Multiple sequence alignment - TraesCS5B01G058500

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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 TraesCS5B01G058500 chr5B 100.000 5385 0 0 1 5385 64268955 64263571 0.000000e+00 9945.0
1 TraesCS5B01G058500 chr5B 85.024 207 25 4 2547 2753 559992027 559992227 7.070000e-49 206.0
2 TraesCS5B01G058500 chr5B 90.991 111 10 0 2638 2748 565929881 565929771 3.360000e-32 150.0
3 TraesCS5B01G058500 chr5B 88.525 122 14 0 3783 3904 559992256 559992377 1.210000e-31 148.0
4 TraesCS5B01G058500 chr5D 95.839 2259 65 13 3148 5385 66755765 66758015 0.000000e+00 3624.0
5 TraesCS5B01G058500 chr5D 93.003 2301 59 39 570 2793 66753273 66755548 0.000000e+00 3264.0
6 TraesCS5B01G058500 chr5D 91.111 180 10 5 2792 2969 66755598 66755773 6.970000e-59 239.0
7 TraesCS5B01G058500 chr5D 85.577 208 25 3 2547 2753 457776977 457777180 4.220000e-51 213.0
8 TraesCS5B01G058500 chr5D 90.164 122 12 0 3783 3904 457777203 457777324 5.580000e-35 159.0
9 TraesCS5B01G058500 chr5D 90.090 111 11 0 2638 2748 460394564 460394454 1.560000e-30 145.0
10 TraesCS5B01G058500 chr5A 94.945 2255 72 16 3145 5385 57376348 57374122 0.000000e+00 3494.0
11 TraesCS5B01G058500 chr5A 91.776 1143 44 18 1691 2793 57377702 57376570 0.000000e+00 1544.0
12 TraesCS5B01G058500 chr5A 90.598 1138 53 27 564 1655 57379027 57377898 0.000000e+00 1459.0
13 TraesCS5B01G058500 chr5A 90.991 111 10 0 2638 2748 580465954 580465844 3.360000e-32 150.0
14 TraesCS5B01G058500 chr5A 86.719 128 17 0 3777 3904 575658591 575658718 5.620000e-30 143.0
15 TraesCS5B01G058500 chr5A 87.952 83 10 0 2626 2708 575658465 575658547 1.230000e-16 99.0
16 TraesCS5B01G058500 chr4B 95.506 534 24 0 1 534 539480981 539481514 0.000000e+00 854.0
17 TraesCS5B01G058500 chr1D 92.697 534 38 1 1 534 62955358 62955890 0.000000e+00 769.0
18 TraesCS5B01G058500 chr1D 92.754 69 5 0 3834 3902 116004666 116004598 3.430000e-17 100.0
19 TraesCS5B01G058500 chr1D 90.411 73 4 2 4073 4144 469519053 469518983 5.740000e-15 93.5
20 TraesCS5B01G058500 chr6D 92.509 534 40 0 1 534 186967738 186968271 0.000000e+00 765.0
21 TraesCS5B01G058500 chr2B 92.509 534 39 1 1 534 118702834 118703366 0.000000e+00 763.0
22 TraesCS5B01G058500 chr2B 97.688 173 4 0 2980 3152 556659032 556659204 1.130000e-76 298.0
23 TraesCS5B01G058500 chr3D 92.179 537 41 1 1 537 102204475 102203940 0.000000e+00 758.0
24 TraesCS5B01G058500 chr3D 86.220 537 68 6 1 534 138184781 138185314 1.300000e-160 577.0
25 TraesCS5B01G058500 chr3D 88.608 79 9 0 3825 3903 81207425 81207503 4.440000e-16 97.1
26 TraesCS5B01G058500 chr7D 91.993 537 42 1 1 537 234177915 234177380 0.000000e+00 752.0
27 TraesCS5B01G058500 chr3B 91.806 537 43 1 1 537 482504340 482503805 0.000000e+00 747.0
28 TraesCS5B01G058500 chr3B 98.246 171 2 1 2982 3152 731267202 731267033 1.130000e-76 298.0
29 TraesCS5B01G058500 chr3B 97.143 175 4 1 2976 3150 178399258 178399085 1.470000e-75 294.0
30 TraesCS5B01G058500 chr3B 96.571 175 5 1 2975 3149 734667209 734667036 6.820000e-74 289.0
31 TraesCS5B01G058500 chr3B 88.608 79 9 0 3825 3903 126921252 126921330 4.440000e-16 97.1
32 TraesCS5B01G058500 chr2D 91.610 441 36 1 97 537 67582885 67582446 4.610000e-170 608.0
33 TraesCS5B01G058500 chr4A 99.401 167 1 0 2981 3147 610810745 610810911 2.440000e-78 303.0
34 TraesCS5B01G058500 chr4A 98.235 170 3 0 2980 3149 676920990 676920821 1.130000e-76 298.0
35 TraesCS5B01G058500 chr7B 98.810 168 2 0 2979 3146 215365510 215365677 3.150000e-77 300.0
36 TraesCS5B01G058500 chr7B 91.566 83 4 2 4063 4144 490337022 490337102 1.590000e-20 111.0
37 TraesCS5B01G058500 chr2A 98.810 168 2 0 2982 3149 632622112 632622279 3.150000e-77 300.0
38 TraesCS5B01G058500 chr1A 97.126 174 5 0 2974 3147 526575513 526575686 1.470000e-75 294.0
39 TraesCS5B01G058500 chr3A 88.608 79 9 0 3825 3903 95477862 95477940 4.440000e-16 97.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G058500 chr5B 64263571 64268955 5384 True 9945.000000 9945 100.000000 1 5385 1 chr5B.!!$R1 5384
1 TraesCS5B01G058500 chr5D 66753273 66758015 4742 False 2375.666667 3624 93.317667 570 5385 3 chr5D.!!$F1 4815
2 TraesCS5B01G058500 chr5A 57374122 57379027 4905 True 2165.666667 3494 92.439667 564 5385 3 chr5A.!!$R2 4821
3 TraesCS5B01G058500 chr4B 539480981 539481514 533 False 854.000000 854 95.506000 1 534 1 chr4B.!!$F1 533
4 TraesCS5B01G058500 chr1D 62955358 62955890 532 False 769.000000 769 92.697000 1 534 1 chr1D.!!$F1 533
5 TraesCS5B01G058500 chr6D 186967738 186968271 533 False 765.000000 765 92.509000 1 534 1 chr6D.!!$F1 533
6 TraesCS5B01G058500 chr2B 118702834 118703366 532 False 763.000000 763 92.509000 1 534 1 chr2B.!!$F1 533
7 TraesCS5B01G058500 chr3D 102203940 102204475 535 True 758.000000 758 92.179000 1 537 1 chr3D.!!$R1 536
