Multiple sequence alignment - TraesCS5A01G204200

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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 TraesCS5A01G204200 chr5A 100.000 7111 0 0 1 7111 413423285 413416175 0.000000e+00 13132.0
1 TraesCS5A01G204200 chr5A 80.843 261 38 7 3095 3347 32837074 32836818 2.020000e-45 195.0
2 TraesCS5A01G204200 chr5B 95.255 2318 81 20 3798 6106 372092541 372094838 0.000000e+00 3644.0
3 TraesCS5A01G204200 chr5B 89.425 2156 143 44 1 2139 372088813 372090900 0.000000e+00 2639.0
4 TraesCS5A01G204200 chr5B 90.646 1625 102 16 2142 3739 372090939 372092540 0.000000e+00 2113.0
5 TraesCS5A01G204200 chr5B 89.095 431 37 7 6397 6823 372095081 372095505 1.760000e-145 527.0
6 TraesCS5A01G204200 chr5B 96.154 104 4 0 6194 6297 372094845 372094948 3.410000e-38 171.0
7 TraesCS5A01G204200 chr5B 98.387 62 1 0 6256 6317 372094948 372095009 7.540000e-20 110.0
8 TraesCS5A01G204200 chr5D 96.771 1982 48 12 3737 5706 320884198 320886175 0.000000e+00 3291.0
9 TraesCS5A01G204200 chr5D 92.547 1610 82 19 2140 3743 320882527 320884104 0.000000e+00 2274.0
10 TraesCS5A01G204200 chr5D 91.313 1485 48 22 668 2139 320880649 320882065 0.000000e+00 1953.0
11 TraesCS5A01G204200 chr5D 96.000 700 17 5 5704 6395 320886288 320886984 0.000000e+00 1127.0
12 TraesCS5A01G204200 chr5D 88.342 386 19 7 6569 6951 320887133 320887495 2.350000e-119 440.0
13 TraesCS5A01G204200 chr5D 91.593 226 16 2 2140 2364 320882102 320882325 6.930000e-80 309.0
14 TraesCS5A01G204200 chr5D 97.468 158 4 0 1982 2139 320882333 320882490 3.270000e-68 270.0
15 TraesCS5A01G204200 chr5D 85.185 216 27 2 7 218 320880395 320880609 4.320000e-52 217.0
16 TraesCS5A01G204200 chr5D 93.023 86 5 1 3724 3808 320884176 320884091 2.690000e-24 124.0
17 TraesCS5A01G204200 chr5D 84.722 72 2 5 6989 7060 320887490 320887552 5.960000e-06 63.9
18 TraesCS5A01G204200 chr3A 92.133 1144 64 13 2608 3741 64996609 64995482 0.000000e+00 1591.0
19 TraesCS5A01G204200 chr3A 95.745 846 29 6 3802 4646 64995474 64994635 0.000000e+00 1356.0
20 TraesCS5A01G204200 chr3D 95.296 829 33 5 3818 4646 53616548 53615726 0.000000e+00 1310.0
21 TraesCS5A01G204200 chr3D 91.844 282 20 2 3445 3723 53616840 53616559 2.410000e-104 390.0
22 TraesCS5A01G204200 chr3D 91.860 86 4 3 3724 3808 595302866 595302949 4.510000e-22 117.0
23 TraesCS5A01G204200 chr3B 98.544 206 3 0 4238 4443 84442047 84441842 1.460000e-96 364.0
24 TraesCS5A01G204200 chr3B 93.665 221 11 2 4029 4246 84443910 84443690 1.910000e-85 327.0
25 TraesCS5A01G204200 chr3B 95.238 189 7 2 4458 4646 84437995 84437809 1.500000e-76 298.0
26 TraesCS5A01G204200 chr7B 87.671 146 18 0 2858 3003 704660896 704661041 3.410000e-38 171.0
27 TraesCS5A01G204200 chr7D 97.333 75 2 0 3729 3803 6767751 6767677 2.080000e-25 128.0
28 TraesCS5A01G204200 chr1A 97.297 74 2 0 3730 3803 84012456 84012383 7.490000e-25 126.0
29 TraesCS5A01G204200 chr6A 96.053 76 3 0 3731 3806 579400083 579400158 2.690000e-24 124.0
30 TraesCS5A01G204200 chr1B 93.902 82 4 1 3724 3804 615124065 615123984 9.690000e-24 122.0
31 TraesCS5A01G204200 chr1B 92.771 83 4 2 3719 3800 428810776 428810857 1.250000e-22 119.0
32 TraesCS5A01G204200 chr1D 91.667 84 7 0 3719 3802 87667493 87667410 4.510000e-22 117.0


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 TraesCS5A01G204200 chr5A 413416175 413423285 7110 True 13132.000000 13132 100.000000 1 7111 1 chr5A.!!$R2 7110
1 TraesCS5A01G204200 chr5B 372088813 372095505 6692 False 1534.000000 3644 93.160333 1 6823 6 chr5B.!!$F1 6822
2 TraesCS5A01G204200 chr5D 320880395 320887552 7157 False 1104.988889 3291 91.549000 7 7060 9 chr5D.!!$F1 7053
3 TraesCS5A01G204200 chr3A 64994635 64996609 1974 True 1473.500000 1591 93.939000 2608 4646 2 chr3A.!!$R1 2038
4 TraesCS5A01G204200 chr3D 53615726 53616840 1114 True 850.000000 1310 93.570000 3445 4646 2 chr3D.!!$R1 1201
5 TraesCS5A01G204200 chr3B 84437809 84443910 6101 True 329.666667 364 95.815667 4029 4646 3 chr3B.!!$R1 617

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
799 829 1.081242 GCCAAACGCACATCACTGG 60.081 57.895 0.00 0.00 37.47 4.00 F
1246 1289 0.102120 CTCCCGATCTGTCTGTCTGC 59.898 60.000 0.00 0.00 0.00 4.26 F
1484 1527 0.242825 TGCGGAGTTCGTCTAGGTTG 59.757 55.000 0.00 0.00 41.72 3.77 F
2507 3043 0.695924 TTTGCTAGCTAGGGCCAACA 59.304 50.000 22.10 7.58 39.73 3.33 F
2763 3299 2.885135 ACCAGCATGTGAATTCCTGA 57.115 45.000 2.27 0.00 0.00 3.86 F
4112 4763 0.737219 GCCATGAGATGCACAAGTCC 59.263 55.000 0.00 0.00 0.00 3.85 F
5019 11162 2.203126 GATCCTGCCCTGGCTTCG 60.203 66.667 9.97 0.00 42.51 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2574 3110 0.035439 ACGGCAAAGACCCCAGTATG 60.035 55.000 0.00 0.0 0.00 2.39 R
2575 3111 0.035439 CACGGCAAAGACCCCAGTAT 60.035 55.000 0.00 0.0 0.00 2.12 R
2920 3456 0.809385 TTTCCTCCAGCGTAGTCTCG 59.191 55.000 0.00 0.0 0.00 4.04 R
3498 4045 0.517316 GGCAAAAGGTACTGTCTGCG 59.483 55.000 0.00 0.0 40.86 5.18 R
4185 4840 3.511477 ACCTTTTGAGACTCTCCTGCTA 58.489 45.455 3.68 0.0 0.00 3.49 R
5148 11301 0.038251 GCAAGGTACAAAGGGCAAGC 60.038 55.000 0.00 0.0 0.00 4.01 R
