Multiple sequence alignment - TraesCS6A01G328900

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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 TraesCS6A01G328900 chr6A 100.000 2372 0 0 1 2372 562401463 562399092 0.000000e+00 4381.0
1 TraesCS6A01G328900 chr6A 81.852 1080 95 62 674 1694 562271674 562272711 0.000000e+00 815.0
2 TraesCS6A01G328900 chr6A 85.526 760 54 25 657 1399 562250560 562251280 0.000000e+00 743.0
3 TraesCS6A01G328900 chr6A 85.429 700 40 22 705 1399 562470722 562470080 0.000000e+00 671.0
4 TraesCS6A01G328900 chr6A 97.333 150 4 0 2223 2372 597448450 597448599 3.030000e-64 255.0
5 TraesCS6A01G328900 chr6A 82.258 124 11 4 1578 1692 291949382 291949261 1.940000e-16 97.1
6 TraesCS6A01G328900 chr6B 88.690 1061 50 32 669 1724 631193058 631194053 0.000000e+00 1230.0
7 TraesCS6A01G328900 chr6B 91.097 629 31 16 943 1556 631246118 631245500 0.000000e+00 828.0
8 TraesCS6A01G328900 chr6B 85.965 798 56 29 731 1523 631741309 631740563 0.000000e+00 802.0
9 TraesCS6A01G328900 chr6B 86.216 740 55 19 670 1399 631535135 631534433 0.000000e+00 758.0
10 TraesCS6A01G328900 chr6B 89.207 593 32 13 811 1399 631844081 631843517 0.000000e+00 712.0
11 TraesCS6A01G328900 chr6B 91.509 106 4 3 1615 1719 631245273 631245172 8.840000e-30 141.0
12 TraesCS6A01G328900 chr6B 89.062 64 2 3 1635 1694 630918920 630918858 9.090000e-10 75.0
13 TraesCS6A01G328900 chr6D 87.453 1068 69 36 673 1724 418770276 418769258 0.000000e+00 1170.0
14 TraesCS6A01G328900 chr6D 89.858 917 46 25 818 1724 418732811 418733690 0.000000e+00 1134.0
15 TraesCS6A01G328900 chr6D 86.724 693 43 22 662 1342 418883209 418882554 0.000000e+00 725.0
16 TraesCS6A01G328900 chr6D 85.160 721 53 20 657 1374 418893004 418892335 0.000000e+00 689.0
17 TraesCS6A01G328900 chr6D 91.813 171 6 2 1739 1909 418769273 418769111 5.100000e-57 231.0
18 TraesCS6A01G328900 chr6D 92.593 108 3 2 2120 2223 418769112 418769006 1.470000e-32 150.0
19 TraesCS6A01G328900 chr7A 92.478 678 22 4 4 654 267565258 267564583 0.000000e+00 942.0
20 TraesCS6A01G328900 chr7A 91.888 678 24 6 4 654 641237032 641237705 0.000000e+00 918.0
21 TraesCS6A01G328900 chr7A 97.368 152 4 0 2221 2372 731695692 731695843 2.340000e-65 259.0
22 TraesCS6A01G328900 chr7A 96.689 151 5 0 2222 2372 562183023 562182873 3.910000e-63 252.0
23 TraesCS6A01G328900 chr7A 96.000 150 6 0 2223 2372 211131281 211131430 6.550000e-61 244.0
24 TraesCS6A01G328900 chr3A 92.035 678 23 6 4 654 700754891 700754218 0.000000e+00 924.0
25 TraesCS6A01G328900 chr3A 96.000 150 6 0 2223 2372 132162175 132162324 6.550000e-61 244.0
26 TraesCS6A01G328900 chr2A 91.150 678 31 7 4 654 24398506 24399181 0.000000e+00 893.0
27 TraesCS6A01G328900 chr2A 93.125 160 9 2 2213 2372 765848231 765848388 1.420000e-57 233.0
28 TraesCS6A01G328900 chr4A 91.016 679 29 7 4 654 608011574 608012248 0.000000e+00 887.0
29 TraesCS6A01G328900 chr4A 91.148 610 26 6 72 654 677965191 677965799 0.000000e+00 802.0
30 TraesCS6A01G328900 chr1A 88.053 678 28 19 4 654 531318248 531318899 0.000000e+00 754.0
31 TraesCS6A01G328900 chr1A 96.000 150 6 0 2223 2372 189706782 189706931 6.550000e-61 244.0
32 TraesCS6A01G328900 chrUn 87.368 475 33 13 205 654 277263923 277263451 9.720000e-144 520.0
33 TraesCS6A01G328900 chrUn 92.000 50 3 1 2045 2093 468662121 468662170 4.230000e-08 69.4
34 TraesCS6A01G328900 chr1D 90.256 390 14 7 288 654 388276982 388276594 2.740000e-134 488.0
35 TraesCS6A01G328900 chr1D 90.000 390 15 6 288 654 387954587 387954975 1.270000e-132 483.0
36 TraesCS6A01G328900 chr1D 94.371 302 15 2 4 305 387954274 387954573 1.660000e-126 462.0
37 TraesCS6A01G328900 chr1D 94.371 302 15 2 4 305 388277295 388276996 1.660000e-126 462.0
38 TraesCS6A01G328900 chr5B 87.140 451 31 12 205 630 589114450 589114898 9.860000e-134 486.0
39 TraesCS6A01G328900 chr5B 89.899 198 19 1 5 201 589111933 589112130 1.090000e-63 254.0
40 TraesCS6A01G328900 chr5A 97.333 150 4 0 2223 2372 568488524 568488375 3.030000e-64 255.0
41 TraesCS6A01G328900 chr5A 96.000 150 6 0 2223 2372 91550045 91550194 6.550000e-61 244.0
42 TraesCS6A01G328900 chr4B 86.957 115 14 1 2045 2159 657622257 657622144 6.880000e-26 128.0
43 TraesCS6A01G328900 chr4B 86.087 115 15 1 2045 2159 322945772 322945659 3.200000e-24 122.0


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 TraesCS6A01G328900 chr6A 562399092 562401463 2371 True 4381.0 4381 100.000000 1 2372 1 chr6A.!!$R2 2371
1 TraesCS6A01G328900 chr6A 562271674 562272711 1037 False 815.0 815 81.852000 674 1694 1 chr6A.!!$F2 1020
2 TraesCS6A01G328900 chr6A 562250560 562251280 720 False 743.0 743 85.526000 657 1399 1 chr6A.!!$F1 742
3 TraesCS6A01G328900 chr6A 562470080 562470722 642 True 671.0 671 85.429000 705 1399 1 chr6A.!!$R3 694
4 TraesCS6A01G328900 chr6B 631193058 631194053 995 False 1230.0 1230 88.690000 669 1724 1 chr6B.!!$F1 1055
5 TraesCS6A01G328900 chr6B 631740563 631741309 746 True 802.0 802 85.965000 731 1523 1 chr6B.!!$R3 792
6 TraesCS6A01G328900 chr6B 631534433 631535135 702 True 758.0 758 86.216000 670 1399 1 chr6B.!!$R2 729
7 TraesCS6A01G328900 chr6B 631843517 631844081 564 True 712.0 712 89.207000 811 1399 1 chr6B.!!$R4 588
