Multiple sequence alignment - TraesCS7A01G065500

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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 TraesCS7A01G065500 chr7A 100.000 4919 0 0 1 4919 32634005 32629087 0.000000e+00 9084.0
1 TraesCS7A01G065500 chr7A 91.667 84 6 1 1869 1951 234630542 234630625 1.120000e-21 115.0
2 TraesCS7A01G065500 chr7A 90.698 86 6 1 4344 4427 155296045 155296130 4.020000e-21 113.0
3 TraesCS7A01G065500 chr4A 95.292 3823 90 40 686 4470 692386234 692382464 0.000000e+00 5980.0
4 TraesCS7A01G065500 chr4A 90.738 637 47 6 1 636 692390151 692389526 0.000000e+00 839.0
5 TraesCS7A01G065500 chr4A 98.131 107 2 0 4811 4917 692382378 692382272 2.340000e-43 187.0
6 TraesCS7A01G065500 chr4A 93.750 112 4 2 3294 3402 597837505 597837394 1.100000e-36 165.0
7 TraesCS7A01G065500 chr4A 98.462 65 1 0 4756 4820 692382457 692382393 1.120000e-21 115.0
8 TraesCS7A01G065500 chr4A 100.000 31 0 0 4703 4733 631371685 631371715 1.910000e-04 58.4
9 TraesCS7A01G065500 chr7D 96.203 3661 64 23 801 4432 32609897 32606283 0.000000e+00 5921.0
10 TraesCS7A01G065500 chr7D 92.340 470 29 4 1 463 32620348 32619879 0.000000e+00 662.0
11 TraesCS7A01G065500 chr7D 90.373 322 28 2 448 769 32611158 32610840 2.120000e-113 420.0
12 TraesCS7A01G065500 chr7D 98.131 107 2 0 4811 4917 32606176 32606070 2.340000e-43 187.0
13 TraesCS7A01G065500 chr7D 84.737 190 15 10 4165 4342 188361235 188361048 1.410000e-40 178.0
14 TraesCS7A01G065500 chr7D 94.118 68 1 1 4756 4820 32606258 32606191 3.130000e-17 100.0
15 TraesCS7A01G065500 chr4B 92.534 4152 180 46 1 4083 38029390 38025300 0.000000e+00 5830.0
16 TraesCS7A01G065500 chr4B 88.314 522 37 13 3414 3918 9948276 9948790 5.450000e-169 604.0
17 TraesCS7A01G065500 chr4B 91.775 231 9 7 4121 4345 9949043 9949269 3.700000e-81 313.0
18 TraesCS7A01G065500 chr4B 96.154 104 3 1 2348 2451 9948089 9947987 8.470000e-38 169.0
19 TraesCS7A01G065500 chr4B 98.361 61 1 0 4756 4816 9949560 9949620 1.870000e-19 108.0
20 TraesCS7A01G065500 chr4B 83.784 111 5 4 4808 4917 9949640 9949738 5.240000e-15 93.5
21 TraesCS7A01G065500 chr4D 96.595 2614 59 15 1182 3777 25695632 25693031 0.000000e+00 4307.0
22 TraesCS7A01G065500 chr4D 89.446 1137 66 23 1 1134 25696964 25695879 0.000000e+00 1386.0
23 TraesCS7A01G065500 chr4D 86.017 1037 66 30 1731 2761 5684371 5685334 0.000000e+00 1038.0
24 TraesCS7A01G065500 chr4D 89.060 649 46 11 3394 4026 5685337 5685976 0.000000e+00 782.0
25 TraesCS7A01G065500 chr4D 84.356 505 47 25 1082 1560 5683735 5684233 2.680000e-127 466.0
26 TraesCS7A01G065500 chr4D 83.628 226 18 12 4134 4342 215457745 215457968 1.400000e-45 195.0
27 TraesCS7A01G065500 chr4D 88.235 136 11 2 1731 1862 182470836 182470702 1.830000e-34 158.0
28 TraesCS7A01G065500 chr4D 94.444 36 2 0 4420 4455 5686072 5686107 6.880000e-04 56.5
29 TraesCS7A01G065500 chr4D 94.444 36 2 0 4420 4455 25692703 25692668 6.880000e-04 56.5
30 TraesCS7A01G065500 chr6B 95.384 1603 59 10 1677 3277 626213761 626215350 0.000000e+00 2536.0
31 TraesCS7A01G065500 chr6B 88.374 1101 66 25 3278 4345 626216565 626217636 0.000000e+00 1267.0
32 TraesCS7A01G065500 chr6B 84.512 297 22 12 970 1259 626212036 626212315 6.270000e-69 272.0
33 TraesCS7A01G065500 chr6B 80.802 349 41 23 1265 1595 626213386 626213726 2.940000e-62 250.0
34 TraesCS7A01G065500 chr6B 81.364 220 31 9 4131 4341 668971067 668971285 2.350000e-38 171.0
35 TraesCS7A01G065500 chr6B 79.535 215 34 3 49 262 76140387 76140592 1.430000e-30 145.0
36 TraesCS7A01G065500 chr6B 81.538 130 19 3 4344 4468 626217719 626217848 8.710000e-18 102.0
37 TraesCS7A01G065500 chr6B 95.082 61 3 0 4756 4816 626217855 626217915 4.050000e-16 97.1
38 TraesCS7A01G065500 chr6B 97.727 44 1 0 1819 1862 669523923 669523966 5.280000e-10 76.8
39 TraesCS7A01G065500 chr3A 79.597 794 109 34 3074 3841 651640693 651639927 2.030000e-143 520.0
40 TraesCS7A01G065500 chr3A 97.908 239 5 0 4467 4705 597888030 597887792 9.850000e-112 414.0
41 TraesCS7A01G065500 chr3A 97.447 235 6 0 4471 4705 111840098 111839864 7.670000e-108 401.0
42 TraesCS7A01G065500 chr3A 96.203 237 9 0 4469 4705 703404295 703404059 5.970000e-104 388.0
43 TraesCS7A01G065500 chr3A 82.511 223 19 13 4138 4342 647752989 647752769 1.410000e-40 178.0
44 TraesCS7A01G065500 chr3A 87.209 86 9 2 4344 4429 521573691 521573608 4.050000e-16 97.1
45 TraesCS7A01G065500 chr3A 94.872 39 2 0 4703 4741 649164211 649164249 1.480000e-05 62.1
46 TraesCS7A01G065500 chr6A 96.234 239 8 1 4468 4705 46548853 46549091 1.660000e-104 390.0
47 TraesCS7A01G065500 chr6A 96.203 237 8 1 4469 4705 422776251 422776016 2.150000e-103 387.0
48 TraesCS7A01G065500 chr6A 93.878 49 2 1 4139 4186 140545071 140545023 6.830000e-09 73.1
49 TraesCS7A01G065500 chr6A 100.000 33 0 0 4703 4735 80803106 80803074 1.480000e-05 62.1
50 TraesCS7A01G065500 chr5A 95.492 244 10 1 4463 4705 538101482 538101239 5.970000e-104 388.0
51 TraesCS7A01G065500 chr3D 96.186 236 7 2 4470 4705 79555099 79555332 7.720000e-103 385.0
52 TraesCS7A01G065500 chr3D 88.971 136 10 2 1731 1862 494379278 494379144 3.940000e-36 163.0
53 TraesCS7A01G065500 chr2A 96.186 236 8 1 4470 4705 52051591 52051357 7.720000e-103 385.0
54 TraesCS7A01G065500 chr2A 92.857 84 5 1 1869 1951 90619405 90619322 2.400000e-23 121.0
55 TraesCS7A01G065500 chr2A 89.024 82 9 0 4344 4425 429161401 429161482 8.710000e-18 102.0
56 TraesCS7A01G065500 chr2A 100.000 33 0 0 4703 4735 61503536 61503568 1.480000e-05 62.1
57 TraesCS7A01G065500 chr2A 100.000 33 0 0 4703 4735 531505083 531505115 1.480000e-05 62.1
