Multiple sequence alignment - TraesCS3B01G518200

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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 TraesCS3B01G518200 chr3B 100.000 4525 0 0 1 4525 761059038 761063562 0.000000e+00 8357.0
1 TraesCS3B01G518200 chr3B 96.831 1641 49 2 2884 4522 761005318 761006957 0.000000e+00 2739.0
2 TraesCS3B01G518200 chr3B 86.887 877 92 11 1 860 761366231 761367101 0.000000e+00 961.0
3 TraesCS3B01G518200 chr3B 85.566 866 81 16 877 1714 761367148 761367997 0.000000e+00 867.0
4 TraesCS3B01G518200 chr3B 92.278 518 36 4 3618 4133 761035221 761035736 0.000000e+00 732.0
5 TraesCS3B01G518200 chr3B 89.768 518 49 4 3618 4133 761104074 761104589 0.000000e+00 660.0
6 TraesCS3B01G518200 chr3B 89.382 518 51 4 3618 4133 761134264 761134779 0.000000e+00 649.0
7 TraesCS3B01G518200 chr3B 94.402 393 22 0 2884 3276 761195772 761196164 5.010000e-169 604.0
8 TraesCS3B01G518200 chr3B 82.067 658 91 17 2885 3526 760480033 760479387 1.850000e-148 536.0
9 TraesCS3B01G518200 chr3B 84.342 479 66 6 2915 3390 761370713 761371185 1.150000e-125 460.0
10 TraesCS3B01G518200 chr3B 80.874 366 55 8 4152 4514 761270016 761270369 1.600000e-69 274.0
11 TraesCS3B01G518200 chr3B 81.633 294 31 17 2586 2876 761392540 761392813 5.890000e-54 222.0
12 TraesCS3B01G518200 chr3B 83.425 181 20 8 2577 2753 761025998 761026172 4.690000e-35 159.0
13 TraesCS3B01G518200 chr3B 85.621 153 10 8 2622 2763 761003056 761003207 2.820000e-32 150.0
14 TraesCS3B01G518200 chr3A 89.481 1350 98 26 2884 4223 705950303 705951618 0.000000e+00 1666.0
15 TraesCS3B01G518200 chr3A 82.893 719 69 20 1017 1714 706015709 706016394 8.380000e-167 597.0
16 TraesCS3B01G518200 chr3A 84.303 567 56 13 1174 1708 706333472 706334037 1.440000e-144 523.0
17 TraesCS3B01G518200 chr3A 82.055 613 83 16 2951 3546 705363007 705362405 8.740000e-137 497.0
18 TraesCS3B01G518200 chr3A 83.789 512 71 7 2884 3390 706019036 706019540 4.100000e-130 475.0
19 TraesCS3B01G518200 chr3A 80.320 625 104 11 255 877 7203879 7204486 5.340000e-124 455.0
20 TraesCS3B01G518200 chr3A 83.041 513 72 8 2884 3390 706336304 706336807 6.900000e-123 451.0
21 TraesCS3B01G518200 chr3A 82.792 308 24 12 2583 2888 706116811 706117091 9.720000e-62 248.0
22 TraesCS3B01G518200 chr3A 81.366 322 37 12 2578 2888 706016693 706017002 1.630000e-59 241.0
23 TraesCS3B01G518200 chr3A 73.913 598 133 14 2897 3491 705877406 705877983 7.620000e-53 219.0
24 TraesCS3B01G518200 chr3A 81.600 250 35 3 4261 4509 705951979 705952218 3.570000e-46 196.0
25 TraesCS3B01G518200 chr3A 79.245 318 32 18 2586 2883 706257209 706257512 1.660000e-44 191.0
26 TraesCS3B01G518200 chr3A 82.222 180 17 4 908 1086 706015475 706015640 1.700000e-29 141.0
27 TraesCS3B01G518200 chr3A 82.659 173 8 8 2583 2754 706401981 706402132 2.840000e-27 134.0
28 TraesCS3B01G518200 chr3A 80.189 212 11 15 2584 2788 705370548 705370361 3.670000e-26 130.0
29 TraesCS3B01G518200 chr3A 95.122 41 2 0 2541 2581 706334219 706334259 1.050000e-06 65.8
30 TraesCS3B01G518200 chr3D 85.887 992 105 16 1 969 572514287 572513308 0.000000e+00 1024.0
31 TraesCS3B01G518200 chr3D 87.679 698 64 7 1041 1716 572511459 572510762 0.000000e+00 793.0
32 TraesCS3B01G518200 chr3D 83.852 514 70 7 2884 3390 572508120 572507613 1.140000e-130 477.0
33 TraesCS3B01G518200 chr3D 87.701 374 38 3 4142 4514 572553387 572553021 3.230000e-116 429.0
34 TraesCS3B01G518200 chr3D 89.809 314 30 1 2078 2389 40804586 40804899 7.050000e-108 401.0
35 TraesCS3B01G518200 chr3D 77.453 581 90 20 709 1252 113008576 113009152 4.400000e-80 309.0
36 TraesCS3B01G518200 chr3D 84.494 316 27 11 2571 2876 572510492 572510189 4.430000e-75 292.0
37 TraesCS3B01G518200 chr3D 80.380 316 42 13 2585 2888 572490135 572489828 5.890000e-54 222.0
38 TraesCS3B01G518200 chr3D 91.781 146 11 1 1943 2087 40804090 40804235 7.680000e-48 202.0
39 TraesCS3B01G518200 chr3D 97.619 42 1 0 2465 2506 572510599 572510558 6.280000e-09 73.1
40 TraesCS3B01G518200 chr3D 96.970 33 1 0 976 1008 572511484 572511452 6.320000e-04 56.5
41 TraesCS3B01G518200 chr5A 84.639 664 93 7 1728 2389 601336420 601335764 0.000000e+00 652.0
42 TraesCS3B01G518200 chr5A 84.804 612 83 7 1783 2389 550640682 550640076 1.390000e-169 606.0
43 TraesCS3B01G518200 chr7D 83.949 623 88 10 258 875 472897789 472897174 1.810000e-163 586.0
44 TraesCS3B01G518200 chr1D 85.019 514 55 7 1200 1692 96699487 96699999 1.880000e-138 503.0
45 TraesCS3B01G518200 chr1D 87.688 398 41 6 242 638 96699085 96699475 1.480000e-124 457.0
46 TraesCS3B01G518200 chr1D 81.569 510 90 4 242 750 113599457 113599963 7.000000e-113 418.0
47 TraesCS3B01G518200 chr5D 81.481 513 90 5 243 753 408483998 408484507 2.520000e-112 416.0
48 TraesCS3B01G518200 chr5D 81.236 453 79 5 255 706 504000652 504001099 1.200000e-95 361.0
49 TraesCS3B01G518200 chr1B 84.673 398 55 6 242 638 156689626 156689234 4.240000e-105 392.0
50 TraesCS3B01G518200 chr1B 77.471 688 95 30 668 1307 14560437 14561112 1.550000e-94 357.0
51 TraesCS3B01G518200 chr5B 87.629 291 33 3 1719 2007 590799735 590799446 7.250000e-88 335.0
52 TraesCS3B01G518200 chrUn 82.895 228 18 11 2569 2790 131949023 131949235 7.730000e-43 185.0
