Multiple sequence alignment - TraesCS4D01G345200

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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 TraesCS4D01G345200 chr4D 100.000 4697 0 0 1 4697 500020536 500015840 0.000000e+00 8674.0
1 TraesCS4D01G345200 chr5A 93.633 2356 112 21 2360 4697 680837241 680834906 0.000000e+00 3485.0
2 TraesCS4D01G345200 chr5A 85.358 601 57 19 1749 2348 680838155 680837585 1.130000e-165 593.0
3 TraesCS4D01G345200 chr5A 86.831 243 21 7 1158 1394 630046780 630047017 1.300000e-65 261.0
4 TraesCS4D01G345200 chr5A 86.512 215 22 7 133 341 680840065 680839852 3.660000e-56 230.0
5 TraesCS4D01G345200 chr1A 91.735 1101 61 12 3017 4108 564613917 564614996 0.000000e+00 1502.0
6 TraesCS4D01G345200 chr1A 90.799 826 47 14 3299 4113 252836173 252835366 0.000000e+00 1077.0
7 TraesCS4D01G345200 chr1A 84.342 479 53 9 1743 2220 564612061 564612518 2.580000e-122 449.0
8 TraesCS4D01G345200 chr1A 90.332 331 22 3 1064 1394 422207265 422207585 4.340000e-115 425.0
9 TraesCS4D01G345200 chr1A 90.698 301 23 3 2366 2663 564612557 564612855 3.410000e-106 396.0
10 TraesCS4D01G345200 chr1A 93.023 258 18 0 2366 2623 252836448 252836191 1.230000e-100 377.0
11 TraesCS4D01G345200 chr1A 81.903 431 53 10 1798 2227 252836887 252836481 1.620000e-89 340.0
12 TraesCS4D01G345200 chr1A 86.818 220 23 2 989 1208 564611716 564611929 1.690000e-59 241.0
13 TraesCS4D01G345200 chr1A 91.589 107 9 0 2835 2941 564612883 564612989 1.050000e-31 148.0
14 TraesCS4D01G345200 chr4B 93.871 979 40 9 3015 3992 643285713 643284754 0.000000e+00 1458.0
15 TraesCS4D01G345200 chr4B 83.838 891 54 53 588 1437 643287984 643287143 0.000000e+00 765.0
16 TraesCS4D01G345200 chr4B 88.721 594 37 10 2361 2927 643286347 643285757 0.000000e+00 699.0
17 TraesCS4D01G345200 chr4B 90.816 490 41 3 1691 2179 643286910 643286424 0.000000e+00 652.0
18 TraesCS4D01G345200 chr4B 86.667 585 45 9 1 575 643293302 643292741 6.680000e-173 617.0
19 TraesCS4D01G345200 chr4B 96.736 337 11 0 4361 4697 643284626 643284290 3.170000e-156 562.0
20 TraesCS4D01G345200 chr2B 83.708 534 60 16 1689 2219 237058456 237057947 3.290000e-131 479.0
21 TraesCS4D01G345200 chr7B 82.397 534 68 19 1689 2219 24712044 24712554 4.310000e-120 442.0
22 TraesCS4D01G345200 chr7B 82.512 406 43 16 1016 1394 24711440 24711844 9.740000e-87 331.0
23 TraesCS4D01G345200 chr7A 89.124 331 25 4 1064 1394 721556024 721556343 7.320000e-108 401.0
24 TraesCS4D01G345200 chr7A 86.831 243 21 7 1158 1394 17541009 17541246 1.300000e-65 261.0
25 TraesCS4D01G345200 chr6A 88.333 240 17 7 1161 1394 575002666 575002432 1.290000e-70 278.0
26 TraesCS4D01G345200 chr6A 87.295 244 18 8 1158 1394 583750378 583750615 2.790000e-67 267.0
27 TraesCS4D01G345200 chr6A 86.667 240 21 7 1161 1394 606002738 606002504 6.030000e-64 255.0
28 TraesCS4D01G345200 chr5B 87.654 243 19 7 1158 1394 37926544 37926781 5.990000e-69 272.0
29 TraesCS4D01G345200 chr3D 87.654 243 19 7 1158 1394 482118351 482118588 5.990000e-69 272.0
30 TraesCS4D01G345200 chr2A 87.243 243 20 7 1158 1394 197933541 197933778 2.790000e-67 267.0
31 TraesCS4D01G345200 chr2A 80.198 202 29 7 3954 4145 293893404 293893204 1.760000e-29 141.0
32 TraesCS4D01G345200 chr5D 80.282 213 39 3 134 343 282300327 282300539 1.750000e-34 158.0
33 TraesCS4D01G345200 chr5D 91.667 60 5 0 3951 4010 434068022 434067963 3.010000e-12 84.2
34 TraesCS4D01G345200 chr3B 76.233 223 40 8 222 437 69006349 69006133 6.430000e-19 106.0


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 TraesCS4D01G345200 chr4D 500015840 500020536 4696 True 8674.0 8674 100.0000 1 4697 1 chr4D.!!$R1 4696
1 TraesCS4D01G345200 chr5A 680834906 680840065 5159 True 1436.0 3485 88.5010 133 4697 3 chr5A.!!$R1 4564
2 TraesCS4D01G345200 chr1A 252835366 252836887 1521 True 598.0 1077 88.5750 1798 4113 3 chr1A.!!$R1 2315
3 TraesCS4D01G345200 chr1A 564611716 564614996 3280 False 547.2 1502 89.0364 989 4108 5 chr1A.!!$F2 3119
4 TraesCS4D01G345200 chr4B 643284290 643287984 3694 True 827.2 1458 90.7964 588 4697 5 chr4B.!!$R2 4109
5 TraesCS4D01G345200 chr4B 643292741 643293302 561 True 617.0 617 86.6670 1 575 1 chr4B.!!$R1 574
6 TraesCS4D01G345200 chr2B 237057947 237058456 509 True 479.0 479 83.7080 1689 2219 1 chr2B.!!$R1 530
7 TraesCS4D01G345200 chr7B 24711440 24712554 1114 False 386.5 442 82.4545 1016 2219 2 chr7B.!!$F1 1203

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
808 1898 0.103026 CGACTCATCCATCGCCTCAA 59.897 55.0 0.0 0.00 0.00 3.02 F
1378 2548 0.170561 CAACTACTCCCTCGACACCG 59.829 60.0 0.0 0.00 37.07 4.94 F
1659 2894 0.238289 AACAACGGAAGCTGCGAATG 59.762 50.0 4.3 5.48 34.49 2.67 F
1661 2896 0.453282 CAACGGAAGCTGCGAATGTG 60.453 55.0 4.3 0.00 34.49 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2051 3322 0.108898 CTCGTCCCTCTGCACAGAAG 60.109 60.000 1.42 0.00 36.94 2.85 R
