Multiple sequence alignment - TraesCS2A01G389300

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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 TraesCS2A01G389300 chr2A 100.000 6799 0 0 1 6799 637975213 637982011 0.000000e+00 12556.0
1 TraesCS2A01G389300 chr2D 95.234 3525 118 35 2577 6095 492659694 492663174 0.000000e+00 5533.0
2 TraesCS2A01G389300 chr2D 95.373 2183 74 12 18 2180 492657242 492659417 0.000000e+00 3446.0
3 TraesCS2A01G389300 chr2D 90.263 647 42 12 6164 6796 492672733 492673372 0.000000e+00 826.0
4 TraesCS2A01G389300 chr2D 89.535 344 31 3 4170 4509 620790581 620790239 1.350000e-116 431.0
5 TraesCS2A01G389300 chr2D 92.096 291 13 5 2251 2534 492659412 492659699 1.060000e-107 401.0
6 TraesCS2A01G389300 chr2B 94.681 2181 67 18 17 2181 578595564 578597711 0.000000e+00 3339.0
7 TraesCS2A01G389300 chr2B 92.185 2124 106 22 2249 4357 578597910 578599988 0.000000e+00 2948.0
8 TraesCS2A01G389300 chr2B 95.946 1628 56 8 4459 6085 578599989 578601607 0.000000e+00 2632.0
9 TraesCS2A01G389300 chr2B 86.527 668 48 15 6164 6799 578601858 578602515 0.000000e+00 697.0
10 TraesCS2A01G389300 chr1D 94.231 52 2 1 2242 2293 118887397 118887447 2.030000e-10 78.7
11 TraesCS2A01G389300 chr1D 95.652 46 2 0 2249 2294 484026285 484026240 2.630000e-09 75.0
12 TraesCS2A01G389300 chr3D 100.000 41 0 0 2248 2288 315481468 315481428 7.310000e-10 76.8
13 TraesCS2A01G389300 chr3B 100.000 41 0 0 2248 2288 404829427 404829467 7.310000e-10 76.8
14 TraesCS2A01G389300 chr1A 95.833 48 0 2 2245 2292 129728255 129728210 7.310000e-10 76.8
15 TraesCS2A01G389300 chr5D 100.000 40 0 0 2249 2288 464690684 464690723 2.630000e-09 75.0
16 TraesCS2A01G389300 chr4D 97.727 44 0 1 2249 2291 94596317 94596274 2.630000e-09 75.0
17 TraesCS2A01G389300 chr7B 93.878 49 1 2 2249 2295 392853858 392853906 9.460000e-09 73.1
18 TraesCS2A01G389300 chr7A 100.000 30 0 0 2169 2198 155989119 155989148 1.000000e-03 56.5
19 TraesCS2A01G389300 chr3A 100.000 30 0 0 2169 2198 414817112 414817141 1.000000e-03 56.5
20 TraesCS2A01G389300 chr1B 100.000 28 0 0 2172 2199 121572527 121572500 1.200000e-02 52.8
21 TraesCS2A01G389300 chr1B 100.000 28 0 0 2172 2199 121718055 121718028 1.200000e-02 52.8


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 TraesCS2A01G389300 chr2A 637975213 637982011 6798 False 12556.000000 12556 100.000000 1 6799 1 chr2A.!!$F1 6798
1 TraesCS2A01G389300 chr2D 492657242 492663174 5932 False 3126.666667 5533 94.234333 18 6095 3 chr2D.!!$F2 6077
2 TraesCS2A01G389300 chr2D 492672733 492673372 639 False 826.000000 826 90.263000 6164 6796 1 chr2D.!!$F1 632
3 TraesCS2A01G389300 chr2B 578595564 578602515 6951 False 2404.000000 3339 92.334750 17 6799 4 chr2B.!!$F1 6782

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
164 170 0.040499 ACTCCACTCCTCCAGTCCTC 59.960 60.000 0.00 0.00 30.26 3.71 F
207 218 0.545309 TTCCTCTCCACCCTCCTGTG 60.545 60.000 0.00 0.00 35.98 3.66 F
933 958 1.143684 GGGGTCATCATGTGCCATACT 59.856 52.381 0.00 0.00 0.00 2.12 F
1315 1340 1.207329 GTATAGGGGCGGATGGTCATC 59.793 57.143 2.52 2.52 37.11 2.92 F
2602 2803 2.028112 TGAGCTAACTTGGGTACTGCTG 60.028 50.000 0.00 0.00 0.00 4.41 F
4388 4600 3.053693 ACCCTTATCAGCCATAACTGCAA 60.054 43.478 0.00 0.00 37.59 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1302 1327 0.107456 ATGACAGATGACCATCCGCC 59.893 55.000 6.40 0.0 38.58 6.13 R
1576 1601 0.747255 TCCTTCCGAGCTCTATGTGC 59.253 55.000 12.85 0.0 0.00 4.57 R
2581 2782 2.028112 CAGCAGTACCCAAGTTAGCTCA 60.028 50.000 0.00 0.0 0.00 4.26 R
2673 2874 2.664916 GCGCATCAAATCGCCAATATT 58.335 42.857 0.30 0.0 45.01 1.28 R
4429 4641 1.333931 CTATGCCATGCTGCACTTCTG 59.666 52.381 3.57 0.0 45.48 3.02 R
6058 6273 0.100503 ACAAGCTGCCGTCAACAAAC 59.899 50.000 0.00 0.0 0.00 2.93 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
30 31 6.283161 GTACCAGTGTACAAAGTTCTTGTC 57.717 41.667 0.00 0.00 45.50 3.18
112 118 4.139786 CCATCTACCATCAAATCACCCAG 58.860 47.826 0.00 0.00 0.00 4.45
160 166 2.370189 CAGAAAACTCCACTCCTCCAGT 59.630 50.000 0.00 0.00 34.67 4.00
161 167 2.635427 AGAAAACTCCACTCCTCCAGTC 59.365 50.000 0.00 0.00 30.26 3.51
162 168 1.353091 AAACTCCACTCCTCCAGTCC 58.647 55.000 0.00 0.00 30.26 3.85
163 169 0.489567 AACTCCACTCCTCCAGTCCT 59.510 55.000 0.00 0.00 30.26 3.85
164 170 0.040499 ACTCCACTCCTCCAGTCCTC 59.960 60.000 0.00 0.00 30.26 3.71
165 171 0.686112 CTCCACTCCTCCAGTCCTCC 60.686 65.000 0.00 0.00 30.26 4.30
207 218 0.545309 TTCCTCTCCACCCTCCTGTG 60.545 60.000 0.00 0.00 35.98 3.66
