Multiple sequence alignment - TraesCS3A01G339800

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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 TraesCS3A01G339800 chr3A 100.000 6200 0 0 1 6200 586875989 586882188 0.000000e+00 11450.0
1 TraesCS3A01G339800 chr3B 95.600 2591 79 9 2711 5293 583844120 583846683 0.000000e+00 4120.0
2 TraesCS3A01G339800 chr3B 93.152 1431 63 7 3999 5420 583849594 583850998 0.000000e+00 2067.0
3 TraesCS3A01G339800 chr3B 93.092 1216 55 11 426 1634 583842637 583843830 0.000000e+00 1753.0
4 TraesCS3A01G339800 chr3B 97.794 816 15 3 1766 2580 389957592 389958405 0.000000e+00 1404.0
5 TraesCS3A01G339800 chr3B 88.305 419 19 7 5697 6085 583851438 583851856 5.620000e-130 475.0
6 TraesCS3A01G339800 chr3B 87.351 419 21 7 5697 6085 583848518 583848934 9.480000e-123 451.0
7 TraesCS3A01G339800 chr3B 83.989 356 35 13 23 365 583842299 583842645 7.750000e-84 322.0
8 TraesCS3A01G339800 chr3B 93.865 163 2 5 5291 5449 583846748 583846906 8.030000e-59 239.0
9 TraesCS3A01G339800 chr3B 92.754 138 8 2 1632 1769 583843953 583844088 1.360000e-46 198.0
10 TraesCS3A01G339800 chr3B 89.216 102 10 1 2620 2720 241678835 241678936 6.520000e-25 126.0
11 TraesCS3A01G339800 chr3B 91.398 93 5 1 6108 6200 583987039 583987128 2.350000e-24 124.0
12 TraesCS3A01G339800 chr3B 91.429 70 5 1 5584 5653 583847880 583847948 1.840000e-15 95.3
13 TraesCS3A01G339800 chr3B 82.609 115 6 4 5598 5698 583851290 583851404 8.560000e-14 89.8
14 TraesCS3A01G339800 chr3B 90.323 62 2 3 5530 5591 583846941 583846998 1.850000e-10 78.7
15 TraesCS3A01G339800 chr3B 95.349 43 0 2 5656 5698 583848444 583848484 4.010000e-07 67.6
16 TraesCS3A01G339800 chr3B 100.000 32 0 0 2577 2608 583844079 583844110 6.710000e-05 60.2
17 TraesCS3A01G339800 chr3D 95.603 2547 60 12 2897 5438 445289011 445291510 0.000000e+00 4036.0
18 TraesCS3A01G339800 chr3D 94.031 1759 63 22 23 1769 445287125 445288853 0.000000e+00 2628.0
19 TraesCS3A01G339800 chr3D 94.340 318 15 1 5883 6200 445292346 445292660 9.340000e-133 484.0
20 TraesCS3A01G339800 chr3D 90.556 180 3 1 5533 5698 445291948 445292127 6.250000e-55 226.0
21 TraesCS3A01G339800 chr3D 97.727 88 2 0 5697 5784 445292161 445292248 1.080000e-32 152.0
22 TraesCS3A01G339800 chr3D 89.796 98 7 3 2612 2707 543613420 543613516 8.440000e-24 122.0
23 TraesCS3A01G339800 chr3D 83.636 110 12 6 2609 2716 297496947 297496842 1.420000e-16 99.0
24 TraesCS3A01G339800 chr5A 98.162 816 11 4 1765 2580 174601594 174600783 0.000000e+00 1421.0
25 TraesCS3A01G339800 chr2A 98.162 816 11 4 1765 2580 518944215 518943404 0.000000e+00 1421.0
26 TraesCS3A01G339800 chr2A 97.800 818 13 4 1765 2580 87864101 87863287 0.000000e+00 1406.0
27 TraesCS3A01G339800 chr2A 97.797 817 15 3 1765 2580 438396950 438397764 0.000000e+00 1406.0
28 TraesCS3A01G339800 chr2A 95.533 806 31 5 1775 2580 523872563 523871763 0.000000e+00 1284.0
29 TraesCS3A01G339800 chr6B 98.039 816 12 4 1765 2580 606303264 606302453 0.000000e+00 1415.0
30 TraesCS3A01G339800 chr6B 88.636 44 5 0 2671 2714 30165751 30165794 3.000000e-03 54.7
31 TraesCS3A01G339800 chr5B 98.039 816 13 3 1766 2580 48316278 48315465 0.000000e+00 1415.0
32 TraesCS3A01G339800 chr5B 94.828 812 30 5 1771 2580 325067528 325066727 0.000000e+00 1256.0
33 TraesCS3A01G339800 chr5B 93.023 86 6 0 2619 2704 142660041 142660126 6.520000e-25 126.0
34 TraesCS3A01G339800 chr5B 87.379 103 10 3 2603 2703 559771508 559771407 1.410000e-21 115.0
35 TraesCS3A01G339800 chr4B 97.914 815 14 3 1767 2580 5372861 5373673 0.000000e+00 1408.0
36 TraesCS3A01G339800 chr2B 97.683 820 16 3 1762 2580 465129792 465128975 0.000000e+00 1406.0
37 TraesCS3A01G339800 chr2B 90.526 95 9 0 2611 2705 387076280 387076186 6.520000e-25 126.0
38 TraesCS3A01G339800 chr6D 96.929 814 12 6 1769 2580 153190770 153191572 0.000000e+00 1352.0
39 TraesCS3A01G339800 chr6D 94.743 818 29 5 1765 2580 148583407 148582602 0.000000e+00 1260.0
40 TraesCS3A01G339800 chr7A 96.117 824 20 5 1760 2580 118150739 118151553 0.000000e+00 1334.0
41 TraesCS3A01G339800 chr7A 91.304 92 7 1 2616 2706 467851819 467851910 2.350000e-24 124.0
42 TraesCS3A01G339800 chrUn 95.545 808 25 4 1775 2580 332285119 332284321 0.000000e+00 1282.0
43 TraesCS3A01G339800 chr6A 95.517 803 32 4 1778 2580 309812646 309811848 0.000000e+00 1280.0
44 TraesCS3A01G339800 chr6A 88.776 98 9 2 2607 2703 27782689 27782785 1.090000e-22 119.0
45 TraesCS3A01G339800 chr7D 95.031 805 32 7 1776 2580 334840436 334841232 0.000000e+00 1258.0
46 TraesCS3A01G339800 chr7D 87.379 103 12 1 2611 2713 497815015 497815116 3.930000e-22 117.0
47 TraesCS3A01G339800 chr4A 94.554 808 30 6 1773 2578 235658149 235658944 0.000000e+00 1236.0
48 TraesCS3A01G339800 chr2D 85.088 114 15 2 2603 2715 648278373 648278485 1.410000e-21 115.0
49 TraesCS3A01G339800 chr1D 87.879 99 11 1 2615 2712 463165367 463165269 1.410000e-21 115.0
50 TraesCS3A01G339800 chr4D 84.848 99 11 4 2619 2716 46029970 46029875 5.120000e-16 97.1
51 TraesCS3A01G339800 chr7B 80.583 103 20 0 2622 2724 362085197 362085095 5.150000e-11 80.5


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 TraesCS3A01G339800 chr3A 586875989 586882188 6199 False 11450.000000 11450 100.000000 1 6200 1 chr3A.!!$F1 6199
1 TraesCS3A01G339800 chr3B 389957592 389958405 813 False 1404.000000 1404 97.794000 1766 2580 1 chr3B.!!$F2 814