6956 13313 0.036875 GACTTGACCCCACCCTCTTG 59.963 60.000 0.00 0.0 0.00 3.02 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
56 57 7.050377 CCCTCTCATTTTTCTATGCTTACTCA 58.950 38.462 0.00 0.00 0.00 3.41
68 69 7.840931 TCTATGCTTACTCAAGAAACTGATGA 58.159 34.615 0.00 0.00 33.20 2.92
75 76 5.440610 ACTCAAGAAACTGATGAAGGTGTT 58.559 37.500 0.00 0.00 0.00 3.32
81 82 7.352079 AGAAACTGATGAAGGTGTTGATTTT 57.648 32.000 0.00 0.00 0.00 1.82
144 149 3.130693 CCGGGGTTTTTACAACAACAAGA 59.869 43.478 0.00 0.00 0.00 3.02
145 150 4.106909 CGGGGTTTTTACAACAACAAGAC 58.893 43.478 0.00 0.00 0.00 3.01
202 207 4.520874 TGATTTTCAATACCTTTCGTGGCA 59.479 37.500 0.00 0.00 0.00 4.92
204 209 2.851263 TCAATACCTTTCGTGGCACT 57.149 45.000 16.72 0.00 0.00 4.40
214 219 3.955771 TTCGTGGCACTCTTAACAAAC 57.044 42.857 16.72 0.00 0.00 2.93
262 280 1.643811 AGGGGCTAAACATGGGCTTAA 59.356 47.619 0.00 0.00 0.00 1.85
285 303 5.679734 TGTTGAGTCTTTGATGCTTTCTC 57.320 39.130 0.00 0.00 0.00 2.87
305 323 9.250624 CTTTCTCAATCCTAAAACCGATAGTAG 57.749 37.037 0.00 0.00 0.00 2.57
331 358 1.603802 CACGTGGTGAGCAACTCAAAT 59.396 47.619 7.95 0.00 42.46 2.32
337 364 5.334802 CGTGGTGAGCAACTCAAATTTGATA 60.335 40.000 20.76 0.28 42.46 2.15
339 366 6.749118 GTGGTGAGCAACTCAAATTTGATATC 59.251 38.462 20.76 13.92 42.46 1.63
340 367 6.127647 TGGTGAGCAACTCAAATTTGATATCC 60.128 38.462 20.76 13.92 42.46 2.59
341 368 6.268566 GTGAGCAACTCAAATTTGATATCCC 58.731 40.000 20.76 9.05 42.46 3.85
342 369 6.096001 GTGAGCAACTCAAATTTGATATCCCT 59.904 38.462 20.76 13.10 42.46 4.20
343 370 7.283127 GTGAGCAACTCAAATTTGATATCCCTA 59.717 37.037 20.76 4.36 42.46 3.53
344 371 7.833682 TGAGCAACTCAAATTTGATATCCCTAA 59.166 33.333 20.76 5.41 37.57 2.69
345 372 8.593945 AGCAACTCAAATTTGATATCCCTAAA 57.406 30.769 20.76 0.00 36.46 1.85
346 373 9.034800 AGCAACTCAAATTTGATATCCCTAAAA 57.965 29.630 20.76 0.00 36.46 1.52
347 374 9.651913 GCAACTCAAATTTGATATCCCTAAAAA 57.348 29.630 20.76 0.00 36.46 1.94
373 400 6.888105 ACTCAAATTTGATGGGAAAAACACT 58.112 32.000 20.76 0.00 36.46 3.55
374 401 6.762661 ACTCAAATTTGATGGGAAAAACACTG 59.237 34.615 20.76 6.99 36.46 3.66
377 404 8.646004 TCAAATTTGATGGGAAAAACACTGATA 58.354 29.630 16.91 0.00 31.01 2.15
461 488 6.260936 CCGCTGACCTAATTCATCATAACTTT 59.739 38.462 0.00 0.00 0.00 2.66
462 489 7.128331 CGCTGACCTAATTCATCATAACTTTG 58.872 38.462 0.00 0.00 0.00 2.77
497 524 3.820557 AGTTGCTTATCACAGGTGTTGT 58.179 40.909 0.00 0.00 41.94 3.32
518 545 7.041440 TGTTGTGTGATAGGTGTAAATCAGTTG 60.041 37.037 0.00 0.00 32.93 3.16
748 776 4.843728 TGTCAGTTGGTGAGAGTTTTTCT 58.156 39.130 0.00 0.00 39.43 2.52
750 778 5.354234 TGTCAGTTGGTGAGAGTTTTTCTTC 59.646 40.000 0.00 0.00 35.87 2.87
752 780 6.761714 GTCAGTTGGTGAGAGTTTTTCTTCTA 59.238 38.462 0.00 0.00 35.87 2.10
799 829 1.081242 GCCAAACGCACATCACTGG 60.081 57.895 0.00 0.00 37.47 4.00
824 855 4.864334 CAGCAGATGCCCCCGTCC 62.864 72.222 0.14 0.00 43.38 4.79
870 905 1.406751 GCTTTGAAGCCTCCTCTCCTC 60.407 57.143 4.38 0.00 46.20 3.71
871 906 2.187100 CTTTGAAGCCTCCTCTCCTCT 58.813 52.381 0.00 0.00 0.00 3.69
872 907 1.859302 TTGAAGCCTCCTCTCCTCTC 58.141 55.000 0.00 0.00 0.00 3.20
973 1009 4.166531 ACAACAAACTAGAGGGGTTAACCA 59.833 41.667 25.71 4.19 42.91 3.67
1060 1102 1.199615 CCTTGTTCTCTCCCCTCTCC 58.800 60.000 0.00 0.00 0.00 3.71
1240 1283 2.835431 CCGCCTCCCGATCTGTCT 60.835 66.667 0.00 0.00 40.02 3.41
1246 1289 0.102120 CTCCCGATCTGTCTGTCTGC 59.898 60.000 0.00 0.00 0.00 4.26
1297 1340 4.542525 AGATTTAGGGTGTGGGTTATTGGA 59.457 41.667 0.00 0.00 0.00 3.53
1301 1344 2.041216 AGGGTGTGGGTTATTGGAGTTC 59.959 50.000 0.00 0.00 0.00 3.01
1352 1395 4.856801 CGCCGAGGGATTGGTGGG 62.857 72.222 0.00 0.00 32.05 4.61
1484 1527 0.242825 TGCGGAGTTCGTCTAGGTTG 59.757 55.000 0.00 0.00 41.72 3.77
1488 1531 1.617357 GGAGTTCGTCTAGGTTGTGGT 59.383 52.381 0.00 0.00 0.00 4.16
1595 1639 3.030291 TGCACAACCAACTTGAATCCTT 58.970 40.909 0.00 0.00 33.59 3.36
1610 1654 4.019681 TGAATCCTTACCATGAACCGAAGT 60.020 41.667 0.00 0.00 0.00 3.01
1611 1655 3.328382 TCCTTACCATGAACCGAAGTG 57.672 47.619 0.00 0.00 0.00 3.16
1612 1656 2.635915 TCCTTACCATGAACCGAAGTGT 59.364 45.455 0.00 0.00 0.00 3.55
1613 1657 3.833650 TCCTTACCATGAACCGAAGTGTA 59.166 43.478 0.00 0.00 0.00 2.90
1701 1745 3.132111 GGACCTTTTCATTTGTGTGTGGT 59.868 43.478 0.00 0.00 0.00 4.16
1702 1746 4.359706 GACCTTTTCATTTGTGTGTGGTC 58.640 43.478 0.00 0.00 35.39 4.02
1848 1896 5.869753 TTTTTCTCTCTGTCTGCTAATGC 57.130 39.130 0.00 0.00 40.20 3.56
1864 1912 1.098050 ATGCGGATTCTTTGGACAGC 58.902 50.000 0.00 0.00 0.00 4.40
1941 1989 6.352565 CCTTCTCTGGAATATGTGAACTTCCT 60.353 42.308 0.00 0.00 39.36 3.36
1978 2026 9.555727 GTTGCCAAAATAGATTAGGACTATGTA 57.444 33.333 0.00 0.00 31.96 2.29
2097 2145 1.553704 GTATTGGAGACAGGGTTCCGT 59.446 52.381 0.00 0.00 44.54 4.69
2143 2227 3.746492 GGACTGTAGCTACCTTTTGTGTG 59.254 47.826 21.01 3.16 0.00 3.82
2203 2288 8.656849 ACTGTATTGCTACTTAGAATTTTGTCG 58.343 33.333 0.00 0.00 0.00 4.35
2214 2299 8.730680 ACTTAGAATTTTGTCGCTCATGTATTT 58.269 29.630 0.00 0.00 0.00 1.40
2219 2304 8.895932 AATTTTGTCGCTCATGTATTTTCTAC 57.104 30.769 0.00 0.00 0.00 2.59
