Multiple sequence alignment - TraesCS4D01G107000

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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 TraesCS4D01G107000 chr4D 100.000 5147 0 0 1 5147 85263841 85258695 0.000000e+00 9505.0
1 TraesCS4D01G107000 chr4D 94.509 4061 206 11 117 4168 85176441 85172389 0.000000e+00 6248.0
2 TraesCS4D01G107000 chr4D 75.908 2532 563 38 1080 3586 1398219 1400728 0.000000e+00 1253.0
3 TraesCS4D01G107000 chr4D 94.025 318 16 1 4518 4835 85166766 85166452 3.610000e-131 479.0
4 TraesCS4D01G107000 chr4D 93.396 318 18 1 4518 4835 84990361 84990675 7.800000e-128 468.0
5 TraesCS4D01G107000 chr4D 92.135 178 11 3 4157 4331 85172367 85172190 1.110000e-61 248.0
6 TraesCS4D01G107000 chr4D 96.528 144 4 1 5004 5147 84990959 84991101 2.400000e-58 237.0
7 TraesCS4D01G107000 chr4D 95.833 144 5 1 5004 5147 85166168 85166026 1.110000e-56 231.0
8 TraesCS4D01G107000 chr4D 85.955 178 17 2 4327 4496 85167007 85166830 3.170000e-42 183.0
9 TraesCS4D01G107000 chr4D 85.714 175 17 2 4327 4493 84990120 84990294 1.470000e-40 178.0
10 TraesCS4D01G107000 chr4D 86.755 151 5 2 4871 5006 85166383 85166233 2.480000e-33 154.0
11 TraesCS4D01G107000 chr4D 86.486 148 5 2 4871 5003 84990744 84990891 1.150000e-31 148.0
12 TraesCS4D01G107000 chr4B 93.821 4402 246 13 117 4496 122301166 122296769 0.000000e+00 6599.0
13 TraesCS4D01G107000 chr4B 85.517 290 15 4 4517 4806 122296713 122296451 1.410000e-70 278.0
14 TraesCS4D01G107000 chr4B 96.528 144 5 0 5004 5147 122295994 122295851 6.660000e-59 239.0
15 TraesCS4D01G107000 chr4B 96.875 128 4 0 4871 4998 122296189 122296062 1.120000e-51 215.0
16 TraesCS4D01G107000 chr4B 100.000 31 0 0 4805 4835 122296288 122296258 2.000000e-04 58.4
17 TraesCS4D01G107000 chr4A 94.329 4267 212 17 117 4369 498989654 498985404 0.000000e+00 6512.0
18 TraesCS4D01G107000 chr4A 88.538 506 39 12 4517 5008 498985243 498984743 3.430000e-166 595.0
19 TraesCS4D01G107000 chr4A 96.528 144 5 0 5004 5147 498984680 498984537 6.660000e-59 239.0
20 TraesCS4D01G107000 chr4A 100.000 42 0 0 4431 4472 498985370 498985329 1.540000e-10 78.7
21 TraesCS4D01G107000 chrUn 75.323 2630 588 50 1079 3679 75441564 75444161 0.000000e+00 1205.0
22 TraesCS4D01G107000 chr3A 75.133 2638 580 65 1080 3679 36300277 36302876 0.000000e+00 1168.0
23 TraesCS4D01G107000 chr3D 75.078 2556 571 56 1080 3597 26300877 26303404 0.000000e+00 1131.0
24 TraesCS4D01G107000 chr3D 74.442 2555 594 49 1088 3613 26222465 26219941 0.000000e+00 1046.0
25 TraesCS4D01G107000 chr3D 79.046 1279 249 17 2330 3597 26282540 26283810 0.000000e+00 859.0


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 TraesCS4D01G107000 chr4D 85258695 85263841 5146 True 9505.000 9505 100.00000 1 5147 1 chr4D.!!$R1 5146
1 TraesCS4D01G107000 chr4D 85172190 85176441 4251 True 3248.000 6248 93.32200 117 4331 2 chr4D.!!$R3 4214
2 TraesCS4D01G107000 chr4D 1398219 1400728 2509 False 1253.000 1253 75.90800 1080 3586 1 chr4D.!!$F1 2506
3 TraesCS4D01G107000 chr4D 85166026 85167007 981 True 261.750 479 90.64200 4327 5147 4 chr4D.!!$R2 820
4 TraesCS4D01G107000 chr4D 84990120 84991101 981 False 257.750 468 90.53100 4327 5147 4 chr4D.!!$F2 820
5 TraesCS4D01G107000 chr4B 122295851 122301166 5315 True 1477.880 6599 94.54820 117 5147 5 chr4B.!!$R1 5030
6 TraesCS4D01G107000 chr4A 498984537 498989654 5117 True 1856.175 6512 94.84875 117 5147 4 chr4A.!!$R1 5030
7 TraesCS4D01G107000 chrUn 75441564 75444161 2597 False 1205.000 1205 75.32300 1079 3679 1 chrUn.!!$F1 2600
8 TraesCS4D01G107000 chr3A 36300277 36302876 2599 False 1168.000 1168 75.13300 1080 3679 1 chr3A.!!$F1 2599
9 TraesCS4D01G107000 chr3D 26300877 26303404 2527 False 1131.000 1131 75.07800 1080 3597 1 chr3D.!!$F2 2517
10 TraesCS4D01G107000 chr3D 26219941 26222465 2524 True 1046.000 1046 74.44200 1088 3613 1 chr3D.!!$R1 2525
11 TraesCS4D01G107000 chr3D 26282540 26283810 1270 False 859.000 859 79.04600 2330 3597 1 chr3D.!!$F1 1267

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
79 80 0.108945 ACTTGTAGCTACGGCCGTTC 60.109 55.000 38.94 27.28 39.73 3.95 F
1650 1667 0.035598 TTGCCAAGTTACCTGCGCTA 59.964 50.000 9.73 0.00 0.00 4.26 F
1704 1721 1.070601 GGCAGGTTTCAACAAGCCATT 59.929 47.619 15.79 0.00 44.65 3.16 F
2665 2685 2.007608 GAAGCATCCCCACTTCGTTAC 58.992 52.381 0.00 0.00 33.56 2.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 1922 2.524306 CCAATGGACCTAAGCACCAAA 58.476 47.619 0.00 0.00 37.24 3.28 R
2581 2601 2.047061 ACACTCACCCAAAGTGCTAGA 58.953 47.619 0.00 0.00 46.48 2.43 R
3189 3212 2.104792 CCTTGTCTCCAGGTTGAAGACA 59.895 50.000 4.86 4.86 37.68 3.41 R
4410 4473 0.179073 ACAATAATGAGGCGCTCGCT 60.179 50.000 7.64 0.00 41.60 4.93 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
30 31 9.346725 GCTAAAGTTAAATATCTATTGCCATGC 57.653 33.333 0.00 0.00 0.00 4.06