8 TraesCS5B01G058500 chr3D 138184781 138185314 533 False 577.000000 577 86.220000 1 534 1 chr3D.!!$F2 533
9 TraesCS5B01G058500 chr7D 234177380 234177915 535 True 752.000000 752 91.993000 1 537 1 chr7D.!!$R1 536
10 TraesCS5B01G058500 chr3B 482503805 482504340 535 True 747.000000 747 91.806000 1 537 1 chr3B.!!$R2 536

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
56 57 0.035439 AGTAATGGAACTGTGCCGGG 60.035 55.000 2.18 0.00 0.00 5.73 F
538 542 0.106469 TCGGTCCATCTCCTCTCAGG 60.106 60.000 0.00 0.00 36.46 3.86 F
1786 2044 0.035036 ATCCATCTCCATCTGCAGCG 59.965 55.000 9.47 1.99 0.00 5.18 F
2053 2318 2.442643 CTTCCCGGCCATGGCATT 60.443 61.111 36.56 0.00 44.11 3.56 F
2817 3169 1.686325 TTCTCATGCTACCTCGGCCC 61.686 60.000 0.00 0.00 0.00 5.80 F
2999 3354 0.410663 TCTACTCCCTCCGTTCCCAA 59.589 55.000 0.00 0.00 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1016 1035 0.440371 CGCTCCTTTCTGCGTTTCTC 59.560 55.000 0.0 0.0 46.09 2.87 R
1795 2053 0.459489 CTGTCTCTCTGCTGGCTACC 59.541 60.000 0.0 0.0 0.00 3.18 R
2797 3100 0.178068 GGCCGAGGTAGCATGAGAAA 59.822 55.000 0.0 0.0 0.00 2.52 R
2984 3339 1.838077 AGTATTTGGGAACGGAGGGAG 59.162 52.381 0.0 0.0 0.00 4.30 R
3892 4253 2.040813 AGAATGCAACACTCACTCCCAT 59.959 45.455 0.0 0.0 0.00 4.00 R
4887 5269 0.842635 GATGCCTCTGTCCATCCCTT 59.157 55.000 0.0 0.0 33.43 3.95 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
56 57 0.035439 AGTAATGGAACTGTGCCGGG 60.035 55.000 2.18 0.00 0.00 5.73
83 84 3.118956 CCTTTCTGATTGAGAGCGGTAGT 60.119 47.826 0.00 0.00 30.18 2.73
140 141 2.162408 GTCTAAGGATGTGCAAACTGCC 59.838 50.000 0.00 0.00 44.23 4.85
206 207 0.468029 CAAGGTTCACCACAAGGCCT 60.468 55.000 0.00 0.00 39.06 5.19
247 248 2.355920 CCAGGATCTTTCTGCAAGCTCT 60.356 50.000 0.00 0.00 29.66 4.09
359 362 4.195334 ATGCCCTGATCCGTGGCC 62.195 66.667 12.97 0.00 44.72 5.36
431 435 3.493524 GGGAAATCGGATCTCCTTGTCTC 60.494 52.174 10.08 0.00 0.00 3.36
458 462 6.340522 CCCACATGCATTATATATCGTCTCA 58.659 40.000 0.00 0.00 0.00 3.27
459 463 6.988580 CCCACATGCATTATATATCGTCTCAT 59.011 38.462 0.00 0.00 0.00 2.90
467 471 0.603569 ATATCGTCTCATCCGGCACC 59.396 55.000 0.00 0.00 0.00 5.01
482 486 1.868987 GCACCCCGTTTACCGCAATT 61.869 55.000 0.00 0.00 34.38 2.32
534 538 0.396417 CCACTCGGTCCATCTCCTCT 60.396 60.000 0.00 0.00 0.00 3.69
537 541 1.317613 CTCGGTCCATCTCCTCTCAG 58.682 60.000 0.00 0.00 0.00 3.35
538 542 0.106469 TCGGTCCATCTCCTCTCAGG 60.106 60.000 0.00 0.00 36.46 3.86
539 543 0.106469 CGGTCCATCTCCTCTCAGGA 60.106 60.000 0.00 0.00 43.43 3.86
540 544 1.686428 CGGTCCATCTCCTCTCAGGAA 60.686 57.143 0.00 0.00 45.28 3.36
541 545 1.760029 GGTCCATCTCCTCTCAGGAAC 59.240 57.143 0.00 0.00 45.28 3.62
542 546 2.625617 GGTCCATCTCCTCTCAGGAACT 60.626 54.545 0.00 0.00 45.28 3.01
543 547 3.373220 GGTCCATCTCCTCTCAGGAACTA 60.373 52.174 0.00 0.00 45.28 2.24
544 548 4.282496 GTCCATCTCCTCTCAGGAACTAA 58.718 47.826 0.00 0.00 45.28 2.24
545 549 4.898861 GTCCATCTCCTCTCAGGAACTAAT 59.101 45.833 0.00 0.00 45.28 1.73
546 550 5.365314 GTCCATCTCCTCTCAGGAACTAATT 59.635 44.000 0.00 0.00 45.28 1.40
547 551 6.551601 GTCCATCTCCTCTCAGGAACTAATTA 59.448 42.308 0.00 0.00 45.28 1.40
548 552 7.070074 GTCCATCTCCTCTCAGGAACTAATTAA 59.930 40.741 0.00 0.00 45.28 1.40
549 553 7.791766 TCCATCTCCTCTCAGGAACTAATTAAT 59.208 37.037 0.00 0.00 45.28 1.40
550 554 8.435982 CCATCTCCTCTCAGGAACTAATTAATT 58.564 37.037 5.89 5.89 45.28 1.40
551 555 9.270640 CATCTCCTCTCAGGAACTAATTAATTG 57.729 37.037 11.05 3.88 45.28 2.32
552 556 8.380742 TCTCCTCTCAGGAACTAATTAATTGT 57.619 34.615 11.05 4.48 45.28 2.71
553 557 8.260818 TCTCCTCTCAGGAACTAATTAATTGTG 58.739 37.037 11.05 6.27 45.28 3.33
554 558 7.338710 TCCTCTCAGGAACTAATTAATTGTGG 58.661 38.462 11.05 3.96 42.51 4.17
555 559 7.037586 TCCTCTCAGGAACTAATTAATTGTGGT 60.038 37.037 11.05 2.33 42.51 4.16
556 560 8.265055 CCTCTCAGGAACTAATTAATTGTGGTA 58.735 37.037 11.05 0.00 37.67 3.25
557 561 9.838339 CTCTCAGGAACTAATTAATTGTGGTAT 57.162 33.333 11.05 0.12 36.02 2.73
619 625 9.209175 GTATTGTGGATCATGGTAATCTAGTTC 57.791 37.037 0.00 0.00 0.00 3.01
620 626 6.174720 TGTGGATCATGGTAATCTAGTTCC 57.825 41.667 0.00 0.00 0.00 3.62
622 628 6.042093 TGTGGATCATGGTAATCTAGTTCCTC 59.958 42.308 0.00 0.00 0.00 3.71
628 637 8.603898 TCATGGTAATCTAGTTCCTCTTAACA 57.396 34.615 0.00 0.00 0.00 2.41
778 792 4.282873 GCGCCTAAACAAATGAATAGCTC 58.717 43.478 0.00 0.00 0.00 4.09
813 827 6.260700 TCAAAAATATTAGCAGAGGGGCTA 57.739 37.500 0.00 0.00 43.70 3.93
1016 1035 2.978018 GAACCCCAAAAGCTCGCCG 61.978 63.158 0.00 0.00 0.00 6.46
1222 1251 0.820871 AGACCATCGACCTGAAGCTC 59.179 55.000 0.00 0.00 0.00 4.09
1324 1353 3.827898 CAGGAGGAGACGGCGACC 61.828 72.222 16.62 14.02 0.00 4.79
1379 1408 3.295273 AGAGCAGCGTCGTCACCA 61.295 61.111 0.00 0.00 0.00 4.17
