Multiple sequence alignment - TraesCS2B01G073900

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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 TraesCS2B01G073900 chr2B 100.000 3155 0 0 1 3155 39979539 39976385 0.000000e+00 5827
1 TraesCS2B01G073900 chr2B 92.984 955 48 4 2159 3109 34592940 34593879 0.000000e+00 1375
2 TraesCS2B01G073900 chr2B 80.905 597 94 17 2161 2755 597541874 597542452 1.330000e-123 453
3 TraesCS2B01G073900 chr2B 93.085 188 13 0 519 706 17028942 17029129 3.100000e-70 276
4 TraesCS2B01G073900 chr2B 93.122 189 12 1 519 707 679893896 679893709 3.100000e-70 276
5 TraesCS2B01G073900 chr2B 81.437 167 19 8 166 326 93898563 93898723 3.300000e-25 126
6 TraesCS2B01G073900 chr4A 95.482 996 29 4 2163 3155 67295541 67296523 0.000000e+00 1576
7 TraesCS2B01G073900 chr4A 96.820 283 7 1 233 515 179068045 179067765 3.680000e-129 472
8 TraesCS2B01G073900 chr4A 93.048 187 13 0 519 705 722877937 722878123 1.110000e-69 274
9 TraesCS2B01G073900 chr4A 77.165 254 48 9 1876 2124 41919409 41919161 4.240000e-29 139
10 TraesCS2B01G073900 chr4A 92.308 52 4 0 1 52 584419402 584419351 1.210000e-09 75
11 TraesCS2B01G073900 chr2A 90.504 1211 70 23 947 2134 27277283 27276095 0.000000e+00 1557
12 TraesCS2B01G073900 chr2A 88.396 767 51 4 1405 2159 27125422 27124682 0.000000e+00 889
13 TraesCS2B01G073900 chr2A 93.647 425 25 2 945 1369 27127119 27126697 4.440000e-178 634
14 TraesCS2B01G073900 chr2A 96.809 282 7 1 233 514 70704025 70704304 1.320000e-128 470
15 TraesCS2B01G073900 chr2A 91.045 201 17 1 519 719 768471938 768471739 1.440000e-68 270
16 TraesCS2B01G073900 chr2A 88.496 113 10 3 55 164 27130988 27130876 1.970000e-27 134
17 TraesCS2B01G073900 chr2D 89.675 1230 83 11 943 2159 24878013 24879211 0.000000e+00 1528
18 TraesCS2B01G073900 chr2D 89.655 116 9 3 52 164 24872913 24873028 9.120000e-31 145
19 TraesCS2B01G073900 chr7B 95.675 948 26 8 2158 3102 641169404 641168469 0.000000e+00 1509
20 TraesCS2B01G073900 chr7B 82.288 909 134 19 2159 3061 637200603 637199716 0.000000e+00 761
21 TraesCS2B01G073900 chr7B 94.118 187 11 0 519 705 142778082 142778268 5.150000e-73 285
22 TraesCS2B01G073900 chr7B 93.048 187 13 0 519 705 679697983 679698169 1.110000e-69 274
23 TraesCS2B01G073900 chr7B 87.037 108 10 3 169 272 494750747 494750640 5.530000e-23 119
24 TraesCS2B01G073900 chr5B 82.854 904 130 17 2164 3061 682377432 682376548 0.000000e+00 787
25 TraesCS2B01G073900 chr5B 96.503 286 7 2 233 518 446884887 446884605 1.320000e-128 470
26 TraesCS2B01G073900 chr5B 95.848 289 10 1 232 520 112364306 112364592 1.710000e-127 466
27 TraesCS2B01G073900 chr5B 93.583 187 12 0 519 705 267776840 267777026 2.400000e-71 279
28 TraesCS2B01G073900 chr5B 93.048 187 13 0 519 705 492255508 492255694 1.110000e-69 274
29 TraesCS2B01G073900 chr1B 81.788 906 139 18 2163 3061 621263435 621264321 0.000000e+00 736
30 TraesCS2B01G073900 chr1B 84.095 591 75 13 2480 3061 32998299 32998879 1.280000e-153 553
31 TraesCS2B01G073900 chr1B 83.224 608 86 12 2462 3061 130833790 130833191 7.700000e-151 544
32 TraesCS2B01G073900 chr1B 80.795 604 99 15 2154 2755 434749137 434749725 1.030000e-124 457
33 TraesCS2B01G073900 chr1B 89.189 111 8 2 166 272 452309441 452309551 5.490000e-28 135
34 TraesCS2B01G073900 chr1B 85.593 118 12 3 160 272 345769621 345769504 5.530000e-23 119
35 TraesCS2B01G073900 chr3A 90.631 555 33 10 166 704 78185936 78185385 0.000000e+00 719
36 TraesCS2B01G073900 chr7D 87.387 555 61 7 2162 2712 595644971 595645520 2.070000e-176 628
37 TraesCS2B01G073900 chr4D 82.642 651 91 16 2428 3068 354834907 354834269 9.890000e-155 556
38 TraesCS2B01G073900 chr4D 77.865 384 74 8 981 1362 422548504 422548878 8.800000e-56 228
39 TraesCS2B01G073900 chr4D 71.429 602 124 37 1503 2091 422549027 422549593 7.150000e-22 115
40 TraesCS2B01G073900 chr6D 83.553 608 84 10 2462 3061 374111155 374111754 3.560000e-154 555
41 TraesCS2B01G073900 chr6D 78.342 374 74 4 989 1362 385787090 385786724 5.260000e-58 235
42 TraesCS2B01G073900 chr6D 76.984 252 54 4 1875 2124 470030315 470030066 1.180000e-29 141
43 TraesCS2B01G073900 chr6B 96.886 289 7 1 232 520 143176386 143176100 1.700000e-132 483
44 TraesCS2B01G073900 chr6B 90.526 95 7 1 166 258 678298418 678298324 1.190000e-24 124
45 TraesCS2B01G073900 chr7A 97.153 281 6 1 234 514 627156431 627156709 1.020000e-129 473
46 TraesCS2B01G073900 chr7A 93.269 312 15 5 236 546 610710714 610710408 3.710000e-124 455
47 TraesCS2B01G073900 chr4B 96.194 289 9 1 232 520 42365678 42365392 3.680000e-129 472
48 TraesCS2B01G073900 chr4B 93.048 187 13 0 519 705 660751859 660751673 1.110000e-69 274
49 TraesCS2B01G073900 chr4B 94.186 86 2 2 161 243 33742905 33742820 9.190000e-26 128
