Multiple sequence alignment - TraesCS2A01G207100

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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 TraesCS2A01G207100 chr2A 100.000 2288 0 0 1 2288 186588321 186590608 0.000000e+00 4189
1 TraesCS2A01G207100 chr6D 92.350 1438 89 10 1 1421 450905943 450907376 0.000000e+00 2026
2 TraesCS2A01G207100 chr6D 91.295 1436 105 7 1 1421 469235201 469236631 0.000000e+00 1941
3 TraesCS2A01G207100 chr6D 90.460 1436 111 6 1 1421 305745348 305746772 0.000000e+00 1869
4 TraesCS2A01G207100 chr6D 87.569 1448 132 18 1 1421 446604648 446603222 0.000000e+00 1633
5 TraesCS2A01G207100 chr6D 86.437 1364 133 15 1 1318 56319518 56320875 0.000000e+00 1447
6 TraesCS2A01G207100 chr6D 90.860 919 69 5 511 1421 275680938 275680027 0.000000e+00 1218
7 TraesCS2A01G207100 chr6D 84.385 935 99 12 1 890 11696618 11695686 0.000000e+00 874
8 TraesCS2A01G207100 chr6D 93.818 550 27 2 1418 1966 20970616 20971159 0.000000e+00 821
9 TraesCS2A01G207100 chr6D 87.810 484 56 2 3 484 275689678 275689196 4.270000e-157 564
10 TraesCS2A01G207100 chr6D 90.179 112 1 3 1313 1421 56329396 56329500 1.100000e-28 137
11 TraesCS2A01G207100 chr7B 90.397 1437 114 10 3 1421 150842097 150843527 0.000000e+00 1868
12 TraesCS2A01G207100 chr7D 90.215 1441 119 11 1 1421 463975846 463974408 0.000000e+00 1860
13 TraesCS2A01G207100 chr7D 89.931 1440 122 5 1 1417 107722787 107721348 0.000000e+00 1834
14 TraesCS2A01G207100 chr7D 93.863 554 24 3 1417 1966 229201601 229201054 0.000000e+00 826
15 TraesCS2A01G207100 chr7D 93.636 550 27 5 1418 1966 388428069 388427527 0.000000e+00 815
16 TraesCS2A01G207100 chr7D 100.000 312 0 0 1977 2288 583142384 583142695 5.480000e-161 577
17 TraesCS2A01G207100 chr7D 99.679 312 1 0 1977 2288 215239594 215239905 2.550000e-159 571
18 TraesCS2A01G207100 chr7D 99.679 312 1 0 1977 2288 468894802 468895113 2.550000e-159 571
19 TraesCS2A01G207100 chr4B 90.222 1442 118 10 1 1421 551784696 551786135 0.000000e+00 1860
20 TraesCS2A01G207100 chr3D 89.799 1441 117 9 1 1413 593766367 593764929 0.000000e+00 1820
21 TraesCS2A01G207100 chr3D 88.765 1433 124 19 1 1413 113913368 113911953 0.000000e+00 1720
22 TraesCS2A01G207100 chr3D 91.667 516 38 5 1 513 575956072 575955559 0.000000e+00 710
23 TraesCS2A01G207100 chr3D 99.679 312 1 0 1977 2288 433266394 433266083 2.550000e-159 571
24 TraesCS2A01G207100 chr2D 89.703 1447 117 9 1 1421 591013960 591015400 0.000000e+00 1818
25 TraesCS2A01G207100 chr2D 91.557 1291 91 4 1 1274 487337180 487335891 0.000000e+00 1764
26 TraesCS2A01G207100 chr2D 89.736 1325 116 8 115 1421 469180817 469182139 0.000000e+00 1676
27 TraesCS2A01G207100 chr2D 93.816 566 28 2 1401 1966 526572877 526573435 0.000000e+00 845
28 TraesCS2A01G207100 chr2D 93.705 556 28 3 1412 1966 491110114 491109565 0.000000e+00 826
29 TraesCS2A01G207100 chr2D 93.490 553 26 5 1418 1966 220120213 220119667 0.000000e+00 813
30 TraesCS2A01G207100 chr2D 99.679 312 1 0 1977 2288 321544076 321544387 2.550000e-159 571
31 TraesCS2A01G207100 chr2D 99.679 312 1 0 1977 2288 517970215 517969904 2.550000e-159 571
32 TraesCS2A01G207100 chr2D 99.679 312 1 0 1977 2288 558843468 558843157 2.550000e-159 571
33 TraesCS2A01G207100 chr5D 89.749 1434 125 9 1 1417 492732810 492731382 0.000000e+00 1814
34 TraesCS2A01G207100 chr5D 88.190 1033 90 7 3 1017 494993674 494994692 0.000000e+00 1203
35 TraesCS2A01G207100 chr5D 93.818 550 26 3 1418 1966 225475898 225475356 0.000000e+00 821
36 TraesCS2A01G207100 chr5D 93.648 551 27 3 1417 1966 405646867 405647410 0.000000e+00 817
37 TraesCS2A01G207100 chr5D 99.679 312 1 0 1977 2288 284912294 284912605 2.550000e-159 571
38 TraesCS2A01G207100 chr1D 89.426 1447 123 11 1 1421 482488479 482487037 0.000000e+00 1797
39 TraesCS2A01G207100 chr1D 87.517 1450 124 15 1 1421 451193551 451192130 0.000000e+00 1622
40 TraesCS2A01G207100 chr1D 86.869 1447 140 14 1 1421 369900540 369901962 0.000000e+00 1574
41 TraesCS2A01G207100 chr1D 88.699 938 86 6 3 925 338633572 338634504 0.000000e+00 1127
42 TraesCS2A01G207100 chr1D 88.367 851 75 5 8 843 429020176 429021017 0.000000e+00 1002
43 TraesCS2A01G207100 chr1D 99.679 312 1 0 1977 2288 217331083 217331394 2.550000e-159 571
44 TraesCS2A01G207100 chr1D 99.679 312 1 0 1977 2288 260515903 260515592 2.550000e-159 571
45 TraesCS2A01G207100 chr4D 90.615 1268 97 10 172 1420 102106757 102105493 0.000000e+00 1663
46 TraesCS2A01G207100 chr4D 88.008 1426 146 16 8 1415 116524566 116523148 0.000000e+00 1663
47 TraesCS2A01G207100 chr4D 87.969 1438 129 18 8 1417 493971118 493969697 0.000000e+00 1657
48 TraesCS2A01G207100 chr4D 89.597 1240 105 9 1 1220 418403006 418401771 0.000000e+00 1554
49 TraesCS2A01G207100 chr4D 88.811 715 62 3 1 697 508924692 508925406 0.000000e+00 861
50 TraesCS2A01G207100 chr4D 94.182 550 25 3 1418 1966 346679055 346678512 0.000000e+00 832
