Multiple sequence alignment - TraesCS6B01G188700

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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 TraesCS6B01G188700 chr6B 100.000 3800 0 0 1 3800 217175671 217171872 0.000000e+00 7018.0
1 TraesCS6B01G188700 chr6B 88.750 80 9 0 374 453 217175208 217175129 8.690000e-17 99.0
2 TraesCS6B01G188700 chr6B 88.750 80 9 0 464 543 217175298 217175219 8.690000e-17 99.0
3 TraesCS6B01G188700 chr6D 94.150 2513 87 26 842 3320 123164899 123162413 0.000000e+00 3771.0
4 TraesCS6B01G188700 chr6D 91.018 167 14 1 3591 3756 123162259 123162093 1.370000e-54 224.0
5 TraesCS6B01G188700 chr6D 93.496 123 5 2 3317 3438 123162371 123162251 3.020000e-41 180.0
6 TraesCS6B01G188700 chr6D 97.778 45 1 0 3756 3800 123162059 123162015 1.130000e-10 78.7
7 TraesCS6B01G188700 chr6A 93.969 2454 96 22 894 3320 157958856 157961284 0.000000e+00 3664.0
8 TraesCS6B01G188700 chr6A 92.353 170 12 1 3588 3756 157961435 157961604 1.360000e-59 241.0
9 TraesCS6B01G188700 chr6A 94.309 123 4 2 3317 3438 157961326 157961446 6.480000e-43 185.0
10 TraesCS6B01G188700 chr6A 97.826 46 1 0 3755 3800 157961640 157961685 3.150000e-11 80.5
11 TraesCS6B01G188700 chr3A 86.889 839 63 21 1 817 739945008 739945821 0.000000e+00 896.0
12 TraesCS6B01G188700 chr3A 91.875 160 6 3 3440 3595 32466919 32466763 2.300000e-52 217.0
13 TraesCS6B01G188700 chr3A 89.552 67 7 0 374 440 739945485 739945551 6.760000e-13 86.1
14 TraesCS6B01G188700 chr2A 100.000 156 0 0 3439 3594 498099121 498099276 4.800000e-74 289.0
15 TraesCS6B01G188700 chr4B 98.693 153 2 0 3440 3592 31525827 31525675 4.840000e-69 272.0
16 TraesCS6B01G188700 chr7B 97.945 146 3 0 3444 3589 231703854 231703709 1.750000e-63 254.0
17 TraesCS6B01G188700 chr7B 99.213 127 0 1 3440 3566 312342132 312342007 1.060000e-55 228.0
18 TraesCS6B01G188700 chr5B 97.945 146 2 1 3444 3589 124768841 124768697 6.300000e-63 252.0
19 TraesCS6B01G188700 chr5B 95.918 147 3 3 3440 3585 682935572 682935428 6.350000e-58 235.0
20 TraesCS6B01G188700 chrUn 93.506 154 7 2 3439 3592 64148602 64148752 3.820000e-55 226.0
21 TraesCS6B01G188700 chr4D 92.857 154 8 2 3439 3592 31546052 31546202 1.780000e-53 220.0
22 TraesCS6B01G188700 chr1B 100.000 50 0 0 3543 3592 584150520 584150471 4.040000e-15 93.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G188700 chr6B 217171872 217175671 3799 True 2405.333333 7018 92.50000 1 3800 3 chr6B.!!$R1 3799
1 TraesCS6B01G188700 chr6D 123162015 123164899 2884 True 1063.425000 3771 94.11050 842 3800 4 chr6D.!!$R1 2958
2 TraesCS6B01G188700 chr6A 157958856 157961685 2829 False 1042.625000 3664 94.61425 894 3800 4 chr6A.!!$F1 2906
3 TraesCS6B01G188700 chr3A 739945008 739945821 813 False 491.050000 896 88.22050 1 817 2 chr3A.!!$F1 816

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
118 126 0.031857 CCGATGCAAAGTTGTTGCCA 59.968 50.000 8.47 0.0 44.32 4.92 F
180 190 0.038892 TCGTCGGTGGAGTAAAGCAC 60.039 55.000 0.00 0.0 0.00 4.40 F
564 585 0.244450 TATCGAGTTCACCGGCGTTT 59.756 50.000 6.01 0.0 0.00 3.60 F
1458 1497 0.249120 ACGCCGACATGATCCAGAAA 59.751 50.000 0.00 0.0 0.00 2.52 F
2341 2380 1.135083 GTAGCGCTCTTGAGGTGCTTA 60.135 52.381 16.34 0.0 46.53 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1642 1681 0.253044 GCTGACTGCTCCACCCAATA 59.747 55.0 0.00 0.0 38.95 1.90 R
1848 1887 0.741915 TTGCAAACCGGAACAAGTCC 59.258 50.0 9.46 0.0 43.90 3.85 R
2307 2346 0.096976 CGCTACCAACTTGATTGCCG 59.903 55.0 0.00 0.0 36.93 5.69 R
2783 2822 0.033504 AGTCTACAACACTGGTGCCG 59.966 55.0 0.00 0.0 0.00 5.69 R
3409 3515 0.038166 CTGCCTGCTTCACCCCTTTA 59.962 55.0 0.00 0.0 0.00 1.85 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.743928 CTGGGGCTCGACTGTTGC 60.744 66.667 0.00 0.00 0.00 4.17
67 68 0.609957 CTGGTGCTCCAAAGGCATCA 60.610 55.000 9.14 1.76 46.73 3.07
68 69 0.040058 TGGTGCTCCAAAGGCATCAT 59.960 50.000 4.68 0.00 44.50 2.45
69 70 0.458669 GGTGCTCCAAAGGCATCATG 59.541 55.000 0.00 0.00 41.86 3.07
70 71 0.458669 GTGCTCCAAAGGCATCATGG 59.541 55.000 0.00 0.00 41.86 3.66
85 86 3.545124 ATGGCGGTGCTGGAAACGA 62.545 57.895 0.00 0.00 0.00 3.85
98 99 1.874345 GAAACGAGGAGGAGGACGCA 61.874 60.000 0.00 0.00 0.00 5.24
100 101 3.827898 CGAGGAGGAGGACGCACC 61.828 72.222 0.00 0.00 39.35 5.01
102 103 4.361971 AGGAGGAGGACGCACCGA 62.362 66.667 0.00 0.00 44.74 4.69
118 126 0.031857 CCGATGCAAAGTTGTTGCCA 59.968 50.000 8.47 0.00 44.32 4.92
142 152 4.961511 TCGGTGGTGCGCAGACAC 62.962 66.667 27.93 27.93 39.94 3.67
152 162 4.152625 GCAGACACGCGTCATGGC 62.153 66.667 9.86 7.86 45.23 4.40
171 181 1.873270 CTGTGGACATCGTCGGTGGA 61.873 60.000 10.81 0.00 32.65 4.02
180 190 0.038892 TCGTCGGTGGAGTAAAGCAC 60.039 55.000 0.00 0.00 0.00 4.40
203 213 2.677524 GGGTGCTGCAATGGAGCA 60.678 61.111 25.19 25.19 44.22 4.26
212 222 1.815003 CAATGGAGCATCGTCGGCA 60.815 57.895 0.00 0.00 34.37 5.69
216 226 2.583593 GAGCATCGTCGGCACTCC 60.584 66.667 0.00 0.00 0.00 3.85
228 238 1.148157 GGCACTCCGACGACATCATG 61.148 60.000 0.00 0.00 0.00 3.07
233 243 2.528743 CCGACGACATCATGCTGCC 61.529 63.158 0.00 0.00 0.00 4.85
237 247 0.393402 ACGACATCATGCTGCCACAT 60.393 50.000 0.00 0.00 0.00 3.21
317 338 2.401766 CCGATGGCACTGCAACTCC 61.402 63.158 2.82 0.00 0.00 3.85
330 351 1.021202 CAACTCCGGTCAAGTTTGCA 58.979 50.000 0.00 0.00 34.79 4.08
