Multiple sequence alignment - TraesCS1B01G384500

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 TraesCS1B01G384500 chr1B 100.000 8482 0 0 1 8482 617815975 617824456 0.000000e+00 15664
1 TraesCS1B01G384500 chr1B 93.878 147 6 2 5514 5660 617821424 617821567 1.430000e-52 219
2 TraesCS1B01G384500 chr1B 93.878 147 6 2 5450 5593 617821488 617821634 1.430000e-52 219
3 TraesCS1B01G384500 chr1B 93.827 81 2 2 5580 5660 617821424 617821501 1.500000e-22 119
4 TraesCS1B01G384500 chr1B 93.827 81 2 2 5450 5527 617821554 617821634 1.500000e-22 119
5 TraesCS1B01G384500 chr1A 93.134 6700 245 86 1884 8476 545522389 545528980 0.000000e+00 9625
6 TraesCS1B01G384500 chr1A 89.164 1292 82 26 619 1887 545521095 545522351 0.000000e+00 1557
7 TraesCS1B01G384500 chr1A 83.333 354 26 14 1 343 545519996 545520327 6.440000e-76 296
8 TraesCS1B01G384500 chr1A 95.238 147 4 2 5514 5660 545525923 545526066 6.620000e-56 230
9 TraesCS1B01G384500 chr1A 96.296 81 0 2 5580 5660 545525923 545526000 6.910000e-26 130
10 TraesCS1B01G384500 chr1A 92.593 81 3 2 5450 5527 545526053 545526133 6.960000e-21 113
11 TraesCS1B01G384500 chr1D 94.807 2850 83 22 1884 4725 450218955 450221747 0.000000e+00 4383
12 TraesCS1B01G384500 chr1D 95.630 1945 55 13 5520 7443 450222430 450224365 0.000000e+00 3094
13 TraesCS1B01G384500 chr1D 87.363 1915 134 51 1 1884 450217081 450218918 0.000000e+00 2097
14 TraesCS1B01G384500 chr1D 88.725 1082 69 19 7446 8482 450224402 450225475 0.000000e+00 1273
15 TraesCS1B01G384500 chr1D 94.251 835 24 9 4765 5593 450221754 450222570 0.000000e+00 1254
16 TraesCS1B01G384500 chr1D 92.593 81 3 2 5450 5527 450222490 450222570 6.960000e-21 113
17 TraesCS1B01G384500 chr1D 93.333 75 4 1 5586 5660 450222430 450222503 9.000000e-20 110
18 TraesCS1B01G384500 chr3D 75.657 875 174 27 4644 5497 58559164 58560020 4.770000e-107 399
19 TraesCS1B01G384500 chr3A 75.941 478 95 12 5006 5478 67556340 67556802 2.380000e-55 228
20 TraesCS1B01G384500 chr3A 75.523 478 97 12 5006 5478 67527737 67528199 5.160000e-52 217


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 TraesCS1B01G384500 chr1B 617815975 617824456 8481 False 3268.000000 15664 95.082000 1 8482 5 chr1B.!!$F1 8481
1 TraesCS1B01G384500 chr1A 545519996 545528980 8984 False 1991.833333 9625 91.626333 1 8476 6 chr1A.!!$F1 8475
2 TraesCS1B01G384500 chr1D 450217081 450225475 8394 False 1760.571429 4383 92.386000 1 8482 7 chr1D.!!$F1 8481
3 TraesCS1B01G384500 chr3D 58559164 58560020 856 False 399.000000 399 75.657000 4644 5497 1 chr3D.!!$F1 853

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
154 164 0.180642 TGAACAACCCGCACCAAGTA 59.819 50.000 0.00 0.00 0.00 2.24 F
400 536 0.323633 TGCACCTAGCCCTACGTACA 60.324 55.000 0.00 0.00 44.83 2.90 F
1199 1741 0.680061 ATTCCCCGATACTTCGCCTC 59.320 55.000 0.00 0.00 44.12 4.70 F
1559 2110 0.681564 TCTGGGTCCTCTCGCTCTTC 60.682 60.000 0.00 0.00 0.00 2.87 F
1681 2232 0.834612 TGTAGGATTTGGGGCTACCG 59.165 55.000 0.00 0.00 44.64 4.02 F
2126 2725 1.136891 ACACTGTCCCTTTTTGCAAGC 59.863 47.619 0.00 0.00 0.00 4.01 F
3324 3927 1.406341 GGCGTGGTATGGCTCTTTACA 60.406 52.381 0.00 0.00 0.00 2.41 F
3600 4204 0.249120 TCTCATGGCCCAACAGTACG 59.751 55.000 0.00 0.00 0.00 3.67 F
4248 4853 0.317160 TCATCGGTTATGCTAGGCCG 59.683 55.000 0.00 0.00 44.95 6.13 F
4929 5543 0.960364 GCCGTTGCAATTCCTCCTCA 60.960 55.000 0.59 0.00 37.47 3.86 F
5848 6484 1.022982 CATGCATCCACGTCTGCTGT 61.023 55.000 13.55 2.71 39.16 4.40 F
7130 7788 0.888619 AGGAGCTTTGACGACGATGA 59.111 50.000 0.00 0.00 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1157 1699 0.450583 GTTCCCGGCGGAGATTTTTC 59.549 55.000 30.79 4.84 40.10 2.29 R
1255 1800 0.588980 GCCGAATTCGCGAATTGGAC 60.589 55.000 40.43 32.11 40.77 4.02 R
2440 3039 1.459450 TCCCTGCGTTAATTGCCTTC 58.541 50.000 0.00 0.00 0.00 3.46 R
2572 3171 1.818642 AGTCCTCATCAAGCAAGCAC 58.181 50.000 0.00 0.00 0.00 4.40 R
3424 4027 2.290960 GGGTGATTAGTTCCCTTGCAGT 60.291 50.000 0.00 0.00 38.29 4.40 R
3425 4028 2.369394 GGGTGATTAGTTCCCTTGCAG 58.631 52.381 0.00 0.00 38.29 4.41 R
5029 5646 0.172803 GCTGAATCTGCCCTTTGCTG 59.827 55.000 0.27 0.00 42.00 4.41 R
5241 5862 4.769688 ACTTCTGAATGACTGAACACACA 58.230 39.130 0.00 0.00 33.92 3.72 R
5826 6462 1.300971 GCAGACGTGGATGCATGTGT 61.301 55.000 17.57 10.34 42.11 3.72 R
