Multiple sequence alignment - TraesCS5A01G511700

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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 TraesCS5A01G511700 chr5A 100.000 3363 0 0 1 3363 675632621 675629259 0.000000e+00 6211.0
1 TraesCS5A01G511700 chr5A 82.780 1115 163 22 1543 2640 675671499 675670397 0.000000e+00 968.0
2 TraesCS5A01G511700 chr5A 93.233 266 14 3 3099 3363 16621190 16621452 4.390000e-104 388.0
3 TraesCS5A01G511700 chr5A 81.154 520 63 22 966 1467 675672136 675671634 5.680000e-103 385.0
4 TraesCS5A01G511700 chr5A 100.000 54 0 0 3574 3627 675629048 675628995 2.300000e-17 100.0
5 TraesCS5A01G511700 chr4D 90.397 2166 129 32 693 2802 496139732 496137590 0.000000e+00 2774.0
6 TraesCS5A01G511700 chr4D 90.962 852 56 8 1358 2196 496348094 496347251 0.000000e+00 1127.0
7 TraesCS5A01G511700 chr4D 85.195 1101 148 12 1543 2640 496631616 496632704 0.000000e+00 1116.0
8 TraesCS5A01G511700 chr4D 93.056 648 22 10 1 638 496140670 496140036 0.000000e+00 926.0
9 TraesCS5A01G511700 chr4D 93.874 604 32 3 2195 2795 496336589 496335988 0.000000e+00 905.0
10 TraesCS5A01G511700 chr4D 91.467 375 19 8 996 1362 496349710 496349341 1.500000e-138 503.0
11 TraesCS5A01G511700 chr4D 88.169 355 18 10 1 345 496350651 496350311 5.640000e-108 401.0
12 TraesCS5A01G511700 chr4D 93.585 265 14 2 3099 3363 123580672 123580411 3.400000e-105 392.0
13 TraesCS5A01G511700 chr4D 81.179 526 61 22 966 1467 496630994 496631505 4.390000e-104 388.0
14 TraesCS5A01G511700 chr4D 92.830 265 17 1 3099 3363 123369724 123369462 2.040000e-102 383.0
15 TraesCS5A01G511700 chr4D 92.857 266 16 2 3099 3363 329121600 329121863 2.040000e-102 383.0
16 TraesCS5A01G511700 chr4D 88.750 320 18 11 429 730 496350285 496349966 3.420000e-100 375.0
17 TraesCS5A01G511700 chr4D 93.007 143 8 2 747 888 496349984 496349843 1.320000e-49 207.0
18 TraesCS5A01G511700 chr4D 89.796 98 8 2 316 413 496372524 496372619 1.370000e-24 124.0
19 TraesCS5A01G511700 chr4D 100.000 35 0 0 662 696 496140034 496140000 8.410000e-07 65.8
20 TraesCS5A01G511700 chr4B 91.446 1134 52 25 951 2051 636065558 636066679 0.000000e+00 1515.0
21 TraesCS5A01G511700 chr4B 84.182 1100 165 7 1543 2638 636610571 636609477 0.000000e+00 1059.0
22 TraesCS5A01G511700 chr4B 93.281 640 41 1 2173 2810 636066687 636067326 0.000000e+00 942.0
23 TraesCS5A01G511700 chr4B 81.213 511 61 21 966 1458 636611179 636610686 2.640000e-101 379.0
24 TraesCS5A01G511700 chr4B 86.351 359 21 11 1 345 636057329 636057673 2.060000e-97 366.0
25 TraesCS5A01G511700 chr4B 93.793 145 5 3 747 888 636065315 636065458 7.890000e-52 215.0
26 TraesCS5A01G511700 chr4B 86.473 207 11 5 429 620 636057699 636057903 1.020000e-50 211.0
27 TraesCS5A01G511700 chr4B 88.525 122 6 3 610 727 636065213 636065330 1.360000e-29 141.0
28 TraesCS5A01G511700 chr4B 87.755 98 10 2 316 413 636240689 636240784 2.960000e-21 113.0
29 TraesCS5A01G511700 chr7D 93.233 266 15 2 3099 3363 382012082 382012345 4.390000e-104 388.0
30 TraesCS5A01G511700 chr7D 93.233 266 15 2 3099 3363 382012788 382013051 4.390000e-104 388.0
31 TraesCS5A01G511700 chr7D 85.859 198 24 3 1250 1445 573924052 573924247 1.320000e-49 207.0
32 TraesCS5A01G511700 chr2D 93.233 266 15 2 3099 3363 635039341 635039078 4.390000e-104 388.0
33 TraesCS5A01G511700 chr7A 92.830 265 17 1 3099 3363 211276936 211277198 2.040000e-102 383.0
34 TraesCS5A01G511700 chr1A 92.857 266 15 3 3099 3363 334074845 334075107 2.040000e-102 383.0
35 TraesCS5A01G511700 chr7B 85.859 198 24 3 1250 1445 632861598 632861403 1.320000e-49 207.0


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 TraesCS5A01G511700 chr5A 675628995 675632621 3626 True 3155.500000 6211 100.000000 1 3627 2 chr5A.!!$R1 3626
1 TraesCS5A01G511700 chr5A 675670397 675672136 1739 True 676.500000 968 81.967000 966 2640 2 chr5A.!!$R2 1674
2 TraesCS5A01G511700 chr4D 496137590 496140670 3080 True 1255.266667 2774 94.484333 1 2802 3 chr4D.!!$R4 2801
3 TraesCS5A01G511700 chr4D 496335988 496336589 601 True 905.000000 905 93.874000 2195 2795 1 chr4D.!!$R3 600
4 TraesCS5A01G511700 chr4D 496630994 496632704 1710 False 752.000000 1116 83.187000 966 2640 2 chr4D.!!$F3 1674
5 TraesCS5A01G511700 chr4D 496347251 496350651 3400 True 522.600000 1127 90.471000 1 2196 5 chr4D.!!$R5 2195
6 TraesCS5A01G511700 chr4B 636609477 636611179 1702 True 719.000000 1059 82.697500 966 2638 2 chr4B.!!$R1 1672
7 TraesCS5A01G511700 chr4B 636065213 636067326 2113 False 703.250000 1515 91.761250 610 2810 4 chr4B.!!$F3 2200
8 TraesCS5A01G511700 chr4B 636057329 636057903 574 False 288.500000 366 86.412000 1 620 2 chr4B.!!$F2 619
9 TraesCS5A01G511700 chr7D 382012082 382013051 969 False 388.000000 388 93.233000 3099 3363 2 chr7D.!!$F2 264

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
424 450 0.035056 ATAAAGAGGCAGCCGCAAGT 60.035 50.0 18.51 4.28 41.24 3.16 F
