Multiple sequence alignment - TraesCS2D01G579100

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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 TraesCS2D01G579100 chr2D 100.000 5530 0 0 1 5530 641609531 641615060 0.000000e+00 10213.0
1 TraesCS2D01G579100 chr2D 80.039 1027 113 42 2144 3129 642415125 642416100 0.000000e+00 676.0
2 TraesCS2D01G579100 chr2D 83.500 600 81 10 2529 3128 642240990 642240409 1.350000e-150 544.0
3 TraesCS2D01G579100 chr2D 78.173 646 118 16 3872 4499 642417633 642418273 1.870000e-104 390.0
4 TraesCS2D01G579100 chr2D 95.021 241 6 4 286 526 641951192 641950958 1.880000e-99 374.0
5 TraesCS2D01G579100 chr2D 94.215 242 8 4 285 526 597897309 597897074 1.130000e-96 364.0
6 TraesCS2D01G579100 chr2D 92.800 250 14 1 1 250 597897556 597897311 5.270000e-95 359.0
7 TraesCS2D01G579100 chr2D 92.400 250 15 1 1 250 641951440 641951195 2.450000e-93 353.0
8 TraesCS2D01G579100 chr2D 80.795 453 62 16 2624 3068 642940578 642941013 1.150000e-86 331.0
9 TraesCS2D01G579100 chr2D 78.832 411 59 16 2655 3053 642443772 642444166 9.200000e-63 252.0
10 TraesCS2D01G579100 chr2D 74.715 526 107 21 1013 1516 642414429 642414950 1.560000e-50 211.0
11 TraesCS2D01G579100 chr2D 87.778 180 14 2 1 180 598048350 598048521 2.610000e-48 204.0
12 TraesCS2D01G579100 chr2D 87.027 185 16 2 1 185 598020159 598020335 9.390000e-48 202.0
13 TraesCS2D01G579100 chr2D 91.667 108 4 2 774 881 641950917 641950815 1.610000e-30 145.0
14 TraesCS2D01G579100 chr2D 93.151 73 5 0 3586 3658 642416602 642416674 2.110000e-19 108.0
15 TraesCS2D01G579100 chr2D 93.478 46 3 0 3903 3948 595120272 595120227 9.940000e-08 69.4
16 TraesCS2D01G579100 chr2D 100.000 31 0 0 4800 4830 641614300 641614330 2.150000e-04 58.4
17 TraesCS2D01G579100 chr2D 100.000 31 0 0 4770 4800 641614330 641614360 2.150000e-04 58.4
18 TraesCS2D01G579100 chr2A 93.008 1416 80 8 2093 3504 766714324 766715724 0.000000e+00 2049.0
19 TraesCS2D01G579100 chr2A 92.764 1147 65 6 3669 4800 766717230 766718373 0.000000e+00 1642.0
20 TraesCS2D01G579100 chr2A 90.801 1098 62 12 999 2089 766713220 766714285 0.000000e+00 1432.0
21 TraesCS2D01G579100 chr2A 97.375 419 6 4 4799 5214 766718342 766718758 0.000000e+00 708.0
22 TraesCS2D01G579100 chr2A 82.238 822 92 30 2316 3127 767560114 767560891 0.000000e+00 660.0
23 TraesCS2D01G579100 chr2A 81.939 825 93 32 2316 3129 767486138 767485359 0.000000e+00 647.0
24 TraesCS2D01G579100 chr2A 84.839 620 74 12 2506 3125 767138508 767139107 1.700000e-169 606.0
25 TraesCS2D01G579100 chr2A 90.231 389 32 2 10 398 766712448 766712830 2.300000e-138 503.0
26 TraesCS2D01G579100 chr2A 79.570 651 110 6 3872 4499 767562501 767563151 1.410000e-120 444.0
27 TraesCS2D01G579100 chr2A 94.882 254 9 3 5277 5530 766719097 766719346 1.440000e-105 394.0
28 TraesCS2D01G579100 chr2A 79.123 479 51 6 3205 3658 767139368 767139822 9.070000e-73 285.0
29 TraesCS2D01G579100 chr2A 86.891 267 16 7 735 994 766712888 766713142 1.170000e-71 281.0
30 TraesCS2D01G579100 chr2A 96.129 155 6 0 3504 3658 766716885 766717039 2.560000e-63 254.0
31 TraesCS2D01G579100 chr2A 78.199 211 46 0 4289 4499 767479823 767479613 9.660000e-28 135.0
32 TraesCS2D01G579100 chr2A 92.647 68 4 1 643 709 766712826 766712893 4.560000e-16 97.1
33 TraesCS2D01G579100 chr2A 95.349 43 2 0 3903 3945 727612544 727612586 9.940000e-08 69.4
34 TraesCS2D01G579100 chr2A 87.931 58 2 1 2450 2502 767138385 767138442 4.620000e-06 63.9
35 TraesCS2D01G579100 chr2B 88.500 600 32 19 303 890 799968306 799968880 0.000000e+00 691.0
36 TraesCS2D01G579100 chr2B 85.246 610 72 10 2519 3128 799352727 799352136 3.660000e-171 612.0
37 TraesCS2D01G579100 chr2B 78.737 649 113 9 3875 4499 799285177 799284530 1.430000e-110 411.0
38 TraesCS2D01G579100 chr2B 83.441 465 41 21 1611 2070 653014166 653013733 3.100000e-107 399.0
39 TraesCS2D01G579100 chr2B 86.034 179 16 3 1 179 799959226 799959395 3.400000e-42 183.0
40 TraesCS2D01G579100 chr2B 93.243 74 5 0 3585 3658 799286206 799286133 5.860000e-20 110.0
41 TraesCS2D01G579100 chrUn 89.737 380 31 6 1611 1986 18146318 18145943 3.880000e-131 479.0
42 TraesCS2D01G579100 chrUn 81.773 406 55 11 2755 3154 31530436 31530044 6.910000e-84 322.0
43 TraesCS2D01G579100 chr5A 82.729 469 50 22 1627 2091 691790448 691790007 6.720000e-104 388.0
44 TraesCS2D01G579100 chr4A 82.723 382 37 14 1713 2091 708036117 708035762 4.160000e-81 313.0


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 TraesCS2D01G579100 chr2D 641609531 641615060 5529 False 3443.266667 10213 100.000000 1 5530 3 chr2D.!!$F5 5529
1 TraesCS2D01G579100 chr2D 642240409 642240990 581 True 544.000000 544 83.500000 2529 3128 1 chr2D.!!$R2 599
2 TraesCS2D01G579100 chr2D 642414429 642418273 3844 False 346.250000 676 81.519500 1013 4499 4 chr2D.!!$F6 3486
3 TraesCS2D01G579100 chr2D 641950815 641951440 625 True 290.666667 374 93.029333 1 881 3 chr2D.!!$R4 880
4 TraesCS2D01G579100 chr2A 766712448 766719346 6898 False 817.788889 2049 92.747556 10 5530 9 chr2A.!!$F2 5520
