Multiple sequence alignment - TraesCS3A01G417600

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 TraesCS3A01G417600 chr3A 100.000 7934 0 0 1 7934 659933231 659941164 0.000000e+00 14652
1 TraesCS3A01G417600 chr3A 91.917 532 33 6 1 530 639697988 639698511 0.000000e+00 736
2 TraesCS3A01G417600 chr3D 92.378 2834 116 33 4603 7352 525728501 525731318 0.000000e+00 3945
3 TraesCS3A01G417600 chr3D 93.484 2394 95 15 531 2897 525724168 525726527 0.000000e+00 3500
4 TraesCS3A01G417600 chr3D 93.163 1726 83 18 2896 4594 525726602 525728319 0.000000e+00 2501
5 TraesCS3A01G417600 chr3D 84.296 433 18 16 7433 7838 525731364 525731773 2.090000e-100 377
6 TraesCS3A01G417600 chr3D 98.387 62 1 0 7873 7934 525731770 525731831 8.420000e-20 110
7 TraesCS3A01G417600 chr3B 93.907 2396 92 15 529 2897 694019057 694021425 0.000000e+00 3567
8 TraesCS3A01G417600 chr3B 92.419 1728 91 16 2896 4594 694021500 694023216 0.000000e+00 2429
9 TraesCS3A01G417600 chr3B 91.800 1756 84 26 4738 6443 694023274 694025019 0.000000e+00 2390
10 TraesCS3A01G417600 chr3B 89.617 732 46 19 6759 7466 694025546 694026271 0.000000e+00 904
11 TraesCS3A01G417600 chr3B 86.950 659 43 25 7311 7934 694026277 694026927 0.000000e+00 701
12 TraesCS3A01G417600 chr3B 95.847 313 11 1 6439 6751 694025130 694025440 9.190000e-139 505
13 TraesCS3A01G417600 chr7A 93.045 532 32 4 1 530 639315090 639315618 0.000000e+00 773
14 TraesCS3A01G417600 chr1A 92.789 527 32 5 1 526 508326618 508326097 0.000000e+00 758
15 TraesCS3A01G417600 chr1A 92.803 528 30 7 1 526 508347628 508347107 0.000000e+00 758
16 TraesCS3A01G417600 chr1A 92.600 527 33 5 1 526 508294403 508293882 0.000000e+00 752
17 TraesCS3A01G417600 chr5A 91.714 531 39 5 1 530 217003131 217003657 0.000000e+00 732
18 TraesCS3A01G417600 chr2A 91.589 535 37 7 1 530 22193011 22193542 0.000000e+00 732
19 TraesCS3A01G417600 chr2A 91.481 540 34 8 1 530 766134762 766134225 0.000000e+00 732
20 TraesCS3A01G417600 chr6A 91.557 533 33 8 1 530 377697731 377697208 0.000000e+00 725


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 TraesCS3A01G417600 chr3A 659933231 659941164 7933 False 14652.000000 14652 100.000000 1 7934 1 chr3A.!!$F2 7933
1 TraesCS3A01G417600 chr3A 639697988 639698511 523 False 736.000000 736 91.917000 1 530 1 chr3A.!!$F1 529
2 TraesCS3A01G417600 chr3D 525724168 525731831 7663 False 2086.600000 3945 92.341600 531 7934 5 chr3D.!!$F1 7403
3 TraesCS3A01G417600 chr3B 694019057 694026927 7870 False 1749.333333 3567 91.756667 529 7934 6 chr3B.!!$F1 7405
4 TraesCS3A01G417600 chr7A 639315090 639315618 528 False 773.000000 773 93.045000 1 530 1 chr7A.!!$F1 529
5 TraesCS3A01G417600 chr1A 508326097 508326618 521 True 758.000000 758 92.789000 1 526 1 chr1A.!!$R2 525
6 TraesCS3A01G417600 chr1A 508347107 508347628 521 True 758.000000 758 92.803000 1 526 1 chr1A.!!$R3 525
7 TraesCS3A01G417600 chr1A 508293882 508294403 521 True 752.000000 752 92.600000 1 526 1 chr1A.!!$R1 525
8 TraesCS3A01G417600 chr5A 217003131 217003657 526 False 732.000000 732 91.714000 1 530 1 chr5A.!!$F1 529
9 TraesCS3A01G417600 chr2A 22193011 22193542 531 False 732.000000 732 91.589000 1 530 1 chr2A.!!$F1 529
10 TraesCS3A01G417600 chr2A 766134225 766134762 537 True 732.000000 732 91.481000 1 530 1 chr2A.!!$R1 529
11 TraesCS3A01G417600 chr6A 377697208 377697731 523 True 725.000000 725 91.557000 1 530 1 chr6A.!!$R1 529

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
519 531 1.229428 CTTTCTGAAAGTGCGGCTGA 58.771 50.0 19.53 0.00 33.80 4.26 F
1347 1372 0.395311 TAGCCCTCTCTACACCACCG 60.395 60.0 0.00 0.00 0.00 4.94 F
1848 1873 0.032615 AGGGTAGAGCTCAGTCCTGG 60.033 60.0 17.77 0.00 0.00 4.45 F
2530 2555 0.469705 AGCCAAGCCAACAATCCACA 60.470 50.0 0.00 0.00 0.00 4.17 F
3385 3499 0.796312 CCAACAGGTATGTGCACGTC 59.204 55.0 16.44 7.36 40.39 4.34 F
5048 5418 0.109179 CCGCCCACAACATCAACATG 60.109 55.0 0.00 0.00 35.92 3.21 F
5259 5632 0.105039 CAAGGATACGGTGGGAGAGC 59.895 60.0 0.00 0.00 46.39 4.09 F
5919 6302 0.822164 GCCGACTACCTTTCTGCCTA 59.178 55.0 0.00 0.00 0.00 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 1600 0.249868 TGGTGTGCTCGAGTCCAAAG 60.250 55.000 15.13 0.00 0.00 2.77 R
2777 2816 1.303236 TGCTACGGCAATGCTGGTT 60.303 52.632 19.15 0.31 46.36 3.67 R
3605 3733 0.675083 TTAACGAGGCGGAACACTGA 59.325 50.000 0.00 0.00 0.00 3.41 R
4305 4453 2.492773 AAGTGCCAGCTGTTGTGCC 61.493 57.895 13.81 3.37 0.00 5.01 R
5083 5453 1.202268 GCCTGCAGAATTGACAGATGC 60.202 52.381 17.39 0.80 37.40 3.91 R
5871 6254 1.481871 CTGGGCAAGCAAAGATGGAT 58.518 50.000 0.00 0.00 0.00 3.41 R
6272 6657 2.468831 GATGACTCGATTCTCAGTGCC 58.531 52.381 4.29 0.00 0.00 5.01 R
7701 8531 0.107831 TCAGTGTGCCTACCCACAAC 59.892 55.000 0.00 0.00 46.28 3.32 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
