Multiple sequence alignment - TraesCS2B01G215600

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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 TraesCS2B01G215600 chr2B 100.000 2651 0 0 1 2651 200895772 200898422 0.000000e+00 4896.0
1 TraesCS2B01G215600 chr2B 87.056 479 50 7 880 1347 201175694 201176171 5.020000e-147 531.0
2 TraesCS2B01G215600 chr2A 93.679 1313 55 9 784 2078 158062520 158061218 0.000000e+00 1940.0
3 TraesCS2B01G215600 chr2A 85.090 1167 105 31 835 1963 158073945 158072810 0.000000e+00 1127.0
4 TraesCS2B01G215600 chr2A 88.285 239 17 2 2109 2347 158061232 158061005 2.600000e-70 276.0
5 TraesCS2B01G215600 chr2D 95.424 743 18 6 1345 2078 143225486 143226221 0.000000e+00 1170.0
6 TraesCS2B01G215600 chr2D 83.851 1158 96 43 835 1963 143221379 143222474 0.000000e+00 1018.0
7 TraesCS2B01G215600 chr2D 82.529 1139 125 37 803 1898 143236112 143237219 0.000000e+00 933.0
8 TraesCS2B01G215600 chr2D 93.705 556 25 2 803 1348 143223991 143224546 0.000000e+00 824.0
9 TraesCS2B01G215600 chr2D 83.646 587 79 13 195 772 572782436 572783014 1.080000e-148 536.0
10 TraesCS2B01G215600 chr2D 86.364 396 32 8 2213 2593 143226243 143226631 1.900000e-111 412.0
11 TraesCS2B01G215600 chr2D 97.222 36 1 0 2109 2144 143226207 143226242 7.920000e-06 62.1
12 TraesCS2B01G215600 chrUn 89.905 634 57 6 150 780 35843795 35844424 0.000000e+00 809.0
13 TraesCS2B01G215600 chrUn 89.905 634 57 6 150 780 321450602 321451231 0.000000e+00 809.0
14 TraesCS2B01G215600 chrUn 89.590 634 59 6 150 780 34061423 34062052 0.000000e+00 798.0
15 TraesCS2B01G215600 chrUn 88.710 62 7 0 2289 2350 100259348 100259287 2.830000e-10 76.8
16 TraesCS2B01G215600 chr7D 84.255 597 81 11 195 785 560738633 560739222 1.060000e-158 569.0
17 TraesCS2B01G215600 chr1A 84.075 584 82 9 195 772 3606001 3605423 1.070000e-153 553.0
18 TraesCS2B01G215600 chr1D 83.276 586 76 13 195 772 398478365 398477794 1.090000e-143 520.0
19 TraesCS2B01G215600 chr1D 82.500 120 16 4 2271 2389 240666608 240666723 1.680000e-17 100.0
20 TraesCS2B01G215600 chr7A 87.059 340 39 4 452 788 626404553 626404890 1.930000e-101 379.0
21 TraesCS2B01G215600 chr7A 78.251 446 70 17 1555 1989 676065837 676065408 7.280000e-66 261.0
22 TraesCS2B01G215600 chr7A 84.836 244 37 0 540 783 116985466 116985223 2.040000e-61 246.0
23 TraesCS2B01G215600 chr4A 84.426 122 14 4 2269 2389 489880084 489879967 6.000000e-22 115.0
24 TraesCS2B01G215600 chr5A 89.231 65 7 0 2286 2350 659169380 659169316 6.080000e-12 82.4
25 TraesCS2B01G215600 chr7B 86.301 73 9 1 2272 2343 626371622 626371694 7.870000e-11 78.7
26 TraesCS2B01G215600 chr6A 100.000 29 0 0 2301 2329 427033920 427033892 1.000000e-03 54.7


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 TraesCS2B01G215600 chr2B 200895772 200898422 2650 False 4896.00 4896 100.0000 1 2651 1 chr2B.!!$F1 2650
1 TraesCS2B01G215600 chr2A 158072810 158073945 1135 True 1127.00 1127 85.0900 835 1963 1 chr2A.!!$R1 1128
2 TraesCS2B01G215600 chr2A 158061005 158062520 1515 True 1108.00 1940 90.9820 784 2347 2 chr2A.!!$R2 1563
3 TraesCS2B01G215600 chr2D 143236112 143237219 1107 False 933.00 933 82.5290 803 1898 1 chr2D.!!$F1 1095
4 TraesCS2B01G215600 chr2D 143221379 143226631 5252 False 697.22 1170 91.3132 803 2593 5 chr2D.!!$F3 1790
5 TraesCS2B01G215600 chr2D 572782436 572783014 578 False 536.00 536 83.6460 195 772 1 chr2D.!!$F2 577
6 TraesCS2B01G215600 chrUn 35843795 35844424 629 False 809.00 809 89.9050 150 780 1 chrUn.!!$F2 630
7 TraesCS2B01G215600 chrUn 321450602 321451231 629 False 809.00 809 89.9050 150 780 1 chrUn.!!$F3 630
8 TraesCS2B01G215600 chrUn 34061423 34062052 629 False 798.00 798 89.5900 150 780 1 chrUn.!!$F1 630
9 TraesCS2B01G215600 chr7D 560738633 560739222 589 False 569.00 569 84.2550 195 785 1 chr7D.!!$F1 590
10 TraesCS2B01G215600 chr1A 3605423 3606001 578 True 553.00 553 84.0750 195 772 1 chr1A.!!$R1 577
11 TraesCS2B01G215600 chr1D 398477794 398478365 571 True 520.00 520 83.2760 195 772 1 chr1D.!!$R1 577

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
134 135 0.032952 TTGGACCCAGTCGTTTCTCG 59.967 55.0 0.00 0.00 41.41 4.04 F
613 622 0.455633 GAACATTTGCTGCTGCGAGG 60.456 55.0 11.21 7.87 43.34 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1106 2948 1.640428 TGCTACTACATCGTTGCTGC 58.360 50.0 0.0 0.0 36.75 5.25 R
2546 5382 0.037326 TGAGTAGCTTCACTTGGCGG 60.037 55.0 0.0 0.0 0.00 6.13 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
18 19 3.955145 TTGTTCCATGGTCGCTCAT 57.045 47.368 12.58 0.00 0.00 2.90
20 21 2.309528 TGTTCCATGGTCGCTCATAC 57.690 50.000 12.58 0.00 0.00 2.39
21 22 1.134521 TGTTCCATGGTCGCTCATACC 60.135 52.381 12.58 0.00 37.53 2.73