8 TraesCS6A01G328900 chr6B 631245172 631246118 946 True 484.5 828 91.303000 943 1719 2 chr6B.!!$R5 776
9 TraesCS6A01G328900 chr6D 418732811 418733690 879 False 1134.0 1134 89.858000 818 1724 1 chr6D.!!$F1 906
10 TraesCS6A01G328900 chr6D 418882554 418883209 655 True 725.0 725 86.724000 662 1342 1 chr6D.!!$R1 680
11 TraesCS6A01G328900 chr6D 418892335 418893004 669 True 689.0 689 85.160000 657 1374 1 chr6D.!!$R2 717
12 TraesCS6A01G328900 chr6D 418769006 418770276 1270 True 517.0 1170 90.619667 673 2223 3 chr6D.!!$R3 1550
13 TraesCS6A01G328900 chr7A 267564583 267565258 675 True 942.0 942 92.478000 4 654 1 chr7A.!!$R1 650
14 TraesCS6A01G328900 chr7A 641237032 641237705 673 False 918.0 918 91.888000 4 654 1 chr7A.!!$F2 650
15 TraesCS6A01G328900 chr3A 700754218 700754891 673 True 924.0 924 92.035000 4 654 1 chr3A.!!$R1 650
16 TraesCS6A01G328900 chr2A 24398506 24399181 675 False 893.0 893 91.150000 4 654 1 chr2A.!!$F1 650
17 TraesCS6A01G328900 chr4A 608011574 608012248 674 False 887.0 887 91.016000 4 654 1 chr4A.!!$F1 650
18 TraesCS6A01G328900 chr4A 677965191 677965799 608 False 802.0 802 91.148000 72 654 1 chr4A.!!$F2 582
19 TraesCS6A01G328900 chr1A 531318248 531318899 651 False 754.0 754 88.053000 4 654 1 chr1A.!!$F2 650
20 TraesCS6A01G328900 chr1D 388276594 388277295 701 True 475.0 488 92.313500 4 654 2 chr1D.!!$R1 650
21 TraesCS6A01G328900 chr1D 387954274 387954975 701 False 472.5 483 92.185500 4 654 2 chr1D.!!$F1 650
22 TraesCS6A01G328900 chr5B 589111933 589114898 2965 False 370.0 486 88.519500 5 630 2 chr5B.!!$F1 625

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
494 2905 1.333931 CAGCCAATACTCGCTACTCGA 59.666 52.381 0.0 0.0 46.29 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2146 4897 0.108329 CCGTCGGGCTATGTCACTTT 60.108 55.0 2.34 0.0 0.0 2.66 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
38 40 6.315642 TCGAGATTGTCTACAGACTACGATTT 59.684 38.462 10.55 0.00 44.99 2.17
49 51 4.091509 CAGACTACGATTTTACAGGTGCAC 59.908 45.833 8.80 8.80 0.00 4.57
238 2557 8.341173 GCTATGTGGAGAAAGACATATTTTCTG 58.659 37.037 5.76 0.00 43.07 3.02
261 2580 6.661669 TGCAATAACGAATGATGATGTGATC 58.338 36.000 0.00 0.00 0.00 2.92
494 2905 1.333931 CAGCCAATACTCGCTACTCGA 59.666 52.381 0.00 0.00 46.29 4.04
551 2964 7.862372 CCTGCATATTGTTGCTTTTTATATCGT 59.138 33.333 0.00 0.00 43.18 3.73
581 2994 5.394005 GCCATTATCTATGTTGTTGCACCAA 60.394 40.000 0.00 0.00 31.99 3.67
600 3013 5.753438 CACCAACTATAATTTCTGCTAGCGA 59.247 40.000 10.77 7.69 0.00 4.93
605 3018 9.031360 CAACTATAATTTCTGCTAGCGACTTAA 57.969 33.333 10.77 2.90 0.00 1.85
655 3068 2.649331 TTTTCTAGCTTCGTCCCTCG 57.351 50.000 0.00 0.00 41.41 4.63
744 3169 2.337246 TACTACAGGCAGCGCACGA 61.337 57.895 11.47 0.00 0.00 4.35
919 3391 1.901833 TGCAATAGAGCAGTGGTCTCA 59.098 47.619 27.27 16.41 40.94 3.27
920 3392 2.502947 TGCAATAGAGCAGTGGTCTCAT 59.497 45.455 27.27 14.95 40.94 2.90
925 3397 3.660970 AGAGCAGTGGTCTCATCTCTA 57.339 47.619 19.05 0.00 35.30 2.43
928 3400 3.030291 AGCAGTGGTCTCATCTCTAAGG 58.970 50.000 0.00 0.00 0.00 2.69
937 3410 3.011821 TCTCATCTCTAAGGACCACCAGT 59.988 47.826 0.00 0.00 38.94 4.00
1235 3714 2.330372 CCGTCGACGAGTTCCTCCA 61.330 63.158 37.65 0.00 43.02 3.86
1534 4065 2.351641 GCAGAGAGATACGGAGATGCTG 60.352 54.545 0.00 0.00 0.00 4.41
1548 4085 1.694133 ATGCTGGAGAGGCAGTAGGC 61.694 60.000 0.00 0.00 43.15 3.93
1550 4087 1.754621 CTGGAGAGGCAGTAGGCGA 60.755 63.158 0.00 0.00 46.16 5.54
1551 4088 1.075970 TGGAGAGGCAGTAGGCGAT 60.076 57.895 0.00 0.00 46.16 4.58
1552 4089 0.687757 TGGAGAGGCAGTAGGCGATT 60.688 55.000 0.00 0.00 46.16 3.34
1553 4090 1.329256 GGAGAGGCAGTAGGCGATTA 58.671 55.000 0.00 0.00 46.16 1.75
1554 4091 1.271102 GGAGAGGCAGTAGGCGATTAG 59.729 57.143 0.00 0.00 46.16 1.73
1555 4092 1.957877 GAGAGGCAGTAGGCGATTAGT 59.042 52.381 0.00 0.00 46.16 2.24
1556 4093 2.362717 GAGAGGCAGTAGGCGATTAGTT 59.637 50.000 0.00 0.00 46.16 2.24
1557 4094 2.766828 AGAGGCAGTAGGCGATTAGTTT 59.233 45.455 0.00 0.00 46.16 2.66
1558 4095 3.958798 AGAGGCAGTAGGCGATTAGTTTA 59.041 43.478 0.00 0.00 46.16 2.01
1559 4096 4.038162 AGAGGCAGTAGGCGATTAGTTTAG 59.962 45.833 0.00 0.00 46.16 1.85
1560 4097 3.069729 AGGCAGTAGGCGATTAGTTTAGG 59.930 47.826 0.00 0.00 46.16 2.69
1561 4098 2.801111 GCAGTAGGCGATTAGTTTAGGC 59.199 50.000 0.00 0.00 0.00 3.93
1562 4099 3.391049 CAGTAGGCGATTAGTTTAGGCC 58.609 50.000 0.00 0.00 44.07 5.19
1563 4100 2.367894 AGTAGGCGATTAGTTTAGGCCC 59.632 50.000 0.00 0.00 44.82 5.80
1564 4101 0.472898 AGGCGATTAGTTTAGGCCCC 59.527 55.000 0.00 0.00 44.82 5.80
1576 4113 4.351111 AGTTTAGGCCCCATTAGTCTATGG 59.649 45.833 0.00 0.00 43.90 2.74
1613 4351 1.314730 TTCGGCCTTGTTGTTCTTCC 58.685 50.000 0.00 0.00 0.00 3.46
1715 4466 5.604565 GTTACAGCCCGGTTTACATATACT 58.395 41.667 0.00 0.00 0.00 2.12
1717 4468 5.874897 ACAGCCCGGTTTACATATACTAA 57.125 39.130 0.00 0.00 0.00 2.24
1718 4469 5.604565 ACAGCCCGGTTTACATATACTAAC 58.395 41.667 0.00 0.00 0.00 2.34
1719 4470 5.129155 ACAGCCCGGTTTACATATACTAACA 59.871 40.000 0.00 0.00 0.00 2.41
1720 4471 6.050432 CAGCCCGGTTTACATATACTAACAA 58.950 40.000 0.00 0.00 0.00 2.83
