Multiple sequence alignment - TraesCS5D01G562300

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G562300 chr5D 100.000 3656 0 0 1 3656 562103427 562099772 0.000000e+00 6752.0
1 TraesCS5D01G562300 chr5D 82.975 511 66 14 1 495 562105450 562104945 3.350000e-120 442.0
2 TraesCS5D01G562300 chr5D 84.776 335 27 16 2992 3319 562100337 562100020 7.620000e-82 315.0
3 TraesCS5D01G562300 chr5D 84.776 335 27 16 3091 3408 562100436 562100109 7.620000e-82 315.0
4 TraesCS5D01G562300 chr5D 85.366 164 19 3 3060 3223 562100178 562100020 8.120000e-37 165.0
5 TraesCS5D01G562300 chr5D 85.366 164 19 3 3250 3408 562100368 562100205 8.120000e-37 165.0
6 TraesCS5D01G562300 chr7B 90.271 2621 118 73 698 3223 421532 424110 0.000000e+00 3301.0
7 TraesCS5D01G562300 chr7B 80.141 710 79 21 1 669 418015 418703 1.190000e-129 473.0
8 TraesCS5D01G562300 chr7B 88.475 295 9 7 3251 3521 424184 424477 2.100000e-87 333.0
9 TraesCS5D01G562300 chr7B 80.376 372 20 28 3076 3433 423875 424207 2.200000e-57 233.0
10 TraesCS5D01G562300 chr7B 88.360 189 10 3 3250 3433 423954 424135 2.210000e-52 217.0
11 TraesCS5D01G562300 chr7B 86.145 166 14 5 3154 3319 424184 424340 1.750000e-38 171.0
12 TraesCS5D01G562300 chr7B 81.928 166 24 4 3058 3223 424181 424340 6.370000e-28 135.0
13 TraesCS5D01G562300 chr7B 97.059 34 1 0 3623 3656 424478 424511 1.420000e-04 58.4
14 TraesCS5D01G562300 chr5B 89.851 1340 55 26 1970 3282 712696676 712697961 0.000000e+00 1646.0
15 TraesCS5D01G562300 chr5B 88.078 411 8 20 1000 1370 712695930 712696339 2.000000e-122 449.0
16 TraesCS5D01G562300 chr5B 89.080 348 17 10 1400 1747 712696342 712696668 2.630000e-111 412.0
17 TraesCS5D01G562300 chr5B 91.626 203 9 3 3192 3392 712697784 712697980 1.290000e-69 274.0
18 TraesCS5D01G562300 chr5B 92.437 119 7 1 3289 3405 712697784 712697902 6.280000e-38 169.0
19 TraesCS5D01G562300 chr5B 88.000 100 2 1 3432 3521 712698371 712698470 3.860000e-20 110.0
20 TraesCS5D01G562300 chr5B 80.916 131 8 11 2904 3024 712698200 712698323 1.810000e-13 87.9
21 TraesCS5D01G562300 chr3A 95.122 123 4 2 3506 3628 46169218 46169098 3.730000e-45 193.0
22 TraesCS5D01G562300 chr6B 97.297 111 3 0 3515 3625 705508976 705508866 4.820000e-44 189.0
23 TraesCS5D01G562300 chr7D 96.460 113 4 0 3515 3627 379324241 379324129 1.730000e-43 187.0
24 TraesCS5D01G562300 chrUn 96.429 112 3 1 3521 3632 30406060 30405950 2.240000e-42 183.0
25 TraesCS5D01G562300 chr5A 94.167 120 7 0 3506 3625 601257428 601257309 2.240000e-42 183.0
26 TraesCS5D01G562300 chr3D 96.429 112 3 1 3518 3628 26258805 26258694 2.240000e-42 183.0
27 TraesCS5D01G562300 chr6A 92.188 128 9 1 3499 3625 50357009 50356882 2.900000e-41 180.0
28 TraesCS5D01G562300 chr6A 92.857 126 6 3 3504 3627 259311254 259311130 2.900000e-41 180.0
29 TraesCS5D01G562300 chr3B 92.437 119 9 0 3508 3626 214547632 214547514 1.750000e-38 171.0


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 TraesCS5D01G562300 chr5D 562099772 562103427 3655 True 1542.400 6752 88.056800 1 3656 5 chr5D.!!$R2 3655
1 TraesCS5D01G562300 chr5D 562104945 562105450 505 True 442.000 442 82.975000 1 495 1 chr5D.!!$R1 494
2 TraesCS5D01G562300 chr7B 418015 424511 6496 False 615.175 3301 86.594375 1 3656 8 chr7B.!!$F1 3655
3 TraesCS5D01G562300 chr5B 712695930 712698470 2540 False 449.700 1646 88.569714 1000 3521 7 chr5B.!!$F1 2521

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
247 287 0.033503 TGGACCACCAGCGATCTCTA 60.034 55.0 0.0 0.0 41.77 2.43 F
1378 4304 0.036858 GAGAGGCTGGTCTGTGTTCC 60.037 60.0 0.0 0.0 0.00 3.62 F
1814 4767 0.025001 CGTTGGCGTGCTTTCGATAG 59.975 55.0 0.0 0.0 0.00 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1410 4357 1.055849 AGCACCACCATGTCTGTGTA 58.944 50.0 7.34 0.0 31.71 2.90 R
2496 5484 0.256464 AGTCTGACCCTCTACCTCCG 59.744 60.0 3.76 0.0 0.00 4.63 R
3609 7046 0.172803 CTTGTACTCCCTCCGTTCCG 59.827 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
60 61 4.620609 TCATAAAAACACATGCACAATCGC 59.379 37.500 0.00 0.00 0.00 4.58
111 130 5.402054 ACTTTGGATATGATTTGGGCCTA 57.598 39.130 4.53 0.00 0.00 3.93
113 132 5.598417 ACTTTGGATATGATTTGGGCCTAAC 59.402 40.000 0.00 0.00 0.00 2.34
133 152 7.873505 GCCTAACTGAGTCCTTATCGAAAATAT 59.126 37.037 0.00 0.00 0.00 1.28
165 184 7.971183 TTTTTATGGGGTTTTCAGTTTATGC 57.029 32.000 0.00 0.00 0.00 3.14
236 276 5.557866 ACTCTAAAAAGTACATGGACCACC 58.442 41.667 3.84 0.00 0.00 4.61
245 285 3.298958 TGGACCACCAGCGATCTC 58.701 61.111 0.00 0.00 41.77 2.75
246 286 1.305297 TGGACCACCAGCGATCTCT 60.305 57.895 0.00 0.00 41.77 3.10
247 287 0.033503 TGGACCACCAGCGATCTCTA 60.034 55.000 0.00 0.00 41.77 2.43
248 288 1.333177 GGACCACCAGCGATCTCTAT 58.667 55.000 0.00 0.00 35.97 1.98
250 290 2.546795 GGACCACCAGCGATCTCTATTG 60.547 54.545 0.00 0.00 35.97 1.90
253 295 2.389059 CACCAGCGATCTCTATTGTCG 58.611 52.381 0.00 0.00 38.34 4.35
258 300 2.032722 AGCGATCTCTATTGTCGTCGTC 60.033 50.000 0.00 0.00 37.66 4.20
288 331 0.179200 GTTGTCGCCGCACCTTTATG 60.179 55.000 0.00 0.00 0.00 1.90