31 32 9.846248 CTAAAGTTAAATATCTATTGCCATGCC 57.154 33.333 0.00 0.00 0.00 4.40
32 33 8.482852 AAAGTTAAATATCTATTGCCATGCCT 57.517 30.769 0.00 0.00 0.00 4.75
33 34 9.586732 AAAGTTAAATATCTATTGCCATGCCTA 57.413 29.630 0.00 0.00 0.00 3.93
34 35 9.759473 AAGTTAAATATCTATTGCCATGCCTAT 57.241 29.630 0.00 0.00 0.00 2.57
40 41 9.925545 AATATCTATTGCCATGCCTATAAATGA 57.074 29.630 0.00 0.00 0.00 2.57
41 42 7.876936 ATCTATTGCCATGCCTATAAATGAG 57.123 36.000 0.00 0.00 0.00 2.90
42 43 6.182627 TCTATTGCCATGCCTATAAATGAGG 58.817 40.000 0.00 0.00 37.12 3.86
43 44 3.159213 TGCCATGCCTATAAATGAGGG 57.841 47.619 0.00 0.00 34.35 4.30
44 45 2.446666 TGCCATGCCTATAAATGAGGGT 59.553 45.455 0.00 0.00 34.35 4.34
45 46 2.821969 GCCATGCCTATAAATGAGGGTG 59.178 50.000 0.00 0.00 34.35 4.61
46 47 2.821969 CCATGCCTATAAATGAGGGTGC 59.178 50.000 0.00 0.00 34.35 5.01
47 48 2.656947 TGCCTATAAATGAGGGTGCC 57.343 50.000 0.00 0.00 34.35 5.01
48 49 1.849692 TGCCTATAAATGAGGGTGCCA 59.150 47.619 0.00 0.00 34.35 4.92
49 50 2.243478 TGCCTATAAATGAGGGTGCCAA 59.757 45.455 0.00 0.00 34.35 4.52
50 51 2.887152 GCCTATAAATGAGGGTGCCAAG 59.113 50.000 0.00 0.00 34.35 3.61
51 52 2.887152 CCTATAAATGAGGGTGCCAAGC 59.113 50.000 0.00 0.00 0.00 4.01
52 53 2.530460 ATAAATGAGGGTGCCAAGCA 57.470 45.000 0.00 0.00 35.60 3.91
53 54 1.838112 TAAATGAGGGTGCCAAGCAG 58.162 50.000 0.00 0.00 40.08 4.24
62 63 2.100605 GTGCCAAGCAGCTAGTTACT 57.899 50.000 0.00 0.00 40.08 2.24
63 64 2.427506 GTGCCAAGCAGCTAGTTACTT 58.572 47.619 0.00 0.00 40.08 2.24
64 65 2.160417 GTGCCAAGCAGCTAGTTACTTG 59.840 50.000 11.55 11.55 40.08 3.16
65 66 2.224523 TGCCAAGCAGCTAGTTACTTGT 60.225 45.455 15.85 0.00 38.24 3.16
66 67 3.007506 TGCCAAGCAGCTAGTTACTTGTA 59.992 43.478 15.85 4.79 38.24 2.41
67 68 3.619038 GCCAAGCAGCTAGTTACTTGTAG 59.381 47.826 15.85 5.48 38.24 2.74
68 69 3.619038 CCAAGCAGCTAGTTACTTGTAGC 59.381 47.826 15.85 0.00 41.77 3.58
74 75 3.370276 GCTAGTTACTTGTAGCTACGGC 58.630 50.000 18.74 7.80 38.92 5.68
75 76 2.955477 AGTTACTTGTAGCTACGGCC 57.045 50.000 18.74 0.00 39.73 6.13
76 77 1.133790 AGTTACTTGTAGCTACGGCCG 59.866 52.381 26.86 26.86 39.73 6.13
77 78 1.135286 GTTACTTGTAGCTACGGCCGT 60.135 52.381 36.01 36.01 39.73 5.68
78 79 1.176527 TACTTGTAGCTACGGCCGTT 58.823 50.000 38.94 22.03 39.73 4.44
79 80 0.108945 ACTTGTAGCTACGGCCGTTC 60.109 55.000 38.94 27.28 39.73 3.95
80 81 0.172803 CTTGTAGCTACGGCCGTTCT 59.827 55.000 38.94 32.11 39.73 3.01
81 82 1.402968 CTTGTAGCTACGGCCGTTCTA 59.597 52.381 38.94 31.05 39.73 2.10
82 83 0.734889 TGTAGCTACGGCCGTTCTAC 59.265 55.000 37.13 37.13 39.73 2.59
83 84 0.734889 GTAGCTACGGCCGTTCTACA 59.265 55.000 37.86 24.37 39.73 2.74
84 85 0.734889 TAGCTACGGCCGTTCTACAC 59.265 55.000 38.94 18.78 39.73 2.90
85 86 1.517913 GCTACGGCCGTTCTACACC 60.518 63.158 38.94 12.94 0.00 4.16
86 87 1.140375 CTACGGCCGTTCTACACCC 59.860 63.158 38.94 0.00 0.00 4.61
87 88 1.597797 CTACGGCCGTTCTACACCCA 61.598 60.000 38.94 14.33 0.00 4.51
88 89 1.184322 TACGGCCGTTCTACACCCAA 61.184 55.000 38.94 11.67 0.00 4.12
89 90 1.301874 CGGCCGTTCTACACCCAAA 60.302 57.895 19.50 0.00 0.00 3.28
90 91 0.675522 CGGCCGTTCTACACCCAAAT 60.676 55.000 19.50 0.00 0.00 2.32
91 92 1.092348 GGCCGTTCTACACCCAAATC 58.908 55.000 0.00 0.00 0.00 2.17
92 93 1.612199 GGCCGTTCTACACCCAAATCA 60.612 52.381 0.00 0.00 0.00 2.57
93 94 1.737793 GCCGTTCTACACCCAAATCAG 59.262 52.381 0.00 0.00 0.00 2.90
94 95 2.614481 GCCGTTCTACACCCAAATCAGA 60.614 50.000 0.00 0.00 0.00 3.27
95 96 3.000727 CCGTTCTACACCCAAATCAGAC 58.999 50.000 0.00 0.00 0.00 3.51
96 97 3.556213 CCGTTCTACACCCAAATCAGACA 60.556 47.826 0.00 0.00 0.00 3.41
97 98 3.679980 CGTTCTACACCCAAATCAGACAG 59.320 47.826 0.00 0.00 0.00 3.51
98 99 3.981071 TCTACACCCAAATCAGACAGG 57.019 47.619 0.00 0.00 0.00 4.00
99 100 3.516586 TCTACACCCAAATCAGACAGGA 58.483 45.455 0.00 0.00 0.00 3.86
100 101 4.104086 TCTACACCCAAATCAGACAGGAT 58.896 43.478 0.00 0.00 0.00 3.24
101 102 3.814504 ACACCCAAATCAGACAGGATT 57.185 42.857 0.00 0.00 39.11 3.01
102 103 4.118168 ACACCCAAATCAGACAGGATTT 57.882 40.909 0.00 0.00 45.75 2.17
103 104 4.482990 ACACCCAAATCAGACAGGATTTT 58.517 39.130 0.00 0.00 43.13 1.82
104 105 5.640147 ACACCCAAATCAGACAGGATTTTA 58.360 37.500 0.00 0.00 43.13 1.52
105 106 6.074648 ACACCCAAATCAGACAGGATTTTAA 58.925 36.000 0.00 0.00 43.13 1.52
106 107 6.725834 ACACCCAAATCAGACAGGATTTTAAT 59.274 34.615 0.00 0.00 43.13 1.40
107 108 7.037438 CACCCAAATCAGACAGGATTTTAATG 58.963 38.462 0.00 0.00 43.13 1.90
108 109 6.725834 ACCCAAATCAGACAGGATTTTAATGT 59.274 34.615 0.00 0.00 43.13 2.71
109 110 7.235399 ACCCAAATCAGACAGGATTTTAATGTT 59.765 33.333 0.00 0.00 43.13 2.71
110 111 8.096414 CCCAAATCAGACAGGATTTTAATGTTT 58.904 33.333 0.00 0.00 43.13 2.83
111 112 9.143631 CCAAATCAGACAGGATTTTAATGTTTC 57.856 33.333 0.00 0.00 43.13 2.78
112 113 9.143631 CAAATCAGACAGGATTTTAATGTTTCC 57.856 33.333 0.00 0.00 43.13 3.13