58 TraesCS7A01G065500 chr1D 96.186 236 8 1 4470 4705 69475972 69475738 7.720000e-103 385.0
59 TraesCS7A01G065500 chr1D 88.971 136 10 2 1731 1862 145884882 145885016 3.940000e-36 163.0
60 TraesCS7A01G065500 chr1D 89.286 84 8 1 1869 1951 393297597 393297514 2.420000e-18 104.0
61 TraesCS7A01G065500 chr1D 83.636 110 9 7 1473 1580 145884659 145884761 1.460000e-15 95.3
62 TraesCS7A01G065500 chr3B 78.031 701 85 35 2645 3316 680750438 680751098 1.290000e-100 377.0
63 TraesCS7A01G065500 chr3B 82.968 411 44 13 2205 2608 680749948 680750339 1.010000e-91 348.0
64 TraesCS7A01G065500 chr3B 88.321 137 15 1 1019 1155 680748888 680749023 3.940000e-36 163.0
65 TraesCS7A01G065500 chr2B 82.192 219 22 12 4138 4342 525628777 525628562 6.550000e-39 172.0
66 TraesCS7A01G065500 chr2B 86.667 90 12 0 4344 4433 27542093 27542004 3.130000e-17 100.0
67 TraesCS7A01G065500 chr2B 94.595 37 2 0 4703 4739 703348325 703348289 1.910000e-04 58.4
68 TraesCS7A01G065500 chr7B 81.197 234 22 12 4135 4349 614234016 614233786 8.470000e-38 169.0
69 TraesCS7A01G065500 chr7B 88.095 84 9 1 4344 4427 471090354 471090436 1.130000e-16 99.0
70 TraesCS7A01G065500 chr5D 88.971 136 10 2 1731 1862 485215545 485215411 3.940000e-36 163.0
71 TraesCS7A01G065500 chr2D 78.175 252 41 6 290 539 541079422 541079661 1.100000e-31 148.0
72 TraesCS7A01G065500 chr1A 92.857 84 5 1 1869 1951 379468713 379468796 2.400000e-23 121.0
73 TraesCS7A01G065500 chr1A 100.000 33 0 0 4703 4735 320384022 320384054 1.480000e-05 62.1
74 TraesCS7A01G065500 chr1A 100.000 33 0 0 4703 4735 565417380 565417348 1.480000e-05 62.1
75 TraesCS7A01G065500 chr1A 97.143 35 1 0 4703 4737 370098868 370098902 5.320000e-05 60.2
76 TraesCS7A01G065500 chrUn 91.026 78 6 1 4344 4421 309799503 309799579 2.420000e-18 104.0
77 TraesCS7A01G065500 chrUn 91.026 78 6 1 4344 4421 315208250 315208326 2.420000e-18 104.0


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 TraesCS7A01G065500 chr7A 32629087 32634005 4918 True 9084.000000 9084 100.000000 1 4919 1 chr7A.!!$R1 4918
1 TraesCS7A01G065500 chr4A 692382272 692390151 7879 True 1780.250000 5980 95.655750 1 4917 4 chr4A.!!$R2 4916
2 TraesCS7A01G065500 chr7D 32606070 32611158 5088 True 1657.000000 5921 94.706250 448 4917 4 chr7D.!!$R3 4469
3 TraesCS7A01G065500 chr4B 38025300 38029390 4090 True 5830.000000 5830 92.534000 1 4083 1 chr4B.!!$R2 4082
4 TraesCS7A01G065500 chr4B 9948276 9949738 1462 False 279.625000 604 90.558500 3414 4917 4 chr4B.!!$F1 1503
5 TraesCS7A01G065500 chr4D 25692668 25696964 4296 True 1916.500000 4307 93.495000 1 4455 3 chr4D.!!$R2 4454
6 TraesCS7A01G065500 chr4D 5683735 5686107 2372 False 585.625000 1038 88.469250 1082 4455 4 chr4D.!!$F2 3373
7 TraesCS7A01G065500 chr6B 626212036 626217915 5879 False 754.016667 2536 87.615333 970 4816 6 chr6B.!!$F4 3846
8 TraesCS7A01G065500 chr3A 651639927 651640693 766 True 520.000000 520 79.597000 3074 3841 1 chr3A.!!$R5 767
9 TraesCS7A01G065500 chr3B 680748888 680751098 2210 False 296.000000 377 83.106667 1019 3316 3 chr3B.!!$F1 2297

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
303 305 0.324091 CCTTTGGCATTCCTCAGGCT 60.324 55.000 0.00 0.00 0.00 4.58 F
490 534 0.978151 TTTTCCAGGTTCGATCCCGA 59.022 50.000 8.95 2.64 43.96 5.14 F
547 633 1.523711 CCGGCCTGACATACGCAAT 60.524 57.895 0.00 0.00 0.00 3.56 F
996 5278 1.934956 CAATCCGCGACTCGACTCG 60.935 63.158 8.23 9.73 41.67 4.18 F
2398 8083 2.034687 TTCTGCCAGCTCAAGCCC 59.965 61.111 0.00 0.00 43.38 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1179 5501 0.247736 AGATGCGAGCTTTCCGAACT 59.752 50.000 0.00 0.0 0.00 3.01 R
1661 7285 2.277969 TCAGACGGCGTTACAAAAACA 58.722 42.857 16.19 0.0 0.00 2.83 R
2173 7850 3.926058 AAACAGGGCATAGGTTACGAT 57.074 42.857 0.00 0.0 0.00 3.73 R
2814 8593 2.042741 TGGCAAGGGCATCATGGG 60.043 61.111 0.00 0.0 43.71 4.00 R
3920 10969 0.764890 AGCACAGGCAGTTGGACTTA 59.235 50.000 0.00 0.0 44.61 2.24 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
89 90 1.413082 CCTAGGGTGTGGCCTATCTCA 60.413 57.143 3.32 0.00 37.43 3.27
141 143 1.832167 GGTCCTTGTTGCAAGCCCA 60.832 57.895 0.00 0.00 0.00 5.36
146 148 2.170166 CCTTGTTGCAAGCCCATAAGA 58.830 47.619 0.00 0.00 0.00 2.10
187 189 2.224992 TGCAAAGGTCCTTGATTGGCTA 60.225 45.455 4.45 0.00 0.00 3.93
288 290 1.648504 GACGCGTAGTATTGCCCTTT 58.351 50.000 13.97 0.00 0.00 3.11
303 305 0.324091 CCTTTGGCATTCCTCAGGCT 60.324 55.000 0.00 0.00 0.00 4.58
321 323 3.628982 GGGTCGGGTTTCGGGTCA 61.629 66.667 0.00 0.00 39.77 4.02
434 436 9.165014 CGAAGAAACTAAAAACATCAATTTCGA 57.835 29.630 0.00 0.00 34.76 3.71
474 476 5.123344 GCCTCCGTGTAAACTGACATATTTT 59.877 40.000 0.00 0.00 0.00 1.82
480 524 6.148811 CGTGTAAACTGACATATTTTCCAGGT 59.851 38.462 0.00 0.00 0.00 4.00
481 525 7.308348 CGTGTAAACTGACATATTTTCCAGGTT 60.308 37.037 0.00 0.00 39.56 3.50
485 529 5.745227 ACTGACATATTTTCCAGGTTCGAT 58.255 37.500 0.00 0.00 0.00 3.59
490 534 0.978151 TTTTCCAGGTTCGATCCCGA 59.022 50.000 8.95 2.64 43.96 5.14
524 610 3.806949 ACAGGTCAAATTTCTAGGCCA 57.193 42.857 5.01 0.00 0.00 5.36
547 633 1.523711 CCGGCCTGACATACGCAAT 60.524 57.895 0.00 0.00 0.00 3.56
564 650 3.443681 CGCAATGGGTCAAATTTCTAGGT 59.556 43.478 0.00 0.00 0.00 3.08
577 681 4.075793 TAGGTCTGAGCCCGGCCT 62.076 66.667 5.55 0.00 0.00 5.19
578 682 2.642183 CTAGGTCTGAGCCCGGCCTA 62.642 65.000 5.55 0.00 0.00 3.93
580 684 2.442272 GTCTGAGCCCGGCCTAGA 60.442 66.667 5.55 7.47 0.00 2.43
676 810 9.783256 ATTTCGTAAATAATAAGCAAAGTGGAC 57.217 29.630 0.00 0.00 0.00 4.02
