Multiple sequence alignment - TraesCS3A01G111600

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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 TraesCS3A01G111600 chr3A 100.000 3660 0 0 1 3660 79234095 79237754 0.000000e+00 6759.0
1 TraesCS3A01G111600 chr3A 84.540 1326 158 23 1619 2931 79265266 79266557 0.000000e+00 1269.0
2 TraesCS3A01G111600 chr3A 83.407 1133 158 12 1675 2799 79295033 79296143 0.000000e+00 1024.0
3 TraesCS3A01G111600 chr3A 83.868 998 144 11 1570 2552 79296766 79297761 0.000000e+00 935.0
4 TraesCS3A01G111600 chr3A 87.660 235 23 3 665 898 79192446 79192675 6.020000e-68 268.0
5 TraesCS3A01G111600 chr3A 97.619 42 1 0 657 698 79201808 79201849 5.070000e-09 73.1
6 TraesCS3A01G111600 chr3B 93.032 2282 141 9 657 2933 114726908 114724640 0.000000e+00 3317.0
7 TraesCS3A01G111600 chr3D 91.001 2267 127 29 657 2885 67632106 67629879 0.000000e+00 2985.0
8 TraesCS3A01G111600 chr3D 90.970 299 26 1 369 666 610423792 610424090 5.690000e-108 401.0
9 TraesCS3A01G111600 chr3D 91.696 289 22 1 369 657 576887134 576887420 2.050000e-107 399.0
10 TraesCS3A01G111600 chr3D 88.217 314 33 2 67 376 559108839 559109152 4.460000e-99 372.0
11 TraesCS3A01G111600 chr3D 74.831 592 124 15 1163 1749 606941039 606941610 1.020000e-60 244.0
12 TraesCS3A01G111600 chr5A 94.158 736 36 5 2930 3660 333432880 333432147 0.000000e+00 1114.0
13 TraesCS3A01G111600 chr5A 92.360 733 49 5 2931 3660 354967621 354968349 0.000000e+00 1037.0
14 TraesCS3A01G111600 chr5A 89.229 752 59 11 2929 3660 14248865 14249614 0.000000e+00 920.0
15 TraesCS3A01G111600 chr5A 89.160 738 48 15 2933 3644 708612653 708613384 0.000000e+00 891.0
16 TraesCS3A01G111600 chr5A 73.525 1492 307 70 1144 2609 706653370 706654799 1.530000e-133 486.0
17 TraesCS3A01G111600 chr7A 92.982 741 39 6 2931 3660 686140524 686141262 0.000000e+00 1068.0
18 TraesCS3A01G111600 chr7A 91.007 745 50 5 2933 3660 77166682 77165938 0.000000e+00 989.0
19 TraesCS3A01G111600 chr7A 78.098 694 124 19 1108 1793 81548325 81548998 7.310000e-112 414.0
20 TraesCS3A01G111600 chr7A 77.557 704 128 20 1073 1770 518658761 518658082 7.360000e-107 398.0
21 TraesCS3A01G111600 chr2A 92.120 736 49 4 2929 3656 125394014 125393280 0.000000e+00 1029.0
22 TraesCS3A01G111600 chr2A 91.973 735 33 10 2933 3660 93983665 93982950 0.000000e+00 1007.0
23 TraesCS3A01G111600 chr2A 91.644 730 45 9 2933 3660 112736035 112735320 0.000000e+00 996.0
24 TraesCS3A01G111600 chr2A 89.315 730 54 8 2933 3660 161629016 161628309 0.000000e+00 894.0
25 TraesCS3A01G111600 chr2A 88.889 747 43 9 2933 3660 699871236 699871961 0.000000e+00 883.0
26 TraesCS3A01G111600 chr2A 85.805 627 58 11 2929 3539 262129417 262130028 1.430000e-178 636.0
27 TraesCS3A01G111600 chr2A 84.641 612 69 12 2933 3539 709102209 709101618 1.460000e-163 586.0
28 TraesCS3A01G111600 chr2A 90.268 298 29 0 369 666 44796918 44797215 1.230000e-104 390.0
29 TraesCS3A01G111600 chr2A 77.233 694 139 18 1122 1807 753106080 753105398 4.430000e-104 388.0
30 TraesCS3A01G111600 chr2A 76.070 631 126 21 1157 1770 72814041 72813419 4.590000e-79 305.0
31 TraesCS3A01G111600 chr7B 73.351 1501 315 60 1121 2598 502316819 502318257 9.200000e-131 477.0
32 TraesCS3A01G111600 chr7B 78.039 724 131 17 1075 1793 502733977 502734677 7.260000e-117 431.0
33 TraesCS3A01G111600 chr7B 91.379 290 23 2 369 656 42844005 42843716 2.650000e-106 396.0
34 TraesCS3A01G111600 chr7B 77.191 719 129 24 1086 1794 25339230 25339923 1.590000e-103 387.0
35 TraesCS3A01G111600 chr7B 76.197 710 141 18 1089 1793 501965735 501966421 2.090000e-92 350.0
36 TraesCS3A01G111600 chr7D 73.108 1506 310 66 1121 2598 477659317 477660755 2.000000e-122 449.0
37 TraesCS3A01G111600 chr7D 77.986 695 127 18 1071 1761 477855621 477856293 2.630000e-111 412.0
38 TraesCS3A01G111600 chr7D 77.545 717 130 21 1086 1794 78115554 78116247 1.580000e-108 403.0
39 TraesCS3A01G111600 chr7D 91.696 289 22 2 369 656 375970183 375970470 2.050000e-107 399.0
40 TraesCS3A01G111600 chr7D 77.098 703 133 18 1073 1770 477641700 477642379 7.420000e-102 381.0
