Multiple sequence alignment - TraesCS4B01G123800

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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 TraesCS4B01G123800 chr4B 100.000 5940 0 0 1 5940 147384178 147378239 0.000000e+00 10970.0
1 TraesCS4B01G123800 chr4A 94.634 3187 142 15 1 3179 471916811 471919976 0.000000e+00 4911.0
2 TraesCS4B01G123800 chr4A 96.552 1508 32 5 3658 5153 471920586 471922085 0.000000e+00 2479.0
3 TraesCS4B01G123800 chr4A 86.730 633 40 19 5144 5735 471923316 471923945 0.000000e+00 664.0
4 TraesCS4B01G123800 chr4A 98.788 165 1 1 3203 3366 471919972 471920136 5.820000e-75 292.0
5 TraesCS4B01G123800 chr4A 98.182 165 3 0 3495 3659 471920281 471920445 7.530000e-74 289.0
6 TraesCS4B01G123800 chr4A 96.386 83 3 0 3366 3448 471920201 471920283 2.890000e-28 137.0
7 TraesCS4B01G123800 chr4D 95.907 2712 60 12 395 3099 103256355 103253688 0.000000e+00 4346.0
8 TraesCS4B01G123800 chr4D 94.112 2157 64 22 3626 5735 103253238 103251098 0.000000e+00 3221.0
9 TraesCS4B01G123800 chr4D 85.529 463 34 22 3130 3568 103253691 103253238 2.520000e-123 453.0
10 TraesCS4B01G123800 chr4D 87.629 194 20 3 218 409 103258262 103258071 7.750000e-54 222.0
11 TraesCS4B01G123800 chr4D 84.756 164 21 3 4 165 344810033 344809872 1.710000e-35 161.0
12 TraesCS4B01G123800 chr4D 97.590 83 2 0 3366 3448 103253390 103253308 6.210000e-30 143.0
13 TraesCS4B01G123800 chr5A 85.775 471 61 6 1926 2393 320561079 320561546 1.490000e-135 494.0
14 TraesCS4B01G123800 chr5A 88.360 189 21 1 2842 3030 320562065 320562252 5.990000e-55 226.0
15 TraesCS4B01G123800 chr5A 92.000 75 5 1 984 1057 320559815 320559889 2.930000e-18 104.0
16 TraesCS4B01G123800 chr5D 85.319 470 64 5 1926 2393 233971401 233970935 1.160000e-131 481.0
17 TraesCS4B01G123800 chr5D 87.500 192 22 2 2842 3033 233970410 233970221 2.790000e-53 220.0
18 TraesCS4B01G123800 chr5D 87.671 146 17 1 4 148 252663570 252663715 1.020000e-37 169.0
19 TraesCS4B01G123800 chr5D 93.333 75 4 1 984 1057 233972678 233972604 6.290000e-20 110.0
20 TraesCS4B01G123800 chr5B 85.523 449 60 5 1926 2372 270861945 270862390 1.170000e-126 464.0
21 TraesCS4B01G123800 chr5B 88.360 189 21 1 2842 3030 270862928 270863115 5.990000e-55 226.0
22 TraesCS4B01G123800 chr5B 90.805 87 5 3 973 1057 270860682 270860767 4.870000e-21 113.0
23 TraesCS4B01G123800 chr5B 89.394 66 7 0 166 231 700362792 700362727 3.810000e-12 84.2
24 TraesCS4B01G123800 chr7B 90.952 210 15 4 5731 5940 658452888 658452683 4.530000e-71 279.0
25 TraesCS4B01G123800 chr7B 87.805 205 23 1 5738 5940 71337653 71337449 7.690000e-59 239.0
26 TraesCS4B01G123800 chr7B 87.560 209 23 2 5735 5940 138137554 138137762 7.690000e-59 239.0
27 TraesCS4B01G123800 chr7B 86.301 73 7 3 165 236 565903654 565903724 6.380000e-10 76.8
28 TraesCS4B01G123800 chr3B 89.474 209 16 6 5735 5940 725857232 725857437 5.910000e-65 259.0
29 TraesCS4B01G123800 chr3B 88.995 209 21 1 5734 5940 668893677 668893885 2.120000e-64 257.0
30 TraesCS4B01G123800 chr3B 87.923 207 21 4 5735 5940 730428167 730428370 2.140000e-59 241.0
31 TraesCS4B01G123800 chr3B 76.282 156 28 7 256 409 31063411 31063559 2.300000e-09 75.0
32 TraesCS4B01G123800 chr2B 88.995 209 18 5 5733 5938 26947044 26947250 2.750000e-63 254.0
33 TraesCS4B01G123800 chr2B 89.268 205 17 4 5738 5940 27074754 27074553 9.880000e-63 252.0
34 TraesCS4B01G123800 chr6B 88.235 204 23 1 5735 5938 707990320 707990522 5.950000e-60 243.0
35 TraesCS4B01G123800 chr1D 87.342 158 19 1 4 160 312168365 312168522 4.730000e-41 180.0
36 TraesCS4B01G123800 chr3D 86.503 163 21 1 4 165 274745659 274745821 1.700000e-40 178.0
37 TraesCS4B01G123800 chr2D 86.335 161 20 2 4 162 404999677 404999837 2.200000e-39 174.0
38 TraesCS4B01G123800 chr2A 88.356 146 16 1 4 148 392673239 392673384 2.200000e-39 174.0
39 TraesCS4B01G123800 chr7D 87.671 146 17 1 4 148 93012845 93012990 1.020000e-37 169.0
40 TraesCS4B01G123800 chr6D 85.625 160 21 2 5 162 83834478 83834637 3.680000e-37 167.0
41 TraesCS4B01G123800 chr7A 84.507 71 10 1 166 236 500683323 500683392 1.070000e-07 69.4


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 TraesCS4B01G123800 chr4B 147378239 147384178 5939 True 10970.000000 10970 100.000000 1 5940 1 chr4B.!!$R1 5939
1 TraesCS4B01G123800 chr4A 471916811 471923945 7134 False 1462.000000 4911 95.212000 1 5735 6 chr4A.!!$F1 5734
2 TraesCS4B01G123800 chr4D 103251098 103258262 7164 True 1677.000000 4346 92.153400 218 5735 5 chr4D.!!$R2 5517
3 TraesCS4B01G123800 chr5A 320559815 320562252 2437 False 274.666667 494 88.711667 984 3030 3 chr5A.!!$F1 2046
4 TraesCS4B01G123800 chr5D 233970221 233972678 2457 True 270.333333 481 88.717333 984 3033 3 chr5D.!!$R1 2049
5 TraesCS4B01G123800 chr5B 270860682 270863115 2433 False 267.666667 464 88.229333 973 3030 3 chr5B.!!$F1 2057

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
72 74 0.759959 TCCGGGCTAACACTGTTCAA 59.240 50.0 0.00 0.00 0.0 2.69 F
679 2418 0.865218 GACGCATCTCACTCGCTCAG 60.865 60.0 0.00 0.00 0.0 3.35 F
2048 4396 0.962356 ATCCTTCAACGCCTGGCAAG 60.962 55.0 20.29 13.91 0.0 4.01 F
3604 6189 1.110442 CTGGTTTGCTTGGTTGTGGA 58.890 50.0 0.00 0.00 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 3756 2.561478 ACACGAGCAAGGGTAAACAT 57.439 45.0 0.00 0.00 0.00 2.71 R