1721 4472 6.018507 CAGCCCGGTTTACATATACTAACAAC 60.019 42.308 0.00 0.00 0.00 3.32
1722 4473 6.051074 GCCCGGTTTACATATACTAACAACT 58.949 40.000 0.00 0.00 0.00 3.16
1723 4474 6.539826 GCCCGGTTTACATATACTAACAACTT 59.460 38.462 0.00 0.00 0.00 2.66
1724 4475 7.066163 GCCCGGTTTACATATACTAACAACTTT 59.934 37.037 0.00 0.00 0.00 2.66
1725 4476 8.949177 CCCGGTTTACATATACTAACAACTTTT 58.051 33.333 0.00 0.00 0.00 2.27
1766 4517 3.584848 ACTACAACTTGATCTGCTTCCCT 59.415 43.478 0.00 0.00 0.00 4.20
1783 4534 5.118664 GCTTCCCTATCGTTTTTCTTTTTGC 59.881 40.000 0.00 0.00 0.00 3.68
1788 4539 6.256757 CCCTATCGTTTTTCTTTTTGCAAACA 59.743 34.615 12.39 4.32 0.00 2.83
1793 4544 6.147821 TCGTTTTTCTTTTTGCAAACATCCAA 59.852 30.769 12.39 2.04 0.00 3.53
1811 4562 6.757947 ACATCCAACTCAAATTGAACAAGTTG 59.242 34.615 17.64 17.64 44.77 3.16
1845 4596 2.996621 GCTAATGCCAATCGCTAGTAGG 59.003 50.000 0.00 0.00 38.78 3.18
1846 4597 1.884235 AATGCCAATCGCTAGTAGGC 58.116 50.000 0.00 0.00 45.41 3.93
1848 4599 2.906047 GCCAATCGCTAGTAGGCAG 58.094 57.895 0.00 0.00 44.59 4.85
1849 4600 0.105039 GCCAATCGCTAGTAGGCAGT 59.895 55.000 0.00 0.00 44.59 4.40
1850 4601 1.340248 GCCAATCGCTAGTAGGCAGTA 59.660 52.381 0.00 0.00 44.59 2.74
1851 4602 2.608261 GCCAATCGCTAGTAGGCAGTAG 60.608 54.545 0.00 0.00 44.59 2.57
1919 4670 2.654939 GCGAGAAGCTTCGTACCTG 58.345 57.895 20.43 9.08 44.04 4.00
1920 4671 0.109226 GCGAGAAGCTTCGTACCTGT 60.109 55.000 20.43 1.00 44.04 4.00
1921 4672 1.669211 GCGAGAAGCTTCGTACCTGTT 60.669 52.381 20.43 0.20 44.04 3.16
1922 4673 2.251893 CGAGAAGCTTCGTACCTGTTC 58.748 52.381 20.43 9.12 35.91 3.18
1923 4674 2.095161 CGAGAAGCTTCGTACCTGTTCT 60.095 50.000 20.43 0.00 35.91 3.01
1924 4675 3.612004 CGAGAAGCTTCGTACCTGTTCTT 60.612 47.826 20.43 0.00 35.91 2.52
1925 4676 3.915536 AGAAGCTTCGTACCTGTTCTTC 58.084 45.455 20.43 0.00 0.00 2.87
1926 4677 2.745515 AGCTTCGTACCTGTTCTTCC 57.254 50.000 0.00 0.00 0.00 3.46
1927 4678 1.968493 AGCTTCGTACCTGTTCTTCCA 59.032 47.619 0.00 0.00 0.00 3.53
1928 4679 2.367567 AGCTTCGTACCTGTTCTTCCAA 59.632 45.455 0.00 0.00 0.00 3.53
1929 4680 3.008049 AGCTTCGTACCTGTTCTTCCAAT 59.992 43.478 0.00 0.00 0.00 3.16
1930 4681 3.371285 GCTTCGTACCTGTTCTTCCAATC 59.629 47.826 0.00 0.00 0.00 2.67
1931 4682 3.226346 TCGTACCTGTTCTTCCAATCG 57.774 47.619 0.00 0.00 0.00 3.34
1932 4683 1.659098 CGTACCTGTTCTTCCAATCGC 59.341 52.381 0.00 0.00 0.00 4.58
1933 4684 2.674177 CGTACCTGTTCTTCCAATCGCT 60.674 50.000 0.00 0.00 0.00 4.93
1934 4685 3.428452 CGTACCTGTTCTTCCAATCGCTA 60.428 47.826 0.00 0.00 0.00 4.26
1935 4686 3.914426 ACCTGTTCTTCCAATCGCTAT 57.086 42.857 0.00 0.00 0.00 2.97
1936 4687 3.798202 ACCTGTTCTTCCAATCGCTATC 58.202 45.455 0.00 0.00 0.00 2.08
1937 4688 2.797156 CCTGTTCTTCCAATCGCTATCG 59.203 50.000 0.00 0.00 0.00 2.92
1938 4689 2.201732 TGTTCTTCCAATCGCTATCGC 58.798 47.619 0.00 0.00 35.26 4.58
1939 4690 2.159099 TGTTCTTCCAATCGCTATCGCT 60.159 45.455 0.00 0.00 35.26 4.93
1940 4691 3.067601 TGTTCTTCCAATCGCTATCGCTA 59.932 43.478 0.00 0.00 35.26 4.26
1941 4692 3.560902 TCTTCCAATCGCTATCGCTAG 57.439 47.619 0.00 0.00 35.26 3.42
1942 4693 2.885266 TCTTCCAATCGCTATCGCTAGT 59.115 45.455 0.00 0.00 35.26 2.57
1943 4694 4.070009 TCTTCCAATCGCTATCGCTAGTA 58.930 43.478 0.00 0.00 35.26 1.82
1944 4695 4.154375 TCTTCCAATCGCTATCGCTAGTAG 59.846 45.833 0.00 0.00 35.26 2.57
1945 4696 2.161808 TCCAATCGCTATCGCTAGTAGC 59.838 50.000 12.41 12.41 40.83 3.58
1946 4697 2.520979 CAATCGCTATCGCTAGTAGCC 58.479 52.381 16.51 1.05 41.10 3.93
1947 4698 1.822506 ATCGCTATCGCTAGTAGCCA 58.177 50.000 16.51 3.96 41.10 4.75
1948 4699 1.157585 TCGCTATCGCTAGTAGCCAG 58.842 55.000 16.51 11.71 41.10 4.85
1949 4700 0.455295 CGCTATCGCTAGTAGCCAGC 60.455 60.000 20.37 20.37 41.10 4.85
1950 4701 0.109039 GCTATCGCTAGTAGCCAGCC 60.109 60.000 19.93 8.33 38.18 4.85
1951 4702 0.528470 CTATCGCTAGTAGCCAGCCC 59.472 60.000 16.51 0.00 38.18 5.19
1952 4703 0.178973 TATCGCTAGTAGCCAGCCCA 60.179 55.000 16.51 0.00 38.18 5.36
1953 4704 1.048724 ATCGCTAGTAGCCAGCCCAA 61.049 55.000 16.51 0.00 38.18 4.12
1954 4705 1.227380 CGCTAGTAGCCAGCCCAAG 60.227 63.158 16.51 0.00 38.18 3.61
1955 4706 1.908483 GCTAGTAGCCAGCCCAAGT 59.092 57.895 11.33 0.00 34.48 3.16
1956 4707 1.120530 GCTAGTAGCCAGCCCAAGTA 58.879 55.000 11.33 0.00 34.48 2.24
1957 4708 1.694696 GCTAGTAGCCAGCCCAAGTAT 59.305 52.381 11.33 0.00 34.48 2.12
1958 4709 2.897969 GCTAGTAGCCAGCCCAAGTATA 59.102 50.000 11.33 0.00 34.48 1.47
1959 4710 3.515901 GCTAGTAGCCAGCCCAAGTATAT 59.484 47.826 11.33 0.00 34.48 0.86
1960 4711 4.710375 GCTAGTAGCCAGCCCAAGTATATA 59.290 45.833 11.33 0.00 34.48 0.86
1961 4712 5.364157 GCTAGTAGCCAGCCCAAGTATATAT 59.636 44.000 11.33 0.00 34.48 0.86
1962 4713 6.550108 GCTAGTAGCCAGCCCAAGTATATATA 59.450 42.308 11.33 0.00 34.48 0.86
1963 4714 7.233757 GCTAGTAGCCAGCCCAAGTATATATAT 59.766 40.741 11.33 0.00 34.48 0.86
1964 4715 7.996758 AGTAGCCAGCCCAAGTATATATATT 57.003 36.000 0.00 0.00 0.00 1.28
1965 4716 8.024145 AGTAGCCAGCCCAAGTATATATATTC 57.976 38.462 0.00 0.00 0.00 1.75
1966 4717 6.253946 AGCCAGCCCAAGTATATATATTCC 57.746 41.667 0.00 0.00 0.00 3.01
1967 4718 5.973124 AGCCAGCCCAAGTATATATATTCCT 59.027 40.000 0.00 0.00 0.00 3.36