453 464 2.353323 GGTGATTACTTGACCCGAACC 58.647 52.381 0.00 0.00 0.00 3.62
564 587 2.030946 CGAATTCGAGACCTGGAAATGC 59.969 50.000 23.29 0.00 43.02 3.56
651 674 7.554959 AGTCTCACAAAAAGGTATTCTAGGA 57.445 36.000 0.00 0.00 0.00 2.94
774 797 2.735663 GGATGAAGCTCATATGTGCTCG 59.264 50.000 27.44 4.11 43.19 5.03
933 958 1.143684 GGGGTCATCATGTGCCATACT 59.856 52.381 0.00 0.00 0.00 2.12
954 979 8.821894 CATACTCTTCTTAAGCTGTATCAAACC 58.178 37.037 0.00 0.00 30.92 3.27
1315 1340 1.207329 GTATAGGGGCGGATGGTCATC 59.793 57.143 2.52 2.52 37.11 2.92
1521 1546 5.479306 TCGCAGGTATCTTATAATTCTGGC 58.521 41.667 0.00 0.00 0.00 4.85
1576 1601 7.106239 TGCTAAGAACTCTCTATTTGGAAAGG 58.894 38.462 0.00 0.00 0.00 3.11
1683 1708 9.494271 CAGAACATATACATTAATGTACTGCCT 57.506 33.333 26.55 21.25 45.11 4.75
1971 1996 5.863935 GGTGATAAACTTGCTTCATGAAACC 59.136 40.000 9.88 5.75 0.00 3.27
2085 2110 6.744112 TGTTCTTGGCCTTTTAGTGTATTTG 58.256 36.000 3.32 0.00 0.00 2.32
2188 2376 8.874744 TTACTGATGTACTACCTCTGTAAACT 57.125 34.615 15.43 0.00 35.75 2.66
2189 2377 7.778185 ACTGATGTACTACCTCTGTAAACTT 57.222 36.000 0.00 0.00 0.00 2.66
2190 2378 8.191534 ACTGATGTACTACCTCTGTAAACTTT 57.808 34.615 0.00 0.00 0.00 2.66
2212 2400 9.377238 ACTTTTATAAGATAATCGGGGTAGTCT 57.623 33.333 0.00 0.00 35.30 3.24
2218 2406 9.993454 ATAAGATAATCGGGGTAGTCTTAAAAC 57.007 33.333 0.00 0.00 33.46 2.43
2219 2407 7.427989 AGATAATCGGGGTAGTCTTAAAACA 57.572 36.000 0.00 0.00 0.00 2.83
2221 2409 9.151177 AGATAATCGGGGTAGTCTTAAAACATA 57.849 33.333 0.00 0.00 0.00 2.29
2222 2410 9.939802 GATAATCGGGGTAGTCTTAAAACATAT 57.060 33.333 0.00 0.00 0.00 1.78
2224 2412 8.446599 AATCGGGGTAGTCTTAAAACATATTG 57.553 34.615 0.00 0.00 0.00 1.90
2225 2413 6.350906 TCGGGGTAGTCTTAAAACATATTGG 58.649 40.000 0.00 0.00 0.00 3.16
2226 2414 6.070078 TCGGGGTAGTCTTAAAACATATTGGT 60.070 38.462 0.00 0.00 0.00 3.67
2227 2415 6.037830 CGGGGTAGTCTTAAAACATATTGGTG 59.962 42.308 0.00 0.00 0.00 4.17
2228 2416 6.320418 GGGGTAGTCTTAAAACATATTGGTGG 59.680 42.308 0.00 0.00 0.00 4.61
2229 2417 6.888088 GGGTAGTCTTAAAACATATTGGTGGT 59.112 38.462 0.00 0.00 0.00 4.16
2230 2418 7.395206 GGGTAGTCTTAAAACATATTGGTGGTT 59.605 37.037 0.00 0.00 0.00 3.67
2231 2419 9.452287 GGTAGTCTTAAAACATATTGGTGGTTA 57.548 33.333 0.00 0.00 0.00 2.85
2233 2421 8.575649 AGTCTTAAAACATATTGGTGGTTAGG 57.424 34.615 0.00 0.00 0.00 2.69
2234 2422 8.168058 AGTCTTAAAACATATTGGTGGTTAGGT 58.832 33.333 0.00 0.00 0.00 3.08
2235 2423 8.799367 GTCTTAAAACATATTGGTGGTTAGGTT 58.201 33.333 0.00 0.00 0.00 3.50
2236 2424 9.369672 TCTTAAAACATATTGGTGGTTAGGTTT 57.630 29.630 0.00 0.00 34.77 3.27
2243 2431 9.362151 ACATATTGGTGGTTAGGTTTATATTGG 57.638 33.333 0.00 0.00 0.00 3.16
2244 2432 9.581289 CATATTGGTGGTTAGGTTTATATTGGA 57.419 33.333 0.00 0.00 0.00 3.53
2247 2435 8.528044 TTGGTGGTTAGGTTTATATTGGAATC 57.472 34.615 0.00 0.00 0.00 2.52
2248 2436 7.644062 TGGTGGTTAGGTTTATATTGGAATCA 58.356 34.615 0.00 0.00 0.00 2.57
2249 2437 7.777910 TGGTGGTTAGGTTTATATTGGAATCAG 59.222 37.037 0.00 0.00 0.00 2.90
2250 2438 7.778382 GGTGGTTAGGTTTATATTGGAATCAGT 59.222 37.037 0.00 0.00 0.00 3.41
2374 2572 6.987403 TTTAAAATAACAGGAAAGCAGGGT 57.013 33.333 0.00 0.00 0.00 4.34
2424 2625 9.020731 CAACCTGTAATAGTAAAGGTGGAAAAT 57.979 33.333 12.79 0.00 45.97 1.82
2512 2713 7.538678 CGGCAATATGATTAGCATTTTAACTCC 59.461 37.037 0.00 0.00 38.44 3.85
2602 2803 2.028112 TGAGCTAACTTGGGTACTGCTG 60.028 50.000 0.00 0.00 0.00 4.41
2673 2874 9.466497 AAATTTCTAAGCTCCTGTTTATGATGA 57.534 29.630 0.00 0.00 0.00 2.92
2688 2889 8.628280 TGTTTATGATGAATATTGGCGATTTGA 58.372 29.630 0.00 0.00 0.00 2.69
2707 2908 4.754372 TGATGCGCTGATTTATGGATTC 57.246 40.909 9.73 0.00 0.00 2.52
2911 3112 7.519970 GCATTCCCTGATGGTATAAACTTTACG 60.520 40.741 0.00 0.00 34.77 3.18
2918 3119 8.046294 TGATGGTATAAACTTTACGCATGTTT 57.954 30.769 0.00 0.00 36.81 2.83
2919 3120 8.516234 TGATGGTATAAACTTTACGCATGTTTT 58.484 29.630 0.00 0.00 35.11 2.43
2977 3178 5.068198 ACCATTGCAGCTGGTCTAATTAATG 59.932 40.000 17.12 5.32 43.59 1.90
3351 3555 7.803659 GCTTATGTTCTCACTTTCACCTTTTAC 59.196 37.037 0.00 0.00 0.00 2.01
3352 3556 8.740123 TTATGTTCTCACTTTCACCTTTTACA 57.260 30.769 0.00 0.00 0.00 2.41
3528 3732 4.890581 TGGTAAGTTGGTAACTGCAAATGT 59.109 37.500 0.00 0.00 41.91 2.71
3595 3799 5.135533 TGATATACTCCTCCACAGTTCCCTA 59.864 44.000 0.00 0.00 0.00 3.53
3690 3895 6.618287 TTGATACTTGAAAATCCTATGCGG 57.382 37.500 0.00 0.00 0.00 5.69
3749 3954 8.889717 CAGTTTCGTTGGGTTTTATACATAGAT 58.110 33.333 0.00 0.00 0.00 1.98
3755 3960 8.134895 CGTTGGGTTTTATACATAGATTGCAAT 58.865 33.333 12.83 12.83 0.00 3.56