2317 3589 1.104579 GCGCAAAAATGAGATACGCG 58.895 50.000 3.53 3.53 43.77 6.01 R
3632 6130 2.237143 CTCCTAGTGCACATTTCAGGGA 59.763 50.000 21.04 13.05 0.00 4.20 R
3732 6230 2.715005 GCACTGTTTGCGAGCACA 59.285 55.556 0.00 0.00 42.79 4.57 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
25 26 6.796705 GCTAGTTAAAGCACTAGGTTTCAA 57.203 37.500 10.10 0.00 44.58 2.69
108 109 4.348168 ACCTTTAAACTTGCTCTCTCCTGA 59.652 41.667 0.00 0.00 0.00 3.86
111 112 5.552870 TTAAACTTGCTCTCTCCTGAAGT 57.447 39.130 0.00 0.00 0.00 3.01
117 118 4.462508 TGCTCTCTCCTGAAGTAATGTG 57.537 45.455 0.00 0.00 0.00 3.21
141 142 3.733380 CGTGCAATATTTTGGCGGAATGA 60.733 43.478 0.00 0.00 33.22 2.57
175 176 0.798776 CTCCAAGTGATTGTGCCGAC 59.201 55.000 0.00 0.00 0.00 4.79
190 193 2.310233 CGACTGGGTCTTGCACACG 61.310 63.158 0.00 0.00 0.00 4.49
256 261 2.034879 CGACTGGGGACATGCACAC 61.035 63.158 0.00 0.00 41.51 3.82
276 282 0.185175 AGGTTTTGGTGGGGACTGTC 59.815 55.000 0.00 0.00 0.00 3.51
319 325 3.927142 CCAAGTTTCACTAGGAAGTAGCG 59.073 47.826 0.00 0.00 36.72 4.26
341 347 4.391830 CGTCCAGTACAAGCACATGTTATT 59.608 41.667 0.00 0.00 34.75 1.40
343 349 6.237835 CGTCCAGTACAAGCACATGTTATTAG 60.238 42.308 0.00 0.00 34.75 1.73
344 350 5.584649 TCCAGTACAAGCACATGTTATTAGC 59.415 40.000 0.00 0.00 34.75 3.09
345 351 5.353956 CCAGTACAAGCACATGTTATTAGCA 59.646 40.000 0.00 0.00 34.75 3.49
346 352 6.250819 CAGTACAAGCACATGTTATTAGCAC 58.749 40.000 0.00 0.00 34.75 4.40
347 353 5.937540 AGTACAAGCACATGTTATTAGCACA 59.062 36.000 0.00 0.00 34.75 4.57
377 383 0.462375 ACCAACGAAAAACCCTTGCC 59.538 50.000 0.00 0.00 0.00 4.52
425 431 2.158667 GGCCTTAATTGCCTAGGTAGCA 60.159 50.000 11.31 0.00 45.70 3.49
444 450 2.358898 GCAGGCGATTTGGTGAATGTAT 59.641 45.455 0.00 0.00 0.00 2.29
445 451 3.548818 GCAGGCGATTTGGTGAATGTATC 60.549 47.826 0.00 0.00 0.00 2.24
496 1567 7.671495 AATAAAAGAAATGCGGCAAAGAAAT 57.329 28.000 6.82 0.00 0.00 2.17
515 1586 1.006086 TTGTATGCGGACAAGATGCG 58.994 50.000 0.00 0.00 46.53 4.73
516 1587 0.809636 TGTATGCGGACAAGATGCGG 60.810 55.000 0.00 0.00 43.46 5.69
520 1591 3.499737 CGGACAAGATGCGGCCAC 61.500 66.667 2.24 0.00 38.73 5.01
545 1616 0.737219 GGAAGCATGACAGCACATCC 59.263 55.000 0.00 0.00 36.85 3.51
546 1617 1.456296 GAAGCATGACAGCACATCCA 58.544 50.000 0.00 0.00 36.85 3.41
548 1619 3.208594 GAAGCATGACAGCACATCCATA 58.791 45.455 0.00 0.00 36.85 2.74
562 1633 1.384525 TCCATAAAAATGGCCGGACG 58.615 50.000 5.05 0.00 41.43 4.79
563 1634 1.099689 CCATAAAAATGGCCGGACGT 58.900 50.000 5.05 0.00 34.56 4.34
564 1635 1.474879 CCATAAAAATGGCCGGACGTT 59.525 47.619 9.64 9.64 34.56 3.99
577 1648 4.595538 ACGTTGCTGCCGTCCGAA 62.596 61.111 0.00 0.00 31.97 4.30
578 1649 4.072088 CGTTGCTGCCGTCCGAAC 62.072 66.667 0.00 0.00 0.00 3.95
579 1650 2.970324 GTTGCTGCCGTCCGAACA 60.970 61.111 0.00 0.00 0.00 3.18
580 1651 2.664851 TTGCTGCCGTCCGAACAG 60.665 61.111 0.00 5.63 34.48 3.16
581 1652 4.680237 TGCTGCCGTCCGAACAGG 62.680 66.667 0.00 0.00 42.97 4.00
591 1662 0.608035 TCCGAACAGGATTTGGTGCC 60.608 55.000 0.00 0.00 45.98 5.01
608 1679 3.334751 CGTGCGTCGAAGTTGGCA 61.335 61.111 0.00 0.00 42.86 4.92
630 1701 2.280628 GAGAAACCACGGTCATCATCC 58.719 52.381 0.00 0.00 0.00 3.51
709 1780 0.471591 ATGGCCAAAAGGAGCAACCA 60.472 50.000 10.96 0.00 42.04 3.67
720 1791 1.589716 GAGCAACCATCCAAAGCGCT 61.590 55.000 2.64 2.64 0.00 5.92
722 1793 1.865788 GCAACCATCCAAAGCGCTCA 61.866 55.000 12.06 0.00 0.00 4.26
799 1889 4.206958 GCATGTGCGACTCATCCA 57.793 55.556 0.00 0.00 0.00 3.41
800 1890 2.699073 GCATGTGCGACTCATCCAT 58.301 52.632 0.00 0.00 0.00 3.41
801 1891 0.585357 GCATGTGCGACTCATCCATC 59.415 55.000 0.00 0.00 0.00 3.51
802 1892 0.857287 CATGTGCGACTCATCCATCG 59.143 55.000 0.00 0.00 41.32 3.84
806 1896 4.643733 CGACTCATCCATCGCCTC 57.356 61.111 0.00 0.00 0.00 4.70
807 1897 1.735973 CGACTCATCCATCGCCTCA 59.264 57.895 0.00 0.00 0.00 3.86
808 1898 0.103026 CGACTCATCCATCGCCTCAA 59.897 55.000 0.00 0.00 0.00 3.02
809 1899 1.576356 GACTCATCCATCGCCTCAAC 58.424 55.000 0.00 0.00 0.00 3.18
810 1900 0.179000 ACTCATCCATCGCCTCAACC 59.821 55.000 0.00 0.00 0.00 3.77
811 1901 0.467384 CTCATCCATCGCCTCAACCT 59.533 55.000 0.00 0.00 0.00 3.50
812 1902 0.465705 TCATCCATCGCCTCAACCTC 59.534 55.000 0.00 0.00 0.00 3.85
813 1903 0.178767 CATCCATCGCCTCAACCTCA 59.821 55.000 0.00 0.00 0.00 3.86
814 1904 0.179000 ATCCATCGCCTCAACCTCAC 59.821 55.000 0.00 0.00 0.00 3.51
815 1905 0.904865 TCCATCGCCTCAACCTCACT 60.905 55.000 0.00 0.00 0.00 3.41
816 1906 0.460987 CCATCGCCTCAACCTCACTC 60.461 60.000 0.00 0.00 0.00 3.51
817 1907 0.803768 CATCGCCTCAACCTCACTCG 60.804 60.000 0.00 0.00 0.00 4.18
818 1908 2.564553 ATCGCCTCAACCTCACTCGC 62.565 60.000 0.00 0.00 0.00 5.03
819 1909 2.659610 GCCTCAACCTCACTCGCT 59.340 61.111 0.00 0.00 0.00 4.93
