Multiple sequence alignment - TraesCS3A01G051200

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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 TraesCS3A01G051200 chr3A 100.000 3343 0 0 1 3343 27576899 27580241 0.000000e+00 6174.0
1 TraesCS3A01G051200 chr3A 85.676 370 36 13 979 1342 194470342 194469984 1.130000e-99 374.0
2 TraesCS3A01G051200 chr3A 95.238 210 5 1 3139 3343 562094973 562095182 8.940000e-86 327.0
3 TraesCS3A01G051200 chr3A 93.333 210 9 1 3139 3343 684742999 684743208 4.190000e-79 305.0
4 TraesCS3A01G051200 chr3A 95.000 60 3 0 3068 3127 9184512 9184453 9.870000e-16 95.3
5 TraesCS3A01G051200 chr3A 90.625 64 6 0 3064 3127 466513102 466513165 5.940000e-13 86.1
6 TraesCS3A01G051200 chr3B 88.746 1715 124 36 979 2638 32276686 32278386 0.000000e+00 2034.0
7 TraesCS3A01G051200 chr3B 89.634 955 55 17 373 1305 32244123 32245055 0.000000e+00 1175.0
8 TraesCS3A01G051200 chr3B 88.750 320 19 11 2745 3056 32278457 32278767 3.150000e-100 375.0
9 TraesCS3A01G051200 chr3B 93.776 241 10 3 979 1214 32265447 32265687 1.140000e-94 357.0
10 TraesCS3A01G051200 chr3B 93.361 241 11 2 979 1214 32072071 32072311 5.310000e-93 351.0
11 TraesCS3A01G051200 chr3B 92.083 240 17 2 979 1217 32075098 32075336 1.490000e-88 337.0
12 TraesCS3A01G051200 chr3B 86.722 241 27 5 1 238 32243636 32243874 2.560000e-66 263.0
13 TraesCS3A01G051200 chr3B 93.919 148 9 0 979 1126 32073317 32073464 1.210000e-54 224.0
14 TraesCS3A01G051200 chr3B 89.474 76 7 1 239 313 32267075 32267150 9.870000e-16 95.3
15 TraesCS3A01G051200 chr3B 92.188 64 5 0 3064 3127 12394498 12394435 1.280000e-14 91.6
16 TraesCS3A01G051200 chr3B 96.078 51 2 0 2700 2750 32278392 32278442 2.140000e-12 84.2
17 TraesCS3A01G051200 chr3B 83.562 73 11 1 241 312 32243919 32243991 2.150000e-07 67.6
18 TraesCS3A01G051200 chr3D 89.888 890 55 17 979 1836 19934806 19935692 0.000000e+00 1112.0
19 TraesCS3A01G051200 chr3D 90.282 710 49 13 979 1680 19954140 19954837 0.000000e+00 911.0
20 TraesCS3A01G051200 chr3D 85.789 760 69 22 1715 2446 19954949 19955697 0.000000e+00 769.0
21 TraesCS3A01G051200 chr3D 88.758 596 29 11 394 989 19904278 19904835 0.000000e+00 695.0
22 TraesCS3A01G051200 chr3D 92.113 355 22 4 18 369 19903790 19904141 2.320000e-136 496.0
23 TraesCS3A01G051200 chr3D 90.860 372 26 7 1044 1408 19913287 19913657 3.000000e-135 492.0
24 TraesCS3A01G051200 chr3D 84.483 522 42 20 2575 3068 19955704 19956214 2.330000e-131 479.0
25 TraesCS3A01G051200 chr3D 89.302 215 22 1 1393 1607 19915306 19915519 5.500000e-68 268.0
26 TraesCS3A01G051200 chr3D 86.307 241 27 5 1 238 19947024 19947261 1.190000e-64 257.0
27 TraesCS3A01G051200 chr3D 90.541 148 10 2 979 1126 19946927 19947070 3.400000e-45 193.0
28 TraesCS3A01G051200 chr3D 89.655 145 11 3 979 1123 19943958 19944098 7.370000e-42 182.0
29 TraesCS3A01G051200 chr3D 88.514 148 13 2 979 1126 19937856 19937999 3.430000e-40 176.0
30 TraesCS3A01G051200 chr3D 89.781 137 9 4 980 1116 19931287 19931418 1.590000e-38 171.0
31 TraesCS3A01G051200 chr3D 85.806 155 10 7 979 1126 19903670 19903819 1.610000e-33 154.0
32 TraesCS3A01G051200 chr2B 98.537 205 3 0 3139 3343 721722218 721722422 2.450000e-96 363.0
33 TraesCS3A01G051200 chr5A 94.762 210 5 2 3139 3343 606887358 606887150 4.160000e-84 322.0
34 TraesCS3A01G051200 chr6A 93.810 210 8 1 3139 3343 531393430 531393221 9.010000e-81 311.0
35 TraesCS3A01G051200 chr6A 93.333 210 7 2 3139 3341 595512419 595512210 1.510000e-78 303.0
36 TraesCS3A01G051200 chr2A 93.810 210 8 1 3139 3343 48257148 48257357 9.010000e-81 311.0
37 TraesCS3A01G051200 chr2A 93.810 210 8 1 3139 3343 516416744 516416535 9.010000e-81 311.0
38 TraesCS3A01G051200 chr4B 92.857 210 10 1 3139 3343 604142043 604142252 1.950000e-77 300.0
39 TraesCS3A01G051200 chr7A 93.548 62 4 0 3066 3127 519569788 519569727 3.550000e-15 93.5
40 TraesCS3A01G051200 chr4A 93.333 60 4 0 3068 3127 642128927 642128868 4.590000e-14 89.8
41 TraesCS3A01G051200 chr1B 93.220 59 4 0 3069 3127 593561898 593561956 1.650000e-13 87.9
42 TraesCS3A01G051200 chr1B 88.889 63 7 0 3065 3127 603219641 603219703 9.940000e-11 78.7
43 TraesCS3A01G051200 chr7D 91.667 60 5 0 3068 3127 119901534 119901593 2.140000e-12 84.2
44 TraesCS3A01G051200 chr5D 90.323 62 6 0 3057 3118 360374603 360374664 7.690000e-12 82.4


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 TraesCS3A01G051200 chr3A 27576899 27580241 3342 False 6174.000000 6174 100.000000 1 3343 1 chr3A.!!$F1 3342
1 TraesCS3A01G051200 chr3B 32276686 32278767 2081 False 831.066667 2034 91.191333 979 3056 3 chr3B.!!$F4 2077
2 TraesCS3A01G051200 chr3B 32243636 32245055 1419 False 501.866667 1175 86.639333 1 1305 3 chr3B.!!$F2 1304
3 TraesCS3A01G051200 chr3B 32072071 32075336 3265 False 304.000000 351 93.121000 979 1217 3 chr3B.!!$F1 238
4 TraesCS3A01G051200 chr3B 32265447 32267150 1703 False 226.150000 357 91.625000 239 1214 2 chr3B.!!$F3 975
5 TraesCS3A01G051200 chr3D 19954140 19956214 2074 False 719.666667 911 86.851333 979 3068 3 chr3D.!!$F5 2089
6 TraesCS3A01G051200 chr3D 19931287 19937999 6712 False 486.333333 1112 89.394333 979 1836 3 chr3D.!!$F3 857
7 TraesCS3A01G051200 chr3D 19903670 19904835 1165 False 448.333333 695 88.892333 18 1126 3 chr3D.!!$F1 1108
