Multiple sequence alignment - TraesCS3B01G324900

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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 TraesCS3B01G324900 chr3B 100.000 4550 0 0 1 4550 525833718 525829169 0.000000e+00 8403.0
1 TraesCS3B01G324900 chr3B 86.262 757 100 2 9 761 222249947 222249191 0.000000e+00 819.0
2 TraesCS3B01G324900 chr3B 90.909 55 5 0 1001 1055 187352153 187352207 1.760000e-09 75.0
3 TraesCS3B01G324900 chr3A 92.244 2411 103 29 1832 4184 519209612 519207228 0.000000e+00 3339.0
4 TraesCS3B01G324900 chr3A 95.577 814 18 7 759 1556 519210446 519209635 0.000000e+00 1288.0
5 TraesCS3B01G324900 chr3A 87.401 754 93 2 9 761 496599165 496598413 0.000000e+00 865.0
6 TraesCS3B01G324900 chr3A 86.260 262 28 5 4185 4445 519205900 519205646 1.250000e-70 278.0
7 TraesCS3B01G324900 chr3A 89.091 55 6 0 1001 1055 142896670 142896724 8.170000e-08 69.4
8 TraesCS3B01G324900 chr3D 94.036 1593 61 14 1850 3415 400276383 400274798 0.000000e+00 2385.0
9 TraesCS3B01G324900 chr3D 90.480 1166 65 28 3414 4550 400274557 400273409 0.000000e+00 1496.0
10 TraesCS3B01G324900 chr3D 93.356 888 21 13 768 1638 400277666 400276800 0.000000e+00 1279.0
11 TraesCS3B01G324900 chr3D 89.091 55 6 0 1001 1055 130933092 130933146 8.170000e-08 69.4
12 TraesCS3B01G324900 chr4B 87.618 743 91 1 9 750 65528961 65528219 0.000000e+00 861.0
13 TraesCS3B01G324900 chr4B 87.349 743 93 1 9 750 65100928 65100186 0.000000e+00 850.0
14 TraesCS3B01G324900 chr1B 86.922 757 98 1 9 764 419276107 419275351 0.000000e+00 848.0
15 TraesCS3B01G324900 chr1B 85.599 743 107 0 9 751 14988946 14988204 0.000000e+00 780.0
16 TraesCS3B01G324900 chr1B 78.411 579 96 22 2610 3167 580633847 580634417 2.600000e-92 350.0
17 TraesCS3B01G324900 chr1B 75.432 521 98 27 903 1403 580631820 580632330 4.580000e-55 226.0
18 TraesCS3B01G324900 chr5B 86.790 757 96 2 9 761 398806716 398807472 0.000000e+00 841.0
19 TraesCS3B01G324900 chr6B 86.472 754 101 1 9 761 683421992 683421239 0.000000e+00 826.0
20 TraesCS3B01G324900 chrUn 85.734 743 106 0 9 751 2466011 2465269 0.000000e+00 785.0
21 TraesCS3B01G324900 chr1A 78.276 580 98 21 2610 3168 527177283 527177855 9.370000e-92 348.0
22 TraesCS3B01G324900 chr1A 89.583 144 14 1 1261 1403 527175253 527175396 1.010000e-41 182.0
23 TraesCS3B01G324900 chr1A 96.875 64 2 0 992 1055 527174608 527174671 1.730000e-19 108.0
24 TraesCS3B01G324900 chr1A 95.238 42 2 0 1144 1185 527175126 527175167 2.940000e-07 67.6
25 TraesCS3B01G324900 chr1D 78.007 582 97 24 2610 3168 429698535 429699108 2.030000e-88 337.0
26 TraesCS3B01G324900 chr1D 88.971 136 15 0 1268 1403 429696895 429697030 7.830000e-38 169.0
27 TraesCS3B01G324900 chr1D 78.713 202 28 15 992 1184 429696443 429696638 2.220000e-23 121.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G324900 chr3B 525829169 525833718 4549 True 8403 8403 100.000000 1 4550 1 chr3B.!!$R2 4549
1 TraesCS3B01G324900 chr3B 222249191 222249947 756 True 819 819 86.262000 9 761 1 chr3B.!!$R1 752
2 TraesCS3B01G324900 chr3A 519205646 519210446 4800 True 1635 3339 91.360333 759 4445 3 chr3A.!!$R2 3686
3 TraesCS3B01G324900 chr3A 496598413 496599165 752 True 865 865 87.401000 9 761 1 chr3A.!!$R1 752
4 TraesCS3B01G324900 chr3D 400273409 400277666 4257 True 1720 2385 92.624000 768 4550 3 chr3D.!!$R1 3782
5 TraesCS3B01G324900 chr4B 65528219 65528961 742 True 861 861 87.618000 9 750 1 chr4B.!!$R2 741
6 TraesCS3B01G324900 chr4B 65100186 65100928 742 True 850 850 87.349000 9 750 1 chr4B.!!$R1 741
7 TraesCS3B01G324900 chr1B 419275351 419276107 756 True 848 848 86.922000 9 764 1 chr1B.!!$R2 755
8 TraesCS3B01G324900 chr1B 14988204 14988946 742 True 780 780 85.599000 9 751 1 chr1B.!!$R1 742
9 TraesCS3B01G324900 chr1B 580631820 580634417 2597 False 288 350 76.921500 903 3167 2 chr1B.!!$F1 2264
10 TraesCS3B01G324900 chr5B 398806716 398807472 756 False 841 841 86.790000 9 761 1 chr5B.!!$F1 752
11 TraesCS3B01G324900 chr6B 683421239 683421992 753 True 826 826 86.472000 9 761 1 chr6B.!!$R1 752
12 TraesCS3B01G324900 chrUn 2465269 2466011 742 True 785 785 85.734000 9 751 1 chrUn.!!$R1 742
13 TraesCS3B01G324900 chr1D 429696443 429699108 2665 False 209 337 81.897000 992 3168 3 chr1D.!!$F1 2176

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
45 46 0.101219 GGGCCGAAGACATCATTTGC 59.899 55.0 0.0 0.0 0.0 3.68 F
172 173 0.240411 GAGTTCAGTACGACGCACCT 59.760 55.0 0.0 0.0 0.0 4.00 F
1634 3008 0.465460 ACACGGCACACTTTGGTCAT 60.465 50.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1611 2985 0.738389 CCAAAGTGTGCCGTGTCTTT 59.262 50.000 0.00 0.0 0.0 2.52 R
1805 3180 1.275856 TGGCTGCAAAATCACAATCCC 59.724 47.619 0.50 0.0 0.0 3.85 R
3574 5518 1.001974 ACAGGCACGAAAGACTGCATA 59.998 47.619 9.44 0.0 34.9 3.14 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 0.325933 CAAGGCTCCATCCTGTGACA 59.674 55.000 0.00 0.00 36.38 3.58