1968 4719 7.139619 AGCCAGCCCAAGTATATATATTCCTA 58.860 38.462 0.00 0.00 0.00 2.94
1969 4720 7.071321 AGCCAGCCCAAGTATATATATTCCTAC 59.929 40.741 0.00 0.00 0.00 3.18
1970 4721 7.147549 GCCAGCCCAAGTATATATATTCCTACA 60.148 40.741 0.00 0.00 0.00 2.74
1971 4722 8.938883 CCAGCCCAAGTATATATATTCCTACAT 58.061 37.037 0.00 0.00 0.00 2.29
1983 4734 6.875972 ATATTCCTACATTAGGCCTACTGG 57.124 41.667 28.15 18.05 45.82 4.00
1997 4748 4.737855 CCTACTGGCTAGCACTAAAGAA 57.262 45.455 18.24 0.00 0.00 2.52
1998 4749 5.086104 CCTACTGGCTAGCACTAAAGAAA 57.914 43.478 18.24 0.07 0.00 2.52
1999 4750 5.488341 CCTACTGGCTAGCACTAAAGAAAA 58.512 41.667 18.24 0.00 0.00 2.29
2000 4751 5.351740 CCTACTGGCTAGCACTAAAGAAAAC 59.648 44.000 18.24 0.00 0.00 2.43
2001 4752 4.974399 ACTGGCTAGCACTAAAGAAAACT 58.026 39.130 18.24 0.00 0.00 2.66
2002 4753 4.757149 ACTGGCTAGCACTAAAGAAAACTG 59.243 41.667 18.24 1.10 0.00 3.16
2003 4754 4.714632 TGGCTAGCACTAAAGAAAACTGT 58.285 39.130 18.24 0.00 0.00 3.55
2004 4755 4.755123 TGGCTAGCACTAAAGAAAACTGTC 59.245 41.667 18.24 0.00 0.00 3.51
2005 4756 4.755123 GGCTAGCACTAAAGAAAACTGTCA 59.245 41.667 18.24 0.00 0.00 3.58
2006 4757 5.412904 GGCTAGCACTAAAGAAAACTGTCAT 59.587 40.000 18.24 0.00 0.00 3.06
2007 4758 6.072452 GGCTAGCACTAAAGAAAACTGTCATT 60.072 38.462 18.24 0.00 0.00 2.57
2008 4759 6.798959 GCTAGCACTAAAGAAAACTGTCATTG 59.201 38.462 10.63 0.00 0.00 2.82
2009 4760 6.076981 AGCACTAAAGAAAACTGTCATTGG 57.923 37.500 0.00 0.00 0.00 3.16
2010 4761 5.010012 AGCACTAAAGAAAACTGTCATTGGG 59.990 40.000 0.00 0.00 0.00 4.12
2011 4762 5.222631 CACTAAAGAAAACTGTCATTGGGC 58.777 41.667 0.00 0.00 0.00 5.36
2012 4763 3.751479 AAAGAAAACTGTCATTGGGCC 57.249 42.857 0.00 0.00 0.00 5.80
2013 4764 2.683211 AGAAAACTGTCATTGGGCCT 57.317 45.000 4.53 0.00 0.00 5.19
2014 4765 2.242043 AGAAAACTGTCATTGGGCCTG 58.758 47.619 4.53 0.00 0.00 4.85
2015 4766 2.158475 AGAAAACTGTCATTGGGCCTGA 60.158 45.455 4.53 0.00 0.00 3.86
2016 4767 1.620822 AAACTGTCATTGGGCCTGAC 58.379 50.000 16.75 16.75 42.68 3.51
2017 4768 0.251341 AACTGTCATTGGGCCTGACC 60.251 55.000 19.76 6.09 41.87 4.02
2029 4780 3.428413 GGCCTGACCCAAGTAGTAAAA 57.572 47.619 0.00 0.00 0.00 1.52
2030 4781 3.344515 GGCCTGACCCAAGTAGTAAAAG 58.655 50.000 0.00 0.00 0.00 2.27
2031 4782 2.747989 GCCTGACCCAAGTAGTAAAAGC 59.252 50.000 0.00 0.00 0.00 3.51
2032 4783 3.559384 GCCTGACCCAAGTAGTAAAAGCT 60.559 47.826 0.00 0.00 0.00 3.74
2033 4784 4.323257 GCCTGACCCAAGTAGTAAAAGCTA 60.323 45.833 0.00 0.00 0.00 3.32
2034 4785 5.176592 CCTGACCCAAGTAGTAAAAGCTAC 58.823 45.833 0.00 0.00 41.07 3.58
2035 4786 5.156608 TGACCCAAGTAGTAAAAGCTACC 57.843 43.478 0.00 0.00 41.54 3.18
2036 4787 4.594062 TGACCCAAGTAGTAAAAGCTACCA 59.406 41.667 0.00 0.00 41.54 3.25
2037 4788 5.072058 TGACCCAAGTAGTAAAAGCTACCAA 59.928 40.000 0.00 0.00 41.54 3.67
2038 4789 5.557866 ACCCAAGTAGTAAAAGCTACCAAG 58.442 41.667 0.00 0.00 41.54 3.61
2039 4790 5.308759 ACCCAAGTAGTAAAAGCTACCAAGA 59.691 40.000 0.00 0.00 41.54 3.02
2040 4791 6.183361 ACCCAAGTAGTAAAAGCTACCAAGAA 60.183 38.462 0.00 0.00 41.54 2.52
2041 4792 6.884836 CCCAAGTAGTAAAAGCTACCAAGAAT 59.115 38.462 0.00 0.00 41.54 2.40
2042 4793 7.065923 CCCAAGTAGTAAAAGCTACCAAGAATC 59.934 40.741 0.00 0.00 41.54 2.52
2043 4794 7.824779 CCAAGTAGTAAAAGCTACCAAGAATCT 59.175 37.037 0.00 0.00 41.54 2.40
2044 4795 9.220767 CAAGTAGTAAAAGCTACCAAGAATCTT 57.779 33.333 0.00 0.00 41.54 2.40
2045 4796 9.794719 AAGTAGTAAAAGCTACCAAGAATCTTT 57.205 29.630 0.00 0.00 41.54 2.52
2046 4797 9.220767 AGTAGTAAAAGCTACCAAGAATCTTTG 57.779 33.333 0.00 0.00 41.54 2.77
2047 4798 9.216117 GTAGTAAAAGCTACCAAGAATCTTTGA 57.784 33.333 0.81 0.00 36.30 2.69
2048 4799 8.329203 AGTAAAAGCTACCAAGAATCTTTGAG 57.671 34.615 0.81 0.00 0.00 3.02
2049 4800 8.157476 AGTAAAAGCTACCAAGAATCTTTGAGA 58.843 33.333 0.81 0.00 0.00 3.27
2050 4801 7.446001 AAAAGCTACCAAGAATCTTTGAGAG 57.554 36.000 0.81 0.00 0.00 3.20
2051 4802 4.512484 AGCTACCAAGAATCTTTGAGAGC 58.488 43.478 13.55 13.55 36.58 4.09
2052 4803 3.308323 GCTACCAAGAATCTTTGAGAGCG 59.692 47.826 0.81 0.00 31.01 5.03
2053 4804 2.704572 ACCAAGAATCTTTGAGAGCGG 58.295 47.619 0.81 0.00 0.00 5.52
2054 4805 2.303022 ACCAAGAATCTTTGAGAGCGGA 59.697 45.455 0.81 0.00 0.00 5.54
2055 4806 3.054802 ACCAAGAATCTTTGAGAGCGGAT 60.055 43.478 0.81 0.00 0.00 4.18
2056 4807 3.559242 CCAAGAATCTTTGAGAGCGGATC 59.441 47.826 0.00 0.00 0.00 3.36
2057 4808 4.186926 CAAGAATCTTTGAGAGCGGATCA 58.813 43.478 0.00 0.00 0.00 2.92
2058 4809 3.791245 AGAATCTTTGAGAGCGGATCAC 58.209 45.455 0.00 0.00 0.00 3.06
2068 4819 4.873129 CGGATCACGCCCCTGACG 62.873 72.222 0.00 0.00 34.82 4.35
2069 4820 3.458163 GGATCACGCCCCTGACGA 61.458 66.667 0.00 0.00 0.00 4.20
2070 4821 2.105128 GATCACGCCCCTGACGAG 59.895 66.667 0.00 0.00 0.00 4.18
2071 4822 4.148825 ATCACGCCCCTGACGAGC 62.149 66.667 0.00 0.00 0.00 5.03
2107 4858 3.983494 CCCGAGATCGCCGCAGAT 61.983 66.667 0.00 0.00 38.18 2.90
2108 4859 2.732468 CCGAGATCGCCGCAGATG 60.732 66.667 0.00 0.00 38.18 2.90
2109 4860 2.332869 CGAGATCGCCGCAGATGA 59.667 61.111 3.01 0.00 0.00 2.92
2110 4861 1.728778 CGAGATCGCCGCAGATGAG 60.729 63.158 3.01 0.00 0.00 2.90
2111 4862 2.021039 GAGATCGCCGCAGATGAGC 61.021 63.158 3.01 0.00 0.00 4.26