820 1910 1.446966 GCCTCAACCTCACTCGCTC 60.447 63.158 0.00 0.00 0.00 5.03
821 1911 1.967535 CCTCAACCTCACTCGCTCA 59.032 57.895 0.00 0.00 0.00 4.26
842 1932 2.093447 ACTCACAAGAATCCCACCGATC 60.093 50.000 0.00 0.00 0.00 3.69
844 1934 0.546598 ACAAGAATCCCACCGATCCC 59.453 55.000 0.00 0.00 0.00 3.85
867 1957 4.103103 GCGACAAAAGGCGCCCTC 62.103 66.667 26.15 9.18 46.93 4.30
869 1959 2.282180 GACAAAAGGCGCCCTCCA 60.282 61.111 26.15 0.00 30.89 3.86
871 1961 2.142357 GACAAAAGGCGCCCTCCAAC 62.142 60.000 26.15 7.70 30.89 3.77
872 1962 2.197324 AAAAGGCGCCCTCCAACA 59.803 55.556 26.15 0.00 30.89 3.33
873 1963 2.200337 AAAAGGCGCCCTCCAACAC 61.200 57.895 26.15 0.00 30.89 3.32
878 1968 3.345808 CGCCCTCCAACACACACG 61.346 66.667 0.00 0.00 0.00 4.49
894 1984 4.293648 CGCACACCCTGTCCGTCA 62.294 66.667 0.00 0.00 0.00 4.35
895 1985 2.665185 GCACACCCTGTCCGTCAC 60.665 66.667 0.00 0.00 0.00 3.67
896 1986 2.355837 CACACCCTGTCCGTCACG 60.356 66.667 0.00 0.00 0.00 4.35
917 2033 2.045242 ACACTCTCCCGCTCGCTA 60.045 61.111 0.00 0.00 0.00 4.26
918 2034 2.408241 ACACTCTCCCGCTCGCTAC 61.408 63.158 0.00 0.00 0.00 3.58
919 2035 2.829458 ACTCTCCCGCTCGCTACC 60.829 66.667 0.00 0.00 0.00 3.18
920 2036 2.517402 CTCTCCCGCTCGCTACCT 60.517 66.667 0.00 0.00 0.00 3.08
921 2037 2.516460 TCTCCCGCTCGCTACCTC 60.516 66.667 0.00 0.00 0.00 3.85
922 2038 2.829003 CTCCCGCTCGCTACCTCA 60.829 66.667 0.00 0.00 0.00 3.86
1155 2283 1.275291 CACATATACTACGGGCAGGGG 59.725 57.143 0.00 0.00 0.00 4.79
1165 2293 2.035783 GGCAGGGGTTCAAGGTCC 59.964 66.667 0.00 0.00 0.00 4.46
1208 2336 1.227793 GCTACCTCCTCATGCAGGC 60.228 63.158 0.00 0.00 43.08 4.85
1217 2349 3.359523 CATGCAGGCACGCACACT 61.360 61.111 3.58 0.00 46.56 3.55
1235 2367 2.479275 CACTCTCACTCACACTGCATTG 59.521 50.000 1.95 1.95 0.00 2.82
1309 2479 3.257561 CGTCCAAGATGGCGAGCG 61.258 66.667 7.21 0.00 38.63 5.03
1378 2548 0.170561 CAACTACTCCCTCGACACCG 59.829 60.000 0.00 0.00 37.07 4.94
1453 2659 2.230750 ACTGCCGACTTACCAGAGTAAC 59.769 50.000 0.00 0.00 34.70 2.50
1454 2660 1.200716 TGCCGACTTACCAGAGTAACG 59.799 52.381 0.00 0.00 34.70 3.18
1455 2661 1.905449 CCGACTTACCAGAGTAACGC 58.095 55.000 0.00 0.00 34.70 4.84
1459 2665 3.187700 GACTTACCAGAGTAACGCCATG 58.812 50.000 0.00 0.00 34.70 3.66
1471 2678 1.002134 CGCCATGGTTTCCACCTCT 60.002 57.895 14.67 0.00 44.61 3.69
1494 2701 4.105486 GTTTGTTTGCAGTGTCCTTCTTC 58.895 43.478 0.00 0.00 0.00 2.87
1524 2736 2.069776 TGGAGGAGCCAAACTGAGG 58.930 57.895 0.00 0.00 45.87 3.86
1527 2739 0.687354 GAGGAGCCAAACTGAGGTCA 59.313 55.000 0.00 0.00 32.12 4.02
1528 2740 1.280421 GAGGAGCCAAACTGAGGTCAT 59.720 52.381 0.00 0.00 32.12 3.06
1529 2741 1.707427 AGGAGCCAAACTGAGGTCATT 59.293 47.619 0.00 0.00 32.12 2.57
1530 2742 1.815003 GGAGCCAAACTGAGGTCATTG 59.185 52.381 0.00 0.00 32.12 2.82
1531 2743 2.508526 GAGCCAAACTGAGGTCATTGT 58.491 47.619 0.00 0.00 0.00 2.71
1532 2744 3.559171 GGAGCCAAACTGAGGTCATTGTA 60.559 47.826 0.00 0.00 32.12 2.41
1533 2745 4.265073 GAGCCAAACTGAGGTCATTGTAT 58.735 43.478 0.00 0.00 0.00 2.29
1535 2747 5.815581 AGCCAAACTGAGGTCATTGTATAA 58.184 37.500 0.00 0.00 0.00 0.98
1539 2751 6.403200 CCAAACTGAGGTCATTGTATAAACCG 60.403 42.308 0.00 0.00 36.87 4.44
1571 2783 2.277057 GCGGCGGCGACATTTTAC 60.277 61.111 36.87 10.85 0.00 2.01
1572 2784 3.029564 GCGGCGGCGACATTTTACA 62.030 57.895 36.87 0.00 0.00 2.41
1573 2785 1.719117 CGGCGGCGACATTTTACAT 59.281 52.632 29.19 0.00 0.00 2.29
1575 2787 1.822581 GGCGGCGACATTTTACATTC 58.177 50.000 12.98 0.00 0.00 2.67
1576 2788 1.533129 GGCGGCGACATTTTACATTCC 60.533 52.381 12.98 0.00 0.00 3.01
1579 2791 3.064271 GCGGCGACATTTTACATTCCTTA 59.936 43.478 12.98 0.00 0.00 2.69
1580 2792 4.584394 CGGCGACATTTTACATTCCTTAC 58.416 43.478 0.00 0.00 0.00 2.34
1581 2793 4.093703 CGGCGACATTTTACATTCCTTACA 59.906 41.667 0.00 0.00 0.00 2.41
1582 2794 5.220777 CGGCGACATTTTACATTCCTTACAT 60.221 40.000 0.00 0.00 0.00 2.29
1583 2795 6.018588 CGGCGACATTTTACATTCCTTACATA 60.019 38.462 0.00 0.00 0.00 2.29
1584 2796 7.130269 GGCGACATTTTACATTCCTTACATAC 58.870 38.462 0.00 0.00 0.00 2.39
1585 2797 7.201661 GGCGACATTTTACATTCCTTACATACA 60.202 37.037 0.00 0.00 0.00 2.29
1586 2798 8.342634 GCGACATTTTACATTCCTTACATACAT 58.657 33.333 0.00 0.00 0.00 2.29
1653 2888 4.813296 AAAAGAGTAACAACGGAAGCTG 57.187 40.909 0.00 0.00 0.00 4.24
1654 2889 1.797025 AGAGTAACAACGGAAGCTGC 58.203 50.000 0.00 0.00 0.00 5.25
1657 2892 0.863144 GTAACAACGGAAGCTGCGAA 59.137 50.000 4.30 0.00 34.49 4.70
1658 2893 1.463444 GTAACAACGGAAGCTGCGAAT 59.537 47.619 4.30 0.00 34.49 3.34
1659 2894 0.238289 AACAACGGAAGCTGCGAATG 59.762 50.000 4.30 5.48 34.49 2.67
1660 2895 0.884704 ACAACGGAAGCTGCGAATGT 60.885 50.000 4.30 5.98 34.49 2.71
1661 2896 0.453282 CAACGGAAGCTGCGAATGTG 60.453 55.000 4.30 0.00 34.49 3.21