53 TraesCS3B01G518200 chr4B 92.857 70 2 3 2691 2758 605377606 605377674 1.040000e-16 99.0
54 TraesCS3B01G518200 chr2D 95.238 42 2 0 26 67 229641855 229641814 2.920000e-07 67.6


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 TraesCS3B01G518200 chr3B 761059038 761063562 4524 False 8357.000000 8357 100.000000 1 4525 1 chr3B.!!$F3 4524
1 TraesCS3B01G518200 chr3B 761003056 761006957 3901 False 1444.500000 2739 91.226000 2622 4522 2 chr3B.!!$F9 1900
2 TraesCS3B01G518200 chr3B 761366231 761371185 4954 False 762.666667 961 85.598333 1 3390 3 chr3B.!!$F10 3389
3 TraesCS3B01G518200 chr3B 761035221 761035736 515 False 732.000000 732 92.278000 3618 4133 1 chr3B.!!$F2 515
4 TraesCS3B01G518200 chr3B 761104074 761104589 515 False 660.000000 660 89.768000 3618 4133 1 chr3B.!!$F4 515
5 TraesCS3B01G518200 chr3B 761134264 761134779 515 False 649.000000 649 89.382000 3618 4133 1 chr3B.!!$F5 515
6 TraesCS3B01G518200 chr3B 760479387 760480033 646 True 536.000000 536 82.067000 2885 3526 1 chr3B.!!$R1 641
7 TraesCS3B01G518200 chr3A 705950303 705952218 1915 False 931.000000 1666 85.540500 2884 4509 2 chr3A.!!$F6 1625
8 TraesCS3B01G518200 chr3A 705362405 705363007 602 True 497.000000 497 82.055000 2951 3546 1 chr3A.!!$R1 595
9 TraesCS3B01G518200 chr3A 7203879 7204486 607 False 455.000000 455 80.320000 255 877 1 chr3A.!!$F1 622
10 TraesCS3B01G518200 chr3A 706015475 706019540 4065 False 363.500000 597 82.567500 908 3390 4 chr3A.!!$F7 2482
11 TraesCS3B01G518200 chr3A 706333472 706336807 3335 False 346.600000 523 87.488667 1174 3390 3 chr3A.!!$F8 2216
12 TraesCS3B01G518200 chr3A 705877406 705877983 577 False 219.000000 219 73.913000 2897 3491 1 chr3A.!!$F2 594
13 TraesCS3B01G518200 chr3D 572507613 572514287 6674 True 452.600000 1024 89.416833 1 3390 6 chr3D.!!$R3 3389
14 TraesCS3B01G518200 chr3D 113008576 113009152 576 False 309.000000 309 77.453000 709 1252 1 chr3D.!!$F1 543
15 TraesCS3B01G518200 chr3D 40804090 40804899 809 False 301.500000 401 90.795000 1943 2389 2 chr3D.!!$F2 446
16 TraesCS3B01G518200 chr5A 601335764 601336420 656 True 652.000000 652 84.639000 1728 2389 1 chr5A.!!$R2 661
17 TraesCS3B01G518200 chr5A 550640076 550640682 606 True 606.000000 606 84.804000 1783 2389 1 chr5A.!!$R1 606
18 TraesCS3B01G518200 chr7D 472897174 472897789 615 True 586.000000 586 83.949000 258 875 1 chr7D.!!$R1 617
19 TraesCS3B01G518200 chr1D 96699085 96699999 914 False 480.000000 503 86.353500 242 1692 2 chr1D.!!$F2 1450
20 TraesCS3B01G518200 chr1D 113599457 113599963 506 False 418.000000 418 81.569000 242 750 1 chr1D.!!$F1 508
21 TraesCS3B01G518200 chr5D 408483998 408484507 509 False 416.000000 416 81.481000 243 753 1 chr5D.!!$F1 510
22 TraesCS3B01G518200 chr1B 14560437 14561112 675 False 357.000000 357 77.471000 668 1307 1 chr1B.!!$F1 639

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
448 462 0.028637 GCTTGCTGCTTTATCTCGCC 59.971 55.0 0.0 0.0 38.95 5.54 F
1419 3506 0.036952 CGCTCAGTGTCCCATCTTGT 60.037 55.0 0.0 0.0 0.00 3.16 F
2738 5401 0.033228 CAGAGCATCGAGGTGATCCC 59.967 60.0 0.0 0.0 42.67 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2107 4724 0.466739 TGTAGGATAGCGGCTTCGGA 60.467 55.0 8.26 0.0 0.0 4.55 R
3080 7964 0.179034 GGCTCGCCCTTCAAGATGAT 60.179 55.0 0.00 0.0 0.0 2.45 R
4085 9031 0.035056 ATGAACAGAGGGAAAGGGCG 60.035 55.0 0.00 0.0 0.0 6.13 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
57 58 6.625300 AGAGTCAATCTTCAAAGCATCAATGC 60.625 38.462 6.88 6.88 44.75 3.56
77 78 3.119388 TGCTTTCTTCATATGCAAGTGCC 60.119 43.478 0.00 0.00 41.18 5.01
82 83 3.379057 TCTTCATATGCAAGTGCCATGTG 59.621 43.478 12.20 9.18 41.18 3.21
128 129 5.126779 AGTTGTATCTCTGTCTCTATGCGA 58.873 41.667 0.00 0.00 0.00 5.10
161 162 8.602472 TCCCCACTTTATTTTAATACAAGCAT 57.398 30.769 0.00 0.00 0.00 3.79
177 178 4.142643 ACAAGCATGGTTTGTTTGCAAAAG 60.143 37.500 14.67 0.00 46.96 2.27
187 190 3.161866 TGTTTGCAAAAGGGGAGGTATC 58.838 45.455 14.67 0.00 0.00 2.24
402 415 4.005650 AGTGTTTGATGTGCGATCTTCAT 58.994 39.130 0.00 0.00 0.00 2.57
448 462 0.028637 GCTTGCTGCTTTATCTCGCC 59.971 55.000 0.00 0.00 38.95 5.54
471 485 7.439955 CGCCAATGATACAACCATAAGTACTAA 59.560 37.037 0.00 0.00 0.00 2.24
516 532 0.603569 GACCTGCTTTGAGTCGGAGA 59.396 55.000 0.00 0.00 0.00 3.71
646 666 1.654023 GCTGCCCAAATACCGTCCAC 61.654 60.000 0.00 0.00 0.00 4.02
647 667 0.322098 CTGCCCAAATACCGTCCACA 60.322 55.000 0.00 0.00 0.00 4.17
648 668 0.322098 TGCCCAAATACCGTCCACAG 60.322 55.000 0.00 0.00 0.00 3.66
655 675 4.253685 CAAATACCGTCCACAGTCATCTT 58.746 43.478 0.00 0.00 0.00 2.40
688 708 3.191581 AGATGTTGTTCGTCTGATCTCGT 59.808 43.478 0.00 0.00 40.49 4.18
706 727 1.064803 CGTACTTTGCCACACTTGCAA 59.935 47.619 0.00 0.00 46.30 4.08
729 750 6.772360 AAAACATGGATTTTTGCAAAACCT 57.228 29.167 23.79 14.22 36.11 3.50
784 807 6.557253 TCTTATAATCTTAGCTGGTGCCCTTA 59.443 38.462 0.00 0.00 40.80 2.69
786 809 4.526438 AATCTTAGCTGGTGCCCTTATT 57.474 40.909 0.00 0.00 40.80 1.40
791 814 2.205342 AGCTGGTGCCCTTATTTCCTA 58.795 47.619 0.00 0.00 40.80 2.94
905 979 8.918202 AAGGTGACTGATAACTTAACAAATGA 57.082 30.769 0.00 0.00 42.68 2.57
906 980 8.918202 AGGTGACTGATAACTTAACAAATGAA 57.082 30.769 0.00 0.00 41.13 2.57
940 1014 3.767673 AGAATCAATCATGGCAAACAGCT 59.232 39.130 0.00 0.00 44.79 4.24
