Multiple sequence alignment - TraesCS2B01G627900

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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 TraesCS2B01G627900 chr2B 100.000 3521 0 0 1 3521 799578238 799574718 0.000000e+00 6503.0
1 TraesCS2B01G627900 chr2B 87.273 330 41 1 2559 2887 799595660 799595331 3.320000e-100 375.0
2 TraesCS2B01G627900 chr2B 82.890 263 35 4 1337 1589 17464224 17463962 9.830000e-56 228.0
3 TraesCS2B01G627900 chr2B 88.800 125 13 1 2559 2682 799597536 799597412 6.090000e-33 152.0
4 TraesCS2B01G627900 chr2B 79.909 219 31 11 3303 3515 93004794 93004583 7.870000e-32 148.0
5 TraesCS2B01G627900 chr2B 84.177 158 19 6 2413 2568 799599386 799599233 7.870000e-32 148.0
6 TraesCS2B01G627900 chr2B 81.461 178 27 6 3330 3505 100349174 100349001 1.320000e-29 141.0
7 TraesCS2B01G627900 chr2B 96.250 80 3 0 666 745 799584308 799584229 7.930000e-27 132.0
8 TraesCS2B01G627900 chr2B 92.157 51 3 1 1627 1676 789132727 789132777 1.750000e-08 71.3
9 TraesCS2B01G627900 chr2B 97.368 38 1 0 1050 1087 799584070 799584033 8.160000e-07 65.8
10 TraesCS2B01G627900 chr2D 87.739 2455 176 55 466 2872 642099699 642102076 0.000000e+00 2750.0
11 TraesCS2B01G627900 chr2D 88.728 1863 143 30 1044 2872 598328706 598330535 0.000000e+00 2215.0
12 TraesCS2B01G627900 chr2D 93.782 579 17 4 466 1044 598328108 598328667 0.000000e+00 852.0
13 TraesCS2B01G627900 chr2D 86.848 479 59 3 2413 2890 642212778 642213253 1.860000e-147 532.0
14 TraesCS2B01G627900 chr2D 94.819 193 8 2 188 380 598327916 598328106 2.050000e-77 300.0
15 TraesCS2B01G627900 chr2D 93.782 193 10 2 188 380 642099507 642099697 4.450000e-74 289.0
16 TraesCS2B01G627900 chr2D 75.000 288 53 12 3234 3507 381866036 381866318 7.990000e-22 115.0
17 TraesCS2B01G627900 chr2A 89.716 1478 108 20 1044 2485 767017985 767019454 0.000000e+00 1847.0
18 TraesCS2B01G627900 chr2A 83.836 829 79 16 1678 2472 766981478 766982285 0.000000e+00 737.0
19 TraesCS2B01G627900 chr2A 89.840 561 30 7 488 1044 767017409 767017946 0.000000e+00 695.0
20 TraesCS2B01G627900 chr2A 90.965 487 37 6 3026 3508 767020239 767020722 0.000000e+00 649.0
21 TraesCS2B01G627900 chr2A 83.101 574 55 15 2472 3034 767019668 767020210 5.280000e-133 484.0
22 TraesCS2B01G627900 chr2A 82.178 606 55 24 2278 2872 767147005 767146442 4.110000e-129 472.0
23 TraesCS2B01G627900 chr2A 84.466 515 33 20 809 1296 766980989 766981483 6.880000e-127 464.0
24 TraesCS2B01G627900 chr2A 86.072 359 25 11 3170 3507 766983225 766983579 2.580000e-96 363.0
25 TraesCS2B01G627900 chr2A 91.429 245 20 1 2543 2786 766982321 766982565 5.630000e-88 335.0
26 TraesCS2B01G627900 chr2A 89.844 128 5 5 1182 1301 767147315 767147188 1.310000e-34 158.0
27 TraesCS2B01G627900 chr2A 78.750 160 12 5 1678 1815 767147200 767147041 1.740000e-13 87.9
28 TraesCS2B01G627900 chr3B 86.486 296 37 3 1385 1677 829275139 829274844 4.380000e-84 322.0
29 TraesCS2B01G627900 chr3B 84.000 100 7 9 3235 3331 818866246 818866153 1.740000e-13 87.9
30 TraesCS2B01G627900 chr7A 81.408 355 45 12 1337 1677 29834924 29834577 1.610000e-68 270.0
31 TraesCS2B01G627900 chr7A 91.579 95 6 2 379 472 108210425 108210518 2.850000e-26 130.0
32 TraesCS2B01G627900 chr7A 90.909 99 4 5 380 475 612025788 612025884 1.030000e-25 128.0
33 TraesCS2B01G627900 chr6A 82.462 325 31 13 1377 1677 447628614 447628292 9.690000e-66 261.0
34 TraesCS2B01G627900 chr6A 76.863 255 43 12 3281 3521 550717241 550716989 2.850000e-26 130.0
35 TraesCS2B01G627900 chr6A 90.000 100 6 3 366 465 607960042 607959947 3.690000e-25 126.0
36 TraesCS2B01G627900 chr1A 79.455 404 50 14 1297 1677 254185246 254184853 4.510000e-64 255.0
37 TraesCS2B01G627900 chr1A 78.505 214 31 11 3302 3505 496125487 496125279 3.690000e-25 126.0
38 TraesCS2B01G627900 chr1A 86.747 83 8 3 3251 3332 517642761 517642681 4.840000e-14 89.8
39 TraesCS2B01G627900 chr4A 81.115 323 38 10 1377 1677 108368932 108368611 1.630000e-58 237.0
40 TraesCS2B01G627900 chr4A 100.000 28 0 0 1650 1677 581149020 581149047 6.000000e-03 52.8
41 TraesCS2B01G627900 chr5B 79.235 366 51 14 1337 1681 615706404 615706043 7.600000e-57 231.0
42 TraesCS2B01G627900 chr5B 91.579 95 7 1 379 473 375770589 375770496 2.850000e-26 130.0
43 TraesCS2B01G627900 chr7D 85.648 216 27 4 1377 1589 550839789 550840003 1.270000e-54 224.0
44 TraesCS2B01G627900 chr7D 91.753 97 6 2 389 485 626199960 626199866 2.210000e-27 134.0
45 TraesCS2B01G627900 chr7D 90.909 99 5 4 376 471 506141364 506141461 2.850000e-26 130.0
46 TraesCS2B01G627900 chr7B 82.500 160 25 3 3358 3515 71134530 71134688 1.700000e-28 137.0
47 TraesCS2B01G627900 chr3A 80.899 178 31 3 3329 3506 696709648 696709822 1.700000e-28 137.0
48 TraesCS2B01G627900 chr3A 89.796 49 5 0 577 625 102107801 102107753 2.930000e-06 63.9
49 TraesCS2B01G627900 chr5D 92.473 93 5 2 379 470 504793016 504792925 7.930000e-27 132.0
50 TraesCS2B01G627900 chr5D 80.447 179 24 10 3336 3510 539864426 539864255 3.690000e-25 126.0
51 TraesCS2B01G627900 chr5D 77.778 207 25 14 3245 3441 445800675 445800870 1.340000e-19 108.0
52 TraesCS2B01G627900 chr6B 91.579 95 6 2 379 472 225523450 225523357 2.850000e-26 130.0
53 TraesCS2B01G627900 chr4D 87.736 106 11 2 373 478 10971621 10971518 4.770000e-24 122.0