113 114 8.655935 AATCAGACAGGATTTTAATGTTTCCT 57.344 30.769 0.00 0.00 39.18 3.36
114 115 8.655935 ATCAGACAGGATTTTAATGTTTCCTT 57.344 30.769 0.00 0.00 36.45 3.36
115 116 8.477419 TCAGACAGGATTTTAATGTTTCCTTT 57.523 30.769 0.00 0.00 36.45 3.11
131 132 3.141398 TCCTTTGCAGTTCAGATGACAC 58.859 45.455 0.00 0.00 0.00 3.67
132 133 2.880268 CCTTTGCAGTTCAGATGACACA 59.120 45.455 0.00 0.00 0.00 3.72
173 174 1.257675 GTTTGTGCAACCGTCAAATGC 59.742 47.619 3.14 0.00 40.45 3.56
210 211 2.487265 GGTGGACATGAACTCAAGGTGT 60.487 50.000 0.00 0.00 0.00 4.16
268 269 5.424121 AATCTTGTTTTCAGAGTTCCGTG 57.576 39.130 0.00 0.00 0.00 4.94
269 270 4.131649 TCTTGTTTTCAGAGTTCCGTGA 57.868 40.909 0.00 0.00 0.00 4.35
278 279 8.690840 GTTTTCAGAGTTCCGTGAAATTTTATG 58.309 33.333 0.00 0.00 41.20 1.90
289 290 7.921214 TCCGTGAAATTTTATGCAAGTGTTTTA 59.079 29.630 0.00 0.00 0.00 1.52
290 291 8.213812 CCGTGAAATTTTATGCAAGTGTTTTAG 58.786 33.333 0.00 0.00 0.00 1.85
291 292 7.735586 CGTGAAATTTTATGCAAGTGTTTTAGC 59.264 33.333 0.00 0.00 0.00 3.09
292 293 8.764287 GTGAAATTTTATGCAAGTGTTTTAGCT 58.236 29.630 0.00 0.00 0.00 3.32
293 294 9.973450 TGAAATTTTATGCAAGTGTTTTAGCTA 57.027 25.926 0.00 0.00 0.00 3.32
295 296 8.466086 AATTTTATGCAAGTGTTTTAGCTAGC 57.534 30.769 6.62 6.62 0.00 3.42
296 297 6.817765 TTTATGCAAGTGTTTTAGCTAGCT 57.182 33.333 23.12 23.12 0.00 3.32
297 298 4.954092 ATGCAAGTGTTTTAGCTAGCTC 57.046 40.909 23.26 7.43 0.00 4.09
299 300 3.244561 TGCAAGTGTTTTAGCTAGCTCCT 60.245 43.478 23.26 5.86 0.00 3.69
303 304 5.228945 AGTGTTTTAGCTAGCTCCTTTCA 57.771 39.130 23.26 12.39 0.00 2.69
330 331 2.489329 CTCCATGGTGCTTGTTAGTTGG 59.511 50.000 12.58 0.00 0.00 3.77
365 366 4.840115 ACAAGGATGATTCCCACAAACAAT 59.160 37.500 0.00 0.00 43.76 2.71
370 371 7.972301 AGGATGATTCCCACAAACAATTTTTA 58.028 30.769 0.00 0.00 43.76 1.52
378 379 6.058183 CCCACAAACAATTTTTAATGGGTCA 58.942 36.000 13.98 0.00 36.16 4.02
401 402 6.663523 TCATATTTCTCCTTCCACCTTTTTCC 59.336 38.462 0.00 0.00 0.00 3.13
432 434 6.071984 CCTCACTCCTACCTGTAGTATGATT 58.928 44.000 3.80 0.00 0.00 2.57
443 448 8.207350 ACCTGTAGTATGATTATTGTATGCCT 57.793 34.615 0.00 0.00 0.00 4.75
452 457 1.696063 ATTGTATGCCTGGATGGTGC 58.304 50.000 0.00 0.00 38.35 5.01
456 461 1.406539 GTATGCCTGGATGGTGCAAAG 59.593 52.381 0.00 0.00 38.69 2.77
457 462 1.610554 ATGCCTGGATGGTGCAAAGC 61.611 55.000 0.00 0.00 38.69 3.51
469 474 3.879295 TGGTGCAAAGCTATATCTGAAGC 59.121 43.478 0.00 0.00 39.08 3.86
472 477 5.009410 GGTGCAAAGCTATATCTGAAGCAAT 59.991 40.000 2.97 0.00 41.32 3.56
535 541 3.096092 TGAAGAAGGTGCCTGTTTTGTT 58.904 40.909 0.00 0.00 0.00 2.83
539 545 3.769300 AGAAGGTGCCTGTTTTGTTTCTT 59.231 39.130 0.00 0.00 0.00 2.52
627 633 7.996644 AGAATTGACCATACCCGTAACATATTT 59.003 33.333 0.00 0.00 0.00 1.40
638 644 5.471797 CCCGTAACATATTTGTCCATATGCA 59.528 40.000 0.00 0.00 39.77 3.96
654 660 3.508744 ATGCAATTGGGTTTTCTAGCG 57.491 42.857 7.72 0.00 0.00 4.26
674 680 3.614390 GCGTCTGCTTCAGTAGTTTAGGT 60.614 47.826 0.00 0.00 38.39 3.08
677 683 5.652518 GTCTGCTTCAGTAGTTTAGGTAGG 58.347 45.833 0.00 0.00 32.61 3.18
699 705 4.467735 GAGGTTCGTGAATCAAAAGCTTC 58.532 43.478 0.00 0.00 30.20 3.86
703 709 2.223144 TCGTGAATCAAAAGCTTCCACG 59.777 45.455 19.03 19.03 32.40 4.94
716 722 2.618053 CTTCCACGTGATTGTAGGACC 58.382 52.381 19.30 0.00 0.00 4.46
822 830 7.538678 GCCTGTAATTTCACTTATGTTGTTCTG 59.461 37.037 0.00 0.00 0.00 3.02
859 867 2.171840 GACAGTAGGCAAGTCCTGAGA 58.828 52.381 0.00 0.00 46.98 3.27
945 958 9.120538 TCAACTATTGGCTATCTAAAAATGACC 57.879 33.333 0.00 0.00 0.00 4.02
947 960 9.700831 AACTATTGGCTATCTAAAAATGACCTT 57.299 29.630 0.00 0.00 0.00 3.50
1026 1039 9.836864 ATGAAGATTACTACAATCATGCAGTTA 57.163 29.630 0.00 0.00 34.88 2.24
1036 1049 3.737559 TCATGCAGTTAATCTTGGGGT 57.262 42.857 0.00 0.00 0.00 4.95
1263 1276 2.968675 ACAAATCGAGGTTTAGTCGGG 58.031 47.619 0.00 0.00 38.02 5.14
1446 1463 0.178990 ACTGTTCCAACCTCAAGGCC 60.179 55.000 0.00 0.00 39.32 5.19
1451 1468 1.681229 TCCAACCTCAAGGCCCTATT 58.319 50.000 0.00 0.00 39.32 1.73
1525 1542 3.429272 CCTTCAAGTGCTGCAACTTTCAA 60.429 43.478 2.77 5.25 38.34 2.69
1568 1585 0.595095 CCTGCTTCTCTTGCCAACAC 59.405 55.000 0.00 0.00 0.00 3.32
1573 1590 2.233271 CTTCTCTTGCCAACACCACAT 58.767 47.619 0.00 0.00 0.00 3.21
1650 1667 0.035598 TTGCCAAGTTACCTGCGCTA 59.964 50.000 9.73 0.00 0.00 4.26
1704 1721 1.070601 GGCAGGTTTCAACAAGCCATT 59.929 47.619 15.79 0.00 44.65 3.16
1733 1750 7.809880 ACCTTTCTACTCTTGTTACCCTTAT 57.190 36.000 0.00 0.00 0.00 1.73
1801 1818 2.810164 ACTCTCTACCCAGTCTCCAAC 58.190 52.381 0.00 0.00 0.00 3.77
1803 1820 2.757868 CTCTCTACCCAGTCTCCAACAG 59.242 54.545 0.00 0.00 0.00 3.16
1832 1849 6.017934 GCATTAGCCGATAACTTCTTTGATGA 60.018 38.462 0.00 0.00 33.58 2.92
1935 1952 2.962859 AGGTCCATTGGCAAACTTTCT 58.037 42.857 3.01 0.00 0.00 2.52
2050 2067 3.181474 GCTAAATGCCTTCTCGGTAGAGT 60.181 47.826 0.00 0.00 39.55 3.24
