Multiple sequence alignment - TraesCS1B01G400500

Loading Multiple Alignment...

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 TraesCS1B01G400500 chr1B 100.000 4889 0 0 1 4889 631068762 631063874 0.000000e+00 9029.0
1 TraesCS1B01G400500 chr1B 88.095 378 41 3 519 894 631068190 631067815 3.470000e-121 446.0
2 TraesCS1B01G400500 chr1B 88.095 378 41 3 573 948 631068244 631067869 3.470000e-121 446.0
3 TraesCS1B01G400500 chr1B 88.037 326 33 4 519 842 631068136 631067815 9.930000e-102 381.0
4 TraesCS1B01G400500 chr1B 83.117 154 22 4 1172 1322 266925417 266925569 2.370000e-28 137.0
5 TraesCS1B01G400500 chr1B 96.875 32 1 0 2008 2039 30547337 30547306 2.000000e-03 54.7
6 TraesCS1B01G400500 chr5D 92.430 3025 180 27 1410 4414 27468730 27471725 0.000000e+00 4272.0
7 TraesCS1B01G400500 chr5D 85.680 1243 173 3 2651 3889 27489483 27488242 0.000000e+00 1304.0
8 TraesCS1B01G400500 chr5D 93.059 778 48 3 573 1344 27467621 27468398 0.000000e+00 1133.0
9 TraesCS1B01G400500 chr5D 90.355 591 36 12 307 894 27467424 27467996 0.000000e+00 756.0
10 TraesCS1B01G400500 chr5D 90.244 451 33 3 4440 4889 27472000 27472440 3.280000e-161 579.0
11 TraesCS1B01G400500 chr5D 96.907 97 3 0 208 304 27467274 27467370 3.920000e-36 163.0
12 TraesCS1B01G400500 chr5D 100.000 36 0 0 1369 1404 27468399 27468434 3.160000e-07 67.6
13 TraesCS1B01G400500 chr5D 91.892 37 3 0 1999 2035 331253995 331254031 9.000000e-03 52.8
14 TraesCS1B01G400500 chr5A 91.425 2484 169 25 1474 3929 18796064 18798531 0.000000e+00 3367.0
15 TraesCS1B01G400500 chr5A 83.092 1242 198 7 2654 3893 18814038 18812807 0.000000e+00 1120.0
16 TraesCS1B01G400500 chr5A 90.537 782 51 9 573 1343 18794963 18795732 0.000000e+00 1013.0
17 TraesCS1B01G400500 chr5A 85.619 598 39 17 307 894 18794771 18795331 7.050000e-163 584.0
18 TraesCS1B01G400500 chr5A 94.712 208 11 0 1 208 227534020 227534227 1.700000e-84 324.0
19 TraesCS1B01G400500 chr5A 90.233 215 20 1 519 732 18795115 18795329 3.730000e-71 279.0
20 TraesCS1B01G400500 chr5A 94.845 97 5 0 208 304 18794363 18794459 8.480000e-33 152.0
21 TraesCS1B01G400500 chr5A 74.231 260 55 9 4576 4831 18798632 18798883 1.120000e-16 99.0
22 TraesCS1B01G400500 chr5A 78.226 124 23 4 4653 4775 702253785 702253665 5.250000e-10 76.8
23 TraesCS1B01G400500 chr5A 97.619 42 1 0 1410 1451 18796020 18796061 6.790000e-09 73.1
24 TraesCS1B01G400500 chr5A 100.000 36 0 0 1364 1399 18795729 18795764 3.160000e-07 67.6
25 TraesCS1B01G400500 chr5B 95.277 1461 68 1 2430 3889 20654218 20652758 0.000000e+00 2314.0
26 TraesCS1B01G400500 chr5B 90.439 1391 110 17 627 2011 20658639 20657266 0.000000e+00 1810.0
27 TraesCS1B01G400500 chr5B 93.892 966 35 12 3122 4075 20166539 20167492 0.000000e+00 1435.0
28 TraesCS1B01G400500 chr5B 92.815 849 55 3 2281 3128 20154431 20155274 0.000000e+00 1225.0
29 TraesCS1B01G400500 chr5B 84.121 1228 181 10 2668 3893 20730214 20731429 0.000000e+00 1175.0
30 TraesCS1B01G400500 chr5B 94.148 769 33 4 4121 4889 20167488 20168244 0.000000e+00 1160.0
31 TraesCS1B01G400500 chr5B 91.763 777 59 3 573 1344 20149334 20150110 0.000000e+00 1075.0
32 TraesCS1B01G400500 chr5B 88.099 647 53 10 1411 2046 20150444 20151077 0.000000e+00 747.0
33 TraesCS1B01G400500 chr5B 87.838 592 38 10 307 894 20149148 20149709 0.000000e+00 664.0
34 TraesCS1B01G400500 chr5B 94.419 430 18 2 2007 2436 20654819 20654396 0.000000e+00 656.0
35 TraesCS1B01G400500 chr5B 89.729 516 25 7 3837 4332 20172987 20173494 6.900000e-178 634.0
36 TraesCS1B01G400500 chr5B 85.686 510 31 12 336 842 20658787 20658317 2.630000e-137 499.0
37 TraesCS1B01G400500 chr5B 88.272 324 34 4 627 948 20149334 20149655 7.680000e-103 385.0
38 TraesCS1B01G400500 chr5B 93.590 234 12 2 2031 2264 20151767 20151997 3.620000e-91 346.0
39 TraesCS1B01G400500 chr5B 89.697 165 17 0 4700 4864 20173743 20173907 1.380000e-50 211.0
40 TraesCS1B01G400500 chr5B 85.714 98 7 6 209 304 20659543 20659451 4.030000e-16 97.1
41 TraesCS1B01G400500 chr5B 73.188 276 62 8 4339 4611 474970668 474970402 6.740000e-14 89.8
42 TraesCS1B01G400500 chr5B 100.000 36 0 0 1369 1404 20150111 20150146 3.160000e-07 67.6
43 TraesCS1B01G400500 chr7B 84.128 1216 183 6 2683 3893 163505577 163504367 0.000000e+00 1168.0
44 TraesCS1B01G400500 chr7B 87.209 86 6 5 4517 4600 8935437 8935355 5.210000e-15 93.5
45 TraesCS1B01G400500 chr7D 83.539 1215 188 8 2685 3893 199413453 199412245 0.000000e+00 1125.0
46 TraesCS1B01G400500 chr7D 83.974 156 18 5 1172 1324 265693084 265693235 5.100000e-30 143.0
47 TraesCS1B01G400500 chr7D 82.911 158 22 3 1172 1324 265692831 265692988 2.370000e-28 137.0
48 TraesCS1B01G400500 chr7D 81.013 158 17 10 1569 1716 197675599 197675445 4.000000e-21 113.0
49 TraesCS1B01G400500 chr7D 97.059 34 0 1 2010 2043 335391343 335391375 6.840000e-04 56.5
50 TraesCS1B01G400500 chr2B 95.775 213 7 2 1 212 782691726 782691515 4.690000e-90 342.0
51 TraesCS1B01G400500 chr2B 95.146 206 10 0 1 206 215925185 215925390 4.720000e-85 326.0
