Multiple sequence alignment - TraesCS5D01G484400

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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 TraesCS5D01G484400 chr5D 100.000 5117 0 0 1 5117 520650128 520655244 0.000000e+00 9450.0
1 TraesCS5D01G484400 chr5D 87.043 656 49 14 891 1524 520639826 520640467 0.000000e+00 708.0
2 TraesCS5D01G484400 chr5D 90.909 264 22 2 4219 4482 421314564 421314825 2.270000e-93 353.0
3 TraesCS5D01G484400 chr5D 88.968 281 29 2 25 304 232587461 232587740 3.790000e-91 346.0
4 TraesCS5D01G484400 chr5D 86.824 296 34 5 25 315 470474085 470473790 4.940000e-85 326.0
5 TraesCS5D01G484400 chr5B 95.482 3453 101 7 792 4216 656046766 656050191 0.000000e+00 5461.0
6 TraesCS5D01G484400 chr5B 85.072 623 58 17 4521 5114 656050229 656050845 2.040000e-168 603.0
7 TraesCS5D01G484400 chr5B 88.926 298 26 7 13 304 226435510 226435214 1.350000e-95 361.0
8 TraesCS5D01G484400 chr5B 88.968 281 29 2 25 304 308095664 308095943 3.790000e-91 346.0
9 TraesCS5D01G484400 chr5B 87.833 263 26 3 548 809 656046060 656046317 2.320000e-78 303.0
10 TraesCS5D01G484400 chr5B 87.500 200 23 2 307 504 488119243 488119442 3.990000e-56 230.0
11 TraesCS5D01G484400 chr5B 80.132 151 18 8 4612 4754 417559577 417559723 9.060000e-18 102.0
12 TraesCS5D01G484400 chr5A 95.331 3384 130 10 832 4213 648854966 648858323 0.000000e+00 5349.0
13 TraesCS5D01G484400 chr5A 86.931 857 51 29 4 841 648853744 648854558 0.000000e+00 905.0
14 TraesCS5D01G484400 chr5A 86.492 533 40 14 4610 5114 648859002 648859530 1.610000e-154 556.0
15 TraesCS5D01G484400 chr5A 90.681 279 21 4 4206 4482 475652398 475652673 2.910000e-97 366.0
16 TraesCS5D01G484400 chr5A 90.458 262 21 3 4228 4488 9609062 9609320 4.910000e-90 342.0
17 TraesCS5D01G484400 chr5A 88.846 260 29 0 4224 4483 52281158 52281417 2.300000e-83 320.0
18 TraesCS5D01G484400 chr5A 83.945 218 22 8 547 753 648790748 648790963 4.040000e-46 196.0
19 TraesCS5D01G484400 chr5A 81.633 147 19 5 4612 4754 454443565 454443707 1.160000e-21 115.0
20 TraesCS5D01G484400 chr7B 81.423 506 68 13 25 505 526002882 526003386 1.730000e-104 390.0
21 TraesCS5D01G484400 chr7B 93.220 59 4 0 2746 2804 43206618 43206560 2.540000e-13 87.9
22 TraesCS5D01G484400 chr4A 91.760 267 17 5 4220 4484 547311770 547311507 2.910000e-97 366.0
23 TraesCS5D01G484400 chr4A 88.732 284 27 5 25 304 5249978 5250260 4.910000e-90 342.0
24 TraesCS5D01G484400 chr6D 89.085 284 25 5 25 304 90122478 90122759 1.050000e-91 348.0
25 TraesCS5D01G484400 chr6D 80.645 217 24 12 4499 4714 81103472 81103671 8.870000e-33 152.0
26 TraesCS5D01G484400 chr6D 94.915 59 3 0 2746 2804 205119221 205119279 5.460000e-15 93.5
27 TraesCS5D01G484400 chr6A 90.114 263 25 1 4224 4486 385432350 385432089 1.760000e-89 340.0
28 TraesCS5D01G484400 chr6A 88.612 281 30 2 25 304 550622190 550622469 1.760000e-89 340.0
29 TraesCS5D01G484400 chr6A 81.301 246 26 13 4493 4736 97608261 97608488 1.130000e-41 182.0
30 TraesCS5D01G484400 chr1D 88.571 280 31 1 25 304 392634017 392633739 6.350000e-89 339.0
31 TraesCS5D01G484400 chr1D 90.038 261 19 1 4224 4484 394489667 394489414 1.060000e-86 331.0
32 TraesCS5D01G484400 chr1D 86.758 219 24 5 292 506 52740476 52740693 6.620000e-59 239.0
33 TraesCS5D01G484400 chr1D 85.787 197 26 2 307 502 445316911 445317106 1.870000e-49 207.0
34 TraesCS5D01G484400 chr1D 96.190 105 4 0 3672 3776 468374589 468374693 6.810000e-39 172.0
35 TraesCS5D01G484400 chr2A 89.961 259 26 0 4224 4482 203902478 203902736 8.210000e-88 335.0
36 TraesCS5D01G484400 chr2A 81.283 187 28 7 4533 4717 619181520 619181701 1.480000e-30 145.0
37 TraesCS5D01G484400 chr4D 89.231 260 25 3 4224 4482 240934136 240934393 6.390000e-84 322.0
38 TraesCS5D01G484400 chrUn 78.824 510 71 24 25 502 21649726 21650230 4.980000e-80 309.0
39 TraesCS5D01G484400 chrUn 93.056 72 5 0 3705 3776 23722077 23722006 7.010000e-19 106.0
40 TraesCS5D01G484400 chr6B 78.346 508 75 24 25 502 162610704 162611206 3.870000e-76 296.0
41 TraesCS5D01G484400 chr6B 90.385 52 5 0 2753 2804 720008501 720008552 9.190000e-08 69.4
42 TraesCS5D01G484400 chr3A 86.070 201 27 1 307 506 673824129 673824329 1.120000e-51 215.0
43 TraesCS5D01G484400 chr7A 86.294 197 26 1 309 504 156570481 156570677 4.010000e-51 213.0
44 TraesCS5D01G484400 chr7A 92.929 99 6 1 3679 3776 671699518 671699420 5.340000e-30 143.0
45 TraesCS5D01G484400 chr3D 87.634 186 19 4 307 490 159768693 159768510 4.010000e-51 213.0
