Multiple sequence alignment - TraesCS1D01G410300

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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 TraesCS1D01G410300 chr1D 100.000 4619 0 0 1 4619 471987347 471982729 0.000000e+00 8530.0
1 TraesCS1D01G410300 chrUn 95.984 996 35 5 916 1907 315063434 315064428 0.000000e+00 1613.0
2 TraesCS1D01G410300 chrUn 96.559 930 29 3 981 1907 298990426 298989497 0.000000e+00 1537.0
3 TraesCS1D01G410300 chrUn 96.559 930 29 3 981 1907 298995246 298994317 0.000000e+00 1537.0
4 TraesCS1D01G410300 chrUn 96.559 930 29 3 981 1907 310653182 310654111 0.000000e+00 1537.0
5 TraesCS1D01G410300 chrUn 90.287 1081 51 15 2753 3783 298987618 298986542 0.000000e+00 1365.0
6 TraesCS1D01G410300 chrUn 90.194 1081 52 15 2753 3783 298992438 298991362 0.000000e+00 1360.0
7 TraesCS1D01G410300 chrUn 90.009 1081 54 13 2753 3783 1390079 1391155 0.000000e+00 1349.0
8 TraesCS1D01G410300 chrUn 89.926 1082 54 13 2753 3783 369184776 369183699 0.000000e+00 1343.0
9 TraesCS1D01G410300 chrUn 90.169 1068 51 13 2766 3783 1467881 1466818 0.000000e+00 1341.0
10 TraesCS1D01G410300 chrUn 89.824 1081 56 14 2753 3783 328231170 328230094 0.000000e+00 1338.0
11 TraesCS1D01G410300 chrUn 90.945 1016 47 13 2753 3727 310655990 310657001 0.000000e+00 1325.0
12 TraesCS1D01G410300 chrUn 95.932 762 29 2 916 1675 464151463 464152224 0.000000e+00 1234.0
13 TraesCS1D01G410300 chrUn 95.187 748 32 4 1163 1907 398882288 398881542 0.000000e+00 1179.0
14 TraesCS1D01G410300 chrUn 92.188 832 33 11 2984 3783 296512753 296511922 0.000000e+00 1147.0
15 TraesCS1D01G410300 chrUn 94.312 756 29 7 1155 1907 315040532 315041276 0.000000e+00 1146.0
16 TraesCS1D01G410300 chrUn 94.422 753 28 7 1158 1907 356741132 356740391 0.000000e+00 1146.0
17 TraesCS1D01G410300 chrUn 92.634 801 48 6 1908 2699 315041575 315042373 0.000000e+00 1142.0
18 TraesCS1D01G410300 chrUn 91.067 806 53 10 1908 2699 328232496 328231696 0.000000e+00 1072.0
19 TraesCS1D01G410300 chrUn 90.447 806 58 9 1908 2699 298988946 298988146 0.000000e+00 1044.0
20 TraesCS1D01G410300 chrUn 90.447 806 58 9 1908 2699 298993766 298992966 0.000000e+00 1044.0
21 TraesCS1D01G410300 chrUn 90.447 806 58 9 1908 2699 310654662 310655462 0.000000e+00 1044.0
22 TraesCS1D01G410300 chrUn 90.335 807 56 11 1908 2699 321653651 321654450 0.000000e+00 1038.0
23 TraesCS1D01G410300 chrUn 90.335 807 56 11 1908 2699 346464195 346464994 0.000000e+00 1038.0
24 TraesCS1D01G410300 chrUn 92.777 623 38 3 2082 2699 374689896 374690516 0.000000e+00 894.0
25 TraesCS1D01G410300 chrUn 91.956 634 29 6 3172 3783 442099272 442099905 0.000000e+00 869.0
26 TraesCS1D01G410300 chrUn 88.404 733 48 14 429 1160 315039554 315040250 0.000000e+00 848.0
27 TraesCS1D01G410300 chrUn 88.404 733 48 14 429 1160 356742113 356741417 0.000000e+00 848.0
28 TraesCS1D01G410300 chrUn 88.907 604 51 9 85 673 413404180 413404782 0.000000e+00 730.0
29 TraesCS1D01G410300 chrUn 88.723 603 54 7 85 673 285708036 285708638 0.000000e+00 725.0
30 TraesCS1D01G410300 chrUn 88.723 603 54 7 85 673 285739862 285740464 0.000000e+00 725.0
31 TraesCS1D01G410300 chrUn 88.723 603 54 7 85 673 294687807 294688409 0.000000e+00 725.0
32 TraesCS1D01G410300 chrUn 88.391 603 56 7 85 673 259633327 259633929 0.000000e+00 713.0
33 TraesCS1D01G410300 chrUn 88.391 603 56 7 85 673 330125882 330125280 0.000000e+00 713.0
34 TraesCS1D01G410300 chrUn 88.079 604 56 9 85 673 1425882 1425280 0.000000e+00 702.0
35 TraesCS1D01G410300 chrUn 88.303 607 28 11 2753 3320 321654978 321655580 0.000000e+00 688.0
36 TraesCS1D01G410300 chrUn 88.303 607 28 11 2753 3320 346465522 346466124 0.000000e+00 688.0
37 TraesCS1D01G410300 chrUn 88.138 607 29 11 2753 3320 374691044 374691646 0.000000e+00 682.0
38 TraesCS1D01G410300 chrUn 88.364 550 50 9 138 673 315061564 315062113 0.000000e+00 649.0
39 TraesCS1D01G410300 chrUn 89.971 349 23 2 91 427 471674988 471675336 1.530000e-119 440.0
40 TraesCS1D01G410300 chrUn 83.051 354 38 13 609 962 1424315 1424646 7.510000e-78 302.0
41 TraesCS1D01G410300 chrUn 83.285 347 38 14 616 962 1477476 1477150 7.510000e-78 302.0
42 TraesCS1D01G410300 chrUn 83.285 347 38 10 616 962 298249502 298249176 7.510000e-78 302.0
43 TraesCS1D01G410300 chrUn 83.285 347 38 11 616 962 350685848 350685522 7.510000e-78 302.0
44 TraesCS1D01G410300 chrUn 83.051 354 38 13 609 962 350735061 350735392 7.510000e-78 302.0
45 TraesCS1D01G410300 chrUn 83.285 347 38 11 616 962 447040883 447040557 7.510000e-78 302.0
46 TraesCS1D01G410300 chrUn 82.768 354 39 13 609 962 259631884 259632215 3.490000e-76 296.0
47 TraesCS1D01G410300 chrUn 82.768 354 39 12 609 962 285706579 285706910 3.490000e-76 296.0
48 TraesCS1D01G410300 chrUn 82.768 354 39 12 609 962 285738405 285738736 3.490000e-76 296.0
49 TraesCS1D01G410300 chrUn 82.768 354 39 12 609 962 294686350 294686681 3.490000e-76 296.0
50 TraesCS1D01G410300 chrUn 81.557 244 10 2 2757 2982 315042896 315043122 7.950000e-38 169.0
51 TraesCS1D01G410300 chrUn 81.557 244 10 2 2757 2982 431445139 431445365 7.950000e-38 169.0