2154 3953 0.103937 GAGTTGATCAGGGAGAGGCG 59.896 60.0 0.00 0.00 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2361 4174 0.040646 TCCCATCACTACCGTGTCCT 59.959 55.0 0.00 0.0 41.89 3.85 R
3576 6099 0.301987 GCCAAGTAGAATTCGCGAGC 59.698 55.0 9.59 0.7 0.00 5.03 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
65 70 2.287547 ACAATGTAAGTGCCTGTTTGCG 60.288 45.455 0.00 0.00 33.50 4.85
84 89 5.536554 TGCGAATTTCAGTTTTGCAAAAA 57.463 30.435 25.40 10.76 39.83 1.94
120 131 7.542130 AGTTTTGAGAAAAGCAAGTAACTTGTG 59.458 33.333 0.00 0.00 42.77 3.33
131 142 2.366916 AGTAACTTGTGCTCTGCAGACT 59.633 45.455 13.74 1.56 40.08 3.24
132 143 1.590932 AACTTGTGCTCTGCAGACTG 58.409 50.000 13.74 5.34 40.08 3.51
133 144 0.883814 ACTTGTGCTCTGCAGACTGC 60.884 55.000 20.86 20.86 45.29 4.40
174 185 3.069729 AGCCTAACATTGGGAGATACGAC 59.930 47.826 0.00 0.00 0.00 4.34
178 189 6.157211 CCTAACATTGGGAGATACGACATAC 58.843 44.000 0.00 0.00 0.00 2.39
180 191 3.887110 ACATTGGGAGATACGACATACGA 59.113 43.478 0.00 0.00 45.77 3.43
181 192 4.523173 ACATTGGGAGATACGACATACGAT 59.477 41.667 0.00 0.00 45.77 3.73
182 193 5.708697 ACATTGGGAGATACGACATACGATA 59.291 40.000 0.00 0.00 45.77 2.92
183 194 5.618056 TTGGGAGATACGACATACGATAC 57.382 43.478 0.00 0.00 45.77 2.24
224 242 0.523966 AGCGACACTGACTGAGCTAC 59.476 55.000 0.00 0.00 36.25 3.58
324 349 1.135286 GCTCCATTAGTTGCACTTGCC 60.135 52.381 0.00 0.00 41.18 4.52
398 424 6.094881 TCAAGCCTAGTTTAATAATGTGCACC 59.905 38.462 15.69 0.00 0.00 5.01
423 449 0.659957 GATAAAGAGGCAGCCGCAAG 59.340 55.000 18.51 0.00 41.24 4.01
424 450 0.035056 ATAAAGAGGCAGCCGCAAGT 60.035 50.000 18.51 4.28 41.24 3.16
426 452 0.250727 AAAGAGGCAGCCGCAAGTAA 60.251 50.000 18.51 0.00 41.24 2.24
427 453 0.250727 AAGAGGCAGCCGCAAGTAAA 60.251 50.000 18.51 0.00 41.24 2.01
428 454 0.674895 AGAGGCAGCCGCAAGTAAAG 60.675 55.000 18.51 0.00 41.24 1.85
638 684 1.523938 GTAGAATCCAGTGGCCGGC 60.524 63.158 21.18 21.18 0.00 6.13
640 686 4.115199 GAATCCAGTGGCCGGCCT 62.115 66.667 43.34 24.91 36.94 5.19
642 688 3.944250 AATCCAGTGGCCGGCCTTG 62.944 63.158 43.34 36.61 36.94 3.61
644 690 4.974721 CCAGTGGCCGGCCTTGTT 62.975 66.667 43.34 24.15 36.94 2.83
645 691 3.365265 CAGTGGCCGGCCTTGTTC 61.365 66.667 43.34 26.78 36.94 3.18
646 692 4.660938 AGTGGCCGGCCTTGTTCC 62.661 66.667 43.34 23.75 36.94 3.62
698 1020 4.028852 TGAAGTTAGTGACCGATCGATG 57.971 45.455 18.66 2.80 0.00 3.84
819 1153 1.686355 TTTCGCCTCCTGCAAAAGAA 58.314 45.000 0.00 0.00 41.33 2.52
820 1154 1.686355 TTCGCCTCCTGCAAAAGAAA 58.314 45.000 0.00 0.00 41.33 2.52
821 1155 1.686355 TCGCCTCCTGCAAAAGAAAA 58.314 45.000 0.00 0.00 41.33 2.29
822 1156 1.608590 TCGCCTCCTGCAAAAGAAAAG 59.391 47.619 0.00 0.00 41.33 2.27
823 1157 1.608590 CGCCTCCTGCAAAAGAAAAGA 59.391 47.619 0.00 0.00 41.33 2.52
978 1388 2.178273 GGATCGCCAAAACACGCC 59.822 61.111 0.00 0.00 0.00 5.68
979 1389 2.202298 GATCGCCAAAACACGCCG 60.202 61.111 0.00 0.00 0.00 6.46
980 1390 2.666862 ATCGCCAAAACACGCCGA 60.667 55.556 0.00 0.00 0.00 5.54
981 1391 1.977594 GATCGCCAAAACACGCCGAT 61.978 55.000 0.00 0.00 40.84 4.18
994 1404 0.917259 CGCCGATCGAGAAACAGAAG 59.083 55.000 18.66 0.00 41.67 2.85
1038 1451 1.030488 TCCTCTACCTCGGCGTTCTG 61.030 60.000 6.85 0.00 0.00 3.02
1039 1452 1.226717 CTCTACCTCGGCGTTCTGC 60.227 63.158 6.85 0.00 45.38 4.26
1040 1453 1.658686 CTCTACCTCGGCGTTCTGCT 61.659 60.000 6.85 0.00 45.43 4.24
1066 1479 1.304713 CTGGCCATGGGTCTGCTTT 60.305 57.895 15.13 0.00 0.00 3.51
1078 1503 2.093711 GGTCTGCTTTCTTCTCCCTCTC 60.094 54.545 0.00 0.00 0.00 3.20
1085 1520 4.767928 GCTTTCTTCTCCCTCTCCGATATA 59.232 45.833 0.00 0.00 0.00 0.86
1106 1541 3.300388 AGATCGATCTCCTGTTGCCTAA 58.700 45.455 22.32 0.00 29.30 2.69
1113 1548 3.096852 TCTCCTGTTGCCTAATTCTCGA 58.903 45.455 0.00 0.00 0.00 4.04
1120 1555 7.012327 TCCTGTTGCCTAATTCTCGATAATTTG 59.988 37.037 13.22 11.26 31.63 2.32
1121 1556 7.012327 CCTGTTGCCTAATTCTCGATAATTTGA 59.988 37.037 13.22 0.00 31.63 2.69
1478 3182 9.344309 CAAGTAACTTGCTTAGTACTAACTCTC 57.656 37.037 11.38 2.62 35.54 3.20
1522 3297 5.997746 TCGAGTGGATGGATTATTTGATTCC 59.002 40.000 0.00 0.00 0.00 3.01
1572 3354 3.574396 ACAACGAGATGGTGAAGAGAGAA 59.426 43.478 0.00 0.00 0.00 2.87
1579 3361 2.603021 TGGTGAAGAGAGAAGCAGAGT 58.397 47.619 0.00 0.00 0.00 3.24
1593 3381 1.337447 GCAGAGTTAGTGCCGTACCAA 60.337 52.381 0.00 0.00 34.67 3.67
1641 3429 0.558220 TCCAGATGGAGACCGAGGAT 59.442 55.000 0.00 0.00 39.78 3.24
1809 3597 4.810661 AGGAGAGAAGCTGCGCGC 62.811 66.667 27.26 27.26 40.35 6.86
2072 3869 4.522971 GGCAGGAGGCTAAACTCG 57.477 61.111 0.00 0.00 44.01 4.18
2073 3870 1.898154 GGCAGGAGGCTAAACTCGA 59.102 57.895 0.00 0.00 44.01 4.04
2074 3871 0.466124 GGCAGGAGGCTAAACTCGAT 59.534 55.000 0.00 0.00 44.01 3.59
2075 3872 1.539280 GGCAGGAGGCTAAACTCGATC 60.539 57.143 0.00 0.00 44.01 3.69
2098 3897 1.200948 GTTCACTTCTTCCATGCAGGC 59.799 52.381 0.00 0.00 37.29 4.85
2117 3916 0.591659 CGACGACTTCACTGACAGGA 59.408 55.000 7.51 0.00 0.00 3.86
2126 3925 1.347707 TCACTGACAGGATTGTGGACC 59.652 52.381 7.51 0.00 37.76 4.46
