Multiple sequence alignment - TraesCS4B01G220700

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 TraesCS4B01G220700 chr4B 100.000 5597 0 0 1 5597 464156114 464161710 0.000000e+00 10336
1 TraesCS4B01G220700 chr4B 86.400 125 13 4 5248 5369 134464631 134464508 3.520000e-27 134
2 TraesCS4B01G220700 chr4D 94.705 1492 51 11 2547 4030 378260993 378262464 0.000000e+00 2292
3 TraesCS4B01G220700 chr4D 93.418 1337 64 12 4045 5374 378262448 378263767 0.000000e+00 1960
4 TraesCS4B01G220700 chr4D 89.490 1608 46 38 1 1550 378258741 378260283 0.000000e+00 1919
5 TraesCS4B01G220700 chr4D 92.133 572 20 10 1605 2166 378260296 378260852 0.000000e+00 784
6 TraesCS4B01G220700 chr4D 91.667 156 13 0 5372 5527 378263831 378263986 3.400000e-52 217
7 TraesCS4B01G220700 chr4D 88.889 171 13 5 2164 2333 295432529 295432364 7.350000e-49 206
8 TraesCS4B01G220700 chr4A 90.894 1186 51 32 704 1873 87415572 87414428 0.000000e+00 1539
9 TraesCS4B01G220700 chr4A 89.954 1085 72 16 4044 5118 87412817 87411760 0.000000e+00 1365
10 TraesCS4B01G220700 chr4A 94.937 869 36 3 3169 4030 87413667 87412800 0.000000e+00 1354
11 TraesCS4B01G220700 chr4A 93.928 527 23 5 2370 2887 87414190 87413664 0.000000e+00 787
12 TraesCS4B01G220700 chr4A 89.344 244 16 2 1933 2166 87414429 87414186 1.180000e-76 298
13 TraesCS4B01G220700 chr4A 84.921 252 24 7 1 252 87417065 87416828 5.600000e-60 243
14 TraesCS4B01G220700 chr4A 89.506 162 5 6 2463 2612 173646530 173646369 1.590000e-45 195
15 TraesCS4B01G220700 chr4A 95.522 67 3 0 2308 2374 285485432 285485366 2.130000e-19 108
16 TraesCS4B01G220700 chr4A 94.030 67 3 1 242 308 87416805 87416740 3.570000e-17 100
17 TraesCS4B01G220700 chr2A 87.319 276 30 5 2899 3171 71348701 71348428 1.510000e-80 311
18 TraesCS4B01G220700 chr2A 91.892 74 5 1 2308 2381 722077223 722077295 9.920000e-18 102
19 TraesCS4B01G220700 chr2A 90.667 75 6 1 2308 2381 690329401 690329327 1.280000e-16 99
20 TraesCS4B01G220700 chr3A 84.641 306 39 7 2873 3171 523754982 523754678 1.180000e-76 298
21 TraesCS4B01G220700 chr2D 86.397 272 33 4 2899 3167 72700521 72700251 1.520000e-75 294
22 TraesCS4B01G220700 chr2D 85.978 271 35 3 2899 3167 72440666 72440397 2.550000e-73 287
23 TraesCS4B01G220700 chr2B 86.029 272 35 3 2899 3167 109981463 109981192 7.090000e-74 289
24 TraesCS4B01G220700 chr2B 85.662 272 36 3 2899 3167 109934832 109934561 3.300000e-72 283
25 TraesCS4B01G220700 chr2B 97.260 73 2 0 5525 5597 615733278 615733206 2.120000e-24 124
26 TraesCS4B01G220700 chr3D 83.660 306 42 7 2873 3171 402804992 402804688 1.190000e-71 281
27 TraesCS4B01G220700 chr3D 82.639 288 43 6 2886 3169 560188335 560188051 1.200000e-61 248
28 TraesCS4B01G220700 chr3D 85.849 212 26 4 2164 2373 371367034 371366825 7.300000e-54 222
29 TraesCS4B01G220700 chr3D 89.216 102 7 4 5276 5374 65137512 65137412 2.120000e-24 124
30 TraesCS4B01G220700 chr3D 87.879 99 8 4 5274 5369 198706520 198706423 4.580000e-21 113
31 TraesCS4B01G220700 chr3D 92.958 71 4 1 2308 2378 197182369 197182300 9.920000e-18 102
32 TraesCS4B01G220700 chr7D 95.683 139 6 0 2176 2314 164749483 164749345 2.030000e-54 224
33 TraesCS4B01G220700 chr7D 85.377 212 27 4 2164 2373 234351369 234351160 3.400000e-52 217
34 TraesCS4B01G220700 chr7D 97.222 72 2 0 5526 5597 118599041 118598970 7.610000e-24 122
35 TraesCS4B01G220700 chr7B 90.588 170 10 3 2164 2330 645515165 645515331 2.620000e-53 220
36 TraesCS4B01G220700 chr7B 87.200 125 12 4 5248 5369 645300407 645300530 7.560000e-29 139
37 TraesCS4B01G220700 chr7B 84.677 124 16 2 5251 5371 59313565 59313688 2.740000e-23 121
38 TraesCS4B01G220700 chr7A 90.588 170 10 3 2164 2330 439786373 439786539 2.620000e-53 220
39 TraesCS4B01G220700 chr5B 90.588 170 10 3 2164 2330 394253629 394253463 2.620000e-53 220
40 TraesCS4B01G220700 chr5B 90.588 170 10 3 2164 2330 394256287 394256121 2.620000e-53 220
41 TraesCS4B01G220700 chr5A 90.588 170 10 3 2164 2330 311019702 311019868 2.620000e-53 220
42 TraesCS4B01G220700 chr5A 90.385 156 3 6 2463 2606 437176163 437176318 1.590000e-45 195
43 TraesCS4B01G220700 chr3B 92.568 148 11 0 2163 2310 630594061 630594208 4.390000e-51 213
44 TraesCS4B01G220700 chr3B 97.222 72 2 0 5526 5597 30526030 30526101 7.610000e-24 122
45 TraesCS4B01G220700 chr3B 94.872 78 3 1 5521 5597 758070259 758070336 2.740000e-23 121
46 TraesCS4B01G220700 chr3B 92.754 69 5 0 2308 2376 450376577 450376645 3.570000e-17 100
47 TraesCS4B01G220700 chr5D 92.517 147 11 0 2164 2310 175786825 175786679 1.580000e-50 211
48 TraesCS4B01G220700 chr5D 83.846 130 17 4 5248 5374 316880740 316880612 2.740000e-23 121
49 TraesCS4B01G220700 chr1A 89.103 156 5 6 2463 2606 539293231 539293386 3.440000e-42 183
50 TraesCS4B01G220700 chr1A 85.827 127 14 4 5248 5371 90351869 90351994 1.270000e-26 132
51 TraesCS4B01G220700 chr1B 82.273 220 29 7 2163 2377 471753555 471753769 1.240000e-41 182
52 TraesCS4B01G220700 chr1B 98.630 73 1 0 5525 5597 416827644 416827572 4.550000e-26 130
53 TraesCS4B01G220700 chr1B 97.260 73 2 0 5525 5597 670172550 670172478 2.120000e-24 124
54 TraesCS4B01G220700 chr1B 93.827 81 5 0 5517 5597 679525579 679525499 7.610000e-24 122
