Multiple sequence alignment - TraesCS5D01G165100

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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 TraesCS5D01G165100 chr5D 100.000 3422 0 0 1 3422 256722465 256725886 0.000000e+00 6320.0
1 TraesCS5D01G165100 chr5D 80.694 663 105 12 13 672 429052286 429051644 8.530000e-136 494.0
2 TraesCS5D01G165100 chr5D 94.286 35 2 0 2932 2966 111300730 111300696 2.000000e-03 54.7
3 TraesCS5D01G165100 chr5A 92.833 1744 64 25 779 2471 341503924 341505657 0.000000e+00 2471.0
4 TraesCS5D01G165100 chr5A 85.558 547 52 6 2800 3324 341552935 341553476 6.460000e-152 547.0
5 TraesCS5D01G165100 chr5A 88.542 96 9 2 673 767 526875315 526875409 7.760000e-22 115.0
6 TraesCS5D01G165100 chr5A 94.737 38 2 0 2926 2963 115703435 115703472 3.690000e-05 60.2
7 TraesCS5D01G165100 chr5B 89.092 2026 143 33 1116 3107 290810988 290812969 0.000000e+00 2446.0
8 TraesCS5D01G165100 chr5B 92.974 427 21 4 795 1214 290810577 290811001 6.280000e-172 614.0
9 TraesCS5D01G165100 chr5B 80.032 626 112 7 50 672 599843610 599842995 5.210000e-123 451.0
10 TraesCS5D01G165100 chr5B 78.241 671 120 19 13 675 571706070 571705418 1.140000e-109 407.0
11 TraesCS5D01G165100 chr7B 84.347 658 84 11 27 673 366042619 366043268 8.060000e-176 627.0
12 TraesCS5D01G165100 chr7B 79.160 667 112 16 13 673 382270206 382269561 1.460000e-118 436.0
13 TraesCS5D01G165100 chr7B 78.218 101 13 3 2869 2969 503264781 503264690 4.770000e-04 56.5
14 TraesCS5D01G165100 chr7A 83.788 660 77 12 21 673 409256107 409256743 1.760000e-167 599.0
15 TraesCS5D01G165100 chr4B 82.477 662 84 16 14 673 368415160 368415791 4.990000e-153 551.0
16 TraesCS5D01G165100 chr4B 79.897 582 100 13 13 587 27269169 27269740 8.840000e-111 411.0
17 TraesCS5D01G165100 chr7D 82.308 650 99 12 27 673 386923048 386922412 1.800000e-152 549.0
18 TraesCS5D01G165100 chr7D 80.139 433 71 11 21 448 503088697 503088275 3.320000e-80 309.0
19 TraesCS5D01G165100 chr1D 80.240 668 106 11 13 673 472399584 472398936 2.390000e-131 479.0
20 TraesCS5D01G165100 chr1D 77.114 402 75 14 2649 3038 295444402 295444006 2.070000e-52 217.0
21 TraesCS5D01G165100 chr1D 82.474 194 30 3 2856 3049 314769253 314769064 2.110000e-37 167.0
22 TraesCS5D01G165100 chr2D 79.619 525 85 14 22 541 10245104 10244597 1.170000e-94 357.0
23 TraesCS5D01G165100 chr1B 78.600 500 93 13 180 673 22726838 22726347 5.510000e-83 318.0
24 TraesCS5D01G165100 chr1B 90.909 88 7 1 671 757 426466167 426466254 2.160000e-22 117.0
25 TraesCS5D01G165100 chr1B 88.000 100 8 3 659 757 169531048 169531144 7.760000e-22 115.0
26 TraesCS5D01G165100 chr6D 75.462 379 75 11 2649 3014 16254846 16254473 5.870000e-38 169.0
27 TraesCS5D01G165100 chr6D 78.095 105 23 0 2856 2960 325751588 325751692 2.200000e-07 67.6
28 TraesCS5D01G165100 chr3D 74.413 426 87 12 2649 3059 303589699 303590117 2.730000e-36 163.0
29 TraesCS5D01G165100 chr3A 81.463 205 33 4 2837 3040 430780183 430779983 2.730000e-36 163.0
30 TraesCS5D01G165100 chr3A 90.909 88 6 2 671 757 692055355 692055441 2.160000e-22 117.0
31 TraesCS5D01G165100 chr2A 88.571 105 10 2 666 769 15399538 15399641 3.590000e-25 126.0
32 TraesCS5D01G165100 chr3B 88.542 96 9 2 664 757 784688021 784688116 7.760000e-22 115.0
33 TraesCS5D01G165100 chr4A 86.538 104 10 4 660 761 605425407 605425306 1.000000e-20 111.0
34 TraesCS5D01G165100 chr6A 89.655 87 8 1 673 758 190660435 190660349 3.610000e-20 110.0
35 TraesCS5D01G165100 chr6A 89.655 87 8 1 673 758 190738358 190738272 3.610000e-20 110.0
36 TraesCS5D01G165100 chr4D 87.692 65 4 3 3288 3350 373852643 373852705 4.740000e-09 73.1


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 TraesCS5D01G165100 chr5D 256722465 256725886 3421 False 6320 6320 100.000 1 3422 1 chr5D.!!$F1 3421
1 TraesCS5D01G165100 chr5D 429051644 429052286 642 True 494 494 80.694 13 672 1 chr5D.!!$R2 659
2 TraesCS5D01G165100 chr5A 341503924 341505657 1733 False 2471 2471 92.833 779 2471 1 chr5A.!!$F2 1692
3 TraesCS5D01G165100 chr5A 341552935 341553476 541 False 547 547 85.558 2800 3324 1 chr5A.!!$F3 524
4 TraesCS5D01G165100 chr5B 290810577 290812969 2392 False 1530 2446 91.033 795 3107 2 chr5B.!!$F1 2312
5 TraesCS5D01G165100 chr5B 599842995 599843610 615 True 451 451 80.032 50 672 1 chr5B.!!$R2 622
6 TraesCS5D01G165100 chr5B 571705418 571706070 652 True 407 407 78.241 13 675 1 chr5B.!!$R1 662
7 TraesCS5D01G165100 chr7B 366042619 366043268 649 False 627 627 84.347 27 673 1 chr7B.!!$F1 646
8 TraesCS5D01G165100 chr7B 382269561 382270206 645 True 436 436 79.160 13 673 1 chr7B.!!$R1 660
9 TraesCS5D01G165100 chr7A 409256107 409256743 636 False 599 599 83.788 21 673 1 chr7A.!!$F1 652
10 TraesCS5D01G165100 chr4B 368415160 368415791 631 False 551 551 82.477 14 673 1 chr4B.!!$F2 659
11 TraesCS5D01G165100 chr4B 27269169 27269740 571 False 411 411 79.897 13 587 1 chr4B.!!$F1 574
12 TraesCS5D01G165100 chr7D 386922412 386923048 636 True 549 549 82.308 27 673 1 chr7D.!!$R1 646
13 TraesCS5D01G165100 chr1D 472398936 472399584 648 True 479 479 80.240 13 673 1 chr1D.!!$R3 660
