Multiple sequence alignment - TraesCS3D01G312800

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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 TraesCS3D01G312800 chr3D 100.000 8621 0 0 1 8621 427209204 427217824 0.000000e+00 15921.0
1 TraesCS3D01G312800 chr3D 89.583 48 3 2 5523 5569 590583480 590583434 9.350000e-05 60.2
2 TraesCS3D01G312800 chr3B 93.475 4276 189 38 432 4663 556859971 556864200 0.000000e+00 6268.0
3 TraesCS3D01G312800 chr3B 89.917 3253 192 63 5173 8347 556864647 556867841 0.000000e+00 4065.0
4 TraesCS3D01G312800 chr3B 93.570 451 22 3 4699 5143 556864199 556864648 0.000000e+00 665.0
5 TraesCS3D01G312800 chr3B 91.513 271 20 3 1 271 556853258 556853525 3.800000e-98 370.0
6 TraesCS3D01G312800 chr3B 95.238 84 3 1 332 415 556859753 556859835 1.950000e-26 132.0
7 TraesCS3D01G312800 chr3A 93.456 4080 123 46 68 4068 559545506 559541492 0.000000e+00 5923.0
8 TraesCS3D01G312800 chr3A 92.662 1758 82 14 5650 7387 559540442 559538712 0.000000e+00 2488.0
9 TraesCS3D01G312800 chr3A 95.740 1244 40 8 7383 8621 559538665 559537430 0.000000e+00 1991.0
10 TraesCS3D01G312800 chr3A 90.976 676 37 6 4699 5365 559541355 559540695 0.000000e+00 889.0
11 TraesCS3D01G312800 chr3A 87.654 162 15 3 6329 6490 1120216 1120372 5.320000e-42 183.0
12 TraesCS3D01G312800 chr3A 98.684 76 1 0 1 76 559545735 559545660 1.510000e-27 135.0
13 TraesCS3D01G312800 chr3A 92.391 92 7 0 5443 5534 559540547 559540456 1.950000e-26 132.0
14 TraesCS3D01G312800 chr6D 93.676 680 32 8 2477 3151 463220886 463220213 0.000000e+00 1007.0
15 TraesCS3D01G312800 chr2D 88.679 159 13 3 6332 6490 22253504 22253351 1.140000e-43 189.0
16 TraesCS3D01G312800 chr2B 87.037 162 16 3 6329 6490 148030642 148030798 2.470000e-40 178.0
17 TraesCS3D01G312800 chr2B 88.158 76 5 4 5523 5596 780813707 780813634 4.290000e-13 87.9
18 TraesCS3D01G312800 chr1A 80.932 236 28 9 5450 5669 247333228 247333462 4.140000e-38 171.0
19 TraesCS3D01G312800 chr5B 83.974 156 18 6 5498 5649 659594515 659594363 9.020000e-30 143.0
20 TraesCS3D01G312800 chr7B 81.564 179 24 5 5498 5668 524521370 524521193 1.170000e-28 139.0
21 TraesCS3D01G312800 chr5D 81.290 155 22 6 5498 5649 480207240 480207390 1.520000e-22 119.0
22 TraesCS3D01G312800 chr1D 83.673 98 11 2 124 221 370523111 370523019 4.290000e-13 87.9


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 TraesCS3D01G312800 chr3D 427209204 427217824 8620 False 15921.000000 15921 100.000000 1 8621 1 chr3D.!!$F1 8620
1 TraesCS3D01G312800 chr3B 556859753 556867841 8088 False 2782.500000 6268 93.050000 332 8347 4 chr3B.!!$F2 8015
2 TraesCS3D01G312800 chr3A 559537430 559545735 8305 True 1926.333333 5923 93.984833 1 8621 6 chr3A.!!$R1 8620
3 TraesCS3D01G312800 chr6D 463220213 463220886 673 True 1007.000000 1007 93.676000 2477 3151 1 chr6D.!!$R1 674

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
429 594 2.283472 ATTCCGCAGCCGCCATTTTC 62.283 55.000 0.00 0.00 33.11 2.29 F
1604 1961 2.269241 GGCTGGCAGGTCACCTAC 59.731 66.667 17.64 0.00 29.64 3.18 F
1626 1983 0.117340 ACTAGGAGCCACCCTCTTGT 59.883 55.000 0.00 0.00 40.57 3.16 F
2679 3037 1.207089 TCATTAGGTGTGGCCTCTTCG 59.793 52.381 3.32 0.00 46.96 3.79 F
4042 4417 0.171679 ATGTGTGCGTGCCATCATTG 59.828 50.000 0.00 0.00 0.00 2.82 F
4675 5065 0.441533 GCTGCTGATTGACACTGACG 59.558 55.000 0.00 0.00 0.00 4.35 F
5145 5549 0.108472 CTTGCGATCTGGACAGCTGA 60.108 55.000 23.35 0.00 0.00 4.26 F
5146 5550 0.321346 TTGCGATCTGGACAGCTGAA 59.679 50.000 23.35 4.44 0.00 3.02 F
5147 5551 0.538584 TGCGATCTGGACAGCTGAAT 59.461 50.000 23.35 0.00 0.00 2.57 F
5337 5751 0.810031 GTATCCATGTTGTCGCCGCT 60.810 55.000 0.00 0.00 0.00 5.52 F
5612 6097 1.017387 CTATGCCCCAAAACGAGCTC 58.983 55.000 2.73 2.73 0.00 4.09 F
5669 6159 1.341209 CCACAAAAGAACTGGCCCTTC 59.659 52.381 0.00 0.42 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1624 1981 1.153249 GCACCTAGGCGGCAATACA 60.153 57.895 18.49 0.00 35.61 2.29 R
2679 3037 1.476891 TGACACTTGCCTAGTCCGATC 59.523 52.381 0.00 0.00 33.85 3.69 R
3559 3924 2.102578 GGCCCAAGATACAGCACAAAT 58.897 47.619 0.00 0.00 0.00 2.32 R
4394 4770 1.492993 AAGCTGGAGGGACAGGAACC 61.493 60.000 0.00 0.00 38.90 3.62 R
5003 5407 0.731417 CAAGTCATGGCTGCTGCTAC 59.269 55.000 15.64 8.75 39.59 3.58 R
5874 6366 1.194547 GTTGCAGATTTCGAGAACGCA 59.805 47.619 0.00 0.00 39.58 5.24 R
6701 7207 1.447099 TGCTTGGGTTGTAGGGGTAA 58.553 50.000 0.00 0.00 0.00 2.85 R
6717 7229 2.884639 AGGTCGCAACTACAATTTTGCT 59.115 40.909 10.08 0.00 44.94 3.91 R
6835 7369 6.160684 TGATGCAAGCATTAATGGCATTATC 58.839 36.000 23.12 15.82 44.52 1.75 R
7334 7872 3.136443 TCCATTTGTGAAGGTGAGACTGT 59.864 43.478 0.00 0.00 0.00 3.55 R
7467 8059 4.008074 CACTACAGTGTTCCAGACCAAT 57.992 45.455 0.00 0.00 40.96 3.16 R
7860 8472 6.840780 AACAATCCCTAAAGTTCATCCAAG 57.159 37.500 0.00 0.00 0.00 3.61 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
27 28 7.543172 CCATCGAAACTTGATTCACAAATGATT 59.457 33.333 0.00 0.00 38.08 2.57
76 77 5.526115 ACATGTTCTGATTGCTCTTTGTTG 58.474 37.500 0.00 0.00 0.00 3.33
