Multiple sequence alignment - TraesCS4A01G212100

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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 TraesCS4A01G212100 chr4A 100.000 3629 0 0 1 3629 507591560 507595188 0.000000e+00 6702.0
1 TraesCS4A01G212100 chr4A 96.129 310 11 1 3321 3629 58839865 58839556 4.180000e-139 505.0
2 TraesCS4A01G212100 chr4A 96.403 139 5 0 3173 3311 507594586 507594724 2.820000e-56 230.0
3 TraesCS4A01G212100 chr4A 96.403 139 5 0 3027 3165 507594732 507594870 2.820000e-56 230.0
4 TraesCS4A01G212100 chr4A 92.308 143 9 2 2878 3020 25495650 25495510 6.140000e-48 202.0
5 TraesCS4A01G212100 chr4A 90.972 144 11 2 2877 3020 584999437 584999296 3.700000e-45 193.0
6 TraesCS4A01G212100 chr4A 95.000 120 6 0 3164 3283 58841066 58840947 4.780000e-44 189.0
7 TraesCS4A01G212100 chr4D 93.010 2432 138 20 454 2868 78779075 78781491 0.000000e+00 3520.0
8 TraesCS4A01G212100 chr4D 78.625 1076 163 27 1490 2553 503606900 503607920 0.000000e+00 651.0
9 TraesCS4A01G212100 chr4B 93.673 2023 84 19 888 2877 110228621 110230632 0.000000e+00 2987.0
10 TraesCS4A01G212100 chr4B 83.131 1482 211 19 1088 2553 667426658 667428116 0.000000e+00 1315.0
11 TraesCS4A01G212100 chr4B 82.843 1463 210 24 1119 2553 649353971 649355420 0.000000e+00 1273.0
12 TraesCS4A01G212100 chr4B 85.455 550 67 6 1 541 110226493 110227038 8.800000e-156 560.0
13 TraesCS4A01G212100 chr4B 90.836 371 18 3 540 894 110227120 110227490 1.960000e-132 483.0
14 TraesCS4A01G212100 chr7A 86.026 1560 201 9 996 2551 518524741 518523195 0.000000e+00 1657.0
15 TraesCS4A01G212100 chr7A 91.667 144 10 2 2877 3020 116779446 116779587 7.950000e-47 198.0
16 TraesCS4A01G212100 chr7A 91.549 142 10 2 2879 3020 483941524 483941385 1.030000e-45 195.0
17 TraesCS4A01G212100 chr7B 85.623 1565 201 16 996 2551 502733921 502735470 0.000000e+00 1622.0
18 TraesCS4A01G212100 chr7B 82.441 1475 245 11 1082 2547 537517250 537515781 0.000000e+00 1277.0
19 TraesCS4A01G212100 chr7D 84.453 1563 223 12 996 2551 477855569 477857118 0.000000e+00 1522.0
20 TraesCS4A01G212100 chr7D 82.012 1501 254 14 1057 2547 509533812 509532318 0.000000e+00 1262.0
21 TraesCS4A01G212100 chr7D 90.972 144 11 2 2877 3020 415867135 415867276 3.700000e-45 193.0
22 TraesCS4A01G212100 chrUn 83.165 1485 210 20 1086 2553 30095185 30096646 0.000000e+00 1321.0
23 TraesCS4A01G212100 chr5A 82.840 1486 212 24 1088 2553 706653340 706654802 0.000000e+00 1291.0
24 TraesCS4A01G212100 chr5A 97.735 309 7 0 3321 3629 566195061 566194753 1.920000e-147 532.0
25 TraesCS4A01G212100 chr5A 94.839 310 15 1 3321 3629 311973370 311973061 1.960000e-132 483.0
26 TraesCS4A01G212100 chr5A 95.541 157 7 0 3164 3320 311973814 311973658 6.020000e-63 252.0
27 TraesCS4A01G212100 chr5A 94.410 161 6 1 3163 3320 566195338 566195178 1.010000e-60 244.0
28 TraesCS4A01G212100 chr5A 94.702 151 8 0 3015 3165 566195337 566195187 6.060000e-58 235.0
29 TraesCS4A01G212100 chr5A 94.245 139 8 0 3027 3165 311973805 311973667 2.840000e-51 213.0
30 TraesCS4A01G212100 chr5A 91.667 144 10 2 2877 3020 646990390 646990531 7.950000e-47 198.0
31 TraesCS4A01G212100 chr5A 96.774 31 1 0 292 322 126894547 126894517 7.000000e-03 52.8
32 TraesCS4A01G212100 chr2B 81.278 1581 242 30 1007 2551 762118358 762116796 0.000000e+00 1230.0
33 TraesCS4A01G212100 chr2D 80.989 1578 238 29 1007 2550 621359830 621358281 0.000000e+00 1195.0
34 TraesCS4A01G212100 chr2D 92.361 144 9 2 2877 3020 521937002 521937143 1.710000e-48 204.0
35 TraesCS4A01G212100 chr2D 90.972 144 12 1 2877 3020 28766598 28766740 3.700000e-45 193.0
36 TraesCS4A01G212100 chr3A 98.382 309 5 0 3321 3629 667657022 667657330 8.860000e-151 544.0
37 TraesCS4A01G212100 chr3A 96.203 158 6 0 3163 3320 667656748 667656905 3.590000e-65 259.0
38 TraesCS4A01G212100 chr3A 94.964 139 7 0 3027 3165 667656758 667656896 6.100000e-53 219.0
39 TraesCS4A01G212100 chr3A 77.657 367 65 13 2219 2574 79236366 79236726 1.320000e-49 207.0
40 TraesCS4A01G212100 chr2A 98.058 309 5 1 3321 3629 479829869 479829562 1.480000e-148 536.0
41 TraesCS4A01G212100 chr2A 95.161 310 14 1 3321 3629 409135088 409135397 4.210000e-134 488.0
42 TraesCS4A01G212100 chr2A 95.161 310 14 1 3321 3629 409185367 409185676 4.210000e-134 488.0
43 TraesCS4A01G212100 chr2A 96.178 157 6 0 3164 3320 409134735 409134891 1.290000e-64 257.0
44 TraesCS4A01G212100 chr2A 96.575 146 5 0 3175 3320 479830131 479829986 3.620000e-60 243.0
45 TraesCS4A01G212100 chr2A 95.918 147 6 0 3173 3319 409183428 409183574 4.680000e-59 239.0
46 TraesCS4A01G212100 chr2A 95.070 142 7 0 3024 3165 409183425 409183566 1.310000e-54 224.0
47 TraesCS4A01G212100 chr2A 95.620 137 6 0 3029 3165 479830131 479829995 1.700000e-53 220.0
48 TraesCS4A01G212100 chr2A 94.964 139 7 0 3027 3165 409134744 409134882 6.100000e-53 219.0
49 TraesCS4A01G212100 chr2A 80.612 98 9 2 3016 3103 177888704 177888801 6.500000e-08 69.4
50 TraesCS4A01G212100 chr1D 96.129 310 11 1 3321 3629 446365826 446366135 4.180000e-139 505.0
51 TraesCS4A01G212100 chr1D 89.809 314 27 5 3319 3629 397166823 397167134 7.300000e-107 398.0
52 TraesCS4A01G212100 chr1D 97.500 160 4 0 3161 3320 446364803 446364962 1.280000e-69 274.0
