Multiple sequence alignment - TraesCS1A01G310000

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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 TraesCS1A01G310000 chr1A 100.000 2851 0 0 598 3448 500825713 500828563 0.000000e+00 5265.0
1 TraesCS1A01G310000 chr1A 100.000 330 0 0 1 330 500825116 500825445 8.180000e-171 610.0
2 TraesCS1A01G310000 chr1D 89.052 1836 146 33 1645 3448 405364638 405366450 0.000000e+00 2226.0
3 TraesCS1A01G310000 chr1D 83.628 623 76 13 746 1362 405363747 405364349 2.320000e-156 562.0
4 TraesCS1A01G310000 chr1D 87.817 197 18 3 1422 1613 405364445 405364640 3.460000e-55 226.0
5 TraesCS1A01G310000 chr1B 91.914 1113 61 18 2226 3329 545206412 545207504 0.000000e+00 1530.0
6 TraesCS1A01G310000 chr1B 88.042 761 60 13 1474 2233 545205302 545206032 0.000000e+00 872.0
7 TraesCS1A01G310000 chr1B 85.526 760 94 8 608 1366 545204458 545205202 0.000000e+00 780.0
8 TraesCS1A01G310000 chr1B 83.142 261 25 4 69 329 545204123 545204364 1.610000e-53 220.0
9 TraesCS1A01G310000 chr1B 92.135 89 6 1 3361 3448 545207506 545207594 1.300000e-24 124.0
10 TraesCS1A01G310000 chr2D 85.665 872 86 27 2583 3448 534365066 534364228 0.000000e+00 881.0
11 TraesCS1A01G310000 chr2B 85.808 761 69 23 2583 3337 635345644 635344917 0.000000e+00 771.0
12 TraesCS1A01G310000 chr3A 88.679 53 3 3 1400 1451 552705836 552705786 1.030000e-05 62.1
13 TraesCS1A01G310000 chr7D 97.059 34 1 0 1411 1444 79210473 79210506 1.340000e-04 58.4
14 TraesCS1A01G310000 chr7B 97.059 34 1 0 1411 1444 709092706 709092673 1.340000e-04 58.4
15 TraesCS1A01G310000 chr6D 97.059 34 1 0 1411 1444 429498229 429498196 1.340000e-04 58.4
16 TraesCS1A01G310000 chr7A 94.444 36 2 0 1411 1446 720719831 720719866 4.810000e-04 56.5
17 TraesCS1A01G310000 chr3B 100.000 30 0 0 1417 1446 755082641 755082612 4.810000e-04 56.5


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 TraesCS1A01G310000 chr1A 500825116 500828563 3447 False 2937.500000 5265 100.000000 1 3448 2 chr1A.!!$F1 3447
1 TraesCS1A01G310000 chr1D 405363747 405366450 2703 False 1004.666667 2226 86.832333 746 3448 3 chr1D.!!$F1 2702
2 TraesCS1A01G310000 chr1B 545204123 545207594 3471 False 705.200000 1530 88.151800 69 3448 5 chr1B.!!$F1 3379
3 TraesCS1A01G310000 chr2D 534364228 534365066 838 True 881.000000 881 85.665000 2583 3448 1 chr2D.!!$R1 865
4 TraesCS1A01G310000 chr2B 635344917 635345644 727 True 771.000000 771 85.808000 2583 3337 1 chr2B.!!$R1 754

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
251 252 0.109723 TTGCTTCCACCACCTGTACC 59.890 55.0 0.00 0.00 0.00 3.34 F
274 275 0.246910 GGTTCTCGTCTTCACCCCTC 59.753 60.0 0.00 0.00 0.00 4.30 F
1213 1227 0.459411 CGCATCACCCATGTACGTGA 60.459 55.0 16.87 9.99 42.85 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1189 1203 0.106769 TACATGGGTGATGCGCCAAT 60.107 50.0 4.18 0.0 35.42 3.16 R
1315 1329 0.400213 AGCTGTCAAAATCCGTGGGA 59.600 50.0 0.00 0.0 35.55 4.37 R
3024 3484 0.666913 AGTGGATCCGATAACCGACG 59.333 55.0 7.39 0.0 41.76 5.12 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
26 27 8.671921 CAAATATATCAAAGAGTTGCACTGAGT 58.328 33.333 0.00 0.00 34.50 3.41
27 28 7.783090 ATATATCAAAGAGTTGCACTGAGTG 57.217 36.000 8.52 8.52 34.50 3.51
28 29 3.541996 TCAAAGAGTTGCACTGAGTGA 57.458 42.857 18.18 0.00 34.94 3.41
29 30 4.077300 TCAAAGAGTTGCACTGAGTGAT 57.923 40.909 18.18 0.00 34.94 3.06
30 31 4.454678 TCAAAGAGTTGCACTGAGTGATT 58.545 39.130 18.18 0.00 34.94 2.57
31 32 4.274214 TCAAAGAGTTGCACTGAGTGATTG 59.726 41.667 18.18 8.69 34.94 2.67
32 33 3.758755 AGAGTTGCACTGAGTGATTGA 57.241 42.857 18.18 0.00 35.23 2.57
33 34 4.283363 AGAGTTGCACTGAGTGATTGAT 57.717 40.909 18.18 0.00 35.23 2.57
34 35 4.001652 AGAGTTGCACTGAGTGATTGATG 58.998 43.478 18.18 0.00 35.23 3.07
35 36 3.748083 AGTTGCACTGAGTGATTGATGT 58.252 40.909 18.18 0.00 35.23 3.06
36 37 3.501062 AGTTGCACTGAGTGATTGATGTG 59.499 43.478 18.18 0.00 35.23 3.21
37 38 3.130280 TGCACTGAGTGATTGATGTGT 57.870 42.857 18.18 0.00 35.23 3.72
38 39 2.809696 TGCACTGAGTGATTGATGTGTG 59.190 45.455 18.18 0.00 35.23 3.82
39 40 2.413765 GCACTGAGTGATTGATGTGTGC 60.414 50.000 18.18 0.00 41.72 4.57
40 41 3.072211 CACTGAGTGATTGATGTGTGCT 58.928 45.455 6.79 0.00 35.23 4.40
41 42 3.501062 CACTGAGTGATTGATGTGTGCTT 59.499 43.478 6.79 0.00 35.23 3.91
42 43 4.692155 CACTGAGTGATTGATGTGTGCTTA 59.308 41.667 6.79 0.00 35.23 3.09
