Multiple sequence alignment - TraesCS2D01G244700

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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 TraesCS2D01G244700 chr2D 100.000 9739 0 0 1 9739 276940164 276930426 0.000000e+00 17985.0
1 TraesCS2D01G244700 chr2D 96.648 1074 31 5 3417 4489 285349014 285350083 0.000000e+00 1779.0
2 TraesCS2D01G244700 chr2D 95.899 1073 38 4 3417 4489 566486268 566485202 0.000000e+00 1733.0
3 TraesCS2D01G244700 chr2D 93.795 693 30 6 1393 2073 276938091 276937400 0.000000e+00 1029.0
4 TraesCS2D01G244700 chr2D 93.795 693 30 6 2074 2765 276938772 276938092 0.000000e+00 1029.0
5 TraesCS2D01G244700 chr2A 97.910 2919 48 4 501 3416 313778165 313775257 0.000000e+00 5040.0
6 TraesCS2D01G244700 chr2A 96.533 1615 25 3 4490 6100 313775264 313773677 0.000000e+00 2643.0
7 TraesCS2D01G244700 chr2A 98.904 1095 12 0 6129 7223 313773066 313771972 0.000000e+00 1956.0
8 TraesCS2D01G244700 chr2A 98.359 1036 14 3 7346 8380 313771972 313770939 0.000000e+00 1816.0
9 TraesCS2D01G244700 chr2A 93.795 693 29 7 2074 2765 313777282 313776603 0.000000e+00 1029.0
10 TraesCS2D01G244700 chr2A 93.094 695 33 7 1393 2073 313776602 313775909 0.000000e+00 1003.0
11 TraesCS2D01G244700 chr2A 97.331 562 11 2 8364 8925 313770893 313770336 0.000000e+00 952.0
12 TraesCS2D01G244700 chr2A 87.840 773 68 9 8990 9739 313769746 313768977 0.000000e+00 883.0
13 TraesCS2D01G244700 chr2A 94.231 312 5 5 5832 6130 313773677 313773366 1.920000e-126 464.0
14 TraesCS2D01G244700 chr2A 83.237 519 53 20 1 502 756946323 756946824 6.940000e-121 446.0
15 TraesCS2D01G244700 chr2A 94.030 134 6 2 7218 7350 321155664 321155532 1.660000e-47 202.0
16 TraesCS2D01G244700 chr2A 97.115 104 3 0 8885 8988 313770340 313770237 1.010000e-39 176.0
17 TraesCS2D01G244700 chr2A 79.429 175 26 9 7885 8053 65517762 65517932 2.220000e-21 115.0
18 TraesCS2D01G244700 chr2B 96.444 1659 49 8 7362 9016 329474218 329472566 0.000000e+00 2728.0
19 TraesCS2D01G244700 chr2B 95.841 1683 36 4 4490 6168 329478636 329476984 0.000000e+00 2689.0
20 TraesCS2D01G244700 chr2B 96.053 1064 29 3 6159 7220 329475280 329474228 0.000000e+00 1720.0
21 TraesCS2D01G244700 chr2B 95.360 1056 30 6 524 1575 329486932 329485892 0.000000e+00 1661.0
22 TraesCS2D01G244700 chr2B 96.590 997 29 3 1570 2565 329480850 329479858 0.000000e+00 1648.0
23 TraesCS2D01G244700 chr2B 97.463 473 7 2 2947 3416 329479099 329478629 0.000000e+00 802.0
24 TraesCS2D01G244700 chr2B 94.380 516 17 5 2251 2765 329480850 329480346 0.000000e+00 782.0
25 TraesCS2D01G244700 chr2B 98.015 403 8 0 2558 2960 329479674 329479272 0.000000e+00 701.0
26 TraesCS2D01G244700 chr2B 93.333 465 28 1 1393 1857 329480345 329479884 0.000000e+00 684.0
27 TraesCS2D01G244700 chr2B 95.215 209 8 2 1866 2073 329479674 329479467 7.290000e-86 329.0
28 TraesCS2D01G244700 chr2B 95.628 183 8 0 2074 2256 329486074 329485892 2.660000e-75 294.0
29 TraesCS2D01G244700 chr2B 92.647 136 8 2 7218 7353 550044049 550044182 2.780000e-45 195.0
30 TraesCS2D01G244700 chr2B 77.982 109 15 8 7963 8069 531051886 531051785 1.060000e-04 60.2
31 TraesCS2D01G244700 chr7D 96.019 1080 38 4 3413 4489 145920052 145918975 0.000000e+00 1751.0
32 TraesCS2D01G244700 chr7D 95.676 1087 38 7 3413 4495 616465909 616464828 0.000000e+00 1738.0
33 TraesCS2D01G244700 chr7D 95.737 1079 36 7 3413 4489 576645035 576643965 0.000000e+00 1729.0
34 TraesCS2D01G244700 chr7D 88.846 520 33 16 1 500 474676756 474676242 5.000000e-172 616.0
35 TraesCS2D01G244700 chr7D 92.701 137 9 1 7213 7349 325567680 325567815 7.720000e-46 196.0
36 TraesCS2D01G244700 chr7D 90.845 142 11 2 7221 7361 194601789 194601649 1.290000e-43 189.0
37 TraesCS2D01G244700 chr7D 88.235 68 7 1 5968 6034 232411231 232411164 8.110000e-11 80.5
38 TraesCS2D01G244700 chr6D 95.918 1078 37 7 3413 4489 446134127 446133056 0.000000e+00 1740.0
39 TraesCS2D01G244700 chr4D 95.790 1069 37 7 3423 4489 369859166 369860228 0.000000e+00 1718.0
40 TraesCS2D01G244700 chr4D 95.790 1069 37 7 3423 4489 369877414 369876352 0.000000e+00 1718.0
41 TraesCS2D01G244700 chr4D 88.136 59 6 1 5970 6027 5531289 5531231 1.760000e-07 69.4
42 TraesCS2D01G244700 chr5D 95.531 1074 43 5 3417 4490 508156424 508157492 0.000000e+00 1712.0
43 TraesCS2D01G244700 chr5D 96.296 54 2 0 5969 6022 278311374 278311321 1.350000e-13 89.8
44 TraesCS2D01G244700 chr5B 89.981 519 28 9 1 505 411792224 411791716 0.000000e+00 649.0
45 TraesCS2D01G244700 chr5B 87.146 529 39 14 1 502 629258253 629258779 3.050000e-159 573.0
46 TraesCS2D01G244700 chr5B 85.316 538 41 20 1 502 629346289 629346824 1.120000e-143 521.0
47 TraesCS2D01G244700 chr7B 89.555 517 28 11 1 502 630138071 630138576 4.960000e-177 632.0
48 TraesCS2D01G244700 chr7A 87.984 516 40 11 1 505 607605389 607604885 3.030000e-164 590.0
49 TraesCS2D01G244700 chr7A 83.237 519 53 20 1 502 85882287 85882788 6.940000e-121 446.0
