Multiple sequence alignment - TraesCS7B01G389600

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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 TraesCS7B01G389600 chr7B 100.000 3155 0 0 1 3155 656285665 656288819 0.000000e+00 5827.0
1 TraesCS7B01G389600 chr7B 85.505 1642 138 52 683 2264 656419394 656420995 0.000000e+00 1622.0
2 TraesCS7B01G389600 chr7B 82.528 538 49 22 675 1204 656274553 656275053 6.250000e-117 431.0
3 TraesCS7B01G389600 chr7B 85.714 154 20 1 416 569 384201149 384201300 9.060000e-36 161.0
4 TraesCS7B01G389600 chr7B 84.167 120 19 0 2798 2917 655113145 655113264 1.990000e-22 117.0
5 TraesCS7B01G389600 chr7B 80.921 152 24 4 2836 2986 656454524 656454671 7.150000e-22 115.0
6 TraesCS7B01G389600 chr7D 91.773 1884 117 20 412 2279 585666212 585668073 0.000000e+00 2586.0
7 TraesCS7B01G389600 chr7D 93.821 1052 62 3 1128 2178 586029335 586030384 0.000000e+00 1580.0
8 TraesCS7B01G389600 chr7D 93.807 985 39 10 2170 3152 586031965 586032929 0.000000e+00 1461.0
9 TraesCS7B01G389600 chr7D 90.830 458 35 2 1825 2279 585657007 585657460 9.680000e-170 606.0
10 TraesCS7B01G389600 chr7D 85.417 384 46 8 2608 2988 585685021 585685397 1.060000e-104 390.0
11 TraesCS7B01G389600 chr7D 81.382 521 55 22 675 1187 585656519 585657005 1.370000e-103 387.0
12 TraesCS7B01G389600 chr7D 94.811 212 11 0 1 212 585666006 585666217 6.520000e-87 331.0
13 TraesCS7B01G389600 chr7D 94.872 117 6 0 3039 3155 263487381 263487265 1.930000e-42 183.0
14 TraesCS7B01G389600 chr7D 78.370 319 32 21 683 970 586028949 586029261 4.180000e-39 172.0
15 TraesCS7B01G389600 chr7D 93.878 98 5 1 771 867 585726919 585727016 2.540000e-31 147.0
16 TraesCS7B01G389600 chr7D 82.895 152 21 4 2836 2986 586386389 586386536 7.100000e-27 132.0
17 TraesCS7B01G389600 chr7D 90.769 65 5 1 2278 2342 37956352 37956415 5.610000e-13 86.1
18 TraesCS7B01G389600 chr7D 95.455 44 2 0 673 716 585726875 585726918 1.570000e-08 71.3
19 TraesCS7B01G389600 chr7A 94.118 1547 88 2 1285 2828 676517622 676519168 0.000000e+00 2350.0
20 TraesCS7B01G389600 chr7A 92.954 1547 106 2 1285 2828 676539463 676541009 0.000000e+00 2250.0
21 TraesCS7B01G389600 chr7A 90.030 1665 98 31 618 2268 676361128 676359518 0.000000e+00 2093.0
22 TraesCS7B01G389600 chr7A 90.830 1385 74 21 414 1785 682176517 682175173 0.000000e+00 1805.0
23 TraesCS7B01G389600 chr7A 84.906 954 78 39 683 1615 677387498 677388406 0.000000e+00 904.0
24 TraesCS7B01G389600 chr7A 91.131 451 27 4 1832 2279 676306140 676306580 1.620000e-167 599.0
25 TraesCS7B01G389600 chr7A 91.051 447 35 3 1825 2268 682175175 682174731 1.620000e-167 599.0
26 TraesCS7B01G389600 chr7A 88.372 344 34 5 1649 1986 677433468 677433811 2.930000e-110 409.0
27 TraesCS7B01G389600 chr7A 89.124 331 16 2 2825 3155 676527225 676527535 8.200000e-106 394.0
28 TraesCS7B01G389600 chr7A 88.822 331 17 2 2825 3155 676549124 676549434 3.820000e-104 388.0
29 TraesCS7B01G389600 chr7A 84.031 382 40 15 2608 2987 676355561 676355199 6.480000e-92 348.0
30 TraesCS7B01G389600 chr7A 79.096 531 54 27 675 1198 676305662 676306142 2.360000e-81 313.0
31 TraesCS7B01G389600 chr7A 92.891 211 13 1 1 211 682176721 682176513 3.950000e-79 305.0
32 TraesCS7B01G389600 chr7A 89.151 212 17 2 1 211 676361438 676361232 3.120000e-65 259.0
33 TraesCS7B01G389600 chr7A 84.404 218 27 7 2367 2584 682178884 682178674 1.150000e-49 207.0
34 TraesCS7B01G389600 chr7A 88.889 108 12 0 2476 2583 676358895 676358788 1.970000e-27 134.0
35 TraesCS7B01G389600 chr7A 91.935 62 5 0 2278 2339 621755562 621755501 1.560000e-13 87.9
36 TraesCS7B01G389600 chr1D 81.920 448 51 20 1018 1458 487948935 487949359 5.010000e-93 351.0
37 TraesCS7B01G389600 chr2B 95.215 209 10 0 205 413 368289652 368289444 6.520000e-87 331.0
38 TraesCS7B01G389600 chr2B 96.970 198 5 1 213 409 573234933 573235130 6.520000e-87 331.0
39 TraesCS7B01G389600 chr2B 94.737 209 9 2 205 412 6723467 6723260 1.090000e-84 324.0
40 TraesCS7B01G389600 chr2B 87.342 158 18 1 416 573 273869924 273869769 2.500000e-41 180.0
41 TraesCS7B01G389600 chr5B 96.000 200 8 0 213 412 496792743 496792942 3.030000e-85 326.0
42 TraesCS7B01G389600 chr5B 95.169 207 9 1 213 418 589370011 589370217 3.030000e-85 326.0
43 TraesCS7B01G389600 chr5B 94.286 210 12 0 213 422 626383669 626383460 3.930000e-84 322.0
44 TraesCS7B01G389600 chr1A 78.558 541 78 28 1018 1530 586949984 586950514 3.930000e-84 322.0
45 TraesCS7B01G389600 chr4B 94.258 209 12 0 209 417 84523721 84523513 1.410000e-83 320.0
46 TraesCS7B01G389600 chr4B 89.691 97 8 2 2278 2373 659354486 659354581 4.270000e-24 122.0
47 TraesCS7B01G389600 chr6B 92.377 223 15 2 202 423 129793190 129793411 1.830000e-82 316.0
48 TraesCS7B01G389600 chr6B 94.017 117 6 1 3039 3155 184482142 184482257 3.230000e-40 176.0
49 TraesCS7B01G389600 chr6B 88.889 72 8 0 140 211 41257098 41257027 4.330000e-14 89.8
50 TraesCS7B01G389600 chr2A 92.727 220 15 1 198 417 343888368 343888150 1.830000e-82 316.0
51 TraesCS7B01G389600 chr2A 90.909 66 5 1 2277 2342 736009700 736009764 1.560000e-13 87.9
52 TraesCS7B01G389600 chr3A 89.744 156 15 1 420 575 701176949 701177103 6.900000e-47 198.0
53 TraesCS7B01G389600 chr3A 89.231 65 7 0 2278 2342 142888863 142888799 7.250000e-12 82.4
54 TraesCS7B01G389600 chr5D 89.542 153 14 1 414 566 487944675 487944825 3.210000e-45 193.0
55 TraesCS7B01G389600 chr5D 94.872 117 6 0 3039 3155 463121475 463121591 1.930000e-42 183.0