46 TraesCS5D01G484400 chr3D 85.500 200 28 1 307 505 518738614 518738415 1.870000e-49 207.0
47 TraesCS5D01G484400 chr3D 74.792 480 74 34 4628 5079 592569033 592569493 6.810000e-39 172.0
48 TraesCS5D01G484400 chr7D 85.366 205 14 4 3665 3869 262576912 262576724 1.120000e-46 198.0
49 TraesCS5D01G484400 chr7D 87.425 167 18 1 2665 2831 262577102 262576939 6.760000e-44 189.0
50 TraesCS5D01G484400 chr2B 93.000 100 7 0 2814 2913 789128477 789128378 4.130000e-31 147.0
51 TraesCS5D01G484400 chr2B 86.275 102 9 3 4612 4713 799382575 799382479 7.010000e-19 106.0
52 TraesCS5D01G484400 chr2D 89.320 103 7 2 4612 4714 642302684 642302586 5.380000e-25 126.0


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 TraesCS5D01G484400 chr5D 520650128 520655244 5116 False 9450.000000 9450 100.000000 1 5117 1 chr5D.!!$F4 5116
1 TraesCS5D01G484400 chr5D 520639826 520640467 641 False 708.000000 708 87.043000 891 1524 1 chr5D.!!$F3 633
2 TraesCS5D01G484400 chr5B 656046060 656050845 4785 False 2122.333333 5461 89.462333 548 5114 3 chr5B.!!$F4 4566
3 TraesCS5D01G484400 chr5A 648853744 648859530 5786 False 2270.000000 5349 89.584667 4 5114 3 chr5A.!!$F6 5110
4 TraesCS5D01G484400 chr7B 526002882 526003386 504 False 390.000000 390 81.423000 25 505 1 chr7B.!!$F1 480
5 TraesCS5D01G484400 chrUn 21649726 21650230 504 False 309.000000 309 78.824000 25 502 1 chrUn.!!$F1 477
6 TraesCS5D01G484400 chr6B 162610704 162611206 502 False 296.000000 296 78.346000 25 502 1 chr6B.!!$F1 477

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
918 1878 0.385029 CTCAGCTCCATGTCTCCTCG 59.615 60.0 0.00 0.00 0.0 4.63 F
1185 2175 0.319555 CGCTCGAGTTCAACTTCCCA 60.320 55.0 15.13 0.00 0.0 4.37 F
2583 3573 0.034380 TCGTCATCTCCCTCGAGGTT 60.034 55.0 29.25 9.04 36.7 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2556 3546 0.179097 GGGAGATGACGAAGCAGTCC 60.179 60.0 0.00 0.0 40.26 3.85 R
2670 3660 0.670854 GAAGGTCGAGCCACTTGGAC 60.671 60.0 11.73 0.0 40.61 4.02 R
4123 5113 0.309302 CTCGGCAGATCCTACACGAG 59.691 60.0 0.00 0.0 41.20 4.18 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
39 46 5.178061 TCATGCACATCGTAGAAAATGAGT 58.822 37.500 0.00 0.00 43.58 3.41
54 61 2.251869 TGAGTGTCCGAAACGTATCG 57.748 50.000 0.00 0.00 42.37 2.92
99 107 2.498167 GTGAGAATGTTGTGCCTGAGT 58.502 47.619 0.00 0.00 0.00 3.41
105 113 2.472695 TGTTGTGCCTGAGTATGGAC 57.527 50.000 0.00 0.00 0.00 4.02
141 152 8.497554 CGTTTGAACAATTCATCCAATTTCATT 58.502 29.630 0.00 0.00 39.84 2.57
215 227 9.494271 GTTGAGTATATGTGGTGTCATATTGAT 57.506 33.333 4.85 0.00 40.25 2.57
376 426 1.546923 CCACGCCGACATATATGGGTA 59.453 52.381 16.96 0.00 0.00 3.69
377 427 2.167693 CCACGCCGACATATATGGGTAT 59.832 50.000 16.96 0.00 0.00 2.73
381 431 2.418197 GCCGACATATATGGGTATGCGT 60.418 50.000 16.96 0.00 35.87 5.24
387 437 4.041075 ACATATATGGGTATGCGTGTTGGA 59.959 41.667 16.96 0.00 35.87 3.53
408 458 1.926511 GCAGTGCCGACCCAAATCAG 61.927 60.000 2.85 0.00 0.00 2.90
415 465 1.740025 CCGACCCAAATCAGAAAGAGC 59.260 52.381 0.00 0.00 0.00 4.09
472 522 1.314730 AAGCGGACAAAATCACCGTT 58.685 45.000 0.00 0.00 46.95 4.44
473 523 0.591170 AGCGGACAAAATCACCGTTG 59.409 50.000 0.00 0.00 46.95 4.10
517 575 2.509964 TGCTCTAAGGGGGAAATCCTTC 59.490 50.000 0.00 0.00 43.02 3.46
589 647 9.771534 AATTTTTCGGTGAAATTCCTTTGAATA 57.228 25.926 0.00 0.00 40.34 1.75
768 826 2.028020 CCTTTTCCTCTTCACGCCTAGT 60.028 50.000 0.00 0.00 0.00 2.57
769 827 3.557264 CCTTTTCCTCTTCACGCCTAGTT 60.557 47.826 0.00 0.00 0.00 2.24
770 828 4.322499 CCTTTTCCTCTTCACGCCTAGTTA 60.322 45.833 0.00 0.00 0.00 2.24
771 829 4.877378 TTTCCTCTTCACGCCTAGTTAA 57.123 40.909 0.00 0.00 0.00 2.01
841 1783 3.445096 TCTTCATGCGTTCTCATCTCAGA 59.555 43.478 0.00 0.00 0.00 3.27
918 1878 0.385029 CTCAGCTCCATGTCTCCTCG 59.615 60.000 0.00 0.00 0.00 4.63
924 1884 0.397675 TCCATGTCTCCTCGGCTCAT 60.398 55.000 0.00 0.00 0.00 2.90
969 1937 4.210746 GCCGACCGGAAAAGATAGAATAAC 59.789 45.833 9.46 0.00 37.50 1.89
1056 2045 4.143333 GAGGCGCGGAACCTGCTA 62.143 66.667 8.83 0.00 37.77 3.49
1164 2154 3.562232 AACCCGGCCTGGAACGAA 61.562 61.111 21.63 0.00 42.00 3.85
1185 2175 0.319555 CGCTCGAGTTCAACTTCCCA 60.320 55.000 15.13 0.00 0.00 4.37
1356 2346 0.952280 CGCTCATCTACTTCCCGCTA 59.048 55.000 0.00 0.00 0.00 4.26
1578 2568 3.056328 GGGCCGGAGAAAGCACAC 61.056 66.667 5.05 0.00 30.81 3.82
1678 2668 4.732106 CGGAAGATGAGCCGGTAC 57.268 61.111 1.90 0.00 43.67 3.34
