Multiple sequence alignment - TraesCS1B01G422600

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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 TraesCS1B01G422600 chr1B 100.000 2558 0 0 1 2558 645529697 645532254 0.000000e+00 4724
1 TraesCS1B01G422600 chr1B 87.770 139 17 0 2274 2412 555355815 555355677 2.040000e-36 163
2 TraesCS1B01G422600 chr1B 87.050 139 18 0 2274 2412 378629860 378629722 9.470000e-35 158
3 TraesCS1B01G422600 chr1B 88.462 130 15 0 2274 2403 610318350 610318479 9.470000e-35 158
4 TraesCS1B01G422600 chr1D 89.575 2072 138 19 229 2265 467628316 467630344 0.000000e+00 2558
5 TraesCS1B01G422600 chr1D 87.562 201 22 3 1 198 77799249 77799449 1.980000e-56 230
6 TraesCS1B01G422600 chr1D 87.000 200 24 2 1 198 77800030 77800229 9.210000e-55 224
7 TraesCS1B01G422600 chr1D 94.068 118 6 1 2405 2522 467644005 467644121 7.270000e-41 178
8 TraesCS1B01G422600 chr1A 91.997 1412 91 9 252 1655 560311483 560310086 0.000000e+00 1962
9 TraesCS1B01G422600 chr1A 87.321 418 48 3 1714 2131 491376534 491376122 8.280000e-130 473
10 TraesCS1B01G422600 chr1A 87.065 201 22 4 1 198 4035328 4035527 9.210000e-55 224
11 TraesCS1B01G422600 chr2D 88.067 419 44 4 1714 2131 645666368 645665955 2.290000e-135 492
12 TraesCS1B01G422600 chr2D 88.060 134 15 1 2273 2406 478820901 478820769 9.470000e-35 158
13 TraesCS1B01G422600 chr7A 87.560 418 47 3 1714 2131 10422949 10423361 1.780000e-131 479
14 TraesCS1B01G422600 chr7A 86.175 217 24 6 1 213 674751672 674751458 1.980000e-56 230
15 TraesCS1B01G422600 chr5B 87.321 418 48 3 1714 2131 638783200 638783612 8.280000e-130 473
16 TraesCS1B01G422600 chr5B 89.474 133 13 1 2274 2406 665813249 665813118 1.570000e-37 167
17 TraesCS1B01G422600 chr5B 89.147 129 14 0 2274 2402 424190768 424190640 7.320000e-36 161
18 TraesCS1B01G422600 chr3B 87.143 420 50 2 1712 2131 92330448 92330033 8.280000e-130 473
19 TraesCS1B01G422600 chr3B 90.576 191 16 2 1 189 47194225 47194415 4.220000e-63 252
20 TraesCS1B01G422600 chr3B 87.050 139 18 0 2274 2412 125703765 125703627 9.470000e-35 158
21 TraesCS1B01G422600 chr2A 86.885 427 50 4 1705 2131 26933191 26932771 8.280000e-130 473
22 TraesCS1B01G422600 chr2A 87.112 419 50 2 1713 2131 138922378 138922792 2.980000e-129 472
23 TraesCS1B01G422600 chr2A 87.442 215 25 2 1 213 62699378 62699164 1.970000e-61 246
24 TraesCS1B01G422600 chr3D 86.854 426 51 3 1707 2131 56362602 56362181 2.980000e-129 472
25 TraesCS1B01G422600 chr3D 89.529 191 18 2 1 189 27679103 27678913 9.150000e-60 241
26 TraesCS1B01G422600 chr7D 91.099 191 15 2 1 189 411893360 411893170 9.080000e-65 257
27 TraesCS1B01G422600 chr7D 80.000 190 23 11 37 224 265008789 265008965 2.670000e-25 126
28 TraesCS1B01G422600 chr7B 89.529 191 18 2 1 189 720307857 720307667 9.150000e-60 241
29 TraesCS1B01G422600 chr7B 88.462 130 15 0 2274 2403 330370970 330371099 9.470000e-35 158
30 TraesCS1B01G422600 chr2B 88.550 131 15 0 2273 2403 29189286 29189416 2.630000e-35 159


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 TraesCS1B01G422600 chr1B 645529697 645532254 2557 False 4724 4724 100.000 1 2558 1 chr1B.!!$F2 2557
1 TraesCS1B01G422600 chr1D 467628316 467630344 2028 False 2558 2558 89.575 229 2265 1 chr1D.!!$F1 2036
2 TraesCS1B01G422600 chr1D 77799249 77800229 980 False 227 230 87.281 1 198 2 chr1D.!!$F3 197
3 TraesCS1B01G422600 chr1A 560310086 560311483 1397 True 1962 1962 91.997 252 1655 1 chr1A.!!$R2 1403

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
219 223 0.035056 AAGATGGGTGCAGCCACTAC 60.035 55.0 38.27 28.99 41.75 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2068 2487 0.105039 AGATCTTGCGGGATTCGGTC 59.895 55.0 0.0 0.0 39.69 4.79 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
23 24 1.586422 TCTGCTCAAACAGTGCACTC 58.414 50.000 18.64 4.26 41.43 3.51
25 26 1.003116 CTGCTCAAACAGTGCACTCAC 60.003 52.381 18.64 1.94 41.43 3.51
90 92 4.576463 GCTCCTCGAATGTTATTTGACCAT 59.424 41.667 0.00 0.00 0.00 3.55
117 120 4.461081 ACTTTCAAGCGCCCATAACATTTA 59.539 37.500 2.29 0.00 0.00 1.40
120 123 4.930963 TCAAGCGCCCATAACATTTATTG 58.069 39.130 2.29 0.00 0.00 1.90
121 124 4.050553 CAAGCGCCCATAACATTTATTGG 58.949 43.478 2.29 0.00 0.00 3.16
123 126 4.465886 AGCGCCCATAACATTTATTGGTA 58.534 39.130 2.29 0.00 0.00 3.25
125 128 5.361285 AGCGCCCATAACATTTATTGGTAAA 59.639 36.000 2.29 0.00 29.37 2.01
130 133 9.040939 GCCCATAACATTTATTGGTAAACATTC 57.959 33.333 0.00 0.00 32.91 2.67
184 188 3.243068 GCTATATTTTCTTGCGTGGGTGG 60.243 47.826 0.00 0.00 0.00 4.61
199 203 2.203001 TGGACCGTGTGTGCACTG 60.203 61.111 19.41 5.23 40.77 3.66
201 205 1.522806 GGACCGTGTGTGCACTGAA 60.523 57.895 19.41 0.02 43.16 3.02
202 206 1.498865 GGACCGTGTGTGCACTGAAG 61.499 60.000 19.41 6.52 43.16 3.02
203 207 0.529773 GACCGTGTGTGCACTGAAGA 60.530 55.000 19.41 0.00 43.16 2.87
204 208 0.106708 ACCGTGTGTGCACTGAAGAT 59.893 50.000 19.41 0.00 43.16 2.40
213 217 2.177950 CACTGAAGATGGGTGCAGC 58.822 57.895 7.55 7.55 31.74 5.25
214 218 1.001641 ACTGAAGATGGGTGCAGCC 60.002 57.895 28.15 28.15 31.74 4.85
215 219 1.001764 CTGAAGATGGGTGCAGCCA 60.002 57.895 37.62 37.62 39.65 4.75
216 220 1.303561 TGAAGATGGGTGCAGCCAC 60.304 57.895 38.27 28.90 41.32 5.01
217 221 1.001641 GAAGATGGGTGCAGCCACT 60.002 57.895 38.27 30.43 41.75 4.00
218 222 0.253044 GAAGATGGGTGCAGCCACTA 59.747 55.000 38.27 18.07 41.75 2.74
