Multiple sequence alignment - TraesCS4D01G275700

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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 TraesCS4D01G275700 chr4D 100.000 4172 0 0 1 4172 446654721 446650550 0.000000e+00 7705.0
1 TraesCS4D01G275700 chr4D 81.074 391 61 12 3403 3785 405036661 405036276 2.440000e-77 300.0
2 TraesCS4D01G275700 chr4D 80.114 352 46 19 3399 3738 446650984 446651323 1.500000e-59 241.0
3 TraesCS4D01G275700 chr4B 93.139 3148 135 35 41 3137 558729053 558725936 0.000000e+00 4542.0
4 TraesCS4D01G275700 chr4B 89.527 296 20 6 3887 4172 558725517 558725223 8.520000e-97 364.0
5 TraesCS4D01G275700 chr4B 93.750 48 3 0 3149 3196 558725895 558725848 5.790000e-09 73.1
6 TraesCS4D01G275700 chr4A 90.058 3299 188 61 23 3221 21050656 21053914 0.000000e+00 4146.0
7 TraesCS4D01G275700 chr4A 87.708 301 19 6 3886 4172 21057721 21058017 6.680000e-88 335.0
8 TraesCS4D01G275700 chr4A 91.176 68 5 1 3244 3311 21057059 21057125 1.600000e-14 91.6
9 TraesCS4D01G275700 chr3A 97.054 679 19 1 2090 2768 202581422 202582099 0.000000e+00 1142.0
10 TraesCS4D01G275700 chr7B 96.613 679 22 1 2090 2768 429274531 429275208 0.000000e+00 1125.0
11 TraesCS4D01G275700 chr7B 84.076 314 41 8 3449 3758 589391951 589391643 1.130000e-75 294.0
12 TraesCS4D01G275700 chr7B 80.060 336 46 14 3449 3779 487331497 487331178 3.240000e-56 230.0
13 TraesCS4D01G275700 chr7B 80.645 155 24 6 1774 1925 408567860 408568011 9.480000e-22 115.0
14 TraesCS4D01G275700 chr2D 84.334 383 49 11 3405 3782 11517185 11516809 8.520000e-97 364.0
15 TraesCS4D01G275700 chr3D 80.570 386 54 15 3403 3784 408126465 408126833 1.140000e-70 278.0
16 TraesCS4D01G275700 chr3D 79.240 342 59 11 3447 3784 408126748 408126415 1.170000e-55 228.0
17 TraesCS4D01G275700 chr2A 78.866 388 68 13 3403 3784 12123908 12124287 2.490000e-62 250.0
18 TraesCS4D01G275700 chr2A 85.577 208 22 7 3587 3791 714735264 714735466 1.180000e-50 211.0
19 TraesCS4D01G275700 chr5A 78.385 384 55 17 3405 3784 667093888 667093529 1.510000e-54 224.0
20 TraesCS4D01G275700 chr1A 78.947 152 24 8 1773 1920 140961528 140961675 3.430000e-16 97.1
21 TraesCS4D01G275700 chr1D 78.146 151 27 6 1773 1920 126473497 126473644 1.600000e-14 91.6
22 TraesCS4D01G275700 chr5D 93.478 46 1 2 1859 1903 543444008 543443964 2.690000e-07 67.6
23 TraesCS4D01G275700 chr2B 97.059 34 1 0 3363 3396 655761782 655761749 1.620000e-04 58.4


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 TraesCS4D01G275700 chr4D 446650550 446654721 4171 True 7705.0 7705 100.000000 1 4172 1 chr4D.!!$R2 4171
1 TraesCS4D01G275700 chr4B 558725223 558729053 3830 True 1659.7 4542 92.138667 41 4172 3 chr4B.!!$R1 4131
2 TraesCS4D01G275700 chr4A 21050656 21058017 7361 False 1524.2 4146 89.647333 23 4172 3 chr4A.!!$F1 4149
3 TraesCS4D01G275700 chr3A 202581422 202582099 677 False 1142.0 1142 97.054000 2090 2768 1 chr3A.!!$F1 678
4 TraesCS4D01G275700 chr7B 429274531 429275208 677 False 1125.0 1125 96.613000 2090 2768 1 chr7B.!!$F2 678

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
433 461 0.179094 GTTCGGTGGATGGATGCGTA 60.179 55.0 0.0 0.0 0.0 4.42 F
1338 1419 0.625849 GGCAGGAAGGATGGGAAGAA 59.374 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1743 1840 0.388649 CGTCAGTCGGTCCCAAGAAG 60.389 60.0 0.0 0.0 35.71 2.85 R
3324 6684 0.034089 AGTTAAGGATGCAGGCCCAC 60.034 55.0 0.0 0.0 0.00 4.61 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
17 18 4.920828 AACCAAACACGCCCTCAT 57.079 50.000 0.00 0.00 0.00 2.90
18 19 2.340427 AACCAAACACGCCCTCATG 58.660 52.632 0.00 0.00 0.00 3.07
19 20 0.467290 AACCAAACACGCCCTCATGT 60.467 50.000 0.00 0.00 0.00 3.21
20 21 1.172180 ACCAAACACGCCCTCATGTG 61.172 55.000 0.00 0.00 41.81 3.21
21 22 1.081242 CAAACACGCCCTCATGTGC 60.081 57.895 0.00 0.00 39.71 4.57
36 37 2.785540 TGTGCATGCAGATGGAGTTA 57.214 45.000 23.41 0.00 29.21 2.24
39 40 0.950116 GCATGCAGATGGAGTTAGCC 59.050 55.000 14.21 0.00 0.00 3.93
194 208 2.045926 ATGTTGCCGTCTCCTGCC 60.046 61.111 0.00 0.00 0.00 4.85
259 273 0.966370 AGTGGCAGTACTCTCCGGTC 60.966 60.000 0.00 0.00 0.00 4.79
260 274 1.076014 TGGCAGTACTCTCCGGTCA 59.924 57.895 0.00 0.00 0.00 4.02
261 275 1.248785 TGGCAGTACTCTCCGGTCAC 61.249 60.000 0.00 0.00 0.00 3.67
433 461 0.179094 GTTCGGTGGATGGATGCGTA 60.179 55.000 0.00 0.00 0.00 4.42
446 474 0.973632 ATGCGTAGTGAACAGGGTGA 59.026 50.000 0.00 0.00 0.00 4.02
481 509 0.813610 CCGTTGTCACAGTGGCAAGA 60.814 55.000 21.09 0.00 43.26 3.02
607 635 3.461773 CTCAGGCCGACCGGTGAT 61.462 66.667 14.63 0.00 42.76 3.06