50 TraesCS2D01G244700 chr7A 82.386 528 55 23 1 505 2869296 2868784 9.040000e-115 425.0
51 TraesCS2D01G244700 chr7A 91.096 146 11 2 7215 7360 657019085 657019228 7.720000e-46 196.0
52 TraesCS2D01G244700 chr4B 84.971 519 56 14 1 502 256160897 256161410 3.140000e-139 507.0
53 TraesCS2D01G244700 chr4B 90.845 142 10 3 7208 7349 568552965 568553103 4.640000e-43 187.0
54 TraesCS2D01G244700 chr3A 84.200 519 48 23 1 502 26422834 26423335 3.180000e-129 473.0
55 TraesCS2D01G244700 chr3A 79.264 516 53 31 1 502 716469645 716470120 2.640000e-80 311.0
56 TraesCS2D01G244700 chr3A 94.615 130 6 1 7220 7349 136477553 136477425 5.970000e-47 200.0
57 TraesCS2D01G244700 chr3A 84.810 79 11 1 5977 6054 572325329 572325407 2.920000e-10 78.7
58 TraesCS2D01G244700 chr6A 83.908 522 50 23 1 505 604390825 604390321 1.480000e-127 468.0
59 TraesCS2D01G244700 chr4A 83.333 522 53 20 1 505 684407461 684406957 1.490000e-122 451.0
60 TraesCS2D01G244700 chr6B 82.552 533 54 25 1 502 615326542 615327066 5.400000e-117 433.0
61 TraesCS2D01G244700 chr1B 94.574 129 6 1 7221 7349 572202438 572202565 2.150000e-46 198.0
62 TraesCS2D01G244700 chr1A 91.549 142 9 3 7218 7358 294514593 294514454 9.980000e-45 193.0
63 TraesCS2D01G244700 chr3B 78.378 148 15 4 6201 6335 68209443 68209300 8.110000e-11 80.5
64 TraesCS2D01G244700 chr3B 87.719 57 7 0 6279 6335 68203565 68203509 6.310000e-07 67.6
65 TraesCS2D01G244700 chr3B 100.000 31 0 0 7889 7919 795178590 795178560 3.800000e-04 58.4
66 TraesCS2D01G244700 chr1D 90.323 62 5 1 5974 6034 396741844 396741783 8.110000e-11 80.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G244700 chr2D 276930426 276940164 9738 True 6681.000000 17985 95.863333 1 9739 3 chr2D.!!$R2 9738
1 TraesCS2D01G244700 chr2D 285349014 285350083 1069 False 1779.000000 1779 96.648000 3417 4489 1 chr2D.!!$F1 1072
2 TraesCS2D01G244700 chr2D 566485202 566486268 1066 True 1733.000000 1733 95.899000 3417 4489 1 chr2D.!!$R1 1072
3 TraesCS2D01G244700 chr2A 313768977 313778165 9188 True 1596.200000 5040 95.511200 501 9739 10 chr2A.!!$R2 9238
4 TraesCS2D01G244700 chr2A 756946323 756946824 501 False 446.000000 446 83.237000 1 502 1 chr2A.!!$F2 501
5 TraesCS2D01G244700 chr2B 329472566 329480850 8284 True 1342.555556 2728 95.926000 1393 9016 9 chr2B.!!$R2 7623
6 TraesCS2D01G244700 chr2B 329485892 329486932 1040 True 977.500000 1661 95.494000 524 2256 2 chr2B.!!$R3 1732
7 TraesCS2D01G244700 chr7D 145918975 145920052 1077 True 1751.000000 1751 96.019000 3413 4489 1 chr7D.!!$R1 1076
8 TraesCS2D01G244700 chr7D 616464828 616465909 1081 True 1738.000000 1738 95.676000 3413 4495 1 chr7D.!!$R6 1082
9 TraesCS2D01G244700 chr7D 576643965 576645035 1070 True 1729.000000 1729 95.737000 3413 4489 1 chr7D.!!$R5 1076
10 TraesCS2D01G244700 chr7D 474676242 474676756 514 True 616.000000 616 88.846000 1 500 1 chr7D.!!$R4 499
11 TraesCS2D01G244700 chr6D 446133056 446134127 1071 True 1740.000000 1740 95.918000 3413 4489 1 chr6D.!!$R1 1076
12 TraesCS2D01G244700 chr4D 369859166 369860228 1062 False 1718.000000 1718 95.790000 3423 4489 1 chr4D.!!$F1 1066
13 TraesCS2D01G244700 chr4D 369876352 369877414 1062 True 1718.000000 1718 95.790000 3423 4489 1 chr4D.!!$R2 1066
14 TraesCS2D01G244700 chr5D 508156424 508157492 1068 False 1712.000000 1712 95.531000 3417 4490 1 chr5D.!!$F1 1073
15 TraesCS2D01G244700 chr5B 411791716 411792224 508 True 649.000000 649 89.981000 1 505 1 chr5B.!!$R1 504
16 TraesCS2D01G244700 chr5B 629258253 629258779 526 False 573.000000 573 87.146000 1 502 1 chr5B.!!$F1 501
17 TraesCS2D01G244700 chr5B 629346289 629346824 535 False 521.000000 521 85.316000 1 502 1 chr5B.!!$F2 501
18 TraesCS2D01G244700 chr7B 630138071 630138576 505 False 632.000000 632 89.555000 1 502 1 chr7B.!!$F1 501
19 TraesCS2D01G244700 chr7A 607604885 607605389 504 True 590.000000 590 87.984000 1 505 1 chr7A.!!$R2 504
20 TraesCS2D01G244700 chr7A 85882287 85882788 501 False 446.000000 446 83.237000 1 502 1 chr7A.!!$F1 501
21 TraesCS2D01G244700 chr7A 2868784 2869296 512 True 425.000000 425 82.386000 1 505 1 chr7A.!!$R1 504
22 TraesCS2D01G244700 chr4B 256160897 256161410 513 False 507.000000 507 84.971000 1 502 1 chr4B.!!$F1 501
23 TraesCS2D01G244700 chr3A 26422834 26423335 501 False 473.000000 473 84.200000 1 502 1 chr3A.!!$F1 501
24 TraesCS2D01G244700 chr6A 604390321 604390825 504 True 468.000000 468 83.908000 1 505 1 chr6A.!!$R1 504
25 TraesCS2D01G244700 chr4A 684406957 684407461 504 True 451.000000 451 83.333000 1 505 1 chr4A.!!$R1 504
26 TraesCS2D01G244700 chr6B 615326542 615327066 524 False 433.000000 433 82.552000 1 502 1 chr6B.!!$F1 501

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
196 244 0.468648 GGACAATCGGAGGTTAGGGG 59.531 60.000 0.00 0.00 0.00 4.79 F
920 1010 0.912486 ACCAACCTATCCAGCCAGTC 59.088 55.000 0.00 0.00 0.00 3.51 F
964 1054 4.127907 TGCTGAAGATGCTCTCATGATTC 58.872 43.478 0.00 0.00 31.96 2.52 F
