Multiple sequence alignment - TraesCS6D01G168500

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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 TraesCS6D01G168500 chr6D 100.000 4762 0 0 1 4762 153854275 153859036 0.000000e+00 8794.0
1 TraesCS6D01G168500 chr6D 88.679 636 34 17 1451 2067 135463539 135462923 0.000000e+00 741.0
2 TraesCS6D01G168500 chr6A 97.361 2766 62 5 1689 4444 206345131 206347895 0.000000e+00 4693.0
3 TraesCS6D01G168500 chr6A 92.672 1119 54 9 561 1665 206344049 206345153 0.000000e+00 1587.0
4 TraesCS6D01G168500 chr6A 87.734 587 35 8 2 557 206343248 206343828 0.000000e+00 651.0
5 TraesCS6D01G168500 chr6A 96.581 117 4 0 4646 4762 206347893 206348009 1.350000e-45 195.0
6 TraesCS6D01G168500 chr1D 89.982 1637 132 7 2203 3838 10549718 10548113 0.000000e+00 2085.0
7 TraesCS6D01G168500 chr1D 90.955 995 77 8 2141 3128 10457995 10457007 0.000000e+00 1327.0
8 TraesCS6D01G168500 chr1D 88.836 636 33 16 1451 2067 254397206 254396590 0.000000e+00 747.0
9 TraesCS6D01G168500 chr1D 88.832 197 16 3 4565 4757 10456612 10456418 2.220000e-58 237.0
10 TraesCS6D01G168500 chr1D 82.772 267 34 6 3913 4174 10542307 10542048 1.330000e-55 228.0
11 TraesCS6D01G168500 chr1A 90.054 1297 104 6 2203 3499 12186279 12185008 0.000000e+00 1657.0
12 TraesCS6D01G168500 chr1A 89.308 636 30 17 1451 2067 554513152 554513768 0.000000e+00 763.0
13 TraesCS6D01G168500 chr1A 88.554 332 29 1 3545 3876 12185007 12184685 1.240000e-105 394.0
14 TraesCS6D01G168500 chr1A 87.543 289 26 8 3913 4194 12184675 12184390 4.600000e-85 326.0
15 TraesCS6D01G168500 chr1A 86.294 197 11 8 4565 4757 12184390 12184206 2.910000e-47 200.0
16 TraesCS6D01G168500 chr5D 89.623 636 28 13 1451 2067 446174688 446175304 0.000000e+00 774.0
17 TraesCS6D01G168500 chr5D 88.679 636 34 17 1451 2067 503277322 503276706 0.000000e+00 741.0
18 TraesCS6D01G168500 chr4D 89.465 636 29 12 1451 2067 30387094 30386478 0.000000e+00 769.0
19 TraesCS6D01G168500 chr3B 89.465 636 29 12 1451 2067 101912079 101912695 0.000000e+00 769.0
20 TraesCS6D01G168500 chr3B 87.479 591 46 15 2993 3578 27506509 27505942 0.000000e+00 656.0
21 TraesCS6D01G168500 chr4A 89.151 636 31 12 1451 2067 73811375 73811991 0.000000e+00 758.0
22 TraesCS6D01G168500 chr4A 87.366 372 36 4 3004 3373 353083687 353083325 2.650000e-112 416.0
23 TraesCS6D01G168500 chr4A 93.434 198 11 1 1451 1648 73809832 73810027 4.660000e-75 292.0
24 TraesCS6D01G168500 chr3D 88.994 636 32 12 1451 2067 589278641 589278025 0.000000e+00 752.0
25 TraesCS6D01G168500 chr3A 88.994 636 32 12 1451 2067 594898720 594898104 0.000000e+00 752.0
26 TraesCS6D01G168500 chrUn 89.137 626 30 18 1451 2057 93408728 93408122 0.000000e+00 745.0
27 TraesCS6D01G168500 chrUn 88.679 636 34 17 1451 2067 346595590 346594974 0.000000e+00 741.0
28 TraesCS6D01G168500 chrUn 88.522 636 35 17 1451 2067 216517699 216517083 0.000000e+00 736.0
29 TraesCS6D01G168500 chrUn 89.203 602 26 14 1485 2067 444245493 444244912 0.000000e+00 715.0
30 TraesCS6D01G168500 chrUn 91.892 407 16 7 1661 2067 389360266 389360655 1.940000e-153 553.0
31 TraesCS6D01G168500 chrUn 88.793 348 18 10 1451 1779 389445940 389446285 1.600000e-109 407.0
32 TraesCS6D01G168500 chr4B 88.208 636 36 17 1451 2067 308697375 308697990 0.000000e+00 723.0
33 TraesCS6D01G168500 chr2D 89.203 602 26 14 1485 2067 272792974 272792393 0.000000e+00 715.0
34 TraesCS6D01G168500 chr2D 88.401 569 45 15 2993 3554 450398989 450399543 0.000000e+00 665.0
35 TraesCS6D01G168500 chr2D 89.960 249 22 2 3330 3578 498869073 498868828 7.690000e-83 318.0
36 TraesCS6D01G168500 chr5A 88.401 569 42 17 2993 3554 220899654 220899103 0.000000e+00 664.0
37 TraesCS6D01G168500 chr1B 84.967 153 11 4 4565 4717 15617078 15616938 1.380000e-30 145.0
38 TraesCS6D01G168500 chr1B 93.333 75 5 0 4565 4639 15459997 15459923 1.400000e-20 111.0
39 TraesCS6D01G168500 chr1B 87.368 95 7 2 4668 4758 15459922 15459829 2.340000e-18 104.0
40 TraesCS6D01G168500 chr1B 95.349 43 2 0 4716 4758 15616830 15616788 8.550000e-08 69.4


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 TraesCS6D01G168500 chr6D 153854275 153859036 4761 False 8794.00 8794 100.00000 1 4762 1 chr6D.!!$F1 4761
1 TraesCS6D01G168500 chr6D 135462923 135463539 616 True 741.00 741 88.67900 1451 2067 1 chr6D.!!$R1 616
2 TraesCS6D01G168500 chr6A 206343248 206348009 4761 False 1781.50 4693 93.58700 2 4762 4 chr6A.!!$F1 4760
3 TraesCS6D01G168500 chr1D 10548113 10549718 1605 True 2085.00 2085 89.98200 2203 3838 1 chr1D.!!$R2 1635
4 TraesCS6D01G168500 chr1D 10456418 10457995 1577 True 782.00 1327 89.89350 2141 4757 2 chr1D.!!$R4 2616
5 TraesCS6D01G168500 chr1D 254396590 254397206 616 True 747.00 747 88.83600 1451 2067 1 chr1D.!!$R3 616
6 TraesCS6D01G168500 chr1A 554513152 554513768 616 False 763.00 763 89.30800 1451 2067 1 chr1A.!!$F1 616
7 TraesCS6D01G168500 chr1A 12184206 12186279 2073 True 644.25 1657 88.11125 2203 4757 4 chr1A.!!$R1 2554
8 TraesCS6D01G168500 chr5D 446174688 446175304 616 False 774.00 774 89.62300 1451 2067 1 chr5D.!!$F1 616
9 TraesCS6D01G168500 chr5D 503276706 503277322 616 True 741.00 741 88.67900 1451 2067 1 chr5D.!!$R1 616
10 TraesCS6D01G168500 chr4D 30386478 30387094 616 True 769.00 769 89.46500 1451 2067 1 chr4D.!!$R1 616
