Multiple sequence alignment - TraesCS6D01G197200

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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 TraesCS6D01G197200 chr6D 100.000 8011 0 0 1 8011 274300739 274308749 0.000000e+00 14794.0
1 TraesCS6D01G197200 chr6B 95.038 3567 115 31 2574 6110 436493677 436497211 0.000000e+00 5550.0
2 TraesCS6D01G197200 chr6B 94.714 1173 52 8 6083 7253 436498089 436499253 0.000000e+00 1814.0
3 TraesCS6D01G197200 chr6B 92.028 991 51 12 811 1775 436492022 436493010 0.000000e+00 1367.0
4 TraesCS6D01G197200 chr6B 95.338 622 16 11 1798 2416 436493068 436493679 0.000000e+00 976.0
5 TraesCS6D01G197200 chr6B 89.911 674 54 7 142 805 668629713 668630382 0.000000e+00 856.0
6 TraesCS6D01G197200 chr6B 92.053 151 9 2 1 149 668629398 668629547 8.150000e-50 209.0
7 TraesCS6D01G197200 chr6B 93.805 113 7 0 3057 3169 67469331 67469219 3.840000e-38 171.0
8 TraesCS6D01G197200 chr6B 87.302 63 8 0 7710 7772 570150359 570150421 1.120000e-08 73.1
9 TraesCS6D01G197200 chr6A 95.946 3429 92 23 4583 8007 392939386 392936001 0.000000e+00 5518.0
10 TraesCS6D01G197200 chr6A 97.436 2028 31 8 2576 4597 392941578 392939566 0.000000e+00 3437.0
11 TraesCS6D01G197200 chr6A 96.606 1532 32 7 895 2414 392943103 392941580 0.000000e+00 2523.0
12 TraesCS6D01G197200 chr6A 91.257 183 14 2 3634 3815 264774706 264774887 1.730000e-61 248.0
13 TraesCS6D01G197200 chr6A 90.000 80 5 2 803 881 392965926 392965849 5.120000e-17 100.0
14 TraesCS6D01G197200 chr7B 92.433 674 41 6 142 805 648101958 648101285 0.000000e+00 953.0
15 TraesCS6D01G197200 chr7B 91.558 154 8 2 1 149 648102277 648102124 2.930000e-49 207.0
16 TraesCS6D01G197200 chr3B 90.634 662 41 5 152 805 823875718 823875070 0.000000e+00 859.0
17 TraesCS6D01G197200 chr3B 96.296 162 6 0 2414 2575 126006045 126005884 4.770000e-67 267.0
18 TraesCS6D01G197200 chr3B 96.226 159 6 0 2417 2575 428100892 428100734 2.220000e-65 261.0
19 TraesCS6D01G197200 chr3B 95.679 162 7 0 2414 2575 780937506 780937345 2.220000e-65 261.0
20 TraesCS6D01G197200 chr3B 92.350 183 11 3 3634 3815 480568160 480568340 2.870000e-64 257.0
21 TraesCS6D01G197200 chr3B 94.040 151 7 1 1 149 823876850 823876700 2.250000e-55 228.0
22 TraesCS6D01G197200 chr3B 94.643 112 6 0 3057 3168 8549076 8549187 2.970000e-39 174.0
23 TraesCS6D01G197200 chr1B 91.304 598 31 7 216 805 671236116 671235532 0.000000e+00 797.0
24 TraesCS6D01G197200 chr1B 95.679 162 7 0 2414 2575 83203805 83203644 2.220000e-65 261.0
25 TraesCS6D01G197200 chr1B 94.040 151 7 1 1 149 671239960 671239810 2.250000e-55 228.0
26 TraesCS6D01G197200 chr1B 95.455 110 5 0 3057 3166 625168435 625168326 8.260000e-40 176.0
27 TraesCS6D01G197200 chr1B 93.056 72 5 0 142 213 671239644 671239573 1.100000e-18 106.0
28 TraesCS6D01G197200 chr1B 86.364 66 5 4 7709 7772 15901643 15901580 1.440000e-07 69.4
29 TraesCS6D01G197200 chr2A 91.023 557 36 8 142 685 729187550 729188105 0.000000e+00 739.0
30 TraesCS6D01G197200 chr2A 91.209 182 15 1 3634 3814 745090403 745090584 6.210000e-61 246.0
31 TraesCS6D01G197200 chr2A 96.026 151 4 1 1 149 729187234 729187384 2.230000e-60 244.0
32 TraesCS6D01G197200 chr2A 89.894 188 16 3 3630 3815 649477564 649477750 1.040000e-58 239.0
33 TraesCS6D01G197200 chr4B 92.188 384 29 1 142 524 488999621 489000004 7.070000e-150 542.0
34 TraesCS6D01G197200 chr4B 91.915 235 19 0 571 805 489000224 489000458 5.990000e-86 329.0
35 TraesCS6D01G197200 chr4B 94.040 151 7 1 1 149 488999305 488999455 2.250000e-55 228.0
36 TraesCS6D01G197200 chr4B 92.063 63 2 3 7710 7771 573690892 573690832 1.430000e-12 86.1
37 TraesCS6D01G197200 chr4B 82.667 75 11 1 1994 2068 428465428 428465500 1.870000e-06 65.8
38 TraesCS6D01G197200 chr5B 96.914 162 5 0 2414 2575 491710533 491710372 1.020000e-68 272.0
39 TraesCS6D01G197200 chr3D 95.294 170 6 2 2414 2583 18133543 18133710 1.330000e-67 268.0
40 TraesCS6D01G197200 chr3D 92.857 182 13 0 3634 3815 409470967 409470786 1.710000e-66 265.0
41 TraesCS6D01G197200 chr3D 95.679 162 7 0 2414 2575 23144025 23144186 2.220000e-65 261.0
42 TraesCS6D01G197200 chr3D 93.143 175 11 1 3634 3807 16131532 16131706 1.030000e-63 255.0
43 TraesCS6D01G197200 chrUn 92.308 182 13 1 3634 3814 71310536 71310355 2.870000e-64 257.0
44 TraesCS6D01G197200 chrUn 94.545 110 5 1 3057 3166 313033773 313033881 1.380000e-37 169.0
45 TraesCS6D01G197200 chrUn 94.545 110 5 1 3057 3166 313037568 313037676 1.380000e-37 169.0
46 TraesCS6D01G197200 chrUn 94.545 110 5 1 3057 3166 327964244 327964352 1.380000e-37 169.0
47 TraesCS6D01G197200 chr2B 94.578 166 9 0 2414 2579 195678777 195678612 2.870000e-64 257.0
48 TraesCS6D01G197200 chr4D 92.571 175 10 3 2409 2583 437295930 437295759 1.730000e-61 248.0
49 TraesCS6D01G197200 chr4D 83.333 66 9 2 2164 2228 362413310 362413246 8.680000e-05 60.2
50 TraesCS6D01G197200 chr7D 94.690 113 6 0 3057 3169 219717860 219717972 8.260000e-40 176.0
51 TraesCS6D01G197200 chr4A 84.906 53 7 1 2017 2068 117281943 117281891 1.500000e-02 52.8


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 TraesCS6D01G197200 chr6D 274300739 274308749 8010 False 14794.000000 14794 100.000000 1 8011 1 chr6D.!!$F1 8010
1 TraesCS6D01G197200 chr6B 436492022 436499253 7231 False 2426.750000 5550 94.279500 811 7253 4 chr6B.!!$F2 6442
2 TraesCS6D01G197200 chr6B 668629398 668630382 984 False 532.500000 856 90.982000 1 805 2 chr6B.!!$F3 804
3 TraesCS6D01G197200 chr6A 392936001 392943103 7102 True 3826.000000 5518 96.662667 895 8007 3 chr6A.!!$R2 7112