183 190 2.427905 GTGTGTACGCGCGTGAGA 60.428 61.111 42.78 25.45 0.00 3.27
296 303 3.056328 GGAACCGAGGCAGTTGGC 61.056 66.667 0.00 0.00 43.74 4.52
366 373 2.494530 GCCAAAACAGTTCGCCCCA 61.495 57.895 0.00 0.00 0.00 4.96
509 521 2.039084 GTCTGAGGAGGCCTTTCTGAAA 59.961 50.000 21.40 2.44 31.76 2.69
511 523 2.039613 CTGAGGAGGCCTTTCTGAAAGT 59.960 50.000 24.18 9.84 36.77 2.66
519 531 1.229428 CTTTCTGAAAGTGCGGCTGA 58.771 50.000 19.53 0.00 33.80 4.26
526 538 1.915614 AAAGTGCGGCTGAAGATGCG 61.916 55.000 0.00 0.00 0.00 4.73
538 550 4.819761 GATGCGCCTGAGCCGTCA 62.820 66.667 4.18 0.00 36.02 4.35
650 662 2.935955 GACGACGCAACCAACAGG 59.064 61.111 0.00 0.00 0.00 4.00
698 710 7.168637 GGAAAAAGAAAGTAAAAATGGTCGGAC 59.831 37.037 0.00 0.00 0.00 4.79
699 711 6.954487 AAAGAAAGTAAAAATGGTCGGACT 57.046 33.333 8.23 0.00 0.00 3.85
700 712 6.555812 AAGAAAGTAAAAATGGTCGGACTC 57.444 37.500 8.23 0.00 0.00 3.36
701 713 5.001874 AGAAAGTAAAAATGGTCGGACTCC 58.998 41.667 8.23 0.00 0.00 3.85
702 714 4.360951 AAGTAAAAATGGTCGGACTCCA 57.639 40.909 8.23 0.00 39.41 3.86
703 715 3.939066 AGTAAAAATGGTCGGACTCCAG 58.061 45.455 8.23 0.00 38.42 3.86
704 716 2.951229 AAAAATGGTCGGACTCCAGT 57.049 45.000 8.23 0.00 38.42 4.00
770 782 3.914364 GCACGCACCAAAAATAAGAGAAG 59.086 43.478 0.00 0.00 0.00 2.85
1077 1099 1.814169 CGGGAAGAAAGCGGTAGGC 60.814 63.158 0.00 0.00 44.05 3.93
1078 1100 1.451567 GGGAAGAAAGCGGTAGGCC 60.452 63.158 0.00 0.00 45.17 5.19
1089 1111 2.820037 GTAGGCCCTCGCTGTTGC 60.820 66.667 0.00 0.00 34.44 4.17
1092 1114 4.096003 GGCCCTCGCTGTTGCCTA 62.096 66.667 0.00 0.00 40.77 3.93
1114 1139 1.796151 CTTACGTAGCCGTCGGTCA 59.204 57.895 13.94 0.00 46.28 4.02
1154 1179 2.603171 CACCATTTTGGCCCCGGT 60.603 61.111 0.00 0.00 42.67 5.28
1177 1202 1.134610 GCCCGACGGAATAGGAGAAAA 60.135 52.381 17.49 0.00 0.00 2.29
1187 1212 4.889409 GGAATAGGAGAAAATGGATGTGCA 59.111 41.667 0.00 0.00 0.00 4.57
1226 1251 6.816640 AGCTAGCATTACGATTGTAGTTCAAA 59.183 34.615 18.83 0.00 39.62 2.69
1309 1334 4.516698 CACCCTCATGCTGAAACCATATAC 59.483 45.833 0.00 0.00 0.00 1.47
1310 1335 4.165950 ACCCTCATGCTGAAACCATATACA 59.834 41.667 0.00 0.00 0.00 2.29
1311 1336 4.758674 CCCTCATGCTGAAACCATATACAG 59.241 45.833 0.00 0.00 0.00 2.74
1347 1372 0.395311 TAGCCCTCTCTACACCACCG 60.395 60.000 0.00 0.00 0.00 4.94
1537 1562 1.388133 GGAGAACCCCCTGCCAAAT 59.612 57.895 0.00 0.00 0.00 2.32
1575 1600 0.606673 GGAGAGGGTTTGGTGTCTGC 60.607 60.000 0.00 0.00 0.00 4.26
1585 1610 0.249868 TGGTGTCTGCTTTGGACTCG 60.250 55.000 0.00 0.00 35.04 4.18
1848 1873 0.032615 AGGGTAGAGCTCAGTCCTGG 60.033 60.000 17.77 0.00 0.00 4.45
1915 1940 2.249139 GACAGTGGTTCCCAGTCTACT 58.751 52.381 0.00 0.00 34.53 2.57
1947 1972 5.606329 TGTCAAAATGGGGAGGAAATTCTTT 59.394 36.000 0.00 0.00 0.00 2.52
2059 2084 9.225436 GATTACTCCCCAGAAAATGATATCTTC 57.775 37.037 3.98 0.00 0.00 2.87
2067 2092 2.086054 AATGATATCTTCGGCCGCTC 57.914 50.000 23.51 10.22 0.00 5.03
2145 2170 5.357742 TGCCTTGACTATGCAGATCTTTA 57.642 39.130 0.00 0.00 0.00 1.85
2232 2257 0.907704 ACCAGCAACCGGGACTATGA 60.908 55.000 6.32 0.00 0.00 2.15
2323 2348 5.864418 ATGCATTAAATTCCACATCTGCT 57.136 34.783 0.00 0.00 0.00 4.24
2455 2480 1.010419 CCCCGTACGTTGAACCTTCG 61.010 60.000 15.21 0.00 0.00 3.79
2517 2542 1.888215 TCTTCTGTTCAGCAGCCAAG 58.112 50.000 0.00 0.00 44.66 3.61
2530 2555 0.469705 AGCCAAGCCAACAATCCACA 60.470 50.000 0.00 0.00 0.00 4.17
2542 2567 5.006552 CCAACAATCCACACAAAACAATGTC 59.993 40.000 0.00 0.00 0.00 3.06
2561 2586 9.261180 ACAATGTCGTGGATAATTCTGTTATAG 57.739 33.333 0.00 0.00 0.00 1.31
2601 2626 2.459555 AGTGAAAAGGGGCCATATGG 57.540 50.000 18.07 18.07 38.53 2.74
2688 2713 4.811555 TGTTCCAAGATTTCACAAGTCG 57.188 40.909 0.00 0.00 0.00 4.18
2750 2775 6.698008 TGAATGCCAACCACTATCTATTTG 57.302 37.500 0.00 0.00 0.00 2.32
2812 2851 5.393027 CCGTAGCAAATTTTACAGAAGGCAT 60.393 40.000 0.00 0.00 0.00 4.40
2813 2852 6.183360 CCGTAGCAAATTTTACAGAAGGCATA 60.183 38.462 0.00 0.00 0.00 3.14
2832 2871 7.790027 AGGCATATAATATGAAGAGTAGCCTG 58.210 38.462 0.00 0.00 45.06 4.85
2833 2872 7.621285 AGGCATATAATATGAAGAGTAGCCTGA 59.379 37.037 0.00 0.00 45.06 3.86
2897 2936 2.301870 TGCCAGTTACACCCAGAACTAG 59.698 50.000 0.00 0.00 34.13 2.57
2899 2938 3.244457 GCCAGTTACACCCAGAACTAGTT 60.244 47.826 8.13 8.13 34.13 2.24
2900 2939 4.315803 CCAGTTACACCCAGAACTAGTTG 58.684 47.826 14.14 0.00 34.13 3.16
2902 2941 3.389983 AGTTACACCCAGAACTAGTTGCA 59.610 43.478 14.14 0.00 34.13 4.08
2903 2942 4.131596 GTTACACCCAGAACTAGTTGCAA 58.868 43.478 14.14 0.00 0.00 4.08
2904 2943 3.290948 ACACCCAGAACTAGTTGCAAA 57.709 42.857 14.14 0.00 0.00 3.68
2905 2944 9.525981 CAGTTACACCCAGAACTAGTTGCAAAC 62.526 44.444 14.14 6.75 39.47 2.93
3016 3130 5.066375 CACTGATTGTTTGTCAAGACTCCAA 59.934 40.000 1.53 2.75 39.55 3.53