52 TraesCS1B01G400500 chr2B 87.097 62 6 1 4263 4324 23019198 23019139 8.780000e-08 69.4
53 TraesCS1B01G400500 chr6A 95.631 206 9 0 1 206 182323137 182322932 1.010000e-86 331.0
54 TraesCS1B01G400500 chr6A 78.832 137 21 7 4654 4788 140076110 140076240 8.720000e-13 86.1
55 TraesCS1B01G400500 chr6A 89.655 58 5 1 4654 4711 329059607 329059663 6.790000e-09 73.1
56 TraesCS1B01G400500 chr6A 94.595 37 2 0 1999 2035 39925606 39925570 1.900000e-04 58.4
57 TraesCS1B01G400500 chr7A 94.660 206 11 0 1 206 700181971 700182176 2.200000e-83 320.0
58 TraesCS1B01G400500 chr7A 94.258 209 12 0 1 209 700528272 700528064 2.200000e-83 320.0
59 TraesCS1B01G400500 chr7A 76.190 336 42 24 1433 1744 515032842 515033163 5.100000e-30 143.0
60 TraesCS1B01G400500 chr7A 93.617 47 1 1 1505 1551 549377777 549377821 8.780000e-08 69.4
61 TraesCS1B01G400500 chr7A 91.892 37 3 0 1999 2035 546229448 546229484 9.000000e-03 52.8
62 TraesCS1B01G400500 chr3A 94.258 209 12 0 1 209 1769124 1768916 2.200000e-83 320.0
63 TraesCS1B01G400500 chr3A 82.166 157 26 2 1168 1322 208074169 208074013 3.070000e-27 134.0
64 TraesCS1B01G400500 chr3A 76.536 179 37 3 4653 4831 691901386 691901213 5.210000e-15 93.5
65 TraesCS1B01G400500 chr2A 94.660 206 11 0 1 206 752550991 752551196 2.200000e-83 320.0
66 TraesCS1B01G400500 chr2A 82.609 115 19 1 4211 4324 392754529 392754643 3.110000e-17 100.0
67 TraesCS1B01G400500 chr2A 83.824 68 10 1 4262 4329 392756951 392757017 4.090000e-06 63.9
68 TraesCS1B01G400500 chrUn 94.231 208 12 0 1 208 184017018 184017225 7.900000e-83 318.0
69 TraesCS1B01G400500 chr6B 85.333 150 17 5 1176 1322 209587535 209587388 3.050000e-32 150.0
70 TraesCS1B01G400500 chr4A 78.090 178 38 1 4654 4831 713387791 713387967 1.440000e-20 111.0
71 TraesCS1B01G400500 chr4A 89.474 57 4 2 4654 4709 740195623 740195678 2.440000e-08 71.3
72 TraesCS1B01G400500 chr3D 76.056 213 34 15 1569 1776 433734396 433734596 1.450000e-15 95.3
73 TraesCS1B01G400500 chr2D 81.579 114 21 0 4209 4322 325338907 325338794 1.450000e-15 95.3


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 TraesCS1B01G400500 chr1B 631063874 631068762 4888 True 2575.500000 9029 91.056750 1 4889 4 chr1B.!!$R2 4888
1 TraesCS1B01G400500 chr5D 27488242 27489483 1241 True 1304.000000 1304 85.680000 2651 3889 1 chr5D.!!$R1 1238
2 TraesCS1B01G400500 chr5D 27467274 27472440 5166 False 1161.766667 4272 93.832500 208 4889 6 chr5D.!!$F2 4681
3 TraesCS1B01G400500 chr5A 18812807 18814038 1231 True 1120.000000 1120 83.092000 2654 3893 1 chr5A.!!$R1 1239
4 TraesCS1B01G400500 chr5A 18794363 18798883 4520 False 704.337500 3367 90.563625 208 4831 8 chr5A.!!$F2 4623
5 TraesCS1B01G400500 chr5B 20166539 20168244 1705 False 1297.500000 1435 94.020000 3122 4889 2 chr5B.!!$F3 1767
6 TraesCS1B01G400500 chr5B 20730214 20731429 1215 False 1175.000000 1175 84.121000 2668 3893 1 chr5B.!!$F1 1225
7 TraesCS1B01G400500 chr5B 20652758 20659543 6785 True 1075.220000 2314 90.307000 209 3889 5 chr5B.!!$R2 3680
8 TraesCS1B01G400500 chr5B 20149148 20155274 6126 False 644.228571 1225 91.768143 307 3128 7 chr5B.!!$F2 2821
9 TraesCS1B01G400500 chr5B 20172987 20173907 920 False 422.500000 634 89.713000 3837 4864 2 chr5B.!!$F4 1027
10 TraesCS1B01G400500 chr7B 163504367 163505577 1210 True 1168.000000 1168 84.128000 2683 3893 1 chr7B.!!$R2 1210
11 TraesCS1B01G400500 chr7D 199412245 199413453 1208 True 1125.000000 1125 83.539000 2685 3893 1 chr7D.!!$R2 1208

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
288 291 0.253044 ATCGGGTCCCATCACTTGTG 59.747 55.0 9.12 0.0 0.0 3.33 F
450 1348 0.390340 GAGATCACAAGGACGCTGCA 60.390 55.0 0.00 0.0 0.0 4.41 F
978 1938 0.529378 GGAAGGAGAAGCGACCGTAA 59.471 55.0 0.00 0.0 0.0 3.18 F
1950 3221 0.594602 CGTGGTGTGTAGTTCTCCGA 59.405 55.0 0.00 0.0 0.0 4.55 F
3135 10173 0.108804 CCAACCTGTCACGCTACGAT 60.109 55.0 0.00 0.0 0.0 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 6471 0.391130 CAGTACTGCCCAGCGCTAAA 60.391 55.0 10.99 0.00 38.78 1.85 R
2245 6673 1.178276 GAACGCTGGAGGAGAAGAGA 58.822 55.0 0.00 0.00 0.00 3.10 R
2727 9765 0.450583 TGTCGCAGATGTCGTACCTC 59.549 55.0 0.00 0.00 40.67 3.85 R
3667 10723 0.250684 ATGTGTTGCACCATCACCGA 60.251 50.0 0.00 0.00 34.35 4.69 R
4126 11205 0.800631 ATGTCATGCACGTGCTCAAG 59.199 50.0 37.59 24.35 42.66 3.02 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 8.924511 TTAAATGAAGAAAGAGATGGTTGAGT 57.075 30.769 0.00 0.00 0.00 3.41
34 35 8.729805 AATGAAGAAAGAGATGGTTGAGTATC 57.270 34.615 0.00 0.00 0.00 2.24
68 69 9.438291 GATACCGTATCATAATAAATGCAATGC 57.562 33.333 12.83 0.00 35.28 3.56
69 70 7.452880 ACCGTATCATAATAAATGCAATGCT 57.547 32.000 6.82 0.00 0.00 3.79
70 71 8.560355 ACCGTATCATAATAAATGCAATGCTA 57.440 30.769 6.82 0.00 0.00 3.49
71 72 8.450964 ACCGTATCATAATAAATGCAATGCTAC 58.549 33.333 6.82 0.00 0.00 3.58
72 73 8.668353 CCGTATCATAATAAATGCAATGCTACT 58.332 33.333 6.82 0.00 0.00 2.57
80 81 7.806409 ATAAATGCAATGCTACTATGTGTCA 57.194 32.000 6.82 0.00 0.00 3.58
