Multiple sequence alignment - TraesCS3D01G106300

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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 TraesCS3D01G106300 chr3D 100.000 2928 0 0 1 2928 58400501 58397574 0.000000e+00 5408.0
1 TraesCS3D01G106300 chr3D 88.889 351 29 7 2582 2927 547454211 547454556 9.700000e-115 424.0
2 TraesCS3D01G106300 chr3D 88.022 359 24 9 2582 2928 170555753 170556104 9.770000e-110 407.0
3 TraesCS3D01G106300 chr3D 90.833 120 10 1 2343 2461 120315100 120314981 3.020000e-35 159.0
4 TraesCS3D01G106300 chr3D 96.226 53 2 0 2086 2138 612596984 612597036 1.450000e-13 87.9
5 TraesCS3D01G106300 chr3D 83.824 68 6 5 1995 2062 120315222 120315160 3.150000e-05 60.2
6 TraesCS3D01G106300 chr3B 86.364 1958 183 45 82 2005 92595955 92594048 0.000000e+00 2060.0
7 TraesCS3D01G106300 chr3B 87.234 470 32 7 2134 2581 92594051 92593588 7.240000e-141 510.0
8 TraesCS3D01G106300 chr3B 88.920 361 29 7 2579 2928 606379167 606379527 4.480000e-118 435.0
9 TraesCS3D01G106300 chr3B 79.714 419 63 18 4 409 92597470 92597061 1.720000e-72 283.0
10 TraesCS3D01G106300 chr3B 90.323 124 11 1 2343 2466 172450831 172450709 8.400000e-36 161.0
11 TraesCS3D01G106300 chr3B 97.826 46 1 0 2221 2266 829267082 829267127 2.420000e-11 80.5
12 TraesCS3D01G106300 chr3B 83.824 68 6 1 1995 2062 172450953 172450891 3.150000e-05 60.2
13 TraesCS3D01G106300 chr3A 88.064 1508 100 29 1135 2581 67360538 67359050 0.000000e+00 1714.0
14 TraesCS3D01G106300 chr3A 90.198 1112 70 22 1 1101 67361617 67360534 0.000000e+00 1413.0
15 TraesCS3D01G106300 chr3A 86.119 353 35 8 2582 2928 157036180 157036524 4.610000e-98 368.0
16 TraesCS3D01G106300 chr3A 82.787 122 15 4 1864 1980 127274758 127274638 1.440000e-18 104.0
17 TraesCS3D01G106300 chr3A 83.824 68 6 1 1995 2062 127274158 127274096 3.150000e-05 60.2
18 TraesCS3D01G106300 chr7A 89.518 353 30 7 2582 2928 596329749 596329398 9.630000e-120 440.0
19 TraesCS3D01G106300 chr1D 88.483 356 32 5 2582 2928 39864313 39864668 3.490000e-114 422.0
20 TraesCS3D01G106300 chr1D 94.231 52 1 1 2088 2139 95836674 95836723 8.700000e-11 78.7
21 TraesCS3D01G106300 chr7D 88.102 353 26 11 2585 2928 533486350 533486005 3.510000e-109 405.0
22 TraesCS3D01G106300 chr1B 87.328 363 32 9 2577 2928 470724390 470724031 1.260000e-108 403.0
23 TraesCS3D01G106300 chr4A 86.197 355 37 8 2584 2928 651801933 651802285 9.910000e-100 374.0
24 TraesCS3D01G106300 chr2A 96.226 53 2 0 2086 2138 58579559 58579611 1.450000e-13 87.9
25 TraesCS3D01G106300 chr2A 92.453 53 3 1 2086 2138 161509279 161509228 1.130000e-09 75.0
26 TraesCS3D01G106300 chr6A 94.118 51 3 0 2088 2138 603775816 603775766 8.700000e-11 78.7
27 TraesCS3D01G106300 chr6A 83.333 72 10 2 305 375 529639844 529639914 6.770000e-07 65.8


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 TraesCS3D01G106300 chr3D 58397574 58400501 2927 True 5408.0 5408 100.000000 1 2928 1 chr3D.!!$R1 2927
1 TraesCS3D01G106300 chr3B 92593588 92597470 3882 True 951.0 2060 84.437333 4 2581 3 chr3B.!!$R1 2577
2 TraesCS3D01G106300 chr3A 67359050 67361617 2567 True 1563.5 1714 89.131000 1 2581 2 chr3A.!!$R1 2580

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
942 2398 0.391597 GACGGGTCTGACCAAGAACA 59.608 55.0 26.94 0.0 45.32 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2806 4346 0.10852 ATGCGAAACGGTATGACGGT 60.109 50.0 0.0 0.0 38.39 4.83 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 40 6.189677 TGTTCTGAAGTCGAACATTGTTTT 57.810 33.333 3.08 0.00 44.03 2.43
38 41 6.616947 TGTTCTGAAGTCGAACATTGTTTTT 58.383 32.000 3.08 0.00 44.03 1.94
254 1696 8.439286 CCAGAAACAACTTTTTGAAATTTCGAA 58.561 29.630 15.57 15.57 33.52 3.71
300 1743 5.467902 TTTTGCATTCTTGAACTTTGTGC 57.532 34.783 0.00 0.00 0.00 4.57
308 1751 7.622672 GCATTCTTGAACTTTGTGCATTTATGG 60.623 37.037 0.00 0.00 0.00 2.74
333 1777 7.793427 GGACATTTTTGAAAATCACGAACATTG 59.207 33.333 0.00 0.00 36.52 2.82
405 1849 8.672823 TCATGATTCCATCTCTAGACATTTTG 57.327 34.615 0.00 0.00 0.00 2.44
415 1859 9.159364 CATCTCTAGACATTTTGTGATTTCTCA 57.841 33.333 0.00 0.00 0.00 3.27
606 2054 6.011277 GCGCTCATTTTTCAAATTCATGAAC 58.989 36.000 11.07 0.00 38.95 3.18
660 2109 5.856156 TCATGAACATGTTTTGAATTGCCT 58.144 33.333 13.36 0.00 39.72 4.75
679 2129 7.403312 TTGCCTAGCATTTTTATATGTGTGT 57.597 32.000 0.00 0.00 38.76 3.72
728 2180 8.885494 TTTTCGAAATCATGAACATTTTTCCT 57.115 26.923 12.12 0.00 0.00 3.36
794 2248 9.611284 TTCACGAACATATTTTGAATTGAGAAG 57.389 29.630 0.00 0.00 0.00 2.85
869 2324 4.334443 CGAATAGTTTGCGAATCCACAAG 58.666 43.478 0.00 0.00 0.00 3.16
931 2387 3.390003 TTTTTGAAGCGACGGGTCT 57.610 47.368 0.00 0.00 0.00 3.85
942 2398 0.391597 GACGGGTCTGACCAAGAACA 59.608 55.000 26.94 0.00 45.32 3.18
1008 2464 6.126409 AGTTGGTCACTCTGTTCCATAAAAA 58.874 36.000 0.00 0.00 0.00 1.94
1046 2502 5.378292 AGACTCATACCATACTATGTGCG 57.622 43.478 0.00 0.00 0.00 5.34
1048 2504 5.302059 AGACTCATACCATACTATGTGCGTT 59.698 40.000 0.00 0.00 0.00 4.84
