Multiple sequence alignment - TraesCS1D01G289900

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G289900 chr1D 100.000 8270 0 0 1 8270 387951660 387943391 0.000000e+00 15272
1 TraesCS1D01G289900 chr1D 93.007 143 9 1 7318 7459 483472744 483472886 3.030000e-49 207
2 TraesCS1D01G289900 chr1B 96.013 5292 151 20 870 6138 521225423 521220169 0.000000e+00 8549
3 TraesCS1D01G289900 chr1B 95.447 1186 43 6 6138 7319 521220120 521218942 0.000000e+00 1881
4 TraesCS1D01G289900 chr1B 88.727 479 39 9 7446 7916 521218940 521218469 9.310000e-159 571
5 TraesCS1D01G289900 chr1A 97.583 2979 58 7 3170 6137 487490068 487487093 0.000000e+00 5090
6 TraesCS1D01G289900 chr1A 95.960 1188 35 8 6138 7321 487487044 487485866 0.000000e+00 1916
7 TraesCS1D01G289900 chr1A 96.268 911 8 3 1891 2794 487491739 487490848 0.000000e+00 1471
8 TraesCS1D01G289900 chr1A 89.907 862 49 16 7444 8270 487485868 487485010 0.000000e+00 1075
9 TraesCS1D01G289900 chr1A 95.560 563 19 4 870 1431 487493065 487492508 0.000000e+00 896
10 TraesCS1D01G289900 chr1A 95.571 429 18 1 1479 1907 487492528 487492101 0.000000e+00 686
11 TraesCS1D01G289900 chr1A 94.366 142 2 1 2792 2933 487490725 487490590 6.500000e-51 213
12 TraesCS1D01G289900 chr1A 100.000 56 0 0 3073 3128 487490123 487490068 4.080000e-18 104
13 TraesCS1D01G289900 chr2D 97.712 874 17 1 1 871 42091166 42090293 0.000000e+00 1500
14 TraesCS1D01G289900 chr2D 94.203 138 8 0 7319 7456 536091026 536091163 2.340000e-50 211
15 TraesCS1D01G289900 chr7B 83.396 530 55 10 160 671 73143115 73142601 2.100000e-125 460
16 TraesCS1D01G289900 chr7B 83.532 419 43 7 456 874 73141813 73141421 1.310000e-97 368
17 TraesCS1D01G289900 chr7B 84.259 216 20 3 456 671 73142606 73142405 1.820000e-46 198
18 TraesCS1D01G289900 chr7B 88.679 159 16 2 456 614 73142410 73142254 8.470000e-45 193
19 TraesCS1D01G289900 chr5A 94.118 170 7 3 6713 6879 320214236 320214405 1.070000e-63 255
20 TraesCS1D01G289900 chr5A 93.333 165 9 2 6717 6879 558675661 558675497 8.290000e-60 243
21 TraesCS1D01G289900 chr5A 96.970 132 4 0 7317 7448 607836674 607836805 1.080000e-53 222
22 TraesCS1D01G289900 chr2A 94.545 165 7 2 6717 6879 135473392 135473228 3.830000e-63 254
23 TraesCS1D01G289900 chr4B 93.529 170 7 4 6712 6879 532434995 532435162 4.960000e-62 250
24 TraesCS1D01G289900 chr4D 93.373 166 10 1 6724 6888 64390627 64390462 2.310000e-60 244
25 TraesCS1D01G289900 chr5D 92.814 167 10 2 6712 6876 314421982 314422148 2.980000e-59 241
26 TraesCS1D01G289900 chr5D 93.617 141 7 2 7312 7452 565275093 565275231 8.410000e-50 209
27 TraesCS1D01G289900 chr5D 94.737 95 5 0 1557 1651 35954302 35954208 1.860000e-31 148
28 TraesCS1D01G289900 chr6A 90.909 176 11 5 6706 6879 609592940 609593112 1.800000e-56 231
29 TraesCS1D01G289900 chr6A 92.466 146 10 1 7309 7453 12317781 12317636 3.030000e-49 207
30 TraesCS1D01G289900 chr7D 94.964 139 7 0 7311 7449 636760670 636760532 1.400000e-52 219
31 TraesCS1D01G289900 chr3D 95.556 135 5 1 7317 7450 283321122 283321256 1.810000e-51 215
32 TraesCS1D01G289900 chr3D 94.245 139 7 1 7320 7458 210622549 210622412 2.340000e-50 211
33 TraesCS1D01G289900 chr3D 95.385 130 6 0 7320 7449 351086751 351086622 3.030000e-49 207


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 TraesCS1D01G289900 chr1D 387943391 387951660 8269 True 15272.000 15272 100.000000 1 8270 1 chr1D.!!$R1 8269
1 TraesCS1D01G289900 chr1B 521218469 521225423 6954 True 3667.000 8549 93.395667 870 7916 3 chr1B.!!$R1 7046
2 TraesCS1D01G289900 chr1A 487485010 487493065 8055 True 1431.375 5090 95.651875 870 8270 8 chr1A.!!$R1 7400
3 TraesCS1D01G289900 chr2D 42090293 42091166 873 True 1500.000 1500 97.712000 1 871 1 chr2D.!!$R1 870
4 TraesCS1D01G289900 chr7B 73141421 73143115 1694 True 304.750 460 84.966500 160 874 4 chr7B.!!$R1 714