54 TraesCS2B01G627900 chr6D 75.912 274 39 22 3250 3507 308936961 308936699 7.990000e-22 115.0
55 TraesCS2B01G627900 chr3D 74.653 288 53 12 3241 3511 547616814 547617098 3.720000e-20 110.0
56 TraesCS2B01G627900 chr3D 77.222 180 37 4 3331 3510 560872717 560872892 6.220000e-18 102.0
57 TraesCS2B01G627900 chr1D 74.627 268 57 10 3251 3515 46461114 46460855 1.340000e-19 108.0


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 TraesCS2B01G627900 chr2B 799574718 799578238 3520 True 6503.000000 6503 100.000000 1 3521 1 chr2B.!!$R4 3520
1 TraesCS2B01G627900 chr2B 799595331 799599386 4055 True 225.000000 375 86.750000 2413 2887 3 chr2B.!!$R6 474
2 TraesCS2B01G627900 chr2D 642099507 642102076 2569 False 1519.500000 2750 90.760500 188 2872 2 chr2D.!!$F4 2684
3 TraesCS2B01G627900 chr2D 598327916 598330535 2619 False 1122.333333 2215 92.443000 188 2872 3 chr2D.!!$F3 2684
4 TraesCS2B01G627900 chr2A 767017409 767020722 3313 False 918.750000 1847 88.405500 488 3508 4 chr2A.!!$F2 3020
5 TraesCS2B01G627900 chr2A 766980989 766983579 2590 False 474.750000 737 86.450750 809 3507 4 chr2A.!!$F1 2698
6 TraesCS2B01G627900 chr2A 767146442 767147315 873 True 239.300000 472 83.590667 1182 2872 3 chr2A.!!$R1 1690

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
111 112 0.299895 CGATGCTCGCATTGTCTGAC 59.700 55.0 5.79 0.00 36.70 3.51 F
1747 1842 0.385751 TTGATCGCCTCGAGATGGAC 59.614 55.0 15.71 3.06 39.91 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1795 1908 0.391228 TCTTGTTCTGCTGTGCCGTA 59.609 50.0 0.0 0.0 0.0 4.02 R
2820 7179 0.034059 CGCCCTCATCTCATGTACCC 59.966 60.0 0.0 0.0 0.0 3.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.951775 AGCTCAACTACTGTGAAGAGG 57.048 47.619 0.00 0.00 0.00 3.69
22 23 3.235200 AGCTCAACTACTGTGAAGAGGT 58.765 45.455 0.00 0.00 0.00 3.85
23 24 3.643792 AGCTCAACTACTGTGAAGAGGTT 59.356 43.478 0.00 0.00 31.71 3.50
24 25 4.101741 AGCTCAACTACTGTGAAGAGGTTT 59.898 41.667 0.00 0.00 31.71 3.27
25 26 5.304614 AGCTCAACTACTGTGAAGAGGTTTA 59.695 40.000 0.00 0.00 31.71 2.01
26 27 5.989777 GCTCAACTACTGTGAAGAGGTTTAA 59.010 40.000 0.00 0.00 0.00 1.52
27 28 6.146347 GCTCAACTACTGTGAAGAGGTTTAAG 59.854 42.308 0.00 0.00 0.00 1.85
28 29 7.356089 TCAACTACTGTGAAGAGGTTTAAGA 57.644 36.000 0.00 0.00 0.00 2.10
29 30 7.963532 TCAACTACTGTGAAGAGGTTTAAGAT 58.036 34.615 0.00 0.00 0.00 2.40
30 31 8.429641 TCAACTACTGTGAAGAGGTTTAAGATT 58.570 33.333 0.00 0.00 0.00 2.40
31 32 9.057089 CAACTACTGTGAAGAGGTTTAAGATTT 57.943 33.333 0.00 0.00 0.00 2.17
32 33 8.608844 ACTACTGTGAAGAGGTTTAAGATTTG 57.391 34.615 0.00 0.00 0.00 2.32
33 34 8.429641 ACTACTGTGAAGAGGTTTAAGATTTGA 58.570 33.333 0.00 0.00 0.00 2.69
34 35 7.497925 ACTGTGAAGAGGTTTAAGATTTGAC 57.502 36.000 0.00 0.00 0.00 3.18
35 36 7.054124 ACTGTGAAGAGGTTTAAGATTTGACA 58.946 34.615 0.00 0.00 0.00 3.58
36 37 7.556275 ACTGTGAAGAGGTTTAAGATTTGACAA 59.444 33.333 0.00 0.00 0.00 3.18
37 38 8.463930 TGTGAAGAGGTTTAAGATTTGACAAT 57.536 30.769 0.00 0.00 0.00 2.71
38 39 8.567948 TGTGAAGAGGTTTAAGATTTGACAATC 58.432 33.333 0.00 0.00 39.45 2.67
39 40 7.746475 GTGAAGAGGTTTAAGATTTGACAATCG 59.254 37.037 0.00 0.00 43.38 3.34
40 41 7.659799 TGAAGAGGTTTAAGATTTGACAATCGA 59.340 33.333 0.00 0.00 43.38 3.59
41 42 8.567285 AAGAGGTTTAAGATTTGACAATCGAT 57.433 30.769 0.00 0.00 43.38 3.59
42 43 7.978982 AGAGGTTTAAGATTTGACAATCGATG 58.021 34.615 0.00 0.00 43.38 3.84
44 45 8.110860 AGGTTTAAGATTTGACAATCGATGTT 57.889 30.769 0.00 0.00 44.12 2.71
45 46 8.237267 AGGTTTAAGATTTGACAATCGATGTTC 58.763 33.333 0.00 0.00 44.12 3.18
46 47 8.237267 GGTTTAAGATTTGACAATCGATGTTCT 58.763 33.333 0.00 0.00 44.12 3.01
47 48 9.612620 GTTTAAGATTTGACAATCGATGTTCTT 57.387 29.630 0.00 7.96 44.12 2.52
48 49 9.611284 TTTAAGATTTGACAATCGATGTTCTTG 57.389 29.630 0.00 0.00 44.12 3.02
49 50 6.808008 AGATTTGACAATCGATGTTCTTGT 57.192 33.333 0.00 0.00 44.12 3.16
50 51 7.905604 AGATTTGACAATCGATGTTCTTGTA 57.094 32.000 0.00 0.00 44.12 2.41
51 52 8.498054 AGATTTGACAATCGATGTTCTTGTAT 57.502 30.769 0.00 0.00 44.12 2.29
52 53 9.599866 AGATTTGACAATCGATGTTCTTGTATA 57.400 29.630 0.00 0.00 44.12 1.47
53 54 9.638300 GATTTGACAATCGATGTTCTTGTATAC 57.362 33.333 0.00 0.00 44.12 1.47
54 55 7.534085 TTGACAATCGATGTTCTTGTATACC 57.466 36.000 0.00 0.00 44.12 2.73
55 56 5.746721 TGACAATCGATGTTCTTGTATACCG 59.253 40.000 0.00 0.00 44.12 4.02
56 57 5.898174 ACAATCGATGTTCTTGTATACCGA 58.102 37.500 0.00 0.00 40.06 4.69
57 58 5.977725 ACAATCGATGTTCTTGTATACCGAG 59.022 40.000 0.00 0.00 40.06 4.63
58 59 3.961182 TCGATGTTCTTGTATACCGAGC 58.039 45.455 0.00 0.26 0.00 5.03
59 60 3.050619 CGATGTTCTTGTATACCGAGCC 58.949 50.000 0.00 0.00 0.00 4.70
60 61 3.490249 CGATGTTCTTGTATACCGAGCCA 60.490 47.826 0.00 0.44 0.00 4.75
61 62 3.965379 TGTTCTTGTATACCGAGCCAA 57.035 42.857 0.00 0.00 0.00 4.52
62 63 3.857052 TGTTCTTGTATACCGAGCCAAG 58.143 45.455 0.00 0.00 36.49 3.61
63 64 2.596904 TCTTGTATACCGAGCCAAGC 57.403 50.000 0.00 0.00 35.42 4.01
64 65 2.108168 TCTTGTATACCGAGCCAAGCT 58.892 47.619 0.00 0.00 43.88 3.74
65 66 3.293337 TCTTGTATACCGAGCCAAGCTA 58.707 45.455 0.00 0.00 39.88 3.32
66 67 3.067742 TCTTGTATACCGAGCCAAGCTAC 59.932 47.826 0.00 0.00 39.88 3.58
67 68 2.380941 TGTATACCGAGCCAAGCTACA 58.619 47.619 0.00 0.00 39.88 2.74
