Multiple sequence alignment - TraesCS3A01G400100

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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 TraesCS3A01G400100 chr3A 100.000 2661 0 0 1 2661 646851299 646848639 0.000000e+00 4915.0
1 TraesCS3A01G400100 chr3A 100.000 1052 0 0 2860 3911 646848440 646847389 0.000000e+00 1943.0
2 TraesCS3A01G400100 chr3D 94.836 2653 106 12 21 2661 509251222 509248589 0.000000e+00 4111.0
3 TraesCS3A01G400100 chr3B 96.287 1966 71 1 696 2661 672101552 672099589 0.000000e+00 3225.0
4 TraesCS3A01G400100 chr3B 89.251 521 38 7 184 698 672102183 672101675 1.530000e-178 636.0
5 TraesCS3A01G400100 chr3B 85.437 309 20 12 2896 3186 672099526 672099225 8.220000e-77 298.0
6 TraesCS3A01G400100 chr3B 85.484 248 15 10 3675 3911 672098682 672098445 5.050000e-59 239.0
7 TraesCS3A01G400100 chr3B 83.401 247 20 11 3419 3658 672098893 672098661 3.960000e-50 209.0
8 TraesCS3A01G400100 chr1A 88.055 1892 205 12 772 2658 448913512 448915387 0.000000e+00 2222.0
9 TraesCS3A01G400100 chr1B 87.699 1886 219 11 772 2655 469969183 469971057 0.000000e+00 2185.0
10 TraesCS3A01G400100 chr1D 87.302 1898 219 13 772 2658 348051612 348053498 0.000000e+00 2150.0
11 TraesCS3A01G400100 chr1D 100.000 31 0 0 2552 2582 299358484 299358454 1.520000e-04 58.4
12 TraesCS3A01G400100 chr7B 88.656 573 36 12 27 581 657584106 657583545 0.000000e+00 671.0
13 TraesCS3A01G400100 chr7B 91.507 471 33 3 114 581 74048145 74048611 3.290000e-180 641.0
14 TraesCS3A01G400100 chr7B 87.587 572 46 15 27 581 42197593 42197030 1.180000e-179 640.0
15 TraesCS3A01G400100 chr5B 92.521 468 28 3 117 581 669145759 669145296 0.000000e+00 664.0
16 TraesCS3A01G400100 chr5B 92.094 468 30 3 117 581 538080163 538079700 0.000000e+00 652.0
17 TraesCS3A01G400100 chr7A 88.266 571 42 14 27 581 580362793 580363354 0.000000e+00 660.0
18 TraesCS3A01G400100 chr5A 91.507 471 32 4 114 581 709007794 709008259 3.290000e-180 641.0
19 TraesCS3A01G400100 chr7D 100.000 31 0 0 2552 2582 404601513 404601543 1.520000e-04 58.4
20 TraesCS3A01G400100 chr5D 100.000 31 0 0 2552 2582 122925984 122925954 1.520000e-04 58.4
21 TraesCS3A01G400100 chr4D 100.000 31 0 0 2552 2582 56410550 56410580 1.520000e-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 TraesCS3A01G400100 chr3A 646847389 646851299 3910 True 3429.0 4915 100.000 1 3911 2 chr3A.!!$R1 3910
1 TraesCS3A01G400100 chr3D 509248589 509251222 2633 True 4111.0 4111 94.836 21 2661 1 chr3D.!!$R1 2640
2 TraesCS3A01G400100 chr3B 672098445 672102183 3738 True 921.4 3225 87.972 184 3911 5 chr3B.!!$R1 3727
3 TraesCS3A01G400100 chr1A 448913512 448915387 1875 False 2222.0 2222 88.055 772 2658 1 chr1A.!!$F1 1886
4 TraesCS3A01G400100 chr1B 469969183 469971057 1874 False 2185.0 2185 87.699 772 2655 1 chr1B.!!$F1 1883
5 TraesCS3A01G400100 chr1D 348051612 348053498 1886 False 2150.0 2150 87.302 772 2658 1 chr1D.!!$F1 1886
6 TraesCS3A01G400100 chr7B 657583545 657584106 561 True 671.0 671 88.656 27 581 1 chr7B.!!$R2 554
7 TraesCS3A01G400100 chr7B 42197030 42197593 563 True 640.0 640 87.587 27 581 1 chr7B.!!$R1 554
8 TraesCS3A01G400100 chr7A 580362793 580363354 561 False 660.0 660 88.266 27 581 1 chr7A.!!$F1 554

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
72 73 0.608640 AGTTGTCGGGACCAAGCTAG 59.391 55.0 0.00 0.00 0.00 3.42 F
1166 1323 0.455005 GGCAAAGAAGAGGCTCATGC 59.545 55.0 18.26 16.82 38.76 4.06 F
2265 2422 0.036022 AGCTGACCTTGGCTGAGAAC 59.964 55.0 0.00 0.00 37.41 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1185 1342 0.449388 CGGAAGCAAAGCACATCTCC 59.551 55.0 0.0 0.0 0.0 3.71 R
2863 3029 0.105224 TCCAGCGAAGTGTTTCCGAA 59.895 50.0 0.0 0.0 0.0 4.30 R
3879 4203 0.028505 CATCAGGCTCGGCATTTTCG 59.971 55.0 0.0 0.0 0.0 3.46 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 4.643795 CCTGATGACACGGGCATT 57.356 55.556 0.00 0.00 0.00 3.56
18 19 2.100846 CCTGATGACACGGGCATTG 58.899 57.895 0.00 0.00 0.00 2.82
19 20 1.378882 CCTGATGACACGGGCATTGG 61.379 60.000 0.00 0.00 0.00 3.16
49 50 2.828877 TGCGCCGTAGCTAATAATGTT 58.171 42.857 4.18 0.00 38.13 2.71
50 51 2.798283 TGCGCCGTAGCTAATAATGTTC 59.202 45.455 4.18 0.00 38.13 3.18
51 52 2.160013 GCGCCGTAGCTAATAATGTTCG 60.160 50.000 0.00 0.00 36.60 3.95
62 63 5.051240 GCTAATAATGTTCGTAGTTGTCGGG 60.051 44.000 0.00 0.00 0.00 5.14
72 73 0.608640 AGTTGTCGGGACCAAGCTAG 59.391 55.000 0.00 0.00 0.00 3.42
128 143 1.891060 GAAGACGGTTCTGTGCTGCG 61.891 60.000 0.00 0.00 29.98 5.18
158 175 2.159707 CGTACGGCTGGTTTGATTTCTG 60.160 50.000 7.57 0.00 0.00 3.02
161 178 1.135575 CGGCTGGTTTGATTTCTGAGC 60.136 52.381 0.00 0.00 0.00 4.26
219 237 4.023980 ACAGATAGTACTACCTGCTTGCA 58.976 43.478 22.24 0.00 0.00 4.08
290 310 3.368843 GGTGTGTTAACGTAGGTGCATAC 59.631 47.826 0.26 0.00 0.00 2.39
295 320 5.514204 GTGTTAACGTAGGTGCATACTACTG 59.486 44.000 21.66 18.07 38.87 2.74
372 397 3.613737 CGTTTTCATCATGCCAATCAACC 59.386 43.478 0.00 0.00 0.00 3.77
401 426 2.106511 TCTATGGGCCAAATCTACCTGC 59.893 50.000 11.89 0.00 0.00 4.85
519 544 1.561542 AGGCTTCAGTGGTATTCAGGG 59.438 52.381 0.00 0.00 0.00 4.45
542 567 5.227238 CATTTATGCTCCACAGTTCAGTC 57.773 43.478 0.00 0.00 0.00 3.51
543 568 4.350368 TTTATGCTCCACAGTTCAGTCA 57.650 40.909 0.00 0.00 0.00 3.41
544 569 2.469274 ATGCTCCACAGTTCAGTCAG 57.531 50.000 0.00 0.00 0.00 3.51
563 588 4.631813 GTCAGACAGCTAGTTACCAAATGG 59.368 45.833 0.00 0.00 42.17 3.16