3756 3961 9.816354 GTTGGGTTTTATACATAGATTGCAATT 57.184 29.630 14.33 6.39 0.00 2.32
3757 3962 9.814899 TTGGGTTTTATACATAGATTGCAATTG 57.185 29.630 14.33 10.62 0.00 2.32
3758 3963 9.194972 TGGGTTTTATACATAGATTGCAATTGA 57.805 29.630 14.33 5.00 0.00 2.57
4067 4276 8.685427 TGATAACCATGTCAATGTCTAAAATGG 58.315 33.333 0.00 0.00 39.20 3.16
4123 4335 5.426509 TCCACAGATAGTCAAACATGGATCT 59.573 40.000 0.00 0.00 30.08 2.75
4136 4348 8.464404 TCAAACATGGATCTGATTCTGATTTTC 58.536 33.333 7.39 2.84 0.00 2.29
4138 4350 8.591114 AACATGGATCTGATTCTGATTTTCTT 57.409 30.769 7.39 0.00 0.00 2.52
4203 4415 7.015584 AGTGCATTTTTAATTTGGAGGACTTCT 59.984 33.333 0.00 0.00 0.00 2.85
4211 4423 4.503714 TTTGGAGGACTTCTTCAACAGT 57.496 40.909 0.00 0.00 40.52 3.55
4286 4498 5.241403 TCTAAAGTTCCCTGAGCAAATGA 57.759 39.130 0.00 0.00 0.00 2.57
4292 4504 4.018960 AGTTCCCTGAGCAAATGATGTAGT 60.019 41.667 0.00 0.00 0.00 2.73
4388 4600 3.053693 ACCCTTATCAGCCATAACTGCAA 60.054 43.478 0.00 0.00 37.59 4.08
4661 4873 4.885325 GGAAAAGGTACAGGACAAGACAAA 59.115 41.667 0.00 0.00 0.00 2.83
4790 5002 2.637165 AGGATGTCTCTTGGGGACTTT 58.363 47.619 0.00 0.00 35.04 2.66
5090 5302 3.049344 AGATCCAGGACCTATTTGGGAC 58.951 50.000 0.00 0.00 41.11 4.46
5216 5428 2.632377 ACATCTATGGAACTTGTGCCG 58.368 47.619 0.00 0.00 0.00 5.69
5420 5632 0.878416 TACTGCAATTTGGTCGCCAC 59.122 50.000 0.00 0.00 30.78 5.01
5460 5672 5.182001 GTGGAATATGTGAAGGTATCATGCC 59.818 44.000 0.00 0.00 40.97 4.40
5529 5741 5.163426 TGCTTTTTGAAGAGCTTCCATTTGA 60.163 36.000 7.69 0.00 39.60 2.69
5631 5844 2.288273 ACACTGACTCGGTCTTAACTGC 60.288 50.000 5.77 0.00 33.15 4.40
5708 5922 1.410850 ATGGCTGTGGGATAGACGGG 61.411 60.000 0.00 0.00 0.00 5.28
5790 6004 1.153842 GGCCGGCAATGTAAACAGC 60.154 57.895 30.85 1.22 0.00 4.40
5814 6028 2.638480 TTAAGCACCACAAGTCTGCT 57.362 45.000 0.00 0.00 43.21 4.24
5914 6129 2.676121 TTGCCAATGAGGGTGCGG 60.676 61.111 0.00 0.00 38.09 5.69
5975 6190 9.837681 TGTATATTTGAGTGATTATAGAGGGGA 57.162 33.333 0.00 0.00 0.00 4.81
5999 6214 9.267084 GGATACCTCAGTTCTTTTTATCTGATC 57.733 37.037 0.00 0.00 36.55 2.92
6034 6249 3.865164 TGTTGACATCTACTAATGCTGCG 59.135 43.478 0.00 0.00 0.00 5.18
6041 6256 3.267483 TCTACTAATGCTGCGTTTTCCC 58.733 45.455 12.93 0.00 0.00 3.97
6042 6257 2.200373 ACTAATGCTGCGTTTTCCCT 57.800 45.000 12.93 0.00 0.00 4.20
6046 6261 0.240945 ATGCTGCGTTTTCCCTTTCG 59.759 50.000 0.00 0.00 0.00 3.46
6049 6264 0.110823 CTGCGTTTTCCCTTTCGACG 60.111 55.000 0.00 0.00 36.85 5.12
6050 6265 0.530211 TGCGTTTTCCCTTTCGACGA 60.530 50.000 0.00 0.00 35.90 4.20
6058 6273 2.573369 TCCCTTTCGACGATAGAGGAG 58.427 52.381 15.73 9.54 41.38 3.69
6068 6283 3.834610 ACGATAGAGGAGTTTGTTGACG 58.165 45.455 0.00 0.00 41.38 4.35
6069 6284 3.179830 CGATAGAGGAGTTTGTTGACGG 58.820 50.000 0.00 0.00 39.76 4.79
6087 6302 3.117589 GCAGCTTGTGAATTGCCTG 57.882 52.632 0.00 0.00 0.00 4.85
6090 6305 1.079612 GCTTGTGAATTGCCTGCCC 60.080 57.895 0.00 0.00 0.00 5.36
6091 6306 1.818959 GCTTGTGAATTGCCTGCCCA 61.819 55.000 0.00 0.00 0.00 5.36
6092 6307 0.899720 CTTGTGAATTGCCTGCCCAT 59.100 50.000 0.00 0.00 0.00 4.00
6093 6308 0.609151 TTGTGAATTGCCTGCCCATG 59.391 50.000 0.00 0.00 0.00 3.66
6094 6309 0.251698 TGTGAATTGCCTGCCCATGA 60.252 50.000 0.00 0.00 0.00 3.07
6096 6311 0.040058 TGAATTGCCTGCCCATGACT 59.960 50.000 0.00 0.00 0.00 3.41
6097 6312 1.284491 TGAATTGCCTGCCCATGACTA 59.716 47.619 0.00 0.00 0.00 2.59
6098 6313 1.952296 GAATTGCCTGCCCATGACTAG 59.048 52.381 0.00 0.00 0.00 2.57
6100 6315 0.913934 TTGCCTGCCCATGACTAGGA 60.914 55.000 11.72 0.00 31.91 2.94
6101 6316 0.695462 TGCCTGCCCATGACTAGGAT 60.695 55.000 11.72 0.00 31.91 3.24
6102 6317 1.352083 GCCTGCCCATGACTAGGATA 58.648 55.000 11.72 0.00 31.91 2.59
6103 6318 1.912043 GCCTGCCCATGACTAGGATAT 59.088 52.381 11.72 0.00 31.91 1.63
6109 6513 7.504403 CCTGCCCATGACTAGGATATATAAAG 58.496 42.308 0.00 0.00 31.91 1.85
6123 6527 9.784376 AGGATATATAAAGCCAGTTCCTATGTA 57.216 33.333 0.00 0.00 30.74 2.29
6127 6531 4.910458 AAAGCCAGTTCCTATGTACAGT 57.090 40.909 0.33 0.00 0.00 3.55
6128 6532 7.670605 ATAAAGCCAGTTCCTATGTACAGTA 57.329 36.000 0.33 0.00 0.00 2.74
6129 6533 6.561519 AAAGCCAGTTCCTATGTACAGTAT 57.438 37.500 0.33 0.00 0.00 2.12
6131 6535 7.857404 AAGCCAGTTCCTATGTACAGTATAT 57.143 36.000 0.33 0.00 0.00 0.86
6133 6537 9.548631 AAGCCAGTTCCTATGTACAGTATATAT 57.451 33.333 0.33 0.00 0.00 0.86
6151 6555 9.853177 AGTATATATAATCCCCTAATGCTTTGC 57.147 33.333 0.00 0.00 0.00 3.68
6152 6556 9.627123 GTATATATAATCCCCTAATGCTTTGCA 57.373 33.333 0.00 0.00 44.86 4.08
