Multiple sequence alignment - TraesCS5D01G180600

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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 TraesCS5D01G180600 chr5D 100.000 4202 0 0 2151 6352 281013336 281009135 0.000000e+00 7760.0
1 TraesCS5D01G180600 chr5D 100.000 1958 0 0 1 1958 281015486 281013529 0.000000e+00 3616.0
2 TraesCS5D01G180600 chr5D 85.819 409 45 10 4029 4431 485395262 485394861 7.610000e-114 422.0
3 TraesCS5D01G180600 chr5D 84.864 403 47 10 4035 4430 555423233 555423628 1.660000e-105 394.0
4 TraesCS5D01G180600 chr5D 91.786 280 23 0 6048 6327 7559988 7559709 2.150000e-104 390.0
5 TraesCS5D01G180600 chr5D 90.625 64 3 2 813 876 281014702 281014642 1.470000e-11 82.4
6 TraesCS5D01G180600 chr5A 95.204 3169 86 21 2167 5296 370267249 370270390 0.000000e+00 4950.0
7 TraesCS5D01G180600 chr5A 95.784 1091 45 1 842 1932 370265936 370267025 0.000000e+00 1759.0
8 TraesCS5D01G180600 chr5A 91.837 784 34 13 5288 6059 370271079 370271844 0.000000e+00 1066.0
9 TraesCS5D01G180600 chr5A 89.902 713 44 16 1 691 370264785 370265491 0.000000e+00 893.0
10 TraesCS5D01G180600 chr5A 96.226 53 1 1 5393 5444 370271130 370271182 1.130000e-12 86.1
11 TraesCS5D01G180600 chr5A 100.000 28 0 0 5366 5393 370271185 370271212 1.200000e-02 52.8
12 TraesCS5D01G180600 chr5B 92.493 1079 42 9 861 1932 318876603 318875557 0.000000e+00 1507.0
13 TraesCS5D01G180600 chr5B 91.187 1112 52 21 2330 3409 318875147 318874050 0.000000e+00 1469.0
14 TraesCS5D01G180600 chr5B 88.619 905 82 10 4441 5328 318873475 318872575 0.000000e+00 1081.0
15 TraesCS5D01G180600 chr5B 86.174 933 63 25 5429 6346 318872568 318871687 0.000000e+00 948.0
16 TraesCS5D01G180600 chr5B 93.793 580 35 1 3439 4018 318874050 318873472 0.000000e+00 870.0
17 TraesCS5D01G180600 chr5B 94.631 149 8 0 2155 2303 318875293 318875145 1.380000e-56 231.0
18 TraesCS5D01G180600 chr5B 90.000 110 9 2 2510 2618 696737370 696737262 2.390000e-29 141.0
19 TraesCS5D01G180600 chr3B 92.230 296 21 2 6045 6339 377115122 377115416 9.850000e-113 418.0
20 TraesCS5D01G180600 chr3B 84.729 406 51 9 4029 4430 141129526 141129128 4.620000e-106 396.0
21 TraesCS5D01G180600 chr3A 91.919 297 22 2 6045 6339 319962314 319962610 1.270000e-111 414.0
22 TraesCS5D01G180600 chr3A 86.992 123 12 4 2518 2639 30994934 30995053 1.110000e-27 135.0
23 TraesCS5D01G180600 chr2D 85.468 406 49 10 4031 4432 639828263 639827864 1.270000e-111 414.0
24 TraesCS5D01G180600 chr2D 90.785 293 26 1 6045 6336 325807321 325807613 2.150000e-104 390.0
25 TraesCS5D01G180600 chr2D 85.271 129 15 2 2513 2640 395940187 395940312 5.170000e-26 130.0
26 TraesCS5D01G180600 chr6D 85.096 416 48 12 4029 4436 392524772 392525181 4.580000e-111 412.0
