Multiple sequence alignment - TraesCS4B01G174200

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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 TraesCS4B01G174200 chr4B 100.000 5051 0 0 1 5051 382194371 382199421 0.000000e+00 9328.0
1 TraesCS4B01G174200 chr4B 92.500 40 1 2 81 119 471271434 471271472 7.060000e-04 56.5
2 TraesCS4B01G174200 chr4D 90.366 3965 165 64 327 4150 305969206 305973094 0.000000e+00 5005.0
3 TraesCS4B01G174200 chr4D 89.381 791 64 11 4274 5048 305973447 305974233 0.000000e+00 977.0
4 TraesCS4B01G174200 chr4D 89.443 341 24 5 1 330 305968719 305969058 2.170000e-113 420.0
5 TraesCS4B01G174200 chr4A 94.638 2406 98 15 670 3053 171220072 171217676 0.000000e+00 3699.0
6 TraesCS4B01G174200 chr4A 90.605 1075 46 11 3110 4163 171216919 171215879 0.000000e+00 1375.0
7 TraesCS4B01G174200 chr4A 96.429 84 0 2 561 644 171220152 171220072 8.820000e-28 135.0
8 TraesCS4B01G174200 chr7A 86.508 252 32 1 4745 4994 21439954 21439703 4.980000e-70 276.0
9 TraesCS4B01G174200 chr7A 84.291 261 37 3 4745 5003 592097128 592097386 8.390000e-63 252.0
10 TraesCS4B01G174200 chr3D 86.220 254 32 2 4745 4996 25385847 25385595 6.440000e-69 272.0
11 TraesCS4B01G174200 chr3D 82.727 110 19 0 21 130 38551768 38551877 1.160000e-16 99.0
12 TraesCS4B01G174200 chr7D 85.771 253 33 2 4745 4995 632139366 632139115 1.080000e-66 265.0
13 TraesCS4B01G174200 chr3A 84.674 261 37 2 4745 5003 464800299 464800558 1.800000e-64 257.0
14 TraesCS4B01G174200 chr3A 86.441 236 29 2 4770 5003 118507279 118507045 6.490000e-64 255.0
15 TraesCS4B01G174200 chr6D 84.739 249 35 2 4758 5004 457643354 457643601 3.910000e-61 246.0
16 TraesCS4B01G174200 chr6D 82.069 290 46 4 4711 4995 67519555 67519267 5.050000e-60 243.0
17 TraesCS4B01G174200 chr6D 84.328 134 17 4 4579 4710 38540363 38540232 1.480000e-25 128.0
18 TraesCS4B01G174200 chr2A 77.673 318 41 13 4745 5034 769978057 769977742 3.130000e-37 167.0
19 TraesCS4B01G174200 chr5D 84.328 134 17 4 4579 4710 51641761 51641630 1.480000e-25 128.0


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 TraesCS4B01G174200 chr4B 382194371 382199421 5050 False 9328.000000 9328 100.000000 1 5051 1 chr4B.!!$F1 5050
1 TraesCS4B01G174200 chr4D 305968719 305974233 5514 False 2134.000000 5005 89.730000 1 5048 3 chr4D.!!$F1 5047
2 TraesCS4B01G174200 chr4A 171215879 171220152 4273 True 1736.333333 3699 93.890667 561 4163 3 chr4A.!!$R1 3602

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
559 722 0.322187 GAAGGTAGCAAAAGCCGGGA 60.322 55.0 2.18 0.0 0.00 5.14 F
781 998 0.391130 TGATAACACAGCCGCAGACC 60.391 55.0 0.00 0.0 0.00 3.85 F
2556 2806 0.179073 AGAATCGCATGGAGTTCCGG 60.179 55.0 0.00 0.0 39.43 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 2519 0.320421 CAGTTGTACCTCCCGTGGTG 60.320 60.0 0.00 0.0 41.05 4.17 R
2745 2995 0.037697 CGCAACACACTGGCCTAGTA 60.038 55.0 3.32 0.0 37.60 1.82 R
4166 5177 0.035343 GCACCTGGTACTTTCCTCCC 60.035 60.0 0.00 0.0 0.00 4.30 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 1.073897 AAGTTGCAGCCTCCACTCC 59.926 57.895 0.00 0.00 0.00 3.85
124 125 1.380650 GAGGAGAAGGAGGAGCGGT 60.381 63.158 0.00 0.00 0.00 5.68
144 150 2.513897 GGGGGCGAGATTGGAACG 60.514 66.667 0.00 0.00 0.00 3.95
149 155 1.643832 GCGAGATTGGAACGGATGC 59.356 57.895 0.00 0.00 0.00 3.91
150 156 0.811616 GCGAGATTGGAACGGATGCT 60.812 55.000 0.00 0.00 0.00 3.79
201 210 1.200252 GCGGCGCTAGATAGAGATTCA 59.800 52.381 26.86 0.00 0.00 2.57
202 211 2.857618 CGGCGCTAGATAGAGATTCAC 58.142 52.381 7.64 0.00 0.00 3.18
205 214 2.414824 GCGCTAGATAGAGATTCACGGG 60.415 54.545 0.00 0.00 0.00 5.28
206 215 3.075148 CGCTAGATAGAGATTCACGGGA 58.925 50.000 0.00 0.00 0.00 5.14
207 216 3.126171 CGCTAGATAGAGATTCACGGGAG 59.874 52.174 0.00 0.00 0.00 4.30
209 218 5.247084 GCTAGATAGAGATTCACGGGAGTA 58.753 45.833 0.00 0.00 44.67 2.59
235 244 7.580910 AGAGAGAGAAGAATGAGAGAAGAGAT 58.419 38.462 0.00 0.00 0.00 2.75
255 267 0.919710 ACCAAACCCTAGCATCTCCC 59.080 55.000 0.00 0.00 0.00 4.30
273 285 2.191513 CATTGGGGATGGAGCAGCG 61.192 63.158 0.00 0.00 31.83 5.18
277 289 1.152881 GGGGATGGAGCAGCGAATT 60.153 57.895 0.00 0.00 0.00 2.17