68 69 2.963101 TGTATACCGAGCCAAGCTACAT 59.037 45.455 0.00 0.00 39.88 2.29
69 70 3.386726 TGTATACCGAGCCAAGCTACATT 59.613 43.478 0.00 0.00 39.88 2.71
70 71 4.585581 TGTATACCGAGCCAAGCTACATTA 59.414 41.667 0.00 0.00 39.88 1.90
71 72 2.311124 ACCGAGCCAAGCTACATTAC 57.689 50.000 0.00 0.00 39.88 1.89
72 73 1.134491 ACCGAGCCAAGCTACATTACC 60.134 52.381 0.00 0.00 39.88 2.85
73 74 1.583054 CGAGCCAAGCTACATTACCC 58.417 55.000 0.00 0.00 39.88 3.69
74 75 1.139058 CGAGCCAAGCTACATTACCCT 59.861 52.381 0.00 0.00 39.88 4.34
75 76 2.565841 GAGCCAAGCTACATTACCCTG 58.434 52.381 0.00 0.00 39.88 4.45
76 77 1.916181 AGCCAAGCTACATTACCCTGT 59.084 47.619 0.00 0.00 36.99 4.00
77 78 3.112263 AGCCAAGCTACATTACCCTGTA 58.888 45.455 0.00 0.00 36.99 2.74
79 80 3.744530 GCCAAGCTACATTACCCTGTAGG 60.745 52.174 11.89 0.00 45.71 3.18
90 91 2.453242 CCTGTAGGTAGGGGCATCC 58.547 63.158 0.00 0.00 34.06 3.51
103 104 2.031616 CATCCCCGATGCTCGCAT 59.968 61.111 3.70 3.70 38.82 4.73
104 105 1.598962 CATCCCCGATGCTCGCATT 60.599 57.895 5.79 0.00 38.82 3.56
105 106 1.598962 ATCCCCGATGCTCGCATTG 60.599 57.895 11.37 11.37 38.82 2.82
106 107 2.329539 ATCCCCGATGCTCGCATTGT 62.330 55.000 15.84 0.00 38.82 2.71
107 108 2.537560 CCCCGATGCTCGCATTGTC 61.538 63.158 15.84 0.48 38.82 3.18
108 109 1.522355 CCCGATGCTCGCATTGTCT 60.522 57.895 15.84 0.00 38.82 3.41
109 110 1.640069 CCGATGCTCGCATTGTCTG 59.360 57.895 15.84 0.27 38.82 3.51
110 111 0.807275 CCGATGCTCGCATTGTCTGA 60.807 55.000 15.84 0.00 38.82 3.27
111 112 0.299895 CGATGCTCGCATTGTCTGAC 59.700 55.000 5.79 0.00 36.70 3.51
112 113 1.649664 GATGCTCGCATTGTCTGACT 58.350 50.000 9.51 0.00 36.70 3.41
113 114 2.796032 CGATGCTCGCATTGTCTGACTA 60.796 50.000 9.51 1.38 36.70 2.59
114 115 1.996292 TGCTCGCATTGTCTGACTAC 58.004 50.000 9.51 0.00 0.00 2.73
115 116 1.546029 TGCTCGCATTGTCTGACTACT 59.454 47.619 9.51 0.00 0.00 2.57
116 117 2.029020 TGCTCGCATTGTCTGACTACTT 60.029 45.455 9.51 0.00 0.00 2.24
117 118 3.192633 TGCTCGCATTGTCTGACTACTTA 59.807 43.478 9.51 0.00 0.00 2.24
118 119 3.794028 GCTCGCATTGTCTGACTACTTAG 59.206 47.826 9.51 1.57 0.00 2.18
119 120 3.770666 TCGCATTGTCTGACTACTTAGC 58.229 45.455 9.51 4.03 0.00 3.09
120 121 3.192633 TCGCATTGTCTGACTACTTAGCA 59.807 43.478 9.51 0.00 0.00 3.49
121 122 3.304559 CGCATTGTCTGACTACTTAGCAC 59.695 47.826 9.51 0.00 0.00 4.40
122 123 4.245660 GCATTGTCTGACTACTTAGCACA 58.754 43.478 9.51 0.00 0.00 4.57
123 124 4.872691 GCATTGTCTGACTACTTAGCACAT 59.127 41.667 9.51 0.00 0.00 3.21
124 125 5.352569 GCATTGTCTGACTACTTAGCACATT 59.647 40.000 9.51 0.00 0.00 2.71
125 126 6.535150 GCATTGTCTGACTACTTAGCACATTA 59.465 38.462 9.51 0.00 0.00 1.90
126 127 7.064609 GCATTGTCTGACTACTTAGCACATTAA 59.935 37.037 9.51 0.00 0.00 1.40
127 128 9.102757 CATTGTCTGACTACTTAGCACATTAAT 57.897 33.333 9.51 0.00 0.00 1.40
128 129 9.672673 ATTGTCTGACTACTTAGCACATTAATT 57.327 29.630 9.51 0.00 0.00 1.40
129 130 9.502091 TTGTCTGACTACTTAGCACATTAATTT 57.498 29.630 9.51 0.00 0.00 1.82
130 131 9.502091 TGTCTGACTACTTAGCACATTAATTTT 57.498 29.630 9.51 0.00 0.00 1.82
257 258 5.817816 CGGCTAATAAAAACAGATGAGAGGT 59.182 40.000 0.00 0.00 0.00 3.85
267 268 6.472686 AACAGATGAGAGGTTATCAGGTAC 57.527 41.667 0.00 0.00 0.00 3.34
330 331 7.038729 ACTCTCTCTGTTCCAATGAATAAGTCA 60.039 37.037 0.00 0.00 41.67 3.41
340 341 6.615316 TCCAATGAATAAGTCATACTCCCTCA 59.385 38.462 0.00 0.00 46.80 3.86
341 342 6.933521 CCAATGAATAAGTCATACTCCCTCAG 59.066 42.308 0.00 0.00 46.80 3.35
350 351 7.741554 AGTCATACTCCCTCAGTTAAGAATT 57.258 36.000 0.00 0.00 36.43 2.17
380 381 5.375773 TGGAGCAATGCATGTAGCTAAATA 58.624 37.500 18.11 5.98 45.94 1.40
381 382 5.239306 TGGAGCAATGCATGTAGCTAAATAC 59.761 40.000 18.11 8.23 45.94 1.89
382 383 5.471456 GGAGCAATGCATGTAGCTAAATACT 59.529 40.000 18.11 0.00 45.94 2.12
383 384 6.348050 GGAGCAATGCATGTAGCTAAATACTC 60.348 42.308 18.11 7.32 45.94 2.59
384 385 5.471456 AGCAATGCATGTAGCTAAATACTCC 59.529 40.000 17.01 0.00 45.94 3.85
385 386 5.471456 GCAATGCATGTAGCTAAATACTCCT 59.529 40.000 0.00 0.00 45.94 3.69
386 387 6.650807 GCAATGCATGTAGCTAAATACTCCTA 59.349 38.462 0.00 0.00 45.94 2.94
387 388 7.173218 GCAATGCATGTAGCTAAATACTCCTAA 59.827 37.037 0.00 0.00 45.94 2.69
388 389 8.499162 CAATGCATGTAGCTAAATACTCCTAAC 58.501 37.037 0.00 0.00 45.94 2.34
389 390 6.213677 TGCATGTAGCTAAATACTCCTAACG 58.786 40.000 0.00 0.00 45.94 3.18
390 391 6.183360 TGCATGTAGCTAAATACTCCTAACGT 60.183 38.462 0.00 0.00 45.94 3.99
391 392 6.362820 GCATGTAGCTAAATACTCCTAACGTC 59.637 42.308 0.00 0.00 41.15 4.34
392 393 7.649973 CATGTAGCTAAATACTCCTAACGTCT 58.350 38.462 0.00 0.00 0.00 4.18
393 394 7.256756 TGTAGCTAAATACTCCTAACGTCTC 57.743 40.000 0.00 0.00 0.00 3.36
394 395 6.825213 TGTAGCTAAATACTCCTAACGTCTCA 59.175 38.462 0.00 0.00 0.00 3.27
395 396 6.134040 AGCTAAATACTCCTAACGTCTCAC 57.866 41.667 0.00 0.00 0.00 3.51
396 397 5.887035 AGCTAAATACTCCTAACGTCTCACT 59.113 40.000 0.00 0.00 0.00 3.41
397 398 7.052873 AGCTAAATACTCCTAACGTCTCACTA 58.947 38.462 0.00 0.00 0.00 2.74
398 399 7.555554 AGCTAAATACTCCTAACGTCTCACTAA 59.444 37.037 0.00 0.00 0.00 2.24
399 400 8.351461 GCTAAATACTCCTAACGTCTCACTAAT 58.649 37.037 0.00 0.00 0.00 1.73
400 401 9.666626 CTAAATACTCCTAACGTCTCACTAATG 57.333 37.037 0.00 0.00 0.00 1.90
401 402 7.642082 AATACTCCTAACGTCTCACTAATGT 57.358 36.000 0.00 0.00 0.00 2.71