8 TraesCS3A01G051200 chr3D 19913287 19915519 2232 False 380.000000 492 90.081000 1044 1607 2 chr3D.!!$F2 563
9 TraesCS3A01G051200 chr3D 19943958 19947261 3303 False 210.666667 257 88.834333 1 1126 3 chr3D.!!$F4 1125

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
563 682 0.545646 TGGATCGCCATCACCATTCA 59.454 50.0 0.0 0.0 39.92 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2472 13051 0.037512 CTCCCTCTCTGCACAGTGTG 60.038 60.0 19.27 19.27 36.51 3.82 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
19 20 2.564721 AACTCCAAAAGGCGCCTGC 61.565 57.895 33.60 0.46 41.71 4.85
38 39 5.528870 CCTGCGAACCAAAGTATTTTTCTT 58.471 37.500 0.00 0.00 35.03 2.52
44 45 9.406828 GCGAACCAAAGTATTTTTCTTCTAAAT 57.593 29.630 0.00 0.00 35.03 1.40
80 81 7.873719 TTCAACAATTACAGAAGTTCAAGGA 57.126 32.000 5.50 0.00 0.00 3.36
110 111 6.640907 CCACTCACAATTAAACAAAACTAGCC 59.359 38.462 0.00 0.00 0.00 3.93
111 112 7.199766 CACTCACAATTAAACAAAACTAGCCA 58.800 34.615 0.00 0.00 0.00 4.75
140 141 5.584253 TGGTGCTTCAACTAGATCTAGAC 57.416 43.478 31.91 18.61 36.97 2.59
147 148 6.512091 GCTTCAACTAGATCTAGACACTACCG 60.512 46.154 31.91 14.59 36.97 4.02
172 173 6.763610 GCAACTGGAGTATTAGCTAGAAACAT 59.236 38.462 0.00 0.00 0.00 2.71
191 192 4.275810 ACATCATGGATCCAACCAAAGAG 58.724 43.478 20.67 6.22 43.47 2.85
192 193 4.018141 ACATCATGGATCCAACCAAAGAGA 60.018 41.667 20.67 7.18 43.47 3.10
194 195 4.335416 TCATGGATCCAACCAAAGAGAAC 58.665 43.478 20.67 0.00 43.47 3.01
195 196 4.043310 TCATGGATCCAACCAAAGAGAACT 59.957 41.667 20.67 0.00 43.47 3.01
201 202 4.703897 TCCAACCAAAGAGAACTACACAG 58.296 43.478 0.00 0.00 0.00 3.66
232 236 1.902918 AAACATCAGCCGCAAGCCA 60.903 52.632 0.00 0.00 45.47 4.75
257 303 2.305635 TCCAGCAACTTAGCATCTTCCA 59.694 45.455 0.00 0.00 36.85 3.53
258 304 2.681848 CCAGCAACTTAGCATCTTCCAG 59.318 50.000 0.00 0.00 36.85 3.86
262 308 4.006319 GCAACTTAGCATCTTCCAGAAGT 58.994 43.478 7.26 0.00 39.38 3.01
263 309 4.094146 GCAACTTAGCATCTTCCAGAAGTC 59.906 45.833 7.26 0.00 39.38 3.01
265 311 3.840666 ACTTAGCATCTTCCAGAAGTCCA 59.159 43.478 7.26 0.00 39.38 4.02
266 312 4.472833 ACTTAGCATCTTCCAGAAGTCCAT 59.527 41.667 7.26 0.00 39.38 3.41
267 313 3.278668 AGCATCTTCCAGAAGTCCATG 57.721 47.619 7.26 5.49 39.38 3.66
268 314 2.842496 AGCATCTTCCAGAAGTCCATGA 59.158 45.455 7.26 0.00 39.38 3.07
269 315 3.118334 AGCATCTTCCAGAAGTCCATGAG 60.118 47.826 7.26 0.00 39.38 2.90
270 316 3.118482 GCATCTTCCAGAAGTCCATGAGA 60.118 47.826 7.26 0.00 39.38 3.27
271 317 4.444591 GCATCTTCCAGAAGTCCATGAGAT 60.445 45.833 7.26 0.00 39.38 2.75
273 319 4.356436 TCTTCCAGAAGTCCATGAGATGA 58.644 43.478 7.26 0.00 39.38 2.92
274 320 4.405036 TCTTCCAGAAGTCCATGAGATGAG 59.595 45.833 7.26 0.00 39.38 2.90
275 321 3.986435 TCCAGAAGTCCATGAGATGAGA 58.014 45.455 0.00 0.00 0.00 3.27
276 322 4.356436 TCCAGAAGTCCATGAGATGAGAA 58.644 43.478 0.00 0.00 0.00 2.87
277 323 4.779489 TCCAGAAGTCCATGAGATGAGAAA 59.221 41.667 0.00 0.00 0.00 2.52
278 324 5.105023 TCCAGAAGTCCATGAGATGAGAAAG 60.105 44.000 0.00 0.00 0.00 2.62
312 359 4.578516 TCGAAAGCAGTCCAAAATGAGAAA 59.421 37.500 0.00 0.00 0.00 2.52
314 361 5.922544 CGAAAGCAGTCCAAAATGAGAAAAT 59.077 36.000 0.00 0.00 0.00 1.82
315 362 6.129009 CGAAAGCAGTCCAAAATGAGAAAATG 60.129 38.462 0.00 0.00 0.00 2.32
317 364 6.022163 AGCAGTCCAAAATGAGAAAATGAG 57.978 37.500 0.00 0.00 0.00 2.90
318 365 4.624452 GCAGTCCAAAATGAGAAAATGAGC 59.376 41.667 0.00 0.00 0.00 4.26
327 392 1.471684 GAGAAAATGAGCAGGTGCCAG 59.528 52.381 0.00 0.00 43.38 4.85
330 395 4.790962 ATGAGCAGGTGCCAGCCG 62.791 66.667 1.88 0.00 43.38 5.52
349 414 1.335506 CGTGTGCAAAACCATACACCC 60.336 52.381 0.00 0.00 40.08 4.61
369 434 2.820197 CCCCCTTAACAGCTTCTCAAAC 59.180 50.000 0.00 0.00 0.00 2.93
472 591 3.230976 GTTGGTTTCCCCATGTCTCTTT 58.769 45.455 0.00 0.00 44.74 2.52
473 592 3.154827 TGGTTTCCCCATGTCTCTTTC 57.845 47.619 0.00 0.00 38.72 2.62
474 593 2.716424 TGGTTTCCCCATGTCTCTTTCT 59.284 45.455 0.00 0.00 38.72 2.52
475 594 3.244911 TGGTTTCCCCATGTCTCTTTCTC 60.245 47.826 0.00 0.00 38.72 2.87
477 596 4.507512 GGTTTCCCCATGTCTCTTTCTCTT 60.508 45.833 0.00 0.00 0.00 2.85
478 597 5.280521 GGTTTCCCCATGTCTCTTTCTCTTA 60.281 44.000 0.00 0.00 0.00 2.10
482 601 4.141824 CCCCATGTCTCTTTCTCTTACTCC 60.142 50.000 0.00 0.00 0.00 3.85
485 604 4.792521 TGTCTCTTTCTCTTACTCCTGC 57.207 45.455 0.00 0.00 0.00 4.85
506 625 2.094258 CGCATCGTCAATGGGCATATAC 59.906 50.000 0.00 0.00 40.89 1.47
513 632 3.059188 GTCAATGGGCATATACCGTTTCG 60.059 47.826 1.35 0.00 35.08 3.46
562 681 3.402186 TGGATCGCCATCACCATTC 57.598 52.632 0.00 0.00 39.92 2.67
563 682 0.545646 TGGATCGCCATCACCATTCA 59.454 50.000 0.00 0.00 39.92 2.57
570 689 4.377021 TCGCCATCACCATTCACTATAAC 58.623 43.478 0.00 0.00 0.00 1.89
603 722 3.678056 ATGAAGAGTTTGTACTGCCGA 57.322 42.857 0.00 0.00 33.84 5.54
727 847 2.094234 GGTTGGTGGTCCATTTATGTGC 60.094 50.000 0.00 0.00 43.91 4.57
825 945 4.471904 AGCTGAGAATCCAATGTCGTAA 57.528 40.909 0.00 0.00 0.00 3.18
826 946 5.028549 AGCTGAGAATCCAATGTCGTAAT 57.971 39.130 0.00 0.00 0.00 1.89
828 948 4.024556 GCTGAGAATCCAATGTCGTAATGG 60.025 45.833 0.00 0.00 35.49 3.16
829 949 5.097742 TGAGAATCCAATGTCGTAATGGT 57.902 39.130 0.00 0.00 35.66 3.55
831 951 5.097742 AGAATCCAATGTCGTAATGGTGA 57.902 39.130 0.00 0.00 35.66 4.02
833 953 2.627945 TCCAATGTCGTAATGGTGAGC 58.372 47.619 0.00 0.00 35.66 4.26
