Multiple sequence alignment - TraesCS4B01G234700

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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 TraesCS4B01G234700 chr4B 100.000 3264 0 0 1 3264 489295603 489292340 0.000000e+00 6028.0
1 TraesCS4B01G234700 chr4B 80.494 1133 145 37 1208 2288 639452215 639453323 0.000000e+00 798.0
2 TraesCS4B01G234700 chr4B 82.263 919 128 15 1216 2121 626068781 626067885 0.000000e+00 761.0
3 TraesCS4B01G234700 chr4B 81.409 667 86 22 1208 1868 667343756 667344390 8.080000e-141 510.0
4 TraesCS4B01G234700 chr4B 84.878 410 44 9 1714 2108 667263801 667264207 6.560000e-107 398.0
5 TraesCS4B01G234700 chr4B 79.227 414 45 18 1915 2289 667345419 667345830 1.940000e-62 250.0
6 TraesCS4B01G234700 chr4B 79.496 278 38 12 1374 1634 667263235 667263510 2.590000e-41 180.0
7 TraesCS4B01G234700 chr4B 94.186 86 3 2 293 376 110358633 110358718 2.640000e-26 130.0
8 TraesCS4B01G234700 chr4B 94.444 72 4 0 2301 2372 667345911 667345982 9.570000e-21 111.0
9 TraesCS4B01G234700 chr4B 92.857 70 5 0 2301 2370 639453418 639453487 5.760000e-18 102.0
10 TraesCS4B01G234700 chr4A 91.997 1462 72 22 1208 2652 54405836 54404403 0.000000e+00 2010.0
11 TraesCS4B01G234700 chr4A 88.506 1044 59 25 2 1038 54406819 54405830 0.000000e+00 1206.0
12 TraesCS4B01G234700 chr4D 94.750 1200 45 5 1208 2394 397158256 397157062 0.000000e+00 1851.0
13 TraesCS4B01G234700 chr4D 94.313 633 23 5 397 1023 397158895 397158270 0.000000e+00 957.0
14 TraesCS4B01G234700 chr4D 83.389 903 123 11 1212 2108 488666010 488665129 0.000000e+00 811.0
15 TraesCS4B01G234700 chr4D 80.750 587 75 19 2702 3264 397155440 397154868 1.080000e-114 424.0
16 TraesCS4B01G234700 chr4D 91.525 295 15 3 1 289 397159231 397158941 6.560000e-107 398.0
17 TraesCS4B01G234700 chr4D 100.000 169 0 0 1040 1208 405768096 405768264 2.450000e-81 313.0
18 TraesCS4B01G234700 chr5A 83.757 905 116 15 1212 2108 670426072 670425191 0.000000e+00 828.0
19 TraesCS4B01G234700 chr5A 80.195 1131 136 47 1208 2292 706678436 706677348 0.000000e+00 767.0
20 TraesCS4B01G234700 chr5A 82.273 220 31 5 1707 1922 706705514 706705299 2.000000e-42 183.0
21 TraesCS4B01G234700 chr5A 92.857 70 4 1 2301 2370 706677260 706677192 2.070000e-17 100.0
22 TraesCS4B01G234700 chr5A 83.654 104 11 5 3048 3149 11074796 11074895 3.470000e-15 93.5
23 TraesCS4B01G234700 chr5A 82.051 78 10 4 2496 2569 331102608 331102531 2.720000e-06 63.9
24 TraesCS4B01G234700 chrUn 82.101 676 83 22 1442 2108 30126390 30125744 7.960000e-151 544.0
25 TraesCS4B01G234700 chrUn 79.127 733 81 29 1707 2371 30131094 30130366 1.070000e-119 440.0
26 TraesCS4B01G234700 chrUn 100.000 171 0 0 1040 1210 74769769 74769939 1.890000e-82 316.0
27 TraesCS4B01G234700 chrUn 93.407 91 4 2 293 381 17148683 17148593 2.040000e-27 134.0
28 TraesCS4B01G234700 chrUn 82.569 109 14 4 2487 2591 352484396 352484503 1.250000e-14 91.6
29 TraesCS4B01G234700 chrUn 82.692 104 13 5 2492 2591 352502277 352502379 1.610000e-13 87.9
30 TraesCS4B01G234700 chr1D 94.118 357 15 2 1208 1558 394263725 394263369 3.710000e-149 538.0
31 TraesCS4B01G234700 chr1D 100.000 171 0 0 1040 1210 486378294 486378124 1.890000e-82 316.0
32 TraesCS4B01G234700 chr1D 76.176 319 45 23 2687 2988 118800503 118800807 4.390000e-29 139.0
33 TraesCS4B01G234700 chr1D 94.318 88 3 2 290 375 104427167 104427254 2.040000e-27 134.0
34 TraesCS4B01G234700 chr3B 95.918 196 6 2 1032 1227 242488269 242488462 1.890000e-82 316.0
35 TraesCS4B01G234700 chr3B 91.398 93 5 3 293 382 452283202 452283110 1.230000e-24 124.0
36 TraesCS4B01G234700 chr3B 87.324 71 7 2 2527 2595 804386886 804386816 2.700000e-11 80.5
37 TraesCS4B01G234700 chr3B 94.444 36 2 0 3229 3264 25190604 25190639 4.550000e-04 56.5
38 TraesCS4B01G234700 chr7B 100.000 170 0 0 1040 1209 699933424 699933593 6.800000e-82 315.0
39 TraesCS4B01G234700 chr7B 90.323 93 8 1 285 376 199802616 199802708 1.590000e-23 121.0
40 TraesCS4B01G234700 chr7B 97.674 43 0 1 255 296 576354325 576354367 4.520000e-09 73.1
41 TraesCS4B01G234700 chr6B 100.000 170 0 0 1041 1210 687560195 687560364 6.800000e-82 315.0
42 TraesCS4B01G234700 chr6D 100.000 169 0 0 1041 1209 455497551 455497383 2.450000e-81 313.0
43 TraesCS4B01G234700 chr1A 97.790 181 1 3 1034 1213 307044401 307044223 3.160000e-80 309.0
44 TraesCS4B01G234700 chr1A 96.739 184 3 3 1038 1220 561526817 561526998 1.470000e-78 303.0
45 TraesCS4B01G234700 chr1A 77.199 307 43 19 2688 2972 130337902 130338203 1.570000e-33 154.0
46 TraesCS4B01G234700 chr1A 100.000 28 0 0 3235 3262 555616036 555616063 6.000000e-03 52.8
47 TraesCS4B01G234700 chr1B 78.505 321 40 22 2691 2988 180523818 180524132 2.000000e-42 183.0
48 TraesCS4B01G234700 chr1B 93.407 91 4 2 291 379 129095802 129095892 2.040000e-27 134.0
49 TraesCS4B01G234700 chr1B 91.398 93 5 3 289 378 526194603 526194695 1.230000e-24 124.0
50 TraesCS4B01G234700 chr6A 93.258 89 3 3 293 379 89972681 89972594 9.510000e-26 128.0
51 TraesCS4B01G234700 chr6A 84.146 82 9 4 3049 3129 441298290 441298212 3.490000e-10 76.8