1700 2690 3.936203 TTCGGAAGCGGTGCCAGT 61.936 61.111 13.22 0.00 0.00 4.00
1708 2698 2.332654 GCGGTGCCAGTTTCCGATT 61.333 57.895 7.01 0.00 46.05 3.34
2142 3132 3.989698 CTGCTTCGACACCGCCGAT 62.990 63.158 0.00 0.00 35.84 4.18
2556 3546 1.934956 CGAGCCGTTCATCGACGAG 60.935 63.158 3.01 0.00 45.47 4.18
2583 3573 0.034380 TCGTCATCTCCCTCGAGGTT 60.034 55.000 29.25 9.04 36.70 3.50
2604 3594 0.448197 GCTACGGCAAGGAAGCTTTC 59.552 55.000 0.00 0.00 38.54 2.62
2652 3642 4.162690 GCCATCGAGAGGCGGGTT 62.163 66.667 14.94 0.00 43.15 4.11
2670 3660 2.582498 GACGATCGGAAGGTGGCG 60.582 66.667 20.98 0.00 0.00 5.69
2725 3715 2.242043 CCATGAGAAAAGTGGGCAAGT 58.758 47.619 0.00 0.00 0.00 3.16
3002 3992 1.816537 GCACCATCTCCGACAGCTA 59.183 57.895 0.00 0.00 0.00 3.32
3951 4941 0.955428 CCACAGGGATGTTCGTGGTG 60.955 60.000 0.00 0.00 43.23 4.17
4087 5077 0.391263 GATCAACTTCTTCCGGCGGT 60.391 55.000 27.32 1.27 0.00 5.68
4101 5091 2.006772 GCGGTTGCCTTCTATGTCG 58.993 57.895 0.00 0.00 33.98 4.35
4123 5113 3.988517 GGAACGTATCATGTAAGGCTAGC 59.011 47.826 6.04 6.04 0.00 3.42
4124 5114 4.262079 GGAACGTATCATGTAAGGCTAGCT 60.262 45.833 15.72 0.00 0.00 3.32
4125 5115 4.506886 ACGTATCATGTAAGGCTAGCTC 57.493 45.455 15.72 4.82 0.00 4.09
4126 5116 3.058155 ACGTATCATGTAAGGCTAGCTCG 60.058 47.826 15.72 5.35 0.00 5.03
4127 5117 3.058155 CGTATCATGTAAGGCTAGCTCGT 60.058 47.826 15.72 5.81 0.00 4.18
4128 5118 2.871182 TCATGTAAGGCTAGCTCGTG 57.129 50.000 15.72 13.46 0.00 4.35
4129 5119 2.100197 TCATGTAAGGCTAGCTCGTGT 58.900 47.619 15.72 0.00 0.00 4.49
4130 5120 3.284617 TCATGTAAGGCTAGCTCGTGTA 58.715 45.455 15.72 0.00 0.00 2.90
4179 5174 2.743752 CGCCATGGACTGCAGTTCG 61.744 63.158 22.65 13.32 0.00 3.95
4187 5182 0.233332 GACTGCAGTTCGAGTTGCAC 59.767 55.000 22.65 9.11 44.72 4.57
4188 5183 1.160329 ACTGCAGTTCGAGTTGCACC 61.160 55.000 15.25 0.00 44.72 5.01
4199 5194 2.987149 CGAGTTGCACCTTGTAGTACTG 59.013 50.000 5.39 0.00 0.00 2.74
4201 5196 2.038557 AGTTGCACCTTGTAGTACTGGG 59.961 50.000 5.39 12.02 0.00 4.45
4215 5210 3.881089 AGTACTGGGTCGTTTTCCTTTTG 59.119 43.478 0.00 0.00 0.00 2.44
4217 5212 3.888583 ACTGGGTCGTTTTCCTTTTGTA 58.111 40.909 0.00 0.00 0.00 2.41
4218 5213 3.881089 ACTGGGTCGTTTTCCTTTTGTAG 59.119 43.478 0.00 0.00 0.00 2.74
4219 5214 3.881089 CTGGGTCGTTTTCCTTTTGTAGT 59.119 43.478 0.00 0.00 0.00 2.73
4221 5216 4.815846 TGGGTCGTTTTCCTTTTGTAGTAC 59.184 41.667 0.00 0.00 0.00 2.73
4222 5217 5.059161 GGGTCGTTTTCCTTTTGTAGTACT 58.941 41.667 0.00 0.00 0.00 2.73
4223 5218 5.178252 GGGTCGTTTTCCTTTTGTAGTACTC 59.822 44.000 0.00 0.00 0.00 2.59
4224 5219 5.987953 GGTCGTTTTCCTTTTGTAGTACTCT 59.012 40.000 0.00 0.00 0.00 3.24
4227 5222 5.407691 CGTTTTCCTTTTGTAGTACTCTCCC 59.592 44.000 0.00 0.00 0.00 4.30
4229 5224 5.997384 TTCCTTTTGTAGTACTCTCCCTC 57.003 43.478 0.00 0.00 0.00 4.30
4231 5226 5.017490 TCCTTTTGTAGTACTCTCCCTCTG 58.983 45.833 0.00 0.00 0.00 3.35
4232 5227 4.160626 CCTTTTGTAGTACTCTCCCTCTGG 59.839 50.000 0.00 0.00 0.00 3.86
4233 5228 4.399483 TTTGTAGTACTCTCCCTCTGGT 57.601 45.455 0.00 0.00 0.00 4.00
4234 5229 3.648507 TGTAGTACTCTCCCTCTGGTC 57.351 52.381 0.00 0.00 0.00 4.02
4235 5230 2.241685 TGTAGTACTCTCCCTCTGGTCC 59.758 54.545 0.00 0.00 0.00 4.46
4236 5231 1.688750 AGTACTCTCCCTCTGGTCCT 58.311 55.000 0.00 0.00 0.00 3.85
4237 5232 2.004589 AGTACTCTCCCTCTGGTCCTT 58.995 52.381 0.00 0.00 0.00 3.36
4238 5233 2.384029 AGTACTCTCCCTCTGGTCCTTT 59.616 50.000 0.00 0.00 0.00 3.11
4239 5234 2.424684 ACTCTCCCTCTGGTCCTTTT 57.575 50.000 0.00 0.00 0.00 2.27
4240 5235 2.707554 ACTCTCCCTCTGGTCCTTTTT 58.292 47.619 0.00 0.00 0.00 1.94
4241 5236 3.870559 ACTCTCCCTCTGGTCCTTTTTA 58.129 45.455 0.00 0.00 0.00 1.52
4242 5237 4.439860 ACTCTCCCTCTGGTCCTTTTTAT 58.560 43.478 0.00 0.00 0.00 1.40
4243 5238 4.852697 ACTCTCCCTCTGGTCCTTTTTATT 59.147 41.667 0.00 0.00 0.00 1.40
4244 5239 5.045505 ACTCTCCCTCTGGTCCTTTTTATTC 60.046 44.000 0.00 0.00 0.00 1.75
4245 5240 5.101529 TCTCCCTCTGGTCCTTTTTATTCT 58.898 41.667 0.00 0.00 0.00 2.40
4246 5241 5.045578 TCTCCCTCTGGTCCTTTTTATTCTG 60.046 44.000 0.00 0.00 0.00 3.02
4247 5242 3.696548 CCCTCTGGTCCTTTTTATTCTGC 59.303 47.826 0.00 0.00 0.00 4.26
4248 5243 4.335416 CCTCTGGTCCTTTTTATTCTGCA 58.665 43.478 0.00 0.00 0.00 4.41
4249 5244 4.952335 CCTCTGGTCCTTTTTATTCTGCAT 59.048 41.667 0.00 0.00 0.00 3.96
4250 5245 6.122277 CCTCTGGTCCTTTTTATTCTGCATA 58.878 40.000 0.00 0.00 0.00 3.14
4251 5246 6.774656 CCTCTGGTCCTTTTTATTCTGCATAT 59.225 38.462 0.00 0.00 0.00 1.78