14 TraesCS5D01G165100 chr2D 10244597 10245104 507 True 357 357 79.619 22 541 1 chr2D.!!$R1 519

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
263 280 0.452184 CGGCGTGACATCTACAGACT 59.548 55.0 0.0 0.0 0.00 3.24 F
1726 1879 0.107459 CAGACCCTGCTAAGAAGGCC 60.107 60.0 0.0 0.0 33.07 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 1910 0.037326 TGGATCAATATCGCCTCCGC 60.037 55.0 0.00 0.0 32.44 5.54 R
2809 3039 0.031721 GGTGAGACCGTCGTTGTCTT 59.968 55.0 5.75 0.0 42.94 3.01 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 114 4.582240 CCCAGATTTAGGCTTTTCAGATCC 59.418 45.833 0.00 0.00 0.00 3.36
107 115 5.195940 CCAGATTTAGGCTTTTCAGATCCA 58.804 41.667 0.00 0.00 0.00 3.41
175 186 1.669440 GTTGTACACCGGCTGGAGA 59.331 57.895 21.41 0.00 39.21 3.71
251 268 4.680237 CAAGGTGGAGCGGCGTGA 62.680 66.667 9.37 0.00 0.00 4.35
261 278 1.138883 GCGGCGTGACATCTACAGA 59.861 57.895 9.37 0.00 0.00 3.41
262 279 1.140407 GCGGCGTGACATCTACAGAC 61.140 60.000 9.37 0.00 0.00 3.51
263 280 0.452184 CGGCGTGACATCTACAGACT 59.548 55.000 0.00 0.00 0.00 3.24
264 281 1.669265 CGGCGTGACATCTACAGACTA 59.331 52.381 0.00 0.00 0.00 2.59
265 282 2.539142 CGGCGTGACATCTACAGACTAC 60.539 54.545 0.00 0.00 0.00 2.73
266 283 2.422479 GGCGTGACATCTACAGACTACA 59.578 50.000 0.00 0.00 0.00 2.74
267 284 3.487711 GGCGTGACATCTACAGACTACAG 60.488 52.174 0.00 0.00 0.00 2.74
322 343 4.899239 GGGTCTCGGCGCTGGATG 62.899 72.222 17.88 7.41 0.00 3.51
391 432 1.290955 CGTTGACGGCAGAAGGGTA 59.709 57.895 0.00 0.00 35.37 3.69
450 494 4.696402 AGACTACGAAAGAAGACGATGACT 59.304 41.667 0.00 0.00 0.00 3.41
453 497 3.566523 ACGAAAGAAGACGATGACTGAC 58.433 45.455 0.00 0.00 0.00 3.51
486 530 4.657408 TGCGCTGCATGTTGGGGA 62.657 61.111 9.73 0.00 31.71 4.81
498 544 1.204146 GTTGGGGATCTGCTAGACCA 58.796 55.000 0.00 0.00 0.00 4.02
513 559 3.953775 CCAGTTGGTGCTCCCGGT 61.954 66.667 0.00 0.00 35.15 5.28
595 642 6.047231 CAGAGCACATCATCAATCTTGTAGA 58.953 40.000 0.00 0.00 0.00 2.59
600 647 7.015974 AGCACATCATCAATCTTGTAGATAGGA 59.984 37.037 0.00 0.00 32.89 2.94
673 727 8.659925 TTTTGCATGACTTTGTTGAATAATGT 57.340 26.923 0.00 0.00 0.00 2.71
674 728 9.755804 TTTTGCATGACTTTGTTGAATAATGTA 57.244 25.926 0.00 0.00 0.00 2.29
675 729 8.741101 TTGCATGACTTTGTTGAATAATGTAC 57.259 30.769 0.00 0.00 0.00 2.90
676 730 8.109705 TGCATGACTTTGTTGAATAATGTACT 57.890 30.769 0.00 0.00 0.00 2.73
677 731 8.236586 TGCATGACTTTGTTGAATAATGTACTC 58.763 33.333 0.00 0.00 0.00 2.59
678 732 7.698130 GCATGACTTTGTTGAATAATGTACTCC 59.302 37.037 0.00 0.00 0.00 3.85
679 733 7.681939 TGACTTTGTTGAATAATGTACTCCC 57.318 36.000 0.00 0.00 0.00 4.30
680 734 7.458397 TGACTTTGTTGAATAATGTACTCCCT 58.542 34.615 0.00 0.00 0.00 4.20
681 735 7.942341 TGACTTTGTTGAATAATGTACTCCCTT 59.058 33.333 0.00 0.00 0.00 3.95
682 736 8.706322 ACTTTGTTGAATAATGTACTCCCTTT 57.294 30.769 0.00 0.00 0.00 3.11
683 737 8.576442 ACTTTGTTGAATAATGTACTCCCTTTG 58.424 33.333 0.00 0.00 0.00 2.77
684 738 8.472007 TTTGTTGAATAATGTACTCCCTTTGT 57.528 30.769 0.00 0.00 0.00 2.83
685 739 9.575868 TTTGTTGAATAATGTACTCCCTTTGTA 57.424 29.630 0.00 0.00 0.00 2.41
686 740 9.575868 TTGTTGAATAATGTACTCCCTTTGTAA 57.424 29.630 0.00 0.00 0.00 2.41
687 741 9.575868 TGTTGAATAATGTACTCCCTTTGTAAA 57.424 29.630 0.00 0.00 0.00 2.01
700 754 8.957466 ACTCCCTTTGTAAAGAAATATAAGTGC 58.043 33.333 5.95 0.00 38.28 4.40
701 755 7.981142 TCCCTTTGTAAAGAAATATAAGTGCG 58.019 34.615 5.95 0.00 38.28 5.34
702 756 7.066525 TCCCTTTGTAAAGAAATATAAGTGCGG 59.933 37.037 5.95 0.00 38.28 5.69
703 757 7.148137 CCCTTTGTAAAGAAATATAAGTGCGGT 60.148 37.037 5.95 0.00 38.28 5.68
704 758 8.885722 CCTTTGTAAAGAAATATAAGTGCGGTA 58.114 33.333 5.95 0.00 38.28 4.02
705 759 9.916397 CTTTGTAAAGAAATATAAGTGCGGTAG 57.084 33.333 0.00 0.00 38.28 3.18
706 760 9.656040 TTTGTAAAGAAATATAAGTGCGGTAGA 57.344 29.630 0.00 0.00 0.00 2.59
707 761 9.826574 TTGTAAAGAAATATAAGTGCGGTAGAT 57.173 29.630 0.00 0.00 0.00 1.98
708 762 9.472361 TGTAAAGAAATATAAGTGCGGTAGATC 57.528 33.333 0.00 0.00 0.00 2.75
709 763 9.472361 GTAAAGAAATATAAGTGCGGTAGATCA 57.528 33.333 0.00 0.00 0.00 2.92
710 764 7.948278 AAGAAATATAAGTGCGGTAGATCAC 57.052 36.000 0.00 0.00 0.00 3.06
711 765 7.291411 AGAAATATAAGTGCGGTAGATCACT 57.709 36.000 0.00 0.00 44.64 3.41
712 766 8.405418 AGAAATATAAGTGCGGTAGATCACTA 57.595 34.615 0.00 0.00 42.19 2.74
713 767 8.516234 AGAAATATAAGTGCGGTAGATCACTAG 58.484 37.037 0.00 0.00 42.19 2.57
714 768 7.762588 AATATAAGTGCGGTAGATCACTAGT 57.237 36.000 0.00 0.00 42.19 2.57
715 769 7.762588 ATATAAGTGCGGTAGATCACTAGTT 57.237 36.000 0.00 0.00 42.19 2.24
716 770 4.803098 AAGTGCGGTAGATCACTAGTTT 57.197 40.909 0.00 0.00 42.19 2.66
717 771 5.909621 AAGTGCGGTAGATCACTAGTTTA 57.090 39.130 0.00 0.00 42.19 2.01
718 772 5.502153 AGTGCGGTAGATCACTAGTTTAG 57.498 43.478 0.00 0.00 41.32 1.85
719 773 4.948621 AGTGCGGTAGATCACTAGTTTAGT 59.051 41.667 0.00 0.00 41.32 2.24
743 797 9.601217 AGTGATCTAAACGCTCTTATATTTGTT 57.399 29.630 0.00 0.00 0.00 2.83
771 825 6.451393 AGAGGAAGTAATAAAGATGCTAGCG 58.549 40.000 10.77 0.00 0.00 4.26
772 826 5.542779 AGGAAGTAATAAAGATGCTAGCGG 58.457 41.667 10.77 0.00 0.00 5.52
773 827 5.304614 AGGAAGTAATAAAGATGCTAGCGGA 59.695 40.000 10.77 0.00 0.00 5.54