2270 4618 1.168714 GGTGACTCACAAGCCATTCC 58.831 55.0 11.34 0.00 35.86 3.01 R
3923 6652 0.252421 AGGGGATGCTGTCTCTGACA 60.252 55.0 0.37 0.37 40.50 3.58 R
5536 9557 0.176910 CCAACCCAACACCACCAAAC 59.823 55.0 0.00 0.00 0.00 2.93 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
24 26 4.031426 GCTTTTTGTACTGTCCGATCTACG 59.969 45.833 0.00 0.00 42.18 3.51
51 53 0.950116 GCTAGATGCCCATCTTGTGC 59.050 55.000 15.27 13.13 45.31 4.57
56 58 2.825836 GCCCATCTTGTGCCTCCG 60.826 66.667 0.00 0.00 0.00 4.63
72 74 0.759959 TCCGGGCTAACACTGTTCAA 59.240 50.000 0.00 0.00 0.00 2.69
87 90 6.051717 CACTGTTCAAGATCTTCCCGAATAT 58.948 40.000 4.57 0.00 0.00 1.28
91 94 5.474578 TCAAGATCTTCCCGAATATCCAG 57.525 43.478 4.57 0.00 0.00 3.86
92 95 3.971245 AGATCTTCCCGAATATCCAGC 57.029 47.619 0.00 0.00 0.00 4.85
93 96 3.515562 AGATCTTCCCGAATATCCAGCT 58.484 45.455 0.00 0.00 0.00 4.24
102 105 1.002087 GAATATCCAGCTACCACCGGG 59.998 57.143 6.32 0.00 41.29 5.73
152 155 2.597805 ACAGCTCCGACCACGACT 60.598 61.111 0.00 0.00 42.66 4.18
156 159 4.477975 CTCCGACCACGACTCCGC 62.478 72.222 0.00 0.00 42.66 5.54
187 190 2.210116 CTACTTGTGAGTTGCGTTGGT 58.790 47.619 0.00 0.00 37.33 3.67
198 201 2.004583 TGCGTTGGTATTTCTCCGAG 57.995 50.000 0.00 0.00 0.00 4.63
199 202 1.546923 TGCGTTGGTATTTCTCCGAGA 59.453 47.619 0.00 0.00 0.00 4.04
214 217 2.961741 TCCGAGAAGGAGAGAATGATGG 59.038 50.000 0.00 0.00 45.98 3.51
216 219 3.005684 CCGAGAAGGAGAGAATGATGGAG 59.994 52.174 0.00 0.00 45.00 3.86
221 224 5.960811 AGAAGGAGAGAATGATGGAGTACAA 59.039 40.000 0.00 0.00 0.00 2.41
226 229 7.232534 AGGAGAGAATGATGGAGTACAATAGAC 59.767 40.741 0.00 0.00 0.00 2.59
274 277 1.346365 TAGCTAGCAAACGTTCGCTG 58.654 50.000 23.56 13.92 39.30 5.18
313 318 5.849081 TGCGAACGTTTAGATGACAATTTTC 59.151 36.000 0.46 0.00 0.00 2.29
332 337 1.420514 TCATTGTACGGGGGTTGACAA 59.579 47.619 0.00 0.00 36.32 3.18
391 396 1.778334 TCACCGTTTGATCTCACGTG 58.222 50.000 9.94 9.94 34.47 4.49
409 414 2.869801 CGTGGCAACTAAAACTGTCAGA 59.130 45.455 6.91 0.00 37.61 3.27
411 416 4.201871 CGTGGCAACTAAAACTGTCAGAAA 60.202 41.667 6.91 0.00 37.61 2.52
412 417 5.646606 GTGGCAACTAAAACTGTCAGAAAA 58.353 37.500 6.91 0.00 37.61 2.29
413 418 6.096695 GTGGCAACTAAAACTGTCAGAAAAA 58.903 36.000 6.91 0.00 37.61 1.94
414 419 6.756542 GTGGCAACTAAAACTGTCAGAAAAAT 59.243 34.615 6.91 0.00 37.61 1.82
415 420 7.918562 GTGGCAACTAAAACTGTCAGAAAAATA 59.081 33.333 6.91 0.00 37.61 1.40
416 421 8.637986 TGGCAACTAAAACTGTCAGAAAAATAT 58.362 29.630 6.91 0.00 37.61 1.28
424 429 9.774742 AAAACTGTCAGAAAAATATATTCGCTC 57.225 29.630 6.91 0.00 32.04 5.03
425 430 8.723942 AACTGTCAGAAAAATATATTCGCTCT 57.276 30.769 6.91 0.00 32.04 4.09
426 431 9.817809 AACTGTCAGAAAAATATATTCGCTCTA 57.182 29.630 6.91 0.00 32.04 2.43
427 432 9.250624 ACTGTCAGAAAAATATATTCGCTCTAC 57.749 33.333 6.91 0.00 32.04 2.59
434 2171 9.274206 GAAAAATATATTCGCTCTACCCTCTTT 57.726 33.333 0.00 0.00 0.00 2.52
446 2183 1.743252 CCTCTTTCCAGCTGACGCC 60.743 63.158 17.39 0.00 36.60 5.68
450 2187 1.294659 CTTTCCAGCTGACGCCTGTC 61.295 60.000 17.39 0.00 45.71 3.51
495 2233 7.980099 ACTAGGACTGAAAATGTCGGTATTAAG 59.020 37.037 0.00 0.00 46.43 1.85
496 2234 6.708285 AGGACTGAAAATGTCGGTATTAAGT 58.292 36.000 0.00 0.00 46.43 2.24
679 2418 0.865218 GACGCATCTCACTCGCTCAG 60.865 60.000 0.00 0.00 0.00 3.35
791 2530 2.567497 GCTTGCCTGCTTTGCCTCA 61.567 57.895 0.00 0.00 0.00 3.86
852 2591 2.690452 CTTCGAGGAGGAGGGGGA 59.310 66.667 0.00 0.00 0.00 4.81
867 2606 1.527370 GGGAACTAGGAGGCGCATT 59.473 57.895 10.83 0.00 0.00 3.56
1322 3228 7.865707 TCTGCTCTACATTTTTGTCTTTCTTC 58.134 34.615 0.00 0.00 0.00 2.87
1323 3229 7.716998 TCTGCTCTACATTTTTGTCTTTCTTCT 59.283 33.333 0.00 0.00 0.00 2.85
1324 3230 8.225603 TGCTCTACATTTTTGTCTTTCTTCTT 57.774 30.769 0.00 0.00 0.00 2.52
1325 3231 8.345565 TGCTCTACATTTTTGTCTTTCTTCTTC 58.654 33.333 0.00 0.00 0.00 2.87
1326 3232 8.563732 GCTCTACATTTTTGTCTTTCTTCTTCT 58.436 33.333 0.00 0.00 0.00 2.85
1331 3237 9.794685 ACATTTTTGTCTTTCTTCTTCTTCTTC 57.205 29.630 0.00 0.00 0.00 2.87
1335 3241 9.454859 TTTTGTCTTTCTTCTTCTTCTTCTTCT 57.545 29.630 0.00 0.00 0.00 2.85
1336 3242 9.454859 TTTGTCTTTCTTCTTCTTCTTCTTCTT 57.545 29.630 0.00 0.00 0.00 2.52
1337 3243 8.655651 TGTCTTTCTTCTTCTTCTTCTTCTTC 57.344 34.615 0.00 0.00 0.00 2.87
1338 3244 8.482128 TGTCTTTCTTCTTCTTCTTCTTCTTCT 58.518 33.333 0.00 0.00 0.00 2.85
1339 3245 9.325198 GTCTTTCTTCTTCTTCTTCTTCTTCTT 57.675 33.333 0.00 0.00 0.00 2.52
1340 3246 9.541143 TCTTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
1341 3247 9.546428 CTTTCTTCTTCTTCTTCTTCTTCTTCT 57.454 33.333 0.00 0.00 0.00 2.85
1342 3248 9.898152 TTTCTTCTTCTTCTTCTTCTTCTTCTT 57.102 29.630 0.00 0.00 0.00 2.52
1343 3249 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
1369 3281 4.630644 TCTTCTTCAGCAGAGATTTGGT 57.369 40.909 0.00 0.00 31.12 3.67
1543 3455 1.546548 GCCCTTCTCCTGTGCTTTCTT 60.547 52.381 0.00 0.00 0.00 2.52
1809 3756 1.132977 TCTGGTCCACTGGTCCTAACA 60.133 52.381 12.06 0.00 32.23 2.41
1833 3781 4.035441 TGTTTACCCTTGCTCGTGTAAAAC 59.965 41.667 0.00 0.00 35.60 2.43
1847 3795 9.298774 GCTCGTGTAAAACTTATACTGTCTATT 57.701 33.333 0.00 0.00 0.00 1.73