5 TraesCS2D01G579100 chr2A 767485359 767486138 779 True 647.000000 647 81.939000 2316 3129 1 chr2A.!!$R2 813
6 TraesCS2D01G579100 chr2A 767560114 767563151 3037 False 552.000000 660 80.904000 2316 4499 2 chr2A.!!$F4 2183
7 TraesCS2D01G579100 chr2A 767138385 767139822 1437 False 318.300000 606 83.964333 2450 3658 3 chr2A.!!$F3 1208
8 TraesCS2D01G579100 chr2B 799968306 799968880 574 False 691.000000 691 88.500000 303 890 1 chr2B.!!$F2 587
9 TraesCS2D01G579100 chr2B 799352136 799352727 591 True 612.000000 612 85.246000 2519 3128 1 chr2B.!!$R2 609
10 TraesCS2D01G579100 chr2B 799284530 799286206 1676 True 260.500000 411 85.990000 3585 4499 2 chr2B.!!$R3 914

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
413 414 0.252197 AGATGTTAACCCCAGGACGC 59.748 55.0 2.48 0.00 0.00 5.19 F
1090 1175 0.590732 CGATTTGCTGCGGAATGAGC 60.591 55.0 0.00 0.00 35.65 4.26 F
1400 1497 0.179111 TCCAGAAGCATAAGGACGCG 60.179 55.0 3.53 3.53 0.00 6.01 F
1557 1660 0.247460 TCGTCCATGCTCTGGTCTTG 59.753 55.0 5.89 0.00 46.08 3.02 F
2914 3198 0.250640 AGCTTGAAGTGGCCACTCTG 60.251 55.0 37.75 25.81 41.58 3.35 F
3689 5585 0.514255 CGAGTGTGTCACTGCATTGG 59.486 55.0 7.14 0.00 45.44 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1216 1313 0.879090 GGAACAAGGTAAGGCCAACG 59.121 55.000 5.01 0.0 40.61 4.10 R
2850 3134 1.483827 TGAGTAGATCTGCAAGGCCTG 59.516 52.381 5.69 1.1 0.00 4.85 R
3399 3877 0.320771 GGGAGCGTGTGTCAGAACAT 60.321 55.000 0.00 0.0 37.81 2.71 R
3412 3890 0.824109 TGAACTACATCAGGGGAGCG 59.176 55.000 0.00 0.0 0.00 5.03 R
4511 7231 0.032615 ACTAGCCACAGAGAGAGGGG 60.033 60.000 0.00 0.0 0.00 4.79 R
4719 7442 0.250295 CCCAGCCAGTTCGACTCAAA 60.250 55.000 0.00 0.0 0.00 2.69 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
99 100 2.834549 AGTAGTAGCAGCACTGATGGTT 59.165 45.455 4.02 0.00 33.06 3.67
152 153 2.005960 CTCGCTACGGTTGAGGAGGG 62.006 65.000 0.00 0.00 0.00 4.30
155 156 1.517832 CTACGGTTGAGGAGGGCAG 59.482 63.158 0.00 0.00 0.00 4.85
166 167 2.500098 GAGGAGGGCAGTAACACATACA 59.500 50.000 0.00 0.00 36.94 2.29
187 188 9.985730 CATACATACCTAATTTTAACCGGTCTA 57.014 33.333 8.04 0.00 0.00 2.59
228 229 2.104451 CCTGCAGAGGCTTATCACTGAT 59.896 50.000 17.39 0.00 41.91 2.90
256 257 1.959985 CGCTGTCCCTCTAGTGATGAT 59.040 52.381 0.00 0.00 0.00 2.45
271 272 2.522836 ATGATCCTCATCACTGACGC 57.477 50.000 0.00 0.00 42.05 5.19
272 273 1.185315 TGATCCTCATCACTGACGCA 58.815 50.000 0.00 0.00 33.80 5.24
311 312 3.919216 GTGATGAGTAGTCACTTGTGCT 58.081 45.455 1.37 0.25 42.04 4.40
408 409 5.188751 AGAAGAGAAGAGATGTTAACCCCAG 59.811 44.000 2.48 0.00 0.00 4.45
410 411 3.775316 GAGAAGAGATGTTAACCCCAGGA 59.225 47.826 2.48 0.00 0.00 3.86
411 412 3.519913 AGAAGAGATGTTAACCCCAGGAC 59.480 47.826 2.48 0.00 0.00 3.85
412 413 1.831736 AGAGATGTTAACCCCAGGACG 59.168 52.381 2.48 0.00 0.00 4.79
413 414 0.252197 AGATGTTAACCCCAGGACGC 59.748 55.000 2.48 0.00 0.00 5.19
548 557 2.414559 CGCGGGTAGAAAAGAGTTACGA 60.415 50.000 0.00 0.00 0.00 3.43
563 572 1.199615 TACGAAGTGATGCCATGGGA 58.800 50.000 15.13 12.25 45.73 4.37
565 574 1.064463 ACGAAGTGATGCCATGGGAAT 60.064 47.619 11.10 0.00 42.51 3.01
566 575 1.335810 CGAAGTGATGCCATGGGAATG 59.664 52.381 11.10 0.00 0.00 2.67
567 576 2.381911 GAAGTGATGCCATGGGAATGT 58.618 47.619 11.10 0.00 0.00 2.71
568 577 1.771565 AGTGATGCCATGGGAATGTG 58.228 50.000 11.10 0.00 0.00 3.21
584 594 7.835822 TGGGAATGTGAACAACAAAATATAGG 58.164 34.615 0.00 0.00 43.61 2.57
627 637 4.106909 TGTATGTCACGGCATAACTAACG 58.893 43.478 0.00 0.00 33.67 3.18
695 705 9.874205 TGATTTTTGGATAAAATAGGAAAGCAG 57.126 29.630 0.00 0.00 35.82 4.24
703 713 4.813750 AAATAGGAAAGCAGCTGCATTT 57.186 36.364 38.24 31.12 45.16 2.32
752 764 7.659652 TTTTTCTTTTTCTTTTCGAGGCAAA 57.340 28.000 0.00 0.00 0.00 3.68
829 841 5.582665 GCCATACTTACTTGTGGAGAAGAAG 59.417 44.000 0.00 0.00 35.29 2.85
830 842 6.574465 GCCATACTTACTTGTGGAGAAGAAGA 60.574 42.308 0.00 0.00 33.39 2.87
831 843 7.386851 CCATACTTACTTGTGGAGAAGAAGAA 58.613 38.462 0.00 0.00 33.39 2.52
849 861 2.092914 AGAATAGGTTCTTCTTGGGCCG 60.093 50.000 0.00 0.00 41.92 6.13
890 902 2.037136 CCGGACTGAGCTTGCTTGG 61.037 63.158 0.00 0.00 0.00 3.61
891 903 2.037136 CGGACTGAGCTTGCTTGGG 61.037 63.158 0.00 0.00 0.00 4.12
892 904 1.073897 GGACTGAGCTTGCTTGGGT 59.926 57.895 0.00 0.00 0.00 4.51
895 907 1.975407 CTGAGCTTGCTTGGGTGGG 60.975 63.158 0.00 0.00 0.00 4.61
896 908 2.416107 CTGAGCTTGCTTGGGTGGGA 62.416 60.000 0.00 0.00 0.00 4.37
897 909 1.973812 GAGCTTGCTTGGGTGGGAC 60.974 63.158 0.00 0.00 0.00 4.46
898 910 2.203480 GCTTGCTTGGGTGGGACA 60.203 61.111 0.00 0.00 0.00 4.02
899 911 2.270986 GCTTGCTTGGGTGGGACAG 61.271 63.158 0.00 0.00 41.80 3.51
931 943 3.502123 ATATACAACCATCCCAACCCG 57.498 47.619 0.00 0.00 0.00 5.28
960 972 3.877508 ACATCGCTATTGAAACCCTAAGC 59.122 43.478 0.00 0.00 0.00 3.09
970 982 2.789409 AACCCTAAGCTGCTAGGTTG 57.211 50.000 23.12 12.33 36.49 3.77
977 989 1.671054 GCTGCTAGGTTGTTCGCCA 60.671 57.895 0.00 0.00 0.00 5.69