1493 1537 1.745489 TGCTCTGCATGCAGCTCAG 60.745 57.895 37.48 30.05 45.94 3.35
1507 1551 0.453793 GCTCAGCTCTGCTCGTCTTA 59.546 55.000 0.00 0.00 36.40 2.10
1508 1552 1.135257 GCTCAGCTCTGCTCGTCTTAA 60.135 52.381 0.00 0.00 36.40 1.85
1519 1576 3.100089 GCTCGTCTTAAGCTCTTCGTAC 58.900 50.000 0.00 0.00 36.80 3.67
1619 1686 1.705337 CGGGCAGTTAACGGCATGAG 61.705 60.000 27.92 14.07 38.83 2.90
1635 1702 1.252175 TGAGTCGCTCTGCTTCTCTT 58.748 50.000 8.07 0.00 31.41 2.85
1655 1722 4.524328 TCTTGCCATGATCGATCTAGCTTA 59.476 41.667 25.02 14.93 0.00 3.09
1656 1723 4.446994 TGCCATGATCGATCTAGCTTAG 57.553 45.455 25.02 8.86 0.00 2.18
1657 1724 3.186119 GCCATGATCGATCTAGCTTAGC 58.814 50.000 25.02 14.12 0.00 3.09
1658 1725 3.119173 GCCATGATCGATCTAGCTTAGCT 60.119 47.826 25.02 12.67 43.41 3.32
1681 1918 5.159273 TGTACTAGTCCATGCATGTTCAA 57.841 39.130 24.58 7.32 0.00 2.69
1721 1970 1.554160 GATCGAGGGCTGATCATGGAT 59.446 52.381 0.00 0.00 41.48 3.41
1723 1972 0.683412 CGAGGGCTGATCATGGATGA 59.317 55.000 0.00 0.00 41.70 2.92
1724 1973 1.337917 CGAGGGCTGATCATGGATGAG 60.338 57.143 0.00 0.00 40.64 2.90
1725 1974 1.698532 GAGGGCTGATCATGGATGAGT 59.301 52.381 0.00 0.00 40.64 3.41
1786 2044 0.035036 ATCCATCTCCATCTGCAGCG 59.965 55.000 9.47 1.99 0.00 5.18
2053 2318 2.442643 CTTCCCGGCCATGGCATT 60.443 61.111 36.56 0.00 44.11 3.56
2054 2319 2.759149 TTCCCGGCCATGGCATTG 60.759 61.111 36.56 24.60 44.11 2.82
2055 2320 4.837797 TCCCGGCCATGGCATTGG 62.838 66.667 36.56 30.97 44.11 3.16
2163 2445 9.334693 CTTGTACAAATCAAGCTGAAACTTATC 57.665 33.333 10.03 0.00 36.38 1.75
2480 2772 4.724074 TCATGAAAGAAACCCATGCATC 57.276 40.909 0.00 0.00 37.99 3.91
2767 3070 2.620115 CCATCGGTATGCATGCTTCTTT 59.380 45.455 20.33 1.25 0.00 2.52
2817 3169 1.686325 TTCTCATGCTACCTCGGCCC 61.686 60.000 0.00 0.00 0.00 5.80
2945 3299 9.877222 CCTAAACCCTAGTCCCATTTATTTATT 57.123 33.333 0.00 0.00 0.00 1.40
2987 3342 9.825109 ATCTAGCTTTTGTTTTCTATCTACTCC 57.175 33.333 0.00 0.00 0.00 3.85
2988 3343 8.258708 TCTAGCTTTTGTTTTCTATCTACTCCC 58.741 37.037 0.00 0.00 0.00 4.30
2989 3344 7.021998 AGCTTTTGTTTTCTATCTACTCCCT 57.978 36.000 0.00 0.00 0.00 4.20
2990 3345 7.106890 AGCTTTTGTTTTCTATCTACTCCCTC 58.893 38.462 0.00 0.00 0.00 4.30
2991 3346 6.316640 GCTTTTGTTTTCTATCTACTCCCTCC 59.683 42.308 0.00 0.00 0.00 4.30
2992 3347 5.593679 TTGTTTTCTATCTACTCCCTCCG 57.406 43.478 0.00 0.00 0.00 4.63
2993 3348 4.607239 TGTTTTCTATCTACTCCCTCCGT 58.393 43.478 0.00 0.00 0.00 4.69
2994 3349 5.021458 TGTTTTCTATCTACTCCCTCCGTT 58.979 41.667 0.00 0.00 0.00 4.44
2995 3350 5.126707 TGTTTTCTATCTACTCCCTCCGTTC 59.873 44.000 0.00 0.00 0.00 3.95
2996 3351 3.505480 TCTATCTACTCCCTCCGTTCC 57.495 52.381 0.00 0.00 0.00 3.62
2997 3352 2.107901 TCTATCTACTCCCTCCGTTCCC 59.892 54.545 0.00 0.00 0.00 3.97
2998 3353 0.635009 ATCTACTCCCTCCGTTCCCA 59.365 55.000 0.00 0.00 0.00 4.37
2999 3354 0.410663 TCTACTCCCTCCGTTCCCAA 59.589 55.000 0.00 0.00 0.00 4.12
3000 3355 1.203212 TCTACTCCCTCCGTTCCCAAA 60.203 52.381 0.00 0.00 0.00 3.28
3001 3356 1.838077 CTACTCCCTCCGTTCCCAAAT 59.162 52.381 0.00 0.00 0.00 2.32
3002 3357 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3003 3358 1.558294 ACTCCCTCCGTTCCCAAATAC 59.442 52.381 0.00 0.00 0.00 1.89
3004 3359 1.838077 CTCCCTCCGTTCCCAAATACT 59.162 52.381 0.00 0.00 0.00 2.12
3005 3360 2.238898 CTCCCTCCGTTCCCAAATACTT 59.761 50.000 0.00 0.00 0.00 2.24
3006 3361 2.026636 TCCCTCCGTTCCCAAATACTTG 60.027 50.000 0.00 0.00 0.00 3.16
3007 3362 2.290705 CCCTCCGTTCCCAAATACTTGT 60.291 50.000 0.00 0.00 0.00 3.16
3008 3363 3.007635 CCTCCGTTCCCAAATACTTGTC 58.992 50.000 0.00 0.00 0.00 3.18
3009 3364 3.307480 CCTCCGTTCCCAAATACTTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
3010 3365 4.324267 CTCCGTTCCCAAATACTTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
3011 3366 4.721132 TCCGTTCCCAAATACTTGTCTTT 58.279 39.130 0.00 0.00 0.00 2.52
3012 3367 4.758165 TCCGTTCCCAAATACTTGTCTTTC 59.242 41.667 0.00 0.00 0.00 2.62
3013 3368 4.760204 CCGTTCCCAAATACTTGTCTTTCT 59.240 41.667 0.00 0.00 0.00 2.52
3014 3369 5.935789 CCGTTCCCAAATACTTGTCTTTCTA 59.064 40.000 0.00 0.00 0.00 2.10
3015 3370 6.092259 CCGTTCCCAAATACTTGTCTTTCTAG 59.908 42.308 0.00 0.00 0.00 2.43
3016 3371 6.092259 CGTTCCCAAATACTTGTCTTTCTAGG 59.908 42.308 0.00 0.00 0.00 3.02
3017 3372 5.497474 TCCCAAATACTTGTCTTTCTAGGC 58.503 41.667 0.00 0.00 0.00 3.93
3018 3373 5.013704 TCCCAAATACTTGTCTTTCTAGGCA 59.986 40.000 0.00 0.00 33.22 4.75
3019 3374 5.888161 CCCAAATACTTGTCTTTCTAGGCAT 59.112 40.000 0.00 0.00 35.56 4.40
3020 3375 6.378280 CCCAAATACTTGTCTTTCTAGGCATT 59.622 38.462 0.00 0.00 35.56 3.56
3021 3376 7.093771 CCCAAATACTTGTCTTTCTAGGCATTT 60.094 37.037 0.00 0.00 35.56 2.32
3022 3377 7.970614 CCAAATACTTGTCTTTCTAGGCATTTC 59.029 37.037 0.00 0.00 35.56 2.17
