Multiple sequence alignment - TraesCS7D01G553800

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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 TraesCS7D01G553800 chr7D 100.000 3464 0 0 1 3464 638189671 638186208 0.000000e+00 6397.0
1 TraesCS7D01G553800 chr7D 96.491 570 15 2 1644 2213 237393376 237392812 0.000000e+00 937.0
2 TraesCS7D01G553800 chr7D 85.876 885 80 22 2455 3325 534148061 534148914 0.000000e+00 900.0
3 TraesCS7D01G553800 chr7D 94.426 592 12 7 1631 2213 237394725 237394146 0.000000e+00 891.0
4 TraesCS7D01G553800 chr7B 90.269 1151 87 9 2277 3422 734772830 734773960 0.000000e+00 1482.0
5 TraesCS7D01G553800 chr7B 89.111 551 39 9 1102 1645 734772195 734772731 0.000000e+00 665.0
6 TraesCS7D01G553800 chr7B 87.324 71 6 2 748 815 734772022 734772092 1.030000e-10 78.7
7 TraesCS7D01G553800 chr7A 91.094 786 37 13 872 1641 727897571 727898339 0.000000e+00 1033.0
8 TraesCS7D01G553800 chr7A 88.575 709 53 13 2331 3038 727898552 727899233 0.000000e+00 835.0
9 TraesCS7D01G553800 chr7A 79.965 569 72 28 196 742 727896890 727897438 7.020000e-102 381.0
10 TraesCS7D01G553800 chr7A 84.267 375 36 6 3049 3423 727899271 727899622 9.200000e-91 344.0
11 TraesCS7D01G553800 chr5D 86.328 885 78 18 2455 3325 52456661 52457516 0.000000e+00 924.0
12 TraesCS7D01G553800 chr2B 86.261 888 75 23 2455 3325 47319486 47318629 0.000000e+00 920.0
13 TraesCS7D01G553800 chr2B 85.892 886 81 18 2455 3325 593396892 593397748 0.000000e+00 904.0
14 TraesCS7D01G553800 chr2B 91.478 575 37 7 1644 2216 76077518 76078082 0.000000e+00 780.0
15 TraesCS7D01G553800 chr4A 85.198 885 86 20 2455 3325 563183510 563182657 0.000000e+00 867.0
16 TraesCS7D01G553800 chr6B 93.715 541 21 6 1098 1626 6148675 6148136 0.000000e+00 798.0
17 TraesCS7D01G553800 chr6B 92.950 539 27 5 1098 1626 79153063 79152526 0.000000e+00 774.0
18 TraesCS7D01G553800 chr6B 89.286 392 28 10 1644 2030 691454866 691455248 2.420000e-131 479.0
19 TraesCS7D01G553800 chr6B 88.804 393 28 12 1644 2030 691452939 691453321 5.230000e-128 468.0
20 TraesCS7D01G553800 chr6B 93.537 294 13 4 1924 2212 142409 142117 1.910000e-117 433.0
21 TraesCS7D01G553800 chr4B 90.104 576 44 8 1644 2213 19984946 19985514 0.000000e+00 736.0
22 TraesCS7D01G553800 chr5B 89.074 421 36 9 1756 2170 439966402 439965986 6.630000e-142 514.0
23 TraesCS7D01G553800 chr5B 86.874 419 52 2 1754 2170 439964374 439963957 1.880000e-127 466.0
24 TraesCS7D01G553800 chr5B 88.272 324 31 5 1895 2213 439967278 439966957 7.020000e-102 381.0
25 TraesCS7D01G553800 chr6A 90.104 384 33 2 1644 2025 10011240 10010860 8.640000e-136 494.0
26 TraesCS7D01G553800 chr1A 91.185 363 29 3 1644 2004 45690557 45690196 1.120000e-134 490.0
27 TraesCS7D01G553800 chr2D 85.507 483 39 18 1762 2219 524442176 524441700 3.130000e-130 475.0
28 TraesCS7D01G553800 chr1B 89.286 364 28 6 1644 2003 616024414 616024770 2.450000e-121 446.0
29 TraesCS7D01G553800 chrUn 83.599 439 43 11 2899 3325 274220449 274220028 5.420000e-103 385.0
30 TraesCS7D01G553800 chrUn 83.599 439 43 11 2899 3325 274228219 274227798 5.420000e-103 385.0
31 TraesCS7D01G553800 chrUn 83.484 442 44 11 2896 3325 291459048 291459472 5.420000e-103 385.0
32 TraesCS7D01G553800 chrUn 83.599 439 43 11 2899 3325 295626074 295625653 5.420000e-103 385.0
33 TraesCS7D01G553800 chr6D 83.951 81 9 4 117 195 376893672 376893750 1.330000e-09 75.0


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 TraesCS7D01G553800 chr7D 638186208 638189671 3463 True 6397.000000 6397 100.000000 1 3464 1 chr7D.!!$R1 3463
1 TraesCS7D01G553800 chr7D 237392812 237394725 1913 True 914.000000 937 95.458500 1631 2213 2 chr7D.!!$R2 582
2 TraesCS7D01G553800 chr7D 534148061 534148914 853 False 900.000000 900 85.876000 2455 3325 1 chr7D.!!$F1 870
3 TraesCS7D01G553800 chr7B 734772022 734773960 1938 False 741.900000 1482 88.901333 748 3422 3 chr7B.!!$F1 2674
4 TraesCS7D01G553800 chr7A 727896890 727899622 2732 False 648.250000 1033 85.975250 196 3423 4 chr7A.!!$F1 3227
5 TraesCS7D01G553800 chr5D 52456661 52457516 855 False 924.000000 924 86.328000 2455 3325 1 chr5D.!!$F1 870
6 TraesCS7D01G553800 chr2B 47318629 47319486 857 True 920.000000 920 86.261000 2455 3325 1 chr2B.!!$R1 870
7 TraesCS7D01G553800 chr2B 593396892 593397748 856 False 904.000000 904 85.892000 2455 3325 1 chr2B.!!$F2 870
8 TraesCS7D01G553800 chr2B 76077518 76078082 564 False 780.000000 780 91.478000 1644 2216 1 chr2B.!!$F1 572
9 TraesCS7D01G553800 chr4A 563182657 563183510 853 True 867.000000 867 85.198000 2455 3325 1 chr4A.!!$R1 870
10 TraesCS7D01G553800 chr6B 6148136 6148675 539 True 798.000000 798 93.715000 1098 1626 1 chr6B.!!$R2 528
11 TraesCS7D01G553800 chr6B 79152526 79153063 537 True 774.000000 774 92.950000 1098 1626 1 chr6B.!!$R3 528
12 TraesCS7D01G553800 chr6B 691452939 691455248 2309 False 473.500000 479 89.045000 1644 2030 2 chr6B.!!$F1 386
13 TraesCS7D01G553800 chr4B 19984946 19985514 568 False 736.000000 736 90.104000 1644 2213 1 chr4B.!!$F1 569
14 TraesCS7D01G553800 chr5B 439963957 439967278 3321 True 453.666667 514 88.073333 1754 2213 3 chr5B.!!$R1 459

