Multiple sequence alignment - TraesCS2D01G033000

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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 TraesCS2D01G033000 chr2D 100.000 3722 0 0 1 3722 12873919 12870198 0.000000e+00 6874.0
1 TraesCS2D01G033000 chr2D 94.444 36 1 1 127 162 12880434 12880400 2.000000e-03 54.7
2 TraesCS2D01G033000 chr2A 94.485 1360 61 7 569 1916 14978166 14976809 0.000000e+00 2084.0
3 TraesCS2D01G033000 chr2A 93.211 1090 57 12 1443 2530 14960908 14959834 0.000000e+00 1587.0
4 TraesCS2D01G033000 chr2A 94.952 416 13 4 2529 2937 14959797 14959383 0.000000e+00 645.0
5 TraesCS2D01G033000 chr2A 87.645 518 35 10 1 496 14978803 14978293 3.220000e-160 575.0
6 TraesCS2D01G033000 chr2A 86.969 353 19 12 3008 3353 14959376 14959044 4.540000e-99 372.0
7 TraesCS2D01G033000 chr2A 89.130 230 17 4 1914 2138 14976277 14976051 2.830000e-71 279.0
8 TraesCS2D01G033000 chr2A 95.455 154 7 0 3350 3503 14959009 14958856 2.870000e-61 246.0
9 TraesCS2D01G033000 chr2A 82.639 144 8 9 3525 3668 14958786 14958660 1.090000e-20 111.0
10 TraesCS2D01G033000 chr2B 93.310 1420 60 14 635 2029 23551073 23549664 0.000000e+00 2063.0
11 TraesCS2D01G033000 chr2B 85.099 557 53 13 15 563 23551655 23551121 3.270000e-150 542.0
12 TraesCS2D01G033000 chr2B 84.091 132 15 4 2604 2733 511601881 511601754 5.050000e-24 122.0
13 TraesCS2D01G033000 chr2B 84.298 121 9 3 2913 3031 511555633 511555521 3.930000e-20 110.0
14 TraesCS2D01G033000 chr2B 81.481 81 12 3 379 457 729880352 729880431 3.100000e-06 63.9
15 TraesCS2D01G033000 chr2B 100.000 28 0 0 2037 2064 490115852 490115825 7.000000e-03 52.8
16 TraesCS2D01G033000 chr4D 82.174 791 125 11 1001 1780 323097949 323097164 0.000000e+00 665.0
17 TraesCS2D01G033000 chr6A 81.922 791 127 11 1001 1780 603249197 603249982 0.000000e+00 654.0
18 TraesCS2D01G033000 chr6A 81.612 794 128 12 999 1780 60973175 60972388 3.130000e-180 641.0
19 TraesCS2D01G033000 chr6A 80.143 841 156 7 999 1832 158317846 158317010 5.280000e-173 617.0
20 TraesCS2D01G033000 chr6A 97.143 35 1 0 2122 2156 233395575 233395609 4.010000e-05 60.2
21 TraesCS2D01G033000 chr3B 80.523 842 147 13 995 1826 40773328 40774162 6.780000e-177 630.0
22 TraesCS2D01G033000 chr6D 80.308 843 153 9 999 1833 121225556 121226393 3.160000e-175 625.0
23 TraesCS2D01G033000 chr6D 80.048 842 155 9 999 1832 121064486 121065322 2.460000e-171 612.0
24 TraesCS2D01G033000 chr6D 74.510 204 33 15 1910 2098 160397380 160397181 1.850000e-08 71.3
25 TraesCS2D01G033000 chr5D 81.173 324 46 10 2604 2919 278647482 278647166 2.870000e-61 246.0
26 TraesCS2D01G033000 chr5D 84.298 121 9 3 2913 3031 278647146 278647034 3.930000e-20 110.0
27 TraesCS2D01G033000 chr5D 97.143 35 1 0 2122 2156 459068766 459068800 4.010000e-05 60.2
28 TraesCS2D01G033000 chr7B 76.856 229 43 6 1915 2138 60607934 60607711 1.820000e-23 121.0
29 TraesCS2D01G033000 chr7B 83.871 93 8 4 2026 2115 89917692 89917604 8.570000e-12 82.4
30 TraesCS2D01G033000 chr1D 73.705 251 42 15 1920 2153 37463202 37463445 3.990000e-10 76.8
31 TraesCS2D01G033000 chr7A 77.778 126 20 5 1985 2108 201996511 201996392 1.850000e-08 71.3
32 TraesCS2D01G033000 chr5A 93.617 47 3 0 2018 2064 476334007 476334053 1.850000e-08 71.3
33 TraesCS2D01G033000 chr7D 97.222 36 1 0 2121 2156 205494466 205494501 1.120000e-05 62.1
34 TraesCS2D01G033000 chr3D 97.222 36 1 0 2121 2156 71506548 71506513 1.120000e-05 62.1
35 TraesCS2D01G033000 chr3D 97.143 35 1 0 2122 2156 278452769 278452803 4.010000e-05 60.2
36 TraesCS2D01G033000 chr3A 97.222 36 1 0 2121 2156 83734683 83734648 1.120000e-05 62.1
37 TraesCS2D01G033000 chr6B 91.111 45 2 1 2037 2081 290590963 290590921 4.010000e-05 60.2
38 TraesCS2D01G033000 chr6B 91.111 45 2 1 2037 2081 290622774 290622732 4.010000e-05 60.2


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 TraesCS2D01G033000 chr2D 12870198 12873919 3721 True 6874.000000 6874 100.0000 1 3722 1 chr2D.!!$R1 3721
1 TraesCS2D01G033000 chr2A 14976051 14978803 2752 True 979.333333 2084 90.4200 1 2138 3 chr2A.!!$R2 2137
2 TraesCS2D01G033000 chr2A 14958660 14960908 2248 True 592.200000 1587 90.6452 1443 3668 5 chr2A.!!$R1 2225
3 TraesCS2D01G033000 chr2B 23549664 23551655 1991 True 1302.500000 2063 89.2045 15 2029 2 chr2B.!!$R4 2014
4 TraesCS2D01G033000 chr4D 323097164 323097949 785 True 665.000000 665 82.1740 1001 1780 1 chr4D.!!$R1 779
5 TraesCS2D01G033000 chr6A 603249197 603249982 785 False 654.000000 654 81.9220 1001 1780 1 chr6A.!!$F2 779
6 TraesCS2D01G033000 chr6A 60972388 60973175 787 True 641.000000 641 81.6120 999 1780 1 chr6A.!!$R1 781
7 TraesCS2D01G033000 chr6A 158317010 158317846 836 True 617.000000 617 80.1430 999 1832 1 chr6A.!!$R2 833
8 TraesCS2D01G033000 chr3B 40773328 40774162 834 False 630.000000 630 80.5230 995 1826 1 chr3B.!!$F1 831
9 TraesCS2D01G033000 chr6D 121225556 121226393 837 False 625.000000 625 80.3080 999 1833 1 chr6D.!!$F2 834
10 TraesCS2D01G033000 chr6D 121064486 121065322 836 False 612.000000 612 80.0480 999 1832 1 chr6D.!!$F1 833

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
