Multiple sequence alignment - TraesCS6B01G423400

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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 TraesCS6B01G423400 chr6B 100.000 5025 0 0 1 5025 693303789 693298765 0.000000e+00 9280.0
1 TraesCS6B01G423400 chr6B 84.911 1014 108 23 3456 4437 693131627 693130627 0.000000e+00 983.0
2 TraesCS6B01G423400 chr6B 86.807 758 53 19 956 1678 693133218 693132473 0.000000e+00 802.0
3 TraesCS6B01G423400 chr6B 88.000 500 44 7 1046 1538 693324353 693323863 1.210000e-160 577.0
4 TraesCS6B01G423400 chr6B 83.444 453 52 12 3 433 693136164 693135713 2.820000e-107 399.0
5 TraesCS6B01G423400 chr6B 86.250 320 33 8 3821 4136 693322792 693322480 2.240000e-88 337.0
6 TraesCS6B01G423400 chr6D 89.971 1725 95 32 1 1670 455908795 455907094 0.000000e+00 2156.0
7 TraesCS6B01G423400 chr6D 92.950 1149 48 12 3299 4437 455906552 455905427 0.000000e+00 1642.0
8 TraesCS6B01G423400 chr6D 83.719 1038 97 39 3456 4437 455898178 455897157 0.000000e+00 915.0
9 TraesCS6B01G423400 chr6D 94.494 563 16 8 2700 3249 455907091 455906531 0.000000e+00 854.0
10 TraesCS6B01G423400 chr6D 86.390 698 55 17 1005 1678 455899764 455899083 0.000000e+00 726.0
11 TraesCS6B01G423400 chr6D 91.188 522 35 3 1028 1538 455970026 455969505 0.000000e+00 699.0
12 TraesCS6B01G423400 chr6D 86.413 552 51 13 2703 3249 455899085 455898553 2.610000e-162 582.0
13 TraesCS6B01G423400 chr6D 85.657 502 48 8 1046 1538 455935638 455935152 1.610000e-139 507.0
14 TraesCS6B01G423400 chr6D 80.125 639 100 19 3501 4136 455968995 455968381 7.670000e-123 451.0
15 TraesCS6B01G423400 chr6D 87.812 320 28 8 3821 4136 455934169 455933857 1.030000e-96 364.0
16 TraesCS6B01G423400 chr6D 85.659 258 37 0 3463 3720 455934512 455934255 6.410000e-69 272.0
17 TraesCS6B01G423400 chr6D 82.946 258 40 4 2442 2698 18770571 18770825 3.910000e-56 230.0
18 TraesCS6B01G423400 chr6D 87.059 170 18 1 2052 2221 463962903 463963068 6.640000e-44 189.0
19 TraesCS6B01G423400 chr6D 100.000 55 0 0 3246 3300 44544909 44544963 8.900000e-18 102.0
20 TraesCS6B01G423400 chr6D 73.810 294 50 17 317 591 137796175 137796460 1.930000e-14 91.6
21 TraesCS6B01G423400 chr6A 86.051 1742 129 37 1 1661 602718723 602717015 0.000000e+00 1766.0
22 TraesCS6B01G423400 chr6A 91.870 984 63 10 3456 4437 602715977 602715009 0.000000e+00 1358.0
23 TraesCS6B01G423400 chr6A 89.600 500 39 6 1046 1538 602740569 602740076 1.540000e-174 623.0
24 TraesCS6B01G423400 chr6A 92.000 450 25 4 2803 3249 602717013 602716572 5.530000e-174 621.0
25 TraesCS6B01G423400 chr6A 84.554 505 52 12 1046 1539 602727028 602726539 1.270000e-130 477.0
26 TraesCS6B01G423400 chr6A 78.548 606 110 15 3497 4100 602739529 602738942 1.020000e-101 381.0
27 TraesCS6B01G423400 chr6A 85.893 319 36 6 3821 4136 602725542 602725230 1.040000e-86 331.0
28 TraesCS6B01G423400 chr6A 83.178 321 43 6 3821 4136 596486128 596486442 2.960000e-72 283.0
29 TraesCS6B01G423400 chr6A 85.659 258 37 0 3463 3720 602725885 602725628 6.410000e-69 272.0
30 TraesCS6B01G423400 chr6A 96.875 160 5 0 3299 3458 602716593 602716434 8.290000e-68 268.0
31 TraesCS6B01G423400 chr6A 81.818 209 38 0 3463 3671 596485824 596486032 5.170000e-40 176.0
32 TraesCS6B01G423400 chr5D 90.979 1042 62 10 1682 2699 82199655 82198622 0.000000e+00 1375.0
33 TraesCS6B01G423400 chr5D 89.011 637 38 15 2080 2691 398781370 398781999 0.000000e+00 760.0
34 TraesCS6B01G423400 chr5D 88.514 444 48 3 4435 4877 3579236 3579677 7.400000e-148 534.0
35 TraesCS6B01G423400 chr5D 91.643 359 28 1 1683 2039 398781021 398781379 3.490000e-136 496.0
36 TraesCS6B01G423400 chr5D 87.879 264 31 1 1682 1945 456594113 456594375 4.890000e-80 309.0
37 TraesCS6B01G423400 chr5D 86.590 261 34 1 1683 1943 443905916 443905657 2.290000e-73 287.0
38 TraesCS6B01G423400 chr5D 100.000 55 0 0 3246 3300 98244636 98244690 8.900000e-18 102.0
39 TraesCS6B01G423400 chr5D 98.182 55 1 0 3246 3300 238700019 238700073 4.140000e-16 97.1
40 TraesCS6B01G423400 chr5D 98.182 55 1 0 3246 3300 434813742 434813796 4.140000e-16 97.1
41 TraesCS6B01G423400 chr5D 76.077 209 21 16 407 591 181878285 181878488 1.160000e-11 82.4
42 TraesCS6B01G423400 chr7A 90.316 1043 65 14 1682 2699 724254054 724255085 0.000000e+00 1334.0
43 TraesCS6B01G423400 chr7A 90.183 438 42 1 4589 5025 505707361 505706924 2.030000e-158 569.0
44 TraesCS6B01G423400 chr7A 89.041 438 47 1 4589 5025 505693649 505693212 4.430000e-150 542.0
45 TraesCS6B01G423400 chr7A 80.952 84 12 3 3513 3594 31687462 31687543 4.200000e-06 63.9
46 TraesCS6B01G423400 chr7A 100.000 31 0 0 436 466 69527811 69527781 1.950000e-04 58.4
47 TraesCS6B01G423400 chr3D 88.225 586 64 5 4436 5019 598721798 598722380 0.000000e+00 695.0
48 TraesCS6B01G423400 chr3D 88.911 505 51 3 4518 5019 581019736 581019234 7.150000e-173 617.0
49 TraesCS6B01G423400 chr3D 91.250 400 34 1 4438 4836 573446424 573446823 1.230000e-150 544.0