53 TraesCS4A01G212100 chr1D 97.122 139 4 0 3027 3165 446364815 446364953 6.060000e-58 235.0
54 TraesCS4A01G212100 chr1A 95.714 140 6 0 3181 3320 105299562 105299701 3.650000e-55 226.0
55 TraesCS4A01G212100 chr1A 94.656 131 7 0 3035 3165 105299562 105299692 1.710000e-48 204.0
56 TraesCS4A01G212100 chr5D 93.617 141 8 1 2877 3017 497021848 497021709 3.670000e-50 209.0


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 TraesCS4A01G212100 chr4A 507591560 507595188 3628 False 2387.333333 6702 97.602000 1 3629 3 chr4A.!!$F1 3628
1 TraesCS4A01G212100 chr4A 58839556 58841066 1510 True 347.000000 505 95.564500 3164 3629 2 chr4A.!!$R3 465
2 TraesCS4A01G212100 chr4D 78779075 78781491 2416 False 3520.000000 3520 93.010000 454 2868 1 chr4D.!!$F1 2414
3 TraesCS4A01G212100 chr4D 503606900 503607920 1020 False 651.000000 651 78.625000 1490 2553 1 chr4D.!!$F2 1063
4 TraesCS4A01G212100 chr4B 110226493 110230632 4139 False 1343.333333 2987 89.988000 1 2877 3 chr4B.!!$F3 2876
5 TraesCS4A01G212100 chr4B 667426658 667428116 1458 False 1315.000000 1315 83.131000 1088 2553 1 chr4B.!!$F2 1465
6 TraesCS4A01G212100 chr4B 649353971 649355420 1449 False 1273.000000 1273 82.843000 1119 2553 1 chr4B.!!$F1 1434
7 TraesCS4A01G212100 chr7A 518523195 518524741 1546 True 1657.000000 1657 86.026000 996 2551 1 chr7A.!!$R2 1555
8 TraesCS4A01G212100 chr7B 502733921 502735470 1549 False 1622.000000 1622 85.623000 996 2551 1 chr7B.!!$F1 1555
9 TraesCS4A01G212100 chr7B 537515781 537517250 1469 True 1277.000000 1277 82.441000 1082 2547 1 chr7B.!!$R1 1465
10 TraesCS4A01G212100 chr7D 477855569 477857118 1549 False 1522.000000 1522 84.453000 996 2551 1 chr7D.!!$F2 1555
11 TraesCS4A01G212100 chr7D 509532318 509533812 1494 True 1262.000000 1262 82.012000 1057 2547 1 chr7D.!!$R1 1490
12 TraesCS4A01G212100 chrUn 30095185 30096646 1461 False 1321.000000 1321 83.165000 1086 2553 1 chrUn.!!$F1 1467
13 TraesCS4A01G212100 chr5A 706653340 706654802 1462 False 1291.000000 1291 82.840000 1088 2553 1 chr5A.!!$F2 1465
14 TraesCS4A01G212100 chr5A 566194753 566195338 585 True 337.000000 532 95.615667 3015 3629 3 chr5A.!!$R3 614
15 TraesCS4A01G212100 chr5A 311973061 311973814 753 True 316.000000 483 94.875000 3027 3629 3 chr5A.!!$R2 602
16 TraesCS4A01G212100 chr2B 762116796 762118358 1562 True 1230.000000 1230 81.278000 1007 2551 1 chr2B.!!$R1 1544
17 TraesCS4A01G212100 chr2D 621358281 621359830 1549 True 1195.000000 1195 80.989000 1007 2550 1 chr2D.!!$R1 1543
18 TraesCS4A01G212100 chr3A 667656748 667657330 582 False 340.666667 544 96.516333 3027 3629 3 chr3A.!!$F2 602
19 TraesCS4A01G212100 chr2A 479829562 479830131 569 True 333.000000 536 96.751000 3029 3629 3 chr2A.!!$R1 600
20 TraesCS4A01G212100 chr2A 409134735 409135397 662 False 321.333333 488 95.434333 3027 3629 3 chr2A.!!$F2 602
21 TraesCS4A01G212100 chr2A 409183425 409185676 2251 False 317.000000 488 95.383000 3024 3629 3 chr2A.!!$F3 605
22 TraesCS4A01G212100 chr1D 446364803 446366135 1332 False 338.000000 505 96.917000 3027 3629 3 chr1D.!!$F2 602

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
433 442 0.447801 CAGAGTGTGCCGGCAATTAC 59.552 55.0 34.66 28.29 0.00 1.89 F
1107 2383 0.106819 ATGGCTTCCTCCAGTGCATC 60.107 55.0 0.00 0.00 39.89 3.91 F
2277 3580 0.037697 AGTACATCGCGTTCTGGCAA 60.038 50.0 5.77 0.00 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 3133 0.108804 CCGACAGCATCACCGTTACT 60.109 55.0 0.0 0.0 0.00 2.24 R
2416 3725 0.811915 CTCTGGGACGTGGTACTGAG 59.188 60.0 0.0 0.0 0.00 3.35 R
3195 4536 0.601576 TTGTGACGGTGAATCCACGG 60.602 55.0 0.0 0.0 44.09 4.94 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
27 28 2.997485 GCAAAAGGAAATGCTCGAGT 57.003 45.000 15.13 0.00 39.46 4.18
37 38 5.757320 AGGAAATGCTCGAGTTAGATGATTG 59.243 40.000 15.13 0.00 0.00 2.67
39 40 6.073873 GGAAATGCTCGAGTTAGATGATTGAG 60.074 42.308 15.13 0.00 0.00 3.02
67 76 7.158697 ACAGCTAATGTAATTATGTATGCCGA 58.841 34.615 0.00 0.00 41.60 5.54
97 106 4.070552 GGCCGCGAGACAGGAACT 62.071 66.667 8.23 0.00 43.88 3.01
104 113 1.476891 GCGAGACAGGAACTATGGTCA 59.523 52.381 0.00 0.00 36.02 4.02
155 164 1.593750 GGCGCTCTGACTAGCATGG 60.594 63.158 7.64 0.00 42.91 3.66
164 173 1.065926 TGACTAGCATGGACTGGCTTG 60.066 52.381 0.00 0.00 41.41 4.01
170 179 1.404391 GCATGGACTGGCTTGATTCTG 59.596 52.381 0.00 0.00 0.00 3.02
173 182 1.034292 GGACTGGCTTGATTCTGGCC 61.034 60.000 0.00 0.00 45.45 5.36
176 185 3.190878 GGCTTGATTCTGGCCGTG 58.809 61.111 0.00 0.00 36.37 4.94
190 199 3.274601 CCGTGGGGCCTAAATTTCA 57.725 52.632 0.84 0.00 0.00 2.69
204 213 9.875691 GGCCTAAATTTCAGTTTTCATTATCTT 57.124 29.630 0.00 0.00 0.00 2.40
237 246 1.529438 TCAAACGGTCAGTCGAATTGC 59.471 47.619 0.00 0.00 33.85 3.56
241 250 0.732880 CGGTCAGTCGAATTGCGTCT 60.733 55.000 0.00 0.00 41.80 4.18
256 265 2.115052 TCTGTTGGTTGGGCGCAT 59.885 55.556 10.83 0.00 0.00 4.73
290 299 4.379143 GAAACGGCCGGACAACGC 62.379 66.667 31.76 7.38 42.52 4.84
297 306 2.642700 CCGGACAACGCCCTTTTG 59.357 61.111 0.00 0.00 42.52 2.44
298 307 2.642700 CGGACAACGCCCTTTTGG 59.357 61.111 0.00 0.00 39.97 3.28
319 328 1.076332 CGACCCAAACGGACAGAATC 58.924 55.000 0.00 0.00 34.64 2.52
343 352 5.047847 CAGATAATATGGACGACCGTTTGT 58.952 41.667 3.45 0.00 39.42 2.83