343 365 0.736672 CGACGGAGAGAGACTCGTCA 60.737 60.000 13.68 0.0 45.76 4.35 F
855 986 0.813821 TCACTCTCCACAGCTCATCG 59.186 55.000 0.00 0.0 0.00 3.84 F
2409 3113 1.632920 TGGTGATGTATGTTGGGAGCA 59.367 47.619 0.00 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2238 2942 1.247567 CCAGCCCTGGTGTTAAACTG 58.752 55.0 6.15 0.0 45.53 3.16 R
2509 3213 0.100503 ACTGCCAAAACGTCTTGCAC 59.899 50.0 0.00 0.0 0.00 4.57 R
3271 4023 0.108329 CCTATCCTTTGTCGTGCCGT 60.108 55.0 0.00 0.0 0.00 5.68 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
32 33 2.175715 AGAATAATCCAGCCCAACTCCC 59.824 50.000 0.00 0.00 0.00 4.30
111 116 1.668101 CTCGGTTTCTCCTCTCCCCG 61.668 65.000 0.00 0.00 36.83 5.73
215 224 2.187946 CCCTGCACCGTCATCCTC 59.812 66.667 0.00 0.00 0.00 3.71
219 228 4.451150 GCACCGTCATCCTCGCCA 62.451 66.667 0.00 0.00 0.00 5.69
256 265 3.195698 GGCAGCGTCATCCCGTTC 61.196 66.667 0.00 0.00 0.00 3.95
257 266 3.195698 GCAGCGTCATCCCGTTCC 61.196 66.667 0.00 0.00 0.00 3.62
258 267 2.511600 CAGCGTCATCCCGTTCCC 60.512 66.667 0.00 0.00 0.00 3.97
259 268 4.143333 AGCGTCATCCCGTTCCCG 62.143 66.667 0.00 0.00 0.00 5.14
342 364 0.737019 ACGACGGAGAGAGACTCGTC 60.737 60.000 0.00 0.00 45.76 4.20
343 365 0.736672 CGACGGAGAGAGACTCGTCA 60.737 60.000 13.68 0.00 45.76 4.35
366 388 4.803908 CGGAAGGCTGAAGGGGGC 62.804 72.222 0.00 0.00 0.00 5.80
424 452 1.520666 CTACGGGTAAGGCCAGTGG 59.479 63.158 5.01 4.20 45.25 4.00
491 527 2.358267 CCACCGTCCACTGTCTCTATAC 59.642 54.545 0.00 0.00 0.00 1.47
499 535 6.038825 CGTCCACTGTCTCTATACTGAGATTT 59.961 42.308 0.00 0.00 43.84 2.17
502 538 8.053355 TCCACTGTCTCTATACTGAGATTTACA 58.947 37.037 0.00 0.00 43.84 2.41
563 599 9.793259 AAGAAAATCACATTCAACTTAGGTAGA 57.207 29.630 0.00 0.00 0.00 2.59
567 603 9.965902 AAATCACATTCAACTTAGGTAGATCTT 57.034 29.630 0.00 0.00 0.00 2.40
662 778 5.573146 GCACATGCCAGAGACTAAATTTAC 58.427 41.667 0.00 0.00 34.31 2.01
695 823 9.981460 ATCCCCTCATTCCAAATTTAGTATATC 57.019 33.333 0.00 0.00 0.00 1.63
855 986 0.813821 TCACTCTCCACAGCTCATCG 59.186 55.000 0.00 0.00 0.00 3.84
1116 1265 2.126812 GTCGACGCGCTCTTCACT 60.127 61.111 5.73 0.00 0.00 3.41
1362 1511 4.293648 CTGTCCGGTCACGTGGCA 62.294 66.667 23.45 0.00 38.78 4.92
1395 1556 4.137872 GCGTTCATCGGGTCGGGA 62.138 66.667 0.00 0.00 40.26 5.14
1862 2027 5.689383 TCACAGGAAATGAGTGCTTAAAC 57.311 39.130 0.00 0.00 33.44 2.01
1863 2028 5.376625 TCACAGGAAATGAGTGCTTAAACT 58.623 37.500 0.00 0.00 33.44 2.66
1871 2036 9.744468 GGAAATGAGTGCTTAAACTAAGAAAAA 57.256 29.630 0.00 0.00 38.02 1.94
1970 2669 6.751888 GGATACTGGTTGCAATATGTTTCAAC 59.248 38.462 0.59 8.77 39.66 3.18
2152 2856 8.429493 TGCATGTTGAGAGAAATAGATTAGTG 57.571 34.615 0.00 0.00 0.00 2.74
2159 2863 7.309091 TGAGAGAAATAGATTAGTGGGGATCT 58.691 38.462 0.00 0.00 36.61 2.75
2166 2870 8.616799 AATAGATTAGTGGGGATCTCCTATTC 57.383 38.462 14.22 4.13 34.60 1.75
2196 2900 2.093447 AGGATTTACTGCTCCAACCTCG 60.093 50.000 0.00 0.00 33.75 4.63
2212 2916 7.735917 TCCAACCTCGTTCATTATATGAGATT 58.264 34.615 0.00 0.00 40.94 2.40
2238 2942 8.573035 TGACATGTTATAAGGAGTTTGAAAACC 58.427 33.333 0.00 0.00 39.71 3.27
2243 2947 8.973182 TGTTATAAGGAGTTTGAAAACCAGTTT 58.027 29.630 2.34 0.00 39.71 2.66
2250 2954 6.347859 AGTTTGAAAACCAGTTTAACACCA 57.652 33.333 2.34 0.00 39.71 4.17
2274 2978 3.056322 GGCTGGATGATTTTTCTGTTGCT 60.056 43.478 0.00 0.00 0.00 3.91
2313 3017 4.229582 TGGGGGTTAGTTAAGCATCAGATT 59.770 41.667 3.80 0.00 35.51 2.40
2314 3018 4.580580 GGGGGTTAGTTAAGCATCAGATTG 59.419 45.833 3.80 0.00 35.51 2.67
2337 3041 2.237392 AGAGATGTTGGTTGGGAGTAGC 59.763 50.000 0.00 0.00 0.00 3.58
2339 3043 2.026822 AGATGTTGGTTGGGAGTAGCTG 60.027 50.000 0.00 0.00 0.00 4.24
2353 3057 6.708949 TGGGAGTAGCTGTTTTACTAAAGTTG 59.291 38.462 0.00 0.00 31.74 3.16
2360 3064 6.489022 AGCTGTTTTACTAAAGTTGGGGTTAG 59.511 38.462 0.00 0.00 34.19 2.34
2389 3093 6.888632 AGCATCAGATTAAAGAGATGTTGGTT 59.111 34.615 12.84 0.00 39.90 3.67
2392 3096 6.542821 TCAGATTAAAGAGATGTTGGTTGGT 58.457 36.000 0.00 0.00 0.00 3.67
2408 3112 2.418368 TGGTGATGTATGTTGGGAGC 57.582 50.000 0.00 0.00 0.00 4.70
2409 3113 1.632920 TGGTGATGTATGTTGGGAGCA 59.367 47.619 0.00 0.00 0.00 4.26
2410 3114 2.241941 TGGTGATGTATGTTGGGAGCAT 59.758 45.455 0.00 0.00 0.00 3.79
2411 3115 3.290710 GGTGATGTATGTTGGGAGCATT 58.709 45.455 0.00 0.00 0.00 3.56
2412 3116 4.080072 TGGTGATGTATGTTGGGAGCATTA 60.080 41.667 0.00 0.00 0.00 1.90
2413 3117 4.516698 GGTGATGTATGTTGGGAGCATTAG 59.483 45.833 0.00 0.00 0.00 1.73
2423 3127 5.472137 TGTTGGGAGCATTAGTAGTTGTTTC 59.528 40.000 0.00 0.00 0.00 2.78
2424 3128 5.499004 TGGGAGCATTAGTAGTTGTTTCT 57.501 39.130 0.00 0.00 0.00 2.52
2425 3129 6.614694 TGGGAGCATTAGTAGTTGTTTCTA 57.385 37.500 0.00 0.00 0.00 2.10
2426 3130 6.403878 TGGGAGCATTAGTAGTTGTTTCTAC 58.596 40.000 0.00 0.00 40.14 2.59
2456 3160 7.831193 AGTTAACTATGGAGTTTTGAGCATGAT 59.169 33.333 6.26 0.00 43.70 2.45
2463 3167 6.131264 TGGAGTTTTGAGCATGATCCATTAT 58.869 36.000 8.78 0.00 30.63 1.28
2473 3177 4.340381 GCATGATCCATTATATCAAGGGGC 59.660 45.833 0.00 0.00 36.95 5.80
