Multiple sequence alignment - TraesCS6A01G196000

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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 TraesCS6A01G196000 chr6A 100.000 6665 0 0 1 6665 283927050 283933714 0.000000e+00 12309.0
1 TraesCS6A01G196000 chr6A 86.239 109 10 3 2878 2984 438036119 438036014 5.460000e-21 113.0
2 TraesCS6A01G196000 chr6A 86.585 82 10 1 6161 6241 283927997 283928078 9.210000e-14 89.8
3 TraesCS6A01G196000 chr6A 86.585 82 10 1 948 1029 283933210 283933290 9.210000e-14 89.8
4 TraesCS6A01G196000 chr6A 76.023 171 34 6 4321 4487 381523238 381523071 1.540000e-11 82.4
5 TraesCS6A01G196000 chr6A 75.969 129 26 5 1967 2093 62652911 62652786 2.010000e-05 62.1
6 TraesCS6A01G196000 chr6D 95.897 2145 51 14 4552 6665 220295177 220297315 0.000000e+00 3439.0
7 TraesCS6A01G196000 chr6D 93.975 1892 86 15 1 1874 220293014 220294895 0.000000e+00 2837.0
8 TraesCS6A01G196000 chr6D 85.243 576 60 16 1871 2434 43038190 43038752 2.700000e-158 569.0
9 TraesCS6A01G196000 chr6D 87.732 269 28 2 3101 3364 220294892 220295160 6.490000e-80 309.0
10 TraesCS6A01G196000 chr6D 84.746 118 13 5 2991 3105 9197348 9197463 5.460000e-21 113.0
11 TraesCS6A01G196000 chr6D 86.585 82 10 1 6161 6241 220293956 220294037 9.210000e-14 89.8
12 TraesCS6A01G196000 chr6D 76.712 146 29 4 4283 4424 81197672 81197528 7.170000e-10 76.8
13 TraesCS6A01G196000 chrUn 92.563 2380 131 24 3896 6241 314077503 314079870 0.000000e+00 3373.0
14 TraesCS6A01G196000 chrUn 92.479 2380 133 24 3896 6241 314073771 314076138 0.000000e+00 3362.0
15 TraesCS6A01G196000 chrUn 93.480 1994 95 18 4281 6241 321289609 321287618 0.000000e+00 2929.0
16 TraesCS6A01G196000 chrUn 95.415 1483 38 16 14 1479 289920245 289918776 0.000000e+00 2335.0
17 TraesCS6A01G196000 chrUn 86.414 1185 132 13 3101 4270 289916967 289915797 0.000000e+00 1269.0
18 TraesCS6A01G196000 chrUn 86.245 1185 134 13 3101 4270 289918220 289917050 0.000000e+00 1258.0
19 TraesCS6A01G196000 chrUn 93.396 424 26 1 6243 6664 314076177 314076600 1.580000e-175 627.0
20 TraesCS6A01G196000 chrUn 93.396 424 26 1 6243 6664 314079909 314080332 1.580000e-175 627.0
21 TraesCS6A01G196000 chrUn 93.396 424 26 1 6243 6664 321287579 321287156 1.580000e-175 627.0
22 TraesCS6A01G196000 chrUn 87.603 484 59 1 3101 3583 403544701 403544218 1.620000e-155 560.0
23 TraesCS6A01G196000 chrUn 91.944 360 17 7 1132 1479 403545616 403545257 1.670000e-135 494.0
24 TraesCS6A01G196000 chrUn 89.623 106 9 2 3000 3103 86394114 86394219 4.190000e-27 134.0
25 TraesCS6A01G196000 chr2A 82.402 1074 111 36 1873 2877 568576189 568577253 0.000000e+00 865.0
26 TraesCS6A01G196000 chr2A 85.965 342 40 3 1911 2252 566451299 566450966 6.350000e-95 359.0
27 TraesCS6A01G196000 chr2A 79.625 427 76 9 3890 4313 547774959 547775377 5.050000e-76 296.0
28 TraesCS6A01G196000 chr2A 80.702 342 62 3 3977 4316 566988132 566987793 5.130000e-66 263.0
29 TraesCS6A01G196000 chr2A 76.170 470 86 12 3585 4041 84365609 84366065 2.420000e-54 224.0
30 TraesCS6A01G196000 chr2A 92.045 88 7 0 3585 3672 547774688 547774775 2.520000e-24 124.0
31 TraesCS6A01G196000 chr2A 100.000 29 0 0 2404 2432 16945527 16945499 3.000000e-03 54.7
32 TraesCS6A01G196000 chr4D 78.185 1311 207 40 3109 4384 371788507 371787241 0.000000e+00 763.0
33 TraesCS6A01G196000 chr4D 80.762 499 76 11 3105 3584 441900150 441899653 8.160000e-99 372.0
34 TraesCS6A01G196000 chr4D 73.718 468 86 22 1436 1868 441900622 441900157 1.500000e-31 148.0
35 TraesCS6A01G196000 chr4D 76.875 160 27 9 1871 2025 30498447 30498601 1.540000e-11 82.4
36 TraesCS6A01G196000 chr7B 76.906 1390 219 62 3110 4434 50980350 50978998 0.000000e+00 695.0
37 TraesCS6A01G196000 chr7B 85.542 415 51 5 2568 2976 633944126 633943715 6.180000e-115 425.0
38 TraesCS6A01G196000 chr7B 81.373 510 52 10 1871 2374 634049387 634048915 6.310000e-100 375.0
39 TraesCS6A01G196000 chr7B 73.922 464 88 12 1436 1866 136290457 136290920 8.950000e-34 156.0
40 TraesCS6A01G196000 chr7B 88.393 112 11 2 2994 3103 633943658 633943547 4.190000e-27 134.0
41 TraesCS6A01G196000 chr5D 85.814 571 38 14 1873 2433 59941113 59941650 3.490000e-157 566.0
42 TraesCS6A01G196000 chr5D 93.043 115 7 1 2812 2926 59941992 59942105 4.130000e-37 167.0
43 TraesCS6A01G196000 chr5D 84.906 53 8 0 1998 2050 7044037 7043985 3.000000e-03 54.7
44 TraesCS6A01G196000 chr1D 78.867 847 133 25 3585 4412 364093761 364094580 1.270000e-146 531.0
45 TraesCS6A01G196000 chr1D 84.185 411 50 13 1873 2276 478800943 478801345 1.050000e-102 385.0
46 TraesCS6A01G196000 chr1D 78.088 502 86 16 3107 3586 364093195 364093694 5.050000e-76 296.0
47 TraesCS6A01G196000 chr1D 84.393 173 24 2 1699 1869 469823429 469823258 4.130000e-37 167.0
48 TraesCS6A01G196000 chr1D 90.244 123 11 1 2983 3105 221298723 221298602 6.920000e-35 159.0
49 TraesCS6A01G196000 chr1D 98.148 54 1 0 2381 2434 389264183 389264236 1.980000e-15 95.3
50 TraesCS6A01G196000 chr1A 77.361 879 153 24 3585 4434 518470987 518470126 4.680000e-131 479.0
51 TraesCS6A01G196000 chr1A 77.778 549 67 31 1873 2380 391944368 391943834 3.040000e-73 287.0
52 TraesCS6A01G196000 chr1A 77.909 507 79 19 3105 3595 127074366 127073877 1.090000e-72 285.0