52 TraesCS4B01G234700 chr6A 81.553 103 10 9 3049 3148 478524199 478524103 3.490000e-10 76.8
53 TraesCS4B01G234700 chr6A 97.619 42 1 0 248 289 122681288 122681247 4.520000e-09 73.1
54 TraesCS4B01G234700 chr6A 84.058 69 6 5 3056 3123 510238000 510237936 9.780000e-06 62.1
55 TraesCS4B01G234700 chr2B 94.118 85 4 1 292 375 482319748 482319664 9.510000e-26 128.0
56 TraesCS4B01G234700 chr2B 95.556 45 2 0 247 291 111483599 111483643 4.520000e-09 73.1
57 TraesCS4B01G234700 chr2D 75.879 199 33 13 2933 3122 305061781 305061973 1.610000e-13 87.9
58 TraesCS4B01G234700 chr2D 100.000 39 0 0 253 291 184122031 184121993 4.520000e-09 73.1
59 TraesCS4B01G234700 chr7D 88.000 75 5 1 2521 2595 632991518 632991588 5.800000e-13 86.1
60 TraesCS4B01G234700 chr3D 80.672 119 16 7 3046 3160 129257813 129257698 5.800000e-13 86.1
61 TraesCS4B01G234700 chr3D 97.674 43 0 1 255 296 213295009 213295051 4.520000e-09 73.1
62 TraesCS4B01G234700 chr2A 79.130 115 20 3 2485 2595 677173621 677173735 3.490000e-10 76.8
63 TraesCS4B01G234700 chr5D 97.674 43 0 1 255 296 229933262 229933304 4.520000e-09 73.1
64 TraesCS4B01G234700 chr5D 78.641 103 13 8 3049 3149 4658972 4659067 3.520000e-05 60.2
65 TraesCS4B01G234700 chr3A 85.135 74 6 4 3049 3121 170997215 170997146 1.620000e-08 71.3
66 TraesCS4B01G234700 chr3A 93.617 47 1 2 245 290 99426175 99426220 5.840000e-08 69.4
67 TraesCS4B01G234700 chr3A 100.000 28 0 0 3235 3262 290410234 290410207 6.000000e-03 52.8
68 TraesCS4B01G234700 chr5B 90.000 50 5 0 241 290 549974408 549974359 7.560000e-07 65.8


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 TraesCS4B01G234700 chr4B 489292340 489295603 3263 True 6028.000000 6028 100.000000 1 3264 1 chr4B.!!$R1 3263
1 TraesCS4B01G234700 chr4B 626067885 626068781 896 True 761.000000 761 82.263000 1216 2121 1 chr4B.!!$R2 905
2 TraesCS4B01G234700 chr4B 639452215 639453487 1272 False 450.000000 798 86.675500 1208 2370 2 chr4B.!!$F2 1162
3 TraesCS4B01G234700 chr4B 667343756 667345982 2226 False 290.333333 510 85.026667 1208 2372 3 chr4B.!!$F4 1164
4 TraesCS4B01G234700 chr4B 667263235 667264207 972 False 289.000000 398 82.187000 1374 2108 2 chr4B.!!$F3 734
5 TraesCS4B01G234700 chr4A 54404403 54406819 2416 True 1608.000000 2010 90.251500 2 2652 2 chr4A.!!$R1 2650
6 TraesCS4B01G234700 chr4D 397154868 397159231 4363 True 907.500000 1851 90.334500 1 3264 4 chr4D.!!$R2 3263
7 TraesCS4B01G234700 chr4D 488665129 488666010 881 True 811.000000 811 83.389000 1212 2108 1 chr4D.!!$R1 896
8 TraesCS4B01G234700 chr5A 670425191 670426072 881 True 828.000000 828 83.757000 1212 2108 1 chr5A.!!$R2 896
9 TraesCS4B01G234700 chr5A 706677192 706678436 1244 True 433.500000 767 86.526000 1208 2370 2 chr5A.!!$R4 1162
10 TraesCS4B01G234700 chrUn 30125744 30131094 5350 True 492.000000 544 80.614000 1442 2371 2 chrUn.!!$R2 929

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
556 580 0.311477 TGTCAACACTAGCGCGTACA 59.689 50.0 8.43 0.0 0.00 2.90 F
1053 1092 0.032912 TGGACCCAGTGGCGTATCTA 60.033 55.0 2.61 0.0 33.59 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2145 8453 1.739466 TCTGATCGTGCATTGAAAGCC 59.261 47.619 0.0 0.0 0.0 4.35 R
2595 10399 1.346395 TGCACCCGTTCTCTGTACATT 59.654 47.619 0.0 0.0 0.0 2.71 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
57 58 1.081892 CTCCAACGCCATCTGAACAG 58.918 55.000 0.00 0.00 0.00 3.16
92 99 2.098831 GCCGTCGCTTCAACCTACC 61.099 63.158 0.00 0.00 0.00 3.18
123 130 1.790755 TCACAAAAGTGTCCCGATCG 58.209 50.000 8.51 8.51 35.07 3.69
172 179 4.489810 TCATTCCACAAACAAACACACAC 58.510 39.130 0.00 0.00 0.00 3.82
202 209 4.495349 GCGCGTACTGATTCAGTAGAACTA 60.495 45.833 23.59 3.90 45.88 2.24
205 212 5.163683 GCGTACTGATTCAGTAGAACTACCA 60.164 44.000 23.59 1.82 45.88 3.25
220 227 7.392766 AGAACTACCAATCCATCCATCAATA 57.607 36.000 0.00 0.00 0.00 1.90
282 289 6.325545 TCCCTCCGTAAAGAAATATAAGAGCA 59.674 38.462 0.00 0.00 0.00 4.26
299 306 6.567602 AAGAGCATTTAGATTGTACTCCCT 57.432 37.500 0.00 0.00 0.00 4.20
300 307 6.168270 AGAGCATTTAGATTGTACTCCCTC 57.832 41.667 0.00 0.00 0.00 4.30
301 308 5.663106 AGAGCATTTAGATTGTACTCCCTCA 59.337 40.000 0.00 0.00 0.00 3.86
302 309 6.328672 AGAGCATTTAGATTGTACTCCCTCAT 59.671 38.462 0.00 0.00 0.00 2.90
303 310 6.529220 AGCATTTAGATTGTACTCCCTCATC 58.471 40.000 0.00 0.00 0.00 2.92
304 311 5.703130 GCATTTAGATTGTACTCCCTCATCC 59.297 44.000 0.00 0.00 0.00 3.51
306 313 3.421394 AGATTGTACTCCCTCATCCCA 57.579 47.619 0.00 0.00 0.00 4.37
307 314 3.946824 AGATTGTACTCCCTCATCCCAT 58.053 45.455 0.00 0.00 0.00 4.00
310 317 6.094302 AGATTGTACTCCCTCATCCCATAAT 58.906 40.000 0.00 0.00 0.00 1.28
312 319 4.566837 TGTACTCCCTCATCCCATAATGT 58.433 43.478 0.00 0.00 0.00 2.71
313 320 5.722290 TGTACTCCCTCATCCCATAATGTA 58.278 41.667 0.00 0.00 0.00 2.29
314 321 6.147473 TGTACTCCCTCATCCCATAATGTAA 58.853 40.000 0.00 0.00 0.00 2.41
315 322 5.832539 ACTCCCTCATCCCATAATGTAAG 57.167 43.478 0.00 0.00 0.00 2.34
317 324 5.308237 ACTCCCTCATCCCATAATGTAAGAC 59.692 44.000 0.00 0.00 0.00 3.01
318 325 4.283467 TCCCTCATCCCATAATGTAAGACG 59.717 45.833 0.00 0.00 0.00 4.18
