Multiple sequence alignment - TraesCS2B01G263700

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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 TraesCS2B01G263700 chr2B 100.000 5287 0 0 1 5287 355390864 355385578 0.000000e+00 9764.0
1 TraesCS2B01G263700 chr2B 79.963 544 78 20 234 760 777557250 777557779 6.470000e-99 372.0
2 TraesCS2B01G263700 chr2B 79.597 397 38 24 1884 2249 652705594 652705978 1.470000e-60 244.0
3 TraesCS2B01G263700 chr2B 78.903 237 21 10 2389 2625 652706069 652706276 3.320000e-27 134.0
4 TraesCS2B01G263700 chr2B 95.455 66 3 0 2389 2454 134846514 134846579 7.240000e-19 106.0
5 TraesCS2B01G263700 chr2D 96.485 3926 71 16 776 4678 293857662 293861543 0.000000e+00 6423.0
6 TraesCS2B01G263700 chr2D 85.336 566 80 3 4720 5283 428854403 428854967 2.740000e-162 582.0
7 TraesCS2B01G263700 chr2D 79.720 572 110 6 4719 5287 309943860 309943292 4.930000e-110 409.0
8 TraesCS2B01G263700 chr2D 96.364 55 2 0 4624 4678 293861525 293861579 2.030000e-14 91.6
9 TraesCS2B01G263700 chr2D 93.443 61 2 1 4624 4684 293861561 293861619 7.290000e-14 89.8
10 TraesCS2B01G263700 chr2A 96.131 3593 83 17 1092 4670 360868372 360871922 0.000000e+00 5814.0
11 TraesCS2B01G263700 chr2A 93.827 162 9 1 776 936 360867974 360868135 5.290000e-60 243.0
12 TraesCS2B01G263700 chr2A 97.778 45 1 0 4643 4687 360872234 360872278 1.580000e-10 78.7
13 TraesCS2B01G263700 chr7D 88.665 1094 98 14 3130 4209 538908536 538909617 0.000000e+00 1310.0
14 TraesCS2B01G263700 chr7D 89.392 641 57 6 2338 2970 538905410 538906047 0.000000e+00 797.0
15 TraesCS2B01G263700 chr7D 82.210 534 77 13 234 760 193493851 193494373 1.350000e-120 444.0
16 TraesCS2B01G263700 chr7D 96.341 82 3 0 1957 2038 538902583 538902664 9.240000e-28 135.0
17 TraesCS2B01G263700 chr7D 80.159 126 6 8 3014 3128 538908370 538908487 5.680000e-10 76.8
18 TraesCS2B01G263700 chr7B 87.978 1098 101 17 3130 4209 581502933 581504017 0.000000e+00 1267.0
19 TraesCS2B01G263700 chr7B 80.387 1759 166 87 2389 4021 661739658 661741363 0.000000e+00 1171.0
20 TraesCS2B01G263700 chr7B 77.954 567 57 40 1740 2249 723874192 723873637 5.180000e-75 292.0
21 TraesCS2B01G263700 chr7B 88.000 200 20 2 4110 4305 661741440 661741639 3.180000e-57 233.0
22 TraesCS2B01G263700 chr7B 78.750 240 22 10 2389 2628 723873546 723873336 3.320000e-27 134.0
23 TraesCS2B01G263700 chr7B 93.651 63 4 0 1 63 549934521 549934459 1.570000e-15 95.3
24 TraesCS2B01G263700 chr7A 98.834 686 6 2 81 766 513543719 513543036 0.000000e+00 1221.0
25 TraesCS2B01G263700 chr7A 83.489 1284 115 50 3130 4349 674105298 674104048 0.000000e+00 1107.0
26 TraesCS2B01G263700 chr7A 88.298 752 73 13 3136 3882 620532635 620533376 0.000000e+00 887.0
27 TraesCS2B01G263700 chr7A 81.545 699 59 37 2389 3039 674106120 674105444 3.650000e-141 512.0
28 TraesCS2B01G263700 chr7A 79.567 416 50 12 3913 4317 620533487 620533878 1.130000e-66 265.0
29 TraesCS2B01G263700 chr7A 91.803 61 2 3 1957 2016 712461752 712461810 1.220000e-11 82.4
30 TraesCS2B01G263700 chr3B 93.109 682 35 7 81 761 482409572 482408902 0.000000e+00 989.0
31 TraesCS2B01G263700 chr3B 91.134 688 53 5 76 762 592303633 592304313 0.000000e+00 926.0
32 TraesCS2B01G263700 chr3B 80.202 495 95 3 4722 5215 223348528 223349020 8.360000e-98 368.0
33 TraesCS2B01G263700 chr5B 84.284 929 87 35 3133 4043 37814673 37813786 0.000000e+00 852.0
34 TraesCS2B01G263700 chr5B 83.793 907 82 37 3130 4019 38518732 38519590 0.000000e+00 800.0
35 TraesCS2B01G263700 chr5B 81.201 383 39 15 2511 2876 37815387 37815021 1.450000e-70 278.0
36 TraesCS2B01G263700 chr5B 82.143 336 31 14 2511 2833 38518013 38518332 1.460000e-65 261.0
37 TraesCS2B01G263700 chr5B 79.545 396 33 28 1740 2093 38516732 38517121 6.840000e-59 239.0
38 TraesCS2B01G263700 chr5A 83.857 923 94 29 3133 4038 31135216 31134332 0.000000e+00 828.0
39 TraesCS2B01G263700 chr5A 79.817 545 86 18 234 760 694512428 694512966 5.000000e-100 375.0
40 TraesCS2B01G263700 chr5A 80.930 430 49 18 3911 4320 31293309 31293725 5.140000e-80 309.0
41 TraesCS2B01G263700 chr5A 81.250 384 37 16 2511 2876 31135931 31135565 1.450000e-70 278.0
42 TraesCS2B01G263700 chr5A 75.418 598 60 40 2512 3052 31292020 31292587 5.370000e-50 209.0
43 TraesCS2B01G263700 chr5A 79.470 151 16 4 3153 3302 31292796 31292932 5.640000e-15 93.5
44 TraesCS2B01G263700 chr4D 88.339 566 66 0 4720 5285 289391784 289392349 0.000000e+00 680.0
45 TraesCS2B01G263700 chr6A 81.090 936 98 43 3130 4020 616800169 616799268 0.000000e+00 675.0
46 TraesCS2B01G263700 chr6A 78.992 714 65 42 2393 3039 616806184 616805489 4.930000e-110 409.0