219 223 0.035056 AAGATGGGTGCAGCCACTAC 60.035 55.000 38.27 28.99 41.75 2.73
220 224 0.911525 AGATGGGTGCAGCCACTACT 60.912 55.000 38.27 30.50 41.75 2.57
221 225 0.035056 GATGGGTGCAGCCACTACTT 60.035 55.000 38.27 23.27 41.75 2.24
222 226 0.405585 ATGGGTGCAGCCACTACTTT 59.594 50.000 38.27 19.90 41.75 2.66
223 227 0.250727 TGGGTGCAGCCACTACTTTC 60.251 55.000 33.13 4.75 41.75 2.62
224 228 0.960861 GGGTGCAGCCACTACTTTCC 60.961 60.000 29.70 1.08 41.75 3.13
225 229 0.960861 GGTGCAGCCACTACTTTCCC 60.961 60.000 4.03 0.00 41.75 3.97
226 230 0.036875 GTGCAGCCACTACTTTCCCT 59.963 55.000 0.00 0.00 38.93 4.20
227 231 0.324943 TGCAGCCACTACTTTCCCTC 59.675 55.000 0.00 0.00 0.00 4.30
418 425 3.269643 TCAGAAGATGTCCCTCAGGTCTA 59.730 47.826 0.00 0.00 0.00 2.59
457 464 2.122783 TCCAAGGAAATACCGGCTTG 57.877 50.000 0.00 5.76 44.74 4.01
468 475 2.255252 CGGCTTGTTGCTTTCCCG 59.745 61.111 0.00 0.00 42.39 5.14
477 484 2.695666 TGTTGCTTTCCCGGAAATTTCA 59.304 40.909 19.49 8.84 30.85 2.69
542 549 2.687935 AGTCAAAAACTGCACATTCGGT 59.312 40.909 0.00 0.00 36.65 4.69
543 550 3.130340 AGTCAAAAACTGCACATTCGGTT 59.870 39.130 0.00 0.00 36.65 4.44
544 551 3.485743 GTCAAAAACTGCACATTCGGTTC 59.514 43.478 0.00 0.00 34.68 3.62
545 552 3.380004 TCAAAAACTGCACATTCGGTTCT 59.620 39.130 0.00 0.00 34.68 3.01
547 554 5.066634 TCAAAAACTGCACATTCGGTTCTAA 59.933 36.000 0.00 0.00 34.68 2.10
610 617 4.074627 TCCCAACATAGACACAACGAAA 57.925 40.909 0.00 0.00 0.00 3.46
625 632 1.754226 ACGAAATTGCCAACCACAGTT 59.246 42.857 0.00 0.00 36.33 3.16
684 703 0.243636 GAATTTTGCGTGTGGGAGGG 59.756 55.000 0.00 0.00 0.00 4.30
685 704 1.184970 AATTTTGCGTGTGGGAGGGG 61.185 55.000 0.00 0.00 0.00 4.79
743 762 7.998753 AAGAAGATTGAAAGAAGCAACAAAG 57.001 32.000 0.00 0.00 0.00 2.77
758 777 2.715046 ACAAAGACCACGATCATGCAT 58.285 42.857 0.00 0.00 0.00 3.96
759 778 2.421073 ACAAAGACCACGATCATGCATG 59.579 45.455 21.07 21.07 0.00 4.06
763 782 0.677414 ACCACGATCATGCATGCACA 60.677 50.000 25.37 13.51 0.00 4.57
783 802 5.909610 GCACACTTTGAATCTTAGACAACAC 59.090 40.000 0.00 0.00 0.00 3.32
796 815 3.109230 GACAACACGTCATCATCTTGC 57.891 47.619 0.00 0.00 44.69 4.01
797 816 2.738846 GACAACACGTCATCATCTTGCT 59.261 45.455 0.00 0.00 44.69 3.91
798 817 2.481568 ACAACACGTCATCATCTTGCTG 59.518 45.455 0.00 0.00 0.00 4.41
799 818 2.462456 ACACGTCATCATCTTGCTGT 57.538 45.000 0.00 0.00 0.00 4.40
800 819 2.341257 ACACGTCATCATCTTGCTGTC 58.659 47.619 0.00 0.00 0.00 3.51
801 820 2.028658 ACACGTCATCATCTTGCTGTCT 60.029 45.455 0.00 0.00 0.00 3.41
802 821 2.998670 CACGTCATCATCTTGCTGTCTT 59.001 45.455 0.00 0.00 0.00 3.01
803 822 2.998670 ACGTCATCATCTTGCTGTCTTG 59.001 45.455 0.00 0.00 0.00 3.02
804 823 2.998670 CGTCATCATCTTGCTGTCTTGT 59.001 45.455 0.00 0.00 0.00 3.16
805 824 3.061831 CGTCATCATCTTGCTGTCTTGTC 59.938 47.826 0.00 0.00 0.00 3.18
806 825 4.252073 GTCATCATCTTGCTGTCTTGTCT 58.748 43.478 0.00 0.00 0.00 3.41
807 826 5.414360 GTCATCATCTTGCTGTCTTGTCTA 58.586 41.667 0.00 0.00 0.00 2.59
808 827 5.290643 GTCATCATCTTGCTGTCTTGTCTAC 59.709 44.000 0.00 0.00 0.00 2.59
809 828 5.186603 TCATCATCTTGCTGTCTTGTCTACT 59.813 40.000 0.00 0.00 0.00 2.57
810 829 6.378280 TCATCATCTTGCTGTCTTGTCTACTA 59.622 38.462 0.00 0.00 0.00 1.82
811 830 6.782082 TCATCTTGCTGTCTTGTCTACTAT 57.218 37.500 0.00 0.00 0.00 2.12
812 831 7.175347 TCATCTTGCTGTCTTGTCTACTATT 57.825 36.000 0.00 0.00 0.00 1.73
813 832 7.261325 TCATCTTGCTGTCTTGTCTACTATTC 58.739 38.462 0.00 0.00 0.00 1.75
814 833 6.842437 TCTTGCTGTCTTGTCTACTATTCT 57.158 37.500 0.00 0.00 0.00 2.40
815 834 6.857956 TCTTGCTGTCTTGTCTACTATTCTC 58.142 40.000 0.00 0.00 0.00 2.87
816 835 5.584253 TGCTGTCTTGTCTACTATTCTCC 57.416 43.478 0.00 0.00 0.00 3.71
942 990 8.582891 ACTTCCCTTCCTATATAAACCTTCAT 57.417 34.615 0.00 0.00 0.00 2.57
1053 1101 2.622942 TCATGCACCACTTTTCCAAGAC 59.377 45.455 0.00 0.00 33.72 3.01
1056 1104 0.951558 CACCACTTTTCCAAGACCCG 59.048 55.000 0.00 0.00 33.72 5.28
1170 1218 0.820482 TCTCCACGACAACCTCGACA 60.820 55.000 0.00 0.00 46.14 4.35
1209 1257 0.605319 AGACATCGAAGGCGCCAAAA 60.605 50.000 31.54 11.53 37.46 2.44
1242 1290 1.594397 GATGAGATGAATGCGACGCAA 59.406 47.619 28.24 11.33 43.62 4.85
1276 1324 3.073650 GGTAGCCATGAGAAAGATGGGAT 59.926 47.826 0.00 0.00 40.80 3.85
1278 1326 3.563223 AGCCATGAGAAAGATGGGATTG 58.437 45.455 0.00 0.00 40.80 2.67
1318 1366 9.601217 AGAAAAGCTGTGAATATATTTCTACGT 57.399 29.630 0.00 0.00 34.79 3.57
1320 1368 9.988350 AAAAGCTGTGAATATATTTCTACGTTG 57.012 29.630 0.00 0.00 0.00 4.10
1324 1372 8.600625 GCTGTGAATATATTTCTACGTTGTTCA 58.399 33.333 0.00 0.00 0.00 3.18
1356 1404 2.157738 CCAAGCTTCCAGGAAGTGAAG 58.842 52.381 27.15 15.73 41.27 3.02
1362 1410 0.620556 TCCAGGAAGTGAAGATGGCC 59.379 55.000 0.00 0.00 0.00 5.36
1448 1496 2.714250 ACAACTTGGGATTAGGTGACCA 59.286 45.455 3.63 0.00 34.42 4.02
1504 1552 7.503549 TGCTAGATATGACATGAACAATGACT 58.496 34.615 0.00 2.07 38.72 3.41
1661 1709 8.383175 TGATTCCAGAACTAAATAACTGGTCTT 58.617 33.333 0.00 0.00 46.68 3.01
1664 1712 8.617290 TCCAGAACTAAATAACTGGTCTTTTC 57.383 34.615 0.00 0.00 46.68 2.29
1686 2041 2.317530 TTTGAAAAAGGGGTTTGGCG 57.682 45.000 0.00 0.00 0.00 5.69
1705 2060 1.587547 GTCTAGCATTGCCACTAGCC 58.412 55.000 4.70 0.00 42.71 3.93
1711 2066 1.336125 GCATTGCCACTAGCCATCTTC 59.664 52.381 0.00 0.00 42.71 2.87
1712 2067 2.928334 CATTGCCACTAGCCATCTTCT 58.072 47.619 0.00 0.00 42.71 2.85
1713 2068 3.285484 CATTGCCACTAGCCATCTTCTT 58.715 45.455 0.00 0.00 42.71 2.52