319 326 4.040461 CCCTCATCCCATAATGTAAGACGT 59.960 45.833 0.00 0.00 0.00 4.34
321 328 6.055588 CCTCATCCCATAATGTAAGACGTTT 58.944 40.000 0.00 0.00 0.00 3.60
323 330 7.067008 CCTCATCCCATAATGTAAGACGTTTTT 59.933 37.037 0.00 0.00 0.00 1.94
324 331 7.757526 TCATCCCATAATGTAAGACGTTTTTG 58.242 34.615 0.00 0.00 0.00 2.44
325 332 6.503589 TCCCATAATGTAAGACGTTTTTGG 57.496 37.500 0.00 0.00 32.97 3.28
326 333 5.099575 CCCATAATGTAAGACGTTTTTGGC 58.900 41.667 0.00 0.00 32.38 4.52
328 335 5.571357 CCATAATGTAAGACGTTTTTGGCAC 59.429 40.000 0.00 0.00 28.92 5.01
329 336 4.911514 AATGTAAGACGTTTTTGGCACT 57.088 36.364 0.00 0.00 0.00 4.40
330 337 7.361371 CCATAATGTAAGACGTTTTTGGCACTA 60.361 37.037 0.00 0.00 28.92 2.74
331 338 4.799419 TGTAAGACGTTTTTGGCACTAC 57.201 40.909 0.00 0.00 0.00 2.73
332 339 4.190001 TGTAAGACGTTTTTGGCACTACA 58.810 39.130 0.00 0.00 0.00 2.74
333 340 3.685836 AAGACGTTTTTGGCACTACAC 57.314 42.857 0.00 0.00 0.00 2.90
335 342 4.062677 AGACGTTTTTGGCACTACACTA 57.937 40.909 0.00 0.00 0.00 2.74
336 343 4.056050 AGACGTTTTTGGCACTACACTAG 58.944 43.478 0.00 0.00 0.00 2.57
337 344 3.800531 ACGTTTTTGGCACTACACTAGT 58.199 40.909 0.00 0.00 40.28 2.57
400 424 2.802787 AGTGAAACAGACCTCGTCAG 57.197 50.000 0.00 0.00 41.43 3.51
512 536 3.010808 ACAAATCCTCCGGGTGGAATTAA 59.989 43.478 20.81 0.00 45.87 1.40
556 580 0.311477 TGTCAACACTAGCGCGTACA 59.689 50.000 8.43 0.00 0.00 2.90
679 707 7.147479 ACCACTATATATGCCTGTTTCTTCTGT 60.147 37.037 0.00 0.00 0.00 3.41
714 742 3.562973 CAGCAAGTCAAGAAAGAAGAGCA 59.437 43.478 0.00 0.00 0.00 4.26
716 744 3.812053 GCAAGTCAAGAAAGAAGAGCAGA 59.188 43.478 0.00 0.00 0.00 4.26
762 794 7.064728 GGTATGTCTTGACCACAAATTCTACTC 59.935 40.741 0.00 0.00 35.65 2.59
894 927 0.451783 GGTAAGCGCATTTGGTCCTG 59.548 55.000 11.47 0.00 0.00 3.86
910 943 2.171448 GTCCTGATTACCTGTGGCATCT 59.829 50.000 0.00 0.00 0.00 2.90
911 944 2.171237 TCCTGATTACCTGTGGCATCTG 59.829 50.000 0.00 0.00 0.00 2.90
912 945 2.171237 CCTGATTACCTGTGGCATCTGA 59.829 50.000 0.00 0.00 0.00 3.27
913 946 3.370846 CCTGATTACCTGTGGCATCTGAA 60.371 47.826 0.00 0.00 0.00 3.02
914 947 4.264253 CTGATTACCTGTGGCATCTGAAA 58.736 43.478 0.00 0.00 0.00 2.69
915 948 4.009675 TGATTACCTGTGGCATCTGAAAC 58.990 43.478 0.00 0.00 0.00 2.78
916 949 2.489938 TACCTGTGGCATCTGAAACC 57.510 50.000 0.00 0.00 0.00 3.27
946 979 8.630054 AGTTAACATGCTGTGAATTTAAGGTA 57.370 30.769 8.61 0.00 0.00 3.08
1020 1053 0.690762 TGTACCAGCAAGAAGGGGTC 59.309 55.000 0.00 0.00 34.88 4.46
1044 1083 4.802051 CCCGGCATGGACCCAGTG 62.802 72.222 0.00 0.00 42.00 3.66
1045 1084 4.802051 CCGGCATGGACCCAGTGG 62.802 72.222 0.63 0.63 42.00 4.00
1048 1087 4.722700 GCATGGACCCAGTGGCGT 62.723 66.667 2.61 2.97 33.59 5.68
1049 1088 2.986290 CATGGACCCAGTGGCGTA 59.014 61.111 2.61 0.00 33.59 4.42
1050 1089 1.526887 CATGGACCCAGTGGCGTAT 59.473 57.895 2.61 0.00 33.59 3.06
1051 1090 0.532862 CATGGACCCAGTGGCGTATC 60.533 60.000 2.61 0.00 33.59 2.24
1052 1091 0.691078 ATGGACCCAGTGGCGTATCT 60.691 55.000 2.61 0.00 33.59 1.98
1053 1092 0.032912 TGGACCCAGTGGCGTATCTA 60.033 55.000 2.61 0.00 33.59 1.98
1054 1093 0.674534 GGACCCAGTGGCGTATCTAG 59.325 60.000 2.61 0.00 33.59 2.43
1055 1094 0.674534 GACCCAGTGGCGTATCTAGG 59.325 60.000 2.61 0.00 33.59 3.02
1056 1095 0.759436 ACCCAGTGGCGTATCTAGGG 60.759 60.000 2.61 0.00 40.66 3.53
1057 1096 1.472662 CCCAGTGGCGTATCTAGGGG 61.473 65.000 2.61 0.00 0.00 4.79
1058 1097 1.472662 CCAGTGGCGTATCTAGGGGG 61.473 65.000 0.00 0.00 0.00 5.40
1059 1098 0.759436 CAGTGGCGTATCTAGGGGGT 60.759 60.000 0.00 0.00 0.00 4.95
1060 1099 0.759436 AGTGGCGTATCTAGGGGGTG 60.759 60.000 0.00 0.00 0.00 4.61
1061 1100 1.458777 TGGCGTATCTAGGGGGTGG 60.459 63.158 0.00 0.00 0.00 4.61
1062 1101 1.152398 GGCGTATCTAGGGGGTGGA 60.152 63.158 0.00 0.00 0.00 4.02
1063 1102 1.470165 GGCGTATCTAGGGGGTGGAC 61.470 65.000 0.00 0.00 0.00 4.02
1064 1103 0.757935 GCGTATCTAGGGGGTGGACA 60.758 60.000 0.00 0.00 0.00 4.02
1065 1104 1.329256 CGTATCTAGGGGGTGGACAG 58.671 60.000 0.00 0.00 0.00 3.51
1066 1105 1.718280 GTATCTAGGGGGTGGACAGG 58.282 60.000 0.00 0.00 0.00 4.00
1067 1106 0.566176 TATCTAGGGGGTGGACAGGG 59.434 60.000 0.00 0.00 0.00 4.45
1068 1107 1.537478 ATCTAGGGGGTGGACAGGGT 61.537 60.000 0.00 0.00 0.00 4.34
1069 1108 1.995626 CTAGGGGGTGGACAGGGTG 60.996 68.421 0.00 0.00 0.00 4.61
1070 1109 3.572715 TAGGGGGTGGACAGGGTGG 62.573 68.421 0.00 0.00 0.00 4.61
1072 1111 3.647771 GGGGTGGACAGGGTGGTC 61.648 72.222 0.00 0.00 37.06 4.02
1092 1131 2.236489 CATGGACCACCCTGGAATTT 57.764 50.000 0.00 0.00 40.96 1.82
1093 1132 2.102578 CATGGACCACCCTGGAATTTC 58.897 52.381 0.00 0.00 40.96 2.17
1094 1133 0.407918 TGGACCACCCTGGAATTTCC 59.592 55.000 8.59 8.59 40.96 3.13
1095 1134 0.324368 GGACCACCCTGGAATTTCCC 60.324 60.000 12.90 0.00 40.96 3.97
1096 1135 0.324368 GACCACCCTGGAATTTCCCC 60.324 60.000 12.90 0.00 40.96 4.81
1097 1136 1.077298 ACCACCCTGGAATTTCCCCA 61.077 55.000 12.90 0.00 40.96 4.96
1098 1137 0.339510 CCACCCTGGAATTTCCCCAT 59.660 55.000 12.90 0.00 40.96 4.00
1099 1138 1.573376 CCACCCTGGAATTTCCCCATA 59.427 52.381 12.90 0.00 40.96 2.74