687 724 5.003160 TGATCGGCAGTATAAAATCCATGG 58.997 41.667 4.97 4.97 0.00 3.66
709 746 4.573607 GGAGTAGTTCGTGGTTTTGTCTTT 59.426 41.667 0.00 0.00 0.00 2.52
723 760 0.723981 GTCTTTGCAGCTCGTGGATC 59.276 55.000 0.00 0.00 0.00 3.36
823 869 1.589414 ACCTCAGATTCTTCCAGGGG 58.411 55.000 7.63 0.00 29.88 4.79
878 932 3.630013 AGGGCAGCTGCTCACGAA 61.630 61.111 38.55 0.00 46.01 3.85
903 967 1.295423 CCAACCGATCGACCCAACT 59.705 57.895 18.66 0.00 0.00 3.16
1150 1231 2.223852 TGCTAACCATAGATTACGCGCA 60.224 45.455 5.73 0.00 0.00 6.09
1151 1232 2.155155 GCTAACCATAGATTACGCGCAC 59.845 50.000 5.73 0.00 0.00 5.34
1182 1263 4.318949 TGCTCTGCTGCCGCTTCA 62.319 61.111 0.70 0.00 36.97 3.02
1192 1273 3.957535 CCGCTTCATCCATGGCGC 61.958 66.667 6.96 0.00 45.21 6.53
1194 1275 3.957535 GCTTCATCCATGGCGCCG 61.958 66.667 23.90 8.36 0.00 6.46
1197 1278 1.848932 CTTCATCCATGGCGCCGATG 61.849 60.000 27.41 27.41 35.71 3.84
1198 1279 4.034258 CATCCATGGCGCCGATGC 62.034 66.667 23.92 1.91 0.00 3.91
1199 1280 4.567488 ATCCATGGCGCCGATGCA 62.567 61.111 23.90 13.28 37.32 3.96
1200 1281 4.792804 TCCATGGCGCCGATGCAA 62.793 61.111 23.90 13.48 37.32 4.08
1201 1282 4.260355 CCATGGCGCCGATGCAAG 62.260 66.667 23.90 10.00 37.32 4.01
1243 1324 2.536811 GCACGTTGCGTTTCATTTTC 57.463 45.000 0.00 0.00 38.32 2.29
1338 1419 0.625849 GGCAGGAAGGATGGGAAGAA 59.374 55.000 0.00 0.00 0.00 2.52
1480 1564 2.801162 CGTGAGGTCGACAGCGTG 60.801 66.667 18.91 0.00 38.98 5.34
1501 1585 4.400109 GCGTCTCGGTCGTCAGCA 62.400 66.667 0.00 0.00 0.00 4.41
1621 1705 4.626081 ACTGTGGCACGCCTGTCC 62.626 66.667 13.77 0.00 38.60 4.02
1662 1755 3.134792 GAGCCAGCTCGTCGAGGA 61.135 66.667 23.09 7.70 33.06 3.71
1663 1756 2.676822 AGCCAGCTCGTCGAGGAA 60.677 61.111 23.09 0.00 0.00 3.36
1743 1840 2.030805 ACACTTCATTTTTCTGCTCGCC 60.031 45.455 0.00 0.00 0.00 5.54
2119 2216 1.065199 GGAACATGCAGGAGATGGACA 60.065 52.381 4.84 0.00 28.84 4.02
2136 2233 1.137825 CAGGTCGAGCGAGGAGAAC 59.862 63.158 9.28 0.00 0.00 3.01
2139 2236 1.226073 GTCGAGCGAGGAGAACGTC 60.226 63.158 0.00 0.00 0.00 4.34
2274 2374 2.441348 TCGGCCATGACGGAGCTA 60.441 61.111 2.24 0.00 36.56 3.32
2309 2409 2.046892 CTGGCACTTGGAGGACCG 60.047 66.667 0.00 0.00 39.42 4.79
2774 2877 1.347320 GTCGGATTCGAGGTGACAAC 58.653 55.000 0.00 0.00 46.91 3.32
2796 2899 5.715070 ACTCTACACTCAAGCATCTTACAC 58.285 41.667 0.00 0.00 0.00 2.90
2811 2914 4.758688 TCTTACACATCGATCAACTGCAT 58.241 39.130 0.00 0.00 0.00 3.96
2812 2915 5.901552 TCTTACACATCGATCAACTGCATA 58.098 37.500 0.00 0.00 0.00 3.14
2814 2917 6.986231 TCTTACACATCGATCAACTGCATATT 59.014 34.615 0.00 0.00 0.00 1.28
2817 2920 7.125536 ACACATCGATCAACTGCATATTATG 57.874 36.000 0.00 0.00 0.00 1.90
2829 2936 4.129380 TGCATATTATGACCACTGCTGTC 58.871 43.478 7.87 0.00 0.00 3.51
2853 2964 9.546909 GTCATTTTAATATCGTGGCATATCTTG 57.453 33.333 0.00 0.00 0.00 3.02
2856 2967 7.667043 TTTAATATCGTGGCATATCTTGTCC 57.333 36.000 0.00 0.00 0.00 4.02
2859 2970 3.627395 TCGTGGCATATCTTGTCCTTT 57.373 42.857 0.00 0.00 0.00 3.11
2978 3096 3.047093 CTCGTTCGTGTGTGTGTTGATA 58.953 45.455 0.00 0.00 0.00 2.15
3058 3180 2.235891 TGGCTCTTCGAGTCAAGTACA 58.764 47.619 0.00 0.00 41.56 2.90
3060 3182 3.246619 GGCTCTTCGAGTCAAGTACAAG 58.753 50.000 0.00 0.00 34.02 3.16
3061 3183 3.305471 GGCTCTTCGAGTCAAGTACAAGT 60.305 47.826 0.00 0.00 34.02 3.16
3062 3184 3.670991 GCTCTTCGAGTCAAGTACAAGTG 59.329 47.826 0.00 0.00 31.39 3.16
3063 3185 4.793353 GCTCTTCGAGTCAAGTACAAGTGT 60.793 45.833 0.00 0.00 31.39 3.55
3064 3186 5.562307 GCTCTTCGAGTCAAGTACAAGTGTA 60.562 44.000 0.00 0.00 31.39 2.90
3065 3187 7.537272 GCTCTTCGAGTCAAGTACAAGTGTAC 61.537 46.154 12.72 12.72 40.29 2.90
3066 3188 9.786002 GCTCTTCGAGTCAAGTACAAGTGTACA 62.786 44.444 20.64 0.00 41.25 2.90
3104 3229 5.177142 GTGCATATCTGTGACATGATGACTC 59.823 44.000 0.00 0.00 0.00 3.36
3113 3238 2.032620 ACATGATGACTCCGAGGTACC 58.967 52.381 2.73 2.73 0.00 3.34
3137 3267 7.120726 ACCAAGTGTAATTAGAAATGTACTGGC 59.879 37.037 0.00 0.00 0.00 4.85
3154 3313 1.134818 TGGCTTATCACTAGTGGCACG 60.135 52.381 22.48 9.41 0.00 5.34
3203 3362 3.132289 TCAAGACTCAAGAGTTCCAACGT 59.868 43.478 3.96 0.00 42.66 3.99
3229 3428 6.071503 ACTCACCCAACATACTAGTACTCAAC 60.072 42.308 4.31 0.00 0.00 3.18
3238 3437 7.828712 ACATACTAGTACTCAACTTGAACCTC 58.171 38.462 4.31 0.00 39.80 3.85
3239 3438 5.725325 ACTAGTACTCAACTTGAACCTCC 57.275 43.478 0.00 0.00 39.80 4.30
3241 3440 4.608948 AGTACTCAACTTGAACCTCCAG 57.391 45.455 0.00 0.00 33.35 3.86
3242 3441 2.938956 ACTCAACTTGAACCTCCAGG 57.061 50.000 0.00 0.00 42.17 4.45
3324 6684 5.630680 GGACAACAGTCATTACAATTTGCTG 59.369 40.000 0.00 0.00 33.90 4.41
