Multiple sequence alignment - TraesCS2B01G414400

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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 TraesCS2B01G414400 chr2B 100.000 1852 0 0 1 1852 592371645 592369794 0.000000e+00 3421.0
1 TraesCS2B01G414400 chr2B 100.000 259 0 0 2090 2348 592369556 592369298 1.630000e-131 479.0
2 TraesCS2B01G414400 chr2A 89.575 1861 107 31 3 1832 649564295 649562491 0.000000e+00 2281.0
3 TraesCS2B01G414400 chr2D 89.975 788 68 8 927 1712 503548434 503547656 0.000000e+00 1007.0
4 TraesCS2B01G414400 chr2D 87.109 256 32 1 2090 2345 503543037 503542783 2.950000e-74 289.0
5 TraesCS2B01G414400 chr2D 88.971 136 14 1 1708 1842 503543232 503543097 1.440000e-37 167.0
6 TraesCS2B01G414400 chr7D 82.400 125 20 2 128 251 53923532 53923655 8.870000e-20 108.0
7 TraesCS2B01G414400 chr1D 84.848 99 11 3 154 251 352937212 352937307 1.920000e-16 97.1
8 TraesCS2B01G414400 chr3D 94.737 38 1 1 34 70 586891553 586891590 9.060000e-05 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G414400 chr2B 592369298 592371645 2347 True 1950 3421 100.000 1 2348 2 chr2B.!!$R1 2347
1 TraesCS2B01G414400 chr2A 649562491 649564295 1804 True 2281 2281 89.575 3 1832 1 chr2A.!!$R1 1829
2 TraesCS2B01G414400 chr2D 503547656 503548434 778 True 1007 1007 89.975 927 1712 1 chr2D.!!$R1 785

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
345 357 0.386476 GATATACGGCCGTCCACACA 59.614 55.0 38.01 17.72 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 2178 0.096976 GCGTTCATCGGTGGTGATTG 59.903 55.0 0.0 0.0 40.26 2.67 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
100 103 8.995027 ACATTTATTATTAGATGGGCAACAGA 57.005 30.769 0.00 0.00 39.74 3.41
125 132 7.520119 TCTATACGCATTTAACACTTGTCAG 57.480 36.000 0.00 0.00 0.00 3.51
130 137 5.741982 ACGCATTTAACACTTGTCAGAAAAC 59.258 36.000 0.00 0.00 0.00 2.43
255 262 8.600449 TTTTTCGAATGCTTGGATTAATTTGT 57.400 26.923 0.00 0.00 0.00 2.83
256 263 9.698309 TTTTTCGAATGCTTGGATTAATTTGTA 57.302 25.926 0.00 0.00 0.00 2.41
287 299 4.687948 CAGATCGGTGCAACTATGATAAGG 59.312 45.833 0.00 0.00 36.74 2.69
293 305 4.202367 GGTGCAACTATGATAAGGGCTAGT 60.202 45.833 0.00 0.00 36.74 2.57
294 306 4.991687 GTGCAACTATGATAAGGGCTAGTC 59.008 45.833 0.00 0.00 0.00 2.59
296 308 5.011125 TGCAACTATGATAAGGGCTAGTCTC 59.989 44.000 0.00 0.00 0.00 3.36
298 310 6.571537 GCAACTATGATAAGGGCTAGTCTCTC 60.572 46.154 0.00 0.00 0.00 3.20
315 327 1.001020 TCACGGGCCGGTAAGACTA 60.001 57.895 31.78 2.73 0.00 2.59
324 336 4.259356 GGCCGGTAAGACTAATTTCAGTT 58.741 43.478 1.90 0.00 0.00 3.16
325 337 5.422145 GGCCGGTAAGACTAATTTCAGTTA 58.578 41.667 1.90 0.00 0.00 2.24
336 348 8.305317 AGACTAATTTCAGTTAGATATACGGCC 58.695 37.037 0.00 0.00 35.96 6.13
338 350 4.924305 TTTCAGTTAGATATACGGCCGT 57.076 40.909 36.01 36.01 0.00 5.68
340 352 2.816087 TCAGTTAGATATACGGCCGTCC 59.184 50.000 38.01 21.73 0.00 4.79
341 353 2.555325 CAGTTAGATATACGGCCGTCCA 59.445 50.000 38.01 24.34 0.00 4.02
342 354 2.555757 AGTTAGATATACGGCCGTCCAC 59.444 50.000 38.01 23.37 0.00 4.02
343 355 2.275134 TAGATATACGGCCGTCCACA 57.725 50.000 38.01 19.09 0.00 4.17
344 356 0.672342 AGATATACGGCCGTCCACAC 59.328 55.000 38.01 22.30 0.00 3.82
345 357 0.386476 GATATACGGCCGTCCACACA 59.614 55.000 38.01 17.72 0.00 3.72
350 371 2.662596 GGCCGTCCACACAGATCA 59.337 61.111 0.00 0.00 0.00 2.92
363 384 2.943690 CACAGATCAGGCTCTTCCATTG 59.056 50.000 0.00 0.00 37.29 2.82
371 392 3.814283 CAGGCTCTTCCATTGAGATAAGC 59.186 47.826 0.00 0.00 37.29 3.09
373 394 3.145286 GCTCTTCCATTGAGATAAGCCC 58.855 50.000 0.00 0.00 33.68 5.19
548 571 1.078709 CACGATTCACATCCGTGCTT 58.921 50.000 0.00 0.00 45.26 3.91
551 574 1.267038 CGATTCACATCCGTGCTTTCG 60.267 52.381 0.00 0.00 43.28 3.46
556 579 1.654105 CACATCCGTGCTTTCGTAGTC 59.346 52.381 0.00 0.00 36.06 2.59
568 591 0.821517 TCGTAGTCGTAGGTCCGGTA 59.178 55.000 0.00 0.00 38.33 4.02
569 592 1.412710 TCGTAGTCGTAGGTCCGGTAT 59.587 52.381 0.00 0.00 38.33 2.73
570 593 2.158957 TCGTAGTCGTAGGTCCGGTATT 60.159 50.000 0.00 0.00 38.33 1.89
571 594 2.032549 CGTAGTCGTAGGTCCGGTATTG 60.033 54.545 0.00 0.00 0.00 1.90
572 595 0.743097 AGTCGTAGGTCCGGTATTGC 59.257 55.000 0.00 0.00 0.00 3.56
573 596 0.743097 GTCGTAGGTCCGGTATTGCT 59.257 55.000 0.00 0.00 0.00 3.91
574 597 0.742505 TCGTAGGTCCGGTATTGCTG 59.257 55.000 0.00 0.00 0.00 4.41
575 598 0.874607 CGTAGGTCCGGTATTGCTGC 60.875 60.000 0.00 0.00 0.00 5.25
579 602 1.166531 GGTCCGGTATTGCTGCATCC 61.167 60.000 1.84 6.08 0.00 3.51
580 603 1.148273 TCCGGTATTGCTGCATCCC 59.852 57.895 1.84 2.86 0.00 3.85
583 606 0.464373 CGGTATTGCTGCATCCCACT 60.464 55.000 1.84 0.00 0.00 4.00
593 616 1.005097 TGCATCCCACTTGCATCTCTT 59.995 47.619 0.00 0.00 44.73 2.85
