Multiple sequence alignment - TraesCS3A01G325800

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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 TraesCS3A01G325800 chr3A 100.000 6493 0 0 1 6493 571173922 571180414 0.000000e+00 11991.0
1 TraesCS3A01G325800 chr3A 99.091 110 0 1 3064 3173 46169209 46169101 5.140000e-46 196.0
2 TraesCS3A01G325800 chr3A 85.600 125 12 4 5514 5637 142884969 142884850 6.830000e-25 126.0
3 TraesCS3A01G325800 chr3D 95.883 3255 108 15 3249 6493 433135484 433138722 0.000000e+00 5245.0
4 TraesCS3A01G325800 chr3D 92.070 1362 60 19 1 1332 433132421 433133764 0.000000e+00 1873.0
5 TraesCS3A01G325800 chr3D 92.377 1220 63 10 1363 2556 433133751 433134966 0.000000e+00 1711.0
6 TraesCS3A01G325800 chr3D 93.987 449 22 2 2620 3067 433134971 433135415 0.000000e+00 675.0
7 TraesCS3A01G325800 chr3D 86.207 87 10 2 5664 5749 3580201 3580116 6.930000e-15 93.5
8 TraesCS3A01G325800 chr3B 94.223 3029 123 21 3189 6206 565267734 565270721 0.000000e+00 4577.0
9 TraesCS3A01G325800 chr3B 92.097 1354 70 18 1 1326 565264627 565265971 0.000000e+00 1873.0
10 TraesCS3A01G325800 chr3B 91.995 862 41 11 1764 2602 565266408 565267264 0.000000e+00 1184.0
11 TraesCS3A01G325800 chr3B 89.823 452 38 3 2620 3067 565267249 565267696 2.030000e-159 573.0
12 TraesCS3A01G325800 chr3B 90.449 356 24 6 1346 1696 565265948 565266298 1.650000e-125 460.0
13 TraesCS3A01G325800 chr3B 95.312 256 9 2 6205 6458 565270881 565271135 2.820000e-108 403.0
14 TraesCS3A01G325800 chr3B 84.651 215 27 4 338 547 670692292 670692505 6.600000e-50 209.0
15 TraesCS3A01G325800 chr3B 100.000 31 0 0 1697 1727 565266379 565266409 2.530000e-04 58.4
16 TraesCS3A01G325800 chr5B 88.780 205 17 5 347 546 128806089 128806292 5.030000e-61 246.0
17 TraesCS3A01G325800 chr5B 88.764 89 9 1 5664 5752 680853425 680853338 2.480000e-19 108.0
18 TraesCS3A01G325800 chr5A 85.714 231 22 8 339 560 689612569 689612341 3.910000e-57 233.0
19 TraesCS3A01G325800 chr5A 89.000 100 9 2 5655 5754 569803298 569803201 8.840000e-24 122.0
20 TraesCS3A01G325800 chr6D 85.909 220 24 5 339 554 263476008 263475792 1.820000e-55 228.0
21 TraesCS3A01G325800 chr7D 88.083 193 19 4 362 552 18282051 18282241 6.550000e-55 226.0
22 TraesCS3A01G325800 chr7D 97.368 114 2 1 3060 3173 474273742 474273630 6.640000e-45 193.0
23 TraesCS3A01G325800 chr7D 88.372 86 10 0 5664 5749 419793198 419793113 3.200000e-18 104.0
24 TraesCS3A01G325800 chrUn 84.783 230 22 9 338 559 85639130 85638906 1.100000e-52 219.0
25 TraesCS3A01G325800 chr6B 84.651 215 25 7 338 548 680323776 680323566 2.370000e-49 207.0
26 TraesCS3A01G325800 chr7A 95.935 123 3 2 3062 3183 269960430 269960309 1.430000e-46 198.0
27 TraesCS3A01G325800 chr6A 98.214 112 1 1 3063 3174 250834513 250834623 1.850000e-45 195.0
28 TraesCS3A01G325800 chr5D 99.083 109 0 1 3065 3173 424123548 424123655 1.850000e-45 195.0
29 TraesCS3A01G325800 chr5D 92.135 89 6 1 5664 5752 539150919 539150832 2.460000e-24 124.0
30 TraesCS3A01G325800 chr4A 97.345 113 1 2 3066 3178 381227047 381226937 2.390000e-44 191.0
31 TraesCS3A01G325800 chr4A 90.244 82 7 1 5668 5749 629378659 629378739 8.900000e-19 106.0
32 TraesCS3A01G325800 chr1D 97.345 113 1 2 3066 3178 447959571 447959461 2.390000e-44 191.0
33 TraesCS3A01G325800 chr1A 95.763 118 2 3 3058 3173 517104209 517104093 3.090000e-43 187.0
34 TraesCS3A01G325800 chr2A 94.262 122 5 2 3063 3183 29450265 29450385 1.110000e-42 185.0
35 TraesCS3A01G325800 chr4D 90.426 94 8 1 5664 5757 450203791 450203699 8.840000e-24 122.0


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 TraesCS3A01G325800 chr3A 571173922 571180414 6492 False 11991.000000 11991 100.000000 1 6493 1 chr3A.!!$F1 6492
1 TraesCS3A01G325800 chr3D 433132421 433138722 6301 False 2376.000000 5245 93.579250 1 6493 4 chr3D.!!$F1 6492
2 TraesCS3A01G325800 chr3B 565264627 565271135 6508 False 1304.057143 4577 93.414143 1 6458 7 chr3B.!!$F2 6457

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
32 33 1.599916 CGCATGTCATGTGCACACAAA 60.600 47.619 24.37 7.38 45.41 2.83 F
888 930 2.955660 GACAAGGGGAAACAACACATCA 59.044 45.455 0.00 0.00 0.00 3.07 F
1666 1720 0.175760 ACGGCGTATCTTGTCTGCAT 59.824 50.000 12.58 0.00 0.00 3.96 F
2687 2851 0.179100 CGGTAGGACCTGACATGCAG 60.179 60.000 3.53 9.40 44.49 4.41 F
3106 3275 0.249120 TCGGTCGCAGAAATGGATGT 59.751 50.000 0.00 0.00 39.69 3.06 F
3597 3788 0.392863 TGGTCATGATGGACGCCAAG 60.393 55.000 0.00 0.00 36.95 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1308 1358 1.078143 GGTTGCACCTCTAGCCAGG 60.078 63.158 0.00 0.0 39.80 4.45 R
2212 2368 0.036388 TCTTGTCCATCGGAGTTGCC 60.036 55.000 0.00 0.0 29.39 4.52 R
3156 3325 0.038744 AGTTACTCCCTCCGTTCCGA 59.961 55.000 0.00 0.0 0.00 4.55 R
4411 4611 0.661483 GAGGCGCTTTTGCTGACAAC 60.661 55.000 7.64 0.0 44.80 3.32 R