3352 6755 2.037902 TGCATCCTTAACTGTCGTTGGA 59.962 45.455 0.00 0.00 34.59 3.53
3353 6756 2.415512 GCATCCTTAACTGTCGTTGGAC 59.584 50.000 0.00 0.00 43.71 4.02
3354 6757 2.825861 TCCTTAACTGTCGTTGGACC 57.174 50.000 0.00 0.00 42.73 4.46
3355 6758 2.040939 TCCTTAACTGTCGTTGGACCA 58.959 47.619 0.00 0.00 42.73 4.02
3356 6759 2.635915 TCCTTAACTGTCGTTGGACCAT 59.364 45.455 0.00 0.00 42.73 3.55
3357 6760 2.742053 CCTTAACTGTCGTTGGACCATG 59.258 50.000 0.00 0.00 42.73 3.66
3358 6761 3.399330 CTTAACTGTCGTTGGACCATGT 58.601 45.455 0.00 0.00 42.73 3.21
3359 6762 1.878953 AACTGTCGTTGGACCATGTC 58.121 50.000 0.00 0.00 42.73 3.06
3360 6763 1.048601 ACTGTCGTTGGACCATGTCT 58.951 50.000 0.00 0.00 42.73 3.41
3361 6764 1.270305 ACTGTCGTTGGACCATGTCTG 60.270 52.381 0.00 0.00 42.73 3.51
3362 6765 5.921360 AACTGTCGTTGGACCATGTCTGG 62.921 52.174 0.00 0.00 42.73 3.86
3370 6773 3.341629 CCATGTCTGGGGCCCTGT 61.342 66.667 25.93 4.48 39.04 4.00
3371 6774 2.044650 CATGTCTGGGGCCCTGTG 60.045 66.667 25.93 13.88 0.00 3.66
3372 6775 4.052518 ATGTCTGGGGCCCTGTGC 62.053 66.667 25.93 19.54 40.16 4.57
3389 6792 3.268986 CGGGCCGCACATTTTGTA 58.731 55.556 15.42 0.00 0.00 2.41
3390 6793 1.154112 CGGGCCGCACATTTTGTAC 60.154 57.895 15.42 0.00 0.00 2.90
3391 6794 1.214325 GGGCCGCACATTTTGTACC 59.786 57.895 0.00 0.00 0.00 3.34
3392 6795 1.528292 GGGCCGCACATTTTGTACCA 61.528 55.000 0.00 0.00 0.00 3.25
3393 6796 0.315568 GGCCGCACATTTTGTACCAA 59.684 50.000 0.00 0.00 0.00 3.67
3394 6797 1.067213 GGCCGCACATTTTGTACCAAT 60.067 47.619 0.00 0.00 0.00 3.16
3395 6798 1.991965 GCCGCACATTTTGTACCAATG 59.008 47.619 11.55 11.55 37.60 2.82
3396 6799 2.605030 CCGCACATTTTGTACCAATGG 58.395 47.619 15.69 0.00 36.15 3.16
3397 6800 2.029470 CCGCACATTTTGTACCAATGGT 60.029 45.455 10.81 10.81 40.16 3.55
3398 6801 3.191581 CCGCACATTTTGTACCAATGGTA 59.808 43.478 8.27 8.27 37.09 3.25
3437 6840 9.270576 CAATTCTAGATGTGTCAAAAGAATTCG 57.729 33.333 0.00 0.35 37.87 3.34
3438 6841 8.777865 ATTCTAGATGTGTCAAAAGAATTCGA 57.222 30.769 0.00 0.00 31.84 3.71
3439 6842 8.601845 TTCTAGATGTGTCAAAAGAATTCGAA 57.398 30.769 0.00 0.00 0.00 3.71
3440 6843 8.601845 TCTAGATGTGTCAAAAGAATTCGAAA 57.398 30.769 0.00 0.00 0.00 3.46
3441 6844 9.219603 TCTAGATGTGTCAAAAGAATTCGAAAT 57.780 29.630 0.00 0.00 0.00 2.17
3460 6863 9.905171 TTCGAAATAATTTGTGAATGTTCATCA 57.095 25.926 0.00 0.00 39.73 3.07
3461 6864 9.340695 TCGAAATAATTTGTGAATGTTCATCAC 57.659 29.630 0.00 0.00 45.82 3.06
3469 6872 5.112220 GTGAATGTTCATCACACATGTGT 57.888 39.130 25.76 25.76 45.13 3.72
3470 6873 4.913345 GTGAATGTTCATCACACATGTGTG 59.087 41.667 40.86 40.86 45.69 3.82
3471 6874 4.579753 TGAATGTTCATCACACATGTGTGT 59.420 37.500 42.53 31.64 45.18 3.72
3472 6875 5.277925 TGAATGTTCATCACACATGTGTGTC 60.278 40.000 42.53 32.88 43.78 3.67
3473 6876 7.408236 TGAATGTTCATCACACATGTGTGTCT 61.408 38.462 42.53 32.31 43.78 3.41
3474 6877 8.168507 TGAATGTTCATCACACATGTGTGTCTA 61.169 37.037 42.53 31.01 43.78 2.59
3482 6885 4.462508 CACATGTGTGTCTACATCCTCT 57.537 45.455 18.03 0.00 39.17 3.69
3483 6886 5.582689 CACATGTGTGTCTACATCCTCTA 57.417 43.478 18.03 0.00 39.17 2.43
3484 6887 5.965922 CACATGTGTGTCTACATCCTCTAA 58.034 41.667 18.03 0.00 39.17 2.10
3485 6888 6.038985 CACATGTGTGTCTACATCCTCTAAG 58.961 44.000 18.03 0.00 39.17 2.18
3486 6889 5.952347 ACATGTGTGTCTACATCCTCTAAGA 59.048 40.000 0.00 0.00 39.17 2.10
3487 6890 6.437477 ACATGTGTGTCTACATCCTCTAAGAA 59.563 38.462 0.00 0.00 39.17 2.52
3488 6891 6.911250 TGTGTGTCTACATCCTCTAAGAAA 57.089 37.500 0.00 0.00 39.39 2.52
3489 6892 7.482169 TGTGTGTCTACATCCTCTAAGAAAT 57.518 36.000 0.00 0.00 39.39 2.17
3490 6893 7.548097 TGTGTGTCTACATCCTCTAAGAAATC 58.452 38.462 0.00 0.00 39.39 2.17
3491 6894 6.981559 GTGTGTCTACATCCTCTAAGAAATCC 59.018 42.308 0.00 0.00 39.39 3.01
3492 6895 6.667848 TGTGTCTACATCCTCTAAGAAATCCA 59.332 38.462 0.00 0.00 0.00 3.41
3493 6896 7.147828 TGTGTCTACATCCTCTAAGAAATCCAG 60.148 40.741 0.00 0.00 0.00 3.86
3494 6897 7.068839 GTGTCTACATCCTCTAAGAAATCCAGA 59.931 40.741 0.00 0.00 0.00 3.86
3495 6898 7.786943 TGTCTACATCCTCTAAGAAATCCAGAT 59.213 37.037 0.00 0.00 0.00 2.90
3496 6899 8.303876 GTCTACATCCTCTAAGAAATCCAGATC 58.696 40.741 0.00 0.00 0.00 2.75
3497 6900 8.007153 TCTACATCCTCTAAGAAATCCAGATCA 58.993 37.037 0.00 0.00 0.00 2.92
3498 6901 7.443302 ACATCCTCTAAGAAATCCAGATCAA 57.557 36.000 0.00 0.00 0.00 2.57
3499 6902 7.865820 ACATCCTCTAAGAAATCCAGATCAAA 58.134 34.615 0.00 0.00 0.00 2.69
3500 6903 8.331740 ACATCCTCTAAGAAATCCAGATCAAAA 58.668 33.333 0.00 0.00 0.00 2.44