52 TraesCS1D01G410300 chrUn 98.438 64 1 0 916 979 333214439 333214502 3.780000e-21 113.0
53 TraesCS1D01G410300 chrUn 98.438 64 1 0 916 979 468001649 468001586 3.780000e-21 113.0
54 TraesCS1D01G410300 chrUn 92.308 78 4 2 9 84 104147820 104147897 4.890000e-20 110.0
55 TraesCS1D01G410300 chrUn 96.610 59 2 0 4559 4617 1466824 1466766 1.060000e-16 99.0
56 TraesCS1D01G410300 chrUn 96.610 59 2 0 4559 4617 298986548 298986490 1.060000e-16 99.0
57 TraesCS1D01G410300 chrUn 96.610 59 2 0 4559 4617 298991368 298991310 1.060000e-16 99.0
58 TraesCS1D01G410300 chrUn 96.610 59 2 0 4559 4617 369183705 369183647 1.060000e-16 99.0
59 TraesCS1D01G410300 chrUn 94.915 59 3 0 4559 4617 1391149 1391207 4.920000e-15 93.5
60 TraesCS1D01G410300 chrUn 93.333 60 3 1 4559 4617 328230100 328230041 2.290000e-13 87.9
61 TraesCS1D01G410300 chrUn 100.000 29 0 0 1 29 103374184 103374212 2.000000e-03 54.7
62 TraesCS1D01G410300 chrUn 94.286 35 2 0 4585 4619 296511905 296511871 2.000000e-03 54.7
63 TraesCS1D01G410300 chr1B 89.851 1074 42 13 2760 3783 656099222 656098166 0.000000e+00 1317.0
64 TraesCS1D01G410300 chr1B 88.920 1083 71 21 91 1160 656102917 656101871 0.000000e+00 1290.0
65 TraesCS1D01G410300 chr1B 92.759 801 47 6 1908 2699 656100546 656099748 0.000000e+00 1147.0
66 TraesCS1D01G410300 chr1B 94.422 753 28 7 1158 1907 656101586 656100845 0.000000e+00 1146.0
67 TraesCS1D01G410300 chr1B 100.000 29 0 0 1 29 572930425 572930453 2.000000e-03 54.7
68 TraesCS1D01G410300 chr1B 94.286 35 2 0 4585 4619 656098149 656098115 2.000000e-03 54.7
69 TraesCS1D01G410300 chr7D 96.901 355 10 1 4203 4557 625198699 625198346 1.110000e-165 593.0
70 TraesCS1D01G410300 chr7D 95.556 360 10 3 4203 4557 100616279 100615921 5.180000e-159 571.0
71 TraesCS1D01G410300 chr7D 90.476 441 26 6 3783 4207 625199188 625198748 6.710000e-158 568.0
72 TraesCS1D01G410300 chr7D 90.000 440 28 6 3784 4207 100616763 100616324 5.220000e-154 555.0
73 TraesCS1D01G410300 chr7D 98.551 69 1 0 26 94 60027562 60027494 6.280000e-24 122.0
74 TraesCS1D01G410300 chr3D 90.661 439 25 6 3784 4207 448626779 448626342 1.860000e-158 569.0
75 TraesCS1D01G410300 chr3D 97.354 189 4 1 4203 4391 448626293 448626106 2.070000e-83 320.0
76 TraesCS1D01G410300 chr3D 95.364 151 6 1 4407 4557 448626120 448625971 5.970000e-59 239.0
77 TraesCS1D01G410300 chr3D 91.954 87 5 1 1 85 564377988 564377902 2.260000e-23 121.0
78 TraesCS1D01G410300 chr2A 93.291 313 19 2 4246 4557 132265472 132265783 1.170000e-125 460.0
79 TraesCS1D01G410300 chr2A 87.901 405 28 7 3824 4207 132264969 132265373 1.510000e-124 457.0
80 TraesCS1D01G410300 chr2D 87.662 154 16 2 4407 4559 106365347 106365196 4.750000e-40 176.0
81 TraesCS1D01G410300 chr2D 98.485 66 0 1 26 90 604310169 604310234 1.050000e-21 115.0
82 TraesCS1D01G410300 chr2D 86.813 91 8 3 4407 4496 34563746 34563659 1.060000e-16 99.0
83 TraesCS1D01G410300 chr5A 88.276 145 13 4 4415 4558 685434420 685434279 2.210000e-38 171.0
84 TraesCS1D01G410300 chr5D 87.943 141 17 0 4417 4557 510920367 510920227 2.860000e-37 167.0
85 TraesCS1D01G410300 chr5D 98.462 65 1 0 26 90 532784095 532784159 1.050000e-21 115.0
86 TraesCS1D01G410300 chr5D 90.741 54 5 0 1141 1194 79118451 79118504 6.410000e-09 73.1
87 TraesCS1D01G410300 chr5B 86.364 154 17 3 4407 4559 22044169 22044319 1.030000e-36 165.0
88 TraesCS1D01G410300 chr6D 100.000 63 0 0 26 88 11559331 11559393 2.920000e-22 117.0
89 TraesCS1D01G410300 chr6D 100.000 63 0 0 26 88 443462786 443462848 2.920000e-22 117.0
90 TraesCS1D01G410300 chr6D 89.286 84 9 0 1 84 12557563 12557646 6.320000e-19 106.0
91 TraesCS1D01G410300 chr6D 100.000 29 0 0 1 29 9718703 9718675 2.000000e-03 54.7
92 TraesCS1D01G410300 chr4D 95.775 71 1 2 28 97 482796422 482796353 3.780000e-21 113.0
93 TraesCS1D01G410300 chr6B 100.000 34 0 0 8 41 92954783 92954816 3.860000e-06 63.9
94 TraesCS1D01G410300 chr6B 100.000 29 0 0 1 29 67176038 67176010 2.000000e-03 54.7
95 TraesCS1D01G410300 chr6B 96.875 32 1 0 1 32 459149078 459149047 2.000000e-03 54.7


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 TraesCS1D01G410300 chr1D 471982729 471987347 4618 True 8530.000000 8530 100.000000 1 4619 1 chr1D.!!$R1 4618
1 TraesCS1D01G410300 chrUn 310653182 310657001 3819 False 1302.000000 1537 92.650333 981 3727 3 chrUn.!!$F16 2746
2 TraesCS1D01G410300 chrUn 464151463 464152224 761 False 1234.000000 1234 95.932000 916 1675 1 chrUn.!!$F9 759
3 TraesCS1D01G410300 chrUn 398881542 398882288 746 True 1179.000000 1179 95.187000 1163 1907 1 chrUn.!!$R6 744
4 TraesCS1D01G410300 chrUn 315061564 315064428 2864 False 1131.000000 1613 92.174000 138 1907 2 chrUn.!!$F18 1769
5 TraesCS1D01G410300 chrUn 298986490 298995246 8756 True 1010.625000 1537 93.464125 981 4617 8 chrUn.!!$R11 3636
6 TraesCS1D01G410300 chrUn 356740391 356742113 1722 True 997.000000 1146 91.413000 429 1907 2 chrUn.!!$R13 1478
7 TraesCS1D01G410300 chrUn 442099272 442099905 633 False 869.000000 869 91.956000 3172 3783 1 chrUn.!!$F8 611
8 TraesCS1D01G410300 chrUn 321653651 321655580 1929 False 863.000000 1038 89.319000 1908 3320 2 chrUn.!!$F19 1412