4 TraesCS6D01G197200 chr7B 648101285 648102277 992 True 580.000000 953 91.995500 1 805 2 chr7B.!!$R1 804
5 TraesCS6D01G197200 chr3B 823875070 823876850 1780 True 543.500000 859 92.337000 1 805 2 chr3B.!!$R4 804
6 TraesCS6D01G197200 chr1B 671235532 671239960 4428 True 377.000000 797 92.800000 1 805 3 chr1B.!!$R4 804
7 TraesCS6D01G197200 chr2A 729187234 729188105 871 False 491.500000 739 93.524500 1 685 2 chr2A.!!$F3 684
8 TraesCS6D01G197200 chr4B 488999305 489000458 1153 False 366.333333 542 92.714333 1 805 3 chr4B.!!$F2 804

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
535 5006 0.320508 GAACCGAAGCGAACCCTCTT 60.321 55.000 0.0 0.0 0.00 2.85 F
536 5007 0.320508 AACCGAAGCGAACCCTCTTC 60.321 55.000 0.0 0.0 36.31 2.87 F
545 5016 0.837940 GAACCCTCTTCGGCCCTATT 59.162 55.000 0.0 0.0 0.00 1.73 F
546 5017 0.837940 AACCCTCTTCGGCCCTATTC 59.162 55.000 0.0 0.0 0.00 1.75 F
2427 7129 1.206610 GGAACTTACTCCCTCCGTTCC 59.793 57.143 0.0 0.0 44.51 3.62 F
3233 7941 1.898574 CAGCCCTTGTGAAACCGCT 60.899 57.895 0.0 0.0 34.36 5.52 F
3725 8435 0.887387 GGTTACCGAGTTGCCTTGCA 60.887 55.000 0.0 0.0 36.47 4.08 F
4199 8924 2.096466 TGAACGCATTTGTAGCTTCACG 60.096 45.455 0.0 0.0 30.15 4.35 F
4670 9594 2.224523 TGCCAGTTTCAGAGGTGGTTAG 60.225 50.000 0.0 0.0 32.20 2.34 F
6375 12208 1.248101 ATTTGGCAGTGGTTACGGGC 61.248 55.000 0.0 0.0 45.43 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 6609 0.036164 TGGAGCCTGAGCGCTAAAAA 59.964 50.000 11.50 0.00 46.67 1.94 R
1922 6617 1.817099 GTTCCATGGAGCCTGAGCG 60.817 63.158 17.35 0.00 46.67 5.03 R
2414 7116 2.547990 ACATTTAGGAACGGAGGGAGT 58.452 47.619 0.00 0.00 0.00 3.85 R
2451 7153 2.563620 TCCGTATGTAGTTTGCAGTGGA 59.436 45.455 0.00 0.00 0.00 4.02 R
3639 8349 3.598299 CCAATATTTGGCACCAAACCAG 58.402 45.455 16.76 7.64 46.80 4.00 R
4899 9824 0.387202 CACACCGGCCAAACATTTCA 59.613 50.000 0.00 0.00 0.00 2.69 R
5582 10511 0.467290 GAGCCAACAAACCCCTGTCA 60.467 55.000 0.00 0.00 0.00 3.58 R
5988 10918 5.359860 ACATGATATTGTACTGTCACCGAGA 59.640 40.000 0.00 0.00 0.00 4.04 R
6478 12311 1.217779 GTGTCAGGAGGAGCAGCTC 59.782 63.158 14.69 14.69 0.00 4.09 R
7330 13166 0.034337 TCGCCGGCAAGTTTAGTTCT 59.966 50.000 28.98 0.00 0.00 3.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 53 7.984422 ATTGATCTGAGTGTCACAAATTACA 57.016 32.000 5.62 0.00 0.00 2.41
53 56 7.389232 TGATCTGAGTGTCACAAATTACATCT 58.611 34.615 5.62 0.00 0.00 2.90
238 4677 4.617959 CGGATACAATCATACAACCGTCT 58.382 43.478 0.00 0.00 35.40 4.18
295 4734 2.345760 GGAAGCCGGGAGTACGACA 61.346 63.158 2.18 0.00 35.47 4.35
407 4853 2.751436 CTGCCGTCCCCAACCATG 60.751 66.667 0.00 0.00 0.00 3.66
533 5004 0.391263 ATGAACCGAAGCGAACCCTC 60.391 55.000 0.00 0.00 0.00 4.30
534 5005 1.292541 GAACCGAAGCGAACCCTCT 59.707 57.895 0.00 0.00 0.00 3.69
535 5006 0.320508 GAACCGAAGCGAACCCTCTT 60.321 55.000 0.00 0.00 0.00 2.85
536 5007 0.320508 AACCGAAGCGAACCCTCTTC 60.321 55.000 0.00 0.00 36.31 2.87
539 5010 2.047179 AAGCGAACCCTCTTCGGC 60.047 61.111 4.77 0.00 41.76 5.54
542 5013 3.391382 CGAACCCTCTTCGGCCCT 61.391 66.667 0.00 0.00 38.19 5.19
543 5014 2.056223 CGAACCCTCTTCGGCCCTA 61.056 63.158 0.00 0.00 38.19 3.53
544 5015 1.400530 CGAACCCTCTTCGGCCCTAT 61.401 60.000 0.00 0.00 38.19 2.57
545 5016 0.837940 GAACCCTCTTCGGCCCTATT 59.162 55.000 0.00 0.00 0.00 1.73
546 5017 0.837940 AACCCTCTTCGGCCCTATTC 59.162 55.000 0.00 0.00 0.00 1.75
548 5019 1.367840 CCTCTTCGGCCCTATTCGG 59.632 63.158 0.00 0.00 0.00 4.30
560 5040 2.276201 CCTATTCGGCAAACATCGTGA 58.724 47.619 0.00 0.00 0.00 4.35
569 5192 2.668279 GCAAACATCGTGAATCGGCTTT 60.668 45.455 0.00 0.00 40.32 3.51
645 5268 4.172512 AGCAGCGGCCCAGAGATG 62.173 66.667 4.82 0.00 42.56 2.90
805 5429 9.542462 GTGGCTATGTTATACTGTTTCTCAATA 57.458 33.333 0.00 0.00 0.00 1.90
838 5462 8.135529 CGAATTTTTCTGGGAAGAAGTTTTACT 58.864 33.333 0.00 0.00 0.00 2.24
839 5463 9.249457 GAATTTTTCTGGGAAGAAGTTTTACTG 57.751 33.333 0.00 0.00 0.00 2.74
843 5467 7.797038 TTCTGGGAAGAAGTTTTACTGTAAC 57.203 36.000 0.00 0.00 0.00 2.50
847 5471 5.407691 GGGAAGAAGTTTTACTGTAACCGAG 59.592 44.000 0.00 0.00 0.00 4.63
852 5476 8.496707 AGAAGTTTTACTGTAACCGAGAAAAA 57.503 30.769 0.00 0.00 0.00 1.94
856 5480 8.501580 AGTTTTACTGTAACCGAGAAAAATAGC 58.498 33.333 0.00 0.00 0.00 2.97
871 5495 8.677148 AGAAAAATAGCTGTCTGACAACTTTA 57.323 30.769 17.83 2.89 0.00 1.85
872 5496 8.560374 AGAAAAATAGCTGTCTGACAACTTTAC 58.440 33.333 17.83 6.77 0.00 2.01
873 5497 6.467723 AAATAGCTGTCTGACAACTTTACG 57.532 37.500 17.83 3.11 0.00 3.18
874 5498 3.454371 AGCTGTCTGACAACTTTACGT 57.546 42.857 12.16 0.00 0.00 3.57
877 5501 5.353938 AGCTGTCTGACAACTTTACGTAAA 58.646 37.500 19.12 19.12 0.00 2.01
879 5503 6.482308 AGCTGTCTGACAACTTTACGTAAATT 59.518 34.615 20.39 12.77 0.00 1.82
880 5504 7.654520 AGCTGTCTGACAACTTTACGTAAATTA 59.345 33.333 20.39 2.85 0.00 1.40
937 5563 1.224870 GGAGTTGCTCTAAGCCCCC 59.775 63.158 0.00 0.00 41.51 5.40
1319 5946 1.216977 CAATCCCTCGCACCACGTA 59.783 57.895 0.00 0.00 44.19 3.57
1681 6330 2.431683 GCCAGACCAGTGCCTTGA 59.568 61.111 0.00 0.00 0.00 3.02
1696 6345 1.747355 CCTTGATGTGGCAGAATCACC 59.253 52.381 11.32 0.00 32.63 4.02
1738 6387 2.746362 GCAAGAAGCTAGTGACTGCATT 59.254 45.455 0.00 0.00 41.15 3.56
1883 6577 8.665685 CCATAGTTTTCTGTAACAGATGGTAAC 58.334 37.037 7.12 8.97 40.39 2.50
1915 6609 4.952460 AGCAATTGTTTCTGCAGAAATGT 58.048 34.783 37.03 24.89 44.69 2.71
1922 6617 6.826893 TGTTTCTGCAGAAATGTTTTTAGC 57.173 33.333 37.03 23.58 44.69 3.09
2038 6734 9.869757 TGTTATATGGATGTATACTGCATGTAC 57.130 33.333 14.88 11.40 33.45 2.90