1917 3866 5.592282 TGCAAACCTGTCTTTATTTCTCACA 59.408 36.000 0.00 0.00 0.00 3.58
2048 4396 0.962356 ATCCTTCAACGCCTGGCAAG 60.962 55.000 20.29 13.91 0.00 4.01
2140 4488 1.441016 CAAAGAGCTTTCGTGCCGC 60.441 57.895 0.00 0.00 0.00 6.53
2270 4618 2.238144 AGATGGACATCAAGGACACAGG 59.762 50.000 14.16 0.00 40.22 4.00
2421 4771 4.520179 TGTGAAATCTGCAGATGCTATGT 58.480 39.130 29.34 10.26 42.66 2.29
2538 4888 5.319043 TCTGAATAACCCTTGGTGAGTTT 57.681 39.130 0.00 0.00 35.34 2.66
2591 5014 7.309990 GGGTATCCATTATGATCAAAATGTGGG 60.310 40.741 0.00 0.00 32.34 4.61
2791 5310 5.794894 ACTGTCATTACCCTGTTAAGTCAG 58.205 41.667 0.00 0.00 35.45 3.51
2872 5391 1.340248 TCTCTGTTTCGTGGTCAGACC 59.660 52.381 13.35 13.35 39.22 3.85
3069 5588 4.894784 TGTTTACTCATTTTCTCGCCTCT 58.105 39.130 0.00 0.00 0.00 3.69
3089 5608 5.418209 CCTCTCTTTTCTTGAATGCCATCTT 59.582 40.000 0.00 0.00 0.00 2.40
3255 5775 4.400567 GCCTTGGCATCTTCTATCAACTTT 59.599 41.667 6.79 0.00 0.00 2.66
3461 6046 8.896722 GGAGATATATACTCCCTCTACCAAAA 57.103 38.462 15.23 0.00 45.64 2.44
3462 6047 9.495382 GGAGATATATACTCCCTCTACCAAAAT 57.505 37.037 15.23 0.00 45.64 1.82
3468 6053 7.750947 ATACTCCCTCTACCAAAATACTTGT 57.249 36.000 0.00 0.00 0.00 3.16
3469 6054 8.849543 ATACTCCCTCTACCAAAATACTTGTA 57.150 34.615 0.00 0.00 0.00 2.41
3470 6055 7.184067 ACTCCCTCTACCAAAATACTTGTAG 57.816 40.000 0.00 0.00 0.00 2.74
3471 6056 6.729569 ACTCCCTCTACCAAAATACTTGTAGT 59.270 38.462 0.00 0.00 0.00 2.73
3472 6057 7.237055 ACTCCCTCTACCAAAATACTTGTAGTT 59.763 37.037 0.00 0.00 0.00 2.24
3473 6058 7.391620 TCCCTCTACCAAAATACTTGTAGTTG 58.608 38.462 0.00 0.00 0.00 3.16
3474 6059 6.598064 CCCTCTACCAAAATACTTGTAGTTGG 59.402 42.308 17.42 17.42 43.60 3.77
3475 6060 6.598064 CCTCTACCAAAATACTTGTAGTTGGG 59.402 42.308 20.55 16.74 42.52 4.12
3476 6061 6.478129 TCTACCAAAATACTTGTAGTTGGGG 58.522 40.000 20.55 15.16 42.52 4.96
3477 6062 5.327737 ACCAAAATACTTGTAGTTGGGGA 57.672 39.130 20.55 0.00 42.52 4.81
3478 6063 5.707495 ACCAAAATACTTGTAGTTGGGGAA 58.293 37.500 20.55 0.00 42.52 3.97
3479 6064 6.137559 ACCAAAATACTTGTAGTTGGGGAAA 58.862 36.000 20.55 0.00 42.52 3.13
3480 6065 6.266786 ACCAAAATACTTGTAGTTGGGGAAAG 59.733 38.462 20.55 0.00 42.52 2.62
3481 6066 6.266786 CCAAAATACTTGTAGTTGGGGAAAGT 59.733 38.462 13.79 0.00 36.00 2.66
3482 6067 7.201965 CCAAAATACTTGTAGTTGGGGAAAGTT 60.202 37.037 13.79 0.00 36.00 2.66
3483 6068 6.894339 AATACTTGTAGTTGGGGAAAGTTG 57.106 37.500 0.00 0.00 33.37 3.16
3484 6069 4.245251 ACTTGTAGTTGGGGAAAGTTGT 57.755 40.909 0.00 0.00 0.00 3.32
3485 6070 5.376756 ACTTGTAGTTGGGGAAAGTTGTA 57.623 39.130 0.00 0.00 0.00 2.41
3486 6071 5.128205 ACTTGTAGTTGGGGAAAGTTGTAC 58.872 41.667 0.00 0.00 0.00 2.90
3487 6072 5.104235 ACTTGTAGTTGGGGAAAGTTGTACT 60.104 40.000 0.00 0.00 0.00 2.73
3488 6073 6.100134 ACTTGTAGTTGGGGAAAGTTGTACTA 59.900 38.462 0.00 0.00 0.00 1.82
3489 6074 6.105397 TGTAGTTGGGGAAAGTTGTACTAG 57.895 41.667 0.00 0.00 0.00 2.57
3490 6075 5.603813 TGTAGTTGGGGAAAGTTGTACTAGT 59.396 40.000 0.00 0.00 0.00 2.57
3491 6076 5.641789 AGTTGGGGAAAGTTGTACTAGTT 57.358 39.130 0.00 0.00 0.00 2.24
3492 6077 6.009908 AGTTGGGGAAAGTTGTACTAGTTT 57.990 37.500 9.47 9.47 0.00 2.66
3493 6078 6.060136 AGTTGGGGAAAGTTGTACTAGTTTC 58.940 40.000 22.01 22.01 36.94 2.78
3494 6079 5.899631 TGGGGAAAGTTGTACTAGTTTCT 57.100 39.130 26.14 3.85 37.52 2.52
3495 6080 6.999705 TGGGGAAAGTTGTACTAGTTTCTA 57.000 37.500 26.14 15.82 37.52 2.10
3496 6081 6.762333 TGGGGAAAGTTGTACTAGTTTCTAC 58.238 40.000 26.14 21.05 37.52 2.59
3497 6082 6.327104 TGGGGAAAGTTGTACTAGTTTCTACA 59.673 38.462 26.14 22.57 37.52 2.74
3498 6083 7.147514 TGGGGAAAGTTGTACTAGTTTCTACAA 60.148 37.037 26.14 16.01 37.52 2.41
3499 6084 7.881751 GGGGAAAGTTGTACTAGTTTCTACAAT 59.118 37.037 26.14 0.00 37.52 2.71
3500 6085 8.933807 GGGAAAGTTGTACTAGTTTCTACAATC 58.066 37.037 26.14 14.60 37.52 2.67
3604 6189 1.110442 CTGGTTTGCTTGGTTGTGGA 58.890 50.000 0.00 0.00 0.00 4.02
3620 6205 1.756538 GTGGATGGTAAGCCAATTGGG 59.243 52.381 25.73 8.01 45.37 4.12
3659 6244 2.040278 TCTGGTTCCCAATTGGAGTCTG 59.960 50.000 26.60 14.60 46.24 3.51
3666 6393 5.620738 TCCCAATTGGAGTCTGAATCTAG 57.379 43.478 26.60 4.15 38.61 2.43
3840 6568 9.035890 AGGCATATGCACTATACTAATCAACTA 57.964 33.333 28.07 0.00 44.36 2.24
4012 6744 1.509923 GCTTGCCTCCACAATGCTC 59.490 57.895 0.00 0.00 0.00 4.26
4083 6815 4.574527 CTCTGTTGAGTGATTACTTGCG 57.425 45.455 0.00 0.00 37.25 4.85
4121 6853 4.729227 TCAGTTCTACGCATAACCATCA 57.271 40.909 0.00 0.00 0.00 3.07
4468 7200 4.320494 GCAGAATCTGACGGTGAATTGTTT 60.320 41.667 15.38 0.00 32.44 2.83
4516 7248 1.989165 CACTTGACTGCTAGAAGCGAC 59.011 52.381 0.00 0.00 46.26 5.19
4973 7705 0.396435 TCGTTCATGTTGCCTGGAGT 59.604 50.000 0.00 0.00 0.00 3.85
4974 7706 1.202758 TCGTTCATGTTGCCTGGAGTT 60.203 47.619 0.00 0.00 0.00 3.01
4994 7726 8.662255 TGGAGTTAAAGGAAATAGGTTCAGTTA 58.338 33.333 0.00 0.00 38.06 2.24
5038 7770 1.725066 GTTTCGTGGGTGTGTGTGG 59.275 57.895 0.00 0.00 0.00 4.17
5039 7771 1.452289 TTTCGTGGGTGTGTGTGGG 60.452 57.895 0.00 0.00 0.00 4.61
5050 7782 2.412937 GTGTGGGTGCACTTGTGC 59.587 61.111 17.98 17.73 36.51 4.57
5153 7893 3.961480 TCTCACTGTGGTCTTATGTGG 57.039 47.619 8.11 0.00 0.00 4.17