6153 6557 8.757982 ATATATAATCCCCTAATGCTTTGCAG 57.242 34.615 0.00 0.00 43.65 4.41
6154 6558 3.386932 AATCCCCTAATGCTTTGCAGA 57.613 42.857 0.00 0.00 43.65 4.26
6155 6559 2.897271 TCCCCTAATGCTTTGCAGAA 57.103 45.000 0.00 0.00 43.65 3.02
6156 6560 2.446435 TCCCCTAATGCTTTGCAGAAC 58.554 47.619 0.00 0.00 43.65 3.01
6157 6561 2.170166 CCCCTAATGCTTTGCAGAACA 58.830 47.619 0.00 0.00 43.65 3.18
6158 6562 2.562298 CCCCTAATGCTTTGCAGAACAA 59.438 45.455 0.00 0.00 43.65 2.83
6159 6563 3.578688 CCCTAATGCTTTGCAGAACAAC 58.421 45.455 0.00 0.00 43.65 3.32
6160 6564 3.256631 CCCTAATGCTTTGCAGAACAACT 59.743 43.478 0.00 0.00 43.65 3.16
6161 6565 4.262164 CCCTAATGCTTTGCAGAACAACTT 60.262 41.667 0.00 0.00 43.65 2.66
6162 6566 4.919754 CCTAATGCTTTGCAGAACAACTTC 59.080 41.667 0.00 0.00 43.65 3.01
6169 6573 5.518848 TTTGCAGAACAACTTCACATCAT 57.481 34.783 0.00 0.00 38.23 2.45
6174 6578 4.682860 CAGAACAACTTCACATCATTTGCC 59.317 41.667 0.00 0.00 0.00 4.52
6177 6581 4.370917 ACAACTTCACATCATTTGCCAAC 58.629 39.130 0.00 0.00 0.00 3.77
6179 6583 4.877378 ACTTCACATCATTTGCCAACAT 57.123 36.364 0.00 0.00 0.00 2.71
6180 6584 5.217978 ACTTCACATCATTTGCCAACATT 57.782 34.783 0.00 0.00 0.00 2.71
6181 6585 6.343716 ACTTCACATCATTTGCCAACATTA 57.656 33.333 0.00 0.00 0.00 1.90
6184 6588 7.546667 ACTTCACATCATTTGCCAACATTATTC 59.453 33.333 0.00 0.00 0.00 1.75
6195 6599 4.261489 GCCAACATTATTCAGATGCAGAGG 60.261 45.833 0.00 0.00 0.00 3.69
6198 6602 6.127535 CCAACATTATTCAGATGCAGAGGTTT 60.128 38.462 0.00 0.00 0.00 3.27
6199 6603 7.318141 CAACATTATTCAGATGCAGAGGTTTT 58.682 34.615 0.00 0.00 0.00 2.43
6200 6604 7.093322 ACATTATTCAGATGCAGAGGTTTTC 57.907 36.000 0.00 0.00 0.00 2.29
6201 6605 5.801350 TTATTCAGATGCAGAGGTTTTCG 57.199 39.130 0.00 0.00 0.00 3.46
6202 6606 3.401033 TTCAGATGCAGAGGTTTTCGA 57.599 42.857 0.00 0.00 0.00 3.71
6203 6607 2.964740 TCAGATGCAGAGGTTTTCGAG 58.035 47.619 0.00 0.00 0.00 4.04
6204 6608 2.562738 TCAGATGCAGAGGTTTTCGAGA 59.437 45.455 0.00 0.00 0.00 4.04
6205 6609 2.670414 CAGATGCAGAGGTTTTCGAGAC 59.330 50.000 0.00 0.00 0.00 3.36
6206 6610 2.003301 GATGCAGAGGTTTTCGAGACC 58.997 52.381 11.05 11.05 37.44 3.85
6210 6614 2.616842 GCAGAGGTTTTCGAGACCAAAA 59.383 45.455 18.69 0.00 39.71 2.44
6231 6635 7.809806 CCAAAACAGGTTCAGATTTTAGTCATC 59.190 37.037 0.00 0.00 0.00 2.92
6232 6636 6.727824 AACAGGTTCAGATTTTAGTCATCG 57.272 37.500 0.00 0.00 0.00 3.84
6234 6638 5.639506 ACAGGTTCAGATTTTAGTCATCGTG 59.360 40.000 0.00 0.00 0.00 4.35
6235 6639 5.639506 CAGGTTCAGATTTTAGTCATCGTGT 59.360 40.000 0.00 0.00 0.00 4.49
6236 6640 5.639506 AGGTTCAGATTTTAGTCATCGTGTG 59.360 40.000 0.00 0.00 0.00 3.82
6251 6655 2.029380 TCGTGTGTACCATCCTTGACTG 60.029 50.000 0.00 0.00 0.00 3.51
6273 6685 4.448395 TGCTAATCAAAACATGTTGCTTGC 59.552 37.500 12.82 10.72 0.00 4.01
6283 6695 1.837648 TGTTGCTTGCATGTTTGTCG 58.162 45.000 1.14 0.00 0.00 4.35
6306 6718 5.049167 GCTCTGATTAGTCTTGGACATGAG 58.951 45.833 0.00 0.00 34.60 2.90
6329 6741 1.079127 CCCGGGAACAGCTGTAGTG 60.079 63.158 22.01 10.38 0.00 2.74
6336 6748 2.236395 GGAACAGCTGTAGTGGTACCAT 59.764 50.000 22.01 9.82 0.00 3.55
6392 6805 4.442705 CGACTAACGTGTGAAATTGTGAC 58.557 43.478 0.00 0.00 37.22 3.67
6445 6858 6.398918 GTGTGCGGATATGGTTCTCTAATAT 58.601 40.000 0.00 0.00 0.00 1.28
6474 6887 0.745845 CCCTGATTGGAGAAGGTGCG 60.746 60.000 0.00 0.00 38.35 5.34
6500 6913 2.957680 GGTCGGGGGTCAAACTTAAAAA 59.042 45.455 0.00 0.00 0.00 1.94
6505 6918 5.242171 TCGGGGGTCAAACTTAAAAAGATTC 59.758 40.000 0.00 0.00 0.00 2.52
6522 6935 2.638480 TTCAATAAGAGGGGATGCCG 57.362 50.000 0.00 0.00 0.00 5.69
6638 7051 4.439289 GCTTTGCAGAATAACTTAGCCTGG 60.439 45.833 0.00 0.00 0.00 4.45
6640 7053 1.950216 GCAGAATAACTTAGCCTGGCC 59.050 52.381 16.57 0.00 0.00 5.36
6647 7060 0.905357 ACTTAGCCTGGCCACTACTG 59.095 55.000 16.57 1.33 0.00 2.74
6650 7063 1.617018 TAGCCTGGCCACTACTGCTG 61.617 60.000 16.57 0.00 0.00 4.41
6689 7105 2.821969 CCTTCTCCATTTGGTTGGACTG 59.178 50.000 0.00 0.00 40.90 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.229936 AGACAAGAACTTTGTACACTGGTA 57.770 37.500 0.00 0.00 31.96 3.25
9 10 5.099042 AGACAAGAACTTTGTACACTGGT 57.901 39.130 0.00 0.00 31.96 4.00
10 11 6.436843 AAAGACAAGAACTTTGTACACTGG 57.563 37.500 0.00 0.00 36.43 4.00
11 12 7.065324 TGGTAAAGACAAGAACTTTGTACACTG 59.935 37.037 0.00 0.00 37.96 3.66
12 13 7.107542 TGGTAAAGACAAGAACTTTGTACACT 58.892 34.615 0.00 0.00 37.96 3.55
13 14 7.311364 TGGTAAAGACAAGAACTTTGTACAC 57.689 36.000 0.00 0.00 37.96 2.90
14 15 7.227910 GGATGGTAAAGACAAGAACTTTGTACA 59.772 37.037 0.00 0.00 37.96 2.90