2265 2357 4.678840 CGGCGGTGTTTCCTAGTATAGTTT 60.679 45.833 0.00 0.00 36.82 2.66 F
2783 3068 2.113860 AAGGAACACACATCCATCGG 57.886 50.000 0.00 0.00 39.55 4.18 F
3791 4270 0.111061 TGCAGTTGCCATCTCAGGTT 59.889 50.000 1.06 0.00 41.18 3.50 F
4603 5094 0.527113 CCATTCATGGCAAACTGCGA 59.473 50.000 0.00 0.00 46.21 5.10 F
5045 5536 1.001631 TTCGATGCTGGAGGGAGGA 59.998 57.895 0.00 0.00 0.00 3.71 F
5658 6151 0.679002 TGATCTGGAAGGCAAGCTGC 60.679 55.000 0.00 0.00 44.08 5.25 F
5700 6193 2.245096 GAGCAGCGTATTTGCACTTTG 58.755 47.619 0.00 0.00 43.92 2.77 F
6602 9395 3.057876 CCTTCTACTACTATGCAGCGAGG 60.058 52.174 0.00 0.00 0.00 4.63 F
7344 10137 0.756903 ACATATTTCCGGACGGAGGG 59.243 55.000 13.64 5.76 46.06 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1421 1512 2.095567 GCATTCAAGACTGTCGTGCATT 60.096 45.455 17.23 3.60 0.00 3.56 R
2450 2544 0.109597 CATGACAAGAAAGGTGCGGC 60.110 55.000 0.00 0.00 0.00 6.53 R
2783 3068 5.819991 TGAGCCATAAATCCTGGGATAATC 58.180 41.667 2.24 0.00 33.97 1.75 R
3421 3895 0.669318 ACACGTGTGGCAGTTATCGG 60.669 55.000 22.71 0.00 34.19 4.18 R
4589 5080 0.311790 ACTTGTCGCAGTTTGCCATG 59.688 50.000 0.00 0.00 41.12 3.66 R
5024 5515 0.103937 CTCCCTCCAGCATCGAAGTC 59.896 60.000 0.00 0.00 0.00 3.01 R
5572 6065 1.163420 TCAAACAGCACGCGGTCAAT 61.163 50.000 12.47 0.00 0.00 2.57 R
7043 9836 3.822192 CCTCACCGGCGATCGTGA 61.822 66.667 17.81 12.98 37.11 4.35 R
7328 10121 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40 R
7331 10124 0.032813 ATTACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30 R
8059 10853 4.517075 GGAGCAATCTTTTATACTGCCTCC 59.483 45.833 0.00 0.00 33.41 4.30 R
9158 12545 0.035458 ACTTGTGCTCGGGGAAGAAG 59.965 55.000 0.00 0.00 0.00 2.85 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
67 68 3.199727 TGCTGCTAGAGAGAGAGAGAGAA 59.800 47.826 0.00 0.00 0.00 2.87
68 69 4.141413 TGCTGCTAGAGAGAGAGAGAGAAT 60.141 45.833 0.00 0.00 0.00 2.40
74 95 3.139025 AGAGAGAGAGAGAGAATGGGAGG 59.861 52.174 0.00 0.00 0.00 4.30
76 112 2.176798 GAGAGAGAGAGAATGGGAGGGA 59.823 54.545 0.00 0.00 0.00 4.20
80 116 1.135960 GAGAGAATGGGAGGGAAGGG 58.864 60.000 0.00 0.00 0.00 3.95
101 139 3.307550 GGGGGAGAAAGAGAACTAACCAC 60.308 52.174 0.00 0.00 0.00 4.16
127 168 4.254709 TCGCCTGCAGCAACCACT 62.255 61.111 8.66 0.00 44.04 4.00
128 169 3.289834 CGCCTGCAGCAACCACTT 61.290 61.111 8.66 0.00 44.04 3.16
129 170 2.647297 GCCTGCAGCAACCACTTC 59.353 61.111 8.66 0.00 42.97 3.01
196 244 0.468648 GGACAATCGGAGGTTAGGGG 59.531 60.000 0.00 0.00 0.00 4.79
198 246 1.558294 GACAATCGGAGGTTAGGGGTT 59.442 52.381 0.00 0.00 0.00 4.11
397 472 1.035932 TTTTCCGCGTGGGTTTGGAA 61.036 50.000 16.49 0.00 38.67 3.53
423 498 1.229076 GGCCGGGGAAATACCACAT 59.771 57.895 2.18 0.00 43.50 3.21
553 637 1.746991 GCTACAGCTTCAGGCCCAC 60.747 63.158 0.00 0.00 43.05 4.61
621 705 4.699522 GCCGTCCGCAACCTCCTT 62.700 66.667 0.00 0.00 37.47 3.36
704 791 1.086757 ACCCCCAATCCCCTTAGCT 59.913 57.895 0.00 0.00 0.00 3.32
736 823 3.528370 CCGCTACGGCTGCTACCT 61.528 66.667 0.00 0.00 41.17 3.08
905 995 2.265367 TCCCAACTAGATCTGCACCAA 58.735 47.619 5.18 0.00 0.00 3.67
920 1010 0.912486 ACCAACCTATCCAGCCAGTC 59.088 55.000 0.00 0.00 0.00 3.51
964 1054 4.127907 TGCTGAAGATGCTCTCATGATTC 58.872 43.478 0.00 0.00 31.96 2.52
1421 1512 5.249780 TCCACAAGGGATTTAGTTGCTAA 57.750 39.130 0.00 0.00 42.15 3.09
2265 2357 4.678840 CGGCGGTGTTTCCTAGTATAGTTT 60.679 45.833 0.00 0.00 36.82 2.66
2266 2358 5.450412 CGGCGGTGTTTCCTAGTATAGTTTA 60.450 44.000 0.00 0.00 36.82 2.01
2329 2423 7.308348 GCAGGACACATTTGTTAGTTTAAGCTA 60.308 37.037 0.00 0.00 35.47 3.32
2783 3068 2.113860 AAGGAACACACATCCATCGG 57.886 50.000 0.00 0.00 39.55 4.18
2911 3196 6.255670 TGCAAATACGAGCTTTGTAGAGTATG 59.744 38.462 6.04 2.74 36.26 2.39
2921 3206 7.796054 AGCTTTGTAGAGTATGGAATATGTGT 58.204 34.615 0.00 0.00 0.00 3.72
2926 3211 9.817809 TTGTAGAGTATGGAATATGTGTTCTTC 57.182 33.333 0.00 0.00 0.00 2.87
3218 3692 9.730705 ATAACTGTGCTATTGTCATATTATGCT 57.269 29.630 0.00 0.00 0.00 3.79
3791 4270 0.111061 TGCAGTTGCCATCTCAGGTT 59.889 50.000 1.06 0.00 41.18 3.50
3798 4277 1.421268 TGCCATCTCAGGTTCAAGTGT 59.579 47.619 0.00 0.00 0.00 3.55
3913 4392 0.883833 ACACTAAGCAGTTGCCATGC 59.116 50.000 0.00 0.00 43.38 4.06
4425 4916 1.812571 AGATTCGTGCACCCACAAATC 59.187 47.619 12.15 12.16 42.83 2.17
4579 5070 4.827692 ACTGCGACAAGTAATGGTTGATA 58.172 39.130 0.00 0.00 0.00 2.15
4580 5071 4.870426 ACTGCGACAAGTAATGGTTGATAG 59.130 41.667 0.00 0.00 0.00 2.08
4581 5072 4.827692 TGCGACAAGTAATGGTTGATAGT 58.172 39.130 0.00 0.00 0.00 2.12
4582 5073 4.629634 TGCGACAAGTAATGGTTGATAGTG 59.370 41.667 0.00 0.00 0.00 2.74
4583 5074 4.034048 GCGACAAGTAATGGTTGATAGTGG 59.966 45.833 0.00 0.00 0.00 4.00
4584 5075 4.034048 CGACAAGTAATGGTTGATAGTGGC 59.966 45.833 0.00 0.00 0.00 5.01
4585 5076 4.270008 ACAAGTAATGGTTGATAGTGGCC 58.730 43.478 0.00 0.00 0.00 5.36
4586 5077 4.263727 ACAAGTAATGGTTGATAGTGGCCA 60.264 41.667 0.00 0.00 35.28 5.36
