Multiple sequence alignment - TraesCS7B01G135100

Loading Multiple Alignment...

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 TraesCS7B01G135100 chr7B 100.000 2687 0 0 1 2687 165104103 165101417 0.000000e+00 4963
1 TraesCS7B01G135100 chr7D 93.793 1160 47 5 788 1922 200770091 200768932 0.000000e+00 1720
2 TraesCS7B01G135100 chr7D 89.231 520 18 18 1913 2415 200768991 200768493 1.370000e-172 616
3 TraesCS7B01G135100 chr7D 91.636 275 6 6 2413 2687 200768451 200768194 5.470000e-97 364
4 TraesCS7B01G135100 chr7A 96.561 785 27 0 948 1732 214306377 214305593 0.000000e+00 1301
5 TraesCS7B01G135100 chr7A 84.221 507 72 7 169 668 512186960 512187465 1.120000e-133 486
6 TraesCS7B01G135100 chr7A 95.074 203 7 2 1908 2107 214305434 214305232 1.550000e-82 316
7 TraesCS7B01G135100 chr7A 89.950 199 19 1 1725 1922 214305567 214305369 3.430000e-64 255
8 TraesCS7B01G135100 chr7A 88.119 202 17 5 2216 2415 214305105 214304909 1.610000e-57 233
9 TraesCS7B01G135100 chr6D 84.722 504 69 7 169 665 48674827 48675329 5.170000e-137 497
10 TraesCS7B01G135100 chr2A 84.646 508 65 12 169 666 719682551 719683055 6.680000e-136 494
11 TraesCS7B01G135100 chr6A 84.356 505 69 9 169 665 65859110 65858608 1.120000e-133 486
12 TraesCS7B01G135100 chr6A 89.881 168 13 2 1 166 512815982 512815817 2.100000e-51 213
13 TraesCS7B01G135100 chr5D 84.149 511 64 16 169 668 165615725 165616229 1.870000e-131 479
14 TraesCS7B01G135100 chr5D 90.566 159 11 2 9 165 218186308 218186464 9.750000e-50 207
15 TraesCS7B01G135100 chr4B 83.694 509 70 11 167 667 504993808 504993305 4.050000e-128 468
16 TraesCS7B01G135100 chr1A 83.465 508 74 9 169 668 287381870 287382375 5.240000e-127 464
17 TraesCS7B01G135100 chr3B 83.203 512 73 12 172 674 780617635 780617128 8.770000e-125 457
18 TraesCS7B01G135100 chr2B 82.846 513 79 7 169 675 557350791 557351300 4.080000e-123 451
19 TraesCS7B01G135100 chr2B 98.788 165 2 0 1 165 779966428 779966264 7.270000e-76 294
20 TraesCS7B01G135100 chr5A 98.788 165 2 0 1 165 553495591 553495755 7.270000e-76 294
21 TraesCS7B01G135100 chr4A 90.909 165 11 2 1 163 446626140 446625978 4.500000e-53 219
22 TraesCS7B01G135100 chr3A 88.690 168 17 2 1 167 26578315 26578481 1.260000e-48 204
23 TraesCS7B01G135100 chr5B 87.647 170 16 3 1 167 586472892 586472725 2.730000e-45 193


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 TraesCS7B01G135100 chr7B 165101417 165104103 2686 True 4963.00 4963 100.000000 1 2687 1 chr7B.!!$R1 2686
1 TraesCS7B01G135100 chr7D 200768194 200770091 1897 True 900.00 1720 91.553333 788 2687 3 chr7D.!!$R1 1899
2 TraesCS7B01G135100 chr7A 214304909 214306377 1468 True 526.25 1301 92.426000 948 2415 4 chr7A.!!$R1 1467
3 TraesCS7B01G135100 chr7A 512186960 512187465 505 False 486.00 486 84.221000 169 668 1 chr7A.!!$F1 499
4 TraesCS7B01G135100 chr6D 48674827 48675329 502 False 497.00 497 84.722000 169 665 1 chr6D.!!$F1 496
5 TraesCS7B01G135100 chr2A 719682551 719683055 504 False 494.00 494 84.646000 169 666 1 chr2A.!!$F1 497
6 TraesCS7B01G135100 chr6A 65858608 65859110 502 True 486.00 486 84.356000 169 665 1 chr6A.!!$R1 496
7 TraesCS7B01G135100 chr5D 165615725 165616229 504 False 479.00 479 84.149000 169 668 1 chr5D.!!$F1 499
8 TraesCS7B01G135100 chr4B 504993305 504993808 503 True 468.00 468 83.694000 167 667 1 chr4B.!!$R1 500
9 TraesCS7B01G135100 chr1A 287381870 287382375 505 False 464.00 464 83.465000 169 668 1 chr1A.!!$F1 499
10 TraesCS7B01G135100 chr3B 780617128 780617635 507 True 457.00 457 83.203000 172 674 1 chr3B.!!$R1 502
11 TraesCS7B01G135100 chr2B 557350791 557351300 509 False 451.00 451 82.846000 169 675 1 chr2B.!!$F1 506

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
776 787 0.037447 TGGACATGTGAAATCCCGCA 59.963 50.0 1.15 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1901 1969 0.17668 CCTGCGACCTAGAAGCACAT 59.823 55.0 0.0 0.0 36.79 3.21 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
26 27 8.891671 ATAAAGCACAATGTTTTCAGTCATTT 57.108 26.923 0.00 0.00 33.01 2.32
27 28 6.592798 AAGCACAATGTTTTCAGTCATTTG 57.407 33.333 0.00 0.00 32.85 2.32
28 29 5.663456 AGCACAATGTTTTCAGTCATTTGT 58.337 33.333 0.00 0.00 32.85 2.83
29 30 6.804677 AGCACAATGTTTTCAGTCATTTGTA 58.195 32.000 0.00 0.00 32.85 2.41
30 31 6.697019 AGCACAATGTTTTCAGTCATTTGTAC 59.303 34.615 0.00 0.00 32.85 2.90
31 32 6.475076 GCACAATGTTTTCAGTCATTTGTACA 59.525 34.615 0.00 0.00 32.85 2.90
32 33 7.009999 GCACAATGTTTTCAGTCATTTGTACAA 59.990 33.333 3.59 3.59 32.85 2.41
33 34 8.533965 CACAATGTTTTCAGTCATTTGTACAAG 58.466 33.333 8.56 0.00 32.85 3.16
34 35 8.250332 ACAATGTTTTCAGTCATTTGTACAAGT 58.750 29.630 8.56 2.66 32.85 3.16
35 36 9.086336 CAATGTTTTCAGTCATTTGTACAAGTT 57.914 29.630 8.56 0.00 32.85 2.66
37 38 9.950680 ATGTTTTCAGTCATTTGTACAAGTTAG 57.049 29.630 8.56 0.85 0.00 2.34