831 5092 4.208686 GCCGAGTAGGACAGCCCG 62.209 72.222 0.00 0.00 45.00 6.13
950 5224 2.592001 CTCGATCTCTCCCGCCGA 60.592 66.667 0.00 0.00 0.00 5.54
996 5278 1.934956 CAATCCGCGACTCGACTCG 60.935 63.158 8.23 9.73 41.67 4.18
997 5279 2.104859 AATCCGCGACTCGACTCGA 61.105 57.895 17.07 0.29 41.67 4.04
999 5281 3.488978 CCGCGACTCGACTCGACT 61.489 66.667 17.07 0.00 41.67 4.18
1223 5711 5.237236 TCTAGGTTTTAGTTCTGGTTGGG 57.763 43.478 0.00 0.00 0.00 4.12
1661 7285 5.415701 GGTTGATGTGTGATGTGGTTATCTT 59.584 40.000 0.00 0.00 0.00 2.40
1897 7557 7.145323 TGCAATTTTACTTTAGGAGTTTCAGC 58.855 34.615 0.00 0.00 39.86 4.26
2007 7676 2.389059 CTTGTCAGTGTCAGAGTGTCG 58.611 52.381 0.00 0.00 0.00 4.35
2173 7850 3.256704 ACCCAACCCTTCTGTCTGATTA 58.743 45.455 0.00 0.00 0.00 1.75
2398 8083 2.034687 TTCTGCCAGCTCAAGCCC 59.965 61.111 0.00 0.00 43.38 5.19
2608 8382 7.225523 GCATAATAAGTTGCCAAATGAGTTG 57.774 36.000 0.00 0.00 36.94 3.16
2814 8593 3.842925 TTTCTGGCCTGCGGGTGAC 62.843 63.158 14.55 4.74 34.45 3.67
2981 8760 8.485578 TTTTACCTAGGAACATGTTGGATTTT 57.514 30.769 17.58 0.00 0.00 1.82
3018 8818 4.058124 TCGTACTAATTCATGCTGATGCC 58.942 43.478 0.00 0.00 38.71 4.40
3654 10693 3.008517 TGCAAGGAGATCCCGGCA 61.009 61.111 10.13 10.13 44.14 5.69
3778 10821 5.448654 TGAAGAGGTGGATTATTGGATTGG 58.551 41.667 0.00 0.00 0.00 3.16
3779 10822 5.193527 TGAAGAGGTGGATTATTGGATTGGA 59.806 40.000 0.00 0.00 0.00 3.53
3780 10823 5.937492 AGAGGTGGATTATTGGATTGGAT 57.063 39.130 0.00 0.00 0.00 3.41
3781 10824 6.285329 AGAGGTGGATTATTGGATTGGATT 57.715 37.500 0.00 0.00 0.00 3.01
3782 10825 6.073314 AGAGGTGGATTATTGGATTGGATTG 58.927 40.000 0.00 0.00 0.00 2.67
3907 10956 8.931385 ACAATGCCTGTTATGTTAATCAATTC 57.069 30.769 0.00 0.00 32.99 2.17
3920 10969 7.589395 TGTTAATCAATTCATTGTGTAAGCGT 58.411 30.769 0.00 0.00 38.84 5.07
4073 11165 1.072331 ACGGTTGATTGGCAGAAGTCT 59.928 47.619 0.00 0.00 0.00 3.24
4090 11182 7.859875 GCAGAAGTCTATATCAAAATTGCCTTC 59.140 37.037 0.00 0.00 0.00 3.46
4111 11203 4.457466 TCAAACTACAAGGGAGTTGAACC 58.543 43.478 0.00 0.00 38.60 3.62
4492 11869 3.936902 TTTTGAACACAGTACAGACGC 57.063 42.857 0.00 0.00 0.00 5.19
4493 11870 2.588027 TTGAACACAGTACAGACGCA 57.412 45.000 0.00 0.00 0.00 5.24
4494 11871 2.588027 TGAACACAGTACAGACGCAA 57.412 45.000 0.00 0.00 0.00 4.85
4496 11873 1.192534 GAACACAGTACAGACGCAAGC 59.807 52.381 0.00 0.00 45.62 4.01
4497 11874 0.939577 ACACAGTACAGACGCAAGCG 60.940 55.000 13.50 13.50 46.03 4.68
4498 11875 2.022129 ACAGTACAGACGCAAGCGC 61.022 57.895 15.09 0.00 44.19 5.92
4499 11876 1.734477 CAGTACAGACGCAAGCGCT 60.734 57.895 15.09 2.64 44.19 5.92
4500 11877 1.444553 AGTACAGACGCAAGCGCTC 60.445 57.895 12.06 11.06 44.19 5.03
4501 11878 1.733041 GTACAGACGCAAGCGCTCA 60.733 57.895 12.06 0.83 44.19 4.26
4502 11879 1.078759 GTACAGACGCAAGCGCTCAT 61.079 55.000 12.06 0.00 44.19 2.90
4503 11880 0.454196 TACAGACGCAAGCGCTCATA 59.546 50.000 12.06 5.16 44.19 2.15
4504 11881 0.179100 ACAGACGCAAGCGCTCATAT 60.179 50.000 12.06 0.00 44.19 1.78
4505 11882 1.067060 ACAGACGCAAGCGCTCATATA 59.933 47.619 12.06 0.00 44.19 0.86
4506 11883 2.127251 CAGACGCAAGCGCTCATATAA 58.873 47.619 12.06 0.00 44.19 0.98
4507 11884 2.539688 CAGACGCAAGCGCTCATATAAA 59.460 45.455 12.06 0.00 44.19 1.40
4508 11885 2.540101 AGACGCAAGCGCTCATATAAAC 59.460 45.455 12.06 0.00 44.19 2.01
4509 11886 1.257936 ACGCAAGCGCTCATATAAACG 59.742 47.619 12.06 8.52 44.19 3.60
4516 11893 3.008456 CGCTCATATAAACGCGCATAC 57.992 47.619 5.73 0.00 39.11 2.39
4517 11894 2.407026 CGCTCATATAAACGCGCATACA 59.593 45.455 5.73 0.00 39.11 2.29
4518 11895 3.718036 CGCTCATATAAACGCGCATACAC 60.718 47.826 5.73 0.00 39.11 2.90
4519 11896 3.428870 GCTCATATAAACGCGCATACACT 59.571 43.478 5.73 0.00 0.00 3.55
4520 11897 4.433022 GCTCATATAAACGCGCATACACTC 60.433 45.833 5.73 0.00 0.00 3.51
4521 11898 4.612943 TCATATAAACGCGCATACACTCA 58.387 39.130 5.73 0.00 0.00 3.41
4522 11899 4.443063 TCATATAAACGCGCATACACTCAC 59.557 41.667 5.73 0.00 0.00 3.51
4523 11900 1.352114 TAAACGCGCATACACTCACC 58.648 50.000 5.73 0.00 0.00 4.02
4524 11901 1.296056 AAACGCGCATACACTCACCC 61.296 55.000 5.73 0.00 0.00 4.61
4525 11902 2.890474 CGCGCATACACTCACCCC 60.890 66.667 8.75 0.00 0.00 4.95
4526 11903 2.584608 GCGCATACACTCACCCCT 59.415 61.111 0.30 0.00 0.00 4.79
4527 11904 1.820581 GCGCATACACTCACCCCTA 59.179 57.895 0.30 0.00 0.00 3.53
4528 11905 0.393077 GCGCATACACTCACCCCTAT 59.607 55.000 0.30 0.00 0.00 2.57
4529 11906 1.873903 GCGCATACACTCACCCCTATG 60.874 57.143 0.30 0.00 0.00 2.23
4530 11907 1.686587 CGCATACACTCACCCCTATGA 59.313 52.381 0.00 0.00 0.00 2.15
4531 11908 2.102420 CGCATACACTCACCCCTATGAA 59.898 50.000 0.00 0.00 0.00 2.57
4532 11909 3.467803 GCATACACTCACCCCTATGAAC 58.532 50.000 0.00 0.00 0.00 3.18
4533 11910 3.717707 CATACACTCACCCCTATGAACG 58.282 50.000 0.00 0.00 0.00 3.95
4534 11911 0.249398 ACACTCACCCCTATGAACGC 59.751 55.000 0.00 0.00 0.00 4.84
4535 11912 0.249120 CACTCACCCCTATGAACGCA 59.751 55.000 0.00 0.00 0.00 5.24
4536 11913 0.249398 ACTCACCCCTATGAACGCAC 59.751 55.000 0.00 0.00 0.00 5.34
4537 11914 0.249120 CTCACCCCTATGAACGCACA 59.751 55.000 0.00 0.00 0.00 4.57
4538 11915 0.036765 TCACCCCTATGAACGCACAC 60.037 55.000 0.00 0.00 0.00 3.82
4539 11916 0.321210 CACCCCTATGAACGCACACA 60.321 55.000 0.00 0.00 0.00 3.72
4540 11917 0.321298 ACCCCTATGAACGCACACAC 60.321 55.000 0.00 0.00 0.00 3.82
4541 11918 1.358725 CCCCTATGAACGCACACACG 61.359 60.000 0.00 0.00 39.50 4.49
4542 11919 1.419922 CCTATGAACGCACACACGC 59.580 57.895 0.00 0.00 36.19 5.34