1085 2542 3.938963 CGACACCATAAAACCTGTAGCAT 59.061 43.478 0.00 0.00 0.00 3.79
1100 2557 3.758023 TGTAGCATGCTAAACAATGTGCT 59.242 39.130 28.44 0.94 43.05 4.40
1101 2558 3.226346 AGCATGCTAAACAATGTGCTG 57.774 42.857 21.21 0.00 39.95 4.41
1102 2559 2.559668 AGCATGCTAAACAATGTGCTGT 59.440 40.909 21.21 0.00 39.95 4.40
1103 2560 2.664568 GCATGCTAAACAATGTGCTGTG 59.335 45.455 11.37 0.00 30.62 3.66
1106 2563 3.213506 TGCTAAACAATGTGCTGTGAGT 58.786 40.909 0.00 0.00 0.00 3.41
1107 2564 3.631686 TGCTAAACAATGTGCTGTGAGTT 59.368 39.130 0.00 0.00 0.00 3.01
1109 2566 5.147162 GCTAAACAATGTGCTGTGAGTTAC 58.853 41.667 0.00 0.00 0.00 2.50
1110 2567 4.568152 AAACAATGTGCTGTGAGTTACC 57.432 40.909 0.00 0.00 0.00 2.85
1111 2568 3.492102 ACAATGTGCTGTGAGTTACCT 57.508 42.857 0.00 0.00 0.00 3.08
1112 2569 3.820557 ACAATGTGCTGTGAGTTACCTT 58.179 40.909 0.00 0.00 0.00 3.50
1113 2570 3.565482 ACAATGTGCTGTGAGTTACCTTG 59.435 43.478 0.00 0.00 0.00 3.61
1114 2571 2.254546 TGTGCTGTGAGTTACCTTGG 57.745 50.000 0.00 0.00 0.00 3.61
1115 2572 1.488812 TGTGCTGTGAGTTACCTTGGT 59.511 47.619 0.00 0.00 0.00 3.67
1116 2573 1.873591 GTGCTGTGAGTTACCTTGGTG 59.126 52.381 2.03 0.00 0.00 4.17
1117 2574 0.875059 GCTGTGAGTTACCTTGGTGC 59.125 55.000 2.03 0.00 0.00 5.01
1118 2575 1.523758 CTGTGAGTTACCTTGGTGCC 58.476 55.000 2.03 0.00 0.00 5.01
1119 2576 0.109723 TGTGAGTTACCTTGGTGCCC 59.890 55.000 2.03 0.00 0.00 5.36
1120 2577 0.608308 GTGAGTTACCTTGGTGCCCC 60.608 60.000 2.03 0.00 0.00 5.80
1131 2588 1.226104 TGGTGCCCCTCTACCTCCTA 61.226 60.000 0.00 0.00 37.84 2.94
1132 2589 0.191314 GGTGCCCCTCTACCTCCTAT 59.809 60.000 0.00 0.00 34.11 2.57
1133 2590 1.432024 GGTGCCCCTCTACCTCCTATA 59.568 57.143 0.00 0.00 34.11 1.31
1183 2641 0.609131 AACATGAAGGCGACAAGGGG 60.609 55.000 0.00 0.00 0.00 4.79
1245 2707 6.346096 TCCCCAACTCTAAATACATCGAAAG 58.654 40.000 0.00 0.00 0.00 2.62
1277 2739 4.379918 GGTCTTTCACTCTTTTGCATAGCC 60.380 45.833 0.00 0.00 0.00 3.93
1322 2786 1.586154 GCTTCCATTCCACCACCACG 61.586 60.000 0.00 0.00 0.00 4.94
1351 2820 3.345808 CCACCACGAGCAACACCG 61.346 66.667 0.00 0.00 0.00 4.94
1557 3029 2.749621 CCAAAGTCCACTCCATAACAGC 59.250 50.000 0.00 0.00 0.00 4.40
1572 3044 1.456518 CAGCGGAGGAGGAGATGGA 60.457 63.158 0.00 0.00 0.00 3.41
1688 3163 1.080501 CCAGCGTTGAAGAGCGAGA 60.081 57.895 0.00 0.00 38.61 4.04
1737 3212 4.083862 GCCCGGCGAGGACTCTTT 62.084 66.667 9.30 0.00 45.00 2.52
1738 3213 2.184579 CCCGGCGAGGACTCTTTC 59.815 66.667 9.30 0.00 45.00 2.62
1779 3260 1.202200 GGATTCAGACGACGAGGACAG 60.202 57.143 0.00 0.00 0.00 3.51
1784 3265 0.956410 AGACGACGAGGACAGTGAGG 60.956 60.000 0.00 0.00 0.00 3.86
1786 3267 1.235948 ACGACGAGGACAGTGAGGAC 61.236 60.000 0.00 0.00 0.00 3.85
1847 3335 0.107456 ATCGATCAATCTTGGCCGCT 59.893 50.000 0.00 0.00 0.00 5.52
1879 3370 9.794719 TGCTGTGATATACTACTAGTTCTGTAT 57.205 33.333 0.00 10.29 0.00 2.29
1917 3419 3.259064 GAGTTTGGCGCTCTGTACATAA 58.741 45.455 7.64 0.00 0.00 1.90
1920 3422 5.050490 AGTTTGGCGCTCTGTACATAATAG 58.950 41.667 7.64 0.00 0.00 1.73
1921 3423 4.665833 TTGGCGCTCTGTACATAATAGT 57.334 40.909 7.64 0.00 0.00 2.12
1922 3424 5.777850 TTGGCGCTCTGTACATAATAGTA 57.222 39.130 7.64 0.00 0.00 1.82
1942 3451 6.808008 AGTAGATGAATAAATGGCAATCCG 57.192 37.500 0.00 0.00 34.14 4.18
1948 3457 4.950475 TGAATAAATGGCAATCCGGTGTTA 59.050 37.500 0.00 0.00 34.14 2.41
1987 3496 2.597510 AGCGTTTCCCCCTGTTGC 60.598 61.111 0.00 0.00 0.00 4.17
2022 3531 5.437060 AGTGCAGTTCTTGAGTAAAGGAAA 58.563 37.500 0.00 0.00 36.46 3.13
2025 3534 5.296780 TGCAGTTCTTGAGTAAAGGAAAGTG 59.703 40.000 0.00 0.00 36.46 3.16
2026 3535 5.278022 GCAGTTCTTGAGTAAAGGAAAGTGG 60.278 44.000 0.00 0.00 36.46 4.00
2027 3536 4.822350 AGTTCTTGAGTAAAGGAAAGTGGC 59.178 41.667 0.00 0.00 36.46 5.01
2028 3537 4.431416 TCTTGAGTAAAGGAAAGTGGCA 57.569 40.909 0.00 0.00 36.46 4.92
2030 3539 5.003804 TCTTGAGTAAAGGAAAGTGGCATC 58.996 41.667 0.00 0.00 36.46 3.91
2031 3540 4.365514 TGAGTAAAGGAAAGTGGCATCA 57.634 40.909 0.00 0.00 0.00 3.07
2033 3542 4.701651 TGAGTAAAGGAAAGTGGCATCATG 59.298 41.667 0.00 0.00 0.00 3.07
2036 3545 2.134789 AGGAAAGTGGCATCATGGAC 57.865 50.000 0.00 0.00 0.00 4.02
2037 3546 1.637553 AGGAAAGTGGCATCATGGACT 59.362 47.619 0.00 0.00 0.00 3.85
2040 3549 3.285484 GAAAGTGGCATCATGGACTCAT 58.715 45.455 0.00 0.00 0.00 2.90
2056 3565 6.124340 TGGACTCATGATCATTTGCATAAGT 58.876 36.000 5.16 0.00 0.00 2.24
2061 3570 4.389890 TGATCATTTGCATAAGTTGGCC 57.610 40.909 0.00 0.00 0.00 5.36
2068 3577 1.035139 GCATAAGTTGGCCTCATGGG 58.965 55.000 3.32 0.00 38.36 4.00
2077 3586 2.202878 CCTCATGGGCACGTACGG 60.203 66.667 21.06 9.73 0.00 4.02
2112 3628 5.545063 TTTTTGAAAAGAAGGATGACCCC 57.455 39.130 0.00 0.00 36.73 4.95
2114 3630 2.358258 TGAAAAGAAGGATGACCCCCT 58.642 47.619 0.00 0.00 36.73 4.79
2146 3662 1.160329 GGGAGATGCATGTACCGTGC 61.160 60.000 9.78 12.07 45.53 5.34
2198 3717 3.831323 TGCTTTTCTCTTCATCACCCAA 58.169 40.909 0.00 0.00 0.00 4.12
2199 3718 4.410099 TGCTTTTCTCTTCATCACCCAAT 58.590 39.130 0.00 0.00 0.00 3.16