292 335 0.107410 TCGCCGCACCTTTATGGAAT 60.107 50.000 0.00 0.00 39.71 3.01
308 351 2.303022 TGGAATCTGACCTGACCTTGTC 59.697 50.000 0.00 0.00 0.00 3.18
319 362 3.007940 CCTGACCTTGTCTATGACAACCA 59.992 47.826 8.81 7.00 45.88 3.67
320 363 3.997021 CTGACCTTGTCTATGACAACCAC 59.003 47.826 8.81 4.72 45.88 4.16
321 364 3.389656 TGACCTTGTCTATGACAACCACA 59.610 43.478 8.81 6.76 45.88 4.17
421 475 6.507900 AGATGACATGAATCTACGTCGATTT 58.492 36.000 15.57 1.07 33.96 2.17
455 509 4.401925 ACAAACTCAAGGAGGATTGAAGG 58.598 43.478 16.02 0.00 38.66 3.46
456 510 2.797177 ACTCAAGGAGGATTGAAGGC 57.203 50.000 0.00 0.00 38.66 4.35
464 518 3.054508 AGGAGGATTGAAGGCTGAAAGAG 60.055 47.826 0.00 0.00 34.07 2.85
495 549 0.976641 TGAAGCGTCATCTCCAACCT 59.023 50.000 0.00 0.00 0.00 3.50
499 553 1.482593 AGCGTCATCTCCAACCTAAGG 59.517 52.381 0.00 0.00 0.00 2.69
501 555 1.473434 CGTCATCTCCAACCTAAGGGC 60.473 57.143 0.00 0.00 35.63 5.19
502 556 1.840635 GTCATCTCCAACCTAAGGGCT 59.159 52.381 0.00 0.00 35.63 5.19
503 557 1.839994 TCATCTCCAACCTAAGGGCTG 59.160 52.381 0.00 0.00 35.63 4.85
514 568 4.507969 AGGGCTGCACCTTTTGAG 57.492 55.556 0.00 0.00 37.69 3.02
517 571 2.278330 GGCTGCACCTTTTGAGGGG 61.278 63.158 0.50 0.00 34.51 4.79
522 576 2.634453 CTGCACCTTTTGAGGGGAAAAT 59.366 45.455 0.00 0.00 33.12 1.82
524 578 4.424842 TGCACCTTTTGAGGGGAAAATAT 58.575 39.130 0.00 0.00 33.12 1.28
551 605 1.192428 CTAAACTACTGGCCCGGAGT 58.808 55.000 6.15 6.15 0.00 3.85
552 606 1.553704 CTAAACTACTGGCCCGGAGTT 59.446 52.381 18.48 18.48 33.60 3.01
554 608 1.125711 AACTACTGGCCCGGAGTTGT 61.126 55.000 22.83 12.78 31.83 3.32
574 628 3.930012 CGCCCGAATCCCTCTCCC 61.930 72.222 0.00 0.00 0.00 4.30
579 633 2.812619 CGAATCCCTCTCCCAGCCC 61.813 68.421 0.00 0.00 0.00 5.19
620 674 1.587054 GGATCCATAGGCTCGTCGG 59.413 63.158 6.95 0.00 0.00 4.79
641 695 0.842635 GAAGCATGGAGGGGATGAGT 59.157 55.000 0.00 0.00 0.00 3.41
720 3579 9.103861 GAGTAAAACCAGATGAAAATCCTAGAG 57.896 37.037 0.00 0.00 0.00 2.43
751 3616 8.578151 TGGAGTAAATACAACAATTTGGGTAAC 58.422 33.333 0.78 0.09 37.00 2.50
763 3628 4.463050 TTTGGGTAACTGGACTTGGAAT 57.537 40.909 0.00 0.00 0.00 3.01
821 3690 3.539791 CAATCCAATGGCCGGCCC 61.540 66.667 41.75 24.44 34.56 5.80
822 3691 4.858942 AATCCAATGGCCGGCCCC 62.859 66.667 41.75 19.91 34.56 5.80
826 3695 4.883354 CAATGGCCGGCCCCTCTC 62.883 72.222 41.75 17.44 34.56 3.20
846 3717 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
872 3743 4.161377 GTGTATTTCTTCCTCTGGCTCTCT 59.839 45.833 0.00 0.00 0.00 3.10
874 3745 3.971245 TTTCTTCCTCTGGCTCTCTTC 57.029 47.619 0.00 0.00 0.00 2.87
875 3746 2.917713 TCTTCCTCTGGCTCTCTTCT 57.082 50.000 0.00 0.00 0.00 2.85
879 3750 1.113788 CCTCTGGCTCTCTTCTCCTG 58.886 60.000 0.00 0.00 0.00 3.86
885 3756 1.557269 GCTCTCTTCTCCTGCCCCAA 61.557 60.000 0.00 0.00 0.00 4.12
895 3766 1.308069 CCTGCCCCAAACATCTCACG 61.308 60.000 0.00 0.00 0.00 4.35
897 3768 2.700773 GCCCCAAACATCTCACGCC 61.701 63.158 0.00 0.00 0.00 5.68
949 3820 4.916314 GGCCGGAGATCCCTCGGA 62.916 72.222 19.05 0.00 40.85 4.55
951 3822 2.210711 GCCGGAGATCCCTCGGATT 61.211 63.158 19.05 0.00 43.27 3.01
952 3823 1.968310 CCGGAGATCCCTCGGATTC 59.032 63.158 12.00 0.00 43.27 2.52
953 3824 1.581954 CGGAGATCCCTCGGATTCG 59.418 63.158 0.00 0.00 43.27 3.34
954 3825 0.889638 CGGAGATCCCTCGGATTCGA 60.890 60.000 0.00 0.00 43.27 3.71
956 3827 1.896465 GGAGATCCCTCGGATTCGATT 59.104 52.381 0.00 0.00 43.27 3.34
957 3828 2.094442 GGAGATCCCTCGGATTCGATTC 60.094 54.545 0.00 0.00 43.27 2.52
958 3829 1.896465 AGATCCCTCGGATTCGATTCC 59.104 52.381 15.04 15.04 43.27 3.01
959 3830 1.618837 GATCCCTCGGATTCGATTCCA 59.381 52.381 22.58 11.16 43.27 3.53
960 3831 1.717032 TCCCTCGGATTCGATTCCAT 58.283 50.000 22.58 0.00 45.04 3.41
961 3832 2.047061 TCCCTCGGATTCGATTCCATT 58.953 47.619 22.58 0.00 45.04 3.16
962 3833 2.037251 TCCCTCGGATTCGATTCCATTC 59.963 50.000 22.58 0.00 45.04 2.67
963 3834 2.061773 CCTCGGATTCGATTCCATTCG 58.938 52.381 22.58 8.01 45.04 3.34
964 3835 2.288213 CCTCGGATTCGATTCCATTCGA 60.288 50.000 22.58 11.65 45.75 3.71
987 3869 3.660054 CGAGTCGAATCGAAGAGAAGA 57.340 47.619 29.50 0.00 45.56 2.87
988 3870 3.603379 CGAGTCGAATCGAAGAGAAGAG 58.397 50.000 29.50 0.00 45.56 2.85
989 3871 3.307512 CGAGTCGAATCGAAGAGAAGAGA 59.692 47.826 29.50 0.00 45.56 3.10
990 3872 4.201734 CGAGTCGAATCGAAGAGAAGAGAA 60.202 45.833 29.50 0.00 45.56 2.87
991 3873 5.503357 CGAGTCGAATCGAAGAGAAGAGAAT 60.503 44.000 29.50 0.00 45.56 2.40
1038 3920 2.434884 CTTGACGCGCTGATGGGT 60.435 61.111 5.73 0.00 37.78 4.51
1200 4082 3.659089 AAAGATCCACGACCCGGCG 62.659 63.158 0.00 0.00 37.29 6.46
1263 4159 7.010091 TCGATTTCGATTTCTTTCGATTCATCA 59.990 33.333 0.00 0.00 46.55 3.07
1266 4162 6.530913 TCGATTTCTTTCGATTCATCATCC 57.469 37.500 0.00 0.00 42.81 3.51
1267 4163 5.466728 TCGATTTCTTTCGATTCATCATCCC 59.533 40.000 0.00 0.00 42.81 3.85
1269 4165 4.778213 TTCTTTCGATTCATCATCCCCT 57.222 40.909 0.00 0.00 0.00 4.79
1273 4169 1.059098 CGATTCATCATCCCCTCCCA 58.941 55.000 0.00 0.00 0.00 4.37
1274 4170 1.421268 CGATTCATCATCCCCTCCCAA 59.579 52.381 0.00 0.00 0.00 4.12
