Multiple sequence alignment - TraesCS1B01G294000

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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 TraesCS1B01G294000 chr1B 100.000 3632 0 0 1 3632 511972279 511975910 0.000000e+00 6708
1 TraesCS1B01G294000 chr1B 83.036 2240 305 37 868 3060 175429793 175427582 0.000000e+00 1962
2 TraesCS1B01G294000 chr1D 93.100 3087 139 40 1 3060 381972954 381975993 0.000000e+00 4453
3 TraesCS1B01G294000 chr1D 82.872 2277 310 41 832 3060 114366058 114363814 0.000000e+00 1971
4 TraesCS1B01G294000 chr1D 93.210 324 21 1 3056 3378 464850233 464850556 3.280000e-130 475
5 TraesCS1B01G294000 chr1D 92.835 321 20 3 3060 3378 184384360 184384041 2.550000e-126 462
6 TraesCS1B01G294000 chr1A 91.519 3113 171 45 1 3060 482247599 482250671 0.000000e+00 4200
7 TraesCS1B01G294000 chr1A 82.777 2276 315 40 832 3060 124897914 124895669 0.000000e+00 1960
8 TraesCS1B01G294000 chr5D 78.676 1632 280 34 885 2464 40929133 40927518 0.000000e+00 1024
9 TraesCS1B01G294000 chr5B 93.808 323 18 2 3058 3378 461609151 461608829 5.450000e-133 484
10 TraesCS1B01G294000 chr5B 94.262 244 13 1 3377 3619 597224505 597224262 4.430000e-99 372
11 TraesCS1B01G294000 chrUn 93.125 320 20 2 3060 3377 154744621 154744940 5.490000e-128 468
12 TraesCS1B01G294000 chrUn 92.857 322 19 4 3060 3378 46246609 46246929 7.100000e-127 464
13 TraesCS1B01G294000 chr6B 92.879 323 21 2 3058 3378 10899137 10899459 5.490000e-128 468
14 TraesCS1B01G294000 chr2D 92.049 327 24 2 3054 3378 608741783 608741457 3.300000e-125 459
15 TraesCS1B01G294000 chr3D 91.592 333 25 3 3049 3378 16536739 16536407 1.190000e-124 457
16 TraesCS1B01G294000 chr3D 91.592 333 25 3 3049 3378 16546438 16546106 1.190000e-124 457
17 TraesCS1B01G294000 chr4B 94.628 242 13 0 3378 3619 547548572 547548331 3.420000e-100 375
18 TraesCS1B01G294000 chr4B 93.827 243 15 0 3377 3619 535719047 535718805 2.060000e-97 366
19 TraesCS1B01G294000 chr4B 93.496 246 16 0 3374 3619 577665367 577665612 2.060000e-97 366
20 TraesCS1B01G294000 chr7B 94.958 238 12 0 3382 3619 679994772 679995009 1.230000e-99 374
21 TraesCS1B01G294000 chr7B 93.902 246 15 0 3374 3619 88556871 88557116 4.430000e-99 372
22 TraesCS1B01G294000 chr7B 94.191 241 14 0 3377 3617 344307075 344306835 5.730000e-98 368
23 TraesCS1B01G294000 chr2B 94.239 243 14 0 3377 3619 493558892 493558650 4.430000e-99 372
24 TraesCS1B01G294000 chr2B 93.522 247 15 1 3371 3616 4776407 4776653 2.060000e-97 366


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 TraesCS1B01G294000 chr1B 511972279 511975910 3631 False 6708 6708 100.000 1 3632 1 chr1B.!!$F1 3631
1 TraesCS1B01G294000 chr1B 175427582 175429793 2211 True 1962 1962 83.036 868 3060 1 chr1B.!!$R1 2192
2 TraesCS1B01G294000 chr1D 381972954 381975993 3039 False 4453 4453 93.100 1 3060 1 chr1D.!!$F1 3059
3 TraesCS1B01G294000 chr1D 114363814 114366058 2244 True 1971 1971 82.872 832 3060 1 chr1D.!!$R1 2228
4 TraesCS1B01G294000 chr1A 482247599 482250671 3072 False 4200 4200 91.519 1 3060 1 chr1A.!!$F1 3059
5 TraesCS1B01G294000 chr1A 124895669 124897914 2245 True 1960 1960 82.777 832 3060 1 chr1A.!!$R1 2228
6 TraesCS1B01G294000 chr5D 40927518 40929133 1615 True 1024 1024 78.676 885 2464 1 chr5D.!!$R1 1579

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
893 959 1.152839 CTCTCGGTCTCTCCTCCCC 60.153 68.421 0.00 0.0 0.0 4.81 F
1412 1532 0.390866 CTCAAGCTGCACTCGTGGAT 60.391 55.000 1.02 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 2146 0.250901 AACCTGCCCATCACAGTGTC 60.251 55.0 0.0 0.0 33.09 3.67 R
3324 3458 0.179092 GCAGCCTTGCCATTGATTCC 60.179 55.0 0.0 0.0 44.74 3.01 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
118 121 4.163552 TGTCAGTCAAATCATCGTACGAC 58.836 43.478 22.14 5.69 0.00 4.34
166 169 2.171003 GATGTGTCAAAAGGGGGAAGG 58.829 52.381 0.00 0.00 0.00 3.46
261 268 8.782533 AATTTCAGTTTCAAGTTCACGTATTC 57.217 30.769 0.00 0.00 0.00 1.75
377 384 9.681692 CAAAATGAACATGAGAACATTCACTAA 57.318 29.630 0.00 0.00 34.15 2.24
457 472 8.328146 GTGACTTTCCTGTTTCTTTATTTTTGC 58.672 33.333 0.00 0.00 0.00 3.68
458 473 8.257306 TGACTTTCCTGTTTCTTTATTTTTGCT 58.743 29.630 0.00 0.00 0.00 3.91
493 515 8.936864 AGAACATGAGCTTGTGTTTACTAATAC 58.063 33.333 15.91 4.48 38.57 1.89
495 517 7.165485 ACATGAGCTTGTGTTTACTAATACCA 58.835 34.615 0.00 0.00 0.00 3.25
513 536 7.896383 AATACCAAAATGCAGGCTCTAATTA 57.104 32.000 0.00 0.00 0.00 1.40
566 589 7.338196 TCTTGTAAAATGACACTTTGGACAAGA 59.662 33.333 17.48 17.48 42.41 3.02
672 714 9.929722 GGAATATTTTTGTTTTTGAGACAAACC 57.070 29.630 2.24 0.00 44.16 3.27
683 725 6.877611 TTTGAGACAAACCTTGAGGAATAC 57.122 37.500 3.59 0.00 38.94 1.89
684 726 5.825593 TGAGACAAACCTTGAGGAATACT 57.174 39.130 3.59 0.00 38.94 2.12
686 728 6.601332 TGAGACAAACCTTGAGGAATACTTT 58.399 36.000 3.59 0.00 38.94 2.66
742 785 5.744666 TTTTAGGACAACTTTGAGGAACG 57.255 39.130 0.00 0.00 0.00 3.95