56 TraesCS7B01G389600 chr6D 94.828 116 6 0 3040 3155 313150559 313150444 6.950000e-42 182.0
57 TraesCS7B01G389600 chr6D 94.017 117 7 0 3039 3155 186963197 186963081 8.990000e-41 178.0
58 TraesCS7B01G389600 chr6A 94.872 117 5 1 3040 3155 14383346 14383230 6.950000e-42 182.0
59 TraesCS7B01G389600 chr4A 86.624 157 19 1 416 572 695116154 695116000 4.180000e-39 172.0
60 TraesCS7B01G389600 chr3B 85.976 164 20 2 416 578 257035497 257035658 4.180000e-39 172.0
61 TraesCS7B01G389600 chr3B 86.667 90 11 1 123 211 31305449 31305538 7.200000e-17 99.0
62 TraesCS7B01G389600 chr3B 90.278 72 5 1 140 211 31521199 31521268 3.350000e-15 93.5
63 TraesCS7B01G389600 chr3D 86.842 152 17 2 421 572 152168867 152168719 1.950000e-37 167.0
64 TraesCS7B01G389600 chr4D 91.860 86 6 1 123 207 325379178 325379263 5.530000e-23 119.0
65 TraesCS7B01G389600 chr1B 88.095 84 9 1 2280 2363 304417583 304417665 7.200000e-17 99.0
66 TraesCS7B01G389600 chrUn 88.889 72 8 0 140 211 234163450 234163379 4.330000e-14 89.8
67 TraesCS7B01G389600 chr2D 85.057 87 12 1 126 211 515540082 515539996 1.560000e-13 87.9


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 TraesCS7B01G389600 chr7B 656285665 656288819 3154 False 5827.0 5827 100.00000 1 3155 1 chr7B.!!$F4 3154
1 TraesCS7B01G389600 chr7B 656419394 656420995 1601 False 1622.0 1622 85.50500 683 2264 1 chr7B.!!$F5 1581
2 TraesCS7B01G389600 chr7B 656274553 656275053 500 False 431.0 431 82.52800 675 1204 1 chr7B.!!$F3 529
3 TraesCS7B01G389600 chr7D 585666006 585668073 2067 False 1458.5 2586 93.29200 1 2279 2 chr7D.!!$F5 2278
4 TraesCS7B01G389600 chr7D 586028949 586032929 3980 False 1071.0 1580 88.66600 683 3152 3 chr7D.!!$F7 2469
5 TraesCS7B01G389600 chr7D 585656519 585657460 941 False 496.5 606 86.10600 675 2279 2 chr7D.!!$F4 1604
6 TraesCS7B01G389600 chr7A 676517622 676519168 1546 False 2350.0 2350 94.11800 1285 2828 1 chr7A.!!$F1 1543
7 TraesCS7B01G389600 chr7A 676539463 676541009 1546 False 2250.0 2250 92.95400 1285 2828 1 chr7A.!!$F3 1543
8 TraesCS7B01G389600 chr7A 677387498 677388406 908 False 904.0 904 84.90600 683 1615 1 chr7A.!!$F5 932
9 TraesCS7B01G389600 chr7A 682174731 682178884 4153 True 729.0 1805 89.79400 1 2584 4 chr7A.!!$R3 2583
10 TraesCS7B01G389600 chr7A 676355199 676361438 6239 True 708.5 2093 88.02525 1 2987 4 chr7A.!!$R2 2986
11 TraesCS7B01G389600 chr7A 676305662 676306580 918 False 456.0 599 85.11350 675 2279 2 chr7A.!!$F7 1604
12 TraesCS7B01G389600 chr1A 586949984 586950514 530 False 322.0 322 78.55800 1018 1530 1 chr1A.!!$F1 512

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
297 2461 0.107410 ATCGGCAAGTTAATCGGCCA 60.107 50.0 2.24 0.0 46.75 5.36 F
351 2515 0.395448 AGGCTACTCGGTGACCCTAC 60.395 60.0 0.00 0.0 0.00 3.18 F
770 2945 0.599558 TGCACAGCAAGCATCCTTTC 59.400 50.0 0.00 0.0 37.02 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1112 3366 0.179094 GGTGGACGTTGCGATGGATA 60.179 55.0 0.00 0.00 0.0 2.59 R
1639 3930 0.456221 GACGCATTCTCCTCCTTCGA 59.544 55.0 0.00 0.00 0.0 3.71 R
2495 6875 0.465460 GGTGATGGCCGGCTGATAAA 60.465 55.0 28.56 7.96 0.0 1.40 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
90 2254 1.271817 TGCATGTGGGTGTTCATAGCA 60.272 47.619 0.00 0.00 0.00 3.49
137 2301 7.013464 GTGAGCATATGTACTACTACCTCTGTT 59.987 40.741 4.29 0.00 0.00 3.16
148 2312 7.970102 ACTACTACCTCTGTTTGGTTTATTGA 58.030 34.615 0.00 0.00 38.88 2.57
152 2316 5.892348 ACCTCTGTTTGGTTTATTGATCCT 58.108 37.500 0.00 0.00 33.34 3.24
229 2393 9.832445 AGTTATATACATTGTTGAGGAAATCGT 57.168 29.630 0.00 0.00 0.00 3.73
234 2398 6.877611 ACATTGTTGAGGAAATCGTTAACT 57.122 33.333 3.71 0.00 33.31 2.24
235 2399 6.668323 ACATTGTTGAGGAAATCGTTAACTG 58.332 36.000 3.71 0.00 33.31 3.16
236 2400 5.682943 TTGTTGAGGAAATCGTTAACTGG 57.317 39.130 3.71 0.00 33.31 4.00
237 2401 4.710324 TGTTGAGGAAATCGTTAACTGGT 58.290 39.130 3.71 0.00 33.31 4.00
238 2402 5.856156 TGTTGAGGAAATCGTTAACTGGTA 58.144 37.500 3.71 0.00 33.31 3.25
239 2403 5.929992 TGTTGAGGAAATCGTTAACTGGTAG 59.070 40.000 3.71 0.00 33.31 3.18
240 2404 4.501071 TGAGGAAATCGTTAACTGGTAGC 58.499 43.478 3.71 0.00 0.00 3.58
241 2405 4.222145 TGAGGAAATCGTTAACTGGTAGCT 59.778 41.667 3.71 0.00 0.00 3.32
242 2406 4.504858 AGGAAATCGTTAACTGGTAGCTG 58.495 43.478 3.71 0.00 0.00 4.24
243 2407 3.063588 GGAAATCGTTAACTGGTAGCTGC 59.936 47.826 3.71 0.00 0.00 5.25
244 2408 3.611766 AATCGTTAACTGGTAGCTGCT 57.388 42.857 7.57 7.57 0.00 4.24
245 2409 2.649331 TCGTTAACTGGTAGCTGCTC 57.351 50.000 4.91 0.00 0.00 4.26
246 2410 1.135489 TCGTTAACTGGTAGCTGCTCG 60.135 52.381 4.91 0.00 0.00 5.03
247 2411 1.641577 GTTAACTGGTAGCTGCTCGG 58.358 55.000 4.91 0.00 0.00 4.63
248 2412 1.067071 GTTAACTGGTAGCTGCTCGGT 60.067 52.381 4.91 0.41 0.00 4.69
249 2413 1.263356 TAACTGGTAGCTGCTCGGTT 58.737 50.000 16.67 16.67 34.74 4.44
250 2414 0.320771 AACTGGTAGCTGCTCGGTTG 60.321 55.000 4.91 0.00 0.00 3.77
251 2415 1.448540 CTGGTAGCTGCTCGGTTGG 60.449 63.158 4.91 0.00 0.00 3.77
252 2416 2.820037 GGTAGCTGCTCGGTTGGC 60.820 66.667 4.91 0.00 0.00 4.52
253 2417 2.266055 GTAGCTGCTCGGTTGGCT 59.734 61.111 4.91 0.00 38.62 4.75
254 2418 2.103042 GTAGCTGCTCGGTTGGCTG 61.103 63.158 4.91 0.00 36.40 4.85
255 2419 3.315142 TAGCTGCTCGGTTGGCTGG 62.315 63.158 4.91 0.00 36.40 4.85
257 2421 3.052082 CTGCTCGGTTGGCTGGTG 61.052 66.667 0.00 0.00 0.00 4.17
258 2422 3.535629 CTGCTCGGTTGGCTGGTGA 62.536 63.158 0.00 0.00 0.00 4.02
259 2423 2.743928 GCTCGGTTGGCTGGTGAG 60.744 66.667 0.00 0.00 0.00 3.51