2112 4863 2.028778 GATCGCCGCAGATGAGCT 59.971 61.111 0.00 0.00 0.00 4.09
2113 4864 1.593750 GATCGCCGCAGATGAGCTT 60.594 57.895 0.00 0.00 0.00 3.74
2114 4865 1.829349 GATCGCCGCAGATGAGCTTG 61.829 60.000 0.00 0.00 0.00 4.01
2115 4866 4.233635 CGCCGCAGATGAGCTTGC 62.234 66.667 0.00 0.00 0.00 4.01
2116 4867 2.823147 GCCGCAGATGAGCTTGCT 60.823 61.111 6.55 0.00 0.00 3.91
2117 4868 2.821688 GCCGCAGATGAGCTTGCTC 61.822 63.158 15.01 15.01 0.00 4.26
2118 4869 2.523507 CCGCAGATGAGCTTGCTCG 61.524 63.158 16.48 5.35 0.00 5.03
2119 4870 1.517913 CGCAGATGAGCTTGCTCGA 60.518 57.895 16.48 7.48 0.00 4.04
2120 4871 1.481019 CGCAGATGAGCTTGCTCGAG 61.481 60.000 16.48 8.45 0.00 4.04
2146 4897 1.610673 GGAGGAGACCCTGACTGCA 60.611 63.158 0.00 0.00 44.53 4.41
2198 4953 4.862574 GCTGTTCTGTACGTATCATCAACA 59.137 41.667 0.00 9.58 0.00 3.33
2203 4958 8.083462 TGTTCTGTACGTATCATCAACAGTTTA 58.917 33.333 11.10 0.00 38.88 2.01
2234 4989 9.366216 TGCTATTTGACAATACTAGTAAGTGTG 57.634 33.333 21.20 13.23 36.36 3.82
2235 4990 8.328864 GCTATTTGACAATACTAGTAAGTGTGC 58.671 37.037 21.20 15.03 36.36 4.57
2236 4991 9.366216 CTATTTGACAATACTAGTAAGTGTGCA 57.634 33.333 21.20 16.39 36.36 4.57
2237 4992 7.416154 TTTGACAATACTAGTAAGTGTGCAC 57.584 36.000 21.20 10.75 36.36 4.57
2238 4993 5.158494 TGACAATACTAGTAAGTGTGCACG 58.842 41.667 21.20 0.00 36.36 5.34
2239 4994 5.130292 ACAATACTAGTAAGTGTGCACGT 57.870 39.130 17.41 3.64 36.36 4.49
2240 4995 4.921515 ACAATACTAGTAAGTGTGCACGTG 59.078 41.667 12.28 12.28 36.36 4.49
2241 4996 1.779569 ACTAGTAAGTGTGCACGTGC 58.220 50.000 33.11 33.11 36.61 5.34
2242 4997 1.067974 ACTAGTAAGTGTGCACGTGCA 59.932 47.619 37.86 37.86 41.10 4.57
2243 4998 3.243468 TACTAGTAAGTGTGCACGTGCAA 60.243 43.478 42.04 28.45 44.14 4.08
2244 4999 5.317225 TACTAGTAAGTGTGCACGTGCAAC 61.317 45.833 42.04 35.35 44.14 4.17
2258 5013 1.503294 TGCAACGCACGTCTATTTGA 58.497 45.000 0.00 0.00 31.71 2.69
2259 5014 1.867865 TGCAACGCACGTCTATTTGAA 59.132 42.857 0.00 0.00 31.71 2.69
2260 5015 2.230864 GCAACGCACGTCTATTTGAAC 58.769 47.619 0.00 0.00 0.00 3.18
2261 5016 2.096417 GCAACGCACGTCTATTTGAACT 60.096 45.455 0.00 0.00 0.00 3.01
2262 5017 3.122278 GCAACGCACGTCTATTTGAACTA 59.878 43.478 0.00 0.00 0.00 2.24
2263 5018 4.376615 GCAACGCACGTCTATTTGAACTAA 60.377 41.667 0.00 0.00 0.00 2.24
2264 5019 5.670341 GCAACGCACGTCTATTTGAACTAAT 60.670 40.000 0.00 0.00 0.00 1.73
2265 5020 6.454583 GCAACGCACGTCTATTTGAACTAATA 60.455 38.462 0.00 0.00 0.00 0.98
2266 5021 7.449827 CAACGCACGTCTATTTGAACTAATAA 58.550 34.615 0.00 0.00 0.00 1.40
2267 5022 7.218145 ACGCACGTCTATTTGAACTAATAAG 57.782 36.000 0.00 0.00 0.00 1.73
2268 5023 6.810182 ACGCACGTCTATTTGAACTAATAAGT 59.190 34.615 0.00 0.00 37.65 2.24
2269 5024 7.111139 CGCACGTCTATTTGAACTAATAAGTG 58.889 38.462 0.00 0.00 35.62 3.16
2270 5025 7.201410 CGCACGTCTATTTGAACTAATAAGTGT 60.201 37.037 0.00 0.00 35.62 3.55
2271 5026 7.898309 GCACGTCTATTTGAACTAATAAGTGTG 59.102 37.037 0.00 0.00 35.62 3.82
2272 5027 7.898309 CACGTCTATTTGAACTAATAAGTGTGC 59.102 37.037 0.00 0.00 35.62 4.57
2273 5028 7.601130 ACGTCTATTTGAACTAATAAGTGTGCA 59.399 33.333 0.00 0.00 35.62 4.57
2274 5029 7.898309 CGTCTATTTGAACTAATAAGTGTGCAC 59.102 37.037 10.75 10.75 35.62 4.57
2275 5030 7.898309 GTCTATTTGAACTAATAAGTGTGCACG 59.102 37.037 13.13 0.00 35.62 5.34
2276 5031 5.994887 TTTGAACTAATAAGTGTGCACGT 57.005 34.783 13.13 2.34 35.62 4.49
2277 5032 4.983215 TGAACTAATAAGTGTGCACGTG 57.017 40.909 12.28 12.28 35.62 4.49
2278 5033 3.185594 TGAACTAATAAGTGTGCACGTGC 59.814 43.478 33.11 33.11 37.54 5.34
2279 5034 2.761559 ACTAATAAGTGTGCACGTGCA 58.238 42.857 37.86 37.86 41.10 4.57
2280 5035 3.562141 AACTAATAAGTGTGCACGTGCAA 59.438 39.130 42.04 27.84 43.95 4.08
2281 5036 4.553938 AACTAATAAGTGTGCACGTGCAAC 60.554 41.667 42.04 35.35 43.95 4.17
2282 5037 6.932164 AACTAATAAGTGTGCACGTGCAACA 61.932 40.000 42.04 34.57 43.95 3.33
2283 5038 8.842213 AACTAATAAGTGTGCACGTGCAACAC 62.842 42.308 39.30 39.30 43.95 3.32
2296 5051 3.696898 GTGCAACACACGTTTATTTGGA 58.303 40.909 0.00 0.00 40.07 3.53
2297 5052 4.295051 GTGCAACACACGTTTATTTGGAT 58.705 39.130 0.00 0.00 40.07 3.41
2298 5053 4.742659 GTGCAACACACGTTTATTTGGATT 59.257 37.500 0.00 0.00 40.07 3.01
2299 5054 5.915758 GTGCAACACACGTTTATTTGGATTA 59.084 36.000 0.00 0.00 40.07 1.75
2300 5055 6.418226 GTGCAACACACGTTTATTTGGATTAA 59.582 34.615 0.00 0.00 40.07 1.40
2301 5056 6.418226 TGCAACACACGTTTATTTGGATTAAC 59.582 34.615 0.00 0.00 31.13 2.01
2302 5057 6.418226 GCAACACACGTTTATTTGGATTAACA 59.582 34.615 0.00 0.00 31.13 2.41
2303 5058 7.566148 GCAACACACGTTTATTTGGATTAACAC 60.566 37.037 0.00 0.00 31.13 3.32
2304 5059 7.028926 ACACACGTTTATTTGGATTAACACA 57.971 32.000 0.00 0.00 0.00 3.72
2305 5060 7.653647 ACACACGTTTATTTGGATTAACACAT 58.346 30.769 0.00 0.00 0.00 3.21
2306 5061 8.138712 ACACACGTTTATTTGGATTAACACATT 58.861 29.630 0.00 0.00 0.00 2.71
2307 5062 9.613957 CACACGTTTATTTGGATTAACACATTA 57.386 29.630 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.946329 TCTGTAGACAATCTCGAGAGGC 59.054 50.000 21.52 10.45 0.00 4.70
9 10 4.545823 GTCTGTAGACAATCTCGAGAGG 57.454 50.000 21.52 17.11 44.18 3.69
38 40 4.650734 TCATGAAATCAGTGCACCTGTAA 58.349 39.130 14.63 0.00 42.19 2.41