43 44 4.692625 ACTGAGTGATTGATGTGTGCTTAC 59.307 41.667 0.00 0.00 0.00 2.34
44 45 4.002982 TGAGTGATTGATGTGTGCTTACC 58.997 43.478 0.00 0.00 0.00 2.85
45 46 3.002791 AGTGATTGATGTGTGCTTACCG 58.997 45.455 0.00 0.00 0.00 4.02
46 47 3.000041 GTGATTGATGTGTGCTTACCGA 59.000 45.455 0.00 0.00 0.00 4.69
47 48 3.062639 GTGATTGATGTGTGCTTACCGAG 59.937 47.826 0.00 0.00 0.00 4.63
48 49 3.056179 TGATTGATGTGTGCTTACCGAGA 60.056 43.478 0.00 0.00 0.00 4.04
49 50 2.654749 TGATGTGTGCTTACCGAGAG 57.345 50.000 0.00 0.00 0.00 3.20
77 78 7.537306 TCGAAGTTTAACATTAAAGAGCATTGC 59.463 33.333 0.00 0.00 33.66 3.56
89 90 5.886960 AAGAGCATTGCGAATTACTCTTT 57.113 34.783 2.38 0.00 38.05 2.52
96 97 9.056005 AGCATTGCGAATTACTCTTTATATCAA 57.944 29.630 2.38 0.00 0.00 2.57
102 103 9.865484 GCGAATTACTCTTTATATCAAAAGGTC 57.135 33.333 0.00 0.00 37.13 3.85
153 154 6.808321 ACCCTACATATTGCTAGTCTTTCA 57.192 37.500 0.00 0.00 0.00 2.69
162 163 8.680903 CATATTGCTAGTCTTTCACAATTTCCT 58.319 33.333 0.00 0.00 33.31 3.36
167 168 8.730680 TGCTAGTCTTTCACAATTTCCTAATTC 58.269 33.333 0.00 0.00 31.63 2.17
170 171 8.034058 AGTCTTTCACAATTTCCTAATTCTCG 57.966 34.615 0.00 0.00 31.63 4.04
171 172 7.661847 AGTCTTTCACAATTTCCTAATTCTCGT 59.338 33.333 0.00 0.00 31.63 4.18
193 194 3.120385 CCTGCTCGCAATCGCACA 61.120 61.111 0.00 0.00 38.40 4.57
196 197 2.325857 GCTCGCAATCGCACATCC 59.674 61.111 0.00 0.00 38.40 3.51
221 222 2.519377 ACAAAGATCACCAACGTCGA 57.481 45.000 0.00 0.00 0.00 4.20
222 223 3.040147 ACAAAGATCACCAACGTCGAT 57.960 42.857 0.00 0.00 0.00 3.59
223 224 2.736721 ACAAAGATCACCAACGTCGATG 59.263 45.455 2.26 2.26 0.00 3.84
226 227 0.999406 GATCACCAACGTCGATGTGG 59.001 55.000 11.82 16.25 0.00 4.17
229 230 0.999406 CACCAACGTCGATGTGGATC 59.001 55.000 24.15 0.00 0.00 3.36
239 240 1.605710 CGATGTGGATCCATTGCTTCC 59.394 52.381 19.62 3.27 0.00 3.46
240 241 2.658285 GATGTGGATCCATTGCTTCCA 58.342 47.619 19.62 9.66 37.20 3.53
242 243 3.594453 TGGATCCATTGCTTCCACC 57.406 52.632 11.44 0.00 34.65 4.61
243 244 0.703488 TGGATCCATTGCTTCCACCA 59.297 50.000 11.44 0.00 34.65 4.17
244 245 1.106285 GGATCCATTGCTTCCACCAC 58.894 55.000 6.95 0.00 0.00 4.16
245 246 1.106285 GATCCATTGCTTCCACCACC 58.894 55.000 0.00 0.00 0.00 4.61
246 247 0.706433 ATCCATTGCTTCCACCACCT 59.294 50.000 0.00 0.00 0.00 4.00
247 248 0.251297 TCCATTGCTTCCACCACCTG 60.251 55.000 0.00 0.00 0.00 4.00
248 249 0.540365 CCATTGCTTCCACCACCTGT 60.540 55.000 0.00 0.00 0.00 4.00
249 250 1.271871 CCATTGCTTCCACCACCTGTA 60.272 52.381 0.00 0.00 0.00 2.74
250 251 1.812571 CATTGCTTCCACCACCTGTAC 59.187 52.381 0.00 0.00 0.00 2.90
251 252 0.109723 TTGCTTCCACCACCTGTACC 59.890 55.000 0.00 0.00 0.00 3.34
262 263 0.316204 ACCTGTACCGTTGGTTCTCG 59.684 55.000 0.00 0.00 37.09 4.04
265 266 1.268899 CTGTACCGTTGGTTCTCGTCT 59.731 52.381 0.00 0.00 37.09 4.18
274 275 0.246910 GGTTCTCGTCTTCACCCCTC 59.753 60.000 0.00 0.00 0.00 4.30
292 293 4.873746 CCTCGCTAGGGAAAATGAGATA 57.126 45.455 11.05 0.00 39.48 1.98
623 624 1.410004 TCTTGTCCTTCCACGAGTGT 58.590 50.000 2.36 0.00 0.00 3.55
627 628 0.663568 GTCCTTCCACGAGTGTCACG 60.664 60.000 2.36 0.00 0.00 4.35
643 644 5.028375 GTGTCACGCCAGCTTTATTTTATC 58.972 41.667 0.00 0.00 0.00 1.75
650 651 6.974622 ACGCCAGCTTTATTTTATCTGATTTG 59.025 34.615 0.00 0.00 0.00 2.32
674 675 4.124970 AGGTTCGGTACAAAAGTGAGTTC 58.875 43.478 0.00 0.00 0.00 3.01
679 680 6.395426 TCGGTACAAAAGTGAGTTCTCTAA 57.605 37.500 0.00 0.00 0.00 2.10
689 690 7.954788 AAGTGAGTTCTCTAAAGATGTTGAC 57.045 36.000 1.53 0.00 0.00 3.18
736 737 6.415573 AGTACAAATATGAAAGGGAGTCCAC 58.584 40.000 12.30 0.06 34.83 4.02
739 740 4.510167 AATATGAAAGGGAGTCCACCAG 57.490 45.455 12.30 0.00 34.83 4.00
740 741 0.995024 ATGAAAGGGAGTCCACCAGG 59.005 55.000 12.30 0.00 34.83 4.45
742 743 0.615850 GAAAGGGAGTCCACCAGGAG 59.384 60.000 12.30 0.00 46.92 3.69
757 759 3.916989 ACCAGGAGGACAAGGAGTATTTT 59.083 43.478 0.00 0.00 38.69 1.82
786 788 5.418310 AGCATTATTTTCATCGTAACCGG 57.582 39.130 0.00 0.00 33.95 5.28
790 792 5.821516 TTATTTTCATCGTAACCGGCAAT 57.178 34.783 0.00 0.00 33.95 3.56
798 800 1.745827 CGTAACCGGCAATGGATTCCT 60.746 52.381 0.00 0.00 0.00 3.36
815 817 5.544176 GGATTCCTTCCATGTAGAGTGGATA 59.456 44.000 0.00 0.00 44.75 2.59
823 825 2.022195 TGTAGAGTGGATAGTGGCGTC 58.978 52.381 0.00 0.00 0.00 5.19
835 837 2.511600 GGCGTCGCAAGCATACCT 60.512 61.111 20.50 0.00 36.08 3.08
838 840 0.508641 GCGTCGCAAGCATACCTATG 59.491 55.000 13.44 0.00 36.78 2.23