5154 7894 3.239449 TCTCACTGTGGTCTTATGTGGT 58.761 45.455 8.11 0.00 0.00 4.16
5155 7895 3.006859 TCTCACTGTGGTCTTATGTGGTG 59.993 47.826 8.11 0.00 0.00 4.17
5156 7896 1.806542 CACTGTGGTCTTATGTGGTGC 59.193 52.381 0.00 0.00 0.00 5.01
5427 9418 1.993370 CTGAGTCGGAAACCTAAAGCG 59.007 52.381 0.00 0.00 0.00 4.68
5460 9451 0.264359 CTCATCTCCACCCTCCCTCT 59.736 60.000 0.00 0.00 0.00 3.69
5510 9531 2.725815 GCGAACGTTGGCAGCAAC 60.726 61.111 27.46 0.00 31.76 4.17
5549 9570 2.025441 CGGCGTTTGGTGGTGTTG 59.975 61.111 0.00 0.00 0.00 3.33
5552 9573 2.419739 GCGTTTGGTGGTGTTGGGT 61.420 57.895 0.00 0.00 0.00 4.51
5567 9588 2.356667 GGTTGGCCTTCCCTCCTG 59.643 66.667 3.32 0.00 0.00 3.86
5585 9606 2.093447 CCTGTATGCTTCGAGGGAAACT 60.093 50.000 0.00 0.00 0.00 2.66
5589 9610 2.631160 TGCTTCGAGGGAAACTTCAA 57.369 45.000 0.00 0.00 35.91 2.69
5596 9617 5.086104 TCGAGGGAAACTTCAAATCTAGG 57.914 43.478 0.00 0.00 35.91 3.02
5613 9634 0.397254 AGGTTCCTGGATCGGACGAT 60.397 55.000 6.95 6.95 37.59 3.73
5620 9641 2.427080 GATCGGACGATCGCGACC 60.427 66.667 12.93 14.99 46.46 4.79
5624 9645 2.183555 GGACGATCGCGACCCTTT 59.816 61.111 12.93 0.00 44.69 3.11
5629 9652 2.033448 ATCGCGACCCTTTTGGCA 59.967 55.556 12.93 0.00 37.83 4.92
5630 9653 2.253414 GATCGCGACCCTTTTGGCAC 62.253 60.000 12.93 0.00 37.83 5.01
5643 9666 2.002018 TTGGCACCGTTTCCCTCCTT 62.002 55.000 0.00 0.00 0.00 3.36
5683 9706 2.841988 GGCCGGCTGAGGAGATCT 60.842 66.667 28.56 0.00 0.00 2.75
5691 9714 0.900421 CTGAGGAGATCTGTGTGGCA 59.100 55.000 0.00 0.00 0.00 4.92
5715 9738 5.130292 CAATGAGGATTGTGAGCAAAGTT 57.870 39.130 0.00 0.00 38.21 2.66
5718 9741 2.229784 GAGGATTGTGAGCAAAGTTGGG 59.770 50.000 0.00 0.00 38.21 4.12
5723 9746 1.148273 TGAGCAAAGTTGGGTCGCT 59.852 52.632 5.02 0.00 35.60 4.93
5735 9758 4.057428 GTCGCTGCGTGTCCTCCT 62.057 66.667 22.48 0.00 0.00 3.69
5736 9759 4.056125 TCGCTGCGTGTCCTCCTG 62.056 66.667 22.48 0.00 0.00 3.86
5737 9760 4.056125 CGCTGCGTGTCCTCCTGA 62.056 66.667 14.93 0.00 0.00 3.86
5738 9761 2.125753 GCTGCGTGTCCTCCTGAG 60.126 66.667 0.00 0.00 0.00 3.35
5739 9762 2.640302 GCTGCGTGTCCTCCTGAGA 61.640 63.158 0.00 0.00 0.00 3.27
5740 9763 1.510383 CTGCGTGTCCTCCTGAGAG 59.490 63.158 0.00 0.00 40.09 3.20
5741 9764 2.183046 GCGTGTCCTCCTGAGAGC 59.817 66.667 0.00 0.00 38.96 4.09
5742 9765 2.640302 GCGTGTCCTCCTGAGAGCA 61.640 63.158 0.00 0.00 38.96 4.26
5743 9766 1.954362 GCGTGTCCTCCTGAGAGCAT 61.954 60.000 0.00 0.00 38.96 3.79
5744 9767 0.102120 CGTGTCCTCCTGAGAGCATC 59.898 60.000 0.00 0.00 38.96 3.91
5755 9778 3.805267 GAGCATCTCCAGCCGTTG 58.195 61.111 0.00 0.00 0.00 4.10
5789 9812 2.003672 CGTAAAATCGCCGTCAGGG 58.996 57.895 0.00 0.00 38.20 4.45
5822 9845 3.243128 AAAAATCGGTCTGGGGACG 57.757 52.632 0.00 0.00 42.97 4.79
5823 9846 0.688487 AAAAATCGGTCTGGGGACGA 59.312 50.000 0.00 0.00 42.97 4.20
5824 9847 0.249398 AAAATCGGTCTGGGGACGAG 59.751 55.000 0.00 0.00 42.97 4.18
5825 9848 0.903454 AAATCGGTCTGGGGACGAGT 60.903 55.000 0.00 0.00 42.97 4.18
5826 9849 1.605058 AATCGGTCTGGGGACGAGTG 61.605 60.000 0.00 0.00 42.97 3.51
5827 9850 3.760035 CGGTCTGGGGACGAGTGG 61.760 72.222 0.00 0.00 42.97 4.00
5828 9851 3.391382 GGTCTGGGGACGAGTGGG 61.391 72.222 0.00 0.00 42.97 4.61
5829 9852 2.603776 GTCTGGGGACGAGTGGGT 60.604 66.667 0.00 0.00 32.47 4.51
5830 9853 2.203182 TCTGGGGACGAGTGGGTT 59.797 61.111 0.00 0.00 0.00 4.11
5831 9854 1.911766 TCTGGGGACGAGTGGGTTC 60.912 63.158 0.00 0.00 0.00 3.62
5832 9855 2.926242 TGGGGACGAGTGGGTTCC 60.926 66.667 0.00 0.00 34.56 3.62
5834 9857 2.926242 GGGACGAGTGGGTTCCCA 60.926 66.667 6.46 6.46 40.26 4.37
5835 9858 2.663196 GGACGAGTGGGTTCCCAG 59.337 66.667 11.21 2.54 36.70 4.45
5836 9859 2.214920 GGACGAGTGGGTTCCCAGT 61.215 63.158 17.11 17.11 42.00 4.00
5839 9862 2.047179 GAGTGGGTTCCCAGTCGC 60.047 66.667 24.35 8.80 43.83 5.19
5840 9863 3.607370 GAGTGGGTTCCCAGTCGCC 62.607 68.421 24.35 8.31 43.83 5.54
5843 9866 4.754667 GGGTTCCCAGTCGCCGAC 62.755 72.222 9.71 9.71 0.00 4.79
5844 9867 4.754667 GGTTCCCAGTCGCCGACC 62.755 72.222 14.60 0.00 32.18 4.79
5845 9868 4.754667 GTTCCCAGTCGCCGACCC 62.755 72.222 14.60 0.00 32.18 4.46
5870 9893 3.423154 GCTCCCAGACGCCGTTTG 61.423 66.667 0.03 0.03 0.00 2.93
5871 9894 2.030562 CTCCCAGACGCCGTTTGT 59.969 61.111 7.03 0.00 0.00 2.83
5872 9895 2.280524 TCCCAGACGCCGTTTGTG 60.281 61.111 7.03 0.00 0.00 3.33
5873 9896 2.590575 CCCAGACGCCGTTTGTGT 60.591 61.111 7.03 0.00 41.39 3.72
5874 9897 2.184167 CCCAGACGCCGTTTGTGTT 61.184 57.895 7.03 0.00 37.96 3.32
5875 9898 0.881159 CCCAGACGCCGTTTGTGTTA 60.881 55.000 7.03 0.00 37.96 2.41
5876 9899 0.938713 CCAGACGCCGTTTGTGTTAA 59.061 50.000 7.03 0.00 37.96 2.01
5877 9900 1.331138 CCAGACGCCGTTTGTGTTAAA 59.669 47.619 7.03 0.00 37.96 1.52
5878 9901 2.223294 CCAGACGCCGTTTGTGTTAAAA 60.223 45.455 7.03 0.00 37.96 1.52
5879 9902 3.427243 CAGACGCCGTTTGTGTTAAAAA 58.573 40.909 0.00 0.00 37.96 1.94
5899 9922 4.919677 AAAAAGTGTTTGGCAAAGTTCG 57.080 36.364 13.94 0.00 0.00 3.95
5900 9923 2.577449 AAGTGTTTGGCAAAGTTCGG 57.423 45.000 13.94 0.00 0.00 4.30
5901 9924 0.102300 AGTGTTTGGCAAAGTTCGGC 59.898 50.000 13.94 0.74 0.00 5.54
5902 9925 0.102300 GTGTTTGGCAAAGTTCGGCT 59.898 50.000 13.94 0.00 0.00 5.52
5903 9926 1.335496 GTGTTTGGCAAAGTTCGGCTA 59.665 47.619 13.94 0.00 0.00 3.93