1675 2911 4.098654 TGCGAATGTGAAAAGGAAAAAGGA 59.901 37.500 0.00 0.00 0.00 3.36
1676 2912 5.047188 GCGAATGTGAAAAGGAAAAAGGAA 58.953 37.500 0.00 0.00 0.00 3.36
1708 2965 4.531332 CGGCTTTCTGCTTATAATGCTTC 58.469 43.478 7.94 0.00 42.39 3.86
1713 2970 5.998454 TTCTGCTTATAATGCTTCAGCTC 57.002 39.130 0.00 0.00 42.66 4.09
1738 2996 3.267483 GACGCCTGGAGTAATTTTGCTA 58.733 45.455 2.13 0.00 0.00 3.49
1739 2997 3.877508 GACGCCTGGAGTAATTTTGCTAT 59.122 43.478 2.13 0.00 0.00 2.97
1740 2998 3.627577 ACGCCTGGAGTAATTTTGCTATG 59.372 43.478 0.00 0.00 0.00 2.23
1741 2999 3.627577 CGCCTGGAGTAATTTTGCTATGT 59.372 43.478 0.00 0.00 0.00 2.29
1791 3049 5.749462 AGAACTTGAAGGGGATAACATCAG 58.251 41.667 0.00 0.00 0.00 2.90
1793 3051 3.266772 ACTTGAAGGGGATAACATCAGCA 59.733 43.478 0.00 0.00 0.00 4.41
1838 3096 1.135689 CAGGCGTATGCAAGTGGAAAC 60.136 52.381 9.59 0.00 45.35 2.78
1871 3129 2.743928 GGGACAGACGCAGGCAAG 60.744 66.667 0.00 0.00 0.00 4.01
1916 3174 2.748605 GTGAGCACGGATCAAGATAGG 58.251 52.381 0.00 0.00 26.97 2.57
1931 3189 1.024579 ATAGGGGTTGCAACTTCGCG 61.025 55.000 27.64 0.00 33.35 5.87
2051 3322 7.367285 TGAACTGACAAAACTAATATTGGTGC 58.633 34.615 5.10 0.00 0.00 5.01
2066 3337 1.372683 GTGCTTCTGTGCAGAGGGA 59.627 57.895 11.47 7.34 44.20 4.20
2150 3422 6.985188 TGATGCAGTTAAGACCAGTAAATC 57.015 37.500 0.00 0.00 0.00 2.17
2173 3445 3.236816 GACTGAATTTGCGTTGTCATGG 58.763 45.455 0.00 0.00 0.00 3.66
2179 3451 1.674359 TTGCGTTGTCATGGTTGAGT 58.326 45.000 0.00 0.00 30.85 3.41
2196 3468 7.644490 TGGTTGAGTGACAATATTGTGTTTAC 58.356 34.615 25.42 16.79 42.43 2.01
2201 3473 9.719355 TGAGTGACAATATTGTGTTTACTATGT 57.281 29.630 25.42 0.00 42.43 2.29
2265 3537 6.577103 TCAACTAGCAAGACCAGATTATCTG 58.423 40.000 14.80 14.80 43.91 2.90
2271 3543 4.337555 GCAAGACCAGATTATCTGTGCAAT 59.662 41.667 22.31 5.61 42.80 3.56
2272 3544 5.528690 GCAAGACCAGATTATCTGTGCAATA 59.471 40.000 22.31 0.00 42.80 1.90
2273 3545 6.512415 GCAAGACCAGATTATCTGTGCAATAC 60.512 42.308 22.31 5.87 42.80 1.89
2274 3546 6.491714 AGACCAGATTATCTGTGCAATACT 57.508 37.500 19.37 6.40 42.80 2.12
2280 3552 9.416794 CCAGATTATCTGTGCAATACTTACTAG 57.583 37.037 19.37 0.00 42.80 2.57
2319 3591 2.314246 ACAGGTATACCTAAGGACCGC 58.686 52.381 24.15 0.00 46.65 5.68
2335 3607 1.062002 ACCGCGTATCTCATTTTTGCG 59.938 47.619 4.92 0.00 43.34 4.85
2351 3624 5.741388 TTTTGCGCCAAATTTTAACACAT 57.259 30.435 4.18 0.00 33.19 3.21
2355 3628 3.923461 GCGCCAAATTTTAACACATGCTA 59.077 39.130 0.00 0.00 0.00 3.49
2356 3629 4.201580 GCGCCAAATTTTAACACATGCTAC 60.202 41.667 0.00 0.00 0.00 3.58
2529 4134 9.017669 GTGCATCTATCTAAGCAAAATTTTGAG 57.982 33.333 30.40 19.80 40.55 3.02
2552 4157 7.755373 TGAGTACAGAGTTTTTACTGATCATCG 59.245 37.037 0.00 0.00 37.54 3.84
2627 4235 3.955650 ACAAGTTACAGGTAGCGTCAT 57.044 42.857 0.00 0.00 0.00 3.06
2651 4262 6.820470 TTTGTATTGCAGCAGTTACAAAAC 57.180 33.333 27.28 9.99 35.38 2.43
2652 4263 4.865776 TGTATTGCAGCAGTTACAAAACC 58.134 39.130 14.69 0.00 36.15 3.27
2656 4268 4.561735 TGCAGCAGTTACAAAACCTAAC 57.438 40.909 0.00 0.00 36.15 2.34
2668 4280 6.203808 ACAAAACCTAACAAAGAAGTGGAC 57.796 37.500 0.00 0.00 0.00 4.02
2670 4282 6.127730 ACAAAACCTAACAAAGAAGTGGACAG 60.128 38.462 0.00 0.00 0.00 3.51
2813 4427 3.225104 ACATGCCATTCTTTGTGTGAGT 58.775 40.909 0.00 0.00 0.00 3.41
2814 4428 4.397420 ACATGCCATTCTTTGTGTGAGTA 58.603 39.130 0.00 0.00 0.00 2.59
2861 4499 4.409901 TCAGCCAGATCACCATTTCAGATA 59.590 41.667 0.00 0.00 0.00 1.98
2894 4532 6.518208 AGAGCTCGTTTCTTACTACTTGAT 57.482 37.500 8.37 0.00 0.00 2.57
2942 4581 9.174166 TGTTCTAAGATAAATTTGGCCTCTTAC 57.826 33.333 3.32 0.00 0.00 2.34
2964 5447 9.907576 CTTACTATGTAAGAAGAAAATTCTGCG 57.092 33.333 10.88 0.00 37.94 5.18
2965 5448 7.308782 ACTATGTAAGAAGAAAATTCTGCGG 57.691 36.000 0.00 0.00 37.94 5.69
2968 5451 3.813529 AAGAAGAAAATTCTGCGGACG 57.186 42.857 0.00 0.00 37.94 4.79
2969 5452 1.464997 AGAAGAAAATTCTGCGGACGC 59.535 47.619 10.13 10.13 37.94 5.19
2970 5453 1.464997 GAAGAAAATTCTGCGGACGCT 59.535 47.619 18.04 0.00 42.51 5.07
2984 5468 5.817988 TGCGGACGCTATATGATCTATTAC 58.182 41.667 18.04 0.00 42.51 1.89
2989 5473 7.853437 CGGACGCTATATGATCTATTACTTCAG 59.147 40.741 0.00 0.00 0.00 3.02
3099 5591 0.979665 ACATATGCCTCGGATCCTGG 59.020 55.000 10.75 12.85 0.00 4.45
3354 5847 3.561097 CCAAACCCCAGTGTGTCATATGA 60.561 47.826 0.00 0.00 28.00 2.15
3388 5885 3.477530 AGTGGTCTAACAAACTTCCTGC 58.522 45.455 0.00 0.00 0.00 4.85
3456 5953 4.511082 GGTTCTTGCTGATCTGATAGAAGC 59.489 45.833 19.94 19.94 34.37 3.86
3485 5982 2.290464 CAACGGGGAACTACACAACAA 58.710 47.619 0.00 0.00 0.00 2.83
3502 5999 6.039382 ACACAACAATTTACTTCAGGAACCTC 59.961 38.462 0.00 0.00 0.00 3.85
3541 6038 6.765915 AATGTTTTCTCCAGGCTATCTTTC 57.234 37.500 0.00 0.00 0.00 2.62
3600 6098 3.119637 TGATGTTGATCAGCAGCATTGTG 60.120 43.478 24.10 0.00 46.68 3.33