2211 3730 2.291365 TCACCCAATGATCGCTTGATG 58.709 47.619 8.89 7.28 30.70 3.07
2333 3873 3.334691 TCTGTTAACACTATGCTGCACC 58.665 45.455 3.57 0.00 0.00 5.01
2334 3874 3.007940 TCTGTTAACACTATGCTGCACCT 59.992 43.478 3.57 0.00 0.00 4.00
2335 3875 3.073678 TGTTAACACTATGCTGCACCTG 58.926 45.455 3.57 2.84 0.00 4.00
2336 3876 1.737838 TAACACTATGCTGCACCTGC 58.262 50.000 3.57 0.00 42.50 4.85
2389 3929 8.322906 TGAACAACAGTTGGAATATAAGACTG 57.677 34.615 17.76 0.00 42.48 3.51
2516 4056 1.346722 GAAGAGTCGTGGGGGAAAAGA 59.653 52.381 0.00 0.00 0.00 2.52
2571 4111 6.203338 GCATTCCATTTTGTCACTGTTTGATT 59.797 34.615 0.00 0.00 36.32 2.57
2581 4121 6.329496 TGTCACTGTTTGATTGAAGGTTTTC 58.671 36.000 0.00 0.00 36.32 2.29
2582 4122 5.455525 GTCACTGTTTGATTGAAGGTTTTCG 59.544 40.000 0.00 0.00 36.32 3.46
2583 4123 4.739716 CACTGTTTGATTGAAGGTTTTCGG 59.260 41.667 0.00 0.00 36.04 4.30
2584 4124 4.642885 ACTGTTTGATTGAAGGTTTTCGGA 59.357 37.500 0.00 0.00 36.04 4.55
2585 4125 5.126384 ACTGTTTGATTGAAGGTTTTCGGAA 59.874 36.000 0.00 0.00 36.04 4.30
2586 4126 5.967088 TGTTTGATTGAAGGTTTTCGGAAA 58.033 33.333 0.00 0.00 36.04 3.13
2587 4127 6.578023 TGTTTGATTGAAGGTTTTCGGAAAT 58.422 32.000 3.67 0.00 36.04 2.17
2588 4128 6.699642 TGTTTGATTGAAGGTTTTCGGAAATC 59.300 34.615 3.67 3.56 36.04 2.17
2589 4129 5.385509 TGATTGAAGGTTTTCGGAAATCC 57.614 39.130 18.64 18.64 36.04 3.01
2590 4130 4.830046 TGATTGAAGGTTTTCGGAAATCCA 59.170 37.500 24.95 10.61 36.04 3.41
2591 4131 5.303078 TGATTGAAGGTTTTCGGAAATCCAA 59.697 36.000 24.95 14.96 36.04 3.53
2592 4132 5.799827 TTGAAGGTTTTCGGAAATCCAAT 57.200 34.783 24.95 16.50 36.04 3.16
2593 4133 5.799827 TGAAGGTTTTCGGAAATCCAATT 57.200 34.783 24.95 15.30 36.04 2.32
2594 4134 5.778862 TGAAGGTTTTCGGAAATCCAATTC 58.221 37.500 24.95 20.80 36.04 2.17
2595 4135 4.434713 AGGTTTTCGGAAATCCAATTCG 57.565 40.909 24.95 0.00 35.14 3.34
2596 4136 3.192633 AGGTTTTCGGAAATCCAATTCGG 59.807 43.478 24.95 0.00 35.14 4.30
2597 4137 2.921121 GTTTTCGGAAATCCAATTCGGC 59.079 45.455 3.67 0.00 35.14 5.54
2598 4138 2.122783 TTCGGAAATCCAATTCGGCT 57.877 45.000 0.00 0.00 35.14 5.52
2599 4139 1.663695 TCGGAAATCCAATTCGGCTC 58.336 50.000 0.00 0.00 35.14 4.70
2600 4140 1.209504 TCGGAAATCCAATTCGGCTCT 59.790 47.619 0.00 0.00 35.14 4.09
2601 4141 1.599542 CGGAAATCCAATTCGGCTCTC 59.400 52.381 0.00 0.00 35.14 3.20
2602 4142 1.599542 GGAAATCCAATTCGGCTCTCG 59.400 52.381 0.00 0.00 36.67 4.04
2603 4143 1.599542 GAAATCCAATTCGGCTCTCGG 59.400 52.381 0.00 0.00 39.77 4.63
2604 4144 0.179045 AATCCAATTCGGCTCTCGGG 60.179 55.000 0.00 0.00 39.77 5.14
2605 4145 1.048724 ATCCAATTCGGCTCTCGGGA 61.049 55.000 0.00 0.00 39.77 5.14
2606 4146 1.227380 CCAATTCGGCTCTCGGGAG 60.227 63.158 8.32 8.32 42.18 4.30
2623 4163 4.837085 GCATATGCTCCTGCCCAT 57.163 55.556 20.64 0.00 38.71 4.00
2624 4164 3.963733 GCATATGCTCCTGCCCATA 57.036 52.632 20.64 0.00 38.71 2.74
2625 4165 2.205022 GCATATGCTCCTGCCCATAA 57.795 50.000 20.64 0.00 38.71 1.90
2626 4166 2.731572 GCATATGCTCCTGCCCATAAT 58.268 47.619 20.64 0.00 38.71 1.28
2627 4167 3.094572 GCATATGCTCCTGCCCATAATT 58.905 45.455 20.64 0.00 38.71 1.40
2628 4168 3.512724 GCATATGCTCCTGCCCATAATTT 59.487 43.478 20.64 0.00 38.71 1.82
2629 4169 4.020839 GCATATGCTCCTGCCCATAATTTT 60.021 41.667 20.64 0.00 38.71 1.82
2630 4170 5.511888 GCATATGCTCCTGCCCATAATTTTT 60.512 40.000 20.64 0.00 38.71 1.94
2681 4221 8.668510 AAAATAGATATGATCACTGTCACACC 57.331 34.615 0.00 0.00 0.00 4.16
2682 4222 6.983906 ATAGATATGATCACTGTCACACCA 57.016 37.500 0.00 0.00 0.00 4.17
2683 4223 5.682234 AGATATGATCACTGTCACACCAA 57.318 39.130 0.00 0.00 0.00 3.67
2684 4224 6.053632 AGATATGATCACTGTCACACCAAA 57.946 37.500 0.00 0.00 0.00 3.28
2685 4225 6.475504 AGATATGATCACTGTCACACCAAAA 58.524 36.000 0.00 0.00 0.00 2.44
2686 4226 4.836125 ATGATCACTGTCACACCAAAAC 57.164 40.909 0.00 0.00 0.00 2.43
2687 4227 2.611751 TGATCACTGTCACACCAAAACG 59.388 45.455 0.00 0.00 0.00 3.60
2688 4228 0.730265 TCACTGTCACACCAAAACGC 59.270 50.000 0.00 0.00 0.00 4.84
2689 4229 0.732571 CACTGTCACACCAAAACGCT 59.267 50.000 0.00 0.00 0.00 5.07
2690 4230 1.937223 CACTGTCACACCAAAACGCTA 59.063 47.619 0.00 0.00 0.00 4.26
2691 4231 1.937899 ACTGTCACACCAAAACGCTAC 59.062 47.619 0.00 0.00 0.00 3.58
2692 4232 1.263217 CTGTCACACCAAAACGCTACC 59.737 52.381 0.00 0.00 0.00 3.18
2693 4233 1.134340 TGTCACACCAAAACGCTACCT 60.134 47.619 0.00 0.00 0.00 3.08
2694 4234 1.263217 GTCACACCAAAACGCTACCTG 59.737 52.381 0.00 0.00 0.00 4.00
2695 4235 1.139256 TCACACCAAAACGCTACCTGA 59.861 47.619 0.00 0.00 0.00 3.86
2696 4236 1.944024 CACACCAAAACGCTACCTGAA 59.056 47.619 0.00 0.00 0.00 3.02
2697 4237 2.356382 CACACCAAAACGCTACCTGAAA 59.644 45.455 0.00 0.00 0.00 2.69
2698 4238 2.616842 ACACCAAAACGCTACCTGAAAG 59.383 45.455 0.00 0.00 0.00 2.62
2699 4239 2.616842 CACCAAAACGCTACCTGAAAGT 59.383 45.455 0.00 0.00 0.00 2.66
2700 4240 3.066203 CACCAAAACGCTACCTGAAAGTT 59.934 43.478 0.00 0.00 0.00 2.66
2701 4241 3.697542 ACCAAAACGCTACCTGAAAGTTT 59.302 39.130 0.00 0.00 36.70 2.66
