Multiple sequence alignment - TraesCS2A01G371600

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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 TraesCS2A01G371600 chr2A 100.000 4255 0 0 1 4255 613990865 613986611 0.000000e+00 7858.0
1 TraesCS2A01G371600 chr2A 76.955 1931 365 51 1138 3010 613991512 613993420 0.000000e+00 1027.0
2 TraesCS2A01G371600 chr2A 89.749 439 37 4 3547 3977 57461694 57461256 4.810000e-154 555.0
3 TraesCS2A01G371600 chr2A 89.367 442 33 11 3545 3977 10750830 10750394 1.040000e-150 544.0
4 TraesCS2A01G371600 chr2A 88.276 435 41 7 3545 3974 221312020 221312449 2.930000e-141 512.0
5 TraesCS2A01G371600 chr2A 92.419 277 21 0 3977 4253 698795091 698794815 3.080000e-106 396.0
6 TraesCS2A01G371600 chr2A 92.115 279 20 2 3976 4253 57459919 57459642 3.990000e-105 392.0
7 TraesCS2A01G371600 chr2A 91.727 278 23 0 3976 4253 718475592 718475315 1.860000e-103 387.0
8 TraesCS2A01G371600 chr2A 90.877 285 22 4 3973 4255 160013638 160013920 3.110000e-101 379.0
9 TraesCS2A01G371600 chr2A 78.498 293 49 10 499 784 712060680 712060395 3.380000e-41 180.0
10 TraesCS2A01G371600 chr2B 92.694 2806 113 36 790 3550 551635570 551632812 0.000000e+00 3962.0
11 TraesCS2A01G371600 chr2B 77.905 1919 353 51 1138 3010 551637877 551639770 0.000000e+00 1129.0
12 TraesCS2A01G371600 chr2B 78.935 432 48 19 47 457 551636025 551635616 1.960000e-63 254.0
13 TraesCS2A01G371600 chr2B 78.214 280 47 9 499 774 661176710 661176979 2.630000e-37 167.0
14 TraesCS2A01G371600 chr2D 96.464 2319 70 7 790 3105 472469274 472466965 0.000000e+00 3818.0
15 TraesCS2A01G371600 chr2D 77.167 1927 362 53 1138 3010 472470512 472472414 0.000000e+00 1050.0
16 TraesCS2A01G371600 chr2D 89.008 373 18 5 3190 3540 472466911 472466540 1.400000e-119 440.0
17 TraesCS2A01G371600 chr2D 81.739 460 41 19 47 487 472469733 472469298 1.130000e-90 344.0
18 TraesCS2A01G371600 chr5B 76.870 1885 365 56 1162 3003 586359895 586358039 0.000000e+00 1000.0
19 TraesCS2A01G371600 chr5B 76.761 142 33 0 1410 1551 107369619 107369760 3.530000e-11 80.5
20 TraesCS2A01G371600 chr5A 76.200 1916 377 61 1138 3003 597688188 597686302 0.000000e+00 939.0
21 TraesCS2A01G371600 chr5A 91.197 284 23 2 3973 4255 462810503 462810785 6.670000e-103 385.0
22 TraesCS2A01G371600 chr5A 91.071 280 25 0 3976 4255 464136123 464135844 3.110000e-101 379.0
23 TraesCS2A01G371600 chr5A 79.137 139 29 0 1413 1551 105416967 105416829 3.500000e-16 97.1
24 TraesCS2A01G371600 chr1D 79.012 1296 233 33 1411 2689 192569688 192570961 0.000000e+00 850.0
25 TraesCS2A01G371600 chr5D 81.063 1035 161 25 1899 2910 478594579 478595601 0.000000e+00 793.0
26 TraesCS2A01G371600 chr5D 78.169 142 31 0 1410 1551 98227871 98228012 1.630000e-14 91.6
27 TraesCS2A01G371600 chr1B 78.164 1296 247 30 1411 2689 266258364 266259640 0.000000e+00 793.0
28 TraesCS2A01G371600 chr7A 75.393 1589 336 43 1142 2695 49991149 49989581 0.000000e+00 717.0
29 TraesCS2A01G371600 chr7A 90.433 439 34 5 3547 3977 366869004 366868566 4.770000e-159 571.0
30 TraesCS2A01G371600 chr7A 91.815 281 22 1 3976 4255 609131580 609131300 1.430000e-104 390.0
31 TraesCS2A01G371600 chr7A 79.412 272 41 11 495 761 724648330 724648069 1.220000e-40 178.0
32 TraesCS2A01G371600 chr7D 74.905 1586 337 46 1142 2689 47454099 47455661 0.000000e+00 667.0
33 TraesCS2A01G371600 chr7D 90.389 437 30 9 3545 3974 549405526 549405957 7.990000e-157 564.0
34 TraesCS2A01G371600 chr7D 79.496 278 44 9 499 772 605758685 605758417 7.270000e-43 185.0
35 TraesCS2A01G371600 chr3A 91.686 433 31 3 3545 3974 540678887 540679317 2.830000e-166 595.0
36 TraesCS2A01G371600 chr3A 90.367 436 35 5 3547 3977 707138410 707137977 2.220000e-157 566.0
37 TraesCS2A01G371600 chr3A 79.681 251 39 8 527 772 649800652 649800895 2.030000e-38 171.0
38 TraesCS2A01G371600 chr3A 89.381 113 12 0 2300 2412 23775094 23775206 4.430000e-30 143.0
39 TraesCS2A01G371600 chr4A 91.475 434 30 5 3547 3974 428261522 428261954 1.320000e-164 590.0
40 TraesCS2A01G371600 chr4A 80.505 277 41 9 499 771 140303542 140303275 2.590000e-47 200.0
41 TraesCS2A01G371600 chr6A 72.870 1596 379 47 1138 2694 104410242 104408662 2.280000e-137 499.0
42 TraesCS2A01G371600 chr6A 88.333 420 43 4 3564 3977 506521635 506521216 2.280000e-137 499.0
43 TraesCS2A01G371600 chr6A 92.832 279 20 0 3977 4255 599257438 599257716 5.120000e-109 405.0
44 TraesCS2A01G371600 chr6D 72.512 1437 341 44 1288 2688 86725152 86726570 2.370000e-112 416.0
45 TraesCS2A01G371600 chr1A 91.549 284 22 2 3973 4255 208880662 208880944 1.430000e-104 390.0
46 TraesCS2A01G371600 chr7B 78.545 275 46 7 499 769 201531925 201532190 7.320000e-38 169.0
47 TraesCS2A01G371600 chr3B 78.261 276 51 6 499 772 11954673 11954405 7.320000e-38 169.0
48 TraesCS2A01G371600 chr6B 77.899 276 50 7 500 772 588948225 588947958 1.220000e-35 161.0


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 TraesCS2A01G371600 chr2A 613986611 613990865 4254 True 7858.0 7858 100.000000 1 4255 1 chr2A.!!$R2 4254