2340 2360 7.290948 TCTCAATTGGCATATCTCCTTCTAGAA 59.709 37.037 5.42 4.81 0.00 2.10
2396 2416 3.177997 TGGAAAGCTTCAAAACCTTGC 57.822 42.857 0.00 0.00 32.14 4.01
2461 2481 6.887002 ACCAAAGGAGATCTTTAGAATTCCAC 59.113 38.462 0.65 0.00 43.32 4.02
2484 2504 8.638873 CCACCACTAAGGGAAATTTATTTATCC 58.361 37.037 0.00 0.00 43.89 2.59
2581 2601 9.956640 CTTCAAATAGGCTATCTGGAGATATTT 57.043 33.333 10.17 0.00 36.53 1.40
2665 2685 2.007608 GAAGCATCCCCACTTCGTTAC 58.992 52.381 0.00 0.00 33.56 2.50
2686 2706 7.745594 CGTTACGCAAAATAAGTAGCCTAAAAA 59.254 33.333 0.00 0.00 0.00 1.94
2697 2717 7.674471 AAGTAGCCTAAAAATTCTCAGTGTC 57.326 36.000 0.00 0.00 0.00 3.67
2751 2771 5.240844 AGTGTTTCTTGGCAACCTACAATAC 59.759 40.000 0.00 0.00 0.00 1.89
2754 2774 4.216411 TCTTGGCAACCTACAATACCTC 57.784 45.455 0.00 0.00 0.00 3.85
2786 2806 3.829886 TTTGTCATTCAACCATCTCGC 57.170 42.857 0.00 0.00 35.61 5.03
2852 2872 3.619419 TGCGGATTGAAGGAAATCATGA 58.381 40.909 0.00 0.00 38.14 3.07
3051 3071 5.323581 TCCATGTCTTCACCATCATTTGAA 58.676 37.500 0.00 0.00 0.00 2.69
3188 3211 8.415553 TCAAGATGGAAATTATGTTGCCATAAG 58.584 33.333 5.41 0.91 44.52 1.73
3189 3212 7.902920 AGATGGAAATTATGTTGCCATAAGT 57.097 32.000 5.41 0.00 44.52 2.24
3359 3382 4.563538 TATGAGTTCATGCCTCGAGGAGG 61.564 52.174 35.69 21.61 43.47 4.30
3414 3437 8.211116 ACTATGAGAGCTCTTTTGATTTGATG 57.789 34.615 19.36 1.93 0.00 3.07
3639 3662 5.021033 ACTCATACTCAGCCTCTTCAATG 57.979 43.478 0.00 0.00 0.00 2.82
3683 3706 6.239887 GGATATGTTGCTCCAGGTAATTCCTA 60.240 42.308 0.00 0.00 46.24 2.94
3801 3824 3.505680 GTGCAACAGGTGGTCATATTTCA 59.494 43.478 0.00 0.00 36.32 2.69
3899 3922 6.446318 TGTTCAAAGATGGACTAAACATTGC 58.554 36.000 0.00 0.00 35.92 3.56
4000 4023 4.673968 TCCTGAAGAAACTCTAGTAGCCA 58.326 43.478 0.00 0.00 0.00 4.75
4028 4051 5.010282 GGAAAATGACCTGGACTGTGTAAT 58.990 41.667 0.00 0.00 0.00 1.89
4050 4073 2.436417 TCAGTGCTAAACATTGGGCTC 58.564 47.619 0.00 0.00 36.68 4.70
4082 4105 4.564116 ATACCCGAACGAGCGCCG 62.564 66.667 15.25 15.25 45.44 6.46
4125 4148 1.030457 GGCTGCATGGAATCAAGGAG 58.970 55.000 0.50 0.00 34.01 3.69
4142 4165 1.691434 GGAGGCTTATCTCAGAGGGTG 59.309 57.143 0.00 0.00 35.58 4.61
4155 4178 4.298626 TCAGAGGGTGCTAAGGTAATCAT 58.701 43.478 0.00 0.00 0.00 2.45
4242 4298 3.872511 TGGCAGCACCATATTTTTGAG 57.127 42.857 0.00 0.00 46.36 3.02
4258 4314 7.846101 ATTTTTGAGGTTTTCAGAGAATCCT 57.154 32.000 0.00 0.00 37.07 3.24
4371 4433 6.952773 AACAGTGGTTTTTCTGCTGTATTA 57.047 33.333 0.00 0.00 39.19 0.98
4372 4434 6.560253 ACAGTGGTTTTTCTGCTGTATTAG 57.440 37.500 0.00 0.00 38.46 1.73
4381 4443 6.743575 TTTCTGCTGTATTAGAAAAGAGGC 57.256 37.500 0.00 0.00 39.29 4.70
4385 4447 3.371595 GCTGTATTAGAAAAGAGGCCCCA 60.372 47.826 0.00 0.00 0.00 4.96
4386 4448 4.855340 CTGTATTAGAAAAGAGGCCCCAA 58.145 43.478 0.00 0.00 0.00 4.12
4387 4449 4.595986 TGTATTAGAAAAGAGGCCCCAAC 58.404 43.478 0.00 0.00 0.00 3.77
4388 4450 3.825908 ATTAGAAAAGAGGCCCCAACA 57.174 42.857 0.00 0.00 0.00 3.33
4422 4485 1.360551 GAGATAAGCGAGCGCCTCA 59.639 57.895 11.66 0.00 43.17 3.86
4425 4488 1.613925 AGATAAGCGAGCGCCTCATTA 59.386 47.619 11.66 4.14 43.17 1.90
4429 4492 0.179073 AGCGAGCGCCTCATTATTGT 60.179 50.000 11.66 0.00 43.17 2.71
4482 4552 1.284982 CTTCTTCCGTGTCACCTGCG 61.285 60.000 0.00 0.00 0.00 5.18
4497 4594 3.039011 ACCTGCGAACCCATTAGTATCT 58.961 45.455 0.00 0.00 0.00 1.98
4530 4642 1.137479 GATTGGTACCCGGTCAATCGA 59.863 52.381 10.07 0.00 37.89 3.59
4667 4779 4.593864 GGAGCCCTCGACCATCGC 62.594 72.222 0.00 0.00 40.21 4.58
4738 4850 4.437682 ACACTTCCTTCACATCCTTTGA 57.562 40.909 0.00 0.00 0.00 2.69
4835 5111 1.137404 GTTGACATCGTGCATGGCC 59.863 57.895 5.98 0.00 40.36 5.36
4837 5113 0.892814 TTGACATCGTGCATGGCCAA 60.893 50.000 10.96 0.00 40.36 4.52
4838 5114 0.892814 TGACATCGTGCATGGCCAAA 60.893 50.000 10.96 0.00 40.36 3.28
4839 5115 0.456653 GACATCGTGCATGGCCAAAC 60.457 55.000 10.96 8.13 33.74 2.93
4840 5116 1.177895 ACATCGTGCATGGCCAAACA 61.178 50.000 10.96 8.54 36.72 2.83
4841 5117 0.733566 CATCGTGCATGGCCAAACAC 60.734 55.000 24.59 24.59 0.00 3.32
4842 5118 0.895100 ATCGTGCATGGCCAAACACT 60.895 50.000 28.72 15.38 0.00 3.55
4843 5119 1.372004 CGTGCATGGCCAAACACTG 60.372 57.895 28.72 21.19 0.00 3.66
4844 5120 1.665599 GTGCATGGCCAAACACTGC 60.666 57.895 26.26 23.10 0.00 4.40
4845 5121 2.132352 TGCATGGCCAAACACTGCA 61.132 52.632 23.71 23.71 40.29 4.41
4846 5122 1.373748 GCATGGCCAAACACTGCAG 60.374 57.895 20.77 13.48 33.13 4.41
4847 5123 1.373748 CATGGCCAAACACTGCAGC 60.374 57.895 10.96 0.00 0.00 5.25
4848 5124 1.833492 ATGGCCAAACACTGCAGCA 60.833 52.632 10.96 0.62 0.00 4.41
4850 5126 2.492773 GGCCAAACACTGCAGCACT 61.493 57.895 15.27 0.00 0.00 4.40
4851 5127 1.438814 GCCAAACACTGCAGCACTT 59.561 52.632 15.27 0.80 0.00 3.16
4853 5129 0.740149 CCAAACACTGCAGCACTTGA 59.260 50.000 15.27 0.00 0.00 3.02
4854 5130 1.534595 CCAAACACTGCAGCACTTGAC 60.535 52.381 15.27 0.00 0.00 3.18