402 403 8.743085 AATACTCCTAACGTCTCACTAATGTA 57.257 34.615 0.00 0.00 0.00 2.29
403 404 8.743085 ATACTCCTAACGTCTCACTAATGTAA 57.257 34.615 0.00 0.00 0.00 2.41
404 405 7.086230 ACTCCTAACGTCTCACTAATGTAAG 57.914 40.000 0.00 0.00 0.00 2.34
405 406 6.883217 ACTCCTAACGTCTCACTAATGTAAGA 59.117 38.462 0.00 0.00 0.00 2.10
406 407 7.081526 TCCTAACGTCTCACTAATGTAAGAC 57.918 40.000 0.00 0.00 35.81 3.01
460 461 4.872664 GTCTTACATTATGAGACGGAGGG 58.127 47.826 0.00 0.00 34.53 4.30
461 462 4.583489 GTCTTACATTATGAGACGGAGGGA 59.417 45.833 0.00 0.00 34.53 4.20
462 463 4.827835 TCTTACATTATGAGACGGAGGGAG 59.172 45.833 0.00 0.00 0.00 4.30
463 464 3.033659 ACATTATGAGACGGAGGGAGT 57.966 47.619 0.00 0.00 0.00 3.85
464 465 4.180377 ACATTATGAGACGGAGGGAGTA 57.820 45.455 0.00 0.00 0.00 2.59
529 530 4.121317 CGTACGGAGGTGGCATAAATTTA 58.879 43.478 7.57 0.00 0.00 1.40
534 535 5.299279 ACGGAGGTGGCATAAATTTAATCAG 59.701 40.000 1.21 0.00 0.00 2.90
536 537 6.207417 CGGAGGTGGCATAAATTTAATCAGAT 59.793 38.462 1.21 0.00 0.00 2.90
611 612 4.486090 CTCGGATCCATAATAAGTGTCGG 58.514 47.826 13.41 0.00 0.00 4.79
621 622 6.404293 CCATAATAAGTGTCGGGGTTTTGAAG 60.404 42.308 0.00 0.00 0.00 3.02
662 663 7.772332 CTAAGGTTACTATTGTGCCTTAGTG 57.228 40.000 25.73 14.35 45.35 2.74
663 664 6.368779 AAGGTTACTATTGTGCCTTAGTGA 57.631 37.500 13.26 0.00 39.38 3.41
664 665 6.368779 AGGTTACTATTGTGCCTTAGTGAA 57.631 37.500 0.00 0.00 31.94 3.18
665 666 6.958767 AGGTTACTATTGTGCCTTAGTGAAT 58.041 36.000 0.00 0.00 31.94 2.57
666 667 7.402862 AGGTTACTATTGTGCCTTAGTGAATT 58.597 34.615 0.00 0.00 31.94 2.17
667 668 8.545472 AGGTTACTATTGTGCCTTAGTGAATTA 58.455 33.333 0.00 0.00 31.94 1.40
742 752 6.037786 TGATGTAACTCTTGTTCCCAGTAG 57.962 41.667 0.00 0.00 37.59 2.57
743 753 4.884668 TGTAACTCTTGTTCCCAGTAGG 57.115 45.455 0.00 0.00 37.59 3.18
744 754 4.485875 TGTAACTCTTGTTCCCAGTAGGA 58.514 43.478 0.00 0.00 45.68 2.94
745 755 5.091552 TGTAACTCTTGTTCCCAGTAGGAT 58.908 41.667 0.00 0.00 46.94 3.24
746 756 6.258354 TGTAACTCTTGTTCCCAGTAGGATA 58.742 40.000 0.00 0.00 46.94 2.59
747 757 6.901300 TGTAACTCTTGTTCCCAGTAGGATAT 59.099 38.462 0.00 0.00 46.94 1.63
748 758 8.063153 TGTAACTCTTGTTCCCAGTAGGATATA 58.937 37.037 0.00 0.00 46.94 0.86
749 759 9.091220 GTAACTCTTGTTCCCAGTAGGATATAT 57.909 37.037 0.00 0.00 46.94 0.86
792 802 1.474077 GAAAGGAGCGCATGAATTGGT 59.526 47.619 11.47 0.00 0.00 3.67
1121 1189 1.495148 TCCTCGATCTAGCCCTCTTCA 59.505 52.381 0.00 0.00 0.00 3.02
1128 1196 2.683768 TCTAGCCCTCTTCATCCCTTC 58.316 52.381 0.00 0.00 0.00 3.46
1140 1208 0.958091 ATCCCTTCTCATCTCTCGCG 59.042 55.000 0.00 0.00 0.00 5.87
1159 1227 3.489785 CGCGTCAAAGTCTTACTGAGTTT 59.510 43.478 0.00 0.00 46.09 2.66
1317 1401 6.183360 GGTTCTATGAGACAGATTTTCAGCAC 60.183 42.308 0.00 0.00 0.00 4.40
1319 1403 3.777106 TGAGACAGATTTTCAGCACCT 57.223 42.857 0.00 0.00 0.00 4.00
1355 1440 5.359576 TGGCATACACCCTTTATGAACATTC 59.640 40.000 0.00 0.00 0.00 2.67
1479 1566 6.264518 GGAGTCCTCACCTGAAAAACAAAATA 59.735 38.462 0.41 0.00 0.00 1.40
1481 1568 7.489160 AGTCCTCACCTGAAAAACAAAATAAC 58.511 34.615 0.00 0.00 0.00 1.89
1559 1646 3.886505 TCCACGAAGGTTATTTGTTGCTT 59.113 39.130 0.00 0.00 39.02 3.91
1572 1659 5.793026 TTTGTTGCTTAAACTTTGCAAGG 57.207 34.783 7.07 7.07 45.55 3.61
1645 1736 5.123344 ACGAATTTACTGTTTATGAGGGTGC 59.877 40.000 0.00 0.00 0.00 5.01
1648 1739 4.901197 TTACTGTTTATGAGGGTGCAGA 57.099 40.909 0.00 0.00 0.00 4.26
1683 1774 3.875134 CTGTTACACCTTTCTCGTGGTTT 59.125 43.478 0.00 0.00 35.46 3.27
1746 1841 0.670706 CTTGATCGCCTCGAGATGGA 59.329 55.000 15.71 8.24 39.91 3.41
1747 1842 0.385751 TTGATCGCCTCGAGATGGAC 59.614 55.000 15.71 3.06 39.91 4.02
1754 1867 3.432051 CTCGAGATGGACGTGGGCC 62.432 68.421 6.58 0.00 0.00 5.80
1785 1898 1.199789 GATGGTGCAACTGATCGCAAA 59.800 47.619 2.04 0.00 40.44 3.68
1908 2021 0.323542 AACGACCAGGAGACGGAGAT 60.324 55.000 0.00 0.00 0.00 2.75
1909 2022 0.323542 ACGACCAGGAGACGGAGATT 60.324 55.000 0.00 0.00 0.00 2.40
2079 2192 2.802247 TCATCAGACAAGTTCGCACAAG 59.198 45.455 0.00 0.00 0.00 3.16
2084 2197 1.663643 GACAAGTTCGCACAAGTCACA 59.336 47.619 5.46 0.00 32.22 3.58
2093 2212 1.741706 GCACAAGTCACATAGCAGCAT 59.258 47.619 0.00 0.00 0.00 3.79
2097 2216 4.269603 CACAAGTCACATAGCAGCATCTAC 59.730 45.833 0.00 0.00 0.00 2.59
2099 2218 3.303938 AGTCACATAGCAGCATCTACCT 58.696 45.455 0.00 0.00 0.00 3.08
2100 2219 3.708631 AGTCACATAGCAGCATCTACCTT 59.291 43.478 0.00 0.00 0.00 3.50
2101 2220 4.054671 GTCACATAGCAGCATCTACCTTC 58.945 47.826 0.00 0.00 0.00 3.46
2103 2222 2.064762 CATAGCAGCATCTACCTTCGC 58.935 52.381 0.00 0.00 0.00 4.70
2164 2289 2.270527 GCACAAGGAGGAGGAGGC 59.729 66.667 0.00 0.00 0.00 4.70
2259 2384 1.063492 TCCGTCTCCCTACCATGCTTA 60.063 52.381 0.00 0.00 0.00 3.09
2314 2445 2.424793 TCCCTTTACACCCTTCCAACT 58.575 47.619 0.00 0.00 0.00 3.16
2391 2523 5.437383 GCGTCTGGCGTAATATTATCTTC 57.563 43.478 2.76 0.00 43.66 2.87
2425 2557 5.571784 ATCTGTATCCATTTGTGCACTTG 57.428 39.130 19.41 12.56 0.00 3.16
2448 2580 5.587443 TGATTTGTGCAGAGACTATGAATGG 59.413 40.000 0.07 0.00 0.00 3.16
2496 2856 5.888691 ATATGGTTATGTGCAACGAAACA 57.111 34.783 0.00 0.00 42.39 2.83
2513 2877 4.263677 CGAAACAATTGATGCAAAGGATCG 59.736 41.667 13.59 0.09 0.00 3.69