4252 5247 7.286316 CCTCTGGTCCTTTTTATTCTGCATATT 59.714 37.037 0.00 0.00 0.00 1.28
4253 5248 9.342308 CTCTGGTCCTTTTTATTCTGCATATTA 57.658 33.333 0.00 0.00 0.00 0.98
4254 5249 9.342308 TCTGGTCCTTTTTATTCTGCATATTAG 57.658 33.333 0.00 0.00 0.00 1.73
4255 5250 9.342308 CTGGTCCTTTTTATTCTGCATATTAGA 57.658 33.333 0.00 0.00 0.00 2.10
4256 5251 9.866655 TGGTCCTTTTTATTCTGCATATTAGAT 57.133 29.630 0.00 0.00 0.00 1.98
4267 5262 8.565896 TTCTGCATATTAGATTTGTGTCAAGT 57.434 30.769 0.00 0.00 0.00 3.16
4268 5263 8.565896 TCTGCATATTAGATTTGTGTCAAGTT 57.434 30.769 0.00 0.00 0.00 2.66
4269 5264 9.665719 TCTGCATATTAGATTTGTGTCAAGTTA 57.334 29.630 0.00 0.00 0.00 2.24
4277 5272 7.755582 AGATTTGTGTCAAGTTAAACTTTGC 57.244 32.000 0.00 0.00 36.03 3.68
4278 5273 7.319646 AGATTTGTGTCAAGTTAAACTTTGCA 58.680 30.769 0.00 0.00 36.03 4.08
4279 5274 7.816995 AGATTTGTGTCAAGTTAAACTTTGCAA 59.183 29.630 0.00 0.00 36.03 4.08
4280 5275 7.715265 TTTGTGTCAAGTTAAACTTTGCAAA 57.285 28.000 12.14 12.14 36.03 3.68
4281 5276 6.942886 TGTGTCAAGTTAAACTTTGCAAAG 57.057 33.333 32.53 32.53 36.03 2.77
4294 5289 6.816134 ACTTTGCAAAGTTTGACCAAATTT 57.184 29.167 33.85 11.08 46.52 1.82
4295 5290 7.913674 ACTTTGCAAAGTTTGACCAAATTTA 57.086 28.000 33.85 0.00 46.52 1.40
4296 5291 8.504812 ACTTTGCAAAGTTTGACCAAATTTAT 57.495 26.923 33.85 10.04 46.52 1.40
4297 5292 9.606631 ACTTTGCAAAGTTTGACCAAATTTATA 57.393 25.926 33.85 0.00 46.52 0.98
4375 5370 8.862325 TTCATAGTGAATCTAACAATGTTGGT 57.138 30.769 9.15 0.00 30.26 3.67
4376 5371 8.862325 TCATAGTGAATCTAACAATGTTGGTT 57.138 30.769 9.15 3.26 31.94 3.67
4377 5372 9.295825 TCATAGTGAATCTAACAATGTTGGTTT 57.704 29.630 9.15 7.18 31.94 3.27
4378 5373 9.345517 CATAGTGAATCTAACAATGTTGGTTTG 57.654 33.333 9.15 0.00 31.94 2.93
4379 5374 6.748132 AGTGAATCTAACAATGTTGGTTTGG 58.252 36.000 9.15 0.00 0.00 3.28
4380 5375 5.405269 GTGAATCTAACAATGTTGGTTTGGC 59.595 40.000 9.15 0.00 0.00 4.52
4381 5376 5.069648 TGAATCTAACAATGTTGGTTTGGCA 59.930 36.000 9.15 0.53 0.00 4.92
4382 5377 5.743636 ATCTAACAATGTTGGTTTGGCAT 57.256 34.783 9.15 0.00 0.00 4.40
4383 5378 5.543507 TCTAACAATGTTGGTTTGGCATT 57.456 34.783 9.15 0.00 33.64 3.56
4388 5383 5.998454 CAATGTTGGTTTGGCATTGTAAA 57.002 34.783 7.96 0.00 42.41 2.01
4389 5384 5.988092 CAATGTTGGTTTGGCATTGTAAAG 58.012 37.500 7.96 0.00 42.41 1.85
4390 5385 4.065321 TGTTGGTTTGGCATTGTAAAGG 57.935 40.909 0.00 0.00 0.00 3.11
4391 5386 3.452627 TGTTGGTTTGGCATTGTAAAGGT 59.547 39.130 0.00 0.00 0.00 3.50
4392 5387 4.080863 TGTTGGTTTGGCATTGTAAAGGTT 60.081 37.500 0.00 0.00 0.00 3.50
4393 5388 5.128827 TGTTGGTTTGGCATTGTAAAGGTTA 59.871 36.000 0.00 0.00 0.00 2.85
4394 5389 5.871396 TGGTTTGGCATTGTAAAGGTTAA 57.129 34.783 0.00 0.00 0.00 2.01
4395 5390 6.426646 TGGTTTGGCATTGTAAAGGTTAAT 57.573 33.333 0.00 0.00 0.00 1.40
4396 5391 7.540474 TGGTTTGGCATTGTAAAGGTTAATA 57.460 32.000 0.00 0.00 0.00 0.98
4397 5392 7.379750 TGGTTTGGCATTGTAAAGGTTAATAC 58.620 34.615 0.00 0.00 0.00 1.89
4398 5393 7.233757 TGGTTTGGCATTGTAAAGGTTAATACT 59.766 33.333 0.00 0.00 0.00 2.12
4399 5394 8.092068 GGTTTGGCATTGTAAAGGTTAATACTT 58.908 33.333 0.00 0.00 0.00 2.24
4400 5395 9.483916 GTTTGGCATTGTAAAGGTTAATACTTT 57.516 29.630 11.34 11.34 40.87 2.66
4427 5422 9.621629 TTTCTATAAGTTTGGTCAAAGTTGAGA 57.378 29.630 20.50 18.66 42.17 3.27
4428 5423 9.793259 TTCTATAAGTTTGGTCAAAGTTGAGAT 57.207 29.630 20.50 12.08 42.17 2.75
4432 5427 7.881775 AAGTTTGGTCAAAGTTGAGATACTT 57.118 32.000 13.71 2.03 41.07 2.24
4433 5428 7.881775 AGTTTGGTCAAAGTTGAGATACTTT 57.118 32.000 0.00 0.00 46.42 2.66
4442 5437 7.979444 AAAGTTGAGATACTTTGATTTCGGA 57.021 32.000 0.00 0.00 44.42 4.55
4443 5438 6.969828 AGTTGAGATACTTTGATTTCGGAC 57.030 37.500 0.00 0.00 0.00 4.79
4444 5439 6.464222 AGTTGAGATACTTTGATTTCGGACA 58.536 36.000 0.00 0.00 0.00 4.02
4445 5440 6.934645 AGTTGAGATACTTTGATTTCGGACAA 59.065 34.615 0.00 0.00 0.00 3.18
4446 5441 7.444183 AGTTGAGATACTTTGATTTCGGACAAA 59.556 33.333 0.00 0.00 35.26 2.83
4447 5442 7.737972 TGAGATACTTTGATTTCGGACAAAA 57.262 32.000 0.00 0.00 35.95 2.44
4448 5443 7.581476 TGAGATACTTTGATTTCGGACAAAAC 58.419 34.615 0.00 0.00 35.95 2.43
4449 5444 7.444183 TGAGATACTTTGATTTCGGACAAAACT 59.556 33.333 0.00 0.00 35.95 2.66
4450 5445 8.166422 AGATACTTTGATTTCGGACAAAACTT 57.834 30.769 0.00 0.00 35.95 2.66
4451 5446 9.280174 AGATACTTTGATTTCGGACAAAACTTA 57.720 29.630 0.00 0.00 35.95 2.24
4455 5450 9.840427 ACTTTGATTTCGGACAAAACTTATATG 57.160 29.630 0.00 0.00 35.95 1.78
