Multiple sequence alignment - TraesCS3D01G490300

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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 TraesCS3D01G490300 chr3D 100.000 1603 0 0 1 1603 584424365 584422763 0.000000e+00 2961.0
1 TraesCS3D01G490300 chr3D 100.000 1564 0 0 1899 3462 584422467 584420904 0.000000e+00 2889.0
2 TraesCS3D01G490300 chr3D 93.865 652 17 6 958 1603 584593660 584593026 0.000000e+00 961.0
3 TraesCS3D01G490300 chr3D 86.677 653 68 15 955 1603 584352707 584352070 0.000000e+00 706.0
4 TraesCS3D01G490300 chr3D 83.826 643 64 13 962 1601 584344411 584343806 3.000000e-160 575.0
5 TraesCS3D01G490300 chr3D 93.072 332 22 1 1899 2229 584592955 584592624 5.190000e-133 484.0
6 TraesCS3D01G490300 chr3D 92.537 335 22 2 1899 2230 584343733 584343399 8.690000e-131 477.0
7 TraesCS3D01G490300 chr3D 91.445 339 20 6 1899 2229 584351999 584351662 1.130000e-124 457.0
8 TraesCS3D01G490300 chr3D 91.579 190 3 1 2531 2707 584415504 584415315 2.060000e-62 250.0
9 TraesCS3D01G490300 chr3D 86.900 229 23 6 2318 2539 584592594 584592366 2.060000e-62 250.0
10 TraesCS3D01G490300 chr3D 76.556 482 72 26 1117 1592 584048843 584049289 3.480000e-55 226.0
11 TraesCS3D01G490300 chr3D 95.556 135 6 0 1025 1159 584349555 584349421 2.090000e-52 217.0
12 TraesCS3D01G490300 chr3D 84.722 216 25 6 2289 2501 584343406 584343196 3.500000e-50 209.0
13 TraesCS3D01G490300 chr3D 75.523 478 87 23 1117 1588 584129942 584130395 1.260000e-49 207.0
14 TraesCS3D01G490300 chr3D 75.152 495 93 20 1117 1601 584456801 584456327 4.530000e-49 206.0
15 TraesCS3D01G490300 chr3D 100.000 39 0 0 2493 2531 584343173 584343135 4.790000e-09 73.1
16 TraesCS3D01G490300 chr3D 97.368 38 1 0 2493 2530 584351428 584351391 8.020000e-07 65.8
17 TraesCS3D01G490300 chr7B 91.124 845 58 8 2619 3462 674977804 674978632 0.000000e+00 1129.0
18 TraesCS3D01G490300 chr7B 93.902 82 5 0 2532 2613 161606392 161606473 1.300000e-24 124.0
19 TraesCS3D01G490300 chr7B 93.902 82 5 0 2532 2613 161624699 161624780 1.300000e-24 124.0
20 TraesCS3D01G490300 chr4B 92.094 721 56 1 2743 3462 16543331 16544051 0.000000e+00 1014.0
21 TraesCS3D01G490300 chr1D 88.277 853 84 11 2619 3462 479824544 479823699 0.000000e+00 1007.0
22 TraesCS3D01G490300 chr1D 89.145 304 27 5 531 832 133536537 133536836 1.170000e-99 374.0
23 TraesCS3D01G490300 chr1D 85.714 77 4 4 469 540 33625392 33625318 1.330000e-09 75.0
24 TraesCS3D01G490300 chr1D 85.075 67 1 6 469 528 492364789 492364853 3.730000e-05 60.2
25 TraesCS3D01G490300 chr5B 87.544 851 96 9 2619 3462 602953234 602954081 0.000000e+00 976.0
26 TraesCS3D01G490300 chr5B 89.157 83 4 1 2531 2613 81603715 81603638 7.910000e-17 99.0
27 TraesCS3D01G490300 chr5B 84.746 59 7 1 469 527 212405843 212405787 1.340000e-04 58.4
28 TraesCS3D01G490300 chr5D 89.204 741 65 13 2619 3349 379812676 379813411 0.000000e+00 911.0
29 TraesCS3D01G490300 chr5D 93.902 82 5 0 2532 2613 548952004 548951923 1.300000e-24 124.0
30 TraesCS3D01G490300 chr5D 93.220 59 4 0 469 527 422944357 422944415 1.710000e-13 87.9
31 TraesCS3D01G490300 chr2D 89.296 710 68 7 2759 3462 504184591 504185298 0.000000e+00 883.0
32 TraesCS3D01G490300 chr2D 82.333 300 27 21 175 470 577545082 577544805 1.610000e-58 237.0
33 TraesCS3D01G490300 chr2D 94.382 89 5 0 2619 2707 190550844 190550756 1.680000e-28 137.0
34 TraesCS3D01G490300 chr2D 96.386 83 3 0 2531 2613 190550963 190550881 1.680000e-28 137.0
35 TraesCS3D01G490300 chr2D 95.122 82 4 0 2532 2613 190568217 190568136 2.800000e-26 130.0
36 TraesCS3D01G490300 chr2D 89.655 87 9 0 871 957 577544365 577544279 1.020000e-20 111.0
37 TraesCS3D01G490300 chr2D 84.000 100 10 5 863 957 494410374 494410276 1.320000e-14 91.6
38 TraesCS3D01G490300 chr1A 85.357 840 96 15 2630 3462 523342291 523341472 0.000000e+00 845.0
39 TraesCS3D01G490300 chr1A 84.551 835 102 16 2635 3462 524714833 524715647 0.000000e+00 802.0
40 TraesCS3D01G490300 chr1A 86.408 309 34 7 526 832 577423991 577424293 7.160000e-87 331.0
41 TraesCS3D01G490300 chr1A 85.149 101 9 5 863 957 577424293 577424393 7.910000e-17 99.0
42 TraesCS3D01G490300 chr3A 84.915 822 96 22 2655 3462 608691251 608690444 0.000000e+00 806.0
43 TraesCS3D01G490300 chr3A 89.062 64 2 2 469 527 478807284 478807221 1.330000e-09 75.0
44 TraesCS3D01G490300 chr3B 87.727 660 51 22 955 1601 781471200 781470558 0.000000e+00 743.0
45 TraesCS3D01G490300 chr3B 92.833 293 20 1 1899 2190 781470485 781470193 1.150000e-114 424.0
46 TraesCS3D01G490300 chr3B 81.073 317 34 16 170 470 11868662 11868968 2.690000e-56 230.0
47 TraesCS3D01G490300 chr3B 89.560 182 16 3 2352 2531 781470137 781469957 9.670000e-56 228.0
48 TraesCS3D01G490300 chr3B 80.696 316 37 15 170 470 115391272 115390966 1.250000e-54 224.0
49 TraesCS3D01G490300 chr3B 80.064 311 41 16 170 470 449038780 449038481 9.730000e-51 211.0
50 TraesCS3D01G490300 chr3B 75.052 477 76 26 1126 1601 781494721 781494287 7.630000e-42 182.0
51 TraesCS3D01G490300 chr3B 82.803 157 23 4 685 838 576819744 576819899 1.680000e-28 137.0
52 TraesCS3D01G490300 chr3B 85.106 94 8 5 869 957 115390653 115390561 1.320000e-14 91.6
53 TraesCS3D01G490300 chr3B 84.211 95 11 1 867 957 576819897 576819991 4.760000e-14 89.8