845 855 3.739830 CGCAAGCATACCTATGGTGTGTA 60.740 47.826 13.49 0.00 44.82 2.90
847 857 4.127171 CAAGCATACCTATGGTGTGTACC 58.873 47.826 13.49 0.00 44.82 3.34
866 876 1.414378 CGGATTTTGGTTGCGAAACC 58.586 50.000 19.28 19.28 43.12 3.27
967 979 4.160736 ACACTTGCCGAATAGAAAAAGC 57.839 40.909 0.00 0.00 0.00 3.51
971 983 5.634859 CACTTGCCGAATAGAAAAAGCAAAT 59.365 36.000 0.00 0.00 39.50 2.32
972 984 6.146021 CACTTGCCGAATAGAAAAAGCAAATT 59.854 34.615 0.00 0.00 39.50 1.82
980 992 7.695618 CGAATAGAAAAAGCAAATTGGAGAGAG 59.304 37.037 0.00 0.00 0.00 3.20
999 1011 1.337703 AGCATTGCGAAAGAAACTGCA 59.662 42.857 2.38 0.00 36.34 4.41
1009 1021 4.377328 CGAAAGAAACTGCAATGATGACGA 60.377 41.667 0.00 0.00 0.00 4.20
1019 1031 5.604565 TGCAATGATGACGATTCTCATAGT 58.395 37.500 0.00 0.00 30.62 2.12
1021 1033 5.119898 GCAATGATGACGATTCTCATAGTCC 59.880 44.000 0.00 0.00 34.87 3.85
1066 1080 1.804151 GAGCGCAACAAACTGATGGTA 59.196 47.619 11.47 0.00 0.00 3.25
1113 1127 8.880878 TGAGTCGCTATTTTGCATATTAGTTA 57.119 30.769 7.58 0.00 0.00 2.24
1142 1156 1.975660 AGTCGGGCTGCAACTTTTTA 58.024 45.000 0.50 0.00 0.00 1.52
1160 1174 9.489084 AACTTTTTAATGGCTTTAATCCTGTTC 57.511 29.630 6.43 0.00 30.03 3.18
1162 1176 3.782889 AATGGCTTTAATCCTGTTCGC 57.217 42.857 0.00 0.00 0.00 4.70
1181 1195 2.794910 CGCGATTCGTCCTATTGATTGT 59.205 45.455 0.00 0.00 0.00 2.71
1203 1217 2.663826 TTTTTATTGGCGCATCACCC 57.336 45.000 10.83 0.00 0.00 4.61
1205 1219 1.774110 TTTATTGGCGCATCACCCAT 58.226 45.000 10.83 0.00 0.00 4.00
1213 1227 0.459411 CGCATCACCCATGTACGTGA 60.459 55.000 16.87 9.99 42.85 4.35
1216 1230 2.159156 GCATCACCCATGTACGTGACTA 60.159 50.000 16.87 0.00 41.56 2.59
1225 1239 5.048921 CCCATGTACGTGACTATCGATAAGT 60.049 44.000 16.87 6.88 0.00 2.24
1231 1245 4.393990 ACGTGACTATCGATAAGTGTGACA 59.606 41.667 6.58 0.00 0.00 3.58
1244 1258 4.927267 AGTGTGACATCCCTTGGAATAA 57.073 40.909 0.00 0.00 34.34 1.40
1274 1288 2.747989 CGGCTATATCTTGCGTCCTAGA 59.252 50.000 0.00 0.00 0.00 2.43
1305 1319 2.316108 TGGCTATAAGAGACCATGCGA 58.684 47.619 0.00 0.00 28.20 5.10
1307 1321 3.324846 TGGCTATAAGAGACCATGCGATT 59.675 43.478 0.00 0.00 28.20 3.34
1314 1328 9.208022 CTATAAGAGACCATGCGATTTTTATGA 57.792 33.333 0.00 0.00 0.00 2.15
1315 1329 6.949352 AAGAGACCATGCGATTTTTATGAT 57.051 33.333 0.00 0.00 0.00 2.45
1321 1335 3.961477 TGCGATTTTTATGATCCCACG 57.039 42.857 0.00 0.00 0.00 4.94
1330 1344 5.828299 TTTATGATCCCACGGATTTTGAC 57.172 39.130 0.00 0.00 43.27 3.18
1331 1345 2.869101 TGATCCCACGGATTTTGACA 57.131 45.000 0.00 0.00 43.27 3.58
1362 1376 3.395639 TCCGATTTGTGTTGTGTCCTAC 58.604 45.455 0.00 0.00 0.00 3.18
1365 1379 4.274950 CCGATTTGTGTTGTGTCCTACTTT 59.725 41.667 0.00 0.00 0.00 2.66
1371 1385 4.102524 TGTGTTGTGTCCTACTTTCTCCAT 59.897 41.667 0.00 0.00 0.00 3.41
1372 1386 4.691216 GTGTTGTGTCCTACTTTCTCCATC 59.309 45.833 0.00 0.00 0.00 3.51
1373 1387 4.254492 GTTGTGTCCTACTTTCTCCATCC 58.746 47.826 0.00 0.00 0.00 3.51
1374 1388 3.516586 TGTGTCCTACTTTCTCCATCCA 58.483 45.455 0.00 0.00 0.00 3.41
1375 1389 3.260884 TGTGTCCTACTTTCTCCATCCAC 59.739 47.826 0.00 0.00 0.00 4.02
1377 1391 3.907474 TGTCCTACTTTCTCCATCCACAA 59.093 43.478 0.00 0.00 0.00 3.33
1379 1393 5.724370 TGTCCTACTTTCTCCATCCACAATA 59.276 40.000 0.00 0.00 0.00 1.90
1381 1395 7.092444 TGTCCTACTTTCTCCATCCACAATATT 60.092 37.037 0.00 0.00 0.00 1.28
1382 1396 8.429641 GTCCTACTTTCTCCATCCACAATATTA 58.570 37.037 0.00 0.00 0.00 0.98
1393 1407 9.979578 TCCATCCACAATATTATATGTTTTTGC 57.020 29.630 0.00 0.00 0.00 3.68
1394 1408 9.761504 CCATCCACAATATTATATGTTTTTGCA 57.238 29.630 0.00 0.00 0.00 4.08
1410 1448 9.927668 ATGTTTTTGCAAGCTATGTTAGTTTAT 57.072 25.926 0.00 0.00 0.00 1.40
1634 1695 8.244802 AGGTAGAATCACGTTATGTATATCTGC 58.755 37.037 0.00 0.00 0.00 4.26
1635 1696 8.244802 GGTAGAATCACGTTATGTATATCTGCT 58.755 37.037 0.00 0.00 0.00 4.24
1636 1697 9.627395 GTAGAATCACGTTATGTATATCTGCTT 57.373 33.333 0.00 0.00 0.00 3.91
1637 1698 8.749841 AGAATCACGTTATGTATATCTGCTTC 57.250 34.615 0.00 0.00 0.00 3.86
1638 1699 7.815068 AGAATCACGTTATGTATATCTGCTTCC 59.185 37.037 0.00 0.00 0.00 3.46
1639 1700 5.458015 TCACGTTATGTATATCTGCTTCCG 58.542 41.667 0.00 0.00 0.00 4.30
1656 1717 4.757149 GCTTCCGATTTGTATTATGGAGCT 59.243 41.667 0.00 0.00 0.00 4.09
1658 1719 6.091441 GCTTCCGATTTGTATTATGGAGCTAG 59.909 42.308 0.00 0.00 0.00 3.42
1660 1721 4.327357 CCGATTTGTATTATGGAGCTAGCG 59.673 45.833 9.55 0.00 0.00 4.26