78 79 3.318839 TGTTCTGATTGCTCTTTGTTGGG 59.681 43.478 0.00 0.00 0.00 4.12
416 581 2.298163 TCTTCCCCGTATTCTATTCCGC 59.702 50.000 0.00 0.00 0.00 5.54
429 594 2.283472 ATTCCGCAGCCGCCATTTTC 62.283 55.000 0.00 0.00 33.11 2.29
540 834 3.462678 GTCTCCCTCCCGCTCACC 61.463 72.222 0.00 0.00 0.00 4.02
655 949 4.315264 AAACCAATGGGCCCCGCT 62.315 61.111 22.27 0.00 37.90 5.52
656 950 2.925117 AAACCAATGGGCCCCGCTA 61.925 57.895 22.27 0.00 37.90 4.26
671 965 4.479993 CTAGCAGCGCCAGCCCTT 62.480 66.667 17.61 3.68 46.67 3.95
672 966 3.984193 CTAGCAGCGCCAGCCCTTT 62.984 63.158 17.61 3.34 46.67 3.11
1524 1881 8.999431 GTTTCCTTCAGTACTTGATACATCAAA 58.001 33.333 6.15 0.00 45.26 2.69
1596 1953 3.918253 TTTACAGGCGGCTGGCAGG 62.918 63.158 37.97 17.17 46.16 4.85
1604 1961 2.269241 GGCTGGCAGGTCACCTAC 59.731 66.667 17.64 0.00 29.64 3.18
1624 1981 1.268283 GCACTAGGAGCCACCCTCTT 61.268 60.000 0.00 0.00 40.57 2.85
1626 1983 0.117340 ACTAGGAGCCACCCTCTTGT 59.883 55.000 0.00 0.00 40.57 3.16
1715 2072 5.767816 AACACTTGTGATAAAACCTGGTC 57.232 39.130 7.83 0.00 0.00 4.02
1716 2073 4.787551 ACACTTGTGATAAAACCTGGTCA 58.212 39.130 7.83 0.00 0.00 4.02
1839 2196 5.059833 GCTGGATATCTAAGTTGGTTCTGG 58.940 45.833 2.05 0.00 0.00 3.86
1930 2287 9.753674 ATCAAGTCCTTCCAATTTACTATTTGA 57.246 29.630 0.00 0.00 0.00 2.69
2264 2622 8.856490 AATTTGAAGTGACATACTGTGTTTTC 57.144 30.769 0.00 0.00 42.36 2.29
2444 2802 6.378710 AAGAGCTTTGTTTGTTCTCCTAAC 57.621 37.500 0.00 0.00 0.00 2.34
2679 3037 1.207089 TCATTAGGTGTGGCCTCTTCG 59.793 52.381 3.32 0.00 46.96 3.79
2748 3106 9.520515 AGTGTGATCACATAAAATAAAGGAAGT 57.479 29.630 30.10 3.37 46.01 3.01
3054 3416 3.625649 AATTGGAGAGGAGAGCAAGAC 57.374 47.619 0.00 0.00 0.00 3.01
3056 3418 1.554836 TGGAGAGGAGAGCAAGACTG 58.445 55.000 0.00 0.00 0.00 3.51
3060 3422 1.617850 AGAGGAGAGCAAGACTGTGTG 59.382 52.381 0.00 0.00 0.00 3.82
3096 3458 5.531287 AGAAGTTGTGACATTTTAGGGTGTC 59.469 40.000 0.00 0.00 43.81 3.67
3097 3459 4.142038 AGTTGTGACATTTTAGGGTGTCC 58.858 43.478 3.38 0.00 43.09 4.02
3143 3505 2.949644 GTGTGGCACTAAGACAACCTTT 59.050 45.455 19.83 0.00 36.65 3.11
3303 3665 7.669427 AGGCAAAATGTGAGAACAATATTTGA 58.331 30.769 14.18 0.00 31.58 2.69
3559 3924 1.885887 GCAGGTTCAGGTTTGCATACA 59.114 47.619 9.57 0.00 36.59 2.29
3859 4224 2.819608 ACGAGCTGGTAATTGTGCAATT 59.180 40.909 13.68 13.68 42.95 2.32
3957 4324 7.959651 GTGCAGATAATGTTAGTTCTTTCTGTG 59.040 37.037 0.00 0.00 0.00 3.66
3996 4363 8.150945 TGATTTCCCTTGAACACTATCTATAGC 58.849 37.037 0.00 0.00 33.68 2.97
4030 4397 7.821595 TTACTGTACTATGTAACATGTGTGC 57.178 36.000 0.00 0.00 0.00 4.57
4042 4417 0.171679 ATGTGTGCGTGCCATCATTG 59.828 50.000 0.00 0.00 0.00 2.82
4059 4434 7.972277 GCCATCATTGTTATATCCATTTAGCTG 59.028 37.037 0.00 0.00 0.00 4.24
4069 4444 3.686016 TCCATTTAGCTGTTGTCCCTTC 58.314 45.455 0.00 0.00 0.00 3.46
4070 4445 2.755103 CCATTTAGCTGTTGTCCCTTCC 59.245 50.000 0.00 0.00 0.00 3.46
4120 4496 0.953727 TGGAGCACTTGCACATTGTC 59.046 50.000 3.62 0.00 45.16 3.18
4125 4501 1.725931 GCACTTGCACATTGTCGTAGC 60.726 52.381 0.00 0.00 41.59 3.58
4130 4506 3.469899 TGCACATTGTCGTAGCATTTC 57.530 42.857 0.00 0.00 0.00 2.17
4140 4516 6.117911 TGTCGTAGCATTTCATGGTTATTG 57.882 37.500 0.00 0.00 41.83 1.90
4154 4530 8.421249 TCATGGTTATTGTTCATTTTCCTCTT 57.579 30.769 0.00 0.00 0.00 2.85
4212 4588 8.682936 AAACAGTACTCATTTCATTCTCAGTT 57.317 30.769 0.00 0.00 0.00 3.16
4213 4589 7.897575 ACAGTACTCATTTCATTCTCAGTTC 57.102 36.000 0.00 0.00 0.00 3.01
4214 4590 7.675062 ACAGTACTCATTTCATTCTCAGTTCT 58.325 34.615 0.00 0.00 0.00 3.01
4215 4591 7.816995 ACAGTACTCATTTCATTCTCAGTTCTC 59.183 37.037 0.00 0.00 0.00 2.87
4216 4592 7.816513 CAGTACTCATTTCATTCTCAGTTCTCA 59.183 37.037 0.00 0.00 0.00 3.27
4217 4593 8.034215 AGTACTCATTTCATTCTCAGTTCTCAG 58.966 37.037 0.00 0.00 0.00 3.35
4218 4594 6.767456 ACTCATTTCATTCTCAGTTCTCAGT 58.233 36.000 0.00 0.00 0.00 3.41
4275 4651 6.993786 TTTGTCACTAGTCATGTTTTGTGA 57.006 33.333 0.00 10.46 32.91 3.58
4291 4667 2.183679 TGTGAAACTTTGGGCCAGTTT 58.816 42.857 20.19 20.19 45.28 2.66
4339 4715 4.583871 CTCCTGTGAAAATAAGCCTCAGT 58.416 43.478 0.00 0.00 0.00 3.41
4373 4749 6.894654 TGTGGAAATAAGCCCATGAGAATAAA 59.105 34.615 0.00 0.00 34.58 1.40
4374 4750 7.564660 TGTGGAAATAAGCCCATGAGAATAAAT 59.435 33.333 0.00 0.00 34.58 1.40
4375 4751 9.077885 GTGGAAATAAGCCCATGAGAATAAATA 57.922 33.333 0.00 0.00 34.58 1.40
4376 4752 9.653516 TGGAAATAAGCCCATGAGAATAAATAA 57.346 29.630 0.00 0.00 0.00 1.40
4379 4755 8.946797 AATAAGCCCATGAGAATAAATAAGCT 57.053 30.769 0.00 0.00 0.00 3.74
4389 4765 9.817809 ATGAGAATAAATAAGCTAACGAGTTCA 57.182 29.630 0.00 0.00 0.00 3.18
4399 4775 4.215613 AGCTAACGAGTTCATTTTGGTTCC 59.784 41.667 0.00 0.00 0.00 3.62
4462 4838 5.365605 TCTGTAATACCCCTGGACTGTATTG 59.634 44.000 18.38 8.54 36.25 1.90
4481 4857 8.846943 TGTATTGTTCTGATATTCAGTTGTGT 57.153 30.769 4.56 0.00 44.58 3.72
4487 4863 9.337396 TGTTCTGATATTCAGTTGTGTTTTAGT 57.663 29.630 4.56 0.00 44.58 2.24