2328 7030 2.163390 CATGGAGCTCGAGCACACG 61.163 63.158 36.87 24.09 45.16 4.49
2413 7115 3.653352 GGGATCCTTAGGCTATGGAACTT 59.347 47.826 27.13 14.89 35.86 2.66
2414 7116 4.844655 GGGATCCTTAGGCTATGGAACTTA 59.155 45.833 27.13 9.60 35.86 2.24
2415 7117 5.280062 GGGATCCTTAGGCTATGGAACTTAC 60.280 48.000 27.13 15.10 35.86 2.34
2416 7118 5.544562 GGATCCTTAGGCTATGGAACTTACT 59.455 44.000 27.13 13.64 35.86 2.24
2417 7119 6.295405 GGATCCTTAGGCTATGGAACTTACTC 60.295 46.154 27.13 19.57 35.86 2.59
2418 7120 4.900054 TCCTTAGGCTATGGAACTTACTCC 59.100 45.833 22.88 0.00 35.88 3.85
2419 7121 4.040584 CCTTAGGCTATGGAACTTACTCCC 59.959 50.000 19.09 0.00 34.22 4.30
2420 7122 3.423058 AGGCTATGGAACTTACTCCCT 57.577 47.619 0.00 0.00 34.22 4.20
2421 7123 3.310193 AGGCTATGGAACTTACTCCCTC 58.690 50.000 0.00 0.00 34.22 4.30
2422 7124 2.369203 GGCTATGGAACTTACTCCCTCC 59.631 54.545 0.00 0.00 34.22 4.30
2423 7125 2.036089 GCTATGGAACTTACTCCCTCCG 59.964 54.545 0.00 0.00 34.22 4.63
2424 7126 2.249309 ATGGAACTTACTCCCTCCGT 57.751 50.000 0.00 0.00 34.22 4.69
2425 7127 2.019807 TGGAACTTACTCCCTCCGTT 57.980 50.000 0.00 0.00 34.22 4.44
2426 7128 1.897802 TGGAACTTACTCCCTCCGTTC 59.102 52.381 0.00 0.00 34.22 3.95
2427 7129 1.206610 GGAACTTACTCCCTCCGTTCC 59.793 57.143 0.00 0.00 44.51 3.62
2428 7130 2.177734 GAACTTACTCCCTCCGTTCCT 58.822 52.381 0.00 0.00 0.00 3.36
2429 7131 3.359950 GAACTTACTCCCTCCGTTCCTA 58.640 50.000 0.00 0.00 0.00 2.94
2430 7132 3.463048 ACTTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
2431 7133 3.782992 ACTTACTCCCTCCGTTCCTAAA 58.217 45.455 0.00 0.00 0.00 1.85
2432 7134 4.359996 ACTTACTCCCTCCGTTCCTAAAT 58.640 43.478 0.00 0.00 0.00 1.40
2433 7135 4.161754 ACTTACTCCCTCCGTTCCTAAATG 59.838 45.833 0.00 0.00 0.00 2.32
2434 7136 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
2435 7137 3.716431 ACTCCCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
2436 7138 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
2437 7139 4.161754 ACTCCCTCCGTTCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
2438 7140 4.098894 TCCCTCCGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
2439 7141 4.161001 TCCCTCCGTTCCTAAATGTAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
2440 7142 4.161754 CCCTCCGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
2441 7143 5.338137 CCCTCCGTTCCTAAATGTAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
2442 7144 6.171213 CCTCCGTTCCTAAATGTAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
2443 7145 6.653740 CCTCCGTTCCTAAATGTAAGTCTTTT 59.346 38.462 0.00 0.00 0.00 2.27
2444 7146 7.174426 CCTCCGTTCCTAAATGTAAGTCTTTTT 59.826 37.037 0.00 0.00 0.00 1.94
2445 7147 9.211485 CTCCGTTCCTAAATGTAAGTCTTTTTA 57.789 33.333 0.00 0.00 0.00 1.52
2446 7148 9.211485 TCCGTTCCTAAATGTAAGTCTTTTTAG 57.789 33.333 7.75 7.75 0.00 1.85
2447 7149 9.211485 CCGTTCCTAAATGTAAGTCTTTTTAGA 57.789 33.333 13.43 2.40 0.00 2.10
2457 7159 8.833231 TGTAAGTCTTTTTAGAGATTCCACTG 57.167 34.615 0.00 0.00 0.00 3.66
2458 7160 6.809630 AAGTCTTTTTAGAGATTCCACTGC 57.190 37.500 0.00 0.00 0.00 4.40
2459 7161 5.869579 AGTCTTTTTAGAGATTCCACTGCA 58.130 37.500 0.00 0.00 0.00 4.41
2460 7162 6.299141 AGTCTTTTTAGAGATTCCACTGCAA 58.701 36.000 0.00 0.00 0.00 4.08
2461 7163 6.772716 AGTCTTTTTAGAGATTCCACTGCAAA 59.227 34.615 0.00 0.00 0.00 3.68
2462 7164 6.858478 GTCTTTTTAGAGATTCCACTGCAAAC 59.142 38.462 0.00 0.00 0.00 2.93
2463 7165 6.772716 TCTTTTTAGAGATTCCACTGCAAACT 59.227 34.615 0.00 0.00 0.00 2.66
2464 7166 7.936847 TCTTTTTAGAGATTCCACTGCAAACTA 59.063 33.333 0.00 0.00 0.00 2.24
2465 7167 7.435068 TTTTAGAGATTCCACTGCAAACTAC 57.565 36.000 0.00 0.00 0.00 2.73
2466 7168 4.623932 AGAGATTCCACTGCAAACTACA 57.376 40.909 0.00 0.00 0.00 2.74
2467 7169 5.171339 AGAGATTCCACTGCAAACTACAT 57.829 39.130 0.00 0.00 0.00 2.29
2468 7170 6.299805 AGAGATTCCACTGCAAACTACATA 57.700 37.500 0.00 0.00 0.00 2.29
2469 7171 6.109359 AGAGATTCCACTGCAAACTACATAC 58.891 40.000 0.00 0.00 0.00 2.39
2470 7172 4.870426 AGATTCCACTGCAAACTACATACG 59.130 41.667 0.00 0.00 0.00 3.06
2471 7173 2.967362 TCCACTGCAAACTACATACGG 58.033 47.619 0.00 0.00 0.00 4.02
2472 7174 2.563620 TCCACTGCAAACTACATACGGA 59.436 45.455 0.00 0.00 0.00 4.69
2473 7175 3.196901 TCCACTGCAAACTACATACGGAT 59.803 43.478 0.00 0.00 0.00 4.18
2474 7176 3.309682 CCACTGCAAACTACATACGGATG 59.690 47.826 5.94 5.94 39.16 3.51
2476 7178 5.106442 CACTGCAAACTACATACGGATGTA 58.894 41.667 19.32 19.32 44.77 2.29
2477 7179 5.753438 CACTGCAAACTACATACGGATGTAT 59.247 40.000 20.64 4.46 45.42 2.29
2478 7180 6.921307 CACTGCAAACTACATACGGATGTATA 59.079 38.462 20.64 1.71 45.42 1.47
2479 7181 7.598869 CACTGCAAACTACATACGGATGTATAT 59.401 37.037 20.64 9.64 45.42 0.86
2480 7182 7.598869 ACTGCAAACTACATACGGATGTATATG 59.401 37.037 20.64 18.49 45.42 1.78
2481 7183 6.871492 TGCAAACTACATACGGATGTATATGG 59.129 38.462 20.64 11.52 45.42 2.74
2482 7184 6.183360 GCAAACTACATACGGATGTATATGGC 60.183 42.308 20.64 16.54 45.42 4.40
2483 7185 5.593679 ACTACATACGGATGTATATGGCC 57.406 43.478 20.64 0.00 45.42 5.36
2484 7186 5.020795 ACTACATACGGATGTATATGGCCA 58.979 41.667 20.64 8.56 45.42 5.36
2485 7187 5.661312 ACTACATACGGATGTATATGGCCAT 59.339 40.000 24.45 24.45 45.42 4.40
2486 7188 6.837048 ACTACATACGGATGTATATGGCCATA 59.163 38.462 27.36 27.36 45.42 2.74
2487 7189 6.747414 ACATACGGATGTATATGGCCATAT 57.253 37.500 34.76 34.76 44.77 1.78
2488 7190 7.136822 ACATACGGATGTATATGGCCATATT 57.863 36.000 36.85 22.98 44.77 1.28