4587 5078 4.796110 AGTAATGGTTGATAGTGGCCAT 57.204 40.909 9.72 0.00 42.90 4.40
4589 5080 5.133221 AGTAATGGTTGATAGTGGCCATTC 58.867 41.667 9.72 7.58 45.43 2.67
4590 5081 3.668141 ATGGTTGATAGTGGCCATTCA 57.332 42.857 9.72 10.46 38.45 2.57
4591 5082 3.668141 TGGTTGATAGTGGCCATTCAT 57.332 42.857 9.72 1.89 0.00 2.57
4592 5083 3.289836 TGGTTGATAGTGGCCATTCATG 58.710 45.455 9.72 0.00 0.00 3.07
4593 5084 6.681816 AATGGTTGATAGTGGCCATTCATGG 61.682 44.000 9.72 0.95 45.43 3.66
4602 5093 3.038946 CCATTCATGGCAAACTGCG 57.961 52.632 0.00 0.00 46.21 5.18
4603 5094 0.527113 CCATTCATGGCAAACTGCGA 59.473 50.000 0.00 0.00 46.21 5.10
4604 5095 1.621107 CATTCATGGCAAACTGCGAC 58.379 50.000 0.00 0.00 46.21 5.19
4605 5096 1.068402 CATTCATGGCAAACTGCGACA 60.068 47.619 0.00 0.00 46.21 4.35
4785 5276 2.525105 TTGGGAAGGTCCTTAATGGC 57.475 50.000 3.42 0.00 36.57 4.40
5024 5515 9.289782 AGCTTAAAAGGGCAGTAGAATATAATG 57.710 33.333 0.00 0.00 0.00 1.90
5045 5536 1.001631 TTCGATGCTGGAGGGAGGA 59.998 57.895 0.00 0.00 0.00 3.71
5572 6065 8.704668 TCATTATTTTCTACCAGCATACTCTGA 58.295 33.333 0.00 0.00 36.19 3.27
5578 6071 3.550437 ACCAGCATACTCTGATTGACC 57.450 47.619 0.00 0.00 36.19 4.02
5658 6151 0.679002 TGATCTGGAAGGCAAGCTGC 60.679 55.000 0.00 0.00 44.08 5.25
5700 6193 2.245096 GAGCAGCGTATTTGCACTTTG 58.755 47.619 0.00 0.00 43.92 2.77
6177 8968 8.864069 AAGATCGTTACTCTTACTCATCATTG 57.136 34.615 0.00 0.00 31.27 2.82
6196 8989 7.849804 TCATTGGAGAATGTTAGTAGAAAGC 57.150 36.000 0.00 0.00 40.09 3.51
6602 9395 3.057876 CCTTCTACTACTATGCAGCGAGG 60.058 52.174 0.00 0.00 0.00 4.63
7146 9939 8.652810 AAATGTGAATTCCTTTGAAGAACTTG 57.347 30.769 2.27 0.00 33.05 3.16
7211 10004 3.133901 TGACCTGTTGTTCTACTTCTGCA 59.866 43.478 0.00 0.00 0.00 4.41
7227 10020 9.262358 CTACTTCTGCATTAGTTTAATACTCCC 57.738 37.037 6.22 0.00 38.33 4.30
7229 10022 7.988028 ACTTCTGCATTAGTTTAATACTCCCTC 59.012 37.037 0.00 0.00 38.33 4.30
7230 10023 6.827727 TCTGCATTAGTTTAATACTCCCTCC 58.172 40.000 0.00 0.00 38.33 4.30
7231 10024 6.385759 TCTGCATTAGTTTAATACTCCCTCCA 59.614 38.462 0.00 0.00 38.33 3.86
7232 10025 7.072454 TCTGCATTAGTTTAATACTCCCTCCAT 59.928 37.037 0.00 0.00 38.33 3.41
7233 10026 7.224297 TGCATTAGTTTAATACTCCCTCCATC 58.776 38.462 0.00 0.00 38.33 3.51
7234 10027 7.072454 TGCATTAGTTTAATACTCCCTCCATCT 59.928 37.037 0.00 0.00 38.33 2.90
7235 10028 7.389053 GCATTAGTTTAATACTCCCTCCATCTG 59.611 40.741 0.00 0.00 38.33 2.90
7236 10029 8.651389 CATTAGTTTAATACTCCCTCCATCTGA 58.349 37.037 0.00 0.00 38.33 3.27
7237 10030 8.618240 TTAGTTTAATACTCCCTCCATCTGAA 57.382 34.615 0.00 0.00 38.33 3.02
7238 10031 7.510675 AGTTTAATACTCCCTCCATCTGAAA 57.489 36.000 0.00 0.00 28.23 2.69
7239 10032 7.928873 AGTTTAATACTCCCTCCATCTGAAAA 58.071 34.615 0.00 0.00 28.23 2.29
7240 10033 8.560903 AGTTTAATACTCCCTCCATCTGAAAAT 58.439 33.333 0.00 0.00 28.23 1.82
7241 10034 9.847224 GTTTAATACTCCCTCCATCTGAAAATA 57.153 33.333 0.00 0.00 0.00 1.40
7242 10035 9.847224 TTTAATACTCCCTCCATCTGAAAATAC 57.153 33.333 0.00 0.00 0.00 1.89
7243 10036 7.698163 AATACTCCCTCCATCTGAAAATACT 57.302 36.000 0.00 0.00 0.00 2.12
7244 10037 7.698163 ATACTCCCTCCATCTGAAAATACTT 57.302 36.000 0.00 0.00 0.00 2.24
7245 10038 5.749462 ACTCCCTCCATCTGAAAATACTTG 58.251 41.667 0.00 0.00 0.00 3.16
7246 10039 5.251700 ACTCCCTCCATCTGAAAATACTTGT 59.748 40.000 0.00 0.00 0.00 3.16
7247 10040 5.745227 TCCCTCCATCTGAAAATACTTGTC 58.255 41.667 0.00 0.00 0.00 3.18
7248 10041 5.250543 TCCCTCCATCTGAAAATACTTGTCA 59.749 40.000 0.00 0.00 0.00 3.58
7249 10042 6.069440 TCCCTCCATCTGAAAATACTTGTCAT 60.069 38.462 0.00 0.00 0.00 3.06
7250 10043 6.261826 CCCTCCATCTGAAAATACTTGTCATC 59.738 42.308 0.00 0.00 0.00 2.92
7251 10044 6.825213 CCTCCATCTGAAAATACTTGTCATCA 59.175 38.462 0.00 0.00 0.00 3.07
7252 10045 7.337689 CCTCCATCTGAAAATACTTGTCATCAA 59.662 37.037 0.00 0.00 0.00 2.57
7253 10046 8.634335 TCCATCTGAAAATACTTGTCATCAAA 57.366 30.769 0.00 0.00 32.87 2.69
7254 10047 9.076781 TCCATCTGAAAATACTTGTCATCAAAA 57.923 29.630 0.00 0.00 32.87 2.44
7255 10048 9.695526 CCATCTGAAAATACTTGTCATCAAAAA 57.304 29.630 0.00 0.00 32.87 1.94
7305 10098 8.977267 ACTAATATACGTCTAGATACATCCCC 57.023 38.462 0.00 0.00 0.00 4.81
7306 10099 8.780003 ACTAATATACGTCTAGATACATCCCCT 58.220 37.037 0.00 0.00 0.00 4.79
7307 10100 9.629878 CTAATATACGTCTAGATACATCCCCTT 57.370 37.037 0.00 0.00 0.00 3.95
7308 10101 8.896722 AATATACGTCTAGATACATCCCCTTT 57.103 34.615 0.00 0.00 0.00 3.11
7309 10102 8.896722 ATATACGTCTAGATACATCCCCTTTT 57.103 34.615 0.00 0.00 0.00 2.27
7310 10103 9.986157 ATATACGTCTAGATACATCCCCTTTTA 57.014 33.333 0.00 0.00 0.00 1.52
7311 10104 8.896722 ATACGTCTAGATACATCCCCTTTTAT 57.103 34.615 0.00 0.00 0.00 1.40
7312 10105 7.613551 ACGTCTAGATACATCCCCTTTTATT 57.386 36.000 0.00 0.00 0.00 1.40
7313 10106 7.668492 ACGTCTAGATACATCCCCTTTTATTC 58.332 38.462 0.00 0.00 0.00 1.75
7314 10107 7.289317 ACGTCTAGATACATCCCCTTTTATTCA 59.711 37.037 0.00 0.00 0.00 2.57