774 828 5.635700 GGAAGTAATAAAGATGCTAGCGGAG 59.364 44.000 10.77 0.00 0.00 4.63
775 829 5.793030 AGTAATAAAGATGCTAGCGGAGT 57.207 39.130 10.77 0.00 0.00 3.85
776 830 6.896021 AGTAATAAAGATGCTAGCGGAGTA 57.104 37.500 10.77 0.00 0.00 2.59
777 831 7.286215 AGTAATAAAGATGCTAGCGGAGTAA 57.714 36.000 10.77 0.00 0.00 2.24
833 888 5.454897 GGAGGTCCCCAGAATAAATGTAGTC 60.455 48.000 0.00 0.00 0.00 2.59
1158 1308 3.160748 GGAGCTGGAGGAGGAGGC 61.161 72.222 0.00 0.00 0.00 4.70
1174 1324 2.490685 GCGGAGAAGGACGAGGAC 59.509 66.667 0.00 0.00 0.00 3.85
1537 1687 4.461119 CAGGAGGTGCTGACCCTA 57.539 61.111 0.00 0.00 44.40 3.53
1575 1725 2.410687 CGCTGGAGCTCCTCGAGAA 61.411 63.158 32.28 11.16 38.34 2.87
1705 1858 1.299926 CTGTACCATCGCTACCGCC 60.300 63.158 0.00 0.00 0.00 6.13
1726 1879 0.107459 CAGACCCTGCTAAGAAGGCC 60.107 60.000 0.00 0.00 33.07 5.19
1754 1910 0.312416 GGAGACGGATGATCAGGACG 59.688 60.000 12.96 12.96 0.00 4.79
1755 1911 0.318275 GAGACGGATGATCAGGACGC 60.318 60.000 14.07 8.68 0.00 5.19
1761 1917 3.157217 ATGATCAGGACGCGGAGGC 62.157 63.158 12.47 0.00 0.00 4.70
1773 1929 0.037326 GCGGAGGCGATATTGATCCA 60.037 55.000 12.70 0.00 0.00 3.41
1870 2038 2.280457 GAGGAGGCGCATGTAGGC 60.280 66.667 10.83 8.42 0.00 3.93
1882 2050 1.043816 ATGTAGGCGATCAGAGTGGG 58.956 55.000 0.00 0.00 0.00 4.61
1886 2054 2.725312 GGCGATCAGAGTGGGCAGA 61.725 63.158 0.00 0.00 0.00 4.26
1981 2200 2.131023 GAAGGGGATGTCAGGAGGATT 58.869 52.381 0.00 0.00 0.00 3.01
2274 2493 0.108662 CACGATCAGTAGCAGGCACA 60.109 55.000 0.00 0.00 0.00 4.57
2365 2593 6.068010 ACTCCCAAAATGTATGTTTGACTCA 58.932 36.000 0.00 0.00 38.05 3.41
2400 2629 6.581388 AAGGAGATCCATTGTAATCCAAGA 57.419 37.500 0.92 0.00 36.25 3.02
2406 2635 8.383318 AGATCCATTGTAATCCAAGAAATACG 57.617 34.615 0.00 0.00 36.25 3.06
2484 2713 2.415168 ACGCGTTTGGTTGACATATCTG 59.585 45.455 5.58 0.00 0.00 2.90
2491 2720 7.060633 GCGTTTGGTTGACATATCTGTTTTTAG 59.939 37.037 0.00 0.00 35.14 1.85
2499 2728 8.984891 TGACATATCTGTTTTTAGGCATTTTG 57.015 30.769 0.00 0.00 35.14 2.44
2518 2747 7.221452 GCATTTTGCCTTGAAGTATACATCAAG 59.779 37.037 30.64 30.64 45.82 3.02
2523 2752 8.177119 TGCCTTGAAGTATACATCAAGTTTTT 57.823 30.769 32.78 8.52 45.19 1.94
2528 2757 9.567776 TTGAAGTATACATCAAGTTTTTGGAGA 57.432 29.630 17.28 0.00 34.97 3.71
2536 2765 7.830739 ACATCAAGTTTTTGGAGAATACCATC 58.169 34.615 0.00 0.00 39.82 3.51
2543 2772 8.383175 AGTTTTTGGAGAATACCATCTTGAGTA 58.617 33.333 0.00 0.00 39.82 2.59
2546 2775 4.954202 TGGAGAATACCATCTTGAGTACGT 59.046 41.667 0.00 0.00 34.77 3.57
2548 2777 5.067413 GGAGAATACCATCTTGAGTACGTCA 59.933 44.000 0.00 0.00 0.00 4.35
2549 2778 6.405508 GGAGAATACCATCTTGAGTACGTCAA 60.406 42.308 0.00 7.31 43.26 3.18
2556 2785 2.806608 TTGAGTACGTCAAGGACCAC 57.193 50.000 0.00 0.00 40.45 4.16
2557 2786 1.694844 TGAGTACGTCAAGGACCACA 58.305 50.000 0.00 0.00 32.79 4.17
2558 2787 2.033372 TGAGTACGTCAAGGACCACAA 58.967 47.619 0.00 0.00 32.79 3.33
2559 2788 2.223876 TGAGTACGTCAAGGACCACAAC 60.224 50.000 0.00 0.00 32.79 3.32
2584 2813 1.459592 GTGTCCATTCTTCGGTTGTCG 59.540 52.381 0.00 0.00 40.90 4.35
2588 2817 0.796312 CATTCTTCGGTTGTCGGTGG 59.204 55.000 0.00 0.00 39.77 4.61
2593 2822 0.178533 TTCGGTTGTCGGTGGTTCTT 59.821 50.000 0.00 0.00 39.77 2.52
2594 2823 0.531090 TCGGTTGTCGGTGGTTCTTG 60.531 55.000 0.00 0.00 39.77 3.02
2595 2824 0.531090 CGGTTGTCGGTGGTTCTTGA 60.531 55.000 0.00 0.00 34.75 3.02
2596 2825 1.876416 CGGTTGTCGGTGGTTCTTGAT 60.876 52.381 0.00 0.00 34.75 2.57
2597 2826 1.804748 GGTTGTCGGTGGTTCTTGATC 59.195 52.381 0.00 0.00 0.00 2.92
2598 2827 1.459592 GTTGTCGGTGGTTCTTGATCG 59.540 52.381 0.00 0.00 0.00 3.69
2599 2828 0.037697 TGTCGGTGGTTCTTGATCGG 60.038 55.000 0.00 0.00 0.00 4.18
2612 2841 3.327464 TCTTGATCGGCCCATGAATGATA 59.673 43.478 0.00 0.00 0.00 2.15
2614 2843 2.905736 TGATCGGCCCATGAATGATAGA 59.094 45.455 0.00 0.00 0.00 1.98
2622 2851 3.922850 CCCATGAATGATAGATCGACGTG 59.077 47.826 0.00 0.00 0.00 4.49
2623 2852 3.922850 CCATGAATGATAGATCGACGTGG 59.077 47.826 0.00 0.00 31.86 4.94
2628 2857 2.640184 TGATAGATCGACGTGGTGAGT 58.360 47.619 0.00 0.00 0.00 3.41
2635 2864 2.283298 TCGACGTGGTGAGTACTATCC 58.717 52.381 0.00 1.87 0.00 2.59
2637 2866 2.617308 CGACGTGGTGAGTACTATCCAT 59.383 50.000 17.72 6.68 32.45 3.41
2641 2870 3.548214 CGTGGTGAGTACTATCCATGACG 60.548 52.174 23.07 16.68 38.73 4.35
2642 2871 3.380637 GTGGTGAGTACTATCCATGACGT 59.619 47.826 17.72 0.00 32.45 4.34
2643 2872 4.021229 TGGTGAGTACTATCCATGACGTT 58.979 43.478 12.67 0.00 0.00 3.99
2647 2876 4.703093 TGAGTACTATCCATGACGTTGTCA 59.297 41.667 1.65 1.65 46.90 3.58
2668 2897 0.945813 CGCCGACCCAAACAACTTTA 59.054 50.000 0.00 0.00 0.00 1.85
2673 2902 3.564511 CGACCCAAACAACTTTATGCAG 58.435 45.455 0.00 0.00 0.00 4.41
2688 2917 5.894298 TTATGCAGGATCATCCTTGTACT 57.106 39.130 2.26 0.00 46.91 2.73
2689 2918 3.827008 TGCAGGATCATCCTTGTACTC 57.173 47.619 2.26 0.00 46.91 2.59
2692 2921 4.125703 GCAGGATCATCCTTGTACTCAAG 58.874 47.826 2.26 0.00 46.91 3.02
2693 2922 4.383552 GCAGGATCATCCTTGTACTCAAGT 60.384 45.833 2.26 0.00 46.91 3.16