45 46 0.101219 GGGCCGAAGACATCATTTGC 59.899 55.000 0.00 0.00 0.00 3.68
54 55 3.461061 AGACATCATTTGCGATGATCGT 58.539 40.909 16.83 12.23 44.67 3.73
126 127 2.353208 GCACTCGAGGAACAGATTGACT 60.353 50.000 18.41 0.00 0.00 3.41
132 133 2.941720 GAGGAACAGATTGACTCATGGC 59.058 50.000 0.00 0.00 0.00 4.40
153 154 2.429907 GATCAGCTCGATCCGGCG 60.430 66.667 0.00 0.00 44.25 6.46
171 172 1.063951 CGAGTTCAGTACGACGCACC 61.064 60.000 0.00 0.00 0.00 5.01
172 173 0.240411 GAGTTCAGTACGACGCACCT 59.760 55.000 0.00 0.00 0.00 4.00
198 199 2.623889 GGCGCTATCTCTTCTTGAGGTA 59.376 50.000 7.64 0.00 42.86 3.08
201 202 3.004944 CGCTATCTCTTCTTGAGGTACCC 59.995 52.174 8.74 0.32 42.86 3.69
204 205 1.356738 TCTCTTCTTGAGGTACCCCGA 59.643 52.381 8.74 0.00 42.86 5.14
210 211 1.346722 CTTGAGGTACCCCGACAACTT 59.653 52.381 8.74 0.00 35.12 2.66
213 214 2.030958 GGTACCCCGACAACTTGCG 61.031 63.158 0.00 0.00 0.00 4.85
214 215 1.301165 GTACCCCGACAACTTGCGT 60.301 57.895 0.00 0.00 0.00 5.24
276 277 4.351192 GTTTTGTCACCATCAACACTGAC 58.649 43.478 0.00 0.00 33.30 3.51
285 286 1.163420 TCAACACTGACGCGGCAATT 61.163 50.000 19.01 8.19 0.00 2.32
289 290 1.604755 ACACTGACGCGGCAATTAAAA 59.395 42.857 19.01 0.00 0.00 1.52
299 300 3.793492 GCGGCAATTAAAAGAGAAGATGC 59.207 43.478 0.00 0.00 0.00 3.91
335 336 4.247781 CGTAGCCCGGTCCTCTAA 57.752 61.111 0.00 0.00 0.00 2.10
345 346 3.958798 CCCGGTCCTCTAACTCATTTCTA 59.041 47.826 0.00 0.00 0.00 2.10
390 391 4.263243 CCTGGAGTTATGGATCCCTTCATC 60.263 50.000 9.90 2.04 34.47 2.92
391 392 3.652869 TGGAGTTATGGATCCCTTCATCC 59.347 47.826 9.90 11.87 42.68 3.51
425 426 1.890510 TGCGCGACGGAGCTATCTA 60.891 57.895 12.10 0.00 39.95 1.98
456 457 3.324268 TGAGGGGTTTTACACACGTCATA 59.676 43.478 0.00 0.00 46.55 2.15
513 514 1.508545 CACTCGCCATGACTCTCGT 59.491 57.895 0.00 0.00 0.00 4.18
525 526 1.173444 ACTCTCGTTCAGTCGTGGCT 61.173 55.000 0.00 0.00 0.00 4.75
546 547 5.066593 GCTCCTATCCTGTTAGAAATTGGG 58.933 45.833 0.00 0.00 0.00 4.12
598 601 7.543756 TGATATTCGGCATATTGTAAGATCGA 58.456 34.615 0.00 0.00 0.00 3.59
600 603 3.909430 TCGGCATATTGTAAGATCGACC 58.091 45.455 0.00 0.00 0.00 4.79
651 654 4.123497 AGCTTGCATAATAGACGTGACA 57.877 40.909 0.00 0.00 0.00 3.58
666 669 2.736719 CGTGACAGAAAGCTGGATCGAT 60.737 50.000 0.00 0.00 46.60 3.59
668 671 4.433615 GTGACAGAAAGCTGGATCGATAA 58.566 43.478 0.00 0.00 46.60 1.75
669 672 4.268884 GTGACAGAAAGCTGGATCGATAAC 59.731 45.833 0.00 0.00 46.60 1.89
678 681 3.570550 GCTGGATCGATAACACTCCTAGT 59.429 47.826 0.00 0.00 0.00 2.57
684 687 6.489361 GGATCGATAACACTCCTAGTTTCCTA 59.511 42.308 0.00 0.00 0.00 2.94
711 714 1.871772 CCTTTTGGCAGACTGCTCG 59.128 57.895 25.92 10.37 44.28 5.03
717 720 2.437359 GCAGACTGCTCGGCCAAT 60.437 61.111 20.41 0.00 40.96 3.16
744 747 7.677511 GCCTTTAAGCAATAAAGCTCTCACTAC 60.678 40.741 13.65 0.00 46.10 2.73
751 754 2.327325 AAGCTCTCACTACTTCCCCA 57.673 50.000 0.00 0.00 0.00 4.96
752 755 2.327325 AGCTCTCACTACTTCCCCAA 57.673 50.000 0.00 0.00 0.00 4.12
753 756 2.621070 AGCTCTCACTACTTCCCCAAA 58.379 47.619 0.00 0.00 0.00 3.28
1089 1096 1.153429 CCCGTCCTCCTTTTAGGCG 60.153 63.158 0.00 0.00 36.51 5.52
1105 1121 3.179433 GCGTTTGCCTTTTCCAGTC 57.821 52.632 0.00 0.00 33.98 3.51
1109 1125 2.357637 CGTTTGCCTTTTCCAGTCTTCA 59.642 45.455 0.00 0.00 0.00 3.02
1441 1643 4.201783 GCAATTATGTGGTCCTGTAACGAC 60.202 45.833 0.00 0.00 0.00 4.34
1569 2942 4.842574 TGTTATGCTGGAGTGCTTATTCA 58.157 39.130 0.00 0.00 0.00 2.57
1584 2957 9.561069 AGTGCTTATTCACTTATTATGGGTAAG 57.439 33.333 0.00 0.00 44.26 2.34
1585 2958 8.784043 GTGCTTATTCACTTATTATGGGTAAGG 58.216 37.037 0.00 0.00 34.28 2.69
1587 2960 8.784043 GCTTATTCACTTATTATGGGTAAGGTG 58.216 37.037 0.00 0.00 34.28 4.00
1611 2985 3.559171 GCTGGAGTGTTGTATTCCTGGAA 60.559 47.826 12.26 12.26 36.22 3.53
1620 2994 3.670625 TGTATTCCTGGAAAAGACACGG 58.329 45.455 14.03 0.00 0.00 4.94
1628 3002 1.404035 GGAAAAGACACGGCACACTTT 59.596 47.619 0.00 0.00 34.67 2.66
1633 3007 1.078072 ACACGGCACACTTTGGTCA 60.078 52.632 0.00 0.00 0.00 4.02
1634 3008 0.465460 ACACGGCACACTTTGGTCAT 60.465 50.000 0.00 0.00 0.00 3.06
1635 3009 0.667993 CACGGCACACTTTGGTCATT 59.332 50.000 0.00 0.00 0.00 2.57
1636 3010 1.066908 CACGGCACACTTTGGTCATTT 59.933 47.619 0.00 0.00 0.00 2.32
1637 3011 1.754226 ACGGCACACTTTGGTCATTTT 59.246 42.857 0.00 0.00 0.00 1.82
1638 3012 2.223711 ACGGCACACTTTGGTCATTTTC 60.224 45.455 0.00 0.00 0.00 2.29
1639 3013 2.034558 CGGCACACTTTGGTCATTTTCT 59.965 45.455 0.00 0.00 0.00 2.52
1640 3014 3.252215 CGGCACACTTTGGTCATTTTCTA 59.748 43.478 0.00 0.00 0.00 2.10
1641 3015 4.082787 CGGCACACTTTGGTCATTTTCTAT 60.083 41.667 0.00 0.00 0.00 1.98
1642 3016 5.123186 CGGCACACTTTGGTCATTTTCTATA 59.877 40.000 0.00 0.00 0.00 1.31
1643 3017 6.555315 GGCACACTTTGGTCATTTTCTATAG 58.445 40.000 0.00 0.00 0.00 1.31