4930 5130 0.179000 CTCCTCCTACGCCTTTGCAT 59.821 55.000 0.00 0.0 37.32 3.96 R
5593 5803 1.098129 GCATCGCTTCTCCCCTTTCC 61.098 60.000 0.00 0.0 0.00 3.13 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 1.599916 CGCATGTCATGTGCACACAAA 60.600 47.619 24.37 7.38 45.41 2.83
38 39 3.384146 TGTCATGTGCACACAAATTTCCT 59.616 39.130 24.37 0.00 45.41 3.36
338 339 7.201835 TGTGTGCCTTTAATGTGCAATATATG 58.798 34.615 0.00 0.00 36.65 1.78
339 340 7.147932 TGTGTGCCTTTAATGTGCAATATATGT 60.148 33.333 0.00 0.00 36.65 2.29
340 341 7.379529 GTGTGCCTTTAATGTGCAATATATGTC 59.620 37.037 0.00 0.00 36.65 3.06
342 343 6.777091 TGCCTTTAATGTGCAATATATGTCCT 59.223 34.615 0.00 0.00 30.85 3.85
344 345 7.596494 CCTTTAATGTGCAATATATGTCCTGG 58.404 38.462 0.00 0.00 0.00 4.45
345 346 7.231317 CCTTTAATGTGCAATATATGTCCTGGT 59.769 37.037 0.00 0.00 0.00 4.00
514 553 3.483085 GCTAGTCAAATACGCGGTCAAAC 60.483 47.826 12.47 1.00 0.00 2.93
565 604 3.778622 ACCCAGAGATAGTAACCACCT 57.221 47.619 0.00 0.00 0.00 4.00
577 616 7.567622 AGATAGTAACCACCTAGGCTATTTTCA 59.432 37.037 9.30 0.00 43.14 2.69
888 930 2.955660 GACAAGGGGAAACAACACATCA 59.044 45.455 0.00 0.00 0.00 3.07
934 976 9.939424 AGTAGACACTAGAGAAATTTATAGGGT 57.061 33.333 10.62 10.62 34.63 4.34
982 1024 3.626924 AACTTGGCGAGGGCGTCT 61.627 61.111 6.71 0.00 43.87 4.18
1059 1101 6.425114 CGGTATAATTGTTTCCCTCATCTCTG 59.575 42.308 0.00 0.00 0.00 3.35
1122 1164 5.008613 TCCAAAGAGTTGTAACATGTCTTGC 59.991 40.000 0.00 0.00 32.40 4.01
1174 1224 7.275920 TGAGTAGATAAGGGCTTGAATTTCTC 58.724 38.462 0.00 0.00 0.00 2.87
1252 1302 8.251721 GCTACCTCGGATTATCTGTTATTGTAT 58.748 37.037 0.57 0.00 0.00 2.29
1337 1388 2.193536 GTGCAACCTGCTCGGGTTT 61.194 57.895 10.27 0.00 46.21 3.27
1338 1389 1.454847 TGCAACCTGCTCGGGTTTT 60.455 52.632 10.27 0.00 46.21 2.43
1339 1390 1.040339 TGCAACCTGCTCGGGTTTTT 61.040 50.000 10.27 0.00 46.21 1.94
1367 1418 2.123683 TTTTTGCGAGGGGGTGCA 60.124 55.556 0.00 0.00 39.81 4.57
1372 1423 4.115199 GCGAGGGGGTGCAATCCT 62.115 66.667 7.21 5.51 0.00 3.24
1417 1468 2.932498 TCTGTTTTGACATGCATTCGC 58.068 42.857 0.00 0.00 39.24 4.70
1521 1575 5.478679 CCTAGATCCAGTCATCGAGGTTATT 59.521 44.000 0.00 0.00 39.60 1.40
1522 1576 5.207110 AGATCCAGTCATCGAGGTTATTG 57.793 43.478 0.00 0.00 0.00 1.90
1568 1622 8.478066 ACAAGTTCTTAATCAAAAGCTTTTCCT 58.522 29.630 21.45 11.08 0.00 3.36
1666 1720 0.175760 ACGGCGTATCTTGTCTGCAT 59.824 50.000 12.58 0.00 0.00 3.96
1777 1915 2.076100 CCAGTATCGTGCTTTGCTTGA 58.924 47.619 0.00 0.00 0.00 3.02
1799 1937 2.045561 TTTCCTTGCTTCGTTCACCA 57.954 45.000 0.00 0.00 0.00 4.17
1968 2123 4.074970 ACCCACTTGCTCTGTTAAGATTG 58.925 43.478 0.00 0.00 0.00 2.67
2038 2193 3.181494 CGAGGCAATTCAAAGCATGATGA 60.181 43.478 0.00 0.00 38.03 2.92
2049 2204 1.177256 GCATGATGAGGCCCCACATC 61.177 60.000 20.96 20.96 41.94 3.06
2100 2255 7.961325 TGGCATCTTCCAAATTTACTTTTTC 57.039 32.000 0.00 0.00 32.18 2.29
2107 2262 7.710475 TCTTCCAAATTTACTTTTTCCAAGCTG 59.290 33.333 0.00 0.00 0.00 4.24
2212 2368 6.456047 CGACAATGACTTGGACATATCACAAG 60.456 42.308 0.00 0.00 45.27 3.16
2399 2562 2.939460 ACAGGTTTTTCGGCATATGC 57.061 45.000 19.79 19.79 41.14 3.14
2521 2684 6.411376 TGAAGGTCTGTTCTAAAACACTTCA 58.589 36.000 14.02 14.02 44.85 3.02
2523 2686 7.556275 TGAAGGTCTGTTCTAAAACACTTCAAT 59.444 33.333 14.97 0.00 44.50 2.57
2565 2729 7.508687 ACACAGTTGGTCAATATATGCATCTA 58.491 34.615 0.19 0.00 0.00 1.98
2588 2752 8.771766 TCTATCAACTACTATTGCTACTGTACG 58.228 37.037 0.00 0.00 0.00 3.67
2589 2753 6.748333 TCAACTACTATTGCTACTGTACGT 57.252 37.500 0.00 0.00 0.00 3.57
2590 2754 7.149569 TCAACTACTATTGCTACTGTACGTT 57.850 36.000 0.00 0.00 0.00 3.99
2591 2755 7.025365 TCAACTACTATTGCTACTGTACGTTG 58.975 38.462 0.00 0.00 32.33 4.10
2592 2756 6.506500 ACTACTATTGCTACTGTACGTTGT 57.493 37.500 0.00 0.00 0.00 3.32
2593 2757 6.549952 ACTACTATTGCTACTGTACGTTGTC 58.450 40.000 0.00 0.00 0.00 3.18
2594 2758 5.381174 ACTATTGCTACTGTACGTTGTCA 57.619 39.130 0.00 0.00 0.00 3.58
2595 2759 5.962433 ACTATTGCTACTGTACGTTGTCAT 58.038 37.500 0.00 0.00 0.00 3.06
2596 2760 5.805486 ACTATTGCTACTGTACGTTGTCATG 59.195 40.000 0.00 0.00 0.00 3.07
2597 2761 3.653539 TGCTACTGTACGTTGTCATGT 57.346 42.857 0.00 0.00 0.00 3.21
2598 2762 3.571571 TGCTACTGTACGTTGTCATGTC 58.428 45.455 0.00 0.00 0.00 3.06
2599 2763 3.254903 TGCTACTGTACGTTGTCATGTCT 59.745 43.478 0.00 0.00 0.00 3.41
2600 2764 4.235360 GCTACTGTACGTTGTCATGTCTT 58.765 43.478 0.00 0.00 0.00 3.01
2601 2765 4.323868 GCTACTGTACGTTGTCATGTCTTC 59.676 45.833 0.00 0.00 0.00 2.87
2602 2766 4.585955 ACTGTACGTTGTCATGTCTTCT 57.414 40.909 0.00 0.00 0.00 2.85
2603 2767 4.945246 ACTGTACGTTGTCATGTCTTCTT 58.055 39.130 0.00 0.00 0.00 2.52
2604 2768 5.357257 ACTGTACGTTGTCATGTCTTCTTT 58.643 37.500 0.00 0.00 0.00 2.52
2605 2769 5.815740 ACTGTACGTTGTCATGTCTTCTTTT 59.184 36.000 0.00 0.00 0.00 2.27
2606 2770 6.315393 ACTGTACGTTGTCATGTCTTCTTTTT 59.685 34.615 0.00 0.00 0.00 1.94
