Multiple sequence alignment - TraesCS5A01G309100

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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 TraesCS5A01G309100 chr5A 100.000 3458 0 0 1 3458 521357252 521360709 0.000000e+00 6386.0
1 TraesCS5A01G309100 chr5A 77.016 1414 274 39 997 2387 521696497 521697882 0.000000e+00 763.0
2 TraesCS5A01G309100 chr5A 94.472 398 21 1 2748 3145 123610649 123610253 2.280000e-171 612.0
3 TraesCS5A01G309100 chr5A 93.300 403 26 1 2743 3145 124917894 124917493 8.260000e-166 593.0
4 TraesCS5A01G309100 chr5A 95.918 294 12 0 3113 3406 123610318 123610025 8.680000e-131 477.0
5 TraesCS5A01G309100 chr5A 95.578 294 13 0 3113 3406 124917558 124917265 4.040000e-129 472.0
6 TraesCS5A01G309100 chr5A 95.312 64 3 0 3115 3178 521360333 521360396 6.110000e-18 102.0
7 TraesCS5A01G309100 chr5A 96.078 51 2 0 3408 3458 123609984 123609934 2.210000e-12 84.2
8 TraesCS5A01G309100 chr5D 92.482 2248 108 27 547 2746 410075114 410077348 0.000000e+00 3158.0
9 TraesCS5A01G309100 chr5D 77.348 1395 266 36 997 2366 410200737 410202106 0.000000e+00 780.0
10 TraesCS5A01G309100 chr5D 74.387 1386 308 32 1000 2366 545207504 545208861 1.810000e-152 549.0
11 TraesCS5A01G309100 chr5D 88.034 351 20 9 134 478 410074752 410075086 2.500000e-106 396.0
12 TraesCS5A01G309100 chr5D 91.336 277 17 3 2748 3019 433247938 433248212 4.210000e-99 372.0
13 TraesCS5A01G309100 chr5D 81.839 446 37 26 2340 2746 419759648 419760088 5.530000e-88 335.0
14 TraesCS5A01G309100 chr5D 96.133 181 6 1 3226 3406 433303737 433303916 9.390000e-76 294.0
15 TraesCS5A01G309100 chr5D 87.826 230 8 6 2534 2746 410077557 410077783 5.730000e-63 252.0
16 TraesCS5A01G309100 chr5D 94.505 91 5 0 40 130 492222074 492221984 1.290000e-29 141.0
17 TraesCS5A01G309100 chr5B 92.044 2250 130 28 536 2746 491878908 491881147 0.000000e+00 3118.0
18 TraesCS5A01G309100 chr5B 79.023 1187 220 24 1187 2366 491952546 491953710 0.000000e+00 785.0
19 TraesCS5A01G309100 chr5B 87.744 359 19 14 129 478 491878240 491878582 2.500000e-106 396.0
20 TraesCS5A01G309100 chr5B 90.196 102 10 0 28 129 72256162 72256061 2.170000e-27 134.0
21 TraesCS5A01G309100 chr5B 90.196 102 10 0 28 129 72823501 72823602 2.170000e-27 134.0
22 TraesCS5A01G309100 chrUn 94.221 398 22 1 2748 3145 317095249 317094853 1.060000e-169 606.0
23 TraesCS5A01G309100 chrUn 94.015 401 23 1 2745 3145 317132363 317132762 1.060000e-169 606.0
24 TraesCS5A01G309100 chrUn 94.221 398 22 1 2748 3145 373027195 373026799 1.060000e-169 606.0
25 TraesCS5A01G309100 chrUn 94.352 301 10 3 3115 3409 317094916 317094617 4.070000e-124 455.0
26 TraesCS5A01G309100 chrUn 94.631 298 9 3 3115 3406 317132699 317132995 4.070000e-124 455.0
27 TraesCS5A01G309100 chrUn 94.352 301 10 3 3115 3409 373026862 373026563 4.070000e-124 455.0
28 TraesCS5A01G309100 chr4A 93.970 398 23 1 2748 3145 391548788 391548392 4.940000e-168 601.0
29 TraesCS5A01G309100 chr4A 92.881 295 11 6 3115 3409 391548455 391548171 1.480000e-113 420.0
30 TraesCS5A01G309100 chr7D 93.216 398 26 1 2748 3145 321088176 321087780 4.970000e-163 584.0
31 TraesCS5A01G309100 chr7D 93.370 362 23 1 2780 3141 48492228 48491868 5.080000e-148 534.0
32 TraesCS5A01G309100 chr7D 95.932 295 12 0 3115 3409 321087843 321087549 2.410000e-131 479.0
33 TraesCS5A01G309100 chr7D 95.593 295 13 0 3115 3409 48491927 48491633 1.120000e-129 473.0
34 TraesCS5A01G309100 chr7D 94.444 90 5 0 40 129 628640544 628640633 4.650000e-29 139.0
35 TraesCS5A01G309100 chr6B 94.118 102 6 0 28 129 531006417 531006316 4.620000e-34 156.0
36 TraesCS5A01G309100 chr3B 94.565 92 5 0 40 131 700336547 700336456 3.600000e-30 143.0
37 TraesCS5A01G309100 chr3D 91.919 99 8 0 28 126 168506502 168506600 4.650000e-29 139.0
38 TraesCS5A01G309100 chr3D 92.391 92 6 1 38 129 252330963 252330873 2.800000e-26 130.0
39 TraesCS5A01G309100 chr2A 91.176 102 9 0 28 129 773281196 773281297 4.650000e-29 139.0
40 TraesCS5A01G309100 chr2D 95.349 43 2 0 2743 2785 301377928 301377886 6.190000e-08 69.4


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 TraesCS5A01G309100 chr5A 521357252 521360709 3457 False 3244.000000 6386 97.656000 1 3458 2 chr5A.!!$F2 3457
1 TraesCS5A01G309100 chr5A 521696497 521697882 1385 False 763.000000 763 77.016000 997 2387 1 chr5A.!!$F1 1390