1644 3018 6.151144 GGCACACTTTGGTCATTTTCTATAGT 59.849 38.462 0.00 0.00 0.00 2.12
1645 3019 7.023575 GCACACTTTGGTCATTTTCTATAGTG 58.976 38.462 0.00 0.00 37.19 2.74
1646 3020 7.308589 GCACACTTTGGTCATTTTCTATAGTGT 60.309 37.037 0.00 0.00 42.99 3.55
1647 3021 8.567948 CACACTTTGGTCATTTTCTATAGTGTT 58.432 33.333 0.00 0.00 41.01 3.32
1648 3022 9.131791 ACACTTTGGTCATTTTCTATAGTGTTT 57.868 29.630 0.00 0.00 40.32 2.83
1649 3023 9.612620 CACTTTGGTCATTTTCTATAGTGTTTC 57.387 33.333 0.00 0.00 0.00 2.78
1650 3024 9.349713 ACTTTGGTCATTTTCTATAGTGTTTCA 57.650 29.630 0.00 0.00 0.00 2.69
1651 3025 9.831737 CTTTGGTCATTTTCTATAGTGTTTCAG 57.168 33.333 0.00 0.00 0.00 3.02
1652 3026 9.567776 TTTGGTCATTTTCTATAGTGTTTCAGA 57.432 29.630 0.00 0.00 0.00 3.27
1653 3027 9.567776 TTGGTCATTTTCTATAGTGTTTCAGAA 57.432 29.630 0.00 0.00 0.00 3.02
1654 3028 9.219603 TGGTCATTTTCTATAGTGTTTCAGAAG 57.780 33.333 0.00 0.00 0.00 2.85
1655 3029 9.436957 GGTCATTTTCTATAGTGTTTCAGAAGA 57.563 33.333 0.00 0.00 0.00 2.87
1664 3038 5.876612 AGTGTTTCAGAAGATCATTCAGC 57.123 39.130 0.00 0.00 0.00 4.26
1665 3039 5.558818 AGTGTTTCAGAAGATCATTCAGCT 58.441 37.500 0.00 0.00 0.00 4.24
1666 3040 6.002704 AGTGTTTCAGAAGATCATTCAGCTT 58.997 36.000 0.00 0.00 0.00 3.74
1667 3041 6.489361 AGTGTTTCAGAAGATCATTCAGCTTT 59.511 34.615 0.00 0.00 0.00 3.51
1668 3042 7.014038 AGTGTTTCAGAAGATCATTCAGCTTTT 59.986 33.333 0.00 0.00 0.00 2.27
1669 3043 7.650903 GTGTTTCAGAAGATCATTCAGCTTTTT 59.349 33.333 0.00 0.00 0.00 1.94
1670 3044 7.864379 TGTTTCAGAAGATCATTCAGCTTTTTC 59.136 33.333 0.00 0.00 0.00 2.29
1671 3045 6.506500 TCAGAAGATCATTCAGCTTTTTCC 57.493 37.500 0.00 0.00 0.00 3.13
1672 3046 6.005823 TCAGAAGATCATTCAGCTTTTTCCA 58.994 36.000 0.00 0.00 0.00 3.53
1673 3047 6.072286 TCAGAAGATCATTCAGCTTTTTCCAC 60.072 38.462 0.00 0.00 0.00 4.02
1674 3048 4.691860 AGATCATTCAGCTTTTTCCACG 57.308 40.909 0.00 0.00 0.00 4.94
1675 3049 4.074970 AGATCATTCAGCTTTTTCCACGT 58.925 39.130 0.00 0.00 0.00 4.49
1676 3050 5.245531 AGATCATTCAGCTTTTTCCACGTA 58.754 37.500 0.00 0.00 0.00 3.57
1677 3051 5.352569 AGATCATTCAGCTTTTTCCACGTAG 59.647 40.000 0.00 0.00 0.00 3.51
1678 3052 3.188460 TCATTCAGCTTTTTCCACGTAGC 59.812 43.478 0.00 0.00 0.00 3.58
1679 3053 2.248280 TCAGCTTTTTCCACGTAGCA 57.752 45.000 8.35 0.00 36.11 3.49
1680 3054 2.778299 TCAGCTTTTTCCACGTAGCAT 58.222 42.857 8.35 0.00 36.11 3.79
1681 3055 2.483877 TCAGCTTTTTCCACGTAGCATG 59.516 45.455 8.35 4.32 36.11 4.06
1682 3056 2.226437 CAGCTTTTTCCACGTAGCATGT 59.774 45.455 8.35 0.00 36.11 3.21
1683 3057 2.484264 AGCTTTTTCCACGTAGCATGTC 59.516 45.455 8.35 0.00 36.11 3.06
1684 3058 2.484264 GCTTTTTCCACGTAGCATGTCT 59.516 45.455 0.93 0.00 33.88 3.41
1685 3059 3.058224 GCTTTTTCCACGTAGCATGTCTT 60.058 43.478 0.93 0.00 33.88 3.01
1686 3060 4.466828 CTTTTTCCACGTAGCATGTCTTG 58.533 43.478 0.00 0.00 0.00 3.02
1687 3061 2.831685 TTCCACGTAGCATGTCTTGT 57.168 45.000 0.00 0.00 0.00 3.16
1688 3062 3.945981 TTCCACGTAGCATGTCTTGTA 57.054 42.857 0.00 0.00 0.00 2.41
1689 3063 3.945981 TCCACGTAGCATGTCTTGTAA 57.054 42.857 0.00 0.00 0.00 2.41
1690 3064 4.465632 TCCACGTAGCATGTCTTGTAAT 57.534 40.909 0.00 0.00 0.00 1.89
1769 3144 9.793252 ATCAAAATATGTTGCTGAAGTGTAATC 57.207 29.630 0.22 0.00 0.00 1.75
1770 3145 8.791675 TCAAAATATGTTGCTGAAGTGTAATCA 58.208 29.630 0.22 0.00 0.00 2.57
1771 3146 9.577110 CAAAATATGTTGCTGAAGTGTAATCAT 57.423 29.630 0.00 0.00 0.00 2.45
1773 3148 9.577110 AAATATGTTGCTGAAGTGTAATCATTG 57.423 29.630 0.00 0.00 0.00 2.82
1774 3149 4.797471 TGTTGCTGAAGTGTAATCATTGC 58.203 39.130 0.00 0.00 0.00 3.56
1775 3150 4.277921 TGTTGCTGAAGTGTAATCATTGCA 59.722 37.500 0.00 0.00 0.00 4.08
1776 3151 4.424061 TGCTGAAGTGTAATCATTGCAC 57.576 40.909 10.44 10.44 45.13 4.57
1788 3163 8.072567 GTGTAATCATTGCACTCATAGAAATCC 58.927 37.037 11.10 0.00 42.10 3.01
1789 3164 7.774625 TGTAATCATTGCACTCATAGAAATCCA 59.225 33.333 0.00 0.00 0.00 3.41
1790 3165 6.879276 ATCATTGCACTCATAGAAATCCAG 57.121 37.500 0.00 0.00 0.00 3.86
1791 3166 5.128205 TCATTGCACTCATAGAAATCCAGG 58.872 41.667 0.00 0.00 0.00 4.45
1792 3167 3.565764 TGCACTCATAGAAATCCAGGG 57.434 47.619 0.00 0.00 0.00 4.45
1793 3168 2.173356 TGCACTCATAGAAATCCAGGGG 59.827 50.000 0.00 0.00 0.00 4.79
1794 3169 2.487986 GCACTCATAGAAATCCAGGGGG 60.488 54.545 0.00 0.00 0.00 5.40
1822 3197 2.678471 GGGGGATTGTGATTTTGCAG 57.322 50.000 0.00 0.00 0.00 4.41
1823 3198 1.405933 GGGGGATTGTGATTTTGCAGC 60.406 52.381 0.00 0.00 0.00 5.25
1824 3199 1.405933 GGGGATTGTGATTTTGCAGCC 60.406 52.381 0.00 0.00 0.00 4.85
1825 3200 1.275856 GGGATTGTGATTTTGCAGCCA 59.724 47.619 0.00 0.00 0.00 4.75
1826 3201 2.093341 GGGATTGTGATTTTGCAGCCAT 60.093 45.455 0.00 0.00 0.00 4.40
1827 3202 2.933906 GGATTGTGATTTTGCAGCCATG 59.066 45.455 0.00 0.00 0.00 3.66
1828 3203 3.368635 GGATTGTGATTTTGCAGCCATGA 60.369 43.478 0.00 0.00 0.00 3.07