27 TraesCS5D01G180600 chr6D 90.268 298 27 2 6033 6329 327021859 327022155 7.720000e-104 388.0
28 TraesCS5D01G180600 chr3D 91.892 296 23 1 6045 6339 255424394 255424689 4.580000e-111 412.0
29 TraesCS5D01G180600 chr3D 90.816 294 26 1 6047 6340 491959957 491960249 5.970000e-105 392.0
30 TraesCS5D01G180600 chr4D 85.167 418 40 12 4029 4432 327379916 327379507 5.930000e-110 409.0
31 TraesCS5D01G180600 chr2A 92.281 285 21 1 6045 6329 43540247 43540530 2.760000e-108 403.0
32 TraesCS5D01G180600 chr2A 86.508 126 11 3 2518 2641 1882078 1882199 4.000000e-27 134.0
33 TraesCS5D01G180600 chr6A 90.604 298 22 4 6046 6340 374422666 374422960 2.150000e-104 390.0
34 TraesCS5D01G180600 chr6A 83.373 415 56 12 4029 4437 606095569 606095976 7.780000e-99 372.0
35 TraesCS5D01G180600 chr6A 86.466 133 13 3 2510 2641 582803720 582803592 2.390000e-29 141.0
36 TraesCS5D01G180600 chr6A 87.705 122 11 2 2521 2641 162832956 162832838 8.590000e-29 139.0
37 TraesCS5D01G180600 chr4B 82.567 413 56 9 4029 4431 120422491 120422897 3.640000e-92 350.0
38 TraesCS5D01G180600 chr7A 85.827 127 12 3 2517 2641 573456806 573456684 5.170000e-26 130.0


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 TraesCS5D01G180600 chr5D 281009135 281015486 6351 True 3819.466667 7760 96.8750 1 6352 3 chr5D.!!$R3 6351
1 TraesCS5D01G180600 chr5A 370264785 370271844 7059 False 1467.816667 4950 94.8255 1 6059 6 chr5A.!!$F1 6058
2 TraesCS5D01G180600 chr5B 318871687 318876603 4916 True 1017.666667 1507 91.1495 861 6346 6 chr5B.!!$R2 5485

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
691 714 0.037590 TCTACCACGCCCTTGCAATT 59.962 50.000 0.00 0.0 37.32 2.32 F
701 724 0.038343 CCTTGCAATTGGAACCGGTG 60.038 55.000 8.52 0.0 0.00 4.94 F
749 772 0.179124 CGAGTGCCAGAGCTTCCTAC 60.179 60.000 0.00 0.0 40.80 3.18 F
1749 2153 0.249073 ACGACCTCATATCTGCACGC 60.249 55.000 0.00 0.0 0.00 5.34 F
1781 2185 1.841944 GATCGTGCGCATTCAATTGTG 59.158 47.619 15.91 0.0 0.00 3.33 F
1941 2345 3.130869 TGAAAATGCCACTGATATGCCAC 59.869 43.478 0.00 0.0 0.00 5.01 F
3765 4259 2.584835 TTTGGCCAGCAACTCTACAT 57.415 45.000 5.11 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1654 2058 0.112995 TGGGGAGAAAACAGCAGCAT 59.887 50.000 0.00 0.00 0.00 3.79 R
1936 2340 1.632589 TTGAGCTGAGACTAGTGGCA 58.367 50.000 0.00 0.00 0.00 4.92 R
1937 2341 2.615869 CTTTGAGCTGAGACTAGTGGC 58.384 52.381 0.00 0.00 0.00 5.01 R
3469 3962 3.201353 TCACGAACCCATTCAAGTTGA 57.799 42.857 0.08 0.08 34.14 3.18 R
3729 4223 5.072329 TGGCCAAATTGGAAATAAAACTCCA 59.928 36.000 17.47 6.40 40.96 3.86 R
3863 4357 1.451567 CCTCATCAGCACAGCAGGG 60.452 63.158 0.00 0.00 0.00 4.45 R
5359 6590 0.034186 TTATGCAGGCACCAGGGAAG 60.034 55.000 0.00 0.00 0.00 3.46 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