23 24 1.300931 CCATGGTCGCTCATACCCG 60.301 63.158 2.57 0.00 36.06 5.28
24 25 1.739667 CATGGTCGCTCATACCCGA 59.260 57.895 0.00 0.00 36.06 5.14
25 26 0.318441 CATGGTCGCTCATACCCGAT 59.682 55.000 0.00 0.00 36.06 4.18
26 27 0.318441 ATGGTCGCTCATACCCGATG 59.682 55.000 0.00 0.00 36.06 3.84
27 28 1.040893 TGGTCGCTCATACCCGATGT 61.041 55.000 0.00 0.00 36.84 3.06
28 29 0.956633 GGTCGCTCATACCCGATGTA 59.043 55.000 0.00 0.00 36.84 2.29
30 31 2.223876 GGTCGCTCATACCCGATGTAAA 60.224 50.000 0.00 0.00 36.84 2.01
32 33 3.244579 GTCGCTCATACCCGATGTAAAAC 59.755 47.826 0.00 0.00 36.84 2.43
33 34 2.542595 CGCTCATACCCGATGTAAAACC 59.457 50.000 0.00 0.00 36.84 3.27
34 35 3.740141 CGCTCATACCCGATGTAAAACCT 60.740 47.826 0.00 0.00 36.84 3.50
35 36 3.560068 GCTCATACCCGATGTAAAACCTG 59.440 47.826 0.00 0.00 36.84 4.00
36 37 4.127171 CTCATACCCGATGTAAAACCTGG 58.873 47.826 0.00 0.00 36.84 4.45
37 38 2.406596 TACCCGATGTAAAACCTGGC 57.593 50.000 0.00 0.00 0.00 4.85
38 39 0.402504 ACCCGATGTAAAACCTGGCA 59.597 50.000 0.00 0.00 0.00 4.92
39 40 0.808755 CCCGATGTAAAACCTGGCAC 59.191 55.000 0.00 0.00 0.00 5.01
42 43 2.159393 CCGATGTAAAACCTGGCACATG 60.159 50.000 8.11 0.00 38.20 3.21
43 44 2.487762 CGATGTAAAACCTGGCACATGT 59.512 45.455 8.11 0.00 39.29 3.21
44 45 3.426159 CGATGTAAAACCTGGCACATGTC 60.426 47.826 0.00 0.00 35.82 3.06
45 46 3.222173 TGTAAAACCTGGCACATGTCT 57.778 42.857 0.00 0.00 35.82 3.41
46 47 2.884012 TGTAAAACCTGGCACATGTCTG 59.116 45.455 0.00 0.00 35.82 3.51
53 54 3.357919 GCACATGTCTGCCTTGCA 58.642 55.556 0.00 0.00 36.92 4.08
54 55 1.888018 GCACATGTCTGCCTTGCAT 59.112 52.632 0.00 0.00 38.13 3.96
55 56 0.457853 GCACATGTCTGCCTTGCATG 60.458 55.000 0.00 0.00 43.84 4.06
56 57 0.457853 CACATGTCTGCCTTGCATGC 60.458 55.000 11.82 11.82 42.50 4.06
57 58 0.896479 ACATGTCTGCCTTGCATGCA 60.896 50.000 18.46 18.46 42.50 3.96
59 60 0.744874 ATGTCTGCCTTGCATGCATC 59.255 50.000 23.37 14.11 38.13 3.91
61 62 0.815734 GTCTGCCTTGCATGCATCTT 59.184 50.000 23.37 0.00 38.13 2.40
63 64 1.897133 TCTGCCTTGCATGCATCTTTT 59.103 42.857 23.37 0.00 38.13 2.27
64 65 1.999735 CTGCCTTGCATGCATCTTTTG 59.000 47.619 23.37 6.95 38.13 2.44
65 66 1.345089 TGCCTTGCATGCATCTTTTGT 59.655 42.857 23.37 0.00 31.71 2.83
66 67 2.224329 TGCCTTGCATGCATCTTTTGTT 60.224 40.909 23.37 0.00 31.71 2.83
68 69 3.395639 CCTTGCATGCATCTTTTGTTGT 58.604 40.909 23.37 0.00 0.00 3.32
69 70 3.185594 CCTTGCATGCATCTTTTGTTGTG 59.814 43.478 23.37 0.60 0.00 3.33
70 71 2.756829 TGCATGCATCTTTTGTTGTGG 58.243 42.857 18.46 0.00 0.00 4.17
72 73 2.070783 CATGCATCTTTTGTTGTGGCC 58.929 47.619 0.00 0.00 0.00 5.36
75 76 1.202627 GCATCTTTTGTTGTGGCCCAA 60.203 47.619 0.00 0.55 0.00 4.12
85 86 2.799126 TGTGGCCCAACTAATACCTG 57.201 50.000 0.00 0.00 0.00 4.00
86 87 1.283613 TGTGGCCCAACTAATACCTGG 59.716 52.381 0.00 0.00 0.00 4.45
87 88 1.283905 GTGGCCCAACTAATACCTGGT 59.716 52.381 4.05 4.05 0.00 4.00
88 89 2.506644 GTGGCCCAACTAATACCTGGTA 59.493 50.000 9.36 9.36 0.00 3.25
89 90 2.506644 TGGCCCAACTAATACCTGGTAC 59.493 50.000 9.09 0.00 0.00 3.34
92 93 4.134563 GCCCAACTAATACCTGGTACATG 58.865 47.826 9.09 4.64 38.20 3.21
94 95 5.751586 CCCAACTAATACCTGGTACATGTT 58.248 41.667 9.09 10.81 38.37 2.71
95 96 6.184789 CCCAACTAATACCTGGTACATGTTT 58.815 40.000 9.09 1.78 38.37 2.83
96 97 6.317893 CCCAACTAATACCTGGTACATGTTTC 59.682 42.308 9.09 0.00 38.37 2.78
97 98 6.036735 CCAACTAATACCTGGTACATGTTTCG 59.963 42.308 9.09 0.00 38.37 3.46
98 99 6.534475 ACTAATACCTGGTACATGTTTCGA 57.466 37.500 9.09 0.00 38.37 3.71
100 101 2.094762 ACCTGGTACATGTTTCGAGC 57.905 50.000 2.30 0.00 38.20 5.03
101 102 1.338769 ACCTGGTACATGTTTCGAGCC 60.339 52.381 2.30 0.00 38.20 4.70
102 103 1.338674 CCTGGTACATGTTTCGAGCCA 60.339 52.381 2.30 2.99 38.20 4.75
103 104 1.732259 CTGGTACATGTTTCGAGCCAC 59.268 52.381 2.30 0.00 38.20 5.01
104 105 0.719465 GGTACATGTTTCGAGCCACG 59.281 55.000 2.30 0.00 44.09 4.94
108 109 1.005037 ATGTTTCGAGCCACGCAGA 60.005 52.632 0.00 0.00 42.26 4.26
110 111 1.664965 GTTTCGAGCCACGCAGACT 60.665 57.895 0.00 0.00 42.26 3.24
112 113 1.221466 TTTCGAGCCACGCAGACTTG 61.221 55.000 0.00 0.00 42.26 3.16
117 118 2.949106 CCACGCAGACTTGGCTTG 59.051 61.111 0.00 0.00 0.00 4.01
118 119 2.620112 CCACGCAGACTTGGCTTGG 61.620 63.158 0.00 0.00 43.06 3.61
119 120 1.597854 CACGCAGACTTGGCTTGGA 60.598 57.895 0.00 0.00 0.00 3.53
120 121 1.598130 ACGCAGACTTGGCTTGGAC 60.598 57.895 0.00 0.00 0.00 4.02
121 122 2.328099 CGCAGACTTGGCTTGGACC 61.328 63.158 0.00 0.00 0.00 4.46
122 123 1.973812 GCAGACTTGGCTTGGACCC 60.974 63.158 0.00 0.00 0.00 4.46
123 124 1.455849 CAGACTTGGCTTGGACCCA 59.544 57.895 0.00 0.00 0.00 4.51
124 125 0.607489 CAGACTTGGCTTGGACCCAG 60.607 60.000 0.00 0.00 33.13 4.45
127 128 1.672356 CTTGGCTTGGACCCAGTCG 60.672 63.158 0.00 0.00 33.13 4.18