2151 3950 1.135915 CGTGGAGTTGATCAGGGAGAG 59.864 57.143 0.00 0.00 0.00 3.20
2154 3953 0.103937 GAGTTGATCAGGGAGAGGCG 59.896 60.000 0.00 0.00 0.00 5.52
2161 3960 4.680537 AGGGAGAGGCGTCACCGT 62.681 66.667 15.30 13.43 46.52 4.83
2164 3963 2.711922 GGAGAGGCGTCACCGTGAT 61.712 63.158 9.41 0.00 46.52 3.06
2225 4024 0.605589 CTGCGAGAGGGTCAAGAAGT 59.394 55.000 0.00 0.00 0.00 3.01
2242 4041 1.752683 AGTTACTGAGCGACCGAGAT 58.247 50.000 0.00 0.00 0.00 2.75
2251 4050 1.874019 CGACCGAGATGGCGTTCTG 60.874 63.158 0.00 0.00 43.94 3.02
2341 4154 0.247736 AGCTGAACCGTGACCTCATC 59.752 55.000 0.00 0.00 0.00 2.92
2361 4174 3.621558 TCGAGAGAGCACTGGAAATAGA 58.378 45.455 0.00 0.00 34.84 1.98
2371 4184 3.446161 CACTGGAAATAGAGGACACGGTA 59.554 47.826 0.00 0.00 0.00 4.02
2518 4331 1.120530 GAGGGCTAATCAGGGACGAA 58.879 55.000 0.00 0.00 0.00 3.85
2524 4337 0.458669 TAATCAGGGACGAAGACGCC 59.541 55.000 0.00 0.00 43.96 5.68
2578 4391 2.809119 CGAGTCTGCTAGATACGTGGAT 59.191 50.000 0.00 0.00 0.00 3.41
2590 4403 5.292765 AGATACGTGGATGAATGCTACAAG 58.707 41.667 0.00 0.00 0.00 3.16
2609 4422 3.151022 GAGGAGTCTCGGGGCCTG 61.151 72.222 5.83 5.83 0.00 4.85
2641 4454 6.183361 TGGCAAAATAAACACACAAATAGGGT 60.183 34.615 0.00 0.00 0.00 4.34
2702 4517 6.926272 TGTAACCTTGGCAATTTGATTTACAC 59.074 34.615 0.00 0.00 0.00 2.90
2819 4637 7.653767 AGAGAGAAAAACAAACATAGTACGG 57.346 36.000 0.00 0.00 0.00 4.02
2820 4638 7.215085 AGAGAGAAAAACAAACATAGTACGGT 58.785 34.615 0.00 0.00 0.00 4.83
2821 4639 7.713942 AGAGAGAAAAACAAACATAGTACGGTT 59.286 33.333 0.00 0.00 0.00 4.44
2822 4640 8.217131 AGAGAAAAACAAACATAGTACGGTTT 57.783 30.769 7.30 7.30 37.69 3.27
2823 4641 8.680001 AGAGAAAAACAAACATAGTACGGTTTT 58.320 29.630 9.61 0.00 39.36 2.43
2824 4642 9.934190 GAGAAAAACAAACATAGTACGGTTTTA 57.066 29.630 9.61 0.00 37.44 1.52
2825 4643 9.940166 AGAAAAACAAACATAGTACGGTTTTAG 57.060 29.630 9.61 4.54 37.44 1.85
2826 4644 9.934190 GAAAAACAAACATAGTACGGTTTTAGA 57.066 29.630 9.61 0.00 37.44 2.10
2830 4648 9.940166 AACAAACATAGTACGGTTTTAGAAAAG 57.060 29.630 9.61 2.46 35.17 2.27
2831 4649 9.328845 ACAAACATAGTACGGTTTTAGAAAAGA 57.671 29.630 9.61 0.00 35.17 2.52
2834 4652 8.543862 ACATAGTACGGTTTTAGAAAAGAAGG 57.456 34.615 0.00 0.00 0.00 3.46
2835 4653 8.152898 ACATAGTACGGTTTTAGAAAAGAAGGT 58.847 33.333 0.00 0.00 0.00 3.50
2836 4654 6.856135 AGTACGGTTTTAGAAAAGAAGGTG 57.144 37.500 0.00 0.00 0.00 4.00
2837 4655 5.761726 AGTACGGTTTTAGAAAAGAAGGTGG 59.238 40.000 0.00 0.00 0.00 4.61
2838 4656 4.784177 ACGGTTTTAGAAAAGAAGGTGGA 58.216 39.130 0.00 0.00 0.00 4.02
2839 4657 5.195185 ACGGTTTTAGAAAAGAAGGTGGAA 58.805 37.500 0.00 0.00 0.00 3.53
2840 4658 5.298527 ACGGTTTTAGAAAAGAAGGTGGAAG 59.701 40.000 0.00 0.00 0.00 3.46
2841 4659 5.529791 GGTTTTAGAAAAGAAGGTGGAAGC 58.470 41.667 0.00 0.00 0.00 3.86
2854 4672 1.268079 GTGGAAGCTTTCACCTTCTGC 59.732 52.381 25.14 0.00 38.91 4.26
2855 4673 1.133823 TGGAAGCTTTCACCTTCTGCA 60.134 47.619 2.32 0.00 38.91 4.41
2856 4674 2.165998 GGAAGCTTTCACCTTCTGCAT 58.834 47.619 0.00 0.00 38.91 3.96
2857 4675 2.163211 GGAAGCTTTCACCTTCTGCATC 59.837 50.000 0.00 0.00 38.91 3.91
2858 4676 1.446907 AGCTTTCACCTTCTGCATCG 58.553 50.000 0.00 0.00 0.00 3.84
2859 4677 0.449388 GCTTTCACCTTCTGCATCGG 59.551 55.000 0.00 0.00 0.00 4.18
2860 4678 1.813513 CTTTCACCTTCTGCATCGGT 58.186 50.000 0.00 0.00 0.00 4.69
2861 4679 2.154462 CTTTCACCTTCTGCATCGGTT 58.846 47.619 0.00 0.00 0.00 4.44
2862 4680 1.522668 TTCACCTTCTGCATCGGTTG 58.477 50.000 0.00 0.00 0.00 3.77
2870 4688 3.187058 GCATCGGTTGCGATGGTT 58.813 55.556 5.90 0.00 44.07 3.67
2871 4689 1.226379 GCATCGGTTGCGATGGTTG 60.226 57.895 5.90 0.00 44.07 3.77
2872 4690 1.226379 CATCGGTTGCGATGGTTGC 60.226 57.895 0.00 0.00 41.25 4.17
2873 4691 2.749865 ATCGGTTGCGATGGTTGCG 61.750 57.895 0.00 0.00 34.24 4.85
2874 4692 3.418913 CGGTTGCGATGGTTGCGA 61.419 61.111 0.00 0.00 34.24 5.10
2875 4693 2.175811 GGTTGCGATGGTTGCGAC 59.824 61.111 0.00 0.00 44.39 5.19
2876 4694 2.202171 GTTGCGATGGTTGCGACG 60.202 61.111 0.00 0.00 37.03 5.12
2880 4698 3.410516 CGATGGTTGCGACGCACA 61.411 61.111 24.42 18.78 38.71 4.57
2881 4699 2.173382 GATGGTTGCGACGCACAC 59.827 61.111 24.42 21.58 38.71 3.82
2882 4700 2.590291 ATGGTTGCGACGCACACA 60.590 55.556 24.42 23.43 38.71 3.72
2883 4701 1.911293 GATGGTTGCGACGCACACAT 61.911 55.000 28.26 28.26 38.71 3.21
2884 4702 1.911293 ATGGTTGCGACGCACACATC 61.911 55.000 24.42 9.37 38.71 3.06
2885 4703 2.173382 GTTGCGACGCACACATCC 59.827 61.111 24.42 2.59 38.71 3.51
2886 4704 2.280457 TTGCGACGCACACATCCA 60.280 55.556 24.42 2.41 38.71 3.41
2887 4705 1.670730 TTGCGACGCACACATCCAT 60.671 52.632 24.42 0.00 38.71 3.41
2888 4706 0.390472 TTGCGACGCACACATCCATA 60.390 50.000 24.42 0.66 38.71 2.74
2889 4707 0.179086 TGCGACGCACACATCCATAT 60.179 50.000 20.50 0.00 31.71 1.78
2890 4708 0.233074 GCGACGCACACATCCATATG 59.767 55.000 16.42 0.00 39.17 1.78
2891 4709 4.927762 TGCGACGCACACATCCATATGT 62.928 50.000 20.50 0.00 39.33 2.29
2892 4710 1.933181 CGACGCACACATCCATATGTT 59.067 47.619 1.24 0.00 44.07 2.71