2474 3178 5.763355 CATGATCCATTATATCAAGGGGCT 58.237 41.667 0.00 0.00 36.95 5.19
2475 3179 6.635645 GCATGATCCATTATATCAAGGGGCTA 60.636 42.308 0.00 0.00 36.95 3.93
2476 3180 7.524290 CATGATCCATTATATCAAGGGGCTAT 58.476 38.462 0.00 0.00 36.95 2.97
2478 3182 8.637108 TGATCCATTATATCAAGGGGCTATTA 57.363 34.615 0.00 0.00 30.52 0.98
2480 3184 9.343539 GATCCATTATATCAAGGGGCTATTAAC 57.656 37.037 0.00 0.00 0.00 2.01
2481 3185 8.225863 TCCATTATATCAAGGGGCTATTAACA 57.774 34.615 0.00 0.00 0.00 2.41
2482 3186 8.845793 TCCATTATATCAAGGGGCTATTAACAT 58.154 33.333 0.00 0.00 0.00 2.71
2483 3187 9.479549 CCATTATATCAAGGGGCTATTAACATT 57.520 33.333 0.00 0.00 0.00 2.71
2486 3190 9.515226 TTATATCAAGGGGCTATTAACATTCAC 57.485 33.333 0.00 0.00 0.00 3.18
2487 3191 5.186256 TCAAGGGGCTATTAACATTCACA 57.814 39.130 0.00 0.00 0.00 3.58
2488 3192 5.765510 TCAAGGGGCTATTAACATTCACAT 58.234 37.500 0.00 0.00 0.00 3.21
2509 3213 4.553330 TTAGGCACCCTCTGTTTCTAAG 57.447 45.455 0.00 0.00 34.61 2.18
2523 3227 5.328691 TGTTTCTAAGTGCAAGACGTTTTG 58.671 37.500 14.13 14.13 0.00 2.44
2543 3285 3.476552 TGGCAGTTTAGAAACAGAGGTG 58.523 45.455 7.82 0.00 41.30 4.00
2559 3301 5.119694 CAGAGGTGGTAGAATTTAGAAGGC 58.880 45.833 0.00 0.00 0.00 4.35
2572 3314 0.417841 AGAAGGCCCCTGGTCTCTAA 59.582 55.000 0.00 0.00 36.17 2.10
2577 3319 0.984995 GCCCCTGGTCTCTAACAACT 59.015 55.000 0.00 0.00 0.00 3.16
2579 3321 2.876079 GCCCCTGGTCTCTAACAACTTG 60.876 54.545 0.00 0.00 0.00 3.16
2606 3348 3.250040 GGGACACTTGTGTATGTTGTCAC 59.750 47.826 6.37 0.00 35.43 3.67
2737 3479 2.082231 TCTGAGCTGAAAGAAGCATGC 58.918 47.619 10.51 10.51 46.08 4.06
2842 3586 0.460109 CGGCCGTGATGATCAAGACA 60.460 55.000 19.50 0.00 0.00 3.41
2844 3588 0.654683 GCCGTGATGATCAAGACAGC 59.345 55.000 9.95 0.00 0.00 4.40
2867 3611 0.796491 CGTCGCTGCTCTCTCTTGTC 60.796 60.000 0.00 0.00 0.00 3.18
2914 3663 1.617018 CCTGCAGGTGATTCCTCGGA 61.617 60.000 25.53 0.00 46.24 4.55
2937 3686 2.328099 GGCAAGCAAGACGGGTCTG 61.328 63.158 1.44 0.00 40.36 3.51
2938 3687 1.598130 GCAAGCAAGACGGGTCTGT 60.598 57.895 1.44 0.00 40.36 3.41
2939 3688 1.845809 GCAAGCAAGACGGGTCTGTG 61.846 60.000 1.44 4.72 40.36 3.66
2940 3689 0.532862 CAAGCAAGACGGGTCTGTGT 60.533 55.000 1.44 0.00 40.36 3.72
2941 3690 0.180406 AAGCAAGACGGGTCTGTGTT 59.820 50.000 1.44 0.00 40.36 3.32
2943 3692 0.586802 GCAAGACGGGTCTGTGTTTC 59.413 55.000 1.44 0.00 40.36 2.78
2944 3693 1.810412 GCAAGACGGGTCTGTGTTTCT 60.810 52.381 1.44 0.00 40.36 2.52
2945 3694 2.135933 CAAGACGGGTCTGTGTTTCTC 58.864 52.381 1.44 0.00 40.36 2.87
2946 3695 1.705873 AGACGGGTCTGTGTTTCTCT 58.294 50.000 0.00 0.00 38.75 3.10
2947 3696 2.872732 AGACGGGTCTGTGTTTCTCTA 58.127 47.619 0.00 0.00 38.75 2.43
2948 3697 2.557490 AGACGGGTCTGTGTTTCTCTAC 59.443 50.000 0.00 0.00 38.75 2.59
2949 3698 1.268899 ACGGGTCTGTGTTTCTCTACG 59.731 52.381 0.00 0.00 0.00 3.51
2950 3699 1.402456 CGGGTCTGTGTTTCTCTACGG 60.402 57.143 0.00 0.00 0.00 4.02
2951 3700 1.067071 GGGTCTGTGTTTCTCTACGGG 60.067 57.143 0.00 0.00 0.00 5.28
2952 3701 1.672145 GGTCTGTGTTTCTCTACGGGC 60.672 57.143 0.00 0.00 0.00 6.13
2953 3702 1.272769 GTCTGTGTTTCTCTACGGGCT 59.727 52.381 0.00 0.00 0.00 5.19
2954 3703 1.272490 TCTGTGTTTCTCTACGGGCTG 59.728 52.381 0.00 0.00 0.00 4.85
2955 3704 0.320374 TGTGTTTCTCTACGGGCTGG 59.680 55.000 0.00 0.00 0.00 4.85
2956 3705 0.391263 GTGTTTCTCTACGGGCTGGG 60.391 60.000 0.00 0.00 0.00 4.45
2957 3706 1.449778 GTTTCTCTACGGGCTGGGC 60.450 63.158 0.00 0.00 0.00 5.36
2958 3707 1.612442 TTTCTCTACGGGCTGGGCT 60.612 57.895 0.00 0.00 0.00 5.19
2959 3708 1.899437 TTTCTCTACGGGCTGGGCTG 61.899 60.000 0.00 1.32 0.00 4.85
2960 3709 3.854669 CTCTACGGGCTGGGCTGG 61.855 72.222 7.84 0.00 0.00 4.85
2961 3710 4.715130 TCTACGGGCTGGGCTGGT 62.715 66.667 7.84 2.97 0.00 4.00
2962 3711 4.162690 CTACGGGCTGGGCTGGTC 62.163 72.222 7.84 0.00 0.00 4.02
2973 3722 4.162690 GCTGGTCCGGGCGAATCT 62.163 66.667 0.00 0.00 0.00 2.40
2974 3723 2.107141 CTGGTCCGGGCGAATCTC 59.893 66.667 0.00 0.00 0.00 2.75
2975 3724 3.447025 CTGGTCCGGGCGAATCTCC 62.447 68.421 0.00 0.00 0.00 3.71
2976 3725 3.155167 GGTCCGGGCGAATCTCCT 61.155 66.667 0.00 0.00 0.00 3.69
2977 3726 2.107141 GTCCGGGCGAATCTCCTG 59.893 66.667 0.00 0.00 0.00 3.86
2978 3727 3.849951 TCCGGGCGAATCTCCTGC 61.850 66.667 0.00 0.00 0.00 4.85
2984 3733 3.085208 GCGAATCTCCTGCCAATCA 57.915 52.632 0.00 0.00 0.00 2.57
2985 3734 1.382522 GCGAATCTCCTGCCAATCAA 58.617 50.000 0.00 0.00 0.00 2.57
2986 3735 1.952296 GCGAATCTCCTGCCAATCAAT 59.048 47.619 0.00 0.00 0.00 2.57
2987 3736 2.031333 GCGAATCTCCTGCCAATCAATC 60.031 50.000 0.00 0.00 0.00 2.67
2988 3737 3.208594 CGAATCTCCTGCCAATCAATCA 58.791 45.455 0.00 0.00 0.00 2.57
2989 3738 3.819337 CGAATCTCCTGCCAATCAATCAT 59.181 43.478 0.00 0.00 0.00 2.45
2990 3739 4.320275 CGAATCTCCTGCCAATCAATCATG 60.320 45.833 0.00 0.00 0.00 3.07
2991 3740 2.304092 TCTCCTGCCAATCAATCATGC 58.696 47.619 0.00 0.00 0.00 4.06
2992 3741 2.028876 CTCCTGCCAATCAATCATGCA 58.971 47.619 0.00 0.00 0.00 3.96
2993 3742 2.628178 CTCCTGCCAATCAATCATGCAT 59.372 45.455 0.00 0.00 0.00 3.96
2994 3743 2.364002 TCCTGCCAATCAATCATGCATG 59.636 45.455 21.07 21.07 0.00 4.06