54 TraesCS3D01G490300 chr1B 87.247 494 30 13 1 470 605459020 605459504 1.830000e-147 532.0
55 TraesCS3D01G490300 chr1B 90.355 394 27 5 526 911 605459501 605459891 1.110000e-139 507.0
56 TraesCS3D01G490300 chr1B 82.748 313 40 10 525 832 608011969 608012272 2.050000e-67 267.0
57 TraesCS3D01G490300 chr4D 83.188 458 33 23 5 438 455317930 455317493 2.520000e-101 379.0
58 TraesCS3D01G490300 chr4D 87.365 277 33 2 682 957 455311845 455311570 2.010000e-82 316.0
59 TraesCS3D01G490300 chr4D 90.244 123 8 2 529 650 455311963 455311844 1.290000e-34 158.0
60 TraesCS3D01G490300 chr4D 88.889 63 4 1 469 528 424579613 424579675 1.330000e-09 75.0
61 TraesCS3D01G490300 chr4D 93.023 43 3 0 500 542 15085454 15085412 2.880000e-06 63.9
62 TraesCS3D01G490300 chr6D 87.171 304 32 6 531 832 414452474 414452176 4.280000e-89 339.0
63 TraesCS3D01G490300 chr6D 86.905 84 8 2 1140 1223 454996491 454996411 1.320000e-14 91.6
64 TraesCS3D01G490300 chr5A 86.084 309 36 7 526 832 551166363 551166666 3.330000e-85 326.0
65 TraesCS3D01G490300 chr5A 80.464 302 43 13 170 460 559990795 559991091 2.090000e-52 217.0
66 TraesCS3D01G490300 chr5A 83.333 114 12 5 863 969 551166666 551166779 7.910000e-17 99.0
67 TraesCS3D01G490300 chr2B 82.848 309 34 11 533 831 23902728 23903027 3.430000e-65 259.0
68 TraesCS3D01G490300 chr2B 81.388 317 33 16 170 470 23902416 23902722 5.780000e-58 235.0
69 TraesCS3D01G490300 chr2B 84.158 101 11 2 867 962 18501731 18501631 3.680000e-15 93.5
70 TraesCS3D01G490300 chr2B 83.178 107 11 3 863 962 18474137 18474031 1.320000e-14 91.6
71 TraesCS3D01G490300 chr2A 80.528 303 41 13 170 460 758605948 758605652 2.090000e-52 217.0
72 TraesCS3D01G490300 chr6A 82.072 251 29 9 221 470 89979318 89979553 2.110000e-47 200.0
73 TraesCS3D01G490300 chr6A 88.095 84 7 2 1140 1223 601264642 601264562 2.840000e-16 97.1
74 TraesCS3D01G490300 chr6A 86.207 87 9 2 1137 1223 602075660 602075743 1.320000e-14 91.6
75 TraesCS3D01G490300 chr6A 89.831 59 4 2 469 527 507552013 507551957 1.330000e-09 75.0
76 TraesCS3D01G490300 chrUn 75.100 498 85 27 1126 1601 45483159 45482679 2.730000e-46 196.0
77 TraesCS3D01G490300 chr7D 95.062 81 4 0 2533 2613 395220109 395220189 1.010000e-25 128.0
78 TraesCS3D01G490300 chr7D 92.222 90 6 1 2619 2707 395220226 395220315 3.630000e-25 126.0
79 TraesCS3D01G490300 chr7D 77.477 222 32 14 2639 2855 585298659 585298451 2.180000e-22 117.0
80 TraesCS3D01G490300 chr7A 90.476 84 8 0 2526 2609 643840136 643840219 1.020000e-20 111.0
81 TraesCS3D01G490300 chr7A 91.525 59 5 0 469 527 20649308 20649250 7.960000e-12 82.4
82 TraesCS3D01G490300 chr6B 87.356 87 8 1 1137 1223 692574485 692574568 2.840000e-16 97.1


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 TraesCS3D01G490300 chr3D 584420904 584424365 3461 True 2925.000 2961 100.00000 1 3462 2 chr3D.!!$R5 3461
1 TraesCS3D01G490300 chr3D 584592366 584593660 1294 True 565.000 961 91.27900 958 2539 3 chr3D.!!$R6 1581
2 TraesCS3D01G490300 chr3D 584349421 584352707 3286 True 361.450 706 92.76150 955 2530 4 chr3D.!!$R4 1575
3 TraesCS3D01G490300 chr3D 584343135 584344411 1276 True 333.525 575 90.27125 962 2531 4 chr3D.!!$R3 1569
4 TraesCS3D01G490300 chr7B 674977804 674978632 828 False 1129.000 1129 91.12400 2619 3462 1 chr7B.!!$F3 843
5 TraesCS3D01G490300 chr4B 16543331 16544051 720 False 1014.000 1014 92.09400 2743 3462 1 chr4B.!!$F1 719
6 TraesCS3D01G490300 chr1D 479823699 479824544 845 True 1007.000 1007 88.27700 2619 3462 1 chr1D.!!$R2 843
7 TraesCS3D01G490300 chr5B 602953234 602954081 847 False 976.000 976 87.54400 2619 3462 1 chr5B.!!$F1 843
8 TraesCS3D01G490300 chr5D 379812676 379813411 735 False 911.000 911 89.20400 2619 3349 1 chr5D.!!$F1 730
9 TraesCS3D01G490300 chr2D 504184591 504185298 707 False 883.000 883 89.29600 2759 3462 1 chr2D.!!$F1 703
10 TraesCS3D01G490300 chr1A 523341472 523342291 819 True 845.000 845 85.35700 2630 3462 1 chr1A.!!$R1 832
11 TraesCS3D01G490300 chr1A 524714833 524715647 814 False 802.000 802 84.55100 2635 3462 1 chr1A.!!$F1 827
12 TraesCS3D01G490300 chr3A 608690444 608691251 807 True 806.000 806 84.91500 2655 3462 1 chr3A.!!$R2 807
13 TraesCS3D01G490300 chr3B 781469957 781471200 1243 True 465.000 743 90.04000 955 2531 3 chr3B.!!$R4 1576
14 TraesCS3D01G490300 chr1B 605459020 605459891 871 False 519.500 532 88.80100 1 911 2 chr1B.!!$F2 910
15 TraesCS3D01G490300 chr2B 23902416 23903027 611 False 247.000 259 82.11800 170 831 2 chr2B.!!$F1 661

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
222 247 0.102481 ACCATCCTCGATCGTTTCCG 59.898 55.0 15.94 2.46 0.00 4.30 F
913 946 0.103572 GGCTGCATTTCATCCGCATT 59.896 50.0 0.50 0.00 34.63 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1310 1390 0.040157 ACACACACACGCATGCATTC 60.040 50.0 19.57 0.0 0.0 2.67 R
2616 2785 0.524862 TTCTAACTGTCGCGTCTCCC 59.475 55.0 5.77 0.0 0.0 4.30 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
75 82 4.415596 AGGCAAATCTGACCATTACCAAA 58.584 39.130 0.00 0.00 0.00 3.28
83 90 4.281435 TCTGACCATTACCAAACACGTAGA 59.719 41.667 0.00 0.00 0.00 2.59
87 94 4.202388 ACCATTACCAAACACGTAGACCTT 60.202 41.667 0.00 0.00 0.00 3.50