50 TraesCS2B01G073900 chr4B 71.795 546 118 31 1511 2048 519404401 519404918 4.270000e-24 122
51 TraesCS2B01G073900 chr4B 93.023 86 3 2 161 243 558183607 558183692 4.270000e-24 122
52 TraesCS2B01G073900 chr4B 95.652 46 2 0 1907 1952 665959298 665959343 1.210000e-09 75
53 TraesCS2B01G073900 chr6A 78.457 376 70 7 989 1362 530252935 530252569 5.260000e-58 235
54 TraesCS2B01G073900 chr1A 93.976 83 3 1 156 236 564593408 564593490 1.190000e-24 124


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 TraesCS2B01G073900 chr2B 39976385 39979539 3154 True 5827.000000 5827 100.000000 1 3155 1 chr2B.!!$R1 3154
1 TraesCS2B01G073900 chr2B 34592940 34593879 939 False 1375.000000 1375 92.984000 2159 3109 1 chr2B.!!$F2 950
2 TraesCS2B01G073900 chr2B 597541874 597542452 578 False 453.000000 453 80.905000 2161 2755 1 chr2B.!!$F4 594
3 TraesCS2B01G073900 chr4A 67295541 67296523 982 False 1576.000000 1576 95.482000 2163 3155 1 chr4A.!!$F1 992
4 TraesCS2B01G073900 chr2A 27276095 27277283 1188 True 1557.000000 1557 90.504000 947 2134 1 chr2A.!!$R1 1187
5 TraesCS2B01G073900 chr2A 27124682 27130988 6306 True 552.333333 889 90.179667 55 2159 3 chr2A.!!$R3 2104
6 TraesCS2B01G073900 chr2D 24878013 24879211 1198 False 1528.000000 1528 89.675000 943 2159 1 chr2D.!!$F2 1216
7 TraesCS2B01G073900 chr7B 641168469 641169404 935 True 1509.000000 1509 95.675000 2158 3102 1 chr7B.!!$R3 944
8 TraesCS2B01G073900 chr7B 637199716 637200603 887 True 761.000000 761 82.288000 2159 3061 1 chr7B.!!$R2 902
9 TraesCS2B01G073900 chr5B 682376548 682377432 884 True 787.000000 787 82.854000 2164 3061 1 chr5B.!!$R2 897
10 TraesCS2B01G073900 chr1B 621263435 621264321 886 False 736.000000 736 81.788000 2163 3061 1 chr1B.!!$F4 898
11 TraesCS2B01G073900 chr1B 32998299 32998879 580 False 553.000000 553 84.095000 2480 3061 1 chr1B.!!$F1 581
12 TraesCS2B01G073900 chr1B 130833191 130833790 599 True 544.000000 544 83.224000 2462 3061 1 chr1B.!!$R1 599
13 TraesCS2B01G073900 chr1B 434749137 434749725 588 False 457.000000 457 80.795000 2154 2755 1 chr1B.!!$F2 601
14 TraesCS2B01G073900 chr3A 78185385 78185936 551 True 719.000000 719 90.631000 166 704 1 chr3A.!!$R1 538
15 TraesCS2B01G073900 chr7D 595644971 595645520 549 False 628.000000 628 87.387000 2162 2712 1 chr7D.!!$F1 550
16 TraesCS2B01G073900 chr4D 354834269 354834907 638 True 556.000000 556 82.642000 2428 3068 1 chr4D.!!$R1 640
17 TraesCS2B01G073900 chr6D 374111155 374111754 599 False 555.000000 555 83.553000 2462 3061 1 chr6D.!!$F1 599

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
757 777 0.034477 CAACCCCGGCTTCTGGTATT 60.034 55.0 0.0 0.0 0.0 1.89 F
846 4364 0.035056 ACTCCCTCCGCCTCAAAATG 60.035 55.0 0.0 0.0 0.0 2.32 F
1330 4872 0.039437 TCAGCAACTTCGTCGGTCTC 60.039 55.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 6666 0.107508 CAGCCAGACGGTTCATCCAT 60.108 55.000 0.00 0.00 35.57 3.41 R
2049 6859 0.525029 GGAAGGCGCAGTACTCGTAC 60.525 60.000 10.83 0.00 36.35 3.67 R
2368 7186 1.000955 GATTAGGGGCATCGATGACGT 59.999 52.381 29.20 21.54 36.40 4.34 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.400054 GGCTAGTCCGGCCCAACT 61.400 66.667 9.47 9.47 43.49 3.16
25 26 2.125106 GCTAGTCCGGCCCAACTG 60.125 66.667 13.63 6.22 0.00 3.16
26 27 2.955881 GCTAGTCCGGCCCAACTGT 61.956 63.158 13.63 0.00 0.00 3.55
27 28 1.677552 CTAGTCCGGCCCAACTGTT 59.322 57.895 13.63 0.00 0.00 3.16
28 29 0.391263 CTAGTCCGGCCCAACTGTTC 60.391 60.000 13.63 0.00 0.00 3.18
29 30 2.162338 TAGTCCGGCCCAACTGTTCG 62.162 60.000 13.63 0.00 0.00 3.95
30 31 4.323477 TCCGGCCCAACTGTTCGG 62.323 66.667 11.00 11.00 41.80 4.30
33 34 3.365265 GGCCCAACTGTTCGGCTG 61.365 66.667 24.81 0.00 42.58 4.85
34 35 3.365265 GCCCAACTGTTCGGCTGG 61.365 66.667 19.98 5.28 39.70 4.85
35 36 2.429930 CCCAACTGTTCGGCTGGA 59.570 61.111 2.98 0.00 0.00 3.86
36 37 1.966451 CCCAACTGTTCGGCTGGAC 60.966 63.158 0.00 0.00 0.00 4.02
37 38 1.071471 CCAACTGTTCGGCTGGACT 59.929 57.895 5.34 0.00 0.00 3.85
38 39 1.230635 CCAACTGTTCGGCTGGACTG 61.231 60.000 9.22 9.22 0.00 3.51
39 40 1.598130 AACTGTTCGGCTGGACTGC 60.598 57.895 10.63 0.00 0.00 4.40
48 49 2.662596 CTGGACTGCCAACGCCTA 59.337 61.111 0.00 0.00 45.41 3.93
49 50 1.221840 CTGGACTGCCAACGCCTAT 59.778 57.895 0.00 0.00 45.41 2.57
50 51 0.811616 CTGGACTGCCAACGCCTATC 60.812 60.000 0.00 0.00 45.41 2.08
51 52 1.220749 GGACTGCCAACGCCTATCA 59.779 57.895 0.00 0.00 0.00 2.15
52 53 1.090052 GGACTGCCAACGCCTATCAC 61.090 60.000 0.00 0.00 0.00 3.06
53 54 0.108138 GACTGCCAACGCCTATCACT 60.108 55.000 0.00 0.00 0.00 3.41
54 55 0.391661 ACTGCCAACGCCTATCACTG 60.392 55.000 0.00 0.00 0.00 3.66
55 56 1.078497 TGCCAACGCCTATCACTGG 60.078 57.895 0.00 0.00 0.00 4.00
