Multiple sequence alignment - TraesCS2B01G196000

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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 TraesCS2B01G196000 chr2B 100.000 3828 0 0 1 3828 173758320 173754493 0.000000e+00 7070
1 TraesCS2B01G196000 chr2B 88.281 128 14 1 3121 3247 712324808 712324935 6.620000e-33 152
2 TraesCS2B01G196000 chr2A 92.299 2805 169 18 160 2929 124660909 124658117 0.000000e+00 3940
3 TraesCS2B01G196000 chr2A 83.240 716 99 12 3130 3828 312268509 312269220 4.170000e-179 638
4 TraesCS2B01G196000 chr2A 89.474 152 7 5 2976 3124 124656922 124656777 2.350000e-42 183
5 TraesCS2B01G196000 chr2D 92.495 2425 112 18 512 2884 120633900 120631494 0.000000e+00 3406
6 TraesCS2B01G196000 chr2D 79.065 535 101 10 150 678 565874361 565874890 1.310000e-94 357
7 TraesCS2B01G196000 chr2D 83.178 107 18 0 2044 2150 33050797 33050691 8.750000e-17 99
8 TraesCS2B01G196000 chr5D 89.976 409 35 4 1420 1828 299407838 299407436 1.220000e-144 523
9 TraesCS2B01G196000 chr5D 73.023 708 156 25 3125 3827 308339154 308339831 2.320000e-52 217
10 TraesCS2B01G196000 chr4A 82.258 558 86 11 150 702 24116705 24116156 1.610000e-128 470
11 TraesCS2B01G196000 chr4A 80.806 521 93 7 150 667 29055451 29055967 5.960000e-108 401
12 TraesCS2B01G196000 chr7B 82.440 541 90 5 149 687 682884944 682885481 5.790000e-128 468
13 TraesCS2B01G196000 chr5B 82.306 503 79 8 180 678 617671579 617671083 9.830000e-116 427
14 TraesCS2B01G196000 chr5B 72.082 437 103 16 3362 3785 28141326 28140896 3.130000e-21 113
15 TraesCS2B01G196000 chr6D 81.181 542 88 13 152 686 107978353 107978887 1.270000e-114 424
16 TraesCS2B01G196000 chr6D 80.522 498 90 5 148 643 405088396 405087904 3.610000e-100 375
17 TraesCS2B01G196000 chrUn 80.971 515 92 6 149 661 143844923 143844413 1.660000e-108 403
18 TraesCS2B01G196000 chrUn 77.019 483 70 28 3124 3570 68660198 68659721 4.940000e-59 239
19 TraesCS2B01G196000 chr3D 77.155 731 135 21 3126 3827 105101827 105101100 2.770000e-106 396
20 TraesCS2B01G196000 chr3D 83.178 107 18 0 2044 2150 3040400 3040506 8.750000e-17 99
21 TraesCS2B01G196000 chr1D 79.541 523 95 11 162 678 16676215 16675699 2.810000e-96 363
22 TraesCS2B01G196000 chr1A 86.364 132 11 7 3125 3255 585657575 585657700 1.850000e-28 137
23 TraesCS2B01G196000 chr7A 84.112 107 17 0 2044 2150 488417268 488417374 1.880000e-18 104


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 TraesCS2B01G196000 chr2B 173754493 173758320 3827 True 7070.0 7070 100.0000 1 3828 1 chr2B.!!$R1 3827
1 TraesCS2B01G196000 chr2A 124656777 124660909 4132 True 2061.5 3940 90.8865 160 3124 2 chr2A.!!$R1 2964
2 TraesCS2B01G196000 chr2A 312268509 312269220 711 False 638.0 638 83.2400 3130 3828 1 chr2A.!!$F1 698
3 TraesCS2B01G196000 chr2D 120631494 120633900 2406 True 3406.0 3406 92.4950 512 2884 1 chr2D.!!$R2 2372
4 TraesCS2B01G196000 chr2D 565874361 565874890 529 False 357.0 357 79.0650 150 678 1 chr2D.!!$F1 528
5 TraesCS2B01G196000 chr5D 308339154 308339831 677 False 217.0 217 73.0230 3125 3827 1 chr5D.!!$F1 702
6 TraesCS2B01G196000 chr4A 24116156 24116705 549 True 470.0 470 82.2580 150 702 1 chr4A.!!$R1 552
7 TraesCS2B01G196000 chr4A 29055451 29055967 516 False 401.0 401 80.8060 150 667 1 chr4A.!!$F1 517
8 TraesCS2B01G196000 chr7B 682884944 682885481 537 False 468.0 468 82.4400 149 687 1 chr7B.!!$F1 538
9 TraesCS2B01G196000 chr6D 107978353 107978887 534 False 424.0 424 81.1810 152 686 1 chr6D.!!$F1 534
10 TraesCS2B01G196000 chrUn 143844413 143844923 510 True 403.0 403 80.9710 149 661 1 chrUn.!!$R2 512
11 TraesCS2B01G196000 chr3D 105101100 105101827 727 True 396.0 396 77.1550 3126 3827 1 chr3D.!!$R1 701
12 TraesCS2B01G196000 chr1D 16675699 16676215 516 True 363.0 363 79.5410 162 678 1 chr1D.!!$R1 516

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
579 582 0.179097 CTTCGGCTCCTTCTAGTGCC 60.179 60.0 0.0 0.0 41.76 5.01 F
1658 1706 0.961857 TGTACAGCCTCCGCTTCGTA 60.962 55.0 0.0 0.0 45.55 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2495 2543 0.388134 TTTACCTCGCTGAGTCGTGC 60.388 55.0 5.15 0.0 0.00 5.34 R
3514 4763 0.107263 TGTGCAACAGGCTCAACAGA 60.107 50.0 0.00 0.0 45.67 3.41 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