11 TraesCS6D01G168500 chr3B 101912079 101912695 616 False 769.00 769 89.46500 1451 2067 1 chr3B.!!$F1 616
12 TraesCS6D01G168500 chr3B 27505942 27506509 567 True 656.00 656 87.47900 2993 3578 1 chr3B.!!$R1 585
13 TraesCS6D01G168500 chr4A 73809832 73811991 2159 False 525.00 758 91.29250 1451 2067 2 chr4A.!!$F1 616
14 TraesCS6D01G168500 chr3D 589278025 589278641 616 True 752.00 752 88.99400 1451 2067 1 chr3D.!!$R1 616
15 TraesCS6D01G168500 chr3A 594898104 594898720 616 True 752.00 752 88.99400 1451 2067 1 chr3A.!!$R1 616
16 TraesCS6D01G168500 chrUn 93408122 93408728 606 True 745.00 745 89.13700 1451 2057 1 chrUn.!!$R1 606
17 TraesCS6D01G168500 chrUn 346594974 346595590 616 True 741.00 741 88.67900 1451 2067 1 chrUn.!!$R3 616
18 TraesCS6D01G168500 chrUn 216517083 216517699 616 True 736.00 736 88.52200 1451 2067 1 chrUn.!!$R2 616
19 TraesCS6D01G168500 chrUn 444244912 444245493 581 True 715.00 715 89.20300 1485 2067 1 chrUn.!!$R4 582
20 TraesCS6D01G168500 chr4B 308697375 308697990 615 False 723.00 723 88.20800 1451 2067 1 chr4B.!!$F1 616
21 TraesCS6D01G168500 chr2D 272792393 272792974 581 True 715.00 715 89.20300 1485 2067 1 chr2D.!!$R1 582
22 TraesCS6D01G168500 chr2D 450398989 450399543 554 False 665.00 665 88.40100 2993 3554 1 chr2D.!!$F1 561
23 TraesCS6D01G168500 chr5A 220899103 220899654 551 True 664.00 664 88.40100 2993 3554 1 chr5A.!!$R1 561

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
75 76 0.103572 TCTGCCCGTTATTACTCGCC 59.896 55.0 0.0 0.00 0.00 5.54 F
536 566 0.108138 GCTATTGCTGGGAGTGTCGT 60.108 55.0 0.0 0.00 36.03 4.34 F
543 573 0.389948 CTGGGAGTGTCGTACCTTGC 60.390 60.0 0.0 0.00 0.00 4.01 F
1659 2948 0.468585 TCCCATTCAGCCATGGATGC 60.469 55.0 25.4 4.55 46.18 3.91 F
3033 4874 0.615331 TCTGGATGAAGTGGACTGCC 59.385 55.0 0.0 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1673 2981 0.606096 AATGGTTAAAGCGCCCAACC 59.394 50.000 22.08 22.08 41.75 3.77 R
2163 3991 3.909732 AGGTGTTTTGATTCCTTGACCA 58.090 40.909 0.00 0.00 0.00 4.02 R
2761 4602 2.256461 GCCCACGCTTGCTTTCAG 59.744 61.111 0.00 0.00 0.00 3.02 R
3708 5579 1.876156 CCTGTCAGTGCCAAGAGAAAC 59.124 52.381 0.00 0.00 0.00 2.78 R
3897 5769 1.135083 CGATATCCGGCCTATCCACAC 60.135 57.143 14.60 0.00 34.01 3.82 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
29 30 3.644861 AAAAACGCGATTCCCCTCT 57.355 47.368 15.93 0.00 0.00 3.69
68 69 3.331293 CCCCCTCTGCCCGTTATT 58.669 61.111 0.00 0.00 0.00 1.40
69 70 2.535224 CCCCCTCTGCCCGTTATTA 58.465 57.895 0.00 0.00 0.00 0.98
71 72 1.129058 CCCCTCTGCCCGTTATTACT 58.871 55.000 0.00 0.00 0.00 2.24
72 73 1.070289 CCCCTCTGCCCGTTATTACTC 59.930 57.143 0.00 0.00 0.00 2.59
73 74 1.269621 CCCTCTGCCCGTTATTACTCG 60.270 57.143 0.00 0.00 0.00 4.18
74 75 1.488527 CTCTGCCCGTTATTACTCGC 58.511 55.000 0.00 0.00 0.00 5.03
75 76 0.103572 TCTGCCCGTTATTACTCGCC 59.896 55.000 0.00 0.00 0.00 5.54
76 77 1.213094 CTGCCCGTTATTACTCGCCG 61.213 60.000 0.00 0.00 0.00 6.46
80 81 1.558383 CGTTATTACTCGCCGCAGC 59.442 57.895 0.00 0.00 0.00 5.25
270 298 4.694233 CAGCCAGCGCACAGACCT 62.694 66.667 11.47 0.00 37.52 3.85
295 323 3.253955 CAGTACGCACTGCCCAAC 58.746 61.111 2.15 0.00 45.44 3.77
297 325 3.053896 GTACGCACTGCCCAACCC 61.054 66.667 0.00 0.00 0.00 4.11
302 330 4.596585 CACTGCCCAACCCCCGTT 62.597 66.667 0.00 0.00 0.00 4.44
323 351 5.504010 CGTTCCCCAATTTCATCATTACTCG 60.504 44.000 0.00 0.00 0.00 4.18
332 360 9.104965 CAATTTCATCATTACTCGTTAGGGTTA 57.895 33.333 0.00 0.00 30.72 2.85
333 361 9.847224 AATTTCATCATTACTCGTTAGGGTTAT 57.153 29.630 0.00 0.00 30.72 1.89
335 363 8.657074 TTCATCATTACTCGTTAGGGTTATTG 57.343 34.615 0.00 0.00 30.72 1.90
336 364 7.788026 TCATCATTACTCGTTAGGGTTATTGT 58.212 34.615 0.00 0.00 30.72 2.71
337 365 7.924412 TCATCATTACTCGTTAGGGTTATTGTC 59.076 37.037 0.00 0.00 30.72 3.18
380 410 1.851304 AACATTGCCCCTGTGTATGG 58.149 50.000 0.00 0.00 0.00 2.74
381 411 0.998928 ACATTGCCCCTGTGTATGGA 59.001 50.000 0.00 0.00 0.00 3.41
407 437 1.076549 TTGTCTGTGCCCAATCCCC 59.923 57.895 0.00 0.00 0.00 4.81
417 447 2.425569 CCAATCCCCGTTGGCATGG 61.426 63.158 0.00 0.00 41.92 3.66
420 450 2.877089 AATCCCCGTTGGCATGGCAT 62.877 55.000 23.96 2.73 0.00 4.40
422 452 2.489275 CCCCGTTGGCATGGCATAC 61.489 63.158 23.96 20.42 0.00 2.39
452 482 2.642154 TTTTCTTTAGCGGTGGACCA 57.358 45.000 0.00 0.00 35.14 4.02
465 495 0.186386 TGGACCACCCGTTCCAAAAT 59.814 50.000 0.00 0.00 37.93 1.82
466 496 0.885879 GGACCACCCGTTCCAAAATC 59.114 55.000 0.00 0.00 0.00 2.17
474 504 2.640184 CCGTTCCAAAATCCTAGACCC 58.360 52.381 0.00 0.00 0.00 4.46
475 505 2.238898 CCGTTCCAAAATCCTAGACCCT 59.761 50.000 0.00 0.00 0.00 4.34
476 506 3.308188 CCGTTCCAAAATCCTAGACCCTT 60.308 47.826 0.00 0.00 0.00 3.95
484 514 0.617820 TCCTAGACCCTTCACTGCCC 60.618 60.000 0.00 0.00 0.00 5.36
497 527 2.038689 TCACTGCCCGTAACAATGGTAA 59.961 45.455 0.00 0.00 0.00 2.85
500 530 4.636648 CACTGCCCGTAACAATGGTAATAA 59.363 41.667 0.00 0.00 0.00 1.40
501 531 4.879545 ACTGCCCGTAACAATGGTAATAAG 59.120 41.667 0.00 0.00 0.00 1.73
506 536 4.035909 CCGTAACAATGGTAATAAGGGCAC 59.964 45.833 0.00 0.00 0.00 5.01
536 566 0.108138 GCTATTGCTGGGAGTGTCGT 60.108 55.000 0.00 0.00 36.03 4.34
543 573 0.389948 CTGGGAGTGTCGTACCTTGC 60.390 60.000 0.00 0.00 0.00 4.01