81 82 6.704289 AAATGCAATGCTACTATGTGTCAT 57.296 33.333 6.82 0.00 0.00 3.06
82 83 5.684550 ATGCAATGCTACTATGTGTCATG 57.315 39.130 6.82 0.00 0.00 3.07
83 84 4.516323 TGCAATGCTACTATGTGTCATGT 58.484 39.130 6.82 0.00 0.00 3.21
84 85 5.669477 TGCAATGCTACTATGTGTCATGTA 58.331 37.500 6.82 0.00 0.00 2.29
85 86 6.290605 TGCAATGCTACTATGTGTCATGTAT 58.709 36.000 6.82 0.00 0.00 2.29
86 87 6.203338 TGCAATGCTACTATGTGTCATGTATG 59.797 38.462 6.82 0.00 0.00 2.39
87 88 6.347969 GCAATGCTACTATGTGTCATGTATGG 60.348 42.308 0.00 0.00 0.00 2.74
88 89 4.631131 TGCTACTATGTGTCATGTATGGC 58.369 43.478 0.00 0.00 0.00 4.40
89 90 4.100808 TGCTACTATGTGTCATGTATGGCA 59.899 41.667 0.00 0.00 40.61 4.92
90 91 5.056480 GCTACTATGTGTCATGTATGGCAA 58.944 41.667 0.03 0.00 44.94 4.52
91 92 5.702670 GCTACTATGTGTCATGTATGGCAAT 59.297 40.000 0.03 1.14 44.94 3.56
92 93 6.873605 GCTACTATGTGTCATGTATGGCAATA 59.126 38.462 0.03 2.13 44.94 1.90
93 94 7.387673 GCTACTATGTGTCATGTATGGCAATAA 59.612 37.037 0.03 0.00 44.94 1.40
94 95 9.271828 CTACTATGTGTCATGTATGGCAATAAA 57.728 33.333 0.03 0.00 44.94 1.40
95 96 8.696043 ACTATGTGTCATGTATGGCAATAAAT 57.304 30.769 0.03 0.00 44.94 1.40
96 97 9.791801 ACTATGTGTCATGTATGGCAATAAATA 57.208 29.630 0.03 0.00 44.94 1.40
99 100 9.970395 ATGTGTCATGTATGGCAATAAATAAAG 57.030 29.630 0.03 0.00 44.94 1.85
100 101 8.965819 TGTGTCATGTATGGCAATAAATAAAGT 58.034 29.630 0.03 0.00 44.94 2.66
101 102 9.450807 GTGTCATGTATGGCAATAAATAAAGTC 57.549 33.333 0.03 0.00 44.94 3.01
102 103 9.183368 TGTCATGTATGGCAATAAATAAAGTCA 57.817 29.630 0.00 0.00 39.82 3.41
137 138 8.467598 ACTAGTACATAATACGATGCATTAGGG 58.532 37.037 0.00 0.00 0.00 3.53
138 139 7.476540 AGTACATAATACGATGCATTAGGGA 57.523 36.000 0.00 0.00 0.00 4.20
139 140 7.548097 AGTACATAATACGATGCATTAGGGAG 58.452 38.462 0.00 0.00 0.00 4.30
140 141 5.734720 ACATAATACGATGCATTAGGGAGG 58.265 41.667 0.00 0.00 0.00 4.30
141 142 5.248477 ACATAATACGATGCATTAGGGAGGT 59.752 40.000 0.00 0.00 0.00 3.85
142 143 6.439375 ACATAATACGATGCATTAGGGAGGTA 59.561 38.462 0.00 0.00 0.00 3.08
143 144 5.407407 AATACGATGCATTAGGGAGGTAG 57.593 43.478 0.00 0.00 0.00 3.18
144 145 2.679082 ACGATGCATTAGGGAGGTAGT 58.321 47.619 0.00 0.00 0.00 2.73
145 146 3.840991 ACGATGCATTAGGGAGGTAGTA 58.159 45.455 0.00 0.00 0.00 1.82
146 147 4.417437 ACGATGCATTAGGGAGGTAGTAT 58.583 43.478 0.00 0.00 0.00 2.12
147 148 4.838986 ACGATGCATTAGGGAGGTAGTATT 59.161 41.667 0.00 0.00 0.00 1.89
148 149 6.014647 ACGATGCATTAGGGAGGTAGTATTA 58.985 40.000 0.00 0.00 0.00 0.98
149 150 6.668283 ACGATGCATTAGGGAGGTAGTATTAT 59.332 38.462 0.00 0.00 0.00 1.28
150 151 7.837689 ACGATGCATTAGGGAGGTAGTATTATA 59.162 37.037 0.00 0.00 0.00 0.98
151 152 8.136165 CGATGCATTAGGGAGGTAGTATTATAC 58.864 40.741 0.00 0.00 0.00 1.47
152 153 8.911018 ATGCATTAGGGAGGTAGTATTATACA 57.089 34.615 5.11 0.00 0.00 2.29
153 154 8.130671 TGCATTAGGGAGGTAGTATTATACAC 57.869 38.462 5.11 1.59 0.00 2.90
154 155 7.954056 TGCATTAGGGAGGTAGTATTATACACT 59.046 37.037 5.11 0.12 0.00 3.55
155 156 9.471702 GCATTAGGGAGGTAGTATTATACACTA 57.528 37.037 5.11 0.00 0.00 2.74
191 192 9.804758 GCATGATACTAACTTATGATACTACCC 57.195 37.037 0.00 0.00 0.00 3.69
200 201 8.904099 AACTTATGATACTACCCATTACAAGC 57.096 34.615 0.00 0.00 0.00 4.01
201 202 8.029782 ACTTATGATACTACCCATTACAAGCA 57.970 34.615 0.00 0.00 0.00 3.91
202 203 8.150945 ACTTATGATACTACCCATTACAAGCAG 58.849 37.037 0.00 0.00 0.00 4.24
203 204 4.703897 TGATACTACCCATTACAAGCAGC 58.296 43.478 0.00 0.00 0.00 5.25
204 205 2.420058 ACTACCCATTACAAGCAGCC 57.580 50.000 0.00 0.00 0.00 4.85
205 206 1.916181 ACTACCCATTACAAGCAGCCT 59.084 47.619 0.00 0.00 0.00 4.58
206 207 3.112263 ACTACCCATTACAAGCAGCCTA 58.888 45.455 0.00 0.00 0.00 3.93
234 235 2.285368 TCGGGGTTCTCATGCCCT 60.285 61.111 6.14 0.00 44.25 5.19
269 272 3.307906 CGGGTTGACCACCTCGGA 61.308 66.667 2.12 0.00 46.38 4.55
288 291 0.253044 ATCGGGTCCCATCACTTGTG 59.747 55.000 9.12 0.00 0.00 3.33
304 307 9.195411 CATCACTTGTGTAATTGCAATTAACTT 57.805 29.630 28.75 10.16 33.05 2.66
305 308 8.572828 TCACTTGTGTAATTGCAATTAACTTG 57.427 30.769 28.75 22.71 37.94 3.16
306 309 8.194104 TCACTTGTGTAATTGCAATTAACTTGT 58.806 29.630 28.75 23.14 37.18 3.16
308 311 8.413229 ACTTGTGTAATTGCAATTAACTTGTCT 58.587 29.630 28.75 6.59 37.18 3.41
316 627 9.643693 AATTGCAATTAACTTGTCTAAATCCAG 57.356 29.630 22.95 0.00 37.18 3.86
398 1296 3.770046 GCCCAACCCTTCCTAGTTTAAA 58.230 45.455 0.00 0.00 0.00 1.52
400 1298 4.084287 CCCAACCCTTCCTAGTTTAAACC 58.916 47.826 14.72 0.00 0.00 3.27
401 1299 4.202641 CCCAACCCTTCCTAGTTTAAACCT 60.203 45.833 14.72 5.30 0.00 3.50
402 1300 5.008331 CCAACCCTTCCTAGTTTAAACCTC 58.992 45.833 14.72 0.00 0.00 3.85
403 1301 5.222068 CCAACCCTTCCTAGTTTAAACCTCT 60.222 44.000 14.72 0.00 0.00 3.69
405 1303 7.455891 CAACCCTTCCTAGTTTAAACCTCTTA 58.544 38.462 14.72 0.20 0.00 2.10
406 1304 7.013823 ACCCTTCCTAGTTTAAACCTCTTAC 57.986 40.000 14.72 0.00 0.00 2.34
408 1306 7.104290 CCCTTCCTAGTTTAAACCTCTTACTG 58.896 42.308 14.72 0.00 0.00 2.74
409 1307 6.594547 CCTTCCTAGTTTAAACCTCTTACTGC 59.405 42.308 14.72 0.00 0.00 4.40