1661 1722 5.161358 CGATTTGTATTATGGAGCTAGCGA 58.839 41.667 9.55 0.00 0.00 4.93
1663 1724 6.020281 CGATTTGTATTATGGAGCTAGCGATC 60.020 42.308 9.55 1.82 0.00 3.69
1672 1733 2.740981 GGAGCTAGCGATCATTTCCATG 59.259 50.000 9.55 0.00 0.00 3.66
1677 1738 4.035558 GCTAGCGATCATTTCCATGTTGAA 59.964 41.667 0.00 0.00 0.00 2.69
1678 1739 5.278169 GCTAGCGATCATTTCCATGTTGAAT 60.278 40.000 0.00 0.00 0.00 2.57
1679 1740 4.928601 AGCGATCATTTCCATGTTGAATG 58.071 39.130 0.00 0.00 33.24 2.67
1680 1741 4.641541 AGCGATCATTTCCATGTTGAATGA 59.358 37.500 14.23 14.23 42.14 2.57
1786 1847 4.512484 GACAAAGGGATCCTCTTTCTCAG 58.488 47.826 19.54 13.44 32.72 3.35
1882 1943 4.265056 GGTCACCGGCACCAACCT 62.265 66.667 16.76 0.00 33.63 3.50
1914 1975 2.707849 TTCGACTACGGCAGCCTCC 61.708 63.158 10.54 0.00 40.21 4.30
1926 1987 1.405526 GCAGCCTCCGAAACATACTGA 60.406 52.381 0.00 0.00 0.00 3.41
1928 1989 1.207329 AGCCTCCGAAACATACTGACC 59.793 52.381 0.00 0.00 0.00 4.02
1936 1997 5.711506 TCCGAAACATACTGACCTACTACAA 59.288 40.000 0.00 0.00 0.00 2.41
1937 1998 6.379133 TCCGAAACATACTGACCTACTACAAT 59.621 38.462 0.00 0.00 0.00 2.71
1940 2001 9.745880 CGAAACATACTGACCTACTACAATATT 57.254 33.333 0.00 0.00 0.00 1.28
2037 2098 2.203582 AGCCGGAAAAACCCCACC 60.204 61.111 5.05 0.00 34.64 4.61
2151 2212 2.683933 AGGAGCCCCACAGGTACG 60.684 66.667 0.00 0.00 38.26 3.67
2152 2213 3.001406 GGAGCCCCACAGGTACGT 61.001 66.667 0.00 0.00 38.26 3.57
2295 2743 4.051167 TCGGGCAGGACGACCCTA 62.051 66.667 0.00 0.00 45.60 3.53
2408 2856 0.179076 CGATCTGCCACTACATGCCA 60.179 55.000 0.00 0.00 0.00 4.92
2411 2859 0.538584 TCTGCCACTACATGCCAGAG 59.461 55.000 0.00 0.00 0.00 3.35
2429 2877 2.303022 AGAGAAGTATGTGGTGTGGGTG 59.697 50.000 0.00 0.00 0.00 4.61
2431 2879 0.404040 AAGTATGTGGTGTGGGTGGG 59.596 55.000 0.00 0.00 0.00 4.61
2432 2880 0.770557 AGTATGTGGTGTGGGTGGGT 60.771 55.000 0.00 0.00 0.00 4.51
2490 2938 2.577700 TCTCGAGCTAAGAGGGATGAC 58.422 52.381 7.81 0.00 36.45 3.06
2545 2993 6.653320 CCAAGCTTAAACTAATGGTCACTACA 59.347 38.462 0.00 0.00 0.00 2.74
2546 2994 7.336931 CCAAGCTTAAACTAATGGTCACTACAT 59.663 37.037 0.00 0.00 0.00 2.29
2593 3046 6.360681 GCATGCACGAATTTGGAGAAATATAC 59.639 38.462 14.21 0.00 31.18 1.47
2611 3064 2.684001 ACGTGGAGTTCTGAACAACA 57.316 45.000 21.50 16.07 0.00 3.33
2662 3115 3.751175 CCAATTGAACACCGGCGATATAT 59.249 43.478 9.30 0.00 0.00 0.86
2663 3116 4.932799 CCAATTGAACACCGGCGATATATA 59.067 41.667 9.30 0.00 0.00 0.86
2698 3151 1.012841 GGCTCTTCTTTGCATCCTCG 58.987 55.000 0.00 0.00 0.00 4.63
2699 3152 1.406069 GGCTCTTCTTTGCATCCTCGA 60.406 52.381 0.00 0.00 0.00 4.04
2728 3181 8.924511 ATAATTTCGATCCCATTGTGTATTCT 57.075 30.769 0.00 0.00 0.00 2.40
2785 3238 0.880278 GCAACTTCGCTGGTGAGTCA 60.880 55.000 0.00 0.00 0.00 3.41
2837 3291 6.531240 CAGCATGACAACAGTTAAAACAAACT 59.469 34.615 0.00 0.00 39.69 2.66
2855 3309 3.669251 ACTAACAGAGGAGAACAGCAC 57.331 47.619 0.00 0.00 0.00 4.40
2866 3323 6.014669 AGAGGAGAACAGCACATATAGGATTC 60.015 42.308 0.00 0.00 0.00 2.52
2878 3337 7.359598 GCACATATAGGATTCGTCAGTTCAATC 60.360 40.741 0.00 0.00 0.00 2.67
2879 3338 7.869937 CACATATAGGATTCGTCAGTTCAATCT 59.130 37.037 0.00 0.00 0.00 2.40
2880 3339 7.869937 ACATATAGGATTCGTCAGTTCAATCTG 59.130 37.037 0.00 0.00 36.85 2.90
2881 3340 4.543590 AGGATTCGTCAGTTCAATCTGT 57.456 40.909 0.00 0.00 36.85 3.41
2882 3341 5.661056 AGGATTCGTCAGTTCAATCTGTA 57.339 39.130 0.00 0.00 36.85 2.74
2883 3342 6.037786 AGGATTCGTCAGTTCAATCTGTAA 57.962 37.500 0.00 0.00 36.85 2.41
2884 3343 6.102663 AGGATTCGTCAGTTCAATCTGTAAG 58.897 40.000 0.00 0.00 36.85 2.34
2927 3387 2.996621 CTCACCGTTGTCCAGAAGAATC 59.003 50.000 0.00 0.00 0.00 2.52
2961 3421 4.028852 TCAAGAACCGATGTGATACGAG 57.971 45.455 0.00 0.00 0.00 4.18
2962 3422 3.692593 TCAAGAACCGATGTGATACGAGA 59.307 43.478 0.00 0.00 0.00 4.04
3069 3529 2.767505 AGTTGCCTCGTCCAAAACTAG 58.232 47.619 0.00 0.00 29.56 2.57
3142 3602 4.445545 GCGCTCCAGTTTTCGCCG 62.446 66.667 0.00 0.00 41.53 6.46
3174 3635 4.168922 CTGCATTTCAGTTCAGAATGCA 57.831 40.909 18.39 18.39 38.48 3.96
3187 3648 7.439056 CAGTTCAGAATGCAAAGTTATTGGTTT 59.561 33.333 0.00 0.00 34.76 3.27
3202 3665 8.253113 AGTTATTGGTTTGCCATCATAAAGAAG 58.747 33.333 0.00 0.00 45.56 2.85
3231 3694 3.955471 TCCACTGGGAATTTCTGTCATC 58.045 45.455 0.00 0.00 41.32 2.92
3233 3696 4.043310 TCCACTGGGAATTTCTGTCATCTT 59.957 41.667 0.00 0.00 41.32 2.40