994 1006 2.533942 CGCCACAAAGAAAAAGGAAACG 59.466 45.455 0.00 0.00 0.00 3.60
995 1007 3.517602 GCCACAAAGAAAAAGGAAACGT 58.482 40.909 0.00 0.00 0.00 3.99
997 1009 4.490743 CCACAAAGAAAAAGGAAACGTGT 58.509 39.130 0.00 0.00 0.00 4.49
1090 1175 0.590732 CGATTTGCTGCGGAATGAGC 60.591 55.000 0.00 0.00 35.65 4.26
1143 1231 5.163364 TGGAAAGAAGGCTTATCTAGAGCAG 60.163 44.000 0.00 0.00 41.89 4.24
1159 1247 2.873472 GAGCAGCATTCTGATGGAAGAG 59.127 50.000 0.00 0.00 42.95 2.85
1163 1251 1.674962 GCATTCTGATGGAAGAGCACC 59.325 52.381 0.00 0.00 38.19 5.01
1164 1252 2.683152 GCATTCTGATGGAAGAGCACCT 60.683 50.000 0.00 0.00 38.19 4.00
1173 1261 0.871057 GAAGAGCACCTCAACTGCAC 59.129 55.000 0.00 0.00 37.08 4.57
1242 1339 3.010420 GCCTTACCTTGTTCCTCATCAC 58.990 50.000 0.00 0.00 0.00 3.06
1350 1447 4.815308 CCATTGGAGAAGCTCAGATTACTG 59.185 45.833 0.00 0.00 44.66 2.74
1351 1448 3.533606 TGGAGAAGCTCAGATTACTGC 57.466 47.619 0.00 0.00 43.17 4.40
1355 1452 4.202243 GGAGAAGCTCAGATTACTGCATCT 60.202 45.833 0.00 0.00 43.17 2.90
1367 1464 5.689383 TTACTGCATCTCTTGTCCAAAAC 57.311 39.130 0.00 0.00 0.00 2.43
1400 1497 0.179111 TCCAGAAGCATAAGGACGCG 60.179 55.000 3.53 3.53 0.00 6.01
1401 1498 1.638467 CAGAAGCATAAGGACGCGC 59.362 57.895 5.73 0.00 0.00 6.86
1536 1639 6.472808 GCTTCCACGACATAAGTAAGTTAGAG 59.527 42.308 0.00 0.00 0.00 2.43
1547 1650 4.745649 AGTAAGTTAGAGTTCGTCCATGC 58.254 43.478 0.00 0.00 0.00 4.06
1549 1652 3.512033 AGTTAGAGTTCGTCCATGCTC 57.488 47.619 0.00 0.00 0.00 4.26
1554 1657 0.247736 AGTTCGTCCATGCTCTGGTC 59.752 55.000 5.89 0.52 46.08 4.02
1555 1658 0.247736 GTTCGTCCATGCTCTGGTCT 59.752 55.000 5.89 0.00 46.08 3.85
1557 1660 0.247460 TCGTCCATGCTCTGGTCTTG 59.753 55.000 5.89 0.00 46.08 3.02
1563 1666 3.776969 TCCATGCTCTGGTCTTGTTATCT 59.223 43.478 5.89 0.00 46.08 1.98
1566 1669 5.366460 CATGCTCTGGTCTTGTTATCTCAT 58.634 41.667 0.00 0.00 0.00 2.90
1573 1676 9.126151 CTCTGGTCTTGTTATCTCATCTAACTA 57.874 37.037 0.00 0.00 31.71 2.24
1626 1761 4.530094 TCCTTAAAATGCTTCATACGCG 57.470 40.909 3.53 3.53 0.00 6.01
1637 1772 1.720805 TCATACGCGTGCAGAATTGT 58.279 45.000 24.59 0.00 0.00 2.71
1657 1792 2.232452 GTCTAGTGGCTGCAGAGAAAGA 59.768 50.000 20.43 9.86 0.00 2.52
1664 1799 2.991866 GGCTGCAGAGAAAGAAAAATGC 59.008 45.455 20.43 0.00 0.00 3.56
1668 1803 5.163982 GCTGCAGAGAAAGAAAAATGCATTC 60.164 40.000 20.43 0.77 42.24 2.67
1674 1809 9.635520 CAGAGAAAGAAAAATGCATTCAGTAAT 57.364 29.630 13.38 0.00 0.00 1.89
1688 1823 6.963805 GCATTCAGTAATTTCAGCAACTAGTC 59.036 38.462 0.00 0.00 0.00 2.59
1692 1827 7.168219 TCAGTAATTTCAGCAACTAGTCCAAT 58.832 34.615 0.00 0.00 0.00 3.16
1757 1892 2.027377 GCTAGGCATCTATCCAGCACAT 60.027 50.000 0.00 0.00 32.10 3.21
1769 1904 4.025040 TCCAGCACATCAGAACAAGAAT 57.975 40.909 0.00 0.00 0.00 2.40
1771 1906 4.937620 TCCAGCACATCAGAACAAGAATAC 59.062 41.667 0.00 0.00 0.00 1.89
1773 1908 5.163784 CCAGCACATCAGAACAAGAATACTG 60.164 44.000 0.00 0.00 0.00 2.74
1927 2063 7.094420 ACAGCAGCAATAAATGTTGTACATACA 60.094 33.333 11.53 11.53 41.84 2.29
1928 2064 7.916977 CAGCAGCAATAAATGTTGTACATACAT 59.083 33.333 14.20 14.20 41.84 2.29
1929 2065 8.469200 AGCAGCAATAAATGTTGTACATACATT 58.531 29.630 20.93 20.93 45.49 2.71
1950 2092 7.231607 ACATTAGAAAACTTGTTGTATACGCG 58.768 34.615 3.53 3.53 0.00 6.01
1978 2120 3.354089 AAACAACATTGCAGAGAACCG 57.646 42.857 0.00 0.00 0.00 4.44
2005 2147 5.458041 AACTTCCATTCCACAAACATGAG 57.542 39.130 0.00 0.00 0.00 2.90
2015 2157 7.912056 TTCCACAAACATGAGAAGAGATAAG 57.088 36.000 0.00 0.00 0.00 1.73
2019 2161 7.824289 CCACAAACATGAGAAGAGATAAGGTAA 59.176 37.037 0.00 0.00 0.00 2.85
2089 2231 0.478072 TGTTGCCATCCTTCCACAGT 59.522 50.000 0.00 0.00 0.00 3.55
2090 2232 1.702401 TGTTGCCATCCTTCCACAGTA 59.298 47.619 0.00 0.00 0.00 2.74
2097 2274 1.991121 TCCTTCCACAGTACACGAGT 58.009 50.000 0.00 0.00 0.00 4.18
2107 2284 3.043586 CAGTACACGAGTCACTTGTCAC 58.956 50.000 0.00 0.00 33.19 3.67
2220 2398 8.125448 GGAATTAGTGCTCATGTCAGAAATTAC 58.875 37.037 0.00 0.00 0.00 1.89
2280 2472 2.927014 GCGTGTCAGAGTTAGGAACAGG 60.927 54.545 0.00 0.00 0.00 4.00
2287 2479 5.998363 GTCAGAGTTAGGAACAGGTCAATTT 59.002 40.000 0.00 0.00 0.00 1.82
2356 2567 2.149973 TGCATCTCAGAGGACTAGCA 57.850 50.000 0.00 0.00 0.00 3.49
2377 2588 3.569250 AACCGTACCATTCAAACATGC 57.431 42.857 0.00 0.00 0.00 4.06
2390 2601 8.028354 CCATTCAAACATGCAGACAATAAGTTA 58.972 33.333 0.00 0.00 0.00 2.24
2421 2632 3.025262 AGTAGCTGCTGGAAGGTAGTAC 58.975 50.000 13.43 0.00 33.17 2.73
2457 2668 2.158957 TCTGGACAGTGAAGTTGTGGAC 60.159 50.000 0.00 0.00 0.00 4.02
2556 2838 2.838736 CACACTAGTGCACAGTTTCCT 58.161 47.619 22.90 0.00 39.21 3.36
2582 2864 2.552315 GGATGTTTGGCTTTGAAGTCGA 59.448 45.455 0.00 0.00 31.96 4.20
2586 2868 3.250762 TGTTTGGCTTTGAAGTCGATGAG 59.749 43.478 0.00 0.00 31.96 2.90
2618 2900 3.804325 CCTGTGTGCTCCTATGTATTTCG 59.196 47.826 0.00 0.00 0.00 3.46
2810 3094 5.209659 CTGTCTCCTATGTACTTTACCCCT 58.790 45.833 0.00 0.00 0.00 4.79