50 TraesCS6B01G423400 chr3D 85.597 243 31 4 3479 3720 457057231 457057470 8.350000e-63 252.0
51 TraesCS6B01G423400 chr3D 83.658 257 41 1 2442 2698 84582919 84582664 1.810000e-59 241.0
52 TraesCS6B01G423400 chr3D 83.399 253 39 3 1681 1931 92363610 92363359 1.090000e-56 231.0
53 TraesCS6B01G423400 chr3D 86.207 145 14 1 1407 1545 457047667 457047811 8.710000e-33 152.0
54 TraesCS6B01G423400 chr3D 98.246 57 1 0 3246 3302 554163717 554163661 3.200000e-17 100.0
55 TraesCS6B01G423400 chr3D 84.375 64 9 1 317 379 394920333 394920270 1.510000e-05 62.1
56 TraesCS6B01G423400 chr3D 100.000 29 0 0 317 345 527684973 527684945 3.000000e-03 54.7
57 TraesCS6B01G423400 chr2B 90.887 417 38 0 4437 4853 741143999 741143583 1.220000e-155 560.0
58 TraesCS6B01G423400 chr2B 90.670 418 39 0 4436 4853 741146183 741145766 1.580000e-154 556.0
59 TraesCS6B01G423400 chr2B 83.200 250 41 1 1682 1931 40505452 40505700 1.410000e-55 228.0
60 TraesCS6B01G423400 chr2B 96.667 60 2 0 3246 3305 693336102 693336043 3.200000e-17 100.0
61 TraesCS6B01G423400 chr4A 87.746 457 49 6 4438 4890 629919978 629920431 1.240000e-145 527.0
62 TraesCS6B01G423400 chr4A 85.185 81 11 1 317 396 599914843 599914763 1.160000e-11 82.4
63 TraesCS6B01G423400 chr1D 86.641 262 33 2 1684 1945 28553272 28553531 6.370000e-74 289.0
64 TraesCS6B01G423400 chr1D 82.800 250 41 2 1682 1931 22030531 22030284 6.550000e-54 222.0
65 TraesCS6B01G423400 chr1D 88.953 172 18 1 4849 5019 42099892 42099721 1.420000e-50 211.0
66 TraesCS6B01G423400 chr1D 98.214 56 1 0 3246 3301 79134979 79135034 1.150000e-16 99.0
67 TraesCS6B01G423400 chr1D 98.182 55 1 0 3246 3300 486210609 486210663 4.140000e-16 97.1
68 TraesCS6B01G423400 chr1D 82.927 82 13 1 316 396 43137253 43137334 6.980000e-09 73.1
69 TraesCS6B01G423400 chr2D 83.721 258 39 3 2443 2699 572032477 572032222 1.810000e-59 241.0
70 TraesCS6B01G423400 chr2D 85.093 161 22 2 3299 3458 484127063 484127222 4.030000e-36 163.0
71 TraesCS6B01G423400 chr5B 82.182 275 46 3 2426 2699 52309665 52309393 3.020000e-57 233.0
72 TraesCS6B01G423400 chr5B 77.273 154 14 12 316 465 153182689 153182825 2.510000e-08 71.3
73 TraesCS6B01G423400 chr7D 83.012 259 39 5 2443 2699 575144777 575144522 3.910000e-56 230.0
74 TraesCS6B01G423400 chr7D 100.000 56 0 0 3246 3301 127017304 127017359 2.470000e-18 104.0
75 TraesCS6B01G423400 chr4D 81.522 276 45 5 2427 2699 93835873 93836145 6.550000e-54 222.0
76 TraesCS6B01G423400 chr7B 92.453 53 3 1 415 466 6797933 6797881 1.940000e-09 75.0
77 TraesCS6B01G423400 chr4B 77.483 151 16 9 317 466 489379086 489379219 1.940000e-09 75.0
78 TraesCS6B01G423400 chr4B 74.877 203 28 17 516 710 113959629 113959442 2.510000e-08 71.3
79 TraesCS6B01G423400 chr1A 92.500 40 3 0 316 355 42550534 42550573 1.950000e-04 58.4


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 TraesCS6B01G423400 chr6B 693298765 693303789 5024 True 9280.000000 9280 100.000000 1 5025 1 chr6B.!!$R1 5024
1 TraesCS6B01G423400 chr6B 693130627 693136164 5537 True 728.000000 983 85.054000 3 4437 3 chr6B.!!$R2 4434
2 TraesCS6B01G423400 chr6B 693322480 693324353 1873 True 457.000000 577 87.125000 1046 4136 2 chr6B.!!$R3 3090
3 TraesCS6B01G423400 chr6D 455905427 455908795 3368 True 1550.666667 2156 92.471667 1 4437 3 chr6D.!!$R2 4436
4 TraesCS6B01G423400 chr6D 455897157 455899764 2607 True 741.000000 915 85.507333 1005 4437 3 chr6D.!!$R1 3432
5 TraesCS6B01G423400 chr6D 455968381 455970026 1645 True 575.000000 699 85.656500 1028 4136 2 chr6D.!!$R4 3108
6 TraesCS6B01G423400 chr6D 455933857 455935638 1781 True 381.000000 507 86.376000 1046 4136 3 chr6D.!!$R3 3090
7 TraesCS6B01G423400 chr6A 602715009 602718723 3714 True 1003.250000 1766 91.699000 1 4437 4 chr6A.!!$R1 4436
8 TraesCS6B01G423400 chr6A 602738942 602740569 1627 True 502.000000 623 84.074000 1046 4100 2 chr6A.!!$R3 3054
9 TraesCS6B01G423400 chr6A 602725230 602727028 1798 True 360.000000 477 85.368667 1046 4136 3 chr6A.!!$R2 3090
10 TraesCS6B01G423400 chr6A 596485824 596486442 618 False 229.500000 283 82.498000 3463 4136 2 chr6A.!!$F1 673
11 TraesCS6B01G423400 chr5D 82198622 82199655 1033 True 1375.000000 1375 90.979000 1682 2699 1 chr5D.!!$R1 1017
12 TraesCS6B01G423400 chr5D 398781021 398781999 978 False 628.000000 760 90.327000 1683 2691 2 chr5D.!!$F7 1008
13 TraesCS6B01G423400 chr7A 724254054 724255085 1031 False 1334.000000 1334 90.316000 1682 2699 1 chr7A.!!$F2 1017
14 TraesCS6B01G423400 chr3D 598721798 598722380 582 False 695.000000 695 88.225000 4436 5019 1 chr3D.!!$F4 583
15 TraesCS6B01G423400 chr3D 581019234 581019736 502 True 617.000000 617 88.911000 4518 5019 1 chr3D.!!$R6 501
16 TraesCS6B01G423400 chr2B 741143583 741146183 2600 True 558.000000 560 90.778500 4436 4853 2 chr2B.!!$R2 417

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
310 331 0.034896 GACTTGGACGGTGATGTGGT 59.965 55.0 0.00 0.0 0.00 4.16 F