2518 4758 1.971481 TGATGCAAAGGATCGATGGG 58.029 50.000 0.54 0.00 0.00 4.00
2523 4763 2.224523 TGCAAAGGATCGATGGGGATAC 60.225 50.000 0.54 0.00 0.00 2.24
2541 4781 4.141459 GGATACCCCCTTTTCGAAGAAGAT 60.141 45.833 16.62 6.40 45.90 2.40
2547 4787 6.724441 ACCCCCTTTTCGAAGAAGATAAAAAT 59.276 34.615 16.62 0.45 45.90 1.82
2649 6605 7.645058 AGGTATTTCCTATGTTTCCATTGTG 57.355 36.000 0.00 0.00 46.10 3.33
2656 6612 4.526262 CCTATGTTTCCATTGTGGTTTCCA 59.474 41.667 0.00 0.00 39.03 3.53
2673 6629 7.065683 GTGGTTTCCATGAATTTGTCAGTTTTT 59.934 33.333 0.00 0.00 40.43 1.94
2761 6734 1.150827 TGACTGCAACTCATCAAGCG 58.849 50.000 0.00 0.00 0.00 4.68
2781 6754 3.305964 CGATGCATTGGATCAAGCAATC 58.694 45.455 16.98 0.00 40.76 2.67
2786 6759 3.304861 GCATTGGATCAAGCAATCGCATA 60.305 43.478 0.00 0.00 42.27 3.14
2798 7157 7.227314 TCAAGCAATCGCATAGATTCAAAGTAT 59.773 33.333 0.00 0.00 45.95 2.12
2804 7163 6.500910 TCGCATAGATTCAAAGTATGTACGT 58.499 36.000 0.00 0.00 0.00 3.57
2820 7179 1.506891 CGTGTGTGTATGCGCGTTG 60.507 57.895 7.78 0.00 34.41 4.10
2824 7183 1.015085 GTGTGTATGCGCGTTGGGTA 61.015 55.000 7.78 0.00 0.00 3.69
2844 7203 3.174507 ATGAGATGAGGGCGCGCAT 62.175 57.895 34.42 21.45 0.00 4.73
2889 7248 1.768684 AAGGGCTGTTCTTCCTCGCA 61.769 55.000 0.00 0.00 0.00 5.10
2900 7259 4.208686 CCTCGCAGGACCGGCTAC 62.209 72.222 14.92 0.00 37.67 3.58
2901 7260 4.554363 CTCGCAGGACCGGCTACG 62.554 72.222 14.92 0.00 40.55 3.51
2929 7288 6.521151 AGCTGACTGAATTTCTAATTTGGG 57.479 37.500 0.00 0.00 0.00 4.12
2950 7309 5.588648 TGGGTCAGTCACTTTTTCTTTACAG 59.411 40.000 0.00 0.00 0.00 2.74
2957 7316 5.464389 GTCACTTTTTCTTTACAGTCGGCTA 59.536 40.000 0.00 0.00 0.00 3.93
2959 7318 6.202188 TCACTTTTTCTTTACAGTCGGCTAAG 59.798 38.462 0.00 0.00 0.00 2.18
2962 7321 7.384387 ACTTTTTCTTTACAGTCGGCTAAGTAG 59.616 37.037 0.00 0.00 0.00 2.57
2967 7326 6.538021 TCTTTACAGTCGGCTAAGTAGTCTAG 59.462 42.308 0.00 0.00 0.00 2.43
2972 7331 3.128242 GTCGGCTAAGTAGTCTAGTTGCA 59.872 47.826 9.81 0.00 0.00 4.08
2977 7336 5.096849 GCTAAGTAGTCTAGTTGCACAGTC 58.903 45.833 9.81 0.00 0.00 3.51
2988 7347 3.886505 AGTTGCACAGTCCGGAATTAAAA 59.113 39.130 5.23 0.00 0.00 1.52
2989 7348 4.522789 AGTTGCACAGTCCGGAATTAAAAT 59.477 37.500 5.23 0.00 0.00 1.82
2993 7352 3.192422 CACAGTCCGGAATTAAAATGCCA 59.808 43.478 5.23 0.00 33.26 4.92
2995 7354 2.427095 AGTCCGGAATTAAAATGCCAGC 59.573 45.455 5.23 0.00 33.26 4.85
2996 7355 2.427095 GTCCGGAATTAAAATGCCAGCT 59.573 45.455 5.23 0.00 33.26 4.24
2997 7356 2.426738 TCCGGAATTAAAATGCCAGCTG 59.573 45.455 6.78 6.78 33.26 4.24
2998 7357 2.195922 CGGAATTAAAATGCCAGCTGC 58.804 47.619 8.66 4.57 33.26 5.25
2999 7358 2.554142 GGAATTAAAATGCCAGCTGCC 58.446 47.619 8.66 0.00 40.16 4.85
3000 7359 2.093553 GGAATTAAAATGCCAGCTGCCA 60.094 45.455 8.66 3.15 40.16 4.92
3024 7383 1.558233 AGCGAGGCCACTACTAAACT 58.442 50.000 5.01 0.00 0.00 2.66
3034 7393 3.940852 CCACTACTAAACTCATGCATGCA 59.059 43.478 25.04 25.04 0.00 3.96
3055 7451 2.405892 GCTAGTGCTGGTTGTGTTTG 57.594 50.000 0.00 0.00 36.03 2.93
3063 7459 4.095782 GTGCTGGTTGTGTTTGAAGTAAGA 59.904 41.667 0.00 0.00 0.00 2.10
3102 7498 3.699779 TTTTTGTTACGCTGACATGCA 57.300 38.095 0.00 0.00 0.00 3.96
3103 7499 3.913548 TTTTGTTACGCTGACATGCAT 57.086 38.095 0.00 0.00 0.00 3.96
3105 7501 5.363979 TTTTGTTACGCTGACATGCATTA 57.636 34.783 0.00 0.00 0.00 1.90
3107 7503 5.559427 TTGTTACGCTGACATGCATTATT 57.441 34.783 0.00 0.00 0.00 1.40
3109 7505 5.568482 TGTTACGCTGACATGCATTATTTC 58.432 37.500 0.00 0.00 0.00 2.17
3110 7506 5.123027 TGTTACGCTGACATGCATTATTTCA 59.877 36.000 0.00 0.00 0.00 2.69
3117 7516 7.412129 CGCTGACATGCATTATTTCACATTTTT 60.412 33.333 0.00 0.00 0.00 1.94
3142 7541 5.957842 AAGAATAGACGCCACAAATCAAA 57.042 34.783 0.00 0.00 0.00 2.69
3171 7570 7.738345 AGAAAAACAAACAAAATTGACTTCCG 58.262 30.769 0.00 0.00 34.38 4.30
3187 7586 8.770850 TTGACTTCCGTTTTCTTAATTTTACG 57.229 30.769 0.00 0.00 0.00 3.18
3188 7587 7.918643 TGACTTCCGTTTTCTTAATTTTACGT 58.081 30.769 0.00 0.00 0.00 3.57
3222 7621 5.556915 ACCCTTTAACGATGATCAAAGACA 58.443 37.500 0.00 0.00 31.11 3.41
3379 7781 6.418057 AAAAGAATGAAATTAGTGGCACCA 57.582 33.333 15.27 4.07 36.07 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.643792 ACCTCTTCACAGTAGTTGAGCTT 59.356 43.478 0.00 0.00 0.00 3.74
1 2 3.235200 ACCTCTTCACAGTAGTTGAGCT 58.765 45.455 0.00 0.00 0.00 4.09
2 3 3.669251 ACCTCTTCACAGTAGTTGAGC 57.331 47.619 0.00 0.00 0.00 4.26
3 4 7.434492 TCTTAAACCTCTTCACAGTAGTTGAG 58.566 38.462 0.00 0.00 0.00 3.02
4 5 7.356089 TCTTAAACCTCTTCACAGTAGTTGA 57.644 36.000 0.00 0.00 0.00 3.18
5 6 8.608844 AATCTTAAACCTCTTCACAGTAGTTG 57.391 34.615 0.00 0.00 0.00 3.16
6 7 9.057089 CAAATCTTAAACCTCTTCACAGTAGTT 57.943 33.333 0.00 0.00 0.00 2.24
7 8 8.429641 TCAAATCTTAAACCTCTTCACAGTAGT 58.570 33.333 0.00 0.00 0.00 2.73
8 9 8.713271 GTCAAATCTTAAACCTCTTCACAGTAG 58.287 37.037 0.00 0.00 0.00 2.57
9 10 8.208224 TGTCAAATCTTAAACCTCTTCACAGTA 58.792 33.333 0.00 0.00 0.00 2.74
10 11 7.054124 TGTCAAATCTTAAACCTCTTCACAGT 58.946 34.615 0.00 0.00 0.00 3.55
11 12 7.496529 TGTCAAATCTTAAACCTCTTCACAG 57.503 36.000 0.00 0.00 0.00 3.66
12 13 7.873719 TTGTCAAATCTTAAACCTCTTCACA 57.126 32.000 0.00 0.00 0.00 3.58
13 14 7.746475 CGATTGTCAAATCTTAAACCTCTTCAC 59.254 37.037 0.00 0.00 40.15 3.18