24 25 6.094193 TGTCATTGTTAATTTGCCATGACA 57.906 33.333 17.16 17.16 43.00 3.58
25 26 6.519382 TGTCATTGTTAATTTGCCATGACAA 58.481 32.000 18.04 0.00 42.50 3.18
26 27 7.160049 TGTCATTGTTAATTTGCCATGACAAT 58.840 30.769 18.04 0.00 42.50 2.71
27 28 7.660617 TGTCATTGTTAATTTGCCATGACAATT 59.339 29.630 18.04 0.00 42.50 2.32
28 29 9.149225 GTCATTGTTAATTTGCCATGACAATTA 57.851 29.630 15.14 0.00 36.04 1.40
29 30 9.887629 TCATTGTTAATTTGCCATGACAATTAT 57.112 25.926 0.00 0.00 36.04 1.28
37 38 9.807649 AATTTGCCATGACAATTATAAAGAGAC 57.192 29.630 0.00 0.00 0.00 3.36
38 39 7.936496 TTGCCATGACAATTATAAAGAGACA 57.064 32.000 0.00 0.00 0.00 3.41
39 40 7.936496 TGCCATGACAATTATAAAGAGACAA 57.064 32.000 0.00 0.00 0.00 3.18
40 41 8.347004 TGCCATGACAATTATAAAGAGACAAA 57.653 30.769 0.00 0.00 0.00 2.83
41 42 8.801299 TGCCATGACAATTATAAAGAGACAAAA 58.199 29.630 0.00 0.00 0.00 2.44
42 43 9.076596 GCCATGACAATTATAAAGAGACAAAAC 57.923 33.333 0.00 0.00 0.00 2.43
82 83 8.644374 TTTTGTAGAGCCTTTGTTTATATGGT 57.356 30.769 0.00 0.00 0.00 3.55
83 84 7.859325 TTGTAGAGCCTTTGTTTATATGGTC 57.141 36.000 0.00 0.00 0.00 4.02
84 85 6.046593 TGTAGAGCCTTTGTTTATATGGTCG 58.953 40.000 0.00 0.00 0.00 4.79
85 86 5.099042 AGAGCCTTTGTTTATATGGTCGT 57.901 39.130 0.00 0.00 0.00 4.34
86 87 5.116882 AGAGCCTTTGTTTATATGGTCGTC 58.883 41.667 0.00 0.00 0.00 4.20
87 88 5.099042 AGCCTTTGTTTATATGGTCGTCT 57.901 39.130 0.00 0.00 0.00 4.18
88 89 5.497474 AGCCTTTGTTTATATGGTCGTCTT 58.503 37.500 0.00 0.00 0.00 3.01
89 90 5.944007 AGCCTTTGTTTATATGGTCGTCTTT 59.056 36.000 0.00 0.00 0.00 2.52
90 91 6.093633 AGCCTTTGTTTATATGGTCGTCTTTC 59.906 38.462 0.00 0.00 0.00 2.62
91 92 6.677187 GCCTTTGTTTATATGGTCGTCTTTCC 60.677 42.308 0.00 0.00 0.00 3.13
92 93 6.598064 CCTTTGTTTATATGGTCGTCTTTCCT 59.402 38.462 0.00 0.00 0.00 3.36
93 94 7.201617 CCTTTGTTTATATGGTCGTCTTTCCTC 60.202 40.741 0.00 0.00 0.00 3.71
94 95 5.345702 TGTTTATATGGTCGTCTTTCCTCG 58.654 41.667 0.00 0.00 0.00 4.63
95 96 5.105635 TGTTTATATGGTCGTCTTTCCTCGT 60.106 40.000 0.00 0.00 0.00 4.18
96 97 3.712091 ATATGGTCGTCTTTCCTCGTC 57.288 47.619 0.00 0.00 0.00 4.20
97 98 1.254026 ATGGTCGTCTTTCCTCGTCA 58.746 50.000 0.00 0.00 0.00 4.35
98 99 1.254026 TGGTCGTCTTTCCTCGTCAT 58.746 50.000 0.00 0.00 0.00 3.06
99 100 2.439409 TGGTCGTCTTTCCTCGTCATA 58.561 47.619 0.00 0.00 0.00 2.15
100 101 2.821378 TGGTCGTCTTTCCTCGTCATAA 59.179 45.455 0.00 0.00 0.00 1.90
101 102 3.119602 TGGTCGTCTTTCCTCGTCATAAG 60.120 47.826 0.00 0.00 0.00 1.73
102 103 3.128242 GGTCGTCTTTCCTCGTCATAAGA 59.872 47.826 0.00 0.00 0.00 2.10
103 104 4.380233 GGTCGTCTTTCCTCGTCATAAGAA 60.380 45.833 0.00 0.00 0.00 2.52
104 105 5.159209 GTCGTCTTTCCTCGTCATAAGAAA 58.841 41.667 0.00 0.00 0.00 2.52
105 106 5.632347 GTCGTCTTTCCTCGTCATAAGAAAA 59.368 40.000 0.00 0.00 0.00 2.29
106 107 5.862323 TCGTCTTTCCTCGTCATAAGAAAAG 59.138 40.000 0.00 0.00 0.00 2.27
107 108 5.444745 CGTCTTTCCTCGTCATAAGAAAAGC 60.445 44.000 0.00 0.00 0.00 3.51
108 109 4.935808 TCTTTCCTCGTCATAAGAAAAGCC 59.064 41.667 0.00 0.00 0.00 4.35
109 110 3.261981 TCCTCGTCATAAGAAAAGCCC 57.738 47.619 0.00 0.00 0.00 5.19
110 111 2.093128 TCCTCGTCATAAGAAAAGCCCC 60.093 50.000 0.00 0.00 0.00 5.80
111 112 2.289565 CTCGTCATAAGAAAAGCCCCC 58.710 52.381 0.00 0.00 0.00 5.40
112 113 1.913419 TCGTCATAAGAAAAGCCCCCT 59.087 47.619 0.00 0.00 0.00 4.79
113 114 2.307686 TCGTCATAAGAAAAGCCCCCTT 59.692 45.455 0.00 0.00 0.00 3.95
114 115 2.683362 CGTCATAAGAAAAGCCCCCTTC 59.317 50.000 0.00 0.00 0.00 3.46
115 116 3.024547 GTCATAAGAAAAGCCCCCTTCC 58.975 50.000 0.00 0.00 0.00 3.46
116 117 2.926329 TCATAAGAAAAGCCCCCTTCCT 59.074 45.455 0.00 0.00 0.00 3.36
117 118 3.336694 TCATAAGAAAAGCCCCCTTCCTT 59.663 43.478 0.00 0.00 0.00 3.36
118 119 2.310779 AAGAAAAGCCCCCTTCCTTC 57.689 50.000 0.00 0.00 0.00 3.46
119 120 1.461321 AGAAAAGCCCCCTTCCTTCT 58.539 50.000 0.00 0.00 0.00 2.85
120 121 1.789536 AGAAAAGCCCCCTTCCTTCTT 59.210 47.619 0.00 0.00 28.47 2.52
121 122 2.171840 GAAAAGCCCCCTTCCTTCTTC 58.828 52.381 0.00 0.00 0.00 2.87
122 123 0.409876 AAAGCCCCCTTCCTTCTTCC 59.590 55.000 0.00 0.00 0.00 3.46
123 124 1.853250 AAGCCCCCTTCCTTCTTCCG 61.853 60.000 0.00 0.00 0.00 4.30
124 125 2.272471 CCCCCTTCCTTCTTCCGC 59.728 66.667 0.00 0.00 0.00 5.54