1016 3072 0.807667 CGAATGCCGGACCAGAAGAG 60.808 60.0 5.05 0.0 33.91 2.85 F
2016 4150 0.967380 GTAAGCCAAGCCACTGCCAT 60.967 55.0 0.00 0.0 38.69 4.40 F
2022 4156 0.968901 CAAGCCACTGCCATCACCAT 60.969 55.0 0.00 0.0 38.69 3.55 F
3255 5579 0.106719 CGGGGTGAATTGGCTATGGT 60.107 55.0 0.00 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2302 4486 1.602237 CGGTGGTGCCTGTTAGGAT 59.398 57.895 0.00 0.0 37.67 3.24 R
2704 4938 1.069500 GGTTGCGCGAATTAACACTGT 60.069 47.619 12.10 0.0 0.00 3.55 R
3236 5560 0.106719 ACCATAGCCAATTCACCCCG 60.107 55.000 0.00 0.0 0.00 5.73 R
3752 6627 0.318275 GACTCATCGTCATCGCCCTC 60.318 60.000 0.00 0.0 42.37 4.30 R
4995 8005 0.034059 GCCCGATCGATCCACTGAAT 59.966 55.000 18.66 0.0 0.00 2.57 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
133 134 3.572604 ACGAGTTAAACGAGCTAGCTT 57.427 42.857 20.42 5.15 34.70 3.74
138 139 4.553323 AGTTAAACGAGCTAGCTTTCGAA 58.447 39.130 27.19 12.42 39.93 3.71
144 145 4.683832 ACGAGCTAGCTTTCGAATTACAT 58.316 39.130 27.19 5.67 39.93 2.29
165 166 0.674534 AGTCGAGCCGAGTTTGACTT 59.325 50.000 5.28 0.00 34.60 3.01
208 219 3.702330 CTGACGCGTTATGGTAATGAGA 58.298 45.455 15.53 0.00 0.00 3.27
215 226 5.460748 CGCGTTATGGTAATGAGATGTAACA 59.539 40.000 0.00 0.00 0.00 2.41
242 263 2.169978 ACTAGAATTACACCCCTTCGCC 59.830 50.000 0.00 0.00 0.00 5.54
302 323 2.623915 CGACGGAGACTTGGACGGT 61.624 63.158 0.00 0.00 0.00 4.83
310 331 0.034896 GACTTGGACGGTGATGTGGT 59.965 55.000 0.00 0.00 0.00 4.16
413 436 8.915871 TCAGAAAAGAAGTTTCACAAGAAATG 57.084 30.769 2.00 0.00 46.98 2.32
537 576 4.202010 GCAGTAAACGCCAATATTCATGGT 60.202 41.667 0.00 0.00 40.23 3.55
590 2605 6.479660 CAGTAATGTGTTTGAACTTGGCAATT 59.520 34.615 0.00 0.00 0.00 2.32
652 2674 6.660887 TTTTCTCAAAACTTCCAAACATGC 57.339 33.333 0.00 0.00 0.00 4.06
733 2758 2.407609 CGTGTACGTTGCGTTGACTTAC 60.408 50.000 0.00 0.00 41.54 2.34
736 2761 3.615937 TGTACGTTGCGTTGACTTACAAA 59.384 39.130 0.00 0.00 41.54 2.83
860 2909 3.566322 TCGCCCCAAAATATTAATCCACG 59.434 43.478 0.00 0.00 0.00 4.94
901 2957 1.888018 CTCCGTCGCTAAACCTCCA 59.112 57.895 0.00 0.00 0.00 3.86
932 2988 2.970324 CACCCACACCCGAACACG 60.970 66.667 0.00 0.00 0.00 4.49
1003 3059 2.202388 TCCGACGACGACGAATGC 60.202 61.111 20.63 0.00 42.66 3.56
1016 3072 0.807667 CGAATGCCGGACCAGAAGAG 60.808 60.000 5.05 0.00 33.91 2.85
1333 3397 4.710695 TCGTGGTACGTGCCTGCG 62.711 66.667 23.67 24.34 43.14 5.18
1556 3682 6.694411 TCGTTCGCTCTTCCACTTTTATATAC 59.306 38.462 0.00 0.00 0.00 1.47
1711 3843 6.732531 TTGCACAAAACATTGACATTGAAA 57.267 29.167 4.40 0.00 0.00 2.69
1718 3850 8.090214 ACAAAACATTGACATTGAAAGATAGGG 58.910 33.333 4.40 0.00 0.00 3.53
1779 3913 5.589050 ACCACTAATTCCGAGGCTAATTTTC 59.411 40.000 0.00 0.00 0.00 2.29
1781 3915 6.990349 CCACTAATTCCGAGGCTAATTTTCTA 59.010 38.462 0.00 0.00 0.00 2.10
1782 3916 7.497909 CCACTAATTCCGAGGCTAATTTTCTAA 59.502 37.037 0.00 0.00 0.00 2.10
1783 3917 8.889717 CACTAATTCCGAGGCTAATTTTCTAAA 58.110 33.333 0.00 0.00 0.00 1.85
1833 3967 5.334802 CCGTTTTGAGCACAATTATGACAGA 60.335 40.000 0.00 0.00 35.85 3.41
2016 4150 0.967380 GTAAGCCAAGCCACTGCCAT 60.967 55.000 0.00 0.00 38.69 4.40
2021 4155 1.604308 CAAGCCACTGCCATCACCA 60.604 57.895 0.00 0.00 38.69 4.17
2022 4156 0.968901 CAAGCCACTGCCATCACCAT 60.969 55.000 0.00 0.00 38.69 3.55
2046 4180 2.529744 GCCACCCCTCCTTCACAGT 61.530 63.158 0.00 0.00 0.00 3.55
2062 4196 4.717313 GTGTCGCCCCACCTTCCC 62.717 72.222 0.00 0.00 0.00 3.97
2159 4342 2.287251 CCCTCCCCTCCGGATTCT 59.713 66.667 3.57 0.00 41.00 2.40
2221 4404 2.124996 CCTCCACCCCTCCTTCCA 59.875 66.667 0.00 0.00 0.00 3.53
2312 4496 2.510906 CCCCGCCATCCTAACAGG 59.489 66.667 0.00 0.00 36.46 4.00
2390 4622 4.093952 CGCCGGAGCAAGCAACAG 62.094 66.667 5.05 0.00 39.83 3.16
2458 4690 1.480954 GTCAGAGGACCCGATTGCTTA 59.519 52.381 0.00 0.00 38.12 3.09
2509 4741 5.907866 TCGTGTCTGGATGTAATTGACTA 57.092 39.130 0.00 0.00 0.00 2.59
2554 4786 0.987294 AGAGGGACCAACCTGTCATG 59.013 55.000 0.00 0.00 42.10 3.07
2590 4822 1.070134 ACCTAAGCGAGCAACTTGTGA 59.930 47.619 0.00 0.00 0.00 3.58
2630 4863 3.306710 GCCTGGGAATTAGTGTTTTTGGG 60.307 47.826 0.00 0.00 0.00 4.12
2699 4933 4.514816 TCGATGTTTTCTGCAATTCACTCA 59.485 37.500 0.00 0.00 0.00 3.41
2700 4934 5.181811 TCGATGTTTTCTGCAATTCACTCAT 59.818 36.000 0.00 0.00 0.00 2.90
2701 4935 5.510674 CGATGTTTTCTGCAATTCACTCATC 59.489 40.000 0.00 0.00 0.00 2.92
2702 4936 6.585695 ATGTTTTCTGCAATTCACTCATCT 57.414 33.333 0.00 0.00 0.00 2.90
2703 4937 5.765176 TGTTTTCTGCAATTCACTCATCTG 58.235 37.500 0.00 0.00 0.00 2.90
2704 4938 5.532032 TGTTTTCTGCAATTCACTCATCTGA 59.468 36.000 0.00 0.00 0.00 3.27
2705 4939 5.618056 TTTCTGCAATTCACTCATCTGAC 57.382 39.130 0.00 0.00 0.00 3.51
2706 4940 4.276058 TCTGCAATTCACTCATCTGACA 57.724 40.909 0.00 0.00 0.00 3.58
2707 4941 4.251268 TCTGCAATTCACTCATCTGACAG 58.749 43.478 0.00 0.00 0.00 3.51
2765 5060 4.487714 GGATGGTCCTATGAAGTGTGAA 57.512 45.455 0.00 0.00 32.53 3.18
2815 5120 5.056553 AGTTCCTGGGTAGCAAGTTTTAA 57.943 39.130 0.00 0.00 0.00 1.52