4855 5131 1.132834 CAAACACTGCAGCACTTGACA 59.867 47.619 15.27 0.00 0.00 3.58
4857 5133 1.233019 ACACTGCAGCACTTGACATC 58.767 50.000 15.27 0.00 0.00 3.06
4860 5136 0.165295 CTGCAGCACTTGACATCGTG 59.835 55.000 0.00 2.03 0.00 4.35
4865 5141 3.215642 CACTTGACATCGTGCAGGA 57.784 52.632 12.13 12.13 0.00 3.86
4866 5142 1.730501 CACTTGACATCGTGCAGGAT 58.269 50.000 15.97 15.97 0.00 3.24
4868 5144 1.276138 ACTTGACATCGTGCAGGATGA 59.724 47.619 41.05 25.21 45.27 2.92
4869 5145 1.931841 CTTGACATCGTGCAGGATGAG 59.068 52.381 41.05 28.93 45.27 2.90
4875 5184 1.078918 CGTGCAGGATGAGGCTGAA 60.079 57.895 0.00 0.00 39.69 3.02
4919 5228 4.930405 TGCGTATCTGTCGGTCAAAATTAA 59.070 37.500 0.00 0.00 0.00 1.40
5080 5471 4.697514 AGTACATAAGCTGCGATGTGATT 58.302 39.130 24.38 12.36 36.92 2.57
5118 5509 5.449304 CAGGTACGTTCTTGGAAAATGAAC 58.551 41.667 0.00 0.00 38.80 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.346725 GCATGGCAATAGATATTTAACTTTAGC 57.653 33.333 0.00 0.00 0.00 3.09
5 6 9.846248 GGCATGGCAATAGATATTTAACTTTAG 57.154 33.333 15.47 0.00 0.00 1.85
6 7 9.586732 AGGCATGGCAATAGATATTTAACTTTA 57.413 29.630 22.64 0.00 0.00 1.85
7 8 8.482852 AGGCATGGCAATAGATATTTAACTTT 57.517 30.769 22.64 0.00 0.00 2.66
8 9 9.759473 ATAGGCATGGCAATAGATATTTAACTT 57.241 29.630 22.64 0.00 0.00 2.66
14 15 9.925545 TCATTTATAGGCATGGCAATAGATATT 57.074 29.630 22.64 0.00 0.00 1.28
15 16 9.570468 CTCATTTATAGGCATGGCAATAGATAT 57.430 33.333 22.64 11.35 0.00 1.63
16 17 7.994911 CCTCATTTATAGGCATGGCAATAGATA 59.005 37.037 22.64 3.99 0.00 1.98
17 18 6.832384 CCTCATTTATAGGCATGGCAATAGAT 59.168 38.462 22.64 6.82 0.00 1.98
18 19 6.182627 CCTCATTTATAGGCATGGCAATAGA 58.817 40.000 22.64 10.68 0.00 1.98
19 20 5.359009 CCCTCATTTATAGGCATGGCAATAG 59.641 44.000 22.64 9.72 32.34 1.73
20 21 5.222316 ACCCTCATTTATAGGCATGGCAATA 60.222 40.000 22.64 6.36 32.34 1.90
21 22 4.091549 CCCTCATTTATAGGCATGGCAAT 58.908 43.478 22.64 9.32 32.34 3.56
22 23 3.117169 ACCCTCATTTATAGGCATGGCAA 60.117 43.478 22.64 7.14 32.34 4.52
23 24 2.446666 ACCCTCATTTATAGGCATGGCA 59.553 45.455 22.64 7.94 32.34 4.92
24 25 2.821969 CACCCTCATTTATAGGCATGGC 59.178 50.000 12.14 12.14 32.34 4.40
25 26 2.821969 GCACCCTCATTTATAGGCATGG 59.178 50.000 0.00 0.00 32.34 3.66
26 27 2.821969 GGCACCCTCATTTATAGGCATG 59.178 50.000 0.00 0.00 32.34 4.06
27 28 2.446666 TGGCACCCTCATTTATAGGCAT 59.553 45.455 0.00 0.00 32.34 4.40
28 29 1.849692 TGGCACCCTCATTTATAGGCA 59.150 47.619 0.00 0.00 32.34 4.75
29 30 2.656947 TGGCACCCTCATTTATAGGC 57.343 50.000 0.00 0.00 32.34 3.93
30 31 2.887152 GCTTGGCACCCTCATTTATAGG 59.113 50.000 0.00 0.00 0.00 2.57
31 32 3.554934 TGCTTGGCACCCTCATTTATAG 58.445 45.455 0.00 0.00 31.71 1.31
32 33 3.554934 CTGCTTGGCACCCTCATTTATA 58.445 45.455 0.00 0.00 33.79 0.98
33 34 2.381911 CTGCTTGGCACCCTCATTTAT 58.618 47.619 0.00 0.00 33.79 1.40
34 35 1.838112 CTGCTTGGCACCCTCATTTA 58.162 50.000 0.00 0.00 33.79 1.40
35 36 1.538687 GCTGCTTGGCACCCTCATTT 61.539 55.000 0.00 0.00 33.79 2.32
36 37 1.980772 GCTGCTTGGCACCCTCATT 60.981 57.895 0.00 0.00 33.79 2.57
37 38 1.565390 TAGCTGCTTGGCACCCTCAT 61.565 55.000 7.79 0.00 33.79 2.90
38 39 2.189191 CTAGCTGCTTGGCACCCTCA 62.189 60.000 7.79 0.00 33.79 3.86
39 40 1.451028 CTAGCTGCTTGGCACCCTC 60.451 63.158 7.79 0.00 33.79 4.30
40 41 1.783250 AACTAGCTGCTTGGCACCCT 61.783 55.000 7.79 0.00 33.79 4.34
41 42 0.035439 TAACTAGCTGCTTGGCACCC 60.035 55.000 7.79 0.00 33.79 4.61
42 43 1.087501 GTAACTAGCTGCTTGGCACC 58.912 55.000 7.79 0.00 33.79 5.01
43 44 2.100605 AGTAACTAGCTGCTTGGCAC 57.899 50.000 7.79 8.25 33.79 5.01
44 45 2.224523 ACAAGTAACTAGCTGCTTGGCA 60.225 45.455 22.64 0.00 41.68 4.92
45 46 2.427506 ACAAGTAACTAGCTGCTTGGC 58.572 47.619 22.64 1.07 41.68 4.52
46 47 3.619038 GCTACAAGTAACTAGCTGCTTGG 59.381 47.826 22.64 10.82 41.68 3.61
47 48 4.499183 AGCTACAAGTAACTAGCTGCTTG 58.501 43.478 18.80 18.80 43.35 4.01
48 49 4.810191 AGCTACAAGTAACTAGCTGCTT 57.190 40.909 7.79 0.00 43.35 3.91
49 50 4.201930 CGTAGCTACAAGTAACTAGCTGCT 60.202 45.833 23.21 7.57 44.42 4.24
50 51 4.036352 CGTAGCTACAAGTAACTAGCTGC 58.964 47.826 23.21 6.99 44.42 5.25
51 52 4.599047 CCGTAGCTACAAGTAACTAGCTG 58.401 47.826 23.21 2.50 44.42 4.24
52 53 3.066481 GCCGTAGCTACAAGTAACTAGCT 59.934 47.826 23.21 4.69 46.08 3.32
53 54 3.370276 GCCGTAGCTACAAGTAACTAGC 58.630 50.000 23.21 7.65 36.40 3.42
54 55 3.547613 CGGCCGTAGCTACAAGTAACTAG 60.548 52.174 23.21 3.89 39.73 2.57
55 56 2.355756 CGGCCGTAGCTACAAGTAACTA 59.644 50.000 23.21 0.00 39.73 2.24
56 57 1.133790 CGGCCGTAGCTACAAGTAACT 59.866 52.381 23.21 0.00 39.73 2.24
57 58 1.135286 ACGGCCGTAGCTACAAGTAAC 60.135 52.381 33.34 6.35 39.73 2.50
58 59 1.176527 ACGGCCGTAGCTACAAGTAA 58.823 50.000 33.34 0.00 39.73 2.24
59 60 1.133025 GAACGGCCGTAGCTACAAGTA 59.867 52.381 34.44 0.00 39.73 2.24
60 61 0.108945 GAACGGCCGTAGCTACAAGT 60.109 55.000 34.44 12.99 39.73 3.16
