Multiple sequence alignment - TraesCS6A01G009200

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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 TraesCS6A01G009200 chr6A 100.000 3727 0 0 1 3727 3854230 3850504 0.000000e+00 6883
1 TraesCS6A01G009200 chr6A 82.857 140 15 6 1178 1309 203805956 203806094 2.350000e-22 117
2 TraesCS6A01G009200 chr6D 90.017 1753 86 35 1882 3567 4774713 4772983 0.000000e+00 2185
3 TraesCS6A01G009200 chr6D 86.685 1472 115 42 452 1884 4776190 4774761 0.000000e+00 1557
4 TraesCS6A01G009200 chr6D 91.753 97 6 2 93 187 4777567 4777471 2.340000e-27 134
5 TraesCS6A01G009200 chr6B 88.250 1549 113 30 1881 3377 9002784 9004315 0.000000e+00 1788
6 TraesCS6A01G009200 chr6B 88.598 1184 57 28 737 1884 9001588 9002729 0.000000e+00 1367
7 TraesCS6A01G009200 chr4A 86.697 218 27 2 2336 2552 732772339 732772123 1.340000e-59 241
8 TraesCS6A01G009200 chr7A 93.902 82 5 0 1481 1562 8375846 8375765 1.410000e-24 124
9 TraesCS6A01G009200 chr4B 93.750 80 5 0 1483 1562 650051745 650051666 1.820000e-23 121
10 TraesCS6A01G009200 chr4B 93.750 80 5 0 1483 1562 650061354 650061275 1.820000e-23 121
11 TraesCS6A01G009200 chr4B 93.750 80 5 0 1483 1562 650120141 650120062 1.820000e-23 121
12 TraesCS6A01G009200 chr4B 93.750 80 5 0 1483 1562 650181803 650181724 1.820000e-23 121


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 TraesCS6A01G009200 chr6A 3850504 3854230 3726 True 6883.0 6883 100.000 1 3727 1 chr6A.!!$R1 3726
1 TraesCS6A01G009200 chr6D 4772983 4777567 4584 True 1292.0 2185 89.485 93 3567 3 chr6D.!!$R1 3474
2 TraesCS6A01G009200 chr6B 9001588 9004315 2727 False 1577.5 1788 88.424 737 3377 2 chr6B.!!$F1 2640

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
26 27 1.069022 AGCAGCTTGTTACAATGCACG 60.069 47.619 20.95 12.5 39.34 5.34 F
762 1782 1.233019 CTATACACATGGCAGCCAGC 58.767 55.000 21.51 0.0 44.65 4.85 F
2587 3736 0.036388 AGGACGGTATGCACCAACAG 60.036 55.000 0.00 0.0 46.14 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1667 2737 0.469494 ACATGCATCTCGGTGCCATA 59.531 50.0 0.0 0.0 44.43 2.74 R
2640 3819 0.248866 CCTGCCAACAACAACGAACC 60.249 55.0 0.0 0.0 0.00 3.62 R
3706 4918 0.030501 TGGTGGTGGTAGGGATAGGG 60.031 60.0 0.0 0.0 0.00 3.53 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
24 25 3.731652 AAAGCAGCTTGTTACAATGCA 57.268 38.095 20.95 0.00 39.34 3.96
25 26 2.712057 AGCAGCTTGTTACAATGCAC 57.288 45.000 20.95 12.50 39.34 4.57
26 27 1.069022 AGCAGCTTGTTACAATGCACG 60.069 47.619 20.95 12.50 39.34 5.34
27 28 1.334960 GCAGCTTGTTACAATGCACGT 60.335 47.619 16.00 0.00 36.88 4.49
28 29 2.095969 GCAGCTTGTTACAATGCACGTA 60.096 45.455 16.00 0.00 36.88 3.57
29 30 3.479006 CAGCTTGTTACAATGCACGTAC 58.521 45.455 17.00 0.00 0.00 3.67
30 31 2.482721 AGCTTGTTACAATGCACGTACC 59.517 45.455 17.00 0.00 0.00 3.34
31 32 2.224549 GCTTGTTACAATGCACGTACCA 59.775 45.455 12.25 0.00 0.00 3.25
32 33 3.805823 CTTGTTACAATGCACGTACCAC 58.194 45.455 0.00 0.00 0.00 4.16
33 34 2.835027 TGTTACAATGCACGTACCACA 58.165 42.857 0.00 0.00 0.00 4.17
34 35 3.403968 TGTTACAATGCACGTACCACAT 58.596 40.909 0.00 0.00 0.00 3.21
35 36 4.566987 TGTTACAATGCACGTACCACATA 58.433 39.130 0.00 0.00 0.00 2.29
36 37 5.179533 TGTTACAATGCACGTACCACATAT 58.820 37.500 0.00 0.00 0.00 1.78
37 38 5.644206 TGTTACAATGCACGTACCACATATT 59.356 36.000 0.00 0.00 0.00 1.28
38 39 6.149640 TGTTACAATGCACGTACCACATATTT 59.850 34.615 0.00 0.00 0.00 1.40
39 40 5.637006 ACAATGCACGTACCACATATTTT 57.363 34.783 0.00 0.00 0.00 1.82
40 41 5.398169 ACAATGCACGTACCACATATTTTG 58.602 37.500 0.00 0.00 0.00 2.44
41 42 5.048364 ACAATGCACGTACCACATATTTTGT 60.048 36.000 0.00 0.00 39.91 2.83
42 43 5.637006 ATGCACGTACCACATATTTTGTT 57.363 34.783 0.00 0.00 36.00 2.83
43 44 5.440234 TGCACGTACCACATATTTTGTTT 57.560 34.783 0.00 0.00 36.00 2.83
44 45 5.215903 TGCACGTACCACATATTTTGTTTG 58.784 37.500 0.00 0.00 36.00 2.93
45 46 5.008712 TGCACGTACCACATATTTTGTTTGA 59.991 36.000 0.00 0.00 36.00 2.69
46 47 5.915758 GCACGTACCACATATTTTGTTTGAA 59.084 36.000 0.00 0.00 36.00 2.69
47 48 6.418226 GCACGTACCACATATTTTGTTTGAAA 59.582 34.615 0.00 0.00 36.00 2.69
48 49 7.115663 GCACGTACCACATATTTTGTTTGAAAT 59.884 33.333 0.00 0.00 36.00 2.17
49 50 9.613957 CACGTACCACATATTTTGTTTGAAATA 57.386 29.630 0.00 0.00 36.00 1.40
69 70 9.566432 TGAAATAATTGCAAAAATACCAAAGGT 57.434 25.926 1.71 0.00 40.16 3.50
74 75 7.722795 ATTGCAAAAATACCAAAGGTAACAC 57.277 32.000 1.71 0.00 41.85 3.32
75 76 6.222038 TGCAAAAATACCAAAGGTAACACA 57.778 33.333 0.00 0.00 41.85 3.72
76 77 6.640518 TGCAAAAATACCAAAGGTAACACAA 58.359 32.000 0.00 0.00 41.85 3.33
77 78 7.275920 TGCAAAAATACCAAAGGTAACACAAT 58.724 30.769 0.00 0.00 41.85 2.71
78 79 7.225538 TGCAAAAATACCAAAGGTAACACAATG 59.774 33.333 0.00 0.00 41.85 2.82
79 80 7.307692 GCAAAAATACCAAAGGTAACACAATGG 60.308 37.037 0.00 0.00 41.85 3.16
80 81 7.604657 AAAATACCAAAGGTAACACAATGGA 57.395 32.000 0.00 0.00 41.85 3.41
81 82 6.834168 AATACCAAAGGTAACACAATGGAG 57.166 37.500 0.00 0.00 41.85 3.86
82 83 4.178956 ACCAAAGGTAACACAATGGAGT 57.821 40.909 0.00 0.00 41.41 3.85
83 84 3.888930 ACCAAAGGTAACACAATGGAGTG 59.111 43.478 0.00 0.00 38.77 3.51
84 85 3.255642 CCAAAGGTAACACAATGGAGTGG 59.744 47.826 0.00 0.00 43.72 4.00
85 86 4.141287 CAAAGGTAACACAATGGAGTGGA 58.859 43.478 0.00 0.00 43.72 4.02