56 57 2.472909 GCCAACGCCTATCACTGGC 61.473 63.158 0.00 0.00 45.27 4.85
76 77 5.944013 TGGCCTTTGCAAAAACTTAAAAAC 58.056 33.333 13.84 0.00 40.13 2.43
93 95 8.153550 ACTTAAAAACATTTATTGGGCACATGA 58.846 29.630 0.00 0.00 0.00 3.07
105 107 1.676746 GCACATGACCATCTGCTGAT 58.323 50.000 0.00 0.00 31.30 2.90
108 110 3.488721 GCACATGACCATCTGCTGATTTC 60.489 47.826 0.00 4.45 31.30 2.17
111 113 5.007430 CACATGACCATCTGCTGATTTCTAC 59.993 44.000 0.00 0.00 0.00 2.59
117 119 6.136857 ACCATCTGCTGATTTCTACCTACTA 58.863 40.000 2.92 0.00 0.00 1.82
122 124 3.318557 GCTGATTTCTACCTACTACGCCT 59.681 47.826 0.00 0.00 0.00 5.52
124 126 4.529897 TGATTTCTACCTACTACGCCTCA 58.470 43.478 0.00 0.00 0.00 3.86
154 156 7.219484 AGTGTCTTTGATTATTTTGGGACAG 57.781 36.000 0.00 0.00 42.39 3.51
155 157 7.004086 AGTGTCTTTGATTATTTTGGGACAGA 58.996 34.615 0.00 0.00 42.39 3.41
158 160 6.659242 GTCTTTGATTATTTTGGGACAGAGGA 59.341 38.462 0.00 0.00 42.39 3.71
159 161 6.886459 TCTTTGATTATTTTGGGACAGAGGAG 59.114 38.462 0.00 0.00 42.39 3.69
160 162 5.779241 TGATTATTTTGGGACAGAGGAGT 57.221 39.130 0.00 0.00 42.39 3.85
161 163 6.884472 TGATTATTTTGGGACAGAGGAGTA 57.116 37.500 0.00 0.00 42.39 2.59
162 164 7.451731 TGATTATTTTGGGACAGAGGAGTAT 57.548 36.000 0.00 0.00 42.39 2.12
164 166 7.775093 TGATTATTTTGGGACAGAGGAGTATTG 59.225 37.037 0.00 0.00 42.39 1.90
195 197 9.263446 GGTTGTAATGGGGAGTATCATATACTA 57.737 37.037 0.00 0.00 36.25 1.82
255 259 1.379044 GCTGGTCACAATGGGGAGG 60.379 63.158 0.00 0.00 0.00 4.30
258 262 0.698238 TGGTCACAATGGGGAGGAAG 59.302 55.000 0.00 0.00 0.00 3.46
272 276 4.101274 GGGGAGGAAGTTAGGAGTAACATC 59.899 50.000 0.00 0.00 41.06 3.06
273 277 4.715297 GGGAGGAAGTTAGGAGTAACATCA 59.285 45.833 3.70 0.00 41.06 3.07
303 307 6.803320 CACTCCAATACAACTTTGCTTATGTG 59.197 38.462 0.00 0.00 0.00 3.21
381 385 4.898829 TCACACACTCCAAGAAACAATG 57.101 40.909 0.00 0.00 0.00 2.82
383 387 4.946772 TCACACACTCCAAGAAACAATGAA 59.053 37.500 0.00 0.00 0.00 2.57
420 424 6.925610 AAATACATCGTTGCATGACACTAT 57.074 33.333 0.00 0.00 0.00 2.12
437 441 7.532199 TGACACTATATAGATGTTCCTACCCA 58.468 38.462 16.79 6.68 0.00 4.51
468 472 6.069994 AGGTAGTAACATAGTCTAGGGAAGC 58.930 44.000 0.00 0.00 0.00 3.86
482 486 4.446994 AGGGAAGCGTGTAAGTTACTAC 57.553 45.455 14.00 9.35 0.00 2.73
508 512 1.686052 GTTCTTGCCCATTGTGACCAA 59.314 47.619 0.00 0.00 34.45 3.67
561 578 7.821595 ATTTATTGACATGCATGACACAAAG 57.178 32.000 32.75 4.14 32.58 2.77
564 581 5.361135 TTGACATGCATGACACAAAGTAG 57.639 39.130 32.75 1.99 32.58 2.57
568 585 4.943093 ACATGCATGACACAAAGTAGCATA 59.057 37.500 32.75 0.00 39.67 3.14
569 586 5.065602 ACATGCATGACACAAAGTAGCATAG 59.934 40.000 32.75 0.00 39.67 2.23
574 591 5.801350 TGACACAAAGTAGCATAGCATTC 57.199 39.130 0.00 0.00 0.00 2.67
576 593 5.704978 TGACACAAAGTAGCATAGCATTCAA 59.295 36.000 0.00 0.00 0.00 2.69
580 597 9.559732 ACACAAAGTAGCATAGCATTCAATATA 57.440 29.630 0.00 0.00 0.00 0.86
586 603 9.534565 AGTAGCATAGCATTCAATATAATACGG 57.465 33.333 0.00 0.00 0.00 4.02
628 645 7.693969 ACACCCTCTCTTTCTTCATTTAATG 57.306 36.000 0.00 0.00 0.00 1.90
634 651 9.334947 CCTCTCTTTCTTCATTTAATGCTATGA 57.665 33.333 0.00 0.00 0.00 2.15
651 668 6.500910 TGCTATGACATCTCATCAAAATTGC 58.499 36.000 0.00 0.00 38.21 3.56
668 685 1.753930 TGCCTAGTTGACATGCATGG 58.246 50.000 29.41 11.12 0.00 3.66
678 695 5.070981 AGTTGACATGCATGGTACTAGCTAT 59.929 40.000 29.41 5.21 0.00 2.97
679 696 5.139435 TGACATGCATGGTACTAGCTATC 57.861 43.478 29.41 14.37 0.00 2.08
680 697 4.169508 GACATGCATGGTACTAGCTATCG 58.830 47.826 29.41 0.42 0.00 2.92
706 723 3.039011 ACCATTACGACCAGCCTTAGAT 58.961 45.455 0.00 0.00 0.00 1.98
724 741 7.470147 GCCTTAGATTAGACACACACTGCTATA 60.470 40.741 0.00 0.00 0.00 1.31
745 765 3.897936 TGCGATTAAGCAACCCCG 58.102 55.556 0.00 0.00 45.06 5.73
746 766 1.747367 TGCGATTAAGCAACCCCGG 60.747 57.895 0.00 0.00 45.06 5.73
748 768 1.451387 CGATTAAGCAACCCCGGCT 60.451 57.895 0.00 0.00 45.15 5.52
753 773 4.351054 AGCAACCCCGGCTTCTGG 62.351 66.667 0.00 0.00 38.81 3.86
754 774 4.660938 GCAACCCCGGCTTCTGGT 62.661 66.667 0.00 0.00 0.00 4.00
755 775 3.074281 CAACCCCGGCTTCTGGTA 58.926 61.111 0.00 0.00 0.00 3.25
756 776 1.607612 CAACCCCGGCTTCTGGTAT 59.392 57.895 0.00 0.00 0.00 2.73
757 777 0.034477 CAACCCCGGCTTCTGGTATT 60.034 55.000 0.00 0.00 0.00 1.89
759 779 1.152963 CCCCGGCTTCTGGTATTGG 60.153 63.158 0.00 0.00 0.00 3.16
760 780 1.823899 CCCGGCTTCTGGTATTGGC 60.824 63.158 0.00 0.00 0.00 4.52
762 782 1.376609 CCGGCTTCTGGTATTGGCAC 61.377 60.000 0.00 0.00 0.00 5.01
763 783 0.676466 CGGCTTCTGGTATTGGCACA 60.676 55.000 0.00 0.00 0.00 4.57
764 784 1.767759 GGCTTCTGGTATTGGCACAT 58.232 50.000 0.00 0.00 39.30 3.21
765 785 1.406539 GGCTTCTGGTATTGGCACATG 59.593 52.381 0.00 0.00 39.30 3.21