51 TraesCS2A01G207100 chr1A 87.877 1427 149 14 8 1417 327011927 327010508 0.000000e+00 1655
52 TraesCS2A01G207100 chrUn 87.500 1424 147 12 1 1396 32170633 32169213 0.000000e+00 1615
53 TraesCS2A01G207100 chrUn 86.632 576 58 5 389 947 472761090 472760517 8.980000e-174 619
54 TraesCS2A01G207100 chrUn 83.378 373 56 5 1 367 300351305 300350933 7.830000e-90 340
55 TraesCS2A01G207100 chrUn 83.378 373 56 5 1 367 300356006 300355634 7.830000e-90 340
56 TraesCS2A01G207100 chrUn 83.378 373 56 5 1 367 470057228 470057600 7.830000e-90 340
57 TraesCS2A01G207100 chrUn 81.711 339 58 3 1 336 317182826 317182489 1.730000e-71 279
58 TraesCS2A01G207100 chrUn 81.627 332 57 4 1 330 267996505 267996834 2.900000e-69 272
59 TraesCS2A01G207100 chr1B 87.539 1292 141 16 136 1417 385028597 385029878 0.000000e+00 1476
60 TraesCS2A01G207100 chr6A 89.233 678 56 5 2 663 497727032 497727708 0.000000e+00 832


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 TraesCS2A01G207100 chr2A 186588321 186590608 2287 False 4189 4189 100.000 1 2288 1 chr2A.!!$F1 2287
1 TraesCS2A01G207100 chr6D 450905943 450907376 1433 False 2026 2026 92.350 1 1421 1 chr6D.!!$F5 1420
2 TraesCS2A01G207100 chr6D 469235201 469236631 1430 False 1941 1941 91.295 1 1421 1 chr6D.!!$F6 1420
3 TraesCS2A01G207100 chr6D 305745348 305746772 1424 False 1869 1869 90.460 1 1421 1 chr6D.!!$F4 1420
4 TraesCS2A01G207100 chr6D 446603222 446604648 1426 True 1633 1633 87.569 1 1421 1 chr6D.!!$R4 1420
5 TraesCS2A01G207100 chr6D 56319518 56320875 1357 False 1447 1447 86.437 1 1318 1 chr6D.!!$F2 1317
6 TraesCS2A01G207100 chr6D 275680027 275680938 911 True 1218 1218 90.860 511 1421 1 chr6D.!!$R2 910
7 TraesCS2A01G207100 chr6D 11695686 11696618 932 True 874 874 84.385 1 890 1 chr6D.!!$R1 889
8 TraesCS2A01G207100 chr6D 20970616 20971159 543 False 821 821 93.818 1418 1966 1 chr6D.!!$F1 548
9 TraesCS2A01G207100 chr7B 150842097 150843527 1430 False 1868 1868 90.397 3 1421 1 chr7B.!!$F1 1418
10 TraesCS2A01G207100 chr7D 463974408 463975846 1438 True 1860 1860 90.215 1 1421 1 chr7D.!!$R4 1420
11 TraesCS2A01G207100 chr7D 107721348 107722787 1439 True 1834 1834 89.931 1 1417 1 chr7D.!!$R1 1416
12 TraesCS2A01G207100 chr7D 229201054 229201601 547 True 826 826 93.863 1417 1966 1 chr7D.!!$R2 549
13 TraesCS2A01G207100 chr7D 388427527 388428069 542 True 815 815 93.636 1418 1966 1 chr7D.!!$R3 548
14 TraesCS2A01G207100 chr4B 551784696 551786135 1439 False 1860 1860 90.222 1 1421 1 chr4B.!!$F1 1420
15 TraesCS2A01G207100 chr3D 593764929 593766367 1438 True 1820 1820 89.799 1 1413 1 chr3D.!!$R4 1412
16 TraesCS2A01G207100 chr3D 113911953 113913368 1415 True 1720 1720 88.765 1 1413 1 chr3D.!!$R1 1412
17 TraesCS2A01G207100 chr3D 575955559 575956072 513 True 710 710 91.667 1 513 1 chr3D.!!$R3 512
18 TraesCS2A01G207100 chr2D 591013960 591015400 1440 False 1818 1818 89.703 1 1421 1 chr2D.!!$F4 1420
19 TraesCS2A01G207100 chr2D 487335891 487337180 1289 True 1764 1764 91.557 1 1274 1 chr2D.!!$R2 1273
20 TraesCS2A01G207100 chr2D 469180817 469182139 1322 False 1676 1676 89.736 115 1421 1 chr2D.!!$F2 1306
21 TraesCS2A01G207100 chr2D 526572877 526573435 558 False 845 845 93.816 1401 1966 1 chr2D.!!$F3 565
22 TraesCS2A01G207100 chr2D 491109565 491110114 549 True 826 826 93.705 1412 1966 1 chr2D.!!$R3 554
23 TraesCS2A01G207100 chr2D 220119667 220120213 546 True 813 813 93.490 1418 1966 1 chr2D.!!$R1 548
24 TraesCS2A01G207100 chr5D 492731382 492732810 1428 True 1814 1814 89.749 1 1417 1 chr5D.!!$R2 1416
25 TraesCS2A01G207100 chr5D 494993674 494994692 1018 False 1203 1203 88.190 3 1017 1 chr5D.!!$F3 1014
26 TraesCS2A01G207100 chr5D 225475356 225475898 542 True 821 821 93.818 1418 1966 1 chr5D.!!$R1 548
27 TraesCS2A01G207100 chr5D 405646867 405647410 543 False 817 817 93.648 1417 1966 1 chr5D.!!$F2 549
28 TraesCS2A01G207100 chr1D 482487037 482488479 1442 True 1797 1797 89.426 1 1421 1 chr1D.!!$R3 1420
29 TraesCS2A01G207100 chr1D 451192130 451193551 1421 True 1622 1622 87.517 1 1421 1 chr1D.!!$R2 1420
30 TraesCS2A01G207100 chr1D 369900540 369901962 1422 False 1574 1574 86.869 1 1421 1 chr1D.!!$F3 1420
31 TraesCS2A01G207100 chr1D 338633572 338634504 932 False 1127 1127 88.699 3 925 1 chr1D.!!$F2 922
32 TraesCS2A01G207100 chr1D 429020176 429021017 841 False 1002 1002 88.367 8 843 1 chr1D.!!$F4 835
33 TraesCS2A01G207100 chr4D 102105493 102106757 1264 True 1663 1663 90.615 172 1420 1 chr4D.!!$R1 1248
34 TraesCS2A01G207100 chr4D 116523148 116524566 1418 True 1663 1663 88.008 8 1415 1 chr4D.!!$R2 1407
35 TraesCS2A01G207100 chr4D 493969697 493971118 1421 True 1657 1657 87.969 8 1417 1 chr4D.!!$R5 1409
36 TraesCS2A01G207100 chr4D 418401771 418403006 1235 True 1554 1554 89.597 1 1220 1 chr4D.!!$R4 1219
