Multiple sequence alignment - TraesCS6D01G398500

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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 TraesCS6D01G398500 chr6D 100.000 3328 0 0 1 3328 469617698 469621025 0.000000e+00 6146
1 TraesCS6D01G398500 chr6D 96.053 228 9 0 3101 3328 281210426 281210199 4.050000e-99 372
2 TraesCS6D01G398500 chr6D 96.053 228 9 0 3101 3328 283046379 283046606 4.050000e-99 372
3 TraesCS6D01G398500 chr6D 96.053 228 9 0 3101 3328 469656814 469657041 4.050000e-99 372
4 TraesCS6D01G398500 chr6D 95.614 228 10 0 3101 3328 281160882 281160655 1.890000e-97 366
5 TraesCS6D01G398500 chr6D 95.614 228 10 0 3101 3328 288112802 288112575 1.890000e-97 366
6 TraesCS6D01G398500 chr6A 98.379 2406 35 4 1 2403 614669412 614671816 0.000000e+00 4224
7 TraesCS6D01G398500 chr6A 95.349 86 2 1 2401 2486 614672054 614672137 5.790000e-28 135
8 TraesCS6D01G398500 chr6B 91.965 1618 108 8 920 2515 715757945 715759562 0.000000e+00 2248
9 TraesCS6D01G398500 chr6B 95.479 376 15 2 455 829 715757574 715757948 1.710000e-167 599
10 TraesCS6D01G398500 chr6B 89.130 368 17 8 2592 2958 715759562 715759907 1.420000e-118 436
11 TraesCS6D01G398500 chr6B 94.697 132 3 1 2964 3091 715759958 715760089 5.630000e-48 202
12 TraesCS6D01G398500 chr6B 89.474 114 9 1 270 383 715757444 715757554 1.240000e-29 141
13 TraesCS6D01G398500 chrUn 95.610 729 28 4 386 1112 75390671 75389945 0.000000e+00 1166
14 TraesCS6D01G398500 chrUn 91.503 612 49 2 1110 1718 368393329 368392718 0.000000e+00 839
15 TraesCS6D01G398500 chrUn 97.656 384 9 0 1 384 74882221 74882604 0.000000e+00 660
16 TraesCS6D01G398500 chr3D 96.491 228 8 0 3101 3328 379898019 379898246 8.720000e-101 377
17 TraesCS6D01G398500 chr3D 94.845 97 4 1 828 923 292887841 292887745 2.070000e-32 150
18 TraesCS6D01G398500 chr3D 90.385 104 9 1 825 927 378055556 378055453 5.790000e-28 135
19 TraesCS6D01G398500 chr5D 96.053 228 9 0 3101 3328 49902373 49902600 4.050000e-99 372
20 TraesCS6D01G398500 chr5D 88.679 106 11 1 825 929 342724292 342724187 9.690000e-26 128
21 TraesCS6D01G398500 chr2D 96.053 228 9 0 3101 3328 431339691 431339464 4.050000e-99 372
22 TraesCS6D01G398500 chr4D 95.633 229 10 0 3100 3328 310893957 310893729 5.250000e-98 368
23 TraesCS6D01G398500 chr3B 90.654 107 8 2 819 923 439865037 439865143 1.240000e-29 141
24 TraesCS6D01G398500 chr3A 92.079 101 6 2 824 923 531452036 531452135 1.240000e-29 141
25 TraesCS6D01G398500 chr4B 90.909 99 7 2 826 923 167348094 167347997 7.490000e-27 132
26 TraesCS6D01G398500 chr5B 90.816 98 8 1 828 924 28937188 28937285 2.690000e-26 130


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 TraesCS6D01G398500 chr6D 469617698 469621025 3327 False 6146.0 6146 100.000 1 3328 1 chr6D.!!$F2 3327
1 TraesCS6D01G398500 chr6A 614669412 614672137 2725 False 2179.5 4224 96.864 1 2486 2 chr6A.!!$F1 2485
2 TraesCS6D01G398500 chr6B 715757444 715760089 2645 False 725.2 2248 92.149 270 3091 5 chr6B.!!$F1 2821
3 TraesCS6D01G398500 chrUn 75389945 75390671 726 True 1166.0 1166 95.610 386 1112 1 chrUn.!!$R1 726
4 TraesCS6D01G398500 chrUn 368392718 368393329 611 True 839.0 839 91.503 1110 1718 1 chrUn.!!$R2 608

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
289 290 0.322975 CCCAGGTGAGTGGTGAGAAG 59.677 60.0 0.00 0.00 35.60 2.85 F
497 498 0.823356 AAGGAAGCACATGCACCGTT 60.823 50.0 6.64 2.59 45.16 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1625 1629 0.614134 ACCCAGTTCCCGAGGAGTAC 60.614 60.0 0.00 0.0 31.21 2.73 R
2492 2756 0.613260 TATCAGCTGCTTCCAACGGT 59.387 50.0 9.47 0.0 0.00 4.83 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
77 78 1.588404 GATCGCACATAGGACACAACG 59.412 52.381 0.00 0.00 0.00 4.10
115 116 2.503356 CCTGTCCCTTAATCTGTCTGCT 59.497 50.000 0.00 0.00 0.00 4.24
218 219 2.021639 AGGATCCTTCATCTTCCCCAGA 60.022 50.000 9.02 0.00 35.33 3.86
289 290 0.322975 CCCAGGTGAGTGGTGAGAAG 59.677 60.000 0.00 0.00 35.60 2.85
497 498 0.823356 AAGGAAGCACATGCACCGTT 60.823 50.000 6.64 2.59 45.16 4.44
590 591 3.062763 GTGGCTGTAGCTGTATGCATAG 58.937 50.000 6.67 0.00 45.94 2.23
696 697 7.661437 ACTCTGATTAAGTACTTGCACATGAAA 59.339 33.333 18.56 2.06 0.00 2.69
704 705 8.801715 AAGTACTTGCACATGAAAATTGTTAG 57.198 30.769 7.48 0.00 0.00 2.34
753 754 4.671831 TGAAATAAGCCCCAACTCAATGA 58.328 39.130 0.00 0.00 0.00 2.57
823 825 7.238486 ACCACCTATTTTGCATTATGTTCAA 57.762 32.000 0.00 0.00 0.00 2.69
1158 1162 1.645704 CGTCGAGATCCTGTCACGGT 61.646 60.000 0.00 0.00 40.65 4.83
1214 1218 1.301716 CACGCACTGGTACTGCCTT 60.302 57.895 0.44 0.00 38.35 4.35
1397 1401 0.990374 AGCTTGTCAGGCTGGAAGAT 59.010 50.000 23.30 17.46 38.73 2.40
1490 1494 2.100989 GAGAGATGGGTCGTGTTACCT 58.899 52.381 0.00 0.00 39.65 3.08