766 786 2.368439 GCTTCTGGTATTGGCACATGA 58.632 47.619 0.00 0.00 39.30 3.07
767 787 2.954318 GCTTCTGGTATTGGCACATGAT 59.046 45.455 0.00 0.00 39.30 2.45
769 789 4.498682 GCTTCTGGTATTGGCACATGATTC 60.499 45.833 0.00 0.00 39.30 2.52
770 790 4.508551 TCTGGTATTGGCACATGATTCT 57.491 40.909 0.00 0.00 39.30 2.40
772 792 4.883585 TCTGGTATTGGCACATGATTCTTC 59.116 41.667 0.00 0.00 39.30 2.87
773 793 4.598022 TGGTATTGGCACATGATTCTTCA 58.402 39.130 0.00 0.00 39.30 3.02
774 794 5.202765 TGGTATTGGCACATGATTCTTCAT 58.797 37.500 0.00 0.00 43.51 2.57
775 795 5.300034 TGGTATTGGCACATGATTCTTCATC 59.700 40.000 0.00 0.00 40.70 2.92
776 796 5.300034 GGTATTGGCACATGATTCTTCATCA 59.700 40.000 0.00 0.00 46.41 3.07
777 797 4.707030 TTGGCACATGATTCTTCATCAC 57.293 40.909 0.00 0.00 45.12 3.06
779 799 2.360165 GGCACATGATTCTTCATCACCC 59.640 50.000 0.00 0.00 45.12 4.61
781 801 3.181493 GCACATGATTCTTCATCACCCAC 60.181 47.826 0.00 0.00 45.12 4.61
782 802 4.267536 CACATGATTCTTCATCACCCACT 58.732 43.478 0.00 0.00 45.12 4.00
783 803 4.334759 CACATGATTCTTCATCACCCACTC 59.665 45.833 0.00 0.00 45.12 3.51
784 804 4.226846 ACATGATTCTTCATCACCCACTCT 59.773 41.667 0.00 0.00 45.12 3.24
785 805 4.212143 TGATTCTTCATCACCCACTCTG 57.788 45.455 0.00 0.00 36.94 3.35
786 806 2.479566 TTCTTCATCACCCACTCTGC 57.520 50.000 0.00 0.00 0.00 4.26
788 808 1.002430 TCTTCATCACCCACTCTGCAC 59.998 52.381 0.00 0.00 0.00 4.57
789 809 0.320683 TTCATCACCCACTCTGCACG 60.321 55.000 0.00 0.00 0.00 5.34
791 811 1.004560 ATCACCCACTCTGCACGTG 60.005 57.895 12.28 12.28 0.00 4.49
794 814 2.357517 CCCACTCTGCACGTGACC 60.358 66.667 22.23 2.42 34.35 4.02
795 815 2.421314 CCACTCTGCACGTGACCA 59.579 61.111 22.23 7.80 34.35 4.02
796 816 1.004560 CCACTCTGCACGTGACCAT 60.005 57.895 22.23 0.00 34.35 3.55
797 817 0.246360 CCACTCTGCACGTGACCATA 59.754 55.000 22.23 0.14 34.35 2.74
798 818 1.134699 CCACTCTGCACGTGACCATAT 60.135 52.381 22.23 0.00 34.35 1.78
812 853 4.030216 TGACCATATGCTGACTTCTACCA 58.970 43.478 0.00 0.00 0.00 3.25
819 860 7.172190 CCATATGCTGACTTCTACCAAACTATG 59.828 40.741 0.00 0.00 0.00 2.23
824 865 7.602644 TGCTGACTTCTACCAAACTATGTTTAG 59.397 37.037 0.00 0.00 0.00 1.85
831 4349 9.933723 TTCTACCAAACTATGTTTAGTTACTCC 57.066 33.333 0.00 0.00 45.77 3.85
836 4354 5.848833 ACTATGTTTAGTTACTCCCTCCG 57.151 43.478 0.00 0.00 34.99 4.63
837 4355 3.538634 ATGTTTAGTTACTCCCTCCGC 57.461 47.619 0.00 0.00 0.00 5.54
839 4357 1.829849 GTTTAGTTACTCCCTCCGCCT 59.170 52.381 0.00 0.00 0.00 5.52
846 4364 0.035056 ACTCCCTCCGCCTCAAAATG 60.035 55.000 0.00 0.00 0.00 2.32
850 4368 1.373570 CCTCCGCCTCAAAATGAGTC 58.626 55.000 6.62 0.00 42.80 3.36
851 4369 1.339055 CCTCCGCCTCAAAATGAGTCA 60.339 52.381 0.00 0.00 42.80 3.41
852 4370 2.426522 CTCCGCCTCAAAATGAGTCAA 58.573 47.619 0.00 0.00 42.80 3.18
853 4371 2.813754 CTCCGCCTCAAAATGAGTCAAA 59.186 45.455 0.00 0.00 42.80 2.69
854 4372 3.218453 TCCGCCTCAAAATGAGTCAAAA 58.782 40.909 0.00 0.00 42.80 2.44
855 4373 3.826157 TCCGCCTCAAAATGAGTCAAAAT 59.174 39.130 0.00 0.00 42.80 1.82
856 4374 5.007034 TCCGCCTCAAAATGAGTCAAAATA 58.993 37.500 0.00 0.00 42.80 1.40
857 4375 5.475220 TCCGCCTCAAAATGAGTCAAAATAA 59.525 36.000 0.00 0.00 42.80 1.40
858 4376 5.801947 CCGCCTCAAAATGAGTCAAAATAAG 59.198 40.000 0.00 0.00 42.80 1.73
859 4377 6.381801 CGCCTCAAAATGAGTCAAAATAAGT 58.618 36.000 0.00 0.00 42.80 2.24
860 4378 6.306356 CGCCTCAAAATGAGTCAAAATAAGTG 59.694 38.462 0.00 0.00 42.80 3.16
861 4379 7.147976 GCCTCAAAATGAGTCAAAATAAGTGT 58.852 34.615 0.00 0.00 42.80 3.55
862 4380 7.327032 GCCTCAAAATGAGTCAAAATAAGTGTC 59.673 37.037 0.00 0.00 42.80 3.67
863 4381 8.571336 CCTCAAAATGAGTCAAAATAAGTGTCT 58.429 33.333 0.00 0.00 42.80 3.41
864 4382 9.956720 CTCAAAATGAGTCAAAATAAGTGTCTT 57.043 29.630 0.00 0.00 39.58 3.01
923 4441 5.179368 TGCTATAAATTGCTACGATCAAGCC 59.821 40.000 13.04 0.00 39.30 4.35
925 4443 6.128172 GCTATAAATTGCTACGATCAAGCCAT 60.128 38.462 13.04 6.27 39.30 4.40
945 4463 5.450965 GCCATTCACACCAATTAAGATCCAG 60.451 44.000 0.00 0.00 0.00 3.86
959 4501 3.370104 AGATCCAGGAGACGAATTCACT 58.630 45.455 6.22 4.10 0.00 3.41
1297 4839 1.738099 GCGCATCAAGGACGTCACT 60.738 57.895 18.91 9.30 0.00 3.41
1316 4858 3.356639 GACGCCGGTCAGATCAGCA 62.357 63.158 1.90 0.00 42.91 4.41
1323 4865 1.670087 CGGTCAGATCAGCAACTTCGT 60.670 52.381 0.00 0.00 0.00 3.85
1330 4872 0.039437 TCAGCAACTTCGTCGGTCTC 60.039 55.000 0.00 0.00 0.00 3.36
1410 4952 4.159321 TGATCCTTCATCATCCGCTCTATC 59.841 45.833 0.00 0.00 36.51 2.08
1597 6394 0.872021 GCTACAGCTTCCGGATGTCG 60.872 60.000 12.37 8.00 44.02 4.35
1638 6435 3.723348 GAACGCGGCCAAGGTGAC 61.723 66.667 12.47 0.00 0.00 3.67
1684 6481 1.599518 GACCACCACCATCGTGCAA 60.600 57.895 0.00 0.00 38.79 4.08