9 TraesCS1D01G410300 chrUn 346464195 346466124 1929 False 863.000000 1038 89.319000 1908 3320 2 chrUn.!!$F20 1412
10 TraesCS1D01G410300 chrUn 328230041 328232496 2455 True 832.633333 1338 91.408000 1908 4617 3 chrUn.!!$R12 2709
11 TraesCS1D01G410300 chrUn 315039554 315043122 3568 False 826.250000 1146 89.226750 429 2982 4 chrUn.!!$F17 2553
12 TraesCS1D01G410300 chrUn 374689896 374691646 1750 False 788.000000 894 90.457500 2082 3320 2 chrUn.!!$F21 1238
13 TraesCS1D01G410300 chrUn 413404180 413404782 602 False 730.000000 730 88.907000 85 673 1 chrUn.!!$F6 588
14 TraesCS1D01G410300 chrUn 1390079 1391207 1128 False 721.250000 1349 92.462000 2753 4617 2 chrUn.!!$F11 1864
15 TraesCS1D01G410300 chrUn 369183647 369184776 1129 True 721.000000 1343 93.268000 2753 4617 2 chrUn.!!$R14 1864
16 TraesCS1D01G410300 chrUn 1466766 1467881 1115 True 720.000000 1341 93.389500 2766 4617 2 chrUn.!!$R9 1851
17 TraesCS1D01G410300 chrUn 330125280 330125882 602 True 713.000000 713 88.391000 85 673 1 chrUn.!!$R4 588
18 TraesCS1D01G410300 chrUn 1425280 1425882 602 True 702.000000 702 88.079000 85 673 1 chrUn.!!$R1 588
19 TraesCS1D01G410300 chrUn 296511871 296512753 882 True 600.850000 1147 93.237000 2984 4619 2 chrUn.!!$R10 1635
20 TraesCS1D01G410300 chrUn 285706579 285708638 2059 False 510.500000 725 85.745500 85 962 2 chrUn.!!$F13 877
21 TraesCS1D01G410300 chrUn 285738405 285740464 2059 False 510.500000 725 85.745500 85 962 2 chrUn.!!$F14 877
22 TraesCS1D01G410300 chrUn 294686350 294688409 2059 False 510.500000 725 85.745500 85 962 2 chrUn.!!$F15 877
23 TraesCS1D01G410300 chrUn 259631884 259633929 2045 False 504.500000 713 85.579500 85 962 2 chrUn.!!$F12 877
24 TraesCS1D01G410300 chr1B 656098115 656102917 4802 True 990.940000 1317 92.047600 91 4619 5 chr1B.!!$R1 4528
25 TraesCS1D01G410300 chr7D 625198346 625199188 842 True 580.500000 593 93.688500 3783 4557 2 chr7D.!!$R3 774
26 TraesCS1D01G410300 chr7D 100615921 100616763 842 True 563.000000 571 92.778000 3784 4557 2 chr7D.!!$R2 773
27 TraesCS1D01G410300 chr3D 448625971 448626779 808 True 376.000000 569 94.459667 3784 4557 3 chr3D.!!$R2 773
28 TraesCS1D01G410300 chr2A 132264969 132265783 814 False 458.500000 460 90.596000 3824 4557 2 chr2A.!!$F1 733

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
58 59 0.033503 AAAGGCCCTTATGAACCGGG 60.034 55.0 6.32 0.00 41.06 5.73 F
1756 9373 0.387239 GCCGTGTTAAAGCTGCTTGG 60.387 55.0 16.73 12.36 0.00 3.61 F
2411 10603 0.030908 CGAAGGTACCGGATGAGCTC 59.969 60.0 9.46 6.82 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1999 10177 0.041238 AGCCCTAGTGAGTGGTAGCA 59.959 55.0 0.00 0.0 0.00 3.49 R
2712 10904 0.036164 TGTAAGCATGTCGTGGCCTT 59.964 50.0 3.32 0.0 0.00 4.35 R
3985 12721 0.397187 CATCTCATGAGGGGAGCAGG 59.603 60.0 22.42 0.0 32.38 4.85 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
18 19 3.040965 TCGTGTAAGAACCGGGACT 57.959 52.632 6.32 0.73 0.00 3.85
19 20 2.198827 TCGTGTAAGAACCGGGACTA 57.801 50.000 6.32 0.00 0.00 2.59
20 21 2.513753 TCGTGTAAGAACCGGGACTAA 58.486 47.619 6.32 0.00 0.00 2.24
21 22 2.890311 TCGTGTAAGAACCGGGACTAAA 59.110 45.455 6.32 0.00 0.00 1.85
22 23 3.057315 TCGTGTAAGAACCGGGACTAAAG 60.057 47.826 6.32 0.00 0.00 1.85
23 24 3.593096 GTGTAAGAACCGGGACTAAAGG 58.407 50.000 6.32 0.00 0.00 3.11
25 26 0.327259 AAGAACCGGGACTAAAGGGC 59.673 55.000 6.32 0.00 0.00 5.19
26 27 1.077930 GAACCGGGACTAAAGGGCC 60.078 63.158 6.32 0.00 44.23 5.80
32 33 3.571748 GGACTAAAGGGCCAGAACC 57.428 57.895 6.18 0.67 44.40 3.62
33 34 0.392595 GGACTAAAGGGCCAGAACCG 60.393 60.000 6.18 0.00 44.40 4.44
34 35 0.392595 GACTAAAGGGCCAGAACCGG 60.393 60.000 6.18 0.00 0.00 5.28
35 36 1.077716 CTAAAGGGCCAGAACCGGG 60.078 63.158 6.32 0.00 0.00 5.73
36 37 1.539372 TAAAGGGCCAGAACCGGGA 60.539 57.895 6.32 0.00 0.00 5.14
37 38 1.844544 TAAAGGGCCAGAACCGGGAC 61.845 60.000 6.32 0.00 0.00 4.46
38 39 4.658786 AGGGCCAGAACCGGGACT 62.659 66.667 6.32 0.73 32.41 3.85
39 40 2.686106 GGGCCAGAACCGGGACTA 60.686 66.667 6.32 0.00 32.41 2.59
41 42 1.681076 GGCCAGAACCGGGACTAAA 59.319 57.895 6.32 0.00 0.00 1.85
42 43 0.392595 GGCCAGAACCGGGACTAAAG 60.393 60.000 6.32 0.00 0.00 1.85
43 44 0.392595 GCCAGAACCGGGACTAAAGG 60.393 60.000 6.32 3.64 0.00 3.11
44 45 0.392595 CCAGAACCGGGACTAAAGGC 60.393 60.000 6.32 0.00 0.00 4.35
45 46 0.392595 CAGAACCGGGACTAAAGGCC 60.393 60.000 6.32 0.00 0.00 5.19
46 47 1.077930 GAACCGGGACTAAAGGCCC 60.078 63.158 11.29 11.29 41.11 5.80
47 48 1.540617 AACCGGGACTAAAGGCCCT 60.541 57.895 18.97 0.00 42.40 5.19
48 49 1.138228 AACCGGGACTAAAGGCCCTT 61.138 55.000 18.97 4.45 42.40 3.95
49 50 0.252835 ACCGGGACTAAAGGCCCTTA 60.253 55.000 18.97 0.00 42.40 2.69
51 52 1.202770 CCGGGACTAAAGGCCCTTATG 60.203 57.143 18.97 3.00 42.40 1.90
52 53 1.766496 CGGGACTAAAGGCCCTTATGA 59.234 52.381 18.97 0.00 42.40 2.15
53 54 2.171870 CGGGACTAAAGGCCCTTATGAA 59.828 50.000 18.97 0.00 42.40 2.57
55 56 3.552875 GGACTAAAGGCCCTTATGAACC 58.447 50.000 0.00 0.00 0.00 3.62
56 57 3.203716 GACTAAAGGCCCTTATGAACCG 58.796 50.000 0.00 0.00 0.00 4.44