1276 4172 0.926293 TTCATCATCCCCTCCCAACC 59.074 55.000 0.00 0.00 0.00 3.77
1281 4177 0.336048 CATCCCCTCCCAACCAACAT 59.664 55.000 0.00 0.00 0.00 2.71
1286 4212 2.292192 CCCCTCCCAACCAACATATGTT 60.292 50.000 15.47 15.47 39.12 2.71
1374 4300 2.125753 GCGAGAGGCTGGTCTGTG 60.126 66.667 0.00 0.00 39.11 3.66
1376 4302 1.668294 CGAGAGGCTGGTCTGTGTT 59.332 57.895 0.00 0.00 0.00 3.32
1378 4304 0.036858 GAGAGGCTGGTCTGTGTTCC 60.037 60.000 0.00 0.00 0.00 3.62
1390 4316 3.576550 GTCTGTGTTCCTCTTCCTCTTCT 59.423 47.826 0.00 0.00 0.00 2.85
1410 4357 4.392047 TCTTCACACACAGATTTGCATCT 58.608 39.130 0.00 0.00 40.79 2.90
1415 4362 4.213906 CACACACAGATTTGCATCTACACA 59.786 41.667 0.00 0.00 37.71 3.72
1418 4365 4.692625 ACACAGATTTGCATCTACACAGAC 59.307 41.667 0.00 0.00 37.71 3.51
1419 4366 4.692155 CACAGATTTGCATCTACACAGACA 59.308 41.667 0.00 0.00 37.71 3.41
1421 4368 5.353400 ACAGATTTGCATCTACACAGACATG 59.647 40.000 0.00 0.00 37.71 3.21
1422 4369 4.880120 AGATTTGCATCTACACAGACATGG 59.120 41.667 0.00 0.00 38.06 3.66
1463 4410 8.908786 TGAATTATCTATCCAGATTCCAACAC 57.091 34.615 0.00 0.00 41.84 3.32
1466 4413 9.512588 AATTATCTATCCAGATTCCAACACATC 57.487 33.333 0.00 0.00 41.84 3.06
1705 4652 1.132500 CATGAGGAAGGTAGACCCCC 58.868 60.000 0.00 0.00 36.42 5.40
1747 4700 8.255905 TGTTTACTAATCTTACTTAGGGTCTGC 58.744 37.037 0.00 0.00 33.79 4.26
1814 4767 0.025001 CGTTGGCGTGCTTTCGATAG 59.975 55.000 0.00 0.00 0.00 2.08
1978 4931 8.477709 CGAAACATCGTCTTACTGATTATTACC 58.522 37.037 0.00 0.00 0.00 2.85
2230 5183 4.569865 GGTTATGGTCTGGTCAGGGAATTT 60.570 45.833 0.00 0.00 0.00 1.82
2248 5201 2.754946 TTCTCGCCGAATACAAGGTT 57.245 45.000 0.00 0.00 0.00 3.50
2279 5251 3.550842 GCGCCAAAAGAGAACAATGTTCT 60.551 43.478 26.63 26.63 0.00 3.01
2281 5253 4.676924 CGCCAAAAGAGAACAATGTTCTTC 59.323 41.667 26.94 19.46 31.16 2.87
2283 5255 5.689068 GCCAAAAGAGAACAATGTTCTTCTG 59.311 40.000 26.94 19.80 31.16 3.02
2284 5256 5.689068 CCAAAAGAGAACAATGTTCTTCTGC 59.311 40.000 26.94 15.47 31.16 4.26
2288 5260 7.807977 AAGAGAACAATGTTCTTCTGCTTTA 57.192 32.000 26.94 0.00 0.00 1.85
2291 5263 7.663081 AGAGAACAATGTTCTTCTGCTTTATGA 59.337 33.333 26.94 0.00 0.00 2.15
2292 5264 7.814642 AGAACAATGTTCTTCTGCTTTATGAG 58.185 34.615 21.73 0.00 0.00 2.90
2293 5265 6.506500 ACAATGTTCTTCTGCTTTATGAGG 57.493 37.500 0.00 0.00 0.00 3.86
2307 5291 2.431954 ATGAGGCCAAGTTCTGATGG 57.568 50.000 5.01 0.00 39.80 3.51
2375 5360 0.902516 AAGGAAGCAGAGGAGCGTCT 60.903 55.000 0.00 0.00 41.74 4.18
2391 5376 1.682684 TCTGAACCGGGAGAGAGGC 60.683 63.158 6.32 0.00 0.00 4.70
2392 5377 2.683933 TGAACCGGGAGAGAGGCC 60.684 66.667 6.32 0.00 0.00 5.19
2412 5397 1.198759 ACCATAACAGAGGCCACCGT 61.199 55.000 5.01 0.00 0.00 4.83
2433 5418 4.561938 CGTGACGACTATAGGGAGAGATCT 60.562 50.000 0.00 0.00 0.00 2.75
2496 5484 0.678950 GAGAGAGGCCCTATGAGCAC 59.321 60.000 0.00 0.00 0.00 4.40
2732 5722 0.441533 CAGTCGCAATGTCTGAGTGC 59.558 55.000 0.00 0.00 42.42 4.40
2854 5847 2.026822 AGGTACCATCTGTTCTTGGCAG 60.027 50.000 15.94 0.00 36.41 4.85
2901 5894 3.363378 CGTGCACTCTGAGATTGTGTTTC 60.363 47.826 16.19 0.00 34.52 2.78
3020 6020 8.157476 ACCTCTGTCTGTCTTACATGTTAAAAT 58.843 33.333 2.30 0.00 0.00 1.82
3021 6021 8.446273 CCTCTGTCTGTCTTACATGTTAAAATG 58.554 37.037 2.30 3.94 0.00 2.32
3022 6022 9.208022 CTCTGTCTGTCTTACATGTTAAAATGA 57.792 33.333 12.75 0.00 0.00 2.57
3023 6023 9.725019 TCTGTCTGTCTTACATGTTAAAATGAT 57.275 29.630 12.75 0.00 0.00 2.45
3088 6088 6.239345 CTGGAAGAAACACTAGACAGGTAACT 60.239 42.308 0.00 0.00 45.15 2.24
3146 6146 9.520515 GATTGATGATATATACAAGGTTGGGTT 57.479 33.333 0.00 0.00 0.00 4.11
3149 6149 5.947663 TGATATATACAAGGTTGGGTTGGG 58.052 41.667 0.00 0.00 0.00 4.12
3150 6150 5.433712 TGATATATACAAGGTTGGGTTGGGT 59.566 40.000 0.00 0.00 0.00 4.51
3168 6168 1.509703 GTCGGACCTGGAAGAAACAC 58.490 55.000 0.00 0.00 34.07 3.32
3172 6172 2.561419 CGGACCTGGAAGAAACACTAGA 59.439 50.000 0.00 0.00 34.07 2.43
3173 6173 3.614390 CGGACCTGGAAGAAACACTAGAC 60.614 52.174 0.00 0.00 34.07 2.59
3181 6181 6.239345 CTGGAAGAAACACTAGACAGGTAACT 60.239 42.308 0.00 0.00 45.15 2.24
3201 6201 6.932356 AACTCGTAATCTCCGTCTTATACA 57.068 37.500 0.00 0.00 0.00 2.29
3202 6202 7.507733 AACTCGTAATCTCCGTCTTATACAT 57.492 36.000 0.00 0.00 0.00 2.29
3203 6203 6.900189 ACTCGTAATCTCCGTCTTATACATG 58.100 40.000 0.00 0.00 0.00 3.21
3204 6204 6.485984 ACTCGTAATCTCCGTCTTATACATGT 59.514 38.462 2.69 2.69 0.00 3.21
3206 6280 8.382030 TCGTAATCTCCGTCTTATACATGTTA 57.618 34.615 2.30 0.00 0.00 2.41
3213 6287 9.878667 TCTCCGTCTTATACATGTTAAAAATGA 57.121 29.630 2.30 0.00 0.00 2.57
3240 6314 8.018537 TGATGATATATATAAGGTTGGGTCGG 57.981 38.462 0.00 0.00 0.00 4.79
3241 6315 7.842236 TGATGATATATATAAGGTTGGGTCGGA 59.158 37.037 0.00 0.00 0.00 4.55
3242 6316 7.414222 TGATATATATAAGGTTGGGTCGGAC 57.586 40.000 0.00 0.00 0.00 4.79
3243 6317 6.381994 TGATATATATAAGGTTGGGTCGGACC 59.618 42.308 19.06 19.06 37.60 4.46
3244 6318 1.113788 TATAAGGTTGGGTCGGACCG 58.886 55.000 20.35 7.84 39.83 4.79