125 126 2.272471 CCCCTTCCTTCTTCCGCC 59.728 66.667 0.00 0.00 0.00 6.13
126 127 2.125106 CCCTTCCTTCTTCCGCCG 60.125 66.667 0.00 0.00 0.00 6.46
127 128 2.125106 CCTTCCTTCTTCCGCCGG 60.125 66.667 0.00 0.00 0.00 6.13
128 129 2.820037 CTTCCTTCTTCCGCCGGC 60.820 66.667 19.07 19.07 0.00 6.13
129 130 4.752879 TTCCTTCTTCCGCCGGCG 62.753 66.667 41.00 41.00 39.44 6.46
147 148 4.899239 CTGCCGCTGATCCGTCCC 62.899 72.222 0.00 0.00 0.00 4.46
216 217 2.837291 TTGGTTGGGGCTGTGTGC 60.837 61.111 0.00 0.00 41.94 4.57
256 257 3.641906 CGGTAGGAATATTGTCTCCCACT 59.358 47.826 0.00 0.00 31.50 4.00
399 401 5.908916 TTTGTTCGTATTCGTTCATGTGA 57.091 34.783 0.00 0.00 38.33 3.58
458 460 1.219124 GCGATGGTTGCTCCTCTGA 59.781 57.895 0.00 0.00 37.07 3.27
481 484 1.248486 GTTGGTCCTTTGAGGCCTTC 58.752 55.000 6.77 0.10 34.61 3.46
484 487 2.047274 TCCTTTGAGGCCTTCGCG 60.047 61.111 6.77 0.00 34.61 5.87
485 488 3.127533 CCTTTGAGGCCTTCGCGG 61.128 66.667 6.77 1.70 35.02 6.46
526 529 2.224670 ACTACAACAAGATTTGCCCGGA 60.225 45.455 0.73 0.00 0.00 5.14
535 538 0.331278 ATTTGCCCGGATCTGGTGAA 59.669 50.000 19.51 10.77 0.00 3.18
553 556 4.115199 GGAGGGGCAATGACGGCT 62.115 66.667 0.00 0.00 0.00 5.52
554 557 2.044946 GAGGGGCAATGACGGCTT 60.045 61.111 0.00 0.00 0.00 4.35
559 562 3.788766 GCAATGACGGCTTCGCGT 61.789 61.111 5.77 0.00 37.41 6.01
569 572 2.881352 CTTCGCGTCTTCGGCTCC 60.881 66.667 5.77 0.00 37.56 4.70
570 573 3.343788 CTTCGCGTCTTCGGCTCCT 62.344 63.158 5.77 0.00 37.56 3.69
579 582 0.179097 CTTCGGCTCCTTCTAGTGCC 60.179 60.000 0.00 0.00 41.76 5.01
590 594 3.701542 CCTTCTAGTGCCTGTAGTCATCA 59.298 47.826 0.00 0.00 0.00 3.07
591 595 4.343526 CCTTCTAGTGCCTGTAGTCATCAT 59.656 45.833 0.00 0.00 0.00 2.45
607 611 5.044919 AGTCATCATTAGGTGGTCCATGAAA 60.045 40.000 0.00 0.00 32.42 2.69
614 618 2.714250 AGGTGGTCCATGAAACTGGTTA 59.286 45.455 0.00 0.00 37.57 2.85
657 661 5.292101 GTGTTCTCTGTACTACCATGATTGC 59.708 44.000 0.00 0.00 0.00 3.56
667 671 8.090831 TGTACTACCATGATTGCTGAATAGATC 58.909 37.037 0.00 0.00 0.00 2.75
668 672 6.471146 ACTACCATGATTGCTGAATAGATCC 58.529 40.000 0.00 0.00 0.00 3.36
782 792 1.283736 GCATGCTTGCCTAATTGCAC 58.716 50.000 11.37 0.00 43.38 4.57
816 826 3.626996 TTCCCTGATGCTGCCGGTG 62.627 63.158 1.90 0.00 0.00 4.94
1025 1041 4.475135 GCCAGGGTCTTCCTCCGC 62.475 72.222 0.00 0.00 46.12 5.54
1041 1057 4.803426 GCGAGGCTCGTCCACCTG 62.803 72.222 34.41 8.03 42.81 4.00
1203 1219 2.224066 GGACTCCTTCATCCGGTATGTG 60.224 54.545 0.00 0.00 36.89 3.21
1218 1238 4.631377 CGGTATGTGCTTCTGATTTCTGAA 59.369 41.667 0.82 0.82 33.68 3.02
1221 1241 2.807967 TGTGCTTCTGATTTCTGAACCG 59.192 45.455 0.00 0.00 31.85 4.44
1259 1279 2.151202 TGCTTGTCTCGGTTGATTTCC 58.849 47.619 0.00 0.00 0.00 3.13
1398 1446 1.449601 ACAATCACGGCGGTCATCC 60.450 57.895 13.24 0.00 0.00 3.51
1437 1485 3.470888 CGGTCGGGGGCTCTGATT 61.471 66.667 0.00 0.00 32.64 2.57
1447 1495 2.517450 GCTCTGATTTCGTCGCCGG 61.517 63.158 0.00 0.00 33.95 6.13
1658 1706 0.961857 TGTACAGCCTCCGCTTCGTA 60.962 55.000 0.00 0.00 45.55 3.43
1926 1974 3.277211 TTGGACCTCGCCGAGTTCG 62.277 63.158 13.83 0.00 39.44 3.95
2547 2595 2.599032 CCCATGGCCTGCTCATGA 59.401 61.111 6.09 0.00 43.25 3.07
2561 2609 3.198417 TGCTCATGACTCCAGCTCATTAA 59.802 43.478 5.60 0.00 34.03 1.40
2591 2639 5.561145 CGAGATTCGAGATACACGGAGAAAT 60.561 44.000 0.00 0.00 43.74 2.17
2598 2646 6.073167 TCGAGATACACGGAGAAATTAGCTAG 60.073 42.308 0.00 0.00 0.00 3.42
2602 2650 8.910944 AGATACACGGAGAAATTAGCTAGTTAA 58.089 33.333 1.46 1.19 0.00 2.01
2603 2651 8.868635 ATACACGGAGAAATTAGCTAGTTAAC 57.131 34.615 1.46 0.00 0.00 2.01
2604 2652 6.104665 ACACGGAGAAATTAGCTAGTTAACC 58.895 40.000 1.46 5.66 0.00 2.85
2605 2653 6.103997 CACGGAGAAATTAGCTAGTTAACCA 58.896 40.000 1.46 0.00 0.00 3.67
2606 2654 6.761714 CACGGAGAAATTAGCTAGTTAACCAT 59.238 38.462 1.46 0.00 0.00 3.55
2607 2655 6.985059 ACGGAGAAATTAGCTAGTTAACCATC 59.015 38.462 1.46 1.38 0.00 3.51
2609 2657 7.169982 CGGAGAAATTAGCTAGTTAACCATCTG 59.830 40.741 1.46 6.28 0.00 2.90
2624 2682 4.870363 ACCATCTGTTATGTGTGTTTTGC 58.130 39.130 0.00 0.00 0.00 3.68
2647 2705 4.538283 CTCGCGTGCTCGGACGAT 62.538 66.667 15.05 0.00 42.10 3.73