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
766 837 0.249398 GCCCTCACCGTTACTGATGT 59.751 55.0 0.00 0.0 0.00 3.06 F
1287 1369 0.319900 AGCACGTCAAGGTACTGCTG 60.320 55.0 3.01 0.0 40.86 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1690 1793 0.376502 GGCGTCTGTACTCGACCTAC 59.623 60.0 9.34 0.0 0.0 3.18 R
3198 7836 0.543749 ATCTTTCCTCCCAAGCTCGG 59.456 55.0 0.00 0.0 0.0 4.63 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
29 30 7.546778 AATTGCAACCAATTTTTAAACTCGT 57.453 28.000 0.00 0.00 46.66 4.18
30 31 5.957910 TGCAACCAATTTTTAAACTCGTG 57.042 34.783 0.00 0.00 0.00 4.35
31 32 5.651530 TGCAACCAATTTTTAAACTCGTGA 58.348 33.333 0.00 0.00 0.00 4.35
32 33 5.746245 TGCAACCAATTTTTAAACTCGTGAG 59.254 36.000 0.00 0.00 0.00 3.51
33 34 5.746721 GCAACCAATTTTTAAACTCGTGAGT 59.253 36.000 0.00 0.00 44.94 3.41
47 48 5.748592 ACTCGTGAGTTTTAATTTGCAGAC 58.251 37.500 0.00 0.00 38.83 3.51
48 49 5.295787 ACTCGTGAGTTTTAATTTGCAGACA 59.704 36.000 0.00 0.00 38.83 3.41
49 50 5.747565 TCGTGAGTTTTAATTTGCAGACAG 58.252 37.500 0.00 0.00 0.00 3.51
50 51 5.295787 TCGTGAGTTTTAATTTGCAGACAGT 59.704 36.000 0.00 0.00 0.00 3.55
51 52 5.971202 CGTGAGTTTTAATTTGCAGACAGTT 59.029 36.000 0.00 0.00 0.00 3.16
52 53 6.472163 CGTGAGTTTTAATTTGCAGACAGTTT 59.528 34.615 0.00 0.00 0.00 2.66
53 54 7.009174 CGTGAGTTTTAATTTGCAGACAGTTTT 59.991 33.333 0.00 0.00 0.00 2.43
54 55 8.655970 GTGAGTTTTAATTTGCAGACAGTTTTT 58.344 29.630 0.00 0.00 0.00 1.94
55 56 8.868916 TGAGTTTTAATTTGCAGACAGTTTTTC 58.131 29.630 0.00 0.00 0.00 2.29
56 57 9.087424 GAGTTTTAATTTGCAGACAGTTTTTCT 57.913 29.630 0.00 0.00 0.00 2.52
61 62 7.858052 AATTTGCAGACAGTTTTTCTATTCG 57.142 32.000 0.00 0.00 0.00 3.34
62 63 6.371809 TTTGCAGACAGTTTTTCTATTCGT 57.628 33.333 0.00 0.00 0.00 3.85
63 64 7.485418 TTTGCAGACAGTTTTTCTATTCGTA 57.515 32.000 0.00 0.00 0.00 3.43
64 65 7.485418 TTGCAGACAGTTTTTCTATTCGTAA 57.515 32.000 0.00 0.00 0.00 3.18
65 66 7.485418 TGCAGACAGTTTTTCTATTCGTAAA 57.515 32.000 0.00 0.00 0.00 2.01
66 67 7.349711 TGCAGACAGTTTTTCTATTCGTAAAC 58.650 34.615 0.00 0.00 0.00 2.01
67 68 7.011576 TGCAGACAGTTTTTCTATTCGTAAACA 59.988 33.333 0.00 0.00 33.94 2.83
68 69 8.015658 GCAGACAGTTTTTCTATTCGTAAACAT 58.984 33.333 0.00 0.00 33.94 2.71
69 70 9.878599 CAGACAGTTTTTCTATTCGTAAACATT 57.121 29.630 0.00 0.00 33.94 2.71
92 93 5.549742 TTTTGGATTGGCAGACATTTTCT 57.450 34.783 0.00 0.00 33.33 2.52
93 94 6.662865 TTTTGGATTGGCAGACATTTTCTA 57.337 33.333 0.00 0.00 31.12 2.10
94 95 6.855763 TTTGGATTGGCAGACATTTTCTAT 57.144 33.333 0.00 0.00 31.12 1.98
95 96 7.953005 TTTGGATTGGCAGACATTTTCTATA 57.047 32.000 0.00 0.00 31.12 1.31
96 97 8.537728 TTTGGATTGGCAGACATTTTCTATAT 57.462 30.769 0.00 0.00 31.12 0.86
97 98 8.537728 TTGGATTGGCAGACATTTTCTATATT 57.462 30.769 0.00 0.00 31.12 1.28
98 99 8.169977 TGGATTGGCAGACATTTTCTATATTC 57.830 34.615 0.00 0.00 31.12 1.75
99 100 7.779326 TGGATTGGCAGACATTTTCTATATTCA 59.221 33.333 0.00 0.00 31.12 2.57
100 101 8.078596 GGATTGGCAGACATTTTCTATATTCAC 58.921 37.037 0.00 0.00 31.12 3.18
101 102 6.603237 TGGCAGACATTTTCTATATTCACG 57.397 37.500 0.00 0.00 31.12 4.35
102 103 6.345298 TGGCAGACATTTTCTATATTCACGA 58.655 36.000 0.00 0.00 31.12 4.35
103 104 6.992123 TGGCAGACATTTTCTATATTCACGAT 59.008 34.615 0.00 0.00 31.12 3.73
104 105 7.171508 TGGCAGACATTTTCTATATTCACGATC 59.828 37.037 0.00 0.00 31.12 3.69
105 106 7.171508 GGCAGACATTTTCTATATTCACGATCA 59.828 37.037 0.00 0.00 31.12 2.92
106 107 8.715998 GCAGACATTTTCTATATTCACGATCAT 58.284 33.333 0.00 0.00 31.12 2.45
138 139 9.597170 TGAAACAAACAATCTTTGAATTCATGA 57.403 25.926 9.40 11.10 35.78 3.07
141 142 8.369218 ACAAACAATCTTTGAATTCATGAACC 57.631 30.769 11.07 6.51 33.83 3.62
142 143 7.442062 ACAAACAATCTTTGAATTCATGAACCC 59.558 33.333 11.07 6.14 33.83 4.11
143 144 6.923199 ACAATCTTTGAATTCATGAACCCT 57.077 33.333 11.07 0.00 0.00 4.34
144 145 7.307131 ACAATCTTTGAATTCATGAACCCTT 57.693 32.000 11.07 0.81 0.00 3.95
145 146 7.738847 ACAATCTTTGAATTCATGAACCCTTT 58.261 30.769 11.07 0.39 0.00 3.11
146 147 8.212995 ACAATCTTTGAATTCATGAACCCTTTT 58.787 29.630 11.07 0.00 0.00 2.27
147 148 9.059260 CAATCTTTGAATTCATGAACCCTTTTT 57.941 29.630 11.07 0.00 0.00 1.94
148 149 8.837788 ATCTTTGAATTCATGAACCCTTTTTC 57.162 30.769 11.07 10.00 0.00 2.29
149 150 7.216494 TCTTTGAATTCATGAACCCTTTTTCC 58.784 34.615 11.07 0.00 0.00 3.13
150 151 6.491714 TTGAATTCATGAACCCTTTTTCCA 57.508 33.333 11.07 0.00 0.00 3.53
151 152 6.684897 TGAATTCATGAACCCTTTTTCCAT 57.315 33.333 11.07 0.00 0.00 3.41
152 153 7.077050 TGAATTCATGAACCCTTTTTCCATT 57.923 32.000 11.07 0.00 0.00 3.16
153 154 7.516452 TGAATTCATGAACCCTTTTTCCATTT 58.484 30.769 11.07 0.00 0.00 2.32
154 155 7.661027 TGAATTCATGAACCCTTTTTCCATTTC 59.339 33.333 11.07 6.47 0.00 2.17
155 156 6.491714 TTCATGAACCCTTTTTCCATTTCA 57.508 33.333 3.38 0.00 0.00 2.69
156 157 6.684897 TCATGAACCCTTTTTCCATTTCAT 57.315 33.333 0.00 0.00 34.73 2.57
157 158 6.465948 TCATGAACCCTTTTTCCATTTCATG 58.534 36.000 13.49 13.49 46.10 3.07
158 159 6.684897 ATGAACCCTTTTTCCATTTCATGA 57.315 33.333 0.00 0.00 33.49 3.07
159 160 6.491714 TGAACCCTTTTTCCATTTCATGAA 57.508 33.333 3.38 3.38 0.00 2.57