376 385 5.624344 TGTAGTAGAAGTCTTGGTTCTCG 57.376 43.478 0.00 0.00 35.78 4.04
384 393 3.698289 AGTCTTGGTTCTCGGATCTGTA 58.302 45.455 0.42 0.00 0.00 2.74
399 408 1.073216 CTGTAGCTCGTGCGTCCTTG 61.073 60.000 3.48 0.00 45.42 3.61
417 426 1.375908 GAATGTGCGCCAGACCAGA 60.376 57.895 4.18 0.00 0.00 3.86
433 442 0.447801 CAGAGTGTGCCGGCAATTAC 59.552 55.000 34.66 28.29 0.00 1.89
437 446 1.472480 AGTGTGCCGGCAATTACATTC 59.528 47.619 34.66 17.06 0.00 2.67
438 447 0.449786 TGTGCCGGCAATTACATTCG 59.550 50.000 34.66 0.00 0.00 3.34
446 455 4.307432 CGGCAATTACATTCGAGTAGGAT 58.693 43.478 0.00 0.00 0.00 3.24
447 456 4.386049 CGGCAATTACATTCGAGTAGGATC 59.614 45.833 0.00 0.00 0.00 3.36
469 478 9.129532 GGATCATAAGGAAAAGAGTGAATGAAT 57.870 33.333 0.00 0.00 0.00 2.57
516 526 0.565679 CTGTTGTTTTCACGCAACGC 59.434 50.000 0.00 0.00 45.54 4.84
536 546 2.543653 GCACACAACCACAATGGAGAAC 60.544 50.000 0.84 0.00 40.96 3.01
541 551 5.063204 CACAACCACAATGGAGAACTCTAA 58.937 41.667 0.84 0.00 40.96 2.10
597 690 7.120285 CAGACATTCTTTTGCCTTCTCTATTGA 59.880 37.037 0.00 0.00 0.00 2.57
600 693 6.560253 TTCTTTTGCCTTCTCTATTGACAC 57.440 37.500 0.00 0.00 0.00 3.67
637 737 9.344309 CGATGCATAGATGATATAGATAGCAAG 57.656 37.037 0.00 0.00 31.87 4.01
640 740 8.142551 TGCATAGATGATATAGATAGCAAGCTG 58.857 37.037 4.53 0.00 31.87 4.24
645 745 4.774200 TGATATAGATAGCAAGCTGAGCCA 59.226 41.667 0.00 0.00 0.00 4.75
651 751 1.598962 GCAAGCTGAGCCAGTCACA 60.599 57.895 0.00 0.00 33.43 3.58
656 756 0.871057 GCTGAGCCAGTCACAAACTC 59.129 55.000 0.00 0.00 35.45 3.01
806 913 5.119588 TCACAACTAGCACGCACTAATTTAC 59.880 40.000 0.00 0.00 0.00 2.01
846 953 2.504461 CTTGAAGCCTTGCACGCTCG 62.504 60.000 7.89 0.00 34.84 5.03
944 2195 9.824216 ATATAAGGAGGTTCATGTAGTAGCTAA 57.176 33.333 0.00 0.00 0.00 3.09
952 2203 7.614583 AGGTTCATGTAGTAGCTAAGTTCAGTA 59.385 37.037 0.00 0.00 0.00 2.74
1027 2291 1.342374 TGCTCAGAGGCCTATCACTCA 60.342 52.381 4.42 0.00 36.20 3.41
1107 2383 0.106819 ATGGCTTCCTCCAGTGCATC 60.107 55.000 0.00 0.00 39.89 3.91
1131 2407 1.410882 GAGAAGATACCCAGCGAGCTT 59.589 52.381 0.00 0.00 0.00 3.74
1140 2416 0.599991 CCAGCGAGCTTGTGTACACA 60.600 55.000 24.62 24.62 39.98 3.72
1160 2436 0.317269 CAGTGCAACGCCAACTTCAG 60.317 55.000 0.00 0.00 45.86 3.02
1469 2760 0.317938 GAGCTGTACTACGCCATCGG 60.318 60.000 0.00 0.00 40.69 4.18
1614 2905 2.034879 CGACGCCAAGCTGGTCAAT 61.035 57.895 0.00 0.00 40.46 2.57
2277 3580 0.037697 AGTACATCGCGTTCTGGCAA 60.038 50.000 5.77 0.00 0.00 4.52
2419 3734 3.359523 CGGTGTCGGACGACCTCA 61.360 66.667 20.57 1.06 43.97 3.86
2499 3817 4.717629 CTCGCGTCGGTGAAGGCA 62.718 66.667 5.77 0.00 31.08 4.75
2611 3929 1.669779 GTGAGCAGAGATTCATGCCAC 59.330 52.381 9.50 12.09 43.60 5.01
2612 3930 1.279846 TGAGCAGAGATTCATGCCACA 59.720 47.619 9.50 8.11 43.60 4.17
2620 3938 1.959282 GATTCATGCCACAAGATCCCC 59.041 52.381 0.00 0.00 0.00 4.81
2621 3939 0.703488 TTCATGCCACAAGATCCCCA 59.297 50.000 0.00 0.00 0.00 4.96
2627 3945 4.805140 TGCCACAAGATCCCCATAATTA 57.195 40.909 0.00 0.00 0.00 1.40
2628 3946 4.728772 TGCCACAAGATCCCCATAATTAG 58.271 43.478 0.00 0.00 0.00 1.73
2629 3947 4.167892 TGCCACAAGATCCCCATAATTAGT 59.832 41.667 0.00 0.00 0.00 2.24
2630 3948 5.371176 TGCCACAAGATCCCCATAATTAGTA 59.629 40.000 0.00 0.00 0.00 1.82
2631 3949 5.705905 GCCACAAGATCCCCATAATTAGTAC 59.294 44.000 0.00 0.00 0.00 2.73
2636 3954 9.220906 ACAAGATCCCCATAATTAGTACAGTAA 57.779 33.333 0.00 0.00 0.00 2.24
2675 4004 2.674796 ACTTCAAGATGACTACGGGC 57.325 50.000 0.00 0.00 0.00 6.13
2677 4006 0.539986 TTCAAGATGACTACGGGCCC 59.460 55.000 13.57 13.57 0.00 5.80
2734 4072 8.211629 ACTGTACAAGTTGTATTTTCTCCTTCT 58.788 33.333 18.35 0.00 34.57 2.85
2739 4077 5.238583 AGTTGTATTTTCTCCTTCTCGTGG 58.761 41.667 0.00 0.00 0.00 4.94
2748 4086 0.668706 CCTTCTCGTGGTGACTGCTG 60.669 60.000 0.00 0.00 0.00 4.41
2759 4097 1.053835 TGACTGCTGGGTGGAGACAA 61.054 55.000 0.00 0.00 46.06 3.18
2877 4218 2.783135 TGAAAATGACAGTCTCAGGCC 58.217 47.619 0.00 0.00 30.20 5.19
2878 4219 2.106338 TGAAAATGACAGTCTCAGGCCA 59.894 45.455 5.01 0.00 30.20 5.36
2879 4220 2.486472 AAATGACAGTCTCAGGCCAG 57.514 50.000 5.01 0.00 30.20 4.85
2880 4221 0.035630 AATGACAGTCTCAGGCCAGC 60.036 55.000 5.01 0.00 30.20 4.85
2881 4222 1.908340 ATGACAGTCTCAGGCCAGCC 61.908 60.000 5.01 0.00 30.20 4.85
2882 4223 3.655810 GACAGTCTCAGGCCAGCCG 62.656 68.421 5.01 0.00 41.95 5.52
2885 4226 3.461773 GTCTCAGGCCAGCCGCTA 61.462 66.667 5.01 0.00 41.95 4.26
2886 4227 3.150335 TCTCAGGCCAGCCGCTAG 61.150 66.667 5.01 2.51 41.95 3.42
2887 4228 4.906792 CTCAGGCCAGCCGCTAGC 62.907 72.222 5.01 4.06 41.95 3.42
2898 4239 4.162690 CGCTAGCCCCAGGGTCAC 62.163 72.222 9.66 0.00 37.65 3.67
2899 4240 3.798511 GCTAGCCCCAGGGTCACC 61.799 72.222 2.29 0.00 37.65 4.02
2900 4241 3.090532 CTAGCCCCAGGGTCACCC 61.091 72.222 3.85 3.85 45.90 4.61
2910 4251 3.781760 GGTCACCCCAGACACGTA 58.218 61.111 0.00 0.00 40.29 3.57
2911 4252 2.283824 GGTCACCCCAGACACGTAT 58.716 57.895 0.00 0.00 40.29 3.06
2912 4253 0.611714 GGTCACCCCAGACACGTATT 59.388 55.000 0.00 0.00 40.29 1.89
2913 4254 1.002773 GGTCACCCCAGACACGTATTT 59.997 52.381 0.00 0.00 40.29 1.40
2914 4255 2.551504 GGTCACCCCAGACACGTATTTT 60.552 50.000 0.00 0.00 40.29 1.82
2915 4256 3.143728 GTCACCCCAGACACGTATTTTT 58.856 45.455 0.00 0.00 38.40 1.94