834 954 2.236146 TCCAATGTCGTAATGGTGAGCT 59.764 45.455 0.00 0.00 35.66 4.09
841 961 1.268589 CGTAATGGTGAGCTCGATCGT 60.269 52.381 15.94 0.00 0.00 3.73
876 996 7.553881 ACACTGCTAAAATGTACATATGTCC 57.446 36.000 12.68 0.56 0.00 4.02
905 1025 6.535508 GCTTCCTAAATACTCGAGTGAATGTT 59.464 38.462 28.12 15.28 0.00 2.71
911 1031 3.305398 ACTCGAGTGAATGTTGGTCTC 57.695 47.619 19.30 0.00 0.00 3.36
928 1048 2.615912 GTCTCTGGCCTTATGCACAATC 59.384 50.000 3.32 0.00 43.89 2.67
934 1054 2.477863 GGCCTTATGCACAATCGTTGTC 60.478 50.000 0.00 0.00 43.23 3.18
962 1082 2.597455 AGTTCCAAGGGTGTTTGATGG 58.403 47.619 0.00 0.00 0.00 3.51
1041 4846 1.432251 CGAACGCGGGTCTATCTGT 59.568 57.895 12.47 0.00 0.00 3.41
1042 4847 0.591741 CGAACGCGGGTCTATCTGTC 60.592 60.000 12.47 0.00 0.00 3.51
1044 4849 0.456221 AACGCGGGTCTATCTGTCAG 59.544 55.000 12.47 0.00 0.00 3.51
1045 4850 1.299468 CGCGGGTCTATCTGTCAGC 60.299 63.158 0.00 0.00 0.00 4.26
1046 4851 1.816537 GCGGGTCTATCTGTCAGCA 59.183 57.895 0.00 0.00 0.00 4.41
1047 4852 0.249238 GCGGGTCTATCTGTCAGCAG 60.249 60.000 0.00 0.00 43.87 4.24
1059 4864 2.864946 CTGTCAGCAGAATCCAGAATCG 59.135 50.000 0.00 0.00 45.28 3.34
1281 6925 3.067461 CCGAAAACCTCAAACCAACATCA 59.933 43.478 0.00 0.00 0.00 3.07
1414 8723 6.147821 GCAAACTACTTACATTCTTGCAGAGA 59.852 38.462 0.00 0.00 38.03 3.10
1421 8730 3.452474 ACATTCTTGCAGAGATACGAGC 58.548 45.455 0.00 0.00 33.49 5.03
1427 8736 2.656002 TGCAGAGATACGAGCCTAAGT 58.344 47.619 0.00 0.00 0.00 2.24
1452 8763 7.991084 TTTCTGATTTCTGAACTGATCATGT 57.009 32.000 0.00 0.00 37.44 3.21
1599 8910 2.180204 GTGCTACGCCGCCATGATT 61.180 57.895 0.00 0.00 0.00 2.57
1679 8990 2.562738 CCAAACCCCATTTCTTCAGTCC 59.437 50.000 0.00 0.00 0.00 3.85
1756 9147 1.909302 GTTCCAAGGATCCCTGAGACA 59.091 52.381 12.24 0.00 32.13 3.41
1892 9605 0.475044 GGTAACCAACCCACCTCACA 59.525 55.000 0.00 0.00 43.16 3.58
1928 9768 2.977914 TCTATGCCACAACTCTGAAGC 58.022 47.619 0.00 0.00 0.00 3.86
1948 10996 4.433615 AGCCTGATAAACTCATACACACG 58.566 43.478 0.00 0.00 32.10 4.49
2038 12515 2.735762 GCTCTACCTCGGTAAGCAACTG 60.736 54.545 17.58 0.00 36.13 3.16
2039 12516 1.203994 TCTACCTCGGTAAGCAACTGC 59.796 52.381 0.00 0.00 42.49 4.40
2045 12522 0.040425 CGGTAAGCAACTGCCAACAC 60.040 55.000 0.00 0.00 43.38 3.32
2047 12524 1.318576 GTAAGCAACTGCCAACACCT 58.681 50.000 0.00 0.00 43.38 4.00
2094 12636 6.381133 TCTTCAGAATCCAATGTACTGAGCTA 59.619 38.462 0.00 0.00 38.52 3.32
2097 12639 4.406972 AGAATCCAATGTACTGAGCTAGCA 59.593 41.667 18.83 0.00 0.00 3.49
2099 12641 3.861840 TCCAATGTACTGAGCTAGCAAC 58.138 45.455 18.83 11.11 0.00 4.17
2108 12651 3.243569 ACTGAGCTAGCAACGATGATACC 60.244 47.826 18.83 0.00 0.00 2.73
2130 12678 3.951775 TCTTTGTTTTGGCAGTTGTGT 57.048 38.095 0.00 0.00 0.00 3.72
2132 12680 4.241681 TCTTTGTTTTGGCAGTTGTGTTC 58.758 39.130 0.00 0.00 0.00 3.18
2134 12682 3.951775 TGTTTTGGCAGTTGTGTTCTT 57.048 38.095 0.00 0.00 0.00 2.52
2232 12780 1.674322 CGTACCCACTTGGCCAAGG 60.674 63.158 41.04 30.03 42.53 3.61
2264 12812 1.762460 GCTCCGGAAGATCCCCAGA 60.762 63.158 5.23 0.00 31.13 3.86
2347 12901 2.923605 GCTCGCACGTCAACTAAACCTA 60.924 50.000 0.00 0.00 0.00 3.08
2364 12918 0.527565 CTACCCAGCCAACAACATGC 59.472 55.000 0.00 0.00 0.00 4.06
2369 12923 2.617788 CCCAGCCAACAACATGCTACTA 60.618 50.000 0.00 0.00 33.16 1.82
2375 12929 4.094442 GCCAACAACATGCTACTACTAACC 59.906 45.833 0.00 0.00 0.00 2.85
2381 12935 5.757099 ACATGCTACTACTAACCAACCTT 57.243 39.130 0.00 0.00 0.00 3.50
2390 12962 7.793948 ACTACTAACCAACCTTTACAGAGAT 57.206 36.000 0.00 0.00 0.00 2.75
2449 13025 0.250338 AAGACCTGAACGAACCCAGC 60.250 55.000 0.00 0.00 0.00 4.85
2460 13039 1.933853 CGAACCCAGCTAACTACATGC 59.066 52.381 0.00 0.00 0.00 4.06
2472 13051 5.333952 GCTAACTACATGCTCATCAATCAGC 60.334 44.000 0.00 0.00 36.08 4.26
2477 13057 2.484742 TGCTCATCAATCAGCACACT 57.515 45.000 0.00 0.00 40.80 3.55
2480 13060 2.159558 GCTCATCAATCAGCACACTGTG 60.160 50.000 6.19 6.19 44.77 3.66
2493 13073 1.229145 ACTGTGCAGAGAGGGAGCT 60.229 57.895 19.13 0.00 0.00 4.09
2506 13086 0.826715 GGGAGCTGCAGACAGATGTA 59.173 55.000 20.43 0.00 44.20 2.29
2507 13087 1.208052 GGGAGCTGCAGACAGATGTAA 59.792 52.381 20.43 0.00 44.20 2.41
2509 13089 3.539604 GGAGCTGCAGACAGATGTAAAT 58.460 45.455 20.43 0.00 44.20 1.40
2552 13179 4.454504 ACCTGAACGAACCAACATATGTTC 59.545 41.667 18.25 6.66 35.83 3.18
2593 13344 2.104729 GAGAGCGAGCCTGCAGAG 59.895 66.667 17.39 6.56 37.31 3.35
2600 13351 0.528033 CGAGCCTGCAGAGAGATGTG 60.528 60.000 17.39 0.00 0.00 3.21
2640 13391 8.918202 ATAAGACCTGAATGTAAAGTGTTTCA 57.082 30.769 0.00 0.00 0.00 2.69
2641 13392 6.619801 AGACCTGAATGTAAAGTGTTTCAC 57.380 37.500 0.00 0.00 34.10 3.18
2653 13415 7.602644 TGTAAAGTGTTTCACTCCTACATGATC 59.397 37.037 0.00 0.00 44.62 2.92
2660 13422 2.798847 CACTCCTACATGATCATGCGTG 59.201 50.000 31.17 23.98 42.39 5.34
2698 13460 4.602259 CCGTGCGACCAGTGGTGT 62.602 66.667 22.50 0.00 35.25 4.16
2721 13484 4.278669 TGGCGATCCTGTAAATCTCTCTAC 59.721 45.833 0.00 0.00 0.00 2.59
2768 13551 3.748568 GGTGCGATATCTTCTTTCCATCC 59.251 47.826 0.34 0.00 0.00 3.51
2802 13585 0.794473 CTTTCCGCTTTCCCGTGTAC 59.206 55.000 0.00 0.00 0.00 2.90
2808 13591 1.677353 GCTTTCCCGTGTACGCGTAC 61.677 60.000 36.15 36.15 38.18 3.67
2819 13602 3.006247 TGTACGCGTACCAGTGTATGTA 58.994 45.455 38.22 18.54 39.02 2.29