61 62 0.172803 AGAACGGCCGTAGCTACAAG 59.827 55.000 34.44 14.59 39.73 3.16
62 63 1.133025 GTAGAACGGCCGTAGCTACAA 59.867 52.381 39.03 23.20 39.73 2.41
63 64 0.734889 GTAGAACGGCCGTAGCTACA 59.265 55.000 39.03 23.72 39.73 2.74
64 65 0.734889 TGTAGAACGGCCGTAGCTAC 59.265 55.000 38.30 38.30 39.73 3.58
65 66 0.734889 GTGTAGAACGGCCGTAGCTA 59.265 55.000 34.44 30.05 39.73 3.32
66 67 1.509923 GTGTAGAACGGCCGTAGCT 59.490 57.895 34.44 31.13 39.73 3.32
67 68 1.517913 GGTGTAGAACGGCCGTAGC 60.518 63.158 34.44 26.05 38.76 3.58
68 69 1.140375 GGGTGTAGAACGGCCGTAG 59.860 63.158 34.44 1.90 0.00 3.51
69 70 1.184322 TTGGGTGTAGAACGGCCGTA 61.184 55.000 34.44 14.39 0.00 4.02
70 71 2.042404 TTTGGGTGTAGAACGGCCGT 62.042 55.000 28.70 28.70 0.00 5.68
71 72 0.675522 ATTTGGGTGTAGAACGGCCG 60.676 55.000 26.86 26.86 0.00 6.13
72 73 1.092348 GATTTGGGTGTAGAACGGCC 58.908 55.000 0.00 0.00 0.00 6.13
73 74 1.737793 CTGATTTGGGTGTAGAACGGC 59.262 52.381 0.00 0.00 0.00 5.68
74 75 3.000727 GTCTGATTTGGGTGTAGAACGG 58.999 50.000 0.00 0.00 0.00 4.44
75 76 3.659786 TGTCTGATTTGGGTGTAGAACG 58.340 45.455 0.00 0.00 0.00 3.95
76 77 4.003648 CCTGTCTGATTTGGGTGTAGAAC 58.996 47.826 0.00 0.00 0.00 3.01
77 78 3.907474 TCCTGTCTGATTTGGGTGTAGAA 59.093 43.478 0.00 0.00 0.00 2.10
78 79 3.516586 TCCTGTCTGATTTGGGTGTAGA 58.483 45.455 0.00 0.00 0.00 2.59
79 80 3.981071 TCCTGTCTGATTTGGGTGTAG 57.019 47.619 0.00 0.00 0.00 2.74
80 81 4.927267 AATCCTGTCTGATTTGGGTGTA 57.073 40.909 0.00 0.00 30.88 2.90
81 82 3.814504 AATCCTGTCTGATTTGGGTGT 57.185 42.857 0.00 0.00 30.88 4.16
82 83 6.588719 TTAAAATCCTGTCTGATTTGGGTG 57.411 37.500 0.21 0.00 42.58 4.61
83 84 6.725834 ACATTAAAATCCTGTCTGATTTGGGT 59.274 34.615 0.21 0.00 42.58 4.51
84 85 7.174107 ACATTAAAATCCTGTCTGATTTGGG 57.826 36.000 0.21 0.00 42.58 4.12
85 86 9.143631 GAAACATTAAAATCCTGTCTGATTTGG 57.856 33.333 0.21 0.00 42.58 3.28
86 87 9.143631 GGAAACATTAAAATCCTGTCTGATTTG 57.856 33.333 0.21 0.00 42.58 2.32
87 88 9.093458 AGGAAACATTAAAATCCTGTCTGATTT 57.907 29.630 0.00 0.00 44.67 2.17
88 89 8.655935 AGGAAACATTAAAATCCTGTCTGATT 57.344 30.769 0.00 0.00 40.73 2.57
89 90 8.655935 AAGGAAACATTAAAATCCTGTCTGAT 57.344 30.769 0.00 0.00 41.39 2.90
90 91 8.359642 CAAAGGAAACATTAAAATCCTGTCTGA 58.640 33.333 0.00 0.00 41.39 3.27
91 92 7.116805 GCAAAGGAAACATTAAAATCCTGTCTG 59.883 37.037 0.00 0.00 41.39 3.51
92 93 7.154656 GCAAAGGAAACATTAAAATCCTGTCT 58.845 34.615 0.00 0.00 41.39 3.41
93 94 6.928492 TGCAAAGGAAACATTAAAATCCTGTC 59.072 34.615 0.00 0.00 41.39 3.51
94 95 6.825610 TGCAAAGGAAACATTAAAATCCTGT 58.174 32.000 0.00 0.00 41.39 4.00
95 96 6.930722 ACTGCAAAGGAAACATTAAAATCCTG 59.069 34.615 0.00 0.00 41.39 3.86
96 97 7.066307 ACTGCAAAGGAAACATTAAAATCCT 57.934 32.000 0.00 0.00 44.08 3.24
97 98 7.440856 TGAACTGCAAAGGAAACATTAAAATCC 59.559 33.333 0.00 0.00 0.00 3.01
98 99 8.364129 TGAACTGCAAAGGAAACATTAAAATC 57.636 30.769 0.00 0.00 0.00 2.17
99 100 8.203485 TCTGAACTGCAAAGGAAACATTAAAAT 58.797 29.630 0.00 0.00 0.00 1.82
100 101 7.551585 TCTGAACTGCAAAGGAAACATTAAAA 58.448 30.769 0.00 0.00 0.00 1.52
101 102 7.106439 TCTGAACTGCAAAGGAAACATTAAA 57.894 32.000 0.00 0.00 0.00 1.52
102 103 6.707440 TCTGAACTGCAAAGGAAACATTAA 57.293 33.333 0.00 0.00 0.00 1.40
103 104 6.489700 TCATCTGAACTGCAAAGGAAACATTA 59.510 34.615 0.00 0.00 0.00 1.90
104 105 5.302568 TCATCTGAACTGCAAAGGAAACATT 59.697 36.000 0.00 0.00 0.00 2.71
105 106 4.828939 TCATCTGAACTGCAAAGGAAACAT 59.171 37.500 0.00 0.00 0.00 2.71
106 107 4.036734 GTCATCTGAACTGCAAAGGAAACA 59.963 41.667 0.00 0.00 0.00 2.83
107 108 4.036734 TGTCATCTGAACTGCAAAGGAAAC 59.963 41.667 0.00 0.00 0.00 2.78
108 109 4.036734 GTGTCATCTGAACTGCAAAGGAAA 59.963 41.667 0.00 0.00 0.00 3.13
109 110 3.565482 GTGTCATCTGAACTGCAAAGGAA 59.435 43.478 0.00 0.00 0.00 3.36
110 111 3.141398 GTGTCATCTGAACTGCAAAGGA 58.859 45.455 0.00 0.00 0.00 3.36
111 112 2.880268 TGTGTCATCTGAACTGCAAAGG 59.120 45.455 0.00 0.00 0.00 3.11
112 113 4.556942 TTGTGTCATCTGAACTGCAAAG 57.443 40.909 0.00 0.00 0.00 2.77
113 114 4.579753 TGATTGTGTCATCTGAACTGCAAA 59.420 37.500 0.00 0.00 0.00 3.68
114 115 4.136051 TGATTGTGTCATCTGAACTGCAA 58.864 39.130 0.00 0.00 0.00 4.08
115 116 3.742385 TGATTGTGTCATCTGAACTGCA 58.258 40.909 0.00 0.00 0.00 4.41
137 138 2.971330 ACAAACATCCCCAAAATCAGCA 59.029 40.909 0.00 0.00 0.00 4.41
142 143 3.475575 GTTGCACAAACATCCCCAAAAT 58.524 40.909 0.00 0.00 38.75 1.82
146 147 1.459455 CGGTTGCACAAACATCCCCA 61.459 55.000 0.00 0.00 40.86 4.96
173 174 0.750546 CACCACCATCATCCTGCCAG 60.751 60.000 0.00 0.00 0.00 4.85
243 244 6.751888 CACGGAACTCTGAAAACAAGATTTTT 59.248 34.615 0.00 0.00 0.00 1.94
245 246 5.588648 TCACGGAACTCTGAAAACAAGATTT 59.411 36.000 0.00 0.00 0.00 2.17
246 247 5.123227 TCACGGAACTCTGAAAACAAGATT 58.877 37.500 0.00 0.00 0.00 2.40
257 258 5.698832 TGCATAAAATTTCACGGAACTCTG 58.301 37.500 0.00 0.00 0.00 3.35