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
734 1731 1.201921 CGCGCAGGTATGTTTCTGAAC 60.202 52.381 8.75 0.0 36.29 3.18 F
1470 2480 1.210478 TGCCTGTGCCCTAAGAAGATC 59.790 52.381 0.00 0.0 36.33 2.75 F
1780 2790 2.230992 TGCTTTAATGCTTTGGCGACAT 59.769 40.909 13.80 0.0 42.32 3.06 F
3449 5304 2.405143 CGAGAGCGGATGTGGAGTA 58.595 57.895 0.00 0.0 0.00 2.59 F
4211 6074 6.748333 ACATTGTCTGTGAATGTCCTAATG 57.252 37.500 0.00 0.0 39.34 1.90 F
4435 6298 0.771127 TCCCTTAAACAGCAGTGCCT 59.229 50.000 12.58 0.0 0.00 4.75 F
4464 6327 1.006281 TCCCCTGCATGAGCTGAAATT 59.994 47.619 0.00 0.0 41.71 1.82 F
5439 7307 1.028905 CCGGAACTGCCAAAAAGACA 58.971 50.000 0.00 0.0 35.94 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 3439 2.816087 CAGTGAGGAGGTCAAACCAATG 59.184 50.000 0.00 0.0 41.95 2.82 R
3449 5304 0.174389 CGTGTGCTGTCAGAGGCTAT 59.826 55.000 3.32 0.0 0.00 2.97 R
3491 5346 1.958288 AGGTCCCACTGCTTGACTAT 58.042 50.000 0.00 0.0 0.00 2.12 R
4435 6298 0.614294 CATGCAGGGGAATTTTGGCA 59.386 50.000 0.00 0.0 35.54 4.92 R
5644 7512 0.104672 TGGAGGACCTCAAAGGGTGA 60.105 55.000 23.06 0.0 40.58 4.02 R
6120 7988 1.155889 CGCAGTCTAACCACATGCAA 58.844 50.000 0.00 0.0 36.70 4.08 R
6363 8281 8.871686 ACAAAATACCTTTTTGACATCTGAAC 57.128 30.769 15.50 0.0 40.73 3.18 R
7428 9353 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.0 0.00 3.28 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
74 75 7.768120 TCAACCATTGTGTTAAAAGCTTCAAAT 59.232 29.630 0.00 0.00 0.00 2.32
126 127 3.677596 ACTTCAAAAACTGGCGTTGTTTG 59.322 39.130 14.95 14.95 37.64 2.93
341 342 3.896648 AAATGCTTCAACCGTGTACTG 57.103 42.857 0.00 0.00 0.00 2.74
452 469 3.127533 GCCGGTGACCATCAGTGC 61.128 66.667 1.90 0.00 0.00 4.40
734 1731 1.201921 CGCGCAGGTATGTTTCTGAAC 60.202 52.381 8.75 0.00 36.29 3.18
972 1982 1.536709 GCAAATTTGAGCCCATAGCCG 60.537 52.381 22.31 0.00 45.47 5.52
980 1990 2.279517 CCCATAGCCGAGTCGCAC 60.280 66.667 7.12 0.84 0.00 5.34
1341 2351 8.277713 CGATCGAGTTCTTTTTGTTTAGGTTAA 58.722 33.333 10.26 0.00 0.00 2.01
1390 2400 5.350365 GTCATAAAGTGGCTGTGAAATCGTA 59.650 40.000 0.00 0.00 0.00 3.43
1412 2422 4.026052 AGTTTGGGGATTGCCTTATTCTG 58.974 43.478 0.00 0.00 0.00 3.02
1439 2449 2.996249 TTTTGGGTACACCGTACACA 57.004 45.000 5.14 5.14 44.64 3.72
1440 2450 3.488778 TTTTGGGTACACCGTACACAT 57.511 42.857 9.86 0.00 44.64 3.21
1441 2451 2.459060 TTGGGTACACCGTACACATG 57.541 50.000 9.86 0.00 44.64 3.21
1442 2452 1.630223 TGGGTACACCGTACACATGA 58.370 50.000 5.14 0.00 44.64 3.07
1470 2480 1.210478 TGCCTGTGCCCTAAGAAGATC 59.790 52.381 0.00 0.00 36.33 2.75
1483 2493 6.287525 CCTAAGAAGATCATGGTTCCTCTTC 58.712 44.000 11.42 11.48 42.44 2.87
1499 2509 7.334671 GGTTCCTCTTCTACATTTTTAGGACAG 59.665 40.741 0.00 0.00 31.58 3.51
1527 2537 4.926832 TCAATTGTGCTTGCAGAATCATTG 59.073 37.500 16.38 12.60 0.00 2.82
1635 2645 2.235650 TCAGGCTCTGATCAAGGAACAG 59.764 50.000 0.00 0.00 35.39 3.16
1644 2654 6.070656 TCTGATCAAGGAACAGGAAAACATT 58.929 36.000 0.00 0.00 34.05 2.71
1780 2790 2.230992 TGCTTTAATGCTTTGGCGACAT 59.769 40.909 13.80 0.00 42.32 3.06
1788 2798 2.872245 TGCTTTGGCGACATATAGCTTC 59.128 45.455 17.90 0.00 42.32 3.86
1809 2826 6.366061 GCTTCCACCATCAATTAACTTTGTTC 59.634 38.462 0.00 0.00 0.00 3.18
1827 2844 7.649306 ACTTTGTTCAAGACACATAAAAGCATC 59.351 33.333 0.00 0.00 38.18 3.91
1854 2871 7.492344 TGGATGATTTGATTATCCATCGTATCG 59.508 37.037 9.57 0.00 46.69 2.92
1876 2893 4.514066 CGGGTAACAGCAAAGTAGAGTTTT 59.486 41.667 0.00 0.00 39.74 2.43
1883 2900 3.691498 GCAAAGTAGAGTTTTTGCGTGT 58.309 40.909 6.23 0.00 46.41 4.49
1933 3328 4.576873 TCAAGAAATTACGAAACACTGCCA 59.423 37.500 0.00 0.00 0.00 4.92
2044 3439 5.342259 GTGGATGTGAAATTTTAGTGCGAAC 59.658 40.000 0.00 0.00 0.00 3.95
2284 3679 5.944007 AGTGTTAGCGGAAATATCCACTTTT 59.056 36.000 0.00 0.00 46.97 2.27