4543 11920 1.288419 CCTATGAACGCACACACGCA 61.288 55.000 0.00 0.00 36.19 5.24
4544 11921 0.179250 CTATGAACGCACACACGCAC 60.179 55.000 0.00 0.00 36.19 5.34
4545 11922 0.876342 TATGAACGCACACACGCACA 60.876 50.000 0.00 0.00 36.19 4.57
4546 11923 2.350760 GAACGCACACACGCACAC 60.351 61.111 0.00 0.00 36.19 3.82
4547 11924 3.783588 GAACGCACACACGCACACC 62.784 63.158 0.00 0.00 36.19 4.16
4550 11927 2.280524 GCACACACGCACACCCTA 60.281 61.111 0.00 0.00 0.00 3.53
4551 11928 2.604174 GCACACACGCACACCCTAC 61.604 63.158 0.00 0.00 0.00 3.18
4552 11929 1.959226 CACACACGCACACCCTACC 60.959 63.158 0.00 0.00 0.00 3.18
4553 11930 2.358247 CACACGCACACCCTACCC 60.358 66.667 0.00 0.00 0.00 3.69
4554 11931 3.633116 ACACGCACACCCTACCCC 61.633 66.667 0.00 0.00 0.00 4.95
4555 11932 3.319198 CACGCACACCCTACCCCT 61.319 66.667 0.00 0.00 0.00 4.79
4556 11933 1.985662 CACGCACACCCTACCCCTA 60.986 63.158 0.00 0.00 0.00 3.53
4557 11934 1.002533 ACGCACACCCTACCCCTAT 59.997 57.895 0.00 0.00 0.00 2.57
4558 11935 1.335132 ACGCACACCCTACCCCTATG 61.335 60.000 0.00 0.00 0.00 2.23
4559 11936 1.046472 CGCACACCCTACCCCTATGA 61.046 60.000 0.00 0.00 0.00 2.15
4560 11937 0.759346 GCACACCCTACCCCTATGAG 59.241 60.000 0.00 0.00 0.00 2.90
4561 11938 0.759346 CACACCCTACCCCTATGAGC 59.241 60.000 0.00 0.00 0.00 4.26
4562 11939 0.341961 ACACCCTACCCCTATGAGCA 59.658 55.000 0.00 0.00 0.00 4.26
4563 11940 0.759346 CACCCTACCCCTATGAGCAC 59.241 60.000 0.00 0.00 0.00 4.40
4564 11941 0.400093 ACCCTACCCCTATGAGCACC 60.400 60.000 0.00 0.00 0.00 5.01
4565 11942 0.104934 CCCTACCCCTATGAGCACCT 60.105 60.000 0.00 0.00 0.00 4.00
4566 11943 1.343069 CCTACCCCTATGAGCACCTC 58.657 60.000 0.00 0.00 0.00 3.85
4567 11944 1.343069 CTACCCCTATGAGCACCTCC 58.657 60.000 0.00 0.00 0.00 4.30
4568 11945 0.469331 TACCCCTATGAGCACCTCCG 60.469 60.000 0.00 0.00 0.00 4.63
4569 11946 1.457643 CCCCTATGAGCACCTCCGA 60.458 63.158 0.00 0.00 0.00 4.55
4570 11947 1.467678 CCCCTATGAGCACCTCCGAG 61.468 65.000 0.00 0.00 0.00 4.63
4571 11948 0.468214 CCCTATGAGCACCTCCGAGA 60.468 60.000 0.00 0.00 0.00 4.04
4572 11949 0.958091 CCTATGAGCACCTCCGAGAG 59.042 60.000 0.00 0.00 0.00 3.20
4573 11950 1.477740 CCTATGAGCACCTCCGAGAGA 60.478 57.143 0.00 0.00 0.00 3.10
4574 11951 1.606668 CTATGAGCACCTCCGAGAGAC 59.393 57.143 0.00 0.00 0.00 3.36
4575 11952 0.033601 ATGAGCACCTCCGAGAGACT 60.034 55.000 0.00 0.00 0.00 3.24
4576 11953 0.962855 TGAGCACCTCCGAGAGACTG 60.963 60.000 0.00 0.22 0.00 3.51
4577 11954 0.678366 GAGCACCTCCGAGAGACTGA 60.678 60.000 0.00 0.00 0.00 3.41
4578 11955 0.679640 AGCACCTCCGAGAGACTGAG 60.680 60.000 0.00 0.00 0.00 3.35
4579 11956 0.963355 GCACCTCCGAGAGACTGAGT 60.963 60.000 0.00 0.00 0.00 3.41
4580 11957 1.091537 CACCTCCGAGAGACTGAGTC 58.908 60.000 3.98 3.98 0.00 3.36
4581 11958 0.391927 ACCTCCGAGAGACTGAGTCG 60.392 60.000 6.99 0.00 37.67 4.18
4583 11960 2.795297 CCGAGAGACTGAGTCGGC 59.205 66.667 6.99 3.72 46.18 5.54
4584 11961 2.041115 CCGAGAGACTGAGTCGGCA 61.041 63.158 6.99 0.00 46.18 5.69
4585 11962 1.380403 CCGAGAGACTGAGTCGGCAT 61.380 60.000 6.99 0.00 46.18 4.40
4586 11963 1.300481 CGAGAGACTGAGTCGGCATA 58.700 55.000 6.99 0.00 37.67 3.14
4587 11964 1.876799 CGAGAGACTGAGTCGGCATAT 59.123 52.381 6.99 0.00 37.67 1.78
4588 11965 2.095969 CGAGAGACTGAGTCGGCATATC 60.096 54.545 6.99 0.00 37.67 1.63
4589 11966 2.881513 GAGAGACTGAGTCGGCATATCA 59.118 50.000 6.99 0.00 37.67 2.15
4590 11967 3.495331 AGAGACTGAGTCGGCATATCAT 58.505 45.455 6.99 0.00 37.67 2.45
4591 11968 3.505680 AGAGACTGAGTCGGCATATCATC 59.494 47.826 6.99 0.00 37.67 2.92
4592 11969 3.495331 AGACTGAGTCGGCATATCATCT 58.505 45.455 6.99 0.00 37.67 2.90
4593 11970 3.894427 AGACTGAGTCGGCATATCATCTT 59.106 43.478 6.99 0.00 37.67 2.40
4594 11971 3.986572 GACTGAGTCGGCATATCATCTTG 59.013 47.826 0.00 0.00 0.00 3.02
4595 11972 3.638627 ACTGAGTCGGCATATCATCTTGA 59.361 43.478 0.00 0.00 0.00 3.02
4596 11973 4.236147 CTGAGTCGGCATATCATCTTGAG 58.764 47.826 0.00 0.00 0.00 3.02
4597 11974 3.891366 TGAGTCGGCATATCATCTTGAGA 59.109 43.478 0.00 0.00 0.00 3.27
4598 11975 4.233789 GAGTCGGCATATCATCTTGAGAC 58.766 47.826 0.00 0.00 0.00 3.36
4599 11976 3.894427 AGTCGGCATATCATCTTGAGACT 59.106 43.478 0.00 0.00 31.84 3.24
4600 11977 4.343526 AGTCGGCATATCATCTTGAGACTT 59.656 41.667 0.00 0.00 32.36 3.01
4601 11978 5.053145 GTCGGCATATCATCTTGAGACTTT 58.947 41.667 0.00 0.00 0.00 2.66
4602 11979 6.040955 AGTCGGCATATCATCTTGAGACTTTA 59.959 38.462 0.00 0.00 32.36 1.85
4603 11980 6.144724 GTCGGCATATCATCTTGAGACTTTAC 59.855 42.308 0.00 0.00 0.00 2.01
4604 11981 5.117745 CGGCATATCATCTTGAGACTTTACG 59.882 44.000 0.00 0.00 0.00 3.18
4605 11982 6.216569 GGCATATCATCTTGAGACTTTACGA 58.783 40.000 0.00 0.00 0.00 3.43
4606 11983 6.701841 GGCATATCATCTTGAGACTTTACGAA 59.298 38.462 0.00 0.00 0.00 3.85
4607 11984 7.095857 GGCATATCATCTTGAGACTTTACGAAG 60.096 40.741 0.00 0.00 38.87 3.79
4628 12005 3.207669 CCGTAGGCGCCTCGTAGT 61.208 66.667 36.73 11.27 46.14 2.73
4629 12006 2.327244 CGTAGGCGCCTCGTAGTC 59.673 66.667 36.73 15.88 0.00 2.59
4630 12007 2.327244 GTAGGCGCCTCGTAGTCG 59.673 66.667 36.73 0.00 38.55 4.18
4631 12008 2.176273 GTAGGCGCCTCGTAGTCGA 61.176 63.158 36.73 10.36 44.12 4.20
4632 12009 2.176273 TAGGCGCCTCGTAGTCGAC 61.176 63.158 36.73 7.70 41.35 4.20
4651 12028 4.115270 GGAACGTCTCCTCCCACT 57.885 61.111 8.87 0.00 41.61 4.00
4652 12029 1.592223 GGAACGTCTCCTCCCACTG 59.408 63.158 8.87 0.00 41.61 3.66
4653 12030 0.898789 GGAACGTCTCCTCCCACTGA 60.899 60.000 8.87 0.00 41.61 3.41
4654 12031 0.966920 GAACGTCTCCTCCCACTGAA 59.033 55.000 0.00 0.00 0.00 3.02