971 2869 1.270094 ACTCGGTTCAATTGTCTCGCA 60.270 47.619 5.13 0.00 0.00 5.10
972 2870 2.002586 CTCGGTTCAATTGTCTCGCAT 58.997 47.619 5.13 0.00 0.00 4.73
973 2871 3.186909 CTCGGTTCAATTGTCTCGCATA 58.813 45.455 5.13 0.00 0.00 3.14
974 2872 3.792401 TCGGTTCAATTGTCTCGCATAT 58.208 40.909 5.13 0.00 0.00 1.78
979 2877 7.115805 TCGGTTCAATTGTCTCGCATATATAAC 59.884 37.037 5.13 0.00 0.00 1.89
1008 2906 3.005684 GCCAAATCACCATCAACAAGTGA 59.994 43.478 0.00 0.00 44.11 3.41
1009 2907 4.501229 GCCAAATCACCATCAACAAGTGAA 60.501 41.667 0.00 0.00 43.29 3.18
1022 2920 3.417101 ACAAGTGAACAAACACACCTCA 58.583 40.909 0.00 0.00 42.45 3.86
1034 2932 1.745087 CACACCTCACCATATTGCACC 59.255 52.381 0.00 0.00 0.00 5.01
1037 2935 0.819259 CCTCACCATATTGCACCCGG 60.819 60.000 0.00 0.00 0.00 5.73
1039 2937 1.225983 CACCATATTGCACCCGGGA 59.774 57.895 32.02 4.18 0.00 5.14
1059 2957 1.705873 AACGAGTGTCTCCAGGAGTT 58.294 50.000 16.65 0.00 0.00 3.01
1081 3116 1.280746 CACGCCACAAAGAGCACAG 59.719 57.895 0.00 0.00 0.00 3.66
1111 3146 4.851639 AGTGGACATTTTCCTATGAGCT 57.148 40.909 0.00 0.00 46.10 4.09
1120 3155 5.401531 TTTTCCTATGAGCTTGTACGTCT 57.598 39.130 0.00 0.00 0.00 4.18
1138 3198 1.071542 TCTTCGGTTGGCAATGAGTGA 59.928 47.619 1.92 4.94 0.00 3.41
1148 3208 2.099263 GGCAATGAGTGACTCGCTAGTA 59.901 50.000 8.23 0.00 35.56 1.82
1303 3376 2.929531 CGCTGATCTCACAGTGTAGT 57.070 50.000 0.00 0.00 41.61 2.73
1319 3403 1.884075 TAGTAGCCAGTGCCACACCG 61.884 60.000 0.00 0.00 38.69 4.94
1405 3492 1.745653 CACACCTCTGATAGTCGCTCA 59.254 52.381 0.00 0.00 0.00 4.26
1406 3493 2.020720 ACACCTCTGATAGTCGCTCAG 58.979 52.381 0.00 0.00 41.23 3.35
1419 3506 0.036952 CGCTCAGTGTCCCATCTTGT 60.037 55.000 0.00 0.00 0.00 3.16
1445 3535 4.956085 TGTATGGTCAATAAGATCCGTGG 58.044 43.478 0.00 0.00 0.00 4.94
1471 3562 1.364269 AAGGTGGATTGGTTACCCGA 58.636 50.000 0.00 0.00 35.03 5.14
1475 3566 2.619590 GGTGGATTGGTTACCCGACATT 60.620 50.000 0.00 0.00 0.00 2.71
1480 3571 5.163141 TGGATTGGTTACCCGACATTCATAT 60.163 40.000 0.00 0.00 0.00 1.78
1481 3572 5.411669 GGATTGGTTACCCGACATTCATATC 59.588 44.000 0.00 0.00 0.00 1.63
1517 3617 4.089361 GTCCCTTGGAATCCAATTGTCTT 58.911 43.478 15.91 0.00 43.07 3.01
1555 3656 0.391130 CTCCGTTGCCAATTCTCCGA 60.391 55.000 0.00 0.00 0.00 4.55
1576 3677 0.174845 TCAATCCCCGCTTGAGTACG 59.825 55.000 0.00 0.00 0.00 3.67
1582 3683 2.434134 CCGCTTGAGTACGTCACGC 61.434 63.158 0.00 11.29 45.01 5.34
1596 3697 1.817447 GTCACGCCCTTCTACTACTGT 59.183 52.381 0.00 0.00 0.00 3.55
1597 3698 2.089980 TCACGCCCTTCTACTACTGTC 58.910 52.381 0.00 0.00 0.00 3.51
1614 3715 1.704628 TGTCCTCCAAATCTGGCTTGA 59.295 47.619 0.00 0.00 43.17 3.02
1692 3802 4.853924 AAATTCTTGCACCGAGTGATTT 57.146 36.364 8.04 2.75 35.23 2.17
1716 3867 2.094752 GGTTTTGTAGAATGCGCCATGT 60.095 45.455 4.18 0.00 0.00 3.21
1717 3868 3.574614 GTTTTGTAGAATGCGCCATGTT 58.425 40.909 4.18 0.00 0.00 2.71
1773 4026 2.552315 AGCAGAATTACAAACCCACACG 59.448 45.455 0.00 0.00 0.00 4.49
1776 4029 4.378046 GCAGAATTACAAACCCACACGTAG 60.378 45.833 0.00 0.00 0.00 3.51
1790 4043 2.299013 ACACGTAGCCACAATCAAGAGA 59.701 45.455 0.00 0.00 0.00 3.10
1804 4057 3.995199 TCAAGAGACATCCAGAACACAC 58.005 45.455 0.00 0.00 0.00 3.82
1807 4060 2.700371 AGAGACATCCAGAACACACACA 59.300 45.455 0.00 0.00 0.00 3.72
1832 4085 4.494484 ACAACACTTTGCAAGAAGAAACC 58.506 39.130 5.15 0.00 36.00 3.27
1833 4086 4.220602 ACAACACTTTGCAAGAAGAAACCT 59.779 37.500 5.15 0.00 36.00 3.50
1862 4118 0.103937 TTGCAAAGAAACGCTTGGGG 59.896 50.000 0.00 0.00 36.80 4.96
1869 4125 1.486726 AGAAACGCTTGGGGATCCTAG 59.513 52.381 12.58 8.10 38.63 3.02
1883 4139 4.336280 GGATCCTAGAAGCAAAACAACCT 58.664 43.478 3.84 0.00 0.00 3.50
1885 4141 4.431416 TCCTAGAAGCAAAACAACCTGA 57.569 40.909 0.00 0.00 0.00 3.86
1899 4155 1.004560 CCTGATGTCGCCGCCATAT 60.005 57.895 0.00 0.00 0.00 1.78
1903 4159 3.182590 ATGTCGCCGCCATATGCCT 62.183 57.895 0.00 0.00 36.24 4.75
1904 4160 2.591715 GTCGCCGCCATATGCCTT 60.592 61.111 0.00 0.00 36.24 4.35
1951 4207 0.467290 GGAGACACCAACTTGCCCAA 60.467 55.000 0.00 0.00 38.79 4.12
1971 4228 6.490040 GCCCAAGATAGAATTAGTGCCATAAA 59.510 38.462 0.00 0.00 0.00 1.40
2039 4296 1.215647 GACCTTGTGGCTCGTCGAT 59.784 57.895 0.00 0.00 36.63 3.59
2127 4744 0.039074 CCGAAGCCGCTATCCTACAG 60.039 60.000 0.00 0.00 0.00 2.74
2130 4747 1.759459 AAGCCGCTATCCTACAGCCC 61.759 60.000 0.00 0.00 35.53 5.19
2138 4755 1.987080 ATCCTACAGCCCCCTTTCTT 58.013 50.000 0.00 0.00 0.00 2.52
2183 4800 1.065928 AGATCGCCGTCGTCATTCC 59.934 57.895 0.00 0.00 36.96 3.01
2188 4805 1.738830 GCCGTCGTCATTCCCGAAA 60.739 57.895 0.00 0.00 35.89 3.46
2263 4882 2.046023 CGGGAGCAAGCACCATCA 60.046 61.111 10.60 0.00 0.00 3.07
2265 4884 1.303561 GGGAGCAAGCACCATCACA 60.304 57.895 10.60 0.00 0.00 3.58
2330 4949 0.537143 CACTGCACCAACCAGGCTTA 60.537 55.000 0.00 0.00 43.14 3.09
2337 4956 0.112412 CCAACCAGGCTTAACCACCT 59.888 55.000 0.00 0.00 43.14 4.00
2353 4972 1.217057 ACCTGCCCAACCAGATCCAT 61.217 55.000 0.00 0.00 34.77 3.41
2402 5021 8.047413 TCGAAGAGGAATTTTTGTAAATACCC 57.953 34.615 0.00 0.00 32.85 3.69
2403 5022 7.886446 TCGAAGAGGAATTTTTGTAAATACCCT 59.114 33.333 0.00 0.00 38.53 4.34
2404 5023 8.520351 CGAAGAGGAATTTTTGTAAATACCCTT 58.480 33.333 0.00 0.00 37.20 3.95