2325 2835 4.264172 ACTTTATGTGCAACCCCCTTATGA 60.264 41.667 0.00 0.00 34.36 2.15
2398 2934 3.006940 TGCCCAAGTTACTGAATTAGCG 58.993 45.455 0.00 0.00 0.00 4.26
2422 2958 4.394729 ACCAAACACAAGTTACATCCGAT 58.605 39.130 0.00 0.00 36.84 4.18
2431 2967 7.221838 ACACAAGTTACATCCGATTTTGTTTTG 59.778 33.333 0.00 0.00 0.00 2.44
2478 3014 5.631026 ACTATTTGCATGACGTTGCTAAAG 58.369 37.500 13.05 12.56 43.18 1.85
2507 3043 0.695924 TTTGCTAGCTAGGGCCAACA 59.304 50.000 22.10 7.58 39.73 3.33
2546 3082 7.016268 AGTCACTAAGTAACCAAGGATCTTTGA 59.984 37.037 18.45 0.00 0.00 2.69
2572 3108 9.383519 ACAAACAATCATAGGTGTAAGATACTG 57.616 33.333 0.00 0.00 0.00 2.74
2573 3109 8.338259 CAAACAATCATAGGTGTAAGATACTGC 58.662 37.037 0.00 0.00 0.00 4.40
2574 3110 6.525629 ACAATCATAGGTGTAAGATACTGCC 58.474 40.000 0.00 0.00 0.00 4.85
2575 3111 6.099701 ACAATCATAGGTGTAAGATACTGCCA 59.900 38.462 0.00 0.00 0.00 4.92
2576 3112 6.942163 ATCATAGGTGTAAGATACTGCCAT 57.058 37.500 0.00 0.00 0.00 4.40
2577 3113 8.314021 CAATCATAGGTGTAAGATACTGCCATA 58.686 37.037 0.00 0.00 0.00 2.74
2578 3114 7.228314 TCATAGGTGTAAGATACTGCCATAC 57.772 40.000 0.00 0.00 0.00 2.39
2579 3115 7.010771 TCATAGGTGTAAGATACTGCCATACT 58.989 38.462 0.00 0.00 0.00 2.12
2620 3156 6.159928 TGGTTACATGGTATGGGGTTATGTAA 59.840 38.462 0.00 0.00 40.13 2.41
2695 3231 3.322828 TCGTAGGTGTAAAGATATGGGGC 59.677 47.826 0.00 0.00 0.00 5.80
2742 3278 6.164417 TGCGGTTATGTAGCCTTTAGATTA 57.836 37.500 0.00 0.00 0.00 1.75
2763 3299 2.885135 ACCAGCATGTGAATTCCTGA 57.115 45.000 2.27 0.00 0.00 3.86
2772 3308 5.337009 GCATGTGAATTCCTGATTCTTTGGT 60.337 40.000 2.27 0.00 43.74 3.67
2781 3317 4.895297 TCCTGATTCTTTGGTTTCTTTGCT 59.105 37.500 0.00 0.00 0.00 3.91
2850 3386 6.815641 TCTGATGTAAAGAAGCTCATTGAGAC 59.184 38.462 17.87 8.66 0.00 3.36
2920 3456 3.072622 ACCAAGGGTCAGTTCTTAAGGAC 59.927 47.826 5.69 5.69 0.00 3.85
2930 3466 3.126686 AGTTCTTAAGGACGAGACTACGC 59.873 47.826 8.29 0.00 36.70 4.42
3041 3578 7.176515 TGTCATAAAATTGTGGAGTTGCATAGT 59.823 33.333 0.00 0.00 0.00 2.12
3086 3623 7.810766 AAAATCATAACAATACCTTTGTGCG 57.189 32.000 0.00 0.00 32.22 5.34
3103 3640 3.312973 TGTGCGTCGGAAGTATTTGTTTT 59.687 39.130 0.00 0.00 0.00 2.43
3114 3651 8.458843 CGGAAGTATTTGTTTTGGATATCAAGT 58.541 33.333 4.83 0.00 36.62 3.16
3158 3695 7.856145 AATGATCTTCAGTGTCTATTGGAAC 57.144 36.000 0.00 0.00 0.00 3.62
3209 3750 8.962884 ATTGCTGATCCTTTTTGTTAAACTTT 57.037 26.923 0.00 0.00 0.00 2.66
3213 3754 8.328146 GCTGATCCTTTTTGTTAAACTTTGTTC 58.672 33.333 0.00 0.00 0.00 3.18
3298 3839 8.844244 AGATGATTGTTATTATTGCTTCTGACC 58.156 33.333 0.00 0.00 0.00 4.02
3302 3843 6.061022 TGTTATTATTGCTTCTGACCCTCA 57.939 37.500 0.00 0.00 0.00 3.86
3397 3938 8.321353 AGTTGGAACTTGATTACACTGATATGA 58.679 33.333 0.00 0.00 35.21 2.15
3481 4028 8.010733 ACCATATATCCAAAACTTTGTCATGG 57.989 34.615 0.00 8.14 36.45 3.66
3490 4037 5.675684 AAACTTTGTCATGGTTCTTTGGT 57.324 34.783 0.00 0.00 0.00 3.67
3498 4045 7.681939 TGTCATGGTTCTTTGGTAGTTATTC 57.318 36.000 0.00 0.00 0.00 1.75
3568 4115 7.637519 GGTACAGTTTAAGTTCGTTGTTTCTTC 59.362 37.037 0.00 0.00 0.00 2.87
3584 4133 6.913170 TGTTTCTTCAATTGGCAGATAGTTC 58.087 36.000 5.42 0.00 0.00 3.01
3594 4143 2.224018 GGCAGATAGTTCAGCTCTGAGG 60.224 54.545 6.83 0.00 41.13 3.86
3682 4232 5.826586 ACGCATTTTTGTCATCTGTTTGTA 58.173 33.333 0.00 0.00 0.00 2.41
3683 4233 6.446318 ACGCATTTTTGTCATCTGTTTGTAT 58.554 32.000 0.00 0.00 0.00 2.29
3687 4239 9.584839 GCATTTTTGTCATCTGTTTGTATTTTC 57.415 29.630 0.00 0.00 0.00 2.29
3760 4410 6.037786 ACATCCGTATGTAGTCCATATTGG 57.962 41.667 0.00 0.00 44.66 3.16
4112 4763 0.737219 GCCATGAGATGCACAAGTCC 59.263 55.000 0.00 0.00 0.00 3.85
4212 4870 6.234177 CAGGAGAGTCTCAAAAGGTTGTTAT 58.766 40.000 21.53 0.00 36.07 1.89
4730 10873 4.855298 TCCTCCCTTAGTTTGGTTATGG 57.145 45.455 0.00 0.00 0.00 2.74
4940 11083 9.843334 CTATACAACTAATACCCTTCGATCTTC 57.157 37.037 0.00 0.00 0.00 2.87
5019 11162 2.203126 GATCCTGCCCTGGCTTCG 60.203 66.667 9.97 0.00 42.51 3.79
5106 11259 4.008916 AGTACTCTCTCCCTCTCTCTCT 57.991 50.000 0.00 0.00 0.00 3.10
5295 11448 7.238710 ACCCTCAAATCTTACAGGTACATTTT 58.761 34.615 0.00 0.00 0.00 1.82
5296 11449 7.176690 ACCCTCAAATCTTACAGGTACATTTTG 59.823 37.037 0.00 0.00 0.00 2.44
5302 11460 6.067263 TCTTACAGGTACATTTTGTGTTGC 57.933 37.500 0.00 0.00 42.29 4.17
5321 11479 1.270518 GCTGCTCTTTCTCCTGTGTCA 60.271 52.381 0.00 0.00 0.00 3.58
5360 11518 6.166279 TGACAGTTGACTAACAGGATCATTC 58.834 40.000 0.00 0.00 39.30 2.67
5611 11771 1.757118 GTGTGCCTCAGACCATAGCTA 59.243 52.381 0.00 0.00 0.00 3.32
5702 11862 1.026584 CCGCATCTGCATTTCCATGA 58.973 50.000 2.72 0.00 42.21 3.07
6120 12395 9.370126 CGTATAAAAGTTCTCTGTCAGTTTTTG 57.630 33.333 0.00 0.00 30.06 2.44
6366 12690 2.789219 ACATAGGCCTACAGGGGATTT 58.211 47.619 16.61 0.00 35.18 2.17
6368 12692 3.531814 ACATAGGCCTACAGGGGATTTTT 59.468 43.478 16.61 0.00 35.18 1.94
6409 12763 1.811679 GCACTAGAGGCCAACGCTC 60.812 63.158 5.01 0.00 34.44 5.03
6414 12768 2.835701 TAGAGGCCAACGCTCGCAAG 62.836 60.000 5.01 0.00 34.44 4.01
6459 12814 4.265320 GCAACAAAACAAGCTTGTAGTGTC 59.735 41.667 32.13 22.86 41.31 3.67