1 TraesCS2A01G371600 chr2A 613991512 613993420 1908 False 1027.0 1027 76.955000 1138 3010 1 chr2A.!!$F3 1872
2 TraesCS2A01G371600 chr2A 57459642 57461694 2052 True 473.5 555 90.932000 3547 4253 2 chr2A.!!$R6 706
3 TraesCS2A01G371600 chr2B 551632812 551636025 3213 True 2108.0 3962 85.814500 47 3550 2 chr2B.!!$R1 3503
4 TraesCS2A01G371600 chr2B 551637877 551639770 1893 False 1129.0 1129 77.905000 1138 3010 1 chr2B.!!$F1 1872
5 TraesCS2A01G371600 chr2D 472466540 472469733 3193 True 1534.0 3818 89.070333 47 3540 3 chr2D.!!$R1 3493
6 TraesCS2A01G371600 chr2D 472470512 472472414 1902 False 1050.0 1050 77.167000 1138 3010 1 chr2D.!!$F1 1872
7 TraesCS2A01G371600 chr5B 586358039 586359895 1856 True 1000.0 1000 76.870000 1162 3003 1 chr5B.!!$R1 1841
8 TraesCS2A01G371600 chr5A 597686302 597688188 1886 True 939.0 939 76.200000 1138 3003 1 chr5A.!!$R3 1865
9 TraesCS2A01G371600 chr1D 192569688 192570961 1273 False 850.0 850 79.012000 1411 2689 1 chr1D.!!$F1 1278
10 TraesCS2A01G371600 chr5D 478594579 478595601 1022 False 793.0 793 81.063000 1899 2910 1 chr5D.!!$F2 1011
11 TraesCS2A01G371600 chr1B 266258364 266259640 1276 False 793.0 793 78.164000 1411 2689 1 chr1B.!!$F1 1278
12 TraesCS2A01G371600 chr7A 49989581 49991149 1568 True 717.0 717 75.393000 1142 2695 1 chr7A.!!$R1 1553
13 TraesCS2A01G371600 chr7D 47454099 47455661 1562 False 667.0 667 74.905000 1142 2689 1 chr7D.!!$F1 1547
14 TraesCS2A01G371600 chr6A 104408662 104410242 1580 True 499.0 499 72.870000 1138 2694 1 chr6A.!!$R1 1556
15 TraesCS2A01G371600 chr6D 86725152 86726570 1418 False 416.0 416 72.512000 1288 2688 1 chr6D.!!$F1 1400

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
236 254 0.030773 TTAGCAGCTGCCTCGTATCG 59.969 55.0 34.39 0.0 43.38 2.92 F
239 257 0.039074 GCAGCTGCCTCGTATCGTAT 60.039 55.0 28.76 0.0 34.31 3.06 F
2366 2485 0.317160 TACCTGCACGACAAGACCAG 59.683 55.0 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1127 1159 1.227853 AACTGGTCGGTGTTCTGCC 60.228 57.895 0.0 0.0 0.00 4.85 R
2710 2838 3.103911 CACGTTCTGGTCGTCGGC 61.104 66.667 0.0 0.0 39.55 5.54 R
3604 3796 0.040514 CGCGCCAAAACAGACAATGA 60.041 50.000 0.0 0.0 0.00 2.57 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
19 20 1.656652 CACTCCATTGACCGATCCAC 58.343 55.000 0.00 0.00 0.00 4.02
20 21 1.208052 CACTCCATTGACCGATCCACT 59.792 52.381 0.00 0.00 0.00 4.00
21 22 1.482593 ACTCCATTGACCGATCCACTC 59.517 52.381 0.00 0.00 0.00 3.51
22 23 1.482182 CTCCATTGACCGATCCACTCA 59.518 52.381 0.00 0.00 0.00 3.41
23 24 1.207089 TCCATTGACCGATCCACTCAC 59.793 52.381 0.00 0.00 0.00 3.51
24 25 1.656652 CATTGACCGATCCACTCACC 58.343 55.000 0.00 0.00 0.00 4.02
25 26 1.208052 CATTGACCGATCCACTCACCT 59.792 52.381 0.00 0.00 0.00 4.00
26 27 0.895530 TTGACCGATCCACTCACCTC 59.104 55.000 0.00 0.00 0.00 3.85
27 28 0.251608 TGACCGATCCACTCACCTCA 60.252 55.000 0.00 0.00 0.00 3.86
28 29 1.115467 GACCGATCCACTCACCTCAT 58.885 55.000 0.00 0.00 0.00 2.90
29 30 1.482593 GACCGATCCACTCACCTCATT 59.517 52.381 0.00 0.00 0.00 2.57
30 31 1.909302 ACCGATCCACTCACCTCATTT 59.091 47.619 0.00 0.00 0.00 2.32
31 32 2.305927 ACCGATCCACTCACCTCATTTT 59.694 45.455 0.00 0.00 0.00 1.82
32 33 2.939103 CCGATCCACTCACCTCATTTTC 59.061 50.000 0.00 0.00 0.00 2.29
33 34 2.939103 CGATCCACTCACCTCATTTTCC 59.061 50.000 0.00 0.00 0.00 3.13
34 35 2.879103 TCCACTCACCTCATTTTCCC 57.121 50.000 0.00 0.00 0.00 3.97
35 36 1.354368 TCCACTCACCTCATTTTCCCC 59.646 52.381 0.00 0.00 0.00 4.81
36 37 1.453155 CACTCACCTCATTTTCCCCG 58.547 55.000 0.00 0.00 0.00 5.73
37 38 0.328258 ACTCACCTCATTTTCCCCGG 59.672 55.000 0.00 0.00 0.00 5.73
38 39 0.328258 CTCACCTCATTTTCCCCGGT 59.672 55.000 0.00 0.00 0.00 5.28
39 40 0.037590 TCACCTCATTTTCCCCGGTG 59.962 55.000 0.00 0.00 44.92 4.94
40 41 0.965363 CACCTCATTTTCCCCGGTGG 60.965 60.000 0.00 0.82 41.01 4.61
41 42 1.382629 CCTCATTTTCCCCGGTGGT 59.617 57.895 0.00 0.00 34.77 4.16
42 43 0.251608 CCTCATTTTCCCCGGTGGTT 60.252 55.000 0.00 0.00 34.77 3.67
43 44 0.887933 CTCATTTTCCCCGGTGGTTG 59.112 55.000 0.00 0.08 34.77 3.77
44 45 0.478942 TCATTTTCCCCGGTGGTTGA 59.521 50.000 0.00 2.33 34.77 3.18
45 46 0.887933 CATTTTCCCCGGTGGTTGAG 59.112 55.000 0.00 0.00 34.77 3.02
52 53 0.965363 CCCGGTGGTTGAGGATTTGG 60.965 60.000 0.00 0.00 0.00 3.28
79 81 5.276868 CCATCTGCTTCGAGGTTTTAATACG 60.277 44.000 0.00 0.00 0.00 3.06
85 87 1.253545 CGAGGTTTTAATACGACGCCG 59.746 52.381 0.00 0.00 42.50 6.46
86 88 1.589779 GAGGTTTTAATACGACGCCGG 59.410 52.381 0.00 0.00 40.78 6.13
96 98 1.219522 ACGACGCCGGTTCTTTTGAG 61.220 55.000 1.90 0.00 40.78 3.02
97 99 0.942410 CGACGCCGGTTCTTTTGAGA 60.942 55.000 1.90 0.00 0.00 3.27
100 112 0.512952 CGCCGGTTCTTTTGAGACTG 59.487 55.000 1.90 0.00 0.00 3.51
103 115 0.512952 CGGTTCTTTTGAGACTGGCG 59.487 55.000 0.00 0.00 0.00 5.69
115 127 2.513897 CTGGCGATTTCCGGGTCC 60.514 66.667 0.00 0.00 39.04 4.46
117 129 2.045731 GGCGATTTCCGGGTCCAA 60.046 61.111 0.00 0.00 39.04 3.53