340 361 1.823470 AAGTTTGCACGGCTGCTCA 60.823 52.632 0.00 0.00 44.57 4.26
343 364 4.560743 TTGCACGGCTGCTCACCA 62.561 61.111 0.00 0.00 44.57 4.17
344 365 4.994471 TGCACGGCTGCTCACCAG 62.994 66.667 0.00 0.00 44.57 4.00
357 378 2.289320 GCTCACCAGAGTCACTTGATGT 60.289 50.000 0.00 0.00 44.00 3.06
412 433 3.198489 GCTACGAGCTTGCCAGGC 61.198 66.667 3.66 3.66 38.45 4.85
443 464 1.126296 GCCAAAGTTACGTCGAAGCTC 59.874 52.381 0.00 0.00 0.00 4.09
444 465 1.725164 CCAAAGTTACGTCGAAGCTCC 59.275 52.381 0.00 0.00 0.00 4.70
523 544 0.517316 CAGTTGCTTGCCGGAGTTAC 59.483 55.000 5.05 0.00 0.00 2.50
531 552 0.664166 TGCCGGAGTTACGTCGAAAC 60.664 55.000 5.05 0.00 0.00 2.78
532 553 0.387750 GCCGGAGTTACGTCGAAACT 60.388 55.000 5.05 1.87 39.84 2.66
533 554 1.334054 CCGGAGTTACGTCGAAACTG 58.666 55.000 6.92 0.00 37.31 3.16
534 555 1.335324 CCGGAGTTACGTCGAAACTGT 60.335 52.381 6.92 0.00 37.31 3.55
535 556 1.712350 CGGAGTTACGTCGAAACTGTG 59.288 52.381 6.92 0.00 37.31 3.66
536 557 2.735823 GGAGTTACGTCGAAACTGTGT 58.264 47.619 6.92 0.00 37.31 3.72
537 558 3.118542 GGAGTTACGTCGAAACTGTGTT 58.881 45.455 6.92 0.00 37.31 3.32
538 559 3.060740 GGAGTTACGTCGAAACTGTGTTG 60.061 47.826 6.92 0.00 37.31 3.33
539 560 2.283351 AGTTACGTCGAAACTGTGTTGC 59.717 45.455 0.00 0.00 35.87 4.17
540 561 1.923899 TACGTCGAAACTGTGTTGCA 58.076 45.000 0.00 0.00 0.00 4.08
551 572 1.596260 CTGTGTTGCAGCCATATCGAG 59.404 52.381 0.00 0.00 38.52 4.04
553 574 2.009774 GTGTTGCAGCCATATCGAGTT 58.990 47.619 0.00 0.00 0.00 3.01
554 575 2.030946 GTGTTGCAGCCATATCGAGTTC 59.969 50.000 0.00 0.00 0.00 3.01
555 576 2.279741 GTTGCAGCCATATCGAGTTCA 58.720 47.619 0.00 0.00 0.00 3.18
556 577 1.939974 TGCAGCCATATCGAGTTCAC 58.060 50.000 0.00 0.00 0.00 3.18
557 578 1.221414 GCAGCCATATCGAGTTCACC 58.779 55.000 0.00 0.00 0.00 4.02
558 579 1.491670 CAGCCATATCGAGTTCACCG 58.508 55.000 0.00 0.00 0.00 4.94
559 580 0.389391 AGCCATATCGAGTTCACCGG 59.611 55.000 0.00 0.00 0.00 5.28
560 581 1.222115 GCCATATCGAGTTCACCGGC 61.222 60.000 0.00 0.00 0.00 6.13
561 582 0.939577 CCATATCGAGTTCACCGGCG 60.940 60.000 0.00 0.00 0.00 6.46
562 583 0.248907 CATATCGAGTTCACCGGCGT 60.249 55.000 6.01 0.00 0.00 5.68
563 584 0.458669 ATATCGAGTTCACCGGCGTT 59.541 50.000 6.01 0.00 0.00 4.84
564 585 0.244450 TATCGAGTTCACCGGCGTTT 59.756 50.000 6.01 0.00 0.00 3.60
565 586 1.012486 ATCGAGTTCACCGGCGTTTC 61.012 55.000 6.01 0.00 0.00 2.78
566 587 1.952133 CGAGTTCACCGGCGTTTCA 60.952 57.895 6.01 0.00 0.00 2.69
567 588 1.568025 GAGTTCACCGGCGTTTCAC 59.432 57.895 6.01 0.00 0.00 3.18
568 589 0.878961 GAGTTCACCGGCGTTTCACT 60.879 55.000 6.01 2.15 0.00 3.41
569 590 0.390124 AGTTCACCGGCGTTTCACTA 59.610 50.000 6.01 0.00 0.00 2.74
691 712 5.278687 CGTTTCTTTTGCAACTAAACGTC 57.721 39.130 27.82 9.08 44.32 4.34
795 816 6.200286 CGGCTTACGTTTGTATGTTATCATCT 59.800 38.462 0.00 0.00 37.93 2.90
799 820 8.780846 TTACGTTTGTATGTTATCATCTGGTT 57.219 30.769 0.00 0.00 35.70 3.67
813 834 6.048732 TCATCTGGTTGATTTGTAGCACTA 57.951 37.500 0.00 0.00 32.05 2.74
817 838 3.244735 TGGTTGATTTGTAGCACTAGCCA 60.245 43.478 0.00 0.00 43.56 4.75
818 839 3.947834 GGTTGATTTGTAGCACTAGCCAT 59.052 43.478 0.00 0.00 43.56 4.40
819 840 5.123227 GGTTGATTTGTAGCACTAGCCATA 58.877 41.667 0.00 0.00 43.56 2.74
820 841 5.588648 GGTTGATTTGTAGCACTAGCCATAA 59.411 40.000 0.00 0.00 43.56 1.90
821 842 6.094881 GGTTGATTTGTAGCACTAGCCATAAA 59.905 38.462 0.00 0.00 43.56 1.40
822 843 7.362574 GGTTGATTTGTAGCACTAGCCATAAAA 60.363 37.037 0.00 0.00 43.56 1.52
823 844 7.880160 TGATTTGTAGCACTAGCCATAAAAT 57.120 32.000 0.00 0.00 43.56 1.82
824 845 8.972458 TGATTTGTAGCACTAGCCATAAAATA 57.028 30.769 0.00 0.00 43.56 1.40
825 846 9.573166 TGATTTGTAGCACTAGCCATAAAATAT 57.427 29.630 0.00 0.00 43.56 1.28
830 851 9.627123 TGTAGCACTAGCCATAAAATATTTTCT 57.373 29.630 16.56 10.22 43.56 2.52
833 854 9.189156 AGCACTAGCCATAAAATATTTTCTTGA 57.811 29.630 16.56 0.23 43.56 3.02
834 855 9.971922 GCACTAGCCATAAAATATTTTCTTGAT 57.028 29.630 16.56 5.24 33.58 2.57
856 877 3.007635 AGCAAATAAGGACGGTACTTGC 58.992 45.455 15.90 10.98 38.33 4.01
953 983 1.134491 CCCTAACAGGCTAAACCCTCG 60.134 57.143 0.00 0.00 40.58 4.63
968 998 1.607148 CCCTCGTTTTCAGTTCCAACC 59.393 52.381 0.00 0.00 0.00 3.77
970 1000 1.607148 CTCGTTTTCAGTTCCAACCCC 59.393 52.381 0.00 0.00 0.00 4.95
972 1002 1.752788 CGTTTTCAGTTCCAACCCCCT 60.753 52.381 0.00 0.00 0.00 4.79
973 1003 1.961394 GTTTTCAGTTCCAACCCCCTC 59.039 52.381 0.00 0.00 0.00 4.30
1117 1156 3.205056 TGCCATATTCTTCCAACCATCCT 59.795 43.478 0.00 0.00 0.00 3.24
1311 1350 3.381333 CTCCATGCTCCAGCTCGCA 62.381 63.158 4.54 4.54 42.66 5.10
1458 1497 0.249120 ACGCCGACATGATCCAGAAA 59.751 50.000 0.00 0.00 0.00 2.52
1557 1596 5.240891 TCTAAGCTGGACAAGTTGAATGAG 58.759 41.667 10.54 1.11 0.00 2.90
1608 1647 1.884235 CACTGGTTGTGGAGAAGGTC 58.116 55.000 0.00 0.00 42.68 3.85
1642 1681 2.034558 CGACAGGCAATGGTGTTCTTTT 59.965 45.455 0.00 0.00 0.00 2.27
1764 1803 1.830477 GAGGTCCTGCAGAAGATGAGT 59.170 52.381 17.39 0.00 0.00 3.41
1770 1809 5.105310 GGTCCTGCAGAAGATGAGTAGTAAA 60.105 44.000 17.39 0.00 0.00 2.01
1780 1819 5.590818 AGATGAGTAGTAAAGAGGTTGGGA 58.409 41.667 0.00 0.00 0.00 4.37
1797 1836 4.228237 TGGGATGGATAAGGAGGTGTAT 57.772 45.455 0.00 0.00 0.00 2.29
1812 1851 7.275920 AGGAGGTGTATGTTATTCTCATTGAC 58.724 38.462 0.00 0.00 0.00 3.18
1848 1887 3.128242 GGAAGATGTTTGAGGATGCAGTG 59.872 47.826 0.00 0.00 0.00 3.66