3031 3145 4.165372 AGACTCCAAAAGGTTCTGTTACCA 59.835 41.667 0.00 0.00 40.82 3.25
3039 3153 7.413657 CCAAAAGGTTCTGTTACCACATATACG 60.414 40.741 0.00 0.00 40.82 3.06
3060 3174 2.692041 GCTTGGCTCCTTAGATGCAATT 59.308 45.455 0.00 0.00 0.00 2.32
3099 3213 5.849357 TCTGTCGCGTTGTAATTGTTTAT 57.151 34.783 5.77 0.00 0.00 1.40
3102 3216 7.133513 TCTGTCGCGTTGTAATTGTTTATTTT 58.866 30.769 5.77 0.00 0.00 1.82
3127 3241 6.973843 TGTTTTTCATCAGTCCAGATTTCTG 58.026 36.000 0.39 0.39 43.40 3.02
3137 3251 3.499918 GTCCAGATTTCTGACCAACACAG 59.500 47.826 9.15 0.00 46.59 3.66
3144 3258 7.120285 CAGATTTCTGACCAACACAGTCATAAT 59.880 37.037 1.15 0.00 46.59 1.28
3164 3278 5.362556 AATTTGATGTGCTGTGACAGTAC 57.637 39.130 24.03 24.03 45.02 2.73
3205 3319 7.964011 GCAATTTAGCATGCACATTTTGTTATT 59.036 29.630 21.98 0.00 42.12 1.40
3234 3348 5.533903 CCCTTCAACATAATGCTCATAGCTT 59.466 40.000 0.00 0.00 42.97 3.74
3246 3360 3.620966 GCTCATAGCTTCTCTGGTTTGGT 60.621 47.826 0.00 0.00 38.45 3.67
3261 3375 3.572255 GGTTTGGTTACCAGCTCATTGAA 59.428 43.478 3.65 0.00 38.12 2.69
3321 3435 8.038351 ACTTTAGAGAAATCTCAAGAACTAGCC 58.962 37.037 12.65 0.00 45.21 3.93
3360 3474 6.479990 CGGATAACTCAGCATTGACAGATAAA 59.520 38.462 0.00 0.00 0.00 1.40
3382 3496 2.226330 TCAACCAACAGGTATGTGCAC 58.774 47.619 10.75 10.75 40.39 4.57
3385 3499 0.796312 CCAACAGGTATGTGCACGTC 59.204 55.000 16.44 7.36 40.39 4.34
3393 3507 4.436515 TGTGCACGTCCACAGAAG 57.563 55.556 8.58 0.00 40.55 2.85
3399 3513 1.948104 CACGTCCACAGAAGTTTCCA 58.052 50.000 0.00 0.00 31.86 3.53
3429 3543 1.171308 CTTGCAATCAGTGGGAGGTG 58.829 55.000 0.00 0.00 0.00 4.00
3441 3555 3.116356 AGTGGGAGGTGGATATGGTATCA 60.116 47.826 0.03 0.00 0.00 2.15
3536 3664 9.841295 AGTAGTAACAAGAAGTTGGAATGTTAA 57.159 29.630 0.00 0.00 41.50 2.01
3605 3733 7.432350 TTCAAAATTTTGTGTTTTGCTGTCT 57.568 28.000 25.98 0.00 43.04 3.41
3719 3850 9.852091 GATGAAGCTCAATTTTAGTTTGATTCT 57.148 29.630 0.00 0.00 32.94 2.40
3768 3899 5.944007 AGACATACCTGTAAAAATGGGACAC 59.056 40.000 0.00 0.00 37.00 3.67
3826 3957 6.605594 GTCACATCCCCAGGTTTTAAATGATA 59.394 38.462 0.00 0.00 0.00 2.15
4047 4178 3.857157 TTCAAGCTCAACTGGTTAGGT 57.143 42.857 0.00 0.00 0.00 3.08
4065 4196 6.313164 GGTTAGGTTTCTTCCGTCATTTCTAG 59.687 42.308 0.00 0.00 0.00 2.43
4194 4325 7.059202 TCATCTATGTGATCAATGCTAGTGT 57.941 36.000 0.00 0.00 32.05 3.55
4195 4326 8.181904 TCATCTATGTGATCAATGCTAGTGTA 57.818 34.615 0.00 0.00 32.05 2.90
4196 4327 8.302438 TCATCTATGTGATCAATGCTAGTGTAG 58.698 37.037 0.00 0.00 32.05 2.74
4197 4328 7.588497 TCTATGTGATCAATGCTAGTGTAGT 57.412 36.000 0.00 0.00 0.00 2.73
4198 4329 7.428826 TCTATGTGATCAATGCTAGTGTAGTG 58.571 38.462 0.00 0.00 0.00 2.74
4199 4330 4.183865 TGTGATCAATGCTAGTGTAGTGC 58.816 43.478 0.00 0.00 0.00 4.40
4266 4399 4.463050 TCTTCCCCTTTGAAGCCTTTAA 57.537 40.909 0.00 0.00 41.23 1.52
4305 4453 9.057089 ACCTTGTGTTTCTTTCTAACTCTATTG 57.943 33.333 0.00 0.00 0.00 1.90
4453 4601 4.592485 TTCTATCTCCTCGATTGCTTCC 57.408 45.455 0.00 0.00 33.48 3.46
4570 4718 5.962031 TGTGATACCCCTGTAGTTCATAACT 59.038 40.000 0.00 0.00 45.40 2.24
4631 4952 6.462207 CCATATGCTATCTGGCCTCAGTATAC 60.462 46.154 3.32 0.00 41.59 1.47
4632 4953 3.844640 TGCTATCTGGCCTCAGTATACA 58.155 45.455 3.32 0.00 41.59 2.29
4666 4987 5.789643 ATGTTCATTGTAGCAAGGTTGTT 57.210 34.783 0.00 0.00 0.00 2.83
4678 4999 3.989817 GCAAGGTTGTTTCCAGCATTTAG 59.010 43.478 0.00 0.00 33.26 1.85
4726 5047 2.582052 CAAGGTGCAGAACTGGGTAAA 58.418 47.619 3.99 0.00 0.00 2.01
4751 5072 1.687612 CAGGAAGATGGCCAGGTGT 59.312 57.895 13.05 0.00 0.00 4.16
4784 5105 5.249163 TGGTAGGTGATGGGATTAGATCATG 59.751 44.000 0.00 0.00 31.40 3.07
4834 5159 8.218338 AGATTGATTTCTCGTTGCTTCAATAT 57.782 30.769 0.00 0.00 34.81 1.28
4980 5350 2.412847 GCACGACTATTGCTTTCCACAC 60.413 50.000 0.00 0.00 37.00 3.82
4981 5351 3.067106 CACGACTATTGCTTTCCACACT 58.933 45.455 0.00 0.00 0.00 3.55
4983 5353 4.327357 CACGACTATTGCTTTCCACACTAG 59.673 45.833 0.00 0.00 0.00 2.57
4989 5359 1.140852 TGCTTTCCACACTAGTGCTGT 59.859 47.619 22.90 0.12 44.53 4.40
4990 5360 1.532868 GCTTTCCACACTAGTGCTGTG 59.467 52.381 22.90 13.29 44.53 3.66
5001 5371 4.624882 CACTAGTGCTGTGATCTTCTGTTC 59.375 45.833 10.54 0.00 37.60 3.18
5002 5372 3.051081 AGTGCTGTGATCTTCTGTTCC 57.949 47.619 0.00 0.00 0.00 3.62
5042 5412 1.097547 CATCCTCCGCCCACAACATC 61.098 60.000 0.00 0.00 0.00 3.06
5046 5416 0.888736 CTCCGCCCACAACATCAACA 60.889 55.000 0.00 0.00 0.00 3.33
5048 5418 0.109179 CCGCCCACAACATCAACATG 60.109 55.000 0.00 0.00 35.92 3.21
5058 5428 6.151004 CACAACATCAACATGAGCATTGTTA 58.849 36.000 0.00 0.00 31.48 2.41
5067 5437 2.781923 TGAGCATTGTTAGCTTCAGCA 58.218 42.857 0.75 0.00 43.58 4.41
5068 5438 2.745821 TGAGCATTGTTAGCTTCAGCAG 59.254 45.455 0.75 0.00 43.58 4.24