37 TraesCS2A01G207100 chr4D 508924692 508925406 714 False 861 861 88.811 1 697 1 chr4D.!!$F1 696
38 TraesCS2A01G207100 chr4D 346678512 346679055 543 True 832 832 94.182 1418 1966 1 chr4D.!!$R3 548
39 TraesCS2A01G207100 chr1A 327010508 327011927 1419 True 1655 1655 87.877 8 1417 1 chr1A.!!$R1 1409
40 TraesCS2A01G207100 chrUn 32169213 32170633 1420 True 1615 1615 87.500 1 1396 1 chrUn.!!$R1 1395
41 TraesCS2A01G207100 chrUn 472760517 472761090 573 True 619 619 86.632 389 947 1 chrUn.!!$R5 558
42 TraesCS2A01G207100 chr1B 385028597 385029878 1281 False 1476 1476 87.539 136 1417 1 chr1B.!!$F1 1281
43 TraesCS2A01G207100 chr6A 497727032 497727708 676 False 832 832 89.233 2 663 1 chr6A.!!$F1 661

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
722 791 0.82999 TCTGTGTTGTGCCTGACTCA 59.17 50.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 2132 0.037605 CCTCGCTTCTACCACGGTTT 60.038 55.0 0.0 0.0 0.0 3.27 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
68 70 1.602323 GTCCATTGTTGTGCGGGGA 60.602 57.895 0.00 0.00 0.00 4.81
160 174 0.899717 ATTGGCATCTGCACCGGTTT 60.900 50.000 2.97 0.00 44.36 3.27
499 520 2.663852 GTCACCAACCGACCACCG 60.664 66.667 0.00 0.00 38.18 4.94
505 526 1.374252 CAACCGACCACCGAGGAAG 60.374 63.158 0.00 0.00 41.22 3.46
506 527 1.532316 AACCGACCACCGAGGAAGA 60.532 57.895 0.00 0.00 41.22 2.87
508 529 1.215647 CCGACCACCGAGGAAGAAG 59.784 63.158 0.00 0.00 41.22 2.85
582 620 5.838955 TGGAGAGGAGGAAAGTTGATAGTA 58.161 41.667 0.00 0.00 0.00 1.82
637 678 3.244112 GCAGGGTGAGTAAATATAGGCGT 60.244 47.826 0.00 0.00 0.00 5.68
722 791 0.829990 TCTGTGTTGTGCCTGACTCA 59.170 50.000 0.00 0.00 0.00 3.41
896 969 1.003349 GATGATGAGGGCATGGAGGAG 59.997 57.143 0.00 0.00 34.11 3.69
1032 1115 2.108157 ACCAAGCACTTCGTCGCA 59.892 55.556 0.00 0.00 0.00 5.10
1150 1233 2.036733 GCCACCTACATAGCCGTTCATA 59.963 50.000 0.00 0.00 0.00 2.15
1157 1240 6.211584 ACCTACATAGCCGTTCATAAGATCAT 59.788 38.462 0.00 0.00 0.00 2.45
1240 1323 1.271325 ACAACGATGGCATTGAGGTCA 60.271 47.619 21.46 0.00 0.00 4.02
1263 1346 3.703556 TCAACAAGTTTGGGAAGCATGAA 59.296 39.130 0.00 0.00 0.00 2.57
1632 1738 0.322546 GACATTCTTTGGGCCGTCCT 60.323 55.000 0.00 0.00 36.20 3.85
1694 1800 3.059099 GGGTGTTCCCGGTTACGA 58.941 61.111 0.00 0.00 44.74 3.43
1696 1802 0.823460 GGGTGTTCCCGGTTACGATA 59.177 55.000 0.00 0.00 44.74 2.92
1774 1881 4.555709 TGGGTGCGAGGCGTTGTT 62.556 61.111 0.00 0.00 0.00 2.83
1838 1948 1.709147 GATTGCACTGCAGGCTACGG 61.709 60.000 19.93 1.14 40.61 4.02
1840 1950 4.767255 GCACTGCAGGCTACGGCT 62.767 66.667 19.93 0.00 38.69 5.52
1841 1951 2.892640 CACTGCAGGCTACGGCTA 59.107 61.111 19.93 0.00 38.69 3.93
1842 1952 1.519455 CACTGCAGGCTACGGCTAC 60.519 63.158 19.93 0.00 38.69 3.58
1849 1959 1.008079 GGCTACGGCTACGCGTTAT 60.008 57.895 20.78 0.86 46.04 1.89
1881 1995 5.371526 AGTGATTGATCGATGGCTGTTAAT 58.628 37.500 0.54 0.00 0.00 1.40
1993 2108 3.991999 ACGCAGCTGCATGACATT 58.008 50.000 36.03 9.62 42.21 2.71
1994 2109 1.798735 ACGCAGCTGCATGACATTC 59.201 52.632 36.03 5.81 42.21 2.67
1995 2110 0.675837 ACGCAGCTGCATGACATTCT 60.676 50.000 36.03 3.03 42.21 2.40
1996 2111 0.450583 CGCAGCTGCATGACATTCTT 59.549 50.000 36.03 0.00 42.21 2.52
1997 2112 1.135489 CGCAGCTGCATGACATTCTTT 60.135 47.619 36.03 0.00 42.21 2.52
1998 2113 2.259618 GCAGCTGCATGACATTCTTTG 58.740 47.619 33.36 0.00 41.59 2.77
1999 2114 2.876091 CAGCTGCATGACATTCTTTGG 58.124 47.619 0.00 0.00 0.00 3.28
2000 2115 1.822990 AGCTGCATGACATTCTTTGGG 59.177 47.619 1.02 0.00 0.00 4.12
2001 2116 1.738030 GCTGCATGACATTCTTTGGGC 60.738 52.381 0.00 0.00 0.00 5.36
2002 2117 0.896923 TGCATGACATTCTTTGGGCC 59.103 50.000 0.00 0.00 0.00 5.80
2003 2118 0.179129 GCATGACATTCTTTGGGCCG 60.179 55.000 0.00 0.00 0.00 6.13
2004 2119 1.176527 CATGACATTCTTTGGGCCGT 58.823 50.000 0.00 0.00 0.00 5.68
2005 2120 1.133025 CATGACATTCTTTGGGCCGTC 59.867 52.381 0.00 0.00 0.00 4.79
2006 2121 0.608035 TGACATTCTTTGGGCCGTCC 60.608 55.000 0.00 0.00 0.00 4.79
2007 2122 0.608035 GACATTCTTTGGGCCGTCCA 60.608 55.000 0.00 0.00 45.43 4.02
2008 2123 0.039618 ACATTCTTTGGGCCGTCCAT 59.960 50.000 0.00 0.00 46.52 3.41
2009 2124 0.457035 CATTCTTTGGGCCGTCCATG 59.543 55.000 0.00 0.00 46.52 3.66
2010 2125 0.331278 ATTCTTTGGGCCGTCCATGA 59.669 50.000 0.00 0.00 46.52 3.07
2011 2126 0.331278 TTCTTTGGGCCGTCCATGAT 59.669 50.000 0.00 0.00 46.52 2.45
2012 2127 0.394216 TCTTTGGGCCGTCCATGATG 60.394 55.000 0.00 0.00 46.52 3.07
2013 2128 1.379710 TTTGGGCCGTCCATGATGG 60.380 57.895 4.74 4.74 46.52 3.51
2014 2129 1.857638 TTTGGGCCGTCCATGATGGA 61.858 55.000 10.75 10.75 45.98 3.41
2034 2149 2.243602 AAAAACCGTGGTAGAAGCGA 57.756 45.000 0.00 0.00 0.00 4.93
2035 2150 1.792006 AAAACCGTGGTAGAAGCGAG 58.208 50.000 0.00 0.00 0.00 5.03
2036 2151 0.037605 AAACCGTGGTAGAAGCGAGG 60.038 55.000 0.00 0.00 0.00 4.63
2037 2152 1.885163 AACCGTGGTAGAAGCGAGGG 61.885 60.000 0.00 0.00 0.00 4.30