3245 6319 1.619807 ATAAGGTTGGGTCGGACCGG 61.620 60.000 20.35 0.00 39.83 5.28
3246 6320 2.728460 TAAGGTTGGGTCGGACCGGA 62.728 60.000 20.35 8.90 39.83 5.14
3247 6321 4.383861 GGTTGGGTCGGACCGGAC 62.384 72.222 20.35 19.05 39.83 4.79
3260 6334 2.678934 CGGACCGGACCTGGAAGA 60.679 66.667 20.77 0.00 34.07 2.87
3282 6356 1.897802 ACAGTAGGAAGGTAACCCGTG 59.102 52.381 0.00 0.00 35.12 4.94
3334 6410 9.520515 GATTGATGATATATACAAGGTTGGGTT 57.479 33.333 0.00 0.00 0.00 4.11
3385 6461 3.698040 GGTAATCCGTCACCTCTGTCTTA 59.302 47.826 0.00 0.00 0.00 2.10
3428 6839 2.168496 CGACCTGGAAGAACAGTAGGA 58.832 52.381 0.00 0.00 36.75 2.94
3442 6869 1.065126 AGTAGGAAGGTCTTGCATGCC 60.065 52.381 16.68 0.00 33.04 4.40
3521 6958 6.166982 GTTTCTGAATGCCTAGTCTTGTACT 58.833 40.000 0.00 0.00 42.62 2.73
3522 6959 5.584253 TCTGAATGCCTAGTCTTGTACTC 57.416 43.478 0.00 0.00 39.80 2.59
3523 6960 4.402793 TCTGAATGCCTAGTCTTGTACTCC 59.597 45.833 0.00 0.00 39.80 3.85
3524 6961 3.451178 TGAATGCCTAGTCTTGTACTCCC 59.549 47.826 0.00 0.00 39.80 4.30
3525 6962 2.921834 TGCCTAGTCTTGTACTCCCT 57.078 50.000 0.00 0.00 39.80 4.20
3526 6963 2.736347 TGCCTAGTCTTGTACTCCCTC 58.264 52.381 0.00 0.00 39.80 4.30
3527 6964 2.033372 GCCTAGTCTTGTACTCCCTCC 58.967 57.143 0.00 0.00 39.80 4.30
3528 6965 2.299521 CCTAGTCTTGTACTCCCTCCG 58.700 57.143 0.00 0.00 39.80 4.63
3529 6966 2.356947 CCTAGTCTTGTACTCCCTCCGT 60.357 54.545 0.00 0.00 39.80 4.69
3530 6967 2.305858 AGTCTTGTACTCCCTCCGTT 57.694 50.000 0.00 0.00 30.33 4.44
3531 6968 2.169330 AGTCTTGTACTCCCTCCGTTC 58.831 52.381 0.00 0.00 30.33 3.95
3532 6969 2.169330 GTCTTGTACTCCCTCCGTTCT 58.831 52.381 0.00 0.00 0.00 3.01
3533 6970 3.009916 AGTCTTGTACTCCCTCCGTTCTA 59.990 47.826 0.00 0.00 30.33 2.10
3534 6971 3.760684 GTCTTGTACTCCCTCCGTTCTAA 59.239 47.826 0.00 0.00 0.00 2.10
3535 6972 4.219288 GTCTTGTACTCCCTCCGTTCTAAA 59.781 45.833 0.00 0.00 0.00 1.85
3536 6973 5.021458 TCTTGTACTCCCTCCGTTCTAAAT 58.979 41.667 0.00 0.00 0.00 1.40
3537 6974 5.482878 TCTTGTACTCCCTCCGTTCTAAATT 59.517 40.000 0.00 0.00 0.00 1.82
3538 6975 6.664816 TCTTGTACTCCCTCCGTTCTAAATTA 59.335 38.462 0.00 0.00 0.00 1.40
3539 6976 6.212888 TGTACTCCCTCCGTTCTAAATTAC 57.787 41.667 0.00 0.00 0.00 1.89
3540 6977 5.954150 TGTACTCCCTCCGTTCTAAATTACT 59.046 40.000 0.00 0.00 0.00 2.24
3541 6978 5.595257 ACTCCCTCCGTTCTAAATTACTC 57.405 43.478 0.00 0.00 0.00 2.59
3542 6979 4.097589 ACTCCCTCCGTTCTAAATTACTCG 59.902 45.833 0.00 0.00 0.00 4.18
3543 6980 4.019174 TCCCTCCGTTCTAAATTACTCGT 58.981 43.478 0.00 0.00 0.00 4.18
3544 6981 4.096984 TCCCTCCGTTCTAAATTACTCGTC 59.903 45.833 0.00 0.00 0.00 4.20
3545 6982 4.142315 CCCTCCGTTCTAAATTACTCGTCA 60.142 45.833 0.00 0.00 0.00 4.35
3546 6983 4.797349 CCTCCGTTCTAAATTACTCGTCAC 59.203 45.833 0.00 0.00 0.00 3.67
3547 6984 5.375417 TCCGTTCTAAATTACTCGTCACA 57.625 39.130 0.00 0.00 0.00 3.58
3548 6985 5.396484 TCCGTTCTAAATTACTCGTCACAG 58.604 41.667 0.00 0.00 0.00 3.66
3549 6986 5.181811 TCCGTTCTAAATTACTCGTCACAGA 59.818 40.000 0.00 0.00 0.00 3.41
3550 6987 5.860182 CCGTTCTAAATTACTCGTCACAGAA 59.140 40.000 0.00 0.00 0.00 3.02
3551 6988 6.364165 CCGTTCTAAATTACTCGTCACAGAAA 59.636 38.462 0.00 0.00 0.00 2.52
3552 6989 7.063074 CCGTTCTAAATTACTCGTCACAGAAAT 59.937 37.037 0.00 0.00 0.00 2.17
3553 6990 7.893236 CGTTCTAAATTACTCGTCACAGAAATG 59.107 37.037 0.00 0.00 0.00 2.32
3554 6991 7.827819 TCTAAATTACTCGTCACAGAAATGG 57.172 36.000 0.00 0.00 0.00 3.16
3555 6992 7.608153 TCTAAATTACTCGTCACAGAAATGGA 58.392 34.615 0.00 0.00 0.00 3.41
3556 6993 8.258007 TCTAAATTACTCGTCACAGAAATGGAT 58.742 33.333 0.00 0.00 0.00 3.41
3557 6994 6.668541 AATTACTCGTCACAGAAATGGATG 57.331 37.500 0.00 0.00 0.00 3.51
3558 6995 3.685139 ACTCGTCACAGAAATGGATGT 57.315 42.857 0.00 0.00 0.00 3.06
3559 6996 4.801330 ACTCGTCACAGAAATGGATGTA 57.199 40.909 0.00 0.00 0.00 2.29
3560 6997 5.344743 ACTCGTCACAGAAATGGATGTAT 57.655 39.130 0.00 0.00 0.00 2.29
3561 6998 5.734720 ACTCGTCACAGAAATGGATGTATT 58.265 37.500 0.00 0.00 0.00 1.89
3562 6999 6.173339 ACTCGTCACAGAAATGGATGTATTT 58.827 36.000 0.00 0.00 33.19 1.40
3563 7000 7.327975 ACTCGTCACAGAAATGGATGTATTTA 58.672 34.615 0.00 0.00 30.78 1.40
3564 7001 7.492669 ACTCGTCACAGAAATGGATGTATTTAG 59.507 37.037 0.00 0.00 30.78 1.85
3565 7002 7.552459 TCGTCACAGAAATGGATGTATTTAGA 58.448 34.615 0.00 0.00 30.78 2.10
3566 7003 8.038351 TCGTCACAGAAATGGATGTATTTAGAA 58.962 33.333 0.00 0.00 30.78 2.10
3567 7004 8.116753 CGTCACAGAAATGGATGTATTTAGAAC 58.883 37.037 0.00 0.00 30.78 3.01
3568 7005 9.167311 GTCACAGAAATGGATGTATTTAGAACT 57.833 33.333 0.00 0.00 30.78 3.01
3597 7034 9.775539 AATACATCTAGATACATCCATACCTGT 57.224 33.333 4.54 0.00 0.00 4.00
3598 7035 7.473735 ACATCTAGATACATCCATACCTGTG 57.526 40.000 4.54 0.00 0.00 3.66
3599 7036 7.241628 ACATCTAGATACATCCATACCTGTGA 58.758 38.462 4.54 0.00 0.00 3.58
3600 7037 7.177568 ACATCTAGATACATCCATACCTGTGAC 59.822 40.741 4.54 0.00 0.00 3.67
3601 7038 6.610830 TCTAGATACATCCATACCTGTGACA 58.389 40.000 0.00 0.00 0.00 3.58
3602 7039 7.066781 TCTAGATACATCCATACCTGTGACAA 58.933 38.462 0.00 0.00 0.00 3.18