2893 4711 3.120041 CGACGCACACATCCATATGTTA 58.880 45.455 1.24 0.00 44.07 2.41
2894 4712 3.060540 CGACGCACACATCCATATGTTAC 60.061 47.826 1.24 0.00 44.07 2.50
2895 4713 3.867857 ACGCACACATCCATATGTTACA 58.132 40.909 1.24 0.00 44.07 2.41
2896 4714 4.257731 ACGCACACATCCATATGTTACAA 58.742 39.130 1.24 0.00 44.07 2.41
2897 4715 4.881273 ACGCACACATCCATATGTTACAAT 59.119 37.500 1.24 0.00 44.07 2.71
2898 4716 6.052360 ACGCACACATCCATATGTTACAATA 58.948 36.000 1.24 0.00 44.07 1.90
2899 4717 6.540551 ACGCACACATCCATATGTTACAATAA 59.459 34.615 1.24 0.00 44.07 1.40
2900 4718 7.066404 ACGCACACATCCATATGTTACAATAAA 59.934 33.333 1.24 0.00 44.07 1.40
2901 4719 7.912773 CGCACACATCCATATGTTACAATAAAA 59.087 33.333 1.24 0.00 44.07 1.52
2902 4720 9.748708 GCACACATCCATATGTTACAATAAAAT 57.251 29.630 1.24 0.00 44.07 1.82
2915 4733 9.964253 TGTTACAATAAAATAAATTGCGCATTG 57.036 25.926 12.75 11.33 37.77 2.82
2916 4734 9.965748 GTTACAATAAAATAAATTGCGCATTGT 57.034 25.926 12.75 16.85 37.77 2.71
2919 4737 9.965748 ACAATAAAATAAATTGCGCATTGTTAC 57.034 25.926 12.75 0.00 37.77 2.50
2920 4738 9.964253 CAATAAAATAAATTGCGCATTGTTACA 57.036 25.926 12.75 0.00 0.00 2.41
2924 4742 9.722056 AAAATAAATTGCGCATTGTTACAAAAA 57.278 22.222 12.75 0.00 0.00 1.94
2980 4798 9.961265 AATGTTTGCATGATTCTAACATATCAG 57.039 29.630 10.25 0.00 38.34 2.90
2981 4799 8.735692 TGTTTGCATGATTCTAACATATCAGA 57.264 30.769 0.00 0.00 34.52 3.27
2982 4800 8.615211 TGTTTGCATGATTCTAACATATCAGAC 58.385 33.333 0.00 0.00 34.52 3.51
2983 4801 7.412137 TTGCATGATTCTAACATATCAGACG 57.588 36.000 0.00 0.00 34.52 4.18
2984 4802 6.748132 TGCATGATTCTAACATATCAGACGA 58.252 36.000 0.00 0.00 34.52 4.20
2985 4803 7.381323 TGCATGATTCTAACATATCAGACGAT 58.619 34.615 0.00 0.00 34.52 3.73
2986 4804 7.874528 TGCATGATTCTAACATATCAGACGATT 59.125 33.333 0.00 0.00 34.52 3.34
2987 4805 9.358872 GCATGATTCTAACATATCAGACGATTA 57.641 33.333 0.00 0.00 34.52 1.75
3022 4840 9.513906 TTGAAAACATGTGAATATAGGAAGACA 57.486 29.630 0.00 0.00 0.00 3.41
3023 4841 9.685276 TGAAAACATGTGAATATAGGAAGACAT 57.315 29.630 0.00 0.00 0.00 3.06
3025 4843 9.911788 AAAACATGTGAATATAGGAAGACATCT 57.088 29.630 0.00 0.00 0.00 2.90
3030 4848 9.664332 ATGTGAATATAGGAAGACATCTAATGC 57.336 33.333 0.00 0.00 0.00 3.56
3031 4849 8.650490 TGTGAATATAGGAAGACATCTAATGCA 58.350 33.333 0.00 0.00 0.00 3.96
3032 4850 9.494271 GTGAATATAGGAAGACATCTAATGCAA 57.506 33.333 0.00 0.00 0.00 4.08
3035 4853 9.458727 AATATAGGAAGACATCTAATGCAATGG 57.541 33.333 0.00 0.00 0.00 3.16
3036 4854 5.378230 AGGAAGACATCTAATGCAATGGA 57.622 39.130 0.00 0.00 0.00 3.41
3037 4855 5.374921 AGGAAGACATCTAATGCAATGGAG 58.625 41.667 0.00 0.00 0.00 3.86
3038 4856 5.131642 AGGAAGACATCTAATGCAATGGAGA 59.868 40.000 0.00 0.00 0.00 3.71
3039 4857 5.238214 GGAAGACATCTAATGCAATGGAGAC 59.762 44.000 0.00 0.00 0.00 3.36
3040 4858 4.375272 AGACATCTAATGCAATGGAGACG 58.625 43.478 0.00 0.00 0.00 4.18
3041 4859 4.100035 AGACATCTAATGCAATGGAGACGA 59.900 41.667 0.00 0.00 0.00 4.20
3042 4860 4.769688 ACATCTAATGCAATGGAGACGAA 58.230 39.130 0.00 0.00 0.00 3.85
3043 4861 5.371526 ACATCTAATGCAATGGAGACGAAT 58.628 37.500 0.00 0.00 0.00 3.34
3044 4862 5.237996 ACATCTAATGCAATGGAGACGAATG 59.762 40.000 0.00 0.00 0.00 2.67
3045 4863 2.857592 AATGCAATGGAGACGAATGC 57.142 45.000 0.00 0.00 36.62 3.56
3046 4864 2.048444 ATGCAATGGAGACGAATGCT 57.952 45.000 0.00 0.00 36.90 3.79
3047 4865 2.689553 TGCAATGGAGACGAATGCTA 57.310 45.000 0.00 0.00 36.90 3.49
3048 4866 3.198409 TGCAATGGAGACGAATGCTAT 57.802 42.857 0.00 0.00 36.90 2.97
3049 4867 4.335400 TGCAATGGAGACGAATGCTATA 57.665 40.909 0.00 0.00 36.90 1.31
3050 4868 4.898320 TGCAATGGAGACGAATGCTATAT 58.102 39.130 0.00 0.00 36.90 0.86
3051 4869 5.308014 TGCAATGGAGACGAATGCTATATT 58.692 37.500 0.00 0.00 36.90 1.28
3052 4870 5.764686 TGCAATGGAGACGAATGCTATATTT 59.235 36.000 0.00 0.00 36.90 1.40
3053 4871 6.262944 TGCAATGGAGACGAATGCTATATTTT 59.737 34.615 0.00 0.00 36.90 1.82
3054 4872 7.141363 GCAATGGAGACGAATGCTATATTTTT 58.859 34.615 0.00 0.00 34.26 1.94
3096 4914 6.503589 TTTTTGTTTCTTTCTTCCGACTCA 57.496 33.333 0.00 0.00 0.00 3.41
3097 4915 6.693315 TTTTGTTTCTTTCTTCCGACTCAT 57.307 33.333 0.00 0.00 0.00 2.90
3130 4948 7.547370 CAGTCTTTCTTCGGAATTCTACTGAAT 59.453 37.037 5.23 0.00 44.08 2.57
3186 5708 5.181622 ACTTATATCCTAAGGTCTCTTCGCG 59.818 44.000 0.00 0.00 34.59 5.87
3199 5721 0.109689 CTTCGCGAAGAACTCTCCGT 60.110 55.000 39.00 0.00 40.79 4.69
3204 5726 1.602165 GCGAAGAACTCTCCGTCAACA 60.602 52.381 0.00 0.00 0.00 3.33
3211 5733 1.269831 ACTCTCCGTCAACAACAGAGC 60.270 52.381 0.00 0.00 33.38 4.09
3308 5831 5.221382 GCTTACGAGTTTACATCCATCCCTA 60.221 44.000 0.00 0.00 0.00 3.53
3354 5877 0.035152 TCTCTCGTAGCCGTTACCCA 60.035 55.000 0.00 0.00 35.01 4.51
3594 6117 1.640428 TGCTCGCGAATTCTACTTGG 58.360 50.000 11.33 0.00 0.00 3.61
3595 6118 0.301987 GCTCGCGAATTCTACTTGGC 59.698 55.000 11.33 1.48 0.00 4.52
3596 6119 1.640428 CTCGCGAATTCTACTTGGCA 58.360 50.000 11.33 0.00 31.06 4.92