4655 12032 1.343465 GAACGTCTCCTCCCACTGAAA 59.657 52.381 0.00 0.00 0.00 2.69
4656 12033 0.969894 ACGTCTCCTCCCACTGAAAG 59.030 55.000 0.00 0.00 42.29 2.62
4657 12034 0.390472 CGTCTCCTCCCACTGAAAGC 60.390 60.000 0.00 0.00 37.60 3.51
4658 12035 0.390472 GTCTCCTCCCACTGAAAGCG 60.390 60.000 0.00 0.00 37.60 4.68
4659 12036 0.832135 TCTCCTCCCACTGAAAGCGT 60.832 55.000 0.00 0.00 37.60 5.07
4660 12037 0.895530 CTCCTCCCACTGAAAGCGTA 59.104 55.000 0.00 0.00 37.60 4.42
4661 12038 1.482593 CTCCTCCCACTGAAAGCGTAT 59.517 52.381 0.00 0.00 37.60 3.06
4662 12039 1.480954 TCCTCCCACTGAAAGCGTATC 59.519 52.381 0.00 0.00 37.60 2.24
4663 12040 1.560923 CTCCCACTGAAAGCGTATCG 58.439 55.000 0.00 0.00 37.60 2.92
4676 12053 2.509052 CGTATCGCCAGAATTCCTGA 57.491 50.000 0.65 0.00 45.78 3.86
4677 12054 2.821546 CGTATCGCCAGAATTCCTGAA 58.178 47.619 0.65 0.00 45.78 3.02
4678 12055 3.194861 CGTATCGCCAGAATTCCTGAAA 58.805 45.455 0.65 0.00 45.78 2.69
4679 12056 3.809832 CGTATCGCCAGAATTCCTGAAAT 59.190 43.478 0.65 0.00 45.78 2.17
4680 12057 4.988540 CGTATCGCCAGAATTCCTGAAATA 59.011 41.667 0.65 0.00 45.78 1.40
4681 12058 5.465390 CGTATCGCCAGAATTCCTGAAATAA 59.535 40.000 0.65 0.00 45.78 1.40
4682 12059 6.018262 CGTATCGCCAGAATTCCTGAAATAAA 60.018 38.462 0.65 0.00 45.78 1.40
4683 12060 6.966534 ATCGCCAGAATTCCTGAAATAAAT 57.033 33.333 0.65 0.00 45.78 1.40
4684 12061 6.377327 TCGCCAGAATTCCTGAAATAAATC 57.623 37.500 0.65 0.00 45.78 2.17
4685 12062 5.299279 TCGCCAGAATTCCTGAAATAAATCC 59.701 40.000 0.65 0.00 45.78 3.01
4686 12063 5.067674 CGCCAGAATTCCTGAAATAAATCCA 59.932 40.000 0.65 0.00 45.78 3.41
4687 12064 6.510536 GCCAGAATTCCTGAAATAAATCCAG 58.489 40.000 0.65 0.00 45.78 3.86
4688 12065 6.462067 GCCAGAATTCCTGAAATAAATCCAGG 60.462 42.308 0.65 0.00 45.78 4.45
4698 12075 7.815840 TGAAATAAATCCAGGATAAATGCGA 57.184 32.000 1.02 0.00 0.00 5.10
4699 12076 7.874940 TGAAATAAATCCAGGATAAATGCGAG 58.125 34.615 1.02 0.00 0.00 5.03
4700 12077 5.886960 ATAAATCCAGGATAAATGCGAGC 57.113 39.130 1.02 0.00 0.00 5.03
4701 12078 2.936919 ATCCAGGATAAATGCGAGCA 57.063 45.000 0.00 0.00 0.00 4.26
4702 12079 1.953559 TCCAGGATAAATGCGAGCAC 58.046 50.000 0.00 0.00 0.00 4.40
4703 12080 0.947244 CCAGGATAAATGCGAGCACC 59.053 55.000 0.00 0.00 0.00 5.01
4704 12081 1.667236 CAGGATAAATGCGAGCACCA 58.333 50.000 0.00 0.00 0.00 4.17
4705 12082 1.331756 CAGGATAAATGCGAGCACCAC 59.668 52.381 0.00 0.00 0.00 4.16
4706 12083 0.663153 GGATAAATGCGAGCACCACC 59.337 55.000 0.00 0.00 0.00 4.61
4707 12084 1.668419 GATAAATGCGAGCACCACCT 58.332 50.000 0.00 0.00 0.00 4.00
4708 12085 2.484770 GGATAAATGCGAGCACCACCTA 60.485 50.000 0.00 0.00 0.00 3.08
4709 12086 2.772077 TAAATGCGAGCACCACCTAA 57.228 45.000 0.00 0.00 0.00 2.69
4710 12087 1.165270 AAATGCGAGCACCACCTAAC 58.835 50.000 0.00 0.00 0.00 2.34
4711 12088 0.676782 AATGCGAGCACCACCTAACC 60.677 55.000 0.00 0.00 0.00 2.85
4712 12089 1.836999 ATGCGAGCACCACCTAACCA 61.837 55.000 0.00 0.00 0.00 3.67
4713 12090 1.078426 GCGAGCACCACCTAACCAT 60.078 57.895 0.00 0.00 0.00 3.55
4714 12091 1.090052 GCGAGCACCACCTAACCATC 61.090 60.000 0.00 0.00 0.00 3.51
4715 12092 0.537188 CGAGCACCACCTAACCATCT 59.463 55.000 0.00 0.00 0.00 2.90
4716 12093 1.471676 CGAGCACCACCTAACCATCTC 60.472 57.143 0.00 0.00 0.00 2.75
4717 12094 1.555075 GAGCACCACCTAACCATCTCA 59.445 52.381 0.00 0.00 0.00 3.27
4718 12095 1.985159 AGCACCACCTAACCATCTCAA 59.015 47.619 0.00 0.00 0.00 3.02
4719 12096 2.084546 GCACCACCTAACCATCTCAAC 58.915 52.381 0.00 0.00 0.00 3.18
4720 12097 2.711542 CACCACCTAACCATCTCAACC 58.288 52.381 0.00 0.00 0.00 3.77
4721 12098 2.039746 CACCACCTAACCATCTCAACCA 59.960 50.000 0.00 0.00 0.00 3.67
4722 12099 2.305927 ACCACCTAACCATCTCAACCAG 59.694 50.000 0.00 0.00 0.00 4.00
4723 12100 2.571653 CCACCTAACCATCTCAACCAGA 59.428 50.000 0.00 0.00 34.78 3.86
4724 12101 3.369892 CCACCTAACCATCTCAACCAGAG 60.370 52.174 0.00 0.00 46.14 3.35
4725 12102 2.840651 ACCTAACCATCTCAACCAGAGG 59.159 50.000 0.00 0.00 44.81 3.69
4726 12103 2.840651 CCTAACCATCTCAACCAGAGGT 59.159 50.000 0.00 0.00 44.81 3.85
4881 12290 9.725019 TGAGGGTGATTAACTAGCAATATTATG 57.275 33.333 0.00 0.00 0.00 1.90
4917 12326 6.611381 TGTTTGCATGTTTCTTCTAGCATAC 58.389 36.000 0.00 0.00 35.49 2.39
4918 12327 6.430925 TGTTTGCATGTTTCTTCTAGCATACT 59.569 34.615 0.00 0.00 35.78 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.338769 GGCCATAGAACACCGTCACTT 60.339 52.381 0.00 0.00 0.00 3.16
14 15 1.216977 CGGCCATAGAACACCGTCA 59.783 57.895 2.24 0.00 40.77 4.35
100 101 2.105821 TGTTTCAAAGGTCCACCGAGAT 59.894 45.455 0.00 0.00 42.08 2.75
141 143 5.295950 CAGCTACTAGCATGCTGTTCTTAT 58.704 41.667 30.42 7.78 45.56 1.73
187 189 1.938585 TCCGTCCAATCTTCTGACCT 58.061 50.000 0.00 0.00 0.00 3.85
242 244 6.837312 ACCCGATGATAAACCAATTAGATCA 58.163 36.000 0.00 0.00 0.00 2.92
288 290 2.679092 CCAGCCTGAGGAATGCCA 59.321 61.111 0.65 0.00 36.29 4.92
303 305 3.628982 GACCCGAAACCCGACCCA 61.629 66.667 0.00 0.00 41.76 4.51
321 323 1.598130 GTCGTGCTTTGACAGGCCT 60.598 57.895 0.00 0.00 36.37 5.19
377 379 4.099881 TCGGGCCTACATATACGTTTTCTT 59.900 41.667 0.84 0.00 0.00 2.52
474 476 2.056223 GGTCGGGATCGAACCTGGA 61.056 63.158 19.45 10.68 46.56 3.86
481 525 1.315690 GTATGTCAGGTCGGGATCGA 58.684 55.000 0.00 0.00 43.86 3.59
485 529 1.252215 TTGCGTATGTCAGGTCGGGA 61.252 55.000 0.00 0.00 0.00 5.14
490 534 3.532896 CCTGTTGCGTATGTCAGGT 57.467 52.632 10.17 0.00 41.51 4.00
524 610 2.041922 TATGTCAGGCCGGGCTCT 60.042 61.111 30.43 15.33 0.00 4.09
547 633 4.565652 GCTCAGACCTAGAAATTTGACCCA 60.566 45.833 0.00 0.00 0.00 4.51