2650 4053 5.174037 TCATTTTCCTACCCAGGTGTAAG 57.826 43.478 0.00 0.00 43.18 2.34
2651 4054 4.600111 TCATTTTCCTACCCAGGTGTAAGT 59.400 41.667 0.00 0.00 43.18 2.24
2652 4055 4.360951 TTTTCCTACCCAGGTGTAAGTG 57.639 45.455 0.00 0.00 43.18 3.16
2653 4056 2.708037 TCCTACCCAGGTGTAAGTGT 57.292 50.000 0.00 0.00 43.18 3.55
2654 4057 3.831642 TCCTACCCAGGTGTAAGTGTA 57.168 47.619 0.00 0.00 43.18 2.90
2655 4058 4.130719 TCCTACCCAGGTGTAAGTGTAA 57.869 45.455 0.00 0.00 43.18 2.41
2686 4089 8.579850 TCAGGTAGTAGAACGTATTTTCCTTA 57.420 34.615 0.00 0.00 0.00 2.69
2751 4154 6.943146 AGGGAGAGAAGTTGATTTAAACCTTC 59.057 38.462 0.00 0.87 0.00 3.46
2933 4461 4.406003 AGTTCTGGCGGTACTATCAAATCT 59.594 41.667 3.52 0.00 0.00 2.40
3021 4549 6.590292 ACCACTAGAAATATTGTTGTCACTCG 59.410 38.462 0.00 0.00 0.00 4.18
3449 5304 2.405143 CGAGAGCGGATGTGGAGTA 58.595 57.895 0.00 0.00 0.00 2.59
4211 6074 6.748333 ACATTGTCTGTGAATGTCCTAATG 57.252 37.500 0.00 0.00 39.34 1.90
4368 6231 8.937634 ATGCAATGATTTGAAGAAATTACTCC 57.062 30.769 0.00 0.00 34.60 3.85
4435 6298 0.771127 TCCCTTAAACAGCAGTGCCT 59.229 50.000 12.58 0.00 0.00 4.75
4464 6327 1.006281 TCCCCTGCATGAGCTGAAATT 59.994 47.619 0.00 0.00 41.71 1.82
4556 6419 6.795399 TCTTCATTCAACCAAAGTCAAACTC 58.205 36.000 0.00 0.00 0.00 3.01
4573 6436 8.873830 AGTCAAACTCAATACTGATATGTTTCG 58.126 33.333 0.00 0.00 29.60 3.46
4678 6541 3.774766 AGGGGTTTCCTATTTTTCATGGC 59.225 43.478 0.00 0.00 45.98 4.40
5329 7197 4.009675 AGAATGCGCAGAATAGAAACCAA 58.990 39.130 18.32 0.00 0.00 3.67
5392 7260 3.561725 AGACGACAAAAGAAAGAGGCAAG 59.438 43.478 0.00 0.00 0.00 4.01
5439 7307 1.028905 CCGGAACTGCCAAAAAGACA 58.971 50.000 0.00 0.00 35.94 3.41
5441 7309 1.676006 CGGAACTGCCAAAAAGACAGT 59.324 47.619 0.00 0.00 46.27 3.55
5722 7590 2.945447 TTCACCGTATCTGGGTAACG 57.055 50.000 0.00 0.00 35.58 3.18
5726 7594 2.684881 CACCGTATCTGGGTAACGTAGT 59.315 50.000 0.00 0.00 38.06 2.73
6008 7876 6.795098 AGCAATGACGATTACAAAGTACAA 57.205 33.333 0.00 0.00 0.00 2.41
6120 7988 7.733047 TCATGGGTATTATACAGTACATGGACT 59.267 37.037 4.17 4.17 36.16 3.85
6363 8281 7.961351 ACAGAGAAGAGGGTTGAAGATATATG 58.039 38.462 0.00 0.00 0.00 1.78
6681 8600 9.056005 TCTTGTCTCGCATAAAAATAGCAATAT 57.944 29.630 0.00 0.00 0.00 1.28
6883 8805 5.848833 TTAGAAACGGAGGGAGTAGATTC 57.151 43.478 0.00 0.00 0.00 2.52
6941 8865 4.744570 TCTAGATGGTCAAACTAGTTGCG 58.255 43.478 9.34 3.88 37.13 4.85
6988 8913 5.987777 TTTGAGCAAAACAAATGATGTGG 57.012 34.783 0.00 0.00 42.99 4.17
7029 8954 4.728772 TGTGCCCCCAATTAGATTAGATG 58.271 43.478 0.00 0.00 0.00 2.90
7087 9012 3.445008 TCAGGAGTAGAATTGCAGGTCT 58.555 45.455 6.48 6.48 0.00 3.85
7131 9056 2.165030 CCCTCTGGTGATTTGAACATGC 59.835 50.000 0.00 0.00 0.00 4.06
7136 9061 1.339711 GTGATTTGAACATGCGCCAC 58.660 50.000 4.18 0.00 0.00 5.01
7153 9078 1.827969 CCACTGGGTTGAGTAGGAGAG 59.172 57.143 0.00 0.00 0.00 3.20
7157 9082 2.569404 CTGGGTTGAGTAGGAGAGCTTT 59.431 50.000 0.00 0.00 0.00 3.51
7176 9101 5.125097 AGCTTTTTATGATCTCCAGCACAAG 59.875 40.000 0.00 0.00 0.00 3.16
7190 9115 5.047164 TCCAGCACAAGTTCGTATAGGTTTA 60.047 40.000 0.00 0.00 0.00 2.01
7219 9144 3.923017 AATTTACCTGCTCACAACTGC 57.077 42.857 0.00 0.00 0.00 4.40
7271 9196 1.696336 GAAGGCCTGGATGAGCTGATA 59.304 52.381 5.69 0.00 0.00 2.15
7320 9245 1.507140 CCTGGGCCTGGAGTAATGTA 58.493 55.000 24.15 0.00 0.00 2.29
7321 9246 1.141053 CCTGGGCCTGGAGTAATGTAC 59.859 57.143 24.15 0.00 0.00 2.90
7322 9247 2.119495 CTGGGCCTGGAGTAATGTACT 58.881 52.381 4.53 0.00 42.86 2.73
7332 9257 2.664015 AGTAATGTACTCCCTCCGTCC 58.336 52.381 0.00 0.00 32.47 4.79
7333 9258 1.685517 GTAATGTACTCCCTCCGTCCC 59.314 57.143 0.00 0.00 0.00 4.46
7334 9259 0.042131 AATGTACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
7335 9260 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
7336 9261 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