2819 5124 4.276431 TCCTGGGTAGCAAGTTTTAAAACG 59.724 41.667 22.04 12.20 43.51 3.60
2846 5160 5.005971 CACAGTGCTTGAAATCAGTTTTTGG 59.994 40.000 0.00 0.00 0.00 3.28
2847 5161 5.111293 CAGTGCTTGAAATCAGTTTTTGGT 58.889 37.500 0.00 0.00 0.00 3.67
3165 5489 8.486210 ACTGTTTCTATGCTGTTATCTTATCCA 58.514 33.333 0.00 0.00 0.00 3.41
3227 5551 5.874261 TGCATTGTGATCTAACTCGATTTCA 59.126 36.000 0.00 0.00 0.00 2.69
3228 5552 6.371271 TGCATTGTGATCTAACTCGATTTCAA 59.629 34.615 0.00 0.00 0.00 2.69
3229 5553 7.066163 TGCATTGTGATCTAACTCGATTTCAAT 59.934 33.333 0.00 0.00 32.62 2.57
3230 5554 7.912250 GCATTGTGATCTAACTCGATTTCAATT 59.088 33.333 0.00 0.00 31.41 2.32
3231 5555 9.430838 CATTGTGATCTAACTCGATTTCAATTC 57.569 33.333 0.00 0.00 31.41 2.17
3232 5556 8.546597 TTGTGATCTAACTCGATTTCAATTCA 57.453 30.769 0.00 0.00 0.00 2.57
3233 5557 8.722480 TGTGATCTAACTCGATTTCAATTCAT 57.278 30.769 0.00 0.00 0.00 2.57
3234 5558 9.166173 TGTGATCTAACTCGATTTCAATTCATT 57.834 29.630 0.00 0.00 0.00 2.57
3235 5559 9.994432 GTGATCTAACTCGATTTCAATTCATTT 57.006 29.630 0.00 0.00 0.00 2.32
3237 5561 9.362911 GATCTAACTCGATTTCAATTCATTTCG 57.637 33.333 0.00 0.00 0.00 3.46
3238 5562 7.684670 TCTAACTCGATTTCAATTCATTTCGG 58.315 34.615 0.00 0.00 0.00 4.30
3239 5563 5.235305 ACTCGATTTCAATTCATTTCGGG 57.765 39.130 0.00 0.00 33.49 5.14
3240 5564 4.096382 ACTCGATTTCAATTCATTTCGGGG 59.904 41.667 0.00 0.00 31.61 5.73
3241 5565 4.013728 TCGATTTCAATTCATTTCGGGGT 58.986 39.130 0.00 0.00 0.00 4.95
3242 5566 4.104776 CGATTTCAATTCATTTCGGGGTG 58.895 43.478 0.00 0.00 0.00 4.61
3243 5567 4.142491 CGATTTCAATTCATTTCGGGGTGA 60.142 41.667 0.00 0.00 0.00 4.02
3244 5568 5.621104 CGATTTCAATTCATTTCGGGGTGAA 60.621 40.000 0.00 0.00 38.57 3.18
3245 5569 5.736951 TTTCAATTCATTTCGGGGTGAAT 57.263 34.783 4.85 4.85 44.55 2.57
3249 5573 1.181786 TCATTTCGGGGTGAATTGGC 58.818 50.000 0.00 0.00 38.11 4.52
3250 5574 1.185315 CATTTCGGGGTGAATTGGCT 58.815 50.000 0.00 0.00 36.22 4.75
3251 5575 2.025793 TCATTTCGGGGTGAATTGGCTA 60.026 45.455 0.00 0.00 38.11 3.93
3252 5576 2.818751 TTTCGGGGTGAATTGGCTAT 57.181 45.000 0.00 0.00 36.22 2.97
3253 5577 2.051334 TTCGGGGTGAATTGGCTATG 57.949 50.000 0.00 0.00 0.00 2.23
3254 5578 0.182537 TCGGGGTGAATTGGCTATGG 59.817 55.000 0.00 0.00 0.00 2.74
3255 5579 0.106719 CGGGGTGAATTGGCTATGGT 60.107 55.000 0.00 0.00 0.00 3.55
3256 5580 1.402787 GGGGTGAATTGGCTATGGTG 58.597 55.000 0.00 0.00 0.00 4.17
3257 5581 1.402787 GGGTGAATTGGCTATGGTGG 58.597 55.000 0.00 0.00 0.00 4.61
3258 5582 1.341976 GGGTGAATTGGCTATGGTGGT 60.342 52.381 0.00 0.00 0.00 4.16
3259 5583 2.456577 GGTGAATTGGCTATGGTGGTT 58.543 47.619 0.00 0.00 0.00 3.67
3260 5584 2.831526 GGTGAATTGGCTATGGTGGTTT 59.168 45.455 0.00 0.00 0.00 3.27
3261 5585 3.368323 GGTGAATTGGCTATGGTGGTTTG 60.368 47.826 0.00 0.00 0.00 2.93
3262 5586 2.233431 TGAATTGGCTATGGTGGTTTGC 59.767 45.455 0.00 0.00 0.00 3.68
3263 5587 2.236489 ATTGGCTATGGTGGTTTGCT 57.764 45.000 0.00 0.00 0.00 3.91
3264 5588 2.008242 TTGGCTATGGTGGTTTGCTT 57.992 45.000 0.00 0.00 0.00 3.91
3265 5589 2.008242 TGGCTATGGTGGTTTGCTTT 57.992 45.000 0.00 0.00 0.00 3.51
3266 5590 3.162147 TGGCTATGGTGGTTTGCTTTA 57.838 42.857 0.00 0.00 0.00 1.85
3267 5591 3.707316 TGGCTATGGTGGTTTGCTTTAT 58.293 40.909 0.00 0.00 0.00 1.40
3268 5592 4.093011 TGGCTATGGTGGTTTGCTTTATT 58.907 39.130 0.00 0.00 0.00 1.40
3269 5593 4.530161 TGGCTATGGTGGTTTGCTTTATTT 59.470 37.500 0.00 0.00 0.00 1.40
3270 5594 5.717178 TGGCTATGGTGGTTTGCTTTATTTA 59.283 36.000 0.00 0.00 0.00 1.40
3271 5595 6.382570 TGGCTATGGTGGTTTGCTTTATTTAT 59.617 34.615 0.00 0.00 0.00 1.40
3272 5596 7.561722 TGGCTATGGTGGTTTGCTTTATTTATA 59.438 33.333 0.00 0.00 0.00 0.98
3273 5597 8.417884 GGCTATGGTGGTTTGCTTTATTTATAA 58.582 33.333 0.00 0.00 0.00 0.98
3274 5598 9.810545 GCTATGGTGGTTTGCTTTATTTATAAA 57.189 29.630 0.00 0.00 0.00 1.40
3284 5608 5.427036 CTTTATTTATAAAGCGGGGCGAA 57.573 39.130 8.78 0.00 41.69 4.70
3285 5609 5.823353 CTTTATTTATAAAGCGGGGCGAAA 58.177 37.500 8.78 0.00 41.69 3.46
3286 5610 3.982576 ATTTATAAAGCGGGGCGAAAG 57.017 42.857 3.94 0.00 0.00 2.62
3458 5783 6.917477 TGAAATCGGTTTTTGTTGATCTTCAG 59.083 34.615 0.00 0.00 0.00 3.02
3503 6342 8.443937 GTCTTCTTGACAAGTTGTAACCATATC 58.556 37.037 14.75 0.00 44.73 1.63
3537 6376 4.966005 CGAAGGTGCTGAACTCGA 57.034 55.556 0.00 0.00 0.00 4.04
3541 6380 0.318762 AAGGTGCTGAACTCGAGGAC 59.681 55.000 18.41 10.59 0.00 3.85
3739 6614 4.430765 GGCGAGGCGGACGAGAAA 62.431 66.667 0.00 0.00 0.00 2.52
3759 6634 2.103538 GCATTACGACGAGGGCGA 59.896 61.111 0.00 0.00 41.64 5.54
3760 6635 1.299926 GCATTACGACGAGGGCGAT 60.300 57.895 0.00 0.00 41.64 4.58
3761 6636 1.548973 GCATTACGACGAGGGCGATG 61.549 60.000 0.00 0.00 41.64 3.84
3762 6637 0.030235 CATTACGACGAGGGCGATGA 59.970 55.000 0.00 0.00 41.64 2.92
3763 6638 0.030369 ATTACGACGAGGGCGATGAC 59.970 55.000 0.00 0.00 41.64 3.06
3764 6639 2.313717 TTACGACGAGGGCGATGACG 62.314 60.000 0.00 0.00 41.64 4.35