53 TraesCS6A01G196000 chr1A 89.756 205 13 5 2907 3105 12375034 12375236 8.580000e-64 255.0
54 TraesCS6A01G196000 chr1A 75.484 465 79 20 1436 1867 432625911 432625449 1.900000e-45 195.0
55 TraesCS6A01G196000 chr7D 81.240 645 59 36 2502 3103 542853616 542854241 1.310000e-126 464.0
56 TraesCS6A01G196000 chr7D 80.556 540 89 10 3774 4308 82607596 82607068 1.040000e-107 401.0
57 TraesCS6A01G196000 chr7D 74.696 411 68 22 1492 1869 500590637 500590230 4.160000e-32 150.0
58 TraesCS6A01G196000 chr7D 86.777 121 13 3 2983 3101 23499350 23499231 1.510000e-26 132.0
59 TraesCS6A01G196000 chr7D 90.000 100 10 0 3585 3684 270711121 270711022 5.420000e-26 130.0
60 TraesCS6A01G196000 chr7D 76.804 194 40 5 1436 1625 186511070 186511262 3.290000e-18 104.0
61 TraesCS6A01G196000 chr7D 91.045 67 6 0 2875 2941 94650312 94650246 2.560000e-14 91.6
62 TraesCS6A01G196000 chr2B 79.671 669 105 14 3584 4235 736121030 736121684 2.830000e-123 453.0
63 TraesCS6A01G196000 chr2B 82.456 342 55 5 3973 4312 493651955 493651617 1.820000e-75 294.0
64 TraesCS6A01G196000 chr2B 89.076 119 10 3 2988 3105 207474850 207474734 1.940000e-30 145.0
65 TraesCS6A01G196000 chr2B 96.296 54 2 0 2381 2434 232891679 232891732 9.210000e-14 89.8
66 TraesCS6A01G196000 chr2B 84.615 91 11 3 2895 2984 207475002 207474914 3.310000e-13 87.9
67 TraesCS6A01G196000 chr2B 78.571 140 20 7 1699 1837 148146103 148146233 4.280000e-12 84.2
68 TraesCS6A01G196000 chr3A 83.377 385 51 8 1870 2252 724134891 724134518 1.780000e-90 344.0
69 TraesCS6A01G196000 chr3A 76.887 212 40 8 4281 4485 61307220 61307429 1.960000e-20 111.0
70 TraesCS6A01G196000 chr3A 76.836 177 34 6 1699 1875 474806391 474806222 7.120000e-15 93.5
71 TraesCS6A01G196000 chr3A 100.000 28 0 0 1436 1463 558863447 558863420 1.200000e-02 52.8
72 TraesCS6A01G196000 chr2D 83.158 380 54 7 3106 3475 50440123 50439744 8.280000e-89 339.0
73 TraesCS6A01G196000 chr2D 77.114 402 50 21 3591 3977 598350167 598349793 1.900000e-45 195.0
74 TraesCS6A01G196000 chr4B 79.134 508 84 14 3105 3590 548766064 548765557 1.390000e-86 331.0
75 TraesCS6A01G196000 chr4B 76.734 447 68 21 1457 1869 548766514 548766070 4.050000e-52 217.0
76 TraesCS6A01G196000 chr3B 76.093 686 124 27 3771 4434 755078114 755077447 8.340000e-84 322.0
77 TraesCS6A01G196000 chr3B 81.373 102 14 3 1729 1827 153538820 153538721 1.990000e-10 78.7
78 TraesCS6A01G196000 chr6B 74.899 745 140 31 3585 4322 695194704 695195408 5.050000e-76 296.0
79 TraesCS6A01G196000 chr6B 94.000 50 2 1 2381 2430 644806152 644806200 2.580000e-09 75.0
80 TraesCS6A01G196000 chr5B 74.429 700 122 32 3811 4487 501099994 501100659 1.440000e-61 248.0
81 TraesCS6A01G196000 chr5B 87.500 112 9 3 2875 2984 434063770 434063662 2.520000e-24 124.0
82 TraesCS6A01G196000 chr5B 94.118 51 3 0 2381 2431 441680646 441680696 1.990000e-10 78.7
83 TraesCS6A01G196000 chr7A 74.840 469 85 16 1436 1871 724609636 724610104 1.480000e-41 182.0
84 TraesCS6A01G196000 chr7A 90.435 115 9 2 2988 3101 671699000 671698887 4.160000e-32 150.0
85 TraesCS6A01G196000 chr3D 79.885 174 33 2 1697 1869 68832545 68832373 7.020000e-25 126.0
86 TraesCS6A01G196000 chr3D 94.118 68 4 0 2654 2721 364518261 364518328 3.290000e-18 104.0
87 TraesCS6A01G196000 chr5A 86.607 112 10 5 2875 2984 468940780 468940672 1.170000e-22 119.0
88 TraesCS6A01G196000 chr4A 80.899 89 17 0 3481 3569 587202830 587202918 3.330000e-08 71.3


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 TraesCS6A01G196000 chr6A 283927050 283933714 6664 False 12309.000000 12309 100.00000 1 6665 1 chr6A.!!$F1 6664
1 TraesCS6A01G196000 chr6D 220293014 220297315 4301 False 1668.700000 3439 91.04725 1 6665 4 chr6D.!!$F3 6664
2 TraesCS6A01G196000 chr6D 43038190 43038752 562 False 569.000000 569 85.24300 1871 2434 1 chr6D.!!$F2 563
3 TraesCS6A01G196000 chrUn 314073771 314080332 6561 False 1997.250000 3373 92.95850 3896 6664 4 chrUn.!!$F2 2768
4 TraesCS6A01G196000 chrUn 321287156 321289609 2453 True 1778.000000 2929 93.43800 4281 6664 2 chrUn.!!$R2 2383
5 TraesCS6A01G196000 chrUn 289915797 289920245 4448 True 1620.666667 2335 89.35800 14 4270 3 chrUn.!!$R1 4256
6 TraesCS6A01G196000 chrUn 403544218 403545616 1398 True 527.000000 560 89.77350 1132 3583 2 chrUn.!!$R3 2451
7 TraesCS6A01G196000 chr2A 568576189 568577253 1064 False 865.000000 865 82.40200 1873 2877 1 chr2A.!!$F2 1004
8 TraesCS6A01G196000 chr2A 547774688 547775377 689 False 210.000000 296 85.83500 3585 4313 2 chr2A.!!$F3 728
9 TraesCS6A01G196000 chr4D 371787241 371788507 1266 True 763.000000 763 78.18500 3109 4384 1 chr4D.!!$R1 1275
10 TraesCS6A01G196000 chr4D 441899653 441900622 969 True 260.000000 372 77.24000 1436 3584 2 chr4D.!!$R2 2148
11 TraesCS6A01G196000 chr7B 50978998 50980350 1352 True 695.000000 695 76.90600 3110 4434 1 chr7B.!!$R1 1324
12 TraesCS6A01G196000 chr7B 633943547 633944126 579 True 279.500000 425 86.96750 2568 3103 2 chr7B.!!$R3 535
13 TraesCS6A01G196000 chr5D 59941113 59942105 992 False 366.500000 566 89.42850 1873 2926 2 chr5D.!!$F1 1053
14 TraesCS6A01G196000 chr1D 364093195 364094580 1385 False 413.500000 531 78.47750 3107 4412 2 chr1D.!!$F3 1305