5904 9927 2.025155 TGTTTGGCAAAGTTCGGCTAA 58.975 42.857 13.94 0.00 0.00 3.09
5905 9928 2.427453 TGTTTGGCAAAGTTCGGCTAAA 59.573 40.909 13.94 6.84 38.01 1.85
5906 9929 3.119101 TGTTTGGCAAAGTTCGGCTAAAA 60.119 39.130 13.94 5.29 41.18 1.52
5907 9930 4.055360 GTTTGGCAAAGTTCGGCTAAAAT 58.945 39.130 13.94 0.00 41.18 1.82
5908 9931 4.329462 TTGGCAAAGTTCGGCTAAAATT 57.671 36.364 0.00 0.00 0.00 1.82
5909 9932 3.908213 TGGCAAAGTTCGGCTAAAATTC 58.092 40.909 0.00 0.00 0.00 2.17
5910 9933 2.914838 GGCAAAGTTCGGCTAAAATTCG 59.085 45.455 0.25 0.00 0.00 3.34
5911 9934 2.914838 GCAAAGTTCGGCTAAAATTCGG 59.085 45.455 0.00 0.00 0.00 4.30
5912 9935 2.913777 AAGTTCGGCTAAAATTCGGC 57.086 45.000 0.00 0.00 0.00 5.54
5913 9936 1.816074 AGTTCGGCTAAAATTCGGCA 58.184 45.000 0.00 0.00 0.00 5.69
5914 9937 2.156098 AGTTCGGCTAAAATTCGGCAA 58.844 42.857 0.00 0.00 0.00 4.52
5915 9938 2.554893 AGTTCGGCTAAAATTCGGCAAA 59.445 40.909 0.00 0.00 0.00 3.68
5916 9939 2.622546 TCGGCTAAAATTCGGCAAAC 57.377 45.000 0.00 0.00 0.00 2.93
5917 9940 2.156098 TCGGCTAAAATTCGGCAAACT 58.844 42.857 0.00 0.00 0.00 2.66
5918 9941 2.095466 TCGGCTAAAATTCGGCAAACTG 60.095 45.455 0.00 0.00 0.00 3.16
5919 9942 2.606108 GGCTAAAATTCGGCAAACTGG 58.394 47.619 0.00 0.00 0.00 4.00
5920 9943 2.606108 GCTAAAATTCGGCAAACTGGG 58.394 47.619 0.00 0.00 0.00 4.45
5921 9944 2.606108 CTAAAATTCGGCAAACTGGGC 58.394 47.619 0.00 0.00 0.00 5.36
5922 9945 0.755686 AAAATTCGGCAAACTGGGCA 59.244 45.000 0.00 0.00 0.00 5.36
5923 9946 0.975887 AAATTCGGCAAACTGGGCAT 59.024 45.000 0.00 0.00 0.00 4.40
5924 9947 1.846007 AATTCGGCAAACTGGGCATA 58.154 45.000 0.00 0.00 0.00 3.14
5925 9948 2.071778 ATTCGGCAAACTGGGCATAT 57.928 45.000 0.00 0.00 0.00 1.78
5926 9949 2.719531 TTCGGCAAACTGGGCATATA 57.280 45.000 0.00 0.00 0.00 0.86
5927 9950 2.949177 TCGGCAAACTGGGCATATAT 57.051 45.000 0.00 0.00 0.00 0.86
5928 9951 3.222173 TCGGCAAACTGGGCATATATT 57.778 42.857 0.00 0.00 0.00 1.28
5929 9952 4.359434 TCGGCAAACTGGGCATATATTA 57.641 40.909 0.00 0.00 0.00 0.98
5930 9953 4.323417 TCGGCAAACTGGGCATATATTAG 58.677 43.478 0.00 0.00 0.00 1.73
5931 9954 4.041075 TCGGCAAACTGGGCATATATTAGA 59.959 41.667 0.00 0.00 0.00 2.10
5932 9955 4.154195 CGGCAAACTGGGCATATATTAGAC 59.846 45.833 0.00 0.00 0.00 2.59
5933 9956 5.070001 GGCAAACTGGGCATATATTAGACA 58.930 41.667 0.00 0.00 0.00 3.41
5934 9957 5.711976 GGCAAACTGGGCATATATTAGACAT 59.288 40.000 0.00 0.00 0.00 3.06
5935 9958 6.349611 GGCAAACTGGGCATATATTAGACATG 60.350 42.308 0.00 0.00 0.00 3.21
5936 9959 6.207417 GCAAACTGGGCATATATTAGACATGT 59.793 38.462 0.00 0.00 0.00 3.21
5937 9960 7.255590 GCAAACTGGGCATATATTAGACATGTT 60.256 37.037 0.00 0.00 0.00 2.71
5938 9961 7.986085 AACTGGGCATATATTAGACATGTTC 57.014 36.000 0.00 0.00 0.00 3.18
5939 9962 6.166279 ACTGGGCATATATTAGACATGTTCG 58.834 40.000 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 42 2.124570 CCGGAGGCACAAGATGGG 60.125 66.667 0.00 0.00 46.14 4.00
56 58 3.944087 AGATCTTGAACAGTGTTAGCCC 58.056 45.455 8.88 0.00 0.00 5.19
61 63 3.071023 TCGGGAAGATCTTGAACAGTGTT 59.929 43.478 14.00 8.61 0.00 3.32
65 67 5.698545 GGATATTCGGGAAGATCTTGAACAG 59.301 44.000 14.00 4.11 38.64 3.16
72 74 3.515562 AGCTGGATATTCGGGAAGATCT 58.484 45.455 13.78 0.00 38.64 2.75
87 90 2.363795 CTCCCGGTGGTAGCTGGA 60.364 66.667 0.00 0.00 37.06 3.86
91 94 3.075005 TGCTCTCCCGGTGGTAGC 61.075 66.667 0.00 4.47 40.17 3.58
92 95 3.082579 GCTGCTCTCCCGGTGGTAG 62.083 68.421 0.00 0.00 0.00 3.18
93 96 3.075005 GCTGCTCTCCCGGTGGTA 61.075 66.667 0.00 0.00 0.00 3.25
102 105 4.527583 CGGAGGCAGGCTGCTCTC 62.528 72.222 35.73 33.74 44.28 3.20
138 141 4.477975 CGGAGTCGTGGTCGGAGC 62.478 72.222 0.00 0.00 37.69 4.70
156 159 4.489771 CAAGTAGCAGGCCGGGGG 62.490 72.222 2.18 0.00 0.00 5.40
158 161 2.436646 CACAAGTAGCAGGCCGGG 60.437 66.667 2.18 0.00 0.00 5.73
161 164 1.160137 CAACTCACAAGTAGCAGGCC 58.840 55.000 0.00 0.00 33.48 5.19
163 166 0.792640 CGCAACTCACAAGTAGCAGG 59.207 55.000 0.00 0.00 33.48 4.85
181 184 3.119245 TCCTTCTCGGAGAAATACCAACG 60.119 47.826 20.08 7.06 36.69 4.10
198 201 5.860941 TGTACTCCATCATTCTCTCCTTC 57.139 43.478 0.00 0.00 0.00 3.46
199 202 6.821616 ATTGTACTCCATCATTCTCTCCTT 57.178 37.500 0.00 0.00 0.00 3.36
245 248 4.246458 CGTTTGCTAGCTAAAAGAGTCCT 58.754 43.478 17.23 0.00 0.00 3.85
274 277 2.981302 GCAAATGCCACCCCTTCC 59.019 61.111 0.00 0.00 34.31 3.46
313 318 1.898902 TTGTCAACCCCCGTACAATG 58.101 50.000 0.00 0.00 0.00 2.82
409 414 9.274206 GAAAGAGGGTAGAGCGAATATATTTTT 57.726 33.333 0.00 0.00 0.00 1.94
411 416 7.016268 TGGAAAGAGGGTAGAGCGAATATATTT 59.984 37.037 0.00 0.00 0.00 1.40
412 417 6.497259 TGGAAAGAGGGTAGAGCGAATATATT 59.503 38.462 0.00 0.00 0.00 1.28
413 418 6.017192 TGGAAAGAGGGTAGAGCGAATATAT 58.983 40.000 0.00 0.00 0.00 0.86
414 419 5.391256 TGGAAAGAGGGTAGAGCGAATATA 58.609 41.667 0.00 0.00 0.00 0.86
415 420 4.223953 TGGAAAGAGGGTAGAGCGAATAT 58.776 43.478 0.00 0.00 0.00 1.28
416 421 3.637229 CTGGAAAGAGGGTAGAGCGAATA 59.363 47.826 0.00 0.00 0.00 1.75
417 422 2.432510 CTGGAAAGAGGGTAGAGCGAAT 59.567 50.000 0.00 0.00 0.00 3.34
418 423 1.825474 CTGGAAAGAGGGTAGAGCGAA 59.175 52.381 0.00 0.00 0.00 4.70
419 424 1.475403 CTGGAAAGAGGGTAGAGCGA 58.525 55.000 0.00 0.00 0.00 4.93