289 301 1.539388 CAGCGAATTGGTGTAAGGCAA 59.461 47.619 0.00 0.00 41.21 4.52
305 317 2.161855 GGCAAGTCACAATGGATCACA 58.838 47.619 0.00 0.00 0.00 3.58
330 342 3.834799 CCACTCGTACCCTCGGCC 61.835 72.222 0.00 0.00 0.00 6.13
364 527 0.411452 TCTGAGAGAGCCCAGGTTCT 59.589 55.000 2.28 2.28 38.38 3.01
383 546 5.278022 GGTTCTCCTGCAAGTCTTAGTTTTG 60.278 44.000 0.00 0.00 0.00 2.44
386 549 4.985538 TCCTGCAAGTCTTAGTTTTGGAT 58.014 39.130 0.00 0.00 0.00 3.41
392 555 6.016610 TGCAAGTCTTAGTTTTGGATGTTACC 60.017 38.462 0.00 0.00 0.00 2.85
407 570 2.135933 GTTACCATCACATAGCGCTCC 58.864 52.381 16.34 0.00 0.00 4.70
417 580 3.380004 CACATAGCGCTCCCCAATAAAAA 59.620 43.478 16.34 0.00 0.00 1.94
423 586 3.447742 CGCTCCCCAATAAAAATTGAGC 58.552 45.455 0.00 0.00 33.55 4.26
444 607 9.681062 TTGAGCCTACAAGCTAATAAATACTTT 57.319 29.630 0.00 0.00 45.15 2.66
464 627 9.893305 ATACTTTTAAGACACTTTGCATTACAC 57.107 29.630 0.00 0.00 0.00 2.90
468 631 9.891828 TTTTAAGACACTTTGCATTACACTATG 57.108 29.630 0.00 0.00 0.00 2.23
473 636 9.062524 AGACACTTTGCATTACACTATGTAAAA 57.937 29.630 5.57 0.00 44.84 1.52
474 637 9.329913 GACACTTTGCATTACACTATGTAAAAG 57.670 33.333 5.57 7.23 44.84 2.27
507 670 5.595885 AGACTAGTGTGATATGCATGACAC 58.404 41.667 21.78 21.78 46.18 3.67
553 716 8.926715 AAAACTAACAAAGAAGGTAGCAAAAG 57.073 30.769 0.00 0.00 0.00 2.27
559 722 0.322187 GAAGGTAGCAAAAGCCGGGA 60.322 55.000 2.18 0.00 0.00 5.14
644 831 5.050490 CGTCCCTGACTACTATTTTCCATG 58.950 45.833 0.00 0.00 0.00 3.66
758 975 2.364317 CTCCTCTCCTTCCCCGCA 60.364 66.667 0.00 0.00 0.00 5.69
774 991 2.529151 CCGCAAATTGATAACACAGCC 58.471 47.619 0.00 0.00 0.00 4.85
779 996 2.401583 ATTGATAACACAGCCGCAGA 57.598 45.000 0.00 0.00 0.00 4.26
781 998 0.391130 TGATAACACAGCCGCAGACC 60.391 55.000 0.00 0.00 0.00 3.85
785 1016 2.740055 CACAGCCGCAGACCTCAC 60.740 66.667 0.00 0.00 0.00 3.51
843 1074 1.674651 GCGGTCCCTCCAAAACCTC 60.675 63.158 0.00 0.00 35.57 3.85
860 1091 1.341531 CCTCTGGCCGATCTCGTTAAT 59.658 52.381 0.00 0.00 37.74 1.40
924 1155 5.376625 TCGCTTGGCTAAATCCAATCTTAT 58.623 37.500 0.00 0.00 44.39 1.73
929 1160 8.239998 GCTTGGCTAAATCCAATCTTATCATAC 58.760 37.037 0.00 0.00 44.39 2.39
967 1199 3.636404 GCTGCGTGCTTTAGTTAGTAC 57.364 47.619 0.00 0.00 38.95 2.73
968 1200 3.251571 GCTGCGTGCTTTAGTTAGTACT 58.748 45.455 0.00 0.00 38.95 2.73
969 1201 3.303760 GCTGCGTGCTTTAGTTAGTACTC 59.696 47.826 0.00 0.00 38.95 2.59
1369 1619 3.613952 TACATCAACGACGCGCCGT 62.614 57.895 16.52 16.52 45.10 5.68
1429 1679 0.613777 CCACACCTCCAAGTACTCCC 59.386 60.000 0.00 0.00 0.00 4.30
1470 1720 1.178276 ACCTCTACGAGCAGTTCCAG 58.822 55.000 0.00 0.00 0.00 3.86
1542 1792 0.468226 AACTCCTCGTGCTGTCCAAA 59.532 50.000 0.00 0.00 0.00 3.28
1612 1862 4.112341 ACGCGTACGAGGACTGGC 62.112 66.667 21.65 0.00 43.93 4.85
1632 1882 2.280524 CGGCACCGGTCAGACAAA 60.281 61.111 2.59 0.00 35.56 2.83
1839 2089 2.027625 GTCCAACCTCAAGACGCGG 61.028 63.158 12.47 0.00 0.00 6.46
1920 2170 1.339929 GAGAAACCCAACCGCAACATT 59.660 47.619 0.00 0.00 0.00 2.71
1923 2173 3.576550 AGAAACCCAACCGCAACATTTAT 59.423 39.130 0.00 0.00 0.00 1.40
2018 2268 0.806102 TGCGAGCTCAAGAATACGGC 60.806 55.000 15.40 6.02 0.00 5.68
2169 2419 2.486042 GTCGTCCTCTGCTCGGTC 59.514 66.667 0.00 0.00 0.00 4.79
2170 2420 2.041686 GTCGTCCTCTGCTCGGTCT 61.042 63.158 0.00 0.00 0.00 3.85
2219 2469 2.887568 CCATGTCGACCAGCTCGC 60.888 66.667 14.12 0.00 42.62 5.03
2424 2674 2.592102 ACTTCATGGTGCAGGACAAT 57.408 45.000 0.00 0.00 0.00 2.71
2433 2683 2.352030 GGTGCAGGACAATCACATGTTG 60.352 50.000 0.00 0.00 32.57 3.33
2437 2687 3.148412 CAGGACAATCACATGTTGGACA 58.852 45.455 0.00 0.00 32.57 4.02
2439 2689 3.569701 AGGACAATCACATGTTGGACAAC 59.430 43.478 8.19 8.19 41.50 3.32
2452 2702 1.973812 GACAACAAGAGCCAGGCCC 60.974 63.158 8.22 0.00 0.00 5.80
2508 2758 1.674441 CTCGGGCAGATCAAGTACGTA 59.326 52.381 0.00 0.00 0.00 3.57
2544 2794 3.181967 ACGCTCACGCAGAATCGC 61.182 61.111 0.00 0.00 45.53 4.58
2556 2806 0.179073 AGAATCGCATGGAGTTCCGG 60.179 55.000 0.00 0.00 39.43 5.14
2689 2939 3.073274 AGCTTGGTTGACTAATCACCC 57.927 47.619 0.00 0.00 37.91 4.61