47 TraesCS2B01G263700 chr6A 82.872 397 55 11 234 627 346346623 346347009 1.410000e-90 344.0
48 TraesCS2B01G263700 chr6A 88.889 198 17 3 4112 4304 616799168 616798971 6.840000e-59 239.0
49 TraesCS2B01G263700 chr1A 82.007 817 88 32 3233 4021 77098178 77098963 1.610000e-179 640.0
50 TraesCS2B01G263700 chr1A 80.877 570 105 3 4720 5287 437714305 437713738 3.760000e-121 446.0
51 TraesCS2B01G263700 chr1A 84.112 214 20 4 4112 4321 543391678 543391881 1.500000e-45 195.0
52 TraesCS2B01G263700 chr6D 81.404 570 102 4 4720 5287 467308663 467308096 3.730000e-126 462.0
53 TraesCS2B01G263700 chr6D 80.844 569 107 2 4720 5287 427097632 427098199 3.760000e-121 446.0
54 TraesCS2B01G263700 chr4A 80.674 564 104 4 4720 5281 519614303 519614863 2.920000e-117 433.0
55 TraesCS2B01G263700 chr1D 80.303 528 79 17 234 758 172864441 172864946 5.000000e-100 375.0
56 TraesCS2B01G263700 chr1D 78.397 574 45 47 1726 2246 447400899 447401446 3.090000e-77 300.0
57 TraesCS2B01G263700 chr1D 81.507 292 22 22 1979 2247 447466980 447467262 1.490000e-50 211.0
58 TraesCS2B01G263700 chr1D 91.463 82 6 1 2591 2671 447441300 447441381 1.560000e-20 111.0
59 TraesCS2B01G263700 chr1B 76.585 568 88 26 237 767 183924023 183924582 2.430000e-68 270.0


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 TraesCS2B01G263700 chr2B 355385578 355390864 5286 True 9764.000000 9764 100.000000 1 5287 1 chr2B.!!$R1 5286
1 TraesCS2B01G263700 chr2B 777557250 777557779 529 False 372.000000 372 79.963000 234 760 1 chr2B.!!$F2 526
2 TraesCS2B01G263700 chr2D 293857662 293861619 3957 False 2201.466667 6423 95.430667 776 4684 3 chr2D.!!$F2 3908
3 TraesCS2B01G263700 chr2D 428854403 428854967 564 False 582.000000 582 85.336000 4720 5283 1 chr2D.!!$F1 563
4 TraesCS2B01G263700 chr2D 309943292 309943860 568 True 409.000000 409 79.720000 4719 5287 1 chr2D.!!$R1 568
5 TraesCS2B01G263700 chr2A 360867974 360872278 4304 False 2045.233333 5814 95.912000 776 4687 3 chr2A.!!$F1 3911
6 TraesCS2B01G263700 chr7D 538902583 538909617 7034 False 579.700000 1310 88.639250 1957 4209 4 chr7D.!!$F2 2252
7 TraesCS2B01G263700 chr7D 193493851 193494373 522 False 444.000000 444 82.210000 234 760 1 chr7D.!!$F1 526
8 TraesCS2B01G263700 chr7B 581502933 581504017 1084 False 1267.000000 1267 87.978000 3130 4209 1 chr7B.!!$F1 1079
9 TraesCS2B01G263700 chr7B 661739658 661741639 1981 False 702.000000 1171 84.193500 2389 4305 2 chr7B.!!$F2 1916
10 TraesCS2B01G263700 chr7B 723873336 723874192 856 True 213.000000 292 78.352000 1740 2628 2 chr7B.!!$R2 888
11 TraesCS2B01G263700 chr7A 513543036 513543719 683 True 1221.000000 1221 98.834000 81 766 1 chr7A.!!$R1 685
12 TraesCS2B01G263700 chr7A 674104048 674106120 2072 True 809.500000 1107 82.517000 2389 4349 2 chr7A.!!$R2 1960
13 TraesCS2B01G263700 chr7A 620532635 620533878 1243 False 576.000000 887 83.932500 3136 4317 2 chr7A.!!$F2 1181
14 TraesCS2B01G263700 chr3B 482408902 482409572 670 True 989.000000 989 93.109000 81 761 1 chr3B.!!$R1 680
15 TraesCS2B01G263700 chr3B 592303633 592304313 680 False 926.000000 926 91.134000 76 762 1 chr3B.!!$F2 686
16 TraesCS2B01G263700 chr5B 37813786 37815387 1601 True 565.000000 852 82.742500 2511 4043 2 chr5B.!!$R1 1532
17 TraesCS2B01G263700 chr5B 38516732 38519590 2858 False 433.333333 800 81.827000 1740 4019 3 chr5B.!!$F1 2279
18 TraesCS2B01G263700 chr5A 31134332 31135931 1599 True 553.000000 828 82.553500 2511 4038 2 chr5A.!!$R1 1527
19 TraesCS2B01G263700 chr5A 694512428 694512966 538 False 375.000000 375 79.817000 234 760 1 chr5A.!!$F1 526
20 TraesCS2B01G263700 chr5A 31292020 31293725 1705 False 203.833333 309 78.606000 2512 4320 3 chr5A.!!$F2 1808
21 TraesCS2B01G263700 chr4D 289391784 289392349 565 False 680.000000 680 88.339000 4720 5285 1 chr4D.!!$F1 565
22 TraesCS2B01G263700 chr6A 616798971 616800169 1198 True 457.000000 675 84.989500 3130 4304 2 chr6A.!!$R2 1174
23 TraesCS2B01G263700 chr6A 616805489 616806184 695 True 409.000000 409 78.992000 2393 3039 1 chr6A.!!$R1 646
24 TraesCS2B01G263700 chr1A 77098178 77098963 785 False 640.000000 640 82.007000 3233 4021 1 chr1A.!!$F1 788
25 TraesCS2B01G263700 chr1A 437713738 437714305 567 True 446.000000 446 80.877000 4720 5287 1 chr1A.!!$R1 567
26 TraesCS2B01G263700 chr6D 467308096 467308663 567 True 462.000000 462 81.404000 4720 5287 1 chr6D.!!$R1 567
27 TraesCS2B01G263700 chr6D 427097632 427098199 567 False 446.000000 446 80.844000 4720 5287 1 chr6D.!!$F1 567
28 TraesCS2B01G263700 chr4A 519614303 519614863 560 False 433.000000 433 80.674000 4720 5281 1 chr4A.!!$F1 561