2038 2153 2.202756 CGTGGTAGAAGCGAGGGC 60.203 66.667 0.00 0.00 40.37 5.19
2039 2154 2.202756 GTGGTAGAAGCGAGGGCG 60.203 66.667 0.00 0.00 46.35 6.13
2040 2155 2.361992 TGGTAGAAGCGAGGGCGA 60.362 61.111 0.00 0.00 46.35 5.54
2041 2156 2.413765 GGTAGAAGCGAGGGCGAG 59.586 66.667 0.00 0.00 46.35 5.03
2042 2157 2.413765 GTAGAAGCGAGGGCGAGG 59.586 66.667 0.00 0.00 46.35 4.63
2043 2158 2.119655 GTAGAAGCGAGGGCGAGGA 61.120 63.158 0.00 0.00 46.35 3.71
2044 2159 1.379443 TAGAAGCGAGGGCGAGGAA 60.379 57.895 0.00 0.00 46.35 3.36
2045 2160 0.968901 TAGAAGCGAGGGCGAGGAAA 60.969 55.000 0.00 0.00 46.35 3.13
2046 2161 1.375523 GAAGCGAGGGCGAGGAAAA 60.376 57.895 0.00 0.00 46.35 2.29
2047 2162 0.744771 GAAGCGAGGGCGAGGAAAAT 60.745 55.000 0.00 0.00 46.35 1.82
2048 2163 0.322546 AAGCGAGGGCGAGGAAAATT 60.323 50.000 0.00 0.00 46.35 1.82
2049 2164 0.322546 AGCGAGGGCGAGGAAAATTT 60.323 50.000 0.00 0.00 46.35 1.82
2050 2165 0.098905 GCGAGGGCGAGGAAAATTTC 59.901 55.000 0.00 0.00 40.82 2.17
2051 2166 0.373716 CGAGGGCGAGGAAAATTTCG 59.626 55.000 0.00 0.00 40.82 3.46
2052 2167 0.733150 GAGGGCGAGGAAAATTTCGG 59.267 55.000 0.00 0.00 37.30 4.30
2053 2168 0.679960 AGGGCGAGGAAAATTTCGGG 60.680 55.000 0.00 0.00 37.30 5.14
2054 2169 1.663379 GGGCGAGGAAAATTTCGGGG 61.663 60.000 0.00 0.00 37.30 5.73
2055 2170 0.678684 GGCGAGGAAAATTTCGGGGA 60.679 55.000 0.00 0.00 37.30 4.81
2056 2171 0.733150 GCGAGGAAAATTTCGGGGAG 59.267 55.000 0.00 0.00 37.30 4.30
2057 2172 1.949079 GCGAGGAAAATTTCGGGGAGT 60.949 52.381 0.00 0.00 37.30 3.85
2058 2173 2.433436 CGAGGAAAATTTCGGGGAGTT 58.567 47.619 0.00 0.00 33.39 3.01
2059 2174 2.418976 CGAGGAAAATTTCGGGGAGTTC 59.581 50.000 0.00 0.00 33.39 3.01
2060 2175 2.753452 GAGGAAAATTTCGGGGAGTTCC 59.247 50.000 0.00 0.00 35.74 3.62
2078 2193 2.575461 CGGTTACGGTGGGAGGTC 59.425 66.667 0.00 0.00 36.18 3.85
2079 2194 2.575461 GGTTACGGTGGGAGGTCG 59.425 66.667 0.00 0.00 0.00 4.79
2080 2195 2.575461 GTTACGGTGGGAGGTCGG 59.425 66.667 0.00 0.00 0.00 4.79
2081 2196 2.681064 TTACGGTGGGAGGTCGGG 60.681 66.667 0.00 0.00 0.00 5.14
2082 2197 4.764771 TACGGTGGGAGGTCGGGG 62.765 72.222 0.00 0.00 0.00 5.73
2105 2220 2.318024 GCGATGCGCGTTTCTCTC 59.682 61.111 8.43 0.00 44.55 3.20
2106 2221 2.610308 CGATGCGCGTTTCTCTCG 59.390 61.111 8.43 0.00 34.64 4.04
2107 2222 2.152699 CGATGCGCGTTTCTCTCGT 61.153 57.895 8.43 0.00 34.64 4.18
2108 2223 0.860203 CGATGCGCGTTTCTCTCGTA 60.860 55.000 8.43 0.00 34.64 3.43
2109 2224 0.566593 GATGCGCGTTTCTCTCGTAC 59.433 55.000 8.43 0.00 0.00 3.67
2110 2225 0.109458 ATGCGCGTTTCTCTCGTACA 60.109 50.000 8.43 0.00 0.00 2.90
2111 2226 1.000233 TGCGCGTTTCTCTCGTACAC 61.000 55.000 8.43 0.00 0.00 2.90
2112 2227 1.971336 CGCGTTTCTCTCGTACACG 59.029 57.895 0.00 0.00 41.45 4.49
2113 2228 0.723790 CGCGTTTCTCTCGTACACGT 60.724 55.000 0.00 0.00 40.80 4.49
2114 2229 1.462378 CGCGTTTCTCTCGTACACGTA 60.462 52.381 0.00 0.00 40.80 3.57
2115 2230 1.901236 GCGTTTCTCTCGTACACGTAC 59.099 52.381 1.19 0.00 40.80 3.67
2136 2251 4.354212 CGTGTGTGCGAGGCGTTG 62.354 66.667 0.00 0.00 0.00 4.10
2137 2252 4.012895 GTGTGTGCGAGGCGTTGG 62.013 66.667 0.00 0.00 0.00 3.77
2147 2262 2.362242 AGGCGTTGGCTCTAACTGA 58.638 52.632 0.00 0.00 39.81 3.41
2148 2263 0.685097 AGGCGTTGGCTCTAACTGAA 59.315 50.000 0.00 0.00 39.81 3.02
2149 2264 0.796927 GGCGTTGGCTCTAACTGAAC 59.203 55.000 0.00 0.00 39.81 3.18
2150 2265 0.796927 GCGTTGGCTCTAACTGAACC 59.203 55.000 0.00 0.00 35.83 3.62
2151 2266 1.439679 CGTTGGCTCTAACTGAACCC 58.560 55.000 0.00 0.00 30.01 4.11
2152 2267 1.439679 GTTGGCTCTAACTGAACCCG 58.560 55.000 0.00 0.00 30.01 5.28
2153 2268 1.001633 GTTGGCTCTAACTGAACCCGA 59.998 52.381 0.00 0.00 30.01 5.14
2154 2269 0.895530 TGGCTCTAACTGAACCCGAG 59.104 55.000 0.00 0.00 30.01 4.63
2155 2270 0.460459 GGCTCTAACTGAACCCGAGC 60.460 60.000 0.00 0.00 44.67 5.03
2156 2271 0.802607 GCTCTAACTGAACCCGAGCG 60.803 60.000 0.00 0.00 37.89 5.03
2157 2272 0.809385 CTCTAACTGAACCCGAGCGA 59.191 55.000 0.00 0.00 0.00 4.93
2158 2273 0.809385 TCTAACTGAACCCGAGCGAG 59.191 55.000 0.00 0.00 0.00 5.03
2159 2274 0.179134 CTAACTGAACCCGAGCGAGG 60.179 60.000 0.00 0.00 0.00 4.63
2160 2275 2.221906 TAACTGAACCCGAGCGAGGC 62.222 60.000 0.00 0.00 0.00 4.70
2163 2278 4.736896 GAACCCGAGCGAGGCGTT 62.737 66.667 0.00 6.93 0.00 4.84
2175 2290 3.890674 GGCGTTGGGCTCTAACTG 58.109 61.111 0.00 0.00 42.94 3.16
2176 2291 1.295423 GGCGTTGGGCTCTAACTGA 59.705 57.895 0.00 0.00 42.94 3.41
2177 2292 0.321298 GGCGTTGGGCTCTAACTGAA 60.321 55.000 0.00 0.00 42.94 3.02
2178 2293 0.796927 GCGTTGGGCTCTAACTGAAC 59.203 55.000 0.00 0.00 39.11 3.18
2179 2294 1.439679 CGTTGGGCTCTAACTGAACC 58.560 55.000 0.00 0.00 0.00 3.62
2181 2296 4.934989 GGGCTCTAACTGAACCCG 57.065 61.111 0.00 0.00 40.85 5.28
2182 2297 2.283824 GGGCTCTAACTGAACCCGA 58.716 57.895 0.00 0.00 40.85 5.14
2183 2298 0.175989 GGGCTCTAACTGAACCCGAG 59.824 60.000 0.00 0.00 40.85 4.63