7337 9262 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
7338 9263 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
7339 9264 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
7340 9265 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
7341 9266 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
7342 9267 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
7343 9268 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
7344 9269 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
7345 9270 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
7346 9271 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
7347 9272 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
7348 9273 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
7349 9274 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
7350 9275 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
7351 9276 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
7352 9277 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
7353 9278 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
7354 9279 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
7355 9280 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
7356 9281 8.923270 TCCCAAAATTCTTGTCTTAGATTTGTT 58.077 29.630 0.00 0.00 28.79 2.83
7357 9282 9.546428 CCCAAAATTCTTGTCTTAGATTTGTTT 57.454 29.630 0.00 0.00 28.79 2.83
7380 9305 9.365311 GTTTAAATACGGATGTATCAAATCACG 57.635 33.333 0.00 0.00 40.42 4.35
7381 9306 8.651391 TTAAATACGGATGTATCAAATCACGT 57.349 30.769 0.00 0.00 40.42 4.49
7382 9307 7.548196 AAATACGGATGTATCAAATCACGTT 57.452 32.000 0.00 0.00 40.42 3.99
7383 9308 7.548196 AATACGGATGTATCAAATCACGTTT 57.452 32.000 0.00 0.00 40.42 3.60
7384 9309 5.873179 ACGGATGTATCAAATCACGTTTT 57.127 34.783 0.00 0.00 31.40 2.43
7385 9310 6.971527 ACGGATGTATCAAATCACGTTTTA 57.028 33.333 0.00 0.00 31.40 1.52
7386 9311 7.000575 ACGGATGTATCAAATCACGTTTTAG 57.999 36.000 0.00 0.00 31.40 1.85
7387 9312 6.592607 ACGGATGTATCAAATCACGTTTTAGT 59.407 34.615 0.00 0.00 31.40 2.24
7388 9313 7.760794 ACGGATGTATCAAATCACGTTTTAGTA 59.239 33.333 0.00 0.00 31.40 1.82
7389 9314 8.761497 CGGATGTATCAAATCACGTTTTAGTAT 58.239 33.333 0.00 0.00 0.00 2.12
7423 9348 8.919777 TCCGTATCTAGATGAATCTAAGACAA 57.080 34.615 15.79 0.00 38.80 3.18
7424 9349 9.004717 TCCGTATCTAGATGAATCTAAGACAAG 57.995 37.037 15.79 0.00 38.80 3.16
7425 9350 9.004717 CCGTATCTAGATGAATCTAAGACAAGA 57.995 37.037 15.79 0.00 38.80 3.02
7433 9358 8.964772 AGATGAATCTAAGACAAGAATTTTGGG 58.035 33.333 0.00 0.00 34.85 4.12
7434 9359 8.884124 ATGAATCTAAGACAAGAATTTTGGGA 57.116 30.769 5.68 0.00 0.00 4.37
7435 9360 8.110860 TGAATCTAAGACAAGAATTTTGGGAC 57.889 34.615 5.68 0.00 0.00 4.46
7436 9361 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
7437 9362 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
7438 9363 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
7439 9364 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
7440 9365 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
7441 9366 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
7442 9367 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
7443 9368 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
7444 9369 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
7528 9453 2.091776 TTTACGGTTGTGTCGTGCGC 62.092 55.000 0.00 0.00 41.24 6.09
7539 9464 4.643385 CGTGCGCGTTGTGGACAC 62.643 66.667 12.43 4.18 34.14 3.67
7544 9469 2.019408 CGCGTTGTGGACACGATCA 61.019 57.895 0.00 0.00 35.91 2.92
7567 9496 2.610479 GCTGTGTTTCGGATCTGACTCA 60.610 50.000 2.94 3.81 0.00 3.41
7568 9497 2.989840 CTGTGTTTCGGATCTGACTCAC 59.010 50.000 21.73 21.73 0.00 3.51
7569 9498 2.628178 TGTGTTTCGGATCTGACTCACT 59.372 45.455 25.47 0.00 0.00 3.41