2815 3099 5.095809 TCCTATGTACTTTACCCCTTGTGT 58.904 41.667 0.00 0.00 0.00 3.72
2870 3154 1.483827 CAGGCCTTGCAGATCTACTCA 59.516 52.381 0.00 0.00 0.00 3.41
2914 3198 0.250640 AGCTTGAAGTGGCCACTCTG 60.251 55.000 37.75 25.81 41.58 3.35
2984 3268 2.091541 CTTCTCTTCTCTCGCTCCAGT 58.908 52.381 0.00 0.00 0.00 4.00
3154 3547 5.252547 TCAGCAGCATTGGTTGATTAGTAA 58.747 37.500 0.00 0.00 31.36 2.24
3176 3569 5.476752 AAGCAGATAACAAATTCGCTCTC 57.523 39.130 0.00 0.00 0.00 3.20
3297 3775 3.697542 TGCAAGCATCTTCAATACTGCAT 59.302 39.130 0.00 0.00 37.09 3.96
3399 3877 5.012458 ACAGCAGCAATATCATAGGCTTCTA 59.988 40.000 0.00 0.00 33.60 2.10
3411 3889 5.422012 TCATAGGCTTCTATGTTCTGACACA 59.578 40.000 11.63 0.00 46.40 3.72
3412 3890 3.931578 AGGCTTCTATGTTCTGACACAC 58.068 45.455 0.00 0.00 38.91 3.82
3511 5194 3.319755 GGTGTCAAGCAATGGTTTCATG 58.680 45.455 0.00 0.00 33.18 3.07
3552 5235 4.937620 CAGTACTATGCCAATGTGTCTGTT 59.062 41.667 0.00 0.00 0.00 3.16
3658 5374 8.362639 CAATCAATAAGACCATTAATTCCTGGG 58.637 37.037 10.16 0.00 36.82 4.45
3660 5376 6.068498 TCAATAAGACCATTAATTCCTGGGGT 60.068 38.462 10.16 0.00 36.82 4.95
3662 5378 3.981212 AGACCATTAATTCCTGGGGTTG 58.019 45.455 10.16 0.00 36.82 3.77
3663 5379 3.596046 AGACCATTAATTCCTGGGGTTGA 59.404 43.478 10.16 0.00 36.82 3.18
3665 5381 3.076785 ACCATTAATTCCTGGGGTTGACA 59.923 43.478 10.16 0.00 36.82 3.58
3667 5383 4.344104 CATTAATTCCTGGGGTTGACACT 58.656 43.478 0.00 0.00 0.00 3.55
3689 5585 0.514255 CGAGTGTGTCACTGCATTGG 59.486 55.000 7.14 0.00 45.44 3.16
3791 5852 4.571984 TGTCGATGATGGTTAAGCAATCAG 59.428 41.667 12.00 7.81 40.61 2.90
3820 5882 5.772825 TTCAGATCCAGTGGTTTTTCTTG 57.227 39.130 9.54 0.23 0.00 3.02
3846 5923 1.883275 CTCTCTCTCTCCGTGTGTGTT 59.117 52.381 0.00 0.00 0.00 3.32
3915 6614 2.552315 TGTTGTTCGCAGGATCCTTTTC 59.448 45.455 13.00 3.34 0.00 2.29
3949 6648 1.757118 CCCTTCTCGTGCTATTCTGGA 59.243 52.381 0.00 0.00 0.00 3.86
3971 6670 4.336889 TGAGTACCCTGTTGACTTTGAG 57.663 45.455 0.00 0.00 0.00 3.02
3998 6697 9.232473 GTTGAACTAAGGATAAAAGATGGAAGT 57.768 33.333 0.00 0.00 0.00 3.01
4014 6713 7.911651 AGATGGAAGTGAGTCTCAAGATAAAA 58.088 34.615 3.51 0.00 0.00 1.52
4146 6845 5.989168 CAGGCCACAATATTATCAGTTCGTA 59.011 40.000 5.01 0.00 0.00 3.43
4171 6870 1.454201 GGAGGGCTGTCTACTTTTGC 58.546 55.000 0.00 0.00 0.00 3.68
4200 6899 2.095617 GGGCAAATTGCTTGTTCATTGC 60.096 45.455 18.04 0.00 44.28 3.56
4303 7023 4.473444 AGGAATGTTGTCACTGTGGAATT 58.527 39.130 8.11 1.66 0.00 2.17
4304 7024 4.279169 AGGAATGTTGTCACTGTGGAATTG 59.721 41.667 8.11 0.00 0.00 2.32
4350 7070 8.708742 TCATAAAAAGTTACACAGAATCTCGTG 58.291 33.333 9.98 9.98 39.10 4.35
4351 7071 5.924475 AAAAGTTACACAGAATCTCGTGG 57.076 39.130 14.14 0.00 37.45 4.94
4381 7101 0.731417 CAGGCTGAGCTTGAATTCGG 59.269 55.000 11.48 0.00 37.87 4.30
4406 7126 1.003116 CGGCATTGTCAGATAAGCAGC 60.003 52.381 0.00 0.00 0.00 5.25
4413 7133 2.305635 TGTCAGATAAGCAGCCAGGAAA 59.694 45.455 0.00 0.00 0.00 3.13
4463 7183 2.027192 TGTCATTGCTTGGTCCCTACTC 60.027 50.000 0.00 0.00 0.00 2.59
4469 7189 1.835494 CTTGGTCCCTACTCGTGAGA 58.165 55.000 3.44 0.00 39.12 3.27
4511 7231 2.772515 AGAGGGGTATGCCTTCACTTAC 59.227 50.000 0.00 0.00 34.45 2.34
4565 7285 4.695928 GTGGGGTGATCAAACTTAGAACTC 59.304 45.833 0.00 0.00 0.00 3.01
4566 7286 3.933332 GGGGTGATCAAACTTAGAACTCG 59.067 47.826 0.00 0.00 0.00 4.18
4567 7287 4.562963 GGGGTGATCAAACTTAGAACTCGT 60.563 45.833 0.00 0.00 0.00 4.18
4568 7288 4.389077 GGGTGATCAAACTTAGAACTCGTG 59.611 45.833 0.00 0.00 0.00 4.35
4586 7309 5.989777 ACTCGTGCTTGTGTAATCTAACTTT 59.010 36.000 0.00 0.00 0.00 2.66
4587 7310 6.073765 ACTCGTGCTTGTGTAATCTAACTTTG 60.074 38.462 0.00 0.00 0.00 2.77
4589 7312 6.480651 TCGTGCTTGTGTAATCTAACTTTGAA 59.519 34.615 0.00 0.00 0.00 2.69
4590 7313 6.792250 CGTGCTTGTGTAATCTAACTTTGAAG 59.208 38.462 0.00 0.00 0.00 3.02
4592 7315 8.770828 GTGCTTGTGTAATCTAACTTTGAAGTA 58.229 33.333 0.00 0.00 38.57 2.24
4593 7316 8.988934 TGCTTGTGTAATCTAACTTTGAAGTAG 58.011 33.333 0.00 0.00 38.57 2.57
4594 7317 9.204570 GCTTGTGTAATCTAACTTTGAAGTAGA 57.795 33.333 0.00 2.15 38.57 2.59
4611 7334 5.407407 AGTAGAGACCTATGTTGTGTTGG 57.593 43.478 0.00 0.00 0.00 3.77
4618 7341 3.826157 ACCTATGTTGTGTTGGGTGATTG 59.174 43.478 0.00 0.00 0.00 2.67
4648 7371 8.251721 GTGTCATCAAACTAAGTAGACCTATGT 58.748 37.037 0.00 0.00 0.00 2.29
4768 7491 9.000486 GTGCCTTTTATTATGTAATACTCCCTC 58.000 37.037 0.00 0.00 0.00 4.30
4789 7512 3.077359 CTGTCTGGTTGTCCATTTCTCC 58.923 50.000 0.00 0.00 43.43 3.71
4790 7513 2.076863 GTCTGGTTGTCCATTTCTCCG 58.923 52.381 0.00 0.00 43.43 4.63
4791 7514 1.974957 TCTGGTTGTCCATTTCTCCGA 59.025 47.619 0.00 0.00 43.43 4.55
4792 7515 2.076863 CTGGTTGTCCATTTCTCCGAC 58.923 52.381 0.00 0.00 43.43 4.79
4793 7516 1.418264 TGGTTGTCCATTTCTCCGACA 59.582 47.619 0.00 0.00 39.03 4.35
4794 7517 2.158740 TGGTTGTCCATTTCTCCGACAA 60.159 45.455 0.00 0.00 42.60 3.18
4795 7518 2.484264 GGTTGTCCATTTCTCCGACAAG 59.516 50.000 2.29 0.00 44.72 3.16
4796 7519 3.139077 GTTGTCCATTTCTCCGACAAGT 58.861 45.455 2.29 0.00 44.72 3.16