4456 5451 9.840427 CTTTGATTTCGGACAAAACTTATATGT 57.160 29.630 0.00 0.00 35.95 2.29
4457 5452 9.619316 TTTGATTTCGGACAAAACTTATATGTG 57.381 29.630 0.00 0.00 33.90 3.21
4458 5453 7.757526 TGATTTCGGACAAAACTTATATGTGG 58.242 34.615 0.00 0.00 0.00 4.17
4459 5454 7.608376 TGATTTCGGACAAAACTTATATGTGGA 59.392 33.333 0.00 0.00 0.00 4.02
4460 5455 6.730960 TTCGGACAAAACTTATATGTGGAC 57.269 37.500 0.00 0.00 0.00 4.02
4461 5456 6.045072 TCGGACAAAACTTATATGTGGACT 57.955 37.500 0.00 0.00 0.00 3.85
4462 5457 7.172868 TCGGACAAAACTTATATGTGGACTA 57.827 36.000 0.00 0.00 0.00 2.59
4463 5458 7.613585 TCGGACAAAACTTATATGTGGACTAA 58.386 34.615 0.00 0.00 0.00 2.24
4464 5459 8.095792 TCGGACAAAACTTATATGTGGACTAAA 58.904 33.333 0.00 0.00 0.00 1.85
4465 5460 8.723311 CGGACAAAACTTATATGTGGACTAAAA 58.277 33.333 0.00 0.00 0.00 1.52
4476 5471 5.531122 TGTGGACTAAAATAGATCGGAGG 57.469 43.478 0.00 0.00 0.00 4.30
4477 5472 4.344102 TGTGGACTAAAATAGATCGGAGGG 59.656 45.833 0.00 0.00 0.00 4.30
4521 5518 6.496571 ACACTTCAGCTATATGTAAGTCGTC 58.503 40.000 0.00 0.00 0.00 4.20
4522 5519 5.621634 CACTTCAGCTATATGTAAGTCGTCG 59.378 44.000 0.00 0.00 0.00 5.12
4525 5522 4.451435 TCAGCTATATGTAAGTCGTCGGAG 59.549 45.833 0.00 0.00 0.00 4.63
4537 5534 5.352643 AGTCGTCGGAGTTTTAAATTTGG 57.647 39.130 0.00 0.00 0.00 3.28
4544 5541 7.691050 CGTCGGAGTTTTAAATTTGGATAAGTC 59.309 37.037 0.00 2.62 0.00 3.01
4581 5579 5.522456 TGATTCTTGTGTCAAGATTTGTGC 58.478 37.500 12.02 0.59 0.00 4.57
4589 5930 6.033341 TGTGTCAAGATTTGTGCTGTTTTAC 58.967 36.000 0.00 0.00 0.00 2.01
4594 5935 7.702348 GTCAAGATTTGTGCTGTTTTACTTTCT 59.298 33.333 0.00 0.00 0.00 2.52
4617 5958 8.275015 TCTTGTGTTGTTTCATGACTTCTTAA 57.725 30.769 0.00 0.00 0.00 1.85
4626 5967 8.292448 TGTTTCATGACTTCTTAAGCTGATTTC 58.708 33.333 0.00 0.00 0.00 2.17
4666 6192 7.669089 TTGGGGTAAGTCAATTTTCTTTTCT 57.331 32.000 0.00 0.00 0.00 2.52
4745 6271 0.681564 TGGACTTGCCGTTGTTTGGT 60.682 50.000 0.00 0.00 40.66 3.67
4750 6276 3.018149 ACTTGCCGTTGTTTGGTTAAGA 58.982 40.909 0.00 0.00 31.53 2.10
4755 6281 4.174762 GCCGTTGTTTGGTTAAGACAAAA 58.825 39.130 6.79 0.00 39.29 2.44
4756 6282 4.626172 GCCGTTGTTTGGTTAAGACAAAAA 59.374 37.500 6.79 0.37 39.29 1.94
4787 6315 5.070001 TGGGCATTAGGCTAATTACACATC 58.930 41.667 16.95 4.35 44.01 3.06
4792 6320 6.568462 GCATTAGGCTAATTACACATCGCATT 60.568 38.462 16.95 0.00 40.25 3.56
4881 6417 2.566833 TTGCTGCACTTCCACTGTAT 57.433 45.000 0.00 0.00 0.00 2.29
4936 6481 6.829229 TCTGTCATTGATTTCTGCTTTGAT 57.171 33.333 0.00 0.00 0.00 2.57
4952 6497 6.615088 TGCTTTGATATTTGTGCTCTCTTTC 58.385 36.000 0.00 0.00 0.00 2.62
5068 6626 3.173965 CCTCCACTCTCTCCCTTTGTTA 58.826 50.000 0.00 0.00 0.00 2.41
5083 6641 8.754991 TCCCTTTGTTATTTTCTGTTTACTGA 57.245 30.769 0.00 0.00 0.00 3.41
5084 6642 9.362151 TCCCTTTGTTATTTTCTGTTTACTGAT 57.638 29.630 0.00 0.00 0.00 2.90
5085 6643 9.981114 CCCTTTGTTATTTTCTGTTTACTGATT 57.019 29.630 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.556451 CATGATCACCTCCCACAGTCA 59.444 52.381 0.00 0.00 0.00 3.41
1 2 1.745141 GCATGATCACCTCCCACAGTC 60.745 57.143 0.00 0.00 0.00 3.51
2 3 0.254178 GCATGATCACCTCCCACAGT 59.746 55.000 0.00 0.00 0.00 3.55
8 9 1.224075 CGATGTGCATGATCACCTCC 58.776 55.000 0.00 0.00 36.17 4.30
17 18 5.163824 ACACTCATTTTCTACGATGTGCATG 60.164 40.000 0.00 0.00 0.00 4.06
39 46 3.294908 CGTCGATACGTTTCGGACA 57.705 52.632 24.64 6.40 44.21 4.02
54 61 3.813166 TGAAACTGAAACCCTTGATCGTC 59.187 43.478 0.00 0.00 0.00 4.20
99 107 2.202690 CGTTGCCGCTCGTCCATA 60.203 61.111 0.00 0.00 0.00 2.74
105 113 1.721133 GTTCAAACGTTGCCGCTCG 60.721 57.895 0.00 6.91 37.70 5.03
141 152 9.982291 GTGAGTTTTCTAATCACGCATTTTATA 57.018 29.630 0.00 0.00 34.55 0.98
231 243 9.834628 CATAGTTTTACAAGCCGAATAAAAAGA 57.165 29.630 0.00 0.00 31.47 2.52
232 244 9.620660 ACATAGTTTTACAAGCCGAATAAAAAG 57.379 29.630 0.00 0.00 31.47 2.27
364 414 4.041075 TCCAACACGCATACCCATATATGT 59.959 41.667 11.73 0.00 35.36 2.29
367 417 3.553302 CGTCCAACACGCATACCCATATA 60.553 47.826 0.00 0.00 42.87 0.86
381 431 4.228567 TCGGCACTGCGTCCAACA 62.229 61.111 0.00 0.00 0.00 3.33
387 437 3.842925 ATTTGGGTCGGCACTGCGT 62.843 57.895 0.00 0.00 0.00 5.24
408 458 3.479269 CGGTGTCCGCGCTCTTTC 61.479 66.667 5.56 0.00 41.17 2.62
429 479 2.670251 CGTTTAGGTTGGCCGCCA 60.670 61.111 8.43 8.43 40.50 5.69
437 487 2.033675 CCGCTTTTTGTCCGTTTAGGTT 59.966 45.455 0.00 0.00 41.99 3.50
441 491 2.286872 TGTCCGCTTTTTGTCCGTTTA 58.713 42.857 0.00 0.00 0.00 2.01