2916 4257 4.317488 GTCACCCCAGACACGTATTTTTA 58.683 43.478 0.00 0.00 38.40 1.52
2917 4258 4.939439 GTCACCCCAGACACGTATTTTTAT 59.061 41.667 0.00 0.00 38.40 1.40
2918 4259 5.413523 GTCACCCCAGACACGTATTTTTATT 59.586 40.000 0.00 0.00 38.40 1.40
2919 4260 6.594937 GTCACCCCAGACACGTATTTTTATTA 59.405 38.462 0.00 0.00 38.40 0.98
2920 4261 7.281549 GTCACCCCAGACACGTATTTTTATTAT 59.718 37.037 0.00 0.00 38.40 1.28
2921 4262 7.830201 TCACCCCAGACACGTATTTTTATTATT 59.170 33.333 0.00 0.00 0.00 1.40
2922 4263 8.463607 CACCCCAGACACGTATTTTTATTATTT 58.536 33.333 0.00 0.00 0.00 1.40
2923 4264 9.027202 ACCCCAGACACGTATTTTTATTATTTT 57.973 29.630 0.00 0.00 0.00 1.82
2942 4283 9.868277 ATTATTTTAAAACATCTGAATTCGGCA 57.132 25.926 9.58 0.00 0.00 5.69
2943 4284 9.698309 TTATTTTAAAACATCTGAATTCGGCAA 57.302 25.926 9.58 0.00 0.00 4.52
2944 4285 8.600449 ATTTTAAAACATCTGAATTCGGCAAA 57.400 26.923 9.58 0.00 0.00 3.68
2945 4286 8.425577 TTTTAAAACATCTGAATTCGGCAAAA 57.574 26.923 9.58 4.72 0.00 2.44
2946 4287 8.600449 TTTAAAACATCTGAATTCGGCAAAAT 57.400 26.923 9.58 0.00 0.00 1.82
2947 4288 8.600449 TTAAAACATCTGAATTCGGCAAAATT 57.400 26.923 9.58 4.88 0.00 1.82
2948 4289 6.710692 AAACATCTGAATTCGGCAAAATTC 57.289 33.333 9.58 13.35 43.10 2.17
2949 4290 4.414852 ACATCTGAATTCGGCAAAATTCG 58.585 39.130 9.58 10.92 44.85 3.34
2950 4291 3.485947 TCTGAATTCGGCAAAATTCGG 57.514 42.857 18.79 18.79 46.50 4.30
2951 4292 1.919918 CTGAATTCGGCAAAATTCGGC 59.080 47.619 15.04 0.00 44.85 5.54
2952 4293 1.277326 GAATTCGGCAAAATTCGGCC 58.723 50.000 9.67 9.67 46.80 6.13
2957 4298 7.095446 GAATTCGGCAAAATTCGGCCAAATT 62.095 40.000 15.32 15.32 46.47 1.82
2959 4300 2.785879 GCAAAATTCGGCCAAATTCG 57.214 45.000 1.18 0.00 0.00 3.34
2960 4301 1.393196 GCAAAATTCGGCCAAATTCGG 59.607 47.619 1.18 0.00 0.00 4.30
2972 4313 2.794350 CCAAATTCGGCATAAATTCGGC 59.206 45.455 0.00 0.00 0.00 5.54
2973 4314 3.490761 CCAAATTCGGCATAAATTCGGCT 60.491 43.478 0.00 0.00 0.00 5.52
2974 4315 4.261405 CCAAATTCGGCATAAATTCGGCTA 60.261 41.667 0.00 0.00 0.00 3.93
2975 4316 5.277825 CAAATTCGGCATAAATTCGGCTAA 58.722 37.500 0.00 0.00 0.00 3.09
2976 4317 3.955771 TTCGGCATAAATTCGGCTAAC 57.044 42.857 0.00 0.00 0.00 2.34
2977 4318 3.188159 TCGGCATAAATTCGGCTAACT 57.812 42.857 0.00 0.00 0.00 2.24
2978 4319 3.537580 TCGGCATAAATTCGGCTAACTT 58.462 40.909 0.00 0.00 0.00 2.66
2979 4320 3.311322 TCGGCATAAATTCGGCTAACTTG 59.689 43.478 0.00 0.00 0.00 3.16
2980 4321 3.311322 CGGCATAAATTCGGCTAACTTGA 59.689 43.478 0.00 0.00 0.00 3.02
2981 4322 4.598062 GGCATAAATTCGGCTAACTTGAC 58.402 43.478 0.00 0.00 0.00 3.18
2982 4323 4.095782 GGCATAAATTCGGCTAACTTGACA 59.904 41.667 0.00 0.00 0.00 3.58
2983 4324 5.221048 GGCATAAATTCGGCTAACTTGACAT 60.221 40.000 0.00 0.00 0.00 3.06
2984 4325 6.265577 GCATAAATTCGGCTAACTTGACATT 58.734 36.000 0.00 0.00 0.00 2.71
2985 4326 6.414987 GCATAAATTCGGCTAACTTGACATTC 59.585 38.462 0.00 0.00 0.00 2.67
2986 4327 5.957842 AAATTCGGCTAACTTGACATTCA 57.042 34.783 0.00 0.00 0.00 2.57
2987 4328 6.515272 AAATTCGGCTAACTTGACATTCAT 57.485 33.333 0.00 0.00 0.00 2.57
2988 4329 7.624360 AAATTCGGCTAACTTGACATTCATA 57.376 32.000 0.00 0.00 0.00 2.15
2989 4330 7.807977 AATTCGGCTAACTTGACATTCATAT 57.192 32.000 0.00 0.00 0.00 1.78
2990 4331 7.807977 ATTCGGCTAACTTGACATTCATATT 57.192 32.000 0.00 0.00 0.00 1.28
2991 4332 6.844696 TCGGCTAACTTGACATTCATATTC 57.155 37.500 0.00 0.00 0.00 1.75
2992 4333 6.345298 TCGGCTAACTTGACATTCATATTCA 58.655 36.000 0.00 0.00 0.00 2.57
2993 4334 6.821160 TCGGCTAACTTGACATTCATATTCAA 59.179 34.615 0.00 0.00 0.00 2.69
2994 4335 6.907212 CGGCTAACTTGACATTCATATTCAAC 59.093 38.462 0.00 0.00 0.00 3.18
2995 4336 7.413988 CGGCTAACTTGACATTCATATTCAACA 60.414 37.037 0.00 0.00 0.00 3.33
2996 4337 8.408601 GGCTAACTTGACATTCATATTCAACAT 58.591 33.333 0.00 0.00 0.00 2.71
2997 4338 9.229784 GCTAACTTGACATTCATATTCAACATG 57.770 33.333 0.00 0.00 0.00 3.21
3000 4341 9.630098 AACTTGACATTCATATTCAACATGTTC 57.370 29.630 8.48 0.00 0.00 3.18
3001 4342 7.964559 ACTTGACATTCATATTCAACATGTTCG 59.035 33.333 8.48 4.95 0.00 3.95
3002 4343 6.784176 TGACATTCATATTCAACATGTTCGG 58.216 36.000 8.48 0.00 0.00 4.30
3003 4344 5.581605 ACATTCATATTCAACATGTTCGGC 58.418 37.500 8.48 0.00 0.00 5.54
3004 4345 5.125257 ACATTCATATTCAACATGTTCGGCA 59.875 36.000 8.48 0.00 0.00 5.69
3005 4346 5.833406 TTCATATTCAACATGTTCGGCAT 57.167 34.783 8.48 0.00 38.60 4.40
3006 4347 5.833406 TCATATTCAACATGTTCGGCATT 57.167 34.783 8.48 0.00 35.19 3.56
3007 4348 6.206395 TCATATTCAACATGTTCGGCATTT 57.794 33.333 8.48 0.00 35.19 2.32
3008 4349 7.326968 TCATATTCAACATGTTCGGCATTTA 57.673 32.000 8.48 0.00 35.19 1.40
3009 4350 7.192913 TCATATTCAACATGTTCGGCATTTAC 58.807 34.615 8.48 0.00 35.19 2.01
3010 4351 4.837896 TTCAACATGTTCGGCATTTACA 57.162 36.364 8.48 0.00 35.19 2.41
3011 4352 5.384063 TTCAACATGTTCGGCATTTACAT 57.616 34.783 8.48 0.00 35.19 2.29
3012 4353 6.502136 TTCAACATGTTCGGCATTTACATA 57.498 33.333 8.48 0.00 35.19 2.29
3013 4354 6.502136 TCAACATGTTCGGCATTTACATAA 57.498 33.333 8.48 0.00 35.19 1.90
3014 4355 6.914259 TCAACATGTTCGGCATTTACATAAA 58.086 32.000 8.48 0.00 35.19 1.40
3015 4356 7.542890 TCAACATGTTCGGCATTTACATAAAT 58.457 30.769 8.48 0.00 35.19 1.40
3016 4357 7.700234 TCAACATGTTCGGCATTTACATAAATC 59.300 33.333 8.48 0.00 35.19 2.17