410 1308 6.675413 TCCTAGTTTAAACCTCTTACTGCA 57.325 37.500 14.72 0.00 0.00 4.41
411 1309 7.069877 TCCTAGTTTAAACCTCTTACTGCAA 57.930 36.000 14.72 0.00 0.00 4.08
412 1310 7.159372 TCCTAGTTTAAACCTCTTACTGCAAG 58.841 38.462 14.72 0.00 42.29 4.01
450 1348 0.390340 GAGATCACAAGGACGCTGCA 60.390 55.000 0.00 0.00 0.00 4.41
561 1461 9.985318 CAAATTTAGAATCTAGTTTGAGCAGAG 57.015 33.333 17.70 0.00 0.00 3.35
623 1525 3.748645 AGTTAGAGCAGAGGGAGAGAA 57.251 47.619 0.00 0.00 0.00 2.87
624 1526 3.631250 AGTTAGAGCAGAGGGAGAGAAG 58.369 50.000 0.00 0.00 0.00 2.85
625 1527 3.268334 AGTTAGAGCAGAGGGAGAGAAGA 59.732 47.826 0.00 0.00 0.00 2.87
626 1528 2.917713 AGAGCAGAGGGAGAGAAGAA 57.082 50.000 0.00 0.00 0.00 2.52
627 1529 2.738743 AGAGCAGAGGGAGAGAAGAAG 58.261 52.381 0.00 0.00 0.00 2.85
628 1530 2.311542 AGAGCAGAGGGAGAGAAGAAGA 59.688 50.000 0.00 0.00 0.00 2.87
629 1531 2.689983 GAGCAGAGGGAGAGAAGAAGAG 59.310 54.545 0.00 0.00 0.00 2.85
630 1532 1.756538 GCAGAGGGAGAGAAGAAGAGG 59.243 57.143 0.00 0.00 0.00 3.69
631 1533 1.756538 CAGAGGGAGAGAAGAAGAGGC 59.243 57.143 0.00 0.00 0.00 4.70
632 1534 1.645919 AGAGGGAGAGAAGAAGAGGCT 59.354 52.381 0.00 0.00 0.00 4.58
633 1535 2.856231 AGAGGGAGAGAAGAAGAGGCTA 59.144 50.000 0.00 0.00 0.00 3.93
634 1536 2.956333 GAGGGAGAGAAGAAGAGGCTAC 59.044 54.545 0.00 0.00 0.00 3.58
635 1537 2.036387 GGGAGAGAAGAAGAGGCTACC 58.964 57.143 0.00 0.00 0.00 3.18
636 1538 2.036387 GGAGAGAAGAAGAGGCTACCC 58.964 57.143 0.00 0.00 0.00 3.69
637 1539 2.624557 GGAGAGAAGAAGAGGCTACCCA 60.625 54.545 0.00 0.00 0.00 4.51
638 1540 2.693074 GAGAGAAGAAGAGGCTACCCAG 59.307 54.545 0.00 0.00 0.00 4.45
652 1554 4.471904 CTACCCAGCACACAGATTTAGA 57.528 45.455 0.00 0.00 0.00 2.10
653 1555 3.788227 ACCCAGCACACAGATTTAGAA 57.212 42.857 0.00 0.00 0.00 2.10
654 1556 4.307032 ACCCAGCACACAGATTTAGAAT 57.693 40.909 0.00 0.00 0.00 2.40
655 1557 5.435686 ACCCAGCACACAGATTTAGAATA 57.564 39.130 0.00 0.00 0.00 1.75
656 1558 6.006275 ACCCAGCACACAGATTTAGAATAT 57.994 37.500 0.00 0.00 0.00 1.28
657 1559 7.136822 ACCCAGCACACAGATTTAGAATATA 57.863 36.000 0.00 0.00 0.00 0.86
658 1560 7.220030 ACCCAGCACACAGATTTAGAATATAG 58.780 38.462 0.00 0.00 0.00 1.31
659 1561 7.147479 ACCCAGCACACAGATTTAGAATATAGT 60.147 37.037 0.00 0.00 0.00 2.12
660 1562 7.716998 CCCAGCACACAGATTTAGAATATAGTT 59.283 37.037 0.00 0.00 0.00 2.24
661 1563 9.764363 CCAGCACACAGATTTAGAATATAGTTA 57.236 33.333 0.00 0.00 0.00 2.24
672 1574 9.830186 ATTTAGAATATAGTTAGAGCAGAGGGA 57.170 33.333 0.00 0.00 0.00 4.20
673 1575 8.871629 TTAGAATATAGTTAGAGCAGAGGGAG 57.128 38.462 0.00 0.00 0.00 4.30
674 1576 7.097623 AGAATATAGTTAGAGCAGAGGGAGA 57.902 40.000 0.00 0.00 0.00 3.71
675 1577 7.175104 AGAATATAGTTAGAGCAGAGGGAGAG 58.825 42.308 0.00 0.00 0.00 3.20
676 1578 6.712114 ATATAGTTAGAGCAGAGGGAGAGA 57.288 41.667 0.00 0.00 0.00 3.10
732 1634 6.191315 TGTAGTTAGAGCAGAAGGAGAGAAT 58.809 40.000 0.00 0.00 0.00 2.40
793 1749 1.756538 CAGAGGGAGAGAAGAAGAGGC 59.243 57.143 0.00 0.00 0.00 4.70
797 1753 2.585432 AGGGAGAGAAGAAGAGGCTACT 59.415 50.000 0.00 0.00 0.00 2.57
801 1757 3.631250 AGAGAAGAAGAGGCTACTCAGG 58.369 50.000 0.00 0.00 46.44 3.86
807 1763 2.310779 AGAGGCTACTCAGGACACAA 57.689 50.000 0.00 0.00 46.44 3.33
809 1765 2.300437 AGAGGCTACTCAGGACACAAAC 59.700 50.000 0.00 0.00 46.44 2.93
846 1803 4.016444 GAGCAGAAGGAGAGAAGAAGAGA 58.984 47.826 0.00 0.00 0.00 3.10
910 1870 3.057174 AGAAGAAGAGGCTACTCAACACG 60.057 47.826 0.00 0.00 46.44 4.49
977 1937 1.651240 CGGAAGGAGAAGCGACCGTA 61.651 60.000 0.00 0.00 36.38 4.02
978 1938 0.529378 GGAAGGAGAAGCGACCGTAA 59.471 55.000 0.00 0.00 0.00 3.18
1020 1980 1.004440 GGCTGCCAACTCGTTCTCT 60.004 57.895 15.17 0.00 0.00 3.10
1023 1983 0.601046 CTGCCAACTCGTTCTCTGCA 60.601 55.000 0.00 0.00 0.00 4.41
1177 2137 5.046878 ACGAATGACATTGGTTAGTACTCCA 60.047 40.000 9.77 0.00 0.00 3.86
1195 2155 8.262227 AGTACTCCATCCGTTCACAAATATAAA 58.738 33.333 0.00 0.00 0.00 1.40
1248 2209 7.822334 ACATATGACTAAAATGAGTGAACGGAA 59.178 33.333 10.38 0.00 0.00 4.30
1252 2213 6.056428 ACTAAAATGAGTGAACGGAAACAC 57.944 37.500 0.00 0.00 37.30 3.32
1268 2229 5.955496 CGGAAACACTAAAATGCGTGTATAC 59.045 40.000 0.00 0.00 43.05 1.47
1334 2302 4.909695 ACAAAGGGGTACTTAGTAGTGGTT 59.090 41.667 0.00 0.00 38.85 3.67
1344 2312 8.412456 GGTACTTAGTAGTGGTTATCTTCTTCC 58.588 40.741 0.00 0.00 35.78 3.46
1360 2328 7.223260 TCTTCTTCCGTTGTCAGTTATCTAA 57.777 36.000 0.00 0.00 0.00 2.10
1446 2705 4.449743 CGAAAGTGTTGTTCTAATCCCGAA 59.550 41.667 0.00 0.00 0.00 4.30
1567 2826 1.026182 TCATCCTGCAATGACGTGGC 61.026 55.000 0.00 0.00 30.76 5.01
1616 2885 8.149647 TGTTTTTGAACATATCATTTTGGAGCT 58.850 29.630 0.00 0.00 38.03 4.09
1660 2930 5.434182 TCCACAAATATCATCTGGTGACA 57.566 39.130 0.00 0.00 40.28 3.58
1783 3053 3.815856 TCTCACATGAGCTTGAGATCC 57.184 47.619 11.06 0.00 42.67 3.36
1787 3057 3.133542 TCACATGAGCTTGAGATCCGAAT 59.866 43.478 0.00 0.00 0.00 3.34
1863 3134 1.453155 CATGTCTTGGTTTCTCCCCG 58.547 55.000 0.00 0.00 34.77 5.73