29 TraesCS2B01G263700 chr1D 172864441 172864946 505 False 375.000000 375 80.303000 234 758 1 chr1D.!!$F1 524
30 TraesCS2B01G263700 chr1D 447400899 447401446 547 False 300.000000 300 78.397000 1726 2246 1 chr1D.!!$F2 520
31 TraesCS2B01G263700 chr1B 183924023 183924582 559 False 270.000000 270 76.585000 237 767 1 chr1B.!!$F1 530

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
60 61 0.032678 AGCGCGCATATGCTTCTAGT 59.967 50.0 35.10 3.94 38.57 2.57 F
730 755 0.035176 TTGGCCTGCAAAATTCCTGC 59.965 50.0 3.32 5.70 40.35 4.85 F
733 758 0.038343 GCCTGCAAAATTCCTGCGAA 60.038 50.0 7.70 0.00 42.97 4.70 F
769 794 0.040958 CGCAGCCTTAATCATTCCGC 60.041 55.0 0.00 0.00 0.00 5.54 F
1468 1579 0.163788 CCGTGATGTGCAACGACTTC 59.836 55.0 10.13 0.00 42.39 3.01 F
2365 5565 0.746659 ATTTATCAAAGCCCCGCAGC 59.253 50.0 0.00 0.00 0.00 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1031 1073 0.030603 GGGGAGGGAAGGAGACAGAT 60.031 60.000 0.00 0.00 0.00 2.90 R
1605 1716 4.142381 GCATATCAAACCCCACAGAAACTC 60.142 45.833 0.00 0.00 0.00 3.01 R
2730 5987 1.238439 GTAGCACAGAGGCAGCAAAA 58.762 50.000 0.00 0.00 35.83 2.44 R
2895 6213 5.533482 TCTTTTTGACTGCTCTGTAGAGAC 58.467 41.667 12.89 5.01 44.74 3.36 R
3372 9197 2.297033 TCAGAGGGTAACAACACCGTAC 59.703 50.000 0.00 0.00 39.69 3.67 R
4420 10625 4.225042 TGTCTGGTTGAGCATAGGTACAAT 59.775 41.667 0.00 0.00 0.00 2.71 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 6.741992 TTGTGCAAGGAAGATGTTATAGTG 57.258 37.500 0.00 0.00 0.00 2.74
25 26 6.048732 TGTGCAAGGAAGATGTTATAGTGA 57.951 37.500 0.00 0.00 0.00 3.41
26 27 6.472016 TGTGCAAGGAAGATGTTATAGTGAA 58.528 36.000 0.00 0.00 0.00 3.18
27 28 6.595326 TGTGCAAGGAAGATGTTATAGTGAAG 59.405 38.462 0.00 0.00 0.00 3.02
28 29 6.818644 GTGCAAGGAAGATGTTATAGTGAAGA 59.181 38.462 0.00 0.00 0.00 2.87
29 30 7.010923 GTGCAAGGAAGATGTTATAGTGAAGAG 59.989 40.741 0.00 0.00 0.00 2.85
30 31 6.018343 GCAAGGAAGATGTTATAGTGAAGAGC 60.018 42.308 0.00 0.00 0.00 4.09
31 32 5.837437 AGGAAGATGTTATAGTGAAGAGCG 58.163 41.667 0.00 0.00 0.00 5.03
32 33 4.985409 GGAAGATGTTATAGTGAAGAGCGG 59.015 45.833 0.00 0.00 0.00 5.52
33 34 5.452077 GGAAGATGTTATAGTGAAGAGCGGT 60.452 44.000 0.00 0.00 0.00 5.68
34 35 6.238953 GGAAGATGTTATAGTGAAGAGCGGTA 60.239 42.308 0.00 0.00 0.00 4.02
35 36 6.074544 AGATGTTATAGTGAAGAGCGGTAC 57.925 41.667 0.00 0.00 0.00 3.34
36 37 5.593095 AGATGTTATAGTGAAGAGCGGTACA 59.407 40.000 0.00 0.00 0.00 2.90
37 38 5.244785 TGTTATAGTGAAGAGCGGTACAG 57.755 43.478 0.00 0.00 0.00 2.74
38 39 2.873133 ATAGTGAAGAGCGGTACAGC 57.127 50.000 10.25 10.25 37.41 4.40
39 40 1.541379 TAGTGAAGAGCGGTACAGCA 58.459 50.000 20.22 0.00 40.15 4.41
40 41 0.679505 AGTGAAGAGCGGTACAGCAA 59.320 50.000 20.22 0.00 40.15 3.91
41 42 1.070134 AGTGAAGAGCGGTACAGCAAA 59.930 47.619 20.22 0.00 40.15 3.68
42 43 1.461127 GTGAAGAGCGGTACAGCAAAG 59.539 52.381 20.22 0.00 40.15 2.77
43 44 0.444260 GAAGAGCGGTACAGCAAAGC 59.556 55.000 20.22 6.44 40.15 3.51
44 45 1.291877 AAGAGCGGTACAGCAAAGCG 61.292 55.000 20.22 0.82 40.15 4.68
54 55 2.025156 GCAAAGCGCGCATATGCT 59.975 55.556 33.66 14.44 44.97 3.79
59 60 2.819667 AGCGCGCATATGCTTCTAG 58.180 52.632 35.10 10.35 38.57 2.43
60 61 0.032678 AGCGCGCATATGCTTCTAGT 59.967 50.000 35.10 3.94 38.57 2.57
61 62 1.269723 AGCGCGCATATGCTTCTAGTA 59.730 47.619 35.10 0.00 38.57 1.82
62 63 2.094494 AGCGCGCATATGCTTCTAGTAT 60.094 45.455 35.10 2.61 38.57 2.12
63 64 3.128764 AGCGCGCATATGCTTCTAGTATA 59.871 43.478 35.10 0.00 38.57 1.47
64 65 3.240861 GCGCGCATATGCTTCTAGTATAC 59.759 47.826 29.10 0.00 39.32 1.47
65 66 3.791887 CGCGCATATGCTTCTAGTATACC 59.208 47.826 24.56 0.00 39.32 2.73
66 67 4.438880 CGCGCATATGCTTCTAGTATACCT 60.439 45.833 24.56 0.00 39.32 3.08
67 68 5.411781 GCGCATATGCTTCTAGTATACCTT 58.588 41.667 24.56 0.00 39.32 3.50
68 69 6.561614 GCGCATATGCTTCTAGTATACCTTA 58.438 40.000 24.56 0.00 39.32 2.69
69 70 7.033791 GCGCATATGCTTCTAGTATACCTTAA 58.966 38.462 24.56 0.00 39.32 1.85
70 71 7.544566 GCGCATATGCTTCTAGTATACCTTAAA 59.455 37.037 24.56 0.00 39.32 1.52
71 72 9.419297 CGCATATGCTTCTAGTATACCTTAAAA 57.581 33.333 24.56 0.00 39.32 1.52
75 76 6.892485 TGCTTCTAGTATACCTTAAAACCCC 58.108 40.000 0.00 0.00 0.00 4.95
76 77 6.675303 TGCTTCTAGTATACCTTAAAACCCCT 59.325 38.462 0.00 0.00 0.00 4.79
77 78 7.183293 TGCTTCTAGTATACCTTAAAACCCCTT 59.817 37.037 0.00 0.00 0.00 3.95
78 79 8.051535 GCTTCTAGTATACCTTAAAACCCCTTT 58.948 37.037 0.00 0.00 0.00 3.11
79 80 9.970553 CTTCTAGTATACCTTAAAACCCCTTTT 57.029 33.333 0.00 0.00 33.92 2.27
155 157 5.128171 AGGAAGTGAAGTTGTGTGTACAGTA 59.872 40.000 0.00 0.00 38.23 2.74