1829 3204 3.747854 TTGTGATTTTGCAGCCATGAA 57.252 38.095 0.00 0.00 0.00 2.57
1830 3205 3.965379 TGTGATTTTGCAGCCATGAAT 57.035 38.095 0.00 0.00 0.00 2.57
1831 3206 5.402997 TTGTGATTTTGCAGCCATGAATA 57.597 34.783 0.00 0.00 0.00 1.75
1832 3207 5.001237 TGTGATTTTGCAGCCATGAATAG 57.999 39.130 0.00 0.00 0.00 1.73
1833 3208 4.705991 TGTGATTTTGCAGCCATGAATAGA 59.294 37.500 0.00 0.00 0.00 1.98
1834 3209 5.185442 TGTGATTTTGCAGCCATGAATAGAA 59.815 36.000 0.00 0.00 0.00 2.10
1835 3210 6.101332 GTGATTTTGCAGCCATGAATAGAAA 58.899 36.000 0.00 0.00 0.00 2.52
1836 3211 6.591062 GTGATTTTGCAGCCATGAATAGAAAA 59.409 34.615 0.00 0.00 0.00 2.29
1837 3212 7.279313 GTGATTTTGCAGCCATGAATAGAAAAT 59.721 33.333 0.00 0.00 0.00 1.82
1868 3505 1.516161 TGCAGAATCGCCTATGATGC 58.484 50.000 0.00 0.00 32.83 3.91
1898 3544 7.721286 AAAGAGTCAGTACAGTGAAAGATTG 57.279 36.000 0.00 0.00 0.00 2.67
1934 3580 7.253422 CAAATTATCCATCCAAGTGTCAAGTC 58.747 38.462 0.00 0.00 0.00 3.01
1996 3642 4.793216 GCATTTTCTGTAACTGGCATTACG 59.207 41.667 12.13 8.80 37.79 3.18
2012 3658 6.368516 TGGCATTACGTTAGTTACCAGTAAAC 59.631 38.462 0.00 0.00 32.11 2.01
2025 3671 9.162764 AGTTACCAGTAAACATAGTTTGCATAG 57.837 33.333 12.05 4.16 0.00 2.23
2026 3672 9.158233 GTTACCAGTAAACATAGTTTGCATAGA 57.842 33.333 12.05 0.00 0.00 1.98
2027 3673 7.611213 ACCAGTAAACATAGTTTGCATAGAC 57.389 36.000 12.05 0.00 0.00 2.59
2031 3678 9.708222 CAGTAAACATAGTTTGCATAGACAATC 57.292 33.333 12.05 0.00 0.00 2.67
2125 3780 2.664081 GGGAGCTGGGGTGTCTCTG 61.664 68.421 0.00 0.00 0.00 3.35
2162 3817 7.163001 AGGAAGAGCTACAAAATGGAAAATC 57.837 36.000 0.00 0.00 0.00 2.17
2218 3883 9.906111 GTTGTTTGATTCAGAAAATTCTTCAAC 57.094 29.630 7.81 0.00 33.62 3.18
2222 3887 5.241506 TGATTCAGAAAATTCTTCAACGCCT 59.758 36.000 0.00 0.00 34.74 5.52
2223 3888 6.429692 TGATTCAGAAAATTCTTCAACGCCTA 59.570 34.615 0.00 0.00 34.74 3.93
2224 3889 5.862924 TCAGAAAATTCTTCAACGCCTAG 57.137 39.130 0.00 0.00 34.74 3.02
2359 4024 6.999705 ATATGTGACCCATATGCCAATTTT 57.000 33.333 0.00 0.00 43.61 1.82
2485 4150 9.770503 CTTCTTTCTCTCATTCAAATACATGTG 57.229 33.333 9.11 0.00 0.00 3.21
2501 4166 5.751243 ACATGTGTCGCTTTTCTTAAAGT 57.249 34.783 0.00 0.00 42.25 2.66
2597 4263 4.003648 GCTTACCTCTTCTGCTGCTTTAA 58.996 43.478 0.00 0.00 0.00 1.52
2783 4449 4.268359 AGAATTTCTGATCCAGGTGAAGC 58.732 43.478 0.00 0.00 31.51 3.86
2940 4608 2.554272 CAACAGCCGCGTGGTAAC 59.446 61.111 17.91 0.00 37.67 2.50
3169 4851 4.642429 ACCAGAAGAAGAATTGTAAGCGT 58.358 39.130 0.00 0.00 0.00 5.07
3205 4887 8.589335 TTGTTCAGTACTTGAGTATCTGTTTC 57.411 34.615 0.00 9.93 37.07 2.78
3207 4889 7.867909 TGTTCAGTACTTGAGTATCTGTTTCAG 59.132 37.037 0.00 0.00 37.07 3.02
3208 4890 7.526142 TCAGTACTTGAGTATCTGTTTCAGT 57.474 36.000 0.00 0.00 34.41 3.41
3209 4891 8.631480 TCAGTACTTGAGTATCTGTTTCAGTA 57.369 34.615 0.00 0.00 34.41 2.74
3257 4947 8.214721 TGTTTAAACATATACGCATTGATCCA 57.785 30.769 17.01 0.00 33.17 3.41
3267 4957 7.692460 ATACGCATTGATCCAATCATATGTT 57.308 32.000 1.90 0.00 39.39 2.71
3268 4958 6.005583 ACGCATTGATCCAATCATATGTTC 57.994 37.500 1.90 0.00 39.39 3.18
3303 4993 0.837272 TAGCTTACCCATGTCAGCCC 59.163 55.000 0.00 0.00 41.66 5.19
3325 5016 4.202243 CCTTTTTGCTTCACCATCTTTGGA 60.202 41.667 0.00 0.00 46.92 3.53
3574 5518 1.102978 GGCCGTAGCAACCATTGAAT 58.897 50.000 0.00 0.00 42.56 2.57
3743 5687 5.305585 ACGGCGGAATGAATAATATTGTCT 58.694 37.500 13.24 0.00 0.00 3.41
3833 5778 3.755628 GTCGCCACGGGTGCTCTA 61.756 66.667 0.00 0.00 32.51 2.43
3834 5779 2.758327 TCGCCACGGGTGCTCTAT 60.758 61.111 0.00 0.00 32.51 1.98
3835 5780 2.586079 CGCCACGGGTGCTCTATG 60.586 66.667 0.00 0.00 0.00 2.23
3836 5781 2.897350 GCCACGGGTGCTCTATGC 60.897 66.667 0.00 0.00 43.25 3.14
3837 5782 2.903357 CCACGGGTGCTCTATGCT 59.097 61.111 0.00 0.00 43.37 3.79
3838 5783 1.221840 CCACGGGTGCTCTATGCTT 59.778 57.895 0.00 0.00 43.37 3.91
3839 5784 0.811616 CCACGGGTGCTCTATGCTTC 60.812 60.000 0.00 0.00 43.37 3.86
3840 5785 0.176680 CACGGGTGCTCTATGCTTCT 59.823 55.000 0.00 0.00 43.37 2.85
3851 5796 5.423610 TGCTCTATGCTTCTATCCCTTATCC 59.576 44.000 0.00 0.00 43.37 2.59
3858 5803 3.897657 TCTATCCCTTATCCGTGACCT 57.102 47.619 0.00 0.00 0.00 3.85
3859 5804 4.194678 TCTATCCCTTATCCGTGACCTT 57.805 45.455 0.00 0.00 0.00 3.50
3860 5805 4.553678 TCTATCCCTTATCCGTGACCTTT 58.446 43.478 0.00 0.00 0.00 3.11
3861 5806 5.708544 TCTATCCCTTATCCGTGACCTTTA 58.291 41.667 0.00 0.00 0.00 1.85
3862 5807 4.684484 ATCCCTTATCCGTGACCTTTAC 57.316 45.455 0.00 0.00 0.00 2.01
3863 5808 2.428171 TCCCTTATCCGTGACCTTTACG 59.572 50.000 0.00 0.00 40.98 3.18
3864 5809 2.428171 CCCTTATCCGTGACCTTTACGA 59.572 50.000 0.00 0.00 43.82 3.43
3865 5810 3.490419 CCCTTATCCGTGACCTTTACGAG 60.490 52.174 0.00 0.00 43.82 4.18
3866 5811 3.379372 CCTTATCCGTGACCTTTACGAGA 59.621 47.826 0.00 0.00 43.82 4.04
3912 5884 4.615682 GCATCTCAGGATCTGTCACTATCG 60.616 50.000 0.00 0.00 32.61 2.92