88 95 4.390909 CCATTACCAAACACGTAGACCTTC 59.609 45.833 0.00 0.00 0.00 3.46
89 96 4.942761 TTACCAAACACGTAGACCTTCT 57.057 40.909 0.00 0.00 0.00 2.85
90 97 6.392354 CATTACCAAACACGTAGACCTTCTA 58.608 40.000 0.00 0.00 0.00 2.10
91 98 4.248691 ACCAAACACGTAGACCTTCTAC 57.751 45.455 3.62 3.62 44.41 2.59
110 122 4.818546 TCTACGTACCTAGTGTTGGATAGC 59.181 45.833 0.00 0.00 0.00 2.97
137 149 2.612721 CCCAAAATTGTTAGCCCACAGC 60.613 50.000 0.00 0.00 44.25 4.40
156 175 2.435805 AGCCACATACAATCAGGTCGAT 59.564 45.455 0.00 0.00 35.12 3.59
164 183 1.759445 CAATCAGGTCGATCTGAGGGT 59.241 52.381 30.49 17.07 45.60 4.34
220 245 2.194271 GACACCATCCTCGATCGTTTC 58.806 52.381 15.94 0.00 0.00 2.78
222 247 0.102481 ACCATCCTCGATCGTTTCCG 59.898 55.000 15.94 2.46 0.00 4.30
253 278 1.338655 GGACCTAGGTCTGAATCGAGC 59.661 57.143 35.12 15.85 44.04 5.03
258 283 1.227380 GGTCTGAATCGAGCGGCAT 60.227 57.895 1.45 0.00 0.00 4.40
264 289 1.202521 TGAATCGAGCGGCATACATGT 60.203 47.619 2.69 2.69 0.00 3.21
275 300 1.333524 GCATACATGTCGCATCAGCAC 60.334 52.381 0.00 0.00 42.27 4.40
280 305 2.743538 GTCGCATCAGCACCAGCA 60.744 61.111 0.00 0.00 45.49 4.41
282 307 1.816679 TCGCATCAGCACCAGCATC 60.817 57.895 0.00 0.00 45.49 3.91
284 309 1.650314 CGCATCAGCACCAGCATCAA 61.650 55.000 0.00 0.00 45.49 2.57
285 310 0.179145 GCATCAGCACCAGCATCAAC 60.179 55.000 0.00 0.00 45.49 3.18
286 311 0.454600 CATCAGCACCAGCATCAACC 59.545 55.000 0.00 0.00 45.49 3.77
287 312 0.330604 ATCAGCACCAGCATCAACCT 59.669 50.000 0.00 0.00 45.49 3.50
288 313 0.607217 TCAGCACCAGCATCAACCTG 60.607 55.000 0.00 0.00 45.49 4.00
289 314 0.607217 CAGCACCAGCATCAACCTGA 60.607 55.000 0.00 0.00 45.49 3.86
290 315 0.111061 AGCACCAGCATCAACCTGAA 59.889 50.000 0.00 0.00 45.49 3.02
291 316 0.242017 GCACCAGCATCAACCTGAAC 59.758 55.000 0.00 0.00 41.58 3.18
292 317 0.883833 CACCAGCATCAACCTGAACC 59.116 55.000 0.00 0.00 32.03 3.62
296 321 0.321653 AGCATCAACCTGAACCGACC 60.322 55.000 0.00 0.00 0.00 4.79
313 338 4.395519 CAAGGTGTGGATTCCGCA 57.604 55.556 14.95 14.95 42.15 5.69
322 347 1.885850 GGATTCCGCACGCCGTTAT 60.886 57.895 0.00 0.00 34.38 1.89
368 393 5.437060 TCTACTAATTGGCAAACATCTCCC 58.563 41.667 3.01 0.00 0.00 4.30
374 399 1.078143 GCAAACATCTCCCGCCTCT 60.078 57.895 0.00 0.00 0.00 3.69
375 400 1.092345 GCAAACATCTCCCGCCTCTC 61.092 60.000 0.00 0.00 0.00 3.20
376 401 0.250234 CAAACATCTCCCGCCTCTCA 59.750 55.000 0.00 0.00 0.00 3.27
377 402 0.539051 AAACATCTCCCGCCTCTCAG 59.461 55.000 0.00 0.00 0.00 3.35
378 403 0.324738 AACATCTCCCGCCTCTCAGA 60.325 55.000 0.00 0.00 0.00 3.27
384 409 1.379176 CCCGCCTCTCAGACTCTCA 60.379 63.158 0.00 0.00 0.00 3.27
390 415 1.202114 CCTCTCAGACTCTCACAGCAC 59.798 57.143 0.00 0.00 0.00 4.40
435 460 4.165950 TCAACCAAGGTATGCCACATAGAT 59.834 41.667 1.54 0.00 37.19 1.98
472 497 8.142994 ACATTTAGATTATGCAAACTACTCCG 57.857 34.615 0.00 0.00 0.00 4.63
473 498 7.769044 ACATTTAGATTATGCAAACTACTCCGT 59.231 33.333 0.00 0.00 0.00 4.69
474 499 9.256477 CATTTAGATTATGCAAACTACTCCGTA 57.744 33.333 0.00 0.00 0.00 4.02
475 500 9.826574 ATTTAGATTATGCAAACTACTCCGTAA 57.173 29.630 0.00 0.00 0.00 3.18
476 501 9.656040 TTTAGATTATGCAAACTACTCCGTAAA 57.344 29.630 0.00 0.00 0.00 2.01
477 502 7.535489 AGATTATGCAAACTACTCCGTAAAC 57.465 36.000 0.00 0.00 0.00 2.01
478 503 7.328737 AGATTATGCAAACTACTCCGTAAACT 58.671 34.615 0.00 0.00 0.00 2.66
479 504 6.956299 TTATGCAAACTACTCCGTAAACTC 57.044 37.500 0.00 0.00 0.00 3.01
480 505 4.325028 TGCAAACTACTCCGTAAACTCA 57.675 40.909 0.00 0.00 0.00 3.41
481 506 4.890088 TGCAAACTACTCCGTAAACTCAT 58.110 39.130 0.00 0.00 0.00 2.90
482 507 6.028146 TGCAAACTACTCCGTAAACTCATA 57.972 37.500 0.00 0.00 0.00 2.15
483 508 6.636705 TGCAAACTACTCCGTAAACTCATAT 58.363 36.000 0.00 0.00 0.00 1.78
484 509 7.774134 TGCAAACTACTCCGTAAACTCATATA 58.226 34.615 0.00 0.00 0.00 0.86
485 510 8.252417 TGCAAACTACTCCGTAAACTCATATAA 58.748 33.333 0.00 0.00 0.00 0.98
486 511 8.753175 GCAAACTACTCCGTAAACTCATATAAG 58.247 37.037 0.00 0.00 0.00 1.73
489 514 7.873910 ACTACTCCGTAAACTCATATAAGAGC 58.126 38.462 4.89 0.00 39.26 4.09
490 515 5.759963 ACTCCGTAAACTCATATAAGAGCG 58.240 41.667 4.89 1.13 39.26 5.03
491 516 5.298777 ACTCCGTAAACTCATATAAGAGCGT 59.701 40.000 4.89 0.00 39.26 5.07
492 517 6.140303 TCCGTAAACTCATATAAGAGCGTT 57.860 37.500 4.89 2.97 39.26 4.84
493 518 6.567050 TCCGTAAACTCATATAAGAGCGTTT 58.433 36.000 4.89 3.37 39.26 3.60
494 519 7.706159 TCCGTAAACTCATATAAGAGCGTTTA 58.294 34.615 4.89 2.52 39.26 2.01
495 520 7.859377 TCCGTAAACTCATATAAGAGCGTTTAG 59.141 37.037 4.89 1.04 39.26 1.85
496 521 7.859377 CCGTAAACTCATATAAGAGCGTTTAGA 59.141 37.037 4.89 0.00 39.26 2.10
497 522 9.395707 CGTAAACTCATATAAGAGCGTTTAGAT 57.604 33.333 4.89 0.00 39.26 1.98
523 548 9.866655 TTACTCTTATATTAGTTTACGGAGGGA 57.133 33.333 0.00 0.00 0.00 4.20
524 549 8.406730 ACTCTTATATTAGTTTACGGAGGGAG 57.593 38.462 0.00 0.00 0.00 4.30
525 550 8.003629 ACTCTTATATTAGTTTACGGAGGGAGT 58.996 37.037 0.00 0.00 0.00 3.85
526 551 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
607 632 9.635520 AGAATTGCATAAAACATGAAGAAGAAG 57.364 29.630 0.00 0.00 0.00 2.85
617 642 5.546526 ACATGAAGAAGAAGAAGAGACCAC 58.453 41.667 0.00 0.00 0.00 4.16
620 645 4.408921 TGAAGAAGAAGAAGAGACCACCAA 59.591 41.667 0.00 0.00 0.00 3.67