2 TraesCS5A01G309100 chr5A 124917265 124917894 629 True 532.500000 593 94.439000 2743 3406 2 chr5A.!!$R2 663
3 TraesCS5A01G309100 chr5A 123609934 123610649 715 True 391.066667 612 95.489333 2748 3458 3 chr5A.!!$R1 710
4 TraesCS5A01G309100 chr5D 410074752 410077783 3031 False 1268.666667 3158 89.447333 134 2746 3 chr5D.!!$F6 2612
5 TraesCS5A01G309100 chr5D 410200737 410202106 1369 False 780.000000 780 77.348000 997 2366 1 chr5D.!!$F1 1369
6 TraesCS5A01G309100 chr5D 545207504 545208861 1357 False 549.000000 549 74.387000 1000 2366 1 chr5D.!!$F5 1366
7 TraesCS5A01G309100 chr5B 491878240 491881147 2907 False 1757.000000 3118 89.894000 129 2746 2 chr5B.!!$F3 2617
8 TraesCS5A01G309100 chr5B 491952546 491953710 1164 False 785.000000 785 79.023000 1187 2366 1 chr5B.!!$F2 1179
9 TraesCS5A01G309100 chrUn 317094617 317095249 632 True 530.500000 606 94.286500 2748 3409 2 chrUn.!!$R1 661
10 TraesCS5A01G309100 chrUn 317132363 317132995 632 False 530.500000 606 94.323000 2745 3406 2 chrUn.!!$F1 661
11 TraesCS5A01G309100 chrUn 373026563 373027195 632 True 530.500000 606 94.286500 2748 3409 2 chrUn.!!$R2 661
12 TraesCS5A01G309100 chr4A 391548171 391548788 617 True 510.500000 601 93.425500 2748 3409 2 chr4A.!!$R1 661
13 TraesCS5A01G309100 chr7D 321087549 321088176 627 True 531.500000 584 94.574000 2748 3409 2 chr7D.!!$R2 661
14 TraesCS5A01G309100 chr7D 48491633 48492228 595 True 503.500000 534 94.481500 2780 3409 2 chr7D.!!$R1 629

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
126 127 0.033504 TGAACTCCTGACTTCGCCAC 59.966 55.0 0.0 0.0 0.00 5.01 F
1031 1339 0.174389 CACAGAGACCACATCCTCGG 59.826 60.0 0.0 0.0 34.75 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1437 1760 1.080025 GCCCGTCTTAGCGAACAGT 60.080 57.895 0.0 0.0 0.0 3.55 R
2820 3640 0.326618 CTGGGGTAGAGGATGTGGGT 60.327 60.000 0.0 0.0 0.0 4.51 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
20 21 3.088194 GTGTTCTGTGTAGTCGGTTGA 57.912 47.619 0.00 0.00 0.00 3.18
21 22 2.793232 GTGTTCTGTGTAGTCGGTTGAC 59.207 50.000 0.00 0.00 45.86 3.18
33 34 4.905412 GTCGGTTGACTACACAGAAATC 57.095 45.455 0.00 0.00 42.08 2.17
34 35 3.678548 GTCGGTTGACTACACAGAAATCC 59.321 47.826 0.00 0.00 42.08 3.01
35 36 3.576982 TCGGTTGACTACACAGAAATCCT 59.423 43.478 0.00 0.00 0.00 3.24
36 37 4.039973 TCGGTTGACTACACAGAAATCCTT 59.960 41.667 0.00 0.00 0.00 3.36
37 38 4.389077 CGGTTGACTACACAGAAATCCTTC 59.611 45.833 0.00 0.00 0.00 3.46
38 39 5.305585 GGTTGACTACACAGAAATCCTTCA 58.694 41.667 0.00 0.00 33.64 3.02
39 40 5.763204 GGTTGACTACACAGAAATCCTTCAA 59.237 40.000 0.00 0.00 33.64 2.69
40 41 6.262273 GGTTGACTACACAGAAATCCTTCAAA 59.738 38.462 0.00 0.00 33.64 2.69
41 42 7.201785 GGTTGACTACACAGAAATCCTTCAAAA 60.202 37.037 0.00 0.00 33.64 2.44
42 43 7.873719 TGACTACACAGAAATCCTTCAAAAA 57.126 32.000 0.00 0.00 33.64 1.94
81 82 8.862325 AATCCAAATACAACTACTTGACATCA 57.138 30.769 0.00 0.00 0.00 3.07
82 83 7.667043 TCCAAATACAACTACTTGACATCAC 57.333 36.000 0.00 0.00 0.00 3.06
83 84 7.220740 TCCAAATACAACTACTTGACATCACA 58.779 34.615 0.00 0.00 0.00 3.58
84 85 7.717436 TCCAAATACAACTACTTGACATCACAA 59.283 33.333 0.00 0.00 0.00 3.33
85 86 8.514594 CCAAATACAACTACTTGACATCACAAT 58.485 33.333 0.00 0.00 0.00 2.71
86 87 9.897744 CAAATACAACTACTTGACATCACAATT 57.102 29.630 0.00 0.00 0.00 2.32
96 97 8.086851 ACTTGACATCACAATTTTAAATTGCC 57.913 30.769 24.90 11.30 32.55 4.52
97 98 7.714377 ACTTGACATCACAATTTTAAATTGCCA 59.286 29.630 24.90 14.78 32.55 4.92
98 99 8.618702 TTGACATCACAATTTTAAATTGCCAT 57.381 26.923 24.90 16.08 32.55 4.40
99 100 8.254178 TGACATCACAATTTTAAATTGCCATC 57.746 30.769 24.90 16.90 32.55 3.51
100 101 7.876582 TGACATCACAATTTTAAATTGCCATCA 59.123 29.630 24.90 18.66 32.55 3.07
101 102 8.031848 ACATCACAATTTTAAATTGCCATCAC 57.968 30.769 24.90 0.00 32.55 3.06
102 103 7.660617 ACATCACAATTTTAAATTGCCATCACA 59.339 29.630 24.90 6.63 32.55 3.58
103 104 8.504815 CATCACAATTTTAAATTGCCATCACAA 58.495 29.630 24.90 7.05 32.55 3.33
104 105 7.859598 TCACAATTTTAAATTGCCATCACAAC 58.140 30.769 24.90 0.00 32.55 3.32
105 106 7.714377 TCACAATTTTAAATTGCCATCACAACT 59.286 29.630 24.90 4.22 32.55 3.16
106 107 8.344098 CACAATTTTAAATTGCCATCACAACTT 58.656 29.630 24.90 3.78 32.55 2.66
107 108 8.901793 ACAATTTTAAATTGCCATCACAACTTT 58.098 25.926 24.90 3.60 32.55 2.66