3235 3698 4.157289 CACTGGGAATTTCTGTCATCTTGG 59.843 45.833 0.00 0.00 0.00 3.61
3236 3699 4.043310 ACTGGGAATTTCTGTCATCTTGGA 59.957 41.667 0.00 0.00 0.00 3.53
3237 3700 4.592942 TGGGAATTTCTGTCATCTTGGAG 58.407 43.478 0.00 0.00 0.00 3.86
3334 3815 4.045104 CCTAGACAACATAGATCACGCAC 58.955 47.826 0.00 0.00 0.00 5.34
3338 3819 4.152402 AGACAACATAGATCACGCACAAAC 59.848 41.667 0.00 0.00 0.00 2.93
3339 3820 3.188460 ACAACATAGATCACGCACAAACC 59.812 43.478 0.00 0.00 0.00 3.27
3365 3848 6.974622 ACTTTAGCCATCAAATAGAAAATGCG 59.025 34.615 0.00 0.00 0.00 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.251729 ACACATCAATCACTCAGTGCAAC 59.748 43.478 0.00 0.00 32.98 4.17
16 17 3.251487 CACACATCAATCACTCAGTGCAA 59.749 43.478 0.00 0.00 32.98 4.08
17 18 2.809696 CACACATCAATCACTCAGTGCA 59.190 45.455 0.00 0.00 32.98 4.57
18 19 2.413765 GCACACATCAATCACTCAGTGC 60.414 50.000 0.00 0.00 43.27 4.40
19 20 3.072211 AGCACACATCAATCACTCAGTG 58.928 45.455 0.00 0.00 34.45 3.66
20 21 3.413846 AGCACACATCAATCACTCAGT 57.586 42.857 0.00 0.00 0.00 3.41
21 22 4.093998 GGTAAGCACACATCAATCACTCAG 59.906 45.833 0.00 0.00 0.00 3.35
22 23 4.002982 GGTAAGCACACATCAATCACTCA 58.997 43.478 0.00 0.00 0.00 3.41
23 24 3.062639 CGGTAAGCACACATCAATCACTC 59.937 47.826 0.00 0.00 0.00 3.51
24 25 3.002791 CGGTAAGCACACATCAATCACT 58.997 45.455 0.00 0.00 0.00 3.41
25 26 3.000041 TCGGTAAGCACACATCAATCAC 59.000 45.455 0.00 0.00 0.00 3.06
26 27 3.056179 TCTCGGTAAGCACACATCAATCA 60.056 43.478 0.00 0.00 0.00 2.57
27 28 3.521560 TCTCGGTAAGCACACATCAATC 58.478 45.455 0.00 0.00 0.00 2.67
28 29 3.525537 CTCTCGGTAAGCACACATCAAT 58.474 45.455 0.00 0.00 0.00 2.57
29 30 2.353704 CCTCTCGGTAAGCACACATCAA 60.354 50.000 0.00 0.00 0.00 2.57
30 31 1.204704 CCTCTCGGTAAGCACACATCA 59.795 52.381 0.00 0.00 0.00 3.07
31 32 1.204941 ACCTCTCGGTAAGCACACATC 59.795 52.381 0.00 0.00 43.29 3.06
32 33 1.204941 GACCTCTCGGTAAGCACACAT 59.795 52.381 0.00 0.00 45.73 3.21
33 34 0.601558 GACCTCTCGGTAAGCACACA 59.398 55.000 0.00 0.00 45.73 3.72
34 35 0.456312 CGACCTCTCGGTAAGCACAC 60.456 60.000 0.00 0.00 45.73 3.82
35 36 0.607217 TCGACCTCTCGGTAAGCACA 60.607 55.000 0.00 0.00 45.73 4.57
36 37 0.524862 TTCGACCTCTCGGTAAGCAC 59.475 55.000 0.00 0.00 45.73 4.40
37 38 0.809385 CTTCGACCTCTCGGTAAGCA 59.191 55.000 0.00 0.00 45.73 3.91
38 39 0.810016 ACTTCGACCTCTCGGTAAGC 59.190 55.000 0.00 0.00 45.73 3.09
39 40 3.572604 AAACTTCGACCTCTCGGTAAG 57.427 47.619 0.00 0.00 45.73 2.34
40 41 4.278170 TGTTAAACTTCGACCTCTCGGTAA 59.722 41.667 0.00 0.00 45.73 2.85
41 42 3.820467 TGTTAAACTTCGACCTCTCGGTA 59.180 43.478 0.00 0.00 45.73 4.02
43 44 3.293311 TGTTAAACTTCGACCTCTCGG 57.707 47.619 0.00 0.00 40.58 4.63
44 45 6.939551 TTAATGTTAAACTTCGACCTCTCG 57.060 37.500 0.00 0.00 41.65 4.04
45 46 8.530269 TCTTTAATGTTAAACTTCGACCTCTC 57.470 34.615 0.00 0.00 0.00 3.20
46 47 7.117956 GCTCTTTAATGTTAAACTTCGACCTCT 59.882 37.037 0.00 0.00 0.00 3.69
47 48 7.095355 TGCTCTTTAATGTTAAACTTCGACCTC 60.095 37.037 0.00 0.00 0.00 3.85
48 49 6.708949 TGCTCTTTAATGTTAAACTTCGACCT 59.291 34.615 0.00 0.00 0.00 3.85
49 50 6.894828 TGCTCTTTAATGTTAAACTTCGACC 58.105 36.000 0.00 0.00 0.00 4.79
50 51 8.840867 CAATGCTCTTTAATGTTAAACTTCGAC 58.159 33.333 0.00 0.00 0.00 4.20
51 52 7.537306 GCAATGCTCTTTAATGTTAAACTTCGA 59.463 33.333 0.00 0.00 0.00 3.71
52 53 7.460120 CGCAATGCTCTTTAATGTTAAACTTCG 60.460 37.037 2.94 0.00 0.00 3.79
53 54 7.537306 TCGCAATGCTCTTTAATGTTAAACTTC 59.463 33.333 2.94 0.00 0.00 3.01
54 55 7.367285 TCGCAATGCTCTTTAATGTTAAACTT 58.633 30.769 2.94 0.00 0.00 2.66
55 56 6.908825 TCGCAATGCTCTTTAATGTTAAACT 58.091 32.000 2.94 0.00 0.00 2.66
56 57 7.561237 TTCGCAATGCTCTTTAATGTTAAAC 57.439 32.000 2.94 0.00 0.00 2.01
57 58 8.755696 AATTCGCAATGCTCTTTAATGTTAAA 57.244 26.923 2.94 0.00 0.00 1.52
58 59 9.284594 GTAATTCGCAATGCTCTTTAATGTTAA 57.715 29.630 2.94 0.00 0.00 2.01
59 60 8.673711 AGTAATTCGCAATGCTCTTTAATGTTA 58.326 29.630 2.94 0.00 0.00 2.41
60 61 7.538575 AGTAATTCGCAATGCTCTTTAATGTT 58.461 30.769 2.94 0.00 0.00 2.71
61 62 7.066284 AGAGTAATTCGCAATGCTCTTTAATGT 59.934 33.333 2.94 0.00 33.23 2.71
62 63 7.412853 AGAGTAATTCGCAATGCTCTTTAATG 58.587 34.615 2.94 0.00 33.23 1.90
63 64 7.559590 AGAGTAATTCGCAATGCTCTTTAAT 57.440 32.000 2.94 0.00 33.23 1.40
64 65 6.985188 AGAGTAATTCGCAATGCTCTTTAA 57.015 33.333 2.94 0.00 33.23 1.52
65 66 6.985188 AAGAGTAATTCGCAATGCTCTTTA 57.015 33.333 2.94 0.00 39.16 1.85