3603 7040 6.166984 AGATACATCCATACCTGTGACAAG 57.833 41.667 0.00 0.00 0.00 3.16
3604 7041 5.663106 AGATACATCCATACCTGTGACAAGT 59.337 40.000 0.00 0.00 0.00 3.16
3605 7042 6.839134 AGATACATCCATACCTGTGACAAGTA 59.161 38.462 0.00 0.00 0.00 2.24
3606 7043 5.755409 ACATCCATACCTGTGACAAGTAA 57.245 39.130 0.00 0.00 0.00 2.24
3607 7044 6.313519 ACATCCATACCTGTGACAAGTAAT 57.686 37.500 0.00 0.00 0.00 1.89
3608 7045 6.721318 ACATCCATACCTGTGACAAGTAATT 58.279 36.000 0.00 0.00 0.00 1.40
3609 7046 6.823689 ACATCCATACCTGTGACAAGTAATTC 59.176 38.462 0.00 0.00 0.00 2.17
3610 7047 5.416083 TCCATACCTGTGACAAGTAATTCG 58.584 41.667 0.00 0.00 0.00 3.34
3611 7048 4.570772 CCATACCTGTGACAAGTAATTCGG 59.429 45.833 0.00 0.00 0.00 4.30
3612 7049 5.416083 CATACCTGTGACAAGTAATTCGGA 58.584 41.667 0.00 0.00 0.00 4.55
3613 7050 4.345859 ACCTGTGACAAGTAATTCGGAA 57.654 40.909 0.00 0.00 0.00 4.30
3614 7051 4.062991 ACCTGTGACAAGTAATTCGGAAC 58.937 43.478 0.00 0.00 0.00 3.62
3650 7087 6.199937 AGATTTAATTTGCACTGCCAGTAG 57.800 37.500 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 4.620609 GCGATTGTGCATGTGTTTTTATGA 59.379 37.500 0.00 0.00 34.15 2.15
60 61 1.373590 CCACGTATGCCGGGAAAAGG 61.374 60.000 0.00 0.00 45.03 3.11
133 152 9.327731 ACTGAAAACCCCATAAAAATGGTATAA 57.672 29.630 3.84 0.00 40.06 0.98
135 154 7.806680 ACTGAAAACCCCATAAAAATGGTAT 57.193 32.000 3.84 0.00 40.06 2.73
141 160 7.509546 TGCATAAACTGAAAACCCCATAAAAA 58.490 30.769 0.00 0.00 0.00 1.94
156 175 7.114811 GGCGGTAATAAAATCATGCATAAACTG 59.885 37.037 0.00 0.00 0.00 3.16
165 184 5.242069 TGTGTGGCGGTAATAAAATCATG 57.758 39.130 0.00 0.00 0.00 3.07
232 262 2.748605 GACAATAGAGATCGCTGGTGG 58.251 52.381 9.48 0.00 0.00 4.61
236 276 2.286477 ACGACGACAATAGAGATCGCTG 60.286 50.000 9.48 0.00 39.47 5.18
238 278 2.286242 TGACGACGACAATAGAGATCGC 60.286 50.000 0.00 0.00 39.47 4.58
239 279 3.536833 CTGACGACGACAATAGAGATCG 58.463 50.000 0.00 0.00 41.60 3.69
240 280 3.560481 TCCTGACGACGACAATAGAGATC 59.440 47.826 0.00 0.00 0.00 2.75
241 281 3.542648 TCCTGACGACGACAATAGAGAT 58.457 45.455 0.00 0.00 0.00 2.75
242 282 2.981898 TCCTGACGACGACAATAGAGA 58.018 47.619 0.00 0.00 0.00 3.10
243 283 3.312697 TCATCCTGACGACGACAATAGAG 59.687 47.826 0.00 0.00 0.00 2.43
244 284 3.275999 TCATCCTGACGACGACAATAGA 58.724 45.455 0.00 0.00 0.00 1.98
245 285 3.622828 CTCATCCTGACGACGACAATAG 58.377 50.000 0.00 0.00 0.00 1.73
246 286 2.223502 GCTCATCCTGACGACGACAATA 60.224 50.000 0.00 0.00 0.00 1.90
247 287 1.469940 GCTCATCCTGACGACGACAAT 60.470 52.381 0.00 0.00 0.00 2.71
248 288 0.109272 GCTCATCCTGACGACGACAA 60.109 55.000 0.00 0.00 0.00 3.18
250 290 1.226717 GGCTCATCCTGACGACGAC 60.227 63.158 0.00 0.00 0.00 4.34
253 295 1.078759 CAACGGCTCATCCTGACGAC 61.079 60.000 0.00 0.00 0.00 4.34
258 300 2.456119 GCGACAACGGCTCATCCTG 61.456 63.158 0.00 0.00 40.15 3.86
288 331 2.569404 AGACAAGGTCAGGTCAGATTCC 59.431 50.000 0.00 0.00 36.50 3.01
292 335 3.764434 GTCATAGACAAGGTCAGGTCAGA 59.236 47.826 0.00 0.00 36.50 3.27
308 351 6.042143 AGCAAAAACTTTGTGGTTGTCATAG 58.958 36.000 1.45 0.00 0.00 2.23
319 362 3.871485 TGATGGCAAGCAAAAACTTTGT 58.129 36.364 0.00 0.00 0.00 2.83
320 363 4.879104 TTGATGGCAAGCAAAAACTTTG 57.121 36.364 0.00 0.00 0.00 2.77
321 364 5.824097 AGATTTGATGGCAAGCAAAAACTTT 59.176 32.000 8.87 0.00 44.28 2.66
374 417 0.834687 TGGGGAAGCGACAGTAGGTT 60.835 55.000 0.00 0.00 0.00 3.50
375 418 0.834687 TTGGGGAAGCGACAGTAGGT 60.835 55.000 0.00 0.00 0.00 3.08
382 425 0.462759 CATCTCCTTGGGGAAGCGAC 60.463 60.000 0.00 0.00 41.69 5.19
421 475 0.672401 GAGTTTGTTCATCGGGGCGA 60.672 55.000 0.00 0.00 41.13 5.54
471 525 4.321230 GGTTGGAGATGACGCTTCATTTTT 60.321 41.667 7.18 0.00 42.95 1.94
474 528 2.026822 AGGTTGGAGATGACGCTTCATT 60.027 45.455 7.18 0.00 42.95 2.57
495 549 1.547675 CCTCAAAAGGTGCAGCCCTTA 60.548 52.381 13.29 0.00 44.14 2.69
499 553 2.278330 CCCCTCAAAAGGTGCAGCC 61.278 63.158 13.29 4.65 41.59 4.85
501 555 1.703411 TTTCCCCTCAAAAGGTGCAG 58.297 50.000 0.00 0.00 41.59 4.41
502 556 2.166907 TTTTCCCCTCAAAAGGTGCA 57.833 45.000 0.00 0.00 41.59 4.57
503 557 5.419542 GAATATTTTCCCCTCAAAAGGTGC 58.580 41.667 0.00 0.00 41.59 5.01
522 576 5.367644 GGGCCAGTAGTTTAGGTTAGGAATA 59.632 44.000 4.39 0.00 0.00 1.75
524 578 3.520721 GGGCCAGTAGTTTAGGTTAGGAA 59.479 47.826 4.39 0.00 0.00 3.36
531 585 0.464452 CTCCGGGCCAGTAGTTTAGG 59.536 60.000 4.39 0.00 0.00 2.69
585 639 3.839432 CGACTCCCTTCCGCCTCC 61.839 72.222 0.00 0.00 0.00 4.30
598 652 0.178987 ACGAGCCTATGGATCCGACT 60.179 55.000 7.39 0.00 34.17 4.18
620 674 0.548031 TCATCCCCTCCATGCTTCAC 59.452 55.000 0.00 0.00 0.00 3.18
657 711 3.274288 GTGATTCTTTCCCTCTTGCGAT 58.726 45.455 0.00 0.00 0.00 4.58
658 712 2.038426 TGTGATTCTTTCCCTCTTGCGA 59.962 45.455 0.00 0.00 0.00 5.10
691 767 8.059798 AGGATTTTCATCTGGTTTTACTCATG 57.940 34.615 0.00 0.00 0.00 3.07
694 770 9.103861 CTCTAGGATTTTCATCTGGTTTTACTC 57.896 37.037 0.00 0.00 0.00 2.59
695 771 8.049721 CCTCTAGGATTTTCATCTGGTTTTACT 58.950 37.037 0.00 0.00 37.39 2.24