5083 5453 4.707030 TCAGCAGCTACCAATTTTGATG 57.293 40.909 0.00 0.00 0.00 3.07
5085 5455 2.827322 AGCAGCTACCAATTTTGATGCA 59.173 40.909 0.00 0.00 34.93 3.96
5092 5462 5.393352 GCTACCAATTTTGATGCATCTGTCA 60.393 40.000 26.32 5.90 0.00 3.58
5093 5463 5.471556 ACCAATTTTGATGCATCTGTCAA 57.528 34.783 26.32 12.08 32.86 3.18
5113 5483 4.456911 TCAATTCTGCAGGCTCTTAAACTG 59.543 41.667 15.13 0.00 35.40 3.16
5167 5537 6.794534 AGTGGAGGGTTTAAATTCAGAGATT 58.205 36.000 0.00 0.00 0.00 2.40
5188 5558 8.159344 AGATTTCTTCCTACAAGTGAGTTTTG 57.841 34.615 0.00 0.00 0.00 2.44
5191 5561 5.057149 TCTTCCTACAAGTGAGTTTTGAGC 58.943 41.667 0.00 0.00 0.00 4.26
5203 5573 8.411318 AGTGAGTTTTGAGCTATTTTGTTTTG 57.589 30.769 0.00 0.00 0.00 2.44
5219 5589 3.261580 GTTTTGCTAATCCCCATGTTGC 58.738 45.455 0.00 0.00 0.00 4.17
5259 5632 0.105039 CAAGGATACGGTGGGAGAGC 59.895 60.000 0.00 0.00 46.39 4.09
5287 5660 8.754991 TCTTGTTTTTCATGGTTACCTAAAGA 57.245 30.769 2.07 0.00 0.00 2.52
5316 5689 1.997606 GGATGCTTGAAATTGCTGTGC 59.002 47.619 0.00 0.00 0.00 4.57
5371 5744 5.360591 CAAAGGATGGAACTAGCTAACGAT 58.639 41.667 0.00 0.00 0.00 3.73
5448 5827 5.802465 TCTAGTCTAGAGAAGGAACGTCAA 58.198 41.667 5.41 0.00 39.91 3.18
5517 5896 8.890124 TGTGTACTTTAGTTTAGCACATACAA 57.110 30.769 0.00 0.00 31.57 2.41
5525 5904 6.443934 AGTTTAGCACATACAAACAACACA 57.556 33.333 0.00 0.00 35.17 3.72
5533 5912 6.202570 GCACATACAAACAACACATTTTCCAT 59.797 34.615 0.00 0.00 0.00 3.41
5555 5934 6.403636 CCATTAAACTTTCCGATCTTGGTCAG 60.404 42.308 0.00 0.00 0.00 3.51
5556 5935 3.771577 AACTTTCCGATCTTGGTCAGT 57.228 42.857 0.00 0.00 0.00 3.41
5577 5956 8.496751 GTCAGTCCTAGAAAATCACTTTGTAAC 58.503 37.037 0.00 0.00 0.00 2.50
5609 5988 2.345760 CCTCATGCACCCTTGTGGC 61.346 63.158 0.00 0.00 42.99 5.01
5619 5999 1.110442 CCCTTGTGGCACTTGTTTCA 58.890 50.000 19.83 0.00 0.00 2.69
5685 6065 2.195741 AGACAGGTAGCGTGTAGACA 57.804 50.000 0.00 0.00 32.46 3.41
5707 6087 6.600388 ACATGACCTATACATGCCATTGTTA 58.400 36.000 0.00 0.00 45.95 2.41
5723 6103 6.517529 GCCATTGTTACCACCATTTGACTTTA 60.518 38.462 0.00 0.00 0.00 1.85
5757 6140 4.974645 TTGGACAGAAAAGAAGCTCCTA 57.025 40.909 0.00 0.00 0.00 2.94
5861 6244 1.152383 GCGACGGAGGATTTAGGTGC 61.152 60.000 0.00 0.00 0.00 5.01
5871 6254 5.362105 AGGATTTAGGTGCGGTATTACAA 57.638 39.130 0.00 0.00 0.00 2.41
5919 6302 0.822164 GCCGACTACCTTTCTGCCTA 59.178 55.000 0.00 0.00 0.00 3.93
5923 6306 2.269172 GACTACCTTTCTGCCTAACGC 58.731 52.381 0.00 0.00 38.31 4.84
6056 6439 4.081420 TCTGATTTTCCTTCCTTCGGAGAG 60.081 45.833 0.00 0.00 38.43 3.20
6077 6460 3.137533 GGCATCTTCTAGCATTCCAGAC 58.862 50.000 0.00 0.00 0.00 3.51
6136 6519 3.698289 TGTCGGAGGTAATCTCTTGAGT 58.302 45.455 0.00 0.00 42.10 3.41
6139 6522 5.103687 GTCGGAGGTAATCTCTTGAGTTTC 58.896 45.833 0.00 0.00 42.10 2.78
6162 6545 3.944087 AGGGCTACTTTCTCACATCAAC 58.056 45.455 0.00 0.00 0.00 3.18
6195 6580 7.625469 TCCCAAACAACCTTAACTTGATTTTT 58.375 30.769 0.00 0.00 0.00 1.94
6272 6657 2.288152 GGAGAGAGAAGAGCTAATGCGG 60.288 54.545 0.00 0.00 45.42 5.69
6324 6709 3.887621 AGCTGAAGGTATTCTTACGCA 57.112 42.857 0.00 0.00 35.50 5.24
6358 6743 4.079253 TCAGTTAATTTTGTCCAGGGCTC 58.921 43.478 0.00 0.00 0.00 4.70
6366 6751 1.201429 TGTCCAGGGCTCTTCTTCCC 61.201 60.000 0.00 0.00 42.94 3.97
6367 6752 1.616628 TCCAGGGCTCTTCTTCCCC 60.617 63.158 0.00 0.00 43.67 4.81
6372 6757 1.767692 GGCTCTTCTTCCCCAACCA 59.232 57.895 0.00 0.00 0.00 3.67
6395 6780 6.942005 CCAATATTGATAAGATGCCTGTACCA 59.058 38.462 17.23 0.00 0.00 3.25
6469 6969 8.906238 AGAAACCCTATTTACTGGTAGACTTA 57.094 34.615 0.00 0.00 0.00 2.24
6470 6970 9.503369 AGAAACCCTATTTACTGGTAGACTTAT 57.497 33.333 0.00 0.00 0.00 1.73
6473 6973 8.480133 ACCCTATTTACTGGTAGACTTATCAG 57.520 38.462 0.00 0.00 42.61 2.90
6480 6980 8.824756 TTACTGGTAGACTTATCAGTCAAGAT 57.175 34.615 9.64 0.00 45.94 2.40
6509 7009 5.165676 TGTATTACTTCGGTTACAGTGCAG 58.834 41.667 0.00 0.00 0.00 4.41
6723 7223 4.286707 TCCTACCAGCAGAGCTAATTGTA 58.713 43.478 0.00 0.00 36.40 2.41
6790 7388 8.491134 TGCCAGTTATATGAACTATACCTTTGT 58.509 33.333 0.00 0.00 0.00 2.83
6928 7528 2.243957 CGTCGCACCAGCAAACTCA 61.244 57.895 0.00 0.00 42.27 3.41
7137 7738 5.374921 ACAGAATAGCCTCCAAGAATCATG 58.625 41.667 0.00 0.00 0.00 3.07
7195 7796 5.298527 GGGGTGGATATGTAAAAGCTGTTAC 59.701 44.000 18.41 18.41 35.02 2.50
7358 7975 6.806249 TCAATACGGATTGAAATGAAACAAGC 59.194 34.615 20.84 0.00 46.75 4.01
7360 7977 5.138125 ACGGATTGAAATGAAACAAGCAT 57.862 34.783 0.00 0.00 34.68 3.79
7361 7978 6.266168 ACGGATTGAAATGAAACAAGCATA 57.734 33.333 0.00 0.00 34.68 3.14
7362 7979 6.092748 ACGGATTGAAATGAAACAAGCATAC 58.907 36.000 0.00 0.00 34.68 2.39
7363 7980 6.092092 CGGATTGAAATGAAACAAGCATACA 58.908 36.000 0.00 0.00 34.68 2.29
7365 7982 7.116090 CGGATTGAAATGAAACAAGCATACAAA 59.884 33.333 0.00 0.00 34.68 2.83