14 15 7.659799 TCGATTGTCAAATCTTAAACCTCTTCA 59.340 33.333 0.00 0.00 40.15 3.02
15 16 8.029642 TCGATTGTCAAATCTTAAACCTCTTC 57.970 34.615 0.00 0.00 40.15 2.87
16 17 7.979444 TCGATTGTCAAATCTTAAACCTCTT 57.021 32.000 0.00 0.00 40.15 2.85
17 18 7.607991 ACATCGATTGTCAAATCTTAAACCTCT 59.392 33.333 0.00 0.00 40.15 3.69
18 19 7.752695 ACATCGATTGTCAAATCTTAAACCTC 58.247 34.615 0.00 0.00 40.15 3.85
19 20 7.687941 ACATCGATTGTCAAATCTTAAACCT 57.312 32.000 0.00 0.00 40.15 3.50
20 21 8.237267 AGAACATCGATTGTCAAATCTTAAACC 58.763 33.333 0.00 0.00 40.15 3.27
21 22 9.612620 AAGAACATCGATTGTCAAATCTTAAAC 57.387 29.630 0.00 0.00 40.15 2.01
22 23 9.611284 CAAGAACATCGATTGTCAAATCTTAAA 57.389 29.630 0.00 0.00 40.15 1.52
23 24 8.783093 ACAAGAACATCGATTGTCAAATCTTAA 58.217 29.630 0.00 0.00 40.15 1.85
24 25 8.322906 ACAAGAACATCGATTGTCAAATCTTA 57.677 30.769 0.00 0.00 40.15 2.10
25 26 7.206981 ACAAGAACATCGATTGTCAAATCTT 57.793 32.000 0.00 1.69 40.15 2.40
26 27 6.808008 ACAAGAACATCGATTGTCAAATCT 57.192 33.333 0.00 0.00 40.15 2.40
27 28 9.638300 GTATACAAGAACATCGATTGTCAAATC 57.362 33.333 4.69 0.00 37.68 2.17
28 29 8.612619 GGTATACAAGAACATCGATTGTCAAAT 58.387 33.333 5.01 0.00 37.68 2.32
29 30 7.201487 CGGTATACAAGAACATCGATTGTCAAA 60.201 37.037 5.01 0.00 37.68 2.69
30 31 6.254804 CGGTATACAAGAACATCGATTGTCAA 59.745 38.462 5.01 0.00 37.68 3.18
31 32 5.746721 CGGTATACAAGAACATCGATTGTCA 59.253 40.000 5.01 0.00 37.68 3.58
32 33 5.975344 TCGGTATACAAGAACATCGATTGTC 59.025 40.000 5.01 1.17 37.68 3.18
33 34 5.898174 TCGGTATACAAGAACATCGATTGT 58.102 37.500 5.01 6.58 41.53 2.71
34 35 5.107837 GCTCGGTATACAAGAACATCGATTG 60.108 44.000 5.01 0.00 0.00 2.67
35 36 4.982916 GCTCGGTATACAAGAACATCGATT 59.017 41.667 5.01 0.00 0.00 3.34
36 37 4.547532 GCTCGGTATACAAGAACATCGAT 58.452 43.478 5.01 0.00 0.00 3.59
37 38 3.243301 GGCTCGGTATACAAGAACATCGA 60.243 47.826 5.01 1.15 0.00 3.59
38 39 3.050619 GGCTCGGTATACAAGAACATCG 58.949 50.000 5.01 0.00 0.00 3.84
39 40 4.054780 TGGCTCGGTATACAAGAACATC 57.945 45.455 5.01 0.00 0.00 3.06
40 41 4.442706 CTTGGCTCGGTATACAAGAACAT 58.557 43.478 5.01 0.00 42.07 2.71
41 42 3.857052 CTTGGCTCGGTATACAAGAACA 58.143 45.455 5.01 3.51 42.07 3.18
42 43 2.608090 GCTTGGCTCGGTATACAAGAAC 59.392 50.000 5.01 0.00 42.07 3.01
43 44 2.500098 AGCTTGGCTCGGTATACAAGAA 59.500 45.455 5.01 0.00 42.07 2.52
44 45 2.108168 AGCTTGGCTCGGTATACAAGA 58.892 47.619 5.01 2.83 42.07 3.02
45 46 2.604046 AGCTTGGCTCGGTATACAAG 57.396 50.000 5.01 2.81 42.31 3.16
46 47 2.761767 TGTAGCTTGGCTCGGTATACAA 59.238 45.455 5.01 0.00 40.44 2.41
47 48 2.380941 TGTAGCTTGGCTCGGTATACA 58.619 47.619 5.01 0.00 40.44 2.29
48 49 3.662247 ATGTAGCTTGGCTCGGTATAC 57.338 47.619 0.00 0.00 40.44 1.47
49 50 4.021719 GGTAATGTAGCTTGGCTCGGTATA 60.022 45.833 0.00 0.00 40.44 1.47
50 51 3.244112 GGTAATGTAGCTTGGCTCGGTAT 60.244 47.826 0.00 0.00 40.44 2.73
51 52 2.101917 GGTAATGTAGCTTGGCTCGGTA 59.898 50.000 0.00 0.00 40.44 4.02
52 53 1.134491 GGTAATGTAGCTTGGCTCGGT 60.134 52.381 0.00 0.00 40.44 4.69
53 54 1.583054 GGTAATGTAGCTTGGCTCGG 58.417 55.000 0.00 0.00 40.44 4.63
54 55 1.139058 AGGGTAATGTAGCTTGGCTCG 59.861 52.381 0.00 0.00 40.44 5.03
55 56 2.092914 ACAGGGTAATGTAGCTTGGCTC 60.093 50.000 0.00 0.00 40.44 4.70
56 57 1.916181 ACAGGGTAATGTAGCTTGGCT 59.084 47.619 0.00 0.00 43.41 4.75
57 58 2.420058 ACAGGGTAATGTAGCTTGGC 57.580 50.000 0.00 0.00 37.55 4.52
72 73 2.453242 GGATGCCCCTACCTACAGG 58.547 63.158 0.00 0.00 42.17 4.00
93 94 1.649664 AGTCAGACAATGCGAGCATC 58.350 50.000 11.26 0.00 35.31 3.91
94 95 2.167281 AGTAGTCAGACAATGCGAGCAT 59.833 45.455 4.52 4.52 38.46 3.79
95 96 1.546029 AGTAGTCAGACAATGCGAGCA 59.454 47.619 2.66 0.00 0.00 4.26
96 97 2.285827 AGTAGTCAGACAATGCGAGC 57.714 50.000 2.66 0.00 0.00 5.03
97 98 3.794028 GCTAAGTAGTCAGACAATGCGAG 59.206 47.826 2.66 0.00 0.00 5.03
98 99 3.192633 TGCTAAGTAGTCAGACAATGCGA 59.807 43.478 2.66 0.00 0.00 5.10
99 100 3.304559 GTGCTAAGTAGTCAGACAATGCG 59.695 47.826 2.66 0.00 0.00 4.73
100 101 4.245660 TGTGCTAAGTAGTCAGACAATGC 58.754 43.478 2.66 0.00 0.00 3.56
101 102 6.974932 AATGTGCTAAGTAGTCAGACAATG 57.025 37.500 2.66 0.00 0.00 2.82
102 103 9.672673 AATTAATGTGCTAAGTAGTCAGACAAT 57.327 29.630 2.66 0.00 0.00 2.71
103 104 9.502091 AAATTAATGTGCTAAGTAGTCAGACAA 57.498 29.630 2.66 0.00 0.00 3.18
104 105 9.502091 AAAATTAATGTGCTAAGTAGTCAGACA 57.498 29.630 2.66 0.00 0.00 3.41
166 167 9.820725 AGTGCACAAATTAATAATATGTTGCAT 57.179 25.926 21.04 0.00 33.79 3.96
215 216 2.677037 GCCGTAGCTGACTACCATTTGT 60.677 50.000 0.00 0.00 45.11 2.83
257 258 8.877195 GGTTCCTGGAATATAAGTACCTGATAA 58.123 37.037 13.07 0.00 0.00 1.75
267 268 7.521871 AGTAGTACGGTTCCTGGAATATAAG 57.478 40.000 13.07 5.39 0.00 1.73
308 309 8.762645 AGTATGACTTATTCATTGGAACAGAGA 58.237 33.333 0.00 0.00 42.87 3.10
312 313 7.054124 GGGAGTATGACTTATTCATTGGAACA 58.946 38.462 0.00 0.00 42.87 3.18
330 331 9.047947 ACAAGTAATTCTTAACTGAGGGAGTAT 57.952 33.333 0.00 0.00 34.66 2.12
340 341 7.817418 TTGCTCCAACAAGTAATTCTTAACT 57.183 32.000 0.00 0.00 34.66 2.24
341 342 7.062255 GCATTGCTCCAACAAGTAATTCTTAAC 59.938 37.037 0.16 0.00 34.66 2.01
350 351 3.156293 ACATGCATTGCTCCAACAAGTA 58.844 40.909 10.49 0.00 31.96 2.24
380 381 6.883217 TCTTACATTAGTGAGACGTTAGGAGT 59.117 38.462 0.00 0.00 35.67 3.85