1100 1139 2.023501 CCACCCTGGAATTTCCCCATAA 60.024 50.000 12.90 0.00 40.96 1.90
1101 1140 3.375207 CCACCCTGGAATTTCCCCATAAT 60.375 47.826 12.90 0.00 40.96 1.28
1102 1141 3.897505 CACCCTGGAATTTCCCCATAATC 59.102 47.826 12.90 0.00 35.03 1.75
1103 1142 3.799578 ACCCTGGAATTTCCCCATAATCT 59.200 43.478 12.90 0.00 35.03 2.40
1104 1143 4.988221 ACCCTGGAATTTCCCCATAATCTA 59.012 41.667 12.90 0.00 35.03 1.98
1105 1144 5.621329 ACCCTGGAATTTCCCCATAATCTAT 59.379 40.000 12.90 0.00 35.03 1.98
1106 1145 6.802660 ACCCTGGAATTTCCCCATAATCTATA 59.197 38.462 12.90 0.00 35.03 1.31
1107 1146 7.468830 ACCCTGGAATTTCCCCATAATCTATAT 59.531 37.037 12.90 0.00 35.03 0.86
1108 1147 9.014049 CCCTGGAATTTCCCCATAATCTATATA 57.986 37.037 12.90 0.00 35.03 0.86
1110 1149 9.566432 CTGGAATTTCCCCATAATCTATATAGC 57.434 37.037 12.90 0.00 35.03 2.97
1111 1150 9.067963 TGGAATTTCCCCATAATCTATATAGCA 57.932 33.333 12.90 0.00 35.03 3.49
1173 1212 8.489990 TTTATGTGAATATTTTGCATTGGTGG 57.510 30.769 0.00 0.00 0.00 4.61
1174 1213 5.735285 TGTGAATATTTTGCATTGGTGGA 57.265 34.783 0.00 0.00 0.00 4.02
1175 1214 5.477510 TGTGAATATTTTGCATTGGTGGAC 58.522 37.500 0.00 0.00 0.00 4.02
1176 1215 4.869861 GTGAATATTTTGCATTGGTGGACC 59.130 41.667 0.00 0.00 0.00 4.46
1177 1216 4.529769 TGAATATTTTGCATTGGTGGACCA 59.470 37.500 0.00 0.00 45.94 4.02
1187 1226 2.361610 GTGGACCACCCTGGCATG 60.362 66.667 14.16 0.00 42.67 4.06
1188 1227 2.858476 TGGACCACCCTGGCATGT 60.858 61.111 0.00 0.00 42.67 3.21
1189 1228 2.440599 GGACCACCCTGGCATGTT 59.559 61.111 0.00 0.00 42.67 2.71
1190 1229 1.978617 GGACCACCCTGGCATGTTG 60.979 63.158 0.00 0.00 42.67 3.33
1191 1230 1.978617 GACCACCCTGGCATGTTGG 60.979 63.158 4.83 4.83 42.67 3.77
1192 1231 2.681064 CCACCCTGGCATGTTGGG 60.681 66.667 15.17 15.17 46.07 4.12
1193 1232 3.384532 CACCCTGGCATGTTGGGC 61.385 66.667 16.24 0.00 44.56 5.36
1194 1233 3.593680 ACCCTGGCATGTTGGGCT 61.594 61.111 16.24 5.04 44.56 5.19
1195 1234 2.237965 ACCCTGGCATGTTGGGCTA 61.238 57.895 16.24 0.00 44.56 3.93
1196 1235 1.454479 CCCTGGCATGTTGGGCTAG 60.454 63.158 6.83 0.00 39.31 3.42
1197 1236 2.123428 CCTGGCATGTTGGGCTAGC 61.123 63.158 6.04 6.04 38.40 3.42
1198 1237 1.077212 CTGGCATGTTGGGCTAGCT 60.077 57.895 15.72 0.00 33.06 3.32
1199 1238 0.181114 CTGGCATGTTGGGCTAGCTA 59.819 55.000 15.72 0.96 33.06 3.32
1200 1239 0.107214 TGGCATGTTGGGCTAGCTAC 60.107 55.000 15.72 10.98 0.00 3.58
1201 1240 1.160329 GGCATGTTGGGCTAGCTACG 61.160 60.000 15.72 1.04 0.00 3.51
1202 1241 1.776034 GCATGTTGGGCTAGCTACGC 61.776 60.000 15.72 6.93 0.00 4.42
1203 1242 1.146263 ATGTTGGGCTAGCTACGCC 59.854 57.895 15.72 19.98 46.83 5.68
1225 1264 1.672356 GCATGGACCAGCAGTTCGT 60.672 57.895 0.00 0.00 0.00 3.85
1301 1346 0.380733 CGTCGTTCCATCCATCTCGA 59.619 55.000 0.00 0.00 0.00 4.04
1316 1361 0.175760 CTCGAAGCTCCGATTTCCCA 59.824 55.000 0.00 0.00 37.96 4.37
1415 1469 2.732094 CCGCCGTCGTCGAACTTT 60.732 61.111 2.98 0.00 39.71 2.66
1451 1505 2.357836 CAGGCTGGCACCCTCAAT 59.642 61.111 6.61 0.00 0.00 2.57
2145 8453 5.088739 CGGTTGTAGCTTGCAAGAAAATAG 58.911 41.667 30.39 9.38 0.00 1.73
2150 8458 4.879197 AGCTTGCAAGAAAATAGGCTTT 57.121 36.364 30.39 0.00 0.00 3.51
2158 8492 5.163923 GCAAGAAAATAGGCTTTCAATGCAC 60.164 40.000 16.64 0.00 43.11 4.57
2260 8598 2.546795 CGTGGCTCTCAGAAGTTTCAGT 60.547 50.000 0.00 0.00 0.00 3.41
2318 8745 2.234300 TTCTGAGTTTGGTCACGGTC 57.766 50.000 0.00 0.00 0.00 4.79
2332 8759 2.232941 TCACGGTCTCCATTTCTACCAC 59.767 50.000 0.00 0.00 32.04 4.16
2372 8799 9.620660 CTGTAACCATTTCAGTTTACCATTTAC 57.379 33.333 0.00 0.00 0.00 2.01
2373 8800 8.291032 TGTAACCATTTCAGTTTACCATTTACG 58.709 33.333 0.00 0.00 0.00 3.18
2374 8801 6.887626 ACCATTTCAGTTTACCATTTACGT 57.112 33.333 0.00 0.00 0.00 3.57
2375 8802 7.982761 ACCATTTCAGTTTACCATTTACGTA 57.017 32.000 0.00 0.00 0.00 3.57
2397 10199 3.017442 TGTGACTAACCAGATCTCCTCG 58.983 50.000 0.00 0.00 0.00 4.63
2403 10205 2.516227 ACCAGATCTCCTCGTCTGAA 57.484 50.000 0.00 0.00 43.50 3.02
2447 10249 9.952030 TCTATTGACTAAAATGTTCCACATACA 57.048 29.630 0.00 0.00 37.97 2.29
2461 10263 8.511321 TGTTCCACATACAATGAATGTTCTAAC 58.489 33.333 0.00 0.00 43.63 2.34
2488 10290 4.686191 TTCCCCGCGGAAATAATAGTTA 57.314 40.909 30.73 0.00 45.54 2.24
2491 10293 3.126343 CCCCGCGGAAATAATAGTTATGC 59.874 47.826 30.73 0.00 0.00 3.14
2492 10294 4.000988 CCCGCGGAAATAATAGTTATGCT 58.999 43.478 30.73 0.00 0.00 3.79
2493 10295 4.454504 CCCGCGGAAATAATAGTTATGCTT 59.545 41.667 30.73 0.00 0.00 3.91
2495 10297 5.305812 CGCGGAAATAATAGTTATGCTTCG 58.694 41.667 0.00 0.00 0.00 3.79
2497 10299 6.183360 CGCGGAAATAATAGTTATGCTTCGAT 60.183 38.462 0.00 0.00 0.00 3.59
2500 10302 9.135843 CGGAAATAATAGTTATGCTTCGATACA 57.864 33.333 0.00 0.00 0.00 2.29
2514 10316 2.905085 TCGATACACCCCCTAAACACAA 59.095 45.455 0.00 0.00 0.00 3.33
2519 10321 3.442076 ACACCCCCTAAACACAAAAACA 58.558 40.909 0.00 0.00 0.00 2.83
2520 10322 3.449377 ACACCCCCTAAACACAAAAACAG 59.551 43.478 0.00 0.00 0.00 3.16
2521 10323 3.449377 CACCCCCTAAACACAAAAACAGT 59.551 43.478 0.00 0.00 0.00 3.55
2561 10363 6.101734 ACCTCTTCATAAGAAAGGGCATGATA 59.898 38.462 0.00 0.00 37.02 2.15