4517 4893 5.402270 GTCGCCCATATGAACATAAAATTGC 59.598 40.000 3.65 0.00 0.00 3.56
4552 4928 7.765819 ACATCATGAAATGTTAGTCGAAGATCA 59.234 33.333 0.00 0.00 46.80 2.92
4553 4929 7.761651 TCATGAAATGTTAGTCGAAGATCAG 57.238 36.000 0.00 0.00 46.80 2.90
4564 4940 4.687948 AGTCGAAGATCAGTTTGTCACATG 59.312 41.667 0.00 0.00 40.67 3.21
4613 4989 7.164122 ACAAACATCATTGTCTCACATAGAGT 58.836 34.615 0.00 0.00 39.23 3.24
4663 5053 3.540617 TGTAGAAAAGTTGTGCTGCTGA 58.459 40.909 0.00 0.00 0.00 4.26
4664 5054 4.136796 TGTAGAAAAGTTGTGCTGCTGAT 58.863 39.130 0.00 0.00 0.00 2.90
4665 5055 4.580167 TGTAGAAAAGTTGTGCTGCTGATT 59.420 37.500 0.00 0.00 0.00 2.57
4666 5056 3.973657 AGAAAAGTTGTGCTGCTGATTG 58.026 40.909 0.00 0.00 0.00 2.67
4667 5057 3.633525 AGAAAAGTTGTGCTGCTGATTGA 59.366 39.130 0.00 0.00 0.00 2.57
4668 5058 3.360249 AAAGTTGTGCTGCTGATTGAC 57.640 42.857 0.00 0.00 0.00 3.18
4669 5059 1.971481 AGTTGTGCTGCTGATTGACA 58.029 45.000 0.00 0.00 0.00 3.58
4670 5060 1.605710 AGTTGTGCTGCTGATTGACAC 59.394 47.619 0.00 0.00 0.00 3.67
4671 5061 1.605710 GTTGTGCTGCTGATTGACACT 59.394 47.619 0.00 0.00 32.49 3.55
4672 5062 1.232119 TGTGCTGCTGATTGACACTG 58.768 50.000 0.00 0.00 32.49 3.66
4673 5063 1.202675 TGTGCTGCTGATTGACACTGA 60.203 47.619 0.00 0.00 32.49 3.41
4674 5064 1.196354 GTGCTGCTGATTGACACTGAC 59.804 52.381 0.00 0.00 0.00 3.51
4675 5065 0.441533 GCTGCTGATTGACACTGACG 59.558 55.000 0.00 0.00 0.00 4.35
4676 5066 1.936656 GCTGCTGATTGACACTGACGA 60.937 52.381 0.00 0.00 0.00 4.20
4677 5067 2.407090 CTGCTGATTGACACTGACGAA 58.593 47.619 0.00 0.00 0.00 3.85
4678 5068 2.802247 CTGCTGATTGACACTGACGAAA 59.198 45.455 0.00 0.00 0.00 3.46
4679 5069 2.543848 TGCTGATTGACACTGACGAAAC 59.456 45.455 0.00 0.00 0.00 2.78
4680 5070 2.802816 GCTGATTGACACTGACGAAACT 59.197 45.455 0.00 0.00 0.00 2.66
4681 5071 3.363378 GCTGATTGACACTGACGAAACTG 60.363 47.826 0.00 0.00 0.00 3.16
4682 5072 4.051237 CTGATTGACACTGACGAAACTGA 58.949 43.478 0.00 0.00 0.00 3.41
4683 5073 4.438148 TGATTGACACTGACGAAACTGAA 58.562 39.130 0.00 0.00 0.00 3.02
4684 5074 4.270084 TGATTGACACTGACGAAACTGAAC 59.730 41.667 0.00 0.00 0.00 3.18
4685 5075 3.239587 TGACACTGACGAAACTGAACA 57.760 42.857 0.00 0.00 0.00 3.18
4686 5076 2.927477 TGACACTGACGAAACTGAACAC 59.073 45.455 0.00 0.00 0.00 3.32
4687 5077 3.187700 GACACTGACGAAACTGAACACT 58.812 45.455 0.00 0.00 0.00 3.55
4688 5078 3.187700 ACACTGACGAAACTGAACACTC 58.812 45.455 0.00 0.00 0.00 3.51
4689 5079 3.119101 ACACTGACGAAACTGAACACTCT 60.119 43.478 0.00 0.00 0.00 3.24
4690 5080 3.243877 CACTGACGAAACTGAACACTCTG 59.756 47.826 0.00 0.00 0.00 3.35
4691 5081 3.130516 ACTGACGAAACTGAACACTCTGA 59.869 43.478 0.00 0.00 0.00 3.27
4692 5082 4.112634 CTGACGAAACTGAACACTCTGAA 58.887 43.478 0.00 0.00 0.00 3.02
4693 5083 3.863424 TGACGAAACTGAACACTCTGAAC 59.137 43.478 0.00 0.00 0.00 3.18
4694 5084 3.857052 ACGAAACTGAACACTCTGAACA 58.143 40.909 0.00 0.00 0.00 3.18
4695 5085 4.442706 ACGAAACTGAACACTCTGAACAT 58.557 39.130 0.00 0.00 0.00 2.71
4696 5086 4.508124 ACGAAACTGAACACTCTGAACATC 59.492 41.667 0.00 0.00 0.00 3.06
4697 5087 4.507756 CGAAACTGAACACTCTGAACATCA 59.492 41.667 0.00 0.00 0.00 3.07
4698 5088 5.178252 CGAAACTGAACACTCTGAACATCAT 59.822 40.000 0.00 0.00 0.00 2.45
4699 5089 5.936686 AACTGAACACTCTGAACATCATG 57.063 39.130 0.00 0.00 0.00 3.07
4777 5167 5.036117 AGTGGTTGTTACAGACACTCATT 57.964 39.130 15.01 0.00 37.86 2.57
4786 5176 4.613925 ACAGACACTCATTGACACTGAT 57.386 40.909 0.00 0.00 32.81 2.90
4913 5307 2.428890 CTCCCAGATCCTACACACACTC 59.571 54.545 0.00 0.00 0.00 3.51
4915 5309 2.167281 CCCAGATCCTACACACACTCTG 59.833 54.545 0.00 0.00 0.00 3.35
4956 5360 4.273480 CAGGTACATTAGCAGCACAATACC 59.727 45.833 0.00 0.00 0.00 2.73
4957 5361 4.080582 AGGTACATTAGCAGCACAATACCA 60.081 41.667 12.73 0.00 0.00 3.25
4958 5362 4.638421 GGTACATTAGCAGCACAATACCAA 59.362 41.667 0.00 0.00 0.00 3.67
4959 5363 4.970662 ACATTAGCAGCACAATACCAAG 57.029 40.909 0.00 0.00 0.00 3.61
4960 5364 4.588899 ACATTAGCAGCACAATACCAAGA 58.411 39.130 0.00 0.00 0.00 3.02
4961 5365 5.009631 ACATTAGCAGCACAATACCAAGAA 58.990 37.500 0.00 0.00 0.00 2.52
4962 5366 5.106157 ACATTAGCAGCACAATACCAAGAAC 60.106 40.000 0.00 0.00 0.00 3.01
5003 5407 1.405463 TGGTGCACGCTATCAGTAGAG 59.595 52.381 11.45 0.00 34.34 2.43
5047 5451 1.613317 ATCGGCCCAGAACGTGATCA 61.613 55.000 0.00 0.00 0.00 2.92
5071 5475 3.244764 CAGATCTGCTGGCTTGTGT 57.755 52.632 10.38 0.00 41.07 3.72
5143 5547 1.220206 CCTTGCGATCTGGACAGCT 59.780 57.895 0.00 0.00 0.00 4.24
5144 5548 1.088340 CCTTGCGATCTGGACAGCTG 61.088 60.000 13.48 13.48 0.00 4.24
5145 5549 0.108472 CTTGCGATCTGGACAGCTGA 60.108 55.000 23.35 0.00 0.00 4.26
5146 5550 0.321346 TTGCGATCTGGACAGCTGAA 59.679 50.000 23.35 4.44 0.00 3.02
5147 5551 0.538584 TGCGATCTGGACAGCTGAAT 59.461 50.000 23.35 0.00 0.00 2.57
5148 5552 1.216122 GCGATCTGGACAGCTGAATC 58.784 55.000 23.35 8.41 0.00 2.52
5149 5553 1.863267 CGATCTGGACAGCTGAATCC 58.137 55.000 23.35 18.45 35.37 3.01
5150 5554 1.137675 CGATCTGGACAGCTGAATCCA 59.862 52.381 23.35 22.12 42.88 3.41