744 787 1.766496 AGGACAACTTTGAGGAACGGA 59.234 47.619 0.00 0.00 0.00 4.69
797 847 2.210116 AGCATACTCCGGTTAATTGCG 58.790 47.619 0.00 0.00 33.99 4.85
820 870 3.359523 GGCCCACGTTCCGAAACC 61.360 66.667 0.00 0.00 31.27 3.27
821 871 3.359523 GCCCACGTTCCGAAACCC 61.360 66.667 0.00 0.00 31.27 4.11
822 872 2.670592 CCCACGTTCCGAAACCCC 60.671 66.667 0.00 0.00 31.27 4.95
823 873 2.670592 CCACGTTCCGAAACCCCC 60.671 66.667 0.00 0.00 31.27 5.40
824 874 2.111460 CACGTTCCGAAACCCCCA 59.889 61.111 0.00 0.00 31.27 4.96
825 875 2.111669 ACGTTCCGAAACCCCCAC 59.888 61.111 0.00 0.00 31.27 4.61
826 876 3.045492 CGTTCCGAAACCCCCACG 61.045 66.667 0.00 0.00 31.27 4.94
827 877 3.359523 GTTCCGAAACCCCCACGC 61.360 66.667 0.00 0.00 0.00 5.34
828 878 3.875023 TTCCGAAACCCCCACGCA 61.875 61.111 0.00 0.00 0.00 5.24
829 879 3.417167 TTCCGAAACCCCCACGCAA 62.417 57.895 0.00 0.00 0.00 4.85
852 913 3.723348 GTCGCCGTTTCAGCCCAC 61.723 66.667 0.00 0.00 0.00 4.61
858 919 2.398554 CGTTTCAGCCCACCATCCG 61.399 63.158 0.00 0.00 0.00 4.18
880 941 4.504461 CGTATCCCAAAAATCAGTCTCTCG 59.496 45.833 0.00 0.00 0.00 4.04
893 959 1.152839 CTCTCGGTCTCTCCTCCCC 60.153 68.421 0.00 0.00 0.00 4.81
1034 1112 4.452733 CGTTGCGACCCTCCCCTC 62.453 72.222 0.00 0.00 0.00 4.30
1039 1117 3.756783 CGACCCTCCCCTCTCCCT 61.757 72.222 0.00 0.00 0.00 4.20
1059 1149 1.826054 CTGCTCCTCCTCCGACGAT 60.826 63.158 0.00 0.00 0.00 3.73
1064 1154 0.835276 TCCTCCTCCGACGATGACTA 59.165 55.000 0.00 0.00 0.00 2.59
1066 1156 2.636403 TCCTCCTCCGACGATGACTATA 59.364 50.000 0.00 0.00 0.00 1.31
1140 1236 3.667282 CAGCACCAGCACCAGCAC 61.667 66.667 0.00 0.00 45.49 4.40
1141 1237 4.962836 AGCACCAGCACCAGCACC 62.963 66.667 0.00 0.00 45.49 5.01
1143 1239 2.981909 CACCAGCACCAGCACCAG 60.982 66.667 0.00 0.00 45.49 4.00
1144 1240 4.962836 ACCAGCACCAGCACCAGC 62.963 66.667 0.00 0.00 45.49 4.85
1145 1241 4.960866 CCAGCACCAGCACCAGCA 62.961 66.667 0.00 0.00 45.49 4.41
1383 1503 2.047274 CCCAATGCGTCGTCCTGT 60.047 61.111 0.00 0.00 0.00 4.00
1412 1532 0.390866 CTCAAGCTGCACTCGTGGAT 60.391 55.000 1.02 0.00 0.00 3.41
1449 1569 1.134560 GACTCTCCGTACAAGGCGATT 59.865 52.381 0.00 0.00 0.00 3.34
1488 1608 2.826702 GTGGAACCTGACGTGGGT 59.173 61.111 0.00 0.00 38.94 4.51
1759 1882 5.278957 GCCAAATTTAAGGAAGTCAAGCAGA 60.279 40.000 0.00 0.00 0.00 4.26
1824 1947 7.585286 TGTCACCTACAATACGTTTATGAAC 57.415 36.000 0.00 0.00 34.29 3.18
1947 2070 0.905809 ATTGCCTTTGCCATGCCTCA 60.906 50.000 0.00 0.00 36.33 3.86
1967 2090 3.036091 CAAGGATTTCCCATGCCAGATT 58.964 45.455 0.00 0.00 37.41 2.40
2020 2146 0.590682 TGCTGGTGTTGTTGCATACG 59.409 50.000 0.00 0.00 0.00 3.06
2044 2170 2.843730 ACTGTGATGGGCAGGTTATGTA 59.156 45.455 0.00 0.00 38.22 2.29
2148 2274 6.481976 TCAACATTGTCATTCGTAGTCTTTGT 59.518 34.615 0.00 0.00 0.00 2.83
2258 2387 3.187637 TGGTTTTTCTACCATCGAAAGCG 59.812 43.478 0.00 0.00 43.14 4.68
2445 2577 2.210961 GGCGTCCTTATAAACAGGCTC 58.789 52.381 7.54 0.00 0.00 4.70
2665 2798 2.625314 TGGATCTAGGAAGCAGACGATG 59.375 50.000 0.00 0.00 0.00 3.84
2717 2850 7.806690 TGTTTTTCTCGTGATCTGAATTTAGG 58.193 34.615 0.00 0.00 0.00 2.69
2725 2858 6.323996 TCGTGATCTGAATTTAGGTGGAGTAT 59.676 38.462 0.00 0.00 0.00 2.12
2747 2880 9.890629 AGTATTATTGTTCTCACTGCTGAATTA 57.109 29.630 0.00 0.00 0.00 1.40
2851 2985 9.491675 TTTACGGAATCTGAAATTGTAAGTGTA 57.508 29.630 0.00 0.00 0.00 2.90
2859 2993 7.037438 TCTGAAATTGTAAGTGTATCGTACCC 58.963 38.462 0.00 0.00 31.69 3.69
3060 3194 1.743996 GGAAGCTTCCTGTGCCTAAG 58.256 55.000 33.98 0.00 44.11 2.18
3061 3195 1.279271 GGAAGCTTCCTGTGCCTAAGA 59.721 52.381 33.98 0.00 44.11 2.10
3062 3196 2.626840 GAAGCTTCCTGTGCCTAAGAG 58.373 52.381 15.97 0.00 0.00 2.85
3063 3197 0.251634 AGCTTCCTGTGCCTAAGAGC 59.748 55.000 0.00 0.00 0.00 4.09
3064 3198 0.036010 GCTTCCTGTGCCTAAGAGCA 60.036 55.000 0.00 0.00 41.46 4.26
3065 3199 1.407989 GCTTCCTGTGCCTAAGAGCAT 60.408 52.381 0.00 0.00 46.24 3.79
3066 3200 2.559440 CTTCCTGTGCCTAAGAGCATC 58.441 52.381 0.00 0.00 46.24 3.91
3108 3242 2.406616 CCCCCATGCGACTTTTCGG 61.407 63.158 0.00 0.00 45.98 4.30
3109 3243 2.485122 CCCATGCGACTTTTCGGC 59.515 61.111 0.00 0.00 45.98 5.54
3110 3244 2.485122 CCATGCGACTTTTCGGCC 59.515 61.111 0.00 0.00 45.98 6.13
3111 3245 2.331893 CCATGCGACTTTTCGGCCA 61.332 57.895 2.24 0.00 45.98 5.36
3112 3246 1.154225 CATGCGACTTTTCGGCCAC 60.154 57.895 2.24 0.00 45.98 5.01
3113 3247 2.332654 ATGCGACTTTTCGGCCACC 61.333 57.895 2.24 0.00 45.98 4.61
3139 3273 2.159181 AAAAATCGGTCCAGTCGCG 58.841 52.632 0.00 0.00 0.00 5.87
3140 3274 1.908066 AAAAATCGGTCCAGTCGCGC 61.908 55.000 0.00 0.00 0.00 6.86
3141 3275 4.814294 AATCGGTCCAGTCGCGCC 62.814 66.667 0.00 0.00 0.00 6.53
3157 3291 4.248908 CCCCAAGGGCCCATTTTT 57.751 55.556 27.56 6.31 35.35 1.94
3158 3292 1.990424 CCCCAAGGGCCCATTTTTC 59.010 57.895 27.56 0.00 35.35 2.29
3159 3293 1.596408 CCCAAGGGCCCATTTTTCG 59.404 57.895 27.56 1.16 0.00 3.46