616 641 4.414337 AGCTATTACTTTCCTGCTGAGG 57.586 45.455 0.00 0.00 41.39 3.86
635 660 0.931662 GCACAGCTGAAGCAAACACG 60.932 55.000 23.35 0.00 45.16 4.49
657 685 5.042593 CGGCCGTAGTAACATTACACATTA 58.957 41.667 19.50 0.00 36.12 1.90
658 686 5.693104 CGGCCGTAGTAACATTACACATTAT 59.307 40.000 19.50 0.00 36.12 1.28
659 687 6.201425 CGGCCGTAGTAACATTACACATTATT 59.799 38.462 19.50 0.00 36.12 1.40
660 688 7.381948 CGGCCGTAGTAACATTACACATTATTA 59.618 37.037 19.50 0.00 36.12 0.98
684 712 6.793492 TTTTTCTTGTTTTGGGTTGAAGTG 57.207 33.333 0.00 0.00 0.00 3.16
705 858 2.413634 GCCGTTATGTTGTAACTGCCAC 60.414 50.000 3.84 0.00 33.49 5.01
722 875 3.890756 TGCCACTTGTGTCATTGATTTCT 59.109 39.130 0.00 0.00 0.00 2.52
755 908 5.774690 ACAATCACTTTGAGGGAAATGCTTA 59.225 36.000 0.00 0.00 38.76 3.09
799 952 5.839621 TGTCTGTCAACTGTAGACTTAACC 58.160 41.667 9.21 0.00 41.01 2.85
852 1009 3.973206 TGGTGATACTAGTGTTGGGTG 57.027 47.619 5.39 0.00 0.00 4.61
1166 1323 0.455005 GGCAAAGAAGAGGCTCATGC 59.545 55.000 18.26 16.82 38.76 4.06
1203 1360 1.742268 GAGGAGATGTGCTTTGCTTCC 59.258 52.381 0.00 0.00 0.00 3.46
1470 1627 5.663106 AGAACCAGGAAACTCATATAGCAGA 59.337 40.000 0.00 0.00 40.21 4.26
1560 1717 4.379302 AAAATCTCAGCTCAAGGAGGTT 57.621 40.909 0.00 0.00 38.40 3.50
1563 1720 1.620819 TCTCAGCTCAAGGAGGTTGAC 59.379 52.381 0.00 0.00 40.45 3.18
1587 1744 3.822735 TCTCAGATTTTGTTGCTGGAAGG 59.177 43.478 0.00 0.00 0.00 3.46
1701 1858 2.266055 GAGAAGGGTGTGAGGGCG 59.734 66.667 0.00 0.00 0.00 6.13
1902 2059 2.814336 GGTCAAGCGTTCTCCAAATCTT 59.186 45.455 0.00 0.00 0.00 2.40
2139 2296 4.778534 AGCAATTGTGAATGTCCTCAAG 57.221 40.909 7.40 0.00 0.00 3.02
2265 2422 0.036022 AGCTGACCTTGGCTGAGAAC 59.964 55.000 0.00 0.00 37.41 3.01
2495 2652 0.321122 CTGAAGGCAGGCGAGAACTT 60.321 55.000 0.00 0.00 38.51 2.66
2568 2725 2.755655 TGACGAGGATGAAGAAGAGGAC 59.244 50.000 0.00 0.00 0.00 3.85
2885 3051 0.534203 GGAAACACTTCGCTGGACCA 60.534 55.000 0.00 0.00 31.77 4.02
2887 3053 0.180406 AAACACTTCGCTGGACCAGT 59.820 50.000 22.58 0.00 33.43 4.00
2895 3061 0.523072 CGCTGGACCAGTTGGAATTG 59.477 55.000 22.58 0.00 38.94 2.32
2896 3062 1.881925 CGCTGGACCAGTTGGAATTGA 60.882 52.381 22.58 0.00 38.94 2.57
2897 3063 2.238521 GCTGGACCAGTTGGAATTGAA 58.761 47.619 22.58 0.00 38.94 2.69
2898 3064 2.827921 GCTGGACCAGTTGGAATTGAAT 59.172 45.455 22.58 0.00 38.94 2.57
2899 3065 3.259123 GCTGGACCAGTTGGAATTGAATT 59.741 43.478 22.58 0.00 38.94 2.17
2900 3066 4.262592 GCTGGACCAGTTGGAATTGAATTT 60.263 41.667 22.58 0.00 38.94 1.82
2901 3067 5.467035 TGGACCAGTTGGAATTGAATTTC 57.533 39.130 4.92 0.00 38.94 2.17
2902 3068 4.022416 TGGACCAGTTGGAATTGAATTTCG 60.022 41.667 4.92 0.00 38.94 3.46
2903 3069 3.913089 ACCAGTTGGAATTGAATTTCGC 58.087 40.909 4.92 0.00 38.94 4.70
2904 3070 2.916716 CCAGTTGGAATTGAATTTCGCG 59.083 45.455 0.00 0.00 37.39 5.87
2915 3081 4.811555 TGAATTTCGCGGAATGATAAGG 57.188 40.909 14.64 0.00 0.00 2.69
2943 3109 3.346631 CTGTGGCCGGCTCAATTGC 62.347 63.158 28.56 8.18 0.00 3.56
2979 3145 0.039165 GCAGCCTGTTTTGGTGTAGC 60.039 55.000 0.00 0.00 0.00 3.58
3019 3185 7.013942 GGTTTATCTGTAACTTTGGTTGGAACT 59.986 37.037 0.00 0.00 36.92 3.01
3021 3187 6.635030 ATCTGTAACTTTGGTTGGAACTTC 57.365 37.500 0.00 0.00 36.92 3.01
3023 3189 6.184789 TCTGTAACTTTGGTTGGAACTTCTT 58.815 36.000 0.00 0.00 36.92 2.52
3025 3191 6.626302 TGTAACTTTGGTTGGAACTTCTTTG 58.374 36.000 0.00 0.00 36.92 2.77
3084 3262 4.571176 GTCGAGGACCCTTAAATCATCAAC 59.429 45.833 0.00 0.00 0.00 3.18
3120 3298 4.508662 GGAACCACCTATCTATATGCTGC 58.491 47.826 0.00 0.00 35.41 5.25
3125 3303 2.423892 ACCTATCTATATGCTGCGACCG 59.576 50.000 0.00 0.00 0.00 4.79
3162 3341 2.352503 ATCTGTGGCGTGCATTTTTC 57.647 45.000 0.00 0.00 0.00 2.29
3163 3342 0.313672 TCTGTGGCGTGCATTTTTCC 59.686 50.000 0.00 0.00 0.00 3.13
3165 3344 0.313672 TGTGGCGTGCATTTTTCCTC 59.686 50.000 0.00 0.00 0.00 3.71
3166 3345 0.598065 GTGGCGTGCATTTTTCCTCT 59.402 50.000 0.00 0.00 0.00 3.69
3167 3346 0.881118 TGGCGTGCATTTTTCCTCTC 59.119 50.000 0.00 0.00 0.00 3.20
3168 3347 0.881118 GGCGTGCATTTTTCCTCTCA 59.119 50.000 0.00 0.00 0.00 3.27
3169 3348 1.474077 GGCGTGCATTTTTCCTCTCAT 59.526 47.619 0.00 0.00 0.00 2.90
3174 3356 4.622740 CGTGCATTTTTCCTCTCATTTTCC 59.377 41.667 0.00 0.00 0.00 3.13
3183 3365 1.741706 CTCTCATTTTCCGTGCTGCAT 59.258 47.619 5.27 0.00 0.00 3.96
3186 3368 3.313249 TCTCATTTTCCGTGCTGCATATG 59.687 43.478 5.27 0.00 0.00 1.78
3187 3369 3.016031 TCATTTTCCGTGCTGCATATGT 58.984 40.909 5.27 0.00 0.00 2.29
3189 3371 3.485947 TTTTCCGTGCTGCATATGTTC 57.514 42.857 5.27 0.00 0.00 3.18
3190 3372 1.006086 TTCCGTGCTGCATATGTTCG 58.994 50.000 5.27 3.10 0.00 3.95
3191 3373 1.010797 CCGTGCTGCATATGTTCGC 60.011 57.895 5.27 5.44 0.00 4.70
3192 3374 1.704387 CCGTGCTGCATATGTTCGCA 61.704 55.000 5.27 7.95 36.52 5.10
3197 3379 2.097444 TGCATATGTTCGCAGTGGC 58.903 52.632 4.29 0.00 33.34 5.01
3198 3380 0.676151 TGCATATGTTCGCAGTGGCA 60.676 50.000 4.29 0.00 41.24 4.92
3199 3381 0.451383 GCATATGTTCGCAGTGGCAA 59.549 50.000 4.29 0.00 41.24 4.52
3216 3398 2.036346 GGCAACAAGTTTTGATCTGCCT 59.964 45.455 18.22 0.00 43.92 4.75
3217 3399 3.255642 GGCAACAAGTTTTGATCTGCCTA 59.744 43.478 18.22 0.00 43.92 3.93
3218 3400 4.229876 GCAACAAGTTTTGATCTGCCTAC 58.770 43.478 0.00 0.00 32.33 3.18
3221 3403 3.074412 CAAGTTTTGATCTGCCTACCGT 58.926 45.455 0.00 0.00 0.00 4.83