2629 2793 5.386810 TTTTGAACGCAAACATTGTCATG 57.613 34.783 0.00 0.00 43.27 3.07
2676 2840 2.973420 GCATGTAGCACGGTAGGAC 58.027 57.895 0.00 0.00 44.79 3.85
2687 2851 0.179100 CGGTAGGACCTGACATGCAG 60.179 60.000 3.53 9.40 44.49 4.41
2703 2867 1.098050 GCAGAAGGCTTATGGTGGTG 58.902 55.000 22.11 0.00 40.25 4.17
2717 2881 4.713824 TGGTGGTGATCGTTCTAACTAG 57.286 45.455 0.00 0.00 0.00 2.57
2728 2892 5.475719 TCGTTCTAACTAGTTGTTCCATGG 58.524 41.667 18.56 4.97 39.89 3.66
2803 2967 1.719529 ATGAGATGCTGAGGGAGGAG 58.280 55.000 0.00 0.00 0.00 3.69
2821 2985 1.742268 GAGAACAAGAGGCTTGCATCC 59.258 52.381 7.06 0.00 0.00 3.51
2871 3035 2.069273 CGTTGCTTTACCAGGACTGAG 58.931 52.381 0.00 0.00 0.00 3.35
2908 3072 2.087646 CAGAGGCTAAGGCAGGAAAAC 58.912 52.381 0.00 0.00 40.87 2.43
2990 3157 6.019779 TCAGCTCAACTCTCTCTAAACTTC 57.980 41.667 0.00 0.00 0.00 3.01
2995 3162 6.588373 GCTCAACTCTCTCTAAACTTCGAAAT 59.412 38.462 0.00 0.00 0.00 2.17
3039 3208 9.076596 CCAGTTTTAGTATCTTAAAAGCAATGC 57.923 33.333 0.00 0.00 34.25 3.56
3040 3209 9.076596 CAGTTTTAGTATCTTAAAAGCAATGCC 57.923 33.333 0.00 0.00 34.25 4.40
3067 3236 8.562892 TGCTAGACGTACCTATATTTGAAGTAC 58.437 37.037 0.00 0.00 0.00 2.73
3068 3237 8.782144 GCTAGACGTACCTATATTTGAAGTACT 58.218 37.037 0.00 0.00 32.89 2.73
3070 3239 8.164058 AGACGTACCTATATTTGAAGTACTCC 57.836 38.462 0.00 0.00 32.89 3.85
3071 3240 7.230309 AGACGTACCTATATTTGAAGTACTCCC 59.770 40.741 0.00 0.00 32.89 4.30
3072 3241 7.065504 ACGTACCTATATTTGAAGTACTCCCT 58.934 38.462 0.00 0.00 32.89 4.20
3073 3242 7.230309 ACGTACCTATATTTGAAGTACTCCCTC 59.770 40.741 0.00 0.00 32.89 4.30
3074 3243 6.997942 ACCTATATTTGAAGTACTCCCTCC 57.002 41.667 0.00 0.00 0.00 4.30
3075 3244 5.539193 ACCTATATTTGAAGTACTCCCTCCG 59.461 44.000 0.00 0.00 0.00 4.63
3076 3245 5.539193 CCTATATTTGAAGTACTCCCTCCGT 59.461 44.000 0.00 0.00 0.00 4.69
3077 3246 5.952347 ATATTTGAAGTACTCCCTCCGTT 57.048 39.130 0.00 0.00 0.00 4.44
3078 3247 3.672767 TTTGAAGTACTCCCTCCGTTC 57.327 47.619 0.00 0.00 0.00 3.95
3079 3248 1.553706 TGAAGTACTCCCTCCGTTCC 58.446 55.000 0.00 0.00 0.00 3.62
3080 3249 1.203087 TGAAGTACTCCCTCCGTTCCA 60.203 52.381 0.00 0.00 0.00 3.53
3081 3250 1.897802 GAAGTACTCCCTCCGTTCCAA 59.102 52.381 0.00 0.00 0.00 3.53
3082 3251 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
3083 3252 2.547990 AGTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
3084 3253 2.910977 AGTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
3085 3254 4.098894 AGTACTCCCTCCGTTCCAAATTA 58.901 43.478 0.00 0.00 0.00 1.40
3086 3255 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
3087 3256 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
3088 3257 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
3089 3258 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
3090 3259 2.277084 CCTCCGTTCCAAATTACTCGG 58.723 52.381 0.00 0.00 39.40 4.63
3091 3260 2.354403 CCTCCGTTCCAAATTACTCGGT 60.354 50.000 0.00 0.00 39.14 4.69
3092 3261 2.928116 CTCCGTTCCAAATTACTCGGTC 59.072 50.000 0.00 0.00 39.14 4.79
3093 3262 1.657094 CCGTTCCAAATTACTCGGTCG 59.343 52.381 0.00 0.00 34.38 4.79
3094 3263 1.060122 CGTTCCAAATTACTCGGTCGC 59.940 52.381 0.00 0.00 0.00 5.19
3095 3264 2.070783 GTTCCAAATTACTCGGTCGCA 58.929 47.619 0.00 0.00 0.00 5.10
3096 3265 2.004583 TCCAAATTACTCGGTCGCAG 57.995 50.000 0.00 0.00 0.00 5.18
3097 3266 1.546923 TCCAAATTACTCGGTCGCAGA 59.453 47.619 0.00 0.00 0.00 4.26
3098 3267 2.028839 TCCAAATTACTCGGTCGCAGAA 60.029 45.455 0.00 0.00 39.69 3.02
3099 3268 2.739913 CCAAATTACTCGGTCGCAGAAA 59.260 45.455 0.00 0.00 39.69 2.52
3100 3269 3.374058 CCAAATTACTCGGTCGCAGAAAT 59.626 43.478 0.00 0.00 39.69 2.17
3101 3270 4.334443 CAAATTACTCGGTCGCAGAAATG 58.666 43.478 0.00 0.00 39.69 2.32
3102 3271 2.004583 TTACTCGGTCGCAGAAATGG 57.995 50.000 0.00 0.00 39.69 3.16
3103 3272 1.179152 TACTCGGTCGCAGAAATGGA 58.821 50.000 0.00 0.00 39.69 3.41
3104 3273 0.537188 ACTCGGTCGCAGAAATGGAT 59.463 50.000 0.00 0.00 39.69 3.41
3105 3274 0.933097 CTCGGTCGCAGAAATGGATG 59.067 55.000 0.00 0.00 39.69 3.51
3106 3275 0.249120 TCGGTCGCAGAAATGGATGT 59.751 50.000 0.00 0.00 39.69 3.06
3107 3276 1.478916 TCGGTCGCAGAAATGGATGTA 59.521 47.619 0.00 0.00 39.69 2.29
3108 3277 2.102420 TCGGTCGCAGAAATGGATGTAT 59.898 45.455 0.00 0.00 39.69 2.29
3109 3278 2.476619 CGGTCGCAGAAATGGATGTATC 59.523 50.000 0.00 0.00 39.69 2.24
3110 3279 3.733337 GGTCGCAGAAATGGATGTATCT 58.267 45.455 0.00 0.00 39.69 1.98
3111 3280 4.558697 CGGTCGCAGAAATGGATGTATCTA 60.559 45.833 0.00 0.00 39.69 1.98
3112 3281 4.926238 GGTCGCAGAAATGGATGTATCTAG 59.074 45.833 0.00 0.00 39.69 2.43
3113 3282 5.279006 GGTCGCAGAAATGGATGTATCTAGA 60.279 44.000 0.00 0.00 39.69 2.43
3114 3283 6.216569 GTCGCAGAAATGGATGTATCTAGAA 58.783 40.000 0.00 0.00 39.69 2.10
3115 3284 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