2898 2965 0.603065 ACGTACATGCAGAGCACAGA 59.397 50.000 0.00 0.00 43.04 3.41
2899 2966 1.205655 ACGTACATGCAGAGCACAGAT 59.794 47.619 0.00 0.00 43.04 2.90
2934 3237 6.078479 CACGCTAATGTAGAGACTTATACCG 58.922 44.000 0.00 0.00 0.00 4.02
2941 3244 1.404391 AGAGACTTATACCGTGCCGTG 59.596 52.381 0.00 0.00 0.00 4.94
2948 3251 1.238625 ATACCGTGCCGTGGGTTTTG 61.239 55.000 0.00 0.00 37.75 2.44
2949 3252 2.605854 TACCGTGCCGTGGGTTTTGT 62.606 55.000 0.00 0.00 37.75 2.83
2974 3785 3.000674 CGCTACGAAGTTCAGTTAGCATG 60.001 47.826 20.11 0.00 37.78 4.06
2982 3793 4.144297 AGTTCAGTTAGCATGGCAAAGAA 58.856 39.130 0.00 0.00 0.00 2.52
2983 3794 4.022849 AGTTCAGTTAGCATGGCAAAGAAC 60.023 41.667 0.00 0.00 34.61 3.01
2984 3795 3.754965 TCAGTTAGCATGGCAAAGAACT 58.245 40.909 0.00 0.00 0.00 3.01
2989 4208 2.716217 AGCATGGCAAAGAACTACTCC 58.284 47.619 0.00 0.00 0.00 3.85
2990 4209 1.745653 GCATGGCAAAGAACTACTCCC 59.254 52.381 0.00 0.00 0.00 4.30
2997 4216 3.878778 CAAAGAACTACTCCCTCCCATG 58.121 50.000 0.00 0.00 0.00 3.66
2998 4217 3.491766 AAGAACTACTCCCTCCCATGA 57.508 47.619 0.00 0.00 0.00 3.07
2999 4218 3.715648 AGAACTACTCCCTCCCATGAT 57.284 47.619 0.00 0.00 0.00 2.45
3000 4219 3.312890 AGAACTACTCCCTCCCATGATG 58.687 50.000 0.00 0.00 0.00 3.07
3001 4220 1.428869 ACTACTCCCTCCCATGATGC 58.571 55.000 0.00 0.00 0.00 3.91
3007 4226 0.256752 CCCTCCCATGATGCAAGACA 59.743 55.000 0.00 0.00 0.00 3.41
3019 4238 5.283294 TGATGCAAGACATTTTTGACACTG 58.717 37.500 0.00 0.00 39.84 3.66
3022 4241 4.642437 TGCAAGACATTTTTGACACTGGTA 59.358 37.500 0.00 0.00 0.00 3.25
3243 4467 4.290622 ACCAAGGTGCCCTGGCTG 62.291 66.667 9.97 0.00 42.51 4.85
3247 4471 0.539438 CAAGGTGCCCTGGCTGTAAA 60.539 55.000 9.97 0.00 42.51 2.01
3262 4486 3.120060 GCTGTAAACTGCCAGACAAGATG 60.120 47.826 0.00 0.00 35.17 2.90
3265 4489 2.486472 AACTGCCAGACAAGATGGAG 57.514 50.000 0.00 0.00 40.51 3.86
3286 4514 3.009143 AGACATGTAGAGGGGTGGAAAAC 59.991 47.826 0.00 0.00 0.00 2.43
3290 4518 3.050089 TGTAGAGGGGTGGAAAACAGAA 58.950 45.455 0.00 0.00 0.00 3.02
3291 4519 2.959465 AGAGGGGTGGAAAACAGAAG 57.041 50.000 0.00 0.00 0.00 2.85
3292 4520 1.425448 AGAGGGGTGGAAAACAGAAGG 59.575 52.381 0.00 0.00 0.00 3.46
3293 4521 0.178961 AGGGGTGGAAAACAGAAGGC 60.179 55.000 0.00 0.00 0.00 4.35
3297 4525 1.970640 GGTGGAAAACAGAAGGCCAAT 59.029 47.619 5.01 0.00 0.00 3.16
3311 4558 8.494433 ACAGAAGGCCAATATGTTCTAATCTAA 58.506 33.333 5.01 0.00 0.00 2.10
3314 4561 7.394144 AGGCCAATATGTTCTAATCTAACCT 57.606 36.000 5.01 0.00 0.00 3.50
3336 4583 3.503827 TGTATCCAATCGGCTATAGCG 57.496 47.619 18.30 13.37 43.26 4.26
3340 4587 0.732880 CCAATCGGCTATAGCGTCGG 60.733 60.000 18.30 10.17 43.26 4.79
3341 4588 1.080705 AATCGGCTATAGCGTCGGC 60.081 57.895 18.30 3.37 43.26 5.54
3381 4628 7.884877 TGACTCCTATTATGCCATAAATGAAGG 59.115 37.037 0.47 6.68 0.00 3.46
3390 4637 4.832266 TGCCATAAATGAAGGAGTTGTGTT 59.168 37.500 0.00 0.00 0.00 3.32
3391 4638 5.163513 GCCATAAATGAAGGAGTTGTGTTG 58.836 41.667 0.00 0.00 0.00 3.33
3396 4643 3.120321 TGAAGGAGTTGTGTTGCGTAT 57.880 42.857 0.00 0.00 0.00 3.06
3408 4655 9.982291 AGTTGTGTTGCGTATTGTTTTATATAG 57.018 29.630 0.00 0.00 0.00 1.31
3414 4661 6.526526 TGCGTATTGTTTTATATAGGCTGGA 58.473 36.000 0.00 0.00 38.36 3.86
3429 4676 1.765314 GCTGGAGGCCATCTCTTAGAA 59.235 52.381 5.01 0.00 42.10 2.10
3435 4682 4.819088 GGAGGCCATCTCTTAGAATTGAAC 59.181 45.833 5.01 0.00 42.10 3.18
3476 4725 2.430465 CCATGAAGTAACTGCAGTGCT 58.570 47.619 22.49 18.51 0.00 4.40
3514 4763 3.474570 GCTGGAGGACGGCCATCT 61.475 66.667 11.69 0.00 46.06 2.90
3539 4788 1.238439 GAGCCTGTTGCACAAAGCTA 58.762 50.000 11.04 0.00 45.94 3.32
3542 4791 2.629617 AGCCTGTTGCACAAAGCTAATT 59.370 40.909 9.97 0.00 45.94 1.40
3590 4839 1.442769 CCAGGTCGAACACATTCCAG 58.557 55.000 1.87 0.00 0.00 3.86
3593 4842 3.338249 CAGGTCGAACACATTCCAGATT 58.662 45.455 1.87 0.00 0.00 2.40
3596 4845 4.020573 AGGTCGAACACATTCCAGATTACA 60.021 41.667 1.87 0.00 0.00 2.41
3623 4872 0.882927 GGCAACAACGTAGCACCAGA 60.883 55.000 0.00 0.00 0.00 3.86
3626 4875 2.412870 CAACAACGTAGCACCAGATGA 58.587 47.619 0.00 0.00 0.00 2.92
3628 4877 2.688507 ACAACGTAGCACCAGATGAAG 58.311 47.619 0.00 0.00 0.00 3.02
3629 4878 2.002586 CAACGTAGCACCAGATGAAGG 58.997 52.381 0.00 0.00 0.00 3.46