564 650 0.691078 AAATCTAGGCCGGGCTCAGA 60.691 55.000 36.44 30.54 0.00 3.27
663 797 2.566913 TGCGAAAGTCCACTTTGCTTA 58.433 42.857 9.45 0.00 45.37 3.09
711 4057 4.555348 TGTAGGAAACGCGAAAAACAAT 57.445 36.364 15.93 0.00 0.00 2.71
790 5051 5.220710 TCCTCCTCTTTCTTCTTTCTGTG 57.779 43.478 0.00 0.00 0.00 3.66
791 5052 5.744594 GCTTCCTCCTCTTTCTTCTTTCTGT 60.745 44.000 0.00 0.00 0.00 3.41
792 5053 4.694982 GCTTCCTCCTCTTTCTTCTTTCTG 59.305 45.833 0.00 0.00 0.00 3.02
793 5054 4.263287 GGCTTCCTCCTCTTTCTTCTTTCT 60.263 45.833 0.00 0.00 0.00 2.52
794 5055 4.006989 GGCTTCCTCCTCTTTCTTCTTTC 58.993 47.826 0.00 0.00 0.00 2.62
795 5056 3.558109 CGGCTTCCTCCTCTTTCTTCTTT 60.558 47.826 0.00 0.00 0.00 2.52
796 5057 2.027653 CGGCTTCCTCCTCTTTCTTCTT 60.028 50.000 0.00 0.00 0.00 2.52
798 5059 1.550976 TCGGCTTCCTCCTCTTTCTTC 59.449 52.381 0.00 0.00 0.00 2.87
799 5060 1.552792 CTCGGCTTCCTCCTCTTTCTT 59.447 52.381 0.00 0.00 0.00 2.52
831 5092 5.682659 TGTGTACTGTATACTCCTCCTCTC 58.317 45.833 14.49 0.00 0.00 3.20
844 5115 0.454600 GCTAGCGGCTGTGTACTGTA 59.545 55.000 13.86 0.00 38.06 2.74
845 5116 1.215647 GCTAGCGGCTGTGTACTGT 59.784 57.895 13.86 0.00 38.06 3.55
846 5117 4.094684 GCTAGCGGCTGTGTACTG 57.905 61.111 13.86 0.00 38.06 2.74
950 5224 0.827368 GCTGAACGGGATCTCTCCTT 59.173 55.000 0.00 0.00 41.74 3.36
1179 5501 0.247736 AGATGCGAGCTTTCCGAACT 59.752 50.000 0.00 0.00 0.00 3.01
1580 7204 2.932614 CCTCACCGACACAATCTTCATC 59.067 50.000 0.00 0.00 0.00 2.92
1661 7285 2.277969 TCAGACGGCGTTACAAAAACA 58.722 42.857 16.19 0.00 0.00 2.83
1950 7610 9.074443 GTCAGTTTTAACTCCTAAGATAGAACG 57.926 37.037 0.00 0.00 37.08 3.95
2007 7676 6.453926 AAAGAGACCCGTTATTCTAGAGTC 57.546 41.667 0.00 0.00 0.00 3.36
2013 7682 4.928020 GTCGAAAAAGAGACCCGTTATTCT 59.072 41.667 0.00 0.00 0.00 2.40
2173 7850 3.926058 AAACAGGGCATAGGTTACGAT 57.074 42.857 0.00 0.00 0.00 3.73
2398 8083 7.226720 GGAACTAACCATGTGTCCATGTAATAG 59.773 40.741 2.38 4.37 45.83 1.73
2559 8250 9.660180 GCCCAAAGAAAACCAATAATTTATACA 57.340 29.630 0.00 0.00 0.00 2.29
2814 8593 2.042741 TGGCAAGGGCATCATGGG 60.043 61.111 0.00 0.00 43.71 4.00
3024 8824 2.674852 CGATGATGGAGGAATTATGCCG 59.325 50.000 0.00 0.00 0.00 5.69
3737 10780 4.043310 TCTTCATGGGAAACTCAGTCCAAT 59.957 41.667 0.00 0.00 36.83 3.16
3778 10821 2.109126 GCCGAGTCACAGGGCAATC 61.109 63.158 4.34 0.00 46.13 2.67
3779 10822 2.045926 GCCGAGTCACAGGGCAAT 60.046 61.111 4.34 0.00 46.13 3.56
3907 10956 4.451096 AGTTGGACTTACGCTTACACAATG 59.549 41.667 0.00 0.00 0.00 2.82
3920 10969 0.764890 AGCACAGGCAGTTGGACTTA 59.235 50.000 0.00 0.00 44.61 2.24
3971 11040 2.432628 CCGTCGACCTTGCCTGTC 60.433 66.667 10.58 0.00 0.00 3.51
4090 11182 4.204012 TGGTTCAACTCCCTTGTAGTTTG 58.796 43.478 0.00 0.00 34.99 2.93
4471 11848 3.685272 TGCGTCTGTACTGTGTTCAAAAA 59.315 39.130 0.00 0.00 0.00 1.94
4473 11850 2.894902 TGCGTCTGTACTGTGTTCAAA 58.105 42.857 0.00 0.00 0.00 2.69
4475 11852 2.469826 CTTGCGTCTGTACTGTGTTCA 58.530 47.619 0.00 0.00 0.00 3.18
4476 11853 1.192534 GCTTGCGTCTGTACTGTGTTC 59.807 52.381 0.00 0.00 0.00 3.18
4477 11854 1.217882 GCTTGCGTCTGTACTGTGTT 58.782 50.000 0.00 0.00 0.00 3.32
4478 11855 0.939577 CGCTTGCGTCTGTACTGTGT 60.940 55.000 6.86 0.00 0.00 3.72
4479 11856 1.775344 CGCTTGCGTCTGTACTGTG 59.225 57.895 6.86 0.00 0.00 3.66
4480 11857 2.022129 GCGCTTGCGTCTGTACTGT 61.022 57.895 16.38 0.00 0.00 3.55
4481 11858 1.678269 GAGCGCTTGCGTCTGTACTG 61.678 60.000 13.26 0.00 45.69 2.74
4482 11859 1.444553 GAGCGCTTGCGTCTGTACT 60.445 57.895 13.26 3.73 45.69 2.73
4483 11860 1.078759 ATGAGCGCTTGCGTCTGTAC 61.079 55.000 13.26 0.00 45.69 2.90
4484 11861 0.454196 TATGAGCGCTTGCGTCTGTA 59.546 50.000 13.26 6.26 45.69 2.74
4485 11862 0.179100 ATATGAGCGCTTGCGTCTGT 60.179 50.000 13.26 7.66 45.69 3.41
4486 11863 1.770957 TATATGAGCGCTTGCGTCTG 58.229 50.000 13.26 0.00 45.69 3.51
4487 11864 2.509052 TTATATGAGCGCTTGCGTCT 57.491 45.000 13.26 13.17 45.69 4.18
4488 11865 2.656632 CGTTTATATGAGCGCTTGCGTC 60.657 50.000 13.26 12.36 45.69 5.19
4489 11866 1.257936 CGTTTATATGAGCGCTTGCGT 59.742 47.619 13.26 3.24 45.69 5.24
4490 11867 1.924408 CGTTTATATGAGCGCTTGCG 58.076 50.000 13.26 10.90 45.69 4.85
4491 11868 1.663494 GCGTTTATATGAGCGCTTGC 58.337 50.000 19.08 0.00 45.48 4.01
4492 11869 1.924408 CGCGTTTATATGAGCGCTTG 58.076 50.000 22.51 7.90 46.56 4.01
4497 11874 3.428870 AGTGTATGCGCGTTTATATGAGC 59.571 43.478 7.78 0.00 36.72 4.26
4498 11875 4.679654 TGAGTGTATGCGCGTTTATATGAG 59.320 41.667 7.78 0.00 0.00 2.90
4499 11876 4.443063 GTGAGTGTATGCGCGTTTATATGA 59.557 41.667 7.78 0.00 0.00 2.15
4500 11877 4.376008 GGTGAGTGTATGCGCGTTTATATG 60.376 45.833 7.78 0.00 0.00 1.78
4501 11878 3.739300 GGTGAGTGTATGCGCGTTTATAT 59.261 43.478 7.78 0.00 0.00 0.86
4502 11879 3.117794 GGTGAGTGTATGCGCGTTTATA 58.882 45.455 7.78 1.67 0.00 0.98
4503 11880 1.931172 GGTGAGTGTATGCGCGTTTAT 59.069 47.619 7.78 2.74 0.00 1.40
4504 11881 1.352114 GGTGAGTGTATGCGCGTTTA 58.648 50.000 7.78 0.00 0.00 2.01
4505 11882 1.296056 GGGTGAGTGTATGCGCGTTT 61.296 55.000 7.78 0.00 0.00 3.60
4506 11883 1.740296 GGGTGAGTGTATGCGCGTT 60.740 57.895 7.78 0.00 0.00 4.84
4507 11884 2.125673 GGGTGAGTGTATGCGCGT 60.126 61.111 8.43 7.55 0.00 6.01
4508 11885 2.011741 TAGGGGTGAGTGTATGCGCG 62.012 60.000 0.00 0.00 0.00 6.86
4509 11886 0.393077 ATAGGGGTGAGTGTATGCGC 59.607 55.000 0.00 0.00 0.00 6.09
4510 11887 1.686587 TCATAGGGGTGAGTGTATGCG 59.313 52.381 0.00 0.00 0.00 4.73
4511 11888 3.467803 GTTCATAGGGGTGAGTGTATGC 58.532 50.000 0.00 0.00 0.00 3.14