381 382 7.188157 GTCTTACATTAGTGAGACGTTAGGAG 58.812 42.308 5.06 0.00 46.86 3.69
382 383 7.081526 GTCTTACATTAGTGAGACGTTAGGA 57.918 40.000 5.06 0.00 46.86 2.94
438 439 4.583489 TCCCTCCGTCTCATAATGTAAGAC 59.417 45.833 0.00 0.00 36.82 3.01
439 440 4.800023 TCCCTCCGTCTCATAATGTAAGA 58.200 43.478 0.00 0.00 0.00 2.10
440 441 4.585162 ACTCCCTCCGTCTCATAATGTAAG 59.415 45.833 0.00 0.00 0.00 2.34
441 442 4.543689 ACTCCCTCCGTCTCATAATGTAA 58.456 43.478 0.00 0.00 0.00 2.41
442 443 4.180377 ACTCCCTCCGTCTCATAATGTA 57.820 45.455 0.00 0.00 0.00 2.29
443 444 3.033659 ACTCCCTCCGTCTCATAATGT 57.966 47.619 0.00 0.00 0.00 2.71
444 445 7.411486 AATATACTCCCTCCGTCTCATAATG 57.589 40.000 0.00 0.00 0.00 1.90
445 446 8.437274 AAAATATACTCCCTCCGTCTCATAAT 57.563 34.615 0.00 0.00 0.00 1.28
446 447 7.850935 AAAATATACTCCCTCCGTCTCATAA 57.149 36.000 0.00 0.00 0.00 1.90
447 448 7.614583 CCTAAAATATACTCCCTCCGTCTCATA 59.385 40.741 0.00 0.00 0.00 2.15
448 449 6.437793 CCTAAAATATACTCCCTCCGTCTCAT 59.562 42.308 0.00 0.00 0.00 2.90
449 450 5.773680 CCTAAAATATACTCCCTCCGTCTCA 59.226 44.000 0.00 0.00 0.00 3.27
450 451 5.774184 ACCTAAAATATACTCCCTCCGTCTC 59.226 44.000 0.00 0.00 0.00 3.36
451 452 5.713807 ACCTAAAATATACTCCCTCCGTCT 58.286 41.667 0.00 0.00 0.00 4.18
452 453 5.537674 TGACCTAAAATATACTCCCTCCGTC 59.462 44.000 0.00 0.00 0.00 4.79
453 454 5.461327 TGACCTAAAATATACTCCCTCCGT 58.539 41.667 0.00 0.00 0.00 4.69
454 455 6.183360 TGTTGACCTAAAATATACTCCCTCCG 60.183 42.308 0.00 0.00 0.00 4.63
455 456 7.133133 TGTTGACCTAAAATATACTCCCTCC 57.867 40.000 0.00 0.00 0.00 4.30
491 492 6.395426 TCCGTACGGAATTACTTGTCATAT 57.605 37.500 33.96 0.00 42.05 1.78
509 510 6.358178 TGATTAAATTTATGCCACCTCCGTA 58.642 36.000 0.00 0.00 0.00 4.02
536 537 5.221823 TGGTCAAACCTAGATGTCATTGACA 60.222 40.000 21.05 21.05 45.11 3.58
592 593 3.326880 ACCCCGACACTTATTATGGATCC 59.673 47.826 4.20 4.20 0.00 3.36
611 612 6.947644 TGAACTAAGGTTACTTCAAAACCC 57.052 37.500 1.47 0.00 46.33 4.11
660 661 7.259161 AGGTCTCGAGTAATTCACTAATTCAC 58.741 38.462 13.13 0.00 37.72 3.18
661 662 7.406031 AGGTCTCGAGTAATTCACTAATTCA 57.594 36.000 13.13 0.00 37.72 2.57
662 663 9.235537 GTTAGGTCTCGAGTAATTCACTAATTC 57.764 37.037 13.13 0.00 37.72 2.17
663 664 8.746530 TGTTAGGTCTCGAGTAATTCACTAATT 58.253 33.333 13.13 0.00 37.72 1.40
664 665 8.289939 TGTTAGGTCTCGAGTAATTCACTAAT 57.710 34.615 13.13 0.00 37.72 1.73
665 666 7.692460 TGTTAGGTCTCGAGTAATTCACTAA 57.308 36.000 13.13 8.68 37.72 2.24
666 667 7.876936 ATGTTAGGTCTCGAGTAATTCACTA 57.123 36.000 13.13 3.35 37.72 2.74
667 668 6.777213 ATGTTAGGTCTCGAGTAATTCACT 57.223 37.500 13.13 4.25 41.47 3.41
742 752 6.777213 ATCCAGACGGACACTTATATATCC 57.223 41.667 0.00 0.00 46.79 2.59
743 753 7.036220 CCAATCCAGACGGACACTTATATATC 58.964 42.308 0.00 0.00 46.79 1.63
744 754 6.070767 CCCAATCCAGACGGACACTTATATAT 60.071 42.308 0.00 0.00 46.79 0.86
745 755 5.245301 CCCAATCCAGACGGACACTTATATA 59.755 44.000 0.00 0.00 46.79 0.86
746 756 4.040461 CCCAATCCAGACGGACACTTATAT 59.960 45.833 0.00 0.00 46.79 0.86
747 757 3.386726 CCCAATCCAGACGGACACTTATA 59.613 47.826 0.00 0.00 46.79 0.98
748 758 2.170607 CCCAATCCAGACGGACACTTAT 59.829 50.000 0.00 0.00 46.79 1.73
749 759 1.553248 CCCAATCCAGACGGACACTTA 59.447 52.381 0.00 0.00 46.79 2.24
750 760 0.324943 CCCAATCCAGACGGACACTT 59.675 55.000 0.00 0.00 46.79 3.16
792 802 2.627699 ACGTACGAGAACCCAAACCTTA 59.372 45.455 24.41 0.00 0.00 2.69
982 1011 2.791260 GCGTACGCGTAATTGCCGT 61.791 57.895 26.17 12.77 40.81 5.68
983 1012 2.054585 GCGTACGCGTAATTGCCG 60.055 61.111 26.17 20.04 40.81 5.69
1121 1189 0.958091 CGCGAGAGATGAGAAGGGAT 59.042 55.000 0.00 0.00 0.00 3.85
1128 1196 2.159448 AGACTTTGACGCGAGAGATGAG 60.159 50.000 15.93 3.55 0.00 2.90
1140 1208 8.819643 ATACTCAAACTCAGTAAGACTTTGAC 57.180 34.615 0.00 0.00 35.50 3.18
1242 1311 0.460284 ACATACCTCGCTTTGCTCCG 60.460 55.000 0.00 0.00 0.00 4.63
1249 1318 2.685897 GAGAGAGACACATACCTCGCTT 59.314 50.000 0.00 0.00 39.16 4.68
1335 1420 9.253832 TGAATTGAATGTTCATAAAGGGTGTAT 57.746 29.630 0.00 0.00 37.00 2.29
1458 1544 7.123547 ACAGTTATTTTGTTTTTCAGGTGAGGA 59.876 33.333 0.00 0.00 0.00 3.71
1505 1592 8.226448 CACAAACAAAAACAAAATAACAGCTCA 58.774 29.630 0.00 0.00 0.00 4.26
1506 1593 8.439286 TCACAAACAAAAACAAAATAACAGCTC 58.561 29.630 0.00 0.00 0.00 4.09
1510 1597 7.361286 GCCCTCACAAACAAAAACAAAATAACA 60.361 33.333 0.00 0.00 0.00 2.41
1513 1600 6.410540 AGCCCTCACAAACAAAAACAAAATA 58.589 32.000 0.00 0.00 0.00 1.40
1559 1646 7.288810 AGATTTGATGTCCTTGCAAAGTTTA 57.711 32.000 0.00 0.00 44.25 2.01
1620 1708 6.542852 CACCCTCATAAACAGTAAATTCGTG 58.457 40.000 0.00 0.00 0.00 4.35
1621 1709 5.123344 GCACCCTCATAAACAGTAAATTCGT 59.877 40.000 0.00 0.00 0.00 3.85
1622 1710 5.123186 TGCACCCTCATAAACAGTAAATTCG 59.877 40.000 0.00 0.00 0.00 3.34
1623 1711 6.374333 TCTGCACCCTCATAAACAGTAAATTC 59.626 38.462 0.00 0.00 0.00 2.17
1625 1713 5.815581 TCTGCACCCTCATAAACAGTAAAT 58.184 37.500 0.00 0.00 0.00 1.40
1626 1714 5.235850 TCTGCACCCTCATAAACAGTAAA 57.764 39.130 0.00 0.00 0.00 2.01
1633 1724 0.991146 TGCCTCTGCACCCTCATAAA 59.009 50.000 0.00 0.00 44.23 1.40
1645 1736 3.160047 AGCTCCCGGATGCCTCTG 61.160 66.667 0.73 0.00 0.00 3.35
1648 1739 1.689233 TAACAGCTCCCGGATGCCT 60.689 57.895 0.73 0.00 34.20 4.75