557 587 7.604927 TGTCGTACCTTGCTGATTAGTTTTTAT 59.395 33.333 0.00 0.00 0.00 1.40
559 589 8.447833 TCGTACCTTGCTGATTAGTTTTTATTG 58.552 33.333 0.00 0.00 0.00 1.90
592 839 5.174037 TGTTGGGAAGATAACCCTGTAAG 57.826 43.478 0.00 0.00 46.82 2.34
696 947 8.324163 AGTATTATGGTGTTGTTCTCTTGTTC 57.676 34.615 0.00 0.00 0.00 3.18
697 948 5.666969 TTATGGTGTTGTTCTCTTGTTCG 57.333 39.130 0.00 0.00 0.00 3.95
698 949 1.668751 TGGTGTTGTTCTCTTGTTCGC 59.331 47.619 0.00 0.00 0.00 4.70
721 980 5.120208 GCTTCTACGATAAACACAGCAAGAA 59.880 40.000 0.00 0.00 0.00 2.52
724 983 7.667043 TCTACGATAAACACAGCAAGAAATT 57.333 32.000 0.00 0.00 0.00 1.82
755 1014 8.129211 AGAAGTTAAACATCAAACAACTACAGC 58.871 33.333 0.00 0.00 0.00 4.40
785 1044 6.973229 GCATTTGGCATTAGACTTTTCATT 57.027 33.333 0.00 0.00 43.97 2.57
786 1045 7.368480 GCATTTGGCATTAGACTTTTCATTT 57.632 32.000 0.00 0.00 43.97 2.32
787 1046 8.477984 GCATTTGGCATTAGACTTTTCATTTA 57.522 30.769 0.00 0.00 43.97 1.40
788 1047 8.598075 GCATTTGGCATTAGACTTTTCATTTAG 58.402 33.333 0.00 0.00 43.97 1.85
789 1048 9.859427 CATTTGGCATTAGACTTTTCATTTAGA 57.141 29.630 0.00 0.00 0.00 2.10
792 1051 8.862325 TGGCATTAGACTTTTCATTTAGAGAA 57.138 30.769 0.00 0.00 0.00 2.87
793 1052 8.730680 TGGCATTAGACTTTTCATTTAGAGAAC 58.269 33.333 0.00 0.00 0.00 3.01
794 1053 8.951243 GGCATTAGACTTTTCATTTAGAGAACT 58.049 33.333 0.00 0.00 0.00 3.01
795 1054 9.980780 GCATTAGACTTTTCATTTAGAGAACTC 57.019 33.333 0.00 0.00 0.00 3.01
814 1073 6.696148 AGAACTCATAAATAAAGTACGCGGAG 59.304 38.462 12.47 4.78 0.00 4.63
836 1095 1.535896 GGACAGAAGCCGAAAAGAACC 59.464 52.381 0.00 0.00 0.00 3.62
837 1096 2.218603 GACAGAAGCCGAAAAGAACCA 58.781 47.619 0.00 0.00 0.00 3.67
840 1099 2.224314 CAGAAGCCGAAAAGAACCAGAC 59.776 50.000 0.00 0.00 0.00 3.51
860 1119 2.224402 ACTGCAGTTTCTCAGGGTCTTC 60.224 50.000 15.25 0.00 34.76 2.87
880 1139 7.099764 GTCTTCTTTCCATCACTGAATCTGTA 58.900 38.462 0.00 0.00 0.00 2.74
887 1146 4.502259 CCATCACTGAATCTGTAGGGTAGC 60.502 50.000 0.00 0.00 0.00 3.58
913 1172 2.094762 TAAGCCGTTTCTGGAGAAGC 57.905 50.000 0.00 0.00 35.21 3.86
946 1205 2.597578 ACCGTGCCCTAATTTCCTTT 57.402 45.000 0.00 0.00 0.00 3.11
953 1212 4.772624 GTGCCCTAATTTCCTTTCTCCTTT 59.227 41.667 0.00 0.00 0.00 3.11
956 1215 5.393135 GCCCTAATTTCCTTTCTCCTTTTCG 60.393 44.000 0.00 0.00 0.00 3.46
978 1237 5.121611 TCGTCTGTGCAGTTTATTTATGGTG 59.878 40.000 0.00 0.00 0.00 4.17
1032 1291 4.819088 GGGGAGAAAGATTCAGCTGATAAC 59.181 45.833 19.04 11.79 0.00 1.89
1059 1318 5.721000 GGTCTCTCCATCTGATGATAGGAAT 59.279 44.000 18.92 0.00 33.10 3.01
1082 1341 1.148310 CTGCAAGTGGAAGGTACGTG 58.852 55.000 0.00 0.00 0.00 4.49
1116 1375 2.681344 CAGAGCACATATCTGCAAAGCA 59.319 45.455 5.72 0.00 39.86 3.91
1235 1494 6.876257 GCAGACTTTATATCTCCATGGTTAGG 59.124 42.308 12.58 1.18 0.00 2.69
1244 1503 5.165961 TCTCCATGGTTAGGAAACAGAAG 57.834 43.478 12.58 0.00 37.34 2.85
1248 1507 4.459337 CCATGGTTAGGAAACAGAAGTTCC 59.541 45.833 2.57 0.00 36.84 3.62
1399 1658 1.732809 GCCTTTTCTCGTTCACCTAGC 59.267 52.381 0.00 0.00 0.00 3.42
1425 1684 6.054295 CCTTGCATCTCTGTATAGCTTTTCT 58.946 40.000 0.00 0.00 0.00 2.52
1441 1700 5.113502 CTTTTCTAGCAAAGGGACACTTG 57.886 43.478 6.95 0.00 39.96 3.16
1448 1707 3.584848 AGCAAAGGGACACTTGTCTATCT 59.415 43.478 9.20 2.77 44.20 1.98
1449 1708 4.042187 AGCAAAGGGACACTTGTCTATCTT 59.958 41.667 9.20 7.93 44.20 2.40
1579 2868 8.039603 TGAATATGCCATACCAATTCGTTATC 57.960 34.615 0.00 0.00 30.79 1.75
1581 2870 8.635765 AATATGCCATACCAATTCGTTATCTT 57.364 30.769 0.00 0.00 0.00 2.40
1652 2941 1.923356 GGAACTTTCCCATTCAGCCA 58.077 50.000 0.00 0.00 41.62 4.75
1653 2942 2.460669 GGAACTTTCCCATTCAGCCAT 58.539 47.619 0.00 0.00 41.62 4.40
1654 2943 2.167075 GGAACTTTCCCATTCAGCCATG 59.833 50.000 0.00 0.00 41.62 3.66
1655 2944 1.856629 ACTTTCCCATTCAGCCATGG 58.143 50.000 7.63 7.63 43.26 3.66
1656 2945 1.358787 ACTTTCCCATTCAGCCATGGA 59.641 47.619 18.40 0.00 46.18 3.41
1657 2946 2.023695 ACTTTCCCATTCAGCCATGGAT 60.024 45.455 18.40 6.18 46.18 3.41
1658 2947 2.076207 TTCCCATTCAGCCATGGATG 57.924 50.000 24.32 24.32 46.18 3.51
1659 2948 0.468585 TCCCATTCAGCCATGGATGC 60.469 55.000 25.40 4.55 46.18 3.91
1662 2970 2.589720 CCATTCAGCCATGGATGCTTA 58.410 47.619 25.40 12.90 46.18 3.09
1670 2978 3.776417 AGCCATGGATGCTTAACCAATTT 59.224 39.130 18.40 0.00 39.69 1.82
1673 2981 8.757363 AGCCATGGATGCTTAACCAATTTTGG 62.757 42.308 18.40 7.79 44.87 3.28
1856 3678 1.872773 AACACCTCTCTGGATCCTCC 58.127 55.000 14.23 0.00 39.71 4.30
1874 3696 7.176340 GGATCCTCCAATTGAAAGATAGATTGG 59.824 40.741 7.12 7.47 46.26 3.16
1934 3756 9.863650 AATTGATCCAATTCTATTGAGTCTGAT 57.136 29.630 1.11 0.00 39.50 2.90
2034 3856 9.725019 TTATGATACCTAGTTGGCATTGATAAG 57.275 33.333 0.00 0.00 40.22 1.73
2044 3866 6.769822 AGTTGGCATTGATAAGAATGACCTAG 59.230 38.462 0.00 0.00 40.22 3.02
2163 3991 4.685575 GCCTTCTCTCTGCTCCATGTATTT 60.686 45.833 0.00 0.00 0.00 1.40
2761 4602 1.152989 CGGAGAGAGCTGCAGCAATC 61.153 60.000 38.24 31.91 45.16 2.67
3002 4843 5.239306 ACACAATGTTGACCTTACAGATGTG 59.761 40.000 16.48 16.48 44.42 3.21
3033 4874 0.615331 TCTGGATGAAGTGGACTGCC 59.385 55.000 0.00 0.00 0.00 4.85
3154 5015 6.757897 TGAGAAATTGTCAAACTCACTGTT 57.242 33.333 12.97 0.00 41.29 3.16