41 TraesCS3A01G111600 chr7D 76.602 671 125 22 1106 1769 509533789 509533144 1.260000e-89 340.0
42 TraesCS3A01G111600 chr7D 76.855 337 65 9 2272 2606 477856789 477857114 1.040000e-40 178.0
43 TraesCS3A01G111600 chr4B 73.002 1489 319 59 1144 2609 667426685 667428113 2.590000e-121 446.0
44 TraesCS3A01G111600 chr4B 72.375 1495 332 57 1148 2609 649353971 649355417 7.360000e-107 398.0
45 TraesCS3A01G111600 chr4B 88.217 314 33 2 67 376 59190421 59190108 4.460000e-99 372.0
46 TraesCS3A01G111600 chr2B 77.437 749 134 26 1075 1807 762118313 762117584 7.310000e-112 414.0
47 TraesCS3A01G111600 chr2B 87.812 320 33 4 61 376 757569453 757569770 1.610000e-98 370.0
48 TraesCS3A01G111600 chr2B 75.829 633 124 21 1157 1770 111081821 111081199 9.940000e-76 294.0
49 TraesCS3A01G111600 chr4D 91.497 294 23 1 365 656 107712728 107712435 1.580000e-108 403.0
50 TraesCS3A01G111600 chr4D 91.438 292 22 3 367 656 8274710 8274420 7.360000e-107 398.0
51 TraesCS3A01G111600 chr4D 88.746 311 28 3 73 376 8275061 8274751 1.240000e-99 374.0
52 TraesCS3A01G111600 chr4D 77.596 366 67 12 2272 2632 78780843 78781198 1.330000e-49 207.0
53 TraesCS3A01G111600 chr5D 91.667 288 24 0 369 656 129239218 129239505 2.050000e-107 399.0
54 TraesCS3A01G111600 chr5D 77.160 683 128 22 1123 1797 371862167 371862829 4.460000e-99 372.0
55 TraesCS3A01G111600 chr5D 77.617 554 91 22 1255 1793 406351717 406351182 4.590000e-79 305.0
56 TraesCS3A01G111600 chr2D 91.667 288 23 1 369 656 617082554 617082840 7.360000e-107 398.0
57 TraesCS3A01G111600 chr2D 88.636 308 31 2 73 376 617082204 617082511 4.460000e-99 372.0
58 TraesCS3A01G111600 chr1D 88.535 314 32 2 67 376 402837828 402838141 9.590000e-101 377.0
59 TraesCS3A01G111600 chr1A 88.636 308 31 3 73 376 40891727 40891420 4.460000e-99 372.0
60 TraesCS3A01G111600 chr1A 74.349 499 98 20 1278 1761 579172247 579172730 6.240000e-43 185.0
61 TraesCS3A01G111600 chr4A 87.898 314 34 2 67 376 702119033 702119346 2.080000e-97 366.0
62 TraesCS3A01G111600 chr4A 87.937 315 33 3 67 376 725941790 725942104 2.080000e-97 366.0
63 TraesCS3A01G111600 chr4A 77.657 367 65 13 2272 2632 507593778 507594133 1.330000e-49 207.0
64 TraesCS3A01G111600 chr1B 74.297 498 100 16 1278 1761 671259106 671259589 6.240000e-43 185.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G111600 chr3A 79234095 79237754 3659 False 6759.0 6759 100.0000 1 3660 1 chr3A.!!$F3 3659
1 TraesCS3A01G111600 chr3A 79265266 79266557 1291 False 1269.0 1269 84.5400 1619 2931 1 chr3A.!!$F4 1312
2 TraesCS3A01G111600 chr3A 79295033 79297761 2728 False 979.5 1024 83.6375 1570 2799 2 chr3A.!!$F5 1229
3 TraesCS3A01G111600 chr3B 114724640 114726908 2268 True 3317.0 3317 93.0320 657 2933 1 chr3B.!!$R1 2276
4 TraesCS3A01G111600 chr3D 67629879 67632106 2227 True 2985.0 2985 91.0010 657 2885 1 chr3D.!!$R1 2228
5 TraesCS3A01G111600 chr3D 606941039 606941610 571 False 244.0 244 74.8310 1163 1749 1 chr3D.!!$F3 586
6 TraesCS3A01G111600 chr5A 333432147 333432880 733 True 1114.0 1114 94.1580 2930 3660 1 chr5A.!!$R1 730
7 TraesCS3A01G111600 chr5A 354967621 354968349 728 False 1037.0 1037 92.3600 2931 3660 1 chr5A.!!$F2 729
8 TraesCS3A01G111600 chr5A 14248865 14249614 749 False 920.0 920 89.2290 2929 3660 1 chr5A.!!$F1 731
9 TraesCS3A01G111600 chr5A 708612653 708613384 731 False 891.0 891 89.1600 2933 3644 1 chr5A.!!$F4 711
10 TraesCS3A01G111600 chr5A 706653370 706654799 1429 False 486.0 486 73.5250 1144 2609 1 chr5A.!!$F3 1465
11 TraesCS3A01G111600 chr7A 686140524 686141262 738 False 1068.0 1068 92.9820 2931 3660 1 chr7A.!!$F2 729
12 TraesCS3A01G111600 chr7A 77165938 77166682 744 True 989.0 989 91.0070 2933 3660 1 chr7A.!!$R1 727
13 TraesCS3A01G111600 chr7A 81548325 81548998 673 False 414.0 414 78.0980 1108 1793 1 chr7A.!!$F1 685
14 TraesCS3A01G111600 chr7A 518658082 518658761 679 True 398.0 398 77.5570 1073 1770 1 chr7A.!!$R2 697
15 TraesCS3A01G111600 chr2A 125393280 125394014 734 True 1029.0 1029 92.1200 2929 3656 1 chr2A.!!$R4 727