1714 2069 3.439857 TTGCCACTAGCCATCTTCTTT 57.560 42.857 0.00 0.00 42.71 2.52
1769 2188 4.507710 TCAATCATGGCAGTACTGAGAAC 58.492 43.478 27.08 12.80 0.00 3.01
1777 2196 2.734079 GCAGTACTGAGAACACTTGAGC 59.266 50.000 27.08 1.99 0.00 4.26
1780 2199 5.398169 CAGTACTGAGAACACTTGAGCTAG 58.602 45.833 18.45 0.00 0.00 3.42
1781 2200 3.951775 ACTGAGAACACTTGAGCTAGG 57.048 47.619 0.00 0.00 0.00 3.02
1782 2201 3.235200 ACTGAGAACACTTGAGCTAGGT 58.765 45.455 0.00 0.00 0.00 3.08
1783 2202 3.006323 ACTGAGAACACTTGAGCTAGGTG 59.994 47.826 0.00 10.40 41.76 4.00
1785 2204 3.834813 TGAGAACACTTGAGCTAGGTGAT 59.165 43.478 16.60 7.64 38.57 3.06
1786 2205 5.016831 TGAGAACACTTGAGCTAGGTGATA 58.983 41.667 16.60 0.00 38.57 2.15
1787 2206 5.480422 TGAGAACACTTGAGCTAGGTGATAA 59.520 40.000 16.60 0.00 38.57 1.75
1789 2208 6.769512 AGAACACTTGAGCTAGGTGATAAAA 58.230 36.000 16.60 0.00 38.57 1.52
1791 2210 7.885399 AGAACACTTGAGCTAGGTGATAAAAAT 59.115 33.333 16.60 0.00 38.57 1.82
1793 2212 9.515226 AACACTTGAGCTAGGTGATAAAAATTA 57.485 29.630 16.60 0.00 38.57 1.40
1794 2213 8.947115 ACACTTGAGCTAGGTGATAAAAATTAC 58.053 33.333 16.60 0.00 38.57 1.89
1795 2214 8.946085 CACTTGAGCTAGGTGATAAAAATTACA 58.054 33.333 0.00 0.00 38.57 2.41
1796 2215 9.515226 ACTTGAGCTAGGTGATAAAAATTACAA 57.485 29.630 0.00 0.00 0.00 2.41
1797 2216 9.774742 CTTGAGCTAGGTGATAAAAATTACAAC 57.225 33.333 0.00 0.00 0.00 3.32
1799 2218 7.885922 TGAGCTAGGTGATAAAAATTACAACCA 59.114 33.333 0.00 0.00 0.00 3.67
1800 2219 8.644374 AGCTAGGTGATAAAAATTACAACCAA 57.356 30.769 0.00 0.00 0.00 3.67
1801 2220 8.739972 AGCTAGGTGATAAAAATTACAACCAAG 58.260 33.333 0.00 0.00 0.00 3.61
1802 2221 8.520351 GCTAGGTGATAAAAATTACAACCAAGT 58.480 33.333 0.00 0.00 0.00 3.16
1810 2229 9.705290 ATAAAAATTACAACCAAGTTCATGGAC 57.295 29.630 0.00 0.00 43.54 4.02
1830 2249 1.404391 CCACCTAGCGACGACTACAAT 59.596 52.381 0.00 0.00 0.00 2.71
1843 2262 2.600867 GACTACAATCACTGAAGCGAGC 59.399 50.000 0.00 0.00 0.00 5.03
1877 2296 2.143419 GTCATCGCCCCTCCCTCAT 61.143 63.158 0.00 0.00 0.00 2.90
1878 2297 1.838846 TCATCGCCCCTCCCTCATC 60.839 63.158 0.00 0.00 0.00 2.92
1883 2302 1.383803 GCCCCTCCCTCATCAGAGT 60.384 63.158 0.00 0.00 40.40 3.24
1884 2303 1.406860 GCCCCTCCCTCATCAGAGTC 61.407 65.000 0.00 0.00 40.40 3.36
1888 2307 1.028905 CTCCCTCATCAGAGTCGGAC 58.971 60.000 0.00 0.00 40.40 4.79
1892 2311 2.611518 CCTCATCAGAGTCGGACAAAC 58.388 52.381 11.27 1.67 40.40 2.93
1899 2318 3.385433 TCAGAGTCGGACAAACCTTGTTA 59.615 43.478 11.27 0.00 45.52 2.41
1905 2324 6.996509 AGTCGGACAAACCTTGTTATAGTAA 58.003 36.000 11.27 0.00 45.52 2.24
1926 2345 2.479566 TAGTAGGGAAGTCGTCGTGT 57.520 50.000 0.00 0.00 0.00 4.49
1947 2366 0.471591 AAGGCCCCAATGAAACAGCA 60.472 50.000 0.00 0.00 0.00 4.41
1973 2392 1.263484 GAGCAGCAACCATCATCGATG 59.737 52.381 19.61 19.61 39.52 3.84
1974 2393 1.134310 AGCAGCAACCATCATCGATGA 60.134 47.619 29.09 29.09 42.09 2.92
1980 2399 3.873361 GCAACCATCATCGATGAAGAGAA 59.127 43.478 30.41 8.45 42.09 2.87
1991 2410 5.763088 TCGATGAAGAGAATTGTAGATCGG 58.237 41.667 0.00 0.00 33.86 4.18
1995 2414 7.096271 CGATGAAGAGAATTGTAGATCGGAAAG 60.096 40.741 0.00 0.00 0.00 2.62
2012 2431 4.517453 CGGAAAGATCAAACCTGTAACCAA 59.483 41.667 0.00 0.00 0.00 3.67
2033 2452 5.513495 CCAAATGAACGAAGACGAACAAAAA 59.487 36.000 0.00 0.00 42.66 1.94
2041 2460 4.610680 CGAAGACGAACAAAAACTGGATCC 60.611 45.833 4.20 4.20 42.66 3.36
2066 2485 7.148507 CCAAATAGATCCATCGAAGATAAGCAC 60.149 40.741 1.60 0.00 45.12 4.40
2068 2487 2.509052 TCCATCGAAGATAAGCACCG 57.491 50.000 0.00 0.00 45.12 4.94
2071 2490 2.128035 CATCGAAGATAAGCACCGACC 58.872 52.381 0.00 0.00 45.12 4.79
2079 2498 2.287457 TAAGCACCGACCGAATCCCG 62.287 60.000 0.00 0.00 38.18 5.14
2081 2500 4.444838 CACCGACCGAATCCCGCA 62.445 66.667 0.00 0.00 36.84 5.69
2083 2502 2.890474 CCGACCGAATCCCGCAAG 60.890 66.667 0.00 0.00 36.84 4.01
2087 2506 0.105039 GACCGAATCCCGCAAGATCT 59.895 55.000 0.00 0.00 43.02 2.75
2092 2511 0.179073 AATCCCGCAAGATCTGACGG 60.179 55.000 23.41 23.41 41.53 4.79
2095 2514 1.880340 CCGCAAGATCTGACGGAGC 60.880 63.158 25.24 9.75 43.31 4.70
2115 2535 2.402564 CCACACCTCCACATATCCTCT 58.597 52.381 0.00 0.00 0.00 3.69
2121 2541 3.161067 CCTCCACATATCCTCTGACGAT 58.839 50.000 0.00 0.00 0.00 3.73
2142 2562 3.157881 TGCTATTCGCCACTAGCTATCT 58.842 45.455 2.62 0.00 40.78 1.98
2154 2574 6.226052 CCACTAGCTATCTTACATGCATGAA 58.774 40.000 32.75 19.66 0.00 2.57
2218 2650 4.799564 TGCAAGATCCCCAAAATAACAC 57.200 40.909 0.00 0.00 0.00 3.32
2219 2651 4.155709 TGCAAGATCCCCAAAATAACACA 58.844 39.130 0.00 0.00 0.00 3.72
2220 2652 4.220382 TGCAAGATCCCCAAAATAACACAG 59.780 41.667 0.00 0.00 0.00 3.66
2221 2653 4.462483 GCAAGATCCCCAAAATAACACAGA 59.538 41.667 0.00 0.00 0.00 3.41
2222 2654 5.622233 GCAAGATCCCCAAAATAACACAGAC 60.622 44.000 0.00 0.00 0.00 3.51
2224 2656 3.885976 TCCCCAAAATAACACAGACCA 57.114 42.857 0.00 0.00 0.00 4.02
2265 2698 4.105057 ACCCAACCAGTATTCAGGTACAAA 59.895 41.667 0.00 0.00 37.07 2.83
2266 2699 4.457949 CCCAACCAGTATTCAGGTACAAAC 59.542 45.833 0.00 0.00 37.07 2.93
2267 2700 5.067273 CCAACCAGTATTCAGGTACAAACA 58.933 41.667 0.00 0.00 37.07 2.83
2268 2701 5.710099 CCAACCAGTATTCAGGTACAAACAT 59.290 40.000 0.00 0.00 37.07 2.71
2269 2702 6.208599 CCAACCAGTATTCAGGTACAAACATT 59.791 38.462 0.00 0.00 37.07 2.71
2270 2703 6.817765 ACCAGTATTCAGGTACAAACATTG 57.182 37.500 0.00 0.00 36.07 2.82