6605 7260 1.546476 AGCCGTCTTACCAGAGTTGAG 59.454 52.381 0.00 0.00 0.00 3.02 R
7467 8163 0.320771 AGCGTCACAAACCCTAGCAG 60.321 55.000 0.00 0.00 0.00 4.24 R
8010 8738 1.389106 GTCCGCACACGAGTTATGAAC 59.611 52.381 0.00 0.00 43.93 3.18 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
144 153 3.254903 GTGAAACCACCTATGAACAACCC 59.745 47.826 0.00 0.00 0.00 4.11
154 164 0.180642 TGAACAACCCGCACCAAGTA 59.819 50.000 0.00 0.00 0.00 2.24
158 168 1.086696 CAACCCGCACCAAGTATCTG 58.913 55.000 0.00 0.00 0.00 2.90
194 204 3.698029 ATGTTAGCATCATTCGTTGGC 57.302 42.857 0.00 0.00 0.00 4.52
220 230 0.951040 GAGAGGTTGAACCACCAGCG 60.951 60.000 17.83 0.00 41.95 5.18
221 231 2.594592 AGGTTGAACCACCAGCGC 60.595 61.111 17.83 0.00 41.95 5.92
224 234 1.008538 GTTGAACCACCAGCGCAAG 60.009 57.895 11.47 1.76 43.44 4.01
225 235 2.192861 TTGAACCACCAGCGCAAGG 61.193 57.895 11.47 14.38 38.28 3.61
235 245 3.178539 GCGCAAGGTCTGTTAGGC 58.821 61.111 0.30 0.00 38.28 3.93
244 254 5.278758 GCAAGGTCTGTTAGGCAACATAAAA 60.279 40.000 3.58 0.00 43.58 1.52
270 280 4.041723 CAGAATGTGTCGGTTTTTGTTCC 58.958 43.478 0.00 0.00 0.00 3.62
274 284 4.457834 TGTGTCGGTTTTTGTTCCATTT 57.542 36.364 0.00 0.00 0.00 2.32
276 286 4.865365 TGTGTCGGTTTTTGTTCCATTTTC 59.135 37.500 0.00 0.00 0.00 2.29
279 289 6.091577 GTGTCGGTTTTTGTTCCATTTTCTTT 59.908 34.615 0.00 0.00 0.00 2.52
281 291 5.517054 TCGGTTTTTGTTCCATTTTCTTTCG 59.483 36.000 0.00 0.00 0.00 3.46
282 292 5.289917 CGGTTTTTGTTCCATTTTCTTTCGT 59.710 36.000 0.00 0.00 0.00 3.85
283 293 6.183360 CGGTTTTTGTTCCATTTTCTTTCGTT 60.183 34.615 0.00 0.00 0.00 3.85
284 294 7.009357 CGGTTTTTGTTCCATTTTCTTTCGTTA 59.991 33.333 0.00 0.00 0.00 3.18
285 295 8.657729 GGTTTTTGTTCCATTTTCTTTCGTTAA 58.342 29.630 0.00 0.00 0.00 2.01
390 526 3.431725 GGCCGTGTTGCACCTAGC 61.432 66.667 0.00 0.00 45.96 3.42
400 536 0.323633 TGCACCTAGCCCTACGTACA 60.324 55.000 0.00 0.00 44.83 2.90
450 586 4.816385 ACAATCAGTTGAAAGATGTCGTGT 59.184 37.500 0.00 0.00 38.71 4.49
459 595 1.931906 AGATGTCGTGTGCATAGCAG 58.068 50.000 0.00 0.00 40.08 4.24
471 607 2.681344 TGCATAGCAGCACTCATCTTTG 59.319 45.455 0.00 0.00 40.11 2.77
472 608 2.541178 GCATAGCAGCACTCATCTTTGC 60.541 50.000 0.00 0.00 39.16 3.68
473 609 2.477845 TAGCAGCACTCATCTTTGCA 57.522 45.000 0.00 0.00 41.48 4.08
474 610 1.835494 AGCAGCACTCATCTTTGCAT 58.165 45.000 0.00 0.00 41.48 3.96
475 611 1.743958 AGCAGCACTCATCTTTGCATC 59.256 47.619 0.00 0.00 41.48 3.91
476 612 1.531264 GCAGCACTCATCTTTGCATCG 60.531 52.381 0.00 0.00 41.48 3.84
477 613 1.063616 CAGCACTCATCTTTGCATCGG 59.936 52.381 0.00 0.00 41.48 4.18
478 614 1.089920 GCACTCATCTTTGCATCGGT 58.910 50.000 0.00 0.00 38.68 4.69
481 617 3.751621 CACTCATCTTTGCATCGGTTTC 58.248 45.455 0.00 0.00 0.00 2.78
482 618 2.416547 ACTCATCTTTGCATCGGTTTCG 59.583 45.455 0.00 0.00 37.82 3.46
522 658 2.644798 ACCACTCTAATCAAACCCTGCT 59.355 45.455 0.00 0.00 0.00 4.24
538 674 8.925700 CAAACCCTGCTTAGATATTTTTGTTTC 58.074 33.333 0.00 0.00 0.00 2.78
539 675 6.852664 ACCCTGCTTAGATATTTTTGTTTCG 58.147 36.000 0.00 0.00 0.00 3.46
540 676 6.433093 ACCCTGCTTAGATATTTTTGTTTCGT 59.567 34.615 0.00 0.00 0.00 3.85
541 677 7.039993 ACCCTGCTTAGATATTTTTGTTTCGTT 60.040 33.333 0.00 0.00 0.00 3.85
542 678 7.812669 CCCTGCTTAGATATTTTTGTTTCGTTT 59.187 33.333 0.00 0.00 0.00 3.60
543 679 8.638565 CCTGCTTAGATATTTTTGTTTCGTTTG 58.361 33.333 0.00 0.00 0.00 2.93
544 680 9.180678 CTGCTTAGATATTTTTGTTTCGTTTGT 57.819 29.630 0.00 0.00 0.00 2.83
545 681 9.522804 TGCTTAGATATTTTTGTTTCGTTTGTT 57.477 25.926 0.00 0.00 0.00 2.83
549 685 7.626446 AGATATTTTTGTTTCGTTTGTTTGGC 58.374 30.769 0.00 0.00 0.00 4.52
606 1118 9.265901 CATCCATACTATCTCTGTTTGTTTAGG 57.734 37.037 0.00 0.00 0.00 2.69
607 1119 8.603898 TCCATACTATCTCTGTTTGTTTAGGA 57.396 34.615 0.00 0.00 0.00 2.94
611 1129 6.174049 ACTATCTCTGTTTGTTTAGGAAGGC 58.826 40.000 0.00 0.00 0.00 4.35
613 1131 4.985538 TCTCTGTTTGTTTAGGAAGGCAT 58.014 39.130 0.00 0.00 0.00 4.40
807 1328 2.378634 GCACTGGGTCTATGGGCCT 61.379 63.158 4.53 0.00 0.00 5.19
974 1513 1.149627 CCCAGGTCAACCGTTTCCA 59.850 57.895 5.41 0.00 42.08 3.53
1079 1618 2.897207 GCCCGCCCCATTAAAACC 59.103 61.111 0.00 0.00 0.00 3.27
1115 1654 0.933700 CTTCTCCTCCTCCTCCTCCT 59.066 60.000 0.00 0.00 0.00 3.69
1116 1655 0.930726 TTCTCCTCCTCCTCCTCCTC 59.069 60.000 0.00 0.00 0.00 3.71