3017 4358 7.333528 ACATGTTCGGCATTTACATAAATCT 57.666 32.000 0.00 0.00 35.19 2.40
3018 4359 8.445275 ACATGTTCGGCATTTACATAAATCTA 57.555 30.769 0.00 0.00 35.19 1.98
3022 4363 7.717436 TGTTCGGCATTTACATAAATCTATCCA 59.283 33.333 0.00 0.00 33.88 3.41
3074 4415 0.441145 GTTCACCGTCACAATACGCC 59.559 55.000 0.00 0.00 41.51 5.68
3091 4432 1.202143 CGCCTCTTCCCGTAAATTTGC 60.202 52.381 0.00 0.00 0.00 3.68
3092 4433 1.202143 GCCTCTTCCCGTAAATTTGCG 60.202 52.381 20.06 20.06 36.02 4.85
3093 4434 1.202143 CCTCTTCCCGTAAATTTGCGC 60.202 52.381 21.35 0.00 34.89 6.09
3094 4435 1.737793 CTCTTCCCGTAAATTTGCGCT 59.262 47.619 21.35 0.00 34.89 5.92
3095 4436 2.156098 TCTTCCCGTAAATTTGCGCTT 58.844 42.857 21.35 0.00 34.89 4.68
3096 4437 2.554893 TCTTCCCGTAAATTTGCGCTTT 59.445 40.909 21.35 3.30 34.89 3.51
3097 4438 2.622546 TCCCGTAAATTTGCGCTTTC 57.377 45.000 21.35 0.00 34.89 2.62
3098 4439 1.880675 TCCCGTAAATTTGCGCTTTCA 59.119 42.857 21.35 1.94 34.89 2.69
3099 4440 2.095466 TCCCGTAAATTTGCGCTTTCAG 60.095 45.455 21.35 8.02 34.89 3.02
3100 4441 2.351350 CCCGTAAATTTGCGCTTTCAGT 60.351 45.455 21.35 0.00 34.89 3.41
3101 4442 3.305110 CCGTAAATTTGCGCTTTCAGTT 58.695 40.909 21.35 0.00 34.89 3.16
3102 4443 3.733727 CCGTAAATTTGCGCTTTCAGTTT 59.266 39.130 21.35 4.16 34.89 2.66
3103 4444 4.208253 CCGTAAATTTGCGCTTTCAGTTTT 59.792 37.500 21.35 1.91 34.89 2.43
3104 4445 5.276631 CCGTAAATTTGCGCTTTCAGTTTTT 60.277 36.000 21.35 0.35 34.89 1.94
3125 4466 6.618287 TTTTCGCTCATATTATCCAAGGTG 57.382 37.500 0.00 0.00 0.00 4.00
3126 4467 4.271696 TCGCTCATATTATCCAAGGTGG 57.728 45.455 0.00 0.00 39.43 4.61
3127 4468 3.646162 TCGCTCATATTATCCAAGGTGGT 59.354 43.478 0.00 0.00 39.03 4.16
3128 4469 4.836175 TCGCTCATATTATCCAAGGTGGTA 59.164 41.667 0.00 0.00 39.03 3.25
3129 4470 4.929808 CGCTCATATTATCCAAGGTGGTAC 59.070 45.833 0.00 0.00 39.03 3.34
3130 4471 5.279506 CGCTCATATTATCCAAGGTGGTACT 60.280 44.000 0.00 0.00 39.03 2.73
3131 4472 6.071560 CGCTCATATTATCCAAGGTGGTACTA 60.072 42.308 0.00 0.00 39.03 1.82
3132 4473 7.363880 CGCTCATATTATCCAAGGTGGTACTAT 60.364 40.741 0.00 0.00 39.03 2.12
3133 4474 8.322091 GCTCATATTATCCAAGGTGGTACTATT 58.678 37.037 0.00 0.00 39.03 1.73
3134 4475 9.877178 CTCATATTATCCAAGGTGGTACTATTC 57.123 37.037 0.00 0.00 39.03 1.75
3135 4476 9.387397 TCATATTATCCAAGGTGGTACTATTCA 57.613 33.333 0.00 0.00 39.03 2.57
3138 4479 5.975988 ATCCAAGGTGGTACTATTCATGT 57.024 39.130 0.00 0.00 39.03 3.21
3139 4480 5.097742 TCCAAGGTGGTACTATTCATGTG 57.902 43.478 0.00 0.00 39.03 3.21
3140 4481 3.627577 CCAAGGTGGTACTATTCATGTGC 59.372 47.826 0.00 0.00 31.35 4.57
3141 4482 4.517285 CAAGGTGGTACTATTCATGTGCT 58.483 43.478 0.00 0.00 0.00 4.40
3142 4483 4.844349 AGGTGGTACTATTCATGTGCTT 57.156 40.909 0.00 0.00 0.00 3.91
3143 4484 5.179452 AGGTGGTACTATTCATGTGCTTT 57.821 39.130 0.00 0.00 0.00 3.51
3144 4485 5.570320 AGGTGGTACTATTCATGTGCTTTT 58.430 37.500 0.00 0.00 0.00 2.27
3145 4486 6.010219 AGGTGGTACTATTCATGTGCTTTTT 58.990 36.000 0.00 0.00 0.00 1.94
3146 4487 7.172342 AGGTGGTACTATTCATGTGCTTTTTA 58.828 34.615 0.00 0.00 0.00 1.52
3147 4488 7.336931 AGGTGGTACTATTCATGTGCTTTTTAG 59.663 37.037 0.00 0.00 0.00 1.85
3148 4489 7.120726 GGTGGTACTATTCATGTGCTTTTTAGT 59.879 37.037 0.00 0.00 0.00 2.24
3149 4490 9.158233 GTGGTACTATTCATGTGCTTTTTAGTA 57.842 33.333 0.00 0.00 0.00 1.82
3150 4491 9.727859 TGGTACTATTCATGTGCTTTTTAGTAA 57.272 29.630 0.00 0.00 0.00 2.24
3158 4499 9.699703 TTCATGTGCTTTTTAGTAATTAAACCC 57.300 29.630 0.00 0.00 31.11 4.11
3159 4500 8.308207 TCATGTGCTTTTTAGTAATTAAACCCC 58.692 33.333 0.00 0.00 31.11 4.95
3160 4501 6.679843 TGTGCTTTTTAGTAATTAAACCCCG 58.320 36.000 0.00 0.00 31.11 5.73
3161 4502 5.574055 GTGCTTTTTAGTAATTAAACCCCGC 59.426 40.000 0.00 0.00 31.11 6.13
3162 4503 5.477637 TGCTTTTTAGTAATTAAACCCCGCT 59.522 36.000 0.00 0.00 31.11 5.52
3195 4536 7.095187 CCCTAATAATAAAGCACGGATTGACTC 60.095 40.741 0.00 0.00 0.00 3.36
3214 5494 0.601576 CCGTGGATTCACCGTCACAA 60.602 55.000 0.00 0.00 40.65 3.33
3227 5507 2.607187 CGTCACAATACGCTTCTTCCT 58.393 47.619 0.00 0.00 35.87 3.36
3236 5516 7.271223 CACAATACGCTTCTTCCTGTAAATTTG 59.729 37.037 0.00 0.00 0.00 2.32
3432 8058 5.409520 TGAGCAGCAAACACTATAAGAACTG 59.590 40.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 6.563753 GCTCAATCATCTAACTCGAGCATTTC 60.564 42.308 13.61 0.00 42.99 2.17
18 19 4.039004 AGCTCAATCATCTAACTCGAGCAT 59.961 41.667 13.61 4.25 45.26 3.79
20 21 3.976169 AGCTCAATCATCTAACTCGAGC 58.024 45.455 13.61 0.00 43.63 5.03
39 40 8.391106 GGCATACATAATTACATTAGCTGTAGC 58.609 37.037 0.00 0.00 41.30 3.58
47 48 9.665719 ATCATGTCGGCATACATAATTACATTA 57.334 29.630 0.16 0.00 38.01 1.90
49 50 8.043113 AGATCATGTCGGCATACATAATTACAT 58.957 33.333 0.16 0.00 38.01 2.29
50 51 7.386059 AGATCATGTCGGCATACATAATTACA 58.614 34.615 0.16 0.00 38.01 2.41
51 52 7.834068 AGATCATGTCGGCATACATAATTAC 57.166 36.000 0.16 0.00 38.01 1.89
53 54 7.044181 CCTAGATCATGTCGGCATACATAATT 58.956 38.462 0.16 0.00 38.01 1.40
54 55 6.407412 CCCTAGATCATGTCGGCATACATAAT 60.407 42.308 0.16 0.00 38.01 1.28
55 56 5.105351 CCCTAGATCATGTCGGCATACATAA 60.105 44.000 0.16 0.00 38.01 1.90
56 57 4.402474 CCCTAGATCATGTCGGCATACATA 59.598 45.833 0.16 0.00 38.01 2.29
61 70 0.979665 CCCCTAGATCATGTCGGCAT 59.020 55.000 0.00 0.00 35.32 4.40