605 628 2.746375 ATCTCTTGCGCGGGGGATT 61.746 57.895 8.83 0.00 0.00 3.01
606 629 1.407656 ATCTCTTGCGCGGGGGATTA 61.408 55.000 8.83 0.00 0.00 1.75
646 669 7.859875 CCTCAGATTTCTCTTGTTTTTGTTCTC 59.140 37.037 0.00 0.00 0.00 2.87
648 671 6.634436 CAGATTTCTCTTGTTTTTGTTCTCGG 59.366 38.462 0.00 0.00 0.00 4.63
673 696 2.661504 TGTTCATTTGAGACGCAACG 57.338 45.000 0.00 0.00 35.91 4.10
705 728 1.063174 GTGCGCATGGAAATGAGACTC 59.937 52.381 15.91 0.00 0.00 3.36
706 729 0.659957 GCGCATGGAAATGAGACTCC 59.340 55.000 0.30 0.00 0.00 3.85
714 737 4.662278 TGGAAATGAGACTCCGGAAAATT 58.338 39.130 5.23 0.00 34.14 1.82
715 738 4.700213 TGGAAATGAGACTCCGGAAAATTC 59.300 41.667 5.23 1.65 34.14 2.17
729 752 4.266714 GGAAAATTCATGAAGGGACGGTA 58.733 43.478 14.54 0.00 0.00 4.02
731 754 6.059484 GGAAAATTCATGAAGGGACGGTATA 58.941 40.000 14.54 0.00 0.00 1.47
734 757 7.745620 AAATTCATGAAGGGACGGTATAATC 57.254 36.000 14.54 0.00 0.00 1.75
735 758 4.514781 TCATGAAGGGACGGTATAATCG 57.485 45.455 0.00 0.00 0.00 3.34
736 759 4.146564 TCATGAAGGGACGGTATAATCGA 58.853 43.478 0.00 0.00 0.00 3.59
737 760 4.585581 TCATGAAGGGACGGTATAATCGAA 59.414 41.667 0.00 0.00 0.00 3.71
738 761 5.245301 TCATGAAGGGACGGTATAATCGAAT 59.755 40.000 0.00 0.00 0.00 3.34
747 771 7.605309 GGGACGGTATAATCGAATTTTTAGGAT 59.395 37.037 0.00 0.00 0.00 3.24
803 827 3.358775 CAAGATTTTGTTGTTCGTCGCA 58.641 40.909 0.00 0.00 0.00 5.10
805 829 4.022464 AGATTTTGTTGTTCGTCGCAAA 57.978 36.364 0.00 0.00 0.00 3.68
827 851 1.285950 GGCCCGTTTCTTGTTGCTC 59.714 57.895 0.00 0.00 0.00 4.26
836 860 5.142962 CGTTTCTTGTTGCTCTCTGAATTC 58.857 41.667 0.00 0.00 0.00 2.17
893 917 8.877195 ACCCTTTCTGTATAATTGACCGTATAT 58.123 33.333 0.00 0.00 0.00 0.86
894 918 9.151471 CCCTTTCTGTATAATTGACCGTATATG 57.849 37.037 0.00 0.00 0.00 1.78
895 919 9.706691 CCTTTCTGTATAATTGACCGTATATGT 57.293 33.333 0.00 0.00 0.00 2.29
904 928 9.787435 ATAATTGACCGTATATGTATTTGTGGT 57.213 29.630 0.00 0.00 0.00 4.16
906 930 8.597662 ATTGACCGTATATGTATTTGTGGTAC 57.402 34.615 0.00 0.00 0.00 3.34
907 931 6.207928 TGACCGTATATGTATTTGTGGTACG 58.792 40.000 0.00 0.00 34.80 3.67
908 932 6.147864 ACCGTATATGTATTTGTGGTACGT 57.852 37.500 0.00 0.00 33.61 3.57
909 933 6.572519 ACCGTATATGTATTTGTGGTACGTT 58.427 36.000 0.00 0.00 33.61 3.99
910 934 7.041107 ACCGTATATGTATTTGTGGTACGTTT 58.959 34.615 0.00 0.00 33.61 3.60
911 935 7.010367 ACCGTATATGTATTTGTGGTACGTTTG 59.990 37.037 0.00 0.00 33.61 2.93
912 936 7.339207 CGTATATGTATTTGTGGTACGTTTGG 58.661 38.462 0.00 0.00 31.59 3.28
913 937 7.222417 CGTATATGTATTTGTGGTACGTTTGGA 59.778 37.037 0.00 0.00 31.59 3.53
914 938 5.873179 ATGTATTTGTGGTACGTTTGGAG 57.127 39.130 0.00 0.00 0.00 3.86
915 939 4.958509 TGTATTTGTGGTACGTTTGGAGA 58.041 39.130 0.00 0.00 0.00 3.71
916 940 5.553123 TGTATTTGTGGTACGTTTGGAGAT 58.447 37.500 0.00 0.00 0.00 2.75
917 941 6.699366 TGTATTTGTGGTACGTTTGGAGATA 58.301 36.000 0.00 0.00 0.00 1.98
962 986 4.576053 TGCTTATTCCCATGAATCTGTTCG 59.424 41.667 0.00 0.00 41.44 3.95
1038 1062 3.244249 GGTCTCTAGTGGAAACTGCAACT 60.244 47.826 0.00 0.00 0.00 3.16
1053 1077 4.278419 ACTGCAACTAGACAAATCAAACCC 59.722 41.667 0.00 0.00 0.00 4.11
1056 1080 4.069304 CAACTAGACAAATCAAACCCGGA 58.931 43.478 0.73 0.00 0.00 5.14
1073 1097 2.161609 CCGGAAATGGACTTGCAAGTAC 59.838 50.000 31.31 31.31 39.88 2.73
1124 1148 4.156455 TGAGAGTTTCAAGAACCAGCTT 57.844 40.909 0.00 0.00 31.34 3.74
1127 1151 1.683385 AGTTTCAAGAACCAGCTTGGC 59.317 47.619 0.00 0.00 42.67 4.52
1180 1204 4.501058 GGTTGATGACGATTACTACTCCCC 60.501 50.000 0.00 0.00 0.00 4.81
1181 1205 2.882761 TGATGACGATTACTACTCCCCG 59.117 50.000 0.00 0.00 0.00 5.73
1186 1210 2.092212 ACGATTACTACTCCCCGGAAGA 60.092 50.000 0.73 0.00 0.00 2.87
1189 1213 2.905415 TACTACTCCCCGGAAGAACA 57.095 50.000 0.73 0.00 0.00 3.18
1202 1226 4.563580 CCGGAAGAACAAGAAGGAGATCAA 60.564 45.833 0.00 0.00 0.00 2.57
1204 1228 4.390297 GGAAGAACAAGAAGGAGATCAACG 59.610 45.833 0.00 0.00 0.00 4.10
1217 1241 4.440802 GGAGATCAACGCTACTGAATCTGT 60.441 45.833 0.00 0.00 0.00 3.41
1362 1386 3.792401 CAAATGAGTCGCCAGGTATGTA 58.208 45.455 0.00 0.00 0.00 2.29
1398 1422 2.485814 GCTCTTCTCTGTTTTTCCGCAT 59.514 45.455 0.00 0.00 0.00 4.73
1400 1424 3.999663 CTCTTCTCTGTTTTTCCGCATCT 59.000 43.478 0.00 0.00 0.00 2.90
1401 1425 3.997021 TCTTCTCTGTTTTTCCGCATCTC 59.003 43.478 0.00 0.00 0.00 2.75
1402 1426 2.699954 TCTCTGTTTTTCCGCATCTCC 58.300 47.619 0.00 0.00 0.00 3.71
1403 1427 1.394917 CTCTGTTTTTCCGCATCTCCG 59.605 52.381 0.00 0.00 0.00 4.63
1404 1428 0.179189 CTGTTTTTCCGCATCTCCGC 60.179 55.000 0.00 0.00 0.00 5.54
1405 1429 0.886938 TGTTTTTCCGCATCTCCGCA 60.887 50.000 0.00 0.00 0.00 5.69
1449 1476 0.613012 AATTCTGTGCAGGGGGCTTC 60.613 55.000 0.00 0.00 45.15 3.86
1503 1530 1.402456 GCCTGGCCGTGTATATAGTCG 60.402 57.143 7.66 0.00 0.00 4.18