1872 1911 1.291906 GTTCCGGTTTGCAATGGGG 59.708 57.895 0.00 1.59 0.00 4.96
1905 1944 1.672881 CCATCGGCTCAGGATTTTGTC 59.327 52.381 0.00 0.00 0.00 3.18
1962 2001 2.170187 GGATCTGAAGCTGGTGATGAGT 59.830 50.000 0.00 0.00 0.00 3.41
2205 2244 4.142182 CGTGTGGAAAAATCAGGGCATAAT 60.142 41.667 0.00 0.00 0.00 1.28
2230 2269 3.462021 GATCCACTTGTATGGTCTGCTC 58.538 50.000 0.00 0.00 40.95 4.26
2258 2297 1.604278 GAAGTATTCCCTTGGCGATGC 59.396 52.381 0.00 0.00 39.83 3.91
2277 2316 2.754552 TGCTGTTGATATGGCAGTTTCC 59.245 45.455 0.00 0.00 33.18 3.13
2307 2346 4.483311 CTGAAATGCTGGAAAGAAGAAGC 58.517 43.478 0.00 0.00 36.18 3.86
2316 2355 2.228822 GGAAAGAAGAAGCGGCAATCAA 59.771 45.455 1.45 0.00 0.00 2.57
2341 2380 1.135083 GTAGCGCTCTTGAGGTGCTTA 60.135 52.381 16.34 0.00 46.53 3.09
2424 2463 3.386402 TGTTGAAAAAGGATGTGGTTCCC 59.614 43.478 0.00 0.00 36.35 3.97
2535 2574 8.706322 AAAGTAATGGATTTCCGCCTTATATT 57.294 30.769 0.00 0.00 39.43 1.28
2536 2575 7.923414 AGTAATGGATTTCCGCCTTATATTC 57.077 36.000 0.00 0.00 39.43 1.75
2550 2589 7.401860 CGCCTTATATTCATCCATTTATCACG 58.598 38.462 0.00 0.00 0.00 4.35
2568 2607 2.988493 CACGCACATTTTGAAATCTGGG 59.012 45.455 7.06 7.06 34.82 4.45
2588 2627 2.745308 CCGTGGATGATGCCCTGGA 61.745 63.158 0.00 0.00 0.00 3.86
2597 2636 1.419012 TGATGCCCTGGATCTGCTAAG 59.581 52.381 0.00 0.00 0.00 2.18
2611 2650 2.900122 GCTAAGCGCAATGTCTTCAA 57.100 45.000 11.47 0.00 38.92 2.69
2618 2657 2.413371 GCGCAATGTCTTCAAAGGAGTC 60.413 50.000 0.30 0.00 0.00 3.36
2627 2666 3.593328 TCTTCAAAGGAGTCCCCATCAAT 59.407 43.478 5.25 0.00 37.41 2.57
2756 2795 6.680874 TGTTCTCGACCTCTTCTATAAGAC 57.319 41.667 0.00 0.00 36.80 3.01
2773 2812 8.191446 TCTATAAGACGAAGATTGAAGAACCTG 58.809 37.037 0.00 0.00 0.00 4.00
2780 2819 2.039480 AGATTGAAGAACCTGCAGCAGA 59.961 45.455 24.90 0.77 32.44 4.26
2781 2820 1.888215 TTGAAGAACCTGCAGCAGAG 58.112 50.000 24.90 15.80 32.44 3.35
2782 2821 0.035881 TGAAGAACCTGCAGCAGAGG 59.964 55.000 24.90 11.76 32.44 3.69
2783 2822 1.303155 AAGAACCTGCAGCAGAGGC 60.303 57.895 24.90 11.66 41.61 4.70
2829 2868 6.775088 TCTTATGTTGAATCGAATTGCTGAC 58.225 36.000 0.00 0.00 0.00 3.51
2843 2882 4.560136 TTGCTGACGCTTGTATTTCAAA 57.440 36.364 0.00 0.00 35.48 2.69
2861 2900 6.371595 TTCAAATGGCATTTTGTATTCCCT 57.628 33.333 22.26 0.00 37.73 4.20
2862 2901 6.371595 TCAAATGGCATTTTGTATTCCCTT 57.628 33.333 22.26 0.00 37.73 3.95
2924 2967 4.214310 TGGATGGCAGAAAACTTCTTTGA 58.786 39.130 0.00 0.00 38.11 2.69
2984 3028 2.795231 TTTTCCTCTCTGCCATGGAG 57.205 50.000 18.40 10.38 0.00 3.86
3038 3085 4.083431 GCTTCATGTAGCAATAGCCATCTG 60.083 45.833 18.39 0.00 43.56 2.90
3073 3120 9.241317 GTCAATTTAAATGATTAGCATCAGTGG 57.759 33.333 0.39 0.00 42.93 4.00
3134 3181 1.195448 GTGTTCAGCTTGATGGTCGTG 59.805 52.381 0.00 0.00 0.00 4.35
3144 3191 1.337728 TGATGGTCGTGCGAACTTGAT 60.338 47.619 11.02 0.00 32.08 2.57
3164 3211 7.819900 ACTTGATTTCTGTCATTCTGGTACTAC 59.180 37.037 0.00 0.00 0.00 2.73
3236 3296 6.013032 CCAATCTCTGTATGGGGATAATGACT 60.013 42.308 0.00 0.00 0.00 3.41
3237 3297 7.180946 CCAATCTCTGTATGGGGATAATGACTA 59.819 40.741 0.00 0.00 0.00 2.59
3263 3323 6.403527 GCATGCATGTTAGTGTATCACAAGAA 60.404 38.462 26.79 0.00 36.74 2.52
3264 3324 6.480524 TGCATGTTAGTGTATCACAAGAAC 57.519 37.500 0.00 4.63 36.74 3.01
3266 3326 5.411361 GCATGTTAGTGTATCACAAGAACCA 59.589 40.000 0.00 0.00 36.74 3.67
3267 3327 6.620733 GCATGTTAGTGTATCACAAGAACCAC 60.621 42.308 0.00 0.00 36.74 4.16
3272 3332 6.169557 AGTGTATCACAAGAACCACTAACA 57.830 37.500 2.80 0.00 37.15 2.41
3273 3333 6.588204 AGTGTATCACAAGAACCACTAACAA 58.412 36.000 2.80 0.00 37.15 2.83
3274 3334 7.224297 AGTGTATCACAAGAACCACTAACAAT 58.776 34.615 2.80 0.00 37.15 2.71
3275 3335 7.719633 AGTGTATCACAAGAACCACTAACAATT 59.280 33.333 2.80 0.00 37.15 2.32
3276 3336 8.015658 GTGTATCACAAGAACCACTAACAATTC 58.984 37.037 0.00 0.00 34.08 2.17
3277 3337 7.936847 TGTATCACAAGAACCACTAACAATTCT 59.063 33.333 0.00 0.00 32.78 2.40
3278 3338 6.861065 TCACAAGAACCACTAACAATTCTC 57.139 37.500 0.00 0.00 31.05 2.87
3279 3339 6.353323 TCACAAGAACCACTAACAATTCTCA 58.647 36.000 0.00 0.00 31.05 3.27
3280 3340 6.998074 TCACAAGAACCACTAACAATTCTCAT 59.002 34.615 0.00 0.00 31.05 2.90
3281 3341 7.041167 TCACAAGAACCACTAACAATTCTCATG 60.041 37.037 0.00 0.00 31.05 3.07
3282 3342 6.207417 ACAAGAACCACTAACAATTCTCATGG 59.793 38.462 0.00 0.00 31.05 3.66
3338 3443 7.394077 TGGTGTAACATCAGATTGATCAAATGT 59.606 33.333 13.09 14.16 39.98 2.71
3354 3459 1.512926 ATGTGCGTGTGAGGAGAAAC 58.487 50.000 0.00 0.00 0.00 2.78
3355 3460 0.176910 TGTGCGTGTGAGGAGAAACA 59.823 50.000 0.00 0.00 0.00 2.83
3356 3461 1.202639 TGTGCGTGTGAGGAGAAACAT 60.203 47.619 0.00 0.00 0.00 2.71
3357 3462 2.036604 TGTGCGTGTGAGGAGAAACATA 59.963 45.455 0.00 0.00 0.00 2.29
3358 3463 3.262420 GTGCGTGTGAGGAGAAACATAT 58.738 45.455 0.00 0.00 0.00 1.78
3359 3464 3.307242 GTGCGTGTGAGGAGAAACATATC 59.693 47.826 0.00 0.00 0.00 1.63
3360 3465 3.195610 TGCGTGTGAGGAGAAACATATCT 59.804 43.478 0.00 0.00 0.00 1.98
3409 3515 3.463045 AAAAATCTGGGCTGGCAGT 57.537 47.368 17.16 0.00 0.00 4.40
3417 3523 2.763902 GGCTGGCAGTAAAGGGGT 59.236 61.111 17.16 0.00 0.00 4.95
3444 3550 3.794737 CAGTGATGCTGCCCATAGT 57.205 52.632 0.00 0.00 38.52 2.12
3445 3551 2.048444 CAGTGATGCTGCCCATAGTT 57.952 50.000 0.00 0.00 38.52 2.24