55 TraesCS4B01G220700 chrUn 85.185 135 17 3 5243 5374 32095530 32095396 9.780000e-28 135
56 TraesCS4B01G220700 chr6B 97.260 73 2 0 5525 5597 290716692 290716764 2.120000e-24 124
57 TraesCS4B01G220700 chr6B 94.805 77 4 0 5521 5597 8927078 8927154 2.740000e-23 121
58 TraesCS4B01G220700 chr6B 92.208 77 6 0 2298 2374 462910224 462910300 5.930000e-20 110


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 TraesCS4B01G220700 chr4B 464156114 464161710 5596 False 10336.000000 10336 100.0000 1 5597 1 chr4B.!!$F1 5596
1 TraesCS4B01G220700 chr4D 378258741 378263986 5245 False 1434.400000 2292 92.2826 1 5527 5 chr4D.!!$F1 5526
2 TraesCS4B01G220700 chr4A 87411760 87417065 5305 True 812.285714 1539 91.1440 1 5118 7 chr4A.!!$R3 5117
3 TraesCS4B01G220700 chr5B 394253463 394256287 2824 True 220.000000 220 90.5880 2164 2330 2 chr5B.!!$R1 166

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
45 46 0.173708 GACACCTCTGGTTAGGCTCG 59.826 60.000 0.00 0.0 40.62 5.03 F
352 400 0.315568 AGTGAGTGACTCTGGTTCGC 59.684 55.000 14.42 0.0 0.00 4.70 F
936 1849 0.337428 ATTTTGATGCTCCAGGGCCT 59.663 50.000 0.00 0.0 0.00 5.19 F
1489 2402 1.299976 GATGAAGGCTGTCCCGGTT 59.700 57.895 0.00 0.0 39.21 4.44 F
2310 3248 1.492764 TTTGGGACGGAGGGAGTATC 58.507 55.000 0.00 0.0 0.00 2.24 F
2447 3392 0.463295 CACAGGATGCTCGCTCCATT 60.463 55.000 9.12 0.0 42.53 3.16 F
3603 5732 0.323629 TTAGGCAACCTTCTGGGACG 59.676 55.000 0.00 0.0 38.76 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1161 2074 1.076014 GTTGGGGTTGGGGTACTGG 59.924 63.158 0.00 0.00 0.00 4.00 R
1419 2332 1.153978 GACGTCGTTGCGGATGGTA 60.154 57.895 0.00 0.00 35.98 3.25 R
2134 3072 1.546476 CCTCCAGAGTACAGACACACC 59.454 57.143 0.00 0.00 0.00 4.16 R
2430 3375 1.783031 GCAATGGAGCGAGCATCCTG 61.783 60.000 12.37 6.73 37.74 3.86 R
3597 5726 1.278127 GAGAAGTCAATTCCCGTCCCA 59.722 52.381 0.00 0.00 38.84 4.37 R
4316 6449 1.005156 TCGCTGCACATACACTGCA 60.005 52.632 0.00 0.00 42.42 4.41 R
4736 6870 0.308684 CAACAGCACACGCATGAACT 59.691 50.000 0.00 0.00 42.27 3.01 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
45 46 0.173708 GACACCTCTGGTTAGGCTCG 59.826 60.000 0.00 0.00 40.62 5.03
49 50 1.439644 CTCTGGTTAGGCTCGGCTC 59.560 63.158 0.00 0.00 0.00 4.70
126 130 6.089417 CAGAAAGCTTTATTAACAAAAGGGCG 59.911 38.462 12.68 0.00 35.04 6.13
127 131 4.450082 AGCTTTATTAACAAAAGGGCGG 57.550 40.909 11.94 0.00 35.04 6.13
128 132 3.194755 AGCTTTATTAACAAAAGGGCGGG 59.805 43.478 11.94 0.00 35.04 6.13
129 133 3.677700 GCTTTATTAACAAAAGGGCGGGG 60.678 47.826 11.94 0.00 35.04 5.73
156 160 8.366359 AGGAATATAAGAATTGTTGCCACTTT 57.634 30.769 0.00 0.00 0.00 2.66
237 280 4.608890 CGCCATTTCACTGCAATTTCAAAC 60.609 41.667 0.00 0.00 0.00 2.93
240 283 2.132740 TCACTGCAATTTCAAACGGC 57.867 45.000 0.00 0.00 0.00 5.68
258 301 1.439693 CTTTTTACACGTGCGGCCG 60.440 57.895 24.05 24.05 0.00 6.13
311 359 2.348666 CACCACTATTACTCGCACTTGC 59.651 50.000 0.00 0.00 37.78 4.01
328 376 1.171549 TGCTTGCATGCTGGAAACGA 61.172 50.000 23.31 0.00 0.00 3.85
331 379 0.874390 TTGCATGCTGGAAACGAGAC 59.126 50.000 20.33 0.00 0.00 3.36
338 386 2.071688 CTGGAAACGAGACCAGTGAG 57.928 55.000 14.61 0.00 45.82 3.51
339 387 1.341531 CTGGAAACGAGACCAGTGAGT 59.658 52.381 14.61 0.00 45.82 3.41
340 388 1.068588 TGGAAACGAGACCAGTGAGTG 59.931 52.381 0.00 0.00 0.00 3.51
341 389 1.340248 GGAAACGAGACCAGTGAGTGA 59.660 52.381 0.00 0.00 0.00 3.41
343 391 1.693627 AACGAGACCAGTGAGTGACT 58.306 50.000 0.00 0.00 34.02 3.41
344 392 1.240256 ACGAGACCAGTGAGTGACTC 58.760 55.000 5.47 5.47 29.75 3.36
345 393 1.202830 ACGAGACCAGTGAGTGACTCT 60.203 52.381 14.42 0.00 29.75 3.24
346 394 1.198867 CGAGACCAGTGAGTGACTCTG 59.801 57.143 14.42 4.53 39.10 3.35
351 399 2.057503 CAGTGAGTGACTCTGGTTCG 57.942 55.000 14.42 0.00 36.73 3.95
352 400 0.315568 AGTGAGTGACTCTGGTTCGC 59.684 55.000 14.42 0.00 0.00 4.70
353 401 0.667792 GTGAGTGACTCTGGTTCGCC 60.668 60.000 14.42 0.00 37.92 5.54
354 402 1.444553 GAGTGACTCTGGTTCGCCG 60.445 63.158 5.12 0.00 41.18 6.46
355 403 2.432628 GTGACTCTGGTTCGCCGG 60.433 66.667 0.00 0.00 45.14 6.13
356 404 4.373116 TGACTCTGGTTCGCCGGC 62.373 66.667 19.07 19.07 43.43 6.13
403 451 1.026718 CACTCCCTCACCGCCAAATC 61.027 60.000 0.00 0.00 0.00 2.17
457 505 1.098712 TCACGTGTGGGGTGAAAAGC 61.099 55.000 16.51 0.00 41.17 3.51
465 513 3.062466 GGTGAAAAGCCTCGCCCC 61.062 66.667 0.20 0.00 39.66 5.80
612 688 4.443621 GGGGGAAAGAAAAGAGACGATAG 58.556 47.826 0.00 0.00 46.19 2.08
677 753 2.097202 CGACACAGACGAGAAAGCAAAG 60.097 50.000 0.00 0.00 0.00 2.77
734 1621 4.964241 CCCTCCCCTCCCCCGATC 62.964 77.778 0.00 0.00 0.00 3.69
736 1623 4.220163 CTCCCCTCCCCCGATCGA 62.220 72.222 18.66 0.00 0.00 3.59
784 1696 2.847715 GGGGAATCGATCGGGGGT 60.848 66.667 16.41 0.00 0.00 4.95
798 1710 1.310216 GGGGGTTCGTTCCAATTCCG 61.310 60.000 1.77 0.00 0.00 4.30
799 1711 0.607217 GGGGTTCGTTCCAATTCCGT 60.607 55.000 1.77 0.00 0.00 4.69
820 1733 2.501610 GCCGCTTCTTCCGATCCT 59.498 61.111 0.00 0.00 0.00 3.24
847 1760 1.228657 GGCGTGCGTCCTCTTTTTCT 61.229 55.000 0.00 0.00 0.00 2.52
877 1790 0.466739 GGGTTTTCTGGGGACGTTGT 60.467 55.000 0.00 0.00 0.00 3.32
879 1792 1.066454 GGTTTTCTGGGGACGTTGTTG 59.934 52.381 0.00 0.00 0.00 3.33