122 134 1.940613 CGATTTCCGGGTCCAATTCTC 59.059 52.381 0.00 0.00 33.91 2.87
125 137 1.358152 TTCCGGGTCCAATTCTCTGT 58.642 50.000 0.00 0.00 0.00 3.41
126 138 2.241281 TCCGGGTCCAATTCTCTGTA 57.759 50.000 0.00 0.00 0.00 2.74
132 144 4.081309 CGGGTCCAATTCTCTGTAACCTTA 60.081 45.833 0.00 0.00 0.00 2.69
133 145 5.429130 GGGTCCAATTCTCTGTAACCTTAG 58.571 45.833 0.00 0.00 0.00 2.18
151 163 4.822350 CCTTAGATGATCCTGACACGAGTA 59.178 45.833 0.00 0.00 0.00 2.59
160 172 6.377429 TGATCCTGACACGAGTAGTAAGAAAT 59.623 38.462 0.00 0.00 0.00 2.17
162 174 5.475909 TCCTGACACGAGTAGTAAGAAATGT 59.524 40.000 0.00 0.00 0.00 2.71
167 185 5.577164 ACACGAGTAGTAAGAAATGTGATGC 59.423 40.000 0.00 0.00 0.00 3.91
187 205 1.134965 CGCCGAGGAGAAGTCAAAGAT 60.135 52.381 0.00 0.00 0.00 2.40
194 212 1.021390 AGAAGTCAAAGATGGGCGCG 61.021 55.000 0.00 0.00 0.00 6.86
195 213 2.583685 GAAGTCAAAGATGGGCGCGC 62.584 60.000 25.94 25.94 0.00 6.86
196 214 4.520846 GTCAAAGATGGGCGCGCG 62.521 66.667 28.44 28.44 0.00 6.86
231 249 3.791539 CAGTTAGCAGCTGCCTCG 58.208 61.111 34.39 15.27 43.38 4.63
232 250 1.079543 CAGTTAGCAGCTGCCTCGT 60.080 57.895 34.39 18.95 43.38 4.18
235 253 1.067821 AGTTAGCAGCTGCCTCGTATC 59.932 52.381 34.39 18.19 43.38 2.24
236 254 0.030773 TTAGCAGCTGCCTCGTATCG 59.969 55.000 34.39 0.00 43.38 2.92
237 255 1.101635 TAGCAGCTGCCTCGTATCGT 61.102 55.000 34.39 15.49 43.38 3.73
238 256 1.101635 AGCAGCTGCCTCGTATCGTA 61.102 55.000 34.39 0.00 43.38 3.43
239 257 0.039074 GCAGCTGCCTCGTATCGTAT 60.039 55.000 28.76 0.00 34.31 3.06
240 258 1.970447 CAGCTGCCTCGTATCGTATC 58.030 55.000 0.00 0.00 0.00 2.24
241 259 1.537638 CAGCTGCCTCGTATCGTATCT 59.462 52.381 0.00 0.00 0.00 1.98
242 260 2.742589 CAGCTGCCTCGTATCGTATCTA 59.257 50.000 0.00 0.00 0.00 1.98
243 261 3.375610 CAGCTGCCTCGTATCGTATCTAT 59.624 47.826 0.00 0.00 0.00 1.98
244 262 3.623960 AGCTGCCTCGTATCGTATCTATC 59.376 47.826 0.00 0.00 0.00 2.08
245 263 3.374367 GCTGCCTCGTATCGTATCTATCA 59.626 47.826 0.00 0.00 0.00 2.15
247 265 3.939592 TGCCTCGTATCGTATCTATCAGG 59.060 47.826 0.00 0.00 0.00 3.86
248 266 3.242804 GCCTCGTATCGTATCTATCAGGC 60.243 52.174 0.00 0.00 37.35 4.85
249 267 4.193090 CCTCGTATCGTATCTATCAGGCT 58.807 47.826 0.00 0.00 0.00 4.58
250 268 5.358090 CCTCGTATCGTATCTATCAGGCTA 58.642 45.833 0.00 0.00 0.00 3.93
251 269 5.464057 CCTCGTATCGTATCTATCAGGCTAG 59.536 48.000 0.00 0.00 0.00 3.42
252 270 5.358090 TCGTATCGTATCTATCAGGCTAGG 58.642 45.833 0.00 0.00 0.00 3.02
253 271 5.128335 TCGTATCGTATCTATCAGGCTAGGA 59.872 44.000 0.00 0.00 0.00 2.94
255 273 7.015001 TCGTATCGTATCTATCAGGCTAGGATA 59.985 40.741 0.00 0.00 0.00 2.59
256 274 7.116662 CGTATCGTATCTATCAGGCTAGGATAC 59.883 44.444 11.33 11.33 37.95 2.24
257 275 6.309389 TCGTATCTATCAGGCTAGGATACA 57.691 41.667 18.84 2.45 41.41 2.29
258 276 6.350103 TCGTATCTATCAGGCTAGGATACAG 58.650 44.000 18.84 14.28 41.41 2.74
259 277 5.008217 CGTATCTATCAGGCTAGGATACAGC 59.992 48.000 18.84 0.00 41.41 4.40
268 286 1.335810 CTAGGATACAGCGTTGCGGTA 59.664 52.381 0.00 4.37 42.50 4.02
300 324 3.840666 ACCACTCACTCCTGTCATAATGT 59.159 43.478 0.00 0.00 0.00 2.71
304 328 6.111382 CACTCACTCCTGTCATAATGTCATT 58.889 40.000 3.06 3.06 0.00 2.57
316 340 2.143876 ATGTCATTGCCCACCTAACC 57.856 50.000 0.00 0.00 0.00 2.85
317 341 1.072266 TGTCATTGCCCACCTAACCT 58.928 50.000 0.00 0.00 0.00 3.50
318 342 2.270858 TGTCATTGCCCACCTAACCTA 58.729 47.619 0.00 0.00 0.00 3.08
319 343 2.645297 TGTCATTGCCCACCTAACCTAA 59.355 45.455 0.00 0.00 0.00 2.69
320 344 3.268334 TGTCATTGCCCACCTAACCTAAT 59.732 43.478 0.00 0.00 0.00 1.73
321 345 4.475381 TGTCATTGCCCACCTAACCTAATA 59.525 41.667 0.00 0.00 0.00 0.98
322 346 5.044772 TGTCATTGCCCACCTAACCTAATAA 60.045 40.000 0.00 0.00 0.00 1.40
323 347 5.531287 GTCATTGCCCACCTAACCTAATAAG 59.469 44.000 0.00 0.00 0.00 1.73
324 348 5.430417 TCATTGCCCACCTAACCTAATAAGA 59.570 40.000 0.00 0.00 0.00 2.10
325 349 5.987019 TTGCCCACCTAACCTAATAAGAT 57.013 39.130 0.00 0.00 0.00 2.40
326 350 7.293771 TCATTGCCCACCTAACCTAATAAGATA 59.706 37.037 0.00 0.00 0.00 1.98
327 351 7.642094 TTGCCCACCTAACCTAATAAGATAT 57.358 36.000 0.00 0.00 0.00 1.63
328 352 7.016153 TGCCCACCTAACCTAATAAGATATG 57.984 40.000 0.00 0.00 0.00 1.78
396 420 1.444724 TACAATGCACGCGTACGCT 60.445 52.632 34.69 20.51 45.53 5.07
397 421 1.679187 TACAATGCACGCGTACGCTG 61.679 55.000 34.69 29.42 45.53 5.18
398 422 3.487202 AATGCACGCGTACGCTGG 61.487 61.111 34.69 26.66 45.53 4.85
440 469 3.599343 CAGCACTGGCATAGTTTGTCTA 58.401 45.455 0.00 0.00 44.61 2.59
487 516 5.970289 TCCTCCTATGATTGTACTCTCCAT 58.030 41.667 0.00 0.00 0.00 3.41
489 518 5.777223 CCTCCTATGATTGTACTCTCCATCA 59.223 44.000 0.00 0.00 0.00 3.07
491 520 7.295322 TCCTATGATTGTACTCTCCATCAAG 57.705 40.000 0.00 0.00 0.00 3.02
492 521 7.069344 TCCTATGATTGTACTCTCCATCAAGA 58.931 38.462 0.00 0.00 0.00 3.02
493 522 7.014711 TCCTATGATTGTACTCTCCATCAAGAC 59.985 40.741 0.00 0.00 0.00 3.01
494 523 4.998788 TGATTGTACTCTCCATCAAGACG 58.001 43.478 0.00 0.00 0.00 4.18
496 525 5.360999 TGATTGTACTCTCCATCAAGACGAT 59.639 40.000 0.00 0.00 33.27 3.73