1583 1587 3.577848 CCTCCCATTTCCATGTGTTTCAA 59.422 43.478 0.00 0.00 0.00 2.69
1625 1629 0.887933 GGGTGGCGGGCATAAATATG 59.112 55.000 7.75 0.00 36.78 1.78
2091 2113 0.531532 CATTGATCGCGAGGAGGCTT 60.532 55.000 16.66 0.00 0.00 4.35
2147 2169 7.815383 TGATATCATGTTTTCCCTATGTTCCT 58.185 34.615 0.00 0.00 0.00 3.36
2153 2175 5.070001 TGTTTTCCCTATGTTCCTCTGTTG 58.930 41.667 0.00 0.00 0.00 3.33
2515 2779 4.067896 CCGTTGGAAGCAGCTGATATATT 58.932 43.478 20.43 0.00 0.00 1.28
2516 2780 4.516698 CCGTTGGAAGCAGCTGATATATTT 59.483 41.667 20.43 0.00 0.00 1.40
2517 2781 5.446709 CGTTGGAAGCAGCTGATATATTTG 58.553 41.667 20.43 0.00 0.00 2.32
2518 2782 5.561532 CGTTGGAAGCAGCTGATATATTTGG 60.562 44.000 20.43 0.00 0.00 3.28
2519 2783 5.052693 TGGAAGCAGCTGATATATTTGGT 57.947 39.130 20.43 0.00 0.00 3.67
2520 2784 6.186420 TGGAAGCAGCTGATATATTTGGTA 57.814 37.500 20.43 0.00 0.00 3.25
2521 2785 6.782986 TGGAAGCAGCTGATATATTTGGTAT 58.217 36.000 20.43 0.00 0.00 2.73
2522 2786 7.917003 TGGAAGCAGCTGATATATTTGGTATA 58.083 34.615 20.43 0.00 0.00 1.47
2523 2787 8.551440 TGGAAGCAGCTGATATATTTGGTATAT 58.449 33.333 20.43 0.00 38.42 0.86
2670 2934 4.711846 GGATCCTTTGGGTGCTTAGAATTT 59.288 41.667 3.84 0.00 0.00 1.82
2676 2940 2.301583 TGGGTGCTTAGAATTTTTGGCC 59.698 45.455 0.00 0.00 0.00 5.36
2679 2943 3.501950 GTGCTTAGAATTTTTGGCCGAG 58.498 45.455 0.00 0.00 0.00 4.63
2684 2948 5.800438 GCTTAGAATTTTTGGCCGAGTTAAG 59.200 40.000 0.00 1.28 0.00 1.85
2703 2967 8.508883 AGTTAAGTGAGTACTACTCCAGTATG 57.491 38.462 12.79 0.00 44.44 2.39
2772 3036 7.048629 CTCAGATGAGCAGTAAGGAATTAGA 57.951 40.000 0.00 0.00 35.13 2.10
2773 3037 7.609097 TCAGATGAGCAGTAAGGAATTAGAT 57.391 36.000 0.00 0.00 0.00 1.98
2776 3040 7.814107 CAGATGAGCAGTAAGGAATTAGATCTC 59.186 40.741 0.00 0.00 0.00 2.75
2778 3042 7.283625 TGAGCAGTAAGGAATTAGATCTCTC 57.716 40.000 0.00 0.00 0.00 3.20
2779 3043 6.016693 TGAGCAGTAAGGAATTAGATCTCTCG 60.017 42.308 0.00 0.00 0.00 4.04
2780 3044 6.065374 AGCAGTAAGGAATTAGATCTCTCGA 58.935 40.000 0.00 0.00 0.00 4.04
2782 3046 7.232534 AGCAGTAAGGAATTAGATCTCTCGAAT 59.767 37.037 0.00 0.00 0.00 3.34
2783 3047 7.328249 GCAGTAAGGAATTAGATCTCTCGAATG 59.672 40.741 0.00 0.00 28.58 2.67
2784 3048 7.812191 CAGTAAGGAATTAGATCTCTCGAATGG 59.188 40.741 0.00 0.00 28.58 3.16
2785 3049 5.146010 AGGAATTAGATCTCTCGAATGGC 57.854 43.478 0.00 0.00 28.58 4.40
2786 3050 4.590647 AGGAATTAGATCTCTCGAATGGCA 59.409 41.667 0.00 0.00 28.58 4.92
2787 3051 4.928615 GGAATTAGATCTCTCGAATGGCAG 59.071 45.833 0.00 0.00 28.58 4.85
2788 3052 5.510520 GGAATTAGATCTCTCGAATGGCAGT 60.511 44.000 0.00 0.00 28.58 4.40
2789 3053 6.294787 GGAATTAGATCTCTCGAATGGCAGTA 60.295 42.308 0.00 0.00 28.58 2.74
2790 3054 5.697473 TTAGATCTCTCGAATGGCAGTAG 57.303 43.478 0.00 0.00 0.00 2.57
2791 3055 2.890311 AGATCTCTCGAATGGCAGTAGG 59.110 50.000 0.00 0.00 0.00 3.18
2792 3056 0.747255 TCTCTCGAATGGCAGTAGGC 59.253 55.000 0.00 0.00 43.74 3.93
2793 3057 0.749649 CTCTCGAATGGCAGTAGGCT 59.250 55.000 0.00 0.00 44.01 4.58
2794 3058 1.957177 CTCTCGAATGGCAGTAGGCTA 59.043 52.381 0.00 0.00 44.01 3.93
2795 3059 1.957177 TCTCGAATGGCAGTAGGCTAG 59.043 52.381 0.00 0.00 44.01 3.42
2796 3060 1.683917 CTCGAATGGCAGTAGGCTAGT 59.316 52.381 0.00 0.00 44.01 2.57
2797 3061 2.885266 CTCGAATGGCAGTAGGCTAGTA 59.115 50.000 0.60 0.00 44.01 1.82
2798 3062 2.885266 TCGAATGGCAGTAGGCTAGTAG 59.115 50.000 0.60 0.00 44.01 2.57
2799 3063 2.608261 CGAATGGCAGTAGGCTAGTAGC 60.608 54.545 14.09 14.09 44.01 3.58
2926 3190 6.271488 TCAGCCAGGAAACAGAAATTATTG 57.729 37.500 0.00 0.00 0.00 1.90
3078 3387 1.153349 GGTTCAGACGCCCAGATCC 60.153 63.158 0.00 0.00 0.00 3.36
3081 3390 0.178767 TTCAGACGCCCAGATCCATG 59.821 55.000 0.00 0.00 0.00 3.66
3082 3391 0.687427 TCAGACGCCCAGATCCATGA 60.687 55.000 0.00 0.00 0.00 3.07
3083 3392 0.249784 CAGACGCCCAGATCCATGAG 60.250 60.000 0.00 0.00 0.00 2.90
3084 3393 1.596477 GACGCCCAGATCCATGAGC 60.596 63.158 0.00 0.00 0.00 4.26
3085 3394 2.664185 CGCCCAGATCCATGAGCG 60.664 66.667 0.00 0.00 37.39 5.03
3086 3395 2.507944 GCCCAGATCCATGAGCGT 59.492 61.111 0.00 0.00 0.00 5.07
3087 3396 1.596477 GCCCAGATCCATGAGCGTC 60.596 63.158 0.00 0.00 0.00 5.19
3088 3397 1.825341 CCCAGATCCATGAGCGTCA 59.175 57.895 0.00 0.00 0.00 4.35
3089 3398 0.178767 CCCAGATCCATGAGCGTCAA 59.821 55.000 0.00 0.00 0.00 3.18
3090 3399 1.293924 CCAGATCCATGAGCGTCAAC 58.706 55.000 0.00 0.00 0.00 3.18
3091 3400 1.134580 CCAGATCCATGAGCGTCAACT 60.135 52.381 0.00 0.00 0.00 3.16
3092 3401 2.625737 CAGATCCATGAGCGTCAACTT 58.374 47.619 0.00 0.00 0.00 2.66
3093 3402 2.350804 CAGATCCATGAGCGTCAACTTG 59.649 50.000 0.00 0.00 0.00 3.16
3094 3403 1.667724 GATCCATGAGCGTCAACTTGG 59.332 52.381 0.00 0.00 34.17 3.61
3095 3404 0.396435 TCCATGAGCGTCAACTTGGT 59.604 50.000 0.00 0.00 34.41 3.67