86 87 4.657814 AAGGTAACACAATGGAGTGGAT 57.342 40.909 0.00 0.00 43.72 3.41
87 88 4.657814 AGGTAACACAATGGAGTGGATT 57.342 40.909 0.00 0.00 43.72 3.01
88 89 4.998051 AGGTAACACAATGGAGTGGATTT 58.002 39.130 0.00 0.00 43.72 2.17
89 90 5.010282 AGGTAACACAATGGAGTGGATTTC 58.990 41.667 0.00 0.00 43.72 2.17
90 91 4.764823 GGTAACACAATGGAGTGGATTTCA 59.235 41.667 0.00 0.00 43.72 2.69
91 92 5.242838 GGTAACACAATGGAGTGGATTTCAA 59.757 40.000 0.00 0.00 43.72 2.69
92 93 5.867903 AACACAATGGAGTGGATTTCAAA 57.132 34.783 0.00 0.00 43.72 2.69
93 94 6.423776 AACACAATGGAGTGGATTTCAAAT 57.576 33.333 0.00 0.00 43.72 2.32
94 95 6.423776 ACACAATGGAGTGGATTTCAAATT 57.576 33.333 0.00 0.00 43.72 1.82
95 96 6.829849 ACACAATGGAGTGGATTTCAAATTT 58.170 32.000 0.00 0.00 43.72 1.82
96 97 7.281841 ACACAATGGAGTGGATTTCAAATTTT 58.718 30.769 0.00 0.00 43.72 1.82
97 98 7.774625 ACACAATGGAGTGGATTTCAAATTTTT 59.225 29.630 0.00 0.00 43.72 1.94
153 154 6.371809 AATACTTGAAACTGCGAAAAGTGA 57.628 33.333 0.00 0.00 33.37 3.41
210 279 9.265862 AGTTTTGGAATGGTATGGAATAATTGA 57.734 29.630 0.00 0.00 0.00 2.57
213 282 9.486123 TTTGGAATGGTATGGAATAATTGAAGA 57.514 29.630 0.00 0.00 0.00 2.87
231 300 5.580661 TGAAGATGTTGTGAAATGTGTGTG 58.419 37.500 0.00 0.00 0.00 3.82
232 301 5.125257 TGAAGATGTTGTGAAATGTGTGTGT 59.875 36.000 0.00 0.00 0.00 3.72
285 355 7.849804 ATGAAACAGTTAAATCTATGCGTCT 57.150 32.000 0.00 0.00 0.00 4.18
286 356 7.060600 TGAAACAGTTAAATCTATGCGTCTG 57.939 36.000 0.00 0.00 0.00 3.51
297 367 1.730501 ATGCGTCTGGAGTGTCATTG 58.269 50.000 0.00 0.00 0.00 2.82
300 370 2.143122 GCGTCTGGAGTGTCATTGAAA 58.857 47.619 0.00 0.00 0.00 2.69
301 371 2.744202 GCGTCTGGAGTGTCATTGAAAT 59.256 45.455 0.00 0.00 0.00 2.17
305 375 6.403636 GCGTCTGGAGTGTCATTGAAATTATT 60.404 38.462 0.00 0.00 0.00 1.40
306 376 7.530010 CGTCTGGAGTGTCATTGAAATTATTT 58.470 34.615 0.00 0.00 0.00 1.40
307 377 7.482743 CGTCTGGAGTGTCATTGAAATTATTTG 59.517 37.037 0.00 0.00 0.00 2.32
308 378 8.514594 GTCTGGAGTGTCATTGAAATTATTTGA 58.485 33.333 0.00 0.00 0.00 2.69
309 379 9.076781 TCTGGAGTGTCATTGAAATTATTTGAA 57.923 29.630 0.00 0.00 0.00 2.69
310 380 9.695526 CTGGAGTGTCATTGAAATTATTTGAAA 57.304 29.630 0.00 0.00 0.00 2.69
356 761 8.807581 AGAACGAAATTTTGAAATCAGTGTTTC 58.192 29.630 12.54 9.78 38.32 2.78
357 762 7.463469 ACGAAATTTTGAAATCAGTGTTTCC 57.537 32.000 12.54 0.00 37.31 3.13
376 781 9.959749 GTGTTTCCTGAAATGTCATAAAAGTAA 57.040 29.630 0.00 0.00 31.85 2.24
444 849 8.087982 TGAATAGGATGAATATTCTTTGACGC 57.912 34.615 16.24 0.00 39.39 5.19
447 852 9.725019 AATAGGATGAATATTCTTTGACGCATA 57.275 29.630 16.24 1.49 0.00 3.14
449 854 8.627208 AGGATGAATATTCTTTGACGCATATT 57.373 30.769 16.24 0.00 0.00 1.28
615 1633 9.801873 TTTGAAACCTTGAGCTATTTATATTGC 57.198 29.630 0.00 0.00 33.44 3.56
617 1635 7.559533 TGAAACCTTGAGCTATTTATATTGCCA 59.440 33.333 0.00 0.00 33.68 4.92
726 1746 8.283699 ACAATAGAGACAGTACTTTCTACTCC 57.716 38.462 11.50 0.00 0.00 3.85
727 1747 7.889073 ACAATAGAGACAGTACTTTCTACTCCA 59.111 37.037 11.50 0.00 0.00 3.86
728 1748 8.402472 CAATAGAGACAGTACTTTCTACTCCAG 58.598 40.741 11.50 0.00 0.00 3.86
729 1749 5.883180 AGAGACAGTACTTTCTACTCCAGT 58.117 41.667 11.50 0.00 0.00 4.00
730 1750 7.018487 AGAGACAGTACTTTCTACTCCAGTA 57.982 40.000 11.50 0.00 0.00 2.74
731 1751 7.635648 AGAGACAGTACTTTCTACTCCAGTAT 58.364 38.462 11.50 0.00 0.00 2.12
732 1752 8.770322 AGAGACAGTACTTTCTACTCCAGTATA 58.230 37.037 11.50 0.00 0.00 1.47
733 1753 8.735692 AGACAGTACTTTCTACTCCAGTATAC 57.264 38.462 9.85 0.00 0.00 1.47
734 1754 8.550585 AGACAGTACTTTCTACTCCAGTATACT 58.449 37.037 9.85 0.00 0.00 2.12
735 1755 9.176460 GACAGTACTTTCTACTCCAGTATACTT 57.824 37.037 1.56 0.00 0.00 2.24
759 1779 2.633860 GGCTATACACATGGCAGCC 58.366 57.895 3.66 3.66 44.54 4.85
762 1782 1.233019 CTATACACATGGCAGCCAGC 58.767 55.000 21.51 0.00 44.65 4.85
791 1811 4.331717 GCCGGAGTTATTCGAATTTCTGAA 59.668 41.667 17.19 0.66 0.00 3.02
1047 2100 4.000620 TCCTACTCCCCGGCCACA 62.001 66.667 2.24 0.00 0.00 4.17
1101 2160 2.680370 CCACTTCCTGGCCTACCCC 61.680 68.421 3.32 0.00 31.36 4.95
1422 2481 3.435186 GGGAAGCCGCACAAGCTC 61.435 66.667 0.00 0.00 40.49 4.09
1464 2523 3.202706 GCGATTGGGGACTTCGGC 61.203 66.667 0.00 0.00 37.23 5.54
1563 2622 3.615351 GCTCCAACTTCCTCTGTCAGTAC 60.615 52.174 0.00 0.00 0.00 2.73
1564 2623 3.829601 CTCCAACTTCCTCTGTCAGTACT 59.170 47.826 0.00 0.00 0.00 2.73
1567 2626 5.419155 TCCAACTTCCTCTGTCAGTACTATG 59.581 44.000 0.00 0.00 0.00 2.23
1579 2638 6.036470 TGTCAGTACTATGCATCTCTTTTCG 58.964 40.000 0.19 0.00 0.00 3.46
1584 2643 7.327275 CAGTACTATGCATCTCTTTTCGTATCC 59.673 40.741 0.19 0.00 0.00 2.59
1589 2648 4.876107 TGCATCTCTTTTCGTATCCTTTCC 59.124 41.667 0.00 0.00 0.00 3.13
1591 2650 5.586643 GCATCTCTTTTCGTATCCTTTCCTT 59.413 40.000 0.00 0.00 0.00 3.36
1592 2651 6.457528 GCATCTCTTTTCGTATCCTTTCCTTG 60.458 42.308 0.00 0.00 0.00 3.61
1593 2652 4.935808 TCTCTTTTCGTATCCTTTCCTTGC 59.064 41.667 0.00 0.00 0.00 4.01
1594 2653 4.007659 TCTTTTCGTATCCTTTCCTTGCC 58.992 43.478 0.00 0.00 0.00 4.52
1595 2654 3.713826 TTTCGTATCCTTTCCTTGCCT 57.286 42.857 0.00 0.00 0.00 4.75
1596 2655 2.691409 TCGTATCCTTTCCTTGCCTG 57.309 50.000 0.00 0.00 0.00 4.85
1607 2673 3.071874 TCCTTGCCTGTTTCATCGATT 57.928 42.857 0.00 0.00 0.00 3.34
1608 2674 2.749076 TCCTTGCCTGTTTCATCGATTG 59.251 45.455 0.00 0.00 0.00 2.67