2405 5024 9.639601 GAAGAGGAATTTTTGTAAATACCCTTG 57.360 33.333 0.00 0.00 37.20 3.61
2406 5025 8.721133 AGAGGAATTTTTGTAAATACCCTTGT 57.279 30.769 0.00 0.00 37.20 3.16
2407 5026 8.585018 AGAGGAATTTTTGTAAATACCCTTGTG 58.415 33.333 0.00 0.00 37.20 3.33
2408 5027 8.485578 AGGAATTTTTGTAAATACCCTTGTGA 57.514 30.769 0.00 0.00 35.29 3.58
2409 5028 8.929487 AGGAATTTTTGTAAATACCCTTGTGAA 58.071 29.630 0.00 0.00 35.29 3.18
2410 5029 9.719355 GGAATTTTTGTAAATACCCTTGTGAAT 57.281 29.630 0.00 0.00 32.85 2.57
2412 5031 9.719355 AATTTTTGTAAATACCCTTGTGAATCC 57.281 29.630 0.00 0.00 32.85 3.01
2413 5032 7.841282 TTTTGTAAATACCCTTGTGAATCCA 57.159 32.000 0.00 0.00 0.00 3.41
2414 5033 7.461182 TTTGTAAATACCCTTGTGAATCCAG 57.539 36.000 0.00 0.00 0.00 3.86
2415 5034 6.381498 TGTAAATACCCTTGTGAATCCAGA 57.619 37.500 0.00 0.00 0.00 3.86
2416 5035 6.414732 TGTAAATACCCTTGTGAATCCAGAG 58.585 40.000 0.00 0.00 0.00 3.35
2417 5036 4.510167 AATACCCTTGTGAATCCAGAGG 57.490 45.455 0.00 0.00 0.00 3.69
2418 5037 2.044793 ACCCTTGTGAATCCAGAGGA 57.955 50.000 0.00 0.00 35.55 3.71
2419 5038 2.348472 ACCCTTGTGAATCCAGAGGAA 58.652 47.619 0.00 0.00 34.34 3.36
2420 5039 2.716424 ACCCTTGTGAATCCAGAGGAAA 59.284 45.455 0.00 0.00 34.34 3.13
2421 5040 3.334881 ACCCTTGTGAATCCAGAGGAAAT 59.665 43.478 0.00 0.00 34.34 2.17
2422 5041 4.202716 ACCCTTGTGAATCCAGAGGAAATT 60.203 41.667 0.00 0.00 34.34 1.82
2423 5042 4.774200 CCCTTGTGAATCCAGAGGAAATTT 59.226 41.667 0.00 0.00 34.34 1.82
2424 5043 5.951747 CCCTTGTGAATCCAGAGGAAATTTA 59.048 40.000 0.00 0.00 34.34 1.40
2425 5044 6.608808 CCCTTGTGAATCCAGAGGAAATTTAT 59.391 38.462 0.00 0.00 34.34 1.40
2426 5045 7.124750 CCCTTGTGAATCCAGAGGAAATTTATT 59.875 37.037 0.00 0.00 34.34 1.40
2427 5046 8.193438 CCTTGTGAATCCAGAGGAAATTTATTC 58.807 37.037 0.00 0.00 34.34 1.75
2428 5047 8.648698 TTGTGAATCCAGAGGAAATTTATTCA 57.351 30.769 6.30 6.30 34.34 2.57
2429 5048 8.055279 TGTGAATCCAGAGGAAATTTATTCAC 57.945 34.615 22.40 22.40 41.10 3.18
2430 5049 7.122650 TGTGAATCCAGAGGAAATTTATTCACC 59.877 37.037 24.37 10.19 40.54 4.02
2431 5050 6.318648 TGAATCCAGAGGAAATTTATTCACCG 59.681 38.462 6.30 0.00 34.34 4.94
2432 5051 3.945285 TCCAGAGGAAATTTATTCACCGC 59.055 43.478 0.00 0.00 0.00 5.68
2433 5052 3.066760 CCAGAGGAAATTTATTCACCGCC 59.933 47.826 0.00 0.00 0.00 6.13
2434 5053 2.943033 AGAGGAAATTTATTCACCGCCG 59.057 45.455 0.00 0.00 0.00 6.46
2435 5054 2.681344 GAGGAAATTTATTCACCGCCGT 59.319 45.455 0.00 0.00 0.00 5.68
2436 5055 2.681344 AGGAAATTTATTCACCGCCGTC 59.319 45.455 0.00 0.00 0.00 4.79
2437 5056 2.420722 GGAAATTTATTCACCGCCGTCA 59.579 45.455 0.00 0.00 0.00 4.35
2438 5057 3.422655 GAAATTTATTCACCGCCGTCAC 58.577 45.455 0.00 0.00 0.00 3.67
2439 5058 2.102070 ATTTATTCACCGCCGTCACA 57.898 45.000 0.00 0.00 0.00 3.58
2440 5059 1.434555 TTTATTCACCGCCGTCACAG 58.565 50.000 0.00 0.00 0.00 3.66
2441 5060 1.017177 TTATTCACCGCCGTCACAGC 61.017 55.000 0.00 0.00 0.00 4.40
2442 5061 2.845752 TATTCACCGCCGTCACAGCC 62.846 60.000 0.00 0.00 0.00 4.85
2451 5070 3.936203 GTCACAGCCACCACCGGA 61.936 66.667 9.46 0.00 0.00 5.14
2452 5071 3.164977 TCACAGCCACCACCGGAA 61.165 61.111 9.46 0.00 0.00 4.30
2453 5072 2.203280 CACAGCCACCACCGGAAA 60.203 61.111 9.46 0.00 0.00 3.13
2454 5073 1.603455 CACAGCCACCACCGGAAAT 60.603 57.895 9.46 0.00 0.00 2.17
2455 5074 1.152830 ACAGCCACCACCGGAAATT 59.847 52.632 9.46 0.00 0.00 1.82
2456 5075 0.469144 ACAGCCACCACCGGAAATTT 60.469 50.000 9.46 0.00 0.00 1.82
2457 5076 1.202952 ACAGCCACCACCGGAAATTTA 60.203 47.619 9.46 0.00 0.00 1.40
2458 5077 2.099405 CAGCCACCACCGGAAATTTAT 58.901 47.619 9.46 0.00 0.00 1.40
2459 5078 2.495669 CAGCCACCACCGGAAATTTATT 59.504 45.455 9.46 0.00 0.00 1.40
2460 5079 2.758423 AGCCACCACCGGAAATTTATTC 59.242 45.455 9.46 0.00 0.00 1.75
2495 5114 1.276989 CACGGTCTAGGCCCAGTTTAA 59.723 52.381 8.07 0.00 0.00 1.52
2506 5125 2.514803 CCCAGTTTAAACCCACCAGAG 58.485 52.381 14.72 0.00 0.00 3.35
2507 5126 2.514803 CCAGTTTAAACCCACCAGAGG 58.485 52.381 14.72 1.45 0.00 3.69
2509 5128 3.146847 CAGTTTAAACCCACCAGAGGAC 58.853 50.000 14.72 0.00 0.00 3.85
2511 5130 2.882761 GTTTAAACCCACCAGAGGACAC 59.117 50.000 7.12 0.00 0.00 3.67
2512 5131 1.809133 TAAACCCACCAGAGGACACA 58.191 50.000 0.00 0.00 0.00 3.72
2513 5132 0.923358 AAACCCACCAGAGGACACAA 59.077 50.000 0.00 0.00 0.00 3.33
2514 5133 0.474184 AACCCACCAGAGGACACAAG 59.526 55.000 0.00 0.00 0.00 3.16
2515 5134 0.694444 ACCCACCAGAGGACACAAGT 60.694 55.000 0.00 0.00 0.00 3.16
2516 5135 0.474184 CCCACCAGAGGACACAAGTT 59.526 55.000 0.00 0.00 0.00 2.66
2517 5136 1.697432 CCCACCAGAGGACACAAGTTA 59.303 52.381 0.00 0.00 0.00 2.24
2518 5137 2.305927 CCCACCAGAGGACACAAGTTAT 59.694 50.000 0.00 0.00 0.00 1.89
2519 5138 3.244911 CCCACCAGAGGACACAAGTTATT 60.245 47.826 0.00 0.00 0.00 1.40
2520 5139 4.019681 CCCACCAGAGGACACAAGTTATTA 60.020 45.833 0.00 0.00 0.00 0.98
2521 5140 5.178797 CCACCAGAGGACACAAGTTATTAG 58.821 45.833 0.00 0.00 0.00 1.73
2522 5141 4.631813 CACCAGAGGACACAAGTTATTAGC 59.368 45.833 0.00 0.00 0.00 3.09
2523 5142 4.192317 CCAGAGGACACAAGTTATTAGCC 58.808 47.826 0.00 0.00 0.00 3.93
2524 5143 4.192317 CAGAGGACACAAGTTATTAGCCC 58.808 47.826 0.00 0.00 0.00 5.19
2525 5144 3.200165 AGAGGACACAAGTTATTAGCCCC 59.800 47.826 0.00 0.00 0.00 5.80