3023 3378 8.514594 CAAATACTTGTCTTTCTAGGCATTTCA 58.485 33.333 0.00 0.00 35.56 2.69
3024 3379 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
3025 3380 6.959639 ACTTGTCTTTCTAGGCATTTCAAA 57.040 33.333 0.00 0.00 35.56 2.69
3026 3381 7.530426 ACTTGTCTTTCTAGGCATTTCAAAT 57.470 32.000 0.00 0.00 35.56 2.32
3027 3382 7.373493 ACTTGTCTTTCTAGGCATTTCAAATG 58.627 34.615 5.68 5.68 35.56 2.32
3028 3383 6.271488 TGTCTTTCTAGGCATTTCAAATGG 57.729 37.500 12.14 0.00 29.10 3.16
3029 3384 6.009589 TGTCTTTCTAGGCATTTCAAATGGA 58.990 36.000 12.14 0.00 29.10 3.41
3030 3385 6.071952 TGTCTTTCTAGGCATTTCAAATGGAC 60.072 38.462 12.14 8.23 29.10 4.02
3031 3386 6.151817 GTCTTTCTAGGCATTTCAAATGGACT 59.848 38.462 12.14 3.08 0.00 3.85
3032 3387 6.375455 TCTTTCTAGGCATTTCAAATGGACTC 59.625 38.462 12.14 0.00 0.00 3.36
3033 3388 5.178096 TCTAGGCATTTCAAATGGACTCA 57.822 39.130 12.14 0.00 0.00 3.41
3034 3389 5.569355 TCTAGGCATTTCAAATGGACTCAA 58.431 37.500 12.14 0.00 0.00 3.02
3035 3390 4.525912 AGGCATTTCAAATGGACTCAAC 57.474 40.909 12.14 0.00 0.00 3.18
3036 3391 3.896888 AGGCATTTCAAATGGACTCAACA 59.103 39.130 12.14 0.00 0.00 3.33
3037 3392 4.529377 AGGCATTTCAAATGGACTCAACAT 59.471 37.500 12.14 0.00 0.00 2.71
3038 3393 5.716228 AGGCATTTCAAATGGACTCAACATA 59.284 36.000 12.14 0.00 0.00 2.29
3039 3394 5.807011 GGCATTTCAAATGGACTCAACATAC 59.193 40.000 12.14 0.00 0.00 2.39
3040 3395 5.512788 GCATTTCAAATGGACTCAACATACG 59.487 40.000 12.14 0.00 0.00 3.06
3041 3396 5.621197 TTTCAAATGGACTCAACATACGG 57.379 39.130 0.00 0.00 0.00 4.02
3042 3397 4.545208 TCAAATGGACTCAACATACGGA 57.455 40.909 0.00 0.00 0.00 4.69
3043 3398 5.097742 TCAAATGGACTCAACATACGGAT 57.902 39.130 0.00 0.00 0.00 4.18
3044 3399 4.875536 TCAAATGGACTCAACATACGGATG 59.124 41.667 5.94 5.94 39.16 3.51
3046 3401 5.607939 AATGGACTCAACATACGGATGTA 57.392 39.130 15.10 0.00 45.93 2.29
3047 3402 5.808366 ATGGACTCAACATACGGATGTAT 57.192 39.130 15.10 0.00 45.93 2.29
3084 3439 9.677567 TTTAAAGTGTAGATTCACTCATTTTGC 57.322 29.630 0.00 0.00 46.25 3.68
3085 3440 6.882610 AAGTGTAGATTCACTCATTTTGCA 57.117 33.333 0.00 0.00 46.25 4.08
3086 3441 6.246420 AGTGTAGATTCACTCATTTTGCAC 57.754 37.500 0.00 0.00 44.07 4.57
3087 3442 5.182001 AGTGTAGATTCACTCATTTTGCACC 59.818 40.000 0.00 0.00 44.07 5.01
3088 3443 3.837213 AGATTCACTCATTTTGCACCG 57.163 42.857 0.00 0.00 0.00 4.94
3089 3444 3.149196 AGATTCACTCATTTTGCACCGT 58.851 40.909 0.00 0.00 0.00 4.83
3090 3445 4.323417 AGATTCACTCATTTTGCACCGTA 58.677 39.130 0.00 0.00 0.00 4.02
3091 3446 4.943705 AGATTCACTCATTTTGCACCGTAT 59.056 37.500 0.00 0.00 0.00 3.06
3092 3447 4.418013 TTCACTCATTTTGCACCGTATG 57.582 40.909 0.00 0.00 0.00 2.39
3093 3448 3.407698 TCACTCATTTTGCACCGTATGT 58.592 40.909 0.00 0.00 0.00 2.29
3094 3449 4.570930 TCACTCATTTTGCACCGTATGTA 58.429 39.130 0.00 0.00 0.00 2.29
3095 3450 4.629634 TCACTCATTTTGCACCGTATGTAG 59.370 41.667 0.00 0.00 0.00 2.74
3096 3451 4.391830 CACTCATTTTGCACCGTATGTAGT 59.608 41.667 0.00 0.00 0.00 2.73
3097 3452 4.630069 ACTCATTTTGCACCGTATGTAGTC 59.370 41.667 0.00 0.00 0.00 2.59
3098 3453 4.570930 TCATTTTGCACCGTATGTAGTCA 58.429 39.130 0.00 0.00 0.00 3.41
3099 3454 4.390603 TCATTTTGCACCGTATGTAGTCAC 59.609 41.667 0.00 0.00 0.00 3.67
3100 3455 3.671008 TTTGCACCGTATGTAGTCACT 57.329 42.857 0.00 0.00 0.00 3.41
3101 3456 3.671008 TTGCACCGTATGTAGTCACTT 57.329 42.857 0.00 0.00 0.00 3.16
3102 3457 2.954316 TGCACCGTATGTAGTCACTTG 58.046 47.619 0.00 0.00 0.00 3.16
3103 3458 2.297880 TGCACCGTATGTAGTCACTTGT 59.702 45.455 0.00 0.00 0.00 3.16
3104 3459 3.243941 TGCACCGTATGTAGTCACTTGTT 60.244 43.478 0.00 0.00 0.00 2.83
3105 3460 3.122948 GCACCGTATGTAGTCACTTGTTG 59.877 47.826 0.00 0.00 0.00 3.33
3106 3461 4.552355 CACCGTATGTAGTCACTTGTTGA 58.448 43.478 0.00 0.00 0.00 3.18
3107 3462 4.986034 CACCGTATGTAGTCACTTGTTGAA 59.014 41.667 0.00 0.00 35.39 2.69
3108 3463 5.464057 CACCGTATGTAGTCACTTGTTGAAA 59.536 40.000 0.00 0.00 35.39 2.69
3109 3464 6.147164 CACCGTATGTAGTCACTTGTTGAAAT 59.853 38.462 0.00 0.00 35.39 2.17
3110 3465 6.367969 ACCGTATGTAGTCACTTGTTGAAATC 59.632 38.462 0.00 0.00 35.39 2.17
3111 3466 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
3112 3467 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
3113 3468 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
3114 3469 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
3122 3477 9.996554 TCACTTGTTGAAATCTCTATAAAGACA 57.003 29.630 0.00 0.00 0.00 3.41
3139 3494 8.943909 ATAAAGACAAGTATTTAGGAACGGAG 57.056 34.615 6.26 0.00 30.97 4.63
3140 3495 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
3141 3496 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
3142 3497 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
3143 3498 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