2741 2991 6.831769 TGACCGTAAGAAAACTAGTACTACG 58.168 40.000 0.00 5.62 43.02 3.51
2742 2992 6.426937 TGACCGTAAGAAAACTAGTACTACGT 59.573 38.462 0.00 0.00 43.02 3.57
2743 2993 7.601130 TGACCGTAAGAAAACTAGTACTACGTA 59.399 37.037 0.00 0.00 43.02 3.57
2744 2994 7.740246 ACCGTAAGAAAACTAGTACTACGTAC 58.260 38.462 0.00 1.66 38.37 3.67
2745 2995 7.603024 ACCGTAAGAAAACTAGTACTACGTACT 59.397 37.037 11.02 11.02 45.86 2.73
2746 2996 9.084164 CCGTAAGAAAACTAGTACTACGTACTA 57.916 37.037 11.96 11.96 43.59 1.82
2747 2997 9.888637 CGTAAGAAAACTAGTACTACGTACTAC 57.111 37.037 9.22 0.00 43.59 2.73
2816 3079 5.065988 GGGTACACGTATGCAGAATTTGAAT 59.934 40.000 0.00 0.00 0.00 2.57
2859 3122 0.792640 AGAAATGAGCACGCGAGTTG 59.207 50.000 15.93 0.69 46.40 3.16
2971 3235 3.932822 ACGTGCAATGGTACTGTTCATA 58.067 40.909 0.00 0.00 0.00 2.15
3074 3375 0.906775 TTTAAGCTACCGGGACCTGG 59.093 55.000 18.66 18.66 0.00 4.45
3097 3401 1.882912 TCCTGTAGCTTGTGTTGCAG 58.117 50.000 0.00 0.00 37.01 4.41
3116 3428 4.692625 TGCAGAACATTTGACTCTTCTAGC 59.307 41.667 0.00 0.00 0.00 3.42
3118 3430 5.164233 CAGAACATTTGACTCTTCTAGCGA 58.836 41.667 0.00 0.00 0.00 4.93
3119 3431 5.635280 CAGAACATTTGACTCTTCTAGCGAA 59.365 40.000 0.00 0.00 0.00 4.70
3122 3434 5.724328 ACATTTGACTCTTCTAGCGAATGA 58.276 37.500 0.00 0.00 37.00 2.57
3135 4124 4.848562 AGCGAATGATATACAACCTCGA 57.151 40.909 0.00 0.00 33.84 4.04
3140 4129 5.853810 CGAATGATATACAACCTCGAGTCAG 59.146 44.000 12.31 2.67 33.84 3.51
3199 4188 2.529780 ATTACCGGACGTCAACAACA 57.470 45.000 18.91 0.00 0.00 3.33
3216 4205 6.695278 TCAACAACAAACATTCTTTCGGATTC 59.305 34.615 0.00 0.00 0.00 2.52
3262 4255 1.289276 CGATGAATCGTCACCATGCA 58.711 50.000 4.53 0.00 44.74 3.96
3263 4256 1.869132 CGATGAATCGTCACCATGCAT 59.131 47.619 4.53 0.00 44.74 3.96
3272 4265 2.164017 CGTCACCATGCATCCATTTTCA 59.836 45.455 0.00 0.00 0.00 2.69
3305 4298 1.983605 CCGACACGACACACTAATGTC 59.016 52.381 0.00 0.00 44.68 3.06
3314 4307 5.517037 GACACACTAATGTCACAGCTAAC 57.483 43.478 1.08 0.00 46.89 2.34
3315 4308 5.215252 ACACACTAATGTCACAGCTAACT 57.785 39.130 0.00 0.00 36.72 2.24
3316 4309 6.340962 ACACACTAATGTCACAGCTAACTA 57.659 37.500 0.00 0.00 36.72 2.24
3317 4310 6.390721 ACACACTAATGTCACAGCTAACTAG 58.609 40.000 0.00 0.00 36.72 2.57
3318 4311 6.015350 ACACACTAATGTCACAGCTAACTAGT 60.015 38.462 0.00 0.00 36.72 2.57
3319 4312 6.528423 CACACTAATGTCACAGCTAACTAGTC 59.472 42.308 0.00 0.00 36.72 2.59
3358 4351 8.079809 CGTTTGACAACCCAGTTATTTTTCTAT 58.920 33.333 0.00 0.00 0.00 1.98
3361 4354 9.802039 TTGACAACCCAGTTATTTTTCTATAGT 57.198 29.630 0.00 0.00 0.00 2.12
3404 4397 3.513119 TCAACACTCAATCAGGAGGAGAG 59.487 47.826 7.50 0.00 39.27 3.20
3429 4422 4.272018 CGAATCTGATCTGGTCCATGTTTC 59.728 45.833 0.00 0.00 0.00 2.78
3530 4523 3.059982 CTGCTCAAGGACGGGACA 58.940 61.111 0.00 0.00 0.00 4.02
3534 4527 2.525629 TCAAGGACGGGACAGGCA 60.526 61.111 0.00 0.00 0.00 4.75
3539 4532 2.112297 GACGGGACAGGCACCAAA 59.888 61.111 0.00 0.00 0.00 3.28
3785 4778 4.024545 ACCACCCCGCCCGTTTAG 62.025 66.667 0.00 0.00 0.00 1.85
3820 4815 0.746204 TTCGCATAGCAATTCCGCCA 60.746 50.000 0.00 0.00 0.00 5.69
3944 4940 1.083806 GCGAGGTTGTGATGCGATCA 61.084 55.000 0.00 0.00 36.84 2.92
3964 4960 6.513884 CGATCAACATTGACATTTCCATAGGG 60.514 42.308 0.00 0.00 40.49 3.53
4006 5017 4.023107 GTGAGACAAGGGGAAAACTAAAGC 60.023 45.833 0.00 0.00 0.00 3.51
4056 5067 1.419374 GGCGGCTAATGTGATACTCG 58.581 55.000 0.00 0.00 0.00 4.18
4103 5114 3.063997 CAGAAAGCGAAACTGTCAACTGT 59.936 43.478 0.00 0.00 34.71 3.55
4107 5118 1.332904 GCGAAACTGTCAACTGTTCCG 60.333 52.381 7.07 7.07 38.24 4.30
4146 5157 2.656646 CAGGTGTGGCTGCTCGTA 59.343 61.111 0.00 0.00 0.00 3.43
4147 5158 1.446792 CAGGTGTGGCTGCTCGTAG 60.447 63.158 0.00 0.00 0.00 3.51
4159 5170 1.034292 GCTCGTAGGACCCGGTACTT 61.034 60.000 7.89 0.00 0.00 2.24
4163 5174 2.029110 TCGTAGGACCCGGTACTTTTTG 60.029 50.000 7.89 0.00 0.00 2.44
4164 5175 2.703416 GTAGGACCCGGTACTTTTTGG 58.297 52.381 7.89 0.00 0.00 3.28
4166 5177 0.609957 GGACCCGGTACTTTTTGGGG 60.610 60.000 0.00 0.00 46.38 4.96
4167 5178 0.609957 GACCCGGTACTTTTTGGGGG 60.610 60.000 0.00 0.00 46.38 5.40