2489 7191 7.573710 ACATACGGATGTATATGGCCATATTT 58.426 34.615 36.85 23.96 44.77 1.40
2490 7192 8.052748 ACATACGGATGTATATGGCCATATTTT 58.947 33.333 36.85 23.65 44.77 1.82
2491 7193 9.554395 CATACGGATGTATATGGCCATATTTTA 57.446 33.333 36.85 24.69 39.28 1.52
2492 7194 9.778741 ATACGGATGTATATGGCCATATTTTAG 57.221 33.333 36.85 25.19 39.52 1.85
2493 7195 7.857456 ACGGATGTATATGGCCATATTTTAGA 58.143 34.615 36.85 21.53 35.71 2.10
2494 7196 7.987458 ACGGATGTATATGGCCATATTTTAGAG 59.013 37.037 36.85 26.03 35.71 2.43
2495 7197 7.987458 CGGATGTATATGGCCATATTTTAGAGT 59.013 37.037 36.85 18.02 35.71 3.24
2505 7207 9.944376 TGGCCATATTTTAGAGTATAGATTCAC 57.056 33.333 0.00 0.00 0.00 3.18
2517 7219 9.995003 AGAGTATAGATTCACTCATTTTGATCC 57.005 33.333 4.70 0.00 42.99 3.36
2518 7220 8.824159 AGTATAGATTCACTCATTTTGATCCG 57.176 34.615 0.00 0.00 0.00 4.18
2519 7221 8.424918 AGTATAGATTCACTCATTTTGATCCGT 58.575 33.333 0.00 0.00 0.00 4.69
2520 7222 9.692749 GTATAGATTCACTCATTTTGATCCGTA 57.307 33.333 0.00 0.00 0.00 4.02
2522 7224 7.721286 AGATTCACTCATTTTGATCCGTATC 57.279 36.000 0.00 0.00 0.00 2.24
2523 7225 7.504403 AGATTCACTCATTTTGATCCGTATCT 58.496 34.615 0.00 0.00 32.93 1.98
2524 7226 8.642432 AGATTCACTCATTTTGATCCGTATCTA 58.358 33.333 0.00 0.00 32.93 1.98
2525 7227 8.824159 ATTCACTCATTTTGATCCGTATCTAG 57.176 34.615 0.00 0.00 32.93 2.43
2526 7228 7.348080 TCACTCATTTTGATCCGTATCTAGT 57.652 36.000 0.00 0.00 32.93 2.57
2527 7229 7.426410 TCACTCATTTTGATCCGTATCTAGTC 58.574 38.462 0.00 0.00 32.93 2.59
2528 7230 6.642950 CACTCATTTTGATCCGTATCTAGTCC 59.357 42.308 0.00 0.00 32.93 3.85
2529 7231 6.323996 ACTCATTTTGATCCGTATCTAGTCCA 59.676 38.462 0.00 0.00 32.93 4.02
2530 7232 7.015682 ACTCATTTTGATCCGTATCTAGTCCAT 59.984 37.037 0.00 0.00 32.93 3.41
2531 7233 8.417273 TCATTTTGATCCGTATCTAGTCCATA 57.583 34.615 0.00 0.00 32.93 2.74
2532 7234 8.523658 TCATTTTGATCCGTATCTAGTCCATAG 58.476 37.037 0.00 0.00 32.93 2.23
2533 7235 7.834881 TTTTGATCCGTATCTAGTCCATAGT 57.165 36.000 0.00 0.00 32.93 2.12
2534 7236 6.819397 TTGATCCGTATCTAGTCCATAGTG 57.181 41.667 0.00 0.00 32.93 2.74
2535 7237 6.123045 TGATCCGTATCTAGTCCATAGTGA 57.877 41.667 0.00 0.00 32.93 3.41
2536 7238 6.540083 TGATCCGTATCTAGTCCATAGTGAA 58.460 40.000 0.00 0.00 32.93 3.18
2537 7239 7.002276 TGATCCGTATCTAGTCCATAGTGAAA 58.998 38.462 0.00 0.00 32.93 2.69
2538 7240 7.670140 TGATCCGTATCTAGTCCATAGTGAAAT 59.330 37.037 0.00 0.00 32.93 2.17
2539 7241 7.450124 TCCGTATCTAGTCCATAGTGAAATC 57.550 40.000 0.00 0.00 32.85 2.17
2540 7242 7.232188 TCCGTATCTAGTCCATAGTGAAATCT 58.768 38.462 0.00 0.00 32.85 2.40
2541 7243 7.390996 TCCGTATCTAGTCCATAGTGAAATCTC 59.609 40.741 0.00 0.00 32.85 2.75
2542 7244 7.392113 CCGTATCTAGTCCATAGTGAAATCTCT 59.608 40.741 0.00 0.00 32.85 3.10
2543 7245 9.438228 CGTATCTAGTCCATAGTGAAATCTCTA 57.562 37.037 0.00 0.00 32.85 2.43
2550 7252 9.660180 AGTCCATAGTGAAATCTCTAAAAAGAC 57.340 33.333 0.00 0.00 0.00 3.01
2551 7253 9.660180 GTCCATAGTGAAATCTCTAAAAAGACT 57.340 33.333 0.00 0.00 0.00 3.24
2570 7272 9.868160 AAAAGACTTATATTTAGGAATGGAGGG 57.132 33.333 0.00 0.00 0.00 4.30
2571 7273 8.814448 AAGACTTATATTTAGGAATGGAGGGA 57.186 34.615 0.00 0.00 0.00 4.20
2572 7274 8.442660 AGACTTATATTTAGGAATGGAGGGAG 57.557 38.462 0.00 0.00 0.00 4.30
2786 7488 8.328758 TCTGATATGGACCTATTTTGTTGTTCT 58.671 33.333 0.00 0.00 0.00 3.01
2787 7489 9.613428 CTGATATGGACCTATTTTGTTGTTCTA 57.387 33.333 0.00 0.00 0.00 2.10
2971 7678 9.838339 TCACCAAAATTTTCTGCCTTAATAAAA 57.162 25.926 0.00 0.00 0.00 1.52
3233 7941 1.898574 CAGCCCTTGTGAAACCGCT 60.899 57.895 0.00 0.00 34.36 5.52
3274 7982 4.684724 TCCCTAGCTCAAAAGGAAGAGTA 58.315 43.478 1.53 0.00 34.58 2.59
3587 8297 9.950680 CAAAAGTAAAGTTCTGCTCTCATTTAA 57.049 29.630 0.00 0.00 0.00 1.52
3639 8349 7.707104 AGCACTTACTTGATTTATGGCATAAC 58.293 34.615 19.11 9.79 0.00 1.89
3655 8365 3.556843 GCATAACTGGTTTGGTGCCAAAT 60.557 43.478 18.00 5.94 45.90 2.32
3725 8435 0.887387 GGTTACCGAGTTGCCTTGCA 60.887 55.000 0.00 0.00 36.47 4.08
4017 8727 5.056894 ACGTACTGCTCTTACGAAATTCT 57.943 39.130 15.98 0.00 44.11 2.40
4199 8924 2.096466 TGAACGCATTTGTAGCTTCACG 60.096 45.455 0.00 0.00 30.15 4.35
4455 9180 6.827586 TTTCTGTCCTATTTACGGCAAAAT 57.172 33.333 0.00 1.12 33.69 1.82
4604 9528 9.897744 ATCACTTAACTGTGTATGTCATTTTTG 57.102 29.630 0.00 0.00 38.90 2.44
4670 9594 2.224523 TGCCAGTTTCAGAGGTGGTTAG 60.225 50.000 0.00 0.00 32.20 2.34
4671 9595 2.224548 GCCAGTTTCAGAGGTGGTTAGT 60.225 50.000 0.00 0.00 32.20 2.24
4672 9596 3.403038 CCAGTTTCAGAGGTGGTTAGTG 58.597 50.000 0.00 0.00 0.00 2.74
4673 9597 3.403038 CAGTTTCAGAGGTGGTTAGTGG 58.597 50.000 0.00 0.00 0.00 4.00
4674 9598 3.046374 AGTTTCAGAGGTGGTTAGTGGT 58.954 45.455 0.00 0.00 0.00 4.16
4675 9599 3.458487 AGTTTCAGAGGTGGTTAGTGGTT 59.542 43.478 0.00 0.00 0.00 3.67
4676 9600 4.657039 AGTTTCAGAGGTGGTTAGTGGTTA 59.343 41.667 0.00 0.00 0.00 2.85
4725 9650 6.601613 TGTATGGACTGCAAGGGTTAATAAAG 59.398 38.462 0.00 0.00 39.30 1.85
5582 10511 6.653740 CGTTCCTAGGTGTTATCCTTTTCTTT 59.346 38.462 9.08 0.00 38.86 2.52
5672 10601 7.361127 GTTGCTCCTTATCAAATGAGATCATG 58.639 38.462 0.00 0.00 36.56 3.07
5915 10845 6.147164 TCCGTTGCTTACTGAAGTTAGATTTG 59.853 38.462 0.80 0.00 34.90 2.32
5939 10869 7.656412 TGTTTTCTTGCATGTGTACATAACAT 58.344 30.769 0.00 0.00 41.10 2.71
5988 10918 7.712264 TTCATCGAGCAAAATTTGAATGTTT 57.288 28.000 10.26 0.00 0.00 2.83
5994 10924 5.600696 AGCAAAATTTGAATGTTTCTCGGT 58.399 33.333 10.26 0.00 0.00 4.69
6348 12181 7.004086 TCCATTTCTTGGTTGATACTGACTTT 58.996 34.615 0.00 0.00 46.52 2.66