7570 9499 3.246619 GTGTTTCGGATCTGACTCACTC 58.753 50.000 21.46 10.52 0.00 3.51
7666 9595 3.959293 TCAGGACTCCGTGATTGTAGTA 58.041 45.455 0.00 0.00 32.82 1.82
7713 9646 7.640313 TCTCTACTTCCTACATAAGGTTCTGA 58.360 38.462 0.00 0.00 46.62 3.27
7728 9663 3.144120 CTGACGCATCCCTCCTCCG 62.144 68.421 0.00 0.00 0.00 4.63
7776 9716 6.238759 CCCTCTCTGTTTTGATCTTTTTCGTT 60.239 38.462 0.00 0.00 0.00 3.85
7816 9756 3.428316 GCACTCGGTTTCCTTGAAAACAA 60.428 43.478 5.55 0.00 38.98 2.83
7817 9757 4.736464 GCACTCGGTTTCCTTGAAAACAAT 60.736 41.667 5.55 0.00 38.98 2.71
7909 9853 3.515104 ACCAAATAAGGGAGTGCCAAATG 59.485 43.478 2.50 0.00 35.15 2.32
7918 9862 3.381590 GGGAGTGCCAAATGAAATCCTAC 59.618 47.826 0.00 0.00 35.15 3.18
7924 9868 4.264352 TGCCAAATGAAATCCTACTCCCTT 60.264 41.667 0.00 0.00 0.00 3.95
7929 9874 4.569719 TGAAATCCTACTCCCTTGTTCC 57.430 45.455 0.00 0.00 0.00 3.62
7941 9886 5.543790 ACTCCCTTGTTCCAAAATAAATGCT 59.456 36.000 0.00 0.00 0.00 3.79
7963 9908 6.314896 TGCTGTGGTTTTAGTTCAAATTTTGG 59.685 34.615 9.18 0.00 0.00 3.28
7966 9911 9.108284 CTGTGGTTTTAGTTCAAATTTTGGAAT 57.892 29.630 9.18 2.49 0.00 3.01
7975 9921 6.327365 AGTTCAAATTTTGGAATGGAGGAGTT 59.673 34.615 9.18 0.00 0.00 3.01
8112 10067 2.337849 ACCCCCAATTGATGCAAAACT 58.662 42.857 7.12 0.00 0.00 2.66
8169 10135 7.231467 TCTTTGGAGTTGAGCTTTATTAACCT 58.769 34.615 0.00 0.00 0.00 3.50
8183 10149 7.392393 GCTTTATTAACCTTTTGTCTACCCAGA 59.608 37.037 0.00 0.00 0.00 3.86
8191 10157 3.334583 TTGTCTACCCAGATCAACAGC 57.665 47.619 0.00 0.00 32.09 4.40
8196 10162 0.957395 ACCCAGATCAACAGCGCAAG 60.957 55.000 11.47 3.78 43.44 4.01
8212 10178 1.068194 GCAAGGCTATAGATCGCTCGT 60.068 52.381 3.21 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 5.177327 CGCCATTTGAAGCTTTTAACACAAT 59.823 36.000 0.00 0.00 0.00 2.71
61 62 2.556189 TCTGCGCCATTTGAAGCTTTTA 59.444 40.909 4.18 0.00 0.00 1.52
104 105 3.586100 AACAACGCCAGTTTTTGAAGT 57.414 38.095 0.00 0.00 38.79 3.01
126 127 1.327764 GCTGCTCATACCGTTGTTAGC 59.672 52.381 0.00 0.00 0.00 3.09
341 342 4.752101 GGTGCACATGGATGTAGATACTTC 59.248 45.833 20.43 0.00 39.39 3.01
440 457 2.171209 CTCCCACGCACTGATGGTCA 62.171 60.000 0.00 0.00 33.80 4.02
452 469 1.804326 CGGTCGTAAAGCTCCCACG 60.804 63.158 8.04 8.04 37.03 4.94
703 1697 4.421479 CTGCGCGAGTCCTTCCGT 62.421 66.667 12.10 0.00 0.00 4.69
913 1910 8.079211 AGAGCATCCGCCTTAATAATCTTATA 57.921 34.615 0.00 0.00 39.83 0.98
914 1911 6.951971 AGAGCATCCGCCTTAATAATCTTAT 58.048 36.000 0.00 0.00 39.83 1.73
972 1982 0.250513 AGAATTCCCTGGTGCGACTC 59.749 55.000 0.65 0.00 0.00 3.36
1304 2314 6.889019 AAGAACTCGATCGGTTAATTTCTC 57.111 37.500 16.41 5.01 0.00 2.87
1368 2378 4.685169 ACGATTTCACAGCCACTTTATG 57.315 40.909 0.00 0.00 0.00 1.90
1390 2400 4.026052 CAGAATAAGGCAATCCCCAAACT 58.974 43.478 0.00 0.00 0.00 2.66
1426 2436 4.170292 AGAGTTCATGTGTACGGTGTAC 57.830 45.455 0.22 0.22 0.00 2.90
1432 2442 2.668457 GGCAGAAGAGTTCATGTGTACG 59.332 50.000 0.00 0.00 0.00 3.67
1433 2443 3.681897 CAGGCAGAAGAGTTCATGTGTAC 59.318 47.826 0.00 0.00 0.00 2.90
1434 2444 3.324846 ACAGGCAGAAGAGTTCATGTGTA 59.675 43.478 0.00 0.00 0.00 2.90
1435 2445 2.105477 ACAGGCAGAAGAGTTCATGTGT 59.895 45.455 0.00 0.00 0.00 3.72
1436 2446 2.483106 CACAGGCAGAAGAGTTCATGTG 59.517 50.000 0.00 0.00 0.00 3.21
1437 2447 2.775890 CACAGGCAGAAGAGTTCATGT 58.224 47.619 0.00 0.00 0.00 3.21
1438 2448 1.467734 GCACAGGCAGAAGAGTTCATG 59.532 52.381 0.00 0.00 40.72 3.07
1439 2449 1.612726 GGCACAGGCAGAAGAGTTCAT 60.613 52.381 0.00 0.00 43.71 2.57
1440 2450 0.250467 GGCACAGGCAGAAGAGTTCA 60.250 55.000 0.00 0.00 43.71 3.18
1441 2451 0.957888 GGGCACAGGCAGAAGAGTTC 60.958 60.000 0.00 0.00 43.71 3.01
1442 2452 1.073897 GGGCACAGGCAGAAGAGTT 59.926 57.895 0.00 0.00 43.71 3.01
1470 2480 7.829211 TCCTAAAAATGTAGAAGAGGAACCATG 59.171 37.037 0.00 0.00 0.00 3.66
1483 2493 9.965824 AATTGAACAACTGTCCTAAAAATGTAG 57.034 29.630 0.00 0.00 0.00 2.74