4512 11889 3.717707 CGTTCATAGGGGTGAGTGTATG 58.282 50.000 0.00 0.00 0.00 2.39
4513 11890 2.102588 GCGTTCATAGGGGTGAGTGTAT 59.897 50.000 0.00 0.00 0.00 2.29
4514 11891 1.479323 GCGTTCATAGGGGTGAGTGTA 59.521 52.381 0.00 0.00 0.00 2.90
4515 11892 0.249398 GCGTTCATAGGGGTGAGTGT 59.751 55.000 0.00 0.00 0.00 3.55
4516 11893 0.249120 TGCGTTCATAGGGGTGAGTG 59.751 55.000 0.00 0.00 0.00 3.51
4517 11894 0.249398 GTGCGTTCATAGGGGTGAGT 59.751 55.000 0.00 0.00 0.00 3.41
4518 11895 0.249120 TGTGCGTTCATAGGGGTGAG 59.751 55.000 0.00 0.00 0.00 3.51
4519 11896 0.036765 GTGTGCGTTCATAGGGGTGA 60.037 55.000 0.00 0.00 0.00 4.02
4520 11897 0.321210 TGTGTGCGTTCATAGGGGTG 60.321 55.000 0.00 0.00 0.00 4.61
4521 11898 0.321298 GTGTGTGCGTTCATAGGGGT 60.321 55.000 0.00 0.00 0.00 4.95
4522 11899 1.358725 CGTGTGTGCGTTCATAGGGG 61.359 60.000 0.00 0.00 0.00 4.79
4523 11900 1.966493 GCGTGTGTGCGTTCATAGGG 61.966 60.000 0.00 0.00 0.00 3.53
4524 11901 1.288419 TGCGTGTGTGCGTTCATAGG 61.288 55.000 0.00 0.00 37.81 2.57
4525 11902 0.179250 GTGCGTGTGTGCGTTCATAG 60.179 55.000 0.00 0.00 37.81 2.23
4526 11903 0.876342 TGTGCGTGTGTGCGTTCATA 60.876 50.000 0.00 0.00 37.81 2.15
4527 11904 2.176926 TGTGCGTGTGTGCGTTCAT 61.177 52.632 0.00 0.00 37.81 2.57
4528 11905 2.815647 TGTGCGTGTGTGCGTTCA 60.816 55.556 0.00 0.00 37.81 3.18
4529 11906 2.350760 GTGTGCGTGTGTGCGTTC 60.351 61.111 0.00 0.00 37.81 3.95
4530 11907 3.871574 GGTGTGCGTGTGTGCGTT 61.872 61.111 0.00 0.00 37.81 4.84
4533 11910 2.280524 TAGGGTGTGCGTGTGTGC 60.281 61.111 0.00 0.00 0.00 4.57
4534 11911 1.959226 GGTAGGGTGTGCGTGTGTG 60.959 63.158 0.00 0.00 0.00 3.82
4535 11912 2.424302 GGTAGGGTGTGCGTGTGT 59.576 61.111 0.00 0.00 0.00 3.72
4536 11913 2.358247 GGGTAGGGTGTGCGTGTG 60.358 66.667 0.00 0.00 0.00 3.82
4537 11914 2.735151 TAGGGGTAGGGTGTGCGTGT 62.735 60.000 0.00 0.00 0.00 4.49
4538 11915 1.335132 ATAGGGGTAGGGTGTGCGTG 61.335 60.000 0.00 0.00 0.00 5.34
4539 11916 1.002533 ATAGGGGTAGGGTGTGCGT 59.997 57.895 0.00 0.00 0.00 5.24
4540 11917 1.046472 TCATAGGGGTAGGGTGTGCG 61.046 60.000 0.00 0.00 0.00 5.34
4541 11918 0.759346 CTCATAGGGGTAGGGTGTGC 59.241 60.000 0.00 0.00 0.00 4.57
4542 11919 0.759346 GCTCATAGGGGTAGGGTGTG 59.241 60.000 0.00 0.00 0.00 3.82
4543 11920 0.341961 TGCTCATAGGGGTAGGGTGT 59.658 55.000 0.00 0.00 0.00 4.16
4544 11921 0.759346 GTGCTCATAGGGGTAGGGTG 59.241 60.000 0.00 0.00 0.00 4.61
4545 11922 0.400093 GGTGCTCATAGGGGTAGGGT 60.400 60.000 0.00 0.00 0.00 4.34
4546 11923 0.104934 AGGTGCTCATAGGGGTAGGG 60.105 60.000 0.00 0.00 0.00 3.53
4547 11924 1.343069 GAGGTGCTCATAGGGGTAGG 58.657 60.000 0.00 0.00 0.00 3.18
4548 11925 1.343069 GGAGGTGCTCATAGGGGTAG 58.657 60.000 0.00 0.00 31.08 3.18
4549 11926 0.469331 CGGAGGTGCTCATAGGGGTA 60.469 60.000 0.00 0.00 31.08 3.69
4550 11927 1.762460 CGGAGGTGCTCATAGGGGT 60.762 63.158 0.00 0.00 31.08 4.95
4551 11928 1.457643 TCGGAGGTGCTCATAGGGG 60.458 63.158 0.00 0.00 31.08 4.79
4552 11929 0.468214 TCTCGGAGGTGCTCATAGGG 60.468 60.000 4.96 0.00 31.08 3.53
4553 11930 0.958091 CTCTCGGAGGTGCTCATAGG 59.042 60.000 4.96 0.00 31.08 2.57
4554 11931 1.606668 GTCTCTCGGAGGTGCTCATAG 59.393 57.143 4.96 0.00 31.08 2.23
4555 11932 1.213182 AGTCTCTCGGAGGTGCTCATA 59.787 52.381 4.96 0.00 31.08 2.15
4556 11933 0.033601 AGTCTCTCGGAGGTGCTCAT 60.034 55.000 4.96 0.00 31.08 2.90
4557 11934 0.962855 CAGTCTCTCGGAGGTGCTCA 60.963 60.000 4.96 0.00 31.08 4.26
4558 11935 0.678366 TCAGTCTCTCGGAGGTGCTC 60.678 60.000 4.96 0.00 0.00 4.26
4559 11936 0.679640 CTCAGTCTCTCGGAGGTGCT 60.680 60.000 4.96 0.00 35.32 4.40
4560 11937 0.963355 ACTCAGTCTCTCGGAGGTGC 60.963 60.000 4.96 0.00 41.46 5.01
4561 11938 1.091537 GACTCAGTCTCTCGGAGGTG 58.908 60.000 4.96 0.00 41.46 4.00
4562 11939 0.391927 CGACTCAGTCTCTCGGAGGT 60.392 60.000 2.61 0.00 41.46 3.85
4563 11940 2.389386 CGACTCAGTCTCTCGGAGG 58.611 63.158 2.61 0.00 41.46 4.30
4567 11944 1.300481 TATGCCGACTCAGTCTCTCG 58.700 55.000 2.61 0.00 0.00 4.04
4568 11945 2.881513 TGATATGCCGACTCAGTCTCTC 59.118 50.000 2.61 0.00 0.00 3.20
4569 11946 2.937519 TGATATGCCGACTCAGTCTCT 58.062 47.619 2.61 0.00 0.00 3.10
4570 11947 3.505680 AGATGATATGCCGACTCAGTCTC 59.494 47.826 2.61 0.00 0.00 3.36
4571 11948 3.495331 AGATGATATGCCGACTCAGTCT 58.505 45.455 2.61 0.00 0.00 3.24
4572 11949 3.932545 AGATGATATGCCGACTCAGTC 57.067 47.619 0.00 0.00 0.00 3.51
4573 11950 3.638627 TCAAGATGATATGCCGACTCAGT 59.361 43.478 0.00 0.00 0.00 3.41
4574 11951 4.022503 TCTCAAGATGATATGCCGACTCAG 60.023 45.833 0.00 0.00 0.00 3.35
4575 11952 3.891366 TCTCAAGATGATATGCCGACTCA 59.109 43.478 0.00 0.00 0.00 3.41
4576 11953 4.022416 AGTCTCAAGATGATATGCCGACTC 60.022 45.833 0.00 0.00 0.00 3.36
4577 11954 3.894427 AGTCTCAAGATGATATGCCGACT 59.106 43.478 0.00 0.00 0.00 4.18
4578 11955 4.250116 AGTCTCAAGATGATATGCCGAC 57.750 45.455 0.00 0.00 0.00 4.79
4579 11956 4.944619 AAGTCTCAAGATGATATGCCGA 57.055 40.909 0.00 0.00 0.00 5.54
4580 11957 5.117745 CGTAAAGTCTCAAGATGATATGCCG 59.882 44.000 0.00 0.00 0.00 5.69
4581 11958 6.216569 TCGTAAAGTCTCAAGATGATATGCC 58.783 40.000 0.00 0.00 0.00 4.40
4582 11959 7.436673 ACTTCGTAAAGTCTCAAGATGATATGC 59.563 37.037 0.00 0.00 42.10 3.14
4583 11960 8.864069 ACTTCGTAAAGTCTCAAGATGATATG 57.136 34.615 0.00 0.00 42.10 1.78
4597 11974 5.742791 CGCCTACGGTGACTTCGTAAAGT 62.743 52.174 0.00 0.00 41.62 2.66
4598 11975 2.257034 GCCTACGGTGACTTCGTAAAG 58.743 52.381 0.00 0.00 41.62 1.85
4599 11976 1.401409 CGCCTACGGTGACTTCGTAAA 60.401 52.381 0.00 0.00 41.62 2.01
4600 11977 0.168788 CGCCTACGGTGACTTCGTAA 59.831 55.000 0.00 0.00 41.62 3.18