533 591 7.592164 GGTTTTCGATCCTTAAATTTTGTTCGA 59.408 33.333 0.00 5.28 33.09 3.71
534 592 7.593644 AGGTTTTCGATCCTTAAATTTTGTTCG 59.406 33.333 0.00 3.10 0.00 3.95
538 596 7.375053 TGGAGGTTTTCGATCCTTAAATTTTG 58.625 34.615 0.00 0.00 33.83 2.44
541 599 7.718334 ATTGGAGGTTTTCGATCCTTAAATT 57.282 32.000 3.79 0.00 33.83 1.82
542 600 7.718334 AATTGGAGGTTTTCGATCCTTAAAT 57.282 32.000 3.79 5.70 33.83 1.40
543 601 7.533289 AAATTGGAGGTTTTCGATCCTTAAA 57.467 32.000 3.79 4.01 33.83 1.52
589 647 5.701224 TGTTGGTTTGAATTCTTAGGGTCT 58.299 37.500 7.05 0.00 0.00 3.85
924 1884 4.193334 CTCAGCGGTGATCGGCGA 62.193 66.667 18.98 13.87 43.21 5.54
969 1937 1.107538 TCGATGGAAGTCGCCTAGGG 61.108 60.000 11.72 0.44 41.22 3.53
1164 2154 0.319641 GGAAGTTGAACTCGAGCGGT 60.320 55.000 13.61 0.00 0.00 5.68
1479 2469 4.133796 GCATCAACCTTGGGCGGC 62.134 66.667 0.00 0.00 0.00 6.53
1562 2552 3.423154 CGTGTGCTTTCTCCGGCC 61.423 66.667 0.00 0.00 0.00 6.13
1566 2556 2.383527 CGCTCCGTGTGCTTTCTCC 61.384 63.158 0.00 0.00 0.00 3.71
1678 2668 2.383527 GCACCGCTTCCGAACTCAG 61.384 63.158 0.00 0.00 36.29 3.35
1708 2698 3.443925 CCTCTCTGACGCCGCTGA 61.444 66.667 0.00 0.00 0.00 4.26
2556 3546 0.179097 GGGAGATGACGAAGCAGTCC 60.179 60.000 0.00 0.00 40.26 3.85
2583 3573 2.125673 GCTTCCTTGCCGTAGCGA 60.126 61.111 0.00 0.00 44.31 4.93
2652 3642 2.577059 GCCACCTTCCGATCGTCA 59.423 61.111 15.09 0.00 0.00 4.35
2670 3660 0.670854 GAAGGTCGAGCCACTTGGAC 60.671 60.000 11.73 0.00 40.61 4.02
2706 3696 2.029649 CCACTTGCCCACTTTTCTCATG 60.030 50.000 0.00 0.00 0.00 3.07
3132 4122 4.096003 CGCACCTTCCCCATCGGT 62.096 66.667 0.00 0.00 0.00 4.69
3339 4329 4.137872 TTCACGGACGGGATCGGC 62.138 66.667 0.00 0.00 45.30 5.54
4087 5077 1.274167 ACGTTCCGACATAGAAGGCAA 59.726 47.619 0.00 0.00 33.48 4.52
4101 5091 3.988517 GCTAGCCTTACATGATACGTTCC 59.011 47.826 2.29 0.00 0.00 3.62
4116 5106 1.144093 AGATCCTACACGAGCTAGCCT 59.856 52.381 12.13 0.00 0.00 4.58
4117 5107 1.268352 CAGATCCTACACGAGCTAGCC 59.732 57.143 12.13 1.79 0.00 3.93
4118 5108 1.335506 GCAGATCCTACACGAGCTAGC 60.336 57.143 6.62 6.62 0.00 3.42
4119 5109 1.268352 GGCAGATCCTACACGAGCTAG 59.732 57.143 0.00 0.00 0.00 3.42
4120 5110 1.319541 GGCAGATCCTACACGAGCTA 58.680 55.000 0.00 0.00 0.00 3.32
4121 5111 1.729470 CGGCAGATCCTACACGAGCT 61.729 60.000 0.00 0.00 0.00 4.09
4122 5112 1.299468 CGGCAGATCCTACACGAGC 60.299 63.158 0.00 0.00 0.00 5.03
4123 5113 0.309302 CTCGGCAGATCCTACACGAG 59.691 60.000 0.00 0.00 41.20 4.18
4124 5114 1.725557 GCTCGGCAGATCCTACACGA 61.726 60.000 0.00 0.00 0.00 4.35
4125 5115 1.299468 GCTCGGCAGATCCTACACG 60.299 63.158 0.00 0.00 0.00 4.49
4126 5116 1.299468 CGCTCGGCAGATCCTACAC 60.299 63.158 0.00 0.00 0.00 2.90
4127 5117 2.490148 CCGCTCGGCAGATCCTACA 61.490 63.158 0.00 0.00 0.00 2.74
4128 5118 2.336809 CCGCTCGGCAGATCCTAC 59.663 66.667 0.00 0.00 0.00 3.18
4129 5119 2.123854 ACCGCTCGGCAGATCCTA 60.124 61.111 8.41 0.00 39.32 2.94
4130 5120 3.842923 CACCGCTCGGCAGATCCT 61.843 66.667 8.41 0.00 39.32 3.24
4152 5147 2.284625 TCCATGGCGACCCAGACT 60.285 61.111 6.96 0.00 46.24 3.24
4179 5174 3.326747 CCAGTACTACAAGGTGCAACTC 58.673 50.000 3.77 0.00 36.74 3.01
4187 5182 3.672767 AAACGACCCAGTACTACAAGG 57.327 47.619 0.00 0.00 0.00 3.61
4188 5183 3.992427 GGAAAACGACCCAGTACTACAAG 59.008 47.826 0.00 0.00 0.00 3.16
4199 5194 5.059161 AGTACTACAAAAGGAAAACGACCC 58.941 41.667 0.00 0.00 0.00 4.46
4201 5196 6.145209 GGAGAGTACTACAAAAGGAAAACGAC 59.855 42.308 0.00 0.00 0.00 4.34
4215 5210 2.510800 AGGACCAGAGGGAGAGTACTAC 59.489 54.545 0.00 0.00 38.05 2.73
4217 5212 1.688750 AGGACCAGAGGGAGAGTACT 58.311 55.000 0.00 0.00 38.05 2.73
4218 5213 2.535836 AAGGACCAGAGGGAGAGTAC 57.464 55.000 0.00 0.00 38.05 2.73
4219 5214 3.562108 AAAAGGACCAGAGGGAGAGTA 57.438 47.619 0.00 0.00 38.05 2.59
4221 5216 5.190726 AGAATAAAAAGGACCAGAGGGAGAG 59.809 44.000 0.00 0.00 38.05 3.20
4222 5217 5.045578 CAGAATAAAAAGGACCAGAGGGAGA 60.046 44.000 0.00 0.00 38.05 3.71
4223 5218 5.189180 CAGAATAAAAAGGACCAGAGGGAG 58.811 45.833 0.00 0.00 38.05 4.30
4224 5219 4.567747 GCAGAATAAAAAGGACCAGAGGGA 60.568 45.833 0.00 0.00 38.05 4.20
4227 5222 7.814264 ATATGCAGAATAAAAAGGACCAGAG 57.186 36.000 0.00 0.00 0.00 3.35
4229 5224 9.342308 TCTAATATGCAGAATAAAAAGGACCAG 57.658 33.333 0.00 0.00 0.00 4.00
4241 5236 9.182214 ACTTGACACAAATCTAATATGCAGAAT 57.818 29.630 0.00 0.00 0.00 2.40
4242 5237 8.565896 ACTTGACACAAATCTAATATGCAGAA 57.434 30.769 0.00 0.00 0.00 3.02