508 537 6.668541 CATCAAGACGATGGTAATGAAAGT 57.331 37.500 0.00 0.00 46.73 2.66
509 538 7.770801 CATCAAGACGATGGTAATGAAAGTA 57.229 36.000 0.00 0.00 46.73 2.24
510 539 8.370493 CATCAAGACGATGGTAATGAAAGTAT 57.630 34.615 0.00 0.00 46.73 2.12
511 540 8.491152 CATCAAGACGATGGTAATGAAAGTATC 58.509 37.037 0.00 0.00 46.73 2.24
512 541 7.552459 TCAAGACGATGGTAATGAAAGTATCA 58.448 34.615 0.00 0.00 43.67 2.15
558 587 8.978874 AATAGTATGCAATTTACATGAGGTGA 57.021 30.769 0.00 0.00 0.00 4.02
559 588 6.683974 AGTATGCAATTTACATGAGGTGAC 57.316 37.500 0.00 0.00 0.00 3.67
560 589 6.179756 AGTATGCAATTTACATGAGGTGACA 58.820 36.000 0.00 0.00 0.00 3.58
561 590 6.830324 AGTATGCAATTTACATGAGGTGACAT 59.170 34.615 0.00 0.00 0.00 3.06
562 591 7.992608 AGTATGCAATTTACATGAGGTGACATA 59.007 33.333 0.00 0.00 0.00 2.29
563 592 6.682423 TGCAATTTACATGAGGTGACATAG 57.318 37.500 0.00 0.00 0.00 2.23
564 593 6.413892 TGCAATTTACATGAGGTGACATAGA 58.586 36.000 0.00 0.00 0.00 1.98
565 594 6.883756 TGCAATTTACATGAGGTGACATAGAA 59.116 34.615 0.00 0.00 0.00 2.10
566 595 7.557358 TGCAATTTACATGAGGTGACATAGAAT 59.443 33.333 0.00 0.00 0.00 2.40
567 596 8.408601 GCAATTTACATGAGGTGACATAGAATT 58.591 33.333 0.00 0.00 0.00 2.17
611 640 9.750783 AAGTGTAGTACTATTATGATACCGGAT 57.249 33.333 9.46 0.00 39.18 4.18
612 641 9.750783 AGTGTAGTACTATTATGATACCGGATT 57.249 33.333 9.46 0.00 38.04 3.01
647 676 9.995003 TTGTATATTACTATGTGTCATGCATGA 57.005 29.630 25.42 25.42 0.00 3.07
663 692 7.984391 TCATGCATGACAATAAATAAAGTCGT 58.016 30.769 25.42 0.00 33.83 4.34
664 693 8.458052 TCATGCATGACAATAAATAAAGTCGTT 58.542 29.630 25.42 0.00 33.83 3.85
665 694 8.736742 CATGCATGACAATAAATAAAGTCGTTC 58.263 33.333 22.59 0.00 33.83 3.95
666 695 6.958752 TGCATGACAATAAATAAAGTCGTTCG 59.041 34.615 0.00 0.00 33.83 3.95
667 696 6.959311 GCATGACAATAAATAAAGTCGTTCGT 59.041 34.615 0.00 0.00 33.83 3.85
668 697 8.111836 GCATGACAATAAATAAAGTCGTTCGTA 58.888 33.333 0.00 0.00 33.83 3.43
669 698 9.961266 CATGACAATAAATAAAGTCGTTCGTAA 57.039 29.630 0.00 0.00 33.83 3.18
767 796 7.986085 ATGATACTATCCATTACAAACAGCC 57.014 36.000 0.00 0.00 0.00 4.85
768 797 7.136822 TGATACTATCCATTACAAACAGCCT 57.863 36.000 0.00 0.00 0.00 4.58
769 798 7.573710 TGATACTATCCATTACAAACAGCCTT 58.426 34.615 0.00 0.00 0.00 4.35
770 799 8.710239 TGATACTATCCATTACAAACAGCCTTA 58.290 33.333 0.00 0.00 0.00 2.69
771 800 9.726438 GATACTATCCATTACAAACAGCCTTAT 57.274 33.333 0.00 0.00 0.00 1.73
772 801 9.726438 ATACTATCCATTACAAACAGCCTTATC 57.274 33.333 0.00 0.00 0.00 1.75
773 802 6.706270 ACTATCCATTACAAACAGCCTTATCG 59.294 38.462 0.00 0.00 0.00 2.92
774 803 5.092554 TCCATTACAAACAGCCTTATCGA 57.907 39.130 0.00 0.00 0.00 3.59
775 804 4.873827 TCCATTACAAACAGCCTTATCGAC 59.126 41.667 0.00 0.00 0.00 4.20
790 819 6.219473 CCTTATCGACAGTCTTGATTAGCAT 58.781 40.000 0.00 0.00 0.00 3.79
791 820 6.703607 CCTTATCGACAGTCTTGATTAGCATT 59.296 38.462 0.00 0.00 0.00 3.56
792 821 7.867909 CCTTATCGACAGTCTTGATTAGCATTA 59.132 37.037 0.00 0.00 0.00 1.90
793 822 8.803201 TTATCGACAGTCTTGATTAGCATTAG 57.197 34.615 0.00 0.00 0.00 1.73
794 823 5.043903 TCGACAGTCTTGATTAGCATTAGC 58.956 41.667 0.00 0.00 42.56 3.09
795 824 4.805719 CGACAGTCTTGATTAGCATTAGCA 59.194 41.667 0.00 0.00 45.49 3.49
798 827 4.274459 CAGTCTTGATTAGCATTAGCACCC 59.726 45.833 0.00 0.00 45.49 4.61
801 830 2.135189 TGATTAGCATTAGCACCCCCT 58.865 47.619 0.00 0.00 45.49 4.79
802 831 2.106511 TGATTAGCATTAGCACCCCCTC 59.893 50.000 0.00 0.00 45.49 4.30
803 832 0.843984 TTAGCATTAGCACCCCCTCC 59.156 55.000 0.00 0.00 45.49 4.30
804 833 1.060163 TAGCATTAGCACCCCCTCCC 61.060 60.000 0.00 0.00 45.49 4.30
805 834 2.927056 CATTAGCACCCCCTCCCC 59.073 66.667 0.00 0.00 0.00 4.81
806 835 2.006415 CATTAGCACCCCCTCCCCA 61.006 63.158 0.00 0.00 0.00 4.96
807 836 2.006991 ATTAGCACCCCCTCCCCAC 61.007 63.158 0.00 0.00 0.00 4.61
808 837 4.752594 TAGCACCCCCTCCCCACC 62.753 72.222 0.00 0.00 0.00 4.61
908 937 4.147322 GGGTCAATGCGTCGCACG 62.147 66.667 24.34 16.87 43.04 5.34
912 942 1.445238 TCAATGCGTCGCACGATCA 60.445 52.632 24.34 0.00 46.05 2.92
918 948 1.966493 GCGTCGCACGATCACCAAAT 61.966 55.000 13.44 0.00 46.05 2.32
921 951 1.083489 TCGCACGATCACCAAATTCC 58.917 50.000 0.00 0.00 0.00 3.01
975 1007 4.595762 TCACACTCTACACTACAAACCC 57.404 45.455 0.00 0.00 0.00 4.11
976 1008 3.322828 TCACACTCTACACTACAAACCCC 59.677 47.826 0.00 0.00 0.00 4.95
985 1017 3.218386 TACAAACCCCCAGGCCTGC 62.218 63.158 28.39 0.00 36.11 4.85
1077 1109 1.819905 CCGCTTTCTCCTCCTCCTC 59.180 63.158 0.00 0.00 0.00 3.71
1081 1113 1.494960 CTTTCTCCTCCTCCTCCCAG 58.505 60.000 0.00 0.00 0.00 4.45
1377 1442 4.101790 GGCATGGCGTTCGTGGTG 62.102 66.667 2.41 0.00 33.10 4.17
2366 2485 0.317160 TACCTGCACGACAAGACCAG 59.683 55.000 0.00 0.00 0.00 4.00
2404 2532 1.202746 GCCAGAGGTTCCAGATCATCC 60.203 57.143 0.00 0.00 0.00 3.51
2915 3049 3.851128 GTACCTGGAGGGCGAGGC 61.851 72.222 0.00 0.00 43.23 4.70
3108 3242 8.567948 TGAATGAATAAACAAGGACAAGAAGTC 58.432 33.333 0.00 0.00 46.83 3.01