3144 3499 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
3145 3500 5.134725 AGTATTTAGGAACGGAGGGAGTA 57.865 43.478 0.00 0.00 0.00 2.59
3363 3719 2.171448 GTCTTCCCTGTCTGTGGCATAT 59.829 50.000 0.00 0.00 0.00 1.78
3530 3886 0.806868 ATGTTGGAGCGTGCATCTTG 59.193 50.000 0.00 0.00 0.00 3.02
3551 3908 4.630111 TGAAAAAGATGCAACCAATGGTC 58.370 39.130 4.95 0.00 33.12 4.02
3564 3921 2.103263 CCAATGGTCGGTTTCCCAAAAA 59.897 45.455 0.00 0.00 33.66 1.94
3647 4008 3.000727 CGGAACTTTATTCGGCACTTCT 58.999 45.455 0.00 0.00 0.00 2.85
3703 4064 4.463539 TGAACTAGCAGTACGTATTTCCCA 59.536 41.667 0.00 0.00 0.00 4.37
3705 4066 5.410355 ACTAGCAGTACGTATTTCCCAAA 57.590 39.130 0.00 0.00 0.00 3.28
3715 4076 6.262193 ACGTATTTCCCAAATTACTGTTGG 57.738 37.500 0.00 0.00 44.42 3.77
3751 4112 5.539048 AGATATTAATCCCAGTGTACGTGC 58.461 41.667 0.00 0.00 31.98 5.34
3820 4181 2.483363 CGAGAGCAAGCTGATGGATCTT 60.483 50.000 0.00 0.00 0.00 2.40
3826 4187 3.065095 GCAAGCTGATGGATCTTCTCAAC 59.935 47.826 0.00 0.00 0.00 3.18
3905 4266 1.544825 CGTCCCATGGGAGTGAGTGT 61.545 60.000 34.67 0.00 46.16 3.55
3911 4272 2.165167 CATGGGAGTGAGTGTTGCATT 58.835 47.619 0.00 0.00 0.00 3.56
4106 4475 2.292521 TGGCCTTGGTCAGTAGATCTCT 60.293 50.000 3.32 0.00 0.00 3.10
4170 4540 5.027460 AGAGGTTTTGTTAAGTTTTGGGGT 58.973 37.500 0.00 0.00 0.00 4.95
4195 4565 8.442384 GTGACTTTTGTTTTGATTGTGAATTGT 58.558 29.630 0.00 0.00 0.00 2.71
4520 4891 3.879892 GTGTCTTCTCCTTTTTGCTCTGT 59.120 43.478 0.00 0.00 0.00 3.41
4616 4994 5.350091 CGGTTTGTCCATCAAAAGTTGTTTT 59.650 36.000 0.00 0.00 45.84 2.43
4774 5155 4.187694 GTTCCACTGAATCATGAGAGGAC 58.812 47.826 0.09 0.00 29.74 3.85
4804 5185 8.349568 TGTTAGAGTAGAGATGCTTTGTTCTA 57.650 34.615 0.00 0.00 0.00 2.10
4887 5269 2.610859 GGAGCCAACTGGGAGGGA 60.611 66.667 0.00 0.00 40.01 4.20
5059 5441 2.308570 TGTCATGATAAAGGGTGCAGGT 59.691 45.455 0.00 0.00 0.00 4.00
5258 5640 1.133668 CCTTTGGAGATCATGTCCCCC 60.134 57.143 0.00 0.00 32.49 5.40
5259 5641 1.849039 CTTTGGAGATCATGTCCCCCT 59.151 52.381 0.00 0.00 32.49 4.79
5349 5731 4.365514 TCCACCAAGAAATTGCTCAGTA 57.634 40.909 0.00 0.00 0.00 2.74
5355 5737 6.421801 CACCAAGAAATTGCTCAGTAAAAAGG 59.578 38.462 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 5.070001 CAGTTCCATTACTTGGTGGAGAAA 58.930 41.667 0.00 0.00 44.74 2.52
56 57 2.363683 CTCTCAATCAGAAAGGCCACC 58.636 52.381 5.01 0.00 0.00 4.61
83 84 4.909088 TCTTTCCCTTGTAAGTACCTTGGA 59.091 41.667 0.00 0.00 0.00 3.53
95 96 1.073923 ACGAAGGCATCTTTCCCTTGT 59.926 47.619 0.00 0.00 41.36 3.16
140 141 3.432517 CTCAACGGAGGAGCTTGAG 57.567 57.895 0.00 0.00 37.51 3.02
167 168 0.818296 CTAAGAGTGCGGCACTACCT 59.182 55.000 33.45 24.16 45.44 3.08
206 207 2.115910 CTGTTTGGGGCTGCCTCA 59.884 61.111 19.38 19.38 28.50 3.86
247 248 1.299648 CCCGTGGCTCAGGAAATCA 59.700 57.895 0.00 0.00 0.00 2.57
338 341 0.107017 CCACGGATCAGGGCATCTTT 60.107 55.000 0.00 0.00 0.00 2.52
431 435 4.877823 ACGATATATAATGCATGTGGGCTG 59.122 41.667 0.00 0.00 34.04 4.85
458 462 2.269883 GTAAACGGGGTGCCGGAT 59.730 61.111 5.05 0.00 37.53 4.18
459 463 4.019312 GGTAAACGGGGTGCCGGA 62.019 66.667 5.05 0.00 37.53 5.14
467 471 1.069091 ACGAAAATTGCGGTAAACGGG 60.069 47.619 0.00 0.00 44.51 5.28
470 474 2.898225 GACGACGAAAATTGCGGTAAAC 59.102 45.455 0.00 0.00 0.00 2.01
550 554 8.634335 ATTGCTATTGTGCATAATATACCACA 57.366 30.769 15.27 7.38 42.96 4.17
552 556 8.892723 GCTATTGCTATTGTGCATAATATACCA 58.107 33.333 15.27 10.52 42.96 3.25
553 557 8.892723 TGCTATTGCTATTGTGCATAATATACC 58.107 33.333 15.27 8.45 42.96 2.73
556 560 9.797556 CAATGCTATTGCTATTGTGCATAATAT 57.202 29.630 15.27 5.56 42.96 1.28
557 561 7.756272 GCAATGCTATTGCTATTGTGCATAATA 59.244 33.333 19.93 14.32 42.96 0.98
558 562 6.588756 GCAATGCTATTGCTATTGTGCATAAT 59.411 34.615 19.93 13.54 42.96 1.28
559 563 5.921976 GCAATGCTATTGCTATTGTGCATAA 59.078 36.000 19.93 0.00 42.96 1.90
560 564 5.463286 GCAATGCTATTGCTATTGTGCATA 58.537 37.500 19.93 0.00 42.96 3.14
561 565 4.304110 GCAATGCTATTGCTATTGTGCAT 58.696 39.130 19.93 8.99 42.96 3.96
562 566 3.708890 GCAATGCTATTGCTATTGTGCA 58.291 40.909 19.93 5.89 41.87 4.57
587 593 2.564771 CATGATCCACAATACGGTGCT 58.435 47.619 0.00 0.00 37.46 4.40
591 597 5.551233 AGATTACCATGATCCACAATACGG 58.449 41.667 0.00 0.00 0.00 4.02
592 598 7.378966 ACTAGATTACCATGATCCACAATACG 58.621 38.462 0.00 0.00 0.00 3.06
813 827 2.270986 CCAGCCTCTTTTGCGCCTT 61.271 57.895 4.18 0.00 0.00 4.35
1016 1035 0.440371 CGCTCCTTTCTGCGTTTCTC 59.560 55.000 0.00 0.00 46.09 2.87
1061 1080 3.056465 TCCTCGCTTCTTCTTCTTCTTCC 60.056 47.826 0.00 0.00 0.00 3.46
1336 1365 0.827368 GCGACCTCTTCATCTTCCCT 59.173 55.000 0.00 0.00 0.00 4.20
1417 1446 0.535335 GGAGATGCACGTACTTGGGA 59.465 55.000 1.12 0.00 0.00 4.37
1493 1537 1.134175 AGAGCTTAAGACGAGCAGAGC 59.866 52.381 6.67 0.00 42.56 4.09