3597 6120 2.205074 CTCGCGAATTCTACTTGGCAT 58.795 47.619 11.33 0.00 31.06 4.40
3598 6121 2.609459 CTCGCGAATTCTACTTGGCATT 59.391 45.455 11.33 0.00 31.06 3.56
3599 6122 2.351418 TCGCGAATTCTACTTGGCATTG 59.649 45.455 6.20 0.00 31.06 2.82
3600 6123 2.454055 GCGAATTCTACTTGGCATTGC 58.546 47.619 3.52 0.00 31.06 3.56
3601 6124 2.098117 GCGAATTCTACTTGGCATTGCT 59.902 45.455 8.82 0.00 31.06 3.91
3602 6125 3.312421 GCGAATTCTACTTGGCATTGCTA 59.688 43.478 8.82 0.00 31.06 3.49
3603 6126 4.201910 GCGAATTCTACTTGGCATTGCTAA 60.202 41.667 8.82 7.99 31.06 3.09
3604 6127 5.676079 GCGAATTCTACTTGGCATTGCTAAA 60.676 40.000 8.84 3.43 31.06 1.85
3605 6128 6.321717 CGAATTCTACTTGGCATTGCTAAAA 58.678 36.000 8.84 0.94 0.00 1.52
3606 6129 6.974622 CGAATTCTACTTGGCATTGCTAAAAT 59.025 34.615 8.84 3.20 0.00 1.82
3607 6130 8.128582 CGAATTCTACTTGGCATTGCTAAAATA 58.871 33.333 8.84 4.06 0.00 1.40
3608 6131 9.237846 GAATTCTACTTGGCATTGCTAAAATAC 57.762 33.333 8.84 0.00 0.00 1.89
3609 6132 7.938140 TTCTACTTGGCATTGCTAAAATACT 57.062 32.000 8.84 0.00 0.00 2.12
3610 6133 7.938140 TCTACTTGGCATTGCTAAAATACTT 57.062 32.000 8.84 0.00 0.00 2.24
3611 6134 8.348285 TCTACTTGGCATTGCTAAAATACTTT 57.652 30.769 8.84 0.00 0.00 2.66
3612 6135 8.243426 TCTACTTGGCATTGCTAAAATACTTTG 58.757 33.333 8.84 0.00 0.00 2.77
3613 6136 6.165577 ACTTGGCATTGCTAAAATACTTTGG 58.834 36.000 8.84 0.00 0.00 3.28
3614 6137 5.736951 TGGCATTGCTAAAATACTTTGGT 57.263 34.783 8.82 0.00 0.00 3.67
3615 6138 6.107901 TGGCATTGCTAAAATACTTTGGTT 57.892 33.333 8.82 0.00 0.00 3.67
3616 6139 5.931146 TGGCATTGCTAAAATACTTTGGTTG 59.069 36.000 8.82 0.00 0.00 3.77
3617 6140 5.931724 GGCATTGCTAAAATACTTTGGTTGT 59.068 36.000 8.82 0.00 0.00 3.32
3618 6141 7.093992 GGCATTGCTAAAATACTTTGGTTGTA 58.906 34.615 8.82 0.00 0.00 2.41
3619 6142 7.600752 GGCATTGCTAAAATACTTTGGTTGTAA 59.399 33.333 8.82 0.00 0.00 2.41
3620 6143 9.150348 GCATTGCTAAAATACTTTGGTTGTAAT 57.850 29.630 0.16 0.00 0.00 1.89
3622 6145 8.958175 TTGCTAAAATACTTTGGTTGTAATCG 57.042 30.769 0.00 0.00 0.00 3.34
3623 6146 8.101654 TGCTAAAATACTTTGGTTGTAATCGT 57.898 30.769 0.00 0.00 0.00 3.73
3624 6147 9.217278 TGCTAAAATACTTTGGTTGTAATCGTA 57.783 29.630 0.00 0.00 0.00 3.43
3625 6148 9.698617 GCTAAAATACTTTGGTTGTAATCGTAG 57.301 33.333 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 61 4.550639 GCAAAACTGAAATTCGCAAACAGG 60.551 41.667 0.00 0.00 33.57 4.00
92 100 9.736023 CAAGTTACTTGCTTTTCTCAAAACTAT 57.264 29.630 12.37 0.00 34.63 2.12
131 142 5.410067 GCTTACATTTTTCTTATGCCTGCA 58.590 37.500 0.00 0.00 0.00 4.41
132 143 4.805719 GGCTTACATTTTTCTTATGCCTGC 59.194 41.667 0.00 0.00 34.63 4.85
133 144 6.212888 AGGCTTACATTTTTCTTATGCCTG 57.787 37.500 0.00 0.00 42.08 4.85
134 145 7.396055 TGTTAGGCTTACATTTTTCTTATGCCT 59.604 33.333 1.56 0.00 44.42 4.75
135 146 7.543756 TGTTAGGCTTACATTTTTCTTATGCC 58.456 34.615 1.56 0.00 36.66 4.40
136 147 9.586435 AATGTTAGGCTTACATTTTTCTTATGC 57.414 29.630 22.34 0.00 42.02 3.14
174 185 2.159503 CCTCGCTAGCCAGTATCGTATG 60.160 54.545 9.66 0.00 0.00 2.39
178 189 0.669077 AACCTCGCTAGCCAGTATCG 59.331 55.000 9.66 0.00 0.00 2.92
179 190 1.681793 TCAACCTCGCTAGCCAGTATC 59.318 52.381 9.66 0.00 0.00 2.24
180 191 1.776662 TCAACCTCGCTAGCCAGTAT 58.223 50.000 9.66 0.00 0.00 2.12
181 192 1.476891 CTTCAACCTCGCTAGCCAGTA 59.523 52.381 9.66 0.00 0.00 2.74
182 193 0.247736 CTTCAACCTCGCTAGCCAGT 59.752 55.000 9.66 0.69 0.00 4.00
183 194 0.532573 TCTTCAACCTCGCTAGCCAG 59.467 55.000 9.66 5.61 0.00 4.85
324 349 4.119862 ACATCAATTTCCCATAGACGTCG 58.880 43.478 10.46 0.00 0.00 5.12
398 424 3.762779 CGGCTGCCTCTTTATCTTTTTG 58.237 45.455 17.92 0.00 0.00 2.44
423 449 9.995957 GATTTGCCTCTTTATCTTCTTCTTTAC 57.004 33.333 0.00 0.00 0.00 2.01
424 450 9.739276 TGATTTGCCTCTTTATCTTCTTCTTTA 57.261 29.630 0.00 0.00 0.00 1.85
426 452 7.887495 AGTGATTTGCCTCTTTATCTTCTTCTT 59.113 33.333 0.00 0.00 0.00 2.52
427 453 7.401246 AGTGATTTGCCTCTTTATCTTCTTCT 58.599 34.615 0.00 0.00 0.00 2.85
428 454 7.622893 AGTGATTTGCCTCTTTATCTTCTTC 57.377 36.000 0.00 0.00 0.00 2.87
638 684 1.466167 CAGCTGAATCACGGAACAAGG 59.534 52.381 8.42 0.00 0.00 3.61
640 686 1.071542 TCCAGCTGAATCACGGAACAA 59.928 47.619 17.39 0.00 0.00 2.83
642 688 1.079503 GTCCAGCTGAATCACGGAAC 58.920 55.000 17.39 0.00 0.00 3.62
643 689 0.684535 TGTCCAGCTGAATCACGGAA 59.315 50.000 17.39 0.00 0.00 4.30
644 690 0.904649 ATGTCCAGCTGAATCACGGA 59.095 50.000 17.39 0.00 0.00 4.69
645 691 1.012086 CATGTCCAGCTGAATCACGG 58.988 55.000 17.39 0.00 0.00 4.94
646 692 1.931841 CTCATGTCCAGCTGAATCACG 59.068 52.381 17.39 3.93 0.00 4.35
698 1020 2.882876 CATGCTTCACCTGCCAGC 59.117 61.111 0.00 0.00 0.00 4.85
841 1179 4.023107 CCAATCTGTATACGTCTCGTCCAT 60.023 45.833 0.00 0.00 41.54 3.41
978 1388 2.189342 GGAGCTTCTGTTTCTCGATCG 58.811 52.381 9.36 9.36 0.00 3.69
979 1389 3.238108 TGGAGCTTCTGTTTCTCGATC 57.762 47.619 0.00 0.00 0.00 3.69
980 1390 3.685139 TTGGAGCTTCTGTTTCTCGAT 57.315 42.857 0.00 0.00 0.00 3.59
981 1391 3.329386 CATTGGAGCTTCTGTTTCTCGA 58.671 45.455 0.00 0.00 0.00 4.04