3119 3253 4.660352 GACAAGAAGTCGTCGTAGTAGT 57.340 45.455 0.00 0.00 37.53 2.73
3120 3254 5.769967 GACAAGAAGTCGTCGTAGTAGTA 57.230 43.478 0.00 0.00 37.53 1.82
3121 3255 5.776519 ACAAGAAGTCGTCGTAGTAGTAG 57.223 43.478 0.00 0.00 0.00 2.57
3122 3256 5.233988 ACAAGAAGTCGTCGTAGTAGTAGT 58.766 41.667 0.00 0.00 0.00 2.73
3123 3257 5.347364 ACAAGAAGTCGTCGTAGTAGTAGTC 59.653 44.000 0.00 0.00 0.00 2.59
3124 3258 4.101942 AGAAGTCGTCGTAGTAGTAGTCG 58.898 47.826 0.00 0.00 0.00 4.18
3125 3259 2.189342 AGTCGTCGTAGTAGTAGTCGC 58.811 52.381 0.00 0.00 0.00 5.19
3126 3260 2.159310 AGTCGTCGTAGTAGTAGTCGCT 60.159 50.000 0.00 0.00 0.00 4.93
3134 3268 0.447011 GTAGTAGTCGCTGCGTGAGT 59.553 55.000 22.48 12.95 0.00 3.41
3140 3274 3.767230 CGCTGCGTGAGTCGTTGG 61.767 66.667 14.93 0.00 42.13 3.77
3148 3282 2.661979 GCGTGAGTCGTTGGTTTGATTC 60.662 50.000 0.00 0.00 42.13 2.52
3190 3324 3.592898 ACGTCATCTGCTGTAACATGA 57.407 42.857 0.00 0.00 0.00 3.07
3191 3325 3.515630 ACGTCATCTGCTGTAACATGAG 58.484 45.455 0.00 0.00 0.00 2.90
3192 3326 2.283617 CGTCATCTGCTGTAACATGAGC 59.716 50.000 0.00 0.00 35.65 4.26
3272 3432 3.838120 TCTAGTCTGCACTCAAACATCG 58.162 45.455 0.00 0.00 33.62 3.84
3354 3532 2.093181 TGGTGGTGGATGTTATCTTCGG 60.093 50.000 0.00 0.00 0.00 4.30
3541 3732 1.007387 GCCGCCTGTTGTTTTCCTG 60.007 57.895 0.00 0.00 0.00 3.86
3543 3734 1.600023 CCGCCTGTTGTTTTCCTGTA 58.400 50.000 0.00 0.00 0.00 2.74
3564 3755 2.097160 GAGCATCTGCAACACGCG 59.903 61.111 3.53 3.53 46.97 6.01
3603 3795 2.836479 AAAACAGTTTTAGCGCGTGT 57.164 40.000 9.67 0.00 0.00 4.49
3604 3796 2.836479 AAACAGTTTTAGCGCGTGTT 57.164 40.000 8.43 5.49 32.75 3.32
3608 3800 2.289547 ACAGTTTTAGCGCGTGTTCATT 59.710 40.909 8.43 0.00 0.00 2.57
3610 3802 2.289547 AGTTTTAGCGCGTGTTCATTGT 59.710 40.909 8.43 0.00 0.00 2.71
3614 3806 0.880278 AGCGCGTGTTCATTGTCTGT 60.880 50.000 8.43 0.00 0.00 3.41
3625 3817 2.747507 ATTGTCTGTTTTGGCGCGGC 62.748 55.000 27.61 27.61 0.00 6.53
3709 3907 3.163594 GACTCGCACAAACAACATATGC 58.836 45.455 1.58 0.00 0.00 3.14
3714 3912 3.001856 CGCACAAACAACATATGCATTCG 60.002 43.478 3.54 0.00 36.02 3.34
3721 3919 6.932901 AACAACATATGCATTCGAAAACAG 57.067 33.333 3.54 0.00 0.00 3.16
3806 4004 9.915629 AACAAACAGTTTATTGTTCAGTACAAA 57.084 25.926 0.00 0.00 44.16 2.83
3881 4080 5.048504 ACAAATCATGATGCTCTTTGTCGTT 60.049 36.000 15.39 0.00 35.70 3.85
3900 4099 0.034186 TCATTCCATGCCCACCACTC 60.034 55.000 0.00 0.00 0.00 3.51
3903 4102 1.434513 TTCCATGCCCACCACTCCTT 61.435 55.000 0.00 0.00 0.00 3.36
3908 4107 1.367346 TGCCCACCACTCCTTAATGA 58.633 50.000 0.00 0.00 0.00 2.57
3913 4112 3.181450 CCCACCACTCCTTAATGAGATCC 60.181 52.174 13.92 0.00 36.22 3.36
3933 4132 5.535753 TCCTTCTGAAGATCATTATGCGA 57.464 39.130 18.68 0.77 0.00 5.10
3974 4173 2.039216 TGATAGGAGGCAACAAAACGGA 59.961 45.455 0.00 0.00 41.41 4.69
3985 5522 1.134310 ACAAAACGGACCGGAGAAAGT 60.134 47.619 20.00 6.01 0.00 2.66
3990 5527 3.479269 GACCGGAGAAAGTGCGCG 61.479 66.667 9.46 0.00 39.00 6.86
4073 5611 3.785859 GCGGCTGGATGAGGGTGA 61.786 66.667 0.00 0.00 0.00 4.02
4084 5622 1.979693 GAGGGTGAGAGGTGCGAGT 60.980 63.158 0.00 0.00 0.00 4.18
4102 5640 2.258591 GAGCGCGTGAGAGTCCAA 59.741 61.111 8.43 0.00 0.00 3.53
4105 5643 2.050351 CGCGTGAGAGTCCAACGT 60.050 61.111 14.53 0.00 0.00 3.99
4112 5650 2.029964 GAGTCCAACGTGCGGGAA 59.970 61.111 5.53 0.00 34.34 3.97
4153 5691 4.829518 GCGATTGCGTTTCGGCCC 62.830 66.667 0.00 0.00 40.36 5.80
4154 5692 3.427425 CGATTGCGTTTCGGCCCA 61.427 61.111 0.00 0.00 33.05 5.36
4172 5710 1.063649 ACGCGCTGGACTACGTATG 59.936 57.895 5.73 0.00 36.91 2.39
4224 5762 1.375013 AACTATTCCGGTTGCGCGT 60.375 52.632 8.43 0.00 0.00 6.01
4226 5764 2.048033 TATTCCGGTTGCGCGTGT 60.048 55.556 8.43 0.00 0.00 4.49
4236 5774 1.763200 TTGCGCGTGTGCTAAAACGA 61.763 50.000 8.43 0.00 42.32 3.85
4239 5777 1.495951 GCGTGTGCTAAAACGAGGG 59.504 57.895 0.00 0.00 42.32 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.482593 GAGTGGATCGGTCAATGGAGT 59.517 52.381 0.00 0.00 0.00 3.85
2 3 1.482182 TGAGTGGATCGGTCAATGGAG 59.518 52.381 0.00 0.00 0.00 3.86
3 4 1.207089 GTGAGTGGATCGGTCAATGGA 59.793 52.381 0.00 0.00 0.00 3.41
4 5 1.656652 GTGAGTGGATCGGTCAATGG 58.343 55.000 0.00 0.00 0.00 3.16
6 7 1.482593 GAGGTGAGTGGATCGGTCAAT 59.517 52.381 0.00 0.00 0.00 2.57
7 8 0.895530 GAGGTGAGTGGATCGGTCAA 59.104 55.000 0.00 0.00 0.00 3.18
8 9 0.251608 TGAGGTGAGTGGATCGGTCA 60.252 55.000 0.00 0.00 0.00 4.02
9 10 1.115467 ATGAGGTGAGTGGATCGGTC 58.885 55.000 0.00 0.00 0.00 4.79
10 11 1.573108 AATGAGGTGAGTGGATCGGT 58.427 50.000 0.00 0.00 0.00 4.69
11 12 2.698855 AAATGAGGTGAGTGGATCGG 57.301 50.000 0.00 0.00 0.00 4.18
12 13 2.939103 GGAAAATGAGGTGAGTGGATCG 59.061 50.000 0.00 0.00 0.00 3.69
13 14 3.282885 GGGAAAATGAGGTGAGTGGATC 58.717 50.000 0.00 0.00 0.00 3.36
14 15 2.024941 GGGGAAAATGAGGTGAGTGGAT 60.025 50.000 0.00 0.00 0.00 3.41
15 16 1.354368 GGGGAAAATGAGGTGAGTGGA 59.646 52.381 0.00 0.00 0.00 4.02
16 17 1.839424 GGGGAAAATGAGGTGAGTGG 58.161 55.000 0.00 0.00 0.00 4.00