3920 5895 2.803956 TCTGTCACTATCGTTCCCACT 58.196 47.619 0.00 0.00 0.00 4.00
3956 5931 3.564225 AGAAACGCCAGTGAAGTAAAAGG 59.436 43.478 0.00 0.00 0.00 3.11
3977 5952 8.893563 AAAGGAACCAATAATTTGATGGACTA 57.106 30.769 9.94 0.00 37.66 2.59
3979 5954 7.643123 AGGAACCAATAATTTGATGGACTAGT 58.357 34.615 0.00 0.00 37.66 2.57
3999 5974 0.031994 TTTTGCTCCGCTTTTCTGCC 59.968 50.000 0.00 0.00 0.00 4.85
4005 5980 2.599659 CTCCGCTTTTCTGCCATTTTC 58.400 47.619 0.00 0.00 0.00 2.29
4017 5992 2.151202 GCCATTTTCGTGTCTTCTCCA 58.849 47.619 0.00 0.00 0.00 3.86
4031 6006 7.166167 GTGTCTTCTCCATACTTTTCCCTTTA 58.834 38.462 0.00 0.00 0.00 1.85
4032 6007 7.829706 GTGTCTTCTCCATACTTTTCCCTTTAT 59.170 37.037 0.00 0.00 0.00 1.40
4033 6008 8.390921 TGTCTTCTCCATACTTTTCCCTTTATT 58.609 33.333 0.00 0.00 0.00 1.40
4034 6009 8.678199 GTCTTCTCCATACTTTTCCCTTTATTG 58.322 37.037 0.00 0.00 0.00 1.90
4035 6010 7.339466 TCTTCTCCATACTTTTCCCTTTATTGC 59.661 37.037 0.00 0.00 0.00 3.56
4036 6011 5.891551 TCTCCATACTTTTCCCTTTATTGCC 59.108 40.000 0.00 0.00 0.00 4.52
4037 6012 5.837829 TCCATACTTTTCCCTTTATTGCCT 58.162 37.500 0.00 0.00 0.00 4.75
4038 6013 6.260663 TCCATACTTTTCCCTTTATTGCCTT 58.739 36.000 0.00 0.00 0.00 4.35
4039 6014 7.415086 TCCATACTTTTCCCTTTATTGCCTTA 58.585 34.615 0.00 0.00 0.00 2.69
4040 6015 8.065007 TCCATACTTTTCCCTTTATTGCCTTAT 58.935 33.333 0.00 0.00 0.00 1.73
4041 6016 8.704668 CCATACTTTTCCCTTTATTGCCTTATT 58.295 33.333 0.00 0.00 0.00 1.40
4042 6017 9.533253 CATACTTTTCCCTTTATTGCCTTATTG 57.467 33.333 0.00 0.00 0.00 1.90
4049 6024 5.530915 CCCTTTATTGCCTTATTGACGATCA 59.469 40.000 0.00 0.00 0.00 2.92
4078 6053 0.950116 GCTAGAAGATGGTGCATGCC 59.050 55.000 16.68 6.42 0.00 4.40
4101 6077 5.338708 CCTCTTCATCTTCCCTGCTCTTTTA 60.339 44.000 0.00 0.00 0.00 1.52
4187 7491 0.464452 GCTCATGTAGCCCTAACCGT 59.536 55.000 6.02 0.00 46.25 4.83
4209 7513 1.000993 GAGTCCCCTGAGCTCCTCA 59.999 63.158 12.15 0.00 38.25 3.86
4210 7514 0.616111 GAGTCCCCTGAGCTCCTCAA 60.616 60.000 12.15 0.00 40.18 3.02
4226 7530 1.347707 CTCAACCCCTTGTAGCTGTCA 59.652 52.381 0.00 0.00 0.00 3.58
4240 7544 0.321122 CTGTCAGAGAAGGCCGCTTT 60.321 55.000 0.00 0.00 0.00 3.51
4278 7582 2.959030 AGGGGTCTTTTCTGCTTGTTTC 59.041 45.455 0.00 0.00 0.00 2.78
4279 7583 2.693074 GGGGTCTTTTCTGCTTGTTTCA 59.307 45.455 0.00 0.00 0.00 2.69
4285 7589 3.414549 TTTCTGCTTGTTTCAACCGAC 57.585 42.857 0.00 0.00 0.00 4.79
4286 7590 2.031258 TCTGCTTGTTTCAACCGACA 57.969 45.000 0.00 0.00 0.00 4.35
4287 7591 2.571212 TCTGCTTGTTTCAACCGACAT 58.429 42.857 0.00 0.00 0.00 3.06
4293 7597 3.328382 TGTTTCAACCGACATAGGAGG 57.672 47.619 0.00 0.00 34.73 4.30
4360 7665 2.693591 GGGTAGTCCGATGATGAAGACA 59.306 50.000 0.00 0.00 33.83 3.41
4361 7666 3.243569 GGGTAGTCCGATGATGAAGACAG 60.244 52.174 0.00 0.00 33.83 3.51
4365 7670 1.410517 TCCGATGATGAAGACAGCCTC 59.589 52.381 0.00 0.00 0.00 4.70
4372 7677 3.133542 TGATGAAGACAGCCTCTGTATGG 59.866 47.826 0.00 0.00 45.44 2.74
4373 7678 2.820178 TGAAGACAGCCTCTGTATGGA 58.180 47.619 0.00 0.00 45.44 3.41
4449 7754 1.407656 GGGATGGCCGGATGTAGACA 61.408 60.000 5.05 0.00 33.83 3.41
4453 7758 0.249120 TGGCCGGATGTAGACAACAG 59.751 55.000 5.05 0.00 42.70 3.16
4463 7768 2.371841 TGTAGACAACAGCCCTTGATGT 59.628 45.455 0.00 0.00 44.52 3.06
4483 7788 8.753497 TGATGTAGACTAGCTCTTTTGATCTA 57.247 34.615 0.00 0.00 0.00 1.98
4488 7793 6.120905 AGACTAGCTCTTTTGATCTACGGTA 58.879 40.000 0.00 0.00 0.00 4.02
4494 7799 2.555732 TTTGATCTACGGTAGGGGGT 57.444 50.000 14.82 0.00 0.00 4.95
4503 7808 1.543944 CGGTAGGGGGTTGTACGGTT 61.544 60.000 0.00 0.00 0.00 4.44
4539 7844 2.582052 CTAGCCACCACTTTTGTTGGA 58.418 47.619 0.00 0.00 33.27 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.832201 GGATGGAGCCTTGGCAGC 60.832 66.667 14.54 5.28 0.00 5.25
1 2 1.453379 CAGGATGGAGCCTTGGCAG 60.453 63.158 14.54 0.00 35.66 4.85
2 3 2.233566 ACAGGATGGAGCCTTGGCA 61.234 57.895 14.54 0.00 43.62 4.92
3 4 1.751927 CACAGGATGGAGCCTTGGC 60.752 63.158 2.97 2.97 43.62 4.52
5 6 0.325933 TGTCACAGGATGGAGCCTTG 59.674 55.000 0.00 0.00 43.62 3.61
7 8 0.545171 CATGTCACAGGATGGAGCCT 59.455 55.000 0.00 0.00 43.62 4.58
24 25 2.026641 CAAATGATGTCTTCGGCCCAT 58.973 47.619 0.00 0.00 0.00 4.00
45 46 3.551046 CCCTGGAAGTAAGACGATCATCG 60.551 52.174 5.22 5.22 46.93 3.84
54 55 1.848652 CTCGGTCCCTGGAAGTAAGA 58.151 55.000 0.00 0.00 0.00 2.10
82 83 2.806945 ATGGACCACATGACCGAAAT 57.193 45.000 0.00 0.00 38.70 2.17
126 127 1.744639 GAGCTGATCCTCGCCATGA 59.255 57.895 0.00 0.00 0.00 3.07
153 154 0.240411 AGGTGCGTCGTACTGAACTC 59.760 55.000 13.25 0.00 0.00 3.01
159 160 2.282674 TCCCAGGTGCGTCGTACT 60.283 61.111 13.25 0.00 0.00 2.73
171 172 0.316841 GAAGAGATAGCGCCTCCCAG 59.683 60.000 2.29 0.00 0.00 4.45
172 173 0.105964 AGAAGAGATAGCGCCTCCCA 60.106 55.000 2.29 0.00 0.00 4.37
210 211 1.677300 CCCAGGCATAACCAACGCA 60.677 57.895 0.00 0.00 43.14 5.24