696 772 8.047310 TCCTCTAGGATTTTCATCTGGTTTTAC 58.953 37.037 0.00 0.00 39.78 2.01
720 3579 7.812669 CCAAATTGTTGTATTTACTCCAACTCC 59.187 37.037 0.00 0.00 39.30 3.85
733 3592 6.311735 AGTCCAGTTACCCAAATTGTTGTAT 58.688 36.000 0.00 0.00 32.40 2.29
734 3593 5.697067 AGTCCAGTTACCCAAATTGTTGTA 58.303 37.500 0.00 0.00 32.40 2.41
742 3607 3.955524 TTCCAAGTCCAGTTACCCAAA 57.044 42.857 0.00 0.00 0.00 3.28
751 3616 6.579666 TGAAATTTCAGATTCCAAGTCCAG 57.420 37.500 16.91 0.00 32.50 3.86
763 3628 6.400568 GCCCAAATCTCAATGAAATTTCAGA 58.599 36.000 24.17 16.48 41.08 3.27
821 3690 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
822 3691 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
823 3692 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
824 3693 4.648762 ACAGAGAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
825 3694 4.403752 CACAGAGAGAGAGAGAGAGAGAGA 59.596 50.000 0.00 0.00 0.00 3.10
826 3695 4.442612 CCACAGAGAGAGAGAGAGAGAGAG 60.443 54.167 0.00 0.00 0.00 3.20
846 3717 3.010420 GCCAGAGGAAGAAATACACCAC 58.990 50.000 0.00 0.00 0.00 4.16
872 3743 1.004745 GAGATGTTTGGGGCAGGAGAA 59.995 52.381 0.00 0.00 0.00 2.87
874 3745 0.329261 TGAGATGTTTGGGGCAGGAG 59.671 55.000 0.00 0.00 0.00 3.69
875 3746 0.038166 GTGAGATGTTTGGGGCAGGA 59.962 55.000 0.00 0.00 0.00 3.86
879 3750 2.700773 GGCGTGAGATGTTTGGGGC 61.701 63.158 0.00 0.00 0.00 5.80
920 3791 0.676782 CTCCGGCCACAAACCCTAAG 60.677 60.000 2.24 0.00 0.00 2.18
952 3823 2.376956 GACTCGACTCGAATGGAATCG 58.623 52.381 2.16 0.00 44.04 3.34
953 3824 2.031807 TCGACTCGACTCGAATGGAATC 59.968 50.000 13.68 0.00 39.71 2.52
954 3825 2.014857 TCGACTCGACTCGAATGGAAT 58.985 47.619 13.68 0.00 39.71 3.01
956 3827 1.445871 TTCGACTCGACTCGAATGGA 58.554 50.000 21.06 4.59 45.44 3.41
957 3828 3.990546 TTCGACTCGACTCGAATGG 57.009 52.632 21.06 0.00 45.44 3.16
963 3834 2.604011 TCTCTTCGATTCGACTCGACTC 59.396 50.000 25.06 4.67 46.53 3.36
964 3835 2.619147 TCTCTTCGATTCGACTCGACT 58.381 47.619 25.06 0.00 46.53 4.18
970 3852 4.668837 CGATTCTCTTCTCTTCGATTCGAC 59.331 45.833 8.55 0.00 34.89 4.20
987 3869 2.160615 CGCGTCCATCTCTATCGATTCT 59.839 50.000 1.71 0.00 0.00 2.40
988 3870 2.510874 CGCGTCCATCTCTATCGATTC 58.489 52.381 1.71 0.00 0.00 2.52
989 3871 1.401670 GCGCGTCCATCTCTATCGATT 60.402 52.381 8.43 0.00 0.00 3.34
990 3872 0.169230 GCGCGTCCATCTCTATCGAT 59.831 55.000 8.43 2.16 0.00 3.59
991 3873 1.164041 TGCGCGTCCATCTCTATCGA 61.164 55.000 8.43 0.00 0.00 3.59
1023 3905 2.434185 GAACCCATCAGCGCGTCA 60.434 61.111 8.43 0.00 0.00 4.35
1038 3920 4.047059 GTCAGGTCCCGCGACGAA 62.047 66.667 8.23 0.00 40.17 3.85
1200 4082 5.139435 AGGATAAAAACCTTTGCTTGAGC 57.861 39.130 0.00 0.00 36.56 4.26
1263 4159 1.994399 TATGTTGGTTGGGAGGGGAT 58.006 50.000 0.00 0.00 0.00 3.85
1266 4162 2.826674 ACATATGTTGGTTGGGAGGG 57.173 50.000 1.41 0.00 0.00 4.30
1273 4169 4.559153 GAAGCTGCAAACATATGTTGGTT 58.441 39.130 21.46 18.54 38.44 3.67
1274 4170 3.366273 CGAAGCTGCAAACATATGTTGGT 60.366 43.478 21.46 11.55 38.44 3.67
1276 4172 4.082274 TCGAAGCTGCAAACATATGTTG 57.918 40.909 21.46 15.57 38.44 3.33
1281 4177 2.028112 AGGACTCGAAGCTGCAAACATA 60.028 45.455 1.02 0.00 0.00 2.29
1286 4212 1.293498 GGAGGACTCGAAGCTGCAA 59.707 57.895 1.02 0.00 0.00 4.08
1374 4300 4.202264 TGTGTGAAGAAGAGGAAGAGGAAC 60.202 45.833 0.00 0.00 0.00 3.62
1376 4302 3.322254 GTGTGTGAAGAAGAGGAAGAGGA 59.678 47.826 0.00 0.00 0.00 3.71
1378 4304 4.038522 TCTGTGTGTGAAGAAGAGGAAGAG 59.961 45.833 0.00 0.00 0.00 2.85
1390 4316 5.049474 GTGTAGATGCAAATCTGTGTGTGAA 60.049 40.000 0.00 0.00 32.36 3.18
1410 4357 1.055849 AGCACCACCATGTCTGTGTA 58.944 50.000 7.34 0.00 31.71 2.90
1415 4362 3.091545 CCAAAATAGCACCACCATGTCT 58.908 45.455 0.00 0.00 0.00 3.41
1418 4365 3.257873 TCAACCAAAATAGCACCACCATG 59.742 43.478 0.00 0.00 0.00 3.66
1419 4366 3.505386 TCAACCAAAATAGCACCACCAT 58.495 40.909 0.00 0.00 0.00 3.55
1421 4368 4.535526 ATTCAACCAAAATAGCACCACC 57.464 40.909 0.00 0.00 0.00 4.61
1422 4369 7.547227 AGATAATTCAACCAAAATAGCACCAC 58.453 34.615 0.00 0.00 0.00 4.16
1463 4410 1.666700 GCAGCAGCAGAAAGAGAGATG 59.333 52.381 0.00 0.00 41.58 2.90
1466 4413 1.080298 CAGCAGCAGCAGAAAGAGAG 58.920 55.000 3.17 0.00 45.49 3.20
1506 4453 1.269778 CCGCGCCTGATCTTCTTATCA 60.270 52.381 0.00 0.00 34.72 2.15
1542 4489 2.989824 ACCTCCACGACGTCCTGG 60.990 66.667 23.08 23.08 0.00 4.45
1705 4652 1.986882 AACACAAAGAGAAGGCCAGG 58.013 50.000 5.01 0.00 0.00 4.45
1747 4700 3.118884 CCCAGGCTTGAATTCAATCCAAG 60.119 47.826 32.16 25.18 42.81 3.61
1814 4767 3.683340 GGATCCGACTTTTTGGTGTCTAC 59.317 47.826 0.00 0.00 0.00 2.59
1891 4844 4.726704 CGAATAATTTGGCGTAGGTTTTCG 59.273 41.667 0.00 0.00 0.00 3.46
1978 4931 6.638096 TCATGTAATTATCACCAATGGCTG 57.362 37.500 0.00 0.00 0.00 4.85
1988 4941 6.363882 TGGTTGAGGCATCATGTAATTATCA 58.636 36.000 0.03 0.00 34.73 2.15
2230 5183 2.756760 ACTAACCTTGTATTCGGCGAGA 59.243 45.455 10.46 1.60 0.00 4.04
2279 5251 3.439857 ACTTGGCCTCATAAAGCAGAA 57.560 42.857 3.32 0.00 0.00 3.02
2281 5253 3.128242 CAGAACTTGGCCTCATAAAGCAG 59.872 47.826 3.32 0.00 0.00 4.24