2184 2299 0.460459 GGCTCTAACTGAACCCGAGC 60.460 60.000 0.00 0.00 44.67 5.03
2185 2300 0.802607 GCTCTAACTGAACCCGAGCG 60.803 60.000 0.00 0.00 37.89 5.03
2186 2301 0.809385 CTCTAACTGAACCCGAGCGA 59.191 55.000 0.00 0.00 0.00 4.93
2187 2302 1.405821 CTCTAACTGAACCCGAGCGAT 59.594 52.381 0.00 0.00 0.00 4.58
2188 2303 1.822990 TCTAACTGAACCCGAGCGATT 59.177 47.619 0.00 0.00 0.00 3.34
2189 2304 1.927174 CTAACTGAACCCGAGCGATTG 59.073 52.381 0.00 0.00 0.00 2.67
2190 2305 1.298859 AACTGAACCCGAGCGATTGC 61.299 55.000 0.00 0.00 43.24 3.56
2191 2306 1.741401 CTGAACCCGAGCGATTGCA 60.741 57.895 7.90 0.00 46.23 4.08
2192 2307 1.970917 CTGAACCCGAGCGATTGCAC 61.971 60.000 7.90 0.00 46.23 4.57
2193 2308 1.741770 GAACCCGAGCGATTGCACT 60.742 57.895 7.90 0.00 46.23 4.40
2194 2309 1.970917 GAACCCGAGCGATTGCACTG 61.971 60.000 7.90 0.00 46.23 3.66
2195 2310 3.869272 CCCGAGCGATTGCACTGC 61.869 66.667 7.90 0.00 46.23 4.40
2196 2311 3.120385 CCGAGCGATTGCACTGCA 61.120 61.111 7.90 0.00 46.23 4.41
2197 2312 2.398429 CGAGCGATTGCACTGCAG 59.602 61.111 13.48 13.48 46.23 4.41
2198 2313 2.789917 GAGCGATTGCACTGCAGG 59.210 61.111 19.93 8.27 46.23 4.85
2199 2314 3.392595 GAGCGATTGCACTGCAGGC 62.393 63.158 19.93 18.37 46.23 4.85
2200 2315 3.437795 GCGATTGCACTGCAGGCT 61.438 61.111 19.93 3.72 40.61 4.58
2201 2316 2.108514 GCGATTGCACTGCAGGCTA 61.109 57.895 19.93 15.26 40.61 3.93
2202 2317 1.717937 CGATTGCACTGCAGGCTAC 59.282 57.895 19.93 12.02 40.61 3.58
2203 2318 1.717937 GATTGCACTGCAGGCTACG 59.282 57.895 19.93 1.81 40.61 3.51
2204 2319 2.315038 GATTGCACTGCAGGCTACGC 62.315 60.000 19.93 12.43 40.61 4.42
2207 2322 2.738521 CACTGCAGGCTACGCGTT 60.739 61.111 20.78 0.80 0.00 4.84
2208 2323 1.445410 CACTGCAGGCTACGCGTTA 60.445 57.895 20.78 2.21 0.00 3.18
2209 2324 1.445582 ACTGCAGGCTACGCGTTAC 60.446 57.895 20.78 10.25 0.00 2.50
2210 2325 1.153823 CTGCAGGCTACGCGTTACT 60.154 57.895 20.78 10.91 0.00 2.24
2211 2326 1.413767 CTGCAGGCTACGCGTTACTG 61.414 60.000 20.78 23.07 0.00 2.74
2212 2327 1.153901 GCAGGCTACGCGTTACTGA 60.154 57.895 29.35 9.66 0.00 3.41
2213 2328 0.734942 GCAGGCTACGCGTTACTGAA 60.735 55.000 29.35 8.99 0.00 3.02
2214 2329 0.989890 CAGGCTACGCGTTACTGAAC 59.010 55.000 20.78 1.03 0.00 3.18
2215 2330 0.108945 AGGCTACGCGTTACTGAACC 60.109 55.000 20.78 3.14 31.28 3.62
2216 2331 1.080435 GGCTACGCGTTACTGAACCC 61.080 60.000 20.78 2.71 31.28 4.11
2217 2332 1.408474 GCTACGCGTTACTGAACCCG 61.408 60.000 20.78 0.00 41.56 5.28
2218 2333 0.168788 CTACGCGTTACTGAACCCGA 59.831 55.000 20.78 0.00 38.80 5.14
2219 2334 0.168788 TACGCGTTACTGAACCCGAG 59.831 55.000 20.78 0.00 38.80 4.63
2220 2335 2.442188 CGCGTTACTGAACCCGAGC 61.442 63.158 0.00 0.00 38.80 5.03
2221 2336 2.442188 GCGTTACTGAACCCGAGCG 61.442 63.158 0.00 0.00 31.28 5.03
2222 2337 1.210931 CGTTACTGAACCCGAGCGA 59.789 57.895 0.00 0.00 31.28 4.93
2223 2338 0.179145 CGTTACTGAACCCGAGCGAT 60.179 55.000 0.00 0.00 31.28 4.58
2224 2339 1.557651 GTTACTGAACCCGAGCGATC 58.442 55.000 0.00 0.00 0.00 3.69
2225 2340 0.099968 TTACTGAACCCGAGCGATCG 59.900 55.000 17.57 17.57 0.00 3.69
2226 2341 0.745486 TACTGAACCCGAGCGATCGA 60.745 55.000 26.68 2.41 34.64 3.59
2227 2342 1.360551 CTGAACCCGAGCGATCGAT 59.639 57.895 26.68 14.21 34.64 3.59
2228 2343 0.661780 CTGAACCCGAGCGATCGATC 60.662 60.000 26.68 22.90 34.64 3.69
2242 2357 3.643763 GATCGATCGATGGCTGTTAACT 58.356 45.455 33.86 7.27 34.60 2.24
2243 2358 2.809446 TCGATCGATGGCTGTTAACTG 58.191 47.619 15.15 7.67 0.00 3.16
2244 2359 2.425668 TCGATCGATGGCTGTTAACTGA 59.574 45.455 15.15 0.00 0.00 3.41
2245 2360 3.119280 TCGATCGATGGCTGTTAACTGAA 60.119 43.478 15.15 4.06 0.00 3.02
2246 2361 3.000322 CGATCGATGGCTGTTAACTGAAC 60.000 47.826 10.26 8.31 38.65 3.18
2247 2362 2.695359 TCGATGGCTGTTAACTGAACC 58.305 47.619 15.89 8.97 37.22 3.62
2248 2363 1.737793 CGATGGCTGTTAACTGAACCC 59.262 52.381 15.89 8.33 37.22 4.11
2249 2364 1.737793 GATGGCTGTTAACTGAACCCG 59.262 52.381 15.89 0.00 37.22 5.28
2250 2365 0.759959 TGGCTGTTAACTGAACCCGA 59.240 50.000 15.89 0.00 37.22 5.14
2251 2366 1.349688 TGGCTGTTAACTGAACCCGAT 59.650 47.619 15.89 0.00 37.22 4.18
2252 2367 2.007608 GGCTGTTAACTGAACCCGATC 58.992 52.381 15.89 0.00 37.22 3.69
2253 2368 1.659098 GCTGTTAACTGAACCCGATCG 59.341 52.381 15.89 8.51 37.22 3.69
2254 2369 2.673043 GCTGTTAACTGAACCCGATCGA 60.673 50.000 18.66 0.00 37.22 3.59
2255 2370 3.179830 CTGTTAACTGAACCCGATCGAG 58.820 50.000 18.66 5.68 37.22 4.04
2256 2371 1.925185 GTTAACTGAACCCGATCGAGC 59.075 52.381 18.66 3.11 31.20 5.03
2257 2372 0.099968 TAACTGAACCCGATCGAGCG 59.900 55.000 17.57 17.57 0.00 5.03
2258 2373 1.592400 AACTGAACCCGATCGAGCGA 61.592 55.000 26.68 2.41 0.00 4.93
2259 2374 1.360551 CTGAACCCGATCGAGCGAT 59.639 57.895 26.68 9.53 37.59 4.58
2260 2375 0.249073 CTGAACCCGATCGAGCGATT 60.249 55.000 26.68 18.12 34.60 3.34