3765 6640 3.872728 CGACGAGGGCGATGACGA 61.873 66.667 0.00 0.00 42.66 4.20
3766 6641 2.722487 GACGAGGGCGATGACGAT 59.278 61.111 0.00 0.00 42.66 3.73
3771 6646 3.897175 CGAGGGCGATGACGATGAGTC 62.897 61.905 0.00 0.00 44.67 3.36
3909 6862 0.739112 GAGCTGGGCGAGTTCTTGAG 60.739 60.000 6.13 0.00 0.00 3.02
3946 6899 0.394565 GCGAGGTATCCATCAGCCTT 59.605 55.000 0.00 0.00 0.00 4.35
3985 6938 1.366319 AGTGGAAGAGTGGCCTCATT 58.634 50.000 3.32 0.00 40.40 2.57
4057 7013 3.094572 CCAGGATTCATTCAACTTGCCT 58.905 45.455 0.00 0.00 0.00 4.75
4159 7145 0.041663 GCGCGCAACTTCTTGTACAA 60.042 50.000 29.10 8.28 0.00 2.41
4196 7182 7.500892 AGTGACAGACATTTGGTTTGTTATACA 59.499 33.333 0.00 0.00 44.16 2.29
4232 7224 0.461163 GTTGGTGGCGCTTTGGTTTT 60.461 50.000 7.64 0.00 0.00 2.43
4246 7241 3.749665 TGGTTTTAGCAGCTTTGCATT 57.250 38.095 0.00 0.00 37.25 3.56
4283 7278 3.510360 TCCTTGTGTCTAGTGGCTACTTC 59.490 47.826 8.46 0.47 38.36 3.01
4313 7311 2.885135 ATGTTGAGATCCTTGTGGCA 57.115 45.000 0.00 0.00 0.00 4.92
4343 7348 3.490419 GCTTTGCATATGCTTCCTCTTGG 60.490 47.826 27.13 9.00 42.66 3.61
4345 7350 1.064537 TGCATATGCTTCCTCTTGGCA 60.065 47.619 27.13 0.47 42.66 4.92
4346 7351 2.236766 GCATATGCTTCCTCTTGGCAT 58.763 47.619 20.64 0.00 46.49 4.40
4347 7352 2.626743 GCATATGCTTCCTCTTGGCATT 59.373 45.455 20.64 0.00 43.02 3.56
4348 7353 3.069158 GCATATGCTTCCTCTTGGCATTT 59.931 43.478 20.64 0.00 43.02 2.32
4349 7354 4.442472 GCATATGCTTCCTCTTGGCATTTT 60.442 41.667 20.64 0.00 43.02 1.82
4350 7355 3.881937 ATGCTTCCTCTTGGCATTTTC 57.118 42.857 0.00 0.00 43.02 2.29
4353 7358 0.521291 TTCCTCTTGGCATTTTCGCG 59.479 50.000 0.00 0.00 0.00 5.87
4356 7361 1.067199 CTCTTGGCATTTTCGCGCAC 61.067 55.000 8.75 0.00 0.00 5.34
4357 7362 2.049618 TTGGCATTTTCGCGCACC 60.050 55.556 8.75 0.00 0.00 5.01
4358 7363 2.476534 CTTGGCATTTTCGCGCACCT 62.477 55.000 8.75 0.00 0.00 4.00
4359 7364 2.081425 TTGGCATTTTCGCGCACCTT 62.081 50.000 8.75 0.00 0.00 3.50
4360 7365 1.237954 TGGCATTTTCGCGCACCTTA 61.238 50.000 8.75 0.00 0.00 2.69
4362 7367 1.466855 GCATTTTCGCGCACCTTATC 58.533 50.000 8.75 0.00 0.00 1.75
4363 7368 1.064060 GCATTTTCGCGCACCTTATCT 59.936 47.619 8.75 0.00 0.00 1.98
4364 7369 2.286833 GCATTTTCGCGCACCTTATCTA 59.713 45.455 8.75 0.00 0.00 1.98
4365 7370 3.058914 GCATTTTCGCGCACCTTATCTAT 60.059 43.478 8.75 0.00 0.00 1.98
4366 7371 4.702392 CATTTTCGCGCACCTTATCTATC 58.298 43.478 8.75 0.00 0.00 2.08
4367 7372 3.728076 TTTCGCGCACCTTATCTATCT 57.272 42.857 8.75 0.00 0.00 1.98
4368 7373 2.991434 TCGCGCACCTTATCTATCTC 57.009 50.000 8.75 0.00 0.00 2.75
4375 7380 5.755861 GCGCACCTTATCTATCTCTCTTTTT 59.244 40.000 0.30 0.00 0.00 1.94
4416 7421 0.325602 AAGGTGCCAAAATGCCATGG 59.674 50.000 7.63 7.63 39.80 3.66
4441 7446 6.358974 TTCTCACTCACATCTGGATTGTTA 57.641 37.500 0.00 0.00 0.00 2.41
4462 7467 4.928661 AGAGTTGTGTCGAATATTGTGC 57.071 40.909 0.00 0.00 0.00 4.57
4476 7481 6.456449 CGAATATTGTGCACAAGGTAGGTTAC 60.456 42.308 33.44 17.12 39.47 2.50
4486 7491 4.040095 ACAAGGTAGGTTACAGTTGGACTC 59.960 45.833 0.00 0.00 31.85 3.36
4516 7521 8.941977 GTTGTATTGTGTTTACATAGGATGTGA 58.058 33.333 2.33 0.00 44.60 3.58
4525 7530 4.537135 ACATAGGATGTGAAGTCGTGTT 57.463 40.909 0.00 0.00 43.01 3.32
4556 7561 2.294791 CACTTGTATCCTAGGCCTCTCG 59.705 54.545 9.68 0.00 0.00 4.04
4563 7568 7.204243 TGTATCCTAGGCCTCTCGTATATAA 57.796 40.000 9.68 0.00 0.00 0.98
4587 7592 2.231964 GGGGTAGACACACGATGTAACA 59.768 50.000 0.00 0.00 43.56 2.41
4607 7612 6.957920 AACATATGCCAACATAATAGCACA 57.042 33.333 1.58 0.00 41.99 4.57
4608 7613 7.528996 AACATATGCCAACATAATAGCACAT 57.471 32.000 1.58 0.00 41.99 3.21
4623 7628 1.176527 CACATGAACGCAGGGGAAAT 58.823 50.000 0.00 0.00 28.62 2.17
4631 7636 4.489771 CAGGGGAAATCGGCGGCT 62.490 66.667 7.21 0.00 0.00 5.52
4665 7670 2.646719 GCGATCGGGTGCGGTATA 59.353 61.111 18.30 0.00 0.00 1.47
4671 7676 2.928801 TCGGGTGCGGTATAGTAGTA 57.071 50.000 0.00 0.00 0.00 1.82
4681 7686 4.758674 GCGGTATAGTAGTAGTGTCATGGA 59.241 45.833 0.00 0.00 0.00 3.41
4690 7695 0.613292 AGTGTCATGGAGAGGAGCGT 60.613 55.000 0.00 0.00 0.00 5.07
4698 7703 1.031029 GGAGAGGAGCGTCCGTAGTT 61.031 60.000 0.00 0.00 42.75 2.24
4784 7792 0.911769 TGCTTGGTCCTCGGATGATT 59.088 50.000 0.00 0.00 0.00 2.57
4785 7793 2.115427 TGCTTGGTCCTCGGATGATTA 58.885 47.619 0.00 0.00 0.00 1.75
4817 7826 8.402798 TGCCTCAGATTTATTTTAACAAGTGA 57.597 30.769 0.00 0.00 0.00 3.41
4841 7851 2.631062 TCAAAGCTAGGTTGTTCGGAGA 59.369 45.455 8.16 0.00 0.00 3.71
4854 7864 3.197549 TGTTCGGAGATCATGGATTGTCA 59.802 43.478 0.00 0.00 35.04 3.58
4858 7868 5.059161 TCGGAGATCATGGATTGTCAATTC 58.941 41.667 0.00 0.00 0.00 2.17
4878 7888 3.565307 TCAGAGGCAGGTTTGATGTTTT 58.435 40.909 0.00 0.00 0.00 2.43
4890 7900 4.530094 TTGATGTTTTGATCGGTATCGC 57.470 40.909 0.00 0.00 34.60 4.58
4906 7916 0.874175 TCGCGGTGAACACAGTTGAG 60.874 55.000 6.13 0.00 0.00 3.02
4915 7925 3.258123 TGAACACAGTTGAGATCGATGGA 59.742 43.478 0.54 0.00 0.00 3.41