38 39 8.402472 TGTTTTCAGTCATTTGTACAAGTTAGG 58.598 33.333 8.56 0.00 0.00 2.69
39 40 8.617809 GTTTTCAGTCATTTGTACAAGTTAGGA 58.382 33.333 8.56 0.00 0.00 2.94
40 41 8.740123 TTTCAGTCATTTGTACAAGTTAGGAA 57.260 30.769 8.56 7.34 0.00 3.36
41 42 8.918202 TTCAGTCATTTGTACAAGTTAGGAAT 57.082 30.769 8.56 0.00 0.00 3.01
42 43 8.918202 TCAGTCATTTGTACAAGTTAGGAATT 57.082 30.769 8.56 0.00 0.00 2.17
55 56 9.586435 ACAAGTTAGGAATTATATGCTTTTTGC 57.414 29.630 0.00 0.00 43.25 3.68
56 57 8.745837 CAAGTTAGGAATTATATGCTTTTTGCG 58.254 33.333 0.00 0.00 46.63 4.85
57 58 7.996385 AGTTAGGAATTATATGCTTTTTGCGT 58.004 30.769 0.00 0.00 46.63 5.24
58 59 7.915397 AGTTAGGAATTATATGCTTTTTGCGTG 59.085 33.333 0.00 0.00 46.63 5.34
59 60 6.449635 AGGAATTATATGCTTTTTGCGTGA 57.550 33.333 0.00 0.00 46.63 4.35
60 61 6.498304 AGGAATTATATGCTTTTTGCGTGAG 58.502 36.000 0.00 0.00 46.63 3.51
61 62 6.318648 AGGAATTATATGCTTTTTGCGTGAGA 59.681 34.615 0.00 0.00 46.63 3.27
62 63 7.013655 AGGAATTATATGCTTTTTGCGTGAGAT 59.986 33.333 0.00 0.00 46.63 2.75
63 64 7.649306 GGAATTATATGCTTTTTGCGTGAGATT 59.351 33.333 0.00 0.00 46.63 2.40
64 65 8.931385 AATTATATGCTTTTTGCGTGAGATTT 57.069 26.923 0.00 0.00 46.63 2.17
65 66 7.969387 TTATATGCTTTTTGCGTGAGATTTC 57.031 32.000 0.00 0.00 46.63 2.17
66 67 3.706802 TGCTTTTTGCGTGAGATTTCA 57.293 38.095 0.00 0.00 46.63 2.69
67 68 3.631144 TGCTTTTTGCGTGAGATTTCAG 58.369 40.909 0.00 0.00 46.63 3.02
68 69 2.406357 GCTTTTTGCGTGAGATTTCAGC 59.594 45.455 0.00 0.00 32.98 4.26
69 70 3.854784 GCTTTTTGCGTGAGATTTCAGCT 60.855 43.478 8.42 0.00 32.98 4.24
70 71 2.975410 TTTGCGTGAGATTTCAGCTG 57.025 45.000 7.63 7.63 32.98 4.24
71 72 1.882912 TTGCGTGAGATTTCAGCTGT 58.117 45.000 14.67 0.00 32.98 4.40
72 73 1.882912 TGCGTGAGATTTCAGCTGTT 58.117 45.000 14.67 0.00 32.98 3.16
73 74 1.800586 TGCGTGAGATTTCAGCTGTTC 59.199 47.619 14.67 9.54 32.98 3.18
74 75 1.800586 GCGTGAGATTTCAGCTGTTCA 59.199 47.619 14.67 8.33 32.98 3.18
75 76 2.224079 GCGTGAGATTTCAGCTGTTCAA 59.776 45.455 14.67 5.92 32.98 2.69
76 77 3.303990 GCGTGAGATTTCAGCTGTTCAAA 60.304 43.478 14.67 7.59 32.98 2.69
77 78 4.789481 GCGTGAGATTTCAGCTGTTCAAAA 60.789 41.667 14.67 7.20 32.98 2.44
78 79 5.273170 CGTGAGATTTCAGCTGTTCAAAAA 58.727 37.500 14.67 6.80 32.98 1.94
79 80 5.397534 CGTGAGATTTCAGCTGTTCAAAAAG 59.602 40.000 14.67 0.00 32.98 2.27
80 81 6.268566 GTGAGATTTCAGCTGTTCAAAAAGT 58.731 36.000 14.67 0.00 32.98 2.66
81 82 7.417612 GTGAGATTTCAGCTGTTCAAAAAGTA 58.582 34.615 14.67 0.00 32.98 2.24
82 83 7.589221 GTGAGATTTCAGCTGTTCAAAAAGTAG 59.411 37.037 14.67 0.00 32.98 2.57
83 84 7.498900 TGAGATTTCAGCTGTTCAAAAAGTAGA 59.501 33.333 14.67 0.00 0.00 2.59
84 85 8.401490 AGATTTCAGCTGTTCAAAAAGTAGAT 57.599 30.769 14.67 0.00 0.00 1.98
85 86 8.854117 AGATTTCAGCTGTTCAAAAAGTAGATT 58.146 29.630 14.67 0.00 0.00 2.40
86 87 9.468532 GATTTCAGCTGTTCAAAAAGTAGATTT 57.531 29.630 14.67 0.00 0.00 2.17
89 90 9.897744 TTCAGCTGTTCAAAAAGTAGATTTATG 57.102 29.630 14.67 0.00 0.00 1.90
90 91 9.066892 TCAGCTGTTCAAAAAGTAGATTTATGT 57.933 29.630 14.67 0.00 0.00 2.29
91 92 9.683069 CAGCTGTTCAAAAAGTAGATTTATGTT 57.317 29.630 5.25 0.00 0.00 2.71
92 93 9.683069 AGCTGTTCAAAAAGTAGATTTATGTTG 57.317 29.630 0.00 0.00 0.00 3.33
93 94 9.677567 GCTGTTCAAAAAGTAGATTTATGTTGA 57.322 29.630 0.00 0.00 0.00 3.18
137 138 8.988934 TCATTGTAGAACATATTTAATCGAGGC 58.011 33.333 0.00 0.00 0.00 4.70
138 139 7.402811 TTGTAGAACATATTTAATCGAGGCG 57.597 36.000 0.00 0.00 0.00 5.52
139 140 6.509656 TGTAGAACATATTTAATCGAGGCGT 58.490 36.000 0.00 0.00 0.00 5.68
140 141 5.907197 AGAACATATTTAATCGAGGCGTG 57.093 39.130 0.00 0.00 0.00 5.34
141 142 5.357257 AGAACATATTTAATCGAGGCGTGT 58.643 37.500 0.00 0.00 0.00 4.49
142 143 5.234329 AGAACATATTTAATCGAGGCGTGTG 59.766 40.000 0.00 0.00 0.00 3.82
143 144 4.439057 ACATATTTAATCGAGGCGTGTGT 58.561 39.130 0.00 0.00 0.00 3.72
144 145 4.270084 ACATATTTAATCGAGGCGTGTGTG 59.730 41.667 0.00 0.00 0.00 3.82
145 146 1.434555 TTTAATCGAGGCGTGTGTGG 58.565 50.000 0.00 0.00 0.00 4.17
146 147 1.017177 TTAATCGAGGCGTGTGTGGC 61.017 55.000 0.00 0.00 0.00 5.01
147 148 2.161078 TAATCGAGGCGTGTGTGGCA 62.161 55.000 0.00 0.00 36.77 4.92
148 149 4.961511 TCGAGGCGTGTGTGGCAC 62.962 66.667 11.55 11.55 44.36 5.01
155 156 3.649096 GTGTGTGGCACGTGCATA 58.351 55.556 38.60 25.42 44.36 3.14
156 157 1.206578 GTGTGTGGCACGTGCATAC 59.793 57.895 38.60 33.29 44.36 2.39
157 158 1.070615 TGTGTGGCACGTGCATACT 59.929 52.632 38.60 0.00 44.36 2.12
158 159 0.533978 TGTGTGGCACGTGCATACTT 60.534 50.000 38.60 0.00 44.36 2.24
159 160 1.270358 TGTGTGGCACGTGCATACTTA 60.270 47.619 38.60 24.41 44.36 2.24
160 161 1.127951 GTGTGGCACGTGCATACTTAC 59.872 52.381 38.60 25.53 44.36 2.34
161 162 1.001520 TGTGGCACGTGCATACTTACT 59.998 47.619 38.60 0.00 44.36 2.24
162 163 2.231721 TGTGGCACGTGCATACTTACTA 59.768 45.455 38.60 18.58 44.36 1.82