266 267 8.764287 AGCTAAAACACTTGCATAAAATTTCAC 58.236 29.630 0.00 0.00 0.00 3.18
269 270 8.925700 GCTAGCTAAAACACTTGCATAAAATTT 58.074 29.630 7.70 0.00 35.20 1.82
278 279 3.339141 AGGAGCTAGCTAAAACACTTGC 58.661 45.455 19.38 0.19 35.30 4.01
299 300 1.887956 GCACCATGGAGCTCCTTGAAA 60.888 52.381 37.67 19.40 42.04 2.69
303 304 0.323178 CAAGCACCATGGAGCTCCTT 60.323 55.000 32.93 24.06 40.95 3.36
311 312 2.238521 ACCAACTAACAAGCACCATGG 58.761 47.619 11.19 11.19 0.00 3.66
330 331 7.545615 GGGAATCATCCTTGTTGTCATTTAAAC 59.454 37.037 0.00 0.00 45.77 2.01
365 366 8.977412 GGAAGGAGAAATATGACCCATTAAAAA 58.023 33.333 0.00 0.00 0.00 1.94
370 371 5.449553 GTGGAAGGAGAAATATGACCCATT 58.550 41.667 0.00 0.00 0.00 3.16
378 379 6.437477 GTGGAAAAAGGTGGAAGGAGAAATAT 59.563 38.462 0.00 0.00 0.00 1.28
401 402 2.692557 CAGGTAGGAGTGAGGAGATGTG 59.307 54.545 0.00 0.00 0.00 3.21
432 434 2.174424 TGCACCATCCAGGCATACAATA 59.826 45.455 0.00 0.00 43.14 1.90
443 448 4.102996 TCAGATATAGCTTTGCACCATCCA 59.897 41.667 0.00 0.00 0.00 3.41
535 541 6.153851 TCACGGATGACCTGTTATAAGAAGAA 59.846 38.462 0.00 0.00 0.00 2.52
599 605 2.710096 ACGGGTATGGTCAATTCTGG 57.290 50.000 0.00 0.00 0.00 3.86
615 621 6.552859 TGCATATGGACAAATATGTTACGG 57.447 37.500 4.56 0.00 40.95 4.02
627 633 4.776837 AGAAAACCCAATTGCATATGGACA 59.223 37.500 17.48 0.00 39.12 4.02
638 644 2.488153 GCAGACGCTAGAAAACCCAATT 59.512 45.455 0.00 0.00 34.30 2.32
654 660 5.418209 TCCTACCTAAACTACTGAAGCAGAC 59.582 44.000 0.82 0.00 35.18 3.51
674 680 4.000988 GCTTTTGATTCACGAACCTCCTA 58.999 43.478 0.00 0.00 0.00 2.94
677 683 4.467735 GAAGCTTTTGATTCACGAACCTC 58.532 43.478 0.00 0.00 43.66 3.85
699 705 0.245539 ACGGTCCTACAATCACGTGG 59.754 55.000 17.00 1.74 32.90 4.94
703 709 4.460948 TTTCCTACGGTCCTACAATCAC 57.539 45.455 0.00 0.00 0.00 3.06
716 722 9.703892 AGATTTGAGATATCTGAATTTCCTACG 57.296 33.333 10.74 0.00 31.32 3.51
772 780 4.013728 TCCAGCCAACGCAAATTTACTAT 58.986 39.130 0.00 0.00 37.52 2.12
822 830 6.586844 CCTACTGTCTTTCTGCAAGTAAGTAC 59.413 42.308 0.00 0.00 41.48 2.73
859 867 8.440771 CCTAACCAATTATACTTCAATCCCTCT 58.559 37.037 0.00 0.00 0.00 3.69
940 953 6.991531 ACATGCAAACACAAAAATAAGGTCAT 59.008 30.769 0.00 0.00 0.00 3.06
941 954 6.344500 ACATGCAAACACAAAAATAAGGTCA 58.656 32.000 0.00 0.00 0.00 4.02
942 955 6.843069 ACATGCAAACACAAAAATAAGGTC 57.157 33.333 0.00 0.00 0.00 3.85
943 956 8.900983 ATTACATGCAAACACAAAAATAAGGT 57.099 26.923 0.00 0.00 0.00 3.50
947 960 9.755804 TCTTGATTACATGCAAACACAAAAATA 57.244 25.926 0.00 0.00 0.00 1.40
948 961 8.659925 TCTTGATTACATGCAAACACAAAAAT 57.340 26.923 0.00 0.00 0.00 1.82
949 962 8.659925 ATCTTGATTACATGCAAACACAAAAA 57.340 26.923 0.00 0.00 0.00 1.94
954 967 7.307694 TGAAGATCTTGATTACATGCAAACAC 58.692 34.615 14.00 0.00 0.00 3.32
1026 1039 3.390639 TGCAAACAATGAACCCCAAGATT 59.609 39.130 0.00 0.00 0.00 2.40
1263 1276 3.679389 TCCAAGTGAAGGAGAGATTTGC 58.321 45.455 0.00 0.00 0.00 3.68
1446 1463 5.440610 AGTTGATTTCTACCCAGCAATAGG 58.559 41.667 0.00 0.00 0.00 2.57
1451 1468 5.245531 CAACTAGTTGATTTCTACCCAGCA 58.754 41.667 28.17 0.00 42.93 4.41
1498 1515 2.878406 GTTGCAGCACTTGAAGGTAAGA 59.122 45.455 0.00 0.00 0.00 2.10
1525 1542 8.506083 AGGGATGATTCCAGTAAGATTGTTAAT 58.494 33.333 0.00 0.00 44.60 1.40
1568 1585 4.719040 GTTAAACTGGTTTAGCGATGTGG 58.281 43.478 6.13 0.00 36.52 4.17
1650 1667 2.802057 GCTACCCGCGTTCAGAATATGT 60.802 50.000 4.92 0.00 0.00 2.29
1704 1721 6.769341 GGGTAACAAGAGTAGAAAGGTTCAAA 59.231 38.462 0.00 0.00 39.74 2.69
1733 1750 5.480073 CCACTTAAATGATTTGGACCAAGGA 59.520 40.000 7.07 0.00 0.00 3.36
1801 1818 3.123804 AGTTATCGGCTAATGCGAACTG 58.876 45.455 0.00 0.00 40.82 3.16
1803 1820 3.802685 AGAAGTTATCGGCTAATGCGAAC 59.197 43.478 0.00 0.00 40.82 3.95
1905 1922 2.524306 CCAATGGACCTAAGCACCAAA 58.476 47.619 0.00 0.00 37.24 3.28
1935 1952 6.657541 ACTCAAGGTTTAACTTTGTGAGTTCA 59.342 34.615 22.30 3.06 45.40 3.18
2050 2067 3.114606 TGTGGCCTTCTAGATGATTCCA 58.885 45.455 3.32 8.22 0.00 3.53
2230 2250 8.822652 ATTTGCAAATTTTTGAGAGTTCCTAG 57.177 30.769 18.99 0.00 40.55 3.02
2396 2416 5.712004 TGTTGCTGGACATGTTCAATATTG 58.288 37.500 8.51 9.29 0.00 1.90
2484 2504 7.435192 GGAAGTTGTCCATCAAAGTTGTTAAAG 59.565 37.037 0.00 0.00 46.97 1.85
2581 2601 2.047061 ACACTCACCCAAAGTGCTAGA 58.953 47.619 0.00 0.00 46.48 2.43
2611 2631 8.511604 ACATTCCAGTCCAACTTTATATCTTG 57.488 34.615 0.00 0.00 0.00 3.02
2619 2639 5.422012 ACTGAAAACATTCCAGTCCAACTTT 59.578 36.000 0.00 0.00 36.51 2.66
2665 2685 8.911247 AGAATTTTTAGGCTACTTATTTTGCG 57.089 30.769 0.00 0.00 0.00 4.85
2697 2717 6.406370 TGACCCAGTAATGTTATTGTGAGAG 58.594 40.000 0.00 0.00 0.00 3.20
2732 2752 4.585879 GAGGTATTGTAGGTTGCCAAGAA 58.414 43.478 0.00 0.00 0.00 2.52
2751 2771 3.849911 TGACAAATCTAGTTGCTCGAGG 58.150 45.455 15.58 0.00 31.29 4.63
2754 2774 5.784750 TGAATGACAAATCTAGTTGCTCG 57.215 39.130 0.00 0.00 31.29 5.03
2852 2872 2.116125 GAGCCCCACCACAAAGCT 59.884 61.111 0.00 0.00 36.25 3.74