2702 4242 4.158949 ACCAAAACGCTACCTGAAAGTTTT 59.841 37.500 0.00 0.00 43.20 2.43
2703 4243 5.106442 CCAAAACGCTACCTGAAAGTTTTT 58.894 37.500 2.39 0.00 41.32 1.94
2704 4244 6.127675 ACCAAAACGCTACCTGAAAGTTTTTA 60.128 34.615 2.39 0.00 41.32 1.52
2705 4245 6.416750 CCAAAACGCTACCTGAAAGTTTTTAG 59.583 38.462 2.39 0.00 41.32 1.85
2706 4246 5.684550 AACGCTACCTGAAAGTTTTTAGG 57.315 39.130 12.39 12.39 46.21 2.69
2707 4247 4.964593 ACGCTACCTGAAAGTTTTTAGGA 58.035 39.130 18.86 5.38 44.27 2.94
2708 4248 4.995487 ACGCTACCTGAAAGTTTTTAGGAG 59.005 41.667 18.86 13.16 44.27 3.69
2709 4249 4.392138 CGCTACCTGAAAGTTTTTAGGAGG 59.608 45.833 18.86 12.40 44.27 4.30
2710 4250 5.557866 GCTACCTGAAAGTTTTTAGGAGGA 58.442 41.667 18.86 6.07 44.27 3.71
2711 4251 6.002082 GCTACCTGAAAGTTTTTAGGAGGAA 58.998 40.000 18.86 4.34 44.27 3.36
2712 4252 6.489022 GCTACCTGAAAGTTTTTAGGAGGAAA 59.511 38.462 18.86 2.49 44.27 3.13
2713 4253 6.961360 ACCTGAAAGTTTTTAGGAGGAAAG 57.039 37.500 18.86 0.00 44.27 2.62
2714 4254 5.302059 ACCTGAAAGTTTTTAGGAGGAAAGC 59.698 40.000 18.86 0.00 44.27 3.51
2715 4255 5.536538 CCTGAAAGTTTTTAGGAGGAAAGCT 59.463 40.000 9.20 0.00 44.27 3.74
2716 4256 6.040955 CCTGAAAGTTTTTAGGAGGAAAGCTT 59.959 38.462 9.20 0.00 44.27 3.74
2717 4257 7.230712 CCTGAAAGTTTTTAGGAGGAAAGCTTA 59.769 37.037 9.20 0.00 44.27 3.09
2718 4258 8.528044 TGAAAGTTTTTAGGAGGAAAGCTTAA 57.472 30.769 0.00 0.00 36.81 1.85
2719 4259 8.630037 TGAAAGTTTTTAGGAGGAAAGCTTAAG 58.370 33.333 0.00 0.00 36.81 1.85
2720 4260 8.534954 AAAGTTTTTAGGAGGAAAGCTTAAGT 57.465 30.769 0.00 0.00 36.81 2.24
2721 4261 9.636789 AAAGTTTTTAGGAGGAAAGCTTAAGTA 57.363 29.630 0.00 0.00 36.81 2.24
2722 4262 9.809395 AAGTTTTTAGGAGGAAAGCTTAAGTAT 57.191 29.630 0.00 0.00 36.30 2.12
2723 4263 9.809395 AGTTTTTAGGAGGAAAGCTTAAGTATT 57.191 29.630 0.00 0.00 0.00 1.89
2730 4270 9.165057 AGGAGGAAAGCTTAAGTATTATGATCT 57.835 33.333 0.00 0.00 0.00 2.75
2731 4271 9.213799 GGAGGAAAGCTTAAGTATTATGATCTG 57.786 37.037 0.00 0.00 0.00 2.90
2732 4272 9.771534 GAGGAAAGCTTAAGTATTATGATCTGT 57.228 33.333 0.00 0.00 0.00 3.41
2733 4273 9.553064 AGGAAAGCTTAAGTATTATGATCTGTG 57.447 33.333 0.00 0.00 0.00 3.66
2734 4274 8.286097 GGAAAGCTTAAGTATTATGATCTGTGC 58.714 37.037 0.00 0.00 0.00 4.57
2735 4275 8.737168 AAAGCTTAAGTATTATGATCTGTGCA 57.263 30.769 0.00 0.00 0.00 4.57
2736 4276 8.737168 AAGCTTAAGTATTATGATCTGTGCAA 57.263 30.769 0.00 0.00 0.00 4.08
2737 4277 8.737168 AGCTTAAGTATTATGATCTGTGCAAA 57.263 30.769 4.02 0.00 0.00 3.68
2738 4278 9.177608 AGCTTAAGTATTATGATCTGTGCAAAA 57.822 29.630 4.02 0.00 0.00 2.44
2739 4279 9.787532 GCTTAAGTATTATGATCTGTGCAAAAA 57.212 29.630 4.02 0.00 0.00 1.94
2759 4299 5.925189 AAAAACAAGTCGAACGACAAATG 57.075 34.783 25.13 21.32 46.76 2.32
2760 4300 4.609691 AAACAAGTCGAACGACAAATGT 57.390 36.364 25.13 21.82 46.76 2.71
2761 4301 4.609691 AACAAGTCGAACGACAAATGTT 57.390 36.364 25.13 24.96 46.76 2.71
2762 4302 5.721876 AACAAGTCGAACGACAAATGTTA 57.278 34.783 26.95 0.00 46.76 2.41
2763 4303 5.074430 ACAAGTCGAACGACAAATGTTAC 57.926 39.130 25.13 0.29 46.76 2.50
2764 4304 4.025480 ACAAGTCGAACGACAAATGTTACC 60.025 41.667 25.13 0.00 46.76 2.85
2765 4305 3.986277 AGTCGAACGACAAATGTTACCT 58.014 40.909 25.13 2.09 46.76 3.08
2766 4306 3.985925 AGTCGAACGACAAATGTTACCTC 59.014 43.478 25.13 0.00 46.76 3.85
2767 4307 3.122445 GTCGAACGACAAATGTTACCTCC 59.878 47.826 20.00 0.00 44.02 4.30
2768 4308 3.061322 CGAACGACAAATGTTACCTCCA 58.939 45.455 0.00 0.00 0.00 3.86
2769 4309 3.495377 CGAACGACAAATGTTACCTCCAA 59.505 43.478 0.00 0.00 0.00 3.53
2770 4310 4.024725 CGAACGACAAATGTTACCTCCAAA 60.025 41.667 0.00 0.00 0.00 3.28
2771 4311 5.334569 CGAACGACAAATGTTACCTCCAAAT 60.335 40.000 0.00 0.00 0.00 2.32
2772 4312 5.371115 ACGACAAATGTTACCTCCAAATG 57.629 39.130 0.00 0.00 0.00 2.32
2773 4313 4.825085 ACGACAAATGTTACCTCCAAATGT 59.175 37.500 0.00 0.00 0.00 2.71
2774 4314 5.300792 ACGACAAATGTTACCTCCAAATGTT 59.699 36.000 0.00 0.00 0.00 2.71
2775 4315 6.487331 ACGACAAATGTTACCTCCAAATGTTA 59.513 34.615 0.00 0.00 0.00 2.41
2776 4316 6.799925 CGACAAATGTTACCTCCAAATGTTAC 59.200 38.462 0.00 0.00 0.00 2.50
2777 4317 7.520776 CGACAAATGTTACCTCCAAATGTTACA 60.521 37.037 0.00 0.00 0.00 2.41
2778 4318 8.189119 ACAAATGTTACCTCCAAATGTTACAT 57.811 30.769 0.00 0.00 36.58 2.29
2779 4319 8.646900 ACAAATGTTACCTCCAAATGTTACATT 58.353 29.630 4.56 4.56 42.91 2.71
2780 4320 9.487790 CAAATGTTACCTCCAAATGTTACATTT 57.512 29.630 16.57 16.57 46.82 2.32
2808 4348 0.658897 TTTTTCACCGACGAAGCACC 59.341 50.000 0.00 0.00 0.00 5.01
2809 4349 1.492319 TTTTCACCGACGAAGCACCG 61.492 55.000 0.00 0.00 0.00 4.94
2810 4350 2.632136 TTTCACCGACGAAGCACCGT 62.632 55.000 0.00 3.04 46.43 4.83
2816 4356 4.904466 ACGAAGCACCGTCATACC 57.096 55.556 0.00 0.00 38.56 2.73
2817 4357 1.153901 ACGAAGCACCGTCATACCG 60.154 57.895 0.00 0.00 38.56 4.02
2818 4358 1.153901 CGAAGCACCGTCATACCGT 60.154 57.895 0.00 0.00 0.00 4.83
2819 4359 0.734942 CGAAGCACCGTCATACCGTT 60.735 55.000 0.00 0.00 0.00 4.44
2820 4360 1.435577 GAAGCACCGTCATACCGTTT 58.564 50.000 0.00 0.00 0.00 3.60