3446 3552 2.372264 CAGTGATGCTGCCCATAGTTT 58.628 47.619 0.00 0.00 38.52 2.66
3447 3553 2.756760 CAGTGATGCTGCCCATAGTTTT 59.243 45.455 0.00 0.00 38.52 2.43
3448 3554 3.194116 CAGTGATGCTGCCCATAGTTTTT 59.806 43.478 0.00 0.00 38.52 1.94
3449 3555 4.398988 CAGTGATGCTGCCCATAGTTTTTA 59.601 41.667 0.00 0.00 38.52 1.52
3450 3556 5.016173 AGTGATGCTGCCCATAGTTTTTAA 58.984 37.500 0.00 0.00 33.29 1.52
3451 3557 5.126061 AGTGATGCTGCCCATAGTTTTTAAG 59.874 40.000 0.00 0.00 33.29 1.85
3452 3558 4.402155 TGATGCTGCCCATAGTTTTTAAGG 59.598 41.667 0.00 0.00 33.29 2.69
3453 3559 2.495669 TGCTGCCCATAGTTTTTAAGGC 59.504 45.455 0.00 0.00 40.87 4.35
3454 3560 2.479560 GCTGCCCATAGTTTTTAAGGCG 60.480 50.000 0.00 0.00 43.46 5.52
3455 3561 2.096248 TGCCCATAGTTTTTAAGGCGG 58.904 47.619 0.00 0.00 43.46 6.13
3456 3562 2.097036 GCCCATAGTTTTTAAGGCGGT 58.903 47.619 0.00 0.00 0.00 5.68
3457 3563 3.281158 GCCCATAGTTTTTAAGGCGGTA 58.719 45.455 0.00 0.00 0.00 4.02
3458 3564 3.695556 GCCCATAGTTTTTAAGGCGGTAA 59.304 43.478 0.00 0.00 0.00 2.85
3459 3565 4.201980 GCCCATAGTTTTTAAGGCGGTAAG 60.202 45.833 0.00 0.00 0.00 2.34
3460 3566 4.337274 CCCATAGTTTTTAAGGCGGTAAGG 59.663 45.833 0.00 0.00 0.00 2.69
3468 3574 2.894919 GGCGGTAAGGCGACCTAA 59.105 61.111 9.52 0.00 37.34 2.69
3469 3575 1.227176 GGCGGTAAGGCGACCTAAG 60.227 63.158 9.52 0.00 37.34 2.18
3470 3576 1.227176 GCGGTAAGGCGACCTAAGG 60.227 63.158 9.52 0.00 37.34 2.69
3471 3577 1.227176 CGGTAAGGCGACCTAAGGC 60.227 63.158 9.52 0.00 37.34 4.35
3472 3578 1.227176 GGTAAGGCGACCTAAGGCG 60.227 63.158 4.54 0.00 39.33 5.52
3473 3579 1.881709 GTAAGGCGACCTAAGGCGC 60.882 63.158 15.21 15.21 43.47 6.53
3474 3580 2.056223 TAAGGCGACCTAAGGCGCT 61.056 57.895 20.95 8.24 43.61 5.92
3475 3581 2.292794 TAAGGCGACCTAAGGCGCTG 62.293 60.000 20.95 0.00 43.61 5.18
3478 3584 4.530857 CGACCTAAGGCGCTGGGG 62.531 72.222 7.64 7.52 0.00 4.96
3479 3585 4.176752 GACCTAAGGCGCTGGGGG 62.177 72.222 7.64 7.91 0.00 5.40
3530 3636 1.981256 CCTAAGGCGGGCATATTTGT 58.019 50.000 3.78 0.00 0.00 2.83
3531 3637 3.134574 CCTAAGGCGGGCATATTTGTA 57.865 47.619 3.78 0.00 0.00 2.41
3532 3638 3.482436 CCTAAGGCGGGCATATTTGTAA 58.518 45.455 3.78 0.00 0.00 2.41
3533 3639 3.502211 CCTAAGGCGGGCATATTTGTAAG 59.498 47.826 3.78 0.00 0.00 2.34
3534 3640 1.981256 AGGCGGGCATATTTGTAAGG 58.019 50.000 3.78 0.00 0.00 2.69
3535 3641 0.313987 GGCGGGCATATTTGTAAGGC 59.686 55.000 0.00 0.00 0.00 4.35
3536 3642 0.040425 GCGGGCATATTTGTAAGGCG 60.040 55.000 0.00 0.00 0.00 5.52
3537 3643 0.040425 CGGGCATATTTGTAAGGCGC 60.040 55.000 0.00 0.00 0.00 6.53
3538 3644 1.318576 GGGCATATTTGTAAGGCGCT 58.681 50.000 7.64 0.00 34.95 5.92
3539 3645 1.001378 GGGCATATTTGTAAGGCGCTG 60.001 52.381 7.64 0.00 34.95 5.18
3540 3646 1.001378 GGCATATTTGTAAGGCGCTGG 60.001 52.381 7.64 0.00 0.00 4.85
3541 3647 1.001378 GCATATTTGTAAGGCGCTGGG 60.001 52.381 7.64 0.00 0.00 4.45
3542 3648 1.608590 CATATTTGTAAGGCGCTGGGG 59.391 52.381 7.64 0.00 0.00 4.96
3543 3649 0.106918 TATTTGTAAGGCGCTGGGGG 60.107 55.000 7.64 0.00 0.00 5.40
3572 3678 3.195698 GCCTAAGCGTCCAAGGCG 61.196 66.667 0.00 0.00 45.82 5.52
3573 3679 2.511600 CCTAAGCGTCCAAGGCGG 60.512 66.667 5.39 0.00 33.62 6.13
3574 3680 2.511600 CTAAGCGTCCAAGGCGGG 60.512 66.667 5.39 0.00 33.62 6.13
3575 3681 2.998480 TAAGCGTCCAAGGCGGGA 60.998 61.111 0.00 0.00 33.62 5.14
3592 3698 3.926821 GGGACGCCTTAAAAACAATGA 57.073 42.857 0.00 0.00 0.00 2.57
3593 3699 4.450082 GGGACGCCTTAAAAACAATGAT 57.550 40.909 0.00 0.00 0.00 2.45
3594 3700 4.173256 GGGACGCCTTAAAAACAATGATG 58.827 43.478 0.00 0.00 0.00 3.07
3595 3701 3.612423 GGACGCCTTAAAAACAATGATGC 59.388 43.478 0.00 0.00 0.00 3.91
3596 3702 4.485163 GACGCCTTAAAAACAATGATGCT 58.515 39.130 0.00 0.00 0.00 3.79
3597 3703 4.236935 ACGCCTTAAAAACAATGATGCTG 58.763 39.130 0.00 0.00 0.00 4.41
3598 3704 3.061161 CGCCTTAAAAACAATGATGCTGC 59.939 43.478 0.00 0.00 0.00 5.25
3599 3705 3.371898 GCCTTAAAAACAATGATGCTGCC 59.628 43.478 0.00 0.00 0.00 4.85
3600 3706 4.567971 CCTTAAAAACAATGATGCTGCCA 58.432 39.130 0.00 0.00 0.00 4.92
3606 3712 4.783621 ATGATGCTGCCACGCCGT 62.784 61.111 0.00 0.00 0.00 5.68
3632 3738 6.877855 ACTATGTTATGATCATCATGACTGCC 59.122 38.462 20.12 0.00 42.00 4.85
3656 3763 7.023575 CCATCTTTGGTGTCTTCTTTTAATCG 58.976 38.462 0.00 0.00 38.30 3.34
3698 3805 2.232452 ACAATCTAGTCGCTGTTCTGCT 59.768 45.455 0.00 0.00 0.00 4.24
3704 3811 4.749310 CGCTGTTCTGCTCCGGCT 62.749 66.667 0.00 0.00 39.59 5.52
3705 3812 2.817396 GCTGTTCTGCTCCGGCTC 60.817 66.667 0.00 0.00 39.59 4.70
3735 3842 3.030291 ACCTGGAACAACATTGCAGAAA 58.970 40.909 9.45 0.00 39.78 2.52
3756 3863 9.424319 CAGAAATACTAGTTAGCACTGAAAGAA 57.576 33.333 0.00 0.00 37.43 2.52
3760 3867 9.944376 AATACTAGTTAGCACTGAAAGAATTGA 57.056 29.630 0.00 0.00 37.43 2.57
3761 3868 7.897575 ACTAGTTAGCACTGAAAGAATTGAG 57.102 36.000 0.00 0.00 37.43 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.113514 TTGCAACAGTCGAGCCCCA 62.114 57.895 0.00 0.00 0.00 4.96
26 27 2.041153 CCAACCCCTTGCAACAGTC 58.959 57.895 0.00 0.00 0.00 3.51
31 32 1.382420 AGTTGCCAACCCCTTGCAA 60.382 52.632 3.45 0.00 0.00 4.08
34 35 1.457455 ACCAGTTGCCAACCCCTTG 60.457 57.895 3.45 0.00 0.00 3.61
57 58 1.140161 CACCGCCATGATGCCTTTG 59.860 57.895 0.00 0.00 0.00 2.77
58 59 2.713967 GCACCGCCATGATGCCTTT 61.714 57.895 0.00 0.00 26.83 3.11