163 164 2.858344 GTGGCACGTGCATACTTACTAG 59.142 50.000 38.60 0.00 44.36 2.57
164 165 2.494471 TGGCACGTGCATACTTACTAGT 59.506 45.455 38.60 0.00 44.36 2.57
165 166 2.858344 GGCACGTGCATACTTACTAGTG 59.142 50.000 38.60 0.00 44.36 2.74
196 197 9.086336 ACAACTACTCAAAAATGTCATTGTTTG 57.914 29.630 17.85 17.85 33.26 2.93
200 201 9.467258 CTACTCAAAAATGTCATTGTTTGATGT 57.533 29.630 22.28 21.76 38.81 3.06
301 303 6.173339 AGACATCGTTATTGTCAGGTCAAAT 58.827 36.000 6.59 0.00 44.73 2.32
305 307 3.485216 CGTTATTGTCAGGTCAAATCCGC 60.485 47.826 0.00 0.00 0.00 5.54
322 324 4.890158 TCCGCTGACCATGTTATATGAT 57.110 40.909 0.00 0.00 0.00 2.45
345 348 7.841729 TGATAAAAATACCCATACACCCACATT 59.158 33.333 0.00 0.00 0.00 2.71
360 363 3.755378 CCCACATTCCAGTTCTCTCTTTG 59.245 47.826 0.00 0.00 0.00 2.77
443 446 7.675619 AGGAAAATAAGAATGTTGTTGGGATCT 59.324 33.333 0.00 0.00 0.00 2.75
449 452 4.536090 AGAATGTTGTTGGGATCTAGTGGA 59.464 41.667 0.00 0.00 0.00 4.02
467 471 3.287222 TGGAGCCCACACTTTATTATGC 58.713 45.455 0.00 0.00 0.00 3.14
484 488 2.673775 TGCTGAGATAGAGGGAGAGG 57.326 55.000 0.00 0.00 0.00 3.69
497 501 1.073923 GGGAGAGGTGACATGTTGGTT 59.926 52.381 0.00 0.00 0.00 3.67
546 550 2.031682 GCAAACACGATTTGAGCTGACT 60.032 45.455 17.29 0.00 0.00 3.41
553 557 4.627035 CACGATTTGAGCTGACTGTAATGA 59.373 41.667 0.00 0.00 0.00 2.57
634 645 5.705441 TGAAAACTCTAATGGCAAGTAGTGG 59.295 40.000 12.45 8.21 0.00 4.00
668 679 6.757947 CAGTGGCATAAATGATAAAAACCCTG 59.242 38.462 0.00 0.00 0.00 4.45
669 680 5.523552 GTGGCATAAATGATAAAAACCCTGC 59.476 40.000 0.00 0.00 0.00 4.85
671 682 6.070309 TGGCATAAATGATAAAAACCCTGCTT 60.070 34.615 0.00 0.00 0.00 3.91
673 684 7.984617 GGCATAAATGATAAAAACCCTGCTTAA 59.015 33.333 0.00 0.00 0.00 1.85
674 685 9.546428 GCATAAATGATAAAAACCCTGCTTAAT 57.454 29.630 0.00 0.00 0.00 1.40
681 692 9.693739 TGATAAAAACCCTGCTTAATAATCTGA 57.306 29.630 0.00 0.00 0.00 3.27
685 696 8.593945 AAAACCCTGCTTAATAATCTGAATGA 57.406 30.769 0.00 0.00 0.00 2.57
686 697 8.773033 AAACCCTGCTTAATAATCTGAATGAT 57.227 30.769 0.00 0.00 36.89 2.45
687 698 8.773033 AACCCTGCTTAATAATCTGAATGATT 57.227 30.769 0.00 0.00 46.22 2.57
688 699 8.773033 ACCCTGCTTAATAATCTGAATGATTT 57.227 30.769 0.00 0.00 42.28 2.17
689 700 9.205513 ACCCTGCTTAATAATCTGAATGATTTT 57.794 29.630 0.00 0.00 42.28 1.82
766 777 7.739498 TCATTGATGATTAGATGGACATGTG 57.261 36.000 1.15 0.00 0.00 3.21
767 778 7.511268 TCATTGATGATTAGATGGACATGTGA 58.489 34.615 1.15 0.00 0.00 3.58
768 779 7.994334 TCATTGATGATTAGATGGACATGTGAA 59.006 33.333 1.15 0.00 0.00 3.18
769 780 8.626526 CATTGATGATTAGATGGACATGTGAAA 58.373 33.333 1.15 0.00 0.00 2.69
770 781 8.756486 TTGATGATTAGATGGACATGTGAAAT 57.244 30.769 1.15 0.00 0.00 2.17
771 782 8.387190 TGATGATTAGATGGACATGTGAAATC 57.613 34.615 1.15 3.42 0.00 2.17
772 783 7.446319 TGATGATTAGATGGACATGTGAAATCC 59.554 37.037 1.15 0.00 0.00 3.01
773 784 6.064060 TGATTAGATGGACATGTGAAATCCC 58.936 40.000 1.15 0.00 0.00 3.85
774 785 2.923121 AGATGGACATGTGAAATCCCG 58.077 47.619 1.15 0.00 0.00 5.14
775 786 1.334869 GATGGACATGTGAAATCCCGC 59.665 52.381 1.15 0.00 0.00 6.13
776 787 0.037447 TGGACATGTGAAATCCCGCA 59.963 50.000 1.15 0.00 0.00 5.69
777 788 1.173043 GGACATGTGAAATCCCGCAA 58.827 50.000 1.15 0.00 0.00 4.85
778 789 1.543802 GGACATGTGAAATCCCGCAAA 59.456 47.619 1.15 0.00 0.00 3.68
779 790 2.029470 GGACATGTGAAATCCCGCAAAA 60.029 45.455 1.15 0.00 0.00 2.44
780 791 3.553922 GGACATGTGAAATCCCGCAAAAA 60.554 43.478 1.15 0.00 0.00 1.94
857 868 0.110192 GTTGCGTGCCTCACTAAAGC 60.110 55.000 0.00 0.00 31.34 3.51
871 882 0.675083 TAAAGCACTCGACCGTTGGA 59.325 50.000 0.00 0.00 0.00 3.53
875 886 3.292936 ACTCGACCGTTGGACGCT 61.293 61.111 2.88 0.00 40.91 5.07
881 892 2.126071 CCGTTGGACGCTCACGAT 60.126 61.111 0.00 0.00 43.93 3.73
896 907 2.116238 CACGATCCCTTCCCTTCCTTA 58.884 52.381 0.00 0.00 0.00 2.69
897 908 2.504175 CACGATCCCTTCCCTTCCTTAA 59.496 50.000 0.00 0.00 0.00 1.85
898 909 2.772515 ACGATCCCTTCCCTTCCTTAAG 59.227 50.000 0.00 0.00 0.00 1.85
899 910 2.485657 CGATCCCTTCCCTTCCTTAAGC 60.486 54.545 0.00 0.00 0.00 3.09
900 911 1.296002 TCCCTTCCCTTCCTTAAGCC 58.704 55.000 0.00 0.00 0.00 4.35
901 912 0.107165 CCCTTCCCTTCCTTAAGCCG 60.107 60.000 0.00 0.00 0.00 5.52
902 913 0.748367 CCTTCCCTTCCTTAAGCCGC 60.748 60.000 0.00 0.00 0.00 6.53
903 914 1.078708 TTCCCTTCCTTAAGCCGCG 60.079 57.895 0.00 0.00 0.00 6.46
927 962 1.112113 TCATCACGCTTCTACTCCCC 58.888 55.000 0.00 0.00 0.00 4.81
928 963 0.249073 CATCACGCTTCTACTCCCCG 60.249 60.000 0.00 0.00 0.00 5.73
929 964 2.017559 ATCACGCTTCTACTCCCCGC 62.018 60.000 0.00 0.00 0.00 6.13
945 980 0.453390 CCGCTTTCCATTTCTGCCTC 59.547 55.000 0.00 0.00 0.00 4.70
953 988 0.539051 CATTTCTGCCTCCCGAGTCT 59.461 55.000 0.00 0.00 0.00 3.24
971 1006 5.070770 AGTCTGATCTCACATCAACTCAC 57.929 43.478 0.00 0.00 0.00 3.51