4797 7520 4.312443 GTTGTCCATTTCTCCGACAAGTA 58.688 43.478 2.29 0.00 44.72 2.24
4798 7521 4.819105 TGTCCATTTCTCCGACAAGTAT 57.181 40.909 0.00 0.00 33.72 2.12
4799 7522 5.160607 TGTCCATTTCTCCGACAAGTATT 57.839 39.130 0.00 0.00 33.72 1.89
4814 7537 5.964958 CAAGTATTGTCTGGTTGTCCATT 57.035 39.130 0.00 0.00 41.43 3.16
4815 7538 6.331369 CAAGTATTGTCTGGTTGTCCATTT 57.669 37.500 0.00 0.00 41.43 2.32
4816 7539 6.381801 CAAGTATTGTCTGGTTGTCCATTTC 58.618 40.000 0.00 0.00 41.43 2.17
4817 7540 5.880901 AGTATTGTCTGGTTGTCCATTTCT 58.119 37.500 0.00 0.00 43.43 2.52
4818 7541 5.940470 AGTATTGTCTGGTTGTCCATTTCTC 59.060 40.000 0.00 0.00 43.43 2.87
4859 7582 6.270231 AGTGGAGGGAGTATATAATTGTGGTC 59.730 42.308 0.00 0.00 0.00 4.02
4862 7585 6.350277 GGAGGGAGTATATAATTGTGGTCGAG 60.350 46.154 0.00 0.00 0.00 4.04
5101 7826 1.200252 CAGTACGACCTGACCTGACAG 59.800 57.143 0.00 0.00 34.23 3.51
5214 7939 8.553459 TTCTGAAGAAGAAGATGTGGAAATAC 57.447 34.615 0.00 0.00 40.09 1.89
5215 7940 7.911651 TCTGAAGAAGAAGATGTGGAAATACT 58.088 34.615 0.00 0.00 29.54 2.12
5216 7941 9.035890 TCTGAAGAAGAAGATGTGGAAATACTA 57.964 33.333 0.00 0.00 29.54 1.82
5217 7942 9.829507 CTGAAGAAGAAGATGTGGAAATACTAT 57.170 33.333 0.00 0.00 0.00 2.12
5218 7943 9.823647 TGAAGAAGAAGATGTGGAAATACTATC 57.176 33.333 0.00 0.00 0.00 2.08
5219 7944 9.267084 GAAGAAGAAGATGTGGAAATACTATCC 57.733 37.037 0.00 0.00 37.48 2.59
5220 7945 7.740805 AGAAGAAGATGTGGAAATACTATCCC 58.259 38.462 0.00 0.00 36.04 3.85
5250 8163 4.340950 GGAAATTAAATCTCCATTGCCCGA 59.659 41.667 0.00 0.00 0.00 5.14
5261 8174 6.303054 TCTCCATTGCCCGAAAATATAATGA 58.697 36.000 0.00 0.00 0.00 2.57
5301 8303 2.879026 AGGAAACGGAGCAAGAAGAAAC 59.121 45.455 0.00 0.00 0.00 2.78
5309 8311 1.652012 CAAGAAGAAACGGCGGCAA 59.348 52.632 13.24 0.00 0.00 4.52
5346 8348 4.302455 ACACGAGAGACAAACAGATCAAG 58.698 43.478 0.00 0.00 0.00 3.02
5355 8357 6.122277 AGACAAACAGATCAAGAAAACCAGA 58.878 36.000 0.00 0.00 0.00 3.86
5356 8358 6.261826 AGACAAACAGATCAAGAAAACCAGAG 59.738 38.462 0.00 0.00 0.00 3.35
5370 8372 5.917545 AAACCAGAGAACCTAAAACCCTA 57.082 39.130 0.00 0.00 0.00 3.53
5371 8373 5.500546 AACCAGAGAACCTAAAACCCTAG 57.499 43.478 0.00 0.00 0.00 3.02
5385 8387 5.741962 AAACCCTAGAGGACTAAAGTGAC 57.258 43.478 0.00 0.00 39.89 3.67
5425 8427 0.250513 GAAATCTCCCAGGAGCACGT 59.749 55.000 8.95 0.00 41.71 4.49
5428 8430 0.689080 ATCTCCCAGGAGCACGTGAT 60.689 55.000 22.23 14.87 41.71 3.06
5461 8463 7.749126 GGGATTAATGACTGAAACGTTTAACTG 59.251 37.037 14.65 9.07 0.00 3.16
5480 8482 6.968131 AACTGCAAAAAGAGAAGGAAAAAC 57.032 33.333 0.00 0.00 0.00 2.43
5483 8485 6.934083 ACTGCAAAAAGAGAAGGAAAAACAAA 59.066 30.769 0.00 0.00 0.00 2.83
5484 8486 7.443879 ACTGCAAAAAGAGAAGGAAAAACAAAA 59.556 29.630 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 6.690957 TCATTGATGTTTGTTCAAACTTCGTC 59.309 34.615 24.86 18.38 38.75 4.20
99 100 8.506437 GTTCATCACAGACTAATGTCAAAATGA 58.494 33.333 0.00 0.00 45.20 2.57
187 188 3.326880 AGGACTTCCAAGACGGTTAACAT 59.673 43.478 8.10 0.00 38.89 2.71
256 257 0.176449 CCATGCGTCAGTGATGAGGA 59.824 55.000 16.74 3.33 0.00 3.71
271 272 3.134623 TCACTAACTGCCCTATGACCATG 59.865 47.826 0.00 0.00 0.00 3.66
272 273 3.384168 TCACTAACTGCCCTATGACCAT 58.616 45.455 0.00 0.00 0.00 3.55
310 311 6.270064 CCCAACACTACTACAAAACCAAAAG 58.730 40.000 0.00 0.00 0.00 2.27
311 312 5.127356 CCCCAACACTACTACAAAACCAAAA 59.873 40.000 0.00 0.00 0.00 2.44
412 413 4.547905 TACTACAGAGCCGCGCGC 62.548 66.667 27.36 23.91 37.98 6.86
413 414 2.352457 CTACTACAGAGCCGCGCG 60.352 66.667 25.67 25.67 0.00 6.86
548 557 2.104967 CACATTCCCATGGCATCACTT 58.895 47.619 6.09 0.00 34.27 3.16
609 619 3.183754 CATCGTTAGTTATGCCGTGACA 58.816 45.455 0.00 0.00 0.00 3.58
616 626 8.794406 CCACATTAAAAACATCGTTAGTTATGC 58.206 33.333 0.00 0.00 0.00 3.14
759 771 0.037160 ATTAACGTCCGTGCCCCTTT 59.963 50.000 0.00 0.00 0.00 3.11
772 784 2.893404 CCGGCCCGTCCATTAACG 60.893 66.667 0.85 0.00 42.24 3.18
829 841 2.289565 CGGCCCAAGAAGAACCTATTC 58.710 52.381 0.00 0.00 34.78 1.75
830 842 1.064685 CCGGCCCAAGAAGAACCTATT 60.065 52.381 0.00 0.00 0.00 1.73
831 843 0.546598 CCGGCCCAAGAAGAACCTAT 59.453 55.000 0.00 0.00 0.00 2.57
849 861 3.008408 TCTCTCCTCGGAGGGACC 58.992 66.667 23.39 0.00 45.85 4.46
891 903 8.482943 TGTATATATAATATGGTGCTGTCCCAC 58.517 37.037 0.00 0.00 34.07 4.61
892 904 8.616799 TGTATATATAATATGGTGCTGTCCCA 57.383 34.615 0.00 0.00 36.16 4.37
895 907 9.884636 TGGTTGTATATATAATATGGTGCTGTC 57.115 33.333 0.00 0.00 0.00 3.51
899 911 9.284968 GGGATGGTTGTATATATAATATGGTGC 57.715 37.037 0.00 0.00 0.00 5.01
905 917 8.487848 CGGGTTGGGATGGTTGTATATATAATA 58.512 37.037 0.00 0.00 0.00 0.98
906 918 7.343357 CGGGTTGGGATGGTTGTATATATAAT 58.657 38.462 0.00 0.00 0.00 1.28
907 919 6.713276 CGGGTTGGGATGGTTGTATATATAA 58.287 40.000 0.00 0.00 0.00 0.98
908 920 5.338544 GCGGGTTGGGATGGTTGTATATATA 60.339 44.000 0.00 0.00 0.00 0.86
909 921 4.566907 GCGGGTTGGGATGGTTGTATATAT 60.567 45.833 0.00 0.00 0.00 0.86