7366 7983 8.772705 GGATTGAAATGAAACAAGCATACAAAA 58.227 29.630 0.00 0.00 34.68 2.44
7369 7986 9.932699 TTGAAATGAAACAAGCATACAAAAATG 57.067 25.926 0.00 0.00 0.00 2.32
7427 8235 7.819900 ACGATTATAATATGAAACAGAGGGAGC 59.180 37.037 0.00 0.00 0.00 4.70
7431 8239 2.486472 ATGAAACAGAGGGAGCACAG 57.514 50.000 0.00 0.00 0.00 3.66
7489 8298 2.198827 TTCACTTCCGTGCCATCAAT 57.801 45.000 0.00 0.00 40.99 2.57
7490 8299 1.737838 TCACTTCCGTGCCATCAATC 58.262 50.000 0.00 0.00 40.99 2.67
7491 8300 1.003003 TCACTTCCGTGCCATCAATCA 59.997 47.619 0.00 0.00 40.99 2.57
7492 8301 1.811965 CACTTCCGTGCCATCAATCAA 59.188 47.619 0.00 0.00 33.82 2.57
7527 8336 2.342910 CAGCATGCCTGAAGTTGAAC 57.657 50.000 15.66 0.00 44.64 3.18
7528 8337 1.884579 CAGCATGCCTGAAGTTGAACT 59.115 47.619 15.66 0.00 44.64 3.01
7529 8338 1.884579 AGCATGCCTGAAGTTGAACTG 59.115 47.619 15.66 0.00 0.00 3.16
7531 8340 2.606308 GCATGCCTGAAGTTGAACTGTG 60.606 50.000 6.36 0.00 0.00 3.66
7532 8341 1.679139 TGCCTGAAGTTGAACTGTGG 58.321 50.000 0.00 2.96 0.00 4.17
7533 8342 0.312102 GCCTGAAGTTGAACTGTGGC 59.688 55.000 16.53 16.53 33.78 5.01
7534 8343 0.954452 CCTGAAGTTGAACTGTGGCC 59.046 55.000 0.00 0.00 0.00 5.36
7535 8344 1.477558 CCTGAAGTTGAACTGTGGCCT 60.478 52.381 3.32 0.00 0.00 5.19
7536 8345 1.876156 CTGAAGTTGAACTGTGGCCTC 59.124 52.381 3.32 0.00 0.00 4.70
7561 8390 7.865385 TCAAATTTGACCAACCTAAGAATTTCG 59.135 33.333 16.91 0.00 31.01 3.46
7701 8531 2.169352 AGGCATGCTGGACTACTACTTG 59.831 50.000 18.92 0.00 0.00 3.16
7793 8626 0.033504 GTCCTCGTCTTCAGTGGCAA 59.966 55.000 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.256464 CTCTCCCTCTCTACCACCGT 59.744 60.000 0.00 0.00 0.00 4.83
165 172 2.728015 CTCACGCGCGTACACACA 60.728 61.111 37.24 13.85 0.00 3.72
420 430 1.751162 CCCAATTTTCGCCGGCCTA 60.751 57.895 23.46 6.42 0.00 3.93
509 521 2.816958 CGCATCTTCAGCCGCACT 60.817 61.111 0.00 0.00 0.00 4.40
526 538 1.520342 GTGATCTGACGGCTCAGGC 60.520 63.158 12.09 0.00 43.87 4.85
538 550 3.148279 GCTCGTCGGGGGTGATCT 61.148 66.667 0.00 0.00 0.00 2.75
650 662 3.786586 GTCGCTGCTGCACTGCTC 61.787 66.667 16.29 2.36 40.84 4.26
665 677 6.381481 TTTTACTTTCTTTTTCCTCGGGTC 57.619 37.500 0.00 0.00 0.00 4.46
704 716 2.680352 GCCCGGTCTCTGTGGAGA 60.680 66.667 0.00 0.00 45.30 3.71
720 732 2.682494 TACCCTCCCACCTCGTGC 60.682 66.667 0.00 0.00 31.34 5.34
843 856 4.964241 GGATCGGGGAGGGAGGGG 62.964 77.778 0.00 0.00 0.00 4.79
1077 1099 1.718757 GCAATAGGCAACAGCGAGGG 61.719 60.000 0.00 0.00 43.97 4.30
1078 1100 1.723870 GCAATAGGCAACAGCGAGG 59.276 57.895 0.00 0.00 43.97 4.63
1114 1139 3.023119 TGATTATCAAGCAATTGCCGGT 58.977 40.909 26.45 16.68 43.38 5.28
1117 1142 4.567959 GGTGTTGATTATCAAGCAATTGCC 59.432 41.667 26.45 9.30 39.20 4.52
1118 1143 5.170021 TGGTGTTGATTATCAAGCAATTGC 58.830 37.500 23.05 23.05 39.20 3.56
1154 1179 4.215742 CCTATTCCGTCGGGCGCA 62.216 66.667 12.29 0.00 39.71 6.09
1198 1223 2.743938 ACAATCGTAATGCTAGCTCGG 58.256 47.619 17.23 1.01 0.00 4.63
1226 1251 6.096987 TCTCTAGGATGAGCTAAAACGATTGT 59.903 38.462 0.00 0.00 34.29 2.71
1331 1356 1.486211 AATCGGTGGTGTAGAGAGGG 58.514 55.000 0.00 0.00 0.00 4.30
1347 1372 5.395486 GCCGAATTAGCATTCAACGTAAATC 59.605 40.000 0.00 0.00 39.14 2.17
1396 1421 5.297776 CAGAAAACAGGACAGTGTCATTCTT 59.702 40.000 24.20 10.08 35.74 2.52
1537 1562 4.225492 TCTCCGGTGTTACCATTATTGGAA 59.775 41.667 10.62 0.00 46.92 3.53
1549 1574 0.688487 CCAAACCCTCTCCGGTGTTA 59.312 55.000 0.00 0.00 35.83 2.41
1553 1578 1.765597 GACACCAAACCCTCTCCGGT 61.766 60.000 0.00 0.00 37.93 5.28
1555 1580 0.320771 CAGACACCAAACCCTCTCCG 60.321 60.000 0.00 0.00 0.00 4.63
1559 1584 1.338020 CAAAGCAGACACCAAACCCTC 59.662 52.381 0.00 0.00 0.00 4.30
1575 1600 0.249868 TGGTGTGCTCGAGTCCAAAG 60.250 55.000 15.13 0.00 0.00 2.77
1585 1610 1.131883 GATGATGTGCTTGGTGTGCTC 59.868 52.381 0.00 0.00 0.00 4.26
1915 1940 2.445145 TCCCCATTTTGACAAGACCTCA 59.555 45.455 0.00 0.00 0.00 3.86
1947 1972 5.184287 TCGATACCATGTACTTGACTCAACA 59.816 40.000 10.20 0.00 0.00 3.33
2059 2084 4.124351 TTACCTCGTGAGCGGCCG 62.124 66.667 24.05 24.05 40.41 6.13
2067 2092 4.116747 AGAGCTTCAATCTTACCTCGTG 57.883 45.455 0.00 0.00 0.00 4.35
2117 2142 3.354948 TGCATAGTCAAGGCAGTCATT 57.645 42.857 0.00 0.00 32.95 2.57
2232 2257 8.891720 CGACCTTAGAACTACTAAAGATACTGT 58.108 37.037 0.00 0.00 40.07 3.55
2254 2279 3.179443 TGATCTAAACCATCAGCGACC 57.821 47.619 0.00 0.00 0.00 4.79
2321 2346 9.875691 AAAAGGATCCTGTTTATCAAAATTAGC 57.124 29.630 17.02 0.00 0.00 3.09
2517 2542 2.898705 TGTTTTGTGTGGATTGTTGGC 58.101 42.857 0.00 0.00 0.00 4.52
2530 2555 7.083858 CAGAATTATCCACGACATTGTTTTGT 58.916 34.615 0.00 0.00 0.00 2.83
2542 2567 5.639506 CCCTGCTATAACAGAATTATCCACG 59.360 44.000 4.66 0.00 40.25 4.94