3116 3285 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
3117 3286 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
3118 3287 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
3119 3288 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
3145 3314 9.775539 AATACATCTAGATACATCCATACCTGT 57.224 33.333 4.54 0.00 0.00 4.00
3146 3315 7.473735 ACATCTAGATACATCCATACCTGTG 57.526 40.000 4.54 0.00 0.00 3.66
3147 3316 7.241628 ACATCTAGATACATCCATACCTGTGA 58.758 38.462 4.54 0.00 0.00 3.58
3148 3317 7.177568 ACATCTAGATACATCCATACCTGTGAC 59.822 40.741 4.54 0.00 0.00 3.67
3149 3318 6.610830 TCTAGATACATCCATACCTGTGACA 58.389 40.000 0.00 0.00 0.00 3.58
3150 3319 7.066781 TCTAGATACATCCATACCTGTGACAA 58.933 38.462 0.00 0.00 0.00 3.18
3151 3320 6.166984 AGATACATCCATACCTGTGACAAG 57.833 41.667 0.00 0.00 0.00 3.16
3152 3321 5.663106 AGATACATCCATACCTGTGACAAGT 59.337 40.000 0.00 0.00 0.00 3.16
3153 3322 6.839134 AGATACATCCATACCTGTGACAAGTA 59.161 38.462 0.00 0.00 0.00 2.24
3154 3323 5.755409 ACATCCATACCTGTGACAAGTAA 57.245 39.130 0.00 0.00 0.00 2.24
3155 3324 6.313519 ACATCCATACCTGTGACAAGTAAT 57.686 37.500 0.00 0.00 0.00 1.89
3156 3325 6.721318 ACATCCATACCTGTGACAAGTAATT 58.279 36.000 0.00 0.00 0.00 1.40
3157 3326 6.823689 ACATCCATACCTGTGACAAGTAATTC 59.176 38.462 0.00 0.00 0.00 2.17
3158 3327 5.416083 TCCATACCTGTGACAAGTAATTCG 58.584 41.667 0.00 0.00 0.00 3.34
3159 3328 4.570772 CCATACCTGTGACAAGTAATTCGG 59.429 45.833 0.00 0.00 0.00 4.30
3160 3329 5.416083 CATACCTGTGACAAGTAATTCGGA 58.584 41.667 0.00 0.00 0.00 4.55
3161 3330 4.345859 ACCTGTGACAAGTAATTCGGAA 57.654 40.909 0.00 0.00 0.00 4.30
3162 3331 4.062991 ACCTGTGACAAGTAATTCGGAAC 58.937 43.478 0.00 0.00 0.00 3.62
3186 3355 4.262617 GAGGGAGTAACTTTGGTGGAATC 58.737 47.826 0.00 0.00 0.00 2.52
3187 3356 3.916989 AGGGAGTAACTTTGGTGGAATCT 59.083 43.478 0.00 0.00 0.00 2.40
3210 3401 8.072321 TCTAGTCTTACAAAGATTGCATCTCT 57.928 34.615 0.00 0.00 39.08 3.10
3232 3423 8.033626 TCTCTAGTTAATTTTCCGTCCTCTTTC 58.966 37.037 0.00 0.00 0.00 2.62
3262 3453 2.159240 TGCACCTCGATGTACACTGATC 60.159 50.000 0.00 0.00 0.00 2.92
3267 3458 4.108336 CCTCGATGTACACTGATCTTGTG 58.892 47.826 14.74 14.74 40.87 3.33
3285 3476 0.944386 TGTTCTTCGTTTGGCAGCTC 59.056 50.000 0.00 0.00 0.00 4.09
3347 3538 3.834231 CCTTTTCAACTTGACCCATCCAT 59.166 43.478 0.00 0.00 0.00 3.41
3348 3539 4.322198 CCTTTTCAACTTGACCCATCCATG 60.322 45.833 0.00 0.00 0.00 3.66
3537 3728 1.790623 GCAAGAAGCAGTGCAAATGTG 59.209 47.619 19.20 9.45 44.79 3.21
3597 3788 0.392863 TGGTCATGATGGACGCCAAG 60.393 55.000 0.00 0.00 36.95 3.61
3612 3803 1.740025 GCCAAGCAGATTGTGGACTAC 59.260 52.381 0.00 0.00 37.17 2.73
3649 3845 8.263940 TGTAAGTTGCCTATAAATCTTGTCAC 57.736 34.615 0.00 0.00 0.00 3.67
3670 3866 5.812127 TCACTGATGATATTTCCAAGTCACG 59.188 40.000 0.00 0.00 0.00 4.35
3735 3931 3.999663 CACATCTTTCTGTCCTGGACTTC 59.000 47.826 26.03 2.01 33.15 3.01
3759 3955 2.158534 ACCAGTGCAAATACCACCAAGA 60.159 45.455 0.00 0.00 33.75 3.02
3776 3972 3.694566 CCAAGATTTACAAGTGGCCTACC 59.305 47.826 3.32 0.00 0.00 3.18
3804 4000 1.815003 GCTACAATGGGGCTATGCATC 59.185 52.381 0.19 0.00 0.00 3.91
3820 4016 5.954296 ATGCATCTGGTATGTATGCTTTC 57.046 39.130 0.00 0.00 44.96 2.62
3821 4017 4.779696 TGCATCTGGTATGTATGCTTTCA 58.220 39.130 7.89 0.00 44.96 2.69
3867 4066 5.359009 AGATGTTTGGCATGAGTATCCAAAG 59.641 40.000 12.95 0.00 46.71 2.77
4139 4339 2.094390 CCACAAAATGCCATCAGGAGTG 60.094 50.000 0.00 0.00 36.89 3.51
4195 4395 6.591834 CAGGTATGGTAAAGAAGACTTGAGTG 59.408 42.308 0.00 0.00 36.39 3.51
4404 4604 0.742281 AAAGCGCACGCATGAGAGAT 60.742 50.000 18.24 0.00 44.88 2.75
4411 4611 2.383450 CACGCATGAGAGATCTCTTCG 58.617 52.381 25.81 24.41 43.25 3.79
4489 4689 5.991606 TCCTGAAACTCTGTAACTGAACATG 59.008 40.000 0.00 0.00 0.00 3.21
4676 4876 3.218453 ACATCAGGATCTCGTACAGGAG 58.782 50.000 0.00 0.00 35.32 3.69
4686 4886 2.163815 CTCGTACAGGAGGAACAACGAT 59.836 50.000 0.00 0.00 38.51 3.73
4697 4897 2.602217 GGAACAACGATGACAGCAACAC 60.602 50.000 0.00 0.00 0.00 3.32
4702 4902 1.965930 GATGACAGCAACACCGCCA 60.966 57.895 0.00 0.00 0.00 5.69
4734 4934 2.434185 GCGTCGTTCCATCTGCCA 60.434 61.111 0.00 0.00 0.00 4.92
4745 4945 4.994471 TCTGCCAGTGCCGCACAG 62.994 66.667 24.97 17.07 36.74 3.66
4779 4979 2.945008 TCTGCTCAAGAACAACCTGTTG 59.055 45.455 8.42 8.42 41.28 3.33
4797 4997 2.046285 GCGCCCAAAGGTATGCACT 61.046 57.895 0.00 0.00 34.57 4.40
4851 5051 4.779475 GCGGCTAGCCATGTATGT 57.221 55.556 32.47 0.00 40.81 2.29
4852 5052 3.906660 GCGGCTAGCCATGTATGTA 57.093 52.632 32.47 0.00 40.81 2.29
4853 5053 1.714794 GCGGCTAGCCATGTATGTAG 58.285 55.000 32.47 14.25 40.81 2.74
4947 5147 1.134521 TGTATGCAAAGGCGTAGGAGG 60.135 52.381 0.00 0.00 41.97 4.30
4990 5190 3.495100 CCATACTGCATCTCAAGGTACCC 60.495 52.174 8.74 0.00 0.00 3.69
5022 5222 2.680312 TTCAGCTCCTCCAAGAATCG 57.320 50.000 0.00 0.00 0.00 3.34