930 942 4.969196 ATAGCGATGTGGCCGGCG 62.969 66.667 22.54 6.34 0.00 6.46
931 943 2.591715 AATAGCGATGTGGCCGGC 60.592 61.111 21.18 21.18 0.00 6.13
938 950 3.877508 GCTTAGGGTTTCAATAGCGATGT 59.122 43.478 0.00 0.00 0.00 3.06
944 956 5.059833 CCTAGCAGCTTAGGGTTTCAATAG 58.940 45.833 0.00 0.00 37.20 1.73
946 958 3.267031 ACCTAGCAGCTTAGGGTTTCAAT 59.733 43.478 14.67 0.00 43.76 2.57
960 972 0.602638 TGTGGCGAACAACCTAGCAG 60.603 55.000 0.00 0.00 35.24 4.24
970 982 3.430333 TCCTTTTTCTTTGTGGCGAAC 57.570 42.857 0.00 0.00 0.00 3.95
977 989 4.154556 TCGACACGTTTCCTTTTTCTTTGT 59.845 37.500 0.00 0.00 0.00 2.83
1085 1170 2.765807 CCCGGGACCTGAGCTCAT 60.766 66.667 18.48 2.44 0.00 2.90
1143 1231 1.674962 GGTGCTCTTCCATCAGAATGC 59.325 52.381 0.00 0.00 35.59 3.56
1159 1247 2.959357 GCTCGTGCAGTTGAGGTGC 61.959 63.158 4.26 0.00 41.59 5.01
1163 1251 2.609825 AACAGCTCGTGCAGTTGAG 58.390 52.632 17.71 6.24 45.12 3.02
1164 1252 4.855105 AACAGCTCGTGCAGTTGA 57.145 50.000 17.71 0.00 45.12 3.18
1216 1313 0.879090 GGAACAAGGTAAGGCCAACG 59.121 55.000 5.01 0.00 40.61 4.10
1242 1339 1.528542 TAGATCCACGGCCTCCTCG 60.529 63.158 0.00 0.00 0.00 4.63
1350 1447 4.232221 CACATGTTTTGGACAAGAGATGC 58.768 43.478 11.10 0.00 42.62 3.91
1351 1448 4.232221 GCACATGTTTTGGACAAGAGATG 58.768 43.478 10.02 10.02 42.62 2.90
1355 1452 2.290367 CTCGCACATGTTTTGGACAAGA 59.710 45.455 0.00 0.00 42.62 3.02
1367 1464 1.521010 CTGGAGAGGCTCGCACATG 60.521 63.158 19.92 3.02 0.00 3.21
1401 1498 1.010350 GCTTGAAGATGGCGATGCG 60.010 57.895 0.00 0.00 0.00 4.73
1411 1508 2.230025 CCTGAGAAGACTCGCTTGAAGA 59.770 50.000 0.00 0.00 45.25 2.87
1518 1621 6.686253 GGACGAACTCTAACTTACTTATGTCG 59.314 42.308 0.00 0.00 0.00 4.35
1547 1650 8.006298 AGTTAGATGAGATAACAAGACCAGAG 57.994 38.462 0.00 0.00 35.92 3.35
1573 1676 7.007116 AGGAAGGAAAGCTGACTAGAAAAATT 58.993 34.615 0.00 0.00 0.00 1.82
1575 1678 5.941788 AGGAAGGAAAGCTGACTAGAAAAA 58.058 37.500 0.00 0.00 0.00 1.94
1580 1715 6.000840 AGAAAAAGGAAGGAAAGCTGACTAG 58.999 40.000 0.00 0.00 0.00 2.57
1582 1717 4.797743 AGAAAAAGGAAGGAAAGCTGACT 58.202 39.130 0.00 0.00 0.00 3.41
1626 1761 2.417933 CAGCCACTAGACAATTCTGCAC 59.582 50.000 0.00 0.00 32.75 4.57
1637 1772 2.529632 TCTTTCTCTGCAGCCACTAGA 58.470 47.619 9.47 3.05 0.00 2.43
1657 1792 7.966246 TGCTGAAATTACTGAATGCATTTTT 57.034 28.000 14.33 8.74 0.00 1.94
1664 1799 7.119699 TGGACTAGTTGCTGAAATTACTGAATG 59.880 37.037 0.00 0.00 0.00 2.67
1668 1803 6.801539 TTGGACTAGTTGCTGAAATTACTG 57.198 37.500 0.00 0.00 0.00 2.74
1674 1809 4.756642 CACTCATTGGACTAGTTGCTGAAA 59.243 41.667 0.00 0.00 0.00 2.69
1675 1810 4.040339 TCACTCATTGGACTAGTTGCTGAA 59.960 41.667 0.00 0.00 0.00 3.02
1688 1823 7.864108 TTGTCTTATATGGTTCACTCATTGG 57.136 36.000 0.00 0.00 0.00 3.16
1692 1827 7.602644 GTGTCTTTGTCTTATATGGTTCACTCA 59.397 37.037 0.00 0.00 0.00 3.41
1757 1892 5.928839 GTCTGAAGCAGTATTCTTGTTCTGA 59.071 40.000 0.00 0.00 32.61 3.27
1769 1904 7.065085 GCTGAAATCATAAAGTCTGAAGCAGTA 59.935 37.037 0.00 0.00 32.61 2.74
1771 1906 6.256686 GCTGAAATCATAAAGTCTGAAGCAG 58.743 40.000 0.00 0.00 0.00 4.24
1773 1908 5.124457 TGGCTGAAATCATAAAGTCTGAAGC 59.876 40.000 0.00 0.00 0.00 3.86
1811 1947 9.726438 ATTGCTAACTAACTGAAGAACTAATGT 57.274 29.630 0.00 0.00 0.00 2.71
1854 1990 9.853177 AATTGCTATTCCTATTGCTAACTAACT 57.147 29.630 0.00 0.00 34.23 2.24
1927 2063 6.091713 AGCGCGTATACAACAAGTTTTCTAAT 59.908 34.615 8.43 0.00 0.00 1.73
1928 2064 5.406175 AGCGCGTATACAACAAGTTTTCTAA 59.594 36.000 8.43 0.00 0.00 2.10
1929 2065 4.925054 AGCGCGTATACAACAAGTTTTCTA 59.075 37.500 8.43 0.00 0.00 2.10
1931 2067 3.838550 CAGCGCGTATACAACAAGTTTTC 59.161 43.478 8.43 0.00 0.00 2.29
1932 2068 3.495377 TCAGCGCGTATACAACAAGTTTT 59.505 39.130 8.43 0.00 0.00 2.43
1934 2070 2.679450 TCAGCGCGTATACAACAAGTT 58.321 42.857 8.43 0.00 0.00 2.66
1936 2072 3.925688 ATTCAGCGCGTATACAACAAG 57.074 42.857 8.43 0.00 0.00 3.16
1950 2092 6.151691 TCTCTGCAATGTTGTTTTATTCAGC 58.848 36.000 0.00 0.00 0.00 4.26
1978 2120 8.519526 TCATGTTTGTGGAATGGAAGTTTATAC 58.480 33.333 0.00 0.00 0.00 1.47
2038 2180 6.707440 TGTTTCTCTGCAATTTCTTGGTTA 57.293 33.333 0.00 0.00 32.72 2.85
2089 2231 2.946990 TCAGTGACAAGTGACTCGTGTA 59.053 45.455 0.00 0.00 38.73 2.90
2090 2232 1.749063 TCAGTGACAAGTGACTCGTGT 59.251 47.619 0.00 0.00 41.08 4.49
2097 2274 3.561310 GTGCTGAATTCAGTGACAAGTGA 59.439 43.478 30.88 6.72 45.45 3.41
2107 2284 2.880268 TGACAAGTGGTGCTGAATTCAG 59.120 45.455 27.82 27.82 46.40 3.02
2117 2295 4.990426 GGAATTTTGGAATGACAAGTGGTG 59.010 41.667 0.00 0.00 0.00 4.17
2220 2398 5.500234 TCTAGGAATTGGTGTGGATTTCTG 58.500 41.667 0.00 0.00 0.00 3.02
2307 2499 7.050377 TGATCAAGCAATACCCTTTTCTCTAG 58.950 38.462 0.00 0.00 0.00 2.43
2356 2567 3.319405 TGCATGTTTGAATGGTACGGTTT 59.681 39.130 0.00 0.00 0.00 3.27
2390 2601 3.396276 TCCAGCAGCTACTCCTACTAGAT 59.604 47.826 0.00 0.00 0.00 1.98
2421 2632 7.872993 TCACTGTCCAGACTTTACTTCATTAAG 59.127 37.037 0.40 0.00 38.77 1.85
2457 2668 3.443045 GCACTGTGGAATGGGCCG 61.443 66.667 10.21 0.00 0.00 6.13