1117 1656 0.996762 TCTCCTCCTCCTCCTCCTCC 60.997 65.000 0.00 0.00 0.00 4.30
1148 1690 1.133869 CGCACCCGAATTCCGAAAC 59.866 57.895 0.00 0.00 41.76 2.78
1199 1741 0.680061 ATTCCCCGATACTTCGCCTC 59.320 55.000 0.00 0.00 44.12 4.70
1200 1742 1.731433 TTCCCCGATACTTCGCCTCG 61.731 60.000 0.00 0.00 44.12 4.63
1201 1743 2.487532 CCCCGATACTTCGCCTCGT 61.488 63.158 0.00 0.00 44.12 4.18
1202 1744 1.168407 CCCCGATACTTCGCCTCGTA 61.168 60.000 0.00 0.00 44.12 3.43
1206 1748 1.739618 GATACTTCGCCTCGTACGTG 58.260 55.000 16.05 13.00 0.00 4.49
1208 1750 2.257286 TACTTCGCCTCGTACGTGCC 62.257 60.000 16.05 1.07 0.00 5.01
1209 1751 3.338126 CTTCGCCTCGTACGTGCCT 62.338 63.158 16.05 0.00 0.00 4.75
1215 1757 4.735132 TCGTACGTGCCTGCCTGC 62.735 66.667 16.05 0.00 0.00 4.85
1230 1775 4.439700 CCTGCCTGCAAGTAAGAATCATTG 60.440 45.833 0.00 0.00 0.00 2.82
1236 1781 6.183360 CCTGCAAGTAAGAATCATTGTCGATT 60.183 38.462 0.00 0.00 38.32 3.34
1241 1786 8.446273 CAAGTAAGAATCATTGTCGATTGAACT 58.554 33.333 0.00 0.00 35.74 3.01
1242 1787 8.553459 AGTAAGAATCATTGTCGATTGAACTT 57.447 30.769 15.39 15.39 35.74 2.66
1245 1790 7.301068 AGAATCATTGTCGATTGAACTTCTC 57.699 36.000 0.00 0.00 35.74 2.87
1247 1792 7.605691 AGAATCATTGTCGATTGAACTTCTCTT 59.394 33.333 0.00 0.00 35.74 2.85
1255 1800 3.508845 TTGAACTTCTCTTCCCCCTTG 57.491 47.619 0.00 0.00 0.00 3.61
1266 1811 2.406616 CCCCCTTGTCCAATTCGCG 61.407 63.158 0.00 0.00 0.00 5.87
1310 1856 0.857287 GCTTTGCTGCTGCTTTGTTC 59.143 50.000 17.00 0.00 40.48 3.18
1311 1857 1.803625 GCTTTGCTGCTGCTTTGTTCA 60.804 47.619 17.00 0.00 40.48 3.18
1316 1862 1.598924 GCTGCTGCTTTGTTCACTGAC 60.599 52.381 8.53 0.00 36.03 3.51
1321 1867 3.793492 GCTGCTTTGTTCACTGACTTTTC 59.207 43.478 0.00 0.00 0.00 2.29
1331 1877 1.003839 TGACTTTTCCTGCGCGGAT 60.004 52.632 20.25 4.79 42.70 4.18
1367 1913 4.400961 GCCTGGAGCTTCGCTGGT 62.401 66.667 0.00 0.00 39.88 4.00
1377 1923 1.764851 CTTCGCTGGTGAGATCGATC 58.235 55.000 17.91 17.91 0.00 3.69
1439 1985 2.890311 CCAGGCCATGTGAGTACAAAAA 59.110 45.455 5.01 0.00 40.84 1.94
1501 2051 5.768752 TGGTTAGGGTGTTTACTTCCTTTT 58.231 37.500 0.00 0.00 0.00 2.27
1502 2052 6.196434 TGGTTAGGGTGTTTACTTCCTTTTT 58.804 36.000 0.00 0.00 0.00 1.94
1503 2053 6.321945 TGGTTAGGGTGTTTACTTCCTTTTTC 59.678 38.462 0.00 0.00 0.00 2.29
1559 2110 0.681564 TCTGGGTCCTCTCGCTCTTC 60.682 60.000 0.00 0.00 0.00 2.87
1579 2130 7.175119 GCTCTTCCCTGTATGAACTTAGTTTTT 59.825 37.037 0.00 0.00 0.00 1.94
1610 2161 7.565323 TTTCTTCAATTTTCAATGTTTGGGG 57.435 32.000 0.00 0.00 0.00 4.96
1640 2191 8.827177 ATAGGCTCGTATTTTGATTATTTCGA 57.173 30.769 0.00 0.00 0.00 3.71
1681 2232 0.834612 TGTAGGATTTGGGGCTACCG 59.165 55.000 0.00 0.00 44.64 4.02
1730 2281 9.977762 GTAAAAGTCTACATGTAAAAATACCCG 57.022 33.333 7.06 0.00 0.00 5.28
1847 2402 5.403512 TCCCCTATACTCTTACAATGGGAG 58.596 45.833 0.00 0.00 34.67 4.30
1871 2426 3.871594 GACAGCTTACCTAATGCGTGAAT 59.128 43.478 0.00 0.00 0.00 2.57
1991 2590 3.687212 TGATGCCACGTGTATAAACCAAG 59.313 43.478 15.65 0.00 0.00 3.61
2031 2630 7.620880 TCCAACTAATAATCAGTGCTACTGTT 58.379 34.615 13.59 10.52 46.03 3.16
2042 2641 8.628882 ATCAGTGCTACTGTTTTAACAAAAAC 57.371 30.769 13.59 6.76 46.03 2.43
2043 2642 7.594714 TCAGTGCTACTGTTTTAACAAAAACA 58.405 30.769 13.88 13.88 46.03 2.83
2126 2725 1.136891 ACACTGTCCCTTTTTGCAAGC 59.863 47.619 0.00 0.00 0.00 4.01
2177 2776 6.811170 CACCTGTAATCACAAAGTGTTGTTTT 59.189 34.615 0.00 0.00 46.01 2.43
2230 2829 2.462456 TGCTGTAGTTCCTTGCAGAG 57.538 50.000 0.00 0.00 0.00 3.35
2440 3039 7.334858 AGACTAAAATAGCCTCCTTCAAGAAG 58.665 38.462 2.83 2.83 38.14 2.85
2572 3171 1.725931 GCCGTTGAAGCATTTCGACAG 60.726 52.381 6.82 0.00 44.63 3.51
2599 3198 1.466167 CTTGATGAGGACTTGTTGCCG 59.534 52.381 0.00 0.00 0.00 5.69
2678 3277 6.153067 GGTCTTAATCTGACCGTATGATCTG 58.847 44.000 0.00 0.00 43.55 2.90
2725 3324 1.808343 GGAAACCGTGTACCAATGTCC 59.192 52.381 0.00 0.00 0.00 4.02
2737 3336 3.711863 ACCAATGTCCATTGCCTATGTT 58.288 40.909 13.34 0.00 45.06 2.71
2904 3506 5.061853 AGCTTATGTGGTCTGATATGCTTG 58.938 41.667 0.00 0.00 33.85 4.01
3132 3735 8.783660 ATAAAGATGGAAGACCTGTCTATGTA 57.216 34.615 0.00 0.00 39.39 2.29
3279 3882 1.597027 AAAACGGCACCTGGACTCG 60.597 57.895 0.00 3.22 0.00 4.18
3285 3888 2.737180 CACCTGGACTCGTGCACT 59.263 61.111 16.19 0.00 0.00 4.40
3324 3927 1.406341 GGCGTGGTATGGCTCTTTACA 60.406 52.381 0.00 0.00 0.00 2.41