936 1849 0.337428 ATTTTGATGCTCCAGGGCCT 59.663 50.000 0.00 0.00 0.00 5.19
953 1866 3.829048 TCGAGATCCGAGCCTGAC 58.171 61.111 2.65 0.00 43.23 3.51
974 1887 4.452733 GTCTCCCCGGGTTCGCAG 62.453 72.222 21.85 7.02 34.56 5.18
1419 2332 2.032681 GAGCACCAGAAGGCCGTT 59.967 61.111 0.00 0.00 39.06 4.44
1488 2401 1.903877 CTGATGAAGGCTGTCCCGGT 61.904 60.000 0.00 0.00 39.21 5.28
1489 2402 1.299976 GATGAAGGCTGTCCCGGTT 59.700 57.895 0.00 0.00 39.21 4.44
1602 2516 2.680312 ATATGTATGCCGGCAGCTAG 57.320 50.000 35.36 0.00 44.23 3.42
1684 2598 2.921121 TGTATGTCGACGTTGATGCTTC 59.079 45.455 16.79 0.00 0.00 3.86
1699 2613 4.646945 TGATGCTTCGAGGAATTAGTCTCT 59.353 41.667 0.00 0.00 0.00 3.10
1737 2651 1.949525 TGCTTTCACTTGCTTGAGGTC 59.050 47.619 0.00 0.00 0.00 3.85
1811 2729 7.539034 TGATTGACGATTCCCTCTATTGATA 57.461 36.000 0.00 0.00 0.00 2.15
1877 2799 8.842358 TTTGTCTACAAAAGTATTACCTGAGG 57.158 34.615 5.82 0.00 42.26 3.86
1892 2814 3.838317 ACCTGAGGACACTAACATGCTTA 59.162 43.478 4.99 0.00 0.00 3.09
2045 2976 9.314321 TCAGAAGTCTTTAGTAAAAACTCTGTG 57.686 33.333 18.12 11.48 0.00 3.66
2046 2977 9.314321 CAGAAGTCTTTAGTAAAAACTCTGTGA 57.686 33.333 2.12 0.00 0.00 3.58
2051 2983 8.640291 GTCTTTAGTAAAAACTCTGTGATCGAG 58.360 37.037 0.00 0.00 34.70 4.04
2061 2993 4.880120 ACTCTGTGATCGAGAATACGGTAA 59.120 41.667 3.44 0.00 32.87 2.85
2063 2995 5.758924 TCTGTGATCGAGAATACGGTAATG 58.241 41.667 0.00 0.00 0.00 1.90
2099 3031 6.051074 TCAATGATCTACAGTTGCCATACAG 58.949 40.000 0.00 0.00 0.00 2.74
2112 3047 2.099756 GCCATACAGTTTGATCCCTTGC 59.900 50.000 0.00 0.00 0.00 4.01
2128 3063 5.202004 TCCCTTGCCAACTGTTAAACTTTA 58.798 37.500 0.00 0.00 0.00 1.85
2134 3072 7.254227 TGCCAACTGTTAAACTTTAGTAGTG 57.746 36.000 0.00 0.00 37.12 2.74
2161 3099 1.895798 CTGTACTCTGGAGGCAGAACA 59.104 52.381 14.53 2.43 37.58 3.18
2162 3100 1.618837 TGTACTCTGGAGGCAGAACAC 59.381 52.381 2.58 0.00 0.00 3.32
2178 3116 5.715070 CAGAACACTACTCCCTCTGTAAAG 58.285 45.833 0.00 0.00 30.98 1.85
2179 3117 5.477291 CAGAACACTACTCCCTCTGTAAAGA 59.523 44.000 0.00 0.00 30.98 2.52
2181 3119 6.553852 AGAACACTACTCCCTCTGTAAAGAAA 59.446 38.462 0.00 0.00 0.00 2.52
2183 3121 8.431910 AACACTACTCCCTCTGTAAAGAAATA 57.568 34.615 0.00 0.00 0.00 1.40
2185 3123 7.674772 ACACTACTCCCTCTGTAAAGAAATACT 59.325 37.037 0.00 0.00 0.00 2.12
2186 3124 8.192110 CACTACTCCCTCTGTAAAGAAATACTC 58.808 40.741 0.00 0.00 0.00 2.59
2187 3125 6.547930 ACTCCCTCTGTAAAGAAATACTCC 57.452 41.667 0.00 0.00 0.00 3.85
2188 3126 5.425862 ACTCCCTCTGTAAAGAAATACTCCC 59.574 44.000 0.00 0.00 0.00 4.30
2189 3127 4.720273 TCCCTCTGTAAAGAAATACTCCCC 59.280 45.833 0.00 0.00 0.00 4.81
2240 3178 8.867112 TTGTCTAAATACGGATGTATCAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
2251 3189 6.748658 CGGATGTATCAAGTCACGTTTTAGTA 59.251 38.462 0.00 0.00 0.00 1.82
2256 3194 9.577110 TGTATCAAGTCACGTTTTAGTATTAGG 57.423 33.333 0.00 0.00 0.00 2.69
2309 3247 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
2310 3248 1.492764 TTTGGGACGGAGGGAGTATC 58.507 55.000 0.00 0.00 0.00 2.24
2330 3271 9.973450 GAGTATCAGAGCATTTAGATCACTAAA 57.027 33.333 0.00 0.00 42.50 1.85
2331 3272 9.979578 AGTATCAGAGCATTTAGATCACTAAAG 57.020 33.333 0.00 0.00 46.97 1.85
2334 3275 9.979578 ATCAGAGCATTTAGATCACTAAAGTAG 57.020 33.333 0.00 0.00 46.97 2.57
2335 3276 8.972127 TCAGAGCATTTAGATCACTAAAGTAGT 58.028 33.333 0.00 0.00 46.97 2.73
2347 3288 5.838531 ACTAAAGTAGTGATCTAAGCGCT 57.161 39.130 2.64 2.64 37.69 5.92
2348 3289 5.823353 ACTAAAGTAGTGATCTAAGCGCTC 58.177 41.667 12.06 0.00 37.69 5.03
2349 3290 4.993029 AAAGTAGTGATCTAAGCGCTCT 57.007 40.909 12.06 3.67 0.00 4.09
2350 3291 4.993029 AAGTAGTGATCTAAGCGCTCTT 57.007 40.909 12.06 2.09 36.35 2.85
2351 3292 6.452494 AAAGTAGTGATCTAAGCGCTCTTA 57.548 37.500 12.06 0.00 33.85 2.10
2353 3294 6.452494 AGTAGTGATCTAAGCGCTCTTAAA 57.548 37.500 12.06 0.00 34.62 1.52
2354 3295 7.045126 AGTAGTGATCTAAGCGCTCTTAAAT 57.955 36.000 12.06 0.00 34.62 1.40
2355 3296 7.493367 AGTAGTGATCTAAGCGCTCTTAAATT 58.507 34.615 12.06 0.00 34.62 1.82
2356 3297 7.982354 AGTAGTGATCTAAGCGCTCTTAAATTT 59.018 33.333 12.06 0.00 34.62 1.82
2357 3298 7.240414 AGTGATCTAAGCGCTCTTAAATTTC 57.760 36.000 12.06 0.76 34.62 2.17
2359 3300 7.550906 AGTGATCTAAGCGCTCTTAAATTTCTT 59.449 33.333 12.06 0.00 34.62 2.52
2360 3301 8.178313 GTGATCTAAGCGCTCTTAAATTTCTTT 58.822 33.333 12.06 0.00 34.62 2.52
2362 3303 9.639636 GATCTAAGCGCTCTTAAATTTCTTTAC 57.360 33.333 12.06 0.00 34.62 2.01
2363 3304 8.542497 TCTAAGCGCTCTTAAATTTCTTTACA 57.458 30.769 12.06 0.00 34.62 2.41
2364 3305 8.656849 TCTAAGCGCTCTTAAATTTCTTTACAG 58.343 33.333 12.06 0.00 34.62 2.74
2365 3306 7.435068 AAGCGCTCTTAAATTTCTTTACAGA 57.565 32.000 12.06 0.00 0.00 3.41
2366 3307 7.066374 AGCGCTCTTAAATTTCTTTACAGAG 57.934 36.000 2.64 0.00 36.48 3.35
2367 3308 6.092807 AGCGCTCTTAAATTTCTTTACAGAGG 59.907 38.462 2.64 0.00 35.45 3.69
2430 3375 5.611796 TGCATTGATTGTGAGACTTACAC 57.388 39.130 0.00 0.00 38.55 2.90
2447 3392 0.463295 CACAGGATGCTCGCTCCATT 60.463 55.000 9.12 0.00 42.53 3.16
2485 3455 7.092846 ACAAGTGTTACTTATGCCCTATTCTCT 60.093 37.037 0.00 0.00 36.03 3.10
2504 3474 1.751351 CTGAGATGGCCTAGTCAACGA 59.249 52.381 3.32 0.00 0.00 3.85