3160 3294 1.079197 CCAAGGGCCCATTTTTCGC 60.079 57.895 27.56 0.00 0.00 4.70
3161 3295 1.079197 CAAGGGCCCATTTTTCGCC 60.079 57.895 27.56 0.00 42.23 5.54
3162 3296 2.645192 AAGGGCCCATTTTTCGCCG 61.645 57.895 27.56 0.00 43.99 6.46
3163 3297 4.141965 GGGCCCATTTTTCGCCGG 62.142 66.667 19.95 0.00 43.99 6.13
3164 3298 4.812476 GGCCCATTTTTCGCCGGC 62.812 66.667 19.07 19.07 38.96 6.13
3165 3299 3.758931 GCCCATTTTTCGCCGGCT 61.759 61.111 26.68 0.00 36.65 5.52
3166 3300 2.489751 CCCATTTTTCGCCGGCTC 59.510 61.111 26.68 0.00 0.00 4.70
3167 3301 2.100216 CCATTTTTCGCCGGCTCG 59.900 61.111 26.68 10.37 0.00 5.03
3179 3313 3.200522 GGCTCGGGCTGAAATTGG 58.799 61.111 7.48 0.00 38.73 3.16
3180 3314 2.491621 GCTCGGGCTGAAATTGGC 59.508 61.111 0.00 0.00 35.22 4.52
3181 3315 2.793946 CTCGGGCTGAAATTGGCG 59.206 61.111 0.00 0.00 0.00 5.69
3182 3316 3.401243 CTCGGGCTGAAATTGGCGC 62.401 63.158 0.00 0.00 37.90 6.53
3183 3317 4.496927 CGGGCTGAAATTGGCGCC 62.497 66.667 22.73 22.73 41.75 6.53
3184 3318 3.381136 GGGCTGAAATTGGCGCCA 61.381 61.111 29.03 29.03 44.23 5.69
3185 3319 2.182537 GGCTGAAATTGGCGCCAG 59.817 61.111 30.75 18.11 42.06 4.85
3186 3320 2.507769 GCTGAAATTGGCGCCAGC 60.508 61.111 30.75 24.15 44.00 4.85
3187 3321 2.202518 CTGAAATTGGCGCCAGCG 60.203 61.111 30.75 7.86 46.35 5.18
3188 3322 3.688475 CTGAAATTGGCGCCAGCGG 62.688 63.158 30.75 20.16 46.35 5.52
3189 3323 3.439540 GAAATTGGCGCCAGCGGA 61.440 61.111 30.75 16.07 46.35 5.54
3190 3324 3.683587 GAAATTGGCGCCAGCGGAC 62.684 63.158 30.75 16.91 46.35 4.79
3204 3338 4.710167 GGACCCAACCCGAACCCG 62.710 72.222 0.00 0.00 0.00 5.28
3247 3381 3.322526 GCCGGGCGAATAGTTTTTG 57.677 52.632 1.81 0.00 0.00 2.44
3248 3382 0.179148 GCCGGGCGAATAGTTTTTGG 60.179 55.000 1.81 0.00 0.00 3.28
3249 3383 0.179148 CCGGGCGAATAGTTTTTGGC 60.179 55.000 0.00 0.00 0.00 4.52
3250 3384 0.179148 CGGGCGAATAGTTTTTGGCC 60.179 55.000 14.11 14.11 46.34 5.36
3251 3385 3.322526 GGCGAATAGTTTTTGGCCG 57.677 52.632 0.00 0.00 40.06 6.13
3252 3386 0.806241 GGCGAATAGTTTTTGGCCGA 59.194 50.000 0.00 0.00 40.06 5.54
3253 3387 1.200484 GGCGAATAGTTTTTGGCCGAA 59.800 47.619 0.00 0.00 40.06 4.30
3254 3388 2.351932 GGCGAATAGTTTTTGGCCGAAA 60.352 45.455 14.56 14.56 40.06 3.46
3255 3389 2.914838 GCGAATAGTTTTTGGCCGAAAG 59.085 45.455 17.68 6.29 0.00 2.62
3256 3390 3.365565 GCGAATAGTTTTTGGCCGAAAGA 60.366 43.478 17.68 8.48 0.00 2.52
3257 3391 4.403453 CGAATAGTTTTTGGCCGAAAGAG 58.597 43.478 17.68 3.11 0.00 2.85
3258 3392 3.850122 ATAGTTTTTGGCCGAAAGAGC 57.150 42.857 17.68 12.17 0.00 4.09
3301 3435 4.856607 CGCCCGCCTCGTCTTCTC 62.857 72.222 0.00 0.00 0.00 2.87
3302 3436 4.516195 GCCCGCCTCGTCTTCTCC 62.516 72.222 0.00 0.00 0.00 3.71
3303 3437 3.839432 CCCGCCTCGTCTTCTCCC 61.839 72.222 0.00 0.00 0.00 4.30
3304 3438 4.194720 CCGCCTCGTCTTCTCCCG 62.195 72.222 0.00 0.00 0.00 5.14
3305 3439 3.132139 CGCCTCGTCTTCTCCCGA 61.132 66.667 0.00 0.00 0.00 5.14
3306 3440 2.490685 GCCTCGTCTTCTCCCGAC 59.509 66.667 0.00 0.00 0.00 4.79
3310 3444 3.441290 CGTCTTCTCCCGACGCCT 61.441 66.667 0.00 0.00 46.12 5.52
3311 3445 2.490685 GTCTTCTCCCGACGCCTC 59.509 66.667 0.00 0.00 0.00 4.70
3312 3446 3.132139 TCTTCTCCCGACGCCTCG 61.132 66.667 0.00 0.00 39.83 4.63
3320 3454 2.809601 CGACGCCTCGGTTTCCTG 60.810 66.667 0.00 0.00 36.16 3.86
3321 3455 3.119096 GACGCCTCGGTTTCCTGC 61.119 66.667 0.00 0.00 0.00 4.85
3325 3459 4.778143 CCTCGGTTTCCTGCGGGG 62.778 72.222 12.87 0.00 0.00 5.73
3326 3460 3.702048 CTCGGTTTCCTGCGGGGA 61.702 66.667 12.87 0.00 43.41 4.81
3333 3467 4.984194 TCCTGCGGGGAATCAATG 57.016 55.556 12.87 0.00 41.91 2.82
3334 3468 1.227102 TCCTGCGGGGAATCAATGG 59.773 57.895 12.87 0.00 41.91 3.16
3335 3469 2.492773 CCTGCGGGGAATCAATGGC 61.493 63.158 2.57 0.00 37.23 4.40
3336 3470 1.753848 CTGCGGGGAATCAATGGCA 60.754 57.895 0.00 0.00 0.00 4.92
3337 3471 1.304796 TGCGGGGAATCAATGGCAA 60.305 52.632 0.00 0.00 0.00 4.52
3338 3472 1.321805 TGCGGGGAATCAATGGCAAG 61.322 55.000 0.00 0.00 0.00 4.01
3339 3473 2.019897 GCGGGGAATCAATGGCAAGG 62.020 60.000 0.00 0.00 0.00 3.61
3340 3474 1.825341 GGGGAATCAATGGCAAGGC 59.175 57.895 0.00 0.00 0.00 4.35
3341 3475 0.688749 GGGGAATCAATGGCAAGGCT 60.689 55.000 0.00 0.00 0.00 4.58
3342 3476 0.462789 GGGAATCAATGGCAAGGCTG 59.537 55.000 0.00 0.00 0.00 4.85
3362 3496 4.479993 GCCGGTCAGCTCTGCCAT 62.480 66.667 1.90 0.00 0.00 4.40
3363 3497 2.270205 CCGGTCAGCTCTGCCATT 59.730 61.111 0.00 0.00 0.00 3.16
3364 3498 2.110967 CCGGTCAGCTCTGCCATTG 61.111 63.158 0.00 0.00 0.00 2.82
3365 3499 1.078918 CGGTCAGCTCTGCCATTGA 60.079 57.895 9.72 0.00 0.00 2.57
3366 3500 0.463295 CGGTCAGCTCTGCCATTGAT 60.463 55.000 9.72 0.00 0.00 2.57
3367 3501 1.760192 GGTCAGCTCTGCCATTGATT 58.240 50.000 0.00 0.00 0.00 2.57
3368 3502 1.674962 GGTCAGCTCTGCCATTGATTC 59.325 52.381 0.00 0.00 0.00 2.52
3369 3503 1.674962 GTCAGCTCTGCCATTGATTCC 59.325 52.381 0.00 0.00 0.00 3.01