6375 12208 1.248101 ATTTGGCAGTGGTTACGGGC 61.248 55.000 0.00 0.00 45.43 6.13
6734 12568 8.911918 TTGTAGCCTTCATCTTTTGTAACTAA 57.088 30.769 0.00 0.00 0.00 2.24
6809 12643 5.551233 TGACTTCTACCCTTCAATCAACAG 58.449 41.667 0.00 0.00 0.00 3.16
6987 12821 4.398044 GGGTCTTGTGTATGTGTTTATGGG 59.602 45.833 0.00 0.00 0.00 4.00
7016 12850 7.340487 CAGCTCCTCCCTTATTTTTCTTATTGT 59.660 37.037 0.00 0.00 0.00 2.71
7063 12897 9.693157 CATTCTTTGTTTTGAAGTTTCAATCAC 57.307 29.630 8.02 8.66 45.65 3.06
7066 12900 7.973388 TCTTTGTTTTGAAGTTTCAATCACGAT 59.027 29.630 8.02 0.00 45.65 3.73
7162 12997 2.367030 TTGGCGCCATCATTTGAAAG 57.633 45.000 33.25 0.00 0.00 2.62
7163 12998 1.255882 TGGCGCCATCATTTGAAAGT 58.744 45.000 29.03 0.00 0.00 2.66
7164 12999 1.067706 TGGCGCCATCATTTGAAAGTG 60.068 47.619 29.03 0.00 0.00 3.16
7165 13000 0.994263 GCGCCATCATTTGAAAGTGC 59.006 50.000 0.00 3.86 32.33 4.40
7166 13001 1.669502 GCGCCATCATTTGAAAGTGCA 60.670 47.619 0.00 0.00 36.93 4.57
7167 13002 2.883574 CGCCATCATTTGAAAGTGCAT 58.116 42.857 0.00 0.00 0.00 3.96
7168 13003 2.855963 CGCCATCATTTGAAAGTGCATC 59.144 45.455 0.00 0.00 0.00 3.91
7169 13004 2.855963 GCCATCATTTGAAAGTGCATCG 59.144 45.455 0.00 0.00 0.00 3.84
7170 13005 3.441163 CCATCATTTGAAAGTGCATCGG 58.559 45.455 0.00 0.00 0.00 4.18
7171 13006 3.129113 CCATCATTTGAAAGTGCATCGGA 59.871 43.478 0.00 0.00 0.00 4.55
7172 13007 4.348656 CATCATTTGAAAGTGCATCGGAG 58.651 43.478 0.00 0.00 0.00 4.63
7173 13008 3.673902 TCATTTGAAAGTGCATCGGAGA 58.326 40.909 0.00 0.00 45.75 3.71
7330 13166 0.821301 TGGCAATTCCAGTCACGCAA 60.821 50.000 0.00 0.00 40.72 4.85
7348 13184 0.872388 AAGAACTAAACTTGCCGGCG 59.128 50.000 23.90 11.34 0.00 6.46
7353 13189 1.002142 ACTAAACTTGCCGGCGAAAAC 60.002 47.619 23.90 0.00 0.00 2.43
7471 13307 6.998673 AGCAATAGGAACCCACATAGAAATAC 59.001 38.462 0.00 0.00 0.00 1.89
7495 13331 2.236741 GCAAACCGCTTAAACCGTAG 57.763 50.000 0.00 0.00 37.77 3.51
7502 13338 3.434299 ACCGCTTAAACCGTAGACAAATG 59.566 43.478 0.00 0.00 0.00 2.32
7508 13344 3.896648 AACCGTAGACAAATGCACAAG 57.103 42.857 0.00 0.00 0.00 3.16
7524 13360 3.622612 GCACAAGCATCCAAACAAACTTT 59.377 39.130 0.00 0.00 41.58 2.66
7547 13383 0.461548 GTGATGGTGATGAGGCGAGA 59.538 55.000 0.00 0.00 0.00 4.04
7548 13384 1.134699 GTGATGGTGATGAGGCGAGAA 60.135 52.381 0.00 0.00 0.00 2.87
7553 13389 2.700371 TGGTGATGAGGCGAGAATATGT 59.300 45.455 0.00 0.00 0.00 2.29
7581 13417 9.616156 TTTATTAGGTTGTGTCAAAAGTGTAGA 57.384 29.630 0.00 0.00 0.00 2.59
7582 13418 9.787435 TTATTAGGTTGTGTCAAAAGTGTAGAT 57.213 29.630 0.00 0.00 0.00 1.98
7653 13489 6.098679 GCTCAGCTAGGATATGTTGATGTAG 58.901 44.000 0.00 0.00 0.00 2.74
7661 13497 6.525629 AGGATATGTTGATGTAGTACAAGCC 58.474 40.000 7.16 1.01 0.00 4.35
7667 13503 7.283625 TGTTGATGTAGTACAAGCCAAAAAT 57.716 32.000 7.16 0.00 0.00 1.82
7680 13516 2.096811 GCCAAAAATCATGTTGTGCACG 60.097 45.455 13.13 0.00 0.00 5.34
7682 13518 4.294232 CCAAAAATCATGTTGTGCACGTA 58.706 39.130 13.13 0.00 0.00 3.57
7749 13585 4.411327 CAACTGTTTGGTTGTGTGTAGTG 58.589 43.478 0.00 0.00 40.92 2.74
7763 13599 3.132111 TGTGTAGTGTCTTGTTCTGCTCA 59.868 43.478 0.00 0.00 0.00 4.26
7772 13608 2.154854 TGTTCTGCTCACCTCTTTCG 57.845 50.000 0.00 0.00 0.00 3.46
7790 13626 1.518056 CGAGCCACTTTGCACCACAT 61.518 55.000 0.00 0.00 0.00 3.21
7798 13634 2.760092 ACTTTGCACCACATTTCACAGT 59.240 40.909 0.00 0.00 0.00 3.55
7807 13643 7.065683 TGCACCACATTTCACAGTAACATATAG 59.934 37.037 0.00 0.00 0.00 1.31
7840 13676 0.718904 TGCGCACAATTAGCAGTACG 59.281 50.000 5.66 0.00 35.81 3.67
7876 13712 8.835467 ATCACGCAATTAACATTGTACATTAC 57.165 30.769 0.00 0.00 41.84 1.89
7893 13729 5.631119 ACATTACCACTTAAACAAGAGCCT 58.369 37.500 0.00 0.00 0.00 4.58
7907 13743 1.364626 GAGCCTCCTGCACAACATCG 61.365 60.000 0.00 0.00 44.83 3.84
7909 13745 1.915614 GCCTCCTGCACAACATCGTG 61.916 60.000 0.00 0.00 40.77 4.35
7970 13806 3.181443 TGGCATACGAGAGGACTAGATCA 60.181 47.826 0.00 0.00 0.00 2.92
7974 13810 2.937519 ACGAGAGGACTAGATCATGCA 58.062 47.619 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.539825 GACACTCAGATCAATTAGAACATATGT 57.460 33.333 1.41 1.41 0.00 2.29
50 53 8.641541 ACATTGTTATTCACCAAAACTTGAGAT 58.358 29.630 0.00 0.00 0.00 2.75
53 56 8.037758 ACAACATTGTTATTCACCAAAACTTGA 58.962 29.630 0.86 0.00 38.47 3.02
154 333 1.338389 GGCTAACAACGCTCCCTTACA 60.338 52.381 0.00 0.00 0.00 2.41
319 4758 1.557269 ATGCTTCGTGCCTTCTCCCT 61.557 55.000 1.30 0.00 42.00 4.20
407 4853 2.753849 TGGGTTAGGCAATGGCGC 60.754 61.111 0.00 0.00 42.47 6.53
539 5010 1.330521 CACGATGTTTGCCGAATAGGG 59.669 52.381 0.00 0.00 41.48 3.53
541 5012 4.518217 GATTCACGATGTTTGCCGAATAG 58.482 43.478 0.00 0.00 0.00 1.73
542 5013 3.000825 CGATTCACGATGTTTGCCGAATA 59.999 43.478 0.00 0.00 45.77 1.75
543 5014 2.223021 CGATTCACGATGTTTGCCGAAT 60.223 45.455 0.00 0.00 45.77 3.34
544 5015 1.127766 CGATTCACGATGTTTGCCGAA 59.872 47.619 0.00 0.00 45.77 4.30
545 5016 0.718904 CGATTCACGATGTTTGCCGA 59.281 50.000 0.00 0.00 45.77 5.54
546 5017 0.247655 CCGATTCACGATGTTTGCCG 60.248 55.000 0.00 0.00 45.77 5.69
548 5019 0.447801 AGCCGATTCACGATGTTTGC 59.552 50.000 0.00 0.00 45.77 3.68
555 5035 4.693566 AGTTTATTGAAAGCCGATTCACGA 59.306 37.500 0.00 0.00 45.77 4.35
560 5040 3.181500 GCCGAGTTTATTGAAAGCCGATT 60.181 43.478 0.00 0.00 0.00 3.34
569 5192 3.493699 CCGAATAGGGCCGAGTTTATTGA 60.494 47.826 0.00 0.00 35.97 2.57
639 5262 2.815945 CGCCTGGCCCATCATCTCT 61.816 63.158 14.12 0.00 0.00 3.10
704 5328 1.806623 GCACTAGATCGATTGGCCGTT 60.807 52.381 0.00 0.00 0.00 4.44
770 5394 1.486211 AACATAGCCACCTACGAGCT 58.514 50.000 0.00 0.00 40.66 4.09