66 67 5.886960 AAGAGTAATTCGCAATGCTCTTT 57.113 34.783 2.94 0.00 39.16 2.52
67 68 5.886960 AAAGAGTAATTCGCAATGCTCTT 57.113 34.783 2.94 0.56 41.55 2.85
142 143 8.951243 AGAATTAGGAAATTGTGAAAGACTAGC 58.049 33.333 0.00 0.00 35.41 3.42
148 149 7.905493 GCTACGAGAATTAGGAAATTGTGAAAG 59.095 37.037 0.00 0.00 35.41 2.62
153 154 5.123936 GGGCTACGAGAATTAGGAAATTGT 58.876 41.667 0.00 0.00 35.41 2.71
189 190 3.058293 TGATCTTTGTTGAACGGATGTGC 60.058 43.478 0.00 0.00 0.00 4.57
193 194 3.750371 TGGTGATCTTTGTTGAACGGAT 58.250 40.909 0.00 0.00 0.00 4.18
196 197 3.242608 ACGTTGGTGATCTTTGTTGAACG 60.243 43.478 0.00 0.00 40.46 3.95
221 222 2.832643 TGGAAGCAATGGATCCACAT 57.167 45.000 18.99 6.29 38.30 3.21
239 240 4.371975 CCAACGGTACAGGTGGTG 57.628 61.111 20.73 3.54 43.80 4.17
242 243 1.792006 GAGAACCAACGGTACAGGTG 58.208 55.000 3.81 3.81 33.12 4.00
243 244 0.316204 CGAGAACCAACGGTACAGGT 59.684 55.000 0.00 0.00 33.12 4.00
244 245 0.316204 ACGAGAACCAACGGTACAGG 59.684 55.000 0.00 0.00 33.12 4.00
245 246 1.268899 AGACGAGAACCAACGGTACAG 59.731 52.381 0.00 0.00 33.12 2.74
246 247 1.321474 AGACGAGAACCAACGGTACA 58.679 50.000 0.00 0.00 33.12 2.90
247 248 2.287788 TGAAGACGAGAACCAACGGTAC 60.288 50.000 0.00 0.00 33.12 3.34
248 249 1.955778 TGAAGACGAGAACCAACGGTA 59.044 47.619 0.00 0.00 33.12 4.02
249 250 0.748450 TGAAGACGAGAACCAACGGT 59.252 50.000 0.00 0.00 37.65 4.83
250 251 1.137513 GTGAAGACGAGAACCAACGG 58.862 55.000 0.00 0.00 0.00 4.44
251 252 1.137513 GGTGAAGACGAGAACCAACG 58.862 55.000 0.00 0.00 32.69 4.10
262 263 1.817209 CCTAGCGAGGGGTGAAGAC 59.183 63.158 4.68 0.00 39.48 3.01
274 275 6.049149 TCACTTTATCTCATTTTCCCTAGCG 58.951 40.000 0.00 0.00 0.00 4.26
288 289 8.560124 AATTACTCATCCTCCTCACTTTATCT 57.440 34.615 0.00 0.00 0.00 1.98
292 293 6.903534 TCCTAATTACTCATCCTCCTCACTTT 59.096 38.462 0.00 0.00 0.00 2.66
597 598 2.679837 CGTGGAAGGACAAGAATCCATG 59.320 50.000 0.00 0.00 43.41 3.66
598 599 2.571653 TCGTGGAAGGACAAGAATCCAT 59.428 45.455 0.00 0.00 43.41 3.41
599 600 1.974957 TCGTGGAAGGACAAGAATCCA 59.025 47.619 0.00 0.00 41.73 3.41
600 601 2.028020 ACTCGTGGAAGGACAAGAATCC 60.028 50.000 0.00 0.00 39.28 3.01
601 602 2.996621 CACTCGTGGAAGGACAAGAATC 59.003 50.000 0.00 0.00 0.00 2.52
602 603 2.368875 ACACTCGTGGAAGGACAAGAAT 59.631 45.455 1.77 0.00 34.19 2.40
603 604 1.760613 ACACTCGTGGAAGGACAAGAA 59.239 47.619 1.77 0.00 34.19 2.52
604 605 1.340248 GACACTCGTGGAAGGACAAGA 59.660 52.381 1.77 0.00 34.19 3.02
605 606 1.068588 TGACACTCGTGGAAGGACAAG 59.931 52.381 1.77 0.00 34.19 3.16
606 607 1.116308 TGACACTCGTGGAAGGACAA 58.884 50.000 1.77 0.00 34.19 3.18
610 611 2.022129 GCGTGACACTCGTGGAAGG 61.022 63.158 3.68 0.00 34.19 3.46
616 617 2.644555 AAAGCTGGCGTGACACTCGT 62.645 55.000 3.68 0.00 0.00 4.18
623 624 5.182487 TCAGATAAAATAAAGCTGGCGTGA 58.818 37.500 0.00 0.00 0.00 4.35
627 628 9.455847 CTACAAATCAGATAAAATAAAGCTGGC 57.544 33.333 0.00 0.00 0.00 4.85
643 644 6.204108 ACTTTTGTACCGAACCTACAAATCAG 59.796 38.462 4.94 3.89 41.48 2.90
650 651 4.625028 ACTCACTTTTGTACCGAACCTAC 58.375 43.478 0.00 0.00 0.00 3.18
689 690 8.498054 ACTCACAAAGTGTTGATATATTCCTG 57.502 34.615 0.00 0.00 36.65 3.86
720 721 2.196595 CCTGGTGGACTCCCTTTCATA 58.803 52.381 0.00 0.00 34.57 2.15
723 724 0.615850 CTCCTGGTGGACTCCCTTTC 59.384 60.000 0.00 0.00 37.46 2.62
724 725 0.842467 CCTCCTGGTGGACTCCCTTT 60.842 60.000 9.20 0.00 37.46 3.11
736 737 4.576330 AAAATACTCCTTGTCCTCCTGG 57.424 45.455 0.00 0.00 0.00 4.45
762 764 6.360329 CCGGTTACGATGAAAATAATGCTAC 58.640 40.000 0.00 0.00 44.60 3.58
815 817 2.100631 GTATGCTTGCGACGCCACT 61.101 57.895 18.69 0.01 0.00 4.00
823 825 1.599071 CACACCATAGGTATGCTTGCG 59.401 52.381 0.00 0.00 32.11 4.85
835 837 3.009253 ACCAAAATCCGGTACACACCATA 59.991 43.478 0.00 0.00 46.14 2.74
838 840 1.900245 ACCAAAATCCGGTACACACC 58.100 50.000 0.00 0.00 41.93 4.16
845 855 1.033574 TTTCGCAACCAAAATCCGGT 58.966 45.000 0.00 0.00 38.85 5.28
866 876 0.900547 GCGCGAATGTTGTGATTTCG 59.099 50.000 12.10 0.00 43.72 3.46
891 903 1.068895 TCTAAACCGACACAAAGCCGA 59.931 47.619 0.00 0.00 0.00 5.54
898 910 4.498345 GGTTTGCATTTCTAAACCGACACA 60.498 41.667 0.16 0.00 44.29 3.72
965 977 2.165845 GCAATGCTCTCTCCAATTTGCT 59.834 45.455 0.00 0.00 36.10 3.91
967 979 2.421073 TCGCAATGCTCTCTCCAATTTG 59.579 45.455 2.94 0.00 0.00 2.32
971 983 2.079158 CTTTCGCAATGCTCTCTCCAA 58.921 47.619 2.94 0.00 0.00 3.53
972 984 1.276138 TCTTTCGCAATGCTCTCTCCA 59.724 47.619 2.94 0.00 0.00 3.86