3632 6130 3.884037 AGAAGGGGTCACAGAAATTGT 57.116 42.857 0.00 0.00 41.94 2.71
3732 6230 7.097192 TGAACATTAAGACGATTCAAGCTACT 58.903 34.615 0.00 0.00 0.00 2.57
3840 6338 7.483691 GGAAGTGTTTTGTTAAGTGTGTTACAG 59.516 37.037 0.00 0.00 0.00 2.74
3857 6355 6.693545 GTGTTACAGTCACTATACTCATCAGC 59.306 42.308 0.00 0.00 33.59 4.26
3869 6367 2.289631 ACTCATCAGCCGTCAATTGACA 60.290 45.455 32.06 16.78 44.99 3.58
3874 6373 2.548057 TCAGCCGTCAATTGACACTTTC 59.452 45.455 32.06 17.78 44.99 2.62
3877 6376 2.808543 GCCGTCAATTGACACTTTCTCT 59.191 45.455 32.06 0.00 44.99 3.10
3905 6404 6.176183 AGCAGCAGTTGTATCTTTATCTGTT 58.824 36.000 0.00 0.00 0.00 3.16
4021 6520 6.922957 TGCAGTTTTGTTTCCTTGAATGATAC 59.077 34.615 0.00 0.00 0.00 2.24
4055 6554 4.018960 AGACTGGGATGAACTGCTTGTAAT 60.019 41.667 0.00 0.00 0.00 1.89
4073 6588 6.255596 TGTAATCTCAGTCACTAGTCACAC 57.744 41.667 0.00 0.00 0.00 3.82
4113 6628 6.015940 ACAAGCAGACAAAAGAAATAGAAGGG 60.016 38.462 0.00 0.00 0.00 3.95
4133 6648 1.133668 GGAATCCCAGCACATTAGCCT 60.134 52.381 0.00 0.00 34.23 4.58
4159 6674 9.565090 TTCAGATCTTCAATATTAAGGACATGG 57.435 33.333 0.00 0.00 0.00 3.66
4195 6710 7.201548 GGACTAAATTTGGCATGCTAATGTTTG 60.202 37.037 24.78 19.84 36.08 2.93
4332 6847 1.264288 GCATGCCGTAAGATTAGCACC 59.736 52.381 6.36 0.00 38.21 5.01
4402 6917 7.182817 ACTGCAAGAACAGGTATAAGTATCA 57.817 36.000 0.00 0.00 42.21 2.15
4461 6976 9.060347 TCATAATAAGCATTCAGAAATGACTCC 57.940 33.333 2.44 0.00 44.25 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 6.039829 AGGAGAGAGCAAGTTTAAAGGTTTTG 59.960 38.462 0.00 0.00 0.00 2.44
90 91 6.665992 TTACTTCAGGAGAGAGCAAGTTTA 57.334 37.500 0.00 0.00 0.00 2.01
92 93 5.012561 ACATTACTTCAGGAGAGAGCAAGTT 59.987 40.000 0.00 0.00 0.00 2.66
97 98 4.429108 GACACATTACTTCAGGAGAGAGC 58.571 47.826 0.00 0.00 0.00 4.09
108 109 6.806249 CCAAAATATTGCACGACACATTACTT 59.194 34.615 0.00 0.00 35.10 2.24
111 112 5.098893 GCCAAAATATTGCACGACACATTA 58.901 37.500 0.00 0.00 35.10 1.90
117 118 1.131504 TCCGCCAAAATATTGCACGAC 59.868 47.619 0.00 0.00 36.98 4.34
175 176 0.532862 ACTTCGTGTGCAAGACCCAG 60.533 55.000 0.00 0.00 0.00 4.45
190 193 1.189403 CCGTCGAGCGTAATCACTTC 58.811 55.000 0.00 0.00 39.32 3.01
256 261 0.106217 ACAGTCCCCACCAAAACCTG 60.106 55.000 0.00 0.00 0.00 4.00
276 282 0.250553 AGATCTCGGTCTCCTAGGCG 60.251 60.000 2.96 0.00 0.00 5.52
319 325 5.880054 AATAACATGTGCTTGTACTGGAC 57.120 39.130 0.00 0.00 0.00 4.02
341 347 8.719560 TTCGTTGGTAATAATAACATGTGCTA 57.280 30.769 0.00 0.00 0.00 3.49
343 349 8.676454 TTTTCGTTGGTAATAATAACATGTGC 57.324 30.769 0.00 0.00 0.00 4.57
345 351 9.628746 GGTTTTTCGTTGGTAATAATAACATGT 57.371 29.630 0.00 0.00 0.00 3.21
346 352 9.078753 GGGTTTTTCGTTGGTAATAATAACATG 57.921 33.333 0.00 0.00 0.00 3.21
347 353 9.027202 AGGGTTTTTCGTTGGTAATAATAACAT 57.973 29.630 0.00 0.00 0.00 2.71
349 355 9.131416 CAAGGGTTTTTCGTTGGTAATAATAAC 57.869 33.333 0.00 0.00 0.00 1.89
351 357 7.314393 GCAAGGGTTTTTCGTTGGTAATAATA 58.686 34.615 0.00 0.00 34.31 0.98
352 358 6.160684 GCAAGGGTTTTTCGTTGGTAATAAT 58.839 36.000 0.00 0.00 34.31 1.28
353 359 5.509332 GGCAAGGGTTTTTCGTTGGTAATAA 60.509 40.000 0.00 0.00 34.31 1.40
377 383 2.028876 TGATGGCATGGCATTCTTGAG 58.971 47.619 32.59 0.00 0.00 3.02
425 431 3.879295 CTGATACATTCACCAAATCGCCT 59.121 43.478 0.00 0.00 0.00 5.52
476 1466 4.815846 ACAATTTCTTTGCCGCATTTCTTT 59.184 33.333 0.00 0.00 39.03 2.52
482 1472 3.189285 GCATACAATTTCTTTGCCGCAT 58.811 40.909 0.00 0.00 39.03 4.73
486 1476 3.179048 GTCCGCATACAATTTCTTTGCC 58.821 45.455 0.00 0.00 39.03 4.52
496 1567 1.006086 CGCATCTTGTCCGCATACAA 58.994 50.000 1.36 1.36 37.75 2.41
519 1590 2.809601 GTCATGCTTCCGACGCGT 60.810 61.111 13.85 13.85 0.00 6.01
520 1591 2.792290 CTGTCATGCTTCCGACGCG 61.792 63.158 3.53 3.53 34.78 6.01
523 1594 0.950555 TGTGCTGTCATGCTTCCGAC 60.951 55.000 0.00 0.00 0.00 4.79
525 1596 0.376152 GATGTGCTGTCATGCTTCCG 59.624 55.000 0.00 0.00 0.00 4.30
529 1600 3.286329 TTATGGATGTGCTGTCATGCT 57.714 42.857 9.05 1.00 37.14 3.79
533 1604 4.381825 GCCATTTTTATGGATGTGCTGTCA 60.382 41.667 8.32 0.00 44.39 3.58
545 1616 2.525055 CAACGTCCGGCCATTTTTATG 58.475 47.619 2.24 0.00 0.00 1.90
546 1617 1.135228 GCAACGTCCGGCCATTTTTAT 60.135 47.619 2.24 0.00 0.00 1.40
548 1619 1.006688 GCAACGTCCGGCCATTTTT 60.007 52.632 2.24 0.00 0.00 1.94
562 1633 2.954753 CTGTTCGGACGGCAGCAAC 61.955 63.158 0.00 0.00 0.00 4.17
563 1634 2.664851 CTGTTCGGACGGCAGCAA 60.665 61.111 0.00 0.00 0.00 3.91
564 1635 4.680237 CCTGTTCGGACGGCAGCA 62.680 66.667 0.00 0.00 33.16 4.41
571 1642 0.521735 GCACCAAATCCTGTTCGGAC 59.478 55.000 0.00 0.00 46.80 4.79
575 1646 0.240945 CACGGCACCAAATCCTGTTC 59.759 55.000 0.00 0.00 0.00 3.18
576 1647 1.805428 GCACGGCACCAAATCCTGTT 61.805 55.000 0.00 0.00 0.00 3.16
577 1648 2.268076 GCACGGCACCAAATCCTGT 61.268 57.895 0.00 0.00 0.00 4.00