1901 3172 7.874940 TCTTTCTGTCCATTATTTTGACACTG 58.125 34.615 0.00 0.00 35.34 3.66
1905 3176 6.206634 TCTGTCCATTATTTTGACACTGGTTC 59.793 38.462 0.00 0.00 35.34 3.62
1923 3194 2.753849 TTTATGTGCTGCGGGCCC 60.754 61.111 13.57 13.57 40.92 5.80
1924 3195 3.575703 TTTATGTGCTGCGGGCCCA 62.576 57.895 24.92 0.93 40.92 5.36
1950 3221 0.594602 CGTGGTGTGTAGTTCTCCGA 59.405 55.000 0.00 0.00 0.00 4.55
1977 3248 1.831736 CTATAGAATCCGCCCCCGATT 59.168 52.381 0.00 0.00 36.29 3.34
2043 6471 5.997384 ACGAAGGGAGTACTAACTGAAAT 57.003 39.130 0.00 0.00 35.56 2.17
2047 6475 8.033626 ACGAAGGGAGTACTAACTGAAATTTAG 58.966 37.037 0.00 0.00 35.56 1.85
2090 6518 0.924090 GCTACAAGATTCGCTCACGG 59.076 55.000 0.00 0.00 40.63 4.94
2091 6519 1.469251 GCTACAAGATTCGCTCACGGA 60.469 52.381 0.00 0.00 40.63 4.69
2094 6522 1.000955 ACAAGATTCGCTCACGGAGTT 59.999 47.619 3.38 0.00 41.61 3.01
2245 6673 1.669999 GGCGAGCAAAATGCCAGGAT 61.670 55.000 0.00 0.00 46.52 3.24
2264 6692 1.178276 TCTCTTCTCCTCCAGCGTTC 58.822 55.000 0.00 0.00 0.00 3.95
2310 9155 7.948357 TCAAGGTATATCAATTACTACTGCGT 58.052 34.615 0.00 0.00 0.00 5.24
2335 9180 7.764443 GTGTCGGGTCATATTGTTATATAGCAT 59.236 37.037 0.00 0.00 0.00 3.79
2336 9181 8.973182 TGTCGGGTCATATTGTTATATAGCATA 58.027 33.333 0.00 0.00 0.00 3.14
2337 9182 9.982651 GTCGGGTCATATTGTTATATAGCATAT 57.017 33.333 0.00 1.07 0.00 1.78
2486 9518 7.353414 ACTGCAGTACATGACATAGATAACT 57.647 36.000 20.16 0.00 0.00 2.24
2489 9521 5.928839 GCAGTACATGACATAGATAACTGGG 59.071 44.000 0.00 0.00 34.95 4.45
2509 9541 1.741770 GAAGGACGACGCAGCCAAT 60.742 57.895 0.00 0.00 0.00 3.16
2590 9625 0.610174 TGCAGGAAGAGCTCATTCGT 59.390 50.000 17.77 14.40 0.00 3.85
2643 9679 3.578456 GCGCTTAGCTTGCTTCCA 58.422 55.556 0.00 0.00 44.04 3.53
2727 9765 3.057547 CTGCGACCTCTCTGACCCG 62.058 68.421 0.00 0.00 0.00 5.28
2865 9903 1.376037 CCAGTCCCGCAAGAACCTC 60.376 63.158 0.00 0.00 43.02 3.85
2901 9939 2.039084 GGTGAATGTCAAGACCCTGAGT 59.961 50.000 0.00 0.00 0.00 3.41
3091 10129 3.240134 GAGCTCCAGCCGTGGTTCA 62.240 63.158 0.87 0.00 45.28 3.18
3135 10173 0.108804 CCAACCTGTCACGCTACGAT 60.109 55.000 0.00 0.00 0.00 3.73
3354 10404 1.368850 GAACGCAGCCAACGACAAC 60.369 57.895 0.00 0.00 0.00 3.32
3831 10887 0.179116 CGGAGCAGGACATCAGACTG 60.179 60.000 0.00 0.00 35.40 3.51
3834 10890 2.170187 GGAGCAGGACATCAGACTGAAT 59.830 50.000 9.70 0.29 34.21 2.57
3896 10955 1.274242 ACTCCGGGAATAGGGGAACTT 60.274 52.381 0.00 0.00 32.37 2.66
3911 10970 5.535406 AGGGGAACTTGATACGTGATACTAG 59.465 44.000 0.00 0.00 0.00 2.57
4041 11120 5.005107 GCTTGCTTCTTTCTTGTTGTTTCAG 59.995 40.000 0.00 0.00 0.00 3.02
4126 11205 2.803956 TCGATCAACCGGAAAACAAGAC 59.196 45.455 9.46 0.00 0.00 3.01
4129 11208 4.537015 GATCAACCGGAAAACAAGACTTG 58.463 43.478 9.46 13.77 0.00 3.16
4438 11518 9.256228 TGTTTGGGGTATGTTTGCTATATTTAA 57.744 29.630 0.00 0.00 0.00 1.52
4609 11938 3.517296 TTTCCAAACATCTGGGTGCTA 57.483 42.857 0.00 0.00 37.06 3.49
4610 11939 3.517296 TTCCAAACATCTGGGTGCTAA 57.483 42.857 0.00 0.00 37.06 3.09
4611 11940 3.737559 TCCAAACATCTGGGTGCTAAT 57.262 42.857 0.00 0.00 37.06 1.73
4614 11943 5.575157 TCCAAACATCTGGGTGCTAATTAA 58.425 37.500 0.00 0.00 37.06 1.40
4622 11951 4.649674 TCTGGGTGCTAATTAAGACTCGAT 59.350 41.667 0.00 0.00 0.00 3.59
4746 12101 7.093552 TGAGGTGAAAAATTGAGAAGGTTTCAA 60.094 33.333 1.79 0.00 39.26 2.69
4790 12146 1.916181 AGAAACCGGACCATCTCCAAT 59.084 47.619 9.46 0.00 39.39 3.16
4842 12198 6.122964 AGTCAGGTTTGAAAAGAAAGTAGCT 58.877 36.000 0.00 0.00 34.49 3.32
4846 12202 7.554835 TCAGGTTTGAAAAGAAAGTAGCTGTTA 59.445 33.333 0.00 0.00 32.98 2.41
4859 12215 6.276832 AGTAGCTGTTACTTTATCGGTTGA 57.723 37.500 0.00 0.00 39.64 3.18
4860 12216 6.331061 AGTAGCTGTTACTTTATCGGTTGAG 58.669 40.000 0.00 0.00 39.64 3.02
4861 12217 5.148651 AGCTGTTACTTTATCGGTTGAGT 57.851 39.130 0.00 0.00 0.00 3.41
4862 12218 5.548406 AGCTGTTACTTTATCGGTTGAGTT 58.452 37.500 0.00 0.00 0.00 3.01
4863 12219 5.995897 AGCTGTTACTTTATCGGTTGAGTTT 59.004 36.000 0.00 0.00 0.00 2.66
4864 12220 7.156673 AGCTGTTACTTTATCGGTTGAGTTTA 58.843 34.615 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.525826 ACTCAACCATCTCTTTCTTCATTTAAT 57.474 29.630 0.00 0.00 0.00 1.40
6 7 8.924511 ACTCAACCATCTCTTTCTTCATTTAA 57.075 30.769 0.00 0.00 0.00 1.52
8 9 9.171877 GATACTCAACCATCTCTTTCTTCATTT 57.828 33.333 0.00 0.00 0.00 2.32
9 10 8.324306 TGATACTCAACCATCTCTTTCTTCATT 58.676 33.333 0.00 0.00 0.00 2.57
10 11 7.855375 TGATACTCAACCATCTCTTTCTTCAT 58.145 34.615 0.00 0.00 0.00 2.57
11 12 7.244886 TGATACTCAACCATCTCTTTCTTCA 57.755 36.000 0.00 0.00 0.00 3.02
12 13 9.255304 GTATGATACTCAACCATCTCTTTCTTC 57.745 37.037 0.00 0.00 0.00 2.87
13 14 8.762645 TGTATGATACTCAACCATCTCTTTCTT 58.237 33.333 4.03 0.00 0.00 2.52
14 15 8.311395 TGTATGATACTCAACCATCTCTTTCT 57.689 34.615 4.03 0.00 0.00 2.52
15 16 8.948631 TTGTATGATACTCAACCATCTCTTTC 57.051 34.615 4.03 0.00 0.00 2.62
16 17 9.334947 CATTGTATGATACTCAACCATCTCTTT 57.665 33.333 4.03 0.00 0.00 2.52
17 18 8.708378 TCATTGTATGATACTCAACCATCTCTT 58.292 33.333 4.03 0.00 33.59 2.85