58 59 0.033503 AAAGGCCCTTATGAACCGGG 60.034 55.000 6.32 0.00 41.06 5.73
59 60 1.933307 AAGGCCCTTATGAACCGGGG 61.933 60.000 6.32 0.00 41.64 5.73
60 61 2.686572 GGCCCTTATGAACCGGGGT 61.687 63.158 6.32 0.00 40.86 4.95
62 63 0.547553 GCCCTTATGAACCGGGGTAA 59.452 55.000 6.32 0.00 40.86 2.85
63 64 1.064537 GCCCTTATGAACCGGGGTAAA 60.065 52.381 6.32 0.00 40.86 2.01
65 66 3.284617 CCCTTATGAACCGGGGTAAAAG 58.715 50.000 6.32 3.70 34.22 2.27
66 67 2.686405 CCTTATGAACCGGGGTAAAAGC 59.314 50.000 6.32 0.00 0.00 3.51
76 77 2.320681 GGGTAAAAGCCCCTTTTCCT 57.679 50.000 6.25 0.00 41.88 3.36
77 78 3.461378 GGGTAAAAGCCCCTTTTCCTA 57.539 47.619 6.25 0.00 41.88 2.94
78 79 3.094572 GGGTAAAAGCCCCTTTTCCTAC 58.905 50.000 6.25 0.98 41.88 3.18
79 80 3.245514 GGGTAAAAGCCCCTTTTCCTACT 60.246 47.826 6.25 0.00 41.88 2.57
80 81 4.018141 GGGTAAAAGCCCCTTTTCCTACTA 60.018 45.833 6.25 0.00 41.88 1.82
81 82 5.191426 GGTAAAAGCCCCTTTTCCTACTAG 58.809 45.833 6.25 0.00 41.88 2.57
82 83 5.280882 GGTAAAAGCCCCTTTTCCTACTAGT 60.281 44.000 0.00 0.00 41.88 2.57
83 84 4.302559 AAAGCCCCTTTTCCTACTAGTG 57.697 45.455 5.39 0.00 28.27 2.74
147 1521 7.966339 TTATGGCTTAGTAAGTAGGAAGACA 57.034 36.000 11.51 0.00 41.07 3.41
187 1561 4.555262 ACCACAATTGCTTAATTCGGTTG 58.445 39.130 5.05 0.00 0.00 3.77
208 1582 0.609957 TCATAGGTCCGTGGACGTGT 60.610 55.000 21.20 13.63 45.41 4.49
256 1630 5.804944 TTTGGATCCTCATTTTTCTTGCA 57.195 34.783 14.23 0.00 0.00 4.08
259 1633 5.540911 TGGATCCTCATTTTTCTTGCAAAC 58.459 37.500 14.23 0.00 0.00 2.93
292 1677 3.429822 CCTTATATTGTCCGGTCACGTGT 60.430 47.826 16.51 0.00 38.78 4.49
304 1689 5.474189 TCCGGTCACGTGTATATGATTGATA 59.526 40.000 16.51 0.00 38.78 2.15
407 1792 3.605749 CTGGACACGCCCGGACATT 62.606 63.158 0.73 0.00 34.45 2.71
408 1793 2.359478 GGACACGCCCGGACATTT 60.359 61.111 0.73 0.00 0.00 2.32
410 1795 2.359478 ACACGCCCGGACATTTCC 60.359 61.111 0.73 0.00 38.77 3.13
417 1805 1.143073 GCCCGGACATTTCCTATCCTT 59.857 52.381 0.73 0.00 40.23 3.36
433 1821 6.730507 TCCTATCCTTCACATATATGGCTTGA 59.269 38.462 16.96 8.76 0.00 3.02
447 1835 2.699846 TGGCTTGAATATGGGGATTTGC 59.300 45.455 0.00 0.00 0.00 3.68
491 1879 2.747446 CAAAGTCAGGATTACGGTTGGG 59.253 50.000 0.00 0.00 0.00 4.12
522 1910 3.415457 ACTTCTTTCTCCTGCCTGAAG 57.585 47.619 0.00 0.00 37.50 3.02
859 3366 9.917887 AAAAATTGTCCTCATCTTCATCTATCT 57.082 29.630 0.00 0.00 0.00 1.98
860 3367 9.917887 AAAATTGTCCTCATCTTCATCTATCTT 57.082 29.630 0.00 0.00 0.00 2.40
861 3368 9.558396 AAATTGTCCTCATCTTCATCTATCTTC 57.442 33.333 0.00 0.00 0.00 2.87
864 3371 7.065504 TGTCCTCATCTTCATCTATCTTCAGA 58.934 38.462 0.00 0.00 0.00 3.27
865 3372 7.562821 TGTCCTCATCTTCATCTATCTTCAGAA 59.437 37.037 0.00 0.00 0.00 3.02
877 3384 9.322773 CATCTATCTTCAGAAATATGTGTGTGT 57.677 33.333 0.00 0.00 0.00 3.72
878 3385 8.707938 TCTATCTTCAGAAATATGTGTGTGTG 57.292 34.615 0.00 0.00 0.00 3.82
879 3386 8.314021 TCTATCTTCAGAAATATGTGTGTGTGT 58.686 33.333 0.00 0.00 0.00 3.72
880 3387 6.544038 TCTTCAGAAATATGTGTGTGTGTG 57.456 37.500 0.00 0.00 0.00 3.82
881 3388 6.054941 TCTTCAGAAATATGTGTGTGTGTGT 58.945 36.000 0.00 0.00 0.00 3.72
882 3389 5.671742 TCAGAAATATGTGTGTGTGTGTG 57.328 39.130 0.00 0.00 0.00 3.82
883 3390 5.122519 TCAGAAATATGTGTGTGTGTGTGT 58.877 37.500 0.00 0.00 0.00 3.72
884 3391 5.007528 TCAGAAATATGTGTGTGTGTGTGTG 59.992 40.000 0.00 0.00 0.00 3.82
885 3392 4.881273 AGAAATATGTGTGTGTGTGTGTGT 59.119 37.500 0.00 0.00 0.00 3.72
886 3393 4.550577 AATATGTGTGTGTGTGTGTGTG 57.449 40.909 0.00 0.00 0.00 3.82
887 3394 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
888 3395 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
889 3396 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
890 3397 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
891 3398 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
892 3399 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
893 3400 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
894 3401 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
895 3402 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
896 3403 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
897 3404 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
898 3405 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
902 3409 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
904 3411 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
909 3416 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57
983 3490 3.450817 TCCTCACAAGAAGTCACAACTCA 59.549 43.478 0.00 0.00 33.48 3.41
1301 8917 1.001764 CATGCTTGAGACCAGGCCA 60.002 57.895 5.01 0.00 43.84 5.36
1361 8977 2.679342 GGCCAGGAGCACCATGGTA 61.679 63.158 19.28 0.00 46.50 3.25
1544 9160 1.699730 TCAACCTCGTCTTCAGGTCA 58.300 50.000 0.00 0.00 44.03 4.02
1748 9365 4.527564 CTCAAGTGAAAGCCGTGTTAAAG 58.472 43.478 0.00 0.00 0.00 1.85
1756 9373 0.387239 GCCGTGTTAAAGCTGCTTGG 60.387 55.000 16.73 12.36 0.00 3.61
1901 9521 8.152023 AGAAACCAGAGGAATGTAAACTCTAT 57.848 34.615 0.00 0.00 39.44 1.98
1932 10110 8.359642 TGGAATATTGGTTGTTCAAAGAAAGAG 58.640 33.333 0.00 0.00 0.00 2.85
1933 10111 8.576442 GGAATATTGGTTGTTCAAAGAAAGAGA 58.424 33.333 0.00 0.00 0.00 3.10