578 1649 2.568090 GCACGGCACCAAATCCTG 59.432 61.111 0.00 0.00 0.00 3.86
579 1650 3.055719 CGCACGGCACCAAATCCT 61.056 61.111 0.00 0.00 0.00 3.24
580 1651 3.322706 GACGCACGGCACCAAATCC 62.323 63.158 0.00 0.00 0.00 3.01
581 1652 2.175811 GACGCACGGCACCAAATC 59.824 61.111 0.00 0.00 0.00 2.17
582 1653 3.722295 CGACGCACGGCACCAAAT 61.722 61.111 0.00 0.00 38.46 2.32
583 1654 4.893601 TCGACGCACGGCACCAAA 62.894 61.111 0.00 0.00 42.82 3.28
584 1655 4.893601 TTCGACGCACGGCACCAA 62.894 61.111 0.00 0.00 42.82 3.67
591 1662 2.667318 ATGCCAACTTCGACGCACG 61.667 57.895 0.00 0.00 44.09 5.34
608 1679 3.535561 GATGATGACCGTGGTTTCTCAT 58.464 45.455 10.05 10.05 0.00 2.90
651 1722 4.029809 ACTGGCCGCCTTGGTACC 62.030 66.667 11.61 4.43 41.21 3.34
691 1762 0.471591 ATGGTTGCTCCTTTTGGCCA 60.472 50.000 0.00 0.00 40.12 5.36
692 1763 0.247460 GATGGTTGCTCCTTTTGGCC 59.753 55.000 0.00 0.00 40.12 5.36
709 1780 0.890542 TGTTGCTGAGCGCTTTGGAT 60.891 50.000 13.26 0.00 40.11 3.41
720 1791 4.560743 TGGTGGCGCTGTTGCTGA 62.561 61.111 7.64 0.00 36.97 4.26
782 1872 0.585357 GATGGATGAGTCGCACATGC 59.415 55.000 0.00 0.00 36.79 4.06
783 1873 0.857287 CGATGGATGAGTCGCACATG 59.143 55.000 0.00 0.00 0.00 3.21
785 1875 4.812814 CGATGGATGAGTCGCACA 57.187 55.556 0.00 0.00 0.00 4.57
789 1879 0.103026 TTGAGGCGATGGATGAGTCG 59.897 55.000 0.00 0.00 40.62 4.18
790 1880 1.576356 GTTGAGGCGATGGATGAGTC 58.424 55.000 0.00 0.00 0.00 3.36
791 1881 0.179000 GGTTGAGGCGATGGATGAGT 59.821 55.000 0.00 0.00 0.00 3.41
792 1882 0.467384 AGGTTGAGGCGATGGATGAG 59.533 55.000 0.00 0.00 0.00 2.90
793 1883 0.465705 GAGGTTGAGGCGATGGATGA 59.534 55.000 0.00 0.00 0.00 2.92
794 1884 0.178767 TGAGGTTGAGGCGATGGATG 59.821 55.000 0.00 0.00 0.00 3.51
795 1885 0.179000 GTGAGGTTGAGGCGATGGAT 59.821 55.000 0.00 0.00 0.00 3.41
796 1886 0.904865 AGTGAGGTTGAGGCGATGGA 60.905 55.000 0.00 0.00 0.00 3.41
797 1887 0.460987 GAGTGAGGTTGAGGCGATGG 60.461 60.000 0.00 0.00 0.00 3.51
798 1888 0.803768 CGAGTGAGGTTGAGGCGATG 60.804 60.000 0.00 0.00 0.00 3.84
799 1889 1.513158 CGAGTGAGGTTGAGGCGAT 59.487 57.895 0.00 0.00 0.00 4.58
800 1890 2.962569 CGAGTGAGGTTGAGGCGA 59.037 61.111 0.00 0.00 0.00 5.54
801 1891 2.811317 GCGAGTGAGGTTGAGGCG 60.811 66.667 0.00 0.00 0.00 5.52
802 1892 1.446966 GAGCGAGTGAGGTTGAGGC 60.447 63.158 0.00 0.00 0.00 4.70
803 1893 0.389166 GTGAGCGAGTGAGGTTGAGG 60.389 60.000 0.00 0.00 0.00 3.86
804 1894 0.600557 AGTGAGCGAGTGAGGTTGAG 59.399 55.000 0.00 0.00 0.00 3.02
805 1895 0.598562 GAGTGAGCGAGTGAGGTTGA 59.401 55.000 0.00 0.00 0.00 3.18
806 1896 0.315251 TGAGTGAGCGAGTGAGGTTG 59.685 55.000 0.00 0.00 0.00 3.77
807 1897 0.315568 GTGAGTGAGCGAGTGAGGTT 59.684 55.000 0.00 0.00 0.00 3.50
808 1898 0.823769 TGTGAGTGAGCGAGTGAGGT 60.824 55.000 0.00 0.00 0.00 3.85
809 1899 0.315251 TTGTGAGTGAGCGAGTGAGG 59.685 55.000 0.00 0.00 0.00 3.86
810 1900 1.268079 TCTTGTGAGTGAGCGAGTGAG 59.732 52.381 0.00 0.00 0.00 3.51
811 1901 1.318576 TCTTGTGAGTGAGCGAGTGA 58.681 50.000 0.00 0.00 0.00 3.41
812 1902 2.140065 TTCTTGTGAGTGAGCGAGTG 57.860 50.000 0.00 0.00 0.00 3.51
813 1903 2.353208 GGATTCTTGTGAGTGAGCGAGT 60.353 50.000 0.00 0.00 0.00 4.18
814 1904 2.266554 GGATTCTTGTGAGTGAGCGAG 58.733 52.381 0.00 0.00 0.00 5.03
815 1905 1.066858 GGGATTCTTGTGAGTGAGCGA 60.067 52.381 0.00 0.00 0.00 4.93
816 1906 1.338105 TGGGATTCTTGTGAGTGAGCG 60.338 52.381 0.00 0.00 0.00 5.03
817 1907 2.079925 GTGGGATTCTTGTGAGTGAGC 58.920 52.381 0.00 0.00 0.00 4.26
818 1908 2.704572 GGTGGGATTCTTGTGAGTGAG 58.295 52.381 0.00 0.00 0.00 3.51
819 1909 1.001974 CGGTGGGATTCTTGTGAGTGA 59.998 52.381 0.00 0.00 0.00 3.41
820 1910 1.001974 TCGGTGGGATTCTTGTGAGTG 59.998 52.381 0.00 0.00 0.00 3.51
821 1911 1.348064 TCGGTGGGATTCTTGTGAGT 58.652 50.000 0.00 0.00 0.00 3.41
851 1941 3.431725 GGAGGGCGCCTTTTGTCG 61.432 66.667 28.56 0.00 31.76 4.35
866 1956 2.109739 GGTGTGCGTGTGTGTTGGA 61.110 57.895 0.00 0.00 0.00 3.53
867 1957 2.407210 GGTGTGCGTGTGTGTTGG 59.593 61.111 0.00 0.00 0.00 3.77
869 1959 2.112198 CAGGGTGTGCGTGTGTGTT 61.112 57.895 0.00 0.00 0.00 3.32
871 1961 2.513666 ACAGGGTGTGCGTGTGTG 60.514 61.111 0.00 0.00 0.00 3.82
872 1962 2.203015 GACAGGGTGTGCGTGTGT 60.203 61.111 0.00 0.00 0.00 3.72
873 1963 2.972505 GGACAGGGTGTGCGTGTG 60.973 66.667 0.00 0.00 0.00 3.82
878 1968 2.665185 GTGACGGACAGGGTGTGC 60.665 66.667 0.00 0.00 35.21 4.57
896 1986 4.459089 GAGCGGGAGAGTGTGCCC 62.459 72.222 0.00 0.00 41.11 5.36
904 2020 2.516460 GAGGTAGCGAGCGGGAGA 60.516 66.667 0.00 0.00 0.00 3.71
917 2033 0.900182 TGATGGCGAGTGAGTGAGGT 60.900 55.000 0.00 0.00 0.00 3.85
918 2034 0.459237 GTGATGGCGAGTGAGTGAGG 60.459 60.000 0.00 0.00 0.00 3.86
919 2035 0.799917 CGTGATGGCGAGTGAGTGAG 60.800 60.000 0.00 0.00 0.00 3.51
920 2036 1.212751 CGTGATGGCGAGTGAGTGA 59.787 57.895 0.00 0.00 0.00 3.41