2561 2586 6.265649 TCACTATTATACTCTTGTCTCCCTGC 59.734 42.308 0.00 0.00 0.00 4.85
2601 2626 7.521261 GCAAGGAATCAGGAAGTATAGAATTGC 60.521 40.741 0.00 0.00 0.00 3.56
2608 2633 5.163195 GGAAGGCAAGGAATCAGGAAGTATA 60.163 44.000 0.00 0.00 0.00 1.47
2688 2713 3.003275 TGCAAAACCGTCATCTTTCTCAC 59.997 43.478 0.00 0.00 0.00 3.51
2771 2796 3.207265 ACGGCAATGCTGGTTCATATA 57.793 42.857 19.15 0.00 39.57 0.86
2777 2816 1.303236 TGCTACGGCAATGCTGGTT 60.303 52.632 19.15 0.31 46.36 3.67
2806 2845 8.263640 CAGGCTACTCTTCATATTATATGCCTT 58.736 37.037 7.31 0.00 43.12 4.35
2808 2847 7.786030 TCAGGCTACTCTTCATATTATATGCC 58.214 38.462 7.31 3.13 36.11 4.40
2839 2878 5.733109 GCGCTAAGTTAACATCTACTTTTGC 59.267 40.000 8.61 3.51 36.16 3.68
2860 2899 5.613358 ACTGGCATTAAATCTAATAGCGC 57.387 39.130 0.00 0.00 0.00 5.92
2861 2900 8.009974 GTGTAACTGGCATTAAATCTAATAGCG 58.990 37.037 0.00 0.00 0.00 4.26
3031 3145 3.895656 TCTAAGGAGCCAAGCGTATATGT 59.104 43.478 0.00 0.00 0.00 2.29
3039 3153 1.755179 TTGCATCTAAGGAGCCAAGC 58.245 50.000 0.00 0.00 0.00 4.01
3060 3174 3.202906 ACAGAACGCTAACAAAGAAGCA 58.797 40.909 0.00 0.00 38.70 3.91
3099 3213 9.097257 GAAATCTGGACTGATGAAAAACAAAAA 57.903 29.630 0.00 0.00 0.00 1.94
3102 3216 7.285172 TCAGAAATCTGGACTGATGAAAAACAA 59.715 33.333 10.37 0.00 43.91 2.83
3112 3226 3.390967 TGTTGGTCAGAAATCTGGACTGA 59.609 43.478 10.37 0.00 43.91 3.41
3113 3227 3.499918 GTGTTGGTCAGAAATCTGGACTG 59.500 47.826 10.37 0.00 43.91 3.51
3127 3241 6.803320 CACATCAAATTATGACTGTGTTGGTC 59.197 38.462 15.19 0.00 41.93 4.02
3137 3251 5.941733 TGTCACAGCACATCAAATTATGAC 58.058 37.500 0.00 0.00 41.93 3.06
3144 3258 4.071961 AGTACTGTCACAGCACATCAAA 57.928 40.909 10.90 0.00 34.37 2.69
3189 3303 5.189539 AGGGCCTAAATAACAAAATGTGCAT 59.810 36.000 2.82 0.00 0.00 3.96
3205 3319 4.207165 GAGCATTATGTTGAAGGGCCTAA 58.793 43.478 6.41 0.00 0.00 2.69
3246 3360 6.003326 TGTCAAATCTTCAATGAGCTGGTAA 58.997 36.000 0.00 0.00 0.00 2.85
3261 3375 6.316390 ACGAAAACTTCTCTGTTGTCAAATCT 59.684 34.615 0.00 0.00 34.69 2.40
3360 3474 3.255642 GTGCACATACCTGTTGGTTGAAT 59.744 43.478 13.17 0.00 46.05 2.57
3382 3496 1.806542 CCATGGAAACTTCTGTGGACG 59.193 52.381 5.56 0.00 35.30 4.79
3385 3499 2.224867 ACCTCCATGGAAACTTCTGTGG 60.225 50.000 17.00 12.32 39.71 4.17
3393 3507 3.069443 TGCAAGAAAACCTCCATGGAAAC 59.931 43.478 17.00 3.92 39.71 2.78
3399 3513 4.021719 CACTGATTGCAAGAAAACCTCCAT 60.022 41.667 4.94 0.00 0.00 3.41
3581 3709 7.172190 TGAGACAGCAAAACACAAAATTTTGAA 59.828 29.630 32.20 1.65 45.75 2.69
3588 3716 4.022416 ACACTGAGACAGCAAAACACAAAA 60.022 37.500 0.00 0.00 34.37 2.44
3591 3719 2.710377 ACACTGAGACAGCAAAACACA 58.290 42.857 0.00 0.00 34.37 3.72
3593 3721 2.682856 GGAACACTGAGACAGCAAAACA 59.317 45.455 0.00 0.00 34.37 2.83
3605 3733 0.675083 TTAACGAGGCGGAACACTGA 59.325 50.000 0.00 0.00 0.00 3.41
3629 3760 7.871853 ACATGTTGTGCTAGTTTAACTTAAGG 58.128 34.615 1.94 0.00 0.00 2.69
3632 3763 7.307751 GCTGACATGTTGTGCTAGTTTAACTTA 60.308 37.037 1.94 0.00 0.00 2.24
3760 3891 5.023452 TCTACACTATGTCTTGTGTCCCAT 58.977 41.667 1.91 0.00 44.94 4.00
3768 3899 7.946655 TTTGTCTTGTCTACACTATGTCTTG 57.053 36.000 0.00 0.00 0.00 3.02
3826 3957 9.202273 GATCTACTGATCGATCTTGCTATTTTT 57.798 33.333 25.02 4.62 39.56 1.94
3856 3987 7.993101 TGTCATTCTCATTCATGGAAGAATTC 58.007 34.615 0.00 0.00 46.67 2.17
4047 4178 5.063438 CGAATGCTAGAAATGACGGAAGAAA 59.937 40.000 0.00 0.00 0.00 2.52
4100 4231 5.246203 TCAGCATTTAGTGAGTCCTACAACT 59.754 40.000 0.00 0.00 0.00 3.16
4149 4280 4.344968 TGATCCATACACGACCAGATCAAT 59.655 41.667 0.00 0.00 37.70 2.57
4189 4320 5.950544 AATATGGGAGTTGCACTACACTA 57.049 39.130 0.00 0.00 27.88 2.74
4191 4322 6.542370 ACATTAATATGGGAGTTGCACTACAC 59.458 38.462 0.00 0.00 36.01 2.90
4192 4323 6.542005 CACATTAATATGGGAGTTGCACTACA 59.458 38.462 0.00 0.00 37.35 2.74
4193 4324 6.765989 TCACATTAATATGGGAGTTGCACTAC 59.234 38.462 0.00 0.00 39.26 2.73
4194 4325 6.894682 TCACATTAATATGGGAGTTGCACTA 58.105 36.000 0.00 0.00 39.26 2.74
4195 4326 5.754782 TCACATTAATATGGGAGTTGCACT 58.245 37.500 0.00 0.00 39.26 4.40
4196 4327 6.449635 TTCACATTAATATGGGAGTTGCAC 57.550 37.500 0.00 0.00 44.68 4.57
4197 4328 8.938801 ATATTCACATTAATATGGGAGTTGCA 57.061 30.769 0.00 0.00 44.68 4.08
4305 4453 2.492773 AAGTGCCAGCTGTTGTGCC 61.493 57.895 13.81 3.37 0.00 5.01
4453 4601 7.420002 TGCAAGATTAAATAGCTAATGCACAG 58.580 34.615 0.00 0.00 42.74 3.66
4506 4654 5.534207 TTTCTCAAACAGCATCAACCATT 57.466 34.783 0.00 0.00 0.00 3.16
4552 4700 6.441222 TCTGATAGTTATGAACTACAGGGGT 58.559 40.000 18.38 0.91 45.99 4.95
4595 4743 7.229506 GCCAGATAGCATATGGAGTTACTTTTT 59.770 37.037 12.23 0.00 44.32 1.94
4596 4744 6.712547 GCCAGATAGCATATGGAGTTACTTTT 59.287 38.462 12.23 0.00 44.32 2.27
4599 4747 4.223923 GGCCAGATAGCATATGGAGTTACT 59.776 45.833 12.23 0.00 44.32 2.24