808 5432 6.873997 ACTTCTTCCCAGAAAAATTCGTTTT 58.126 32.000 0.00 0.00 42.28 2.43
809 5433 6.465439 ACTTCTTCCCAGAAAAATTCGTTT 57.535 33.333 0.00 0.00 38.63 3.60
810 5434 6.465439 AACTTCTTCCCAGAAAAATTCGTT 57.535 33.333 0.00 0.00 38.63 3.85
811 5435 6.465439 AAACTTCTTCCCAGAAAAATTCGT 57.535 33.333 0.00 0.00 38.63 3.85
812 5436 8.135529 AGTAAAACTTCTTCCCAGAAAAATTCG 58.864 33.333 0.00 0.00 38.63 3.34
813 5437 9.249457 CAGTAAAACTTCTTCCCAGAAAAATTC 57.751 33.333 0.00 0.00 38.63 2.17
814 5438 8.758829 ACAGTAAAACTTCTTCCCAGAAAAATT 58.241 29.630 0.00 0.00 38.63 1.82
815 5439 8.306313 ACAGTAAAACTTCTTCCCAGAAAAAT 57.694 30.769 0.00 0.00 38.63 1.82
816 5440 7.712204 ACAGTAAAACTTCTTCCCAGAAAAA 57.288 32.000 0.00 0.00 38.63 1.94
817 5441 8.680001 GTTACAGTAAAACTTCTTCCCAGAAAA 58.320 33.333 0.00 0.00 38.63 2.29
818 5442 7.283807 GGTTACAGTAAAACTTCTTCCCAGAAA 59.716 37.037 0.00 0.00 38.63 2.52
819 5443 6.769341 GGTTACAGTAAAACTTCTTCCCAGAA 59.231 38.462 0.00 0.00 36.62 3.02
820 5444 6.293698 GGTTACAGTAAAACTTCTTCCCAGA 58.706 40.000 0.00 0.00 0.00 3.86
821 5445 5.178809 CGGTTACAGTAAAACTTCTTCCCAG 59.821 44.000 0.00 0.00 0.00 4.45
822 5446 5.058490 CGGTTACAGTAAAACTTCTTCCCA 58.942 41.667 0.00 0.00 0.00 4.37
823 5447 5.299949 TCGGTTACAGTAAAACTTCTTCCC 58.700 41.667 0.00 0.00 0.00 3.97
824 5448 6.218746 TCTCGGTTACAGTAAAACTTCTTCC 58.781 40.000 0.00 0.00 0.00 3.46
825 5449 7.704789 TTCTCGGTTACAGTAAAACTTCTTC 57.295 36.000 0.00 0.00 0.00 2.87
826 5450 8.496707 TTTTCTCGGTTACAGTAAAACTTCTT 57.503 30.769 0.00 0.00 0.00 2.52
827 5451 8.496707 TTTTTCTCGGTTACAGTAAAACTTCT 57.503 30.769 0.00 0.00 0.00 2.85
830 5454 8.501580 GCTATTTTTCTCGGTTACAGTAAAACT 58.498 33.333 0.00 0.00 0.00 2.66
838 5462 5.637810 CAGACAGCTATTTTTCTCGGTTACA 59.362 40.000 0.00 0.00 0.00 2.41
839 5463 5.867716 TCAGACAGCTATTTTTCTCGGTTAC 59.132 40.000 0.00 0.00 0.00 2.50
843 5467 4.245660 TGTCAGACAGCTATTTTTCTCGG 58.754 43.478 0.00 0.00 0.00 4.63
847 5471 7.530861 CGTAAAGTTGTCAGACAGCTATTTTTC 59.469 37.037 19.28 8.19 38.76 2.29
852 5476 5.135508 ACGTAAAGTTGTCAGACAGCTAT 57.864 39.130 19.28 8.02 38.76 2.97
955 5582 8.487313 AGGTAAAGCGTTTTGAAAAGAAAAAT 57.513 26.923 7.57 0.00 0.00 1.82
1093 5720 1.457831 GTGGGGGTAGGAGATCGCT 60.458 63.158 0.00 0.00 0.00 4.93
1681 6330 0.257039 GGAGGGTGATTCTGCCACAT 59.743 55.000 0.00 0.00 36.31 3.21
1738 6387 1.997311 CTCCATGTCCAGGCTCCCA 60.997 63.158 0.00 0.00 0.00 4.37
1915 6609 0.036164 TGGAGCCTGAGCGCTAAAAA 59.964 50.000 11.50 0.00 46.67 1.94
1922 6617 1.817099 GTTCCATGGAGCCTGAGCG 60.817 63.158 17.35 0.00 46.67 5.03
2292 6991 2.746279 TGGTGCCCTTCTTTTCTGAA 57.254 45.000 0.00 0.00 0.00 3.02
2328 7030 4.036734 TGAAGAAACAAGAGTGTGGCATTC 59.963 41.667 0.00 0.00 38.27 2.67
2413 7115 3.716431 ACATTTAGGAACGGAGGGAGTA 58.284 45.455 0.00 0.00 0.00 2.59
2414 7116 2.547990 ACATTTAGGAACGGAGGGAGT 58.452 47.619 0.00 0.00 0.00 3.85
2415 7117 4.161754 ACTTACATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
2416 7118 4.098894 ACTTACATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
2417 7119 4.161754 AGACTTACATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
2418 7120 5.340439 AGACTTACATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
2419 7121 7.668525 AAAAGACTTACATTTAGGAACGGAG 57.331 36.000 0.00 0.00 0.00 4.63
2420 7122 9.211485 CTAAAAAGACTTACATTTAGGAACGGA 57.789 33.333 8.91 0.00 33.69 4.69
2421 7123 9.211485 TCTAAAAAGACTTACATTTAGGAACGG 57.789 33.333 13.94 0.00 36.48 4.44
2431 7133 9.442047 CAGTGGAATCTCTAAAAAGACTTACAT 57.558 33.333 0.00 0.00 0.00 2.29
2432 7134 7.387948 GCAGTGGAATCTCTAAAAAGACTTACA 59.612 37.037 0.00 0.00 0.00 2.41
2433 7135 7.387948 TGCAGTGGAATCTCTAAAAAGACTTAC 59.612 37.037 0.00 0.00 0.00 2.34
2434 7136 7.450074 TGCAGTGGAATCTCTAAAAAGACTTA 58.550 34.615 0.00 0.00 0.00 2.24
2435 7137 6.299141 TGCAGTGGAATCTCTAAAAAGACTT 58.701 36.000 0.00 0.00 0.00 3.01
2436 7138 5.869579 TGCAGTGGAATCTCTAAAAAGACT 58.130 37.500 0.00 0.00 0.00 3.24
2437 7139 6.560253 TTGCAGTGGAATCTCTAAAAAGAC 57.440 37.500 0.00 0.00 0.00 3.01
2438 7140 6.772716 AGTTTGCAGTGGAATCTCTAAAAAGA 59.227 34.615 0.00 0.00 0.00 2.52
2439 7141 6.974965 AGTTTGCAGTGGAATCTCTAAAAAG 58.025 36.000 0.00 0.00 0.00 2.27
2440 7142 6.959639 AGTTTGCAGTGGAATCTCTAAAAA 57.040 33.333 0.00 0.00 0.00 1.94
2441 7143 6.995686 TGTAGTTTGCAGTGGAATCTCTAAAA 59.004 34.615 10.82 0.00 0.00 1.52
2442 7144 6.530120 TGTAGTTTGCAGTGGAATCTCTAAA 58.470 36.000 10.82 2.01 0.00 1.85
2443 7145 6.109156 TGTAGTTTGCAGTGGAATCTCTAA 57.891 37.500 10.82 0.00 0.00 2.10
2444 7146 5.738619 TGTAGTTTGCAGTGGAATCTCTA 57.261 39.130 10.82 5.97 0.00 2.43
2445 7147 4.623932 TGTAGTTTGCAGTGGAATCTCT 57.376 40.909 10.82 6.81 0.00 3.10
2446 7148 5.005779 CGTATGTAGTTTGCAGTGGAATCTC 59.994 44.000 10.82 5.07 0.00 2.75
2447 7149 4.870426 CGTATGTAGTTTGCAGTGGAATCT 59.130 41.667 11.99 11.99 0.00 2.40
2448 7150 4.034048 CCGTATGTAGTTTGCAGTGGAATC 59.966 45.833 0.00 0.00 0.00 2.52
2449 7151 3.938963 CCGTATGTAGTTTGCAGTGGAAT 59.061 43.478 0.00 0.00 0.00 3.01
2450 7152 3.007074 TCCGTATGTAGTTTGCAGTGGAA 59.993 43.478 0.00 0.00 0.00 3.53
2451 7153 2.563620 TCCGTATGTAGTTTGCAGTGGA 59.436 45.455 0.00 0.00 0.00 4.02
2452 7154 2.967362 TCCGTATGTAGTTTGCAGTGG 58.033 47.619 0.00 0.00 0.00 4.00
2453 7155 3.932710 ACATCCGTATGTAGTTTGCAGTG 59.067 43.478 0.00 0.00 44.66 3.66
2454 7156 4.202245 ACATCCGTATGTAGTTTGCAGT 57.798 40.909 0.00 0.00 44.66 4.40
2465 7167 8.450578 AAAATATGGCCATATACATCCGTATG 57.549 34.615 33.47 0.00 38.79 2.39