1609 2675 2.749076 CCTTGCCTGTTTCATCGATTGA 59.251 45.455 0.00 0.00 0.00 2.57
1610 2676 3.379372 CCTTGCCTGTTTCATCGATTGAT 59.621 43.478 0.00 0.00 33.34 2.57
1611 2677 4.497006 CCTTGCCTGTTTCATCGATTGATC 60.497 45.833 0.00 0.00 33.34 2.92
1612 2678 2.945008 TGCCTGTTTCATCGATTGATCC 59.055 45.455 0.00 0.00 33.34 3.36
1613 2679 2.032549 GCCTGTTTCATCGATTGATCCG 60.033 50.000 0.00 0.00 33.34 4.18
1614 2680 3.198068 CCTGTTTCATCGATTGATCCGT 58.802 45.455 0.00 0.00 33.34 4.69
1615 2681 3.623060 CCTGTTTCATCGATTGATCCGTT 59.377 43.478 0.00 0.00 33.34 4.44
1616 2682 4.260375 CCTGTTTCATCGATTGATCCGTTC 60.260 45.833 0.00 0.00 33.34 3.95
1659 2729 2.159240 GGCCGGAGATTGAAATGAAACC 60.159 50.000 5.05 0.00 0.00 3.27
1667 2737 7.260603 GGAGATTGAAATGAAACCGATTGATT 58.739 34.615 0.00 0.00 0.00 2.57
1671 2741 8.876275 ATTGAAATGAAACCGATTGATTATGG 57.124 30.769 0.00 0.00 0.00 2.74
1673 2743 5.850557 AATGAAACCGATTGATTATGGCA 57.149 34.783 0.00 0.00 0.00 4.92
1690 2760 1.900237 GCACCGAGATGCATGTTTTC 58.100 50.000 2.46 0.00 45.39 2.29
1693 2763 1.470098 ACCGAGATGCATGTTTTCTGC 59.530 47.619 2.46 0.00 40.10 4.26
1706 2776 3.796178 TGTTTTCTGCTGATTTTTGACGC 59.204 39.130 0.00 0.00 0.00 5.19
1848 2918 3.281158 CCATCATCATGGTACTGCACAA 58.719 45.455 0.00 0.00 44.46 3.33
1864 2934 5.106396 ACTGCACAATCACTAATTCTTGCTC 60.106 40.000 0.00 0.00 35.64 4.26
1910 3038 5.255687 TCATGAACACCTTGCTGACATATT 58.744 37.500 0.00 0.00 0.00 1.28
1911 3039 5.711506 TCATGAACACCTTGCTGACATATTT 59.288 36.000 0.00 0.00 0.00 1.40
1946 3074 2.807622 GCGACGGGTACGGGTATT 59.192 61.111 0.00 0.00 46.48 1.89
2017 3145 9.298774 CGAGGACTACAAGGTTAGTAATTTTAG 57.701 37.037 0.00 0.00 0.00 1.85
2083 3213 3.194116 CCAATTCCAACTATGCTTGCACT 59.806 43.478 0.00 0.00 0.00 4.40
2085 3215 5.068198 CCAATTCCAACTATGCTTGCACTAT 59.932 40.000 0.00 0.00 0.00 2.12
2092 3222 8.253810 TCCAACTATGCTTGCACTATATCTATC 58.746 37.037 0.00 0.00 0.00 2.08
2133 3263 6.539464 AGTGTTTAATTACCAACGAGACACAA 59.461 34.615 0.00 0.00 37.81 3.33
2134 3264 6.849305 GTGTTTAATTACCAACGAGACACAAG 59.151 38.462 0.00 0.00 36.00 3.16
2135 3265 6.539464 TGTTTAATTACCAACGAGACACAAGT 59.461 34.615 0.00 0.00 0.00 3.16
2136 3266 7.710044 TGTTTAATTACCAACGAGACACAAGTA 59.290 33.333 0.00 0.00 0.00 2.24
2137 3267 7.642071 TTAATTACCAACGAGACACAAGTAC 57.358 36.000 0.00 0.00 0.00 2.73
2138 3268 4.652421 TTACCAACGAGACACAAGTACA 57.348 40.909 0.00 0.00 0.00 2.90
2145 3276 3.615496 ACGAGACACAAGTACAACACAAC 59.385 43.478 0.00 0.00 0.00 3.32
2158 3289 7.916552 AGTACAACACAACATCAGAGTTAAAC 58.083 34.615 0.00 0.00 0.00 2.01
2162 3293 6.604735 ACACAACATCAGAGTTAAACTGTC 57.395 37.500 9.66 0.00 36.81 3.51
2166 3297 7.328493 CACAACATCAGAGTTAAACTGTCGATA 59.672 37.037 9.66 0.00 36.81 2.92
2168 3299 7.993821 ACATCAGAGTTAAACTGTCGATATG 57.006 36.000 9.66 8.41 36.81 1.78
2208 3341 1.379576 GGCTTGGCATGGCTCTTCT 60.380 57.895 21.08 0.00 0.00 2.85
2251 3384 2.691011 CTCTGCTCTACAAGGAGGTACC 59.309 54.545 2.73 2.73 43.33 3.34
2259 3392 6.442541 TCTACAAGGAGGTACCAAATTCAA 57.557 37.500 15.94 0.00 42.04 2.69
2260 3393 6.235664 TCTACAAGGAGGTACCAAATTCAAC 58.764 40.000 15.94 0.00 42.04 3.18
2261 3394 4.149598 ACAAGGAGGTACCAAATTCAACC 58.850 43.478 15.94 4.27 42.04 3.77
2264 3397 2.492088 GGAGGTACCAAATTCAACCTGC 59.508 50.000 15.94 0.00 42.40 4.85
2282 3421 3.024547 CTGCCTAGCTAGTACTGTTGGA 58.975 50.000 19.31 2.78 0.00 3.53
2477 3626 0.325110 CAAGGAGGAGCTCTGGGAGA 60.325 60.000 14.64 0.00 0.00 3.71
2563 3712 1.141665 CATCATGGTCGACCTCGCA 59.858 57.895 33.39 15.47 39.60 5.10
2587 3736 0.036388 AGGACGGTATGCACCAACAG 60.036 55.000 0.00 0.00 46.14 3.16
2589 3738 1.076332 GACGGTATGCACCAACAGTC 58.924 55.000 11.29 11.29 46.14 3.51
2592 3741 1.678728 CGGTATGCACCAACAGTCCAT 60.679 52.381 0.00 0.00 46.14 3.41
2608 3784 2.686915 GTCCATTCATCTTGCTCTTGGG 59.313 50.000 0.00 0.00 0.00 4.12
2611 3787 3.129988 CCATTCATCTTGCTCTTGGGAAC 59.870 47.826 0.00 0.00 0.00 3.62
2629 3805 5.686159 GGAACCTTGCTAATGATGAGATG 57.314 43.478 0.00 0.00 0.00 2.90
2640 3819 8.349983 TGCTAATGATGAGATGATGAAATGTTG 58.650 33.333 0.00 0.00 0.00 3.33
2644 3823 7.092137 TGATGAGATGATGAAATGTTGGTTC 57.908 36.000 0.00 0.00 0.00 3.62
2656 3835 1.273688 GTTGGTTCGTTGTTGTTGGC 58.726 50.000 0.00 0.00 0.00 4.52
2663 3842 0.673437 CGTTGTTGTTGGCAGGGATT 59.327 50.000 0.00 0.00 0.00 3.01
2732 3911 6.293516 GGAACGTCGAAGTATACTGATCATCT 60.294 42.308 6.06 0.00 0.00 2.90
2797 3997 3.558033 TGTTTGTCCCACCTAGTTTTCC 58.442 45.455 0.00 0.00 0.00 3.13
2856 4057 4.160814 TCGGCCATATATACGCCTTGTATT 59.839 41.667 16.77 0.00 41.01 1.89
2866 4067 2.992744 GCCTTGTATTTAGCGACGAC 57.007 50.000 0.00 0.00 0.00 4.34
2879 4080 4.664677 ACGACTGAGTGGCACGGC 62.665 66.667 12.71 9.25 0.00 5.68
2892 4093 1.796151 CACGGCGAGCATCAAATGT 59.204 52.632 16.62 0.00 33.17 2.71
2893 4094 0.168788 CACGGCGAGCATCAAATGTT 59.831 50.000 16.62 0.00 33.17 2.71
2902 4103 5.348451 GCGAGCATCAAATGTTAAACCAATT 59.652 36.000 0.00 0.00 33.17 2.32
2916 4117 2.205022 CCAATTGTTGGCTCCTCTGA 57.795 50.000 4.43 0.00 45.17 3.27
2918 4119 2.426024 CCAATTGTTGGCTCCTCTGATG 59.574 50.000 4.43 0.00 45.17 3.07
2921 4122 1.588239 TGTTGGCTCCTCTGATGGAT 58.412 50.000 0.00 0.00 35.30 3.41
2941 4142 9.247126 GATGGATCGATCAATGTAGATATTGAG 57.753 37.037 25.93 0.00 46.70 3.02
3011 4212 6.311935 CACTATTTGCAGCTGTTTTTATGCAT 59.688 34.615 16.64 3.79 32.14 3.96