3222 3404 2.699954 AGTTTTGATCTGCCTACCGTG 58.300 47.619 0.00 0.00 0.00 4.94
3223 3405 1.130561 GTTTTGATCTGCCTACCGTGC 59.869 52.381 0.00 0.00 0.00 5.34
3225 3407 2.279517 GATCTGCCTACCGTGCGG 60.280 66.667 9.29 9.29 42.03 5.69
3235 3417 4.347096 CCGTGCGGTTTGTACAGA 57.653 55.556 1.93 0.00 31.89 3.41
3236 3418 2.150424 CCGTGCGGTTTGTACAGAG 58.850 57.895 1.93 0.00 31.89 3.35
3237 3419 0.319211 CCGTGCGGTTTGTACAGAGA 60.319 55.000 1.93 0.00 31.89 3.10
3238 3420 1.493772 CGTGCGGTTTGTACAGAGAA 58.506 50.000 0.00 0.00 31.89 2.87
3239 3421 1.455786 CGTGCGGTTTGTACAGAGAAG 59.544 52.381 0.00 0.00 31.89 2.85
3241 3423 3.128349 GTGCGGTTTGTACAGAGAAGAA 58.872 45.455 0.00 0.00 32.79 2.52
3242 3424 3.746492 GTGCGGTTTGTACAGAGAAGAAT 59.254 43.478 0.00 0.00 32.79 2.40
3243 3425 4.927425 GTGCGGTTTGTACAGAGAAGAATA 59.073 41.667 0.00 0.00 32.79 1.75
3245 3427 4.927425 GCGGTTTGTACAGAGAAGAATACA 59.073 41.667 0.00 0.00 0.00 2.29
3246 3428 5.062308 GCGGTTTGTACAGAGAAGAATACAG 59.938 44.000 0.00 0.00 0.00 2.74
3247 3429 5.062308 CGGTTTGTACAGAGAAGAATACAGC 59.938 44.000 0.00 0.00 0.00 4.40
3248 3430 5.351740 GGTTTGTACAGAGAAGAATACAGCC 59.648 44.000 0.00 0.00 0.00 4.85
3251 3433 5.265191 TGTACAGAGAAGAATACAGCCTCT 58.735 41.667 0.00 0.00 34.83 3.69
3254 3436 3.069443 CAGAGAAGAATACAGCCTCTCCC 59.931 52.174 0.00 0.00 32.42 4.30
3255 3437 2.367241 GAGAAGAATACAGCCTCTCCCC 59.633 54.545 0.00 0.00 0.00 4.81
3256 3438 1.069358 GAAGAATACAGCCTCTCCCCG 59.931 57.143 0.00 0.00 0.00 5.73
3257 3439 0.760945 AGAATACAGCCTCTCCCCGG 60.761 60.000 0.00 0.00 0.00 5.73
3275 3457 4.069232 CGGCAGGAGCGTCTTCCA 62.069 66.667 5.72 0.00 43.41 3.53
3276 3458 2.125350 GGCAGGAGCGTCTTCCAG 60.125 66.667 5.72 0.00 43.41 3.86
3279 3461 2.604686 AGGAGCGTCTTCCAGCCA 60.605 61.111 5.72 0.00 39.84 4.75
3280 3462 2.125350 GGAGCGTCTTCCAGCCAG 60.125 66.667 0.00 0.00 37.20 4.85
3281 3463 2.817396 GAGCGTCTTCCAGCCAGC 60.817 66.667 0.00 0.00 0.00 4.85
3282 3464 3.308014 GAGCGTCTTCCAGCCAGCT 62.308 63.158 0.00 0.00 37.69 4.24
3283 3465 2.817396 GCGTCTTCCAGCCAGCTC 60.817 66.667 0.00 0.00 0.00 4.09
3284 3466 2.977178 CGTCTTCCAGCCAGCTCT 59.023 61.111 0.00 0.00 0.00 4.09
3285 3467 1.153667 CGTCTTCCAGCCAGCTCTC 60.154 63.158 0.00 0.00 0.00 3.20
3286 3468 1.153667 GTCTTCCAGCCAGCTCTCG 60.154 63.158 0.00 0.00 0.00 4.04
3287 3469 2.186384 CTTCCAGCCAGCTCTCGG 59.814 66.667 0.00 0.00 0.00 4.63
3288 3470 2.283894 TTCCAGCCAGCTCTCGGA 60.284 61.111 0.00 0.00 0.00 4.55
3289 3471 1.684386 CTTCCAGCCAGCTCTCGGAT 61.684 60.000 0.00 0.00 0.00 4.18
3291 3473 0.178950 TCCAGCCAGCTCTCGGATAT 60.179 55.000 0.00 0.00 0.00 1.63
3292 3474 0.246086 CCAGCCAGCTCTCGGATATC 59.754 60.000 0.00 0.00 0.00 1.63
3294 3476 1.214062 GCCAGCTCTCGGATATCGG 59.786 63.158 3.94 3.94 39.77 4.18
3295 3477 1.886585 CCAGCTCTCGGATATCGGG 59.113 63.158 10.11 0.00 41.61 5.14
3296 3478 1.599606 CCAGCTCTCGGATATCGGGG 61.600 65.000 10.11 7.11 40.39 5.73
3297 3479 1.979693 AGCTCTCGGATATCGGGGC 60.980 63.158 10.11 7.85 40.39 5.80
3298 3480 2.276116 GCTCTCGGATATCGGGGCA 61.276 63.158 10.11 0.00 40.39 5.36
3299 3481 1.886585 CTCTCGGATATCGGGGCAG 59.113 63.158 10.11 3.55 40.39 4.85
3300 3482 0.896019 CTCTCGGATATCGGGGCAGT 60.896 60.000 10.11 0.00 40.39 4.40
3301 3483 0.894184 TCTCGGATATCGGGGCAGTC 60.894 60.000 10.11 0.00 40.39 3.51
3302 3484 1.152631 TCGGATATCGGGGCAGTCA 60.153 57.895 10.11 0.00 39.77 3.41
3303 3485 1.006102 CGGATATCGGGGCAGTCAC 60.006 63.158 2.40 0.00 34.75 3.67
3304 3486 1.371558 GGATATCGGGGCAGTCACC 59.628 63.158 0.00 0.00 0.00 4.02
3305 3487 1.122019 GGATATCGGGGCAGTCACCT 61.122 60.000 0.00 0.00 0.00 4.00
3306 3488 0.034059 GATATCGGGGCAGTCACCTG 59.966 60.000 0.00 0.00 41.91 4.00
3307 3489 0.691078 ATATCGGGGCAGTCACCTGT 60.691 55.000 0.00 0.00 41.02 4.00
3308 3490 0.032912 TATCGGGGCAGTCACCTGTA 60.033 55.000 0.00 0.00 41.02 2.74
3309 3491 1.330655 ATCGGGGCAGTCACCTGTAG 61.331 60.000 0.00 0.00 41.02 2.74
3310 3492 1.982395 CGGGGCAGTCACCTGTAGA 60.982 63.158 0.00 0.00 41.02 2.59
3311 3493 1.597461 GGGGCAGTCACCTGTAGAC 59.403 63.158 0.00 0.00 41.02 2.59
3312 3494 1.192146 GGGGCAGTCACCTGTAGACA 61.192 60.000 0.00 0.00 41.02 3.41
3313 3495 0.247736 GGGCAGTCACCTGTAGACAG 59.752 60.000 2.50 2.50 41.02 3.51
3314 3496 1.257743 GGCAGTCACCTGTAGACAGA 58.742 55.000 11.31 0.00 46.59 3.41
3315 3497 1.067495 GGCAGTCACCTGTAGACAGAC 60.067 57.143 11.31 2.18 46.59 3.51
3316 3498 1.889829 GCAGTCACCTGTAGACAGACT 59.110 52.381 11.31 4.45 46.59 3.24
3317 3499 2.094957 GCAGTCACCTGTAGACAGACTC 60.095 54.545 11.31 0.00 46.59 3.36
3318 3500 2.490115 CAGTCACCTGTAGACAGACTCC 59.510 54.545 11.31 0.00 46.59 3.85
3319 3501 1.819903 GTCACCTGTAGACAGACTCCC 59.180 57.143 11.31 0.00 46.59 4.30
3320 3502 1.427753 TCACCTGTAGACAGACTCCCA 59.572 52.381 11.31 0.00 46.59 4.37
3321 3503 1.546476 CACCTGTAGACAGACTCCCAC 59.454 57.143 11.31 0.00 46.59 4.61
3322 3504 1.429687 ACCTGTAGACAGACTCCCACT 59.570 52.381 11.31 0.00 46.59 4.00
3323 3505 1.821753 CCTGTAGACAGACTCCCACTG 59.178 57.143 11.31 0.00 46.59 3.66
3346 3532 3.785325 TCCCACACTCCATCATCCATTTA 59.215 43.478 0.00 0.00 0.00 1.40
3348 3534 4.763793 CCCACACTCCATCATCCATTTATC 59.236 45.833 0.00 0.00 0.00 1.75
3349 3535 4.453478 CCACACTCCATCATCCATTTATCG 59.547 45.833 0.00 0.00 0.00 2.92
3350 3536 4.453478 CACACTCCATCATCCATTTATCGG 59.547 45.833 0.00 0.00 0.00 4.18
3355 3541 7.772292 CACTCCATCATCCATTTATCGGAATAT 59.228 37.037 0.00 0.00 35.77 1.28