4600 4748 4.223923 AGGCCAGATAGCATATGGAGTTAC 59.776 45.833 5.01 0.00 44.32 2.50
4601 4749 4.429505 AGGCCAGATAGCATATGGAGTTA 58.570 43.478 5.01 0.00 44.32 2.24
4603 4751 2.836981 GAGGCCAGATAGCATATGGAGT 59.163 50.000 5.01 0.86 44.32 3.85
4604 4752 2.836372 TGAGGCCAGATAGCATATGGAG 59.164 50.000 5.01 0.00 44.32 3.86
4605 4753 2.836372 CTGAGGCCAGATAGCATATGGA 59.164 50.000 5.01 0.00 44.32 3.41
4606 4754 2.570752 ACTGAGGCCAGATAGCATATGG 59.429 50.000 5.01 5.69 44.38 2.74
4607 4755 3.977134 ACTGAGGCCAGATAGCATATG 57.023 47.619 5.01 0.00 43.02 1.78
4660 4981 2.298729 TGGCTAAATGCTGGAAACAACC 59.701 45.455 0.00 0.00 42.06 3.77
4666 4987 3.084039 CAACTCTGGCTAAATGCTGGAA 58.916 45.455 0.00 0.00 42.39 3.53
4678 4999 1.227853 ACAACGGTCCAACTCTGGC 60.228 57.895 0.00 0.00 43.17 4.85
4688 5009 2.798976 TGGTACAGTACACAACGGTC 57.201 50.000 12.89 0.00 37.67 4.79
4689 5010 2.224113 CCTTGGTACAGTACACAACGGT 60.224 50.000 12.89 0.00 42.39 4.83
4691 5012 2.798283 CACCTTGGTACAGTACACAACG 59.202 50.000 12.89 9.97 42.39 4.10
4726 5047 1.380302 GCCATCTTCCTGGTGGTGT 59.620 57.895 3.34 0.00 38.63 4.16
4751 5072 2.238646 CCATCACCTACCAAGCCAACTA 59.761 50.000 0.00 0.00 0.00 2.24
4784 5105 2.552373 CCCAAGTTTGTCTACCTCACCC 60.552 54.545 0.00 0.00 0.00 4.61
4834 5159 3.754965 AGGCTGAGCACTGTATTCAAAA 58.245 40.909 6.82 0.00 0.00 2.44
4841 5166 2.598565 CCCTATAGGCTGAGCACTGTA 58.401 52.381 13.85 3.20 0.00 2.74
4917 5283 6.211785 GCCTTATAGGGAAGCTATCAAGTAGT 59.788 42.308 4.79 0.00 35.37 2.73
4963 5333 4.093556 GCACTAGTGTGGAAAGCAATAGTC 59.906 45.833 23.44 0.00 43.14 2.59
4980 5350 4.180057 GGAACAGAAGATCACAGCACTAG 58.820 47.826 0.00 0.00 0.00 2.57
4981 5351 3.367395 CGGAACAGAAGATCACAGCACTA 60.367 47.826 0.00 0.00 0.00 2.74
4983 5353 1.728971 CGGAACAGAAGATCACAGCAC 59.271 52.381 0.00 0.00 0.00 4.40
4989 5359 1.218047 CCGGCGGAACAGAAGATCA 59.782 57.895 24.41 0.00 0.00 2.92
4990 5360 2.174319 GCCGGCGGAACAGAAGATC 61.174 63.158 33.44 3.13 0.00 2.75
5042 5412 5.050644 TGAAGCTAACAATGCTCATGTTG 57.949 39.130 11.06 0.00 40.95 3.33
5046 5416 3.349927 TGCTGAAGCTAACAATGCTCAT 58.650 40.909 3.61 0.00 40.22 2.90
5048 5418 3.402058 CTGCTGAAGCTAACAATGCTC 57.598 47.619 3.61 0.00 40.22 4.26
5067 5437 4.708421 ACAGATGCATCAAAATTGGTAGCT 59.292 37.500 27.81 0.00 0.00 3.32
5068 5438 5.002464 ACAGATGCATCAAAATTGGTAGC 57.998 39.130 27.81 0.00 0.00 3.58
5083 5453 1.202268 GCCTGCAGAATTGACAGATGC 60.202 52.381 17.39 0.80 37.40 3.91
5085 5455 2.239150 AGAGCCTGCAGAATTGACAGAT 59.761 45.455 17.39 0.00 33.22 2.90
5092 5462 4.655963 TCAGTTTAAGAGCCTGCAGAATT 58.344 39.130 17.39 6.60 0.00 2.17
5093 5463 4.260170 CTCAGTTTAAGAGCCTGCAGAAT 58.740 43.478 17.39 2.14 0.00 2.40
5113 5483 6.377327 TCAAGTTTCAACTCATTTGACCTC 57.623 37.500 0.00 0.00 44.28 3.85
5167 5537 5.527582 GCTCAAAACTCACTTGTAGGAAGAA 59.472 40.000 0.00 0.00 0.00 2.52
5188 5558 6.042777 GGGGATTAGCAAAACAAAATAGCTC 58.957 40.000 0.00 0.00 36.80 4.09
5191 5561 7.330262 ACATGGGGATTAGCAAAACAAAATAG 58.670 34.615 0.00 0.00 0.00 1.73
5203 5573 3.825143 AATTGCAACATGGGGATTAGC 57.175 42.857 0.00 0.00 0.00 3.09
5219 5589 7.603404 TCCTTGAAAGGTGCATTCATAAAATTG 59.397 33.333 8.91 0.00 46.54 2.32
5252 5625 3.744660 TGAAAAACAAGAGAGCTCTCCC 58.255 45.455 34.87 16.52 43.88 4.30
5259 5632 6.884280 AGGTAACCATGAAAAACAAGAGAG 57.116 37.500 0.00 0.00 37.17 3.20
5346 5719 2.426842 AGCTAGTTCCATCCTTTGGC 57.573 50.000 0.00 0.00 46.01 4.52
5403 5776 9.464714 CTAGAAACTTTGCGTCTGTGTATATAT 57.535 33.333 0.00 0.00 0.00 0.86
5404 5777 8.464404 ACTAGAAACTTTGCGTCTGTGTATATA 58.536 33.333 0.00 0.00 0.00 0.86
5405 5778 7.321153 ACTAGAAACTTTGCGTCTGTGTATAT 58.679 34.615 0.00 0.00 0.00 0.86
5406 5779 6.684686 ACTAGAAACTTTGCGTCTGTGTATA 58.315 36.000 0.00 0.00 0.00 1.47
5407 5780 5.539048 ACTAGAAACTTTGCGTCTGTGTAT 58.461 37.500 0.00 0.00 0.00 2.29
5448 5827 5.046014 AGCCTCAACAGTAGATTGAAGATGT 60.046 40.000 0.00 0.00 35.70 3.06
5517 5896 8.888716 GGAAAGTTTAATGGAAAATGTGTTGTT 58.111 29.630 0.00 0.00 0.00 2.83
5525 5904 8.034804 CCAAGATCGGAAAGTTTAATGGAAAAT 58.965 33.333 0.00 0.00 0.00 1.82
5533 5912 5.617252 ACTGACCAAGATCGGAAAGTTTAA 58.383 37.500 0.00 0.00 0.00 1.52
5555 5934 8.837389 ACAAGTTACAAAGTGATTTTCTAGGAC 58.163 33.333 0.00 0.00 0.00 3.85
5556 5935 8.836413 CACAAGTTACAAAGTGATTTTCTAGGA 58.164 33.333 0.00 0.00 33.99 2.94
5566 5945 8.347035 GGCTAAAATACACAAGTTACAAAGTGA 58.653 33.333 8.38 0.00 35.97 3.41
5577 5956 5.335127 GTGCATGAGGCTAAAATACACAAG 58.665 41.667 0.00 0.00 45.15 3.16
5685 6065 6.003950 GGTAACAATGGCATGTATAGGTCAT 58.996 40.000 0.00 0.00 33.81 3.06
5707 6087 9.881773 ATATGGATATTAAAGTCAAATGGTGGT 57.118 29.630 0.00 0.00 0.00 4.16
5757 6140 7.721399 ACAGGAATGTTTCTCAATTTAGAGTGT 59.279 33.333 0.00 0.00 36.97 3.55
5861 6244 6.201517 CAAGCAAAGATGGATTGTAATACCG 58.798 40.000 0.00 0.00 0.00 4.02