67 76 2.520536 GCGGCCCCCTAGATCATGT 61.521 63.158 0.00 0.00 0.00 3.21
135 144 0.460811 CATGCTAGTCAGAGCGCCAA 60.461 55.000 2.29 0.00 45.99 4.52
146 155 1.279496 TCAAGCCAGTCCATGCTAGT 58.721 50.000 0.00 0.00 36.66 2.57
155 164 2.486796 GGCCAGAATCAAGCCAGTC 58.513 57.895 0.00 0.00 46.34 3.51
173 182 1.834188 ACTGAAATTTAGGCCCCACG 58.166 50.000 0.00 0.00 0.00 4.94
175 184 4.227197 TGAAAACTGAAATTTAGGCCCCA 58.773 39.130 0.00 0.00 0.00 4.96
176 185 4.882842 TGAAAACTGAAATTTAGGCCCC 57.117 40.909 0.00 0.00 0.00 5.80
214 223 4.783242 CAATTCGACTGACCGTTTGAATT 58.217 39.130 0.00 5.78 39.50 2.17
215 224 3.364964 GCAATTCGACTGACCGTTTGAAT 60.365 43.478 0.00 0.00 34.47 2.57
227 236 1.148310 CCAACAGACGCAATTCGACT 58.852 50.000 4.65 1.57 43.45 4.18
229 238 1.262950 CAACCAACAGACGCAATTCGA 59.737 47.619 4.65 0.00 41.67 3.71
237 246 4.025401 GCGCCCAACCAACAGACG 62.025 66.667 0.00 0.00 0.00 4.18
241 250 3.301554 CCATGCGCCCAACCAACA 61.302 61.111 4.18 0.00 0.00 3.33
256 265 2.359850 CTACCTTTGCGCTGGCCA 60.360 61.111 9.73 4.71 38.85 5.36
264 273 1.500396 CGGCCGTTTCTACCTTTGC 59.500 57.895 19.50 0.00 0.00 3.68
268 277 1.474332 TTGTCCGGCCGTTTCTACCT 61.474 55.000 26.12 0.00 0.00 3.08
290 299 1.834822 TTTGGGTCGGCCAAAAGGG 60.835 57.895 9.07 0.00 32.89 3.95
292 301 1.007849 CGTTTGGGTCGGCCAAAAG 60.008 57.895 9.41 5.74 38.30 2.27
297 306 4.629523 TGTCCGTTTGGGTCGGCC 62.630 66.667 0.00 0.00 46.49 6.13
298 307 2.999739 TTCTGTCCGTTTGGGTCGGC 63.000 60.000 0.00 0.00 46.49 5.54
319 328 3.936372 ACGGTCGTCCATATTATCTGG 57.064 47.619 0.00 0.00 34.93 3.86
324 333 3.055963 ACCACAAACGGTCGTCCATATTA 60.056 43.478 0.00 0.00 32.11 0.98
327 336 0.680618 ACCACAAACGGTCGTCCATA 59.319 50.000 0.00 0.00 32.11 2.74
329 338 1.227321 GACCACAAACGGTCGTCCA 60.227 57.895 0.00 0.00 45.77 4.02
337 346 2.911819 ACAACAGTTGACCACAAACG 57.088 45.000 20.56 0.00 37.77 3.60
338 347 4.957759 ACTACAACAGTTGACCACAAAC 57.042 40.909 20.56 0.00 37.77 2.93
343 352 5.597182 AGACTTCTACTACAACAGTTGACCA 59.403 40.000 20.56 3.83 38.50 4.02
349 358 6.324254 AGAACCAAGACTTCTACTACAACAGT 59.676 38.462 0.00 0.00 41.62 3.55
350 359 6.750148 AGAACCAAGACTTCTACTACAACAG 58.250 40.000 0.00 0.00 0.00 3.16
351 360 6.514541 CGAGAACCAAGACTTCTACTACAACA 60.515 42.308 0.00 0.00 0.00 3.33
376 385 0.592754 GACGCACGAGCTACAGATCC 60.593 60.000 2.73 0.00 39.10 3.36
384 393 1.016130 CATTCAAGGACGCACGAGCT 61.016 55.000 2.73 0.00 39.10 4.09
399 408 1.364626 CTCTGGTCTGGCGCACATTC 61.365 60.000 10.83 0.00 0.00 2.67
417 426 1.472480 GAATGTAATTGCCGGCACACT 59.528 47.619 32.95 14.53 36.07 3.55
433 442 8.144478 TCTTTTCCTTATGATCCTACTCGAATG 58.856 37.037 0.00 0.00 0.00 2.67
437 446 6.920758 CACTCTTTTCCTTATGATCCTACTCG 59.079 42.308 0.00 0.00 0.00 4.18
438 447 8.012957 TCACTCTTTTCCTTATGATCCTACTC 57.987 38.462 0.00 0.00 0.00 2.59
446 455 9.958180 TGTATTCATTCACTCTTTTCCTTATGA 57.042 29.630 0.00 0.00 0.00 2.15
516 526 2.951642 AGTTCTCCATTGTGGTTGTGTG 59.048 45.455 0.00 0.00 39.03 3.82
562 655 3.593442 AAAGAATGTCTGGTTGTGGGA 57.407 42.857 0.00 0.00 0.00 4.37
597 690 0.042188 GCATCGCGCATTAATCGTGT 60.042 50.000 8.75 5.88 41.79 4.49
637 737 0.871057 GAGTTTGTGACTGGCTCAGC 59.129 55.000 0.00 0.00 39.19 4.26
640 740 1.967319 TTGGAGTTTGTGACTGGCTC 58.033 50.000 0.00 0.00 39.19 4.70
645 745 2.936498 CGTGAGTTTGGAGTTTGTGACT 59.064 45.455 0.00 0.00 42.70 3.41
651 751 1.021968 GTGGCGTGAGTTTGGAGTTT 58.978 50.000 0.00 0.00 0.00 2.66
656 756 4.214545 TGTTAATTAGTGGCGTGAGTTTGG 59.785 41.667 0.00 0.00 0.00 3.28
806 913 1.405105 CCAACTAAATCGGGCATGGTG 59.595 52.381 0.00 0.00 0.00 4.17
846 953 1.803334 TGTTAACTGCCGTCCATGTC 58.197 50.000 7.22 0.00 0.00 3.06
943 2194 1.417890 AGTGCTGTGCCTACTGAACTT 59.582 47.619 0.00 0.00 40.59 2.66
944 2195 1.001406 GAGTGCTGTGCCTACTGAACT 59.999 52.381 0.00 0.00 44.62 3.01
1027 2291 4.202398 TGAGAAGAAGGTGACAGAAAGCAT 60.202 41.667 0.00 0.00 0.00 3.79
1107 2383 0.390860 CGCTGGGTATCTTCTCCCTG 59.609 60.000 0.00 0.00 43.74 4.45
1140 2416 1.029408 TGAAGTTGGCGTTGCACTGT 61.029 50.000 0.00 0.00 0.00 3.55
1392 2683 1.069765 CCAGTGGTTGACGCTCACT 59.930 57.895 0.00 0.00 41.81 3.41
1842 3133 0.108804 CCGACAGCATCACCGTTACT 60.109 55.000 0.00 0.00 0.00 2.24
1843 3134 1.082117 CCCGACAGCATCACCGTTAC 61.082 60.000 0.00 0.00 0.00 2.50
1917 3211 4.388499 AACCGCTCGCCCATCGTT 62.388 61.111 0.00 0.00 39.67 3.85
2116 3410 1.827399 AAGATGTCCTTCCACGCGGT 61.827 55.000 12.47 0.00 0.00 5.68
2407 3716 0.957395 GTGGTACTGAGGTCGTCCGA 60.957 60.000 0.00 0.00 39.05 4.55
2416 3725 0.811915 CTCTGGGACGTGGTACTGAG 59.188 60.000 0.00 0.00 0.00 3.35
2419 3734 2.341101 CGCTCTGGGACGTGGTACT 61.341 63.158 0.00 0.00 0.00 2.73
2499 3817 1.224592 GTCCATTGGATCCACGGCT 59.775 57.895 15.91 0.00 32.73 5.52
2675 4004 2.960163 AGGGAAGTAGACTAATCCGGG 58.040 52.381 0.00 0.00 32.56 5.73
2677 4006 3.385111 AGCAAGGGAAGTAGACTAATCCG 59.615 47.826 8.69 0.00 32.56 4.18
2711 4042 7.384387 ACGAGAAGGAGAAAATACAACTTGTAC 59.616 37.037 3.67 0.00 35.42 2.90
2734 4072 2.842462 ACCCAGCAGTCACCACGA 60.842 61.111 0.00 0.00 0.00 4.35
2739 4077 1.004440 GTCTCCACCCAGCAGTCAC 60.004 63.158 0.00 0.00 0.00 3.67
2748 4086 6.051179 AGAGTAATTAAGTTGTCTCCACCC 57.949 41.667 0.00 0.00 0.00 4.61
2881 4222 4.162690 GTGACCCTGGGGCTAGCG 62.163 72.222 21.75 0.00 39.32 4.26