4243 5238 8.565896 AACTTGACACAAATCTAATATGCAGA 57.434 30.769 0.00 0.00 0.00 4.26
4251 5246 9.296400 GCAAAGTTTAACTTGACACAAATCTAA 57.704 29.630 11.35 0.00 38.66 2.10
4252 5247 8.462811 TGCAAAGTTTAACTTGACACAAATCTA 58.537 29.630 11.35 0.00 38.66 1.98
4253 5248 7.319646 TGCAAAGTTTAACTTGACACAAATCT 58.680 30.769 11.35 0.00 38.66 2.40
4254 5249 7.518731 TGCAAAGTTTAACTTGACACAAATC 57.481 32.000 11.35 0.00 38.66 2.17
4255 5250 7.897575 TTGCAAAGTTTAACTTGACACAAAT 57.102 28.000 11.35 0.00 38.66 2.32
4256 5251 7.439655 ACTTTGCAAAGTTTAACTTGACACAAA 59.560 29.630 33.85 15.74 46.52 2.83
4257 5252 6.926272 ACTTTGCAAAGTTTAACTTGACACAA 59.074 30.769 33.85 10.17 46.52 3.33
4258 5253 6.451393 ACTTTGCAAAGTTTAACTTGACACA 58.549 32.000 33.85 5.31 46.52 3.72
4259 5254 6.944557 ACTTTGCAAAGTTTAACTTGACAC 57.055 33.333 33.85 2.49 46.52 3.67
4349 5344 9.295825 ACCAACATTGTTAGATTCACTATGAAA 57.704 29.630 0.86 0.00 40.12 2.69
4350 5345 8.862325 ACCAACATTGTTAGATTCACTATGAA 57.138 30.769 0.86 0.00 41.09 2.57
4351 5346 8.862325 AACCAACATTGTTAGATTCACTATGA 57.138 30.769 0.86 0.00 33.28 2.15
4352 5347 9.345517 CAAACCAACATTGTTAGATTCACTATG 57.654 33.333 0.86 0.00 34.64 2.23
4353 5348 8.522830 CCAAACCAACATTGTTAGATTCACTAT 58.477 33.333 0.86 0.00 0.00 2.12
4354 5349 7.523052 GCCAAACCAACATTGTTAGATTCACTA 60.523 37.037 0.86 0.00 0.00 2.74
4355 5350 6.738453 GCCAAACCAACATTGTTAGATTCACT 60.738 38.462 0.86 0.00 0.00 3.41
4356 5351 5.405269 GCCAAACCAACATTGTTAGATTCAC 59.595 40.000 0.86 0.00 0.00 3.18
4357 5352 5.069648 TGCCAAACCAACATTGTTAGATTCA 59.930 36.000 0.86 0.00 0.00 2.57
4358 5353 5.537188 TGCCAAACCAACATTGTTAGATTC 58.463 37.500 0.86 0.00 0.00 2.52
4359 5354 5.543507 TGCCAAACCAACATTGTTAGATT 57.456 34.783 0.86 0.00 0.00 2.40
4360 5355 5.743636 ATGCCAAACCAACATTGTTAGAT 57.256 34.783 0.86 0.00 0.00 1.98
4361 5356 5.295950 CAATGCCAAACCAACATTGTTAGA 58.704 37.500 0.86 0.00 43.53 2.10
4362 5357 5.594724 CAATGCCAAACCAACATTGTTAG 57.405 39.130 0.86 0.00 43.53 2.34
4367 5362 5.062528 CCTTTACAATGCCAAACCAACATT 58.937 37.500 0.00 0.00 34.42 2.71
4368 5363 4.102367 ACCTTTACAATGCCAAACCAACAT 59.898 37.500 0.00 0.00 0.00 2.71
4369 5364 3.452627 ACCTTTACAATGCCAAACCAACA 59.547 39.130 0.00 0.00 0.00 3.33
4370 5365 4.066646 ACCTTTACAATGCCAAACCAAC 57.933 40.909 0.00 0.00 0.00 3.77
4371 5366 4.762289 AACCTTTACAATGCCAAACCAA 57.238 36.364 0.00 0.00 0.00 3.67
4372 5367 5.871396 TTAACCTTTACAATGCCAAACCA 57.129 34.783 0.00 0.00 0.00 3.67
4373 5368 7.608153 AGTATTAACCTTTACAATGCCAAACC 58.392 34.615 0.00 0.00 0.00 3.27
4374 5369 9.483916 AAAGTATTAACCTTTACAATGCCAAAC 57.516 29.630 1.17 0.00 30.59 2.93
4401 5396 9.621629 TCTCAACTTTGACCAAACTTATAGAAA 57.378 29.630 0.00 0.00 32.90 2.52
4402 5397 9.793259 ATCTCAACTTTGACCAAACTTATAGAA 57.207 29.630 0.00 0.00 32.90 2.10
4406 5401 9.574516 AAGTATCTCAACTTTGACCAAACTTAT 57.425 29.630 0.00 0.00 36.26 1.73
4407 5402 8.974060 AAGTATCTCAACTTTGACCAAACTTA 57.026 30.769 0.00 0.00 36.26 2.24
4408 5403 7.881775 AAGTATCTCAACTTTGACCAAACTT 57.118 32.000 0.00 0.00 36.26 2.66
4409 5404 7.881775 AAAGTATCTCAACTTTGACCAAACT 57.118 32.000 1.41 0.00 45.60 2.66
4419 5414 6.934645 TGTCCGAAATCAAAGTATCTCAACTT 59.065 34.615 0.00 0.00 41.46 2.66
4420 5415 6.464222 TGTCCGAAATCAAAGTATCTCAACT 58.536 36.000 0.00 0.00 0.00 3.16
4421 5416 6.721571 TGTCCGAAATCAAAGTATCTCAAC 57.278 37.500 0.00 0.00 0.00 3.18
4422 5417 7.737972 TTTGTCCGAAATCAAAGTATCTCAA 57.262 32.000 0.00 0.00 0.00 3.02
4423 5418 7.444183 AGTTTTGTCCGAAATCAAAGTATCTCA 59.556 33.333 0.00 0.00 35.47 3.27
4424 5419 7.807680 AGTTTTGTCCGAAATCAAAGTATCTC 58.192 34.615 0.00 0.00 35.47 2.75
4425 5420 7.745620 AGTTTTGTCCGAAATCAAAGTATCT 57.254 32.000 0.00 0.00 35.47 1.98
4429 5424 9.840427 CATATAAGTTTTGTCCGAAATCAAAGT 57.160 29.630 0.00 0.00 35.47 2.66
4430 5425 9.840427 ACATATAAGTTTTGTCCGAAATCAAAG 57.160 29.630 0.00 0.00 35.47 2.77
4431 5426 9.619316 CACATATAAGTTTTGTCCGAAATCAAA 57.381 29.630 0.00 0.00 32.75 2.69
4432 5427 8.240682 CCACATATAAGTTTTGTCCGAAATCAA 58.759 33.333 0.00 0.00 0.00 2.57
4433 5428 7.608376 TCCACATATAAGTTTTGTCCGAAATCA 59.392 33.333 0.00 0.00 0.00 2.57
4434 5429 7.908601 GTCCACATATAAGTTTTGTCCGAAATC 59.091 37.037 0.00 0.00 0.00 2.17
4435 5430 7.610305 AGTCCACATATAAGTTTTGTCCGAAAT 59.390 33.333 0.00 0.00 0.00 2.17
4436 5431 6.938030 AGTCCACATATAAGTTTTGTCCGAAA 59.062 34.615 0.00 0.00 0.00 3.46
4437 5432 6.469410 AGTCCACATATAAGTTTTGTCCGAA 58.531 36.000 0.00 0.00 0.00 4.30