1965 10143 3.385755 GGGATCAAGTGCATTAGCCAATT 59.614 43.478 0.00 0.00 41.13 2.32
1974 10152 9.669353 CAAGTGCATTAGCCAATTACTATTTAG 57.331 33.333 0.00 0.00 41.13 1.85
1977 10155 6.208599 TGCATTAGCCAATTACTATTTAGCCC 59.791 38.462 0.00 0.00 41.13 5.19
1991 10169 2.566529 GCCCGGTGCTAAAGTTGC 59.433 61.111 0.00 0.00 36.87 4.17
1999 10177 1.681264 GTGCTAAAGTTGCCACTGGTT 59.319 47.619 0.00 0.00 31.60 3.67
2042 10220 2.806608 TCAGTTCAGTTACCGTGGTC 57.193 50.000 0.00 0.00 0.00 4.02
2049 10227 0.974383 AGTTACCGTGGTCTTGGGAG 59.026 55.000 0.00 0.00 0.00 4.30
2050 10228 0.683412 GTTACCGTGGTCTTGGGAGT 59.317 55.000 0.00 0.00 0.00 3.85
2051 10229 1.895131 GTTACCGTGGTCTTGGGAGTA 59.105 52.381 0.00 0.00 0.00 2.59
2052 10230 1.549203 TACCGTGGTCTTGGGAGTAC 58.451 55.000 0.00 0.00 0.00 2.73
2054 10232 0.902531 CCGTGGTCTTGGGAGTACAT 59.097 55.000 0.00 0.00 0.00 2.29
2055 10233 1.405526 CCGTGGTCTTGGGAGTACATG 60.406 57.143 0.00 0.00 0.00 3.21
2166 10354 5.363005 AGGTATATGTCTTTTCTGCCGTAGT 59.637 40.000 0.00 0.00 0.00 2.73
2169 10357 7.707893 GGTATATGTCTTTTCTGCCGTAGTTTA 59.292 37.037 0.00 0.00 0.00 2.01
2174 10362 5.006941 GTCTTTTCTGCCGTAGTTTACACAA 59.993 40.000 0.00 0.00 0.00 3.33
2411 10603 0.030908 CGAAGGTACCGGATGAGCTC 59.969 60.000 9.46 6.82 0.00 4.09
2415 10607 0.671251 GGTACCGGATGAGCTCTCAG 59.329 60.000 16.19 10.27 43.61 3.35
2444 10636 5.129320 TGCTTACCTGAATGAAGAGAGCATA 59.871 40.000 0.00 0.00 0.00 3.14
2691 10883 2.224042 TGCTCTATAATGTGCAGACCCG 60.224 50.000 0.00 0.00 33.38 5.28
2699 10891 0.323302 TGTGCAGACCCGATGCTAAA 59.677 50.000 0.00 0.00 44.17 1.85
2700 10892 1.271108 TGTGCAGACCCGATGCTAAAA 60.271 47.619 0.00 0.00 44.17 1.52
2701 10893 1.810151 GTGCAGACCCGATGCTAAAAA 59.190 47.619 0.00 0.00 44.17 1.94
2702 10894 2.423538 GTGCAGACCCGATGCTAAAAAT 59.576 45.455 0.00 0.00 44.17 1.82
2703 10895 3.625764 GTGCAGACCCGATGCTAAAAATA 59.374 43.478 0.00 0.00 44.17 1.40
2705 10897 4.702612 TGCAGACCCGATGCTAAAAATAAA 59.297 37.500 0.00 0.00 44.17 1.40
2709 10901 7.591426 GCAGACCCGATGCTAAAAATAAAATAG 59.409 37.037 0.00 0.00 40.59 1.73
2710 10902 7.591426 CAGACCCGATGCTAAAAATAAAATAGC 59.409 37.037 0.00 0.00 41.84 2.97
2712 10904 8.685838 ACCCGATGCTAAAAATAAAATAGCTA 57.314 30.769 0.00 0.00 41.97 3.32
2713 10905 9.127277 ACCCGATGCTAAAAATAAAATAGCTAA 57.873 29.630 0.00 0.00 41.97 3.09
2714 10906 9.612620 CCCGATGCTAAAAATAAAATAGCTAAG 57.387 33.333 0.00 0.00 41.97 2.18
2715 10907 9.612620 CCGATGCTAAAAATAAAATAGCTAAGG 57.387 33.333 0.00 2.88 41.97 2.69
2716 10908 9.118236 CGATGCTAAAAATAAAATAGCTAAGGC 57.882 33.333 0.00 0.00 41.97 4.35
2717 10909 9.411801 GATGCTAAAAATAAAATAGCTAAGGCC 57.588 33.333 0.00 0.00 41.97 5.19
2718 10910 8.299990 TGCTAAAAATAAAATAGCTAAGGCCA 57.700 30.769 5.01 0.00 41.97 5.36
2719 10911 8.194769 TGCTAAAAATAAAATAGCTAAGGCCAC 58.805 33.333 5.01 0.00 41.97 5.01
2721 10913 7.399245 AAAAATAAAATAGCTAAGGCCACGA 57.601 32.000 5.01 0.00 39.73 4.35
2722 10914 6.373186 AAATAAAATAGCTAAGGCCACGAC 57.627 37.500 5.01 0.00 39.73 4.34
2725 10917 2.533266 ATAGCTAAGGCCACGACATG 57.467 50.000 5.01 0.00 39.73 3.21
2729 11267 1.742411 GCTAAGGCCACGACATGCTTA 60.742 52.381 5.01 0.00 0.00 3.09
2732 11270 0.036164 AGGCCACGACATGCTTACAA 59.964 50.000 5.01 0.00 0.00 2.41
2733 11271 1.094785 GGCCACGACATGCTTACAAT 58.905 50.000 0.00 0.00 0.00 2.71
2736 11274 3.486875 GGCCACGACATGCTTACAATAAC 60.487 47.826 0.00 0.00 0.00 1.89
2739 11277 5.276868 GCCACGACATGCTTACAATAACTAG 60.277 44.000 0.00 0.00 0.00 2.57
2799 11471 3.577968 ATATATGGCCACCCTCTACCA 57.422 47.619 8.16 0.00 36.43 3.25
2831 11503 3.364267 CGATGATAACAATCGGCATGGTG 60.364 47.826 0.00 0.00 34.52 4.17
2844 11516 2.549992 GGCATGGTGGCTATAACGATGA 60.550 50.000 0.00 0.00 40.14 2.92
2897 11569 0.865769 GAGCACGAATTGGTGACGTT 59.134 50.000 22.97 6.01 40.38 3.99
3083 11773 3.319972 CCCATATGAATTGTTGGAGCCAG 59.680 47.826 3.65 0.00 0.00 4.85
3161 11851 8.333235 TCTAAAGTTATTGTGACCATGGGTATT 58.667 33.333 18.09 0.00 35.25 1.89
3162 11852 7.790782 AAAGTTATTGTGACCATGGGTATTT 57.209 32.000 18.09 0.00 35.25 1.40
3270 11982 0.772124 AGGGCCTTGTGGAGAAGGAA 60.772 55.000 0.00 0.00 44.87 3.36
3293 12005 2.708325 AGCTGGTCTCTTTCAACCTTCT 59.292 45.455 0.00 0.00 36.47 2.85
3294 12006 3.137360 AGCTGGTCTCTTTCAACCTTCTT 59.863 43.478 0.00 0.00 36.47 2.52
3399 12111 1.918262 TCAAGCTGGGATCCACAAGAT 59.082 47.619 15.23 3.54 38.17 2.40
3402 12114 2.133520 AGCTGGGATCCACAAGATGAT 58.866 47.619 15.23 0.00 34.42 2.45
3775 12498 3.434309 ACCAAGTACGCTAGAAACCCTA 58.566 45.455 0.00 0.00 0.00 3.53
3776 12499 3.194329 ACCAAGTACGCTAGAAACCCTAC 59.806 47.826 0.00 0.00 0.00 3.18
3777 12500 3.429960 CCAAGTACGCTAGAAACCCTACC 60.430 52.174 0.00 0.00 0.00 3.18
3778 12501 3.091633 AGTACGCTAGAAACCCTACCA 57.908 47.619 0.00 0.00 0.00 3.25
3779 12502 3.639952 AGTACGCTAGAAACCCTACCAT 58.360 45.455 0.00 0.00 0.00 3.55
3780 12503 4.028825 AGTACGCTAGAAACCCTACCATT 58.971 43.478 0.00 0.00 0.00 3.16
3781 12504 3.994931 ACGCTAGAAACCCTACCATTT 57.005 42.857 0.00 0.00 0.00 2.32
3823 12546 3.178046 TGGTACTCCCTAACAAGATGCA 58.822 45.455 0.00 0.00 0.00 3.96