982 1017 3.632145 ACATCAACTCACAACCTTCCAAC 59.368 43.478 0.00 0.00 0.00 3.77
991 1026 2.169769 ACAACCTTCCAACTCAGAACGA 59.830 45.455 0.00 0.00 0.00 3.85
1689 1724 2.496817 GTCCTGTGCGCCTAGGAG 59.503 66.667 24.88 11.38 43.42 3.69
1694 1729 0.176680 CTGTGCGCCTAGGAGACAAT 59.823 55.000 17.75 0.00 0.00 2.71
1744 1812 2.224548 ACCTCTTGTTTACTCCCTGTGC 60.225 50.000 0.00 0.00 0.00 4.57
1862 1930 8.337741 ACGAAATAACGCTTCTCTAATTCTAC 57.662 34.615 0.00 0.00 36.70 2.59
1875 1943 0.179108 ATTCTACGGTCGCAGGCTTC 60.179 55.000 0.00 0.00 0.00 3.86
1876 1944 2.202756 CTACGGTCGCAGGCTTCC 60.203 66.667 0.00 0.00 0.00 3.46
1877 1945 2.678934 TACGGTCGCAGGCTTCCT 60.679 61.111 0.00 0.00 0.00 3.36
1889 1957 3.463048 AGGCTTCCTGGTGAATTCATT 57.537 42.857 12.12 0.00 29.57 2.57
1890 1958 3.359950 AGGCTTCCTGGTGAATTCATTC 58.640 45.455 12.12 8.00 32.89 2.67
1891 1959 2.098117 GGCTTCCTGGTGAATTCATTCG 59.902 50.000 12.12 2.87 39.62 3.34
1892 1960 2.098117 GCTTCCTGGTGAATTCATTCGG 59.902 50.000 12.12 11.74 39.62 4.30
1893 1961 3.609853 CTTCCTGGTGAATTCATTCGGA 58.390 45.455 12.12 13.76 39.62 4.55
1894 1962 3.266510 TCCTGGTGAATTCATTCGGAG 57.733 47.619 12.12 3.69 39.62 4.63
1895 1963 2.092968 TCCTGGTGAATTCATTCGGAGG 60.093 50.000 12.12 11.97 39.62 4.30
1896 1964 2.092968 CCTGGTGAATTCATTCGGAGGA 60.093 50.000 12.12 0.00 39.62 3.71
1897 1965 3.609853 CTGGTGAATTCATTCGGAGGAA 58.390 45.455 12.12 0.00 39.62 3.36
1898 1966 4.009675 CTGGTGAATTCATTCGGAGGAAA 58.990 43.478 12.12 0.00 39.62 3.13
1899 1967 3.756434 TGGTGAATTCATTCGGAGGAAAC 59.244 43.478 12.12 0.00 39.62 2.78
1900 1968 3.181510 GGTGAATTCATTCGGAGGAAACG 60.182 47.826 12.12 0.00 39.62 3.60
1901 1969 3.682858 GTGAATTCATTCGGAGGAAACGA 59.317 43.478 12.12 0.00 39.62 3.85
1902 1970 4.332819 GTGAATTCATTCGGAGGAAACGAT 59.667 41.667 12.12 0.00 40.38 3.73
1903 1971 4.332543 TGAATTCATTCGGAGGAAACGATG 59.667 41.667 3.38 0.00 40.38 3.84
1904 1972 3.328382 TTCATTCGGAGGAAACGATGT 57.672 42.857 0.00 0.00 40.38 3.06
1905 1973 2.616960 TCATTCGGAGGAAACGATGTG 58.383 47.619 0.00 0.00 40.38 3.21
1906 1974 1.062587 CATTCGGAGGAAACGATGTGC 59.937 52.381 0.00 0.00 40.38 4.57
1907 1975 0.320374 TTCGGAGGAAACGATGTGCT 59.680 50.000 0.00 0.00 40.38 4.40
1908 1976 0.320374 TCGGAGGAAACGATGTGCTT 59.680 50.000 0.00 0.00 35.12 3.91
1909 1977 0.721718 CGGAGGAAACGATGTGCTTC 59.278 55.000 0.00 0.00 0.00 3.86
1910 1978 1.673033 CGGAGGAAACGATGTGCTTCT 60.673 52.381 0.00 0.00 0.00 2.85
1911 1979 2.416836 CGGAGGAAACGATGTGCTTCTA 60.417 50.000 0.00 0.00 0.00 2.10
1912 1980 3.190874 GGAGGAAACGATGTGCTTCTAG 58.809 50.000 0.00 0.00 0.00 2.43
1913 1981 3.190874 GAGGAAACGATGTGCTTCTAGG 58.809 50.000 0.00 0.00 0.00 3.02
1914 1982 2.567615 AGGAAACGATGTGCTTCTAGGT 59.432 45.455 0.00 0.00 0.00 3.08
1915 1983 2.930682 GGAAACGATGTGCTTCTAGGTC 59.069 50.000 0.00 0.00 0.00 3.85
1916 1984 2.279582 AACGATGTGCTTCTAGGTCG 57.720 50.000 0.00 0.00 35.42 4.79
1917 1985 0.179134 ACGATGTGCTTCTAGGTCGC 60.179 55.000 0.00 0.00 32.78 5.19
1918 1986 0.179137 CGATGTGCTTCTAGGTCGCA 60.179 55.000 0.00 0.00 0.00 5.10
1919 1987 1.565305 GATGTGCTTCTAGGTCGCAG 58.435 55.000 2.47 0.00 33.84 5.18
1920 1988 0.176680 ATGTGCTTCTAGGTCGCAGG 59.823 55.000 2.47 0.00 33.84 4.85
1921 1989 1.811679 GTGCTTCTAGGTCGCAGGC 60.812 63.158 2.47 0.00 33.84 4.85
1962 2030 2.354805 GGAAACGATGTGCTTCTAGGGT 60.355 50.000 0.00 0.00 0.00 4.34
1968 2036 0.898326 TGTGCTTCTAGGGTCGCAGA 60.898 55.000 0.00 0.00 32.38 4.26
2037 2106 7.642978 CGATGATCAGAGAATTTCCAACATTTC 59.357 37.037 0.09 0.00 0.00 2.17
2092 2161 8.268850 ACGATTCAAAGCTTATTTGTATGACT 57.731 30.769 0.00 0.00 0.00 3.41
2160 2229 8.821894 GTTATTCTGACTTCCTGCTTTATACTG 58.178 37.037 0.00 0.00 0.00 2.74
2161 2230 6.360370 TTCTGACTTCCTGCTTTATACTGT 57.640 37.500 0.00 0.00 0.00 3.55
2163 2232 6.864342 TCTGACTTCCTGCTTTATACTGTAC 58.136 40.000 0.00 0.00 0.00 2.90
2164 2233 6.663953 TCTGACTTCCTGCTTTATACTGTACT 59.336 38.462 0.00 0.00 0.00 2.73
2167 2236 6.407202 ACTTCCTGCTTTATACTGTACTTGG 58.593 40.000 0.00 0.00 0.00 3.61
2168 2237 4.766375 TCCTGCTTTATACTGTACTTGGC 58.234 43.478 0.00 0.00 0.00 4.52
2170 2239 4.941263 CCTGCTTTATACTGTACTTGGCAA 59.059 41.667 0.00 0.00 0.00 4.52
2172 2241 6.095440 CCTGCTTTATACTGTACTTGGCAAAT 59.905 38.462 0.00 0.00 0.00 2.32
2242 2362 3.806949 ATTCTCCCTGCAAACCTGTTA 57.193 42.857 0.00 0.00 0.00 2.41
2243 2363 3.806949 TTCTCCCTGCAAACCTGTTAT 57.193 42.857 0.00 0.00 0.00 1.89
2286 2406 9.480053 AATTTGAAAGAATTTGTTCGATGATGT 57.520 25.926 0.00 0.00 39.27 3.06
2287 2407 7.856492 TTGAAAGAATTTGTTCGATGATGTG 57.144 32.000 0.00 0.00 39.27 3.21
2353 2493 2.666022 TCGTGATTGCGTCATTACACAG 59.334 45.455 0.00 0.00 39.48 3.66
2411 2552 1.001974 CCAGCCTGCACACTGTTACTA 59.998 52.381 9.70 0.00 31.76 1.82
2420 2605 6.372659 CCTGCACACTGTTACTAGAAAATCAT 59.627 38.462 0.00 0.00 0.00 2.45