1018 1428 0.748729 AGAACGCCGAGGTAGAGGAG 60.749 60.000 0.00 0.00 0.00 3.69
1038 1451 1.751927 CATGGCCAGGAACAGGAGC 60.752 63.158 13.35 0.00 37.04 4.70
1039 1452 1.077212 CCATGGCCAGGAACAGGAG 60.077 63.158 21.32 0.00 37.04 3.69
1040 1453 2.615465 CCCATGGCCAGGAACAGGA 61.615 63.158 21.32 0.00 37.04 3.86
1066 1479 5.996644 GATCTATATCGGAGAGGGAGAAGA 58.003 45.833 0.00 0.00 43.63 2.87
1085 1520 1.786937 AGGCAACAGGAGATCGATCT 58.213 50.000 27.63 27.63 38.67 2.75
1090 1525 4.054671 CGAGAATTAGGCAACAGGAGATC 58.945 47.826 0.00 0.00 41.41 2.75
1113 1548 8.415553 TCATGCCGAGAAAATCAATCAAATTAT 58.584 29.630 0.00 0.00 0.00 1.28
1120 1555 4.621068 TGTCATGCCGAGAAAATCAATC 57.379 40.909 0.00 0.00 0.00 2.67
1121 1556 4.037208 GGATGTCATGCCGAGAAAATCAAT 59.963 41.667 0.00 0.00 0.00 2.57
1132 1567 3.274586 CCGCTGGATGTCATGCCG 61.275 66.667 1.44 0.00 0.00 5.69
1421 3125 1.374252 GAGTCGCTTGAAGCCGGAA 60.374 57.895 12.13 0.00 38.18 4.30
1467 3171 7.368833 TGTGCAAACTAGAAGAGAGTTAGTAC 58.631 38.462 0.00 0.00 36.10 2.73
1478 3182 4.686091 TCGATCAGTTGTGCAAACTAGAAG 59.314 41.667 12.06 10.63 0.00 2.85
1522 3297 6.092092 TCCTATGTGAACAATTGAATTTGCG 58.908 36.000 13.59 0.00 0.00 4.85
1572 3354 0.531200 GGTACGGCACTAACTCTGCT 59.469 55.000 0.00 0.00 34.84 4.24
1579 3361 2.702261 GGTGAATTGGTACGGCACTAA 58.298 47.619 0.00 0.00 31.50 2.24
1593 3381 0.400213 TTCCCAGCTGTTCGGTGAAT 59.600 50.000 13.81 0.00 43.75 2.57
1641 3429 1.173043 GGAAATTCATCACGTGGCCA 58.827 50.000 17.00 0.00 0.00 5.36
1809 3597 3.726517 CCGAAGCCACCGTGCAAG 61.727 66.667 0.00 0.00 0.00 4.01
1935 3723 1.461127 CTGAACTTTGTAGCGTGGCTC 59.539 52.381 0.00 0.00 40.44 4.70
2057 3854 2.223923 CCAGATCGAGTTTAGCCTCCTG 60.224 54.545 0.00 0.00 0.00 3.86
2072 3869 3.376546 GCATGGAAGAAGTGAACCAGATC 59.623 47.826 0.00 0.00 35.84 2.75
2073 3870 3.245016 TGCATGGAAGAAGTGAACCAGAT 60.245 43.478 0.00 0.00 35.84 2.90
2074 3871 2.106338 TGCATGGAAGAAGTGAACCAGA 59.894 45.455 0.00 0.00 35.84 3.86
2075 3872 2.486982 CTGCATGGAAGAAGTGAACCAG 59.513 50.000 0.00 0.00 35.84 4.00
2098 3897 0.591659 TCCTGTCAGTGAAGTCGTCG 59.408 55.000 0.00 0.00 0.00 5.12
2126 3925 2.679837 CCCTGATCAACTCCACGAAATG 59.320 50.000 0.00 0.00 0.00 2.32
2138 3937 0.614697 TGACGCCTCTCCCTGATCAA 60.615 55.000 0.00 0.00 0.00 2.57
2154 3953 0.249322 CCCACGGATATCACGGTGAC 60.249 60.000 13.92 0.50 41.41 3.67
2161 3960 0.826256 CCTCGTCCCCACGGATATCA 60.826 60.000 4.83 0.00 46.70 2.15
2164 3963 2.123597 CCCTCGTCCCCACGGATA 60.124 66.667 0.00 0.00 46.70 2.59
2205 4004 0.108424 CTTCTTGACCCTCTCGCAGG 60.108 60.000 0.00 0.00 43.01 4.85
2217 4016 2.351447 CGGTCGCTCAGTAACTTCTTGA 60.351 50.000 0.00 0.00 0.00 3.02
2225 4024 0.738975 CCATCTCGGTCGCTCAGTAA 59.261 55.000 0.00 0.00 0.00 2.24
2251 4050 1.134788 AGAACCGGTCCGATGTTCATC 60.135 52.381 25.64 0.00 40.58 2.92
2341 4154 3.243367 CCTCTATTTCCAGTGCTCTCTCG 60.243 52.174 0.00 0.00 0.00 4.04
2361 4174 0.040646 TCCCATCACTACCGTGTCCT 59.959 55.000 0.00 0.00 41.89 3.85
2371 4184 3.732938 GGAGCACCTCCCATCACT 58.267 61.111 0.00 0.00 44.36 3.41
2578 4391 2.501723 GACTCCTCCCTTGTAGCATTCA 59.498 50.000 0.00 0.00 0.00 2.57
2609 4422 4.506288 GTGTGTTTATTTTGCCAACCAGAC 59.494 41.667 0.00 0.00 0.00 3.51
2641 4454 1.097232 GCACTGCATATGCCTTCACA 58.903 50.000 24.54 4.10 41.18 3.58
2642 4455 1.065102 CTGCACTGCATATGCCTTCAC 59.935 52.381 24.54 10.93 42.69 3.18
2702 4517 2.480419 GACAACTGGGACTCATGTTTCG 59.520 50.000 0.00 0.00 0.00 3.46
2810 4628 8.440833 CACCTTCTTTTCTAAAACCGTACTATG 58.559 37.037 0.00 0.00 0.00 2.23
2811 4629 7.605309 CCACCTTCTTTTCTAAAACCGTACTAT 59.395 37.037 0.00 0.00 0.00 2.12
2812 4630 6.930722 CCACCTTCTTTTCTAAAACCGTACTA 59.069 38.462 0.00 0.00 0.00 1.82
2813 4631 5.761726 CCACCTTCTTTTCTAAAACCGTACT 59.238 40.000 0.00 0.00 0.00 2.73
2814 4632 5.759763 TCCACCTTCTTTTCTAAAACCGTAC 59.240 40.000 0.00 0.00 0.00 3.67
2815 4633 5.927819 TCCACCTTCTTTTCTAAAACCGTA 58.072 37.500 0.00 0.00 0.00 4.02
2816 4634 4.784177 TCCACCTTCTTTTCTAAAACCGT 58.216 39.130 0.00 0.00 0.00 4.83
2817 4635 5.758924 CTTCCACCTTCTTTTCTAAAACCG 58.241 41.667 0.00 0.00 0.00 4.44
2818 4636 5.302059 AGCTTCCACCTTCTTTTCTAAAACC 59.698 40.000 0.00 0.00 0.00 3.27
2819 4637 6.392625 AGCTTCCACCTTCTTTTCTAAAAC 57.607 37.500 0.00 0.00 0.00 2.43
2820 4638 7.123547 TGAAAGCTTCCACCTTCTTTTCTAAAA 59.876 33.333 0.00 0.00 0.00 1.52
2821 4639 6.605594 TGAAAGCTTCCACCTTCTTTTCTAAA 59.394 34.615 0.00 0.00 0.00 1.85
2822 4640 6.039382 GTGAAAGCTTCCACCTTCTTTTCTAA 59.961 38.462 4.14 0.00 0.00 2.10
2823 4641 5.531287 GTGAAAGCTTCCACCTTCTTTTCTA 59.469 40.000 4.14 0.00 0.00 2.10
2824 4642 4.339530 GTGAAAGCTTCCACCTTCTTTTCT 59.660 41.667 4.14 0.00 0.00 2.52
2825 4643 4.499865 GGTGAAAGCTTCCACCTTCTTTTC 60.500 45.833 26.24 3.59 46.94 2.29
2826 4644 3.384789 GGTGAAAGCTTCCACCTTCTTTT 59.615 43.478 26.24 0.00 46.94 2.27
2827 4645 2.959030 GGTGAAAGCTTCCACCTTCTTT 59.041 45.455 26.24 0.00 46.94 2.52
2828 4646 2.587522 GGTGAAAGCTTCCACCTTCTT 58.412 47.619 26.24 0.00 46.94 2.52