243 244 1.602605 GACAAAACCTGGGTCGGGG 60.603 63.158 0.00 0.00 33.40 5.73
276 277 3.740044 TCTTCTCTTTTAATTGCCGCG 57.260 42.857 0.00 0.00 0.00 6.46
285 286 5.014123 TCCTCCTTTGGCATCTTCTCTTTTA 59.986 40.000 0.00 0.00 0.00 1.52
289 290 2.504996 CTCCTCCTTTGGCATCTTCTCT 59.495 50.000 0.00 0.00 0.00 3.10
299 300 2.679716 CCCCTGCTCCTCCTTTGG 59.320 66.667 0.00 0.00 0.00 3.28
327 328 5.361285 TGCTCCTAGAAATGAGTTAGAGGAC 59.639 44.000 0.00 0.00 30.44 3.85
335 336 3.181456 GCTCCATGCTCCTAGAAATGAGT 60.181 47.826 0.00 0.00 38.95 3.41
345 346 0.333993 ATGGTTTGCTCCATGCTCCT 59.666 50.000 7.60 0.00 45.26 3.69
377 378 1.696965 CCTCTGGGATGAAGGGATCCA 60.697 57.143 15.23 0.00 43.51 3.41
390 391 3.790437 ACTGCCATCGCCTCTGGG 61.790 66.667 0.00 0.00 34.16 4.45
391 392 2.513204 CACTGCCATCGCCTCTGG 60.513 66.667 0.00 0.00 36.81 3.86
419 420 2.546795 CCCCTCAAGCTTGCGTAGATAG 60.547 54.545 21.99 11.42 0.00 2.08
425 426 0.755327 AAAACCCCTCAAGCTTGCGT 60.755 50.000 21.99 11.39 0.00 5.24
430 431 2.583143 GTGTGTAAAACCCCTCAAGCT 58.417 47.619 0.00 0.00 0.00 3.74
456 457 1.326213 CCGAGCAGTCCATCTCCACT 61.326 60.000 0.00 0.00 0.00 4.00
513 514 1.112113 GGATAGGAGCCACGACTGAA 58.888 55.000 0.00 0.00 0.00 3.02
525 526 5.293643 TCCCCAATTTCTAACAGGATAGGA 58.706 41.667 0.00 0.00 0.00 2.94
582 585 4.084537 CCGTTGGTCGATCTTACAATATGC 60.085 45.833 0.00 0.00 42.86 3.14
598 601 1.204146 ATATGAGCAGGACCGTTGGT 58.796 50.000 0.00 0.00 39.44 3.67
600 603 3.009723 ACAAATATGAGCAGGACCGTTG 58.990 45.455 0.00 0.00 0.00 4.10
638 641 4.461431 TCCAGCTTTCTGTCACGTCTATTA 59.539 41.667 0.00 0.00 38.66 0.98
642 645 1.040646 TCCAGCTTTCTGTCACGTCT 58.959 50.000 0.00 0.00 38.66 4.18
651 654 4.442192 GGAGTGTTATCGATCCAGCTTTCT 60.442 45.833 0.00 0.00 0.00 2.52
666 669 9.186837 CTACTGATTAGGAAACTAGGAGTGTTA 57.813 37.037 0.00 0.00 45.45 2.41
668 671 6.097129 GCTACTGATTAGGAAACTAGGAGTGT 59.903 42.308 0.00 0.00 45.45 3.55
669 672 6.461788 GGCTACTGATTAGGAAACTAGGAGTG 60.462 46.154 0.00 0.00 45.45 3.51
678 681 4.705023 GCCAAAAGGCTACTGATTAGGAAA 59.295 41.667 0.00 0.00 0.00 3.13
684 687 3.084786 GTCTGCCAAAAGGCTACTGATT 58.915 45.455 8.11 0.00 35.66 2.57
714 717 6.335777 AGAGCTTTATTGCTTAAAGGCATTG 58.664 36.000 16.43 0.00 44.69 2.82
717 720 5.009631 TGAGAGCTTTATTGCTTAAAGGCA 58.990 37.500 16.43 0.00 44.69 4.75
720 723 8.485976 AGTAGTGAGAGCTTTATTGCTTAAAG 57.514 34.615 12.61 12.61 46.45 1.85
981 988 3.449018 CCATCGGGATCTATCTACCAAGG 59.551 52.174 0.00 0.00 35.59 3.61
1089 1096 3.381590 AGTGAAGACTGGAAAAGGCAAAC 59.618 43.478 0.00 0.00 35.71 2.93
1109 1125 3.726607 CAGAAAAGTCAGTCAGCAGAGT 58.273 45.455 0.00 0.00 0.00 3.24
1441 1643 1.446907 AGAATGACTTGCTCCAAGCG 58.553 50.000 4.96 0.00 46.26 4.68
1512 2885 8.515695 TGAACAAAATGCATCTAGAGATTCAT 57.484 30.769 0.00 0.00 39.47 2.57
1569 2942 5.437060 CAGCACACCTTACCCATAATAAGT 58.563 41.667 0.00 0.00 0.00 2.24
1584 2957 2.185004 ATACAACACTCCAGCACACC 57.815 50.000 0.00 0.00 0.00 4.16
1585 2958 2.484264 GGAATACAACACTCCAGCACAC 59.516 50.000 0.00 0.00 0.00 3.82
1587 2960 2.744202 CAGGAATACAACACTCCAGCAC 59.256 50.000 0.00 0.00 0.00 4.40
1611 2985 0.738389 CCAAAGTGTGCCGTGTCTTT 59.262 50.000 0.00 0.00 0.00 2.52
1620 2994 7.023575 CACTATAGAAAATGACCAAAGTGTGC 58.976 38.462 6.78 0.00 0.00 4.57
1628 3002 9.219603 CTTCTGAAACACTATAGAAAATGACCA 57.780 33.333 6.78 0.00 0.00 4.02
1638 3012 8.763356 GCTGAATGATCTTCTGAAACACTATAG 58.237 37.037 0.00 0.00 0.00 1.31
1639 3013 8.481314 AGCTGAATGATCTTCTGAAACACTATA 58.519 33.333 12.59 0.00 0.00 1.31
1640 3014 7.337167 AGCTGAATGATCTTCTGAAACACTAT 58.663 34.615 12.59 0.00 0.00 2.12
1641 3015 6.705302 AGCTGAATGATCTTCTGAAACACTA 58.295 36.000 12.59 0.00 0.00 2.74
1642 3016 5.558818 AGCTGAATGATCTTCTGAAACACT 58.441 37.500 12.59 2.17 0.00 3.55
1643 3017 5.876612 AGCTGAATGATCTTCTGAAACAC 57.123 39.130 12.59 0.00 0.00 3.32
1644 3018 6.889301 AAAGCTGAATGATCTTCTGAAACA 57.111 33.333 12.59 0.00 0.00 2.83
1645 3019 7.328005 GGAAAAAGCTGAATGATCTTCTGAAAC 59.672 37.037 12.59 0.00 0.00 2.78
1646 3020 7.014518 TGGAAAAAGCTGAATGATCTTCTGAAA 59.985 33.333 12.59 0.00 0.00 2.69
1647 3021 6.491062 TGGAAAAAGCTGAATGATCTTCTGAA 59.509 34.615 12.59 0.00 0.00 3.02
1648 3022 6.005823 TGGAAAAAGCTGAATGATCTTCTGA 58.994 36.000 12.59 0.00 0.00 3.27
1649 3023 6.091437 GTGGAAAAAGCTGAATGATCTTCTG 58.909 40.000 0.00 1.46 0.00 3.02
1650 3024 5.106396 CGTGGAAAAAGCTGAATGATCTTCT 60.106 40.000 0.00 0.00 0.00 2.85
1651 3025 5.091431 CGTGGAAAAAGCTGAATGATCTTC 58.909 41.667 0.00 0.00 0.00 2.87
1652 3026 4.520492 ACGTGGAAAAAGCTGAATGATCTT 59.480 37.500 0.00 0.00 0.00 2.40
1653 3027 4.074970 ACGTGGAAAAAGCTGAATGATCT 58.925 39.130 0.00 0.00 0.00 2.75
1654 3028 4.425577 ACGTGGAAAAAGCTGAATGATC 57.574 40.909 0.00 0.00 0.00 2.92
1655 3029 4.142600 GCTACGTGGAAAAAGCTGAATGAT 60.143 41.667 1.81 0.00 32.18 2.45
1656 3030 3.188460 GCTACGTGGAAAAAGCTGAATGA 59.812 43.478 1.81 0.00 32.18 2.57