16 TraesCS3A01G111600 chr2A 93982950 93983665 715 True 1007.0 1007 91.9730 2933 3660 1 chr2A.!!$R2 727
17 TraesCS3A01G111600 chr2A 112735320 112736035 715 True 996.0 996 91.6440 2933 3660 1 chr2A.!!$R3 727
18 TraesCS3A01G111600 chr2A 161628309 161629016 707 True 894.0 894 89.3150 2933 3660 1 chr2A.!!$R5 727
19 TraesCS3A01G111600 chr2A 699871236 699871961 725 False 883.0 883 88.8890 2933 3660 1 chr2A.!!$F3 727
20 TraesCS3A01G111600 chr2A 262129417 262130028 611 False 636.0 636 85.8050 2929 3539 1 chr2A.!!$F2 610
21 TraesCS3A01G111600 chr2A 709101618 709102209 591 True 586.0 586 84.6410 2933 3539 1 chr2A.!!$R6 606
22 TraesCS3A01G111600 chr2A 753105398 753106080 682 True 388.0 388 77.2330 1122 1807 1 chr2A.!!$R7 685
23 TraesCS3A01G111600 chr2A 72813419 72814041 622 True 305.0 305 76.0700 1157 1770 1 chr2A.!!$R1 613
24 TraesCS3A01G111600 chr7B 502316819 502318257 1438 False 477.0 477 73.3510 1121 2598 1 chr7B.!!$F3 1477
25 TraesCS3A01G111600 chr7B 502733977 502734677 700 False 431.0 431 78.0390 1075 1793 1 chr7B.!!$F4 718
26 TraesCS3A01G111600 chr7B 25339230 25339923 693 False 387.0 387 77.1910 1086 1794 1 chr7B.!!$F1 708
27 TraesCS3A01G111600 chr7B 501965735 501966421 686 False 350.0 350 76.1970 1089 1793 1 chr7B.!!$F2 704
28 TraesCS3A01G111600 chr7D 477659317 477660755 1438 False 449.0 449 73.1080 1121 2598 1 chr7D.!!$F4 1477
29 TraesCS3A01G111600 chr7D 78115554 78116247 693 False 403.0 403 77.5450 1086 1794 1 chr7D.!!$F1 708
30 TraesCS3A01G111600 chr7D 477641700 477642379 679 False 381.0 381 77.0980 1073 1770 1 chr7D.!!$F3 697
31 TraesCS3A01G111600 chr7D 509533144 509533789 645 True 340.0 340 76.6020 1106 1769 1 chr7D.!!$R1 663
32 TraesCS3A01G111600 chr7D 477855621 477857114 1493 False 295.0 412 77.4205 1071 2606 2 chr7D.!!$F5 1535
33 TraesCS3A01G111600 chr4B 667426685 667428113 1428 False 446.0 446 73.0020 1144 2609 1 chr4B.!!$F2 1465
34 TraesCS3A01G111600 chr4B 649353971 649355417 1446 False 398.0 398 72.3750 1148 2609 1 chr4B.!!$F1 1461
35 TraesCS3A01G111600 chr2B 762117584 762118313 729 True 414.0 414 77.4370 1075 1807 1 chr2B.!!$R2 732
36 TraesCS3A01G111600 chr2B 111081199 111081821 622 True 294.0 294 75.8290 1157 1770 1 chr2B.!!$R1 613
37 TraesCS3A01G111600 chr4D 8274420 8275061 641 True 386.0 398 90.0920 73 656 2 chr4D.!!$R2 583
38 TraesCS3A01G111600 chr5D 371862167 371862829 662 False 372.0 372 77.1600 1123 1797 1 chr5D.!!$F2 674
39 TraesCS3A01G111600 chr5D 406351182 406351717 535 True 305.0 305 77.6170 1255 1793 1 chr5D.!!$R1 538
40 TraesCS3A01G111600 chr2D 617082204 617082840 636 False 385.0 398 90.1515 73 656 2 chr2D.!!$F1 583

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
22 23 0.027455 CTGTTCGCACAAAACGCTCA 59.973 50.0 0.0 0.0 30.36 4.26 F
52 53 0.102844 CAACAACAGCCACAACCCAG 59.897 55.0 0.0 0.0 0.00 4.45 F
261 269 0.250513 GTTCAGGAAGGCGAGATGGT 59.749 55.0 0.0 0.0 0.00 3.55 F
1932 2076 0.393077 CAACACCGTCTTCCAGACCT 59.607 55.0 0.0 0.0 42.12 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1003 1076 0.878416 TAATTTGCTCGGTGTGGTGC 59.122 50.000 0.0 0.0 0.00 5.01 R
1443 1561 1.380650 AGGCCTCCTCGTCCTTCTC 60.381 63.158 0.0 0.0 0.00 2.87 R
2177 2328 0.617820 ACAGGTGCTCCCGGTAGATT 60.618 55.000 0.0 0.0 40.14 2.40 R
3482 4669 0.106819 GAGTACGAGGAGGTAGCCCA 60.107 60.000 0.0 0.0 0.00 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
18 19 3.437845 CTCCTGTTCGCACAAAACG 57.562 52.632 0.00 0.00 30.36 3.60
19 20 0.657368 CTCCTGTTCGCACAAAACGC 60.657 55.000 0.00 0.00 30.36 4.84
20 21 1.092921 TCCTGTTCGCACAAAACGCT 61.093 50.000 0.00 0.00 30.36 5.07
21 22 0.657368 CCTGTTCGCACAAAACGCTC 60.657 55.000 0.00 0.00 30.36 5.03
22 23 0.027455 CTGTTCGCACAAAACGCTCA 59.973 50.000 0.00 0.00 30.36 4.26
23 24 0.660488 TGTTCGCACAAAACGCTCAT 59.340 45.000 0.00 0.00 0.00 2.90
24 25 1.044725 GTTCGCACAAAACGCTCATG 58.955 50.000 0.00 0.00 0.00 3.07
25 26 0.660488 TTCGCACAAAACGCTCATGT 59.340 45.000 0.00 0.00 0.00 3.21
26 27 0.660488 TCGCACAAAACGCTCATGTT 59.340 45.000 0.00 0.00 0.00 2.71