189 191 7.710475 CAGGTTTTCAAAGCAAAGGAATAAAGA 59.290 33.333 4.41 0.00 38.79 2.52
243 245 3.384789 TGCTAGCCGTATCAAATCTGTCT 59.615 43.478 13.29 0.00 0.00 3.41
643 668 4.267349 AGTACAGGTATGTGACGCTTTT 57.733 40.909 0.00 0.00 40.79 2.27
715 740 5.535753 ATTTATTCCTATGGCAGTTTGGC 57.464 39.130 0.00 0.00 44.03 4.52
727 752 2.145536 CAGTTTGGCCTGCAAAATTCC 58.854 47.619 3.32 0.00 0.00 3.01
728 753 2.049372 AGTTTGGCCTGCAAAATTCCT 58.951 42.857 3.32 0.00 0.00 3.36
729 754 2.145536 GTTTGGCCTGCAAAATTCCTG 58.854 47.619 3.32 0.00 0.00 3.86
730 755 0.035176 TTGGCCTGCAAAATTCCTGC 59.965 50.000 3.32 5.70 40.35 4.85
731 756 1.446618 GGCCTGCAAAATTCCTGCG 60.447 57.895 0.00 3.78 42.97 5.18
732 757 1.586028 GCCTGCAAAATTCCTGCGA 59.414 52.632 7.70 0.00 42.97 5.10
733 758 0.038343 GCCTGCAAAATTCCTGCGAA 60.038 50.000 7.70 0.00 42.97 4.70
734 759 1.605202 GCCTGCAAAATTCCTGCGAAA 60.605 47.619 7.70 0.00 42.97 3.46
735 760 2.932187 GCCTGCAAAATTCCTGCGAAAT 60.932 45.455 7.70 0.00 42.97 2.17
736 761 3.328505 CCTGCAAAATTCCTGCGAAATT 58.671 40.909 7.70 0.00 42.97 1.82
737 762 3.368843 CCTGCAAAATTCCTGCGAAATTC 59.631 43.478 7.70 0.00 42.97 2.17
738 763 3.324993 TGCAAAATTCCTGCGAAATTCC 58.675 40.909 7.70 0.00 42.97 3.01
739 764 2.672874 GCAAAATTCCTGCGAAATTCCC 59.327 45.455 0.00 0.00 0.00 3.97
740 765 3.864160 GCAAAATTCCTGCGAAATTCCCA 60.864 43.478 0.00 0.00 0.00 4.37
741 766 4.506758 CAAAATTCCTGCGAAATTCCCAT 58.493 39.130 0.00 0.00 0.00 4.00
742 767 3.806625 AATTCCTGCGAAATTCCCATG 57.193 42.857 0.00 0.00 0.00 3.66
743 768 0.817013 TTCCTGCGAAATTCCCATGC 59.183 50.000 0.00 0.00 0.00 4.06
744 769 1.064621 CCTGCGAAATTCCCATGCG 59.935 57.895 0.00 0.00 0.00 4.73
746 771 2.278792 GCGAAATTCCCATGCGCC 60.279 61.111 4.18 0.00 41.65 6.53
747 772 2.024588 CGAAATTCCCATGCGCCG 59.975 61.111 4.18 0.00 0.00 6.46
748 773 2.468670 CGAAATTCCCATGCGCCGA 61.469 57.895 4.18 0.00 0.00 5.54
749 774 1.806568 GAAATTCCCATGCGCCGAA 59.193 52.632 4.18 1.44 0.00 4.30
750 775 0.525455 GAAATTCCCATGCGCCGAAC 60.525 55.000 4.18 0.00 0.00 3.95
760 785 3.115892 CGCCGAACGCAGCCTTAA 61.116 61.111 0.00 0.00 37.30 1.85
761 786 2.461110 CGCCGAACGCAGCCTTAAT 61.461 57.895 0.00 0.00 37.30 1.40
762 787 1.352056 GCCGAACGCAGCCTTAATC 59.648 57.895 0.00 0.00 37.47 1.75
763 788 1.366111 GCCGAACGCAGCCTTAATCA 61.366 55.000 0.00 0.00 37.47 2.57
764 789 1.299541 CCGAACGCAGCCTTAATCAT 58.700 50.000 0.00 0.00 0.00 2.45
765 790 1.670811 CCGAACGCAGCCTTAATCATT 59.329 47.619 0.00 0.00 0.00 2.57
766 791 2.286418 CCGAACGCAGCCTTAATCATTC 60.286 50.000 0.00 0.00 0.00 2.67
767 792 2.286418 CGAACGCAGCCTTAATCATTCC 60.286 50.000 0.00 0.00 0.00 3.01
768 793 1.299541 ACGCAGCCTTAATCATTCCG 58.700 50.000 0.00 0.00 0.00 4.30
769 794 0.040958 CGCAGCCTTAATCATTCCGC 60.041 55.000 0.00 0.00 0.00 5.54
770 795 1.312815 GCAGCCTTAATCATTCCGCT 58.687 50.000 0.00 0.00 0.00 5.52
771 796 1.002033 GCAGCCTTAATCATTCCGCTG 60.002 52.381 8.31 8.31 45.05 5.18
772 797 1.002033 CAGCCTTAATCATTCCGCTGC 60.002 52.381 0.00 0.00 37.51 5.25
773 798 1.024271 GCCTTAATCATTCCGCTGCA 58.976 50.000 0.00 0.00 0.00 4.41
774 799 1.268743 GCCTTAATCATTCCGCTGCAC 60.269 52.381 0.00 0.00 0.00 4.57
812 837 0.178903 AAGGCAGAGGTGACACCCTA 60.179 55.000 21.32 0.00 39.75 3.53
924 950 0.391263 CAGCTTACCCCCACTCGTTC 60.391 60.000 0.00 0.00 0.00 3.95
1031 1073 3.446442 ACTCACCGTAAGTTCCCTCTA 57.554 47.619 0.00 0.00 0.00 2.43
1036 1078 3.700038 CACCGTAAGTTCCCTCTATCTGT 59.300 47.826 0.00 0.00 0.00 3.41
1041 1083 4.618378 AAGTTCCCTCTATCTGTCTCCT 57.382 45.455 0.00 0.00 0.00 3.69
1252 1362 1.405821 CTGATCGAGTTTAGAGGCGGT 59.594 52.381 0.00 0.00 0.00 5.68
1468 1579 0.163788 CCGTGATGTGCAACGACTTC 59.836 55.000 10.13 0.00 42.39 3.01
1516 1627 7.690952 ATGCTTAACACCGGAGTAAATTTTA 57.309 32.000 9.46 0.00 0.00 1.52
1605 1716 3.573967 ACAGTCAAATTAACTGGCTTGGG 59.426 43.478 19.51 0.00 46.73 4.12
1670 1781 5.879237 TCTTTTGGCATTACATGATCGTTC 58.121 37.500 0.00 0.00 0.00 3.95
1691 1802 7.484641 TCGTTCTCATGTTTCTTTTGAGTTTTG 59.515 33.333 0.00 0.00 38.39 2.44
2155 2892 6.648725 GCCTTATTTGTCCATTTTTGCACTTA 59.351 34.615 0.00 0.00 0.00 2.24
2267 5439 3.162666 CCATTCATCATCCCCCATTCTG 58.837 50.000 0.00 0.00 0.00 3.02
2268 5440 2.369983 TTCATCATCCCCCATTCTGC 57.630 50.000 0.00 0.00 0.00 4.26
2272 5444 2.925966 TCATCCCCCATTCTGCTTTT 57.074 45.000 0.00 0.00 0.00 2.27
2317 5517 9.712305 CCTTATTCATAGTAATGACGGAATCTT 57.288 33.333 0.00 0.00 41.87 2.40
2365 5565 0.746659 ATTTATCAAAGCCCCGCAGC 59.253 50.000 0.00 0.00 0.00 5.25
2490 5706 2.426842 AGCAGAGCCAAACCTTATCC 57.573 50.000 0.00 0.00 0.00 2.59