7315 10108 8.314751 CGTCTAGATACATCCCCTTTTATTCAT 58.685 37.037 0.00 0.00 0.00 2.57
7320 10113 9.713684 AGATACATCCCCTTTTATTCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
7323 10116 8.378115 ACATCCCCTTTTATTCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
7324 10117 8.260114 ACATCCCCTTTTATTCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
7325 10118 7.789202 TCCCCTTTTATTCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
7326 10119 7.610865 TCCCCTTTTATTCATTTTGATGACAC 58.389 34.615 0.00 0.00 0.00 3.67
7327 10120 7.234371 TCCCCTTTTATTCATTTTGATGACACA 59.766 33.333 0.00 0.00 0.00 3.72
7328 10121 8.042515 CCCCTTTTATTCATTTTGATGACACAT 58.957 33.333 0.00 0.00 0.00 3.21
7335 10128 8.861033 ATTCATTTTGATGACACATATTTCCG 57.139 30.769 0.00 0.00 0.00 4.30
7336 10129 6.794374 TCATTTTGATGACACATATTTCCGG 58.206 36.000 0.00 0.00 0.00 5.14
7337 10130 6.601217 TCATTTTGATGACACATATTTCCGGA 59.399 34.615 0.00 0.00 0.00 5.14
7338 10131 5.811399 TTTGATGACACATATTTCCGGAC 57.189 39.130 1.83 0.00 0.00 4.79
7339 10132 3.453424 TGATGACACATATTTCCGGACG 58.547 45.455 1.83 0.00 0.00 4.79
7340 10133 2.303163 TGACACATATTTCCGGACGG 57.697 50.000 1.83 3.96 0.00 4.79
7341 10134 1.826096 TGACACATATTTCCGGACGGA 59.174 47.619 1.83 9.76 43.52 4.69
7342 10135 2.159156 TGACACATATTTCCGGACGGAG 60.159 50.000 13.64 4.57 46.06 4.63
7343 10136 1.138266 ACACATATTTCCGGACGGAGG 59.862 52.381 13.64 0.00 46.06 4.30
7344 10137 0.756903 ACATATTTCCGGACGGAGGG 59.243 55.000 13.64 5.76 46.06 4.30
7383 10176 1.490490 TGCTGGGAACTTCAGTCTGTT 59.510 47.619 0.00 0.00 34.89 3.16
7862 10656 9.855021 TCTTTCTTTTTAGTTTGCATATTAGGC 57.145 29.630 0.00 0.00 0.00 3.93
8091 10885 9.740710 AGTATAAAAGATTGCTCCTGTTAGTTT 57.259 29.630 0.00 0.00 0.00 2.66
8299 11096 5.945784 AGGTAAAGCATGATTAGCTGAACAA 59.054 36.000 17.41 0.00 42.53 2.83
8433 11292 2.046892 GCAGGTCACGCAGTCCAT 60.047 61.111 0.00 0.00 41.61 3.41
8602 11461 4.305524 AGATCAAGATCCAGGTCCAAGAT 58.694 43.478 6.45 0.00 38.58 2.40
8612 11471 1.154205 GGTCCAAGATCCGTGATGCG 61.154 60.000 0.00 0.00 40.95 4.73
8927 11822 5.405571 CCGGTGAAGTTTATCGATAAGATGG 59.594 44.000 16.89 8.71 40.40 3.51
8965 11860 0.034863 TGGATTTCTTACCACGGGGC 60.035 55.000 1.73 0.00 37.90 5.80
8988 11883 3.055747 TCCACGTGGTATAAGATGCAACA 60.056 43.478 32.74 6.62 36.34 3.33
9016 12401 6.149633 AGTTGCCAACTTTTCGATTGATAAC 58.850 36.000 3.74 3.78 39.04 1.89
9018 12403 4.095610 GCCAACTTTTCGATTGATAACGG 58.904 43.478 0.00 0.00 0.00 4.44
9022 12407 0.653636 TTTCGATTGATAACGGCGGC 59.346 50.000 13.24 0.00 0.00 6.53
9037 12422 0.308993 GCGGCTGCTACAAATCATCC 59.691 55.000 11.21 0.00 38.39 3.51
9044 12429 3.785486 TGCTACAAATCATCCGACTGAG 58.215 45.455 0.00 0.00 0.00 3.35
9045 12430 2.541762 GCTACAAATCATCCGACTGAGC 59.458 50.000 0.00 0.00 0.00 4.26
9046 12431 2.768253 ACAAATCATCCGACTGAGCA 57.232 45.000 0.00 0.00 0.00 4.26
9049 12434 0.904649 AATCATCCGACTGAGCACCA 59.095 50.000 0.00 0.00 0.00 4.17
9050 12435 0.904649 ATCATCCGACTGAGCACCAA 59.095 50.000 0.00 0.00 0.00 3.67
9051 12436 0.684535 TCATCCGACTGAGCACCAAA 59.315 50.000 0.00 0.00 0.00 3.28
9052 12437 1.278985 TCATCCGACTGAGCACCAAAT 59.721 47.619 0.00 0.00 0.00 2.32
9096 12483 0.861837 GATTCATCGTGCCTAAGCCG 59.138 55.000 0.00 0.00 38.69 5.52
9121 12508 1.495584 TTGGTCAACGCTGCTTCGTC 61.496 55.000 0.00 0.00 42.46 4.20
9158 12545 2.822399 CGTAGGTCCATGGCTCCC 59.178 66.667 18.09 12.79 0.00 4.30
9197 12584 2.445438 GCAGTTCACCGCTAGTCGC 61.445 63.158 0.00 0.00 36.73 5.19
9212 12599 0.386858 GTCGCTGACAGTAGCAACGA 60.387 55.000 3.99 0.39 43.87 3.85
9256 12643 2.586079 CGATGGAAGCGGCGATGT 60.586 61.111 12.98 0.00 45.34 3.06
9257 12644 2.874694 CGATGGAAGCGGCGATGTG 61.875 63.158 12.98 0.00 45.34 3.21
9331 12718 1.063649 GGCTGATGTTGCGATGCAG 59.936 57.895 0.00 0.00 40.61 4.41
9339 12726 3.413861 TGCGATGCAGCACACGAC 61.414 61.111 22.60 15.41 42.92 4.34
9437 12824 2.817834 GTAATGCAGCGCCACCGA 60.818 61.111 2.29 0.00 36.29 4.69
9497 12884 2.183504 TTGCAACGCCACACACGAT 61.184 52.632 0.00 0.00 0.00 3.73
9605 13013 2.361610 CGGCCATGGTGGAAGCTT 60.362 61.111 14.67 0.00 40.96 3.74
9615 13023 2.101770 GGAAGCTTGCGATGCAGC 59.898 61.111 2.10 0.00 40.61 5.25
9649 13057 0.677731 GGGAGCTGCTATGCAACACA 60.678 55.000 0.15 0.00 38.41 3.72
9650 13058 1.386533 GGAGCTGCTATGCAACACAT 58.613 50.000 0.15 0.00 43.18 3.21
9651 13059 1.065102 GGAGCTGCTATGCAACACATG 59.935 52.381 0.15 0.00 40.06 3.21
9660 13068 2.898181 TGCAACACATGAATGCTACG 57.102 45.000 18.00 0.00 40.66 3.51
9661 13069 2.421619 TGCAACACATGAATGCTACGA 58.578 42.857 18.00 1.57 40.66 3.43
9662 13070 3.009026 TGCAACACATGAATGCTACGAT 58.991 40.909 18.00 0.00 40.66 3.73
9675 13083 1.217585 CTACGATGATGCAGCCACGG 61.218 60.000 18.60 6.26 0.00 4.94
9724 13132 1.353091 GTCTTCCCCTCCTCTGTTGT 58.647 55.000 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 116 3.326880 TGTGGTTAGTTCTCTTTCTCCCC 59.673 47.826 0.00 0.00 0.00 4.81