2526 5145 2.241430 AGGACACAAGTTATTAGCCCCC 59.759 50.000 0.00 0.00 0.00 5.40
2527 5146 2.025699 GGACACAAGTTATTAGCCCCCA 60.026 50.000 0.00 0.00 0.00 4.96
2528 5147 3.562609 GGACACAAGTTATTAGCCCCCAA 60.563 47.826 0.00 0.00 0.00 4.12
2529 5148 4.083565 GACACAAGTTATTAGCCCCCAAA 58.916 43.478 0.00 0.00 0.00 3.28
2530 5149 4.484912 ACACAAGTTATTAGCCCCCAAAA 58.515 39.130 0.00 0.00 0.00 2.44
2531 5150 4.902448 ACACAAGTTATTAGCCCCCAAAAA 59.098 37.500 0.00 0.00 0.00 1.94
2532 5151 5.011635 ACACAAGTTATTAGCCCCCAAAAAG 59.988 40.000 0.00 0.00 0.00 2.27
2533 5152 5.245075 CACAAGTTATTAGCCCCCAAAAAGA 59.755 40.000 0.00 0.00 0.00 2.52
2534 5153 5.841783 ACAAGTTATTAGCCCCCAAAAAGAA 59.158 36.000 0.00 0.00 0.00 2.52
2535 5154 6.327887 ACAAGTTATTAGCCCCCAAAAAGAAA 59.672 34.615 0.00 0.00 0.00 2.52
2536 5155 7.147461 ACAAGTTATTAGCCCCCAAAAAGAAAA 60.147 33.333 0.00 0.00 0.00 2.29
2545 5164 3.709141 CCCCAAAAAGAAAAACCAGAGGA 59.291 43.478 0.00 0.00 0.00 3.71
2605 5259 2.683933 TCCTCTCCCGCTCCCAAC 60.684 66.667 0.00 0.00 0.00 3.77
2620 5278 1.343075 CCCAACCACCTCCTAGCTAGA 60.343 57.143 22.70 7.45 0.00 2.43
2662 5325 2.334653 CAAGCTTTTTCCGGCGCA 59.665 55.556 10.83 0.00 0.00 6.09
2738 5401 0.033228 CAGAGCATCGAGGTGATCCC 59.967 60.000 0.00 0.00 42.67 3.85
2774 5450 1.452108 CCTCTCCGATTTGGTGCCC 60.452 63.158 0.00 0.00 39.52 5.36
2778 5454 0.609131 CTCCGATTTGGTGCCCTGTT 60.609 55.000 0.00 0.00 39.52 3.16
2779 5455 0.178975 TCCGATTTGGTGCCCTGTTT 60.179 50.000 0.00 0.00 39.52 2.83
2792 5468 5.452636 GGTGCCCTGTTTAACTGAAAAATCA 60.453 40.000 3.54 0.00 0.00 2.57
2795 5471 6.267471 TGCCCTGTTTAACTGAAAAATCATCT 59.733 34.615 3.54 0.00 0.00 2.90
2800 5476 7.806690 TGTTTAACTGAAAAATCATCTCCTCG 58.193 34.615 0.00 0.00 0.00 4.63
2814 5490 5.987953 TCATCTCCTCGCATTTCAAAGATAG 59.012 40.000 0.00 0.00 0.00 2.08
2818 5494 7.500992 TCTCCTCGCATTTCAAAGATAGTAAT 58.499 34.615 0.00 0.00 0.00 1.89
2917 7796 6.900568 TGGTTGTTGCATTTTCTTAACTTG 57.099 33.333 0.00 0.00 0.00 3.16
2929 7812 8.755018 CATTTTCTTAACTTGTCCACACAATTC 58.245 33.333 0.00 0.00 41.82 2.17
3222 8106 1.004560 CTGTGAAGGCGCTCAAGGA 60.005 57.895 7.64 0.00 0.00 3.36
3280 8164 1.006400 ACTAACTAGGTAGGTGCCCGT 59.994 52.381 19.00 0.00 0.00 5.28
3369 8262 0.611618 TTGCAGTTGCGGGATTGGAT 60.612 50.000 0.00 0.00 45.83 3.41
3417 8315 1.700739 TGGGATGTAGGTTTCGTTGGT 59.299 47.619 0.00 0.00 0.00 3.67
3566 8467 9.691362 GCTTTTGAATTTTATTCCAGACTACAA 57.309 29.630 0.00 0.00 0.00 2.41
3578 8481 4.220821 TCCAGACTACAACCACTGAGATTC 59.779 45.833 0.00 0.00 32.90 2.52
3584 8487 4.264460 ACAACCACTGAGATTCTGAGAC 57.736 45.455 7.17 0.00 0.00 3.36
3591 8494 5.063186 CCACTGAGATTCTGAGACGAATTTG 59.937 44.000 7.17 0.00 33.96 2.32
3727 8630 3.041946 AGAGGAACACCTTCACAAGTCT 58.958 45.455 0.00 0.00 33.73 3.24
3939 8843 1.864711 CGTGTTTGGTCTGATTCGTGT 59.135 47.619 0.00 0.00 0.00 4.49
3950 8854 3.743911 TCTGATTCGTGTAAATGCGTTGT 59.256 39.130 0.00 0.00 0.00 3.32
4048 8994 3.679502 GCTTTTTGTGCTGTGTGACTTTT 59.320 39.130 0.00 0.00 0.00 2.27
4058 9004 4.142600 GCTGTGTGACTTTTTGTGTCTTCT 60.143 41.667 0.00 0.00 35.63 2.85
4085 9031 1.432270 CGCTTCCGCCCATCTTTCTC 61.432 60.000 0.00 0.00 0.00 2.87
4101 9047 0.836400 TCTCGCCCTTTCCCTCTGTT 60.836 55.000 0.00 0.00 0.00 3.16
4150 9133 2.753452 CTCAAGCCTCGACTACCTTACA 59.247 50.000 0.00 0.00 0.00 2.41
4226 9210 3.097614 GCATCGTCCTATGGGTAGGTAT 58.902 50.000 0.00 0.00 46.43 2.73
4393 9700 5.234116 CCAGTTTGTACAACTTGCAATTTCC 59.766 40.000 8.07 0.00 28.89 3.13
4404 9711 1.611491 TGCAATTTCCGGTCCACTTTC 59.389 47.619 0.00 0.00 0.00 2.62
4453 9760 5.570205 TGGAGTGGTTTTAACTCATACCA 57.430 39.130 5.97 0.00 44.86 3.25
4511 9818 4.010349 CCTTTCCTCCTCGCAAATACTTT 58.990 43.478 0.00 0.00 0.00 2.66
4522 9829 4.752604 TCGCAAATACTTTGTTACTGCTCA 59.247 37.500 1.97 0.00 42.56 4.26
4523 9830 5.411361 TCGCAAATACTTTGTTACTGCTCAT 59.589 36.000 1.97 0.00 42.56 2.90
4524 9831 5.509272 CGCAAATACTTTGTTACTGCTCATG 59.491 40.000 1.97 0.00 42.56 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 5.563876 AGATTGACTCTGCCATGATGTAT 57.436 39.130 0.00 0.00 31.12 2.29
23 24 4.196971 TGAAGATTGACTCTGCCATGATG 58.803 43.478 0.00 0.00 33.29 3.07
57 58 4.707030 TGGCACTTGCATATGAAGAAAG 57.293 40.909 6.97 6.62 44.36 2.62
60 61 3.379057 CACATGGCACTTGCATATGAAGA 59.621 43.478 18.83 0.00 44.36 2.87
102 103 7.282450 TCGCATAGAGACAGAGATACAACTAAA 59.718 37.037 0.00 0.00 0.00 1.85
161 162 1.909302 TCCCCTTTTGCAAACAAACCA 59.091 42.857 12.39 0.00 45.29 3.67
177 178 5.446260 TTTTCACTAAAGGATACCTCCCC 57.554 43.478 0.00 0.00 43.21 4.81
259 272 7.761409 TGTGGACAATGATCAATAAAGCTTAC 58.239 34.615 0.00 0.00 0.00 2.34
295 308 4.338964 TCCATCCCATTGATCATTTTCGTG 59.661 41.667 0.00 0.00 0.00 4.35
298 311 6.659745 TGATCCATCCCATTGATCATTTTC 57.340 37.500 0.00 0.00 39.81 2.29
303 316 3.204831 TGGTTGATCCATCCCATTGATCA 59.795 43.478 0.00 0.00 42.20 2.92
309 322 4.079038 TCATCTTTGGTTGATCCATCCCAT 60.079 41.667 0.00 0.00 46.60 4.00
310 323 3.269118 TCATCTTTGGTTGATCCATCCCA 59.731 43.478 0.00 0.00 46.60 4.37
332 345 1.293062 ACACTCTTGATCAGGGGCAT 58.707 50.000 4.28 0.00 0.00 4.40
333 346 1.067295 AACACTCTTGATCAGGGGCA 58.933 50.000 4.28 0.00 0.00 5.36
471 485 3.375699 ACGACATTGAGAGGGGAACTAT 58.624 45.455 0.00 0.00 0.00 2.12