2609 3579 6.303054 TCTCTAAACCAACATGTTTCCATCA 58.697 36.000 8.77 0.00 39.15 3.07
2663 3722 3.223940 TCCCCAGTACCATTTTCCCTA 57.776 47.619 0.00 0.00 0.00 3.53
2871 4002 5.579511 GCATGCATCTTGCTACATTTTTCTT 59.420 36.000 14.21 0.00 45.31 2.52
2920 4051 9.998106 TTGCTTTGTAGGAATTCTATAGGATAC 57.002 33.333 5.23 0.00 0.00 2.24
2921 4052 9.154632 TGCTTTGTAGGAATTCTATAGGATACA 57.845 33.333 5.23 0.00 41.41 2.29
2922 4053 9.998106 GCTTTGTAGGAATTCTATAGGATACAA 57.002 33.333 5.23 1.71 41.41 2.41
2966 4097 9.447279 TCTATAGATCCCTTTGATTTGTAGGAA 57.553 33.333 0.00 0.00 33.02 3.36
2968 4099 8.930846 ATAGATCCCTTTGATTTGTAGGAATG 57.069 34.615 0.00 0.00 32.41 2.67
2971 4102 5.509498 TCCCTTTGATTTGTAGGAATGGAG 58.491 41.667 0.00 0.00 0.00 3.86
2975 4106 4.137116 TGATTTGTAGGAATGGAGTCCG 57.863 45.455 4.30 0.00 43.03 4.79
3046 4179 5.957771 ACATTAGCTCAGACCTATTGGAA 57.042 39.130 0.00 0.00 37.04 3.53
3126 4259 5.240891 TGTCATCTCATTTCCTGTGACTTC 58.759 41.667 0.00 0.00 37.46 3.01
3140 4273 5.545723 CCTGTGACTTCCCTATTCCTATGAT 59.454 44.000 0.00 0.00 0.00 2.45
3141 4274 6.043706 CCTGTGACTTCCCTATTCCTATGATT 59.956 42.308 0.00 0.00 0.00 2.57
3142 4275 7.420680 CCTGTGACTTCCCTATTCCTATGATTT 60.421 40.741 0.00 0.00 0.00 2.17
3143 4276 7.872138 TGTGACTTCCCTATTCCTATGATTTT 58.128 34.615 0.00 0.00 0.00 1.82
3144 4277 7.993183 TGTGACTTCCCTATTCCTATGATTTTC 59.007 37.037 0.00 0.00 0.00 2.29
3145 4278 7.445707 GTGACTTCCCTATTCCTATGATTTTCC 59.554 40.741 0.00 0.00 0.00 3.13
3146 4279 7.350921 TGACTTCCCTATTCCTATGATTTTCCT 59.649 37.037 0.00 0.00 0.00 3.36
3147 4280 8.814448 ACTTCCCTATTCCTATGATTTTCCTA 57.186 34.615 0.00 0.00 0.00 2.94
3148 4281 9.411848 ACTTCCCTATTCCTATGATTTTCCTAT 57.588 33.333 0.00 0.00 0.00 2.57
3149 4282 9.898152 CTTCCCTATTCCTATGATTTTCCTATC 57.102 37.037 0.00 0.00 0.00 2.08
3150 4283 8.393959 TCCCTATTCCTATGATTTTCCTATCC 57.606 38.462 0.00 0.00 0.00 2.59
3151 4284 8.193874 TCCCTATTCCTATGATTTTCCTATCCT 58.806 37.037 0.00 0.00 0.00 3.24
3152 4285 9.507381 CCCTATTCCTATGATTTTCCTATCCTA 57.493 37.037 0.00 0.00 0.00 2.94
3262 4399 6.748333 ACTATACGAAGCACACTGTACTTA 57.252 37.500 0.00 0.00 0.00 2.24
3281 4418 8.439971 TGTACTTATCCTTCCTGCAAATATGAT 58.560 33.333 0.00 0.00 0.00 2.45
3284 4421 7.885399 ACTTATCCTTCCTGCAAATATGATACC 59.115 37.037 0.00 0.00 0.00 2.73
3341 4478 9.424319 TGCTAGAGCTGTATTGCTATTTAATAC 57.576 33.333 2.72 0.00 44.17 1.89
3507 5636 4.147321 TCTTTGCAAAGGAAGAGCTCAAT 58.853 39.130 33.01 3.78 36.67 2.57
3579 5708 0.850100 TCAAAGAGGGTCTTGGCCAA 59.150 50.000 19.25 19.25 36.71 4.52
3597 5726 4.937201 CCAAAAGTTTAGGCAACCTTCT 57.063 40.909 0.00 0.00 35.77 2.85
3603 5732 0.323629 TTAGGCAACCTTCTGGGACG 59.676 55.000 0.00 0.00 38.76 4.79
4022 6151 9.601217 AGAAGCTTATTTGTGAATATCTACGTT 57.399 29.630 0.00 0.00 0.00 3.99
4024 6153 9.988350 AAGCTTATTTGTGAATATCTACGTTTG 57.012 29.630 0.00 0.00 0.00 2.93
4025 6154 9.378551 AGCTTATTTGTGAATATCTACGTTTGA 57.621 29.630 0.00 0.00 0.00 2.69
4026 6155 9.982291 GCTTATTTGTGAATATCTACGTTTGAA 57.018 29.630 0.00 0.00 0.00 2.69
4088 6217 9.725019 ATTAAGCTATAATGCTGCAGTTATGTA 57.275 29.630 16.64 3.64 43.24 2.29
4089 6218 9.725019 TTAAGCTATAATGCTGCAGTTATGTAT 57.275 29.630 16.64 8.78 43.24 2.29
4091 6220 8.261492 AGCTATAATGCTGCAGTTATGTATTC 57.739 34.615 16.64 0.00 42.33 1.75
4092 6221 8.099537 AGCTATAATGCTGCAGTTATGTATTCT 58.900 33.333 16.64 0.97 42.33 2.40
4093 6222 8.386606 GCTATAATGCTGCAGTTATGTATTCTC 58.613 37.037 16.64 0.00 0.00 2.87
4094 6223 7.678947 ATAATGCTGCAGTTATGTATTCTCC 57.321 36.000 16.64 0.00 0.00 3.71
4213 6344 9.582431 TTTACTGATCCAGAAAAATCTACTACG 57.418 33.333 0.45 0.00 35.18 3.51
4215 6346 7.837863 ACTGATCCAGAAAAATCTACTACGAA 58.162 34.615 0.45 0.00 35.18 3.85
4216 6347 7.976734 ACTGATCCAGAAAAATCTACTACGAAG 59.023 37.037 0.45 0.00 35.18 3.79
4236 6367 7.464358 ACGAAGTACAATAATTCACTGATTGC 58.536 34.615 0.00 0.00 41.94 3.56
4267 6398 2.430465 CAGTGCTATGAGCTGTTTGGT 58.570 47.619 0.00 0.00 42.97 3.67
4271 6402 4.003648 GTGCTATGAGCTGTTTGGTAACT 58.996 43.478 0.00 0.00 42.97 2.24
4280 6411 5.865085 AGCTGTTTGGTAACTGATTCTGTA 58.135 37.500 0.00 0.00 35.81 2.74
4306 6439 4.400884 AGCATCTCTAGTAACTGACACTGG 59.599 45.833 0.00 0.00 0.00 4.00
4316 6449 6.476378 AGTAACTGACACTGGATATTTTGCT 58.524 36.000 0.00 0.00 0.00 3.91
4525 6658 0.740868 GCAGCCTATCACGAACAGCA 60.741 55.000 0.00 0.00 0.00 4.41
4730 6864 1.871676 CGATGCCAAGATGAGGACATG 59.128 52.381 0.00 0.00 36.82 3.21
4736 6870 4.080413 TGCCAAGATGAGGACATGTGATAA 60.080 41.667 1.15 0.00 36.82 1.75
5118 7256 3.431905 GAGCATCATCTGACTGGTGTCAT 60.432 47.826 0.00 0.00 43.22 3.06
5134 7272 4.154015 GGTGTCATGTTCGATTTGTGATGA 59.846 41.667 0.00 0.00 0.00 2.92
5173 7311 5.015733 GTGAAAGCTCATTTGATCGTTACG 58.984 41.667 0.00 0.00 33.05 3.18
5188 7326 7.140705 TGATCGTTACGTTGTCTCTTCTTTTA 58.859 34.615 4.24 0.00 0.00 1.52
5192 7330 3.400255 ACGTTGTCTCTTCTTTTAGGCC 58.600 45.455 0.00 0.00 0.00 5.19
5247 7455 4.654724 AGGACTAGGGAAACTATAAGGCAC 59.345 45.833 0.00 0.00 0.00 5.01
5269 7494 7.655490 GCACCTTTGCTTCATAGAATATGAAT 58.345 34.615 11.52 0.00 46.17 2.57
5307 7532 7.493971 AGAAAATTCATAGGAAGTGAGATGACG 59.506 37.037 0.00 0.00 36.25 4.35