3356 3542 8.331740 ACTCCATCATCCATTTATCGGAATATT 58.668 33.333 0.00 0.00 35.77 1.28
3390 3576 6.563381 GCGATGTACCAAACCTACGAATAATG 60.563 42.308 0.00 0.00 0.00 1.90
3392 3578 7.384115 CGATGTACCAAACCTACGAATAATGAT 59.616 37.037 0.00 0.00 0.00 2.45
3393 3579 9.701098 GATGTACCAAACCTACGAATAATGATA 57.299 33.333 0.00 0.00 0.00 2.15
3408 3594 9.672673 CGAATAATGATAACCTTATCCAATCCT 57.327 33.333 3.16 0.00 38.98 3.24
3412 3598 6.354794 TGATAACCTTATCCAATCCTACCG 57.645 41.667 3.16 0.00 38.98 4.02
3413 3599 5.842328 TGATAACCTTATCCAATCCTACCGT 59.158 40.000 3.16 0.00 38.98 4.83
3414 3600 4.417426 AACCTTATCCAATCCTACCGTG 57.583 45.455 0.00 0.00 0.00 4.94
3415 3601 2.104281 ACCTTATCCAATCCTACCGTGC 59.896 50.000 0.00 0.00 0.00 5.34
3417 3603 0.677288 TATCCAATCCTACCGTGCGG 59.323 55.000 9.29 9.29 42.03 5.69
3468 3777 1.677217 GCTCTTCGTGATGGGCTCTTT 60.677 52.381 0.69 0.00 0.00 2.52
3470 3779 3.077359 CTCTTCGTGATGGGCTCTTTTT 58.923 45.455 0.00 0.00 0.00 1.94
3471 3780 3.074412 TCTTCGTGATGGGCTCTTTTTC 58.926 45.455 0.00 0.00 0.00 2.29
3472 3781 2.859165 TCGTGATGGGCTCTTTTTCT 57.141 45.000 0.00 0.00 0.00 2.52
3474 3783 1.470098 CGTGATGGGCTCTTTTTCTGG 59.530 52.381 0.00 0.00 0.00 3.86
3475 3784 2.795329 GTGATGGGCTCTTTTTCTGGA 58.205 47.619 0.00 0.00 0.00 3.86
3476 3785 3.359950 GTGATGGGCTCTTTTTCTGGAT 58.640 45.455 0.00 0.00 0.00 3.41
3479 3788 4.949856 TGATGGGCTCTTTTTCTGGATTAC 59.050 41.667 0.00 0.00 0.00 1.89
3488 3797 8.178313 GCTCTTTTTCTGGATTACTACATGAAC 58.822 37.037 0.00 0.00 0.00 3.18
3489 3798 9.219603 CTCTTTTTCTGGATTACTACATGAACA 57.780 33.333 0.00 0.00 0.00 3.18
3501 3810 6.182039 ACTACATGAACAATGGATCAAACG 57.818 37.500 0.00 0.00 40.94 3.60
3502 3811 4.439305 ACATGAACAATGGATCAAACGG 57.561 40.909 0.00 0.00 40.94 4.44
3503 3812 3.826157 ACATGAACAATGGATCAAACGGT 59.174 39.130 0.00 0.00 40.94 4.83
3504 3813 4.280677 ACATGAACAATGGATCAAACGGTT 59.719 37.500 0.00 0.00 40.94 4.44
3505 3814 4.497473 TGAACAATGGATCAAACGGTTC 57.503 40.909 0.00 2.63 35.09 3.62
3506 3815 3.058570 TGAACAATGGATCAAACGGTTCG 60.059 43.478 0.00 0.00 36.77 3.95
3507 3816 1.199097 ACAATGGATCAAACGGTTCGC 59.801 47.619 0.00 0.00 0.00 4.70
3508 3817 0.446222 AATGGATCAAACGGTTCGCG 59.554 50.000 0.00 0.00 0.00 5.87
3509 3818 0.390603 ATGGATCAAACGGTTCGCGA 60.391 50.000 3.71 3.71 0.00 5.87
3510 3819 0.390603 TGGATCAAACGGTTCGCGAT 60.391 50.000 10.88 0.00 0.00 4.58
3511 3820 1.135053 TGGATCAAACGGTTCGCGATA 60.135 47.619 10.88 0.00 0.00 2.92
3512 3821 2.132762 GGATCAAACGGTTCGCGATAT 58.867 47.619 10.88 0.00 0.00 1.63
3513 3822 2.155155 GGATCAAACGGTTCGCGATATC 59.845 50.000 10.88 3.58 0.00 1.63
3514 3823 1.563111 TCAAACGGTTCGCGATATCC 58.437 50.000 10.88 12.38 0.00 2.59
3516 3825 1.661617 CAAACGGTTCGCGATATCCAA 59.338 47.619 10.88 0.00 0.00 3.53
3517 3826 1.567504 AACGGTTCGCGATATCCAAG 58.432 50.000 10.88 4.44 0.00 3.61
3551 3861 2.266055 CCTCCCCGTGCAAGAGAC 59.734 66.667 0.00 0.00 0.00 3.36
3554 3864 3.636231 CCCCGTGCAAGAGACCCA 61.636 66.667 0.00 0.00 0.00 4.51
3556 3866 1.746615 CCCGTGCAAGAGACCCATG 60.747 63.158 0.00 0.00 0.00 3.66
3559 3869 0.742281 CGTGCAAGAGACCCATGAGG 60.742 60.000 0.00 0.00 43.78 3.86
3563 3873 0.617413 CAAGAGACCCATGAGGCAGT 59.383 55.000 0.00 0.00 40.58 4.40
3564 3874 0.908198 AAGAGACCCATGAGGCAGTC 59.092 55.000 0.00 0.00 40.58 3.51
3565 3875 0.042431 AGAGACCCATGAGGCAGTCT 59.958 55.000 0.00 0.00 38.60 3.24
3566 3876 0.177604 GAGACCCATGAGGCAGTCTG 59.822 60.000 0.00 0.00 36.80 3.51
3567 3877 1.222936 GACCCATGAGGCAGTCTGG 59.777 63.158 1.14 0.00 40.58 3.86
3643 3957 1.633852 GCTGACAAAGCGCAGAGAGG 61.634 60.000 11.47 0.00 43.45 3.69
3651 3965 4.827835 ACAAAGCGCAGAGAGGAGTATATA 59.172 41.667 11.47 0.00 0.00 0.86
3652 3966 5.478679 ACAAAGCGCAGAGAGGAGTATATAT 59.521 40.000 11.47 0.00 0.00 0.86
3653 3967 5.828299 AAGCGCAGAGAGGAGTATATATC 57.172 43.478 11.47 0.00 0.00 1.63
3654 3968 5.110814 AGCGCAGAGAGGAGTATATATCT 57.889 43.478 11.47 0.00 0.00 1.98
3655 3969 5.505780 AGCGCAGAGAGGAGTATATATCTT 58.494 41.667 11.47 0.00 0.00 2.40
3656 3970 5.949354 AGCGCAGAGAGGAGTATATATCTTT 59.051 40.000 11.47 0.00 0.00 2.52
3657 3971 6.094881 AGCGCAGAGAGGAGTATATATCTTTC 59.905 42.308 11.47 0.00 0.00 2.62
3658 3972 6.094881 GCGCAGAGAGGAGTATATATCTTTCT 59.905 42.308 0.30 0.00 0.00 2.52
3659 3973 7.362574 GCGCAGAGAGGAGTATATATCTTTCTT 60.363 40.741 0.30 0.00 0.00 2.52
3660 3974 8.519526 CGCAGAGAGGAGTATATATCTTTCTTT 58.480 37.037 0.00 0.00 0.00 2.52
3683 3997 2.930826 TTTGCGGAAAAGAGAGGAGT 57.069 45.000 0.00 0.00 0.00 3.85
3684 3998 4.345859 TTTTGCGGAAAAGAGAGGAGTA 57.654 40.909 11.06 0.00 0.00 2.59
3685 3999 4.553330 TTTGCGGAAAAGAGAGGAGTAT 57.447 40.909 0.00 0.00 0.00 2.12
3686 4000 5.670792 TTTGCGGAAAAGAGAGGAGTATA 57.329 39.130 0.00 0.00 0.00 1.47
3756 4075 2.951457 TCGTCCTTGTCGAATATGCA 57.049 45.000 0.00 0.00 34.36 3.96
3758 4077 1.255342 CGTCCTTGTCGAATATGCACG 59.745 52.381 0.00 0.00 0.00 5.34
3759 4078 1.593006 GTCCTTGTCGAATATGCACGG 59.407 52.381 0.00 0.00 0.00 4.94
3760 4079 0.304705 CCTTGTCGAATATGCACGGC 59.695 55.000 0.00 0.00 34.64 5.68
3761 4080 0.043053 CTTGTCGAATATGCACGGCG 60.043 55.000 4.80 4.80 36.91 6.46
3762 4081 0.738063 TTGTCGAATATGCACGGCGT 60.738 50.000 6.77 6.77 36.91 5.68
3763 4082 1.143373 TGTCGAATATGCACGGCGTC 61.143 55.000 10.85 6.01 36.91 5.19
3764 4083 1.942223 TCGAATATGCACGGCGTCG 60.942 57.895 10.85 8.42 43.02 5.12