87 123 4.767928 ACGAGATCTGTGGTTAGTTCTCTT 59.232 41.667 0.00 0.00 39.62 2.85
101 139 1.588403 CTGCAGGCGACGAGATCTG 60.588 63.158 5.57 1.35 0.00 2.90
127 168 2.461695 CAGAACCCTAGCTCTGGAGAA 58.538 52.381 8.37 0.00 36.27 2.87
128 169 2.151502 CAGAACCCTAGCTCTGGAGA 57.848 55.000 8.37 0.00 36.27 3.71
170 214 1.343478 ACCTCCGATTGTCCCATCTCT 60.343 52.381 0.00 0.00 0.00 3.10
196 244 3.423154 CACGAAGCCCTGCCGAAC 61.423 66.667 0.00 0.00 0.00 3.95
216 264 4.430765 CCCCTGGTTCGACGACCG 62.431 72.222 0.00 0.00 42.83 4.79
289 347 0.972983 CAGAAGCGGAAGGAGGAGGA 60.973 60.000 0.00 0.00 0.00 3.71
290 348 1.261238 ACAGAAGCGGAAGGAGGAGG 61.261 60.000 0.00 0.00 0.00 4.30
291 349 0.174617 GACAGAAGCGGAAGGAGGAG 59.825 60.000 0.00 0.00 0.00 3.69
292 350 1.595993 CGACAGAAGCGGAAGGAGGA 61.596 60.000 0.00 0.00 0.00 3.71
397 472 2.395180 ATTTCCCCGGCCCAAACCTT 62.395 55.000 0.00 0.00 0.00 3.50
553 637 2.573609 ATCGGTTTCCTTCCGCGGAG 62.574 60.000 29.20 21.10 46.49 4.63
618 702 1.190643 GTCAGGACTCAGGAGGAAGG 58.809 60.000 0.83 0.00 0.00 3.46
619 703 1.190643 GGTCAGGACTCAGGAGGAAG 58.809 60.000 0.83 0.00 0.00 3.46
620 704 0.787084 AGGTCAGGACTCAGGAGGAA 59.213 55.000 0.83 0.00 0.00 3.36
621 705 1.566703 CTAGGTCAGGACTCAGGAGGA 59.433 57.143 0.83 0.00 0.00 3.71
729 816 3.083349 ATGGCAGCGGAGGTAGCA 61.083 61.111 0.00 0.00 35.08 3.49
736 823 4.838152 GAAGGCGATGGCAGCGGA 62.838 66.667 27.38 0.00 42.47 5.54
905 995 2.559381 AAGAGACTGGCTGGATAGGT 57.441 50.000 0.00 0.00 0.00 3.08
920 1010 5.284079 CAACAAACATCCCAACAGAAAGAG 58.716 41.667 0.00 0.00 0.00 2.85
1003 1093 5.456265 GTTCAGATTCTTCTTGAACTTGGC 58.544 41.667 8.81 0.00 37.22 4.52
1069 1159 3.251004 GCAACCTCAAACGTGATTCTCTT 59.749 43.478 0.00 0.00 31.85 2.85
1421 1512 2.095567 GCATTCAAGACTGTCGTGCATT 60.096 45.455 17.23 3.60 0.00 3.56
1547 1638 2.292016 CACCGCCACAACACTCAAATTA 59.708 45.455 0.00 0.00 0.00 1.40
1825 1916 5.049129 GGAGATATCATGTAAAAGCAGTGGC 60.049 44.000 5.32 0.00 41.61 5.01
2230 2322 2.115911 ACCGCCGCAACACTCAAAA 61.116 52.632 0.00 0.00 0.00 2.44
2278 2372 4.810345 ACCTTTATGTGGAAGTGGGAAAA 58.190 39.130 0.00 0.00 0.00 2.29
2329 2423 8.548877 AGGAAGACAACAATACAACACCTATAT 58.451 33.333 0.00 0.00 0.00 0.86
2338 2432 6.353323 TGAACAGAGGAAGACAACAATACAA 58.647 36.000 0.00 0.00 0.00 2.41
2450 2544 0.109597 CATGACAAGAAAGGTGCGGC 60.110 55.000 0.00 0.00 0.00 6.53
2783 3068 5.819991 TGAGCCATAAATCCTGGGATAATC 58.180 41.667 2.24 0.00 33.97 1.75
3151 3622 9.342308 CTTCAGAGGCTATAACCAATAAAATCA 57.658 33.333 0.00 0.00 0.00 2.57
3218 3692 9.502091 ACAGTACATACATTCTTTTAGCAGAAA 57.498 29.630 0.00 0.00 36.36 2.52
3410 3884 1.807742 CAGTTATCGGCGTCCCAAAAA 59.192 47.619 6.85 0.00 0.00 1.94
3411 3885 1.444836 CAGTTATCGGCGTCCCAAAA 58.555 50.000 6.85 0.00 0.00 2.44
3421 3895 0.669318 ACACGTGTGGCAGTTATCGG 60.669 55.000 22.71 0.00 34.19 4.18
3791 4270 3.256383 CCAAAATGGCATCTGACACTTGA 59.744 43.478 0.00 0.00 34.80 3.02
3798 4277 3.256383 CAGTTGTCCAAAATGGCATCTGA 59.744 43.478 17.52 0.00 40.14 3.27
3913 4392 4.154195 GCAACTGTAGTAAACCAGACCATG 59.846 45.833 0.00 0.00 32.93 3.66
4585 5076 1.068402 TGTCGCAGTTTGCCATGAATG 60.068 47.619 0.00 0.00 41.12 2.67
4586 5077 1.246649 TGTCGCAGTTTGCCATGAAT 58.753 45.000 0.00 0.00 41.12 2.57
4587 5078 1.001487 CTTGTCGCAGTTTGCCATGAA 60.001 47.619 0.00 0.00 41.12 2.57
4588 5079 0.592637 CTTGTCGCAGTTTGCCATGA 59.407 50.000 0.00 0.00 41.12 3.07
4589 5080 0.311790 ACTTGTCGCAGTTTGCCATG 59.688 50.000 0.00 0.00 41.12 3.66
4590 5081 1.890876 TACTTGTCGCAGTTTGCCAT 58.109 45.000 0.00 0.00 41.12 4.40
4591 5082 1.535028 CATACTTGTCGCAGTTTGCCA 59.465 47.619 0.00 0.00 41.12 4.92
4592 5083 1.535462 ACATACTTGTCGCAGTTTGCC 59.465 47.619 0.00 0.00 41.12 4.52
4593 5084 2.223144 TCACATACTTGTCGCAGTTTGC 59.777 45.455 0.00 0.00 35.13 3.68
4594 5085 4.668576 ATCACATACTTGTCGCAGTTTG 57.331 40.909 0.00 0.00 32.34 2.93
4595 5086 5.577164 GTCTATCACATACTTGTCGCAGTTT 59.423 40.000 0.00 0.00 32.34 2.66
4596 5087 5.103000 GTCTATCACATACTTGTCGCAGTT 58.897 41.667 0.00 0.00 32.34 3.16
4597 5088 4.440250 GGTCTATCACATACTTGTCGCAGT 60.440 45.833 0.00 0.00 32.34 4.40
4598 5089 4.045104 GGTCTATCACATACTTGTCGCAG 58.955 47.826 0.00 0.00 32.34 5.18
4599 5090 3.181479 GGGTCTATCACATACTTGTCGCA 60.181 47.826 0.00 0.00 32.34 5.10
4600 5091 3.181479 TGGGTCTATCACATACTTGTCGC 60.181 47.826 0.00 0.00 32.34 5.19
4601 5092 4.649088 TGGGTCTATCACATACTTGTCG 57.351 45.455 0.00 0.00 32.34 4.35
4602 5093 5.581085 GTGTTGGGTCTATCACATACTTGTC 59.419 44.000 0.00 0.00 32.34 3.18
4603 5094 5.488341 GTGTTGGGTCTATCACATACTTGT 58.512 41.667 0.00 0.00 36.15 3.16
4604 5095 4.876107 GGTGTTGGGTCTATCACATACTTG 59.124 45.833 0.00 0.00 33.17 3.16
4605 5096 4.534500 TGGTGTTGGGTCTATCACATACTT 59.466 41.667 0.00 0.00 33.17 2.24
4809 5300 1.457346 CAGATTCAGAACCCAGTGCC 58.543 55.000 0.00 0.00 0.00 5.01
4961 5452 6.360370 TCAAGTACTGAGAAAGCTTACCAT 57.640 37.500 0.00 0.00 0.00 3.55