1815 6622 3.078305 CCATATACCTCTCTTCCCCTCCT 59.922 52.174 0.00 0.00 0.00 3.69
1817 6624 1.695065 TACCTCTCTTCCCCTCCTCA 58.305 55.000 0.00 0.00 0.00 3.86
1826 6636 0.339859 TCCCCTCCTCAGCAGTGTAT 59.660 55.000 0.00 0.00 0.00 2.29
1833 6643 4.946157 CCTCCTCAGCAGTGTATTGAATTT 59.054 41.667 0.00 0.00 0.00 1.82
1834 6644 5.163683 CCTCCTCAGCAGTGTATTGAATTTG 60.164 44.000 0.00 0.00 0.00 2.32
1836 6646 5.769662 TCCTCAGCAGTGTATTGAATTTGTT 59.230 36.000 0.00 0.00 0.00 2.83
1837 6647 6.265196 TCCTCAGCAGTGTATTGAATTTGTTT 59.735 34.615 0.00 0.00 0.00 2.83
1838 6648 7.446931 TCCTCAGCAGTGTATTGAATTTGTTTA 59.553 33.333 0.00 0.00 0.00 2.01
1839 6649 8.081633 CCTCAGCAGTGTATTGAATTTGTTTAA 58.918 33.333 0.00 0.00 0.00 1.52
1840 6650 9.121517 CTCAGCAGTGTATTGAATTTGTTTAAG 57.878 33.333 0.00 0.00 0.00 1.85
1841 6651 8.629158 TCAGCAGTGTATTGAATTTGTTTAAGT 58.371 29.630 0.00 0.00 0.00 2.24
1842 6652 8.693504 CAGCAGTGTATTGAATTTGTTTAAGTG 58.306 33.333 0.00 0.00 0.00 3.16
1843 6653 7.867403 AGCAGTGTATTGAATTTGTTTAAGTGG 59.133 33.333 0.00 0.00 0.00 4.00
1844 6654 7.865385 GCAGTGTATTGAATTTGTTTAAGTGGA 59.135 33.333 0.00 0.00 0.00 4.02
1845 6655 9.743057 CAGTGTATTGAATTTGTTTAAGTGGAA 57.257 29.630 0.00 0.00 0.00 3.53
1846 6656 9.744468 AGTGTATTGAATTTGTTTAAGTGGAAC 57.256 29.630 0.00 0.00 0.00 3.62
1847 6657 8.687301 GTGTATTGAATTTGTTTAAGTGGAACG 58.313 33.333 0.00 0.00 45.86 3.95
1848 6658 8.622157 TGTATTGAATTTGTTTAAGTGGAACGA 58.378 29.630 0.00 0.00 45.86 3.85
1849 6659 9.620660 GTATTGAATTTGTTTAAGTGGAACGAT 57.379 29.630 0.00 0.00 45.86 3.73
1850 6660 7.922505 TTGAATTTGTTTAAGTGGAACGATG 57.077 32.000 0.00 0.00 45.86 3.84
1851 6661 5.918011 TGAATTTGTTTAAGTGGAACGATGC 59.082 36.000 0.00 0.00 45.86 3.91
1852 6662 5.705609 ATTTGTTTAAGTGGAACGATGCT 57.294 34.783 0.00 0.00 45.86 3.79
1853 6663 4.481930 TTGTTTAAGTGGAACGATGCTG 57.518 40.909 0.00 0.00 45.86 4.41
1854 6664 3.472652 TGTTTAAGTGGAACGATGCTGT 58.527 40.909 0.00 0.00 45.86 4.40
1855 6665 4.633175 TGTTTAAGTGGAACGATGCTGTA 58.367 39.130 0.00 0.00 45.86 2.74
1856 6666 5.057819 TGTTTAAGTGGAACGATGCTGTAA 58.942 37.500 0.00 0.00 45.86 2.41
1857 6667 5.703592 TGTTTAAGTGGAACGATGCTGTAAT 59.296 36.000 0.00 0.00 45.86 1.89
1858 6668 5.794687 TTAAGTGGAACGATGCTGTAATG 57.205 39.130 0.00 0.00 45.86 1.90
1859 6669 2.632377 AGTGGAACGATGCTGTAATGG 58.368 47.619 0.00 0.00 45.86 3.16
1860 6670 2.236146 AGTGGAACGATGCTGTAATGGA 59.764 45.455 0.00 0.00 45.86 3.41
1861 6671 3.118261 AGTGGAACGATGCTGTAATGGAT 60.118 43.478 0.00 0.00 45.86 3.41
1862 6672 3.002656 GTGGAACGATGCTGTAATGGATG 59.997 47.826 0.00 0.00 0.00 3.51
2046 6856 2.488820 GTCTACCGTCCCTGCGAC 59.511 66.667 0.00 0.00 38.21 5.19
2082 6892 1.104630 CCTTCCAGTACTCGGAGGAC 58.895 60.000 9.16 12.62 31.40 3.85
2131 6947 2.348971 GCTTTCTGCGGAGTAGCTAAAC 59.651 50.000 20.20 0.00 41.03 2.01
2139 6955 4.036498 TGCGGAGTAGCTAAACATCTAGAC 59.964 45.833 0.00 0.00 38.13 2.59
2140 6956 4.036498 GCGGAGTAGCTAAACATCTAGACA 59.964 45.833 0.00 0.00 0.00 3.41
2143 6959 6.293190 CGGAGTAGCTAAACATCTAGACAGAG 60.293 46.154 0.00 0.00 33.22 3.35
2159 6975 1.463831 CAGAGCAGCTGTGTGATGAAC 59.536 52.381 16.64 0.00 39.85 3.18
2160 6976 1.347050 AGAGCAGCTGTGTGATGAACT 59.653 47.619 16.64 0.00 33.12 3.01
2161 6977 2.149578 GAGCAGCTGTGTGATGAACTT 58.850 47.619 16.64 0.00 33.12 2.66
2162 6978 2.551459 GAGCAGCTGTGTGATGAACTTT 59.449 45.455 16.64 0.00 33.12 2.66
2181 6997 8.966868 TGAACTTTTTATTTTTGAGACAGAGGT 58.033 29.630 0.00 0.00 0.00 3.85
2368 7186 0.842030 ATCACCTCTCCCCAAGCACA 60.842 55.000 0.00 0.00 0.00 4.57
2425 7243 1.530852 CGACTTCGCTGCAAACAAACA 60.531 47.619 0.00 0.00 0.00 2.83
2745 7580 1.178534 CCCCCATCAACGTTGTTGCT 61.179 55.000 26.68 10.61 0.00 3.91
2934 7774 2.759535 TCACAGAGGAAGAGAGAGCATG 59.240 50.000 0.00 0.00 0.00 4.06
3083 7928 2.039787 TCCACGCATCCACCCCTA 59.960 61.111 0.00 0.00 0.00 3.53
3119 7964 1.452110 CAGCAACATCCCATCACGAA 58.548 50.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.125106 CAGTTGGGCCGGACTAGC 60.125 66.667 7.57 1.95 0.00 3.42
9 10 0.391263 GAACAGTTGGGCCGGACTAG 60.391 60.000 7.57 9.05 0.00 2.57
12 13 3.047877 CGAACAGTTGGGCCGGAC 61.048 66.667 5.05 0.00 0.00 4.79
13 14 4.323477 CCGAACAGTTGGGCCGGA 62.323 66.667 5.05 0.00 42.49 5.14
18 19 1.966451 GTCCAGCCGAACAGTTGGG 60.966 63.158 9.96 9.96 0.00 4.12
19 20 1.071471 AGTCCAGCCGAACAGTTGG 59.929 57.895 0.00 0.00 0.00 3.77
20 21 1.845809 GCAGTCCAGCCGAACAGTTG 61.846 60.000 0.00 0.00 0.00 3.16
21 22 1.598130 GCAGTCCAGCCGAACAGTT 60.598 57.895 0.00 0.00 0.00 3.16
22 23 2.031163 GCAGTCCAGCCGAACAGT 59.969 61.111 0.00 0.00 0.00 3.55
23 24 2.743928 GGCAGTCCAGCCGAACAG 60.744 66.667 0.00 0.00 46.12 3.16
30 31 2.876368 ATAGGCGTTGGCAGTCCAGC 62.876 60.000 4.90 0.14 44.53 4.85