27 28 1.064803 TCGCACAAAACGCTCATGTTT 59.935 42.857 0.00 0.00 43.60 2.83
28 29 2.288186 TCGCACAAAACGCTCATGTTTA 59.712 40.909 0.00 0.00 41.01 2.01
29 30 3.039405 CGCACAAAACGCTCATGTTTAA 58.961 40.909 0.00 0.00 41.01 1.52
30 31 3.483922 CGCACAAAACGCTCATGTTTAAA 59.516 39.130 0.00 0.00 41.01 1.52
31 32 4.148000 CGCACAAAACGCTCATGTTTAAAT 59.852 37.500 0.00 0.00 41.01 1.40
32 33 5.598783 GCACAAAACGCTCATGTTTAAATC 58.401 37.500 0.00 0.00 41.01 2.17
33 34 5.388371 GCACAAAACGCTCATGTTTAAATCC 60.388 40.000 0.00 0.00 41.01 3.01
34 35 5.689514 CACAAAACGCTCATGTTTAAATCCA 59.310 36.000 0.00 0.00 41.01 3.41
35 36 6.199908 CACAAAACGCTCATGTTTAAATCCAA 59.800 34.615 0.00 0.00 41.01 3.53
36 37 6.200097 ACAAAACGCTCATGTTTAAATCCAAC 59.800 34.615 0.00 0.00 41.01 3.77
37 38 5.446143 AACGCTCATGTTTAAATCCAACA 57.554 34.783 0.00 0.00 38.49 3.33
38 39 5.446143 ACGCTCATGTTTAAATCCAACAA 57.554 34.783 0.00 0.00 37.67 2.83
39 40 5.219633 ACGCTCATGTTTAAATCCAACAAC 58.780 37.500 0.00 0.00 37.67 3.32
40 41 5.218885 CGCTCATGTTTAAATCCAACAACA 58.781 37.500 0.00 0.00 37.67 3.33
41 42 5.343058 CGCTCATGTTTAAATCCAACAACAG 59.657 40.000 0.00 0.00 37.67 3.16
42 43 5.119125 GCTCATGTTTAAATCCAACAACAGC 59.881 40.000 0.00 0.00 37.67 4.40
43 44 5.537188 TCATGTTTAAATCCAACAACAGCC 58.463 37.500 0.00 0.00 37.67 4.85
44 45 5.069648 TCATGTTTAAATCCAACAACAGCCA 59.930 36.000 0.00 0.00 37.67 4.75
45 46 4.688021 TGTTTAAATCCAACAACAGCCAC 58.312 39.130 0.00 0.00 31.05 5.01
46 47 4.160439 TGTTTAAATCCAACAACAGCCACA 59.840 37.500 0.00 0.00 31.05 4.17
47 48 5.112686 GTTTAAATCCAACAACAGCCACAA 58.887 37.500 0.00 0.00 0.00 3.33
48 49 2.888834 AATCCAACAACAGCCACAAC 57.111 45.000 0.00 0.00 0.00 3.32
49 50 1.039856 ATCCAACAACAGCCACAACC 58.960 50.000 0.00 0.00 0.00 3.77
50 51 1.040339 TCCAACAACAGCCACAACCC 61.040 55.000 0.00 0.00 0.00 4.11
51 52 1.326213 CCAACAACAGCCACAACCCA 61.326 55.000 0.00 0.00 0.00 4.51
52 53 0.102844 CAACAACAGCCACAACCCAG 59.897 55.000 0.00 0.00 0.00 4.45
53 54 0.324275 AACAACAGCCACAACCCAGT 60.324 50.000 0.00 0.00 0.00 4.00
54 55 0.548989 ACAACAGCCACAACCCAGTA 59.451 50.000 0.00 0.00 0.00 2.74
55 56 1.238439 CAACAGCCACAACCCAGTAG 58.762 55.000 0.00 0.00 0.00 2.57
56 57 1.136828 AACAGCCACAACCCAGTAGA 58.863 50.000 0.00 0.00 0.00 2.59
57 58 1.362224 ACAGCCACAACCCAGTAGAT 58.638 50.000 0.00 0.00 0.00 1.98
58 59 2.546899 ACAGCCACAACCCAGTAGATA 58.453 47.619 0.00 0.00 0.00 1.98
59 60 3.115390 ACAGCCACAACCCAGTAGATAT 58.885 45.455 0.00 0.00 0.00 1.63
60 61 4.295201 ACAGCCACAACCCAGTAGATATA 58.705 43.478 0.00 0.00 0.00 0.86
61 62 4.907875 ACAGCCACAACCCAGTAGATATAT 59.092 41.667 0.00 0.00 0.00 0.86
62 63 5.012148 ACAGCCACAACCCAGTAGATATATC 59.988 44.000 4.42 4.42 0.00 1.63
63 64 5.247110 CAGCCACAACCCAGTAGATATATCT 59.753 44.000 18.99 18.99 40.86 1.98
64 65 6.437477 CAGCCACAACCCAGTAGATATATCTA 59.563 42.308 16.95 16.95 38.32 1.98
65 66 7.124901 CAGCCACAACCCAGTAGATATATCTAT 59.875 40.741 22.34 10.92 41.09 1.98
66 67 7.343316 AGCCACAACCCAGTAGATATATCTATC 59.657 40.741 22.34 16.16 41.09 2.08
67 68 7.343316 GCCACAACCCAGTAGATATATCTATCT 59.657 40.741 22.34 17.72 44.94 1.98
68 69 8.908903 CCACAACCCAGTAGATATATCTATCTC 58.091 40.741 22.34 11.86 42.51 2.75
69 70 8.908903 CACAACCCAGTAGATATATCTATCTCC 58.091 40.741 22.34 11.55 42.51 3.71
70 71 8.851876 ACAACCCAGTAGATATATCTATCTCCT 58.148 37.037 22.34 13.34 42.51 3.69
71 72 9.707957 CAACCCAGTAGATATATCTATCTCCTT 57.292 37.037 22.34 10.81 42.51 3.36
83 84 4.845541 TCTATCTCCTTCTCCTCCTCCTA 58.154 47.826 0.00 0.00 0.00 2.94
144 145 2.752238 CAGGTCCGCCTCGTCTCT 60.752 66.667 0.00 0.00 44.97 3.10
148 149 1.748122 GTCCGCCTCGTCTCTGGTA 60.748 63.158 0.00 0.00 0.00 3.25
154 162 1.479021 GCCTCGTCTCTGGTATAGGGT 60.479 57.143 0.00 0.00 0.00 4.34
166 174 0.471022 TATAGGGTCATGGAGGCGCA 60.471 55.000 10.83 0.00 37.23 6.09
175 183 3.785859 GGAGGCGCAGTGGATCCA 61.786 66.667 11.44 11.44 0.00 3.41
183 191 1.993653 CAGTGGATCCAGGCAAGGA 59.006 57.895 16.81 0.99 43.01 3.36
185 193 0.548682 AGTGGATCCAGGCAAGGACT 60.549 55.000 16.81 2.67 41.30 3.85