2820 13603 3.627123 TGTACGCGTACCAGTGTATGTAT 59.373 43.478 38.22 3.43 39.02 2.29
2821 13604 3.344904 ACGCGTACCAGTGTATGTATC 57.655 47.619 11.67 0.00 36.51 2.24
2822 13605 2.947652 ACGCGTACCAGTGTATGTATCT 59.052 45.455 11.67 0.00 36.51 1.98
2853 13636 2.106683 GTCGACCGCCATGGAAAGG 61.107 63.158 18.40 17.35 42.00 3.11
2895 13683 2.812358 CCATTGATGCATGGTGGATG 57.188 50.000 2.46 0.80 33.39 3.51
2903 13691 1.842007 CATGGTGGATGGAGGAGGG 59.158 63.158 0.00 0.00 0.00 4.30
2985 13785 0.034767 CCTGGAGCTGAGGCAATCAA 60.035 55.000 0.00 0.00 41.70 2.57
3047 13848 1.591504 GCTCCGATCTCCCGAGGATC 61.592 65.000 0.00 0.00 36.99 3.36
3074 13875 4.564110 GCCCCCTCGCGGCTAAAT 62.564 66.667 6.13 0.00 43.48 1.40
3075 13876 2.192175 CCCCCTCGCGGCTAAATT 59.808 61.111 6.13 0.00 0.00 1.82
3076 13877 1.453197 CCCCCTCGCGGCTAAATTT 60.453 57.895 6.13 0.00 0.00 1.82
3077 13878 1.444917 CCCCCTCGCGGCTAAATTTC 61.445 60.000 6.13 0.00 0.00 2.17
3078 13879 1.641677 CCCTCGCGGCTAAATTTCG 59.358 57.895 6.13 0.00 0.00 3.46
3079 13880 1.087771 CCCTCGCGGCTAAATTTCGT 61.088 55.000 6.13 0.00 0.00 3.85
3080 13881 0.026285 CCTCGCGGCTAAATTTCGTG 59.974 55.000 6.13 0.00 35.98 4.35
3081 13882 0.719465 CTCGCGGCTAAATTTCGTGT 59.281 50.000 6.13 0.00 36.07 4.49
3082 13883 1.127951 CTCGCGGCTAAATTTCGTGTT 59.872 47.619 6.13 0.00 36.07 3.32
3083 13884 1.532007 TCGCGGCTAAATTTCGTGTTT 59.468 42.857 6.13 0.00 36.07 2.83
3084 13885 2.031857 TCGCGGCTAAATTTCGTGTTTT 60.032 40.909 6.13 0.00 36.07 2.43
3085 13886 2.088360 CGCGGCTAAATTTCGTGTTTTG 59.912 45.455 0.00 0.00 0.00 2.44
3086 13887 3.301706 GCGGCTAAATTTCGTGTTTTGA 58.698 40.909 0.00 0.00 0.00 2.69
3087 13888 3.118972 GCGGCTAAATTTCGTGTTTTGAC 59.881 43.478 0.00 0.00 0.00 3.18
3088 13889 3.666797 CGGCTAAATTTCGTGTTTTGACC 59.333 43.478 0.00 0.00 0.00 4.02
3089 13890 3.985279 GGCTAAATTTCGTGTTTTGACCC 59.015 43.478 0.00 0.00 0.00 4.46
3090 13891 4.261867 GGCTAAATTTCGTGTTTTGACCCT 60.262 41.667 0.00 0.00 0.00 4.34
3091 13892 5.286438 GCTAAATTTCGTGTTTTGACCCTT 58.714 37.500 0.00 0.00 0.00 3.95
3092 13893 5.751509 GCTAAATTTCGTGTTTTGACCCTTT 59.248 36.000 0.00 0.00 0.00 3.11
3093 13894 6.256975 GCTAAATTTCGTGTTTTGACCCTTTT 59.743 34.615 0.00 0.00 0.00 2.27
3094 13895 6.656314 AAATTTCGTGTTTTGACCCTTTTC 57.344 33.333 0.00 0.00 0.00 2.29
3095 13896 5.592104 ATTTCGTGTTTTGACCCTTTTCT 57.408 34.783 0.00 0.00 0.00 2.52
3096 13897 6.702716 ATTTCGTGTTTTGACCCTTTTCTA 57.297 33.333 0.00 0.00 0.00 2.10
3097 13898 6.512342 TTTCGTGTTTTGACCCTTTTCTAA 57.488 33.333 0.00 0.00 0.00 2.10
3098 13899 6.702716 TTCGTGTTTTGACCCTTTTCTAAT 57.297 33.333 0.00 0.00 0.00 1.73
3099 13900 7.804843 TTCGTGTTTTGACCCTTTTCTAATA 57.195 32.000 0.00 0.00 0.00 0.98
3100 13901 7.989416 TCGTGTTTTGACCCTTTTCTAATAT 57.011 32.000 0.00 0.00 0.00 1.28
3101 13902 8.036273 TCGTGTTTTGACCCTTTTCTAATATC 57.964 34.615 0.00 0.00 0.00 1.63
3102 13903 7.881232 TCGTGTTTTGACCCTTTTCTAATATCT 59.119 33.333 0.00 0.00 0.00 1.98
3103 13904 8.512138 CGTGTTTTGACCCTTTTCTAATATCTT 58.488 33.333 0.00 0.00 0.00 2.40
3108 13909 9.509956 TTTGACCCTTTTCTAATATCTTTTCGA 57.490 29.630 0.00 0.00 0.00 3.71
3109 13910 8.718102 TGACCCTTTTCTAATATCTTTTCGAG 57.282 34.615 0.00 0.00 0.00 4.04
3110 13911 8.537016 TGACCCTTTTCTAATATCTTTTCGAGA 58.463 33.333 0.00 0.00 39.13 4.04
3111 13912 9.549078 GACCCTTTTCTAATATCTTTTCGAGAT 57.451 33.333 0.00 0.00 46.74 2.75
3112 13913 9.549078 ACCCTTTTCTAATATCTTTTCGAGATC 57.451 33.333 0.00 0.00 44.04 2.75
3113 13914 9.771534 CCCTTTTCTAATATCTTTTCGAGATCT 57.228 33.333 0.00 0.00 44.04 2.75
3124 13925 7.873719 TCTTTTCGAGATCTGATTCTAGTCT 57.126 36.000 0.00 0.00 0.00 3.24
3125 13926 7.702386 TCTTTTCGAGATCTGATTCTAGTCTG 58.298 38.462 0.00 0.00 0.00 3.51
3126 13927 7.554476 TCTTTTCGAGATCTGATTCTAGTCTGA 59.446 37.037 0.00 0.00 0.00 3.27
3127 13928 6.612247 TTCGAGATCTGATTCTAGTCTGAC 57.388 41.667 0.00 0.00 0.00 3.51
3128 13929 5.924356 TCGAGATCTGATTCTAGTCTGACT 58.076 41.667 15.57 15.57 0.00 3.41
3129 13930 7.056844 TCGAGATCTGATTCTAGTCTGACTA 57.943 40.000 16.17 16.17 0.00 2.59
3131 13932 6.929049 CGAGATCTGATTCTAGTCTGACTAGT 59.071 42.308 32.73 21.13 46.31 2.57
3132 13933 8.085909 CGAGATCTGATTCTAGTCTGACTAGTA 58.914 40.741 32.73 27.29 46.31 1.82
3133 13934 9.772973 GAGATCTGATTCTAGTCTGACTAGTAA 57.227 37.037 32.73 26.40 46.31 2.24
3139 13940 8.572185 TGATTCTAGTCTGACTAGTAATCATGC 58.428 37.037 33.98 23.83 46.31 4.06
3140 13941 7.881775 TTCTAGTCTGACTAGTAATCATGCA 57.118 36.000 32.73 15.63 46.31 3.96
3141 13942 7.265647 TCTAGTCTGACTAGTAATCATGCAC 57.734 40.000 32.73 0.00 46.31 4.57
3142 13943 4.926244 AGTCTGACTAGTAATCATGCACG 58.074 43.478 8.91 0.00 0.00 5.34
3143 13944 4.399618 AGTCTGACTAGTAATCATGCACGT 59.600 41.667 8.91 0.00 0.00 4.49
3144 13945 4.735822 GTCTGACTAGTAATCATGCACGTC 59.264 45.833 0.00 0.00 0.00 4.34
3145 13946 4.640647 TCTGACTAGTAATCATGCACGTCT 59.359 41.667 0.00 0.00 0.00 4.18
3146 13947 4.921547 TGACTAGTAATCATGCACGTCTC 58.078 43.478 0.00 0.00 0.00 3.36
3147 13948 3.953766 ACTAGTAATCATGCACGTCTCG 58.046 45.455 0.00 0.00 0.00 4.04
3148 13949 3.626217 ACTAGTAATCATGCACGTCTCGA 59.374 43.478 0.00 0.00 0.00 4.04
3149 13950 3.717400 AGTAATCATGCACGTCTCGAT 57.283 42.857 0.00 0.00 0.00 3.59
3150 13951 3.633235 AGTAATCATGCACGTCTCGATC 58.367 45.455 0.00 0.00 0.00 3.69