4182 5193 2.308185 GGGGGAGGAAAGTACCAGG 58.692 63.158 0.00 0.00 0.00 4.45
4183 5194 0.549413 GGGGGAGGAAAGTACCAGGT 60.549 60.000 0.00 0.00 0.00 4.00
4184 5195 0.618981 GGGGAGGAAAGTACCAGGTG 59.381 60.000 0.76 0.00 0.00 4.00
4185 5196 0.035343 GGGAGGAAAGTACCAGGTGC 60.035 60.000 0.76 0.00 0.00 5.01
4186 5197 0.984995 GGAGGAAAGTACCAGGTGCT 59.015 55.000 3.93 3.93 0.00 4.40
4187 5198 2.185387 GGAGGAAAGTACCAGGTGCTA 58.815 52.381 11.13 0.00 0.00 3.49
4188 5199 2.772515 GGAGGAAAGTACCAGGTGCTAT 59.227 50.000 11.13 0.00 0.00 2.97
4189 5200 3.200165 GGAGGAAAGTACCAGGTGCTATT 59.800 47.826 11.13 7.61 0.00 1.73
4190 5201 4.324331 GGAGGAAAGTACCAGGTGCTATTT 60.324 45.833 11.13 2.25 0.00 1.40
4191 5202 5.254115 GAGGAAAGTACCAGGTGCTATTTT 58.746 41.667 11.13 1.47 0.00 1.82
4192 5203 5.254115 AGGAAAGTACCAGGTGCTATTTTC 58.746 41.667 11.13 10.84 0.00 2.29
4193 5204 4.398358 GGAAAGTACCAGGTGCTATTTTCC 59.602 45.833 18.70 18.70 30.24 3.13
4194 5205 4.929146 AAGTACCAGGTGCTATTTTCCT 57.071 40.909 11.13 0.00 0.00 3.36
4195 5206 4.929146 AGTACCAGGTGCTATTTTCCTT 57.071 40.909 8.75 0.00 0.00 3.36
4196 5207 5.256806 AGTACCAGGTGCTATTTTCCTTT 57.743 39.130 8.75 0.00 0.00 3.11
4197 5208 5.010282 AGTACCAGGTGCTATTTTCCTTTG 58.990 41.667 8.75 0.00 0.00 2.77
4198 5209 3.165071 ACCAGGTGCTATTTTCCTTTGG 58.835 45.455 0.00 0.00 0.00 3.28
4199 5210 3.181423 ACCAGGTGCTATTTTCCTTTGGA 60.181 43.478 0.00 0.00 0.00 3.53
4200 5211 3.831911 CCAGGTGCTATTTTCCTTTGGAA 59.168 43.478 0.00 0.00 40.27 3.53
4215 5226 8.704849 TTCCTTTGGAAACATTAAGAATCTGA 57.295 30.769 0.00 0.00 38.93 3.27
4216 5227 8.884124 TCCTTTGGAAACATTAAGAATCTGAT 57.116 30.769 0.00 0.00 42.32 2.90
4217 5228 8.742777 TCCTTTGGAAACATTAAGAATCTGATG 58.257 33.333 5.63 5.63 42.32 3.07
4218 5229 8.526147 CCTTTGGAAACATTAAGAATCTGATGT 58.474 33.333 6.68 6.68 42.32 3.06
4235 5246 5.716228 TCTGATGTTGGATTTTTAGGCATGT 59.284 36.000 0.00 0.00 0.00 3.21
4236 5247 5.964758 TGATGTTGGATTTTTAGGCATGTC 58.035 37.500 0.00 0.00 0.00 3.06
4237 5248 5.479724 TGATGTTGGATTTTTAGGCATGTCA 59.520 36.000 0.00 0.00 0.00 3.58
4238 5249 5.798125 TGTTGGATTTTTAGGCATGTCAA 57.202 34.783 0.00 0.00 0.00 3.18
4239 5250 6.166984 TGTTGGATTTTTAGGCATGTCAAA 57.833 33.333 0.00 0.00 0.00 2.69
4240 5251 6.767456 TGTTGGATTTTTAGGCATGTCAAAT 58.233 32.000 0.00 0.00 0.00 2.32
4246 5257 8.632679 GGATTTTTAGGCATGTCAAATCTGATA 58.367 33.333 16.58 0.00 35.21 2.15
4258 5269 8.093659 TGTCAAATCTGATATTTTTCACGACA 57.906 30.769 0.00 0.00 33.05 4.35
4277 5288 9.303537 TCACGACAATTTATATTAACATGACGA 57.696 29.630 15.27 0.00 0.00 4.20
4301 5620 8.593842 CGATGATAAATTTATTTTGCAAGCACA 58.406 29.630 11.92 2.44 0.00 4.57
4335 5654 9.551734 TCTGACAATATAATTGAACTGAGATGG 57.448 33.333 6.64 0.00 0.00 3.51
4336 5655 9.334947 CTGACAATATAATTGAACTGAGATGGT 57.665 33.333 6.64 0.00 0.00 3.55
4350 5669 2.744202 GAGATGGTTTTGTCATGCTCGT 59.256 45.455 0.00 0.00 0.00 4.18
4371 5690 5.471797 TCGTCAAATAAACTTGCCATTCTCA 59.528 36.000 0.00 0.00 0.00 3.27
4374 5693 7.329226 CGTCAAATAAACTTGCCATTCTCAAAT 59.671 33.333 0.00 0.00 0.00 2.32
4442 5762 1.764723 TGATGGCAGATCTGTAGTGGG 59.235 52.381 23.38 0.00 0.00 4.61
4483 5804 5.453903 GCTCAAGCCTTCAATCCAGAGTATA 60.454 44.000 0.00 0.00 34.31 1.47
4531 5852 5.011533 CCACATTTTAGGTTTCAATCCCACA 59.988 40.000 0.00 0.00 0.00 4.17
4643 5964 9.757859 TTTGGACGATTTAAATACGTTTATGAC 57.242 29.630 19.47 10.44 40.29 3.06
4683 6004 4.722193 CCGATGTGGCAAGGAAGT 57.278 55.556 0.00 0.00 0.00 3.01
4704 6025 4.517832 AGTCAACTCCGTTTATTTTGACCC 59.482 41.667 8.72 0.00 44.69 4.46
4707 6028 3.069289 ACTCCGTTTATTTTGACCCGTC 58.931 45.455 0.00 0.00 0.00 4.79
4709 6030 3.474600 TCCGTTTATTTTGACCCGTCAA 58.525 40.909 6.17 6.17 46.72 3.18
4720 6041 2.236146 TGACCCGTCAAAGCATCTACAT 59.764 45.455 0.00 0.00 36.53 2.29
4731 6052 2.501723 AGCATCTACATCCGGACTTTGT 59.498 45.455 6.12 10.83 0.00 2.83
4743 6064 3.062122 GGACTTTGTAAATCCGGTCCA 57.938 47.619 0.00 0.00 41.75 4.02
4745 6066 3.189910 GGACTTTGTAAATCCGGTCCAAC 59.810 47.826 0.00 0.00 41.75 3.77
4746 6067 2.809696 ACTTTGTAAATCCGGTCCAACG 59.190 45.455 0.00 0.00 0.00 4.10
4749 6070 0.737019 GTAAATCCGGTCCAACGCGA 60.737 55.000 15.93 0.00 0.00 5.87