260 2424 2.743718 CTCGGTTGGCTGGTGAGT 59.256 61.111 0.00 0.00 0.00 3.41
261 2425 1.972198 CTCGGTTGGCTGGTGAGTA 59.028 57.895 0.00 0.00 0.00 2.59
262 2426 0.108615 CTCGGTTGGCTGGTGAGTAG 60.109 60.000 0.00 0.00 0.00 2.57
263 2427 1.079127 CGGTTGGCTGGTGAGTAGG 60.079 63.158 0.00 0.00 0.00 3.18
264 2428 1.299976 GGTTGGCTGGTGAGTAGGG 59.700 63.158 0.00 0.00 0.00 3.53
265 2429 1.299976 GTTGGCTGGTGAGTAGGGG 59.700 63.158 0.00 0.00 0.00 4.79
266 2430 1.159905 TTGGCTGGTGAGTAGGGGA 59.840 57.895 0.00 0.00 0.00 4.81
267 2431 0.253160 TTGGCTGGTGAGTAGGGGAT 60.253 55.000 0.00 0.00 0.00 3.85
268 2432 0.253160 TGGCTGGTGAGTAGGGGATT 60.253 55.000 0.00 0.00 0.00 3.01
269 2433 1.009060 TGGCTGGTGAGTAGGGGATTA 59.991 52.381 0.00 0.00 0.00 1.75
270 2434 2.124411 GGCTGGTGAGTAGGGGATTAA 58.876 52.381 0.00 0.00 0.00 1.40
271 2435 2.711547 GGCTGGTGAGTAGGGGATTAAT 59.288 50.000 0.00 0.00 0.00 1.40
272 2436 3.138468 GGCTGGTGAGTAGGGGATTAATT 59.862 47.826 0.00 0.00 0.00 1.40
273 2437 4.137543 GCTGGTGAGTAGGGGATTAATTG 58.862 47.826 0.00 0.00 0.00 2.32
274 2438 4.718961 CTGGTGAGTAGGGGATTAATTGG 58.281 47.826 0.00 0.00 0.00 3.16
275 2439 3.117663 TGGTGAGTAGGGGATTAATTGGC 60.118 47.826 0.00 0.00 0.00 4.52
276 2440 3.138468 GGTGAGTAGGGGATTAATTGGCT 59.862 47.826 0.00 0.00 0.00 4.75
277 2441 4.349930 GGTGAGTAGGGGATTAATTGGCTA 59.650 45.833 0.00 0.00 0.00 3.93
278 2442 5.163131 GGTGAGTAGGGGATTAATTGGCTAA 60.163 44.000 0.00 0.00 0.00 3.09
279 2443 6.467339 GGTGAGTAGGGGATTAATTGGCTAAT 60.467 42.308 0.00 0.00 0.00 1.73
280 2444 6.655425 GTGAGTAGGGGATTAATTGGCTAATC 59.345 42.308 0.00 0.00 37.50 1.75
281 2445 5.805728 AGTAGGGGATTAATTGGCTAATCG 58.194 41.667 0.00 0.00 38.61 3.34
282 2446 4.034285 AGGGGATTAATTGGCTAATCGG 57.966 45.455 0.00 0.00 38.61 4.18
283 2447 2.492088 GGGGATTAATTGGCTAATCGGC 59.508 50.000 0.00 0.00 38.61 5.54
293 2457 2.869801 TGGCTAATCGGCAAGTTAATCG 59.130 45.455 0.00 0.00 46.25 3.34
294 2458 2.223377 GGCTAATCGGCAAGTTAATCGG 59.777 50.000 0.00 0.00 38.25 4.18
295 2459 2.349532 GCTAATCGGCAAGTTAATCGGC 60.350 50.000 0.00 0.00 0.00 5.54
296 2460 1.021968 AATCGGCAAGTTAATCGGCC 58.978 50.000 0.00 0.00 42.98 6.13
297 2461 0.107410 ATCGGCAAGTTAATCGGCCA 60.107 50.000 2.24 0.00 46.75 5.36
298 2462 0.107410 TCGGCAAGTTAATCGGCCAT 60.107 50.000 2.24 0.00 46.75 4.40
299 2463 0.738389 CGGCAAGTTAATCGGCCATT 59.262 50.000 2.24 4.55 46.75 3.16
300 2464 1.134175 CGGCAAGTTAATCGGCCATTT 59.866 47.619 2.24 0.00 46.75 2.32
301 2465 2.356382 CGGCAAGTTAATCGGCCATTTA 59.644 45.455 2.24 0.00 46.75 1.40
302 2466 3.181495 CGGCAAGTTAATCGGCCATTTAA 60.181 43.478 2.24 3.07 46.75 1.52
303 2467 4.499019 CGGCAAGTTAATCGGCCATTTAAT 60.499 41.667 2.24 0.00 46.75 1.40
304 2468 4.982295 GGCAAGTTAATCGGCCATTTAATC 59.018 41.667 2.24 1.98 45.70 1.75
305 2469 5.451242 GGCAAGTTAATCGGCCATTTAATCA 60.451 40.000 2.24 0.00 45.70 2.57
306 2470 6.039616 GCAAGTTAATCGGCCATTTAATCAA 58.960 36.000 2.24 0.00 0.00 2.57
307 2471 6.701400 GCAAGTTAATCGGCCATTTAATCAAT 59.299 34.615 2.24 0.00 0.00 2.57
308 2472 7.224557 GCAAGTTAATCGGCCATTTAATCAATT 59.775 33.333 2.24 0.00 0.00 2.32
309 2473 9.743057 CAAGTTAATCGGCCATTTAATCAATTA 57.257 29.630 2.24 0.00 0.00 1.40
313 2477 9.619316 TTAATCGGCCATTTAATCAATTAATCG 57.381 29.630 2.24 0.00 32.78 3.34
314 2478 6.007936 TCGGCCATTTAATCAATTAATCGG 57.992 37.500 2.24 2.40 32.78 4.18
315 2479 5.765677 TCGGCCATTTAATCAATTAATCGGA 59.234 36.000 2.24 0.00 32.78 4.55
316 2480 5.856455 CGGCCATTTAATCAATTAATCGGAC 59.144 40.000 2.24 9.25 32.60 4.79
317 2481 6.514212 CGGCCATTTAATCAATTAATCGGACA 60.514 38.462 2.24 0.00 34.22 4.02
318 2482 7.206687 GGCCATTTAATCAATTAATCGGACAA 58.793 34.615 0.00 0.00 34.49 3.18
319 2483 7.872483 GGCCATTTAATCAATTAATCGGACAAT 59.128 33.333 0.00 0.00 34.49 2.71
320 2484 9.260002 GCCATTTAATCAATTAATCGGACAATT 57.740 29.630 11.86 0.00 32.78 2.32
327 2491 7.795482 TCAATTAATCGGACAATTTATCGGT 57.205 32.000 0.00 0.00 0.00 4.69
328 2492 8.215926 TCAATTAATCGGACAATTTATCGGTT 57.784 30.769 0.00 0.00 0.00 4.44
329 2493 8.679100 TCAATTAATCGGACAATTTATCGGTTT 58.321 29.630 0.00 0.00 0.00 3.27
330 2494 9.938670 CAATTAATCGGACAATTTATCGGTTTA 57.061 29.630 0.00 0.00 0.00 2.01
334 2498 7.900782 ATCGGACAATTTATCGGTTTATAGG 57.099 36.000 0.00 0.00 0.00 2.57
335 2499 5.697633 TCGGACAATTTATCGGTTTATAGGC 59.302 40.000 0.00 0.00 0.00 3.93
336 2500 5.699458 CGGACAATTTATCGGTTTATAGGCT 59.301 40.000 0.00 0.00 0.00 4.58
337 2501 6.869913 CGGACAATTTATCGGTTTATAGGCTA 59.130 38.462 0.00 0.00 0.00 3.93
338 2502 7.148689 CGGACAATTTATCGGTTTATAGGCTAC 60.149 40.741 0.00 0.00 0.00 3.58
339 2503 7.876582 GGACAATTTATCGGTTTATAGGCTACT 59.123 37.037 0.00 0.00 0.00 2.57
340 2504 8.828688 ACAATTTATCGGTTTATAGGCTACTC 57.171 34.615 0.00 0.00 0.00 2.59
341 2505 7.597743 ACAATTTATCGGTTTATAGGCTACTCG 59.402 37.037 0.00 0.00 0.00 4.18
342 2506 5.633830 TTATCGGTTTATAGGCTACTCGG 57.366 43.478 0.00 0.00 0.00 4.63
343 2507 2.936202 TCGGTTTATAGGCTACTCGGT 58.064 47.619 0.00 0.00 0.00 4.69
344 2508 2.620115 TCGGTTTATAGGCTACTCGGTG 59.380 50.000 0.00 0.00 0.00 4.94
345 2509 2.620115 CGGTTTATAGGCTACTCGGTGA 59.380 50.000 0.00 0.00 0.00 4.02
346 2510 3.549625 CGGTTTATAGGCTACTCGGTGAC 60.550 52.174 0.00 0.00 0.00 3.67
347 2511 3.243670 GGTTTATAGGCTACTCGGTGACC 60.244 52.174 0.00 0.00 0.00 4.02
348 2512 2.283145 TATAGGCTACTCGGTGACCC 57.717 55.000 0.00 0.00 0.00 4.46
349 2513 0.556747 ATAGGCTACTCGGTGACCCT 59.443 55.000 0.00 0.00 0.00 4.34
350 2514 1.216064 TAGGCTACTCGGTGACCCTA 58.784 55.000 0.00 0.00 0.00 3.53