3501 6904 9.352191 CATCCTCTAAGAAATCCAGATCAAAAT 57.648 33.333 0.00 0.00 0.00 1.82
3537 6940 9.794685 ACAAAGAGAAACAAGAAAGAGAAATTC 57.205 29.630 0.00 0.00 0.00 2.17
3538 6941 9.793252 CAAAGAGAAACAAGAAAGAGAAATTCA 57.207 29.630 0.00 0.00 0.00 2.57
3540 6943 7.647228 AGAGAAACAAGAAAGAGAAATTCAGC 58.353 34.615 0.00 0.00 0.00 4.26
3541 6944 7.284034 AGAGAAACAAGAAAGAGAAATTCAGCA 59.716 33.333 0.00 0.00 0.00 4.41
3542 6945 7.949434 AGAAACAAGAAAGAGAAATTCAGCAT 58.051 30.769 0.00 0.00 0.00 3.79
3543 6946 7.866393 AGAAACAAGAAAGAGAAATTCAGCATG 59.134 33.333 0.00 0.00 37.54 4.06
3585 6988 7.584987 AGAAAAGGATGAATAGTGTCAAAACG 58.415 34.615 0.00 0.00 0.00 3.60
3586 6989 7.444183 AGAAAAGGATGAATAGTGTCAAAACGA 59.556 33.333 0.00 0.00 0.00 3.85
3587 6990 6.481954 AAGGATGAATAGTGTCAAAACGAC 57.518 37.500 0.00 0.00 45.61 4.34
3602 7005 8.601243 GTCAAAACGACACTATTCAAATATGG 57.399 34.615 0.00 0.00 44.69 2.74
3603 7006 8.447833 GTCAAAACGACACTATTCAAATATGGA 58.552 33.333 0.00 0.00 44.69 3.41
3604 7007 9.173021 TCAAAACGACACTATTCAAATATGGAT 57.827 29.630 0.00 0.00 0.00 3.41
3605 7008 9.787532 CAAAACGACACTATTCAAATATGGATT 57.212 29.630 0.00 0.00 0.00 3.01
3609 7012 9.396022 ACGACACTATTCAAATATGGATTTTCT 57.604 29.630 0.00 0.00 32.73 2.52
3610 7013 9.869844 CGACACTATTCAAATATGGATTTTCTC 57.130 33.333 0.00 0.00 32.73 2.87
3649 7052 9.830975 TTCTGTATATTTCGGATTTTGATCTGA 57.169 29.630 0.00 0.00 34.38 3.27
3650 7053 9.830975 TCTGTATATTTCGGATTTTGATCTGAA 57.169 29.630 6.57 6.57 42.39 3.02
3676 7079 7.931578 TTTTTAGGGGTTGTAGACACATATG 57.068 36.000 0.00 0.00 33.76 1.78
3677 7080 6.630203 TTTAGGGGTTGTAGACACATATGT 57.370 37.500 1.41 1.41 43.71 2.29
3701 7104 9.127006 TGTGATGAACATTCACAAATTATTTCG 57.873 29.630 4.15 0.00 40.81 3.46
3702 7105 9.340695 GTGATGAACATTCACAAATTATTTCGA 57.659 29.630 0.00 0.00 40.49 3.71
3730 7133 9.796120 TTTTTGACACGTCTAGAATTGAAATTT 57.204 25.926 8.51 0.00 0.00 1.82
3731 7134 9.796120 TTTTGACACGTCTAGAATTGAAATTTT 57.204 25.926 8.51 0.00 0.00 1.82
3732 7135 9.445786 TTTGACACGTCTAGAATTGAAATTTTC 57.554 29.630 8.51 2.05 0.00 2.29
3733 7136 8.148807 TGACACGTCTAGAATTGAAATTTTCA 57.851 30.769 7.74 7.74 38.04 2.69
3747 7150 8.830201 TTGAAATTTTCAAAGTGATACCATGG 57.170 30.769 19.57 11.19 45.94 3.66
3748 7151 7.385267 TGAAATTTTCAAAGTGATACCATGGG 58.615 34.615 18.09 0.00 36.59 4.00
3749 7152 7.234371 TGAAATTTTCAAAGTGATACCATGGGA 59.766 33.333 18.09 8.35 36.59 4.37
3750 7153 6.780457 ATTTTCAAAGTGATACCATGGGAG 57.220 37.500 18.09 0.00 0.00 4.30
3751 7154 3.281727 TCAAAGTGATACCATGGGAGC 57.718 47.619 18.09 11.94 0.00 4.70
3752 7155 2.575735 TCAAAGTGATACCATGGGAGCA 59.424 45.455 11.97 11.97 0.00 4.26
3753 7156 2.684881 CAAAGTGATACCATGGGAGCAC 59.315 50.000 33.89 33.89 0.00 4.40
3754 7157 1.885049 AGTGATACCATGGGAGCACT 58.115 50.000 37.07 37.07 31.48 4.40
3755 7158 2.200081 AGTGATACCATGGGAGCACTT 58.800 47.619 37.07 23.16 31.98 3.16
3756 7159 2.092753 AGTGATACCATGGGAGCACTTG 60.093 50.000 37.07 0.00 31.98 3.16
3757 7160 2.092968 GTGATACCATGGGAGCACTTGA 60.093 50.000 33.63 1.01 0.00 3.02
3758 7161 2.171237 TGATACCATGGGAGCACTTGAG 59.829 50.000 11.97 0.00 0.00 3.02
3759 7162 1.656587 TACCATGGGAGCACTTGAGT 58.343 50.000 18.09 0.00 0.00 3.41
3763 7166 2.014857 CATGGGAGCACTTGAGTGATG 58.985 52.381 14.98 5.53 45.57 3.07
3764 7167 0.325933 TGGGAGCACTTGAGTGATGG 59.674 55.000 14.98 0.00 45.57 3.51
3765 7168 0.326264 GGGAGCACTTGAGTGATGGT 59.674 55.000 14.98 0.00 45.57 3.55
3766 7169 1.555075 GGGAGCACTTGAGTGATGGTA 59.445 52.381 14.98 0.00 45.57 3.25
3767 7170 2.171448 GGGAGCACTTGAGTGATGGTAT 59.829 50.000 14.98 0.00 45.57 2.73
3768 7171 3.462021 GGAGCACTTGAGTGATGGTATC 58.538 50.000 14.98 0.00 45.57 2.24
3769 7172 3.118629 GGAGCACTTGAGTGATGGTATCA 60.119 47.826 14.98 0.00 45.57 2.15
3797 7204 1.768077 CTCCCCATGTCCCTCTCCC 60.768 68.421 0.00 0.00 0.00 4.30
3821 7231 2.276201 CGCCAAACACGGATCAAGATA 58.724 47.619 0.00 0.00 0.00 1.98
3851 7266 5.972107 AAAACAAGGATCAAGAGACCATG 57.028 39.130 0.00 0.00 0.00 3.66
3857 7272 2.617308 GGATCAAGAGACCATGTGCATG 59.383 50.000 5.26 5.26 38.51 4.06
3887 7702 3.455152 CGGTATCTGATCCGGCCA 58.545 61.111 2.24 0.00 42.61 5.36
3930 7746 6.767524 TGATGCGTATCCCTGTTTTATTTT 57.232 33.333 11.17 0.00 32.09 1.82
4074 7893 4.133373 ATGCCGCCCATCAAGCCT 62.133 61.111 0.00 0.00 0.00 4.58
4095 7921 4.503991 CCTCTTATAAAGCGAGGGCATCTT 60.504 45.833 10.19 0.00 43.41 2.40
4110 7936 2.267426 CATCTTGACGTACGGCATTGA 58.733 47.619 27.01 24.76 30.63 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.150536 ACATGAGGGCGTGTTTGGT 59.849 52.632 0.00 0.00 41.35 3.67