2 TraesCS3A01G339800 chr3B 583842299 583851856 9557 False 770.507692 4120 91.370615 23 6085 13 chr3B.!!$F4 6062
3 TraesCS3A01G339800 chr3D 445287125 445292660 5535 False 1505.200000 4036 94.451400 23 6200 5 chr3D.!!$F2 6177
4 TraesCS3A01G339800 chr5A 174600783 174601594 811 True 1421.000000 1421 98.162000 1765 2580 1 chr5A.!!$R1 815
5 TraesCS3A01G339800 chr2A 518943404 518944215 811 True 1421.000000 1421 98.162000 1765 2580 1 chr2A.!!$R2 815
6 TraesCS3A01G339800 chr2A 87863287 87864101 814 True 1406.000000 1406 97.800000 1765 2580 1 chr2A.!!$R1 815
7 TraesCS3A01G339800 chr2A 438396950 438397764 814 False 1406.000000 1406 97.797000 1765 2580 1 chr2A.!!$F1 815
8 TraesCS3A01G339800 chr2A 523871763 523872563 800 True 1284.000000 1284 95.533000 1775 2580 1 chr2A.!!$R3 805
9 TraesCS3A01G339800 chr6B 606302453 606303264 811 True 1415.000000 1415 98.039000 1765 2580 1 chr6B.!!$R1 815
10 TraesCS3A01G339800 chr5B 48315465 48316278 813 True 1415.000000 1415 98.039000 1766 2580 1 chr5B.!!$R1 814
11 TraesCS3A01G339800 chr5B 325066727 325067528 801 True 1256.000000 1256 94.828000 1771 2580 1 chr5B.!!$R2 809
12 TraesCS3A01G339800 chr4B 5372861 5373673 812 False 1408.000000 1408 97.914000 1767 2580 1 chr4B.!!$F1 813
13 TraesCS3A01G339800 chr2B 465128975 465129792 817 True 1406.000000 1406 97.683000 1762 2580 1 chr2B.!!$R2 818
14 TraesCS3A01G339800 chr6D 153190770 153191572 802 False 1352.000000 1352 96.929000 1769 2580 1 chr6D.!!$F1 811
15 TraesCS3A01G339800 chr6D 148582602 148583407 805 True 1260.000000 1260 94.743000 1765 2580 1 chr6D.!!$R1 815
16 TraesCS3A01G339800 chr7A 118150739 118151553 814 False 1334.000000 1334 96.117000 1760 2580 1 chr7A.!!$F1 820
17 TraesCS3A01G339800 chrUn 332284321 332285119 798 True 1282.000000 1282 95.545000 1775 2580 1 chrUn.!!$R1 805
18 TraesCS3A01G339800 chr6A 309811848 309812646 798 True 1280.000000 1280 95.517000 1778 2580 1 chr6A.!!$R1 802
19 TraesCS3A01G339800 chr7D 334840436 334841232 796 False 1258.000000 1258 95.031000 1776 2580 1 chr7D.!!$F1 804
20 TraesCS3A01G339800 chr4A 235658149 235658944 795 False 1236.000000 1236 94.554000 1773 2578 1 chr4A.!!$F1 805

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
997 1017 1.019673 CTGCAGGGGAACATCAATCG 58.980 55.0 5.57 0.0 0.00 3.34 F
1742 1893 0.738389 AACAGAAAACTGCACCACCG 59.262 50.0 0.00 0.0 0.00 4.94 F
1757 1908 1.036707 CACCGTTGTTTTCCCCACAT 58.963 50.0 0.00 0.0 0.00 3.21 F
2677 2840 0.249741 ACACTAGTGCCGAAAACGCT 60.250 50.0 22.90 0.0 0.00 5.07 F
4191 4360 0.044855 ATCTCTGGCCTACCCACCTT 59.955 55.0 3.32 0.0 39.18 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2658 2821 0.249741 AGCGTTTTCGGCACTAGTGT 60.250 50.0 23.44 0.00 44.29 3.55 R
2660 2823 0.317479 AGAGCGTTTTCGGCACTAGT 59.683 50.0 0.00 0.00 44.29 2.57 R
3444 3613 1.144969 TGTTCGGTTCGAGCATGTTC 58.855 50.0 0.53 0.00 41.62 3.18 R
4578 4751 0.675837 TGAGCAGCTGCAGATTCCAC 60.676 55.0 38.24 18.44 45.16 4.02 R
6096 11050 0.103983 TATCCCCATCATGGAGCCCA 60.104 55.0 4.75 0.00 40.96 5.36 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
19 20 2.969628 GACTGACGGATCCATCTGTT 57.030 50.000 19.57 5.81 45.91 3.16
20 21 2.544685 GACTGACGGATCCATCTGTTG 58.455 52.381 19.57 5.68 45.91 3.33
21 22 1.902508 ACTGACGGATCCATCTGTTGT 59.097 47.619 13.88 0.16 45.91 3.32
89 90 5.352569 CCTAGTCTGTTAGAATTTGCACCTG 59.647 44.000 0.00 0.00 0.00 4.00
111 112 8.458843 ACCTGAACCTACAAATTTTAATCATCG 58.541 33.333 0.00 0.00 0.00 3.84
323 337 1.209504 CCGAGGTGGGTATCAACATGT 59.790 52.381 0.00 0.00 34.94 3.21
373 387 5.248477 AGGCAGTCTGGTAGTATTTCTTTCA 59.752 40.000 1.14 0.00 0.00 2.69
408 425 4.442706 CTCCGCATCACCAATTAAGTACT 58.557 43.478 0.00 0.00 0.00 2.73
535 552 1.144969 GAAACATTGGTCGCGACTCA 58.855 50.000 35.50 27.87 0.00 3.41
695 713 1.454572 GGTGTGGATGTGTGCTGCAA 61.455 55.000 2.77 0.00 0.00 4.08
791 809 3.571401 ACTTCTGGGTTTCTTGCATTGAG 59.429 43.478 0.00 0.00 0.00 3.02
799 817 5.337813 GGGTTTCTTGCATTGAGGATTTGAT 60.338 40.000 0.00 0.00 0.00 2.57
888 908 4.438913 TCCCCATTTGGATAGCTATAGCT 58.561 43.478 29.24 29.24 46.14 3.32
936 956 3.425892 GCATAGCTCAGTTTGCTCACTTG 60.426 47.826 0.00 0.00 41.46 3.16
947 967 1.206072 CTCACTTGCTGCTGCGAAC 59.794 57.895 11.21 0.00 43.34 3.95
997 1017 1.019673 CTGCAGGGGAACATCAATCG 58.980 55.000 5.57 0.00 0.00 3.34
1146 1166 2.522638 CGTCGGTATGGCGCCTTTC 61.523 63.158 29.70 19.07 0.00 2.62
1172 1192 2.813908 CGCCTACCGCAACCTCAC 60.814 66.667 0.00 0.00 37.30 3.51
1223 1243 6.127423 GCCTTCTACTTTGAGAGGTACATACA 60.127 42.308 0.00 0.00 0.00 2.29
1224 1244 7.418025 GCCTTCTACTTTGAGAGGTACATACAT 60.418 40.741 0.00 0.00 0.00 2.29
1225 1245 9.132923 CCTTCTACTTTGAGAGGTACATACATA 57.867 37.037 0.00 0.00 0.00 2.29
1226 1246 9.953697 CTTCTACTTTGAGAGGTACATACATAC 57.046 37.037 0.00 0.00 0.00 2.39
1270 1292 8.547967 TTAGCTAGGTATTTGTTCTGTTCTTG 57.452 34.615 1.80 0.00 0.00 3.02
1325 1347 9.508642 TCATGTCTTATAGACTGTAGGATAGTG 57.491 37.037 8.18 0.00 45.27 2.74
1476 1498 1.004044 AGTGCTGCAACCTCTTAGCAT 59.996 47.619 2.77 0.00 46.48 3.79
1515 1537 7.281999 TGTTCATGTTCACTGAAGTATTTGTCA 59.718 33.333 0.00 0.00 33.49 3.58
1578 1600 6.479972 TTTTATATCACCGTCCTGTCAGAT 57.520 37.500 0.00 0.00 0.00 2.90
1590 1612 2.188524 CTGTCAGATTCCATCGTGTCG 58.811 52.381 0.00 0.00 0.00 4.35
1628 1654 8.295569 AGAGATTTGTTAACACGACTAAGAAC 57.704 34.615 8.07 0.00 0.00 3.01
1739 1890 4.734398 AAATGAACAGAAAACTGCACCA 57.266 36.364 0.00 0.00 0.00 4.17