2882 4223 3.798511 GGTGACCCTGGGGCTAGC 61.799 72.222 21.75 12.10 39.32 3.42
2894 4235 2.467566 AAATACGTGTCTGGGGTGAC 57.532 50.000 0.00 0.00 37.47 3.67
2895 4236 3.495434 AAAAATACGTGTCTGGGGTGA 57.505 42.857 0.00 0.00 0.00 4.02
2896 4237 5.890424 AATAAAAATACGTGTCTGGGGTG 57.110 39.130 0.00 0.00 0.00 4.61
2897 4238 8.584063 AAATAATAAAAATACGTGTCTGGGGT 57.416 30.769 0.00 0.00 0.00 4.95
2916 4257 9.868277 TGCCGAATTCAGATGTTTTAAAATAAT 57.132 25.926 3.52 1.57 0.00 1.28
2917 4258 9.698309 TTGCCGAATTCAGATGTTTTAAAATAA 57.302 25.926 3.52 0.00 0.00 1.40
2918 4259 9.698309 TTTGCCGAATTCAGATGTTTTAAAATA 57.302 25.926 3.52 1.41 0.00 1.40
2919 4260 8.600449 TTTGCCGAATTCAGATGTTTTAAAAT 57.400 26.923 3.52 0.00 0.00 1.82
2920 4261 8.425577 TTTTGCCGAATTCAGATGTTTTAAAA 57.574 26.923 6.22 0.00 0.00 1.52
2921 4262 8.600449 ATTTTGCCGAATTCAGATGTTTTAAA 57.400 26.923 6.22 0.00 0.00 1.52
2922 4263 8.600449 AATTTTGCCGAATTCAGATGTTTTAA 57.400 26.923 6.22 0.00 0.00 1.52
2923 4264 7.061673 CGAATTTTGCCGAATTCAGATGTTTTA 59.938 33.333 17.06 0.00 43.12 1.52
2924 4265 6.128849 CGAATTTTGCCGAATTCAGATGTTTT 60.129 34.615 17.06 0.00 43.12 2.43
2925 4266 5.345741 CGAATTTTGCCGAATTCAGATGTTT 59.654 36.000 17.06 0.00 43.12 2.83
2926 4267 4.858692 CGAATTTTGCCGAATTCAGATGTT 59.141 37.500 17.06 0.00 43.12 2.71
2927 4268 4.414852 CGAATTTTGCCGAATTCAGATGT 58.585 39.130 17.06 0.00 43.12 3.06
2928 4269 3.792956 CCGAATTTTGCCGAATTCAGATG 59.207 43.478 17.06 5.62 43.12 2.90
2929 4270 3.734902 GCCGAATTTTGCCGAATTCAGAT 60.735 43.478 17.06 0.00 43.12 2.90
2930 4271 2.415357 GCCGAATTTTGCCGAATTCAGA 60.415 45.455 17.06 0.00 43.12 3.27
2931 4272 1.919918 GCCGAATTTTGCCGAATTCAG 59.080 47.619 17.06 10.09 43.12 3.02
2932 4273 1.403514 GGCCGAATTTTGCCGAATTCA 60.404 47.619 17.06 0.00 43.12 2.57
2933 4274 1.277326 GGCCGAATTTTGCCGAATTC 58.723 50.000 10.33 10.33 40.80 2.17
2934 4275 3.434258 GGCCGAATTTTGCCGAATT 57.566 47.368 3.72 0.00 38.00 2.17
2940 4281 1.393196 CCGAATTTGGCCGAATTTTGC 59.607 47.619 28.14 16.49 29.75 3.68
2951 4292 2.794350 GCCGAATTTATGCCGAATTTGG 59.206 45.455 7.44 7.44 45.12 3.28
2952 4293 3.705604 AGCCGAATTTATGCCGAATTTG 58.294 40.909 0.00 0.00 0.00 2.32
2953 4294 5.067283 AGTTAGCCGAATTTATGCCGAATTT 59.933 36.000 0.00 0.00 0.00 1.82
2954 4295 4.578928 AGTTAGCCGAATTTATGCCGAATT 59.421 37.500 0.00 0.00 0.00 2.17
2955 4296 4.134563 AGTTAGCCGAATTTATGCCGAAT 58.865 39.130 0.00 0.00 0.00 3.34
2956 4297 3.537580 AGTTAGCCGAATTTATGCCGAA 58.462 40.909 0.00 0.00 0.00 4.30
2957 4298 3.188159 AGTTAGCCGAATTTATGCCGA 57.812 42.857 0.00 0.00 0.00 5.54
2958 4299 3.311322 TCAAGTTAGCCGAATTTATGCCG 59.689 43.478 0.00 0.00 0.00 5.69
2959 4300 4.095782 TGTCAAGTTAGCCGAATTTATGCC 59.904 41.667 0.00 0.00 0.00 4.40
2960 4301 5.229921 TGTCAAGTTAGCCGAATTTATGC 57.770 39.130 0.00 0.00 0.00 3.14
2961 4302 7.471721 TGAATGTCAAGTTAGCCGAATTTATG 58.528 34.615 0.00 0.00 0.00 1.90
2962 4303 7.624360 TGAATGTCAAGTTAGCCGAATTTAT 57.376 32.000 0.00 0.00 0.00 1.40
2963 4304 7.624360 ATGAATGTCAAGTTAGCCGAATTTA 57.376 32.000 0.00 0.00 0.00 1.40
2964 4305 5.957842 TGAATGTCAAGTTAGCCGAATTT 57.042 34.783 0.00 0.00 0.00 1.82
2965 4306 7.807977 ATATGAATGTCAAGTTAGCCGAATT 57.192 32.000 0.00 0.00 0.00 2.17
2966 4307 7.498900 TGAATATGAATGTCAAGTTAGCCGAAT 59.501 33.333 0.00 0.00 0.00 3.34
2967 4308 6.821160 TGAATATGAATGTCAAGTTAGCCGAA 59.179 34.615 0.00 0.00 0.00 4.30
2968 4309 6.345298 TGAATATGAATGTCAAGTTAGCCGA 58.655 36.000 0.00 0.00 0.00 5.54
2969 4310 6.603237 TGAATATGAATGTCAAGTTAGCCG 57.397 37.500 0.00 0.00 0.00 5.52
2970 4311 7.761409 TGTTGAATATGAATGTCAAGTTAGCC 58.239 34.615 0.00 0.00 32.15 3.93
2971 4312 9.229784 CATGTTGAATATGAATGTCAAGTTAGC 57.770 33.333 0.00 0.00 32.15 3.09
2974 4315 9.630098 GAACATGTTGAATATGAATGTCAAGTT 57.370 29.630 17.58 0.00 32.15 2.66
2975 4316 7.964559 CGAACATGTTGAATATGAATGTCAAGT 59.035 33.333 17.58 0.00 32.15 3.16
2976 4317 7.430211 CCGAACATGTTGAATATGAATGTCAAG 59.570 37.037 17.58 0.00 32.15 3.02
2977 4318 7.249858 CCGAACATGTTGAATATGAATGTCAA 58.750 34.615 17.58 0.00 31.29 3.18
2978 4319 6.677675 GCCGAACATGTTGAATATGAATGTCA 60.678 38.462 17.58 0.00 31.29 3.58
2979 4320 5.682862 GCCGAACATGTTGAATATGAATGTC 59.317 40.000 17.58 0.00 31.29 3.06
2980 4321 5.125257 TGCCGAACATGTTGAATATGAATGT 59.875 36.000 17.58 0.00 32.99 2.71
2981 4322 5.580661 TGCCGAACATGTTGAATATGAATG 58.419 37.500 17.58 0.00 0.00 2.67
2982 4323 5.833406 TGCCGAACATGTTGAATATGAAT 57.167 34.783 17.58 0.00 0.00 2.57
2983 4324 5.833406 ATGCCGAACATGTTGAATATGAA 57.167 34.783 17.58 0.00 37.70 2.57
2984 4325 5.833406 AATGCCGAACATGTTGAATATGA 57.167 34.783 17.58 0.00 39.60 2.15
2985 4326 6.971756 TGTAAATGCCGAACATGTTGAATATG 59.028 34.615 17.58 0.08 39.60 1.78
2986 4327 7.094508 TGTAAATGCCGAACATGTTGAATAT 57.905 32.000 17.58 2.62 39.60 1.28
2987 4328 6.502136 TGTAAATGCCGAACATGTTGAATA 57.498 33.333 17.58 0.06 39.60 1.75
2988 4329 5.384063 TGTAAATGCCGAACATGTTGAAT 57.616 34.783 17.58 0.00 39.60 2.57
2989 4330 4.837896 TGTAAATGCCGAACATGTTGAA 57.162 36.364 17.58 0.00 39.60 2.69
2990 4331 6.502136 TTATGTAAATGCCGAACATGTTGA 57.498 33.333 17.58 0.00 39.60 3.18
2991 4332 7.701924 AGATTTATGTAAATGCCGAACATGTTG 59.298 33.333 17.58 8.34 39.60 3.33
2992 4333 7.771183 AGATTTATGTAAATGCCGAACATGTT 58.229 30.769 11.78 11.78 39.60 2.71