1532 1559 5.793817 TGTAGACATCATGTTGCTGTAGTT 58.206 37.500 3.61 0.00 25.39 2.24
1533 1560 6.930731 TGTAGACATCATGTTGCTGTAGTTA 58.069 36.000 3.61 0.00 25.39 2.24
1617 1644 5.584649 ACTGAACAAATTTCGAAGTCTGTCA 59.415 36.000 0.00 0.84 0.00 3.58
1639 1666 6.363357 GTCACTGTGCAATGTTTTATTTCCTC 59.637 38.462 2.12 0.00 0.00 3.71
1658 1685 1.347707 TCGTGAATCCATATGGGCTCC 59.652 52.381 21.78 9.21 36.21 4.70
1725 1752 1.955080 CGGTAAGAACCTCTAGCCGAT 59.045 52.381 11.20 0.00 42.50 4.18
1726 1753 3.144506 CGGTAAGAACCTCTAGCCGATA 58.855 50.000 11.20 0.00 42.50 2.92
1739 1766 5.247084 TCTAGCCGATACCTAGAAAGCTAG 58.753 45.833 9.32 9.32 46.11 3.42
1746 1776 6.437094 CGATACCTAGAAAGCTAGTACAACC 58.563 44.000 0.00 0.00 42.11 3.77
1757 1787 6.963049 AGCTAGTACAACCGAGTAAAATTG 57.037 37.500 0.00 0.00 0.00 2.32
1786 1816 3.183801 ACCCCACTAAACCGGATCTAAA 58.816 45.455 9.46 0.00 0.00 1.85
1834 1864 2.773993 AAAAATTAGTCCTCCGCCGA 57.226 45.000 0.00 0.00 0.00 5.54
1835 1865 2.773993 AAAATTAGTCCTCCGCCGAA 57.226 45.000 0.00 0.00 0.00 4.30
1836 1866 2.773993 AAATTAGTCCTCCGCCGAAA 57.226 45.000 0.00 0.00 0.00 3.46
1837 1867 3.277142 AAATTAGTCCTCCGCCGAAAT 57.723 42.857 0.00 0.00 0.00 2.17
1838 1868 2.528041 ATTAGTCCTCCGCCGAAATC 57.472 50.000 0.00 0.00 0.00 2.17
1839 1869 0.462789 TTAGTCCTCCGCCGAAATCC 59.537 55.000 0.00 0.00 0.00 3.01
1840 1870 1.397390 TAGTCCTCCGCCGAAATCCC 61.397 60.000 0.00 0.00 0.00 3.85
1841 1871 3.476419 TCCTCCGCCGAAATCCCC 61.476 66.667 0.00 0.00 0.00 4.81
1842 1872 4.564110 CCTCCGCCGAAATCCCCC 62.564 72.222 0.00 0.00 0.00 5.40
2106 2136 2.687566 TTCCCTCTTCTCCCGCCC 60.688 66.667 0.00 0.00 0.00 6.13
2125 2155 4.394712 CGCGGCTCCACCTTTCCT 62.395 66.667 0.00 0.00 35.61 3.36
2126 2156 2.747855 GCGGCTCCACCTTTCCTG 60.748 66.667 0.00 0.00 35.61 3.86
2127 2157 2.750350 CGGCTCCACCTTTCCTGT 59.250 61.111 0.00 0.00 35.61 4.00
2128 2158 1.376037 CGGCTCCACCTTTCCTGTC 60.376 63.158 0.00 0.00 35.61 3.51
2129 2159 1.376037 GGCTCCACCTTTCCTGTCG 60.376 63.158 0.00 0.00 34.51 4.35
2130 2160 2.035442 GCTCCACCTTTCCTGTCGC 61.035 63.158 0.00 0.00 0.00 5.19
2131 2161 1.376037 CTCCACCTTTCCTGTCGCC 60.376 63.158 0.00 0.00 0.00 5.54
2132 2162 2.742372 CCACCTTTCCTGTCGCCG 60.742 66.667 0.00 0.00 0.00 6.46
2133 2163 2.742372 CACCTTTCCTGTCGCCGG 60.742 66.667 0.00 0.00 0.00 6.13
2134 2164 4.699522 ACCTTTCCTGTCGCCGGC 62.700 66.667 19.07 19.07 0.00 6.13
2135 2165 4.394712 CCTTTCCTGTCGCCGGCT 62.395 66.667 26.68 0.00 0.00 5.52
2136 2166 2.815647 CTTTCCTGTCGCCGGCTC 60.816 66.667 26.68 17.76 0.00 4.70
2137 2167 4.388499 TTTCCTGTCGCCGGCTCC 62.388 66.667 26.68 15.20 0.00 4.70
2151 2181 3.411517 CTCCCCACCCGCCTCAAT 61.412 66.667 0.00 0.00 0.00 2.57
2152 2182 3.406595 CTCCCCACCCGCCTCAATC 62.407 68.421 0.00 0.00 0.00 2.67
2153 2183 3.727258 CCCCACCCGCCTCAATCA 61.727 66.667 0.00 0.00 0.00 2.57
2154 2184 2.438434 CCCACCCGCCTCAATCAC 60.438 66.667 0.00 0.00 0.00 3.06
2155 2185 2.438434 CCACCCGCCTCAATCACC 60.438 66.667 0.00 0.00 0.00 4.02
2156 2186 2.350895 CACCCGCCTCAATCACCA 59.649 61.111 0.00 0.00 0.00 4.17
2157 2187 2.040544 CACCCGCCTCAATCACCAC 61.041 63.158 0.00 0.00 0.00 4.16
2158 2188 2.438434 CCCGCCTCAATCACCACC 60.438 66.667 0.00 0.00 0.00 4.61
2159 2189 2.819595 CCGCCTCAATCACCACCG 60.820 66.667 0.00 0.00 0.00 4.94
2160 2190 2.264480 CGCCTCAATCACCACCGA 59.736 61.111 0.00 0.00 0.00 4.69
2161 2191 1.153369 CGCCTCAATCACCACCGAT 60.153 57.895 0.00 0.00 0.00 4.18
2162 2192 1.431488 CGCCTCAATCACCACCGATG 61.431 60.000 0.00 0.00 0.00 3.84
2163 2193 0.107703 GCCTCAATCACCACCGATGA 60.108 55.000 0.00 0.00 0.00 2.92
2164 2194 1.678728 GCCTCAATCACCACCGATGAA 60.679 52.381 0.00 0.00 0.00 2.57
2165 2195 2.009774 CCTCAATCACCACCGATGAAC 58.990 52.381 0.00 0.00 0.00 3.18
2166 2196 1.660607 CTCAATCACCACCGATGAACG 59.339 52.381 0.00 0.00 42.18 3.95
2167 2197 0.096976 CAATCACCACCGATGAACGC 59.903 55.000 0.00 0.00 41.07 4.84
2168 2198 1.024579 AATCACCACCGATGAACGCC 61.025 55.000 0.00 0.00 41.07 5.68
2169 2199 2.178876 ATCACCACCGATGAACGCCA 62.179 55.000 0.00 0.00 41.07 5.69
2170 2200 2.358247 ACCACCGATGAACGCCAC 60.358 61.111 0.00 0.00 41.07 5.01
2171 2201 3.124921 CCACCGATGAACGCCACC 61.125 66.667 0.00 0.00 41.07 4.61
2172 2202 2.358125 CACCGATGAACGCCACCA 60.358 61.111 0.00 0.00 41.07 4.17
2173 2203 1.745115 CACCGATGAACGCCACCAT 60.745 57.895 0.00 0.00 41.07 3.55
2174 2204 1.449601 ACCGATGAACGCCACCATC 60.450 57.895 0.00 0.00 41.07 3.51
2176 2206 2.709475 GATGAACGCCACCATCGC 59.291 61.111 0.00 0.00 31.20 4.58
2177 2207 1.815421 GATGAACGCCACCATCGCT 60.815 57.895 0.00 0.00 31.20 4.93
2178 2208 2.040213 GATGAACGCCACCATCGCTG 62.040 60.000 0.00 0.00 31.20 5.18
2180 2210 3.950794 GAACGCCACCATCGCTGGA 62.951 63.158 13.24 0.00 46.37 3.86