2466 7168 9.778741 CTAAAATATGGCCATATACATCCGTAT 57.221 33.333 33.47 15.35 41.34 3.06
2467 7169 8.983789 TCTAAAATATGGCCATATACATCCGTA 58.016 33.333 33.47 17.70 33.86 4.02
2468 7170 7.857456 TCTAAAATATGGCCATATACATCCGT 58.143 34.615 33.47 16.71 33.86 4.69
2469 7171 7.987458 ACTCTAAAATATGGCCATATACATCCG 59.013 37.037 33.47 22.83 33.86 4.18
2479 7181 9.944376 GTGAATCTATACTCTAAAATATGGCCA 57.056 33.333 8.56 8.56 0.00 5.36
2491 7193 9.995003 GGATCAAAATGAGTGAATCTATACTCT 57.005 33.333 0.00 0.00 42.86 3.24
2492 7194 8.920665 CGGATCAAAATGAGTGAATCTATACTC 58.079 37.037 0.00 0.00 42.77 2.59
2493 7195 8.424918 ACGGATCAAAATGAGTGAATCTATACT 58.575 33.333 0.00 0.00 0.00 2.12
2494 7196 8.594881 ACGGATCAAAATGAGTGAATCTATAC 57.405 34.615 0.00 0.00 0.00 1.47
2496 7198 9.429359 GATACGGATCAAAATGAGTGAATCTAT 57.571 33.333 1.67 0.00 31.78 1.98
2497 7199 8.642432 AGATACGGATCAAAATGAGTGAATCTA 58.358 33.333 10.99 0.00 34.17 1.98
2498 7200 7.504403 AGATACGGATCAAAATGAGTGAATCT 58.496 34.615 10.99 0.00 34.17 2.40
2499 7201 7.721286 AGATACGGATCAAAATGAGTGAATC 57.279 36.000 10.99 0.00 34.17 2.52
2500 7202 8.424918 ACTAGATACGGATCAAAATGAGTGAAT 58.575 33.333 10.99 0.00 34.17 2.57
2501 7203 7.782049 ACTAGATACGGATCAAAATGAGTGAA 58.218 34.615 10.99 0.00 34.17 3.18
2502 7204 7.348080 ACTAGATACGGATCAAAATGAGTGA 57.652 36.000 10.99 0.00 34.17 3.41
2503 7205 6.642950 GGACTAGATACGGATCAAAATGAGTG 59.357 42.308 10.99 0.00 34.17 3.51
2504 7206 6.323996 TGGACTAGATACGGATCAAAATGAGT 59.676 38.462 10.99 2.97 34.17 3.41
2505 7207 6.749139 TGGACTAGATACGGATCAAAATGAG 58.251 40.000 10.99 0.00 34.17 2.90
2506 7208 6.724893 TGGACTAGATACGGATCAAAATGA 57.275 37.500 10.99 0.00 34.17 2.57
2507 7209 8.307483 ACTATGGACTAGATACGGATCAAAATG 58.693 37.037 10.99 0.00 34.17 2.32
2508 7210 8.307483 CACTATGGACTAGATACGGATCAAAAT 58.693 37.037 10.99 0.00 34.17 1.82
2509 7211 7.504574 TCACTATGGACTAGATACGGATCAAAA 59.495 37.037 10.99 0.00 34.17 2.44
2510 7212 7.002276 TCACTATGGACTAGATACGGATCAAA 58.998 38.462 10.99 0.00 34.17 2.69
2511 7213 6.540083 TCACTATGGACTAGATACGGATCAA 58.460 40.000 10.99 0.00 34.17 2.57
2512 7214 6.123045 TCACTATGGACTAGATACGGATCA 57.877 41.667 10.99 0.00 34.17 2.92
2513 7215 7.450124 TTTCACTATGGACTAGATACGGATC 57.550 40.000 0.00 0.00 0.00 3.36
2514 7216 7.891183 AGATTTCACTATGGACTAGATACGGAT 59.109 37.037 0.00 0.00 0.00 4.18
2515 7217 7.232188 AGATTTCACTATGGACTAGATACGGA 58.768 38.462 0.00 0.00 0.00 4.69
2516 7218 7.392113 AGAGATTTCACTATGGACTAGATACGG 59.608 40.741 0.00 0.00 0.00 4.02
2517 7219 8.330466 AGAGATTTCACTATGGACTAGATACG 57.670 38.462 0.00 0.00 0.00 3.06
2524 7226 9.660180 GTCTTTTTAGAGATTTCACTATGGACT 57.340 33.333 0.00 0.00 0.00 3.85
2525 7227 9.660180 AGTCTTTTTAGAGATTTCACTATGGAC 57.340 33.333 0.00 0.00 0.00 4.02
2544 7246 9.868160 CCCTCCATTCCTAAATATAAGTCTTTT 57.132 33.333 0.00 0.00 0.00 2.27
2545 7247 9.237706 TCCCTCCATTCCTAAATATAAGTCTTT 57.762 33.333 0.00 0.00 0.00 2.52
2546 7248 8.814448 TCCCTCCATTCCTAAATATAAGTCTT 57.186 34.615 0.00 0.00 0.00 3.01
2547 7249 8.019652 ACTCCCTCCATTCCTAAATATAAGTCT 58.980 37.037 0.00 0.00 0.00 3.24
2548 7250 8.208575 ACTCCCTCCATTCCTAAATATAAGTC 57.791 38.462 0.00 0.00 0.00 3.01
2549 7251 9.102453 GTACTCCCTCCATTCCTAAATATAAGT 57.898 37.037 0.00 0.00 0.00 2.24
2550 7252 8.251721 CGTACTCCCTCCATTCCTAAATATAAG 58.748 40.741 0.00 0.00 0.00 1.73
2551 7253 7.731688 ACGTACTCCCTCCATTCCTAAATATAA 59.268 37.037 0.00 0.00 0.00 0.98
2552 7254 7.243824 ACGTACTCCCTCCATTCCTAAATATA 58.756 38.462 0.00 0.00 0.00 0.86
2553 7255 6.082707 ACGTACTCCCTCCATTCCTAAATAT 58.917 40.000 0.00 0.00 0.00 1.28
2554 7256 5.461327 ACGTACTCCCTCCATTCCTAAATA 58.539 41.667 0.00 0.00 0.00 1.40
2555 7257 4.296056 ACGTACTCCCTCCATTCCTAAAT 58.704 43.478 0.00 0.00 0.00 1.40
2556 7258 3.716431 ACGTACTCCCTCCATTCCTAAA 58.284 45.455 0.00 0.00 0.00 1.85
2557 7259 3.393426 ACGTACTCCCTCCATTCCTAA 57.607 47.619 0.00 0.00 0.00 2.69
2558 7260 3.393426 AACGTACTCCCTCCATTCCTA 57.607 47.619 0.00 0.00 0.00 2.94
2559 7261 2.249309 AACGTACTCCCTCCATTCCT 57.751 50.000 0.00 0.00 0.00 3.36
2560 7262 4.684484 AATAACGTACTCCCTCCATTCC 57.316 45.455 0.00 0.00 0.00 3.01
2561 7263 5.055144 GGAAATAACGTACTCCCTCCATTC 58.945 45.833 0.00 0.00 0.00 2.67
2562 7264 4.472108 TGGAAATAACGTACTCCCTCCATT 59.528 41.667 0.00 0.00 0.00 3.16
2563 7265 4.035112 TGGAAATAACGTACTCCCTCCAT 58.965 43.478 0.00 0.00 0.00 3.41
2564 7266 3.443052 TGGAAATAACGTACTCCCTCCA 58.557 45.455 0.00 0.00 0.00 3.86
2565 7267 4.684484 ATGGAAATAACGTACTCCCTCC 57.316 45.455 0.00 0.00 0.00 4.30
2566 7268 7.713942 ACAAATATGGAAATAACGTACTCCCTC 59.286 37.037 0.00 0.00 0.00 4.30
2567 7269 7.571025 ACAAATATGGAAATAACGTACTCCCT 58.429 34.615 0.00 0.00 0.00 4.20
2568 7270 7.797038 ACAAATATGGAAATAACGTACTCCC 57.203 36.000 0.00 0.00 0.00 4.30
2969 7676 9.606631 TTAACTGCACATTTTCCAAAAGTATTT 57.393 25.926 0.00 0.00 42.41 1.40
2970 7677 9.260002 CTTAACTGCACATTTTCCAAAAGTATT 57.740 29.630 0.00 0.00 0.00 1.89
2971 7678 8.421002 ACTTAACTGCACATTTTCCAAAAGTAT 58.579 29.630 0.00 0.00 0.00 2.12
2972 7679 7.777095 ACTTAACTGCACATTTTCCAAAAGTA 58.223 30.769 0.00 0.00 0.00 2.24
3639 8349 3.598299 CCAATATTTGGCACCAAACCAG 58.402 45.455 16.76 7.64 46.80 4.00
3897 8607 8.699749 GCAACAGTACTTTTACAATTTCCATTC 58.300 33.333 0.00 0.00 0.00 2.67
4017 8727 9.393512 CATTCAAAATTTGGAAATATGCCCTTA 57.606 29.630 11.99 0.00 0.00 2.69
4055 8765 7.281549 GTGGACCCAAAAATGTATAACTACGAT 59.718 37.037 0.00 0.00 0.00 3.73
4604 9528 3.807071 CACCAAAGCAAAACCACCAATAC 59.193 43.478 0.00 0.00 0.00 1.89