1537 1604 5.388288 GCTCGCGTTTTTATGTTTTGTTTTG 59.612 36.000 5.77 0.00 0.00 2.44
1539 1606 4.026393 GGCTCGCGTTTTTATGTTTTGTTT 60.026 37.500 5.77 0.00 0.00 2.83
1540 1607 3.487942 GGCTCGCGTTTTTATGTTTTGTT 59.512 39.130 5.77 0.00 0.00 2.83
1541 1608 3.047093 GGCTCGCGTTTTTATGTTTTGT 58.953 40.909 5.77 0.00 0.00 2.83
1542 1609 3.305110 AGGCTCGCGTTTTTATGTTTTG 58.695 40.909 5.77 0.00 0.00 2.44
1543 1610 3.636282 AGGCTCGCGTTTTTATGTTTT 57.364 38.095 5.77 0.00 0.00 2.43
1544 1611 4.214758 AGTTAGGCTCGCGTTTTTATGTTT 59.785 37.500 5.77 0.00 0.00 2.83
1545 1612 3.749609 AGTTAGGCTCGCGTTTTTATGTT 59.250 39.130 5.77 0.00 0.00 2.71
1546 1613 3.332034 AGTTAGGCTCGCGTTTTTATGT 58.668 40.909 5.77 0.00 0.00 2.29
1550 1617 3.396560 AGTTAGTTAGGCTCGCGTTTTT 58.603 40.909 5.77 0.00 0.00 1.94
1619 1686 1.357991 GGCAAGAGAAGCAGAGCGAC 61.358 60.000 0.00 0.00 0.00 5.19
1635 1702 3.367806 GCTAAGCTAGATCGATCATGGCA 60.368 47.826 26.47 11.24 0.00 4.92
1655 1722 3.198635 ACATGCATGGACTAGTACAAGCT 59.801 43.478 29.83 16.27 38.80 3.74
1656 1723 3.535561 ACATGCATGGACTAGTACAAGC 58.464 45.455 29.41 25.10 38.52 4.01
1657 1724 5.178061 TGAACATGCATGGACTAGTACAAG 58.822 41.667 29.41 9.18 0.00 3.16
1658 1725 5.159273 TGAACATGCATGGACTAGTACAA 57.841 39.130 29.41 0.00 0.00 2.41
1708 1957 3.831333 TCTCTACTCATCCATGATCAGCC 59.169 47.826 0.09 0.00 36.02 4.85
1709 1958 4.082081 CCTCTCTACTCATCCATGATCAGC 60.082 50.000 0.09 0.00 36.02 4.26
1721 1970 3.465210 ACCCATCATCTCCTCTCTACTCA 59.535 47.826 0.00 0.00 0.00 3.41
1723 1972 3.465210 TCACCCATCATCTCCTCTCTACT 59.535 47.826 0.00 0.00 0.00 2.57
1724 1973 3.826157 CTCACCCATCATCTCCTCTCTAC 59.174 52.174 0.00 0.00 0.00 2.59
1725 1974 3.724209 TCTCACCCATCATCTCCTCTCTA 59.276 47.826 0.00 0.00 0.00 2.43
1791 2049 2.202851 CTCTGCTGGCTACCGCTG 60.203 66.667 0.00 0.00 36.09 5.18
1792 2050 2.363018 TCTCTGCTGGCTACCGCT 60.363 61.111 0.00 0.00 36.09 5.52
1795 2053 0.459489 CTGTCTCTCTGCTGGCTACC 59.541 60.000 0.00 0.00 0.00 3.18
1938 2196 1.883084 GATGATGGCGACGTGGACC 60.883 63.158 0.00 2.46 0.00 4.46
2053 2318 5.513614 CCATATCTTGATACAGTGGATGCCA 60.514 44.000 0.00 0.00 0.00 4.92
2054 2319 4.940046 CCATATCTTGATACAGTGGATGCC 59.060 45.833 0.00 0.00 0.00 4.40
2055 2320 4.394300 GCCATATCTTGATACAGTGGATGC 59.606 45.833 11.04 0.00 0.00 3.91
2056 2321 5.554070 TGCCATATCTTGATACAGTGGATG 58.446 41.667 11.04 0.00 0.00 3.51
2057 2322 5.830799 TGCCATATCTTGATACAGTGGAT 57.169 39.130 11.04 0.00 0.00 3.41
2058 2323 5.513614 CCATGCCATATCTTGATACAGTGGA 60.514 44.000 11.04 0.00 0.00 4.02
2059 2324 4.698780 CCATGCCATATCTTGATACAGTGG 59.301 45.833 0.00 5.02 0.00 4.00
2220 2502 9.696572 ACTTTTTACCTACCTTTTTCTTCTTCT 57.303 29.630 0.00 0.00 0.00 2.85
2450 2742 4.026052 GGTTTCTTTCATGATCCATGGGT 58.974 43.478 13.02 3.70 41.66 4.51
2452 2744 4.025360 TGGGTTTCTTTCATGATCCATGG 58.975 43.478 4.97 4.97 41.66 3.66
2793 3096 3.681897 GCCGAGGTAGCATGAGAAATATG 59.318 47.826 0.00 0.00 0.00 1.78
2796 3099 1.202698 GGCCGAGGTAGCATGAGAAAT 60.203 52.381 0.00 0.00 0.00 2.17
2797 3100 0.178068 GGCCGAGGTAGCATGAGAAA 59.822 55.000 0.00 0.00 0.00 2.52
2798 3101 1.686325 GGGCCGAGGTAGCATGAGAA 61.686 60.000 0.00 0.00 0.00 2.87
2799 3102 2.134287 GGGCCGAGGTAGCATGAGA 61.134 63.158 0.00 0.00 0.00 3.27
2801 3104 3.536917 CGGGCCGAGGTAGCATGA 61.537 66.667 24.41 0.00 0.00 3.07
2804 3107 3.766691 GAACGGGCCGAGGTAGCA 61.767 66.667 35.78 0.00 0.00 3.49
2805 3108 4.867599 CGAACGGGCCGAGGTAGC 62.868 72.222 35.78 13.07 0.00 3.58
2806 3109 4.203076 CCGAACGGGCCGAGGTAG 62.203 72.222 35.78 17.65 0.00 3.18
2840 3192 7.786305 TTTACACACTTATATATACGCTCGC 57.214 36.000 0.00 0.00 0.00 5.03
2879 3233 2.821546 TCAGCGGTCTAATATGCACAC 58.178 47.619 0.00 0.00 0.00 3.82
2984 3339 1.838077 AGTATTTGGGAACGGAGGGAG 59.162 52.381 0.00 0.00 0.00 4.30
2985 3340 1.961133 AGTATTTGGGAACGGAGGGA 58.039 50.000 0.00 0.00 0.00 4.20
2986 3341 2.290705 ACAAGTATTTGGGAACGGAGGG 60.291 50.000 2.81 0.00 38.66 4.30
2987 3342 3.007635 GACAAGTATTTGGGAACGGAGG 58.992 50.000 2.81 0.00 38.66 4.30
2988 3343 3.939066 AGACAAGTATTTGGGAACGGAG 58.061 45.455 2.81 0.00 38.66 4.63
2989 3344 4.360951 AAGACAAGTATTTGGGAACGGA 57.639 40.909 2.81 0.00 38.66 4.69
2990 3345 4.760204 AGAAAGACAAGTATTTGGGAACGG 59.240 41.667 2.81 0.00 38.66 4.44
2991 3346 5.941948 AGAAAGACAAGTATTTGGGAACG 57.058 39.130 2.81 0.00 38.66 3.95
2992 3347 6.127980 GCCTAGAAAGACAAGTATTTGGGAAC 60.128 42.308 2.81 0.00 38.66 3.62
2993 3348 5.944007 GCCTAGAAAGACAAGTATTTGGGAA 59.056 40.000 2.81 0.00 38.66 3.97
2994 3349 5.013704 TGCCTAGAAAGACAAGTATTTGGGA 59.986 40.000 2.81 0.00 38.66 4.37
2995 3350 5.253330 TGCCTAGAAAGACAAGTATTTGGG 58.747 41.667 2.81 0.00 38.66 4.12
2996 3351 7.396540 AATGCCTAGAAAGACAAGTATTTGG 57.603 36.000 2.81 0.00 38.66 3.28