15 TraesCS6A01G196000 chr1A 518470126 518470987 861 True 479.000000 479 77.36100 3585 4434 1 chr1A.!!$R4 849
16 TraesCS6A01G196000 chr1A 391943834 391944368 534 True 287.000000 287 77.77800 1873 2380 1 chr1A.!!$R2 507
17 TraesCS6A01G196000 chr7D 542853616 542854241 625 False 464.000000 464 81.24000 2502 3103 1 chr7D.!!$F2 601
18 TraesCS6A01G196000 chr7D 82607068 82607596 528 True 401.000000 401 80.55600 3774 4308 1 chr7D.!!$R2 534
19 TraesCS6A01G196000 chr2B 736121030 736121684 654 False 453.000000 453 79.67100 3584 4235 1 chr2B.!!$F3 651
20 TraesCS6A01G196000 chr4B 548765557 548766514 957 True 274.000000 331 77.93400 1457 3590 2 chr4B.!!$R1 2133
21 TraesCS6A01G196000 chr3B 755077447 755078114 667 True 322.000000 322 76.09300 3771 4434 1 chr3B.!!$R2 663
22 TraesCS6A01G196000 chr6B 695194704 695195408 704 False 296.000000 296 74.89900 3585 4322 1 chr6B.!!$F2 737
23 TraesCS6A01G196000 chr5B 501099994 501100659 665 False 248.000000 248 74.42900 3811 4487 1 chr5B.!!$F2 676

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
197 203 1.682854 CATAGAAATTGGGCCACGCAT 59.317 47.619 5.23 0.0 0.00 4.73 F
1481 1499 0.389391 CCTCCCGCATTCATCTACGT 59.611 55.000 0.00 0.0 0.00 3.57 F
2121 2389 0.173029 CTGACACGCATGAGCTCTCT 59.827 55.000 16.19 0.0 39.10 3.10 F
3013 3427 0.182775 GGGGGCAACGAGTGGATAAT 59.817 55.000 0.00 0.0 37.60 1.28 F
3225 3641 0.253160 TACCTGGCCATCTCCCTGTT 60.253 55.000 5.51 0.0 0.00 3.16 F
4291 6192 0.179040 GGTCACGAGTTTTGGGTGGA 60.179 55.000 0.00 0.0 32.65 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2290 0.531090 TAAACATATCGCCGGCGCTT 60.531 50.000 42.78 32.37 39.59 4.68 R
3373 3807 0.179179 GAGTACGTCGACCGGGAAAG 60.179 60.000 10.58 0.00 42.24 2.62 R
3750 5455 0.539438 ACCACCACAATTCGCACCAT 60.539 50.000 0.00 0.00 0.00 3.55 R
4279 6180 0.251787 GCCCTGATCCACCCAAAACT 60.252 55.000 0.00 0.00 0.00 2.66 R
5219 7136 0.110238 CAACCAACGAGCGAACCATG 60.110 55.000 0.00 0.00 0.00 3.66 R
5990 7920 1.067250 GCAACCCGAGCAAAGCAAA 59.933 52.632 0.00 0.00 0.00 3.68 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
146 152 2.193248 CCATTTCCCGGGCTCTCC 59.807 66.667 18.49 0.00 0.00 3.71
147 153 2.378634 CCATTTCCCGGGCTCTCCT 61.379 63.158 18.49 0.00 0.00 3.69
197 203 1.682854 CATAGAAATTGGGCCACGCAT 59.317 47.619 5.23 0.00 0.00 4.73
416 422 5.735285 TCTTGATTTCTTCTCTCTGCTCA 57.265 39.130 0.00 0.00 0.00 4.26
463 469 6.207810 GGTCTAACCTGAGATCTATCAACGAT 59.792 42.308 0.00 0.00 34.73 3.73
895 901 5.990996 ACGCCAGTTTTGATTGATTCATTTT 59.009 32.000 0.00 0.00 33.34 1.82
918 924 8.859517 TTTGCTAAACTGCGTTTTAATTAGTT 57.140 26.923 10.96 0.00 37.01 2.24
919 925 9.947669 TTTGCTAAACTGCGTTTTAATTAGTTA 57.052 25.926 10.96 0.00 37.01 2.24
1293 1299 7.344352 AGCTCTTCTTTCCATCTGACTAATAGT 59.656 37.037 0.00 0.00 0.00 2.12
1409 1417 2.012237 CAAGCTAGACGCCATGCTG 58.988 57.895 0.00 0.00 40.39 4.41
1426 1434 6.567321 GCCATGCTGATTGTAAGTGCTATTAG 60.567 42.308 0.00 0.00 0.00 1.73
1452 1470 0.608856 ATGCATCTCCAACGGCAACA 60.609 50.000 0.00 0.00 40.02 3.33
1481 1499 0.389391 CCTCCCGCATTCATCTACGT 59.611 55.000 0.00 0.00 0.00 3.57
1505 1724 1.499049 GAAATCAGTCCGCGGATACC 58.501 55.000 33.58 19.17 0.00 2.73
1533 1752 4.202080 CGGAAGGTCGACATCCAATACTAA 60.202 45.833 28.55 0.00 32.58 2.24
1576 1796 4.250464 ACTCGAATCAACGGCAGAAATTA 58.750 39.130 0.00 0.00 0.00 1.40
1743 1991 0.467384 CTCCTCCATCATCGTTGCCT 59.533 55.000 0.00 0.00 0.00 4.75
1761 2011 2.342648 GTCGCCGTTGGAGGAGTT 59.657 61.111 0.00 0.00 32.66 3.01
1815 2065 3.211963 GCGGCAATGCTTCCCGAT 61.212 61.111 4.82 0.00 44.55 4.18
1847 2097 1.410517 GCTCACGGATGATCCTCTTCA 59.589 52.381 10.18 0.00 33.30 3.02
1923 2176 3.070018 CTCAGGAGCACTTTTTCATCGT 58.930 45.455 0.00 0.00 0.00 3.73
1929 2182 1.334599 GCACTTTTTCATCGTCGGCAA 60.335 47.619 0.00 0.00 0.00 4.52
1964 2217 0.466922 CTCATGCCCCAAGGATCACC 60.467 60.000 0.00 0.00 33.47 4.02
2037 2290 1.383664 CCCCTGAGAGGCATCTGGA 60.384 63.158 5.17 0.00 39.90 3.86
2080 2333 2.576832 GCAAAGGCCCACATGCAGT 61.577 57.895 13.06 0.00 38.63 4.40
2112 2376 1.603802 CACTTTTCACCTGACACGCAT 59.396 47.619 0.00 0.00 0.00 4.73
2118 2386 1.079543 ACCTGACACGCATGAGCTC 60.080 57.895 6.82 6.82 39.10 4.09
2121 2389 0.173029 CTGACACGCATGAGCTCTCT 59.827 55.000 16.19 0.00 39.10 3.10
2154 2422 4.528596 TCTCTCCTCGTCTTTTCTTCCAAT 59.471 41.667 0.00 0.00 0.00 3.16
2182 2459 4.421479 CTCGCCGTCTCTTGCCGT 62.421 66.667 0.00 0.00 0.00 5.68
2441 2808 3.902086 GAGCGGACGGCCTCCTAC 61.902 72.222 5.33 9.99 45.17 3.18
2444 2811 3.834799 CGGACGGCCTCCTACACC 61.835 72.222 5.33 2.70 36.80 4.16
2445 2812 2.682494 GGACGGCCTCCTACACCA 60.682 66.667 0.00 0.00 35.89 4.17
2449 2816 3.075005 GGCCTCCTACACCAGCGA 61.075 66.667 0.00 0.00 0.00 4.93
2455 2822 4.063967 CTACACCAGCGACGGCCA 62.064 66.667 2.24 0.00 41.24 5.36
2610 3018 1.676635 GCATGAGCCAGACCTTGCA 60.677 57.895 0.00 0.00 34.72 4.08
2654 3064 4.100084 CCACTGCTCATCCGGCCA 62.100 66.667 2.24 0.00 0.00 5.36
2681 3091 3.984193 GACGCCATGGCCAGAGCTT 62.984 63.158 30.79 16.45 39.73 3.74
2752 3166 4.641645 TGCCCCCACGAGCACTTG 62.642 66.667 0.00 0.00 33.08 3.16
2763 3177 3.352222 GCACTTGCGAGCTGCTGT 61.352 61.111 7.01 0.00 46.63 4.40