6503 12858 8.236586 CCAAATTCGTGAAATCACTATTCTTCA 58.763 33.333 11.45 0.00 44.34 3.02
6509 12864 9.219603 TCGTGAAATCACTATTCTTCAATTTCT 57.780 29.630 11.45 0.00 44.34 2.52
6525 12880 0.671781 TTCTGAAGAGGCTTGCTCGC 60.672 55.000 0.00 0.00 0.00 5.03
6544 12899 2.047560 GGACCGACCTTGAACCCG 60.048 66.667 0.00 0.00 35.41 5.28
6548 12903 0.107066 ACCGACCTTGAACCCGTTTT 60.107 50.000 0.00 0.00 0.00 2.43
6552 12907 2.304092 GACCTTGAACCCGTTTTCCTT 58.696 47.619 0.00 0.00 0.00 3.36
6577 12932 2.887151 ATTGTCTCCTTGGGGTCTTG 57.113 50.000 0.00 0.00 0.00 3.02
6591 12946 1.523758 GTCTTGGCACGGTGAAGAAT 58.476 50.000 13.29 0.00 0.00 2.40
6605 12960 3.826157 GTGAAGAATCCCACCATTGTCAA 59.174 43.478 0.00 0.00 0.00 3.18
6606 12961 4.463891 GTGAAGAATCCCACCATTGTCAAT 59.536 41.667 0.00 0.00 0.00 2.57
6607 12962 4.463539 TGAAGAATCCCACCATTGTCAATG 59.536 41.667 17.24 17.24 38.63 2.82
6610 12965 0.614415 TCCCACCATTGTCAATGCCC 60.614 55.000 18.52 0.00 37.57 5.36
6611 12966 0.903924 CCCACCATTGTCAATGCCCA 60.904 55.000 18.52 0.00 37.57 5.36
6612 12967 1.196911 CCACCATTGTCAATGCCCAT 58.803 50.000 18.52 2.71 37.57 4.00
6613 12968 1.137479 CCACCATTGTCAATGCCCATC 59.863 52.381 18.52 0.00 37.57 3.51
6614 12969 1.105457 ACCATTGTCAATGCCCATCG 58.895 50.000 18.52 7.66 37.57 3.84
6656 13012 3.457610 CCACTTTGAACATGTGGCTTT 57.542 42.857 0.00 0.00 43.61 3.51
6676 13032 1.687660 TGCAGAAATGCCACACACAAT 59.312 42.857 0.00 0.00 0.00 2.71
6685 13041 1.550072 GCCACACACAATATGGGCTTT 59.450 47.619 0.00 0.00 38.37 3.51
6744 13101 1.269102 ACGTCTTGTCTGGTCTCAACG 60.269 52.381 0.00 0.00 0.00 4.10
6855 13212 2.273449 CTCGCAGGGGATTTGGCT 59.727 61.111 0.00 0.00 0.00 4.75
6865 13222 1.313091 GGATTTGGCTCGGGTGGAAC 61.313 60.000 0.00 0.00 0.00 3.62
6895 13252 1.741770 GCTGGCTCAAATCCGTCGT 60.742 57.895 0.00 0.00 0.00 4.34
6915 13272 4.477975 GTCTCCGTCGAGCCACCG 62.478 72.222 0.00 0.00 35.94 4.94
6965 13322 2.935481 TGGAGGGCCAAGAGGGTG 60.935 66.667 6.18 0.00 42.49 4.61
6966 13323 3.732849 GGAGGGCCAAGAGGGTGG 61.733 72.222 6.18 0.00 42.05 4.61
6967 13324 3.732849 GAGGGCCAAGAGGGTGGG 61.733 72.222 6.18 0.00 39.26 4.61
6970 13327 4.048470 GGCCAAGAGGGTGGGGTC 62.048 72.222 0.00 0.00 39.26 4.46
6971 13328 3.256960 GCCAAGAGGGTGGGGTCA 61.257 66.667 0.00 0.00 39.26 4.02
6972 13329 2.840753 GCCAAGAGGGTGGGGTCAA 61.841 63.158 0.00 0.00 39.26 3.18
6973 13330 1.380302 CCAAGAGGGTGGGGTCAAG 59.620 63.158 0.00 0.00 34.77 3.02
6974 13331 1.427072 CCAAGAGGGTGGGGTCAAGT 61.427 60.000 0.00 0.00 34.77 3.16
6975 13332 0.036875 CAAGAGGGTGGGGTCAAGTC 59.963 60.000 0.00 0.00 0.00 3.01
6976 13333 0.401395 AAGAGGGTGGGGTCAAGTCA 60.401 55.000 0.00 0.00 0.00 3.41
6977 13334 0.401395 AGAGGGTGGGGTCAAGTCAA 60.401 55.000 0.00 0.00 0.00 3.18
6978 13335 0.036875 GAGGGTGGGGTCAAGTCAAG 59.963 60.000 0.00 0.00 0.00 3.02
6979 13336 0.401395 AGGGTGGGGTCAAGTCAAGA 60.401 55.000 0.00 0.00 0.00 3.02
6980 13337 0.250770 GGGTGGGGTCAAGTCAAGAC 60.251 60.000 0.00 0.00 35.29 3.01
6986 13343 2.235546 GTCAAGTCAAGACCACGCC 58.764 57.895 0.00 0.00 0.00 5.68
6987 13344 1.070786 TCAAGTCAAGACCACGCCC 59.929 57.895 0.00 0.00 0.00 6.13
6988 13345 2.030562 AAGTCAAGACCACGCCCG 59.969 61.111 0.00 0.00 0.00 6.13
6989 13346 4.681978 AGTCAAGACCACGCCCGC 62.682 66.667 0.00 0.00 0.00 6.13
7021 13378 0.179100 CGATCCACCGCATCTGTTCT 60.179 55.000 0.00 0.00 0.00 3.01
7022 13379 1.293924 GATCCACCGCATCTGTTCTG 58.706 55.000 0.00 0.00 0.00 3.02
7023 13380 0.615331 ATCCACCGCATCTGTTCTGT 59.385 50.000 0.00 0.00 0.00 3.41
7024 13381 0.320683 TCCACCGCATCTGTTCTGTG 60.321 55.000 0.00 0.00 0.00 3.66
7026 13383 1.003355 ACCGCATCTGTTCTGTGGG 60.003 57.895 7.70 0.00 46.37 4.61
7027 13384 1.003355 CCGCATCTGTTCTGTGGGT 60.003 57.895 0.00 0.00 39.99 4.51
7028 13385 1.021390 CCGCATCTGTTCTGTGGGTC 61.021 60.000 0.00 0.00 39.99 4.46
7029 13386 1.354337 CGCATCTGTTCTGTGGGTCG 61.354 60.000 0.00 0.00 0.00 4.79
7030 13387 0.037326 GCATCTGTTCTGTGGGTCGA 60.037 55.000 0.00 0.00 0.00 4.20
7040 13397 2.842462 TGGGTCGATCGATGGGGG 60.842 66.667 22.50 0.00 0.00 5.40
7060 13417 2.415491 GGCCGTCTTCCAAAAATACAGC 60.415 50.000 0.00 0.00 0.00 4.40
7061 13418 2.227865 GCCGTCTTCCAAAAATACAGCA 59.772 45.455 0.00 0.00 0.00 4.41
7062 13419 3.821841 CCGTCTTCCAAAAATACAGCAC 58.178 45.455 0.00 0.00 0.00 4.40
7063 13420 3.365969 CCGTCTTCCAAAAATACAGCACC 60.366 47.826 0.00 0.00 0.00 5.01
7064 13421 3.252215 CGTCTTCCAAAAATACAGCACCA 59.748 43.478 0.00 0.00 0.00 4.17
7065 13422 4.546570 GTCTTCCAAAAATACAGCACCAC 58.453 43.478 0.00 0.00 0.00 4.16
7066 13423 4.278419 GTCTTCCAAAAATACAGCACCACT 59.722 41.667 0.00 0.00 0.00 4.00
7067 13424 5.472137 GTCTTCCAAAAATACAGCACCACTA 59.528 40.000 0.00 0.00 0.00 2.74
7068 13425 5.705441 TCTTCCAAAAATACAGCACCACTAG 59.295 40.000 0.00 0.00 0.00 2.57
7069 13426 4.980573 TCCAAAAATACAGCACCACTAGT 58.019 39.130 0.00 0.00 0.00 2.57
7081 13438 3.659786 CACCACTAGTGTCAAAATCGGA 58.340 45.455 21.18 0.00 41.93 4.55
7082 13439 3.679980 CACCACTAGTGTCAAAATCGGAG 59.320 47.826 21.18 4.19 41.93 4.63
7083 13440 2.673368 CCACTAGTGTCAAAATCGGAGC 59.327 50.000 21.18 0.00 0.00 4.70