2571 10375 8.593945 AAGAAAGGGCATGATAGTCATTTTAA 57.406 30.769 0.00 0.00 34.28 1.52
2586 10390 8.965986 AGTCATTTTAAAAACTCTTTATCCGC 57.034 30.769 4.44 0.00 0.00 5.54
2595 10399 3.141398 ACTCTTTATCCGCCGTATACGA 58.859 45.455 26.37 6.85 43.02 3.43
2612 10427 1.891150 ACGAATGTACAGAGAACGGGT 59.109 47.619 0.33 0.00 0.00 5.28
2617 10432 1.007336 GTACAGAGAACGGGTGCACG 61.007 60.000 11.45 2.44 40.31 5.34
2668 10484 3.451178 AGGCAACGTGATAACATACCTCT 59.549 43.478 0.00 0.00 46.39 3.69
2669 10485 4.081087 AGGCAACGTGATAACATACCTCTT 60.081 41.667 0.00 0.00 46.39 2.85
2675 10491 7.113658 ACGTGATAACATACCTCTTTCTCAT 57.886 36.000 0.00 0.00 0.00 2.90
2676 10492 7.556844 ACGTGATAACATACCTCTTTCTCATT 58.443 34.615 0.00 0.00 0.00 2.57
2677 10493 7.707035 ACGTGATAACATACCTCTTTCTCATTC 59.293 37.037 0.00 0.00 0.00 2.67
2678 10494 7.923344 CGTGATAACATACCTCTTTCTCATTCT 59.077 37.037 0.00 0.00 0.00 2.40
2679 10495 9.606631 GTGATAACATACCTCTTTCTCATTCTT 57.393 33.333 0.00 0.00 0.00 2.52
2683 10499 7.929941 ACATACCTCTTTCTCATTCTTTTCC 57.070 36.000 0.00 0.00 0.00 3.13
2684 10500 7.694093 ACATACCTCTTTCTCATTCTTTTCCT 58.306 34.615 0.00 0.00 0.00 3.36
2685 10501 7.826744 ACATACCTCTTTCTCATTCTTTTCCTC 59.173 37.037 0.00 0.00 0.00 3.71
2686 10502 6.446909 ACCTCTTTCTCATTCTTTTCCTCT 57.553 37.500 0.00 0.00 0.00 3.69
2687 10503 6.846988 ACCTCTTTCTCATTCTTTTCCTCTT 58.153 36.000 0.00 0.00 0.00 2.85
2688 10504 7.293828 ACCTCTTTCTCATTCTTTTCCTCTTT 58.706 34.615 0.00 0.00 0.00 2.52
2689 10505 7.446931 ACCTCTTTCTCATTCTTTTCCTCTTTC 59.553 37.037 0.00 0.00 0.00 2.62
2690 10506 7.665145 CCTCTTTCTCATTCTTTTCCTCTTTCT 59.335 37.037 0.00 0.00 0.00 2.52
2691 10507 8.986929 TCTTTCTCATTCTTTTCCTCTTTCTT 57.013 30.769 0.00 0.00 0.00 2.52
2692 10508 9.061435 TCTTTCTCATTCTTTTCCTCTTTCTTC 57.939 33.333 0.00 0.00 0.00 2.87
2693 10509 8.986929 TTTCTCATTCTTTTCCTCTTTCTTCT 57.013 30.769 0.00 0.00 0.00 2.85
2694 10510 8.986929 TTCTCATTCTTTTCCTCTTTCTTCTT 57.013 30.769 0.00 0.00 0.00 2.52
2695 10511 8.986929 TCTCATTCTTTTCCTCTTTCTTCTTT 57.013 30.769 0.00 0.00 0.00 2.52
2696 10512 8.844244 TCTCATTCTTTTCCTCTTTCTTCTTTG 58.156 33.333 0.00 0.00 0.00 2.77
2697 10513 7.428826 TCATTCTTTTCCTCTTTCTTCTTTGC 58.571 34.615 0.00 0.00 0.00 3.68
2698 10514 7.286316 TCATTCTTTTCCTCTTTCTTCTTTGCT 59.714 33.333 0.00 0.00 0.00 3.91
2699 10515 7.410120 TTCTTTTCCTCTTTCTTCTTTGCTT 57.590 32.000 0.00 0.00 0.00 3.91
2700 10516 7.410120 TCTTTTCCTCTTTCTTCTTTGCTTT 57.590 32.000 0.00 0.00 0.00 3.51
2708 10524 8.939929 CCTCTTTCTTCTTTGCTTTTTCTTTTT 58.060 29.630 0.00 0.00 0.00 1.94
2738 10554 7.685481 TCTTCCTTTTTCCCTTTTTCTTGTTT 58.315 30.769 0.00 0.00 0.00 2.83
2740 10556 7.252612 TCCTTTTTCCCTTTTTCTTGTTTCT 57.747 32.000 0.00 0.00 0.00 2.52
2867 10691 9.996554 TTTCTTTTCTTTTCTTTTTCTGTTCCT 57.003 25.926 0.00 0.00 0.00 3.36
2868 10692 9.996554 TTCTTTTCTTTTCTTTTTCTGTTCCTT 57.003 25.926 0.00 0.00 0.00 3.36
2869 10693 9.996554 TCTTTTCTTTTCTTTTTCTGTTCCTTT 57.003 25.926 0.00 0.00 0.00 3.11
2958 10783 8.696410 ACTATTTTCAAATTTGTGAACGTGTT 57.304 26.923 17.47 2.48 37.24 3.32
2972 10797 5.895889 GTGAACGTGTTTTCAAAATTGATGC 59.104 36.000 0.00 0.00 37.24 3.91
2980 10805 7.429051 GTGTTTTCAAAATTGATGCACCTTTTC 59.571 33.333 0.00 0.00 37.00 2.29
2981 10806 7.336427 TGTTTTCAAAATTGATGCACCTTTTCT 59.664 29.630 0.00 0.00 37.00 2.52
2982 10807 7.481275 TTTCAAAATTGATGCACCTTTTCTC 57.519 32.000 0.00 0.00 37.00 2.87
2985 10810 7.046652 TCAAAATTGATGCACCTTTTCTCAAA 58.953 30.769 1.13 0.00 31.01 2.69
2987 10812 8.347035 CAAAATTGATGCACCTTTTCTCAAATT 58.653 29.630 1.13 0.00 30.39 1.82
2988 10813 7.662604 AATTGATGCACCTTTTCTCAAATTC 57.337 32.000 1.13 0.00 30.39 2.17
2989 10814 5.787953 TGATGCACCTTTTCTCAAATTCA 57.212 34.783 0.00 0.00 0.00 2.57
2990 10815 6.349243 TGATGCACCTTTTCTCAAATTCAT 57.651 33.333 0.00 0.00 0.00 2.57
2991 10816 6.392354 TGATGCACCTTTTCTCAAATTCATC 58.608 36.000 0.00 0.00 0.00 2.92
2992 10817 4.797471 TGCACCTTTTCTCAAATTCATCG 58.203 39.130 0.00 0.00 0.00 3.84
2993 10818 4.518590 TGCACCTTTTCTCAAATTCATCGA 59.481 37.500 0.00 0.00 0.00 3.59
2994 10819 5.009510 TGCACCTTTTCTCAAATTCATCGAA 59.990 36.000 0.00 0.00 0.00 3.71
2995 10820 5.920273 GCACCTTTTCTCAAATTCATCGAAA 59.080 36.000 0.00 0.00 0.00 3.46
3044 10869 7.138692 AGAAAATTGATGAACCTTCTCGAAG 57.861 36.000 0.00 0.00 38.14 3.79
3073 10898 9.913451 GATGAACATTTTTCAAAATCAACGAAA 57.087 25.926 0.00 0.00 36.52 3.46
3179 11027 7.388460 ACTTTGTTTGCAAAATCCATGAAAA 57.612 28.000 14.67 4.40 43.17 2.29
3233 11081 2.355132 TGTGTACGTTTTGCAAATCCGT 59.645 40.909 28.66 28.66 35.68 4.69
3240 11088 3.489047 CGTTTTGCAAATCCGTGAACATT 59.511 39.130 13.65 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 0.744771 GGCGACATTTCTGGAGGACC 60.745 60.000 0.00 0.00 0.00 4.46
92 99 0.453793 TTTTGTGAAGGGTGTGCACG 59.546 50.000 13.13 0.00 35.37 5.34
123 130 5.050159 GGTTGATTTGATTTGTTGTTGGAGC 60.050 40.000 0.00 0.00 0.00 4.70
202 209 8.961293 ATTGTTATATTGATGGATGGATTGGT 57.039 30.769 0.00 0.00 0.00 3.67
205 212 9.096823 AGCAATTGTTATATTGATGGATGGATT 57.903 29.630 7.40 0.00 37.65 3.01
220 227 8.032451 ACCGCAAATAAGTTTAGCAATTGTTAT 58.968 29.630 7.40 0.00 0.00 1.89