2765 3179 1.082300 CACTTGCGAGCTGCTGTTG 60.082 57.895 7.01 0.00 46.63 3.33
2767 3181 3.606065 CTTGCGAGCTGCTGTTGCC 62.606 63.158 7.01 0.00 46.63 4.52
2768 3182 4.631247 TGCGAGCTGCTGTTGCCT 62.631 61.111 7.01 0.00 46.63 4.75
2769 3183 3.797546 GCGAGCTGCTGTTGCCTC 61.798 66.667 7.01 0.00 41.73 4.70
2770 3184 3.123620 CGAGCTGCTGTTGCCTCC 61.124 66.667 7.01 0.00 38.71 4.30
2771 3185 2.350514 GAGCTGCTGTTGCCTCCT 59.649 61.111 7.01 0.00 38.71 3.69
2772 3186 2.033757 AGCTGCTGTTGCCTCCTG 59.966 61.111 0.00 0.00 38.71 3.86
2774 3188 3.429141 CTGCTGTTGCCTCCTGCG 61.429 66.667 0.00 0.00 45.60 5.18
2777 3191 3.730761 CTGTTGCCTCCTGCGCAC 61.731 66.667 5.66 0.00 45.60 5.34
2812 3226 4.587189 CGCGGCCCTACCTGCTAC 62.587 72.222 0.00 0.00 36.28 3.58
2814 3228 2.732619 GCGGCCCTACCTGCTACTT 61.733 63.158 0.00 0.00 35.76 2.24
2815 3229 1.144057 CGGCCCTACCTGCTACTTG 59.856 63.158 0.00 0.00 35.61 3.16
2816 3230 1.153147 GGCCCTACCTGCTACTTGC 60.153 63.158 0.00 0.00 43.25 4.01
2817 3231 1.521681 GCCCTACCTGCTACTTGCG 60.522 63.158 0.00 0.00 46.63 4.85
2818 3232 1.521681 CCCTACCTGCTACTTGCGC 60.522 63.158 0.00 0.00 46.63 6.09
2819 3233 1.521681 CCTACCTGCTACTTGCGCC 60.522 63.158 4.18 0.00 46.63 6.53
2820 3234 1.878522 CTACCTGCTACTTGCGCCG 60.879 63.158 4.18 0.00 46.63 6.46
2823 3237 2.202743 CTGCTACTTGCGCCGCTA 60.203 61.111 11.67 0.48 46.63 4.26
2824 3238 1.592669 CTGCTACTTGCGCCGCTAT 60.593 57.895 11.67 0.00 46.63 2.97
2825 3239 1.153449 TGCTACTTGCGCCGCTATT 60.153 52.632 11.67 0.00 46.63 1.73
2827 3241 1.276844 CTACTTGCGCCGCTATTGC 59.723 57.895 11.67 0.00 0.00 3.56
2828 3242 1.153449 TACTTGCGCCGCTATTGCT 60.153 52.632 11.67 0.00 36.97 3.91
2830 3244 4.178214 TTGCGCCGCTATTGCTGC 62.178 61.111 11.67 5.52 44.27 5.25
2833 3247 3.643978 CGCCGCTATTGCTGCCTC 61.644 66.667 9.65 0.00 44.77 4.70
2834 3248 3.282920 GCCGCTATTGCTGCCTCC 61.283 66.667 4.28 0.00 42.39 4.30
2835 3249 2.507944 CCGCTATTGCTGCCTCCT 59.492 61.111 0.00 0.00 36.97 3.69
2836 3250 1.890979 CCGCTATTGCTGCCTCCTG 60.891 63.158 0.00 0.00 36.97 3.86
2837 3251 2.541120 CGCTATTGCTGCCTCCTGC 61.541 63.158 0.00 0.00 41.77 4.85
2838 3252 2.541120 GCTATTGCTGCCTCCTGCG 61.541 63.158 0.00 0.00 45.60 5.18
2839 3253 2.514592 TATTGCTGCCTCCTGCGC 60.515 61.111 0.00 0.00 45.60 6.09
2907 3321 4.796231 CCGTCGGCGACCTCCTTG 62.796 72.222 31.86 17.55 41.33 3.61
2908 3322 4.796231 CGTCGGCGACCTCCTTGG 62.796 72.222 31.86 13.91 41.33 3.61
2912 3326 4.388499 GGCGACCTCCTTGGCGAA 62.388 66.667 0.00 0.00 40.22 4.70
2913 3327 2.815647 GCGACCTCCTTGGCGAAG 60.816 66.667 0.74 0.74 40.22 3.79
2920 3334 2.124151 CCTTGGCGAAGGGGATGG 60.124 66.667 19.17 0.00 44.76 3.51
2921 3335 2.679342 CCTTGGCGAAGGGGATGGA 61.679 63.158 19.17 0.00 44.76 3.41
2923 3337 1.915078 CTTGGCGAAGGGGATGGACT 61.915 60.000 0.00 0.00 0.00 3.85
2925 3339 2.506472 GCGAAGGGGATGGACTCC 59.494 66.667 0.00 0.00 44.11 3.85
2926 3340 2.815308 CGAAGGGGATGGACTCCG 59.185 66.667 0.00 0.00 46.01 4.63
2930 3344 3.234730 GGGGATGGACTCCGCGAT 61.235 66.667 8.23 0.00 45.94 4.58
2931 3345 2.029666 GGGATGGACTCCGCGATG 59.970 66.667 8.23 1.41 46.01 3.84
2933 3347 1.144057 GGATGGACTCCGCGATGTT 59.856 57.895 8.23 0.00 33.29 2.71
2937 3351 1.810030 GGACTCCGCGATGTTGTCC 60.810 63.158 8.23 13.40 40.05 4.02
2938 3352 2.126071 ACTCCGCGATGTTGTCCG 60.126 61.111 8.23 0.00 0.00 4.79
2943 3357 2.809601 GCGATGTTGTCCGCGACT 60.810 61.111 8.23 0.00 42.02 4.18
2944 3358 3.071459 GCGATGTTGTCCGCGACTG 62.071 63.158 8.23 0.00 42.02 3.51
2987 3401 2.103143 CGAGCAGCAGGAGGTACG 59.897 66.667 0.00 0.00 0.00 3.67
2988 3402 2.701780 CGAGCAGCAGGAGGTACGT 61.702 63.158 0.00 0.00 0.00 3.57
2989 3403 1.153745 GAGCAGCAGGAGGTACGTG 60.154 63.158 0.00 0.00 37.43 4.49
2995 3409 3.379445 AGGAGGTACGTGCGTGGG 61.379 66.667 2.90 0.00 0.00 4.61
2996 3410 4.446413 GGAGGTACGTGCGTGGGG 62.446 72.222 2.90 0.00 0.00 4.96
2997 3411 4.446413 GAGGTACGTGCGTGGGGG 62.446 72.222 2.90 0.00 0.00 5.40
3011 3425 3.316029 GGGGGCAACGAGTGGATA 58.684 61.111 0.00 0.00 37.60 2.59
3013 3427 0.182775 GGGGGCAACGAGTGGATAAT 59.817 55.000 0.00 0.00 37.60 1.28
3014 3428 1.409661 GGGGGCAACGAGTGGATAATT 60.410 52.381 0.00 0.00 37.60 1.40
3015 3429 2.375146 GGGGCAACGAGTGGATAATTT 58.625 47.619 0.00 0.00 37.60 1.82
3016 3430 2.758423 GGGGCAACGAGTGGATAATTTT 59.242 45.455 0.00 0.00 37.60 1.82
3017 3431 3.194755 GGGGCAACGAGTGGATAATTTTT 59.805 43.478 0.00 0.00 37.60 1.94
3019 3433 4.082463 GGGCAACGAGTGGATAATTTTTCA 60.082 41.667 0.00 0.00 37.60 2.69
3020 3434 5.394115 GGGCAACGAGTGGATAATTTTTCAT 60.394 40.000 0.00 0.00 37.60 2.57
3023 3437 6.265577 CAACGAGTGGATAATTTTTCATCCC 58.734 40.000 3.08 0.00 40.11 3.85
3025 3439 4.024048 CGAGTGGATAATTTTTCATCCCCG 60.024 45.833 3.08 1.55 40.11 5.73
3026 3440 4.215109 AGTGGATAATTTTTCATCCCCGG 58.785 43.478 0.00 0.00 40.11 5.73
3028 3442 4.037565 GTGGATAATTTTTCATCCCCGGAC 59.962 45.833 0.73 0.00 40.11 4.79
3029 3443 4.079443 TGGATAATTTTTCATCCCCGGACT 60.079 41.667 0.73 0.00 40.11 3.85
3030 3444 5.132985 TGGATAATTTTTCATCCCCGGACTA 59.867 40.000 0.73 0.00 40.11 2.59
3031 3445 6.066032 GGATAATTTTTCATCCCCGGACTAA 58.934 40.000 0.73 0.00 35.61 2.24
3032 3446 6.548251 GGATAATTTTTCATCCCCGGACTAAA 59.452 38.462 0.73 0.00 35.61 1.85