4924 7934 2.752903 TGAGATCGATGGAAAGACGTCA 59.247 45.455 19.50 0.00 0.00 4.35
4965 7975 1.134560 GAGTAGCGGAAATCAGACGGT 59.865 52.381 0.00 0.00 41.50 4.83
4990 8000 2.644555 AAGCAGTCAAGACGTGCGGT 62.645 55.000 0.00 7.81 39.07 5.68
4995 8005 0.666274 GTCAAGACGTGCGGTGATCA 60.666 55.000 0.00 0.00 0.00 2.92
5021 8031 2.048784 ATCGATCGGGCGAGCATG 60.049 61.111 16.41 0.00 44.26 4.06
5022 8032 2.755542 GATCGATCGGGCGAGCATGT 62.756 60.000 16.41 0.00 45.17 3.21
5023 8033 1.524008 ATCGATCGGGCGAGCATGTA 61.524 55.000 16.41 0.00 44.26 2.29
5024 8034 2.016704 CGATCGGGCGAGCATGTAC 61.017 63.158 7.38 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 3.444916 GGCTCGACTCATGTAATTCGAA 58.555 45.455 0.00 0.00 39.83 3.71
138 139 2.025155 ACTCGGCTCGACTCATGTAAT 58.975 47.619 0.00 0.00 0.00 1.89
144 145 0.039437 GTCAAACTCGGCTCGACTCA 60.039 55.000 0.00 0.00 0.00 3.41
215 226 6.598064 CGAAGGGGTGTAATTCTAGTTGATTT 59.402 38.462 0.00 0.00 0.00 2.17
220 231 3.370209 GGCGAAGGGGTGTAATTCTAGTT 60.370 47.826 0.00 0.00 0.00 2.24
230 251 3.692406 GTCTCGGCGAAGGGGTGT 61.692 66.667 12.13 0.00 0.00 4.16
242 263 2.019951 CAACCAACCGTCGGTCTCG 61.020 63.158 19.16 10.42 34.99 4.04
302 323 0.611896 TCTCTCTGGCGACCACATCA 60.612 55.000 0.00 0.00 0.00 3.07
310 331 3.891366 TCATGTGATATTCTCTCTGGCGA 59.109 43.478 0.00 0.00 0.00 5.54
315 336 8.105829 ACTTGGTTTTCATGTGATATTCTCTCT 58.894 33.333 0.00 0.00 33.23 3.10
357 379 2.294829 CGTCATTTCACGTGGTTTTCG 58.705 47.619 17.00 10.16 34.95 3.46
495 533 1.741706 GCAGACACTGACCAATGATGG 59.258 52.381 2.81 0.00 41.30 3.51
506 544 0.512952 GGCGTTTACTGCAGACACTG 59.487 55.000 23.35 8.16 34.12 3.66
537 576 6.329496 ACGAGCTTTGAAAGAACAAATTCAA 58.671 32.000 9.48 0.00 42.17 2.69
590 2605 3.392947 TGATGTTAAGAGGGTGGTGTTCA 59.607 43.478 0.00 0.00 0.00 3.18
700 2722 1.458827 ACGTACACGAGACGAGAGAAC 59.541 52.381 9.04 0.00 42.98 3.01
733 2758 1.795872 TCTTCGCATACGTGTGGTTTG 59.204 47.619 14.49 0.00 41.18 2.93
736 2761 0.885879 TCTCTTCGCATACGTGTGGT 59.114 50.000 14.49 0.00 41.18 4.16
762 2797 3.000819 TGGGAGGCACTACGTGGG 61.001 66.667 3.26 0.00 43.09 4.61
914 2970 3.284449 GTGTTCGGGTGTGGGTGC 61.284 66.667 0.00 0.00 0.00 5.01
932 2988 2.667969 GCCACGGATTTGATTCTTTTGC 59.332 45.455 0.00 0.00 0.00 3.68
969 3025 0.394625 GGAGGAGAGTGCGAGGTAGT 60.395 60.000 0.00 0.00 0.00 2.73
970 3026 1.440938 CGGAGGAGAGTGCGAGGTAG 61.441 65.000 0.00 0.00 32.11 3.18
971 3027 1.451567 CGGAGGAGAGTGCGAGGTA 60.452 63.158 0.00 0.00 32.11 3.08
972 3028 2.752238 CGGAGGAGAGTGCGAGGT 60.752 66.667 0.00 0.00 32.11 3.85
1003 3059 2.885861 CGGTCTCTTCTGGTCCGG 59.114 66.667 0.00 0.00 37.92 5.14
1296 3360 2.997315 CTGTCGTGGAGGAGGGCA 60.997 66.667 0.00 0.00 0.00 5.36
1493 3566 2.687200 ATCCAGGCCCAGTGCGTA 60.687 61.111 0.00 0.00 42.61 4.42
1556 3682 2.620115 AGCAACATTCAGACACACAAGG 59.380 45.455 0.00 0.00 0.00 3.61
1626 3758 2.783284 CACGAAGCAACAACACAATCAC 59.217 45.455 0.00 0.00 0.00 3.06
1671 3803 4.142622 TGTGCAATTCACTCCGATCAAATC 60.143 41.667 0.00 0.00 45.81 2.17
1680 3812 5.049167 TCAATGTTTTGTGCAATTCACTCC 58.951 37.500 0.00 0.00 45.81 3.85
1693 3825 8.090214 ACCCTATCTTTCAATGTCAATGTTTTG 58.910 33.333 0.00 0.00 0.00 2.44
1701 3833 4.661222 TGCAACCCTATCTTTCAATGTCA 58.339 39.130 0.00 0.00 0.00 3.58
1718 3850 3.625764 TGTAGAAGTGTGGTTTCTGCAAC 59.374 43.478 3.79 0.00 41.94 4.17
1798 3932 2.673833 CTCAAAACGGTCTAAGCGAGT 58.326 47.619 5.47 0.00 42.41 4.18
1833 3967 1.607612 CCTGTTTAGCGGGACCCAT 59.392 57.895 12.15 0.18 46.81 4.00
1953 4087 4.007940 GGCAGTGAAAACGCGCGA 62.008 61.111 39.36 11.25 0.00 5.87
1956 4090 2.252260 CTGGGCAGTGAAAACGCG 59.748 61.111 3.53 3.53 0.00 6.01
2016 4150 2.668632 GGTGGCTTCCGATGGTGA 59.331 61.111 0.00 0.00 0.00 4.02
2021 4155 3.090532 GGAGGGGTGGCTTCCGAT 61.091 66.667 0.00 0.00 0.00 4.18
2022 4156 3.864983 AAGGAGGGGTGGCTTCCGA 62.865 63.158 0.00 0.00 36.11 4.55
2197 4380 4.250170 AGGGGTGGAGGTCACGGT 62.250 66.667 0.00 0.00 46.96 4.83
2203 4386 2.125225 GGAAGGAGGGGTGGAGGT 59.875 66.667 0.00 0.00 0.00 3.85
2302 4486 1.602237 CGGTGGTGCCTGTTAGGAT 59.398 57.895 0.00 0.00 37.67 3.24
2325 4509 1.461268 TCCACTCCCTTCCAGTGCA 60.461 57.895 0.00 0.00 40.10 4.57
2330 4514 2.610859 GGCCTCCACTCCCTTCCA 60.611 66.667 0.00 0.00 0.00 3.53
2458 4690 5.638530 TTTGCAAAAGGACCCCTAAAAAT 57.361 34.783 10.02 0.00 31.13 1.82
2544 4776 2.479566 AAGCACGATCATGACAGGTT 57.520 45.000 0.00 0.00 0.00 3.50
2630 4863 6.885735 AATCACAAGTTTACAGTTTTGTGC 57.114 33.333 10.43 0.00 46.07 4.57
2643 4876 4.641989 ACAGTCTTGCAGAAATCACAAGTT 59.358 37.500 12.85 4.39 41.22 2.66
2699 4933 2.348666 GCGCGAATTAACACTGTCAGAT 59.651 45.455 12.10 0.00 0.00 2.90
2700 4934 1.724623 GCGCGAATTAACACTGTCAGA 59.275 47.619 12.10 0.00 0.00 3.27
2701 4935 1.459209 TGCGCGAATTAACACTGTCAG 59.541 47.619 12.10 0.00 0.00 3.51
2702 4936 1.503294 TGCGCGAATTAACACTGTCA 58.497 45.000 12.10 0.00 0.00 3.58
2703 4937 2.230864 GTTGCGCGAATTAACACTGTC 58.769 47.619 12.10 0.00 0.00 3.51