2181 2211 3.545124 AACGCCACCATCGCTGGAA 62.545 57.895 13.24 0.00 46.37 3.53
2182 2212 2.514592 CGCCACCATCGCTGGAAT 60.515 61.111 13.24 0.00 46.37 3.01
2183 2213 2.827051 CGCCACCATCGCTGGAATG 61.827 63.158 13.24 0.19 46.37 2.67
2184 2214 2.484062 GCCACCATCGCTGGAATGG 61.484 63.158 13.24 11.31 46.37 3.16
2185 2215 1.825191 CCACCATCGCTGGAATGGG 60.825 63.158 13.24 4.13 46.37 4.00
2186 2216 1.077501 CACCATCGCTGGAATGGGT 60.078 57.895 13.24 0.00 46.37 4.51
2187 2217 1.077501 ACCATCGCTGGAATGGGTG 60.078 57.895 13.24 0.00 46.37 4.61
2188 2218 1.825191 CCATCGCTGGAATGGGTGG 60.825 63.158 0.00 0.00 46.37 4.61
2189 2219 2.124151 ATCGCTGGAATGGGTGGC 60.124 61.111 0.00 0.00 0.00 5.01
2190 2220 3.721370 ATCGCTGGAATGGGTGGCC 62.721 63.158 0.00 0.00 0.00 5.36
2191 2221 4.738998 CGCTGGAATGGGTGGCCA 62.739 66.667 0.00 0.00 0.00 5.36
2192 2222 2.283821 GCTGGAATGGGTGGCCAA 60.284 61.111 7.24 0.00 0.00 4.52
2193 2223 2.353610 GCTGGAATGGGTGGCCAAG 61.354 63.158 7.24 0.00 0.00 3.61
2194 2224 1.383799 CTGGAATGGGTGGCCAAGA 59.616 57.895 7.24 0.00 0.00 3.02
2195 2225 0.967380 CTGGAATGGGTGGCCAAGAC 60.967 60.000 7.24 0.25 0.00 3.01
2196 2226 1.682344 GGAATGGGTGGCCAAGACC 60.682 63.158 7.24 11.63 0.00 3.85
2201 2231 2.843545 GGTGGCCAAGACCCTTCA 59.156 61.111 7.24 0.00 0.00 3.02
2202 2232 1.603739 GGTGGCCAAGACCCTTCAC 60.604 63.158 7.24 0.00 0.00 3.18
2203 2233 1.603739 GTGGCCAAGACCCTTCACC 60.604 63.158 7.24 0.00 0.00 4.02
2204 2234 2.081787 TGGCCAAGACCCTTCACCA 61.082 57.895 0.61 0.00 0.00 4.17
2205 2235 1.603739 GGCCAAGACCCTTCACCAC 60.604 63.158 0.00 0.00 0.00 4.16
2206 2236 1.603739 GCCAAGACCCTTCACCACC 60.604 63.158 0.00 0.00 0.00 4.61
2207 2237 1.302511 CCAAGACCCTTCACCACCG 60.303 63.158 0.00 0.00 0.00 4.94
2208 2238 1.966451 CAAGACCCTTCACCACCGC 60.966 63.158 0.00 0.00 0.00 5.68
2209 2239 3.192103 AAGACCCTTCACCACCGCC 62.192 63.158 0.00 0.00 0.00 6.13
2235 2265 2.159181 CGTCATCGGAAACCACACC 58.841 57.895 0.00 0.00 0.00 4.16
2236 2266 1.296056 CGTCATCGGAAACCACACCC 61.296 60.000 0.00 0.00 0.00 4.61
2237 2267 1.004320 TCATCGGAAACCACACCCG 60.004 57.895 0.00 0.00 44.22 5.28
2238 2268 1.302192 CATCGGAAACCACACCCGT 60.302 57.895 0.00 0.00 43.40 5.28
2239 2269 1.302192 ATCGGAAACCACACCCGTG 60.302 57.895 0.00 0.00 43.40 4.94
2240 2270 3.656045 CGGAAACCACACCCGTGC 61.656 66.667 0.00 0.00 42.17 5.34
2241 2271 2.203294 GGAAACCACACCCGTGCT 60.203 61.111 0.00 0.00 42.17 4.40
2242 2272 2.551912 GGAAACCACACCCGTGCTG 61.552 63.158 0.00 0.00 42.17 4.41
2243 2273 3.194272 GAAACCACACCCGTGCTGC 62.194 63.158 0.00 0.00 42.17 5.25
2263 2293 3.743636 CCCGCGCCGAAAAATGGT 61.744 61.111 0.00 0.00 0.00 3.55
2264 2294 2.257067 CCGCGCCGAAAAATGGTT 59.743 55.556 0.00 0.00 0.00 3.67
2265 2295 2.085844 CCGCGCCGAAAAATGGTTG 61.086 57.895 0.00 0.00 0.00 3.77
2266 2296 1.081774 CGCGCCGAAAAATGGTTGA 60.082 52.632 0.00 0.00 0.00 3.18
2267 2297 1.065031 CGCGCCGAAAAATGGTTGAG 61.065 55.000 0.00 0.00 0.00 3.02
2268 2298 0.732538 GCGCCGAAAAATGGTTGAGG 60.733 55.000 0.00 0.00 0.00 3.86
2269 2299 0.878416 CGCCGAAAAATGGTTGAGGA 59.122 50.000 0.00 0.00 0.00 3.71
2270 2300 1.472480 CGCCGAAAAATGGTTGAGGAT 59.528 47.619 0.00 0.00 0.00 3.24
2271 2301 2.094752 CGCCGAAAAATGGTTGAGGATT 60.095 45.455 0.00 0.00 0.00 3.01
2272 2302 3.127895 CGCCGAAAAATGGTTGAGGATTA 59.872 43.478 0.00 0.00 0.00 1.75
2273 2303 4.380023 CGCCGAAAAATGGTTGAGGATTAA 60.380 41.667 0.00 0.00 0.00 1.40
2274 2304 5.474825 GCCGAAAAATGGTTGAGGATTAAA 58.525 37.500 0.00 0.00 0.00 1.52
2275 2305 5.929415 GCCGAAAAATGGTTGAGGATTAAAA 59.071 36.000 0.00 0.00 0.00 1.52
2276 2306 6.425417 GCCGAAAAATGGTTGAGGATTAAAAA 59.575 34.615 0.00 0.00 0.00 1.94
2277 2307 7.119116 GCCGAAAAATGGTTGAGGATTAAAAAT 59.881 33.333 0.00 0.00 0.00 1.82
2278 2308 8.442384 CCGAAAAATGGTTGAGGATTAAAAATG 58.558 33.333 0.00 0.00 0.00 2.32
2279 2309 8.987890 CGAAAAATGGTTGAGGATTAAAAATGT 58.012 29.630 0.00 0.00 0.00 2.71
2285 2315 8.885494 TGGTTGAGGATTAAAAATGTTCTTTG 57.115 30.769 0.00 0.00 0.00 2.77
2286 2316 8.700051 TGGTTGAGGATTAAAAATGTTCTTTGA 58.300 29.630 0.00 0.00 0.00 2.69
2287 2317 8.978539 GGTTGAGGATTAAAAATGTTCTTTGAC 58.021 33.333 0.00 0.00 0.00 3.18
2288 2318 8.978539 GTTGAGGATTAAAAATGTTCTTTGACC 58.021 33.333 0.00 0.00 0.00 4.02
2289 2319 7.666623 TGAGGATTAAAAATGTTCTTTGACCC 58.333 34.615 0.00 0.00 0.00 4.46
2290 2320 7.288852 TGAGGATTAAAAATGTTCTTTGACCCA 59.711 33.333 0.00 0.00 0.00 4.51
2291 2321 7.441836 AGGATTAAAAATGTTCTTTGACCCAC 58.558 34.615 0.00 0.00 0.00 4.61
2292 2322 6.649141 GGATTAAAAATGTTCTTTGACCCACC 59.351 38.462 0.00 0.00 0.00 4.61
2293 2323 6.546428 TTAAAAATGTTCTTTGACCCACCA 57.454 33.333 0.00 0.00 0.00 4.17
2294 2324 4.400529 AAAATGTTCTTTGACCCACCAC 57.599 40.909 0.00 0.00 0.00 4.16