5024 5515 0.103937 CTCCCTCCAGCATCGAAGTC 59.896 60.000 0.00 0.00 0.00 3.01
5028 5519 0.829602 GATCCTCCCTCCAGCATCGA 60.830 60.000 0.00 0.00 0.00 3.59
5375 5866 7.118971 GCAGGGAATCAATTCAGCTAGTATTAG 59.881 40.741 5.19 0.00 38.53 1.73
5572 6065 1.163420 TCAAACAGCACGCGGTCAAT 61.163 50.000 12.47 0.00 0.00 2.57
5574 6067 1.163420 ATTCAAACAGCACGCGGTCA 61.163 50.000 12.47 0.00 0.00 4.02
5578 6071 2.095969 TCCTAAATTCAAACAGCACGCG 60.096 45.455 3.53 3.53 0.00 6.01
5700 6193 4.793216 CGAGCAATAAATTGGCAAGTACAC 59.207 41.667 5.96 0.00 38.21 2.90
6177 8968 7.712639 TCATCATGCTTTCTACTAACATTCTCC 59.287 37.037 0.00 0.00 0.00 3.71
6196 8989 7.010275 CAGACAGACACAGTAAAGATCATCATG 59.990 40.741 0.00 0.00 0.00 3.07
6467 9260 4.483476 ACTTTCATCTTTGTGTAACGGC 57.517 40.909 0.00 0.00 42.39 5.68
6952 9745 5.833406 ACGTGGCAAATCAATAATCATGA 57.167 34.783 0.00 0.00 0.00 3.07
7043 9836 3.822192 CCTCACCGGCGATCGTGA 61.822 66.667 17.81 12.98 37.11 4.35
7146 9939 4.883585 TGCCACAATTCCATGAGATTAGAC 59.116 41.667 0.00 0.00 0.00 2.59
7211 10004 8.798975 TCAGATGGAGGGAGTATTAAACTAAT 57.201 34.615 0.00 0.00 39.07 1.73
7223 10016 5.749462 ACAAGTATTTTCAGATGGAGGGAG 58.251 41.667 0.00 0.00 0.00 4.30
7224 10017 5.250543 TGACAAGTATTTTCAGATGGAGGGA 59.749 40.000 0.00 0.00 0.00 4.20
7225 10018 5.500234 TGACAAGTATTTTCAGATGGAGGG 58.500 41.667 0.00 0.00 0.00 4.30
7226 10019 6.825213 TGATGACAAGTATTTTCAGATGGAGG 59.175 38.462 0.00 0.00 0.00 4.30
7227 10020 7.854557 TGATGACAAGTATTTTCAGATGGAG 57.145 36.000 0.00 0.00 0.00 3.86
7229 10022 9.695526 TTTTTGATGACAAGTATTTTCAGATGG 57.304 29.630 0.00 0.00 37.32 3.51
7279 10072 9.406113 GGGGATGTATCTAGACGTATATTAGTT 57.594 37.037 0.00 0.00 0.00 2.24
7280 10073 8.780003 AGGGGATGTATCTAGACGTATATTAGT 58.220 37.037 0.00 0.00 0.00 2.24
7281 10074 9.629878 AAGGGGATGTATCTAGACGTATATTAG 57.370 37.037 0.00 0.00 0.00 1.73
7282 10075 9.986157 AAAGGGGATGTATCTAGACGTATATTA 57.014 33.333 0.00 0.00 0.00 0.98
7283 10076 8.896722 AAAGGGGATGTATCTAGACGTATATT 57.103 34.615 0.00 0.00 0.00 1.28
7284 10077 8.896722 AAAAGGGGATGTATCTAGACGTATAT 57.103 34.615 0.00 0.00 0.00 0.86
7285 10078 9.986157 ATAAAAGGGGATGTATCTAGACGTATA 57.014 33.333 0.00 0.00 0.00 1.47
7286 10079 8.896722 ATAAAAGGGGATGTATCTAGACGTAT 57.103 34.615 0.00 0.00 0.00 3.06
7287 10080 8.716674 AATAAAAGGGGATGTATCTAGACGTA 57.283 34.615 0.00 0.00 0.00 3.57
7288 10081 7.289317 TGAATAAAAGGGGATGTATCTAGACGT 59.711 37.037 0.00 0.00 0.00 4.34
7289 10082 7.667557 TGAATAAAAGGGGATGTATCTAGACG 58.332 38.462 0.00 0.00 0.00 4.18
7294 10087 9.713684 TCAAAATGAATAAAAGGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
7297 10090 9.486123 TCATCAAAATGAATAAAAGGGGATGTA 57.514 29.630 0.00 0.00 38.97 2.29
7298 10091 8.260114 GTCATCAAAATGAATAAAAGGGGATGT 58.740 33.333 0.00 0.00 43.42 3.06
7299 10092 8.259411 TGTCATCAAAATGAATAAAAGGGGATG 58.741 33.333 0.00 0.00 43.42 3.51
7300 10093 8.260114 GTGTCATCAAAATGAATAAAAGGGGAT 58.740 33.333 0.00 0.00 43.42 3.85
7301 10094 7.234371 TGTGTCATCAAAATGAATAAAAGGGGA 59.766 33.333 0.00 0.00 43.42 4.81
7302 10095 7.385267 TGTGTCATCAAAATGAATAAAAGGGG 58.615 34.615 0.00 0.00 43.42 4.79
7309 10102 9.949174 CGGAAATATGTGTCATCAAAATGAATA 57.051 29.630 0.00 0.00 43.42 1.75
7310 10103 7.922278 CCGGAAATATGTGTCATCAAAATGAAT 59.078 33.333 0.00 0.00 43.42 2.57
7311 10104 7.121907 TCCGGAAATATGTGTCATCAAAATGAA 59.878 33.333 0.00 0.00 43.42 2.57
7312 10105 6.601217 TCCGGAAATATGTGTCATCAAAATGA 59.399 34.615 0.00 0.00 39.63 2.57
7313 10106 6.692681 GTCCGGAAATATGTGTCATCAAAATG 59.307 38.462 5.23 0.00 0.00 2.32
7314 10107 6.458206 CGTCCGGAAATATGTGTCATCAAAAT 60.458 38.462 5.23 0.00 0.00 1.82
7315 10108 5.163804 CGTCCGGAAATATGTGTCATCAAAA 60.164 40.000 5.23 0.00 0.00 2.44
7316 10109 4.331443 CGTCCGGAAATATGTGTCATCAAA 59.669 41.667 5.23 0.00 0.00 2.69
7317 10110 3.868661 CGTCCGGAAATATGTGTCATCAA 59.131 43.478 5.23 0.00 0.00 2.57
7318 10111 3.453424 CGTCCGGAAATATGTGTCATCA 58.547 45.455 5.23 0.00 0.00 3.07
7319 10112 2.800544 CCGTCCGGAAATATGTGTCATC 59.199 50.000 5.23 0.00 37.50 2.92
7320 10113 2.432874 TCCGTCCGGAAATATGTGTCAT 59.567 45.455 5.23 0.00 42.05 3.06
7321 10114 1.826096 TCCGTCCGGAAATATGTGTCA 59.174 47.619 5.23 0.00 42.05 3.58
7322 10115 2.470821 CTCCGTCCGGAAATATGTGTC 58.529 52.381 5.23 0.00 44.66 3.67
7323 10116 1.138266 CCTCCGTCCGGAAATATGTGT 59.862 52.381 5.23 0.00 44.66 3.72
7324 10117 1.540363 CCCTCCGTCCGGAAATATGTG 60.540 57.143 5.23 0.00 44.66 3.21
7325 10118 0.756903 CCCTCCGTCCGGAAATATGT 59.243 55.000 5.23 0.00 44.66 2.29
7326 10119 1.000955 CTCCCTCCGTCCGGAAATATG 59.999 57.143 5.23 0.00 44.66 1.78
7327 10120 1.339097 CTCCCTCCGTCCGGAAATAT 58.661 55.000 5.23 0.00 44.66 1.28
7328 10121 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
7329 10122 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
7330 10123 0.251742 TTACTCCCTCCGTCCGGAAA 60.252 55.000 5.23 0.00 44.66 3.13
7331 10124 0.032813 ATTACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