2696 2925 5.485353 AGGATCATCCTTGTACTCAAGTTGA 59.515 40.000 0.00 5.25 46.91 3.18
2705 2934 5.339008 TGTACTCAAGTTGAAGTGTCTGT 57.661 39.130 7.06 2.20 0.00 3.41
2716 2945 0.244994 AGTGTCTGTCGATGCCACTC 59.755 55.000 0.00 0.00 30.94 3.51
2727 2956 2.695359 GATGCCACTCGAGTTTACCAA 58.305 47.619 17.26 0.00 0.00 3.67
2739 2969 2.558359 AGTTTACCAAGCACTTGCCATC 59.442 45.455 4.82 0.00 43.38 3.51
2740 2970 1.164411 TTACCAAGCACTTGCCATCG 58.836 50.000 4.82 0.00 43.38 3.84
2748 2978 0.742281 CACTTGCCATCGTCCCAGAG 60.742 60.000 0.00 0.00 0.00 3.35
2752 2982 1.153349 GCCATCGTCCCAGAGGAAC 60.153 63.158 0.00 0.00 46.38 3.62
2753 2983 1.522569 CCATCGTCCCAGAGGAACC 59.477 63.158 0.00 0.00 46.38 3.62
2754 2984 1.522569 CATCGTCCCAGAGGAACCC 59.477 63.158 0.00 0.00 46.38 4.11
2758 2988 3.319198 TCCCAGAGGAACCCGTGC 61.319 66.667 0.00 0.00 40.08 5.34
2759 2989 4.410400 CCCAGAGGAACCCGTGCC 62.410 72.222 0.00 0.00 33.47 5.01
2761 2991 4.003788 CAGAGGAACCCGTGCCGT 62.004 66.667 0.00 0.00 0.00 5.68
2776 3006 1.227438 CCGTGGACAAACACCGACT 60.227 57.895 0.00 0.00 38.11 4.18
2777 3007 1.495584 CCGTGGACAAACACCGACTG 61.496 60.000 0.00 0.00 38.11 3.51
2791 3021 0.317160 CGACTGTGCTTGTAGGGTGA 59.683 55.000 0.00 0.00 0.00 4.02
2794 3024 1.488812 ACTGTGCTTGTAGGGTGACAA 59.511 47.619 0.00 0.00 36.98 3.18
2809 3039 3.689161 GGTGACAATCCGAATGATCAACA 59.311 43.478 0.00 0.00 31.61 3.33
2820 3050 4.386230 GAATGATCAACAAGACAACGACG 58.614 43.478 0.00 0.00 0.00 5.12
2822 3052 2.132762 GATCAACAAGACAACGACGGT 58.867 47.619 0.00 0.00 0.00 4.83
2831 3061 1.372997 CAACGACGGTCTCACCCTG 60.373 63.158 6.57 0.00 33.75 4.45
2836 3066 2.989824 CGGTCTCACCCTGGACGT 60.990 66.667 0.00 0.00 33.75 4.34
2846 3076 0.320421 CCCTGGACGTCATTGTTCGT 60.320 55.000 18.91 8.70 43.00 3.85
2854 3084 5.272167 GACGTCATTGTTCGTCCAATTAA 57.728 39.130 11.55 0.00 46.83 1.40
2911 3141 0.252197 ACCATCCTAAAGGTGACCGC 59.748 55.000 0.00 0.00 36.60 5.68
2921 3151 0.620556 AGGTGACCGCCTTCAATGAT 59.379 50.000 0.00 0.00 34.71 2.45
2993 3223 4.646572 CCTTGGATGCCTAGGAAGTTATC 58.353 47.826 14.75 7.33 46.83 1.75
3016 3246 7.807977 TCTCTGCATCTTTAAGACTTTTTGT 57.192 32.000 0.00 0.00 0.00 2.83
3017 3247 7.642669 TCTCTGCATCTTTAAGACTTTTTGTG 58.357 34.615 0.00 0.00 0.00 3.33
3032 3262 6.805713 ACTTTTTGTGTGGGATGTTTAAGAG 58.194 36.000 0.00 0.00 0.00 2.85
3035 3265 5.766150 TTGTGTGGGATGTTTAAGAGTTG 57.234 39.130 0.00 0.00 0.00 3.16
3041 3271 2.084546 GATGTTTAAGAGTTGGCCGCT 58.915 47.619 0.00 0.00 0.00 5.52
3063 3293 4.584327 ACTGCTTGTCATTTAACAACCC 57.416 40.909 0.00 0.00 35.39 4.11
3082 3326 3.638160 ACCCGAGTGTGTGTTAAGACTTA 59.362 43.478 4.21 0.00 0.00 2.24
3111 3355 1.328680 CTGCTATGCCTGTTTACTGCG 59.671 52.381 0.00 0.00 0.00 5.18
3119 3363 1.514678 CTGTTTACTGCGGCCAAGCA 61.515 55.000 2.24 3.96 45.96 3.91
3136 3380 5.578005 CAAGCATGGATCAGAAAAGTGAT 57.422 39.130 0.00 0.00 40.00 3.06
3141 3385 6.541641 AGCATGGATCAGAAAAGTGATTCTAC 59.458 38.462 0.00 0.00 37.56 2.59
3145 3389 7.679783 TGGATCAGAAAAGTGATTCTACTTGA 58.320 34.615 0.00 0.00 40.58 3.02
3146 3390 8.156820 TGGATCAGAAAAGTGATTCTACTTGAA 58.843 33.333 0.00 0.00 40.58 2.69
3208 3453 0.038892 GGACAAGGTGCACTGCATTG 60.039 55.000 17.98 17.46 41.91 2.82
3211 3456 0.319211 CAAGGTGCACTGCATTGTGG 60.319 55.000 17.98 0.00 41.91 4.17
3224 3469 3.270027 GCATTGTGGCCGCTATATATGA 58.730 45.455 18.96 0.00 0.00 2.15
3225 3470 3.063997 GCATTGTGGCCGCTATATATGAC 59.936 47.826 18.96 0.00 0.00 3.06
3227 3472 1.890489 TGTGGCCGCTATATATGACGT 59.110 47.619 18.96 0.00 0.00 4.34
3232 3477 3.119602 GGCCGCTATATATGACGTTCTCA 60.120 47.826 0.00 0.00 0.00 3.27
3233 3478 4.440250 GGCCGCTATATATGACGTTCTCAT 60.440 45.833 0.00 0.00 42.68 2.90
3247 3492 6.806739 TGACGTTCTCATTACAAGATACACAG 59.193 38.462 0.00 0.00 0.00 3.66
3255 3500 8.877808 TCATTACAAGATACACAGATCATGTC 57.122 34.615 5.95 0.00 41.41 3.06
3256 3501 7.649306 TCATTACAAGATACACAGATCATGTCG 59.351 37.037 5.95 1.31 41.41 4.35
3266 3518 0.921347 GATCATGTCGTACACGTGGC 59.079 55.000 21.57 11.29 41.80 5.01
3297 3549 0.553819 AACCAAGTTGTAGGTGGGCA 59.446 50.000 1.45 0.00 38.37 5.36
3328 3580 3.522731 CCTGAGGCGGACGAGGAG 61.523 72.222 0.00 0.00 0.00 3.69
3329 3581 2.752238 CTGAGGCGGACGAGGAGT 60.752 66.667 0.00 0.00 0.00 3.85
3330 3582 3.057547 CTGAGGCGGACGAGGAGTG 62.058 68.421 0.00 0.00 0.00 3.51
3331 3583 3.827898 GAGGCGGACGAGGAGTGG 61.828 72.222 0.00 0.00 0.00 4.00
3359 3611 4.766088 GTCCGTTCGACGTCCGGG 62.766 72.222 25.03 14.79 40.58 5.73
3363 3615 3.673484 GTTCGACGTCCGGGTGGA 61.673 66.667 10.58 0.00 43.88 4.02
3371 3623 4.089105 TCCGGGTGGATGCAAAAC 57.911 55.556 0.00 0.00 40.17 2.43
3372 3624 1.969064 TCCGGGTGGATGCAAAACG 60.969 57.895 0.00 0.00 40.17 3.60
3373 3625 2.566010 CGGGTGGATGCAAAACGG 59.434 61.111 0.00 0.00 0.00 4.44
3374 3626 2.969827 GGGTGGATGCAAAACGGG 59.030 61.111 0.00 0.00 0.00 5.28
3375 3627 2.261361 GGTGGATGCAAAACGGGC 59.739 61.111 0.00 0.00 0.00 6.13
3376 3628 2.126502 GTGGATGCAAAACGGGCG 60.127 61.111 0.00 0.00 0.00 6.13
3377 3629 2.596046 TGGATGCAAAACGGGCGT 60.596 55.556 0.00 0.00 0.00 5.68
3378 3630 1.302591 TGGATGCAAAACGGGCGTA 60.303 52.632 0.00 0.00 0.00 4.42