3260 5130 5.625921 AGCAGAAGAAGCAGAAGATTTTC 57.374 39.130 0.00 0.00 0.00 2.29
3492 5363 1.065491 TGGGACGTGGAATGGATCTTG 60.065 52.381 0.00 0.00 0.00 3.02
3677 5548 0.826715 CAGGAGCTCCAATTCCTCGA 59.173 55.000 33.90 0.00 41.86 4.04
3829 5700 6.415206 ACTACATGTGCTACCGGTTATATT 57.585 37.500 15.04 0.00 0.00 1.28
3897 5769 2.730090 GCTTGTTGTGCATCCATCTTCG 60.730 50.000 0.00 0.00 0.00 3.79
3910 5782 0.389391 ATCTTCGTGTGGATAGGCCG 59.611 55.000 0.00 0.00 40.66 6.13
3978 5851 7.168219 TGACAGCTTTACCAATGAGTCTAAAT 58.832 34.615 0.00 0.00 0.00 1.40
3992 5865 6.273825 TGAGTCTAAATACGATTCTTCAGGC 58.726 40.000 0.00 0.00 0.00 4.85
4047 5961 8.718102 ATGTAAACAAGCTACCTTATGTGTAG 57.282 34.615 0.00 0.00 38.95 2.74
4161 6076 4.104102 ACACTGATGGTTTCCTGGTTCTTA 59.896 41.667 0.00 0.00 0.00 2.10
4162 6077 5.070001 CACTGATGGTTTCCTGGTTCTTAA 58.930 41.667 0.00 0.00 0.00 1.85
4302 6217 9.941325 AATTAATATTGCTTGTGAACAATTCCA 57.059 25.926 0.00 0.00 37.63 3.53
4335 6250 2.935849 AGCTTTTCTTTTTGGGCAAACG 59.064 40.909 0.00 0.00 0.00 3.60
4340 6255 2.657143 TCTTTTTGGGCAAACGGTAGT 58.343 42.857 0.00 0.00 0.00 2.73
4341 6256 2.359531 TCTTTTTGGGCAAACGGTAGTG 59.640 45.455 0.00 0.00 0.00 2.74
4383 6298 6.844388 ACCACTATGGATAGTTGATAGGTGAA 59.156 38.462 0.84 0.00 41.44 3.18
4391 6306 6.939163 GGATAGTTGATAGGTGAAGCATCAAT 59.061 38.462 0.00 0.00 39.95 2.57
4443 6358 2.680805 CGAAGCACAATACTGGGACCAT 60.681 50.000 0.00 0.00 0.00 3.55
4444 6359 3.356290 GAAGCACAATACTGGGACCATT 58.644 45.455 0.00 0.00 0.00 3.16
4445 6360 2.726821 AGCACAATACTGGGACCATTG 58.273 47.619 0.00 0.00 36.07 2.82
4446 6361 2.041620 AGCACAATACTGGGACCATTGT 59.958 45.455 3.59 3.59 42.17 2.71
4447 6362 2.825532 GCACAATACTGGGACCATTGTT 59.174 45.455 6.17 0.00 40.09 2.83
4448 6363 3.119495 GCACAATACTGGGACCATTGTTC 60.119 47.826 6.17 0.00 40.09 3.18
4449 6364 4.335416 CACAATACTGGGACCATTGTTCT 58.665 43.478 6.17 0.00 40.09 3.01
4450 6365 4.156556 CACAATACTGGGACCATTGTTCTG 59.843 45.833 6.17 0.00 40.09 3.02
4451 6366 4.202567 ACAATACTGGGACCATTGTTCTGT 60.203 41.667 3.59 0.00 39.27 3.41
4452 6367 2.276732 ACTGGGACCATTGTTCTGTG 57.723 50.000 0.00 0.00 0.00 3.66
4453 6368 1.202927 ACTGGGACCATTGTTCTGTGG 60.203 52.381 0.00 0.00 41.35 4.17
4463 6378 5.944007 ACCATTGTTCTGTGGTATTTAGACC 59.056 40.000 0.00 0.00 46.49 3.85
4464 6379 6.180472 CCATTGTTCTGTGGTATTTAGACCT 58.820 40.000 0.00 0.00 40.46 3.85
4465 6380 7.037873 ACCATTGTTCTGTGGTATTTAGACCTA 60.038 37.037 0.00 0.00 46.49 3.08
4466 6381 7.280205 CCATTGTTCTGTGGTATTTAGACCTAC 59.720 40.741 0.00 0.00 40.46 3.18
4467 6382 7.549147 TTGTTCTGTGGTATTTAGACCTACT 57.451 36.000 0.00 0.00 40.46 2.57
4468 6383 7.549147 TGTTCTGTGGTATTTAGACCTACTT 57.451 36.000 0.00 0.00 40.46 2.24
4469 6384 7.609056 TGTTCTGTGGTATTTAGACCTACTTC 58.391 38.462 0.00 0.00 40.46 3.01
4470 6385 7.453752 TGTTCTGTGGTATTTAGACCTACTTCT 59.546 37.037 0.00 0.00 40.46 2.85
4471 6386 8.964772 GTTCTGTGGTATTTAGACCTACTTCTA 58.035 37.037 0.00 0.00 40.46 2.10
4472 6387 8.749026 TCTGTGGTATTTAGACCTACTTCTAG 57.251 38.462 0.00 0.00 40.46 2.43
4473 6388 8.334734 TCTGTGGTATTTAGACCTACTTCTAGT 58.665 37.037 0.00 0.00 40.46 2.57
4474 6389 8.289939 TGTGGTATTTAGACCTACTTCTAGTG 57.710 38.462 0.00 0.00 40.46 2.74
4475 6390 7.341256 TGTGGTATTTAGACCTACTTCTAGTGG 59.659 40.741 0.00 0.00 40.46 4.00
4476 6391 6.323225 TGGTATTTAGACCTACTTCTAGTGGC 59.677 42.308 0.00 0.00 40.46 5.01
4477 6392 6.323225 GGTATTTAGACCTACTTCTAGTGGCA 59.677 42.308 0.00 0.00 36.47 4.92
4478 6393 5.916661 TTTAGACCTACTTCTAGTGGCAG 57.083 43.478 0.00 0.00 29.67 4.85
4479 6394 3.741245 AGACCTACTTCTAGTGGCAGA 57.259 47.619 0.00 0.00 0.00 4.26
4480 6395 4.258457 AGACCTACTTCTAGTGGCAGAT 57.742 45.455 0.00 0.00 0.00 2.90
4481 6396 4.615513 AGACCTACTTCTAGTGGCAGATT 58.384 43.478 0.00 0.00 0.00 2.40
4482 6397 5.026790 AGACCTACTTCTAGTGGCAGATTT 58.973 41.667 0.00 0.00 0.00 2.17
4483 6398 5.091261 ACCTACTTCTAGTGGCAGATTTG 57.909 43.478 0.00 0.00 0.00 2.32
4484 6399 4.777896 ACCTACTTCTAGTGGCAGATTTGA 59.222 41.667 0.00 0.00 0.00 2.69
4485 6400 5.426833 ACCTACTTCTAGTGGCAGATTTGAT 59.573 40.000 0.00 0.00 0.00 2.57
4486 6401 5.988561 CCTACTTCTAGTGGCAGATTTGATC 59.011 44.000 0.00 0.00 0.00 2.92
4487 6402 4.775236 ACTTCTAGTGGCAGATTTGATCC 58.225 43.478 0.00 0.00 0.00 3.36
4488 6403 4.472833 ACTTCTAGTGGCAGATTTGATCCT 59.527 41.667 0.00 0.00 0.00 3.24
4489 6404 5.663106 ACTTCTAGTGGCAGATTTGATCCTA 59.337 40.000 0.00 0.00 0.00 2.94
4490 6405 6.328672 ACTTCTAGTGGCAGATTTGATCCTAT 59.671 38.462 0.00 0.00 0.00 2.57
4491 6406 7.510685 ACTTCTAGTGGCAGATTTGATCCTATA 59.489 37.037 0.00 0.00 0.00 1.31
4492 6407 7.233389 TCTAGTGGCAGATTTGATCCTATAC 57.767 40.000 0.00 0.00 0.00 1.47
4493 6408 7.013220 TCTAGTGGCAGATTTGATCCTATACT 58.987 38.462 0.00 0.00 0.00 2.12
4494 6409 6.107901 AGTGGCAGATTTGATCCTATACTC 57.892 41.667 0.00 0.00 0.00 2.59
4495 6410 5.843421 AGTGGCAGATTTGATCCTATACTCT 59.157 40.000 0.00 0.00 0.00 3.24
4496 6411 7.013220 AGTGGCAGATTTGATCCTATACTCTA 58.987 38.462 0.00 0.00 0.00 2.43
4497 6412 7.178274 AGTGGCAGATTTGATCCTATACTCTAG 59.822 40.741 0.00 0.00 0.00 2.43
4498 6413 7.013220 TGGCAGATTTGATCCTATACTCTAGT 58.987 38.462 0.00 0.00 0.00 2.57
4499 6414 7.039434 TGGCAGATTTGATCCTATACTCTAGTG 60.039 40.741 0.00 0.00 0.00 2.74