2 3 1.580942 CACATGAGGGCGTGTTTGG 59.419 57.895 0.00 0.00 42.20 3.28
3 4 1.081242 GCACATGAGGGCGTGTTTG 60.081 57.895 0.00 0.00 42.20 2.93
4 5 0.895100 ATGCACATGAGGGCGTGTTT 60.895 50.000 0.00 0.00 42.20 2.83
5 6 1.303561 ATGCACATGAGGGCGTGTT 60.304 52.632 0.00 0.00 42.20 3.32
6 7 2.042259 CATGCACATGAGGGCGTGT 61.042 57.895 17.04 0.00 44.87 4.49
7 8 2.795973 CATGCACATGAGGGCGTG 59.204 61.111 4.57 8.09 41.20 5.34
8 9 3.136123 GCATGCACATGAGGGCGT 61.136 61.111 14.21 0.00 41.20 5.68
9 10 3.120979 CTGCATGCACATGAGGGCG 62.121 63.158 18.46 0.00 41.20 6.13
10 11 1.107538 ATCTGCATGCACATGAGGGC 61.108 55.000 18.46 0.22 41.20 5.19
11 12 0.668535 CATCTGCATGCACATGAGGG 59.331 55.000 26.37 11.77 41.20 4.30
12 13 0.668535 CCATCTGCATGCACATGAGG 59.331 55.000 30.47 21.29 41.20 3.86
13 14 1.604278 CTCCATCTGCATGCACATGAG 59.396 52.381 30.47 22.03 41.20 2.90
14 15 1.064979 ACTCCATCTGCATGCACATGA 60.065 47.619 30.47 21.13 41.20 3.07
15 16 1.389555 ACTCCATCTGCATGCACATG 58.610 50.000 24.32 24.32 41.60 3.21
16 17 2.139323 AACTCCATCTGCATGCACAT 57.861 45.000 18.46 9.93 0.00 3.21
17 18 2.635714 CTAACTCCATCTGCATGCACA 58.364 47.619 18.46 7.34 0.00 4.57
18 19 1.332997 GCTAACTCCATCTGCATGCAC 59.667 52.381 18.46 0.00 0.00 4.57
19 20 1.671979 GCTAACTCCATCTGCATGCA 58.328 50.000 21.29 21.29 0.00 3.96
20 21 0.950116 GGCTAACTCCATCTGCATGC 59.050 55.000 11.82 11.82 0.00 4.06
21 22 1.224075 CGGCTAACTCCATCTGCATG 58.776 55.000 0.00 0.00 0.00 4.06
89 90 0.390472 GCTATAGGGCTCATCGCACC 60.390 60.000 1.04 0.00 45.64 5.01
259 273 3.410516 TGACGGCGACAATGCGTG 61.411 61.111 16.62 0.00 35.06 5.34
260 274 3.411351 GTGACGGCGACAATGCGT 61.411 61.111 16.62 0.00 35.06 5.24
261 275 4.147322 GGTGACGGCGACAATGCG 62.147 66.667 16.62 0.00 35.06 4.73
289 303 1.153309 GCATTTGGAGCAATGCCCC 60.153 57.895 0.00 0.00 34.23 5.80
295 309 4.271661 TGATACATCTGCATTTGGAGCAA 58.728 39.130 0.00 0.00 42.17 3.91
433 461 1.418908 CCCACCTCACCCTGTTCACT 61.419 60.000 0.00 0.00 0.00 3.41
457 485 3.808036 ACTGTGACAACGGTGCAC 58.192 55.556 17.54 17.54 44.50 4.57
607 635 1.653094 GGATTGGATTTGTGCGGCGA 61.653 55.000 12.98 0.00 0.00 5.54
669 702 6.534634 ACTACTCCATGGATTTTATACTGCC 58.465 40.000 16.63 0.00 0.00 4.85
687 724 5.499047 CAAAGACAAAACCACGAACTACTC 58.501 41.667 0.00 0.00 0.00 2.59
709 746 1.395045 CCTAGGATCCACGAGCTGCA 61.395 60.000 15.82 0.00 0.00 4.41
823 869 2.125350 CTCTGCCCTCAGGTTCGC 60.125 66.667 0.00 0.00 40.69 4.70
835 881 1.202627 CCATTCCTAGCTGGTCTCTGC 60.203 57.143 0.00 0.00 38.00 4.26
878 932 0.175073 GTCGATCGGTTGGTTAGCCT 59.825 55.000 16.41 0.00 35.27 4.58
1058 1134 1.792949 CTCCAACGTAGCAGTCAACAC 59.207 52.381 0.00 0.00 0.00 3.32
1059 1135 1.411246 ACTCCAACGTAGCAGTCAACA 59.589 47.619 0.00 0.00 0.00 3.33
1150 1231 1.165270 GAGCAGCCAACCGTAATTGT 58.835 50.000 0.00 0.00 0.00 2.71
1151 1232 1.131126 CAGAGCAGCCAACCGTAATTG 59.869 52.381 0.00 0.00 0.00 2.32
1182 1263 4.567488 TGCATCGGCGCCATGGAT 62.567 61.111 28.98 18.32 45.35 3.41
1192 1273 1.097547 CCCTACTTGCCTTGCATCGG 61.098 60.000 0.00 0.00 38.76 4.18
1194 1275 1.098050 CACCCTACTTGCCTTGCATC 58.902 55.000 0.00 0.00 38.76 3.91
1197 1278 1.098050 CATCACCCTACTTGCCTTGC 58.902 55.000 0.00 0.00 0.00 4.01
1198 1279 2.026822 ACTCATCACCCTACTTGCCTTG 60.027 50.000 0.00 0.00 0.00 3.61
1199 1280 2.269940 ACTCATCACCCTACTTGCCTT 58.730 47.619 0.00 0.00 0.00 4.35
1200 1281 1.958288 ACTCATCACCCTACTTGCCT 58.042 50.000 0.00 0.00 0.00 4.75
1201 1282 2.500098 TGTACTCATCACCCTACTTGCC 59.500 50.000 0.00 0.00 0.00 4.52
1243 1324 2.508887 GACCTCTGCTGCTCTGCG 60.509 66.667 0.00 0.00 35.36 5.18
1300 1381 2.041115 GCCGGCCAAGAAGTTCCTC 61.041 63.158 18.11 0.00 0.00 3.71
1615 1699 4.785453 GCCTTGCGGGAGGACAGG 62.785 72.222 4.90 0.00 39.25 4.00
1644 1737 4.200283 CCTCGACGAGCTGGCTCC 62.200 72.222 19.55 3.38 39.77 4.70
1650 1743 3.816524 CCGCTTCCTCGACGAGCT 61.817 66.667 19.55 0.00 34.33 4.09
1743 1840 0.388649 CGTCAGTCGGTCCCAAGAAG 60.389 60.000 0.00 0.00 35.71 2.85
2119 2216 2.400158 CGTTCTCCTCGCTCGACCT 61.400 63.158 0.00 0.00 0.00 3.85
2136 2233 1.330829 TCCATCTCGACGATCTTGACG 59.669 52.381 0.00 0.00 0.00 4.35
2139 2236 2.725490 CTGTCCATCTCGACGATCTTG 58.275 52.381 0.00 0.00 35.40 3.02
2774 2877 5.714047 TGTGTAAGATGCTTGAGTGTAGAG 58.286 41.667 0.00 0.00 0.00 2.43
2796 2899 6.369615 TGGTCATAATATGCAGTTGATCGATG 59.630 38.462 0.54 0.00 0.00 3.84
2817 2920 6.037172 ACGATATTAAAATGACAGCAGTGGTC 59.963 38.462 0.00 0.00 35.83 4.02
2829 2936 9.546909 GACAAGATATGCCACGATATTAAAATG 57.453 33.333 0.00 0.00 0.00 2.32
2834 2941 6.605471 AGGACAAGATATGCCACGATATTA 57.395 37.500 0.00 0.00 0.00 0.98