129 130 1.990160 TTGGCTTGGACCCAGTCGTT 61.990 55.000 0.00 0.00 33.13 3.85
130 131 1.228154 GGCTTGGACCCAGTCGTTT 60.228 57.895 0.00 0.00 32.65 3.60
131 132 1.235281 GGCTTGGACCCAGTCGTTTC 61.235 60.000 0.00 0.00 32.65 2.78
132 133 0.250338 GCTTGGACCCAGTCGTTTCT 60.250 55.000 0.00 0.00 32.65 2.52
133 134 1.797025 CTTGGACCCAGTCGTTTCTC 58.203 55.000 0.00 0.00 32.65 2.87
134 135 0.032952 TTGGACCCAGTCGTTTCTCG 59.967 55.000 0.00 0.00 41.41 4.04
135 136 1.080025 GGACCCAGTCGTTTCTCGG 60.080 63.158 0.00 0.00 40.32 4.63
137 138 1.813728 GACCCAGTCGTTTCTCGGGT 61.814 60.000 0.00 0.00 40.32 5.28
139 140 0.822164 CCCAGTCGTTTCTCGGGTAT 59.178 55.000 0.00 0.00 40.32 2.73
140 141 1.206371 CCCAGTCGTTTCTCGGGTATT 59.794 52.381 0.00 0.00 40.32 1.89
141 142 2.428171 CCCAGTCGTTTCTCGGGTATTA 59.572 50.000 0.00 0.00 40.32 0.98
143 144 3.129988 CCAGTCGTTTCTCGGGTATTACT 59.870 47.826 0.00 0.00 40.32 2.24
144 145 4.336433 CCAGTCGTTTCTCGGGTATTACTA 59.664 45.833 0.00 0.00 40.32 1.82
145 146 5.009410 CCAGTCGTTTCTCGGGTATTACTAT 59.991 44.000 0.00 0.00 40.32 2.12
146 147 6.205464 CCAGTCGTTTCTCGGGTATTACTATA 59.795 42.308 0.00 0.00 40.32 1.31
147 148 7.296660 CAGTCGTTTCTCGGGTATTACTATAG 58.703 42.308 0.00 0.00 40.32 1.31
148 149 6.072783 AGTCGTTTCTCGGGTATTACTATAGC 60.073 42.308 0.00 0.00 40.32 2.97
173 174 7.676004 CCAAAACCAAGGGTTACTTAAATGAT 58.324 34.615 0.32 0.00 46.20 2.45
181 182 6.911308 AGGGTTACTTAAATGATGGCACTAT 58.089 36.000 0.00 0.00 0.00 2.12
191 192 6.778834 AATGATGGCACTATCAATTGACAA 57.221 33.333 11.07 0.99 40.21 3.18
206 207 5.886960 ATTGACAATGGAACTAGCTCAAC 57.113 39.130 0.00 0.00 0.00 3.18
222 223 3.813166 GCTCAACCGCTGGCTAATAAATA 59.187 43.478 0.00 0.00 0.00 1.40
260 262 4.141620 CCTGTGGGAGATATAACTGCTTGT 60.142 45.833 1.67 0.00 33.58 3.16
278 280 5.163864 TGCTTGTCTAATCATGTTTAGCACG 60.164 40.000 15.81 14.59 31.80 5.34
281 283 6.880822 TGTCTAATCATGTTTAGCACGTAC 57.119 37.500 15.81 10.40 0.00 3.67
320 322 4.927422 TGCTTAATATTTAACCAAGCCGC 58.073 39.130 14.40 0.00 40.66 6.53
322 324 4.202070 GCTTAATATTTAACCAAGCCGCCA 60.202 41.667 8.20 0.00 36.46 5.69
397 399 4.019792 TGACTGATTGTGGTGCAGTAAT 57.980 40.909 0.00 0.00 42.47 1.89
398 400 5.159273 TGACTGATTGTGGTGCAGTAATA 57.841 39.130 0.00 0.00 42.47 0.98
411 413 7.691050 GTGGTGCAGTAATAAATCGACTTAAAC 59.309 37.037 0.00 0.00 0.00 2.01
487 489 2.123248 TTTGGCCGGCATCTCTGTCA 62.123 55.000 30.85 11.59 0.00 3.58
491 493 1.893062 CCGGCATCTCTGTCAGTCA 59.107 57.895 0.00 0.00 0.00 3.41
516 519 0.901580 ACACCCCACGATTCGGTACT 60.902 55.000 11.29 0.00 0.00 2.73
532 537 3.932710 CGGTACTTGTTCTGCATGTGTAT 59.067 43.478 0.00 0.00 36.88 2.29
538 543 4.284829 TGTTCTGCATGTGTATCAGGAA 57.715 40.909 0.00 0.00 0.00 3.36
570 579 4.755266 TTACTACCTGAGCCAGAATTCC 57.245 45.455 0.65 0.00 32.44 3.01
613 622 0.455633 GAACATTTGCTGCTGCGAGG 60.456 55.000 11.21 7.87 43.34 4.63
627 636 1.384989 GCGAGGAGACGAATCCAGGA 61.385 60.000 12.15 0.00 42.26 3.86
670 679 7.180229 ACCAGCCATATACTACATGCTGTAATA 59.820 37.037 8.31 0.00 31.67 0.98
671 680 8.040727 CCAGCCATATACTACATGCTGTAATAA 58.959 37.037 8.31 0.00 31.67 1.40
713 722 1.872952 CGATTCATAAATGCGCTGGGA 59.127 47.619 9.73 0.00 0.00 4.37
772 781 1.225376 CTAGACGCCGTGCACCAAAA 61.225 55.000 12.15 0.00 0.00 2.44
780 789 1.923864 CCGTGCACCAAAACAACTTTC 59.076 47.619 12.15 0.00 0.00 2.62
785 794 2.611518 CACCAAAACAACTTTCCGCAA 58.388 42.857 0.00 0.00 0.00 4.85
786 795 2.996621 CACCAAAACAACTTTCCGCAAA 59.003 40.909 0.00 0.00 0.00 3.68
787 796 3.433615 CACCAAAACAACTTTCCGCAAAA 59.566 39.130 0.00 0.00 0.00 2.44
788 797 4.094146 CACCAAAACAACTTTCCGCAAAAT 59.906 37.500 0.00 0.00 0.00 1.82
789 798 4.697828 ACCAAAACAACTTTCCGCAAAATT 59.302 33.333 0.00 0.00 0.00 1.82
790 799 5.875359 ACCAAAACAACTTTCCGCAAAATTA 59.125 32.000 0.00 0.00 0.00 1.40
792 801 6.036626 CCAAAACAACTTTCCGCAAAATTACT 59.963 34.615 0.00 0.00 0.00 2.24
793 802 6.822073 AAACAACTTTCCGCAAAATTACTC 57.178 33.333 0.00 0.00 0.00 2.59
795 804 3.824414 ACTTTCCGCAAAATTACTCCG 57.176 42.857 0.00 0.00 0.00 4.63
796 805 3.143728 ACTTTCCGCAAAATTACTCCGT 58.856 40.909 0.00 0.00 0.00 4.69
797 806 3.058501 ACTTTCCGCAAAATTACTCCGTG 60.059 43.478 0.00 0.00 0.00 4.94
798 807 2.459060 TCCGCAAAATTACTCCGTGA 57.541 45.000 0.00 0.00 0.00 4.35
799 808 2.768698 TCCGCAAAATTACTCCGTGAA 58.231 42.857 0.00 0.00 0.00 3.18
801 810 3.187637 TCCGCAAAATTACTCCGTGAAAG 59.812 43.478 0.00 0.00 0.00 2.62
809 818 1.578583 ACTCCGTGAAAGGTGAAACG 58.421 50.000 0.00 0.00 38.12 3.60
879 2709 5.637006 TGGATAAGAAATCAACCCAAACG 57.363 39.130 0.00 0.00 0.00 3.60
915 2745 2.874694 CGCATCTCAACGCATCCCG 61.875 63.158 0.00 0.00 44.21 5.14
983 2825 4.940593 GCAAACCAGCGCCGCAAA 62.941 61.111 13.36 0.00 0.00 3.68