4768 6089 4.039357 CGAGCACGTCCACGGACT 62.039 66.667 14.12 0.23 44.95 3.85
4805 6128 4.752101 CCTTAAAATAGACTCTGCATCCGG 59.248 45.833 0.00 0.00 0.00 5.14
4810 6133 1.040339 AGACTCTGCATCCGGGTCTC 61.040 60.000 0.00 0.00 32.66 3.36
4831 6154 5.548056 TCTCCCATATTTCAACCCCTAGATC 59.452 44.000 0.00 0.00 0.00 2.75
4854 6177 6.286758 TCCATACAAAGCATGCAAAAGAAAA 58.713 32.000 21.98 0.00 0.00 2.29
4864 6187 8.015185 AGCATGCAAAAGAAAATCCTACATAT 57.985 30.769 21.98 0.00 0.00 1.78
4885 6208 9.139734 ACATATTACCCTAACTAATCTTCGTCA 57.860 33.333 0.00 0.00 0.00 4.35
4910 6233 0.373716 GATGTCCACGATTTCGGTGC 59.626 55.000 4.84 0.00 44.95 5.01
4912 6235 2.433491 TCCACGATTTCGGTGCCG 60.433 61.111 3.94 3.94 44.95 5.69
4945 6268 2.829458 GACGCGTAGGAGGGCTCT 60.829 66.667 13.97 0.00 0.00 4.09
4947 6270 3.905678 CGCGTAGGAGGGCTCTGG 61.906 72.222 0.00 0.00 0.00 3.86
4960 6283 1.757423 GCTCTGGCTCATCCTCCTCC 61.757 65.000 0.00 0.00 35.26 4.30
4977 6300 0.397675 TCCTGCTCGACCTCATCCAT 60.398 55.000 0.00 0.00 0.00 3.41
4983 6306 1.000283 CTCGACCTCATCCATGTAGGC 60.000 57.143 0.00 0.00 37.29 3.93
5016 6349 3.473647 CTCCATCTCCTGCCGGCA 61.474 66.667 30.59 30.59 0.00 5.69
5039 6372 2.895372 GTATGGCCTCCGCAACCG 60.895 66.667 3.32 0.00 36.38 4.44
5041 6374 2.661066 TATGGCCTCCGCAACCGAA 61.661 57.895 3.32 0.00 36.38 4.30
5048 6381 0.108615 CTCCGCAACCGAATCTGAGT 60.109 55.000 0.00 0.00 36.29 3.41
5049 6382 0.389817 TCCGCAACCGAATCTGAGTG 60.390 55.000 0.00 0.00 36.29 3.51
5050 6383 1.361668 CCGCAACCGAATCTGAGTGG 61.362 60.000 0.00 0.00 36.29 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.073897 GGAGTGGAGGCTGCAACTT 59.926 57.895 11.29 0.00 0.00 2.66
17 18 2.596851 GGAGGAGTGGAGGCTGCAA 61.597 63.158 11.29 0.00 0.00 4.08
22 23 1.194781 TTGTCAGGAGGAGTGGAGGC 61.195 60.000 0.00 0.00 0.00 4.70
32 33 2.375766 GCGTCTGCGTTGTCAGGAG 61.376 63.158 0.00 0.00 40.81 3.69
98 99 0.914644 CTCCTTCTCCTCCATTGCCA 59.085 55.000 0.00 0.00 0.00 4.92
137 143 1.153449 CCGCTAGCATCCGTTCCAA 60.153 57.895 16.45 0.00 0.00 3.53
188 197 7.016366 TCTCTTACTCCCGTGAATCTCTATCTA 59.984 40.741 0.00 0.00 0.00 1.98
190 199 5.998981 TCTCTTACTCCCGTGAATCTCTATC 59.001 44.000 0.00 0.00 0.00 2.08
201 210 4.304048 TTCTTCTCTCTCTTACTCCCGT 57.696 45.455 0.00 0.00 0.00 5.28
202 211 4.884744 TCATTCTTCTCTCTCTTACTCCCG 59.115 45.833 0.00 0.00 0.00 5.14
205 214 8.506168 TTCTCTCATTCTTCTCTCTCTTACTC 57.494 38.462 0.00 0.00 0.00 2.59
206 215 8.328758 TCTTCTCTCATTCTTCTCTCTCTTACT 58.671 37.037 0.00 0.00 0.00 2.24
207 216 8.506168 TCTTCTCTCATTCTTCTCTCTCTTAC 57.494 38.462 0.00 0.00 0.00 2.34
208 217 8.548025 TCTCTTCTCTCATTCTTCTCTCTCTTA 58.452 37.037 0.00 0.00 0.00 2.10
209 218 7.405292 TCTCTTCTCTCATTCTTCTCTCTCTT 58.595 38.462 0.00 0.00 0.00 2.85
235 244 2.124411 GGGAGATGCTAGGGTTTGGTA 58.876 52.381 0.00 0.00 0.00 3.25
255 267 2.191513 CGCTGCTCCATCCCCAATG 61.192 63.158 0.00 0.00 34.93 2.82
273 285 3.568007 TGTGACTTGCCTTACACCAATTC 59.432 43.478 0.00 0.00 33.08 2.17
277 289 2.719531 TTGTGACTTGCCTTACACCA 57.280 45.000 0.00 0.00 33.08 4.17
289 301 3.401033 TTCGTGTGATCCATTGTGACT 57.599 42.857 0.00 0.00 0.00 3.41
330 342 4.039151 TCTCAGAGCTTAGAGCATTTCG 57.961 45.455 10.55 0.00 45.56 3.46
364 527 4.431416 TCCAAAACTAAGACTTGCAGGA 57.569 40.909 1.40 0.00 0.00 3.86
392 555 0.179048 TTGGGGAGCGCTATGTGATG 60.179 55.000 11.50 0.00 0.00 3.07
399 562 4.274147 TCAATTTTTATTGGGGAGCGCTA 58.726 39.130 11.50 0.00 32.65 4.26
407 570 5.812127 GCTTGTAGGCTCAATTTTTATTGGG 59.188 40.000 0.00 0.00 35.19 4.12
417 580 9.853177 AAGTATTTATTAGCTTGTAGGCTCAAT 57.147 29.630 0.00 0.00 42.97 2.57
444 607 8.615878 ACATAGTGTAATGCAAAGTGTCTTAA 57.384 30.769 0.00 0.00 0.00 1.85
531 694 5.009710 GGCTTTTGCTACCTTCTTTGTTAGT 59.990 40.000 0.00 0.00 46.54 2.24
629 816 8.328758 TCCAGAAATGACATGGAAAATAGTAGT 58.671 33.333 0.00 0.00 40.13 2.73
630 817 8.737168 TCCAGAAATGACATGGAAAATAGTAG 57.263 34.615 0.00 0.00 40.13 2.57
644 831 3.008485 ACTCCCACTCTTCCAGAAATGAC 59.992 47.826 0.00 0.00 0.00 3.06
702 889 2.985456 GGCCAGAGGGAGTGACTG 59.015 66.667 0.00 0.00 35.59 3.51