1653 1744 0.834687 AAGGTGTAACAGCTCCCGGA 60.835 55.000 0.73 0.00 41.59 5.14
1683 1774 2.517127 AGACCCCGAGGAAGAGGTATAA 59.483 50.000 0.00 0.00 36.73 0.98
1746 1841 1.905512 GTTAGGATCAGGCCCACGT 59.094 57.895 0.00 0.00 0.00 4.49
1747 1842 1.227263 CGTTAGGATCAGGCCCACG 60.227 63.158 0.00 0.00 0.00 4.94
1754 1867 2.602257 TGCACCATCGTTAGGATCAG 57.398 50.000 0.00 0.00 31.28 2.90
1795 1908 0.391228 TCTTGTTCTGCTGTGCCGTA 59.609 50.000 0.00 0.00 0.00 4.02
1842 1955 2.034048 TACGTTGGCCAGAGTGCACA 62.034 55.000 21.04 2.82 0.00 4.57
1908 2021 1.280133 CCTTGAGCCTCCTCATCACAA 59.720 52.381 0.00 0.00 46.84 3.33
1909 2022 0.907486 CCTTGAGCCTCCTCATCACA 59.093 55.000 0.00 0.00 46.84 3.58
2004 2117 7.660208 TCTTTCTATTAACCCCATCTAATTCGC 59.340 37.037 0.00 0.00 0.00 4.70
2079 2192 3.742433 AGGTAGATGCTGCTATGTGAC 57.258 47.619 0.00 0.00 0.00 3.67
2084 2197 1.001406 GGCGAAGGTAGATGCTGCTAT 59.999 52.381 0.00 0.00 0.00 2.97
2093 2212 1.684734 GGAGTGGGGCGAAGGTAGA 60.685 63.158 0.00 0.00 0.00 2.59
2097 2216 4.101448 CTGGGAGTGGGGCGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
2103 2222 1.303643 GTTTGAGCTGGGAGTGGGG 60.304 63.158 0.00 0.00 0.00 4.96
2391 2523 5.039920 TGGATACAGATTTGTCATCCAGG 57.960 43.478 16.62 0.00 46.17 4.45
2425 2557 5.587844 ACCATTCATAGTCTCTGCACAAATC 59.412 40.000 0.00 0.00 0.00 2.17
2462 2594 6.149308 GCACATAACCATATATACTTGCTGCA 59.851 38.462 0.00 0.00 0.00 4.41
2496 2856 3.319972 CCCATCGATCCTTTGCATCAATT 59.680 43.478 0.00 0.00 0.00 2.32
2518 4758 3.199289 TCTTCTTCGAAAAGGGGGTATCC 59.801 47.826 15.40 0.00 33.03 2.59
2523 4763 6.584185 TTTTTATCTTCTTCGAAAAGGGGG 57.416 37.500 15.40 0.00 33.03 5.40
2532 4772 7.948278 AGGGACGATATTTTTATCTTCTTCG 57.052 36.000 0.00 0.00 0.00 3.79
2541 4781 8.062065 AGCAAATGAAAGGGACGATATTTTTA 57.938 30.769 0.00 0.00 0.00 1.52
2547 4787 5.924356 TGATAGCAAATGAAAGGGACGATA 58.076 37.500 0.00 0.00 0.00 2.92
2634 6590 6.071447 TCATGGAAACCACAATGGAAACATAG 60.071 38.462 0.84 0.00 43.96 2.23
2647 6603 5.200368 ACTGACAAATTCATGGAAACCAC 57.800 39.130 0.00 0.00 35.80 4.16
2649 6605 7.408910 CAAAAACTGACAAATTCATGGAAACC 58.591 34.615 0.00 0.00 32.17 3.27
2656 6612 7.274447 ACACATCCAAAAACTGACAAATTCAT 58.726 30.769 0.00 0.00 32.17 2.57
2738 6711 3.057736 GCTTGATGAGTTGCAGTCATGTT 60.058 43.478 16.17 0.00 38.32 2.71
2761 6734 3.305964 CGATTGCTTGATCCAATGCATC 58.694 45.455 0.00 0.00 33.34 3.91
2781 6754 6.198403 ACACGTACATACTTTGAATCTATGCG 59.802 38.462 0.00 0.00 0.00 4.73
2786 6759 6.220930 ACACACACGTACATACTTTGAATCT 58.779 36.000 0.00 0.00 0.00 2.40
2798 7157 1.338526 CGCGCATACACACACGTACA 61.339 55.000 8.75 0.00 0.00 2.90
2804 7163 2.321333 CCCAACGCGCATACACACA 61.321 57.895 5.73 0.00 0.00 3.72
2820 7179 0.034059 CGCCCTCATCTCATGTACCC 59.966 60.000 0.00 0.00 0.00 3.69
2824 7183 2.107750 CGCGCCCTCATCTCATGT 59.892 61.111 0.00 0.00 0.00 3.21
2900 7259 1.734465 GAAATTCAGTCAGCTGGTCCG 59.266 52.381 15.13 0.23 42.78 4.79
2901 7260 3.064900 AGAAATTCAGTCAGCTGGTCC 57.935 47.619 15.13 2.19 42.78 4.46
2902 7261 6.749923 AATTAGAAATTCAGTCAGCTGGTC 57.250 37.500 15.13 7.79 42.78 4.02
2921 7280 7.654022 AAGAAAAAGTGACTGACCCAAATTA 57.346 32.000 0.00 0.00 0.00 1.40
2929 7288 6.411652 CGACTGTAAAGAAAAAGTGACTGAC 58.588 40.000 0.00 0.00 0.00 3.51
2950 7309 3.128242 TGCAACTAGACTACTTAGCCGAC 59.872 47.826 0.00 0.00 0.00 4.79
2957 7316 3.057456 CGGACTGTGCAACTAGACTACTT 60.057 47.826 0.00 0.00 38.04 2.24
2959 7318 2.415625 CCGGACTGTGCAACTAGACTAC 60.416 54.545 0.00 0.00 38.04 2.73
2962 7321 0.601558 TCCGGACTGTGCAACTAGAC 59.398 55.000 0.00 0.00 38.04 2.59
2967 7326 3.907894 TTTAATTCCGGACTGTGCAAC 57.092 42.857 1.83 0.00 37.35 4.17
2972 7331 3.426615 TGGCATTTTAATTCCGGACTGT 58.573 40.909 1.83 0.00 0.00 3.55
2977 7336 2.813061 CAGCTGGCATTTTAATTCCGG 58.187 47.619 5.57 0.00 32.10 5.14
2993 7352 2.047465 CTCGCTTGAGTGGCAGCT 60.047 61.111 0.00 0.00 34.89 4.24
2995 7354 3.123620 GCCTCGCTTGAGTGGCAG 61.124 66.667 11.43 0.00 46.64 4.85
2997 7356 4.704833 TGGCCTCGCTTGAGTGGC 62.705 66.667 3.32 8.54 46.68 5.01
2998 7357 1.888436 TAGTGGCCTCGCTTGAGTGG 61.888 60.000 3.32 0.00 38.10 4.00
2999 7358 0.737715 GTAGTGGCCTCGCTTGAGTG 60.738 60.000 3.32 0.00 38.10 3.51
3000 7359 0.900647 AGTAGTGGCCTCGCTTGAGT 60.901 55.000 3.32 0.00 38.10 3.41
3024 7383 0.736636 GCACTAGCTTGCATGCATGA 59.263 50.000 31.38 14.25 42.49 3.07
3117 7516 7.441890 TTGATTTGTGGCGTCTATTCTTTAA 57.558 32.000 0.00 0.00 0.00 1.52
3207 7606 5.121298 CACAAGTGATGTCTTTGATCATCGT 59.879 40.000 0.00 0.00 41.46 3.73
3209 7608 5.106436 TGCACAAGTGATGTCTTTGATCATC 60.106 40.000 4.04 0.00 41.46 2.92
3215 7614 3.488310 GCTTTGCACAAGTGATGTCTTTG 59.512 43.478 4.04 0.00 41.46 2.77
3367 7769 4.045022 AGGGTAATACTGGTGCCACTAAT 58.955 43.478 0.00 0.00 0.00 1.73
3371 7773 2.026636 TGAAGGGTAATACTGGTGCCAC 60.027 50.000 0.00 0.00 0.00 5.01
3377 7779 7.394816 TCTTTCTTCTTGAAGGGTAATACTGG 58.605 38.462 10.08 0.00 35.89 4.00
3378 7780 8.848474 TTCTTTCTTCTTGAAGGGTAATACTG 57.152 34.615 10.08 0.00 35.89 2.74
3379 7781 9.862149 TTTTCTTTCTTCTTGAAGGGTAATACT 57.138 29.630 10.08 0.00 35.89 2.12
3426 7844 9.693739 TTCTTACCAGGCTTCATTATTTTCATA 57.306 29.630 0.00 0.00 0.00 2.15
3429 7847 8.686334 TCATTCTTACCAGGCTTCATTATTTTC 58.314 33.333 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.