2272 2705 6.775629 ACCAGTATTCAGGTACAAACATTGTT 59.224 34.615 0.54 0.00 42.22 2.83
2273 2706 7.286775 ACCAGTATTCAGGTACAAACATTGTTT 59.713 33.333 8.97 8.97 42.22 2.83
2274 2707 7.594758 CCAGTATTCAGGTACAAACATTGTTTG 59.405 37.037 31.05 31.05 42.22 2.93
2275 2708 8.134895 CAGTATTCAGGTACAAACATTGTTTGT 58.865 33.333 36.50 36.50 42.22 2.83
2276 2709 9.344772 AGTATTCAGGTACAAACATTGTTTGTA 57.655 29.630 34.83 34.83 42.22 2.41
2283 2716 5.767816 ACAAACATTGTTTGTACTCCCTC 57.232 39.130 34.95 0.00 42.22 4.30
2284 2717 4.583073 ACAAACATTGTTTGTACTCCCTCC 59.417 41.667 34.95 0.00 42.22 4.30
2285 2718 3.053831 ACATTGTTTGTACTCCCTCCG 57.946 47.619 0.00 0.00 36.57 4.63
2286 2719 2.370849 ACATTGTTTGTACTCCCTCCGT 59.629 45.455 0.00 0.00 36.57 4.69
2287 2720 3.181448 ACATTGTTTGTACTCCCTCCGTT 60.181 43.478 0.00 0.00 36.57 4.44
2288 2721 2.825861 TGTTTGTACTCCCTCCGTTC 57.174 50.000 0.00 0.00 0.00 3.95
2289 2722 1.345415 TGTTTGTACTCCCTCCGTTCC 59.655 52.381 0.00 0.00 0.00 3.62
2290 2723 1.345415 GTTTGTACTCCCTCCGTTCCA 59.655 52.381 0.00 0.00 0.00 3.53
2291 2724 1.719529 TTGTACTCCCTCCGTTCCAA 58.280 50.000 0.00 0.00 0.00 3.53
2292 2725 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
2293 2726 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
2294 2727 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
2295 2728 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
2296 2729 4.472108 TGTACTCCCTCCGTTCCAAAATAT 59.528 41.667 0.00 0.00 0.00 1.28
2297 2730 5.662208 TGTACTCCCTCCGTTCCAAAATATA 59.338 40.000 0.00 0.00 0.00 0.86
2298 2731 5.703730 ACTCCCTCCGTTCCAAAATATAA 57.296 39.130 0.00 0.00 0.00 0.98
2299 2732 5.681639 ACTCCCTCCGTTCCAAAATATAAG 58.318 41.667 0.00 0.00 0.00 1.73
2300 2733 5.191124 ACTCCCTCCGTTCCAAAATATAAGT 59.809 40.000 0.00 0.00 0.00 2.24
2301 2734 5.677567 TCCCTCCGTTCCAAAATATAAGTC 58.322 41.667 0.00 0.00 0.00 3.01
2302 2735 5.427481 TCCCTCCGTTCCAAAATATAAGTCT 59.573 40.000 0.00 0.00 0.00 3.24
2303 2736 5.527582 CCCTCCGTTCCAAAATATAAGTCTG 59.472 44.000 0.00 0.00 0.00 3.51
2304 2737 6.113411 CCTCCGTTCCAAAATATAAGTCTGT 58.887 40.000 0.00 0.00 0.00 3.41
2305 2738 6.598064 CCTCCGTTCCAAAATATAAGTCTGTT 59.402 38.462 0.00 0.00 0.00 3.16
2306 2739 7.120726 CCTCCGTTCCAAAATATAAGTCTGTTT 59.879 37.037 0.00 0.00 0.00 2.83
2307 2740 9.158233 CTCCGTTCCAAAATATAAGTCTGTTTA 57.842 33.333 0.00 0.00 0.00 2.01
2308 2741 9.158233 TCCGTTCCAAAATATAAGTCTGTTTAG 57.842 33.333 0.00 0.00 0.00 1.85
2309 2742 9.158233 CCGTTCCAAAATATAAGTCTGTTTAGA 57.842 33.333 0.00 0.00 0.00 2.10
2343 2776 6.130298 TGAATTACATACGGAGCAAAATGG 57.870 37.500 0.00 0.00 0.00 3.16
2347 2780 2.290641 ACATACGGAGCAAAATGGGTGA 60.291 45.455 0.00 0.00 0.00 4.02
2349 2782 1.923356 ACGGAGCAAAATGGGTGAAT 58.077 45.000 0.00 0.00 0.00 2.57
2350 2783 1.818674 ACGGAGCAAAATGGGTGAATC 59.181 47.619 0.00 0.00 0.00 2.52
2353 2786 3.065371 CGGAGCAAAATGGGTGAATCTAC 59.935 47.826 0.00 0.00 0.00 2.59
2357 2790 6.212888 AGCAAAATGGGTGAATCTACATTC 57.787 37.500 0.00 0.00 39.24 2.67
2359 2792 7.118723 AGCAAAATGGGTGAATCTACATTCTA 58.881 34.615 0.00 0.00 39.49 2.10
2361 2794 8.250332 GCAAAATGGGTGAATCTACATTCTAAA 58.750 33.333 0.00 0.00 39.49 1.85
2366 2799 8.657074 TGGGTGAATCTACATTCTAAATTACG 57.343 34.615 0.00 0.00 39.49 3.18
2368 2801 8.762426 GGGTGAATCTACATTCTAAATTACGTC 58.238 37.037 0.00 0.00 39.49 4.34
2369 2802 9.530633 GGTGAATCTACATTCTAAATTACGTCT 57.469 33.333 0.00 0.00 39.49 4.18
2413 2932 9.869844 GTTCATATTGAAATCTTTAGATGACGG 57.130 33.333 0.00 0.00 38.22 4.79
2414 2933 8.087982 TCATATTGAAATCTTTAGATGACGGC 57.912 34.615 0.00 0.00 34.49 5.68
2416 2935 5.801350 TTGAAATCTTTAGATGACGGCTG 57.199 39.130 0.00 0.00 34.49 4.85
2417 2936 5.084818 TGAAATCTTTAGATGACGGCTGA 57.915 39.130 0.00 0.00 34.49 4.26
2418 2937 5.111989 TGAAATCTTTAGATGACGGCTGAG 58.888 41.667 0.00 0.00 34.49 3.35
2420 2939 1.757118 TCTTTAGATGACGGCTGAGGG 59.243 52.381 0.00 0.00 0.00 4.30
2421 2940 0.178068 TTTAGATGACGGCTGAGGGC 59.822 55.000 0.00 0.00 40.90 5.19
2422 2941 0.975556 TTAGATGACGGCTGAGGGCA 60.976 55.000 0.00 0.00 44.01 5.36
2423 2942 0.975556 TAGATGACGGCTGAGGGCAA 60.976 55.000 0.00 0.00 44.01 4.52
2424 2943 2.045926 ATGACGGCTGAGGGCAAC 60.046 61.111 0.00 0.00 44.01 4.17
2425 2944 2.803155 GATGACGGCTGAGGGCAACA 62.803 60.000 0.00 0.00 44.01 3.33
2426 2945 2.743928 GACGGCTGAGGGCAACAG 60.744 66.667 0.00 5.93 44.01 3.16
2433 2952 0.737219 CTGAGGGCAACAGCAATAGC 59.263 55.000 0.00 0.00 42.56 2.97
2465 2984 4.053469 GCTAGTCCAAGCTAGGAAGAAG 57.947 50.000 0.00 0.00 39.92 2.85
2466 2985 3.702045 GCTAGTCCAAGCTAGGAAGAAGA 59.298 47.826 0.00 0.00 39.92 2.87
2467 2986 4.343814 GCTAGTCCAAGCTAGGAAGAAGAT 59.656 45.833 0.00 0.00 39.92 2.40
2468 2987 5.508994 GCTAGTCCAAGCTAGGAAGAAGATC 60.509 48.000 0.00 0.00 39.92 2.75
2469 2988 4.357325 AGTCCAAGCTAGGAAGAAGATCA 58.643 43.478 0.00 0.00 39.92 2.92
2470 2989 4.968080 AGTCCAAGCTAGGAAGAAGATCAT 59.032 41.667 0.00 0.00 39.92 2.45
2471 2990 5.055812 GTCCAAGCTAGGAAGAAGATCATG 58.944 45.833 0.00 0.00 39.92 3.07
2472 2991 4.964897 TCCAAGCTAGGAAGAAGATCATGA 59.035 41.667 0.00 0.00 33.93 3.07
2473 2992 5.426509 TCCAAGCTAGGAAGAAGATCATGAA 59.573 40.000 0.00 0.00 33.93 2.57
2474 2993 5.526846 CCAAGCTAGGAAGAAGATCATGAAC 59.473 44.000 0.00 0.00 0.00 3.18
2475 2994 5.946942 AGCTAGGAAGAAGATCATGAACA 57.053 39.130 0.00 0.00 0.00 3.18
2476 2995 5.916318 AGCTAGGAAGAAGATCATGAACAG 58.084 41.667 0.00 0.00 0.00 3.16