212 220 5.419542 GGGAGGGCTTCATTTTTAATTGTC 58.580 41.667 0.00 0.00 0.00 3.18
213 221 5.419542 GGAGGGCTTCATTTTTAATTGTCC 58.580 41.667 0.00 0.00 0.00 4.02
218 226 7.998383 AGGGCTTCATTTTTAATTGTCCTTTTT 59.002 29.630 0.00 0.00 0.00 1.94
240 248 8.528044 TTTTAATCTTGTTAGGGTTTGTGTCT 57.472 30.769 0.00 0.00 0.00 3.41
242 250 6.391227 AATCTTGTTAGGGTTTGTGTCTTG 57.609 37.500 0.00 0.00 0.00 3.02
243 251 4.850680 TCTTGTTAGGGTTTGTGTCTTGT 58.149 39.130 0.00 0.00 0.00 3.16
258 266 1.902508 TCTTGTTCAGGAAGGCGAGAT 59.097 47.619 0.00 0.00 0.00 2.75
261 269 0.250513 GTTCAGGAAGGCGAGATGGT 59.749 55.000 0.00 0.00 0.00 3.55
265 273 2.268920 GAAGGCGAGATGGTGGCA 59.731 61.111 0.00 0.00 0.00 4.92
279 287 0.833287 GTGGCAGCTCCCTGAAGATA 59.167 55.000 0.00 0.00 41.77 1.98
288 296 5.700373 CAGCTCCCTGAAGATAGAATAAAGC 59.300 44.000 0.00 0.00 41.77 3.51
299 307 0.535328 GAATAAAGCTCTCCCCGCCC 60.535 60.000 0.00 0.00 0.00 6.13
361 369 4.436998 GGAGGTGTGTCTCCGGCG 62.437 72.222 0.00 0.00 43.19 6.46
432 490 1.903404 GGTTGCTGTTCTGGGGTGG 60.903 63.158 0.00 0.00 0.00 4.61
443 501 0.620410 CTGGGGTGGTGGTCCTATGA 60.620 60.000 0.00 0.00 34.23 2.15
446 504 0.620700 GGGTGGTGGTCCTATGAGGT 60.621 60.000 0.00 0.00 36.53 3.85
447 505 1.286248 GGTGGTGGTCCTATGAGGTT 58.714 55.000 0.00 0.00 36.53 3.50
467 525 2.203972 TTAGCACGACGACTTCCCGG 62.204 60.000 0.00 0.00 0.00 5.73
487 545 4.321452 CCGGCTGTCTACTACAACAAGTTA 60.321 45.833 0.00 0.00 37.74 2.24
494 552 3.688694 ACTACAACAAGTTATGCCCGA 57.311 42.857 0.00 0.00 0.00 5.14
499 557 0.981183 ACAAGTTATGCCCGACTCCA 59.019 50.000 0.00 0.00 0.00 3.86
501 559 1.066143 CAAGTTATGCCCGACTCCAGT 60.066 52.381 0.00 0.00 0.00 4.00
522 580 3.564218 GGAGGGGCGATGATGGCT 61.564 66.667 0.00 0.00 34.31 4.75
543 601 2.126463 CGTCTTCGGCTCGCTTCA 60.126 61.111 0.00 0.00 0.00 3.02
564 622 1.129998 GTGCTTGTAGTCGTCGCTAGA 59.870 52.381 0.00 0.00 0.00 2.43
572 630 3.128852 AGTCGTCGCTAGATGGTCTAT 57.871 47.619 0.00 0.00 34.23 1.98
636 694 7.390996 ACTGCCATGATTGAAGATGAATAGATC 59.609 37.037 0.00 0.00 0.00 2.75
646 704 8.425577 TGAAGATGAATAGATCGGAAGTTTTC 57.574 34.615 0.00 0.00 0.00 2.29
663 721 7.766738 GGAAGTTTTCCCAGAAAAACATGTTTA 59.233 33.333 23.53 3.95 46.68 2.01
666 724 8.973182 AGTTTTCCCAGAAAAACATGTTTAGTA 58.027 29.630 23.53 3.73 46.68 1.82
711 774 8.240883 AGTGATTCGTTAACTAGTTGACATTC 57.759 34.615 25.01 18.50 0.00 2.67
718 781 6.018588 CGTTAACTAGTTGACATTCACCACAA 60.019 38.462 25.01 3.45 0.00 3.33
741 806 8.450964 ACAAAATGTACTGTAGGAATCAAATCG 58.549 33.333 0.00 0.00 0.00 3.34
814 886 2.554032 GGGATGAAGGCCGTCATTAATG 59.446 50.000 31.00 9.29 38.38 1.90
878 950 1.833860 CGAGGAGACGAAGATCAAGC 58.166 55.000 0.00 0.00 35.09 4.01
879 951 1.833860 GAGGAGACGAAGATCAAGCG 58.166 55.000 0.00 0.00 0.00 4.68
885 957 1.921230 GACGAAGATCAAGCGAACTCC 59.079 52.381 8.53 0.00 0.00 3.85
900 972 3.600388 GAACTCCACAGGTCAACCATAG 58.400 50.000 1.33 0.00 36.21 2.23
901 973 1.279271 ACTCCACAGGTCAACCATAGC 59.721 52.381 1.33 0.00 38.89 2.97
934 1006 9.361315 CATTAGCAAAGTCAAATCATCATCAAA 57.639 29.630 0.00 0.00 0.00 2.69
957 1029 4.692625 ACTCATTATAAGCAGCATTAGCCG 59.307 41.667 0.00 0.00 43.56 5.52
961 1034 2.273449 AGCAGCATTAGCCGGCTT 59.727 55.556 37.74 16.15 46.02 4.35
990 1063 4.553323 CATAATAAGCTTGGCTGCCATTC 58.447 43.478 24.03 16.63 39.62 2.67
1001 1074 1.078918 TGCCATTCGCAGTCTCCAG 60.079 57.895 0.00 0.00 44.64 3.86
1003 1076 1.364626 GCCATTCGCAGTCTCCAGTG 61.365 60.000 0.00 0.00 37.47 3.66
1031 1122 2.233271 CCGAGCAAATTATCCATGGCT 58.767 47.619 6.96 0.00 0.00 4.75
1448 1566 3.459063 GTCCGTCCGGGGGAGAAG 61.459 72.222 14.51 0.00 33.31 2.85
1511 1647 1.011019 CGAGCTCTACTACGCCGTG 60.011 63.158 12.85 0.00 0.00 4.94
1863 2006 1.740296 AAATGGGAGACGTTCGCGG 60.740 57.895 6.13 0.00 46.45 6.46
1932 2076 0.393077 CAACACCGTCTTCCAGACCT 59.607 55.000 0.00 0.00 42.12 3.85
2030 2174 1.919600 GCAGGGAGATGAGCTGGGTT 61.920 60.000 0.00 0.00 0.00 4.11
2067 2217 4.504916 CCCTGAGCAGCTCCGACG 62.505 72.222 20.16 5.64 0.00 5.12
2096 2247 1.530771 CCTGGAGGGGATGCTGAAG 59.469 63.158 0.00 0.00 0.00 3.02