17 18 1.453155 CGGGGAAAATGAGGTGAGTG 58.547 55.000 0.00 0.00 0.00 3.51
18 19 0.328258 CCGGGGAAAATGAGGTGAGT 59.672 55.000 0.00 0.00 0.00 3.41
19 20 0.328258 ACCGGGGAAAATGAGGTGAG 59.672 55.000 6.32 0.00 33.37 3.51
20 21 2.470311 ACCGGGGAAAATGAGGTGA 58.530 52.632 6.32 0.00 33.37 4.02
21 22 2.566824 CACCGGGGAAAATGAGGTG 58.433 57.895 6.32 0.00 45.01 4.00
22 23 1.382629 CCACCGGGGAAAATGAGGT 59.617 57.895 4.41 0.00 40.01 3.85
23 24 0.251608 AACCACCGGGGAAAATGAGG 60.252 55.000 4.41 0.00 41.15 3.86
24 25 0.887933 CAACCACCGGGGAAAATGAG 59.112 55.000 4.41 0.00 41.15 2.90
25 26 0.478942 TCAACCACCGGGGAAAATGA 59.521 50.000 4.41 0.06 41.15 2.57
26 27 0.887933 CTCAACCACCGGGGAAAATG 59.112 55.000 4.41 0.00 41.15 2.32
27 28 0.251608 CCTCAACCACCGGGGAAAAT 60.252 55.000 4.41 0.00 41.15 1.82
28 29 1.151908 CCTCAACCACCGGGGAAAA 59.848 57.895 4.41 0.00 41.15 2.29
29 30 1.137594 ATCCTCAACCACCGGGGAAA 61.138 55.000 4.41 0.00 41.15 3.13
30 31 1.137594 AATCCTCAACCACCGGGGAA 61.138 55.000 4.41 0.00 41.15 3.97
31 32 1.137594 AAATCCTCAACCACCGGGGA 61.138 55.000 4.41 0.00 41.15 4.81
32 33 0.965363 CAAATCCTCAACCACCGGGG 60.965 60.000 6.32 0.00 44.81 5.73
33 34 0.965363 CCAAATCCTCAACCACCGGG 60.965 60.000 6.32 0.00 41.29 5.73
34 35 0.037590 TCCAAATCCTCAACCACCGG 59.962 55.000 0.00 0.00 0.00 5.28
35 36 2.017049 GATCCAAATCCTCAACCACCG 58.983 52.381 0.00 0.00 0.00 4.94
36 37 2.379005 GGATCCAAATCCTCAACCACC 58.621 52.381 6.95 0.00 46.97 4.61
52 53 2.611225 AACCTCGAAGCAGATGGATC 57.389 50.000 0.00 0.00 0.00 3.36
56 57 5.518847 TCGTATTAAAACCTCGAAGCAGATG 59.481 40.000 0.00 0.00 0.00 2.90
79 81 0.511653 GTCTCAAAAGAACCGGCGTC 59.488 55.000 6.01 0.00 31.93 5.19
85 87 1.878953 TCGCCAGTCTCAAAAGAACC 58.121 50.000 0.00 0.00 31.93 3.62
86 88 4.467735 GAAATCGCCAGTCTCAAAAGAAC 58.532 43.478 0.00 0.00 31.93 3.01
96 98 1.814169 GACCCGGAAATCGCCAGTC 60.814 63.158 0.73 0.00 37.59 3.51
97 99 2.267961 GACCCGGAAATCGCCAGT 59.732 61.111 0.73 0.00 37.59 4.00
100 112 1.035385 AATTGGACCCGGAAATCGCC 61.035 55.000 0.73 0.00 37.59 5.54
103 115 2.945668 CAGAGAATTGGACCCGGAAATC 59.054 50.000 0.73 0.00 0.00 2.17
115 127 8.428063 AGGATCATCTAAGGTTACAGAGAATTG 58.572 37.037 0.00 0.00 0.00 2.32
117 129 7.786943 TCAGGATCATCTAAGGTTACAGAGAAT 59.213 37.037 0.00 0.00 0.00 2.40
122 134 6.276847 GTGTCAGGATCATCTAAGGTTACAG 58.723 44.000 0.00 0.00 0.00 2.74
125 137 5.198207 TCGTGTCAGGATCATCTAAGGTTA 58.802 41.667 0.00 0.00 0.00 2.85
126 138 4.023980 TCGTGTCAGGATCATCTAAGGTT 58.976 43.478 0.00 0.00 0.00 3.50
132 144 3.892284 ACTACTCGTGTCAGGATCATCT 58.108 45.455 0.00 0.00 0.00 2.90
133 145 5.527951 TCTTACTACTCGTGTCAGGATCATC 59.472 44.000 0.00 0.00 0.00 2.92
151 163 1.665679 CGGCGCATCACATTTCTTACT 59.334 47.619 10.83 0.00 0.00 2.24
160 172 2.563050 CTTCTCCTCGGCGCATCACA 62.563 60.000 10.83 0.00 0.00 3.58
162 174 2.284798 GACTTCTCCTCGGCGCATCA 62.285 60.000 10.83 0.00 0.00 3.07
167 185 0.243907 TCTTTGACTTCTCCTCGGCG 59.756 55.000 0.00 0.00 0.00 6.46
194 212 0.789383 CGACGAAATTGAGTTGGCGC 60.789 55.000 0.00 0.00 0.00 6.53
195 213 0.789383 GCGACGAAATTGAGTTGGCG 60.789 55.000 0.00 0.00 0.00 5.69
196 214 0.237235 TGCGACGAAATTGAGTTGGC 59.763 50.000 0.00 4.25 0.00 4.52
206 224 0.319555 AGCTGCTAACTGCGACGAAA 60.320 50.000 0.00 0.00 46.63 3.46
231 249 7.932491 TGTATCCTAGCCTGATAGATACGATAC 59.068 40.741 0.00 0.00 31.13 2.24
232 250 8.030913 TGTATCCTAGCCTGATAGATACGATA 57.969 38.462 0.00 0.00 0.00 2.92
235 253 5.008217 GCTGTATCCTAGCCTGATAGATACG 59.992 48.000 0.00 0.00 35.15 3.06
236 254 5.008217 CGCTGTATCCTAGCCTGATAGATAC 59.992 48.000 0.00 0.00 37.90 2.24
237 255 5.126779 CGCTGTATCCTAGCCTGATAGATA 58.873 45.833 0.00 0.00 37.90 1.98
238 256 3.951037 CGCTGTATCCTAGCCTGATAGAT 59.049 47.826 0.00 0.00 37.90 1.98
239 257 3.244946 ACGCTGTATCCTAGCCTGATAGA 60.245 47.826 0.00 0.00 37.90 1.98
240 258 3.085533 ACGCTGTATCCTAGCCTGATAG 58.914 50.000 0.00 0.00 37.90 2.08
241 259 3.156288 ACGCTGTATCCTAGCCTGATA 57.844 47.619 0.00 0.00 37.90 2.15
242 260 2.002505 ACGCTGTATCCTAGCCTGAT 57.997 50.000 0.00 0.00 37.90 2.90
243 261 1.409064 CAACGCTGTATCCTAGCCTGA 59.591 52.381 0.00 0.00 37.90 3.86
244 262 1.858091 CAACGCTGTATCCTAGCCTG 58.142 55.000 0.00 0.00 37.90 4.85
245 263 0.105039 GCAACGCTGTATCCTAGCCT 59.895 55.000 0.00 0.00 37.90 4.58
247 265 1.215655 CCGCAACGCTGTATCCTAGC 61.216 60.000 0.00 0.00 37.80 3.42
248 266 0.102481 ACCGCAACGCTGTATCCTAG 59.898 55.000 0.00 0.00 0.00 3.02
249 267 1.391577 TACCGCAACGCTGTATCCTA 58.608 50.000 0.00 0.00 0.00 2.94
250 268 0.750850 ATACCGCAACGCTGTATCCT 59.249 50.000 0.00 0.00 34.77 3.24
251 269 0.859232 CATACCGCAACGCTGTATCC 59.141 55.000 0.72 0.00 36.97 2.59
252 270 1.521423 GTCATACCGCAACGCTGTATC 59.479 52.381 0.72 0.00 36.97 2.24
253 271 1.567504 GTCATACCGCAACGCTGTAT 58.432 50.000 0.00 0.00 38.98 2.29
255 273 2.092291 CGTCATACCGCAACGCTGT 61.092 57.895 0.00 0.00 0.00 4.40
256 274 2.695055 CGTCATACCGCAACGCTG 59.305 61.111 0.00 0.00 0.00 5.18
268 286 0.681733 AGTGAGTGGTTGAGCGTCAT 59.318 50.000 0.00 0.00 0.00 3.06