5163 5567 3.125376 AATCCAGGGATCCAGGCGC 62.125 63.158 15.23 0.00 33.08 6.53
5166 5570 3.536917 CAGGGATCCAGGCGCGTA 61.537 66.667 15.23 0.00 0.00 4.42
5181 5585 2.357760 GTAGGCGTGCGTTGGGAA 60.358 61.111 0.00 0.00 0.00 3.97
5238 5642 2.392181 CGAGAGGACGAGCGACTGT 61.392 63.158 0.00 0.00 35.09 3.55
5262 5668 2.587247 GCTGGACAGAGGAGTGGCA 61.587 63.158 3.00 0.00 0.00 4.92
5287 5693 3.082701 GCAGAGCAGAGGGAGGCT 61.083 66.667 0.00 0.00 44.48 4.58
5317 5723 1.736645 CGTCTACCCAGCACCAACG 60.737 63.158 0.00 0.00 0.00 4.10
5319 5725 1.839747 TCTACCCAGCACCAACGGT 60.840 57.895 0.00 0.00 35.62 4.83
5328 5734 1.004277 AGCACCAACGGTATCCATGTT 59.996 47.619 0.00 0.00 32.11 2.71
5333 5747 1.062002 CAACGGTATCCATGTTGTCGC 59.938 52.381 0.00 0.00 38.47 5.19
5337 5751 0.810031 GTATCCATGTTGTCGCCGCT 60.810 55.000 0.00 0.00 0.00 5.52
5366 5780 4.162690 GCATCGGGAGGCGAGGTT 62.163 66.667 0.00 0.00 0.00 3.50
5368 5782 2.683933 ATCGGGAGGCGAGGTTGT 60.684 61.111 0.00 0.00 0.00 3.32
5369 5783 2.722201 ATCGGGAGGCGAGGTTGTC 61.722 63.158 0.00 0.00 0.00 3.18
5416 5882 2.870411 GACGGGGAAATCCTATTTCACG 59.130 50.000 18.60 18.60 36.82 4.35
5436 5902 4.150454 AGGAGAGGGGCGAGAGGG 62.150 72.222 0.00 0.00 0.00 4.30
5441 5907 3.117648 AGGGGCGAGAGGGGGATA 61.118 66.667 0.00 0.00 0.00 2.59
5454 5938 2.089350 AGGGGGATAGATAAGGGCAGTT 60.089 50.000 0.00 0.00 0.00 3.16
5544 6028 4.410400 CGGGAAGCTGACCACCCC 62.410 72.222 11.49 0.00 39.20 4.95
5585 6070 2.507471 AGGAGAGGGCTGTGGAAATAAG 59.493 50.000 0.00 0.00 0.00 1.73
5605 6090 4.316025 AGTTAAGCTCTATGCCCCAAAA 57.684 40.909 0.00 0.00 44.23 2.44
5612 6097 1.017387 CTATGCCCCAAAACGAGCTC 58.983 55.000 2.73 2.73 0.00 4.09
5669 6159 1.341209 CCACAAAAGAACTGGCCCTTC 59.659 52.381 0.00 0.42 0.00 3.46
5695 6186 3.811497 GTGGGTAAACAGTACTGGTTCAC 59.189 47.826 28.90 24.46 40.14 3.18
5874 6366 5.782893 TTTTGTAGCAAACCATAGCTTGT 57.217 34.783 0.00 0.00 42.05 3.16
5882 6374 1.726853 ACCATAGCTTGTGCGTTCTC 58.273 50.000 0.00 0.00 45.42 2.87
5915 6407 5.878406 ACCTTCATTATCTCGAGGTTCAT 57.122 39.130 13.56 0.66 37.44 2.57
5995 6487 5.057149 GGAAGTGAGTTAGAAGCTGTCAAA 58.943 41.667 0.00 0.00 0.00 2.69
6164 6656 9.959775 GAATCTTTGAGTAACGATTTCTTACAG 57.040 33.333 0.00 0.00 35.61 2.74
6247 6739 6.405397 GCTTCGGCCCTAATTTTTCTATTTGA 60.405 38.462 0.00 0.00 34.32 2.69
6268 6765 3.804786 TGCCATGCTAATTGGACATTG 57.195 42.857 0.00 0.00 36.26 2.82
6271 6768 4.114794 GCCATGCTAATTGGACATTGTTC 58.885 43.478 0.00 0.00 36.26 3.18
6474 6971 9.551734 CATCATCAAGACTCATATTCAGGTTTA 57.448 33.333 0.00 0.00 0.00 2.01
6506 7004 6.966435 ACATTTTATTGAAAAATCCTGGCG 57.034 33.333 0.00 0.00 38.04 5.69
6529 7027 7.081976 GCGTTAATTTGTGTTTCTCTTGGTAT 58.918 34.615 0.00 0.00 0.00 2.73
6592 7091 3.636153 ACCAGTCTGCTTTAAGATCCC 57.364 47.619 0.00 0.00 0.00 3.85
6659 7165 8.999431 ACATACTTTACGTGATCATGTCTTTTT 58.001 29.630 23.61 8.71 0.00 1.94
6678 7184 6.887545 TCTTTTTGGTTCTGTCCAGTTAGAAA 59.112 34.615 0.00 0.00 38.80 2.52
6717 7229 2.784682 ACAAGTTACCCCTACAACCCAA 59.215 45.455 0.00 0.00 0.00 4.12
6744 7256 2.004583 TGTAGTTGCGACCTACATGC 57.995 50.000 0.00 0.00 0.00 4.06
6775 7309 6.047231 TGATTATTCTGTGTGATCTCTGCAG 58.953 40.000 7.63 7.63 0.00 4.41
6776 7310 5.665916 TTATTCTGTGTGATCTCTGCAGA 57.334 39.130 17.19 17.19 34.80 4.26
6777 7311 4.548451 ATTCTGTGTGATCTCTGCAGAA 57.452 40.909 18.85 23.69 46.03 3.02
6778 7312 4.548451 TTCTGTGTGATCTCTGCAGAAT 57.452 40.909 18.85 13.72 40.07 2.40
6779 7313 5.665916 TTCTGTGTGATCTCTGCAGAATA 57.334 39.130 18.85 9.42 40.07 1.75
6780 7314 5.866159 TCTGTGTGATCTCTGCAGAATAT 57.134 39.130 18.85 14.03 33.84 1.28
6781 7315 5.598769 TCTGTGTGATCTCTGCAGAATATG 58.401 41.667 18.85 6.09 33.84 1.78
6782 7316 4.700700 TGTGTGATCTCTGCAGAATATGG 58.299 43.478 18.85 5.68 30.24 2.74
6783 7317 4.162888 TGTGTGATCTCTGCAGAATATGGT 59.837 41.667 18.85 1.38 30.24 3.55
6784 7318 4.510711 GTGTGATCTCTGCAGAATATGGTG 59.489 45.833 18.85 4.10 30.24 4.17
6785 7319 4.162888 TGTGATCTCTGCAGAATATGGTGT 59.837 41.667 18.85 0.00 30.24 4.16
6786 7320 4.510711 GTGATCTCTGCAGAATATGGTGTG 59.489 45.833 18.85 2.53 30.24 3.82
6787 7321 4.406649 TGATCTCTGCAGAATATGGTGTGA 59.593 41.667 18.85 8.39 30.24 3.58
6788 7322 4.824479 TCTCTGCAGAATATGGTGTGAA 57.176 40.909 18.85 0.00 0.00 3.18
6789 7323 5.363562 TCTCTGCAGAATATGGTGTGAAT 57.636 39.130 18.85 0.00 0.00 2.57
6790 7324 5.748402 TCTCTGCAGAATATGGTGTGAATT 58.252 37.500 18.85 0.00 0.00 2.17
6791 7325 5.587443 TCTCTGCAGAATATGGTGTGAATTG 59.413 40.000 18.85 0.00 0.00 2.32
6792 7326 5.255687 TCTGCAGAATATGGTGTGAATTGT 58.744 37.500 15.67 0.00 0.00 2.71
6793 7327 6.413892 TCTGCAGAATATGGTGTGAATTGTA 58.586 36.000 15.67 0.00 0.00 2.41
6794 7328 7.056006 TCTGCAGAATATGGTGTGAATTGTAT 58.944 34.615 15.67 0.00 0.00 2.29
6795 7329 7.227314 TCTGCAGAATATGGTGTGAATTGTATC 59.773 37.037 15.67 0.00 0.00 2.24
6796 7330 6.827762 TGCAGAATATGGTGTGAATTGTATCA 59.172 34.615 0.00 0.00 0.00 2.15
6860 7394 3.446310 TGCCATTAATGCTTGCATCAG 57.554 42.857 10.11 0.11 0.00 2.90
6900 7434 4.176271 GCCATACCAATTGCTGTTTCTTC 58.824 43.478 0.00 0.00 0.00 2.87