2995 3744 2.135139 CTGCCAATCAATCATGCATGC 58.865 47.619 22.25 11.82 0.00 4.06
2996 3745 1.202592 TGCCAATCAATCATGCATGCC 60.203 47.619 22.25 0.00 0.00 4.40
2997 3746 1.778334 CCAATCAATCATGCATGCCG 58.222 50.000 22.25 12.08 0.00 5.69
2998 3747 1.067974 CCAATCAATCATGCATGCCGT 59.932 47.619 22.25 7.49 0.00 5.68
2999 3748 2.124122 CAATCAATCATGCATGCCGTG 58.876 47.619 22.25 17.61 0.00 4.94
3000 3749 1.395635 ATCAATCATGCATGCCGTGT 58.604 45.000 22.25 4.94 0.00 4.49
3001 3750 0.734309 TCAATCATGCATGCCGTGTC 59.266 50.000 22.25 0.00 0.00 3.67
3002 3751 0.452585 CAATCATGCATGCCGTGTCA 59.547 50.000 22.25 2.92 0.00 3.58
3003 3752 0.736636 AATCATGCATGCCGTGTCAG 59.263 50.000 22.25 0.00 0.00 3.51
3004 3753 0.393402 ATCATGCATGCCGTGTCAGT 60.393 50.000 22.25 0.72 0.00 3.41
3005 3754 1.135939 CATGCATGCCGTGTCAGTG 59.864 57.895 14.93 0.00 0.00 3.66
3006 3755 2.693762 ATGCATGCCGTGTCAGTGC 61.694 57.895 16.68 0.00 36.39 4.40
3017 3766 1.583404 GTGTCAGTGCGTTTTGCTTTG 59.417 47.619 0.00 0.00 46.63 2.77
3059 3808 4.800249 GCCCATCAATGTTTGAGCAAGAAA 60.800 41.667 0.00 0.00 43.98 2.52
3077 3826 4.583871 AGAAACTGAAGTAGCCATCCTTG 58.416 43.478 0.00 0.00 0.00 3.61
3087 3836 1.153289 CCATCCTTGGACTGGAGCG 60.153 63.158 10.57 0.00 46.92 5.03
3127 3879 5.955488 TGACTATGTACTCAACTCTCAAGC 58.045 41.667 0.00 0.00 0.00 4.01
3128 3880 5.712446 TGACTATGTACTCAACTCTCAAGCT 59.288 40.000 0.00 0.00 0.00 3.74
3129 3881 5.960113 ACTATGTACTCAACTCTCAAGCTG 58.040 41.667 0.00 0.00 0.00 4.24
3130 3882 4.881019 ATGTACTCAACTCTCAAGCTGT 57.119 40.909 0.00 0.00 0.00 4.40
3131 3883 4.672587 TGTACTCAACTCTCAAGCTGTT 57.327 40.909 0.00 0.00 0.00 3.16
3132 3884 5.023533 TGTACTCAACTCTCAAGCTGTTT 57.976 39.130 0.00 0.00 0.00 2.83
3133 3885 6.156748 TGTACTCAACTCTCAAGCTGTTTA 57.843 37.500 0.00 0.00 0.00 2.01
3134 3886 6.759272 TGTACTCAACTCTCAAGCTGTTTAT 58.241 36.000 0.00 0.00 0.00 1.40
3135 3887 7.217200 TGTACTCAACTCTCAAGCTGTTTATT 58.783 34.615 0.00 0.00 0.00 1.40
3136 3888 7.715249 TGTACTCAACTCTCAAGCTGTTTATTT 59.285 33.333 0.00 0.00 0.00 1.40
3137 3889 6.963796 ACTCAACTCTCAAGCTGTTTATTTG 58.036 36.000 0.00 0.00 0.00 2.32
3138 3890 5.762045 TCAACTCTCAAGCTGTTTATTTGC 58.238 37.500 0.00 0.00 0.00 3.68
3139 3891 5.299028 TCAACTCTCAAGCTGTTTATTTGCA 59.701 36.000 0.00 0.00 0.00 4.08
3140 3892 5.368256 ACTCTCAAGCTGTTTATTTGCAG 57.632 39.130 0.00 0.00 35.93 4.41
3141 3893 4.217118 ACTCTCAAGCTGTTTATTTGCAGG 59.783 41.667 0.00 0.00 33.62 4.85
3208 3960 5.882557 ACACATATGTCAGGAAAGATTGTCC 59.117 40.000 5.07 0.00 31.55 4.02
3209 3961 5.007039 CACATATGTCAGGAAAGATTGTCCG 59.993 44.000 5.07 0.00 40.36 4.79
3222 3974 0.032952 TTGTCCGGTGAGAAGGAACG 59.967 55.000 0.00 0.00 38.41 3.95
3223 3975 1.737008 GTCCGGTGAGAAGGAACGC 60.737 63.158 0.00 0.00 38.41 4.84
3224 3976 2.434359 CCGGTGAGAAGGAACGCC 60.434 66.667 0.00 0.00 0.00 5.68
3226 3978 2.434359 GGTGAGAAGGAACGCCGG 60.434 66.667 0.00 0.00 39.96 6.13
3227 3979 2.654877 GTGAGAAGGAACGCCGGA 59.345 61.111 5.05 0.00 39.96 5.14
3228 3980 1.005394 GTGAGAAGGAACGCCGGAA 60.005 57.895 5.05 0.00 39.96 4.30
3229 3981 1.005394 TGAGAAGGAACGCCGGAAC 60.005 57.895 5.05 0.00 39.96 3.62
3296 4055 3.309954 GCACGACAAAGGATAGGTTGATC 59.690 47.826 0.00 0.00 0.00 2.92
3313 4072 0.249238 ATCGACGGCTGCTTCATCTC 60.249 55.000 0.00 0.00 0.00 2.75
3314 4073 1.153765 CGACGGCTGCTTCATCTCA 60.154 57.895 0.00 0.00 0.00 3.27
3316 4075 1.005340 GACGGCTGCTTCATCTCAAG 58.995 55.000 0.00 0.00 0.00 3.02
3342 4101 2.280628 CAAATCCCTTCTAGCACGGTC 58.719 52.381 0.00 0.00 0.00 4.79
3386 4183 2.107031 TCGGGGTAGCAGTATGTAGCTA 59.893 50.000 0.00 0.00 42.05 3.32
3460 4257 8.124199 AGTTTTTGTGTTTGTATACTTGTACCG 58.876 33.333 4.17 0.00 0.00 4.02
3481 4278 2.583024 TCAATGCAACCAGTCCATGA 57.417 45.000 0.00 0.00 0.00 3.07
3504 4301 2.937519 TGTGTGTAAAACATGGGAGCA 58.062 42.857 0.00 0.00 41.97 4.26
3505 4302 2.621055 TGTGTGTAAAACATGGGAGCAC 59.379 45.455 0.00 0.38 41.97 4.40
3506 4303 2.884639 GTGTGTAAAACATGGGAGCACT 59.115 45.455 0.00 0.00 41.97 4.40
3508 4305 3.957497 TGTGTAAAACATGGGAGCACTTT 59.043 39.130 0.00 0.00 32.36 2.66
3509 4306 4.037446 TGTGTAAAACATGGGAGCACTTTC 59.963 41.667 0.00 0.00 32.36 2.62
3510 4307 3.572255 TGTAAAACATGGGAGCACTTTCC 59.428 43.478 0.00 0.00 36.46 3.13
3518 4315 2.861147 GGAGCACTTTCCCAAGTACT 57.139 50.000 0.00 0.00 41.69 2.73
3519 4316 3.975168 GGAGCACTTTCCCAAGTACTA 57.025 47.619 0.00 0.00 41.69 1.82
3520 4317 3.597255 GGAGCACTTTCCCAAGTACTAC 58.403 50.000 0.00 0.00 41.69 2.73
3521 4318 3.007614 GGAGCACTTTCCCAAGTACTACA 59.992 47.826 0.00 0.00 41.69 2.74
3522 4319 4.504340 GGAGCACTTTCCCAAGTACTACAA 60.504 45.833 0.00 0.00 41.69 2.41
3523 4320 5.242795 AGCACTTTCCCAAGTACTACAAT 57.757 39.130 0.00 0.00 41.69 2.71
3536 4381 7.119262 CCAAGTACTACAATAAAAGGTGACCTG 59.881 40.741 4.15 0.00 32.13 4.00
3546 4391 0.838122 AGGTGACCTGGTCCTTCTGG 60.838 60.000 23.42 0.00 29.57 3.86
3560 4405 8.331931 TGGTCCTTCTGGAAGTGTATATTATT 57.668 34.615 9.15 0.00 45.18 1.40
3626 4471 4.283467 TGTATAGGCAGTCAGTTCAACTGT 59.717 41.667 17.27 0.00 46.03 3.55
3627 4472 2.717639 AGGCAGTCAGTTCAACTGTT 57.282 45.000 17.27 4.59 46.03 3.16