985 2827 3.977244 AAACCAGCGCCGCAAAGG 61.977 61.111 13.36 12.93 44.97 3.11
1117 2959 2.110967 CCCTCCAGCAGCAACGATG 61.111 63.158 0.00 0.00 0.00 3.84
1167 3009 1.810755 CCCTGCTTTTCGTTTCTACCC 59.189 52.381 0.00 0.00 0.00 3.69
1560 4360 4.926860 TTGTGCATTATGTCGTCTTCAG 57.073 40.909 0.00 0.00 0.00 3.02
1765 4574 9.017669 CAACTAGTCCGTATTTCTGTATTGTAC 57.982 37.037 0.00 0.00 0.00 2.90
1941 4762 4.024893 GCTTCGTTTGTGTCAATCTCTGAA 60.025 41.667 0.00 0.00 35.22 3.02
2069 4890 5.412640 TGCATGGAATCATCAAATGTTCAC 58.587 37.500 0.00 0.00 0.00 3.18
2070 4891 4.807304 GCATGGAATCATCAAATGTTCACC 59.193 41.667 0.00 0.00 0.00 4.02
2071 4892 5.394883 GCATGGAATCATCAAATGTTCACCT 60.395 40.000 0.00 0.00 0.00 4.00
2072 4893 6.183360 GCATGGAATCATCAAATGTTCACCTA 60.183 38.462 0.00 0.00 0.00 3.08
2073 4894 7.423199 CATGGAATCATCAAATGTTCACCTAG 58.577 38.462 0.00 0.00 0.00 3.02
2074 4895 6.484288 TGGAATCATCAAATGTTCACCTAGT 58.516 36.000 0.00 0.00 0.00 2.57
2075 4896 6.947733 TGGAATCATCAAATGTTCACCTAGTT 59.052 34.615 0.00 0.00 0.00 2.24
2076 4897 8.106462 TGGAATCATCAAATGTTCACCTAGTTA 58.894 33.333 0.00 0.00 0.00 2.24
2077 4898 9.125026 GGAATCATCAAATGTTCACCTAGTTAT 57.875 33.333 0.00 0.00 0.00 1.89
2139 4960 7.490402 ACCTAGTTATCGAACTGTTTTATTCCG 59.510 37.037 0.00 0.00 45.74 4.30
2154 4975 2.561733 TTCCGTTGCTCTGACTATCG 57.438 50.000 0.00 0.00 0.00 2.92
2163 4984 2.601266 GCTCTGACTATCGAACGCTCTC 60.601 54.545 0.00 0.00 0.00 3.20
2167 4988 4.017380 TGACTATCGAACGCTCTCTTTC 57.983 45.455 0.00 0.00 0.00 2.62
2176 4997 4.201570 CGAACGCTCTCTTTCTTCAATCTG 60.202 45.833 0.00 0.00 0.00 2.90
2177 4998 3.594134 ACGCTCTCTTTCTTCAATCTGG 58.406 45.455 0.00 0.00 0.00 3.86
2232 5053 5.222079 TGCAGAATTGTACTGTAGAACCA 57.778 39.130 0.00 0.00 37.64 3.67
2276 5097 1.618343 CCAACCCTGACCCATTTGTTC 59.382 52.381 0.00 0.00 0.00 3.18
2277 5098 2.315176 CAACCCTGACCCATTTGTTCA 58.685 47.619 0.00 0.00 0.00 3.18
2284 5105 5.454471 CCCTGACCCATTTGTTCAAAAATCA 60.454 40.000 2.11 3.93 0.00 2.57
2285 5106 6.232692 CCTGACCCATTTGTTCAAAAATCAT 58.767 36.000 2.11 0.00 0.00 2.45
2286 5107 6.369615 CCTGACCCATTTGTTCAAAAATCATC 59.630 38.462 2.11 0.00 0.00 2.92
2287 5108 7.065120 TGACCCATTTGTTCAAAAATCATCT 57.935 32.000 2.11 0.00 0.00 2.90
2338 5160 2.986019 CCATCCATCCAACCCTATACCA 59.014 50.000 0.00 0.00 0.00 3.25
2343 5165 4.080015 TCCATCCAACCCTATACCACAAAG 60.080 45.833 0.00 0.00 0.00 2.77
2388 5210 8.503458 TGAAAAACCATGATTTGTGATTTGTT 57.497 26.923 0.00 0.00 0.00 2.83
2389 5211 9.605275 TGAAAAACCATGATTTGTGATTTGTTA 57.395 25.926 0.00 0.00 0.00 2.41
2391 5213 9.612066 AAAAACCATGATTTGTGATTTGTTAGT 57.388 25.926 0.00 0.00 0.00 2.24
2408 5244 5.344884 TGTTAGTAGCTTTTTGTTTGGTGC 58.655 37.500 0.00 0.00 0.00 5.01
2411 5247 4.826556 AGTAGCTTTTTGTTTGGTGCAAA 58.173 34.783 0.00 0.00 34.47 3.68
2415 5251 3.728566 GCTTTTTGTTTGGTGCAAAGCTG 60.729 43.478 6.70 0.00 43.91 4.24
2451 5287 2.358957 TCATGGCTTCCGTCAAATCTG 58.641 47.619 0.00 0.00 0.00 2.90
2469 5305 6.648879 AATCTGCTTACCAAGTAAAGCAAA 57.351 33.333 10.58 0.00 34.52 3.68
2500 5336 5.522460 CCTACTAAACACAATACCATGACGG 59.478 44.000 0.00 0.00 42.50 4.79
2514 5350 4.220821 ACCATGACGGATAGTGGCTAATAG 59.779 45.833 0.00 0.00 38.63 1.73
2542 5378 4.816385 TCATAAGATTTGGCGGAAAGCTAG 59.184 41.667 0.00 0.00 39.42 3.42
2543 5379 1.745653 AAGATTTGGCGGAAAGCTAGC 59.254 47.619 6.62 6.62 39.42 3.42
2544 5380 2.619074 AAGATTTGGCGGAAAGCTAGCT 60.619 45.455 12.68 12.68 39.42 3.32
2545 5381 4.125207 AAGATTTGGCGGAAAGCTAGCTT 61.125 43.478 24.42 24.42 39.42 3.74
2546 5382 5.929538 AAGATTTGGCGGAAAGCTAGCTTC 61.930 45.833 29.42 20.94 39.42 3.86
2558 5394 1.363744 CTAGCTTCCGCCAAGTGAAG 58.636 55.000 0.00 0.00 40.72 3.02
2574 5410 6.457934 CCAAGTGAAGCTACTCATAAGCATTG 60.458 42.308 0.00 0.00 42.62 2.82
2576 5412 5.104776 AGTGAAGCTACTCATAAGCATTGGA 60.105 40.000 0.00 0.00 42.62 3.53
2578 5414 3.722147 AGCTACTCATAAGCATTGGACG 58.278 45.455 0.00 0.00 42.62 4.79
2581 5417 3.627395 ACTCATAAGCATTGGACGGAA 57.373 42.857 0.00 0.00 0.00 4.30
2583 5419 3.689649 ACTCATAAGCATTGGACGGAAAC 59.310 43.478 0.00 0.00 0.00 2.78
2587 5423 2.403252 AGCATTGGACGGAAACCTAG 57.597 50.000 0.00 0.00 0.00 3.02
2597 5433 2.467566 GGAAACCTAGCTTCCGTCAA 57.532 50.000 0.00 0.00 33.40 3.18
2598 5434 2.774687 GGAAACCTAGCTTCCGTCAAA 58.225 47.619 0.00 0.00 33.40 2.69
2599 5435 3.344515 GGAAACCTAGCTTCCGTCAAAT 58.655 45.455 0.00 0.00 33.40 2.32
2600 5436 3.127030 GGAAACCTAGCTTCCGTCAAATG 59.873 47.826 0.00 0.00 33.40 2.32
2601 5437 3.695830 AACCTAGCTTCCGTCAAATGA 57.304 42.857 0.00 0.00 0.00 2.57
2602 5438 3.695830 ACCTAGCTTCCGTCAAATGAA 57.304 42.857 0.00 0.00 0.00 2.57
2603 5439 3.600388 ACCTAGCTTCCGTCAAATGAAG 58.400 45.455 0.00 0.00 40.72 3.02