2821 4361 1.392510 GAAGCACCGTCATACCGTTTC 59.607 52.381 0.00 0.00 0.00 2.78
2822 4362 0.734942 AGCACCGTCATACCGTTTCG 60.735 55.000 0.00 0.00 0.00 3.46
2823 4363 1.705727 CACCGTCATACCGTTTCGC 59.294 57.895 0.00 0.00 0.00 4.70
2824 4364 1.009903 CACCGTCATACCGTTTCGCA 61.010 55.000 0.00 0.00 0.00 5.10
2825 4365 0.108520 ACCGTCATACCGTTTCGCAT 60.109 50.000 0.00 0.00 0.00 4.73
2826 4366 0.300491 CCGTCATACCGTTTCGCATG 59.700 55.000 0.00 0.00 0.00 4.06
2827 4367 1.273688 CGTCATACCGTTTCGCATGA 58.726 50.000 0.00 0.00 0.00 3.07
2828 4368 1.656594 CGTCATACCGTTTCGCATGAA 59.343 47.619 0.00 0.00 32.02 2.57
2829 4369 2.092995 CGTCATACCGTTTCGCATGAAA 59.907 45.455 0.00 0.00 41.69 2.69
2830 4370 3.423776 CGTCATACCGTTTCGCATGAAAA 60.424 43.478 0.00 0.00 45.22 2.29
2831 4371 4.658071 GTCATACCGTTTCGCATGAAAAT 58.342 39.130 0.00 0.00 45.22 1.82
2832 4372 5.092781 GTCATACCGTTTCGCATGAAAATT 58.907 37.500 0.00 0.00 45.22 1.82
2833 4373 5.003402 GTCATACCGTTTCGCATGAAAATTG 59.997 40.000 0.00 0.00 45.22 2.32
2834 4374 2.671596 ACCGTTTCGCATGAAAATTGG 58.328 42.857 0.00 5.47 45.22 3.16
2835 4375 1.389784 CCGTTTCGCATGAAAATTGGC 59.610 47.619 0.00 0.00 45.22 4.52
2836 4376 2.057316 CGTTTCGCATGAAAATTGGCA 58.943 42.857 0.00 0.00 45.22 4.92
2837 4377 2.474359 CGTTTCGCATGAAAATTGGCAA 59.526 40.909 0.68 0.68 45.22 4.52
2838 4378 3.422085 CGTTTCGCATGAAAATTGGCAAG 60.422 43.478 5.96 0.00 45.22 4.01
2839 4379 1.712401 TCGCATGAAAATTGGCAAGC 58.288 45.000 5.96 0.34 0.00 4.01
2840 4380 1.000618 TCGCATGAAAATTGGCAAGCA 59.999 42.857 5.96 1.74 0.00 3.91
2841 4381 1.127213 CGCATGAAAATTGGCAAGCAC 59.873 47.619 5.96 0.00 0.00 4.40
2842 4382 2.144730 GCATGAAAATTGGCAAGCACA 58.855 42.857 5.96 4.00 0.00 4.57
2843 4383 2.096119 GCATGAAAATTGGCAAGCACAC 60.096 45.455 5.96 0.00 0.00 3.82
2844 4384 3.395639 CATGAAAATTGGCAAGCACACT 58.604 40.909 5.96 0.00 0.00 3.55
2845 4385 3.540314 TGAAAATTGGCAAGCACACTT 57.460 38.095 5.96 0.00 36.19 3.16
2857 4397 5.478233 CAAGCACACTTGTTACACTAACA 57.522 39.130 0.00 0.00 46.84 2.41
2870 4410 8.771920 TGTTACACTAACAAGAACATCTATGG 57.228 34.615 0.00 0.00 44.95 2.74
2871 4411 7.822334 TGTTACACTAACAAGAACATCTATGGG 59.178 37.037 0.00 0.00 44.95 4.00
2872 4412 6.620877 ACACTAACAAGAACATCTATGGGA 57.379 37.500 0.00 0.00 0.00 4.37
2873 4413 7.016153 ACACTAACAAGAACATCTATGGGAA 57.984 36.000 0.00 0.00 0.00 3.97
2874 4414 7.458397 ACACTAACAAGAACATCTATGGGAAA 58.542 34.615 0.00 0.00 0.00 3.13
2875 4415 7.942341 ACACTAACAAGAACATCTATGGGAAAA 59.058 33.333 0.00 0.00 0.00 2.29
2876 4416 8.960591 CACTAACAAGAACATCTATGGGAAAAT 58.039 33.333 0.00 0.00 0.00 1.82
2877 4417 9.178758 ACTAACAAGAACATCTATGGGAAAATC 57.821 33.333 0.00 0.00 0.00 2.17
2878 4418 9.177608 CTAACAAGAACATCTATGGGAAAATCA 57.822 33.333 0.00 0.00 0.00 2.57
2879 4419 7.636150 ACAAGAACATCTATGGGAAAATCAG 57.364 36.000 0.00 0.00 0.00 2.90
2880 4420 7.405292 ACAAGAACATCTATGGGAAAATCAGA 58.595 34.615 0.00 0.00 0.00 3.27
2881 4421 7.890127 ACAAGAACATCTATGGGAAAATCAGAA 59.110 33.333 0.00 0.00 0.00 3.02
2882 4422 8.910944 CAAGAACATCTATGGGAAAATCAGAAT 58.089 33.333 0.00 0.00 0.00 2.40
2883 4423 9.484806 AAGAACATCTATGGGAAAATCAGAATT 57.515 29.630 0.00 0.00 0.00 2.17
2884 4424 9.484806 AGAACATCTATGGGAAAATCAGAATTT 57.515 29.630 0.00 0.00 36.64 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 1598 8.116136 GCGACTTCAGAAAATGTTTCAAAATTT 58.884 29.630 3.74 0.00 0.00 1.82
165 1605 3.900703 GTCGCGACTTCAGAAAATGTTTC 59.099 43.478 31.12 0.00 0.00 2.78
297 1740 9.545611 GATTTTCAAAAATGTCCATAAATGCAC 57.454 29.630 5.48 0.00 38.64 4.57
300 1743 9.743937 CGTGATTTTCAAAAATGTCCATAAATG 57.256 29.630 5.48 0.00 38.64 2.32
308 1751 8.327429 ACAATGTTCGTGATTTTCAAAAATGTC 58.673 29.630 5.48 0.00 38.64 3.06
321 1765 8.832521 TCAGTAACTTAAAACAATGTTCGTGAT 58.167 29.630 0.00 0.00 0.00 3.06
392 1836 9.823098 CTTTGAGAAATCACAAAATGTCTAGAG 57.177 33.333 7.30 0.00 36.34 2.43
397 1841 8.862550 AGTTCTTTGAGAAATCACAAAATGTC 57.137 30.769 7.30 0.95 35.75 3.06
766 2220 9.558648 TCTCAATTCAAAATATGTTCGTGAATG 57.441 29.630 12.08 8.45 38.57 2.67
769 2223 8.998377 TCTTCTCAATTCAAAATATGTTCGTGA 58.002 29.630 0.00 0.00 0.00 4.35
794 2248 6.578919 AGAAAATCTTCGCGACTTCAAAAATC 59.421 34.615 9.15 0.00 36.61 2.17
800 2255 4.055360 TCAAGAAAATCTTCGCGACTTCA 58.945 39.130 9.15 0.00 33.78 3.02
801 2256 4.647291 TCAAGAAAATCTTCGCGACTTC 57.353 40.909 9.15 7.12 33.78 3.01
926 2382 0.106149 ACGTGTTCTTGGTCAGACCC 59.894 55.000 17.59 1.36 37.50 4.46
931 2387 0.460722 TTCCGACGTGTTCTTGGTCA 59.539 50.000 0.00 0.00 0.00 4.02
942 2398 3.362797 TCAGCGCTCTTCCGACGT 61.363 61.111 7.13 0.00 0.00 4.34
1046 2502 2.225491 TGTCGCTGGTATTCTTTGCAAC 59.775 45.455 0.00 0.00 0.00 4.17
1048 2504 1.804151 GTGTCGCTGGTATTCTTTGCA 59.196 47.619 0.00 0.00 0.00 4.08
1085 2542 3.213506 ACTCACAGCACATTGTTTAGCA 58.786 40.909 1.11 0.00 0.00 3.49
1114 2571 2.994957 TATAGGAGGTAGAGGGGCAC 57.005 55.000 0.00 0.00 0.00 5.01
1115 2572 2.025226 CGATATAGGAGGTAGAGGGGCA 60.025 54.545 0.00 0.00 0.00 5.36