15 16 7.227910 TGGATGGTAAAGACAAGAACTTTGTAC 59.772 37.037 0.00 0.00 37.96 2.90
30 31 6.823182 TGTATTGTGTCAGATGGATGGTAAAG 59.177 38.462 0.00 0.00 0.00 1.85
82 88 2.118679 TGATGGTAGATGGAGGGTGTG 58.881 52.381 0.00 0.00 0.00 3.82
83 89 2.568546 TGATGGTAGATGGAGGGTGT 57.431 50.000 0.00 0.00 0.00 4.16
112 118 4.760047 ATCGGTGGCTGGCACGAC 62.760 66.667 25.26 13.31 38.24 4.34
160 166 1.625879 TAGCTGGGGAGGAGGAGGA 60.626 63.158 0.00 0.00 0.00 3.71
161 167 1.152355 CTAGCTGGGGAGGAGGAGG 60.152 68.421 0.00 0.00 0.00 4.30
162 168 0.469144 GTCTAGCTGGGGAGGAGGAG 60.469 65.000 0.00 0.00 0.00 3.69
163 169 1.621377 GTCTAGCTGGGGAGGAGGA 59.379 63.158 0.00 0.00 0.00 3.71
164 170 1.830408 CGTCTAGCTGGGGAGGAGG 60.830 68.421 0.00 0.00 0.00 4.30
165 171 1.830408 CCGTCTAGCTGGGGAGGAG 60.830 68.421 0.00 0.00 0.00 3.69
207 218 1.610327 GGGGAGGAAGAGGAAAGGC 59.390 63.158 0.00 0.00 0.00 4.35
349 360 1.226323 CGACGCGGTGAAGTAGGAG 60.226 63.158 12.47 0.00 0.00 3.69
395 406 1.675552 ACCTCAAAAACCAGTGTCCG 58.324 50.000 0.00 0.00 0.00 4.79
453 464 3.778718 CACGCGAAAAATTTACAGGATCG 59.221 43.478 15.93 0.00 0.00 3.69
564 587 1.601903 ACAACCACATGTGCTACAACG 59.398 47.619 20.81 7.36 30.82 4.10
576 599 4.371624 AATTCAGATCTCCACAACCACA 57.628 40.909 0.00 0.00 0.00 4.17
579 602 5.163854 CGTACAAATTCAGATCTCCACAACC 60.164 44.000 0.00 0.00 0.00 3.77
651 674 8.958506 CCTAATATCCGCTAAACTGTCTAGTAT 58.041 37.037 0.00 0.00 35.69 2.12
774 797 0.675633 AGCATGTGTTCAGGGCAAAC 59.324 50.000 0.00 0.00 32.59 2.93
856 881 2.287915 TCTGCGACAAAAGAGAAACAGC 59.712 45.455 0.00 0.00 0.00 4.40
933 958 5.250774 AGGGGTTTGATACAGCTTAAGAAGA 59.749 40.000 6.67 0.00 0.00 2.87
1302 1327 0.107456 ATGACAGATGACCATCCGCC 59.893 55.000 6.40 0.00 38.58 6.13
1315 1340 5.428496 TCAGCTTTCTTGTTTGATGACAG 57.572 39.130 0.00 0.00 0.00 3.51
1521 1546 6.686630 TGCATGTAAAGTAAAATGTTGGAGG 58.313 36.000 0.00 0.00 0.00 4.30
1576 1601 0.747255 TCCTTCCGAGCTCTATGTGC 59.253 55.000 12.85 0.00 0.00 4.57
1683 1708 4.508551 AATACTGGATGTTGCAGGATGA 57.491 40.909 0.00 0.00 38.52 2.92
1738 1763 5.766150 TTGATTGGCGGGTAATCAAATAG 57.234 39.130 9.86 0.00 46.04 1.73
1880 1905 7.425606 CAGTGCAAAAGGTAGAAGTTTTACAT 58.574 34.615 5.97 0.00 0.00 2.29
1881 1906 6.679392 GCAGTGCAAAAGGTAGAAGTTTTACA 60.679 38.462 11.09 0.00 0.00 2.41
1999 2024 7.804843 ATCATCTTCTTCATGAGATTTCCAC 57.195 36.000 0.00 0.00 33.74 4.02
2062 2087 6.977213 TCAAATACACTAAAAGGCCAAGAAC 58.023 36.000 5.01 0.00 0.00 3.01
2163 2190 8.874744 AGTTTACAGAGGTAGTACATCAGTAA 57.125 34.615 21.70 21.70 38.47 2.24
2192 2380 9.993454 GTTTTAAGACTACCCCGATTATCTTAT 57.007 33.333 0.00 0.00 30.85 1.73
2193 2381 8.980596 TGTTTTAAGACTACCCCGATTATCTTA 58.019 33.333 0.00 0.00 0.00 2.10
2194 2382 7.854337 TGTTTTAAGACTACCCCGATTATCTT 58.146 34.615 0.00 0.00 0.00 2.40
2196 2384 9.939802 ATATGTTTTAAGACTACCCCGATTATC 57.060 33.333 0.00 0.00 0.00 1.75
2198 2386 9.550406 CAATATGTTTTAAGACTACCCCGATTA 57.450 33.333 0.00 0.00 0.00 1.75
2199 2387 7.501225 CCAATATGTTTTAAGACTACCCCGATT 59.499 37.037 0.00 0.00 0.00 3.34
2200 2388 6.996282 CCAATATGTTTTAAGACTACCCCGAT 59.004 38.462 0.00 0.00 0.00 4.18
2202 2390 6.037830 CACCAATATGTTTTAAGACTACCCCG 59.962 42.308 0.00 0.00 0.00 5.73
2203 2391 6.320418 CCACCAATATGTTTTAAGACTACCCC 59.680 42.308 0.00 0.00 0.00 4.95
2204 2392 6.888088 ACCACCAATATGTTTTAAGACTACCC 59.112 38.462 0.00 0.00 0.00 3.69
2205 2393 7.933215 ACCACCAATATGTTTTAAGACTACC 57.067 36.000 0.00 0.00 0.00 3.18
2207 2395 9.675464 CCTAACCACCAATATGTTTTAAGACTA 57.325 33.333 0.00 0.00 0.00 2.59
2208 2396 8.168058 ACCTAACCACCAATATGTTTTAAGACT 58.832 33.333 0.00 0.00 0.00 3.24
2209 2397 8.344446 ACCTAACCACCAATATGTTTTAAGAC 57.656 34.615 0.00 0.00 0.00 3.01
2210 2398 8.943594 AACCTAACCACCAATATGTTTTAAGA 57.056 30.769 0.00 0.00 0.00 2.10
2217 2405 9.362151 CCAATATAAACCTAACCACCAATATGT 57.638 33.333 0.00 0.00 0.00 2.29
2218 2406 9.581289 TCCAATATAAACCTAACCACCAATATG 57.419 33.333 0.00 0.00 0.00 1.78
2221 2409 9.143155 GATTCCAATATAAACCTAACCACCAAT 57.857 33.333 0.00 0.00 0.00 3.16
2222 2410 8.116669 TGATTCCAATATAAACCTAACCACCAA 58.883 33.333 0.00 0.00 0.00 3.67
2223 2411 7.644062 TGATTCCAATATAAACCTAACCACCA 58.356 34.615 0.00 0.00 0.00 4.17
2224 2412 7.778382 ACTGATTCCAATATAAACCTAACCACC 59.222 37.037 0.00 0.00 0.00 4.61
2225 2413 8.621286 CACTGATTCCAATATAAACCTAACCAC 58.379 37.037 0.00 0.00 0.00 4.16
2226 2414 8.553153 TCACTGATTCCAATATAAACCTAACCA 58.447 33.333 0.00 0.00 0.00 3.67
2227 2415 8.837389 GTCACTGATTCCAATATAAACCTAACC 58.163 37.037 0.00 0.00 0.00 2.85
2228 2416 8.837389 GGTCACTGATTCCAATATAAACCTAAC 58.163 37.037 0.00 0.00 0.00 2.34