1742 1893 0.738389 AACAGAAAACTGCACCACCG 59.262 50.000 0.00 0.00 0.00 4.94
1753 1904 1.737201 CACCACCGTTGTTTTCCCC 59.263 57.895 0.00 0.00 0.00 4.81
1754 1905 1.038130 CACCACCGTTGTTTTCCCCA 61.038 55.000 0.00 0.00 0.00 4.96
1755 1906 1.038681 ACCACCGTTGTTTTCCCCAC 61.039 55.000 0.00 0.00 0.00 4.61
1756 1907 1.038130 CCACCGTTGTTTTCCCCACA 61.038 55.000 0.00 0.00 0.00 4.17
1757 1908 1.036707 CACCGTTGTTTTCCCCACAT 58.963 50.000 0.00 0.00 0.00 3.21
1758 1909 1.036707 ACCGTTGTTTTCCCCACATG 58.963 50.000 0.00 0.00 0.00 3.21
1761 1912 1.883275 CGTTGTTTTCCCCACATGCTA 59.117 47.619 0.00 0.00 0.00 3.49
2191 2343 3.493176 CCATCTCAACATACGCATCTCCA 60.493 47.826 0.00 0.00 0.00 3.86
2454 2606 2.933834 GGTACCACCTGGCCACCT 60.934 66.667 7.15 0.00 39.35 4.00
2455 2607 2.351276 GTACCACCTGGCCACCTG 59.649 66.667 0.00 0.00 39.32 4.00
2466 2618 2.765969 CCACCTGGCCATCAAGGT 59.234 61.111 5.51 7.37 40.61 3.50
2469 2621 1.063717 CCACCTGGCCATCAAGGTTAT 60.064 52.381 11.60 0.00 40.61 1.89
2470 2622 2.174639 CCACCTGGCCATCAAGGTTATA 59.825 50.000 11.60 0.00 40.61 0.98
2472 2624 2.849943 ACCTGGCCATCAAGGTTATACA 59.150 45.455 5.51 0.00 40.61 2.29
2631 2794 8.625467 AACCTTATATTATACTCCCTCCATCC 57.375 38.462 0.00 0.00 0.00 3.51
2632 2795 7.140304 ACCTTATATTATACTCCCTCCATCCC 58.860 42.308 0.00 0.00 0.00 3.85
2633 2796 7.139619 CCTTATATTATACTCCCTCCATCCCA 58.860 42.308 0.00 0.00 0.00 4.37
2634 2797 7.796637 CCTTATATTATACTCCCTCCATCCCAT 59.203 40.741 0.00 0.00 0.00 4.00
2635 2798 9.898576 CTTATATTATACTCCCTCCATCCCATA 57.101 37.037 0.00 0.00 0.00 2.74
2642 2805 8.805145 ATACTCCCTCCATCCCATAATATAAG 57.195 38.462 0.00 0.00 0.00 1.73
2643 2806 6.826727 ACTCCCTCCATCCCATAATATAAGA 58.173 40.000 0.00 0.00 0.00 2.10
2644 2807 6.905776 ACTCCCTCCATCCCATAATATAAGAG 59.094 42.308 0.00 0.00 0.00 2.85
2645 2808 5.667626 TCCCTCCATCCCATAATATAAGAGC 59.332 44.000 0.00 0.00 0.00 4.09
2646 2809 5.453903 CCCTCCATCCCATAATATAAGAGCG 60.454 48.000 0.00 0.00 0.00 5.03
2647 2810 5.129485 CCTCCATCCCATAATATAAGAGCGT 59.871 44.000 0.00 0.00 0.00 5.07
2648 2811 6.352222 CCTCCATCCCATAATATAAGAGCGTT 60.352 42.308 0.00 0.00 0.00 4.84
2649 2812 7.016153 TCCATCCCATAATATAAGAGCGTTT 57.984 36.000 0.00 0.00 0.00 3.60
2650 2813 7.458397 TCCATCCCATAATATAAGAGCGTTTT 58.542 34.615 0.00 0.00 0.00 2.43
2651 2814 7.606456 TCCATCCCATAATATAAGAGCGTTTTC 59.394 37.037 0.00 0.00 0.00 2.29
2655 2818 8.525316 TCCCATAATATAAGAGCGTTTTCGATA 58.475 33.333 0.00 0.00 43.74 2.92
2656 2819 8.592998 CCCATAATATAAGAGCGTTTTCGATAC 58.407 37.037 0.00 0.00 43.74 2.24
2657 2820 9.355215 CCATAATATAAGAGCGTTTTCGATACT 57.645 33.333 0.00 0.00 43.74 2.12
2661 2824 8.725212 ATATAAGAGCGTTTTCGATACTACAC 57.275 34.615 0.00 0.00 43.74 2.90
2662 2825 4.698583 AGAGCGTTTTCGATACTACACT 57.301 40.909 0.00 0.00 43.74 3.55
2663 2826 5.808042 AGAGCGTTTTCGATACTACACTA 57.192 39.130 0.00 0.00 43.74 2.74
2664 2827 5.808403 AGAGCGTTTTCGATACTACACTAG 58.192 41.667 0.00 0.00 43.74 2.57
2665 2828 5.353678 AGAGCGTTTTCGATACTACACTAGT 59.646 40.000 0.00 0.00 43.74 2.57
2666 2829 5.451662 GAGCGTTTTCGATACTACACTAGTG 59.548 44.000 21.44 21.44 43.74 2.74
2667 2830 7.902403 GAGCGTTTTCGATACTACACTAGTGC 61.902 46.154 22.90 4.37 43.74 4.40
2668 2831 5.945775 GTTTTCGATACTACACTAGTGCC 57.054 43.478 22.90 4.63 39.81 5.01
2669 2832 3.957671 TTCGATACTACACTAGTGCCG 57.042 47.619 22.90 15.55 39.81 5.69
2670 2833 3.183793 TCGATACTACACTAGTGCCGA 57.816 47.619 22.90 16.97 39.81 5.54
2671 2834 3.534554 TCGATACTACACTAGTGCCGAA 58.465 45.455 22.90 6.90 39.29 4.30
2672 2835 3.940852 TCGATACTACACTAGTGCCGAAA 59.059 43.478 22.90 5.45 39.29 3.46
2673 2836 4.395854 TCGATACTACACTAGTGCCGAAAA 59.604 41.667 22.90 4.37 39.29 2.29
2674 2837 4.498323 CGATACTACACTAGTGCCGAAAAC 59.502 45.833 22.90 8.29 39.81 2.43
2675 2838 2.669364 ACTACACTAGTGCCGAAAACG 58.331 47.619 22.90 5.03 37.69 3.60
2676 2839 1.389106 CTACACTAGTGCCGAAAACGC 59.611 52.381 22.90 0.00 0.00 4.84
2677 2840 0.249741 ACACTAGTGCCGAAAACGCT 60.250 50.000 22.90 0.00 0.00 5.07
2678 2841 0.438830 CACTAGTGCCGAAAACGCTC 59.561 55.000 10.54 0.00 0.00 5.03
2679 2842 0.317479 ACTAGTGCCGAAAACGCTCT 59.683 50.000 0.00 0.00 34.63 4.09
2680 2843 1.270147 ACTAGTGCCGAAAACGCTCTT 60.270 47.619 0.00 0.00 32.65 2.85
2681 2844 2.029649 ACTAGTGCCGAAAACGCTCTTA 60.030 45.455 0.00 0.00 32.65 2.10
2682 2845 2.094762 AGTGCCGAAAACGCTCTTAT 57.905 45.000 0.00 0.00 0.00 1.73
2683 2846 3.241067 AGTGCCGAAAACGCTCTTATA 57.759 42.857 0.00 0.00 0.00 0.98
2684 2847 3.793559 AGTGCCGAAAACGCTCTTATAT 58.206 40.909 0.00 0.00 0.00 0.86
2685 2848 4.189231 AGTGCCGAAAACGCTCTTATATT 58.811 39.130 0.00 0.00 0.00 1.28
2686 2849 5.353938 AGTGCCGAAAACGCTCTTATATTA 58.646 37.500 0.00 0.00 0.00 0.98
2687 2850 5.989777 AGTGCCGAAAACGCTCTTATATTAT 59.010 36.000 0.00 0.00 0.00 1.28
2688 2851 6.071463 GTGCCGAAAACGCTCTTATATTATG 58.929 40.000 0.00 0.00 0.00 1.90
2689 2852 5.178623 TGCCGAAAACGCTCTTATATTATGG 59.821 40.000 0.00 0.00 0.00 2.74
2690 2853 5.390567 GCCGAAAACGCTCTTATATTATGGG 60.391 44.000 0.00 0.00 0.00 4.00
2691 2854 5.929992 CCGAAAACGCTCTTATATTATGGGA 59.070 40.000 0.00 0.00 0.00 4.37
2692 2855 6.128634 CCGAAAACGCTCTTATATTATGGGAC 60.129 42.308 0.00 0.00 0.00 4.46
2693 2856 6.399669 CGAAAACGCTCTTATATTATGGGACG 60.400 42.308 0.00 0.00 0.00 4.79
2694 2857 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
2695 2858 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