300 324 5.430417 TCTTATTAGGTTAGGTGGGCAATGA 59.570 40.000 0.00 0.00 0.00 2.57
304 328 6.561070 ACATATCTTATTAGGTTAGGTGGGCA 59.439 38.462 0.00 0.00 0.00 5.36
340 364 6.625081 CGGGAGTCAAAGTCAAAAAGAAGTTT 60.625 38.462 0.00 0.00 0.00 2.66
419 448 2.430465 AGACAAACTATGCCAGTGCTG 58.570 47.619 0.00 0.00 37.63 4.41
440 469 5.411831 TTCAGAGCAAGATCACACTACAT 57.588 39.130 0.00 0.00 0.00 2.29
445 474 4.260170 AGGATTTCAGAGCAAGATCACAC 58.740 43.478 0.00 0.00 0.00 3.82
487 516 7.552459 TGATACTTTCATTACCATCGTCTTGA 58.448 34.615 0.00 0.00 0.00 3.02
491 520 9.477484 AGTTATGATACTTTCATTACCATCGTC 57.523 33.333 2.20 0.00 42.62 4.20
533 562 8.840321 GTCACCTCATGTAAATTGCATACTATT 58.160 33.333 0.00 0.00 0.00 1.73
534 563 7.992608 TGTCACCTCATGTAAATTGCATACTAT 59.007 33.333 0.00 0.00 0.00 2.12
535 564 7.334858 TGTCACCTCATGTAAATTGCATACTA 58.665 34.615 0.00 0.00 0.00 1.82
536 565 6.179756 TGTCACCTCATGTAAATTGCATACT 58.820 36.000 0.00 0.00 0.00 2.12
537 566 6.435430 TGTCACCTCATGTAAATTGCATAC 57.565 37.500 0.00 0.00 0.00 2.39
538 567 8.210265 TCTATGTCACCTCATGTAAATTGCATA 58.790 33.333 0.00 0.00 0.00 3.14
539 568 7.056006 TCTATGTCACCTCATGTAAATTGCAT 58.944 34.615 0.00 0.00 0.00 3.96
540 569 6.413892 TCTATGTCACCTCATGTAAATTGCA 58.586 36.000 0.00 0.00 0.00 4.08
541 570 6.925610 TCTATGTCACCTCATGTAAATTGC 57.074 37.500 0.00 0.00 0.00 3.56
585 614 9.750783 ATCCGGTATCATAATAGTACTACACTT 57.249 33.333 4.31 0.00 38.80 3.16
586 615 9.750783 AATCCGGTATCATAATAGTACTACACT 57.249 33.333 4.31 0.00 41.62 3.55
621 650 9.995003 TCATGCATGACACATAGTAATATACAA 57.005 29.630 25.42 0.00 0.00 2.41
638 667 7.984391 ACGACTTTATTTATTGTCATGCATGA 58.016 30.769 25.42 25.42 0.00 3.07
639 668 8.619146 AACGACTTTATTTATTGTCATGCATG 57.381 30.769 21.07 21.07 0.00 4.06
640 669 7.639850 CGAACGACTTTATTTATTGTCATGCAT 59.360 33.333 0.00 0.00 0.00 3.96
641 670 6.958752 CGAACGACTTTATTTATTGTCATGCA 59.041 34.615 0.00 0.00 0.00 3.96
642 671 6.959311 ACGAACGACTTTATTTATTGTCATGC 59.041 34.615 0.14 0.00 0.00 4.06
643 672 9.961266 TTACGAACGACTTTATTTATTGTCATG 57.039 29.630 0.14 0.00 0.00 3.07
741 770 9.502091 GGCTGTTTGTAATGGATAGTATCATAA 57.498 33.333 12.19 0.00 0.00 1.90
742 771 8.880244 AGGCTGTTTGTAATGGATAGTATCATA 58.120 33.333 12.19 1.05 0.00 2.15
743 772 7.749666 AGGCTGTTTGTAATGGATAGTATCAT 58.250 34.615 12.19 1.61 0.00 2.45
744 773 7.136822 AGGCTGTTTGTAATGGATAGTATCA 57.863 36.000 12.19 0.00 0.00 2.15
745 774 9.726438 ATAAGGCTGTTTGTAATGGATAGTATC 57.274 33.333 1.11 1.11 0.00 2.24
746 775 9.726438 GATAAGGCTGTTTGTAATGGATAGTAT 57.274 33.333 0.00 0.00 0.00 2.12
747 776 7.870954 CGATAAGGCTGTTTGTAATGGATAGTA 59.129 37.037 0.00 0.00 0.00 1.82
748 777 6.706270 CGATAAGGCTGTTTGTAATGGATAGT 59.294 38.462 0.00 0.00 0.00 2.12
749 778 6.929049 TCGATAAGGCTGTTTGTAATGGATAG 59.071 38.462 0.00 0.00 0.00 2.08
750 779 6.704493 GTCGATAAGGCTGTTTGTAATGGATA 59.296 38.462 0.00 0.00 0.00 2.59
751 780 5.527582 GTCGATAAGGCTGTTTGTAATGGAT 59.472 40.000 0.00 0.00 0.00 3.41
752 781 4.873827 GTCGATAAGGCTGTTTGTAATGGA 59.126 41.667 0.00 0.00 0.00 3.41
753 782 4.634004 TGTCGATAAGGCTGTTTGTAATGG 59.366 41.667 0.00 0.00 0.00 3.16
754 783 5.351465 ACTGTCGATAAGGCTGTTTGTAATG 59.649 40.000 0.00 0.00 32.53 1.90
755 784 5.488341 ACTGTCGATAAGGCTGTTTGTAAT 58.512 37.500 0.00 0.00 32.53 1.89
756 785 4.890088 ACTGTCGATAAGGCTGTTTGTAA 58.110 39.130 0.00 0.00 32.53 2.41
757 786 4.219944 AGACTGTCGATAAGGCTGTTTGTA 59.780 41.667 5.69 0.00 36.74 2.41
758 787 3.006967 AGACTGTCGATAAGGCTGTTTGT 59.993 43.478 5.69 0.00 36.74 2.83
759 788 3.589988 AGACTGTCGATAAGGCTGTTTG 58.410 45.455 5.69 0.00 36.74 2.93
760 789 3.963428 AGACTGTCGATAAGGCTGTTT 57.037 42.857 5.69 0.00 36.74 2.83
761 790 3.258372 TCAAGACTGTCGATAAGGCTGTT 59.742 43.478 7.17 0.00 36.74 3.16
762 791 2.826128 TCAAGACTGTCGATAAGGCTGT 59.174 45.455 7.17 0.00 39.38 4.40
763 792 3.510388 TCAAGACTGTCGATAAGGCTG 57.490 47.619 7.17 3.07 31.66 4.85
764 793 4.744795 AATCAAGACTGTCGATAAGGCT 57.255 40.909 1.52 0.71 33.06 4.58
765 794 4.446051 GCTAATCAAGACTGTCGATAAGGC 59.554 45.833 1.52 0.00 0.00 4.35
766 795 5.592054 TGCTAATCAAGACTGTCGATAAGG 58.408 41.667 1.52 0.00 0.00 2.69
767 796 7.706281 AATGCTAATCAAGACTGTCGATAAG 57.294 36.000 1.52 0.00 0.00 1.73
768 797 7.382488 GCTAATGCTAATCAAGACTGTCGATAA 59.618 37.037 1.52 0.00 36.03 1.75
769 798 6.863645 GCTAATGCTAATCAAGACTGTCGATA 59.136 38.462 1.52 0.00 36.03 2.92
770 799 5.694006 GCTAATGCTAATCAAGACTGTCGAT 59.306 40.000 1.52 0.00 36.03 3.59
771 800 5.043903 GCTAATGCTAATCAAGACTGTCGA 58.956 41.667 1.52 0.00 36.03 4.20
772 801 4.805719 TGCTAATGCTAATCAAGACTGTCG 59.194 41.667 1.52 0.00 40.48 4.35
773 802 5.007136 GGTGCTAATGCTAATCAAGACTGTC 59.993 44.000 0.00 0.00 40.48 3.51
774 803 4.878397 GGTGCTAATGCTAATCAAGACTGT 59.122 41.667 0.00 0.00 40.48 3.55
775 804 4.274459 GGGTGCTAATGCTAATCAAGACTG 59.726 45.833 0.00 0.00 40.48 3.51
790 819 2.612746 GTGGGGAGGGGGTGCTAA 60.613 66.667 0.00 0.00 0.00 3.09
791 820 4.752594 GGTGGGGAGGGGGTGCTA 62.753 72.222 0.00 0.00 0.00 3.49