2730 5987 7.902920 AATTAAAGGATGGACATGCTTATGT 57.097 32.000 17.49 6.91 46.58 2.29
2895 6213 1.263217 GTTGTTCACTGTGCTTACCGG 59.737 52.381 0.00 0.00 0.00 5.28
3128 8863 1.350071 CCTCATAGAGCAGCAGGGAT 58.650 55.000 0.00 0.00 0.00 3.85
3151 8933 8.703743 GGATATCCAGCTATATGAAGTCTGAAT 58.296 37.037 17.34 0.00 35.64 2.57
3503 9331 7.759489 TGAAGAGGTATAGTTGCAACATTTT 57.241 32.000 30.11 12.97 0.00 1.82
3591 9437 4.893524 CCTCCTTTGTTACTTTGGAACCTT 59.106 41.667 0.00 0.00 0.00 3.50
4022 10161 5.807520 CCACATAGAGACACATGTAAGACAC 59.192 44.000 0.00 0.00 33.66 3.67
4023 10162 6.350528 CCACATAGAGACACATGTAAGACACT 60.351 42.308 0.00 0.00 33.66 3.55
4024 10163 7.093354 CACATAGAGACACATGTAAGACACTT 58.907 38.462 0.00 0.00 33.66 3.16
4025 10164 8.244113 CACATAGAGACACATGTAAGACACTTA 58.756 37.037 0.00 0.00 33.66 2.24
4026 10165 8.244802 ACATAGAGACACATGTAAGACACTTAC 58.755 37.037 12.81 12.81 33.66 2.34
4027 10166 5.700846 AGAGACACATGTAAGACACTTACG 58.299 41.667 14.18 6.24 0.00 3.18
4028 10167 5.472478 AGAGACACATGTAAGACACTTACGA 59.528 40.000 14.18 6.68 0.00 3.43
4029 10168 6.016527 AGAGACACATGTAAGACACTTACGAA 60.017 38.462 14.18 2.07 0.00 3.85
4043 10219 6.888430 ACACTTACGAAAACAGCTTATTCTG 58.112 36.000 0.00 0.00 39.86 3.02
4053 10229 9.346725 GAAAACAGCTTATTCTGAATAAACCTG 57.653 33.333 27.65 27.65 38.01 4.00
4420 10625 6.100004 GTGACCGATTCAAACTCTTCTATCA 58.900 40.000 0.00 0.00 35.39 2.15
4473 10678 2.283173 GTTTGCCCCTGGAGGTGG 60.283 66.667 0.00 0.00 0.00 4.61
4595 10800 4.783242 CAGTTTGTGCACCATACTAACAC 58.217 43.478 15.69 0.00 36.62 3.32
4684 11264 1.845791 TGCTCATTCATCTTGGGGCTA 59.154 47.619 0.00 0.00 0.00 3.93
4685 11265 2.444388 TGCTCATTCATCTTGGGGCTAT 59.556 45.455 0.00 0.00 0.00 2.97
4686 11266 3.117398 TGCTCATTCATCTTGGGGCTATT 60.117 43.478 0.00 0.00 0.00 1.73
4687 11267 3.893813 GCTCATTCATCTTGGGGCTATTT 59.106 43.478 0.00 0.00 0.00 1.40
4688 11268 4.343239 GCTCATTCATCTTGGGGCTATTTT 59.657 41.667 0.00 0.00 0.00 1.82
4689 11269 5.163374 GCTCATTCATCTTGGGGCTATTTTT 60.163 40.000 0.00 0.00 0.00 1.94
4703 11283 2.026879 TTTTTGCGCGGTGCCTTC 59.973 55.556 8.83 0.00 45.60 3.46
4704 11284 3.815569 TTTTTGCGCGGTGCCTTCG 62.816 57.895 8.83 0.00 45.60 3.79
4717 11297 3.558674 CCTTCGATGGCAGGAAAGT 57.441 52.632 4.15 0.00 30.81 2.66
4765 11345 2.047655 TCCCGTAAGCTTGCCACG 60.048 61.111 9.86 11.30 35.50 4.94
4798 11378 2.380410 GCTCAACCGCGTCGAATGT 61.380 57.895 4.92 0.00 0.00 2.71
4814 11395 3.430374 CGAATGTCTAAATCTGGTCCGGT 60.430 47.826 0.00 0.00 0.00 5.28
4850 11431 3.695606 GCGTCCACCTGCTCCTCA 61.696 66.667 0.00 0.00 0.00 3.86
4864 11445 2.503061 CTCACCATGGCCCTCTCG 59.497 66.667 13.04 0.00 0.00 4.04
4924 11505 0.620556 TCCTCTGGCATGGAAGGAAC 59.379 55.000 6.87 0.00 0.00 3.62
4930 11511 2.032634 GCATGGAAGGAACGACGCA 61.033 57.895 0.00 0.00 0.00 5.24
4953 11534 1.272490 CGTTGGCTCCTGTCTAGTCAA 59.728 52.381 0.00 0.00 36.26 3.18
4970 11551 2.752807 AACTGGGCACGGGTCTGTT 61.753 57.895 0.00 0.00 0.00 3.16
5073 11654 3.518998 CACCGATCCCTCGCGACT 61.519 66.667 3.71 0.00 43.66 4.18
5092 11673 3.118531 ACTATGGTCCCATCTTCAGCTT 58.881 45.455 1.17 0.00 37.82 3.74
5095 11676 0.106967 GGTCCCATCTTCAGCTTCCC 60.107 60.000 0.00 0.00 0.00 3.97
5098 11679 0.106819 CCCATCTTCAGCTTCCCCAG 60.107 60.000 0.00 0.00 0.00 4.45
5133 11714 3.309296 TCCAATTCTTCCGAGCCTCTAT 58.691 45.455 0.00 0.00 0.00 1.98
5240 11821 1.280457 CCTGTCAGCCCTAGTTCCTT 58.720 55.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.939730 TCACTATAACATCTTCCTTGCACAAA 59.060 34.615 0.00 0.00 0.00 2.83
3 4 6.818644 TCTTCACTATAACATCTTCCTTGCAC 59.181 38.462 0.00 0.00 0.00 4.57
5 6 6.018343 GCTCTTCACTATAACATCTTCCTTGC 60.018 42.308 0.00 0.00 0.00 4.01
6 7 6.199908 CGCTCTTCACTATAACATCTTCCTTG 59.800 42.308 0.00 0.00 0.00 3.61
7 8 6.276847 CGCTCTTCACTATAACATCTTCCTT 58.723 40.000 0.00 0.00 0.00 3.36
8 9 5.221342 CCGCTCTTCACTATAACATCTTCCT 60.221 44.000 0.00 0.00 0.00 3.36
9 10 4.985409 CCGCTCTTCACTATAACATCTTCC 59.015 45.833 0.00 0.00 0.00 3.46
10 11 5.593010 ACCGCTCTTCACTATAACATCTTC 58.407 41.667 0.00 0.00 0.00 2.87
11 12 5.599999 ACCGCTCTTCACTATAACATCTT 57.400 39.130 0.00 0.00 0.00 2.40
12 13 5.593095 TGTACCGCTCTTCACTATAACATCT 59.407 40.000 0.00 0.00 0.00 2.90
13 14 5.828747 TGTACCGCTCTTCACTATAACATC 58.171 41.667 0.00 0.00 0.00 3.06
14 15 5.736492 GCTGTACCGCTCTTCACTATAACAT 60.736 44.000 1.52 0.00 0.00 2.71
15 16 4.439700 GCTGTACCGCTCTTCACTATAACA 60.440 45.833 1.52 0.00 0.00 2.41
16 17 4.043073 GCTGTACCGCTCTTCACTATAAC 58.957 47.826 1.52 0.00 0.00 1.89
17 18 3.697542 TGCTGTACCGCTCTTCACTATAA 59.302 43.478 10.75 0.00 0.00 0.98