676 702 5.181009 CCACTCTACTGATGAGAATGCAAA 58.819 41.667 0.00 0.00 35.66 3.68
688 715 6.976636 TGAGAATGCAAACGACATGTATAA 57.023 33.333 0.00 0.00 0.00 0.98
694 721 9.674208 GAATGCAAACGACATGTATAAATTTTG 57.326 29.630 0.00 3.94 0.00 2.44
699 726 7.696992 AACGACATGTATAAATTTTGGGAGT 57.303 32.000 0.00 0.00 0.00 3.85
702 729 7.556275 ACGACATGTATAAATTTTGGGAGTGAT 59.444 33.333 0.00 0.00 0.00 3.06
742 769 3.096092 GTTTGATGGTTTGATGGGCCTA 58.904 45.455 4.53 0.00 0.00 3.93
748 775 1.136891 GGTTTGATGGGCCTATTGTGC 59.863 52.381 1.86 0.00 0.00 4.57
752 779 1.210722 TGATGGGCCTATTGTGCGTAA 59.789 47.619 1.86 0.00 0.00 3.18
848 875 9.656040 TGTTTGATATTGCAATGAAATTAGCTT 57.344 25.926 22.27 0.00 32.46 3.74
854 881 4.022603 TGCAATGAAATTAGCTTAGGCCA 58.977 39.130 5.01 0.00 34.40 5.36
869 896 5.392595 GCTTAGGCCACATTTCGTCAAAATA 60.393 40.000 5.01 0.00 35.77 1.40
907 940 1.551883 ACTTTGGGGCTGCATTTCATC 59.448 47.619 0.50 0.00 0.00 2.92
911 944 2.417257 GGGCTGCATTTCATCCGCA 61.417 57.895 0.50 0.00 31.77 5.69
912 945 1.737816 GGCTGCATTTCATCCGCAT 59.262 52.632 0.50 0.00 34.63 4.73
913 946 0.103572 GGCTGCATTTCATCCGCATT 59.896 50.000 0.50 0.00 34.63 3.56
914 947 1.205657 GCTGCATTTCATCCGCATTG 58.794 50.000 0.00 0.00 34.63 2.82
915 948 1.470285 GCTGCATTTCATCCGCATTGT 60.470 47.619 0.00 0.00 34.63 2.71
916 949 2.456989 CTGCATTTCATCCGCATTGTC 58.543 47.619 0.00 0.00 34.63 3.18
917 950 1.134753 TGCATTTCATCCGCATTGTCC 59.865 47.619 0.00 0.00 0.00 4.02
918 951 1.406539 GCATTTCATCCGCATTGTCCT 59.593 47.619 0.00 0.00 0.00 3.85
919 952 2.797087 GCATTTCATCCGCATTGTCCTG 60.797 50.000 0.00 0.00 0.00 3.86
920 953 2.198827 TTTCATCCGCATTGTCCTGT 57.801 45.000 0.00 0.00 0.00 4.00
921 954 2.198827 TTCATCCGCATTGTCCTGTT 57.801 45.000 0.00 0.00 0.00 3.16
922 955 1.737838 TCATCCGCATTGTCCTGTTC 58.262 50.000 0.00 0.00 0.00 3.18
923 956 0.374758 CATCCGCATTGTCCTGTTCG 59.625 55.000 0.00 0.00 0.00 3.95
924 957 1.369091 ATCCGCATTGTCCTGTTCGC 61.369 55.000 0.00 0.00 0.00 4.70
925 958 2.480555 CGCATTGTCCTGTTCGCC 59.519 61.111 0.00 0.00 0.00 5.54
926 959 2.877691 GCATTGTCCTGTTCGCCC 59.122 61.111 0.00 0.00 0.00 6.13
927 960 2.700773 GCATTGTCCTGTTCGCCCC 61.701 63.158 0.00 0.00 0.00 5.80
928 961 2.046285 CATTGTCCTGTTCGCCCCC 61.046 63.158 0.00 0.00 0.00 5.40
945 978 2.949447 CCCCCTATGTTCAAATCCTGG 58.051 52.381 0.00 0.00 0.00 4.45
946 979 2.310538 CCCCTATGTTCAAATCCTGGC 58.689 52.381 0.00 0.00 0.00 4.85
947 980 2.091665 CCCCTATGTTCAAATCCTGGCT 60.092 50.000 0.00 0.00 0.00 4.75
948 981 3.217626 CCCTATGTTCAAATCCTGGCTC 58.782 50.000 0.00 0.00 0.00 4.70
949 982 3.217626 CCTATGTTCAAATCCTGGCTCC 58.782 50.000 0.00 0.00 0.00 4.70
950 983 1.755179 ATGTTCAAATCCTGGCTCCG 58.245 50.000 0.00 0.00 0.00 4.63
951 984 0.960364 TGTTCAAATCCTGGCTCCGC 60.960 55.000 0.00 0.00 0.00 5.54
1022 1055 1.808945 CAAGCCGAAAGTTGCTCTCAT 59.191 47.619 0.00 0.00 36.66 2.90
1023 1056 1.731720 AGCCGAAAGTTGCTCTCATC 58.268 50.000 0.00 0.00 30.33 2.92
1024 1057 1.277557 AGCCGAAAGTTGCTCTCATCT 59.722 47.619 0.00 0.00 30.33 2.90
1025 1058 2.497675 AGCCGAAAGTTGCTCTCATCTA 59.502 45.455 0.00 0.00 30.33 1.98
1026 1059 3.055819 AGCCGAAAGTTGCTCTCATCTAA 60.056 43.478 0.00 0.00 30.33 2.10
1027 1060 3.873952 GCCGAAAGTTGCTCTCATCTAAT 59.126 43.478 0.00 0.00 0.00 1.73
1028 1061 4.333926 GCCGAAAGTTGCTCTCATCTAATT 59.666 41.667 0.00 0.00 0.00 1.40
1029 1062 5.523916 GCCGAAAGTTGCTCTCATCTAATTA 59.476 40.000 0.00 0.00 0.00 1.40
1030 1063 6.292596 GCCGAAAGTTGCTCTCATCTAATTAG 60.293 42.308 6.11 6.11 0.00 1.73
1031 1064 6.292596 CCGAAAGTTGCTCTCATCTAATTAGC 60.293 42.308 7.67 0.00 0.00 3.09
1032 1065 6.478344 CGAAAGTTGCTCTCATCTAATTAGCT 59.522 38.462 7.67 0.00 34.28 3.32
1033 1066 7.649705 CGAAAGTTGCTCTCATCTAATTAGCTA 59.350 37.037 7.67 0.00 34.28 3.32
1034 1067 8.885494 AAAGTTGCTCTCATCTAATTAGCTAG 57.115 34.615 7.67 5.16 34.28 3.42
1035 1068 6.454795 AGTTGCTCTCATCTAATTAGCTAGC 58.545 40.000 6.62 6.62 34.28 3.42
1036 1069 6.267471 AGTTGCTCTCATCTAATTAGCTAGCT 59.733 38.462 23.12 23.12 34.28 3.32
1037 1070 6.266168 TGCTCTCATCTAATTAGCTAGCTC 57.734 41.667 23.26 1.62 34.28 4.09
1038 1071 5.772169 TGCTCTCATCTAATTAGCTAGCTCA 59.228 40.000 23.26 11.58 34.28 4.26
1039 1072 6.092748 GCTCTCATCTAATTAGCTAGCTCAC 58.907 44.000 23.26 0.00 0.00 3.51
1040 1073 6.247727 TCTCATCTAATTAGCTAGCTCACG 57.752 41.667 23.26 6.79 0.00 4.35
1041 1074 5.998363 TCTCATCTAATTAGCTAGCTCACGA 59.002 40.000 23.26 12.06 0.00 4.35
1042 1075 6.148645 TCTCATCTAATTAGCTAGCTCACGAG 59.851 42.308 23.26 14.64 0.00 4.18
1090 1147 0.322008 GAGCCAAGTCCAAGGACCAG 60.322 60.000 15.36 8.36 45.59 4.00
1101 1166 0.984995 AAGGACCAGGCAGACTAACC 59.015 55.000 0.00 0.00 0.00 2.85
1237 1313 2.607282 CGCCGACTACATATCCCTTCAC 60.607 54.545 0.00 0.00 0.00 3.18
1307 1387 2.202756 GATCGACCACTGACCGGC 60.203 66.667 0.00 0.00 0.00 6.13
1308 1388 3.718210 GATCGACCACTGACCGGCC 62.718 68.421 0.00 0.00 0.00 6.13
1458 1555 3.757248 AATCCGATGGGCTCCGTGC 62.757 63.158 0.00 0.00 41.94 5.34
1506 1603 2.203337 GGCTGAACACACTGGGCA 60.203 61.111 0.00 0.00 0.00 5.36
1569 1666 3.991051 CACCTCACTCGCACCCGT 61.991 66.667 0.00 0.00 35.54 5.28
1571 1668 3.991051 CCTCACTCGCACCCGTGT 61.991 66.667 0.00 0.00 41.33 4.49