479 495 2.347697 TCGTGAACGACATTGAGAGG 57.652 50.000 0.50 0.00 44.22 3.69
525 541 7.825761 TGCAGAAGACTTGATGATTCAGAATTA 59.174 33.333 0.00 0.00 32.27 1.40
530 546 5.642491 TCTTGCAGAAGACTTGATGATTCAG 59.358 40.000 0.00 0.00 32.98 3.02
610 630 2.349886 GCAGCTCCTTTATCGTTGTCTG 59.650 50.000 0.00 0.00 0.00 3.51
611 631 2.622436 GCAGCTCCTTTATCGTTGTCT 58.378 47.619 0.00 0.00 0.00 3.41
620 640 2.682563 CGGTATTTGGGCAGCTCCTTTA 60.683 50.000 0.00 0.00 34.39 1.85
622 642 0.394352 CGGTATTTGGGCAGCTCCTT 60.394 55.000 0.00 0.00 34.39 3.36
646 666 0.520404 GCAGTGTGCCAAGATGACTG 59.480 55.000 0.00 0.00 37.42 3.51
647 667 0.109153 TGCAGTGTGCCAAGATGACT 59.891 50.000 0.00 0.00 44.23 3.41
648 668 0.520404 CTGCAGTGTGCCAAGATGAC 59.480 55.000 5.25 0.00 44.23 3.06
655 675 0.466007 ACAACATCTGCAGTGTGCCA 60.466 50.000 14.67 0.00 44.23 4.92
674 694 3.499048 GCAAAGTACGAGATCAGACGAA 58.501 45.455 12.38 0.00 0.00 3.85
706 727 6.458070 CGAGGTTTTGCAAAAATCCATGTTTT 60.458 34.615 25.40 7.22 32.94 2.43
707 728 5.007528 CGAGGTTTTGCAAAAATCCATGTTT 59.992 36.000 25.40 7.89 0.00 2.83
729 750 2.279073 CCTAGGGAGCCACCTCGA 59.721 66.667 0.00 0.00 42.09 4.04
784 807 6.484288 TGGAGATGACAACACAATAGGAAAT 58.516 36.000 0.00 0.00 0.00 2.17
786 809 5.013079 ACTGGAGATGACAACACAATAGGAA 59.987 40.000 0.00 0.00 0.00 3.36
791 814 4.978099 AGAACTGGAGATGACAACACAAT 58.022 39.130 0.00 0.00 0.00 2.71
856 879 4.928601 TGGATACACGAAGAGGTTTATCG 58.071 43.478 0.00 0.00 46.17 2.92
906 980 8.304596 GCCATGATTGATTCTTTATCACATGAT 58.695 33.333 14.76 0.00 43.58 2.45
918 992 3.767673 AGCTGTTTGCCATGATTGATTCT 59.232 39.130 0.00 0.00 44.23 2.40
940 1014 0.320421 GAACCGAGTGCCAAGCAGTA 60.320 55.000 0.00 0.00 42.74 2.74
1008 2906 4.261994 GCAATATGGTGAGGTGTGTTTGTT 60.262 41.667 0.00 0.00 0.00 2.83
1009 2907 3.255642 GCAATATGGTGAGGTGTGTTTGT 59.744 43.478 0.00 0.00 0.00 2.83
1022 2920 0.333312 TTTCCCGGGTGCAATATGGT 59.667 50.000 22.86 0.00 0.00 3.55
1034 2932 1.080025 GGAGACACTCGTTTCCCGG 60.080 63.158 0.00 0.00 39.93 5.73
1037 2935 0.966920 TCCTGGAGACACTCGTTTCC 59.033 55.000 0.00 0.00 44.88 3.13
1039 2937 1.705873 ACTCCTGGAGACACTCGTTT 58.294 50.000 29.71 1.03 35.60 3.60
1059 2957 1.671054 GCTCTTTGTGGCGTGGCTA 60.671 57.895 0.00 0.00 0.00 3.93
1081 3116 3.939592 GGAAAATGTCCACTACTAGCACC 59.060 47.826 0.00 0.00 46.97 5.01
1111 3146 0.104487 TGCCAACCGAAGACGTACAA 59.896 50.000 0.00 0.00 37.88 2.41
1120 3155 1.202758 AGTCACTCATTGCCAACCGAA 60.203 47.619 0.00 0.00 0.00 4.30
1138 3198 3.767673 TGTTCCTTTGGATACTAGCGAGT 59.232 43.478 4.47 4.47 39.92 4.18
1148 3208 9.492730 AGGAAAAATATGTATGTTCCTTTGGAT 57.507 29.630 10.37 0.00 44.49 3.41
1303 3376 2.920384 TCGGTGTGGCACTGGCTA 60.920 61.111 19.83 0.00 40.76 3.93
1319 3403 5.331876 ACAAGTGAGGTACAAGATAGCTC 57.668 43.478 0.00 6.26 41.11 4.09
1369 3453 7.552687 TCAGAGGTGTGTTTACCAATTGATATC 59.447 37.037 7.12 0.00 43.37 1.63
1419 3506 4.503123 CGGATCTTATTGACCATACAGCCA 60.503 45.833 0.00 0.00 0.00 4.75
1445 3535 0.681175 ACCAATCCACCTTTGCTTGC 59.319 50.000 0.00 0.00 0.00 4.01
1471 3562 2.727123 TGTTGGGCCGATATGAATGT 57.273 45.000 0.00 0.00 0.00 2.71
1475 3566 1.540146 CGTCATGTTGGGCCGATATGA 60.540 52.381 24.75 24.75 0.00 2.15
1480 3571 2.047655 GACGTCATGTTGGGCCGA 60.048 61.111 11.55 0.00 0.00 5.54
1481 3572 3.124921 GGACGTCATGTTGGGCCG 61.125 66.667 18.91 0.00 0.00 6.13
1517 3617 5.538813 ACGGAGCTTCAACTCATATATGGTA 59.461 40.000 12.78 0.00 38.50 3.25
1555 3656 2.741878 CGTACTCAAGCGGGGATTGATT 60.742 50.000 0.00 0.00 37.33 2.57
1576 3677 1.817447 ACAGTAGTAGAAGGGCGTGAC 59.183 52.381 0.00 0.00 0.00 3.67
1582 3683 3.383698 TGGAGGACAGTAGTAGAAGGG 57.616 52.381 0.00 0.00 0.00 3.95
1614 3715 6.795144 TGAATGCAGAATTGGGTAATCATT 57.205 33.333 0.00 0.00 0.00 2.57
1669 3770 3.624326 TCACTCGGTGCAAGAATTTTG 57.376 42.857 0.00 0.00 32.98 2.44
1692 3802 1.271102 GGCGCATTCTACAAAACCCAA 59.729 47.619 10.83 0.00 0.00 4.12
1728 3981 7.170828 GCTCATGAATAAATGACACGTGGTATA 59.829 37.037 21.57 5.93 33.08 1.47
1729 3982 6.017934 GCTCATGAATAAATGACACGTGGTAT 60.018 38.462 21.57 10.69 33.08 2.73
1730 3983 5.293324 GCTCATGAATAAATGACACGTGGTA 59.707 40.000 21.57 8.57 33.08 3.25
1732 3985 4.094739 TGCTCATGAATAAATGACACGTGG 59.905 41.667 21.57 1.66 33.08 4.94
1773 4026 3.873952 GGATGTCTCTTGATTGTGGCTAC 59.126 47.826 0.00 0.00 0.00 3.58
1776 4029 2.681848 CTGGATGTCTCTTGATTGTGGC 59.318 50.000 0.00 0.00 0.00 5.01
1790 4043 3.133901 TGTACTGTGTGTGTTCTGGATGT 59.866 43.478 0.00 0.00 0.00 3.06
1804 4057 4.614555 TCTTGCAAAGTGTTGTACTGTG 57.385 40.909 0.00 0.00 46.34 3.66
1807 4060 6.322491 GTTTCTTCTTGCAAAGTGTTGTACT 58.678 36.000 0.00 0.00 46.34 2.73
1862 4118 5.003804 TCAGGTTGTTTTGCTTCTAGGATC 58.996 41.667 0.00 0.00 0.00 3.36
1869 4125 3.300009 CGACATCAGGTTGTTTTGCTTC 58.700 45.455 0.00 0.00 0.00 3.86
1883 4139 1.960763 GCATATGGCGGCGACATCA 60.961 57.895 34.32 18.74 31.56 3.07
1885 4141 2.669569 GGCATATGGCGGCGACAT 60.670 61.111 32.82 32.82 46.16 3.06
1899 4155 2.637025 GCTTTTGCGACGAAGGCA 59.363 55.556 0.00 0.00 38.93 4.75
1951 4207 9.905713 TTGTCTTTTATGGCACTAATTCTATCT 57.094 29.630 0.00 0.00 0.00 1.98
1971 4228 1.331756 CTCACAACGCAGCTTTGTCTT 59.668 47.619 14.12 0.00 34.91 3.01