3370 3504 1.562942 TCAGCTCTGCCATTGATTCCT 59.437 47.619 0.00 0.00 0.00 3.36
3371 3505 1.948145 CAGCTCTGCCATTGATTCCTC 59.052 52.381 0.00 0.00 0.00 3.71
3372 3506 0.942962 GCTCTGCCATTGATTCCTCG 59.057 55.000 0.00 0.00 0.00 4.63
3373 3507 0.942962 CTCTGCCATTGATTCCTCGC 59.057 55.000 0.00 0.00 0.00 5.03
3374 3508 0.811219 TCTGCCATTGATTCCTCGCG 60.811 55.000 0.00 0.00 0.00 5.87
3375 3509 1.779025 CTGCCATTGATTCCTCGCGG 61.779 60.000 6.13 0.00 0.00 6.46
3376 3510 2.546494 GCCATTGATTCCTCGCGGG 61.546 63.158 6.13 0.59 0.00 6.13
3377 3511 2.546494 CCATTGATTCCTCGCGGGC 61.546 63.158 6.13 0.00 34.39 6.13
3378 3512 1.524621 CATTGATTCCTCGCGGGCT 60.525 57.895 6.13 0.00 34.39 5.19
3379 3513 1.227674 ATTGATTCCTCGCGGGCTC 60.228 57.895 6.13 7.55 34.39 4.70
3380 3514 1.690219 ATTGATTCCTCGCGGGCTCT 61.690 55.000 6.13 0.00 34.39 4.09
3381 3515 1.899437 TTGATTCCTCGCGGGCTCTT 61.899 55.000 6.13 0.00 34.39 2.85
3382 3516 1.592939 GATTCCTCGCGGGCTCTTC 60.593 63.158 6.13 0.00 34.39 2.87
3383 3517 2.022240 GATTCCTCGCGGGCTCTTCT 62.022 60.000 6.13 0.00 34.39 2.85
3384 3518 2.022240 ATTCCTCGCGGGCTCTTCTC 62.022 60.000 6.13 0.00 34.39 2.87
3385 3519 4.214327 CCTCGCGGGCTCTTCTCC 62.214 72.222 6.13 0.00 0.00 3.71
3386 3520 4.214327 CTCGCGGGCTCTTCTCCC 62.214 72.222 6.13 0.00 40.43 4.30
3390 3524 3.474570 CGGGCTCTTCTCCCCCAG 61.475 72.222 0.00 0.00 40.75 4.45
3391 3525 3.803162 GGGCTCTTCTCCCCCAGC 61.803 72.222 0.00 0.00 38.70 4.85
3392 3526 3.803162 GGCTCTTCTCCCCCAGCC 61.803 72.222 0.00 0.00 44.63 4.85
3393 3527 3.803162 GCTCTTCTCCCCCAGCCC 61.803 72.222 0.00 0.00 0.00 5.19
3394 3528 2.041928 CTCTTCTCCCCCAGCCCT 59.958 66.667 0.00 0.00 0.00 5.19
3395 3529 2.041265 TCTTCTCCCCCAGCCCTC 59.959 66.667 0.00 0.00 0.00 4.30
3396 3530 3.093172 CTTCTCCCCCAGCCCTCC 61.093 72.222 0.00 0.00 0.00 4.30
3397 3531 4.760220 TTCTCCCCCAGCCCTCCC 62.760 72.222 0.00 0.00 0.00 4.30
3405 3539 4.787280 CAGCCCTCCCTCTCCCGT 62.787 72.222 0.00 0.00 0.00 5.28
3406 3540 4.787280 AGCCCTCCCTCTCCCGTG 62.787 72.222 0.00 0.00 0.00 4.94
3429 3563 4.506255 CCGCCCAACCCCTCCATC 62.506 72.222 0.00 0.00 0.00 3.51
3430 3564 3.411517 CGCCCAACCCCTCCATCT 61.412 66.667 0.00 0.00 0.00 2.90
3431 3565 2.597903 GCCCAACCCCTCCATCTC 59.402 66.667 0.00 0.00 0.00 2.75
3432 3566 3.061905 GCCCAACCCCTCCATCTCC 62.062 68.421 0.00 0.00 0.00 3.71
3433 3567 2.386935 CCCAACCCCTCCATCTCCC 61.387 68.421 0.00 0.00 0.00 4.30
3434 3568 1.308216 CCAACCCCTCCATCTCCCT 60.308 63.158 0.00 0.00 0.00 4.20
3435 3569 1.348775 CCAACCCCTCCATCTCCCTC 61.349 65.000 0.00 0.00 0.00 4.30
3436 3570 1.004891 AACCCCTCCATCTCCCTCC 59.995 63.158 0.00 0.00 0.00 4.30
3437 3571 2.122189 CCCCTCCATCTCCCTCCC 60.122 72.222 0.00 0.00 0.00 4.30
3438 3572 2.122189 CCCTCCATCTCCCTCCCC 60.122 72.222 0.00 0.00 0.00 4.81
3439 3573 2.731461 CCCTCCATCTCCCTCCCCT 61.731 68.421 0.00 0.00 0.00 4.79
3440 3574 1.319799 CCTCCATCTCCCTCCCCTT 59.680 63.158 0.00 0.00 0.00 3.95
3441 3575 0.327964 CCTCCATCTCCCTCCCCTTT 60.328 60.000 0.00 0.00 0.00 3.11
3442 3576 1.135960 CTCCATCTCCCTCCCCTTTC 58.864 60.000 0.00 0.00 0.00 2.62
3443 3577 0.327576 TCCATCTCCCTCCCCTTTCC 60.328 60.000 0.00 0.00 0.00 3.13
3444 3578 1.356494 CCATCTCCCTCCCCTTTCCC 61.356 65.000 0.00 0.00 0.00 3.97
3445 3579 1.384643 ATCTCCCTCCCCTTTCCCG 60.385 63.158 0.00 0.00 0.00 5.14
3446 3580 1.898190 ATCTCCCTCCCCTTTCCCGA 61.898 60.000 0.00 0.00 0.00 5.14
3447 3581 1.384643 CTCCCTCCCCTTTCCCGAT 60.385 63.158 0.00 0.00 0.00 4.18
3448 3582 1.692749 TCCCTCCCCTTTCCCGATG 60.693 63.158 0.00 0.00 0.00 3.84
3449 3583 2.757124 CCCTCCCCTTTCCCGATGG 61.757 68.421 0.00 0.00 0.00 3.51
3450 3584 2.193248 CTCCCCTTTCCCGATGGC 59.807 66.667 0.00 0.00 0.00 4.40
3451 3585 3.416880 TCCCCTTTCCCGATGGCC 61.417 66.667 0.00 0.00 0.00 5.36
3452 3586 4.875713 CCCCTTTCCCGATGGCCG 62.876 72.222 0.00 0.00 38.18 6.13
3453 3587 3.792736 CCCTTTCCCGATGGCCGA 61.793 66.667 0.00 0.00 41.76 5.54
3454 3588 2.203070 CCTTTCCCGATGGCCGAG 60.203 66.667 0.00 0.00 41.76 4.63
3455 3589 2.897350 CTTTCCCGATGGCCGAGC 60.897 66.667 0.00 0.00 41.76 5.03
3456 3590 4.830765 TTTCCCGATGGCCGAGCG 62.831 66.667 0.00 1.57 41.76 5.03
3460 3594 3.564027 CCGATGGCCGAGCGTTTC 61.564 66.667 10.99 0.00 41.76 2.78
3461 3595 2.509336 CGATGGCCGAGCGTTTCT 60.509 61.111 0.00 0.00 41.76 2.52
3462 3596 2.517450 CGATGGCCGAGCGTTTCTC 61.517 63.158 0.00 0.00 41.76 2.87
3463 3597 2.125106 ATGGCCGAGCGTTTCTCC 60.125 61.111 0.00 0.00 38.62 3.71
3464 3598 4.735132 TGGCCGAGCGTTTCTCCG 62.735 66.667 0.00 0.00 38.62 4.63
3466 3600 4.430765 GCCGAGCGTTTCTCCGGA 62.431 66.667 2.93 2.93 38.62 5.14
3467 3601 2.202623 CCGAGCGTTTCTCCGGAG 60.203 66.667 26.32 26.32 38.62 4.63
3468 3602 2.697761 CCGAGCGTTTCTCCGGAGA 61.698 63.158 30.49 30.49 38.62 3.71
3469 3603 1.514443 CGAGCGTTTCTCCGGAGAC 60.514 63.158 33.75 22.15 38.62 3.36
3521 3655 2.981909 TCCGCGAACAGGAGTCGT 60.982 61.111 8.23 0.00 33.19 4.34