2611 5447 6.910536 CTTCCGTCAAATGAAGCTATACTT 57.089 37.500 0.00 0.00 42.98 2.24
2625 5461 6.074544 AGCTATACTTCCAGCTACTAAACG 57.925 41.667 0.00 0.00 46.14 3.60
2626 5462 4.680567 GCTATACTTCCAGCTACTAAACGC 59.319 45.833 0.00 0.00 34.86 4.84
2627 5463 2.381725 ACTTCCAGCTACTAAACGCC 57.618 50.000 0.00 0.00 0.00 5.68
2628 5464 1.621814 ACTTCCAGCTACTAAACGCCA 59.378 47.619 0.00 0.00 0.00 5.69
2629 5465 2.038033 ACTTCCAGCTACTAAACGCCAA 59.962 45.455 0.00 0.00 0.00 4.52
2630 5466 2.843401 TCCAGCTACTAAACGCCAAA 57.157 45.000 0.00 0.00 0.00 3.28
2631 5467 3.343941 TCCAGCTACTAAACGCCAAAT 57.656 42.857 0.00 0.00 0.00 2.32
2632 5468 3.006940 TCCAGCTACTAAACGCCAAATG 58.993 45.455 0.00 0.00 0.00 2.32
2633 5469 3.006940 CCAGCTACTAAACGCCAAATGA 58.993 45.455 0.00 0.00 0.00 2.57
2634 5470 3.438781 CCAGCTACTAAACGCCAAATGAA 59.561 43.478 0.00 0.00 0.00 2.57
2635 5471 4.083003 CCAGCTACTAAACGCCAAATGAAA 60.083 41.667 0.00 0.00 0.00 2.69
2636 5472 4.851558 CAGCTACTAAACGCCAAATGAAAC 59.148 41.667 0.00 0.00 0.00 2.78
2637 5473 4.760204 AGCTACTAAACGCCAAATGAAACT 59.240 37.500 0.00 0.00 0.00 2.66
2638 5474 5.086727 GCTACTAAACGCCAAATGAAACTC 58.913 41.667 0.00 0.00 0.00 3.01
2639 5475 4.499037 ACTAAACGCCAAATGAAACTCC 57.501 40.909 0.00 0.00 0.00 3.85
2640 5476 3.886505 ACTAAACGCCAAATGAAACTCCA 59.113 39.130 0.00 0.00 0.00 3.86
2641 5477 2.793278 AACGCCAAATGAAACTCCAC 57.207 45.000 0.00 0.00 0.00 4.02
2642 5478 0.958822 ACGCCAAATGAAACTCCACC 59.041 50.000 0.00 0.00 0.00 4.61
2643 5479 1.247567 CGCCAAATGAAACTCCACCT 58.752 50.000 0.00 0.00 0.00 4.00
2644 5480 2.224670 ACGCCAAATGAAACTCCACCTA 60.225 45.455 0.00 0.00 0.00 3.08
2645 5481 2.817258 CGCCAAATGAAACTCCACCTAA 59.183 45.455 0.00 0.00 0.00 2.69
2646 5482 3.443681 CGCCAAATGAAACTCCACCTAAT 59.556 43.478 0.00 0.00 0.00 1.73
2647 5483 4.438744 CGCCAAATGAAACTCCACCTAATC 60.439 45.833 0.00 0.00 0.00 1.75
2648 5484 4.706962 GCCAAATGAAACTCCACCTAATCT 59.293 41.667 0.00 0.00 0.00 2.40
2649 5485 5.885912 GCCAAATGAAACTCCACCTAATCTA 59.114 40.000 0.00 0.00 0.00 1.98
2650 5486 6.038714 GCCAAATGAAACTCCACCTAATCTAG 59.961 42.308 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.809083 GGGTATGAGCGACCATGGAACAA 62.809 52.174 21.47 0.00 38.86 2.83
1 2 4.381433 GGGTATGAGCGACCATGGAACA 62.381 54.545 21.47 10.74 38.86 3.18
3 4 0.468226 GGGTATGAGCGACCATGGAA 59.532 55.000 21.47 0.00 38.86 3.53
4 5 1.744320 CGGGTATGAGCGACCATGGA 61.744 60.000 21.47 0.00 38.86 3.41
5 6 1.300931 CGGGTATGAGCGACCATGG 60.301 63.158 11.19 11.19 38.86 3.66
6 7 0.318441 ATCGGGTATGAGCGACCATG 59.682 55.000 0.00 0.00 38.86 3.66
8 9 1.040893 ACATCGGGTATGAGCGACCA 61.041 55.000 0.00 0.00 38.86 4.02
10 11 2.787601 TTACATCGGGTATGAGCGAC 57.212 50.000 0.00 0.00 39.07 5.19
11 12 3.450578 GTTTTACATCGGGTATGAGCGA 58.549 45.455 0.00 0.00 39.07 4.93
13 14 3.560068 CAGGTTTTACATCGGGTATGAGC 59.440 47.826 0.00 0.00 39.07 4.26
14 15 4.127171 CCAGGTTTTACATCGGGTATGAG 58.873 47.826 0.00 0.00 39.07 2.90
15 16 3.683281 GCCAGGTTTTACATCGGGTATGA 60.683 47.826 0.00 0.00 39.07 2.15
16 17 2.616842 GCCAGGTTTTACATCGGGTATG 59.383 50.000 0.00 0.00 41.74 2.39
17 18 2.240160 TGCCAGGTTTTACATCGGGTAT 59.760 45.455 0.00 0.00 0.00 2.73
18 19 1.629353 TGCCAGGTTTTACATCGGGTA 59.371 47.619 0.00 0.00 0.00 3.69
19 20 0.402504 TGCCAGGTTTTACATCGGGT 59.597 50.000 0.00 0.00 0.00 5.28
20 21 0.808755 GTGCCAGGTTTTACATCGGG 59.191 55.000 0.00 0.00 0.00 5.14
21 22 1.529226 TGTGCCAGGTTTTACATCGG 58.471 50.000 0.00 0.00 0.00 4.18
23 24 3.758554 AGACATGTGCCAGGTTTTACATC 59.241 43.478 1.15 0.00 31.84 3.06
24 25 3.507233 CAGACATGTGCCAGGTTTTACAT 59.493 43.478 1.15 0.00 34.31 2.29
25 26 2.884012 CAGACATGTGCCAGGTTTTACA 59.116 45.455 1.15 0.00 0.00 2.41
26 27 2.351738 GCAGACATGTGCCAGGTTTTAC 60.352 50.000 1.15 0.00 37.49 2.01
27 28 1.885887 GCAGACATGTGCCAGGTTTTA 59.114 47.619 1.15 0.00 37.49 1.52
28 29 0.675633 GCAGACATGTGCCAGGTTTT 59.324 50.000 1.15 0.00 37.49 2.43
30 31 4.085876 GCAGACATGTGCCAGGTT 57.914 55.556 1.15 0.00 37.49 3.50
36 37 0.457853 CATGCAAGGCAGACATGTGC 60.458 55.000 1.15 0.27 43.65 4.57
37 38 3.713936 CATGCAAGGCAGACATGTG 57.286 52.632 1.15 0.00 43.65 3.21
48 49 3.185594 CCACAACAAAAGATGCATGCAAG 59.814 43.478 26.68 12.56 0.00 4.01
49 50 3.132160 CCACAACAAAAGATGCATGCAA 58.868 40.909 26.68 8.49 0.00 4.08
50 51 2.756829 CCACAACAAAAGATGCATGCA 58.243 42.857 25.04 25.04 0.00 3.96
51 52 1.461897 GCCACAACAAAAGATGCATGC 59.538 47.619 11.82 11.82 0.00 4.06
53 54 1.002315 GGGCCACAACAAAAGATGCAT 59.998 47.619 4.39 0.00 0.00 3.96
54 55 0.392336 GGGCCACAACAAAAGATGCA 59.608 50.000 4.39 0.00 0.00 3.96
55 56 0.392336 TGGGCCACAACAAAAGATGC 59.608 50.000 0.00 0.00 0.00 3.91
56 57 2.906691 TTGGGCCACAACAAAAGATG 57.093 45.000 5.23 0.00 33.18 2.90