4438 5433 6.045072 AGTCCACATATAAGTTTTGTCCGA 57.955 37.500 0.00 0.00 0.00 4.55
4439 5434 7.837202 TTAGTCCACATATAAGTTTTGTCCG 57.163 36.000 0.00 0.00 0.00 4.79
4450 5445 8.967918 CCTCCGATCTATTTTAGTCCACATATA 58.032 37.037 0.00 0.00 0.00 0.86
4451 5446 7.093289 CCCTCCGATCTATTTTAGTCCACATAT 60.093 40.741 0.00 0.00 0.00 1.78
4452 5447 6.210784 CCCTCCGATCTATTTTAGTCCACATA 59.789 42.308 0.00 0.00 0.00 2.29
4453 5448 5.012148 CCCTCCGATCTATTTTAGTCCACAT 59.988 44.000 0.00 0.00 0.00 3.21
4454 5449 4.344102 CCCTCCGATCTATTTTAGTCCACA 59.656 45.833 0.00 0.00 0.00 4.17
4455 5450 4.587684 TCCCTCCGATCTATTTTAGTCCAC 59.412 45.833 0.00 0.00 0.00 4.02
4456 5451 4.811498 TCCCTCCGATCTATTTTAGTCCA 58.189 43.478 0.00 0.00 0.00 4.02
4457 5452 4.833938 ACTCCCTCCGATCTATTTTAGTCC 59.166 45.833 0.00 0.00 0.00 3.85
4458 5453 6.716173 AGTACTCCCTCCGATCTATTTTAGTC 59.284 42.308 0.00 0.00 0.00 2.59
4459 5454 6.612741 AGTACTCCCTCCGATCTATTTTAGT 58.387 40.000 0.00 0.00 0.00 2.24
4460 5455 7.527568 AAGTACTCCCTCCGATCTATTTTAG 57.472 40.000 0.00 0.00 0.00 1.85
4461 5456 7.176340 GCTAAGTACTCCCTCCGATCTATTTTA 59.824 40.741 0.00 0.00 0.00 1.52
4462 5457 6.015265 GCTAAGTACTCCCTCCGATCTATTTT 60.015 42.308 0.00 0.00 0.00 1.82
4463 5458 5.477637 GCTAAGTACTCCCTCCGATCTATTT 59.522 44.000 0.00 0.00 0.00 1.40
4464 5459 5.011586 GCTAAGTACTCCCTCCGATCTATT 58.988 45.833 0.00 0.00 0.00 1.73
4465 5460 4.290196 AGCTAAGTACTCCCTCCGATCTAT 59.710 45.833 0.00 0.00 0.00 1.98
4466 5461 3.651904 AGCTAAGTACTCCCTCCGATCTA 59.348 47.826 0.00 0.00 0.00 1.98
4467 5462 2.444010 AGCTAAGTACTCCCTCCGATCT 59.556 50.000 0.00 0.00 0.00 2.75
4468 5463 2.866351 AGCTAAGTACTCCCTCCGATC 58.134 52.381 0.00 0.00 0.00 3.69
4469 5464 3.395273 ACTAGCTAAGTACTCCCTCCGAT 59.605 47.826 0.00 0.00 36.36 4.18
4470 5465 2.776536 ACTAGCTAAGTACTCCCTCCGA 59.223 50.000 0.00 0.00 36.36 4.55
4471 5466 3.211718 ACTAGCTAAGTACTCCCTCCG 57.788 52.381 0.00 0.00 36.36 4.63
4472 5467 6.363882 TCTTTACTAGCTAAGTACTCCCTCC 58.636 44.000 0.00 0.00 40.48 4.30
4473 5468 7.338957 TGTTCTTTACTAGCTAAGTACTCCCTC 59.661 40.741 0.00 0.00 40.48 4.30
4474 5469 7.122501 GTGTTCTTTACTAGCTAAGTACTCCCT 59.877 40.741 0.00 0.00 40.48 4.20
4475 5470 7.122501 AGTGTTCTTTACTAGCTAAGTACTCCC 59.877 40.741 0.00 0.00 40.48 4.30
4476 5471 8.054152 AGTGTTCTTTACTAGCTAAGTACTCC 57.946 38.462 0.00 0.00 40.48 3.85
4477 5472 9.558648 GAAGTGTTCTTTACTAGCTAAGTACTC 57.441 37.037 0.00 9.90 40.48 2.59
4513 5510 6.705381 TCCAAATTTAAAACTCCGACGACTTA 59.295 34.615 0.00 0.00 0.00 2.24
4521 5518 9.855021 ATTGACTTATCCAAATTTAAAACTCCG 57.145 29.630 0.00 0.00 0.00 4.63
4537 5534 9.727627 GAATCATGGTCTGAAAATTGACTTATC 57.272 33.333 0.00 0.00 37.44 1.75
4544 5541 7.149973 ACACAAGAATCATGGTCTGAAAATTG 58.850 34.615 0.00 0.00 37.44 2.32
4552 5549 5.233083 TCTTGACACAAGAATCATGGTCT 57.767 39.130 11.06 0.00 0.00 3.85
4581 5579 8.514136 TGAAACAACACAAGAAAGTAAAACAG 57.486 30.769 0.00 0.00 0.00 3.16
4589 5930 7.253422 AGAAGTCATGAAACAACACAAGAAAG 58.747 34.615 0.00 0.00 0.00 2.62
4594 5935 6.972328 GCTTAAGAAGTCATGAAACAACACAA 59.028 34.615 6.67 0.00 0.00 3.33
4617 5958 3.080319 GAGGCAAGTCAAGAAATCAGCT 58.920 45.455 0.00 0.00 0.00 4.24
4626 5967 2.157738 CCCAAAGAGAGGCAAGTCAAG 58.842 52.381 0.00 0.00 0.00 3.02
4666 6192 3.258123 GGCAAGTCAAAAATCCAGCCTAA 59.742 43.478 0.00 0.00 37.89 2.69
4756 6282 9.996554 GTAATTAGCCTAATGCCCAATAATTTT 57.003 29.630 0.00 0.00 42.71 1.82
4757 6283 9.153479 TGTAATTAGCCTAATGCCCAATAATTT 57.847 29.630 0.00 0.00 42.71 1.82
4758 6284 8.585018 GTGTAATTAGCCTAATGCCCAATAATT 58.415 33.333 0.00 0.00 42.71 1.40
4759 6285 7.728083 TGTGTAATTAGCCTAATGCCCAATAAT 59.272 33.333 0.00 0.00 42.71 1.28
4760 6286 7.063593 TGTGTAATTAGCCTAATGCCCAATAA 58.936 34.615 0.00 0.00 42.71 1.40
4792 6320 6.765915 AGCAAAAGCAAAAACCCATAAAAA 57.234 29.167 0.00 0.00 0.00 1.94
4866 6402 3.550820 ACAAACATACAGTGGAAGTGCA 58.449 40.909 0.00 0.00 42.38 4.57
4874 6410 1.790043 TCACGCGACAAACATACAGTG 59.210 47.619 15.93 0.00 0.00 3.66
4881 6417 3.406728 TGAATTTTCACGCGACAAACA 57.593 38.095 15.93 2.82 31.01 2.83
4936 6481 7.172190 CAGAACAGAAGAAAGAGAGCACAAATA 59.828 37.037 0.00 0.00 0.00 1.40
4952 6497 4.521943 CAAAAGAACTCGCAGAACAGAAG 58.478 43.478 0.00 0.00 34.09 2.85
4989 6540 7.976414 AAGGAATTCCCAAATATGTGATTGA 57.024 32.000 21.22 0.00 37.41 2.57
4995 6546 8.067488 AGGATGTTAAGGAATTCCCAAATATGT 58.933 33.333 21.22 6.39 37.41 2.29


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

AutoCloner maintained by Alex Coulton.