4601 11978 1.796151 CGCCTACGGTGACTTCGTA 59.204 57.895 0.00 0.00 41.38 3.43
4602 11979 2.564975 CGCCTACGGTGACTTCGT 59.435 61.111 0.00 0.00 43.64 3.85
4603 11980 2.879462 GCGCCTACGGTGACTTCG 60.879 66.667 0.00 0.00 40.57 3.79
4604 11981 2.508663 GGCGCCTACGGTGACTTC 60.509 66.667 22.15 0.00 38.38 3.01
4607 11984 4.849329 CGAGGCGCCTACGGTGAC 62.849 72.222 32.97 14.51 42.50 3.67
4608 11985 3.974835 TACGAGGCGCCTACGGTGA 62.975 63.158 34.97 23.77 40.57 4.02
4609 11986 3.465296 CTACGAGGCGCCTACGGTG 62.465 68.421 34.97 26.78 40.57 4.94
4610 11987 3.207669 CTACGAGGCGCCTACGGT 61.208 66.667 34.97 30.33 40.57 4.83
4611 11988 3.178569 GACTACGAGGCGCCTACGG 62.179 68.421 34.97 27.37 40.57 4.02
4612 11989 2.327244 GACTACGAGGCGCCTACG 59.673 66.667 32.97 32.67 44.07 3.51
4613 11990 2.327244 CGACTACGAGGCGCCTAC 59.673 66.667 32.97 21.51 41.27 3.18
4623 12000 2.863153 ACGTTCCCGTCGACTACG 59.137 61.111 14.70 18.15 46.28 3.51
4635 12012 0.966920 TTCAGTGGGAGGAGACGTTC 59.033 55.000 0.00 0.00 0.00 3.95
4636 12013 1.344763 CTTTCAGTGGGAGGAGACGTT 59.655 52.381 0.00 0.00 0.00 3.99
4637 12014 0.969894 CTTTCAGTGGGAGGAGACGT 59.030 55.000 0.00 0.00 0.00 4.34
4638 12015 0.390472 GCTTTCAGTGGGAGGAGACG 60.390 60.000 0.00 0.00 0.00 4.18
4639 12016 0.390472 CGCTTTCAGTGGGAGGAGAC 60.390 60.000 0.00 0.00 0.00 3.36
4640 12017 0.832135 ACGCTTTCAGTGGGAGGAGA 60.832 55.000 0.00 0.00 0.00 3.71
4641 12018 0.895530 TACGCTTTCAGTGGGAGGAG 59.104 55.000 0.00 0.00 0.00 3.69
4642 12019 1.480954 GATACGCTTTCAGTGGGAGGA 59.519 52.381 0.00 0.00 0.00 3.71
4643 12020 1.802880 CGATACGCTTTCAGTGGGAGG 60.803 57.143 0.00 0.00 0.00 4.30
4644 12021 1.560923 CGATACGCTTTCAGTGGGAG 58.439 55.000 0.00 0.00 0.00 4.30
4645 12022 3.733236 CGATACGCTTTCAGTGGGA 57.267 52.632 0.00 0.00 0.00 4.37
4657 12034 2.509052 TCAGGAATTCTGGCGATACG 57.491 50.000 5.23 0.00 43.53 3.06
4658 12035 6.861065 TTATTTCAGGAATTCTGGCGATAC 57.139 37.500 5.23 0.00 43.53 2.24
4659 12036 7.174946 GGATTTATTTCAGGAATTCTGGCGATA 59.825 37.037 5.23 0.00 43.53 2.92
4660 12037 6.015940 GGATTTATTTCAGGAATTCTGGCGAT 60.016 38.462 5.23 0.00 43.53 4.58
4661 12038 5.299279 GGATTTATTTCAGGAATTCTGGCGA 59.701 40.000 5.23 0.00 43.53 5.54
4662 12039 5.067674 TGGATTTATTTCAGGAATTCTGGCG 59.932 40.000 5.23 0.00 43.53 5.69
4663 12040 6.469782 TGGATTTATTTCAGGAATTCTGGC 57.530 37.500 5.23 0.00 43.53 4.85
4672 12049 7.040478 TCGCATTTATCCTGGATTTATTTCAGG 60.040 37.037 15.55 0.00 46.91 3.86
4673 12050 7.874940 TCGCATTTATCCTGGATTTATTTCAG 58.125 34.615 15.55 1.04 0.00 3.02
4674 12051 7.522073 GCTCGCATTTATCCTGGATTTATTTCA 60.522 37.037 15.55 0.00 0.00 2.69
4675 12052 6.803807 GCTCGCATTTATCCTGGATTTATTTC 59.196 38.462 15.55 0.09 0.00 2.17
4676 12053 6.265196 TGCTCGCATTTATCCTGGATTTATTT 59.735 34.615 15.55 0.00 0.00 1.40
4677 12054 5.769662 TGCTCGCATTTATCCTGGATTTATT 59.230 36.000 15.55 0.00 0.00 1.40
4678 12055 5.182001 GTGCTCGCATTTATCCTGGATTTAT 59.818 40.000 15.55 5.99 0.00 1.40
4679 12056 4.515191 GTGCTCGCATTTATCCTGGATTTA 59.485 41.667 15.55 3.70 0.00 1.40
4680 12057 3.316308 GTGCTCGCATTTATCCTGGATTT 59.684 43.478 15.55 0.00 0.00 2.17
4681 12058 2.880890 GTGCTCGCATTTATCCTGGATT 59.119 45.455 15.55 0.00 0.00 3.01
4682 12059 2.498167 GTGCTCGCATTTATCCTGGAT 58.502 47.619 14.66 14.66 0.00 3.41
4683 12060 1.475034 GGTGCTCGCATTTATCCTGGA 60.475 52.381 0.00 0.00 0.00 3.86
4684 12061 0.947244 GGTGCTCGCATTTATCCTGG 59.053 55.000 0.00 0.00 0.00 4.45
4685 12062 1.331756 GTGGTGCTCGCATTTATCCTG 59.668 52.381 0.00 0.00 0.00 3.86
4686 12063 1.668419 GTGGTGCTCGCATTTATCCT 58.332 50.000 0.00 0.00 0.00 3.24
4687 12064 0.663153 GGTGGTGCTCGCATTTATCC 59.337 55.000 0.00 0.00 0.00 2.59
4688 12065 1.668419 AGGTGGTGCTCGCATTTATC 58.332 50.000 0.00 0.00 0.00 1.75
4689 12066 2.943033 GTTAGGTGGTGCTCGCATTTAT 59.057 45.455 0.00 0.00 0.00 1.40
4690 12067 2.352388 GTTAGGTGGTGCTCGCATTTA 58.648 47.619 0.00 0.00 0.00 1.40
4691 12068 1.165270 GTTAGGTGGTGCTCGCATTT 58.835 50.000 0.00 0.00 0.00 2.32
4692 12069 0.676782 GGTTAGGTGGTGCTCGCATT 60.677 55.000 0.00 0.00 0.00 3.56
4693 12070 1.078426 GGTTAGGTGGTGCTCGCAT 60.078 57.895 0.00 0.00 0.00 4.73
4694 12071 1.836999 ATGGTTAGGTGGTGCTCGCA 61.837 55.000 0.00 0.00 0.00 5.10
4695 12072 1.078426 ATGGTTAGGTGGTGCTCGC 60.078 57.895 0.00 0.00 0.00 5.03
4696 12073 0.537188 AGATGGTTAGGTGGTGCTCG 59.463 55.000 0.00 0.00 0.00 5.03
4697 12074 1.555075 TGAGATGGTTAGGTGGTGCTC 59.445 52.381 0.00 0.00 0.00 4.26
4698 12075 1.656587 TGAGATGGTTAGGTGGTGCT 58.343 50.000 0.00 0.00 0.00 4.40
4699 12076 2.084546 GTTGAGATGGTTAGGTGGTGC 58.915 52.381 0.00 0.00 0.00 5.01
4700 12077 2.039746 TGGTTGAGATGGTTAGGTGGTG 59.960 50.000 0.00 0.00 0.00 4.17
4701 12078 2.305927 CTGGTTGAGATGGTTAGGTGGT 59.694 50.000 0.00 0.00 0.00 4.16
4702 12079 2.571653 TCTGGTTGAGATGGTTAGGTGG 59.428 50.000 0.00 0.00 0.00 4.61
4703 12080 3.369892 CCTCTGGTTGAGATGGTTAGGTG 60.370 52.174 0.00 0.00 45.39 4.00
4704 12081 2.840651 CCTCTGGTTGAGATGGTTAGGT 59.159 50.000 0.00 0.00 45.39 3.08
4705 12082 2.840651 ACCTCTGGTTGAGATGGTTAGG 59.159 50.000 0.00 0.00 45.39 2.69
4706 12083 4.559862 AACCTCTGGTTGAGATGGTTAG 57.440 45.455 0.71 0.00 45.07 2.34
4754 12131 2.496070 TGTCGATCTTACACCTCCTTGG 59.504 50.000 0.00 0.00 42.93 3.61
4771 12148 4.714632 ACATTTGGTATAATCCCCTGTCG 58.285 43.478 0.00 0.00 0.00 4.35
4845 12254 5.652452 AGTTAATCACCCTCAAGTTATTGCC 59.348 40.000 0.00 0.00 36.30 4.52
4881 12290 2.747396 TGCAAACAGGGCAAATGATC 57.253 45.000 0.00 0.00 38.54 2.92


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

AutoCloner maintained by Alex Coulton.