18 19 3.284617 TGCTGTACCGCTCTTCACTATA 58.715 45.455 10.75 0.00 0.00 1.31
19 20 2.100197 TGCTGTACCGCTCTTCACTAT 58.900 47.619 10.75 0.00 0.00 2.12
20 21 1.541379 TGCTGTACCGCTCTTCACTA 58.459 50.000 10.75 0.00 0.00 2.74
21 22 0.679505 TTGCTGTACCGCTCTTCACT 59.320 50.000 10.75 0.00 0.00 3.41
22 23 1.461127 CTTTGCTGTACCGCTCTTCAC 59.539 52.381 10.75 0.00 0.00 3.18
23 24 1.795768 CTTTGCTGTACCGCTCTTCA 58.204 50.000 10.75 0.00 0.00 3.02
24 25 0.444260 GCTTTGCTGTACCGCTCTTC 59.556 55.000 10.75 0.00 0.00 2.87
25 26 1.291877 CGCTTTGCTGTACCGCTCTT 61.292 55.000 10.75 0.00 0.00 2.85
26 27 1.738099 CGCTTTGCTGTACCGCTCT 60.738 57.895 10.75 0.00 0.00 4.09
27 28 2.778679 CGCTTTGCTGTACCGCTC 59.221 61.111 10.75 0.00 0.00 5.03
28 29 3.423154 GCGCTTTGCTGTACCGCT 61.423 61.111 10.75 0.00 41.28 5.52
29 30 4.794241 CGCGCTTTGCTGTACCGC 62.794 66.667 5.56 1.80 43.27 5.68
30 31 4.794241 GCGCGCTTTGCTGTACCG 62.794 66.667 26.67 0.00 43.27 4.02
31 32 1.701545 TATGCGCGCTTTGCTGTACC 61.702 55.000 33.29 0.00 43.27 3.34
32 33 0.304705 ATATGCGCGCTTTGCTGTAC 59.695 50.000 33.29 0.00 43.27 2.90
33 34 0.304401 CATATGCGCGCTTTGCTGTA 59.696 50.000 33.29 9.65 43.27 2.74
34 35 1.063006 CATATGCGCGCTTTGCTGT 59.937 52.632 33.29 11.34 43.27 4.40
35 36 2.290789 GCATATGCGCGCTTTGCTG 61.291 57.895 31.51 23.45 43.27 4.41
36 37 1.996786 AAGCATATGCGCGCTTTGCT 61.997 50.000 34.03 34.03 46.04 3.91
37 38 1.587088 AAGCATATGCGCGCTTTGC 60.587 52.632 31.64 31.64 46.04 3.68
38 39 4.696078 AAGCATATGCGCGCTTTG 57.304 50.000 33.29 25.18 46.04 2.77
49 50 8.654094 GGGGTTTTAAGGTATACTAGAAGCATA 58.346 37.037 2.25 0.00 0.00 3.14
50 51 7.350124 AGGGGTTTTAAGGTATACTAGAAGCAT 59.650 37.037 2.25 0.00 0.00 3.79
51 52 6.675303 AGGGGTTTTAAGGTATACTAGAAGCA 59.325 38.462 2.25 0.00 0.00 3.91
52 53 7.134362 AGGGGTTTTAAGGTATACTAGAAGC 57.866 40.000 2.25 0.32 0.00 3.86
53 54 9.970553 AAAAGGGGTTTTAAGGTATACTAGAAG 57.029 33.333 2.25 0.00 0.00 2.85
56 57 9.842775 CCTAAAAGGGGTTTTAAGGTATACTAG 57.157 37.037 2.25 0.00 0.00 2.57
57 58 8.274322 GCCTAAAAGGGGTTTTAAGGTATACTA 58.726 37.037 2.25 0.00 35.37 1.82
58 59 7.036352 AGCCTAAAAGGGGTTTTAAGGTATACT 60.036 37.037 2.25 0.00 35.37 2.12
59 60 7.067859 CAGCCTAAAAGGGGTTTTAAGGTATAC 59.932 40.741 0.00 0.00 35.37 1.47
60 61 7.120716 CAGCCTAAAAGGGGTTTTAAGGTATA 58.879 38.462 0.00 0.00 35.37 1.47
61 62 5.955959 CAGCCTAAAAGGGGTTTTAAGGTAT 59.044 40.000 0.00 0.00 35.37 2.73
62 63 5.326900 CAGCCTAAAAGGGGTTTTAAGGTA 58.673 41.667 0.00 0.00 35.37 3.08
63 64 4.157246 CAGCCTAAAAGGGGTTTTAAGGT 58.843 43.478 0.00 0.00 35.37 3.50
64 65 3.056107 GCAGCCTAAAAGGGGTTTTAAGG 60.056 47.826 0.00 0.00 35.37 2.69
65 66 3.366985 CGCAGCCTAAAAGGGGTTTTAAG 60.367 47.826 0.00 0.00 35.37 1.85
66 67 2.559231 CGCAGCCTAAAAGGGGTTTTAA 59.441 45.455 0.00 0.00 35.37 1.52
67 68 2.164338 CGCAGCCTAAAAGGGGTTTTA 58.836 47.619 0.00 0.00 35.37 1.52
68 69 0.966179 CGCAGCCTAAAAGGGGTTTT 59.034 50.000 0.00 0.00 35.37 2.43
69 70 0.178973 ACGCAGCCTAAAAGGGGTTT 60.179 50.000 0.00 0.00 35.37 3.27
70 71 0.178973 AACGCAGCCTAAAAGGGGTT 60.179 50.000 0.00 0.00 35.37 4.11
71 72 0.608308 GAACGCAGCCTAAAAGGGGT 60.608 55.000 0.00 0.00 35.37 4.95
72 73 1.644786 CGAACGCAGCCTAAAAGGGG 61.645 60.000 0.00 0.00 35.37 4.79
73 74 0.672401 TCGAACGCAGCCTAAAAGGG 60.672 55.000 0.00 0.00 35.37 3.95
74 75 1.136057 GTTCGAACGCAGCCTAAAAGG 60.136 52.381 13.36 0.00 38.80 3.11
75 76 1.798813 AGTTCGAACGCAGCCTAAAAG 59.201 47.619 21.87 0.00 0.00 2.27
76 77 1.529438 CAGTTCGAACGCAGCCTAAAA 59.471 47.619 21.87 0.00 0.00 1.52
77 78 1.144969 CAGTTCGAACGCAGCCTAAA 58.855 50.000 21.87 0.00 0.00 1.85
78 79 0.669318 CCAGTTCGAACGCAGCCTAA 60.669 55.000 21.87 0.00 0.00 2.69
79 80 1.080093 CCAGTTCGAACGCAGCCTA 60.080 57.895 21.87 0.00 0.00 3.93
189 191 4.664150 AACCCGAACACACATCATTTTT 57.336 36.364 0.00 0.00 0.00 1.94
707 732 2.145536 GGAATTTTGCAGGCCAAACTG 58.854 47.619 5.01 0.00 42.81 3.16
708 733 2.049372 AGGAATTTTGCAGGCCAAACT 58.951 42.857 5.01 0.00 42.81 2.66
709 734 2.145536 CAGGAATTTTGCAGGCCAAAC 58.854 47.619 5.01 0.00 42.81 2.93
710 735 1.542987 GCAGGAATTTTGCAGGCCAAA 60.543 47.619 5.01 0.00 41.48 3.28
711 736 0.035176 GCAGGAATTTTGCAGGCCAA 59.965 50.000 5.01 0.00 41.17 4.52
712 737 1.672898 GCAGGAATTTTGCAGGCCA 59.327 52.632 5.01 0.00 41.17 5.36
713 738 1.446618 CGCAGGAATTTTGCAGGCC 60.447 57.895 13.97 0.00 41.59 5.19
714 739 0.038343 TTCGCAGGAATTTTGCAGGC 60.038 50.000 13.97 0.00 41.59 4.85
715 740 2.437200 TTTCGCAGGAATTTTGCAGG 57.563 45.000 13.97 2.09 41.59 4.85
716 741 3.368843 GGAATTTCGCAGGAATTTTGCAG 59.631 43.478 13.97 8.27 41.59 4.41