2159 2266 5.050363 CAGAGCGTAACACACACATTAAAGT 60.050 40.000 0.00 0.00 0.00 2.66
2197 2309 1.319374 CGTACGTGATTTAGCGTGTGG 59.681 52.381 7.22 0.00 41.68 4.17
2209 2321 1.154488 CGTGTGGTTCATTTCGGCG 60.154 57.895 0.00 0.00 0.00 6.46
2217 2329 2.096819 GGTTCATTTCGGCGCTTTGATA 59.903 45.455 7.64 0.00 0.00 2.15
2219 2331 2.627945 TCATTTCGGCGCTTTGATAGT 58.372 42.857 7.64 0.00 0.00 2.12
2230 2342 5.220719 GGCGCTTTGATAGTACGGTAAAAAT 60.221 40.000 7.64 0.00 0.00 1.82
2231 2343 6.018832 GGCGCTTTGATAGTACGGTAAAAATA 60.019 38.462 7.64 0.00 0.00 1.40
2232 2344 7.061634 GCGCTTTGATAGTACGGTAAAAATAG 58.938 38.462 0.00 0.00 0.00 1.73
2233 2345 7.061634 CGCTTTGATAGTACGGTAAAAATAGC 58.938 38.462 0.00 0.00 0.00 2.97
2234 2346 7.042925 CGCTTTGATAGTACGGTAAAAATAGCT 60.043 37.037 0.00 0.00 0.00 3.32
2235 2347 8.610035 GCTTTGATAGTACGGTAAAAATAGCTT 58.390 33.333 0.00 0.00 0.00 3.74
2237 2349 9.880157 TTTGATAGTACGGTAAAAATAGCTTCT 57.120 29.630 0.00 0.00 0.00 2.85
2238 2350 9.880157 TTGATAGTACGGTAAAAATAGCTTCTT 57.120 29.630 0.00 0.00 0.00 2.52
2239 2351 9.525409 TGATAGTACGGTAAAAATAGCTTCTTC 57.475 33.333 0.00 0.00 0.00 2.87
2240 2352 9.747293 GATAGTACGGTAAAAATAGCTTCTTCT 57.253 33.333 0.00 0.00 0.00 2.85
2242 2354 8.843885 AGTACGGTAAAAATAGCTTCTTCTTT 57.156 30.769 0.00 0.00 0.00 2.52
2243 2355 9.281371 AGTACGGTAAAAATAGCTTCTTCTTTT 57.719 29.630 0.00 0.00 0.00 2.27
2244 2356 9.888878 GTACGGTAAAAATAGCTTCTTCTTTTT 57.111 29.630 0.00 0.48 35.58 1.94
2348 2475 4.017126 TCTTCTCATCTCGTCTGCCTTTA 58.983 43.478 0.00 0.00 0.00 1.85
2349 2476 4.097135 TCTTCTCATCTCGTCTGCCTTTAG 59.903 45.833 0.00 0.00 0.00 1.85
2377 2511 5.910637 AAGCGTCTTGTTATTTGTTCGTA 57.089 34.783 0.00 0.00 0.00 3.43
2429 2564 1.645751 CGTACGACGTCCTAAGTTTGC 59.354 52.381 10.44 0.00 36.74 3.68
2434 2569 2.915463 CGACGTCCTAAGTTTGCTGTAG 59.085 50.000 10.58 0.00 0.00 2.74
2450 2588 2.008329 TGTAGTTTTCCAACGCGTGTT 58.992 42.857 14.98 8.91 38.03 3.32
2469 2607 8.414173 CGCGTGTTAATGTAATAAATAAATGCC 58.586 33.333 0.00 0.00 0.00 4.40
2470 2608 8.696175 GCGTGTTAATGTAATAAATAAATGCCC 58.304 33.333 0.00 0.00 0.00 5.36
2477 2615 6.146760 TGTAATAAATAAATGCCCCCATGGT 58.853 36.000 11.73 0.00 36.04 3.55
2480 2618 3.929955 AATAAATGCCCCCATGGTTTG 57.070 42.857 11.73 0.00 36.04 2.93
2485 2623 2.649129 GCCCCCATGGTTTGTCAGC 61.649 63.158 11.73 0.00 36.04 4.26
2541 2710 5.160641 ACAAAGTTGTGTGTGATGTGAAAC 58.839 37.500 0.00 0.00 40.49 2.78
2542 2711 5.278709 ACAAAGTTGTGTGTGATGTGAAACA 60.279 36.000 0.00 0.00 46.72 2.83
2560 2729 7.428826 GTGAAACAAGGAAGACAAATGAATCT 58.571 34.615 0.00 0.00 36.32 2.40
2561 2730 7.592903 GTGAAACAAGGAAGACAAATGAATCTC 59.407 37.037 0.00 0.00 36.32 2.75
2562 2731 7.503566 TGAAACAAGGAAGACAAATGAATCTCT 59.496 33.333 0.00 0.00 0.00 3.10
2563 2732 8.924511 AAACAAGGAAGACAAATGAATCTCTA 57.075 30.769 0.00 0.00 0.00 2.43
2565 2734 8.729805 ACAAGGAAGACAAATGAATCTCTATC 57.270 34.615 0.00 0.00 0.00 2.08
2567 2736 9.044150 CAAGGAAGACAAATGAATCTCTATCTC 57.956 37.037 0.00 0.00 0.00 2.75
2568 2737 8.551682 AGGAAGACAAATGAATCTCTATCTCT 57.448 34.615 0.00 0.00 0.00 3.10
2569 2738 8.991275 AGGAAGACAAATGAATCTCTATCTCTT 58.009 33.333 0.00 0.00 0.00 2.85
2575 2744 9.258826 ACAAATGAATCTCTATCTCTTTCATCG 57.741 33.333 0.00 0.00 36.33 3.84
2576 2745 9.473640 CAAATGAATCTCTATCTCTTTCATCGA 57.526 33.333 0.00 0.00 36.33 3.59
2580 2749 9.022884 TGAATCTCTATCTCTTTCATCGATGAT 57.977 33.333 27.75 14.70 36.56 2.45
2582 2751 8.812513 ATCTCTATCTCTTTCATCGATGATCT 57.187 34.615 27.75 11.74 36.56 2.75
2583 2752 8.267620 TCTCTATCTCTTTCATCGATGATCTC 57.732 38.462 27.75 0.00 36.56 2.75
2584 2753 8.102676 TCTCTATCTCTTTCATCGATGATCTCT 58.897 37.037 27.75 13.30 36.56 3.10
2585 2754 8.042944 TCTATCTCTTTCATCGATGATCTCTG 57.957 38.462 27.75 16.52 36.56 3.35
2586 2755 6.653526 ATCTCTTTCATCGATGATCTCTGT 57.346 37.500 27.75 11.19 36.56 3.41
2588 2757 6.964908 TCTCTTTCATCGATGATCTCTGTAC 58.035 40.000 27.75 0.00 36.56 2.90
2590 2759 7.230309 TCTCTTTCATCGATGATCTCTGTACAT 59.770 37.037 27.75 0.00 36.56 2.29
2591 2760 7.720442 TCTTTCATCGATGATCTCTGTACATT 58.280 34.615 27.75 0.00 36.56 2.71
2592 2761 8.850156 TCTTTCATCGATGATCTCTGTACATTA 58.150 33.333 27.75 6.22 36.56 1.90
2593 2762 9.636879 CTTTCATCGATGATCTCTGTACATTAT 57.363 33.333 27.75 0.00 36.56 1.28
2606 2775 9.480861 TCTCTGTACATTATATATCCCTGAAGG 57.519 37.037 0.00 0.00 0.00 3.46
2616 2785 2.809601 CCTGAAGGGACGCGTTCG 60.810 66.667 15.53 0.00 42.43 3.95
2617 2786 2.809601 CTGAAGGGACGCGTTCGG 60.810 66.667 15.53 8.32 40.69 4.30
2664 2833 0.601841 CGCCTGTCGGTTTACAAGGT 60.602 55.000 0.00 0.00 33.78 3.50
2737 2911 4.543590 ATCTCCGCCTTGATTATGTAGG 57.456 45.455 0.00 0.00 0.00 3.18
2745 2920 5.702670 CGCCTTGATTATGTAGGTCATCATT 59.297 40.000 0.00 0.00 37.91 2.57
2770 2946 4.163078 TGAAAAATGCTCCTCCAAAAACCA 59.837 37.500 0.00 0.00 0.00 3.67
2954 3959 5.998454 AAAAGAGTGCAATATCAGGATCG 57.002 39.130 0.00 0.00 0.00 3.69
3156 4837 7.910683 GCAATACACTTTCTAATTGCTCCTTAC 59.089 37.037 10.71 0.00 46.71 2.34
3170 4851 3.679389 CTCCTTACAACCTGTCTGCATT 58.321 45.455 0.00 0.00 0.00 3.56
3241 4924 3.843422 ACCAATCAATCCCACTTGAACA 58.157 40.909 0.00 0.00 38.55 3.18
3309 4993 9.421806 TGATGCTTCATTCAAATTAACGATTTT 57.578 25.926 0.00 0.00 35.79 1.82