5321 7546 2.015736 ATGACGTGCATCTCAACTCC 57.984 50.000 0.00 0.00 28.85 3.85
5327 7552 5.105513 TGACGTGCATCTCAACTCCTATAAA 60.106 40.000 0.00 0.00 0.00 1.40
5328 7553 5.352284 ACGTGCATCTCAACTCCTATAAAG 58.648 41.667 0.00 0.00 0.00 1.85
5351 7938 7.959689 AGAAATAGATGTCTGTGATGCATAC 57.040 36.000 0.00 0.00 0.00 2.39
5365 7952 9.162793 CTGTGATGCATACGATAAGAATTTTTC 57.837 33.333 0.00 0.00 0.00 2.29
5366 7953 8.672815 TGTGATGCATACGATAAGAATTTTTCA 58.327 29.630 0.00 0.00 0.00 2.69
5367 7954 9.669353 GTGATGCATACGATAAGAATTTTTCAT 57.331 29.630 0.00 0.00 0.00 2.57
5392 8046 5.414454 TGAATCAATTCCTACGAACCAAAGG 59.586 40.000 0.00 0.00 35.97 3.11
5396 8050 3.622166 TTCCTACGAACCAAAGGGATC 57.378 47.619 0.00 0.00 38.05 3.36
5476 8130 0.038744 TCCTACGGACGAAAGGAGGT 59.961 55.000 13.65 0.00 34.46 3.85
5490 8144 5.126384 CGAAAGGAGGTCTAAGAAGTGAGAT 59.874 44.000 0.00 0.00 0.00 2.75
5499 8153 6.818644 GGTCTAAGAAGTGAGATGCATTGTAA 59.181 38.462 0.00 0.00 0.00 2.41
5516 8170 7.962373 TGCATTGTAACTCAAATTCTATGAACG 59.038 33.333 0.00 0.00 39.62 3.95
5527 8181 7.279090 TCAAATTCTATGAACGGCGATAGAAAA 59.721 33.333 24.23 10.62 41.97 2.29
5528 8182 7.548196 AATTCTATGAACGGCGATAGAAAAA 57.452 32.000 24.23 10.07 41.97 1.94
5529 8183 5.961395 TCTATGAACGGCGATAGAAAAAC 57.039 39.130 16.62 0.00 39.76 2.43
5530 8184 5.412640 TCTATGAACGGCGATAGAAAAACA 58.587 37.500 16.62 0.00 39.76 2.83
5531 8185 4.600012 ATGAACGGCGATAGAAAAACAG 57.400 40.909 16.62 0.00 39.76 3.16
5532 8186 3.395639 TGAACGGCGATAGAAAAACAGT 58.604 40.909 16.62 0.00 39.76 3.55
5533 8187 3.810941 TGAACGGCGATAGAAAAACAGTT 59.189 39.130 16.62 0.00 39.76 3.16
5534 8188 4.273969 TGAACGGCGATAGAAAAACAGTTT 59.726 37.500 16.62 0.00 39.76 2.66
5535 8189 4.823790 ACGGCGATAGAAAAACAGTTTT 57.176 36.364 16.62 5.37 39.70 2.43
5536 8190 4.533222 ACGGCGATAGAAAAACAGTTTTG 58.467 39.130 16.62 0.05 37.07 2.44
5537 8191 3.360758 CGGCGATAGAAAAACAGTTTTGC 59.639 43.478 12.13 10.32 37.07 3.68
5538 8192 4.546570 GGCGATAGAAAAACAGTTTTGCT 58.453 39.130 21.05 21.05 41.40 3.91
5539 8193 5.615984 CGGCGATAGAAAAACAGTTTTGCTA 60.616 40.000 23.53 23.53 43.17 3.49
5540 8194 5.795441 GGCGATAGAAAAACAGTTTTGCTAG 59.205 40.000 24.79 16.32 42.49 3.42
5541 8195 6.348213 GGCGATAGAAAAACAGTTTTGCTAGA 60.348 38.462 24.79 10.99 42.49 2.43
5542 8196 7.075741 GCGATAGAAAAACAGTTTTGCTAGAA 58.924 34.615 24.79 10.38 42.49 2.10
5543 8197 7.059602 GCGATAGAAAAACAGTTTTGCTAGAAC 59.940 37.037 24.79 18.38 42.49 3.01
5544 8198 8.283291 CGATAGAAAAACAGTTTTGCTAGAACT 58.717 33.333 24.79 12.86 42.49 3.01
5545 8199 9.600646 GATAGAAAAACAGTTTTGCTAGAACTC 57.399 33.333 24.79 16.48 42.49 3.01
5546 8200 7.391148 AGAAAAACAGTTTTGCTAGAACTCA 57.609 32.000 16.71 0.00 36.75 3.41
5547 8201 8.000780 AGAAAAACAGTTTTGCTAGAACTCAT 57.999 30.769 16.71 0.00 36.75 2.90
5548 8202 8.131731 AGAAAAACAGTTTTGCTAGAACTCATC 58.868 33.333 16.71 4.41 36.75 2.92
5549 8203 7.573968 AAAACAGTTTTGCTAGAACTCATCT 57.426 32.000 10.62 0.00 42.48 2.90
5550 8204 8.677148 AAAACAGTTTTGCTAGAACTCATCTA 57.323 30.769 10.62 0.00 39.71 1.98
5551 8205 8.677148 AAACAGTTTTGCTAGAACTCATCTAA 57.323 30.769 0.00 0.00 40.12 2.10
5552 8206 8.677148 AACAGTTTTGCTAGAACTCATCTAAA 57.323 30.769 0.00 0.00 40.12 1.85
5553 8207 8.854614 ACAGTTTTGCTAGAACTCATCTAAAT 57.145 30.769 0.00 0.00 40.12 1.40
5554 8208 8.725148 ACAGTTTTGCTAGAACTCATCTAAATG 58.275 33.333 0.00 0.00 40.12 2.32
5555 8209 8.180267 CAGTTTTGCTAGAACTCATCTAAATGG 58.820 37.037 0.00 0.00 40.12 3.16
5556 8210 7.337942 AGTTTTGCTAGAACTCATCTAAATGGG 59.662 37.037 0.00 0.00 40.12 4.00
5557 8211 6.560003 TTGCTAGAACTCATCTAAATGGGA 57.440 37.500 0.00 0.00 40.12 4.37
5558 8212 6.753913 TGCTAGAACTCATCTAAATGGGAT 57.246 37.500 0.00 0.00 40.12 3.85
5559 8213 7.855784 TGCTAGAACTCATCTAAATGGGATA 57.144 36.000 0.00 0.00 40.12 2.59
5560 8214 8.441311 TGCTAGAACTCATCTAAATGGGATAT 57.559 34.615 0.00 0.00 40.12 1.63
5561 8215 9.547279 TGCTAGAACTCATCTAAATGGGATATA 57.453 33.333 0.00 0.00 40.12 0.86
5576 8230 9.659135 AAATGGGATATAATTTGGTCTCATTCA 57.341 29.630 10.37 0.00 40.02 2.57
5577 8231 8.641498 ATGGGATATAATTTGGTCTCATTCAC 57.359 34.615 0.00 0.00 27.57 3.18
5578 8232 7.004086 TGGGATATAATTTGGTCTCATTCACC 58.996 38.462 0.00 0.00 0.00 4.02
5579 8233 7.147141 TGGGATATAATTTGGTCTCATTCACCT 60.147 37.037 0.00 0.00 34.66 4.00
5580 8234 7.725844 GGGATATAATTTGGTCTCATTCACCTT 59.274 37.037 0.00 0.00 34.66 3.50
5581 8235 9.136323 GGATATAATTTGGTCTCATTCACCTTT 57.864 33.333 0.00 0.00 34.66 3.11
5587 8241 7.391148 TTTGGTCTCATTCACCTTTTATAGC 57.609 36.000 0.00 0.00 34.66 2.97
5588 8242 5.437060 TGGTCTCATTCACCTTTTATAGCC 58.563 41.667 0.00 0.00 34.66 3.93
5589 8243 5.045213 TGGTCTCATTCACCTTTTATAGCCA 60.045 40.000 0.00 0.00 34.66 4.75
5590 8244 6.064717 GGTCTCATTCACCTTTTATAGCCAT 58.935 40.000 0.00 0.00 0.00 4.40
5591 8245 6.547510 GGTCTCATTCACCTTTTATAGCCATT 59.452 38.462 0.00 0.00 0.00 3.16
5592 8246 7.420800 GTCTCATTCACCTTTTATAGCCATTG 58.579 38.462 0.00 0.00 0.00 2.82
5593 8247 6.547141 TCTCATTCACCTTTTATAGCCATTGG 59.453 38.462 0.00 0.00 0.00 3.16
5594 8248 6.430864 TCATTCACCTTTTATAGCCATTGGA 58.569 36.000 6.95 0.00 0.00 3.53
5595 8249 7.068702 TCATTCACCTTTTATAGCCATTGGAT 58.931 34.615 6.95 1.78 0.00 3.41