1116 2573 2.657143 CGATATAGGAGGTAGAGGGGC 58.343 57.143 0.00 0.00 0.00 5.80
1117 2574 2.242708 AGCGATATAGGAGGTAGAGGGG 59.757 54.545 0.00 0.00 0.00 4.79
1118 2575 3.201266 AGAGCGATATAGGAGGTAGAGGG 59.799 52.174 0.00 0.00 0.00 4.30
1119 2576 4.448210 GAGAGCGATATAGGAGGTAGAGG 58.552 52.174 0.00 0.00 0.00 3.69
1120 2577 4.116961 CGAGAGCGATATAGGAGGTAGAG 58.883 52.174 0.00 0.00 40.82 2.43
1183 2641 2.000429 TTAGTCGCTAAGGAAACGCC 58.000 50.000 0.00 0.00 0.00 5.68
1245 2707 3.809905 AGAGTGAAAGACCAGTTGGAAC 58.190 45.455 4.92 0.00 38.94 3.62
1277 2739 1.152673 GGAATAAGCTGGGCTGGGG 60.153 63.158 0.00 0.00 39.62 4.96
1529 2998 0.320508 GAGTGGACTTTGGTCGGGTC 60.321 60.000 0.00 0.00 42.97 4.46
1557 3029 0.397816 AACCTCCATCTCCTCCTCCG 60.398 60.000 0.00 0.00 0.00 4.63
1750 3231 0.656259 CGTCTGAATCCGAGTCGCTA 59.344 55.000 7.12 0.00 0.00 4.26
1786 3267 4.752879 AACCACGCCACGATCCCG 62.753 66.667 0.00 0.00 42.50 5.14
1847 3335 8.465273 ACTAGTAGTATATCACAGCACAATGA 57.535 34.615 0.00 0.00 0.00 2.57
1879 3370 3.980646 ACTCGCAAAAGCATACACAAA 57.019 38.095 0.00 0.00 0.00 2.83
1895 3386 0.666274 TGTACAGAGCGCCAAACTCG 60.666 55.000 2.29 0.00 39.23 4.18
1917 3419 7.554118 CCGGATTGCCATTTATTCATCTACTAT 59.446 37.037 0.00 0.00 0.00 2.12
1920 3422 5.473504 ACCGGATTGCCATTTATTCATCTAC 59.526 40.000 9.46 0.00 0.00 2.59
1921 3423 5.473162 CACCGGATTGCCATTTATTCATCTA 59.527 40.000 9.46 0.00 0.00 1.98
1922 3424 4.279169 CACCGGATTGCCATTTATTCATCT 59.721 41.667 9.46 0.00 0.00 2.90
1942 3451 3.929094 TCCGGAGTTGTACAATAACACC 58.071 45.455 12.26 7.05 36.03 4.16
1948 3457 3.196901 TGCATACTCCGGAGTTGTACAAT 59.803 43.478 40.23 24.09 42.54 2.71
1987 3496 9.462174 CTCAAGAACTGCACTATCTATTCTAAG 57.538 37.037 0.00 0.00 0.00 2.18
2031 3540 6.776116 ACTTATGCAAATGATCATGAGTCCAT 59.224 34.615 9.46 10.11 35.48 3.41
2033 3542 6.630444 ACTTATGCAAATGATCATGAGTCC 57.370 37.500 9.46 0.00 35.48 3.85
2036 3545 5.690409 GCCAACTTATGCAAATGATCATGAG 59.310 40.000 9.46 6.13 33.94 2.90
2037 3546 5.452216 GGCCAACTTATGCAAATGATCATGA 60.452 40.000 9.46 0.00 0.00 3.07
2040 3549 4.025360 AGGCCAACTTATGCAAATGATCA 58.975 39.130 5.01 0.00 0.00 2.92
2041 3550 4.098349 TGAGGCCAACTTATGCAAATGATC 59.902 41.667 5.01 0.00 0.00 2.92
2042 3551 4.025360 TGAGGCCAACTTATGCAAATGAT 58.975 39.130 5.01 0.00 0.00 2.45
2043 3552 3.429492 TGAGGCCAACTTATGCAAATGA 58.571 40.909 5.01 0.00 0.00 2.57
2044 3553 3.872511 TGAGGCCAACTTATGCAAATG 57.127 42.857 5.01 0.00 0.00 2.32
2045 3554 3.133362 CCATGAGGCCAACTTATGCAAAT 59.867 43.478 5.01 0.00 40.75 2.32
2047 3556 2.101783 CCATGAGGCCAACTTATGCAA 58.898 47.619 5.01 0.00 40.75 4.08
2048 3557 1.685803 CCCATGAGGCCAACTTATGCA 60.686 52.381 5.01 0.00 40.75 3.96
2049 3558 1.035139 CCCATGAGGCCAACTTATGC 58.965 55.000 5.01 0.00 40.75 3.14
2061 3570 1.809619 CACCGTACGTGCCCATGAG 60.810 63.158 15.21 0.00 35.18 2.90
2101 3617 2.003548 GAGGCAGGGGGTCATCCTT 61.004 63.158 0.00 0.00 35.33 3.36
2103 3619 2.367512 AGAGGCAGGGGGTCATCC 60.368 66.667 0.00 0.00 0.00 3.51
2125 3641 0.908910 ACGGTACATGCATCTCCCAA 59.091 50.000 0.00 0.00 0.00 4.12
2127 3643 2.992089 CACGGTACATGCATCTCCC 58.008 57.895 0.00 0.00 0.00 4.30
2165 3681 7.054124 TGAAGAGAAAAGCAAAAGGAACTAGA 58.946 34.615 0.00 0.00 38.49 2.43
2198 3717 5.633830 AAGTTGTTTCATCAAGCGATCAT 57.366 34.783 0.00 0.00 0.00 2.45
2199 3718 6.204688 ACTTAAGTTGTTTCATCAAGCGATCA 59.795 34.615 1.12 0.00 0.00 2.92
2211 3730 9.145865 TGGTTTTTCATTGACTTAAGTTGTTTC 57.854 29.630 10.02 0.00 0.00 2.78
2280 3820 0.687354 TGAGTGGTCTCCTGCTTTCC 59.313 55.000 0.00 0.00 39.75 3.13
2318 3858 2.559785 GCAGGTGCAGCATAGTGTT 58.440 52.632 19.63 0.00 41.59 3.32
2333 3873 0.877071 CCTTGCCACTAACAGTGCAG 59.123 55.000 0.64 0.00 44.63 4.41
2334 3874 0.472044 TCCTTGCCACTAACAGTGCA 59.528 50.000 0.64 0.93 44.63 4.57
2335 3875 1.604604 TTCCTTGCCACTAACAGTGC 58.395 50.000 0.64 0.00 44.63 4.40
2336 3876 3.476552 TCTTTCCTTGCCACTAACAGTG 58.523 45.455 0.00 0.00 45.53 3.66
2337 3877 3.857157 TCTTTCCTTGCCACTAACAGT 57.143 42.857 0.00 0.00 0.00 3.55
2338 3878 3.441572 CCATCTTTCCTTGCCACTAACAG 59.558 47.826 0.00 0.00 0.00 3.16
2339 3879 3.420893 CCATCTTTCCTTGCCACTAACA 58.579 45.455 0.00 0.00 0.00 2.41
2340 3880 2.164422 GCCATCTTTCCTTGCCACTAAC 59.836 50.000 0.00 0.00 0.00 2.34
2341 3881 2.224992 TGCCATCTTTCCTTGCCACTAA 60.225 45.455 0.00 0.00 0.00 2.24
2389 3929 5.123820 TGTTCTTATGCACATCTGGTTAAGC 59.876 40.000 0.00 0.00 0.00 3.09
2503 4043 3.744238 AAACATTTCTTTTCCCCCACG 57.256 42.857 0.00 0.00 0.00 4.94
2516 4056 8.109634 ACCCTGAGAATGTCACTATAAACATTT 58.890 33.333 2.60 0.00 44.06 2.32
2571 4111 5.563867 CGAATTGGATTTCCGAAAACCTTCA 60.564 40.000 18.10 5.95 39.43 3.02
2581 4121 1.599542 GAGAGCCGAATTGGATTTCCG 59.400 52.381 0.00 0.00 42.00 4.30
2582 4122 1.599542 CGAGAGCCGAATTGGATTTCC 59.400 52.381 0.00 0.00 42.00 3.13
2583 4123 1.599542 CCGAGAGCCGAATTGGATTTC 59.400 52.381 0.00 0.00 42.00 2.17
2584 4124 1.668419 CCGAGAGCCGAATTGGATTT 58.332 50.000 0.00 0.00 42.00 2.17
2585 4125 0.179045 CCCGAGAGCCGAATTGGATT 60.179 55.000 0.00 0.00 42.00 3.01