6902 7436 5.125417 GCCATACCAATTGCTGTTTCTTCTA 59.875 40.000 0.00 0.00 0.00 2.10
6960 7498 8.149973 TCCTCACAACAGAATAAACAAACTAC 57.850 34.615 0.00 0.00 0.00 2.73
6961 7499 7.771361 TCCTCACAACAGAATAAACAAACTACA 59.229 33.333 0.00 0.00 0.00 2.74
6997 7535 4.831107 TGCTTCTTTTTGTGCTCCTTTTT 58.169 34.783 0.00 0.00 0.00 1.94
7041 7579 9.588096 AACTTAGGTGGAAAACTATCAATTTCT 57.412 29.630 0.00 0.00 36.15 2.52
7207 7745 3.684305 TCATCTCGTTATGCAACAACCAG 59.316 43.478 8.49 6.05 34.05 4.00
7432 8024 6.785488 TCATTGATGTTCTGTAACTGTCAC 57.215 37.500 0.00 0.00 36.51 3.67
7467 8059 5.596836 AACAGTGGAATTTCTCTTTTGCA 57.403 34.783 0.00 0.00 0.00 4.08
7860 8472 2.986479 CTGTTATTTTTCAGGCGCCAAC 59.014 45.455 31.54 21.06 0.00 3.77
8062 8675 2.158943 GGAGCCAGCTAGATTTAACGGT 60.159 50.000 0.00 0.00 0.00 4.83
8086 8699 4.318121 GCACTTCAACTACAAGTTCACTCG 60.318 45.833 0.00 0.00 36.03 4.18
8206 8836 4.149598 TGTTACCTTGTGACTAGCTCAGA 58.850 43.478 0.00 0.00 0.00 3.27
8231 8861 3.760684 GGGAAACTTGTGATTCTCAGCAT 59.239 43.478 0.00 0.00 0.00 3.79
8249 8879 5.097529 CAGCATTCACGTTATCTTTTGCAT 58.902 37.500 0.00 0.00 0.00 3.96
8355 8986 8.501580 CGATTACACATCATCAGCAGATAAAAT 58.498 33.333 0.00 0.00 31.88 1.82
8358 8989 7.400599 ACACATCATCAGCAGATAAAATTGT 57.599 32.000 0.00 0.00 31.88 2.71
8397 9028 1.985460 TACACCCGCCCAAGTGTTGT 61.985 55.000 0.62 0.00 44.65 3.32
8437 9068 1.371558 GGGCAGTTGTCCGAGTTCT 59.628 57.895 0.00 0.00 0.00 3.01
8511 9142 2.338257 CACACGCGGGGCAAATTT 59.662 55.556 15.46 0.00 0.00 1.82
8515 9146 2.202427 CGCGGGGCAAATTTCGTC 60.202 61.111 0.00 0.00 0.00 4.20
8516 9147 2.958576 GCGGGGCAAATTTCGTCA 59.041 55.556 0.00 0.00 0.00 4.35
8532 9163 1.062148 CGTCAAGATACTCGAGCACGA 59.938 52.381 13.61 6.00 46.56 4.35
8545 9176 2.651361 CACGAGACTCCAAGGCGT 59.349 61.111 0.00 0.00 35.33 5.68
8564 9195 0.973632 TGTCCTCGTGTACATTGCCT 59.026 50.000 0.00 0.00 0.00 4.75
8565 9196 1.346395 TGTCCTCGTGTACATTGCCTT 59.654 47.619 0.00 0.00 0.00 4.35
8566 9197 2.224426 TGTCCTCGTGTACATTGCCTTT 60.224 45.455 0.00 0.00 0.00 3.11
8567 9198 2.812011 GTCCTCGTGTACATTGCCTTTT 59.188 45.455 0.00 0.00 0.00 2.27
8592 9223 1.203928 CAAAGGCGATCTCTACTGCG 58.796 55.000 0.00 0.00 0.00 5.18
8599 9230 1.071107 CGATCTCTACTGCGACGAGAC 60.071 57.143 0.00 0.00 36.70 3.36
8606 9237 0.741574 ACTGCGACGAGACGAGAGAT 60.742 55.000 0.00 0.00 35.09 2.75
8609 9240 0.315544 GCGACGAGACGAGAGATCAC 60.316 60.000 0.00 0.00 35.09 3.06
8616 9247 3.487711 CGAGACGAGAGATCACCGATTTT 60.488 47.826 8.11 0.00 0.00 1.82
8617 9248 4.035278 AGACGAGAGATCACCGATTTTC 57.965 45.455 8.11 0.00 0.00 2.29
8618 9249 3.697045 AGACGAGAGATCACCGATTTTCT 59.303 43.478 8.11 0.00 0.00 2.52
8620 9251 5.357314 AGACGAGAGATCACCGATTTTCTAA 59.643 40.000 8.11 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 6.096036 TGTTTTTCGAACAAAGAGCAATCAA 58.904 32.000 0.00 0.00 0.00 2.57
76 77 6.260714 AGCAATCAGAAAATGTTTGTTTTCCC 59.739 34.615 8.11 0.00 45.01 3.97
78 79 7.127686 CCAGCAATCAGAAAATGTTTGTTTTC 58.872 34.615 4.42 4.42 44.51 2.29
334 499 4.129148 CCAGCAACTAGGGGGCCC 62.129 72.222 15.76 15.76 0.00 5.80
335 500 3.339093 ACCAGCAACTAGGGGGCC 61.339 66.667 0.00 0.00 0.00 5.80
416 581 1.672737 GGAAAAGGAAAATGGCGGCTG 60.673 52.381 11.43 0.00 0.00 4.85
429 594 2.956987 CGCACTGCTGGGAAAAGG 59.043 61.111 0.00 0.00 31.89 3.11
623 917 1.006571 GTTTGTCTCGTCTGGCGGA 60.007 57.895 0.30 0.00 41.72 5.54
655 949 3.567579 AAAAGGGCTGGCGCTGCTA 62.568 57.895 20.97 0.80 39.23 3.49
656 950 4.982701 AAAAGGGCTGGCGCTGCT 62.983 61.111 20.97 1.38 39.23 4.24
672 966 1.824045 CGCCCTTTAGGTGGGGAAAAA 60.824 52.381 1.80 0.00 45.18 1.94
677 971 2.590092 CTCGCCCTTTAGGTGGGG 59.410 66.667 0.00 0.00 43.66 4.96
682 976 1.123928 ATCTGGACTCGCCCTTTAGG 58.876 55.000 0.00 0.00 39.47 2.69
786 1096 4.322385 GTCGCGCGGCCTGTTTTT 62.322 61.111 31.69 0.00 0.00 1.94
903 1225 3.144193 CTCGAAGCTCCTCCCGCT 61.144 66.667 0.00 0.00 39.94 5.52
1233 1558 3.701532 AATAGCTGACGTCTAGCACTC 57.298 47.619 29.03 10.59 43.53 3.51
1385 1736 3.484721 GCTATAGCGCATGTGCACATATG 60.485 47.826 30.92 24.96 42.21 1.78
1414 1768 8.779354 AACACTTCTACCTCATTACTCAAATC 57.221 34.615 0.00 0.00 0.00 2.17
1477 1834 7.987458 GGAAACAGACATCCAATCAGAGTATAA 59.013 37.037 0.00 0.00 35.71 0.98
1524 1881 3.266510 TGCTTCGCCTCAGATACAAAT 57.733 42.857 0.00 0.00 0.00 2.32
1560 1917 2.350863 AATCACTGACTCCCCTTCCT 57.649 50.000 0.00 0.00 0.00 3.36
1604 1961 3.077556 AGGGTGGCTCCTAGTGCG 61.078 66.667 5.46 0.00 34.92 5.34
1624 1981 1.153249 GCACCTAGGCGGCAATACA 60.153 57.895 18.49 0.00 35.61 2.29
1626 1983 2.508928 GGCACCTAGGCGGCAATA 59.491 61.111 23.14 0.00 35.61 1.90
1693 2050 5.067283 GTGACCAGGTTTTATCACAAGTGTT 59.933 40.000 0.00 0.00 40.95 3.32
1694 2051 4.578928 GTGACCAGGTTTTATCACAAGTGT 59.421 41.667 0.00 0.00 40.95 3.55
2105 2462 5.767816 AGATAAATGGAATGTAAACGGGC 57.232 39.130 0.00 0.00 0.00 6.13
2402 2760 7.385267 AGCTCTTTTACTCAGGATATATGCTG 58.615 38.462 24.14 24.14 46.17 4.41