5596 8250 6.713762 TTCACCTTTTATAGCCATTGGATG 57.286 37.500 6.95 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.796796 CTCCGCTTTTGCTAGTGGC 59.203 57.895 8.27 0.00 43.92 5.01
29 30 2.359967 GCCGAGCCTAACCAGAGGT 61.360 63.158 0.00 0.00 39.02 3.85
49 50 2.930826 AGTGGTAGTGGTCAGGTTTG 57.069 50.000 0.00 0.00 0.00 2.93
126 130 6.239317 GGCAACAATTCTTATATTCCTTCCCC 60.239 42.308 0.00 0.00 0.00 4.81
127 131 6.749139 GGCAACAATTCTTATATTCCTTCCC 58.251 40.000 0.00 0.00 0.00 3.97
156 160 2.391724 GACGGAGGGGCTTGTTGTCA 62.392 60.000 0.00 0.00 0.00 3.58
163 167 2.203938 TTGGAGACGGAGGGGCTT 60.204 61.111 0.00 0.00 0.00 4.35
237 280 1.439693 CCGCACGTGTAAAAAGCCG 60.440 57.895 18.38 9.11 0.00 5.52
240 283 1.439693 CGGCCGCACGTGTAAAAAG 60.440 57.895 14.67 1.12 0.00 2.27
258 301 3.122971 GCCGCACGGTAAACTCCC 61.123 66.667 11.27 0.00 37.65 4.30
311 359 1.135859 GTCTCGTTTCCAGCATGCAAG 60.136 52.381 21.98 11.91 31.97 4.01
328 376 1.626686 CCAGAGTCACTCACTGGTCT 58.373 55.000 7.77 0.00 45.53 3.85
337 385 2.651361 CGGCGAACCAGAGTCACT 59.349 61.111 0.00 0.00 34.57 3.41
338 386 2.432628 CCGGCGAACCAGAGTCAC 60.433 66.667 9.30 0.00 34.57 3.67
339 387 4.373116 GCCGGCGAACCAGAGTCA 62.373 66.667 12.58 0.00 34.57 3.41
366 414 3.805207 AGTGATGGCCTATTTTCGGTAC 58.195 45.455 3.32 0.00 0.00 3.34
367 415 3.181458 GGAGTGATGGCCTATTTTCGGTA 60.181 47.826 3.32 0.00 0.00 4.02
595 670 5.696724 CACACCACTATCGTCTCTTTTCTTT 59.303 40.000 0.00 0.00 0.00 2.52
784 1696 1.619526 CGCGACGGAATTGGAACGAA 61.620 55.000 0.00 0.00 0.00 3.85
837 1750 5.305386 ACCCAAGAATCCAAAGAAAAAGAGG 59.695 40.000 0.00 0.00 0.00 3.69
838 1751 6.410942 ACCCAAGAATCCAAAGAAAAAGAG 57.589 37.500 0.00 0.00 0.00 2.85
840 1753 7.770433 AGAAAACCCAAGAATCCAAAGAAAAAG 59.230 33.333 0.00 0.00 0.00 2.27
842 1755 7.047271 CAGAAAACCCAAGAATCCAAAGAAAA 58.953 34.615 0.00 0.00 0.00 2.29
847 1760 3.645687 CCCAGAAAACCCAAGAATCCAAA 59.354 43.478 0.00 0.00 0.00 3.28
877 1790 1.203557 TCCCAATTCCTCTCCTCCCAA 60.204 52.381 0.00 0.00 0.00 4.12
879 1792 1.135960 CTCCCAATTCCTCTCCTCCC 58.864 60.000 0.00 0.00 0.00 4.30
936 1849 1.824329 GGTCAGGCTCGGATCTCGA 60.824 63.158 6.21 6.21 46.77 4.04
965 1878 4.778143 ATCACCCGCTGCGAACCC 62.778 66.667 25.45 0.00 0.00 4.11
968 1881 2.125552 CAGATCACCCGCTGCGAA 60.126 61.111 25.45 6.23 0.00 4.70
969 1882 4.819761 GCAGATCACCCGCTGCGA 62.820 66.667 25.45 3.10 46.66 5.10
1161 2074 1.076014 GTTGGGGTTGGGGTACTGG 59.924 63.158 0.00 0.00 0.00 4.00
1260 2173 3.174987 CCCCTGTGGTGGTGGTCA 61.175 66.667 0.00 0.00 0.00 4.02
1419 2332 1.153978 GACGTCGTTGCGGATGGTA 60.154 57.895 0.00 0.00 35.98 3.25
1488 2401 1.374252 GAAGGCGACGAGGAAGCAA 60.374 57.895 0.00 0.00 0.00 3.91
1489 2402 2.261671 GAAGGCGACGAGGAAGCA 59.738 61.111 0.00 0.00 0.00 3.91
1576 2490 2.087501 CCGGCATACATATAACGGCA 57.912 50.000 0.00 0.00 34.54 5.69
1684 2598 4.878971 TCAGAGACAGAGACTAATTCCTCG 59.121 45.833 0.00 0.00 34.75 4.63
1699 2613 2.770232 AGCATCACCATCATCAGAGACA 59.230 45.455 0.00 0.00 0.00 3.41
1737 2651 4.638421 TGAAATAGACAAATACCGCCCTTG 59.362 41.667 0.00 0.00 0.00 3.61
1877 2799 6.270815 TCGTCCTTATAAGCATGTTAGTGTC 58.729 40.000 6.99 0.00 0.00 3.67
1892 2814 3.561143 AGATGACTGAGCTCGTCCTTAT 58.439 45.455 25.43 17.05 0.00 1.73
2045 2976 5.624344 TCCTCATTACCGTATTCTCGATC 57.376 43.478 0.00 0.00 0.00 3.69
2046 2977 5.710567 TCATCCTCATTACCGTATTCTCGAT 59.289 40.000 0.00 0.00 0.00 3.59
2051 2983 7.494625 TGAAACTTCATCCTCATTACCGTATTC 59.505 37.037 0.00 0.00 31.01 1.75
2061 2993 8.270030 TGTAGATCATTGAAACTTCATCCTCAT 58.730 33.333 0.00 0.00 37.00 2.90
2063 2995 7.768120 ACTGTAGATCATTGAAACTTCATCCTC 59.232 37.037 0.00 0.00 37.00 3.71
2099 3031 1.963515 ACAGTTGGCAAGGGATCAAAC 59.036 47.619 0.00 0.00 0.00 2.93
2112 3047 7.281549 ACACCACTACTAAAGTTTAACAGTTGG 59.718 37.037 0.00 14.80 35.76 3.77
2128 3063 3.821600 CAGAGTACAGACACACCACTACT 59.178 47.826 0.00 0.00 0.00 2.57
2134 3072 1.546476 CCTCCAGAGTACAGACACACC 59.454 57.143 0.00 0.00 0.00 4.16
2161 3099 7.342541 GGAGTATTTCTTTACAGAGGGAGTAGT 59.657 40.741 0.00 0.00 0.00 2.73
2162 3100 7.201929 GGGAGTATTTCTTTACAGAGGGAGTAG 60.202 44.444 0.00 0.00 0.00 2.57
2187 3125 1.967779 ACAAGAATTTTTGGACGGGGG 59.032 47.619 12.83 0.00 32.32 5.40
2188 3126 2.890945 AGACAAGAATTTTTGGACGGGG 59.109 45.455 12.83 0.00 32.32 5.73
2189 3127 4.584327 AAGACAAGAATTTTTGGACGGG 57.416 40.909 12.83 0.00 32.32 5.28
2236 3174 9.578439 GATGTACCTAATACTAAAACGTGACTT 57.422 33.333 0.00 0.00 34.56 3.01
2240 3178 8.922058 ACAGATGTACCTAATACTAAAACGTG 57.078 34.615 0.00 0.00 34.56 4.49
2278 3216 5.378332 TCCGTCCCAAAATTCTTGTCTTAA 58.622 37.500 0.00 0.00 0.00 1.85
2309 3247 8.972127 ACTACTTTAGTGATCTAAATGCTCTGA 58.028 33.333 0.00 0.00 42.75 3.27
2330 3271 6.452494 TTTAAGAGCGCTTAGATCACTACT 57.548 37.500 13.26 0.00 37.84 2.57
2331 3272 7.701809 AATTTAAGAGCGCTTAGATCACTAC 57.298 36.000 13.26 0.00 37.84 2.73
2334 3275 7.240414 AGAAATTTAAGAGCGCTTAGATCAC 57.760 36.000 13.26 9.97 37.84 3.06
2335 3276 7.849804 AAGAAATTTAAGAGCGCTTAGATCA 57.150 32.000 13.26 0.00 37.84 2.92
2336 3277 9.639636 GTAAAGAAATTTAAGAGCGCTTAGATC 57.360 33.333 13.26 0.00 37.84 2.75
2337 3278 9.162764 TGTAAAGAAATTTAAGAGCGCTTAGAT 57.837 29.630 13.26 8.56 37.84 1.98