31 32 0.811616 GATAGGCGTTGGCAGTCCAG 60.812 60.000 4.90 0.00 44.53 3.86
32 33 1.220749 GATAGGCGTTGGCAGTCCA 59.779 57.895 4.90 0.00 42.47 4.02
33 34 1.090052 GTGATAGGCGTTGGCAGTCC 61.090 60.000 0.00 0.00 42.47 3.85
34 35 0.108138 AGTGATAGGCGTTGGCAGTC 60.108 55.000 0.00 0.00 42.47 3.51
35 36 0.391661 CAGTGATAGGCGTTGGCAGT 60.392 55.000 0.00 0.00 42.47 4.40
36 37 1.091771 CCAGTGATAGGCGTTGGCAG 61.092 60.000 0.00 0.00 42.47 4.85
37 38 1.078497 CCAGTGATAGGCGTTGGCA 60.078 57.895 0.00 0.00 42.47 4.92
38 39 2.472909 GCCAGTGATAGGCGTTGGC 61.473 63.158 3.49 3.49 46.39 4.52
39 40 3.813596 GCCAGTGATAGGCGTTGG 58.186 61.111 0.00 0.00 43.15 3.77
45 46 1.838112 TTGCAAAGGCCAGTGATAGG 58.162 50.000 5.01 0.00 40.13 2.57
46 47 3.940209 TTTTGCAAAGGCCAGTGATAG 57.060 42.857 12.41 0.00 40.13 2.08
47 48 3.640967 AGTTTTTGCAAAGGCCAGTGATA 59.359 39.130 12.41 0.00 40.13 2.15
48 49 2.435437 AGTTTTTGCAAAGGCCAGTGAT 59.565 40.909 12.41 0.00 40.13 3.06
49 50 1.830477 AGTTTTTGCAAAGGCCAGTGA 59.170 42.857 12.41 0.00 40.13 3.41
50 51 2.314323 AGTTTTTGCAAAGGCCAGTG 57.686 45.000 12.41 2.83 40.13 3.66
51 52 4.479786 TTAAGTTTTTGCAAAGGCCAGT 57.520 36.364 12.41 0.00 40.13 4.00
52 53 5.809719 TTTTAAGTTTTTGCAAAGGCCAG 57.190 34.783 12.41 0.00 40.13 4.85
53 54 5.473504 TGTTTTTAAGTTTTTGCAAAGGCCA 59.526 32.000 12.41 0.00 40.13 5.36
54 55 5.944013 TGTTTTTAAGTTTTTGCAAAGGCC 58.056 33.333 12.41 0.00 40.13 5.19
55 56 8.459521 AAATGTTTTTAAGTTTTTGCAAAGGC 57.540 26.923 12.41 9.21 41.68 4.35
76 77 4.342951 AGATGGTCATGTGCCCAATAAATG 59.657 41.667 5.79 0.00 33.66 2.32
93 95 4.965532 AGTAGGTAGAAATCAGCAGATGGT 59.034 41.667 0.00 0.00 33.90 3.55
105 107 5.726980 TTTTGAGGCGTAGTAGGTAGAAA 57.273 39.130 0.00 0.00 0.00 2.52
108 110 6.696148 CACTTATTTTGAGGCGTAGTAGGTAG 59.304 42.308 0.00 0.00 0.00 3.18
111 113 5.416947 ACACTTATTTTGAGGCGTAGTAGG 58.583 41.667 0.00 0.00 0.00 3.18
117 119 4.819630 TCAAAGACACTTATTTTGAGGCGT 59.180 37.500 0.00 0.00 36.28 5.68
154 156 1.282157 ACAACCAGCCCAATACTCCTC 59.718 52.381 0.00 0.00 0.00 3.71
155 157 1.372501 ACAACCAGCCCAATACTCCT 58.627 50.000 0.00 0.00 0.00 3.69
158 160 3.627237 CCCATTACAACCAGCCCAATACT 60.627 47.826 0.00 0.00 0.00 2.12
159 161 2.693074 CCCATTACAACCAGCCCAATAC 59.307 50.000 0.00 0.00 0.00 1.89
160 162 2.358721 CCCCATTACAACCAGCCCAATA 60.359 50.000 0.00 0.00 0.00 1.90
161 163 1.622173 CCCCATTACAACCAGCCCAAT 60.622 52.381 0.00 0.00 0.00 3.16
162 164 0.252012 CCCCATTACAACCAGCCCAA 60.252 55.000 0.00 0.00 0.00 4.12
164 166 0.395724 CTCCCCATTACAACCAGCCC 60.396 60.000 0.00 0.00 0.00 5.19
195 197 9.247861 TCATACACTAGTATCATATGCATGACT 57.752 33.333 10.16 7.28 43.89 3.41
220 224 4.161102 ACCAGCCTTAGGGATGTAGTATC 58.839 47.826 8.46 0.00 46.66 2.24
228 232 1.668826 TTGTGACCAGCCTTAGGGAT 58.331 50.000 0.00 0.00 33.58 3.85
230 234 1.683011 CCATTGTGACCAGCCTTAGGG 60.683 57.143 0.00 0.00 0.00 3.53
255 259 6.145696 GTGTGTGTGATGTTACTCCTAACTTC 59.854 42.308 0.00 0.00 37.46 3.01
258 262 5.539048 AGTGTGTGTGATGTTACTCCTAAC 58.461 41.667 0.00 0.00 33.92 2.34
272 276 5.273170 CAAAGTTGTATTGGAGTGTGTGTG 58.727 41.667 0.00 0.00 0.00 3.82
273 277 4.202010 GCAAAGTTGTATTGGAGTGTGTGT 60.202 41.667 0.00 0.00 0.00 3.72
303 307 6.995091 ACCTCTCTCTTCATTAAATATGTGCC 59.005 38.462 0.00 0.00 0.00 5.01
420 424 7.111136 TCCATAGTGGGTAGGAACATCTATA 57.889 40.000 0.00 0.00 38.32 1.31
468 472 8.857216 CAAGAACATAAGGTAGTAACTTACACG 58.143 37.037 9.87 4.86 33.63 4.49
482 486 3.763360 TCACAATGGGCAAGAACATAAGG 59.237 43.478 0.00 0.00 0.00 2.69
508 512 9.535170 AGTACTACATGATACTATGCATTAGGT 57.465 33.333 3.54 4.70 29.70 3.08
535 552 9.356433 CTTTGTGTCATGCATGTCAATAAATAA 57.644 29.630 24.86 12.24 0.00 1.40
545 562 3.148412 TGCTACTTTGTGTCATGCATGT 58.852 40.909 25.43 6.98 0.00 3.21
561 578 9.314321 ACCGTATTATATTGAATGCTATGCTAC 57.686 33.333 0.00 0.00 0.00 3.58
593 610 9.440761 AAGAAAGAGAGGGTGTAGTATCATATT 57.559 33.333 0.00 0.00 0.00 1.28
628 645 5.919141 GGCAATTTTGATGAGATGTCATAGC 59.081 40.000 5.15 2.26 43.92 2.97
634 651 6.660521 TCAACTAGGCAATTTTGATGAGATGT 59.339 34.615 0.00 0.00 0.00 3.06
637 654 6.003326 TGTCAACTAGGCAATTTTGATGAGA 58.997 36.000 0.00 0.00 30.96 3.27
650 667 1.755179 ACCATGCATGTCAACTAGGC 58.245 50.000 24.58 0.00 0.00 3.93
651 668 4.142609 AGTACCATGCATGTCAACTAGG 57.857 45.455 24.58 9.74 0.00 3.02
668 685 7.542477 TCGTAATGGTAGTACGATAGCTAGTAC 59.458 40.741 13.00 13.00 46.13 2.73
679 696 2.542411 GGCTGGTCGTAATGGTAGTACG 60.542 54.545 2.81 2.81 44.45 3.67
680 697 2.692041 AGGCTGGTCGTAATGGTAGTAC 59.308 50.000 0.00 0.00 0.00 2.73
706 723 6.183360 CGCAATTTATAGCAGTGTGTGTCTAA 60.183 38.462 0.00 0.00 0.00 2.10
741 761 1.152963 CCAATACCAGAAGCCGGGG 60.153 63.158 2.18 0.00 31.45 5.73
742 762 1.823899 GCCAATACCAGAAGCCGGG 60.824 63.158 2.18 0.00 0.00 5.73