2696 2859 4.525487 ACGCTCTTATATTATGGGACGGAA 59.475 41.667 0.00 0.00 0.00 4.30
2697 2860 5.103000 CGCTCTTATATTATGGGACGGAAG 58.897 45.833 0.00 0.00 0.00 3.46
2698 2861 5.105877 CGCTCTTATATTATGGGACGGAAGA 60.106 44.000 0.00 0.00 0.00 2.87
2699 2862 6.571731 CGCTCTTATATTATGGGACGGAAGAA 60.572 42.308 0.00 0.00 0.00 2.52
2700 2863 6.814146 GCTCTTATATTATGGGACGGAAGAAG 59.186 42.308 0.00 0.00 0.00 2.85
2738 2901 8.029642 CAGGTATACTGTGGTTTCTAGTTTTG 57.970 38.462 2.25 0.00 42.42 2.44
2791 2954 0.618458 TCACCCACATAGGCAGTTCC 59.382 55.000 0.00 0.00 35.39 3.62
2803 2966 3.412386 AGGCAGTTCCAAACATACTGAC 58.588 45.455 0.00 0.00 46.09 3.51
2821 2984 4.098960 ACTGACGGTCAAGTAGAAAGTTCA 59.901 41.667 12.54 0.00 0.00 3.18
2835 2998 9.788960 AGTAGAAAGTTCAATTGTGAAAAGAAC 57.211 29.630 5.13 0.70 45.29 3.01
2893 3056 5.554822 TTTACGTAGTCATTTGGAATGGC 57.445 39.130 0.00 0.00 43.93 4.40
2898 3061 4.096231 CGTAGTCATTTGGAATGGCAATGA 59.904 41.667 7.86 0.00 35.10 2.57
2933 3096 9.185680 ACCAAAACTTTGTACTTATCAGAACTT 57.814 29.630 0.00 0.00 36.45 2.66
3064 3229 7.270779 TCATGACATTTCCATGTGTTTGAAAA 58.729 30.769 0.00 0.00 44.22 2.29
3190 3359 6.202379 GGTGCTTTCCTTTCCGTTCTATATAC 59.798 42.308 0.00 0.00 0.00 1.47
3241 3410 6.696583 TGTTGTTGATGTATAACCGTATACCG 59.303 38.462 0.00 0.00 40.96 4.02
3549 3718 6.884295 TCCAGGAATTTTACACTTACCATGAG 59.116 38.462 0.00 0.00 0.00 2.90
3690 3859 4.804139 CGTACGTCCAGCATTCTAATTTCT 59.196 41.667 7.22 0.00 0.00 2.52
3896 4065 7.989416 TTCAAAACGGATGGAGTAGTTATTT 57.011 32.000 0.00 0.00 0.00 1.40
3897 4066 9.504708 TTTCAAAACGGATGGAGTAGTTATTTA 57.495 29.630 0.00 0.00 0.00 1.40
3898 4067 8.483307 TCAAAACGGATGGAGTAGTTATTTAC 57.517 34.615 0.00 0.00 0.00 2.01
4054 4223 4.518970 TCTGAAAATGCTGGTCTACAAACC 59.481 41.667 0.00 0.00 39.94 3.27
4063 4232 5.012664 TGCTGGTCTACAAACCTATTCAGAA 59.987 40.000 0.00 0.00 40.20 3.02
4125 4294 2.435938 ATCGGTGCGGCGATTTGT 60.436 55.556 12.98 0.00 0.00 2.83
4191 4360 0.044855 ATCTCTGGCCTACCCACCTT 59.955 55.000 3.32 0.00 39.18 3.50
4201 4370 0.688487 TACCCACCTTCTGAAACCGG 59.312 55.000 0.00 0.00 0.00 5.28
4515 4688 4.293648 CTGGCGTGTGTGTCGGGA 62.294 66.667 0.00 0.00 0.00 5.14
4545 4718 1.607612 GGTGGTGATCGGGGTCATT 59.392 57.895 0.00 0.00 0.00 2.57
4578 4751 2.420568 AATGGCATGGGCGCTCAAG 61.421 57.895 17.15 12.43 42.47 3.02
4605 4778 3.108289 CAGCTGCTCACCGTCGTG 61.108 66.667 0.00 0.00 41.72 4.35
4648 4821 5.105635 CCAGTAGCAATTTGATGTGACCATT 60.106 40.000 0.00 0.00 0.00 3.16
4650 4823 4.100707 AGCAATTTGATGTGACCATTCG 57.899 40.909 0.00 0.00 0.00 3.34
4899 5072 4.201990 GGTGAGAATGGATTTCTGTCATGC 60.202 45.833 0.00 0.00 44.88 4.06
4914 5087 3.441222 TGTCATGCGCATCTTCAGAAATT 59.559 39.130 22.51 0.00 0.00 1.82
4928 5101 4.450976 TCAGAAATTGGATGGTCGTATGG 58.549 43.478 0.00 0.00 0.00 2.74
4929 5102 3.565482 CAGAAATTGGATGGTCGTATGGG 59.435 47.826 0.00 0.00 0.00 4.00
4972 5145 1.131883 GGCAAGCTGCTAACAGTGATG 59.868 52.381 0.90 0.00 46.30 3.07
4973 5146 1.808945 GCAAGCTGCTAACAGTGATGT 59.191 47.619 0.90 0.00 46.30 3.06
4974 5147 2.227388 GCAAGCTGCTAACAGTGATGTT 59.773 45.455 0.90 0.00 46.30 2.71
4975 5148 3.436704 GCAAGCTGCTAACAGTGATGTTA 59.563 43.478 0.90 1.31 46.30 2.41
4976 5149 4.670221 GCAAGCTGCTAACAGTGATGTTAC 60.670 45.833 0.90 0.00 46.30 2.50
4977 5150 4.543590 AGCTGCTAACAGTGATGTTACT 57.456 40.909 0.00 0.00 46.30 2.24
4978 5151 8.734103 GCAAGCTGCTAACAGTGATGTTACTG 62.734 46.154 0.90 4.49 46.30 2.74
4992 5165 9.741647 AGTGATGTTACTGATGCATATATATCG 57.258 33.333 0.00 0.00 0.00 2.92
4993 5166 9.736023 GTGATGTTACTGATGCATATATATCGA 57.264 33.333 0.00 0.00 0.00 3.59
5006 5179 6.147821 GCATATATATCGAAACCTGCTTGTGT 59.852 38.462 0.00 0.00 0.00 3.72
5121 5294 2.818274 GAGGCGGCGAACGGAAAT 60.818 61.111 12.98 0.00 44.51 2.17
5242 5415 3.319137 AGACAGTATTTGCGCAGAAGA 57.681 42.857 11.31 2.72 0.00 2.87
5391 5637 2.158943 CCTCCCACCCTCTAAAATCGTC 60.159 54.545 0.00 0.00 0.00 4.20
5449 5695 9.458727 CATAAAGCATTCATATCCCTAGAATGT 57.541 33.333 13.78 0.55 46.33 2.71
5452 5698 9.866655 AAAGCATTCATATCCCTAGAATGTTTA 57.133 29.630 13.93 0.00 45.79 2.01
5455 5701 8.725148 GCATTCATATCCCTAGAATGTTTACAG 58.275 37.037 13.78 0.00 46.33 2.74
5456 5702 9.224267 CATTCATATCCCTAGAATGTTTACAGG 57.776 37.037 0.00 0.00 42.12 4.00
5457 5703 7.931015 TCATATCCCTAGAATGTTTACAGGT 57.069 36.000 0.00 0.00 0.00 4.00
5458 5704 8.331931 TCATATCCCTAGAATGTTTACAGGTT 57.668 34.615 0.00 0.00 0.00 3.50
5459 5705 8.429641 TCATATCCCTAGAATGTTTACAGGTTC 58.570 37.037 0.00 0.00 0.00 3.62
5460 5706 5.431179 TCCCTAGAATGTTTACAGGTTCC 57.569 43.478 0.00 0.00 0.00 3.62
5461 5707 5.098663 TCCCTAGAATGTTTACAGGTTCCT 58.901 41.667 0.00 0.00 0.00 3.36
5466 5712 6.301169 AGAATGTTTACAGGTTCCTCTAGG 57.699 41.667 0.00 0.00 0.00 3.02
5467 5713 3.975168 TGTTTACAGGTTCCTCTAGGC 57.025 47.619 0.00 0.00 34.44 3.93
5468 5714 3.517612 TGTTTACAGGTTCCTCTAGGCT 58.482 45.455 0.00 0.00 34.44 4.58
5469 5715 3.514309 TGTTTACAGGTTCCTCTAGGCTC 59.486 47.826 0.00 0.00 34.44 4.70
5471 5717 4.875578 TTACAGGTTCCTCTAGGCTCTA 57.124 45.455 0.00 0.00 34.44 2.43
5473 5719 1.960689 CAGGTTCCTCTAGGCTCTAGC 59.039 57.143 0.00 0.00 41.14 3.42
5501 5747 1.508256 CCCCCACTAGGTAAGAAGGG 58.492 60.000 0.00 0.00 41.14 3.95
5504 5750 2.265526 CCACTAGGTAAGAAGGGGGT 57.734 55.000 0.00 0.00 32.21 4.95
5505 5751 1.838077 CCACTAGGTAAGAAGGGGGTG 59.162 57.143 0.00 0.00 32.21 4.61