2997 3352 8.514594 TGAAATGCCTAGAAAGACAAGTATTTG 58.485 33.333 0.00 0.00 40.24 2.32
2998 3353 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
2999 3354 8.635765 TTGAAATGCCTAGAAAGACAAGTATT 57.364 30.769 0.00 0.00 0.00 1.89
3000 3355 8.635765 TTTGAAATGCCTAGAAAGACAAGTAT 57.364 30.769 0.00 0.00 0.00 2.12
3001 3356 8.514594 CATTTGAAATGCCTAGAAAGACAAGTA 58.485 33.333 4.82 0.00 0.00 2.24
3002 3357 6.959639 TTTGAAATGCCTAGAAAGACAAGT 57.040 33.333 0.00 0.00 0.00 3.16
3003 3358 6.810182 CCATTTGAAATGCCTAGAAAGACAAG 59.190 38.462 12.26 0.00 0.00 3.16
3004 3359 6.493115 TCCATTTGAAATGCCTAGAAAGACAA 59.507 34.615 12.26 0.00 0.00 3.18
3005 3360 6.009589 TCCATTTGAAATGCCTAGAAAGACA 58.990 36.000 12.26 0.00 0.00 3.41
3006 3361 6.151817 AGTCCATTTGAAATGCCTAGAAAGAC 59.848 38.462 12.26 10.86 0.00 3.01
3007 3362 6.248433 AGTCCATTTGAAATGCCTAGAAAGA 58.752 36.000 12.26 0.00 0.00 2.52
3008 3363 6.151648 TGAGTCCATTTGAAATGCCTAGAAAG 59.848 38.462 12.26 0.00 0.00 2.62
3009 3364 6.009589 TGAGTCCATTTGAAATGCCTAGAAA 58.990 36.000 12.26 0.00 0.00 2.52
3010 3365 5.569355 TGAGTCCATTTGAAATGCCTAGAA 58.431 37.500 12.26 0.00 0.00 2.10
3011 3366 5.178096 TGAGTCCATTTGAAATGCCTAGA 57.822 39.130 12.26 1.83 0.00 2.43
3012 3367 5.183713 TGTTGAGTCCATTTGAAATGCCTAG 59.816 40.000 12.26 0.00 0.00 3.02
3013 3368 5.076182 TGTTGAGTCCATTTGAAATGCCTA 58.924 37.500 12.26 0.00 0.00 3.93
3014 3369 3.896888 TGTTGAGTCCATTTGAAATGCCT 59.103 39.130 12.26 9.70 0.00 4.75
3015 3370 4.255833 TGTTGAGTCCATTTGAAATGCC 57.744 40.909 12.26 5.23 0.00 4.40
3016 3371 5.512788 CGTATGTTGAGTCCATTTGAAATGC 59.487 40.000 12.26 0.23 0.00 3.56
3017 3372 6.029607 CCGTATGTTGAGTCCATTTGAAATG 58.970 40.000 10.84 10.84 0.00 2.32
3018 3373 5.943416 TCCGTATGTTGAGTCCATTTGAAAT 59.057 36.000 0.00 0.00 0.00 2.17
3019 3374 5.309638 TCCGTATGTTGAGTCCATTTGAAA 58.690 37.500 0.00 0.00 0.00 2.69
3020 3375 4.900684 TCCGTATGTTGAGTCCATTTGAA 58.099 39.130 0.00 0.00 0.00 2.69
3021 3376 4.545208 TCCGTATGTTGAGTCCATTTGA 57.455 40.909 0.00 0.00 0.00 2.69
3022 3377 4.635765 ACATCCGTATGTTGAGTCCATTTG 59.364 41.667 0.00 0.00 44.07 2.32
3023 3378 4.843728 ACATCCGTATGTTGAGTCCATTT 58.156 39.130 0.00 0.00 44.07 2.32
3024 3379 4.487714 ACATCCGTATGTTGAGTCCATT 57.512 40.909 0.00 0.00 44.07 3.16
3025 3380 5.541845 CATACATCCGTATGTTGAGTCCAT 58.458 41.667 0.00 0.00 46.70 3.41
3026 3381 4.944048 CATACATCCGTATGTTGAGTCCA 58.056 43.478 0.00 0.00 46.70 4.02
3064 3419 5.393962 GGTGCAAAATGAGTGAATCTACAC 58.606 41.667 0.00 0.00 40.60 2.90
3065 3420 4.154015 CGGTGCAAAATGAGTGAATCTACA 59.846 41.667 0.00 0.00 0.00 2.74
3066 3421 4.154195 ACGGTGCAAAATGAGTGAATCTAC 59.846 41.667 0.00 0.00 0.00 2.59
3067 3422 4.323417 ACGGTGCAAAATGAGTGAATCTA 58.677 39.130 0.00 0.00 0.00 1.98
3068 3423 3.149196 ACGGTGCAAAATGAGTGAATCT 58.851 40.909 0.00 0.00 0.00 2.40
3069 3424 3.559238 ACGGTGCAAAATGAGTGAATC 57.441 42.857 0.00 0.00 0.00 2.52
3070 3425 4.458989 ACATACGGTGCAAAATGAGTGAAT 59.541 37.500 0.00 0.00 0.00 2.57
3071 3426 3.818210 ACATACGGTGCAAAATGAGTGAA 59.182 39.130 0.00 0.00 0.00 3.18
3072 3427 3.407698 ACATACGGTGCAAAATGAGTGA 58.592 40.909 0.00 0.00 0.00 3.41
3073 3428 3.829886 ACATACGGTGCAAAATGAGTG 57.170 42.857 0.00 0.00 0.00 3.51
3074 3429 4.575885 ACTACATACGGTGCAAAATGAGT 58.424 39.130 0.00 0.00 0.00 3.41
3075 3430 4.629634 TGACTACATACGGTGCAAAATGAG 59.370 41.667 0.00 0.00 0.00 2.90
3076 3431 4.390603 GTGACTACATACGGTGCAAAATGA 59.609 41.667 0.00 0.00 0.00 2.57
3077 3432 4.391830 AGTGACTACATACGGTGCAAAATG 59.608 41.667 0.00 0.00 0.00 2.32
3078 3433 4.575885 AGTGACTACATACGGTGCAAAAT 58.424 39.130 0.00 0.00 0.00 1.82
3079 3434 3.997762 AGTGACTACATACGGTGCAAAA 58.002 40.909 0.00 0.00 0.00 2.44
3080 3435 3.671008 AGTGACTACATACGGTGCAAA 57.329 42.857 0.00 0.00 0.00 3.68
3081 3436 3.243941 ACAAGTGACTACATACGGTGCAA 60.244 43.478 0.00 0.00 0.00 4.08
3082 3437 2.297880 ACAAGTGACTACATACGGTGCA 59.702 45.455 0.00 0.00 0.00 4.57
3083 3438 2.955614 ACAAGTGACTACATACGGTGC 58.044 47.619 0.00 0.00 0.00 5.01
3084 3439 4.552355 TCAACAAGTGACTACATACGGTG 58.448 43.478 0.00 0.00 0.00 4.94
3085 3440 4.859304 TCAACAAGTGACTACATACGGT 57.141 40.909 0.00 0.00 0.00 4.83
3086 3441 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
3087 3442 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
3088 3443 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
3096 3451 9.996554 TGTCTTTATAGAGATTTCAACAAGTGA 57.003 29.630 0.00 0.00 0.00 3.41
3114 3469 7.985752 CCTCCGTTCCTAAATACTTGTCTTTAT 59.014 37.037 0.00 0.00 0.00 1.40
3115 3470 7.325694 CCTCCGTTCCTAAATACTTGTCTTTA 58.674 38.462 0.00 0.00 0.00 1.85
3116 3471 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
3117 3472 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
3118 3473 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