3779 4098 3.672447 TCGGCGTGCGTGGTAGAA 61.672 61.111 6.85 0.00 0.00 2.10
3793 4112 2.194271 GGTAGAAAGACGCAGATTCCG 58.806 52.381 0.00 0.00 0.00 4.30
3798 4117 4.094684 GACGCAGATTCCGTCCTG 57.905 61.111 2.79 0.00 46.78 3.86
3843 4162 1.001406 AGCTAGTAGCATTCCATCCGC 59.999 52.381 23.77 0.00 45.56 5.54
3856 4175 1.616628 ATCCGCCCCCAACTCTTCT 60.617 57.895 0.00 0.00 0.00 2.85
3870 4189 0.033504 TCTTCTGGCGCTCTCGTTTT 59.966 50.000 7.64 0.00 38.14 2.43
3874 4198 0.951040 CTGGCGCTCTCGTTTTTCCT 60.951 55.000 7.64 0.00 38.14 3.36
3875 4199 1.227999 TGGCGCTCTCGTTTTTCCTG 61.228 55.000 7.64 0.00 38.14 3.86
3879 4203 1.660333 CGCTCTCGTTTTTCCTGCAAC 60.660 52.381 0.00 0.00 0.00 4.17
3892 4216 1.067199 CTGCAACGAAAATGCCGAGC 61.067 55.000 0.00 0.00 43.16 5.03
3896 4220 0.605319 AACGAAAATGCCGAGCCTGA 60.605 50.000 0.00 0.00 0.00 3.86
3898 4222 0.028505 CGAAAATGCCGAGCCTGATG 59.971 55.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.378882 CCAATGCCCGTGTCATCAGG 61.379 60.000 0.00 0.00 0.00 3.86
1 2 1.378882 CCCAATGCCCGTGTCATCAG 61.379 60.000 0.00 0.00 0.00 2.90
2 3 1.378382 CCCAATGCCCGTGTCATCA 60.378 57.895 0.00 0.00 0.00 3.07
3 4 2.774799 GCCCAATGCCCGTGTCATC 61.775 63.158 0.00 0.00 0.00 2.92
4 5 2.755469 GCCCAATGCCCGTGTCAT 60.755 61.111 0.00 0.00 0.00 3.06
11 12 3.238755 AAAACAGCGCCCAATGCCC 62.239 57.895 2.29 0.00 36.24 5.36
12 13 2.028733 CAAAACAGCGCCCAATGCC 61.029 57.895 2.29 0.00 36.24 4.40
13 14 2.670210 GCAAAACAGCGCCCAATGC 61.670 57.895 2.29 5.30 0.00 3.56
14 15 3.553039 GCAAAACAGCGCCCAATG 58.447 55.556 2.29 0.00 0.00 2.82
49 50 0.599558 CTTGGTCCCGACAACTACGA 59.400 55.000 0.00 0.00 0.00 3.43
50 51 1.012486 GCTTGGTCCCGACAACTACG 61.012 60.000 0.00 0.00 0.00 3.51
51 52 0.320697 AGCTTGGTCCCGACAACTAC 59.679 55.000 0.00 0.00 0.00 2.73
62 63 7.603024 ACAAAACAGATTAGTACTAGCTTGGTC 59.397 37.037 2.23 0.00 0.00 4.02
128 143 1.418342 CCAGCCGTACGTGCACATAC 61.418 60.000 24.11 15.66 0.00 2.39
295 320 8.425577 TGAGCAGACTAATGAAAATAACTAGC 57.574 34.615 0.00 0.00 0.00 3.42
372 397 4.342092 AGATTTGGCCCATAGAATTTTCGG 59.658 41.667 0.00 0.00 0.00 4.30
541 566 4.832248 CCATTTGGTAACTAGCTGTCTGA 58.168 43.478 0.00 0.00 37.61 3.27
542 567 3.375299 GCCATTTGGTAACTAGCTGTCTG 59.625 47.826 0.00 0.00 37.57 3.51
543 568 3.264450 AGCCATTTGGTAACTAGCTGTCT 59.736 43.478 0.00 0.00 37.57 3.41
544 569 3.610911 AGCCATTTGGTAACTAGCTGTC 58.389 45.455 0.00 0.00 37.57 3.51
616 641 0.931662 CGTGTTTGCTTCAGCTGTGC 60.932 55.000 21.35 21.35 42.66 4.57
627 652 0.164432 GTTACTACGGCCGTGTTTGC 59.836 55.000 40.02 22.39 0.00 3.68
635 660 7.486802 AATAATGTGTAATGTTACTACGGCC 57.513 36.000 0.00 0.00 34.77 6.13
657 685 9.679661 ACTTCAACCCAAAACAAGAAAAATAAT 57.320 25.926 0.00 0.00 0.00 1.28
658 686 8.940952 CACTTCAACCCAAAACAAGAAAAATAA 58.059 29.630 0.00 0.00 0.00 1.40
659 687 7.065204 GCACTTCAACCCAAAACAAGAAAAATA 59.935 33.333 0.00 0.00 0.00 1.40
660 688 6.128035 GCACTTCAACCCAAAACAAGAAAAAT 60.128 34.615 0.00 0.00 0.00 1.82
671 699 2.054232 TAACGGCACTTCAACCCAAA 57.946 45.000 0.00 0.00 0.00 3.28
684 712 1.807742 TGGCAGTTACAACATAACGGC 59.192 47.619 11.84 11.84 44.10 5.68
722 875 8.698973 TCCCTCAAAGTGATTGTTTTACATAA 57.301 30.769 0.00 0.00 40.11 1.90
745 898 7.432252 CGTCAATTGGTAAAGATAAGCATTTCC 59.568 37.037 5.42 0.00 0.00 3.13
755 908 6.655003 AGACAACATCGTCAATTGGTAAAGAT 59.345 34.615 5.42 0.00 38.43 2.40
799 952 7.014092 ACAAAACACCAATTAGCAAAACATG 57.986 32.000 0.00 0.00 0.00 3.21
1016 1173 1.452108 GTCCGGGGCTGGAAATCTG 60.452 63.158 0.00 0.00 40.44 2.90
1166 1323 2.833338 TCCTCAATCCTTTTGGCATTGG 59.167 45.455 0.00 0.00 37.53 3.16
1167 1324 3.765511 TCTCCTCAATCCTTTTGGCATTG 59.234 43.478 0.00 0.00 40.12 2.82
1185 1342 0.449388 CGGAAGCAAAGCACATCTCC 59.551 55.000 0.00 0.00 0.00 3.71
1203 1360 3.487042 CCTTCTTGAAATGCTCATCTGCG 60.487 47.826 0.00 0.00 32.78 5.18
1560 1717 4.216902 CCAGCAACAAAATCTGAGATGTCA 59.783 41.667 0.00 0.00 0.00 3.58
1563 1720 5.381174 TTCCAGCAACAAAATCTGAGATG 57.619 39.130 0.00 0.00 0.00 2.90
1587 1744 0.750911 CAAGGGCTTCATCCTCAGGC 60.751 60.000 0.00 0.00 32.59 4.85
1701 1858 4.214119 TGTGATTTTAGCAGCTCTGTGAAC 59.786 41.667 0.00 0.00 0.00 3.18
1902 2059 2.368548 TGCTGAGCACCTAAAACTCTCA 59.631 45.455 1.40 0.00 31.71 3.27
1929 2086 3.649981 CCACTCCACCATCAGATCCTATT 59.350 47.826 0.00 0.00 0.00 1.73
2205 2362 1.446618 CAAGCATTCCGCCAAAGGC 60.447 57.895 0.00 0.00 46.75 4.35
2265 2422 2.587194 CCGGCATCCTTCAGCTCG 60.587 66.667 0.00 0.00 0.00 5.03
2326 2483 1.873903 GCTCACGTCAAGCTCCTTCAA 60.874 52.381 11.33 0.00 36.80 2.69
2544 2701 3.243704 CCTCTTCTTCATCCTCGTCATCC 60.244 52.174 0.00 0.00 0.00 3.51
2556 2713 4.646492 TCATCATCATCGTCCTCTTCTTCA 59.354 41.667 0.00 0.00 0.00 3.02
2568 2725 4.153655 CCATACTTTGCCTCATCATCATCG 59.846 45.833 0.00 0.00 0.00 3.84
2859 3025 1.000506 AGCGAAGTGTTTCCGAAGCTA 59.999 47.619 0.00 0.00 28.59 3.32
2860 3026 0.249911 AGCGAAGTGTTTCCGAAGCT 60.250 50.000 0.00 0.00 0.00 3.74
2861 3027 0.110644 CAGCGAAGTGTTTCCGAAGC 60.111 55.000 0.00 0.00 0.00 3.86
2862 3028 0.512952 CCAGCGAAGTGTTTCCGAAG 59.487 55.000 0.00 0.00 0.00 3.79
2863 3029 0.105224 TCCAGCGAAGTGTTTCCGAA 59.895 50.000 0.00 0.00 0.00 4.30
2864 3030 0.599204 GTCCAGCGAAGTGTTTCCGA 60.599 55.000 0.00 0.00 0.00 4.55
2865 3031 1.566018 GGTCCAGCGAAGTGTTTCCG 61.566 60.000 0.00 0.00 0.00 4.30
2866 3032 0.534203 TGGTCCAGCGAAGTGTTTCC 60.534 55.000 0.00 0.00 0.00 3.13