2444 2802 5.110814 TCCAGGAATTACCACCATAACAG 57.889 43.478 0.00 0.00 42.04 3.16
2547 2905 7.370383 AGTTTACAAAATGCACTATCAACTGG 58.630 34.615 0.00 0.00 0.00 4.00
2679 3037 1.476891 TGACACTTGCCTAGTCCGATC 59.523 52.381 0.00 0.00 33.85 3.69
2736 3094 6.523840 TGCTTCATTTGCACTTCCTTTATTT 58.476 32.000 0.00 0.00 35.31 1.40
2846 3204 5.412594 GGTTCATGTTCACTAGATGCTTCAA 59.587 40.000 0.00 0.00 0.00 2.69
2940 3300 9.828852 TGCTGGTATTTACTTTTTATTAACACG 57.171 29.630 0.00 0.00 0.00 4.49
2947 3307 9.942850 ATTTTGCTGCTGGTATTTACTTTTTAT 57.057 25.926 0.00 0.00 0.00 1.40
2984 3344 2.833794 TCTCAAGGTCAACAAAGGTCG 58.166 47.619 0.00 0.00 0.00 4.79
3029 3389 2.303022 TGCTCTCCTCTCCAATTTTCGT 59.697 45.455 0.00 0.00 0.00 3.85
3054 3416 8.136165 ACAACTTCTAACTTCTACTACACACAG 58.864 37.037 0.00 0.00 0.00 3.66
3056 3418 8.133627 TCACAACTTCTAACTTCTACTACACAC 58.866 37.037 0.00 0.00 0.00 3.82
3060 3422 9.694137 AATGTCACAACTTCTAACTTCTACTAC 57.306 33.333 0.00 0.00 0.00 2.73
3096 3458 3.794564 GTCACTGCAAAAACTTAAACCGG 59.205 43.478 0.00 0.00 0.00 5.28
3097 3459 4.499040 CAGTCACTGCAAAAACTTAAACCG 59.501 41.667 0.00 0.00 0.00 4.44
3237 3599 7.071273 ACCATCTGACAATTCCAAATATCCAT 58.929 34.615 0.00 0.00 0.00 3.41
3303 3665 6.266131 TCATGCCTAAGTCCCTAAAATGAT 57.734 37.500 0.00 0.00 0.00 2.45
3308 3670 6.062095 GCTTTATCATGCCTAAGTCCCTAAA 58.938 40.000 0.00 0.00 0.00 1.85
3559 3924 2.102578 GGCCCAAGATACAGCACAAAT 58.897 47.619 0.00 0.00 0.00 2.32
3887 4252 9.900710 CTGTACAGCTGTAAAGTATCTAATAGG 57.099 37.037 29.08 6.53 32.47 2.57
3957 4324 7.712797 TCAAGGGAAATCAGTTAAGAAACAAC 58.287 34.615 0.00 0.00 38.12 3.32
3996 4363 8.801913 GTTACATAGTACAGTAAAAAGTAGGCG 58.198 37.037 0.00 0.00 32.55 5.52
4030 4397 5.885230 ATGGATATAACAATGATGGCACG 57.115 39.130 0.00 0.00 0.00 5.34
4042 4417 6.998673 AGGGACAACAGCTAAATGGATATAAC 59.001 38.462 0.00 0.00 0.00 1.89
4069 4444 3.091545 TGGTGAACTTAGGTACCTACGG 58.908 50.000 24.82 20.04 34.32 4.02
4070 4445 3.428589 GCTGGTGAACTTAGGTACCTACG 60.429 52.174 21.65 21.22 34.32 3.51
4110 4486 2.810852 TGAAATGCTACGACAATGTGCA 59.189 40.909 0.00 0.00 38.05 4.57
4111 4487 3.469899 TGAAATGCTACGACAATGTGC 57.530 42.857 0.00 0.00 0.00 4.57
4120 4496 6.550843 TGAACAATAACCATGAAATGCTACG 58.449 36.000 0.00 0.00 44.97 3.51
4125 4501 9.439500 AGGAAAATGAACAATAACCATGAAATG 57.561 29.630 0.00 0.00 46.21 2.32
4186 4562 8.682936 ACTGAGAATGAAATGAGTACTGTTTT 57.317 30.769 0.00 0.00 0.00 2.43
4187 4563 8.682936 AACTGAGAATGAAATGAGTACTGTTT 57.317 30.769 0.00 0.84 0.00 2.83
4212 4588 8.319057 AGTTGTATTACATCCCATTACTGAGA 57.681 34.615 0.00 0.00 0.00 3.27
4213 4589 8.964476 AAGTTGTATTACATCCCATTACTGAG 57.036 34.615 0.00 0.00 0.00 3.35
4214 4590 9.747898 AAAAGTTGTATTACATCCCATTACTGA 57.252 29.630 0.00 0.00 0.00 3.41
4215 4591 9.787532 CAAAAGTTGTATTACATCCCATTACTG 57.212 33.333 0.00 0.00 0.00 2.74
4216 4592 9.747898 TCAAAAGTTGTATTACATCCCATTACT 57.252 29.630 0.00 0.00 0.00 2.24
4218 4594 9.967451 TCTCAAAAGTTGTATTACATCCCATTA 57.033 29.630 0.00 0.00 0.00 1.90
4291 4667 2.747396 CATAAGCTGCAGCCCAAAAA 57.253 45.000 34.39 14.20 43.38 1.94
4339 4715 4.705023 GGGCTTATTTCCACAAGAGCTTAA 59.295 41.667 0.00 0.00 0.00 1.85
4373 4749 7.361799 GGAACCAAAATGAACTCGTTAGCTTAT 60.362 37.037 0.00 0.00 0.00 1.73
4374 4750 6.072893 GGAACCAAAATGAACTCGTTAGCTTA 60.073 38.462 0.00 0.00 0.00 3.09
4375 4751 5.278315 GGAACCAAAATGAACTCGTTAGCTT 60.278 40.000 0.00 0.00 0.00 3.74
4376 4752 4.215613 GGAACCAAAATGAACTCGTTAGCT 59.784 41.667 0.00 0.00 0.00 3.32
4379 4755 5.127491 ACAGGAACCAAAATGAACTCGTTA 58.873 37.500 0.00 0.00 0.00 3.18
4389 4765 1.786441 TGGAGGGACAGGAACCAAAAT 59.214 47.619 0.00 0.00 0.00 1.82
4394 4770 1.492993 AAGCTGGAGGGACAGGAACC 61.493 60.000 0.00 0.00 38.90 3.62
4399 4775 4.335416 TCAAAATTAAGCTGGAGGGACAG 58.665 43.478 0.00 0.00 41.41 3.51
4481 4857 5.473846 TCATATGGGCGACAAAACACTAAAA 59.526 36.000 2.13 0.00 0.00 1.52
4487 4863 3.149981 TGTTCATATGGGCGACAAAACA 58.850 40.909 2.13 0.75 0.00 2.83
4552 4928 1.682854 CCACCTTGCATGTGACAAACT 59.317 47.619 16.17 0.00 35.74 2.66
4553 4929 1.680735 TCCACCTTGCATGTGACAAAC 59.319 47.619 16.17 0.00 35.74 2.93
4564 4940 3.507233 TGTGAGAAAATGATCCACCTTGC 59.493 43.478 0.00 0.00 0.00 4.01
4663 5053 4.034048 GTGTTCAGTTTCGTCAGTGTCAAT 59.966 41.667 0.00 0.00 0.00 2.57
4664 5054 3.369756 GTGTTCAGTTTCGTCAGTGTCAA 59.630 43.478 0.00 0.00 0.00 3.18
4665 5055 2.927477 GTGTTCAGTTTCGTCAGTGTCA 59.073 45.455 0.00 0.00 0.00 3.58
4666 5056 3.187700 AGTGTTCAGTTTCGTCAGTGTC 58.812 45.455 0.00 0.00 0.00 3.67
4667 5057 3.119101 AGAGTGTTCAGTTTCGTCAGTGT 60.119 43.478 0.00 0.00 0.00 3.55
4668 5058 3.243877 CAGAGTGTTCAGTTTCGTCAGTG 59.756 47.826 0.00 0.00 0.00 3.66
4669 5059 3.130516 TCAGAGTGTTCAGTTTCGTCAGT 59.869 43.478 0.00 0.00 0.00 3.41
4670 5060 3.706698 TCAGAGTGTTCAGTTTCGTCAG 58.293 45.455 0.00 0.00 0.00 3.51
4671 5061 3.793797 TCAGAGTGTTCAGTTTCGTCA 57.206 42.857 0.00 0.00 0.00 4.35
4672 5062 3.863424 TGTTCAGAGTGTTCAGTTTCGTC 59.137 43.478 0.00 0.00 0.00 4.20
4673 5063 3.857052 TGTTCAGAGTGTTCAGTTTCGT 58.143 40.909 0.00 0.00 0.00 3.85