5506 5752 2.547990 CACTAGGTAAGAAGGGGGTGT 58.452 52.381 0.00 0.00 0.00 4.16
5507 5753 3.567219 CCACTAGGTAAGAAGGGGGTGTA 60.567 52.174 0.00 0.00 32.21 2.90
5508 5754 3.705072 CACTAGGTAAGAAGGGGGTGTAG 59.295 52.174 0.00 0.00 0.00 2.74
5509 5755 3.599698 ACTAGGTAAGAAGGGGGTGTAGA 59.400 47.826 0.00 0.00 0.00 2.59
5510 5756 3.117552 AGGTAAGAAGGGGGTGTAGAG 57.882 52.381 0.00 0.00 0.00 2.43
5511 5757 2.117051 GGTAAGAAGGGGGTGTAGAGG 58.883 57.143 0.00 0.00 0.00 3.69
5512 5758 2.117051 GTAAGAAGGGGGTGTAGAGGG 58.883 57.143 0.00 0.00 0.00 4.30
5513 5759 0.914902 AAGAAGGGGGTGTAGAGGGC 60.915 60.000 0.00 0.00 0.00 5.19
5514 5760 1.615424 GAAGGGGGTGTAGAGGGCA 60.615 63.158 0.00 0.00 0.00 5.36
5515 5761 1.911702 GAAGGGGGTGTAGAGGGCAC 61.912 65.000 0.00 0.00 36.22 5.01
5516 5762 2.285442 GGGGGTGTAGAGGGCACT 60.285 66.667 0.00 0.00 37.07 4.40
5517 5763 1.002533 GGGGGTGTAGAGGGCACTA 59.997 63.158 0.00 0.00 37.07 2.74
5518 5764 0.400093 GGGGGTGTAGAGGGCACTAT 60.400 60.000 0.00 0.00 37.07 2.12
5519 5765 0.759346 GGGGTGTAGAGGGCACTATG 59.241 60.000 0.00 0.00 37.07 2.23
5520 5766 0.759346 GGGTGTAGAGGGCACTATGG 59.241 60.000 0.00 0.00 37.07 2.74
5521 5767 1.691482 GGGTGTAGAGGGCACTATGGA 60.691 57.143 0.00 0.00 37.07 3.41
5522 5768 1.413077 GGTGTAGAGGGCACTATGGAC 59.587 57.143 0.00 0.00 37.07 4.02
5523 5769 2.389715 GTGTAGAGGGCACTATGGACT 58.610 52.381 0.00 0.00 34.30 3.85
5524 5770 3.563223 GTGTAGAGGGCACTATGGACTA 58.437 50.000 0.00 0.00 34.30 2.59
5525 5771 3.570550 GTGTAGAGGGCACTATGGACTAG 59.429 52.174 0.00 0.00 34.30 2.57
5526 5772 3.204606 TGTAGAGGGCACTATGGACTAGT 59.795 47.826 0.00 0.00 41.53 2.57
5527 5773 4.414514 TGTAGAGGGCACTATGGACTAGTA 59.585 45.833 0.00 0.00 38.68 1.82
5528 5774 4.107127 AGAGGGCACTATGGACTAGTAG 57.893 50.000 0.00 0.00 38.68 2.57
5660 10549 0.817229 GAGCTTGGAGTGCTATGCCC 60.817 60.000 0.00 0.00 41.30 5.36
5849 10778 1.607467 GCCAGGCCAGGAATGTTGT 60.607 57.895 20.27 0.00 0.00 3.32
5855 10784 2.024414 GGCCAGGAATGTTGTGGTATC 58.976 52.381 0.00 0.00 33.51 2.24
5878 10807 0.036306 ACAAACCGAACTAGCCCTGG 59.964 55.000 0.00 0.00 0.00 4.45
5880 10809 0.613777 AAACCGAACTAGCCCTGGAG 59.386 55.000 0.00 0.00 0.00 3.86
5881 10810 0.544595 AACCGAACTAGCCCTGGAGT 60.545 55.000 0.00 0.00 0.00 3.85
5905 10859 3.334054 GCCCAACTCCTGCCTCCT 61.334 66.667 0.00 0.00 0.00 3.69
5912 10866 0.616111 ACTCCTGCCTCCTACCACAG 60.616 60.000 0.00 0.00 0.00 3.66
5955 10909 1.517257 CGGATGTCACACCGCTCTC 60.517 63.158 5.97 0.00 42.55 3.20
5978 10932 1.270550 CACCTTTGTGGAGCCATTGTC 59.729 52.381 0.00 0.00 38.90 3.18
6041 10995 4.156182 GCACACGGATTTTGTTTAGTAGC 58.844 43.478 0.00 0.00 0.00 3.58
6053 11007 1.196104 TTAGTAGCGGGGTGTTGCCT 61.196 55.000 0.00 0.00 37.43 4.75
6096 11050 3.227614 GGTACAAGGTGACCCAATGTTT 58.772 45.455 10.03 0.00 35.44 2.83
6188 11142 9.503369 AATAGAGGTTACAACTAGGGTCTATTT 57.497 33.333 0.00 0.00 34.01 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.093973 ACAACAGATGGATCCGTCAGTC 60.094 50.000 31.14 13.25 31.87 3.51
1 2 1.902508 ACAACAGATGGATCCGTCAGT 59.097 47.619 31.14 26.94 33.98 3.41
2 3 2.167281 AGACAACAGATGGATCCGTCAG 59.833 50.000 31.14 26.31 34.59 3.51
3 4 2.179427 AGACAACAGATGGATCCGTCA 58.821 47.619 31.14 4.63 34.59 4.35
4 5 2.969628 AGACAACAGATGGATCCGTC 57.030 50.000 24.30 24.30 0.00 4.79
5 6 3.096852 TGTAGACAACAGATGGATCCGT 58.903 45.455 6.04 6.04 33.01 4.69
6 7 3.801114 TGTAGACAACAGATGGATCCG 57.199 47.619 7.39 0.00 33.01 4.18
7 8 7.121168 TCAAATTTGTAGACAACAGATGGATCC 59.879 37.037 17.47 4.20 39.87 3.36
8 9 8.044060 TCAAATTTGTAGACAACAGATGGATC 57.956 34.615 17.47 0.00 39.87 3.36
9 10 8.408043 TTCAAATTTGTAGACAACAGATGGAT 57.592 30.769 17.47 0.00 39.87 3.41
10 11 7.815840 TTCAAATTTGTAGACAACAGATGGA 57.184 32.000 17.47 0.00 39.87 3.41
11 12 9.480053 AAATTCAAATTTGTAGACAACAGATGG 57.520 29.630 17.47 0.00 39.87 3.51
89 90 7.254852 TGGCGATGATTAAAATTTGTAGGTTC 58.745 34.615 0.00 0.00 0.00 3.62
111 112 7.483307 TCAATCTTGTCTAGCAAATTATTGGC 58.517 34.615 17.32 0.00 36.53 4.52
323 337 0.328450 ATGCCCTCCCATCCCTAACA 60.328 55.000 0.00 0.00 0.00 2.41
373 387 1.304134 GCGGAGGGAACAATTGGGT 60.304 57.895 10.83 0.00 0.00 4.51
416 433 7.490657 TTTAGCTTACTCCAGAGGTTTATGA 57.509 36.000 0.00 0.00 0.00 2.15
462 479 0.702383 CGGCTGAAATTGCGAAAACG 59.298 50.000 0.00 0.00 0.00 3.60
535 552 0.393077 CTGAGGTTCTGGTTGGTCGT 59.607 55.000 0.00 0.00 0.00 4.34
643 661 2.995466 ATAATATGCATGCCGTGTGC 57.005 45.000 16.68 0.00 42.81 4.57
695 713 4.479993 GCCTCTGGCTGCGACCAT 62.480 66.667 0.73 0.00 46.69 3.55
714 732 2.300967 TGGGACAGATGCCTGGGAC 61.301 63.158 0.00 0.00 44.60 4.46
717 735 2.124983 CGTGGGACAGATGCCTGG 60.125 66.667 0.00 0.00 44.60 4.45
791 809 3.264104 CCACATGTTTGGCATCAAATCC 58.736 45.455 0.00 0.00 43.73 3.01
920 940 1.334779 GCAGCAAGTGAGCAAACTGAG 60.335 52.381 0.00 0.00 36.85 3.35
947 967 1.278238 GTACCGAGGTTGAAGATGCG 58.722 55.000 0.00 0.00 0.00 4.73
1146 1166 3.584052 CGGTAGGCGAGGAGGACG 61.584 72.222 0.00 0.00 0.00 4.79
1223 1243 0.978146 AAGCGACAGGGCCAGAGTAT 60.978 55.000 6.18 0.00 0.00 2.12
1224 1244 1.605058 GAAGCGACAGGGCCAGAGTA 61.605 60.000 6.18 0.00 0.00 2.59
1225 1245 2.925170 AAGCGACAGGGCCAGAGT 60.925 61.111 6.18 0.01 0.00 3.24
1226 1246 2.125350 GAAGCGACAGGGCCAGAG 60.125 66.667 6.18 0.00 0.00 3.35
1281 1303 4.450419 ACATGAAGAAAAGAAGAGACGCTG 59.550 41.667 0.00 0.00 0.00 5.18
1325 1347 4.025145 CGGTCAAACAAAACAGAGTAGGAC 60.025 45.833 0.00 0.00 0.00 3.85