2495 2680 8.334263 TCTACAAAATGATTATGTGCTGAACA 57.666 30.769 0.00 0.00 44.79 3.18
2529 2714 4.333926 GCATACTTCTGGAACATCAACCTC 59.666 45.833 0.00 0.00 38.20 3.85
2530 2715 3.425162 ACTTCTGGAACATCAACCTCC 57.575 47.619 0.00 0.00 38.20 4.30
2531 2716 2.982488 ACTTCTGGAACATCAACCTCCT 59.018 45.455 0.00 0.00 38.20 3.69
2532 2717 4.168101 ACTTCTGGAACATCAACCTCCTA 58.832 43.478 0.00 0.00 38.20 2.94
2534 2719 2.501723 TCTGGAACATCAACCTCCTAGC 59.498 50.000 0.00 0.00 38.20 3.42
2535 2720 2.237143 CTGGAACATCAACCTCCTAGCA 59.763 50.000 0.00 0.00 38.20 3.49
2536 2721 2.846206 TGGAACATCAACCTCCTAGCAT 59.154 45.455 0.00 0.00 0.00 3.79
2537 2722 3.118261 TGGAACATCAACCTCCTAGCATC 60.118 47.826 0.00 0.00 0.00 3.91
2538 2723 3.135530 GGAACATCAACCTCCTAGCATCT 59.864 47.826 0.00 0.00 0.00 2.90
2539 2724 3.834489 ACATCAACCTCCTAGCATCTG 57.166 47.619 0.00 0.00 0.00 2.90
2540 2725 3.110705 ACATCAACCTCCTAGCATCTGT 58.889 45.455 0.00 0.00 0.00 3.41
2541 2726 4.290093 ACATCAACCTCCTAGCATCTGTA 58.710 43.478 0.00 0.00 0.00 2.74
2542 2727 4.904251 ACATCAACCTCCTAGCATCTGTAT 59.096 41.667 0.00 0.00 0.00 2.29
2543 2728 6.077993 ACATCAACCTCCTAGCATCTGTATA 58.922 40.000 0.00 0.00 0.00 1.47
2600 2785 7.765695 ACATGGTTTCAACATAATCTTCACT 57.234 32.000 0.00 0.00 0.00 3.41
2640 2825 8.265055 CACCTGATACTTACTTCCAAAGGATTA 58.735 37.037 0.00 0.00 27.23 1.75
2655 2840 3.963383 GGATTACACCAAGCCGTATTG 57.037 47.619 0.00 0.00 31.84 1.90
2656 2841 3.275999 GGATTACACCAAGCCGTATTGT 58.724 45.455 0.00 0.00 31.84 2.71
2657 2842 3.692593 GGATTACACCAAGCCGTATTGTT 59.307 43.478 0.00 0.00 31.84 2.83
2658 2843 4.438200 GGATTACACCAAGCCGTATTGTTG 60.438 45.833 0.00 0.00 31.84 3.33
2659 2844 1.975660 ACACCAAGCCGTATTGTTGT 58.024 45.000 0.00 0.00 31.74 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.979578 AAATGACTGAAAACATTGTGCTTTATA 57.020 25.926 0.00 0.00 36.92 0.98
1 2 8.767085 CAAATGACTGAAAACATTGTGCTTTAT 58.233 29.630 0.00 0.00 36.92 1.40
2 3 7.763528 ACAAATGACTGAAAACATTGTGCTTTA 59.236 29.630 0.00 0.00 36.92 1.85
3 4 6.594937 ACAAATGACTGAAAACATTGTGCTTT 59.405 30.769 0.00 0.00 36.92 3.51
4 5 6.108015 ACAAATGACTGAAAACATTGTGCTT 58.892 32.000 0.00 0.00 36.92 3.91
5 6 5.663456 ACAAATGACTGAAAACATTGTGCT 58.337 33.333 0.00 0.00 36.92 4.40
6 7 5.971895 ACAAATGACTGAAAACATTGTGC 57.028 34.783 0.00 0.00 36.92 4.57
7 8 7.984002 TGTACAAATGACTGAAAACATTGTG 57.016 32.000 0.00 0.00 36.92 3.33
8 9 8.250332 ACTTGTACAAATGACTGAAAACATTGT 58.750 29.630 10.03 0.00 36.92 2.71
9 10 8.633075 ACTTGTACAAATGACTGAAAACATTG 57.367 30.769 10.03 0.00 36.92 2.82
11 12 9.950680 CTAACTTGTACAAATGACTGAAAACAT 57.049 29.630 10.03 0.00 0.00 2.71
12 13 8.402472 CCTAACTTGTACAAATGACTGAAAACA 58.598 33.333 10.03 0.00 0.00 2.83
13 14 8.617809 TCCTAACTTGTACAAATGACTGAAAAC 58.382 33.333 10.03 0.00 0.00 2.43
14 15 8.740123 TCCTAACTTGTACAAATGACTGAAAA 57.260 30.769 10.03 0.00 0.00 2.29
15 16 8.740123 TTCCTAACTTGTACAAATGACTGAAA 57.260 30.769 10.03 0.00 0.00 2.69
16 17 8.918202 ATTCCTAACTTGTACAAATGACTGAA 57.082 30.769 10.03 8.72 0.00 3.02
17 18 8.918202 AATTCCTAACTTGTACAAATGACTGA 57.082 30.769 10.03 0.06 0.00 3.41
29 30 9.586435 GCAAAAAGCATATAATTCCTAACTTGT 57.414 29.630 0.00 0.00 44.79 3.16
30 31 8.745837 CGCAAAAAGCATATAATTCCTAACTTG 58.254 33.333 0.00 0.00 46.13 3.16
31 32 8.466798 ACGCAAAAAGCATATAATTCCTAACTT 58.533 29.630 0.00 0.00 46.13 2.66
32 33 7.915397 CACGCAAAAAGCATATAATTCCTAACT 59.085 33.333 0.00 0.00 46.13 2.24
33 34 7.913297 TCACGCAAAAAGCATATAATTCCTAAC 59.087 33.333 0.00 0.00 46.13 2.34
34 35 7.990917 TCACGCAAAAAGCATATAATTCCTAA 58.009 30.769 0.00 0.00 46.13 2.69
35 36 7.497579 TCTCACGCAAAAAGCATATAATTCCTA 59.502 33.333 0.00 0.00 46.13 2.94
36 37 6.318648 TCTCACGCAAAAAGCATATAATTCCT 59.681 34.615 0.00 0.00 46.13 3.36
37 38 6.494842 TCTCACGCAAAAAGCATATAATTCC 58.505 36.000 0.00 0.00 46.13 3.01
38 39 8.566008 AATCTCACGCAAAAAGCATATAATTC 57.434 30.769 0.00 0.00 46.13 2.17
39 40 8.931385 AAATCTCACGCAAAAAGCATATAATT 57.069 26.923 0.00 0.00 46.13 1.40
40 41 8.190122 TGAAATCTCACGCAAAAAGCATATAAT 58.810 29.630 0.00 0.00 46.13 1.28
41 42 7.534282 TGAAATCTCACGCAAAAAGCATATAA 58.466 30.769 0.00 0.00 46.13 0.98
42 43 7.082700 TGAAATCTCACGCAAAAAGCATATA 57.917 32.000 0.00 0.00 46.13 0.86
43 44 5.953183 TGAAATCTCACGCAAAAAGCATAT 58.047 33.333 0.00 0.00 46.13 1.78
44 45 5.369685 TGAAATCTCACGCAAAAAGCATA 57.630 34.783 0.00 0.00 46.13 3.14
45 46 4.232221 CTGAAATCTCACGCAAAAAGCAT 58.768 39.130 0.00 0.00 46.13 3.79
46 47 3.631144 CTGAAATCTCACGCAAAAAGCA 58.369 40.909 0.00 0.00 46.13 3.91
47 48 2.406357 GCTGAAATCTCACGCAAAAAGC 59.594 45.455 0.00 0.00 40.87 3.51
48 49 3.667261 CAGCTGAAATCTCACGCAAAAAG 59.333 43.478 8.42 0.00 31.78 2.27
49 50 3.066621 ACAGCTGAAATCTCACGCAAAAA 59.933 39.130 23.35 0.00 31.78 1.94