4500 6415 7.177568 GGCAGATTTGATCCTATACTCTAGTGA 59.822 40.741 0.00 0.00 0.00 3.41
4501 6416 8.026607 GCAGATTTGATCCTATACTCTAGTGAC 58.973 40.741 0.00 0.00 0.00 3.67
4502 6417 9.295825 CAGATTTGATCCTATACTCTAGTGACT 57.704 37.037 0.00 0.00 0.00 3.41
4503 6418 9.295825 AGATTTGATCCTATACTCTAGTGACTG 57.704 37.037 0.00 0.00 0.00 3.51
4504 6419 9.073475 GATTTGATCCTATACTCTAGTGACTGT 57.927 37.037 0.00 0.00 0.00 3.55
4505 6420 8.453238 TTTGATCCTATACTCTAGTGACTGTC 57.547 38.462 0.00 0.00 0.00 3.51
4506 6421 6.535540 TGATCCTATACTCTAGTGACTGTCC 58.464 44.000 5.17 0.00 0.00 4.02
4507 6422 6.330514 TGATCCTATACTCTAGTGACTGTCCT 59.669 42.308 5.17 4.83 0.00 3.85
4508 6423 6.578313 TCCTATACTCTAGTGACTGTCCTT 57.422 41.667 5.17 0.00 0.00 3.36
4509 6424 6.358178 TCCTATACTCTAGTGACTGTCCTTG 58.642 44.000 5.17 3.79 0.00 3.61
4510 6425 6.069556 TCCTATACTCTAGTGACTGTCCTTGT 60.070 42.308 5.17 5.36 0.00 3.16
4511 6426 6.603997 CCTATACTCTAGTGACTGTCCTTGTT 59.396 42.308 5.17 0.00 0.00 2.83
4512 6427 4.857509 ACTCTAGTGACTGTCCTTGTTC 57.142 45.455 5.17 0.00 0.00 3.18
4513 6428 3.574826 ACTCTAGTGACTGTCCTTGTTCC 59.425 47.826 5.17 0.00 0.00 3.62
4514 6429 3.829601 CTCTAGTGACTGTCCTTGTTCCT 59.170 47.826 5.17 0.00 0.00 3.36
4515 6430 4.223953 TCTAGTGACTGTCCTTGTTCCTT 58.776 43.478 5.17 0.00 0.00 3.36
4516 6431 3.199880 AGTGACTGTCCTTGTTCCTTG 57.800 47.619 5.17 0.00 0.00 3.61
4517 6432 1.604278 GTGACTGTCCTTGTTCCTTGC 59.396 52.381 5.17 0.00 0.00 4.01
4518 6433 1.211703 TGACTGTCCTTGTTCCTTGCA 59.788 47.619 5.17 0.00 0.00 4.08
4519 6434 2.297701 GACTGTCCTTGTTCCTTGCAA 58.702 47.619 0.00 0.00 0.00 4.08
4520 6435 2.687935 GACTGTCCTTGTTCCTTGCAAA 59.312 45.455 0.00 0.00 0.00 3.68
4521 6436 2.689983 ACTGTCCTTGTTCCTTGCAAAG 59.310 45.455 0.00 0.00 45.69 2.77
4536 6451 6.470557 CTTGCAAAGGTATGAAATGGTTTG 57.529 37.500 0.00 0.00 41.27 2.93
4537 6452 5.543507 TGCAAAGGTATGAAATGGTTTGT 57.456 34.783 0.00 0.00 29.54 2.83
4538 6453 6.656632 TGCAAAGGTATGAAATGGTTTGTA 57.343 33.333 0.00 0.00 29.54 2.41
4539 6454 7.055667 TGCAAAGGTATGAAATGGTTTGTAA 57.944 32.000 0.00 0.00 29.54 2.41
4540 6455 7.500992 TGCAAAGGTATGAAATGGTTTGTAAA 58.499 30.769 0.00 0.00 29.54 2.01
4541 6456 7.439655 TGCAAAGGTATGAAATGGTTTGTAAAC 59.560 33.333 0.00 0.00 38.17 2.01
4542 6457 7.655732 GCAAAGGTATGAAATGGTTTGTAAACT 59.344 33.333 7.36 0.00 38.89 2.66
4543 6458 8.977505 CAAAGGTATGAAATGGTTTGTAAACTG 58.022 33.333 7.36 0.00 38.89 3.16
4544 6459 7.833285 AGGTATGAAATGGTTTGTAAACTGT 57.167 32.000 7.36 0.00 38.89 3.55
4545 6460 7.657336 AGGTATGAAATGGTTTGTAAACTGTG 58.343 34.615 7.36 0.00 38.89 3.66
4546 6461 7.286775 AGGTATGAAATGGTTTGTAAACTGTGT 59.713 33.333 7.36 0.00 38.89 3.72
4547 6462 8.569641 GGTATGAAATGGTTTGTAAACTGTGTA 58.430 33.333 7.36 0.00 38.89 2.90
4550 6465 7.429633 TGAAATGGTTTGTAAACTGTGTATGG 58.570 34.615 7.36 0.00 38.89 2.74
4551 6466 4.839668 TGGTTTGTAAACTGTGTATGGC 57.160 40.909 7.36 0.00 38.89 4.40
4552 6467 4.465886 TGGTTTGTAAACTGTGTATGGCT 58.534 39.130 7.36 0.00 38.89 4.75
4553 6468 4.890581 TGGTTTGTAAACTGTGTATGGCTT 59.109 37.500 7.36 0.00 38.89 4.35
4554 6469 5.219633 GGTTTGTAAACTGTGTATGGCTTG 58.780 41.667 7.36 0.00 38.89 4.01
4555 6470 5.221165 GGTTTGTAAACTGTGTATGGCTTGT 60.221 40.000 7.36 0.00 38.89 3.16
4556 6471 6.270064 GTTTGTAAACTGTGTATGGCTTGTT 58.730 36.000 0.41 0.00 36.03 2.83
4557 6472 5.431420 TGTAAACTGTGTATGGCTTGTTG 57.569 39.130 0.00 0.00 0.00 3.33
4558 6473 3.369546 AAACTGTGTATGGCTTGTTGC 57.630 42.857 0.00 0.00 41.94 4.17
4559 6474 2.276732 ACTGTGTATGGCTTGTTGCT 57.723 45.000 0.00 0.00 42.39 3.91
4560 6475 1.881973 ACTGTGTATGGCTTGTTGCTG 59.118 47.619 0.00 0.00 42.39 4.41
4561 6476 2.153645 CTGTGTATGGCTTGTTGCTGA 58.846 47.619 0.00 0.00 42.39 4.26
4562 6477 1.879380 TGTGTATGGCTTGTTGCTGAC 59.121 47.619 0.00 0.00 42.39 3.51
4563 6478 1.200020 GTGTATGGCTTGTTGCTGACC 59.800 52.381 0.00 0.00 42.39 4.02
4564 6479 1.202867 TGTATGGCTTGTTGCTGACCA 60.203 47.619 0.00 0.00 42.39 4.02
4573 6488 3.853831 TGTTGCTGACCAAATATGCTG 57.146 42.857 0.00 0.00 34.68 4.41
4616 6531 7.732025 TCCATTTGACTAGAAGTAACTGTTCA 58.268 34.615 0.00 0.00 0.00 3.18
4657 6572 9.645059 CTACATTTTTCTCACATCTTACTCAGA 57.355 33.333 0.00 0.00 35.33 3.27
4727 6646 8.978874 ACTGCATATTTGATACATGTTTAGGA 57.021 30.769 2.30 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 1.213094 CTGCGGCGAGTAATAACGGG 61.213 60.000 12.98 0.00 0.00 5.28
267 295 2.102588 AGTGCGTACTGAAGACAAAGGT 59.897 45.455 4.99 0.00 35.34 3.50
295 323 0.325203 ATGAAATTGGGGAACGGGGG 60.325 55.000 0.00 0.00 0.00 5.40
297 325 1.846007 TGATGAAATTGGGGAACGGG 58.154 50.000 0.00 0.00 0.00 5.28
300 328 5.357032 ACGAGTAATGATGAAATTGGGGAAC 59.643 40.000 0.00 0.00 0.00 3.62
302 330 5.110814 ACGAGTAATGATGAAATTGGGGA 57.889 39.130 0.00 0.00 0.00 4.81
351 381 5.025453 ACAGGGGCAATGTTTTCTCAATAT 58.975 37.500 0.00 0.00 0.00 1.28
380 410 3.006940 TGGGCACAGACAACGAATATTC 58.993 45.455 5.30 5.30 0.00 1.75
381 411 3.066291 TGGGCACAGACAACGAATATT 57.934 42.857 0.00 0.00 0.00 1.28
407 437 3.628005 CAAGTATGCCATGCCAACG 57.372 52.632 0.00 0.00 0.00 4.10
420 450 6.370593 CGCTAAAGAAAATTGACAGCAAGTA 58.629 36.000 0.00 0.00 37.45 2.24
422 452 4.618489 CCGCTAAAGAAAATTGACAGCAAG 59.382 41.667 0.00 0.00 37.45 4.01
452 482 2.026542 GGTCTAGGATTTTGGAACGGGT 60.027 50.000 0.00 0.00 0.00 5.28