3096 3405 0.798776 CCATGAGCGTCAACTTGGTC 59.201 55.000 0.00 0.00 0.00 4.02
3097 3406 0.798776 CATGAGCGTCAACTTGGTCC 59.201 55.000 0.00 0.00 0.00 4.46
3098 3407 0.396435 ATGAGCGTCAACTTGGTCCA 59.604 50.000 0.00 0.00 0.00 4.02
3099 3408 0.531974 TGAGCGTCAACTTGGTCCAC 60.532 55.000 0.00 0.00 0.00 4.02
3100 3409 0.249911 GAGCGTCAACTTGGTCCACT 60.250 55.000 0.00 0.00 0.00 4.00
3101 3410 0.532862 AGCGTCAACTTGGTCCACTG 60.533 55.000 0.00 0.00 0.00 3.66
3102 3411 0.814010 GCGTCAACTTGGTCCACTGT 60.814 55.000 0.00 0.00 0.00 3.55
3103 3412 1.539496 GCGTCAACTTGGTCCACTGTA 60.539 52.381 0.00 0.00 0.00 2.74
3104 3413 2.828877 CGTCAACTTGGTCCACTGTAA 58.171 47.619 0.00 0.00 0.00 2.41
3105 3414 2.542595 CGTCAACTTGGTCCACTGTAAC 59.457 50.000 0.00 0.00 0.00 2.50
3106 3415 2.542595 GTCAACTTGGTCCACTGTAACG 59.457 50.000 0.00 0.00 0.00 3.18
3107 3416 1.263217 CAACTTGGTCCACTGTAACGC 59.737 52.381 0.00 0.00 0.00 4.84
3108 3417 0.756903 ACTTGGTCCACTGTAACGCT 59.243 50.000 0.00 0.00 0.00 5.07
3109 3418 1.270147 ACTTGGTCCACTGTAACGCTC 60.270 52.381 0.00 0.00 0.00 5.03
3110 3419 0.753867 TTGGTCCACTGTAACGCTCA 59.246 50.000 0.00 0.00 0.00 4.26
3111 3420 0.032952 TGGTCCACTGTAACGCTCAC 59.967 55.000 0.00 0.00 0.00 3.51
3113 3422 0.039798 GTCCACTGTAACGCTCACGA 60.040 55.000 0.00 0.00 43.93 4.35
3114 3423 0.885879 TCCACTGTAACGCTCACGAT 59.114 50.000 0.00 0.00 43.93 3.73
3115 3424 0.992072 CCACTGTAACGCTCACGATG 59.008 55.000 0.00 0.00 43.93 3.84
3116 3425 0.366871 CACTGTAACGCTCACGATGC 59.633 55.000 0.00 0.00 43.93 3.91
3123 3432 4.966005 GCTCACGATGCGGCTATA 57.034 55.556 0.00 0.00 0.00 1.31
3124 3433 3.425578 GCTCACGATGCGGCTATAT 57.574 52.632 0.00 0.00 0.00 0.86
3125 3434 1.272781 GCTCACGATGCGGCTATATC 58.727 55.000 0.00 0.00 0.00 1.63
3126 3435 1.135257 GCTCACGATGCGGCTATATCT 60.135 52.381 0.00 0.00 0.00 1.98
3127 3436 2.791567 CTCACGATGCGGCTATATCTC 58.208 52.381 0.00 0.00 0.00 2.75
3128 3437 1.130561 TCACGATGCGGCTATATCTCG 59.869 52.381 0.00 3.21 0.00 4.04
3134 3443 2.713303 CGGCTATATCTCGCACGTG 58.287 57.895 12.28 12.28 0.00 4.49
3135 3444 0.040336 CGGCTATATCTCGCACGTGT 60.040 55.000 18.38 0.00 0.00 4.49
3136 3445 1.687628 GGCTATATCTCGCACGTGTC 58.312 55.000 18.38 8.63 0.00 3.67
3137 3446 1.319172 GCTATATCTCGCACGTGTCG 58.681 55.000 18.38 20.01 0.00 4.35
3138 3447 1.070108 GCTATATCTCGCACGTGTCGA 60.070 52.381 25.57 25.57 34.52 4.20
3142 3451 4.700365 CTCGCACGTGTCGAGGCA 62.700 66.667 34.47 17.29 46.82 4.75
3143 3452 4.994201 TCGCACGTGTCGAGGCAC 62.994 66.667 24.25 0.00 36.12 5.01
3153 3462 2.478989 TCGAGGCACGACTTAGAGG 58.521 57.895 2.07 0.00 46.45 3.69
3154 3463 1.226717 CGAGGCACGACTTAGAGGC 60.227 63.158 0.00 0.00 45.77 4.70
3155 3464 1.890894 GAGGCACGACTTAGAGGCA 59.109 57.895 0.00 0.00 0.00 4.75
3156 3465 0.461961 GAGGCACGACTTAGAGGCAT 59.538 55.000 0.00 0.00 0.00 4.40
3157 3466 1.681793 GAGGCACGACTTAGAGGCATA 59.318 52.381 0.00 0.00 0.00 3.14
3158 3467 2.100916 GAGGCACGACTTAGAGGCATAA 59.899 50.000 0.00 0.00 0.00 1.90
3159 3468 2.159085 AGGCACGACTTAGAGGCATAAC 60.159 50.000 0.00 0.00 0.00 1.89
3160 3469 2.202566 GCACGACTTAGAGGCATAACC 58.797 52.381 0.00 0.00 39.61 2.85
3161 3470 2.460918 CACGACTTAGAGGCATAACCG 58.539 52.381 0.00 0.00 46.52 4.44
3162 3471 1.202382 ACGACTTAGAGGCATAACCGC 60.202 52.381 0.00 0.00 46.52 5.68
3163 3472 1.202371 CGACTTAGAGGCATAACCGCA 60.202 52.381 0.00 0.00 46.52 5.69
3164 3473 2.545952 CGACTTAGAGGCATAACCGCAT 60.546 50.000 0.00 0.00 46.52 4.73
3165 3474 3.467803 GACTTAGAGGCATAACCGCATT 58.532 45.455 0.00 0.00 46.52 3.56
3166 3475 3.206150 ACTTAGAGGCATAACCGCATTG 58.794 45.455 0.00 0.00 46.52 2.82
3167 3476 3.206150 CTTAGAGGCATAACCGCATTGT 58.794 45.455 0.00 0.00 46.52 2.71
3168 3477 4.141801 ACTTAGAGGCATAACCGCATTGTA 60.142 41.667 0.00 0.00 46.52 2.41
3169 3478 2.838736 AGAGGCATAACCGCATTGTAG 58.161 47.619 0.00 0.00 46.52 2.74
3170 3479 1.873591 GAGGCATAACCGCATTGTAGG 59.126 52.381 0.00 0.00 46.52 3.18
3171 3480 1.211949 AGGCATAACCGCATTGTAGGT 59.788 47.619 0.98 0.98 46.52 3.08
3172 3481 2.436542 AGGCATAACCGCATTGTAGGTA 59.563 45.455 6.42 0.00 46.52 3.08
3173 3482 3.072476 AGGCATAACCGCATTGTAGGTAT 59.928 43.478 6.42 0.00 46.52 2.73
3174 3483 3.818773 GGCATAACCGCATTGTAGGTATT 59.181 43.478 6.42 0.00 40.37 1.89
3175 3484 4.320202 GGCATAACCGCATTGTAGGTATTG 60.320 45.833 6.42 8.09 40.37 1.90
3176 3485 4.274950 GCATAACCGCATTGTAGGTATTGT 59.725 41.667 6.42 0.00 40.37 2.71
3177 3486 5.560183 GCATAACCGCATTGTAGGTATTGTC 60.560 44.000 6.42 2.60 40.37 3.18
3178 3487 2.546778 ACCGCATTGTAGGTATTGTCG 58.453 47.619 4.50 0.00 39.30 4.35
3179 3488 1.260561 CCGCATTGTAGGTATTGTCGC 59.739 52.381 0.00 0.00 0.00 5.19
3180 3489 1.930503 CGCATTGTAGGTATTGTCGCA 59.069 47.619 0.00 0.00 0.00 5.10