7084 13441 3.589988 CACTAGTGTCAAAATCGGAGCT 58.410 45.455 15.06 0.00 0.00 4.09
7085 13442 3.369147 CACTAGTGTCAAAATCGGAGCTG 59.631 47.826 15.06 0.00 0.00 4.24
7086 13443 2.550830 AGTGTCAAAATCGGAGCTGT 57.449 45.000 0.00 0.00 0.00 4.40
7087 13444 2.417719 AGTGTCAAAATCGGAGCTGTC 58.582 47.619 0.00 0.00 0.00 3.51
7088 13445 2.143122 GTGTCAAAATCGGAGCTGTCA 58.857 47.619 0.00 0.00 0.00 3.58
7089 13446 2.158449 GTGTCAAAATCGGAGCTGTCAG 59.842 50.000 0.00 0.00 0.00 3.51
7090 13447 2.224281 TGTCAAAATCGGAGCTGTCAGT 60.224 45.455 0.93 0.00 0.00 3.41
7091 13448 2.808543 GTCAAAATCGGAGCTGTCAGTT 59.191 45.455 0.93 0.00 0.00 3.16
7092 13449 2.807967 TCAAAATCGGAGCTGTCAGTTG 59.192 45.455 0.93 0.00 0.00 3.16
7093 13450 1.160137 AAATCGGAGCTGTCAGTTGC 58.840 50.000 0.93 0.00 0.00 4.17
7094 13451 0.322975 AATCGGAGCTGTCAGTTGCT 59.677 50.000 6.63 0.00 42.82 3.91
7095 13452 0.322975 ATCGGAGCTGTCAGTTGCTT 59.677 50.000 6.63 0.00 39.91 3.91
7096 13453 0.966179 TCGGAGCTGTCAGTTGCTTA 59.034 50.000 6.63 0.00 39.91 3.09
7097 13454 1.071605 CGGAGCTGTCAGTTGCTTAC 58.928 55.000 6.63 0.00 39.91 2.34
7098 13455 1.071605 GGAGCTGTCAGTTGCTTACG 58.928 55.000 0.93 0.00 39.91 3.18
7099 13456 0.440371 GAGCTGTCAGTTGCTTACGC 59.560 55.000 0.93 0.00 39.91 4.42
7100 13457 1.130613 GCTGTCAGTTGCTTACGCG 59.869 57.895 3.53 3.53 39.65 6.01
7101 13458 1.557443 GCTGTCAGTTGCTTACGCGT 61.557 55.000 19.17 19.17 39.65 6.01
7102 13459 0.161658 CTGTCAGTTGCTTACGCGTG 59.838 55.000 24.59 7.20 39.65 5.34
7103 13460 0.528901 TGTCAGTTGCTTACGCGTGT 60.529 50.000 24.59 6.91 39.65 4.49
7104 13461 0.111266 GTCAGTTGCTTACGCGTGTG 60.111 55.000 24.59 15.36 39.65 3.82
7105 13462 1.204062 CAGTTGCTTACGCGTGTGG 59.796 57.895 24.59 12.61 39.65 4.17
7106 13463 2.127383 GTTGCTTACGCGTGTGGC 60.127 61.111 24.59 21.91 39.65 5.01
7107 13464 3.350612 TTGCTTACGCGTGTGGCC 61.351 61.111 24.59 0.00 39.65 5.36
7108 13465 4.610714 TGCTTACGCGTGTGGCCA 62.611 61.111 24.59 0.00 39.65 5.36
7109 13466 3.124921 GCTTACGCGTGTGGCCAT 61.125 61.111 24.59 0.00 38.94 4.40
7110 13467 3.089784 CTTACGCGTGTGGCCATC 58.910 61.111 24.59 4.56 38.94 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.310022 TTTGGTTCCCGGACTCATATTT 57.690 40.909 0.73 0.00 0.00 1.40
14 15 2.595172 GGCGTTTTGGTTCCCGGA 60.595 61.111 0.73 0.00 0.00 5.14
16 17 3.676605 GGGGCGTTTTGGTTCCCG 61.677 66.667 0.00 0.00 39.66 5.14
56 57 6.966534 AATCAACACCTTCATCAGTTTCTT 57.033 33.333 0.00 0.00 0.00 2.52
68 69 2.676748 TGCCAGGAAAATCAACACCTT 58.323 42.857 0.00 0.00 0.00 3.50
75 76 5.221682 ACACAATCAAATGCCAGGAAAATCA 60.222 36.000 0.00 0.00 0.00 2.57
81 82 2.596346 ACACACAATCAAATGCCAGGA 58.404 42.857 0.00 0.00 0.00 3.86
125 126 5.716094 ACTGTCTTGTTGTTGTAAAAACCC 58.284 37.500 0.00 0.00 0.00 4.11
197 202 6.373186 AACTAAGTTTGTTAAGAGTGCCAC 57.627 37.500 0.57 0.00 0.00 5.01
236 252 3.642141 CCCATGTTTAGCCCCTTTATGT 58.358 45.455 0.00 0.00 0.00 2.29
250 266 4.666512 AGACTCAACATTAAGCCCATGTT 58.333 39.130 0.00 0.92 44.14 2.71
262 280 5.766670 TGAGAAAGCATCAAAGACTCAACAT 59.233 36.000 0.00 0.00 31.51 2.71
266 284 5.413833 GGATTGAGAAAGCATCAAAGACTCA 59.586 40.000 0.00 0.00 39.92 3.41
285 303 6.421202 GTCTGCTACTATCGGTTTTAGGATTG 59.579 42.308 0.00 0.00 0.00 2.67
318 336 6.189859 AGGGATATCAAATTTGAGTTGCTCA 58.810 36.000 24.17 0.93 41.08 4.26
345 372 9.018582 TGTTTTTCCCATCAAATTTGAGTTTTT 57.981 25.926 24.17 6.24 41.08 1.94
346 373 8.458052 GTGTTTTTCCCATCAAATTTGAGTTTT 58.542 29.630 24.17 6.61 41.08 2.43
347 374 7.828717 AGTGTTTTTCCCATCAAATTTGAGTTT 59.171 29.630 24.17 6.97 41.08 2.66
348 375 7.280652 CAGTGTTTTTCCCATCAAATTTGAGTT 59.719 33.333 24.17 7.69 41.08 3.01
349 376 6.762661 CAGTGTTTTTCCCATCAAATTTGAGT 59.237 34.615 24.17 11.17 41.08 3.41
350 377 6.985645 TCAGTGTTTTTCCCATCAAATTTGAG 59.014 34.615 24.17 15.99 41.08 3.02
351 378 6.882656 TCAGTGTTTTTCCCATCAAATTTGA 58.117 32.000 22.52 22.52 42.14 2.69
352 379 7.733402 ATCAGTGTTTTTCCCATCAAATTTG 57.267 32.000 12.15 12.15 0.00 2.32
356 383 9.921637 GTTAATATCAGTGTTTTTCCCATCAAA 57.078 29.630 0.00 0.00 0.00 2.69
357 384 9.083422 TGTTAATATCAGTGTTTTTCCCATCAA 57.917 29.630 0.00 0.00 0.00 2.57
358 385 8.642935 TGTTAATATCAGTGTTTTTCCCATCA 57.357 30.769 0.00 0.00 0.00 3.07
359 386 8.190784 CCTGTTAATATCAGTGTTTTTCCCATC 58.809 37.037 0.00 0.00 0.00 3.51
360 387 7.673926 ACCTGTTAATATCAGTGTTTTTCCCAT 59.326 33.333 0.00 0.00 0.00 4.00
361 388 7.007723 ACCTGTTAATATCAGTGTTTTTCCCA 58.992 34.615 0.00 0.00 0.00 4.37
362 389 7.462571 ACCTGTTAATATCAGTGTTTTTCCC 57.537 36.000 0.00 0.00 0.00 3.97
437 464 6.851222 AAGTTATGATGAATTAGGTCAGCG 57.149 37.500 0.00 0.00 36.71 5.18
461 488 8.366401 TGATAAGCAACTTTGGAATTGAAATCA 58.634 29.630 0.00 0.00 0.00 2.57
462 489 8.650714 GTGATAAGCAACTTTGGAATTGAAATC 58.349 33.333 0.00 0.00 0.00 2.17
497 524 5.555966 TGCAACTGATTTACACCTATCACA 58.444 37.500 0.00 0.00 0.00 3.58
499 526 7.334858 TGTATGCAACTGATTTACACCTATCA 58.665 34.615 0.00 0.00 0.00 2.15
518 545 7.383102 AGCCTAGCAACATTATTATGTATGC 57.617 36.000 16.97 16.97 44.14 3.14
553 581 9.878599 CAGTACTAAACAGTAAATCAACAAAGG 57.121 33.333 0.00 0.00 0.00 3.11