2477 2996 4.511082 GCTAGGAAGAAGATCATGAACAGC 59.489 45.833 0.00 0.00 0.00 4.40
2478 2997 4.564782 AGGAAGAAGATCATGAACAGCA 57.435 40.909 0.00 0.00 0.00 4.41
2479 2998 4.515361 AGGAAGAAGATCATGAACAGCAG 58.485 43.478 0.00 0.00 0.00 4.24
2480 2999 3.626670 GGAAGAAGATCATGAACAGCAGG 59.373 47.826 0.00 0.00 0.00 4.85
2481 3000 3.996921 AGAAGATCATGAACAGCAGGT 57.003 42.857 0.00 0.00 0.00 4.00
2482 3001 3.607741 AGAAGATCATGAACAGCAGGTG 58.392 45.455 0.00 0.00 0.00 4.00
2483 3002 2.414994 AGATCATGAACAGCAGGTGG 57.585 50.000 0.00 0.00 0.00 4.61
2484 3003 0.737219 GATCATGAACAGCAGGTGGC 59.263 55.000 0.00 0.00 45.30 5.01
2485 3004 0.682209 ATCATGAACAGCAGGTGGCC 60.682 55.000 0.00 0.00 46.50 5.36
2486 3005 1.604308 CATGAACAGCAGGTGGCCA 60.604 57.895 0.00 0.00 46.50 5.36
2487 3006 1.303888 ATGAACAGCAGGTGGCCAG 60.304 57.895 5.11 0.00 46.50 4.85
2488 3007 1.782201 ATGAACAGCAGGTGGCCAGA 61.782 55.000 5.11 0.00 46.50 3.86
2489 3008 1.228245 GAACAGCAGGTGGCCAGAA 60.228 57.895 5.11 0.00 46.50 3.02
2490 3009 1.228367 AACAGCAGGTGGCCAGAAG 60.228 57.895 5.11 0.00 46.50 2.85
2491 3010 1.708993 AACAGCAGGTGGCCAGAAGA 61.709 55.000 5.11 0.00 46.50 2.87
2492 3011 1.073722 CAGCAGGTGGCCAGAAGAA 59.926 57.895 5.11 0.00 46.50 2.52
2493 3012 1.073897 AGCAGGTGGCCAGAAGAAC 59.926 57.895 5.11 0.00 46.50 3.01
2494 3013 2.328099 GCAGGTGGCCAGAAGAACG 61.328 63.158 5.11 0.00 36.11 3.95
2495 3014 1.071471 CAGGTGGCCAGAAGAACGT 59.929 57.895 5.11 0.00 0.00 3.99
2496 3015 1.071471 AGGTGGCCAGAAGAACGTG 59.929 57.895 5.11 0.00 0.00 4.49
2497 3016 2.617274 GGTGGCCAGAAGAACGTGC 61.617 63.158 5.11 0.00 0.00 5.34
2498 3017 1.598130 GTGGCCAGAAGAACGTGCT 60.598 57.895 5.11 0.00 0.00 4.40
2499 3018 1.597854 TGGCCAGAAGAACGTGCTG 60.598 57.895 0.00 0.00 0.00 4.41
2501 3020 3.257933 CCAGAAGAACGTGCTGGC 58.742 61.111 0.00 0.00 42.30 4.85
2502 3021 2.671177 CCAGAAGAACGTGCTGGCG 61.671 63.158 0.00 0.00 42.30 5.69
2504 3023 1.956170 AGAAGAACGTGCTGGCGTG 60.956 57.895 0.00 0.00 45.00 5.34
2505 3024 2.954753 GAAGAACGTGCTGGCGTGG 61.955 63.158 0.00 0.00 45.00 4.94
2512 3031 4.765449 TGCTGGCGTGGCAGCTAG 62.765 66.667 37.21 15.80 46.62 3.42
2533 3052 4.799473 CGTGCGCGCATCAGGTTG 62.799 66.667 38.62 16.53 0.00 3.77
2534 3053 4.465512 GTGCGCGCATCAGGTTGG 62.466 66.667 38.62 0.00 0.00 3.77
2540 3059 4.424711 GCATCAGGTTGGCCGGGA 62.425 66.667 2.18 0.00 40.50 5.14
2541 3060 2.438434 CATCAGGTTGGCCGGGAC 60.438 66.667 2.18 0.00 40.50 4.46
2556 3075 2.165319 GGGACGACACAGTTTTAGCT 57.835 50.000 0.00 0.00 0.00 3.32
2557 3076 1.798813 GGGACGACACAGTTTTAGCTG 59.201 52.381 0.00 0.00 41.92 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.976793 AGTCAAAATGTGAGTGCACTG 57.023 42.857 27.27 8.21 45.36 3.66
60 61 7.224753 TCAAATAACATTCGAGGAGCTCAATAC 59.775 37.037 17.19 0.00 0.00 1.89
61 62 7.224753 GTCAAATAACATTCGAGGAGCTCAATA 59.775 37.037 17.19 0.00 0.00 1.90
62 63 6.037610 GTCAAATAACATTCGAGGAGCTCAAT 59.962 38.462 17.19 2.72 0.00 2.57
63 64 5.351465 GTCAAATAACATTCGAGGAGCTCAA 59.649 40.000 17.19 0.74 0.00 3.02
64 65 4.870426 GTCAAATAACATTCGAGGAGCTCA 59.130 41.667 17.19 0.00 0.00 4.26
67 69 3.938963 TGGTCAAATAACATTCGAGGAGC 59.061 43.478 0.00 0.00 0.00 4.70
90 92 1.327303 ATGGGCGCTTGAAAGTTTGA 58.673 45.000 7.64 0.00 0.00 2.69
103 106 6.565234 TGTTTACCAATAAATGTTATGGGCG 58.435 36.000 1.89 0.00 37.26 6.13
117 120 9.480053 CTGAATTTTGTGAGAATGTTTACCAAT 57.520 29.630 0.00 0.00 0.00 3.16
120 123 9.696917 ATTCTGAATTTTGTGAGAATGTTTACC 57.303 29.630 0.00 0.00 34.56 2.85
155 159 6.364706 CCACGCAAGAAAATATAGCAAAACAA 59.635 34.615 0.00 0.00 43.62 2.83
157 161 5.288472 CCCACGCAAGAAAATATAGCAAAAC 59.712 40.000 0.00 0.00 43.62 2.43
163 167 4.035208 GTCCACCCACGCAAGAAAATATAG 59.965 45.833 0.00 0.00 43.62 1.31
168 172 1.104577 GGTCCACCCACGCAAGAAAA 61.105 55.000 0.00 0.00 43.62 2.29
191 195 3.327600 CACCCATCTTCAGTGCACA 57.672 52.632 21.04 0.00 0.00 4.57
198 202 1.303561 GTGGCTGCACCCATCTTCA 60.304 57.895 3.54 0.00 37.20 3.02
199 203 0.253044 TAGTGGCTGCACCCATCTTC 59.747 55.000 3.54 0.00 37.20 2.87
201 205 0.911525 AGTAGTGGCTGCACCCATCT 60.912 55.000 3.54 6.25 37.20 2.90
202 206 0.035056 AAGTAGTGGCTGCACCCATC 60.035 55.000 3.54 0.00 37.20 3.51
203 207 0.405585 AAAGTAGTGGCTGCACCCAT 59.594 50.000 3.54 0.00 37.20 4.00
204 208 0.250727 GAAAGTAGTGGCTGCACCCA 60.251 55.000 0.50 0.00 37.83 4.51
210 214 2.859165 TTGAGGGAAAGTAGTGGCTG 57.141 50.000 0.00 0.00 0.00 4.85
213 217 5.183904 CCAAGAAATTGAGGGAAAGTAGTGG 59.816 44.000 0.00 0.00 0.00 4.00
214 218 6.003950 TCCAAGAAATTGAGGGAAAGTAGTG 58.996 40.000 0.00 0.00 0.00 2.74
215 219 6.004574 GTCCAAGAAATTGAGGGAAAGTAGT 58.995 40.000 0.00 0.00 0.00 2.73
216 220 5.122396 CGTCCAAGAAATTGAGGGAAAGTAG 59.878 44.000 0.00 0.00 0.00 2.57
217 221 5.001232 CGTCCAAGAAATTGAGGGAAAGTA 58.999 41.667 0.00 0.00 0.00 2.24
218 222 3.821033 CGTCCAAGAAATTGAGGGAAAGT 59.179 43.478 0.00 0.00 0.00 2.66
219 223 4.072131 TCGTCCAAGAAATTGAGGGAAAG 58.928 43.478 0.00 0.00 0.00 2.62
220 224 4.093472 TCGTCCAAGAAATTGAGGGAAA 57.907 40.909 0.00 0.00 0.00 3.13
221 225 3.780804 TCGTCCAAGAAATTGAGGGAA 57.219 42.857 0.00 0.00 0.00 3.97
222 226 3.263170 TCATCGTCCAAGAAATTGAGGGA 59.737 43.478 0.00 0.00 0.00 4.20
223 227 3.609853 TCATCGTCCAAGAAATTGAGGG 58.390 45.455 0.00 0.00 0.00 4.30
224 228 4.455533 TGTTCATCGTCCAAGAAATTGAGG 59.544 41.667 0.00 0.00 0.00 3.86
225 229 5.385617 GTGTTCATCGTCCAAGAAATTGAG 58.614 41.667 0.00 0.00 0.00 3.02