1657 3031 3.058293 TGCTACGTGGAAAAAGCTGAATG 60.058 43.478 1.81 0.00 35.95 2.67
1658 3032 3.146066 TGCTACGTGGAAAAAGCTGAAT 58.854 40.909 1.81 0.00 35.95 2.57
1659 3033 2.566913 TGCTACGTGGAAAAAGCTGAA 58.433 42.857 1.81 0.00 35.95 3.02
1660 3034 2.248280 TGCTACGTGGAAAAAGCTGA 57.752 45.000 1.81 0.00 35.95 4.26
1661 3035 2.226437 ACATGCTACGTGGAAAAAGCTG 59.774 45.455 1.81 3.72 35.95 4.24
1662 3036 2.484264 GACATGCTACGTGGAAAAAGCT 59.516 45.455 1.81 0.00 35.95 3.74
1663 3037 2.484264 AGACATGCTACGTGGAAAAAGC 59.516 45.455 1.81 0.02 35.51 3.51
1664 3038 4.024048 ACAAGACATGCTACGTGGAAAAAG 60.024 41.667 1.81 0.00 0.00 2.27
1665 3039 3.880490 ACAAGACATGCTACGTGGAAAAA 59.120 39.130 1.81 0.00 0.00 1.94
1666 3040 3.472652 ACAAGACATGCTACGTGGAAAA 58.527 40.909 1.81 0.00 0.00 2.29
1667 3041 3.120321 ACAAGACATGCTACGTGGAAA 57.880 42.857 1.81 0.00 0.00 3.13
1668 3042 2.831685 ACAAGACATGCTACGTGGAA 57.168 45.000 1.81 0.00 0.00 3.53
1669 3043 3.945981 TTACAAGACATGCTACGTGGA 57.054 42.857 1.81 0.00 0.00 4.02
1670 3044 6.844696 AATATTACAAGACATGCTACGTGG 57.155 37.500 0.00 0.00 0.00 4.94
1688 3062 8.094548 GGGGCACTTCTTCAAAGTAAAAATATT 58.905 33.333 0.00 0.00 0.00 1.28
1689 3063 7.234577 TGGGGCACTTCTTCAAAGTAAAAATAT 59.765 33.333 0.00 0.00 0.00 1.28
1690 3064 6.551601 TGGGGCACTTCTTCAAAGTAAAAATA 59.448 34.615 0.00 0.00 0.00 1.40
1709 3083 3.199946 CCAGATAAGAGTAAAGTGGGGCA 59.800 47.826 0.00 0.00 0.00 5.36
1753 3128 4.618489 GTGCAATGATTACACTTCAGCAAC 59.382 41.667 1.34 0.00 0.00 4.17
1759 3134 7.776933 TCTATGAGTGCAATGATTACACTTC 57.223 36.000 11.99 6.73 44.40 3.01
1760 3135 8.565896 TTTCTATGAGTGCAATGATTACACTT 57.434 30.769 11.99 0.92 44.40 3.16
1769 3144 4.277672 CCCTGGATTTCTATGAGTGCAATG 59.722 45.833 0.00 0.00 0.00 2.82
1770 3145 4.467769 CCCTGGATTTCTATGAGTGCAAT 58.532 43.478 0.00 0.00 0.00 3.56
1771 3146 3.371917 CCCCTGGATTTCTATGAGTGCAA 60.372 47.826 0.00 0.00 0.00 4.08
1772 3147 2.173356 CCCCTGGATTTCTATGAGTGCA 59.827 50.000 0.00 0.00 0.00 4.57
1773 3148 2.487986 CCCCCTGGATTTCTATGAGTGC 60.488 54.545 0.00 0.00 0.00 4.40
1774 3149 3.498774 CCCCCTGGATTTCTATGAGTG 57.501 52.381 0.00 0.00 0.00 3.51
1803 3178 1.405933 GCTGCAAAATCACAATCCCCC 60.406 52.381 0.00 0.00 0.00 5.40
1804 3179 1.405933 GGCTGCAAAATCACAATCCCC 60.406 52.381 0.50 0.00 0.00 4.81
1805 3180 1.275856 TGGCTGCAAAATCACAATCCC 59.724 47.619 0.50 0.00 0.00 3.85
1806 3181 2.747396 TGGCTGCAAAATCACAATCC 57.253 45.000 0.50 0.00 0.00 3.01
1807 3182 3.852286 TCATGGCTGCAAAATCACAATC 58.148 40.909 0.50 0.00 0.00 2.67
1808 3183 3.965379 TCATGGCTGCAAAATCACAAT 57.035 38.095 0.50 0.00 0.00 2.71
1809 3184 3.747854 TTCATGGCTGCAAAATCACAA 57.252 38.095 0.50 0.00 0.00 3.33
1810 3185 3.965379 ATTCATGGCTGCAAAATCACA 57.035 38.095 0.50 0.00 0.00 3.58
1811 3186 5.252969 TCTATTCATGGCTGCAAAATCAC 57.747 39.130 0.50 0.00 0.00 3.06
1812 3187 5.918426 TTCTATTCATGGCTGCAAAATCA 57.082 34.783 0.50 0.00 0.00 2.57
1813 3188 7.279313 ACATTTTCTATTCATGGCTGCAAAATC 59.721 33.333 0.50 0.00 0.00 2.17
1814 3189 7.107542 ACATTTTCTATTCATGGCTGCAAAAT 58.892 30.769 0.50 0.00 0.00 1.82
1815 3190 6.465948 ACATTTTCTATTCATGGCTGCAAAA 58.534 32.000 0.50 0.00 0.00 2.44
1816 3191 6.040209 ACATTTTCTATTCATGGCTGCAAA 57.960 33.333 0.50 0.00 0.00 3.68
1817 3192 5.664294 ACATTTTCTATTCATGGCTGCAA 57.336 34.783 0.50 0.00 0.00 4.08
1818 3193 6.964807 ATACATTTTCTATTCATGGCTGCA 57.035 33.333 0.50 0.00 0.00 4.41
1819 3194 7.306983 GCAAATACATTTTCTATTCATGGCTGC 60.307 37.037 0.00 0.00 0.00 5.25
1820 3195 7.924412 AGCAAATACATTTTCTATTCATGGCTG 59.076 33.333 0.00 0.00 0.00 4.85
1821 3196 8.015185 AGCAAATACATTTTCTATTCATGGCT 57.985 30.769 0.00 0.00 0.00 4.75
1822 3197 9.748708 TTAGCAAATACATTTTCTATTCATGGC 57.251 29.630 0.00 0.00 28.49 4.40
1898 3544 6.434028 TGGATGGATAATTTGCAGTATTAGGC 59.566 38.462 8.66 0.00 0.00 3.93
1934 3580 7.299787 GGTAAGAACCAAAATTAGAGTACCG 57.700 40.000 0.00 0.00 45.98 4.02
1996 3642 8.776470 TGCAAACTATGTTTACTGGTAACTAAC 58.224 33.333 0.00 0.00 37.61 2.34
2125 3780 4.512484 AGCTCTTCCTTCTGTGATAAAGC 58.488 43.478 0.00 0.00 0.00 3.51
2162 3817 8.706492 AACTGACATTATTGGTTGCATATTTG 57.294 30.769 0.00 0.00 0.00 2.32
2218 3883 3.366476 GGTCACTATGCTGATACTAGGCG 60.366 52.174 0.00 0.00 0.00 5.52
2222 3887 6.127338 GCATATGGGTCACTATGCTGATACTA 60.127 42.308 4.56 0.00 44.33 1.82
2223 3888 5.337894 GCATATGGGTCACTATGCTGATACT 60.338 44.000 4.56 0.00 44.33 2.12
2224 3889 4.872691 GCATATGGGTCACTATGCTGATAC 59.127 45.833 4.56 0.00 44.33 2.24
2384 4049 4.319177 ACTTCTAACAGAATGGACACTGC 58.681 43.478 0.00 0.00 43.62 4.40
2485 4150 6.296365 ACTACCAACTTTAAGAAAAGCGAC 57.704 37.500 0.00 0.00 45.06 5.19
2570 4235 3.745458 GCAGCAGAAGAGGTAAGCATATC 59.255 47.826 0.00 0.00 0.00 1.63
2580 4246 6.017400 TCATTTTTAAAGCAGCAGAAGAGG 57.983 37.500 0.00 0.00 0.00 3.69