980 992 1.769733 TGCAGTTTCTTTCGCAATGC 58.230 45.000 0.00 0.00 0.00 3.56
999 1011 6.041409 ACAGGACTATGAGAATCGTCATCATT 59.959 38.462 0.00 0.00 38.21 2.57
1009 1021 4.282496 AGGACGAACAGGACTATGAGAAT 58.718 43.478 0.00 0.00 0.00 2.40
1019 1031 0.395312 GAACCCAAGGACGAACAGGA 59.605 55.000 0.00 0.00 0.00 3.86
1021 1033 0.249741 ACGAACCCAAGGACGAACAG 60.250 55.000 10.56 0.00 32.99 3.16
1066 1080 9.927081 ACTCATAAATTTACCTGAATGAGGATT 57.073 29.630 21.76 6.70 46.33 3.01
1107 1121 8.400186 GCAGCCCGACTAAAAATAATTAACTAA 58.600 33.333 0.00 0.00 0.00 2.24
1113 1127 5.185056 AGTTGCAGCCCGACTAAAAATAATT 59.815 36.000 0.00 0.00 36.38 1.40
1117 1131 2.514803 AGTTGCAGCCCGACTAAAAAT 58.485 42.857 0.00 0.00 36.38 1.82
1142 1156 2.097466 CGCGAACAGGATTAAAGCCATT 59.903 45.455 0.00 0.00 0.00 3.16
1162 1176 6.530913 AATGACAATCAATAGGACGAATCG 57.469 37.500 0.00 0.00 0.00 3.34
1181 1195 3.430098 GGGTGATGCGCCAATAAAAATGA 60.430 43.478 4.18 0.00 35.42 2.57
1189 1203 0.106769 TACATGGGTGATGCGCCAAT 60.107 50.000 4.18 0.00 35.42 3.16
1203 1217 6.357240 CACACTTATCGATAGTCACGTACATG 59.643 42.308 5.09 0.00 37.40 3.21
1205 1219 5.581874 TCACACTTATCGATAGTCACGTACA 59.418 40.000 5.09 0.00 37.40 2.90
1213 1227 5.141182 AGGGATGTCACACTTATCGATAGT 58.859 41.667 5.09 3.74 37.40 2.12
1216 1230 4.443457 CCAAGGGATGTCACACTTATCGAT 60.443 45.833 2.16 2.16 31.86 3.59
1225 1239 5.640147 ACTTTTATTCCAAGGGATGTCACA 58.360 37.500 0.00 0.00 0.00 3.58
1231 1245 6.062095 CCGTATGACTTTTATTCCAAGGGAT 58.938 40.000 0.00 0.00 0.00 3.85
1244 1258 4.923871 CGCAAGATATAGCCGTATGACTTT 59.076 41.667 0.00 0.00 43.02 2.66
1274 1288 8.052748 TGGTCTCTTATAGCCAAAACATATGTT 58.947 33.333 15.47 15.47 40.50 2.71
1305 1319 7.093552 TGTCAAAATCCGTGGGATCATAAAAAT 60.094 33.333 0.00 0.00 42.27 1.82
1307 1321 5.712446 TGTCAAAATCCGTGGGATCATAAAA 59.288 36.000 0.00 0.00 42.27 1.52
1314 1328 1.004745 AGCTGTCAAAATCCGTGGGAT 59.995 47.619 0.00 0.00 45.46 3.85
1315 1329 0.400213 AGCTGTCAAAATCCGTGGGA 59.600 50.000 0.00 0.00 35.55 4.37
1349 1363 4.067972 TGGAGAAAGTAGGACACAACAC 57.932 45.455 0.00 0.00 0.00 3.32
1371 1385 9.311916 GCTTGCAAAAACATATAATATTGTGGA 57.688 29.630 0.00 0.00 0.00 4.02
1372 1386 9.316730 AGCTTGCAAAAACATATAATATTGTGG 57.683 29.630 0.00 0.00 0.00 4.17
1382 1396 9.927668 AAACTAACATAGCTTGCAAAAACATAT 57.072 25.926 0.00 0.00 0.00 1.78
1384 1398 9.927668 ATAAACTAACATAGCTTGCAAAAACAT 57.072 25.926 0.00 0.00 0.00 2.71
1416 1454 9.621629 ACTCCCTCTATCTCATAATATAAGACG 57.378 37.037 0.00 0.00 0.00 4.18
1470 1523 9.959721 ACCACAAAATAATCAGTAGTGTTCTAT 57.040 29.630 0.00 0.00 0.00 1.98
1537 1597 0.739813 GTGGGATTGTCGACGAAGGG 60.740 60.000 10.11 0.00 0.00 3.95
1546 1606 2.093447 ACGATGAAGAGGTGGGATTGTC 60.093 50.000 0.00 0.00 0.00 3.18
1610 1671 9.627395 AAGCAGATATACATAACGTGATTCTAC 57.373 33.333 0.00 0.00 0.00 2.59
1615 1676 6.072119 TCGGAAGCAGATATACATAACGTGAT 60.072 38.462 0.00 0.00 0.00 3.06
1616 1677 5.239963 TCGGAAGCAGATATACATAACGTGA 59.760 40.000 0.00 0.00 0.00 4.35
1617 1678 5.458015 TCGGAAGCAGATATACATAACGTG 58.542 41.667 0.00 0.00 0.00 4.49
1618 1679 5.700722 TCGGAAGCAGATATACATAACGT 57.299 39.130 0.00 0.00 0.00 3.99
1619 1680 7.116376 ACAAATCGGAAGCAGATATACATAACG 59.884 37.037 0.00 0.00 0.00 3.18
1620 1681 8.311650 ACAAATCGGAAGCAGATATACATAAC 57.688 34.615 0.00 0.00 0.00 1.89
1626 1687 9.599866 CCATAATACAAATCGGAAGCAGATATA 57.400 33.333 0.00 0.00 0.00 0.86
1627 1688 8.321353 TCCATAATACAAATCGGAAGCAGATAT 58.679 33.333 0.00 0.00 0.00 1.63
1628 1689 7.676004 TCCATAATACAAATCGGAAGCAGATA 58.324 34.615 0.00 0.00 0.00 1.98
1629 1690 6.533730 TCCATAATACAAATCGGAAGCAGAT 58.466 36.000 0.00 0.00 0.00 2.90
1630 1691 5.924356 TCCATAATACAAATCGGAAGCAGA 58.076 37.500 0.00 0.00 0.00 4.26
1631 1692 5.334414 GCTCCATAATACAAATCGGAAGCAG 60.334 44.000 0.00 0.00 0.00 4.24
1632 1693 4.515191 GCTCCATAATACAAATCGGAAGCA 59.485 41.667 0.00 0.00 0.00 3.91
1633 1694 4.757149 AGCTCCATAATACAAATCGGAAGC 59.243 41.667 0.00 0.00 0.00 3.86
1634 1695 6.091441 GCTAGCTCCATAATACAAATCGGAAG 59.909 42.308 7.70 0.00 0.00 3.46
1635 1696 5.932303 GCTAGCTCCATAATACAAATCGGAA 59.068 40.000 7.70 0.00 0.00 4.30
1636 1697 5.479306 GCTAGCTCCATAATACAAATCGGA 58.521 41.667 7.70 0.00 0.00 4.55
1637 1698 4.327357 CGCTAGCTCCATAATACAAATCGG 59.673 45.833 13.93 0.00 0.00 4.18
1638 1699 5.161358 TCGCTAGCTCCATAATACAAATCG 58.839 41.667 13.93 0.00 0.00 3.34