2261 2376 0.248907 TGAACCCGATCGAGCGATTC 60.249 55.000 26.68 25.06 34.60 2.52
2262 2377 0.940047 GAACCCGATCGAGCGATTCC 60.940 60.000 26.68 7.18 34.60 3.01
2263 2378 1.392710 AACCCGATCGAGCGATTCCT 61.393 55.000 26.68 0.68 34.60 3.36
2264 2379 1.364171 CCCGATCGAGCGATTCCTT 59.636 57.895 26.68 0.00 34.60 3.36
2265 2380 0.664767 CCCGATCGAGCGATTCCTTC 60.665 60.000 26.68 0.00 34.60 3.46
2274 2389 3.650409 CGATTCCTTCGCTACTGCT 57.350 52.632 0.00 0.00 41.69 4.24
2275 2390 1.203928 CGATTCCTTCGCTACTGCTG 58.796 55.000 0.00 0.00 41.69 4.41
2276 2391 0.933796 GATTCCTTCGCTACTGCTGC 59.066 55.000 0.00 0.00 36.97 5.25
2277 2392 0.539051 ATTCCTTCGCTACTGCTGCT 59.461 50.000 0.00 0.00 36.97 4.24
2278 2393 1.182667 TTCCTTCGCTACTGCTGCTA 58.817 50.000 0.00 0.00 36.97 3.49
2279 2394 1.182667 TCCTTCGCTACTGCTGCTAA 58.817 50.000 0.00 0.00 36.97 3.09
2280 2395 1.135083 TCCTTCGCTACTGCTGCTAAC 60.135 52.381 0.00 0.00 36.97 2.34
2281 2396 1.134965 CCTTCGCTACTGCTGCTAACT 60.135 52.381 0.00 0.00 36.97 2.24
2282 2397 1.923204 CTTCGCTACTGCTGCTAACTG 59.077 52.381 0.00 0.00 36.97 3.16
2283 2398 1.173913 TCGCTACTGCTGCTAACTGA 58.826 50.000 0.00 0.00 36.97 3.41
2284 2399 1.544246 TCGCTACTGCTGCTAACTGAA 59.456 47.619 0.00 0.00 36.97 3.02
2285 2400 1.923204 CGCTACTGCTGCTAACTGAAG 59.077 52.381 0.00 0.00 36.97 3.02
2287 2402 2.275318 CTACTGCTGCTAACTGAAGCC 58.725 52.381 0.00 0.00 46.96 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 25 3.240134 GAAGGCCAGCCACTCGACA 62.240 63.158 12.03 0.00 38.92 4.35
97 108 1.381928 TACGTGGCAGATCGACCTCC 61.382 60.000 0.00 0.00 0.00 4.30
499 520 1.304617 CCTTGGGGCCTTCTTCCTC 59.695 63.158 0.84 0.00 0.00 3.71
505 526 2.360585 CCTTCCCTTGGGGCCTTC 59.639 66.667 0.84 0.00 43.94 3.46
506 527 3.276081 CCCTTCCCTTGGGGCCTT 61.276 66.667 0.84 0.00 43.94 4.35
582 620 3.142579 ACCCATCCCATCTCTTCTCTT 57.857 47.619 0.00 0.00 0.00 2.85
637 678 2.158310 TCACTCTTCCTCCTCTCCAACA 60.158 50.000 0.00 0.00 0.00 3.33
722 791 2.352651 CTCGATCCGCACACAATTCATT 59.647 45.455 0.00 0.00 0.00 2.57
798 868 0.185901 GGCATTGGATGAAGGGGCTA 59.814 55.000 0.00 0.00 0.00 3.93
928 1010 3.517612 GGCCATCCTCCTAATGGTAGTA 58.482 50.000 0.00 0.00 44.65 1.82
1032 1115 1.006102 CTTGAACTCCGTCGGCACT 60.006 57.895 6.34 0.00 0.00 4.40
1150 1233 3.326006 ACCATGTAGCCGATCATGATCTT 59.674 43.478 28.48 17.93 42.52 2.40
1157 1240 0.464036 GGTCACCATGTAGCCGATCA 59.536 55.000 0.00 0.00 0.00 2.92
1240 1323 3.896888 TCATGCTTCCCAAACTTGTTGAT 59.103 39.130 0.00 0.00 0.00 2.57
1250 1333 1.076024 AGGCTTCTTCATGCTTCCCAA 59.924 47.619 0.00 0.00 0.00 4.12
1263 1346 1.298014 CTTGGCGGAGAAGGCTTCT 59.702 57.895 28.94 28.94 44.21 2.85
1440 1545 1.757118 TCGTTTGGCCCAAAATGTCAA 59.243 42.857 11.20 0.00 35.03 3.18
1694 1800 4.468769 TCGGCCCCGACCACCTAT 62.469 66.667 5.12 0.00 44.01 2.57
1714 1821 1.713937 CGCGCAAACCTCCATGCATA 61.714 55.000 8.75 0.00 42.68 3.14
1773 1880 1.201647 CGCTCGGGTTCAGTTAGAGAA 59.798 52.381 0.00 0.00 0.00 2.87
1774 1881 0.809385 CGCTCGGGTTCAGTTAGAGA 59.191 55.000 0.00 0.00 0.00 3.10
1843 1953 1.717194 TCACTCGGGTTCAATAACGC 58.283 50.000 0.00 0.00 43.25 4.84
1849 1959 2.232696 TCGATCAATCACTCGGGTTCAA 59.767 45.455 0.00 0.00 35.64 2.69
1881 1995 0.174845 AATCGCTCGATCGGGTTCAA 59.825 50.000 17.85 0.00 33.08 2.69
1976 2091 0.675837 AGAATGTCATGCAGCTGCGT 60.676 50.000 32.11 30.01 45.83 5.24
1977 2092 0.450583 AAGAATGTCATGCAGCTGCG 59.549 50.000 32.11 19.83 45.83 5.18
1978 2093 2.259618 CAAAGAATGTCATGCAGCTGC 58.740 47.619 31.89 31.89 42.50 5.25
1979 2094 2.416836 CCCAAAGAATGTCATGCAGCTG 60.417 50.000 10.11 10.11 0.00 4.24
1980 2095 1.822990 CCCAAAGAATGTCATGCAGCT 59.177 47.619 0.00 0.00 0.00 4.24
1981 2096 1.738030 GCCCAAAGAATGTCATGCAGC 60.738 52.381 0.00 0.00 0.00 5.25
1982 2097 1.134907 GGCCCAAAGAATGTCATGCAG 60.135 52.381 0.00 0.00 0.00 4.41
1983 2098 0.896923 GGCCCAAAGAATGTCATGCA 59.103 50.000 0.00 0.00 0.00 3.96
1984 2099 0.179129 CGGCCCAAAGAATGTCATGC 60.179 55.000 0.00 0.00 0.00 4.06
1985 2100 1.133025 GACGGCCCAAAGAATGTCATG 59.867 52.381 0.00 0.00 0.00 3.07
1986 2101 1.463674 GACGGCCCAAAGAATGTCAT 58.536 50.000 0.00 0.00 0.00 3.06
1987 2102 0.608035 GGACGGCCCAAAGAATGTCA 60.608 55.000 0.00 0.00 34.14 3.58
1988 2103 0.608035 TGGACGGCCCAAAGAATGTC 60.608 55.000 3.83 0.00 43.29 3.06
1989 2104 1.458486 TGGACGGCCCAAAGAATGT 59.542 52.632 3.83 0.00 43.29 2.71
1990 2105 4.413928 TGGACGGCCCAAAGAATG 57.586 55.556 3.83 0.00 43.29 2.67
2015 2130 2.140717 CTCGCTTCTACCACGGTTTTT 58.859 47.619 0.00 0.00 0.00 1.94
2016 2131 1.607251 CCTCGCTTCTACCACGGTTTT 60.607 52.381 0.00 0.00 0.00 2.43
2017 2132 0.037605 CCTCGCTTCTACCACGGTTT 60.038 55.000 0.00 0.00 0.00 3.27
2018 2133 1.590147 CCTCGCTTCTACCACGGTT 59.410 57.895 0.00 0.00 0.00 4.44
2019 2134 2.348888 CCCTCGCTTCTACCACGGT 61.349 63.158 0.00 0.00 0.00 4.83
2020 2135 2.494918 CCCTCGCTTCTACCACGG 59.505 66.667 0.00 0.00 0.00 4.94