2801 4467 7.776969 AGAAATCCAATCATACTGTGTTGCTAT 59.223 33.333 0.00 0.00 0.00 2.97
3169 4851 5.023533 AGTACTGAACAAGCAAGAGAACA 57.976 39.130 0.00 0.00 0.00 3.18
3246 4936 6.250344 AGAACATATGATTGGATCAATGCG 57.750 37.500 10.38 0.00 43.50 4.73
3277 4967 5.366482 TGACATGGGTAAGCTAGCAATTA 57.634 39.130 18.83 4.83 0.00 1.40
3325 5016 6.716628 AGAGTACATGTCATGAAAACAATGGT 59.283 34.615 19.77 0.00 0.00 3.55
3451 5385 3.287222 AGTTTAAGGCTGTCAGTTGCAA 58.713 40.909 0.00 0.00 0.00 4.08
3463 5397 5.935789 TGTACCTACATGACAAGTTTAAGGC 59.064 40.000 0.00 0.00 0.00 4.35
3574 5518 1.001974 ACAGGCACGAAAGACTGCATA 59.998 47.619 9.44 0.00 34.90 3.14
3659 5603 1.967066 ACAGGACAGATCATCGATCCC 59.033 52.381 0.00 0.00 39.66 3.85
3743 5687 0.323629 GACGGAGGAACCATTGTCCA 59.676 55.000 0.00 0.00 38.90 4.02
3793 5738 0.033366 GCATTTCAAAACGTGCCCCT 59.967 50.000 0.00 0.00 0.00 4.79
3833 5778 4.021016 GTCACGGATAAGGGATAGAAGCAT 60.021 45.833 0.00 0.00 0.00 3.79
3834 5779 3.321111 GTCACGGATAAGGGATAGAAGCA 59.679 47.826 0.00 0.00 0.00 3.91
3835 5780 3.306156 GGTCACGGATAAGGGATAGAAGC 60.306 52.174 0.00 0.00 0.00 3.86
3836 5781 4.153411 AGGTCACGGATAAGGGATAGAAG 58.847 47.826 0.00 0.00 0.00 2.85
3837 5782 4.194678 AGGTCACGGATAAGGGATAGAA 57.805 45.455 0.00 0.00 0.00 2.10
3838 5783 3.897657 AGGTCACGGATAAGGGATAGA 57.102 47.619 0.00 0.00 0.00 1.98
3839 5784 4.957684 AAAGGTCACGGATAAGGGATAG 57.042 45.455 0.00 0.00 0.00 2.08
3840 5785 4.279169 CGTAAAGGTCACGGATAAGGGATA 59.721 45.833 0.00 0.00 35.78 2.59
3851 5796 7.637229 TCTAAATATCTCTCGTAAAGGTCACG 58.363 38.462 0.00 0.00 40.72 4.35
3858 5803 7.331934 GCATGGCATCTAAATATCTCTCGTAAA 59.668 37.037 0.00 0.00 0.00 2.01
3859 5804 6.813649 GCATGGCATCTAAATATCTCTCGTAA 59.186 38.462 0.00 0.00 0.00 3.18
3860 5805 6.153510 AGCATGGCATCTAAATATCTCTCGTA 59.846 38.462 0.00 0.00 0.00 3.43
3861 5806 5.046735 AGCATGGCATCTAAATATCTCTCGT 60.047 40.000 0.00 0.00 0.00 4.18
3862 5807 5.417811 AGCATGGCATCTAAATATCTCTCG 58.582 41.667 0.00 0.00 0.00 4.04
3863 5808 7.495279 CCTTAGCATGGCATCTAAATATCTCTC 59.505 40.741 15.41 0.00 0.00 3.20
3864 5809 7.337167 CCTTAGCATGGCATCTAAATATCTCT 58.663 38.462 15.41 0.00 0.00 3.10
3865 5810 7.551035 CCTTAGCATGGCATCTAAATATCTC 57.449 40.000 15.41 0.00 0.00 2.75
3912 5884 4.832248 TGATCTGTACAATCAGTGGGAAC 58.168 43.478 13.39 0.00 36.85 3.62
3920 5895 3.932710 GGCGTTTCTGATCTGTACAATCA 59.067 43.478 15.39 15.39 0.00 2.57
3940 5915 3.219281 TGGTTCCTTTTACTTCACTGGC 58.781 45.455 0.00 0.00 0.00 4.85
3999 5974 6.727824 AAGTATGGAGAAGACACGAAAATG 57.272 37.500 0.00 0.00 0.00 2.32
4005 5980 3.933332 GGGAAAAGTATGGAGAAGACACG 59.067 47.826 0.00 0.00 0.00 4.49
4017 5992 9.487442 TCAATAAGGCAATAAAGGGAAAAGTAT 57.513 29.630 0.00 0.00 0.00 2.12
4031 6006 7.099266 TCAAAATGATCGTCAATAAGGCAAT 57.901 32.000 0.00 0.00 0.00 3.56
4032 6007 6.507958 TCAAAATGATCGTCAATAAGGCAA 57.492 33.333 0.00 0.00 0.00 4.52
4033 6008 6.698008 ATCAAAATGATCGTCAATAAGGCA 57.302 33.333 0.00 0.00 29.59 4.75
4049 6024 5.298777 GCACCATCTTCTAGCAGATCAAAAT 59.701 40.000 1.49 0.00 30.50 1.82
4078 6053 3.910568 AAGAGCAGGGAAGATGAAGAG 57.089 47.619 0.00 0.00 0.00 2.85
4101 6077 2.158325 TCCTTTGAATCAAAGTGGGCCT 60.158 45.455 27.68 0.00 46.40 5.19
4209 7513 1.625818 CTCTGACAGCTACAAGGGGTT 59.374 52.381 0.00 0.00 0.00 4.11
4210 7514 1.203187 TCTCTGACAGCTACAAGGGGT 60.203 52.381 0.00 0.00 0.00 4.95
4240 7544 3.706563 CTGCCGCTAGAGCTTCGCA 62.707 63.158 0.00 4.13 39.32 5.10
4261 7565 3.791353 CGGTTGAAACAAGCAGAAAAGAC 59.209 43.478 12.75 0.00 0.00 3.01
4273 7577 2.027561 CCCTCCTATGTCGGTTGAAACA 60.028 50.000 0.00 0.00 0.00 2.83
4278 7582 1.146263 GCCCCTCCTATGTCGGTTG 59.854 63.158 0.00 0.00 0.00 3.77
4279 7583 1.003051 AGCCCCTCCTATGTCGGTT 59.997 57.895 0.00 0.00 0.00 4.44
4303 7607 0.606673 GCTTCCACCTCACCTCCAAC 60.607 60.000 0.00 0.00 0.00 3.77
4328 7632 0.685458 GGACTACCCCTAGCGACCAA 60.685 60.000 0.00 0.00 0.00 3.67
4361 7666 0.390860 ACGAGCATCCATACAGAGGC 59.609 55.000 0.00 0.00 43.72 4.70
4365 7670 0.179076 TGGCACGAGCATCCATACAG 60.179 55.000 7.26 0.00 44.61 2.74
4372 7677 0.654683 GATTCTGTGGCACGAGCATC 59.345 55.000 13.77 12.31 44.61 3.91
4373 7678 0.036105 TGATTCTGTGGCACGAGCAT 60.036 50.000 13.77 7.45 44.61 3.79
4449 7754 3.118592 GCTAGTCTACATCAAGGGCTGTT 60.119 47.826 0.00 0.00 0.00 3.16
4453 7758 2.962421 AGAGCTAGTCTACATCAAGGGC 59.038 50.000 0.00 0.00 31.71 5.19
4457 7762 8.072321 AGATCAAAAGAGCTAGTCTACATCAA 57.928 34.615 0.00 0.00 32.65 2.57
4463 7768 6.120905 ACCGTAGATCAAAAGAGCTAGTCTA 58.879 40.000 0.00 0.00 32.65 2.59
4483 7788 1.984026 CCGTACAACCCCCTACCGT 60.984 63.158 0.00 0.00 0.00 4.83
4488 7793 1.763120 GGAAACCGTACAACCCCCT 59.237 57.895 0.00 0.00 0.00 4.79
4503 7808 0.248289 CTAGGTTTTCTCCCGCGGAA 59.752 55.000 30.73 4.60 0.00 4.30
4514 7819 3.371034 ACAAAAGTGGTGGCTAGGTTTT 58.629 40.909 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.