244 251 0.245813 GGAGGGAGTACACGACAACC 59.754 60.000 0.00 0.00 0.00 3.77
282 289 5.911178 TGGGATGAGGGAGTACAATCTAAAT 59.089 40.000 0.00 0.00 0.00 1.40
287 294 5.825593 TTATGGGATGAGGGAGTACAATC 57.174 43.478 0.00 0.00 0.00 2.67
289 296 4.975147 ACATTATGGGATGAGGGAGTACAA 59.025 41.667 0.00 0.00 0.00 2.41
290 297 4.566837 ACATTATGGGATGAGGGAGTACA 58.433 43.478 0.00 0.00 0.00 2.90
291 298 6.497259 TCTTACATTATGGGATGAGGGAGTAC 59.503 42.308 0.00 0.00 0.00 2.73
293 300 5.308237 GTCTTACATTATGGGATGAGGGAGT 59.692 44.000 0.00 0.00 0.00 3.85
295 302 4.283467 CGTCTTACATTATGGGATGAGGGA 59.717 45.833 0.00 0.00 0.00 4.20
296 303 4.040461 ACGTCTTACATTATGGGATGAGGG 59.960 45.833 0.00 0.00 0.00 4.30
297 304 5.215252 ACGTCTTACATTATGGGATGAGG 57.785 43.478 0.00 1.34 0.00 3.86
298 305 7.553881 AAAACGTCTTACATTATGGGATGAG 57.446 36.000 0.00 0.00 0.00 2.90
299 306 7.148154 CCAAAAACGTCTTACATTATGGGATGA 60.148 37.037 0.00 0.00 0.00 2.92
300 307 6.972328 CCAAAAACGTCTTACATTATGGGATG 59.028 38.462 0.00 0.74 0.00 3.51
301 308 6.405397 GCCAAAAACGTCTTACATTATGGGAT 60.405 38.462 0.00 0.00 0.00 3.85
302 309 5.106078 GCCAAAAACGTCTTACATTATGGGA 60.106 40.000 0.00 0.00 0.00 4.37
303 310 5.099575 GCCAAAAACGTCTTACATTATGGG 58.900 41.667 0.00 0.00 0.00 4.00
304 311 5.571357 GTGCCAAAAACGTCTTACATTATGG 59.429 40.000 0.00 0.00 0.00 2.74
306 313 6.569179 AGTGCCAAAAACGTCTTACATTAT 57.431 33.333 0.00 0.00 0.00 1.28
307 314 6.482641 TGTAGTGCCAAAAACGTCTTACATTA 59.517 34.615 0.00 0.00 0.00 1.90
310 317 4.034279 GTGTAGTGCCAAAAACGTCTTACA 59.966 41.667 0.00 0.00 0.00 2.41
312 319 4.444536 AGTGTAGTGCCAAAAACGTCTTA 58.555 39.130 0.00 0.00 0.00 2.10
313 320 3.275999 AGTGTAGTGCCAAAAACGTCTT 58.724 40.909 0.00 0.00 0.00 3.01
314 321 2.914059 AGTGTAGTGCCAAAAACGTCT 58.086 42.857 0.00 0.00 0.00 4.18
315 322 3.805971 ACTAGTGTAGTGCCAAAAACGTC 59.194 43.478 0.00 0.00 37.69 4.34
342 349 6.092944 TCCGTCGCATAATGTAAGACATTTTT 59.907 34.615 9.92 0.00 45.80 1.94
343 350 5.583061 TCCGTCGCATAATGTAAGACATTTT 59.417 36.000 9.92 0.33 45.80 1.82
344 351 5.113383 TCCGTCGCATAATGTAAGACATTT 58.887 37.500 9.92 0.00 45.80 2.32
346 353 4.299155 CTCCGTCGCATAATGTAAGACAT 58.701 43.478 0.00 0.00 41.31 3.06
347 354 3.490249 CCTCCGTCGCATAATGTAAGACA 60.490 47.826 0.00 0.00 32.57 3.41
348 355 3.050619 CCTCCGTCGCATAATGTAAGAC 58.949 50.000 0.00 0.00 0.00 3.01
349 356 2.035449 CCCTCCGTCGCATAATGTAAGA 59.965 50.000 0.00 0.00 0.00 2.10
350 357 2.035449 TCCCTCCGTCGCATAATGTAAG 59.965 50.000 0.00 0.00 0.00 2.34
351 358 2.033372 TCCCTCCGTCGCATAATGTAA 58.967 47.619 0.00 0.00 0.00 2.41
352 359 1.611977 CTCCCTCCGTCGCATAATGTA 59.388 52.381 0.00 0.00 0.00 2.29
353 360 0.389391 CTCCCTCCGTCGCATAATGT 59.611 55.000 0.00 0.00 0.00 2.71
354 361 0.389391 ACTCCCTCCGTCGCATAATG 59.611 55.000 0.00 0.00 0.00 1.90
355 362 1.612463 GTACTCCCTCCGTCGCATAAT 59.388 52.381 0.00 0.00 0.00 1.28
356 363 1.027357 GTACTCCCTCCGTCGCATAA 58.973 55.000 0.00 0.00 0.00 1.90
357 364 0.182061 AGTACTCCCTCCGTCGCATA 59.818 55.000 0.00 0.00 0.00 3.14
358 365 0.683504 AAGTACTCCCTCCGTCGCAT 60.684 55.000 0.00 0.00 0.00 4.73
359 366 0.896940 AAAGTACTCCCTCCGTCGCA 60.897 55.000 0.00 0.00 0.00 5.10
360 367 0.179142 GAAAGTACTCCCTCCGTCGC 60.179 60.000 0.00 0.00 0.00 5.19
361 368 1.461559 AGAAAGTACTCCCTCCGTCG 58.538 55.000 0.00 0.00 0.00 5.12
362 369 3.377798 CACTAGAAAGTACTCCCTCCGTC 59.622 52.174 0.00 0.00 33.48 4.79
556 580 2.030562 CGTTTGGTCCGCTCCACT 59.969 61.111 0.00 0.00 37.20 4.00
679 707 2.605818 GACTTGCTGTCGTGTGTACAAA 59.394 45.455 0.00 0.00 35.81 2.83
714 742 4.283212 CCTCAAACCTCTGTTCTCTTCTCT 59.717 45.833 0.00 0.00 32.15 3.10
716 744 3.970640 ACCTCAAACCTCTGTTCTCTTCT 59.029 43.478 0.00 0.00 32.15 2.85
762 794 4.407296 AGAGGAACACCAAGCTTATAGAGG 59.593 45.833 0.00 0.00 0.00 3.69
894 927 3.378427 GGTTTCAGATGCCACAGGTAATC 59.622 47.826 0.00 0.00 0.00 1.75
910 943 5.830912 CAGCATGTTAACTTTCAGGTTTCA 58.169 37.500 7.22 0.00 0.00 2.69
946 979 6.094603 CAGCCATTGCAAGAAGAACTTATACT 59.905 38.462 4.94 0.00 41.13 2.12
954 987 1.999648 ACCAGCCATTGCAAGAAGAA 58.000 45.000 4.94 0.00 41.13 2.52
1031 1070 2.608970 ATACGCCACTGGGTCCATGC 62.609 60.000 0.00 0.00 38.74 4.06
1032 1071 0.532862 GATACGCCACTGGGTCCATG 60.533 60.000 0.00 0.00 38.74 3.66
1033 1072 0.691078 AGATACGCCACTGGGTCCAT 60.691 55.000 0.00 0.00 38.74 3.41
1034 1073 0.032912 TAGATACGCCACTGGGTCCA 60.033 55.000 0.00 0.00 38.74 4.02
1035 1074 0.674534 CTAGATACGCCACTGGGTCC 59.325 60.000 0.00 0.00 38.74 4.46
1036 1075 0.674534 CCTAGATACGCCACTGGGTC 59.325 60.000 0.00 0.00 38.74 4.46
1037 1076 0.759436 CCCTAGATACGCCACTGGGT 60.759 60.000 0.00 0.00 41.13 4.51
1038 1077 1.472662 CCCCTAGATACGCCACTGGG 61.473 65.000 0.00 0.00 35.10 4.45
1039 1078 1.472662 CCCCCTAGATACGCCACTGG 61.473 65.000 0.00 0.00 0.00 4.00
1040 1079 0.759436 ACCCCCTAGATACGCCACTG 60.759 60.000 0.00 0.00 0.00 3.66
1041 1080 0.759436 CACCCCCTAGATACGCCACT 60.759 60.000 0.00 0.00 0.00 4.00
1042 1081 1.746517 CACCCCCTAGATACGCCAC 59.253 63.158 0.00 0.00 0.00 5.01
1043 1082 1.458777 CCACCCCCTAGATACGCCA 60.459 63.158 0.00 0.00 0.00 5.69