2295 2325 2.746279 ATGTTCTTTGACCCACCACA 57.254 45.000 0.00 0.00 0.00 4.17
2296 2326 1.757682 TGTTCTTTGACCCACCACAC 58.242 50.000 0.00 0.00 0.00 3.82
2297 2327 1.283613 TGTTCTTTGACCCACCACACT 59.716 47.619 0.00 0.00 0.00 3.55
2298 2328 1.676006 GTTCTTTGACCCACCACACTG 59.324 52.381 0.00 0.00 0.00 3.66
2299 2329 0.182537 TCTTTGACCCACCACACTGG 59.817 55.000 0.00 0.00 45.02 4.00
2300 2330 1.454847 TTTGACCCACCACACTGGC 60.455 57.895 0.00 0.00 42.67 4.85
2301 2331 3.765894 TTGACCCACCACACTGGCG 62.766 63.158 0.00 0.00 42.67 5.69
2317 2347 4.690719 CGGTGGCTGCCGTTACCA 62.691 66.667 22.15 0.00 46.11 3.25
2318 2348 2.281900 GGTGGCTGCCGTTACCAA 60.282 61.111 18.84 0.00 34.63 3.67
2319 2349 2.332654 GGTGGCTGCCGTTACCAAG 61.333 63.158 18.84 0.00 34.63 3.61
2320 2350 2.033448 TGGCTGCCGTTACCAAGG 59.967 61.111 14.98 0.00 0.00 3.61
2326 2356 2.744709 CCGTTACCAAGGCCGGTG 60.745 66.667 12.27 7.50 40.39 4.94
2327 2357 2.744709 CGTTACCAAGGCCGGTGG 60.745 66.667 22.96 22.96 40.39 4.61
2328 2358 2.360726 GTTACCAAGGCCGGTGGG 60.361 66.667 26.65 16.21 40.39 4.61
2329 2359 3.653078 TTACCAAGGCCGGTGGGG 61.653 66.667 26.65 14.61 40.39 4.96
2330 2360 4.986774 TACCAAGGCCGGTGGGGT 62.987 66.667 26.65 18.82 40.39 4.95
2338 2368 3.381136 CCGGTGGGGTGGCAATTG 61.381 66.667 0.00 0.00 0.00 2.32
2339 2369 4.067913 CGGTGGGGTGGCAATTGC 62.068 66.667 22.47 22.47 41.14 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 96 6.846283 GTGTTAAATGCGTATAGATCTGTTGC 59.154 38.462 5.18 7.42 0.00 4.17
100 103 7.979537 TCTGACAAGTGTTAAATGCGTATAGAT 59.020 33.333 0.00 0.00 0.00 1.98
102 105 7.520119 TCTGACAAGTGTTAAATGCGTATAG 57.480 36.000 0.00 0.00 0.00 1.31
106 109 5.493133 TTTCTGACAAGTGTTAAATGCGT 57.507 34.783 0.00 0.00 0.00 5.24
107 110 5.741510 TGTTTTCTGACAAGTGTTAAATGCG 59.258 36.000 0.00 0.00 0.00 4.73
130 137 7.799447 CCATGCATTCACAAAATGTTAAAGTTG 59.201 33.333 0.00 0.00 0.00 3.16
138 145 4.603989 TGACCATGCATTCACAAAATGT 57.396 36.364 0.00 0.00 0.00 2.71
254 261 5.121768 AGTTGCACCGATCTGTGTTTATTAC 59.878 40.000 17.23 7.81 38.52 1.89
255 262 5.242434 AGTTGCACCGATCTGTGTTTATTA 58.758 37.500 17.23 0.00 38.52 0.98
256 263 4.072131 AGTTGCACCGATCTGTGTTTATT 58.928 39.130 17.23 0.00 38.52 1.40
270 277 3.214696 AGCCCTTATCATAGTTGCACC 57.785 47.619 0.00 0.00 0.00 5.01
287 299 2.787567 GGCCCGTGAGAGACTAGCC 61.788 68.421 0.00 0.00 34.37 3.93
293 305 2.036098 TTACCGGCCCGTGAGAGA 59.964 61.111 0.00 0.00 0.00 3.10
294 306 2.050350 TCTTACCGGCCCGTGAGAG 61.050 63.158 13.48 6.27 0.00 3.20
296 308 1.033746 TAGTCTTACCGGCCCGTGAG 61.034 60.000 0.00 9.34 0.00 3.51
298 310 0.462789 ATTAGTCTTACCGGCCCGTG 59.537 55.000 0.00 0.00 0.00 4.94
315 327 5.850614 ACGGCCGTATATCTAACTGAAATT 58.149 37.500 33.34 0.00 0.00 1.82
324 336 1.881973 GTGTGGACGGCCGTATATCTA 59.118 52.381 34.36 14.41 36.79 1.98
325 337 0.672342 GTGTGGACGGCCGTATATCT 59.328 55.000 34.36 7.22 36.79 1.98
331 343 3.296709 GATCTGTGTGGACGGCCGT 62.297 63.158 34.89 34.89 36.79 5.68
332 344 2.509336 GATCTGTGTGGACGGCCG 60.509 66.667 26.86 26.86 36.79 6.13
334 346 1.448540 CCTGATCTGTGTGGACGGC 60.449 63.158 0.00 0.00 0.00 5.68
336 348 0.459237 GAGCCTGATCTGTGTGGACG 60.459 60.000 0.00 0.00 0.00 4.79
338 350 1.552337 GAAGAGCCTGATCTGTGTGGA 59.448 52.381 0.00 0.00 0.00 4.02
340 352 1.277273 TGGAAGAGCCTGATCTGTGTG 59.723 52.381 0.00 0.00 37.63 3.82
341 353 1.649321 TGGAAGAGCCTGATCTGTGT 58.351 50.000 0.00 0.00 37.63 3.72
342 354 2.943690 CAATGGAAGAGCCTGATCTGTG 59.056 50.000 0.00 0.00 37.63 3.66
343 355 2.842496 TCAATGGAAGAGCCTGATCTGT 59.158 45.455 0.00 0.00 37.63 3.41
344 356 3.134262 TCTCAATGGAAGAGCCTGATCTG 59.866 47.826 0.00 0.00 37.63 2.90
345 357 3.382278 TCTCAATGGAAGAGCCTGATCT 58.618 45.455 0.00 0.00 37.63 2.75
350 371 3.181446 GGCTTATCTCAATGGAAGAGCCT 60.181 47.826 14.91 0.00 40.74 4.58
363 384 0.912486 ATATGGGCCGGGCTTATCTC 59.088 55.000 28.80 10.51 0.00 2.75
548 571 0.036388 ACCGGACCTACGACTACGAA 60.036 55.000 9.46 0.00 42.66 3.85
551 574 2.287248 GCAATACCGGACCTACGACTAC 60.287 54.545 9.46 0.00 35.47 2.73
556 579 0.874607 GCAGCAATACCGGACCTACG 60.875 60.000 9.46 0.00 0.00 3.51
568 591 1.895238 GCAAGTGGGATGCAGCAAT 59.105 52.632 3.51 0.00 43.29 3.56
569 592 3.368822 GCAAGTGGGATGCAGCAA 58.631 55.556 3.51 0.00 43.29 3.91
574 597 1.404391 CAAGAGATGCAAGTGGGATGC 59.596 52.381 0.00 0.00 44.08 3.91
588 611 1.407656 ATAATCCCCCGCGCAAGAGA 61.408 55.000 8.75 0.00 40.82 3.10
593 616 1.883275 CAAATTATAATCCCCCGCGCA 59.117 47.619 8.75 0.00 0.00 6.09
646 669 4.151070 CGTCTCAAATGAACAATCAACCG 58.849 43.478 0.00 0.00 39.49 4.44
648 671 4.536065 TGCGTCTCAAATGAACAATCAAC 58.464 39.130 0.00 0.00 39.49 3.18
681 704 1.987770 CTCATTTCCATGCGCACAAAC 59.012 47.619 14.90 0.00 0.00 2.93