7332 10125 0.032813 AATTACTCCCTCCGTCCGGA 60.033 55.000 0.00 0.00 42.90 5.14
7333 10126 0.828677 AAATTACTCCCTCCGTCCGG 59.171 55.000 0.00 0.00 0.00 5.14
7334 10127 1.755380 AGAAATTACTCCCTCCGTCCG 59.245 52.381 0.00 0.00 0.00 4.79
7335 10128 4.344390 ACATAGAAATTACTCCCTCCGTCC 59.656 45.833 0.00 0.00 0.00 4.79
7336 10129 5.532664 ACATAGAAATTACTCCCTCCGTC 57.467 43.478 0.00 0.00 0.00 4.79
7337 10130 5.424252 TCAACATAGAAATTACTCCCTCCGT 59.576 40.000 0.00 0.00 0.00 4.69
7338 10131 5.914033 TCAACATAGAAATTACTCCCTCCG 58.086 41.667 0.00 0.00 0.00 4.63
7339 10132 7.255277 GCATTCAACATAGAAATTACTCCCTCC 60.255 40.741 0.00 0.00 0.00 4.30
7340 10133 7.500559 AGCATTCAACATAGAAATTACTCCCTC 59.499 37.037 0.00 0.00 0.00 4.30
7341 10134 7.284034 CAGCATTCAACATAGAAATTACTCCCT 59.716 37.037 0.00 0.00 0.00 4.20
7342 10135 7.420800 CAGCATTCAACATAGAAATTACTCCC 58.579 38.462 0.00 0.00 0.00 4.30
7343 10136 7.420800 CCAGCATTCAACATAGAAATTACTCC 58.579 38.462 0.00 0.00 0.00 3.85
7344 10137 7.283127 TCCCAGCATTCAACATAGAAATTACTC 59.717 37.037 0.00 0.00 0.00 2.59
7383 10176 2.170607 GAGTAATTGCCACCAGCCTCTA 59.829 50.000 0.00 0.00 42.71 2.43
8054 10848 6.037830 GCAATCTTTTATACTGCCTCCGTTTA 59.962 38.462 0.00 0.00 0.00 2.01
8059 10853 4.517075 GGAGCAATCTTTTATACTGCCTCC 59.483 45.833 0.00 0.00 33.41 4.30
8131 10925 5.227569 TCAGAATGCTAACAGACTTGGAA 57.772 39.130 0.00 0.00 34.76 3.53
8299 11096 5.615289 ACTTCAGCAAAGAGTATGTGACTT 58.385 37.500 5.93 0.00 39.06 3.01
8567 11426 6.071672 TGGATCTTGATCTTCCTCTATTAGCG 60.072 42.308 10.03 0.00 0.00 4.26
8612 11471 0.255318 TAGGAGACCTGGACCTCGAC 59.745 60.000 0.00 0.00 34.61 4.20
8965 11860 3.452755 TGCATCTTATACCACGTGGAG 57.547 47.619 40.21 26.05 38.94 3.86
8988 11883 5.298276 TCAATCGAAAAGTTGGCAACTAAGT 59.702 36.000 31.34 19.54 41.91 2.24
9016 12401 1.439353 ATGATTTGTAGCAGCCGCCG 61.439 55.000 0.00 0.00 39.83 6.46
9018 12403 0.308993 GGATGATTTGTAGCAGCCGC 59.691 55.000 0.00 0.00 36.39 6.53
9022 12407 3.785486 TCAGTCGGATGATTTGTAGCAG 58.215 45.455 0.00 0.00 0.00 4.24
9045 12430 0.606401 ACCCGACTGAGCATTTGGTG 60.606 55.000 0.00 0.00 0.00 4.17
9046 12431 0.321653 GACCCGACTGAGCATTTGGT 60.322 55.000 0.00 0.00 0.00 3.67
9049 12434 0.687354 ACTGACCCGACTGAGCATTT 59.313 50.000 0.00 0.00 0.00 2.32
9050 12435 1.478510 CTACTGACCCGACTGAGCATT 59.521 52.381 0.00 0.00 0.00 3.56
9051 12436 1.107114 CTACTGACCCGACTGAGCAT 58.893 55.000 0.00 0.00 0.00 3.79
9052 12437 1.595993 GCTACTGACCCGACTGAGCA 61.596 60.000 0.00 0.00 0.00 4.26
9054 12439 1.810532 GGCTACTGACCCGACTGAG 59.189 63.158 0.00 0.00 0.00 3.35
9096 12483 0.166814 GCAGCGTTGACCAATCTGAC 59.833 55.000 2.38 6.48 0.00 3.51
9158 12545 0.035458 ACTTGTGCTCGGGGAAGAAG 59.965 55.000 0.00 0.00 0.00 2.85
9197 12584 0.039437 ACCGTCGTTGCTACTGTCAG 60.039 55.000 0.00 0.00 0.00 3.51
9232 12619 4.005472 CGCTTCCATCGCCATCGC 62.005 66.667 0.00 0.00 35.26 4.58
9252 12639 4.101790 CAACCACCGCGCCACATC 62.102 66.667 0.00 0.00 0.00 3.06
9273 12660 3.375472 ATCGTCGCTGGCTGCATCA 62.375 57.895 16.76 0.00 43.06 3.07
9283 12670 0.459899 TGTGCTAATCCATCGTCGCT 59.540 50.000 0.00 0.00 0.00 4.93
9291 12678 1.745115 GCTGCCGTGTGCTAATCCA 60.745 57.895 0.00 0.00 42.00 3.41
9312 12699 2.332362 CTGCATCGCAACATCAGCCC 62.332 60.000 0.00 0.00 38.41 5.19
9321 12708 2.664518 TCGTGTGCTGCATCGCAA 60.665 55.556 19.64 6.46 42.32 4.85
9386 12773 3.276846 GCCGTGTGTTGAGCCGTT 61.277 61.111 0.00 0.00 0.00 4.44
9405 12792 2.965716 ATTACAGCTCCCGCCATGGC 62.966 60.000 27.67 27.67 36.60 4.40
9421 12808 2.817834 GTCGGTGGCGCTGCATTA 60.818 61.111 7.64 0.00 0.00 1.90
9433 12820 4.891727 GCATCCGCCATCGTCGGT 62.892 66.667 1.22 0.00 46.49 4.69
9471 12858 3.894947 GGCGTTGCAACACCCGTT 61.895 61.111 28.01 0.00 35.01 4.44
9485 12872 1.741401 ATGGTCATCGTGTGTGGCG 60.741 57.895 0.00 0.00 0.00 5.69
9488 12875 0.954938 TGCCATGGTCATCGTGTGTG 60.955 55.000 14.67 0.00 0.00 3.82
9497 12884 2.672908 CAGCTCCTGCCATGGTCA 59.327 61.111 14.67 10.98 40.80 4.02
9533 12941 4.451150 TGCGTCGCTCCACCCATC 62.451 66.667 19.50 0.00 0.00 3.51
9589 12997 3.010413 GCAAGCTTCCACCATGGCC 62.010 63.158 13.04 0.00 37.47 5.36
9590 12998 2.575461 GCAAGCTTCCACCATGGC 59.425 61.111 13.04 0.00 37.47 4.40
9649 13057 2.483106 GCTGCATCATCGTAGCATTCAT 59.517 45.455 0.00 0.00 43.34 2.57
9650 13058 1.869132 GCTGCATCATCGTAGCATTCA 59.131 47.619 0.00 0.00 43.34 2.57
9651 13059 1.196354 GGCTGCATCATCGTAGCATTC 59.804 52.381 0.50 0.00 45.38 2.67
9660 13068 3.945434 CGCCGTGGCTGCATCATC 61.945 66.667 9.55 0.00 39.32 2.92
9675 13083 1.308069 TGCCTGAATTGAAGCTCCGC 61.308 55.000 0.00 0.00 0.00 5.54
9701 13109 3.471806 GAGGAGGGGAAGACCGGC 61.472 72.222 0.00 0.00 41.60 6.13
9703 13111 0.905337 AACAGAGGAGGGGAAGACCG 60.905 60.000 0.00 0.00 41.60 4.79
9707 13115 0.326264 CCACAACAGAGGAGGGGAAG 59.674 60.000 0.00 0.00 0.00 3.46
9708 13116 0.401395 ACCACAACAGAGGAGGGGAA 60.401 55.000 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.