589 617 5.206587 GGACAGTAGGGGAGTTATGACTTA 58.793 45.833 0.00 0.00 35.88 2.24
590 618 4.031611 GGACAGTAGGGGAGTTATGACTT 58.968 47.826 0.00 0.00 35.88 3.01
591 619 3.012502 TGGACAGTAGGGGAGTTATGACT 59.987 47.826 0.00 0.00 39.32 3.41
592 620 3.371965 TGGACAGTAGGGGAGTTATGAC 58.628 50.000 0.00 0.00 0.00 3.06
594 622 5.131142 AGAATTGGACAGTAGGGGAGTTATG 59.869 44.000 0.00 0.00 0.00 1.90
595 623 5.289510 AGAATTGGACAGTAGGGGAGTTAT 58.710 41.667 0.00 0.00 0.00 1.89
596 624 4.695606 AGAATTGGACAGTAGGGGAGTTA 58.304 43.478 0.00 0.00 0.00 2.24
597 625 3.532102 AGAATTGGACAGTAGGGGAGTT 58.468 45.455 0.00 0.00 0.00 3.01
598 626 3.207044 AGAATTGGACAGTAGGGGAGT 57.793 47.619 0.00 0.00 0.00 3.85
599 627 4.717280 ACTAAGAATTGGACAGTAGGGGAG 59.283 45.833 0.00 0.00 0.00 4.30
600 628 4.695606 ACTAAGAATTGGACAGTAGGGGA 58.304 43.478 0.00 0.00 0.00 4.81
601 629 6.749036 ATACTAAGAATTGGACAGTAGGGG 57.251 41.667 0.00 0.00 0.00 4.79
602 630 9.462606 AAAAATACTAAGAATTGGACAGTAGGG 57.537 33.333 0.00 0.00 0.00 3.53
799 829 1.271656 GGGGCATCTGCTGATTATTGC 59.728 52.381 2.92 5.90 41.70 3.56
870 905 4.201542 CGGTTTTTGTTTTTGACGTTGGAG 60.202 41.667 0.00 0.00 0.00 3.86
871 906 3.673809 CGGTTTTTGTTTTTGACGTTGGA 59.326 39.130 0.00 0.00 0.00 3.53
872 907 3.673809 TCGGTTTTTGTTTTTGACGTTGG 59.326 39.130 0.00 0.00 0.00 3.77
940 976 7.446013 CCCCTCTAGTTTGTTGTATTTGTAACA 59.554 37.037 0.00 0.00 0.00 2.41
941 977 7.446319 ACCCCTCTAGTTTGTTGTATTTGTAAC 59.554 37.037 0.00 0.00 0.00 2.50
942 978 7.519927 ACCCCTCTAGTTTGTTGTATTTGTAA 58.480 34.615 0.00 0.00 0.00 2.41
943 979 7.081857 ACCCCTCTAGTTTGTTGTATTTGTA 57.918 36.000 0.00 0.00 0.00 2.41
944 980 5.948842 ACCCCTCTAGTTTGTTGTATTTGT 58.051 37.500 0.00 0.00 0.00 2.83
945 981 6.894339 AACCCCTCTAGTTTGTTGTATTTG 57.106 37.500 0.00 0.00 0.00 2.32
973 1009 1.820481 CGTGGACGGGTGGTTTTGT 60.820 57.895 0.00 0.00 35.37 2.83
1025 1067 3.733960 GGAGGCGGCGTGTTTTCC 61.734 66.667 9.37 0.00 0.00 3.13
1032 1074 3.591254 GAGAACAAGGAGGCGGCGT 62.591 63.158 9.37 0.00 0.00 5.68
1317 1360 4.383602 CGAAAACCGTGCCCAGCG 62.384 66.667 0.00 0.00 0.00 5.18
1370 1413 4.771356 GCACACGACTCGCGCCTA 62.771 66.667 0.00 0.00 46.04 3.93
1402 1445 2.173669 ACAGATTGGATTCGCGGCG 61.174 57.895 17.70 17.70 0.00 6.46
1484 1527 1.132199 CTACACATCGACGCGACCAC 61.132 60.000 15.93 0.00 39.18 4.16
1488 1531 1.085893 TAACCTACACATCGACGCGA 58.914 50.000 15.93 4.51 41.13 5.87
1595 1639 4.811969 ACATACACTTCGGTTCATGGTA 57.188 40.909 0.00 0.00 0.00 3.25
1610 1654 3.067742 GCGACCCTTAGCTTCTACATACA 59.932 47.826 0.00 0.00 0.00 2.29
1611 1655 3.318557 AGCGACCCTTAGCTTCTACATAC 59.681 47.826 0.00 0.00 41.52 2.39
1612 1656 3.563223 AGCGACCCTTAGCTTCTACATA 58.437 45.455 0.00 0.00 41.52 2.29
1613 1657 2.362717 GAGCGACCCTTAGCTTCTACAT 59.637 50.000 0.00 0.00 44.69 2.29
1701 1745 4.290155 GCTTGCAATTTCAAGAGTTTCGA 58.710 39.130 20.11 0.00 44.61 3.71
1702 1746 3.426525 GGCTTGCAATTTCAAGAGTTTCG 59.573 43.478 20.11 0.00 44.61 3.46
1748 1793 0.563173 TAGCCCATAGACCTCCAGCT 59.437 55.000 0.00 0.00 0.00 4.24
1814 1862 7.498570 AGACAGAGAGAAAAATAATCCAGCATC 59.501 37.037 0.00 0.00 0.00 3.91
1848 1896 0.449388 GCTGCTGTCCAAAGAATCCG 59.551 55.000 0.00 0.00 0.00 4.18
1852 1900 2.957680 TCAATTGCTGCTGTCCAAAGAA 59.042 40.909 0.00 0.00 0.00 2.52
1864 1912 8.922058 ATGTATTTCTAAAGCTTCAATTGCTG 57.078 30.769 0.00 0.00 41.03 4.41
2143 2227 1.524008 CCCCTTCCGTTTCTGTTGCC 61.524 60.000 0.00 0.00 0.00 4.52
2154 2238 5.952526 AATAATTAATAACGCCCCTTCCG 57.047 39.130 0.00 0.00 0.00 4.30
2202 2287 6.199154 CACTAGTGGTAGAAAATACATGAGCG 59.801 42.308 15.49 0.00 0.00 5.03
2203 2288 7.265673 TCACTAGTGGTAGAAAATACATGAGC 58.734 38.462 22.48 0.00 0.00 4.26
2241 2326 6.303054 TCAGTCAGTCAACCCAAATATTTCA 58.697 36.000 0.00 0.00 0.00 2.69
2398 2934 4.751098 TCGGATGTAACTTGTGTTTGGTAC 59.249 41.667 0.00 0.00 37.59 3.34
2422 2958 9.522804 GTGGTGTATCTGTATTTCAAAACAAAA 57.477 29.630 0.00 0.00 0.00 2.44
2431 2967 9.216117 AGTTTACAAGTGGTGTATCTGTATTTC 57.784 33.333 0.00 0.00 42.37 2.17
2478 3014 1.673168 AGCTAGCAAATGCAGTAGCC 58.327 50.000 18.83 5.88 42.38 3.93
2516 3052 3.746492 CCTTGGTTACTTAGTGACTGCAC 59.254 47.826 7.21 0.00 45.49 4.57
2546 3082 9.383519 CAGTATCTTACACCTATGATTGTTTGT 57.616 33.333 0.00 0.00 0.00 2.83
2574 3110 0.035439 ACGGCAAAGACCCCAGTATG 60.035 55.000 0.00 0.00 0.00 2.39
2575 3111 0.035439 CACGGCAAAGACCCCAGTAT 60.035 55.000 0.00 0.00 0.00 2.12
2576 3112 1.373435 CACGGCAAAGACCCCAGTA 59.627 57.895 0.00 0.00 0.00 2.74
2577 3113 2.113139 CACGGCAAAGACCCCAGT 59.887 61.111 0.00 0.00 0.00 4.00
2578 3114 2.113139 ACACGGCAAAGACCCCAG 59.887 61.111 0.00 0.00 0.00 4.45
2579 3115 2.203280 CACACGGCAAAGACCCCA 60.203 61.111 0.00 0.00 0.00 4.96
2620 3156 5.041191 CCATGCTGGTAGAATCTAAAGGT 57.959 43.478 0.00 0.00 31.35 3.50
2655 3191 1.665735 CGATTGTTTGGCAAAGACCCG 60.666 52.381 13.94 13.44 40.91 5.28
2695 3231 2.030007 CCATGTAACCACACTGCAAAGG 60.030 50.000 0.00 0.00 37.54 3.11
2742 3278 4.508551 TCAGGAATTCACATGCTGGTAT 57.491 40.909 7.93 0.00 36.93 2.73
2763 3299 7.301868 TCCAATAGCAAAGAAACCAAAGAAT 57.698 32.000 0.00 0.00 0.00 2.40