3181 3490 2.350192 CGCATTGTAGGTATTGTCGCAA 59.650 45.455 0.00 0.00 0.00 4.85
3182 3491 3.544048 CGCATTGTAGGTATTGTCGCAAG 60.544 47.826 0.00 0.00 0.00 4.01
3196 3505 2.099141 CGCAAGAAGGGTCATCTTCA 57.901 50.000 7.26 0.00 44.01 3.02
3197 3506 1.734465 CGCAAGAAGGGTCATCTTCAC 59.266 52.381 7.26 0.00 44.01 3.18
3198 3507 2.783135 GCAAGAAGGGTCATCTTCACA 58.217 47.619 7.26 0.00 44.01 3.58
3199 3508 2.485814 GCAAGAAGGGTCATCTTCACAC 59.514 50.000 7.26 0.00 44.01 3.82
3200 3509 3.743521 CAAGAAGGGTCATCTTCACACA 58.256 45.455 7.26 0.00 44.01 3.72
3201 3510 4.136796 CAAGAAGGGTCATCTTCACACAA 58.863 43.478 7.26 0.00 44.01 3.33
3202 3511 4.647564 AGAAGGGTCATCTTCACACAAT 57.352 40.909 7.26 0.00 44.01 2.71
3203 3512 4.583871 AGAAGGGTCATCTTCACACAATC 58.416 43.478 7.26 0.00 44.01 2.67
3204 3513 3.356529 AGGGTCATCTTCACACAATCC 57.643 47.619 0.00 0.00 0.00 3.01
3205 3514 2.025887 AGGGTCATCTTCACACAATCCC 60.026 50.000 0.00 0.00 0.00 3.85
3206 3515 2.290896 GGGTCATCTTCACACAATCCCA 60.291 50.000 0.00 0.00 33.33 4.37
3207 3516 3.624777 GGTCATCTTCACACAATCCCAT 58.375 45.455 0.00 0.00 0.00 4.00
3208 3517 3.379372 GGTCATCTTCACACAATCCCATG 59.621 47.826 0.00 0.00 0.00 3.66
3209 3518 4.012374 GTCATCTTCACACAATCCCATGT 58.988 43.478 0.00 0.00 0.00 3.21
3210 3519 5.185454 GTCATCTTCACACAATCCCATGTA 58.815 41.667 0.00 0.00 30.84 2.29
3211 3520 5.647658 GTCATCTTCACACAATCCCATGTAA 59.352 40.000 0.00 0.00 30.84 2.41
3212 3521 6.319658 GTCATCTTCACACAATCCCATGTAAT 59.680 38.462 0.00 0.00 30.84 1.89
3213 3522 6.319405 TCATCTTCACACAATCCCATGTAATG 59.681 38.462 0.00 0.00 46.21 1.90
3237 3546 9.918630 ATGAACAAGAATGAGATAAAAAGTTGG 57.081 29.630 0.00 0.00 0.00 3.77
3238 3547 7.867403 TGAACAAGAATGAGATAAAAAGTTGGC 59.133 33.333 0.00 0.00 0.00 4.52
3239 3548 7.530426 ACAAGAATGAGATAAAAAGTTGGCT 57.470 32.000 0.00 0.00 0.00 4.75
3240 3549 7.955918 ACAAGAATGAGATAAAAAGTTGGCTT 58.044 30.769 0.00 0.00 36.30 4.35
3241 3550 9.077885 ACAAGAATGAGATAAAAAGTTGGCTTA 57.922 29.630 0.00 0.00 33.95 3.09
3242 3551 9.346725 CAAGAATGAGATAAAAAGTTGGCTTAC 57.653 33.333 0.00 0.00 33.95 2.34
3243 3552 8.635765 AGAATGAGATAAAAAGTTGGCTTACA 57.364 30.769 0.00 0.00 33.95 2.41
3244 3553 9.077885 AGAATGAGATAAAAAGTTGGCTTACAA 57.922 29.630 0.00 0.00 36.54 2.41
3245 3554 9.860898 GAATGAGATAAAAAGTTGGCTTACAAT 57.139 29.630 0.00 0.00 41.95 2.71
3246 3555 9.860898 AATGAGATAAAAAGTTGGCTTACAATC 57.139 29.630 0.00 0.00 41.95 2.67
3247 3556 7.526608 TGAGATAAAAAGTTGGCTTACAATCG 58.473 34.615 0.00 0.00 41.95 3.34
3248 3557 6.852664 AGATAAAAAGTTGGCTTACAATCGG 58.147 36.000 0.00 0.00 41.95 4.18
3249 3558 3.297830 AAAAGTTGGCTTACAATCGGC 57.702 42.857 0.00 0.00 41.95 5.54
3250 3559 1.904287 AAGTTGGCTTACAATCGGCA 58.096 45.000 0.00 0.00 41.95 5.69
3251 3560 1.165270 AGTTGGCTTACAATCGGCAC 58.835 50.000 0.00 0.00 41.95 5.01
3252 3561 1.165270 GTTGGCTTACAATCGGCACT 58.835 50.000 0.00 0.00 41.95 4.40
3253 3562 1.539827 GTTGGCTTACAATCGGCACTT 59.460 47.619 0.00 0.00 41.95 3.16
3254 3563 1.448985 TGGCTTACAATCGGCACTTC 58.551 50.000 0.00 0.00 0.00 3.01
3255 3564 1.271108 TGGCTTACAATCGGCACTTCA 60.271 47.619 0.00 0.00 0.00 3.02
3256 3565 1.130561 GGCTTACAATCGGCACTTCAC 59.869 52.381 0.00 0.00 0.00 3.18
3257 3566 1.804151 GCTTACAATCGGCACTTCACA 59.196 47.619 0.00 0.00 0.00 3.58
3258 3567 2.412847 GCTTACAATCGGCACTTCACAC 60.413 50.000 0.00 0.00 0.00 3.82
3259 3568 2.535012 TACAATCGGCACTTCACACA 57.465 45.000 0.00 0.00 0.00 3.72
3260 3569 1.674359 ACAATCGGCACTTCACACAA 58.326 45.000 0.00 0.00 0.00 3.33
3261 3570 2.229792 ACAATCGGCACTTCACACAAT 58.770 42.857 0.00 0.00 0.00 2.71
3262 3571 2.030893 ACAATCGGCACTTCACACAATG 60.031 45.455 0.00 0.00 0.00 2.82
3263 3572 0.523072 ATCGGCACTTCACACAATGC 59.477 50.000 0.00 0.00 37.35 3.56
3264 3573 0.817229 TCGGCACTTCACACAATGCA 60.817 50.000 0.00 0.00 39.92 3.96
3265 3574 0.241749 CGGCACTTCACACAATGCAT 59.758 50.000 0.00 0.00 39.92 3.96
3266 3575 1.468127 CGGCACTTCACACAATGCATA 59.532 47.619 0.00 0.00 39.92 3.14
3267 3576 2.095314 CGGCACTTCACACAATGCATAA 60.095 45.455 0.00 0.00 39.92 1.90
3268 3577 3.427909 CGGCACTTCACACAATGCATAAT 60.428 43.478 0.00 0.00 39.92 1.28
3269 3578 4.497300 GGCACTTCACACAATGCATAATT 58.503 39.130 0.00 0.00 39.92 1.40
3270 3579 4.931002 GGCACTTCACACAATGCATAATTT 59.069 37.500 0.00 0.00 39.92 1.82
3271 3580 6.098679 GGCACTTCACACAATGCATAATTTA 58.901 36.000 0.00 0.00 39.92 1.40
3272 3581 6.589523 GGCACTTCACACAATGCATAATTTAA 59.410 34.615 0.00 0.00 39.92 1.52
3273 3582 7.117523 GGCACTTCACACAATGCATAATTTAAA 59.882 33.333 0.00 0.00 39.92 1.52
3274 3583 7.951565 GCACTTCACACAATGCATAATTTAAAC 59.048 33.333 0.00 0.00 38.00 2.01
3275 3584 8.976471 CACTTCACACAATGCATAATTTAAACA 58.024 29.630 0.00 0.00 0.00 2.83