2704 4938 1.069500 GGTTGCGCGAATTAACACTGT 60.069 47.619 12.10 0.00 0.00 3.55
2705 4939 1.196808 AGGTTGCGCGAATTAACACTG 59.803 47.619 12.10 0.00 0.00 3.66
2706 4940 1.196808 CAGGTTGCGCGAATTAACACT 59.803 47.619 12.10 5.84 0.00 3.55
2707 4941 1.602191 CAGGTTGCGCGAATTAACAC 58.398 50.000 12.10 0.00 0.00 3.32
2783 5078 1.339727 ACCCAGGAACTATGCCGAAAC 60.340 52.381 0.00 0.00 36.02 2.78
2846 5160 6.473455 CCTTTCAAACAGTTTCAAGATCACAC 59.527 38.462 13.18 0.00 0.00 3.82
2847 5161 6.405731 CCCTTTCAAACAGTTTCAAGATCACA 60.406 38.462 13.18 0.00 0.00 3.58
3136 5460 9.890629 ATAAGATAACAGCATAGAAACAGTCAA 57.109 29.630 0.00 0.00 0.00 3.18
3228 5552 2.168313 GCCAATTCACCCCGAAATGAAT 59.832 45.455 3.13 3.13 45.36 2.57
3229 5553 1.548269 GCCAATTCACCCCGAAATGAA 59.452 47.619 0.00 0.00 36.75 2.57
3230 5554 1.181786 GCCAATTCACCCCGAAATGA 58.818 50.000 0.00 0.00 36.75 2.57
3231 5555 1.185315 AGCCAATTCACCCCGAAATG 58.815 50.000 0.00 0.00 37.12 2.32
3232 5556 2.818751 TAGCCAATTCACCCCGAAAT 57.181 45.000 0.00 0.00 37.12 2.17
3233 5557 2.374184 CATAGCCAATTCACCCCGAAA 58.626 47.619 0.00 0.00 37.12 3.46
3234 5558 1.409521 CCATAGCCAATTCACCCCGAA 60.410 52.381 0.00 0.00 38.22 4.30
3235 5559 0.182537 CCATAGCCAATTCACCCCGA 59.817 55.000 0.00 0.00 0.00 5.14
3236 5560 0.106719 ACCATAGCCAATTCACCCCG 60.107 55.000 0.00 0.00 0.00 5.73
3237 5561 1.402787 CACCATAGCCAATTCACCCC 58.597 55.000 0.00 0.00 0.00 4.95
3238 5562 1.341976 ACCACCATAGCCAATTCACCC 60.342 52.381 0.00 0.00 0.00 4.61
3239 5563 2.143876 ACCACCATAGCCAATTCACC 57.856 50.000 0.00 0.00 0.00 4.02
3240 5564 3.848726 CAAACCACCATAGCCAATTCAC 58.151 45.455 0.00 0.00 0.00 3.18
3241 5565 2.233431 GCAAACCACCATAGCCAATTCA 59.767 45.455 0.00 0.00 0.00 2.57
3242 5566 2.497273 AGCAAACCACCATAGCCAATTC 59.503 45.455 0.00 0.00 0.00 2.17
3243 5567 2.539302 AGCAAACCACCATAGCCAATT 58.461 42.857 0.00 0.00 0.00 2.32
3244 5568 2.236489 AGCAAACCACCATAGCCAAT 57.764 45.000 0.00 0.00 0.00 3.16
3245 5569 2.008242 AAGCAAACCACCATAGCCAA 57.992 45.000 0.00 0.00 0.00 4.52
3246 5570 2.008242 AAAGCAAACCACCATAGCCA 57.992 45.000 0.00 0.00 0.00 4.75
3247 5571 4.736126 AATAAAGCAAACCACCATAGCC 57.264 40.909 0.00 0.00 0.00 3.93
3248 5572 9.810545 TTTATAAATAAAGCAAACCACCATAGC 57.189 29.630 0.00 0.00 0.00 2.97
3263 5587 5.733937 GCTTTCGCCCCGCTTTATAAATAAA 60.734 40.000 0.00 0.00 0.00 1.40
3264 5588 4.261280 GCTTTCGCCCCGCTTTATAAATAA 60.261 41.667 0.00 0.00 0.00 1.40
3265 5589 3.251487 GCTTTCGCCCCGCTTTATAAATA 59.749 43.478 0.00 0.00 0.00 1.40
3266 5590 2.034179 GCTTTCGCCCCGCTTTATAAAT 59.966 45.455 0.00 0.00 0.00 1.40
3267 5591 1.402613 GCTTTCGCCCCGCTTTATAAA 59.597 47.619 0.00 0.00 0.00 1.40
3268 5592 1.018910 GCTTTCGCCCCGCTTTATAA 58.981 50.000 0.00 0.00 0.00 0.98
3269 5593 2.697819 GCTTTCGCCCCGCTTTATA 58.302 52.632 0.00 0.00 0.00 0.98
3270 5594 3.509659 GCTTTCGCCCCGCTTTAT 58.490 55.556 0.00 0.00 0.00 1.40
3280 5604 2.691984 TTACCGAAAAAGGCTTTCGC 57.308 45.000 13.76 7.41 46.89 4.70
3282 5606 7.410407 CGAAATGAATTACCGAAAAAGGCTTTC 60.410 37.037 13.76 0.41 33.69 2.62
3283 5607 6.364976 CGAAATGAATTACCGAAAAAGGCTTT 59.635 34.615 6.68 6.68 33.69 3.51
3284 5608 5.861787 CGAAATGAATTACCGAAAAAGGCTT 59.138 36.000 0.00 0.00 33.69 4.35
3285 5609 5.399013 CGAAATGAATTACCGAAAAAGGCT 58.601 37.500 0.00 0.00 33.69 4.58
3286 5610 4.561213 CCGAAATGAATTACCGAAAAAGGC 59.439 41.667 0.00 0.00 33.69 4.35
3287 5611 5.099575 CCCGAAATGAATTACCGAAAAAGG 58.900 41.667 0.00 0.00 37.30 3.11
3288 5612 5.099575 CCCCGAAATGAATTACCGAAAAAG 58.900 41.667 0.00 0.00 0.00 2.27
3289 5613 4.523558 ACCCCGAAATGAATTACCGAAAAA 59.476 37.500 0.00 0.00 0.00 1.94
3290 5614 4.080687 ACCCCGAAATGAATTACCGAAAA 58.919 39.130 0.00 0.00 0.00 2.29
3291 5615 3.688235 ACCCCGAAATGAATTACCGAAA 58.312 40.909 0.00 0.00 0.00 3.46
3292 5616 3.353370 ACCCCGAAATGAATTACCGAA 57.647 42.857 0.00 0.00 0.00 4.30
3293 5617 3.353370 AACCCCGAAATGAATTACCGA 57.647 42.857 0.00 0.00 0.00 4.69
3294 5618 5.761165 ATTAACCCCGAAATGAATTACCG 57.239 39.130 0.00 0.00 0.00 4.02
3295 5619 6.127281 ACCAATTAACCCCGAAATGAATTACC 60.127 38.462 0.00 0.00 0.00 2.85
3296 5620 6.754675 CACCAATTAACCCCGAAATGAATTAC 59.245 38.462 0.00 0.00 0.00 1.89
3297 5621 6.628398 GCACCAATTAACCCCGAAATGAATTA 60.628 38.462 0.00 0.00 0.00 1.40
3458 5783 3.498397 AGACGATGACCAATCAACAACAC 59.502 43.478 0.00 0.00 38.69 3.32
3503 6342 0.319555 TCGGAGAACCTGTCGCAAAG 60.320 55.000 0.00 0.00 0.00 2.77
3537 6376 1.134220 TCTCAAACCAGCAAACGTCCT 60.134 47.619 0.00 0.00 0.00 3.85
3541 6380 1.879380 TGGATCTCAAACCAGCAAACG 59.121 47.619 0.00 0.00 0.00 3.60
3739 6614 1.808390 GCCCTCGTCGTAATGCGTT 60.808 57.895 0.00 0.00 42.13 4.84
3752 6627 0.318275 GACTCATCGTCATCGCCCTC 60.318 60.000 0.00 0.00 42.37 4.30
3753 6628 1.736586 GACTCATCGTCATCGCCCT 59.263 57.895 0.00 0.00 42.37 5.19
3754 6629 1.300233 GGACTCATCGTCATCGCCC 60.300 63.158 0.00 0.00 44.68 6.13
3755 6630 1.658717 CGGACTCATCGTCATCGCC 60.659 63.158 0.00 0.00 44.68 5.54