18 19 8.255111 TCATTGTATGATACTCAACCATCTCT 57.745 34.615 4.03 0.00 33.59 3.10
42 43 9.438291 GCATTGCATTTATTATGATACGGTATC 57.562 33.333 18.97 18.97 35.74 2.24
43 44 9.177608 AGCATTGCATTTATTATGATACGGTAT 57.822 29.630 11.91 0.00 0.00 2.73
44 45 8.560355 AGCATTGCATTTATTATGATACGGTA 57.440 30.769 11.91 0.00 0.00 4.02
45 46 7.452880 AGCATTGCATTTATTATGATACGGT 57.547 32.000 11.91 0.00 0.00 4.83
46 47 8.668353 AGTAGCATTGCATTTATTATGATACGG 58.332 33.333 11.91 0.00 41.95 4.02
54 55 9.336171 TGACACATAGTAGCATTGCATTTATTA 57.664 29.630 11.91 0.00 0.00 0.98
55 56 8.224389 TGACACATAGTAGCATTGCATTTATT 57.776 30.769 11.91 0.00 0.00 1.40
56 57 7.806409 TGACACATAGTAGCATTGCATTTAT 57.194 32.000 11.91 2.57 0.00 1.40
57 58 7.282901 ACATGACACATAGTAGCATTGCATTTA 59.717 33.333 11.91 0.17 0.00 1.40
58 59 6.095860 ACATGACACATAGTAGCATTGCATTT 59.904 34.615 11.91 0.00 0.00 2.32
59 60 5.591472 ACATGACACATAGTAGCATTGCATT 59.409 36.000 11.91 0.00 0.00 3.56
60 61 5.128205 ACATGACACATAGTAGCATTGCAT 58.872 37.500 11.91 0.00 0.00 3.96
61 62 4.516323 ACATGACACATAGTAGCATTGCA 58.484 39.130 11.91 0.00 0.00 4.08
62 63 6.347969 CCATACATGACACATAGTAGCATTGC 60.348 42.308 0.00 0.00 0.00 3.56
63 64 6.347969 GCCATACATGACACATAGTAGCATTG 60.348 42.308 0.00 0.00 0.00 2.82
64 65 5.702670 GCCATACATGACACATAGTAGCATT 59.297 40.000 0.00 0.00 0.00 3.56
65 66 5.221702 TGCCATACATGACACATAGTAGCAT 60.222 40.000 0.00 0.00 0.00 3.79
66 67 4.100808 TGCCATACATGACACATAGTAGCA 59.899 41.667 0.00 0.00 0.00 3.49
67 68 4.631131 TGCCATACATGACACATAGTAGC 58.369 43.478 0.00 0.00 0.00 3.58
68 69 8.831715 TTATTGCCATACATGACACATAGTAG 57.168 34.615 0.00 0.00 0.00 2.57
69 70 9.791801 ATTTATTGCCATACATGACACATAGTA 57.208 29.630 0.00 0.00 0.00 1.82
70 71 8.696043 ATTTATTGCCATACATGACACATAGT 57.304 30.769 0.00 0.00 0.00 2.12
73 74 9.970395 CTTTATTTATTGCCATACATGACACAT 57.030 29.630 0.00 0.00 0.00 3.21
74 75 8.965819 ACTTTATTTATTGCCATACATGACACA 58.034 29.630 0.00 0.00 0.00 3.72
75 76 9.450807 GACTTTATTTATTGCCATACATGACAC 57.549 33.333 0.00 0.00 0.00 3.67
76 77 9.183368 TGACTTTATTTATTGCCATACATGACA 57.817 29.630 0.00 0.00 0.00 3.58
111 112 8.467598 CCCTAATGCATCGTATTATGTACTAGT 58.532 37.037 0.00 0.00 0.00 2.57
112 113 8.683615 TCCCTAATGCATCGTATTATGTACTAG 58.316 37.037 0.00 0.00 0.00 2.57
113 114 8.584063 TCCCTAATGCATCGTATTATGTACTA 57.416 34.615 0.00 0.00 0.00 1.82
114 115 7.363880 CCTCCCTAATGCATCGTATTATGTACT 60.364 40.741 0.00 0.00 0.00 2.73
115 116 6.757010 CCTCCCTAATGCATCGTATTATGTAC 59.243 42.308 0.00 0.00 0.00 2.90
116 117 6.439375 ACCTCCCTAATGCATCGTATTATGTA 59.561 38.462 0.00 0.00 0.00 2.29
117 118 5.248477 ACCTCCCTAATGCATCGTATTATGT 59.752 40.000 0.00 0.00 0.00 2.29
118 119 5.734720 ACCTCCCTAATGCATCGTATTATG 58.265 41.667 0.00 0.00 0.00 1.90
119 120 6.668283 ACTACCTCCCTAATGCATCGTATTAT 59.332 38.462 0.00 0.00 0.00 1.28
120 121 6.014647 ACTACCTCCCTAATGCATCGTATTA 58.985 40.000 0.00 0.00 0.00 0.98
121 122 4.838986 ACTACCTCCCTAATGCATCGTATT 59.161 41.667 0.00 0.00 0.00 1.89
122 123 4.417437 ACTACCTCCCTAATGCATCGTAT 58.583 43.478 0.00 0.00 0.00 3.06
123 124 3.840991 ACTACCTCCCTAATGCATCGTA 58.159 45.455 0.00 0.00 0.00 3.43
124 125 2.679082 ACTACCTCCCTAATGCATCGT 58.321 47.619 0.00 0.00 0.00 3.73
125 126 5.407407 AATACTACCTCCCTAATGCATCG 57.593 43.478 0.00 0.00 0.00 3.84
126 127 8.978472 TGTATAATACTACCTCCCTAATGCATC 58.022 37.037 0.00 0.00 0.00 3.91
127 128 8.759782 GTGTATAATACTACCTCCCTAATGCAT 58.240 37.037 0.00 0.00 0.00 3.96
128 129 7.954056 AGTGTATAATACTACCTCCCTAATGCA 59.046 37.037 0.00 0.00 0.00 3.96
129 130 8.363761 AGTGTATAATACTACCTCCCTAATGC 57.636 38.462 0.00 0.00 0.00 3.56
165 166 9.804758 GGGTAGTATCATAAGTTAGTATCATGC 57.195 37.037 0.00 0.00 0.00 4.06
174 175 9.991906 GCTTGTAATGGGTAGTATCATAAGTTA 57.008 33.333 0.00 0.00 0.00 2.24
175 176 8.491134 TGCTTGTAATGGGTAGTATCATAAGTT 58.509 33.333 0.00 0.00 0.00 2.66
176 177 8.029782 TGCTTGTAATGGGTAGTATCATAAGT 57.970 34.615 0.00 0.00 0.00 2.24
177 178 7.118390 GCTGCTTGTAATGGGTAGTATCATAAG 59.882 40.741 0.00 0.00 0.00 1.73
178 179 6.934645 GCTGCTTGTAATGGGTAGTATCATAA 59.065 38.462 0.00 0.00 0.00 1.90
179 180 6.464222 GCTGCTTGTAATGGGTAGTATCATA 58.536 40.000 0.00 0.00 0.00 2.15
180 181 5.308825 GCTGCTTGTAATGGGTAGTATCAT 58.691 41.667 0.00 0.00 0.00 2.45
181 182 4.444306 GGCTGCTTGTAATGGGTAGTATCA 60.444 45.833 0.00 0.00 0.00 2.15
182 183 4.065789 GGCTGCTTGTAATGGGTAGTATC 58.934 47.826 0.00 0.00 0.00 2.24
183 184 3.716872 AGGCTGCTTGTAATGGGTAGTAT 59.283 43.478 0.00 0.00 0.00 2.12
184 185 3.112263 AGGCTGCTTGTAATGGGTAGTA 58.888 45.455 0.00 0.00 0.00 1.82
185 186 1.916181 AGGCTGCTTGTAATGGGTAGT 59.084 47.619 0.00 0.00 0.00 2.73
186 187 2.717639 AGGCTGCTTGTAATGGGTAG 57.282 50.000 0.00 0.00 0.00 3.18
187 188 3.684413 GCTTAGGCTGCTTGTAATGGGTA 60.684 47.826 0.00 0.00 35.22 3.69
188 189 2.945890 GCTTAGGCTGCTTGTAATGGGT 60.946 50.000 0.00 0.00 35.22 4.51
189 190 1.678101 GCTTAGGCTGCTTGTAATGGG 59.322 52.381 0.00 0.00 35.22 4.00
190 191 1.331756 CGCTTAGGCTGCTTGTAATGG 59.668 52.381 0.00 0.00 36.09 3.16