3164 4373 9.906660 TGCTAAAAAGAAGTTAATTGTACCATG 57.093 29.630 0.00 0.00 0.00 3.66
3191 4400 1.176527 AGATTGATTTGTGGGCCGTG 58.823 50.000 0.00 0.00 0.00 4.94
3193 4402 1.133025 GATTGATTTGTGGGCCGTGAG 59.867 52.381 0.00 0.00 0.00 3.51
3259 4468 2.114616 CAGAGCCACCCATTACTCTCT 58.885 52.381 0.00 0.00 37.40 3.10
3382 4594 2.227388 AGTGGTAAACGTAGGACTCACG 59.773 50.000 0.00 0.00 44.80 4.35
3462 4674 8.754080 AGTGTAGAGAACATTCAACTAAGCTAT 58.246 33.333 0.00 0.00 41.10 2.97
3490 4702 9.042008 GTAGTTGGTTTGTGATCAATACGATAT 57.958 33.333 0.00 0.00 33.17 1.63
3497 4709 9.244799 GTTTGTGATCAATACGATATCAGTACA 57.755 33.333 0.00 0.00 33.17 2.90
3568 4780 9.621629 TTCATAAATATATTCGGTTTCTGTGGT 57.378 29.630 0.00 0.00 0.00 4.16
3569 4781 9.621629 TCATAAATATATTCGGTTTCTGTGGTT 57.378 29.630 0.00 0.00 0.00 3.67
3572 4784 8.446599 AAATATATTCGGTTTCTGTGGTTAGG 57.553 34.615 0.00 0.00 0.00 2.69
3573 4785 2.554370 TTCGGTTTCTGTGGTTAGGG 57.446 50.000 0.00 0.00 0.00 3.53
3574 4786 1.426751 TCGGTTTCTGTGGTTAGGGT 58.573 50.000 0.00 0.00 0.00 4.34
3575 4787 1.071071 TCGGTTTCTGTGGTTAGGGTG 59.929 52.381 0.00 0.00 0.00 4.61
3576 4788 1.880646 CGGTTTCTGTGGTTAGGGTGG 60.881 57.143 0.00 0.00 0.00 4.61
3577 4789 1.144298 GGTTTCTGTGGTTAGGGTGGT 59.856 52.381 0.00 0.00 0.00 4.16
3578 4790 2.227194 GTTTCTGTGGTTAGGGTGGTG 58.773 52.381 0.00 0.00 0.00 4.17
3579 4791 1.809133 TTCTGTGGTTAGGGTGGTGA 58.191 50.000 0.00 0.00 0.00 4.02
3580 4792 1.053424 TCTGTGGTTAGGGTGGTGAC 58.947 55.000 0.00 0.00 0.00 3.67
3581 4793 0.036306 CTGTGGTTAGGGTGGTGACC 59.964 60.000 0.00 0.00 42.27 4.02
3582 4794 1.004200 GTGGTTAGGGTGGTGACCG 60.004 63.158 0.00 0.00 44.23 4.79
3583 4795 2.218454 TGGTTAGGGTGGTGACCGG 61.218 63.158 0.00 0.00 44.23 5.28
3584 4796 2.666812 GTTAGGGTGGTGACCGGG 59.333 66.667 6.32 0.00 44.23 5.73
3585 4797 1.914764 GTTAGGGTGGTGACCGGGA 60.915 63.158 6.32 0.00 44.23 5.14
3586 4798 1.611261 TTAGGGTGGTGACCGGGAG 60.611 63.158 6.32 0.00 44.23 4.30
3587 4799 2.390777 TTAGGGTGGTGACCGGGAGT 62.391 60.000 6.32 0.00 44.23 3.85
3588 4800 2.793317 TAGGGTGGTGACCGGGAGTC 62.793 65.000 6.32 0.00 44.23 3.36
3589 4801 3.703127 GGTGGTGACCGGGAGTCC 61.703 72.222 6.32 0.00 45.68 3.85
3609 4821 4.555709 GACACCCGCCCACACACA 62.556 66.667 0.00 0.00 0.00 3.72
3610 4822 4.868116 ACACCCGCCCACACACAC 62.868 66.667 0.00 0.00 0.00 3.82
3611 4823 4.866224 CACCCGCCCACACACACA 62.866 66.667 0.00 0.00 0.00 3.72
3612 4824 4.116585 ACCCGCCCACACACACAA 62.117 61.111 0.00 0.00 0.00 3.33
3613 4825 3.286751 CCCGCCCACACACACAAG 61.287 66.667 0.00 0.00 0.00 3.16
3614 4826 2.203139 CCGCCCACACACACAAGA 60.203 61.111 0.00 0.00 0.00 3.02
3615 4827 1.821759 CCGCCCACACACACAAGAA 60.822 57.895 0.00 0.00 0.00 2.52
3616 4828 1.380403 CCGCCCACACACACAAGAAA 61.380 55.000 0.00 0.00 0.00 2.52
3617 4829 0.453793 CGCCCACACACACAAGAAAA 59.546 50.000 0.00 0.00 0.00 2.29
3618 4830 1.135257 CGCCCACACACACAAGAAAAA 60.135 47.619 0.00 0.00 0.00 1.94
3639 4851 7.797121 AAAAAGTCCATTTGGTATCCAGAAT 57.203 32.000 0.00 0.00 33.81 2.40
3640 4852 7.410120 AAAAGTCCATTTGGTATCCAGAATC 57.590 36.000 0.00 0.00 33.81 2.52
3641 4853 5.983333 AGTCCATTTGGTATCCAGAATCT 57.017 39.130 0.00 0.00 33.81 2.40
3642 4854 6.332976 AGTCCATTTGGTATCCAGAATCTT 57.667 37.500 0.00 0.00 33.81 2.40
3643 4855 6.125029 AGTCCATTTGGTATCCAGAATCTTG 58.875 40.000 0.00 0.00 33.81 3.02
3644 4856 6.069440 AGTCCATTTGGTATCCAGAATCTTGA 60.069 38.462 0.00 0.00 33.81 3.02
3645 4857 6.774656 GTCCATTTGGTATCCAGAATCTTGAT 59.225 38.462 2.34 2.34 33.81 2.57
3646 4858 7.939039 GTCCATTTGGTATCCAGAATCTTGATA 59.061 37.037 0.45 0.45 33.81 2.15
3647 4859 8.501904 TCCATTTGGTATCCAGAATCTTGATAA 58.498 33.333 5.73 0.00 33.81 1.75
3648 4860 9.135189 CCATTTGGTATCCAGAATCTTGATAAA 57.865 33.333 5.73 0.71 33.81 1.40
3651 4863 8.519799 TTGGTATCCAGAATCTTGATAAAACC 57.480 34.615 5.73 6.69 33.81 3.27
3652 4864 7.872138 TGGTATCCAGAATCTTGATAAAACCT 58.128 34.615 12.91 0.00 0.00 3.50
3653 4865 7.993183 TGGTATCCAGAATCTTGATAAAACCTC 59.007 37.037 12.91 0.19 0.00 3.85
3654 4866 7.993183 GGTATCCAGAATCTTGATAAAACCTCA 59.007 37.037 5.73 0.00 0.00 3.86
3655 4867 7.872113 ATCCAGAATCTTGATAAAACCTCAC 57.128 36.000 0.00 0.00 0.00 3.51
3656 4868 6.180472 TCCAGAATCTTGATAAAACCTCACC 58.820 40.000 0.00 0.00 0.00 4.02
3657 4869 6.012508 TCCAGAATCTTGATAAAACCTCACCT 60.013 38.462 0.00 0.00 0.00 4.00
3658 4870 6.317391 CCAGAATCTTGATAAAACCTCACCTC 59.683 42.308 0.00 0.00 0.00 3.85
3659 4871 6.881065 CAGAATCTTGATAAAACCTCACCTCA 59.119 38.462 0.00 0.00 0.00 3.86
3660 4872 7.555554 CAGAATCTTGATAAAACCTCACCTCAT 59.444 37.037 0.00 0.00 0.00 2.90
3661 4873 7.555554 AGAATCTTGATAAAACCTCACCTCATG 59.444 37.037 0.00 0.00 0.00 3.07
3662 4874 6.126863 TCTTGATAAAACCTCACCTCATGT 57.873 37.500 0.00 0.00 0.00 3.21
3663 4875 5.939883 TCTTGATAAAACCTCACCTCATGTG 59.060 40.000 0.00 0.00 46.88 3.21
3673 4885 1.561643 ACCTCATGTGATCACTCGGT 58.438 50.000 25.55 20.75 0.00 4.69
3674 4886 1.478510 ACCTCATGTGATCACTCGGTC 59.521 52.381 25.55 0.00 0.00 4.79
3675 4887 1.753649 CCTCATGTGATCACTCGGTCT 59.246 52.381 25.55 2.18 0.00 3.85
3676 4888 2.480932 CCTCATGTGATCACTCGGTCTG 60.481 54.545 25.55 13.10 0.00 3.51
3677 4889 1.134995 TCATGTGATCACTCGGTCTGC 60.135 52.381 25.55 0.00 0.00 4.26
3678 4890 1.134877 CATGTGATCACTCGGTCTGCT 60.135 52.381 25.55 0.00 0.00 4.24