3151 13952 1.481240 AATCATGCACGTCTCGATCG 58.519 50.000 9.36 9.36 0.00 3.69
3152 13953 0.382158 ATCATGCACGTCTCGATCGT 59.618 50.000 15.94 9.42 42.33 3.73
3153 13954 1.011333 TCATGCACGTCTCGATCGTA 58.989 50.000 15.94 1.59 39.55 3.43
3154 13955 1.399089 TCATGCACGTCTCGATCGTAA 59.601 47.619 15.94 1.23 39.55 3.18
3155 13956 2.159490 TCATGCACGTCTCGATCGTAAA 60.159 45.455 15.94 0.00 39.55 2.01
3156 13957 2.334971 TGCACGTCTCGATCGTAAAA 57.665 45.000 15.94 0.00 39.55 1.52
3157 13958 1.980844 TGCACGTCTCGATCGTAAAAC 59.019 47.619 15.94 8.21 39.55 2.43
3158 13959 1.980844 GCACGTCTCGATCGTAAAACA 59.019 47.619 15.94 0.00 39.55 2.83
3159 13960 2.597305 GCACGTCTCGATCGTAAAACAT 59.403 45.455 15.94 0.00 39.55 2.71
3160 13961 3.539592 GCACGTCTCGATCGTAAAACATG 60.540 47.826 15.94 8.93 39.55 3.21
3161 13962 3.606777 CACGTCTCGATCGTAAAACATGT 59.393 43.478 15.94 0.00 39.55 3.21
3162 13963 3.606777 ACGTCTCGATCGTAAAACATGTG 59.393 43.478 15.94 0.00 39.78 3.21
3163 13964 3.849708 CGTCTCGATCGTAAAACATGTGA 59.150 43.478 15.94 0.00 0.00 3.58
3164 13965 4.322539 CGTCTCGATCGTAAAACATGTGAA 59.677 41.667 15.94 0.00 0.00 3.18
3165 13966 5.004440 CGTCTCGATCGTAAAACATGTGAAT 59.996 40.000 15.94 0.00 0.00 2.57
3166 13967 6.453791 CGTCTCGATCGTAAAACATGTGAATT 60.454 38.462 15.94 0.00 0.00 2.17
3167 13968 6.895040 GTCTCGATCGTAAAACATGTGAATTC 59.105 38.462 15.94 0.00 0.00 2.17
3168 13969 6.588373 TCTCGATCGTAAAACATGTGAATTCA 59.412 34.615 15.94 3.38 0.00 2.57
3169 13970 6.530567 TCGATCGTAAAACATGTGAATTCAC 58.469 36.000 28.10 28.10 46.59 3.18
3236 14037 8.479313 TGGATACATAATGTTTGATATCGCTC 57.521 34.615 0.00 0.00 46.17 5.03
3237 14038 8.093927 TGGATACATAATGTTTGATATCGCTCA 58.906 33.333 0.00 0.00 46.17 4.26
3238 14039 8.935844 GGATACATAATGTTTGATATCGCTCAA 58.064 33.333 0.00 0.00 33.42 3.02
3242 14043 9.454585 ACATAATGTTTGATATCGCTCAAATTG 57.545 29.630 9.72 0.00 44.48 2.32
3243 14044 9.454585 CATAATGTTTGATATCGCTCAAATTGT 57.545 29.630 9.72 0.62 44.48 2.71
3248 14049 9.853555 TGTTTGATATCGCTCAAATTGTATTTT 57.146 25.926 9.72 0.00 44.48 1.82
3255 14056 7.104326 TCGCTCAAATTGTATTTTCAAAAGC 57.896 32.000 0.00 0.00 0.00 3.51
3264 14065 6.125327 TGTATTTTCAAAAGCGAGACACAA 57.875 33.333 0.00 0.00 0.00 3.33
3265 14066 6.734137 TGTATTTTCAAAAGCGAGACACAAT 58.266 32.000 0.00 0.00 0.00 2.71
3266 14067 7.866729 TGTATTTTCAAAAGCGAGACACAATA 58.133 30.769 0.00 0.00 0.00 1.90
3268 14069 6.371809 TTTTCAAAAGCGAGACACAATAGT 57.628 33.333 0.00 0.00 0.00 2.12
3282 14083 4.414852 CACAATAGTGGTTATGTTGCTGC 58.585 43.478 0.00 0.00 42.13 5.25
3284 14085 4.706476 ACAATAGTGGTTATGTTGCTGCAT 59.294 37.500 1.84 0.00 0.00 3.96
3285 14086 5.885352 ACAATAGTGGTTATGTTGCTGCATA 59.115 36.000 1.84 0.00 0.00 3.14
3286 14087 6.038603 ACAATAGTGGTTATGTTGCTGCATAG 59.961 38.462 1.84 0.00 33.48 2.23
3287 14088 4.220693 AGTGGTTATGTTGCTGCATAGA 57.779 40.909 1.84 0.00 33.48 1.98
3288 14089 4.194640 AGTGGTTATGTTGCTGCATAGAG 58.805 43.478 1.84 0.00 33.48 2.43
3289 14090 3.941483 GTGGTTATGTTGCTGCATAGAGT 59.059 43.478 1.84 0.00 33.48 3.24
3290 14091 5.104941 AGTGGTTATGTTGCTGCATAGAGTA 60.105 40.000 1.84 0.00 33.48 2.59
3291 14092 5.584649 GTGGTTATGTTGCTGCATAGAGTAA 59.415 40.000 1.84 0.00 33.48 2.24
3292 14093 6.260936 GTGGTTATGTTGCTGCATAGAGTAAT 59.739 38.462 1.84 0.00 33.48 1.89
3293 14094 7.441157 GTGGTTATGTTGCTGCATAGAGTAATA 59.559 37.037 1.84 0.00 33.48 0.98
3294 14095 7.990314 TGGTTATGTTGCTGCATAGAGTAATAA 59.010 33.333 1.84 0.00 33.48 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.297830 AAAATACTTTGGTTCGCAGGC 57.702 42.857 0.00 0.00 0.00 4.85
38 39 7.048629 TGTTGAAAGCCATTGTTCATTTAGA 57.951 32.000 0.00 0.00 33.90 2.10
44 45 6.577103 TGTAATTGTTGAAAGCCATTGTTCA 58.423 32.000 0.00 0.00 31.99 3.18
50 51 6.655078 ACTTCTGTAATTGTTGAAAGCCAT 57.345 33.333 0.00 0.00 0.00 4.40
80 81 7.340999 AGTTTTGTTTAATTGTGAGTGGGTACT 59.659 33.333 0.00 0.00 40.66 2.73
116 117 6.155221 TGTCTAGATCTAGTTGAAGCACCATT 59.845 38.462 25.54 0.00 34.84 3.16
118 119 5.016831 TGTCTAGATCTAGTTGAAGCACCA 58.983 41.667 25.54 3.39 34.84 4.17
119 120 5.126384 AGTGTCTAGATCTAGTTGAAGCACC 59.874 44.000 25.54 10.94 34.84 5.01
120 121 6.202516 AGTGTCTAGATCTAGTTGAAGCAC 57.797 41.667 25.54 21.83 34.84 4.40
121 122 6.319152 GGTAGTGTCTAGATCTAGTTGAAGCA 59.681 42.308 25.54 14.38 34.84 3.91
122 123 6.512091 CGGTAGTGTCTAGATCTAGTTGAAGC 60.512 46.154 25.54 16.99 34.84 3.86
140 141 2.961526 ATACTCCAGTTGCGGTAGTG 57.038 50.000 0.00 0.00 0.00 2.74
147 148 6.106673 TGTTTCTAGCTAATACTCCAGTTGC 58.893 40.000 0.00 0.00 0.00 4.17
172 173 4.043310 AGTTCTCTTTGGTTGGATCCATGA 59.957 41.667 17.06 0.00 37.33 3.07
191 192 5.047847 TGACAACTGCTAACTGTGTAGTTC 58.952 41.667 0.00 0.00 43.53 3.01
192 193 8.486961 TGTTTGACAACTGCTAACTGTGTAGTT 61.487 37.037 0.00 0.00 40.71 2.24
194 195 5.293324 TGTTTGACAACTGCTAACTGTGTAG 59.707 40.000 0.00 0.00 33.58 2.74
195 196 5.179533 TGTTTGACAACTGCTAACTGTGTA 58.820 37.500 0.00 0.00 33.58 2.90
201 202 4.222114 GCTGATGTTTGACAACTGCTAAC 58.778 43.478 11.13 0.00 40.70 2.34
232 236 4.026356 AGATGCTAAGTTGCTGGAAGTT 57.974 40.909 7.17 7.17 35.30 2.66
257 303 6.617782 TTCTTTCTCATCTCATGGACTTCT 57.382 37.500 0.00 0.00 0.00 2.85
258 304 7.626028 GCTTTTCTTTCTCATCTCATGGACTTC 60.626 40.741 0.00 0.00 0.00 3.01
262 308 5.413833 GTGCTTTTCTTTCTCATCTCATGGA 59.586 40.000 0.00 0.00 0.00 3.41