2229 2417 8.778059 AGGTCACTGATTCCAATATAAACCTAA 58.222 33.333 0.00 0.00 30.76 2.69
2230 2418 8.331931 AGGTCACTGATTCCAATATAAACCTA 57.668 34.615 0.00 0.00 30.76 3.08
2231 2419 7.213178 AGGTCACTGATTCCAATATAAACCT 57.787 36.000 0.00 0.00 0.00 3.50
2232 2420 8.974060 TTAGGTCACTGATTCCAATATAAACC 57.026 34.615 0.00 0.00 0.00 3.27
2235 2423 9.104965 CGTTTTAGGTCACTGATTCCAATATAA 57.895 33.333 0.00 0.00 0.00 0.98
2236 2424 8.262227 ACGTTTTAGGTCACTGATTCCAATATA 58.738 33.333 0.00 0.00 0.00 0.86
2237 2425 7.110155 ACGTTTTAGGTCACTGATTCCAATAT 58.890 34.615 0.00 0.00 0.00 1.28
2238 2426 6.469410 ACGTTTTAGGTCACTGATTCCAATA 58.531 36.000 0.00 0.00 0.00 1.90
2239 2427 5.313712 ACGTTTTAGGTCACTGATTCCAAT 58.686 37.500 0.00 0.00 0.00 3.16
2240 2428 4.710324 ACGTTTTAGGTCACTGATTCCAA 58.290 39.130 0.00 0.00 0.00 3.53
2241 2429 4.039973 AGACGTTTTAGGTCACTGATTCCA 59.960 41.667 0.00 0.00 35.60 3.53
2242 2430 4.566987 AGACGTTTTAGGTCACTGATTCC 58.433 43.478 0.00 0.00 35.60 3.01
2243 2431 7.829378 ATAAGACGTTTTAGGTCACTGATTC 57.171 36.000 4.75 0.00 35.60 2.52
2244 2432 9.715121 TTTATAAGACGTTTTAGGTCACTGATT 57.285 29.630 4.75 0.00 35.60 2.57
2245 2433 9.715121 TTTTATAAGACGTTTTAGGTCACTGAT 57.285 29.630 4.75 0.00 35.60 2.90
2246 2434 9.199982 CTTTTATAAGACGTTTTAGGTCACTGA 57.800 33.333 4.75 0.00 35.60 3.41
2247 2435 8.985805 ACTTTTATAAGACGTTTTAGGTCACTG 58.014 33.333 4.75 0.00 35.60 3.66
2248 2436 9.551734 AACTTTTATAAGACGTTTTAGGTCACT 57.448 29.630 4.75 0.00 35.60 3.41
2303 2491 7.394923 CCACAAATATGTTTAAGACTACCCCAA 59.605 37.037 0.00 0.00 37.82 4.12
2305 2493 6.888088 ACCACAAATATGTTTAAGACTACCCC 59.112 38.462 0.00 0.00 37.82 4.95
2325 2514 7.450124 TTTGTTGTACTCAAACTTAACCACA 57.550 32.000 10.91 0.00 35.20 4.17
2424 2625 9.444600 GTTCCTGTTCAATTACTGTATTCCTTA 57.555 33.333 0.00 0.00 0.00 2.69
2486 2687 7.538678 GGAGTTAAAATGCTAATCATATTGCCG 59.461 37.037 0.00 0.00 34.33 5.69
2512 2713 2.513204 CATGCTGCCACGGGAGAG 60.513 66.667 9.03 0.00 35.50 3.20
2569 2770 6.239008 CCCAAGTTAGCTCATTTCAAAGTGAA 60.239 38.462 0.00 0.00 34.03 3.18
2578 2779 4.010349 GCAGTACCCAAGTTAGCTCATTT 58.990 43.478 0.00 0.00 0.00 2.32
2581 2782 2.028112 CAGCAGTACCCAAGTTAGCTCA 60.028 50.000 0.00 0.00 0.00 4.26
2673 2874 2.664916 GCGCATCAAATCGCCAATATT 58.335 42.857 0.30 0.00 45.01 1.28
2688 2889 4.217118 GGAAGAATCCATAAATCAGCGCAT 59.783 41.667 11.47 0.00 45.79 4.73
2754 2955 8.520351 GTTGCTGGAGGTAAACAATATAAAACT 58.480 33.333 0.00 0.00 0.00 2.66
2931 3132 3.322862 TGCCTCTATATTGGGCCTTACA 58.677 45.455 4.53 0.00 44.71 2.41
2991 3192 7.989741 CACAGACAATCCCTACAAAGATAGAAT 59.010 37.037 0.00 0.00 0.00 2.40
2992 3193 7.038302 ACACAGACAATCCCTACAAAGATAGAA 60.038 37.037 0.00 0.00 0.00 2.10
2994 3195 6.644347 ACACAGACAATCCCTACAAAGATAG 58.356 40.000 0.00 0.00 0.00 2.08
2995 3196 6.620877 ACACAGACAATCCCTACAAAGATA 57.379 37.500 0.00 0.00 0.00 1.98
2996 3197 5.505181 ACACAGACAATCCCTACAAAGAT 57.495 39.130 0.00 0.00 0.00 2.40
2997 3198 4.974645 ACACAGACAATCCCTACAAAGA 57.025 40.909 0.00 0.00 0.00 2.52
2998 3199 4.216257 CCAACACAGACAATCCCTACAAAG 59.784 45.833 0.00 0.00 0.00 2.77
3206 3410 5.063880 ACAGTCCAAATAAGTGAGTTGTCC 58.936 41.667 0.00 0.00 30.99 4.02
3528 3732 8.715191 AGTGAAACAAAATAAATGTGAAAGCA 57.285 26.923 0.00 0.00 41.43 3.91
3595 3799 4.999950 TGCAAATGTCCAACAACAAGTTTT 59.000 33.333 0.00 0.00 38.74 2.43
3713 3918 5.123227 ACCCAACGAAACTGTATATCATGG 58.877 41.667 0.00 0.00 0.00 3.66
3764 3969 7.069331 TGGTCTCCAAAATGTAACTTTGACAAT 59.931 33.333 0.00 0.00 0.00 2.71
3776 3981 4.834496 ACATTGACATGGTCTCCAAAATGT 59.166 37.500 0.00 12.35 36.95 2.71
4029 4238 8.009622 TGACATGGTTATCAATATGCATGTTT 57.990 30.769 10.16 0.00 32.96 2.83
4177 4389 6.670695 AGTCCTCCAAATTAAAAATGCACT 57.329 33.333 0.00 0.00 0.00 4.40
4203 4415 7.282224 GGGTTATCATATGCTGTTACTGTTGAA 59.718 37.037 0.00 0.00 0.00 2.69
4211 4423 9.688091 TTAAAAGTGGGTTATCATATGCTGTTA 57.312 29.630 0.00 0.00 0.00 2.41
4243 4455 9.737427 TTTAGATCGAATGCAAACTTACAAAAA 57.263 25.926 0.00 0.00 0.00 1.94
4286 4498 6.342338 AGACTTACGAGGACAAAACTACAT 57.658 37.500 0.00 0.00 0.00 2.29
4362 4574 5.746065 GCAGTTATGGCTGATAAGGGTACAT 60.746 44.000 0.00 0.00 38.70 2.29
4363 4575 4.444306 GCAGTTATGGCTGATAAGGGTACA 60.444 45.833 0.00 0.00 38.70 2.90
4367 4579 3.213206 TGCAGTTATGGCTGATAAGGG 57.787 47.619 3.00 0.00 38.70 3.95
4375 4587 6.780457 ATTTCTATGTTTGCAGTTATGGCT 57.220 33.333 0.00 0.00 0.00 4.75
4406 4618 9.890629 TCTGCAAATACTTGATAGTAGACAAAT 57.109 29.630 0.00 0.00 40.09 2.32
4429 4641 1.333931 CTATGCCATGCTGCACTTCTG 59.666 52.381 3.57 0.00 45.48 3.02