160 161 6.287525 TGAACCCTTTTTCCATTTCATGAAC 58.712 36.000 7.89 0.00 0.00 3.18
161 162 5.885449 ACCCTTTTTCCATTTCATGAACA 57.115 34.783 7.89 0.11 0.00 3.18
162 163 6.438186 ACCCTTTTTCCATTTCATGAACAT 57.562 33.333 7.89 2.64 0.00 2.71
163 164 6.232692 ACCCTTTTTCCATTTCATGAACATG 58.767 36.000 7.89 13.99 40.09 3.21
164 165 6.183361 ACCCTTTTTCCATTTCATGAACATGT 60.183 34.615 7.89 0.00 39.72 3.21
165 166 6.711645 CCCTTTTTCCATTTCATGAACATGTT 59.288 34.615 11.78 11.78 39.72 2.71
166 167 7.229106 CCCTTTTTCCATTTCATGAACATGTTT 59.771 33.333 13.36 0.00 39.72 2.83
167 168 8.623030 CCTTTTTCCATTTCATGAACATGTTTT 58.377 29.630 13.36 0.59 39.72 2.43
168 169 9.440784 CTTTTTCCATTTCATGAACATGTTTTG 57.559 29.630 13.36 13.44 39.72 2.44
169 170 7.493743 TTTCCATTTCATGAACATGTTTTGG 57.506 32.000 13.36 15.81 39.72 3.28
170 171 6.416631 TCCATTTCATGAACATGTTTTGGA 57.583 33.333 13.36 19.84 39.72 3.53
171 172 7.006865 TCCATTTCATGAACATGTTTTGGAT 57.993 32.000 13.36 8.82 39.72 3.41
172 173 7.451732 TCCATTTCATGAACATGTTTTGGATT 58.548 30.769 13.36 2.92 39.72 3.01
173 174 7.937942 TCCATTTCATGAACATGTTTTGGATTT 59.062 29.630 13.36 0.00 39.72 2.17
174 175 8.018520 CCATTTCATGAACATGTTTTGGATTTG 58.981 33.333 13.36 9.09 39.72 2.32
175 176 6.542574 TTCATGAACATGTTTTGGATTTGC 57.457 33.333 13.36 0.00 39.72 3.68
176 177 4.685165 TCATGAACATGTTTTGGATTTGCG 59.315 37.500 13.36 0.00 39.72 4.85
177 178 4.313277 TGAACATGTTTTGGATTTGCGA 57.687 36.364 13.36 0.00 0.00 5.10
178 179 4.686972 TGAACATGTTTTGGATTTGCGAA 58.313 34.783 13.36 0.00 0.00 4.70
179 180 4.505922 TGAACATGTTTTGGATTTGCGAAC 59.494 37.500 13.36 0.00 0.00 3.95
180 181 4.052159 ACATGTTTTGGATTTGCGAACA 57.948 36.364 0.00 0.00 35.04 3.18
181 182 4.630111 ACATGTTTTGGATTTGCGAACAT 58.370 34.783 0.00 0.00 40.46 2.71
182 183 5.055812 ACATGTTTTGGATTTGCGAACATT 58.944 33.333 0.00 0.00 38.48 2.71
183 184 5.526846 ACATGTTTTGGATTTGCGAACATTT 59.473 32.000 0.00 0.00 38.48 2.32
184 185 6.038050 ACATGTTTTGGATTTGCGAACATTTT 59.962 30.769 0.00 0.00 38.48 1.82
185 186 6.428385 TGTTTTGGATTTGCGAACATTTTT 57.572 29.167 0.00 0.00 0.00 1.94
209 210 9.814899 TTTTGAATTTGCTAACATCTTCTGAAA 57.185 25.926 0.00 0.00 0.00 2.69
211 212 8.975410 TGAATTTGCTAACATCTTCTGAAATG 57.025 30.769 9.50 9.50 0.00 2.32
213 214 9.630098 GAATTTGCTAACATCTTCTGAAATGAA 57.370 29.630 14.92 6.17 0.00 2.57
250 252 9.389755 TCATCCGTGAACATATTTTCAAATCTA 57.610 29.630 5.88 0.00 37.24 1.98
306 308 7.250569 TCAGGATAAGAATTGTTTGAATTCGC 58.749 34.615 0.04 0.00 40.56 4.70
314 316 5.745653 ATTGTTTGAATTCGCGAACATTC 57.254 34.783 26.00 23.74 40.73 2.67
328 332 4.563976 GCGAACATTCTTTGAATTCATGGG 59.436 41.667 9.40 2.96 0.00 4.00
348 353 5.708948 TGGGCATCTTTTAAATTCACGAAG 58.291 37.500 0.00 0.00 0.00 3.79
350 355 6.015856 TGGGCATCTTTTAAATTCACGAAGAA 60.016 34.615 0.00 0.00 41.28 2.52
414 425 9.829507 TCAAATCCATGAACAATTTGTAACTTT 57.170 25.926 1.76 0.00 39.96 2.66
415 426 9.866936 CAAATCCATGAACAATTTGTAACTTTG 57.133 29.630 1.76 3.69 36.24 2.77
418 429 8.417780 TCCATGAACAATTTGTAACTTTGTTG 57.582 30.769 1.76 0.00 42.07 3.33
488 514 7.231607 TGAAACAGTTTTTATAATCGACGAGC 58.768 34.615 3.01 0.00 0.00 5.03
489 515 6.715344 AACAGTTTTTATAATCGACGAGCA 57.285 33.333 3.01 0.00 0.00 4.26
490 516 6.715344 ACAGTTTTTATAATCGACGAGCAA 57.285 33.333 3.01 0.00 0.00 3.91
491 517 7.303634 ACAGTTTTTATAATCGACGAGCAAT 57.696 32.000 3.01 0.00 0.00 3.56
492 518 7.748847 ACAGTTTTTATAATCGACGAGCAATT 58.251 30.769 3.01 0.00 0.00 2.32
493 519 8.234546 ACAGTTTTTATAATCGACGAGCAATTT 58.765 29.630 3.01 0.00 0.00 1.82
494 520 9.061610 CAGTTTTTATAATCGACGAGCAATTTT 57.938 29.630 3.01 0.00 0.00 1.82
495 521 9.620660 AGTTTTTATAATCGACGAGCAATTTTT 57.379 25.926 3.01 0.00 0.00 1.94
496 522 9.656834 GTTTTTATAATCGACGAGCAATTTTTG 57.343 29.630 3.01 0.00 0.00 2.44
497 523 9.613957 TTTTTATAATCGACGAGCAATTTTTGA 57.386 25.926 3.01 0.00 0.00 2.69
498 524 9.613957 TTTTATAATCGACGAGCAATTTTTGAA 57.386 25.926 3.01 0.00 0.00 2.69
499 525 8.820628 TTATAATCGACGAGCAATTTTTGAAG 57.179 30.769 3.01 0.00 0.00 3.02
500 526 4.749245 ATCGACGAGCAATTTTTGAAGT 57.251 36.364 3.01 0.00 0.00 3.01
501 527 4.128554 TCGACGAGCAATTTTTGAAGTC 57.871 40.909 0.00 0.00 0.00 3.01
502 528 3.558006 TCGACGAGCAATTTTTGAAGTCA 59.442 39.130 0.00 0.00 32.99 3.41
503 529 4.213270 TCGACGAGCAATTTTTGAAGTCAT 59.787 37.500 0.00 0.00 32.99 3.06
504 530 4.319115 CGACGAGCAATTTTTGAAGTCATG 59.681 41.667 0.00 0.00 32.99 3.07
505 531 5.437289 ACGAGCAATTTTTGAAGTCATGA 57.563 34.783 0.00 0.00 0.00 3.07
506 532 5.830912 ACGAGCAATTTTTGAAGTCATGAA 58.169 33.333 0.00 0.00 0.00 2.57
507 533 6.449698 ACGAGCAATTTTTGAAGTCATGAAT 58.550 32.000 0.00 0.00 0.00 2.57
508 534 7.592938 ACGAGCAATTTTTGAAGTCATGAATA 58.407 30.769 0.00 0.00 0.00 1.75
509 535 8.246180 ACGAGCAATTTTTGAAGTCATGAATAT 58.754 29.630 0.00 0.00 0.00 1.28
510 536 9.079833 CGAGCAATTTTTGAAGTCATGAATATT 57.920 29.630 0.00 0.00 0.00 1.28
512 538 9.715121 AGCAATTTTTGAAGTCATGAATATTGT 57.285 25.926 12.88 0.00 0.00 2.71
685 719 7.428020 TGACAAACAAAAGATGAAATGAGGAG 58.572 34.615 0.00 0.00 0.00 3.69
687 721 8.010733 ACAAACAAAAGATGAAATGAGGAGAA 57.989 30.769 0.00 0.00 0.00 2.87