351 2515 0.395448 AGGCTACTCGGTGACCCTAC 60.395 60.000 0.00 0.00 0.00 3.18
352 2516 1.722636 GGCTACTCGGTGACCCTACG 61.723 65.000 0.00 0.00 0.00 3.51
353 2517 0.745845 GCTACTCGGTGACCCTACGA 60.746 60.000 0.00 0.00 35.14 3.43
355 2519 4.315588 CTCGGTGACCCTACGAGT 57.684 61.111 0.00 0.00 46.43 4.18
356 2520 3.465990 CTCGGTGACCCTACGAGTA 57.534 57.895 0.00 0.00 46.43 2.59
357 2521 1.297664 CTCGGTGACCCTACGAGTAG 58.702 60.000 0.00 3.39 46.43 2.57
358 2522 0.615331 TCGGTGACCCTACGAGTAGT 59.385 55.000 9.15 0.00 32.29 2.73
359 2523 0.731417 CGGTGACCCTACGAGTAGTG 59.269 60.000 9.15 0.78 0.00 2.74
360 2524 1.676916 CGGTGACCCTACGAGTAGTGA 60.677 57.143 9.15 0.00 0.00 3.41
361 2525 2.652590 GGTGACCCTACGAGTAGTGAT 58.347 52.381 9.15 0.00 0.00 3.06
362 2526 3.022406 GGTGACCCTACGAGTAGTGATT 58.978 50.000 9.15 0.00 0.00 2.57
363 2527 4.202441 GGTGACCCTACGAGTAGTGATTA 58.798 47.826 9.15 0.00 0.00 1.75
364 2528 4.641989 GGTGACCCTACGAGTAGTGATTAA 59.358 45.833 9.15 0.00 0.00 1.40
365 2529 5.301298 GGTGACCCTACGAGTAGTGATTAAT 59.699 44.000 9.15 0.00 0.00 1.40
366 2530 6.437094 GTGACCCTACGAGTAGTGATTAATC 58.563 44.000 8.60 8.60 0.00 1.75
372 2536 4.956034 CGAGTAGTGATTAATCGGCAAG 57.044 45.455 10.80 0.00 43.89 4.01
373 2537 4.360563 CGAGTAGTGATTAATCGGCAAGT 58.639 43.478 10.80 0.00 43.89 3.16
374 2538 4.804139 CGAGTAGTGATTAATCGGCAAGTT 59.196 41.667 10.80 0.00 43.89 2.66
375 2539 5.975344 CGAGTAGTGATTAATCGGCAAGTTA 59.025 40.000 10.80 0.00 43.89 2.24
376 2540 6.474427 CGAGTAGTGATTAATCGGCAAGTTAA 59.526 38.462 10.80 0.00 43.89 2.01
377 2541 7.514747 CGAGTAGTGATTAATCGGCAAGTTAAC 60.515 40.741 10.80 0.00 43.89 2.01
378 2542 7.328737 AGTAGTGATTAATCGGCAAGTTAACT 58.671 34.615 10.80 1.12 0.00 2.24
379 2543 6.422776 AGTGATTAATCGGCAAGTTAACTG 57.577 37.500 9.34 4.88 0.00 3.16
380 2544 5.354234 AGTGATTAATCGGCAAGTTAACTGG 59.646 40.000 9.34 7.35 0.00 4.00
381 2545 5.123344 GTGATTAATCGGCAAGTTAACTGGT 59.877 40.000 9.34 0.00 0.00 4.00
382 2546 5.708230 TGATTAATCGGCAAGTTAACTGGTT 59.292 36.000 9.34 1.66 0.00 3.67
383 2547 6.879993 TGATTAATCGGCAAGTTAACTGGTTA 59.120 34.615 9.34 0.65 0.00 2.85
384 2548 7.390996 TGATTAATCGGCAAGTTAACTGGTTAA 59.609 33.333 9.34 9.79 33.48 2.01
385 2549 7.690952 TTAATCGGCAAGTTAACTGGTTAAT 57.309 32.000 9.34 0.00 37.37 1.40
386 2550 6.584185 AATCGGCAAGTTAACTGGTTAATT 57.416 33.333 9.34 4.73 37.37 1.40
387 2551 5.365403 TCGGCAAGTTAACTGGTTAATTG 57.635 39.130 9.34 2.83 37.37 2.32
388 2552 4.216687 TCGGCAAGTTAACTGGTTAATTGG 59.783 41.667 9.34 11.39 37.37 3.16
389 2553 4.617298 CGGCAAGTTAACTGGTTAATTGGG 60.617 45.833 9.34 10.36 37.37 4.12
390 2554 4.282449 GGCAAGTTAACTGGTTAATTGGGT 59.718 41.667 9.34 0.00 37.37 4.51
391 2555 5.227152 GCAAGTTAACTGGTTAATTGGGTG 58.773 41.667 9.34 0.03 37.37 4.61
392 2556 5.010213 GCAAGTTAACTGGTTAATTGGGTGA 59.990 40.000 9.34 0.00 37.37 4.02
393 2557 6.461788 GCAAGTTAACTGGTTAATTGGGTGAA 60.462 38.462 9.34 0.00 37.37 3.18
394 2558 7.666623 CAAGTTAACTGGTTAATTGGGTGAAT 58.333 34.615 9.34 0.00 37.37 2.57
395 2559 7.849322 AGTTAACTGGTTAATTGGGTGAATT 57.151 32.000 7.48 0.00 37.37 2.17
396 2560 7.892609 AGTTAACTGGTTAATTGGGTGAATTC 58.107 34.615 7.48 0.00 37.37 2.17
397 2561 7.728532 AGTTAACTGGTTAATTGGGTGAATTCT 59.271 33.333 7.48 0.00 37.37 2.40
398 2562 6.994421 AACTGGTTAATTGGGTGAATTCTT 57.006 33.333 7.05 0.00 35.74 2.52
399 2563 6.345096 ACTGGTTAATTGGGTGAATTCTTG 57.655 37.500 7.05 0.00 35.74 3.02
400 2564 6.074648 ACTGGTTAATTGGGTGAATTCTTGA 58.925 36.000 7.05 0.00 35.74 3.02
401 2565 6.553100 ACTGGTTAATTGGGTGAATTCTTGAA 59.447 34.615 7.05 0.00 35.74 2.69
402 2566 6.754193 TGGTTAATTGGGTGAATTCTTGAAC 58.246 36.000 7.05 0.00 35.74 3.18
403 2567 5.861787 GGTTAATTGGGTGAATTCTTGAACG 59.138 40.000 7.05 0.00 35.74 3.95
404 2568 4.519540 AATTGGGTGAATTCTTGAACGG 57.480 40.909 7.05 0.00 26.83 4.44
405 2569 1.904287 TGGGTGAATTCTTGAACGGG 58.096 50.000 7.05 0.00 0.00 5.28
406 2570 1.173913 GGGTGAATTCTTGAACGGGG 58.826 55.000 7.05 0.00 0.00 5.73
407 2571 1.173913 GGTGAATTCTTGAACGGGGG 58.826 55.000 7.05 0.00 0.00 5.40
408 2572 1.546998 GGTGAATTCTTGAACGGGGGT 60.547 52.381 7.05 0.00 0.00 4.95
409 2573 2.235891 GTGAATTCTTGAACGGGGGTT 58.764 47.619 7.05 0.00 0.00 4.11
410 2574 3.414269 GTGAATTCTTGAACGGGGGTTA 58.586 45.455 7.05 0.00 0.00 2.85
546 2711 4.855298 TTGACCCAAACTATAAGGAGGG 57.145 45.455 0.00 0.00 42.07 4.30
548 2713 2.778270 GACCCAAACTATAAGGAGGGCT 59.222 50.000 0.00 0.00 39.97 5.19
552 2717 6.155367 ACCCAAACTATAAGGAGGGCTAATA 58.845 40.000 0.00 0.00 39.97 0.98
555 2720 8.170730 CCCAAACTATAAGGAGGGCTAATAAAT 58.829 37.037 0.00 0.00 0.00 1.40
569 2734 5.221581 GGCTAATAAATCAGGACGGAGGTAA 60.222 44.000 0.00 0.00 0.00 2.85
572 2737 7.760340 GCTAATAAATCAGGACGGAGGTAATAG 59.240 40.741 0.00 0.00 0.00 1.73
768 2943 4.506039 TGCACAGCAAGCATCCTT 57.494 50.000 0.00 0.00 37.02 3.36
769 2944 2.736197 TGCACAGCAAGCATCCTTT 58.264 47.368 0.00 0.00 37.02 3.11
770 2945 0.599558 TGCACAGCAAGCATCCTTTC 59.400 50.000 0.00 0.00 37.02 2.62
771 2946 0.886563 GCACAGCAAGCATCCTTTCT 59.113 50.000 0.00 0.00 0.00 2.52
772 2947 1.271656 GCACAGCAAGCATCCTTTCTT 59.728 47.619 0.00 0.00 0.00 2.52
862 3064 4.974645 AACCTTTCCTCACACATGACTA 57.025 40.909 0.00 0.00 0.00 2.59
920 3139 3.484547 CCAAGAACGTACGCCGGC 61.485 66.667 19.07 19.07 42.24 6.13
921 3140 3.484547 CAAGAACGTACGCCGGCC 61.485 66.667 23.46 5.88 42.24 6.13
1011 3239 1.985662 CCATGCCATGCCAACACCT 60.986 57.895 0.00 0.00 0.00 4.00