4441 4653 5.473066 AAACTTTTTCAGTGCTATGCCAT 57.527 34.783 0.00 0.00 35.12 4.40
4631 4843 1.094785 CTGTACCTTTTCCATGCCCG 58.905 55.000 0.00 0.00 0.00 6.13
4661 4873 8.753133 TCTGTATAGACATCAGACAATTCAACT 58.247 33.333 0.00 0.00 34.24 3.16
4790 5002 1.001974 GCTGTACCACCTGATGTGTCA 59.998 52.381 0.00 0.00 43.85 3.58
5090 5302 2.958355 AGTGTCCCACTTTGGTTCATTG 59.042 45.455 0.00 0.00 42.59 2.82
5216 5428 6.041423 ACAACCCATTTCTCATCCAAATTC 57.959 37.500 0.00 0.00 0.00 2.17
5460 5672 2.843701 ACTTGAGCAAGGACAGAAGTG 58.156 47.619 14.14 0.00 42.53 3.16
5580 5793 8.848474 ACTAGAAGCAAACAATTATACTGTGT 57.152 30.769 0.00 0.00 0.00 3.72
5588 5801 9.116067 AGTGTTGTTACTAGAAGCAAACAATTA 57.884 29.630 0.00 0.00 42.07 1.40
5589 5802 7.915397 CAGTGTTGTTACTAGAAGCAAACAATT 59.085 33.333 0.00 0.00 42.07 2.32
5631 5844 0.321671 ACCTGTCAATGTCGGACCAG 59.678 55.000 5.55 5.14 34.36 4.00
5708 5922 4.742201 TTGACGCGGCAGAGCTCC 62.742 66.667 17.30 0.00 34.40 4.70
5790 6004 4.142600 GCAGACTTGTGGTGCTTAAATAGG 60.143 45.833 0.00 0.00 34.23 2.57
5814 6028 2.872245 CCTCAAAAACTCGTGAAGCTCA 59.128 45.455 0.00 0.00 0.00 4.26
5914 6129 1.289380 GTCTGACCGACCAGTCACC 59.711 63.158 0.00 0.00 41.78 4.02
5975 6190 9.829507 CAGATCAGATAAAAAGAACTGAGGTAT 57.170 33.333 0.00 0.00 41.55 2.73
5976 6191 9.035890 TCAGATCAGATAAAAAGAACTGAGGTA 57.964 33.333 0.00 0.00 41.55 3.08
5977 6192 7.911651 TCAGATCAGATAAAAAGAACTGAGGT 58.088 34.615 0.00 0.00 41.55 3.85
5979 6194 9.820725 AGATCAGATCAGATAAAAAGAACTGAG 57.179 33.333 13.14 0.00 42.06 3.35
6007 6222 7.756722 GCAGCATTAGTAGATGTCAACAAAAAT 59.243 33.333 0.00 0.00 0.00 1.82
6008 6223 7.083858 GCAGCATTAGTAGATGTCAACAAAAA 58.916 34.615 0.00 0.00 0.00 1.94
6014 6229 4.123497 ACGCAGCATTAGTAGATGTCAA 57.877 40.909 0.00 0.00 0.00 3.18
6016 6231 5.470845 AAAACGCAGCATTAGTAGATGTC 57.529 39.130 0.00 0.00 0.00 3.06
6017 6232 4.332819 GGAAAACGCAGCATTAGTAGATGT 59.667 41.667 0.00 0.00 0.00 3.06
6023 6238 2.200373 AGGGAAAACGCAGCATTAGT 57.800 45.000 0.00 0.00 0.00 2.24
6034 6249 3.864003 CCTCTATCGTCGAAAGGGAAAAC 59.136 47.826 0.00 0.00 0.00 2.43
6041 6256 4.734917 ACAAACTCCTCTATCGTCGAAAG 58.265 43.478 0.00 0.00 0.00 2.62
6042 6257 4.778534 ACAAACTCCTCTATCGTCGAAA 57.221 40.909 0.00 0.00 0.00 3.46
6046 6261 3.852536 CGTCAACAAACTCCTCTATCGTC 59.147 47.826 0.00 0.00 0.00 4.20
6049 6264 2.930682 GCCGTCAACAAACTCCTCTATC 59.069 50.000 0.00 0.00 0.00 2.08
6050 6265 2.301870 TGCCGTCAACAAACTCCTCTAT 59.698 45.455 0.00 0.00 0.00 1.98
6058 6273 0.100503 ACAAGCTGCCGTCAACAAAC 59.899 50.000 0.00 0.00 0.00 2.93
6068 6283 4.584688 GGCAATTCACAAGCTGCC 57.415 55.556 0.00 0.00 46.95 4.85
6069 6284 1.012486 GCAGGCAATTCACAAGCTGC 61.012 55.000 0.00 0.00 0.00 5.25
6085 6300 6.989169 GCTTTATATATCCTAGTCATGGGCAG 59.011 42.308 0.00 0.00 0.00 4.85
6086 6301 6.126768 GGCTTTATATATCCTAGTCATGGGCA 60.127 42.308 0.00 0.00 0.00 5.36
6087 6302 6.126768 TGGCTTTATATATCCTAGTCATGGGC 60.127 42.308 0.00 0.00 0.00 5.36
6090 6305 9.593134 GAACTGGCTTTATATATCCTAGTCATG 57.407 37.037 0.00 0.00 0.00 3.07
6091 6306 8.763601 GGAACTGGCTTTATATATCCTAGTCAT 58.236 37.037 0.00 0.00 0.00 3.06
6092 6307 7.956315 AGGAACTGGCTTTATATATCCTAGTCA 59.044 37.037 0.00 0.00 37.18 3.41
6093 6308 8.368962 AGGAACTGGCTTTATATATCCTAGTC 57.631 38.462 0.00 0.00 37.18 2.59
6096 6311 9.784376 ACATAGGAACTGGCTTTATATATCCTA 57.216 33.333 6.85 6.85 41.52 2.94
6097 6312 8.686739 ACATAGGAACTGGCTTTATATATCCT 57.313 34.615 0.00 0.00 41.52 3.24
6098 6313 9.819267 GTACATAGGAACTGGCTTTATATATCC 57.181 37.037 0.00 0.00 41.52 2.59
6101 6316 9.375974 ACTGTACATAGGAACTGGCTTTATATA 57.624 33.333 0.00 0.00 41.52 0.86
6102 6317 8.263854 ACTGTACATAGGAACTGGCTTTATAT 57.736 34.615 0.00 0.00 41.52 0.86
6103 6318 7.670605 ACTGTACATAGGAACTGGCTTTATA 57.329 36.000 0.00 0.00 41.52 0.98
6125 6529 9.853177 GCAAAGCATTAGGGGATTATATATACT 57.147 33.333 0.00 0.00 0.00 2.12
6126 6530 9.627123 TGCAAAGCATTAGGGGATTATATATAC 57.373 33.333 0.00 0.00 31.71 1.47
6127 6531 9.851686 CTGCAAAGCATTAGGGGATTATATATA 57.148 33.333 0.00 0.00 38.13 0.86
6128 6532 8.560039 TCTGCAAAGCATTAGGGGATTATATAT 58.440 33.333 0.00 0.00 38.13 0.86
6129 6533 7.927788 TCTGCAAAGCATTAGGGGATTATATA 58.072 34.615 0.00 0.00 38.13 0.86
6131 6535 6.199557 TCTGCAAAGCATTAGGGGATTATA 57.800 37.500 0.00 0.00 38.13 0.98
6133 6537 4.518278 TCTGCAAAGCATTAGGGGATTA 57.482 40.909 0.00 0.00 38.13 1.75
6134 6538 3.386932 TCTGCAAAGCATTAGGGGATT 57.613 42.857 0.00 0.00 38.13 3.01
6135 6539 3.026694 GTTCTGCAAAGCATTAGGGGAT 58.973 45.455 0.00 0.00 38.13 3.85