3379 3631 0.889638 TGGATGCAAAACGGGCGTAA 60.890 50.000 0.00 0.00 0.00 3.18
3380 3632 0.454196 GGATGCAAAACGGGCGTAAT 59.546 50.000 0.00 0.00 0.00 1.89
3381 3633 1.135228 GGATGCAAAACGGGCGTAATT 60.135 47.619 0.00 0.00 0.00 1.40
3382 3634 2.601804 GATGCAAAACGGGCGTAATTT 58.398 42.857 0.00 0.00 0.00 1.82
3383 3635 2.510768 TGCAAAACGGGCGTAATTTT 57.489 40.000 0.00 0.00 0.00 1.82
3384 3636 3.637998 TGCAAAACGGGCGTAATTTTA 57.362 38.095 0.00 0.00 0.00 1.52
3385 3637 3.306818 TGCAAAACGGGCGTAATTTTAC 58.693 40.909 0.00 0.00 0.00 2.01
3386 3638 3.243301 TGCAAAACGGGCGTAATTTTACA 60.243 39.130 1.76 0.00 33.28 2.41
3387 3639 3.921630 GCAAAACGGGCGTAATTTTACAT 59.078 39.130 1.76 0.00 33.28 2.29
3388 3640 4.386350 GCAAAACGGGCGTAATTTTACATT 59.614 37.500 1.76 0.00 33.28 2.71
3389 3641 5.666670 GCAAAACGGGCGTAATTTTACATTG 60.667 40.000 1.76 0.00 33.28 2.82
3390 3642 3.768468 ACGGGCGTAATTTTACATTGG 57.232 42.857 1.76 0.00 33.28 3.16
3391 3643 3.345414 ACGGGCGTAATTTTACATTGGA 58.655 40.909 1.76 0.00 33.28 3.53
3392 3644 3.757493 ACGGGCGTAATTTTACATTGGAA 59.243 39.130 1.76 0.00 33.28 3.53
3393 3645 4.217983 ACGGGCGTAATTTTACATTGGAAA 59.782 37.500 0.00 0.00 33.28 3.13
3394 3646 5.105675 ACGGGCGTAATTTTACATTGGAAAT 60.106 36.000 0.00 0.00 33.28 2.17
3395 3647 5.808030 CGGGCGTAATTTTACATTGGAAATT 59.192 36.000 13.78 13.78 38.56 1.82
3396 3648 6.973474 CGGGCGTAATTTTACATTGGAAATTA 59.027 34.615 12.42 12.42 36.92 1.40
3397 3649 7.166804 CGGGCGTAATTTTACATTGGAAATTAG 59.833 37.037 14.98 11.88 37.99 1.73
3398 3650 7.436970 GGGCGTAATTTTACATTGGAAATTAGG 59.563 37.037 21.01 21.01 41.63 2.69
3400 3652 8.918961 CGTAATTTTACATTGGAAATTAGGCA 57.081 30.769 17.42 0.00 37.99 4.75
3401 3653 9.019764 CGTAATTTTACATTGGAAATTAGGCAG 57.980 33.333 17.42 9.66 37.99 4.85
3402 3654 9.313118 GTAATTTTACATTGGAAATTAGGCAGG 57.687 33.333 14.98 0.00 37.99 4.85
3403 3655 6.926630 TTTTACATTGGAAATTAGGCAGGT 57.073 33.333 0.00 0.00 0.00 4.00
3404 3656 6.524101 TTTACATTGGAAATTAGGCAGGTC 57.476 37.500 0.00 0.00 0.00 3.85
3405 3657 3.016736 ACATTGGAAATTAGGCAGGTCG 58.983 45.455 0.00 0.00 0.00 4.79
3406 3658 2.122783 TTGGAAATTAGGCAGGTCGG 57.877 50.000 0.00 0.00 0.00 4.79
3407 3659 1.281419 TGGAAATTAGGCAGGTCGGA 58.719 50.000 0.00 0.00 0.00 4.55
3408 3660 1.065709 TGGAAATTAGGCAGGTCGGAC 60.066 52.381 0.00 0.00 0.00 4.79
3409 3661 1.287425 GAAATTAGGCAGGTCGGACG 58.713 55.000 1.43 0.00 0.00 4.79
3410 3662 0.743345 AAATTAGGCAGGTCGGACGC 60.743 55.000 1.43 0.67 0.00 5.19
3411 3663 2.901051 AATTAGGCAGGTCGGACGCG 62.901 60.000 3.53 3.53 0.00 6.01
3415 3667 2.813908 GCAGGTCGGACGCGAAAT 60.814 61.111 15.93 0.00 0.00 2.17
3416 3668 3.081133 CAGGTCGGACGCGAAATG 58.919 61.111 15.93 0.00 0.00 2.32
3417 3669 1.445410 CAGGTCGGACGCGAAATGA 60.445 57.895 15.93 1.43 0.00 2.57
3418 3670 1.011968 CAGGTCGGACGCGAAATGAA 61.012 55.000 15.93 0.00 0.00 2.57
3419 3671 1.012486 AGGTCGGACGCGAAATGAAC 61.012 55.000 15.93 7.78 0.00 3.18
3420 3672 1.286354 GGTCGGACGCGAAATGAACA 61.286 55.000 15.93 0.00 0.00 3.18
3421 3673 0.509499 GTCGGACGCGAAATGAACAA 59.491 50.000 15.93 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.404654 CGTGGGCCAAGCTTTCGC 62.405 66.667 8.40 0.69 0.00 4.70
2 3 2.668212 TCGTGGGCCAAGCTTTCG 60.668 61.111 15.12 10.12 0.00 3.46
3 4 2.982744 GCTCGTGGGCCAAGCTTTC 61.983 63.158 20.50 1.25 33.23 2.62
8 9 3.726517 CAACGCTCGTGGGCCAAG 61.727 66.667 8.40 11.48 0.00 3.61
9 10 2.661840 TAACAACGCTCGTGGGCCAA 62.662 55.000 8.40 0.00 0.00 4.52
10 11 3.166490 TAACAACGCTCGTGGGCCA 62.166 57.895 0.00 0.00 0.00 5.36
11 12 2.357760 TAACAACGCTCGTGGGCC 60.358 61.111 0.00 0.00 0.00 5.80
16 17 1.656441 ACGAGGTAACAACGCTCGT 59.344 52.632 0.00 0.00 44.40 4.18
106 114 1.202222 GCAAGAACCTCGCCATCATTG 60.202 52.381 0.00 0.00 0.00 2.82
107 115 1.098050 GCAAGAACCTCGCCATCATT 58.902 50.000 0.00 0.00 0.00 2.57
175 186 3.494223 GCCACCAAGCCAAACACTTATTT 60.494 43.478 0.00 0.00 0.00 1.40
207 218 2.604914 CGCACGAGAAGCATACAAAGAT 59.395 45.455 0.00 0.00 0.00 2.40
251 268 6.822170 TCGTCAATACTGTAGTCTGTAGATGT 59.178 38.462 0.00 0.00 32.98 3.06
261 278 4.634883 ACTCATCGTCGTCAATACTGTAGT 59.365 41.667 0.00 0.00 0.00 2.73
262 279 5.158101 ACTCATCGTCGTCAATACTGTAG 57.842 43.478 0.00 0.00 0.00 2.74
263 280 5.152923 GACTCATCGTCGTCAATACTGTA 57.847 43.478 0.00 0.00 32.04 2.74
264 281 4.017380 GACTCATCGTCGTCAATACTGT 57.983 45.455 0.00 0.00 32.04 3.55
289 309 4.020617 CCCGCTGGACCTTGCTGA 62.021 66.667 8.09 0.00 0.00 4.26
450 494 0.038618 ATGCGCACGTTGTAGAGTCA 60.039 50.000 14.90 0.00 0.00 3.41
453 497 1.059369 GCATGCGCACGTTGTAGAG 59.941 57.895 14.90 0.00 38.36 2.43
473 517 0.395311 AGCAGATCCCCAACATGCAG 60.395 55.000 0.00 0.00 39.34 4.41
483 527 1.139853 CCAACTGGTCTAGCAGATCCC 59.860 57.143 15.62 0.00 0.00 3.85
498 544 1.677552 CTAACCGGGAGCACCAACT 59.322 57.895 6.32 0.00 40.22 3.16
568 615 4.482952 AGATTGATGATGTGCTCTGACA 57.517 40.909 0.00 0.00 0.00 3.58
574 621 7.015974 TCCTATCTACAAGATTGATGATGTGCT 59.984 37.037 0.00 0.00 36.20 4.40
621 673 4.785346 ACATAGATCACTCCAAAGCCAT 57.215 40.909 0.00 0.00 0.00 4.40
653 705 8.184192 GGGAGTACATTATTCAACAAAGTCATG 58.816 37.037 0.00 0.00 0.00 3.07