1408 1430 1.628340 TGGATCCGAACACCATCAAGT 59.372 47.619 7.39 0.00 0.00 3.16
1515 1537 8.960591 CACACAAGGGACAAAGATAGAATAAAT 58.039 33.333 0.00 0.00 0.00 1.40
1572 1594 2.186076 GACGACACGATGGAATCTGAC 58.814 52.381 0.00 0.00 42.58 3.51
1578 1600 1.202143 CGATCTGACGACACGATGGAA 60.202 52.381 0.00 0.00 35.09 3.53
1739 1890 1.036707 CATGTGGGGAAAACAACGGT 58.963 50.000 0.00 0.00 0.00 4.83
1742 1893 3.509575 TCATAGCATGTGGGGAAAACAAC 59.490 43.478 0.00 0.00 0.00 3.32
1753 1904 5.280164 TGTTGTTGTTGTTCATAGCATGTG 58.720 37.500 0.00 0.00 0.00 3.21
1754 1905 5.512753 TGTTGTTGTTGTTCATAGCATGT 57.487 34.783 0.00 0.00 0.00 3.21
1755 1906 5.747675 TGTTGTTGTTGTTGTTCATAGCATG 59.252 36.000 0.00 0.00 0.00 4.06
1756 1907 5.900425 TGTTGTTGTTGTTGTTCATAGCAT 58.100 33.333 0.00 0.00 0.00 3.79
1757 1908 5.316327 TGTTGTTGTTGTTGTTCATAGCA 57.684 34.783 0.00 0.00 0.00 3.49
1758 1909 5.574830 TGTTGTTGTTGTTGTTGTTCATAGC 59.425 36.000 0.00 0.00 0.00 2.97
1761 1912 5.755375 TGTTGTTGTTGTTGTTGTTGTTCAT 59.245 32.000 0.00 0.00 0.00 2.57
2191 2343 3.637911 TGTTCAACAGTTAGGTGTGGT 57.362 42.857 0.00 0.00 35.97 4.16
2262 2414 1.445582 GTTCTACAGGACGGCGGTG 60.446 63.158 13.24 8.30 0.00 4.94
2452 2604 3.576078 TGTATAACCTTGATGGCCAGG 57.424 47.619 13.05 9.74 40.22 4.45
2454 2606 4.787135 TGATGTATAACCTTGATGGCCA 57.213 40.909 8.56 8.56 40.22 5.36
2455 2607 4.887071 TGTTGATGTATAACCTTGATGGCC 59.113 41.667 0.00 0.00 40.22 5.36
2457 2609 5.824624 AGCTGTTGATGTATAACCTTGATGG 59.175 40.000 0.00 0.00 42.93 3.51
2459 2611 7.796054 ACTAGCTGTTGATGTATAACCTTGAT 58.204 34.615 0.00 0.00 0.00 2.57
2460 2612 7.182817 ACTAGCTGTTGATGTATAACCTTGA 57.817 36.000 0.00 0.00 0.00 3.02
2461 2613 8.198109 ACTACTAGCTGTTGATGTATAACCTTG 58.802 37.037 0.00 0.00 0.00 3.61
2462 2614 8.307582 ACTACTAGCTGTTGATGTATAACCTT 57.692 34.615 0.00 0.00 0.00 3.50
2463 2615 7.899648 ACTACTAGCTGTTGATGTATAACCT 57.100 36.000 0.00 0.00 0.00 3.50
2464 2616 8.848182 AGTACTACTAGCTGTTGATGTATAACC 58.152 37.037 0.00 0.00 0.00 2.85
2465 2617 9.666626 CAGTACTACTAGCTGTTGATGTATAAC 57.333 37.037 0.00 0.00 0.00 1.89
2466 2618 9.623000 TCAGTACTACTAGCTGTTGATGTATAA 57.377 33.333 0.00 0.00 0.00 0.98
2469 2621 7.933215 TTCAGTACTACTAGCTGTTGATGTA 57.067 36.000 0.00 0.00 0.00 2.29
2470 2622 6.835819 TTCAGTACTACTAGCTGTTGATGT 57.164 37.500 0.00 0.00 0.00 3.06
2472 2624 6.625300 CGGTTTCAGTACTACTAGCTGTTGAT 60.625 42.308 0.00 0.00 0.00 2.57
2609 2772 8.805145 ATGGGATGGAGGGAGTATAATATAAG 57.195 38.462 0.00 0.00 0.00 1.73
2618 2781 7.961940 TCTTATATTATGGGATGGAGGGAGTA 58.038 38.462 0.00 0.00 0.00 2.59
2619 2782 6.826727 TCTTATATTATGGGATGGAGGGAGT 58.173 40.000 0.00 0.00 0.00 3.85
2620 2783 6.183361 GCTCTTATATTATGGGATGGAGGGAG 60.183 46.154 0.00 0.00 0.00 4.30
2621 2784 5.667626 GCTCTTATATTATGGGATGGAGGGA 59.332 44.000 0.00 0.00 0.00 4.20
2622 2785 5.453903 CGCTCTTATATTATGGGATGGAGGG 60.454 48.000 0.00 0.00 0.00 4.30
2623 2786 5.129485 ACGCTCTTATATTATGGGATGGAGG 59.871 44.000 0.00 0.00 0.00 4.30
2624 2787 6.227298 ACGCTCTTATATTATGGGATGGAG 57.773 41.667 0.00 0.00 0.00 3.86
2625 2788 6.620877 AACGCTCTTATATTATGGGATGGA 57.379 37.500 0.00 0.00 0.00 3.41
2626 2789 7.413000 CGAAAACGCTCTTATATTATGGGATGG 60.413 40.741 0.00 0.00 0.00 3.51
2627 2790 7.330946 TCGAAAACGCTCTTATATTATGGGATG 59.669 37.037 0.00 0.00 0.00 3.51
2628 2791 7.383687 TCGAAAACGCTCTTATATTATGGGAT 58.616 34.615 0.00 0.00 0.00 3.85
2629 2792 6.751157 TCGAAAACGCTCTTATATTATGGGA 58.249 36.000 0.00 0.00 0.00 4.37
2630 2793 7.596749 ATCGAAAACGCTCTTATATTATGGG 57.403 36.000 0.00 0.00 0.00 4.00
2631 2794 9.355215 AGTATCGAAAACGCTCTTATATTATGG 57.645 33.333 0.00 0.00 0.00 2.74
2635 2798 9.178427 GTGTAGTATCGAAAACGCTCTTATATT 57.822 33.333 0.00 0.00 0.00 1.28
2636 2799 8.566260 AGTGTAGTATCGAAAACGCTCTTATAT 58.434 33.333 0.00 0.00 0.00 0.86
2637 2800 7.923888 AGTGTAGTATCGAAAACGCTCTTATA 58.076 34.615 0.00 0.00 0.00 0.98
2638 2801 6.793349 AGTGTAGTATCGAAAACGCTCTTAT 58.207 36.000 0.00 0.00 0.00 1.73
2639 2802 6.187125 AGTGTAGTATCGAAAACGCTCTTA 57.813 37.500 0.00 0.00 0.00 2.10
2640 2803 5.056894 AGTGTAGTATCGAAAACGCTCTT 57.943 39.130 0.00 0.00 0.00 2.85
2641 2804 4.698583 AGTGTAGTATCGAAAACGCTCT 57.301 40.909 0.00 0.00 0.00 4.09
2642 2805 5.451662 CACTAGTGTAGTATCGAAAACGCTC 59.548 44.000 15.06 2.73 37.23 5.03
2643 2806 5.330295 CACTAGTGTAGTATCGAAAACGCT 58.670 41.667 15.06 9.71 37.23 5.07
2644 2807 4.027864 GCACTAGTGTAGTATCGAAAACGC 60.028 45.833 23.44 0.00 37.23 4.84
2645 2808 4.498323 GGCACTAGTGTAGTATCGAAAACG 59.502 45.833 23.44 0.00 37.23 3.60
2646 2809 4.498323 CGGCACTAGTGTAGTATCGAAAAC 59.502 45.833 23.44 2.54 37.23 2.43
2647 2810 4.395854 TCGGCACTAGTGTAGTATCGAAAA 59.604 41.667 23.44 2.02 38.49 2.29
2648 2811 3.940852 TCGGCACTAGTGTAGTATCGAAA 59.059 43.478 23.44 2.60 38.49 3.46
2649 2812 3.534554 TCGGCACTAGTGTAGTATCGAA 58.465 45.455 23.44 6.76 38.49 3.71
2650 2813 3.183793 TCGGCACTAGTGTAGTATCGA 57.816 47.619 23.44 17.92 38.83 3.59
2651 2814 3.957671 TTCGGCACTAGTGTAGTATCG 57.042 47.619 23.44 16.27 37.23 2.92
2652 2815 4.498323 CGTTTTCGGCACTAGTGTAGTATC 59.502 45.833 23.44 6.09 37.13 2.24
2653 2816 4.418392 CGTTTTCGGCACTAGTGTAGTAT 58.582 43.478 23.44 0.00 37.13 2.12
2654 2817 3.825308 CGTTTTCGGCACTAGTGTAGTA 58.175 45.455 23.44 9.39 37.13 1.82
2655 2818 2.669364 CGTTTTCGGCACTAGTGTAGT 58.331 47.619 23.44 0.00 38.50 2.73
2656 2819 1.389106 GCGTTTTCGGCACTAGTGTAG 59.611 52.381 23.44 17.04 44.29 2.74