691 725 7.006509 ACAAAAGATGAAATGAGGAGAAAGGA 58.993 34.615 0.00 0.00 0.00 3.36
716 750 1.940613 AGAAAAACAGACGTGCACTCC 59.059 47.619 16.19 6.25 0.00 3.85
758 827 4.047125 CCATGGGCCCTCACCGTT 62.047 66.667 25.70 0.00 0.00 4.44
766 837 0.249398 GCCCTCACCGTTACTGATGT 59.751 55.000 0.00 0.00 0.00 3.06
775 846 2.344441 CCGTTACTGATGTGTACGCTTG 59.656 50.000 8.10 0.00 35.62 4.01
814 888 4.680537 ACGCGACCTCCTCACCCT 62.681 66.667 15.93 0.00 0.00 4.34
818 892 2.760385 GACCTCCTCACCCTCCCG 60.760 72.222 0.00 0.00 0.00 5.14
819 893 4.400251 ACCTCCTCACCCTCCCGG 62.400 72.222 0.00 0.00 37.81 5.73
902 982 2.041686 GGCGACTCCTCTCGTCTGT 61.042 63.158 0.00 0.00 35.34 3.41
903 983 1.135731 GCGACTCCTCTCGTCTGTG 59.864 63.158 0.00 0.00 35.99 3.66
904 984 1.797441 CGACTCCTCTCGTCTGTGG 59.203 63.158 0.00 0.00 0.00 4.17
906 986 0.609681 GACTCCTCTCGTCTGTGGGT 60.610 60.000 0.00 0.00 0.00 4.51
908 988 2.219325 CTCCTCTCGTCTGTGGGTGC 62.219 65.000 0.00 0.00 0.00 5.01
919 1001 1.979693 GTGGGTGCGTCCTCTCTCT 60.980 63.158 0.00 0.00 36.25 3.10
925 1007 0.681564 TGCGTCCTCTCTCTTCTCCC 60.682 60.000 0.00 0.00 0.00 4.30
951 1033 2.438434 CCTGGGTTCGGTCCATGC 60.438 66.667 0.00 0.00 33.29 4.06
954 1036 0.680921 CTGGGTTCGGTCCATGCATT 60.681 55.000 0.00 0.00 33.29 3.56
956 1038 1.384222 GGGTTCGGTCCATGCATTCC 61.384 60.000 0.00 0.00 0.00 3.01
989 1071 2.039418 TGCTGACACTCACAGTACCTT 58.961 47.619 0.00 0.00 37.64 3.50
1039 1121 2.158957 TGTTCTTGTCTTCTCACGCCTT 60.159 45.455 0.00 0.00 0.00 4.35
1080 1162 4.824515 CGGAGGCCCCTCTCGAGT 62.825 72.222 13.13 0.00 42.38 4.18
1081 1163 2.835895 GGAGGCCCCTCTCGAGTC 60.836 72.222 13.13 0.00 42.38 3.36
1082 1164 2.277404 GAGGCCCCTCTCGAGTCT 59.723 66.667 13.13 0.00 39.80 3.24
1083 1165 1.826487 GAGGCCCCTCTCGAGTCTC 60.826 68.421 13.13 0.00 39.80 3.36
1096 1178 1.945776 GAGTCTCGAAGCAAACGCGG 61.946 60.000 12.47 0.00 0.00 6.46
1260 1342 1.460305 CCCCCTCACCATCTCCGAT 60.460 63.158 0.00 0.00 0.00 4.18
1287 1369 0.319900 AGCACGTCAAGGTACTGCTG 60.320 55.000 3.01 0.00 40.86 4.41
1427 1530 5.007234 TCCTTGTCATTTAGAACGTGTGTTG 59.993 40.000 0.00 0.00 38.78 3.33
1690 1793 0.316937 GACCAACATGTGTGTGCGTG 60.317 55.000 0.00 0.00 38.92 5.34
1732 1835 4.530857 GTGGCCGCGTCCATAGCT 62.531 66.667 13.92 0.00 38.57 3.32
1752 1855 0.250597 GTGGTCAGTTAGCCGGGTTT 60.251 55.000 13.43 0.00 0.00 3.27
1889 5375 4.611564 AGTCCAGGTAAGGTAGAGTCAT 57.388 45.455 0.00 0.00 0.00 3.06
2136 5625 5.244178 TGTGTCTCCTCTTTCTTCTACCTTC 59.756 44.000 0.00 0.00 0.00 3.46
2137 5626 5.244178 GTGTCTCCTCTTTCTTCTACCTTCA 59.756 44.000 0.00 0.00 0.00 3.02
2138 5627 6.019748 TGTCTCCTCTTTCTTCTACCTTCAT 58.980 40.000 0.00 0.00 0.00 2.57
2139 5628 6.498651 TGTCTCCTCTTTCTTCTACCTTCATT 59.501 38.462 0.00 0.00 0.00 2.57
2153 5676 2.416027 CCTTCATTCGTGCGAGAGAGAA 60.416 50.000 0.00 0.00 0.00 2.87
2216 5739 2.358003 GCTCTGCGCCAACAGACT 60.358 61.111 4.18 0.00 41.72 3.24
2218 5741 2.666190 TCTGCGCCAACAGACTGC 60.666 61.111 4.18 0.00 41.72 4.40
2231 5844 2.103771 ACAGACTGCACTCATGTTGACT 59.896 45.455 1.25 0.00 0.00 3.41
2235 5848 5.410746 CAGACTGCACTCATGTTGACTAATT 59.589 40.000 0.00 0.00 0.00 1.40
2255 6383 8.955794 ACTAATTTAGGGCTTATTTCCTGGATA 58.044 33.333 8.26 0.00 34.75 2.59
2289 6434 5.355350 AGCTGTTAATCATAGCTGAAACACC 59.645 40.000 0.00 0.00 45.40 4.16
2310 6455 2.092681 CGTGAACGATGTCAGATTGTGG 59.907 50.000 0.00 0.00 43.02 4.17
2333 6478 9.051679 GTGGATTATGCAAAAATAAATAACCCC 57.948 33.333 0.00 0.00 0.00 4.95
2339 6540 8.876303 ATGCAAAAATAAATAACCCCAAACAT 57.124 26.923 0.00 0.00 0.00 2.71
2341 6542 9.965902 TGCAAAAATAAATAACCCCAAACATAT 57.034 25.926 0.00 0.00 0.00 1.78
2379 6580 6.872920 TGTACTTCTGTTTTTGCCATCTTTT 58.127 32.000 0.00 0.00 0.00 2.27
2413 6841 1.762708 AACTGGTGTTGGTGTTCTGG 58.237 50.000 0.00 0.00 34.71 3.86
2476 6904 8.688151 TGTGGTTTTAACTGCTATTAACTTTGT 58.312 29.630 0.00 0.00 0.00 2.83
2517 7101 8.378565 CAAGTGATGGGGTTATATCTGATTACT 58.621 37.037 0.00 0.00 0.00 2.24
2518 7102 8.140112 AGTGATGGGGTTATATCTGATTACTC 57.860 38.462 0.00 0.00 0.00 2.59
2520 7104 7.181125 GTGATGGGGTTATATCTGATTACTCCT 59.819 40.741 13.74 4.14 30.51 3.69
2523 7107 8.840200 TGGGGTTATATCTGATTACTCCTATC 57.160 38.462 13.74 0.00 30.51 2.08
2525 7109 8.697292 GGGGTTATATCTGATTACTCCTATCAC 58.303 40.741 0.00 0.00 0.00 3.06
2526 7110 9.256228 GGGTTATATCTGATTACTCCTATCACA 57.744 37.037 0.00 0.00 0.00 3.58
2652 7239 9.959721 AGTAATTATCACATGTTAGTTTCCAGT 57.040 29.630 0.00 0.00 0.00 4.00
2854 7445 7.887381 TCTTTTTGTTAGAGTTGGTGTTTTCA 58.113 30.769 0.00 0.00 0.00 2.69
2880 7484 4.023963 GGGTTCTTTTCAGTTGACAGCTAC 60.024 45.833 0.00 0.00 0.00 3.58
2932 7536 0.679002 CCCAGGAATGGCACTGTCTG 60.679 60.000 0.00 0.00 32.90 3.51
2957 7561 2.685202 GGGTACTGAAGCCTGGAGT 58.315 57.895 0.00 0.00 42.89 3.85
2958 7562 0.984995 GGGTACTGAAGCCTGGAGTT 59.015 55.000 0.00 0.00 42.89 3.01
2959 7563 2.185387 GGGTACTGAAGCCTGGAGTTA 58.815 52.381 0.00 0.00 42.89 2.24
2960 7564 2.772515 GGGTACTGAAGCCTGGAGTTAT 59.227 50.000 0.00 0.00 42.89 1.89
2961 7565 3.200165 GGGTACTGAAGCCTGGAGTTATT 59.800 47.826 0.00 0.00 42.89 1.40
2962 7566 4.443621 GGTACTGAAGCCTGGAGTTATTC 58.556 47.826 0.00 0.00 0.00 1.75