2502 2720 7.821134 AGGTATATAGCTTTTCCCATCATCT 57.179 36.000 8.67 0.00 0.00 2.90
2556 2838 4.892934 ACTTCAAAGCCAAACATCCACTTA 59.107 37.500 0.00 0.00 0.00 2.24
2618 2900 5.582269 AGAAAGAAAAAGGAAGCAAAAGCAC 59.418 36.000 0.00 0.00 0.00 4.40
2651 2933 6.829229 TGATTGCATTGACTGAGAAATTCT 57.171 33.333 0.00 0.00 0.00 2.40
2653 2935 8.092068 TGAAATGATTGCATTGACTGAGAAATT 58.908 29.630 0.00 0.00 43.71 1.82
2709 2991 9.636789 AACTACTAAACAAAGGGAAGTACAATT 57.363 29.630 0.00 0.00 0.00 2.32
2750 3032 9.448438 ACATCAATGTGTGTAGTGTTATAATGT 57.552 29.630 0.00 0.00 40.03 2.71
2753 3035 8.233868 GCAACATCAATGTGTGTAGTGTTATAA 58.766 33.333 0.00 0.00 41.61 0.98
2754 3036 7.389053 TGCAACATCAATGTGTGTAGTGTTATA 59.611 33.333 0.00 0.00 41.61 0.98
2755 3037 6.206438 TGCAACATCAATGTGTGTAGTGTTAT 59.794 34.615 0.00 0.00 41.61 1.89
2756 3038 5.529060 TGCAACATCAATGTGTGTAGTGTTA 59.471 36.000 0.00 0.00 41.61 2.41
2757 3039 4.337836 TGCAACATCAATGTGTGTAGTGTT 59.662 37.500 0.00 0.00 41.61 3.32
2810 3094 1.843851 GGGATGATACCAGGGACACAA 59.156 52.381 0.00 0.00 0.00 3.33
2815 3099 1.513991 AGGATGGGATGATACCAGGGA 59.486 52.381 1.45 0.00 42.15 4.20
2850 3134 1.483827 TGAGTAGATCTGCAAGGCCTG 59.516 52.381 5.69 1.10 0.00 4.85
2870 3154 8.044060 TGTCATTTAGCTCAAAGATTTCGAAT 57.956 30.769 0.00 0.00 0.00 3.34
2914 3198 2.503375 CGACCACGCCGTAGACAC 60.503 66.667 0.00 0.00 0.00 3.67
2984 3268 7.449395 TCTTTAGTGAGTACTTGGCAGTTAGTA 59.551 37.037 0.00 0.00 38.36 1.82
3077 3365 9.729023 CCGACATATTAATTTTCTATGTTTGCA 57.271 29.630 0.00 0.00 36.48 4.08
3105 3394 2.659428 AGAACCAGCAAAGCCATATCC 58.341 47.619 0.00 0.00 0.00 2.59
3154 3547 5.064452 CAGAGAGCGAATTTGTTATCTGCTT 59.936 40.000 17.80 0.00 0.00 3.91
3176 3569 4.400884 ACCACTAGACTAGATGTTGCTCAG 59.599 45.833 16.55 0.36 0.00 3.35
3247 3725 6.471233 TCCAGAATACATCTTGACTTCGAT 57.529 37.500 0.00 0.00 35.73 3.59
3297 3775 1.210478 GCCTGTATTCTGCCTGGAAGA 59.790 52.381 0.00 0.00 34.07 2.87
3399 3877 0.320771 GGGAGCGTGTGTCAGAACAT 60.321 55.000 0.00 0.00 37.81 2.71
3411 3889 0.824759 GAACTACATCAGGGGAGCGT 59.175 55.000 0.00 0.00 0.00 5.07
3412 3890 0.824109 TGAACTACATCAGGGGAGCG 59.176 55.000 0.00 0.00 0.00 5.03
3552 5235 8.871125 GTTATTAGAAGGTAGAATGGGAGATCA 58.129 37.037 0.00 0.00 0.00 2.92
3609 5316 2.867624 TGAATGTTCCTCTTGCTGCTT 58.132 42.857 0.00 0.00 0.00 3.91
3665 5381 0.249073 GCAGTGACACACTCGACAGT 60.249 55.000 8.59 0.00 43.43 3.55
3667 5383 0.389025 ATGCAGTGACACACTCGACA 59.611 50.000 8.59 4.25 43.43 4.35
3689 5585 0.679960 GACCTACAATGCCCACCACC 60.680 60.000 0.00 0.00 0.00 4.61
3731 5627 6.810911 ACACAAATAACAAATGTAACTGCCA 58.189 32.000 0.00 0.00 0.00 4.92
3772 5833 6.203530 TCGAATCTGATTGCTTAACCATCATC 59.796 38.462 7.78 0.00 0.00 2.92
3791 5852 4.065321 ACCACTGGATCTGAATCGAATC 57.935 45.455 0.71 0.00 32.24 2.52
3820 5882 2.093658 ACACGGAGAGAGAGAGAGAGAC 60.094 54.545 0.00 0.00 0.00 3.36
3863 5940 9.002600 TCATTATCATTACTAATGCCATGTGAC 57.997 33.333 4.13 0.00 38.77 3.67
3915 6614 1.228367 AAGGGCCAGTCAAGTGCAG 60.228 57.895 6.18 0.00 0.00 4.41
3949 6648 4.263068 CCTCAAAGTCAACAGGGTACTCAT 60.263 45.833 0.00 0.00 0.00 2.90
3971 6670 8.575649 TTCCATCTTTTATCCTTAGTTCAACC 57.424 34.615 0.00 0.00 0.00 3.77
3998 6697 9.159364 CTGATCAATGTTTTATCTTGAGACTCA 57.841 33.333 0.00 0.00 32.82 3.41
4014 6713 6.013725 TGGTGGTTAGTAGAACTGATCAATGT 60.014 38.462 0.00 0.00 26.03 2.71
4146 6845 3.246416 AGTAGACAGCCCTCCGATAAT 57.754 47.619 0.00 0.00 0.00 1.28
4151 6850 1.726853 CAAAAGTAGACAGCCCTCCG 58.273 55.000 0.00 0.00 0.00 4.63
4200 6899 2.048597 TTGCCGACGTGCAGTAGG 60.049 61.111 10.21 9.87 46.78 3.18
4209 6926 0.098025 AACAACACAACTTGCCGACG 59.902 50.000 0.00 0.00 0.00 5.12
4249 6966 5.414765 GGAACGTAACCTTCCAGATTTTCAT 59.585 40.000 0.00 0.00 37.68 2.57
4254 6971 4.635699 AAGGAACGTAACCTTCCAGATT 57.364 40.909 17.54 0.00 43.22 2.40
4292 7012 4.339247 AGTGAACCTTTCAATTCCACAGTG 59.661 41.667 0.00 0.00 42.15 3.66
4303 7023 4.286808 TGATGATCCTCAGTGAACCTTTCA 59.713 41.667 0.00 0.00 37.33 2.69
4304 7024 4.836825 TGATGATCCTCAGTGAACCTTTC 58.163 43.478 0.00 0.00 0.00 2.62
4381 7101 0.463654 TATCTGACAATGCCGGGCAC 60.464 55.000 26.48 12.38 43.04 5.01
4387 7107 1.336125 GGCTGCTTATCTGACAATGCC 59.664 52.381 0.00 0.00 0.00 4.40
4406 7126 5.711976 AGAATCACCAATAACACTTTCCTGG 59.288 40.000 0.00 0.00 0.00 4.45
4413 7133 5.355350 GCAGCTTAGAATCACCAATAACACT 59.645 40.000 0.00 0.00 0.00 3.55
4463 7183 3.616821 TGTTGTCAAGTTTGTCTCTCACG 59.383 43.478 0.00 0.00 0.00 4.35
4469 7189 3.023119 TGCCATGTTGTCAAGTTTGTCT 58.977 40.909 0.00 0.00 0.00 3.41
4475 7195 1.546323 CCCTCTGCCATGTTGTCAAGT 60.546 52.381 0.00 0.00 0.00 3.16
4511 7231 0.032615 ACTAGCCACAGAGAGAGGGG 60.033 60.000 0.00 0.00 0.00 4.79
4565 7285 6.223138 TCAAAGTTAGATTACACAAGCACG 57.777 37.500 0.00 0.00 0.00 5.34
4566 7286 7.639945 ACTTCAAAGTTAGATTACACAAGCAC 58.360 34.615 0.00 0.00 35.21 4.40
4567 7287 7.801716 ACTTCAAAGTTAGATTACACAAGCA 57.198 32.000 0.00 0.00 35.21 3.91