59 60 3.142838 GCACCGCCATGATGCCTT 61.143 61.111 0.00 0.00 26.83 4.35
67 68 3.055719 CGTTTCCAGCACCGCCAT 61.056 61.111 0.00 0.00 0.00 4.40
68 69 4.243008 TCGTTTCCAGCACCGCCA 62.243 61.111 0.00 0.00 0.00 5.69
69 70 3.423154 CTCGTTTCCAGCACCGCC 61.423 66.667 0.00 0.00 0.00 6.13
70 71 3.423154 CCTCGTTTCCAGCACCGC 61.423 66.667 0.00 0.00 0.00 5.68
85 86 3.663815 ATCGGTGCGTCCTCCTCCT 62.664 63.158 0.00 0.00 0.00 3.69
98 99 0.031994 GGCAACAACTTTGCATCGGT 59.968 50.000 10.90 0.00 46.58 4.69
114 122 0.959867 CACCACCGATGACAATGGCA 60.960 55.000 0.00 0.00 35.49 4.92
118 126 2.398554 GCGCACCACCGATGACAAT 61.399 57.895 0.30 0.00 0.00 2.71
142 152 3.490759 GTCCACAGCCATGACGCG 61.491 66.667 3.53 3.53 0.00 6.01
148 158 1.153568 CGACGATGTCCACAGCCAT 60.154 57.895 0.00 0.00 0.00 4.40
149 159 2.261361 CGACGATGTCCACAGCCA 59.739 61.111 0.00 0.00 0.00 4.75
150 160 2.509336 CCGACGATGTCCACAGCC 60.509 66.667 0.00 0.00 0.00 4.85
151 161 2.094659 CACCGACGATGTCCACAGC 61.095 63.158 0.00 0.00 0.00 4.40
152 162 1.446099 CCACCGACGATGTCCACAG 60.446 63.158 0.00 0.00 0.00 3.66
171 181 2.358247 CCCGTGGCGTGCTTTACT 60.358 61.111 0.00 0.00 0.00 2.24
184 194 2.360350 CTCCATTGCAGCACCCGT 60.360 61.111 0.00 0.00 0.00 5.28
212 222 0.179127 CAGCATGATGTCGTCGGAGT 60.179 55.000 1.88 0.00 39.69 3.85
216 226 1.810853 TGGCAGCATGATGTCGTCG 60.811 57.895 11.45 0.00 39.69 5.12
233 243 2.351418 CCATTGTAGCACCACGTATGTG 59.649 50.000 8.18 8.18 46.00 3.21
237 247 1.404986 GCTCCATTGTAGCACCACGTA 60.405 52.381 0.00 0.00 39.83 3.57
248 258 2.514592 CCGGCGATGCTCCATTGT 60.515 61.111 9.30 0.00 0.00 2.71
260 270 4.368808 CACAACACGAAGCCGGCG 62.369 66.667 23.20 9.91 40.78 6.46
317 338 2.051345 GCCGTGCAAACTTGACCG 60.051 61.111 0.00 0.00 0.00 4.79
330 351 2.919856 ACTCTGGTGAGCAGCCGT 60.920 61.111 6.80 3.77 43.85 5.68
340 361 2.498167 GCAACATCAAGTGACTCTGGT 58.502 47.619 0.00 0.00 0.00 4.00
343 364 2.533266 ACGCAACATCAAGTGACTCT 57.467 45.000 0.00 0.00 0.00 3.24
344 365 2.908634 CAACGCAACATCAAGTGACTC 58.091 47.619 0.00 0.00 0.00 3.36
384 405 2.789203 CTCGTAGCAAAGCGCCGAC 61.789 63.158 2.29 0.00 44.04 4.79
385 406 2.506217 CTCGTAGCAAAGCGCCGA 60.506 61.111 2.29 2.64 44.04 5.54
420 441 2.661979 GCTTCGACGTAACTTTGGCAAG 60.662 50.000 0.00 0.00 35.92 4.01
421 442 1.262151 GCTTCGACGTAACTTTGGCAA 59.738 47.619 0.00 0.00 0.00 4.52
422 443 0.863144 GCTTCGACGTAACTTTGGCA 59.137 50.000 0.00 0.00 0.00 4.92
423 444 1.126296 GAGCTTCGACGTAACTTTGGC 59.874 52.381 0.00 0.00 0.00 4.52
424 445 1.725164 GGAGCTTCGACGTAACTTTGG 59.275 52.381 0.00 0.00 0.00 3.28
425 446 1.385743 CGGAGCTTCGACGTAACTTTG 59.614 52.381 9.41 0.00 0.00 2.77
426 447 1.000938 ACGGAGCTTCGACGTAACTTT 60.001 47.619 24.16 0.00 39.30 2.66
458 479 2.340999 GACGAGCTCGACGAAACTG 58.659 57.895 40.58 10.53 43.02 3.16
459 480 4.843101 GACGAGCTCGACGAAACT 57.157 55.556 40.58 18.13 43.02 2.66
523 544 3.420968 CTGCAACACAGTTTCGACG 57.579 52.632 0.00 0.00 41.86 5.12
532 553 1.066215 ACTCGATATGGCTGCAACACA 60.066 47.619 0.50 0.00 0.00 3.72
533 554 1.656652 ACTCGATATGGCTGCAACAC 58.343 50.000 0.50 0.00 0.00 3.32
534 555 2.279741 GAACTCGATATGGCTGCAACA 58.720 47.619 0.50 0.00 0.00 3.33
535 556 2.030946 GTGAACTCGATATGGCTGCAAC 59.969 50.000 0.50 0.00 0.00 4.17
536 557 2.279741 GTGAACTCGATATGGCTGCAA 58.720 47.619 0.50 0.00 0.00 4.08
537 558 1.473257 GGTGAACTCGATATGGCTGCA 60.473 52.381 0.50 0.00 0.00 4.41
538 559 1.221414 GGTGAACTCGATATGGCTGC 58.779 55.000 0.00 0.00 0.00 5.25
539 560 1.491670 CGGTGAACTCGATATGGCTG 58.508 55.000 0.00 0.00 0.00 4.85
540 561 0.389391 CCGGTGAACTCGATATGGCT 59.611 55.000 0.00 0.00 0.00 4.75
543 564 0.248907 ACGCCGGTGAACTCGATATG 60.249 55.000 24.59 0.00 0.00 1.78
544 565 0.458669 AACGCCGGTGAACTCGATAT 59.541 50.000 24.59 0.00 0.00 1.63
546 567 1.005394 AAACGCCGGTGAACTCGAT 60.005 52.632 24.59 0.00 0.00 3.59
547 568 1.662446 GAAACGCCGGTGAACTCGA 60.662 57.895 24.59 0.00 0.00 4.04
549 570 0.878961 AGTGAAACGCCGGTGAACTC 60.879 55.000 24.59 14.63 45.86 3.01
551 572 1.127951 CATAGTGAAACGCCGGTGAAC 59.872 52.381 24.59 13.71 45.86 3.18
553 574 0.604073 TCATAGTGAAACGCCGGTGA 59.396 50.000 24.59 0.09 45.86 4.02
554 575 0.999406 CTCATAGTGAAACGCCGGTG 59.001 55.000 14.93 14.93 45.86 4.94
555 576 0.739813 GCTCATAGTGAAACGCCGGT 60.740 55.000 1.90 0.00 45.86 5.28
556 577 1.429148 GGCTCATAGTGAAACGCCGG 61.429 60.000 0.00 0.00 45.86 6.13
557 578 1.752501 CGGCTCATAGTGAAACGCCG 61.753 60.000 14.00 14.00 46.82 6.46
558 579 0.459585 TCGGCTCATAGTGAAACGCC 60.460 55.000 0.00 0.00 45.86 5.68
559 580 0.645868 GTCGGCTCATAGTGAAACGC 59.354 55.000 0.00 0.00 45.86 4.84
560 581 1.278238 GGTCGGCTCATAGTGAAACG 58.722 55.000 0.00 0.00 45.86 3.60
561 582 1.278238 CGGTCGGCTCATAGTGAAAC 58.722 55.000 0.00 0.00 0.00 2.78
562 583 0.174845 CCGGTCGGCTCATAGTGAAA 59.825 55.000 0.00 0.00 0.00 2.69
563 584 1.813859 CCGGTCGGCTCATAGTGAA 59.186 57.895 0.00 0.00 0.00 3.18
564 585 3.521605 CCGGTCGGCTCATAGTGA 58.478 61.111 0.00 0.00 0.00 3.41
691 712 2.031516 CGCTGAGCCTCCACAACTG 61.032 63.158 0.00 0.00 0.00 3.16
764 785 2.355009 AAACGTAAGCCGCGTCGT 60.355 55.556 4.92 5.06 42.10 4.34
768 789 0.717224 ACATACAAACGTAAGCCGCG 59.283 50.000 0.00 0.00 45.62 6.46
771 792 7.345192 CAGATGATAACATACAAACGTAAGCC 58.655 38.462 0.00 0.00 37.67 4.35
795 816 3.244735 TGGCTAGTGCTACAAATCAACCA 60.245 43.478 0.00 0.00 39.59 3.67