108 109 9.171701 CAATTTTAAATTGCCATCACAACTTTG 57.828 29.630 16.05 0.00 31.03 2.77
109 110 8.674263 ATTTTAAATTGCCATCACAACTTTGA 57.326 26.923 0.00 0.00 31.03 2.69
110 111 8.498054 TTTTAAATTGCCATCACAACTTTGAA 57.502 26.923 0.00 0.00 31.03 2.69
111 112 5.989551 AAATTGCCATCACAACTTTGAAC 57.010 34.783 0.00 0.00 31.03 3.18
112 113 4.942761 ATTGCCATCACAACTTTGAACT 57.057 36.364 0.00 0.00 31.03 3.01
113 114 3.988379 TGCCATCACAACTTTGAACTC 57.012 42.857 0.00 0.00 0.00 3.01
114 115 2.622942 TGCCATCACAACTTTGAACTCC 59.377 45.455 0.00 0.00 0.00 3.85
115 116 2.887152 GCCATCACAACTTTGAACTCCT 59.113 45.455 0.00 0.00 0.00 3.69
116 117 3.304928 GCCATCACAACTTTGAACTCCTG 60.305 47.826 0.00 0.00 0.00 3.86
117 118 4.136796 CCATCACAACTTTGAACTCCTGA 58.863 43.478 0.00 0.00 0.00 3.86
118 119 4.023707 CCATCACAACTTTGAACTCCTGAC 60.024 45.833 0.00 0.00 0.00 3.51
119 120 4.487714 TCACAACTTTGAACTCCTGACT 57.512 40.909 0.00 0.00 0.00 3.41
120 121 4.843728 TCACAACTTTGAACTCCTGACTT 58.156 39.130 0.00 0.00 0.00 3.01
121 122 4.876107 TCACAACTTTGAACTCCTGACTTC 59.124 41.667 0.00 0.00 0.00 3.01
122 123 3.871594 ACAACTTTGAACTCCTGACTTCG 59.128 43.478 0.00 0.00 0.00 3.79
123 124 2.484889 ACTTTGAACTCCTGACTTCGC 58.515 47.619 0.00 0.00 0.00 4.70
124 125 1.801178 CTTTGAACTCCTGACTTCGCC 59.199 52.381 0.00 0.00 0.00 5.54
125 126 0.756294 TTGAACTCCTGACTTCGCCA 59.244 50.000 0.00 0.00 0.00 5.69
126 127 0.033504 TGAACTCCTGACTTCGCCAC 59.966 55.000 0.00 0.00 0.00 5.01
127 128 0.318762 GAACTCCTGACTTCGCCACT 59.681 55.000 0.00 0.00 0.00 4.00
138 139 2.032528 CGCCACTGGTGTCCACAT 59.967 61.111 0.00 0.00 0.00 3.21
159 160 3.482436 TGTAAAAGGTTGCACGGATCTT 58.518 40.909 0.00 0.00 0.00 2.40
166 167 5.722021 AGGTTGCACGGATCTTTAAAAAT 57.278 34.783 0.00 0.00 0.00 1.82
222 224 8.930846 ACATTAATCCTTAGCTAGAATGCATT 57.069 30.769 12.83 12.83 34.99 3.56
223 225 8.790718 ACATTAATCCTTAGCTAGAATGCATTG 58.209 33.333 18.59 3.53 34.99 2.82
244 251 1.460497 GATCTCACCCCCTCCCTCC 60.460 68.421 0.00 0.00 0.00 4.30
305 316 0.404040 TCGCCCATGGAAAGGACTTT 59.596 50.000 15.22 0.00 35.14 2.66
325 336 0.831711 GGAGGTGCCACCCATTTTGT 60.832 55.000 11.06 0.00 39.75 2.83
345 356 2.203280 CCCTTCACCAACCGTGCA 60.203 61.111 0.00 0.00 42.69 4.57
347 358 1.586154 CCCTTCACCAACCGTGCATC 61.586 60.000 0.00 0.00 42.69 3.91
384 395 1.404035 GATTGGCCATTCCCGTGTAAC 59.596 52.381 6.09 0.00 0.00 2.50
413 424 1.689243 ATGCACGATGCCTCTGCCTA 61.689 55.000 7.38 0.00 44.23 3.93
414 425 1.884926 GCACGATGCCTCTGCCTAC 60.885 63.158 0.00 0.00 37.42 3.18
486 506 2.124736 TACGTACGTCCCTCCCCG 60.125 66.667 26.53 0.00 0.00 5.73
506 526 3.055719 CATGCCGCACCTTCCGTT 61.056 61.111 0.00 0.00 0.00 4.44
507 527 2.282180 ATGCCGCACCTTCCGTTT 60.282 55.556 0.00 0.00 0.00 3.60
508 528 1.901464 ATGCCGCACCTTCCGTTTT 60.901 52.632 0.00 0.00 0.00 2.43
512 532 1.161843 CCGCACCTTCCGTTTTGTAT 58.838 50.000 0.00 0.00 0.00 2.29
544 823 1.830477 ACTGCATGTTCTCTCCCTCTC 59.170 52.381 0.00 0.00 0.00 3.20
574 853 2.216898 GCATGTAGAGGCTTGACCATC 58.783 52.381 0.00 0.00 43.14 3.51
578 857 3.928754 TGTAGAGGCTTGACCATCCTAT 58.071 45.455 0.00 0.00 43.14 2.57
579 858 5.074746 TGTAGAGGCTTGACCATCCTATA 57.925 43.478 0.00 0.00 43.14 1.31
580 859 4.833380 TGTAGAGGCTTGACCATCCTATAC 59.167 45.833 12.56 12.56 42.17 1.47
581 860 3.243724 AGAGGCTTGACCATCCTATACC 58.756 50.000 0.00 0.00 43.14 2.73
582 861 2.972713 GAGGCTTGACCATCCTATACCA 59.027 50.000 0.00 0.00 43.14 3.25
583 862 2.706190 AGGCTTGACCATCCTATACCAC 59.294 50.000 0.00 0.00 43.14 4.16
653 939 2.055100 GCTAGCGCTACTGTTCATAGC 58.945 52.381 14.45 10.33 41.43 2.97
654 940 2.543861 GCTAGCGCTACTGTTCATAGCA 60.544 50.000 14.45 0.00 44.46 3.49
730 1019 2.233922 TCGATCTTGTCCCTTCAACTCC 59.766 50.000 0.00 0.00 0.00 3.85
817 1106 3.320733 ACACGATCGATCTTGACGTAG 57.679 47.619 31.58 17.08 35.78 3.51
884 1185 1.742880 CACGGTCACATGAGCTGGG 60.743 63.158 0.00 1.03 40.17 4.45
935 1238 1.390123 GCACGCTACACACATACACTG 59.610 52.381 0.00 0.00 0.00 3.66
939 1242 2.671070 CGCTACACACATACACTGCAGA 60.671 50.000 23.35 0.00 0.00 4.26
972 1280 3.419915 CAAAACATTCAAGAGATCGCGG 58.580 45.455 6.13 0.00 0.00 6.46
986 1294 2.190578 GCGGGATAAGCAGCAGGT 59.809 61.111 0.00 0.00 34.19 4.00
988 1296 1.592669 CGGGATAAGCAGCAGGTCG 60.593 63.158 0.00 0.00 0.00 4.79
989 1297 1.823295 GGGATAAGCAGCAGGTCGA 59.177 57.895 0.00 0.00 0.00 4.20