3030 7635 2.703798 CGGTTGATGCAGCCAAGGG 61.704 63.158 0.00 0.00 34.32 3.95
3038 7643 0.185901 TGCAGCCAAGGGAAAGAAGT 59.814 50.000 0.00 0.00 0.00 3.01
3040 7645 1.986882 CAGCCAAGGGAAAGAAGTGT 58.013 50.000 0.00 0.00 0.00 3.55
3056 7686 4.980805 GTGGAACAGGTGGCGCGA 62.981 66.667 12.10 0.00 41.80 5.87
3073 7704 0.309302 CGACTGATGCTAGACCTCCG 59.691 60.000 0.00 0.00 0.00 4.63
3078 7709 2.370647 GATGCTAGACCTCCGGTGCC 62.371 65.000 0.00 0.00 35.25 5.01
3088 7719 1.228124 TCCGGTGCCCAACAAAGAG 60.228 57.895 0.00 0.00 0.00 2.85
3091 7722 1.247567 CGGTGCCCAACAAAGAGATT 58.752 50.000 0.00 0.00 0.00 2.40
3102 7733 8.903820 GCCCAACAAAGAGATTAATAGTACAAT 58.096 33.333 0.00 0.00 0.00 2.71
3123 7754 1.119684 GTGTTTGGGGCCAATATCCC 58.880 55.000 4.39 0.00 43.42 3.85
3128 7759 0.991355 TGGGGCCAATATCCCGAAGT 60.991 55.000 4.39 0.00 46.03 3.01
3148 7779 6.502074 AAGTAGGGTTCTAATCCAGATTCC 57.498 41.667 0.00 0.00 31.77 3.01
3158 7789 0.909610 TCCAGATTCCGAGTGCCCTT 60.910 55.000 0.00 0.00 0.00 3.95
3191 7829 4.196778 TGGTTGGCAAGCGTCCCA 62.197 61.111 22.82 13.07 0.00 4.37
3198 7836 1.090052 GGCAAGCGTCCCATACTGAC 61.090 60.000 0.00 0.00 0.00 3.51
3206 7844 0.824109 TCCCATACTGACCGAGCTTG 59.176 55.000 0.00 0.00 0.00 4.01
3257 7895 3.244561 TGAAGACCTGAGGTGTTTCATCC 60.245 47.826 15.68 2.99 39.34 3.51
3262 7900 3.117512 ACCTGAGGTGTTTCATCCAGTTT 60.118 43.478 1.77 0.00 32.98 2.66
3276 7914 3.173151 TCCAGTTTGACAGCTAGGATCA 58.827 45.455 0.00 0.00 0.00 2.92
3282 7920 5.104610 AGTTTGACAGCTAGGATCACATCAT 60.105 40.000 0.00 0.00 0.00 2.45
3292 7930 4.676109 AGGATCACATCATGGGAAACAAA 58.324 39.130 0.00 0.00 31.08 2.83
3300 7939 4.163441 TCATGGGAAACAAACTCTCACA 57.837 40.909 0.00 0.00 0.00 3.58
3305 7944 3.498777 GGGAAACAAACTCTCACAGCTAC 59.501 47.826 0.00 0.00 0.00 3.58
3423 8062 7.327975 TCGATTGGTAATGATGTAGTGACTTT 58.672 34.615 0.00 0.00 0.00 2.66
3424 8063 7.822334 TCGATTGGTAATGATGTAGTGACTTTT 59.178 33.333 0.00 0.00 0.00 2.27
3426 8065 9.559958 GATTGGTAATGATGTAGTGACTTTTTG 57.440 33.333 0.00 0.00 0.00 2.44
3427 8066 8.458573 TTGGTAATGATGTAGTGACTTTTTGT 57.541 30.769 0.00 0.00 0.00 2.83
3428 8067 8.458573 TGGTAATGATGTAGTGACTTTTTGTT 57.541 30.769 0.00 0.00 0.00 2.83
3429 8068 8.349245 TGGTAATGATGTAGTGACTTTTTGTTG 58.651 33.333 0.00 0.00 0.00 3.33
3431 8070 9.730420 GTAATGATGTAGTGACTTTTTGTTGTT 57.270 29.630 0.00 0.00 0.00 2.83
3434 8073 7.471721 TGATGTAGTGACTTTTTGTTGTTGAG 58.528 34.615 0.00 0.00 0.00 3.02
3436 8075 5.941058 TGTAGTGACTTTTTGTTGTTGAGGA 59.059 36.000 0.00 0.00 0.00 3.71
3437 8076 5.975693 AGTGACTTTTTGTTGTTGAGGAA 57.024 34.783 0.00 0.00 0.00 3.36
3438 8077 5.709966 AGTGACTTTTTGTTGTTGAGGAAC 58.290 37.500 0.00 0.00 0.00 3.62
3441 8080 5.072040 ACTTTTTGTTGTTGAGGAACTGG 57.928 39.130 0.00 0.00 41.55 4.00
3442 8081 3.518634 TTTTGTTGTTGAGGAACTGGC 57.481 42.857 0.00 0.00 41.55 4.85
3443 8082 2.136298 TTGTTGTTGAGGAACTGGCA 57.864 45.000 0.00 0.00 41.55 4.92
3444 8083 1.679139 TGTTGTTGAGGAACTGGCAG 58.321 50.000 14.16 14.16 41.55 4.85
3445 8084 1.211703 TGTTGTTGAGGAACTGGCAGA 59.788 47.619 23.66 0.00 41.55 4.26
3446 8085 2.158623 TGTTGTTGAGGAACTGGCAGAT 60.159 45.455 23.66 9.90 41.55 2.90
3447 8086 2.189594 TGTTGAGGAACTGGCAGATG 57.810 50.000 23.66 0.00 41.55 2.90
3448 8087 1.699083 TGTTGAGGAACTGGCAGATGA 59.301 47.619 23.66 0.00 41.55 2.92
3449 8088 2.079925 GTTGAGGAACTGGCAGATGAC 58.920 52.381 23.66 8.26 41.55 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.267084 ACGAGTTTAAAAATTGGTTGCAATTAT 57.733 25.926 0.59 0.00 34.06 1.28
4 5 8.543774 CACGAGTTTAAAAATTGGTTGCAATTA 58.456 29.630 0.59 0.00 34.06 1.40
6 7 6.758886 TCACGAGTTTAAAAATTGGTTGCAAT 59.241 30.769 0.59 0.00 0.00 3.56
7 8 6.100004 TCACGAGTTTAAAAATTGGTTGCAA 58.900 32.000 0.00 0.00 0.00 4.08
24 25 5.295787 TGTCTGCAAATTAAAACTCACGAGT 59.704 36.000 0.00 0.00 44.94 4.18
25 26 5.747565 TGTCTGCAAATTAAAACTCACGAG 58.252 37.500 0.00 0.00 0.00 4.18
26 27 5.295787 ACTGTCTGCAAATTAAAACTCACGA 59.704 36.000 0.00 0.00 0.00 4.35
27 28 5.510671 ACTGTCTGCAAATTAAAACTCACG 58.489 37.500 0.00 0.00 0.00 4.35
28 29 7.755582 AAACTGTCTGCAAATTAAAACTCAC 57.244 32.000 0.00 0.00 0.00 3.51
29 30 8.770438 AAAAACTGTCTGCAAATTAAAACTCA 57.230 26.923 0.00 0.00 0.00 3.41
30 31 9.087424 AGAAAAACTGTCTGCAAATTAAAACTC 57.913 29.630 0.00 0.00 0.00 3.01
35 36 9.393249 CGAATAGAAAAACTGTCTGCAAATTAA 57.607 29.630 0.00 0.00 0.00 1.40
36 37 8.564574 ACGAATAGAAAAACTGTCTGCAAATTA 58.435 29.630 0.00 0.00 0.00 1.40
37 38 7.425606 ACGAATAGAAAAACTGTCTGCAAATT 58.574 30.769 0.00 0.00 0.00 1.82
38 39 6.970484 ACGAATAGAAAAACTGTCTGCAAAT 58.030 32.000 0.00 0.00 0.00 2.32
39 40 6.371809 ACGAATAGAAAAACTGTCTGCAAA 57.628 33.333 0.00 0.00 0.00 3.68
40 41 7.485418 TTACGAATAGAAAAACTGTCTGCAA 57.515 32.000 0.00 0.00 0.00 4.08
41 42 7.011576 TGTTTACGAATAGAAAAACTGTCTGCA 59.988 33.333 0.00 0.00 33.57 4.41
42 43 7.349711 TGTTTACGAATAGAAAAACTGTCTGC 58.650 34.615 0.00 0.00 33.57 4.26
43 44 9.878599 AATGTTTACGAATAGAAAAACTGTCTG 57.121 29.630 0.00 0.00 33.57 3.51
69 70 5.927819 AGAAAATGTCTGCCAATCCAAAAA 58.072 33.333 0.00 0.00 34.29 1.94
70 71 5.549742 AGAAAATGTCTGCCAATCCAAAA 57.450 34.783 0.00 0.00 34.29 2.44