3522 3656 2.805353 CCGCGAACAGGAGTCGTG 60.805 66.667 8.23 11.22 37.16 4.35
3523 3657 2.805353 CGCGAACAGGAGTCGTGG 60.805 66.667 16.69 1.01 34.28 4.94
3524 3658 3.112709 GCGAACAGGAGTCGTGGC 61.113 66.667 16.69 7.21 0.00 5.01
3525 3659 2.651361 CGAACAGGAGTCGTGGCT 59.349 61.111 16.69 3.82 0.00 4.75
3526 3660 1.444553 CGAACAGGAGTCGTGGCTC 60.445 63.158 16.69 11.28 34.89 4.70
3532 3666 4.580835 GAGTCGTGGCTCCTGTTC 57.419 61.111 0.00 0.00 0.00 3.18
3533 3667 1.079750 GAGTCGTGGCTCCTGTTCC 60.080 63.158 0.00 0.00 0.00 3.62
3534 3668 1.816863 GAGTCGTGGCTCCTGTTCCA 61.817 60.000 0.00 0.00 0.00 3.53
3535 3669 1.374758 GTCGTGGCTCCTGTTCCAG 60.375 63.158 0.00 0.00 32.15 3.86
3547 3681 2.267642 TTCCAGGCGAACATCCCG 59.732 61.111 0.00 0.00 0.00 5.14
3548 3682 3.323758 TTCCAGGCGAACATCCCGG 62.324 63.158 0.00 0.00 0.00 5.73
3555 3689 3.195698 GAACATCCCGGCGCTGTC 61.196 66.667 16.49 0.42 0.00 3.51
3585 3719 4.796231 CGGGCCGACGGACTGAAG 62.796 72.222 25.21 6.69 40.17 3.02
3586 3720 4.452733 GGGCCGACGGACTGAAGG 62.453 72.222 21.47 0.00 0.00 3.46
3588 3722 4.070552 GCCGACGGACTGAAGGCT 62.071 66.667 20.50 0.00 44.06 4.58
3589 3723 2.182030 CCGACGGACTGAAGGCTC 59.818 66.667 8.64 0.00 0.00 4.70
3590 3724 2.636412 CCGACGGACTGAAGGCTCA 61.636 63.158 8.64 0.00 0.00 4.26
3597 3731 3.571119 CTGAAGGCTCAGCAACGG 58.429 61.111 0.00 0.00 42.66 4.44
3598 3732 2.032528 TGAAGGCTCAGCAACGGG 59.967 61.111 0.00 0.00 0.00 5.28
3599 3733 2.747855 GAAGGCTCAGCAACGGGG 60.748 66.667 0.00 0.00 0.00 5.73
3600 3734 4.351054 AAGGCTCAGCAACGGGGG 62.351 66.667 0.00 0.00 0.00 5.40
3602 3736 4.785453 GGCTCAGCAACGGGGGAG 62.785 72.222 0.00 0.00 0.00 4.30
3603 3737 4.021925 GCTCAGCAACGGGGGAGT 62.022 66.667 0.00 0.00 0.00 3.85
3604 3738 2.046892 CTCAGCAACGGGGGAGTG 60.047 66.667 0.00 0.00 0.00 3.51
3605 3739 4.329545 TCAGCAACGGGGGAGTGC 62.330 66.667 0.00 0.00 0.00 4.40
3616 3750 4.506255 GGAGTGCCCATTCCCCCG 62.506 72.222 0.00 0.00 31.68 5.73
3617 3751 3.728373 GAGTGCCCATTCCCCCGT 61.728 66.667 0.00 0.00 0.00 5.28
3618 3752 3.264845 AGTGCCCATTCCCCCGTT 61.265 61.111 0.00 0.00 0.00 4.44
3619 3753 2.283604 GTGCCCATTCCCCCGTTT 60.284 61.111 0.00 0.00 0.00 3.60
3620 3754 1.000646 GTGCCCATTCCCCCGTTTA 60.001 57.895 0.00 0.00 0.00 2.01
3621 3755 1.035385 GTGCCCATTCCCCCGTTTAG 61.035 60.000 0.00 0.00 0.00 1.85
3622 3756 1.455032 GCCCATTCCCCCGTTTAGG 60.455 63.158 0.00 0.00 40.63 2.69
3631 3765 3.074281 CCGTTTAGGGCTGGACCA 58.926 61.111 0.00 0.00 42.05 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 9.677567 GACAGTGCATCTTCTAAATTAAACAAA 57.322 29.630 0.00 0.00 0.00 2.83
76 77 8.507249 ACTGACAGTGCATCTTCTAAATTAAAC 58.493 33.333 7.47 0.00 0.00 2.01
118 121 6.095440 ACAAGAAACTGGGGATCATTATTTCG 59.905 38.462 0.00 0.00 31.96 3.46
166 169 5.746990 AGTAGGGTCATATATCTGCAACC 57.253 43.478 0.00 0.00 0.00 3.77
231 237 7.759433 ACGTGAACTTGAAACTGAAATTTCATT 59.241 29.630 20.76 13.01 45.55 2.57
261 268 6.905076 CGTTCCATTTCCATGTAAGAATAACG 59.095 38.462 0.00 0.00 0.00 3.18
271 278 2.094078 CCATTGCGTTCCATTTCCATGT 60.094 45.455 0.00 0.00 0.00 3.21
418 425 6.322201 ACAGGAAAGTCACATTTCATTTCACT 59.678 34.615 2.05 0.00 40.29 3.41
457 472 5.361285 ACAAGCTCATGTTCTACCCTAGTAG 59.639 44.000 0.00 0.00 46.34 2.57
458 473 5.127194 CACAAGCTCATGTTCTACCCTAGTA 59.873 44.000 0.00 0.00 0.00 1.82
492 514 9.759473 ATATATAATTAGAGCCTGCATTTTGGT 57.241 29.630 0.00 0.00 0.00 3.67
513 536 8.893563 TTTTCAACAGTGGGAGGAAAATATAT 57.106 30.769 0.00 0.00 33.83 0.86
587 610 4.855340 ACTCCCTCACAAGAAAAACAGAA 58.145 39.130 0.00 0.00 0.00 3.02
652 694 7.172361 CCTCAAGGTTTGTCTCAAAAACAAAAA 59.828 33.333 3.24 0.00 45.35 1.94
653 695 6.648725 CCTCAAGGTTTGTCTCAAAAACAAAA 59.351 34.615 3.24 0.00 45.35 2.44
657 699 5.576447 TCCTCAAGGTTTGTCTCAAAAAC 57.424 39.130 0.00 0.00 36.90 2.43
663 705 7.511959 AAAAGTATTCCTCAAGGTTTGTCTC 57.488 36.000 0.00 0.00 36.34 3.36
664 706 7.898014 AAAAAGTATTCCTCAAGGTTTGTCT 57.102 32.000 0.00 0.00 36.34 3.41
693 736 4.993705 TCCATTCCTCAAAGTTACACCT 57.006 40.909 0.00 0.00 0.00 4.00
694 737 6.590234 AAATCCATTCCTCAAAGTTACACC 57.410 37.500 0.00 0.00 0.00 4.16
724 767 1.766496 TCCGTTCCTCAAAGTTGTCCT 59.234 47.619 0.00 0.00 0.00 3.85
727 770 3.689649 GCATATCCGTTCCTCAAAGTTGT 59.310 43.478 0.00 0.00 0.00 3.32
729 772 4.080863 AGAGCATATCCGTTCCTCAAAGTT 60.081 41.667 0.00 0.00 0.00 2.66
730 773 3.452627 AGAGCATATCCGTTCCTCAAAGT 59.547 43.478 0.00 0.00 0.00 2.66
731 774 3.806521 CAGAGCATATCCGTTCCTCAAAG 59.193 47.826 0.00 0.00 0.00 2.77
732 775 3.197766 ACAGAGCATATCCGTTCCTCAAA 59.802 43.478 0.00 0.00 0.00 2.69
737 780 4.508124 CAGTTAACAGAGCATATCCGTTCC 59.492 45.833 8.61 0.00 0.00 3.62
738 781 4.508124 CCAGTTAACAGAGCATATCCGTTC 59.492 45.833 8.61 0.00 0.00 3.95
739 782 4.081087 ACCAGTTAACAGAGCATATCCGTT 60.081 41.667 8.61 0.00 0.00 4.44
740 783 3.451178 ACCAGTTAACAGAGCATATCCGT 59.549 43.478 8.61 0.00 0.00 4.69