2283 5255 3.347216 TCAGAACTTGGCCTCATAAAGC 58.653 45.455 3.32 0.00 0.00 3.51
2284 5256 4.337555 CCATCAGAACTTGGCCTCATAAAG 59.662 45.833 3.32 0.39 0.00 1.85
2288 5260 1.637553 ACCATCAGAACTTGGCCTCAT 59.362 47.619 3.32 0.00 36.41 2.90
2291 5263 2.269940 ACTACCATCAGAACTTGGCCT 58.730 47.619 3.32 0.00 36.41 5.19
2292 5264 2.749621 CAACTACCATCAGAACTTGGCC 59.250 50.000 0.00 0.00 36.41 5.36
2293 5265 2.162408 GCAACTACCATCAGAACTTGGC 59.838 50.000 0.00 0.00 36.41 4.52
2307 5291 2.666026 GCAGCCTGAAAAAGCAACTAC 58.334 47.619 0.00 0.00 0.00 2.73
2375 5360 2.683933 GGCCTCTCTCCCGGTTCA 60.684 66.667 0.00 0.00 0.00 3.18
2391 5376 0.394352 GGTGGCCTCTGTTATGGTGG 60.394 60.000 3.32 0.00 0.00 4.61
2392 5377 0.744414 CGGTGGCCTCTGTTATGGTG 60.744 60.000 3.32 0.00 0.00 4.17
2412 5397 5.188163 CCTAGATCTCTCCCTATAGTCGTCA 59.812 48.000 0.00 0.00 0.00 4.35
2433 5418 1.327690 GGTCACGGTCATGCTCCCTA 61.328 60.000 0.00 0.00 0.00 3.53
2475 5463 1.062581 TGCTCATAGGGCCTCTCTCTT 60.063 52.381 10.74 0.00 0.00 2.85
2496 5484 0.256464 AGTCTGACCCTCTACCTCCG 59.744 60.000 3.76 0.00 0.00 4.63
2640 5628 8.416329 ACTTGAAATGATTAATAACCATGCCTC 58.584 33.333 0.00 0.00 0.00 4.70
2939 5933 2.168313 TCATCATACGGCTTTCAGCTCA 59.832 45.455 0.00 0.00 41.99 4.26
3146 6146 0.765135 TTTCTTCCAGGTCCGACCCA 60.765 55.000 14.32 0.00 39.75 4.51
3149 6149 1.070289 AGTGTTTCTTCCAGGTCCGAC 59.930 52.381 0.00 0.00 0.00 4.79
3150 6150 1.420430 AGTGTTTCTTCCAGGTCCGA 58.580 50.000 0.00 0.00 0.00 4.55
3168 6168 5.050227 CGGAGATTACGAGTTACCTGTCTAG 60.050 48.000 0.00 0.00 0.00 2.43
3172 6172 3.350833 ACGGAGATTACGAGTTACCTGT 58.649 45.455 0.00 0.00 34.93 4.00
3173 6173 3.626670 AGACGGAGATTACGAGTTACCTG 59.373 47.826 0.00 0.00 34.93 4.00
3181 6181 6.872628 ACATGTATAAGACGGAGATTACGA 57.127 37.500 0.00 0.00 34.93 3.43
3187 6187 9.878667 TCATTTTTAACATGTATAAGACGGAGA 57.121 29.630 0.00 0.00 0.00 3.71
3223 6297 2.892852 CGGTCCGACCCAACCTTATATA 59.107 50.000 4.91 0.00 33.75 0.86
3224 6298 1.690352 CGGTCCGACCCAACCTTATAT 59.310 52.381 4.91 0.00 33.75 0.86
3225 6299 1.113788 CGGTCCGACCCAACCTTATA 58.886 55.000 4.91 0.00 33.75 0.98
3226 6300 1.619807 CCGGTCCGACCCAACCTTAT 61.620 60.000 14.39 0.00 33.75 1.73
3227 6301 2.285024 CCGGTCCGACCCAACCTTA 61.285 63.158 14.39 0.00 33.75 2.69
3228 6302 3.633116 CCGGTCCGACCCAACCTT 61.633 66.667 14.39 0.00 33.75 3.50
3229 6303 4.626402 TCCGGTCCGACCCAACCT 62.626 66.667 14.39 0.00 33.75 3.50
3243 6317 1.823169 TTTCTTCCAGGTCCGGTCCG 61.823 60.000 12.29 3.60 0.00 4.79
3244 6318 0.321387 GTTTCTTCCAGGTCCGGTCC 60.321 60.000 10.05 10.05 0.00 4.46
3245 6319 0.395312 TGTTTCTTCCAGGTCCGGTC 59.605 55.000 0.00 0.00 0.00 4.79
3246 6320 0.396811 CTGTTTCTTCCAGGTCCGGT 59.603 55.000 0.00 0.00 0.00 5.28
3247 6321 0.396811 ACTGTTTCTTCCAGGTCCGG 59.603 55.000 0.00 0.00 34.16 5.14
3248 6322 2.353803 CCTACTGTTTCTTCCAGGTCCG 60.354 54.545 0.00 0.00 34.16 4.79
3249 6323 2.904434 TCCTACTGTTTCTTCCAGGTCC 59.096 50.000 0.00 0.00 34.16 4.46
3250 6324 4.563786 CCTTCCTACTGTTTCTTCCAGGTC 60.564 50.000 0.00 0.00 34.16 3.85
3251 6325 3.328050 CCTTCCTACTGTTTCTTCCAGGT 59.672 47.826 0.00 0.00 34.16 4.00
3252 6326 3.328050 ACCTTCCTACTGTTTCTTCCAGG 59.672 47.826 0.00 0.00 34.16 4.45
3253 6327 4.625607 ACCTTCCTACTGTTTCTTCCAG 57.374 45.455 0.00 0.00 36.01 3.86
3254 6328 5.221783 GGTTACCTTCCTACTGTTTCTTCCA 60.222 44.000 0.00 0.00 0.00 3.53
3255 6329 5.243981 GGTTACCTTCCTACTGTTTCTTCC 58.756 45.833 0.00 0.00 0.00 3.46
3256 6330 5.243981 GGGTTACCTTCCTACTGTTTCTTC 58.756 45.833 0.00 0.00 0.00 2.87
3257 6331 4.262765 CGGGTTACCTTCCTACTGTTTCTT 60.263 45.833 0.00 0.00 33.28 2.52
3258 6332 3.260128 CGGGTTACCTTCCTACTGTTTCT 59.740 47.826 0.00 0.00 33.28 2.52
3259 6333 3.007290 ACGGGTTACCTTCCTACTGTTTC 59.993 47.826 0.00 0.00 33.28 2.78
3260 6334 2.974794 ACGGGTTACCTTCCTACTGTTT 59.025 45.455 0.00 0.00 33.28 2.83
3334 6410 0.765135 TTTCTTCCAGGTCCGGTCCA 60.765 55.000 20.28 0.00 0.00 4.02
3385 6461 8.181573 GTCGTATCATCAACCATTTTAACATGT 58.818 33.333 0.00 0.00 0.00 3.21
3428 6839 2.633967 TCAATTTGGCATGCAAGACCTT 59.366 40.909 21.36 1.86 0.00 3.50
3442 6869 7.409697 CCAACCTTCTATACGTCATCAATTTG 58.590 38.462 0.00 0.00 0.00 2.32
3521 6958 4.019174 ACGAGTAATTTAGAACGGAGGGA 58.981 43.478 0.00 0.00 0.00 4.20
3522 6959 4.142315 TGACGAGTAATTTAGAACGGAGGG 60.142 45.833 0.00 0.00 0.00 4.30
3523 6960 4.797349 GTGACGAGTAATTTAGAACGGAGG 59.203 45.833 0.00 0.00 0.00 4.30
3524 6961 5.396484 TGTGACGAGTAATTTAGAACGGAG 58.604 41.667 0.00 0.00 0.00 4.63
3525 6962 5.181811 TCTGTGACGAGTAATTTAGAACGGA 59.818 40.000 0.00 0.00 0.00 4.69
3526 6963 5.396484 TCTGTGACGAGTAATTTAGAACGG 58.604 41.667 0.00 0.00 0.00 4.44
3527 6964 6.922980 TTCTGTGACGAGTAATTTAGAACG 57.077 37.500 0.00 0.00 0.00 3.95
3528 6965 8.169268 CCATTTCTGTGACGAGTAATTTAGAAC 58.831 37.037 0.00 0.00 0.00 3.01
3529 6966 8.092068 TCCATTTCTGTGACGAGTAATTTAGAA 58.908 33.333 0.00 0.00 0.00 2.10
3530 6967 7.608153 TCCATTTCTGTGACGAGTAATTTAGA 58.392 34.615 0.00 0.00 0.00 2.10
3531 6968 7.827819 TCCATTTCTGTGACGAGTAATTTAG 57.172 36.000 0.00 0.00 0.00 1.85