3879 12603 7.202011 GCATGGGTATTCTAGACCTTTTCTCTA 60.202 40.741 0.00 0.00 37.13 2.43
3919 12643 7.831753 TGTTTTTATCCCATTCGAATTAAGCA 58.168 30.769 8.21 3.37 0.00 3.91
3939 12664 0.525455 CATTGTCCGCGACGATCTCA 60.525 55.000 8.23 0.00 34.75 3.27
3985 12721 1.821136 CTGGCTTTGTCTTCCCCATTC 59.179 52.381 0.00 0.00 0.00 2.67
4082 12818 9.778741 TCTATACACATGGATTCCTGTTAATTC 57.221 33.333 3.95 0.00 0.00 2.17
4122 12858 0.171455 GTACGAGGACTGTGCTCCTG 59.829 60.000 21.38 12.14 41.11 3.86
4177 12921 4.980805 GTCACCGGCCACTTCGCA 62.981 66.667 0.00 0.00 0.00 5.10
4488 13306 3.008049 AGGACTTGTGTTGGAGTACCATC 59.992 47.826 0.00 0.00 46.34 3.51
4503 13321 5.018809 AGTACCATCTAAGGTTAACCGTGA 58.981 41.667 21.65 18.35 43.08 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.198827 TAGTCCCGGTTCTTACACGA 57.801 50.000 0.00 0.00 0.00 4.35
1 2 3.248266 CTTTAGTCCCGGTTCTTACACG 58.752 50.000 0.00 0.00 0.00 4.49
2 3 3.593096 CCTTTAGTCCCGGTTCTTACAC 58.407 50.000 0.00 0.00 0.00 2.90
3 4 2.568509 CCCTTTAGTCCCGGTTCTTACA 59.431 50.000 0.00 0.00 0.00 2.41
4 5 2.679059 GCCCTTTAGTCCCGGTTCTTAC 60.679 54.545 0.00 0.00 0.00 2.34
5 6 1.556451 GCCCTTTAGTCCCGGTTCTTA 59.444 52.381 0.00 0.00 0.00 2.10
6 7 0.327259 GCCCTTTAGTCCCGGTTCTT 59.673 55.000 0.00 0.00 0.00 2.52
7 8 1.559965 GGCCCTTTAGTCCCGGTTCT 61.560 60.000 0.00 0.15 0.00 3.01
8 9 1.077930 GGCCCTTTAGTCCCGGTTC 60.078 63.158 0.00 0.00 0.00 3.62
9 10 1.848886 CTGGCCCTTTAGTCCCGGTT 61.849 60.000 0.00 0.00 0.00 4.44
10 11 2.204029 TGGCCCTTTAGTCCCGGT 60.204 61.111 0.00 0.00 0.00 5.28
11 12 1.559065 TTCTGGCCCTTTAGTCCCGG 61.559 60.000 0.00 0.00 0.00 5.73
12 13 0.392595 GTTCTGGCCCTTTAGTCCCG 60.393 60.000 0.00 0.00 0.00 5.14
13 14 0.034380 GGTTCTGGCCCTTTAGTCCC 60.034 60.000 0.00 0.00 0.00 4.46
14 15 0.392595 CGGTTCTGGCCCTTTAGTCC 60.393 60.000 0.00 0.00 0.00 3.85
15 16 0.392595 CCGGTTCTGGCCCTTTAGTC 60.393 60.000 0.00 0.00 0.00 2.59
16 17 1.683441 CCGGTTCTGGCCCTTTAGT 59.317 57.895 0.00 0.00 0.00 2.24
18 19 1.539372 TCCCGGTTCTGGCCCTTTA 60.539 57.895 0.00 0.00 0.00 1.85
19 20 2.856988 TCCCGGTTCTGGCCCTTT 60.857 61.111 0.00 0.00 0.00 3.11
20 21 2.758852 TAGTCCCGGTTCTGGCCCTT 62.759 60.000 0.00 0.00 0.00 3.95
21 22 2.758852 TTAGTCCCGGTTCTGGCCCT 62.759 60.000 0.00 0.00 0.00 5.19
22 23 1.844544 TTTAGTCCCGGTTCTGGCCC 61.845 60.000 0.00 0.00 0.00 5.80
23 24 0.392595 CTTTAGTCCCGGTTCTGGCC 60.393 60.000 0.00 0.00 0.00 5.36
25 26 0.392595 GCCTTTAGTCCCGGTTCTGG 60.393 60.000 0.00 0.00 0.00 3.86
26 27 0.392595 GGCCTTTAGTCCCGGTTCTG 60.393 60.000 0.00 0.00 0.00 3.02
28 29 1.077930 GGGCCTTTAGTCCCGGTTC 60.078 63.158 0.84 0.00 32.00 3.62
29 30 3.084304 GGGCCTTTAGTCCCGGTT 58.916 61.111 0.84 0.00 32.00 4.44
33 34 3.552875 GTTCATAAGGGCCTTTAGTCCC 58.447 50.000 26.29 4.98 42.94 4.46
34 35 3.552875 GGTTCATAAGGGCCTTTAGTCC 58.447 50.000 26.29 16.19 0.00 3.85
35 36 3.203716 CGGTTCATAAGGGCCTTTAGTC 58.796 50.000 26.29 11.28 0.00 2.59
36 37 2.092592 CCGGTTCATAAGGGCCTTTAGT 60.093 50.000 26.29 8.42 0.00 2.24
37 38 2.572290 CCGGTTCATAAGGGCCTTTAG 58.428 52.381 26.29 17.10 0.00 1.85
38 39 1.213430 CCCGGTTCATAAGGGCCTTTA 59.787 52.381 26.29 10.10 38.51 1.85
39 40 0.033503 CCCGGTTCATAAGGGCCTTT 60.034 55.000 26.29 5.08 38.51 3.11
41 42 2.383601 CCCCGGTTCATAAGGGCCT 61.384 63.158 0.00 0.00 43.74 5.19
42 43 1.347243 TACCCCGGTTCATAAGGGCC 61.347 60.000 0.00 0.00 43.96 5.80
43 44 0.547553 TTACCCCGGTTCATAAGGGC 59.452 55.000 0.00 0.00 43.96 5.19
44 45 3.284617 CTTTTACCCCGGTTCATAAGGG 58.715 50.000 0.00 0.00 45.75 3.95
45 46 2.686405 GCTTTTACCCCGGTTCATAAGG 59.314 50.000 0.00 0.00 0.00 2.69
46 47 2.686405 GGCTTTTACCCCGGTTCATAAG 59.314 50.000 0.00 0.00 0.00 1.73
47 48 2.621147 GGGCTTTTACCCCGGTTCATAA 60.621 50.000 0.00 0.00 45.00 1.90
48 49 1.064537 GGGCTTTTACCCCGGTTCATA 60.065 52.381 0.00 0.00 45.00 2.15
49 50 0.323999 GGGCTTTTACCCCGGTTCAT 60.324 55.000 0.00 0.00 45.00 2.57
51 52 4.007457 GGGCTTTTACCCCGGTTC 57.993 61.111 0.00 0.00 45.00 3.62
58 59 4.043608 AGTAGGAAAAGGGGCTTTTACC 57.956 45.455 0.00 0.00 43.22 2.85
59 60 5.646793 CACTAGTAGGAAAAGGGGCTTTTAC 59.353 44.000 1.45 0.00 42.72 2.01
60 61 5.311385 ACACTAGTAGGAAAAGGGGCTTTTA 59.689 40.000 1.45 0.00 42.72 1.52
62 63 3.656264 ACACTAGTAGGAAAAGGGGCTTT 59.344 43.478 1.45 0.00 34.94 3.51
63 64 3.257578 ACACTAGTAGGAAAAGGGGCTT 58.742 45.455 1.45 0.00 0.00 4.35
65 66 4.831674 TTACACTAGTAGGAAAAGGGGC 57.168 45.455 1.45 0.00 0.00 5.80
66 67 7.909485 TCTATTACACTAGTAGGAAAAGGGG 57.091 40.000 1.45 0.00 0.00 4.79
76 77 9.759473 ACCCTTACAAGTTCTATTACACTAGTA 57.241 33.333 0.00 0.00 0.00 1.82
77 78 8.661752 ACCCTTACAAGTTCTATTACACTAGT 57.338 34.615 0.00 0.00 0.00 2.57
78 79 9.939802 AAACCCTTACAAGTTCTATTACACTAG 57.060 33.333 0.00 0.00 0.00 2.57
79 80 9.715121 CAAACCCTTACAAGTTCTATTACACTA 57.285 33.333 0.00 0.00 0.00 2.74
80 81 8.215736 ACAAACCCTTACAAGTTCTATTACACT 58.784 33.333 0.00 0.00 0.00 3.55
81 82 8.387190 ACAAACCCTTACAAGTTCTATTACAC 57.613 34.615 0.00 0.00 0.00 2.90
82 83 8.842280 CAACAAACCCTTACAAGTTCTATTACA 58.158 33.333 0.00 0.00 0.00 2.41
83 84 7.806487 GCAACAAACCCTTACAAGTTCTATTAC 59.194 37.037 0.00 0.00 0.00 1.89