50 51 2.618241 ACAGCTGAAATCTCACGCAAAA 59.382 40.909 23.35 0.00 31.78 2.44
51 52 2.221169 ACAGCTGAAATCTCACGCAAA 58.779 42.857 23.35 0.00 31.78 3.68
52 53 1.882912 ACAGCTGAAATCTCACGCAA 58.117 45.000 23.35 0.00 31.78 4.85
53 54 1.800586 GAACAGCTGAAATCTCACGCA 59.199 47.619 23.35 0.00 31.78 5.24
54 55 1.800586 TGAACAGCTGAAATCTCACGC 59.199 47.619 23.35 0.00 0.00 5.34
55 56 4.472691 TTTGAACAGCTGAAATCTCACG 57.527 40.909 23.35 0.00 0.00 4.35
56 57 6.268566 ACTTTTTGAACAGCTGAAATCTCAC 58.731 36.000 23.35 2.86 0.00 3.51
57 58 6.455360 ACTTTTTGAACAGCTGAAATCTCA 57.545 33.333 23.35 11.38 0.00 3.27
58 59 7.865707 TCTACTTTTTGAACAGCTGAAATCTC 58.134 34.615 23.35 8.91 0.00 2.75
59 60 7.807977 TCTACTTTTTGAACAGCTGAAATCT 57.192 32.000 23.35 0.00 0.00 2.40
60 61 9.468532 AAATCTACTTTTTGAACAGCTGAAATC 57.531 29.630 23.35 15.48 0.00 2.17
63 64 9.897744 CATAAATCTACTTTTTGAACAGCTGAA 57.102 29.630 23.35 0.48 30.05 3.02
64 65 9.066892 ACATAAATCTACTTTTTGAACAGCTGA 57.933 29.630 23.35 0.00 32.19 4.26
65 66 9.683069 AACATAAATCTACTTTTTGAACAGCTG 57.317 29.630 13.48 13.48 32.19 4.24
66 67 9.683069 CAACATAAATCTACTTTTTGAACAGCT 57.317 29.630 0.00 0.00 32.19 4.24
67 68 9.677567 TCAACATAAATCTACTTTTTGAACAGC 57.322 29.630 0.00 0.00 32.19 4.40
111 112 8.988934 GCCTCGATTAAATATGTTCTACAATGA 58.011 33.333 0.00 0.00 0.00 2.57
112 113 7.952101 CGCCTCGATTAAATATGTTCTACAATG 59.048 37.037 0.00 0.00 0.00 2.82
113 114 7.656137 ACGCCTCGATTAAATATGTTCTACAAT 59.344 33.333 0.00 0.00 0.00 2.71
114 115 6.982141 ACGCCTCGATTAAATATGTTCTACAA 59.018 34.615 0.00 0.00 0.00 2.41
115 116 6.419710 CACGCCTCGATTAAATATGTTCTACA 59.580 38.462 0.00 0.00 0.00 2.74
116 117 6.420008 ACACGCCTCGATTAAATATGTTCTAC 59.580 38.462 0.00 0.00 0.00 2.59
117 118 6.419710 CACACGCCTCGATTAAATATGTTCTA 59.580 38.462 0.00 0.00 0.00 2.10
118 119 5.234329 CACACGCCTCGATTAAATATGTTCT 59.766 40.000 0.00 0.00 0.00 3.01
119 120 5.006358 ACACACGCCTCGATTAAATATGTTC 59.994 40.000 0.00 0.00 0.00 3.18
120 121 4.873827 ACACACGCCTCGATTAAATATGTT 59.126 37.500 0.00 0.00 0.00 2.71
121 122 4.270084 CACACACGCCTCGATTAAATATGT 59.730 41.667 0.00 0.00 0.00 2.29
122 123 4.318760 CCACACACGCCTCGATTAAATATG 60.319 45.833 0.00 0.00 0.00 1.78
123 124 3.807622 CCACACACGCCTCGATTAAATAT 59.192 43.478 0.00 0.00 0.00 1.28
124 125 3.191669 CCACACACGCCTCGATTAAATA 58.808 45.455 0.00 0.00 0.00 1.40
125 126 2.006888 CCACACACGCCTCGATTAAAT 58.993 47.619 0.00 0.00 0.00 1.40
126 127 1.434555 CCACACACGCCTCGATTAAA 58.565 50.000 0.00 0.00 0.00 1.52
127 128 1.017177 GCCACACACGCCTCGATTAA 61.017 55.000 0.00 0.00 0.00 1.40
128 129 1.447140 GCCACACACGCCTCGATTA 60.447 57.895 0.00 0.00 0.00 1.75
129 130 2.742372 GCCACACACGCCTCGATT 60.742 61.111 0.00 0.00 0.00 3.34
130 131 4.002506 TGCCACACACGCCTCGAT 62.003 61.111 0.00 0.00 0.00 3.59
131 132 4.961511 GTGCCACACACGCCTCGA 62.962 66.667 0.00 0.00 40.07 4.04
138 139 1.206578 GTATGCACGTGCCACACAC 59.793 57.895 35.72 21.37 46.45 3.82
139 140 0.533978 AAGTATGCACGTGCCACACA 60.534 50.000 35.72 18.87 41.18 3.72
140 141 1.127951 GTAAGTATGCACGTGCCACAC 59.872 52.381 35.72 27.79 41.18 3.82
141 142 1.001520 AGTAAGTATGCACGTGCCACA 59.998 47.619 35.72 19.66 41.18 4.17
142 143 1.722011 AGTAAGTATGCACGTGCCAC 58.278 50.000 35.72 30.44 41.18 5.01
143 144 2.494471 ACTAGTAAGTATGCACGTGCCA 59.506 45.455 35.72 24.03 35.40 4.92
144 145 2.858344 CACTAGTAAGTATGCACGTGCC 59.142 50.000 35.72 21.46 35.62 5.01
145 146 3.766151 TCACTAGTAAGTATGCACGTGC 58.234 45.455 33.11 33.11 36.52 5.34
146 147 4.982999 ACTCACTAGTAAGTATGCACGTG 58.017 43.478 12.28 12.28 33.48 4.49
147 148 5.640189 AACTCACTAGTAAGTATGCACGT 57.360 39.130 0.00 0.00 33.75 4.49
148 149 6.549061 TGTAACTCACTAGTAAGTATGCACG 58.451 40.000 0.00 0.00 33.75 5.34
149 150 8.027771 AGTTGTAACTCACTAGTAAGTATGCAC 58.972 37.037 0.00 0.00 33.75 4.57
150 151 8.118976 AGTTGTAACTCACTAGTAAGTATGCA 57.881 34.615 0.00 0.00 33.75 3.96
151 152 9.500864 GTAGTTGTAACTCACTAGTAAGTATGC 57.499 37.037 0.00 0.00 40.37 3.14
155 156 8.915057 TGAGTAGTTGTAACTCACTAGTAAGT 57.085 34.615 0.00 0.00 46.38 2.24
196 197 4.201685 GCATTTTTGAGCAAGCATCACATC 60.202 41.667 0.00 0.00 0.00 3.06
200 201 2.037381 TGGCATTTTTGAGCAAGCATCA 59.963 40.909 0.00 0.00 0.00 3.07
254 256 7.545265 GTCTAATGGCATTTTTGAGCAAACATA 59.455 33.333 19.21 0.00 0.00 2.29
301 303 4.890158 ATCATATAACATGGTCAGCGGA 57.110 40.909 0.00 0.00 0.00 5.54
322 324 6.608002 GGAATGTGGGTGTATGGGTATTTTTA 59.392 38.462 0.00 0.00 0.00 1.52
333 336 3.846588 AGAGAACTGGAATGTGGGTGTAT 59.153 43.478 0.00 0.00 0.00 2.29
345 348 4.753516 TTGTGACAAAGAGAGAACTGGA 57.246 40.909 0.00 0.00 0.00 3.86
360 363 2.423538 GGCCCACACTTATCATTGTGAC 59.576 50.000 3.30 0.00 45.03 3.67
449 452 4.080356 TCTCAGCATAATAAAGTGTGGGCT 60.080 41.667 0.00 0.00 0.00 5.19
464 468 2.450500 ACCTCTCCCTCTATCTCAGCAT 59.549 50.000 0.00 0.00 0.00 3.79