683 706 1.199789 GTCTCATTTCCATGCGCACAA 59.800 47.619 14.90 2.56 0.00 3.33
685 708 1.063174 GAGTCTCATTTCCATGCGCAC 59.937 52.381 14.90 0.00 0.00 5.34
705 728 2.097466 CGTCCCTTCATGAATTTTCCGG 59.903 50.000 8.96 5.40 0.00 5.14
706 729 2.097466 CCGTCCCTTCATGAATTTTCCG 59.903 50.000 8.96 7.94 0.00 4.30
714 737 4.146564 TCGATTATACCGTCCCTTCATGA 58.853 43.478 0.00 0.00 0.00 3.07
715 738 4.514781 TCGATTATACCGTCCCTTCATG 57.485 45.455 0.00 0.00 0.00 3.07
729 752 7.014230 CACACCCCATCCTAAAAATTCGATTAT 59.986 37.037 0.00 0.00 0.00 1.28
731 754 5.127031 CACACCCCATCCTAAAAATTCGATT 59.873 40.000 0.00 0.00 0.00 3.34
734 757 3.428862 GCACACCCCATCCTAAAAATTCG 60.429 47.826 0.00 0.00 0.00 3.34
735 758 3.769300 AGCACACCCCATCCTAAAAATTC 59.231 43.478 0.00 0.00 0.00 2.17
736 759 3.790126 AGCACACCCCATCCTAAAAATT 58.210 40.909 0.00 0.00 0.00 1.82
737 760 3.473113 AGCACACCCCATCCTAAAAAT 57.527 42.857 0.00 0.00 0.00 1.82
738 761 2.990740 AGCACACCCCATCCTAAAAA 57.009 45.000 0.00 0.00 0.00 1.94
747 771 0.327924 CCATGAACTAGCACACCCCA 59.672 55.000 0.00 0.00 0.00 4.96
803 827 1.480789 ACAAGAAACGGGCCAAGTTT 58.519 45.000 23.16 23.16 43.60 2.66
805 829 0.744281 CAACAAGAAACGGGCCAAGT 59.256 50.000 4.39 0.00 0.00 3.16
893 917 4.958509 TCTCCAAACGTACCACAAATACA 58.041 39.130 0.00 0.00 0.00 2.29
894 918 6.036408 GGTATCTCCAAACGTACCACAAATAC 59.964 42.308 0.00 0.00 37.21 1.89
895 919 6.108015 GGTATCTCCAAACGTACCACAAATA 58.892 40.000 0.00 0.00 37.21 1.40
896 920 4.939439 GGTATCTCCAAACGTACCACAAAT 59.061 41.667 0.00 0.00 37.21 2.32
897 921 4.202336 TGGTATCTCCAAACGTACCACAAA 60.202 41.667 0.00 0.00 44.12 2.83
898 922 3.324268 TGGTATCTCCAAACGTACCACAA 59.676 43.478 0.00 0.00 44.12 3.33
899 923 2.898612 TGGTATCTCCAAACGTACCACA 59.101 45.455 0.00 0.00 44.12 4.17
900 924 3.598019 TGGTATCTCCAAACGTACCAC 57.402 47.619 0.00 0.00 44.12 4.16
910 934 6.957631 ACAAGTGATATGTTTGGTATCTCCA 58.042 36.000 0.00 0.00 45.60 3.86
911 935 7.679638 GCAACAAGTGATATGTTTGGTATCTCC 60.680 40.741 0.00 0.00 38.90 3.71
912 936 7.148255 TGCAACAAGTGATATGTTTGGTATCTC 60.148 37.037 0.00 0.00 38.90 2.75
913 937 6.658816 TGCAACAAGTGATATGTTTGGTATCT 59.341 34.615 0.00 0.00 38.90 1.98
914 938 6.851609 TGCAACAAGTGATATGTTTGGTATC 58.148 36.000 0.00 0.00 38.90 2.24
915 939 6.832520 TGCAACAAGTGATATGTTTGGTAT 57.167 33.333 0.00 0.00 38.90 2.73
916 940 6.619744 CATGCAACAAGTGATATGTTTGGTA 58.380 36.000 0.00 0.00 38.90 3.25
917 941 5.472148 CATGCAACAAGTGATATGTTTGGT 58.528 37.500 0.00 0.00 38.90 3.67
962 986 2.935201 CTGCCTGCAATCTCTACTCAAC 59.065 50.000 0.00 0.00 0.00 3.18
985 1009 0.729116 CTCATGGAATTCGTGCGCTT 59.271 50.000 9.73 0.00 32.54 4.68
1038 1062 4.461081 CCATTTCCGGGTTTGATTTGTCTA 59.539 41.667 0.00 0.00 0.00 2.59
1053 1077 2.159707 CGTACTTGCAAGTCCATTTCCG 60.160 50.000 34.29 20.14 40.37 4.30
1056 1080 3.472652 TGACGTACTTGCAAGTCCATTT 58.527 40.909 34.29 15.85 40.37 2.32
1073 1097 2.698855 ATTGAGGGTGGATCTTGACG 57.301 50.000 0.00 0.00 0.00 4.35
1124 1148 0.321298 GGTGAAGAAGTAAGGCGCCA 60.321 55.000 31.54 5.56 0.00 5.69
1127 1151 2.996621 CAGAAGGTGAAGAAGTAAGGCG 59.003 50.000 0.00 0.00 0.00 5.52
1180 1204 4.193826 TGATCTCCTTCTTGTTCTTCCG 57.806 45.455 0.00 0.00 0.00 4.30
1181 1205 4.390297 CGTTGATCTCCTTCTTGTTCTTCC 59.610 45.833 0.00 0.00 0.00 3.46
1186 1210 3.409026 AGCGTTGATCTCCTTCTTGTT 57.591 42.857 0.00 0.00 0.00 2.83
1189 1213 3.764434 TCAGTAGCGTTGATCTCCTTCTT 59.236 43.478 0.00 0.00 0.00 2.52
1202 1226 1.751924 GGAGGACAGATTCAGTAGCGT 59.248 52.381 0.00 0.00 0.00 5.07
1204 1228 2.111384 TGGGAGGACAGATTCAGTAGC 58.889 52.381 0.00 0.00 0.00 3.58
1362 1386 0.330604 AGAGCATGGGCAACATCTGT 59.669 50.000 0.00 0.00 44.61 3.41
1403 1427 7.823780 TGAATTTGATTTCACGGCATCATTGC 61.824 38.462 0.00 0.00 38.13 3.56
1404 1428 5.577554 TGAATTTGATTTCACGGCATCATTG 59.422 36.000 0.00 0.00 30.82 2.82
1405 1429 5.722263 TGAATTTGATTTCACGGCATCATT 58.278 33.333 0.00 0.00 30.82 2.57
1418 1445 6.395629 CCTGCACAGAATTCTGAATTTGATT 58.604 36.000 36.15 13.01 46.59 2.57
1421 1448 4.491676 CCCTGCACAGAATTCTGAATTTG 58.508 43.478 36.15 25.32 46.59 2.32
1449 1476 2.095567 CCAACTCAGCGATCAAACAAGG 60.096 50.000 0.00 0.00 0.00 3.61
1503 1530 3.375299 GCAACATGATGTCTACAACCTCC 59.625 47.826 0.00 0.00 0.00 4.30
1532 1559 6.320418 TCAGATTTCGTAGTACTTGCCAGATA 59.680 38.462 0.00 0.00 0.00 1.98
1533 1560 5.127194 TCAGATTTCGTAGTACTTGCCAGAT 59.873 40.000 0.00 0.00 0.00 2.90
1617 1644 5.009610 ACGAGGAAATAAAACATTGCACAGT 59.990 36.000 0.00 0.00 0.00 3.55
1639 1666 1.349026 AGGAGCCCATATGGATTCACG 59.651 52.381 24.00 6.19 37.39 4.35
1725 1752 5.500234 TCGGTTGTACTAGCTTTCTAGGTA 58.500 41.667 0.00 0.00 45.15 3.08
1726 1753 4.338879 TCGGTTGTACTAGCTTTCTAGGT 58.661 43.478 0.00 0.00 45.15 3.08
1739 1766 6.716898 ACTAGCAATTTTACTCGGTTGTAC 57.283 37.500 0.00 0.00 0.00 2.90