3276 3585 9.709495 ACTTCACACAATGCATAATTTAAACAT 57.291 25.926 0.00 0.00 0.00 2.71
3297 3606 8.846943 AACATACATCATTCAGAGTACAAACA 57.153 30.769 0.00 0.00 0.00 2.83
3298 3607 8.846943 ACATACATCATTCAGAGTACAAACAA 57.153 30.769 0.00 0.00 0.00 2.83
3299 3608 8.939929 ACATACATCATTCAGAGTACAAACAAG 58.060 33.333 0.00 0.00 0.00 3.16
3300 3609 6.808008 ACATCATTCAGAGTACAAACAAGG 57.192 37.500 0.00 0.00 0.00 3.61
3301 3610 6.299141 ACATCATTCAGAGTACAAACAAGGT 58.701 36.000 0.00 0.00 0.00 3.50
3302 3611 6.428159 ACATCATTCAGAGTACAAACAAGGTC 59.572 38.462 0.00 0.00 0.00 3.85
3303 3612 5.305585 TCATTCAGAGTACAAACAAGGTCC 58.694 41.667 0.00 0.00 0.00 4.46
3304 3613 3.380479 TCAGAGTACAAACAAGGTCCG 57.620 47.619 0.00 0.00 0.00 4.79
3305 3614 2.960384 TCAGAGTACAAACAAGGTCCGA 59.040 45.455 0.00 0.00 0.00 4.55
3306 3615 3.057734 CAGAGTACAAACAAGGTCCGAC 58.942 50.000 0.00 0.00 0.00 4.79
3307 3616 2.963782 AGAGTACAAACAAGGTCCGACT 59.036 45.455 0.00 0.00 0.00 4.18
3308 3617 4.022589 CAGAGTACAAACAAGGTCCGACTA 60.023 45.833 0.00 0.00 0.00 2.59
3309 3618 4.022503 AGAGTACAAACAAGGTCCGACTAC 60.023 45.833 0.00 0.00 0.00 2.73
3310 3619 2.144482 ACAAACAAGGTCCGACTACG 57.856 50.000 0.00 0.00 39.43 3.51
3324 3633 4.735662 CGACTACGGAACCAAAATGAAA 57.264 40.909 0.00 0.00 35.72 2.69
3325 3634 4.708601 CGACTACGGAACCAAAATGAAAG 58.291 43.478 0.00 0.00 35.72 2.62
3326 3635 4.449743 CGACTACGGAACCAAAATGAAAGA 59.550 41.667 0.00 0.00 35.72 2.52
3327 3636 5.049954 CGACTACGGAACCAAAATGAAAGAA 60.050 40.000 0.00 0.00 35.72 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
218 219 3.237268 TCTGCCTACAACACCCAATTT 57.763 42.857 0.00 0.00 0.00 1.82
289 290 7.821846 ACTCTTTCATGAGGATAAGAGTGTTTC 59.178 37.037 27.89 0.00 43.86 2.78
497 498 3.282885 TGCACCACTATCAACAACAACA 58.717 40.909 0.00 0.00 0.00 3.33
590 591 6.739112 AGTAACAAGAAACTCAAAATCAGGC 58.261 36.000 0.00 0.00 0.00 4.85
823 825 5.333566 TTTTGGGATGAAGGGAGTACTTT 57.666 39.130 0.00 0.00 0.00 2.66
1214 1218 1.062428 AGGTGTTCGGGATGGGAGATA 60.062 52.381 0.00 0.00 0.00 1.98
1397 1401 1.425066 AGGAGAAGGCCATCACAACAA 59.575 47.619 11.19 0.00 0.00 2.83
1490 1494 2.666190 GAGTCAGCTGGCAACGCA 60.666 61.111 22.50 0.00 38.34 5.24
1583 1587 3.652274 CCGCCAATCTTTCAACACAATT 58.348 40.909 0.00 0.00 0.00 2.32
1625 1629 0.614134 ACCCAGTTCCCGAGGAGTAC 60.614 60.000 0.00 0.00 31.21 2.73
2074 2096 1.153568 CAAGCCTCCTCGCGATCAA 60.154 57.895 10.36 0.00 0.00 2.57
2091 2113 0.662619 CCAAAAGTGCAGAGAACGCA 59.337 50.000 0.00 0.00 36.94 5.24
2147 2169 1.269723 ACACTCGAATCGCTCAACAGA 59.730 47.619 0.00 0.00 0.00 3.41
2153 2175 0.806492 GGGGAACACTCGAATCGCTC 60.806 60.000 0.00 0.00 0.00 5.03
2478 2739 3.560896 TCCAACGGTAAGCAAAACTACAC 59.439 43.478 0.00 0.00 0.00 2.90
2492 2756 0.613260 TATCAGCTGCTTCCAACGGT 59.387 50.000 9.47 0.00 0.00 4.83
2575 2839 9.915629 TGTCACGTGCAACATATACAATATATA 57.084 29.630 11.67 0.00 35.74 0.86
2576 2840 8.825667 TGTCACGTGCAACATATACAATATAT 57.174 30.769 11.67 0.00 35.74 0.86
2577 2841 8.138712 TCTGTCACGTGCAACATATACAATATA 58.861 33.333 11.67 0.00 35.74 0.86
2578 2842 6.983890 TCTGTCACGTGCAACATATACAATAT 59.016 34.615 11.67 0.00 35.74 1.28
2579 2843 6.334202 TCTGTCACGTGCAACATATACAATA 58.666 36.000 11.67 0.00 35.74 1.90
2580 2844 5.175127 TCTGTCACGTGCAACATATACAAT 58.825 37.500 11.67 0.00 35.74 2.71
2581 2845 4.561105 TCTGTCACGTGCAACATATACAA 58.439 39.130 11.67 0.00 35.74 2.41
2582 2846 4.181309 TCTGTCACGTGCAACATATACA 57.819 40.909 11.67 6.48 35.74 2.29
2583 2847 5.107259 TGTTTCTGTCACGTGCAACATATAC 60.107 40.000 11.67 9.49 35.74 1.47
2584 2848 4.991687 TGTTTCTGTCACGTGCAACATATA 59.008 37.500 11.67 0.00 35.74 0.86
2585 2849 3.812609 TGTTTCTGTCACGTGCAACATAT 59.187 39.130 11.67 0.00 35.74 1.78
2586 2850 3.198872 TGTTTCTGTCACGTGCAACATA 58.801 40.909 11.67 0.75 35.74 2.29
2587 2851 2.013400 TGTTTCTGTCACGTGCAACAT 58.987 42.857 11.67 0.00 35.74 2.71
2588 2852 1.443802 TGTTTCTGTCACGTGCAACA 58.556 45.000 11.67 10.36 35.74 3.33
2589 2853 2.287915 AGATGTTTCTGTCACGTGCAAC 59.712 45.455 11.67 5.46 0.00 4.17
2590 2854 2.560504 AGATGTTTCTGTCACGTGCAA 58.439 42.857 11.67 0.00 0.00 4.08
2591 2855 2.238942 AGATGTTTCTGTCACGTGCA 57.761 45.000 11.67 11.44 0.00 4.57
2597 2861 6.918067 TCTAAGAGGAAGATGTTTCTGTCA 57.082 37.500 0.00 0.00 30.72 3.58
2633 2897 7.185304 ACCCAAAGGATCCATATTCATATAGCT 59.815 37.037 15.82 0.00 36.73 3.32
2670 2934 2.922740 ACTCACTTAACTCGGCCAAA 57.077 45.000 2.24 0.00 0.00 3.28
2676 2940 5.642919 ACTGGAGTAGTACTCACTTAACTCG 59.357 44.000 27.41 10.02 46.79 4.18
2679 2943 8.278729 ACATACTGGAGTAGTACTCACTTAAC 57.721 38.462 27.41 12.42 46.79 2.01
2684 2948 7.804843 ACATACATACTGGAGTAGTACTCAC 57.195 40.000 27.41 18.31 46.79 3.51
2766 3030 5.543507 ACTGCCATTCGAGAGATCTAATT 57.456 39.130 0.00 0.00 41.60 1.40