3630 4879 1.557099 ACGTAGCACCAGATGAAGGA 58.443 50.000 0.00 0.00 0.00 3.36
3668 4917 3.439476 GGCAGATATCACAATCCTGATGC 59.561 47.826 5.32 1.79 32.86 3.91
3671 4920 4.151867 CAGATATCACAATCCTGATGCGTG 59.848 45.833 5.32 4.40 32.86 5.34
3677 4926 1.524355 CAATCCTGATGCGTGACGATC 59.476 52.381 10.10 9.66 0.00 3.69
3715 4964 7.361457 TCTTCATCATATTATCCCGGGTATC 57.639 40.000 22.86 0.00 0.00 2.24
3716 4965 6.326583 TCTTCATCATATTATCCCGGGTATCC 59.673 42.308 22.86 0.00 0.00 2.59
3721 4970 0.192566 TTATCCCGGGTATCCAGCCT 59.807 55.000 22.86 0.00 40.40 4.58
3722 4971 0.192566 TATCCCGGGTATCCAGCCTT 59.807 55.000 22.86 0.00 40.40 4.35
3726 4975 1.766461 CGGGTATCCAGCCTTCCCT 60.766 63.158 0.00 0.00 40.40 4.20
3731 4980 3.046374 GGTATCCAGCCTTCCCTAGAAA 58.954 50.000 0.00 0.00 0.00 2.52
3736 4985 4.172807 TCCAGCCTTCCCTAGAAAAGTAA 58.827 43.478 0.00 0.00 0.00 2.24
3740 4989 4.008330 GCCTTCCCTAGAAAAGTAACCAC 58.992 47.826 0.00 0.00 0.00 4.16
3761 5010 5.525012 CCACAAGAAGATGCGATATTTGAGA 59.475 40.000 0.00 0.00 0.00 3.27
3767 5016 7.901029 AGAAGATGCGATATTTGAGAGGAATA 58.099 34.615 0.00 0.00 0.00 1.75
3792 5041 0.743097 GTCCCAAATCCATGAGCTGC 59.257 55.000 0.00 0.00 0.00 5.25
3794 5043 0.458669 CCCAAATCCATGAGCTGCAC 59.541 55.000 1.02 0.00 0.00 4.57
3801 5050 0.039798 CCATGAGCTGCACACACAAC 60.040 55.000 0.90 0.00 0.00 3.32
3806 5055 0.173255 AGCTGCACACACAACAAACC 59.827 50.000 1.02 0.00 0.00 3.27
3810 5059 0.534873 GCACACACAACAAACCCCTT 59.465 50.000 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.519382 TGTCATGGCAAATTAACAATGACAA 58.481 32.000 20.60 10.14 42.50 3.18
1 2 6.094193 TGTCATGGCAAATTAACAATGACA 57.906 33.333 19.63 19.63 43.00 3.58
2 3 7.599630 ATTGTCATGGCAAATTAACAATGAC 57.400 32.000 18.05 16.18 36.34 3.06
3 4 9.887629 ATAATTGTCATGGCAAATTAACAATGA 57.112 25.926 18.05 4.61 37.40 2.57
11 12 9.807649 GTCTCTTTATAATTGTCATGGCAAATT 57.192 29.630 18.05 13.61 31.63 1.82
12 13 8.970020 TGTCTCTTTATAATTGTCATGGCAAAT 58.030 29.630 18.05 11.69 31.63 2.32
13 14 8.347004 TGTCTCTTTATAATTGTCATGGCAAA 57.653 30.769 18.05 1.16 31.63 3.68
14 15 7.936496 TGTCTCTTTATAATTGTCATGGCAA 57.064 32.000 16.33 16.33 0.00 4.52
15 16 7.936496 TTGTCTCTTTATAATTGTCATGGCA 57.064 32.000 0.00 0.00 0.00 4.92
16 17 9.076596 GTTTTGTCTCTTTATAATTGTCATGGC 57.923 33.333 0.00 0.00 0.00 4.40
56 57 9.084533 ACCATATAAACAAAGGCTCTACAAAAA 57.915 29.630 0.00 0.00 0.00 1.94
57 58 8.644374 ACCATATAAACAAAGGCTCTACAAAA 57.356 30.769 0.00 0.00 0.00 2.44
58 59 7.065324 CGACCATATAAACAAAGGCTCTACAAA 59.935 37.037 0.00 0.00 0.00 2.83
59 60 6.537301 CGACCATATAAACAAAGGCTCTACAA 59.463 38.462 0.00 0.00 0.00 2.41
60 61 6.046593 CGACCATATAAACAAAGGCTCTACA 58.953 40.000 0.00 0.00 0.00 2.74
61 62 6.047231 ACGACCATATAAACAAAGGCTCTAC 58.953 40.000 0.00 0.00 0.00 2.59
62 63 6.097839 AGACGACCATATAAACAAAGGCTCTA 59.902 38.462 0.00 0.00 0.00 2.43
63 64 5.099042 ACGACCATATAAACAAAGGCTCT 57.901 39.130 0.00 0.00 0.00 4.09
64 65 5.116882 AGACGACCATATAAACAAAGGCTC 58.883 41.667 0.00 0.00 0.00 4.70
65 66 5.099042 AGACGACCATATAAACAAAGGCT 57.901 39.130 0.00 0.00 0.00 4.58
66 67 5.813080 AAGACGACCATATAAACAAAGGC 57.187 39.130 0.00 0.00 0.00 4.35
67 68 6.598064 AGGAAAGACGACCATATAAACAAAGG 59.402 38.462 0.00 0.00 0.00 3.11
68 69 7.464178 CGAGGAAAGACGACCATATAAACAAAG 60.464 40.741 0.00 0.00 0.00 2.77
69 70 6.311935 CGAGGAAAGACGACCATATAAACAAA 59.688 38.462 0.00 0.00 0.00 2.83
70 71 5.808540 CGAGGAAAGACGACCATATAAACAA 59.191 40.000 0.00 0.00 0.00 2.83
71 72 5.105635 ACGAGGAAAGACGACCATATAAACA 60.106 40.000 0.00 0.00 0.00 2.83
72 73 5.346522 ACGAGGAAAGACGACCATATAAAC 58.653 41.667 0.00 0.00 0.00 2.01
73 74 5.125900 TGACGAGGAAAGACGACCATATAAA 59.874 40.000 0.00 0.00 0.00 1.40
74 75 4.641541 TGACGAGGAAAGACGACCATATAA 59.358 41.667 0.00 0.00 0.00 0.98
75 76 4.201657 TGACGAGGAAAGACGACCATATA 58.798 43.478 0.00 0.00 0.00 0.86
76 77 3.021695 TGACGAGGAAAGACGACCATAT 58.978 45.455 0.00 0.00 0.00 1.78
77 78 2.439409 TGACGAGGAAAGACGACCATA 58.561 47.619 0.00 0.00 0.00 2.74
78 79 1.254026 TGACGAGGAAAGACGACCAT 58.746 50.000 0.00 0.00 0.00 3.55
79 80 1.254026 ATGACGAGGAAAGACGACCA 58.746 50.000 0.00 0.00 0.00 4.02
80 81 3.128242 TCTTATGACGAGGAAAGACGACC 59.872 47.826 0.00 0.00 0.00 4.79