2867 3033 0.868406 CTGGTCCAGCGAAGTGTTTC 59.132 55.000 5.79 0.00 0.00 2.78
2868 3034 0.180406 ACTGGTCCAGCGAAGTGTTT 59.820 50.000 19.40 0.00 34.37 2.83
2869 3035 0.180406 AACTGGTCCAGCGAAGTGTT 59.820 50.000 19.40 1.58 34.37 3.32
2870 3036 0.532862 CAACTGGTCCAGCGAAGTGT 60.533 55.000 19.40 0.00 34.37 3.55
2871 3037 1.230635 CCAACTGGTCCAGCGAAGTG 61.231 60.000 19.40 9.07 34.37 3.16
2872 3038 1.071471 CCAACTGGTCCAGCGAAGT 59.929 57.895 19.40 0.00 34.37 3.01
2873 3039 0.250295 TTCCAACTGGTCCAGCGAAG 60.250 55.000 19.40 5.67 34.37 3.79
2876 3042 0.523072 CAATTCCAACTGGTCCAGCG 59.477 55.000 19.40 10.22 34.37 5.18
2885 3051 2.817258 TCCGCGAAATTCAATTCCAACT 59.183 40.909 8.23 0.00 0.00 3.16
2887 3053 3.924918 TTCCGCGAAATTCAATTCCAA 57.075 38.095 8.23 0.00 0.00 3.53
2895 3061 5.007724 AGTTCCTTATCATTCCGCGAAATTC 59.992 40.000 8.23 0.00 0.00 2.17
2896 3062 4.881850 AGTTCCTTATCATTCCGCGAAATT 59.118 37.500 8.23 0.00 0.00 1.82
2897 3063 4.451900 AGTTCCTTATCATTCCGCGAAAT 58.548 39.130 8.23 0.00 0.00 2.17
2898 3064 3.869065 AGTTCCTTATCATTCCGCGAAA 58.131 40.909 8.23 0.00 0.00 3.46
2899 3065 3.454375 GAGTTCCTTATCATTCCGCGAA 58.546 45.455 8.23 0.00 0.00 4.70
2900 3066 2.543031 CGAGTTCCTTATCATTCCGCGA 60.543 50.000 8.23 0.00 0.00 5.87
2901 3067 1.787155 CGAGTTCCTTATCATTCCGCG 59.213 52.381 0.00 0.00 0.00 6.46
2902 3068 2.795470 GACGAGTTCCTTATCATTCCGC 59.205 50.000 0.00 0.00 0.00 5.54
2903 3069 3.043586 CGACGAGTTCCTTATCATTCCG 58.956 50.000 0.00 0.00 0.00 4.30
2904 3070 2.795470 GCGACGAGTTCCTTATCATTCC 59.205 50.000 0.00 0.00 0.00 3.01
2915 3081 3.112709 GGCCACAGCGACGAGTTC 61.113 66.667 0.00 0.00 41.24 3.01
2943 3109 2.391389 GCTCGGCTCGGTTCAAAGG 61.391 63.158 0.00 0.00 0.00 3.11
2944 3110 1.630244 CTGCTCGGCTCGGTTCAAAG 61.630 60.000 0.00 0.00 0.00 2.77
3046 3214 0.596577 TCGACCAGAGAACCAAGACG 59.403 55.000 0.00 0.00 0.00 4.18
3084 3262 3.016736 GTGGTTCCCAACATATCACAGG 58.983 50.000 0.00 0.00 34.18 4.00
3104 3282 2.423892 CGGTCGCAGCATATAGATAGGT 59.576 50.000 0.00 0.00 0.00 3.08
3105 3283 2.796383 GCGGTCGCAGCATATAGATAGG 60.796 54.545 10.67 0.00 41.49 2.57
3106 3284 2.098280 AGCGGTCGCAGCATATAGATAG 59.902 50.000 17.71 0.00 44.88 2.08
3108 3286 0.891373 AGCGGTCGCAGCATATAGAT 59.109 50.000 17.71 0.00 44.88 1.98
3110 3288 0.242286 AGAGCGGTCGCAGCATATAG 59.758 55.000 17.71 0.00 44.88 1.31
3114 3292 2.046892 AAAGAGCGGTCGCAGCAT 60.047 55.556 17.71 0.00 44.88 3.79
3115 3293 2.738521 GAAAGAGCGGTCGCAGCA 60.739 61.111 17.71 0.00 44.88 4.41
3116 3294 3.843240 CGAAAGAGCGGTCGCAGC 61.843 66.667 17.71 8.88 44.88 5.25
3117 3295 3.181967 CCGAAAGAGCGGTCGCAG 61.182 66.667 17.71 2.42 46.07 5.18
3134 3312 1.863454 CACGCCACAGATATCAAGCTC 59.137 52.381 5.32 0.00 0.00 4.09
3144 3323 0.313672 GGAAAAATGCACGCCACAGA 59.686 50.000 0.00 0.00 0.00 3.41
3145 3324 0.314935 AGGAAAAATGCACGCCACAG 59.685 50.000 0.00 0.00 0.00 3.66
3162 3341 0.449388 GCAGCACGGAAAATGAGAGG 59.551 55.000 0.00 0.00 0.00 3.69
3163 3342 1.159285 TGCAGCACGGAAAATGAGAG 58.841 50.000 0.00 0.00 0.00 3.20
3165 3344 3.065786 ACATATGCAGCACGGAAAATGAG 59.934 43.478 0.00 0.00 0.00 2.90
3166 3345 3.016031 ACATATGCAGCACGGAAAATGA 58.984 40.909 0.00 0.00 0.00 2.57
3167 3346 3.425577 ACATATGCAGCACGGAAAATG 57.574 42.857 0.00 0.00 0.00 2.32
3168 3347 3.487376 CGAACATATGCAGCACGGAAAAT 60.487 43.478 0.00 0.00 0.00 1.82
3169 3348 2.159585 CGAACATATGCAGCACGGAAAA 60.160 45.455 0.00 0.00 0.00 2.29
3174 3356 1.715000 TGCGAACATATGCAGCACG 59.285 52.632 13.95 0.00 35.90 5.34
3183 3365 1.535028 CTTGTTGCCACTGCGAACATA 59.465 47.619 0.00 0.00 41.78 2.29
3186 3368 0.100503 AACTTGTTGCCACTGCGAAC 59.899 50.000 0.00 0.00 41.78 3.95
3187 3369 0.814457 AAACTTGTTGCCACTGCGAA 59.186 45.000 0.00 0.00 41.78 4.70
3189 3371 0.922717 CAAAACTTGTTGCCACTGCG 59.077 50.000 0.00 0.00 41.78 5.18
3190 3372 2.292103 TCAAAACTTGTTGCCACTGC 57.708 45.000 0.00 0.00 38.26 4.40
3191 3373 4.046462 CAGATCAAAACTTGTTGCCACTG 58.954 43.478 0.00 0.00 0.00 3.66
3192 3374 3.491447 GCAGATCAAAACTTGTTGCCACT 60.491 43.478 0.00 0.00 32.06 4.00
3193 3375 2.796593 GCAGATCAAAACTTGTTGCCAC 59.203 45.455 0.00 0.00 32.06 5.01
3194 3376 2.224018 GGCAGATCAAAACTTGTTGCCA 60.224 45.455 18.42 0.00 44.74 4.92
3195 3377 2.036346 AGGCAGATCAAAACTTGTTGCC 59.964 45.455 16.91 16.91 45.20 4.52
3197 3379 4.613622 CGGTAGGCAGATCAAAACTTGTTG 60.614 45.833 0.00 0.00 0.00 3.33
3198 3380 3.502211 CGGTAGGCAGATCAAAACTTGTT 59.498 43.478 0.00 0.00 0.00 2.83
3199 3381 3.074412 CGGTAGGCAGATCAAAACTTGT 58.926 45.455 0.00 0.00 0.00 3.16
3201 3383 3.074412 CACGGTAGGCAGATCAAAACTT 58.926 45.455 0.00 0.00 0.00 2.66
3202 3384 2.699954 CACGGTAGGCAGATCAAAACT 58.300 47.619 0.00 0.00 0.00 2.66
3204 3386 1.448985 GCACGGTAGGCAGATCAAAA 58.551 50.000 0.00 0.00 0.00 2.44
3206 3388 1.153647 CGCACGGTAGGCAGATCAA 60.154 57.895 0.00 0.00 0.00 2.57
3208 3390 2.279517 CCGCACGGTAGGCAGATC 60.280 66.667 0.00 0.00 0.00 2.75
3218 3400 0.319211 TCTCTGTACAAACCGCACGG 60.319 55.000 7.71 7.71 42.03 4.94
3221 3403 3.462483 TTCTTCTCTGTACAAACCGCA 57.538 42.857 0.00 0.00 0.00 5.69
3222 3404 4.927425 TGTATTCTTCTCTGTACAAACCGC 59.073 41.667 0.00 0.00 0.00 5.68
3223 3405 5.062308 GCTGTATTCTTCTCTGTACAAACCG 59.938 44.000 0.00 0.00 0.00 4.44
3225 3407 6.166982 AGGCTGTATTCTTCTCTGTACAAAC 58.833 40.000 0.00 0.00 0.00 2.93
3226 3408 6.211584 AGAGGCTGTATTCTTCTCTGTACAAA 59.788 38.462 0.00 0.00 34.01 2.83