991 1299 1.291132 GGATAAGCAGCAGGTCGAAC 58.709 55.000 0.00 0.00 0.00 3.95
992 1300 0.924090 GATAAGCAGCAGGTCGAACG 59.076 55.000 0.00 0.00 0.00 3.95
993 1301 0.460284 ATAAGCAGCAGGTCGAACGG 60.460 55.000 0.00 0.00 0.00 4.44
1024 1332 2.786539 GATGGCGCACAGAGACCACA 62.787 60.000 10.83 0.00 34.36 4.17
1031 1339 0.174389 CACAGAGACCACATCCTCGG 59.826 60.000 0.00 0.00 34.75 4.63
1590 1913 2.933287 AACCTGTCCGGCATGGGA 60.933 61.111 0.00 0.00 38.76 4.37
1870 2205 2.671619 GCGGCTACAACTTGGCCA 60.672 61.111 0.00 0.00 45.50 5.36
2462 2823 1.750399 CCCCGTTGGCTTGATCTGG 60.750 63.158 0.00 0.00 0.00 3.86
2464 2825 0.107017 CCCGTTGGCTTGATCTGGAT 60.107 55.000 0.00 0.00 0.00 3.41
2486 2847 2.148446 ACGTACCTAGTGCATGGGTA 57.852 50.000 10.13 10.13 41.89 3.69
2494 2855 1.133809 AGTGCATGGGTACAGGGTGT 61.134 55.000 0.00 0.00 31.27 4.16
2508 2869 1.152830 GGTGTTTGGGCTCCTGGAA 59.847 57.895 0.00 0.00 0.00 3.53
2509 2870 0.469144 GGTGTTTGGGCTCCTGGAAA 60.469 55.000 0.00 0.00 0.00 3.13
2511 2872 0.178964 TGTTTGGGCTCCTGGAAAGG 60.179 55.000 0.00 0.00 0.00 3.11
2512 2873 0.112412 GTTTGGGCTCCTGGAAAGGA 59.888 55.000 0.00 0.00 36.40 3.36
2515 2900 0.549902 TGGGCTCCTGGAAAGGATCA 60.550 55.000 0.00 0.00 37.34 2.92
2540 2925 0.525242 CAGTGTTGTTTGTGCCGTGG 60.525 55.000 0.00 0.00 0.00 4.94
2671 3490 7.038154 TCTGGGTTTTCTCACTTTTATTGTG 57.962 36.000 0.00 0.00 36.82 3.33
2672 3491 6.040391 TCTGGGTTTTCTCACTTTTATTGTGG 59.960 38.462 0.00 0.00 36.21 4.17
2673 3492 5.659079 TGGGTTTTCTCACTTTTATTGTGGT 59.341 36.000 0.00 0.00 36.21 4.16
2695 3514 1.740025 CTTCGATCTTGTTTCCTGCCC 59.260 52.381 0.00 0.00 0.00 5.36
2702 3521 1.266989 CTTGTTTCCTGCCCTTCGTTC 59.733 52.381 0.00 0.00 0.00 3.95
2703 3522 0.181587 TGTTTCCTGCCCTTCGTTCA 59.818 50.000 0.00 0.00 0.00 3.18
2727 3547 1.742831 TCCATGGCGTATTTTGACTGC 59.257 47.619 6.96 0.00 0.00 4.40
2746 3566 6.265196 TGACTGCTTTCAACTTTGGTCATAAT 59.735 34.615 0.00 0.00 0.00 1.28
2752 3572 7.598493 GCTTTCAACTTTGGTCATAATTAGCAA 59.402 33.333 0.00 0.00 32.84 3.91
2820 3640 1.699083 TGACTCAAAGACCCATGCAGA 59.301 47.619 0.00 0.00 0.00 4.26
2851 3671 2.849943 TCTACCCCAGCCATGTAATTGT 59.150 45.455 0.00 0.00 0.00 2.71
2923 3743 0.662619 CAATGCGCCCGAACATATGT 59.337 50.000 4.18 1.41 0.00 2.29
2932 3752 1.593006 CCGAACATATGTCAAGGCGAC 59.407 52.381 9.23 0.00 45.61 5.19
2944 3764 0.320771 AAGGCGACGAGTTCAAGCAT 60.321 50.000 0.00 0.00 0.00 3.79
2952 3772 1.689959 GAGTTCAAGCATTTGCACGG 58.310 50.000 5.20 0.00 45.16 4.94
3081 3901 0.594284 GTACACCGAGCCTCATACGC 60.594 60.000 0.00 0.00 0.00 4.42
3082 3902 1.731433 TACACCGAGCCTCATACGCC 61.731 60.000 0.00 0.00 0.00 5.68
3083 3903 3.537874 ACCGAGCCTCATACGCCC 61.538 66.667 0.00 0.00 0.00 6.13
3084 3904 3.227276 CCGAGCCTCATACGCCCT 61.227 66.667 0.00 0.00 0.00 5.19
3085 3905 2.336809 CGAGCCTCATACGCCCTC 59.663 66.667 0.00 0.00 0.00 4.30
3086 3906 2.196925 CGAGCCTCATACGCCCTCT 61.197 63.158 0.00 0.00 0.00 3.69
3087 3907 1.663173 GAGCCTCATACGCCCTCTC 59.337 63.158 0.00 0.00 0.00 3.20
3088 3908 2.136196 GAGCCTCATACGCCCTCTCG 62.136 65.000 0.00 0.00 0.00 4.04
3089 3909 2.336809 CCTCATACGCCCTCTCGC 59.663 66.667 0.00 0.00 0.00 5.03
3090 3910 2.196925 CCTCATACGCCCTCTCGCT 61.197 63.158 0.00 0.00 0.00 4.93
3091 3911 1.736586 CTCATACGCCCTCTCGCTT 59.263 57.895 0.00 0.00 0.00 4.68
3092 3912 0.318275 CTCATACGCCCTCTCGCTTC 60.318 60.000 0.00 0.00 0.00 3.86
3093 3913 0.752009 TCATACGCCCTCTCGCTTCT 60.752 55.000 0.00 0.00 0.00 2.85
3094 3914 0.952280 CATACGCCCTCTCGCTTCTA 59.048 55.000 0.00 0.00 0.00 2.10
3095 3915 1.337071 CATACGCCCTCTCGCTTCTAA 59.663 52.381 0.00 0.00 0.00 2.10
3096 3916 1.466856 TACGCCCTCTCGCTTCTAAA 58.533 50.000 0.00 0.00 0.00 1.85
3097 3917 0.824759 ACGCCCTCTCGCTTCTAAAT 59.175 50.000 0.00 0.00 0.00 1.40
3098 3918 1.202428 ACGCCCTCTCGCTTCTAAATC 60.202 52.381 0.00 0.00 0.00 2.17
3099 3919 1.202417 CGCCCTCTCGCTTCTAAATCA 60.202 52.381 0.00 0.00 0.00 2.57
3100 3920 2.738643 CGCCCTCTCGCTTCTAAATCAA 60.739 50.000 0.00 0.00 0.00 2.57
3101 3921 3.471680 GCCCTCTCGCTTCTAAATCAAT 58.528 45.455 0.00 0.00 0.00 2.57
3102 3922 3.249559 GCCCTCTCGCTTCTAAATCAATG 59.750 47.826 0.00 0.00 0.00 2.82
3103 3923 4.446371 CCCTCTCGCTTCTAAATCAATGT 58.554 43.478 0.00 0.00 0.00 2.71
3104 3924 4.878397 CCCTCTCGCTTCTAAATCAATGTT 59.122 41.667 0.00 0.00 0.00 2.71