3424 4027 5.621193 AGGGATTGAAGAACTTCTCGAAAA 58.379 37.500 14.31 2.40 40.14 2.29
3425 4028 5.470437 AGGGATTGAAGAACTTCTCGAAAAC 59.530 40.000 14.31 1.64 40.14 2.43
3465 4068 1.392853 CGACTGCAGAAGATTGACAGC 59.607 52.381 23.35 0.00 31.46 4.40
3600 4204 0.249120 TCTCATGGCCCAACAGTACG 59.751 55.000 0.00 0.00 0.00 3.67
3663 4267 5.705441 CCGGATGTACATAATTAATGCTGGT 59.295 40.000 8.71 0.00 39.39 4.00
3915 4519 5.308014 TCTTGTCTGTGCATGTCTATGTTT 58.692 37.500 0.00 0.00 36.65 2.83
4101 4705 5.591472 CCAAAGAGAGGATATTTCATGCACA 59.409 40.000 0.00 0.00 0.00 4.57
4102 4706 6.238676 CCAAAGAGAGGATATTTCATGCACAG 60.239 42.308 0.00 0.00 0.00 3.66
4103 4707 5.627182 AGAGAGGATATTTCATGCACAGT 57.373 39.130 0.00 0.00 0.00 3.55
4248 4853 0.317160 TCATCGGTTATGCTAGGCCG 59.683 55.000 0.00 0.00 44.95 6.13
4406 5011 1.003580 TGGGTCTGAAGTGGAAGATGC 59.996 52.381 0.00 0.00 0.00 3.91
4440 5045 2.107378 TGCACCAAAGACCCTCATAACA 59.893 45.455 0.00 0.00 0.00 2.41
4509 5114 5.940192 TGTTGAGCGTACAATCAAGAAAT 57.060 34.783 9.39 0.00 36.16 2.17
4534 5139 3.067742 GGCATTATCAGCAGTTCAGCATT 59.932 43.478 0.00 0.00 36.85 3.56
4735 5340 8.115490 AGAAGCAAAGTCTAATTACAGCAAAT 57.885 30.769 0.00 0.00 0.00 2.32
4929 5543 0.960364 GCCGTTGCAATTCCTCCTCA 60.960 55.000 0.59 0.00 37.47 3.86
4961 5576 9.528489 TTTCTATAAGCATAAAAACTTGGAGGT 57.472 29.630 0.00 0.00 0.00 3.85
4976 5591 4.668138 TGGAGGTACAGCCCTAAAAATT 57.332 40.909 0.00 0.00 38.26 1.82
5029 5646 7.412853 CAAGCAACTAGAATGATTATGTCCAC 58.587 38.462 0.00 0.00 0.00 4.02
5150 5767 2.189676 TGAGCAAATGGGCAATGGAAT 58.810 42.857 0.00 0.00 35.83 3.01
5478 6111 6.128090 TGCTGAAACTGATCAAATGCTTCTAG 60.128 38.462 0.00 0.00 0.00 2.43
5547 6181 8.846943 TGAAACTGATCAAATGCTTCTACTAA 57.153 30.769 0.00 0.00 0.00 2.24
5554 6188 6.817765 TCAAATGCTTCTACTAACAAAGGG 57.182 37.500 0.00 0.00 0.00 3.95
5572 6206 9.506018 AACAAAGGGAAATGGAATTATTCTTTG 57.494 29.630 4.87 0.00 43.64 2.77
5577 6211 9.050154 AGGGAAATGGAATTATTCTTTGAACAT 57.950 29.630 4.87 0.00 33.67 2.71
5593 6227 9.086336 TCTTTGAACATTCATTTGAACTGAAAC 57.914 29.630 2.06 0.00 36.30 2.78
5610 6244 7.138692 ACTGAAACTGATCAAATGCTTCTAC 57.861 36.000 0.00 0.00 0.00 2.59
5848 6484 1.022982 CATGCATCCACGTCTGCTGT 61.023 55.000 13.55 2.71 39.16 4.40
5951 6587 6.712547 CAGTGTCTTCTTCCTCAGGTATTTTT 59.287 38.462 0.00 0.00 0.00 1.94
6085 6725 5.997384 AAATAGTTACCGAGTCCAAGAGT 57.003 39.130 0.00 0.00 0.00 3.24
6091 6731 3.157750 ACCGAGTCCAAGAGTTAGTCT 57.842 47.619 0.00 0.00 36.94 3.24
6092 6732 4.298103 ACCGAGTCCAAGAGTTAGTCTA 57.702 45.455 0.00 0.00 32.65 2.59
6202 6857 4.017499 ACCACCATAACCCTTTGAGCTAAT 60.017 41.667 0.00 0.00 0.00 1.73
6280 6935 5.567430 AGTGTAACCCTGAAAATAACCCTC 58.433 41.667 0.00 0.00 37.80 4.30
6293 6948 2.978156 AACCCTCCTGCTTGATTGAA 57.022 45.000 0.00 0.00 0.00 2.69
6323 6978 4.786927 GCGCACTGTATTGTGTGTTTGTTA 60.787 41.667 0.30 0.00 46.54 2.41
6404 7059 3.000041 CACATTCGAAGGAATTCGGACA 59.000 45.455 17.88 0.00 40.90 4.02
6453 7108 1.234615 CGTGACCCTTTTCGCCATGT 61.235 55.000 0.00 0.00 0.00 3.21
6605 7260 3.181474 CCTACACGGAGAAGGAAATCCTC 60.181 52.174 1.68 0.00 39.63 3.71
7039 7697 4.192317 GGTACTGCCATCTTAAGGTCTTG 58.808 47.826 1.85 0.00 37.17 3.02
7068 7726 1.588404 CTTCTGTACTAATGCGTGCCG 59.412 52.381 0.00 0.00 0.00 5.69
7119 7777 3.717452 ATTCTGCTTCTGAGGAGCTTT 57.283 42.857 14.82 0.00 40.81 3.51
7129 7787 1.272781 GAGGAGCTTTGACGACGATG 58.727 55.000 0.00 0.00 0.00 3.84
7130 7788 0.888619 AGGAGCTTTGACGACGATGA 59.111 50.000 0.00 0.00 0.00 2.92
7271 7930 4.625311 TGTCGTGAGTGTAAATGCATGTAG 59.375 41.667 0.00 0.00 0.00 2.74
7283 7943 5.581126 AATGCATGTAGTTTGTGTATGGG 57.419 39.130 0.00 0.00 0.00 4.00
7296 7956 1.349688 TGTATGGGAAAGAAGGCGTGT 59.650 47.619 0.00 0.00 0.00 4.49
7360 8020 1.065418 GGATCCTGAAATCACCACGGT 60.065 52.381 3.84 0.00 0.00 4.83
7361 8021 2.169769 GGATCCTGAAATCACCACGGTA 59.830 50.000 3.84 0.00 0.00 4.02
7467 8163 5.291128 CGTGTATGAACCTATTGTGACCTTC 59.709 44.000 0.00 0.00 0.00 3.46
7519 8215 5.856126 TGTCGCATCTTTTTAATTCGACT 57.144 34.783 12.06 0.00 43.35 4.18
7565 8261 1.374947 CAAGGGAGGGCTCGTTTCA 59.625 57.895 0.00 0.00 0.00 2.69
7566 8262 0.035056 CAAGGGAGGGCTCGTTTCAT 60.035 55.000 0.00 0.00 0.00 2.57
7572 8268 1.740025 GAGGGCTCGTTTCATTGAAGG 59.260 52.381 0.00 0.00 0.00 3.46