717 742 3.324993 GGAATTTCGCAGGAATTTTGCA 58.675 40.909 13.97 0.00 41.59 4.08
718 743 2.672874 GGGAATTTCGCAGGAATTTTGC 59.327 45.455 8.46 5.96 38.18 3.68
719 744 3.924144 TGGGAATTTCGCAGGAATTTTG 58.076 40.909 11.71 0.00 34.23 2.44
720 745 4.506758 CATGGGAATTTCGCAGGAATTTT 58.493 39.130 19.62 0.73 42.55 1.82
721 746 3.679639 GCATGGGAATTTCGCAGGAATTT 60.680 43.478 26.03 5.87 42.55 1.82
722 747 2.159057 GCATGGGAATTTCGCAGGAATT 60.159 45.455 26.03 6.51 42.55 2.17
723 748 1.410153 GCATGGGAATTTCGCAGGAAT 59.590 47.619 26.03 6.84 42.55 3.01
724 749 0.817013 GCATGGGAATTTCGCAGGAA 59.183 50.000 26.03 3.45 42.55 3.36
725 750 1.375853 CGCATGGGAATTTCGCAGGA 61.376 55.000 26.03 3.78 42.55 3.86
726 751 1.064621 CGCATGGGAATTTCGCAGG 59.935 57.895 19.90 19.90 42.66 4.85
727 752 1.587088 GCGCATGGGAATTTCGCAG 60.587 57.895 19.23 12.95 42.66 5.18
728 753 2.489285 GCGCATGGGAATTTCGCA 59.511 55.556 17.21 17.21 44.50 5.10
729 754 2.278792 GGCGCATGGGAATTTCGC 60.279 61.111 14.90 8.51 44.39 4.70
730 755 1.987704 TTCGGCGCATGGGAATTTCG 61.988 55.000 14.90 8.45 0.00 3.46
731 756 0.525455 GTTCGGCGCATGGGAATTTC 60.525 55.000 14.90 0.00 0.00 2.17
732 757 1.510844 GTTCGGCGCATGGGAATTT 59.489 52.632 14.90 0.00 0.00 1.82
733 758 2.760159 CGTTCGGCGCATGGGAATT 61.760 57.895 14.90 0.00 0.00 2.17
734 759 3.202001 CGTTCGGCGCATGGGAAT 61.202 61.111 14.90 0.00 0.00 3.01
744 769 1.352056 GATTAAGGCTGCGTTCGGC 59.648 57.895 11.22 0.00 43.83 5.54
745 770 1.299541 ATGATTAAGGCTGCGTTCGG 58.700 50.000 11.22 0.00 0.00 4.30
746 771 2.286418 GGAATGATTAAGGCTGCGTTCG 60.286 50.000 11.22 0.00 0.00 3.95
747 772 2.286418 CGGAATGATTAAGGCTGCGTTC 60.286 50.000 11.22 0.00 0.00 3.95
748 773 1.670811 CGGAATGATTAAGGCTGCGTT 59.329 47.619 12.54 12.54 0.00 4.84
749 774 1.299541 CGGAATGATTAAGGCTGCGT 58.700 50.000 0.00 0.00 0.00 5.24
750 775 0.040958 GCGGAATGATTAAGGCTGCG 60.041 55.000 0.00 0.00 0.00 5.18
751 776 1.002033 CAGCGGAATGATTAAGGCTGC 60.002 52.381 10.31 0.00 40.99 5.25
753 778 1.312815 GCAGCGGAATGATTAAGGCT 58.687 50.000 0.00 0.00 0.00 4.58
754 779 1.024271 TGCAGCGGAATGATTAAGGC 58.976 50.000 0.00 0.00 0.00 4.35
755 780 2.292267 AGTGCAGCGGAATGATTAAGG 58.708 47.619 0.00 0.00 0.00 2.69
756 781 3.242870 GGAAGTGCAGCGGAATGATTAAG 60.243 47.826 0.00 0.00 0.00 1.85
757 782 2.682856 GGAAGTGCAGCGGAATGATTAA 59.317 45.455 0.00 0.00 0.00 1.40
758 783 2.288666 GGAAGTGCAGCGGAATGATTA 58.711 47.619 0.00 0.00 0.00 1.75
759 784 1.098050 GGAAGTGCAGCGGAATGATT 58.902 50.000 0.00 0.00 0.00 2.57
760 785 0.749454 GGGAAGTGCAGCGGAATGAT 60.749 55.000 0.00 0.00 0.00 2.45
761 786 1.377202 GGGAAGTGCAGCGGAATGA 60.377 57.895 0.00 0.00 0.00 2.57
762 787 0.962356 AAGGGAAGTGCAGCGGAATG 60.962 55.000 0.00 0.00 0.00 2.67
763 788 0.962356 CAAGGGAAGTGCAGCGGAAT 60.962 55.000 0.00 0.00 0.00 3.01
764 789 1.600636 CAAGGGAAGTGCAGCGGAA 60.601 57.895 0.00 0.00 0.00 4.30
765 790 2.032528 CAAGGGAAGTGCAGCGGA 59.967 61.111 0.00 0.00 0.00 5.54
766 791 3.741476 GCAAGGGAAGTGCAGCGG 61.741 66.667 0.00 0.00 41.80 5.52
767 792 2.670934 AGCAAGGGAAGTGCAGCG 60.671 61.111 0.00 0.00 44.74 5.18
768 793 2.960170 CAGCAAGGGAAGTGCAGC 59.040 61.111 0.00 0.00 44.74 5.25
769 794 2.633509 GGCAGCAAGGGAAGTGCAG 61.634 63.158 0.00 0.00 44.74 4.41
770 795 2.598394 GGCAGCAAGGGAAGTGCA 60.598 61.111 0.00 0.00 44.74 4.57
771 796 3.741476 CGGCAGCAAGGGAAGTGC 61.741 66.667 0.00 0.00 42.55 4.40
772 797 3.741476 GCGGCAGCAAGGGAAGTG 61.741 66.667 3.18 0.00 44.35 3.16
812 837 2.591072 CCTGTCTGCAGCTGGGACT 61.591 63.158 17.12 0.00 41.26 3.85
924 950 2.959516 TGTACTGTCGGAGATGCTTTG 58.040 47.619 0.00 0.00 40.67 2.77
1031 1073 0.030603 GGGGAGGGAAGGAGACAGAT 60.031 60.000 0.00 0.00 0.00 2.90
1036 1078 0.855855 TCAGAGGGGAGGGAAGGAGA 60.856 60.000 0.00 0.00 0.00 3.71
1041 1083 1.612442 CGGTTCAGAGGGGAGGGAA 60.612 63.158 0.00 0.00 0.00 3.97
1117 1224 2.807045 CGAGCTCGTGTGCTGGAC 60.807 66.667 27.79 0.00 44.17 4.02
1252 1362 2.104792 CCTTTCTCCACCAGTCACTCAA 59.895 50.000 0.00 0.00 0.00 3.02
1468 1579 6.428385 AAAGCTCGGAATAAATCAGAACAG 57.572 37.500 0.00 0.00 31.61 3.16
1516 1627 5.104941 TCAATGACATTTCGAGGATGGTAGT 60.105 40.000 13.36 1.66 0.00 2.73
1605 1716 4.142381 GCATATCAAACCCCACAGAAACTC 60.142 45.833 0.00 0.00 0.00 3.01
1670 1781 8.537223 CATGTCAAAACTCAAAAGAAACATGAG 58.463 33.333 0.00 0.00 42.37 2.90
1691 1802 6.421377 TGTATTCATAACACAGTGCATGTC 57.579 37.500 13.05 6.12 41.41 3.06
1968 2123 4.792068 AGGAATCCTGCAAAATCGGAATA 58.208 39.130 0.00 0.00 29.57 1.75
2155 2892 7.634671 TGAAAGCATCATGTCATTAATCTGT 57.365 32.000 0.00 0.00 31.50 3.41