147 1521 4.347000 TGTGGTTGTAGAGGCTCTAAGTTT 59.653 41.667 25.07 1.05 29.58 2.66
187 1561 1.065928 CGTCCACGGACCTATGAGC 59.934 63.158 10.61 0.00 41.76 4.26
208 1582 0.535335 GTGCCAAGATACTGACCGGA 59.465 55.000 9.46 0.00 0.00 5.14
256 1630 6.311735 ACAATATAAGGACTGTGGTTGGTTT 58.688 36.000 0.00 0.00 0.00 3.27
259 1633 4.881850 GGACAATATAAGGACTGTGGTTGG 59.118 45.833 0.00 0.00 0.00 3.77
304 1689 9.853177 TTCTTTCTCTTTATTGTCTTCCTCTTT 57.147 29.630 0.00 0.00 0.00 2.52
356 1741 2.156098 GTAGGATTTTGCCAACCACGA 58.844 47.619 0.00 0.00 0.00 4.35
407 1792 7.237471 TCAAGCCATATATGTGAAGGATAGGAA 59.763 37.037 11.73 0.00 0.00 3.36
408 1793 6.730507 TCAAGCCATATATGTGAAGGATAGGA 59.269 38.462 11.73 0.00 0.00 2.94
417 1805 6.217280 TCCCCATATTCAAGCCATATATGTGA 59.783 38.462 11.73 6.24 32.76 3.58
433 1821 2.586425 CAGTCCGCAAATCCCCATATT 58.414 47.619 0.00 0.00 0.00 1.28
447 1835 2.456119 GGCATGTTCGAGCAGTCCG 61.456 63.158 8.26 0.00 0.00 4.79
491 1879 6.475727 GCAGGAGAAAGAAGTTTAAAAACCAC 59.524 38.462 2.02 0.00 39.71 4.16
522 1910 0.608640 ATCGGACAACCCAGTCACTC 59.391 55.000 0.00 0.00 40.29 3.51
636 2024 2.074230 TTTGCTGGCCTTTCTGCGTG 62.074 55.000 3.32 0.00 34.88 5.34
643 2031 2.095978 CTGCTGCTTTGCTGGCCTTT 62.096 55.000 3.32 0.00 0.00 3.11
837 3344 8.260099 TGAAGATAGATGAAGATGAGGACAAT 57.740 34.615 0.00 0.00 0.00 2.71
858 3365 6.138088 CACACACACACACATATTTCTGAAG 58.862 40.000 0.00 0.00 0.00 3.02
859 3366 5.588246 ACACACACACACACATATTTCTGAA 59.412 36.000 0.00 0.00 0.00 3.02
860 3367 5.007528 CACACACACACACACATATTTCTGA 59.992 40.000 0.00 0.00 0.00 3.27
861 3368 5.207033 CACACACACACACACATATTTCTG 58.793 41.667 0.00 0.00 0.00 3.02
864 3371 4.397730 ACACACACACACACACACATATTT 59.602 37.500 0.00 0.00 0.00 1.40
865 3372 3.944650 ACACACACACACACACACATATT 59.055 39.130 0.00 0.00 0.00 1.28
868 3375 1.468127 CACACACACACACACACACAT 59.532 47.619 0.00 0.00 0.00 3.21
869 3376 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
870 3377 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
871 3378 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
873 3380 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
874 3381 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
875 3382 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
877 3384 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
878 3385 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
879 3386 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
880 3387 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
881 3388 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
882 3389 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
883 3390 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
884 3391 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
885 3392 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
886 3393 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
887 3394 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
888 3395 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
889 3396 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
890 3397 0.454285 GCACACACACACACACACAC 60.454 55.000 0.00 0.00 0.00 3.82
891 3398 1.581727 GGCACACACACACACACACA 61.582 55.000 0.00 0.00 0.00 3.72
892 3399 1.136565 GGCACACACACACACACAC 59.863 57.895 0.00 0.00 0.00 3.82
893 3400 2.043405 GGGCACACACACACACACA 61.043 57.895 0.00 0.00 0.00 3.72
894 3401 2.770589 GGGGCACACACACACACAC 61.771 63.158 0.00 0.00 0.00 3.82
895 3402 2.439338 GGGGCACACACACACACA 60.439 61.111 0.00 0.00 0.00 3.72
896 3403 3.216292 GGGGGCACACACACACAC 61.216 66.667 0.00 0.00 0.00 3.82
897 3404 3.414136 GAGGGGGCACACACACACA 62.414 63.158 0.00 0.00 0.00 3.72
898 3405 1.764571 TAGAGGGGGCACACACACAC 61.765 60.000 0.00 0.00 0.00 3.82
902 3409 3.279434 CTTTTATAGAGGGGGCACACAC 58.721 50.000 0.00 0.00 0.00 3.82
904 3411 2.932261 CCTTTTATAGAGGGGGCACAC 58.068 52.381 0.00 0.00 0.00 3.82
983 3490 3.041211 TCCATGGCTAGCTATCACTTGT 58.959 45.455 15.72 0.00 0.00 3.16
1544 9160 1.220206 CTTCTGCAGCCGATCCAGT 59.780 57.895 9.47 0.00 0.00 4.00
1748 9365 3.758554 TGTTTAAGAGATTCCCAAGCAGC 59.241 43.478 0.00 0.00 0.00 5.25
1756 9373 8.099364 TCATGTGAGTTTGTTTAAGAGATTCC 57.901 34.615 0.00 0.00 0.00 3.01
1901 9521 9.083422 TCTTTGAACAACCAATATTCCACATTA 57.917 29.630 0.00 0.00 0.00 1.90
1922 10094 6.062095 TCCCTAAAAGTGGTCTCTTTCTTTG 58.938 40.000 0.00 0.00 36.75 2.77
1932 10110 3.440522 GCACTTGATCCCTAAAAGTGGTC 59.559 47.826 19.02 5.38 46.98 4.02
1933 10111 3.181434 TGCACTTGATCCCTAAAAGTGGT 60.181 43.478 19.02 0.00 46.98 4.16
1974 10152 2.566529 GCAACTTTAGCACCGGGC 59.433 61.111 6.32 6.61 45.30 6.13
1977 10155 0.238289 CAGTGGCAACTTTAGCACCG 59.762 55.000 0.00 0.00 32.98 4.94
1983 10161 2.065899 AGCAACCAGTGGCAACTTTA 57.934 45.000 9.78 0.00 32.98 1.85
1999 10177 0.041238 AGCCCTAGTGAGTGGTAGCA 59.959 55.000 0.00 0.00 0.00 3.49
2007 10185 4.586421 TGAACTGATATGAGCCCTAGTGAG 59.414 45.833 0.00 0.00 0.00 3.51
2011 10189 5.543507 AACTGAACTGATATGAGCCCTAG 57.456 43.478 0.00 0.00 0.00 3.02