81 82 4.352600 TCTTATGACGAGGAAAGACGAC 57.647 45.455 0.00 0.00 0.00 4.34
82 83 5.381174 TTTCTTATGACGAGGAAAGACGA 57.619 39.130 0.00 0.00 0.00 4.20
83 84 5.444745 GCTTTTCTTATGACGAGGAAAGACG 60.445 44.000 8.65 0.00 40.61 4.18
84 85 5.163844 GGCTTTTCTTATGACGAGGAAAGAC 60.164 44.000 8.65 2.53 40.61 3.01
85 86 4.935808 GGCTTTTCTTATGACGAGGAAAGA 59.064 41.667 8.65 0.00 40.61 2.52
86 87 4.095036 GGGCTTTTCTTATGACGAGGAAAG 59.905 45.833 0.00 0.00 40.94 2.62
87 88 4.007659 GGGCTTTTCTTATGACGAGGAAA 58.992 43.478 0.00 0.00 0.00 3.13
88 89 3.606687 GGGCTTTTCTTATGACGAGGAA 58.393 45.455 0.00 0.00 0.00 3.36
89 90 2.093128 GGGGCTTTTCTTATGACGAGGA 60.093 50.000 0.00 0.00 0.00 3.71
90 91 2.289565 GGGGCTTTTCTTATGACGAGG 58.710 52.381 0.00 0.00 0.00 4.63
91 92 2.092914 AGGGGGCTTTTCTTATGACGAG 60.093 50.000 0.00 0.00 0.00 4.18
92 93 1.913419 AGGGGGCTTTTCTTATGACGA 59.087 47.619 0.00 0.00 0.00 4.20
93 94 2.420058 AGGGGGCTTTTCTTATGACG 57.580 50.000 0.00 0.00 0.00 4.35
94 95 3.024547 GGAAGGGGGCTTTTCTTATGAC 58.975 50.000 0.00 0.00 0.00 3.06
95 96 2.926329 AGGAAGGGGGCTTTTCTTATGA 59.074 45.455 0.00 0.00 0.00 2.15
96 97 3.388552 AGGAAGGGGGCTTTTCTTATG 57.611 47.619 0.00 0.00 0.00 1.90
97 98 3.598324 AGAAGGAAGGGGGCTTTTCTTAT 59.402 43.478 0.00 0.00 0.00 1.73
98 99 2.993863 AGAAGGAAGGGGGCTTTTCTTA 59.006 45.455 0.00 0.00 0.00 2.10
99 100 1.789536 AGAAGGAAGGGGGCTTTTCTT 59.210 47.619 0.00 0.00 0.00 2.52
100 101 1.461321 AGAAGGAAGGGGGCTTTTCT 58.539 50.000 0.00 0.00 0.00 2.52
101 102 2.171840 GAAGAAGGAAGGGGGCTTTTC 58.828 52.381 0.00 0.00 0.00 2.29
102 103 1.203187 GGAAGAAGGAAGGGGGCTTTT 60.203 52.381 0.00 0.00 0.00 2.27
103 104 0.409876 GGAAGAAGGAAGGGGGCTTT 59.590 55.000 0.00 0.00 0.00 3.51
104 105 1.853250 CGGAAGAAGGAAGGGGGCTT 61.853 60.000 0.00 0.00 0.00 4.35
105 106 2.301738 CGGAAGAAGGAAGGGGGCT 61.302 63.158 0.00 0.00 0.00 5.19
106 107 2.272471 CGGAAGAAGGAAGGGGGC 59.728 66.667 0.00 0.00 0.00 5.80
107 108 2.272471 GCGGAAGAAGGAAGGGGG 59.728 66.667 0.00 0.00 0.00 5.40
108 109 2.272471 GGCGGAAGAAGGAAGGGG 59.728 66.667 0.00 0.00 0.00 4.79
109 110 2.125106 CGGCGGAAGAAGGAAGGG 60.125 66.667 0.00 0.00 0.00 3.95
110 111 2.125106 CCGGCGGAAGAAGGAAGG 60.125 66.667 24.41 0.00 0.00 3.46
111 112 2.820037 GCCGGCGGAAGAAGGAAG 60.820 66.667 33.44 0.00 0.00 3.46
112 113 4.752879 CGCCGGCGGAAGAAGGAA 62.753 66.667 40.50 0.00 35.56 3.36
130 131 4.899239 GGGACGGATCAGCGGCAG 62.899 72.222 1.45 0.00 0.00 4.85
132 133 4.593864 GAGGGACGGATCAGCGGC 62.594 72.222 0.00 0.00 0.00 6.53
133 134 3.917760 GGAGGGACGGATCAGCGG 61.918 72.222 0.00 0.00 0.00 5.52
134 135 3.917760 GGGAGGGACGGATCAGCG 61.918 72.222 0.00 0.00 0.00 5.18
135 136 3.551407 GGGGAGGGACGGATCAGC 61.551 72.222 0.00 0.00 0.00 4.26
136 137 2.844839 GGGGGAGGGACGGATCAG 60.845 72.222 0.00 0.00 0.00 2.90
137 138 4.853142 CGGGGGAGGGACGGATCA 62.853 72.222 0.00 0.00 0.00 2.92
164 165 6.322969 CCTAACAAAAACTAAAACAGGGTCCT 59.677 38.462 0.00 0.00 0.00 3.85
177 178 9.143155 ACCAAGATATTGAACCTAACAAAAACT 57.857 29.630 0.54 0.00 0.00 2.66
216 217 4.143333 AGGGACATCGCGAACCCG 62.143 66.667 29.65 16.58 46.13 5.28
217 218 2.202892 GAGGGACATCGCGAACCC 60.203 66.667 29.36 29.36 42.36 4.11
222 223 2.331805 CTACCGAGGGACATCGCG 59.668 66.667 0.00 0.00 41.37 5.87
245 246 2.478292 GGGATAGGAAGTGGGAGACAA 58.522 52.381 0.00 0.00 0.00 3.18
273 274 0.989890 GACGACACTATTCGCACCAC 59.010 55.000 0.00 0.00 43.06 4.16
386 388 6.429692 TCAAACCTGTAATCACATGAACGAAT 59.570 34.615 0.00 0.00 33.14 3.34
458 460 1.244019 GCCTCAAAGGACCAACGCAT 61.244 55.000 0.00 0.00 37.67 4.73
484 487 1.282930 GACAACCGAGAAGTCGTGCC 61.283 60.000 0.00 0.00 45.30 5.01
485 488 0.318784 AGACAACCGAGAAGTCGTGC 60.319 55.000 0.00 0.00 45.30 5.34
486 489 2.225963 AGTAGACAACCGAGAAGTCGTG 59.774 50.000 0.00 0.00 45.30 4.35
516 519 0.331278 TTCACCAGATCCGGGCAAAT 59.669 50.000 0.00 0.00 0.00 2.32
526 529 0.846427 TTGCCCCTCCTTCACCAGAT 60.846 55.000 0.00 0.00 0.00 2.90
535 538 4.115199 GCCGTCATTGCCCCTCCT 62.115 66.667 0.00 0.00 0.00 3.69
553 556 2.814183 GAAGGAGCCGAAGACGCGAA 62.814 60.000 15.93 0.00 38.29 4.70
554 557 3.338126 GAAGGAGCCGAAGACGCGA 62.338 63.158 15.93 0.00 38.29 5.87
559 562 0.818296 GCACTAGAAGGAGCCGAAGA 59.182 55.000 0.00 0.00 0.00 2.87