1044 1083 1.152398 TCCACCCCCTAGATACGCC 60.152 63.158 0.00 0.00 0.00 5.68
1045 1084 0.757935 TGTCCACCCCCTAGATACGC 60.758 60.000 0.00 0.00 0.00 4.42
1046 1085 1.329256 CTGTCCACCCCCTAGATACG 58.671 60.000 0.00 0.00 0.00 3.06
1047 1086 1.718280 CCTGTCCACCCCCTAGATAC 58.282 60.000 0.00 0.00 0.00 2.24
1048 1087 0.566176 CCCTGTCCACCCCCTAGATA 59.434 60.000 0.00 0.00 0.00 1.98
1049 1088 1.318380 CCCTGTCCACCCCCTAGAT 59.682 63.158 0.00 0.00 0.00 1.98
1050 1089 2.181773 ACCCTGTCCACCCCCTAGA 61.182 63.158 0.00 0.00 0.00 2.43
1051 1090 1.995626 CACCCTGTCCACCCCCTAG 60.996 68.421 0.00 0.00 0.00 3.02
1052 1091 2.124085 CACCCTGTCCACCCCCTA 59.876 66.667 0.00 0.00 0.00 3.53
1055 1094 3.647771 GACCACCCTGTCCACCCC 61.648 72.222 0.00 0.00 0.00 4.95
1061 1100 1.299976 GTCCATGGACCACCCTGTC 59.700 63.158 31.37 5.53 39.08 3.51
1062 1101 3.495729 GTCCATGGACCACCCTGT 58.504 61.111 31.37 0.00 39.08 4.00
1073 1112 2.102578 GAAATTCCAGGGTGGTCCATG 58.897 52.381 0.00 0.00 44.12 3.66
1074 1113 1.007118 GGAAATTCCAGGGTGGTCCAT 59.993 52.381 7.23 0.00 39.03 3.41
1075 1114 0.407918 GGAAATTCCAGGGTGGTCCA 59.592 55.000 7.23 0.00 39.03 4.02
1076 1115 0.324368 GGGAAATTCCAGGGTGGTCC 60.324 60.000 14.68 0.00 38.64 4.46
1077 1116 0.324368 GGGGAAATTCCAGGGTGGTC 60.324 60.000 14.68 0.00 38.64 4.02
1078 1117 1.077298 TGGGGAAATTCCAGGGTGGT 61.077 55.000 14.68 0.00 38.64 4.16
1079 1118 0.339510 ATGGGGAAATTCCAGGGTGG 59.660 55.000 14.68 0.00 38.64 4.61
1080 1119 3.396685 TTATGGGGAAATTCCAGGGTG 57.603 47.619 14.68 0.00 38.64 4.61
1081 1120 3.799578 AGATTATGGGGAAATTCCAGGGT 59.200 43.478 14.68 0.00 38.64 4.34
1082 1121 4.475919 AGATTATGGGGAAATTCCAGGG 57.524 45.455 14.68 0.00 38.64 4.45
1084 1123 9.566432 GCTATATAGATTATGGGGAAATTCCAG 57.434 37.037 14.68 0.00 38.64 3.86
1085 1124 9.067963 TGCTATATAGATTATGGGGAAATTCCA 57.932 33.333 14.68 0.00 38.64 3.53
1147 1186 9.111613 CCACCAATGCAAAATATTCACATAAAT 57.888 29.630 0.00 0.00 0.00 1.40
1148 1187 8.316946 TCCACCAATGCAAAATATTCACATAAA 58.683 29.630 0.00 0.00 0.00 1.40
1149 1188 7.763528 GTCCACCAATGCAAAATATTCACATAA 59.236 33.333 0.00 0.00 0.00 1.90
1150 1189 7.264221 GTCCACCAATGCAAAATATTCACATA 58.736 34.615 0.00 0.00 0.00 2.29
1151 1190 6.108015 GTCCACCAATGCAAAATATTCACAT 58.892 36.000 0.00 0.00 0.00 3.21
1152 1191 5.477510 GTCCACCAATGCAAAATATTCACA 58.522 37.500 0.00 0.00 0.00 3.58
1153 1192 4.869861 GGTCCACCAATGCAAAATATTCAC 59.130 41.667 0.00 0.00 35.64 3.18
1154 1193 4.529769 TGGTCCACCAATGCAAAATATTCA 59.470 37.500 0.00 0.00 44.35 2.57
1155 1194 5.083533 TGGTCCACCAATGCAAAATATTC 57.916 39.130 0.00 0.00 44.35 1.75
1170 1209 2.361610 CATGCCAGGGTGGTCCAC 60.362 66.667 14.13 14.13 40.46 4.02
1171 1210 2.468868 AACATGCCAGGGTGGTCCA 61.469 57.895 0.00 0.00 40.46 4.02
1172 1211 1.978617 CAACATGCCAGGGTGGTCC 60.979 63.158 0.00 0.00 40.46 4.46
1173 1212 1.978617 CCAACATGCCAGGGTGGTC 60.979 63.158 4.99 0.00 40.46 4.02
1174 1213 2.118076 CCAACATGCCAGGGTGGT 59.882 61.111 4.99 0.00 40.46 4.16
1175 1214 2.681064 CCCAACATGCCAGGGTGG 60.681 66.667 6.42 6.42 41.55 4.61
1176 1215 2.497792 TAGCCCAACATGCCAGGGTG 62.498 60.000 16.46 0.00 44.69 4.61
1177 1216 2.215451 CTAGCCCAACATGCCAGGGT 62.215 60.000 16.46 11.28 44.69 4.34
1178 1217 1.454479 CTAGCCCAACATGCCAGGG 60.454 63.158 12.20 12.20 45.68 4.45
1179 1218 2.123428 GCTAGCCCAACATGCCAGG 61.123 63.158 2.29 0.00 0.00 4.45
1180 1219 0.181114 TAGCTAGCCCAACATGCCAG 59.819 55.000 12.13 0.00 0.00 4.85
1181 1220 0.107214 GTAGCTAGCCCAACATGCCA 60.107 55.000 12.13 0.00 0.00 4.92
1182 1221 1.160329 CGTAGCTAGCCCAACATGCC 61.160 60.000 12.13 0.00 0.00 4.40
1183 1222 2.311294 CGTAGCTAGCCCAACATGC 58.689 57.895 12.13 0.00 0.00 4.06
1206 1245 1.672030 CGAACTGCTGGTCCATGCA 60.672 57.895 13.30 13.30 37.63 3.96
1214 1253 2.743928 GGCTCCACGAACTGCTGG 60.744 66.667 0.00 0.00 0.00 4.85
1240 1282 1.630369 AGTACTGCTCTTGATGGCCAA 59.370 47.619 10.96 0.00 0.00 4.52
1301 1346 0.329596 AGCTTGGGAAATCGGAGCTT 59.670 50.000 0.00 0.00 40.55 3.74
1316 1361 1.961277 CGACGAGCCACCAAAGCTT 60.961 57.895 0.00 0.00 41.75 3.74
1403 1457 2.993449 AGGAGAGAAAGTTCGACGAC 57.007 50.000 0.00 0.00 0.00 4.34
1451 1505 4.082523 CAGGCGCCTCCGGAGAAA 62.083 66.667 33.39 0.00 40.77 2.52
1683 2020 4.743644 CGAAGGGTAACTAATTAAGCTCGG 59.256 45.833 0.00 0.00 0.00 4.63
2145 8453 1.739466 TCTGATCGTGCATTGAAAGCC 59.261 47.619 0.00 0.00 0.00 4.35
2150 8458 4.330894 GTCAATCTTCTGATCGTGCATTGA 59.669 41.667 0.00 0.00 31.51 2.57
2158 8492 5.579904 ACTCAACATGTCAATCTTCTGATCG 59.420 40.000 0.00 0.00 31.51 3.69
2260 8598 6.206634 ACAAATCGCTTCCATTCTACTTTCAA 59.793 34.615 0.00 0.00 0.00 2.69
2318 8745 4.214119 CACACAACAGTGGTAGAAATGGAG 59.786 45.833 0.00 0.00 37.58 3.86
2332 8759 4.188462 TGGTTACAGACTTCACACAACAG 58.812 43.478 0.00 0.00 0.00 3.16
2372 8799 4.580995 AGGAGATCTGGTTAGTCACATACG 59.419 45.833 0.00 0.00 0.00 3.06
2373 8800 5.278071 CGAGGAGATCTGGTTAGTCACATAC 60.278 48.000 0.00 0.00 0.00 2.39
2374 8801 4.822350 CGAGGAGATCTGGTTAGTCACATA 59.178 45.833 0.00 0.00 0.00 2.29
2375 8802 3.634448 CGAGGAGATCTGGTTAGTCACAT 59.366 47.826 0.00 0.00 0.00 3.21