2177 2328 0.323725 GCAAGGCAGGATGGGAAAGA 60.324 55.000 0.00 0.00 35.86 2.52
2234 2385 0.399075 TGATGATCATGGAGCCGCAT 59.601 50.000 14.30 0.00 0.00 4.73
2312 2463 1.438651 GCGTGCTCTACAACATCCAA 58.561 50.000 0.00 0.00 0.00 3.53
2426 2595 2.531942 AACCCGAGGGAGGCCTTT 60.532 61.111 16.26 0.00 38.96 3.11
2469 2638 4.947147 GGCAGAACACGGTGGGCA 62.947 66.667 13.48 0.00 0.00 5.36
2637 2811 1.202313 CCTAGGCTACAACGAGTGAGC 60.202 57.143 0.00 0.00 32.66 4.26
2645 2819 0.784778 CAACGAGTGAGCGAACTTCC 59.215 55.000 0.00 0.00 34.83 3.46
2656 2830 4.340950 TGAGCGAACTTCCCAAAAGAAAAT 59.659 37.500 0.00 0.00 0.00 1.82
2684 2859 2.674796 AGTGATAACGAGTGAAGGCC 57.325 50.000 0.00 0.00 0.00 5.19
2688 2863 2.028839 TGATAACGAGTGAAGGCCGAAA 60.029 45.455 0.00 0.00 0.00 3.46
2868 3045 3.389221 CGTTGGATTGAAAACCAAAGGG 58.611 45.455 6.37 0.00 45.75 3.95
2887 3065 3.003763 GGCACCCCTCTCCTCGTT 61.004 66.667 0.00 0.00 0.00 3.85
2926 3106 6.386342 TCTTCATTCTTGAGATCTTCCTCCAT 59.614 38.462 0.00 0.00 32.27 3.41
3429 4616 3.822192 CCGGACCATCTCGTCGCA 61.822 66.667 0.00 0.00 33.30 5.10
3482 4669 2.185350 CGTCGGAGAAGCCATGCT 59.815 61.111 0.00 0.00 42.56 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.027455 TGAGCGTTTTGTGCGAACAG 59.973 50.000 0.00 0.00 37.44 3.16
5 6 1.044725 CATGAGCGTTTTGTGCGAAC 58.955 50.000 0.00 0.00 37.44 3.95
7 8 0.660488 AACATGAGCGTTTTGTGCGA 59.340 45.000 0.00 0.00 37.44 5.10
8 9 1.476074 AAACATGAGCGTTTTGTGCG 58.524 45.000 0.00 0.00 35.58 5.34
9 10 5.388371 GGATTTAAACATGAGCGTTTTGTGC 60.388 40.000 0.00 0.00 39.70 4.57
10 11 5.689514 TGGATTTAAACATGAGCGTTTTGTG 59.310 36.000 0.00 0.00 39.70 3.33
11 12 5.837437 TGGATTTAAACATGAGCGTTTTGT 58.163 33.333 0.00 0.00 39.70 2.83
12 13 6.199908 TGTTGGATTTAAACATGAGCGTTTTG 59.800 34.615 0.00 0.00 39.70 2.44
13 14 6.276847 TGTTGGATTTAAACATGAGCGTTTT 58.723 32.000 0.00 0.00 39.70 2.43
14 15 5.837437 TGTTGGATTTAAACATGAGCGTTT 58.163 33.333 0.00 0.00 41.78 3.60
15 16 5.446143 TGTTGGATTTAAACATGAGCGTT 57.554 34.783 0.00 0.00 32.71 4.84
16 17 5.219633 GTTGTTGGATTTAAACATGAGCGT 58.780 37.500 0.00 0.00 37.38 5.07
17 18 5.218885 TGTTGTTGGATTTAAACATGAGCG 58.781 37.500 0.00 0.00 37.38 5.03
18 19 5.119125 GCTGTTGTTGGATTTAAACATGAGC 59.881 40.000 0.00 0.00 37.38 4.26
19 20 5.634859 GGCTGTTGTTGGATTTAAACATGAG 59.365 40.000 0.00 0.00 37.38 2.90
20 21 5.069648 TGGCTGTTGTTGGATTTAAACATGA 59.930 36.000 0.00 0.00 37.38 3.07
21 22 5.177327 GTGGCTGTTGTTGGATTTAAACATG 59.823 40.000 0.00 0.00 37.38 3.21
22 23 5.163364 TGTGGCTGTTGTTGGATTTAAACAT 60.163 36.000 0.00 0.00 37.38 2.71
23 24 4.160439 TGTGGCTGTTGTTGGATTTAAACA 59.840 37.500 0.00 0.00 35.78 2.83
24 25 4.688021 TGTGGCTGTTGTTGGATTTAAAC 58.312 39.130 0.00 0.00 0.00 2.01
25 26 5.112686 GTTGTGGCTGTTGTTGGATTTAAA 58.887 37.500 0.00 0.00 0.00 1.52
26 27 4.442192 GGTTGTGGCTGTTGTTGGATTTAA 60.442 41.667 0.00 0.00 0.00 1.52
27 28 3.068873 GGTTGTGGCTGTTGTTGGATTTA 59.931 43.478 0.00 0.00 0.00 1.40
28 29 2.158971 GGTTGTGGCTGTTGTTGGATTT 60.159 45.455 0.00 0.00 0.00 2.17
29 30 1.412343 GGTTGTGGCTGTTGTTGGATT 59.588 47.619 0.00 0.00 0.00 3.01
30 31 1.039856 GGTTGTGGCTGTTGTTGGAT 58.960 50.000 0.00 0.00 0.00 3.41
31 32 1.040339 GGGTTGTGGCTGTTGTTGGA 61.040 55.000 0.00 0.00 0.00 3.53
32 33 1.326213 TGGGTTGTGGCTGTTGTTGG 61.326 55.000 0.00 0.00 0.00 3.77
33 34 0.102844 CTGGGTTGTGGCTGTTGTTG 59.897 55.000 0.00 0.00 0.00 3.33
34 35 0.324275 ACTGGGTTGTGGCTGTTGTT 60.324 50.000 0.00 0.00 0.00 2.83
35 36 0.548989 TACTGGGTTGTGGCTGTTGT 59.451 50.000 0.00 0.00 0.00 3.32
36 37 1.202758 TCTACTGGGTTGTGGCTGTTG 60.203 52.381 0.00 0.00 0.00 3.33
37 38 1.136828 TCTACTGGGTTGTGGCTGTT 58.863 50.000 0.00 0.00 0.00 3.16
38 39 1.362224 ATCTACTGGGTTGTGGCTGT 58.638 50.000 0.00 0.00 0.00 4.40
39 40 3.845781 ATATCTACTGGGTTGTGGCTG 57.154 47.619 0.00 0.00 0.00 4.85
40 41 5.407049 AGATATATCTACTGGGTTGTGGCT 58.593 41.667 13.76 0.00 34.85 4.75
41 42 5.746990 AGATATATCTACTGGGTTGTGGC 57.253 43.478 13.76 0.00 34.85 5.01
42 43 8.830915 AGATAGATATATCTACTGGGTTGTGG 57.169 38.462 22.01 0.00 41.77 4.17