263 309 5.415077 AGTGCTTTTCTTTCTCATCTCATGG 59.585 40.000 0.00 0.00 0.00 3.66
265 311 7.521871 AAAGTGCTTTTCTTTCTCATCTCAT 57.478 32.000 0.00 0.00 30.57 2.90
266 312 6.293081 CGAAAGTGCTTTTCTTTCTCATCTCA 60.293 38.462 13.78 0.00 44.69 3.27
267 313 6.073548 TCGAAAGTGCTTTTCTTTCTCATCTC 60.074 38.462 13.78 0.00 44.69 2.75
268 314 5.760253 TCGAAAGTGCTTTTCTTTCTCATCT 59.240 36.000 13.78 0.00 44.69 2.90
269 315 5.990408 TCGAAAGTGCTTTTCTTTCTCATC 58.010 37.500 13.78 0.00 44.69 2.92
270 316 6.377327 TTCGAAAGTGCTTTTCTTTCTCAT 57.623 33.333 13.78 0.00 44.69 2.90
271 317 5.811399 TTCGAAAGTGCTTTTCTTTCTCA 57.189 34.783 13.78 1.71 44.69 3.27
273 319 5.037385 GCTTTCGAAAGTGCTTTTCTTTCT 58.963 37.500 32.32 0.00 44.69 2.52
274 320 4.798387 TGCTTTCGAAAGTGCTTTTCTTTC 59.202 37.500 32.32 15.61 42.47 2.62
275 321 4.743493 TGCTTTCGAAAGTGCTTTTCTTT 58.257 34.783 32.32 5.10 42.47 2.52
276 322 4.142381 ACTGCTTTCGAAAGTGCTTTTCTT 60.142 37.500 32.32 10.58 42.47 2.52
277 323 3.378427 ACTGCTTTCGAAAGTGCTTTTCT 59.622 39.130 32.32 11.15 42.47 2.52
278 324 3.695816 ACTGCTTTCGAAAGTGCTTTTC 58.304 40.909 32.32 17.89 41.46 2.29
312 359 2.362120 GGCTGGCACCTGCTCATT 60.362 61.111 16.79 0.00 41.70 2.57
327 392 0.312416 TGTATGGTTTTGCACACGGC 59.688 50.000 0.00 0.00 45.13 5.68
330 395 1.000394 GGGGTGTATGGTTTTGCACAC 60.000 52.381 0.00 0.00 40.40 3.82
331 396 1.333177 GGGGTGTATGGTTTTGCACA 58.667 50.000 0.00 0.00 33.88 4.57
349 414 2.484264 CGTTTGAGAAGCTGTTAAGGGG 59.516 50.000 0.00 0.00 0.00 4.79
359 424 0.668535 AAACAGGCCGTTTGAGAAGC 59.331 50.000 20.08 0.00 46.22 3.86
369 434 1.841663 CGTGGTTCTCAAACAGGCCG 61.842 60.000 0.00 0.00 37.10 6.13
415 534 2.238898 ACCAGGGTAGTGGATACTTTGC 59.761 50.000 0.00 0.00 40.44 3.68
472 591 0.382158 CGATGCGCAGGAGTAAGAGA 59.618 55.000 18.32 0.00 0.00 3.10
473 592 0.101399 ACGATGCGCAGGAGTAAGAG 59.899 55.000 18.32 1.39 0.00 2.85
474 593 0.100682 GACGATGCGCAGGAGTAAGA 59.899 55.000 18.32 0.00 0.00 2.10
475 594 0.179137 TGACGATGCGCAGGAGTAAG 60.179 55.000 18.32 4.14 0.00 2.34
477 596 0.459899 ATTGACGATGCGCAGGAGTA 59.540 50.000 18.32 1.93 0.00 2.59
478 597 1.086067 CATTGACGATGCGCAGGAGT 61.086 55.000 18.32 15.64 0.00 3.85
482 601 2.711311 CCCATTGACGATGCGCAG 59.289 61.111 18.32 5.51 34.25 5.18
485 604 1.159285 ATATGCCCATTGACGATGCG 58.841 50.000 0.00 0.00 34.25 4.73
506 625 8.895932 AAAGAATAGATTGAAATTCGAAACGG 57.104 30.769 0.00 0.00 37.22 4.44
579 698 4.452455 CGGCAGTACAAACTCTTCATTTCT 59.548 41.667 0.00 0.00 31.97 2.52
580 699 4.451096 TCGGCAGTACAAACTCTTCATTTC 59.549 41.667 0.00 0.00 31.97 2.17
587 706 3.740115 ACATTTCGGCAGTACAAACTCT 58.260 40.909 0.00 0.00 31.97 3.24
727 847 4.035792 TCAACACGGACAATAAAGTTGTGG 59.964 41.667 0.00 0.00 37.97 4.17
825 945 1.227089 GCACGATCGAGCTCACCAT 60.227 57.895 27.01 1.72 0.00 3.55
826 946 2.181777 GCACGATCGAGCTCACCA 59.818 61.111 27.01 0.00 0.00 4.17
831 951 0.527169 CATGTGAGCACGATCGAGCT 60.527 55.000 34.89 34.89 44.25 4.09
833 953 1.585668 GTTCATGTGAGCACGATCGAG 59.414 52.381 24.34 16.03 0.00 4.04
834 954 1.067915 TGTTCATGTGAGCACGATCGA 60.068 47.619 24.34 0.00 30.24 3.59
841 961 2.837532 TAGCAGTGTTCATGTGAGCA 57.162 45.000 0.00 0.00 32.82 4.26
876 996 3.181489 ACTCGAGTATTTAGGAAGCACCG 60.181 47.826 18.46 0.00 44.74 4.94
905 1025 0.253044 GTGCATAAGGCCAGAGACCA 59.747 55.000 5.01 0.00 43.89 4.02
911 1031 1.382522 ACGATTGTGCATAAGGCCAG 58.617 50.000 5.01 0.00 43.89 4.85
928 1048 4.739716 CCTTGGAACTTCAAAATGACAACG 59.260 41.667 0.00 0.00 0.00 4.10
934 1054 4.670896 ACACCCTTGGAACTTCAAAATG 57.329 40.909 0.00 0.00 0.00 2.32
962 1082 0.178970 ATGATGCATCCTCCTTGGGC 60.179 55.000 23.67 0.00 36.20 5.36
1039 4844 2.897436 CGATTCTGGATTCTGCTGACA 58.103 47.619 0.00 0.00 0.00 3.58
1041 4846 1.207811 TGCGATTCTGGATTCTGCTGA 59.792 47.619 0.00 0.00 0.00 4.26
1042 4847 1.660167 TGCGATTCTGGATTCTGCTG 58.340 50.000 0.00 0.00 0.00 4.41
1044 4849 1.332997 CCTTGCGATTCTGGATTCTGC 59.667 52.381 0.00 0.00 0.00 4.26
1045 4850 2.636830 ACCTTGCGATTCTGGATTCTG 58.363 47.619 0.00 0.00 0.00 3.02
1046 4851 3.356529 AACCTTGCGATTCTGGATTCT 57.643 42.857 0.00 0.00 0.00 2.40
1047 4852 3.428045 CCAAACCTTGCGATTCTGGATTC 60.428 47.826 0.00 0.00 0.00 2.52
1281 6925 2.190538 CCTCCTCCCATTGCCATTTTT 58.809 47.619 0.00 0.00 0.00 1.94
1414 8723 7.278868 CAGAAATCAGAAAACTTAGGCTCGTAT 59.721 37.037 0.00 0.00 0.00 3.06
1421 8730 8.383318 TCAGTTCAGAAATCAGAAAACTTAGG 57.617 34.615 0.00 0.00 0.00 2.69
1427 8736 8.294577 CACATGATCAGTTCAGAAATCAGAAAA 58.705 33.333 0.00 0.00 37.89 2.29
1452 8763 2.101965 GCTGCAACGCAACACACA 59.898 55.556 0.00 0.00 38.41 3.72
1541 8852 2.432628 CCGCCACCTCGAACAGAC 60.433 66.667 0.00 0.00 0.00 3.51
1599 8910 3.776969 AGATGAAGAAGGTGAGCATGGTA 59.223 43.478 0.00 0.00 0.00 3.25
1679 8990 4.679654 GCTAATTCTGAAACAAAACCGTGG 59.320 41.667 0.00 0.00 0.00 4.94
1727 9118 2.484287 ATCCTTGGAACCGGCCTGTG 62.484 60.000 0.00 0.00 0.00 3.66
1892 9605 5.072736 TGGCATAGATCAGATCAGGATTGTT 59.927 40.000 13.14 0.00 0.00 2.83
1928 9768 4.433615 AGCGTGTGTATGAGTTTATCAGG 58.566 43.478 0.00 0.00 42.53 3.86
1948 10996 1.738099 CACCACCGTCTGCAGTAGC 60.738 63.158 14.67 4.68 42.57 3.58
2038 12515 1.160137 CTGCTACTGAAGGTGTTGGC 58.840 55.000 0.00 0.00 0.00 4.52
2039 12516 2.839486 TCTGCTACTGAAGGTGTTGG 57.161 50.000 0.00 0.00 0.00 3.77