63 64 5.750352 AGCCCATGAACTTGAAAATTCAT 57.250 34.783 0.00 0.00 44.52 2.57
308 312 9.678941 GTACATGCTTTTTAATCTATAAAGGGC 57.321 33.333 0.00 0.00 30.53 5.19
354 358 3.503363 GGTGCTAGCAGGCAAGCG 61.503 66.667 20.03 0.00 44.18 4.68
400 404 4.336993 CGAGTGGTAAGCTAATGAGAGAGT 59.663 45.833 0.00 0.00 0.00 3.24
402 406 4.404073 AGTGGTAAGCTAATGAGAGAGTGG 59.596 45.833 0.00 0.00 0.00 4.00
413 417 3.808728 TGAGAGAGTGGTCCAACTTTTG 58.191 45.455 0.00 0.00 0.00 2.44
493 516 2.192979 CCACACATGGCGGCCTAT 59.807 61.111 21.46 9.27 39.82 2.57
494 517 1.453745 CCACACATGGCGGCCTATT 60.454 57.895 21.46 1.98 39.82 1.73
537 560 7.219726 GCTTAGCAAGATTATGAGCTTCAAAAC 59.780 37.037 0.00 0.00 38.47 2.43
576 599 5.576774 TCGTGTACATAATTGCAAGACTCAG 59.423 40.000 4.94 0.00 0.00 3.35
617 640 4.279420 GGCAAGACTCAAAACCAATCTTCT 59.721 41.667 0.00 0.00 0.00 2.85
621 644 2.893489 ACTCAAAACCAATCTTCTGGCC 59.107 45.455 0.00 0.00 40.45 5.36
625 648 0.112995 AACCAATCTTCTGGCCTGCA 59.887 50.000 3.32 0.00 40.45 4.41
626 649 0.112995 ACCAATCTTCTGGCCTGCAA 59.887 50.000 3.32 0.00 40.45 4.08
653 676 2.210144 GAGCACCATAAGGGCCACCA 62.210 60.000 6.18 0.00 42.05 4.17
680 703 9.032420 GTTCCTTCTTAAATATCTTCTACCACG 57.968 37.037 0.00 0.00 0.00 4.94
691 714 0.037590 TCTACCACGCCCTTGCAATT 59.962 50.000 0.00 0.00 37.32 2.32
692 715 0.171007 CTACCACGCCCTTGCAATTG 59.829 55.000 0.00 0.00 37.32 2.32
693 716 1.247419 TACCACGCCCTTGCAATTGG 61.247 55.000 7.72 5.08 37.49 3.16
694 717 2.274645 CCACGCCCTTGCAATTGGA 61.275 57.895 17.01 0.23 34.81 3.53
695 718 1.664873 CACGCCCTTGCAATTGGAA 59.335 52.632 17.01 12.14 37.32 3.53
696 719 0.667184 CACGCCCTTGCAATTGGAAC 60.667 55.000 17.01 0.00 37.32 3.62
697 720 1.079888 CGCCCTTGCAATTGGAACC 60.080 57.895 17.01 0.00 37.32 3.62
698 721 1.079888 GCCCTTGCAATTGGAACCG 60.080 57.895 17.01 2.84 37.47 4.44
699 722 1.591183 CCCTTGCAATTGGAACCGG 59.409 57.895 8.47 9.40 0.00 5.28
700 723 1.184970 CCCTTGCAATTGGAACCGGT 61.185 55.000 8.47 0.00 0.00 5.28
701 724 0.038343 CCTTGCAATTGGAACCGGTG 60.038 55.000 8.52 0.00 0.00 4.94
702 725 0.673437 CTTGCAATTGGAACCGGTGT 59.327 50.000 8.52 0.00 0.00 4.16
703 726 0.387202 TTGCAATTGGAACCGGTGTG 59.613 50.000 8.52 0.77 0.00 3.82
704 727 0.466372 TGCAATTGGAACCGGTGTGA 60.466 50.000 8.52 0.00 0.00 3.58
705 728 0.671251 GCAATTGGAACCGGTGTGAA 59.329 50.000 8.52 0.52 0.00 3.18
706 729 1.272212 GCAATTGGAACCGGTGTGAAT 59.728 47.619 8.52 3.36 0.00 2.57
707 730 2.926159 GCAATTGGAACCGGTGTGAATG 60.926 50.000 8.52 4.94 0.00 2.67
708 731 2.286365 ATTGGAACCGGTGTGAATGT 57.714 45.000 8.52 0.00 0.00 2.71
709 732 2.060050 TTGGAACCGGTGTGAATGTT 57.940 45.000 8.52 0.00 0.00 2.71