799 820 7.880160 ATTTTATGGCTAGTGCTACAAATCA 57.120 32.000 0.00 0.00 39.59 2.57
823 844 8.836413 CCGTCCTTATTTGCTATCAAGAAAATA 58.164 33.333 0.00 0.00 38.92 1.40
824 845 7.339466 ACCGTCCTTATTTGCTATCAAGAAAAT 59.661 33.333 0.00 0.00 42.61 1.82
825 846 6.657541 ACCGTCCTTATTTGCTATCAAGAAAA 59.342 34.615 0.00 0.00 34.63 2.29
826 847 6.177610 ACCGTCCTTATTTGCTATCAAGAAA 58.822 36.000 0.00 0.00 33.12 2.52
827 848 5.741011 ACCGTCCTTATTTGCTATCAAGAA 58.259 37.500 0.00 0.00 33.12 2.52
828 849 5.353394 ACCGTCCTTATTTGCTATCAAGA 57.647 39.130 0.00 0.00 33.12 3.02
829 850 6.281405 AGTACCGTCCTTATTTGCTATCAAG 58.719 40.000 0.00 0.00 33.12 3.02
830 851 6.229936 AGTACCGTCCTTATTTGCTATCAA 57.770 37.500 0.00 0.00 0.00 2.57
831 852 5.864418 AGTACCGTCCTTATTTGCTATCA 57.136 39.130 0.00 0.00 0.00 2.15
832 853 5.050295 GCAAGTACCGTCCTTATTTGCTATC 60.050 44.000 4.08 0.00 38.48 2.08
833 854 4.814771 GCAAGTACCGTCCTTATTTGCTAT 59.185 41.667 4.08 0.00 38.48 2.97
834 855 4.186159 GCAAGTACCGTCCTTATTTGCTA 58.814 43.478 4.08 0.00 38.48 3.49
835 856 3.007635 GCAAGTACCGTCCTTATTTGCT 58.992 45.455 4.08 0.00 38.48 3.91
836 857 2.096980 GGCAAGTACCGTCCTTATTTGC 59.903 50.000 2.95 2.95 39.93 3.68
837 858 3.340034 TGGCAAGTACCGTCCTTATTTG 58.660 45.455 0.00 0.00 0.00 2.32
838 859 3.706600 TGGCAAGTACCGTCCTTATTT 57.293 42.857 0.00 0.00 0.00 1.40
839 860 3.706600 TTGGCAAGTACCGTCCTTATT 57.293 42.857 0.00 0.00 0.00 1.40
840 861 3.706600 TTTGGCAAGTACCGTCCTTAT 57.293 42.857 0.00 0.00 0.00 1.73
847 868 3.719173 TTTTCCTTTTGGCAAGTACCG 57.281 42.857 0.00 0.00 40.12 4.02
856 877 7.506474 CGTTTTCGGAAATATTTTCCTTTTGG 58.494 34.615 15.09 2.14 39.94 3.28
899 929 3.806507 GCTGTTTGGGCATTTGGAATGAA 60.807 43.478 4.92 0.00 0.00 2.57
930 960 3.520721 GAGGGTTTAGCCTGTTAGGGTTA 59.479 47.826 5.00 0.00 45.25 2.85
953 983 1.961394 GAGGGGGTTGGAACTGAAAAC 59.039 52.381 0.00 0.00 0.00 2.43
1212 1251 4.397832 GCGGCGGGGTAGTTGGAA 62.398 66.667 9.78 0.00 0.00 3.53
1236 1275 1.639635 ATGCGGCCCAGGAGAAGAAT 61.640 55.000 0.00 0.00 0.00 2.40
1524 1563 5.991933 TGTCCAGCTTAGATATCTCATCC 57.008 43.478 8.95 0.00 0.00 3.51
1531 1570 7.568349 TCATTCAACTTGTCCAGCTTAGATAT 58.432 34.615 0.00 0.00 0.00 1.63
1557 1596 2.258726 GGTCACCTCAACGCCCAAC 61.259 63.158 0.00 0.00 0.00 3.77
1642 1681 0.253044 GCTGACTGCTCCACCCAATA 59.747 55.000 0.00 0.00 38.95 1.90
1734 1773 1.305381 CAGGACCTCCCGGAACTCT 60.305 63.158 0.73 0.00 40.87 3.24
1764 1803 6.329197 CCTTATCCATCCCAACCTCTTTACTA 59.671 42.308 0.00 0.00 0.00 1.82
1770 1809 3.321950 CTCCTTATCCATCCCAACCTCT 58.678 50.000 0.00 0.00 0.00 3.69
1780 1819 8.511748 AGAATAACATACACCTCCTTATCCAT 57.488 34.615 0.00 0.00 0.00 3.41
1797 1836 7.223584 TGAGAAACCTGTCAATGAGAATAACA 58.776 34.615 0.00 0.00 0.00 2.41
1809 1848 3.967326 TCTTCCTCTTGAGAAACCTGTCA 59.033 43.478 0.00 0.00 0.00 3.58
1812 1851 4.904241 ACATCTTCCTCTTGAGAAACCTG 58.096 43.478 0.00 0.00 0.00 4.00
1848 1887 0.741915 TTGCAAACCGGAACAAGTCC 59.258 50.000 9.46 0.00 43.90 3.85
1962 2001 3.430790 CCTTCTGATAGATCCGCACAACA 60.431 47.826 0.00 0.00 0.00 3.33
2205 2244 4.588899 CAGACCATACAAGTGGATCCAAA 58.411 43.478 18.20 0.00 42.02 3.28
2230 2269 4.265073 CCAAGGGAATACTTCTGAACCAG 58.735 47.826 0.00 0.00 0.00 4.00
2253 2292 2.216046 ACTGCCATATCAACAGCATCG 58.784 47.619 0.00 0.00 34.72 3.84
2277 2316 0.815734 CCAGCATTTCAGGGAAGCAG 59.184 55.000 0.00 0.00 0.00 4.24
2286 2325 3.058016 CGCTTCTTCTTTCCAGCATTTCA 60.058 43.478 0.00 0.00 32.17 2.69
2307 2346 0.096976 CGCTACCAACTTGATTGCCG 59.903 55.000 0.00 0.00 36.93 5.69
2316 2355 0.247736 CCTCAAGAGCGCTACCAACT 59.752 55.000 11.50 0.00 0.00 3.16
2356 2395 2.185004 TCCTTTGCTTCCTTCTTCCG 57.815 50.000 0.00 0.00 0.00 4.30
2364 2403 0.951558 TGAACGCTTCCTTTGCTTCC 59.048 50.000 0.00 0.00 0.00 3.46
2424 2463 6.653320 TCAAATACTTGTAGGTACTTTGCCAG 59.347 38.462 0.00 0.00 41.75 4.85
2535 2574 5.833406 AAATGTGCGTGATAAATGGATGA 57.167 34.783 0.00 0.00 0.00 2.92
2536 2575 6.035217 TCAAAATGTGCGTGATAAATGGATG 58.965 36.000 0.00 0.00 0.00 3.51
2550 2589 3.588955 GGTCCCAGATTTCAAAATGTGC 58.411 45.455 7.00 0.00 38.08 4.57
2568 2607 1.524621 CAGGGCATCATCCACGGTC 60.525 63.158 0.00 0.00 0.00 4.79
2597 2636 1.537202 ACTCCTTTGAAGACATTGCGC 59.463 47.619 0.00 0.00 0.00 6.09
2611 2650 3.852578 ACTGTTATTGATGGGGACTCCTT 59.147 43.478 0.00 0.00 36.20 3.36
2618 2657 5.591099 GCATGTAAACTGTTATTGATGGGG 58.409 41.667 0.00 0.00 0.00 4.96
2627 2666 4.822036 AACAAGCGCATGTAAACTGTTA 57.178 36.364 19.71 0.00 32.02 2.41
2700 2739 2.100197 CGGACACTTCCAGGAGATACA 58.900 52.381 0.00 0.00 43.00 2.29
2720 2759 1.126846 CGAGAACATCTGCGTGGTTTC 59.873 52.381 0.00 0.00 0.00 2.78
2756 2795 2.159599 GCTGCAGGTTCTTCAATCTTCG 60.160 50.000 17.12 0.00 0.00 3.79
2780 2819 2.731691 CTACAACACTGGTGCCGCCT 62.732 60.000 0.00 0.00 38.35 5.52
2781 2820 2.281208 TACAACACTGGTGCCGCC 60.281 61.111 0.00 0.00 37.90 6.13
2782 2821 1.301401 TCTACAACACTGGTGCCGC 60.301 57.895 0.00 0.00 0.00 6.53
2783 2822 0.033504 AGTCTACAACACTGGTGCCG 59.966 55.000 0.00 0.00 0.00 5.69
2784 2823 3.611766 ATAGTCTACAACACTGGTGCC 57.388 47.619 0.00 0.00 0.00 5.01
2785 2824 4.822026 AGAATAGTCTACAACACTGGTGC 58.178 43.478 0.00 0.00 29.93 5.01
2786 2825 8.035394 ACATAAGAATAGTCTACAACACTGGTG 58.965 37.037 0.00 0.00 32.16 4.17
2787 2826 8.135382 ACATAAGAATAGTCTACAACACTGGT 57.865 34.615 0.00 0.00 32.16 4.00