3679 4891 0.244721 TGTGATCACTCGGTCTGCTG 59.755 55.000 25.55 0.00 0.00 4.41
3680 4892 1.080995 GTGATCACTCGGTCTGCTGC 61.081 60.000 18.83 0.00 0.00 5.25
3681 4893 1.253593 TGATCACTCGGTCTGCTGCT 61.254 55.000 0.00 0.00 0.00 4.24
3682 4894 0.805322 GATCACTCGGTCTGCTGCTG 60.805 60.000 0.00 0.00 0.00 4.41
3683 4895 2.849120 ATCACTCGGTCTGCTGCTGC 62.849 60.000 8.89 8.89 40.20 5.25
3684 4896 4.385405 ACTCGGTCTGCTGCTGCC 62.385 66.667 13.47 5.64 38.71 4.85
3707 4919 1.503542 GTGCACACACATAGCAGCC 59.496 57.895 13.17 0.00 46.61 4.85
3708 4920 1.675310 TGCACACACATAGCAGCCC 60.675 57.895 0.00 0.00 33.75 5.19
3709 4921 1.377725 GCACACACATAGCAGCCCT 60.378 57.895 0.00 0.00 0.00 5.19
3710 4922 0.107703 GCACACACATAGCAGCCCTA 60.108 55.000 0.00 0.00 0.00 3.53
3711 4923 1.475751 GCACACACATAGCAGCCCTAT 60.476 52.381 0.00 0.00 37.22 2.57
3712 4924 2.487934 CACACACATAGCAGCCCTATC 58.512 52.381 0.00 0.00 34.49 2.08
3713 4925 1.417890 ACACACATAGCAGCCCTATCC 59.582 52.381 0.00 0.00 34.49 2.59
3714 4926 1.059913 ACACATAGCAGCCCTATCCC 58.940 55.000 0.00 0.00 34.49 3.85
3715 4927 1.356124 CACATAGCAGCCCTATCCCT 58.644 55.000 0.00 0.00 34.49 4.20
3716 4928 2.158158 ACACATAGCAGCCCTATCCCTA 60.158 50.000 0.00 0.00 34.49 3.53
3717 4929 2.234908 CACATAGCAGCCCTATCCCTAC 59.765 54.545 0.00 0.00 34.49 3.18
3718 4930 1.834263 CATAGCAGCCCTATCCCTACC 59.166 57.143 0.00 0.00 34.49 3.18
3719 4931 0.864659 TAGCAGCCCTATCCCTACCA 59.135 55.000 0.00 0.00 0.00 3.25
3720 4932 0.764752 AGCAGCCCTATCCCTACCAC 60.765 60.000 0.00 0.00 0.00 4.16
3721 4933 1.769716 GCAGCCCTATCCCTACCACC 61.770 65.000 0.00 0.00 0.00 4.61
3722 4934 0.399949 CAGCCCTATCCCTACCACCA 60.400 60.000 0.00 0.00 0.00 4.17
3723 4935 0.400093 AGCCCTATCCCTACCACCAC 60.400 60.000 0.00 0.00 0.00 4.16
3724 4936 1.416480 GCCCTATCCCTACCACCACC 61.416 65.000 0.00 0.00 0.00 4.61
3725 4937 0.030501 CCCTATCCCTACCACCACCA 60.031 60.000 0.00 0.00 0.00 4.17
3726 4938 1.416013 CCCTATCCCTACCACCACCAT 60.416 57.143 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.270808 GTGCATTGTAACAAGCTGCTTTTT 59.729 37.500 13.10 15.32 34.02 1.94
3 4 3.803778 GTGCATTGTAACAAGCTGCTTTT 59.196 39.130 13.10 12.52 34.02 2.27
5 6 2.605338 CGTGCATTGTAACAAGCTGCTT 60.605 45.455 9.53 9.53 34.02 3.91
6 7 1.069022 CGTGCATTGTAACAAGCTGCT 60.069 47.619 0.00 0.00 34.02 4.24
7 8 1.330306 CGTGCATTGTAACAAGCTGC 58.670 50.000 0.00 0.00 0.00 5.25
8 9 2.686558 ACGTGCATTGTAACAAGCTG 57.313 45.000 0.00 0.00 0.00 4.24
10 11 2.224549 TGGTACGTGCATTGTAACAAGC 59.775 45.455 15.08 2.20 36.62 4.01
11 12 3.248841 TGTGGTACGTGCATTGTAACAAG 59.751 43.478 18.01 0.00 40.90 3.16
12 13 3.203716 TGTGGTACGTGCATTGTAACAA 58.796 40.909 18.01 8.73 40.90 2.83
13 14 2.835027 TGTGGTACGTGCATTGTAACA 58.165 42.857 13.84 13.84 37.18 2.41
14 15 5.728351 ATATGTGGTACGTGCATTGTAAC 57.272 39.130 5.86 9.49 0.00 2.50
15 16 6.745159 AAATATGTGGTACGTGCATTGTAA 57.255 33.333 5.86 0.00 0.00 2.41
16 17 6.149640 ACAAAATATGTGGTACGTGCATTGTA 59.850 34.615 5.86 0.00 41.93 2.41
17 18 5.048364 ACAAAATATGTGGTACGTGCATTGT 60.048 36.000 5.86 0.00 41.93 2.71
18 19 5.398169 ACAAAATATGTGGTACGTGCATTG 58.602 37.500 5.86 1.02 41.93 2.82
19 20 5.637006 ACAAAATATGTGGTACGTGCATT 57.363 34.783 5.86 0.00 41.93 3.56
20 21 5.637006 AACAAAATATGTGGTACGTGCAT 57.363 34.783 5.86 4.20 42.99 3.96
21 22 5.008712 TCAAACAAAATATGTGGTACGTGCA 59.991 36.000 5.86 0.00 42.99 4.57
22 23 5.453648 TCAAACAAAATATGTGGTACGTGC 58.546 37.500 0.00 0.00 42.99 5.34
23 24 7.916128 TTTCAAACAAAATATGTGGTACGTG 57.084 32.000 0.00 0.00 42.99 4.49
43 44 9.566432 ACCTTTGGTATTTTTGCAATTATTTCA 57.434 25.926 0.00 0.00 32.11 2.69
48 49 9.262358 GTGTTACCTTTGGTATTTTTGCAATTA 57.738 29.630 0.00 0.00 38.05 1.40
49 50 7.770897 TGTGTTACCTTTGGTATTTTTGCAATT 59.229 29.630 0.00 0.00 38.05 2.32
50 51 7.275920 TGTGTTACCTTTGGTATTTTTGCAAT 58.724 30.769 0.00 0.00 38.05 3.56
51 52 6.640518 TGTGTTACCTTTGGTATTTTTGCAA 58.359 32.000 0.00 0.00 38.05 4.08
52 53 6.222038 TGTGTTACCTTTGGTATTTTTGCA 57.778 33.333 0.00 0.00 38.05 4.08
53 54 7.307692 CCATTGTGTTACCTTTGGTATTTTTGC 60.308 37.037 0.00 0.00 38.05 3.68
54 55 7.928706 TCCATTGTGTTACCTTTGGTATTTTTG 59.071 33.333 0.00 0.00 38.05 2.44
55 56 8.024145 TCCATTGTGTTACCTTTGGTATTTTT 57.976 30.769 0.00 0.00 38.05 1.94
56 57 7.289084 ACTCCATTGTGTTACCTTTGGTATTTT 59.711 33.333 0.00 0.00 38.05 1.82
57 58 6.780522 ACTCCATTGTGTTACCTTTGGTATTT 59.219 34.615 0.00 0.00 38.05 1.40
58 59 6.208599 CACTCCATTGTGTTACCTTTGGTATT 59.791 38.462 0.00 0.00 38.05 1.89
59 60 5.710099 CACTCCATTGTGTTACCTTTGGTAT 59.290 40.000 0.00 0.00 38.05 2.73
60 61 5.067273 CACTCCATTGTGTTACCTTTGGTA 58.933 41.667 0.00 0.00 36.26 3.25
61 62 3.888930 CACTCCATTGTGTTACCTTTGGT 59.111 43.478 0.00 0.00 35.11 3.67
62 63 3.255642 CCACTCCATTGTGTTACCTTTGG 59.744 47.826 0.00 0.00 36.30 3.28
63 64 4.141287 TCCACTCCATTGTGTTACCTTTG 58.859 43.478 0.00 0.00 36.30 2.77
64 65 4.447138 TCCACTCCATTGTGTTACCTTT 57.553 40.909 0.00 0.00 36.30 3.11
65 66 4.657814 ATCCACTCCATTGTGTTACCTT 57.342 40.909 0.00 0.00 36.30 3.50
66 67 4.657814 AATCCACTCCATTGTGTTACCT 57.342 40.909 0.00 0.00 36.30 3.08
67 68 4.764823 TGAAATCCACTCCATTGTGTTACC 59.235 41.667 0.00 0.00 36.30 2.85
68 69 5.957842 TGAAATCCACTCCATTGTGTTAC 57.042 39.130 0.00 0.00 36.30 2.50
69 70 6.968263 TTTGAAATCCACTCCATTGTGTTA 57.032 33.333 0.00 0.00 36.30 2.41