226 230 4.215399 GGTGTTCATCGTCCAAGAAATTGA 59.785 41.667 0.00 0.00 0.00 2.57
227 231 4.475944 GGTGTTCATCGTCCAAGAAATTG 58.524 43.478 0.00 0.00 0.00 2.32
418 425 7.201857 CCTTGGAAAAAGAACAAGACTTGATCT 60.202 37.037 21.95 20.46 43.55 2.75
457 464 3.243737 ACTGAAATTTCCGGGAAAGCAAC 60.244 43.478 25.00 16.43 34.92 4.17
468 475 4.846779 TGGTGCTTACACTGAAATTTCC 57.153 40.909 15.48 0.00 46.57 3.13
477 484 4.067896 GCTATATGCATGGTGCTTACACT 58.932 43.478 10.16 0.00 45.31 3.55
569 576 4.576463 GGGAAACATACAGGACATGATGTC 59.424 45.833 16.95 16.95 46.23 3.06
588 595 3.755112 TCGTTGTGTCTATGTTGGGAA 57.245 42.857 0.00 0.00 0.00 3.97
610 617 2.600470 CACAAACTGTGGTTGGCAAT 57.400 45.000 1.92 0.00 44.27 3.56
625 632 8.694540 TGTGGTACTAGTTAGTTTAGTTCACAA 58.305 33.333 0.00 0.00 38.96 3.33
658 665 1.007964 CACGCAAAATTCGGTGCCA 60.008 52.632 3.84 0.00 37.47 4.92
684 703 4.086706 TGTTTCCTGGAAAAGTCTCTCC 57.913 45.455 22.66 8.98 33.14 3.71
685 704 4.697828 GGATGTTTCCTGGAAAAGTCTCTC 59.302 45.833 22.66 9.66 39.14 3.20
743 762 0.028505 GTGCATGCATGATCGTGGTC 59.971 55.000 30.64 10.13 0.00 4.02
758 777 5.588246 TGTTGTCTAAGATTCAAAGTGTGCA 59.412 36.000 0.00 0.00 0.00 4.57
759 778 5.909610 GTGTTGTCTAAGATTCAAAGTGTGC 59.090 40.000 0.00 0.00 0.00 4.57
763 782 6.526566 GACGTGTTGTCTAAGATTCAAAGT 57.473 37.500 0.00 0.00 44.58 2.66
783 802 2.998670 ACAAGACAGCAAGATGATGACG 59.001 45.455 2.23 0.00 35.45 4.35
796 815 6.723298 ATGGGAGAATAGTAGACAAGACAG 57.277 41.667 0.00 0.00 0.00 3.51
797 816 7.839705 ACTTATGGGAGAATAGTAGACAAGACA 59.160 37.037 0.00 0.00 0.00 3.41
798 817 8.240267 ACTTATGGGAGAATAGTAGACAAGAC 57.760 38.462 0.00 0.00 0.00 3.01
799 818 8.840200 AACTTATGGGAGAATAGTAGACAAGA 57.160 34.615 0.00 0.00 0.00 3.02
800 819 9.892130 AAAACTTATGGGAGAATAGTAGACAAG 57.108 33.333 0.00 0.00 0.00 3.16
942 990 5.192927 GGTGTGGGAAAGATCATGTATCAA 58.807 41.667 0.00 0.00 37.03 2.57
1053 1101 1.417890 AGGATGAGAATACCAAGCGGG 59.582 52.381 0.00 0.00 44.81 6.13
1056 1104 6.238869 GGATGAAAAGGATGAGAATACCAAGC 60.239 42.308 0.00 0.00 0.00 4.01
1209 1257 7.042187 GCATTCATCTCATCGTATTCACTCTTT 60.042 37.037 0.00 0.00 0.00 2.52
1221 1269 0.160392 GCGTCGCATTCATCTCATCG 59.840 55.000 13.44 0.00 0.00 3.84
1242 1290 0.760567 TGGCTACCTCCGCATCTGAT 60.761 55.000 0.00 0.00 0.00 2.90
1251 1299 3.495806 CCATCTTTCTCATGGCTACCTCC 60.496 52.174 0.00 0.00 34.59 4.30
1276 1324 7.149973 CAGCTTTTCTCTTGATCAAAATCCAA 58.850 34.615 9.88 0.00 0.00 3.53
1278 1326 6.585322 CACAGCTTTTCTCTTGATCAAAATCC 59.415 38.462 9.88 0.00 0.00 3.01
1318 1366 0.922717 GGTTCGTCGTCGTTGAACAA 59.077 50.000 23.50 0.00 42.86 2.83
1320 1368 0.922717 TTGGTTCGTCGTCGTTGAAC 59.077 50.000 17.90 17.90 40.90 3.18
1324 1372 0.529119 AAGCTTGGTTCGTCGTCGTT 60.529 50.000 0.00 0.00 38.33 3.85
1356 1404 4.021192 TCATCAAAAACCAAGAAGGCCATC 60.021 41.667 5.01 1.19 43.14 3.51
1362 1410 7.922278 TCATTGTTCTCATCAAAAACCAAGAAG 59.078 33.333 0.00 0.00 0.00 2.85
1406 1454 0.661780 GAGGATTCGTCGCAGATCCG 60.662 60.000 13.08 0.00 40.67 4.18
1411 1459 0.456142 TTGTCGAGGATTCGTCGCAG 60.456 55.000 20.71 0.00 46.72 5.18
1426 1474 3.244770 TGGTCACCTAATCCCAAGTTGTC 60.245 47.826 1.45 0.00 0.00 3.18
1448 1496 2.044492 TCAGACTCATTGACCCCTACCT 59.956 50.000 0.00 0.00 0.00 3.08
1504 1552 4.756203 ACTCCATCAGATCTATCCTCCA 57.244 45.455 0.00 0.00 0.00 3.86
1661 1709 5.184096 GCCAAACCCCTTTTTCAAAAAGAAA 59.816 36.000 22.03 0.95 44.21 2.52
1664 1712 3.064682 CGCCAAACCCCTTTTTCAAAAAG 59.935 43.478 14.77 14.77 0.00 2.27
1676 1739 0.679960 AATGCTAGACGCCAAACCCC 60.680 55.000 0.00 0.00 38.05 4.95
1686 2041 1.134401 TGGCTAGTGGCAATGCTAGAC 60.134 52.381 13.18 11.15 46.03 2.59
1769 2188 8.946085 TGTAATTTTTATCACCTAGCTCAAGTG 58.054 33.333 0.00 0.00 0.00 3.16
1780 2199 9.705290 ATGAACTTGGTTGTAATTTTTATCACC 57.295 29.630 0.00 0.00 0.00 4.02
1782 2201 9.703892 CCATGAACTTGGTTGTAATTTTTATCA 57.296 29.630 0.00 0.00 31.74 2.15
1783 2202 9.921637 TCCATGAACTTGGTTGTAATTTTTATC 57.078 29.630 0.00 0.00 38.01 1.75
1785 2204 8.145122 GGTCCATGAACTTGGTTGTAATTTTTA 58.855 33.333 0.00 0.00 38.01 1.52
1786 2205 6.989759 GGTCCATGAACTTGGTTGTAATTTTT 59.010 34.615 0.00 0.00 38.01 1.94
1787 2206 6.098982 TGGTCCATGAACTTGGTTGTAATTTT 59.901 34.615 0.00 0.00 38.01 1.82
1789 2208 5.010617 GTGGTCCATGAACTTGGTTGTAATT 59.989 40.000 0.00 0.00 38.01 1.40
1791 2210 3.886505 GTGGTCCATGAACTTGGTTGTAA 59.113 43.478 0.00 0.00 38.01 2.41
1793 2212 2.306847 GTGGTCCATGAACTTGGTTGT 58.693 47.619 0.00 0.00 38.01 3.32
1794 2213 1.613437 GGTGGTCCATGAACTTGGTTG 59.387 52.381 0.00 0.00 38.01 3.77
1795 2214 1.499007 AGGTGGTCCATGAACTTGGTT 59.501 47.619 0.00 0.00 38.01 3.67
1796 2215 1.149101 AGGTGGTCCATGAACTTGGT 58.851 50.000 0.00 0.00 38.01 3.67
1797 2216 2.941415 GCTAGGTGGTCCATGAACTTGG 60.941 54.545 0.00 0.00 38.18 3.61
1799 2218 1.066143 CGCTAGGTGGTCCATGAACTT 60.066 52.381 0.00 0.00 35.89 2.66
1800 2219 0.537188 CGCTAGGTGGTCCATGAACT 59.463 55.000 0.00 0.00 35.89 3.01
1801 2220 0.535335 TCGCTAGGTGGTCCATGAAC 59.465 55.000 0.00 0.00 35.89 3.18
1802 2221 0.535335 GTCGCTAGGTGGTCCATGAA 59.465 55.000 0.00 0.00 35.89 2.57
1803 2222 1.663379 CGTCGCTAGGTGGTCCATGA 61.663 60.000 0.00 0.00 35.89 3.07
1810 2229 0.806868 TTGTAGTCGTCGCTAGGTGG 59.193 55.000 0.00 0.00 0.00 4.61
1830 2249 1.080501 CTTCGGCTCGCTTCAGTGA 60.081 57.895 0.00 0.00 0.00 3.41
1877 2296 1.760613 ACAAGGTTTGTCCGACTCTGA 59.239 47.619 0.00 0.00 40.56 3.27