2788 2827 8.873830 CAACATAAGAATAGTCTACAACACTGG 58.126 37.037 0.00 0.00 32.16 4.00
2789 2828 9.639601 TCAACATAAGAATAGTCTACAACACTG 57.360 33.333 0.00 0.00 32.16 3.66
2829 2868 5.783100 AAATGCCATTTGAAATACAAGCG 57.217 34.783 0.97 0.00 39.77 4.68
2843 2882 5.499313 CCAAAAGGGAATACAAAATGCCAT 58.501 37.500 0.00 0.00 40.01 4.40
2861 2900 2.900716 GGCCAGTTACAAAGCCAAAA 57.099 45.000 0.00 0.00 45.07 2.44
2924 2967 4.851639 AGAGGACAAGTAGGCATTTCAT 57.148 40.909 0.00 0.00 0.00 2.57
2991 3038 6.642131 GCATATAAATATGTGGCACAAACAGG 59.358 38.462 25.95 8.46 44.16 4.00
3048 3095 9.187996 TCCACTGATGCTAATCATTTAAATTGA 57.812 29.630 0.00 0.76 41.97 2.57
3063 3110 1.271597 GGAAACTGGTCCACTGATGCT 60.272 52.381 0.00 0.00 37.65 3.79
3134 3181 5.084722 CAGAATGACAGAAATCAAGTTCGC 58.915 41.667 0.00 0.00 39.69 4.70
3144 3191 6.873605 CACATGTAGTACCAGAATGACAGAAA 59.126 38.462 0.00 0.00 39.69 2.52
3198 3245 9.469807 CATACAGAGATTGGAGTTTCTATGTAC 57.530 37.037 8.95 0.00 44.70 2.90
3199 3246 8.642432 CCATACAGAGATTGGAGTTTCTATGTA 58.358 37.037 9.13 9.13 45.46 2.29
3200 3247 7.419518 CCCATACAGAGATTGGAGTTTCTATGT 60.420 40.741 5.64 5.64 44.25 2.29
3201 3248 6.933521 CCCATACAGAGATTGGAGTTTCTATG 59.066 42.308 0.00 0.00 37.26 2.23
3202 3249 6.043706 CCCCATACAGAGATTGGAGTTTCTAT 59.956 42.308 0.00 0.00 31.94 1.98
3203 3250 5.366768 CCCCATACAGAGATTGGAGTTTCTA 59.633 44.000 0.00 0.00 31.94 2.10
3204 3251 4.164988 CCCCATACAGAGATTGGAGTTTCT 59.835 45.833 0.00 0.00 31.94 2.52
3205 3252 4.164221 TCCCCATACAGAGATTGGAGTTTC 59.836 45.833 0.00 0.00 31.94 2.78
3206 3253 4.111577 TCCCCATACAGAGATTGGAGTTT 58.888 43.478 0.00 0.00 31.94 2.66
3208 3255 3.421394 TCCCCATACAGAGATTGGAGT 57.579 47.619 0.00 0.00 31.94 3.85
3236 3296 5.669477 TGTGATACACTAACATGCATGCTA 58.331 37.500 26.53 17.58 35.11 3.49
3237 3297 4.516323 TGTGATACACTAACATGCATGCT 58.484 39.130 26.53 17.37 35.11 3.79
3263 3323 4.927267 TCCCATGAGAATTGTTAGTGGT 57.073 40.909 0.00 0.00 0.00 4.16
3264 3324 5.256474 ACTTCCCATGAGAATTGTTAGTGG 58.744 41.667 0.00 0.00 0.00 4.00
3266 3326 6.380079 AGACTTCCCATGAGAATTGTTAGT 57.620 37.500 0.00 0.00 0.00 2.24
3271 3331 8.159447 TGGAATATAGACTTCCCATGAGAATTG 58.841 37.037 0.00 0.00 41.29 2.32
3272 3332 8.280258 TGGAATATAGACTTCCCATGAGAATT 57.720 34.615 0.00 0.00 41.29 2.17
3273 3333 7.878621 TGGAATATAGACTTCCCATGAGAAT 57.121 36.000 0.00 0.00 41.29 2.40
3274 3334 7.878621 ATGGAATATAGACTTCCCATGAGAA 57.121 36.000 0.00 0.00 41.29 2.87
3275 3335 7.513781 TGAATGGAATATAGACTTCCCATGAGA 59.486 37.037 0.00 0.00 41.29 3.27
3276 3336 7.683578 TGAATGGAATATAGACTTCCCATGAG 58.316 38.462 0.00 0.00 41.29 2.90
3277 3337 7.631510 TGAATGGAATATAGACTTCCCATGA 57.368 36.000 0.00 0.00 41.29 3.07
3278 3338 7.886970 ACATGAATGGAATATAGACTTCCCATG 59.113 37.037 0.00 13.93 41.17 3.66
3279 3339 7.993416 ACATGAATGGAATATAGACTTCCCAT 58.007 34.615 0.00 0.00 41.29 4.00
3280 3340 7.392766 ACATGAATGGAATATAGACTTCCCA 57.607 36.000 0.00 0.00 41.29 4.37
3281 3341 9.965902 ATTACATGAATGGAATATAGACTTCCC 57.034 33.333 0.00 0.00 39.49 3.97
3338 3443 3.195610 AGATATGTTTCTCCTCACACGCA 59.804 43.478 0.00 0.00 0.00 5.24
3354 3459 7.011202 GCCAGCATATCAACTGACATAGATATG 59.989 40.741 18.36 18.36 46.57 1.78
3355 3460 7.046652 GCCAGCATATCAACTGACATAGATAT 58.953 38.462 0.00 0.00 35.90 1.63
3356 3461 6.401394 GCCAGCATATCAACTGACATAGATA 58.599 40.000 0.00 0.00 35.90 1.98
3357 3462 5.243981 GCCAGCATATCAACTGACATAGAT 58.756 41.667 0.00 0.00 35.90 1.98
3358 3463 4.503817 GGCCAGCATATCAACTGACATAGA 60.504 45.833 0.00 0.00 35.90 1.98
3359 3464 3.750130 GGCCAGCATATCAACTGACATAG 59.250 47.826 0.00 0.00 35.90 2.23
3360 3465 3.136260 TGGCCAGCATATCAACTGACATA 59.864 43.478 0.00 0.00 35.90 2.29
3405 3511 1.168714 CTGCTTCACCCCTTTACTGC 58.831 55.000 0.00 0.00 0.00 4.40
3406 3512 1.826385 CCTGCTTCACCCCTTTACTG 58.174 55.000 0.00 0.00 0.00 2.74
3409 3515 0.038166 CTGCCTGCTTCACCCCTTTA 59.962 55.000 0.00 0.00 0.00 1.85
3417 3523 3.991999 GCATCACTGCCTGCTTCA 58.008 55.556 0.00 0.00 42.88 3.02
3438 3544 4.201980 GCCTTACCGCCTTAAAAACTATGG 60.202 45.833 0.00 0.00 0.00 2.74
3439 3545 4.495184 CGCCTTACCGCCTTAAAAACTATG 60.495 45.833 0.00 0.00 0.00 2.23
3440 3546 3.624410 CGCCTTACCGCCTTAAAAACTAT 59.376 43.478 0.00 0.00 0.00 2.12
3441 3547 3.002102 CGCCTTACCGCCTTAAAAACTA 58.998 45.455 0.00 0.00 0.00 2.24
3442 3548 1.808343 CGCCTTACCGCCTTAAAAACT 59.192 47.619 0.00 0.00 0.00 2.66
3443 3549 1.805943 TCGCCTTACCGCCTTAAAAAC 59.194 47.619 0.00 0.00 0.00 2.43
3444 3550 1.805943 GTCGCCTTACCGCCTTAAAAA 59.194 47.619 0.00 0.00 0.00 1.94
3445 3551 1.441738 GTCGCCTTACCGCCTTAAAA 58.558 50.000 0.00 0.00 0.00 1.52
3446 3552 0.391528 GGTCGCCTTACCGCCTTAAA 60.392 55.000 0.00 0.00 0.00 1.52
3447 3553 1.218854 GGTCGCCTTACCGCCTTAA 59.781 57.895 0.00 0.00 0.00 1.85
3448 3554 0.395586 TAGGTCGCCTTACCGCCTTA 60.396 55.000 3.71 0.00 44.77 2.69
3449 3555 1.259840 TTAGGTCGCCTTACCGCCTT 61.260 55.000 3.71 0.00 44.77 4.35
3450 3556 1.673808 CTTAGGTCGCCTTACCGCCT 61.674 60.000 3.71 0.00 44.77 5.52
3451 3557 1.227176 CTTAGGTCGCCTTACCGCC 60.227 63.158 3.71 0.00 44.77 6.13
3452 3558 1.227176 CCTTAGGTCGCCTTACCGC 60.227 63.158 3.71 0.00 44.77 5.68
3453 3559 1.227176 GCCTTAGGTCGCCTTACCG 60.227 63.158 0.00 0.00 44.77 4.02
3454 3560 1.227176 CGCCTTAGGTCGCCTTACC 60.227 63.158 0.00 0.00 40.06 2.85
3455 3561 1.881709 GCGCCTTAGGTCGCCTTAC 60.882 63.158 22.66 2.55 40.38 2.34