466 470 2.158534 TCACCTCTCCCTCTATCTCAGC 60.159 54.545 0.00 0.00 0.00 4.26
467 471 3.117701 TGTCACCTCTCCCTCTATCTCAG 60.118 52.174 0.00 0.00 0.00 3.35
484 488 3.081061 TGCCTATGAACCAACATGTCAC 58.919 45.455 0.00 0.00 0.00 3.67
524 528 2.031682 GTCAGCTCAAATCGTGTTTGCT 60.032 45.455 9.97 4.07 32.61 3.91
532 536 5.292834 ACATCATTACAGTCAGCTCAAATCG 59.707 40.000 0.00 0.00 0.00 3.34
546 550 5.936187 AAATGCCAATGGACATCATTACA 57.064 34.783 2.05 0.00 43.70 2.41
573 578 4.793071 CCGTCACTTTGTTATGCAAATGA 58.207 39.130 0.00 0.00 45.00 2.57
577 582 1.950216 TGCCGTCACTTTGTTATGCAA 59.050 42.857 0.00 0.00 34.87 4.08
608 613 7.094205 CCACTACTTGCCATTAGAGTTTTCAAT 60.094 37.037 0.00 0.00 0.00 2.57
616 621 4.141620 ACATCCCACTACTTGCCATTAGAG 60.142 45.833 0.00 0.00 0.00 2.43
634 645 4.887071 TCATTTATGCCACTGGTTACATCC 59.113 41.667 0.00 0.00 0.00 3.51
742 753 7.511268 TCACATGTCCATCTAATCATCAATGA 58.489 34.615 0.00 0.00 41.70 2.57
743 754 7.739498 TCACATGTCCATCTAATCATCAATG 57.261 36.000 0.00 0.00 0.00 2.82
744 755 8.756486 TTTCACATGTCCATCTAATCATCAAT 57.244 30.769 0.00 0.00 0.00 2.57
745 756 8.756486 ATTTCACATGTCCATCTAATCATCAA 57.244 30.769 0.00 0.00 0.00 2.57
746 757 7.446319 GGATTTCACATGTCCATCTAATCATCA 59.554 37.037 0.00 0.00 32.23 3.07
747 758 7.094463 GGGATTTCACATGTCCATCTAATCATC 60.094 40.741 0.00 0.00 33.62 2.92
748 759 6.718454 GGGATTTCACATGTCCATCTAATCAT 59.282 38.462 0.00 0.00 33.62 2.45
749 760 6.064060 GGGATTTCACATGTCCATCTAATCA 58.936 40.000 0.00 0.00 33.62 2.57
750 761 5.180117 CGGGATTTCACATGTCCATCTAATC 59.820 44.000 0.00 0.00 33.62 1.75
751 762 5.065914 CGGGATTTCACATGTCCATCTAAT 58.934 41.667 0.00 0.00 33.62 1.73
752 763 4.450976 CGGGATTTCACATGTCCATCTAA 58.549 43.478 0.00 0.00 33.62 2.10
753 764 3.744214 GCGGGATTTCACATGTCCATCTA 60.744 47.826 0.00 0.00 33.62 1.98
754 765 2.923121 CGGGATTTCACATGTCCATCT 58.077 47.619 0.00 0.00 33.62 2.90
755 766 1.334869 GCGGGATTTCACATGTCCATC 59.665 52.381 0.00 0.00 33.62 3.51
756 767 1.340893 TGCGGGATTTCACATGTCCAT 60.341 47.619 0.00 0.00 33.62 3.41
757 768 0.037447 TGCGGGATTTCACATGTCCA 59.963 50.000 0.00 0.00 33.62 4.02
758 769 1.173043 TTGCGGGATTTCACATGTCC 58.827 50.000 0.00 0.00 0.00 4.02
759 770 3.296322 TTTTGCGGGATTTCACATGTC 57.704 42.857 0.00 0.00 0.00 3.06
760 771 3.742433 TTTTTGCGGGATTTCACATGT 57.258 38.095 0.00 0.00 0.00 3.21
779 790 9.492973 CCCTTTCACATATTCATCTTTTTGTTT 57.507 29.630 0.00 0.00 0.00 2.83
780 791 7.603784 GCCCTTTCACATATTCATCTTTTTGTT 59.396 33.333 0.00 0.00 0.00 2.83
781 792 7.099120 GCCCTTTCACATATTCATCTTTTTGT 58.901 34.615 0.00 0.00 0.00 2.83
782 793 6.536224 GGCCCTTTCACATATTCATCTTTTTG 59.464 38.462 0.00 0.00 0.00 2.44
783 794 6.213195 TGGCCCTTTCACATATTCATCTTTTT 59.787 34.615 0.00 0.00 0.00 1.94
784 795 5.721000 TGGCCCTTTCACATATTCATCTTTT 59.279 36.000 0.00 0.00 0.00 2.27
785 796 5.127682 GTGGCCCTTTCACATATTCATCTTT 59.872 40.000 0.00 0.00 35.39 2.52
786 797 4.646492 GTGGCCCTTTCACATATTCATCTT 59.354 41.667 0.00 0.00 35.39 2.40
794 805 1.377987 GCGGTGGCCCTTTCACATA 60.378 57.895 0.00 0.00 36.90 2.29
857 868 3.103911 GCGTCCAACGGTCGAGTG 61.104 66.667 3.85 0.00 42.82 3.51
871 882 2.722201 GGGAAGGGATCGTGAGCGT 61.722 63.158 0.00 0.00 39.49 5.07
875 886 0.042731 AGGAAGGGAAGGGATCGTGA 59.957 55.000 0.00 0.00 0.00 4.35
881 892 1.296002 GGCTTAAGGAAGGGAAGGGA 58.704 55.000 4.29 0.00 32.84 4.20
896 907 4.529219 TGATGATCCGCGCGGCTT 62.529 61.111 42.78 31.68 34.68 4.35
927 962 0.453390 GGAGGCAGAAATGGAAAGCG 59.547 55.000 0.00 0.00 0.00 4.68
928 963 0.820226 GGGAGGCAGAAATGGAAAGC 59.180 55.000 0.00 0.00 0.00 3.51
929 964 1.098050 CGGGAGGCAGAAATGGAAAG 58.902 55.000 0.00 0.00 0.00 2.62
945 980 2.027385 TGATGTGAGATCAGACTCGGG 58.973 52.381 0.00 0.00 39.49 5.14
953 988 4.040829 AGGTTGTGAGTTGATGTGAGATCA 59.959 41.667 0.00 0.00 0.00 2.92
971 1006 2.833794 TCGTTCTGAGTTGGAAGGTTG 58.166 47.619 0.00 0.00 32.54 3.77
982 1017 3.365364 GCCATTGGAAGTTTCGTTCTGAG 60.365 47.826 6.95 0.00 0.00 3.35
991 1026 2.635443 CCGCCGCCATTGGAAGTTT 61.635 57.895 6.95 0.00 0.00 2.66
1233 1268 2.758737 AGGTAGAAGGCGTCCCGG 60.759 66.667 0.00 0.00 35.76 5.73
1672 1707 2.052690 TCTCCTAGGCGCACAGGAC 61.053 63.158 21.59 0.00 35.99 3.85
1689 1724 3.927142 ACCGAAAACTCAGATCGATTGTC 59.073 43.478 0.00 0.00 38.82 3.18
1694 1729 2.557056 ACTCACCGAAAACTCAGATCGA 59.443 45.455 0.00 0.00 38.82 3.59
1813 1881 7.573656 CGTCATGGATCAGAACAAATTTGAAGA 60.574 37.037 24.64 15.01 0.00 2.87
1875 1943 2.092968 TCCTCCGAATGAATTCACCAGG 60.093 50.000 11.07 13.61 36.61 4.45
1876 1944 3.266510 TCCTCCGAATGAATTCACCAG 57.733 47.619 11.07 4.66 36.61 4.00
1877 1945 3.712016 TTCCTCCGAATGAATTCACCA 57.288 42.857 11.07 0.00 36.61 4.17
1878 1946 3.181510 CGTTTCCTCCGAATGAATTCACC 60.182 47.826 11.07 4.97 36.61 4.02
1879 1947 3.682858 TCGTTTCCTCCGAATGAATTCAC 59.317 43.478 11.07 0.00 36.61 3.18