3033 3447 7.232737 GGATAATTTTTCATCCCCGGACTAAAT 59.767 37.037 0.73 0.00 35.61 1.40
3034 3448 5.852282 ATTTTTCATCCCCGGACTAAATG 57.148 39.130 0.73 0.00 0.00 2.32
3035 3449 4.310022 TTTTCATCCCCGGACTAAATGT 57.690 40.909 0.73 0.00 0.00 2.71
3036 3450 4.310022 TTTCATCCCCGGACTAAATGTT 57.690 40.909 0.73 0.00 0.00 2.71
3037 3451 3.275617 TCATCCCCGGACTAAATGTTG 57.724 47.619 0.73 0.00 0.00 3.33
3038 3452 1.676006 CATCCCCGGACTAAATGTTGC 59.324 52.381 0.73 0.00 0.00 4.17
3039 3453 0.391927 TCCCCGGACTAAATGTTGCG 60.392 55.000 0.73 0.00 0.00 4.85
3040 3454 1.427819 CCCGGACTAAATGTTGCGC 59.572 57.895 0.73 0.00 0.00 6.09
3042 3456 1.060308 CGGACTAAATGTTGCGCCG 59.940 57.895 4.18 0.00 0.00 6.46
3043 3457 1.427819 GGACTAAATGTTGCGCCGG 59.572 57.895 4.18 0.00 0.00 6.13
3044 3458 1.226295 GACTAAATGTTGCGCCGGC 60.226 57.895 19.07 19.07 40.52 6.13
3087 3501 2.061790 GCCTCCTAGGGGCTCAATGG 62.062 65.000 25.84 4.51 45.57 3.16
3088 3502 1.453669 CTCCTAGGGGCTCAATGGC 59.546 63.158 9.46 0.00 40.96 4.40
3089 3503 1.004758 TCCTAGGGGCTCAATGGCT 59.995 57.895 9.46 0.00 41.48 4.75
3090 3504 1.150081 CCTAGGGGCTCAATGGCTG 59.850 63.158 0.00 0.00 41.48 4.85
3091 3505 1.150081 CTAGGGGCTCAATGGCTGG 59.850 63.158 0.00 0.00 41.48 4.85
3092 3506 1.307778 TAGGGGCTCAATGGCTGGA 60.308 57.895 0.00 0.00 41.48 3.86
3094 3508 2.683465 GGGGCTCAATGGCTGGAGA 61.683 63.158 5.11 0.00 41.48 3.71
3099 3513 1.595466 CTCAATGGCTGGAGATGCTC 58.405 55.000 0.00 0.00 32.87 4.26
3103 3517 3.200605 TCAATGGCTGGAGATGCTCTTAA 59.799 43.478 0.00 0.00 0.00 1.85
3225 3641 0.253160 TACCTGGCCATCTCCCTGTT 60.253 55.000 5.51 0.00 0.00 3.16
3340 3761 3.148279 GGCGGGATGTCGGAGTCT 61.148 66.667 0.00 0.00 0.00 3.24
3357 3778 3.687125 AGTCTGTGAACTAGGATCGACA 58.313 45.455 0.00 0.00 0.00 4.35
3364 3798 3.280295 GAACTAGGATCGACAGAGTCCA 58.720 50.000 4.88 0.00 34.42 4.02
3373 3807 0.458716 GACAGAGTCCAACTAGCGCC 60.459 60.000 2.29 0.00 0.00 6.53
3374 3808 0.900647 ACAGAGTCCAACTAGCGCCT 60.901 55.000 2.29 0.00 0.00 5.52
3403 3837 3.812019 CGTACTCCTGCGCCGTCT 61.812 66.667 4.18 0.00 0.00 4.18
3548 4000 2.035442 GGCGCTCCTCCTTCACAAC 61.035 63.158 7.64 0.00 0.00 3.32
3639 5344 0.908198 GACATCACAGGGAGGAGCTT 59.092 55.000 0.00 0.00 0.00 3.74
3672 5377 4.715523 CGGGCCGTTGGTGTGGAT 62.716 66.667 19.97 0.00 0.00 3.41
3676 5381 1.599518 GCCGTTGGTGTGGATGACA 60.600 57.895 0.00 0.00 0.00 3.58
3763 5468 4.713946 ACCGATGGTGCGAATTGT 57.286 50.000 0.00 0.00 32.98 2.71
3764 5469 2.170738 ACCGATGGTGCGAATTGTG 58.829 52.632 0.00 0.00 32.98 3.33
3765 5470 1.305219 ACCGATGGTGCGAATTGTGG 61.305 55.000 0.00 0.00 32.98 4.17
3766 5471 1.305219 CCGATGGTGCGAATTGTGGT 61.305 55.000 0.00 0.00 0.00 4.16
3870 5578 3.382832 CAACGGCCTCGGAGTCCT 61.383 66.667 7.77 0.00 41.39 3.85
3972 5768 2.520741 GGCGAGGAGGAGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
3973 5769 2.520741 GCGAGGAGGAGGAGGAGG 60.521 72.222 0.00 0.00 0.00 4.30
3974 5770 3.063197 GCGAGGAGGAGGAGGAGGA 62.063 68.421 0.00 0.00 0.00 3.71
3975 5771 1.150536 CGAGGAGGAGGAGGAGGAG 59.849 68.421 0.00 0.00 0.00 3.69
3976 5772 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
3977 5773 2.018086 AGGAGGAGGAGGAGGAGGG 61.018 68.421 0.00 0.00 0.00 4.30
3998 5794 1.474143 GGAGGAAGAAGAAGGATGCGG 60.474 57.143 0.00 0.00 0.00 5.69
4003 5799 0.976641 AGAAGAAGGATGCGGTGTGA 59.023 50.000 0.00 0.00 0.00 3.58
4101 5897 1.003233 GAATGGAGTTGGTTCCTCGGT 59.997 52.381 0.00 0.00 38.12 4.69
4105 5901 1.345415 GGAGTTGGTTCCTCGGTAACA 59.655 52.381 0.00 0.00 34.27 2.41
4108 5904 2.370849 AGTTGGTTCCTCGGTAACATGT 59.629 45.455 0.00 0.00 0.00 3.21
4178 6068 1.062886 CCTCCCTCCTCTGGTCACATA 60.063 57.143 0.00 0.00 0.00 2.29
4291 6192 0.179040 GGTCACGAGTTTTGGGTGGA 60.179 55.000 0.00 0.00 32.65 4.02
4319 6223 4.033776 CAGAAGCGGGCTTGGGGA 62.034 66.667 11.17 0.00 36.26 4.81
4340 6246 0.689623 CCAGACTCCTGCAAACCTCT 59.310 55.000 0.00 0.00 39.07 3.69
4341 6247 1.902508 CCAGACTCCTGCAAACCTCTA 59.097 52.381 0.00 0.00 39.07 2.43
4356 6262 6.017109 GCAAACCTCTACATTTTTGTCTCTGA 60.017 38.462 0.00 0.00 32.57 3.27
4379 6285 6.654582 TGATTTTCAGGAGAAATCATGTTCGA 59.345 34.615 7.87 0.00 42.90 3.71
4405 6311 0.534427 TCGCGGACCGATACAGATCT 60.534 55.000 20.50 0.00 41.89 2.75
4412 6318 0.855349 CCGATACAGATCTGCGTTGC 59.145 55.000 22.83 7.06 0.00 4.17
4425 6331 0.567509 GCGTTGCATAATTTCTGCGC 59.432 50.000 0.00 0.00 42.62 6.09
4434 6340 0.605319 AATTTCTGCGCTCCGGACAA 60.605 50.000 9.73 0.79 0.00 3.18
4435 6341 0.392998 ATTTCTGCGCTCCGGACAAT 60.393 50.000 9.73 2.86 0.00 2.71
4439 6345 2.434185 GCGCTCCGGACAATGTCA 60.434 61.111 15.86 0.00 33.68 3.58
4488 6394 1.393603 GCCTTGAAGATGCCCTTACC 58.606 55.000 0.00 0.00 34.68 2.85
4524 6441 3.924114 ACGTATGGATTGATTGGACCA 57.076 42.857 0.00 0.00 36.83 4.02
4534 6451 4.494091 TTGATTGGACCAAGAGAGATCC 57.506 45.455 13.43 0.00 0.00 3.36
4547 6464 4.865905 AGAGAGATCCTGAACTGAGCTAA 58.134 43.478 0.00 0.00 0.00 3.09
4566 6483 5.293569 AGCTAAAGTAATGGTCGTAATGCAC 59.706 40.000 0.00 0.00 0.00 4.57
5257 7174 3.921119 TGTTGATGGTGAAGTTGCATC 57.079 42.857 0.00 0.00 0.00 3.91
5298 7215 2.025441 CTGGAGAGCTACTCGCGC 59.975 66.667 0.00 0.00 45.76 6.86