2107 4724 0.466739 TGTAGGATAGCGGCTTCGGA 60.467 55.000 8.26 0.00 0.00 4.55
2127 4744 3.373565 CGGCACAAGAAAGGGGGC 61.374 66.667 0.00 0.00 0.00 5.80
2130 4747 1.852067 CGGTTCGGCACAAGAAAGGG 61.852 60.000 0.00 0.00 0.00 3.95
2183 4800 1.927174 CGCTGGTGTTATCTCTTTCGG 59.073 52.381 0.00 0.00 0.00 4.30
2188 4805 0.824759 GGGTCGCTGGTGTTATCTCT 59.175 55.000 0.00 0.00 0.00 3.10
2247 4866 1.303561 TGTGATGGTGCTTGCTCCC 60.304 57.895 10.65 3.60 0.00 4.30
2330 4949 1.729267 ATCTGGTTGGGCAGGTGGTT 61.729 55.000 0.00 0.00 0.00 3.67
2337 4956 1.619432 GGAAATGGATCTGGTTGGGCA 60.619 52.381 0.00 0.00 0.00 5.36
2353 4972 2.038426 TGCTCCTCTTTGTCATCGGAAA 59.962 45.455 0.00 0.00 0.00 3.13
2389 5008 7.726291 TCTGGATTCACAAGGGTATTTACAAAA 59.274 33.333 0.00 0.00 0.00 2.44
2390 5009 7.235079 TCTGGATTCACAAGGGTATTTACAAA 58.765 34.615 0.00 0.00 0.00 2.83
2391 5010 6.785076 TCTGGATTCACAAGGGTATTTACAA 58.215 36.000 0.00 0.00 0.00 2.41
2392 5011 6.381498 TCTGGATTCACAAGGGTATTTACA 57.619 37.500 0.00 0.00 0.00 2.41
2393 5012 5.823045 CCTCTGGATTCACAAGGGTATTTAC 59.177 44.000 0.00 0.00 0.00 2.01
2394 5013 5.729229 TCCTCTGGATTCACAAGGGTATTTA 59.271 40.000 0.00 0.00 0.00 1.40
2395 5014 4.540099 TCCTCTGGATTCACAAGGGTATTT 59.460 41.667 0.00 0.00 0.00 1.40
2396 5015 4.111577 TCCTCTGGATTCACAAGGGTATT 58.888 43.478 0.00 0.00 0.00 1.89
2397 5016 3.736094 TCCTCTGGATTCACAAGGGTAT 58.264 45.455 0.00 0.00 0.00 2.73
2398 5017 3.199442 TCCTCTGGATTCACAAGGGTA 57.801 47.619 0.00 0.00 0.00 3.69
2399 5018 2.044793 TCCTCTGGATTCACAAGGGT 57.955 50.000 0.00 0.00 0.00 4.34
2400 5019 3.439857 TTTCCTCTGGATTCACAAGGG 57.560 47.619 0.00 0.00 0.00 3.95
2401 5020 5.990120 AAATTTCCTCTGGATTCACAAGG 57.010 39.130 0.00 0.00 0.00 3.61
2402 5021 8.742777 TGAATAAATTTCCTCTGGATTCACAAG 58.257 33.333 0.00 0.00 0.00 3.16
2403 5022 8.522830 GTGAATAAATTTCCTCTGGATTCACAA 58.477 33.333 23.39 1.36 40.74 3.33
2404 5023 7.122650 GGTGAATAAATTTCCTCTGGATTCACA 59.877 37.037 26.47 4.86 41.82 3.58
2405 5024 7.484140 GGTGAATAAATTTCCTCTGGATTCAC 58.516 38.462 21.69 21.69 40.53 3.18
2406 5025 6.318648 CGGTGAATAAATTTCCTCTGGATTCA 59.681 38.462 0.00 0.04 0.00 2.57
2407 5026 6.729187 CGGTGAATAAATTTCCTCTGGATTC 58.271 40.000 0.00 0.00 0.00 2.52
2408 5027 5.067805 GCGGTGAATAAATTTCCTCTGGATT 59.932 40.000 0.00 0.00 0.00 3.01
2409 5028 4.580580 GCGGTGAATAAATTTCCTCTGGAT 59.419 41.667 0.00 0.00 0.00 3.41
2410 5029 3.945285 GCGGTGAATAAATTTCCTCTGGA 59.055 43.478 0.00 0.00 0.00 3.86
2411 5030 3.066760 GGCGGTGAATAAATTTCCTCTGG 59.933 47.826 0.00 0.00 0.00 3.86
2412 5031 3.242739 CGGCGGTGAATAAATTTCCTCTG 60.243 47.826 0.00 0.00 0.00 3.35
2413 5032 2.943033 CGGCGGTGAATAAATTTCCTCT 59.057 45.455 0.00 0.00 0.00 3.69
2414 5033 2.681344 ACGGCGGTGAATAAATTTCCTC 59.319 45.455 13.24 0.00 0.00 3.71
2415 5034 2.681344 GACGGCGGTGAATAAATTTCCT 59.319 45.455 13.24 0.00 0.00 3.36
2416 5035 2.420722 TGACGGCGGTGAATAAATTTCC 59.579 45.455 13.24 0.00 0.00 3.13
2417 5036 3.120130 TGTGACGGCGGTGAATAAATTTC 60.120 43.478 13.24 0.00 0.00 2.17
2418 5037 2.814919 TGTGACGGCGGTGAATAAATTT 59.185 40.909 13.24 0.00 0.00 1.82
2419 5038 2.418628 CTGTGACGGCGGTGAATAAATT 59.581 45.455 13.24 0.00 0.00 1.82
2420 5039 2.006888 CTGTGACGGCGGTGAATAAAT 58.993 47.619 13.24 0.00 0.00 1.40
2421 5040 1.434555 CTGTGACGGCGGTGAATAAA 58.565 50.000 13.24 0.00 0.00 1.40
2422 5041 1.017177 GCTGTGACGGCGGTGAATAA 61.017 55.000 13.24 0.00 0.00 1.40
2423 5042 1.447140 GCTGTGACGGCGGTGAATA 60.447 57.895 13.24 0.00 0.00 1.75
2424 5043 2.742372 GCTGTGACGGCGGTGAAT 60.742 61.111 13.24 0.00 0.00 2.57
2425 5044 4.980805 GGCTGTGACGGCGGTGAA 62.981 66.667 13.24 0.00 36.46 3.18
2434 5053 2.951475 TTTCCGGTGGTGGCTGTGAC 62.951 60.000 0.00 0.00 0.00 3.67
2435 5054 2.063015 ATTTCCGGTGGTGGCTGTGA 62.063 55.000 0.00 0.00 0.00 3.58
2436 5055 1.178534 AATTTCCGGTGGTGGCTGTG 61.179 55.000 0.00 0.00 0.00 3.66
2437 5056 0.469144 AAATTTCCGGTGGTGGCTGT 60.469 50.000 0.00 0.00 0.00 4.40
2438 5057 1.540267 TAAATTTCCGGTGGTGGCTG 58.460 50.000 0.00 0.00 0.00 4.85
2439 5058 2.525105 ATAAATTTCCGGTGGTGGCT 57.475 45.000 0.00 0.00 0.00 4.75
2440 5059 2.494073 TGAATAAATTTCCGGTGGTGGC 59.506 45.455 0.00 0.00 0.00 5.01
2441 5060 3.119280 GGTGAATAAATTTCCGGTGGTGG 60.119 47.826 0.00 0.00 0.00 4.61
2442 5061 3.426963 CGGTGAATAAATTTCCGGTGGTG 60.427 47.826 0.00 0.00 35.53 4.17
2443 5062 2.750712 CGGTGAATAAATTTCCGGTGGT 59.249 45.455 0.00 0.00 35.53 4.16
2444 5063 2.098443 CCGGTGAATAAATTTCCGGTGG 59.902 50.000 20.68 2.75 44.58 4.61
2445 5064 3.414549 CCGGTGAATAAATTTCCGGTG 57.585 47.619 20.68 2.74 44.58 4.94
2448 5067 1.066454 GGGCCGGTGAATAAATTTCCG 59.934 52.381 1.90 7.99 37.33 4.30
2449 5068 2.104170 TGGGCCGGTGAATAAATTTCC 58.896 47.619 1.90 0.00 0.00 3.13
2450 5069 3.878160 TTGGGCCGGTGAATAAATTTC 57.122 42.857 1.90 0.00 0.00 2.17
2451 5070 4.835284 ATTTGGGCCGGTGAATAAATTT 57.165 36.364 1.90 0.00 0.00 1.82
2452 5071 4.512484 CAATTTGGGCCGGTGAATAAATT 58.488 39.130 1.90 7.19 0.00 1.82
2453 5072 3.681313 GCAATTTGGGCCGGTGAATAAAT 60.681 43.478 1.90 1.05 0.00 1.40
2454 5073 2.354203 GCAATTTGGGCCGGTGAATAAA 60.354 45.455 1.90 0.00 0.00 1.40
2455 5074 1.205893 GCAATTTGGGCCGGTGAATAA 59.794 47.619 1.90 0.00 0.00 1.40
2456 5075 0.820871 GCAATTTGGGCCGGTGAATA 59.179 50.000 1.90 0.00 0.00 1.75