6137 6541 2.170166 TGTTCTGCAAAGCATTAGGGG 58.830 47.619 0.00 0.00 38.13 4.79
6138 6542 3.256631 AGTTGTTCTGCAAAGCATTAGGG 59.743 43.478 0.00 0.00 38.13 3.53
6140 6544 5.400485 GTGAAGTTGTTCTGCAAAGCATTAG 59.600 40.000 0.00 0.00 38.13 1.73
6142 6546 4.114794 GTGAAGTTGTTCTGCAAAGCATT 58.885 39.130 0.00 0.00 38.13 3.56
6145 6549 3.149436 TGTGAAGTTGTTCTGCAAAGC 57.851 42.857 0.00 0.00 39.03 3.51
6146 6550 4.923893 TGATGTGAAGTTGTTCTGCAAAG 58.076 39.130 0.00 0.00 39.03 2.77
6147 6551 4.979943 TGATGTGAAGTTGTTCTGCAAA 57.020 36.364 0.00 0.00 39.03 3.68
6148 6552 5.518848 AATGATGTGAAGTTGTTCTGCAA 57.481 34.783 0.00 0.00 32.81 4.08
6149 6553 5.283294 CAAATGATGTGAAGTTGTTCTGCA 58.717 37.500 0.00 0.00 33.38 4.41
6150 6554 4.149396 GCAAATGATGTGAAGTTGTTCTGC 59.851 41.667 0.00 0.00 33.38 4.26
6151 6555 4.682860 GGCAAATGATGTGAAGTTGTTCTG 59.317 41.667 0.00 0.00 33.38 3.02
6152 6556 4.341806 TGGCAAATGATGTGAAGTTGTTCT 59.658 37.500 0.00 0.00 33.38 3.01
6153 6557 4.619973 TGGCAAATGATGTGAAGTTGTTC 58.380 39.130 0.00 0.00 0.00 3.18
6154 6558 4.669206 TGGCAAATGATGTGAAGTTGTT 57.331 36.364 0.00 0.00 0.00 2.83
6155 6559 4.141981 TGTTGGCAAATGATGTGAAGTTGT 60.142 37.500 0.00 0.00 0.00 3.32
6156 6560 4.370049 TGTTGGCAAATGATGTGAAGTTG 58.630 39.130 0.00 0.00 0.00 3.16
6157 6561 4.669206 TGTTGGCAAATGATGTGAAGTT 57.331 36.364 0.00 0.00 0.00 2.66
6158 6562 4.877378 ATGTTGGCAAATGATGTGAAGT 57.123 36.364 0.00 0.00 0.00 3.01
6159 6563 7.546316 TGAATAATGTTGGCAAATGATGTGAAG 59.454 33.333 0.00 0.00 0.00 3.02
6160 6564 7.384477 TGAATAATGTTGGCAAATGATGTGAA 58.616 30.769 0.00 0.00 0.00 3.18
6161 6565 6.932947 TGAATAATGTTGGCAAATGATGTGA 58.067 32.000 0.00 0.00 0.00 3.58
6162 6566 7.036829 TCTGAATAATGTTGGCAAATGATGTG 58.963 34.615 0.00 0.00 0.00 3.21
6169 6573 5.185442 TCTGCATCTGAATAATGTTGGCAAA 59.815 36.000 0.00 0.00 0.00 3.68
6174 6578 6.446781 AACCTCTGCATCTGAATAATGTTG 57.553 37.500 0.00 0.00 0.00 3.33
6177 6581 6.037500 TCGAAAACCTCTGCATCTGAATAATG 59.962 38.462 0.00 0.00 0.00 1.90
6179 6583 5.487433 TCGAAAACCTCTGCATCTGAATAA 58.513 37.500 0.00 0.00 0.00 1.40
6180 6584 5.084818 TCGAAAACCTCTGCATCTGAATA 57.915 39.130 0.00 0.00 0.00 1.75
6181 6585 3.937706 CTCGAAAACCTCTGCATCTGAAT 59.062 43.478 0.00 0.00 0.00 2.57
6184 6588 2.670414 GTCTCGAAAACCTCTGCATCTG 59.330 50.000 0.00 0.00 0.00 2.90
6195 6599 4.142556 TGAACCTGTTTTGGTCTCGAAAAC 60.143 41.667 11.23 11.23 41.63 2.43
6198 6602 3.118555 TCTGAACCTGTTTTGGTCTCGAA 60.119 43.478 0.00 0.00 39.83 3.71
6199 6603 2.432874 TCTGAACCTGTTTTGGTCTCGA 59.567 45.455 0.00 0.00 39.83 4.04
6200 6604 2.833794 TCTGAACCTGTTTTGGTCTCG 58.166 47.619 0.00 0.00 39.83 4.04
6201 6605 5.774498 AAATCTGAACCTGTTTTGGTCTC 57.226 39.130 0.00 0.00 39.83 3.36
6202 6606 6.833933 ACTAAAATCTGAACCTGTTTTGGTCT 59.166 34.615 0.00 0.00 39.83 3.85
6203 6607 7.039313 ACTAAAATCTGAACCTGTTTTGGTC 57.961 36.000 0.00 0.00 39.83 4.02
6204 6608 6.605594 TGACTAAAATCTGAACCTGTTTTGGT 59.394 34.615 3.18 3.18 43.11 3.67
6205 6609 7.038154 TGACTAAAATCTGAACCTGTTTTGG 57.962 36.000 0.00 0.00 0.00 3.28
6206 6610 7.535258 CGATGACTAAAATCTGAACCTGTTTTG 59.465 37.037 0.00 0.00 0.00 2.44
6210 6614 5.639506 CACGATGACTAAAATCTGAACCTGT 59.360 40.000 0.00 0.00 0.00 4.00
6234 6638 7.074626 TTGATTAGCAGTCAAGGATGGTACAC 61.075 42.308 0.00 0.00 34.25 2.90
6235 6639 5.045942 TTGATTAGCAGTCAAGGATGGTACA 60.046 40.000 0.00 0.00 35.27 2.90
6236 6640 5.023533 TGATTAGCAGTCAAGGATGGTAC 57.976 43.478 0.00 0.00 0.00 3.34
6251 6655 4.448395 TGCAAGCAACATGTTTTGATTAGC 59.552 37.500 21.68 14.67 33.40 3.09
6273 6685 4.867047 AGACTAATCAGAGCGACAAACATG 59.133 41.667 0.00 0.00 0.00 3.21
6283 6695 5.016051 TCATGTCCAAGACTAATCAGAGC 57.984 43.478 0.00 0.00 33.15 4.09
6306 6718 4.021925 AGCTGTTCCCGGGTGAGC 62.022 66.667 22.86 24.11 0.00 4.26
6336 6748 0.904394 GGCTTTGGCTTCCCATCCAA 60.904 55.000 0.00 0.00 41.78 3.53
6371 6784 4.442705 CGTCACAATTTCACACGTTAGTC 58.557 43.478 0.00 0.00 0.00 2.59
6392 6805 3.322514 TCAGGCCTCTGAAAAACCG 57.677 52.632 0.00 0.00 46.08 4.44
6445 6858 1.675310 CAATCAGGGAGCCGTTGCA 60.675 57.895 0.00 0.00 41.13 4.08
6500 6913 3.244700 CGGCATCCCCTCTTATTGAATCT 60.245 47.826 0.00 0.00 0.00 2.40
6505 6918 0.179020 TGCGGCATCCCCTCTTATTG 60.179 55.000 0.00 0.00 0.00 1.90
6522 6935 1.387295 GGCCCTACCAGATTGCTTGC 61.387 60.000 0.00 0.00 38.86 4.01
6647 7060 4.876652 GCACCTTTGCTAAGCAGC 57.123 55.556 2.02 4.91 46.17 5.25
6746 7185 2.916716 GCACGTGGCAAAATCAAGTATG 59.083 45.455 18.88 0.00 43.97 2.39


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

AutoCloner maintained by Alex Coulton.