1012 3240 0.683828 CCATGCCATGCCAACACCTA 60.684 55.000 0.00 0.00 0.00 3.08
1013 3241 1.184431 CATGCCATGCCAACACCTAA 58.816 50.000 0.00 0.00 0.00 2.69
1094 3348 3.565482 GTCACAGTTCACAACACCATCAT 59.435 43.478 0.00 0.00 0.00 2.45
1100 3354 3.507162 TCACAACACCATCATCAACCT 57.493 42.857 0.00 0.00 0.00 3.50
1112 3366 5.457197 CCATCATCAACCTACCAATCCATCT 60.457 44.000 0.00 0.00 0.00 2.90
1639 3930 3.454082 CACCAAGCCTAAGGAAGAGATCT 59.546 47.826 0.00 0.00 0.00 2.75
1641 3932 3.243704 CCAAGCCTAAGGAAGAGATCTCG 60.244 52.174 16.97 1.55 34.09 4.04
1660 3951 0.528684 GAAGGAGGAGAATGCGTCCG 60.529 60.000 0.00 0.00 45.15 4.79
1734 4025 0.250640 AAGCCAGCAGACACAAGGAG 60.251 55.000 0.00 0.00 0.00 3.69
1741 4032 0.036577 CAGACACAAGGAGGAGCAGG 60.037 60.000 0.00 0.00 0.00 4.85
1742 4033 1.197430 AGACACAAGGAGGAGCAGGG 61.197 60.000 0.00 0.00 0.00 4.45
1927 4224 3.056628 CGCAGCGAGGAAGAGAAAT 57.943 52.632 9.98 0.00 0.00 2.17
1987 4284 2.032681 AGAAGAAGGCCACGGCAC 59.967 61.111 10.83 0.00 44.11 5.01
2103 4400 2.824041 GTGGTCGCCATCGCCATT 60.824 61.111 1.90 0.00 41.37 3.16
2269 6174 6.695278 TGTAAAGTCATTTGTGCAAGTAAAGC 59.305 34.615 0.00 0.00 0.00 3.51
2319 6227 4.113815 CCCCGGCCTCTGCATCAA 62.114 66.667 0.00 0.00 40.13 2.57
2326 6234 2.945008 CGGCCTCTGCATCAAAAAGATA 59.055 45.455 0.00 0.00 40.13 1.98
2342 6250 6.673154 AAAAGATACATACGGCCACTTTAC 57.327 37.500 2.24 0.00 0.00 2.01
2363 6271 9.736023 CTTTACTAGAGCAAGTTCAACAAAAAT 57.264 29.630 0.00 0.00 0.00 1.82
2436 6345 6.184789 GGTGAAATCTACCAGGGATTACAAA 58.815 40.000 0.00 0.00 38.12 2.83
2437 6346 6.318900 GGTGAAATCTACCAGGGATTACAAAG 59.681 42.308 0.00 0.00 38.12 2.77
2495 6875 7.284489 ACAGTTTGTTTGTACATAGAACCATGT 59.716 33.333 0.00 0.00 41.88 3.21
2605 6985 1.763545 GGAAGAAGGGCGAGGACTATT 59.236 52.381 0.00 0.00 0.00 1.73
2683 10265 7.623278 AGGACTAGGAAGAAGAGAATGATCTTT 59.377 37.037 0.00 0.00 39.63 2.52
2901 10483 8.450578 TGCCATTCTAACATCTTTAATAGTGG 57.549 34.615 0.00 0.00 0.00 4.00
2902 10484 7.013274 TGCCATTCTAACATCTTTAATAGTGGC 59.987 37.037 0.00 0.00 44.44 5.01
2933 10515 1.725169 TTCTTGGTGGGGTGAAGGGG 61.725 60.000 0.00 0.00 0.00 4.79
3016 10600 8.079211 AGTCTAACATACATGCTAGAAAAGGA 57.921 34.615 4.36 0.00 37.26 3.36
3052 10636 5.384063 AATTGTATGAACGTTGCATGGAA 57.616 34.783 5.00 0.00 0.00 3.53
3087 10671 4.948847 TCTACGCACATGCAAGATCTATT 58.051 39.130 4.49 0.00 42.21 1.73
3106 10690 9.897744 GATCTATTCATAGAGATGCATAGCTAC 57.102 37.037 0.00 0.00 42.20 3.58
3149 10733 3.252974 ACCCTTGAAGATCACTAAGCG 57.747 47.619 0.00 0.00 0.00 4.68
3150 10734 2.832129 ACCCTTGAAGATCACTAAGCGA 59.168 45.455 0.00 0.00 0.00 4.93
3153 10737 4.331168 CCCTTGAAGATCACTAAGCGAAAG 59.669 45.833 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 2254 2.042686 AACATGCACATATCCGCACT 57.957 45.000 0.00 0.00 41.79 4.40
137 2301 8.801882 AAATACGAAGAGGATCAATAAACCAA 57.198 30.769 0.00 0.00 37.82 3.67
148 2312 3.279434 GGGCACAAAATACGAAGAGGAT 58.721 45.455 0.00 0.00 0.00 3.24
152 2316 3.482436 AGTTGGGCACAAAATACGAAGA 58.518 40.909 1.02 0.00 38.54 2.87
208 2372 9.661563 AGTTAACGATTTCCTCAACAATGTATA 57.338 29.630 0.00 0.00 0.00 1.47
209 2373 8.450964 CAGTTAACGATTTCCTCAACAATGTAT 58.549 33.333 0.00 0.00 0.00 2.29
210 2374 7.094975 CCAGTTAACGATTTCCTCAACAATGTA 60.095 37.037 0.00 0.00 0.00 2.29
211 2375 6.293955 CCAGTTAACGATTTCCTCAACAATGT 60.294 38.462 0.00 0.00 0.00 2.71
212 2376 6.086222 CCAGTTAACGATTTCCTCAACAATG 58.914 40.000 0.00 0.00 0.00 2.82
213 2377 5.768164 ACCAGTTAACGATTTCCTCAACAAT 59.232 36.000 0.00 0.00 0.00 2.71
214 2378 5.127491 ACCAGTTAACGATTTCCTCAACAA 58.873 37.500 0.00 0.00 0.00 2.83
215 2379 4.710324 ACCAGTTAACGATTTCCTCAACA 58.290 39.130 0.00 0.00 0.00 3.33
216 2380 5.163884 GCTACCAGTTAACGATTTCCTCAAC 60.164 44.000 0.00 0.00 0.00 3.18
217 2381 4.933400 GCTACCAGTTAACGATTTCCTCAA 59.067 41.667 0.00 0.00 0.00 3.02
218 2382 4.222145 AGCTACCAGTTAACGATTTCCTCA 59.778 41.667 0.00 0.00 0.00 3.86
219 2383 4.567159 CAGCTACCAGTTAACGATTTCCTC 59.433 45.833 0.00 0.00 0.00 3.71
220 2384 4.504858 CAGCTACCAGTTAACGATTTCCT 58.495 43.478 0.00 0.00 0.00 3.36
221 2385 3.063588 GCAGCTACCAGTTAACGATTTCC 59.936 47.826 0.00 0.00 0.00 3.13
222 2386 3.933332 AGCAGCTACCAGTTAACGATTTC 59.067 43.478 0.00 0.00 0.00 2.17
223 2387 3.933332 GAGCAGCTACCAGTTAACGATTT 59.067 43.478 0.00 0.00 0.00 2.17
224 2388 3.522553 GAGCAGCTACCAGTTAACGATT 58.477 45.455 0.00 0.00 0.00 3.34
225 2389 2.479730 CGAGCAGCTACCAGTTAACGAT 60.480 50.000 0.00 0.00 0.00 3.73
226 2390 1.135489 CGAGCAGCTACCAGTTAACGA 60.135 52.381 0.00 0.00 0.00 3.85
227 2391 1.269166 CGAGCAGCTACCAGTTAACG 58.731 55.000 0.00 0.00 0.00 3.18
228 2392 1.067071 ACCGAGCAGCTACCAGTTAAC 60.067 52.381 0.00 0.00 0.00 2.01
229 2393 1.263356 ACCGAGCAGCTACCAGTTAA 58.737 50.000 0.00 0.00 0.00 2.01
230 2394 1.067142 CAACCGAGCAGCTACCAGTTA 60.067 52.381 0.00 0.00 0.00 2.24
231 2395 0.320771 CAACCGAGCAGCTACCAGTT 60.321 55.000 0.00 0.00 0.00 3.16
232 2396 1.293498 CAACCGAGCAGCTACCAGT 59.707 57.895 0.00 0.00 0.00 4.00
233 2397 1.448540 CCAACCGAGCAGCTACCAG 60.449 63.158 0.00 0.00 0.00 4.00
234 2398 2.662596 CCAACCGAGCAGCTACCA 59.337 61.111 0.00 0.00 0.00 3.25
235 2399 2.820037 GCCAACCGAGCAGCTACC 60.820 66.667 0.00 0.00 0.00 3.18
236 2400 2.103042 CAGCCAACCGAGCAGCTAC 61.103 63.158 0.00 0.00 33.33 3.58
237 2401 2.265739 CAGCCAACCGAGCAGCTA 59.734 61.111 0.00 0.00 33.33 3.32
238 2402 4.711949 CCAGCCAACCGAGCAGCT 62.712 66.667 0.00 0.00 35.52 4.24