3330 5025 8.757982 ATTTTAGAATGATTAGTGGATGCAGT 57.242 30.769 0.00 0.00 0.00 4.40
3357 5052 7.976734 CACTAAAATATGTCTTCTCGACTTCCT 59.023 37.037 0.00 0.00 43.25 3.36
3411 5106 7.963532 ACAAAAACTAGTCTGTGATCTAGGAA 58.036 34.615 0.00 0.00 38.24 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 90 3.760684 CCAACACTAGGTACGTAGAAGGT 59.239 47.826 25.31 17.24 0.00 3.50
87 94 4.818546 GCTATCCAACACTAGGTACGTAGA 59.181 45.833 25.31 6.10 0.00 2.59
88 95 4.023365 GGCTATCCAACACTAGGTACGTAG 60.023 50.000 18.68 18.68 0.00 3.51
89 96 3.885297 GGCTATCCAACACTAGGTACGTA 59.115 47.826 0.00 0.00 0.00 3.57
90 97 2.692041 GGCTATCCAACACTAGGTACGT 59.308 50.000 0.00 0.00 0.00 3.57
91 98 2.035576 GGGCTATCCAACACTAGGTACG 59.964 54.545 0.00 0.00 35.00 3.67
92 99 3.036091 TGGGCTATCCAACACTAGGTAC 58.964 50.000 0.00 0.00 43.84 3.34
93 100 3.408157 TGGGCTATCCAACACTAGGTA 57.592 47.619 0.00 0.00 43.84 3.08
94 101 2.263895 TGGGCTATCCAACACTAGGT 57.736 50.000 0.00 0.00 43.84 3.08
110 122 2.615240 GGCTAACAATTTTGGGCTTGGG 60.615 50.000 0.00 0.00 0.00 4.12
115 127 1.346068 TGTGGGCTAACAATTTTGGGC 59.654 47.619 0.00 3.16 0.00 5.36
137 149 4.053983 CAGATCGACCTGATTGTATGTGG 58.946 47.826 0.00 0.00 37.47 4.17
156 175 5.183331 GCGATGTATTGTCTATACCCTCAGA 59.817 44.000 2.56 0.00 38.69 3.27
164 183 6.052360 TGGCAAAAGCGATGTATTGTCTATA 58.948 36.000 0.00 0.00 0.00 1.31
245 270 1.457303 GACATGTATGCCGCTCGATTC 59.543 52.381 0.00 0.00 0.00 2.52
253 278 0.509929 CTGATGCGACATGTATGCCG 59.490 55.000 17.23 9.70 36.72 5.69
258 283 0.248843 TGGTGCTGATGCGACATGTA 59.751 50.000 0.00 0.00 43.34 2.29
264 289 1.816679 GATGCTGGTGCTGATGCGA 60.817 57.895 0.00 0.00 43.34 5.10
275 300 0.321564 TCGGTTCAGGTTGATGCTGG 60.322 55.000 0.00 0.00 0.00 4.85
280 305 1.271379 CCTTGGTCGGTTCAGGTTGAT 60.271 52.381 0.00 0.00 0.00 2.57
282 307 0.179029 ACCTTGGTCGGTTCAGGTTG 60.179 55.000 0.00 0.00 31.94 3.77
284 309 1.342672 ACACCTTGGTCGGTTCAGGT 61.343 55.000 0.00 0.00 34.29 4.00
285 310 0.884704 CACACCTTGGTCGGTTCAGG 60.885 60.000 0.00 0.00 34.29 3.86
286 311 0.884704 CCACACCTTGGTCGGTTCAG 60.885 60.000 0.00 0.00 41.10 3.02
287 312 1.147376 CCACACCTTGGTCGGTTCA 59.853 57.895 0.00 0.00 41.10 3.18
288 313 0.036306 ATCCACACCTTGGTCGGTTC 59.964 55.000 5.10 0.00 46.97 3.62
289 314 0.476771 AATCCACACCTTGGTCGGTT 59.523 50.000 5.10 0.00 46.97 4.44
290 315 0.036306 GAATCCACACCTTGGTCGGT 59.964 55.000 5.10 0.00 46.97 4.69
291 316 0.676782 GGAATCCACACCTTGGTCGG 60.677 60.000 0.00 0.00 46.97 4.79
292 317 1.019278 CGGAATCCACACCTTGGTCG 61.019 60.000 0.00 0.00 46.97 4.79
296 321 1.875963 GTGCGGAATCCACACCTTG 59.124 57.895 9.18 0.00 33.50 3.61
313 338 1.133790 GTGGTAGACTCATAACGGCGT 59.866 52.381 6.77 6.77 0.00 5.68
322 347 2.493675 CAGCTAGCTTGTGGTAGACTCA 59.506 50.000 16.46 0.00 44.52 3.41
368 393 0.451383 CTGTGAGAGTCTGAGAGGCG 59.549 60.000 0.00 0.00 0.00 5.52
374 399 1.959848 CCGTGCTGTGAGAGTCTGA 59.040 57.895 0.00 0.00 0.00 3.27
375 400 1.735920 GCCGTGCTGTGAGAGTCTG 60.736 63.158 0.00 0.00 0.00 3.51
376 401 1.467678 AAGCCGTGCTGTGAGAGTCT 61.468 55.000 0.00 0.00 39.62 3.24
377 402 1.005630 AAGCCGTGCTGTGAGAGTC 60.006 57.895 0.00 0.00 39.62 3.36
378 403 1.301244 CAAGCCGTGCTGTGAGAGT 60.301 57.895 0.00 0.00 39.62 3.24
401 426 4.559862 ACCTTGGTTGAGATTAGACAGG 57.440 45.455 0.00 0.00 0.00 4.00
404 429 4.816925 GGCATACCTTGGTTGAGATTAGAC 59.183 45.833 0.00 0.00 0.00 2.59
449 474 9.826574 TTACGGAGTAGTTTGCATAATCTAAAT 57.173 29.630 0.00 0.00 46.93 1.40
452 477 8.472413 AGTTTACGGAGTAGTTTGCATAATCTA 58.528 33.333 0.00 0.00 46.93 1.98
460 485 8.638685 TTATATGAGTTTACGGAGTAGTTTGC 57.361 34.615 0.00 0.00 46.93 3.68
469 494 5.762825 ACGCTCTTATATGAGTTTACGGA 57.237 39.130 15.05 0.00 36.51 4.69
470 495 6.823678 AAACGCTCTTATATGAGTTTACGG 57.176 37.500 15.05 3.73 35.19 4.02
471 496 8.778141 TCTAAACGCTCTTATATGAGTTTACG 57.222 34.615 15.05 12.31 37.38 3.18
497 522 9.866655 TCCCTCCGTAAACTAATATAAGAGTAA 57.133 33.333 0.00 0.00 0.00 2.24
498 523 9.512588 CTCCCTCCGTAAACTAATATAAGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
499 524 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
500 525 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
505 530 9.819754 ACTAATACTCCCTCCGTAAACTAATAT 57.180 33.333 0.00 0.00 0.00 1.28
506 531 9.646522 AACTAATACTCCCTCCGTAAACTAATA 57.353 33.333 0.00 0.00 0.00 0.98
507 532 8.544687 AACTAATACTCCCTCCGTAAACTAAT 57.455 34.615 0.00 0.00 0.00 1.73
508 533 7.961326 AACTAATACTCCCTCCGTAAACTAA 57.039 36.000 0.00 0.00 0.00 2.24
509 534 8.494433 TCTAACTAATACTCCCTCCGTAAACTA 58.506 37.037 0.00 0.00 0.00 2.24
510 535 7.349598 TCTAACTAATACTCCCTCCGTAAACT 58.650 38.462 0.00 0.00 0.00 2.66
511 536 7.573968 TCTAACTAATACTCCCTCCGTAAAC 57.426 40.000 0.00 0.00 0.00 2.01
512 537 8.773033 ATTCTAACTAATACTCCCTCCGTAAA 57.227 34.615 0.00 0.00 0.00 2.01
513 538 8.000709 TGATTCTAACTAATACTCCCTCCGTAA 58.999 37.037 0.00 0.00 0.00 3.18
514 539 7.520798 TGATTCTAACTAATACTCCCTCCGTA 58.479 38.462 0.00 0.00 0.00 4.02
515 540 6.371278 TGATTCTAACTAATACTCCCTCCGT 58.629 40.000 0.00 0.00 0.00 4.69
516 541 6.896021 TGATTCTAACTAATACTCCCTCCG 57.104 41.667 0.00 0.00 0.00 4.63
576 601 9.453572 TCTTCATGTTTTATGCAATTCTAGACT 57.546 29.630 0.00 0.00 0.00 3.24