5050 5250 6.156949 ACTTTCTCCTCCAGTAATCTTGCATA 59.843 38.462 0.00 0.00 0.00 3.14
5051 5251 6.753913 TTCTCCTCCAGTAATCTTGCATAT 57.246 37.500 0.00 0.00 0.00 1.78
5139 5339 2.190538 TCATGATCCTCCAGAACAGCA 58.809 47.619 0.00 0.00 29.81 4.41
5147 5347 1.135915 CTCCAGAACAGCAGCTACGAT 59.864 52.381 0.00 0.00 0.00 3.73
5153 5353 0.603065 ACAGCAGCTACGATGTGTCA 59.397 50.000 0.00 0.00 0.00 3.58
5213 5413 2.945080 TGAATGAGATCATGAGCCCC 57.055 50.000 7.49 0.42 36.56 5.80
5262 5462 1.686110 CTCTACCCCACCGGCTTCT 60.686 63.158 0.00 0.00 33.26 2.85
5525 5728 6.378280 CCAGGTAATTCTGCTTCCTGTTAAAT 59.622 38.462 8.38 0.00 42.63 1.40
5593 5803 0.171007 CTGTTATTTGCACAGGGGCG 59.829 55.000 0.00 0.00 38.43 6.13
5901 6111 6.648192 ACTCTCTGCAACTTTCAGCTTATAT 58.352 36.000 0.00 0.00 0.00 0.86
5957 6167 4.173036 AGACCTGTTGTTGTTGTTGTTG 57.827 40.909 0.00 0.00 0.00 3.33
5958 6168 3.572255 AGACCTGTTGTTGTTGTTGTTGT 59.428 39.130 0.00 0.00 0.00 3.32
5959 6169 4.038642 AGACCTGTTGTTGTTGTTGTTGTT 59.961 37.500 0.00 0.00 0.00 2.83
5960 6170 4.054671 ACCTGTTGTTGTTGTTGTTGTTG 58.945 39.130 0.00 0.00 0.00 3.33
5961 6171 3.120718 CCTGTTGTTGTTGTTGTTGTTGC 60.121 43.478 0.00 0.00 0.00 4.17
5962 6172 3.722147 TGTTGTTGTTGTTGTTGTTGCT 58.278 36.364 0.00 0.00 0.00 3.91
5963 6173 3.492383 TGTTGTTGTTGTTGTTGTTGCTG 59.508 39.130 0.00 0.00 0.00 4.41
5972 6182 3.738282 TGTTGTTGTTGCTGTTGTTGTTC 59.262 39.130 0.00 0.00 0.00 3.18
6206 6416 6.822170 ACTACCATTGCATGCATATCAGATAG 59.178 38.462 23.37 17.44 0.00 2.08
6295 6668 6.486657 ACCAAGTGTATCGCATAATATTTGCT 59.513 34.615 15.72 5.78 37.96 3.91
6453 6828 5.009911 CCTTGTCACAAGATTCACAAATCCA 59.990 40.000 19.75 0.00 41.97 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 7.735326 TTCCACTATCCTAAACTTCTAGCTT 57.265 36.000 0.00 0.00 0.00 3.74
62 63 7.400627 ACTTTCCACTATCCTAAACTTCTAGCT 59.599 37.037 0.00 0.00 0.00 3.32
65 66 8.660295 TCACTTTCCACTATCCTAAACTTCTA 57.340 34.615 0.00 0.00 0.00 2.10
134 135 2.301738 GCTAGCCCCACTTCACCCT 61.302 63.158 2.29 0.00 0.00 4.34
306 307 0.466555 TTAAAGGCACACAAGGCGGT 60.467 50.000 0.00 0.00 39.37 5.68
338 339 5.618236 ACAAAAGGACTAGTAAACCAGGAC 58.382 41.667 0.00 0.00 0.00 3.85
339 340 5.899631 ACAAAAGGACTAGTAAACCAGGA 57.100 39.130 0.00 0.00 0.00 3.86
340 341 6.238925 CCAAACAAAAGGACTAGTAAACCAGG 60.239 42.308 0.00 0.00 0.00 4.45
342 343 5.595133 CCCAAACAAAAGGACTAGTAAACCA 59.405 40.000 0.00 0.00 0.00 3.67
344 345 6.319405 TGACCCAAACAAAAGGACTAGTAAAC 59.681 38.462 0.00 0.00 0.00 2.01
345 346 6.424883 TGACCCAAACAAAAGGACTAGTAAA 58.575 36.000 0.00 0.00 0.00 2.01
473 512 9.225436 TGACTAGCAAAATGTTAATACATGTCA 57.775 29.630 0.00 0.00 44.14 3.58
553 592 7.685849 TGAAAATAGCCTAGGTGGTTACTAT 57.314 36.000 11.31 4.66 34.30 2.12
565 604 6.096846 GGAGCAAAAAGGATGAAAATAGCCTA 59.903 38.462 0.00 0.00 34.86 3.93
752 794 6.095432 AGAGTAGCTAATACAATGCTCCTG 57.905 41.667 0.00 0.00 38.15 3.86
815 857 3.204467 TTACCCCTGGCCTGCACAC 62.204 63.158 3.32 0.00 0.00 3.82
816 858 2.856494 TTACCCCTGGCCTGCACA 60.856 61.111 3.32 0.00 0.00 4.57
817 859 2.044946 CTTACCCCTGGCCTGCAC 60.045 66.667 3.32 0.00 0.00 4.57
818 860 3.338250 CCTTACCCCTGGCCTGCA 61.338 66.667 3.32 0.00 0.00 4.41
819 861 4.822628 GCCTTACCCCTGGCCTGC 62.823 72.222 3.32 0.00 43.11 4.85
888 930 3.508012 ACTTCACTCGAATGTAGAGCACT 59.492 43.478 7.53 0.00 39.23 4.40
934 976 5.128663 TCGACCAAATCAGAATCTATCCACA 59.871 40.000 0.00 0.00 0.00 4.17
982 1024 2.501316 TCATCTTGGGCTCGAAAGATCA 59.499 45.455 7.03 0.00 40.36 2.92
1059 1101 7.435068 TGCAAGAAAACTTCCAACTAGTATC 57.565 36.000 0.00 0.00 0.00 2.24
1147 1189 7.718753 AGAAATTCAAGCCCTTATCTACTCATG 59.281 37.037 0.00 0.00 0.00 3.07
1151 1193 7.200434 TGAGAAATTCAAGCCCTTATCTACT 57.800 36.000 0.00 0.00 31.34 2.57
1152 1194 6.484977 CCTGAGAAATTCAAGCCCTTATCTAC 59.515 42.308 0.00 0.00 34.81 2.59
1153 1195 6.386927 TCCTGAGAAATTCAAGCCCTTATCTA 59.613 38.462 0.00 0.00 34.81 1.98
1154 1196 5.192522 TCCTGAGAAATTCAAGCCCTTATCT 59.807 40.000 0.00 0.00 34.81 1.98
1155 1197 5.440610 TCCTGAGAAATTCAAGCCCTTATC 58.559 41.667 0.00 0.00 34.81 1.75
1156 1198 5.192522 TCTCCTGAGAAATTCAAGCCCTTAT 59.807 40.000 0.00 0.00 34.81 1.73
1157 1199 4.536090 TCTCCTGAGAAATTCAAGCCCTTA 59.464 41.667 0.00 0.00 34.81 2.69
1158 1200 3.331889 TCTCCTGAGAAATTCAAGCCCTT 59.668 43.478 0.00 0.00 34.81 3.95
1174 1224 8.387190 TGCAAGATATATTTCAACATCTCCTG 57.613 34.615 0.00 0.00 0.00 3.86
1252 1302 8.573035 GGAAAACATGTCCTAGTTGATGTAAAA 58.427 33.333 0.00 0.00 31.94 1.52
1265 1315 7.437713 TGTAGATCTATGGAAAACATGTCCT 57.562 36.000 5.57 0.00 40.82 3.85
1308 1358 1.078143 GGTTGCACCTCTAGCCAGG 60.078 63.158 0.00 0.00 39.80 4.45
1350 1401 1.758514 TTGCACCCCCTCGCAAAAA 60.759 52.632 0.00 0.00 44.71 1.94
1351 1402 2.123683 TTGCACCCCCTCGCAAAA 60.124 55.556 0.00 0.00 44.71 2.44
1354 1405 4.424711 GGATTGCACCCCCTCGCA 62.425 66.667 0.00 0.00 36.05 5.10