240 2404 3.052082 CACCAGCCAACCGAGCAG 61.052 66.667 0.00 0.00 0.00 4.24
241 2405 3.535629 CTCACCAGCCAACCGAGCA 62.536 63.158 0.00 0.00 0.00 4.26
242 2406 2.167398 TACTCACCAGCCAACCGAGC 62.167 60.000 0.00 0.00 0.00 5.03
243 2407 0.108615 CTACTCACCAGCCAACCGAG 60.109 60.000 0.00 0.00 0.00 4.63
244 2408 1.541310 CCTACTCACCAGCCAACCGA 61.541 60.000 0.00 0.00 0.00 4.69
245 2409 1.079127 CCTACTCACCAGCCAACCG 60.079 63.158 0.00 0.00 0.00 4.44
246 2410 1.299976 CCCTACTCACCAGCCAACC 59.700 63.158 0.00 0.00 0.00 3.77
247 2411 1.198759 TCCCCTACTCACCAGCCAAC 61.199 60.000 0.00 0.00 0.00 3.77
248 2412 0.253160 ATCCCCTACTCACCAGCCAA 60.253 55.000 0.00 0.00 0.00 4.52
249 2413 0.253160 AATCCCCTACTCACCAGCCA 60.253 55.000 0.00 0.00 0.00 4.75
250 2414 1.802553 TAATCCCCTACTCACCAGCC 58.197 55.000 0.00 0.00 0.00 4.85
251 2415 4.137543 CAATTAATCCCCTACTCACCAGC 58.862 47.826 0.00 0.00 0.00 4.85
252 2416 4.718961 CCAATTAATCCCCTACTCACCAG 58.281 47.826 0.00 0.00 0.00 4.00
253 2417 3.117663 GCCAATTAATCCCCTACTCACCA 60.118 47.826 0.00 0.00 0.00 4.17
254 2418 3.138468 AGCCAATTAATCCCCTACTCACC 59.862 47.826 0.00 0.00 0.00 4.02
255 2419 4.439253 AGCCAATTAATCCCCTACTCAC 57.561 45.455 0.00 0.00 0.00 3.51
256 2420 6.520061 CGATTAGCCAATTAATCCCCTACTCA 60.520 42.308 0.00 0.00 36.93 3.41
257 2421 5.875359 CGATTAGCCAATTAATCCCCTACTC 59.125 44.000 0.00 0.00 36.93 2.59
258 2422 5.280521 CCGATTAGCCAATTAATCCCCTACT 60.281 44.000 0.00 0.00 36.93 2.57
259 2423 4.941873 CCGATTAGCCAATTAATCCCCTAC 59.058 45.833 0.00 0.00 36.93 3.18
260 2424 4.566907 GCCGATTAGCCAATTAATCCCCTA 60.567 45.833 0.00 0.00 36.93 3.53
261 2425 3.814316 GCCGATTAGCCAATTAATCCCCT 60.814 47.826 0.00 0.00 36.93 4.79
262 2426 2.492088 GCCGATTAGCCAATTAATCCCC 59.508 50.000 0.00 0.00 36.93 4.81
263 2427 3.153919 TGCCGATTAGCCAATTAATCCC 58.846 45.455 0.00 0.00 36.93 3.85
264 2428 4.278419 ACTTGCCGATTAGCCAATTAATCC 59.722 41.667 0.00 0.00 36.93 3.01
265 2429 5.438761 ACTTGCCGATTAGCCAATTAATC 57.561 39.130 0.00 0.00 36.92 1.75
266 2430 5.852282 AACTTGCCGATTAGCCAATTAAT 57.148 34.783 0.00 0.00 0.00 1.40
267 2431 6.761099 TTAACTTGCCGATTAGCCAATTAA 57.239 33.333 0.00 0.00 0.00 1.40
268 2432 6.293190 CGATTAACTTGCCGATTAGCCAATTA 60.293 38.462 0.00 0.00 0.00 1.40
269 2433 5.505654 CGATTAACTTGCCGATTAGCCAATT 60.506 40.000 0.00 0.00 0.00 2.32
270 2434 4.024048 CGATTAACTTGCCGATTAGCCAAT 60.024 41.667 0.00 0.00 0.00 3.16
271 2435 3.311322 CGATTAACTTGCCGATTAGCCAA 59.689 43.478 0.00 0.00 0.00 4.52
272 2436 2.869801 CGATTAACTTGCCGATTAGCCA 59.130 45.455 0.00 0.00 0.00 4.75
273 2437 2.223377 CCGATTAACTTGCCGATTAGCC 59.777 50.000 0.00 0.00 0.00 3.93
274 2438 2.349532 GCCGATTAACTTGCCGATTAGC 60.350 50.000 0.00 0.00 0.00 3.09
275 2439 2.223377 GGCCGATTAACTTGCCGATTAG 59.777 50.000 0.00 0.00 33.59 1.73
276 2440 2.215196 GGCCGATTAACTTGCCGATTA 58.785 47.619 0.00 0.00 33.59 1.75
277 2441 1.021968 GGCCGATTAACTTGCCGATT 58.978 50.000 0.00 0.00 33.59 3.34
278 2442 2.702847 GGCCGATTAACTTGCCGAT 58.297 52.632 0.00 0.00 33.59 4.18
279 2443 4.211986 GGCCGATTAACTTGCCGA 57.788 55.556 0.00 0.00 33.59 5.54
281 2445 2.959507 AAATGGCCGATTAACTTGCC 57.040 45.000 0.00 4.44 44.27 4.52
282 2446 5.587289 TGATTAAATGGCCGATTAACTTGC 58.413 37.500 13.26 6.21 0.00 4.01
283 2447 8.647143 AATTGATTAAATGGCCGATTAACTTG 57.353 30.769 13.26 0.00 0.00 3.16
287 2451 9.619316 CGATTAATTGATTAAATGGCCGATTAA 57.381 29.630 13.33 13.33 36.02 1.40
288 2452 8.240682 CCGATTAATTGATTAAATGGCCGATTA 58.759 33.333 4.10 0.00 36.02 1.75
289 2453 7.040062 TCCGATTAATTGATTAAATGGCCGATT 60.040 33.333 4.10 0.00 36.02 3.34
290 2454 6.432783 TCCGATTAATTGATTAAATGGCCGAT 59.567 34.615 4.10 0.00 36.02 4.18
291 2455 5.765677 TCCGATTAATTGATTAAATGGCCGA 59.234 36.000 4.10 0.00 36.02 5.54
292 2456 5.856455 GTCCGATTAATTGATTAAATGGCCG 59.144 40.000 4.10 0.00 36.02 6.13
293 2457 6.744112 TGTCCGATTAATTGATTAAATGGCC 58.256 36.000 4.10 0.00 36.02 5.36
294 2458 8.816640 ATTGTCCGATTAATTGATTAAATGGC 57.183 30.769 4.10 3.91 36.02 4.40
301 2465 8.846211 ACCGATAAATTGTCCGATTAATTGATT 58.154 29.630 4.10 0.00 0.00 2.57
302 2466 8.391075 ACCGATAAATTGTCCGATTAATTGAT 57.609 30.769 4.10 0.00 0.00 2.57
303 2467 7.795482 ACCGATAAATTGTCCGATTAATTGA 57.205 32.000 4.10 0.00 0.00 2.57
304 2468 8.850454 AAACCGATAAATTGTCCGATTAATTG 57.150 30.769 0.00 0.00 0.00 2.32
308 2472 9.426837 CCTATAAACCGATAAATTGTCCGATTA 57.573 33.333 0.00 0.00 0.00 1.75
309 2473 7.094933 GCCTATAAACCGATAAATTGTCCGATT 60.095 37.037 0.00 0.00 0.00 3.34
310 2474 6.370718 GCCTATAAACCGATAAATTGTCCGAT 59.629 38.462 0.00 0.00 0.00 4.18
311 2475 5.697633 GCCTATAAACCGATAAATTGTCCGA 59.302 40.000 0.00 0.00 0.00 4.55
312 2476 5.699458 AGCCTATAAACCGATAAATTGTCCG 59.301 40.000 0.00 0.00 0.00 4.79
313 2477 7.876582 AGTAGCCTATAAACCGATAAATTGTCC 59.123 37.037 0.00 0.00 0.00 4.02
314 2478 8.828688 AGTAGCCTATAAACCGATAAATTGTC 57.171 34.615 0.00 0.00 0.00 3.18
315 2479 7.597743 CGAGTAGCCTATAAACCGATAAATTGT 59.402 37.037 0.00 0.00 0.00 2.71
316 2480 7.063074 CCGAGTAGCCTATAAACCGATAAATTG 59.937 40.741 0.00 0.00 0.00 2.32
317 2481 7.095270 CCGAGTAGCCTATAAACCGATAAATT 58.905 38.462 0.00 0.00 0.00 1.82
318 2482 6.210185 ACCGAGTAGCCTATAAACCGATAAAT 59.790 38.462 0.00 0.00 0.00 1.40
319 2483 5.536161 ACCGAGTAGCCTATAAACCGATAAA 59.464 40.000 0.00 0.00 0.00 1.40
320 2484 5.048504 CACCGAGTAGCCTATAAACCGATAA 60.049 44.000 0.00 0.00 0.00 1.75
321 2485 4.456911 CACCGAGTAGCCTATAAACCGATA 59.543 45.833 0.00 0.00 0.00 2.92