2767 3031 5.184864 CCTACTGCCATTCGAGAGATCTAAT 59.815 44.000 0.00 0.00 41.60 1.73
2768 3032 4.520874 CCTACTGCCATTCGAGAGATCTAA 59.479 45.833 0.00 0.00 41.60 2.10
2769 3033 4.075682 CCTACTGCCATTCGAGAGATCTA 58.924 47.826 0.00 0.00 41.60 1.98
2770 3034 2.890311 CCTACTGCCATTCGAGAGATCT 59.110 50.000 0.00 0.00 41.60 2.75
2771 3035 2.609244 GCCTACTGCCATTCGAGAGATC 60.609 54.545 0.00 0.00 41.60 2.75
2772 3036 1.342819 GCCTACTGCCATTCGAGAGAT 59.657 52.381 0.00 0.00 41.60 2.75
2773 3037 0.747255 GCCTACTGCCATTCGAGAGA 59.253 55.000 0.00 0.00 39.20 3.10
2776 3040 1.683917 ACTAGCCTACTGCCATTCGAG 59.316 52.381 0.00 0.00 42.71 4.04
2778 3042 2.608261 GCTACTAGCCTACTGCCATTCG 60.608 54.545 0.00 0.00 42.71 3.34
2779 3043 3.033368 GCTACTAGCCTACTGCCATTC 57.967 52.381 0.00 0.00 42.71 2.67
2826 3090 2.211353 CGGTTCCCGCAAAAGAAAAA 57.789 45.000 0.00 0.00 41.17 1.94
2827 3091 3.949031 CGGTTCCCGCAAAAGAAAA 57.051 47.368 0.00 0.00 41.17 2.29
2926 3190 8.699283 ACAGTTAATTCTCGTTGTTACCTATC 57.301 34.615 0.00 0.00 0.00 2.08
2958 3222 7.949434 AGGGTACACTTTGCTATATACAGTAC 58.051 38.462 0.00 0.00 0.00 2.73
2960 3224 6.041751 GGAGGGTACACTTTGCTATATACAGT 59.958 42.308 0.00 0.00 0.00 3.55
2961 3225 6.041637 TGGAGGGTACACTTTGCTATATACAG 59.958 42.308 0.00 0.00 0.00 2.74
2962 3226 5.900699 TGGAGGGTACACTTTGCTATATACA 59.099 40.000 0.00 0.00 0.00 2.29
3064 3373 0.249784 CTCATGGATCTGGGCGTCTG 60.250 60.000 0.00 0.00 0.00 3.51
3078 3387 0.798776 GGACCAAGTTGACGCTCATG 59.201 55.000 3.87 0.00 0.00 3.07
3081 3390 0.249911 AGTGGACCAAGTTGACGCTC 60.250 55.000 3.87 0.00 0.00 5.03
3082 3391 0.532862 CAGTGGACCAAGTTGACGCT 60.533 55.000 3.87 3.60 0.00 5.07
3083 3392 0.814010 ACAGTGGACCAAGTTGACGC 60.814 55.000 3.87 1.22 0.00 5.19
3084 3393 2.519377 TACAGTGGACCAAGTTGACG 57.481 50.000 3.87 0.00 0.00 4.35
3085 3394 2.542595 CGTTACAGTGGACCAAGTTGAC 59.457 50.000 3.87 0.78 0.00 3.18
3086 3395 2.828877 CGTTACAGTGGACCAAGTTGA 58.171 47.619 3.87 0.00 0.00 3.18
3087 3396 1.263217 GCGTTACAGTGGACCAAGTTG 59.737 52.381 0.00 0.00 0.00 3.16
3088 3397 1.140252 AGCGTTACAGTGGACCAAGTT 59.860 47.619 0.00 0.00 0.00 2.66
3089 3398 0.756903 AGCGTTACAGTGGACCAAGT 59.243 50.000 0.00 0.23 0.00 3.16
3090 3399 1.270094 TGAGCGTTACAGTGGACCAAG 60.270 52.381 0.00 0.00 0.00 3.61
3091 3400 0.753867 TGAGCGTTACAGTGGACCAA 59.246 50.000 0.00 0.00 0.00 3.67
3092 3401 0.032952 GTGAGCGTTACAGTGGACCA 59.967 55.000 0.00 0.00 0.00 4.02
3093 3402 1.007336 CGTGAGCGTTACAGTGGACC 61.007 60.000 0.00 0.00 0.00 4.46
3094 3403 0.039798 TCGTGAGCGTTACAGTGGAC 60.040 55.000 0.00 0.00 39.49 4.02
3095 3404 0.885879 ATCGTGAGCGTTACAGTGGA 59.114 50.000 0.00 0.00 39.49 4.02
3096 3405 0.992072 CATCGTGAGCGTTACAGTGG 59.008 55.000 0.00 0.00 39.49 4.00
3097 3406 0.366871 GCATCGTGAGCGTTACAGTG 59.633 55.000 0.00 0.00 39.49 3.66
3098 3407 2.738147 GCATCGTGAGCGTTACAGT 58.262 52.632 0.00 0.00 39.49 3.55
3106 3415 1.135257 AGATATAGCCGCATCGTGAGC 60.135 52.381 0.00 0.00 0.00 4.26
3107 3416 2.789436 CGAGATATAGCCGCATCGTGAG 60.789 54.545 0.00 0.00 0.00 3.51
3108 3417 1.130561 CGAGATATAGCCGCATCGTGA 59.869 52.381 0.00 0.00 0.00 4.35
3109 3418 1.539341 CGAGATATAGCCGCATCGTG 58.461 55.000 0.00 0.00 0.00 4.35
3110 3419 3.998924 CGAGATATAGCCGCATCGT 57.001 52.632 0.00 0.00 0.00 3.73
3116 3425 0.040336 ACACGTGCGAGATATAGCCG 60.040 55.000 17.22 2.81 34.76 5.52
3117 3426 1.687628 GACACGTGCGAGATATAGCC 58.312 55.000 17.22 0.00 0.00 3.93
3118 3427 1.070108 TCGACACGTGCGAGATATAGC 60.070 52.381 24.25 0.00 33.33 2.97
3119 3428 2.943843 TCGACACGTGCGAGATATAG 57.056 50.000 24.25 3.00 33.33 1.31
3126 3435 4.994201 GTGCCTCGACACGTGCGA 62.994 66.667 25.57 25.57 36.23 5.10
3135 3444 1.654954 GCCTCTAAGTCGTGCCTCGA 61.655 60.000 0.00 0.00 46.83 4.04
3136 3445 1.226717 GCCTCTAAGTCGTGCCTCG 60.227 63.158 0.00 0.00 41.41 4.63
3137 3446 0.461961 ATGCCTCTAAGTCGTGCCTC 59.538 55.000 0.00 0.00 0.00 4.70
3138 3447 1.776662 TATGCCTCTAAGTCGTGCCT 58.223 50.000 0.00 0.00 0.00 4.75
3139 3448 2.202566 GTTATGCCTCTAAGTCGTGCC 58.797 52.381 0.00 0.00 0.00 5.01
3140 3449 2.202566 GGTTATGCCTCTAAGTCGTGC 58.797 52.381 0.00 0.00 0.00 5.34
3141 3450 2.460918 CGGTTATGCCTCTAAGTCGTG 58.539 52.381 0.00 0.00 34.25 4.35
3142 3451 1.202382 GCGGTTATGCCTCTAAGTCGT 60.202 52.381 0.00 0.00 34.25 4.34
3143 3452 1.202371 TGCGGTTATGCCTCTAAGTCG 60.202 52.381 0.00 0.00 34.25 4.18
3144 3453 2.596904 TGCGGTTATGCCTCTAAGTC 57.403 50.000 0.00 0.00 34.25 3.01
3145 3454 3.206150 CAATGCGGTTATGCCTCTAAGT 58.794 45.455 0.00 0.00 34.25 2.24
3146 3455 3.206150 ACAATGCGGTTATGCCTCTAAG 58.794 45.455 0.00 0.00 34.25 2.18
3147 3456 3.275617 ACAATGCGGTTATGCCTCTAA 57.724 42.857 0.00 0.00 34.25 2.10
3148 3457 3.244078 CCTACAATGCGGTTATGCCTCTA 60.244 47.826 0.00 0.00 34.25 2.43