1355 1406 4.115199 AGGATTGCACCCCCTCGC 62.115 66.667 0.91 0.00 0.00 5.03
1356 1407 2.124570 CAGGATTGCACCCCCTCG 60.125 66.667 0.91 0.00 0.00 4.63
1366 1417 1.725641 TGCTGTAACGAGCAGGATTG 58.274 50.000 0.00 0.00 44.16 2.67
1417 1468 7.337689 TGAACATGAAGAACCTGGATTAGAATG 59.662 37.037 0.00 0.34 0.00 2.67
1456 1510 5.718649 ATTGGTTACATGAACGATTCTCG 57.281 39.130 0.00 0.00 46.93 4.04
1500 1554 4.651503 ACAATAACCTCGATGACTGGATCT 59.348 41.667 0.00 0.00 0.00 2.75
1521 1575 5.133941 TGTTAGAACAACAAATGGGCTACA 58.866 37.500 0.00 0.00 35.67 2.74
1522 1576 5.699097 TGTTAGAACAACAAATGGGCTAC 57.301 39.130 0.00 0.00 35.67 3.58
1568 1622 4.020218 CCAGATCTGTAAAGTGTCTCCCAA 60.020 45.833 21.11 0.00 0.00 4.12
1752 1890 2.930887 GCAAAGCACGATACTGGACAGA 60.931 50.000 6.29 0.00 0.00 3.41
1777 1915 2.357952 GGTGAACGAAGCAAGGAAAACT 59.642 45.455 0.00 0.00 0.00 2.66
1915 2068 3.308595 CGGACATACGTGTATGCAAACAT 59.691 43.478 17.62 0.00 45.06 2.71
1922 2075 1.337071 AGCTCCGGACATACGTGTATG 59.663 52.381 16.42 16.42 46.24 2.39
1968 2123 3.662247 AATATGCTCTACAGTACCGCC 57.338 47.619 0.00 0.00 0.00 6.13
2038 2193 2.075355 TTTTGTCCGATGTGGGGCCT 62.075 55.000 0.84 0.00 38.76 5.19
2099 2254 7.390996 TCCGTTGTAAATATTAAACAGCTTGGA 59.609 33.333 12.66 10.58 0.00 3.53
2100 2255 7.531716 TCCGTTGTAAATATTAAACAGCTTGG 58.468 34.615 12.66 9.12 0.00 3.61
2107 2262 9.706846 AATTACGCTCCGTTGTAAATATTAAAC 57.293 29.630 0.00 0.00 41.54 2.01
2166 2322 3.050275 GCTGGACGGTCCTGTTGC 61.050 66.667 27.91 21.15 37.74 4.17
2212 2368 0.036388 TCTTGTCCATCGGAGTTGCC 60.036 55.000 0.00 0.00 29.39 4.52
2370 2533 4.499019 GCCGAAAAACCTGTTCATTCAAGA 60.499 41.667 8.37 0.00 0.00 3.02
2399 2562 3.989698 ATTCTCGTCAGGGTGCGCG 62.990 63.158 0.00 0.00 0.00 6.86
2521 2684 6.319658 ACTGTGTCACTGAGATTTCACAAATT 59.680 34.615 15.96 0.00 32.44 1.82
2523 2686 5.185454 ACTGTGTCACTGAGATTTCACAAA 58.815 37.500 15.96 0.00 32.44 2.83
2565 2729 7.330900 ACGTACAGTAGCAATAGTAGTTGAT 57.669 36.000 0.00 0.00 0.00 2.57
2578 2742 3.834610 AGACATGACAACGTACAGTAGC 58.165 45.455 0.00 0.00 0.00 3.58
2606 2770 5.349817 ACATGACAATGTTTGCGTTCAAAAA 59.650 32.000 0.00 0.00 44.94 1.94
2607 2771 4.867047 ACATGACAATGTTTGCGTTCAAAA 59.133 33.333 0.00 0.00 44.94 2.44
2608 2772 4.428209 ACATGACAATGTTTGCGTTCAAA 58.572 34.783 0.00 0.00 44.94 2.69
2609 2773 4.039151 ACATGACAATGTTTGCGTTCAA 57.961 36.364 0.00 0.00 44.94 2.69
2610 2774 3.706802 ACATGACAATGTTTGCGTTCA 57.293 38.095 0.00 0.00 44.94 3.18
2629 2793 6.568869 AGTCTGTAGCTAATGATGTGAAGAC 58.431 40.000 0.00 0.00 0.00 3.01
2669 2833 1.195115 TCTGCATGTCAGGTCCTACC 58.805 55.000 14.50 0.00 43.06 3.18
2676 2840 2.408271 TAAGCCTTCTGCATGTCAGG 57.592 50.000 14.50 7.12 44.83 3.86
2687 2851 2.213499 CGATCACCACCATAAGCCTTC 58.787 52.381 0.00 0.00 0.00 3.46
2803 2967 0.449388 CGGATGCAAGCCTCTTGTTC 59.551 55.000 8.18 5.98 43.22 3.18
2821 2985 2.322161 CAAAATGAAGTCTTGGCTGCG 58.678 47.619 0.00 0.00 0.00 5.18
2827 2991 2.232208 GGAGGGGCAAAATGAAGTCTTG 59.768 50.000 0.00 0.00 0.00 3.02
2908 3072 0.236711 CCTGTTGCTTCAGTTGCTCG 59.763 55.000 7.65 0.00 34.02 5.03
2990 3157 6.895728 TGGAACAAAATCTGCCGAATATTTCG 60.896 38.462 2.77 2.77 44.95 3.46
2995 3162 4.331968 ACTGGAACAAAATCTGCCGAATA 58.668 39.130 0.00 0.00 38.70 1.75
2999 3166 3.369546 AAACTGGAACAAAATCTGCCG 57.630 42.857 0.00 0.00 38.70 5.69
3037 3206 2.359981 ATAGGTACGTCTAGCAGGCA 57.640 50.000 0.00 0.00 0.00 4.75
3038 3207 5.048224 TCAAATATAGGTACGTCTAGCAGGC 60.048 44.000 0.00 0.00 0.00 4.85
3039 3208 6.570672 TCAAATATAGGTACGTCTAGCAGG 57.429 41.667 0.00 0.00 0.00 4.85
3040 3209 7.649973 ACTTCAAATATAGGTACGTCTAGCAG 58.350 38.462 0.00 0.00 0.00 4.24
3067 3236 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
3068 3237 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
3069 3238 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
3070 3239 2.277084 CCGAGTAATTTGGAACGGAGG 58.723 52.381 0.00 0.00 42.40 4.30
3071 3240 2.928116 GACCGAGTAATTTGGAACGGAG 59.072 50.000 0.00 0.00 42.40 4.63
3072 3241 2.671914 CGACCGAGTAATTTGGAACGGA 60.672 50.000 0.00 0.00 42.40 4.69
3073 3242 1.657094 CGACCGAGTAATTTGGAACGG 59.343 52.381 0.00 0.00 44.77 4.44
3074 3243 1.060122 GCGACCGAGTAATTTGGAACG 59.940 52.381 0.00 0.00 37.03 3.95
3075 3244 2.070783 TGCGACCGAGTAATTTGGAAC 58.929 47.619 0.00 0.00 34.08 3.62
3076 3245 2.028839 TCTGCGACCGAGTAATTTGGAA 60.029 45.455 0.00 0.00 34.08 3.53
3077 3246 1.546923 TCTGCGACCGAGTAATTTGGA 59.453 47.619 0.00 0.00 34.08 3.53
3078 3247 2.004583 TCTGCGACCGAGTAATTTGG 57.995 50.000 0.00 0.00 36.29 3.28
3079 3248 4.334443 CATTTCTGCGACCGAGTAATTTG 58.666 43.478 0.00 0.00 0.00 2.32
3080 3249 3.374058 CCATTTCTGCGACCGAGTAATTT 59.626 43.478 0.00 0.00 0.00 1.82
3081 3250 2.936498 CCATTTCTGCGACCGAGTAATT 59.064 45.455 0.00 0.00 0.00 1.40
3082 3251 2.167693 TCCATTTCTGCGACCGAGTAAT 59.832 45.455 0.00 0.00 0.00 1.89