1639 1700 6.813649 TGATCGCTAGCTCCATAATACAAATC 59.186 38.462 13.93 0.00 0.00 2.17
1656 1717 5.821995 TCATTCAACATGGAAATGATCGCTA 59.178 36.000 12.79 0.00 0.00 4.26
1658 1719 4.923893 TCATTCAACATGGAAATGATCGC 58.076 39.130 12.79 0.00 0.00 4.58
1660 1721 7.516155 CGCAATTCATTCAACATGGAAATGATC 60.516 37.037 15.84 0.00 0.00 2.92
1661 1722 6.256975 CGCAATTCATTCAACATGGAAATGAT 59.743 34.615 15.84 4.74 0.00 2.45
1663 1724 5.349270 ACGCAATTCATTCAACATGGAAATG 59.651 36.000 0.00 4.27 0.00 2.32
1672 1733 3.805823 ACACGTACGCAATTCATTCAAC 58.194 40.909 16.72 0.00 0.00 3.18
1677 1738 2.803386 TCACAACACGTACGCAATTCAT 59.197 40.909 16.72 0.00 0.00 2.57
1678 1739 2.202566 TCACAACACGTACGCAATTCA 58.797 42.857 16.72 0.00 0.00 2.57
1679 1740 2.220133 ACTCACAACACGTACGCAATTC 59.780 45.455 16.72 0.00 0.00 2.17
1680 1741 2.033236 CACTCACAACACGTACGCAATT 60.033 45.455 16.72 4.18 0.00 2.32
1745 1806 2.674380 GCCTTGAGGTGCTGTGGG 60.674 66.667 0.00 0.00 37.57 4.61
1786 1847 4.072088 CGTCGAACAGGTTGCGCC 62.072 66.667 4.18 0.00 37.58 6.53
1909 1970 1.207329 AGGTCAGTATGTTTCGGAGGC 59.793 52.381 0.00 0.00 37.40 4.70
1914 1975 9.745880 AATATTGTAGTAGGTCAGTATGTTTCG 57.254 33.333 0.00 0.00 37.40 3.46
1917 1978 7.652105 CGCAATATTGTAGTAGGTCAGTATGTT 59.348 37.037 16.61 0.00 37.40 2.71
1926 1987 2.547218 CCGGCGCAATATTGTAGTAGGT 60.547 50.000 16.61 0.00 0.00 3.08
1928 1989 2.066262 CCCGGCGCAATATTGTAGTAG 58.934 52.381 16.61 9.16 0.00 2.57
2056 2117 2.892425 CGAACTCCATGGCCGCTC 60.892 66.667 6.96 0.51 0.00 5.03
2408 2856 2.303022 CACCCACACCACATACTTCTCT 59.697 50.000 0.00 0.00 0.00 3.10
2411 2859 1.613255 CCCACCCACACCACATACTTC 60.613 57.143 0.00 0.00 0.00 3.01
2448 2896 7.757173 CGAGATTCATACTTCACCGATCATAAT 59.243 37.037 0.00 0.00 0.00 1.28
2490 2938 6.617879 TCATATTACGGTGGAGATTGATACG 58.382 40.000 0.00 0.00 0.00 3.06
2558 3011 6.257423 CAAATTCGTGCATGCAGTTCTTATA 58.743 36.000 23.41 1.10 0.00 0.98
2559 3012 4.970662 AATTCGTGCATGCAGTTCTTAT 57.029 36.364 23.41 6.25 0.00 1.73
2593 3046 2.540101 GACTGTTGTTCAGAACTCCACG 59.460 50.000 14.51 7.60 46.27 4.94
2611 3064 3.435671 CGTTTCCGGCTTGAAATTAGACT 59.564 43.478 0.00 0.00 36.68 3.24
2662 3115 3.778619 CCAAGTCATGGTGCCGATA 57.221 52.632 0.00 0.00 44.85 2.92
2663 3116 4.643795 CCAAGTCATGGTGCCGAT 57.356 55.556 0.00 0.00 44.85 4.18
2698 3151 8.154649 ACACAATGGGATCGAAATTATAAGTC 57.845 34.615 0.00 0.00 0.00 3.01
2699 3152 9.793259 ATACACAATGGGATCGAAATTATAAGT 57.207 29.630 0.00 0.00 0.00 2.24
2728 3181 5.935945 TCCTTATTCTCCAAACTTGTGTCA 58.064 37.500 0.00 0.00 0.00 3.58
2785 3238 2.522185 ACAGGTGAAATTGCAGAGCAT 58.478 42.857 0.00 0.00 38.76 3.79
2837 3291 5.939764 ATATGTGCTGTTCTCCTCTGTTA 57.060 39.130 0.00 0.00 0.00 2.41
2855 3309 7.869937 ACAGATTGAACTGACGAATCCTATATG 59.130 37.037 0.00 0.00 40.63 1.78
2866 3323 5.223382 ACAGTCTTACAGATTGAACTGACG 58.777 41.667 7.27 0.00 40.63 4.35
2927 3387 2.482142 GGTTCTTGATAGCGAGAGGGTG 60.482 54.545 0.00 0.00 35.96 4.61
3024 3484 0.666913 AGTGGATCCGATAACCGACG 59.333 55.000 7.39 0.00 41.76 5.12
3069 3529 1.705873 TCTAAAGAGGAGGCGGATCC 58.294 55.000 0.00 0.00 39.89 3.36
3142 3602 4.401525 CTGAAATGCAGTGACAGAGAAC 57.598 45.455 13.76 0.00 39.85 3.01
3187 3648 6.432162 GGATATTGCTCTTCTTTATGATGGCA 59.568 38.462 0.00 0.00 0.00 4.92
3202 3665 5.009410 CAGAAATTCCCAGTGGATATTGCTC 59.991 44.000 11.95 5.45 41.40 4.26
3226 3689 6.758886 CAGGTTTGATAGTACTCCAAGATGAC 59.241 42.308 0.00 0.90 0.00 3.06
3227 3690 6.440647 ACAGGTTTGATAGTACTCCAAGATGA 59.559 38.462 0.00 0.00 0.00 2.92
3228 3691 6.644347 ACAGGTTTGATAGTACTCCAAGATG 58.356 40.000 0.00 7.79 0.00 2.90
3231 3694 7.122948 ACTCTACAGGTTTGATAGTACTCCAAG 59.877 40.741 0.00 0.00 0.00 3.61
3233 3696 6.491383 ACTCTACAGGTTTGATAGTACTCCA 58.509 40.000 0.00 0.00 0.00 3.86
3235 3698 6.538021 TCGACTCTACAGGTTTGATAGTACTC 59.462 42.308 0.00 0.00 0.00 2.59
3236 3699 6.413052 TCGACTCTACAGGTTTGATAGTACT 58.587 40.000 0.00 0.00 0.00 2.73
3237 3700 6.674694 TCGACTCTACAGGTTTGATAGTAC 57.325 41.667 0.00 0.00 0.00 2.73
3334 3815 7.156876 TCTATTTGATGGCTAAAGTGGTTTG 57.843 36.000 0.00 0.00 0.00 2.93
3338 3819 7.223387 GCATTTTCTATTTGATGGCTAAAGTGG 59.777 37.037 0.00 0.00 0.00 4.00
3339 3820 7.043854 CGCATTTTCTATTTGATGGCTAAAGTG 60.044 37.037 0.00 0.00 0.00 3.16
3421 3906 7.393234 TCTGGGAGGTACTGTATTTTCAAATTG 59.607 37.037 0.00 0.00 41.55 2.32


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

AutoCloner maintained by Alex Coulton.