758 975 3.081061 TCTGCGGCTGTGTTATCAATTT 58.919 40.909 0.00 0.00 0.00 1.82
774 991 1.216710 GAAGGAGGTGAGGTCTGCG 59.783 63.158 0.00 0.00 0.00 5.18
779 996 1.258676 GAGTTCGAAGGAGGTGAGGT 58.741 55.000 0.00 0.00 0.00 3.85
781 998 0.533032 GGGAGTTCGAAGGAGGTGAG 59.467 60.000 0.00 0.00 0.00 3.51
785 1016 2.893398 CGGGGAGTTCGAAGGAGG 59.107 66.667 0.00 0.00 0.00 4.30
843 1074 2.135933 GGAATTAACGAGATCGGCCAG 58.864 52.381 2.24 0.00 44.95 4.85
860 1091 3.554934 ACTTGATTTGTCTGCACTGGAA 58.445 40.909 0.00 0.00 0.00 3.53
924 1155 1.001706 CTAGGCGCGCAACTAGTATGA 60.002 52.381 34.42 4.25 33.63 2.15
929 1160 2.202743 TGCTAGGCGCGCAACTAG 60.203 61.111 34.42 31.16 43.27 2.57
951 1183 5.163814 ACGTAGGAGTACTAACTAAAGCACG 60.164 44.000 13.47 13.47 35.56 5.34
994 1226 2.751436 TTCTGGCCGCATGCTTCC 60.751 61.111 17.13 16.26 40.92 3.46
995 1227 2.768492 CCTTCTGGCCGCATGCTTC 61.768 63.158 17.13 6.82 40.92 3.86
1429 1679 1.144936 GCGGGATGAAGGTGAGGAG 59.855 63.158 0.00 0.00 0.00 3.69
1470 1720 2.089600 AGTAGATGTAGGCCACCCTC 57.910 55.000 5.01 0.00 41.75 4.30
1632 1882 1.639534 CGTGCGGTTGTTCTCGTTT 59.360 52.632 0.00 0.00 0.00 3.60
1839 2089 0.887387 TGGTTTCCTGCTTGGCGTAC 60.887 55.000 0.00 0.00 35.26 3.67
1888 2138 1.734465 GGGTTTCTCGCACTTGATGAG 59.266 52.381 0.00 0.00 0.00 2.90
2031 2281 2.736995 CCGGTGTACACTGCCACG 60.737 66.667 26.53 19.21 36.39 4.94
2169 2419 1.216710 GCCGGTGAGGAGAGACAAG 59.783 63.158 1.90 0.00 45.00 3.16
2170 2420 0.904865 ATGCCGGTGAGGAGAGACAA 60.905 55.000 1.90 0.00 45.00 3.18
2219 2469 2.818921 TGTGGAAAAAGGGGATGATGG 58.181 47.619 0.00 0.00 0.00 3.51
2269 2519 0.320421 CAGTTGTACCTCCCGTGGTG 60.320 60.000 0.00 0.00 41.05 4.17
2433 2683 1.973812 GGCCTGGCTCTTGTTGTCC 60.974 63.158 19.68 0.00 0.00 4.02
2437 2687 4.351054 CCGGGCCTGGCTCTTGTT 62.351 66.667 20.35 0.00 0.00 2.83
2439 2689 4.351054 AACCGGGCCTGGCTCTTG 62.351 66.667 31.77 10.19 0.00 3.02
2544 2794 3.499737 GCGCACCGGAACTCCATG 61.500 66.667 9.46 0.00 35.14 3.66
2689 2939 3.609214 AACGCCGCCGCTCAAAATG 62.609 57.895 0.00 0.00 38.22 2.32
2741 2991 3.846360 CAACACACTGGCCTAGTAGTAC 58.154 50.000 3.32 0.00 37.60 2.73
2742 2992 2.232941 GCAACACACTGGCCTAGTAGTA 59.767 50.000 3.32 0.00 37.60 1.82
2743 2993 1.002087 GCAACACACTGGCCTAGTAGT 59.998 52.381 3.32 5.65 37.60 2.73
2744 2994 1.726853 GCAACACACTGGCCTAGTAG 58.273 55.000 3.32 5.04 37.60 2.57
2745 2995 0.037697 CGCAACACACTGGCCTAGTA 60.038 55.000 3.32 0.00 37.60 1.82
2746 2996 1.301716 CGCAACACACTGGCCTAGT 60.302 57.895 3.32 2.75 41.36 2.57
2747 2997 1.301716 ACGCAACACACTGGCCTAG 60.302 57.895 3.32 2.01 0.00 3.02
2748 2998 1.596752 CACGCAACACACTGGCCTA 60.597 57.895 3.32 0.00 0.00 3.93
2749 2999 2.901840 CACGCAACACACTGGCCT 60.902 61.111 3.32 0.00 0.00 5.19
2750 3000 4.629115 GCACGCAACACACTGGCC 62.629 66.667 0.00 0.00 0.00 5.36
2816 3079 1.851021 CGGCGTGTGGATGCAGAAAA 61.851 55.000 0.00 0.00 35.60 2.29
2878 3142 8.047413 TCTAACTATCGAAATGTGTCAGTGTA 57.953 34.615 0.00 0.00 0.00 2.90
2879 3143 6.920817 TCTAACTATCGAAATGTGTCAGTGT 58.079 36.000 0.00 0.00 0.00 3.55
2971 3235 5.163723 CGATCAGTGGCATAACAAATCAGTT 60.164 40.000 0.00 0.00 35.55 3.16
3074 3375 3.253188 TGCAACACAAGCTACAGGATTTC 59.747 43.478 0.00 0.00 0.00 2.17
3097 3401 6.311445 TCATTCGCTAGAAGAGTCAAATGTTC 59.689 38.462 0.00 0.00 40.09 3.18
3116 3428 5.758924 TGACTCGAGGTTGTATATCATTCG 58.241 41.667 18.41 0.00 0.00 3.34
3118 3430 6.321435 TCACTGACTCGAGGTTGTATATCATT 59.679 38.462 18.41 0.01 0.00 2.57
3119 3431 5.828328 TCACTGACTCGAGGTTGTATATCAT 59.172 40.000 18.41 0.00 0.00 2.45
3122 3434 5.828328 TGATCACTGACTCGAGGTTGTATAT 59.172 40.000 18.41 8.56 0.00 0.86
3135 4124 1.625818 GGTCAACCCTGATCACTGACT 59.374 52.381 16.25 0.00 37.23 3.41
3140 4129 1.745489 GGCGGTCAACCCTGATCAC 60.745 63.158 0.00 0.00 31.50 3.06
3199 4188 7.441017 TCAAATTGGAATCCGAAAGAATGTTT 58.559 30.769 0.00 0.00 0.00 2.83
3216 4205 3.623060 CGATACACCCAGTCTCAAATTGG 59.377 47.826 0.00 0.00 0.00 3.16
3262 4255 4.150359 GCTCTCATCCCATGAAAATGGAT 58.850 43.478 6.31 0.00 44.39 3.41
3263 4256 3.559069 GCTCTCATCCCATGAAAATGGA 58.441 45.455 6.31 0.00 44.39 3.41
3272 4265 1.383109 TGTCGGGCTCTCATCCCAT 60.383 57.895 0.00 0.00 44.11 4.00