2835 2942 5.489792 AGGACAAGATATGCCACGATATT 57.510 39.130 0.00 0.00 0.00 1.28
2836 2943 5.489792 AAGGACAAGATATGCCACGATAT 57.510 39.130 0.00 0.00 0.00 1.63
2945 3058 3.119459 ACACGAACGAGACTATCAAGCAT 60.119 43.478 0.14 0.00 0.00 3.79
2978 3096 5.104109 ACACTCTACTAGGCTCTGATCTCTT 60.104 44.000 0.00 0.00 0.00 2.85
3081 3206 5.286267 AGTCATCATGTCACAGATATGCA 57.714 39.130 0.00 0.00 32.47 3.96
3104 3229 5.587388 TCTAATTACACTTGGTACCTCGG 57.413 43.478 14.36 5.67 0.00 4.63
3113 3238 8.268850 AGCCAGTACATTTCTAATTACACTTG 57.731 34.615 0.00 0.00 0.00 3.16
3137 3267 2.094182 ACACCGTGCCACTAGTGATAAG 60.094 50.000 24.68 13.52 34.33 1.73
3141 3271 1.330234 TTACACCGTGCCACTAGTGA 58.670 50.000 24.68 1.84 34.33 3.41
3154 3313 3.791353 GCAAATTGCGAGCTTATTACACC 59.209 43.478 0.90 0.00 31.71 4.16
3203 3362 6.724351 TGAGTACTAGTATGTTGGGTGAGTA 58.276 40.000 5.75 0.00 0.00 2.59
3288 6648 0.034574 TGTTGTCCACAGCAACTGGT 60.035 50.000 9.16 0.00 44.54 4.00
3312 6672 1.617850 CAGGCCCACAGCAAATTGTAA 59.382 47.619 0.00 0.00 46.50 2.41
3314 6674 2.051941 CAGGCCCACAGCAAATTGT 58.948 52.632 0.00 0.00 46.50 2.71
3315 6675 1.375013 GCAGGCCCACAGCAAATTG 60.375 57.895 0.00 0.00 46.50 2.32
3316 6676 1.196104 ATGCAGGCCCACAGCAAATT 61.196 50.000 12.84 0.00 46.50 1.82
3317 6677 1.610554 GATGCAGGCCCACAGCAAAT 61.611 55.000 12.84 0.00 46.50 2.32
3318 6678 2.203669 ATGCAGGCCCACAGCAAA 60.204 55.556 12.84 0.00 46.50 3.68
3324 6684 0.034089 AGTTAAGGATGCAGGCCCAC 60.034 55.000 0.00 0.00 0.00 4.61
3352 6755 3.341629 CAGGGCCCCAGACATGGT 61.342 66.667 21.43 0.00 46.10 3.55
3354 6757 2.044650 CACAGGGCCCCAGACATG 60.045 66.667 21.43 12.09 0.00 3.21
3355 6758 4.052518 GCACAGGGCCCCAGACAT 62.053 66.667 21.43 0.00 36.11 3.06
3372 6775 1.154112 GTACAAAATGTGCGGCCCG 60.154 57.895 0.00 0.00 0.00 6.13
3373 6776 1.214325 GGTACAAAATGTGCGGCCC 59.786 57.895 0.00 0.00 33.61 5.80
3374 6777 1.960612 TGGTACAAAATGTGCGGCC 59.039 52.632 0.00 0.00 33.61 6.13
3386 6789 9.521841 TGAAATTTTCATAGTACCATTGGTACA 57.478 29.630 35.77 25.45 46.11 2.90
3411 6814 9.270576 CGAATTCTTTTGACACATCTAGAATTG 57.729 33.333 11.34 0.00 37.76 2.32
3412 6815 9.219603 TCGAATTCTTTTGACACATCTAGAATT 57.780 29.630 3.52 0.00 38.89 2.17
3413 6816 8.777865 TCGAATTCTTTTGACACATCTAGAAT 57.222 30.769 3.52 0.00 33.48 2.40
3414 6817 8.601845 TTCGAATTCTTTTGACACATCTAGAA 57.398 30.769 3.52 0.00 0.00 2.10
3415 6818 8.601845 TTTCGAATTCTTTTGACACATCTAGA 57.398 30.769 0.00 0.00 0.00 2.43
3434 6837 9.905171 TGATGAACATTCACAAATTATTTCGAA 57.095 25.926 0.00 0.00 40.49 3.71
3435 6838 9.340695 GTGATGAACATTCACAAATTATTTCGA 57.659 29.630 0.00 0.00 40.49 3.71
3436 6839 9.127006 TGTGATGAACATTCACAAATTATTTCG 57.873 29.630 4.15 0.00 40.81 3.46
3438 6841 9.761504 TGTGTGATGAACATTCACAAATTATTT 57.238 25.926 16.99 0.00 44.53 1.40
3439 6842 9.932207 ATGTGTGATGAACATTCACAAATTATT 57.068 25.926 20.33 8.76 44.53 1.40
3440 6843 9.361315 CATGTGTGATGAACATTCACAAATTAT 57.639 29.630 20.33 11.68 44.53 1.28
3441 6844 8.358895 ACATGTGTGATGAACATTCACAAATTA 58.641 29.630 20.33 10.62 44.53 1.40
3442 6845 7.211573 ACATGTGTGATGAACATTCACAAATT 58.788 30.769 20.33 9.66 44.53 1.82
3443 6846 6.751157 ACATGTGTGATGAACATTCACAAAT 58.249 32.000 20.33 16.45 44.53 2.32
3444 6847 6.146601 ACATGTGTGATGAACATTCACAAA 57.853 33.333 20.33 15.46 44.53 2.83
3445 6848 5.771153 ACATGTGTGATGAACATTCACAA 57.229 34.783 20.33 12.54 44.53 3.33
3462 6865 5.952347 TCTTAGAGGATGTAGACACACATGT 59.048 40.000 0.00 0.00 43.71 3.21
3463 6866 6.456795 TCTTAGAGGATGTAGACACACATG 57.543 41.667 0.00 0.00 39.25 3.21
3464 6867 7.482169 TTTCTTAGAGGATGTAGACACACAT 57.518 36.000 0.00 0.00 41.83 3.21
3465 6868 6.911250 TTTCTTAGAGGATGTAGACACACA 57.089 37.500 0.00 0.00 37.54 3.72
3466 6869 6.981559 GGATTTCTTAGAGGATGTAGACACAC 59.018 42.308 0.00 0.00 37.54 3.82
3467 6870 6.667848 TGGATTTCTTAGAGGATGTAGACACA 59.332 38.462 0.00 0.00 39.52 3.72
3468 6871 7.068839 TCTGGATTTCTTAGAGGATGTAGACAC 59.931 40.741 0.00 0.00 0.00 3.67
3469 6872 7.126061 TCTGGATTTCTTAGAGGATGTAGACA 58.874 38.462 0.00 0.00 0.00 3.41
3470 6873 7.589958 TCTGGATTTCTTAGAGGATGTAGAC 57.410 40.000 0.00 0.00 0.00 2.59
3471 6874 8.007153 TGATCTGGATTTCTTAGAGGATGTAGA 58.993 37.037 0.00 0.00 0.00 2.59
3472 6875 8.187913 TGATCTGGATTTCTTAGAGGATGTAG 57.812 38.462 0.00 0.00 0.00 2.74
3473 6876 8.553085 TTGATCTGGATTTCTTAGAGGATGTA 57.447 34.615 0.00 0.00 0.00 2.29
3474 6877 7.443302 TTGATCTGGATTTCTTAGAGGATGT 57.557 36.000 0.00 0.00 0.00 3.06
3475 6878 8.743085 TTTTGATCTGGATTTCTTAGAGGATG 57.257 34.615 0.00 0.00 0.00 3.51