2042 10220 5.182001 CCTTTTTCTCACATGTACTCCCAAG 59.818 44.000 0.00 0.00 0.00 3.61
2049 10227 9.959749 TTTGAAATACCTTTTTCTCACATGTAC 57.040 29.630 0.00 0.00 36.71 2.90
2051 10229 9.696917 GATTTGAAATACCTTTTTCTCACATGT 57.303 29.630 0.00 0.00 36.71 3.21
2052 10230 9.143631 GGATTTGAAATACCTTTTTCTCACATG 57.856 33.333 0.00 0.00 36.71 3.21
2054 10232 8.477419 AGGATTTGAAATACCTTTTTCTCACA 57.523 30.769 0.00 0.00 36.71 3.58
2055 10233 9.841880 GTAGGATTTGAAATACCTTTTTCTCAC 57.158 33.333 12.05 2.71 36.71 3.51
2100 10284 5.119125 CACACGTGCTATATGTCCATATGTG 59.881 44.000 17.22 10.19 35.71 3.21
2142 10330 4.755266 ACGGCAGAAAAGACATATACCT 57.245 40.909 0.00 0.00 0.00 3.08
2143 10331 5.598769 ACTACGGCAGAAAAGACATATACC 58.401 41.667 0.00 0.00 0.00 2.73
2144 10332 7.535489 AAACTACGGCAGAAAAGACATATAC 57.465 36.000 0.00 0.00 0.00 1.47
2146 10334 7.064253 GTGTAAACTACGGCAGAAAAGACATAT 59.936 37.037 0.00 0.00 0.00 1.78
2444 10636 4.384208 GGTGGAGTACTCTTGCCAATGTAT 60.384 45.833 21.88 0.00 31.18 2.29
2487 10679 5.104067 ACAGGTCCTTTTGGTACTCTTCTTT 60.104 40.000 0.00 0.00 41.38 2.52
2691 10883 9.411801 GGCCTTAGCTATTTTATTTTTAGCATC 57.588 33.333 0.00 0.00 40.60 3.91
2699 10891 5.883673 TGTCGTGGCCTTAGCTATTTTATTT 59.116 36.000 3.32 0.00 39.73 1.40
2700 10892 5.433526 TGTCGTGGCCTTAGCTATTTTATT 58.566 37.500 3.32 0.00 39.73 1.40
2701 10893 5.031066 TGTCGTGGCCTTAGCTATTTTAT 57.969 39.130 3.32 0.00 39.73 1.40
2702 10894 4.475051 TGTCGTGGCCTTAGCTATTTTA 57.525 40.909 3.32 0.00 39.73 1.52
2703 10895 3.343941 TGTCGTGGCCTTAGCTATTTT 57.656 42.857 3.32 0.00 39.73 1.82
2705 10897 2.838736 CATGTCGTGGCCTTAGCTATT 58.161 47.619 3.32 0.00 39.73 1.73
2709 10901 1.026718 AAGCATGTCGTGGCCTTAGC 61.027 55.000 3.32 0.00 38.76 3.09
2710 10902 1.933853 GTAAGCATGTCGTGGCCTTAG 59.066 52.381 3.32 0.00 0.00 2.18
2712 10904 0.036164 TGTAAGCATGTCGTGGCCTT 59.964 50.000 3.32 0.00 0.00 4.35
2713 10905 0.036164 TTGTAAGCATGTCGTGGCCT 59.964 50.000 3.32 0.00 0.00 5.19
2714 10906 1.094785 ATTGTAAGCATGTCGTGGCC 58.905 50.000 0.00 0.00 0.00 5.36
2715 10907 3.374058 AGTTATTGTAAGCATGTCGTGGC 59.626 43.478 0.00 0.00 0.00 5.01
2716 10908 6.040247 TCTAGTTATTGTAAGCATGTCGTGG 58.960 40.000 0.00 0.00 0.00 4.94
2717 10909 7.488150 TCTTCTAGTTATTGTAAGCATGTCGTG 59.512 37.037 0.00 0.00 0.00 4.35
2718 10910 7.544622 TCTTCTAGTTATTGTAAGCATGTCGT 58.455 34.615 0.00 0.00 0.00 4.34
2719 10911 7.987268 TCTTCTAGTTATTGTAAGCATGTCG 57.013 36.000 0.00 0.00 0.00 4.35
2799 11471 2.329267 TGTTATCATCGGGCCAGAGAT 58.671 47.619 12.27 15.35 0.00 2.75
2810 11482 3.058016 CCACCATGCCGATTGTTATCATC 60.058 47.826 0.00 0.00 0.00 2.92
2831 11503 5.980116 CAGCTACCATATCATCGTTATAGCC 59.020 44.000 0.00 0.00 35.48 3.93
2844 11516 2.867109 GTGGCCATCAGCTACCATAT 57.133 50.000 9.72 0.00 46.71 1.78
2897 11569 3.864243 ACTACGTGTCCAAGTTTCACAA 58.136 40.909 0.00 0.00 33.04 3.33
3083 11773 0.811219 TCAGCGATGTGTGCTATGCC 60.811 55.000 0.00 0.00 41.72 4.40
3154 11844 8.348354 AGTTTTCCTCCCAAATATAAATACCCA 58.652 33.333 0.00 0.00 0.00 4.51
3270 11982 3.584733 AGGTTGAAAGAGACCAGCTTT 57.415 42.857 0.00 0.00 38.42 3.51
3294 12006 2.163412 GTCCACAGATGGCGCATAAAAA 59.837 45.455 10.83 0.00 46.80 1.94
3325 12037 1.111116 TTGTTCTCCTCGACCACGGT 61.111 55.000 0.00 0.00 40.21 4.83
3399 12111 3.253230 GACATCATCGTGTGTGTCATCA 58.747 45.455 14.46 0.00 38.07 3.07
3402 12114 1.696988 CGACATCATCGTGTGTGTCA 58.303 50.000 16.92 0.00 46.25 3.58
3491 12203 2.677979 GCCTCGCCGAAGTGTTTCC 61.678 63.158 0.00 0.00 0.00 3.13
3775 12498 7.881751 GGGTACAGTAAAAACTCTCTAAATGGT 59.118 37.037 0.00 0.00 0.00 3.55
3776 12499 8.101419 AGGGTACAGTAAAAACTCTCTAAATGG 58.899 37.037 0.00 0.00 0.00 3.16
3777 12500 8.936864 CAGGGTACAGTAAAAACTCTCTAAATG 58.063 37.037 0.00 0.00 0.00 2.32
3778 12501 8.101419 CCAGGGTACAGTAAAAACTCTCTAAAT 58.899 37.037 0.00 0.00 0.00 1.40
3779 12502 7.071572 ACCAGGGTACAGTAAAAACTCTCTAAA 59.928 37.037 0.00 0.00 0.00 1.85
3780 12503 6.556116 ACCAGGGTACAGTAAAAACTCTCTAA 59.444 38.462 0.00 0.00 0.00 2.10
3781 12504 6.080009 ACCAGGGTACAGTAAAAACTCTCTA 58.920 40.000 0.00 0.00 0.00 2.43
3823 12546 7.349859 TGGATGGTTAGATTTATTGGTACTCCT 59.650 37.037 0.00 0.00 34.23 3.69
3908 12632 2.095213 GCGGACAATGTGCTTAATTCGA 59.905 45.455 2.94 0.00 0.00 3.71
3910 12634 2.095213 TCGCGGACAATGTGCTTAATTC 59.905 45.455 6.13 0.00 0.00 2.17
3919 12643 0.525668 GAGATCGTCGCGGACAATGT 60.526 55.000 6.13 0.00 32.09 2.71
3939 12664 1.826487 GGCCGGGAACAAACAGTGT 60.826 57.895 2.18 0.00 44.64 3.55
3965 12690 1.821136 GAATGGGGAAGACAAAGCCAG 59.179 52.381 0.00 0.00 0.00 4.85
3967 12692 1.186200 GGAATGGGGAAGACAAAGCC 58.814 55.000 0.00 0.00 0.00 4.35
3985 12721 0.397187 CATCTCATGAGGGGAGCAGG 59.603 60.000 22.42 0.00 32.38 4.85
4082 12818 1.202222 GGCGCAACTCAATTGATCTGG 60.202 52.381 10.83 0.00 41.23 3.86
4122 12858 1.519455 CCCTTCGCGGATGTCTGTC 60.519 63.158 6.13 0.00 33.16 3.51
4163 12901 2.186903 CTATGCGAAGTGGCCGGT 59.813 61.111 1.90 0.00 0.00 5.28
4488 13306 7.438459 CCATCTTAATCTCACGGTTAACCTTAG 59.562 40.741 22.12 15.33 0.00 2.18
4503 13321 4.600547 TGAGCCATCCATCCATCTTAATCT 59.399 41.667 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.