744 764 0.676466 TGTGCCAATACCAGAAGCCG 60.676 55.000 0.00 0.00 0.00 5.52
745 765 1.406539 CATGTGCCAATACCAGAAGCC 59.593 52.381 0.00 0.00 0.00 4.35
746 766 2.368439 TCATGTGCCAATACCAGAAGC 58.632 47.619 0.00 0.00 0.00 3.86
748 768 4.858850 AGAATCATGTGCCAATACCAGAA 58.141 39.130 0.00 0.00 0.00 3.02
749 769 4.508551 AGAATCATGTGCCAATACCAGA 57.491 40.909 0.00 0.00 0.00 3.86
750 770 4.641541 TGAAGAATCATGTGCCAATACCAG 59.358 41.667 0.00 0.00 0.00 4.00
751 771 4.598022 TGAAGAATCATGTGCCAATACCA 58.402 39.130 0.00 0.00 0.00 3.25
752 772 5.300034 TGATGAAGAATCATGTGCCAATACC 59.700 40.000 0.00 0.00 46.30 2.73
753 773 6.204359 GTGATGAAGAATCATGTGCCAATAC 58.796 40.000 0.00 0.00 46.90 1.89
754 774 5.300034 GGTGATGAAGAATCATGTGCCAATA 59.700 40.000 0.00 0.00 46.90 1.90
755 775 4.098960 GGTGATGAAGAATCATGTGCCAAT 59.901 41.667 0.00 0.00 46.90 3.16
756 776 3.444742 GGTGATGAAGAATCATGTGCCAA 59.555 43.478 0.00 0.00 46.90 4.52
757 777 3.018856 GGTGATGAAGAATCATGTGCCA 58.981 45.455 0.00 0.00 46.90 4.92
759 779 3.018856 TGGGTGATGAAGAATCATGTGC 58.981 45.455 0.00 0.00 46.90 4.57
760 780 4.267536 AGTGGGTGATGAAGAATCATGTG 58.732 43.478 0.00 0.00 46.90 3.21
762 782 4.575236 CAGAGTGGGTGATGAAGAATCATG 59.425 45.833 0.00 0.00 46.90 3.07
763 783 4.778579 CAGAGTGGGTGATGAAGAATCAT 58.221 43.478 0.00 0.00 46.90 2.45
764 784 3.620719 GCAGAGTGGGTGATGAAGAATCA 60.621 47.826 0.00 0.00 43.24 2.57
765 785 2.941720 GCAGAGTGGGTGATGAAGAATC 59.058 50.000 0.00 0.00 35.67 2.52
766 786 2.306805 TGCAGAGTGGGTGATGAAGAAT 59.693 45.455 0.00 0.00 0.00 2.40
767 787 1.699083 TGCAGAGTGGGTGATGAAGAA 59.301 47.619 0.00 0.00 0.00 2.52
769 789 1.446907 GTGCAGAGTGGGTGATGAAG 58.553 55.000 0.00 0.00 0.00 3.02
770 790 0.320683 CGTGCAGAGTGGGTGATGAA 60.321 55.000 0.00 0.00 0.00 2.57
772 792 1.004560 ACGTGCAGAGTGGGTGATG 60.005 57.895 0.00 0.00 0.00 3.07
773 793 1.004560 CACGTGCAGAGTGGGTGAT 60.005 57.895 0.82 0.00 36.06 3.06
774 794 2.131067 TCACGTGCAGAGTGGGTGA 61.131 57.895 11.67 8.82 39.86 4.02
775 795 1.956170 GTCACGTGCAGAGTGGGTG 60.956 63.158 11.67 6.92 39.86 4.61
776 796 2.421739 GTCACGTGCAGAGTGGGT 59.578 61.111 11.67 0.00 39.86 4.51
777 797 2.357517 GGTCACGTGCAGAGTGGG 60.358 66.667 11.67 0.00 39.86 4.61
779 799 1.929169 CATATGGTCACGTGCAGAGTG 59.071 52.381 11.67 14.25 40.71 3.51
781 801 0.933097 GCATATGGTCACGTGCAGAG 59.067 55.000 11.67 0.00 37.52 3.35
782 802 0.536724 AGCATATGGTCACGTGCAGA 59.463 50.000 11.67 1.28 39.94 4.26
783 803 0.654160 CAGCATATGGTCACGTGCAG 59.346 55.000 11.67 0.00 39.94 4.41
784 804 0.248843 TCAGCATATGGTCACGTGCA 59.751 50.000 11.67 4.24 39.94 4.57
785 805 0.652592 GTCAGCATATGGTCACGTGC 59.347 55.000 11.67 6.03 37.84 5.34
786 806 2.299993 AGTCAGCATATGGTCACGTG 57.700 50.000 9.94 9.94 0.00 4.49
788 808 3.170791 AGAAGTCAGCATATGGTCACG 57.829 47.619 3.96 0.00 0.00 4.35
789 809 4.141937 TGGTAGAAGTCAGCATATGGTCAC 60.142 45.833 3.96 1.91 0.00 3.67
791 811 4.672587 TGGTAGAAGTCAGCATATGGTC 57.327 45.455 3.96 0.00 0.00 4.02
794 814 7.712639 ACATAGTTTGGTAGAAGTCAGCATATG 59.287 37.037 0.00 0.00 0.00 1.78
795 815 7.796054 ACATAGTTTGGTAGAAGTCAGCATAT 58.204 34.615 0.00 0.00 0.00 1.78
796 816 7.182817 ACATAGTTTGGTAGAAGTCAGCATA 57.817 36.000 0.00 0.00 0.00 3.14
797 817 6.054860 ACATAGTTTGGTAGAAGTCAGCAT 57.945 37.500 0.00 0.00 0.00 3.79
798 818 5.483685 ACATAGTTTGGTAGAAGTCAGCA 57.516 39.130 0.00 0.00 0.00 4.41
812 853 6.637657 CGGAGGGAGTAACTAAACATAGTTT 58.362 40.000 6.56 0.51 40.43 2.66
819 860 1.829849 AGGCGGAGGGAGTAACTAAAC 59.170 52.381 0.00 0.00 0.00 2.01
824 865 0.611714 TTTGAGGCGGAGGGAGTAAC 59.388 55.000 0.00 0.00 0.00 2.50
830 4348 2.785868 CTCATTTTGAGGCGGAGGG 58.214 57.895 0.00 0.00 40.71 4.30
854 4372 8.244113 GCTGGTGCTAAATTAAAAGACACTTAT 58.756 33.333 0.00 0.00 36.03 1.73
855 4373 7.572353 CGCTGGTGCTAAATTAAAAGACACTTA 60.572 37.037 0.00 0.00 36.97 2.24
856 4374 6.447162 GCTGGTGCTAAATTAAAAGACACTT 58.553 36.000 0.00 0.00 36.03 3.16
857 4375 5.334879 CGCTGGTGCTAAATTAAAAGACACT 60.335 40.000 0.00 0.00 36.97 3.55
858 4376 4.851558 CGCTGGTGCTAAATTAAAAGACAC 59.148 41.667 0.00 0.00 36.97 3.67
859 4377 4.517453 ACGCTGGTGCTAAATTAAAAGACA 59.483 37.500 0.00 0.00 36.97 3.41
860 4378 5.043189 ACGCTGGTGCTAAATTAAAAGAC 57.957 39.130 0.00 0.00 36.97 3.01
861 4379 5.699097 AACGCTGGTGCTAAATTAAAAGA 57.301 34.783 0.00 0.00 36.97 2.52
862 4380 6.837992 TCTAACGCTGGTGCTAAATTAAAAG 58.162 36.000 0.00 0.00 36.97 2.27
863 4381 6.804770 TCTAACGCTGGTGCTAAATTAAAA 57.195 33.333 0.00 0.00 36.97 1.52
864 4382 6.995511 ATCTAACGCTGGTGCTAAATTAAA 57.004 33.333 0.00 0.00 36.97 1.52
865 4383 6.183360 CCAATCTAACGCTGGTGCTAAATTAA 60.183 38.462 0.00 0.00 36.97 1.40
866 4384 5.295787 CCAATCTAACGCTGGTGCTAAATTA 59.704 40.000 0.00 0.00 36.97 1.40