70 71 5.867903 TTTGAAATCCACTCCATTGTGTT 57.132 34.783 0.00 0.00 36.30 3.32
71 72 6.423776 AATTTGAAATCCACTCCATTGTGT 57.576 33.333 0.00 0.00 36.30 3.72
72 73 7.733402 AAAATTTGAAATCCACTCCATTGTG 57.267 32.000 0.00 0.00 37.66 3.33
187 188 9.486123 TCTTCAATTATTCCATACCATTCCAAA 57.514 29.630 0.00 0.00 0.00 3.28
189 190 9.081204 CATCTTCAATTATTCCATACCATTCCA 57.919 33.333 0.00 0.00 0.00 3.53
190 191 9.082313 ACATCTTCAATTATTCCATACCATTCC 57.918 33.333 0.00 0.00 0.00 3.01
193 262 9.425248 ACAACATCTTCAATTATTCCATACCAT 57.575 29.630 0.00 0.00 0.00 3.55
210 279 5.581126 ACACACACATTTCACAACATCTT 57.419 34.783 0.00 0.00 0.00 2.40
258 327 8.487313 ACGCATAGATTTAACTGTTTCATACA 57.513 30.769 0.00 0.00 34.95 2.29
264 333 6.170506 TCCAGACGCATAGATTTAACTGTTT 58.829 36.000 0.00 0.00 0.00 2.83
330 735 8.702163 AAACACTGATTTCAAAATTTCGTTCT 57.298 26.923 0.00 0.00 0.00 3.01
332 737 7.763985 AGGAAACACTGATTTCAAAATTTCGTT 59.236 29.630 0.00 0.00 39.85 3.85
334 739 7.434897 TCAGGAAACACTGATTTCAAAATTTCG 59.565 33.333 0.00 0.00 42.26 3.46
336 741 9.447157 TTTCAGGAAACACTGATTTCAAAATTT 57.553 25.926 0.00 0.00 46.07 1.82
339 744 8.040132 ACATTTCAGGAAACACTGATTTCAAAA 58.960 29.630 0.00 7.91 46.07 2.44
343 748 6.738114 TGACATTTCAGGAAACACTGATTTC 58.262 36.000 0.00 0.00 46.07 2.17
344 749 6.713762 TGACATTTCAGGAAACACTGATTT 57.286 33.333 0.00 0.00 46.07 2.17
376 781 8.934023 TCCCAGACATATTTTAAACTTTGACT 57.066 30.769 3.60 0.63 0.00 3.41
395 800 8.646004 TCAACAAACATTTCAAATTATCCCAGA 58.354 29.630 0.00 0.00 0.00 3.86
396 801 8.830201 TCAACAAACATTTCAAATTATCCCAG 57.170 30.769 0.00 0.00 0.00 4.45
538 1555 8.645730 TTTTAGGTCCAATTTCCGTTTAAAAC 57.354 30.769 0.00 0.00 0.00 2.43
578 1596 9.413734 AGCTCAAGGTTTCAAAAATAGCTATAT 57.586 29.630 6.68 0.00 36.10 0.86
579 1597 8.807948 AGCTCAAGGTTTCAAAAATAGCTATA 57.192 30.769 6.68 0.00 36.10 1.31
581 1599 8.807948 ATAGCTCAAGGTTTCAAAAATAGCTA 57.192 30.769 0.00 0.00 42.36 3.32
705 1725 7.018487 ACTGGAGTAGAAAGTACTGTCTCTA 57.982 40.000 19.17 11.39 0.00 2.43
717 1737 9.662947 GCCTTTAAAAGTATACTGGAGTAGAAA 57.337 33.333 6.06 0.71 33.52 2.52
718 1738 9.043548 AGCCTTTAAAAGTATACTGGAGTAGAA 57.956 33.333 6.06 0.00 33.52 2.10
719 1739 8.605325 AGCCTTTAAAAGTATACTGGAGTAGA 57.395 34.615 6.06 0.00 33.52 2.59
725 1745 9.826574 TGTGTATAGCCTTTAAAAGTATACTGG 57.173 33.333 6.06 3.22 30.33 4.00
729 1749 9.280174 GCCATGTGTATAGCCTTTAAAAGTATA 57.720 33.333 0.00 0.00 0.00 1.47
730 1750 7.777910 TGCCATGTGTATAGCCTTTAAAAGTAT 59.222 33.333 0.00 0.00 0.00 2.12
731 1751 7.113437 TGCCATGTGTATAGCCTTTAAAAGTA 58.887 34.615 0.00 0.00 0.00 2.24
732 1752 5.949354 TGCCATGTGTATAGCCTTTAAAAGT 59.051 36.000 0.00 0.00 0.00 2.66
733 1753 6.449635 TGCCATGTGTATAGCCTTTAAAAG 57.550 37.500 0.00 0.00 0.00 2.27
734 1754 5.163561 GCTGCCATGTGTATAGCCTTTAAAA 60.164 40.000 0.00 0.00 0.00 1.52
735 1755 4.338118 GCTGCCATGTGTATAGCCTTTAAA 59.662 41.667 0.00 0.00 0.00 1.52
762 1782 0.776451 CGAATAACTCCGGCGAATCG 59.224 55.000 9.30 0.00 0.00 3.34
767 1787 2.864343 AGAAATTCGAATAACTCCGGCG 59.136 45.455 11.83 0.00 0.00 6.46
1023 2076 3.851128 GGGGAGTAGGACGGCAGC 61.851 72.222 0.00 0.00 0.00 5.25
1029 2082 3.468140 GTGGCCGGGGAGTAGGAC 61.468 72.222 2.18 0.00 35.66 3.85
1072 2125 3.319198 GAAGTGGCTGGACGGGGA 61.319 66.667 0.00 0.00 0.00 4.81
1074 2127 3.322466 AGGAAGTGGCTGGACGGG 61.322 66.667 0.00 0.00 0.00 5.28
1075 2128 2.046892 CAGGAAGTGGCTGGACGG 60.047 66.667 0.00 0.00 0.00 4.79
1266 2325 2.426023 GTGTTGAGGAGGCACCGT 59.574 61.111 0.00 0.00 44.74 4.83
1275 2334 2.358737 GTGAGCCGGGTGTTGAGG 60.359 66.667 12.94 0.00 0.00 3.86
1422 2481 2.336809 GCGATGGAGTAGAGCCGG 59.663 66.667 0.00 0.00 0.00 6.13
1450 2509 2.240162 GAGTCGCCGAAGTCCCCAAT 62.240 60.000 0.00 0.00 0.00 3.16
1452 2511 3.379445 GAGTCGCCGAAGTCCCCA 61.379 66.667 0.00 0.00 0.00 4.96
1464 2523 1.442184 CGACACGGTCTTGGAGTCG 60.442 63.158 0.00 0.00 44.64 4.18
1563 2622 7.095439 GGAAAGGATACGAAAAGAGATGCATAG 60.095 40.741 0.00 0.00 46.39 2.23
1564 2623 6.706270 GGAAAGGATACGAAAAGAGATGCATA 59.294 38.462 0.00 0.00 46.39 3.14
1567 2626 5.119694 AGGAAAGGATACGAAAAGAGATGC 58.880 41.667 0.00 0.00 46.39 3.91
1579 2638 4.079253 TGAAACAGGCAAGGAAAGGATAC 58.921 43.478 0.00 0.00 0.00 2.24
1584 2643 2.813754 TCGATGAAACAGGCAAGGAAAG 59.186 45.455 0.00 0.00 0.00 2.62
1589 2648 4.497006 GGATCAATCGATGAAACAGGCAAG 60.497 45.833 0.00 0.00 42.54 4.01
1591 2650 2.945008 GGATCAATCGATGAAACAGGCA 59.055 45.455 0.00 0.00 42.54 4.75
1592 2651 2.032549 CGGATCAATCGATGAAACAGGC 60.033 50.000 0.00 0.00 42.54 4.85
1593 2652 3.198068 ACGGATCAATCGATGAAACAGG 58.802 45.455 0.00 0.00 42.54 4.00
1594 2653 4.329801 TGAACGGATCAATCGATGAAACAG 59.670 41.667 0.00 2.34 42.54 3.16
1595 2654 4.249661 TGAACGGATCAATCGATGAAACA 58.750 39.130 0.00 0.00 42.54 2.83
1596 2655 4.857871 TGAACGGATCAATCGATGAAAC 57.142 40.909 0.00 0.00 42.54 2.78
1607 2673 3.248363 GCGATTGATTGATGAACGGATCA 59.752 43.478 0.00 0.00 43.67 2.92
1608 2674 3.496130 AGCGATTGATTGATGAACGGATC 59.504 43.478 0.00 0.00 0.00 3.36
1609 2675 3.249320 CAGCGATTGATTGATGAACGGAT 59.751 43.478 0.00 0.00 29.11 4.18
1610 2676 2.609002 CAGCGATTGATTGATGAACGGA 59.391 45.455 0.00 0.00 29.11 4.69
1611 2677 2.609002 TCAGCGATTGATTGATGAACGG 59.391 45.455 0.00 0.00 33.95 4.44
1612 2678 3.931285 TCAGCGATTGATTGATGAACG 57.069 42.857 0.00 0.00 33.95 3.95