3511 6914 9.794685 GAATTTCTCTTTCTTGTTTCTCTTTGT 57.205 29.630 0.00 0.00 0.00 2.83
3512 6915 9.793252 TGAATTTCTCTTTCTTGTTTCTCTTTG 57.207 29.630 0.00 0.00 0.00 2.77
3514 6917 8.134261 GCTGAATTTCTCTTTCTTGTTTCTCTT 58.866 33.333 0.00 0.00 0.00 2.85
3515 6918 7.284034 TGCTGAATTTCTCTTTCTTGTTTCTCT 59.716 33.333 0.00 0.00 0.00 3.10
3516 6919 7.420800 TGCTGAATTTCTCTTTCTTGTTTCTC 58.579 34.615 0.00 0.00 0.00 2.87
3517 6920 7.338800 TGCTGAATTTCTCTTTCTTGTTTCT 57.661 32.000 0.00 0.00 0.00 2.52
3518 6921 7.864379 TCATGCTGAATTTCTCTTTCTTGTTTC 59.136 33.333 0.00 0.00 0.00 2.78
3519 6922 7.719483 TCATGCTGAATTTCTCTTTCTTGTTT 58.281 30.769 0.00 0.00 0.00 2.83
3520 6923 7.281040 TCATGCTGAATTTCTCTTTCTTGTT 57.719 32.000 0.00 0.00 0.00 2.83
3521 6924 6.889301 TCATGCTGAATTTCTCTTTCTTGT 57.111 33.333 0.00 0.00 0.00 3.16
3522 6925 9.504710 CTATTCATGCTGAATTTCTCTTTCTTG 57.495 33.333 14.02 0.00 44.03 3.02
3523 6926 9.240734 ACTATTCATGCTGAATTTCTCTTTCTT 57.759 29.630 14.02 0.00 44.03 2.52
3524 6927 8.675504 CACTATTCATGCTGAATTTCTCTTTCT 58.324 33.333 14.02 0.00 44.03 2.52
3525 6928 8.457261 ACACTATTCATGCTGAATTTCTCTTTC 58.543 33.333 14.02 0.00 44.03 2.62
3526 6929 8.345724 ACACTATTCATGCTGAATTTCTCTTT 57.654 30.769 14.02 0.00 44.03 2.52
3527 6930 7.609146 TGACACTATTCATGCTGAATTTCTCTT 59.391 33.333 14.02 0.00 44.03 2.85
3528 6931 7.108194 TGACACTATTCATGCTGAATTTCTCT 58.892 34.615 14.02 0.00 44.03 3.10
3529 6932 7.312657 TGACACTATTCATGCTGAATTTCTC 57.687 36.000 14.02 7.25 44.03 2.87
3530 6933 7.692460 TTGACACTATTCATGCTGAATTTCT 57.308 32.000 14.02 0.00 44.03 2.52
3559 6962 8.717821 CGTTTTGACACTATTCATCCTTTTCTA 58.282 33.333 0.00 0.00 0.00 2.10
3560 6963 7.444183 TCGTTTTGACACTATTCATCCTTTTCT 59.556 33.333 0.00 0.00 0.00 2.52
3561 6964 7.581476 TCGTTTTGACACTATTCATCCTTTTC 58.419 34.615 0.00 0.00 0.00 2.29
3562 6965 7.504924 TCGTTTTGACACTATTCATCCTTTT 57.495 32.000 0.00 0.00 0.00 2.27
3578 6981 8.554835 TCCATATTTGAATAGTGTCGTTTTGA 57.445 30.769 0.00 0.00 0.00 2.69
3579 6982 9.787532 AATCCATATTTGAATAGTGTCGTTTTG 57.212 29.630 0.00 0.00 0.00 2.44
3583 6986 9.396022 AGAAAATCCATATTTGAATAGTGTCGT 57.604 29.630 0.00 0.00 35.46 4.34
3584 6987 9.869844 GAGAAAATCCATATTTGAATAGTGTCG 57.130 33.333 0.00 0.00 35.46 4.35
3623 7026 9.830975 TCAGATCAAAATCCGAAATATACAGAA 57.169 29.630 0.00 0.00 31.78 3.02
3624 7027 9.830975 TTCAGATCAAAATCCGAAATATACAGA 57.169 29.630 0.00 0.00 27.73 3.41
3652 7055 7.392113 CACATATGTGTCTACAACCCCTAAAAA 59.608 37.037 24.91 0.00 40.84 1.94
3653 7056 6.882140 CACATATGTGTCTACAACCCCTAAAA 59.118 38.462 24.91 0.00 40.84 1.52
3654 7057 6.213802 TCACATATGTGTCTACAACCCCTAAA 59.786 38.462 30.03 7.11 45.76 1.85
3655 7058 5.722441 TCACATATGTGTCTACAACCCCTAA 59.278 40.000 30.03 7.71 45.76 2.69
3656 7059 5.274015 TCACATATGTGTCTACAACCCCTA 58.726 41.667 30.03 8.12 45.76 3.53
3657 7060 4.101114 TCACATATGTGTCTACAACCCCT 58.899 43.478 30.03 0.00 45.76 4.79
3658 7061 4.481368 TCACATATGTGTCTACAACCCC 57.519 45.455 30.03 0.00 45.76 4.95
3659 7062 5.670485 TCATCACATATGTGTCTACAACCC 58.330 41.667 30.03 0.00 45.76 4.11
3660 7063 6.593770 TGTTCATCACATATGTGTCTACAACC 59.406 38.462 30.03 14.78 45.76 3.77
3661 7064 7.595311 TGTTCATCACATATGTGTCTACAAC 57.405 36.000 30.03 23.99 45.76 3.32
3662 7065 8.791327 AATGTTCATCACATATGTGTCTACAA 57.209 30.769 30.03 14.17 46.23 2.41
3663 7066 8.040132 TGAATGTTCATCACATATGTGTCTACA 58.960 33.333 30.03 26.37 46.23 2.74
3664 7067 8.331022 GTGAATGTTCATCACATATGTGTCTAC 58.669 37.037 30.03 22.90 46.23 2.59
3665 7068 8.424274 GTGAATGTTCATCACATATGTGTCTA 57.576 34.615 30.03 15.53 46.23 2.59
3666 7069 7.312657 GTGAATGTTCATCACATATGTGTCT 57.687 36.000 30.03 18.48 46.23 3.41
3676 7079 9.340695 TCGAAATAATTTGTGAATGTTCATCAC 57.659 29.630 0.00 0.00 45.82 3.06
3704 7107 9.796120 AAATTTCAATTCTAGACGTGTCAAAAA 57.204 25.926 0.00 0.00 0.00 1.94
3705 7108 9.796120 AAAATTTCAATTCTAGACGTGTCAAAA 57.204 25.926 0.00 0.00 0.00 2.44
3706 7109 9.445786 GAAAATTTCAATTCTAGACGTGTCAAA 57.554 29.630 0.00 0.00 0.00 2.69
3707 7110 8.616942 TGAAAATTTCAATTCTAGACGTGTCAA 58.383 29.630 5.87 0.00 36.59 3.18
3708 7111 8.148807 TGAAAATTTCAATTCTAGACGTGTCA 57.851 30.769 5.87 0.00 36.59 3.58
3723 7126 7.234371 TCCCATGGTATCACTTTGAAAATTTCA 59.766 33.333 11.73 4.03 38.04 2.69
3724 7127 7.610865 TCCCATGGTATCACTTTGAAAATTTC 58.389 34.615 11.73 0.00 0.00 2.17
3725 7128 7.552050 TCCCATGGTATCACTTTGAAAATTT 57.448 32.000 11.73 0.00 0.00 1.82
3726 7129 6.351286 GCTCCCATGGTATCACTTTGAAAATT 60.351 38.462 11.73 0.00 0.00 1.82
3727 7130 5.127682 GCTCCCATGGTATCACTTTGAAAAT 59.872 40.000 11.73 0.00 0.00 1.82