191 192 2.279741 TCGCTTAGGCTGCTTGTAATG 58.720 47.619 0.00 0.00 36.09 1.90
192 193 2.691409 TCGCTTAGGCTGCTTGTAAT 57.309 45.000 0.00 0.00 36.09 1.89
193 194 2.279741 CATCGCTTAGGCTGCTTGTAA 58.720 47.619 0.00 0.00 36.09 2.41
194 195 1.473257 CCATCGCTTAGGCTGCTTGTA 60.473 52.381 0.00 0.00 36.09 2.41
195 196 0.745845 CCATCGCTTAGGCTGCTTGT 60.746 55.000 0.00 0.00 36.09 3.16
196 197 2.020131 CCATCGCTTAGGCTGCTTG 58.980 57.895 0.00 0.00 36.09 4.01
197 198 4.547859 CCATCGCTTAGGCTGCTT 57.452 55.556 0.00 0.00 36.09 3.91
234 235 1.402259 CCGCCAAACACGCCATTAATA 59.598 47.619 0.00 0.00 0.00 0.98
269 272 0.253044 CACAAGTGATGGGACCCGAT 59.747 55.000 5.91 0.18 32.54 4.18
304 307 2.094182 GTCAGCGACCTGGATTTAGACA 60.094 50.000 0.00 0.00 39.61 3.41
305 308 2.166664 AGTCAGCGACCTGGATTTAGAC 59.833 50.000 0.00 3.06 39.61 2.59
306 309 2.457598 AGTCAGCGACCTGGATTTAGA 58.542 47.619 0.00 0.00 39.61 2.10
308 311 2.935238 GCAAGTCAGCGACCTGGATTTA 60.935 50.000 0.00 0.00 39.61 1.40
310 313 0.674895 GCAAGTCAGCGACCTGGATT 60.675 55.000 0.00 0.00 39.61 3.01
311 314 1.078848 GCAAGTCAGCGACCTGGAT 60.079 57.895 0.00 0.00 39.61 3.41
316 627 1.739562 CTCCTGCAAGTCAGCGACC 60.740 63.158 5.29 0.00 41.50 4.79
409 1307 3.419828 TGCGTGGTTGCAGACTTG 58.580 55.556 0.00 0.00 40.62 3.16
450 1348 1.974343 TTTGTTTGCGGGCGCCTAT 60.974 52.632 28.56 0.00 41.09 2.57
500 1398 2.717485 GCCTGTGGCGCATATGTG 59.283 61.111 10.83 12.04 39.62 3.21
561 1461 3.838903 TGGGTAAACTCTTCTTCTCTCCC 59.161 47.826 0.00 0.00 0.00 4.30
631 1533 4.471904 TCTAAATCTGTGTGCTGGGTAG 57.528 45.455 0.00 0.00 0.00 3.18
632 1534 4.901197 TTCTAAATCTGTGTGCTGGGTA 57.099 40.909 0.00 0.00 0.00 3.69
633 1535 3.788227 TTCTAAATCTGTGTGCTGGGT 57.212 42.857 0.00 0.00 0.00 4.51
634 1536 7.220030 ACTATATTCTAAATCTGTGTGCTGGG 58.780 38.462 0.00 0.00 0.00 4.45
635 1537 8.668510 AACTATATTCTAAATCTGTGTGCTGG 57.331 34.615 0.00 0.00 0.00 4.85
646 1548 9.830186 TCCCTCTGCTCTAACTATATTCTAAAT 57.170 33.333 0.00 0.00 0.00 1.40
647 1549 9.303116 CTCCCTCTGCTCTAACTATATTCTAAA 57.697 37.037 0.00 0.00 0.00 1.85
648 1550 8.670490 TCTCCCTCTGCTCTAACTATATTCTAA 58.330 37.037 0.00 0.00 0.00 2.10
649 1551 8.220898 TCTCCCTCTGCTCTAACTATATTCTA 57.779 38.462 0.00 0.00 0.00 2.10
650 1552 7.018149 TCTCTCCCTCTGCTCTAACTATATTCT 59.982 40.741 0.00 0.00 0.00 2.40
651 1553 7.172342 TCTCTCCCTCTGCTCTAACTATATTC 58.828 42.308 0.00 0.00 0.00 1.75
652 1554 7.097623 TCTCTCCCTCTGCTCTAACTATATT 57.902 40.000 0.00 0.00 0.00 1.28
653 1555 6.712114 TCTCTCCCTCTGCTCTAACTATAT 57.288 41.667 0.00 0.00 0.00 0.86
654 1556 6.330514 TCTTCTCTCCCTCTGCTCTAACTATA 59.669 42.308 0.00 0.00 0.00 1.31
655 1557 5.133660 TCTTCTCTCCCTCTGCTCTAACTAT 59.866 44.000 0.00 0.00 0.00 2.12
656 1558 4.475381 TCTTCTCTCCCTCTGCTCTAACTA 59.525 45.833 0.00 0.00 0.00 2.24
657 1559 3.268334 TCTTCTCTCCCTCTGCTCTAACT 59.732 47.826 0.00 0.00 0.00 2.24
658 1560 3.626930 TCTTCTCTCCCTCTGCTCTAAC 58.373 50.000 0.00 0.00 0.00 2.34
659 1561 4.017958 TCTTCTTCTCTCCCTCTGCTCTAA 60.018 45.833 0.00 0.00 0.00 2.10
660 1562 3.525609 TCTTCTTCTCTCCCTCTGCTCTA 59.474 47.826 0.00 0.00 0.00 2.43
661 1563 2.311542 TCTTCTTCTCTCCCTCTGCTCT 59.688 50.000 0.00 0.00 0.00 4.09
662 1564 2.689983 CTCTTCTTCTCTCCCTCTGCTC 59.310 54.545 0.00 0.00 0.00 4.26
663 1565 2.624029 CCTCTTCTTCTCTCCCTCTGCT 60.624 54.545 0.00 0.00 0.00 4.24
664 1566 1.756538 CCTCTTCTTCTCTCCCTCTGC 59.243 57.143 0.00 0.00 0.00 4.26
665 1567 1.756538 GCCTCTTCTTCTCTCCCTCTG 59.243 57.143 0.00 0.00 0.00 3.35
666 1568 1.645919 AGCCTCTTCTTCTCTCCCTCT 59.354 52.381 0.00 0.00 0.00 3.69
667 1569 2.159179 AGCCTCTTCTTCTCTCCCTC 57.841 55.000 0.00 0.00 0.00 4.30
668 1570 2.585432 AGTAGCCTCTTCTTCTCTCCCT 59.415 50.000 0.00 0.00 0.00 4.20
669 1571 2.956333 GAGTAGCCTCTTCTTCTCTCCC 59.044 54.545 0.00 0.00 34.69 4.30
670 1572 3.626930 TGAGTAGCCTCTTCTTCTCTCC 58.373 50.000 0.00 0.00 38.61 3.71
671 1573 3.632145 CCTGAGTAGCCTCTTCTTCTCTC 59.368 52.174 0.00 0.00 38.61 3.20
672 1574 3.268334 TCCTGAGTAGCCTCTTCTTCTCT 59.732 47.826 0.00 0.00 38.61 3.10
673 1575 3.380320 GTCCTGAGTAGCCTCTTCTTCTC 59.620 52.174 0.00 0.00 38.61 2.87
674 1576 3.245443 TGTCCTGAGTAGCCTCTTCTTCT 60.245 47.826 0.00 0.00 38.61 2.85
675 1577 3.093057 TGTCCTGAGTAGCCTCTTCTTC 58.907 50.000 0.00 0.00 38.61 2.87
676 1578 2.829120 GTGTCCTGAGTAGCCTCTTCTT 59.171 50.000 0.00 0.00 38.61 2.52
732 1634 2.304761 CTGTGCCCTGGGTAAACTCTTA 59.695 50.000 15.56 0.00 0.00 2.10
793 1749 7.155328 ACATTCTAAGTTTGTGTCCTGAGTAG 58.845 38.462 0.00 0.00 0.00 2.57
797 1753 7.062749 ACTACATTCTAAGTTTGTGTCCTGA 57.937 36.000 0.00 0.00 0.00 3.86
801 1757 8.648968 GCTCTAACTACATTCTAAGTTTGTGTC 58.351 37.037 0.00 0.00 37.19 3.67
807 1763 8.254508 CCTTCTGCTCTAACTACATTCTAAGTT 58.745 37.037 0.00 0.00 39.25 2.66
809 1765 8.001881 TCCTTCTGCTCTAACTACATTCTAAG 57.998 38.462 0.00 0.00 0.00 2.18
881 1840 2.640284 AGCCTCTTCTTCTCTCCCTT 57.360 50.000 0.00 0.00 0.00 3.95
910 1870 8.475639 TCTGGTCCAACTACATTCTAAATCTAC 58.524 37.037 0.00 0.00 0.00 2.59