71 72 6.855763 ATAGAAAATGTCTGCCAATCCAAA 57.144 33.333 0.00 0.00 37.12 3.28
72 73 8.537728 AATATAGAAAATGTCTGCCAATCCAA 57.462 30.769 0.00 0.00 37.12 3.53
73 74 7.779326 TGAATATAGAAAATGTCTGCCAATCCA 59.221 33.333 0.00 0.00 37.12 3.41
74 75 8.078596 GTGAATATAGAAAATGTCTGCCAATCC 58.921 37.037 0.00 0.00 37.12 3.01
75 76 7.800380 CGTGAATATAGAAAATGTCTGCCAATC 59.200 37.037 0.00 0.00 37.12 2.67
76 77 7.498900 TCGTGAATATAGAAAATGTCTGCCAAT 59.501 33.333 0.00 0.00 37.12 3.16
77 78 6.821160 TCGTGAATATAGAAAATGTCTGCCAA 59.179 34.615 0.00 0.00 37.12 4.52
78 79 6.345298 TCGTGAATATAGAAAATGTCTGCCA 58.655 36.000 0.00 0.00 37.12 4.92
79 80 6.844696 TCGTGAATATAGAAAATGTCTGCC 57.155 37.500 0.00 0.00 37.12 4.85
80 81 8.076714 TGATCGTGAATATAGAAAATGTCTGC 57.923 34.615 0.00 0.00 37.12 4.26
112 113 9.597170 TCATGAATTCAAAGATTGTTTGTTTCA 57.403 25.926 13.09 19.25 37.21 2.69
115 116 8.829612 GGTTCATGAATTCAAAGATTGTTTGTT 58.170 29.630 13.09 0.00 0.00 2.83
116 117 7.442062 GGGTTCATGAATTCAAAGATTGTTTGT 59.558 33.333 13.09 0.00 0.00 2.83
117 118 7.658575 AGGGTTCATGAATTCAAAGATTGTTTG 59.341 33.333 13.09 2.91 0.00 2.93
118 119 7.738847 AGGGTTCATGAATTCAAAGATTGTTT 58.261 30.769 13.09 0.00 0.00 2.83
119 120 7.307131 AGGGTTCATGAATTCAAAGATTGTT 57.693 32.000 13.09 0.00 0.00 2.83
120 121 6.923199 AGGGTTCATGAATTCAAAGATTGT 57.077 33.333 13.09 0.00 0.00 2.71
121 122 8.611654 AAAAGGGTTCATGAATTCAAAGATTG 57.388 30.769 13.09 5.94 0.00 2.67
122 123 9.276590 GAAAAAGGGTTCATGAATTCAAAGATT 57.723 29.630 13.09 3.46 0.00 2.40
123 124 7.879677 GGAAAAAGGGTTCATGAATTCAAAGAT 59.120 33.333 13.09 0.00 0.00 2.40
124 125 7.147585 TGGAAAAAGGGTTCATGAATTCAAAGA 60.148 33.333 13.09 10.81 0.00 2.52
125 126 6.991531 TGGAAAAAGGGTTCATGAATTCAAAG 59.008 34.615 13.09 8.51 0.00 2.77
126 127 6.893583 TGGAAAAAGGGTTCATGAATTCAAA 58.106 32.000 13.09 0.00 0.00 2.69
127 128 6.491714 TGGAAAAAGGGTTCATGAATTCAA 57.508 33.333 13.09 0.81 0.00 2.69
128 129 6.684897 ATGGAAAAAGGGTTCATGAATTCA 57.315 33.333 12.12 11.26 0.00 2.57
129 130 7.661027 TGAAATGGAAAAAGGGTTCATGAATTC 59.339 33.333 12.12 9.75 0.00 2.17
130 131 7.516452 TGAAATGGAAAAAGGGTTCATGAATT 58.484 30.769 12.12 0.00 0.00 2.17
131 132 7.077050 TGAAATGGAAAAAGGGTTCATGAAT 57.923 32.000 12.12 0.00 0.00 2.57
132 133 6.491714 TGAAATGGAAAAAGGGTTCATGAA 57.508 33.333 3.38 3.38 0.00 2.57
133 134 6.684897 ATGAAATGGAAAAAGGGTTCATGA 57.315 33.333 0.00 0.00 35.09 3.07
134 135 6.465948 TCATGAAATGGAAAAAGGGTTCATG 58.534 36.000 14.90 14.90 46.73 3.07
135 136 6.684897 TCATGAAATGGAAAAAGGGTTCAT 57.315 33.333 0.00 0.00 46.73 2.57
136 137 6.126940 TGTTCATGAAATGGAAAAAGGGTTCA 60.127 34.615 10.35 0.00 46.73 3.18
137 138 6.287525 TGTTCATGAAATGGAAAAAGGGTTC 58.712 36.000 10.35 0.00 46.73 3.62
138 139 6.245890 TGTTCATGAAATGGAAAAAGGGTT 57.754 33.333 10.35 0.00 46.73 4.11
139 140 5.885449 TGTTCATGAAATGGAAAAAGGGT 57.115 34.783 10.35 0.00 46.73 4.34
140 141 6.232692 ACATGTTCATGAAATGGAAAAAGGG 58.767 36.000 22.95 6.49 46.73 3.95
141 142 7.733402 AACATGTTCATGAAATGGAAAAAGG 57.267 32.000 22.95 0.36 46.73 3.11
142 143 9.440784 CAAAACATGTTCATGAAATGGAAAAAG 57.559 29.630 22.95 11.54 46.73 2.27
143 144 8.404000 CCAAAACATGTTCATGAAATGGAAAAA 58.596 29.630 22.95 0.00 46.73 1.94
144 145 7.772292 TCCAAAACATGTTCATGAAATGGAAAA 59.228 29.630 22.95 10.44 46.73 2.29
145 146 7.278135 TCCAAAACATGTTCATGAAATGGAAA 58.722 30.769 22.95 10.87 46.73 3.13
146 147 6.824553 TCCAAAACATGTTCATGAAATGGAA 58.175 32.000 22.95 13.35 46.73 3.53
147 148 6.416631 TCCAAAACATGTTCATGAAATGGA 57.583 33.333 22.95 20.01 46.73 3.41
148 149 7.675962 AATCCAAAACATGTTCATGAAATGG 57.324 32.000 22.95 18.55 46.73 3.16
150 151 7.571613 CGCAAATCCAAAACATGTTCATGAAAT 60.572 33.333 20.21 12.76 0.00 2.17
151 152 6.292757 CGCAAATCCAAAACATGTTCATGAAA 60.293 34.615 20.21 11.48 0.00 2.69
152 153 5.177142 CGCAAATCCAAAACATGTTCATGAA 59.823 36.000 20.21 3.38 0.00 2.57
153 154 4.685165 CGCAAATCCAAAACATGTTCATGA 59.315 37.500 20.21 13.59 0.00 3.07
154 155 4.685165 TCGCAAATCCAAAACATGTTCATG 59.315 37.500 12.39 13.61 0.00 3.07
155 156 4.880759 TCGCAAATCCAAAACATGTTCAT 58.119 34.783 12.39 0.93 0.00 2.57
156 157 4.313277 TCGCAAATCCAAAACATGTTCA 57.687 36.364 12.39 0.00 0.00 3.18
157 158 4.505922 TGTTCGCAAATCCAAAACATGTTC 59.494 37.500 12.39 0.00 0.00 3.18
158 159 4.437239 TGTTCGCAAATCCAAAACATGTT 58.563 34.783 4.92 4.92 0.00 2.71
159 160 4.052159 TGTTCGCAAATCCAAAACATGT 57.948 36.364 0.00 0.00 0.00 3.21
160 161 5.594724 AATGTTCGCAAATCCAAAACATG 57.405 34.783 0.00 0.00 39.71 3.21
161 162 6.616774 AAAATGTTCGCAAATCCAAAACAT 57.383 29.167 0.00 0.00 41.09 2.71
162 163 6.428385 AAAAATGTTCGCAAATCCAAAACA 57.572 29.167 0.00 0.00 34.64 2.83
182 183 9.814899 TTCAGAAGATGTTAGCAAATTCAAAAA 57.185 25.926 8.95 0.40 0.00 1.94
183 184 9.814899 TTTCAGAAGATGTTAGCAAATTCAAAA 57.185 25.926 8.95 6.70 0.00 2.44
184 185 9.985730 ATTTCAGAAGATGTTAGCAAATTCAAA 57.014 25.926 8.95 3.87 0.00 2.69
185 186 9.414295 CATTTCAGAAGATGTTAGCAAATTCAA 57.586 29.630 8.95 0.00 0.00 2.69
186 187 8.795513 TCATTTCAGAAGATGTTAGCAAATTCA 58.204 29.630 8.95 0.00 0.00 2.57