65 66 2.291282 CCAGGTATTAGTTGGGCCACAA 60.291 50.000 5.23 3.45 36.54 3.33
66 67 1.283613 CCAGGTATTAGTTGGGCCACA 59.716 52.381 5.23 0.00 0.00 4.17
68 69 1.676248 ACCAGGTATTAGTTGGGCCA 58.324 50.000 0.00 0.00 36.28 5.36
69 70 2.506644 TGTACCAGGTATTAGTTGGGCC 59.493 50.000 1.54 0.00 36.28 5.80
70 71 3.918294 TGTACCAGGTATTAGTTGGGC 57.082 47.619 1.54 0.00 36.28 5.36
72 73 6.036735 CGAAACATGTACCAGGTATTAGTTGG 59.963 42.308 1.54 1.49 37.98 3.77
75 76 6.534475 TCGAAACATGTACCAGGTATTAGT 57.466 37.500 1.54 0.00 0.00 2.24
76 77 5.462398 GCTCGAAACATGTACCAGGTATTAG 59.538 44.000 1.54 0.00 0.00 1.73
77 78 5.353938 GCTCGAAACATGTACCAGGTATTA 58.646 41.667 1.54 0.00 0.00 0.98
78 79 4.189231 GCTCGAAACATGTACCAGGTATT 58.811 43.478 1.54 0.00 0.00 1.89
80 81 2.093869 GGCTCGAAACATGTACCAGGTA 60.094 50.000 0.00 0.00 0.00 3.08
82 83 1.338674 TGGCTCGAAACATGTACCAGG 60.339 52.381 0.00 0.00 0.00 4.45
83 84 1.732259 GTGGCTCGAAACATGTACCAG 59.268 52.381 0.00 0.00 0.00 4.00
84 85 1.803334 GTGGCTCGAAACATGTACCA 58.197 50.000 0.00 0.00 0.00 3.25
85 86 0.719465 CGTGGCTCGAAACATGTACC 59.281 55.000 2.21 0.00 42.86 3.34
86 87 0.094730 GCGTGGCTCGAAACATGTAC 59.905 55.000 13.77 0.00 42.86 2.90
87 88 0.319986 TGCGTGGCTCGAAACATGTA 60.320 50.000 13.77 3.30 42.86 2.29
88 89 1.568612 CTGCGTGGCTCGAAACATGT 61.569 55.000 13.77 0.00 42.86 3.21
89 90 1.133253 CTGCGTGGCTCGAAACATG 59.867 57.895 13.77 0.00 42.86 3.21
92 93 1.222115 AAGTCTGCGTGGCTCGAAAC 61.222 55.000 13.77 6.89 42.86 2.78
94 95 1.664649 CAAGTCTGCGTGGCTCGAA 60.665 57.895 13.77 0.28 42.86 3.71
95 96 2.049156 CAAGTCTGCGTGGCTCGA 60.049 61.111 13.77 0.00 42.86 4.04
96 97 3.114616 CCAAGTCTGCGTGGCTCG 61.115 66.667 4.32 4.32 37.43 5.03
100 101 2.949106 CAAGCCAAGTCTGCGTGG 59.051 61.111 0.00 0.00 45.27 4.94
101 102 1.597854 TCCAAGCCAAGTCTGCGTG 60.598 57.895 0.00 0.00 37.85 5.34
102 103 1.598130 GTCCAAGCCAAGTCTGCGT 60.598 57.895 0.00 0.00 0.00 5.24
103 104 2.328099 GGTCCAAGCCAAGTCTGCG 61.328 63.158 0.00 0.00 0.00 5.18
104 105 1.973812 GGGTCCAAGCCAAGTCTGC 60.974 63.158 0.00 0.00 35.40 4.26
108 109 1.456287 GACTGGGTCCAAGCCAAGT 59.544 57.895 0.00 0.00 46.28 3.16
110 111 1.990160 AACGACTGGGTCCAAGCCAA 61.990 55.000 0.00 0.00 46.28 4.52
112 113 1.228154 AAACGACTGGGTCCAAGCC 60.228 57.895 0.00 0.00 36.00 4.35
115 116 0.032952 CGAGAAACGACTGGGTCCAA 59.967 55.000 0.00 0.00 45.77 3.53
116 117 1.663739 CGAGAAACGACTGGGTCCA 59.336 57.895 0.00 0.00 45.77 4.02
117 118 1.080025 CCGAGAAACGACTGGGTCC 60.080 63.158 0.00 0.00 45.77 4.46
118 119 1.080025 CCCGAGAAACGACTGGGTC 60.080 63.158 0.00 0.00 45.77 4.46
119 120 3.057337 CCCGAGAAACGACTGGGT 58.943 61.111 0.00 0.00 45.77 4.51
120 121 0.822164 ATACCCGAGAAACGACTGGG 59.178 55.000 0.00 2.71 45.77 4.45
121 122 2.667473 AATACCCGAGAAACGACTGG 57.333 50.000 0.00 0.00 45.77 4.00
122 123 4.367386 AGTAATACCCGAGAAACGACTG 57.633 45.455 0.00 0.00 45.77 3.51
123 124 6.072783 GCTATAGTAATACCCGAGAAACGACT 60.073 42.308 0.84 0.00 45.77 4.18
124 125 6.082984 GCTATAGTAATACCCGAGAAACGAC 58.917 44.000 0.84 0.00 45.77 4.34
127 128 6.336842 TGGCTATAGTAATACCCGAGAAAC 57.663 41.667 0.84 0.00 0.00 2.78
129 130 6.982160 TTTGGCTATAGTAATACCCGAGAA 57.018 37.500 0.84 0.00 0.00 2.87
130 131 6.239402 GGTTTTGGCTATAGTAATACCCGAGA 60.239 42.308 14.63 0.00 0.00 4.04
131 132 5.930569 GGTTTTGGCTATAGTAATACCCGAG 59.069 44.000 14.63 0.00 0.00 4.63
132 133 5.366186 TGGTTTTGGCTATAGTAATACCCGA 59.634 40.000 18.96 4.30 0.00 5.14
133 134 5.613329 TGGTTTTGGCTATAGTAATACCCG 58.387 41.667 18.96 0.00 0.00 5.28
134 135 6.489022 CCTTGGTTTTGGCTATAGTAATACCC 59.511 42.308 18.96 6.86 0.00 3.69
135 136 6.489022 CCCTTGGTTTTGGCTATAGTAATACC 59.511 42.308 16.84 16.84 0.00 2.73
137 138 7.215743 ACCCTTGGTTTTGGCTATAGTAATA 57.784 36.000 0.84 0.00 27.29 0.98
139 140 5.523883 ACCCTTGGTTTTGGCTATAGTAA 57.476 39.130 0.84 0.00 27.29 2.24
140 141 5.523883 AACCCTTGGTTTTGGCTATAGTA 57.476 39.130 0.84 0.00 44.33 1.82
141 142 4.397919 AACCCTTGGTTTTGGCTATAGT 57.602 40.909 0.84 0.00 44.33 2.12
143 144 5.523883 AGTAACCCTTGGTTTTGGCTATA 57.476 39.130 3.49 0.00 44.33 1.31
144 145 4.397919 AGTAACCCTTGGTTTTGGCTAT 57.602 40.909 3.49 0.00 44.33 2.97
145 146 3.887916 AGTAACCCTTGGTTTTGGCTA 57.112 42.857 3.49 0.00 44.33 3.93
146 147 2.767644 AGTAACCCTTGGTTTTGGCT 57.232 45.000 3.49 0.00 44.33 4.75
147 148 4.940905 TTAAGTAACCCTTGGTTTTGGC 57.059 40.909 3.49 0.00 44.33 4.52
148 149 7.056844 TCATTTAAGTAACCCTTGGTTTTGG 57.943 36.000 3.49 0.00 44.33 3.28
173 174 4.598022 TCCATTGTCAATTGATAGTGCCA 58.402 39.130 18.43 6.20 0.00 4.92
181 182 5.559770 TGAGCTAGTTCCATTGTCAATTGA 58.440 37.500 3.38 3.38 0.00 2.57
191 192 3.460648 GCGGTTGAGCTAGTTCCAT 57.539 52.632 3.94 0.00 0.00 3.41