594 619 5.512232 GGTGGTCTCTTCTTCTTCTTCATGT 60.512 44.000 0.00 0.00 0.00 3.21
605 630 7.074653 TGTTAGTTATTGGTGGTCTCTTCTT 57.925 36.000 0.00 0.00 0.00 2.52
606 631 6.681729 TGTTAGTTATTGGTGGTCTCTTCT 57.318 37.500 0.00 0.00 0.00 2.85
607 632 7.923414 ATTGTTAGTTATTGGTGGTCTCTTC 57.077 36.000 0.00 0.00 0.00 2.87
617 642 7.818930 ACAATGGCTTCAATTGTTAGTTATTGG 59.181 33.333 23.73 15.78 35.23 3.16
620 645 9.777297 AAAACAATGGCTTCAATTGTTAGTTAT 57.223 25.926 13.24 1.73 44.69 1.89
676 702 6.882140 TCACTCCCAAAATTTATACATGTCGT 59.118 34.615 0.00 0.00 0.00 4.34
699 726 7.542534 AACGTCAAGTTTTGTAGTGTTATCA 57.457 32.000 0.00 0.00 40.88 2.15
714 741 4.261572 CCATCAAACCATCAAACGTCAAGT 60.262 41.667 0.00 0.00 0.00 3.16
715 742 4.229096 CCATCAAACCATCAAACGTCAAG 58.771 43.478 0.00 0.00 0.00 3.02
742 769 7.386851 AGCCTAGATGTATATTTACGCACAAT 58.613 34.615 0.00 0.00 0.00 2.71
775 802 7.823310 TGCAATTACATTGAAATGGCTACAATT 59.177 29.630 7.87 3.25 42.83 2.32
813 840 8.710551 TCATTGCAATATCAAACAAACAATGAC 58.289 29.630 12.53 0.00 44.13 3.06
834 861 5.581126 TGTGGCCTAAGCTAATTTCATTG 57.419 39.130 3.32 0.00 39.73 2.82
842 869 3.267483 GACGAAATGTGGCCTAAGCTAA 58.733 45.455 3.32 0.00 39.73 3.09
848 875 8.458573 AATATATTTTGACGAAATGTGGCCTA 57.541 30.769 3.32 0.00 38.40 3.93
896 929 2.456989 GACAATGCGGATGAAATGCAG 58.543 47.619 0.00 0.00 42.65 4.41
907 940 2.480555 GCGAACAGGACAATGCGG 59.519 61.111 0.00 0.00 0.00 5.69
911 944 2.355115 GGGGGCGAACAGGACAAT 59.645 61.111 0.00 0.00 0.00 2.71
925 958 2.949447 CCAGGATTTGAACATAGGGGG 58.051 52.381 0.00 0.00 0.00 5.40
926 959 2.091665 AGCCAGGATTTGAACATAGGGG 60.092 50.000 0.00 0.00 0.00 4.79
927 960 3.217626 GAGCCAGGATTTGAACATAGGG 58.782 50.000 0.00 0.00 0.00 3.53
928 961 3.217626 GGAGCCAGGATTTGAACATAGG 58.782 50.000 0.00 0.00 0.00 2.57
929 962 2.874701 CGGAGCCAGGATTTGAACATAG 59.125 50.000 0.00 0.00 0.00 2.23
930 963 2.917933 CGGAGCCAGGATTTGAACATA 58.082 47.619 0.00 0.00 0.00 2.29
931 964 1.755179 CGGAGCCAGGATTTGAACAT 58.245 50.000 0.00 0.00 0.00 2.71
932 965 3.248043 CGGAGCCAGGATTTGAACA 57.752 52.632 0.00 0.00 0.00 3.18
949 982 4.082523 ATGTGACGGTCAGGGGCG 62.083 66.667 11.83 0.00 0.00 6.13
950 983 1.327690 TAGATGTGACGGTCAGGGGC 61.328 60.000 11.83 0.00 0.00 5.80
951 984 1.414158 ATAGATGTGACGGTCAGGGG 58.586 55.000 11.83 0.00 0.00 4.79
952 985 4.665833 TTTATAGATGTGACGGTCAGGG 57.334 45.455 11.83 0.00 0.00 4.45
953 986 6.157211 GGTATTTATAGATGTGACGGTCAGG 58.843 44.000 11.83 0.00 0.00 3.86
954 987 6.641314 GTGGTATTTATAGATGTGACGGTCAG 59.359 42.308 11.83 0.00 0.00 3.51
955 988 6.461927 GGTGGTATTTATAGATGTGACGGTCA 60.462 42.308 6.76 6.76 0.00 4.02
956 989 5.924825 GGTGGTATTTATAGATGTGACGGTC 59.075 44.000 0.00 0.00 0.00 4.79
960 993 6.042781 TGGGAGGTGGTATTTATAGATGTGAC 59.957 42.308 0.00 0.00 0.00 3.67
1035 1068 5.392165 GGCTGGTAGTTATATAGCTCGTGAG 60.392 48.000 1.93 0.00 34.89 3.51
1036 1069 4.458295 GGCTGGTAGTTATATAGCTCGTGA 59.542 45.833 1.93 0.00 34.89 4.35
1037 1070 4.217767 TGGCTGGTAGTTATATAGCTCGTG 59.782 45.833 1.93 0.00 34.89 4.35
1038 1071 4.404640 TGGCTGGTAGTTATATAGCTCGT 58.595 43.478 1.93 0.00 34.89 4.18
1039 1072 4.675671 GCTGGCTGGTAGTTATATAGCTCG 60.676 50.000 1.93 0.00 34.89 5.03
1040 1073 4.464597 AGCTGGCTGGTAGTTATATAGCTC 59.535 45.833 1.93 0.00 34.16 4.09
1041 1074 4.421131 AGCTGGCTGGTAGTTATATAGCT 58.579 43.478 4.41 4.41 34.89 3.32
1042 1075 4.810191 AGCTGGCTGGTAGTTATATAGC 57.190 45.455 0.00 0.00 0.00 2.97
1043 1076 5.163499 GGCTAGCTGGCTGGTAGTTATATAG 60.163 48.000 22.23 6.86 45.65 1.31
1044 1077 4.710375 GGCTAGCTGGCTGGTAGTTATATA 59.290 45.833 22.23 0.00 45.65 0.86
1045 1078 3.515901 GGCTAGCTGGCTGGTAGTTATAT 59.484 47.826 22.23 0.00 45.65 0.86
1090 1147 4.130118 CCATGATTAGTGGTTAGTCTGCC 58.870 47.826 0.00 0.00 31.96 4.85
1101 1166 2.617308 CAGAGCTTGGCCATGATTAGTG 59.383 50.000 22.21 10.83 0.00 2.74
1237 1313 4.778415 CTCGGTCACTCACGGCCG 62.778 72.222 26.86 26.86 44.95 6.13
1307 1387 2.100797 CACACGCATGCATTCCGG 59.899 61.111 19.57 0.00 0.00 5.14
1308 1388 1.512522 CACACACGCATGCATTCCG 60.513 57.895 19.57 13.34 0.00 4.30
1309 1389 0.730155 CACACACACGCATGCATTCC 60.730 55.000 19.57 0.00 0.00 3.01
1310 1390 0.040157 ACACACACACGCATGCATTC 60.040 50.000 19.57 0.00 0.00 2.67
1506 1603 1.115326 TCGATGCGGGACATGGAGAT 61.115 55.000 0.00 0.00 38.44 2.75
1553 1650 3.991051 CACGGGTGCGAGTGAGGT 61.991 66.667 0.00 0.00 40.56 3.85
1569 1666 3.298958 GAGGATCTCGGTGGCACA 58.701 61.111 20.82 0.00 0.00 4.57
1907 2004 0.594028 CGTAGTGCATCATACCGCGT 60.594 55.000 4.92 0.00 0.00 6.01
2197 2309 2.262572 ATCAAAGCGCCGAAATGAAC 57.737 45.000 2.29 0.00 0.00 3.18
2209 2321 8.139521 AGCTATTTTTACCGTACTATCAAAGC 57.860 34.615 0.00 0.00 0.00 3.51
2217 2329 8.843885 AAAGAAGAAGCTATTTTTACCGTACT 57.156 30.769 0.00 0.00 0.00 2.73
2275 2387 8.925700 CGTAGGTTTTTACCGTACTATCTTTTT 58.074 33.333 0.00 0.00 34.28 1.94
2276 2388 8.088365 ACGTAGGTTTTTACCGTACTATCTTTT 58.912 33.333 0.00 0.00 34.28 2.27
2277 2389 7.542130 CACGTAGGTTTTTACCGTACTATCTTT 59.458 37.037 0.00 0.00 34.28 2.52
2278 2390 7.029563 CACGTAGGTTTTTACCGTACTATCTT 58.970 38.462 0.00 0.00 34.28 2.40
2279 2391 6.555315 CACGTAGGTTTTTACCGTACTATCT 58.445 40.000 0.00 0.00 34.28 1.98