420 425 0.179097 GCTGGAAAGAGGGTAGAGCG 60.179 60.000 0.00 0.00 0.00 5.03
421 426 1.134551 CAGCTGGAAAGAGGGTAGAGC 60.135 57.143 5.57 0.00 0.00 4.09
422 427 2.167487 GTCAGCTGGAAAGAGGGTAGAG 59.833 54.545 15.13 0.00 0.00 2.43
423 428 2.180276 GTCAGCTGGAAAGAGGGTAGA 58.820 52.381 15.13 0.00 0.00 2.59
424 429 1.134965 CGTCAGCTGGAAAGAGGGTAG 60.135 57.143 15.13 0.00 0.00 3.18
425 430 0.895530 CGTCAGCTGGAAAGAGGGTA 59.104 55.000 15.13 0.00 0.00 3.69
426 431 1.674057 CGTCAGCTGGAAAGAGGGT 59.326 57.895 15.13 0.00 0.00 4.34
427 432 1.743252 GCGTCAGCTGGAAAGAGGG 60.743 63.158 15.13 0.00 41.01 4.30
446 2183 5.605564 TTTTCGGTGATGTTATGTGACAG 57.394 39.130 0.00 0.00 32.19 3.51
450 2187 6.370442 TCCTAGTTTTTCGGTGATGTTATGTG 59.630 38.462 0.00 0.00 0.00 3.21
452 2189 6.594159 AGTCCTAGTTTTTCGGTGATGTTATG 59.406 38.462 0.00 0.00 0.00 1.90
504 2243 7.496591 ACGACTTTCACCAAATTTACAGTCTTA 59.503 33.333 0.00 0.00 0.00 2.10
679 2418 2.126031 GCTTGGGTCGTCGTCTCC 60.126 66.667 0.00 0.00 0.00 3.71
791 2530 1.268899 CGTACGAGGAGAACAAGGTGT 59.731 52.381 10.44 0.00 0.00 4.16
852 2591 4.835927 CGAATGCGCCTCCTAGTT 57.164 55.556 4.18 0.00 0.00 2.24
871 2610 3.520862 CATGCGGTCATGCCACCC 61.521 66.667 6.92 0.00 43.00 4.61
1322 3228 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
1323 3229 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
1324 3230 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
1325 3231 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
1326 3232 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
1327 3233 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
1328 3234 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
1329 3235 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
1330 3236 8.700051 TGAAGAAGAAGAAGAAGAAGAAGAAGA 58.300 33.333 0.00 0.00 0.00 2.87
1331 3237 8.885494 TGAAGAAGAAGAAGAAGAAGAAGAAG 57.115 34.615 0.00 0.00 0.00 2.85
1332 3238 7.440856 GCTGAAGAAGAAGAAGAAGAAGAAGAA 59.559 37.037 0.00 0.00 0.00 2.52
1333 3239 6.928492 GCTGAAGAAGAAGAAGAAGAAGAAGA 59.072 38.462 0.00 0.00 0.00 2.87
1334 3240 6.705381 TGCTGAAGAAGAAGAAGAAGAAGAAG 59.295 38.462 0.00 0.00 0.00 2.85
1335 3241 6.586344 TGCTGAAGAAGAAGAAGAAGAAGAA 58.414 36.000 0.00 0.00 0.00 2.52
1336 3242 6.041409 TCTGCTGAAGAAGAAGAAGAAGAAGA 59.959 38.462 0.00 0.00 37.67 2.87
1337 3243 6.222389 TCTGCTGAAGAAGAAGAAGAAGAAG 58.778 40.000 0.00 0.00 37.67 2.85
1338 3244 6.041409 TCTCTGCTGAAGAAGAAGAAGAAGAA 59.959 38.462 0.00 0.00 40.35 2.52
1339 3245 5.538053 TCTCTGCTGAAGAAGAAGAAGAAGA 59.462 40.000 0.00 0.00 40.35 2.87
1340 3246 5.782047 TCTCTGCTGAAGAAGAAGAAGAAG 58.218 41.667 0.00 0.00 40.35 2.85
1341 3247 5.798125 TCTCTGCTGAAGAAGAAGAAGAA 57.202 39.130 0.00 0.00 40.35 2.52
1342 3248 5.999205 ATCTCTGCTGAAGAAGAAGAAGA 57.001 39.130 0.00 0.00 40.35 2.87
1343 3249 6.128227 CCAAATCTCTGCTGAAGAAGAAGAAG 60.128 42.308 0.00 0.00 40.35 2.85
1369 3281 3.530535 TGAGCAAATGCATACGCTAAGA 58.469 40.909 19.58 7.20 45.16 2.10
1464 3376 6.492429 ACAGGTCAGCGGTCTACAAATATATA 59.508 38.462 0.00 0.00 0.00 0.86
1543 3455 5.358725 GCGAAAAACAAGGGGATAGGATAAA 59.641 40.000 0.00 0.00 0.00 1.40
1809 3756 2.561478 ACACGAGCAAGGGTAAACAT 57.439 45.000 0.00 0.00 0.00 2.71
1895 3843 7.264373 AGTGTGAGAAATAAAGACAGGTTTG 57.736 36.000 0.00 0.00 0.00 2.93
1917 3866 5.065914 AGACATGTCATAGCAACAACAAGT 58.934 37.500 27.02 0.00 0.00 3.16
2048 4396 6.603201 TGGAAATGTCCTTGGTATCTTCAATC 59.397 38.462 2.89 0.00 45.22 2.67
2140 4488 3.691609 GCCTCCTTCACCAAGAACATAAG 59.308 47.826 0.00 0.00 31.61 1.73
2270 4618 1.168714 GGTGACTCACAAGCCATTCC 58.831 55.000 11.34 0.00 35.86 3.01
2370 4720 8.542926 ACTGCATGCATAACTAGGATATATCAA 58.457 33.333 22.97 1.39 0.00 2.57
2421 4771 3.979101 TGACTGCATGAACCACAGATA 57.021 42.857 0.00 0.00 35.38 1.98
2507 4857 9.408648 CACCAAGGGTTATTCAGATTAAGTAAT 57.591 33.333 0.00 0.00 31.02 1.89
2591 5014 8.738645 ATGACCTTTACCATCTTATCAACTTC 57.261 34.615 0.00 0.00 0.00 3.01
2872 5391 1.340600 TGCCCCAGGAAATTAACCTCG 60.341 52.381 1.71 0.00 35.35 4.63
3069 5588 5.771666 AGTGAAGATGGCATTCAAGAAAAGA 59.228 36.000 0.00 0.00 38.34 2.52
3089 5608 7.450074 TCAGCTTAAGGTTTTCTTATCAGTGA 58.550 34.615 3.96 0.00 37.74 3.41
3448 6033 7.391620 CAACTACAAGTATTTTGGTAGAGGGA 58.608 38.462 0.00 0.00 37.31 4.20
3449 6034 6.598064 CCAACTACAAGTATTTTGGTAGAGGG 59.402 42.308 0.00 0.00 37.31 4.30
3450 6035 6.598064 CCCAACTACAAGTATTTTGGTAGAGG 59.402 42.308 14.71 0.00 37.31 3.69
3451 6036 6.598064 CCCCAACTACAAGTATTTTGGTAGAG 59.402 42.308 14.71 0.00 37.31 2.43
3452 6037 6.272792 TCCCCAACTACAAGTATTTTGGTAGA 59.727 38.462 14.71 10.51 37.31 2.59
3453 6038 6.478129 TCCCCAACTACAAGTATTTTGGTAG 58.522 40.000 14.71 0.00 39.23 3.18
3454 6039 6.451292 TCCCCAACTACAAGTATTTTGGTA 57.549 37.500 14.71 5.30 0.00 3.25
3455 6040 5.327737 TCCCCAACTACAAGTATTTTGGT 57.672 39.130 14.71 0.00 0.00 3.67
3456 6041 6.266786 ACTTTCCCCAACTACAAGTATTTTGG 59.733 38.462 11.25 11.25 0.00 3.28
3457 6042 7.284919 ACTTTCCCCAACTACAAGTATTTTG 57.715 36.000 0.00 0.00 0.00 2.44
3458 6043 7.343574 ACAACTTTCCCCAACTACAAGTATTTT 59.656 33.333 0.00 0.00 0.00 1.82
3459 6044 6.837048 ACAACTTTCCCCAACTACAAGTATTT 59.163 34.615 0.00 0.00 0.00 1.40