206 207 9.744468 ATAAAACTTTTATTTATTAGCCAGCGG 57.256 29.630 1.48 0.00 30.72 5.52
222 223 8.950007 TCTCCCACAGGATTAATAAAACTTTT 57.050 30.769 0.00 0.00 42.93 2.27
291 293 9.846248 GCTTGGTTAAATATTAAGCATCCTATG 57.154 33.333 13.53 0.00 42.35 2.23
320 322 1.613437 ACCAAGACAAAAATCGCCTGG 59.387 47.619 0.00 0.00 0.00 4.45
322 324 2.582052 TGACCAAGACAAAAATCGCCT 58.418 42.857 0.00 0.00 0.00 5.52
367 369 5.622914 GCACCACAATCAGTCATTATTGCTT 60.623 40.000 0.00 0.00 36.72 3.91
385 387 5.796350 AAGTCGATTTATTACTGCACCAC 57.204 39.130 0.00 0.00 0.00 4.16
397 399 6.656314 ATCATGCACGTTTAAGTCGATTTA 57.344 33.333 8.66 0.00 0.00 1.40
398 400 5.545658 ATCATGCACGTTTAAGTCGATTT 57.454 34.783 0.00 0.00 0.00 2.17
411 413 3.121227 CGAGCACATAGTTATCATGCACG 60.121 47.826 0.00 0.00 42.24 5.34
487 489 1.761174 GTGGGGTGTGGTCATGACT 59.239 57.895 24.50 0.00 0.00 3.41
491 493 0.035439 GAATCGTGGGGTGTGGTCAT 60.035 55.000 0.00 0.00 0.00 3.06
516 519 4.284829 TCCTGATACACATGCAGAACAA 57.715 40.909 0.00 0.00 0.00 2.83
532 537 4.993705 AGTAAATTGGACCAGTTCCTGA 57.006 40.909 2.25 0.00 46.10 3.86
538 543 4.323562 GCTCAGGTAGTAAATTGGACCAGT 60.324 45.833 0.00 0.00 34.18 4.00
548 553 4.783227 AGGAATTCTGGCTCAGGTAGTAAA 59.217 41.667 5.23 0.00 31.51 2.01
585 594 1.402968 CAGCAAATGTTCCCCGATCTG 59.597 52.381 0.00 0.00 0.00 2.90
613 622 2.347731 GTTTGGTCCTGGATTCGTCTC 58.652 52.381 0.00 0.00 0.00 3.36
627 636 1.348366 TGGTATAGTGCACGGTTTGGT 59.652 47.619 12.01 0.00 0.00 3.67
713 722 3.005554 CTCTCGTTTGCATGTGGATCTT 58.994 45.455 0.00 0.00 0.00 2.40
772 781 4.555906 CGGAGTAATTTTGCGGAAAGTTGT 60.556 41.667 18.15 7.12 0.00 3.32
780 789 3.488489 CTTTCACGGAGTAATTTTGCGG 58.512 45.455 8.07 0.00 41.61 5.69
785 794 5.277634 CGTTTCACCTTTCACGGAGTAATTT 60.278 40.000 0.00 0.00 41.61 1.82
786 795 4.212636 CGTTTCACCTTTCACGGAGTAATT 59.787 41.667 0.00 0.00 41.61 1.40
787 796 3.744426 CGTTTCACCTTTCACGGAGTAAT 59.256 43.478 0.00 0.00 41.61 1.89
788 797 3.125316 CGTTTCACCTTTCACGGAGTAA 58.875 45.455 0.00 0.00 41.61 2.24
789 798 2.746269 CGTTTCACCTTTCACGGAGTA 58.254 47.619 0.00 0.00 41.61 2.59
795 804 2.249844 TCTCCCGTTTCACCTTTCAC 57.750 50.000 0.00 0.00 0.00 3.18
796 805 2.171870 ACTTCTCCCGTTTCACCTTTCA 59.828 45.455 0.00 0.00 0.00 2.69
797 806 2.847441 ACTTCTCCCGTTTCACCTTTC 58.153 47.619 0.00 0.00 0.00 2.62
798 807 3.292492 AACTTCTCCCGTTTCACCTTT 57.708 42.857 0.00 0.00 0.00 3.11
799 808 3.292492 AAACTTCTCCCGTTTCACCTT 57.708 42.857 0.00 0.00 29.08 3.50
801 810 2.034179 CCAAAACTTCTCCCGTTTCACC 59.966 50.000 0.00 0.00 33.76 4.02
809 818 2.026729 CCTCTCCTCCAAAACTTCTCCC 60.027 54.545 0.00 0.00 0.00 4.30
879 2709 1.744114 GCGGAGAGAAAGATGGGTTCC 60.744 57.143 0.00 0.00 0.00 3.62
915 2745 7.611467 TCCATTTATATAGGATGCATGTGGAAC 59.389 37.037 2.46 0.00 37.35 3.62
957 2794 1.577328 CGCTGGTTTGCAGTGTAGGG 61.577 60.000 0.00 0.00 0.00 3.53
983 2825 2.749621 GCCATTGATCTCACGTTTTCCT 59.250 45.455 0.00 0.00 0.00 3.36
985 2827 3.492313 GTGCCATTGATCTCACGTTTTC 58.508 45.455 0.00 0.00 0.00 2.29
1106 2948 1.640428 TGCTACTACATCGTTGCTGC 58.360 50.000 0.00 0.00 36.75 5.25
1117 2959 2.352388 TGCCGATGGTTTTGCTACTAC 58.648 47.619 0.00 0.00 0.00 2.73
1293 3145 2.542907 CGGCGCAGTTCTGTTGGTT 61.543 57.895 10.83 0.00 0.00 3.67
1550 4346 6.145534 TCACAATGTTCATAACTGAAGACGAC 59.854 38.462 0.00 0.00 41.96 4.34
1583 4383 2.636893 GGTCCTGCTGTCAGATCCATAT 59.363 50.000 3.32 0.00 42.95 1.78
1592 4392 4.314440 GCACGGGTCCTGCTGTCA 62.314 66.667 0.00 0.00 0.00 3.58
1941 4762 7.703058 ACCAATAAATTTTCTCCAAGACGAT 57.297 32.000 0.00 0.00 0.00 3.73
2098 4919 9.672086 CGATAACTAGGTGAACAAAAATTCAAA 57.328 29.630 0.00 0.00 40.22 2.69
2099 4920 9.058174 TCGATAACTAGGTGAACAAAAATTCAA 57.942 29.630 0.00 0.00 40.22 2.69
2100 4921 8.610248 TCGATAACTAGGTGAACAAAAATTCA 57.390 30.769 0.00 0.00 36.23 2.57
2101 4922 9.326339 GTTCGATAACTAGGTGAACAAAAATTC 57.674 33.333 4.94 0.00 38.93 2.17
2102 4923 9.063615 AGTTCGATAACTAGGTGAACAAAAATT 57.936 29.630 10.97 0.00 44.26 1.82
2103 4924 8.504005 CAGTTCGATAACTAGGTGAACAAAAAT 58.496 33.333 10.97 0.00 44.28 1.82
2104 4925 7.496591 ACAGTTCGATAACTAGGTGAACAAAAA 59.503 33.333 10.97 0.00 44.28 1.94
2105 4926 6.987992 ACAGTTCGATAACTAGGTGAACAAAA 59.012 34.615 10.97 0.00 44.28 2.44
2106 4927 6.518493 ACAGTTCGATAACTAGGTGAACAAA 58.482 36.000 10.97 0.00 44.28 2.83
2107 4928 6.092955 ACAGTTCGATAACTAGGTGAACAA 57.907 37.500 10.97 0.00 44.28 2.83
2108 4929 5.717078 ACAGTTCGATAACTAGGTGAACA 57.283 39.130 10.97 0.00 44.28 3.18
2109 4930 7.417496 AAAACAGTTCGATAACTAGGTGAAC 57.583 36.000 2.06 2.06 44.28 3.18
2110 4931 9.715121 AATAAAACAGTTCGATAACTAGGTGAA 57.285 29.630 0.00 0.00 44.28 3.18
2111 4932 9.362539 GAATAAAACAGTTCGATAACTAGGTGA 57.637 33.333 0.00 0.00 44.28 4.02