187 188 9.630098 TTCATTTCAGAAGATGTTAGCAAATTC 57.370 29.630 0.00 0.60 0.00 2.17
188 189 9.635520 CTTCATTTCAGAAGATGTTAGCAAATT 57.364 29.630 0.00 0.00 46.18 1.82
189 190 9.017509 TCTTCATTTCAGAAGATGTTAGCAAAT 57.982 29.630 2.50 0.00 46.62 2.32
190 191 8.394971 TCTTCATTTCAGAAGATGTTAGCAAA 57.605 30.769 2.50 0.00 46.62 3.68
191 192 7.984422 TCTTCATTTCAGAAGATGTTAGCAA 57.016 32.000 2.50 0.00 46.62 3.91
220 221 9.534565 TTTGAAAATATGTTCACGGATGAAAAA 57.465 25.926 7.88 0.00 46.40 1.94
227 228 9.389755 TCATAGATTTGAAAATATGTTCACGGA 57.610 29.630 7.88 0.00 37.24 4.69
281 283 7.250569 GCGAATTCAAACAATTCTTATCCTGA 58.749 34.615 6.22 0.00 35.17 3.86
286 288 7.081349 TGTTCGCGAATTCAAACAATTCTTAT 58.919 30.769 26.23 0.00 35.17 1.73
290 292 5.745653 ATGTTCGCGAATTCAAACAATTC 57.254 34.783 26.23 7.76 35.46 2.17
291 293 5.920273 AGAATGTTCGCGAATTCAAACAATT 59.080 32.000 27.69 16.06 35.46 2.32
295 297 5.398122 TCAAAGAATGTTCGCGAATTCAAAC 59.602 36.000 27.69 16.28 35.63 2.93
306 308 4.563976 GCCCATGAATTCAAAGAATGTTCG 59.436 41.667 13.09 0.00 0.00 3.95
314 316 8.550710 TTTAAAAGATGCCCATGAATTCAAAG 57.449 30.769 13.09 8.19 0.00 2.77
348 353 9.453325 AATTCATGTTCACAATTGCAAAAATTC 57.547 25.926 1.71 0.00 0.00 2.17
350 355 8.622157 TGAATTCATGTTCACAATTGCAAAAAT 58.378 25.926 1.71 0.00 33.41 1.82
388 398 9.829507 AAAGTTACAAATTGTTCATGGATTTGA 57.170 25.926 20.87 9.77 41.14 2.69
463 489 7.095565 TGCTCGTCGATTATAAAAACTGTTTCA 60.096 33.333 6.20 0.00 0.00 2.69
464 490 7.231607 TGCTCGTCGATTATAAAAACTGTTTC 58.768 34.615 6.20 0.00 0.00 2.78
467 493 6.715344 TTGCTCGTCGATTATAAAAACTGT 57.285 33.333 0.00 0.00 0.00 3.55
476 502 6.842163 ACTTCAAAAATTGCTCGTCGATTAT 58.158 32.000 0.00 0.00 0.00 1.28
477 503 6.073494 TGACTTCAAAAATTGCTCGTCGATTA 60.073 34.615 0.00 0.00 0.00 1.75
480 506 3.558006 TGACTTCAAAAATTGCTCGTCGA 59.442 39.130 0.00 0.00 0.00 4.20
657 691 7.707893 CCTCATTTCATCTTTTGTTTGTCAGTT 59.292 33.333 0.00 0.00 0.00 3.16
660 694 7.285172 TCTCCTCATTTCATCTTTTGTTTGTCA 59.715 33.333 0.00 0.00 0.00 3.58
664 698 8.146412 CCTTTCTCCTCATTTCATCTTTTGTTT 58.854 33.333 0.00 0.00 0.00 2.83
699 733 0.180406 AGGGAGTGCACGTCTGTTTT 59.820 50.000 12.01 0.00 0.00 2.43
742 778 1.451387 GTAACGGTGAGGGCCCATG 60.451 63.158 27.56 10.97 0.00 3.66
744 780 2.203877 AGTAACGGTGAGGGCCCA 60.204 61.111 27.56 0.00 0.00 5.36
755 791 2.222508 GCAAGCGTACACATCAGTAACG 60.223 50.000 0.00 0.00 38.57 3.18
758 827 1.548719 AGGCAAGCGTACACATCAGTA 59.451 47.619 0.00 0.00 0.00 2.74
785 859 3.754530 TCGCGTGCCGATCCAAGA 61.755 61.111 5.77 0.00 41.89 3.02
820 894 3.827898 GAGGGTGAGGAGGTCGCG 61.828 72.222 0.00 0.00 36.43 5.87
821 895 3.462678 GGAGGGTGAGGAGGTCGC 61.463 72.222 0.00 0.00 34.63 5.19
822 896 2.760385 GGGAGGGTGAGGAGGTCG 60.760 72.222 0.00 0.00 0.00 4.79
823 897 2.760385 CGGGAGGGTGAGGAGGTC 60.760 72.222 0.00 0.00 0.00 3.85
882 956 3.126225 GACGAGAGGAGTCGCCGT 61.126 66.667 0.00 0.00 44.06 5.68
902 982 1.228894 AAGAGAGAGGACGCACCCA 60.229 57.895 0.00 0.00 40.05 4.51
903 983 0.968393 AGAAGAGAGAGGACGCACCC 60.968 60.000 0.00 0.00 40.05 4.61
904 984 0.454196 GAGAAGAGAGAGGACGCACC 59.546 60.000 0.00 0.00 39.35 5.01
906 986 0.681564 GGGAGAAGAGAGAGGACGCA 60.682 60.000 0.00 0.00 0.00 5.24
908 988 1.720694 GCGGGAGAAGAGAGAGGACG 61.721 65.000 0.00 0.00 0.00 4.79
919 1001 4.332543 AGGGAGGTGGCGGGAGAA 62.333 66.667 0.00 0.00 0.00 2.87
925 1007 4.410400 GAACCCAGGGAGGTGGCG 62.410 72.222 14.54 0.00 40.05 5.69
939 1021 1.721487 CGGAATGCATGGACCGAAC 59.279 57.895 25.59 2.03 46.94 3.95
951 1033 3.644805 GCAATGATGTTTTGCGGAATG 57.355 42.857 0.00 0.00 39.98 2.67
959 1041 4.338964 TGTGAGTGTCAGCAATGATGTTTT 59.661 37.500 0.00 0.00 0.00 2.43
963 1045 3.072211 ACTGTGAGTGTCAGCAATGATG 58.928 45.455 0.00 0.00 36.50 3.07
968 1050 2.039418 AGGTACTGTGAGTGTCAGCAA 58.961 47.619 0.00 0.00 37.18 3.91
989 1071 4.112634 CTCGGCAAATCGAAGTATTCTGA 58.887 43.478 0.00 0.00 44.75 3.27
1076 1158 1.412606 GCGTTTGCTTCGAGACTCG 59.587 57.895 18.91 18.91 38.67 4.18
1077 1159 1.412606 CGCGTTTGCTTCGAGACTC 59.587 57.895 0.00 0.00 39.65 3.36
1078 1160 2.022129 CCGCGTTTGCTTCGAGACT 61.022 57.895 4.92 0.00 39.65 3.24
1079 1161 2.470286 CCGCGTTTGCTTCGAGAC 59.530 61.111 4.92 0.00 39.65 3.36
1080 1162 2.736995 CCCGCGTTTGCTTCGAGA 60.737 61.111 4.92 0.00 39.65 4.04
1081 1163 3.041940 ACCCGCGTTTGCTTCGAG 61.042 61.111 4.92 0.00 39.65 4.04
1082 1164 3.342627 CACCCGCGTTTGCTTCGA 61.343 61.111 4.92 0.00 39.65 3.71
1083 1165 3.645975 ACACCCGCGTTTGCTTCG 61.646 61.111 4.92 0.00 39.65 3.79
1260 1342 0.817634 CCTTGACGTGCTCCCAAACA 60.818 55.000 0.00 0.00 0.00 2.83
1287 1369 1.066002 TCTTGCACAAGTTTCAGCAGC 59.934 47.619 10.05 0.00 38.35 5.25
1427 1530 2.937149 GCCCTACGTCCTGAAGAAAATC 59.063 50.000 0.00 0.00 0.00 2.17
1605 1708 1.613630 TCCCTGTTGAGCTCCCTCC 60.614 63.158 12.15 0.00 37.29 4.30
1690 1793 0.376502 GGCGTCTGTACTCGACCTAC 59.623 60.000 9.34 0.00 0.00 3.18
1732 1835 1.412453 AACCCGGCTAACTGACCACA 61.412 55.000 0.00 0.00 0.00 4.17
1752 1855 1.153469 TCGCTCTGCAACACACACA 60.153 52.632 0.00 0.00 0.00 3.72
1889 5375 2.073056 CACGCATGCACTAACTAACCA 58.927 47.619 19.57 0.00 0.00 3.67
2136 5625 2.851235 CTCTTTCTCTCTCGCACGAATG 59.149 50.000 0.00 0.00 0.00 2.67