4674 5064 4.507756 TGATGTTCAGAGTGTTCAGTTTCG 59.492 41.667 0.00 0.00 0.00 3.46
4675 5065 5.991328 TGATGTTCAGAGTGTTCAGTTTC 57.009 39.130 0.00 0.00 0.00 2.78
4676 5066 5.824624 ACATGATGTTCAGAGTGTTCAGTTT 59.175 36.000 0.00 0.00 0.00 2.66
4677 5067 5.237996 CACATGATGTTCAGAGTGTTCAGTT 59.762 40.000 0.00 0.00 34.02 3.16
4678 5068 4.753610 CACATGATGTTCAGAGTGTTCAGT 59.246 41.667 0.00 0.00 34.02 3.41
4679 5069 4.153655 CCACATGATGTTCAGAGTGTTCAG 59.846 45.833 0.00 0.00 35.73 3.02
4680 5070 4.067192 CCACATGATGTTCAGAGTGTTCA 58.933 43.478 0.00 0.00 35.73 3.18
4681 5071 4.318332 TCCACATGATGTTCAGAGTGTTC 58.682 43.478 0.00 0.00 35.73 3.18
4682 5072 4.356405 TCCACATGATGTTCAGAGTGTT 57.644 40.909 0.00 0.00 35.73 3.32
4683 5073 4.321718 CTTCCACATGATGTTCAGAGTGT 58.678 43.478 0.00 0.00 35.73 3.55
4684 5074 3.126514 GCTTCCACATGATGTTCAGAGTG 59.873 47.826 0.00 6.11 36.62 3.51
4685 5075 3.008813 AGCTTCCACATGATGTTCAGAGT 59.991 43.478 0.00 0.00 0.00 3.24
4686 5076 3.607741 AGCTTCCACATGATGTTCAGAG 58.392 45.455 0.00 0.00 0.00 3.35
4687 5077 3.008266 TGAGCTTCCACATGATGTTCAGA 59.992 43.478 0.00 0.00 34.75 3.27
4688 5078 3.340928 TGAGCTTCCACATGATGTTCAG 58.659 45.455 0.00 0.00 34.75 3.02
4689 5079 3.421919 TGAGCTTCCACATGATGTTCA 57.578 42.857 0.00 0.00 36.47 3.18
4690 5080 3.943381 TGATGAGCTTCCACATGATGTTC 59.057 43.478 0.00 0.00 0.00 3.18
4691 5081 3.945921 CTGATGAGCTTCCACATGATGTT 59.054 43.478 0.00 0.00 0.00 2.71
4692 5082 3.542648 CTGATGAGCTTCCACATGATGT 58.457 45.455 0.00 0.00 0.00 3.06
4693 5083 2.290916 GCTGATGAGCTTCCACATGATG 59.709 50.000 0.00 0.00 42.52 3.07
4694 5084 2.092592 TGCTGATGAGCTTCCACATGAT 60.093 45.455 5.57 0.00 46.39 2.45
4695 5085 1.279846 TGCTGATGAGCTTCCACATGA 59.720 47.619 5.57 0.00 46.39 3.07
4696 5086 1.400846 GTGCTGATGAGCTTCCACATG 59.599 52.381 5.57 0.00 46.39 3.21
4697 5087 1.747709 GTGCTGATGAGCTTCCACAT 58.252 50.000 5.57 0.00 46.39 3.21
4698 5088 0.671472 CGTGCTGATGAGCTTCCACA 60.671 55.000 5.57 0.00 46.39 4.17
4699 5089 0.390340 TCGTGCTGATGAGCTTCCAC 60.390 55.000 5.57 0.00 46.39 4.02
4777 5167 2.029110 TCGTCAGCATCAATCAGTGTCA 60.029 45.455 0.00 0.00 0.00 3.58
4786 5176 3.202097 TGTTCAGTTTCGTCAGCATCAA 58.798 40.909 0.00 0.00 0.00 2.57
4913 5307 2.528797 GTGCGAACACCCAGTACAG 58.471 57.895 0.00 0.00 41.21 2.74
4956 5360 3.627395 TGGCCACCATACTAGTTCTTG 57.373 47.619 0.00 0.00 0.00 3.02
4957 5361 3.780294 TGATGGCCACCATACTAGTTCTT 59.220 43.478 8.16 0.00 45.26 2.52
4958 5362 3.384168 TGATGGCCACCATACTAGTTCT 58.616 45.455 8.16 0.00 45.26 3.01
4959 5363 3.495100 CCTGATGGCCACCATACTAGTTC 60.495 52.174 8.16 0.00 45.26 3.01
4960 5364 2.439507 CCTGATGGCCACCATACTAGTT 59.560 50.000 8.16 0.00 45.26 2.24
4961 5365 2.050144 CCTGATGGCCACCATACTAGT 58.950 52.381 8.16 0.00 45.26 2.57
4962 5366 2.050144 ACCTGATGGCCACCATACTAG 58.950 52.381 8.16 0.00 45.26 2.57
5003 5407 0.731417 CAAGTCATGGCTGCTGCTAC 59.269 55.000 15.64 8.75 39.59 3.58
5143 5547 1.699054 CGCCTGGATCCCTGGATTCA 61.699 60.000 21.12 6.96 44.09 2.57
5144 5548 1.072159 CGCCTGGATCCCTGGATTC 59.928 63.158 21.12 0.00 44.09 2.52
5145 5549 3.125376 GCGCCTGGATCCCTGGATT 62.125 63.158 21.12 0.00 44.09 3.01
5146 5550 3.564218 GCGCCTGGATCCCTGGAT 61.564 66.667 21.12 0.00 44.09 3.41
5149 5553 3.506059 CTACGCGCCTGGATCCCTG 62.506 68.421 9.90 0.70 0.00 4.45
5150 5554 3.227276 CTACGCGCCTGGATCCCT 61.227 66.667 9.90 0.00 0.00 4.20
5166 5570 1.743995 GTATTCCCAACGCACGCCT 60.744 57.895 0.00 0.00 0.00 5.52
5238 5642 2.997315 CCTCTGTCCAGCCGTCCA 60.997 66.667 0.00 0.00 0.00 4.02
5262 5668 4.664267 TCTGCTCTGCCCCACCCT 62.664 66.667 0.00 0.00 0.00 4.34
5287 5693 2.036098 TAGACGCGTTCCTCCCCA 59.964 61.111 15.53 0.00 0.00 4.96
5317 5723 1.772063 GCGGCGACAACATGGATACC 61.772 60.000 12.98 0.00 0.00 2.73
5319 5725 0.809636 CAGCGGCGACAACATGGATA 60.810 55.000 12.98 0.00 0.00 2.59
5328 5734 3.449227 CCTACTCCAGCGGCGACA 61.449 66.667 12.98 0.00 0.00 4.35
5337 5751 3.536917 CGATGCCGCCCTACTCCA 61.537 66.667 0.00 0.00 0.00 3.86
5351 5765 2.683933 ACAACCTCGCCTCCCGAT 60.684 61.111 0.00 0.00 46.31 4.18
5405 5871 2.667470 CTCTCCTCCCGTGAAATAGGA 58.333 52.381 0.00 0.00 36.69 2.94
5416 5882 4.144727 TCTCGCCCCTCTCCTCCC 62.145 72.222 0.00 0.00 0.00 4.30
5436 5902 2.106511 TGCAACTGCCCTTATCTATCCC 59.893 50.000 0.00 0.00 41.18 3.85
5437 5903 3.492102 TGCAACTGCCCTTATCTATCC 57.508 47.619 0.00 0.00 41.18 2.59
5438 5904 5.048434 GGAAATGCAACTGCCCTTATCTATC 60.048 44.000 0.00 0.00 41.18 2.08
5439 5905 4.829492 GGAAATGCAACTGCCCTTATCTAT 59.171 41.667 0.00 0.00 41.18 1.98
5441 5907 3.026694 GGAAATGCAACTGCCCTTATCT 58.973 45.455 0.00 0.00 41.18 1.98
5454 5938 4.749099 GCACACAATTACAAAGGAAATGCA 59.251 37.500 0.00 0.00 0.00 3.96
5535 6019 1.623625 AAAAAGCTGGGGGTGGTCA 59.376 52.632 0.00 0.00 0.00 4.02
5585 6070 3.181500 CGTTTTGGGGCATAGAGCTTAAC 60.181 47.826 0.00 0.00 44.79 2.01
5605 6090 3.489229 GCCAAAAACTCAAAAGAGCTCGT 60.489 43.478 8.37 1.01 0.00 4.18
5612 6097 8.663911 TGTCAAATTAAGCCAAAAACTCAAAAG 58.336 29.630 0.00 0.00 0.00 2.27