3105 3925 6.049149 CCCTCTCGCTTCTAAATCAATGTTA 58.951 40.000 0.00 0.00 0.00 2.41
3106 3926 6.708054 CCCTCTCGCTTCTAAATCAATGTTAT 59.292 38.462 0.00 0.00 0.00 1.89
3107 3927 7.872993 CCCTCTCGCTTCTAAATCAATGTTATA 59.127 37.037 0.00 0.00 0.00 0.98
3108 3928 8.920665 CCTCTCGCTTCTAAATCAATGTTATAG 58.079 37.037 0.00 0.00 0.00 1.31
3109 3929 9.684448 CTCTCGCTTCTAAATCAATGTTATAGA 57.316 33.333 0.00 0.00 0.00 1.98
3110 3930 9.464714 TCTCGCTTCTAAATCAATGTTATAGAC 57.535 33.333 0.00 0.00 0.00 2.59
3111 3931 9.469807 CTCGCTTCTAAATCAATGTTATAGACT 57.530 33.333 0.00 0.00 0.00 3.24
3112 3932 9.464714 TCGCTTCTAAATCAATGTTATAGACTC 57.535 33.333 0.00 0.00 0.00 3.36
3113 3933 9.249457 CGCTTCTAAATCAATGTTATAGACTCA 57.751 33.333 0.00 0.00 0.00 3.41
3252 4072 2.887152 AGGAAAGTTCATGTGCTTCACC 59.113 45.455 0.00 6.40 32.73 4.02
3289 4115 2.118313 TTCCGAGTCCTCATACGTCA 57.882 50.000 0.00 0.00 0.00 4.35
3393 4219 3.815962 TCGATCCACATCTAGCTACTCAC 59.184 47.826 0.00 0.00 0.00 3.51
3406 4232 1.687123 CTACTCACCCCGATCCGATTT 59.313 52.381 0.00 0.00 0.00 2.17
3409 4235 0.616371 TCACCCCGATCCGATTTGTT 59.384 50.000 0.00 0.00 0.00 2.83
3410 4236 1.832366 TCACCCCGATCCGATTTGTTA 59.168 47.619 0.00 0.00 0.00 2.41
3411 4237 2.236644 TCACCCCGATCCGATTTGTTAA 59.763 45.455 0.00 0.00 0.00 2.01
3413 4239 3.064820 CACCCCGATCCGATTTGTTAAAG 59.935 47.826 0.00 0.00 0.00 1.85
3414 4240 3.275999 CCCCGATCCGATTTGTTAAAGT 58.724 45.455 0.00 0.00 0.00 2.66
3452 4317 4.767255 GGGCTGGAGAGGTGCACG 62.767 72.222 11.45 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.793232 GTCAACCGACTACACAGAACAC 59.207 50.000 0.00 0.00 39.22 3.32
1 2 3.088194 GTCAACCGACTACACAGAACA 57.912 47.619 0.00 0.00 39.22 3.18
12 13 3.678548 GGATTTCTGTGTAGTCAACCGAC 59.321 47.826 0.00 0.00 42.95 4.79
13 14 3.576982 AGGATTTCTGTGTAGTCAACCGA 59.423 43.478 0.00 0.00 0.00 4.69
14 15 3.926616 AGGATTTCTGTGTAGTCAACCG 58.073 45.455 0.00 0.00 0.00 4.44
15 16 5.305585 TGAAGGATTTCTGTGTAGTCAACC 58.694 41.667 0.00 0.00 34.31 3.77
16 17 6.861065 TTGAAGGATTTCTGTGTAGTCAAC 57.139 37.500 0.00 0.00 34.31 3.18
17 18 7.873719 TTTTGAAGGATTTCTGTGTAGTCAA 57.126 32.000 0.00 0.00 34.31 3.18
18 19 7.873719 TTTTTGAAGGATTTCTGTGTAGTCA 57.126 32.000 0.00 0.00 34.31 3.41
55 56 9.952030 TGATGTCAAGTAGTTGTATTTGGATTA 57.048 29.630 10.08 0.00 34.98 1.75
56 57 8.730680 GTGATGTCAAGTAGTTGTATTTGGATT 58.269 33.333 10.08 0.00 34.98 3.01
57 58 7.882791 TGTGATGTCAAGTAGTTGTATTTGGAT 59.117 33.333 10.08 0.00 34.98 3.41
58 59 7.220740 TGTGATGTCAAGTAGTTGTATTTGGA 58.779 34.615 10.08 0.00 34.98 3.53
59 60 7.433708 TGTGATGTCAAGTAGTTGTATTTGG 57.566 36.000 10.08 0.00 34.98 3.28
60 61 9.897744 AATTGTGATGTCAAGTAGTTGTATTTG 57.102 29.630 10.08 0.00 34.98 2.32
70 71 9.202273 GGCAATTTAAAATTGTGATGTCAAGTA 57.798 29.630 0.00 0.00 0.00 2.24
71 72 7.714377 TGGCAATTTAAAATTGTGATGTCAAGT 59.286 29.630 0.00 0.00 0.00 3.16
72 73 8.085720 TGGCAATTTAAAATTGTGATGTCAAG 57.914 30.769 0.00 0.00 0.00 3.02
73 74 8.618702 ATGGCAATTTAAAATTGTGATGTCAA 57.381 26.923 0.00 0.00 0.00 3.18
74 75 7.876582 TGATGGCAATTTAAAATTGTGATGTCA 59.123 29.630 0.00 0.00 0.00 3.58
75 76 8.170553 GTGATGGCAATTTAAAATTGTGATGTC 58.829 33.333 0.00 0.00 0.00 3.06
76 77 7.660617 TGTGATGGCAATTTAAAATTGTGATGT 59.339 29.630 0.00 0.00 0.00 3.06
77 78 8.030744 TGTGATGGCAATTTAAAATTGTGATG 57.969 30.769 0.00 0.00 0.00 3.07
78 79 8.505625 GTTGTGATGGCAATTTAAAATTGTGAT 58.494 29.630 0.00 0.00 0.00 3.06
79 80 7.714377 AGTTGTGATGGCAATTTAAAATTGTGA 59.286 29.630 0.00 0.00 0.00 3.58
80 81 7.863666 AGTTGTGATGGCAATTTAAAATTGTG 58.136 30.769 0.00 0.00 0.00 3.33
81 82 8.449251 AAGTTGTGATGGCAATTTAAAATTGT 57.551 26.923 0.00 0.00 0.00 2.71
82 83 9.171701 CAAAGTTGTGATGGCAATTTAAAATTG 57.828 29.630 0.00 0.00 30.02 2.32
83 84 9.118300 TCAAAGTTGTGATGGCAATTTAAAATT 57.882 25.926 0.00 0.00 30.02 1.82
84 85 8.674263 TCAAAGTTGTGATGGCAATTTAAAAT 57.326 26.923 0.00 0.00 30.02 1.82
85 86 8.394121 GTTCAAAGTTGTGATGGCAATTTAAAA 58.606 29.630 0.00 0.00 30.02 1.52
86 87 7.768120 AGTTCAAAGTTGTGATGGCAATTTAAA 59.232 29.630 0.00 0.00 30.02 1.52
87 88 7.271511 AGTTCAAAGTTGTGATGGCAATTTAA 58.728 30.769 0.00 0.00 30.02 1.52
88 89 6.815089 AGTTCAAAGTTGTGATGGCAATTTA 58.185 32.000 0.00 0.00 30.02 1.40
89 90 5.673514 AGTTCAAAGTTGTGATGGCAATTT 58.326 33.333 0.00 0.00 31.15 1.82