569 572 4.991153 TGATGACTACAGGCACTAGAAG 57.009 45.455 0.00 0.00 36.02 2.85
570 573 5.939764 AATGATGACTACAGGCACTAGAA 57.060 39.130 0.00 0.00 36.02 2.10
579 582 4.405680 TGGACCACCTAATGATGACTACAG 59.594 45.833 0.00 0.00 37.04 2.74
590 594 3.333680 ACCAGTTTCATGGACCACCTAAT 59.666 43.478 0.00 0.00 43.57 1.73
591 595 2.714250 ACCAGTTTCATGGACCACCTAA 59.286 45.455 0.00 0.00 43.57 2.69
779 789 1.302832 CTGTGGAAGAGTGGGGTGC 60.303 63.158 0.00 0.00 0.00 5.01
782 792 0.036875 GGAACTGTGGAAGAGTGGGG 59.963 60.000 0.00 0.00 40.98 4.96
816 826 0.539669 CACACCCCCAAACCCTCTTC 60.540 60.000 0.00 0.00 0.00 2.87
1025 1041 4.803426 GCAGGTGGACGAGCCTCG 62.803 72.222 13.52 13.52 46.93 4.63
1203 1219 1.201965 CGCGGTTCAGAAATCAGAAGC 60.202 52.381 0.00 7.45 36.79 3.86
1221 1241 3.281359 AACAATTTCTGGCCGCCGC 62.281 57.895 4.58 0.00 0.00 6.53
1259 1279 1.406539 CTCCCCAAAAATGGCGATGAG 59.593 52.381 0.00 0.00 0.00 2.90
1322 1370 0.531200 ACTCCGGCGTCCTCTTAAAG 59.469 55.000 6.01 0.00 0.00 1.85
1598 1646 2.260743 GTCTCGTCCGGGAACACC 59.739 66.667 0.00 0.00 0.00 4.16
1754 1802 3.332493 GACGCCGTAGAACGCCAGA 62.332 63.158 0.00 0.00 40.91 3.86
1769 1817 3.071459 GAACGCCAGCGACATGACG 62.071 63.158 20.32 13.27 42.83 4.35
2010 2058 2.185350 CTTGGCGACGAGGAGCAT 59.815 61.111 0.00 0.00 38.28 3.79
2276 2324 1.028330 ACTTCGCCGTCATCCGTCTA 61.028 55.000 0.00 0.00 33.66 2.59
2342 2390 3.391665 GATCCAGCCCAGGGACACG 62.392 68.421 10.89 0.00 37.23 4.49
2495 2543 0.388134 TTTACCTCGCTGAGTCGTGC 60.388 55.000 5.15 0.00 0.00 5.34
2561 2609 3.312973 GTGTATCTCGAATCTCGGTCAGT 59.687 47.826 0.00 0.00 40.88 3.41
2591 2639 8.537016 ACACATAACAGATGGTTAACTAGCTAA 58.463 33.333 9.55 0.00 44.70 3.09
2598 2646 7.096230 GCAAAACACACATAACAGATGGTTAAC 60.096 37.037 0.00 0.00 44.70 2.01
2602 2650 4.556501 CGCAAAACACACATAACAGATGGT 60.557 41.667 0.00 0.00 0.00 3.55
2603 2651 3.913763 CGCAAAACACACATAACAGATGG 59.086 43.478 0.00 0.00 0.00 3.51
2604 2652 3.361644 GCGCAAAACACACATAACAGATG 59.638 43.478 0.30 0.00 0.00 2.90
2605 2653 3.004210 TGCGCAAAACACACATAACAGAT 59.996 39.130 8.16 0.00 0.00 2.90
2606 2654 2.356069 TGCGCAAAACACACATAACAGA 59.644 40.909 8.16 0.00 0.00 3.41
2607 2655 2.720578 CTGCGCAAAACACACATAACAG 59.279 45.455 13.05 0.00 0.00 3.16
2609 2657 2.050691 CCTGCGCAAAACACACATAAC 58.949 47.619 13.05 0.00 0.00 1.89
2898 2965 7.937649 TCTACATTAGCGTGTTACACTATCAT 58.062 34.615 13.86 0.00 33.62 2.45
2899 2966 7.281549 TCTCTACATTAGCGTGTTACACTATCA 59.718 37.037 13.86 0.00 33.62 2.15
2934 3237 0.317186 CGTAACAAAACCCACGGCAC 60.317 55.000 0.00 0.00 0.00 5.01
2941 3244 2.802247 ACTTCGTAGCGTAACAAAACCC 59.198 45.455 0.00 0.00 0.00 4.11
2948 3251 4.029972 GCTAACTGAACTTCGTAGCGTAAC 59.970 45.833 0.00 0.00 0.00 2.50
2949 3252 4.161333 GCTAACTGAACTTCGTAGCGTAA 58.839 43.478 0.00 0.00 0.00 3.18
2974 3785 1.065345 GGGAGGGAGTAGTTCTTTGCC 60.065 57.143 0.00 0.00 0.00 4.52
2982 3793 1.344393 TGCATCATGGGAGGGAGTAGT 60.344 52.381 0.00 0.00 0.00 2.73
2983 3794 1.427809 TGCATCATGGGAGGGAGTAG 58.572 55.000 0.00 0.00 0.00 2.57
2984 3795 1.770658 CTTGCATCATGGGAGGGAGTA 59.229 52.381 0.00 0.00 0.00 2.59
2989 4208 2.359981 ATGTCTTGCATCATGGGAGG 57.640 50.000 0.00 0.00 30.67 4.30
2990 4209 4.730949 AAAATGTCTTGCATCATGGGAG 57.269 40.909 0.00 0.00 36.67 4.30
2997 4216 4.682860 CCAGTGTCAAAAATGTCTTGCATC 59.317 41.667 0.00 0.00 36.67 3.91
2998 4217 4.099881 ACCAGTGTCAAAAATGTCTTGCAT 59.900 37.500 0.00 0.00 40.03 3.96
2999 4218 3.446873 ACCAGTGTCAAAAATGTCTTGCA 59.553 39.130 0.00 0.00 0.00 4.08
3000 4219 4.045636 ACCAGTGTCAAAAATGTCTTGC 57.954 40.909 0.00 0.00 0.00 4.01
3001 4220 6.151691 CCATACCAGTGTCAAAAATGTCTTG 58.848 40.000 0.00 0.00 0.00 3.02
3007 4226 3.756434 CGTCCCATACCAGTGTCAAAAAT 59.244 43.478 0.00 0.00 0.00 1.82
3019 4238 2.440817 CCACCCTCCGTCCCATACC 61.441 68.421 0.00 0.00 0.00 2.73
3058 4277 5.184711 TGTTCTTTCTTTGCCATGCTTTTT 58.815 33.333 0.00 0.00 0.00 1.94
3059 4278 4.768583 TGTTCTTTCTTTGCCATGCTTTT 58.231 34.783 0.00 0.00 0.00 2.27
3060 4279 4.405116 TGTTCTTTCTTTGCCATGCTTT 57.595 36.364 0.00 0.00 0.00 3.51
3061 4280 4.612264 ATGTTCTTTCTTTGCCATGCTT 57.388 36.364 0.00 0.00 0.00 3.91
3062 4281 5.726980 TTATGTTCTTTCTTTGCCATGCT 57.273 34.783 0.00 0.00 0.00 3.79