2586 4126 1.048724 TCCCGAGAGCCGAATTGGAT 61.049 55.000 0.00 0.00 42.00 3.41
2587 4127 1.676678 CTCCCGAGAGCCGAATTGGA 61.677 60.000 0.00 0.00 42.00 3.53
2588 4128 1.227380 CTCCCGAGAGCCGAATTGG 60.227 63.158 0.00 0.00 41.76 3.16
2589 4129 4.427394 CTCCCGAGAGCCGAATTG 57.573 61.111 0.00 0.00 41.76 2.32
2606 4146 2.205022 TTATGGGCAGGAGCATATGC 57.795 50.000 20.36 20.36 44.61 3.14
2607 4147 5.733620 AAAATTATGGGCAGGAGCATATG 57.266 39.130 0.00 0.00 44.61 1.78
2655 4195 9.113838 GGTGTGACAGTGATCATATCTATTTTT 57.886 33.333 0.00 0.00 0.00 1.94
2656 4196 8.267183 TGGTGTGACAGTGATCATATCTATTTT 58.733 33.333 0.00 0.00 0.00 1.82
2657 4197 7.795047 TGGTGTGACAGTGATCATATCTATTT 58.205 34.615 0.00 0.00 0.00 1.40
2658 4198 7.365497 TGGTGTGACAGTGATCATATCTATT 57.635 36.000 0.00 0.00 0.00 1.73
2659 4199 6.983906 TGGTGTGACAGTGATCATATCTAT 57.016 37.500 0.00 0.00 0.00 1.98
2660 4200 6.790232 TTGGTGTGACAGTGATCATATCTA 57.210 37.500 0.00 0.00 0.00 1.98
2661 4201 5.682234 TTGGTGTGACAGTGATCATATCT 57.318 39.130 0.00 0.00 0.00 1.98
2662 4202 6.546395 GTTTTGGTGTGACAGTGATCATATC 58.454 40.000 0.00 0.00 0.00 1.63
2663 4203 5.122239 CGTTTTGGTGTGACAGTGATCATAT 59.878 40.000 0.00 0.00 0.00 1.78
2664 4204 4.450757 CGTTTTGGTGTGACAGTGATCATA 59.549 41.667 0.00 0.00 0.00 2.15
2665 4205 3.250762 CGTTTTGGTGTGACAGTGATCAT 59.749 43.478 0.00 0.00 0.00 2.45
2666 4206 2.611751 CGTTTTGGTGTGACAGTGATCA 59.388 45.455 0.00 0.00 0.00 2.92
2667 4207 2.602217 GCGTTTTGGTGTGACAGTGATC 60.602 50.000 0.00 0.00 0.00 2.92
2668 4208 1.333619 GCGTTTTGGTGTGACAGTGAT 59.666 47.619 0.00 0.00 0.00 3.06
2669 4209 0.730265 GCGTTTTGGTGTGACAGTGA 59.270 50.000 0.00 0.00 0.00 3.41
2670 4210 0.732571 AGCGTTTTGGTGTGACAGTG 59.267 50.000 0.00 0.00 0.00 3.66
2671 4211 1.937899 GTAGCGTTTTGGTGTGACAGT 59.062 47.619 0.00 0.00 0.00 3.55
2672 4212 1.263217 GGTAGCGTTTTGGTGTGACAG 59.737 52.381 0.00 0.00 0.00 3.51
2673 4213 1.134340 AGGTAGCGTTTTGGTGTGACA 60.134 47.619 0.00 0.00 0.00 3.58
2674 4214 1.263217 CAGGTAGCGTTTTGGTGTGAC 59.737 52.381 0.00 0.00 0.00 3.67
2675 4215 1.139256 TCAGGTAGCGTTTTGGTGTGA 59.861 47.619 0.00 0.00 0.00 3.58
2676 4216 1.588674 TCAGGTAGCGTTTTGGTGTG 58.411 50.000 0.00 0.00 0.00 3.82
2677 4217 2.335316 TTCAGGTAGCGTTTTGGTGT 57.665 45.000 0.00 0.00 0.00 4.16
2678 4218 2.616842 ACTTTCAGGTAGCGTTTTGGTG 59.383 45.455 0.00 0.00 0.00 4.17
2679 4219 2.927028 ACTTTCAGGTAGCGTTTTGGT 58.073 42.857 0.00 0.00 0.00 3.67
2680 4220 3.982576 AACTTTCAGGTAGCGTTTTGG 57.017 42.857 0.00 0.00 0.00 3.28
2681 4221 6.416750 CCTAAAAACTTTCAGGTAGCGTTTTG 59.583 38.462 7.92 0.00 37.71 2.44
2682 4222 6.319405 TCCTAAAAACTTTCAGGTAGCGTTTT 59.681 34.615 2.92 2.92 38.87 2.43
2683 4223 5.824097 TCCTAAAAACTTTCAGGTAGCGTTT 59.176 36.000 0.00 0.00 0.00 3.60
2684 4224 5.370679 TCCTAAAAACTTTCAGGTAGCGTT 58.629 37.500 0.00 0.00 0.00 4.84
2685 4225 4.964593 TCCTAAAAACTTTCAGGTAGCGT 58.035 39.130 0.00 0.00 0.00 5.07
2686 4226 4.392138 CCTCCTAAAAACTTTCAGGTAGCG 59.608 45.833 0.00 0.00 0.00 4.26
2687 4227 5.557866 TCCTCCTAAAAACTTTCAGGTAGC 58.442 41.667 0.00 0.00 0.00 3.58
2688 4228 7.308649 GCTTTCCTCCTAAAAACTTTCAGGTAG 60.309 40.741 0.00 0.00 0.00 3.18
2689 4229 6.489022 GCTTTCCTCCTAAAAACTTTCAGGTA 59.511 38.462 0.00 0.00 0.00 3.08
2690 4230 5.302059 GCTTTCCTCCTAAAAACTTTCAGGT 59.698 40.000 0.00 0.00 0.00 4.00
2691 4231 5.536538 AGCTTTCCTCCTAAAAACTTTCAGG 59.463 40.000 0.00 0.00 0.00 3.86
2692 4232 6.641169 AGCTTTCCTCCTAAAAACTTTCAG 57.359 37.500 0.00 0.00 0.00 3.02
2693 4233 8.528044 TTAAGCTTTCCTCCTAAAAACTTTCA 57.472 30.769 3.20 0.00 0.00 2.69
2694 4234 8.630917 ACTTAAGCTTTCCTCCTAAAAACTTTC 58.369 33.333 3.20 0.00 0.00 2.62
2695 4235 8.534954 ACTTAAGCTTTCCTCCTAAAAACTTT 57.465 30.769 3.20 0.00 0.00 2.66
2696 4236 9.809395 ATACTTAAGCTTTCCTCCTAAAAACTT 57.191 29.630 3.20 0.00 0.00 2.66
2697 4237 9.809395 AATACTTAAGCTTTCCTCCTAAAAACT 57.191 29.630 3.20 0.00 0.00 2.66
2704 4244 9.165057 AGATCATAATACTTAAGCTTTCCTCCT 57.835 33.333 3.20 0.00 0.00 3.69
2705 4245 9.213799 CAGATCATAATACTTAAGCTTTCCTCC 57.786 37.037 3.20 0.00 0.00 4.30
2706 4246 9.771534 ACAGATCATAATACTTAAGCTTTCCTC 57.228 33.333 3.20 0.00 0.00 3.71
2707 4247 9.553064 CACAGATCATAATACTTAAGCTTTCCT 57.447 33.333 3.20 0.00 0.00 3.36
2708 4248 8.286097 GCACAGATCATAATACTTAAGCTTTCC 58.714 37.037 3.20 0.00 0.00 3.13
2709 4249 8.830580 TGCACAGATCATAATACTTAAGCTTTC 58.169 33.333 3.20 0.00 0.00 2.62
2710 4250 8.737168 TGCACAGATCATAATACTTAAGCTTT 57.263 30.769 3.20 0.00 0.00 3.51
2711 4251 8.737168 TTGCACAGATCATAATACTTAAGCTT 57.263 30.769 3.48 3.48 0.00 3.74
2712 4252 8.737168 TTTGCACAGATCATAATACTTAAGCT 57.263 30.769 1.29 0.00 0.00 3.74
2713 4253 9.787532 TTTTTGCACAGATCATAATACTTAAGC 57.212 29.630 1.29 0.00 0.00 3.09
2737 4277 5.395642 ACATTTGTCGTTCGACTTGTTTTT 58.604 33.333 22.49 2.85 36.23 1.94
2738 4278 4.976987 ACATTTGTCGTTCGACTTGTTTT 58.023 34.783 22.49 4.19 36.23 2.43
2739 4279 4.609691 ACATTTGTCGTTCGACTTGTTT 57.390 36.364 22.49 5.52 36.23 2.83