7595 8291 1.448722 CGTGACGTGTTCAAAAACCG 58.551 50.000 0.00 0.00 35.39 4.44
7597 8293 2.474196 CGTGACGTGTTCAAAAACCGAA 60.474 45.455 0.00 0.00 35.39 4.30
7610 8306 8.705134 GTTCAAAAACCGAAATTCCGAATTAAT 58.295 29.630 6.79 0.00 0.00 1.40
7618 8314 7.094118 ACCGAAATTCCGAATTAATGAAAAGGA 60.094 33.333 6.79 0.00 0.00 3.36
7677 8373 5.669164 AGAGTATCCTTGTCTTGGTCTTC 57.331 43.478 0.00 0.00 33.66 2.87
7685 8381 5.070001 CCTTGTCTTGGTCTTCAATGGTTA 58.930 41.667 0.00 0.00 34.45 2.85
7686 8382 5.048713 CCTTGTCTTGGTCTTCAATGGTTAC 60.049 44.000 0.00 0.00 34.45 2.50
7742 8453 5.048921 ACTTGCTGTTCAATGTTGAGATGAG 60.049 40.000 0.00 0.00 38.61 2.90
7764 8475 1.523758 CCATGCGGCCTTATTACCTC 58.476 55.000 0.00 0.00 0.00 3.85
7765 8476 1.148310 CATGCGGCCTTATTACCTCG 58.852 55.000 0.00 0.00 0.00 4.63
7766 8477 0.602905 ATGCGGCCTTATTACCTCGC 60.603 55.000 0.00 0.00 42.90 5.03
7767 8478 1.227438 GCGGCCTTATTACCTCGCA 60.227 57.895 0.00 0.00 42.27 5.10
7819 8546 4.860907 GGTTCAGCTTCATAATTTGCACAG 59.139 41.667 0.00 0.00 0.00 3.66
7837 8564 6.156932 GCACAGGCAAAATTTTGATACTTC 57.843 37.500 30.40 13.71 40.55 3.01
7838 8565 5.695816 GCACAGGCAAAATTTTGATACTTCA 59.304 36.000 30.40 0.00 40.55 3.02
7859 8587 5.964758 TCAGATGGTTGCCAATATTTTGAC 58.035 37.500 0.00 0.00 36.95 3.18
7862 8590 5.481473 AGATGGTTGCCAATATTTTGACACT 59.519 36.000 0.00 0.00 36.95 3.55
7863 8591 5.543507 TGGTTGCCAATATTTTGACACTT 57.456 34.783 0.00 0.00 34.60 3.16
7893 8621 5.541845 TCCATAGCCAATTCTAGTTCGATG 58.458 41.667 0.00 0.00 0.00 3.84
7913 8641 4.209307 TGTTCTTACCAACAGTGACACA 57.791 40.909 8.59 0.00 32.36 3.72
7925 8653 3.056891 ACAGTGACACAACCAAAACCAAG 60.057 43.478 8.59 0.00 0.00 3.61
8010 8738 3.571401 ACTGCTGAAAAATGTCCTTCAGG 59.429 43.478 12.37 1.63 45.71 3.86
8081 8809 9.976511 ATACTTTCTCGAATTATATTTGTCCGA 57.023 29.630 0.00 0.00 0.00 4.55
8311 9062 3.736100 CCAAGCATCAACGGCGCA 61.736 61.111 10.83 0.00 36.08 6.09
8406 9165 1.079256 CTCCCTCCACCACTCCTCA 59.921 63.158 0.00 0.00 0.00 3.86
8478 9237 4.711399 AGAACCGTAAGTAAATATGCCCC 58.289 43.478 0.00 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 12 7.650504 CAGCAGCAGTTTACTATACCGTTTATA 59.349 37.037 0.00 0.00 0.00 0.98
175 185 1.742831 GGCCAACGAATGATGCTAACA 59.257 47.619 0.00 0.00 0.00 2.41
207 217 2.192861 CCTTGCGCTGGTGGTTCAA 61.193 57.895 9.73 0.00 0.00 2.69
220 230 1.604604 TGTTGCCTAACAGACCTTGC 58.395 50.000 0.00 0.00 41.66 4.01
229 239 9.855021 ACATTCTGTTATTTTATGTTGCCTAAC 57.145 29.630 0.00 0.00 37.32 2.34
230 240 9.853555 CACATTCTGTTATTTTATGTTGCCTAA 57.146 29.630 0.00 0.00 0.00 2.69
231 241 9.019656 ACACATTCTGTTATTTTATGTTGCCTA 57.980 29.630 0.00 0.00 0.00 3.93
232 242 7.895759 ACACATTCTGTTATTTTATGTTGCCT 58.104 30.769 0.00 0.00 0.00 4.75
233 243 7.008266 CGACACATTCTGTTATTTTATGTTGCC 59.992 37.037 0.00 0.00 31.03 4.52
234 244 7.008266 CCGACACATTCTGTTATTTTATGTTGC 59.992 37.037 0.00 0.00 31.03 4.17
235 245 8.020819 ACCGACACATTCTGTTATTTTATGTTG 58.979 33.333 0.00 0.00 31.03 3.33
244 254 6.385649 ACAAAAACCGACACATTCTGTTAT 57.614 33.333 0.00 0.00 30.93 1.89
314 324 8.915654 GTTTCGCAAAAGATTTACTTCATCATT 58.084 29.630 0.00 0.00 37.93 2.57
335 345 9.514822 TCGTTTCGTTTGTAAAATATAGTTTCG 57.485 29.630 0.66 0.00 0.00 3.46
345 468 7.166142 GTGGATTGAATCGTTTCGTTTGTAAAA 59.834 33.333 0.00 0.00 34.39 1.52
390 526 2.651455 TCAGACCATCTGTACGTAGGG 58.349 52.381 0.00 0.00 44.58 3.53
400 536 4.375272 CGATACTGCAAATCAGACCATCT 58.625 43.478 8.88 0.00 45.72 2.90
450 586 2.681344 CAAAGATGAGTGCTGCTATGCA 59.319 45.455 0.00 0.00 41.05 3.96
459 595 1.089920 ACCGATGCAAAGATGAGTGC 58.910 50.000 0.00 0.00 41.29 4.40
471 607 4.609691 TTTTTCCTATCGAAACCGATGC 57.390 40.909 10.18 0.00 45.33 3.91
489 625 5.833131 TGATTAGAGTGGTTGGCTTCTTTTT 59.167 36.000 0.00 0.00 0.00 1.94
490 626 5.385198 TGATTAGAGTGGTTGGCTTCTTTT 58.615 37.500 0.00 0.00 0.00 2.27
494 630 4.082733 GGTTTGATTAGAGTGGTTGGCTTC 60.083 45.833 0.00 0.00 0.00 3.86
498 634 3.758554 CAGGGTTTGATTAGAGTGGTTGG 59.241 47.826 0.00 0.00 0.00 3.77
543 679 9.819267 ATATCTAGTAGTCTTGTTTAGCCAAAC 57.181 33.333 0.34 0.34 43.67 2.93
545 681 9.422681 AGATATCTAGTAGTCTTGTTTAGCCAA 57.577 33.333 2.53 0.00 0.00 4.52
546 682 8.851145 CAGATATCTAGTAGTCTTGTTTAGCCA 58.149 37.037 4.54 0.00 0.00 4.75
547 683 8.852135 ACAGATATCTAGTAGTCTTGTTTAGCC 58.148 37.037 4.54 0.00 0.00 3.93