1880 1948 3.932822 TCGTTTCCTCCGAATGAATTCA 58.067 40.909 11.26 11.26 36.61 2.57
1881 1949 4.332819 ACATCGTTTCCTCCGAATGAATTC 59.667 41.667 0.00 0.00 37.93 2.17
1882 1950 4.094887 CACATCGTTTCCTCCGAATGAATT 59.905 41.667 0.00 0.00 37.93 2.17
1883 1951 3.623060 CACATCGTTTCCTCCGAATGAAT 59.377 43.478 0.00 0.00 37.93 2.57
1884 1952 3.000041 CACATCGTTTCCTCCGAATGAA 59.000 45.455 0.00 0.00 37.93 2.57
1885 1953 2.616960 CACATCGTTTCCTCCGAATGA 58.383 47.619 0.00 0.00 37.93 2.57
1886 1954 1.062587 GCACATCGTTTCCTCCGAATG 59.937 52.381 0.00 0.00 37.93 2.67
1887 1955 1.066143 AGCACATCGTTTCCTCCGAAT 60.066 47.619 0.00 0.00 37.93 3.34
1888 1956 0.320374 AGCACATCGTTTCCTCCGAA 59.680 50.000 0.00 0.00 37.93 4.30
1889 1957 0.320374 AAGCACATCGTTTCCTCCGA 59.680 50.000 0.00 0.00 38.89 4.55
1890 1958 0.721718 GAAGCACATCGTTTCCTCCG 59.278 55.000 0.00 0.00 0.00 4.63
1891 1959 2.100605 AGAAGCACATCGTTTCCTCC 57.899 50.000 0.00 0.00 35.55 4.30
1892 1960 3.190874 CCTAGAAGCACATCGTTTCCTC 58.809 50.000 0.00 0.00 35.55 3.71
1893 1961 2.567615 ACCTAGAAGCACATCGTTTCCT 59.432 45.455 0.00 0.00 35.55 3.36
1894 1962 2.930682 GACCTAGAAGCACATCGTTTCC 59.069 50.000 0.00 0.00 35.55 3.13
1895 1963 2.599082 CGACCTAGAAGCACATCGTTTC 59.401 50.000 0.00 0.00 35.20 2.78
1896 1964 2.607187 CGACCTAGAAGCACATCGTTT 58.393 47.619 0.00 0.00 0.00 3.60
1897 1965 1.736032 GCGACCTAGAAGCACATCGTT 60.736 52.381 0.00 0.00 32.32 3.85
1898 1966 0.179134 GCGACCTAGAAGCACATCGT 60.179 55.000 0.00 0.00 32.32 3.73
1899 1967 0.179137 TGCGACCTAGAAGCACATCG 60.179 55.000 0.00 0.00 35.81 3.84
1900 1968 1.565305 CTGCGACCTAGAAGCACATC 58.435 55.000 0.00 0.00 36.79 3.06
1901 1969 0.176680 CCTGCGACCTAGAAGCACAT 59.823 55.000 0.00 0.00 36.79 3.21
1902 1970 1.591703 CCTGCGACCTAGAAGCACA 59.408 57.895 0.00 0.00 36.79 4.57
1903 1971 1.811679 GCCTGCGACCTAGAAGCAC 60.812 63.158 0.00 0.00 36.79 4.40
1904 1972 2.579201 GCCTGCGACCTAGAAGCA 59.421 61.111 0.00 0.00 39.25 3.91
1905 1973 2.202946 GGCCTGCGACCTAGAAGC 60.203 66.667 0.00 0.00 0.00 3.86
1906 1974 2.060980 AGGGCCTGCGACCTAGAAG 61.061 63.158 4.50 0.00 34.71 2.85
1907 1975 2.038975 AGGGCCTGCGACCTAGAA 59.961 61.111 4.50 0.00 34.71 2.10
1908 1976 2.759973 CAGGGCCTGCGACCTAGA 60.760 66.667 22.68 0.00 34.71 2.43
1909 1977 3.854669 CCAGGGCCTGCGACCTAG 61.855 72.222 28.51 8.71 34.71 3.02
1910 1978 4.715130 ACCAGGGCCTGCGACCTA 62.715 66.667 28.51 0.00 34.71 3.08
1913 1981 3.628646 ATTCACCAGGGCCTGCGAC 62.629 63.158 28.51 0.00 0.00 5.19
1914 1982 2.905996 AATTCACCAGGGCCTGCGA 61.906 57.895 28.51 22.17 0.00 5.10
1915 1983 2.361610 AATTCACCAGGGCCTGCG 60.362 61.111 28.51 22.11 0.00 5.18
1916 1984 0.685458 ATCAATTCACCAGGGCCTGC 60.685 55.000 28.51 0.00 0.00 4.85
1917 1985 1.753073 GAATCAATTCACCAGGGCCTG 59.247 52.381 27.04 27.04 36.80 4.85
1918 1986 1.683011 CGAATCAATTCACCAGGGCCT 60.683 52.381 0.00 0.00 36.61 5.19
1919 1987 0.740737 CGAATCAATTCACCAGGGCC 59.259 55.000 0.00 0.00 36.61 5.80
1920 1988 0.740737 CCGAATCAATTCACCAGGGC 59.259 55.000 3.81 0.00 36.61 5.19
1921 1989 2.292267 CTCCGAATCAATTCACCAGGG 58.708 52.381 3.81 0.00 36.61 4.45
1962 2030 3.541996 ATAACACCATGATGTCTGCGA 57.458 42.857 0.00 0.00 30.55 5.10
1968 2036 6.602803 TGTCTATGCAAATAACACCATGATGT 59.397 34.615 0.00 0.00 0.00 3.06
1970 2038 7.056006 TCTGTCTATGCAAATAACACCATGAT 58.944 34.615 0.00 0.00 0.00 2.45
2037 2106 1.227380 CATCTCGGGGCGGAGAAAG 60.227 63.158 10.37 4.03 45.53 2.62
2092 2161 2.941064 GAGTTGCAGCTGCTATGAATGA 59.059 45.455 36.61 13.65 42.66 2.57
2187 2256 5.716228 AGCACATGGAGAATTTCAACCATAA 59.284 36.000 20.00 2.46 40.55 1.90
2284 2404 1.153726 ACAACGACGAGTGCACACA 60.154 52.632 21.04 0.00 0.00 3.72
2285 2405 1.272715 CACAACGACGAGTGCACAC 59.727 57.895 21.04 12.49 0.00 3.82
2286 2406 1.880796 CCACAACGACGAGTGCACA 60.881 57.895 21.04 0.00 34.48 4.57
2287 2407 1.426041 AACCACAACGACGAGTGCAC 61.426 55.000 9.40 9.40 34.48 4.57
2495 2680 8.149647 TGTTCCAGAAGTATGCAAAATTTCAAT 58.850 29.630 9.38 0.00 0.00 2.57
2600 2785 1.481363 TCAGGTGTGAACCACGTTACA 59.519 47.619 0.00 0.00 45.52 2.41
2652 2837 9.897744 CTGATGTTAGAACAACAATACAACAAT 57.102 29.630 6.78 0.00 40.46 2.71
2653 2838 9.114952 TCTGATGTTAGAACAACAATACAACAA 57.885 29.630 6.78 0.00 40.46 2.83
2654 2839 8.556194 GTCTGATGTTAGAACAACAATACAACA 58.444 33.333 6.78 0.00 40.46 3.33
2655 2840 8.015658 GGTCTGATGTTAGAACAACAATACAAC 58.984 37.037 6.78 2.00 40.46 3.32
2656 2841 7.717436 TGGTCTGATGTTAGAACAACAATACAA 59.283 33.333 6.78 0.62 41.21 2.41
2657 2842 7.172532 GTGGTCTGATGTTAGAACAACAATACA 59.827 37.037 6.78 3.78 45.30 2.29
2658 2843 7.519002 GTGGTCTGATGTTAGAACAACAATAC 58.481 38.462 6.78 7.63 45.30 1.89
2659 2844 7.667043 GTGGTCTGATGTTAGAACAACAATA 57.333 36.000 6.78 0.00 45.30 1.90


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

AutoCloner maintained by Alex Coulton.