655 707 7.458397 AGGGAGTACATTATTCAACAAAGTCA 58.542 34.615 0.00 0.00 0.00 3.41
659 711 8.472007 ACAAAGGGAGTACATTATTCAACAAA 57.528 30.769 0.00 0.00 0.00 2.83
674 728 8.957466 GCACTTATATTTCTTTACAAAGGGAGT 58.043 33.333 2.04 0.00 36.67 3.85
675 729 8.122952 CGCACTTATATTTCTTTACAAAGGGAG 58.877 37.037 2.04 0.00 36.67 4.30
676 730 7.066525 CCGCACTTATATTTCTTTACAAAGGGA 59.933 37.037 2.04 0.00 36.67 4.20
677 731 7.148137 ACCGCACTTATATTTCTTTACAAAGGG 60.148 37.037 2.04 0.00 36.67 3.95
678 732 7.758495 ACCGCACTTATATTTCTTTACAAAGG 58.242 34.615 2.04 0.00 36.67 3.11
679 733 9.916397 CTACCGCACTTATATTTCTTTACAAAG 57.084 33.333 0.00 0.00 37.36 2.77
680 734 9.656040 TCTACCGCACTTATATTTCTTTACAAA 57.344 29.630 0.00 0.00 0.00 2.83
681 735 9.826574 ATCTACCGCACTTATATTTCTTTACAA 57.173 29.630 0.00 0.00 0.00 2.41
682 736 9.472361 GATCTACCGCACTTATATTTCTTTACA 57.528 33.333 0.00 0.00 0.00 2.41
683 737 9.472361 TGATCTACCGCACTTATATTTCTTTAC 57.528 33.333 0.00 0.00 0.00 2.01
684 738 9.472361 GTGATCTACCGCACTTATATTTCTTTA 57.528 33.333 0.00 0.00 32.44 1.85
685 739 8.204836 AGTGATCTACCGCACTTATATTTCTTT 58.795 33.333 0.00 0.00 42.33 2.52
686 740 7.727181 AGTGATCTACCGCACTTATATTTCTT 58.273 34.615 0.00 0.00 42.33 2.52
687 741 7.291411 AGTGATCTACCGCACTTATATTTCT 57.709 36.000 0.00 0.00 42.33 2.52
688 742 8.298140 ACTAGTGATCTACCGCACTTATATTTC 58.702 37.037 0.00 0.00 42.33 2.17
689 743 8.179509 ACTAGTGATCTACCGCACTTATATTT 57.820 34.615 0.00 0.00 42.33 1.40
690 744 7.762588 ACTAGTGATCTACCGCACTTATATT 57.237 36.000 0.00 0.00 42.33 1.28
691 745 7.762588 AACTAGTGATCTACCGCACTTATAT 57.237 36.000 0.00 0.00 42.33 0.86
692 746 7.578310 AAACTAGTGATCTACCGCACTTATA 57.422 36.000 0.00 0.00 42.33 0.98
693 747 6.466885 AAACTAGTGATCTACCGCACTTAT 57.533 37.500 0.00 0.00 42.33 1.73
694 748 5.909621 AAACTAGTGATCTACCGCACTTA 57.090 39.130 0.00 0.00 42.33 2.24
695 749 4.803098 AAACTAGTGATCTACCGCACTT 57.197 40.909 0.00 0.00 42.33 3.16
696 750 4.948621 ACTAAACTAGTGATCTACCGCACT 59.051 41.667 0.00 0.00 46.31 4.40
697 751 5.246145 ACTAAACTAGTGATCTACCGCAC 57.754 43.478 0.00 0.00 37.69 5.34
717 771 9.601217 AACAAATATAAGAGCGTTTAGATCACT 57.399 29.630 0.00 0.00 37.82 3.41
745 799 8.247562 CGCTAGCATCTTTATTACTTCCTCTAT 58.752 37.037 16.45 0.00 0.00 1.98
746 800 7.309255 CCGCTAGCATCTTTATTACTTCCTCTA 60.309 40.741 16.45 0.00 0.00 2.43
747 801 6.451393 CGCTAGCATCTTTATTACTTCCTCT 58.549 40.000 16.45 0.00 0.00 3.69
748 802 5.635700 CCGCTAGCATCTTTATTACTTCCTC 59.364 44.000 16.45 0.00 0.00 3.71
749 803 5.304614 TCCGCTAGCATCTTTATTACTTCCT 59.695 40.000 16.45 0.00 0.00 3.36
750 804 5.539048 TCCGCTAGCATCTTTATTACTTCC 58.461 41.667 16.45 0.00 0.00 3.46
751 805 6.217294 ACTCCGCTAGCATCTTTATTACTTC 58.783 40.000 16.45 0.00 0.00 3.01
752 806 6.163135 ACTCCGCTAGCATCTTTATTACTT 57.837 37.500 16.45 0.00 0.00 2.24
753 807 5.793030 ACTCCGCTAGCATCTTTATTACT 57.207 39.130 16.45 0.00 0.00 2.24
754 808 8.535690 AATTACTCCGCTAGCATCTTTATTAC 57.464 34.615 16.45 0.00 0.00 1.89
755 809 9.555727 AAAATTACTCCGCTAGCATCTTTATTA 57.444 29.630 16.45 0.00 0.00 0.98
756 810 8.451908 AAAATTACTCCGCTAGCATCTTTATT 57.548 30.769 16.45 4.55 0.00 1.40
757 811 8.451908 AAAAATTACTCCGCTAGCATCTTTAT 57.548 30.769 16.45 0.00 0.00 1.40
758 812 7.859325 AAAAATTACTCCGCTAGCATCTTTA 57.141 32.000 16.45 0.00 0.00 1.85
759 813 6.759497 AAAAATTACTCCGCTAGCATCTTT 57.241 33.333 16.45 0.00 0.00 2.52
792 846 6.183360 GGGACCTCCAGAGCATTTTATTTTAC 60.183 42.308 0.00 0.00 37.91 2.01
793 847 5.891551 GGGACCTCCAGAGCATTTTATTTTA 59.108 40.000 0.00 0.00 37.91 1.52
833 888 1.602920 GCTTTCCCTTTCTTGGTTGCG 60.603 52.381 0.00 0.00 0.00 4.85
1008 1065 3.461061 CTCTGCCTCAAATTATGCGAGA 58.539 45.455 0.00 0.00 31.05 4.04
1141 1291 3.160748 GCCTCCTCCTCCAGCTCC 61.161 72.222 0.00 0.00 0.00 4.70
1158 1308 2.792599 CGTCCTCGTCCTTCTCCG 59.207 66.667 0.00 0.00 0.00 4.63
1537 1687 4.250305 ACCGCGTTGTTGGGCTCT 62.250 61.111 4.92 0.00 0.00 4.09
1754 1910 0.037326 TGGATCAATATCGCCTCCGC 60.037 55.000 0.00 0.00 32.44 5.54
1755 1911 1.714794 GTGGATCAATATCGCCTCCG 58.285 55.000 0.00 0.00 32.44 4.63
1761 1917 2.051423 CGTCACCGTGGATCAATATCG 58.949 52.381 0.00 0.00 32.44 2.92
1773 1929 3.991051 CCTGCTCACCGTCACCGT 61.991 66.667 0.00 0.00 0.00 4.83
1870 2038 0.247460 TGTTCTGCCCACTCTGATCG 59.753 55.000 0.00 0.00 0.00 3.69
1882 2050 0.514691 CGTCTTCCTGCTTGTTCTGC 59.485 55.000 0.00 0.00 0.00 4.26
1886 2054 1.048601 TCTCCGTCTTCCTGCTTGTT 58.951 50.000 0.00 0.00 0.00 2.83
1946 2165 3.008049 TCCCCTTCTTCTCCGAGAAAAAG 59.992 47.826 14.87 14.87 33.26 2.27
1948 2167 2.616524 TCCCCTTCTTCTCCGAGAAAA 58.383 47.619 11.94 8.39 35.38 2.29
1949 2168 2.320681 TCCCCTTCTTCTCCGAGAAA 57.679 50.000 11.94 0.00 35.38 2.52
1981 2200 3.258228 ATCCTGTGGAAGCAGCGCA 62.258 57.895 11.47 0.00 34.34 6.09
2231 2450 1.462283 CAAGCACGGATCAACAGAGTG 59.538 52.381 0.00 0.00 36.05 3.51
2274 2493 9.002600 TGACCAAACGTACGACATATATAGTAT 57.997 33.333 24.41 0.00 0.00 2.12
2365 2593 6.821616 ATGGATCTCCTTACTCATTTCAGT 57.178 37.500 0.00 0.00 36.82 3.41
2400 2629 6.145048 CGAACCGAATAGCTTTATCCGTATTT 59.855 38.462 0.00 0.00 0.00 1.40
2406 2635 5.346281 CAGATCGAACCGAATAGCTTTATCC 59.654 44.000 0.00 0.00 39.99 2.59