867 4385 4.096382 CCAATCTAACGCTGGTGCTAAATT 59.904 41.667 0.00 0.00 36.97 1.82
868 4386 3.627577 CCAATCTAACGCTGGTGCTAAAT 59.372 43.478 0.00 0.00 36.97 1.40
874 4392 0.999406 CGTCCAATCTAACGCTGGTG 59.001 55.000 0.00 0.00 31.48 4.17
881 4399 0.370273 CAGCGTGCGTCCAATCTAAC 59.630 55.000 0.00 0.00 0.00 2.34
897 4415 5.845985 TGATCGTAGCAATTTATAGCAGC 57.154 39.130 0.00 0.00 0.00 5.25
923 4441 5.887598 TCCTGGATCTTAATTGGTGTGAATG 59.112 40.000 0.00 0.00 0.00 2.67
925 4443 5.250543 TCTCCTGGATCTTAATTGGTGTGAA 59.749 40.000 0.00 0.00 0.00 3.18
945 4463 2.631418 TCGTGAGTGAATTCGTCTCC 57.369 50.000 20.25 13.69 0.00 3.71
959 4501 0.953471 CGGCATTCTGGGTTTCGTGA 60.953 55.000 0.00 0.00 0.00 4.35
1260 4802 1.592669 ATGCTCTCGTACGCCATGC 60.593 57.895 11.24 12.22 0.00 4.06
1297 4839 2.885113 CTGATCTGACCGGCGTCA 59.115 61.111 6.01 9.00 46.91 4.35
1348 4890 1.984570 CTCTCACCAGAAGGCGGGA 60.985 63.158 0.00 0.00 39.06 5.14
1391 4933 4.533919 AAGATAGAGCGGATGATGAAGG 57.466 45.455 0.00 0.00 0.00 3.46
1410 4952 3.196039 TGGGATCCATGCATGTCAAAAAG 59.804 43.478 24.58 8.13 0.00 2.27
1520 6317 4.785453 GACGCCCAGGCCTTCCAG 62.785 72.222 0.00 0.00 37.98 3.86
1684 6481 4.640690 AGGCCCTCCACCTCGTGT 62.641 66.667 0.00 0.00 28.76 4.49
1815 6622 8.629158 ACTTAAACAAATTCAATACACTGCTGA 58.371 29.630 0.00 0.00 0.00 4.26
1817 6624 7.867403 CCACTTAAACAAATTCAATACACTGCT 59.133 33.333 0.00 0.00 0.00 4.24
1826 6636 6.419413 GCATCGTTCCACTTAAACAAATTCAA 59.581 34.615 0.00 0.00 0.00 2.69
1833 6643 3.472652 ACAGCATCGTTCCACTTAAACA 58.527 40.909 0.00 0.00 0.00 2.83
1834 6644 5.600908 TTACAGCATCGTTCCACTTAAAC 57.399 39.130 0.00 0.00 0.00 2.01
1836 6646 4.634004 CCATTACAGCATCGTTCCACTTAA 59.366 41.667 0.00 0.00 0.00 1.85
1837 6647 4.081365 TCCATTACAGCATCGTTCCACTTA 60.081 41.667 0.00 0.00 0.00 2.24
1838 6648 3.009723 CCATTACAGCATCGTTCCACTT 58.990 45.455 0.00 0.00 0.00 3.16
1839 6649 2.236146 TCCATTACAGCATCGTTCCACT 59.764 45.455 0.00 0.00 0.00 4.00
1840 6650 2.627945 TCCATTACAGCATCGTTCCAC 58.372 47.619 0.00 0.00 0.00 4.02
1841 6651 3.118445 TCATCCATTACAGCATCGTTCCA 60.118 43.478 0.00 0.00 0.00 3.53
1842 6652 3.466836 TCATCCATTACAGCATCGTTCC 58.533 45.455 0.00 0.00 0.00 3.62
1843 6653 4.260784 GGTTCATCCATTACAGCATCGTTC 60.261 45.833 0.00 0.00 35.97 3.95
1844 6654 3.627577 GGTTCATCCATTACAGCATCGTT 59.372 43.478 0.00 0.00 35.97 3.85
1845 6655 3.206150 GGTTCATCCATTACAGCATCGT 58.794 45.455 0.00 0.00 35.97 3.73
1846 6656 2.221749 CGGTTCATCCATTACAGCATCG 59.778 50.000 0.00 0.00 35.57 3.84
1847 6657 3.206150 ACGGTTCATCCATTACAGCATC 58.794 45.455 0.00 0.00 35.57 3.91
1848 6658 3.118261 AGACGGTTCATCCATTACAGCAT 60.118 43.478 0.00 0.00 35.57 3.79
1849 6659 2.236146 AGACGGTTCATCCATTACAGCA 59.764 45.455 0.00 0.00 35.57 4.41
1850 6660 2.609459 CAGACGGTTCATCCATTACAGC 59.391 50.000 0.00 0.00 35.57 4.40
1851 6661 3.198068 CCAGACGGTTCATCCATTACAG 58.802 50.000 0.00 0.00 35.57 2.74
1852 6662 2.679639 GCCAGACGGTTCATCCATTACA 60.680 50.000 0.00 0.00 35.57 2.41
1853 6663 1.940613 GCCAGACGGTTCATCCATTAC 59.059 52.381 0.00 0.00 35.57 1.89
1854 6664 1.837439 AGCCAGACGGTTCATCCATTA 59.163 47.619 0.00 0.00 35.57 1.90
1855 6665 0.620556 AGCCAGACGGTTCATCCATT 59.379 50.000 0.00 0.00 35.57 3.16
1856 6666 0.107508 CAGCCAGACGGTTCATCCAT 60.108 55.000 0.00 0.00 35.57 3.41
1857 6667 1.296392 CAGCCAGACGGTTCATCCA 59.704 57.895 0.00 0.00 35.57 3.41
1858 6668 2.109126 GCAGCCAGACGGTTCATCC 61.109 63.158 0.00 0.00 33.28 3.51
1859 6669 1.364626 CTGCAGCCAGACGGTTCATC 61.365 60.000 0.00 0.00 41.77 2.92
1860 6670 1.376424 CTGCAGCCAGACGGTTCAT 60.376 57.895 0.00 0.00 41.77 2.57
1861 6671 2.031012 CTGCAGCCAGACGGTTCA 59.969 61.111 0.00 0.00 41.77 3.18
1862 6672 2.743928 CCTGCAGCCAGACGGTTC 60.744 66.667 8.66 0.00 41.77 3.62
2046 6856 2.277756 GCGCAGTACTCGTACGGG 60.278 66.667 15.01 15.01 40.80 5.28
2049 6859 0.525029 GGAAGGCGCAGTACTCGTAC 60.525 60.000 10.83 0.00 36.35 3.67
2140 6956 1.347050 AGTTCATCACACAGCTGCTCT 59.653 47.619 15.27 0.00 0.00 4.09
2143 6959 3.360249 AAAAGTTCATCACACAGCTGC 57.640 42.857 15.27 0.00 0.00 5.25
2173 6989 5.003804 TGAGGCAAATCTTTTACCTCTGTC 58.996 41.667 16.41 0.00 45.86 3.51
2368 7186 1.000955 GATTAGGGGCATCGATGACGT 59.999 52.381 29.20 21.54 36.40 4.34
2425 7243 1.890894 CGGTGAGGGTTGAGTCGAT 59.109 57.895 0.00 0.00 0.00 3.59
2745 7580 1.845664 TGGTGCTGGGGCTTCTGTA 60.846 57.895 0.00 0.00 39.59 2.74
2934 7774 2.383527 CCTTGAAGGCGTCGACAGC 61.384 63.158 17.16 18.55 0.00 4.40
3083 7928 1.614525 TGCTGTGGGATCTGGCTCT 60.615 57.895 0.00 0.00 0.00 4.09
3119 7964 2.236223 CTGTGCATCGAGGCCTCTGT 62.236 60.000 29.73 15.56 0.00 3.41


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

AutoCloner maintained by Alex Coulton.