921 2037 1.073216 GTCGTGATGGCGAGTGAGTG 61.073 60.000 0.00 0.00 41.85 3.51
922 2038 1.213013 GTCGTGATGGCGAGTGAGT 59.787 57.895 0.00 0.00 41.85 3.41
1155 2283 1.531578 GCGTTCTTGAGGACCTTGAAC 59.468 52.381 18.29 18.29 35.17 3.18
1165 2293 1.738099 CGTCCCAGGCGTTCTTGAG 60.738 63.158 0.00 0.00 0.00 3.02
1208 2336 0.249031 TGTGAGTGAGAGTGTGCGTG 60.249 55.000 0.00 0.00 0.00 5.34
1217 2349 1.417517 ACCAATGCAGTGTGAGTGAGA 59.582 47.619 13.82 0.00 0.00 3.27
1247 2394 3.544834 CGTTGCCGATCAATCAATCTGTC 60.545 47.826 0.00 0.00 36.99 3.51
1309 2479 2.181021 CGTGCAGTACCTCGTCCC 59.819 66.667 0.00 0.00 0.00 4.46
1378 2548 1.834822 ATCTACCTGGAGAGGCGGC 60.835 63.158 0.00 0.00 44.33 6.53
1411 2591 2.126346 GCATGCTGCCGTGAAACC 60.126 61.111 11.37 0.00 37.42 3.27
1438 2644 3.187700 CATGGCGTTACTCTGGTAAGTC 58.812 50.000 0.00 0.00 38.42 3.01
1453 2659 1.002134 AGAGGTGGAAACCATGGCG 60.002 57.895 13.04 0.00 35.28 5.69
1454 2660 0.251341 ACAGAGGTGGAAACCATGGC 60.251 55.000 13.04 0.00 35.28 4.40
1455 2661 2.292828 AACAGAGGTGGAAACCATGG 57.707 50.000 11.19 11.19 35.28 3.66
1459 2665 3.780902 CAAACAAACAGAGGTGGAAACC 58.219 45.455 0.00 0.00 0.00 3.27
1471 2678 3.088532 AGAAGGACACTGCAAACAAACA 58.911 40.909 0.00 0.00 0.00 2.83
1494 2701 0.179089 CTCCTCCATTGCTCACCTCG 60.179 60.000 0.00 0.00 0.00 4.63
1524 2736 6.537301 TCCTGAATGTCGGTTTATACAATGAC 59.463 38.462 0.00 0.00 0.00 3.06
1527 2739 7.228706 GGATTCCTGAATGTCGGTTTATACAAT 59.771 37.037 0.00 0.00 0.00 2.71
1528 2740 6.540914 GGATTCCTGAATGTCGGTTTATACAA 59.459 38.462 0.00 0.00 0.00 2.41
1529 2741 6.053005 GGATTCCTGAATGTCGGTTTATACA 58.947 40.000 0.00 0.00 0.00 2.29
1530 2742 5.176958 CGGATTCCTGAATGTCGGTTTATAC 59.823 44.000 0.30 0.00 0.00 1.47
1531 2743 5.294356 CGGATTCCTGAATGTCGGTTTATA 58.706 41.667 0.30 0.00 0.00 0.98
1532 2744 4.127171 CGGATTCCTGAATGTCGGTTTAT 58.873 43.478 0.30 0.00 0.00 1.40
1533 2745 3.527533 CGGATTCCTGAATGTCGGTTTA 58.472 45.455 0.30 0.00 0.00 2.01
1535 2747 2.012051 GCGGATTCCTGAATGTCGGTT 61.012 52.381 0.30 0.00 0.00 4.44
1539 2751 1.776034 GCCGCGGATTCCTGAATGTC 61.776 60.000 33.48 1.16 0.00 3.06
1560 2772 7.690228 TGTATGTAAGGAATGTAAAATGTCGC 58.310 34.615 0.00 0.00 0.00 5.19
1639 2874 1.463056 CATTCGCAGCTTCCGTTGTTA 59.537 47.619 3.74 0.00 0.00 2.41
1645 2880 0.516877 TTTCACATTCGCAGCTTCCG 59.483 50.000 0.00 0.00 0.00 4.30
1646 2881 2.589014 CTTTTCACATTCGCAGCTTCC 58.411 47.619 0.00 0.00 0.00 3.46
1650 2885 2.704725 TTCCTTTTCACATTCGCAGC 57.295 45.000 0.00 0.00 0.00 5.25
1652 2887 4.098654 TCCTTTTTCCTTTTCACATTCGCA 59.901 37.500 0.00 0.00 0.00 5.10
1653 2888 4.616953 TCCTTTTTCCTTTTCACATTCGC 58.383 39.130 0.00 0.00 0.00 4.70
1654 2889 7.095649 GGATTTCCTTTTTCCTTTTCACATTCG 60.096 37.037 0.00 0.00 0.00 3.34
1657 2892 7.379059 AGGATTTCCTTTTTCCTTTTCACAT 57.621 32.000 0.00 0.00 46.09 3.21
1658 2893 6.806668 AGGATTTCCTTTTTCCTTTTCACA 57.193 33.333 0.00 0.00 46.09 3.58
1676 2912 0.393537 CAGAAAGCCGGCAGAGGATT 60.394 55.000 31.54 10.30 42.38 3.01
1687 2923 6.015458 GCTGAAGCATTATAAGCAGAAAGCC 61.015 44.000 0.00 0.00 42.38 4.35
1708 2965 2.183811 CCAGGCGTCAGAGAGCTG 59.816 66.667 0.00 0.00 43.67 4.24
1713 2970 2.969628 AATTACTCCAGGCGTCAGAG 57.030 50.000 5.62 5.62 0.00 3.35
1719 2976 3.627577 ACATAGCAAAATTACTCCAGGCG 59.372 43.478 0.00 0.00 0.00 5.52
1720 2977 4.399303 ACACATAGCAAAATTACTCCAGGC 59.601 41.667 0.00 0.00 0.00 4.85
1738 2996 1.875514 CAAGTAGCTGCACACACACAT 59.124 47.619 4.12 0.00 0.00 3.21
1739 2997 1.298602 CAAGTAGCTGCACACACACA 58.701 50.000 4.12 0.00 0.00 3.72
1740 2998 0.588252 CCAAGTAGCTGCACACACAC 59.412 55.000 4.12 0.00 0.00 3.82
1741 2999 0.467804 TCCAAGTAGCTGCACACACA 59.532 50.000 4.12 0.00 0.00 3.72
1791 3049 1.072159 ACTGAGAAGCCACCTGTGC 59.928 57.895 0.00 0.00 0.00 4.57
1793 3051 1.072159 GCACTGAGAAGCCACCTGT 59.928 57.895 0.00 0.00 0.00 4.00
1823 3081 1.963747 GCACGTTTCCACTTGCATAC 58.036 50.000 0.00 0.00 45.41 2.39
1838 3096 2.249309 CCGTTGACAAGCTGCACG 59.751 61.111 1.02 1.31 0.00 5.34
1915 3173 4.038080 CCGCGAAGTTGCAACCCC 62.038 66.667 25.62 16.11 34.15 4.95
1916 3174 4.700365 GCCGCGAAGTTGCAACCC 62.700 66.667 25.62 16.46 34.15 4.11
1931 3189 2.036089 CTCTTCGGAGGGTACATAAGCC 59.964 54.545 0.00 0.00 46.88 4.35
2051 3322 0.108898 CTCGTCCCTCTGCACAGAAG 60.109 60.000 1.42 0.00 36.94 2.85
2066 3337 2.170607 CCCAGGTATTTGATCCACTCGT 59.829 50.000 0.00 0.00 0.00 4.18
2150 3422 3.607422 TGACAACGCAAATTCAGTCAG 57.393 42.857 0.00 0.00 32.76 3.51
2242 3514 6.841443 CAGATAATCTGGTCTTGCTAGTTG 57.159 41.667 0.00 0.00 40.71 3.16
2263 3535 8.981724 TCTACAAACTAGTAAGTATTGCACAG 57.018 34.615 0.00 0.00 33.75 3.66
2306 3578 2.158769 TGAGATACGCGGTCCTTAGGTA 60.159 50.000 12.47 0.00 0.00 3.08
2307 3579 1.316651 GAGATACGCGGTCCTTAGGT 58.683 55.000 12.47 0.00 0.00 3.08
2317 3589 1.104579 GCGCAAAAATGAGATACGCG 58.895 50.000 3.53 3.53 43.77 6.01