805 834 3.185299 TAACGTGGGTGCCTGGGTG 62.185 63.158 0.00 0.00 0.00 4.61
806 835 2.850130 TAACGTGGGTGCCTGGGT 60.850 61.111 0.00 0.00 0.00 4.51
807 836 2.046314 CTAACGTGGGTGCCTGGG 60.046 66.667 0.00 0.00 0.00 4.45
808 837 2.746277 GCTAACGTGGGTGCCTGG 60.746 66.667 0.00 0.00 0.00 4.45
809 838 1.599518 TTGCTAACGTGGGTGCCTG 60.600 57.895 0.00 0.00 0.00 4.85
810 839 1.599797 GTTGCTAACGTGGGTGCCT 60.600 57.895 0.00 0.00 0.00 4.75
811 840 1.894756 TGTTGCTAACGTGGGTGCC 60.895 57.895 0.00 0.00 0.00 5.01
812 841 1.281656 GTGTTGCTAACGTGGGTGC 59.718 57.895 0.00 0.00 0.00 5.01
908 937 1.264288 GCGATCCGGAATTTGGTGATC 59.736 52.381 9.01 0.00 0.00 2.92
912 942 1.308998 GATGCGATCCGGAATTTGGT 58.691 50.000 9.01 0.00 0.00 3.67
918 948 0.804544 GTGAACGATGCGATCCGGAA 60.805 55.000 9.01 0.00 0.00 4.30
921 951 1.631072 GTGTGAACGATGCGATCCG 59.369 57.895 0.00 0.00 0.00 4.18
1077 1109 1.755008 GAGGACGAGGAGGACTGGG 60.755 68.421 0.00 0.00 0.00 4.45
1081 1113 1.820481 CGAGGAGGACGAGGAGGAC 60.820 68.421 0.00 0.00 0.00 3.85
1127 1159 1.227853 AACTGGTCGGTGTTCTGCC 60.228 57.895 0.00 0.00 0.00 4.85
2710 2838 3.103911 CACGTTCTGGTCGTCGGC 61.104 66.667 0.00 0.00 39.55 5.54
3079 3213 5.621197 TGTCCTTGTTTATTCATTCACCG 57.379 39.130 0.00 0.00 0.00 4.94
3108 3242 1.331854 GCAGCGACTACTACTACGACG 60.332 57.143 0.00 0.00 0.00 5.12
3111 3245 0.649475 ACGCAGCGACTACTACTACG 59.351 55.000 24.65 0.00 0.00 3.51
3114 3248 0.727970 CTCACGCAGCGACTACTACT 59.272 55.000 24.65 0.00 0.00 2.57
3116 3250 0.725686 GACTCACGCAGCGACTACTA 59.274 55.000 24.65 0.00 0.00 1.82
3117 3251 1.502640 GACTCACGCAGCGACTACT 59.497 57.895 24.65 0.00 0.00 2.57
3118 3252 1.863880 CGACTCACGCAGCGACTAC 60.864 63.158 24.65 7.68 34.51 2.73
3119 3253 1.848932 AACGACTCACGCAGCGACTA 61.849 55.000 24.65 5.00 46.94 2.59
3120 3254 3.195591 AACGACTCACGCAGCGACT 62.196 57.895 24.65 0.00 46.94 4.18
3121 3255 2.729862 AACGACTCACGCAGCGAC 60.730 61.111 24.65 6.24 46.94 5.19
3122 3256 2.729491 CAACGACTCACGCAGCGA 60.729 61.111 24.65 0.00 46.94 4.93
3123 3257 3.767230 CCAACGACTCACGCAGCG 61.767 66.667 14.82 14.82 46.94 5.18
3124 3258 1.772063 AAACCAACGACTCACGCAGC 61.772 55.000 0.00 0.00 46.94 5.25
3125 3259 0.042188 CAAACCAACGACTCACGCAG 60.042 55.000 0.00 0.00 46.94 5.18
3126 3260 0.460459 TCAAACCAACGACTCACGCA 60.460 50.000 0.00 0.00 46.94 5.24
3134 3268 4.286297 AGATGAGGAATCAAACCAACGA 57.714 40.909 0.00 0.00 37.81 3.85
3140 3274 5.174035 CGTCACGATAGATGAGGAATCAAAC 59.826 44.000 0.00 0.00 37.81 2.93
3190 3324 1.421646 ACTAGGAAAAGTGCCACTGCT 59.578 47.619 0.00 0.00 38.71 4.24
3191 3325 1.897560 ACTAGGAAAAGTGCCACTGC 58.102 50.000 0.00 0.00 38.26 4.40
3192 3326 3.997021 CACTACTAGGAAAAGTGCCACTG 59.003 47.826 0.00 0.00 34.73 3.66
3227 3375 7.661437 AGAAAAACATCACTGTATTACTGCTCA 59.339 33.333 1.03 0.00 33.36 4.26
3272 3432 4.052518 ACTCCCAGGCATGGCACC 62.053 66.667 22.64 0.17 46.19 5.01
3455 3645 2.509336 CCGTCACGGTCATCCTGC 60.509 66.667 8.54 0.00 42.73 4.85
3541 3732 3.302740 GCGTGTTGCAGATGCTCTTATAC 60.303 47.826 6.35 0.00 45.45 1.47
3543 3734 1.667724 GCGTGTTGCAGATGCTCTTAT 59.332 47.619 6.35 0.00 45.45 1.73
3591 3782 2.546368 AGACAATGAACACGCGCTAAAA 59.454 40.909 5.73 0.00 0.00 1.52
3603 3795 1.599171 CGCGCCAAAACAGACAATGAA 60.599 47.619 0.00 0.00 0.00 2.57
3604 3796 0.040514 CGCGCCAAAACAGACAATGA 60.041 50.000 0.00 0.00 0.00 2.57
3608 3800 3.959975 GCCGCGCCAAAACAGACA 61.960 61.111 0.00 0.00 0.00 3.41
3709 3907 6.810888 TCTTTTTGCTTCTGTTTTCGAATG 57.189 33.333 0.00 0.00 0.00 2.67
3714 3912 8.442384 TGTTTTGATCTTTTTGCTTCTGTTTTC 58.558 29.630 0.00 0.00 0.00 2.29
3721 3919 8.947304 TTTGTTTGTTTTGATCTTTTTGCTTC 57.053 26.923 0.00 0.00 0.00 3.86
3811 4009 8.575589 TGAACTATTTGTTATGTTCATTGCACT 58.424 29.630 0.00 0.00 42.25 4.40
3814 4012 9.190858 TGTTGAACTATTTGTTATGTTCATTGC 57.809 29.630 7.98 3.93 45.09 3.56
3851 4050 3.103738 GAGCATCATGATTTGTGCGTTC 58.896 45.455 5.16 0.00 37.41 3.95
3900 4099 7.733969 TGATCTTCAGAAGGATCTCATTAAGG 58.266 38.462 10.42 0.00 39.09 2.69
3908 4107 6.014755 TCGCATAATGATCTTCAGAAGGATCT 60.015 38.462 10.42 1.44 39.09 2.75
3913 4112 5.619513 GCATCGCATAATGATCTTCAGAAG 58.380 41.667 3.45 3.45 0.00 2.85
3933 4132 2.202878 CCATTCGACGTCCCGCAT 60.203 61.111 10.58 0.00 0.00 4.73
3995 5532 3.341469 TTCCCCAGCCTATCCCCGT 62.341 63.158 0.00 0.00 0.00 5.28
4084 5622 2.561037 TTGGACTCTCACGCGCTCA 61.561 57.895 5.73 0.00 0.00 4.26
4092 5630 2.338620 CCGCACGTTGGACTCTCA 59.661 61.111 0.00 0.00 0.00 3.27
4112 5650 3.051392 GCTTATTTGCTGCGCCCGT 62.051 57.895 4.18 0.00 0.00 5.28
4153 5691 1.063649 ATACGTAGTCCAGCGCGTG 59.936 57.895 8.43 4.73 43.93 5.34
4154 5692 1.063649 CATACGTAGTCCAGCGCGT 59.936 57.895 8.43 0.00 43.93 6.01
4195 5733 0.178068 GGAATAGTTGCTCCAGCGGA 59.822 55.000 0.00 0.00 45.83 5.54
4224 5762 3.305064 GCAAAATCCCTCGTTTTAGCACA 60.305 43.478 0.00 0.00 0.00 4.57
4226 5764 2.095466 CGCAAAATCCCTCGTTTTAGCA 60.095 45.455 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.