2513 2742 8.526147 CAAGATGGTATTCTCCAAAAACTTGAT 58.474 33.333 0.00 0.00 41.09 2.57
2518 2747 7.454260 ACTCAAGATGGTATTCTCCAAAAAC 57.546 36.000 0.00 0.00 41.09 2.43
2523 2752 4.954202 ACGTACTCAAGATGGTATTCTCCA 59.046 41.667 0.00 0.00 42.01 3.86
2543 2772 1.065709 ACAAGTTGTGGTCCTTGACGT 60.066 47.619 7.96 0.00 40.36 4.34
2555 2784 3.312421 CGAAGAATGGACACACAAGTTGT 59.688 43.478 1.64 1.64 39.97 3.32
2556 2785 3.303990 CCGAAGAATGGACACACAAGTTG 60.304 47.826 0.00 0.00 0.00 3.16
2557 2786 2.878406 CCGAAGAATGGACACACAAGTT 59.122 45.455 0.00 0.00 0.00 2.66
2558 2787 2.158813 ACCGAAGAATGGACACACAAGT 60.159 45.455 0.00 0.00 0.00 3.16
2559 2788 2.494059 ACCGAAGAATGGACACACAAG 58.506 47.619 0.00 0.00 0.00 3.16
2584 2813 1.749258 GGGCCGATCAAGAACCACC 60.749 63.158 0.00 0.00 0.00 4.61
2588 2817 1.750193 TTCATGGGCCGATCAAGAAC 58.250 50.000 0.00 0.00 0.00 3.01
2593 2822 2.905736 TCTATCATTCATGGGCCGATCA 59.094 45.455 0.00 0.00 0.00 2.92
2594 2823 3.616956 TCTATCATTCATGGGCCGATC 57.383 47.619 0.00 0.00 0.00 3.69
2595 2824 3.431346 CGATCTATCATTCATGGGCCGAT 60.431 47.826 0.00 0.00 0.00 4.18
2596 2825 2.094026 CGATCTATCATTCATGGGCCGA 60.094 50.000 0.00 0.00 0.00 5.54
2597 2826 2.094026 TCGATCTATCATTCATGGGCCG 60.094 50.000 0.00 0.00 0.00 6.13
2598 2827 3.265791 GTCGATCTATCATTCATGGGCC 58.734 50.000 0.00 0.00 0.00 5.80
2599 2828 2.926200 CGTCGATCTATCATTCATGGGC 59.074 50.000 0.00 0.00 0.00 5.36
2612 2841 2.110901 AGTACTCACCACGTCGATCT 57.889 50.000 0.00 0.00 0.00 2.75
2614 2843 2.877168 GGATAGTACTCACCACGTCGAT 59.123 50.000 0.00 0.00 0.00 3.59
2622 2851 4.142227 ACAACGTCATGGATAGTACTCACC 60.142 45.833 0.00 4.92 0.00 4.02
2623 2852 4.995124 ACAACGTCATGGATAGTACTCAC 58.005 43.478 0.00 0.00 0.00 3.51
2641 2870 1.716826 TTTGGGTCGGCGTTGACAAC 61.717 55.000 6.85 8.34 40.72 3.32
2642 2871 1.451567 TTTGGGTCGGCGTTGACAA 60.452 52.632 6.85 5.90 40.72 3.18
2643 2872 2.181521 GTTTGGGTCGGCGTTGACA 61.182 57.895 6.85 0.00 40.72 3.58
2647 2876 1.033202 AAGTTGTTTGGGTCGGCGTT 61.033 50.000 6.85 0.00 0.00 4.84
2688 2917 3.793797 TCGACAGACACTTCAACTTGA 57.206 42.857 0.00 0.00 0.00 3.02
2689 2918 3.363378 GCATCGACAGACACTTCAACTTG 60.363 47.826 0.00 0.00 0.00 3.16
2692 2921 1.461127 GGCATCGACAGACACTTCAAC 59.539 52.381 0.00 0.00 0.00 3.18
2693 2922 1.069978 TGGCATCGACAGACACTTCAA 59.930 47.619 0.00 0.00 0.00 2.69
2696 2925 0.681733 AGTGGCATCGACAGACACTT 59.318 50.000 19.55 6.99 39.16 3.16
2716 2945 1.069227 GGCAAGTGCTTGGTAAACTCG 60.069 52.381 13.07 0.00 40.74 4.18
2722 2951 0.036164 ACGATGGCAAGTGCTTGGTA 59.964 50.000 13.07 0.00 40.74 3.25
2727 2956 2.045926 GGGACGATGGCAAGTGCT 60.046 61.111 15.10 0.00 41.70 4.40
2739 2969 2.995574 ACGGGTTCCTCTGGGACG 60.996 66.667 0.00 0.00 42.05 4.79
2740 2970 2.663196 CACGGGTTCCTCTGGGAC 59.337 66.667 0.00 0.00 42.05 4.46
2758 2988 1.227438 AGTCGGTGTTTGTCCACGG 60.227 57.895 0.00 0.00 36.16 4.94
2759 2989 0.808453 ACAGTCGGTGTTTGTCCACG 60.808 55.000 0.00 0.00 34.94 4.94
2761 2991 3.073086 CACAGTCGGTGTTTGTCCA 57.927 52.632 0.00 0.00 42.75 4.02
2776 3006 2.552155 GGATTGTCACCCTACAAGCACA 60.552 50.000 7.22 0.00 45.31 4.57
2777 3007 2.084546 GGATTGTCACCCTACAAGCAC 58.915 52.381 7.22 0.00 45.31 4.40
2781 3011 3.262151 TCATTCGGATTGTCACCCTACAA 59.738 43.478 0.00 0.00 43.16 2.41
2784 3014 3.709141 TGATCATTCGGATTGTCACCCTA 59.291 43.478 0.00 0.00 36.00 3.53
2791 3021 5.003160 TGTCTTGTTGATCATTCGGATTGT 58.997 37.500 0.00 0.00 36.00 2.71
2794 3024 4.093408 CGTTGTCTTGTTGATCATTCGGAT 59.907 41.667 0.00 0.00 39.53 4.18
2809 3039 0.031721 GGTGAGACCGTCGTTGTCTT 59.968 55.000 5.75 0.00 42.94 3.01
2820 3050 1.258445 ATGACGTCCAGGGTGAGACC 61.258 60.000 14.12 0.00 37.60 3.85
2822 3052 0.608130 CAATGACGTCCAGGGTGAGA 59.392 55.000 14.12 0.00 0.00 3.27
2836 3066 6.765989 CCCTATCTTAATTGGACGAACAATGA 59.234 38.462 9.41 1.01 40.71 2.57
2846 3076 6.674861 TGACAAGGTACCCTATCTTAATTGGA 59.325 38.462 8.74 0.00 31.13 3.53
2849 3079 6.677076 AGGTGACAAGGTACCCTATCTTAATT 59.323 38.462 8.74 0.00 37.70 1.40
2854 3084 3.778622 AGGTGACAAGGTACCCTATCT 57.221 47.619 8.74 0.00 37.70 1.98
2910 3140 1.936547 GACGTCCTCATCATTGAAGGC 59.063 52.381 3.51 0.00 0.00 4.35
2911 3141 2.159240 TCGACGTCCTCATCATTGAAGG 60.159 50.000 10.58 0.00 0.00 3.46
2921 3151 2.114625 ACCACCTCGACGTCCTCA 59.885 61.111 10.58 0.00 0.00 3.86
2993 3223 7.377928 CACACAAAAAGTCTTAAAGATGCAGAG 59.622 37.037 0.00 0.00 0.00 3.35
3016 3246 3.153919 GCCAACTCTTAAACATCCCACA 58.846 45.455 0.00 0.00 0.00 4.17
3017 3247 2.492088 GGCCAACTCTTAAACATCCCAC 59.508 50.000 0.00 0.00 0.00 4.61
3063 3293 4.868067 ACCTAAGTCTTAACACACACTCG 58.132 43.478 0.00 0.00 0.00 4.18
3082 3326 2.224867 ACAGGCATAGCAGAAACAACCT 60.225 45.455 0.00 0.00 0.00 3.50
3111 3355 1.477553 TTTCTGATCCATGCTTGGCC 58.522 50.000 13.75 0.00 43.29 5.36
3119 3363 8.324306 TCAAGTAGAATCACTTTTCTGATCCAT 58.676 33.333 0.00 0.00 36.61 3.41
3168 3412 3.004629 CCTTTGTGTGTGCAGCAGAAATA 59.995 43.478 11.97 0.00 30.57 1.40
3178 3422 1.102978 ACCTTGTCCTTTGTGTGTGC 58.897 50.000 0.00 0.00 0.00 4.57
3208 3453 2.649331 ACGTCATATATAGCGGCCAC 57.351 50.000 2.24 0.00 0.00 5.01