3119 3474 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
3120 3475 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
3121 3476 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
3122 3477 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
3123 3478 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
3124 3479 4.892345 ACTACTCCCTCCGTTCCTAAATAC 59.108 45.833 0.00 0.00 0.00 1.89
3125 3480 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
3126 3481 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
3127 3482 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
3128 3483 4.414846 AGATACTACTCCCTCCGTTCCTAA 59.585 45.833 0.00 0.00 0.00 2.69
3129 3484 3.979347 AGATACTACTCCCTCCGTTCCTA 59.021 47.826 0.00 0.00 0.00 2.94
3130 3485 2.784682 AGATACTACTCCCTCCGTTCCT 59.215 50.000 0.00 0.00 0.00 3.36
3131 3486 3.226682 AGATACTACTCCCTCCGTTCC 57.773 52.381 0.00 0.00 0.00 3.62
3132 3487 3.752747 GCTAGATACTACTCCCTCCGTTC 59.247 52.174 0.00 0.00 0.00 3.95
3133 3488 3.395273 AGCTAGATACTACTCCCTCCGTT 59.605 47.826 0.00 0.00 0.00 4.44
3134 3489 2.981081 AGCTAGATACTACTCCCTCCGT 59.019 50.000 0.00 0.00 0.00 4.69
3135 3490 3.244630 ACAGCTAGATACTACTCCCTCCG 60.245 52.174 0.00 0.00 0.00 4.63
3136 3491 4.376225 ACAGCTAGATACTACTCCCTCC 57.624 50.000 0.00 0.00 0.00 4.30
3137 3492 5.935789 CACTACAGCTAGATACTACTCCCTC 59.064 48.000 0.00 0.00 0.00 4.30
3138 3493 5.370289 ACACTACAGCTAGATACTACTCCCT 59.630 44.000 0.00 0.00 0.00 4.20
3139 3494 5.623169 ACACTACAGCTAGATACTACTCCC 58.377 45.833 0.00 0.00 0.00 4.30
3140 3495 6.205270 GGAACACTACAGCTAGATACTACTCC 59.795 46.154 0.00 0.00 0.00 3.85
3141 3496 6.993902 AGGAACACTACAGCTAGATACTACTC 59.006 42.308 0.00 0.00 0.00 2.59
3142 3497 6.768861 CAGGAACACTACAGCTAGATACTACT 59.231 42.308 0.00 0.00 0.00 2.57
3143 3498 6.766944 TCAGGAACACTACAGCTAGATACTAC 59.233 42.308 0.00 0.00 0.00 2.73
3144 3499 6.896883 TCAGGAACACTACAGCTAGATACTA 58.103 40.000 0.00 0.00 0.00 1.82
3145 3500 5.756918 TCAGGAACACTACAGCTAGATACT 58.243 41.667 0.00 0.00 0.00 2.12
3204 3560 9.587772 CATGTACCATATATAGCCAGTAACTTC 57.412 37.037 0.00 0.00 0.00 3.01
3363 3719 5.958380 ACATATGGTAGAGAGACAAGGACAA 59.042 40.000 7.80 0.00 0.00 3.18
3530 3886 3.674753 CGACCATTGGTTGCATCTTTTTC 59.325 43.478 10.29 0.00 35.25 2.29
3564 3921 9.097257 CAACAGAGAAAAACCAATAATTGTTGT 57.903 29.630 13.13 0.29 37.78 3.32
3647 4008 8.109705 TGTTATGGTCTACTAGTTAACAACGA 57.890 34.615 8.61 0.00 36.23 3.85
3690 4051 7.094677 ACCAACAGTAATTTGGGAAATACGTAC 60.095 37.037 0.00 0.00 46.85 3.67
3693 4054 6.090129 CACCAACAGTAATTTGGGAAATACG 58.910 40.000 6.10 0.00 46.85 3.06
3703 4064 4.098914 TCCAGAGCACCAACAGTAATTT 57.901 40.909 0.00 0.00 0.00 1.82
3705 4066 3.788227 TTCCAGAGCACCAACAGTAAT 57.212 42.857 0.00 0.00 0.00 1.89
3715 4076 8.103305 TGGGATTAATATCTAATTCCAGAGCAC 58.897 37.037 10.99 0.00 37.59 4.40
3820 4181 2.651455 ACATACTCGGATCCGTTGAGA 58.349 47.619 32.15 18.64 40.74 3.27
3826 4187 3.474007 CGGAACATACTCGGATCCG 57.526 57.895 28.62 28.62 45.88 4.18
3892 4253 2.040813 AGAATGCAACACTCACTCCCAT 59.959 45.455 0.00 0.00 0.00 4.00
3905 4266 5.595133 TGCATATGGAGAATCAAGAATGCAA 59.405 36.000 4.56 0.00 38.20 4.08
3911 4272 7.387119 GCATTATGCATATGGAGAATCAAGA 57.613 36.000 13.43 0.00 44.26 3.02
4106 4475 4.801330 TCCGCTGATCTGAAACTTAAGA 57.199 40.909 10.09 0.00 0.00 2.10
4162 4532 5.228945 TCAAAACAAAAGTCACCCCAAAA 57.771 34.783 0.00 0.00 0.00 2.44
4170 4540 8.545229 ACAATTCACAATCAAAACAAAAGTCA 57.455 26.923 0.00 0.00 0.00 3.41
4204 4575 5.528320 CCTTGGTGCTGAAACAATTCAAAAT 59.472 36.000 0.00 0.00 44.64 1.82
4299 4670 5.310594 AGGGATGAGCAAGCAAGGTTATATA 59.689 40.000 0.00 0.00 0.00 0.86
4300 4671 4.105377 AGGGATGAGCAAGCAAGGTTATAT 59.895 41.667 0.00 0.00 0.00 0.86
4508 4879 5.654497 AGGAAGAACAAACAGAGCAAAAAG 58.346 37.500 0.00 0.00 0.00 2.27
4572 4950 3.443681 CCGCAAGAGGAAAAATATGGTGT 59.556 43.478 0.00 0.00 43.02 4.16
4577 4955 5.336451 GGACAAACCGCAAGAGGAAAAATAT 60.336 40.000 0.00 0.00 43.02 1.28
4616 4994 5.104982 TGACAGTCACACCATGCTGATAATA 60.105 40.000 0.00 0.00 36.51 0.98
4774 5155 7.763528 ACAAAGCATCTCTACTCTAACATTGAG 59.236 37.037 0.00 0.00 37.55 3.02
4781 5162 8.417106 CCATAGAACAAAGCATCTCTACTCTAA 58.583 37.037 0.00 0.00 0.00 2.10
4804 5185 2.984562 TGTATGTCGACAATGCACCAT 58.015 42.857 24.13 5.75 0.00 3.55
4887 5269 0.842635 GATGCCTCTGTCCATCCCTT 59.157 55.000 0.00 0.00 33.43 3.95
5258 5640 2.617308 CTCAAGGCTGGCATCATTACAG 59.383 50.000 3.38 0.00 35.40 2.74
5259 5641 2.025981 ACTCAAGGCTGGCATCATTACA 60.026 45.455 3.38 0.00 0.00 2.41
5349 5731 9.367160 CAATAATATCCATAGTGACCCCTTTTT 57.633 33.333 0.00 0.00 0.00 1.94
5355 5737 9.574516 AAGAAACAATAATATCCATAGTGACCC 57.425 33.333 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.