43 44 8.908903 GGAGATAGATATATCTACTGGGTTGTG 58.091 40.741 22.01 0.00 41.77 3.33
44 45 8.851876 AGGAGATAGATATATCTACTGGGTTGT 58.148 37.037 19.32 6.41 44.05 3.32
45 46 9.707957 AAGGAGATAGATATATCTACTGGGTTG 57.292 37.037 20.45 0.00 44.75 3.77
46 47 9.930158 GAAGGAGATAGATATATCTACTGGGTT 57.070 37.037 20.45 13.86 44.75 4.11
47 48 9.303922 AGAAGGAGATAGATATATCTACTGGGT 57.696 37.037 20.45 7.32 44.75 4.51
48 49 9.793259 GAGAAGGAGATAGATATATCTACTGGG 57.207 40.741 20.45 0.00 44.75 4.45
49 50 9.793259 GGAGAAGGAGATAGATATATCTACTGG 57.207 40.741 20.45 0.00 44.75 4.00
53 54 9.983410 AGGAGGAGAAGGAGATAGATATATCTA 57.017 37.037 21.86 21.86 43.00 1.98
54 55 8.892312 AGGAGGAGAAGGAGATAGATATATCT 57.108 38.462 18.99 18.99 39.35 1.98
55 56 8.164070 GGAGGAGGAGAAGGAGATAGATATATC 58.836 44.444 4.42 4.42 0.00 1.63
56 57 7.861887 AGGAGGAGGAGAAGGAGATAGATATAT 59.138 40.741 0.00 0.00 0.00 0.86
57 58 7.210610 AGGAGGAGGAGAAGGAGATAGATATA 58.789 42.308 0.00 0.00 0.00 0.86
58 59 6.045251 AGGAGGAGGAGAAGGAGATAGATAT 58.955 44.000 0.00 0.00 0.00 1.63
59 60 5.429518 AGGAGGAGGAGAAGGAGATAGATA 58.570 45.833 0.00 0.00 0.00 1.98
60 61 4.259626 AGGAGGAGGAGAAGGAGATAGAT 58.740 47.826 0.00 0.00 0.00 1.98
61 62 3.687045 AGGAGGAGGAGAAGGAGATAGA 58.313 50.000 0.00 0.00 0.00 1.98
62 63 4.352595 TGTAGGAGGAGGAGAAGGAGATAG 59.647 50.000 0.00 0.00 0.00 2.08
63 64 4.316872 TGTAGGAGGAGGAGAAGGAGATA 58.683 47.826 0.00 0.00 0.00 1.98
64 65 3.135279 TGTAGGAGGAGGAGAAGGAGAT 58.865 50.000 0.00 0.00 0.00 2.75
65 66 2.574587 TGTAGGAGGAGGAGAAGGAGA 58.425 52.381 0.00 0.00 0.00 3.71
66 67 3.053245 TCTTGTAGGAGGAGGAGAAGGAG 60.053 52.174 0.00 0.00 0.00 3.69
67 68 2.927007 TCTTGTAGGAGGAGGAGAAGGA 59.073 50.000 0.00 0.00 0.00 3.36
68 69 3.390175 TCTTGTAGGAGGAGGAGAAGG 57.610 52.381 0.00 0.00 0.00 3.46
69 70 5.020132 TCTTTCTTGTAGGAGGAGGAGAAG 58.980 45.833 0.00 0.00 0.00 2.85
70 71 5.011982 TCTTTCTTGTAGGAGGAGGAGAA 57.988 43.478 0.00 0.00 0.00 2.87
71 72 4.676799 TCTTTCTTGTAGGAGGAGGAGA 57.323 45.455 0.00 0.00 0.00 3.71
83 84 5.296035 CACGAACCCTAACTTTCTTTCTTGT 59.704 40.000 0.00 0.00 0.00 3.16
144 145 1.729586 GCCTCCATGACCCTATACCA 58.270 55.000 0.00 0.00 0.00 3.25
148 149 1.762522 CTGCGCCTCCATGACCCTAT 61.763 60.000 4.18 0.00 0.00 2.57
154 162 2.315781 GATCCACTGCGCCTCCATGA 62.316 60.000 4.18 0.00 0.00 3.07
166 174 0.548682 AGTCCTTGCCTGGATCCACT 60.549 55.000 11.44 0.19 38.52 4.00
185 193 2.439553 AAAATGAAGCCCTCCCGCCA 62.440 55.000 0.00 0.00 0.00 5.69
212 220 8.201464 ACACAAACCCTAACAAGATTAAAAAGG 58.799 33.333 0.00 0.00 0.00 3.11
213 221 9.244799 GACACAAACCCTAACAAGATTAAAAAG 57.755 33.333 0.00 0.00 0.00 2.27
218 226 7.057894 ACAAGACACAAACCCTAACAAGATTA 58.942 34.615 0.00 0.00 0.00 1.75
240 248 1.339055 CCATCTCGCCTTCCTGAACAA 60.339 52.381 0.00 0.00 0.00 2.83
242 250 0.250513 ACCATCTCGCCTTCCTGAAC 59.749 55.000 0.00 0.00 0.00 3.18
243 251 0.250234 CACCATCTCGCCTTCCTGAA 59.750 55.000 0.00 0.00 0.00 3.02
258 266 2.853542 TTCAGGGAGCTGCCACCA 60.854 61.111 27.56 6.36 38.95 4.17
261 269 1.126488 CTATCTTCAGGGAGCTGCCA 58.874 55.000 27.56 5.20 38.95 4.92
265 273 5.606329 AGCTTTATTCTATCTTCAGGGAGCT 59.394 40.000 0.00 0.00 0.00 4.09
279 287 0.470341 GGCGGGGAGAGCTTTATTCT 59.530 55.000 0.00 0.00 34.52 2.40
312 320 2.638154 GATACTAGACGCGCCGCT 59.362 61.111 5.73 3.63 0.00 5.52
317 325 1.463805 CACCAACGATACTAGACGCG 58.536 55.000 3.53 3.53 0.00 6.01
326 334 1.374885 CACACGCCCACCAACGATA 60.375 57.895 0.00 0.00 0.00 2.92
361 369 5.946486 AGGATCCAAACCAAAGATAGATCC 58.054 41.667 15.82 7.85 45.65 3.36
388 446 5.277154 CCGCCGATGAAGAATAACGTAAATT 60.277 40.000 0.00 0.00 0.00 1.82
391 449 3.117794 CCGCCGATGAAGAATAACGTAA 58.882 45.455 0.00 0.00 0.00 3.18
401 459 3.864686 CAACCGCCGCCGATGAAG 61.865 66.667 0.00 0.00 36.29 3.02
432 490 3.939592 GTGCTAAAACCTCATAGGACCAC 59.060 47.826 0.00 0.00 37.67 4.16
443 501 2.401351 GAAGTCGTCGTGCTAAAACCT 58.599 47.619 0.00 0.00 0.00 3.50
446 504 1.787012 GGGAAGTCGTCGTGCTAAAA 58.213 50.000 0.00 0.00 0.00 1.52
447 505 0.387622 CGGGAAGTCGTCGTGCTAAA 60.388 55.000 0.00 0.00 0.00 1.85