3305 4298 2.989840 GTGCTGTGACTAGTTAGCTGTG 59.010 50.000 20.94 2.90 37.10 3.66
3306 4299 2.628178 TGTGCTGTGACTAGTTAGCTGT 59.372 45.455 20.94 0.00 37.10 4.40
3307 4300 2.989840 GTGTGCTGTGACTAGTTAGCTG 59.010 50.000 20.94 10.27 37.10 4.24
3308 4301 2.028930 GGTGTGCTGTGACTAGTTAGCT 60.029 50.000 20.94 0.00 37.10 3.32
3309 4302 2.028930 AGGTGTGCTGTGACTAGTTAGC 60.029 50.000 16.35 16.35 36.72 3.09
3310 4303 3.944055 AGGTGTGCTGTGACTAGTTAG 57.056 47.619 0.00 0.00 0.00 2.34
3311 4304 3.305131 CGAAGGTGTGCTGTGACTAGTTA 60.305 47.826 0.00 0.00 0.00 2.24
3312 4305 2.545952 CGAAGGTGTGCTGTGACTAGTT 60.546 50.000 0.00 0.00 0.00 2.24
3313 4306 1.000163 CGAAGGTGTGCTGTGACTAGT 60.000 52.381 0.00 0.00 0.00 2.57
3314 4307 1.000163 ACGAAGGTGTGCTGTGACTAG 60.000 52.381 0.00 0.00 0.00 2.57
3315 4308 1.037493 ACGAAGGTGTGCTGTGACTA 58.963 50.000 0.00 0.00 0.00 2.59
3316 4309 0.178068 AACGAAGGTGTGCTGTGACT 59.822 50.000 0.00 0.00 0.00 3.41
3317 4310 1.014352 AAACGAAGGTGTGCTGTGAC 58.986 50.000 0.00 0.00 0.00 3.67
3318 4311 1.013596 CAAACGAAGGTGTGCTGTGA 58.986 50.000 0.00 0.00 0.00 3.58
3319 4312 1.013596 TCAAACGAAGGTGTGCTGTG 58.986 50.000 0.00 0.00 31.00 3.66
3372 4365 9.739276 TCCTGATTGAGTGTTGAATTTTACTAT 57.261 29.630 0.00 0.00 0.00 2.12
3373 4366 9.219603 CTCCTGATTGAGTGTTGAATTTTACTA 57.780 33.333 0.00 0.00 0.00 1.82
3388 4381 2.649190 TCGTCTCTCCTCCTGATTGAG 58.351 52.381 0.00 0.00 0.00 3.02
3389 4382 2.808906 TCGTCTCTCCTCCTGATTGA 57.191 50.000 0.00 0.00 0.00 2.57
3396 4389 3.253188 CAGATCAGATTCGTCTCTCCTCC 59.747 52.174 0.00 0.00 0.00 4.30
3404 4397 3.181471 ACATGGACCAGATCAGATTCGTC 60.181 47.826 0.00 0.00 0.00 4.20
3575 4568 1.795170 GCACGATGGTGTTGCAGGTT 61.795 55.000 9.74 0.00 46.13 3.50
3647 4640 4.361971 TGCTCGTCGGGGGACTCT 62.362 66.667 0.00 0.00 0.00 3.24
3804 4799 2.129607 CAAATGGCGGAATTGCTATGC 58.870 47.619 0.00 0.00 36.09 3.14
3820 4815 6.760770 ACAAATCAATTTCACCAACGTCAAAT 59.239 30.769 0.00 0.00 0.00 2.32
3944 4940 5.888161 GTCTCCCTATGGAAATGTCAATGTT 59.112 40.000 0.00 0.00 41.17 2.71
3964 4960 6.366877 GTCTCACTACTCCTATATGACGTCTC 59.633 46.154 17.92 0.00 0.00 3.36
4006 5017 1.282817 TTCGTGACACCAACTGAACG 58.717 50.000 0.00 0.00 35.87 3.95
4103 5114 3.353836 GCTTGCACGGAAGCGGAA 61.354 61.111 7.55 0.00 39.10 4.30
4107 5118 3.259425 CTGTGGCTTGCACGGAAGC 62.259 63.158 14.20 14.20 46.49 3.86
4146 5157 0.402887 CCCAAAAAGTACCGGGTCCT 59.597 55.000 6.32 0.00 33.67 3.85
4147 5158 0.609957 CCCCAAAAAGTACCGGGTCC 60.610 60.000 6.32 0.00 36.92 4.46
4164 5175 0.549413 ACCTGGTACTTTCCTCCCCC 60.549 60.000 0.00 0.00 0.00 5.40
4165 5176 0.618981 CACCTGGTACTTTCCTCCCC 59.381 60.000 0.00 0.00 0.00 4.81
4166 5177 0.035343 GCACCTGGTACTTTCCTCCC 60.035 60.000 0.00 0.00 0.00 4.30
4167 5178 0.984995 AGCACCTGGTACTTTCCTCC 59.015 55.000 0.00 0.00 0.00 4.30
4168 5179 4.489306 AATAGCACCTGGTACTTTCCTC 57.511 45.455 4.61 0.00 0.00 3.71
4169 5180 4.929146 AAATAGCACCTGGTACTTTCCT 57.071 40.909 4.61 0.00 0.00 3.36
4170 5181 5.562506 GAAAATAGCACCTGGTACTTTCC 57.437 43.478 4.61 0.00 37.90 3.13
4171 5182 5.254115 AGGAAAATAGCACCTGGTACTTTC 58.746 41.667 4.61 9.04 40.99 2.62
4172 5183 5.256806 AGGAAAATAGCACCTGGTACTTT 57.743 39.130 4.61 0.00 31.38 2.66
4173 5184 4.929146 AGGAAAATAGCACCTGGTACTT 57.071 40.909 4.61 0.00 32.39 2.24
4174 5185 4.929146 AAGGAAAATAGCACCTGGTACT 57.071 40.909 4.71 4.71 34.03 2.73
4175 5186 4.157840 CCAAAGGAAAATAGCACCTGGTAC 59.842 45.833 0.00 0.00 34.03 3.34
4176 5187 4.043561 TCCAAAGGAAAATAGCACCTGGTA 59.956 41.667 0.00 0.00 34.03 3.25
4177 5188 3.165071 CCAAAGGAAAATAGCACCTGGT 58.835 45.455 0.00 0.00 34.03 4.00
4178 5189 3.430453 TCCAAAGGAAAATAGCACCTGG 58.570 45.455 0.00 0.00 34.03 4.45
4190 5201 8.704849 TCAGATTCTTAATGTTTCCAAAGGAA 57.295 30.769 0.00 0.00 40.27 3.36
4191 5202 8.742777 CATCAGATTCTTAATGTTTCCAAAGGA 58.257 33.333 0.00 0.00 0.00 3.36
4192 5203 8.526147 ACATCAGATTCTTAATGTTTCCAAAGG 58.474 33.333 5.87 0.00 0.00 3.11
4193 5204 9.918630 AACATCAGATTCTTAATGTTTCCAAAG 57.081 29.630 14.31 0.00 38.78 2.77
4194 5205 9.695526 CAACATCAGATTCTTAATGTTTCCAAA 57.304 29.630 16.26 0.00 39.62 3.28