3460 6045 6.370453 ACAACTTTCCCCAACTACAAGTATT 58.630 36.000 0.00 0.00 0.00 1.89
3461 6046 5.948842 ACAACTTTCCCCAACTACAAGTAT 58.051 37.500 0.00 0.00 0.00 2.12
3462 6047 5.376756 ACAACTTTCCCCAACTACAAGTA 57.623 39.130 0.00 0.00 0.00 2.24
3463 6048 4.245251 ACAACTTTCCCCAACTACAAGT 57.755 40.909 0.00 0.00 0.00 3.16
3464 6049 5.374071 AGTACAACTTTCCCCAACTACAAG 58.626 41.667 0.00 0.00 0.00 3.16
3465 6050 5.376756 AGTACAACTTTCCCCAACTACAA 57.623 39.130 0.00 0.00 0.00 2.41
3466 6051 5.603813 ACTAGTACAACTTTCCCCAACTACA 59.396 40.000 0.00 0.00 0.00 2.74
3467 6052 6.106648 ACTAGTACAACTTTCCCCAACTAC 57.893 41.667 0.00 0.00 0.00 2.73
3468 6053 6.752285 AACTAGTACAACTTTCCCCAACTA 57.248 37.500 0.00 0.00 0.00 2.24
3469 6054 5.641789 AACTAGTACAACTTTCCCCAACT 57.358 39.130 0.00 0.00 0.00 3.16
3470 6055 6.060136 AGAAACTAGTACAACTTTCCCCAAC 58.940 40.000 0.00 0.00 0.00 3.77
3471 6056 6.256643 AGAAACTAGTACAACTTTCCCCAA 57.743 37.500 0.00 0.00 0.00 4.12
3472 6057 5.899631 AGAAACTAGTACAACTTTCCCCA 57.100 39.130 0.00 0.00 0.00 4.96
3473 6058 6.762333 TGTAGAAACTAGTACAACTTTCCCC 58.238 40.000 0.00 0.00 0.00 4.81
3474 6059 8.843885 ATTGTAGAAACTAGTACAACTTTCCC 57.156 34.615 10.39 0.00 40.90 3.97
3475 6060 9.708092 AGATTGTAGAAACTAGTACAACTTTCC 57.292 33.333 10.39 0.94 40.90 3.13
3489 6074 9.997482 TGTCAGTTTTAACAAGATTGTAGAAAC 57.003 29.630 19.08 19.08 41.31 2.78
3492 6077 9.337396 ACATGTCAGTTTTAACAAGATTGTAGA 57.663 29.630 0.00 0.00 41.31 2.59
3493 6078 9.950680 AACATGTCAGTTTTAACAAGATTGTAG 57.049 29.630 0.00 0.00 41.31 2.74
3620 6205 0.312102 GAAAGACTGCCAAGTGCCAC 59.688 55.000 0.00 0.00 40.16 5.01
3923 6652 0.252421 AGGGGATGCTGTCTCTGACA 60.252 55.000 0.37 0.37 40.50 3.58
3924 6653 0.908198 AAGGGGATGCTGTCTCTGAC 59.092 55.000 0.00 0.00 0.00 3.51
4083 6815 3.197265 ACTGAAAACAAACAAGGCATGC 58.803 40.909 9.90 9.90 0.00 4.06
4516 7248 1.674611 CGACGCCAAAGCTGTAGACG 61.675 60.000 0.00 0.00 36.60 4.18
4754 7486 1.374125 CCACCACGTCGCTCATCAA 60.374 57.895 0.00 0.00 0.00 2.57
4994 7726 4.183101 CAATCCACGGCTTGCAAATTTAT 58.817 39.130 0.00 0.00 0.00 1.40
5050 7782 3.121496 GCAAAACAAGAAAATACGCACGG 60.121 43.478 0.00 0.00 0.00 4.94
5109 7849 0.541863 TAGAGGGCCTTACAAGCAGC 59.458 55.000 7.89 0.00 0.00 5.25
5110 7850 1.834263 ACTAGAGGGCCTTACAAGCAG 59.166 52.381 7.89 0.00 0.00 4.24
5111 7851 1.952621 ACTAGAGGGCCTTACAAGCA 58.047 50.000 7.89 0.00 0.00 3.91
5112 7852 3.351794 AAACTAGAGGGCCTTACAAGC 57.648 47.619 7.89 0.00 0.00 4.01
5113 7853 5.167303 AGAAAACTAGAGGGCCTTACAAG 57.833 43.478 7.89 5.66 0.00 3.16
5114 7854 4.595781 TGAGAAAACTAGAGGGCCTTACAA 59.404 41.667 7.89 0.00 0.00 2.41
5153 7893 3.186119 GCTCACTCTGTCTTATCAGCAC 58.814 50.000 0.00 0.00 35.63 4.40
5154 7894 2.167281 GGCTCACTCTGTCTTATCAGCA 59.833 50.000 0.00 0.00 35.63 4.41
5155 7895 2.482839 GGGCTCACTCTGTCTTATCAGC 60.483 54.545 0.00 0.00 35.63 4.26
5156 7896 3.030291 AGGGCTCACTCTGTCTTATCAG 58.970 50.000 0.00 0.00 36.85 2.90
5277 9257 4.576330 ACTAATTCACTCCCTGGAAAGG 57.424 45.455 0.00 0.00 0.00 3.11
5290 9270 6.422333 TGAAGCCATTCCACATACTAATTCA 58.578 36.000 0.00 0.00 34.28 2.57
5510 9531 0.671781 CAGACCAACCTGAAGAGGCG 60.672 60.000 0.00 0.00 44.33 5.52
5536 9557 0.176910 CCAACCCAACACCACCAAAC 59.823 55.000 0.00 0.00 0.00 2.93
5549 9570 2.941583 AGGAGGGAAGGCCAACCC 60.942 66.667 24.27 24.27 45.88 4.11
5552 9573 0.918983 CATACAGGAGGGAAGGCCAA 59.081 55.000 5.01 0.00 35.15 4.52
5567 9588 3.596214 TGAAGTTTCCCTCGAAGCATAC 58.404 45.455 0.00 0.00 32.00 2.39
5585 9606 4.141711 CCGATCCAGGAACCTAGATTTGAA 60.142 45.833 0.00 0.00 0.00 2.69
5589 9610 2.966516 GTCCGATCCAGGAACCTAGATT 59.033 50.000 0.00 0.00 42.77 2.40
5596 9617 0.317938 CGATCGTCCGATCCAGGAAC 60.318 60.000 20.48 0.00 45.95 3.62
5613 9634 2.975799 GTGCCAAAAGGGTCGCGA 60.976 61.111 3.71 3.71 39.65 5.87
5620 9641 1.112916 AGGGAAACGGTGCCAAAAGG 61.113 55.000 0.00 0.00 41.19 3.11
5622 9643 1.110518 GGAGGGAAACGGTGCCAAAA 61.111 55.000 0.00 0.00 41.19 2.44
5623 9644 1.529713 GGAGGGAAACGGTGCCAAA 60.530 57.895 0.00 0.00 41.19 3.28
5624 9645 2.002018 AAGGAGGGAAACGGTGCCAA 62.002 55.000 0.00 0.00 41.19 4.52
5629 9652 0.400594 CTCCAAAGGAGGGAAACGGT 59.599 55.000 5.13 0.00 45.43 4.83
5630 9653 3.249687 CTCCAAAGGAGGGAAACGG 57.750 57.895 5.13 0.00 45.43 4.44
5643 9666 2.304761 ACTCCAAATACGAAGCCTCCAA 59.695 45.455 0.00 0.00 0.00 3.53
5683 9706 2.291209 ATCCTCATTGTTGCCACACA 57.709 45.000 0.00 0.00 30.32 3.72
5696 9719 2.886523 CCAACTTTGCTCACAATCCTCA 59.113 45.455 0.00 0.00 35.21 3.86
5718 9741 4.057428 AGGAGGACACGCAGCGAC 62.057 66.667 24.65 12.06 0.00 5.19
5723 9746 2.640302 GCTCTCAGGAGGACACGCA 61.640 63.158 0.00 0.00 39.80 5.24
5735 9758 1.260538 AACGGCTGGAGATGCTCTCA 61.261 55.000 13.06 0.00 45.12 3.27
5736 9759 0.809241 CAACGGCTGGAGATGCTCTC 60.809 60.000 0.00 5.01 42.66 3.20
5737 9760 1.220206 CAACGGCTGGAGATGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
5738 9761 3.805267 CAACGGCTGGAGATGCTC 58.195 61.111 0.00 0.00 0.00 4.26
5758 9781 3.982372 TTTACGCGCTCGCTGAGGG 62.982 63.158 5.73 14.97 43.96 4.30
5759 9782 1.421410 ATTTTACGCGCTCGCTGAGG 61.421 55.000 5.73 0.00 39.84 3.86
5760 9783 0.043822 GATTTTACGCGCTCGCTGAG 60.044 55.000 5.73 0.00 39.84 3.35
5761 9784 1.739093 CGATTTTACGCGCTCGCTGA 61.739 55.000 5.73 0.00 39.84 4.26