3149 3458 2.485479 CCTACAATGCGGTTATGCCTCT 60.485 50.000 0.00 0.00 34.25 3.69
3150 3459 1.873591 CCTACAATGCGGTTATGCCTC 59.126 52.381 0.00 0.00 34.25 4.70
3151 3460 1.211949 ACCTACAATGCGGTTATGCCT 59.788 47.619 0.00 0.00 34.25 4.75
3152 3461 1.675552 ACCTACAATGCGGTTATGCC 58.324 50.000 0.00 0.00 0.00 4.40
3153 3462 4.274950 ACAATACCTACAATGCGGTTATGC 59.725 41.667 0.18 0.00 34.76 3.14
3154 3463 5.333035 CGACAATACCTACAATGCGGTTATG 60.333 44.000 0.18 3.66 34.76 1.90
3155 3464 4.748102 CGACAATACCTACAATGCGGTTAT 59.252 41.667 0.18 0.00 34.76 1.89
3156 3465 4.114073 CGACAATACCTACAATGCGGTTA 58.886 43.478 0.18 0.00 34.76 2.85
3157 3466 2.933906 CGACAATACCTACAATGCGGTT 59.066 45.455 0.18 0.00 34.76 4.44
3158 3467 2.546778 CGACAATACCTACAATGCGGT 58.453 47.619 0.62 0.62 37.31 5.68
3159 3468 1.260561 GCGACAATACCTACAATGCGG 59.739 52.381 0.00 0.00 0.00 5.69
3160 3469 1.930503 TGCGACAATACCTACAATGCG 59.069 47.619 0.00 0.00 0.00 4.73
3161 3470 3.621268 TCTTGCGACAATACCTACAATGC 59.379 43.478 0.00 0.00 0.00 3.56
3162 3471 5.220662 CCTTCTTGCGACAATACCTACAATG 60.221 44.000 0.00 0.00 0.00 2.82
3163 3472 4.876107 CCTTCTTGCGACAATACCTACAAT 59.124 41.667 0.00 0.00 0.00 2.71
3164 3473 4.250464 CCTTCTTGCGACAATACCTACAA 58.750 43.478 0.00 0.00 0.00 2.41
3165 3474 3.369052 CCCTTCTTGCGACAATACCTACA 60.369 47.826 0.00 0.00 0.00 2.74
3166 3475 3.195661 CCCTTCTTGCGACAATACCTAC 58.804 50.000 0.00 0.00 0.00 3.18
3167 3476 2.835764 ACCCTTCTTGCGACAATACCTA 59.164 45.455 0.00 0.00 0.00 3.08
3168 3477 1.628846 ACCCTTCTTGCGACAATACCT 59.371 47.619 0.00 0.00 0.00 3.08
3169 3478 2.007608 GACCCTTCTTGCGACAATACC 58.992 52.381 0.00 0.00 0.00 2.73
3170 3479 2.695359 TGACCCTTCTTGCGACAATAC 58.305 47.619 0.00 0.00 0.00 1.89
3171 3480 3.197766 AGATGACCCTTCTTGCGACAATA 59.802 43.478 0.00 0.00 0.00 1.90
3172 3481 2.026822 AGATGACCCTTCTTGCGACAAT 60.027 45.455 0.00 0.00 0.00 2.71
3173 3482 1.347707 AGATGACCCTTCTTGCGACAA 59.652 47.619 0.00 0.00 0.00 3.18
3174 3483 0.976641 AGATGACCCTTCTTGCGACA 59.023 50.000 0.00 0.00 0.00 4.35
3175 3484 2.003301 GAAGATGACCCTTCTTGCGAC 58.997 52.381 0.00 0.00 39.44 5.19
3176 3485 1.623311 TGAAGATGACCCTTCTTGCGA 59.377 47.619 0.00 0.00 42.20 5.10
3177 3486 1.734465 GTGAAGATGACCCTTCTTGCG 59.266 52.381 0.00 0.00 42.20 4.85
3178 3487 2.485814 GTGTGAAGATGACCCTTCTTGC 59.514 50.000 0.00 0.00 42.20 4.01
3179 3488 3.743521 TGTGTGAAGATGACCCTTCTTG 58.256 45.455 0.00 0.00 42.20 3.02
3180 3489 4.437682 TTGTGTGAAGATGACCCTTCTT 57.562 40.909 0.00 0.00 42.20 2.52
3181 3490 4.566488 GGATTGTGTGAAGATGACCCTTCT 60.566 45.833 0.00 0.00 42.20 2.85
3182 3491 3.691609 GGATTGTGTGAAGATGACCCTTC 59.308 47.826 0.00 0.00 42.09 3.46
3183 3492 3.562176 GGGATTGTGTGAAGATGACCCTT 60.562 47.826 0.00 0.00 32.93 3.95
3184 3493 2.025887 GGGATTGTGTGAAGATGACCCT 60.026 50.000 0.00 0.00 32.93 4.34
3185 3494 2.290896 TGGGATTGTGTGAAGATGACCC 60.291 50.000 0.00 0.00 35.82 4.46
3186 3495 3.071874 TGGGATTGTGTGAAGATGACC 57.928 47.619 0.00 0.00 0.00 4.02
3187 3496 4.012374 ACATGGGATTGTGTGAAGATGAC 58.988 43.478 0.00 0.00 0.00 3.06
3188 3497 4.305539 ACATGGGATTGTGTGAAGATGA 57.694 40.909 0.00 0.00 0.00 2.92
3189 3498 6.319405 TCATTACATGGGATTGTGTGAAGATG 59.681 38.462 0.00 0.00 0.00 2.90
3190 3499 6.425735 TCATTACATGGGATTGTGTGAAGAT 58.574 36.000 0.00 0.00 0.00 2.40
3191 3500 5.814481 TCATTACATGGGATTGTGTGAAGA 58.186 37.500 0.00 0.00 0.00 2.87
3192 3501 6.072008 TGTTCATTACATGGGATTGTGTGAAG 60.072 38.462 0.00 0.00 36.80 3.02
3193 3502 5.772169 TGTTCATTACATGGGATTGTGTGAA 59.228 36.000 0.00 0.00 35.28 3.18
3194 3503 5.320277 TGTTCATTACATGGGATTGTGTGA 58.680 37.500 0.00 0.00 0.00 3.58
3195 3504 5.641783 TGTTCATTACATGGGATTGTGTG 57.358 39.130 0.00 0.00 0.00 3.82
3196 3505 6.009589 TCTTGTTCATTACATGGGATTGTGT 58.990 36.000 0.00 0.00 36.44 3.72
3197 3506 6.513806 TCTTGTTCATTACATGGGATTGTG 57.486 37.500 0.00 0.00 36.44 3.33
3198 3507 7.396907 TCATTCTTGTTCATTACATGGGATTGT 59.603 33.333 0.00 0.00 36.44 2.71
3199 3508 7.774134 TCATTCTTGTTCATTACATGGGATTG 58.226 34.615 0.00 0.00 36.44 2.67
3200 3509 7.835682 TCTCATTCTTGTTCATTACATGGGATT 59.164 33.333 0.00 0.00 36.44 3.01
3201 3510 7.348815 TCTCATTCTTGTTCATTACATGGGAT 58.651 34.615 0.00 0.00 36.44 3.85
3202 3511 6.720309 TCTCATTCTTGTTCATTACATGGGA 58.280 36.000 0.00 0.00 36.44 4.37
3203 3512 7.578310 ATCTCATTCTTGTTCATTACATGGG 57.422 36.000 0.00 0.00 36.44 4.00
3211 3520 9.918630 CCAACTTTTTATCTCATTCTTGTTCAT 57.081 29.630 0.00 0.00 0.00 2.57
3212 3521 7.867403 GCCAACTTTTTATCTCATTCTTGTTCA 59.133 33.333 0.00 0.00 0.00 3.18
3213 3522 8.084684 AGCCAACTTTTTATCTCATTCTTGTTC 58.915 33.333 0.00 0.00 0.00 3.18
3214 3523 7.955918 AGCCAACTTTTTATCTCATTCTTGTT 58.044 30.769 0.00 0.00 0.00 2.83