570 1082 9.689976 CAGAGATAGTATGGATGAAAAGTACAG 57.310 37.037 0.00 0.00 0.00 2.74
575 1087 9.388506 ACAAACAGAGATAGTATGGATGAAAAG 57.611 33.333 0.00 0.00 0.00 2.27
580 1092 9.265901 CCTAAACAAACAGAGATAGTATGGATG 57.734 37.037 0.00 0.00 0.00 3.51
581 1093 9.213777 TCCTAAACAAACAGAGATAGTATGGAT 57.786 33.333 0.00 0.00 0.00 3.41
583 1095 9.319143 CTTCCTAAACAAACAGAGATAGTATGG 57.681 37.037 0.00 0.00 0.00 2.74
584 1096 9.319143 CCTTCCTAAACAAACAGAGATAGTATG 57.681 37.037 0.00 0.00 0.00 2.39
585 1097 7.988028 GCCTTCCTAAACAAACAGAGATAGTAT 59.012 37.037 0.00 0.00 0.00 2.12
586 1098 7.038587 TGCCTTCCTAAACAAACAGAGATAGTA 60.039 37.037 0.00 0.00 0.00 1.82
587 1099 6.174049 GCCTTCCTAAACAAACAGAGATAGT 58.826 40.000 0.00 0.00 0.00 2.12
588 1100 6.173339 TGCCTTCCTAAACAAACAGAGATAG 58.827 40.000 0.00 0.00 0.00 2.08
589 1101 6.121776 TGCCTTCCTAAACAAACAGAGATA 57.878 37.500 0.00 0.00 0.00 1.98
590 1102 4.985538 TGCCTTCCTAAACAAACAGAGAT 58.014 39.130 0.00 0.00 0.00 2.75
591 1103 4.431416 TGCCTTCCTAAACAAACAGAGA 57.569 40.909 0.00 0.00 0.00 3.10
592 1104 4.616835 GCATGCCTTCCTAAACAAACAGAG 60.617 45.833 6.36 0.00 0.00 3.35
604 1116 3.301794 TGATACATTGCATGCCTTCCT 57.698 42.857 16.68 0.00 0.00 3.36
605 1117 3.570975 TGATGATACATTGCATGCCTTCC 59.429 43.478 16.68 0.00 0.00 3.46
606 1118 4.841443 TGATGATACATTGCATGCCTTC 57.159 40.909 16.68 6.07 0.00 3.46
607 1119 6.904463 TTATGATGATACATTGCATGCCTT 57.096 33.333 16.68 0.00 0.00 4.35
794 1315 2.832498 GCTCAGGCCCATAGACCC 59.168 66.667 0.00 0.00 0.00 4.46
1037 1576 1.748500 GGCAGGGAGAAGAAGCAGC 60.749 63.158 0.00 0.00 0.00 5.25
1038 1577 1.449246 CGGCAGGGAGAAGAAGCAG 60.449 63.158 0.00 0.00 0.00 4.24
1039 1578 2.665000 CGGCAGGGAGAAGAAGCA 59.335 61.111 0.00 0.00 0.00 3.91
1079 1618 0.610687 AAGCTTCTCCTTCTCCCACG 59.389 55.000 0.00 0.00 0.00 4.94
1137 1679 2.000447 CACCTCTCGGTTTCGGAATTC 59.000 52.381 0.00 0.00 42.13 2.17
1148 1690 2.271800 CGGAGATTTTTCACCTCTCGG 58.728 52.381 0.00 0.00 36.99 4.63
1157 1699 0.450583 GTTCCCGGCGGAGATTTTTC 59.549 55.000 30.79 4.84 40.10 2.29
1190 1732 2.126580 GCACGTACGAGGCGAAGT 60.127 61.111 24.41 0.00 0.00 3.01
1191 1733 2.879462 GGCACGTACGAGGCGAAG 60.879 66.667 24.41 3.60 0.00 3.79
1200 1742 2.668212 TTGCAGGCAGGCACGTAC 60.668 61.111 3.20 0.00 44.86 3.67
1201 1743 1.822114 TACTTGCAGGCAGGCACGTA 61.822 55.000 13.73 13.73 43.41 3.57
1202 1744 2.674563 TTACTTGCAGGCAGGCACGT 62.675 55.000 15.38 15.38 46.36 4.49
1206 1748 1.403323 GATTCTTACTTGCAGGCAGGC 59.597 52.381 3.06 0.00 0.00 4.85
1208 1750 4.157289 ACAATGATTCTTACTTGCAGGCAG 59.843 41.667 0.00 0.00 0.00 4.85
1209 1751 4.081406 ACAATGATTCTTACTTGCAGGCA 58.919 39.130 0.00 0.00 0.00 4.75
1215 1757 8.446273 AGTTCAATCGACAATGATTCTTACTTG 58.554 33.333 0.00 0.00 36.46 3.16
1230 1775 3.263261 GGGGAAGAGAAGTTCAATCGAC 58.737 50.000 5.50 0.00 0.00 4.20
1236 1781 2.372172 GACAAGGGGGAAGAGAAGTTCA 59.628 50.000 5.50 0.00 0.00 3.18
1241 1786 1.827792 TTGGACAAGGGGGAAGAGAA 58.172 50.000 0.00 0.00 0.00 2.87
1242 1787 2.059756 ATTGGACAAGGGGGAAGAGA 57.940 50.000 0.00 0.00 0.00 3.10
1245 1790 1.463674 CGAATTGGACAAGGGGGAAG 58.536 55.000 0.00 0.00 0.00 3.46
1247 1792 1.001393 GCGAATTGGACAAGGGGGA 60.001 57.895 0.00 0.00 0.00 4.81
1255 1800 0.588980 GCCGAATTCGCGAATTGGAC 60.589 55.000 40.43 32.11 40.77 4.02
1301 1847 4.016444 AGGAAAAGTCAGTGAACAAAGCA 58.984 39.130 0.00 0.00 0.00 3.91
1303 1849 4.354587 GCAGGAAAAGTCAGTGAACAAAG 58.645 43.478 0.00 0.00 0.00 2.77
1310 1856 1.205064 CGCGCAGGAAAAGTCAGTG 59.795 57.895 8.75 0.00 0.00 3.66
1311 1857 1.961277 CCGCGCAGGAAAAGTCAGT 60.961 57.895 8.75 0.00 45.00 3.41
1367 1913 1.903890 GGCTCCGGGATCGATCTCA 60.904 63.158 24.53 5.62 39.00 3.27
1439 1985 8.097662 TCCATAAAAGGAAACAAACAAACACTT 58.902 29.630 0.00 0.00 33.93 3.16
1440 1986 7.616313 TCCATAAAAGGAAACAAACAAACACT 58.384 30.769 0.00 0.00 33.93 3.55
1441 1987 7.835634 TCCATAAAAGGAAACAAACAAACAC 57.164 32.000 0.00 0.00 33.93 3.32
1477 2027 4.635699 AGGAAGTAAACACCCTAACCAG 57.364 45.455 0.00 0.00 0.00 4.00
1583 2134 9.288124 CCCAAACATTGAAAATTGAAGAAAAAC 57.712 29.630 0.00 0.00 0.00 2.43
1586 2137 7.115414 ACCCCAAACATTGAAAATTGAAGAAA 58.885 30.769 0.00 0.00 0.00 2.52
1587 2138 6.657875 ACCCCAAACATTGAAAATTGAAGAA 58.342 32.000 0.00 0.00 0.00 2.52
1588 2139 6.245890 ACCCCAAACATTGAAAATTGAAGA 57.754 33.333 0.00 0.00 0.00 2.87