710 733 1.600023 TGGAACCGGTGTGAATGTTC 58.400 50.000 8.52 0.00 37.08 3.18
711 734 0.879090 GGAACCGGTGTGAATGTTCC 59.121 55.000 8.52 4.58 46.95 3.62
712 735 1.892209 GAACCGGTGTGAATGTTCCT 58.108 50.000 8.52 0.00 32.83 3.36
713 736 1.804748 GAACCGGTGTGAATGTTCCTC 59.195 52.381 8.52 0.00 32.83 3.71
714 737 0.762418 ACCGGTGTGAATGTTCCTCA 59.238 50.000 6.12 0.00 0.00 3.86
715 738 1.270839 ACCGGTGTGAATGTTCCTCAG 60.271 52.381 6.12 0.00 0.00 3.35
716 739 1.442769 CGGTGTGAATGTTCCTCAGG 58.557 55.000 0.00 0.00 0.00 3.86
717 740 1.168714 GGTGTGAATGTTCCTCAGGC 58.831 55.000 0.00 0.00 0.00 4.85
718 741 1.168714 GTGTGAATGTTCCTCAGGCC 58.831 55.000 0.00 0.00 0.00 5.19
719 742 0.770499 TGTGAATGTTCCTCAGGCCA 59.230 50.000 5.01 0.00 0.00 5.36
720 743 1.144708 TGTGAATGTTCCTCAGGCCAA 59.855 47.619 5.01 0.00 0.00 4.52
721 744 1.541588 GTGAATGTTCCTCAGGCCAAC 59.458 52.381 5.01 0.00 0.00 3.77
722 745 1.144708 TGAATGTTCCTCAGGCCAACA 59.855 47.619 5.01 6.81 34.61 3.33
723 746 2.225091 TGAATGTTCCTCAGGCCAACAT 60.225 45.455 5.01 9.19 41.50 2.71
745 768 2.099431 CAGCGAGTGCCAGAGCTTC 61.099 63.158 0.00 0.00 44.31 3.86
748 771 1.949847 GCGAGTGCCAGAGCTTCCTA 61.950 60.000 0.00 0.00 40.80 2.94
749 772 0.179124 CGAGTGCCAGAGCTTCCTAC 60.179 60.000 0.00 0.00 40.80 3.18
777 1175 6.350277 GCAAGAGCTTGGACTAGAGTAGTTTA 60.350 42.308 11.78 0.00 38.88 2.01
782 1180 9.438228 GAGCTTGGACTAGAGTAGTTTATTTTT 57.562 33.333 0.00 0.00 39.59 1.94
783 1181 9.438228 AGCTTGGACTAGAGTAGTTTATTTTTC 57.562 33.333 0.00 0.00 39.59 2.29
784 1182 9.438228 GCTTGGACTAGAGTAGTTTATTTTTCT 57.562 33.333 0.00 0.00 39.59 2.52
809 1207 9.936759 CTTTTATTTTGAGAAGAGGACTAGAGT 57.063 33.333 0.00 0.00 0.00 3.24
812 1210 9.756571 TTATTTTGAGAAGAGGACTAGAGTAGT 57.243 33.333 0.00 0.00 42.86 2.73
813 1211 8.658840 ATTTTGAGAAGAGGACTAGAGTAGTT 57.341 34.615 0.00 0.00 39.59 2.24
814 1212 8.480133 TTTTGAGAAGAGGACTAGAGTAGTTT 57.520 34.615 0.00 0.00 39.59 2.66
815 1213 8.480133 TTTGAGAAGAGGACTAGAGTAGTTTT 57.520 34.615 0.00 0.00 39.59 2.43
816 1214 8.480133 TTGAGAAGAGGACTAGAGTAGTTTTT 57.520 34.615 0.00 0.00 39.59 1.94
837 1235 3.685139 TTTTGACAGGCAGGACTAGAG 57.315 47.619 0.00 0.00 0.00 2.43
838 1236 2.310779 TTGACAGGCAGGACTAGAGT 57.689 50.000 0.00 0.00 0.00 3.24
839 1237 3.451402 TTGACAGGCAGGACTAGAGTA 57.549 47.619 0.00 0.00 0.00 2.59
840 1238 3.006112 TGACAGGCAGGACTAGAGTAG 57.994 52.381 0.00 0.00 0.00 2.57
841 1239 2.309162 TGACAGGCAGGACTAGAGTAGT 59.691 50.000 0.00 0.00 42.86 2.73
842 1240 3.245300 TGACAGGCAGGACTAGAGTAGTT 60.245 47.826 0.00 0.00 39.59 2.24
843 1241 3.764972 GACAGGCAGGACTAGAGTAGTTT 59.235 47.826 0.00 0.00 39.59 2.66
844 1242 4.161102 ACAGGCAGGACTAGAGTAGTTTT 58.839 43.478 0.00 0.00 39.59 2.43
845 1243 4.593634 ACAGGCAGGACTAGAGTAGTTTTT 59.406 41.667 0.00 0.00 39.59 1.94