4670 9594 1.134788 CCTCCCGAGTCATGTAACCAC 60.135 57.143 0.00 0.00 0.00 4.16
4671 9595 1.191535 CCTCCCGAGTCATGTAACCA 58.808 55.000 0.00 0.00 0.00 3.67
4672 9596 1.481871 TCCTCCCGAGTCATGTAACC 58.518 55.000 0.00 0.00 0.00 2.85
4673 9597 2.758979 TCTTCCTCCCGAGTCATGTAAC 59.241 50.000 0.00 0.00 0.00 2.50
4674 9598 3.024547 CTCTTCCTCCCGAGTCATGTAA 58.975 50.000 0.00 0.00 0.00 2.41
4675 9599 2.656002 CTCTTCCTCCCGAGTCATGTA 58.344 52.381 0.00 0.00 0.00 2.29
4676 9600 1.479709 CTCTTCCTCCCGAGTCATGT 58.520 55.000 0.00 0.00 0.00 3.21
4899 9824 0.387202 CACACCGGCCAAACATTTCA 59.613 50.000 0.00 0.00 0.00 2.69
5003 9928 3.066621 TGGTGCAGAACAACAATTGACTC 59.933 43.478 13.59 2.85 45.14 3.36
5004 9929 3.023119 TGGTGCAGAACAACAATTGACT 58.977 40.909 13.59 0.00 45.14 3.41
5005 9930 3.435105 TGGTGCAGAACAACAATTGAC 57.565 42.857 13.59 0.00 45.14 3.18
5582 10511 0.467290 GAGCCAACAAACCCCTGTCA 60.467 55.000 0.00 0.00 0.00 3.58
5672 10601 7.281100 CAGGATAGAAAAGAATAAGGTGACACC 59.719 40.741 17.43 17.43 38.99 4.16
5915 10845 9.787532 ATATGTTATGTACACATGCAAGAAAAC 57.212 29.630 0.00 0.99 40.19 2.43
5988 10918 5.359860 ACATGATATTGTACTGTCACCGAGA 59.640 40.000 0.00 0.00 0.00 4.04
5994 10924 6.643388 AGAGCAACATGATATTGTACTGTCA 58.357 36.000 0.00 0.00 0.00 3.58
6348 12181 4.414337 AACCACTGCCAAATAAAAGCAA 57.586 36.364 0.00 0.00 35.79 3.91
6375 12208 1.813102 AGGAAGGCTTGGATAGGAGG 58.187 55.000 3.46 0.00 0.00 4.30
6478 12311 1.217779 GTGTCAGGAGGAGCAGCTC 59.782 63.158 14.69 14.69 0.00 4.09
6708 12542 9.515226 TTAGTTACAAAAGATGAAGGCTACAAT 57.485 29.630 0.00 0.00 0.00 2.71
6734 12568 2.746362 GCAGATGCAGTGTTAAAGAGCT 59.254 45.455 0.00 0.00 41.59 4.09
6987 12821 3.653835 AAAATAAGGGAGGAGCTGGAC 57.346 47.619 0.00 0.00 0.00 4.02
7016 12850 7.549134 AGAATGATGACAGCATAAACGACTTAA 59.451 33.333 6.62 0.00 34.11 1.85
7063 12897 2.995258 CAGGCAAATTCCACCAAAATCG 59.005 45.455 0.00 0.00 0.00 3.34
7066 12900 2.768527 TGACAGGCAAATTCCACCAAAA 59.231 40.909 0.00 0.00 0.00 2.44
7162 12997 1.202222 CCATTGCTTTCTCCGATGCAC 60.202 52.381 0.00 0.00 35.01 4.57
7163 12998 1.097232 CCATTGCTTTCTCCGATGCA 58.903 50.000 0.00 0.00 0.00 3.96
7164 12999 0.383231 CCCATTGCTTTCTCCGATGC 59.617 55.000 0.00 0.00 0.00 3.91
7165 13000 0.383231 GCCCATTGCTTTCTCCGATG 59.617 55.000 0.00 0.00 36.87 3.84
7166 13001 1.097547 CGCCCATTGCTTTCTCCGAT 61.098 55.000 0.00 0.00 38.05 4.18
7167 13002 1.745115 CGCCCATTGCTTTCTCCGA 60.745 57.895 0.00 0.00 38.05 4.55
7168 13003 2.793946 CGCCCATTGCTTTCTCCG 59.206 61.111 0.00 0.00 38.05 4.63
7169 13004 0.748005 TAGCGCCCATTGCTTTCTCC 60.748 55.000 2.29 0.00 43.71 3.71
7170 13005 1.265365 GATAGCGCCCATTGCTTTCTC 59.735 52.381 2.29 0.00 43.71 2.87
7171 13006 1.312815 GATAGCGCCCATTGCTTTCT 58.687 50.000 2.29 0.00 43.71 2.52
7172 13007 1.024271 TGATAGCGCCCATTGCTTTC 58.976 50.000 2.29 0.00 43.71 2.62
7173 13008 1.338973 CATGATAGCGCCCATTGCTTT 59.661 47.619 2.29 0.00 43.71 3.51
7255 13091 7.874016 ACCTAACGTGTGACACTTATATTTCAA 59.126 33.333 14.42 0.00 31.34 2.69
7272 13108 3.979789 TGCCATGCACCTAACGTG 58.020 55.556 0.00 0.00 46.03 4.49
7319 13155 3.131396 AGTTTAGTTCTTGCGTGACTGG 58.869 45.455 0.00 0.00 0.00 4.00
7321 13157 4.795970 CAAGTTTAGTTCTTGCGTGACT 57.204 40.909 0.00 0.00 36.38 3.41
7330 13166 0.034337 TCGCCGGCAAGTTTAGTTCT 59.966 50.000 28.98 0.00 0.00 3.01
7348 13184 5.440685 CACATGACAACTCCTAACGTTTTC 58.559 41.667 5.91 0.00 0.00 2.29
7353 13189 2.668457 GAGCACATGACAACTCCTAACG 59.332 50.000 0.00 0.00 0.00 3.18
7487 13323 3.550030 GCTTGTGCATTTGTCTACGGTTT 60.550 43.478 0.00 0.00 39.41 3.27
7502 13338 2.825205 AGTTTGTTTGGATGCTTGTGC 58.175 42.857 0.00 0.00 40.20 4.57
7508 13344 5.537188 TCACCATAAAGTTTGTTTGGATGC 58.463 37.500 16.49 0.00 0.00 3.91
7524 13360 1.070601 CGCCTCATCACCATCACCATA 59.929 52.381 0.00 0.00 0.00 2.74
7653 13489 5.333263 GCACAACATGATTTTTGGCTTGTAC 60.333 40.000 0.00 0.00 0.00 2.90
7661 13497 4.975502 ACTACGTGCACAACATGATTTTTG 59.024 37.500 18.64 0.00 38.75 2.44
7667 13503 3.198872 TCAAACTACGTGCACAACATGA 58.801 40.909 18.64 9.96 38.75 3.07
7682 13518 9.607285 CGCTAAAACATAACAAACTATCAAACT 57.393 29.630 0.00 0.00 0.00 2.66
7745 13581 2.965831 AGGTGAGCAGAACAAGACACTA 59.034 45.455 0.00 0.00 0.00 2.74
7749 13585 2.829741 AGAGGTGAGCAGAACAAGAC 57.170 50.000 0.00 0.00 0.00 3.01
7772 13608 0.675633 AATGTGGTGCAAAGTGGCTC 59.324 50.000 0.00 0.00 34.04 4.70
7790 13626 8.261522 TGGTATGTGCTATATGTTACTGTGAAA 58.738 33.333 0.00 0.00 0.00 2.69
7798 13634 7.307692 CGCATGTTTGGTATGTGCTATATGTTA 60.308 37.037 0.00 0.00 33.82 2.41
7840 13676 8.334016 TGTTAATTGCGTGATAAAATGTATGC 57.666 30.769 0.00 0.00 0.00 3.14
7876 13712 3.077359 CAGGAGGCTCTTGTTTAAGTGG 58.923 50.000 17.73 0.00 35.38 4.00
7893 13729 0.682292 TACCACGATGTTGTGCAGGA 59.318 50.000 0.00 0.00 38.55 3.86
7907 13743 8.409358 AATATTTGCTCAGGGAATAATACCAC 57.591 34.615 0.00 0.00 0.00 4.16
7909 13745 8.635765 TGAATATTTGCTCAGGGAATAATACC 57.364 34.615 0.00 0.00 0.00 2.73
7950 13786 4.674101 GCATGATCTAGTCCTCTCGTATGC 60.674 50.000 0.00 0.00 0.00 3.14
7956 13792 3.554752 GGCTTGCATGATCTAGTCCTCTC 60.555 52.174 3.33 0.00 0.00 3.20
7970 13806 0.892755 CAAGGTGACATGGCTTGCAT 59.107 50.000 0.00 0.00 0.00 3.96
7974 13810 4.080129 ACATCTATCAAGGTGACATGGCTT 60.080 41.667 0.00 0.00 35.72 4.35
7983 13819 2.357009 GCCAAGCACATCTATCAAGGTG 59.643 50.000 0.00 0.00 39.95 4.00
7984 13820 2.025981 TGCCAAGCACATCTATCAAGGT 60.026 45.455 0.00 0.00 31.71 3.50


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

AutoCloner maintained by Alex Coulton.