3227 3409 5.717178 AGAGGCTGTATTCTTCTCTGTACAA 59.283 40.000 0.00 0.00 34.01 2.41
3228 3410 5.265191 AGAGGCTGTATTCTTCTCTGTACA 58.735 41.667 0.00 0.00 34.01 2.90
3229 3411 5.221165 GGAGAGGCTGTATTCTTCTCTGTAC 60.221 48.000 0.00 0.00 35.25 2.90
3230 3412 4.890581 GGAGAGGCTGTATTCTTCTCTGTA 59.109 45.833 0.00 0.00 35.25 2.74
3231 3413 3.704061 GGAGAGGCTGTATTCTTCTCTGT 59.296 47.826 0.00 0.00 35.25 3.41
3232 3414 3.069443 GGGAGAGGCTGTATTCTTCTCTG 59.931 52.174 0.00 0.00 35.25 3.35
3233 3415 3.304829 GGGAGAGGCTGTATTCTTCTCT 58.695 50.000 0.00 0.00 37.50 3.10
3234 3416 2.367241 GGGGAGAGGCTGTATTCTTCTC 59.633 54.545 0.00 0.00 0.00 2.87
3235 3417 2.403561 GGGGAGAGGCTGTATTCTTCT 58.596 52.381 0.00 0.00 0.00 2.85
3236 3418 1.069358 CGGGGAGAGGCTGTATTCTTC 59.931 57.143 0.00 0.00 0.00 2.87
3237 3419 1.123928 CGGGGAGAGGCTGTATTCTT 58.876 55.000 0.00 0.00 0.00 2.52
3238 3420 0.760945 CCGGGGAGAGGCTGTATTCT 60.761 60.000 0.00 0.00 0.00 2.40
3239 3421 1.749033 CCGGGGAGAGGCTGTATTC 59.251 63.158 0.00 0.00 0.00 1.75
3258 3440 3.997064 CTGGAAGACGCTCCTGCCG 62.997 68.421 1.03 0.00 34.38 5.69
3259 3441 2.125350 CTGGAAGACGCTCCTGCC 60.125 66.667 1.03 0.00 36.35 4.85
3261 3443 2.125350 GGCTGGAAGACGCTCCTG 60.125 66.667 1.03 1.78 36.35 3.86
3269 3451 2.354401 CCGAGAGCTGGCTGGAAGA 61.354 63.158 0.00 0.00 34.07 2.87
3270 3452 1.684386 ATCCGAGAGCTGGCTGGAAG 61.684 60.000 0.00 0.00 31.42 3.46
3271 3453 0.397114 TATCCGAGAGCTGGCTGGAA 60.397 55.000 0.00 0.00 31.42 3.53
3272 3454 0.178950 ATATCCGAGAGCTGGCTGGA 60.179 55.000 0.00 1.10 0.00 3.86
3273 3455 0.246086 GATATCCGAGAGCTGGCTGG 59.754 60.000 0.00 0.00 0.00 4.85
3274 3456 0.109365 CGATATCCGAGAGCTGGCTG 60.109 60.000 0.00 0.00 41.76 4.85
3275 3457 1.247419 CCGATATCCGAGAGCTGGCT 61.247 60.000 0.00 0.00 41.76 4.75
3276 3458 1.214062 CCGATATCCGAGAGCTGGC 59.786 63.158 0.00 0.00 41.76 4.85
3279 3461 1.979693 GCCCCGATATCCGAGAGCT 60.980 63.158 0.00 0.00 41.76 4.09
3280 3462 2.219325 CTGCCCCGATATCCGAGAGC 62.219 65.000 0.00 0.00 41.76 4.09
3281 3463 0.896019 ACTGCCCCGATATCCGAGAG 60.896 60.000 0.00 0.00 41.76 3.20
3282 3464 0.894184 GACTGCCCCGATATCCGAGA 60.894 60.000 0.00 0.00 41.76 4.04
3283 3465 1.179174 TGACTGCCCCGATATCCGAG 61.179 60.000 0.00 0.00 41.76 4.63
3284 3466 1.152631 TGACTGCCCCGATATCCGA 60.153 57.895 0.00 0.00 41.76 4.55
3285 3467 1.006102 GTGACTGCCCCGATATCCG 60.006 63.158 0.00 0.00 38.18 4.18
3286 3468 1.122019 AGGTGACTGCCCCGATATCC 61.122 60.000 0.00 0.00 41.13 2.59
3287 3469 2.442056 AGGTGACTGCCCCGATATC 58.558 57.895 0.00 0.00 41.13 1.63
3288 3470 4.728780 AGGTGACTGCCCCGATAT 57.271 55.556 0.00 0.00 41.13 1.63
3298 3480 2.555670 GGGAGTCTGTCTACAGGTGACT 60.556 54.545 10.11 6.72 43.91 3.41
3299 3481 1.819903 GGGAGTCTGTCTACAGGTGAC 59.180 57.143 10.11 2.09 43.91 3.67
3300 3482 1.427753 TGGGAGTCTGTCTACAGGTGA 59.572 52.381 10.11 0.00 43.91 4.02
3301 3483 1.546476 GTGGGAGTCTGTCTACAGGTG 59.454 57.143 10.11 0.00 43.91 4.00
3302 3484 1.429687 AGTGGGAGTCTGTCTACAGGT 59.570 52.381 10.11 0.00 43.91 4.00
3303 3485 1.821753 CAGTGGGAGTCTGTCTACAGG 59.178 57.143 10.11 0.00 43.91 4.00
3304 3486 2.520069 ACAGTGGGAGTCTGTCTACAG 58.480 52.381 3.64 3.64 41.52 2.74
3305 3487 2.677542 ACAGTGGGAGTCTGTCTACA 57.322 50.000 0.00 0.00 41.52 2.74
3310 3492 1.122019 GTGGGACAGTGGGAGTCTGT 61.122 60.000 0.00 0.00 46.86 3.41
3311 3493 1.121407 TGTGGGACAGTGGGAGTCTG 61.121 60.000 0.00 0.00 41.80 3.51
3312 3494 1.122019 GTGTGGGACAGTGGGAGTCT 61.122 60.000 0.00 0.00 41.80 3.24
3313 3495 1.122019 AGTGTGGGACAGTGGGAGTC 61.122 60.000 0.00 0.00 41.80 3.36
3314 3496 1.074471 AGTGTGGGACAGTGGGAGT 60.074 57.895 0.00 0.00 41.80 3.85
3315 3497 1.674057 GAGTGTGGGACAGTGGGAG 59.326 63.158 0.00 0.00 41.80 4.30
3316 3498 1.841556 GGAGTGTGGGACAGTGGGA 60.842 63.158 0.00 0.00 41.80 4.37
3317 3499 1.492133 ATGGAGTGTGGGACAGTGGG 61.492 60.000 0.00 0.00 41.80 4.61
3318 3500 0.036010 GATGGAGTGTGGGACAGTGG 60.036 60.000 0.00 0.00 41.80 4.00
3319 3501 0.686789 TGATGGAGTGTGGGACAGTG 59.313 55.000 0.00 0.00 41.80 3.66
3320 3502 1.556911 GATGATGGAGTGTGGGACAGT 59.443 52.381 0.00 0.00 41.80 3.55
3321 3503 1.134280 GGATGATGGAGTGTGGGACAG 60.134 57.143 0.00 0.00 41.80 3.51
3322 3504 0.911769 GGATGATGGAGTGTGGGACA 59.088 55.000 0.00 0.00 0.00 4.02
3323 3505 0.911769 TGGATGATGGAGTGTGGGAC 59.088 55.000 0.00 0.00 0.00 4.46
3364 3550 1.820519 TCGTAGGTTTGGTACATCGCT 59.179 47.619 0.00 0.00 39.30 4.93
3369 3555 9.316730 GTTATCATTATTCGTAGGTTTGGTACA 57.683 33.333 0.00 0.00 0.00 2.90
3370 3556 8.768019 GGTTATCATTATTCGTAGGTTTGGTAC 58.232 37.037 0.00 0.00 0.00 3.34
3371 3557 8.707449 AGGTTATCATTATTCGTAGGTTTGGTA 58.293 33.333 0.00 0.00 0.00 3.25
3372 3558 7.571025 AGGTTATCATTATTCGTAGGTTTGGT 58.429 34.615 0.00 0.00 0.00 3.67
3373 3559 8.446599 AAGGTTATCATTATTCGTAGGTTTGG 57.553 34.615 0.00 0.00 0.00 3.28
3390 3576 6.164176 CACGGTAGGATTGGATAAGGTTATC 58.836 44.000 1.64 1.64 39.01 1.75
3392 3578 4.202284 GCACGGTAGGATTGGATAAGGTTA 60.202 45.833 0.00 0.00 0.00 2.85
3393 3579 3.433173 GCACGGTAGGATTGGATAAGGTT 60.433 47.826 0.00 0.00 0.00 3.50
3417 3603 4.374399 TCCTTCAAGAAAACGGTACTGAC 58.626 43.478 9.17 0.00 0.00 3.51
3418 3604 4.675976 TCCTTCAAGAAAACGGTACTGA 57.324 40.909 9.17 0.00 0.00 3.41
3419 3605 5.701290 AGAATCCTTCAAGAAAACGGTACTG 59.299 40.000 0.00 0.00 0.00 2.74
3420 3606 5.701290 CAGAATCCTTCAAGAAAACGGTACT 59.299 40.000 0.00 0.00 0.00 2.73
3421 3607 5.617087 GCAGAATCCTTCAAGAAAACGGTAC 60.617 44.000 0.00 0.00 0.00 3.34