3456 3562 2.056223 AGCGCCTTAGGTCGCCTTA 61.056 57.895 26.94 0.00 44.56 2.69
3457 3563 3.391382 AGCGCCTTAGGTCGCCTT 61.391 61.111 26.94 13.59 44.56 4.35
3458 3564 4.148825 CAGCGCCTTAGGTCGCCT 62.149 66.667 26.94 16.35 44.56 5.52
3461 3567 4.530857 CCCCAGCGCCTTAGGTCG 62.531 72.222 2.29 9.97 0.00 4.79
3462 3568 4.176752 CCCCCAGCGCCTTAGGTC 62.177 72.222 2.29 0.00 0.00 3.85
3511 3617 1.981256 ACAAATATGCCCGCCTTAGG 58.019 50.000 0.00 0.00 0.00 2.69
3512 3618 3.502211 CCTTACAAATATGCCCGCCTTAG 59.498 47.826 0.00 0.00 0.00 2.18
3513 3619 3.482436 CCTTACAAATATGCCCGCCTTA 58.518 45.455 0.00 0.00 0.00 2.69
3514 3620 2.306847 CCTTACAAATATGCCCGCCTT 58.693 47.619 0.00 0.00 0.00 4.35
3515 3621 1.981256 CCTTACAAATATGCCCGCCT 58.019 50.000 0.00 0.00 0.00 5.52
3516 3622 0.313987 GCCTTACAAATATGCCCGCC 59.686 55.000 0.00 0.00 0.00 6.13
3517 3623 0.040425 CGCCTTACAAATATGCCCGC 60.040 55.000 0.00 0.00 0.00 6.13
3518 3624 0.040425 GCGCCTTACAAATATGCCCG 60.040 55.000 0.00 0.00 0.00 6.13
3519 3625 1.001378 CAGCGCCTTACAAATATGCCC 60.001 52.381 2.29 0.00 0.00 5.36
3520 3626 1.001378 CCAGCGCCTTACAAATATGCC 60.001 52.381 2.29 0.00 0.00 4.40
3521 3627 1.001378 CCCAGCGCCTTACAAATATGC 60.001 52.381 2.29 0.00 0.00 3.14
3522 3628 1.608590 CCCCAGCGCCTTACAAATATG 59.391 52.381 2.29 0.00 0.00 1.78
3523 3629 1.478654 CCCCCAGCGCCTTACAAATAT 60.479 52.381 2.29 0.00 0.00 1.28
3524 3630 0.106918 CCCCCAGCGCCTTACAAATA 60.107 55.000 2.29 0.00 0.00 1.40
3525 3631 1.379843 CCCCCAGCGCCTTACAAAT 60.380 57.895 2.29 0.00 0.00 2.32
3526 3632 2.034999 CCCCCAGCGCCTTACAAA 59.965 61.111 2.29 0.00 0.00 2.83
3556 3662 2.511600 CCGCCTTGGACGCTTAGG 60.512 66.667 0.00 0.00 42.00 2.69
3557 3663 2.511600 CCCGCCTTGGACGCTTAG 60.512 66.667 0.00 0.00 42.00 2.18
3558 3664 2.998480 TCCCGCCTTGGACGCTTA 60.998 61.111 0.00 0.00 42.00 3.09
3559 3665 4.699522 GTCCCGCCTTGGACGCTT 62.700 66.667 0.00 0.00 44.98 4.68
3571 3677 2.226912 TCATTGTTTTTAAGGCGTCCCG 59.773 45.455 0.00 0.00 35.76 5.14
3572 3678 3.926821 TCATTGTTTTTAAGGCGTCCC 57.073 42.857 0.00 0.00 0.00 4.46
3573 3679 3.612423 GCATCATTGTTTTTAAGGCGTCC 59.388 43.478 0.00 0.00 0.00 4.79
3574 3680 4.324402 CAGCATCATTGTTTTTAAGGCGTC 59.676 41.667 0.00 0.00 0.00 5.19
3575 3681 4.236935 CAGCATCATTGTTTTTAAGGCGT 58.763 39.130 0.00 0.00 0.00 5.68
3576 3682 3.061161 GCAGCATCATTGTTTTTAAGGCG 59.939 43.478 0.00 0.00 0.00 5.52
3577 3683 3.371898 GGCAGCATCATTGTTTTTAAGGC 59.628 43.478 0.00 0.00 0.00 4.35
3578 3684 4.389687 GTGGCAGCATCATTGTTTTTAAGG 59.610 41.667 0.00 0.00 0.00 2.69
3579 3685 4.090354 CGTGGCAGCATCATTGTTTTTAAG 59.910 41.667 0.00 0.00 0.00 1.85
3580 3686 3.986572 CGTGGCAGCATCATTGTTTTTAA 59.013 39.130 0.00 0.00 0.00 1.52
3581 3687 3.573598 CGTGGCAGCATCATTGTTTTTA 58.426 40.909 0.00 0.00 0.00 1.52
3582 3688 2.406130 CGTGGCAGCATCATTGTTTTT 58.594 42.857 0.00 0.00 0.00 1.94
3583 3689 1.936203 GCGTGGCAGCATCATTGTTTT 60.936 47.619 0.00 0.00 37.05 2.43
3584 3690 0.388907 GCGTGGCAGCATCATTGTTT 60.389 50.000 0.00 0.00 37.05 2.83
3585 3691 1.213537 GCGTGGCAGCATCATTGTT 59.786 52.632 0.00 0.00 37.05 2.83
3586 3692 2.703798 GGCGTGGCAGCATCATTGT 61.704 57.895 10.33 0.00 39.27 2.71
3587 3693 2.103538 GGCGTGGCAGCATCATTG 59.896 61.111 10.33 0.00 39.27 2.82
3588 3694 2.867793 TACGGCGTGGCAGCATCATT 62.868 55.000 24.86 0.00 39.27 2.57
3589 3695 3.384275 TACGGCGTGGCAGCATCAT 62.384 57.895 24.86 0.00 39.27 2.45
3590 3696 4.075854 TACGGCGTGGCAGCATCA 62.076 61.111 24.86 0.00 39.27 3.07
3591 3697 2.622903 TAGTACGGCGTGGCAGCATC 62.623 60.000 24.86 2.84 39.27 3.91
3592 3698 2.028125 ATAGTACGGCGTGGCAGCAT 62.028 55.000 24.86 4.25 39.27 3.79
3593 3699 2.717044 ATAGTACGGCGTGGCAGCA 61.717 57.895 24.86 0.00 39.27 4.41
3594 3700 2.106332 ATAGTACGGCGTGGCAGC 59.894 61.111 24.86 7.49 0.00 5.25
3595 3701 0.459585 AACATAGTACGGCGTGGCAG 60.460 55.000 24.86 11.05 0.00 4.85
3596 3702 0.816373 TAACATAGTACGGCGTGGCA 59.184 50.000 24.86 7.30 0.00 4.92
3597 3703 1.790623 CATAACATAGTACGGCGTGGC 59.209 52.381 24.86 15.37 0.00 5.01
3598 3704 3.358707 TCATAACATAGTACGGCGTGG 57.641 47.619 24.86 9.23 0.00 4.94
3599 3705 4.542735 TGATCATAACATAGTACGGCGTG 58.457 43.478 24.86 7.97 0.00 5.34
3600 3706 4.841443 TGATCATAACATAGTACGGCGT 57.159 40.909 19.64 19.64 0.00 5.68
3606 3712 8.037166 GGCAGTCATGATGATCATAACATAGTA 58.963 37.037 11.10 0.00 34.28 1.82
3632 3738 7.584987 ACGATTAAAAGAAGACACCAAAGATG 58.415 34.615 0.00 0.00 0.00 2.90
3656 3763 5.927030 TGTTTGATTCTGTCGCTCAATTAC 58.073 37.500 0.00 0.00 0.00 1.89
3698 3805 0.251653 AGGTGTGAGTTAGAGCCGGA 60.252 55.000 5.05 0.00 0.00 5.14
3704 3811 3.452990 TGTTGTTCCAGGTGTGAGTTAGA 59.547 43.478 0.00 0.00 0.00 2.10
3705 3812 3.804036 TGTTGTTCCAGGTGTGAGTTAG 58.196 45.455 0.00 0.00 0.00 2.34
3735 3842 9.593134 CTCAATTCTTTCAGTGCTAACTAGTAT 57.407 33.333 0.00 0.00 33.79 2.12
3756 3863 1.347707 TGAAACGAGCCTGGACTCAAT 59.652 47.619 15.25 3.62 36.42 2.57
3758 3865 0.318441 CTGAAACGAGCCTGGACTCA 59.682 55.000 15.25 2.04 36.42 3.41
3759 3866 1.016653 GCTGAAACGAGCCTGGACTC 61.017 60.000 0.00 2.84 32.35 3.36
3760 3867 1.004440 GCTGAAACGAGCCTGGACT 60.004 57.895 0.00 0.00 32.35 3.85
3761 3868 0.884704 TTGCTGAAACGAGCCTGGAC 60.885 55.000 0.00 0.00 38.28 4.02


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

AutoCloner maintained by Alex Coulton.