3083 3252 1.546923 TCCATTTCTGCGACCGAGTAA 59.453 47.619 0.00 0.00 0.00 2.24
3084 3253 1.179152 TCCATTTCTGCGACCGAGTA 58.821 50.000 0.00 0.00 0.00 2.59
3085 3254 0.537188 ATCCATTTCTGCGACCGAGT 59.463 50.000 0.00 0.00 0.00 4.18
3086 3255 0.933097 CATCCATTTCTGCGACCGAG 59.067 55.000 0.00 0.00 0.00 4.63
3087 3256 0.249120 ACATCCATTTCTGCGACCGA 59.751 50.000 0.00 0.00 0.00 4.69
3088 3257 1.934589 TACATCCATTTCTGCGACCG 58.065 50.000 0.00 0.00 0.00 4.79
3089 3258 3.733337 AGATACATCCATTTCTGCGACC 58.267 45.455 0.00 0.00 0.00 4.79
3090 3259 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
3091 3260 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
3092 3261 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
3093 3262 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
3119 3288 9.775539 ACAGGTATGGATGTATCTAGATGTATT 57.224 33.333 15.79 0.00 0.00 1.89
3120 3289 9.194972 CACAGGTATGGATGTATCTAGATGTAT 57.805 37.037 15.79 9.11 0.00 2.29
3121 3290 8.390921 TCACAGGTATGGATGTATCTAGATGTA 58.609 37.037 15.79 4.44 0.00 2.29
3122 3291 7.177568 GTCACAGGTATGGATGTATCTAGATGT 59.822 40.741 15.79 1.25 0.00 3.06
3123 3292 7.177392 TGTCACAGGTATGGATGTATCTAGATG 59.823 40.741 15.79 0.00 0.00 2.90
3124 3293 7.241628 TGTCACAGGTATGGATGTATCTAGAT 58.758 38.462 10.73 10.73 0.00 1.98
3125 3294 6.610830 TGTCACAGGTATGGATGTATCTAGA 58.389 40.000 0.00 0.00 0.00 2.43
3126 3295 6.901081 TGTCACAGGTATGGATGTATCTAG 57.099 41.667 0.00 0.00 0.00 2.43
3127 3296 6.839134 ACTTGTCACAGGTATGGATGTATCTA 59.161 38.462 0.00 0.00 0.00 1.98
3128 3297 5.663106 ACTTGTCACAGGTATGGATGTATCT 59.337 40.000 0.00 0.00 0.00 1.98
3129 3298 5.918608 ACTTGTCACAGGTATGGATGTATC 58.081 41.667 0.00 0.00 0.00 2.24
3130 3299 5.957771 ACTTGTCACAGGTATGGATGTAT 57.042 39.130 0.00 0.00 0.00 2.29
3131 3300 6.860790 TTACTTGTCACAGGTATGGATGTA 57.139 37.500 0.00 0.00 0.00 2.29
3132 3301 5.755409 TTACTTGTCACAGGTATGGATGT 57.245 39.130 0.00 0.00 0.00 3.06
3133 3302 6.018751 CGAATTACTTGTCACAGGTATGGATG 60.019 42.308 0.00 0.00 0.00 3.51
3134 3303 6.049149 CGAATTACTTGTCACAGGTATGGAT 58.951 40.000 0.00 0.00 0.00 3.41
3135 3304 5.416083 CGAATTACTTGTCACAGGTATGGA 58.584 41.667 0.00 0.00 0.00 3.41
3136 3305 4.570772 CCGAATTACTTGTCACAGGTATGG 59.429 45.833 0.00 0.00 0.00 2.74
3137 3306 5.416083 TCCGAATTACTTGTCACAGGTATG 58.584 41.667 0.00 0.00 0.00 2.39
3138 3307 5.670792 TCCGAATTACTTGTCACAGGTAT 57.329 39.130 0.00 0.00 0.00 2.73
3139 3308 5.232463 GTTCCGAATTACTTGTCACAGGTA 58.768 41.667 0.00 0.00 0.00 3.08
3140 3309 4.062991 GTTCCGAATTACTTGTCACAGGT 58.937 43.478 0.00 0.00 0.00 4.00
3141 3310 3.122948 CGTTCCGAATTACTTGTCACAGG 59.877 47.826 0.00 0.00 0.00 4.00
3142 3311 3.122948 CCGTTCCGAATTACTTGTCACAG 59.877 47.826 0.00 0.00 0.00 3.66
3143 3312 3.061322 CCGTTCCGAATTACTTGTCACA 58.939 45.455 0.00 0.00 0.00 3.58
3144 3313 3.319755 TCCGTTCCGAATTACTTGTCAC 58.680 45.455 0.00 0.00 0.00 3.67
3145 3314 3.581755 CTCCGTTCCGAATTACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
3146 3315 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
3147 3316 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
3148 3317 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
3149 3318 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
3150 3319 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
3151 3320 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
3152 3321 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
3153 3322 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
3154 3323 1.479730 GTTACTCCCTCCGTTCCGAAT 59.520 52.381 0.00 0.00 0.00 3.34
3155 3324 0.890683 GTTACTCCCTCCGTTCCGAA 59.109 55.000 0.00 0.00 0.00 4.30
3156 3325 0.038744 AGTTACTCCCTCCGTTCCGA 59.961 55.000 0.00 0.00 0.00 4.55
3157 3326 0.893447 AAGTTACTCCCTCCGTTCCG 59.107 55.000 0.00 0.00 0.00 4.30
3158 3327 2.614734 CCAAAGTTACTCCCTCCGTTCC 60.615 54.545 0.00 0.00 0.00 3.62
3159 3328 2.038164 ACCAAAGTTACTCCCTCCGTTC 59.962 50.000 0.00 0.00 0.00 3.95
3160 3329 2.052468 ACCAAAGTTACTCCCTCCGTT 58.948 47.619 0.00 0.00 0.00 4.44
3161 3330 1.346722 CACCAAAGTTACTCCCTCCGT 59.653 52.381 0.00 0.00 0.00 4.69
3162 3331 1.338769 CCACCAAAGTTACTCCCTCCG 60.339 57.143 0.00 0.00 0.00 4.63
3163 3332 1.982958 TCCACCAAAGTTACTCCCTCC 59.017 52.381 0.00 0.00 0.00 4.30
3164 3333 3.782656 TTCCACCAAAGTTACTCCCTC 57.217 47.619 0.00 0.00 0.00 4.30
3165 3334 3.916989 AGATTCCACCAAAGTTACTCCCT 59.083 43.478 0.00 0.00 0.00 4.20
3166 3335 4.302559 AGATTCCACCAAAGTTACTCCC 57.697 45.455 0.00 0.00 0.00 4.30
3167 3336 6.051179 ACTAGATTCCACCAAAGTTACTCC 57.949 41.667 0.00 0.00 0.00 3.85
3168 3337 6.937392 AGACTAGATTCCACCAAAGTTACTC 58.063 40.000 0.00 0.00 0.00 2.59
3169 3338 6.936968 AGACTAGATTCCACCAAAGTTACT 57.063 37.500 0.00 0.00 0.00 2.24
3170 3339 8.092687 TGTAAGACTAGATTCCACCAAAGTTAC 58.907 37.037 0.00 0.00 0.00 2.50
