00 0.00 0.00 3.61
1835 1919 6.543430 TGTTTAGCCAAATCATAATGCCTT 57.457 33.333 0.00 0.00 0.00 4.35
1837 1921 7.790823 ATTTGTTTAGCCAAATCATAATGCC 57.209 32.000 0.00 0.00 40.15 4.40
1844 1928 7.975616 GCTTGAGATATTTGTTTAGCCAAATCA 59.024 33.333 2.67 0.00 42.49 2.57
1846 1930 7.839907 TGCTTGAGATATTTGTTTAGCCAAAT 58.160 30.769 4.73 4.73 44.81 2.32
1847 1931 7.225784 TGCTTGAGATATTTGTTTAGCCAAA 57.774 32.000 0.00 0.00 38.58 3.28
1848 1932 6.832520 TGCTTGAGATATTTGTTTAGCCAA 57.167 33.333 0.00 0.00 0.00 4.52
1850 1934 7.254218 GCAAATGCTTGAGATATTTGTTTAGCC 60.254 37.037 15.86 3.17 41.49 3.93
1878 2060 2.288825 ACAAACTTCATCTTCCTCGCGA 60.289 45.455 9.26 9.26 0.00 5.87
1879 2061 2.069273 ACAAACTTCATCTTCCTCGCG 58.931 47.619 0.00 0.00 0.00 5.87
1881 2063 4.787598 CCAAACAAACTTCATCTTCCTCG 58.212 43.478 0.00 0.00 0.00 4.63
1882 2064 4.279420 AGCCAAACAAACTTCATCTTCCTC 59.721 41.667 0.00 0.00 0.00 3.71
1883 2065 4.218312 AGCCAAACAAACTTCATCTTCCT 58.782 39.130 0.00 0.00 0.00 3.36
1884 2066 4.590850 AGCCAAACAAACTTCATCTTCC 57.409 40.909 0.00 0.00 0.00 3.46
1885 2067 8.419076 TTTTTAGCCAAACAAACTTCATCTTC 57.581 30.769 0.00 0.00 0.00 2.87
1927 2156 0.608640 GAGTCCCGACATCCAACACT 59.391 55.000 0.00 0.00 0.00 3.55
1937 2166 2.432628 CTTGGTGCGAGTCCCGAC 60.433 66.667 0.00 0.00 41.76 4.79
1950 2179 4.394300 TGTTTTTCAACAACAATGCCTTGG 59.606 37.500 6.67 0.00 40.10 3.61
1993 2222 9.881773 AGATTAACCCATGGTAAACATAATGAT 57.118 29.630 11.73 0.00 37.84 2.45
2056 2289 1.434513 AAGACCCAACCATCCTGCCA 61.435 55.000 0.00 0.00 0.00 4.92
2090 2323 5.261216 TGAATTGGGGAGTAATTTGAGGAC 58.739 41.667 0.00 0.00 0.00 3.85
2100 2333 1.992557 ACAGCCTTGAATTGGGGAGTA 59.007 47.619 0.00 0.00 0.00 2.59
2153 2426 1.115467 ACAGGTCAGGGAATAGCTCG 58.885 55.000 0.00 0.00 0.00 5.03
2184 2457 6.204688 TGTTTGATGGAAGTTGTATCACTGAC 59.795 38.462 0.00 0.00 31.11 3.51
2208 2481 4.070716 AGATTTGCAGAGAGAACAACCTG 58.929 43.478 0.00 0.00 0.00 4.00
2222 2495 1.144708 TGGTGAACCTCCAGATTTGCA 59.855 47.619 0.37 0.00 36.82 4.08
2236 2509 0.682852 CCGTGGTAGAACCTGGTGAA 59.317 55.000 0.00 0.00 39.58 3.18
2237 2510 0.470456 ACCGTGGTAGAACCTGGTGA 60.470 55.000 0.00 0.00 43.05 4.02
2238 2511 0.395312 AACCGTGGTAGAACCTGGTG 59.605 55.000 0.00 0.00 43.60 4.17
2239 2512 0.683412 GAACCGTGGTAGAACCTGGT 59.317 55.000 0.00 0.00 45.36 4.00
2240 2513 0.389426 CGAACCGTGGTAGAACCTGG 60.389 60.000 0.00 0.00 39.58 4.45
2241 2514 0.389426 CCGAACCGTGGTAGAACCTG 60.389 60.000 0.00 0.00 39.58 4.00
2242 2515 1.969862 CCGAACCGTGGTAGAACCT 59.030 57.895 0.00 0.00 39.58 3.50
2243 2516 1.739196 GCCGAACCGTGGTAGAACC 60.739 63.158 0.00 0.00 39.22 3.62
2244 2517 1.739196 GGCCGAACCGTGGTAGAAC 60.739 63.158 0.00 0.00 0.00 3.01
2245 2518 2.658422 GGCCGAACCGTGGTAGAA 59.342 61.111 0.00 0.00 0.00 2.10
2249 2522 3.912745 GATTGGGCCGAACCGTGGT 62.913 63.158 0.76 0.00 40.62 4.16
2254 2527 2.154462 CTATGATGATTGGGCCGAACC 58.846 52.381 0.76 0.00 37.93 3.62


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

AutoCloner maintained by Alex Coulton.