322 2486 3.255149 CACCGAGTAGCCTATAAACCGAT 59.745 47.826 0.00 0.00 0.00 4.18
323 2487 2.620115 CACCGAGTAGCCTATAAACCGA 59.380 50.000 0.00 0.00 0.00 4.69
324 2488 2.620115 TCACCGAGTAGCCTATAAACCG 59.380 50.000 0.00 0.00 0.00 4.44
325 2489 3.243670 GGTCACCGAGTAGCCTATAAACC 60.244 52.174 0.00 0.00 0.00 3.27
326 2490 3.243670 GGGTCACCGAGTAGCCTATAAAC 60.244 52.174 0.00 0.00 0.00 2.01
327 2491 2.961062 GGGTCACCGAGTAGCCTATAAA 59.039 50.000 0.00 0.00 0.00 1.40
328 2492 2.176364 AGGGTCACCGAGTAGCCTATAA 59.824 50.000 0.00 0.00 41.72 0.98
329 2493 1.779092 AGGGTCACCGAGTAGCCTATA 59.221 52.381 0.00 0.00 41.72 1.31
330 2494 0.556747 AGGGTCACCGAGTAGCCTAT 59.443 55.000 0.00 0.00 41.72 2.57
331 2495 1.133976 GTAGGGTCACCGAGTAGCCTA 60.134 57.143 0.00 0.00 43.24 3.93
332 2496 0.395448 GTAGGGTCACCGAGTAGCCT 60.395 60.000 6.78 6.78 45.33 4.58
333 2497 1.722636 CGTAGGGTCACCGAGTAGCC 61.723 65.000 0.00 0.00 43.47 3.93
334 2498 0.745845 TCGTAGGGTCACCGAGTAGC 60.746 60.000 0.00 0.00 43.47 3.58
335 2499 1.297664 CTCGTAGGGTCACCGAGTAG 58.702 60.000 0.00 0.00 42.26 2.57
336 2500 3.465990 CTCGTAGGGTCACCGAGTA 57.534 57.895 0.00 0.00 42.26 2.59
337 2501 4.315588 CTCGTAGGGTCACCGAGT 57.684 61.111 0.00 0.00 42.26 4.18
339 2503 0.615331 ACTACTCGTAGGGTCACCGA 59.385 55.000 8.77 0.00 43.47 4.69
340 2504 0.731417 CACTACTCGTAGGGTCACCG 59.269 60.000 8.77 0.00 43.47 4.94
341 2505 2.119801 TCACTACTCGTAGGGTCACC 57.880 55.000 6.26 0.00 37.80 4.02
342 2506 5.824904 TTAATCACTACTCGTAGGGTCAC 57.175 43.478 6.26 0.00 37.80 3.67
343 2507 5.237996 CGATTAATCACTACTCGTAGGGTCA 59.762 44.000 15.57 0.00 37.80 4.02
344 2508 5.334724 CCGATTAATCACTACTCGTAGGGTC 60.335 48.000 15.57 0.00 37.80 4.46
345 2509 4.518211 CCGATTAATCACTACTCGTAGGGT 59.482 45.833 15.57 0.00 37.80 4.34
346 2510 4.615452 GCCGATTAATCACTACTCGTAGGG 60.615 50.000 15.57 4.62 37.92 3.53
347 2511 4.023450 TGCCGATTAATCACTACTCGTAGG 60.023 45.833 15.57 5.48 37.49 3.18
348 2512 5.104562 TGCCGATTAATCACTACTCGTAG 57.895 43.478 15.57 2.66 39.04 3.51
349 2513 5.066893 ACTTGCCGATTAATCACTACTCGTA 59.933 40.000 15.57 0.00 32.34 3.43
350 2514 4.142227 ACTTGCCGATTAATCACTACTCGT 60.142 41.667 15.57 1.10 32.34 4.18
351 2515 4.360563 ACTTGCCGATTAATCACTACTCG 58.639 43.478 15.57 1.02 33.64 4.18
352 2516 7.491696 AGTTAACTTGCCGATTAATCACTACTC 59.508 37.037 15.57 0.00 0.00 2.59
353 2517 7.277981 CAGTTAACTTGCCGATTAATCACTACT 59.722 37.037 15.57 2.97 0.00 2.57
354 2518 7.399523 CAGTTAACTTGCCGATTAATCACTAC 58.600 38.462 15.57 2.27 0.00 2.73
355 2519 6.537301 CCAGTTAACTTGCCGATTAATCACTA 59.463 38.462 15.57 3.38 0.00 2.74
356 2520 5.354234 CCAGTTAACTTGCCGATTAATCACT 59.646 40.000 15.57 5.09 0.00 3.41
357 2521 5.123344 ACCAGTTAACTTGCCGATTAATCAC 59.877 40.000 15.57 7.31 0.00 3.06
358 2522 5.250200 ACCAGTTAACTTGCCGATTAATCA 58.750 37.500 15.57 0.00 0.00 2.57
359 2523 5.813080 ACCAGTTAACTTGCCGATTAATC 57.187 39.130 5.07 5.30 0.00 1.75
360 2524 7.690952 TTAACCAGTTAACTTGCCGATTAAT 57.309 32.000 5.07 0.00 30.78 1.40
361 2525 7.690952 ATTAACCAGTTAACTTGCCGATTAA 57.309 32.000 5.07 4.36 37.80 1.40
362 2526 7.362229 CCAATTAACCAGTTAACTTGCCGATTA 60.362 37.037 5.07 0.00 37.80 1.75
363 2527 6.386654 CAATTAACCAGTTAACTTGCCGATT 58.613 36.000 5.07 1.86 37.80 3.34
364 2528 5.105917 CCAATTAACCAGTTAACTTGCCGAT 60.106 40.000 5.07 0.00 37.80 4.18
365 2529 4.216687 CCAATTAACCAGTTAACTTGCCGA 59.783 41.667 5.07 0.00 37.80 5.54
366 2530 4.481463 CCAATTAACCAGTTAACTTGCCG 58.519 43.478 5.07 0.00 37.80 5.69
367 2531 4.282449 ACCCAATTAACCAGTTAACTTGCC 59.718 41.667 5.07 0.00 37.80 4.52
368 2532 5.010213 TCACCCAATTAACCAGTTAACTTGC 59.990 40.000 5.07 0.00 37.80 4.01
369 2533 6.642707 TCACCCAATTAACCAGTTAACTTG 57.357 37.500 5.07 5.14 37.80 3.16
370 2534 7.849322 ATTCACCCAATTAACCAGTTAACTT 57.151 32.000 5.07 0.00 37.80 2.66
371 2535 7.728532 AGAATTCACCCAATTAACCAGTTAACT 59.271 33.333 8.44 1.12 37.80 2.24
372 2536 7.892609 AGAATTCACCCAATTAACCAGTTAAC 58.107 34.615 8.44 0.00 37.80 2.01
373 2537 8.364142 CAAGAATTCACCCAATTAACCAGTTAA 58.636 33.333 8.44 5.51 39.12 2.01
374 2538 7.726291 TCAAGAATTCACCCAATTAACCAGTTA 59.274 33.333 8.44 0.00 34.60 2.24
375 2539 6.553100 TCAAGAATTCACCCAATTAACCAGTT 59.447 34.615 8.44 0.00 34.60 3.16
376 2540 6.074648 TCAAGAATTCACCCAATTAACCAGT 58.925 36.000 8.44 0.00 34.60 4.00
377 2541 6.588719 TCAAGAATTCACCCAATTAACCAG 57.411 37.500 8.44 0.00 34.60 4.00
378 2542 6.515862 CGTTCAAGAATTCACCCAATTAACCA 60.516 38.462 8.44 0.00 34.60 3.67
379 2543 5.861787 CGTTCAAGAATTCACCCAATTAACC 59.138 40.000 8.44 0.00 34.60 2.85
380 2544 5.861787 CCGTTCAAGAATTCACCCAATTAAC 59.138 40.000 8.44 0.38 34.60 2.01
381 2545 5.047660 CCCGTTCAAGAATTCACCCAATTAA 60.048 40.000 8.44 0.00 34.60 1.40
382 2546 4.461081 CCCGTTCAAGAATTCACCCAATTA 59.539 41.667 8.44 0.00 34.60 1.40
383 2547 3.258123 CCCGTTCAAGAATTCACCCAATT 59.742 43.478 8.44 0.00 37.41 2.32
384 2548 2.825532 CCCGTTCAAGAATTCACCCAAT 59.174 45.455 8.44 0.00 0.00 3.16
385 2549 2.235016 CCCGTTCAAGAATTCACCCAA 58.765 47.619 8.44 0.00 0.00 4.12
386 2550 1.546773 CCCCGTTCAAGAATTCACCCA 60.547 52.381 8.44 0.00 0.00 4.51
387 2551 1.173913 CCCCGTTCAAGAATTCACCC 58.826 55.000 8.44 0.00 0.00 4.61
388 2552 1.173913 CCCCCGTTCAAGAATTCACC 58.826 55.000 8.44 0.00 0.00 4.02
389 2553 1.905637 ACCCCCGTTCAAGAATTCAC 58.094 50.000 8.44 0.00 0.00 3.18
390 2554 2.668144 AACCCCCGTTCAAGAATTCA 57.332 45.000 8.44 0.00 0.00 2.57
391 2555 9.901172 ATATATATAACCCCCGTTCAAGAATTC 57.099 33.333 0.00 0.00 33.17 2.17