5626 6111 5.745769 GGAGCAGCTTATTGTCAAATTAAGC 59.254 40.000 17.63 17.63 42.29 3.09
5632 6117 3.485394 TGTGGAGCAGCTTATTGTCAAA 58.515 40.909 0.00 0.00 0.00 2.69
5633 6118 3.138884 TGTGGAGCAGCTTATTGTCAA 57.861 42.857 0.00 0.00 0.00 3.18
5634 6119 2.857186 TGTGGAGCAGCTTATTGTCA 57.143 45.000 0.00 0.00 0.00 3.58
5669 6159 4.394729 ACCAGTACTGTTTACCCACAATG 58.605 43.478 21.18 4.00 0.00 2.82
5695 6186 8.424918 AGTTGTATTGTATCCCATTACTGAGAG 58.575 37.037 0.00 0.00 33.19 3.20
5874 6366 1.194547 GTTGCAGATTTCGAGAACGCA 59.805 47.619 0.00 0.00 39.58 5.24
5882 6374 6.369059 AGATAATGAAGGTTGCAGATTTCG 57.631 37.500 0.00 0.00 0.00 3.46
6016 6508 4.842531 TGCTATTGGACCATCTTCTGAA 57.157 40.909 0.00 0.00 0.00 3.02
6164 6656 8.748380 AGCAAAATTCTGCAACTACTATTTTC 57.252 30.769 6.51 0.00 45.18 2.29
6169 6661 6.446318 CCAAAGCAAAATTCTGCAACTACTA 58.554 36.000 6.51 0.00 45.18 1.82
6247 6739 3.707611 ACAATGTCCAATTAGCATGGCAT 59.292 39.130 0.00 0.00 37.88 4.40
6282 6779 9.647797 CATACTTGGAACTAGTTACATGTGTTA 57.352 33.333 33.80 22.16 40.59 2.41
6494 6991 5.606505 ACACAAATTAACGCCAGGATTTTT 58.393 33.333 0.00 0.00 0.00 1.94
6506 7004 9.394477 GTGATACCAAGAGAAACACAAATTAAC 57.606 33.333 0.00 0.00 0.00 2.01
6545 7043 3.823281 ATCACCAGCAGATCAAGAGAG 57.177 47.619 0.00 0.00 0.00 3.20
6553 7051 3.716353 TGGTATACCAATCACCAGCAGAT 59.284 43.478 22.59 0.00 44.35 2.90
6633 7139 8.547967 AAAAGACATGATCACGTAAAGTATGT 57.452 30.769 0.00 0.00 0.00 2.29
6643 7149 5.149273 CAGAACCAAAAAGACATGATCACG 58.851 41.667 0.00 0.00 0.00 4.35
6659 7165 4.764050 TGTTTCTAACTGGACAGAACCA 57.236 40.909 6.29 0.00 38.33 3.67
6701 7207 1.447099 TGCTTGGGTTGTAGGGGTAA 58.553 50.000 0.00 0.00 0.00 2.85
6717 7229 2.884639 AGGTCGCAACTACAATTTTGCT 59.115 40.909 10.08 0.00 44.94 3.91
6744 7256 8.899427 AGATCACACAGAATAATCAATGTAGG 57.101 34.615 0.00 0.00 0.00 3.18
6775 7309 8.893219 TCTCTGATACAATTCACACCATATTC 57.107 34.615 0.00 0.00 0.00 1.75
6776 7310 9.857656 AATCTCTGATACAATTCACACCATATT 57.142 29.630 0.00 0.00 0.00 1.28
6777 7311 9.857656 AAATCTCTGATACAATTCACACCATAT 57.142 29.630 0.00 0.00 0.00 1.78
6778 7312 9.330063 GAAATCTCTGATACAATTCACACCATA 57.670 33.333 0.00 0.00 0.00 2.74
6779 7313 7.830697 TGAAATCTCTGATACAATTCACACCAT 59.169 33.333 0.00 0.00 0.00 3.55
6780 7314 7.119699 GTGAAATCTCTGATACAATTCACACCA 59.880 37.037 13.48 0.00 42.73 4.17
6781 7315 7.335422 AGTGAAATCTCTGATACAATTCACACC 59.665 37.037 17.55 1.28 44.55 4.16
6782 7316 8.261492 AGTGAAATCTCTGATACAATTCACAC 57.739 34.615 17.55 0.00 44.55 3.82
6783 7317 8.096414 TGAGTGAAATCTCTGATACAATTCACA 58.904 33.333 17.55 3.91 44.55 3.58
6784 7318 8.484641 TGAGTGAAATCTCTGATACAATTCAC 57.515 34.615 11.70 11.70 43.23 3.18
6785 7319 9.506018 TTTGAGTGAAATCTCTGATACAATTCA 57.494 29.630 0.00 0.00 35.68 2.57
6830 7364 7.499563 TGCAAGCATTAATGGCATTATCATTTT 59.500 29.630 19.88 9.06 36.40 1.82
6835 7369 6.160684 TGATGCAAGCATTAATGGCATTATC 58.839 36.000 23.12 15.82 44.52 1.75
6960 7498 9.640974 CAAAAAGAAGCAAAATTGTATCACTTG 57.359 29.630 0.00 0.00 0.00 3.16
6961 7499 9.382275 ACAAAAAGAAGCAAAATTGTATCACTT 57.618 25.926 0.00 0.00 29.89 3.16
6997 7535 8.536175 ACCTAAGTTTGTTTGATTTTCAGGAAA 58.464 29.630 0.00 0.00 0.00 3.13
7085 7623 6.659242 CCAACCAGATAAGTAAGGTGTCAAAT 59.341 38.462 0.00 0.00 33.93 2.32
7207 7745 8.056407 ACTCCTTTTCCATAAAATACAAGAGC 57.944 34.615 0.00 0.00 34.18 4.09
7334 7872 3.136443 TCCATTTGTGAAGGTGAGACTGT 59.864 43.478 0.00 0.00 0.00 3.55
7432 8024 7.687941 AATTCCACTGTTTATCCTGTACAAG 57.312 36.000 0.00 0.00 0.00 3.16
7467 8059 4.008074 CACTACAGTGTTCCAGACCAAT 57.992 45.455 0.00 0.00 40.96 3.16
7860 8472 6.840780 AACAATCCCTAAAGTTCATCCAAG 57.159 37.500 0.00 0.00 0.00 3.61
7937 8550 6.949715 ACCGTATTTCCAACATAAGAAGGTA 58.050 36.000 0.00 0.00 28.07 3.08
8062 8675 4.513442 AGTGAACTTGTAGTTGAAGTGCA 58.487 39.130 0.00 0.00 38.80 4.57
8086 8699 4.654091 TCAGCAGCTTTATTATTTGCCC 57.346 40.909 0.00 0.00 35.44 5.36
8137 8750 1.524621 CGTGATGCAGATCCCCACC 60.525 63.158 0.00 0.00 0.00 4.61
8206 8836 4.392940 CTGAGAATCACAAGTTTCCCAGT 58.607 43.478 0.00 0.00 42.56 4.00
8231 8861 4.455533 AGAGCATGCAAAAGATAACGTGAA 59.544 37.500 21.98 0.00 0.00 3.18
8249 8879 1.881973 CAAGCTACAAGCCAAAGAGCA 59.118 47.619 0.00 0.00 43.77 4.26
8371 9002 2.437895 GGGCGGGTGTAAAGAGGC 60.438 66.667 0.00 0.00 0.00 4.70
8397 9028 1.877680 CGACCACCTCTGTTGCATTGA 60.878 52.381 0.00 0.00 0.00 2.57
8411 9042 2.203153 ACAACTGCCCACGACCAC 60.203 61.111 0.00 0.00 0.00 4.16
8511 9142 1.062148 CGTGCTCGAGTATCTTGACGA 59.938 52.381 15.13 0.00 39.71 4.20
8532 9163 3.060866 GGACACGCCTTGGAGTCT 58.939 61.111 0.00 0.00 0.00 3.24
8545 9176 0.973632 AGGCAATGTACACGAGGACA 59.026 50.000 0.00 0.00 0.00 4.02
8566 9197 5.179368 CAGTAGAGATCGCCTTTGTGAAAAA 59.821 40.000 0.00 0.00 34.04 1.94
8567 9198 4.690748 CAGTAGAGATCGCCTTTGTGAAAA 59.309 41.667 0.00 0.00 34.04 2.29
8578 9209 0.383737 CTCGTCGCAGTAGAGATCGC 60.384 60.000 0.00 0.00 35.10 4.58
8592 9223 0.302288 CGGTGATCTCTCGTCTCGTC 59.698 60.000 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.