2829 4647 2.278332 GGTGAAAGCTTCCACCTTCT 57.722 50.000 26.24 0.00 46.94 2.85
2840 4658 0.449388 CCGATGCAGAAGGTGAAAGC 59.551 55.000 0.00 0.00 0.00 3.51
2841 4659 1.813513 ACCGATGCAGAAGGTGAAAG 58.186 50.000 9.38 0.00 36.81 2.62
2842 4660 1.879380 CAACCGATGCAGAAGGTGAAA 59.121 47.619 10.70 0.00 38.44 2.69
2843 4661 1.522668 CAACCGATGCAGAAGGTGAA 58.477 50.000 10.70 0.00 38.44 3.18
2844 4662 3.231734 CAACCGATGCAGAAGGTGA 57.768 52.632 10.70 0.00 38.44 4.02
2857 4675 3.418913 TCGCAACCATCGCAACCG 61.419 61.111 0.00 0.00 0.00 4.44
2858 4676 2.175811 GTCGCAACCATCGCAACC 59.824 61.111 0.00 0.00 0.00 3.77
2859 4677 2.202171 CGTCGCAACCATCGCAAC 60.202 61.111 0.00 0.00 0.00 4.17
2860 4678 4.083600 GCGTCGCAACCATCGCAA 62.084 61.111 13.44 0.00 46.40 4.85
2863 4681 3.410516 TGTGCGTCGCAACCATCG 61.411 61.111 23.58 0.00 41.47 3.84
2864 4682 1.911293 ATGTGTGCGTCGCAACCATC 61.911 55.000 23.58 9.77 41.47 3.51
2865 4683 1.911293 GATGTGTGCGTCGCAACCAT 61.911 55.000 23.58 24.27 41.47 3.55
2866 4684 2.590291 ATGTGTGCGTCGCAACCA 60.590 55.556 23.58 20.70 41.47 3.67
2867 4685 2.173382 GATGTGTGCGTCGCAACC 59.827 61.111 23.58 15.52 41.47 3.77
2868 4686 1.911293 ATGGATGTGTGCGTCGCAAC 61.911 55.000 23.58 20.78 41.47 4.17
2869 4687 0.390472 TATGGATGTGTGCGTCGCAA 60.390 50.000 23.58 7.07 41.47 4.85
2870 4688 0.179086 ATATGGATGTGTGCGTCGCA 60.179 50.000 17.58 17.58 40.97 5.10
2871 4689 0.233074 CATATGGATGTGTGCGTCGC 59.767 55.000 11.10 11.10 0.00 5.19
2872 4690 1.570813 ACATATGGATGTGTGCGTCG 58.429 50.000 7.80 0.00 44.90 5.12
2873 4691 3.868661 TGTAACATATGGATGTGTGCGTC 59.131 43.478 7.80 0.00 45.93 5.19
2874 4692 3.867857 TGTAACATATGGATGTGTGCGT 58.132 40.909 7.80 0.00 45.93 5.24
2875 4693 4.873768 TTGTAACATATGGATGTGTGCG 57.126 40.909 7.80 0.00 45.93 5.34
2876 4694 9.748708 ATTTTATTGTAACATATGGATGTGTGC 57.251 29.630 7.80 0.00 45.93 4.57
2889 4707 9.964253 CAATGCGCAATTTATTTTATTGTAACA 57.036 25.926 17.11 0.00 35.82 2.41
2890 4708 9.965748 ACAATGCGCAATTTATTTTATTGTAAC 57.034 25.926 17.11 0.00 36.20 2.50
2893 4711 9.965748 GTAACAATGCGCAATTTATTTTATTGT 57.034 25.926 17.11 13.66 38.66 2.71
2894 4712 9.964253 TGTAACAATGCGCAATTTATTTTATTG 57.036 25.926 17.11 12.94 36.34 1.90
2898 4716 9.722056 TTTTTGTAACAATGCGCAATTTATTTT 57.278 22.222 17.11 0.00 0.00 1.82
2954 4772 9.961265 CTGATATGTTAGAATCATGCAAACATT 57.039 29.630 14.05 2.47 40.32 2.71
2955 4773 9.346005 TCTGATATGTTAGAATCATGCAAACAT 57.654 29.630 13.50 13.50 42.00 2.71
2956 4774 8.615211 GTCTGATATGTTAGAATCATGCAAACA 58.385 33.333 0.00 0.00 34.81 2.83
2957 4775 7.795734 CGTCTGATATGTTAGAATCATGCAAAC 59.204 37.037 0.00 0.00 31.95 2.93
2958 4776 7.710475 TCGTCTGATATGTTAGAATCATGCAAA 59.290 33.333 0.00 0.00 31.95 3.68
2959 4777 7.209475 TCGTCTGATATGTTAGAATCATGCAA 58.791 34.615 0.00 0.00 31.95 4.08
2960 4778 6.748132 TCGTCTGATATGTTAGAATCATGCA 58.252 36.000 0.00 0.00 31.95 3.96
2961 4779 7.824704 ATCGTCTGATATGTTAGAATCATGC 57.175 36.000 0.00 0.00 31.95 4.06
2996 4814 9.513906 TGTCTTCCTATATTCACATGTTTTCAA 57.486 29.630 0.00 0.00 0.00 2.69
2997 4815 9.685276 ATGTCTTCCTATATTCACATGTTTTCA 57.315 29.630 0.00 0.00 0.00 2.69
2999 4817 9.911788 AGATGTCTTCCTATATTCACATGTTTT 57.088 29.630 0.00 0.00 0.00 2.43
3004 4822 9.664332 GCATTAGATGTCTTCCTATATTCACAT 57.336 33.333 0.00 0.00 0.00 3.21
3005 4823 8.650490 TGCATTAGATGTCTTCCTATATTCACA 58.350 33.333 0.00 0.00 0.00 3.58
3006 4824 9.494271 TTGCATTAGATGTCTTCCTATATTCAC 57.506 33.333 0.00 0.00 0.00 3.18
3009 4827 9.458727 CCATTGCATTAGATGTCTTCCTATATT 57.541 33.333 0.00 0.00 0.00 1.28
3010 4828 8.829746 TCCATTGCATTAGATGTCTTCCTATAT 58.170 33.333 0.00 0.00 0.00 0.86
3011 4829 8.206126 TCCATTGCATTAGATGTCTTCCTATA 57.794 34.615 0.00 0.00 0.00 1.31
3012 4830 7.016957 TCTCCATTGCATTAGATGTCTTCCTAT 59.983 37.037 0.00 0.00 0.00 2.57
3013 4831 6.327365 TCTCCATTGCATTAGATGTCTTCCTA 59.673 38.462 0.00 0.00 0.00 2.94
3014 4832 5.131642 TCTCCATTGCATTAGATGTCTTCCT 59.868 40.000 0.00 0.00 0.00 3.36
3015 4833 5.238214 GTCTCCATTGCATTAGATGTCTTCC 59.762 44.000 0.00 0.00 0.00 3.46
3016 4834 5.050499 CGTCTCCATTGCATTAGATGTCTTC 60.050 44.000 0.00 0.00 0.00 2.87
3017 4835 4.813161 CGTCTCCATTGCATTAGATGTCTT 59.187 41.667 0.00 0.00 0.00 3.01
3018 4836 4.100035 TCGTCTCCATTGCATTAGATGTCT 59.900 41.667 0.00 0.00 0.00 3.41
3019 4837 4.371786 TCGTCTCCATTGCATTAGATGTC 58.628 43.478 0.00 0.00 0.00 3.06
3020 4838 4.406648 TCGTCTCCATTGCATTAGATGT 57.593 40.909 0.00 0.00 0.00 3.06
3021 4839 5.686834 CATTCGTCTCCATTGCATTAGATG 58.313 41.667 0.00 0.00 0.00 2.90
3022 4840 4.214971 GCATTCGTCTCCATTGCATTAGAT 59.785 41.667 0.00 0.00 33.58 1.98
3023 4841 3.561310 GCATTCGTCTCCATTGCATTAGA 59.439 43.478 0.00 0.00 33.58 2.10
3024 4842 3.562973 AGCATTCGTCTCCATTGCATTAG 59.437 43.478 0.00 0.00 35.79 1.73
3025 4843 3.544684 AGCATTCGTCTCCATTGCATTA 58.455 40.909 0.00 0.00 35.79 1.90
3026 4844 2.372264 AGCATTCGTCTCCATTGCATT 58.628 42.857 0.00 0.00 35.79 3.56
3027 4845 2.048444 AGCATTCGTCTCCATTGCAT 57.952 45.000 0.00 0.00 35.79 3.96