2339 3280 8.656849 TCTGTAAAGAAATTTAAGAGCGCTTAG 58.343 33.333 13.26 0.00 37.84 2.18
2340 3281 8.542497 TCTGTAAAGAAATTTAAGAGCGCTTA 57.458 30.769 13.26 5.74 35.56 3.09
2341 3282 7.361286 CCTCTGTAAAGAAATTTAAGAGCGCTT 60.361 37.037 13.26 8.09 38.15 4.68
2342 3283 6.092807 CCTCTGTAAAGAAATTTAAGAGCGCT 59.907 38.462 11.27 11.27 0.00 5.92
2343 3284 6.251549 CCTCTGTAAAGAAATTTAAGAGCGC 58.748 40.000 0.00 0.00 0.00 5.92
2344 3285 6.594159 TCCCTCTGTAAAGAAATTTAAGAGCG 59.406 38.462 0.00 0.00 0.00 5.03
2345 3286 7.608376 AGTCCCTCTGTAAAGAAATTTAAGAGC 59.392 37.037 0.00 0.00 0.00 4.09
2347 3288 9.939802 GTAGTCCCTCTGTAAAGAAATTTAAGA 57.060 33.333 0.00 0.00 0.00 2.10
2348 3289 9.720769 TGTAGTCCCTCTGTAAAGAAATTTAAG 57.279 33.333 0.00 0.00 0.00 1.85
2354 3295 9.667107 CAAATATGTAGTCCCTCTGTAAAGAAA 57.333 33.333 0.00 0.00 0.00 2.52
2355 3296 8.265055 CCAAATATGTAGTCCCTCTGTAAAGAA 58.735 37.037 0.00 0.00 0.00 2.52
2356 3297 7.147549 CCCAAATATGTAGTCCCTCTGTAAAGA 60.148 40.741 0.00 0.00 0.00 2.52
2357 3298 6.992715 CCCAAATATGTAGTCCCTCTGTAAAG 59.007 42.308 0.00 0.00 0.00 1.85
2359 3300 5.968167 ACCCAAATATGTAGTCCCTCTGTAA 59.032 40.000 0.00 0.00 0.00 2.41
2360 3301 5.535029 ACCCAAATATGTAGTCCCTCTGTA 58.465 41.667 0.00 0.00 0.00 2.74
2362 3303 5.368989 GAACCCAAATATGTAGTCCCTCTG 58.631 45.833 0.00 0.00 0.00 3.35
2363 3304 4.412528 GGAACCCAAATATGTAGTCCCTCT 59.587 45.833 0.00 0.00 0.00 3.69
2364 3305 4.412528 AGGAACCCAAATATGTAGTCCCTC 59.587 45.833 0.00 0.00 0.00 4.30
2365 3306 4.166144 CAGGAACCCAAATATGTAGTCCCT 59.834 45.833 0.00 0.00 0.00 4.20
2366 3307 4.461198 CAGGAACCCAAATATGTAGTCCC 58.539 47.826 0.00 0.00 0.00 4.46
2367 3308 3.883489 GCAGGAACCCAAATATGTAGTCC 59.117 47.826 0.00 0.00 0.00 3.85
2430 3375 1.783031 GCAATGGAGCGAGCATCCTG 61.783 60.000 12.37 6.73 37.74 3.86
2447 3392 6.443934 AGTAACACTTGTGTTAACAATGCA 57.556 33.333 22.76 1.22 45.12 3.96
2485 3455 1.847328 TCGTTGACTAGGCCATCTCA 58.153 50.000 5.01 0.00 0.00 3.27
2609 3579 6.976934 AACAGTTCCAAACATAACTCCAAT 57.023 33.333 0.00 0.00 0.00 3.16
2620 3590 6.294010 GGATGAAGACCTTAACAGTTCCAAAC 60.294 42.308 0.00 0.00 0.00 2.93
2724 3855 5.891451 AAGAAAGACTTGCTTGGTACAAAC 58.109 37.500 7.70 0.00 39.88 2.93
2871 4002 8.474831 GCAAAGGAGGCCTTAAAATTATCTTTA 58.525 33.333 6.77 0.00 43.92 1.85
2891 4022 7.993183 TCCTATAGAATTCCTACAAAGCAAAGG 59.007 37.037 0.00 0.00 0.00 3.11
2966 4097 4.090090 CCTACATAGGAATCGGACTCCAT 58.910 47.826 8.37 0.00 46.63 3.41
3046 4179 9.753674 TCACTTGGTTCATAGGATAAGAATTTT 57.246 29.630 0.00 0.00 30.42 1.82
3126 4259 8.399284 AGGATAGGAAAATCATAGGAATAGGG 57.601 38.462 0.00 0.00 0.00 3.53
3140 4273 6.901615 TCCTTTGGTCATAGGATAGGAAAA 57.098 37.500 6.14 0.00 30.83 2.29
3141 4274 6.183361 CCATCCTTTGGTCATAGGATAGGAAA 60.183 42.308 18.11 0.00 44.11 3.13
3142 4275 5.310594 CCATCCTTTGGTCATAGGATAGGAA 59.689 44.000 18.11 0.00 44.11 3.36
3143 4276 4.846367 CCATCCTTTGGTCATAGGATAGGA 59.154 45.833 18.11 0.00 44.11 2.94
3144 4277 5.171339 CCATCCTTTGGTCATAGGATAGG 57.829 47.826 18.11 16.97 44.11 2.57
3166 4299 5.789710 TTTCGCAACCTATTACACTTAGC 57.210 39.130 0.00 0.00 0.00 3.09
3262 4399 5.248640 CGGTATCATATTTGCAGGAAGGAT 58.751 41.667 0.00 0.00 0.00 3.24
3281 4418 6.549433 AAATCCTCTACAAACATACCGGTA 57.451 37.500 18.46 18.46 0.00 4.02
3284 4421 5.646360 ACCAAAATCCTCTACAAACATACCG 59.354 40.000 0.00 0.00 0.00 4.02
3341 4478 8.492748 ACAACATGAAAGTACAACAATACTACG 58.507 33.333 0.00 0.00 34.18 3.51
3383 4520 7.907214 TCTTTTGTCTGTATTAAGGAAGCTC 57.093 36.000 0.00 0.00 0.00 4.09
3579 5708 3.117284 TCCCAGAAGGTTGCCTAAACTTT 60.117 43.478 0.00 0.00 43.67 2.66
3597 5726 1.278127 GAGAAGTCAATTCCCGTCCCA 59.722 52.381 0.00 0.00 38.84 4.37
3603 5732 2.100605 ACGCTGAGAAGTCAATTCCC 57.899 50.000 0.00 0.00 38.84 3.97
4031 6160 6.369340 TCAAACGTAGATATCGGCAAGAAAAA 59.631 34.615 0.00 0.00 0.00 1.94
4032 6161 5.870433 TCAAACGTAGATATCGGCAAGAAAA 59.130 36.000 0.00 0.00 0.00 2.29
4033 6162 5.412640 TCAAACGTAGATATCGGCAAGAAA 58.587 37.500 0.00 0.00 0.00 2.52
4034 6163 5.001237 TCAAACGTAGATATCGGCAAGAA 57.999 39.130 0.00 0.00 0.00 2.52
4035 6164 4.642445 TCAAACGTAGATATCGGCAAGA 57.358 40.909 0.00 0.00 0.00 3.02
4036 6165 4.804139 ACTTCAAACGTAGATATCGGCAAG 59.196 41.667 0.00 0.00 0.00 4.01
4037 6166 4.751060 ACTTCAAACGTAGATATCGGCAA 58.249 39.130 0.00 0.00 0.00 4.52
4038 6167 4.380841 ACTTCAAACGTAGATATCGGCA 57.619 40.909 0.00 0.00 0.00 5.69
4039 6168 6.817270 TTAACTTCAAACGTAGATATCGGC 57.183 37.500 0.00 0.00 0.00 5.54
4109 6240 8.934507 AGTGTAATAACAGACTAAATCTCTGC 57.065 34.615 0.00 0.00 39.08 4.26
4139 6270 7.874016 TCACACTCGGTAAACAAAACTGTATAT 59.126 33.333 0.00 0.00 0.00 0.86
4144 6275 4.868450 TCACACTCGGTAAACAAAACTG 57.132 40.909 0.00 0.00 0.00 3.16
4145 6276 5.365619 AGATCACACTCGGTAAACAAAACT 58.634 37.500 0.00 0.00 0.00 2.66
4146 6277 5.668558 AGATCACACTCGGTAAACAAAAC 57.331 39.130 0.00 0.00 0.00 2.43
4147 6278 5.818336 TCAAGATCACACTCGGTAAACAAAA 59.182 36.000 0.00 0.00 0.00 2.44
4148 6279 5.361427 TCAAGATCACACTCGGTAAACAAA 58.639 37.500 0.00 0.00 0.00 2.83
4208 6339 9.871238 AATCAGTGAATTATTGTACTTCGTAGT 57.129 29.630 0.00 0.00 38.44 2.73
4213 6344 8.454106 ACAGCAATCAGTGAATTATTGTACTTC 58.546 33.333 0.00 0.00 33.96 3.01