3628 4473 2.292267 AGGCAGTCAGTTCAACTGTTG 58.708 47.619 17.27 16.48 46.03 3.33
3629 4474 2.017049 GGCAGTCAGTTCAACTGTTGT 58.983 47.619 17.27 0.60 46.03 3.32
3630 4475 2.423538 GGCAGTCAGTTCAACTGTTGTT 59.576 45.455 17.27 5.03 46.03 2.83
3653 4498 4.370364 TTTTTGAGGCAGTCAGTTCAAC 57.630 40.909 0.00 0.00 36.21 3.18
3668 4513 2.455674 TCAACTGACCTGGTCGAATG 57.544 50.000 21.15 17.87 34.95 2.67
3669 4514 1.001974 TCAACTGACCTGGTCGAATGG 59.998 52.381 21.15 10.05 34.95 3.16
3670 4515 0.324943 AACTGACCTGGTCGAATGGG 59.675 55.000 21.15 9.52 34.95 4.00
3671 4516 1.450312 CTGACCTGGTCGAATGGGC 60.450 63.158 21.15 0.00 34.95 5.36
3672 4517 2.124695 GACCTGGTCGAATGGGCC 60.125 66.667 11.71 0.00 0.00 5.80
3673 4518 3.699134 GACCTGGTCGAATGGGCCC 62.699 68.421 17.59 17.59 0.00 5.80
3674 4519 3.411517 CCTGGTCGAATGGGCCCT 61.412 66.667 25.70 2.15 0.00 5.19
3675 4520 2.124570 CTGGTCGAATGGGCCCTG 60.125 66.667 25.70 10.53 0.00 4.45
3676 4521 3.704231 CTGGTCGAATGGGCCCTGG 62.704 68.421 25.70 9.52 0.00 4.45
3677 4522 3.728373 GGTCGAATGGGCCCTGGT 61.728 66.667 25.70 7.89 0.00 4.00
3678 4523 2.355115 GTCGAATGGGCCCTGGTT 59.645 61.111 25.70 15.34 0.00 3.67
3679 4524 1.749258 GTCGAATGGGCCCTGGTTC 60.749 63.158 25.70 21.65 0.00 3.62
3680 4525 2.440247 CGAATGGGCCCTGGTTCC 60.440 66.667 25.70 5.24 0.00 3.62
3681 4526 2.440247 GAATGGGCCCTGGTTCCG 60.440 66.667 25.70 0.00 0.00 4.30
3682 4527 3.264845 AATGGGCCCTGGTTCCGT 61.265 61.111 25.70 0.00 0.00 4.69
3683 4528 2.781431 GAATGGGCCCTGGTTCCGTT 62.781 60.000 25.70 1.05 32.96 4.44
3684 4529 2.380571 AATGGGCCCTGGTTCCGTTT 62.381 55.000 25.70 0.00 0.00 3.60
3685 4530 2.203582 GGGCCCTGGTTCCGTTTT 60.204 61.111 17.04 0.00 0.00 2.43
3686 4531 1.835267 GGGCCCTGGTTCCGTTTTT 60.835 57.895 17.04 0.00 0.00 1.94
3687 4532 1.365999 GGCCCTGGTTCCGTTTTTG 59.634 57.895 0.00 0.00 0.00 2.44
3688 4533 1.365999 GCCCTGGTTCCGTTTTTGG 59.634 57.895 0.00 0.00 0.00 3.28
3689 4534 1.365999 CCCTGGTTCCGTTTTTGGC 59.634 57.895 0.00 0.00 0.00 4.52
3690 4535 1.395826 CCCTGGTTCCGTTTTTGGCA 61.396 55.000 0.00 0.00 0.00 4.92
3691 4536 0.678950 CCTGGTTCCGTTTTTGGCAT 59.321 50.000 0.00 0.00 0.00 4.40
3692 4537 1.605202 CCTGGTTCCGTTTTTGGCATG 60.605 52.381 0.00 0.00 0.00 4.06
3693 4538 0.390860 TGGTTCCGTTTTTGGCATGG 59.609 50.000 0.00 0.00 0.00 3.66
3694 4539 0.948623 GGTTCCGTTTTTGGCATGGC 60.949 55.000 13.29 13.29 0.00 4.40
3695 4540 0.249657 GTTCCGTTTTTGGCATGGCA 60.250 50.000 19.43 19.43 0.00 4.92
3696 4541 0.465705 TTCCGTTTTTGGCATGGCAA 59.534 45.000 29.00 29.00 0.00 4.52
3697 4542 0.249657 TCCGTTTTTGGCATGGCAAC 60.250 50.000 32.02 21.22 0.00 4.17
3710 4555 1.909700 TGGCAACATCCAGGAAACTC 58.090 50.000 0.00 0.00 46.17 3.01
3711 4556 0.804989 GGCAACATCCAGGAAACTCG 59.195 55.000 0.00 0.00 40.21 4.18
3712 4557 0.804989 GCAACATCCAGGAAACTCGG 59.195 55.000 0.00 0.00 40.21 4.63
3713 4558 0.804989 CAACATCCAGGAAACTCGGC 59.195 55.000 0.00 0.00 40.21 5.54
3714 4559 0.322546 AACATCCAGGAAACTCGGCC 60.323 55.000 0.00 0.00 40.21 6.13
3715 4560 1.452108 CATCCAGGAAACTCGGCCC 60.452 63.158 0.00 0.00 40.21 5.80
3716 4561 3.031417 ATCCAGGAAACTCGGCCCG 62.031 63.158 0.00 0.00 40.21 6.13
3717 4562 4.778143 CCAGGAAACTCGGCCCGG 62.778 72.222 1.90 0.00 40.21 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.505742 GGGAGTTGGGCTGGATTATTCTAG 60.506 50.000 0.00 0.00 33.79 2.43
111 116 2.958355 CTGGAGACTGGAGAGAGGAATC 59.042 54.545 0.00 0.00 0.00 2.52
201 210 4.451150 GGCGAGGATGACGGTGCA 62.451 66.667 0.00 0.00 0.00 4.57
424 452 3.304726 GGGCACAGAAAAAGCTTCAGTAC 60.305 47.826 0.00 0.00 0.00 2.73
567 603 7.903145 TGGCAGAATAGAGTTGTTCTTTACTA 58.097 34.615 0.00 0.00 37.36 1.82
662 778 1.068121 GGAATGAGGGGATAGGTGGG 58.932 60.000 0.00 0.00 0.00 4.61
695 823 3.521560 TGATTTGGTAGCTAGCTTGACG 58.478 45.455 24.88 0.00 0.00 4.35
855 986 5.063060 GGAATTGCAATTGATTGAGCAGTTC 59.937 40.000 28.67 10.34 46.43 3.01
892 1040 7.331934 GCTGATGCTTGATATAATACGAAGGAA 59.668 37.037 0.00 0.00 36.03 3.36
893 1041 6.813649 GCTGATGCTTGATATAATACGAAGGA 59.186 38.462 0.00 0.00 36.03 3.36
990 1139 1.021390 CGGCCTCCATGTCACTTGAC 61.021 60.000 0.00 2.19 44.97 3.18
1373 1534 3.927163 GACCCGATGAACGCCACGT 62.927 63.158 0.00 0.00 43.97 4.49
1871 2036 3.726144 GGCAGCCAGGCTCCTCTT 61.726 66.667 12.53 0.00 36.40 2.85
1970 2669 9.773328 AAATACTCATGTTACAATCAAACATCG 57.227 29.630 0.00 0.00 43.84 3.84
2152 2856 7.458170 TCCTAAATAGTTGAATAGGAGATCCCC 59.542 40.741 0.00 0.00 39.13 4.81
2166 2870 8.398665 GTTGGAGCAGTAAATCCTAAATAGTTG 58.601 37.037 0.00 0.00 36.50 3.16
2212 2916 8.573035 GGTTTTCAAACTCCTTATAACATGTCA 58.427 33.333 0.00 0.00 38.89 3.58
2238 2942 1.247567 CCAGCCCTGGTGTTAAACTG 58.752 55.000 6.15 0.00 45.53 3.16
2250 2954 3.463048 ACAGAAAAATCATCCAGCCCT 57.537 42.857 0.00 0.00 0.00 5.19
2313 3017 2.711009 ACTCCCAACCAACATCTCTTCA 59.289 45.455 0.00 0.00 0.00 3.02
2314 3018 3.425162 ACTCCCAACCAACATCTCTTC 57.575 47.619 0.00 0.00 0.00 2.87
2337 3041 7.812690 ACTAACCCCAACTTTAGTAAAACAG 57.187 36.000 0.00 0.00 36.88 3.16
2353 3057 7.773690 TCTTTAATCTGATGCTTAACTAACCCC 59.226 37.037 0.00 0.00 0.00 4.95