49 51 4.523173 AGCCAATAGCCATCATGAAATCAG 59.477 41.667 0.00 0.00 45.47 2.90
238 2557 5.787062 CGATCACATCATCATTCGTTATTGC 59.213 40.000 0.00 0.00 0.00 3.56
551 2964 5.290493 ACAACATAGATAATGGCCGAGAA 57.710 39.130 0.00 0.00 40.16 2.87
581 2994 7.652507 GGTTAAGTCGCTAGCAGAAATTATAGT 59.347 37.037 16.45 0.00 0.00 2.12
600 3013 2.460027 ACCGCTTCCCAGGTTAAGT 58.540 52.632 1.72 0.00 37.49 2.24
605 3018 2.430367 GTCAACCGCTTCCCAGGT 59.570 61.111 0.00 0.00 43.68 4.00
655 3068 4.773117 GTCGAGACGGCGGGTGAC 62.773 72.222 13.24 9.89 0.00 3.67
697 3116 0.606604 TCCTTGCTACGGAACCTCAC 59.393 55.000 0.00 0.00 0.00 3.51
698 3117 0.606604 GTCCTTGCTACGGAACCTCA 59.393 55.000 0.00 0.00 31.13 3.86
700 3119 1.590147 CGTCCTTGCTACGGAACCT 59.410 57.895 0.00 0.00 36.71 3.50
726 3148 2.180769 CGTGCGCTGCCTGTAGTA 59.819 61.111 9.73 0.00 0.00 1.82
727 3149 3.633094 CTCGTGCGCTGCCTGTAGT 62.633 63.158 9.73 0.00 0.00 2.73
728 3150 2.882777 CTCGTGCGCTGCCTGTAG 60.883 66.667 9.73 0.00 0.00 2.74
759 3184 3.026630 TGGAAGATTAGATTAGCCGCG 57.973 47.619 0.00 0.00 0.00 6.46
808 3248 4.142752 GGTTTTTATAGGACTTGCACGGTC 60.143 45.833 9.72 9.72 0.00 4.79
809 3249 3.754850 GGTTTTTATAGGACTTGCACGGT 59.245 43.478 0.00 0.00 0.00 4.83
851 3296 2.512745 GTGTGTGTGGTGCGGTGA 60.513 61.111 0.00 0.00 0.00 4.02
914 3386 3.366396 TGGTGGTCCTTAGAGATGAGAC 58.634 50.000 0.00 0.00 34.23 3.36
919 3391 3.301274 GCTACTGGTGGTCCTTAGAGAT 58.699 50.000 0.00 0.00 34.23 2.75
920 3392 2.042569 TGCTACTGGTGGTCCTTAGAGA 59.957 50.000 0.00 0.00 34.23 3.10
925 3397 1.127567 TGCTGCTACTGGTGGTCCTT 61.128 55.000 0.00 0.00 34.23 3.36
928 3400 1.743252 GCTGCTGCTACTGGTGGTC 60.743 63.158 8.53 0.00 36.03 4.02
984 3457 1.226542 CATGATGGTGGCAGCTCCT 59.773 57.895 18.53 2.43 35.26 3.69
1483 4006 3.754850 TGTACGTGTAGTGTAGATGTGCT 59.245 43.478 0.00 0.00 0.00 4.40
1490 4013 5.050227 GCCTCTCTATGTACGTGTAGTGTAG 60.050 48.000 0.00 0.00 0.00 2.74
1534 4065 1.271102 CTAATCGCCTACTGCCTCTCC 59.729 57.143 0.00 0.00 36.24 3.71
1548 4085 4.969484 ACTAATGGGGCCTAAACTAATCG 58.031 43.478 0.84 0.00 0.00 3.34
1550 4087 7.257053 CCATAGACTAATGGGGCCTAAACTAAT 60.257 40.741 0.84 0.00 42.41 1.73
1551 4088 6.043938 CCATAGACTAATGGGGCCTAAACTAA 59.956 42.308 0.84 0.00 42.41 2.24
1552 4089 5.546499 CCATAGACTAATGGGGCCTAAACTA 59.454 44.000 0.84 0.00 42.41 2.24
1553 4090 4.351111 CCATAGACTAATGGGGCCTAAACT 59.649 45.833 0.84 0.00 42.41 2.66
1554 4091 4.652822 CCATAGACTAATGGGGCCTAAAC 58.347 47.826 0.84 0.00 42.41 2.01
1555 4092 4.993705 CCATAGACTAATGGGGCCTAAA 57.006 45.455 0.84 0.00 42.41 1.85
1564 4101 9.896645 ATAAGCAATATGGACCATAGACTAATG 57.103 33.333 18.90 11.36 29.42 1.90
1576 4113 5.393962 GCCGAAATCATAAGCAATATGGAC 58.606 41.667 9.00 0.73 41.53 4.02
1726 4477 1.202952 AGTACATGTCCCCCGCAAAAA 60.203 47.619 0.00 0.00 0.00 1.94
1727 4478 0.402504 AGTACATGTCCCCCGCAAAA 59.597 50.000 0.00 0.00 0.00 2.44
1728 4479 1.065998 GTAGTACATGTCCCCCGCAAA 60.066 52.381 0.00 0.00 0.00 3.68
1729 4480 0.538118 GTAGTACATGTCCCCCGCAA 59.462 55.000 0.00 0.00 0.00 4.85
1730 4481 0.615261 TGTAGTACATGTCCCCCGCA 60.615 55.000 0.00 0.00 0.00 5.69
1731 4482 0.538118 TTGTAGTACATGTCCCCCGC 59.462 55.000 0.00 0.00 0.00 6.13
1732 4483 1.829222 AGTTGTAGTACATGTCCCCCG 59.171 52.381 0.00 0.00 0.00 5.73
1733 4484 3.262405 TCAAGTTGTAGTACATGTCCCCC 59.738 47.826 0.00 0.00 0.00 5.40
1734 4485 4.546829 TCAAGTTGTAGTACATGTCCCC 57.453 45.455 0.00 0.00 0.00 4.81
1735 4486 5.812642 CAGATCAAGTTGTAGTACATGTCCC 59.187 44.000 0.00 0.00 0.00 4.46
1736 4487 5.292101 GCAGATCAAGTTGTAGTACATGTCC 59.708 44.000 0.00 0.00 0.00 4.02
1737 4488 6.102663 AGCAGATCAAGTTGTAGTACATGTC 58.897 40.000 0.00 0.00 0.00 3.06
1738 4489 6.042638 AGCAGATCAAGTTGTAGTACATGT 57.957 37.500 2.69 2.69 0.00 3.21
1739 4490 6.036517 GGAAGCAGATCAAGTTGTAGTACATG 59.963 42.308 3.28 0.00 0.00 3.21
1740 4491 6.109359 GGAAGCAGATCAAGTTGTAGTACAT 58.891 40.000 3.28 0.00 0.00 2.29
1741 4492 5.479306 GGAAGCAGATCAAGTTGTAGTACA 58.521 41.667 0.00 0.00 0.00 2.90
1742 4493 4.870991 GGGAAGCAGATCAAGTTGTAGTAC 59.129 45.833 2.11 0.00 0.00 2.73
1766 4517 7.492669 TGGATGTTTGCAAAAAGAAAAACGATA 59.507 29.630 14.67 0.00 35.71 2.92
1783 4534 7.278424 ACTTGTTCAATTTGAGTTGGATGTTTG 59.722 33.333 0.00 0.00 0.00 2.93
1793 4544 6.697019 CGAATTCCAACTTGTTCAATTTGAGT 59.303 34.615 14.23 0.00 0.00 3.41
1811 4562 1.268743 GCATTAGCACTGCCGAATTCC 60.269 52.381 0.00 0.00 41.58 3.01
1845 4596 1.519408 TTTCGAACTTGGGCTACTGC 58.481 50.000 0.00 0.00 38.76 4.40
1846 4597 3.537793 GTTTTCGAACTTGGGCTACTG 57.462 47.619 0.00 0.00 0.00 2.74
1909 4660 3.612860 CGATTGGAAGAACAGGTACGAAG 59.387 47.826 0.00 0.00 0.00 3.79
1910 4661 3.581755 CGATTGGAAGAACAGGTACGAA 58.418 45.455 0.00 0.00 0.00 3.85
1911 4662 2.673043 GCGATTGGAAGAACAGGTACGA 60.673 50.000 0.00 0.00 0.00 3.43
1912 4663 1.659098 GCGATTGGAAGAACAGGTACG 59.341 52.381 0.00 0.00 0.00 3.67
1913 4664 2.973945 AGCGATTGGAAGAACAGGTAC 58.026 47.619 0.00 0.00 0.00 3.34
1914 4665 4.499188 CGATAGCGATTGGAAGAACAGGTA 60.499 45.833 0.00 0.00 40.82 3.08
1915 4666 3.738281 CGATAGCGATTGGAAGAACAGGT 60.738 47.826 0.00 0.00 40.82 4.00
1916 4667 2.797156 CGATAGCGATTGGAAGAACAGG 59.203 50.000 0.00 0.00 40.82 4.00