2021 2136 2.202756 GCCCTCGCTTCTACCACG 60.203 66.667 0.00 0.00 0.00 4.94
2022 2137 2.202756 CGCCCTCGCTTCTACCAC 60.203 66.667 0.00 0.00 0.00 4.16
2023 2138 2.361992 TCGCCCTCGCTTCTACCA 60.362 61.111 0.00 0.00 35.26 3.25
2024 2139 2.413765 CTCGCCCTCGCTTCTACC 59.586 66.667 0.00 0.00 35.26 3.18
2025 2140 1.664321 TTCCTCGCCCTCGCTTCTAC 61.664 60.000 0.00 0.00 35.26 2.59
2026 2141 0.968901 TTTCCTCGCCCTCGCTTCTA 60.969 55.000 0.00 0.00 35.26 2.10
2027 2142 1.827399 TTTTCCTCGCCCTCGCTTCT 61.827 55.000 0.00 0.00 35.26 2.85
2028 2143 0.744771 ATTTTCCTCGCCCTCGCTTC 60.745 55.000 0.00 0.00 35.26 3.86
2029 2144 0.322546 AATTTTCCTCGCCCTCGCTT 60.323 50.000 0.00 0.00 35.26 4.68
2030 2145 0.322546 AAATTTTCCTCGCCCTCGCT 60.323 50.000 0.00 0.00 35.26 4.93
2031 2146 0.098905 GAAATTTTCCTCGCCCTCGC 59.901 55.000 0.00 0.00 35.26 5.03
2032 2147 0.373716 CGAAATTTTCCTCGCCCTCG 59.626 55.000 3.61 0.00 0.00 4.63
2033 2148 0.733150 CCGAAATTTTCCTCGCCCTC 59.267 55.000 3.61 0.00 33.70 4.30
2034 2149 0.679960 CCCGAAATTTTCCTCGCCCT 60.680 55.000 3.61 0.00 33.70 5.19
2035 2150 1.663379 CCCCGAAATTTTCCTCGCCC 61.663 60.000 3.61 0.00 33.70 6.13
2036 2151 0.678684 TCCCCGAAATTTTCCTCGCC 60.679 55.000 3.61 0.00 33.70 5.54
2037 2152 0.733150 CTCCCCGAAATTTTCCTCGC 59.267 55.000 3.61 0.00 33.70 5.03
2038 2153 2.109425 ACTCCCCGAAATTTTCCTCG 57.891 50.000 3.61 0.00 34.83 4.63
2039 2154 2.753452 GGAACTCCCCGAAATTTTCCTC 59.247 50.000 3.61 0.00 31.54 3.71
2040 2155 2.803956 GGAACTCCCCGAAATTTTCCT 58.196 47.619 3.61 0.00 31.54 3.36
2061 2176 2.575461 GACCTCCCACCGTAACCG 59.425 66.667 0.00 0.00 0.00 4.44
2062 2177 2.575461 CGACCTCCCACCGTAACC 59.425 66.667 0.00 0.00 0.00 2.85
2063 2178 2.575461 CCGACCTCCCACCGTAAC 59.425 66.667 0.00 0.00 0.00 2.50
2064 2179 2.681064 CCCGACCTCCCACCGTAA 60.681 66.667 0.00 0.00 0.00 3.18
2065 2180 4.764771 CCCCGACCTCCCACCGTA 62.765 72.222 0.00 0.00 0.00 4.02
2089 2204 0.860203 TACGAGAGAAACGCGCATCG 60.860 55.000 5.73 9.78 45.03 3.84
2090 2205 0.566593 GTACGAGAGAAACGCGCATC 59.433 55.000 5.73 4.50 45.03 3.91
2091 2206 0.109458 TGTACGAGAGAAACGCGCAT 60.109 50.000 5.73 0.00 45.03 4.73
2092 2207 1.000233 GTGTACGAGAGAAACGCGCA 61.000 55.000 5.73 0.00 45.03 6.09
2093 2208 1.694962 GTGTACGAGAGAAACGCGC 59.305 57.895 5.73 0.00 45.03 6.86
2094 2209 1.971336 CGTGTACGAGAGAAACGCG 59.029 57.895 3.53 3.53 46.44 6.01
2095 2210 1.901236 GTACGTGTACGAGAGAAACGC 59.099 52.381 11.79 0.00 43.02 4.84
2119 2234 4.354212 CAACGCCTCGCACACACG 62.354 66.667 0.00 0.00 0.00 4.49
2120 2235 4.012895 CCAACGCCTCGCACACAC 62.013 66.667 0.00 0.00 0.00 3.82
2124 2239 3.642778 TAGAGCCAACGCCTCGCAC 62.643 63.158 0.00 0.00 34.57 5.34
2125 2240 2.938086 TTAGAGCCAACGCCTCGCA 61.938 57.895 0.00 0.00 34.57 5.10
2126 2241 2.125673 TTAGAGCCAACGCCTCGC 60.126 61.111 0.00 0.00 34.57 5.03
2127 2242 1.078759 CAGTTAGAGCCAACGCCTCG 61.079 60.000 0.00 0.00 34.57 4.63
2128 2243 0.246635 TCAGTTAGAGCCAACGCCTC 59.753 55.000 0.00 0.00 34.57 4.70
2129 2244 0.685097 TTCAGTTAGAGCCAACGCCT 59.315 50.000 0.00 0.00 34.57 5.52
2130 2245 0.796927 GTTCAGTTAGAGCCAACGCC 59.203 55.000 0.00 0.00 34.57 5.68
2131 2246 0.796927 GGTTCAGTTAGAGCCAACGC 59.203 55.000 0.00 0.00 46.12 4.84
2136 2251 0.460459 GCTCGGGTTCAGTTAGAGCC 60.460 60.000 4.58 0.00 46.00 4.70
2137 2252 3.052181 GCTCGGGTTCAGTTAGAGC 57.948 57.895 0.00 0.00 45.74 4.09
2138 2253 0.809385 TCGCTCGGGTTCAGTTAGAG 59.191 55.000 0.00 0.00 0.00 2.43
2139 2254 0.809385 CTCGCTCGGGTTCAGTTAGA 59.191 55.000 0.00 0.00 0.00 2.10
2140 2255 0.179134 CCTCGCTCGGGTTCAGTTAG 60.179 60.000 0.00 0.00 0.00 2.34
2141 2256 1.888018 CCTCGCTCGGGTTCAGTTA 59.112 57.895 0.00 0.00 0.00 2.24
2142 2257 2.657237 CCTCGCTCGGGTTCAGTT 59.343 61.111 0.00 0.00 0.00 3.16
2143 2258 4.070552 GCCTCGCTCGGGTTCAGT 62.071 66.667 0.00 0.00 0.00 3.41
2146 2261 4.736896 AACGCCTCGCTCGGGTTC 62.737 66.667 0.00 0.00 31.40 3.62
2154 2269 3.659089 TTAGAGCCCAACGCCTCGC 62.659 63.158 0.00 0.00 38.78 5.03
2155 2270 1.810030 GTTAGAGCCCAACGCCTCG 60.810 63.158 0.00 0.00 38.78 4.63
2156 2271 0.741221 CAGTTAGAGCCCAACGCCTC 60.741 60.000 0.00 0.00 38.78 4.70
2157 2272 1.192146 TCAGTTAGAGCCCAACGCCT 61.192 55.000 0.00 0.00 38.78 5.52
2158 2273 0.321298 TTCAGTTAGAGCCCAACGCC 60.321 55.000 0.00 0.00 38.78 5.68
2159 2274 0.796927 GTTCAGTTAGAGCCCAACGC 59.203 55.000 0.00 0.00 37.98 4.84
2160 2275 1.439679 GGTTCAGTTAGAGCCCAACG 58.560 55.000 0.00 0.00 41.44 4.10
2165 2280 0.460459 GCTCGGGTTCAGTTAGAGCC 60.460 60.000 4.58 0.00 46.00 4.70
2166 2281 3.052181 GCTCGGGTTCAGTTAGAGC 57.948 57.895 0.00 0.00 45.74 4.09
2167 2282 0.809385 TCGCTCGGGTTCAGTTAGAG 59.191 55.000 0.00 0.00 0.00 2.43
2168 2283 1.471119 ATCGCTCGGGTTCAGTTAGA 58.529 50.000 0.00 0.00 0.00 2.10
2169 2284 1.927174 CAATCGCTCGGGTTCAGTTAG 59.073 52.381 0.00 0.00 0.00 2.34
2170 2285 2.004583 CAATCGCTCGGGTTCAGTTA 57.995 50.000 0.00 0.00 0.00 2.24