2360 3064 9.713740 CAACATCTCTTTAATCTGATGCTTAAC 57.286 33.333 0.00 0.00 39.68 2.01
2389 3093 1.632920 TGCTCCCAACATACATCACCA 59.367 47.619 0.00 0.00 0.00 4.17
2392 3096 5.372343 ACTAATGCTCCCAACATACATCA 57.628 39.130 0.00 0.00 0.00 3.07
2425 3129 9.000486 GCTCAAAACTCCATAGTTAACTTTAGT 58.000 33.333 14.49 9.32 45.37 2.24
2426 3130 8.999431 TGCTCAAAACTCCATAGTTAACTTTAG 58.001 33.333 14.49 8.72 45.37 1.85
2427 3131 8.911918 TGCTCAAAACTCCATAGTTAACTTTA 57.088 30.769 14.49 0.00 45.37 1.85
2430 3134 7.168219 TCATGCTCAAAACTCCATAGTTAACT 58.832 34.615 13.68 13.68 45.37 2.24
2431 3135 7.377766 TCATGCTCAAAACTCCATAGTTAAC 57.622 36.000 0.00 0.00 45.37 2.01
2432 3136 7.283127 GGATCATGCTCAAAACTCCATAGTTAA 59.717 37.037 0.00 0.00 45.37 2.01
2433 3137 6.767902 GGATCATGCTCAAAACTCCATAGTTA 59.232 38.462 0.00 0.00 45.37 2.24
2456 3160 8.225863 TGTTAATAGCCCCTTGATATAATGGA 57.774 34.615 0.00 0.00 0.00 3.41
2463 3167 6.905736 TGTGAATGTTAATAGCCCCTTGATA 58.094 36.000 0.00 0.00 0.00 2.15
2473 3177 6.772716 AGGGTGCCTAATGTGAATGTTAATAG 59.227 38.462 0.00 0.00 28.47 1.73
2474 3178 6.668645 AGGGTGCCTAATGTGAATGTTAATA 58.331 36.000 0.00 0.00 28.47 0.98
2475 3179 5.518865 AGGGTGCCTAATGTGAATGTTAAT 58.481 37.500 0.00 0.00 28.47 1.40
2476 3180 4.929479 AGGGTGCCTAATGTGAATGTTAA 58.071 39.130 0.00 0.00 28.47 2.01
2478 3182 3.010584 AGAGGGTGCCTAATGTGAATGTT 59.989 43.478 0.00 0.00 31.76 2.71
2480 3184 2.947652 CAGAGGGTGCCTAATGTGAATG 59.052 50.000 0.00 0.00 31.76 2.67
2481 3185 2.578021 ACAGAGGGTGCCTAATGTGAAT 59.422 45.455 0.00 0.00 33.93 2.57
2482 3186 1.985159 ACAGAGGGTGCCTAATGTGAA 59.015 47.619 0.00 0.00 33.93 3.18
2483 3187 1.656587 ACAGAGGGTGCCTAATGTGA 58.343 50.000 0.00 0.00 33.93 3.58
2484 3188 2.496899 AACAGAGGGTGCCTAATGTG 57.503 50.000 0.00 0.00 34.96 3.21
2485 3189 2.644798 AGAAACAGAGGGTGCCTAATGT 59.355 45.455 0.00 0.00 35.85 2.71
2486 3190 3.356529 AGAAACAGAGGGTGCCTAATG 57.643 47.619 0.00 0.00 31.76 1.90
2487 3191 4.536489 ACTTAGAAACAGAGGGTGCCTAAT 59.464 41.667 0.00 0.00 31.76 1.73
2488 3192 3.908103 ACTTAGAAACAGAGGGTGCCTAA 59.092 43.478 0.00 0.00 31.76 2.69
2509 3213 0.100503 ACTGCCAAAACGTCTTGCAC 59.899 50.000 0.00 0.00 0.00 4.57
2523 3227 2.814336 CCACCTCTGTTTCTAAACTGCC 59.186 50.000 7.09 0.00 39.59 4.85
2543 3285 3.435169 CCAGGGGCCTTCTAAATTCTACC 60.435 52.174 0.84 0.00 0.00 3.18
2559 3301 2.637872 TCAAGTTGTTAGAGACCAGGGG 59.362 50.000 2.11 0.00 0.00 4.79
2606 3348 2.521547 AAGCTGGGAAATCTTCAGGG 57.478 50.000 0.00 0.00 0.00 4.45
2643 3385 5.581874 ACAAATCACCTGCAAAGAAACAAAG 59.418 36.000 0.00 0.00 0.00 2.77
2827 3571 1.851053 CTCGCTGTCTTGATCATCACG 59.149 52.381 0.00 4.50 0.00 4.35
2862 3606 2.399611 GAATTCGGCCGCGACAAG 59.600 61.111 23.51 0.00 0.00 3.16
2867 3611 2.278336 TACTCGAATTCGGCCGCG 60.278 61.111 26.47 18.88 40.29 6.46
2914 3663 1.961277 CCGTCTTGCTTGCCTTCGT 60.961 57.895 0.00 0.00 0.00 3.85
2937 3686 0.391263 CCCAGCCCGTAGAGAAACAC 60.391 60.000 0.00 0.00 0.00 3.32
2938 3687 1.980052 CCCAGCCCGTAGAGAAACA 59.020 57.895 0.00 0.00 0.00 2.83
2939 3688 1.449778 GCCCAGCCCGTAGAGAAAC 60.450 63.158 0.00 0.00 0.00 2.78
2940 3689 1.612442 AGCCCAGCCCGTAGAGAAA 60.612 57.895 0.00 0.00 0.00 2.52
2941 3690 2.038975 AGCCCAGCCCGTAGAGAA 59.961 61.111 0.00 0.00 0.00 2.87
2943 3692 3.854669 CCAGCCCAGCCCGTAGAG 61.855 72.222 0.00 0.00 0.00 2.43
2944 3693 4.715130 ACCAGCCCAGCCCGTAGA 62.715 66.667 0.00 0.00 0.00 2.59
2945 3694 4.162690 GACCAGCCCAGCCCGTAG 62.163 72.222 0.00 0.00 0.00 3.51
2956 3705 4.162690 AGATTCGCCCGGACCAGC 62.163 66.667 0.73 0.00 0.00 4.85
2957 3706 2.107141 GAGATTCGCCCGGACCAG 59.893 66.667 0.73 0.00 0.00 4.00
2958 3707 3.467226 GGAGATTCGCCCGGACCA 61.467 66.667 0.73 0.00 0.00 4.02
2959 3708 3.155167 AGGAGATTCGCCCGGACC 61.155 66.667 0.73 0.00 0.00 4.46
2960 3709 2.107141 CAGGAGATTCGCCCGGAC 59.893 66.667 0.73 0.00 0.00 4.79
2961 3710 3.849951 GCAGGAGATTCGCCCGGA 61.850 66.667 0.73 0.00 0.00 5.14
2962 3711 4.918201 GGCAGGAGATTCGCCCGG 62.918 72.222 2.46 0.00 40.07 5.73
2963 3712 2.947938 ATTGGCAGGAGATTCGCCCG 62.948 60.000 2.46 0.00 45.63 6.13
2964 3713 1.152881 ATTGGCAGGAGATTCGCCC 60.153 57.895 2.46 0.00 45.63 6.13
2965 3714 0.464373 TGATTGGCAGGAGATTCGCC 60.464 55.000 0.00 0.00 46.43 5.54
2966 3715 1.382522 TTGATTGGCAGGAGATTCGC 58.617 50.000 0.00 0.00 0.00 4.70
2967 3716 3.208594 TGATTGATTGGCAGGAGATTCG 58.791 45.455 0.00 0.00 0.00 3.34
2968 3717 4.558898 GCATGATTGATTGGCAGGAGATTC 60.559 45.833 0.00 0.00 0.00 2.52
2969 3718 3.321111 GCATGATTGATTGGCAGGAGATT 59.679 43.478 0.00 0.00 0.00 2.40
2970 3719 2.891580 GCATGATTGATTGGCAGGAGAT 59.108 45.455 0.00 0.00 0.00 2.75
2971 3720 2.304092 GCATGATTGATTGGCAGGAGA 58.696 47.619 0.00 0.00 0.00 3.71
2972 3721 2.028876 TGCATGATTGATTGGCAGGAG 58.971 47.619 0.00 0.00 0.00 3.69
2973 3722 2.146920 TGCATGATTGATTGGCAGGA 57.853 45.000 0.00 0.00 0.00 3.86
2974 3723 2.754472 CATGCATGATTGATTGGCAGG 58.246 47.619 22.59 0.00 37.96 4.85
2975 3724 2.135139 GCATGCATGATTGATTGGCAG 58.865 47.619 30.64 0.00 37.96 4.85
2976 3725 1.202592 GGCATGCATGATTGATTGGCA 60.203 47.619 30.64 0.00 39.03 4.92