4568 7288 9.204570 TCTACTTCAAAGTTAGATTACACAAGC 57.795 33.333 0.00 0.00 40.37 4.01
4586 7309 6.455647 CAACACAACATAGGTCTCTACTTCA 58.544 40.000 0.00 0.00 0.00 3.02
4587 7310 5.869888 CCAACACAACATAGGTCTCTACTTC 59.130 44.000 0.00 0.00 0.00 3.01
4589 7312 4.223032 CCCAACACAACATAGGTCTCTACT 59.777 45.833 0.00 0.00 0.00 2.57
4590 7313 4.020485 ACCCAACACAACATAGGTCTCTAC 60.020 45.833 0.00 0.00 0.00 2.59
4592 7315 2.979678 ACCCAACACAACATAGGTCTCT 59.020 45.455 0.00 0.00 0.00 3.10
4593 7316 3.074412 CACCCAACACAACATAGGTCTC 58.926 50.000 0.00 0.00 0.00 3.36
4594 7317 2.708861 TCACCCAACACAACATAGGTCT 59.291 45.455 0.00 0.00 0.00 3.85
4611 7334 4.024048 AGTTTGATGACACGTTCAATCACC 60.024 41.667 10.02 3.29 37.92 4.02
4618 7341 6.089150 GGTCTACTTAGTTTGATGACACGTTC 59.911 42.308 0.00 0.00 0.00 3.95
4719 7442 0.250295 CCCAGCCAGTTCGACTCAAA 60.250 55.000 0.00 0.00 0.00 2.69
4791 7514 4.431416 TGGACAACCAGACAATACTTGT 57.569 40.909 0.00 0.00 43.57 3.16
4799 7522 6.833027 GTCGGAGAAATGGACAACCAGACA 62.833 50.000 0.00 0.00 45.13 3.41
4800 7523 4.413777 GTCGGAGAAATGGACAACCAGAC 61.414 52.174 0.00 0.00 45.13 3.51
4801 7524 2.289444 GTCGGAGAAATGGACAACCAGA 60.289 50.000 0.00 0.00 45.13 3.86
4802 7525 2.076863 GTCGGAGAAATGGACAACCAG 58.923 52.381 0.00 0.00 45.13 4.00
4803 7526 1.418264 TGTCGGAGAAATGGACAACCA 59.582 47.619 0.00 0.00 45.78 3.67
4804 7527 2.178912 TGTCGGAGAAATGGACAACC 57.821 50.000 0.00 0.00 39.69 3.77
4805 7528 3.139077 ACTTGTCGGAGAAATGGACAAC 58.861 45.455 2.02 0.00 43.52 3.32
4806 7529 3.485463 ACTTGTCGGAGAAATGGACAA 57.515 42.857 5.80 5.80 45.46 3.18
4807 7530 4.819105 ATACTTGTCGGAGAAATGGACA 57.181 40.909 0.00 0.00 39.69 4.02
4808 7531 6.148811 TGAAAATACTTGTCGGAGAAATGGAC 59.851 38.462 0.00 0.00 39.69 4.02
4809 7532 6.234920 TGAAAATACTTGTCGGAGAAATGGA 58.765 36.000 0.00 0.00 39.69 3.41
4810 7533 6.494893 TGAAAATACTTGTCGGAGAAATGG 57.505 37.500 0.00 0.00 39.69 3.16
4811 7534 7.535258 CACTTGAAAATACTTGTCGGAGAAATG 59.465 37.037 0.00 0.00 39.69 2.32
4812 7535 7.308589 CCACTTGAAAATACTTGTCGGAGAAAT 60.309 37.037 0.00 0.00 39.69 2.17
4813 7536 6.017440 CCACTTGAAAATACTTGTCGGAGAAA 60.017 38.462 0.00 0.00 39.69 2.52
4814 7537 5.468746 CCACTTGAAAATACTTGTCGGAGAA 59.531 40.000 0.00 0.00 39.69 2.87
4815 7538 4.994852 CCACTTGAAAATACTTGTCGGAGA 59.005 41.667 0.00 0.00 0.00 3.71
4816 7539 4.994852 TCCACTTGAAAATACTTGTCGGAG 59.005 41.667 0.00 0.00 0.00 4.63
4817 7540 4.963373 TCCACTTGAAAATACTTGTCGGA 58.037 39.130 0.00 0.00 0.00 4.55
4818 7541 4.154195 CCTCCACTTGAAAATACTTGTCGG 59.846 45.833 0.00 0.00 0.00 4.79
4859 7582 5.763444 ACTACATTCGTCAATTTGACTCG 57.237 39.130 23.29 13.76 44.85 4.18
4862 7585 7.908193 AACAAACTACATTCGTCAATTTGAC 57.092 32.000 17.76 17.76 43.65 3.18
4997 7722 5.808366 TTTCTACTATGATGCTACCCCAG 57.192 43.478 0.00 0.00 0.00 4.45
5023 7748 8.602424 CCCAGTGTGATTAATCAAGGGTATATA 58.398 37.037 24.64 1.17 38.75 0.86
5024 7749 7.461749 CCCAGTGTGATTAATCAAGGGTATAT 58.538 38.462 24.64 6.77 38.75 0.86
5025 7750 6.183361 CCCCAGTGTGATTAATCAAGGGTATA 60.183 42.308 27.58 5.25 38.75 1.47
5052 7777 2.362120 ATGCTGCACTCAAGGGCC 60.362 61.111 3.57 0.00 0.00 5.80
5101 7826 4.258702 TCTTCCACTCTGTTTCTAGCAC 57.741 45.455 0.00 0.00 0.00 4.40
5200 7925 5.132648 TGCTGGGATAGTATTTCCACATCTT 59.867 40.000 3.00 0.00 34.77 2.40
5211 7936 9.605951 ATTTAATTTCCATTGCTGGGATAGTAT 57.394 29.630 0.00 0.00 43.34 2.12
5212 7937 9.077885 GATTTAATTTCCATTGCTGGGATAGTA 57.922 33.333 0.00 0.00 43.34 1.82
5213 7938 7.786464 AGATTTAATTTCCATTGCTGGGATAGT 59.214 33.333 0.00 0.00 43.34 2.12
5214 7939 8.186709 AGATTTAATTTCCATTGCTGGGATAG 57.813 34.615 0.00 0.00 43.34 2.08
5215 7940 7.233348 GGAGATTTAATTTCCATTGCTGGGATA 59.767 37.037 9.33 0.00 43.34 2.59
5216 7941 6.042437 GGAGATTTAATTTCCATTGCTGGGAT 59.958 38.462 9.33 0.00 43.34 3.85
5217 7942 5.363580 GGAGATTTAATTTCCATTGCTGGGA 59.636 40.000 9.33 0.00 43.34 4.37
5218 7943 5.129155 TGGAGATTTAATTTCCATTGCTGGG 59.871 40.000 12.44 0.00 43.34 4.45
5219 7944 6.224665 TGGAGATTTAATTTCCATTGCTGG 57.775 37.500 12.44 0.00 44.64 4.85
5309 8311 4.539083 TGTTGCCGTCCGTGCTGT 62.539 61.111 0.00 0.00 0.00 4.40
5346 8348 5.138276 AGGGTTTTAGGTTCTCTGGTTTTC 58.862 41.667 0.00 0.00 0.00 2.29
5355 8357 5.026093 AGTCCTCTAGGGTTTTAGGTTCT 57.974 43.478 0.00 0.00 36.25 3.01
5356 8358 6.864151 TTAGTCCTCTAGGGTTTTAGGTTC 57.136 41.667 0.00 0.00 36.25 3.62
5370 8372 7.125792 TCTCTTTTTGTCACTTTAGTCCTCT 57.874 36.000 0.00 0.00 0.00 3.69
5371 8373 7.787725 TTCTCTTTTTGTCACTTTAGTCCTC 57.212 36.000 0.00 0.00 0.00 3.71
5385 8387 7.575332 TTTCGTTTCTGGTTTTCTCTTTTTG 57.425 32.000 0.00 0.00 0.00 2.44
5425 8427 4.887071 CAGTCATTAATCCCCCGAAAATCA 59.113 41.667 0.00 0.00 0.00 2.57
5428 8430 4.577988 TCAGTCATTAATCCCCCGAAAA 57.422 40.909 0.00 0.00 0.00 2.29
5461 8463 7.243487 CCTTTTGTTTTTCCTTCTCTTTTTGC 58.757 34.615 0.00 0.00 0.00 3.68
5480 8482 1.585297 CCTTGTTTGGCTGCCTTTTG 58.415 50.000 21.03 5.25 0.00 2.44


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

AutoCloner maintained by Alex Coulton.