3028 4846 2.689553 TAGCATTCGTCTCCATTGCA 57.310 45.000 0.00 0.00 35.79 4.08
3029 4847 5.869753 AATATAGCATTCGTCTCCATTGC 57.130 39.130 0.00 0.00 0.00 3.56
3073 4891 6.503589 TGAGTCGGAAGAAAGAAACAAAAA 57.496 33.333 0.00 0.00 45.01 1.94
3074 4892 6.693315 ATGAGTCGGAAGAAAGAAACAAAA 57.307 33.333 0.00 0.00 45.01 2.44
3075 4893 6.494842 CAATGAGTCGGAAGAAAGAAACAAA 58.505 36.000 0.00 0.00 45.01 2.83
3076 4894 5.505654 GCAATGAGTCGGAAGAAAGAAACAA 60.506 40.000 0.00 0.00 45.01 2.83
3077 4895 4.024048 GCAATGAGTCGGAAGAAAGAAACA 60.024 41.667 0.00 0.00 45.01 2.83
3078 4896 4.467735 GCAATGAGTCGGAAGAAAGAAAC 58.532 43.478 0.00 0.00 45.01 2.78
3079 4897 3.502211 GGCAATGAGTCGGAAGAAAGAAA 59.498 43.478 0.00 0.00 45.01 2.52
3080 4898 3.074412 GGCAATGAGTCGGAAGAAAGAA 58.926 45.455 0.00 0.00 45.01 2.52
3081 4899 2.038426 TGGCAATGAGTCGGAAGAAAGA 59.962 45.455 0.00 0.00 45.01 2.52
3082 4900 2.426522 TGGCAATGAGTCGGAAGAAAG 58.573 47.619 0.00 0.00 45.01 2.62
3083 4901 2.552315 GTTGGCAATGAGTCGGAAGAAA 59.448 45.455 1.92 0.00 45.01 2.52
3084 4902 2.151202 GTTGGCAATGAGTCGGAAGAA 58.849 47.619 1.92 0.00 45.01 2.52
3085 4903 1.071542 TGTTGGCAATGAGTCGGAAGA 59.928 47.619 1.92 0.00 38.16 2.87
3086 4904 1.466167 CTGTTGGCAATGAGTCGGAAG 59.534 52.381 1.92 0.00 0.00 3.46
3087 4905 1.202758 ACTGTTGGCAATGAGTCGGAA 60.203 47.619 1.92 0.00 0.00 4.30
3088 4906 0.396435 ACTGTTGGCAATGAGTCGGA 59.604 50.000 1.92 0.00 0.00 4.55
3089 4907 0.798776 GACTGTTGGCAATGAGTCGG 59.201 55.000 20.10 8.75 0.00 4.79
3090 4908 1.800805 AGACTGTTGGCAATGAGTCG 58.199 50.000 24.80 7.43 39.89 4.18
3091 4909 3.817647 AGAAAGACTGTTGGCAATGAGTC 59.182 43.478 24.25 24.25 35.97 3.36
3092 4910 3.825328 AGAAAGACTGTTGGCAATGAGT 58.175 40.909 13.01 13.01 0.00 3.41
3093 4911 4.612259 CGAAGAAAGACTGTTGGCAATGAG 60.612 45.833 1.92 5.42 0.00 2.90
3094 4912 3.250762 CGAAGAAAGACTGTTGGCAATGA 59.749 43.478 1.92 0.00 0.00 2.57
3095 4913 3.558505 CGAAGAAAGACTGTTGGCAATG 58.441 45.455 1.92 2.21 0.00 2.82
3096 4914 2.554032 CCGAAGAAAGACTGTTGGCAAT 59.446 45.455 1.92 0.00 0.00 3.56
3097 4915 1.946768 CCGAAGAAAGACTGTTGGCAA 59.053 47.619 0.00 0.00 0.00 4.52
3186 5708 3.454375 TGTTGTTGACGGAGAGTTCTTC 58.546 45.455 0.00 0.00 0.00 2.87
3199 5721 3.876914 CAGGTTAGTTGCTCTGTTGTTGA 59.123 43.478 0.00 0.00 0.00 3.18
3204 5726 1.421646 AGGCAGGTTAGTTGCTCTGTT 59.578 47.619 0.00 0.00 41.27 3.16
3248 5771 6.071320 GGGATAATCAGCCAGGTCTTATTTT 58.929 40.000 0.00 0.00 0.00 1.82
3262 5785 2.890814 ACCGAGGGTAGGGATAATCAG 58.109 52.381 0.00 0.00 32.11 2.90
3308 5831 7.812690 AAAATAAAGAAAACTGTACCCGACT 57.187 32.000 0.00 0.00 0.00 4.18
3323 5846 7.486647 ACGGCTACGAGAGATAAAAATAAAGA 58.513 34.615 0.00 0.00 44.60 2.52
3337 5860 1.255882 TTTGGGTAACGGCTACGAGA 58.744 50.000 0.00 0.00 44.60 4.04
3573 6096 3.381045 CCAAGTAGAATTCGCGAGCATA 58.619 45.455 9.59 0.00 0.00 3.14
3574 6097 2.205074 CCAAGTAGAATTCGCGAGCAT 58.795 47.619 9.59 0.00 0.00 3.79
3575 6098 1.640428 CCAAGTAGAATTCGCGAGCA 58.360 50.000 9.59 0.00 0.00 4.26
3576 6099 0.301987 GCCAAGTAGAATTCGCGAGC 59.698 55.000 9.59 0.70 0.00 5.03
3577 6100 1.640428 TGCCAAGTAGAATTCGCGAG 58.360 50.000 9.59 0.00 0.00 5.03
3578 6101 2.309528 ATGCCAAGTAGAATTCGCGA 57.690 45.000 3.71 3.71 0.00 5.87
3579 6102 2.708514 CAATGCCAAGTAGAATTCGCG 58.291 47.619 0.00 0.00 0.00 5.87
3580 6103 2.098117 AGCAATGCCAAGTAGAATTCGC 59.902 45.455 0.00 0.00 0.00 4.70
3581 6104 5.484173 TTAGCAATGCCAAGTAGAATTCG 57.516 39.130 0.00 0.00 0.00 3.34
3582 6105 9.237846 GTATTTTAGCAATGCCAAGTAGAATTC 57.762 33.333 0.00 0.00 0.00 2.17
3583 6106 8.971073 AGTATTTTAGCAATGCCAAGTAGAATT 58.029 29.630 0.00 0.00 0.00 2.17
3584 6107 8.525290 AGTATTTTAGCAATGCCAAGTAGAAT 57.475 30.769 0.00 0.00 0.00 2.40
3585 6108 7.938140 AGTATTTTAGCAATGCCAAGTAGAA 57.062 32.000 0.00 0.00 0.00 2.10
3586 6109 7.938140 AAGTATTTTAGCAATGCCAAGTAGA 57.062 32.000 0.00 0.00 0.00 2.59
3587 6110 7.489113 CCAAAGTATTTTAGCAATGCCAAGTAG 59.511 37.037 0.00 0.00 35.03 2.57
3588 6111 7.039363 ACCAAAGTATTTTAGCAATGCCAAGTA 60.039 33.333 0.00 0.00 35.03 2.24
3589 6112 6.165577 CCAAAGTATTTTAGCAATGCCAAGT 58.834 36.000 0.00 0.00 35.03 3.16
3590 6113 6.165577 ACCAAAGTATTTTAGCAATGCCAAG 58.834 36.000 0.00 0.00 35.03 3.61
3591 6114 6.107901 ACCAAAGTATTTTAGCAATGCCAA 57.892 33.333 0.00 0.00 35.03 4.52
3592 6115 5.736951 ACCAAAGTATTTTAGCAATGCCA 57.263 34.783 0.00 0.00 35.03 4.92
3593 6116 5.931724 ACAACCAAAGTATTTTAGCAATGCC 59.068 36.000 0.00 0.00 35.03 4.40
3594 6117 8.527567 TTACAACCAAAGTATTTTAGCAATGC 57.472 30.769 0.00 0.00 35.03 3.56
3596 6119 9.567848 CGATTACAACCAAAGTATTTTAGCAAT 57.432 29.630 0.00 0.00 35.03 3.56
3597 6120 8.569641 ACGATTACAACCAAAGTATTTTAGCAA 58.430 29.630 0.00 0.00 35.03 3.91
3598 6121 8.101654 ACGATTACAACCAAAGTATTTTAGCA 57.898 30.769 0.00 0.00 35.03 3.49
3599 6122 9.698617 CTACGATTACAACCAAAGTATTTTAGC 57.301 33.333 0.00 0.00 35.03 3.09


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

AutoCloner maintained by Alex Coulton.