3532 6969 7.822334 ACATCCATTTCTGTGACGAGTAATTTA 59.178 33.333 0.00 0.00 0.00 1.40
3533 6970 6.655003 ACATCCATTTCTGTGACGAGTAATTT 59.345 34.615 0.00 0.00 0.00 1.82
3534 6971 6.173339 ACATCCATTTCTGTGACGAGTAATT 58.827 36.000 0.00 0.00 0.00 1.40
3535 6972 5.734720 ACATCCATTTCTGTGACGAGTAAT 58.265 37.500 0.00 0.00 0.00 1.89
3536 6973 5.147330 ACATCCATTTCTGTGACGAGTAA 57.853 39.130 0.00 0.00 0.00 2.24
3537 6974 4.801330 ACATCCATTTCTGTGACGAGTA 57.199 40.909 0.00 0.00 0.00 2.59
3538 6975 3.685139 ACATCCATTTCTGTGACGAGT 57.315 42.857 0.00 0.00 0.00 4.18
3539 6976 6.668541 AAATACATCCATTTCTGTGACGAG 57.331 37.500 0.00 0.00 0.00 4.18
3540 6977 7.552459 TCTAAATACATCCATTTCTGTGACGA 58.448 34.615 0.00 0.00 30.84 4.20
3541 6978 7.770801 TCTAAATACATCCATTTCTGTGACG 57.229 36.000 0.00 0.00 30.84 4.35
3542 6979 9.167311 AGTTCTAAATACATCCATTTCTGTGAC 57.833 33.333 0.00 0.00 30.84 3.67
3571 7008 9.775539 ACAGGTATGGATGTATCTAGATGTATT 57.224 33.333 15.79 0.00 0.00 1.89
3572 7009 9.194972 CACAGGTATGGATGTATCTAGATGTAT 57.805 37.037 15.79 9.11 0.00 2.29
3573 7010 8.390921 TCACAGGTATGGATGTATCTAGATGTA 58.609 37.037 15.79 4.44 0.00 2.29
3574 7011 7.177568 GTCACAGGTATGGATGTATCTAGATGT 59.822 40.741 15.79 1.25 0.00 3.06
3575 7012 7.177392 TGTCACAGGTATGGATGTATCTAGATG 59.823 40.741 15.79 0.00 0.00 2.90
3576 7013 7.241628 TGTCACAGGTATGGATGTATCTAGAT 58.758 38.462 10.73 10.73 0.00 1.98
3577 7014 6.610830 TGTCACAGGTATGGATGTATCTAGA 58.389 40.000 0.00 0.00 0.00 2.43
3578 7015 6.901081 TGTCACAGGTATGGATGTATCTAG 57.099 41.667 0.00 0.00 0.00 2.43
3579 7016 6.839134 ACTTGTCACAGGTATGGATGTATCTA 59.161 38.462 0.00 0.00 0.00 1.98
3580 7017 5.663106 ACTTGTCACAGGTATGGATGTATCT 59.337 40.000 0.00 0.00 0.00 1.98
3581 7018 5.918608 ACTTGTCACAGGTATGGATGTATC 58.081 41.667 0.00 0.00 0.00 2.24
3582 7019 5.957771 ACTTGTCACAGGTATGGATGTAT 57.042 39.130 0.00 0.00 0.00 2.29
3583 7020 6.860790 TTACTTGTCACAGGTATGGATGTA 57.139 37.500 0.00 0.00 0.00 2.29
3584 7021 5.755409 TTACTTGTCACAGGTATGGATGT 57.245 39.130 0.00 0.00 0.00 3.06
3585 7022 6.018751 CGAATTACTTGTCACAGGTATGGATG 60.019 42.308 0.00 0.00 0.00 3.51
3586 7023 6.049149 CGAATTACTTGTCACAGGTATGGAT 58.951 40.000 0.00 0.00 0.00 3.41
3587 7024 5.416083 CGAATTACTTGTCACAGGTATGGA 58.584 41.667 0.00 0.00 0.00 3.41
3588 7025 4.570772 CCGAATTACTTGTCACAGGTATGG 59.429 45.833 0.00 0.00 0.00 2.74
3589 7026 5.416083 TCCGAATTACTTGTCACAGGTATG 58.584 41.667 0.00 0.00 0.00 2.39
3590 7027 5.670792 TCCGAATTACTTGTCACAGGTAT 57.329 39.130 0.00 0.00 0.00 2.73
3591 7028 5.232463 GTTCCGAATTACTTGTCACAGGTA 58.768 41.667 0.00 0.00 0.00 3.08
3592 7029 4.062991 GTTCCGAATTACTTGTCACAGGT 58.937 43.478 0.00 0.00 0.00 4.00
3593 7030 3.122948 CGTTCCGAATTACTTGTCACAGG 59.877 47.826 0.00 0.00 0.00 4.00
3594 7031 3.122948 CCGTTCCGAATTACTTGTCACAG 59.877 47.826 0.00 0.00 0.00 3.66
3595 7032 3.061322 CCGTTCCGAATTACTTGTCACA 58.939 45.455 0.00 0.00 0.00 3.58
3596 7033 3.319755 TCCGTTCCGAATTACTTGTCAC 58.680 45.455 0.00 0.00 0.00 3.67
3597 7034 3.581755 CTCCGTTCCGAATTACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
3598 7035 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
3599 7036 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
3600 7037 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
3601 7038 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
3602 7039 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
3603 7040 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
3604 7041 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
3605 7042 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
3606 7043 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
3607 7044 0.251297 TGTACTCCCTCCGTTCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
3608 7045 0.251297 TTGTACTCCCTCCGTTCCGA 60.251 55.000 0.00 0.00 0.00 4.55
3609 7046 0.172803 CTTGTACTCCCTCCGTTCCG 59.827 60.000 0.00 0.00 0.00 4.30
3610 7047 1.553706 TCTTGTACTCCCTCCGTTCC 58.446 55.000 0.00 0.00 0.00 3.62
3611 7048 3.889520 AATCTTGTACTCCCTCCGTTC 57.110 47.619 0.00 0.00 0.00 3.95
3612 7049 5.750352 TTAAATCTTGTACTCCCTCCGTT 57.250 39.130 0.00 0.00 0.00 4.44
3613 7050 5.952347 ATTAAATCTTGTACTCCCTCCGT 57.048 39.130 0.00 0.00 0.00 4.69
3614 7051 6.458342 GCAAATTAAATCTTGTACTCCCTCCG 60.458 42.308 0.00 0.00 0.00 4.63
3615 7052 6.377146 TGCAAATTAAATCTTGTACTCCCTCC 59.623 38.462 0.00 0.00 0.00 4.30
3616 7053 7.121315 AGTGCAAATTAAATCTTGTACTCCCTC 59.879 37.037 10.96 0.00 42.52 4.30
3617 7054 6.948309 AGTGCAAATTAAATCTTGTACTCCCT 59.052 34.615 10.96 0.00 42.52 4.20
3618 7055 7.029563 CAGTGCAAATTAAATCTTGTACTCCC 58.970 38.462 12.79 0.00 43.74 4.30
3619 7056 6.528072 GCAGTGCAAATTAAATCTTGTACTCC 59.472 38.462 11.09 4.74 43.74 3.85
3620 7057 6.528072 GGCAGTGCAAATTAAATCTTGTACTC 59.472 38.462 18.61 9.55 43.74 2.59
3621 7058 6.015519 TGGCAGTGCAAATTAAATCTTGTACT 60.016 34.615 18.61 10.96 45.61 2.73


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

AutoCloner maintained by Alex Coulton.