1932 4683 0.528470 GGGCTGGCTACTAGCGATAG 59.472 60.000 6.08 6.08 43.62 2.08
1933 4684 0.178973 TGGGCTGGCTACTAGCGATA 60.179 55.000 0.00 0.00 43.62 2.92
1934 4685 1.048724 TTGGGCTGGCTACTAGCGAT 61.049 55.000 0.00 0.00 43.62 4.58
1935 4686 1.676678 CTTGGGCTGGCTACTAGCGA 61.677 60.000 0.00 0.00 43.62 4.93
1936 4687 1.227380 CTTGGGCTGGCTACTAGCG 60.227 63.158 0.00 0.00 43.62 4.26
1937 4688 1.120530 TACTTGGGCTGGCTACTAGC 58.879 55.000 0.00 0.00 41.46 3.42
1938 4689 8.713708 ATATATATACTTGGGCTGGCTACTAG 57.286 38.462 0.00 0.00 0.00 2.57
1939 4690 9.144298 GAATATATATACTTGGGCTGGCTACTA 57.856 37.037 0.00 0.00 0.00 1.82
1940 4691 7.071321 GGAATATATATACTTGGGCTGGCTACT 59.929 40.741 0.00 0.00 0.00 2.57
1941 4692 7.071321 AGGAATATATATACTTGGGCTGGCTAC 59.929 40.741 0.00 0.00 0.00 3.58
1942 4693 7.139619 AGGAATATATATACTTGGGCTGGCTA 58.860 38.462 0.00 0.00 0.00 3.93
1943 4694 5.973124 AGGAATATATATACTTGGGCTGGCT 59.027 40.000 0.00 0.00 0.00 4.75
1944 4695 6.253946 AGGAATATATATACTTGGGCTGGC 57.746 41.667 0.00 0.00 0.00 4.85
1945 4696 8.319057 TGTAGGAATATATATACTTGGGCTGG 57.681 38.462 0.00 0.00 0.00 4.85
1976 4727 4.737855 TTCTTTAGTGCTAGCCAGTAGG 57.262 45.455 13.29 0.00 31.27 3.18
1977 4728 6.091441 CAGTTTTCTTTAGTGCTAGCCAGTAG 59.909 42.308 13.29 3.56 31.27 2.57
1978 4729 5.932303 CAGTTTTCTTTAGTGCTAGCCAGTA 59.068 40.000 13.29 5.03 0.00 2.74
1979 4730 4.757149 CAGTTTTCTTTAGTGCTAGCCAGT 59.243 41.667 13.29 6.03 0.00 4.00
1980 4731 4.757149 ACAGTTTTCTTTAGTGCTAGCCAG 59.243 41.667 13.29 0.52 0.00 4.85
1981 4732 4.714632 ACAGTTTTCTTTAGTGCTAGCCA 58.285 39.130 13.29 0.00 0.00 4.75
1982 4733 4.755123 TGACAGTTTTCTTTAGTGCTAGCC 59.245 41.667 13.29 3.49 0.00 3.93
1983 4734 5.924475 TGACAGTTTTCTTTAGTGCTAGC 57.076 39.130 8.10 8.10 0.00 3.42
1984 4735 7.301054 CCAATGACAGTTTTCTTTAGTGCTAG 58.699 38.462 0.00 0.00 0.00 3.42
1985 4736 6.206634 CCCAATGACAGTTTTCTTTAGTGCTA 59.793 38.462 0.00 0.00 0.00 3.49
1986 4737 5.010012 CCCAATGACAGTTTTCTTTAGTGCT 59.990 40.000 0.00 0.00 0.00 4.40
1987 4738 5.222631 CCCAATGACAGTTTTCTTTAGTGC 58.777 41.667 0.00 0.00 0.00 4.40
1988 4739 5.222631 GCCCAATGACAGTTTTCTTTAGTG 58.777 41.667 0.00 0.00 0.00 2.74
1989 4740 4.280929 GGCCCAATGACAGTTTTCTTTAGT 59.719 41.667 0.00 0.00 0.00 2.24
1990 4741 4.524328 AGGCCCAATGACAGTTTTCTTTAG 59.476 41.667 0.00 0.00 0.00 1.85
1991 4742 4.280677 CAGGCCCAATGACAGTTTTCTTTA 59.719 41.667 0.00 0.00 0.00 1.85
1992 4743 3.070015 CAGGCCCAATGACAGTTTTCTTT 59.930 43.478 0.00 0.00 0.00 2.52
1993 4744 2.629617 CAGGCCCAATGACAGTTTTCTT 59.370 45.455 0.00 0.00 0.00 2.52
1994 4745 2.158475 TCAGGCCCAATGACAGTTTTCT 60.158 45.455 0.00 0.00 0.00 2.52
1995 4746 2.029918 GTCAGGCCCAATGACAGTTTTC 60.030 50.000 16.58 0.00 45.18 2.29
1996 4747 1.963515 GTCAGGCCCAATGACAGTTTT 59.036 47.619 16.58 0.00 45.18 2.43
1997 4748 1.620822 GTCAGGCCCAATGACAGTTT 58.379 50.000 16.58 0.00 45.18 2.66
1998 4749 3.346426 GTCAGGCCCAATGACAGTT 57.654 52.632 16.58 0.00 45.18 3.16
2009 4760 3.344515 CTTTTACTACTTGGGTCAGGCC 58.655 50.000 0.00 0.00 0.00 5.19
2010 4761 2.747989 GCTTTTACTACTTGGGTCAGGC 59.252 50.000 0.00 0.00 0.00 4.85
2011 4762 4.287766 AGCTTTTACTACTTGGGTCAGG 57.712 45.455 0.00 0.00 0.00 3.86
2012 4763 5.176592 GGTAGCTTTTACTACTTGGGTCAG 58.823 45.833 0.00 0.00 41.88 3.51
2013 4764 4.594062 TGGTAGCTTTTACTACTTGGGTCA 59.406 41.667 0.00 0.00 41.88 4.02
2014 4765 5.156608 TGGTAGCTTTTACTACTTGGGTC 57.843 43.478 0.00 0.00 41.88 4.46
2015 4766 5.308759 TCTTGGTAGCTTTTACTACTTGGGT 59.691 40.000 0.00 0.00 41.88 4.51
2016 4767 5.801380 TCTTGGTAGCTTTTACTACTTGGG 58.199 41.667 0.00 0.00 41.88 4.12
2017 4768 7.824779 AGATTCTTGGTAGCTTTTACTACTTGG 59.175 37.037 0.00 0.00 41.88 3.61
2018 4769 8.779354 AGATTCTTGGTAGCTTTTACTACTTG 57.221 34.615 0.00 0.00 41.88 3.16
2019 4770 9.794719 AAAGATTCTTGGTAGCTTTTACTACTT 57.205 29.630 0.00 0.00 41.88 2.24
2020 4771 9.220767 CAAAGATTCTTGGTAGCTTTTACTACT 57.779 33.333 0.00 0.00 41.88 2.57
2021 4772 9.216117 TCAAAGATTCTTGGTAGCTTTTACTAC 57.784 33.333 0.00 0.00 41.54 2.73
2022 4773 9.436957 CTCAAAGATTCTTGGTAGCTTTTACTA 57.563 33.333 0.00 0.00 0.00 1.82
2023 4774 8.157476 TCTCAAAGATTCTTGGTAGCTTTTACT 58.843 33.333 0.00 0.00 0.00 2.24
2024 4775 8.324163 TCTCAAAGATTCTTGGTAGCTTTTAC 57.676 34.615 0.00 0.00 0.00 2.01
2025 4776 7.119846 GCTCTCAAAGATTCTTGGTAGCTTTTA 59.880 37.037 16.86 0.00 34.41 1.52
2026 4777 6.072230 GCTCTCAAAGATTCTTGGTAGCTTTT 60.072 38.462 16.86 0.00 34.41 2.27
2027 4778 5.414144 GCTCTCAAAGATTCTTGGTAGCTTT 59.586 40.000 16.86 0.00 34.41 3.51
2028 4779 4.940654 GCTCTCAAAGATTCTTGGTAGCTT 59.059 41.667 16.86 0.00 34.41 3.74
2029 4780 4.512484 GCTCTCAAAGATTCTTGGTAGCT 58.488 43.478 16.86 0.00 34.41 3.32
2030 4781 3.308323 CGCTCTCAAAGATTCTTGGTAGC 59.692 47.826 15.30 15.30 34.14 3.58
2031 4782 3.868077 CCGCTCTCAAAGATTCTTGGTAG 59.132 47.826 0.00 1.34 0.00 3.18
2032 4783 3.513912 TCCGCTCTCAAAGATTCTTGGTA 59.486 43.478 0.00 0.00 0.00 3.25
2033 4784 2.303022 TCCGCTCTCAAAGATTCTTGGT 59.697 45.455 0.00 0.00 0.00 3.67
2034 4785 2.977914 TCCGCTCTCAAAGATTCTTGG 58.022 47.619 0.00 0.00 0.00 3.61
2035 4786 4.033817 GTGATCCGCTCTCAAAGATTCTTG 59.966 45.833 0.00 0.00 0.00 3.02