5540 7460 1.140652 GCTCATGAGGAAGAAGGAGGG 59.859 57.143 23.89 0.00 0.00 4.30
5629 7549 0.965866 CTCCTACGTGGACAGCCTCA 60.966 60.000 0.00 0.00 40.56 3.86
5705 7627 3.972971 GAGAGCCAGGCCAGCACAG 62.973 68.421 18.87 0.00 0.00 3.66
5834 7759 1.005804 CATCACCGGCTCGATCGATG 61.006 60.000 19.78 13.64 0.00 3.84
5860 7785 1.320344 CCGGACTCGTTCATCCCTCA 61.320 60.000 0.00 0.00 33.95 3.86
5879 7809 4.825634 CCTCACATATACAGTAGACCGGAA 59.174 45.833 9.46 0.00 0.00 4.30
5986 7916 1.198408 CGACATGTGCATGCAAGAACT 59.802 47.619 24.58 3.72 42.39 3.01
6030 7960 2.293122 TGTTGTACGTACGTGGCTACTT 59.707 45.455 30.25 3.43 0.00 2.24
6095 8056 2.514902 CGGGCAAACACATTGTATTCG 58.485 47.619 0.00 0.00 41.32 3.34
6194 8156 7.617041 ATTACCATTCTAGCTTGTTCTGTTC 57.383 36.000 0.00 0.00 0.00 3.18
6241 8240 3.929610 AGAGATTTGCGAAACTACTGCTC 59.070 43.478 0.00 0.00 0.00 4.26
6354 8353 0.329596 GGCTCCTGGTCACAAAGGAT 59.670 55.000 0.00 0.00 41.74 3.24
6394 8395 1.953231 GCCCGCCTAGTTAGTCGGTT 61.953 60.000 7.72 0.00 40.23 4.44
6491 8492 2.741612 AGAGATCGACGTACTAGACCG 58.258 52.381 0.00 0.00 0.00 4.79
6558 8559 2.297912 CGTCCTTCGTTTGTCGCGT 61.298 57.895 5.77 0.00 39.67 6.01
6600 8601 1.373497 AAGAGACACAAGCTCCGCG 60.373 57.895 0.00 0.00 32.82 6.46
6636 8637 2.940994 TCCGGTGATCAAACCAGAAA 57.059 45.000 0.00 0.00 40.53 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 127 1.153086 CCGGGAAATGGGCAGAGAG 60.153 63.158 0.00 0.00 0.00 3.20
146 152 1.593265 GGCATTGCCCTGTTTGGAG 59.407 57.895 17.28 0.00 44.06 3.86
147 153 3.790223 GGCATTGCCCTGTTTGGA 58.210 55.556 17.28 0.00 44.06 3.53
189 195 1.098050 AAATCCTTCTGATGCGTGGC 58.902 50.000 0.00 0.00 32.68 5.01
191 197 4.271049 ACGATTAAATCCTTCTGATGCGTG 59.729 41.667 0.00 0.00 32.68 5.34
197 203 4.095334 TCGACGACGATTAAATCCTTCTGA 59.905 41.667 5.75 0.00 43.81 3.27
416 422 4.141959 CCAAAGAGGACCAAACAACACAAT 60.142 41.667 0.00 0.00 41.22 2.71
463 469 1.355971 GACAAGAGCCGCAATAACGA 58.644 50.000 0.00 0.00 34.06 3.85
918 924 5.587043 CGACCAAATTAACTGGCACCTTATA 59.413 40.000 5.50 0.00 37.48 0.98
919 925 4.398044 CGACCAAATTAACTGGCACCTTAT 59.602 41.667 5.50 0.00 37.48 1.73
1293 1299 8.275187 ACCCCAAGATGTTACAATGATAGATA 57.725 34.615 0.00 0.00 0.00 1.98
1297 1303 7.123547 GGAAAACCCCAAGATGTTACAATGATA 59.876 37.037 0.00 0.00 0.00 2.15
1301 1307 5.402630 AGGAAAACCCCAAGATGTTACAAT 58.597 37.500 0.00 0.00 34.66 2.71
1397 1405 2.283298 CTTACAATCAGCATGGCGTCT 58.717 47.619 0.00 0.00 36.16 4.18
1426 1434 3.365364 GCCGTTGGAGATGCATAATAAGC 60.365 47.826 0.00 0.00 0.00 3.09
1481 1499 2.589720 TCCGCGGACTGATTTCCTATA 58.410 47.619 27.28 0.00 32.88 1.31
1505 1724 1.334779 GGATGTCGACCTTCCGTATCG 60.335 57.143 14.12 0.00 37.20 2.92
1513 1732 4.441079 CGGTTAGTATTGGATGTCGACCTT 60.441 45.833 14.12 0.00 0.00 3.50
1533 1752 5.001232 AGTTACTGTGAAAATGTATGCGGT 58.999 37.500 0.00 0.00 0.00 5.68
1607 1827 4.082845 TCCACTTTAAATGAAATCCGGCA 58.917 39.130 0.00 0.00 0.00 5.69
1609 1829 9.248291 CAAATATCCACTTTAAATGAAATCCGG 57.752 33.333 0.00 0.00 0.00 5.14
1678 1911 8.535335 CATTGGCTAGTATATGATAGTTCAGGT 58.465 37.037 0.00 0.00 34.73 4.00
1743 1991 2.504274 AACTCCTCCAACGGCGACA 61.504 57.895 16.62 0.00 0.00 4.35
1847 2097 2.651361 CACGACGCAAGAGGAGGT 59.349 61.111 0.00 0.00 43.62 3.85
1869 2119 4.156477 GGGACTAGTGGAGATGCTCTAAT 58.844 47.826 0.00 0.00 0.00 1.73
1923 2176 2.159382 GGAGACCTTTTTCATTGCCGA 58.841 47.619 0.00 0.00 0.00 5.54
1929 2182 3.760684 GCATGAGTGGAGACCTTTTTCAT 59.239 43.478 0.00 0.00 0.00 2.57
1975 2228 4.165779 CAGGCGCTAAAATTTGACGAATT 58.834 39.130 7.64 0.00 39.63 2.17
2037 2290 0.531090 TAAACATATCGCCGGCGCTT 60.531 50.000 42.78 32.37 39.59 4.68
2080 2333 3.829601 GGTGAAAAGTGAGAGGAGAGAGA 59.170 47.826 0.00 0.00 0.00 3.10
2112 2376 3.378512 AGAGAGAGAGAGAGAGAGCTCA 58.621 50.000 17.77 0.00 43.81 4.26
2118 2386 3.005261 CGAGGAGAGAGAGAGAGAGAGAG 59.995 56.522 0.00 0.00 0.00 3.20
2121 2389 2.693591 GACGAGGAGAGAGAGAGAGAGA 59.306 54.545 0.00 0.00 0.00 3.10
2385 2711 1.218047 CGATGGCGGAGGTTGAAGA 59.782 57.895 0.00 0.00 0.00 2.87
2594 3002 1.378250 GCTGCAAGGTCTGGCTCAT 60.378 57.895 0.00 0.00 0.00 2.90
2639 3047 4.479993 GCTGGCCGGATGAGCAGT 62.480 66.667 18.31 0.00 32.70 4.40
2739 3153 3.114616 CTCGCAAGTGCTCGTGGG 61.115 66.667 11.49 11.49 39.32 4.61
2747 3161 1.082300 CAACAGCAGCTCGCAAGTG 60.082 57.895 10.16 3.51 46.13 3.16
2748 3162 2.901292 GCAACAGCAGCTCGCAAGT 61.901 57.895 10.16 5.90 46.13 3.16
2749 3163 2.126965 GCAACAGCAGCTCGCAAG 60.127 61.111 10.16 5.38 46.13 4.01
2751 3165 4.631247 AGGCAACAGCAGCTCGCA 62.631 61.111 9.61 0.00 46.13 5.10
2752 3166 3.797546 GAGGCAACAGCAGCTCGC 61.798 66.667 0.00 0.00 42.91 5.03
2753 3167 3.123620 GGAGGCAACAGCAGCTCG 61.124 66.667 0.00 0.00 41.41 5.03
2755 3169 2.033757 CAGGAGGCAACAGCAGCT 59.966 61.111 0.00 0.00 41.41 4.24
2757 3171 3.429141 CGCAGGAGGCAACAGCAG 61.429 66.667 0.00 0.00 45.17 4.24
2760 3174 3.730761 GTGCGCAGGAGGCAACAG 61.731 66.667 12.22 0.00 45.17 3.16
2795 3209 4.587189 GTAGCAGGTAGGGCCGCG 62.587 72.222 0.00 0.00 43.70 6.46
2796 3210 2.732619 AAGTAGCAGGTAGGGCCGC 61.733 63.158 0.00 0.00 43.70 6.53
2798 3212 1.153147 GCAAGTAGCAGGTAGGGCC 60.153 63.158 0.00 0.00 44.79 5.80