2977 3726 1.508632 GGCATGCATGATTGATTGGC 58.491 50.000 30.64 10.76 0.00 4.52
2978 3727 1.067974 ACGGCATGCATGATTGATTGG 59.932 47.619 30.64 10.75 0.00 3.16
2979 3728 2.124122 CACGGCATGCATGATTGATTG 58.876 47.619 30.64 12.78 0.00 2.67
2980 3729 1.752498 ACACGGCATGCATGATTGATT 59.248 42.857 30.64 6.11 0.00 2.57
2981 3730 1.335810 GACACGGCATGCATGATTGAT 59.664 47.619 30.64 11.66 0.00 2.57
2982 3731 0.734309 GACACGGCATGCATGATTGA 59.266 50.000 30.64 0.00 0.00 2.57
2983 3732 0.452585 TGACACGGCATGCATGATTG 59.547 50.000 30.64 22.47 0.00 2.67
2984 3733 0.736636 CTGACACGGCATGCATGATT 59.263 50.000 30.64 10.02 0.00 2.57
2985 3734 0.393402 ACTGACACGGCATGCATGAT 60.393 50.000 30.64 11.66 0.00 2.45
2986 3735 1.003476 ACTGACACGGCATGCATGA 60.003 52.632 30.64 6.34 0.00 3.07
2987 3736 1.135939 CACTGACACGGCATGCATG 59.864 57.895 22.70 22.70 0.00 4.06
2988 3737 2.693762 GCACTGACACGGCATGCAT 61.694 57.895 21.36 3.56 36.30 3.96
2989 3738 3.356267 GCACTGACACGGCATGCA 61.356 61.111 21.36 0.00 36.30 3.96
2990 3739 4.450122 CGCACTGACACGGCATGC 62.450 66.667 9.90 9.90 0.00 4.06
2991 3740 2.116736 AAACGCACTGACACGGCATG 62.117 55.000 0.00 0.00 0.00 4.06
2992 3741 1.444119 AAAACGCACTGACACGGCAT 61.444 50.000 0.00 0.00 0.00 4.40
2993 3742 2.109739 AAAACGCACTGACACGGCA 61.110 52.632 0.00 0.00 0.00 5.69
2994 3743 1.654137 CAAAACGCACTGACACGGC 60.654 57.895 0.00 0.00 0.00 5.68
2995 3744 1.654137 GCAAAACGCACTGACACGG 60.654 57.895 0.00 0.00 41.79 4.94
2996 3745 0.248054 AAGCAAAACGCACTGACACG 60.248 50.000 0.00 0.00 46.13 4.49
2997 3746 1.583404 CAAAGCAAAACGCACTGACAC 59.417 47.619 0.00 0.00 46.13 3.67
2998 3747 1.201181 ACAAAGCAAAACGCACTGACA 59.799 42.857 0.00 0.00 46.13 3.58
2999 3748 1.846175 GACAAAGCAAAACGCACTGAC 59.154 47.619 0.00 0.00 46.13 3.51
3000 3749 1.742831 AGACAAAGCAAAACGCACTGA 59.257 42.857 0.00 0.00 46.13 3.41
3001 3750 2.111756 GAGACAAAGCAAAACGCACTG 58.888 47.619 0.00 0.00 46.13 3.66
3002 3751 1.742831 TGAGACAAAGCAAAACGCACT 59.257 42.857 0.00 0.00 46.13 4.40
3003 3752 2.111756 CTGAGACAAAGCAAAACGCAC 58.888 47.619 0.00 0.00 46.13 5.34
3004 3753 1.742831 ACTGAGACAAAGCAAAACGCA 59.257 42.857 0.00 0.00 46.13 5.24
3005 3754 2.475200 ACTGAGACAAAGCAAAACGC 57.525 45.000 0.00 0.00 42.91 4.84
3006 3755 2.531508 GCAACTGAGACAAAGCAAAACG 59.468 45.455 0.00 0.00 0.00 3.60
3017 3766 1.262683 GCTGACACAAGCAACTGAGAC 59.737 52.381 0.00 0.00 43.01 3.36
3077 3826 1.594331 AGTTTCAAACGCTCCAGTCC 58.406 50.000 0.00 0.00 36.23 3.85
3127 3879 5.186996 ACAAGTCACCTGCAAATAAACAG 57.813 39.130 0.00 0.00 0.00 3.16
3128 3880 5.105554 ACAACAAGTCACCTGCAAATAAACA 60.106 36.000 0.00 0.00 0.00 2.83
3129 3881 5.231991 CACAACAAGTCACCTGCAAATAAAC 59.768 40.000 0.00 0.00 0.00 2.01
3130 3882 5.347342 CACAACAAGTCACCTGCAAATAAA 58.653 37.500 0.00 0.00 0.00 1.40
3131 3883 4.202101 CCACAACAAGTCACCTGCAAATAA 60.202 41.667 0.00 0.00 0.00 1.40
3132 3884 3.317711 CCACAACAAGTCACCTGCAAATA 59.682 43.478 0.00 0.00 0.00 1.40
3133 3885 2.101249 CCACAACAAGTCACCTGCAAAT 59.899 45.455 0.00 0.00 0.00 2.32
3134 3886 1.476085 CCACAACAAGTCACCTGCAAA 59.524 47.619 0.00 0.00 0.00 3.68
3135 3887 1.102154 CCACAACAAGTCACCTGCAA 58.898 50.000 0.00 0.00 0.00 4.08
3136 3888 0.751277 CCCACAACAAGTCACCTGCA 60.751 55.000 0.00 0.00 0.00 4.41
3137 3889 2.032981 CCCACAACAAGTCACCTGC 58.967 57.895 0.00 0.00 0.00 4.85
3138 3890 1.785041 CGCCCACAACAAGTCACCTG 61.785 60.000 0.00 0.00 0.00 4.00
3139 3891 1.525995 CGCCCACAACAAGTCACCT 60.526 57.895 0.00 0.00 0.00 4.00
3140 3892 2.551912 CCGCCCACAACAAGTCACC 61.552 63.158 0.00 0.00 0.00 4.02
3141 3893 1.381165 AACCGCCCACAACAAGTCAC 61.381 55.000 0.00 0.00 0.00 3.67
3208 3960 2.809601 CGGCGTTCCTTCTCACCG 60.810 66.667 0.00 0.00 0.00 4.94
3209 3961 2.434359 CCGGCGTTCCTTCTCACC 60.434 66.667 6.01 0.00 0.00 4.02
3225 3977 3.202706 GATTCTGCCGGCCGTTCC 61.203 66.667 26.77 12.58 0.00 3.62
3226 3978 3.202706 GGATTCTGCCGGCCGTTC 61.203 66.667 26.77 18.01 0.00 3.95
3244 3996 0.539518 GCTTCCCTTCCCTCTGACTC 59.460 60.000 0.00 0.00 0.00 3.36
3271 4023 0.108329 CCTATCCTTTGTCGTGCCGT 60.108 55.000 0.00 0.00 0.00 5.68
3272 4024 0.108329 ACCTATCCTTTGTCGTGCCG 60.108 55.000 0.00 0.00 0.00 5.69
3282 4041 1.068741 GCCGTCGATCAACCTATCCTT 59.931 52.381 0.00 0.00 0.00 3.36
3287 4046 1.141019 GCAGCCGTCGATCAACCTA 59.859 57.895 0.00 0.00 0.00 3.08
3288 4047 2.125512 GCAGCCGTCGATCAACCT 60.126 61.111 0.00 0.00 0.00 3.50
3290 4049 1.014044 TGAAGCAGCCGTCGATCAAC 61.014 55.000 0.00 0.00 0.00 3.18
3296 4055 0.737367 TTGAGATGAAGCAGCCGTCG 60.737 55.000 0.00 0.00 0.00 5.12
3313 4072 2.872337 GAAGGGATTTGCGCGGCTTG 62.872 60.000 8.83 0.00 34.07 4.01
3314 4073 2.676471 AAGGGATTTGCGCGGCTT 60.676 55.556 8.83 0.00 34.07 4.35
3316 4075 1.776034 CTAGAAGGGATTTGCGCGGC 61.776 60.000 8.83 0.00 34.07 6.53
3342 4101 5.013547 ACTCCTATAACTCCCATCATCTCG 58.986 45.833 0.00 0.00 0.00 4.04
3386 4183 9.739276 TTCATCATCAGTACTAAGGAAACAAAT 57.261 29.630 0.00 0.00 0.00 2.32
3401 4198 4.142447 GCTTGACAGCATTTCATCATCAGT 60.142 41.667 0.00 0.00 46.49 3.41
3456 4253 2.627945 GACTGGTTGCATTGATCGGTA 58.372 47.619 0.00 0.00 0.00 4.02