3179 4398 0.326927 CTTTCGGTCCCCAGGCTTTA 59.673 55.000 0.00 0.00 0.00 1.85
3243 4467 3.674997 TCCATCTTGTCTGGCAGTTTAC 58.325 45.455 15.27 6.12 33.56 2.01
3247 4471 1.277557 GTCTCCATCTTGTCTGGCAGT 59.722 52.381 15.27 0.00 33.56 4.40
3255 4479 3.708631 CCCTCTACATGTCTCCATCTTGT 59.291 47.826 0.00 0.00 0.00 3.16
3256 4480 3.070734 CCCCTCTACATGTCTCCATCTTG 59.929 52.174 0.00 0.00 0.00 3.02
3257 4481 3.310954 ACCCCTCTACATGTCTCCATCTT 60.311 47.826 0.00 0.00 0.00 2.40
3262 4486 1.123928 CCACCCCTCTACATGTCTCC 58.876 60.000 0.00 0.00 0.00 3.71
3265 4489 3.244770 TGTTTTCCACCCCTCTACATGTC 60.245 47.826 0.00 0.00 0.00 3.06
3273 4497 1.911057 CCTTCTGTTTTCCACCCCTC 58.089 55.000 0.00 0.00 0.00 4.30
3274 4498 0.178961 GCCTTCTGTTTTCCACCCCT 60.179 55.000 0.00 0.00 0.00 4.79
3286 4514 8.778358 GTTAGATTAGAACATATTGGCCTTCTG 58.222 37.037 11.82 3.78 0.00 3.02
3290 4518 7.394144 AGGTTAGATTAGAACATATTGGCCT 57.606 36.000 3.32 0.00 0.00 5.19
3291 4519 9.167311 CATAGGTTAGATTAGAACATATTGGCC 57.833 37.037 0.00 0.00 32.91 5.36
3292 4520 9.726438 ACATAGGTTAGATTAGAACATATTGGC 57.274 33.333 0.00 0.00 32.91 4.52
3311 4558 5.069251 GCTATAGCCGATTGGATACATAGGT 59.931 44.000 14.13 0.00 39.36 3.08
3314 4561 4.643334 ACGCTATAGCCGATTGGATACATA 59.357 41.667 19.00 0.00 39.36 2.29
3325 4572 4.021631 CGCCGACGCTATAGCCGA 62.022 66.667 20.62 0.00 37.91 5.54
3336 4583 1.593006 CATAAACAGGATGACGCCGAC 59.407 52.381 0.00 0.00 39.69 4.79
3366 4613 5.018809 ACACAACTCCTTCATTTATGGCAT 58.981 37.500 4.88 4.88 0.00 4.40
3381 4628 8.889849 ATATAAAACAATACGCAACACAACTC 57.110 30.769 0.00 0.00 0.00 3.01
3390 4637 6.526526 TCCAGCCTATATAAAACAATACGCA 58.473 36.000 0.00 0.00 0.00 5.24
3391 4638 6.092259 CCTCCAGCCTATATAAAACAATACGC 59.908 42.308 0.00 0.00 0.00 4.42
3414 4661 5.045286 AGTGTTCAATTCTAAGAGATGGCCT 60.045 40.000 3.32 0.00 0.00 5.19
3429 4676 3.338249 CCGGAATGACAGAGTGTTCAAT 58.662 45.455 0.00 0.00 0.00 2.57
3435 4682 0.107508 ATGCCCGGAATGACAGAGTG 60.108 55.000 0.73 0.00 0.00 3.51
3476 4725 5.921976 CAGCAAGTTTCACATTCTATTTGCA 59.078 36.000 8.34 0.00 41.40 4.08
3482 4731 4.041567 TCCTCCAGCAAGTTTCACATTCTA 59.958 41.667 0.00 0.00 0.00 2.10
3512 4761 0.469494 TGCAACAGGCTCAACAGAGA 59.531 50.000 0.00 0.00 45.15 3.10
3514 4763 0.107263 TGTGCAACAGGCTCAACAGA 60.107 50.000 0.00 0.00 45.67 3.41
3539 4788 4.103311 GCCTCCAACTCTATGGACCTAATT 59.897 45.833 0.00 0.00 44.52 1.40
3542 4791 2.023404 TGCCTCCAACTCTATGGACCTA 60.023 50.000 0.00 0.00 44.52 3.08
3590 4839 1.296727 GTTGCCCGGCTACTGTAATC 58.703 55.000 15.80 0.00 32.12 1.75
3593 4842 0.320946 GTTGTTGCCCGGCTACTGTA 60.321 55.000 22.14 7.52 35.51 2.74
3596 4845 1.818959 TACGTTGTTGCCCGGCTACT 61.819 55.000 22.14 7.05 35.51 2.57
3623 4872 4.141756 CCTGCTAGTGAATCTGTCCTTCAT 60.142 45.833 0.00 0.00 35.26 2.57
3626 4875 2.503356 CCCTGCTAGTGAATCTGTCCTT 59.497 50.000 0.00 0.00 0.00 3.36
3628 4877 1.474143 GCCCTGCTAGTGAATCTGTCC 60.474 57.143 0.00 0.00 0.00 4.02
3629 4878 1.208052 TGCCCTGCTAGTGAATCTGTC 59.792 52.381 0.00 0.00 0.00 3.51
3630 4879 1.209019 CTGCCCTGCTAGTGAATCTGT 59.791 52.381 0.00 0.00 0.00 3.41
3677 4926 1.847818 TGAAGAAACAGTGGACGTCG 58.152 50.000 9.92 0.00 0.00 5.12
3715 4964 4.262617 GTTACTTTTCTAGGGAAGGCTGG 58.737 47.826 9.74 0.00 32.61 4.85
3716 4965 4.262617 GGTTACTTTTCTAGGGAAGGCTG 58.737 47.826 9.74 0.00 32.61 4.85
3721 4970 6.503560 TCTTGTGGTTACTTTTCTAGGGAA 57.496 37.500 0.00 0.00 0.00 3.97
3722 4971 6.328148 TCTTCTTGTGGTTACTTTTCTAGGGA 59.672 38.462 0.00 0.00 0.00 4.20
3726 4975 6.147164 CGCATCTTCTTGTGGTTACTTTTCTA 59.853 38.462 0.00 0.00 0.00 2.10
3731 4980 4.002906 TCGCATCTTCTTGTGGTTACTT 57.997 40.909 0.00 0.00 0.00 2.24
3736 4985 5.185454 TCAAATATCGCATCTTCTTGTGGT 58.815 37.500 0.00 0.00 0.00 4.16
3740 4989 5.987953 TCCTCTCAAATATCGCATCTTCTTG 59.012 40.000 0.00 0.00 0.00 3.02
3761 5010 3.181433 GGATTTGGGACCGGATTATTCCT 60.181 47.826 9.46 0.00 40.17 3.36
3767 5016 1.568597 TCATGGATTTGGGACCGGATT 59.431 47.619 9.46 0.00 0.00 3.01
3792 5041 2.232452 TCAAAGGGGTTTGTTGTGTGTG 59.768 45.455 0.00 0.00 33.82 3.82
3794 5043 3.520569 CTTCAAAGGGGTTTGTTGTGTG 58.479 45.455 0.00 0.00 33.82 3.82


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

AutoCloner maintained by Alex Coulton.