2740 4280 4.609691 AACATTTGTCGTTCGACTTGTT 57.390 36.364 22.49 22.36 36.23 2.83
2741 4281 4.025480 GGTAACATTTGTCGTTCGACTTGT 60.025 41.667 22.49 19.09 36.23 3.16
2742 4282 4.210537 AGGTAACATTTGTCGTTCGACTTG 59.789 41.667 22.49 18.60 41.41 3.16
2743 4283 4.374399 AGGTAACATTTGTCGTTCGACTT 58.626 39.130 22.49 12.53 41.41 3.01
2744 4284 3.985925 GAGGTAACATTTGTCGTTCGACT 59.014 43.478 22.49 7.20 41.41 4.18
2745 4285 3.122445 GGAGGTAACATTTGTCGTTCGAC 59.878 47.826 16.85 16.85 41.41 4.20
2746 4286 3.243805 TGGAGGTAACATTTGTCGTTCGA 60.244 43.478 0.00 0.00 41.41 3.71
2747 4287 3.061322 TGGAGGTAACATTTGTCGTTCG 58.939 45.455 0.00 0.00 41.41 3.95
2748 4288 5.427036 TTTGGAGGTAACATTTGTCGTTC 57.573 39.130 0.00 0.00 41.41 3.95
2749 4289 5.300792 ACATTTGGAGGTAACATTTGTCGTT 59.699 36.000 0.00 0.00 41.41 3.85
2750 4290 4.825085 ACATTTGGAGGTAACATTTGTCGT 59.175 37.500 0.00 0.00 41.41 4.34
2751 4291 5.371115 ACATTTGGAGGTAACATTTGTCG 57.629 39.130 0.00 0.00 41.41 4.35
2752 4292 7.653647 TGTAACATTTGGAGGTAACATTTGTC 58.346 34.615 0.00 0.00 41.41 3.18
2753 4293 7.589958 TGTAACATTTGGAGGTAACATTTGT 57.410 32.000 0.00 0.00 41.41 2.83
2754 4294 9.487790 AAATGTAACATTTGGAGGTAACATTTG 57.512 29.630 8.75 0.00 41.92 2.32
2789 4329 0.658897 GGTGCTTCGTCGGTGAAAAA 59.341 50.000 0.00 0.00 0.00 1.94
2790 4330 1.492319 CGGTGCTTCGTCGGTGAAAA 61.492 55.000 0.00 0.00 0.00 2.29
2791 4331 1.952133 CGGTGCTTCGTCGGTGAAA 60.952 57.895 0.00 0.00 0.00 2.69
2792 4332 2.355363 CGGTGCTTCGTCGGTGAA 60.355 61.111 0.00 0.00 0.00 3.18
2793 4333 3.598715 ACGGTGCTTCGTCGGTGA 61.599 61.111 0.00 0.00 39.34 4.02
2799 4339 1.153901 CGGTATGACGGTGCTTCGT 60.154 57.895 4.72 4.72 46.83 3.85
2800 4340 0.734942 AACGGTATGACGGTGCTTCG 60.735 55.000 0.00 0.00 38.39 3.79
2801 4341 1.392510 GAAACGGTATGACGGTGCTTC 59.607 52.381 0.00 0.00 38.39 3.86
2802 4342 1.435577 GAAACGGTATGACGGTGCTT 58.564 50.000 0.00 0.00 38.39 3.91
2803 4343 0.734942 CGAAACGGTATGACGGTGCT 60.735 55.000 0.00 0.00 38.39 4.40
2804 4344 1.705727 CGAAACGGTATGACGGTGC 59.294 57.895 0.00 0.00 38.39 5.01
2805 4345 1.009903 TGCGAAACGGTATGACGGTG 61.010 55.000 0.00 0.00 38.39 4.94
2806 4346 0.108520 ATGCGAAACGGTATGACGGT 60.109 50.000 0.00 0.00 38.39 4.83
2807 4347 0.300491 CATGCGAAACGGTATGACGG 59.700 55.000 0.00 0.00 38.39 4.79
2808 4348 1.273688 TCATGCGAAACGGTATGACG 58.726 50.000 0.00 0.00 34.69 4.35
2809 4349 3.733024 TTTCATGCGAAACGGTATGAC 57.267 42.857 0.00 0.00 38.49 3.06
2810 4350 4.955925 ATTTTCATGCGAAACGGTATGA 57.044 36.364 0.00 0.00 40.84 2.15
2811 4351 4.265085 CCAATTTTCATGCGAAACGGTATG 59.735 41.667 0.00 0.00 40.84 2.39
2812 4352 4.420168 CCAATTTTCATGCGAAACGGTAT 58.580 39.130 0.00 0.00 40.84 2.73
2813 4353 3.827625 CCAATTTTCATGCGAAACGGTA 58.172 40.909 0.00 0.00 40.84 4.02
2814 4354 2.671596 CCAATTTTCATGCGAAACGGT 58.328 42.857 0.00 0.00 40.84 4.83
2815 4355 1.389784 GCCAATTTTCATGCGAAACGG 59.610 47.619 0.00 0.00 40.84 4.44
2816 4356 2.057316 TGCCAATTTTCATGCGAAACG 58.943 42.857 0.00 0.00 40.84 3.60
2817 4357 3.665060 GCTTGCCAATTTTCATGCGAAAC 60.665 43.478 0.00 0.00 40.84 2.78
2818 4358 2.479656 GCTTGCCAATTTTCATGCGAAA 59.520 40.909 0.00 0.00 39.38 3.46
2819 4359 2.067766 GCTTGCCAATTTTCATGCGAA 58.932 42.857 0.00 0.00 0.00 4.70
2820 4360 1.000618 TGCTTGCCAATTTTCATGCGA 59.999 42.857 0.00 0.00 36.51 5.10
2821 4361 1.127213 GTGCTTGCCAATTTTCATGCG 59.873 47.619 8.87 0.00 36.51 4.73
2822 4362 2.096119 GTGTGCTTGCCAATTTTCATGC 60.096 45.455 7.31 7.31 34.96 4.06
2823 4363 3.395639 AGTGTGCTTGCCAATTTTCATG 58.604 40.909 0.00 0.00 0.00 3.07
2824 4364 3.756933 AGTGTGCTTGCCAATTTTCAT 57.243 38.095 0.00 0.00 0.00 2.57
2825 4365 3.196463 CAAGTGTGCTTGCCAATTTTCA 58.804 40.909 0.00 0.00 44.54 2.69
2826 4366 3.865224 CAAGTGTGCTTGCCAATTTTC 57.135 42.857 0.00 0.00 44.54 2.29
2845 4385 7.822334 CCCATAGATGTTCTTGTTAGTGTAACA 59.178 37.037 0.00 0.00 46.13 2.41
2846 4386 8.038944 TCCCATAGATGTTCTTGTTAGTGTAAC 58.961 37.037 0.00 0.00 39.11 2.50
2847 4387 8.141298 TCCCATAGATGTTCTTGTTAGTGTAA 57.859 34.615 0.00 0.00 0.00 2.41
2848 4388 7.727578 TCCCATAGATGTTCTTGTTAGTGTA 57.272 36.000 0.00 0.00 0.00 2.90
2849 4389 6.620877 TCCCATAGATGTTCTTGTTAGTGT 57.379 37.500 0.00 0.00 0.00 3.55
2850 4390 7.921786 TTTCCCATAGATGTTCTTGTTAGTG 57.078 36.000 0.00 0.00 0.00 2.74
2851 4391 9.178758 GATTTTCCCATAGATGTTCTTGTTAGT 57.821 33.333 0.00 0.00 0.00 2.24
2852 4392 9.177608 TGATTTTCCCATAGATGTTCTTGTTAG 57.822 33.333 0.00 0.00 0.00 2.34
2853 4393 9.177608 CTGATTTTCCCATAGATGTTCTTGTTA 57.822 33.333 0.00 0.00 0.00 2.41
2854 4394 7.890127 TCTGATTTTCCCATAGATGTTCTTGTT 59.110 33.333 0.00 0.00 0.00 2.83
2855 4395 7.405292 TCTGATTTTCCCATAGATGTTCTTGT 58.595 34.615 0.00 0.00 0.00 3.16
2856 4396 7.870509 TCTGATTTTCCCATAGATGTTCTTG 57.129 36.000 0.00 0.00 0.00 3.02
2857 4397 9.484806 AATTCTGATTTTCCCATAGATGTTCTT 57.515 29.630 0.00 0.00 0.00 2.52
2858 4398 9.484806 AAATTCTGATTTTCCCATAGATGTTCT 57.515 29.630 0.00 0.00 31.48 3.01


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

AutoCloner maintained by Alex Coulton.