1486 2496 8.542132 CACAATTGAACAACTGTCCTAAAAATG 58.458 33.333 13.59 0.00 27.10 2.32
1499 2509 3.446799 TCTGCAAGCACAATTGAACAAC 58.553 40.909 13.59 0.00 31.55 3.32
1527 2537 4.035091 GGTGCTTTTGATTTGTTTTCCCAC 59.965 41.667 0.00 0.00 0.00 4.61
1765 2775 3.480470 AGCTATATGTCGCCAAAGCATT 58.520 40.909 2.42 0.00 39.83 3.56
1780 2790 8.902806 CAAAGTTAATTGATGGTGGAAGCTATA 58.097 33.333 0.00 0.00 30.89 1.31
1788 2798 7.382218 GTCTTGAACAAAGTTAATTGATGGTGG 59.618 37.037 0.00 0.00 37.18 4.61
1809 2826 5.885230 TCCAGATGCTTTTATGTGTCTTG 57.115 39.130 0.00 0.00 0.00 3.02
1854 2871 6.206498 CAAAAACTCTACTTTGCTGTTACCC 58.794 40.000 0.00 0.00 0.00 3.69
1876 2893 7.706281 AAAATCATCAAATTAACACACGCAA 57.294 28.000 0.00 0.00 0.00 4.85
1933 3328 5.828859 AGTGAGTAGAACAGTGTACTGAAGT 59.171 40.000 18.18 3.59 46.59 3.01
2044 3439 2.816087 CAGTGAGGAGGTCAAACCAATG 59.184 50.000 0.00 0.00 41.95 2.82
2284 3679 5.798125 TCAAATGGTGCCAAAATAGTTCA 57.202 34.783 0.00 0.00 0.00 3.18
2650 4053 9.050601 ACGTTCTACTACCTGATATAGTTACAC 57.949 37.037 0.00 0.00 34.66 2.90
2751 4154 3.198068 TGCTAGGCTCAAGATTTAAGCG 58.802 45.455 0.00 0.00 36.89 4.68
2933 4461 3.072476 AGGAAGGAACCTCATTTTCGACA 59.928 43.478 0.00 0.00 34.98 4.35
2965 4493 1.675007 TGAGAGAGAGACAGGGAGGA 58.325 55.000 0.00 0.00 0.00 3.71
3021 4549 3.888930 TGACCCAAACAAATCCTTCTGAC 59.111 43.478 0.00 0.00 0.00 3.51
3052 4580 9.277783 GAGATACAGCATTTAACCTGATTGTAT 57.722 33.333 10.97 10.97 32.95 2.29
3061 4589 6.743575 ACAGTTGAGATACAGCATTTAACC 57.256 37.500 0.00 0.00 32.13 2.85
3070 4598 7.063898 CACAATAGGTCAACAGTTGAGATACAG 59.936 40.741 16.68 8.37 41.01 2.74
3160 5015 8.466798 ACAAATCCTGGTAATTTATGCAACTAC 58.533 33.333 0.00 0.00 0.00 2.73
3227 5082 8.303156 TCAAATCAAGACAAAGAAAACAGAACA 58.697 29.630 0.00 0.00 0.00 3.18
3449 5304 0.174389 CGTGTGCTGTCAGAGGCTAT 59.826 55.000 3.32 0.00 0.00 2.97
3491 5346 1.958288 AGGTCCCACTGCTTGACTAT 58.042 50.000 0.00 0.00 0.00 2.12
3608 5464 7.538678 AGTCATCGCAATCAAAAAGTTATTCAC 59.461 33.333 0.00 0.00 0.00 3.18
3616 5472 4.635765 TCCCTAGTCATCGCAATCAAAAAG 59.364 41.667 0.00 0.00 0.00 2.27
4324 6187 3.370978 GCATGCTTGCGTTCTTAACTCTA 59.629 43.478 11.37 0.00 39.49 2.43
4368 6231 4.023193 ACTTTCAAAGTGTAGCATTTCCCG 60.023 41.667 0.68 0.00 41.01 5.14
4435 6298 0.614294 CATGCAGGGGAATTTTGGCA 59.386 50.000 0.00 0.00 35.54 4.92
4464 6327 8.845227 TCAATTATGACTGTTGAACTTGCTAAA 58.155 29.630 0.00 0.00 0.00 1.85
4631 6494 4.660303 ACTGTCCCATGATAATGCTCCTTA 59.340 41.667 0.00 0.00 0.00 2.69
4678 6541 7.803279 ACACAGGAGAACCTAAAACTAAAAG 57.197 36.000 0.00 0.00 45.94 2.27
5329 7197 2.908940 GCTGCCTGCCACTGTTGT 60.909 61.111 0.00 0.00 35.15 3.32
5439 7307 1.601171 GCTCACCTCTCCATGCACT 59.399 57.895 0.00 0.00 0.00 4.40
5441 7309 1.276859 ATGGCTCACCTCTCCATGCA 61.277 55.000 0.00 0.00 39.01 3.96
5644 7512 0.104672 TGGAGGACCTCAAAGGGTGA 60.105 55.000 23.06 0.00 40.58 4.02
5722 7590 5.099042 ACATCCAAAGGGTGTATGACTAC 57.901 43.478 0.00 0.00 34.93 2.73
5726 7594 4.085733 CCAAACATCCAAAGGGTGTATGA 58.914 43.478 1.81 0.00 34.93 2.15
6008 7876 6.426587 AGAAACATAGGCATTTACATCCACT 58.573 36.000 0.00 0.00 0.00 4.00
6120 7988 1.155889 CGCAGTCTAACCACATGCAA 58.844 50.000 0.00 0.00 36.70 4.08
6363 8281 8.871686 ACAAAATACCTTTTTGACATCTGAAC 57.128 30.769 15.50 0.00 40.73 3.18
6883 8805 5.354234 AGAATTACTAGCACCCAAAACATCG 59.646 40.000 0.00 0.00 0.00 3.84
6914 8838 7.387948 GCAACTAGTTTGACCATCTAGAAAAGA 59.612 37.037 5.07 0.00 37.39 2.52
6915 8839 7.522374 GCAACTAGTTTGACCATCTAGAAAAG 58.478 38.462 5.07 0.00 37.39 2.27
6916 8840 6.147164 CGCAACTAGTTTGACCATCTAGAAAA 59.853 38.462 5.07 0.00 37.39 2.29
6917 8841 5.637810 CGCAACTAGTTTGACCATCTAGAAA 59.362 40.000 5.07 0.00 37.39 2.52
6918 8842 5.168569 CGCAACTAGTTTGACCATCTAGAA 58.831 41.667 5.07 0.00 37.39 2.10