90 91 5.280654 AGTTCAAAGTTGTGATGGCAATT 57.719 34.783 0.00 0.00 0.00 2.32
91 92 4.262164 GGAGTTCAAAGTTGTGATGGCAAT 60.262 41.667 0.00 0.00 0.00 3.56
92 93 3.068024 GGAGTTCAAAGTTGTGATGGCAA 59.932 43.478 0.00 0.00 0.00 4.52
93 94 2.622942 GGAGTTCAAAGTTGTGATGGCA 59.377 45.455 0.00 0.00 0.00 4.92
94 95 2.887152 AGGAGTTCAAAGTTGTGATGGC 59.113 45.455 0.00 0.00 0.00 4.40
95 96 4.023707 GTCAGGAGTTCAAAGTTGTGATGG 60.024 45.833 0.00 0.00 0.00 3.51
96 97 4.818546 AGTCAGGAGTTCAAAGTTGTGATG 59.181 41.667 0.00 0.00 0.00 3.07
97 98 5.041191 AGTCAGGAGTTCAAAGTTGTGAT 57.959 39.130 0.00 0.00 0.00 3.06
98 99 4.487714 AGTCAGGAGTTCAAAGTTGTGA 57.512 40.909 0.00 0.00 0.00 3.58
99 100 4.260375 CGAAGTCAGGAGTTCAAAGTTGTG 60.260 45.833 15.12 0.00 39.99 3.33
100 101 3.871594 CGAAGTCAGGAGTTCAAAGTTGT 59.128 43.478 15.12 0.00 39.99 3.32
101 102 3.303395 GCGAAGTCAGGAGTTCAAAGTTG 60.303 47.826 15.12 1.67 39.99 3.16
102 103 2.872858 GCGAAGTCAGGAGTTCAAAGTT 59.127 45.455 15.12 0.00 39.99 2.66
103 104 2.484889 GCGAAGTCAGGAGTTCAAAGT 58.515 47.619 15.12 0.00 39.99 2.66
104 105 1.801178 GGCGAAGTCAGGAGTTCAAAG 59.199 52.381 15.12 2.84 39.99 2.77
105 106 1.140052 TGGCGAAGTCAGGAGTTCAAA 59.860 47.619 15.12 0.06 36.97 2.69
106 107 0.756294 TGGCGAAGTCAGGAGTTCAA 59.244 50.000 15.12 0.35 36.97 2.69
107 108 2.436521 TGGCGAAGTCAGGAGTTCA 58.563 52.632 15.12 0.00 36.97 3.18
115 116 1.069090 GACACCAGTGGCGAAGTCA 59.931 57.895 9.78 0.00 43.93 3.41
116 117 1.668151 GGACACCAGTGGCGAAGTC 60.668 63.158 9.78 12.09 40.25 3.01
117 118 2.426023 GGACACCAGTGGCGAAGT 59.574 61.111 9.78 2.68 40.25 3.01
118 119 1.961277 GTGGACACCAGTGGCGAAG 60.961 63.158 9.78 0.00 40.25 3.79
119 120 2.050836 ATGTGGACACCAGTGGCGAA 62.051 55.000 9.78 0.00 40.25 4.70
120 121 2.515979 ATGTGGACACCAGTGGCGA 61.516 57.895 9.78 0.00 40.25 5.54
121 122 2.032528 ATGTGGACACCAGTGGCG 59.967 61.111 9.78 1.17 40.25 5.69
122 123 0.036164 TACATGTGGACACCAGTGGC 59.964 55.000 9.78 0.00 38.06 5.01
123 124 2.559698 TTACATGTGGACACCAGTGG 57.440 50.000 9.11 7.91 32.34 4.00
124 125 3.253188 CCTTTTACATGTGGACACCAGTG 59.747 47.826 9.11 0.00 32.34 3.66
125 126 3.117663 ACCTTTTACATGTGGACACCAGT 60.118 43.478 9.11 1.53 32.34 4.00
126 127 3.486383 ACCTTTTACATGTGGACACCAG 58.514 45.455 9.11 0.00 32.34 4.00
127 128 3.586470 ACCTTTTACATGTGGACACCA 57.414 42.857 9.11 0.00 0.00 4.17
138 139 3.134574 AGATCCGTGCAACCTTTTACA 57.865 42.857 0.00 0.00 0.00 2.41
186 187 9.388672 AGCTAAGGATTAATGTATACCTGGTAA 57.611 33.333 11.17 0.00 0.00 2.85
187 188 8.967779 AGCTAAGGATTAATGTATACCTGGTA 57.032 34.615 9.36 9.36 0.00 3.25
188 189 7.873699 AGCTAAGGATTAATGTATACCTGGT 57.126 36.000 4.05 4.05 0.00 4.00
209 211 4.202192 TGAGATCGACAATGCATTCTAGCT 60.202 41.667 9.53 0.00 34.99 3.32
217 219 0.107703 GGGGTGAGATCGACAATGCA 60.108 55.000 0.00 0.00 0.00 3.96
218 220 0.815615 GGGGGTGAGATCGACAATGC 60.816 60.000 0.00 0.00 0.00 3.56
219 221 0.833287 AGGGGGTGAGATCGACAATG 59.167 55.000 0.00 0.00 0.00 2.82
220 222 1.123928 GAGGGGGTGAGATCGACAAT 58.876 55.000 0.00 0.00 0.00 2.71
221 223 0.976073 GGAGGGGGTGAGATCGACAA 60.976 60.000 0.00 0.00 0.00 3.18
222 224 1.381327 GGAGGGGGTGAGATCGACA 60.381 63.158 0.00 0.00 0.00 4.35
223 225 2.134933 GGGAGGGGGTGAGATCGAC 61.135 68.421 0.00 0.00 0.00 4.20
244 251 3.444642 GTGTCGACACGCTAACGG 58.555 61.111 31.03 0.00 46.04 4.44
305 316 0.831288 CAAAATGGGTGGCACCTCCA 60.831 55.000 33.87 24.87 44.18 3.86
321 332 1.770294 GGTTGGTGAAGGGTGACAAA 58.230 50.000 0.00 0.00 0.00 2.83
325 336 3.650023 ACGGTTGGTGAAGGGTGA 58.350 55.556 0.00 0.00 0.00 4.02
365 376 1.470051 GTTACACGGGAATGGCCAAT 58.530 50.000 10.96 0.00 38.95 3.16
384 395 0.026674 CATCGTGCATGCTTACACCG 59.973 55.000 20.33 11.00 33.09 4.94
385 396 3.903876 CATCGTGCATGCTTACACC 57.096 52.632 20.33 0.00 33.09 4.16
405 416 2.105930 GGCGCTGAGTAGGCAGAG 59.894 66.667 7.64 0.00 38.14 3.35
406 417 3.461773 GGGCGCTGAGTAGGCAGA 61.462 66.667 7.64 0.00 38.14 4.26
494 514 2.073816 AGATACAAAACGGAAGGTGCG 58.926 47.619 0.00 0.00 37.19 5.34
498 518 3.518590 ACGCTAGATACAAAACGGAAGG 58.481 45.455 0.00 0.00 0.00 3.46
499 519 4.206609 GCTACGCTAGATACAAAACGGAAG 59.793 45.833 0.00 0.00 0.00 3.46
503 523 3.242248 GTGGCTACGCTAGATACAAAACG 59.758 47.826 0.00 0.00 0.00 3.60
504 524 4.267928 CAGTGGCTACGCTAGATACAAAAC 59.732 45.833 0.00 0.00 35.22 2.43