3215 3524 7.530426 AGCCAACTTTTTATCTCATTCTTGT 57.470 32.000 0.00 0.00 0.00 3.16
3216 3525 9.346725 GTAAGCCAACTTTTTATCTCATTCTTG 57.653 33.333 0.00 0.00 37.33 3.02
3217 3526 9.077885 TGTAAGCCAACTTTTTATCTCATTCTT 57.922 29.630 0.00 0.00 37.33 2.52
3218 3527 8.635765 TGTAAGCCAACTTTTTATCTCATTCT 57.364 30.769 0.00 0.00 37.33 2.40
3219 3528 9.860898 ATTGTAAGCCAACTTTTTATCTCATTC 57.139 29.630 0.00 0.00 37.33 2.67
3220 3529 9.860898 GATTGTAAGCCAACTTTTTATCTCATT 57.139 29.630 0.00 0.00 37.33 2.57
3221 3530 8.184192 CGATTGTAAGCCAACTTTTTATCTCAT 58.816 33.333 0.00 0.00 37.33 2.90
3222 3531 7.361713 CCGATTGTAAGCCAACTTTTTATCTCA 60.362 37.037 0.00 0.00 37.33 3.27
3223 3532 6.967199 CCGATTGTAAGCCAACTTTTTATCTC 59.033 38.462 0.00 0.00 37.33 2.75
3224 3533 6.625081 GCCGATTGTAAGCCAACTTTTTATCT 60.625 38.462 0.00 0.00 37.33 1.98
3225 3534 5.515270 GCCGATTGTAAGCCAACTTTTTATC 59.485 40.000 0.00 0.00 37.33 1.75
3226 3535 5.047660 TGCCGATTGTAAGCCAACTTTTTAT 60.048 36.000 0.00 0.00 37.33 1.40
3227 3536 4.278669 TGCCGATTGTAAGCCAACTTTTTA 59.721 37.500 0.00 0.00 37.33 1.52
3228 3537 3.068873 TGCCGATTGTAAGCCAACTTTTT 59.931 39.130 0.00 0.00 37.33 1.94
3229 3538 2.625790 TGCCGATTGTAAGCCAACTTTT 59.374 40.909 0.00 0.00 37.33 2.27
3230 3539 2.030274 GTGCCGATTGTAAGCCAACTTT 60.030 45.455 0.00 0.00 37.33 2.66
3231 3540 1.539827 GTGCCGATTGTAAGCCAACTT 59.460 47.619 0.00 0.00 40.07 2.66
3232 3541 1.165270 GTGCCGATTGTAAGCCAACT 58.835 50.000 0.00 0.00 35.44 3.16
3233 3542 1.165270 AGTGCCGATTGTAAGCCAAC 58.835 50.000 0.00 0.00 35.44 3.77
3234 3543 1.810151 GAAGTGCCGATTGTAAGCCAA 59.190 47.619 0.00 0.00 37.49 4.52
3235 3544 1.271108 TGAAGTGCCGATTGTAAGCCA 60.271 47.619 0.00 0.00 0.00 4.75
3236 3545 1.130561 GTGAAGTGCCGATTGTAAGCC 59.869 52.381 0.00 0.00 0.00 4.35
3237 3546 1.804151 TGTGAAGTGCCGATTGTAAGC 59.196 47.619 0.00 0.00 0.00 3.09
3238 3547 2.805671 TGTGTGAAGTGCCGATTGTAAG 59.194 45.455 0.00 0.00 0.00 2.34
3239 3548 2.839975 TGTGTGAAGTGCCGATTGTAA 58.160 42.857 0.00 0.00 0.00 2.41
3240 3549 2.535012 TGTGTGAAGTGCCGATTGTA 57.465 45.000 0.00 0.00 0.00 2.41
3241 3550 1.674359 TTGTGTGAAGTGCCGATTGT 58.326 45.000 0.00 0.00 0.00 2.71
3242 3551 2.587956 CATTGTGTGAAGTGCCGATTG 58.412 47.619 0.00 0.00 0.00 2.67
3243 3552 1.068333 GCATTGTGTGAAGTGCCGATT 60.068 47.619 0.00 0.00 0.00 3.34
3244 3553 0.523072 GCATTGTGTGAAGTGCCGAT 59.477 50.000 0.00 0.00 0.00 4.18
3245 3554 0.817229 TGCATTGTGTGAAGTGCCGA 60.817 50.000 0.00 0.00 36.79 5.54
3246 3555 0.241749 ATGCATTGTGTGAAGTGCCG 59.758 50.000 0.00 0.00 36.79 5.69
3247 3556 3.574284 TTATGCATTGTGTGAAGTGCC 57.426 42.857 3.54 0.00 36.79 5.01
3248 3557 7.579589 TTAAATTATGCATTGTGTGAAGTGC 57.420 32.000 3.54 0.00 38.05 4.40
3249 3558 8.976471 TGTTTAAATTATGCATTGTGTGAAGTG 58.024 29.630 3.54 0.00 0.00 3.16
3250 3559 9.709495 ATGTTTAAATTATGCATTGTGTGAAGT 57.291 25.926 3.54 0.00 0.00 3.01
3271 3580 9.283768 TGTTTGTACTCTGAATGATGTATGTTT 57.716 29.630 0.00 0.00 0.00 2.83
3272 3581 8.846943 TGTTTGTACTCTGAATGATGTATGTT 57.153 30.769 0.00 0.00 0.00 2.71
3273 3582 8.846943 TTGTTTGTACTCTGAATGATGTATGT 57.153 30.769 0.00 0.00 0.00 2.29
3274 3583 8.393366 CCTTGTTTGTACTCTGAATGATGTATG 58.607 37.037 0.00 0.00 0.00 2.39
3275 3584 8.103305 ACCTTGTTTGTACTCTGAATGATGTAT 58.897 33.333 0.00 0.00 0.00 2.29
3276 3585 7.450074 ACCTTGTTTGTACTCTGAATGATGTA 58.550 34.615 0.00 0.00 0.00 2.29
3277 3586 6.299141 ACCTTGTTTGTACTCTGAATGATGT 58.701 36.000 0.00 0.00 0.00 3.06
3278 3587 6.128172 GGACCTTGTTTGTACTCTGAATGATG 60.128 42.308 0.00 0.00 0.00 3.07
3279 3588 5.940470 GGACCTTGTTTGTACTCTGAATGAT 59.060 40.000 0.00 0.00 0.00 2.45
3280 3589 5.305585 GGACCTTGTTTGTACTCTGAATGA 58.694 41.667 0.00 0.00 0.00 2.57
3281 3590 4.152402 CGGACCTTGTTTGTACTCTGAATG 59.848 45.833 0.00 0.00 0.00 2.67
3282 3591 4.039973 TCGGACCTTGTTTGTACTCTGAAT 59.960 41.667 0.00 0.00 0.00 2.57
3283 3592 3.385433 TCGGACCTTGTTTGTACTCTGAA 59.615 43.478 0.00 0.00 0.00 3.02
3284 3593 2.960384 TCGGACCTTGTTTGTACTCTGA 59.040 45.455 0.00 0.00 0.00 3.27
3285 3594 3.057734 GTCGGACCTTGTTTGTACTCTG 58.942 50.000 0.00 0.00 0.00 3.35
3286 3595 2.963782 AGTCGGACCTTGTTTGTACTCT 59.036 45.455 4.14 0.00 0.00 3.24
3287 3596 3.382048 AGTCGGACCTTGTTTGTACTC 57.618 47.619 4.14 0.00 0.00 2.59
3288 3597 3.304928 CGTAGTCGGACCTTGTTTGTACT 60.305 47.826 4.14 0.00 0.00 2.73
3289 3598 2.982470 CGTAGTCGGACCTTGTTTGTAC 59.018 50.000 4.14 0.00 0.00 2.90
3290 3599 3.287312 CGTAGTCGGACCTTGTTTGTA 57.713 47.619 4.14 0.00 0.00 2.41
3291 3600 2.144482 CGTAGTCGGACCTTGTTTGT 57.856 50.000 4.14 0.00 0.00 2.83
3303 3612 4.449743 TCTTTCATTTTGGTTCCGTAGTCG 59.550 41.667 0.00 0.00 0.00 4.18
3304 3613 5.934935 TCTTTCATTTTGGTTCCGTAGTC 57.065 39.130 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.