2397 10199 9.088512 AGAATACATTAGAACACGAATTCAGAC 57.911 33.333 6.22 0.00 0.00 3.51
2438 10240 6.876789 ACGTTAGAACATTCATTGTATGTGGA 59.123 34.615 9.34 0.00 37.68 4.02
2445 10247 6.128007 GGAATCCACGTTAGAACATTCATTGT 60.128 38.462 0.00 0.00 41.53 2.71
2447 10249 5.357032 GGGAATCCACGTTAGAACATTCATT 59.643 40.000 0.09 0.00 0.00 2.57
2480 10282 6.295462 GGGGGTGTATCGAAGCATAACTATTA 60.295 42.308 0.00 0.00 0.00 0.98
2483 10285 3.322828 GGGGGTGTATCGAAGCATAACTA 59.677 47.826 0.00 0.00 0.00 2.24
2485 10287 2.104281 AGGGGGTGTATCGAAGCATAAC 59.896 50.000 0.00 0.00 0.00 1.89
2486 10288 2.404559 AGGGGGTGTATCGAAGCATAA 58.595 47.619 0.00 0.00 0.00 1.90
2488 10290 2.097110 TAGGGGGTGTATCGAAGCAT 57.903 50.000 0.00 0.00 0.00 3.79
2491 10293 3.055675 TGTGTTTAGGGGGTGTATCGAAG 60.056 47.826 0.00 0.00 0.00 3.79
2492 10294 2.905085 TGTGTTTAGGGGGTGTATCGAA 59.095 45.455 0.00 0.00 0.00 3.71
2493 10295 2.538222 TGTGTTTAGGGGGTGTATCGA 58.462 47.619 0.00 0.00 0.00 3.59
2495 10297 5.302313 TGTTTTTGTGTTTAGGGGGTGTATC 59.698 40.000 0.00 0.00 0.00 2.24
2497 10299 4.607239 TGTTTTTGTGTTTAGGGGGTGTA 58.393 39.130 0.00 0.00 0.00 2.90
2500 10302 3.715287 ACTGTTTTTGTGTTTAGGGGGT 58.285 40.909 0.00 0.00 0.00 4.95
2514 10316 9.668497 GAGGTATGGACTAATCTAAACTGTTTT 57.332 33.333 11.48 0.00 0.00 2.43
2519 10321 8.840200 TGAAGAGGTATGGACTAATCTAAACT 57.160 34.615 0.00 0.00 0.00 2.66
2531 10333 5.163195 GCCCTTTCTTATGAAGAGGTATGGA 60.163 44.000 13.53 0.00 39.03 3.41
2538 10340 7.222872 ACTATCATGCCCTTTCTTATGAAGAG 58.777 38.462 0.00 0.00 39.03 2.85
2561 10363 8.027189 GGCGGATAAAGAGTTTTTAAAATGACT 58.973 33.333 0.55 3.23 0.00 3.41
2571 10375 4.741676 CGTATACGGCGGATAAAGAGTTTT 59.258 41.667 14.45 0.00 35.37 2.43
2581 10385 2.553602 TGTACATTCGTATACGGCGGAT 59.446 45.455 24.18 10.59 40.29 4.18
2582 10386 1.946081 TGTACATTCGTATACGGCGGA 59.054 47.619 24.18 1.23 40.29 5.54
2586 10390 4.902448 CGTTCTCTGTACATTCGTATACGG 59.098 45.833 24.18 11.48 40.29 4.02
2595 10399 1.346395 TGCACCCGTTCTCTGTACATT 59.654 47.619 0.00 0.00 0.00 2.71
2617 10432 2.671963 GTTGGTTGTCGAGGGGGC 60.672 66.667 0.00 0.00 0.00 5.80
2651 10467 6.525578 TGAGAAAGAGGTATGTTATCACGT 57.474 37.500 0.00 0.00 0.00 4.49
2668 10484 8.986929 AGAAGAAAGAGGAAAAGAATGAGAAA 57.013 30.769 0.00 0.00 0.00 2.52
2669 10485 8.986929 AAGAAGAAAGAGGAAAAGAATGAGAA 57.013 30.769 0.00 0.00 0.00 2.87
2675 10491 7.410120 AAGCAAAGAAGAAAGAGGAAAAGAA 57.590 32.000 0.00 0.00 0.00 2.52
2676 10492 7.410120 AAAGCAAAGAAGAAAGAGGAAAAGA 57.590 32.000 0.00 0.00 0.00 2.52
2677 10493 8.484641 AAAAAGCAAAGAAGAAAGAGGAAAAG 57.515 30.769 0.00 0.00 0.00 2.27
2678 10494 8.314021 AGAAAAAGCAAAGAAGAAAGAGGAAAA 58.686 29.630 0.00 0.00 0.00 2.29
2679 10495 7.840931 AGAAAAAGCAAAGAAGAAAGAGGAAA 58.159 30.769 0.00 0.00 0.00 3.13
2680 10496 7.410120 AGAAAAAGCAAAGAAGAAAGAGGAA 57.590 32.000 0.00 0.00 0.00 3.36
2681 10497 7.410120 AAGAAAAAGCAAAGAAGAAAGAGGA 57.590 32.000 0.00 0.00 0.00 3.71
2682 10498 8.484641 AAAAGAAAAAGCAAAGAAGAAAGAGG 57.515 30.769 0.00 0.00 0.00 3.69
2708 10524 8.146053 AGAAAAAGGGAAAAAGGAAGAAGAAA 57.854 30.769 0.00 0.00 0.00 2.52
2783 10599 8.655651 ACAAGACTGTTTGAAAAACAAGAAAA 57.344 26.923 6.97 0.00 39.77 2.29
2842 10666 9.996554 AAGGAACAGAAAAAGAAAAGAAAAGAA 57.003 25.926 0.00 0.00 0.00 2.52
2922 10746 9.739786 CAAATTTGAAAATAGTTTATCGGTTGC 57.260 29.630 13.08 0.00 0.00 4.17
2931 10755 9.145865 ACACGTTCACAAATTTGAAAATAGTTT 57.854 25.926 24.64 11.36 37.24 2.66
2934 10758 9.965748 AAAACACGTTCACAAATTTGAAAATAG 57.034 25.926 24.64 15.67 37.24 1.73
2941 10765 8.652592 ATTTTGAAAACACGTTCACAAATTTG 57.347 26.923 16.67 16.67 37.24 2.32
2954 10779 5.989551 AGGTGCATCAATTTTGAAAACAC 57.010 34.783 0.00 11.94 41.13 3.32
2958 10783 7.046652 TGAGAAAAGGTGCATCAATTTTGAAA 58.953 30.769 0.00 0.00 41.13 2.69
2972 10797 7.928908 TTTTCGATGAATTTGAGAAAAGGTG 57.071 32.000 0.00 0.00 36.34 4.00
3017 10842 8.256611 TCGAGAAGGTTCATCAATTTTCTAAG 57.743 34.615 0.00 0.00 0.00 2.18
3020 10845 6.712547 ACTTCGAGAAGGTTCATCAATTTTCT 59.287 34.615 16.16 0.00 42.53 2.52
3021 10846 6.798959 CACTTCGAGAAGGTTCATCAATTTTC 59.201 38.462 16.16 0.00 42.53 2.29
3027 10852 2.897326 TCCACTTCGAGAAGGTTCATCA 59.103 45.455 16.16 0.00 42.53 3.07
3044 10869 7.793427 CGTTGATTTTGAAAAATGTTCATCCAC 59.207 33.333 5.76 0.00 38.64 4.02
3148 10994 8.498054 TGGATTTTGCAAACAAAGTTTAATGA 57.502 26.923 12.39 0.00 46.08 2.57
3149 10995 9.171701 CATGGATTTTGCAAACAAAGTTTAATG 57.828 29.630 12.39 3.35 46.08 1.90
3151 10997 8.498054 TCATGGATTTTGCAAACAAAGTTTAA 57.502 26.923 12.39 0.00 46.08 1.52
3153 10999 6.998968 TCATGGATTTTGCAAACAAAGTTT 57.001 29.167 12.39 0.00 46.08 2.66
3156 11002 8.859517 AATTTTCATGGATTTTGCAAACAAAG 57.140 26.923 12.39 4.81 46.08 2.77
3202 11050 9.872757 TTTGCAAAACGTACACAAATTTAAAAA 57.127 22.222 10.02 0.00 0.00 1.94
3207 11055 6.508721 CGGATTTGCAAAACGTACACAAATTT 60.509 34.615 23.41 2.35 40.13 1.82
3219 11067 5.402464 AAATGTTCACGGATTTGCAAAAC 57.598 34.783 17.19 13.72 0.00 2.43


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

AutoCloner maintained by Alex Coulton.