2799 3213 1.521681 CGCAAGTAGCAGGTAGGGC 60.522 63.158 0.00 0.00 46.13 5.19
2800 3214 1.521681 GCGCAAGTAGCAGGTAGGG 60.522 63.158 0.30 0.00 46.13 3.53
2802 3216 1.878522 CGGCGCAAGTAGCAGGTAG 60.879 63.158 10.83 0.00 46.13 3.18
2803 3217 2.183300 CGGCGCAAGTAGCAGGTA 59.817 61.111 10.83 0.00 46.13 3.08
2805 3219 2.978452 ATAGCGGCGCAAGTAGCAGG 62.978 60.000 35.02 0.00 46.13 4.85
2806 3220 1.154205 AATAGCGGCGCAAGTAGCAG 61.154 55.000 35.02 0.00 46.13 4.24
2807 3221 1.153449 AATAGCGGCGCAAGTAGCA 60.153 52.632 35.02 9.68 46.13 3.49
2808 3222 1.276844 CAATAGCGGCGCAAGTAGC 59.723 57.895 35.02 6.32 41.00 3.58
2809 3223 1.276844 GCAATAGCGGCGCAAGTAG 59.723 57.895 35.02 19.55 41.68 2.57
2810 3224 3.405464 GCAATAGCGGCGCAAGTA 58.595 55.556 35.02 18.38 41.68 2.24
2820 3234 2.541120 CGCAGGAGGCAGCAATAGC 61.541 63.158 0.00 0.00 45.17 2.97
2821 3235 2.541120 GCGCAGGAGGCAGCAATAG 61.541 63.158 0.30 0.00 45.17 1.73
2822 3236 2.514592 GCGCAGGAGGCAGCAATA 60.515 61.111 0.30 0.00 45.17 1.90
2890 3304 4.796231 CAAGGAGGTCGCCGACGG 62.796 72.222 10.29 10.29 40.63 4.79
2891 3305 4.796231 CCAAGGAGGTCGCCGACG 62.796 72.222 11.60 0.00 42.01 5.12
2895 3309 4.388499 TTCGCCAAGGAGGTCGCC 62.388 66.667 0.00 0.00 40.61 5.54
2896 3310 2.815647 CTTCGCCAAGGAGGTCGC 60.816 66.667 0.00 0.00 40.61 5.19
2904 3318 1.452108 GTCCATCCCCTTCGCCAAG 60.452 63.158 0.00 0.00 0.00 3.61
2905 3319 1.910580 GAGTCCATCCCCTTCGCCAA 61.911 60.000 0.00 0.00 0.00 4.52
2906 3320 2.285368 AGTCCATCCCCTTCGCCA 60.285 61.111 0.00 0.00 0.00 5.69
2907 3321 2.506472 GAGTCCATCCCCTTCGCC 59.494 66.667 0.00 0.00 0.00 5.54
2908 3322 2.506472 GGAGTCCATCCCCTTCGC 59.494 66.667 3.60 0.00 43.01 4.70
2909 3323 2.815308 CGGAGTCCATCCCCTTCG 59.185 66.667 10.49 0.00 46.50 3.79
2910 3324 2.506472 GCGGAGTCCATCCCCTTC 59.494 66.667 10.49 0.00 46.50 3.46
2911 3325 3.470888 CGCGGAGTCCATCCCCTT 61.471 66.667 10.49 0.00 46.50 3.95
2912 3326 3.758133 ATCGCGGAGTCCATCCCCT 62.758 63.158 10.49 0.00 46.50 4.79
2913 3327 3.234730 ATCGCGGAGTCCATCCCC 61.235 66.667 10.49 0.00 46.50 4.81
2914 3328 2.029666 CATCGCGGAGTCCATCCC 59.970 66.667 10.49 0.00 46.50 3.85
2915 3329 1.144057 AACATCGCGGAGTCCATCC 59.856 57.895 10.49 0.00 45.64 3.51
2917 3331 0.460284 GACAACATCGCGGAGTCCAT 60.460 55.000 10.49 0.00 0.00 3.41
2918 3332 1.080093 GACAACATCGCGGAGTCCA 60.080 57.895 10.49 0.00 0.00 4.02
2920 3334 2.158959 CGGACAACATCGCGGAGTC 61.159 63.158 6.13 7.48 0.00 3.36
2921 3335 2.126071 CGGACAACATCGCGGAGT 60.126 61.111 6.13 1.64 0.00 3.85
2927 3341 3.071459 GCAGTCGCGGACAACATCG 62.071 63.158 6.13 0.00 34.60 3.84
2968 3382 3.461773 TACCTCCTGCTGCTCGCC 61.462 66.667 0.00 0.00 38.05 5.54
2969 3383 2.202810 GTACCTCCTGCTGCTCGC 60.203 66.667 0.00 0.00 39.77 5.03
2971 3385 1.153745 CACGTACCTCCTGCTGCTC 60.154 63.158 0.00 0.00 0.00 4.26
2972 3386 2.973899 CACGTACCTCCTGCTGCT 59.026 61.111 0.00 0.00 0.00 4.24
2973 3387 2.815647 GCACGTACCTCCTGCTGC 60.816 66.667 0.00 0.00 0.00 5.25
2974 3388 2.507102 CGCACGTACCTCCTGCTG 60.507 66.667 0.00 0.00 0.00 4.41
2977 3391 2.126071 CCACGCACGTACCTCCTG 60.126 66.667 0.00 0.00 0.00 3.86
2979 3393 4.446413 CCCCACGCACGTACCTCC 62.446 72.222 0.00 0.00 0.00 4.30
2980 3394 4.446413 CCCCCACGCACGTACCTC 62.446 72.222 0.00 0.00 0.00 3.85
2995 3409 2.052782 AATTATCCACTCGTTGCCCC 57.947 50.000 0.00 0.00 0.00 5.80
2996 3410 4.082463 TGAAAAATTATCCACTCGTTGCCC 60.082 41.667 0.00 0.00 0.00 5.36
2997 3411 5.054390 TGAAAAATTATCCACTCGTTGCC 57.946 39.130 0.00 0.00 0.00 4.52
2998 3412 5.743872 GGATGAAAAATTATCCACTCGTTGC 59.256 40.000 0.00 0.00 41.97 4.17
3000 3414 5.359860 GGGGATGAAAAATTATCCACTCGTT 59.640 40.000 7.18 0.00 42.42 3.85
3001 3415 4.887655 GGGGATGAAAAATTATCCACTCGT 59.112 41.667 7.18 0.00 42.42 4.18
3002 3416 4.024048 CGGGGATGAAAAATTATCCACTCG 60.024 45.833 5.82 3.95 43.31 4.18
3004 3418 4.079443 TCCGGGGATGAAAAATTATCCACT 60.079 41.667 0.00 0.00 43.31 4.00
3005 3419 4.037565 GTCCGGGGATGAAAAATTATCCAC 59.962 45.833 0.00 2.79 43.74 4.02
3007 3421 4.470602 AGTCCGGGGATGAAAAATTATCC 58.529 43.478 0.00 0.00 41.71 2.59
3008 3422 7.576861 TTTAGTCCGGGGATGAAAAATTATC 57.423 36.000 0.00 0.00 0.00 1.75
3010 3424 6.893005 ACATTTAGTCCGGGGATGAAAAATTA 59.107 34.615 0.00 0.00 0.00 1.40
3011 3425 5.719563 ACATTTAGTCCGGGGATGAAAAATT 59.280 36.000 0.00 0.00 0.00 1.82
3013 3427 4.668636 ACATTTAGTCCGGGGATGAAAAA 58.331 39.130 0.00 0.00 0.00 1.94
3014 3428 4.310022 ACATTTAGTCCGGGGATGAAAA 57.690 40.909 0.00 0.00 0.00 2.29
3015 3429 4.013728 CAACATTTAGTCCGGGGATGAAA 58.986 43.478 0.00 0.00 0.00 2.69
3016 3430 3.616219 CAACATTTAGTCCGGGGATGAA 58.384 45.455 0.00 0.00 0.00 2.57
3017 3431 2.682563 GCAACATTTAGTCCGGGGATGA 60.683 50.000 0.00 0.00 0.00 2.92
3019 3433 1.745827 CGCAACATTTAGTCCGGGGAT 60.746 52.381 0.00 0.00 0.00 3.85
3020 3434 0.391927 CGCAACATTTAGTCCGGGGA 60.392 55.000 0.00 0.00 0.00 4.81
3023 3437 1.427819 GGCGCAACATTTAGTCCGG 59.572 57.895 10.83 0.00 0.00 5.14
3025 3439 1.427819 CCGGCGCAACATTTAGTCC 59.572 57.895 10.83 0.00 0.00 3.85
3026 3440 1.226295 GCCGGCGCAACATTTAGTC 60.226 57.895 12.58 0.00 34.03 2.59
3028 3442 1.226379 CTGCCGGCGCAACATTTAG 60.226 57.895 23.90 6.04 46.66 1.85
3029 3443 2.874019 CTGCCGGCGCAACATTTA 59.126 55.556 23.90 0.00 46.66 1.40