3756 6631 0.930742 GTCGGACTCATCGTCATCGC 60.931 60.000 0.00 0.00 44.68 4.58
3757 6632 0.654760 CGTCGGACTCATCGTCATCG 60.655 60.000 6.57 0.00 44.68 3.84
3758 6633 0.656259 TCGTCGGACTCATCGTCATC 59.344 55.000 6.57 0.00 44.68 2.92
3759 6634 0.658368 CTCGTCGGACTCATCGTCAT 59.342 55.000 6.57 0.00 44.68 3.06
3760 6635 1.366854 CCTCGTCGGACTCATCGTCA 61.367 60.000 6.57 0.00 44.68 4.35
3761 6636 1.088340 TCCTCGTCGGACTCATCGTC 61.088 60.000 6.57 0.00 42.07 4.20
3762 6637 1.078637 TCCTCGTCGGACTCATCGT 60.079 57.895 6.57 0.00 36.69 3.73
3763 6638 1.644372 CTCCTCGTCGGACTCATCG 59.356 63.158 6.57 0.00 36.69 3.84
3764 6639 0.464013 TCCTCCTCGTCGGACTCATC 60.464 60.000 6.57 0.00 36.69 2.92
3765 6640 0.464735 CTCCTCCTCGTCGGACTCAT 60.465 60.000 6.57 0.00 36.69 2.90
3766 6641 1.078356 CTCCTCCTCGTCGGACTCA 60.078 63.158 6.57 0.00 36.69 3.41
3771 6646 2.517402 CCTCCTCCTCCTCGTCGG 60.517 72.222 0.00 0.00 0.00 4.79
3946 6899 3.655777 ACTTCCCACTTTTGGTCTCCATA 59.344 43.478 0.00 0.00 42.10 2.74
3985 6938 1.144716 GATCTCGATGCCCTGCACA 59.855 57.895 0.00 0.00 43.04 4.57
4057 7013 8.713708 TCCTTATTTCATTTACTTTTGACCCA 57.286 30.769 0.00 0.00 0.00 4.51
4159 7145 4.879197 TGTCTGTCACTCATGAGTCATT 57.121 40.909 25.58 1.03 40.20 2.57
4196 7182 5.181245 CCACCAACGTCTGAATCAACTTATT 59.819 40.000 0.00 0.00 0.00 1.40
4201 7187 1.069227 GCCACCAACGTCTGAATCAAC 60.069 52.381 0.00 0.00 0.00 3.18
4246 7241 4.104102 ACACAAGGATCTCAACCTAACCAA 59.896 41.667 0.00 0.00 36.67 3.67
4283 7278 3.496130 GGATCTCAACATAACCAGATGCG 59.504 47.826 0.00 0.00 0.00 4.73
4313 7311 1.202486 GCATATGCAAAGCAGCCACAT 60.202 47.619 22.84 0.00 43.65 3.21
4343 7348 1.064060 AGATAAGGTGCGCGAAAATGC 59.936 47.619 12.10 0.00 0.00 3.56
4345 7350 4.632153 AGATAGATAAGGTGCGCGAAAAT 58.368 39.130 12.10 0.00 0.00 1.82
4346 7351 4.049186 GAGATAGATAAGGTGCGCGAAAA 58.951 43.478 12.10 0.00 0.00 2.29
4347 7352 3.318275 AGAGATAGATAAGGTGCGCGAAA 59.682 43.478 12.10 0.00 0.00 3.46
4348 7353 2.885266 AGAGATAGATAAGGTGCGCGAA 59.115 45.455 12.10 0.00 0.00 4.70
4349 7354 2.484651 GAGAGATAGATAAGGTGCGCGA 59.515 50.000 12.10 0.00 0.00 5.87
4350 7355 2.486203 AGAGAGATAGATAAGGTGCGCG 59.514 50.000 0.00 0.00 0.00 6.86
4375 7380 7.947332 ACCTTATCTATCTCTCTGCAGATACAA 59.053 37.037 18.63 3.74 34.75 2.41
4416 7421 5.426504 ACAATCCAGATGTGAGTGAGAATC 58.573 41.667 0.00 0.00 32.49 2.52
4441 7446 4.152402 GTGCACAATATTCGACACAACTCT 59.848 41.667 13.17 0.00 0.00 3.24
4462 7467 4.062991 GTCCAACTGTAACCTACCTTGTG 58.937 47.826 0.00 0.00 0.00 3.33
4476 7481 6.706270 ACACAATACAACTAAGAGTCCAACTG 59.294 38.462 0.00 0.00 0.00 3.16
4516 7521 4.396522 AGTGTCCTACTAGAACACGACTT 58.603 43.478 0.00 0.00 46.11 3.01
4556 7561 4.320494 CGTGTGTCTACCCCCGTTATATAC 60.320 50.000 0.00 0.00 0.00 1.47
4563 7568 1.304713 ATCGTGTGTCTACCCCCGT 60.305 57.895 0.00 0.00 0.00 5.28
4587 7592 7.573656 CGTTCATGTGCTATTATGTTGGCATAT 60.574 37.037 0.00 0.00 37.42 1.78
4607 7612 0.748005 CCGATTTCCCCTGCGTTCAT 60.748 55.000 0.00 0.00 0.00 2.57
4608 7613 1.376683 CCGATTTCCCCTGCGTTCA 60.377 57.895 0.00 0.00 0.00 3.18
4631 7636 4.738998 CCCTGGATGCCGGCACAA 62.739 66.667 35.50 19.38 0.00 3.33
4641 7646 3.550431 CACCCGATCGCCCTGGAT 61.550 66.667 10.32 0.00 0.00 3.41
4652 7657 2.104792 ACTACTACTATACCGCACCCGA 59.895 50.000 0.00 0.00 36.29 5.14
4665 7670 4.787551 CTCCTCTCCATGACACTACTACT 58.212 47.826 0.00 0.00 0.00 2.57
4671 7676 0.613292 ACGCTCCTCTCCATGACACT 60.613 55.000 0.00 0.00 0.00 3.55
4681 7686 1.666054 CTAACTACGGACGCTCCTCT 58.334 55.000 0.00 0.00 33.30 3.69
4698 7703 2.203182 CTACATCCCCGGGGCCTA 59.797 66.667 36.68 19.63 34.68 3.93
4784 7792 9.616156 TTAAAATAAATCTGAGGCATACCGTTA 57.384 29.630 0.00 0.00 42.76 3.18
4785 7793 8.403236 GTTAAAATAAATCTGAGGCATACCGTT 58.597 33.333 0.00 0.00 42.76 4.44
4817 7826 5.128827 TCTCCGAACAACCTAGCTTTGATAT 59.871 40.000 3.66 0.00 0.00 1.63
4823 7833 2.832129 TGATCTCCGAACAACCTAGCTT 59.168 45.455 0.00 0.00 0.00 3.74
4841 7851 4.583489 GCCTCTGAATTGACAATCCATGAT 59.417 41.667 0.05 0.00 0.00 2.45
4854 7864 3.771216 ACATCAAACCTGCCTCTGAATT 58.229 40.909 0.00 0.00 0.00 2.17
4858 7868 3.318839 TCAAAACATCAAACCTGCCTCTG 59.681 43.478 0.00 0.00 0.00 3.35
4878 7888 0.248743 GTTCACCGCGATACCGATCA 60.249 55.000 8.23 0.00 38.22 2.92
4890 7900 1.721389 CGATCTCAACTGTGTTCACCG 59.279 52.381 0.37 0.00 0.00 4.94
4906 7916 2.860735 CCTTGACGTCTTTCCATCGATC 59.139 50.000 17.92 0.00 0.00 3.69
4915 7925 1.714794 CTCATCGCCTTGACGTCTTT 58.285 50.000 17.92 0.00 0.00 2.52
4924 7934 1.091771 CCGTGATTGCTCATCGCCTT 61.092 55.000 4.91 0.00 39.00 4.35
4959 7969 0.671781 GACTGCTTGCATGACCGTCT 60.672 55.000 3.33 0.00 0.00 4.18
4965 7975 1.150827 CGTCTTGACTGCTTGCATGA 58.849 50.000 3.33 0.00 0.00 3.07
4990 8000 3.305608 CCGATCGATCCACTGAATGATCA 60.306 47.826 18.66 0.00 37.77 2.92
4995 8005 0.034059 GCCCGATCGATCCACTGAAT 59.966 55.000 18.66 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.