2045 12522 2.355209 GGGGAGTTTCTGCTACTGAAGG 60.355 54.545 0.00 0.00 0.00 3.46
2047 12524 2.334977 TGGGGAGTTTCTGCTACTGAA 58.665 47.619 0.00 0.00 0.00 3.02
2108 12651 4.183101 ACACAACTGCCAAAACAAAGATG 58.817 39.130 0.00 0.00 0.00 2.90
2130 12678 0.669318 GGCACCGTCATCGTGAAGAA 60.669 55.000 0.00 0.00 35.01 2.52
2132 12680 2.444624 CGGCACCGTCATCGTGAAG 61.445 63.158 0.00 0.00 35.01 3.02
2134 12682 4.429212 CCGGCACCGTCATCGTGA 62.429 66.667 8.49 0.00 37.81 4.35
2330 12884 2.071540 GGGTAGGTTTAGTTGACGTGC 58.928 52.381 0.00 0.00 0.00 5.34
2347 12901 0.112218 TAGCATGTTGTTGGCTGGGT 59.888 50.000 0.00 0.00 38.55 4.51
2364 12918 8.345724 TCTCTGTAAAGGTTGGTTAGTAGTAG 57.654 38.462 0.00 0.00 0.00 2.57
2369 12923 5.479375 TCGATCTCTGTAAAGGTTGGTTAGT 59.521 40.000 0.00 0.00 0.00 2.24
2375 12929 2.854777 CGCTCGATCTCTGTAAAGGTTG 59.145 50.000 0.00 0.00 0.00 3.77
2381 12935 1.332065 CAGCTCGCTCGATCTCTGTAA 59.668 52.381 0.00 0.00 0.00 2.41
2449 13025 5.756833 TGCTGATTGATGAGCATGTAGTTAG 59.243 40.000 0.87 0.00 42.02 2.34
2460 13039 3.741805 CACAGTGTGCTGATTGATGAG 57.258 47.619 10.97 0.00 45.28 2.90
2472 13051 0.037512 CTCCCTCTCTGCACAGTGTG 60.038 60.000 19.27 19.27 36.51 3.82
2477 13057 3.385469 CAGCTCCCTCTCTGCACA 58.615 61.111 0.00 0.00 0.00 4.57
2487 13067 0.826715 TACATCTGTCTGCAGCTCCC 59.173 55.000 9.47 0.00 42.29 4.30
2488 13068 2.680312 TTACATCTGTCTGCAGCTCC 57.320 50.000 9.47 0.00 42.29 4.70
2493 13073 9.461312 AACCTTATAAATTTACATCTGTCTGCA 57.539 29.630 0.00 0.00 0.00 4.41
2506 13086 9.588096 AGGTCTTGTTCTGAACCTTATAAATTT 57.412 29.630 17.26 0.00 0.00 1.82
2507 13087 9.014297 CAGGTCTTGTTCTGAACCTTATAAATT 57.986 33.333 17.26 0.00 33.11 1.82
2509 13089 7.741785 TCAGGTCTTGTTCTGAACCTTATAAA 58.258 34.615 17.26 3.70 37.11 1.40
2529 13109 4.015872 ACATATGTTGGTTCGTTCAGGT 57.984 40.909 1.41 0.00 0.00 4.00
2568 13195 1.135915 CAGGCTCGCTCTCTGTAATGT 59.864 52.381 0.00 0.00 0.00 2.71
2593 13344 8.964476 TTATTCTGAACCTAAATCCACATCTC 57.036 34.615 0.00 0.00 0.00 2.75
2600 13351 7.565680 TCAGGTCTTATTCTGAACCTAAATCC 58.434 38.462 0.00 0.00 37.11 3.01
2640 13391 2.804572 GCACGCATGATCATGTAGGAGT 60.805 50.000 31.09 21.08 40.80 3.85
2641 13392 1.797046 GCACGCATGATCATGTAGGAG 59.203 52.381 31.09 22.22 40.80 3.69
2692 13454 0.036765 TTACAGGATCGCCACACCAC 60.037 55.000 0.00 0.00 36.29 4.16
2693 13455 0.687920 TTTACAGGATCGCCACACCA 59.312 50.000 0.00 0.00 36.29 4.17
2694 13456 1.940613 GATTTACAGGATCGCCACACC 59.059 52.381 0.00 0.00 36.29 4.16
2695 13457 2.866762 GAGATTTACAGGATCGCCACAC 59.133 50.000 0.00 0.00 36.29 3.82
2696 13458 2.766263 AGAGATTTACAGGATCGCCACA 59.234 45.455 0.00 0.00 36.29 4.17
2697 13459 3.068873 AGAGAGATTTACAGGATCGCCAC 59.931 47.826 0.00 0.00 36.29 5.01
2698 13460 3.300388 AGAGAGATTTACAGGATCGCCA 58.700 45.455 0.00 0.00 36.29 5.69
2768 13551 0.254462 GAAAGGAGGAAGCAGGGGAG 59.746 60.000 0.00 0.00 0.00 4.30
2802 13585 3.242969 ACAGATACATACACTGGTACGCG 60.243 47.826 3.53 3.53 36.17 6.01
2808 13591 5.886992 TCACGTAACAGATACATACACTGG 58.113 41.667 0.00 0.00 36.17 4.00
2819 13602 2.097036 TCGACCCATCACGTAACAGAT 58.903 47.619 0.00 0.00 0.00 2.90
2820 13603 1.200716 GTCGACCCATCACGTAACAGA 59.799 52.381 3.51 0.00 0.00 3.41
2821 13604 1.625616 GTCGACCCATCACGTAACAG 58.374 55.000 3.51 0.00 0.00 3.16
2822 13605 0.244450 GGTCGACCCATCACGTAACA 59.756 55.000 24.75 0.00 0.00 2.41
2853 13636 2.155279 GAGCCCTTGTGTTCTTCCTTC 58.845 52.381 0.00 0.00 0.00 3.46
2895 13683 4.154347 CGCTGTCTGCCCTCCTCC 62.154 72.222 0.00 0.00 38.78 4.30
2941 13737 6.452494 AATATAATCTCTACCCGTCCGATG 57.548 41.667 0.00 0.00 0.00 3.84
2951 13747 6.665680 TCAGCTCCAGGGAATATAATCTCTAC 59.334 42.308 0.00 0.00 0.00 2.59
3068 13869 4.866921 AGGGTCAAAACACGAAATTTAGC 58.133 39.130 0.00 0.00 32.44 3.09
3069 13870 7.704899 AGAAAAGGGTCAAAACACGAAATTTAG 59.295 33.333 0.00 0.00 32.44 1.85
3070 13871 7.548967 AGAAAAGGGTCAAAACACGAAATTTA 58.451 30.769 0.00 0.00 32.44 1.40
3071 13872 6.403049 AGAAAAGGGTCAAAACACGAAATTT 58.597 32.000 0.00 0.00 32.44 1.82
3072 13873 5.972935 AGAAAAGGGTCAAAACACGAAATT 58.027 33.333 0.00 0.00 32.44 1.82
3073 13874 5.592104 AGAAAAGGGTCAAAACACGAAAT 57.408 34.783 0.00 0.00 32.44 2.17
3074 13875 6.512342 TTAGAAAAGGGTCAAAACACGAAA 57.488 33.333 0.00 0.00 32.44 3.46
3075 13876 6.702716 ATTAGAAAAGGGTCAAAACACGAA 57.297 33.333 0.00 0.00 32.44 3.85
3076 13877 7.881232 AGATATTAGAAAAGGGTCAAAACACGA 59.119 33.333 0.00 0.00 32.44 4.35
3077 13878 8.040716 AGATATTAGAAAAGGGTCAAAACACG 57.959 34.615 0.00 0.00 32.44 4.49
3082 13883 9.509956 TCGAAAAGATATTAGAAAAGGGTCAAA 57.490 29.630 0.00 0.00 0.00 2.69
3083 13884 9.162764 CTCGAAAAGATATTAGAAAAGGGTCAA 57.837 33.333 0.00 0.00 0.00 3.18
3084 13885 8.537016 TCTCGAAAAGATATTAGAAAAGGGTCA 58.463 33.333 0.00 0.00 0.00 4.02
3085 13886 8.943909 TCTCGAAAAGATATTAGAAAAGGGTC 57.056 34.615 0.00 0.00 0.00 4.46
3086 13887 9.549078 GATCTCGAAAAGATATTAGAAAAGGGT 57.451 33.333 0.00 0.00 45.06 4.34
3087 13888 9.771534 AGATCTCGAAAAGATATTAGAAAAGGG 57.228 33.333 0.00 0.00 45.06 3.95
3098 13899 9.567776 AGACTAGAATCAGATCTCGAAAAGATA 57.432 33.333 0.00 0.00 45.06 1.98
3100 13901 7.554476 TCAGACTAGAATCAGATCTCGAAAAGA 59.446 37.037 0.00 0.00 38.72 2.52
3101 13902 7.643764 GTCAGACTAGAATCAGATCTCGAAAAG 59.356 40.741 0.00 0.00 0.00 2.27
3102 13903 7.338196 AGTCAGACTAGAATCAGATCTCGAAAA 59.662 37.037 0.00 0.00 0.00 2.29