2319 3591 2.823196 TGGCGCAAAAATGAGATACG 57.177 45.000 10.83 0.00 0.00 3.06
2335 3607 6.155827 TGAGTAGCATGTGTTAAAATTTGGC 58.844 36.000 0.00 0.00 0.00 4.52
2351 3624 5.683681 TGCATTAGGAATGAATGAGTAGCA 58.316 37.500 3.38 0.00 41.46 3.49
2355 3628 8.985315 TTAATCTGCATTAGGAATGAATGAGT 57.015 30.769 3.38 0.70 41.46 3.41
2356 3629 9.281371 TCTTAATCTGCATTAGGAATGAATGAG 57.719 33.333 3.38 0.00 41.46 2.90
2529 4134 6.812160 ACCGATGATCAGTAAAAACTCTGTAC 59.188 38.462 0.09 0.00 33.89 2.90
2532 4137 5.639506 ACACCGATGATCAGTAAAAACTCTG 59.360 40.000 0.09 0.00 0.00 3.35
2534 4139 6.812160 AGTACACCGATGATCAGTAAAAACTC 59.188 38.462 0.09 0.00 0.00 3.01
2552 4157 3.381908 AGCAGCAGTAGATACAGTACACC 59.618 47.826 0.00 0.00 0.00 4.16
2623 4228 6.148948 TGTAACTGCTGCAATACAAAATGAC 58.851 36.000 19.57 1.29 0.00 3.06
2651 4262 3.499918 CAGCTGTCCACTTCTTTGTTAGG 59.500 47.826 5.25 0.00 0.00 2.69
2652 4263 4.380531 TCAGCTGTCCACTTCTTTGTTAG 58.619 43.478 14.67 0.00 0.00 2.34
2656 4268 3.058432 CACATCAGCTGTCCACTTCTTTG 60.058 47.826 14.67 0.52 35.29 2.77
2668 4280 4.895224 AAATAGACATGCACATCAGCTG 57.105 40.909 7.63 7.63 34.99 4.24
2670 4282 6.016860 TGGAATAAATAGACATGCACATCAGC 60.017 38.462 0.00 0.00 0.00 4.26
2861 4499 4.319177 AGAAACGAGCTCTTGTTAGCATT 58.681 39.130 12.85 0.00 45.30 3.56
2927 4566 9.178758 CTTCTTACATAGTAAGAGGCCAAATTT 57.821 33.333 16.39 0.00 35.30 1.82
2930 4569 7.490657 TCTTCTTACATAGTAAGAGGCCAAA 57.509 36.000 18.60 5.71 35.30 3.28
2942 4581 7.402640 GTCCGCAGAATTTTCTTCTTACATAG 58.597 38.462 0.00 0.00 34.74 2.23
2961 5444 4.983671 AATAGATCATATAGCGTCCGCA 57.016 40.909 14.70 0.44 44.88 5.69
2964 5447 8.894731 TCTGAAGTAATAGATCATATAGCGTCC 58.105 37.037 0.00 0.00 0.00 4.79
2998 5482 8.927675 TGGTAGTAAACATAAAGTGGTCATTT 57.072 30.769 0.00 0.00 0.00 2.32
3000 5484 8.548877 AGATGGTAGTAAACATAAAGTGGTCAT 58.451 33.333 0.00 0.00 0.00 3.06
3010 5494 9.880157 GGTTTGAGTTAGATGGTAGTAAACATA 57.120 33.333 0.00 0.00 0.00 2.29
3011 5495 8.603304 AGGTTTGAGTTAGATGGTAGTAAACAT 58.397 33.333 0.00 0.00 0.00 2.71
3013 5497 7.333672 CCAGGTTTGAGTTAGATGGTAGTAAAC 59.666 40.741 0.00 0.00 0.00 2.01
3021 5512 4.651778 TGAACCAGGTTTGAGTTAGATGG 58.348 43.478 6.21 0.00 0.00 3.51
3099 5591 7.414540 CCAAAAATGTGGATAGCTTGTACTCTC 60.415 40.741 0.00 0.00 41.65 3.20
3212 5704 7.324178 AGATAACTGTCATTACCAAGTGTCTC 58.676 38.462 0.00 0.00 0.00 3.36
3289 5781 7.872138 TCACCCTGATTAAGTGGAATAAGATT 58.128 34.615 0.00 0.00 32.29 2.40
3290 5782 7.451731 TCACCCTGATTAAGTGGAATAAGAT 57.548 36.000 0.00 0.00 32.29 2.40
3294 5786 6.386927 ACTCATCACCCTGATTAAGTGGAATA 59.613 38.462 0.00 0.00 34.28 1.75
3388 5885 7.543520 GCTCCATCTGACCAATCTTTTTAAAAG 59.456 37.037 10.89 10.89 0.00 2.27
3485 5982 3.695830 TGCGAGGTTCCTGAAGTAAAT 57.304 42.857 0.00 0.00 0.00 1.40
3519 6016 5.196695 GGAAAGATAGCCTGGAGAAAACAT 58.803 41.667 0.00 0.00 0.00 2.71
3541 6038 6.358974 AATGGTTTAATTCAACAGAAGGGG 57.641 37.500 4.96 0.00 0.00 4.79
3600 6098 2.761767 GACCCCTTCTTCCTGAGTAGTC 59.238 54.545 0.00 0.00 0.00 2.59
3632 6130 2.237143 CTCCTAGTGCACATTTCAGGGA 59.763 50.000 21.04 13.05 0.00 4.20
3732 6230 2.715005 GCACTGTTTGCGAGCACA 59.285 55.556 0.00 0.00 42.79 4.57
3816 6314 7.878036 ACTGTAACACACTTAACAAAACACTT 58.122 30.769 0.00 0.00 0.00 3.16
3840 6338 3.315470 TGACGGCTGATGAGTATAGTGAC 59.685 47.826 0.00 0.00 0.00 3.67
3857 6355 5.926542 TCTTAGAGAAAGTGTCAATTGACGG 59.073 40.000 28.55 10.11 39.70 4.79
3869 6367 4.202305 ACAACTGCTGCTCTTAGAGAAAGT 60.202 41.667 14.14 0.79 36.51 2.66
3874 6373 5.261209 AGATACAACTGCTGCTCTTAGAG 57.739 43.478 4.63 4.63 0.00 2.43
3877 6376 7.708322 CAGATAAAGATACAACTGCTGCTCTTA 59.292 37.037 0.00 0.00 32.66 2.10
3905 6404 7.602265 TCTGTGATCACTTTATCAAAACGATCA 59.398 33.333 25.55 0.00 37.61 2.92
4021 6520 8.887717 CAGTTCATCCCAGTCTTATAAAGAAAG 58.112 37.037 0.00 0.00 39.67 2.62
4038 6537 5.181748 ACTGAGATTACAAGCAGTTCATCC 58.818 41.667 0.00 0.00 38.34 3.51
4055 6554 8.809468 ATTAATAGTGTGACTAGTGACTGAGA 57.191 34.615 13.79 0.00 33.66 3.27
4113 6628 1.133668 AGGCTAATGTGCTGGGATTCC 60.134 52.381 0.00 0.00 0.00 3.01
4133 6648 9.565090 CCATGTCCTTAATATTGAAGATCTGAA 57.435 33.333 0.00 0.00 0.00 3.02
4159 6674 4.988540 GCCAAATTTAGTCCTCAAACCAAC 59.011 41.667 0.00 0.00 0.00 3.77
4195 6710 1.911057 AGCCAACTTTCTACCTTGCC 58.089 50.000 0.00 0.00 0.00 4.52
4259 6774 3.674997 TGTCTGGCAATGTCCTAAACTC 58.325 45.455 0.00 0.00 0.00 3.01
4332 6847 7.864108 TTGATCACATAAAAGGTATCACCAG 57.136 36.000 0.00 0.00 41.95 4.00
4402 6917 5.590259 CCAACTAATTGTGCTTATGGTAGCT 59.410 40.000 0.00 0.00 36.23 3.32
4455 6970 0.333652 TCTGACCATACCGGGAGTCA 59.666 55.000 6.32 7.58 40.22 3.41
4461 6976 2.963101 TGACCTTATCTGACCATACCGG 59.037 50.000 0.00 0.00 42.50 5.28


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

AutoCloner maintained by Alex Coulton.