3423 3609 3.253432 GCAGAATCCTTCAAGAAAACGGT 59.747 43.478 0.00 0.00 0.00 4.83
3424 3610 3.503748 AGCAGAATCCTTCAAGAAAACGG 59.496 43.478 0.00 0.00 0.00 4.44
3425 3611 4.756084 AGCAGAATCCTTCAAGAAAACG 57.244 40.909 0.00 0.00 0.00 3.60
3426 3612 4.683320 GCAAGCAGAATCCTTCAAGAAAAC 59.317 41.667 0.00 0.00 0.00 2.43
3468 3777 8.106462 TCCATTGTTCATGTAGTAATCCAGAAA 58.894 33.333 0.00 0.00 0.00 2.52
3470 3779 7.194112 TCCATTGTTCATGTAGTAATCCAGA 57.806 36.000 0.00 0.00 0.00 3.86
3471 3780 7.716560 TGATCCATTGTTCATGTAGTAATCCAG 59.283 37.037 0.00 0.00 0.00 3.86
3472 3781 7.572814 TGATCCATTGTTCATGTAGTAATCCA 58.427 34.615 0.00 0.00 0.00 3.41
3474 3783 9.722056 GTTTGATCCATTGTTCATGTAGTAATC 57.278 33.333 0.00 0.00 0.00 1.75
3475 3784 8.397906 CGTTTGATCCATTGTTCATGTAGTAAT 58.602 33.333 0.00 0.00 0.00 1.89
3476 3785 7.148323 CCGTTTGATCCATTGTTCATGTAGTAA 60.148 37.037 0.00 0.00 0.00 2.24
3479 3788 5.123820 ACCGTTTGATCCATTGTTCATGTAG 59.876 40.000 0.00 0.00 0.00 2.74
3488 3797 1.790123 CGCGAACCGTTTGATCCATTG 60.790 52.381 0.00 0.00 0.00 2.82
3489 3798 0.446222 CGCGAACCGTTTGATCCATT 59.554 50.000 0.00 0.00 0.00 3.16
3501 3810 0.861837 CTGCTTGGATATCGCGAACC 59.138 55.000 15.24 17.55 0.00 3.62
3502 3811 0.233332 GCTGCTTGGATATCGCGAAC 59.767 55.000 15.24 7.89 0.00 3.95
3503 3812 0.179086 TGCTGCTTGGATATCGCGAA 60.179 50.000 15.24 2.68 0.00 4.70
3504 3813 0.033920 ATGCTGCTTGGATATCGCGA 59.966 50.000 13.09 13.09 0.00 5.87
3505 3814 0.165295 CATGCTGCTTGGATATCGCG 59.835 55.000 0.00 0.00 0.00 5.87
3506 3815 1.233019 ACATGCTGCTTGGATATCGC 58.767 50.000 18.21 0.00 0.00 4.58
3507 3816 3.620374 GGATACATGCTGCTTGGATATCG 59.380 47.826 18.21 0.00 0.00 2.92
3508 3817 4.582869 TGGATACATGCTGCTTGGATATC 58.417 43.478 18.21 15.40 46.17 1.63
3509 3818 4.645863 TGGATACATGCTGCTTGGATAT 57.354 40.909 18.21 8.86 46.17 1.63
3551 3861 0.911769 TTACCAGACTGCCTCATGGG 59.088 55.000 0.00 0.00 37.13 4.00
3554 3864 2.906389 TCTGTTTACCAGACTGCCTCAT 59.094 45.455 0.00 0.00 45.34 2.90
3564 3874 3.120546 CGTGCTGTTGATCTGTTTACCAG 60.121 47.826 0.00 0.00 42.97 4.00
3565 3875 2.805671 CGTGCTGTTGATCTGTTTACCA 59.194 45.455 0.00 0.00 0.00 3.25
3566 3876 3.064207 TCGTGCTGTTGATCTGTTTACC 58.936 45.455 0.00 0.00 0.00 2.85
3567 3877 3.493129 TGTCGTGCTGTTGATCTGTTTAC 59.507 43.478 0.00 0.00 0.00 2.01
3577 3887 4.354212 CCGCGTGTCGTGCTGTTG 62.354 66.667 4.92 0.00 35.94 3.33
3624 3938 1.633852 CCTCTCTGCGCTTTGTCAGC 61.634 60.000 9.73 0.00 46.31 4.26
3625 3939 0.037882 TCCTCTCTGCGCTTTGTCAG 60.038 55.000 9.73 0.00 0.00 3.51
3629 3943 2.593346 ATACTCCTCTCTGCGCTTTG 57.407 50.000 9.73 0.00 0.00 2.77
3662 3976 3.551846 ACTCCTCTCTTTTCCGCAAAAA 58.448 40.909 0.00 0.00 35.56 1.94
3663 3977 3.208747 ACTCCTCTCTTTTCCGCAAAA 57.791 42.857 0.00 0.00 0.00 2.44
3664 3978 2.930826 ACTCCTCTCTTTTCCGCAAA 57.069 45.000 0.00 0.00 0.00 3.68
3665 3979 5.871396 ATATACTCCTCTCTTTTCCGCAA 57.129 39.130 0.00 0.00 0.00 4.85
3666 3980 6.948886 AGATATATACTCCTCTCTTTTCCGCA 59.051 38.462 0.00 0.00 0.00 5.69
3667 3981 7.338449 AGAGATATATACTCCTCTCTTTTCCGC 59.662 40.741 7.50 0.00 41.19 5.54
3668 3982 8.801882 AGAGATATATACTCCTCTCTTTTCCG 57.198 38.462 7.50 0.00 41.19 4.30
3669 3983 9.185680 GGAGAGATATATACTCCTCTCTTTTCC 57.814 40.741 23.64 14.55 46.52 3.13
3670 3984 9.747898 TGGAGAGATATATACTCCTCTCTTTTC 57.252 37.037 25.59 13.39 46.52 2.29
3673 3987 9.753674 CTTTGGAGAGATATATACTCCTCTCTT 57.246 37.037 25.59 9.07 46.52 2.85
3674 3988 7.834181 GCTTTGGAGAGATATATACTCCTCTCT 59.166 40.741 25.59 18.70 46.52 3.10
3680 3994 6.929625 TGCTGCTTTGGAGAGATATATACTC 58.070 40.000 0.00 9.57 34.95 2.59
3681 3995 6.924913 TGCTGCTTTGGAGAGATATATACT 57.075 37.500 0.00 0.00 0.00 2.12
3682 3996 7.065563 CCATTGCTGCTTTGGAGAGATATATAC 59.934 40.741 13.89 0.00 31.94 1.47
3683 3997 7.108194 CCATTGCTGCTTTGGAGAGATATATA 58.892 38.462 13.89 0.00 31.94 0.86
3684 3998 5.944599 CCATTGCTGCTTTGGAGAGATATAT 59.055 40.000 13.89 0.00 31.94 0.86
3685 3999 5.311265 CCATTGCTGCTTTGGAGAGATATA 58.689 41.667 13.89 0.00 31.94 0.86
3686 4000 4.142790 CCATTGCTGCTTTGGAGAGATAT 58.857 43.478 13.89 0.00 31.94 1.63
3761 4080 3.902162 TTCTACCACGCACGCCGAC 62.902 63.158 2.93 0.00 41.02 4.79
3762 4081 3.210223 TTTCTACCACGCACGCCGA 62.210 57.895 2.93 0.00 41.02 5.54
3763 4082 2.726691 CTTTCTACCACGCACGCCG 61.727 63.158 0.00 0.00 44.21 6.46
3764 4083 1.373748 TCTTTCTACCACGCACGCC 60.374 57.895 0.00 0.00 0.00 5.68
3811 4130 2.552585 TACTAGCTTGACGTGCCCGC 62.553 60.000 1.04 0.00 37.70 6.13
3812 4131 0.525668 CTACTAGCTTGACGTGCCCG 60.526 60.000 1.04 0.00 40.83 6.13
3824 4143 1.433534 GCGGATGGAATGCTACTAGC 58.566 55.000 0.61 0.61 42.82 3.42
3825 4144 1.338200 GGGCGGATGGAATGCTACTAG 60.338 57.143 0.00 0.00 29.44 2.57
3826 4145 0.685097 GGGCGGATGGAATGCTACTA 59.315 55.000 0.00 0.00 29.44 1.82
3843 4162 2.045926 CGCCAGAAGAGTTGGGGG 60.046 66.667 0.81 0.00 42.97 5.40
3856 4175 1.070786 AGGAAAAACGAGAGCGCCA 59.929 52.632 2.29 0.00 42.48 5.69
3870 4189 0.039617 CGGCATTTTCGTTGCAGGAA 60.040 50.000 0.00 0.00 41.95 3.36
3874 4198 1.081509 GCTCGGCATTTTCGTTGCA 60.082 52.632 0.00 0.00 41.95 4.08
3875 4199 1.801512 GGCTCGGCATTTTCGTTGC 60.802 57.895 0.00 0.00 39.41 4.17
3879 4203 0.028505 CATCAGGCTCGGCATTTTCG 59.971 55.000 0.00 0.00 0.00 3.46
3892 4216 2.639970 TTTGGCACGGTTCATCAGG 58.360 52.632 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.