467 525 5.063564 GGCATAACTTGTTGTAGTAGACAGC 59.936 44.000 0.00 0.00 39.88 4.40
487 545 1.524002 CATCACTGGAGTCGGGCAT 59.476 57.895 0.00 0.00 0.00 4.40
499 557 0.765903 ATCATCGCCCCTCCATCACT 60.766 55.000 0.00 0.00 0.00 3.41
501 559 1.756665 CATCATCGCCCCTCCATCA 59.243 57.895 0.00 0.00 0.00 3.07
528 586 1.080501 CACTGAAGCGAGCCGAAGA 60.081 57.895 0.00 0.00 0.00 2.87
543 601 1.130749 CTAGCGACGACTACAAGCACT 59.869 52.381 0.00 0.00 0.00 4.40
564 622 7.579940 AATTACATCCAGATCCATAGACCAT 57.420 36.000 0.00 0.00 0.00 3.55
646 704 8.110860 AGACATACTAAACATGTTTTTCTGGG 57.889 34.615 27.66 15.53 36.76 4.45
663 721 6.267928 ACTCCACTGTTTCAACTAGACATACT 59.732 38.462 0.00 0.00 0.00 2.12
666 724 5.070446 TCACTCCACTGTTTCAACTAGACAT 59.930 40.000 0.00 0.00 0.00 3.06
679 737 4.602340 AGTTAACGAATCACTCCACTGT 57.398 40.909 0.00 0.00 0.00 3.55
711 774 6.429692 TGATTCCTACAGTACATTTTGTGGTG 59.570 38.462 0.00 0.00 0.00 4.17
718 781 7.110155 ACCGATTTGATTCCTACAGTACATTT 58.890 34.615 0.00 0.00 0.00 2.32
741 806 5.307926 AGTTGTACTTAAGCTACTCGACC 57.692 43.478 1.29 0.00 0.00 4.79
878 950 0.105964 TGGTTGACCTGTGGAGTTCG 59.894 55.000 1.34 0.00 36.82 3.95
879 951 2.568623 ATGGTTGACCTGTGGAGTTC 57.431 50.000 1.34 0.00 36.82 3.01
885 957 1.470098 GCTTGCTATGGTTGACCTGTG 59.530 52.381 1.34 0.00 36.82 3.66
900 972 4.100707 TGACTTTGCTAATGATGCTTGC 57.899 40.909 0.00 0.00 0.00 4.01
901 973 6.809689 TGATTTGACTTTGCTAATGATGCTTG 59.190 34.615 0.00 0.00 0.00 4.01
934 1006 4.692625 CGGCTAATGCTGCTTATAATGAGT 59.307 41.667 0.00 0.00 38.88 3.41
957 1029 5.343249 CAAGCTTATTATGGTTGTGAAGCC 58.657 41.667 0.00 0.00 40.07 4.35
961 1034 4.398988 CAGCCAAGCTTATTATGGTTGTGA 59.601 41.667 15.93 0.00 39.67 3.58
990 1063 2.740055 GGTGCACTGGAGACTGCG 60.740 66.667 17.98 0.00 34.44 5.18
1001 1074 1.795170 ATTTGCTCGGTGTGGTGCAC 61.795 55.000 8.80 8.80 46.97 4.57
1003 1076 0.878416 TAATTTGCTCGGTGTGGTGC 59.122 50.000 0.00 0.00 0.00 5.01
1007 1080 3.243168 CCATGGATAATTTGCTCGGTGTG 60.243 47.826 5.56 0.00 0.00 3.82
1439 1557 1.758906 CTCCTCGTCCTTCTCCCCC 60.759 68.421 0.00 0.00 0.00 5.40
1440 1558 1.758906 CCTCCTCGTCCTTCTCCCC 60.759 68.421 0.00 0.00 0.00 4.81
1441 1559 2.428085 GCCTCCTCGTCCTTCTCCC 61.428 68.421 0.00 0.00 0.00 4.30
1442 1560 2.428085 GGCCTCCTCGTCCTTCTCC 61.428 68.421 0.00 0.00 0.00 3.71
1443 1561 1.380650 AGGCCTCCTCGTCCTTCTC 60.381 63.158 0.00 0.00 0.00 2.87
1444 1562 1.380650 GAGGCCTCCTCGTCCTTCT 60.381 63.158 23.19 0.00 41.08 2.85
1445 1563 3.212275 GAGGCCTCCTCGTCCTTC 58.788 66.667 23.19 0.00 41.08 3.46
1932 2076 2.046892 GCAGCTGCCGAGGAAGAA 60.047 61.111 28.76 0.00 34.31 2.52
2002 2146 3.991924 ATCTCCCTGCAGTCGCCCT 62.992 63.158 13.81 0.00 37.32 5.19
2067 2217 2.358737 CTCCAGGGGCACGTTGAC 60.359 66.667 0.00 0.00 0.00 3.18
2096 2247 2.983592 CCCAGGTTGTTGGTCCGC 60.984 66.667 0.00 0.00 36.45 5.54
2165 2316 2.706190 CCGGTAGATTCTTTCCCATCCT 59.294 50.000 0.00 0.00 0.00 3.24
2168 2319 2.706190 CTCCCGGTAGATTCTTTCCCAT 59.294 50.000 0.00 0.00 0.00 4.00
2177 2328 0.617820 ACAGGTGCTCCCGGTAGATT 60.618 55.000 0.00 0.00 40.14 2.40
2312 2463 1.602237 CCACCAGAAGGCCACGTAT 59.398 57.895 5.01 0.00 39.06 3.06
2426 2595 1.287815 CAGGTCGCGGTAGTTGACA 59.712 57.895 6.13 0.00 34.32 3.58
2617 2786 1.202313 GCTCACTCGTTGTAGCCTAGG 60.202 57.143 3.67 3.67 0.00 3.02
2625 2794 1.488527 GAAGTTCGCTCACTCGTTGT 58.511 50.000 0.00 0.00 0.00 3.32
2637 2811 9.862585 CATTTTTATTTTCTTTTGGGAAGTTCG 57.137 29.630 0.00 0.00 0.00 3.95
2656 2830 8.717821 CCTTCACTCGTTATCACTTCATTTTTA 58.282 33.333 0.00 0.00 0.00 1.52
2684 2859 1.497991 TCCGCACTCTTCACTTTTCG 58.502 50.000 0.00 0.00 0.00 3.46
2688 2863 2.839486 TCAATCCGCACTCTTCACTT 57.161 45.000 0.00 0.00 0.00 3.16
2887 3065 0.473694 TGAAGAAGGGACTGGGCTGA 60.474 55.000 0.00 0.00 40.86 4.26
2997 3177 0.963355 GCCCCCAGTGCGTGATTTAA 60.963 55.000 0.00 0.00 0.00 1.52
3267 4317 3.092511 GGGAGGGATGCAGCAGGA 61.093 66.667 3.51 0.00 0.00 3.86
3482 4669 0.106819 GAGTACGAGGAGGTAGCCCA 60.107 60.000 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.