3030 3444 4.722855 GCTGCCGGCGCAACATTT 62.723 61.111 29.64 0.00 46.66 2.32
3070 3484 1.059006 AGCCATTGAGCCCCTAGGAG 61.059 60.000 11.48 0.00 33.47 3.69
3073 3487 1.150081 CCAGCCATTGAGCCCCTAG 59.850 63.158 0.00 0.00 0.00 3.02
3075 3489 2.614969 TCCAGCCATTGAGCCCCT 60.615 61.111 0.00 0.00 0.00 4.79
3077 3491 0.822532 CATCTCCAGCCATTGAGCCC 60.823 60.000 0.00 0.00 0.00 5.19
3078 3492 1.453762 GCATCTCCAGCCATTGAGCC 61.454 60.000 0.00 0.00 0.00 4.70
3081 3495 3.794737 GAGCATCTCCAGCCATTGA 57.205 52.632 0.00 0.00 0.00 2.57
3172 3586 4.193334 CTCACCGAGATCGCCGCA 62.193 66.667 0.00 0.00 38.18 5.69
3225 3641 3.749064 GTCGTCTCTGCCGCCTCA 61.749 66.667 0.00 0.00 0.00 3.86
3340 3761 3.687125 ACTCTGTCGATCCTAGTTCACA 58.313 45.455 0.00 0.00 0.00 3.58
3357 3778 0.977395 AAAGGCGCTAGTTGGACTCT 59.023 50.000 7.64 0.00 0.00 3.24
3364 3798 2.267961 CCGGGAAAGGCGCTAGTT 59.732 61.111 7.64 0.00 0.00 2.24
3373 3807 0.179179 GAGTACGTCGACCGGGAAAG 60.179 60.000 10.58 0.00 42.24 2.62
3374 3808 1.586154 GGAGTACGTCGACCGGGAAA 61.586 60.000 10.58 0.00 42.24 3.13
3487 3930 4.767255 CAAGGAGGAGCGCCGCTT 62.767 66.667 15.07 0.00 39.88 4.68
3572 4024 2.048127 GCCGCGTCAAGGAAGAGT 60.048 61.111 4.92 0.00 0.00 3.24
3672 5377 2.983592 TGCTCCGTCGCTCTGTCA 60.984 61.111 0.00 0.00 0.00 3.58
3750 5455 0.539438 ACCACCACAATTCGCACCAT 60.539 50.000 0.00 0.00 0.00 3.55
3758 5463 3.302344 GCCGCCACCACCACAATT 61.302 61.111 0.00 0.00 0.00 2.32
3781 5489 2.418910 CGACGAGGAGGACCAGCAT 61.419 63.158 0.00 0.00 38.94 3.79
3848 5556 3.649277 CTCCGAGGCCGTTGTCCTG 62.649 68.421 0.00 0.00 33.24 3.86
3931 5679 0.830648 CCCCTTACATCTCTGGCGAA 59.169 55.000 0.00 0.00 0.00 4.70
3952 5700 3.151022 CTCCTCCTCCTCGCCCAC 61.151 72.222 0.00 0.00 0.00 4.61
3956 5704 2.520741 CCTCCTCCTCCTCCTCGC 60.521 72.222 0.00 0.00 0.00 5.03
3972 5768 1.208706 CTTCTTCTTCCTCCCCCTCC 58.791 60.000 0.00 0.00 0.00 4.30
3973 5769 1.208706 CCTTCTTCTTCCTCCCCCTC 58.791 60.000 0.00 0.00 0.00 4.30
3974 5770 0.800239 TCCTTCTTCTTCCTCCCCCT 59.200 55.000 0.00 0.00 0.00 4.79
3975 5771 1.492599 CATCCTTCTTCTTCCTCCCCC 59.507 57.143 0.00 0.00 0.00 5.40
3976 5772 1.133945 GCATCCTTCTTCTTCCTCCCC 60.134 57.143 0.00 0.00 0.00 4.81
3977 5773 1.474143 CGCATCCTTCTTCTTCCTCCC 60.474 57.143 0.00 0.00 0.00 4.30
4101 5897 2.161410 GCTTCAATGCGGACACATGTTA 59.839 45.455 0.00 0.00 0.00 2.41
4194 6085 2.969016 CTGAGAGCACGCAGAGGT 59.031 61.111 9.18 0.00 44.55 3.85
4275 6175 1.806542 CTGATCCACCCAAAACTCGTG 59.193 52.381 0.00 0.00 0.00 4.35
4279 6180 0.251787 GCCCTGATCCACCCAAAACT 60.252 55.000 0.00 0.00 0.00 2.66
4291 6192 2.586792 GCTTCTGACCGCCCTGAT 59.413 61.111 0.00 0.00 0.00 2.90
4319 6223 1.280421 GAGGTTTGCAGGAGTCTGGAT 59.720 52.381 0.00 0.00 40.98 3.41
4356 6262 7.308435 GTTCGAACATGATTTCTCCTGAAAAT 58.692 34.615 23.12 0.00 44.22 1.82
4405 6311 1.893759 CGCAGAAATTATGCAACGCA 58.106 45.000 13.21 0.00 44.05 5.24
4412 6318 1.261619 GTCCGGAGCGCAGAAATTATG 59.738 52.381 11.47 0.00 0.00 1.90
4434 6340 5.066893 CCTTTCACAATCATTCGGATGACAT 59.933 40.000 9.01 0.00 44.64 3.06
4435 6341 4.395854 CCTTTCACAATCATTCGGATGACA 59.604 41.667 9.01 0.00 44.64 3.58
4439 6345 5.982890 AAACCTTTCACAATCATTCGGAT 57.017 34.783 0.00 0.00 38.05 4.18
4446 6352 3.816523 GGACCGTAAACCTTTCACAATCA 59.183 43.478 0.00 0.00 0.00 2.57
4524 6441 3.711863 AGCTCAGTTCAGGATCTCTCTT 58.288 45.455 0.00 0.00 0.00 2.85
4534 6451 5.289675 CGACCATTACTTTAGCTCAGTTCAG 59.710 44.000 3.89 0.00 0.00 3.02
4566 6483 3.362295 CGCCACCAAACATTCATATTCG 58.638 45.455 0.00 0.00 0.00 3.34
4570 6487 0.814457 GCCGCCACCAAACATTCATA 59.186 50.000 0.00 0.00 0.00 2.15
5219 7136 0.110238 CAACCAACGAGCGAACCATG 60.110 55.000 0.00 0.00 0.00 3.66
5257 7174 1.977594 GCGTAACCAACATCCTGCCG 61.978 60.000 0.00 0.00 0.00 5.69
5298 7215 2.840066 CGCCAGGCTCTCTAGGACG 61.840 68.421 10.54 0.00 0.00 4.79
5394 7311 2.042537 ATCTCCAGCTGCCTCCGA 60.043 61.111 8.66 0.00 0.00 4.55
5705 7627 2.476185 CCCGTTGTTGCTTTGATCGATC 60.476 50.000 18.72 18.72 0.00 3.69
5834 7759 4.814294 AACGAGTCCGGCCGATGC 62.814 66.667 30.73 16.14 40.78 3.91
5860 7785 4.454678 TCGTTCCGGTCTACTGTATATGT 58.545 43.478 0.00 0.00 0.00 2.29
5879 7809 1.405821 CCGTCCTCTAGAATTGCTCGT 59.594 52.381 0.00 0.00 0.00 4.18
5986 7916 1.363443 CCCGAGCAAAGCAAAGCAA 59.637 52.632 0.00 0.00 0.00 3.91
5990 7920 1.067250 GCAACCCGAGCAAAGCAAA 59.933 52.632 0.00 0.00 0.00 3.68
6030 7960 4.816984 GCGTCTCCTCTCCCGGGA 62.817 72.222 25.06 25.06 0.00 5.14
6110 8071 5.340439 AACCGAGTCTAGAAATGGTTAGG 57.660 43.478 17.60 6.41 37.90 2.69
6194 8156 2.482336 TCATCACGTCCAAATCCAAACG 59.518 45.455 0.00 0.00 40.77 3.60
6241 8240 5.633182 CCAATCCGTTAAACAACAGATTTGG 59.367 40.000 0.00 0.00 29.89 3.28
6354 8353 2.588596 CACACGTGCCTCACTGCA 60.589 61.111 17.22 0.00 39.37 4.41
6394 8395 1.412079 AAAGCAATGTTGGTCTGCCA 58.588 45.000 0.00 0.00 44.38 4.92
6408 8409 1.289160 ACTCATGCCCTCCTAAAGCA 58.711 50.000 0.00 0.00 41.50 3.91
6410 8411 2.025887 ACCAACTCATGCCCTCCTAAAG 60.026 50.000 0.00 0.00 0.00 1.85
6491 8492 1.139095 CTCTCGGACCTACGGCAAC 59.861 63.158 0.00 0.00 0.00 4.17
6600 8601 1.523758 GGATCAATGGCCGATACACC 58.476 55.000 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.