1613 2679 5.475273 TCTTCAGCGATTGATTGATGAAC 57.525 39.130 7.61 0.00 40.53 3.18
1614 2680 6.688637 AATCTTCAGCGATTGATTGATGAA 57.311 33.333 10.52 10.52 42.47 2.57
1639 2709 2.477863 CGGTTTCATTTCAATCTCCGGC 60.478 50.000 0.00 0.00 34.24 6.13
1640 2710 3.006940 TCGGTTTCATTTCAATCTCCGG 58.993 45.455 0.00 0.00 37.72 5.14
1659 2729 2.754472 TCTCGGTGCCATAATCAATCG 58.246 47.619 0.00 0.00 0.00 3.34
1667 2737 0.469494 ACATGCATCTCGGTGCCATA 59.531 50.000 0.00 0.00 44.43 2.74
1671 2741 1.470098 AGAAAACATGCATCTCGGTGC 59.530 47.619 0.00 0.00 45.25 5.01
1673 2743 1.470098 GCAGAAAACATGCATCTCGGT 59.530 47.619 0.00 0.00 43.31 4.69
1690 2760 1.808945 AGAGGCGTCAAAAATCAGCAG 59.191 47.619 9.41 0.00 0.00 4.24
1693 2763 3.499918 AGAACAGAGGCGTCAAAAATCAG 59.500 43.478 9.41 0.00 0.00 2.90
1706 2776 2.686235 CTCAGCAGACAAGAACAGAGG 58.314 52.381 0.00 0.00 0.00 3.69
1848 2918 9.582431 CATTCATTTTGAGCAAGAATTAGTGAT 57.418 29.630 0.00 0.00 0.00 3.06
1864 2934 4.836736 AGCCTATCCATCCCATTCATTTTG 59.163 41.667 0.00 0.00 0.00 2.44
2083 3213 6.071391 TGGCTGATTTCAGTGCGATAGATATA 60.071 38.462 9.21 0.00 45.45 0.86
2085 3215 4.039124 TGGCTGATTTCAGTGCGATAGATA 59.961 41.667 9.21 0.00 45.45 1.98
2092 3222 2.548178 ACTGGCTGATTTCAGTGCG 58.452 52.632 9.21 1.21 45.45 5.34
2133 3263 7.769044 AGTTTAACTCTGATGTTGTGTTGTACT 59.231 33.333 0.00 0.00 0.00 2.73
2134 3264 7.850982 CAGTTTAACTCTGATGTTGTGTTGTAC 59.149 37.037 0.00 0.00 35.20 2.90
2135 3265 7.551262 ACAGTTTAACTCTGATGTTGTGTTGTA 59.449 33.333 12.10 0.00 36.81 2.41
2136 3266 6.374333 ACAGTTTAACTCTGATGTTGTGTTGT 59.626 34.615 12.10 0.00 36.81 3.32
2137 3267 6.785191 ACAGTTTAACTCTGATGTTGTGTTG 58.215 36.000 12.10 0.00 36.81 3.33
2138 3268 6.238103 CGACAGTTTAACTCTGATGTTGTGTT 60.238 38.462 12.10 0.00 36.81 3.32
2145 3276 6.476706 TGCATATCGACAGTTTAACTCTGATG 59.523 38.462 12.10 7.19 36.81 3.07
2158 3289 4.345288 CACCAATGTTTGCATATCGACAG 58.655 43.478 0.00 0.00 34.39 3.51
2162 3293 3.148026 TGCACCAATGTTTGCATATCG 57.852 42.857 3.02 0.00 43.79 2.92
2168 3299 2.222007 TGAACTGCACCAATGTTTGC 57.778 45.000 0.00 0.00 39.33 3.68
2251 3384 4.265073 ACTAGCTAGGCAGGTTGAATTTG 58.735 43.478 24.35 0.00 33.61 2.32
2259 3392 2.761208 CAACAGTACTAGCTAGGCAGGT 59.239 50.000 24.35 13.82 36.25 4.00
2260 3393 2.101582 CCAACAGTACTAGCTAGGCAGG 59.898 54.545 24.35 13.22 0.00 4.85
2261 3394 3.024547 TCCAACAGTACTAGCTAGGCAG 58.975 50.000 24.35 15.08 0.00 4.85
2264 3397 5.662674 ACTTTCCAACAGTACTAGCTAGG 57.337 43.478 24.35 9.25 0.00 3.02
2282 3421 5.243981 CAGATGGATCACTGTCTGAACTTT 58.756 41.667 9.11 0.00 40.30 2.66
2477 3626 2.107204 AGGTGTTGTCCTTCTTGAGCAT 59.893 45.455 0.00 0.00 33.52 3.79
2563 3712 1.078426 GTGCATACCGTCCTTGGCT 60.078 57.895 0.00 0.00 0.00 4.75
2587 3736 2.686915 CCCAAGAGCAAGATGAATGGAC 59.313 50.000 0.00 0.00 0.00 4.02
2589 3738 3.008835 TCCCAAGAGCAAGATGAATGG 57.991 47.619 0.00 0.00 0.00 3.16
2592 3741 2.376518 AGGTTCCCAAGAGCAAGATGAA 59.623 45.455 0.00 0.00 0.00 2.57
2608 3784 6.709397 TCATCATCTCATCATTAGCAAGGTTC 59.291 38.462 0.00 0.00 0.00 3.62
2611 3787 7.506328 TTTCATCATCTCATCATTAGCAAGG 57.494 36.000 0.00 0.00 0.00 3.61
2615 3791 7.808381 CCAACATTTCATCATCTCATCATTAGC 59.192 37.037 0.00 0.00 0.00 3.09
2618 3794 7.655521 ACCAACATTTCATCATCTCATCATT 57.344 32.000 0.00 0.00 0.00 2.57
2629 3805 5.040635 ACAACAACGAACCAACATTTCATC 58.959 37.500 0.00 0.00 0.00 2.92
2640 3819 0.248866 CCTGCCAACAACAACGAACC 60.249 55.000 0.00 0.00 0.00 3.62
2644 3823 0.673437 AATCCCTGCCAACAACAACG 59.327 50.000 0.00 0.00 0.00 4.10
2656 3835 3.641434 AGTCAATCCAGTCAATCCCTG 57.359 47.619 0.00 0.00 0.00 4.45
2663 3842 4.040339 TGCTTCTTGTAGTCAATCCAGTCA 59.960 41.667 0.00 0.00 32.82 3.41
2732 3911 2.296792 CCATGGTAATGGCACGATGAA 58.703 47.619 2.57 0.00 46.89 2.57
2781 3981 6.066690 AGTAAAAAGGAAAACTAGGTGGGAC 58.933 40.000 0.00 0.00 0.00 4.46
2797 3997 4.803613 GCACAACCAAACTGGAGTAAAAAG 59.196 41.667 0.00 0.00 40.96 2.27
2856 4057 1.211969 GCCACTCAGTCGTCGCTAA 59.788 57.895 0.00 0.00 0.00 3.09
2879 4080 6.365789 ACAATTGGTTTAACATTTGATGCTCG 59.634 34.615 10.83 0.00 36.04 5.03
2902 4103 1.487976 GATCCATCAGAGGAGCCAACA 59.512 52.381 0.00 0.00 41.90 3.33
2916 4117 8.975295 TCTCAATATCTACATTGATCGATCCAT 58.025 33.333 22.31 14.32 42.49 3.41
2918 4119 8.246871 TGTCTCAATATCTACATTGATCGATCC 58.753 37.037 22.31 5.50 42.49 3.36
2921 4122 7.940850 TGTGTCTCAATATCTACATTGATCGA 58.059 34.615 0.00 0.00 42.49 3.59
2941 4142 0.741221 GAGCTCGGGACCAATGTGTC 60.741 60.000 0.00 0.00 34.42 3.67
3164 4373 4.142381 GCCCACAAATCAATCTACAACTCC 60.142 45.833 0.00 0.00 0.00 3.85
3191 4400 0.253044 TTGCACTATGAGCCCCACTC 59.747 55.000 0.00 0.00 46.45 3.51
3193 4402 1.406539 CAATTGCACTATGAGCCCCAC 59.593 52.381 0.00 0.00 0.00 4.61
3222 4431 2.272471 GGGCTTGTAGTGGGCCTC 59.728 66.667 4.53 0.00 44.70 4.70
3259 4468 2.226912 CCTTGCGGTTTTATTTGTCGGA 59.773 45.455 0.00 0.00 0.00 4.55
3382 4594 2.139118 GCGATTCTCTCAATAGTGGCC 58.861 52.381 0.00 0.00 0.00 5.36
3462 4674 7.604549 TCGTATTGATCACAAACCAACTACTA 58.395 34.615 0.00 0.00 39.54 1.82
3463 4675 6.460781 TCGTATTGATCACAAACCAACTACT 58.539 36.000 0.00 0.00 39.54 2.57
3567 4779 1.896122 CTCCCGGTCACCACCCTAAC 61.896 65.000 0.00 0.00 40.01 2.34
3568 4780 1.611261 CTCCCGGTCACCACCCTAA 60.611 63.158 0.00 0.00 40.01 2.69
3569 4781 2.038329 CTCCCGGTCACCACCCTA 59.962 66.667 0.00 0.00 40.01 3.53