6919 8843 4.381612 CCGCAACTAGTTTGACCATCTAGA 60.382 45.833 5.07 0.00 37.39 2.43
6920 8844 3.865745 CCGCAACTAGTTTGACCATCTAG 59.134 47.826 5.07 0.00 37.39 2.43
6941 8865 4.571984 GGCTGCATAACCATTTGAAAATCC 59.428 41.667 0.50 0.00 0.00 3.01
6988 8913 1.812571 CATACAGTCTGTTGGGGTTGC 59.187 52.381 11.54 0.00 0.00 4.17
7029 8954 1.407618 AGAACAAAGAACAAACGGGGC 59.592 47.619 0.00 0.00 0.00 5.80
7068 8993 3.198853 GGAAGACCTGCAATTCTACTCCT 59.801 47.826 7.35 0.00 0.00 3.69
7131 9056 1.079127 CCTACTCAACCCAGTGGCG 60.079 63.158 2.61 0.00 33.59 5.69
7136 9061 1.859302 AGCTCTCCTACTCAACCCAG 58.141 55.000 0.00 0.00 0.00 4.45
7153 9078 4.970662 TGTGCTGGAGATCATAAAAAGC 57.029 40.909 0.00 0.00 0.00 3.51
7157 9082 4.631377 CGAACTTGTGCTGGAGATCATAAA 59.369 41.667 0.00 0.00 0.00 1.40
7190 9115 5.362430 TGTGAGCAGGTAAATTTGGAACTTT 59.638 36.000 0.00 0.00 0.00 2.66
7219 9144 3.742882 CCCTGCACAGATGATGTTATACG 59.257 47.826 0.00 0.00 41.41 3.06
7320 9245 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
7321 9246 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
7322 9247 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
7323 9248 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
7324 9249 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
7325 9250 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
7326 9251 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
7327 9252 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
7328 9253 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
7329 9254 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
7330 9255 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
7331 9256 9.546428 AAACAAATCTAAGACAAGAATTTTGGG 57.454 29.630 0.00 0.00 33.04 4.12
7354 9279 9.365311 CGTGATTTGATACATCCGTATTTAAAC 57.635 33.333 0.00 0.00 38.48 2.01
7355 9280 9.100554 ACGTGATTTGATACATCCGTATTTAAA 57.899 29.630 0.00 0.00 38.48 1.52
7356 9281 8.651391 ACGTGATTTGATACATCCGTATTTAA 57.349 30.769 0.00 0.00 38.48 1.52
7357 9282 8.651391 AACGTGATTTGATACATCCGTATTTA 57.349 30.769 0.00 0.00 38.48 1.40
7358 9283 7.548196 AACGTGATTTGATACATCCGTATTT 57.452 32.000 0.00 0.00 38.48 1.40
7359 9284 7.548196 AAACGTGATTTGATACATCCGTATT 57.452 32.000 0.00 0.00 38.48 1.89
7360 9285 7.548196 AAAACGTGATTTGATACATCCGTAT 57.452 32.000 0.00 0.00 41.16 3.06
7361 9286 6.971527 AAAACGTGATTTGATACATCCGTA 57.028 33.333 0.00 0.00 31.50 4.02
7362 9287 5.873179 AAAACGTGATTTGATACATCCGT 57.127 34.783 0.00 0.00 32.42 4.69
7363 9288 7.000575 ACTAAAACGTGATTTGATACATCCG 57.999 36.000 0.00 0.00 0.00 4.18
7397 9322 9.521841 TTGTCTTAGATTCATCTAGATACGGAT 57.478 33.333 4.54 0.00 40.23 4.18
7398 9323 8.919777 TTGTCTTAGATTCATCTAGATACGGA 57.080 34.615 4.54 0.00 40.23 4.69
7399 9324 9.004717 TCTTGTCTTAGATTCATCTAGATACGG 57.995 37.037 4.54 0.00 40.23 4.02
7407 9332 8.964772 CCCAAAATTCTTGTCTTAGATTCATCT 58.035 33.333 0.00 0.00 40.86 2.90
7408 9333 8.960591 TCCCAAAATTCTTGTCTTAGATTCATC 58.039 33.333 0.00 0.00 0.00 2.92
7409 9334 8.743714 GTCCCAAAATTCTTGTCTTAGATTCAT 58.256 33.333 0.00 0.00 0.00 2.57
7410 9335 7.094805 CGTCCCAAAATTCTTGTCTTAGATTCA 60.095 37.037 0.00 0.00 0.00 2.57
7411 9336 7.244192 CGTCCCAAAATTCTTGTCTTAGATTC 58.756 38.462 0.00 0.00 0.00 2.52
7412 9337 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
7413 9338 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
7414 9339 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
7415 9340 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
7416 9341 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
7417 9342 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
7418 9343 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
7419 9344 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
7420 9345 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