741 784 3.804325 CACCAGTTAACAGAGCATATCCG 59.196 47.826 8.61 0.00 0.00 4.18
742 785 3.561725 GCACCAGTTAACAGAGCATATCC 59.438 47.826 8.61 0.00 0.00 2.59
744 787 4.194640 CAGCACCAGTTAACAGAGCATAT 58.805 43.478 16.34 0.00 0.00 1.78
815 865 2.732016 GGTTTGCGTGGGGGTTTC 59.268 61.111 0.00 0.00 0.00 2.78
852 913 4.207165 ACTGATTTTTGGGATACGGATGG 58.793 43.478 0.00 0.00 37.60 3.51
854 915 5.131142 AGAGACTGATTTTTGGGATACGGAT 59.869 40.000 0.00 0.00 37.60 4.18
858 919 4.811557 CCGAGAGACTGATTTTTGGGATAC 59.188 45.833 0.00 0.00 0.00 2.24
1034 1112 1.457455 GAGGAGGAGCAGGAGGGAG 60.457 68.421 0.00 0.00 0.00 4.30
1039 1117 2.043852 GTCGGAGGAGGAGCAGGA 60.044 66.667 0.00 0.00 0.00 3.86
1059 1149 1.470285 GGCTTGGCGTCGTTATAGTCA 60.470 52.381 0.00 0.00 0.00 3.41
1064 1154 2.124860 GGGGCTTGGCGTCGTTAT 60.125 61.111 0.00 0.00 0.00 1.89
1066 1156 4.699522 GAGGGGCTTGGCGTCGTT 62.700 66.667 0.00 0.00 0.00 3.85
1254 1353 4.599500 AGCACACTGGGGGTCCCT 62.599 66.667 8.15 0.00 45.70 4.20
1383 1503 3.008375 AGTGCAGCTTGAGAAGGATGTTA 59.992 43.478 0.00 0.00 0.00 2.41
1412 1532 1.372128 TCGTCGTCGTCGTCAGAGA 60.372 57.895 11.41 0.00 38.33 3.10
1449 1569 1.076412 AGCCTCTCGCATCCAGAGA 60.076 57.895 0.00 0.00 40.02 3.10
1488 1608 3.374988 CCGTGATAAGTGTGGAGTACGTA 59.625 47.826 0.00 0.00 0.00 3.57
1759 1882 7.985589 TCCTTGGTTCTACTCTCCTTTAAAAT 58.014 34.615 0.00 0.00 0.00 1.82
1766 1889 3.777522 CCAATCCTTGGTTCTACTCTCCT 59.222 47.826 0.00 0.00 45.93 3.69
1824 1947 0.895530 TACCTTTCTGGCAGAGACCG 59.104 55.000 17.91 9.06 40.22 4.79
1947 2070 3.052338 AGAATCTGGCATGGGAAATCCTT 60.052 43.478 0.00 0.00 36.20 3.36
1967 2090 3.055312 TGACGTACTCCTCTCTAGCAAGA 60.055 47.826 0.00 0.00 0.00 3.02
2020 2146 0.250901 AACCTGCCCATCACAGTGTC 60.251 55.000 0.00 0.00 33.09 3.67
2044 2170 1.436752 ACCCCTCCAATGTCCCATTTT 59.563 47.619 0.00 0.00 0.00 1.82
2148 2274 2.004583 CGGAGCACTTTCGACCAATA 57.995 50.000 0.00 0.00 0.00 1.90
2282 2411 1.180029 ATTTCCTGCTGCCATGTCAC 58.820 50.000 0.00 0.00 0.00 3.67
2445 2577 2.539476 GGGATTTTGCCATTGTAAGCG 58.461 47.619 0.00 0.00 0.00 4.68
2665 2798 6.228616 AGAAAGAGTAAGCTACCTCCAATC 57.771 41.667 8.53 5.70 0.00 2.67
2717 2850 6.036517 CAGCAGTGAGAACAATAATACTCCAC 59.963 42.308 0.00 0.00 0.00 4.02
2725 2858 7.334421 GGACTAATTCAGCAGTGAGAACAATAA 59.666 37.037 0.00 0.00 32.98 1.40
2747 2880 6.666678 ACATCCTATTGTCATTCATTGGACT 58.333 36.000 0.00 0.00 35.11 3.85
2851 2985 2.790433 AGCACAACAATTGGGTACGAT 58.210 42.857 10.83 0.00 36.14 3.73
3090 3224 2.406616 CCGAAAAGTCGCATGGGGG 61.407 63.158 10.21 0.00 46.28 5.40
3091 3225 3.051392 GCCGAAAAGTCGCATGGGG 62.051 63.158 10.21 0.00 46.28 4.96
3092 3226 2.485122 GCCGAAAAGTCGCATGGG 59.515 61.111 2.76 2.76 46.28 4.00
3093 3227 2.331893 TGGCCGAAAAGTCGCATGG 61.332 57.895 0.00 0.00 46.28 3.66
3094 3228 1.154225 GTGGCCGAAAAGTCGCATG 60.154 57.895 0.00 0.00 46.28 4.06
3095 3229 2.332654 GGTGGCCGAAAAGTCGCAT 61.333 57.895 0.00 0.00 46.28 4.73
3096 3230 2.975799 GGTGGCCGAAAAGTCGCA 60.976 61.111 0.00 0.00 46.28 5.10
3121 3255 1.908066 GCGCGACTGGACCGATTTTT 61.908 55.000 12.10 0.00 0.00 1.94
3122 3256 2.388232 GCGCGACTGGACCGATTTT 61.388 57.895 12.10 0.00 0.00 1.82
3123 3257 2.813908 GCGCGACTGGACCGATTT 60.814 61.111 12.10 0.00 0.00 2.17
3124 3258 4.814294 GGCGCGACTGGACCGATT 62.814 66.667 12.10 0.00 0.00 3.34
3141 3275 1.596408 CGAAAAATGGGCCCTTGGG 59.404 57.895 25.70 0.32 0.00 4.12
3142 3276 1.079197 GCGAAAAATGGGCCCTTGG 60.079 57.895 25.70 11.33 0.00 3.61
3143 3277 1.079197 GGCGAAAAATGGGCCCTTG 60.079 57.895 25.70 7.14 41.01 3.61
3144 3278 2.645192 CGGCGAAAAATGGGCCCTT 61.645 57.895 25.70 15.22 43.99 3.95
3145 3279 3.068064 CGGCGAAAAATGGGCCCT 61.068 61.111 25.70 5.48 43.99 5.19
3146 3280 4.141965 CCGGCGAAAAATGGGCCC 62.142 66.667 17.59 17.59 43.99 5.80
3147 3281 4.812476 GCCGGCGAAAAATGGGCC 62.812 66.667 12.58 0.00 43.42 5.80
3148 3282 3.699955 GAGCCGGCGAAAAATGGGC 62.700 63.158 23.20 0.00 44.07 5.36
3149 3283 2.489751 GAGCCGGCGAAAAATGGG 59.510 61.111 23.20 0.00 0.00 4.00
3150 3284 2.100216 CGAGCCGGCGAAAAATGG 59.900 61.111 23.20 0.00 0.00 3.16
3151 3285 2.100216 CCGAGCCGGCGAAAAATG 59.900 61.111 23.20 6.69 41.17 2.32
3152 3286 3.131478 CCCGAGCCGGCGAAAAAT 61.131 61.111 23.20 0.68 46.86 1.82
3161 3295 2.764314 CCAATTTCAGCCCGAGCCG 61.764 63.158 0.00 0.00 41.25 5.52
3162 3296 3.068729 GCCAATTTCAGCCCGAGCC 62.069 63.158 0.00 0.00 41.25 4.70
3163 3297 2.491621 GCCAATTTCAGCCCGAGC 59.508 61.111 0.00 0.00 40.32 5.03
3164 3298 2.793946 CGCCAATTTCAGCCCGAG 59.206 61.111 0.00 0.00 0.00 4.63
3165 3299 3.439540 GCGCCAATTTCAGCCCGA 61.440 61.111 0.00 0.00 0.00 5.14
3166 3300 4.496927 GGCGCCAATTTCAGCCCG 62.497 66.667 24.80 0.00 43.54 6.13
3169 3303 2.507769 GCTGGCGCCAATTTCAGC 60.508 61.111 32.09 24.77 44.34 4.26
3170 3304 2.202518 CGCTGGCGCCAATTTCAG 60.203 61.111 32.09 18.77 0.00 3.02
3171 3305 3.746889 CCGCTGGCGCCAATTTCA 61.747 61.111 32.09 6.08 38.24 2.69