1232 2193 6.687081 TTAGTGTTTCCGTTCACTCATTTT 57.313 33.333 1.08 0.00 42.77 1.82
1313 2278 7.194761 AGATAACCACTACTAAGTACCCCTTT 58.805 38.462 0.00 0.00 33.48 3.11
1334 2302 7.406031 AGATAACTGACAACGGAAGAAGATA 57.594 36.000 0.00 0.00 0.00 1.98
1344 2312 8.926710 ACAAAAGATCTTAGATAACTGACAACG 58.073 33.333 8.75 0.00 0.00 4.10
1360 2328 5.289510 ACCCTATCCCACTACAAAAGATCT 58.710 41.667 0.00 0.00 0.00 2.75
1446 2705 0.900182 TCACCCGAGCTCACATGAGT 60.900 55.000 15.40 0.00 43.85 3.41
1591 2860 8.538409 AGCTCCAAAATGATATGTTCAAAAAC 57.462 30.769 0.00 0.00 38.03 2.43
1604 2873 8.505625 GCAAAAATAATTGAAGCTCCAAAATGA 58.494 29.630 0.00 0.00 31.84 2.57
1751 3021 4.453478 GCTCATGTGAGATTGAGTGAACAA 59.547 41.667 13.94 0.00 44.74 2.83
1783 3053 3.843117 GACCCGAGGCGGCTATTCG 62.843 68.421 13.24 12.16 46.86 3.34
1787 3057 3.363410 TTAGGACCCGAGGCGGCTA 62.363 63.158 13.24 0.00 46.86 3.93
1803 3073 5.825593 AACATGAGAGGAAAGTGGAGTTA 57.174 39.130 0.00 0.00 0.00 2.24
1901 3172 0.451783 CCCGCAGCACATAAAGAACC 59.548 55.000 0.00 0.00 0.00 3.62
1905 3176 2.800736 GGCCCGCAGCACATAAAG 59.199 61.111 0.00 0.00 46.50 1.85
1923 3194 1.601903 ACTACACACCACGCAAACATG 59.398 47.619 0.00 0.00 0.00 3.21
1924 3195 1.961793 ACTACACACCACGCAAACAT 58.038 45.000 0.00 0.00 0.00 2.71
1950 3221 3.009143 GGGGCGGATTCTATAGGAAACAT 59.991 47.826 0.00 0.00 37.49 2.71
2043 6471 0.391130 CAGTACTGCCCAGCGCTAAA 60.391 55.000 10.99 0.00 38.78 1.85
2090 6518 5.756833 TCCCGTTTTGAGACTAGAAAAACTC 59.243 40.000 17.31 0.00 40.16 3.01
2091 6519 5.677567 TCCCGTTTTGAGACTAGAAAAACT 58.322 37.500 17.31 0.00 40.16 2.66
2094 6522 5.699458 GTGATCCCGTTTTGAGACTAGAAAA 59.301 40.000 0.00 0.00 0.00 2.29
2198 6626 2.545113 GGACTGCAGAACGACTACACAA 60.545 50.000 23.35 0.00 0.00 3.33
2245 6673 1.178276 GAACGCTGGAGGAGAAGAGA 58.822 55.000 0.00 0.00 0.00 3.10
2264 6692 8.571336 CCTTGAATAGAATTATTAGGTGCCAAG 58.429 37.037 0.00 0.00 30.80 3.61
2310 9155 7.234661 TGCTATATAACAATATGACCCGACA 57.765 36.000 0.00 0.00 0.00 4.35
2338 9183 8.847816 ACACATATCTACTACCCTGATACCTAT 58.152 37.037 0.00 0.00 0.00 2.57
2486 9518 2.599281 TGCGTCGTCCTTCTCCCA 60.599 61.111 0.00 0.00 0.00 4.37
2489 9521 2.507324 GGCTGCGTCGTCCTTCTC 60.507 66.667 0.00 0.00 0.00 2.87
2509 9541 3.204382 GGTCCCTTCTTTCCCCATCATTA 59.796 47.826 0.00 0.00 0.00 1.90
2558 9590 5.426504 CTCTTCCTGCATCTTGTCATTAGT 58.573 41.667 0.00 0.00 0.00 2.24
2590 9625 2.160205 ACGTCTCCATCGAGTTCTTGA 58.840 47.619 0.00 0.00 37.40 3.02
2613 9648 2.740580 GCTAAGCGCAACCTACCATGTA 60.741 50.000 11.47 0.00 38.92 2.29
2727 9765 0.450583 TGTCGCAGATGTCGTACCTC 59.549 55.000 0.00 0.00 40.67 3.85
2865 9903 3.138798 ACCTCGACGATGTCCCCG 61.139 66.667 0.00 0.00 0.00 5.73
3091 10129 4.219115 AGGATGAGACGATACTTGTCCAT 58.781 43.478 0.00 0.00 37.04 3.41
3135 10173 3.985279 CGTCCTTGTTGAAGTCGACAATA 59.015 43.478 19.50 0.00 45.99 1.90
3354 10404 1.300620 TTTCTCCGTGACAGTGCCG 60.301 57.895 0.00 0.00 0.00 5.69
3447 10500 3.537206 GAACCCGGCTGTCTGCACT 62.537 63.158 0.00 0.00 45.15 4.40
3454 10507 4.379243 CAGCTCGAACCCGGCTGT 62.379 66.667 13.78 0.00 45.84 4.40
3667 10723 0.250684 ATGTGTTGCACCATCACCGA 60.251 50.000 0.00 0.00 34.35 4.69
3831 10887 2.424956 GGGAGCAAATCTGGTGACATTC 59.575 50.000 0.00 0.00 41.51 2.67
3834 10890 0.770499 TGGGAGCAAATCTGGTGACA 59.230 50.000 0.00 0.00 39.59 3.58
3873 10929 0.689745 TCCCCTATTCCCGGAGTGTG 60.690 60.000 0.73 0.00 0.00 3.82
3896 10955 6.824553 ACAGAGGTACTAGTATCACGTATCA 58.175 40.000 15.51 0.00 41.55 2.15
3911 10970 6.821665 TGCATTACATTTAGGAACAGAGGTAC 59.178 38.462 0.00 0.00 0.00 3.34
4041 11120 7.763172 AATTCTTGTCTATTGATCTGACGAC 57.237 36.000 0.00 0.00 33.81 4.34
4126 11205 0.800631 ATGTCATGCACGTGCTCAAG 59.199 50.000 37.59 24.35 42.66 3.02
4129 11208 1.346197 CGATGTCATGCACGTGCTC 59.654 57.895 37.59 25.07 42.66 4.26
4204 11284 3.979495 CACTTGCAGCTCAAATTTGACTC 59.021 43.478 16.91 11.38 33.65 3.36
4438 11518 9.880157 AAATGCTTAGAAATGCAATTAATGACT 57.120 25.926 0.00 0.00 42.74 3.41
4499 11828 5.386810 TTTTGCAACAATGACACAAATCG 57.613 34.783 0.00 0.00 30.95 3.34
4510 11839 9.995957 GTTTTTGTAACCTAATTTTGCAACAAT 57.004 25.926 0.00 0.00 29.61 2.71
4609 11938 6.644347 ACATGTTCAGGATCGAGTCTTAATT 58.356 36.000 0.00 0.00 0.00 1.40
4610 11939 6.227298 ACATGTTCAGGATCGAGTCTTAAT 57.773 37.500 0.00 0.00 0.00 1.40
4611 11940 5.661056 ACATGTTCAGGATCGAGTCTTAA 57.339 39.130 0.00 0.00 0.00 1.85
4614 11943 3.634448 CCTACATGTTCAGGATCGAGTCT 59.366 47.826 8.78 0.00 33.42 3.24
4751 12107 7.548075 CGGTTTCTAATTAGTGTAGGTGACAAT 59.452 37.037 12.19 0.00 40.66 2.71
4766 12122 4.152284 GGAGATGGTCCGGTTTCTAATT 57.848 45.455 0.00 0.00 34.84 1.40
4790 12146 6.617538 TCCCTCCCGATACTTAGATTCTTTA 58.382 40.000 0.00 0.00 0.00 1.85
4804 12160 0.905357 CTGACTTGTTCCCTCCCGAT 59.095 55.000 0.00 0.00 0.00 4.18
4842 12198 8.891671 ACTTAAACTCAACCGATAAAGTAACA 57.108 30.769 0.00 0.00 0.00 2.41
4846 12202 8.441312 TCAAACTTAAACTCAACCGATAAAGT 57.559 30.769 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.