1589 2140 6.940831 AACCCCAAACATTGAAAATTGAAG 57.059 33.333 0.00 0.00 0.00 3.02
1590 2141 8.807948 TTTAACCCCAAACATTGAAAATTGAA 57.192 26.923 0.00 0.00 0.00 2.69
1591 2142 8.986929 ATTTAACCCCAAACATTGAAAATTGA 57.013 26.923 0.00 0.00 0.00 2.57
1681 2232 5.183904 ACTGTTAAATGAAGAACATGCTCCC 59.816 40.000 0.00 0.00 39.39 4.30
1713 2264 6.070653 ACAGGAGTCGGGTATTTTTACATGTA 60.071 38.462 0.08 0.08 0.00 2.29
1847 2402 2.348666 CACGCATTAGGTAAGCTGTCAC 59.651 50.000 0.00 0.00 0.00 3.67
1959 2558 3.122297 CACGTGGCATCAAAAACACAAT 58.878 40.909 7.95 0.00 33.62 2.71
1963 2562 5.690997 TTATACACGTGGCATCAAAAACA 57.309 34.783 21.57 0.00 0.00 2.83
2036 2635 8.702438 CCTTGCACTGATTATTAGTTGTTTTTG 58.298 33.333 0.00 0.00 0.00 2.44
2042 2641 7.383102 AGAACCTTGCACTGATTATTAGTTG 57.617 36.000 0.00 0.00 0.00 3.16
2043 2642 7.575720 GCAAGAACCTTGCACTGATTATTAGTT 60.576 37.037 22.33 0.00 44.34 2.24
2044 2643 6.127897 GCAAGAACCTTGCACTGATTATTAGT 60.128 38.462 22.33 0.00 44.34 2.24
2093 2692 3.303791 GGGACAGTGTCGTCAATTTTGTC 60.304 47.826 16.89 0.00 37.66 3.18
2126 2725 2.205022 TGAAGATTCAGCAAGGGTGG 57.795 50.000 0.00 0.00 32.50 4.61
2177 2776 5.603596 CCAAATACAGTTACCCGTATGCTA 58.396 41.667 0.00 0.00 0.00 3.49
2230 2829 4.464597 AGTGGGCTAGCTAGATAATAGTGC 59.535 45.833 25.15 6.11 0.00 4.40
2283 2882 4.450976 TGTAGTCAAAGCAAAAGCAGAGA 58.549 39.130 0.00 0.00 0.00 3.10
2284 2883 4.818534 TGTAGTCAAAGCAAAAGCAGAG 57.181 40.909 0.00 0.00 0.00 3.35
2440 3039 1.459450 TCCCTGCGTTAATTGCCTTC 58.541 50.000 0.00 0.00 0.00 3.46
2572 3171 1.818642 AGTCCTCATCAAGCAAGCAC 58.181 50.000 0.00 0.00 0.00 4.40
2599 3198 3.058570 TGTGGTAATCGTCATGTTGTTGC 60.059 43.478 0.00 0.00 0.00 4.17
2611 3210 2.804527 CCTCAGCATCATGTGGTAATCG 59.195 50.000 0.00 0.00 36.63 3.34
2678 3277 3.384789 GTGGGGCTATTGGAAAGAAATCC 59.615 47.826 0.00 0.00 40.10 3.01
2725 3324 4.439700 CCTCTTGAGCAAACATAGGCAATG 60.440 45.833 0.00 0.00 41.74 2.82
2737 3336 5.129320 TCTGTAATGATAGCCTCTTGAGCAA 59.871 40.000 0.00 0.00 0.00 3.91
2904 3506 3.099141 TCCCAAATTCCTTTCTCCATGC 58.901 45.455 0.00 0.00 0.00 4.06
3037 3640 6.648192 ACTCAGAGTAATCAAATTCCTGAGG 58.352 40.000 17.33 0.00 46.06 3.86
3132 3735 7.175104 TGGCATCAACTTTTCCTATTAACTCT 58.825 34.615 0.00 0.00 0.00 3.24
3166 3769 5.404946 TCGGTCTATAGTTGTTACTTGCAC 58.595 41.667 0.00 0.00 35.78 4.57
3285 3888 3.741075 CGCCTTGCACATCCAGAATAGTA 60.741 47.826 0.00 0.00 0.00 1.82
3324 3927 5.221126 GGTTGAGACTTGAGAGCAATGTTTT 60.221 40.000 0.00 0.00 32.68 2.43
3424 4027 2.290960 GGGTGATTAGTTCCCTTGCAGT 60.291 50.000 0.00 0.00 38.29 4.40
3425 4028 2.369394 GGGTGATTAGTTCCCTTGCAG 58.631 52.381 0.00 0.00 38.29 4.41
3545 4149 5.765510 AGCCCACATGACAGGAAATAATAA 58.234 37.500 0.00 0.00 0.00 1.40
3546 4150 5.387113 AGCCCACATGACAGGAAATAATA 57.613 39.130 0.00 0.00 0.00 0.98
3547 4151 4.255510 AGCCCACATGACAGGAAATAAT 57.744 40.909 0.00 0.00 0.00 1.28
3563 4167 7.340232 GCCATGAGAAATATAATGATAAGCCCA 59.660 37.037 0.00 0.00 0.00 5.36
3600 4204 5.005779 CAGCATTCTGAACACGTTAGATACC 59.994 44.000 0.00 0.00 42.95 2.73
3663 4267 4.272489 CCCATAACATCTTGAAGCCTTGA 58.728 43.478 0.00 0.00 0.00 3.02
3771 4375 7.576750 TCTGTGTACTGAATCGATTAACAAC 57.423 36.000 11.38 8.23 0.00 3.32
3819 4423 4.781775 TGGTTCCAAGAACCTTCAAGTA 57.218 40.909 23.21 2.83 40.88 2.24
3915 4519 3.844211 AGGCATTAGTCTGGAAACCTACA 59.156 43.478 0.00 0.00 0.00 2.74
4248 4853 0.243636 AACTTACATTTGGGCGCTGC 59.756 50.000 7.64 0.00 0.00 5.25
4344 4949 4.619679 TGCCCTTTCCCTGCTTTAATATT 58.380 39.130 0.00 0.00 0.00 1.28
4345 4950 4.218312 CTGCCCTTTCCCTGCTTTAATAT 58.782 43.478 0.00 0.00 0.00 1.28
4346 4951 3.011257 ACTGCCCTTTCCCTGCTTTAATA 59.989 43.478 0.00 0.00 0.00 0.98
4347 4952 2.225369 ACTGCCCTTTCCCTGCTTTAAT 60.225 45.455 0.00 0.00 0.00 1.40
4348 4953 1.146982 ACTGCCCTTTCCCTGCTTTAA 59.853 47.619 0.00 0.00 0.00 1.52
4349 4954 0.777446 ACTGCCCTTTCCCTGCTTTA 59.223 50.000 0.00 0.00 0.00 1.85
4406 5011 4.160439 TCTTTGGTGCAGTAGGAGATGTAG 59.840 45.833 0.00 0.00 0.00 2.74
4440 5045 1.573857 ACAGGGGTCAAAGAAGGGTTT 59.426 47.619 0.00 0.00 0.00 3.27
4509 5114 3.538591 CTGAACTGCTGATAATGCCAGA 58.461 45.455 0.00 0.00 33.65 3.86
4534 5139 4.640364 TGACAATGTTACTGATGCAGACA 58.360 39.130 0.82 0.00 35.18 3.41
4762 5367 7.125053 AGTTTTAGCTTCTAGGCTCTTAGATGT 59.875 37.037 0.00 0.00 42.97 3.06