3172 3306 3.439540 TCCGCTGGCGCCAATTTC 61.440 61.111 32.09 17.90 38.24 2.17
3173 3307 3.747976 GTCCGCTGGCGCCAATTT 61.748 61.111 32.09 0.00 38.24 1.82
3183 3317 4.323477 TTCGGGTTGGGTCCGCTG 62.323 66.667 0.00 0.00 46.43 5.18
3184 3318 4.324991 GTTCGGGTTGGGTCCGCT 62.325 66.667 0.00 0.00 46.43 5.52
3187 3321 4.710167 CGGGTTCGGGTTGGGTCC 62.710 72.222 0.00 0.00 0.00 4.46
3229 3363 0.179148 CCAAAAACTATTCGCCCGGC 60.179 55.000 0.00 0.00 0.00 6.13
3230 3364 0.179148 GCCAAAAACTATTCGCCCGG 60.179 55.000 0.00 0.00 0.00 5.73
3231 3365 0.179148 GGCCAAAAACTATTCGCCCG 60.179 55.000 0.00 0.00 0.00 6.13
3232 3366 0.179148 CGGCCAAAAACTATTCGCCC 60.179 55.000 2.24 0.00 32.61 6.13
3233 3367 0.806241 TCGGCCAAAAACTATTCGCC 59.194 50.000 2.24 0.00 0.00 5.54
3234 3368 2.622546 TTCGGCCAAAAACTATTCGC 57.377 45.000 2.24 0.00 0.00 4.70
3235 3369 4.403453 CTCTTTCGGCCAAAAACTATTCG 58.597 43.478 2.24 0.00 0.00 3.34
3236 3370 4.166523 GCTCTTTCGGCCAAAAACTATTC 58.833 43.478 2.24 0.00 0.00 1.75
3237 3371 4.174411 GCTCTTTCGGCCAAAAACTATT 57.826 40.909 2.24 0.00 0.00 1.73
3238 3372 3.850122 GCTCTTTCGGCCAAAAACTAT 57.150 42.857 2.24 0.00 0.00 2.12
3284 3418 4.856607 GAGAAGACGAGGCGGGCG 62.857 72.222 0.00 0.00 0.00 6.13
3285 3419 4.516195 GGAGAAGACGAGGCGGGC 62.516 72.222 0.00 0.00 0.00 6.13
3286 3420 3.839432 GGGAGAAGACGAGGCGGG 61.839 72.222 0.00 0.00 0.00 6.13
3287 3421 4.194720 CGGGAGAAGACGAGGCGG 62.195 72.222 0.00 0.00 0.00 6.13
3288 3422 3.132139 TCGGGAGAAGACGAGGCG 61.132 66.667 0.00 0.00 34.67 5.52
3289 3423 2.490685 GTCGGGAGAAGACGAGGC 59.509 66.667 0.00 0.00 42.89 4.70
3295 3429 3.132139 CGAGGCGTCGGGAGAAGA 61.132 66.667 20.58 0.00 42.87 2.87
3303 3437 2.809601 CAGGAAACCGAGGCGTCG 60.810 66.667 21.30 21.30 46.39 5.12
3304 3438 3.119096 GCAGGAAACCGAGGCGTC 61.119 66.667 0.00 0.00 0.00 5.19
3318 3452 1.321805 TTGCCATTGATTCCCCGCAG 61.322 55.000 0.00 0.00 0.00 5.18
3319 3453 1.304796 TTGCCATTGATTCCCCGCA 60.305 52.632 0.00 0.00 0.00 5.69
3320 3454 1.438814 CTTGCCATTGATTCCCCGC 59.561 57.895 0.00 0.00 0.00 6.13
3321 3455 2.019897 GCCTTGCCATTGATTCCCCG 62.020 60.000 0.00 0.00 0.00 5.73
3322 3456 0.688749 AGCCTTGCCATTGATTCCCC 60.689 55.000 0.00 0.00 0.00 4.81
3323 3457 0.462789 CAGCCTTGCCATTGATTCCC 59.537 55.000 0.00 0.00 0.00 3.97
3324 3458 0.179092 GCAGCCTTGCCATTGATTCC 60.179 55.000 0.00 0.00 44.74 3.01
3325 3459 3.357504 GCAGCCTTGCCATTGATTC 57.642 52.632 0.00 0.00 44.74 2.52
3345 3479 3.984193 AATGGCAGAGCTGACCGGC 62.984 63.158 0.00 0.00 37.98 6.13
3346 3480 2.110967 CAATGGCAGAGCTGACCGG 61.111 63.158 0.00 0.00 37.98 5.28
3347 3481 0.463295 ATCAATGGCAGAGCTGACCG 60.463 55.000 0.03 0.00 37.98 4.79
3348 3482 1.674962 GAATCAATGGCAGAGCTGACC 59.325 52.381 0.03 2.80 37.98 4.02
3349 3483 1.674962 GGAATCAATGGCAGAGCTGAC 59.325 52.381 0.85 0.00 39.62 3.51
3350 3484 1.562942 AGGAATCAATGGCAGAGCTGA 59.437 47.619 0.85 0.00 0.00 4.26
3351 3485 1.948145 GAGGAATCAATGGCAGAGCTG 59.052 52.381 0.00 0.00 0.00 4.24
3352 3486 1.474677 CGAGGAATCAATGGCAGAGCT 60.475 52.381 0.00 0.00 0.00 4.09
3353 3487 0.942962 CGAGGAATCAATGGCAGAGC 59.057 55.000 0.00 0.00 0.00 4.09
3354 3488 0.942962 GCGAGGAATCAATGGCAGAG 59.057 55.000 0.00 0.00 0.00 3.35
3355 3489 0.811219 CGCGAGGAATCAATGGCAGA 60.811 55.000 0.00 0.00 0.00 4.26
3356 3490 1.645455 CGCGAGGAATCAATGGCAG 59.355 57.895 0.00 0.00 0.00 4.85
3357 3491 3.812203 CGCGAGGAATCAATGGCA 58.188 55.556 0.00 0.00 0.00 4.92
3369 3503 4.214327 GGGAGAAGAGCCCGCGAG 62.214 72.222 8.23 0.00 35.50 5.03
3374 3508 3.803162 GCTGGGGGAGAAGAGCCC 61.803 72.222 0.00 0.00 45.25 5.19
3375 3509 3.803162 GGCTGGGGGAGAAGAGCC 61.803 72.222 0.00 0.00 44.10 4.70
3376 3510 3.803162 GGGCTGGGGGAGAAGAGC 61.803 72.222 0.00 0.00 0.00 4.09
3377 3511 2.041928 AGGGCTGGGGGAGAAGAG 59.958 66.667 0.00 0.00 0.00 2.85
3378 3512 2.041265 GAGGGCTGGGGGAGAAGA 59.959 66.667 0.00 0.00 0.00 2.87
3379 3513 3.093172 GGAGGGCTGGGGGAGAAG 61.093 72.222 0.00 0.00 0.00 2.85
3380 3514 4.760220 GGGAGGGCTGGGGGAGAA 62.760 72.222 0.00 0.00 0.00 2.87
3388 3522 4.787280 ACGGGAGAGGGAGGGCTG 62.787 72.222 0.00 0.00 0.00 4.85
3389 3523 4.787280 CACGGGAGAGGGAGGGCT 62.787 72.222 0.00 0.00 0.00 5.19
3412 3546 4.506255 GATGGAGGGGTTGGGCGG 62.506 72.222 0.00 0.00 0.00 6.13
3413 3547 3.406595 GAGATGGAGGGGTTGGGCG 62.407 68.421 0.00 0.00 0.00 6.13
3414 3548 2.597903 GAGATGGAGGGGTTGGGC 59.402 66.667 0.00 0.00 0.00 5.36
3415 3549 2.386935 GGGAGATGGAGGGGTTGGG 61.387 68.421 0.00 0.00 0.00 4.12
3416 3550 1.308216 AGGGAGATGGAGGGGTTGG 60.308 63.158 0.00 0.00 0.00 3.77
3417 3551 1.348775 GGAGGGAGATGGAGGGGTTG 61.349 65.000 0.00 0.00 0.00 3.77
3418 3552 1.004891 GGAGGGAGATGGAGGGGTT 59.995 63.158 0.00 0.00 0.00 4.11
3419 3553 2.706071 GGAGGGAGATGGAGGGGT 59.294 66.667 0.00 0.00 0.00 4.95
3420 3554 2.122189 GGGAGGGAGATGGAGGGG 60.122 72.222 0.00 0.00 0.00 4.79