395 2559 9.717994 TGATATATATATAACCCCCGTTCAAGA 57.282 33.333 6.54 0.00 33.17 3.02
396 2560 9.760077 GTGATATATATATAACCCCCGTTCAAG 57.240 37.037 8.58 0.00 33.17 3.02
397 2561 9.269494 TGTGATATATATATAACCCCCGTTCAA 57.731 33.333 15.14 0.00 33.17 2.69
398 2562 8.841754 TGTGATATATATATAACCCCCGTTCA 57.158 34.615 15.14 1.33 33.17 3.18
401 2565 9.895138 GTTTTGTGATATATATATAACCCCCGT 57.105 33.333 15.14 0.00 0.00 5.28
546 2711 4.338379 ACCTCCGTCCTGATTTATTAGC 57.662 45.455 0.00 0.00 0.00 3.09
548 2713 7.731688 ACCTATTACCTCCGTCCTGATTTATTA 59.268 37.037 0.00 0.00 0.00 0.98
552 2717 4.101119 CACCTATTACCTCCGTCCTGATTT 59.899 45.833 0.00 0.00 0.00 2.17
555 2720 2.024655 ACACCTATTACCTCCGTCCTGA 60.025 50.000 0.00 0.00 0.00 3.86
718 2889 1.447838 GGCAAGCCAACTCGATCGA 60.448 57.895 18.32 18.32 35.81 3.59
719 2890 1.448540 AGGCAAGCCAACTCGATCG 60.449 57.895 14.40 9.36 38.92 3.69
720 2891 1.986575 GCAGGCAAGCCAACTCGATC 61.987 60.000 14.40 0.00 38.92 3.69
721 2892 2.042831 GCAGGCAAGCCAACTCGAT 61.043 57.895 14.40 0.00 38.92 3.59
862 3064 4.720649 AGACGTGTAGCTACATTCATGT 57.279 40.909 28.37 20.18 44.48 3.21
921 3140 9.477405 TAGGAAACCTTTGGATGGATTAGTCCG 62.477 44.444 0.00 0.00 40.27 4.79
922 3141 4.645136 GGAAACCTTTGGATGGATTAGTCC 59.355 45.833 0.00 0.00 45.31 3.85
923 3142 5.510430 AGGAAACCTTTGGATGGATTAGTC 58.490 41.667 0.00 0.00 0.00 2.59
1012 3240 9.702726 GCATGATGCGTCGTTTATATATTTATT 57.297 29.630 0.00 0.00 31.71 1.40
1013 3241 8.335356 GGCATGATGCGTCGTTTATATATTTAT 58.665 33.333 11.75 0.00 46.21 1.40
1094 3348 5.223655 TGGATAGATGGATTGGTAGGTTGA 58.776 41.667 0.00 0.00 0.00 3.18
1100 3354 3.837731 TGCGATGGATAGATGGATTGGTA 59.162 43.478 0.00 0.00 0.00 3.25
1112 3366 0.179094 GGTGGACGTTGCGATGGATA 60.179 55.000 0.00 0.00 0.00 2.59
1491 3782 4.657969 CCAGGTTTATCCCTCTTCATCTCT 59.342 45.833 0.00 0.00 36.75 3.10
1497 3788 3.610911 CACACCAGGTTTATCCCTCTTC 58.389 50.000 0.00 0.00 36.75 2.87
1565 3856 3.000080 CTGCCGTCGACGTCTTTGC 62.000 63.158 33.49 28.02 37.74 3.68
1615 3906 0.991920 TCTTCCTTAGGCTTGGTGGG 59.008 55.000 0.00 0.00 0.00 4.61
1639 3930 0.456221 GACGCATTCTCCTCCTTCGA 59.544 55.000 0.00 0.00 0.00 3.71
1641 3932 0.528684 CGGACGCATTCTCCTCCTTC 60.529 60.000 0.00 0.00 0.00 3.46
1660 3951 1.450312 CCTCGTCCATGGCCTTGTC 60.450 63.158 16.81 8.93 0.00 3.18
1725 4016 0.768221 TTCCCTGCTCCTCCTTGTGT 60.768 55.000 0.00 0.00 0.00 3.72
1734 4025 0.746204 GTGCTAGCTTTCCCTGCTCC 60.746 60.000 17.23 0.00 41.46 4.70
1741 4032 0.605589 ACCGTTGGTGCTAGCTTTCC 60.606 55.000 17.23 15.39 32.98 3.13
1742 4033 2.928416 ACCGTTGGTGCTAGCTTTC 58.072 52.632 17.23 6.44 32.98 2.62
1806 4103 4.760047 ATCTCGTGTGTGGCCGGC 62.760 66.667 21.18 21.18 0.00 6.13
1902 4199 3.226429 TTCCTCGCTGCGCTGTCTT 62.226 57.895 18.65 0.00 0.00 3.01
1987 4284 2.863153 CTCTTTCCAGCCGTTGCG 59.137 61.111 0.00 0.00 44.33 4.85
2103 4400 2.433145 CCGAGCGAGAAAGCAGCA 60.433 61.111 0.00 0.00 40.15 4.41
2285 6190 2.728007 GGGGATGACCTCCTTTTCAAG 58.272 52.381 0.00 0.00 44.28 3.02
2306 6213 3.696051 TGTATCTTTTTGATGCAGAGGCC 59.304 43.478 0.00 0.00 41.66 5.19
2318 6226 6.882678 AGTAAAGTGGCCGTATGTATCTTTTT 59.117 34.615 0.00 0.00 0.00 1.94
2319 6227 6.412214 AGTAAAGTGGCCGTATGTATCTTTT 58.588 36.000 0.00 0.00 0.00 2.27
2326 6234 3.181478 GCTCTAGTAAAGTGGCCGTATGT 60.181 47.826 0.00 0.00 0.00 2.29
2363 6271 6.694447 ACTTCGGTTGTAGCAAGACTATTTA 58.306 36.000 0.00 0.00 32.15 1.40
2436 6345 2.093764 GCTCTGTATGTGCCAAGAGTCT 60.094 50.000 0.00 0.00 0.00 3.24
2437 6346 2.275318 GCTCTGTATGTGCCAAGAGTC 58.725 52.381 0.00 0.00 0.00 3.36
2495 6875 0.465460 GGTGATGGCCGGCTGATAAA 60.465 55.000 28.56 7.96 0.00 1.40
2901 10483 5.291971 CCCACCAAGAAAAATATAGCATGC 58.708 41.667 10.51 10.51 0.00 4.06
2902 10484 5.363580 ACCCCACCAAGAAAAATATAGCATG 59.636 40.000 0.00 0.00 0.00 4.06
2933 10515 5.949233 AGAATTGAACACAACGCTTTTTC 57.051 34.783 0.00 0.00 0.00 2.29
2989 10573 9.988815 CCTTTTCTAGCATGTATGTTAGACTAT 57.011 33.333 15.22 0.00 45.91 2.12
2990 10574 9.197306 TCCTTTTCTAGCATGTATGTTAGACTA 57.803 33.333 15.22 6.74 45.91 2.59
2991 10575 8.079211 TCCTTTTCTAGCATGTATGTTAGACT 57.921 34.615 15.22 0.00 45.91 3.24
2992 10576 8.894768 ATCCTTTTCTAGCATGTATGTTAGAC 57.105 34.615 15.22 0.00 45.91 2.59
2993 10577 9.330063 CAATCCTTTTCTAGCATGTATGTTAGA 57.670 33.333 12.55 12.55 45.03 2.10
2994 10578 9.113838 ACAATCCTTTTCTAGCATGTATGTTAG 57.886 33.333 8.83 8.83 41.27 2.34
2995 10579 9.461312 AACAATCCTTTTCTAGCATGTATGTTA 57.539 29.630 0.00 0.00 0.00 2.41
2996 10580 7.944729 ACAATCCTTTTCTAGCATGTATGTT 57.055 32.000 0.00 0.00 0.00 2.71
2997 10581 7.944729 AACAATCCTTTTCTAGCATGTATGT 57.055 32.000 0.00 0.00 0.00 2.29
2998 10582 9.294030 GAAAACAATCCTTTTCTAGCATGTATG 57.706 33.333 0.00 0.00 37.23 2.39
2999 10583 9.023962 TGAAAACAATCCTTTTCTAGCATGTAT 57.976 29.630 0.00 0.00 39.78 2.29
3000 10584 8.402798 TGAAAACAATCCTTTTCTAGCATGTA 57.597 30.769 0.00 0.00 39.78 2.29
3001 10585 7.288810 TGAAAACAATCCTTTTCTAGCATGT 57.711 32.000 0.00 0.00 39.78 3.21
3031 10615 5.384063 TTTCCATGCAACGTTCATACAAT 57.616 34.783 0.00 0.00 0.00 2.71
3062 10646 4.194640 AGATCTTGCATGTGCGTAGAATT 58.805 39.130 11.82 3.59 45.83 2.17
3063 10647 3.801698 AGATCTTGCATGTGCGTAGAAT 58.198 40.909 11.82 4.07 45.83 2.40
3087 10671 5.491982 TCTCGTAGCTATGCATCTCTATGA 58.508 41.667 20.12 20.12 34.84 2.15
3106 10690 1.068434 GAAGATGCTCTCCCCTTCTCG 59.932 57.143 0.00 0.00 33.98 4.04


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

AutoCloner maintained by Alex Coulton.