2137 5626 2.750166 TCTCTTTCTCTCTCGCACGAAT 59.250 45.455 0.00 0.00 0.00 3.34
2138 5627 2.152016 TCTCTTTCTCTCTCGCACGAA 58.848 47.619 0.00 0.00 0.00 3.85
2139 5628 1.735018 CTCTCTTTCTCTCTCGCACGA 59.265 52.381 0.00 0.00 0.00 4.35
2153 5676 1.037030 CAGCTCCCTCTCGCTCTCTT 61.037 60.000 0.00 0.00 33.45 2.85
2203 5726 3.279116 GTGCAGTCTGTTGGCGCA 61.279 61.111 10.83 0.00 37.93 6.09
2216 5739 5.647658 CCCTAAATTAGTCAACATGAGTGCA 59.352 40.000 0.00 0.00 31.49 4.57
2218 5741 5.882557 AGCCCTAAATTAGTCAACATGAGTG 59.117 40.000 0.00 0.00 31.49 3.51
2231 5844 9.753674 CATATCCAGGAAATAAGCCCTAAATTA 57.246 33.333 0.00 0.00 0.00 1.40
2235 5848 6.780198 ACATATCCAGGAAATAAGCCCTAA 57.220 37.500 0.00 0.00 0.00 2.69
2255 6383 7.989741 AGCTATGATTAACAGCTTTGTCTACAT 59.010 33.333 0.00 0.00 31.02 2.29
2289 6434 2.092681 CCACAATCTGACATCGTTCACG 59.907 50.000 0.00 0.00 41.45 4.35
2350 6551 2.604614 GCAAAAACAGAAGTACAGCGGG 60.605 50.000 0.00 0.00 0.00 6.13
2379 6580 2.092429 ACCAGTTTCAGGAAGAAGCACA 60.092 45.455 0.00 0.00 39.64 4.57
2413 6841 3.579685 GCCGAGGCCAAAGTTCTC 58.420 61.111 5.01 0.00 34.56 2.87
2476 6904 6.884295 CCCATCACTTGAAGTAAGGTTATTGA 59.116 38.462 0.00 0.00 40.84 2.57
2491 7075 8.378565 AGTAATCAGATATAACCCCATCACTTG 58.621 37.037 0.00 0.00 0.00 3.16
2494 7078 7.181125 AGGAGTAATCAGATATAACCCCATCAC 59.819 40.741 0.00 0.00 0.00 3.06
2517 7101 6.318648 GCAAATGGTTACAAGATGTGATAGGA 59.681 38.462 0.00 0.00 0.00 2.94
2518 7102 6.095300 TGCAAATGGTTACAAGATGTGATAGG 59.905 38.462 0.00 0.00 0.00 2.57
2520 7104 6.095300 CCTGCAAATGGTTACAAGATGTGATA 59.905 38.462 0.00 0.00 0.00 2.15
2523 7107 4.022068 ACCTGCAAATGGTTACAAGATGTG 60.022 41.667 0.00 0.00 33.34 3.21
2525 7109 4.218200 TGACCTGCAAATGGTTACAAGATG 59.782 41.667 0.00 0.00 38.03 2.90
2526 7110 4.406456 TGACCTGCAAATGGTTACAAGAT 58.594 39.130 0.00 0.00 38.03 2.40
2527 7111 3.826524 TGACCTGCAAATGGTTACAAGA 58.173 40.909 0.00 0.00 38.03 3.02
2528 7112 4.022068 ACATGACCTGCAAATGGTTACAAG 60.022 41.667 0.00 0.00 38.03 3.16
2529 7113 3.894427 ACATGACCTGCAAATGGTTACAA 59.106 39.130 0.00 0.00 38.03 2.41
2838 7429 3.201266 ACCCAGTGAAAACACCAACTCTA 59.799 43.478 0.00 0.00 0.00 2.43
2854 7445 3.947834 CTGTCAACTGAAAAGAACCCAGT 59.052 43.478 0.00 0.00 42.34 4.00
2861 7452 5.294306 CACAAGTAGCTGTCAACTGAAAAGA 59.706 40.000 0.00 0.00 0.00 2.52
2932 7536 1.348036 AGGCTTCAGTACCCTTGTCAC 59.652 52.381 0.00 0.00 0.00 3.67
2940 7544 4.162509 AGAATAACTCCAGGCTTCAGTACC 59.837 45.833 0.00 0.00 0.00 3.34
2957 7561 7.056006 TGCTGCATCTCTTGGAATAAGAATAA 58.944 34.615 0.00 0.00 0.00 1.40
2958 7562 6.594744 TGCTGCATCTCTTGGAATAAGAATA 58.405 36.000 0.00 0.00 0.00 1.75
2959 7563 5.443283 TGCTGCATCTCTTGGAATAAGAAT 58.557 37.500 0.00 0.00 0.00 2.40
2960 7564 4.847198 TGCTGCATCTCTTGGAATAAGAA 58.153 39.130 0.00 0.00 0.00 2.52
2961 7565 4.449131 CTGCTGCATCTCTTGGAATAAGA 58.551 43.478 1.31 0.00 0.00 2.10
2962 7566 3.003482 GCTGCTGCATCTCTTGGAATAAG 59.997 47.826 11.11 0.00 39.41 1.73
3030 7635 2.618709 CCACCTGTTCCACACTTCTTTC 59.381 50.000 0.00 0.00 0.00 2.62
3040 7645 4.980805 GTCGCGCCACCTGTTCCA 62.981 66.667 0.00 0.00 0.00 3.53
3088 7719 7.704899 GCCCCAAACACAATTGTACTATTAATC 59.295 37.037 11.53 0.00 33.55 1.75
3091 7722 5.419471 GGCCCCAAACACAATTGTACTATTA 59.581 40.000 11.53 0.00 33.55 0.98
3102 7733 2.183679 GGATATTGGCCCCAAACACAA 58.816 47.619 0.00 0.00 39.55 3.33
3123 7754 5.793030 ATCTGGATTAGAACCCTACTTCG 57.207 43.478 0.00 0.00 39.30 3.79
3128 7759 4.811498 TCGGAATCTGGATTAGAACCCTA 58.189 43.478 0.00 0.00 39.30 3.53
3148 7779 2.031516 CAGTCAGCAAGGGCACTCG 61.032 63.158 0.00 0.00 44.61 4.18
3158 7789 2.519622 CCAGGTCCCACAGTCAGCA 61.520 63.158 0.00 0.00 0.00 4.41
3191 7829 1.115467 CTCCCAAGCTCGGTCAGTAT 58.885 55.000 0.00 0.00 0.00 2.12
3198 7836 0.543749 ATCTTTCCTCCCAAGCTCGG 59.456 55.000 0.00 0.00 0.00 4.63
3206 7844 1.039785 GCCTTGGCATCTTTCCTCCC 61.040 60.000 6.79 0.00 0.00 4.30
3257 7895 3.930336 TGTGATCCTAGCTGTCAAACTG 58.070 45.455 0.00 0.00 0.00 3.16
3262 7900 3.070590 CCATGATGTGATCCTAGCTGTCA 59.929 47.826 0.00 0.00 0.00 3.58
3276 7914 4.520492 GTGAGAGTTTGTTTCCCATGATGT 59.480 41.667 0.00 0.00 0.00 3.06
3282 7920 2.092429 AGCTGTGAGAGTTTGTTTCCCA 60.092 45.455 0.00 0.00 0.00 4.37
3292 7930 4.073549 AGTTAGTTCGTAGCTGTGAGAGT 58.926 43.478 0.00 0.00 0.00 3.24
3300 7939 2.492484 CCTGACCAGTTAGTTCGTAGCT 59.508 50.000 0.00 0.00 0.00 3.32
3305 7944 2.296471 ACTGTCCTGACCAGTTAGTTCG 59.704 50.000 0.00 0.00 0.00 3.95
3423 8062 2.426738 CTGCCAGTTCCTCAACAACAAA 59.573 45.455 0.00 0.00 34.60 2.83
3424 8063 2.023673 CTGCCAGTTCCTCAACAACAA 58.976 47.619 0.00 0.00 34.60 2.83
3426 8065 1.967319 TCTGCCAGTTCCTCAACAAC 58.033 50.000 0.00 0.00 34.60 3.32
3427 8066 2.106338 TCATCTGCCAGTTCCTCAACAA 59.894 45.455 0.00 0.00 34.60 2.83
3428 8067 1.699083 TCATCTGCCAGTTCCTCAACA 59.301 47.619 0.00 0.00 34.60 3.33
3429 8068 2.079925 GTCATCTGCCAGTTCCTCAAC 58.920 52.381 0.00 0.00 0.00 3.18
3431 8070 1.277273 CAGTCATCTGCCAGTTCCTCA 59.723 52.381 0.00 0.00 34.79 3.86


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

AutoCloner maintained by Alex Coulton.