506 526 3.737047 GCAGTGGCTACGCTAGATACAAA 60.737 47.826 9.15 0.00 35.22 2.83
507 527 2.223735 GCAGTGGCTACGCTAGATACAA 60.224 50.000 9.15 0.00 35.22 2.41
508 528 1.337071 GCAGTGGCTACGCTAGATACA 59.663 52.381 9.15 0.00 35.22 2.29
512 532 0.103026 CATGCAGTGGCTACGCTAGA 59.897 55.000 15.37 0.04 41.91 2.43
523 543 1.554160 AGAGGGAGAGAACATGCAGTG 59.446 52.381 0.00 0.00 0.00 3.66
532 552 2.041350 ACGTACCAAGAGAGGGAGAGAA 59.959 50.000 0.00 0.00 0.00 2.87
533 553 1.634459 ACGTACCAAGAGAGGGAGAGA 59.366 52.381 0.00 0.00 0.00 3.10
534 554 1.746220 CACGTACCAAGAGAGGGAGAG 59.254 57.143 0.00 0.00 0.00 3.20
544 823 2.540515 CCTCTACATGCACGTACCAAG 58.459 52.381 0.00 0.00 0.00 3.61
574 853 2.426023 GCCGGGCAGTGGTATAGG 59.574 66.667 15.62 0.00 0.00 2.57
580 859 3.083848 TATACGTGCCGGGCAGTGG 62.084 63.158 24.58 16.95 40.08 4.00
581 860 1.881252 GTATACGTGCCGGGCAGTG 60.881 63.158 24.58 20.20 40.08 3.66
582 861 2.497770 GTATACGTGCCGGGCAGT 59.502 61.111 24.58 22.83 40.08 4.40
583 862 2.657296 CGTATACGTGCCGGGCAG 60.657 66.667 24.58 18.35 40.08 4.85
653 939 2.180017 GCCATGAAAGCAGCCGTG 59.820 61.111 0.00 0.00 0.00 4.94
654 940 3.434319 CGCCATGAAAGCAGCCGT 61.434 61.111 0.00 0.00 0.00 5.68
730 1019 1.267732 GCTTTGAGATCGATGCAACCG 60.268 52.381 0.54 5.62 32.44 4.44
776 1065 1.977594 GCCCGCGTAACATGGTTGAG 61.978 60.000 4.92 0.00 0.00 3.02
779 1068 1.601197 TTGCCCGCGTAACATGGTT 60.601 52.632 4.92 0.00 0.00 3.67
805 1094 3.423123 CCGTTGCAAACTACGTCAAGATC 60.423 47.826 0.00 0.00 46.99 2.75
817 1106 2.803451 TGAATTGTGTCCGTTGCAAAC 58.197 42.857 0.00 0.00 45.31 2.93
818 1107 3.379240 CATGAATTGTGTCCGTTGCAAA 58.621 40.909 0.00 0.00 0.00 3.68
820 1109 1.269174 CCATGAATTGTGTCCGTTGCA 59.731 47.619 0.00 0.00 0.00 4.08
821 1110 1.981254 CCATGAATTGTGTCCGTTGC 58.019 50.000 0.00 0.00 0.00 4.17
822 1111 1.728825 CGCCATGAATTGTGTCCGTTG 60.729 52.381 0.00 0.00 0.00 4.10
823 1112 0.521291 CGCCATGAATTGTGTCCGTT 59.479 50.000 0.00 0.00 0.00 4.44
824 1113 0.605319 ACGCCATGAATTGTGTCCGT 60.605 50.000 0.00 0.00 0.00 4.69
825 1114 0.179192 CACGCCATGAATTGTGTCCG 60.179 55.000 0.00 0.00 0.00 4.79
826 1115 0.456653 GCACGCCATGAATTGTGTCC 60.457 55.000 0.00 0.00 34.86 4.02
884 1185 2.662700 CTCTTATATGGTGCGTCGTCC 58.337 52.381 0.00 0.00 0.00 4.79
935 1238 2.704725 TTTGGACGCTGATTTTCTGC 57.295 45.000 0.00 0.00 37.88 4.26
939 1242 4.942852 TGAATGTTTTGGACGCTGATTTT 58.057 34.783 0.00 0.00 0.00 1.82
972 1280 1.291132 GTTCGACCTGCTGCTTATCC 58.709 55.000 0.00 0.00 0.00 2.59
986 1294 1.929806 CTCCATGTCCGTCCGTTCGA 61.930 60.000 0.00 0.00 0.00 3.71
988 1296 0.460311 ATCTCCATGTCCGTCCGTTC 59.540 55.000 0.00 0.00 0.00 3.95
989 1297 0.175760 CATCTCCATGTCCGTCCGTT 59.824 55.000 0.00 0.00 0.00 4.44
991 1299 1.068083 CCATCTCCATGTCCGTCCG 59.932 63.158 0.00 0.00 0.00 4.79
992 1300 1.227674 GCCATCTCCATGTCCGTCC 60.228 63.158 0.00 0.00 0.00 4.79
993 1301 1.592669 CGCCATCTCCATGTCCGTC 60.593 63.158 0.00 0.00 0.00 4.79
1185 1508 4.329545 GCGAAGTCCACCAGCCCA 62.330 66.667 0.00 0.00 0.00 5.36
1437 1760 1.080025 GCCCGTCTTAGCGAACAGT 60.080 57.895 0.00 0.00 0.00 3.55
1770 2099 1.733041 CGATGCGGTGTTCGACAGT 60.733 57.895 0.00 0.00 42.43 3.55
1870 2205 1.454111 CGTCGTCCTCCTCCCTCAT 60.454 63.158 0.00 0.00 0.00 2.90
2462 2823 3.552273 CCCATGCACTAGGTACGTACATC 60.552 52.174 26.02 10.66 0.00 3.06
2464 2825 1.752498 CCCATGCACTAGGTACGTACA 59.248 52.381 26.02 6.81 0.00 2.90
2486 2847 2.084930 AGGAGCCCAAACACCCTGT 61.085 57.895 0.00 0.00 0.00 4.00
2487 2848 1.604593 CAGGAGCCCAAACACCCTG 60.605 63.158 0.00 0.00 38.48 4.45
2494 2855 2.562953 TCCTTTCCAGGAGCCCAAA 58.437 52.632 0.00 0.00 45.20 3.28
2508 2869 2.975489 ACAACACTGTCCTCTGATCCTT 59.025 45.455 0.00 0.00 0.00 3.36
2509 2870 2.614259 ACAACACTGTCCTCTGATCCT 58.386 47.619 0.00 0.00 0.00 3.24
2511 2872 4.024556 CACAAACAACACTGTCCTCTGATC 60.025 45.833 0.00 0.00 33.45 2.92
2512 2873 3.879295 CACAAACAACACTGTCCTCTGAT 59.121 43.478 0.00 0.00 33.45 2.90
2515 2900 2.017049 GCACAAACAACACTGTCCTCT 58.983 47.619 0.00 0.00 33.45 3.69
2545 3348 4.211374 AGCAAGCAAAGTGAAAGTACGTAG 59.789 41.667 0.00 0.00 0.00 3.51
2671 3490 3.371285 GCAGGAAACAAGATCGAAGTACC 59.629 47.826 0.00 0.00 0.00 3.34
2672 3491 3.371285 GGCAGGAAACAAGATCGAAGTAC 59.629 47.826 0.00 0.00 0.00 2.73
2673 3492 3.596214 GGCAGGAAACAAGATCGAAGTA 58.404 45.455 0.00 0.00 0.00 2.24