3051 3071 8.078060 TGAAAGAAACTTTGGGAAGATTTCTT 57.922 30.769 15.52 15.52 44.19 2.52
3188 3211 2.910688 TGTCTCCAGGTTGAAGACAC 57.089 50.000 4.86 0.00 35.00 3.67
3189 3212 2.104792 CCTTGTCTCCAGGTTGAAGACA 59.895 50.000 4.86 4.86 37.68 3.41
3359 3382 3.190874 GAGTACAGTAGTCCATGCAAGC 58.809 50.000 4.20 0.00 0.00 4.01
3405 3428 7.933033 TGAGCTACTGTAATATGCATCAAATCA 59.067 33.333 0.19 0.00 0.00 2.57
3414 3437 5.059833 AGCCTTTGAGCTACTGTAATATGC 58.940 41.667 0.00 0.00 42.70 3.14
3639 3662 7.336931 ACATATCCAATAGTTCCATTTATCGCC 59.663 37.037 0.00 0.00 0.00 5.54
3713 3736 3.584406 TGAGCAGAAGTTACTCTCAGC 57.416 47.619 0.00 1.93 31.07 4.26
3758 3781 5.620654 GCACATTCTGTAGTTCACATGCAAT 60.621 40.000 0.00 0.00 37.83 3.56
3801 3824 2.480416 GCTGTAGACATCGCTAGCAGTT 60.480 50.000 16.45 0.02 0.00 3.16
3899 3922 8.006741 AGGAAAATTCATTTCAACGAATTTCG 57.993 30.769 16.84 16.84 46.13 3.46
3925 3948 8.727149 AGGTTCAATAATTTCTGATATCCTGGA 58.273 33.333 0.00 0.00 0.00 3.86
3996 4019 3.094572 CAGGTCATTTTCCTTCATGGCT 58.905 45.455 0.00 0.00 35.26 4.75
4000 4023 4.202609 ACAGTCCAGGTCATTTTCCTTCAT 60.203 41.667 0.00 0.00 32.37 2.57
4028 4051 3.230134 AGCCCAATGTTTAGCACTGAAA 58.770 40.909 0.00 0.00 0.00 2.69
4050 4073 2.438254 TATGGCTTGGTGCAGCGG 60.438 61.111 11.91 7.83 45.15 5.52
4082 4105 1.080298 GCCACTTCCTGCATGTTGC 60.080 57.895 0.00 0.00 45.29 4.17
4125 4148 1.127343 AGCACCCTCTGAGATAAGCC 58.873 55.000 6.17 0.00 0.00 4.35
4155 4178 4.764308 TGCAGCACCATACACTAAAAATGA 59.236 37.500 0.00 0.00 0.00 2.57
4213 4269 1.993956 TGGTGCTGCCAAATGTAGTT 58.006 45.000 0.00 0.00 45.94 2.24
4269 4329 8.020861 ACGCGTCAAAGTATTTAAAACTATGA 57.979 30.769 5.58 0.00 35.03 2.15
4290 4350 1.264557 TGACACCAAATACCAAACGCG 59.735 47.619 3.53 3.53 0.00 6.01
4351 4413 7.817418 TTTCTAATACAGCAGAAAAACCACT 57.183 32.000 0.00 0.00 37.72 4.00
4371 4433 1.713078 AGATGTTGGGGCCTCTTTTCT 59.287 47.619 3.07 0.00 0.00 2.52
4372 4434 2.222227 AGATGTTGGGGCCTCTTTTC 57.778 50.000 3.07 0.00 0.00 2.29
4408 4471 2.135139 CAATAATGAGGCGCTCGCTTA 58.865 47.619 7.64 5.33 41.60 3.09
4410 4473 0.179073 ACAATAATGAGGCGCTCGCT 60.179 50.000 7.64 0.00 41.60 4.93
4550 4662 1.194547 CACACTACACACGCATGGAAC 59.805 52.381 0.00 0.00 0.00 3.62
4560 4672 4.673320 CGATTGATCGTACCACACTACACA 60.673 45.833 5.26 0.00 44.74 3.72
4562 4674 4.023739 CGATTGATCGTACCACACTACA 57.976 45.455 5.26 0.00 44.74 2.74
4667 4779 1.124297 GTGAAGTATGTGTGCACGACG 59.876 52.381 13.13 0.00 0.00 5.12
4835 5111 1.132834 TGTCAAGTGCTGCAGTGTTTG 59.867 47.619 16.64 15.95 0.00 2.93
4837 5113 1.605710 GATGTCAAGTGCTGCAGTGTT 59.394 47.619 16.64 3.51 0.00 3.32
4838 5114 1.233019 GATGTCAAGTGCTGCAGTGT 58.767 50.000 16.64 0.00 0.00 3.55
4839 5115 0.165295 CGATGTCAAGTGCTGCAGTG 59.835 55.000 16.64 8.77 0.00 3.66
4840 5116 0.250038 ACGATGTCAAGTGCTGCAGT 60.250 50.000 16.64 2.34 0.00 4.40
4841 5117 0.165295 CACGATGTCAAGTGCTGCAG 59.835 55.000 10.11 10.11 0.00 4.41
4842 5118 2.237416 CACGATGTCAAGTGCTGCA 58.763 52.632 0.00 0.00 0.00 4.41
4847 5123 1.395954 CATCCTGCACGATGTCAAGTG 59.604 52.381 15.23 7.27 41.01 3.16
4848 5124 1.276138 TCATCCTGCACGATGTCAAGT 59.724 47.619 20.57 0.00 40.50 3.16
4850 5126 1.405933 CCTCATCCTGCACGATGTCAA 60.406 52.381 20.57 5.74 40.50 3.18
4851 5127 0.176449 CCTCATCCTGCACGATGTCA 59.824 55.000 20.57 6.33 40.50 3.58
4853 5129 1.153289 GCCTCATCCTGCACGATGT 60.153 57.895 20.57 0.00 40.50 3.06
4854 5130 1.145598 AGCCTCATCCTGCACGATG 59.854 57.895 16.82 16.82 40.92 3.84
4855 5131 1.145598 CAGCCTCATCCTGCACGAT 59.854 57.895 0.00 0.00 0.00 3.73
4857 5133 0.463295 ATTCAGCCTCATCCTGCACG 60.463 55.000 0.00 0.00 0.00 5.34
4860 5136 2.158696 ACCTAATTCAGCCTCATCCTGC 60.159 50.000 0.00 0.00 0.00 4.85
4861 5137 3.390639 AGACCTAATTCAGCCTCATCCTG 59.609 47.826 0.00 0.00 0.00 3.86
4862 5138 3.663198 AGACCTAATTCAGCCTCATCCT 58.337 45.455 0.00 0.00 0.00 3.24
4863 5139 4.591072 ACTAGACCTAATTCAGCCTCATCC 59.409 45.833 0.00 0.00 0.00 3.51
4864 5140 5.799827 ACTAGACCTAATTCAGCCTCATC 57.200 43.478 0.00 0.00 0.00 2.92
4865 5141 5.426833 ACAACTAGACCTAATTCAGCCTCAT 59.573 40.000 0.00 0.00 0.00 2.90
4866 5142 4.777896 ACAACTAGACCTAATTCAGCCTCA 59.222 41.667 0.00 0.00 0.00 3.86
4867 5143 5.105310 TGACAACTAGACCTAATTCAGCCTC 60.105 44.000 0.00 0.00 0.00 4.70
4868 5144 4.777896 TGACAACTAGACCTAATTCAGCCT 59.222 41.667 0.00 0.00 0.00 4.58
4869 5145 5.086104 TGACAACTAGACCTAATTCAGCC 57.914 43.478 0.00 0.00 0.00 4.85
4875 5184 5.615289 GCATGGATGACAACTAGACCTAAT 58.385 41.667 0.00 0.00 0.00 1.73
4919 5228 1.980772 GGCCAGCATTGTCTTGCCT 60.981 57.895 0.00 0.00 43.83 4.75
5006 5397 6.966435 ATTTGGAAAAGAATGGCAAATACG 57.034 33.333 0.00 0.00 0.00 3.06
5118 5509 4.722194 CACGTTGTGATTTACTCCCAATG 58.278 43.478 0.00 0.00 35.23 2.82


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

AutoCloner maintained by Alex Coulton.