1746 1776 5.644636 TGGGGTAAACTAGCAATTTTACTCG 59.355 40.000 11.39 0.00 38.89 4.18
1757 1787 3.264947 CGGTTTAGTGGGGTAAACTAGC 58.735 50.000 6.49 0.00 41.03 3.42
1786 1816 7.127955 ACTCCCTTATCAGATTTGGTACTTCAT 59.872 37.037 0.00 0.00 0.00 2.57
1820 1850 0.462789 GGATTTCGGCGGAGGACTAA 59.537 55.000 7.21 0.00 0.00 2.24
1822 1852 2.732619 GGGATTTCGGCGGAGGACT 61.733 63.158 7.21 0.00 0.00 3.85
1823 1853 2.203029 GGGATTTCGGCGGAGGAC 60.203 66.667 7.21 0.00 0.00 3.85
1824 1854 3.476419 GGGGATTTCGGCGGAGGA 61.476 66.667 7.21 0.00 0.00 3.71
1825 1855 4.564110 GGGGGATTTCGGCGGAGG 62.564 72.222 7.21 0.00 0.00 4.30
2089 2119 2.687566 GGGCGGGAGAAGAGGGAA 60.688 66.667 0.00 0.00 0.00 3.97
2108 2138 4.394712 AGGAAAGGTGGAGCCGCG 62.395 66.667 0.00 0.00 43.70 6.46
2109 2139 2.747855 CAGGAAAGGTGGAGCCGC 60.748 66.667 0.00 0.00 43.70 6.53
2110 2140 1.376037 GACAGGAAAGGTGGAGCCG 60.376 63.158 0.00 0.00 43.70 5.52
2111 2141 1.376037 CGACAGGAAAGGTGGAGCC 60.376 63.158 0.00 0.00 37.58 4.70
2112 2142 2.035442 GCGACAGGAAAGGTGGAGC 61.035 63.158 0.00 0.00 0.00 4.70
2113 2143 1.376037 GGCGACAGGAAAGGTGGAG 60.376 63.158 0.00 0.00 0.00 3.86
2114 2144 2.747686 GGCGACAGGAAAGGTGGA 59.252 61.111 0.00 0.00 0.00 4.02
2115 2145 2.742372 CGGCGACAGGAAAGGTGG 60.742 66.667 0.00 0.00 0.00 4.61
2116 2146 2.742372 CCGGCGACAGGAAAGGTG 60.742 66.667 9.30 0.00 0.00 4.00
2117 2147 4.699522 GCCGGCGACAGGAAAGGT 62.700 66.667 12.58 0.00 0.00 3.50
2118 2148 4.394712 AGCCGGCGACAGGAAAGG 62.395 66.667 23.20 0.00 0.00 3.11
2119 2149 2.815647 GAGCCGGCGACAGGAAAG 60.816 66.667 23.20 0.00 0.00 2.62
2120 2150 4.388499 GGAGCCGGCGACAGGAAA 62.388 66.667 23.20 0.00 0.00 3.13
2134 2164 3.406595 GATTGAGGCGGGTGGGGAG 62.407 68.421 0.00 0.00 0.00 4.30
2135 2165 3.407967 GATTGAGGCGGGTGGGGA 61.408 66.667 0.00 0.00 0.00 4.81
2136 2166 3.727258 TGATTGAGGCGGGTGGGG 61.727 66.667 0.00 0.00 0.00 4.96
2137 2167 2.438434 GTGATTGAGGCGGGTGGG 60.438 66.667 0.00 0.00 0.00 4.61
2138 2168 2.438434 GGTGATTGAGGCGGGTGG 60.438 66.667 0.00 0.00 0.00 4.61
2139 2169 2.040544 GTGGTGATTGAGGCGGGTG 61.041 63.158 0.00 0.00 0.00 4.61
2140 2170 2.351276 GTGGTGATTGAGGCGGGT 59.649 61.111 0.00 0.00 0.00 5.28
2141 2171 2.438434 GGTGGTGATTGAGGCGGG 60.438 66.667 0.00 0.00 0.00 6.13
2142 2172 2.593468 ATCGGTGGTGATTGAGGCGG 62.593 60.000 0.00 0.00 0.00 6.13
2143 2173 1.153369 ATCGGTGGTGATTGAGGCG 60.153 57.895 0.00 0.00 0.00 5.52
2144 2174 0.107703 TCATCGGTGGTGATTGAGGC 60.108 55.000 0.00 0.00 0.00 4.70
2145 2175 2.009774 GTTCATCGGTGGTGATTGAGG 58.990 52.381 0.00 0.00 0.00 3.86
2146 2176 1.660607 CGTTCATCGGTGGTGATTGAG 59.339 52.381 0.00 0.00 35.71 3.02
2147 2177 1.720805 CGTTCATCGGTGGTGATTGA 58.279 50.000 0.00 0.00 35.71 2.57
2148 2178 0.096976 GCGTTCATCGGTGGTGATTG 59.903 55.000 0.00 0.00 40.26 2.67
2149 2179 1.024579 GGCGTTCATCGGTGGTGATT 61.025 55.000 0.00 0.00 40.26 2.57
2150 2180 1.449601 GGCGTTCATCGGTGGTGAT 60.450 57.895 0.00 0.00 40.26 3.06
2151 2181 2.047655 GGCGTTCATCGGTGGTGA 60.048 61.111 0.00 0.00 40.26 4.02
2152 2182 2.358125 TGGCGTTCATCGGTGGTG 60.358 61.111 0.00 0.00 40.26 4.17
2153 2183 2.358247 GTGGCGTTCATCGGTGGT 60.358 61.111 0.00 0.00 40.26 4.16
2154 2184 3.124921 GGTGGCGTTCATCGGTGG 61.125 66.667 0.00 0.00 40.26 4.61
2155 2185 1.705337 GATGGTGGCGTTCATCGGTG 61.705 60.000 0.00 0.00 40.26 4.94
2156 2186 1.449601 GATGGTGGCGTTCATCGGT 60.450 57.895 0.00 0.00 40.26 4.69
2157 2187 3.409856 GATGGTGGCGTTCATCGG 58.590 61.111 0.00 0.00 40.26 4.18
2159 2189 1.815421 AGCGATGGTGGCGTTCATC 60.815 57.895 0.00 4.98 37.12 2.92
2160 2190 2.108514 CAGCGATGGTGGCGTTCAT 61.109 57.895 0.00 0.00 35.00 2.57
2161 2191 2.741985 CAGCGATGGTGGCGTTCA 60.742 61.111 0.00 0.00 35.00 3.18
2162 2192 3.499737 CCAGCGATGGTGGCGTTC 61.500 66.667 12.68 0.00 44.28 3.95
2168 2198 1.077501 ACCCATTCCAGCGATGGTG 60.078 57.895 20.97 11.62 42.03 4.17
2169 2199 1.077501 CACCCATTCCAGCGATGGT 60.078 57.895 20.97 0.00 42.03 3.55
2170 2200 1.825191 CCACCCATTCCAGCGATGG 60.825 63.158 15.12 15.12 42.99 3.51
2171 2201 2.484062 GCCACCCATTCCAGCGATG 61.484 63.158 0.00 0.00 0.00 3.84
2172 2202 2.124151 GCCACCCATTCCAGCGAT 60.124 61.111 0.00 0.00 0.00 4.58
2173 2203 4.424711 GGCCACCCATTCCAGCGA 62.425 66.667 0.00 0.00 0.00 4.93
2174 2204 4.738998 TGGCCACCCATTCCAGCG 62.739 66.667 0.00 0.00 35.79 5.18
2175 2205 2.283821 TTGGCCACCCATTCCAGC 60.284 61.111 3.88 0.00 41.78 4.85
2176 2206 0.967380 GTCTTGGCCACCCATTCCAG 60.967 60.000 3.88 0.00 41.78 3.86
2177 2207 1.076549 GTCTTGGCCACCCATTCCA 59.923 57.895 3.88 0.00 41.78 3.53
2178 2208 1.682344 GGTCTTGGCCACCCATTCC 60.682 63.158 3.88 0.00 41.78 3.01
2179 2209 4.018409 GGTCTTGGCCACCCATTC 57.982 61.111 3.88 0.00 41.78 2.67