3460 4257 3.018856 TCATGGACTGGTTGCATTGATC 58.981 45.455 0.00 0.00 33.06 2.92
3481 4278 3.255642 GCTCCCATGTTTTACACACATGT 59.744 43.478 11.15 0.00 46.95 3.21
3500 4297 4.267349 TGTAGTACTTGGGAAAGTGCTC 57.733 45.455 11.67 6.05 43.17 4.26
3503 4300 8.512138 CCTTTTATTGTAGTACTTGGGAAAGTG 58.488 37.037 0.00 0.00 34.37 3.16
3504 4301 8.222637 ACCTTTTATTGTAGTACTTGGGAAAGT 58.777 33.333 0.00 0.00 36.82 2.66
3505 4302 8.512138 CACCTTTTATTGTAGTACTTGGGAAAG 58.488 37.037 0.00 5.16 0.00 2.62
3506 4303 8.219178 TCACCTTTTATTGTAGTACTTGGGAAA 58.781 33.333 0.00 0.00 0.00 3.13
3508 4305 7.163441 GTCACCTTTTATTGTAGTACTTGGGA 58.837 38.462 0.00 0.00 0.00 4.37
3509 4306 6.373495 GGTCACCTTTTATTGTAGTACTTGGG 59.627 42.308 0.00 0.00 0.00 4.12
3510 4307 7.119262 CAGGTCACCTTTTATTGTAGTACTTGG 59.881 40.741 0.00 0.00 0.00 3.61
3511 4308 7.119262 CCAGGTCACCTTTTATTGTAGTACTTG 59.881 40.741 0.00 0.00 0.00 3.16
3512 4309 7.166167 CCAGGTCACCTTTTATTGTAGTACTT 58.834 38.462 0.00 0.00 0.00 2.24
3513 4310 6.271624 ACCAGGTCACCTTTTATTGTAGTACT 59.728 38.462 0.00 0.00 0.00 2.73
3514 4311 6.470278 ACCAGGTCACCTTTTATTGTAGTAC 58.530 40.000 0.00 0.00 0.00 2.73
3515 4312 6.296030 GGACCAGGTCACCTTTTATTGTAGTA 60.296 42.308 21.75 0.00 33.68 1.82
3516 4313 5.514310 GGACCAGGTCACCTTTTATTGTAGT 60.514 44.000 21.75 0.00 33.68 2.73
3518 4315 4.600111 AGGACCAGGTCACCTTTTATTGTA 59.400 41.667 21.75 0.00 33.68 2.41
3519 4316 3.397955 AGGACCAGGTCACCTTTTATTGT 59.602 43.478 21.75 0.00 33.68 2.71
3520 4317 4.034285 AGGACCAGGTCACCTTTTATTG 57.966 45.455 21.75 0.00 33.68 1.90
3521 4318 4.354087 AGAAGGACCAGGTCACCTTTTATT 59.646 41.667 21.75 2.62 42.98 1.40
3522 4319 3.916989 AGAAGGACCAGGTCACCTTTTAT 59.083 43.478 21.75 5.04 42.98 1.40
3523 4320 3.072476 CAGAAGGACCAGGTCACCTTTTA 59.928 47.826 21.75 0.00 42.98 1.52
3579 4424 9.077885 ACATGTACAGTACAATTTTCTCCAAAT 57.922 29.630 17.43 0.00 42.76 2.32
3592 4437 5.889289 TGACTGCCTATACATGTACAGTACA 59.111 40.000 20.67 15.90 43.80 2.90
3593 4438 6.039493 ACTGACTGCCTATACATGTACAGTAC 59.961 42.308 20.67 15.80 38.42 2.73
3594 4439 6.127101 ACTGACTGCCTATACATGTACAGTA 58.873 40.000 20.67 11.84 38.42 2.74
3595 4440 4.956700 ACTGACTGCCTATACATGTACAGT 59.043 41.667 20.73 20.73 40.85 3.55
3596 4441 5.521906 ACTGACTGCCTATACATGTACAG 57.478 43.478 7.96 12.97 0.00 2.74
3653 4498 1.450312 GCCCATTCGACCAGGTCAG 60.450 63.158 20.13 12.10 32.09 3.51
3658 4503 2.124570 CAGGGCCCATTCGACCAG 60.125 66.667 27.56 0.00 0.00 4.00
3668 4513 1.835267 AAAAACGGAACCAGGGCCC 60.835 57.895 16.46 16.46 0.00 5.80
3669 4514 1.365999 CAAAAACGGAACCAGGGCC 59.634 57.895 0.00 0.00 0.00 5.80
3670 4515 1.365999 CCAAAAACGGAACCAGGGC 59.634 57.895 0.00 0.00 0.00 5.19
3671 4516 1.365999 GCCAAAAACGGAACCAGGG 59.634 57.895 0.00 0.00 0.00 4.45
3672 4517 0.678950 ATGCCAAAAACGGAACCAGG 59.321 50.000 0.00 0.00 0.00 4.45
3673 4518 1.605202 CCATGCCAAAAACGGAACCAG 60.605 52.381 0.00 0.00 0.00 4.00
3674 4519 0.390860 CCATGCCAAAAACGGAACCA 59.609 50.000 0.00 0.00 0.00 3.67
3675 4520 0.948623 GCCATGCCAAAAACGGAACC 60.949 55.000 0.00 0.00 0.00 3.62
3676 4521 0.249657 TGCCATGCCAAAAACGGAAC 60.250 50.000 0.00 0.00 0.00 3.62
3677 4522 0.465705 TTGCCATGCCAAAAACGGAA 59.534 45.000 0.00 0.00 0.00 4.30
3678 4523 0.249657 GTTGCCATGCCAAAAACGGA 60.250 50.000 0.00 0.00 0.00 4.69
3679 4524 0.531532 TGTTGCCATGCCAAAAACGG 60.532 50.000 0.00 0.00 0.00 4.44
3680 4525 1.460359 GATGTTGCCATGCCAAAAACG 59.540 47.619 0.00 0.00 0.00 3.60
3681 4526 1.805943 GGATGTTGCCATGCCAAAAAC 59.194 47.619 0.00 0.00 33.62 2.43
3682 4527 1.419012 TGGATGTTGCCATGCCAAAAA 59.581 42.857 0.00 0.00 38.55 1.94
3683 4528 1.002201 CTGGATGTTGCCATGCCAAAA 59.998 47.619 0.00 0.00 38.55 2.44
3684 4529 0.609151 CTGGATGTTGCCATGCCAAA 59.391 50.000 0.00 0.00 38.55 3.28
3685 4530 1.259142 CCTGGATGTTGCCATGCCAA 61.259 55.000 0.00 0.00 38.55 4.52
3686 4531 1.683025 CCTGGATGTTGCCATGCCA 60.683 57.895 0.00 0.00 38.55 4.92
3687 4532 0.971959 TTCCTGGATGTTGCCATGCC 60.972 55.000 0.00 0.00 38.55 4.40
3688 4533 0.896923 TTTCCTGGATGTTGCCATGC 59.103 50.000 0.00 0.00 39.66 4.06
3689 4534 2.165030 GAGTTTCCTGGATGTTGCCATG 59.835 50.000 0.00 0.00 37.30 3.66
3690 4535 2.450476 GAGTTTCCTGGATGTTGCCAT 58.550 47.619 0.00 0.00 37.30 4.40
3691 4536 1.881925 CGAGTTTCCTGGATGTTGCCA 60.882 52.381 0.00 0.00 36.30 4.92
3692 4537 0.804989 CGAGTTTCCTGGATGTTGCC 59.195 55.000 0.00 0.00 0.00 4.52
3693 4538 0.804989 CCGAGTTTCCTGGATGTTGC 59.195 55.000 0.00 0.00 0.00 4.17
3694 4539 0.804989 GCCGAGTTTCCTGGATGTTG 59.195 55.000 0.00 0.00 0.00 3.33
3695 4540 0.322546 GGCCGAGTTTCCTGGATGTT 60.323 55.000 0.00 0.00 0.00 2.71
3696 4541 1.299976 GGCCGAGTTTCCTGGATGT 59.700 57.895 0.00 0.00 0.00 3.06
3697 4542 1.452108 GGGCCGAGTTTCCTGGATG 60.452 63.158 0.00 0.00 0.00 3.51
3698 4543 2.998949 GGGCCGAGTTTCCTGGAT 59.001 61.111 0.00 0.00 0.00 3.41
3699 4544 3.702048 CGGGCCGAGTTTCCTGGA 61.702 66.667 24.41 0.00 0.00 3.86
3700 4545 4.778143 CCGGGCCGAGTTTCCTGG 62.778 72.222 30.79 2.47 42.07 4.45


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

AutoCloner maintained by Alex Coulton.