2036 4787 4.187694 GTGATCCGCTCTCAAAGATTCTT 58.812 43.478 0.00 0.00 0.00 2.52
2037 4788 3.736433 CGTGATCCGCTCTCAAAGATTCT 60.736 47.826 0.00 0.00 0.00 2.40
2038 4789 2.537625 CGTGATCCGCTCTCAAAGATTC 59.462 50.000 0.00 0.00 0.00 2.52
2039 4790 2.544685 CGTGATCCGCTCTCAAAGATT 58.455 47.619 0.00 0.00 0.00 2.40
2040 4791 2.215907 CGTGATCCGCTCTCAAAGAT 57.784 50.000 0.00 0.00 0.00 2.40
2041 4792 3.721625 CGTGATCCGCTCTCAAAGA 57.278 52.632 0.00 0.00 0.00 2.52
2051 4802 4.873129 CGTCAGGGGCGTGATCCG 62.873 72.222 0.00 0.00 40.40 4.18
2052 4803 3.432051 CTCGTCAGGGGCGTGATCC 62.432 68.421 0.00 0.00 0.00 3.36
2053 4804 2.105128 CTCGTCAGGGGCGTGATC 59.895 66.667 0.00 0.00 0.00 2.92
2054 4805 4.148825 GCTCGTCAGGGGCGTGAT 62.149 66.667 0.00 0.00 0.00 3.06
2090 4841 3.983494 ATCTGCGGCGATCTCGGG 61.983 66.667 12.98 0.00 40.23 5.14
2091 4842 2.732468 CATCTGCGGCGATCTCGG 60.732 66.667 12.98 0.00 40.23 4.63
2092 4843 1.728778 CTCATCTGCGGCGATCTCG 60.729 63.158 12.98 0.00 43.27 4.04
2093 4844 2.021039 GCTCATCTGCGGCGATCTC 61.021 63.158 12.98 0.00 0.00 2.75
2094 4845 2.025767 AAGCTCATCTGCGGCGATCT 62.026 55.000 12.98 0.00 38.13 2.75
2095 4846 1.593750 AAGCTCATCTGCGGCGATC 60.594 57.895 12.98 0.00 38.13 3.69
2096 4847 1.886313 CAAGCTCATCTGCGGCGAT 60.886 57.895 12.98 0.00 38.13 4.58
2097 4848 2.510012 CAAGCTCATCTGCGGCGA 60.510 61.111 12.98 0.00 38.13 5.54
2098 4849 4.233635 GCAAGCTCATCTGCGGCG 62.234 66.667 0.51 0.51 38.13 6.46
2099 4850 2.821688 GAGCAAGCTCATCTGCGGC 61.822 63.158 16.69 0.00 42.31 6.53
2100 4851 2.523507 CGAGCAAGCTCATCTGCGG 61.524 63.158 20.75 0.21 42.86 5.69
2101 4852 1.481019 CTCGAGCAAGCTCATCTGCG 61.481 60.000 20.75 7.46 42.86 5.18
2102 4853 1.152989 CCTCGAGCAAGCTCATCTGC 61.153 60.000 20.75 0.00 42.86 4.26
2103 4854 0.459078 TCCTCGAGCAAGCTCATCTG 59.541 55.000 20.75 5.72 42.86 2.90
2104 4855 0.746063 CTCCTCGAGCAAGCTCATCT 59.254 55.000 20.75 0.00 42.86 2.90
2105 4856 0.459489 ACTCCTCGAGCAAGCTCATC 59.541 55.000 20.75 0.00 42.86 2.92
2106 4857 0.459489 GACTCCTCGAGCAAGCTCAT 59.541 55.000 20.75 0.13 42.86 2.90
2107 4858 1.886585 GACTCCTCGAGCAAGCTCA 59.113 57.895 20.75 8.13 42.86 4.26
2108 4859 1.226547 CGACTCCTCGAGCAAGCTC 60.227 63.158 6.99 11.94 43.06 4.09
2109 4860 1.675972 TCGACTCCTCGAGCAAGCT 60.676 57.895 6.99 0.00 44.14 3.74
2110 4861 2.878429 TCGACTCCTCGAGCAAGC 59.122 61.111 6.99 2.76 44.14 4.01
2116 4867 0.976590 TCTCCTCCTCGACTCCTCGA 60.977 60.000 0.00 0.00 46.85 4.04
2117 4868 0.812412 GTCTCCTCCTCGACTCCTCG 60.812 65.000 0.00 0.00 41.65 4.63
2118 4869 0.464916 GGTCTCCTCCTCGACTCCTC 60.465 65.000 0.00 0.00 0.00 3.71
2119 4870 1.610873 GGTCTCCTCCTCGACTCCT 59.389 63.158 0.00 0.00 0.00 3.69
2120 4871 1.454295 GGGTCTCCTCCTCGACTCC 60.454 68.421 0.00 0.00 0.00 3.85
2135 4886 0.546122 TGTCACTTTGCAGTCAGGGT 59.454 50.000 0.00 0.00 0.00 4.34
2146 4897 0.108329 CCGTCGGGCTATGTCACTTT 60.108 55.000 2.34 0.00 0.00 2.66
2239 4994 1.503294 TCAAATAGACGTGCGTTGCA 58.497 45.000 0.00 0.00 35.60 4.08
2240 4995 2.096417 AGTTCAAATAGACGTGCGTTGC 60.096 45.455 0.00 0.00 0.00 4.17
2241 4996 3.788434 AGTTCAAATAGACGTGCGTTG 57.212 42.857 0.00 0.00 0.00 4.10
2242 4997 7.330208 ACTTATTAGTTCAAATAGACGTGCGTT 59.670 33.333 0.00 0.00 0.00 4.84
2243 4998 6.810182 ACTTATTAGTTCAAATAGACGTGCGT 59.190 34.615 0.00 0.00 0.00 5.24
2244 4999 7.111139 CACTTATTAGTTCAAATAGACGTGCG 58.889 38.462 0.00 0.00 30.26 5.34
2245 5000 7.898309 CACACTTATTAGTTCAAATAGACGTGC 59.102 37.037 0.00 0.00 30.26 5.34
2246 5001 7.898309 GCACACTTATTAGTTCAAATAGACGTG 59.102 37.037 0.00 0.00 30.26 4.49
2247 5002 7.601130 TGCACACTTATTAGTTCAAATAGACGT 59.399 33.333 0.00 0.00 30.26 4.34
2248 5003 7.898309 GTGCACACTTATTAGTTCAAATAGACG 59.102 37.037 13.17 0.00 30.26 4.18
2249 5004 7.898309 CGTGCACACTTATTAGTTCAAATAGAC 59.102 37.037 18.64 0.00 30.26 2.59
2250 5005 7.601130 ACGTGCACACTTATTAGTTCAAATAGA 59.399 33.333 18.64 0.00 30.26 1.98
2251 5006 7.688167 CACGTGCACACTTATTAGTTCAAATAG 59.312 37.037 18.64 0.00 30.26 1.73
2252 5007 7.514805 CACGTGCACACTTATTAGTTCAAATA 58.485 34.615 18.64 0.00 30.26 1.40
2253 5008 6.370593 CACGTGCACACTTATTAGTTCAAAT 58.629 36.000 18.64 0.00 30.26 2.32
2254 5009 5.743467 CACGTGCACACTTATTAGTTCAAA 58.257 37.500 18.64 0.00 30.26 2.69
2255 5010 4.319190 GCACGTGCACACTTATTAGTTCAA 60.319 41.667 34.52 0.00 41.59 2.69
2256 5011 3.185594 GCACGTGCACACTTATTAGTTCA 59.814 43.478 34.52 0.00 41.59 3.18
2257 5012 3.732943 GCACGTGCACACTTATTAGTTC 58.267 45.455 34.52 0.00 41.59 3.01
2258 5013 3.806316 GCACGTGCACACTTATTAGTT 57.194 42.857 34.52 0.00 41.59 2.24
2275 5030 3.696898 TCCAAATAAACGTGTGTTGCAC 58.303 40.909 0.00 0.00 44.36 4.57
2276 5031 4.576216 ATCCAAATAAACGTGTGTTGCA 57.424 36.364 0.00 0.00 38.62 4.08
2277 5032 6.418226 TGTTAATCCAAATAAACGTGTGTTGC 59.582 34.615 0.00 0.00 38.62 4.17
2278 5033 7.432545 TGTGTTAATCCAAATAAACGTGTGTTG 59.567 33.333 0.00 0.00 38.62 3.33
2279 5034 7.481642 TGTGTTAATCCAAATAAACGTGTGTT 58.518 30.769 0.00 0.00 40.98 3.32
2280 5035 7.028926 TGTGTTAATCCAAATAAACGTGTGT 57.971 32.000 0.00 0.00 0.00 3.72
2281 5036 8.514136 AATGTGTTAATCCAAATAAACGTGTG 57.486 30.769 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.