2772 3308 5.726980 ACAGCATTCCAATAGCAAAGAAA 57.273 34.783 0.00 0.00 0.00 2.52
2781 3317 9.853555 CAATTACAAAGTTACAGCATTCCAATA 57.146 29.630 0.00 0.00 0.00 1.90
2850 3386 2.233271 ACACATTCTGCCCTTGTGAAG 58.767 47.619 9.08 0.00 42.59 3.02
2920 3456 0.809385 TTTCCTCCAGCGTAGTCTCG 59.191 55.000 0.00 0.00 0.00 4.04
3081 3618 2.157834 ACAAATACTTCCGACGCACA 57.842 45.000 0.00 0.00 0.00 4.57
3086 3623 7.981142 TGATATCCAAAACAAATACTTCCGAC 58.019 34.615 0.00 0.00 0.00 4.79
3114 3651 4.572985 TTACGTTCCGAGAGTTCAAGAA 57.427 40.909 0.00 0.00 0.00 2.52
3139 3676 5.540337 AGACAGTTCCAATAGACACTGAAGA 59.460 40.000 5.20 0.00 37.21 2.87
3158 3695 8.209917 AGAAACACCTACAACTTTTAAGACAG 57.790 34.615 0.00 0.00 0.00 3.51
3298 3839 4.702131 CCCTTATTCTGTGAAAGGTTGAGG 59.298 45.833 0.00 0.00 38.49 3.86
3302 3843 4.202567 TGAGCCCTTATTCTGTGAAAGGTT 60.203 41.667 0.00 0.00 38.49 3.50
3415 3962 2.917343 GCGCCAAAAGAACATAAAGAGC 59.083 45.455 0.00 0.00 0.00 4.09
3451 3998 6.038936 ACAAAGTTTTGGATATATGGTACGGC 59.961 38.462 9.22 0.00 42.34 5.68
3481 4028 5.407387 TGTCTGCGAATAACTACCAAAGAAC 59.593 40.000 0.00 0.00 0.00 3.01
3490 4037 5.909621 AAGGTACTGTCTGCGAATAACTA 57.090 39.130 0.00 0.00 40.86 2.24
3498 4045 0.517316 GGCAAAAGGTACTGTCTGCG 59.483 55.000 0.00 0.00 40.86 5.18
3584 4133 5.720371 ACTATATAGTTGCCTCAGAGCTG 57.280 43.478 9.71 0.00 31.13 4.24
3611 4161 9.582431 TGAACTTCGTAAAATCTACCATTCTAG 57.418 33.333 0.00 0.00 0.00 2.43
3620 4170 9.917129 TCATAGTTGTGAACTTCGTAAAATCTA 57.083 29.630 0.00 0.00 42.81 1.98
3683 4233 9.990360 AAGTTTGACTTAACCAGAAAAAGAAAA 57.010 25.926 0.00 0.00 36.52 2.29
3687 4239 8.458843 TGAGAAGTTTGACTTAACCAGAAAAAG 58.541 33.333 0.00 0.00 38.80 2.27
3729 4281 8.728337 TGGACTACATACGGATGTATATAGAC 57.272 38.462 20.64 10.95 45.42 2.59
3734 4286 8.909923 CCAATATGGACTACATACGGATGTATA 58.090 37.037 20.64 11.30 42.60 1.47
3735 4287 7.618117 TCCAATATGGACTACATACGGATGTAT 59.382 37.037 20.64 9.39 43.13 2.29
3825 4476 9.658799 TCAAAAAGTAGAATCTCACCAATAGAG 57.341 33.333 0.00 0.00 34.42 2.43
4185 4840 3.511477 ACCTTTTGAGACTCTCCTGCTA 58.489 45.455 3.68 0.00 0.00 3.49
4474 10615 6.725364 AGATCATGTCAAATGGGTTAAGAGT 58.275 36.000 0.00 0.00 0.00 3.24
4730 10873 9.793252 ATTTGTGTATATTGAAGAACATTGAGC 57.207 29.630 0.00 0.00 0.00 4.26
4872 11015 3.630312 AGTTGTGTAAAACATGCCGTTCT 59.370 39.130 0.00 0.00 38.99 3.01
4877 11020 7.543868 TGCAATATAAGTTGTGTAAAACATGCC 59.456 33.333 0.00 0.00 38.99 4.40
4940 11083 3.744660 GGCTCAGGAATACCCTACATTG 58.255 50.000 0.00 0.00 45.60 2.82
5019 11162 2.257676 GCAGGTTGAGCTGCTTGC 59.742 61.111 23.62 5.47 42.73 4.01
5106 11259 2.997315 CCGCAGACCACAGAGGGA 60.997 66.667 0.00 0.00 43.89 4.20
5148 11301 0.038251 GCAAGGTACAAAGGGCAAGC 60.038 55.000 0.00 0.00 0.00 4.01
5295 11448 1.141657 AGGAGAAAGAGCAGCAACACA 59.858 47.619 0.00 0.00 0.00 3.72
5296 11449 1.534595 CAGGAGAAAGAGCAGCAACAC 59.465 52.381 0.00 0.00 0.00 3.32
5302 11460 2.827800 TGACACAGGAGAAAGAGCAG 57.172 50.000 0.00 0.00 0.00 4.24
5321 11479 9.080097 AGTCAACTGTCATAAGTAGACTACTTT 57.920 33.333 28.25 15.65 46.27 2.66
5677 11837 1.660560 AAATGCAGATGCGGGCAGTC 61.661 55.000 0.00 0.00 44.24 3.51
5702 11862 6.423604 GTGCCACAAATAAGCATAACAAAGTT 59.576 34.615 0.00 0.00 39.04 2.66
6207 12482 2.354729 GCACACATAGGCCACCCA 59.645 61.111 5.01 0.00 0.00 4.51
6366 12690 9.818796 GCAAAACAAATTTAGACAAAGTCAAAA 57.181 25.926 0.00 0.00 34.60 2.44
6368 12692 8.439286 GTGCAAAACAAATTTAGACAAAGTCAA 58.561 29.630 0.00 0.00 34.60 3.18
6369 12693 7.816995 AGTGCAAAACAAATTTAGACAAAGTCA 59.183 29.630 0.00 0.00 34.60 3.41
6414 12768 2.409975 ACAAATGTTGCAATCTGCTGC 58.590 42.857 0.59 0.00 45.31 5.25
6415 12769 3.611113 GCTACAAATGTTGCAATCTGCTG 59.389 43.478 13.73 0.00 45.31 4.41
6416 12770 3.841643 GCTACAAATGTTGCAATCTGCT 58.158 40.909 13.73 0.00 45.31 4.24
6432 12786 4.448537 ACAAGCTTGTTTTGTTGCTACA 57.551 36.364 26.36 0.00 38.47 2.74
6433 12787 5.455525 CACTACAAGCTTGTTTTGTTGCTAC 59.544 40.000 35.20 0.00 42.35 3.58
6459 12814 5.478233 TTTGGCACTGCATACGTTATTAG 57.522 39.130 2.82 0.00 0.00 1.73
6503 12858 2.746362 CGAGCAAGCCTCTTCAGAAATT 59.254 45.455 0.00 0.00 38.49 1.82
6525 12880 2.047560 GGTTCAAGGTCGGTCCGG 60.048 66.667 12.29 0.00 41.99 5.14
6544 12899 6.650427 AGGAGACAATTTACCAAGGAAAAC 57.350 37.500 0.00 0.00 0.00 2.43
6548 12903 4.508405 CCCAAGGAGACAATTTACCAAGGA 60.508 45.833 0.00 0.00 0.00 3.36
6552 12907 2.719705 ACCCCAAGGAGACAATTTACCA 59.280 45.455 0.00 0.00 36.73 3.25
6577 12932 1.002624 TGGGATTCTTCACCGTGCC 60.003 57.895 0.00 0.00 0.00 5.01
6591 12946 0.614415 GGGCATTGACAATGGTGGGA 60.614 55.000 25.64 0.00 39.31 4.37
6598 12953 1.392589 GACCGATGGGCATTGACAAT 58.607 50.000 0.00 0.00 36.48 2.71
6605 12960 0.251916 TTTTCTCGACCGATGGGCAT 59.748 50.000 0.00 0.00 36.48 4.40
6606 12961 0.251916 ATTTTCTCGACCGATGGGCA 59.748 50.000 0.00 0.00 36.48 5.36
6607 12962 0.938008 GATTTTCTCGACCGATGGGC 59.062 55.000 0.00 0.00 36.48 5.36
6676 13032 2.039480 TGGCATTTTTGCAAAGCCCATA 59.961 40.909 28.33 14.16 44.60 2.74
6685 13041 1.000060 GAGCTGAGTGGCATTTTTGCA 60.000 47.619 0.00 0.00 36.33 4.08