3728 7131 4.462483 GCTCCCATGGTATCACTTTGAAAA 59.538 41.667 11.73 0.00 0.00 2.29
3729 7132 4.016444 GCTCCCATGGTATCACTTTGAAA 58.984 43.478 11.73 0.00 0.00 2.69
3730 7133 3.010027 TGCTCCCATGGTATCACTTTGAA 59.990 43.478 11.73 0.00 0.00 2.69
3731 7134 2.575735 TGCTCCCATGGTATCACTTTGA 59.424 45.455 11.73 0.00 0.00 2.69
3732 7135 2.684881 GTGCTCCCATGGTATCACTTTG 59.315 50.000 11.73 0.00 0.00 2.77
3733 7136 2.578021 AGTGCTCCCATGGTATCACTTT 59.422 45.455 18.62 4.59 31.51 2.66
3734 7137 2.200081 AGTGCTCCCATGGTATCACTT 58.800 47.619 18.62 8.13 31.51 3.16
3735 7138 1.885049 AGTGCTCCCATGGTATCACT 58.115 50.000 18.62 18.62 0.00 3.41
3736 7139 2.092968 TCAAGTGCTCCCATGGTATCAC 60.093 50.000 11.73 14.14 0.00 3.06
3737 7140 2.171237 CTCAAGTGCTCCCATGGTATCA 59.829 50.000 11.73 1.84 0.00 2.15
3738 7141 2.171448 ACTCAAGTGCTCCCATGGTATC 59.829 50.000 11.73 0.00 0.00 2.24
3739 7142 2.092753 CACTCAAGTGCTCCCATGGTAT 60.093 50.000 11.73 0.00 39.39 2.73
3740 7143 1.278985 CACTCAAGTGCTCCCATGGTA 59.721 52.381 11.73 0.00 39.39 3.25
3741 7144 0.037303 CACTCAAGTGCTCCCATGGT 59.963 55.000 11.73 0.00 39.39 3.55
3742 7145 0.325933 TCACTCAAGTGCTCCCATGG 59.674 55.000 4.14 4.14 45.25 3.66
3743 7146 2.014857 CATCACTCAAGTGCTCCCATG 58.985 52.381 5.25 0.61 45.25 3.66
3744 7147 1.064906 CCATCACTCAAGTGCTCCCAT 60.065 52.381 5.25 0.00 45.25 4.00
3745 7148 0.325933 CCATCACTCAAGTGCTCCCA 59.674 55.000 5.25 0.00 45.25 4.37
3746 7149 0.326264 ACCATCACTCAAGTGCTCCC 59.674 55.000 5.25 0.00 45.25 4.30
3747 7150 3.118629 TGATACCATCACTCAAGTGCTCC 60.119 47.826 5.25 0.00 45.25 4.70
3748 7151 4.128925 TGATACCATCACTCAAGTGCTC 57.871 45.455 5.25 0.00 45.25 4.26
3759 7162 6.013379 GGGGAGAATATCAAGTGATACCATCA 60.013 42.308 3.15 0.00 39.57 3.07
3760 7163 6.013379 TGGGGAGAATATCAAGTGATACCATC 60.013 42.308 3.15 3.60 39.57 3.51
3761 7164 5.851693 TGGGGAGAATATCAAGTGATACCAT 59.148 40.000 3.15 0.00 39.57 3.55
3762 7165 5.223655 TGGGGAGAATATCAAGTGATACCA 58.776 41.667 3.15 3.21 39.57 3.25
3763 7166 5.825593 TGGGGAGAATATCAAGTGATACC 57.174 43.478 3.15 1.04 39.57 2.73
3764 7167 6.773638 ACATGGGGAGAATATCAAGTGATAC 58.226 40.000 3.15 0.00 39.57 2.24
3765 7168 6.013379 GGACATGGGGAGAATATCAAGTGATA 60.013 42.308 3.56 3.56 40.85 2.15
3766 7169 5.222007 GGACATGGGGAGAATATCAAGTGAT 60.222 44.000 0.00 0.00 38.51 3.06
3767 7170 4.103153 GGACATGGGGAGAATATCAAGTGA 59.897 45.833 0.00 0.00 0.00 3.41
3768 7171 4.392940 GGACATGGGGAGAATATCAAGTG 58.607 47.826 0.00 0.00 0.00 3.16
3769 7172 3.395941 GGGACATGGGGAGAATATCAAGT 59.604 47.826 0.00 0.00 0.00 3.16
3770 7173 3.654806 AGGGACATGGGGAGAATATCAAG 59.345 47.826 0.00 0.00 0.00 3.02
3771 7174 3.652869 GAGGGACATGGGGAGAATATCAA 59.347 47.826 0.00 0.00 0.00 2.57
3772 7175 3.116199 AGAGGGACATGGGGAGAATATCA 60.116 47.826 0.00 0.00 0.00 2.15
3773 7176 3.517500 GAGAGGGACATGGGGAGAATATC 59.482 52.174 0.00 0.00 0.00 1.63
3774 7177 3.525862 GAGAGGGACATGGGGAGAATAT 58.474 50.000 0.00 0.00 0.00 1.28
3775 7178 2.427889 GGAGAGGGACATGGGGAGAATA 60.428 54.545 0.00 0.00 0.00 1.75
3776 7179 1.697291 GGAGAGGGACATGGGGAGAAT 60.697 57.143 0.00 0.00 0.00 2.40
3777 7180 0.326618 GGAGAGGGACATGGGGAGAA 60.327 60.000 0.00 0.00 0.00 2.87
3778 7181 1.314867 GGAGAGGGACATGGGGAGA 59.685 63.158 0.00 0.00 0.00 3.71
3779 7182 1.768077 GGGAGAGGGACATGGGGAG 60.768 68.421 0.00 0.00 0.00 4.30
3780 7183 2.372688 GGGAGAGGGACATGGGGA 59.627 66.667 0.00 0.00 0.00 4.81
3781 7184 3.164269 CGGGAGAGGGACATGGGG 61.164 72.222 0.00 0.00 0.00 4.96
3782 7185 3.164269 CCGGGAGAGGGACATGGG 61.164 72.222 0.00 0.00 0.00 4.00
3833 7243 2.681848 GCACATGGTCTCTTGATCCTTG 59.318 50.000 0.00 0.00 34.15 3.61
3835 7245 1.911357 TGCACATGGTCTCTTGATCCT 59.089 47.619 0.00 0.00 0.00 3.24
3836 7246 2.408271 TGCACATGGTCTCTTGATCC 57.592 50.000 0.00 0.00 0.00 3.36
3837 7247 2.033049 GCATGCACATGGTCTCTTGATC 59.967 50.000 14.21 0.00 39.16 2.92
3839 7249 1.456296 GCATGCACATGGTCTCTTGA 58.544 50.000 14.21 0.00 39.16 3.02
3841 7251 0.321919 ACGCATGCACATGGTCTCTT 60.322 50.000 19.57 0.00 39.16 2.85
3842 7252 0.321919 AACGCATGCACATGGTCTCT 60.322 50.000 19.57 0.00 39.16 3.10
3878 7293 0.896940 ATGCATTGGATGGCCGGATC 60.897 55.000 5.05 0.00 36.79 3.36
3975 7791 6.894339 TGATTAGCGGAATCTGACATACTA 57.106 37.500 13.44 0.00 43.90 1.82
4074 7893 4.100963 TCAAGATGCCCTCGCTTTATAAGA 59.899 41.667 0.00 0.00 35.36 2.10
4095 7921 2.267426 CAAGATCAATGCCGTACGTCA 58.733 47.619 15.21 8.26 0.00 4.35
4110 7936 2.878406 GCTGGTAACACACACACAAGAT 59.122 45.455 0.00 0.00 46.17 2.40


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

AutoCloner maintained by Alex Coulton.