3103 13904 6.826231 AGTCAGACTAGAATCAGATCTCGAAA 59.174 38.462 0.00 0.00 0.00 3.46
3104 13905 6.353323 AGTCAGACTAGAATCAGATCTCGAA 58.647 40.000 0.00 0.00 0.00 3.71
3105 13906 5.924356 AGTCAGACTAGAATCAGATCTCGA 58.076 41.667 0.00 0.00 0.00 4.04
3119 13920 5.589050 ACGTGCATGATTACTAGTCAGACTA 59.411 40.000 14.17 10.02 0.00 2.59
3120 13921 4.399618 ACGTGCATGATTACTAGTCAGACT 59.600 41.667 14.17 8.50 0.00 3.24
3121 13922 4.673441 ACGTGCATGATTACTAGTCAGAC 58.327 43.478 14.17 0.00 0.00 3.51
3122 13923 4.640647 AGACGTGCATGATTACTAGTCAGA 59.359 41.667 14.17 0.00 0.00 3.27
3123 13924 4.926244 AGACGTGCATGATTACTAGTCAG 58.074 43.478 14.17 0.00 0.00 3.51
3124 13925 4.495844 CGAGACGTGCATGATTACTAGTCA 60.496 45.833 14.17 0.00 0.00 3.41
3125 13926 3.969352 CGAGACGTGCATGATTACTAGTC 59.031 47.826 14.17 0.00 0.00 2.59
3126 13927 3.626217 TCGAGACGTGCATGATTACTAGT 59.374 43.478 14.17 0.00 0.00 2.57
3127 13928 4.210832 TCGAGACGTGCATGATTACTAG 57.789 45.455 14.17 6.88 0.00 2.57
3128 13929 4.610680 CGATCGAGACGTGCATGATTACTA 60.611 45.833 14.17 0.00 0.00 1.82
3129 13930 3.633235 GATCGAGACGTGCATGATTACT 58.367 45.455 14.17 6.19 0.00 2.24
3130 13931 2.402049 CGATCGAGACGTGCATGATTAC 59.598 50.000 14.17 1.25 0.00 1.89
3131 13932 2.032924 ACGATCGAGACGTGCATGATTA 59.967 45.455 24.34 0.00 42.37 1.75
3132 13933 1.202302 ACGATCGAGACGTGCATGATT 60.202 47.619 24.34 0.00 42.37 2.57
3133 13934 0.382158 ACGATCGAGACGTGCATGAT 59.618 50.000 24.34 0.00 42.37 2.45
3134 13935 1.011333 TACGATCGAGACGTGCATGA 58.989 50.000 24.34 6.89 43.73 3.07
3135 13936 1.822581 TTACGATCGAGACGTGCATG 58.177 50.000 24.34 3.82 43.73 4.06
3136 13937 2.554806 TTTACGATCGAGACGTGCAT 57.445 45.000 24.34 0.00 43.73 3.96
3137 13938 1.980844 GTTTTACGATCGAGACGTGCA 59.019 47.619 24.34 11.96 43.73 4.57
3138 13939 1.980844 TGTTTTACGATCGAGACGTGC 59.019 47.619 24.34 14.28 43.73 5.34
3139 13940 3.606777 ACATGTTTTACGATCGAGACGTG 59.393 43.478 24.34 23.08 43.73 4.49
3140 13941 3.606777 CACATGTTTTACGATCGAGACGT 59.393 43.478 24.34 20.49 45.75 4.34
3141 13942 3.849708 TCACATGTTTTACGATCGAGACG 59.150 43.478 24.34 12.09 0.00 4.18
3142 13943 5.756950 TTCACATGTTTTACGATCGAGAC 57.243 39.130 24.34 13.95 0.00 3.36
3143 13944 6.588373 TGAATTCACATGTTTTACGATCGAGA 59.412 34.615 24.34 6.22 0.00 4.04
3144 13945 6.678663 GTGAATTCACATGTTTTACGATCGAG 59.321 38.462 29.43 3.39 45.75 4.04
3145 13946 6.530567 GTGAATTCACATGTTTTACGATCGA 58.469 36.000 29.43 2.23 45.75 3.59
3146 13947 6.759261 GTGAATTCACATGTTTTACGATCG 57.241 37.500 29.43 14.88 45.75 3.69
3209 14010 9.453572 AGCGATATCAAACATTATGTATCCATT 57.546 29.630 0.00 0.00 32.29 3.16
3210 14011 9.102757 GAGCGATATCAAACATTATGTATCCAT 57.897 33.333 0.00 0.00 34.97 3.41
3211 14012 8.093927 TGAGCGATATCAAACATTATGTATCCA 58.906 33.333 0.00 0.00 0.00 3.41
3212 14013 8.479313 TGAGCGATATCAAACATTATGTATCC 57.521 34.615 0.00 0.00 0.00 2.59
3229 14030 8.859156 GCTTTTGAAAATACAATTTGAGCGATA 58.141 29.630 2.79 0.00 0.00 2.92
3230 14031 7.410728 CGCTTTTGAAAATACAATTTGAGCGAT 60.411 33.333 13.32 0.00 41.56 4.58
3231 14032 6.129221 CGCTTTTGAAAATACAATTTGAGCGA 60.129 34.615 13.32 0.00 41.56 4.93
3232 14033 6.002911 CGCTTTTGAAAATACAATTTGAGCG 58.997 36.000 2.79 5.51 38.04 5.03
3233 14034 7.104326 TCGCTTTTGAAAATACAATTTGAGC 57.896 32.000 2.79 0.00 0.00 4.26
3234 14035 8.420189 GTCTCGCTTTTGAAAATACAATTTGAG 58.580 33.333 2.79 0.00 0.00 3.02
3235 14036 7.918033 TGTCTCGCTTTTGAAAATACAATTTGA 59.082 29.630 2.79 0.00 0.00 2.69
3236 14037 7.998212 GTGTCTCGCTTTTGAAAATACAATTTG 59.002 33.333 0.00 0.00 0.00 2.32
3237 14038 7.704472 TGTGTCTCGCTTTTGAAAATACAATTT 59.296 29.630 0.00 0.00 0.00 1.82
3238 14039 7.199766 TGTGTCTCGCTTTTGAAAATACAATT 58.800 30.769 0.00 0.00 0.00 2.32
3239 14040 6.734137 TGTGTCTCGCTTTTGAAAATACAAT 58.266 32.000 0.00 0.00 0.00 2.71
3240 14041 6.125327 TGTGTCTCGCTTTTGAAAATACAA 57.875 33.333 0.00 0.00 0.00 2.41
3241 14042 5.743026 TGTGTCTCGCTTTTGAAAATACA 57.257 34.783 0.00 0.00 0.00 2.29
3242 14043 8.015658 ACTATTGTGTCTCGCTTTTGAAAATAC 58.984 33.333 0.00 0.00 0.00 1.89
3243 14044 8.015087 CACTATTGTGTCTCGCTTTTGAAAATA 58.985 33.333 0.00 0.00 39.24 1.40
3244 14045 6.857964 CACTATTGTGTCTCGCTTTTGAAAAT 59.142 34.615 0.00 0.00 39.24 1.82
3245 14046 6.198687 CACTATTGTGTCTCGCTTTTGAAAA 58.801 36.000 0.00 0.00 39.24 2.29
3246 14047 5.277779 CCACTATTGTGTCTCGCTTTTGAAA 60.278 40.000 6.55 0.00 42.34 2.69
3247 14048 4.213270 CCACTATTGTGTCTCGCTTTTGAA 59.787 41.667 6.55 0.00 42.34 2.69
3248 14049 3.745975 CCACTATTGTGTCTCGCTTTTGA 59.254 43.478 6.55 0.00 42.34 2.69
3249 14050 3.498397 ACCACTATTGTGTCTCGCTTTTG 59.502 43.478 6.55 0.00 42.34 2.44
3253 14054 4.081642 ACATAACCACTATTGTGTCTCGCT 60.082 41.667 6.55 0.00 42.34 4.93
3255 14056 5.445939 GCAACATAACCACTATTGTGTCTCG 60.446 44.000 6.55 0.00 42.34 4.04
3264 14065 5.928976 TCTATGCAGCAACATAACCACTAT 58.071 37.500 0.00 0.00 32.29 2.12
3265 14066 5.104941 ACTCTATGCAGCAACATAACCACTA 60.105 40.000 0.00 0.00 32.29 2.74
3266 14067 4.194640 CTCTATGCAGCAACATAACCACT 58.805 43.478 0.00 0.00 32.29 4.00
3268 14069 4.220693 ACTCTATGCAGCAACATAACCA 57.779 40.909 0.00 0.00 32.29 3.67
3269 14070 6.867662 ATTACTCTATGCAGCAACATAACC 57.132 37.500 0.00 0.00 32.29 2.85


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

AutoCloner maintained by Alex Coulton.