5871 6254 1.481871 CTGGGCAAGCAAAGATGGAT 58.518 50.000 0.00 0.00 0.00 3.41
6056 6439 3.137533 GTCTGGAATGCTAGAAGATGCC 58.862 50.000 0.00 0.00 33.09 4.40
6077 6460 4.117685 TGTCAATCATTCTGAGCTGATCG 58.882 43.478 0.00 0.00 30.98 3.69
6136 6519 5.483937 TGATGTGAGAAAGTAGCCCTAGAAA 59.516 40.000 0.00 0.00 0.00 2.52
6139 6522 5.112686 GTTGATGTGAGAAAGTAGCCCTAG 58.887 45.833 0.00 0.00 0.00 3.02
6195 6580 4.810345 AGAGTGGTTAAATTTTGGGTCCA 58.190 39.130 0.00 0.00 0.00 4.02
6272 6657 2.468831 GATGACTCGATTCTCAGTGCC 58.531 52.381 4.29 0.00 0.00 5.01
6324 6709 8.491331 ACAAAATTAACTGAAACAAATGTGCT 57.509 26.923 0.00 0.00 0.00 4.40
6358 6743 7.779798 TCTTATCAATATTGGTTGGGGAAGAAG 59.220 37.037 15.36 6.46 0.00 2.85
6366 6751 6.266103 ACAGGCATCTTATCAATATTGGTTGG 59.734 38.462 15.36 5.15 0.00 3.77
6367 6752 7.281040 ACAGGCATCTTATCAATATTGGTTG 57.719 36.000 15.36 4.82 0.00 3.77
6395 6780 6.245890 GCCTAGGGCTTAATCATCTCATAT 57.754 41.667 11.72 0.00 46.69 1.78
6480 6980 7.809331 CACTGTAACCGAAGTAATACAAGTGTA 59.191 37.037 0.00 0.00 30.99 2.90
6509 7009 7.809806 ACAAAAGAGTAACTTGCATAAGATTGC 59.190 33.333 0.00 0.00 43.07 3.56
6723 7223 6.949715 AGATGAAGAAAGCTCTCAAAGATCT 58.050 36.000 0.00 0.00 0.00 2.75
6810 7408 5.173312 CAGGCACGTATAGATAAACTGTTCG 59.827 44.000 0.00 0.00 36.81 3.95
6928 7528 6.803154 ACTAAAGCTTCATTTTCGCTAGTT 57.197 33.333 0.00 0.00 32.90 2.24
7137 7738 5.179555 GCGACAAAATATAAGATGGGAGGAC 59.820 44.000 0.00 0.00 0.00 3.85
7195 7796 3.003275 ACAACCGTACAACAATTGCTGAG 59.997 43.478 15.55 6.35 0.00 3.35
7271 7872 5.376625 TCCTTCTGTGCTTCTGTTAACATT 58.623 37.500 9.13 0.00 0.00 2.71
7287 7888 4.440802 CGGAACTACTCAAGGATCCTTCTG 60.441 50.000 24.67 20.28 34.65 3.02
7340 7957 7.887996 TTGTATGCTTGTTTCATTTCAATCC 57.112 32.000 0.00 0.00 0.00 3.01
7365 7982 9.019764 GTCGCATTTTAGTGTATAATTGCATTT 57.980 29.630 0.00 0.00 32.85 2.32
7366 7983 8.405531 AGTCGCATTTTAGTGTATAATTGCATT 58.594 29.630 0.00 0.00 32.85 3.56
7367 7984 7.930217 AGTCGCATTTTAGTGTATAATTGCAT 58.070 30.769 0.00 0.00 32.85 3.96
7368 7985 7.315247 AGTCGCATTTTAGTGTATAATTGCA 57.685 32.000 0.00 0.00 32.85 4.08
7408 8025 5.425217 TCTGTGCTCCCTCTGTTTCATATTA 59.575 40.000 0.00 0.00 0.00 0.98
7409 8026 4.225942 TCTGTGCTCCCTCTGTTTCATATT 59.774 41.667 0.00 0.00 0.00 1.28
7411 8028 3.173151 TCTGTGCTCCCTCTGTTTCATA 58.827 45.455 0.00 0.00 0.00 2.15
7412 8029 1.980765 TCTGTGCTCCCTCTGTTTCAT 59.019 47.619 0.00 0.00 0.00 2.57
7413 8030 1.423584 TCTGTGCTCCCTCTGTTTCA 58.576 50.000 0.00 0.00 0.00 2.69
7414 8031 2.746362 CAATCTGTGCTCCCTCTGTTTC 59.254 50.000 0.00 0.00 0.00 2.78
7427 8235 7.588854 CACAGTTCAATTCACTTACAATCTGTG 59.411 37.037 0.00 0.00 40.66 3.66
7431 8239 5.858581 GCCACAGTTCAATTCACTTACAATC 59.141 40.000 0.00 0.00 0.00 2.67
7489 8298 2.487762 CTGCCGCCTTTTCTATGTTTGA 59.512 45.455 0.00 0.00 0.00 2.69
7490 8299 2.867429 CTGCCGCCTTTTCTATGTTTG 58.133 47.619 0.00 0.00 0.00 2.93
7491 8300 1.202348 GCTGCCGCCTTTTCTATGTTT 59.798 47.619 0.00 0.00 0.00 2.83
7492 8301 0.811281 GCTGCCGCCTTTTCTATGTT 59.189 50.000 0.00 0.00 0.00 2.71
7514 8323 0.312102 GCCACAGTTCAACTTCAGGC 59.688 55.000 8.48 8.48 32.24 4.85
7515 8324 0.954452 GGCCACAGTTCAACTTCAGG 59.046 55.000 0.00 0.00 0.00 3.86
7516 8325 1.876156 GAGGCCACAGTTCAACTTCAG 59.124 52.381 5.01 0.00 0.00 3.02
7518 8327 1.967319 TGAGGCCACAGTTCAACTTC 58.033 50.000 5.01 0.00 0.00 3.01
7519 8328 2.435372 TTGAGGCCACAGTTCAACTT 57.565 45.000 5.01 0.00 0.00 2.66
7521 8330 3.733443 AATTTGAGGCCACAGTTCAAC 57.267 42.857 5.01 0.00 31.11 3.18
7523 8332 3.068024 GTCAAATTTGAGGCCACAGTTCA 59.932 43.478 21.05 0.00 37.98 3.18
7524 8333 3.552890 GGTCAAATTTGAGGCCACAGTTC 60.553 47.826 21.05 5.46 37.98 3.01
7525 8334 2.365293 GGTCAAATTTGAGGCCACAGTT 59.635 45.455 21.05 0.87 37.98 3.16
7527 8336 1.962807 TGGTCAAATTTGAGGCCACAG 59.037 47.619 21.05 0.00 37.98 3.66
7528 8337 2.079170 TGGTCAAATTTGAGGCCACA 57.921 45.000 21.05 11.99 37.98 4.17
7529 8338 2.547855 GGTTGGTCAAATTTGAGGCCAC 60.548 50.000 23.33 18.54 37.98 5.01
7531 8340 1.970640 AGGTTGGTCAAATTTGAGGCC 59.029 47.619 21.05 18.76 37.98 5.19
7532 8341 4.522789 TCTTAGGTTGGTCAAATTTGAGGC 59.477 41.667 21.05 10.37 37.98 4.70
7533 8342 6.648879 TTCTTAGGTTGGTCAAATTTGAGG 57.351 37.500 21.05 0.00 37.98 3.86
7534 8343 9.196552 GAAATTCTTAGGTTGGTCAAATTTGAG 57.803 33.333 21.05 6.54 37.98 3.02
7535 8344 7.865385 CGAAATTCTTAGGTTGGTCAAATTTGA 59.135 33.333 16.91 16.91 34.20 2.69
7536 8345 7.116233 CCGAAATTCTTAGGTTGGTCAAATTTG 59.884 37.037 12.15 12.15 0.00 2.32
7701 8531 0.107831 TCAGTGTGCCTACCCACAAC 59.892 55.000 0.00 0.00 46.28 3.32
7793 8626 2.291605 GCCTTTATGGAGGAGTTTGGGT 60.292 50.000 0.69 0.00 39.25 4.51


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

AutoCloner maintained by Alex Coulton.