4961 5576 7.398904 AGGAATGCTTAAATTTTTAGGGCTGTA 59.601 33.333 0.00 0.00 0.00 2.74
5029 5646 0.172803 GCTGAATCTGCCCTTTGCTG 59.827 55.000 0.27 0.00 42.00 4.41
5241 5862 4.769688 ACTTCTGAATGACTGAACACACA 58.230 39.130 0.00 0.00 33.92 3.72
5547 6181 8.879227 TCAAAGAATAATTCCATTTCCCTTTGT 58.121 29.630 0.00 0.00 39.06 2.83
5572 6206 8.807667 ATCAGTTTCAGTTCAAATGAATGTTC 57.192 30.769 0.22 0.00 36.60 3.18
5593 6227 8.180267 CCTTTGTTAGTAGAAGCATTTGATCAG 58.820 37.037 0.00 0.00 0.00 2.90
5610 6244 9.657419 AAGAATAATTCCATTTGCCTTTGTTAG 57.343 29.630 0.00 0.00 0.00 2.34
5660 6294 2.659428 GAGTATTTGGATGCAAGGGCT 58.341 47.619 0.00 0.00 41.91 5.19
5826 6462 1.300971 GCAGACGTGGATGCATGTGT 61.301 55.000 17.57 10.34 42.11 3.72
5848 6484 3.343617 CTTTCTTCAATAGTGGGGCGAA 58.656 45.455 0.00 0.00 0.00 4.70
5951 6587 8.516234 TGAGAGTAAAAAGTAAAGCAACAACAA 58.484 29.630 0.00 0.00 0.00 2.83
6072 6712 4.641094 ACATAGACTAACTCTTGGACTCGG 59.359 45.833 0.00 0.00 0.00 4.63
6222 6877 9.635404 AGCATGACTAGACTAGACTAAACTAAT 57.365 33.333 16.55 0.00 0.00 1.73
6225 6880 9.635404 AATAGCATGACTAGACTAGACTAAACT 57.365 33.333 16.55 8.85 33.29 2.66
6404 7059 2.044650 AGCCATGCGACAGCCAAT 60.045 55.556 0.00 0.00 44.33 3.16
6453 7108 2.097036 TCTGCTCGGGATACTTCGAAA 58.903 47.619 0.00 0.00 34.87 3.46
6605 7260 1.546476 AGCCGTCTTACCAGAGTTGAG 59.454 52.381 0.00 0.00 0.00 3.02
6802 7459 9.283768 TCTCTTTAAACATAGCAAATTCAGACA 57.716 29.630 0.00 0.00 0.00 3.41
7003 7660 2.028112 GCAGTACCATCTTCAGGTGTCA 60.028 50.000 0.00 0.00 40.26 3.58
7039 7697 5.044558 GCATTAGTACAGAAGAGGTAGCAC 58.955 45.833 0.00 0.00 0.00 4.40
7271 7930 3.365969 CGCCTTCTTTCCCATACACAAAC 60.366 47.826 0.00 0.00 0.00 2.93
7283 7943 5.581085 ACAGATATACAACACGCCTTCTTTC 59.419 40.000 0.00 0.00 0.00 2.62
7296 7956 9.283768 CAGCCCAATATACAAACAGATATACAA 57.716 33.333 0.00 0.00 0.00 2.41
7360 8020 7.722363 ACGACAACTCCAACACATCATATATA 58.278 34.615 0.00 0.00 0.00 0.86
7361 8021 6.582636 ACGACAACTCCAACACATCATATAT 58.417 36.000 0.00 0.00 0.00 0.86
7443 8105 4.755411 AGGTCACAATAGGTTCATACACG 58.245 43.478 0.00 0.00 0.00 4.49
7444 8106 6.313905 CAGAAGGTCACAATAGGTTCATACAC 59.686 42.308 0.00 0.00 0.00 2.90
7447 8143 5.189736 AGCAGAAGGTCACAATAGGTTCATA 59.810 40.000 0.00 0.00 0.00 2.15
7455 8151 3.450904 ACCCTAGCAGAAGGTCACAATA 58.549 45.455 0.00 0.00 34.56 1.90
7467 8163 0.320771 AGCGTCACAAACCCTAGCAG 60.321 55.000 0.00 0.00 0.00 4.24
7519 8215 4.466726 TCAAATTTCCATCACCATGCATCA 59.533 37.500 0.00 0.00 0.00 3.07
7565 8261 3.856508 CGTCACGCGTCCTTCAAT 58.143 55.556 9.86 0.00 35.54 2.57
7595 8291 8.466798 TCCTCCTTTTCATTAATTCGGAATTTC 58.533 33.333 20.04 0.00 32.38 2.17
7597 8293 7.954666 TCCTCCTTTTCATTAATTCGGAATT 57.045 32.000 18.97 18.97 34.90 2.17
7610 8306 4.578928 CCTTTTCGACTTTCCTCCTTTTCA 59.421 41.667 0.00 0.00 0.00 2.69
7618 8314 4.209307 GAGGATCCTTTTCGACTTTCCT 57.791 45.455 17.42 0.00 34.89 3.36
7677 8373 8.816640 ACTTTATTTTTCAGCAGTAACCATTG 57.183 30.769 0.00 0.00 0.00 2.82
7685 8381 5.068987 TCAGCCAACTTTATTTTTCAGCAGT 59.931 36.000 0.00 0.00 0.00 4.40
7686 8382 5.531634 TCAGCCAACTTTATTTTTCAGCAG 58.468 37.500 0.00 0.00 0.00 4.24
7712 8423 6.671190 TCAACATTGAACAGCAAGTTATGAG 58.329 36.000 10.13 4.85 41.51 2.90
7765 8476 0.372334 AACGGTGTAATCGCGAATGC 59.628 50.000 15.24 9.62 37.91 3.56
7766 8477 2.034339 GGTAACGGTGTAATCGCGAATG 60.034 50.000 15.24 0.00 0.00 2.67
7767 8478 2.195922 GGTAACGGTGTAATCGCGAAT 58.804 47.619 15.24 7.65 0.00 3.34
7781 8508 1.801771 TGAACCGCATTCTTGGTAACG 59.198 47.619 0.00 0.00 37.54 3.18
7819 8546 7.099120 ACCATCTGAAGTATCAAAATTTTGCC 58.901 34.615 23.36 14.24 38.05 4.52
7832 8559 7.395772 TCAAAATATTGGCAACCATCTGAAGTA 59.604 33.333 0.00 0.00 37.15 2.24
7893 8621 4.201881 GGTTGTGTCACTGTTGGTAAGAAC 60.202 45.833 4.27 0.00 0.00 3.01
7913 8641 5.692115 AACCAGAATTCTTGGTTTTGGTT 57.308 34.783 24.72 20.84 44.49 3.67
7925 8653 4.248058 CCAAGCCAAATCAACCAGAATTC 58.752 43.478 0.00 0.00 0.00 2.17
7991 8719 4.037923 TGAACCTGAAGGACATTTTTCAGC 59.962 41.667 2.62 0.00 45.60 4.26
8010 8738 1.389106 GTCCGCACACGAGTTATGAAC 59.611 52.381 0.00 0.00 43.93 3.18
8081 8809 5.063060 GCGAGGTAAAATAGTTTGTGTCGAT 59.937 40.000 15.14 0.00 30.71 3.59
8311 9062 1.403780 GCCACCTACACGAGACGAATT 60.404 52.381 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.