456 486 4.700692 GTGAAGGGTCTAGGATTTTGGAAC 59.299 45.833 0.00 0.00 0.00 3.62
457 487 4.601857 AGTGAAGGGTCTAGGATTTTGGAA 59.398 41.667 0.00 0.00 0.00 3.53
459 489 4.265073 CAGTGAAGGGTCTAGGATTTTGG 58.735 47.826 0.00 0.00 0.00 3.28
460 490 3.691609 GCAGTGAAGGGTCTAGGATTTTG 59.308 47.826 0.00 0.00 0.00 2.44
461 491 3.308473 GGCAGTGAAGGGTCTAGGATTTT 60.308 47.826 0.00 0.00 0.00 1.82
465 495 0.617820 GGGCAGTGAAGGGTCTAGGA 60.618 60.000 0.00 0.00 0.00 2.94
466 496 1.908483 GGGCAGTGAAGGGTCTAGG 59.092 63.158 0.00 0.00 0.00 3.02
474 504 1.468520 CCATTGTTACGGGCAGTGAAG 59.531 52.381 0.00 0.00 0.00 3.02
475 505 1.202830 ACCATTGTTACGGGCAGTGAA 60.203 47.619 0.00 0.00 0.00 3.18
476 506 0.398696 ACCATTGTTACGGGCAGTGA 59.601 50.000 0.00 0.00 0.00 3.41
484 514 4.636648 TGTGCCCTTATTACCATTGTTACG 59.363 41.667 0.00 0.00 0.00 3.18
500 530 7.010156 GCAATAGCATCACATATTGTGCCCT 62.010 44.000 2.77 2.35 43.53 5.19
501 531 4.853332 GCAATAGCATCACATATTGTGCCC 60.853 45.833 2.77 0.00 43.53 5.36
506 536 4.763279 TCCCAGCAATAGCATCACATATTG 59.237 41.667 0.00 0.00 45.49 1.90
536 566 9.290988 TCACAATAAAAACTAATCAGCAAGGTA 57.709 29.630 0.00 0.00 0.00 3.08
557 587 4.952957 TCTTCCCAACAAATTCAGTCACAA 59.047 37.500 0.00 0.00 0.00 3.33
559 589 5.712152 ATCTTCCCAACAAATTCAGTCAC 57.288 39.130 0.00 0.00 0.00 3.67
608 855 8.189119 AGAACAAGTCAAATAAATAAAGGCCA 57.811 30.769 5.01 0.00 0.00 5.36
610 857 9.691362 TTGAGAACAAGTCAAATAAATAAAGGC 57.309 29.630 0.00 0.00 30.89 4.35
684 935 3.004002 TCGTAGAAGCGAACAAGAGAACA 59.996 43.478 0.00 0.00 37.99 3.18
685 936 3.562505 TCGTAGAAGCGAACAAGAGAAC 58.437 45.455 0.00 0.00 37.99 3.01
686 937 3.909776 TCGTAGAAGCGAACAAGAGAA 57.090 42.857 0.00 0.00 37.99 2.87
688 939 5.571741 TGTTTATCGTAGAAGCGAACAAGAG 59.428 40.000 0.00 0.00 44.38 2.85
689 940 5.344128 GTGTTTATCGTAGAAGCGAACAAGA 59.656 40.000 0.00 0.00 44.38 3.02
690 941 5.118050 TGTGTTTATCGTAGAAGCGAACAAG 59.882 40.000 0.00 0.00 44.38 3.16
691 942 4.983538 TGTGTTTATCGTAGAAGCGAACAA 59.016 37.500 0.00 0.00 44.38 2.83
696 947 2.921121 TGCTGTGTTTATCGTAGAAGCG 59.079 45.455 0.00 0.00 43.58 4.68
697 948 4.625742 TCTTGCTGTGTTTATCGTAGAAGC 59.374 41.667 0.00 0.00 43.58 3.86
698 949 6.706055 TTCTTGCTGTGTTTATCGTAGAAG 57.294 37.500 0.00 0.00 43.58 2.85
742 1001 1.613437 CCCTTGGGCTGTAGTTGTTTG 59.387 52.381 0.00 0.00 0.00 2.93
744 1003 0.539669 GCCCTTGGGCTGTAGTTGTT 60.540 55.000 22.47 0.00 0.00 2.83
753 1012 3.004946 GCCAAATGCCCTTGGGCT 61.005 61.111 28.37 13.36 45.21 5.19
755 1014 1.139455 CTAATGCCAAATGCCCTTGGG 59.861 52.381 14.04 0.32 45.21 4.12
766 1025 8.862325 TCTCTAAATGAAAAGTCTAATGCCAA 57.138 30.769 0.00 0.00 0.00 4.52
785 1044 9.229784 CGCGTACTTTATTTATGAGTTCTCTAA 57.770 33.333 0.00 0.00 0.00 2.10
786 1045 7.859377 CCGCGTACTTTATTTATGAGTTCTCTA 59.141 37.037 4.92 0.00 0.00 2.43
787 1046 6.696148 CCGCGTACTTTATTTATGAGTTCTCT 59.304 38.462 4.92 0.00 0.00 3.10
788 1047 6.694411 TCCGCGTACTTTATTTATGAGTTCTC 59.306 38.462 4.92 0.00 0.00 2.87
789 1048 6.567050 TCCGCGTACTTTATTTATGAGTTCT 58.433 36.000 4.92 0.00 0.00 3.01
790 1049 6.074463 CCTCCGCGTACTTTATTTATGAGTTC 60.074 42.308 4.92 0.00 0.00 3.01
792 1051 5.287226 CCTCCGCGTACTTTATTTATGAGT 58.713 41.667 4.92 0.00 0.00 3.41
793 1052 4.684703 CCCTCCGCGTACTTTATTTATGAG 59.315 45.833 4.92 0.00 0.00 2.90
794 1053 4.501915 CCCCTCCGCGTACTTTATTTATGA 60.502 45.833 4.92 0.00 0.00 2.15
795 1054 3.744426 CCCCTCCGCGTACTTTATTTATG 59.256 47.826 4.92 0.00 0.00 1.90
796 1055 3.642848 TCCCCTCCGCGTACTTTATTTAT 59.357 43.478 4.92 0.00 0.00 1.40
797 1056 3.030291 TCCCCTCCGCGTACTTTATTTA 58.970 45.455 4.92 0.00 0.00 1.40
810 1069 4.148825 CGGCTTCTGTCCCCTCCG 62.149 72.222 0.00 0.00 0.00 4.63
814 1073 0.036306 TCTTTTCGGCTTCTGTCCCC 59.964 55.000 0.00 0.00 0.00 4.81
836 1095 1.071385 ACCCTGAGAAACTGCAGTCTG 59.929 52.381 21.95 11.19 0.00 3.51
837 1096 1.346068 GACCCTGAGAAACTGCAGTCT 59.654 52.381 21.95 14.23 0.00 3.24
840 1099 2.038295 AGAAGACCCTGAGAAACTGCAG 59.962 50.000 13.48 13.48 0.00 4.41
860 1119 5.121811 CCCTACAGATTCAGTGATGGAAAG 58.878 45.833 0.00 0.00 0.00 2.62
880 1139 1.413077 CGGCTTAAGCTTAGCTACCCT 59.587 52.381 25.88 0.00 38.25 4.34
887 1146 3.596214 TCCAGAAACGGCTTAAGCTTAG 58.404 45.455 25.88 18.95 41.70 2.18
913 1172 1.068474 CACGGTTCTTTACGCTGGAG 58.932 55.000 0.00 0.00 0.00 3.86
929 1188 2.683362 GGAGAAAGGAAATTAGGGCACG 59.317 50.000 0.00 0.00 0.00 5.34
946 1205 1.412710 ACTGCACAGACGAAAAGGAGA 59.587 47.619 4.31 0.00 0.00 3.71
953 1212 5.703592 ACCATAAATAAACTGCACAGACGAA 59.296 36.000 4.31 0.00 0.00 3.85
956 1215 5.095490 GCACCATAAATAAACTGCACAGAC 58.905 41.667 4.31 0.00 0.00 3.51
978 1237 6.405842 CCATTTAACTGAGGTGGGAAATAAGC 60.406 42.308 0.00 0.00 0.00 3.09
1059 1318 1.055849 TACCTTCCACTTGCAGCTCA 58.944 50.000 0.00 0.00 0.00 4.26
1082 1341 3.904571 TGTGCTCTGACAAATTCAATGC 58.095 40.909 0.00 0.00 32.21 3.56
1123 1382 7.933215 TGGATGAGAATAAATATGCATCCAG 57.067 36.000 15.99 0.00 31.64 3.86
1154 1413 8.899427 TTTCCAATTTACTGATTTCATTTGCA 57.101 26.923 0.00 0.00 0.00 4.08
1229 1488 4.969484 TCAGGAACTTCTGTTTCCTAACC 58.031 43.478 3.34 0.00 34.60 2.85
1235 1494 9.660180 ATTATTAGACTCAGGAACTTCTGTTTC 57.340 33.333 0.00 0.00 34.60 2.78
1399 1658 4.333913 AGCTATACAGAGATGCAAGGTG 57.666 45.455 0.00 0.00 0.00 4.00