2695 3514 1.328680 CGCCATGGATTCTGAACGAAG 59.671 52.381 18.40 0.00 34.56 3.79
2702 3521 4.336433 AGTCAAAATACGCCATGGATTCTG 59.664 41.667 18.40 3.66 0.00 3.02
2703 3522 4.336433 CAGTCAAAATACGCCATGGATTCT 59.664 41.667 18.40 0.00 0.00 2.40
2727 3547 9.474920 TTTGCTAATTATGACCAAAGTTGAAAG 57.525 29.630 0.00 0.00 0.00 2.62
2746 3566 0.387878 CGCACGGGCATTTTTGCTAA 60.388 50.000 11.77 0.00 41.24 3.09
2752 3572 2.355718 GCAACGCACGGGCATTTT 60.356 55.556 11.77 0.00 41.24 1.82
2774 3594 2.477189 CGGCGTGTGAGTTTGTTTCTTT 60.477 45.455 0.00 0.00 0.00 2.52
2775 3595 1.063469 CGGCGTGTGAGTTTGTTTCTT 59.937 47.619 0.00 0.00 0.00 2.52
2820 3640 0.326618 CTGGGGTAGAGGATGTGGGT 60.327 60.000 0.00 0.00 0.00 4.51
2851 3671 1.479323 CGAGGGTGGAAGGACGATAAA 59.521 52.381 0.00 0.00 0.00 1.40
2923 3743 0.944311 GCTTGAACTCGTCGCCTTGA 60.944 55.000 0.00 0.00 0.00 3.02
2932 3752 1.321016 CGTGCAAATGCTTGAACTCG 58.679 50.000 6.97 0.00 38.78 4.18
2944 3764 1.308783 TGACAAGTGTGCCGTGCAAA 61.309 50.000 0.00 0.00 41.47 3.68
2952 3772 2.731217 GTGGTTCAATGACAAGTGTGC 58.269 47.619 0.00 0.00 0.00 4.57
3035 3855 0.254178 CCAGGAGCATGGTGTAGCTT 59.746 55.000 0.00 0.00 42.04 3.74
3081 3901 4.446371 ACATTGATTTAGAAGCGAGAGGG 58.554 43.478 0.00 0.00 0.00 4.30
3082 3902 7.721286 ATAACATTGATTTAGAAGCGAGAGG 57.279 36.000 0.00 0.00 0.00 3.69
3083 3903 9.684448 TCTATAACATTGATTTAGAAGCGAGAG 57.316 33.333 0.00 0.00 0.00 3.20
3084 3904 9.464714 GTCTATAACATTGATTTAGAAGCGAGA 57.535 33.333 0.00 0.00 0.00 4.04
3085 3905 9.469807 AGTCTATAACATTGATTTAGAAGCGAG 57.530 33.333 0.00 0.00 0.00 5.03
3086 3906 9.464714 GAGTCTATAACATTGATTTAGAAGCGA 57.535 33.333 0.00 0.00 0.00 4.93
3087 3907 9.249457 TGAGTCTATAACATTGATTTAGAAGCG 57.751 33.333 0.00 0.00 0.00 4.68
3090 3910 9.832445 GGGTGAGTCTATAACATTGATTTAGAA 57.168 33.333 0.00 0.00 0.00 2.10
3091 3911 9.213777 AGGGTGAGTCTATAACATTGATTTAGA 57.786 33.333 0.00 0.00 0.00 2.10
3092 3912 9.482627 GAGGGTGAGTCTATAACATTGATTTAG 57.517 37.037 0.00 0.00 0.00 1.85
3093 3913 9.213777 AGAGGGTGAGTCTATAACATTGATTTA 57.786 33.333 0.00 0.00 0.00 1.40
3094 3914 8.095452 AGAGGGTGAGTCTATAACATTGATTT 57.905 34.615 0.00 0.00 0.00 2.17
3095 3915 7.470702 CGAGAGGGTGAGTCTATAACATTGATT 60.471 40.741 0.00 0.00 0.00 2.57
3096 3916 6.015856 CGAGAGGGTGAGTCTATAACATTGAT 60.016 42.308 0.00 0.00 0.00 2.57
3097 3917 5.299531 CGAGAGGGTGAGTCTATAACATTGA 59.700 44.000 0.00 0.00 0.00 2.57
3098 3918 5.524284 CGAGAGGGTGAGTCTATAACATTG 58.476 45.833 0.00 0.00 0.00 2.82
3099 3919 4.038162 GCGAGAGGGTGAGTCTATAACATT 59.962 45.833 0.00 0.00 0.00 2.71
3100 3920 3.570550 GCGAGAGGGTGAGTCTATAACAT 59.429 47.826 0.00 0.00 0.00 2.71
3101 3921 2.950309 GCGAGAGGGTGAGTCTATAACA 59.050 50.000 0.00 0.00 0.00 2.41
3102 3922 3.215975 AGCGAGAGGGTGAGTCTATAAC 58.784 50.000 0.00 0.00 0.00 1.89
3103 3923 3.579534 AGCGAGAGGGTGAGTCTATAA 57.420 47.619 0.00 0.00 0.00 0.98
3104 3924 3.136809 AGAAGCGAGAGGGTGAGTCTATA 59.863 47.826 0.00 0.00 0.00 1.31
3105 3925 2.092103 AGAAGCGAGAGGGTGAGTCTAT 60.092 50.000 0.00 0.00 0.00 1.98
3106 3926 1.282447 AGAAGCGAGAGGGTGAGTCTA 59.718 52.381 0.00 0.00 0.00 2.59
3107 3927 0.039035 AGAAGCGAGAGGGTGAGTCT 59.961 55.000 0.00 0.00 0.00 3.24
3108 3928 0.172352 CAGAAGCGAGAGGGTGAGTC 59.828 60.000 0.00 0.00 0.00 3.36
3109 3929 0.251386 TCAGAAGCGAGAGGGTGAGT 60.251 55.000 0.00 0.00 0.00 3.41
3110 3930 0.891373 TTCAGAAGCGAGAGGGTGAG 59.109 55.000 0.00 0.00 0.00 3.51
3111 3931 1.478510 GATTCAGAAGCGAGAGGGTGA 59.521 52.381 0.00 0.00 0.00 4.02
3112 3932 1.205655 TGATTCAGAAGCGAGAGGGTG 59.794 52.381 0.00 0.00 0.00 4.61
3113 3933 1.561643 TGATTCAGAAGCGAGAGGGT 58.438 50.000 0.00 0.00 0.00 4.34
3238 4058 0.107643 TCCACGGTGAAGCACATGAA 59.892 50.000 10.28 0.00 35.86 2.57
3393 4219 3.064820 CACTTTAACAAATCGGATCGGGG 59.935 47.826 0.00 0.00 0.00 5.73
3406 4232 7.030768 GGTTTACTGCTTTGAACACTTTAACA 58.969 34.615 0.00 0.00 0.00 2.41
3409 4235 5.889289 AGGGTTTACTGCTTTGAACACTTTA 59.111 36.000 0.00 0.00 32.10 1.85
3410 4236 4.709886 AGGGTTTACTGCTTTGAACACTTT 59.290 37.500 0.00 0.00 32.10 2.66
3411 4237 4.278310 AGGGTTTACTGCTTTGAACACTT 58.722 39.130 0.00 0.00 32.10 3.16
3413 4239 4.215613 CCTAGGGTTTACTGCTTTGAACAC 59.784 45.833 0.00 0.00 0.00 3.32
3414 4240 4.394729 CCTAGGGTTTACTGCTTTGAACA 58.605 43.478 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.