2457 5076 1.190833 TGCAATTTGGGCCGGTGAAT 61.191 50.000 1.90 0.00 0.00 2.57
2458 5077 1.834378 TGCAATTTGGGCCGGTGAA 60.834 52.632 1.90 0.00 0.00 3.18
2459 5078 2.203552 TGCAATTTGGGCCGGTGA 60.204 55.556 1.90 0.00 0.00 4.02
2460 5079 2.048316 GTGCAATTTGGGCCGGTG 60.048 61.111 1.90 0.00 0.00 4.94
2495 5114 0.474184 CTTGTGTCCTCTGGTGGGTT 59.526 55.000 0.00 0.00 0.00 4.11
2506 5125 2.025699 TGGGGGCTAATAACTTGTGTCC 60.026 50.000 0.00 0.00 0.00 4.02
2507 5126 3.359695 TGGGGGCTAATAACTTGTGTC 57.640 47.619 0.00 0.00 0.00 3.67
2509 5128 5.245075 TCTTTTTGGGGGCTAATAACTTGTG 59.755 40.000 0.00 0.00 0.00 3.33
2511 5130 5.993748 TCTTTTTGGGGGCTAATAACTTG 57.006 39.130 0.00 0.00 0.00 3.16
2512 5131 7.381789 TTTTCTTTTTGGGGGCTAATAACTT 57.618 32.000 0.00 0.00 0.00 2.66
2513 5132 7.221450 GTTTTTCTTTTTGGGGGCTAATAACT 58.779 34.615 0.00 0.00 0.00 2.24
2514 5133 6.428771 GGTTTTTCTTTTTGGGGGCTAATAAC 59.571 38.462 0.00 0.00 0.00 1.89
2515 5134 6.101296 TGGTTTTTCTTTTTGGGGGCTAATAA 59.899 34.615 0.00 0.00 0.00 1.40
2516 5135 5.607171 TGGTTTTTCTTTTTGGGGGCTAATA 59.393 36.000 0.00 0.00 0.00 0.98
2517 5136 4.413851 TGGTTTTTCTTTTTGGGGGCTAAT 59.586 37.500 0.00 0.00 0.00 1.73
2518 5137 3.780850 TGGTTTTTCTTTTTGGGGGCTAA 59.219 39.130 0.00 0.00 0.00 3.09
2519 5138 3.385115 TGGTTTTTCTTTTTGGGGGCTA 58.615 40.909 0.00 0.00 0.00 3.93
2520 5139 2.172505 CTGGTTTTTCTTTTTGGGGGCT 59.827 45.455 0.00 0.00 0.00 5.19
2521 5140 2.171659 TCTGGTTTTTCTTTTTGGGGGC 59.828 45.455 0.00 0.00 0.00 5.80
2522 5141 3.181455 CCTCTGGTTTTTCTTTTTGGGGG 60.181 47.826 0.00 0.00 0.00 5.40
2523 5142 3.709141 TCCTCTGGTTTTTCTTTTTGGGG 59.291 43.478 0.00 0.00 0.00 4.96
2524 5143 4.161377 TGTCCTCTGGTTTTTCTTTTTGGG 59.839 41.667 0.00 0.00 0.00 4.12
2525 5144 5.109210 GTGTCCTCTGGTTTTTCTTTTTGG 58.891 41.667 0.00 0.00 0.00 3.28
2526 5145 4.798387 CGTGTCCTCTGGTTTTTCTTTTTG 59.202 41.667 0.00 0.00 0.00 2.44
2527 5146 4.703093 TCGTGTCCTCTGGTTTTTCTTTTT 59.297 37.500 0.00 0.00 0.00 1.94
2528 5147 4.266714 TCGTGTCCTCTGGTTTTTCTTTT 58.733 39.130 0.00 0.00 0.00 2.27
2529 5148 3.877508 CTCGTGTCCTCTGGTTTTTCTTT 59.122 43.478 0.00 0.00 0.00 2.52
2530 5149 3.118371 ACTCGTGTCCTCTGGTTTTTCTT 60.118 43.478 0.00 0.00 0.00 2.52
2531 5150 2.434702 ACTCGTGTCCTCTGGTTTTTCT 59.565 45.455 0.00 0.00 0.00 2.52
2532 5151 2.801111 GACTCGTGTCCTCTGGTTTTTC 59.199 50.000 6.35 0.00 37.24 2.29
2533 5152 2.169769 TGACTCGTGTCCTCTGGTTTTT 59.830 45.455 14.57 0.00 42.28 1.94
2534 5153 1.760613 TGACTCGTGTCCTCTGGTTTT 59.239 47.619 14.57 0.00 42.28 2.43
2535 5154 1.410004 TGACTCGTGTCCTCTGGTTT 58.590 50.000 14.57 0.00 42.28 3.27
2536 5155 1.341531 CTTGACTCGTGTCCTCTGGTT 59.658 52.381 14.57 0.00 42.28 3.67
2738 5401 3.489513 GGGAGGGGTCGGAATGGG 61.490 72.222 0.00 0.00 0.00 4.00
2774 5450 7.959651 CGAGGAGATGATTTTTCAGTTAAACAG 59.040 37.037 0.00 0.00 0.00 3.16
2778 5454 5.937540 TGCGAGGAGATGATTTTTCAGTTAA 59.062 36.000 0.00 0.00 0.00 2.01
2779 5455 5.487433 TGCGAGGAGATGATTTTTCAGTTA 58.513 37.500 0.00 0.00 0.00 2.24
2792 5468 5.923204 ACTATCTTTGAAATGCGAGGAGAT 58.077 37.500 0.00 0.00 0.00 2.75
2795 5471 9.778741 ATTATTACTATCTTTGAAATGCGAGGA 57.221 29.630 0.00 0.00 0.00 3.71
2814 5490 8.224437 GCAAGAGAGGCGAAGATTTATTATTAC 58.776 37.037 0.00 0.00 0.00 1.89
2818 5494 5.918608 AGCAAGAGAGGCGAAGATTTATTA 58.081 37.500 0.00 0.00 36.08 0.98
2876 5573 3.620488 ACCAACAGCATATAACACCAGG 58.380 45.455 0.00 0.00 0.00 4.45
2877 5574 4.458989 ACAACCAACAGCATATAACACCAG 59.541 41.667 0.00 0.00 0.00 4.00
2917 7796 4.079253 ACATAACCTGGAATTGTGTGGAC 58.921 43.478 0.00 0.00 31.10 4.02
2929 7812 3.009033 TGGAGAGGACAAACATAACCTGG 59.991 47.826 0.00 0.00 32.53 4.45
3036 7920 4.090057 GCTCCGCCGCTTGTGAAC 62.090 66.667 0.00 0.00 0.00 3.18
3077 7961 0.464373 TCGCCCTTCAAGATGATGCC 60.464 55.000 0.00 0.00 0.00 4.40
3080 7964 0.179034 GGCTCGCCCTTCAAGATGAT 60.179 55.000 0.00 0.00 0.00 2.45
3280 8164 6.575244 ATTATCAGGACACAATTCCACCTA 57.425 37.500 0.00 0.00 38.25 3.08
3369 8262 5.344743 AGTTTCAACAGAGAGACAGAACA 57.655 39.130 0.00 0.00 0.00 3.18
3417 8315 9.462174 GTTTGTGATCATCAGATGTTTAAAACA 57.538 29.630 10.34 5.45 46.94 2.83
3566 8467 2.796557 TCGTCTCAGAATCTCAGTGGT 58.203 47.619 0.00 0.00 0.00 4.16
3578 8481 4.214980 ACAAACAGCAAATTCGTCTCAG 57.785 40.909 0.00 0.00 0.00 3.35
3584 8487 2.032979 GGCCAAACAAACAGCAAATTCG 60.033 45.455 0.00 0.00 0.00 3.34
3591 8494 1.219646 CATGTGGCCAAACAAACAGC 58.780 50.000 7.24 0.00 32.81 4.40
3727 8630 5.200483 GGTCAAGATCCAAACATATCCCAA 58.800 41.667 0.00 0.00 0.00 4.12
4048 8994 1.581934 CGAACCAGCAGAAGACACAA 58.418 50.000 0.00 0.00 0.00 3.33
4085 9031 0.035056 ATGAACAGAGGGAAAGGGCG 60.035 55.000 0.00 0.00 0.00 6.13
4101 9047 1.014044 GCACGAGGCAAGACGAATGA 61.014 55.000 0.00 0.00 43.97 2.57
4226 9210 1.112113 GAGAATGCGGACAGGGAGTA 58.888 55.000 0.00 0.00 0.00 2.59
4313 9620 1.299316 CAACTGCAACCACGCCTTG 60.299 57.895 0.00 0.00 0.00 3.61
4314 9621 1.447317 CTCAACTGCAACCACGCCTT 61.447 55.000 0.00 0.00 0.00 4.35
4404 9711 5.180117 GCCATATAGCCACATACAGAAACTG 59.820 44.000 0.00 0.00 37.52 3.16
4453 9760 8.186163 CACTAATGCATTCACACAAGATATTGT 58.814 33.333 16.86 0.00 35.14 2.71
4482 9789 1.915078 CGAGGAGGAAAGGCATGGGT 61.915 60.000 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.