2657 2820 1.000060 AGCGTTTTCGGCACTAGTGTA 60.000 47.619 23.44 7.59 44.29 2.90
2658 2821 0.249741 AGCGTTTTCGGCACTAGTGT 60.250 50.000 23.44 0.00 44.29 3.55
2659 2822 0.438830 GAGCGTTTTCGGCACTAGTG 59.561 55.000 18.93 18.93 44.29 2.74
2660 2823 0.317479 AGAGCGTTTTCGGCACTAGT 59.683 50.000 0.00 0.00 44.29 2.57
2661 2824 1.429463 AAGAGCGTTTTCGGCACTAG 58.571 50.000 0.00 0.00 44.29 2.57
2662 2825 2.728690 TAAGAGCGTTTTCGGCACTA 57.271 45.000 0.00 0.00 44.29 2.74
2663 2826 2.094762 ATAAGAGCGTTTTCGGCACT 57.905 45.000 0.00 0.00 44.29 4.40
2664 2827 4.531659 AATATAAGAGCGTTTTCGGCAC 57.468 40.909 0.00 0.00 44.29 5.01
2665 2828 5.178623 CCATAATATAAGAGCGTTTTCGGCA 59.821 40.000 0.00 0.00 44.29 5.69
2666 2829 5.390567 CCCATAATATAAGAGCGTTTTCGGC 60.391 44.000 0.00 0.00 44.29 5.54
2667 2830 5.929992 TCCCATAATATAAGAGCGTTTTCGG 59.070 40.000 0.00 0.00 44.29 4.30
2669 2832 6.128634 CCGTCCCATAATATAAGAGCGTTTTC 60.129 42.308 0.00 0.00 0.00 2.29
2670 2833 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
2671 2834 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
2672 2835 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
2673 2836 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
2674 2837 4.713824 TCCGTCCCATAATATAAGAGCG 57.286 45.455 0.00 0.00 0.00 5.03
2675 2838 6.282199 TCTTCCGTCCCATAATATAAGAGC 57.718 41.667 0.00 0.00 0.00 4.09
2676 2839 7.897864 ACTTCTTCCGTCCCATAATATAAGAG 58.102 38.462 0.00 0.00 0.00 2.85
2677 2840 7.850935 ACTTCTTCCGTCCCATAATATAAGA 57.149 36.000 0.00 0.00 0.00 2.10
2681 2844 8.204836 GCATATACTTCTTCCGTCCCATAATAT 58.795 37.037 0.00 0.00 0.00 1.28
2682 2845 7.399191 AGCATATACTTCTTCCGTCCCATAATA 59.601 37.037 0.00 0.00 0.00 0.98
2683 2846 6.213600 AGCATATACTTCTTCCGTCCCATAAT 59.786 38.462 0.00 0.00 0.00 1.28
2684 2847 5.542635 AGCATATACTTCTTCCGTCCCATAA 59.457 40.000 0.00 0.00 0.00 1.90
2685 2848 5.084519 AGCATATACTTCTTCCGTCCCATA 58.915 41.667 0.00 0.00 0.00 2.74
2686 2849 3.904339 AGCATATACTTCTTCCGTCCCAT 59.096 43.478 0.00 0.00 0.00 4.00
2687 2850 3.305720 AGCATATACTTCTTCCGTCCCA 58.694 45.455 0.00 0.00 0.00 4.37
2688 2851 5.464030 TTAGCATATACTTCTTCCGTCCC 57.536 43.478 0.00 0.00 0.00 4.46
2689 2852 5.348997 GCATTAGCATATACTTCTTCCGTCC 59.651 44.000 0.00 0.00 41.58 4.79
2690 2853 6.396459 GCATTAGCATATACTTCTTCCGTC 57.604 41.667 0.00 0.00 41.58 4.79
2715 2878 8.501580 GTTCAAAACTAGAAACCACAGTATACC 58.498 37.037 0.00 0.00 0.00 2.73
2738 2901 5.510323 CGTAGAACCAACTTTGTTGTTGTTC 59.490 40.000 16.97 16.97 44.01 3.18
2791 2954 5.466819 TCTACTTGACCGTCAGTATGTTTG 58.533 41.667 0.64 0.00 37.40 2.93
2803 2966 6.018262 TCACAATTGAACTTTCTACTTGACCG 60.018 38.462 13.59 0.00 0.00 4.79
2893 3056 4.685924 AGTTTTGGTGCTTCTTGTCATTG 58.314 39.130 0.00 0.00 0.00 2.82
2898 3061 4.535526 ACAAAGTTTTGGTGCTTCTTGT 57.464 36.364 9.22 0.00 42.34 3.16
2899 3062 5.650543 AGTACAAAGTTTTGGTGCTTCTTG 58.349 37.500 9.22 0.00 42.34 3.02
2933 3096 7.795482 TCTTTCCTCGAAATGTAAAGACAAA 57.205 32.000 0.00 0.00 39.59 2.83
2985 3148 3.176708 ACACTTGACACACGCGTATATC 58.823 45.455 13.44 10.25 0.00 1.63
2990 3153 1.202325 TCTAACACTTGACACACGCGT 60.202 47.619 5.58 5.58 0.00 6.01
2992 3155 3.120792 TCTTCTAACACTTGACACACGC 58.879 45.455 0.00 0.00 0.00 5.34
3190 3359 4.320164 GCCGATTGATGTATCTAACGTACG 59.680 45.833 15.01 15.01 0.00 3.67
3241 3410 2.095718 AGCAGCGTTTTCTTTCCGAATC 60.096 45.455 0.00 0.00 0.00 2.52
3397 3566 7.712639 AGAAATTGTGCTGTGATACGAGATTAT 59.287 33.333 0.00 0.00 0.00 1.28
3444 3613 1.144969 TGTTCGGTTCGAGCATGTTC 58.855 50.000 0.53 0.00 41.62 3.18
3549 3718 3.204306 TCATCTCCCTGCATTCATCAC 57.796 47.619 0.00 0.00 0.00 3.06
3690 3859 6.766944 ACAATTCTGATGTCAAATTGCCAAAA 59.233 30.769 19.13 0.00 41.76 2.44
3896 4065 4.344359 TTTGTGCACCTGTGATGTAGTA 57.656 40.909 15.69 0.00 0.00 1.82
3897 4066 2.928801 TTGTGCACCTGTGATGTAGT 57.071 45.000 15.69 0.00 0.00 2.73
3898 4067 5.163723 CCTTATTTGTGCACCTGTGATGTAG 60.164 44.000 15.69 0.36 0.00 2.74
4054 4223 4.511617 TCAGCCGCTCTATTCTGAATAG 57.488 45.455 24.84 24.84 41.77 1.73
4063 4232 1.542108 GCCAATCTTCAGCCGCTCTAT 60.542 52.381 0.00 0.00 0.00 1.98
4157 4326 1.716826 GAGATGCAGCAGCTTGCCTC 61.717 60.000 15.84 7.62 46.52 4.70
4191 4360 1.004560 CTGCAGCTCCGGTTTCAGA 60.005 57.895 0.00 0.00 0.00 3.27
4201 4370 2.031163 ACCAACCGACTGCAGCTC 59.969 61.111 15.27 9.81 0.00 4.09
4545 4718 1.215382 CATTGGACGCCTGTCGAGA 59.785 57.895 0.00 0.00 46.49 4.04
4578 4751 0.675837 TGAGCAGCTGCAGATTCCAC 60.676 55.000 38.24 18.44 45.16 4.02
4605 4778 4.117685 CTGGCCACTTAATTACCGAGTAC 58.882 47.826 0.00 0.00 0.00 2.73
4670 4843 3.144506 GCAAGCTGTAGCATATCCATGT 58.855 45.455 6.65 0.00 45.16 3.21
4899 5072 3.379372 ACCATCCAATTTCTGAAGATGCG 59.621 43.478 10.31 7.53 34.35 4.73
4914 5087 0.396435 GCATCCCATACGACCATCCA 59.604 55.000 0.00 0.00 0.00 3.41
4928 5101 4.083802 GGATTCGCTACAGTAAATGCATCC 60.084 45.833 0.00 0.00 0.00 3.51
4929 5102 4.376413 CGGATTCGCTACAGTAAATGCATC 60.376 45.833 0.00 0.00 0.00 3.91
4972 5145 9.587772 AGGTTTCGATATATATGCATCAGTAAC 57.412 33.333 0.19 0.00 0.00 2.50
4973 5146 9.586435 CAGGTTTCGATATATATGCATCAGTAA 57.414 33.333 0.19 0.00 0.00 2.24
4974 5147 7.706607 GCAGGTTTCGATATATATGCATCAGTA 59.293 37.037 0.19 0.00 32.79 2.74
4975 5148 6.536582 GCAGGTTTCGATATATATGCATCAGT 59.463 38.462 0.19 0.00 32.79 3.41
4976 5149 6.760298 AGCAGGTTTCGATATATATGCATCAG 59.240 38.462 0.19 0.00 34.93 2.90