3171 3340 8.197592 TGTAAGACTAGATTCCACCAAAGTTA 57.802 34.615 0.00 0.00 0.00 2.24
3172 3341 7.074653 TGTAAGACTAGATTCCACCAAAGTT 57.925 36.000 0.00 0.00 0.00 2.66
3210 3401 6.690530 TCGAAAGAGGACGGAAAATTAACTA 58.309 36.000 0.00 0.00 34.84 2.24
3262 3453 2.719798 CTGCCAAACGAAGAACACAAG 58.280 47.619 0.00 0.00 0.00 3.16
3267 3458 1.195674 GAGAGCTGCCAAACGAAGAAC 59.804 52.381 0.00 0.00 0.00 3.01
3347 3538 5.770919 TCTCTCTTCCAGTGATATTCTCCA 58.229 41.667 0.00 0.00 0.00 3.86
3348 3539 6.723298 TTCTCTCTTCCAGTGATATTCTCC 57.277 41.667 0.00 0.00 0.00 3.71
3537 3728 4.381079 GCCTCGGTCATGAATCCTAGTATC 60.381 50.000 0.00 0.00 0.00 2.24
3597 3788 3.562973 CCATGATGTAGTCCACAATCTGC 59.437 47.826 0.00 0.00 41.55 4.26
3612 3803 5.179045 GGCAACTTACAGAATCCATGATG 57.821 43.478 0.00 0.00 0.00 3.07
3649 3845 4.571984 TGCGTGACTTGGAAATATCATCAG 59.428 41.667 0.00 0.00 0.00 2.90
3661 3857 2.118683 CAAATTGTGTGCGTGACTTGG 58.881 47.619 0.00 0.00 0.00 3.61
3670 3866 3.929094 ACAATGGGATCAAATTGTGTGC 58.071 40.909 19.06 0.00 43.56 4.57
3735 3931 1.812571 GGTGGTATTTGCACTGGTCAG 59.187 52.381 0.00 0.00 0.00 3.51
3759 3955 3.686016 CACTGGTAGGCCACTTGTAAAT 58.314 45.455 5.01 0.00 40.46 1.40
3776 3972 1.033746 CCCCATTGTAGCCTGCACTG 61.034 60.000 0.00 0.00 0.00 3.66
3804 4000 7.798596 AGAGAAATGAAAGCATACATACCAG 57.201 36.000 0.00 0.00 33.44 4.00
3820 4016 8.498054 TCTCTTGGCTAAAACATAGAGAAATG 57.502 34.615 0.00 0.00 36.23 2.32
3821 4017 9.118300 CATCTCTTGGCTAAAACATAGAGAAAT 57.882 33.333 0.00 0.00 40.81 2.17
4139 4339 2.205911 GAATTCAGGCTCCGAACTAGC 58.794 52.381 0.00 0.00 39.33 3.42
4386 4586 1.150567 GATCTCTCATGCGTGCGCTT 61.151 55.000 17.49 8.59 42.51 4.68
4404 4604 2.287915 GCTTTTGCTGACAACGAAGAGA 59.712 45.455 0.00 0.00 43.35 3.10
4411 4611 0.661483 GAGGCGCTTTTGCTGACAAC 60.661 55.000 7.64 0.00 44.80 3.32
4489 4689 6.621613 AGAAAACTTGTTTGTTTCTCAGGAC 58.378 36.000 0.00 0.00 38.98 3.85
4641 4841 1.080093 GATGTCGTCTTCCGTGCCA 60.080 57.895 0.00 0.00 37.94 4.92
4666 4866 1.608055 TCGTTGTTCCTCCTGTACGA 58.392 50.000 0.00 0.00 35.89 3.43
4676 4876 1.601903 TGTTGCTGTCATCGTTGTTCC 59.398 47.619 0.00 0.00 0.00 3.62
4686 4886 1.965930 GATGGCGGTGTTGCTGTCA 60.966 57.895 0.00 0.00 42.98 3.58
4697 4897 4.735132 ACACGGACACGATGGCGG 62.735 66.667 0.00 0.00 44.60 6.13
4734 4934 4.626081 GTCACCCTGTGCGGCACT 62.626 66.667 30.81 10.62 35.11 4.40
4742 4942 1.878102 GCAGATCAAACGTCACCCTGT 60.878 52.381 0.00 0.00 0.00 4.00
4745 4945 1.079503 GAGCAGATCAAACGTCACCC 58.920 55.000 0.00 0.00 0.00 4.61
4779 4979 1.993369 GAGTGCATACCTTTGGGCGC 61.993 60.000 0.00 0.00 37.05 6.53
4797 4997 3.257624 TGCACATGCCAAACATAACATGA 59.742 39.130 0.00 0.00 41.93 3.07
4852 5052 9.367444 GTGAGTAAAACATAGCATTAGTACACT 57.633 33.333 0.00 0.00 0.00 3.55
4853 5053 9.146984 TGTGAGTAAAACATAGCATTAGTACAC 57.853 33.333 0.00 0.00 0.00 2.90
4930 5130 0.179000 CTCCTCCTACGCCTTTGCAT 59.821 55.000 0.00 0.00 37.32 3.96
4947 5147 5.188434 TGGAGACAACATCATCAATTCCTC 58.812 41.667 0.00 0.00 37.44 3.71
4990 5190 3.508793 AGGAGCTGAAATTGGATGTGTTG 59.491 43.478 0.00 0.00 0.00 3.33
5022 5222 3.198853 AGATTACTGGAGGAGAAAGTGGC 59.801 47.826 0.00 0.00 0.00 5.01
5139 5339 1.139734 CGCCTGACACATCGTAGCT 59.860 57.895 0.00 0.00 0.00 3.32
5147 5347 2.030412 ATGAACGCGCCTGACACA 59.970 55.556 5.73 0.00 0.00 3.72
5153 5353 1.153628 GTAGACCATGAACGCGCCT 60.154 57.895 5.73 0.00 0.00 5.52
5198 5398 1.834996 GCTGGGGCTCATGATCTCA 59.165 57.895 0.00 0.00 35.22 3.27
5262 5462 2.593978 CTCGACGGGGAGGAGGTA 59.406 66.667 0.00 0.00 0.00 3.08
5484 5684 7.931015 ATTACCTGGGTACATTCTAGATGAA 57.069 36.000 0.00 0.00 39.24 2.57
5525 5728 4.883021 AGATAGGTGAGGACTAGTGGAA 57.117 45.455 0.00 0.00 0.00 3.53
5593 5803 1.098129 GCATCGCTTCTCCCCTTTCC 61.098 60.000 0.00 0.00 0.00 3.13
5847 6057 1.349026 CTGACCATACATAGGCCAGGG 59.651 57.143 5.01 0.00 0.00 4.45
5957 6167 3.987220 ACAACAAGAACAACAACAGCAAC 59.013 39.130 0.00 0.00 0.00 4.17
5958 6168 4.250116 ACAACAAGAACAACAACAGCAA 57.750 36.364 0.00 0.00 0.00 3.91
5959 6169 3.932545 ACAACAAGAACAACAACAGCA 57.067 38.095 0.00 0.00 0.00 4.41
5960 6170 3.987220 ACAACAACAAGAACAACAACAGC 59.013 39.130 0.00 0.00 0.00 4.40
5961 6171 5.461737 ACAACAACAACAAGAACAACAACAG 59.538 36.000 0.00 0.00 0.00 3.16
5962 6172 5.352284 ACAACAACAACAAGAACAACAACA 58.648 33.333 0.00 0.00 0.00 3.33
5963 6173 5.898630 ACAACAACAACAAGAACAACAAC 57.101 34.783 0.00 0.00 0.00 3.32
6160 6370 5.003160 AGTAACAATGTGCTATTGTGCAGA 58.997 37.500 16.85 0.00 44.20 4.26
6206 6416 8.621286 CCAAGTTATTGAACTGGTGGTATATTC 58.379 37.037 1.85 0.00 45.50 1.75
6228 6599 0.251077 ACTTGCTTCAGCCCTCCAAG 60.251 55.000 0.00 0.00 41.18 3.61
6282 6653 6.039270 TGGTGGAGTACAAGCAAATATTATGC 59.961 38.462 12.09 12.09 44.15 3.14
6295 6668 3.756434 GCAGCTTTATTGGTGGAGTACAA 59.244 43.478 0.00 0.00 36.12 2.41


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

AutoCloner maintained by Alex Coulton.