1878 2297 2.240493 ACAAGGTTTGTCCGACTCTG 57.760 50.000 0.00 0.00 40.56 3.35
1883 2302 9.590451 CTATTTACTATAACAAGGTTTGTCCGA 57.410 33.333 0.00 0.00 44.59 4.55
1884 2303 9.374838 ACTATTTACTATAACAAGGTTTGTCCG 57.625 33.333 0.00 0.00 44.59 4.79
1899 2318 6.995091 ACGACGACTTCCCTACTATTTACTAT 59.005 38.462 0.00 0.00 0.00 2.12
1905 2324 3.350833 ACACGACGACTTCCCTACTATT 58.649 45.455 0.00 0.00 0.00 1.73
1911 2330 1.271656 CCTTAACACGACGACTTCCCT 59.728 52.381 0.00 0.00 0.00 4.20
1919 2338 0.675522 ATTGGGGCCTTAACACGACG 60.676 55.000 0.84 0.00 0.00 5.12
1926 2345 1.899142 GCTGTTTCATTGGGGCCTTAA 59.101 47.619 0.84 0.00 0.00 1.85
1947 2366 0.607489 GATGGTTGCTGCTCTGGTGT 60.607 55.000 0.00 0.00 0.00 4.16
1973 2392 8.293114 GATCTTTCCGATCTACAATTCTCTTC 57.707 38.462 0.00 0.00 44.21 2.87
1991 2410 7.657336 TCATTTGGTTACAGGTTTGATCTTTC 58.343 34.615 0.00 0.00 0.00 2.62
1995 2414 5.856455 CGTTCATTTGGTTACAGGTTTGATC 59.144 40.000 0.00 0.00 0.00 2.92
2003 2422 4.446385 TCGTCTTCGTTCATTTGGTTACAG 59.554 41.667 0.00 0.00 38.33 2.74
2012 2431 5.737290 CAGTTTTTGTTCGTCTTCGTTCATT 59.263 36.000 0.00 0.00 38.33 2.57
2041 2460 7.148507 GGTGCTTATCTTCGATGGATCTATTTG 60.149 40.741 4.94 0.00 0.00 2.32
2061 2480 2.267961 GGGATTCGGTCGGTGCTT 59.732 61.111 0.00 0.00 0.00 3.91
2066 2485 2.644555 ATCTTGCGGGATTCGGTCGG 62.645 60.000 0.00 0.00 39.69 4.79
2068 2487 0.105039 AGATCTTGCGGGATTCGGTC 59.895 55.000 0.00 0.00 39.69 4.79
2071 2490 1.212616 GTCAGATCTTGCGGGATTCG 58.787 55.000 0.00 0.00 42.76 3.34
2079 2498 1.086634 GTGGCTCCGTCAGATCTTGC 61.087 60.000 0.00 0.00 0.00 4.01
2081 2500 0.247736 GTGTGGCTCCGTCAGATCTT 59.752 55.000 0.00 0.00 0.00 2.40
2083 2502 1.153549 GGTGTGGCTCCGTCAGATC 60.154 63.158 0.00 0.00 0.00 2.75
2087 2506 3.311110 GGAGGTGTGGCTCCGTCA 61.311 66.667 0.00 0.00 0.00 4.35
2092 2511 1.202698 GGATATGTGGAGGTGTGGCTC 60.203 57.143 0.00 0.00 0.00 4.70
2095 2514 2.103771 CAGAGGATATGTGGAGGTGTGG 59.896 54.545 0.00 0.00 0.00 4.17
2108 2527 4.686839 CGAATAGCATCGTCAGAGGATA 57.313 45.455 5.28 0.00 38.01 2.59
2142 2562 4.684877 GCAATCCACATTCATGCATGTAA 58.315 39.130 25.43 17.92 35.51 2.41
2224 2656 3.650942 TGGGTACATCCAGTTCTCAAACT 59.349 43.478 0.00 0.00 46.80 2.66
2265 2698 2.370849 ACGGAGGGAGTACAAACAATGT 59.629 45.455 0.00 0.00 46.36 2.71
2266 2699 3.053831 ACGGAGGGAGTACAAACAATG 57.946 47.619 0.00 0.00 0.00 2.82
2267 2700 3.558533 GGAACGGAGGGAGTACAAACAAT 60.559 47.826 0.00 0.00 0.00 2.71
2268 2701 2.224354 GGAACGGAGGGAGTACAAACAA 60.224 50.000 0.00 0.00 0.00 2.83
2269 2702 1.345415 GGAACGGAGGGAGTACAAACA 59.655 52.381 0.00 0.00 0.00 2.83
2270 2703 1.345415 TGGAACGGAGGGAGTACAAAC 59.655 52.381 0.00 0.00 0.00 2.93
2271 2704 1.719529 TGGAACGGAGGGAGTACAAA 58.280 50.000 0.00 0.00 0.00 2.83
2272 2705 1.719529 TTGGAACGGAGGGAGTACAA 58.280 50.000 0.00 0.00 0.00 2.41
2273 2706 1.719529 TTTGGAACGGAGGGAGTACA 58.280 50.000 0.00 0.00 0.00 2.90
2274 2707 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
2275 2708 6.384886 ACTTATATTTTGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
2276 2709 5.191124 ACTTATATTTTGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
2277 2710 5.681639 ACTTATATTTTGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2278 2711 5.427481 AGACTTATATTTTGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2279 2712 5.527582 CAGACTTATATTTTGGAACGGAGGG 59.472 44.000 0.00 0.00 0.00 4.30
2280 2713 6.113411 ACAGACTTATATTTTGGAACGGAGG 58.887 40.000 0.00 0.00 0.00 4.30
2281 2714 7.611213 AACAGACTTATATTTTGGAACGGAG 57.389 36.000 0.00 0.00 0.00 4.63
2282 2715 7.989416 AAACAGACTTATATTTTGGAACGGA 57.011 32.000 0.00 0.00 0.00 4.69
2283 2716 9.158233 TCTAAACAGACTTATATTTTGGAACGG 57.842 33.333 0.00 0.00 0.00 4.44
2318 2751 7.040755 CCCATTTTGCTCCGTATGTAATTCATA 60.041 37.037 0.00 0.00 37.91 2.15
2319 2752 6.239008 CCCATTTTGCTCCGTATGTAATTCAT 60.239 38.462 0.00 0.00 40.25 2.57
2320 2753 5.067153 CCCATTTTGCTCCGTATGTAATTCA 59.933 40.000 0.00 0.00 0.00 2.57
2321 2754 5.067283 ACCCATTTTGCTCCGTATGTAATTC 59.933 40.000 0.00 0.00 0.00 2.17
2329 2762 2.570415 TTCACCCATTTTGCTCCGTA 57.430 45.000 0.00 0.00 0.00 4.02
2331 2764 2.094675 AGATTCACCCATTTTGCTCCG 58.905 47.619 0.00 0.00 0.00 4.63
2332 2765 4.016444 TGTAGATTCACCCATTTTGCTCC 58.984 43.478 0.00 0.00 0.00 4.70
2333 2766 5.841957 ATGTAGATTCACCCATTTTGCTC 57.158 39.130 0.00 0.00 0.00 4.26
2334 2767 5.954150 AGAATGTAGATTCACCCATTTTGCT 59.046 36.000 14.46 0.00 40.59 3.91
2341 2774 8.262227 ACGTAATTTAGAATGTAGATTCACCCA 58.738 33.333 14.46 0.00 40.59 4.51
2342 2775 8.658499 ACGTAATTTAGAATGTAGATTCACCC 57.342 34.615 14.46 0.00 40.59 4.61
2343 2776 9.530633 AGACGTAATTTAGAATGTAGATTCACC 57.469 33.333 14.46 0.00 40.59 4.02
2363 2796 9.551734 AACTACATACAGATGTATACAGACGTA 57.448 33.333 11.91 11.57 45.42 3.57
2365 2798 8.557029 TGAACTACATACAGATGTATACAGACG 58.443 37.037 11.91 4.38 45.42 4.18
2388 2907 8.559536 GCCGTCATCTAAAGATTTCAATATGAA 58.440 33.333 0.00 0.00 34.03 2.57
2389 2908 7.933577 AGCCGTCATCTAAAGATTTCAATATGA 59.066 33.333 0.00 0.00 31.21 2.15
2391 2910 7.933577 TCAGCCGTCATCTAAAGATTTCAATAT 59.066 33.333 0.00 0.00 31.21 1.28
2393 2912 6.115446 TCAGCCGTCATCTAAAGATTTCAAT 58.885 36.000 0.00 0.00 31.21 2.57
2401 2920 1.808133 GCCCTCAGCCGTCATCTAAAG 60.808 57.143 0.00 0.00 34.35 1.85
2405 2924 2.293318 TTGCCCTCAGCCGTCATCT 61.293 57.895 0.00 0.00 42.71 2.90