2267 5439 6.863645 GGACCAGAAACAGAAATAAGAAAAGC 59.136 38.462 0.00 0.00 0.00 3.51
2268 5440 8.171164 AGGACCAGAAACAGAAATAAGAAAAG 57.829 34.615 0.00 0.00 0.00 2.27
2272 5444 9.449719 GAATAAGGACCAGAAACAGAAATAAGA 57.550 33.333 0.00 0.00 0.00 2.10
2317 5517 4.220724 AGGAAGTTAGTACTCACACACCA 58.779 43.478 9.77 0.00 31.99 4.17
2730 5987 1.238439 GTAGCACAGAGGCAGCAAAA 58.762 50.000 0.00 0.00 35.83 2.44
2895 6213 5.533482 TCTTTTTGACTGCTCTGTAGAGAC 58.467 41.667 12.89 5.01 44.74 3.36
3081 8720 4.223953 TCAAATAGCCCAGGTAGAGGTAG 58.776 47.826 0.00 0.00 0.00 3.18
3082 8721 4.274794 TCAAATAGCCCAGGTAGAGGTA 57.725 45.455 0.00 0.00 0.00 3.08
3083 8722 3.130734 TCAAATAGCCCAGGTAGAGGT 57.869 47.619 0.00 0.00 0.00 3.85
3084 8723 5.738909 CATATCAAATAGCCCAGGTAGAGG 58.261 45.833 0.00 0.00 0.00 3.69
3085 8724 5.181748 GCATATCAAATAGCCCAGGTAGAG 58.818 45.833 0.00 0.00 0.00 2.43
3086 8725 4.019321 GGCATATCAAATAGCCCAGGTAGA 60.019 45.833 0.00 0.00 41.25 2.59
3151 8933 4.218635 CCACCGCTTATGAAGAGCTAGATA 59.781 45.833 0.00 0.00 37.99 1.98
3302 9121 3.691118 TCAGGCTGATGCATACTTTCAAC 59.309 43.478 14.43 0.00 41.91 3.18
3372 9197 2.297033 TCAGAGGGTAACAACACCGTAC 59.703 50.000 0.00 0.00 39.69 3.67
3591 9437 9.684448 GTCTCGATTAAATCATCAATAGTCTGA 57.316 33.333 0.00 0.00 0.00 3.27
4025 10164 8.021396 GGTTTATTCAGAATAAGCTGTTTTCGT 58.979 33.333 22.18 0.00 35.62 3.85
4026 10165 8.237267 AGGTTTATTCAGAATAAGCTGTTTTCG 58.763 33.333 22.18 0.00 35.62 3.46
4027 10166 9.346725 CAGGTTTATTCAGAATAAGCTGTTTTC 57.653 33.333 22.18 9.95 35.62 2.29
4028 10167 9.077885 TCAGGTTTATTCAGAATAAGCTGTTTT 57.922 29.630 24.83 11.15 35.62 2.43
4029 10168 8.515414 GTCAGGTTTATTCAGAATAAGCTGTTT 58.485 33.333 24.83 12.63 35.62 2.83
4043 10219 9.447040 GCTTTATAAAATCGGTCAGGTTTATTC 57.553 33.333 0.00 0.00 30.59 1.75
4048 10224 6.827586 TTGCTTTATAAAATCGGTCAGGTT 57.172 33.333 0.00 0.00 0.00 3.50
4053 10229 8.170553 TCGTTAGTTTGCTTTATAAAATCGGTC 58.829 33.333 0.00 0.00 0.00 4.79
4361 10566 4.722203 TTGCACAAACACAAAAACAGTG 57.278 36.364 0.00 0.00 42.56 3.66
4420 10625 4.225042 TGTCTGGTTGAGCATAGGTACAAT 59.775 41.667 0.00 0.00 0.00 2.71
4473 10678 5.115472 CACACGAAACACAAATGAATAGCAC 59.885 40.000 0.00 0.00 0.00 4.40
4686 11266 2.026879 GAAGGCACCGCGCAAAAA 59.973 55.556 8.75 0.00 45.17 1.94
4687 11267 4.320928 CGAAGGCACCGCGCAAAA 62.321 61.111 8.75 0.00 45.17 2.44
4699 11279 1.089920 CACTTTCCTGCCATCGAAGG 58.910 55.000 1.31 1.31 34.65 3.46
4700 11280 0.449388 GCACTTTCCTGCCATCGAAG 59.551 55.000 0.00 0.00 0.00 3.79
4701 11281 2.555123 GCACTTTCCTGCCATCGAA 58.445 52.632 0.00 0.00 0.00 3.71
4702 11282 4.301505 GCACTTTCCTGCCATCGA 57.698 55.556 0.00 0.00 0.00 3.59
4708 11288 2.116125 AGGTGGGCACTTTCCTGC 59.884 61.111 0.00 0.00 36.33 4.85
4709 11289 2.270986 GCAGGTGGGCACTTTCCTG 61.271 63.158 16.93 16.93 46.96 3.86
4710 11290 1.133809 TAGCAGGTGGGCACTTTCCT 61.134 55.000 0.00 0.00 35.83 3.36
4711 11291 0.960861 GTAGCAGGTGGGCACTTTCC 60.961 60.000 0.00 0.00 35.83 3.13
4712 11292 0.960861 GGTAGCAGGTGGGCACTTTC 60.961 60.000 0.00 0.00 35.83 2.62
4713 11293 1.074951 GGTAGCAGGTGGGCACTTT 59.925 57.895 0.00 0.00 35.83 2.66
4714 11294 2.757077 GGTAGCAGGTGGGCACTT 59.243 61.111 0.00 0.00 35.83 3.16
4715 11295 3.330720 GGGTAGCAGGTGGGCACT 61.331 66.667 0.00 0.00 35.83 4.40
4716 11296 4.426313 GGGGTAGCAGGTGGGCAC 62.426 72.222 0.00 0.00 35.83 5.01
4717 11297 4.675303 AGGGGTAGCAGGTGGGCA 62.675 66.667 0.00 0.00 35.83 5.36
4791 11371 3.181479 CCGGACCAGATTTAGACATTCGA 60.181 47.826 0.00 0.00 0.00 3.71
4798 11378 5.021458 AGAACTTACCGGACCAGATTTAGA 58.979 41.667 9.46 0.00 0.00 2.10
4814 11395 2.767536 GCATGGCGCTCAGAACTTA 58.232 52.632 7.64 0.00 37.77 2.24
4833 11414 3.695606 TGAGGAGCAGGTGGACGC 61.696 66.667 0.00 0.00 0.00 5.19
4864 11445 2.044650 TGCTTGAGGATGGCAGGC 60.045 61.111 0.00 0.00 38.65 4.85
4867 11448 1.300963 GGTCTGCTTGAGGATGGCA 59.699 57.895 0.00 0.00 34.66 4.92
4883 11464 1.002087 GTCACGGAGGATTCTGTTGGT 59.998 52.381 0.00 0.00 41.01 3.67
4930 11511 2.214181 CTAGACAGGAGCCAACGCGT 62.214 60.000 5.58 5.58 41.18 6.01
4935 11516 2.300152 CAGTTGACTAGACAGGAGCCAA 59.700 50.000 0.00 0.00 0.00 4.52
4953 11534 3.168528 AACAGACCCGTGCCCAGT 61.169 61.111 0.00 0.00 0.00 4.00
5073 11654 2.439507 GGAAGCTGAAGATGGGACCATA 59.560 50.000 3.36 0.00 36.70 2.74
5133 11714 1.005805 CATCCCCAATGGTCCAAGACA 59.994 52.381 0.00 0.00 33.68 3.41
5218 11799 1.229658 AACTAGGGCTGACAGGGCT 60.230 57.895 4.26 0.00 0.00 5.19
5225 11806 0.895530 CGTCAAGGAACTAGGGCTGA 59.104 55.000 0.00 0.00 38.49 4.26


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

AutoCloner maintained by Alex Coulton.