2280 2392 5.230097 GCACGTAGGTTTTTACCGTACTATC 59.770 44.000 0.00 0.00 34.28 2.08
2281 2393 5.102313 GCACGTAGGTTTTTACCGTACTAT 58.898 41.667 0.00 0.00 34.28 2.12
2282 2394 4.481463 GCACGTAGGTTTTTACCGTACTA 58.519 43.478 0.00 0.00 34.28 1.82
2283 2395 3.317150 GCACGTAGGTTTTTACCGTACT 58.683 45.455 0.00 0.00 34.28 2.73
2284 2396 2.090503 CGCACGTAGGTTTTTACCGTAC 59.909 50.000 0.00 0.00 34.28 3.67
2285 2397 2.287909 ACGCACGTAGGTTTTTACCGTA 60.288 45.455 0.00 0.00 34.28 4.02
2286 2398 1.139163 CGCACGTAGGTTTTTACCGT 58.861 50.000 0.00 0.00 34.28 4.83
2287 2399 1.139163 ACGCACGTAGGTTTTTACCG 58.861 50.000 0.00 0.00 34.28 4.02
2288 2400 2.090503 CGTACGCACGTAGGTTTTTACC 59.909 50.000 0.52 0.00 43.31 2.85
2289 2401 3.338405 CGTACGCACGTAGGTTTTTAC 57.662 47.619 0.52 0.00 43.31 2.01
2348 2475 5.067283 ACAAATAACAAGACGCTTTTCACCT 59.933 36.000 0.00 0.00 0.00 4.00
2349 2476 5.278604 ACAAATAACAAGACGCTTTTCACC 58.721 37.500 0.00 0.00 0.00 4.02
2377 2511 3.491619 CGATACCTGCATACAGCTCAACT 60.492 47.826 0.00 0.00 45.94 3.16
2429 2564 1.595794 ACACGCGTTGGAAAACTACAG 59.404 47.619 10.22 0.00 0.00 2.74
2434 2569 3.364946 ACATTAACACGCGTTGGAAAAC 58.635 40.909 10.22 0.00 36.52 2.43
2450 2588 8.820831 CCATGGGGGCATTTATTTATTACATTA 58.179 33.333 2.85 0.00 0.00 1.90
2469 2607 1.303236 TCGCTGACAAACCATGGGG 60.303 57.895 18.09 7.76 41.29 4.96
2470 2608 0.606401 AGTCGCTGACAAACCATGGG 60.606 55.000 18.09 0.00 34.60 4.00
2477 2615 0.601046 CAGGCTGAGTCGCTGACAAA 60.601 55.000 9.42 0.00 34.60 2.83
2480 2618 2.778309 AAGCAGGCTGAGTCGCTGAC 62.778 60.000 20.86 0.00 34.26 3.51
2485 2623 2.086054 AAGTAAAGCAGGCTGAGTCG 57.914 50.000 20.86 0.00 0.00 4.18
2531 2700 6.320926 TCATTTGTCTTCCTTGTTTCACATCA 59.679 34.615 0.00 0.00 0.00 3.07
2532 2701 6.738114 TCATTTGTCTTCCTTGTTTCACATC 58.262 36.000 0.00 0.00 0.00 3.06
2533 2702 6.713762 TCATTTGTCTTCCTTGTTTCACAT 57.286 33.333 0.00 0.00 0.00 3.21
2534 2703 6.522625 TTCATTTGTCTTCCTTGTTTCACA 57.477 33.333 0.00 0.00 0.00 3.58
2538 2707 7.830099 AGAGATTCATTTGTCTTCCTTGTTT 57.170 32.000 0.00 0.00 0.00 2.83
2539 2708 9.171877 GATAGAGATTCATTTGTCTTCCTTGTT 57.828 33.333 0.00 0.00 0.00 2.83
2541 2710 8.961294 AGATAGAGATTCATTTGTCTTCCTTG 57.039 34.615 0.00 0.00 0.00 3.61
2542 2711 8.991275 AGAGATAGAGATTCATTTGTCTTCCTT 58.009 33.333 0.00 0.00 0.00 3.36
2550 2719 9.473640 TCGATGAAAGAGATAGAGATTCATTTG 57.526 33.333 0.00 0.00 0.00 2.32
2553 2722 9.022884 TCATCGATGAAAGAGATAGAGATTCAT 57.977 33.333 25.44 0.00 33.08 2.57
2554 2723 8.401490 TCATCGATGAAAGAGATAGAGATTCA 57.599 34.615 25.44 0.00 33.08 2.57
2555 2724 9.507280 GATCATCGATGAAAGAGATAGAGATTC 57.493 37.037 30.41 14.76 40.69 2.52
2556 2725 9.246670 AGATCATCGATGAAAGAGATAGAGATT 57.753 33.333 30.41 9.97 40.69 2.40
2557 2726 8.812513 AGATCATCGATGAAAGAGATAGAGAT 57.187 34.615 30.41 10.41 40.69 2.75
2558 2727 8.102676 AGAGATCATCGATGAAAGAGATAGAGA 58.897 37.037 30.41 4.64 40.69 3.10
2560 2729 7.665145 ACAGAGATCATCGATGAAAGAGATAGA 59.335 37.037 30.41 5.39 40.69 1.98
2561 2730 7.819644 ACAGAGATCATCGATGAAAGAGATAG 58.180 38.462 30.41 17.27 40.69 2.08
2562 2731 7.757941 ACAGAGATCATCGATGAAAGAGATA 57.242 36.000 30.41 6.91 40.69 1.98
2563 2732 6.653526 ACAGAGATCATCGATGAAAGAGAT 57.346 37.500 30.41 14.14 40.69 2.75
2565 2734 6.733145 TGTACAGAGATCATCGATGAAAGAG 58.267 40.000 30.41 20.41 40.69 2.85
2567 2736 7.943413 AATGTACAGAGATCATCGATGAAAG 57.057 36.000 30.41 19.48 40.69 2.62
2580 2749 9.480861 CCTTCAGGGATATATAATGTACAGAGA 57.519 37.037 0.33 0.00 37.23 3.10
2600 2769 2.809601 CCGAACGCGTCCCTTCAG 60.810 66.667 14.44 2.97 35.23 3.02
2601 2770 4.367023 CCCGAACGCGTCCCTTCA 62.367 66.667 14.44 0.00 35.23 3.02
2602 2771 3.984200 CTCCCGAACGCGTCCCTTC 62.984 68.421 14.44 5.19 35.23 3.46
2603 2772 4.065281 CTCCCGAACGCGTCCCTT 62.065 66.667 14.44 0.00 35.23 3.95
2605 2774 4.790861 GTCTCCCGAACGCGTCCC 62.791 72.222 14.44 6.90 35.23 4.46
2611 2780 4.394078 TGTCGCGTCTCCCGAACG 62.394 66.667 5.77 0.00 42.87 3.95
2612 2781 2.504244 CTGTCGCGTCTCCCGAAC 60.504 66.667 5.77 0.00 39.56 3.95
2613 2782 1.236616 TAACTGTCGCGTCTCCCGAA 61.237 55.000 5.77 0.00 39.56 4.30
2614 2783 1.642037 CTAACTGTCGCGTCTCCCGA 61.642 60.000 5.77 0.00 39.56 5.14
2615 2784 1.226323 CTAACTGTCGCGTCTCCCG 60.226 63.158 5.77 0.00 40.40 5.14
2616 2785 0.524862 TTCTAACTGTCGCGTCTCCC 59.475 55.000 5.77 0.00 0.00 4.30
2617 2786 2.342910 TTTCTAACTGTCGCGTCTCC 57.657 50.000 5.77 0.00 0.00 3.71
2697 2871 6.575267 GGAGATTAGGAGGAGTGTTAAGAAC 58.425 44.000 0.00 0.00 0.00 3.01
2745 2920 5.588246 GGTTTTTGGAGGAGCATTTTTCAAA 59.412 36.000 0.00 0.00 0.00 2.69
2795 2972 8.537728 AAGGAGTTTTTCATGGCATATTATGA 57.462 30.769 7.87 0.00 0.00 2.15
2862 3839 9.461312 AATGAGGCAATTGTAATACAAGAACTA 57.539 29.630 11.70 0.00 41.94 2.24
2954 3959 3.637229 TGATAACCTGTTCGAGATCTCCC 59.363 47.826 17.13 6.00 0.00 4.30
3156 4837 4.566545 TTACACAAATGCAGACAGGTTG 57.433 40.909 0.00 0.00 33.20 3.77
3241 4924 7.692460 TCACAGAATGATGAACTTTGCTAAT 57.308 32.000 0.00 0.00 39.69 1.73
3309 4993 6.098838 AGTGACTGCATCCACTAATCATTCTA 59.901 38.462 16.55 0.00 41.38 2.10
3411 5106 8.248771 TGCTGGGTATATATTAGATCCCCATAT 58.751 37.037 2.45 0.00 39.79 1.78


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

AutoCloner maintained by Alex Coulton.