4215 6346 7.066284 GGACAGCAATCAGTGAATTATTGTACT 59.934 37.037 0.00 0.00 33.96 2.73
4216 6347 7.148255 TGGACAGCAATCAGTGAATTATTGTAC 60.148 37.037 0.00 0.45 33.96 2.90
4236 6367 3.875727 CTCATAGCACTGGAAATGGACAG 59.124 47.826 0.00 0.00 40.48 3.51
4267 6398 9.278978 CTAGAGATGCTAGTACAGAATCAGTTA 57.721 37.037 12.89 4.82 41.42 2.24
4306 6439 4.736793 GCACATACACTGCAGCAAAATATC 59.263 41.667 15.27 0.00 34.56 1.63
4316 6449 1.005156 TCGCTGCACATACACTGCA 60.005 52.632 0.00 0.00 42.42 4.41
4710 6844 1.871676 CATGTCCTCATCTTGGCATCG 59.128 52.381 0.00 0.00 31.15 3.84
4730 6864 2.416547 AGCACACGCATGAACTTATCAC 59.583 45.455 0.00 0.00 42.27 3.06
4736 6870 0.308684 CAACAGCACACGCATGAACT 59.691 50.000 0.00 0.00 42.27 3.01
4839 6973 1.661463 AATCTGGAGGCACCTTCTGA 58.339 50.000 6.99 6.99 39.86 3.27
4908 7043 4.594920 AGAACCCAGAGAAGAGAAATGTGA 59.405 41.667 0.00 0.00 0.00 3.58
5134 7272 8.134895 TGAGCTTTCACAAAAAGAATAACGATT 58.865 29.630 1.85 0.00 0.00 3.34
5141 7279 8.897872 ATCAAATGAGCTTTCACAAAAAGAAT 57.102 26.923 1.85 0.00 0.00 2.40
5173 7311 6.392625 AAAAGGCCTAAAAGAAGAGACAAC 57.607 37.500 5.16 0.00 0.00 3.32
5188 7326 0.537371 CTGTGAACCGGAAAAGGCCT 60.537 55.000 9.46 0.00 33.69 5.19
5192 7330 5.914033 TCTATATCCTGTGAACCGGAAAAG 58.086 41.667 9.46 0.00 32.12 2.27
5228 7436 5.632034 AAGGTGCCTTATAGTTTCCCTAG 57.368 43.478 0.93 0.00 34.05 3.02
5287 7512 4.678044 GCACGTCATCTCACTTCCTATGAA 60.678 45.833 0.00 0.00 30.60 2.57
5307 7532 7.849804 TTTCTTTATAGGAGTTGAGATGCAC 57.150 36.000 0.00 0.00 0.00 4.57
5327 7552 6.644181 CGTATGCATCACAGACATCTATTTCT 59.356 38.462 0.19 0.00 40.66 2.52
5328 7553 6.642540 TCGTATGCATCACAGACATCTATTTC 59.357 38.462 0.19 0.00 40.66 2.17
5365 7952 6.435430 TGGTTCGTAGGAATTGATTCAATG 57.565 37.500 12.50 0.00 38.53 2.82
5366 7953 7.362920 CCTTTGGTTCGTAGGAATTGATTCAAT 60.363 37.037 6.06 6.06 38.53 2.57
5367 7954 6.072175 CCTTTGGTTCGTAGGAATTGATTCAA 60.072 38.462 0.75 0.75 38.53 2.69
5370 7957 4.705023 CCCTTTGGTTCGTAGGAATTGATT 59.295 41.667 0.50 0.00 34.05 2.57
5374 8028 4.524053 GATCCCTTTGGTTCGTAGGAATT 58.476 43.478 0.50 0.00 34.05 2.17
5383 8037 5.745312 AATTCTTTGGATCCCTTTGGTTC 57.255 39.130 9.90 0.00 0.00 3.62
5409 8063 9.460019 TCACATGACATATGAATTTTGTAGGAA 57.540 29.630 10.38 0.00 0.00 3.36
5410 8064 9.631257 ATCACATGACATATGAATTTTGTAGGA 57.369 29.630 10.38 1.80 0.00 2.94
5459 8113 1.461559 AGACCTCCTTTCGTCCGTAG 58.538 55.000 0.00 0.00 0.00 3.51
5462 8116 2.089980 TCTTAGACCTCCTTTCGTCCG 58.910 52.381 0.00 0.00 0.00 4.79
5476 8130 7.615403 AGTTACAATGCATCTCACTTCTTAGA 58.385 34.615 0.00 0.00 0.00 2.10
5490 8144 7.962373 CGTTCATAGAATTTGAGTTACAATGCA 59.038 33.333 0.00 0.00 38.36 3.96
5499 8153 3.857052 TCGCCGTTCATAGAATTTGAGT 58.143 40.909 0.00 0.00 0.00 3.41
5516 8170 4.546570 AGCAAAACTGTTTTTCTATCGCC 58.453 39.130 14.91 2.28 32.27 5.54
5527 8181 8.677148 TTTAGATGAGTTCTAGCAAAACTGTT 57.323 30.769 0.32 0.00 38.19 3.16
5528 8182 8.725148 CATTTAGATGAGTTCTAGCAAAACTGT 58.275 33.333 0.32 0.00 38.19 3.55
5529 8183 8.180267 CCATTTAGATGAGTTCTAGCAAAACTG 58.820 37.037 0.32 0.00 38.19 3.16
5530 8184 7.337942 CCCATTTAGATGAGTTCTAGCAAAACT 59.662 37.037 0.00 0.00 38.19 2.66
5531 8185 7.336931 TCCCATTTAGATGAGTTCTAGCAAAAC 59.663 37.037 0.00 0.00 38.19 2.43
5532 8186 7.402054 TCCCATTTAGATGAGTTCTAGCAAAA 58.598 34.615 0.00 0.00 38.19 2.44
5533 8187 6.957631 TCCCATTTAGATGAGTTCTAGCAAA 58.042 36.000 0.00 0.00 38.19 3.68
5534 8188 6.560003 TCCCATTTAGATGAGTTCTAGCAA 57.440 37.500 0.00 0.00 38.19 3.91
5535 8189 6.753913 ATCCCATTTAGATGAGTTCTAGCA 57.246 37.500 0.00 0.00 38.19 3.49
5550 8204 9.659135 TGAATGAGACCAAATTATATCCCATTT 57.341 29.630 0.00 0.00 0.00 2.32
5551 8205 9.082313 GTGAATGAGACCAAATTATATCCCATT 57.918 33.333 0.00 0.00 0.00 3.16
5552 8206 7.671398 GGTGAATGAGACCAAATTATATCCCAT 59.329 37.037 0.00 0.00 33.25 4.00
5553 8207 7.004086 GGTGAATGAGACCAAATTATATCCCA 58.996 38.462 0.00 0.00 33.25 4.37
5554 8208 7.234355 AGGTGAATGAGACCAAATTATATCCC 58.766 38.462 0.00 0.00 35.76 3.85
5555 8209 8.697507 AAGGTGAATGAGACCAAATTATATCC 57.302 34.615 0.00 0.00 35.76 2.59
5561 8215 8.470002 GCTATAAAAGGTGAATGAGACCAAATT 58.530 33.333 0.00 0.00 35.76 1.82
5562 8216 7.068716 GGCTATAAAAGGTGAATGAGACCAAAT 59.931 37.037 0.00 0.00 35.76 2.32
5563 8217 6.377146 GGCTATAAAAGGTGAATGAGACCAAA 59.623 38.462 0.00 0.00 35.76 3.28
5564 8218 5.885912 GGCTATAAAAGGTGAATGAGACCAA 59.114 40.000 0.00 0.00 35.76 3.67
5565 8219 5.045213 TGGCTATAAAAGGTGAATGAGACCA 60.045 40.000 0.00 0.00 35.76 4.02
5566 8220 5.437060 TGGCTATAAAAGGTGAATGAGACC 58.563 41.667 0.00 0.00 0.00 3.85
5567 8221 7.420800 CAATGGCTATAAAAGGTGAATGAGAC 58.579 38.462 0.00 0.00 0.00 3.36
5568 8222 6.547141 CCAATGGCTATAAAAGGTGAATGAGA 59.453 38.462 0.00 0.00 0.00 3.27
5569 8223 6.547141 TCCAATGGCTATAAAAGGTGAATGAG 59.453 38.462 0.00 0.00 0.00 2.90
5570 8224 6.430864 TCCAATGGCTATAAAAGGTGAATGA 58.569 36.000 0.00 0.00 0.00 2.57
5571 8225 6.713762 TCCAATGGCTATAAAAGGTGAATG 57.286 37.500 0.00 0.00 0.00 2.67
5572 8226 7.294017 CATCCAATGGCTATAAAAGGTGAAT 57.706 36.000 0.00 0.00 0.00 2.57
5573 8227 6.713762 CATCCAATGGCTATAAAAGGTGAA 57.286 37.500 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.