7421 9346 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
7422 9347 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
7423 9348 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
7424 9349 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
7425 9350 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
7426 9351 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
7427 9352 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
7428 9353 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
7429 9354 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
7430 9355 0.549950 CTACTACTCCCTCCGTCCCA 59.450 60.000 0.00 0.00 0.00 4.37
7431 9356 0.842635 TCTACTACTCCCTCCGTCCC 59.157 60.000 0.00 0.00 0.00 4.46
7432 9357 1.767681 TCTCTACTACTCCCTCCGTCC 59.232 57.143 0.00 0.00 0.00 4.79
7433 9358 3.469739 CTTCTCTACTACTCCCTCCGTC 58.530 54.545 0.00 0.00 0.00 4.79
7434 9359 2.421811 GCTTCTCTACTACTCCCTCCGT 60.422 54.545 0.00 0.00 0.00 4.69
7435 9360 2.223745 GCTTCTCTACTACTCCCTCCG 58.776 57.143 0.00 0.00 0.00 4.63
7436 9361 2.091775 TGGCTTCTCTACTACTCCCTCC 60.092 54.545 0.00 0.00 0.00 4.30
7437 9362 2.953648 GTGGCTTCTCTACTACTCCCTC 59.046 54.545 0.00 0.00 0.00 4.30
7438 9363 2.358405 GGTGGCTTCTCTACTACTCCCT 60.358 54.545 0.00 0.00 0.00 4.20
7439 9364 2.033372 GGTGGCTTCTCTACTACTCCC 58.967 57.143 0.00 0.00 0.00 4.30
7440 9365 2.033372 GGGTGGCTTCTCTACTACTCC 58.967 57.143 0.00 0.00 0.00 3.85
7441 9366 1.677052 CGGGTGGCTTCTCTACTACTC 59.323 57.143 0.00 0.00 0.00 2.59
7442 9367 1.685491 CCGGGTGGCTTCTCTACTACT 60.685 57.143 0.00 0.00 0.00 2.57
7443 9368 0.745468 CCGGGTGGCTTCTCTACTAC 59.255 60.000 0.00 0.00 0.00 2.73
7444 9369 3.202548 CCGGGTGGCTTCTCTACTA 57.797 57.895 0.00 0.00 0.00 1.82
7469 9394 1.668419 GGCATTACAGGTTCGCAGAT 58.332 50.000 0.00 0.00 35.04 2.90
7528 9453 0.095245 GCATGATCGTGTCCACAACG 59.905 55.000 16.18 0.00 0.00 4.10
7539 9464 1.358877 TCCGAAACACAGCATGATCG 58.641 50.000 0.00 11.21 39.69 3.69
7544 9469 2.027745 AGTCAGATCCGAAACACAGCAT 60.028 45.455 0.00 0.00 0.00 3.79
7567 9496 1.871080 CACAGAAACAGGAAGCGAGT 58.129 50.000 0.00 0.00 0.00 4.18
7568 9497 0.514691 GCACAGAAACAGGAAGCGAG 59.485 55.000 0.00 0.00 0.00 5.03
7569 9498 0.884704 GGCACAGAAACAGGAAGCGA 60.885 55.000 0.00 0.00 0.00 4.93
7570 9499 1.576421 GGCACAGAAACAGGAAGCG 59.424 57.895 0.00 0.00 0.00 4.68
7677 9606 8.969260 TGTAGGAAGTAGAGATAATGACGTAA 57.031 34.615 0.00 0.00 0.00 3.18
7713 9646 3.148279 GTCGGAGGAGGGATGCGT 61.148 66.667 0.00 0.00 32.85 5.24
7745 9680 1.132527 TCAAAACAGAGAGGGGGAGGA 60.133 52.381 0.00 0.00 0.00 3.71
7748 9683 2.921221 AGATCAAAACAGAGAGGGGGA 58.079 47.619 0.00 0.00 0.00 4.81
7776 9716 6.037500 CCGAGTGCAAAAATATCAGAGATGAA 59.962 38.462 0.00 0.00 0.00 2.57
7816 9756 7.014615 GTGAATAAAAGATGGGCCAGTTGATAT 59.985 37.037 13.78 5.27 0.00 1.63
7817 9757 6.321181 GTGAATAAAAGATGGGCCAGTTGATA 59.679 38.462 13.78 2.86 0.00 2.15
7909 9853 4.569719 TGGAACAAGGGAGTAGGATTTC 57.430 45.455 0.00 0.00 31.92 2.17
7924 9868 5.543507 ACCACAGCATTTATTTTGGAACA 57.456 34.783 0.00 0.00 0.00 3.18
7929 9874 9.039870 TGAACTAAAACCACAGCATTTATTTTG 57.960 29.630 0.00 0.00 0.00 2.44
7941 9886 8.887717 CATTCCAAAATTTGAACTAAAACCACA 58.112 29.630 7.37 0.00 0.00 4.17
7987 9933 7.766278 AGAGTGTTATTTATCTGGACATGTGAC 59.234 37.037 1.15 0.00 0.00 3.67
7988 9934 7.851228 AGAGTGTTATTTATCTGGACATGTGA 58.149 34.615 1.15 0.00 0.00 3.58
7989 9935 9.599866 TTAGAGTGTTATTTATCTGGACATGTG 57.400 33.333 1.15 0.00 0.00 3.21
8112 10067 4.469657 ACCTTGAATGCTTTGTAACCAGA 58.530 39.130 0.00 0.00 0.00 3.86
8169 10135 4.072131 GCTGTTGATCTGGGTAGACAAAA 58.928 43.478 0.00 0.00 35.34 2.44
8191 10157 1.623359 GAGCGATCTATAGCCTTGCG 58.377 55.000 0.00 0.00 0.00 4.85
8196 10162 1.341606 GCAACGAGCGATCTATAGCC 58.658 55.000 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.