1425 1684 4.777896 AGATAGACAAGTGTCCCTTTGCTA 59.222 41.667 7.82 0.00 45.85 3.49
1431 1690 7.444792 CGTAGTATAAGATAGACAAGTGTCCCT 59.555 40.741 7.82 1.05 45.85 4.20
1579 2868 5.382616 TGGAATCTCATCCATCATCCAAAG 58.617 41.667 0.00 0.00 44.52 2.77
1649 2938 3.825143 AATTGGTTAAGCATCCATGGC 57.175 42.857 6.96 0.00 33.50 4.40
1650 2939 4.877251 CCAAAATTGGTTAAGCATCCATGG 59.123 41.667 8.40 4.97 43.43 3.66
1670 2978 1.465200 GGTTAAAGCGCCCAACCCAA 61.465 55.000 19.52 0.00 36.51 4.12
1673 2981 0.606096 AATGGTTAAAGCGCCCAACC 59.394 50.000 22.08 22.08 41.75 3.77
1787 3609 7.417612 CCATCTCGAAATATTTCCGATTGTTT 58.582 34.615 20.01 2.24 33.68 2.83
1856 3678 6.367983 TCCCTCCCAATCTATCTTTCAATTG 58.632 40.000 0.00 0.00 0.00 2.32
2163 3991 3.909732 AGGTGTTTTGATTCCTTGACCA 58.090 40.909 0.00 0.00 0.00 4.02
2761 4602 2.256461 GCCCACGCTTGCTTTCAG 59.744 61.111 0.00 0.00 0.00 3.02
3002 4843 4.576463 ACTTCATCCAGAACAAACACAGAC 59.424 41.667 0.00 0.00 31.61 3.51
3033 4874 4.717877 TCTCTGAATCCTCTCTCTAGCAG 58.282 47.826 0.00 0.00 0.00 4.24
3260 5130 7.910304 AGTGCTGCTTACTTTTTATTATCTCG 58.090 34.615 0.00 0.00 0.00 4.04
3440 5311 7.011950 CCTGTACAAACAACAACAGATACTTCA 59.988 37.037 0.00 0.00 41.47 3.02
3492 5363 8.856490 AACAAAATCACTTGATGTACTTTCAC 57.144 30.769 0.00 0.00 34.49 3.18
3677 5548 8.924511 TGGTGAATTTTGAATTAGAGAGTTCT 57.075 30.769 0.00 0.00 37.46 3.01
3708 5579 1.876156 CCTGTCAGTGCCAAGAGAAAC 59.124 52.381 0.00 0.00 0.00 2.78
3809 5680 3.813166 GCAATATAACCGGTAGCACATGT 59.187 43.478 8.00 0.00 0.00 3.21
3810 5681 4.065088 AGCAATATAACCGGTAGCACATG 58.935 43.478 8.00 4.59 0.00 3.21
3829 5700 4.022935 CCTCAGCTATCAAACAACAAAGCA 60.023 41.667 0.00 0.00 32.42 3.91
3897 5769 1.135083 CGATATCCGGCCTATCCACAC 60.135 57.143 14.60 0.00 34.01 3.82
3910 5782 6.522054 TCAGGAGTTACAAATTCCGATATCC 58.478 40.000 0.00 0.00 41.76 2.59
3978 5851 2.236146 ACACATGGCCTGAAGAATCGTA 59.764 45.455 3.32 0.00 0.00 3.43
3992 5865 5.981315 GCATAAATTGATTCCAGACACATGG 59.019 40.000 0.00 0.00 42.11 3.66
4288 6203 8.154203 TCACTACTCTTATGGAATTGTTCACAA 58.846 33.333 0.00 0.00 40.51 3.33
4302 6217 8.787852 CCAAAAAGAAAAGCTCACTACTCTTAT 58.212 33.333 0.00 0.00 30.54 1.73
4341 6256 7.178097 CCATAGTGGTATAGGTTTACTACCCTC 59.822 44.444 0.00 0.00 39.24 4.30
4366 6281 5.858381 TGATGCTTCACCTATCAACTATCC 58.142 41.667 0.00 0.00 0.00 2.59
4391 6306 6.294473 ACAAAATGGACCATTAAATTGTGCA 58.706 32.000 25.01 0.00 33.72 4.57
4443 6358 7.549147 AGTAGGTCTAAATACCACAGAACAA 57.451 36.000 0.00 0.00 42.40 2.83
4444 6359 7.453752 AGAAGTAGGTCTAAATACCACAGAACA 59.546 37.037 0.00 0.00 42.40 3.18
4445 6360 7.838884 AGAAGTAGGTCTAAATACCACAGAAC 58.161 38.462 0.00 0.00 42.40 3.01
4446 6361 9.186837 CTAGAAGTAGGTCTAAATACCACAGAA 57.813 37.037 0.00 0.00 42.40 3.02
4447 6362 8.334734 ACTAGAAGTAGGTCTAAATACCACAGA 58.665 37.037 0.00 0.00 42.40 3.41
4448 6363 8.407064 CACTAGAAGTAGGTCTAAATACCACAG 58.593 40.741 0.00 0.00 42.40 3.66
4449 6364 7.341256 CCACTAGAAGTAGGTCTAAATACCACA 59.659 40.741 0.00 0.00 42.40 4.17
4450 6365 7.683945 GCCACTAGAAGTAGGTCTAAATACCAC 60.684 44.444 0.00 0.00 42.40 4.16
4451 6366 6.323225 GCCACTAGAAGTAGGTCTAAATACCA 59.677 42.308 0.00 0.00 42.40 3.25
4452 6367 6.323225 TGCCACTAGAAGTAGGTCTAAATACC 59.677 42.308 0.00 0.00 40.06 2.73
4453 6368 7.284944 TCTGCCACTAGAAGTAGGTCTAAATAC 59.715 40.741 0.00 0.00 29.74 1.89
4454 6369 7.351952 TCTGCCACTAGAAGTAGGTCTAAATA 58.648 38.462 0.00 0.00 29.74 1.40
4455 6370 6.195700 TCTGCCACTAGAAGTAGGTCTAAAT 58.804 40.000 0.00 0.00 29.74 1.40
4456 6371 5.577100 TCTGCCACTAGAAGTAGGTCTAAA 58.423 41.667 0.00 0.00 29.74 1.85
4457 6372 5.188988 TCTGCCACTAGAAGTAGGTCTAA 57.811 43.478 0.00 0.00 29.74 2.10
4458 6373 4.857130 TCTGCCACTAGAAGTAGGTCTA 57.143 45.455 0.00 0.00 0.00 2.59
4459 6374 3.741245 TCTGCCACTAGAAGTAGGTCT 57.259 47.619 0.00 0.00 0.00 3.85
4460 6375 5.105310 TCAAATCTGCCACTAGAAGTAGGTC 60.105 44.000 0.00 0.00 0.00 3.85
4461 6376 4.777896 TCAAATCTGCCACTAGAAGTAGGT 59.222 41.667 0.00 0.00 0.00 3.08
4462 6377 5.344743 TCAAATCTGCCACTAGAAGTAGG 57.655 43.478 0.00 0.00 0.00 3.18
4463 6378 5.988561 GGATCAAATCTGCCACTAGAAGTAG 59.011 44.000 0.00 0.00 0.00 2.57
4464 6379 5.663106 AGGATCAAATCTGCCACTAGAAGTA 59.337 40.000 0.00 0.00 0.00 2.24
4465 6380 4.472833 AGGATCAAATCTGCCACTAGAAGT 59.527 41.667 0.00 0.00 0.00 3.01
4466 6381 5.033589 AGGATCAAATCTGCCACTAGAAG 57.966 43.478 0.00 0.00 0.00 2.85
4467 6382 6.753913 ATAGGATCAAATCTGCCACTAGAA 57.246 37.500 0.00 0.00 0.00 2.10
4468 6383 7.013220 AGTATAGGATCAAATCTGCCACTAGA 58.987 38.462 0.00 0.00 0.00 2.43
4469 6384 7.178274 AGAGTATAGGATCAAATCTGCCACTAG 59.822 40.741 0.00 0.00 0.00 2.57
4470 6385 7.013220 AGAGTATAGGATCAAATCTGCCACTA 58.987 38.462 0.00 0.00 0.00 2.74
4471 6386 5.843421 AGAGTATAGGATCAAATCTGCCACT 59.157 40.000 0.00 0.00 0.00 4.00
4472 6387 6.107901 AGAGTATAGGATCAAATCTGCCAC 57.892 41.667 0.00 0.00 0.00 5.01
4473 6388 7.013220 ACTAGAGTATAGGATCAAATCTGCCA 58.987 38.462 0.00 0.00 0.00 4.92
4474 6389 7.177568 TCACTAGAGTATAGGATCAAATCTGCC 59.822 40.741 0.00 0.00 0.00 4.85
4475 6390 8.026607 GTCACTAGAGTATAGGATCAAATCTGC 58.973 40.741 0.00 0.00 0.00 4.26
4476 6391 9.295825 AGTCACTAGAGTATAGGATCAAATCTG 57.704 37.037 0.00 0.00 0.00 2.90