6744 13101 2.750301 AAAAGTTCTCAAACGTCGCC 57.250 45.000 0.00 0.00 40.48 5.54
6823 13180 2.202544 GAGTCTGCGACTGCGAGG 60.203 66.667 14.47 0.00 43.53 4.63
6824 13181 2.575525 CGAGTCTGCGACTGCGAG 60.576 66.667 14.47 2.28 43.53 5.03
6825 13182 4.760840 GCGAGTCTGCGACTGCGA 62.761 66.667 21.47 0.00 43.53 5.10
6827 13184 3.177920 CTGCGAGTCTGCGACTGC 61.178 66.667 14.47 16.16 43.53 4.40
6828 13185 2.505777 CCTGCGAGTCTGCGACTG 60.506 66.667 14.47 8.92 43.53 3.51
6829 13186 3.753434 CCCTGCGAGTCTGCGACT 61.753 66.667 10.33 10.33 46.42 4.18
6830 13187 4.803426 CCCCTGCGAGTCTGCGAC 62.803 72.222 0.00 1.15 37.81 5.19
6832 13189 2.859273 AAATCCCCTGCGAGTCTGCG 62.859 60.000 0.00 0.00 37.81 5.18
6833 13190 1.078143 AAATCCCCTGCGAGTCTGC 60.078 57.895 0.00 0.77 0.00 4.26
6834 13191 0.745845 CCAAATCCCCTGCGAGTCTG 60.746 60.000 0.00 0.00 0.00 3.51
6835 13192 1.604378 CCAAATCCCCTGCGAGTCT 59.396 57.895 0.00 0.00 0.00 3.24
6836 13193 2.115291 GCCAAATCCCCTGCGAGTC 61.115 63.158 0.00 0.00 0.00 3.36
6855 13212 2.933287 AGCCATGGTTCCACCCGA 60.933 61.111 14.67 0.00 37.50 5.14
6873 13230 1.033746 ACGGATTTGAGCCAGCCATG 61.034 55.000 0.00 0.00 0.00 3.66
6874 13231 0.749454 GACGGATTTGAGCCAGCCAT 60.749 55.000 0.00 0.00 0.00 4.40
6875 13232 1.377202 GACGGATTTGAGCCAGCCA 60.377 57.895 0.00 0.00 0.00 4.75
6876 13233 2.464459 CGACGGATTTGAGCCAGCC 61.464 63.158 0.00 0.00 0.00 4.85
6877 13234 1.741770 ACGACGGATTTGAGCCAGC 60.742 57.895 0.00 0.00 0.00 4.85
6953 13310 4.048470 GACCCCACCCTCTTGGCC 62.048 72.222 0.00 0.00 37.83 5.36
6954 13311 2.771328 CTTGACCCCACCCTCTTGGC 62.771 65.000 0.00 0.00 37.83 4.52
6955 13312 1.380302 CTTGACCCCACCCTCTTGG 59.620 63.158 0.00 0.00 41.37 3.61
6956 13313 0.036875 GACTTGACCCCACCCTCTTG 59.963 60.000 0.00 0.00 0.00 3.02
6957 13314 0.401395 TGACTTGACCCCACCCTCTT 60.401 55.000 0.00 0.00 0.00 2.85
6958 13315 0.401395 TTGACTTGACCCCACCCTCT 60.401 55.000 0.00 0.00 0.00 3.69
6959 13316 0.036875 CTTGACTTGACCCCACCCTC 59.963 60.000 0.00 0.00 0.00 4.30
6960 13317 0.401395 TCTTGACTTGACCCCACCCT 60.401 55.000 0.00 0.00 0.00 4.34
6961 13318 0.250770 GTCTTGACTTGACCCCACCC 60.251 60.000 0.00 0.00 0.00 4.61
6962 13319 0.250770 GGTCTTGACTTGACCCCACC 60.251 60.000 1.76 0.00 46.01 4.61
6963 13320 3.324207 GGTCTTGACTTGACCCCAC 57.676 57.895 1.76 0.00 46.01 4.61
6968 13325 1.228657 GGGCGTGGTCTTGACTTGAC 61.229 60.000 0.61 0.00 0.00 3.18
6969 13326 1.070786 GGGCGTGGTCTTGACTTGA 59.929 57.895 0.61 0.00 0.00 3.02
6970 13327 2.317609 CGGGCGTGGTCTTGACTTG 61.318 63.158 0.61 0.00 0.00 3.16
6971 13328 2.030562 CGGGCGTGGTCTTGACTT 59.969 61.111 0.61 0.00 0.00 3.01
6972 13329 4.681978 GCGGGCGTGGTCTTGACT 62.682 66.667 0.61 0.00 0.00 3.41
7021 13378 2.431454 CCCCATCGATCGACCCACA 61.431 63.158 22.06 0.00 0.00 4.17
7022 13379 2.421739 CCCCATCGATCGACCCAC 59.578 66.667 22.06 0.00 0.00 4.61
7023 13380 2.842462 CCCCCATCGATCGACCCA 60.842 66.667 22.06 0.00 0.00 4.51
7024 13381 4.315941 GCCCCCATCGATCGACCC 62.316 72.222 22.06 1.47 0.00 4.46
7025 13382 4.315941 GGCCCCCATCGATCGACC 62.316 72.222 22.06 12.28 0.00 4.79
7026 13383 4.664677 CGGCCCCCATCGATCGAC 62.665 72.222 22.06 6.26 0.00 4.20
7028 13385 4.664677 GACGGCCCCCATCGATCG 62.665 72.222 9.36 9.36 0.00 3.69
7029 13386 2.717139 GAAGACGGCCCCCATCGATC 62.717 65.000 0.00 0.00 0.00 3.69
7030 13387 2.768344 AAGACGGCCCCCATCGAT 60.768 61.111 0.00 0.00 0.00 3.59
7040 13397 2.227865 TGCTGTATTTTTGGAAGACGGC 59.772 45.455 9.66 9.66 41.74 5.68
7061 13418 3.864921 GCTCCGATTTTGACACTAGTGGT 60.865 47.826 26.12 12.20 34.19 4.16
7062 13419 2.673368 GCTCCGATTTTGACACTAGTGG 59.327 50.000 26.12 9.07 34.19 4.00
7063 13420 3.369147 CAGCTCCGATTTTGACACTAGTG 59.631 47.826 21.44 21.44 0.00 2.74
7064 13421 3.006967 ACAGCTCCGATTTTGACACTAGT 59.993 43.478 0.00 0.00 0.00 2.57
7065 13422 3.589988 ACAGCTCCGATTTTGACACTAG 58.410 45.455 0.00 0.00 0.00 2.57
7066 13423 3.006430 TGACAGCTCCGATTTTGACACTA 59.994 43.478 0.00 0.00 0.00 2.74
7067 13424 2.224281 TGACAGCTCCGATTTTGACACT 60.224 45.455 0.00 0.00 0.00 3.55
7068 13425 2.143122 TGACAGCTCCGATTTTGACAC 58.857 47.619 0.00 0.00 0.00 3.67
7069 13426 2.224281 ACTGACAGCTCCGATTTTGACA 60.224 45.455 1.25 0.00 0.00 3.58
7070 13427 2.417719 ACTGACAGCTCCGATTTTGAC 58.582 47.619 1.25 0.00 0.00 3.18
7071 13428 2.807967 CAACTGACAGCTCCGATTTTGA 59.192 45.455 1.25 0.00 0.00 2.69
7072 13429 2.666619 GCAACTGACAGCTCCGATTTTG 60.667 50.000 1.25 0.00 0.00 2.44
7073 13430 1.537202 GCAACTGACAGCTCCGATTTT 59.463 47.619 1.25 0.00 0.00 1.82
7074 13431 1.160137 GCAACTGACAGCTCCGATTT 58.840 50.000 1.25 0.00 0.00 2.17
7075 13432 0.322975 AGCAACTGACAGCTCCGATT 59.677 50.000 1.25 0.00 36.00 3.34
7076 13433 0.322975 AAGCAACTGACAGCTCCGAT 59.677 50.000 1.25 0.00 40.90 4.18
7077 13434 0.966179 TAAGCAACTGACAGCTCCGA 59.034 50.000 1.25 0.00 40.90 4.55
7078 13435 1.071605 GTAAGCAACTGACAGCTCCG 58.928 55.000 1.25 0.00 40.90 4.63
7079 13436 1.071605 CGTAAGCAACTGACAGCTCC 58.928 55.000 1.25 0.00 40.90 4.70
7093 13450 3.089784 GATGGCCACACGCGTAAG 58.910 61.111 13.44 7.37 38.94 2.34


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

AutoCloner maintained by Alex Coulton.