2171 2286 1.298859 GCAATCGCTCGGGTTCAGTT 61.299 55.000 0.00 0.00 34.30 3.16
2172 2287 1.741770 GCAATCGCTCGGGTTCAGT 60.742 57.895 0.00 0.00 34.30 3.41
2173 2288 1.741401 TGCAATCGCTCGGGTTCAG 60.741 57.895 0.00 0.00 39.64 3.02
2174 2289 2.032634 GTGCAATCGCTCGGGTTCA 61.033 57.895 0.00 0.00 39.64 3.18
2175 2290 1.741770 AGTGCAATCGCTCGGGTTC 60.742 57.895 0.00 0.00 39.64 3.62
2176 2291 2.034879 CAGTGCAATCGCTCGGGTT 61.035 57.895 0.00 0.00 39.64 4.11
2177 2292 2.434884 CAGTGCAATCGCTCGGGT 60.435 61.111 0.00 0.00 39.64 5.28
2178 2293 3.869272 GCAGTGCAATCGCTCGGG 61.869 66.667 11.09 0.00 39.64 5.14
2179 2294 3.092192 CTGCAGTGCAATCGCTCGG 62.092 63.158 20.22 0.34 38.41 4.63
2180 2295 2.398429 CTGCAGTGCAATCGCTCG 59.602 61.111 20.22 1.15 38.41 5.03
2181 2296 2.789917 CCTGCAGTGCAATCGCTC 59.210 61.111 20.22 0.00 38.41 5.03
2182 2297 2.526450 TAGCCTGCAGTGCAATCGCT 62.526 55.000 27.35 27.35 38.41 4.93
2183 2298 2.108514 TAGCCTGCAGTGCAATCGC 61.109 57.895 20.22 19.44 38.41 4.58
2184 2299 1.717937 GTAGCCTGCAGTGCAATCG 59.282 57.895 20.22 10.48 38.41 3.34
2185 2300 1.717937 CGTAGCCTGCAGTGCAATC 59.282 57.895 20.22 13.26 38.41 2.67
2186 2301 3.895025 CGTAGCCTGCAGTGCAAT 58.105 55.556 20.22 10.59 38.41 3.56
2203 2318 2.442188 CGCTCGGGTTCAGTAACGC 61.442 63.158 0.00 0.00 43.25 4.84
2204 2319 0.179145 ATCGCTCGGGTTCAGTAACG 60.179 55.000 0.00 0.00 36.39 3.18
2205 2320 1.557651 GATCGCTCGGGTTCAGTAAC 58.442 55.000 0.00 0.00 34.66 2.50
2206 2321 0.099968 CGATCGCTCGGGTTCAGTAA 59.900 55.000 0.26 0.00 41.27 2.24
2207 2322 0.745486 TCGATCGCTCGGGTTCAGTA 60.745 55.000 11.09 0.00 45.10 2.74
2208 2323 1.384989 ATCGATCGCTCGGGTTCAGT 61.385 55.000 11.09 0.00 45.10 3.41
2209 2324 0.661780 GATCGATCGCTCGGGTTCAG 60.662 60.000 11.09 0.00 45.10 3.02
2210 2325 1.359117 GATCGATCGCTCGGGTTCA 59.641 57.895 11.09 0.00 45.10 3.18
2211 2326 1.726322 CGATCGATCGCTCGGGTTC 60.726 63.158 32.34 0.00 45.10 3.62
2212 2327 2.331805 CGATCGATCGCTCGGGTT 59.668 61.111 32.34 0.00 45.10 4.11
2216 2331 2.520284 AGCCATCGATCGATCGCTCG 62.520 60.000 34.94 29.69 43.65 5.03
2217 2332 1.069924 CAGCCATCGATCGATCGCTC 61.070 60.000 36.82 24.71 43.65 5.03
2218 2333 1.080907 CAGCCATCGATCGATCGCT 60.081 57.895 34.94 34.94 46.95 4.93
2221 2336 3.426859 CAGTTAACAGCCATCGATCGATC 59.573 47.826 27.20 17.11 31.62 3.69
2222 2337 3.068165 TCAGTTAACAGCCATCGATCGAT 59.932 43.478 24.60 24.60 34.81 3.59
2223 2338 2.425668 TCAGTTAACAGCCATCGATCGA 59.574 45.455 21.86 21.86 0.00 3.59
2224 2339 2.809446 TCAGTTAACAGCCATCGATCG 58.191 47.619 9.36 9.36 0.00 3.69
2225 2340 3.309954 GGTTCAGTTAACAGCCATCGATC 59.690 47.826 8.61 0.00 40.08 3.69
2226 2341 3.270877 GGTTCAGTTAACAGCCATCGAT 58.729 45.455 8.61 0.00 40.08 3.59
2227 2342 2.614481 GGGTTCAGTTAACAGCCATCGA 60.614 50.000 8.61 0.00 40.08 3.59
2228 2343 1.737793 GGGTTCAGTTAACAGCCATCG 59.262 52.381 8.61 0.00 40.08 3.84
2229 2344 1.737793 CGGGTTCAGTTAACAGCCATC 59.262 52.381 8.61 0.00 40.08 3.51
2230 2345 1.349688 TCGGGTTCAGTTAACAGCCAT 59.650 47.619 8.61 0.00 40.08 4.40
2231 2346 0.759959 TCGGGTTCAGTTAACAGCCA 59.240 50.000 8.61 0.00 40.08 4.75
2232 2347 2.007608 GATCGGGTTCAGTTAACAGCC 58.992 52.381 8.61 5.52 40.08 4.85
2233 2348 1.659098 CGATCGGGTTCAGTTAACAGC 59.341 52.381 7.38 0.00 40.08 4.40
2234 2349 3.179830 CTCGATCGGGTTCAGTTAACAG 58.820 50.000 16.41 0.00 40.08 3.16
2235 2350 2.673043 GCTCGATCGGGTTCAGTTAACA 60.673 50.000 17.85 0.00 40.08 2.41
2236 2351 1.925185 GCTCGATCGGGTTCAGTTAAC 59.075 52.381 17.85 0.00 37.36 2.01
2237 2352 1.468565 CGCTCGATCGGGTTCAGTTAA 60.469 52.381 17.85 0.00 0.00 2.01
2238 2353 0.099968 CGCTCGATCGGGTTCAGTTA 59.900 55.000 17.85 0.00 0.00 2.24
2239 2354 1.153823 CGCTCGATCGGGTTCAGTT 60.154 57.895 17.85 0.00 0.00 3.16
2240 2355 1.384989 ATCGCTCGATCGGGTTCAGT 61.385 55.000 17.85 0.00 0.00 3.41
2241 2356 0.249073 AATCGCTCGATCGGGTTCAG 60.249 55.000 17.85 6.63 33.08 3.02
2242 2357 0.248907 GAATCGCTCGATCGGGTTCA 60.249 55.000 17.85 0.59 33.08 3.18
2243 2358 0.940047 GGAATCGCTCGATCGGGTTC 60.940 60.000 17.85 12.27 33.08 3.62
2244 2359 1.067582 GGAATCGCTCGATCGGGTT 59.932 57.895 17.85 2.47 33.08 4.11
2245 2360 1.392710 AAGGAATCGCTCGATCGGGT 61.393 55.000 17.85 0.00 33.08 5.28
2246 2361 0.664767 GAAGGAATCGCTCGATCGGG 60.665 60.000 16.41 14.14 33.08 5.14
2247 2362 0.999228 CGAAGGAATCGCTCGATCGG 60.999 60.000 16.41 7.26 45.89 4.18
2248 2363 2.414950 CGAAGGAATCGCTCGATCG 58.585 57.895 9.36 9.36 45.89 3.69
2266 2381 1.663135 GCTTCAGTTAGCAGCAGTAGC 59.337 52.381 0.00 0.00 40.89 3.58
2267 2382 2.275318 GGCTTCAGTTAGCAGCAGTAG 58.725 52.381 0.00 0.00 43.02 2.57
2268 2383 2.386661 GGCTTCAGTTAGCAGCAGTA 57.613 50.000 0.00 0.00 43.02 2.74
2269 2384 3.239861 GGCTTCAGTTAGCAGCAGT 57.760 52.632 0.00 0.00 43.02 4.40


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

AutoCloner maintained by Alex Coulton.