5762 9785 1.365339 CGATTTTACGCGCTCGCTG 60.365 57.895 5.73 8.36 39.84 5.18
5763 9786 2.995482 CGATTTTACGCGCTCGCT 59.005 55.556 5.73 2.52 39.84 4.93
5771 9794 1.426041 CCCCTGACGGCGATTTTACG 61.426 60.000 16.62 0.00 0.00 3.18
5772 9795 1.093496 CCCCCTGACGGCGATTTTAC 61.093 60.000 16.62 0.00 0.00 2.01
5773 9796 1.222387 CCCCCTGACGGCGATTTTA 59.778 57.895 16.62 0.00 0.00 1.52
5774 9797 2.045340 CCCCCTGACGGCGATTTT 60.045 61.111 16.62 0.00 0.00 1.82
5775 9798 4.796495 GCCCCCTGACGGCGATTT 62.796 66.667 16.62 0.00 36.47 2.17
5804 9827 0.688487 TCGTCCCCAGACCGATTTTT 59.312 50.000 0.00 0.00 40.12 1.94
5805 9828 0.249398 CTCGTCCCCAGACCGATTTT 59.751 55.000 0.00 0.00 40.12 1.82
5806 9829 0.903454 ACTCGTCCCCAGACCGATTT 60.903 55.000 0.00 0.00 40.12 2.17
5807 9830 1.305046 ACTCGTCCCCAGACCGATT 60.305 57.895 0.00 0.00 40.12 3.34
5808 9831 2.052690 CACTCGTCCCCAGACCGAT 61.053 63.158 0.00 0.00 40.12 4.18
5809 9832 2.675423 CACTCGTCCCCAGACCGA 60.675 66.667 0.00 0.00 40.12 4.69
5810 9833 3.760035 CCACTCGTCCCCAGACCG 61.760 72.222 0.00 0.00 40.12 4.79
5811 9834 3.391382 CCCACTCGTCCCCAGACC 61.391 72.222 0.00 0.00 40.12 3.85
5812 9835 2.168666 GAACCCACTCGTCCCCAGAC 62.169 65.000 0.00 0.00 39.83 3.51
5813 9836 1.911766 GAACCCACTCGTCCCCAGA 60.912 63.158 0.00 0.00 0.00 3.86
5814 9837 2.663196 GAACCCACTCGTCCCCAG 59.337 66.667 0.00 0.00 0.00 4.45
5815 9838 2.926242 GGAACCCACTCGTCCCCA 60.926 66.667 0.00 0.00 0.00 4.96
5828 9851 4.754667 GGGTCGGCGACTGGGAAC 62.755 72.222 35.42 19.68 32.47 3.62
5853 9876 3.423154 CAAACGGCGTCTGGGAGC 61.423 66.667 15.17 0.00 0.00 4.70
5854 9877 2.030562 ACAAACGGCGTCTGGGAG 59.969 61.111 18.56 5.18 0.00 4.30
5855 9878 2.280524 CACAAACGGCGTCTGGGA 60.281 61.111 18.56 0.00 0.00 4.37
5856 9879 0.881159 TAACACAAACGGCGTCTGGG 60.881 55.000 15.06 15.06 0.00 4.45
5857 9880 0.938713 TTAACACAAACGGCGTCTGG 59.061 50.000 18.56 10.87 0.00 3.86
5858 9881 2.741122 TTTAACACAAACGGCGTCTG 57.259 45.000 15.17 13.72 0.00 3.51
5859 9882 3.761311 TTTTTAACACAAACGGCGTCT 57.239 38.095 15.17 0.00 0.00 4.18
5878 9901 3.682377 CCGAACTTTGCCAAACACTTTTT 59.318 39.130 0.00 0.00 0.00 1.94
5879 9902 3.258228 CCGAACTTTGCCAAACACTTTT 58.742 40.909 0.00 0.00 0.00 2.27
5880 9903 2.887337 CCGAACTTTGCCAAACACTTT 58.113 42.857 0.00 0.00 0.00 2.66
5881 9904 1.470805 GCCGAACTTTGCCAAACACTT 60.471 47.619 0.00 0.00 0.00 3.16
5882 9905 0.102300 GCCGAACTTTGCCAAACACT 59.898 50.000 0.00 0.00 0.00 3.55
5883 9906 0.102300 AGCCGAACTTTGCCAAACAC 59.898 50.000 0.00 0.00 0.00 3.32
5884 9907 1.681538 TAGCCGAACTTTGCCAAACA 58.318 45.000 0.00 0.00 0.00 2.83
5885 9908 2.785713 TTAGCCGAACTTTGCCAAAC 57.214 45.000 0.00 0.00 0.00 2.93
5886 9909 3.802948 TTTTAGCCGAACTTTGCCAAA 57.197 38.095 0.00 0.00 0.00 3.28
5887 9910 4.303282 GAATTTTAGCCGAACTTTGCCAA 58.697 39.130 0.00 0.00 0.00 4.52
5888 9911 3.610585 CGAATTTTAGCCGAACTTTGCCA 60.611 43.478 0.00 0.00 0.00 4.92
5889 9912 2.914838 CGAATTTTAGCCGAACTTTGCC 59.085 45.455 0.00 0.00 0.00 4.52
5890 9913 2.914838 CCGAATTTTAGCCGAACTTTGC 59.085 45.455 0.00 0.00 0.00 3.68
5891 9914 2.914838 GCCGAATTTTAGCCGAACTTTG 59.085 45.455 0.00 0.00 0.00 2.77
5892 9915 2.554893 TGCCGAATTTTAGCCGAACTTT 59.445 40.909 0.00 0.00 0.00 2.66
5893 9916 2.156098 TGCCGAATTTTAGCCGAACTT 58.844 42.857 0.00 0.00 0.00 2.66
5894 9917 1.816074 TGCCGAATTTTAGCCGAACT 58.184 45.000 0.00 0.00 0.00 3.01
5895 9918 2.622546 TTGCCGAATTTTAGCCGAAC 57.377 45.000 0.00 0.00 0.00 3.95
5896 9919 2.554893 AGTTTGCCGAATTTTAGCCGAA 59.445 40.909 0.00 0.00 0.00 4.30
5897 9920 2.095466 CAGTTTGCCGAATTTTAGCCGA 60.095 45.455 0.00 0.00 0.00 5.54
5898 9921 2.250188 CAGTTTGCCGAATTTTAGCCG 58.750 47.619 0.00 0.00 0.00 5.52
5899 9922 2.606108 CCAGTTTGCCGAATTTTAGCC 58.394 47.619 0.00 0.00 0.00 3.93
5900 9923 2.606108 CCCAGTTTGCCGAATTTTAGC 58.394 47.619 0.00 0.00 0.00 3.09
5901 9924 2.029470 TGCCCAGTTTGCCGAATTTTAG 60.029 45.455 0.00 0.00 0.00 1.85
5902 9925 1.964223 TGCCCAGTTTGCCGAATTTTA 59.036 42.857 0.00 0.00 0.00 1.52
5903 9926 0.755686 TGCCCAGTTTGCCGAATTTT 59.244 45.000 0.00 0.00 0.00 1.82
5904 9927 0.975887 ATGCCCAGTTTGCCGAATTT 59.024 45.000 0.00 0.00 0.00 1.82
5905 9928 1.846007 TATGCCCAGTTTGCCGAATT 58.154 45.000 0.00 0.00 0.00 2.17
5906 9929 2.071778 ATATGCCCAGTTTGCCGAAT 57.928 45.000 0.00 0.00 0.00 3.34
5907 9930 2.719531 TATATGCCCAGTTTGCCGAA 57.280 45.000 0.00 0.00 0.00 4.30
5908 9931 2.949177 ATATATGCCCAGTTTGCCGA 57.051 45.000 0.00 0.00 0.00 5.54
5909 9932 4.154195 GTCTAATATATGCCCAGTTTGCCG 59.846 45.833 0.00 0.00 0.00 5.69
5910 9933 5.070001 TGTCTAATATATGCCCAGTTTGCC 58.930 41.667 0.00 0.00 0.00 4.52
5911 9934 6.207417 ACATGTCTAATATATGCCCAGTTTGC 59.793 38.462 0.00 0.00 30.12 3.68
5912 9935 7.750229 ACATGTCTAATATATGCCCAGTTTG 57.250 36.000 0.00 0.00 30.12 2.93
5913 9936 7.173218 CGAACATGTCTAATATATGCCCAGTTT 59.827 37.037 0.00 0.00 30.12 2.66
5914 9937 6.650807 CGAACATGTCTAATATATGCCCAGTT 59.349 38.462 0.00 0.00 30.12 3.16
5915 9938 6.166279 CGAACATGTCTAATATATGCCCAGT 58.834 40.000 0.00 0.00 30.12 4.00
5916 9939 6.653273 CGAACATGTCTAATATATGCCCAG 57.347 41.667 0.00 0.00 30.12 4.45


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

AutoCloner maintained by Alex Coulton.