4477 6392 9.295825 CAGTCACTAGAGTATAGGATCAAATCT 57.704 37.037 0.00 0.00 0.00 2.40
4478 6393 9.073475 ACAGTCACTAGAGTATAGGATCAAATC 57.927 37.037 0.00 0.00 0.00 2.17
4479 6394 9.073475 GACAGTCACTAGAGTATAGGATCAAAT 57.927 37.037 0.00 0.00 0.00 2.32
4480 6395 7.502895 GGACAGTCACTAGAGTATAGGATCAAA 59.497 40.741 2.17 0.00 0.00 2.69
4481 6396 6.999272 GGACAGTCACTAGAGTATAGGATCAA 59.001 42.308 2.17 0.00 0.00 2.57
4482 6397 6.330514 AGGACAGTCACTAGAGTATAGGATCA 59.669 42.308 2.17 0.00 0.00 2.92
4483 6398 6.775708 AGGACAGTCACTAGAGTATAGGATC 58.224 44.000 2.17 0.00 0.00 3.36
4484 6399 6.773583 AGGACAGTCACTAGAGTATAGGAT 57.226 41.667 2.17 0.00 0.00 3.24
4485 6400 6.069556 ACAAGGACAGTCACTAGAGTATAGGA 60.070 42.308 2.17 0.00 0.00 2.94
4486 6401 6.123651 ACAAGGACAGTCACTAGAGTATAGG 58.876 44.000 2.17 0.00 0.00 2.57
4487 6402 7.201750 GGAACAAGGACAGTCACTAGAGTATAG 60.202 44.444 2.17 0.00 0.00 1.31
4488 6403 6.602406 GGAACAAGGACAGTCACTAGAGTATA 59.398 42.308 2.17 0.00 0.00 1.47
4489 6404 5.419471 GGAACAAGGACAGTCACTAGAGTAT 59.581 44.000 2.17 0.00 0.00 2.12
4490 6405 4.765856 GGAACAAGGACAGTCACTAGAGTA 59.234 45.833 2.17 0.00 0.00 2.59
4491 6406 3.574826 GGAACAAGGACAGTCACTAGAGT 59.425 47.826 2.17 0.00 0.00 3.24
4492 6407 3.829601 AGGAACAAGGACAGTCACTAGAG 59.170 47.826 2.17 0.00 0.00 2.43
4493 6408 3.845860 AGGAACAAGGACAGTCACTAGA 58.154 45.455 2.17 0.00 0.00 2.43
4494 6409 4.310769 CAAGGAACAAGGACAGTCACTAG 58.689 47.826 2.17 0.00 0.00 2.57
4495 6410 3.494398 GCAAGGAACAAGGACAGTCACTA 60.494 47.826 2.17 0.00 0.00 2.74
4496 6411 2.746472 GCAAGGAACAAGGACAGTCACT 60.746 50.000 2.17 0.00 0.00 3.41
4497 6412 1.604278 GCAAGGAACAAGGACAGTCAC 59.396 52.381 2.17 0.00 0.00 3.67
4498 6413 1.211703 TGCAAGGAACAAGGACAGTCA 59.788 47.619 2.17 0.00 0.00 3.41
4499 6414 1.967319 TGCAAGGAACAAGGACAGTC 58.033 50.000 0.00 0.00 0.00 3.51
4500 6415 2.435372 TTGCAAGGAACAAGGACAGT 57.565 45.000 0.00 0.00 0.00 3.55
4501 6416 3.360249 CTTTGCAAGGAACAAGGACAG 57.640 47.619 1.58 0.00 0.00 3.51
4513 6428 5.990996 ACAAACCATTTCATACCTTTGCAAG 59.009 36.000 0.00 0.00 0.00 4.01
4514 6429 5.923204 ACAAACCATTTCATACCTTTGCAA 58.077 33.333 0.00 0.00 0.00 4.08
4515 6430 5.543507 ACAAACCATTTCATACCTTTGCA 57.456 34.783 0.00 0.00 0.00 4.08
4516 6431 7.655732 AGTTTACAAACCATTTCATACCTTTGC 59.344 33.333 1.27 0.00 39.71 3.68
4517 6432 8.977505 CAGTTTACAAACCATTTCATACCTTTG 58.022 33.333 1.27 0.00 39.71 2.77
4518 6433 8.700973 ACAGTTTACAAACCATTTCATACCTTT 58.299 29.630 1.27 0.00 39.71 3.11
4519 6434 8.141268 CACAGTTTACAAACCATTTCATACCTT 58.859 33.333 1.27 0.00 39.71 3.50
4520 6435 7.286775 ACACAGTTTACAAACCATTTCATACCT 59.713 33.333 1.27 0.00 39.71 3.08
4521 6436 7.430441 ACACAGTTTACAAACCATTTCATACC 58.570 34.615 1.27 0.00 39.71 2.73
4524 6439 8.087750 CCATACACAGTTTACAAACCATTTCAT 58.912 33.333 1.27 0.00 39.71 2.57
4525 6440 7.429633 CCATACACAGTTTACAAACCATTTCA 58.570 34.615 1.27 0.00 39.71 2.69
4526 6441 6.364976 GCCATACACAGTTTACAAACCATTTC 59.635 38.462 1.27 0.00 39.71 2.17
4527 6442 6.041523 AGCCATACACAGTTTACAAACCATTT 59.958 34.615 1.27 0.00 39.71 2.32
4528 6443 5.538433 AGCCATACACAGTTTACAAACCATT 59.462 36.000 1.27 0.00 39.71 3.16
4529 6444 5.076873 AGCCATACACAGTTTACAAACCAT 58.923 37.500 1.27 0.00 39.71 3.55
4530 6445 4.465886 AGCCATACACAGTTTACAAACCA 58.534 39.130 1.27 0.00 39.71 3.67
4531 6446 5.219633 CAAGCCATACACAGTTTACAAACC 58.780 41.667 1.27 0.00 39.71 3.27
4532 6447 5.827666 ACAAGCCATACACAGTTTACAAAC 58.172 37.500 0.00 0.00 39.17 2.93
4533 6448 6.269315 CAACAAGCCATACACAGTTTACAAA 58.731 36.000 0.00 0.00 0.00 2.83
4534 6449 5.734786 GCAACAAGCCATACACAGTTTACAA 60.735 40.000 0.00 0.00 37.23 2.41
4535 6450 4.261405 GCAACAAGCCATACACAGTTTACA 60.261 41.667 0.00 0.00 37.23 2.41
4536 6451 4.226761 GCAACAAGCCATACACAGTTTAC 58.773 43.478 0.00 0.00 37.23 2.01
4537 6452 4.497473 GCAACAAGCCATACACAGTTTA 57.503 40.909 0.00 0.00 37.23 2.01
4538 6453 3.369546 GCAACAAGCCATACACAGTTT 57.630 42.857 0.00 0.00 37.23 2.66
4550 6465 2.925563 GCATATTTGGTCAGCAACAAGC 59.074 45.455 0.00 0.00 46.19 4.01
4551 6466 4.171005 CAGCATATTTGGTCAGCAACAAG 58.829 43.478 0.00 0.00 0.00 3.16
4552 6467 3.573538 ACAGCATATTTGGTCAGCAACAA 59.426 39.130 0.00 0.00 0.00 2.83
4553 6468 3.156293 ACAGCATATTTGGTCAGCAACA 58.844 40.909 0.00 0.00 0.00 3.33
4554 6469 3.855689 ACAGCATATTTGGTCAGCAAC 57.144 42.857 0.00 0.00 0.00 4.17
4555 6470 4.870123 AAACAGCATATTTGGTCAGCAA 57.130 36.364 0.00 0.00 0.00 3.91
4556 6471 4.870123 AAAACAGCATATTTGGTCAGCA 57.130 36.364 0.00 0.00 0.00 4.41
4557 6472 5.576774 GGTTAAAACAGCATATTTGGTCAGC 59.423 40.000 0.00 0.00 0.00 4.26
4558 6473 6.808212 CAGGTTAAAACAGCATATTTGGTCAG 59.192 38.462 0.00 0.00 0.00 3.51
4559 6474 6.491745 TCAGGTTAAAACAGCATATTTGGTCA 59.508 34.615 0.00 0.00 0.00 4.02
4560 6475 6.919721 TCAGGTTAAAACAGCATATTTGGTC 58.080 36.000 0.00 0.00 0.00 4.02
4561 6476 6.909550 TCAGGTTAAAACAGCATATTTGGT 57.090 33.333 0.00 0.00 0.00 3.67
4562 6477 8.776376 ATTTCAGGTTAAAACAGCATATTTGG 57.224 30.769 0.00 0.00 0.00 3.28
4633 6548 7.389053 GGTCTGAGTAAGATGTGAGAAAAATGT 59.611 37.037 0.00 0.00 37.23 2.71
4640 6555 4.323569 AGGGTCTGAGTAAGATGTGAGA 57.676 45.455 0.00 0.00 37.23 3.27


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

AutoCloner maintained by Alex Coulton.