2112 4933 8.601476 GGAATAAAACAGTTCGATAACTAGGTG 58.399 37.037 0.00 0.00 44.28 4.00
2113 4934 7.490402 CGGAATAAAACAGTTCGATAACTAGGT 59.510 37.037 0.00 0.00 44.28 3.08
2139 4960 1.584308 GCGTTCGATAGTCAGAGCAAC 59.416 52.381 0.00 0.00 37.40 4.17
2154 4975 4.092675 CCAGATTGAAGAAAGAGAGCGTTC 59.907 45.833 0.00 0.00 33.44 3.95
2163 4984 5.105473 ACCATCATTGCCAGATTGAAGAAAG 60.105 40.000 0.00 0.00 0.00 2.62
2167 4988 3.952323 AGACCATCATTGCCAGATTGAAG 59.048 43.478 0.00 0.00 0.00 3.02
2176 4997 2.613691 CTTTTGCAGACCATCATTGCC 58.386 47.619 0.00 0.00 37.03 4.52
2177 4998 2.231964 TCCTTTTGCAGACCATCATTGC 59.768 45.455 0.00 0.00 38.30 3.56
2232 5053 2.797786 TGCCCTTAAGCAACGGTTTAT 58.202 42.857 0.00 0.00 40.56 1.40
2263 5084 6.930164 CAGATGATTTTTGAACAAATGGGTCA 59.070 34.615 0.82 4.55 0.00 4.02
2276 5097 5.051891 GACACCAGTCCAGATGATTTTTG 57.948 43.478 0.00 0.00 38.89 2.44
2379 5201 8.539674 CCAAACAAAAAGCTACTAACAAATCAC 58.460 33.333 0.00 0.00 0.00 3.06
2388 5210 5.584253 TTGCACCAAACAAAAAGCTACTA 57.416 34.783 0.00 0.00 0.00 1.82
2389 5211 4.464069 TTGCACCAAACAAAAAGCTACT 57.536 36.364 0.00 0.00 0.00 2.57
2390 5212 4.494035 GCTTTGCACCAAACAAAAAGCTAC 60.494 41.667 10.35 0.00 45.79 3.58
2391 5213 3.620821 GCTTTGCACCAAACAAAAAGCTA 59.379 39.130 10.35 0.00 45.79 3.32
2392 5214 2.419673 GCTTTGCACCAAACAAAAAGCT 59.580 40.909 10.35 0.00 45.79 3.74
2411 5247 7.094463 GCCATGAAATCACTATAATTAGCAGCT 60.094 37.037 0.00 0.00 0.00 4.24
2415 5251 8.239998 GGAAGCCATGAAATCACTATAATTAGC 58.760 37.037 0.00 0.00 0.00 3.09
2431 5267 2.358957 CAGATTTGACGGAAGCCATGA 58.641 47.619 0.00 0.00 0.00 3.07
2451 5287 6.876804 CAAATGTTTGCTTTACTTGGTAAGC 58.123 36.000 0.00 0.00 29.41 3.09
2469 5305 6.717540 TGGTATTGTGTTTAGTAGGCAAATGT 59.282 34.615 0.00 0.00 0.00 2.71
2500 5336 9.179909 TCTTATGAGTAGCTATTAGCCACTATC 57.820 37.037 15.37 6.64 43.05 2.08
2514 5350 3.728845 TCCGCCAAATCTTATGAGTAGC 58.271 45.455 0.00 0.00 0.00 3.58
2523 5359 1.745653 GCTAGCTTTCCGCCAAATCTT 59.254 47.619 7.70 0.00 40.39 2.40
2525 5361 1.383523 AGCTAGCTTTCCGCCAAATC 58.616 50.000 12.68 0.00 40.39 2.17
2543 5379 1.079503 GTAGCTTCACTTGGCGGAAG 58.920 55.000 0.00 0.00 42.62 3.46
2544 5380 0.685097 AGTAGCTTCACTTGGCGGAA 59.315 50.000 0.00 0.00 0.00 4.30
2545 5381 0.246635 GAGTAGCTTCACTTGGCGGA 59.753 55.000 0.00 0.00 0.00 5.54
2546 5382 0.037326 TGAGTAGCTTCACTTGGCGG 60.037 55.000 0.00 0.00 0.00 6.13
2547 5383 2.015736 ATGAGTAGCTTCACTTGGCG 57.984 50.000 0.00 0.00 0.00 5.69
2558 5394 2.802816 CCGTCCAATGCTTATGAGTAGC 59.197 50.000 0.00 0.00 39.10 3.58
2574 5410 3.455328 GGAAGCTAGGTTTCCGTCC 57.545 57.895 8.87 0.99 33.62 4.79
2578 5414 2.467566 TTGACGGAAGCTAGGTTTCC 57.532 50.000 8.87 10.24 39.11 3.13
2581 5417 3.695830 TCATTTGACGGAAGCTAGGTT 57.304 42.857 6.94 6.94 0.00 3.50
2603 5439 4.680567 GCGTTTAGTAGCTGGAAGTATAGC 59.319 45.833 0.00 0.00 40.18 2.97
2604 5440 5.221130 GGCGTTTAGTAGCTGGAAGTATAG 58.779 45.833 0.00 0.00 35.30 1.31
2605 5441 4.646040 TGGCGTTTAGTAGCTGGAAGTATA 59.354 41.667 0.00 0.00 35.30 1.47
2606 5442 3.449737 TGGCGTTTAGTAGCTGGAAGTAT 59.550 43.478 0.00 0.00 35.30 2.12
2607 5443 2.827322 TGGCGTTTAGTAGCTGGAAGTA 59.173 45.455 0.00 0.00 35.30 2.24
2608 5444 1.621814 TGGCGTTTAGTAGCTGGAAGT 59.378 47.619 0.00 0.00 35.30 3.01
2609 5445 2.380084 TGGCGTTTAGTAGCTGGAAG 57.620 50.000 0.00 0.00 0.00 3.46
2610 5446 2.843401 TTGGCGTTTAGTAGCTGGAA 57.157 45.000 0.00 0.00 0.00 3.53
2611 5447 2.843401 TTTGGCGTTTAGTAGCTGGA 57.157 45.000 0.00 0.00 0.00 3.86
2612 5448 3.006940 TCATTTGGCGTTTAGTAGCTGG 58.993 45.455 0.00 0.00 0.00 4.85
2613 5449 4.678509 TTCATTTGGCGTTTAGTAGCTG 57.321 40.909 0.00 0.00 0.00 4.24
2614 5450 4.760204 AGTTTCATTTGGCGTTTAGTAGCT 59.240 37.500 0.00 0.00 0.00 3.32
2615 5451 5.043189 AGTTTCATTTGGCGTTTAGTAGC 57.957 39.130 0.00 0.00 0.00 3.58
2616 5452 5.180492 TGGAGTTTCATTTGGCGTTTAGTAG 59.820 40.000 0.00 0.00 0.00 2.57
2617 5453 5.049267 GTGGAGTTTCATTTGGCGTTTAGTA 60.049 40.000 0.00 0.00 0.00 1.82
2618 5454 3.886505 TGGAGTTTCATTTGGCGTTTAGT 59.113 39.130 0.00 0.00 0.00 2.24
2619 5455 4.226761 GTGGAGTTTCATTTGGCGTTTAG 58.773 43.478 0.00 0.00 0.00 1.85
2620 5456 3.004944 GGTGGAGTTTCATTTGGCGTTTA 59.995 43.478 0.00 0.00 0.00 2.01
2621 5457 2.223947 GGTGGAGTTTCATTTGGCGTTT 60.224 45.455 0.00 0.00 0.00 3.60
2622 5458 1.339929 GGTGGAGTTTCATTTGGCGTT 59.660 47.619 0.00 0.00 0.00 4.84
2623 5459 0.958822 GGTGGAGTTTCATTTGGCGT 59.041 50.000 0.00 0.00 0.00 5.68
2624 5460 1.247567 AGGTGGAGTTTCATTTGGCG 58.752 50.000 0.00 0.00 0.00 5.69
2625 5461 4.706962 AGATTAGGTGGAGTTTCATTTGGC 59.293 41.667 0.00 0.00 0.00 4.52
2626 5462 7.559590 CTAGATTAGGTGGAGTTTCATTTGG 57.440 40.000 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.