3211 3456 4.092771 TGAGAACGTCATATATAGCGGC 57.907 45.455 11.22 0.00 0.00 6.53
3224 3469 6.920817 TCTGTGTATCTTGTAATGAGAACGT 58.079 36.000 0.00 0.00 0.00 3.99
3225 3470 7.702348 TGATCTGTGTATCTTGTAATGAGAACG 59.298 37.037 0.00 0.00 0.00 3.95
3227 3472 9.538508 CATGATCTGTGTATCTTGTAATGAGAA 57.461 33.333 0.00 0.00 0.00 2.87
3232 3477 7.492524 ACGACATGATCTGTGTATCTTGTAAT 58.507 34.615 0.00 0.00 41.64 1.89
3233 3478 6.863275 ACGACATGATCTGTGTATCTTGTAA 58.137 36.000 0.00 0.00 41.64 2.41
3247 3492 0.921347 GCCACGTGTACGACATGATC 59.079 55.000 15.65 0.00 43.02 2.92
3255 3500 1.202211 TGCTAGTATGCCACGTGTACG 60.202 52.381 15.65 2.43 46.33 3.67
3256 3501 2.190981 GTGCTAGTATGCCACGTGTAC 58.809 52.381 15.65 10.57 0.00 2.90
3266 3518 4.072131 ACAACTTGGTTGGTGCTAGTATG 58.928 43.478 13.75 0.00 46.50 2.39
3313 3565 3.062466 CACTCCTCGTCCGCCTCA 61.062 66.667 0.00 0.00 0.00 3.86
3346 3598 2.998279 ATCCACCCGGACGTCGAAC 61.998 63.158 9.92 0.00 46.79 3.95
3347 3599 2.677524 ATCCACCCGGACGTCGAA 60.678 61.111 9.92 0.00 46.79 3.71
3348 3600 3.445687 CATCCACCCGGACGTCGA 61.446 66.667 9.92 0.00 46.79 4.20
3350 3602 3.599285 TTGCATCCACCCGGACGTC 62.599 63.158 7.13 7.13 46.79 4.34
3351 3603 2.684192 TTTTGCATCCACCCGGACGT 62.684 55.000 0.73 0.00 46.79 4.34
3352 3604 1.969064 TTTTGCATCCACCCGGACG 60.969 57.895 0.73 0.00 46.79 4.79
3353 3605 1.584495 GTTTTGCATCCACCCGGAC 59.416 57.895 0.73 0.00 46.79 4.79
3355 3607 2.566010 CGTTTTGCATCCACCCGG 59.434 61.111 0.00 0.00 0.00 5.73
3356 3608 2.566010 CCGTTTTGCATCCACCCG 59.434 61.111 0.00 0.00 0.00 5.28
3357 3609 2.969827 CCCGTTTTGCATCCACCC 59.030 61.111 0.00 0.00 0.00 4.61
3358 3610 2.261361 GCCCGTTTTGCATCCACC 59.739 61.111 0.00 0.00 0.00 4.61
3359 3611 1.579084 TACGCCCGTTTTGCATCCAC 61.579 55.000 0.00 0.00 0.00 4.02
3360 3612 0.889638 TTACGCCCGTTTTGCATCCA 60.890 50.000 0.00 0.00 0.00 3.41
3361 3613 0.454196 ATTACGCCCGTTTTGCATCC 59.546 50.000 0.00 0.00 0.00 3.51
3362 3614 2.271821 AATTACGCCCGTTTTGCATC 57.728 45.000 0.00 0.00 0.00 3.91
3363 3615 2.734276 AAATTACGCCCGTTTTGCAT 57.266 40.000 0.00 0.00 0.00 3.96
3364 3616 2.510768 AAAATTACGCCCGTTTTGCA 57.489 40.000 0.00 0.00 0.00 4.08
3365 3617 3.306818 TGTAAAATTACGCCCGTTTTGC 58.693 40.909 0.00 0.00 36.45 3.68
3366 3618 5.164041 CCAATGTAAAATTACGCCCGTTTTG 60.164 40.000 0.00 0.00 36.45 2.44
3367 3619 4.924462 CCAATGTAAAATTACGCCCGTTTT 59.076 37.500 0.00 0.00 36.45 2.43
3368 3620 4.217983 TCCAATGTAAAATTACGCCCGTTT 59.782 37.500 0.00 0.00 36.45 3.60
3369 3621 3.757493 TCCAATGTAAAATTACGCCCGTT 59.243 39.130 0.00 0.00 36.45 4.44
3370 3622 3.345414 TCCAATGTAAAATTACGCCCGT 58.655 40.909 0.00 0.00 36.45 5.28
3371 3623 4.358494 TTCCAATGTAAAATTACGCCCG 57.642 40.909 0.00 0.00 36.45 6.13
3372 3624 7.436970 CCTAATTTCCAATGTAAAATTACGCCC 59.563 37.037 6.67 0.00 36.66 6.13
3373 3625 7.042992 GCCTAATTTCCAATGTAAAATTACGCC 60.043 37.037 14.02 3.81 35.56 5.68
3374 3626 7.489757 TGCCTAATTTCCAATGTAAAATTACGC 59.510 33.333 16.01 16.01 38.46 4.42
3375 3627 8.918961 TGCCTAATTTCCAATGTAAAATTACG 57.081 30.769 6.67 5.43 36.66 3.18
3376 3628 9.313118 CCTGCCTAATTTCCAATGTAAAATTAC 57.687 33.333 6.67 0.00 36.66 1.89
3377 3629 9.041354 ACCTGCCTAATTTCCAATGTAAAATTA 57.959 29.630 9.13 9.13 36.66 1.40
3378 3630 7.917003 ACCTGCCTAATTTCCAATGTAAAATT 58.083 30.769 8.12 8.12 38.34 1.82
3379 3631 7.494922 ACCTGCCTAATTTCCAATGTAAAAT 57.505 32.000 0.00 0.00 0.00 1.82
3380 3632 6.349777 CGACCTGCCTAATTTCCAATGTAAAA 60.350 38.462 0.00 0.00 0.00 1.52
3381 3633 5.124776 CGACCTGCCTAATTTCCAATGTAAA 59.875 40.000 0.00 0.00 0.00 2.01
3382 3634 4.638421 CGACCTGCCTAATTTCCAATGTAA 59.362 41.667 0.00 0.00 0.00 2.41
3383 3635 4.196193 CGACCTGCCTAATTTCCAATGTA 58.804 43.478 0.00 0.00 0.00 2.29
3384 3636 3.016736 CGACCTGCCTAATTTCCAATGT 58.983 45.455 0.00 0.00 0.00 2.71
3385 3637 2.358898 CCGACCTGCCTAATTTCCAATG 59.641 50.000 0.00 0.00 0.00 2.82
3386 3638 2.241176 TCCGACCTGCCTAATTTCCAAT 59.759 45.455 0.00 0.00 0.00 3.16
3387 3639 1.631388 TCCGACCTGCCTAATTTCCAA 59.369 47.619 0.00 0.00 0.00 3.53
3388 3640 1.065709 GTCCGACCTGCCTAATTTCCA 60.066 52.381 0.00 0.00 0.00 3.53
3389 3641 1.664873 GTCCGACCTGCCTAATTTCC 58.335 55.000 0.00 0.00 0.00 3.13
3390 3642 1.287425 CGTCCGACCTGCCTAATTTC 58.713 55.000 0.00 0.00 0.00 2.17
3391 3643 0.743345 GCGTCCGACCTGCCTAATTT 60.743 55.000 0.00 0.00 0.00 1.82
3392 3644 1.153429 GCGTCCGACCTGCCTAATT 60.153 57.895 0.00 0.00 0.00 1.40
3393 3645 2.499685 GCGTCCGACCTGCCTAAT 59.500 61.111 0.00 0.00 0.00 1.73
3394 3646 4.124351 CGCGTCCGACCTGCCTAA 62.124 66.667 0.00 0.00 36.29 2.69
3398 3650 2.813908 ATTTCGCGTCCGACCTGC 60.814 61.111 5.77 0.00 44.30 4.85
3399 3651 1.011968 TTCATTTCGCGTCCGACCTG 61.012 55.000 5.77 0.00 44.30 4.00
3400 3652 1.012486 GTTCATTTCGCGTCCGACCT 61.012 55.000 5.77 0.00 44.30 3.85
3401 3653 1.286354 TGTTCATTTCGCGTCCGACC 61.286 55.000 5.77 0.00 44.30 4.79
3402 3654 0.509499 TTGTTCATTTCGCGTCCGAC 59.491 50.000 5.77 0.00 44.30 4.79
3403 3655 2.901905 TTGTTCATTTCGCGTCCGA 58.098 47.368 5.77 0.00 42.66 4.55


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

AutoCloner maintained by Alex Coulton.