3570 4782 4.250170 ACTCCCGGTCACCACCCT 62.250 66.667 0.00 0.00 40.01 4.34
3571 4783 3.703127 GACTCCCGGTCACCACCC 61.703 72.222 0.00 0.00 43.94 4.61
3572 4784 3.703127 GGACTCCCGGTCACCACC 61.703 72.222 0.00 0.00 46.16 4.61
3592 4804 4.555709 TGTGTGTGGGCGGGTGTC 62.556 66.667 0.00 0.00 0.00 3.67
3593 4805 4.868116 GTGTGTGTGGGCGGGTGT 62.868 66.667 0.00 0.00 0.00 4.16
3594 4806 4.866224 TGTGTGTGTGGGCGGGTG 62.866 66.667 0.00 0.00 0.00 4.61
3595 4807 4.116585 TTGTGTGTGTGGGCGGGT 62.117 61.111 0.00 0.00 0.00 5.28
3596 4808 3.286751 CTTGTGTGTGTGGGCGGG 61.287 66.667 0.00 0.00 0.00 6.13
3597 4809 1.380403 TTTCTTGTGTGTGTGGGCGG 61.380 55.000 0.00 0.00 0.00 6.13
3598 4810 0.453793 TTTTCTTGTGTGTGTGGGCG 59.546 50.000 0.00 0.00 0.00 6.13
3599 4811 2.663826 TTTTTCTTGTGTGTGTGGGC 57.336 45.000 0.00 0.00 0.00 5.36
3615 4827 7.675619 AGATTCTGGATACCAAATGGACTTTTT 59.324 33.333 6.42 0.00 38.94 1.94
3616 4828 7.184862 AGATTCTGGATACCAAATGGACTTTT 58.815 34.615 6.42 0.00 38.94 2.27
3617 4829 6.735556 AGATTCTGGATACCAAATGGACTTT 58.264 36.000 6.42 0.00 38.94 2.66
3618 4830 6.332976 AGATTCTGGATACCAAATGGACTT 57.667 37.500 6.42 0.00 38.94 3.01
3619 4831 5.983333 AGATTCTGGATACCAAATGGACT 57.017 39.130 6.42 0.00 38.94 3.85
3620 4832 6.122277 TCAAGATTCTGGATACCAAATGGAC 58.878 40.000 6.42 0.00 38.94 4.02
3621 4833 6.325993 TCAAGATTCTGGATACCAAATGGA 57.674 37.500 6.42 0.00 38.94 3.41
3622 4834 8.696043 TTATCAAGATTCTGGATACCAAATGG 57.304 34.615 9.86 0.00 42.17 3.16
3625 4837 8.966868 GGTTTTATCAAGATTCTGGATACCAAA 58.033 33.333 9.86 6.95 27.27 3.28
3626 4838 8.336235 AGGTTTTATCAAGATTCTGGATACCAA 58.664 33.333 17.98 9.56 27.75 3.67
3627 4839 7.872138 AGGTTTTATCAAGATTCTGGATACCA 58.128 34.615 17.98 5.20 27.75 3.25
3628 4840 7.993183 TGAGGTTTTATCAAGATTCTGGATACC 59.007 37.037 9.86 10.72 27.27 2.73
3629 4841 8.831550 GTGAGGTTTTATCAAGATTCTGGATAC 58.168 37.037 9.86 2.79 27.27 2.24
3630 4842 7.993183 GGTGAGGTTTTATCAAGATTCTGGATA 59.007 37.037 6.67 6.67 0.00 2.59
3631 4843 6.830838 GGTGAGGTTTTATCAAGATTCTGGAT 59.169 38.462 8.60 8.60 0.00 3.41
3632 4844 6.012508 AGGTGAGGTTTTATCAAGATTCTGGA 60.013 38.462 0.00 0.00 0.00 3.86
3633 4845 6.183347 AGGTGAGGTTTTATCAAGATTCTGG 58.817 40.000 0.00 0.00 0.00 3.86
3634 4846 6.881065 TGAGGTGAGGTTTTATCAAGATTCTG 59.119 38.462 0.00 0.00 0.00 3.02
3635 4847 7.020827 TGAGGTGAGGTTTTATCAAGATTCT 57.979 36.000 0.00 0.00 0.00 2.40
3636 4848 7.337942 ACATGAGGTGAGGTTTTATCAAGATTC 59.662 37.037 0.00 0.00 0.00 2.52
3637 4849 7.177878 ACATGAGGTGAGGTTTTATCAAGATT 58.822 34.615 0.00 0.00 0.00 2.40
3638 4850 6.725364 ACATGAGGTGAGGTTTTATCAAGAT 58.275 36.000 0.00 0.00 0.00 2.40
3639 4851 6.126863 ACATGAGGTGAGGTTTTATCAAGA 57.873 37.500 0.00 0.00 0.00 3.02
3654 4866 1.478510 GACCGAGTGATCACATGAGGT 59.521 52.381 27.02 25.56 33.78 3.85
3655 4867 1.753649 AGACCGAGTGATCACATGAGG 59.246 52.381 27.02 22.96 0.00 3.86
3656 4868 2.807044 CAGACCGAGTGATCACATGAG 58.193 52.381 27.02 14.68 0.00 2.90
3657 4869 1.134995 GCAGACCGAGTGATCACATGA 60.135 52.381 27.02 0.00 0.00 3.07
3658 4870 1.134877 AGCAGACCGAGTGATCACATG 60.135 52.381 27.02 17.77 0.00 3.21
3659 4871 1.134877 CAGCAGACCGAGTGATCACAT 60.135 52.381 27.02 12.53 0.00 3.21
3660 4872 0.244721 CAGCAGACCGAGTGATCACA 59.755 55.000 27.02 0.00 0.00 3.58
3661 4873 1.080995 GCAGCAGACCGAGTGATCAC 61.081 60.000 18.47 18.47 0.00 3.06
3662 4874 1.216444 GCAGCAGACCGAGTGATCA 59.784 57.895 0.00 0.00 0.00 2.92
3663 4875 0.805322 CAGCAGCAGACCGAGTGATC 60.805 60.000 0.00 0.00 0.00 2.92
3664 4876 1.217511 CAGCAGCAGACCGAGTGAT 59.782 57.895 0.00 0.00 0.00 3.06
3665 4877 2.653115 CAGCAGCAGACCGAGTGA 59.347 61.111 0.00 0.00 0.00 3.41
3666 4878 3.117171 GCAGCAGCAGACCGAGTG 61.117 66.667 0.00 0.00 41.58 3.51
3667 4879 4.385405 GGCAGCAGCAGACCGAGT 62.385 66.667 2.65 0.00 44.61 4.18
3689 4901 1.503542 GGCTGCTATGTGTGTGCAC 59.496 57.895 10.75 10.75 45.44 4.57
3690 4902 1.675310 GGGCTGCTATGTGTGTGCA 60.675 57.895 0.00 0.00 35.30 4.57
3691 4903 0.107703 TAGGGCTGCTATGTGTGTGC 60.108 55.000 0.00 0.00 0.00 4.57
3692 4904 2.487934 GATAGGGCTGCTATGTGTGTG 58.512 52.381 0.00 0.00 0.00 3.82
3693 4905 1.417890 GGATAGGGCTGCTATGTGTGT 59.582 52.381 0.00 0.00 0.00 3.72
3694 4906 1.271054 GGGATAGGGCTGCTATGTGTG 60.271 57.143 0.00 0.00 0.00 3.82
3695 4907 1.059913 GGGATAGGGCTGCTATGTGT 58.940 55.000 0.00 0.00 0.00 3.72
3696 4908 1.356124 AGGGATAGGGCTGCTATGTG 58.644 55.000 0.00 0.00 0.00 3.21
3697 4909 2.541466 GTAGGGATAGGGCTGCTATGT 58.459 52.381 0.00 0.00 0.00 2.29
3698 4910 1.834263 GGTAGGGATAGGGCTGCTATG 59.166 57.143 0.00 0.00 0.00 2.23
3699 4911 1.437149 TGGTAGGGATAGGGCTGCTAT 59.563 52.381 0.00 0.00 0.00 2.97
3700 4912 0.864659 TGGTAGGGATAGGGCTGCTA 59.135 55.000 0.00 0.00 0.00 3.49
3701 4913 0.764752 GTGGTAGGGATAGGGCTGCT 60.765 60.000 0.00 0.00 0.00 4.24
3702 4914 1.755384 GTGGTAGGGATAGGGCTGC 59.245 63.158 0.00 0.00 0.00 5.25
3703 4915 0.399949 TGGTGGTAGGGATAGGGCTG 60.400 60.000 0.00 0.00 0.00 4.85
3704 4916 0.400093 GTGGTGGTAGGGATAGGGCT 60.400 60.000 0.00 0.00 0.00 5.19
3705 4917 1.416480 GGTGGTGGTAGGGATAGGGC 61.416 65.000 0.00 0.00 0.00 5.19
3706 4918 0.030501 TGGTGGTGGTAGGGATAGGG 60.031 60.000 0.00 0.00 0.00 3.53
3707 4919 2.118403 ATGGTGGTGGTAGGGATAGG 57.882 55.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.