2407 2926 2.045926 GTTGCCCTCAGCCGTCAT 60.046 61.111 0.00 0.00 42.71 3.06
2409 2928 2.743928 CTGTTGCCCTCAGCCGTC 60.744 66.667 0.00 0.00 42.71 4.79
2414 2933 0.737219 GCTATTGCTGTTGCCCTCAG 59.263 55.000 0.00 0.00 38.71 3.35
2416 2935 1.026718 ACGCTATTGCTGTTGCCCTC 61.027 55.000 0.00 0.00 38.71 4.30
2417 2936 0.251916 TACGCTATTGCTGTTGCCCT 59.748 50.000 0.00 0.00 38.71 5.19
2418 2937 0.657840 CTACGCTATTGCTGTTGCCC 59.342 55.000 0.00 0.00 38.71 5.36
2420 2939 1.009829 AGCTACGCTATTGCTGTTGC 58.990 50.000 16.38 16.38 38.04 4.17
2421 2940 3.706698 TCTAGCTACGCTATTGCTGTTG 58.293 45.455 0.00 0.34 40.54 3.33
2422 2941 4.363999 CTTCTAGCTACGCTATTGCTGTT 58.636 43.478 0.00 0.00 40.54 3.16
2423 2942 3.797184 GCTTCTAGCTACGCTATTGCTGT 60.797 47.826 0.00 0.18 40.54 4.40
2424 2943 2.728839 GCTTCTAGCTACGCTATTGCTG 59.271 50.000 0.00 0.00 40.54 4.41
2425 2944 3.019933 GCTTCTAGCTACGCTATTGCT 57.980 47.619 0.00 0.00 40.54 3.91
2444 2963 3.702045 TCTTCTTCCTAGCTTGGACTAGC 59.298 47.826 16.99 0.00 38.68 3.42
2445 2964 5.596361 TGATCTTCTTCCTAGCTTGGACTAG 59.404 44.000 16.99 12.47 39.54 2.57
2446 2965 5.519808 TGATCTTCTTCCTAGCTTGGACTA 58.480 41.667 16.99 5.02 35.58 2.59
2447 2966 4.357325 TGATCTTCTTCCTAGCTTGGACT 58.643 43.478 16.99 0.00 35.58 3.85
2448 2967 4.744795 TGATCTTCTTCCTAGCTTGGAC 57.255 45.455 16.99 4.20 35.58 4.02
2449 2968 4.964897 TCATGATCTTCTTCCTAGCTTGGA 59.035 41.667 13.28 13.28 0.00 3.53
2450 2969 5.287674 TCATGATCTTCTTCCTAGCTTGG 57.712 43.478 8.03 8.03 0.00 3.61
2451 2970 6.111382 TGTTCATGATCTTCTTCCTAGCTTG 58.889 40.000 0.00 0.00 0.00 4.01
2452 2971 6.305272 TGTTCATGATCTTCTTCCTAGCTT 57.695 37.500 0.00 0.00 0.00 3.74
2453 2972 5.684552 GCTGTTCATGATCTTCTTCCTAGCT 60.685 44.000 0.00 0.00 0.00 3.32
2454 2973 4.511082 GCTGTTCATGATCTTCTTCCTAGC 59.489 45.833 0.00 0.00 0.00 3.42
2455 2974 5.668471 TGCTGTTCATGATCTTCTTCCTAG 58.332 41.667 0.00 0.00 0.00 3.02
2456 2975 5.396101 CCTGCTGTTCATGATCTTCTTCCTA 60.396 44.000 0.00 0.00 0.00 2.94
2457 2976 4.515361 CTGCTGTTCATGATCTTCTTCCT 58.485 43.478 0.00 0.00 0.00 3.36
2458 2977 3.626670 CCTGCTGTTCATGATCTTCTTCC 59.373 47.826 0.00 0.00 0.00 3.46
2459 2978 4.094590 CACCTGCTGTTCATGATCTTCTTC 59.905 45.833 0.00 0.00 0.00 2.87
2460 2979 4.008330 CACCTGCTGTTCATGATCTTCTT 58.992 43.478 0.00 0.00 0.00 2.52
2461 2980 3.607741 CACCTGCTGTTCATGATCTTCT 58.392 45.455 0.00 0.00 0.00 2.85
2462 2981 2.681848 CCACCTGCTGTTCATGATCTTC 59.318 50.000 0.00 0.00 0.00 2.87
2463 2982 2.719739 CCACCTGCTGTTCATGATCTT 58.280 47.619 0.00 0.00 0.00 2.40
2464 2983 1.681166 GCCACCTGCTGTTCATGATCT 60.681 52.381 0.00 0.00 36.87 2.75
2465 2984 0.737219 GCCACCTGCTGTTCATGATC 59.263 55.000 0.00 0.00 36.87 2.92
2466 2985 0.682209 GGCCACCTGCTGTTCATGAT 60.682 55.000 0.00 0.00 40.92 2.45
2467 2986 1.303561 GGCCACCTGCTGTTCATGA 60.304 57.895 0.00 0.00 40.92 3.07
2468 2987 1.592400 CTGGCCACCTGCTGTTCATG 61.592 60.000 0.00 0.00 40.92 3.07
2469 2988 1.303888 CTGGCCACCTGCTGTTCAT 60.304 57.895 0.00 0.00 40.92 2.57
2470 2989 1.993701 TTCTGGCCACCTGCTGTTCA 61.994 55.000 0.00 0.00 40.92 3.18
2471 2990 1.228245 TTCTGGCCACCTGCTGTTC 60.228 57.895 0.00 0.00 40.92 3.18
2472 2991 1.228367 CTTCTGGCCACCTGCTGTT 60.228 57.895 0.00 0.00 40.92 3.16
2473 2992 1.708993 TTCTTCTGGCCACCTGCTGT 61.709 55.000 0.00 0.00 40.92 4.40
2474 2993 1.073722 TTCTTCTGGCCACCTGCTG 59.926 57.895 0.00 0.00 40.92 4.41
2475 2994 1.073897 GTTCTTCTGGCCACCTGCT 59.926 57.895 0.00 0.00 40.92 4.24
2476 2995 2.328099 CGTTCTTCTGGCCACCTGC 61.328 63.158 0.00 0.00 40.16 4.85
2477 2996 1.071471 ACGTTCTTCTGGCCACCTG 59.929 57.895 0.00 0.00 0.00 4.00
2478 2997 1.071471 CACGTTCTTCTGGCCACCT 59.929 57.895 0.00 0.00 0.00 4.00
2479 2998 2.617274 GCACGTTCTTCTGGCCACC 61.617 63.158 0.00 0.00 0.00 4.61
2480 2999 1.598130 AGCACGTTCTTCTGGCCAC 60.598 57.895 0.00 0.00 0.00 5.01
2481 3000 1.597854 CAGCACGTTCTTCTGGCCA 60.598 57.895 4.71 4.71 0.00 5.36
2482 3001 2.328099 CCAGCACGTTCTTCTGGCC 61.328 63.158 0.00 0.00 40.63 5.36
2483 3002 3.257933 CCAGCACGTTCTTCTGGC 58.742 61.111 9.18 0.00 40.63 4.85
2485 3004 1.956170 ACGCCAGCACGTTCTTCTG 60.956 57.895 0.00 0.00 45.75 3.02
2486 3005 1.956170 CACGCCAGCACGTTCTTCT 60.956 57.895 0.00 0.00 45.75 2.85
2487 3006 2.551270 CACGCCAGCACGTTCTTC 59.449 61.111 0.00 0.00 45.75 2.87
2488 3007 2.972505 CCACGCCAGCACGTTCTT 60.973 61.111 0.00 0.00 45.75 2.52
2502 3021 3.181967 CACGTCGCTAGCTGCCAC 61.182 66.667 13.93 3.20 38.78 5.01
2516 3035 4.799473 CAACCTGATGCGCGCACG 62.799 66.667 39.05 26.13 44.07 5.34
2517 3036 4.465512 CCAACCTGATGCGCGCAC 62.466 66.667 39.05 28.53 0.00 5.34
2523 3042 4.424711 TCCCGGCCAACCTGATGC 62.425 66.667 2.24 0.00 0.00 3.91
2524 3043 2.438434 GTCCCGGCCAACCTGATG 60.438 66.667 2.24 0.00 0.00 3.07
2525 3044 4.096003 CGTCCCGGCCAACCTGAT 62.096 66.667 2.24 0.00 0.00 2.90
2530 3049 4.612412 TGTGTCGTCCCGGCCAAC 62.612 66.667 2.24 0.00 0.00 3.77
2531 3050 4.308458 CTGTGTCGTCCCGGCCAA 62.308 66.667 2.24 0.00 0.00 4.52
2533 3052 3.819877 AAACTGTGTCGTCCCGGCC 62.820 63.158 0.00 0.00 0.00 6.13
2534 3053 0.600782 TAAAACTGTGTCGTCCCGGC 60.601 55.000 0.00 0.00 0.00 6.13
2535 3054 1.425412 CTAAAACTGTGTCGTCCCGG 58.575 55.000 0.00 0.00 0.00 5.73
2536 3055 0.788391 GCTAAAACTGTGTCGTCCCG 59.212 55.000 0.00 0.00 0.00 5.14
2537 3056 1.798813 CAGCTAAAACTGTGTCGTCCC 59.201 52.381 0.00 0.00 32.78 4.46


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

AutoCloner maintained by Alex Coulton.