2184 2214 1.603739 GTGAAGGGTCTTGGCCACC 60.604 63.158 3.88 2.81 0.00 4.61
2185 2215 1.603739 GGTGAAGGGTCTTGGCCAC 60.604 63.158 3.88 0.00 0.00 5.01
2186 2216 2.081787 TGGTGAAGGGTCTTGGCCA 61.082 57.895 0.00 0.00 0.00 5.36
2187 2217 1.603739 GTGGTGAAGGGTCTTGGCC 60.604 63.158 0.00 0.00 0.00 5.36
2188 2218 1.603739 GGTGGTGAAGGGTCTTGGC 60.604 63.158 0.00 0.00 0.00 4.52
2189 2219 1.302511 CGGTGGTGAAGGGTCTTGG 60.303 63.158 0.00 0.00 0.00 3.61
2190 2220 1.966451 GCGGTGGTGAAGGGTCTTG 60.966 63.158 0.00 0.00 0.00 3.02
2191 2221 2.430367 GCGGTGGTGAAGGGTCTT 59.570 61.111 0.00 0.00 0.00 3.01
2192 2222 3.637273 GGCGGTGGTGAAGGGTCT 61.637 66.667 0.00 0.00 0.00 3.85
2217 2247 1.296056 GGGTGTGGTTTCCGATGACG 61.296 60.000 0.00 0.00 39.43 4.35
2218 2248 1.296056 CGGGTGTGGTTTCCGATGAC 61.296 60.000 0.00 0.00 45.96 3.06
2219 2249 1.004320 CGGGTGTGGTTTCCGATGA 60.004 57.895 0.00 0.00 45.96 2.92
2220 2250 1.302192 ACGGGTGTGGTTTCCGATG 60.302 57.895 8.02 0.00 45.96 3.84
2221 2251 1.302192 CACGGGTGTGGTTTCCGAT 60.302 57.895 8.02 0.00 45.96 4.18
2222 2252 2.109387 CACGGGTGTGGTTTCCGA 59.891 61.111 8.02 0.00 45.96 4.55
2223 2253 3.656045 GCACGGGTGTGGTTTCCG 61.656 66.667 0.25 0.00 46.51 4.30
2246 2276 3.275832 AACCATTTTTCGGCGCGGG 62.276 57.895 15.48 2.58 0.00 6.13
2247 2277 2.085844 CAACCATTTTTCGGCGCGG 61.086 57.895 8.83 8.94 0.00 6.46
2248 2278 1.065031 CTCAACCATTTTTCGGCGCG 61.065 55.000 0.00 0.00 0.00 6.86
2249 2279 0.732538 CCTCAACCATTTTTCGGCGC 60.733 55.000 0.00 0.00 0.00 6.53
2250 2280 0.878416 TCCTCAACCATTTTTCGGCG 59.122 50.000 0.00 0.00 0.00 6.46
2251 2281 3.592898 AATCCTCAACCATTTTTCGGC 57.407 42.857 0.00 0.00 0.00 5.54
2252 2282 7.954788 TTTTTAATCCTCAACCATTTTTCGG 57.045 32.000 0.00 0.00 0.00 4.30
2253 2283 8.987890 ACATTTTTAATCCTCAACCATTTTTCG 58.012 29.630 0.00 0.00 0.00 3.46
2259 2289 9.492973 CAAAGAACATTTTTAATCCTCAACCAT 57.507 29.630 0.00 0.00 0.00 3.55
2260 2290 8.700051 TCAAAGAACATTTTTAATCCTCAACCA 58.300 29.630 0.00 0.00 0.00 3.67
2261 2291 8.978539 GTCAAAGAACATTTTTAATCCTCAACC 58.021 33.333 0.00 0.00 0.00 3.77
2262 2292 8.978539 GGTCAAAGAACATTTTTAATCCTCAAC 58.021 33.333 0.00 0.00 0.00 3.18
2263 2293 8.147704 GGGTCAAAGAACATTTTTAATCCTCAA 58.852 33.333 0.00 0.00 0.00 3.02
2264 2294 7.288852 TGGGTCAAAGAACATTTTTAATCCTCA 59.711 33.333 0.00 0.00 0.00 3.86
2265 2295 7.598869 GTGGGTCAAAGAACATTTTTAATCCTC 59.401 37.037 0.00 0.00 0.00 3.71
2266 2296 7.441836 GTGGGTCAAAGAACATTTTTAATCCT 58.558 34.615 0.00 0.00 0.00 3.24
2267 2297 6.649141 GGTGGGTCAAAGAACATTTTTAATCC 59.351 38.462 0.00 0.00 0.00 3.01
2268 2298 7.170828 GTGGTGGGTCAAAGAACATTTTTAATC 59.829 37.037 0.00 0.00 0.00 1.75
2269 2299 6.989759 GTGGTGGGTCAAAGAACATTTTTAAT 59.010 34.615 0.00 0.00 0.00 1.40
2270 2300 6.070767 TGTGGTGGGTCAAAGAACATTTTTAA 60.071 34.615 0.00 0.00 0.00 1.52
2271 2301 5.422331 TGTGGTGGGTCAAAGAACATTTTTA 59.578 36.000 0.00 0.00 0.00 1.52
2272 2302 4.223923 TGTGGTGGGTCAAAGAACATTTTT 59.776 37.500 0.00 0.00 0.00 1.94
2273 2303 3.772025 TGTGGTGGGTCAAAGAACATTTT 59.228 39.130 0.00 0.00 0.00 1.82
2274 2304 3.132111 GTGTGGTGGGTCAAAGAACATTT 59.868 43.478 0.00 0.00 0.00 2.32
2275 2305 2.693074 GTGTGGTGGGTCAAAGAACATT 59.307 45.455 0.00 0.00 0.00 2.71
2276 2306 2.091885 AGTGTGGTGGGTCAAAGAACAT 60.092 45.455 0.00 0.00 0.00 2.71
2277 2307 1.283613 AGTGTGGTGGGTCAAAGAACA 59.716 47.619 0.00 0.00 0.00 3.18
2278 2308 1.676006 CAGTGTGGTGGGTCAAAGAAC 59.324 52.381 0.00 0.00 0.00 3.01
2279 2309 1.409521 CCAGTGTGGTGGGTCAAAGAA 60.410 52.381 0.00 0.00 33.46 2.52
2280 2310 0.182537 CCAGTGTGGTGGGTCAAAGA 59.817 55.000 0.00 0.00 33.46 2.52
2281 2311 1.455383 GCCAGTGTGGTGGGTCAAAG 61.455 60.000 0.00 0.00 40.46 2.77
2282 2312 1.454847 GCCAGTGTGGTGGGTCAAA 60.455 57.895 0.00 0.00 40.46 2.69
2283 2313 2.194597 GCCAGTGTGGTGGGTCAA 59.805 61.111 0.00 0.00 40.46 3.18
2284 2314 4.248842 CGCCAGTGTGGTGGGTCA 62.249 66.667 0.00 0.00 44.04 4.02
2301 2331 2.281900 TTGGTAACGGCAGCCACC 60.282 61.111 13.30 12.47 42.51 4.61
2302 2332 2.332654 CCTTGGTAACGGCAGCCAC 61.333 63.158 13.30 1.44 42.51 5.01
2303 2333 2.033448 CCTTGGTAACGGCAGCCA 59.967 61.111 13.30 0.00 42.51 4.75
2304 2334 3.440415 GCCTTGGTAACGGCAGCC 61.440 66.667 0.00 0.00 45.59 4.85
2310 2340 2.744709 CCACCGGCCTTGGTAACG 60.745 66.667 0.00 0.00 41.38 3.18
2311 2341 2.360726 CCCACCGGCCTTGGTAAC 60.361 66.667 16.90 0.00 41.38 2.50
2312 2342 3.653078 CCCCACCGGCCTTGGTAA 61.653 66.667 16.90 0.00 41.38 2.85
2313 2343 4.986774 ACCCCACCGGCCTTGGTA 62.987 66.667 16.90 0.00 41.38 3.25
2321 2351 3.381136 CAATTGCCACCCCACCGG 61.381 66.667 0.00 0.00 37.81 5.28
2322 2352 4.067913 GCAATTGCCACCCCACCG 62.068 66.667 20.06 0.00 34.31 4.94


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

AutoCloner maintained by Alex Coulton.