4977 5150 6.643388 AGCAGGTTTCGATATATATGCATCA 58.357 36.000 0.19 0.00 34.93 3.07
4978 5151 7.065085 ACAAGCAGGTTTCGATATATATGCATC 59.935 37.037 0.19 0.00 34.93 3.91
4979 5152 6.881065 ACAAGCAGGTTTCGATATATATGCAT 59.119 34.615 3.79 3.79 34.93 3.96
4980 5153 6.147656 CACAAGCAGGTTTCGATATATATGCA 59.852 38.462 0.00 0.00 34.93 3.96
4981 5154 6.147821 ACACAAGCAGGTTTCGATATATATGC 59.852 38.462 0.00 0.00 0.00 3.14
4982 5155 7.658179 ACACAAGCAGGTTTCGATATATATG 57.342 36.000 0.00 0.00 0.00 1.78
4983 5156 8.677148 AAACACAAGCAGGTTTCGATATATAT 57.323 30.769 0.00 0.00 32.00 0.86
4984 5157 8.138365 GAAACACAAGCAGGTTTCGATATATA 57.862 34.615 0.00 0.00 42.17 0.86
4985 5158 7.016361 GAAACACAAGCAGGTTTCGATATAT 57.984 36.000 0.00 0.00 42.17 0.86
4986 5159 6.417191 GAAACACAAGCAGGTTTCGATATA 57.583 37.500 0.00 0.00 42.17 0.86
4987 5160 5.296813 GAAACACAAGCAGGTTTCGATAT 57.703 39.130 0.00 0.00 42.17 1.63
4988 5161 4.742438 GAAACACAAGCAGGTTTCGATA 57.258 40.909 0.00 0.00 42.17 2.92
4989 5162 3.626028 GAAACACAAGCAGGTTTCGAT 57.374 42.857 0.00 0.00 42.17 3.59
4993 5166 1.136891 GCTGGAAACACAAGCAGGTTT 59.863 47.619 0.00 0.00 39.74 3.27
5052 5225 0.550147 TCCCTTTCCCCCAGAGGAAG 60.550 60.000 0.00 0.00 46.44 3.46
5136 5309 1.915614 GCACGCTGTCCAGTCCATTG 61.916 60.000 0.00 0.00 0.00 2.82
5142 5315 3.106986 AACCTGCACGCTGTCCAGT 62.107 57.895 0.00 0.00 0.00 4.00
5232 5405 2.071540 CTTTCATCTGTCTTCTGCGCA 58.928 47.619 10.98 10.98 0.00 6.09
5242 5415 6.537355 TCTTGATTTGACTCCTTTCATCTGT 58.463 36.000 0.00 0.00 0.00 3.41
5449 5695 4.062490 AGAGCCTAGAGGAACCTGTAAA 57.938 45.455 0.00 0.00 37.39 2.01
5450 5696 3.759815 AGAGCCTAGAGGAACCTGTAA 57.240 47.619 0.00 0.00 37.39 2.41
5452 5698 2.688515 GCTAGAGCCTAGAGGAACCTGT 60.689 54.545 11.96 0.00 37.39 4.00
5482 5728 1.508256 CCCTTCTTACCTAGTGGGGG 58.492 60.000 0.00 0.00 40.03 5.40
5483 5729 1.508256 CCCCTTCTTACCTAGTGGGG 58.492 60.000 0.00 0.00 45.34 4.96
5484 5730 1.274242 ACCCCCTTCTTACCTAGTGGG 60.274 57.143 0.00 0.00 37.98 4.61
5485 5731 1.838077 CACCCCCTTCTTACCTAGTGG 59.162 57.143 0.00 0.00 39.83 4.00
5486 5732 2.547990 ACACCCCCTTCTTACCTAGTG 58.452 52.381 0.00 0.00 0.00 2.74
5487 5733 3.599698 TCTACACCCCCTTCTTACCTAGT 59.400 47.826 0.00 0.00 0.00 2.57
5488 5734 4.216708 CTCTACACCCCCTTCTTACCTAG 58.783 52.174 0.00 0.00 0.00 3.02
5489 5735 3.052338 CCTCTACACCCCCTTCTTACCTA 60.052 52.174 0.00 0.00 0.00 3.08
5490 5736 2.292984 CCTCTACACCCCCTTCTTACCT 60.293 54.545 0.00 0.00 0.00 3.08
5491 5737 2.117051 CCTCTACACCCCCTTCTTACC 58.883 57.143 0.00 0.00 0.00 2.85
5492 5738 2.117051 CCCTCTACACCCCCTTCTTAC 58.883 57.143 0.00 0.00 0.00 2.34
5493 5739 1.624391 GCCCTCTACACCCCCTTCTTA 60.624 57.143 0.00 0.00 0.00 2.10
5494 5740 0.914902 GCCCTCTACACCCCCTTCTT 60.915 60.000 0.00 0.00 0.00 2.52
5495 5741 1.307084 GCCCTCTACACCCCCTTCT 60.307 63.158 0.00 0.00 0.00 2.85
5496 5742 1.615424 TGCCCTCTACACCCCCTTC 60.615 63.158 0.00 0.00 0.00 3.46
5497 5743 1.923909 GTGCCCTCTACACCCCCTT 60.924 63.158 0.00 0.00 31.67 3.95
5498 5744 1.524720 TAGTGCCCTCTACACCCCCT 61.525 60.000 0.00 0.00 38.87 4.79
5499 5745 0.400093 ATAGTGCCCTCTACACCCCC 60.400 60.000 0.00 0.00 38.87 5.40
5500 5746 0.759346 CATAGTGCCCTCTACACCCC 59.241 60.000 0.00 0.00 38.87 4.95
5501 5747 0.759346 CCATAGTGCCCTCTACACCC 59.241 60.000 0.00 0.00 38.87 4.61
5502 5748 1.413077 GTCCATAGTGCCCTCTACACC 59.587 57.143 0.00 0.00 38.87 4.16
5503 5749 2.389715 AGTCCATAGTGCCCTCTACAC 58.610 52.381 0.00 0.00 38.35 2.90
5504 5750 2.848678 AGTCCATAGTGCCCTCTACA 57.151 50.000 0.00 0.00 0.00 2.74
5505 5751 3.834938 ACTAGTCCATAGTGCCCTCTAC 58.165 50.000 0.00 0.00 43.35 2.59
5506 5752 4.664064 ACTACTAGTCCATAGTGCCCTCTA 59.336 45.833 0.00 0.00 44.69 2.43
5507 5753 3.464080 ACTACTAGTCCATAGTGCCCTCT 59.536 47.826 0.00 0.00 44.69 3.69
5508 5754 3.834938 ACTACTAGTCCATAGTGCCCTC 58.165 50.000 0.00 0.00 44.69 4.30
5509 5755 3.975479 ACTACTAGTCCATAGTGCCCT 57.025 47.619 0.00 0.00 44.69 5.19
5510 5756 5.354842 AAAACTACTAGTCCATAGTGCCC 57.645 43.478 0.00 0.00 44.69 5.36
5534 6123 4.819630 CACCAACCAAACTACTCTTTGCTA 59.180 41.667 0.00 0.00 30.87 3.49
5642 7120 1.225704 GGGCATAGCACTCCAAGCT 59.774 57.895 0.00 0.00 45.77 3.74
5648 7127 3.610911 ACAAAACTAGGGCATAGCACTC 58.389 45.455 6.03 0.00 38.16 3.51
5660 10549 4.120589 GCCTAATCGGGAGACAAAACTAG 58.879 47.826 0.00 0.00 44.82 2.57
5704 10628 6.995511 AAATTATGAAGTACTTAGCGCCAA 57.004 33.333 8.42 0.00 0.00 4.52
5809 10733 2.186160 TGCCTGGAACGTGCAACTG 61.186 57.895 0.00 0.00 30.85 3.16
5849 10778 2.036217 AGTTCGGTTTGTGTCGATACCA 59.964 45.455 10.00 0.00 35.25 3.25
5855 10784 0.788391 GGCTAGTTCGGTTTGTGTCG 59.212 55.000 0.00 0.00 0.00 4.35
5878 10807 0.591659 GGAGTTGGGCGTGAAAACTC 59.408 55.000 6.29 6.29 45.87 3.01
5880 10809 0.310854 CAGGAGTTGGGCGTGAAAAC 59.689 55.000 0.00 0.00 0.00 2.43
5881 10810 1.452145 GCAGGAGTTGGGCGTGAAAA 61.452 55.000 0.00 0.00 0.00 2.29
5905 10859 2.203728 ACGAGGTGGCCTGTGGTA 60.204 61.111 3.32 0.00 31.76 3.25
5978 10932 2.286654 GGTACTCGACGAAATACCCTCG 60.287 54.545 20.20 1.10 42.06 4.63
6041 10995 2.034066 ACATGAGGCAACACCCCG 59.966 61.111 0.00 0.00 40.58 5.73
6053 11007 2.595386 CGTGTTCATCTGACGACATGA 58.405 47.619 0.00 0.00 35.05 3.07
6092 11046 0.324552 CCCATCATGGAGCCCAAACA 60.325 55.000 4.75 0.00 40.96 2.83
6096 11050 0.103983 TATCCCCATCATGGAGCCCA 60.104 55.000 4.75 0.00 40.96 5.36


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

AutoCloner maintained by Alex Coulton.