2993 4334 7.333528 AGATTTATGTAAATGCCGAACATGT 57.666 32.000 2.90 0.00 39.60 3.21
2994 4335 9.546909 GATAGATTTATGTAAATGCCGAACATG 57.453 33.333 2.90 0.00 39.60 3.21
2995 4336 8.730680 GGATAGATTTATGTAAATGCCGAACAT 58.269 33.333 2.90 0.00 42.30 2.71
2996 4337 7.717436 TGGATAGATTTATGTAAATGCCGAACA 59.283 33.333 2.90 0.00 36.13 3.18
2997 4338 8.094798 TGGATAGATTTATGTAAATGCCGAAC 57.905 34.615 2.90 0.00 36.13 3.95
2998 4339 8.862325 ATGGATAGATTTATGTAAATGCCGAA 57.138 30.769 2.90 0.00 36.13 4.30
2999 4340 9.952030 TTATGGATAGATTTATGTAAATGCCGA 57.048 29.630 2.90 0.00 36.13 5.54
3074 4415 1.737793 AGCGCAAATTTACGGGAAGAG 59.262 47.619 11.47 0.00 0.00 2.85
3101 4442 6.039270 CCACCTTGGATAATATGAGCGAAAAA 59.961 38.462 0.00 0.00 40.96 1.94
3102 4443 5.530915 CCACCTTGGATAATATGAGCGAAAA 59.469 40.000 0.00 0.00 40.96 2.29
3103 4444 5.063204 CCACCTTGGATAATATGAGCGAAA 58.937 41.667 0.00 0.00 40.96 3.46
3104 4445 4.102524 ACCACCTTGGATAATATGAGCGAA 59.897 41.667 0.00 0.00 40.96 4.70
3105 4446 3.646162 ACCACCTTGGATAATATGAGCGA 59.354 43.478 0.00 0.00 40.96 4.93
3106 4447 4.008074 ACCACCTTGGATAATATGAGCG 57.992 45.455 0.00 0.00 40.96 5.03
3107 4448 6.115448 AGTACCACCTTGGATAATATGAGC 57.885 41.667 0.00 0.00 40.96 4.26
3108 4449 9.877178 GAATAGTACCACCTTGGATAATATGAG 57.123 37.037 0.00 0.00 40.96 2.90
3109 4450 9.387397 TGAATAGTACCACCTTGGATAATATGA 57.613 33.333 0.00 0.00 40.96 2.15
3112 4453 9.166222 ACATGAATAGTACCACCTTGGATAATA 57.834 33.333 0.00 0.00 40.96 0.98
3113 4454 7.939039 CACATGAATAGTACCACCTTGGATAAT 59.061 37.037 0.00 0.00 40.96 1.28
3114 4455 7.279615 CACATGAATAGTACCACCTTGGATAA 58.720 38.462 0.00 0.00 40.96 1.75
3115 4456 6.687901 GCACATGAATAGTACCACCTTGGATA 60.688 42.308 0.00 0.00 40.96 2.59
3116 4457 5.684704 CACATGAATAGTACCACCTTGGAT 58.315 41.667 0.00 0.00 40.96 3.41
3117 4458 4.625324 GCACATGAATAGTACCACCTTGGA 60.625 45.833 0.00 0.00 40.96 3.53
3118 4459 3.627577 GCACATGAATAGTACCACCTTGG 59.372 47.826 0.00 0.00 45.02 3.61
3119 4460 4.517285 AGCACATGAATAGTACCACCTTG 58.483 43.478 0.00 0.00 0.00 3.61
3120 4461 4.844349 AGCACATGAATAGTACCACCTT 57.156 40.909 0.00 0.00 0.00 3.50
3121 4462 4.844349 AAGCACATGAATAGTACCACCT 57.156 40.909 0.00 0.00 0.00 4.00
3122 4463 5.897377 AAAAGCACATGAATAGTACCACC 57.103 39.130 0.00 0.00 0.00 4.61
3123 4464 8.040716 ACTAAAAAGCACATGAATAGTACCAC 57.959 34.615 0.00 0.00 0.00 4.16
3124 4465 9.727859 TTACTAAAAAGCACATGAATAGTACCA 57.272 29.630 0.00 0.00 0.00 3.25
3132 4473 9.699703 GGGTTTAATTACTAAAAAGCACATGAA 57.300 29.630 0.00 0.00 33.42 2.57
3133 4474 8.308207 GGGGTTTAATTACTAAAAAGCACATGA 58.692 33.333 0.00 0.00 34.86 3.07
3134 4475 7.274686 CGGGGTTTAATTACTAAAAAGCACATG 59.725 37.037 0.00 0.00 34.50 3.21
3135 4476 7.317390 CGGGGTTTAATTACTAAAAAGCACAT 58.683 34.615 3.72 0.00 34.50 3.21
3136 4477 6.679843 CGGGGTTTAATTACTAAAAAGCACA 58.320 36.000 3.72 0.00 34.50 4.57
3137 4478 5.574055 GCGGGGTTTAATTACTAAAAAGCAC 59.426 40.000 3.13 0.00 33.42 4.40
3138 4479 5.477637 AGCGGGGTTTAATTACTAAAAAGCA 59.522 36.000 3.13 0.00 33.42 3.91
3139 4480 5.957798 AGCGGGGTTTAATTACTAAAAAGC 58.042 37.500 0.00 0.00 31.22 3.51
3140 4481 9.117183 AGATAGCGGGGTTTAATTACTAAAAAG 57.883 33.333 0.00 0.00 31.22 2.27
3143 4484 9.933723 GATAGATAGCGGGGTTTAATTACTAAA 57.066 33.333 0.00 0.00 0.00 1.85
3144 4485 8.534496 GGATAGATAGCGGGGTTTAATTACTAA 58.466 37.037 0.00 0.00 0.00 2.24
3145 4486 7.124750 GGGATAGATAGCGGGGTTTAATTACTA 59.875 40.741 0.00 0.00 0.00 1.82
3146 4487 6.070366 GGGATAGATAGCGGGGTTTAATTACT 60.070 42.308 0.00 0.00 0.00 2.24
3147 4488 6.070366 AGGGATAGATAGCGGGGTTTAATTAC 60.070 42.308 0.00 0.00 0.00 1.89
3148 4489 6.027482 AGGGATAGATAGCGGGGTTTAATTA 58.973 40.000 0.00 0.00 0.00 1.40
3149 4490 4.850386 AGGGATAGATAGCGGGGTTTAATT 59.150 41.667 0.00 0.00 0.00 1.40
3150 4491 4.436079 AGGGATAGATAGCGGGGTTTAAT 58.564 43.478 0.00 0.00 0.00 1.40
3151 4492 3.865571 AGGGATAGATAGCGGGGTTTAA 58.134 45.455 0.00 0.00 0.00 1.52
3152 4493 3.555117 AGGGATAGATAGCGGGGTTTA 57.445 47.619 0.00 0.00 0.00 2.01
3153 4494 2.417719 AGGGATAGATAGCGGGGTTT 57.582 50.000 0.00 0.00 0.00 3.27
3154 4495 3.555117 TTAGGGATAGATAGCGGGGTT 57.445 47.619 0.00 0.00 0.00 4.11
3155 4496 3.778622 ATTAGGGATAGATAGCGGGGT 57.221 47.619 0.00 0.00 0.00 4.95
3156 4497 7.850935 TTATTATTAGGGATAGATAGCGGGG 57.149 40.000 0.00 0.00 0.00 5.73
3157 4498 7.873505 GCTTTATTATTAGGGATAGATAGCGGG 59.126 40.741 0.00 0.00 0.00 6.13
3158 4499 8.421784 TGCTTTATTATTAGGGATAGATAGCGG 58.578 37.037 0.00 0.00 0.00 5.52
3159 4500 9.250624 GTGCTTTATTATTAGGGATAGATAGCG 57.749 37.037 0.00 0.00 0.00 4.26
3160 4501 9.250624 CGTGCTTTATTATTAGGGATAGATAGC 57.749 37.037 0.00 0.00 0.00 2.97
3161 4502 9.751542 CCGTGCTTTATTATTAGGGATAGATAG 57.248 37.037 0.00 0.00 0.00 2.08
3162 4503 9.483489 TCCGTGCTTTATTATTAGGGATAGATA 57.517 33.333 0.00 0.00 0.00 1.98
3195 4536 0.601576 TTGTGACGGTGAATCCACGG 60.602 55.000 0.00 0.00 44.09 4.94
3214 5494 5.447279 CGCAAATTTACAGGAAGAAGCGTAT 60.447 40.000 0.00 0.00 37.05 3.06
3227 5507 6.654793 AAAAACTGAAAGCGCAAATTTACA 57.345 29.167 11.47 1.87 37.60 2.41
3432 8058 4.421948 ACGTTTAGATCTGTCGTGGATTC 58.578 43.478 16.52 0.00 33.55 2.52


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

AutoCloner maintained by Alex Coulton.