3421 3555 2.122189 GGGGAGGGAGATGGAGGG 60.122 72.222 0.00 0.00 0.00 4.30
3422 3556 0.327964 AAAGGGGAGGGAGATGGAGG 60.328 60.000 0.00 0.00 0.00 4.30
3423 3557 1.135960 GAAAGGGGAGGGAGATGGAG 58.864 60.000 0.00 0.00 0.00 3.86
3424 3558 0.327576 GGAAAGGGGAGGGAGATGGA 60.328 60.000 0.00 0.00 0.00 3.41
3425 3559 1.356494 GGGAAAGGGGAGGGAGATGG 61.356 65.000 0.00 0.00 0.00 3.51
3426 3560 1.700042 CGGGAAAGGGGAGGGAGATG 61.700 65.000 0.00 0.00 0.00 2.90
3427 3561 1.384643 CGGGAAAGGGGAGGGAGAT 60.385 63.158 0.00 0.00 0.00 2.75
3428 3562 1.898190 ATCGGGAAAGGGGAGGGAGA 61.898 60.000 0.00 0.00 0.00 3.71
3429 3563 1.384643 ATCGGGAAAGGGGAGGGAG 60.385 63.158 0.00 0.00 0.00 4.30
3430 3564 1.692749 CATCGGGAAAGGGGAGGGA 60.693 63.158 0.00 0.00 0.00 4.20
3431 3565 2.757124 CCATCGGGAAAGGGGAGGG 61.757 68.421 0.00 0.00 35.59 4.30
3432 3566 2.919043 CCATCGGGAAAGGGGAGG 59.081 66.667 0.00 0.00 35.59 4.30
3433 3567 2.193248 GCCATCGGGAAAGGGGAG 59.807 66.667 0.00 0.00 35.59 4.30
3434 3568 3.416880 GGCCATCGGGAAAGGGGA 61.417 66.667 0.00 0.00 35.59 4.81
3435 3569 4.875713 CGGCCATCGGGAAAGGGG 62.876 72.222 2.24 0.00 35.59 4.79
3436 3570 3.757248 CTCGGCCATCGGGAAAGGG 62.757 68.421 2.24 0.00 43.26 3.95
3437 3571 2.203070 CTCGGCCATCGGGAAAGG 60.203 66.667 2.24 0.00 43.26 3.11
3438 3572 2.897350 GCTCGGCCATCGGGAAAG 60.897 66.667 2.24 0.00 43.26 2.62
3439 3573 4.830765 CGCTCGGCCATCGGGAAA 62.831 66.667 2.24 0.00 43.26 3.13
3443 3577 3.564027 GAAACGCTCGGCCATCGG 61.564 66.667 2.24 0.00 39.77 4.18
3444 3578 2.509336 AGAAACGCTCGGCCATCG 60.509 61.111 2.24 5.00 40.90 3.84
3445 3579 2.174319 GGAGAAACGCTCGGCCATC 61.174 63.158 2.24 0.00 44.91 3.51
3446 3580 2.125106 GGAGAAACGCTCGGCCAT 60.125 61.111 2.24 0.00 44.91 4.40
3447 3581 4.735132 CGGAGAAACGCTCGGCCA 62.735 66.667 2.24 0.00 44.91 5.36
3449 3583 4.430765 TCCGGAGAAACGCTCGGC 62.431 66.667 0.00 0.00 44.91 5.54
3450 3584 2.202623 CTCCGGAGAAACGCTCGG 60.203 66.667 28.21 0.00 44.91 4.63
3451 3585 1.514443 GTCTCCGGAGAAACGCTCG 60.514 63.158 35.18 5.38 44.91 5.03
3452 3586 1.514443 CGTCTCCGGAGAAACGCTC 60.514 63.158 35.18 20.20 43.17 5.03
3453 3587 1.924320 CTCGTCTCCGGAGAAACGCT 61.924 60.000 35.18 0.00 39.48 5.07
3454 3588 1.514443 CTCGTCTCCGGAGAAACGC 60.514 63.158 35.18 21.30 39.48 4.84
3455 3589 1.136984 CCTCGTCTCCGGAGAAACG 59.863 63.158 35.18 32.21 39.48 3.60
3456 3590 1.153804 GCCTCGTCTCCGGAGAAAC 60.154 63.158 35.18 22.94 39.48 2.78
3457 3591 2.697761 CGCCTCGTCTCCGGAGAAA 61.698 63.158 35.18 23.99 39.48 2.52
3458 3592 3.132139 CGCCTCGTCTCCGGAGAA 61.132 66.667 35.18 20.17 39.48 2.87
3504 3638 2.981909 ACGACTCCTGTTCGCGGA 60.982 61.111 6.13 0.00 0.00 5.54
3505 3639 2.805353 CACGACTCCTGTTCGCGG 60.805 66.667 6.13 0.00 0.00 6.46
3506 3640 2.805353 CCACGACTCCTGTTCGCG 60.805 66.667 0.00 0.00 0.00 5.87
3507 3641 3.112709 GCCACGACTCCTGTTCGC 61.113 66.667 0.00 0.00 0.00 4.70
3508 3642 1.444553 GAGCCACGACTCCTGTTCG 60.445 63.158 0.00 0.00 0.00 3.95
3509 3643 4.580835 GAGCCACGACTCCTGTTC 57.419 61.111 0.00 0.00 0.00 3.18
3515 3649 1.079750 GGAACAGGAGCCACGACTC 60.080 63.158 0.00 0.00 35.86 3.36
3516 3650 1.837051 TGGAACAGGAGCCACGACT 60.837 57.895 0.00 0.00 0.00 4.18
3517 3651 2.741092 TGGAACAGGAGCCACGAC 59.259 61.111 0.00 0.00 0.00 4.34
3530 3664 2.267642 CGGGATGTTCGCCTGGAA 59.732 61.111 0.00 0.00 0.00 3.53
3568 3702 4.796231 CTTCAGTCCGTCGGCCCG 62.796 72.222 6.34 0.00 0.00 6.13
3569 3703 4.452733 CCTTCAGTCCGTCGGCCC 62.453 72.222 6.34 0.00 0.00 5.80
3571 3705 3.991536 GAGCCTTCAGTCCGTCGGC 62.992 68.421 6.34 1.61 40.99 5.54
3572 3706 2.182030 GAGCCTTCAGTCCGTCGG 59.818 66.667 4.39 4.39 0.00 4.79
3573 3707 1.153939 CTGAGCCTTCAGTCCGTCG 60.154 63.158 0.00 0.00 44.74 5.12
3574 3708 4.900154 CTGAGCCTTCAGTCCGTC 57.100 61.111 0.00 0.00 44.74 4.79
3581 3715 2.032528 CCCGTTGCTGAGCCTTCA 59.967 61.111 0.23 0.00 0.00 3.02
3582 3716 2.747855 CCCCGTTGCTGAGCCTTC 60.748 66.667 0.23 0.00 0.00 3.46
3583 3717 4.351054 CCCCCGTTGCTGAGCCTT 62.351 66.667 0.23 0.00 0.00 4.35
3585 3719 4.785453 CTCCCCCGTTGCTGAGCC 62.785 72.222 0.23 0.00 0.00 4.70
3586 3720 4.021925 ACTCCCCCGTTGCTGAGC 62.022 66.667 0.00 0.00 0.00 4.26
3587 3721 2.046892 CACTCCCCCGTTGCTGAG 60.047 66.667 0.00 0.00 0.00 3.35
3588 3722 4.329545 GCACTCCCCCGTTGCTGA 62.330 66.667 0.00 0.00 0.00 4.26
3599 3733 4.506255 CGGGGGAATGGGCACTCC 62.506 72.222 0.00 0.00 0.00 3.85
3600 3734 2.781431 AAACGGGGGAATGGGCACTC 62.781 60.000 0.00 0.00 0.00 3.51
3601 3735 1.502527 TAAACGGGGGAATGGGCACT 61.503 55.000 0.00 0.00 0.00 4.40
3602 3736 1.000646 TAAACGGGGGAATGGGCAC 60.001 57.895 0.00 0.00 0.00 5.01
3603 3737 1.304952 CTAAACGGGGGAATGGGCA 59.695 57.895 0.00 0.00 0.00 5.36
3604 3738 1.455032 CCTAAACGGGGGAATGGGC 60.455 63.158 0.00 0.00 0.00 5.36
3614 3748 3.074281 TGGTCCAGCCCTAAACGG 58.926 61.111 0.00 0.00 36.04 4.44


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

AutoCloner maintained by Alex Coulton.