4195 5206 8.306038 CCAACATCAGATTCTTAATGTTTCCAA 58.694 33.333 16.26 0.00 39.62 3.53
4196 5207 7.669304 TCCAACATCAGATTCTTAATGTTTCCA 59.331 33.333 16.26 6.02 39.62 3.53
4197 5208 8.055279 TCCAACATCAGATTCTTAATGTTTCC 57.945 34.615 16.26 0.00 39.62 3.13
4205 5216 8.686334 GCCTAAAAATCCAACATCAGATTCTTA 58.314 33.333 0.00 0.00 31.54 2.10
4206 5217 7.178983 TGCCTAAAAATCCAACATCAGATTCTT 59.821 33.333 0.00 0.00 31.54 2.52
4207 5218 6.664816 TGCCTAAAAATCCAACATCAGATTCT 59.335 34.615 0.00 0.00 31.54 2.40
4208 5219 6.866480 TGCCTAAAAATCCAACATCAGATTC 58.134 36.000 0.00 0.00 31.54 2.52
4209 5220 6.855763 TGCCTAAAAATCCAACATCAGATT 57.144 33.333 0.00 0.00 34.18 2.40
4210 5221 6.381994 ACATGCCTAAAAATCCAACATCAGAT 59.618 34.615 0.00 0.00 0.00 2.90
4211 5222 5.716228 ACATGCCTAAAAATCCAACATCAGA 59.284 36.000 0.00 0.00 0.00 3.27
4212 5223 5.969423 ACATGCCTAAAAATCCAACATCAG 58.031 37.500 0.00 0.00 0.00 2.90
4213 5224 5.479724 TGACATGCCTAAAAATCCAACATCA 59.520 36.000 0.00 0.00 0.00 3.07
4214 5225 5.964758 TGACATGCCTAAAAATCCAACATC 58.035 37.500 0.00 0.00 0.00 3.06
4215 5226 5.999205 TGACATGCCTAAAAATCCAACAT 57.001 34.783 0.00 0.00 0.00 2.71
4216 5227 5.798125 TTGACATGCCTAAAAATCCAACA 57.202 34.783 0.00 0.00 0.00 3.33
4217 5228 7.063780 CAGATTTGACATGCCTAAAAATCCAAC 59.936 37.037 12.06 0.00 37.76 3.77
4218 5229 7.039152 TCAGATTTGACATGCCTAAAAATCCAA 60.039 33.333 12.06 0.00 37.76 3.53
4275 5286 8.593842 TGTGCTTGCAAAATAAATTTATCATCG 58.406 29.630 11.08 2.64 0.00 3.84
4289 5608 7.279536 TGTCAGAAAATTATTGTGCTTGCAAAA 59.720 29.630 0.00 0.33 31.63 2.44
4310 5629 9.334947 ACCATCTCAGTTCAATTATATTGTCAG 57.665 33.333 0.00 0.00 0.00 3.51
4328 5647 2.743664 CGAGCATGACAAAACCATCTCA 59.256 45.455 0.00 0.00 0.00 3.27
4335 5654 6.636850 AGTTTATTTGACGAGCATGACAAAAC 59.363 34.615 0.00 4.90 37.14 2.43
4336 5655 6.734137 AGTTTATTTGACGAGCATGACAAAA 58.266 32.000 0.00 0.00 37.14 2.44
4419 5739 4.224594 CCCACTACAGATCTGCCATCATAT 59.775 45.833 22.83 3.03 0.00 1.78
4433 5753 5.453480 GGCTAGGATTAAAGACCCACTACAG 60.453 48.000 0.00 0.00 0.00 2.74
4442 5762 4.408182 TGAGCAGGCTAGGATTAAAGAC 57.592 45.455 0.00 0.00 0.00 3.01
4523 5844 4.104102 TGAAAGTGGTAGTTCTGTGGGATT 59.896 41.667 0.00 0.00 0.00 3.01
4531 5852 3.751698 GCCGATTTGAAAGTGGTAGTTCT 59.248 43.478 1.04 0.00 0.00 3.01
4590 5911 7.119262 CCGATCACTATTTGAAAGTGGTAGTTT 59.881 37.037 3.60 0.00 43.69 2.66
4614 5935 5.207305 ACGTATTTAAATCGTCCAAACCG 57.793 39.130 15.37 5.38 32.26 4.44
4632 5953 2.093869 GGTCCTGCCTGTCATAAACGTA 60.094 50.000 0.00 0.00 0.00 3.57
4643 5964 1.150081 GATGGATGGGTCCTGCCTG 59.850 63.158 0.00 0.00 45.32 4.85
4704 6025 1.860950 CCGGATGTAGATGCTTTGACG 59.139 52.381 0.00 0.00 0.00 4.35
4707 6028 3.185246 AGTCCGGATGTAGATGCTTTG 57.815 47.619 7.81 0.00 0.00 2.77
4709 6030 3.055094 ACAAAGTCCGGATGTAGATGCTT 60.055 43.478 7.81 0.00 0.00 3.91
4731 6052 0.737019 GTCGCGTTGGACCGGATTTA 60.737 55.000 9.46 0.00 0.00 1.40
4762 6083 2.520020 TGACCCGTCACAGTCCGT 60.520 61.111 0.00 0.00 34.14 4.69
4774 6095 5.875359 CAGAGTCTATTTTAAGGTGTGACCC 59.125 44.000 0.00 0.00 39.75 4.46
4782 6103 4.752101 CCGGATGCAGAGTCTATTTTAAGG 59.248 45.833 0.00 0.00 0.00 2.69
4785 6106 3.709653 ACCCGGATGCAGAGTCTATTTTA 59.290 43.478 0.73 0.00 0.00 1.52
4810 6133 4.353788 TGGATCTAGGGGTTGAAATATGGG 59.646 45.833 0.00 0.00 0.00 4.00
4831 6154 6.542574 TTTTCTTTTGCATGCTTTGTATGG 57.457 33.333 20.33 1.44 0.00 2.74
4864 6187 7.124599 TCCAATGACGAAGATTAGTTAGGGTAA 59.875 37.037 0.00 0.00 0.00 2.85
4867 6190 5.914033 TCCAATGACGAAGATTAGTTAGGG 58.086 41.667 0.00 0.00 0.00 3.53
4929 6252 3.141488 CAGAGCCCTCCTACGCGT 61.141 66.667 19.17 19.17 0.00 6.01
4933 6256 0.762461 ATGAGCCAGAGCCCTCCTAC 60.762 60.000 0.00 0.00 41.25 3.18
4945 6268 2.068821 GCAGGAGGAGGATGAGCCA 61.069 63.158 0.00 0.00 40.02 4.75
4947 6270 1.747774 GAGCAGGAGGAGGATGAGC 59.252 63.158 0.00 0.00 0.00 4.26
4960 6283 0.463204 ACATGGATGAGGTCGAGCAG 59.537 55.000 18.15 0.00 0.00 4.24
4977 6300 3.120105 CGGAGATGCTCGCCTACA 58.880 61.111 4.89 0.00 33.90 2.74


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

AutoCloner maintained by Alex Coulton.