846 1244 5.172205 CAGGCAGGACTAGAGTAGTTTTTC 58.828 45.833 0.00 0.00 39.59 2.29
927 1325 1.408127 GCCCAAACAAACAGCCCTTTT 60.408 47.619 0.00 0.00 0.00 2.27
1009 1407 2.102420 ACTGAACGACACAACCATCTCA 59.898 45.455 0.00 0.00 0.00 3.27
1146 1544 0.748367 CCGACTCCTGAGATCACCGA 60.748 60.000 0.22 0.00 0.00 4.69
1153 1551 2.225791 CTGAGATCACCGACGCCCAA 62.226 60.000 0.00 0.00 0.00 4.12
1348 1752 3.787001 CTCCCCACCGCTCCTTCC 61.787 72.222 0.00 0.00 0.00 3.46
1364 1768 0.828022 TTCCCTCGGTATTGCGATGT 59.172 50.000 0.00 0.00 0.00 3.06
1365 1769 0.828022 TCCCTCGGTATTGCGATGTT 59.172 50.000 0.00 0.00 0.00 2.71
1374 1778 0.738063 ATTGCGATGTTCCGTGCGTA 60.738 50.000 0.00 0.00 0.00 4.42
1440 1844 8.793592 GTTTGGTTAGAGAGGTGTAAATTTGAT 58.206 33.333 0.00 0.00 0.00 2.57
1476 1880 1.334869 GAGCAACTTGGATAATGGGCG 59.665 52.381 0.00 0.00 0.00 6.13
1556 1960 1.726791 CGAAGGTGACAACGAAGATGG 59.273 52.381 0.00 0.00 33.36 3.51
1599 2003 4.329392 GAGACGGGAAAAGGGTTATCAAA 58.671 43.478 0.00 0.00 0.00 2.69
1654 2058 1.007038 GTACCGGTGACTGCGAACA 60.007 57.895 19.93 0.00 0.00 3.18
1718 2122 5.749109 GGTGGACATATAACTCTTCTCAACG 59.251 44.000 0.00 0.00 0.00 4.10
1749 2153 0.249073 ACGACCTCATATCTGCACGC 60.249 55.000 0.00 0.00 0.00 5.34
1781 2185 1.841944 GATCGTGCGCATTCAATTGTG 59.158 47.619 15.91 0.00 0.00 3.33
1845 2249 5.783111 TGTCATCTCTTGTTCAATCGAGAA 58.217 37.500 8.01 0.00 36.26 2.87
1931 2335 4.768968 AGTGCTATTTCTGAAAATGCCACT 59.231 37.500 20.14 18.19 39.74 4.00
1932 2336 4.860907 GTGCTATTTCTGAAAATGCCACTG 59.139 41.667 20.14 4.20 35.96 3.66
1933 2337 4.766373 TGCTATTTCTGAAAATGCCACTGA 59.234 37.500 20.14 6.16 35.84 3.41
1934 2338 5.419788 TGCTATTTCTGAAAATGCCACTGAT 59.580 36.000 20.14 1.19 35.84 2.90
1935 2339 6.602803 TGCTATTTCTGAAAATGCCACTGATA 59.397 34.615 20.14 5.15 35.84 2.15
1936 2340 7.286087 TGCTATTTCTGAAAATGCCACTGATAT 59.714 33.333 20.14 0.62 35.84 1.63
1937 2341 7.594015 GCTATTTCTGAAAATGCCACTGATATG 59.406 37.037 6.95 0.00 35.84 1.78
1938 2342 4.906065 TCTGAAAATGCCACTGATATGC 57.094 40.909 0.00 0.00 0.00 3.14
1939 2343 3.633525 TCTGAAAATGCCACTGATATGCC 59.366 43.478 0.00 0.00 0.00 4.40
1940 2344 3.363627 TGAAAATGCCACTGATATGCCA 58.636 40.909 0.00 0.00 0.00 4.92
1941 2345 3.130869 TGAAAATGCCACTGATATGCCAC 59.869 43.478 0.00 0.00 0.00 5.01
2729 3214 8.620416 GCATTGTTAAAAACTTCCCTTGAAAAT 58.380 29.630 0.00 0.00 0.00 1.82
2863 3349 3.181483 GGTTTTCTCAGCAGCCATTATGG 60.181 47.826 6.92 6.92 41.55 2.74
2882 3368 3.799719 TGGCAGATGATATCCCTGAGAT 58.200 45.455 20.15 0.00 39.15 2.75
3031 3518 7.155328 TCTCTTTCCAAGTCTCAGTAATTGAC 58.845 38.462 0.00 0.00 0.00 3.18
3146 3633 9.526713 AATTGTTTGTTATATTGCGATGCATAA 57.473 25.926 0.00 0.00 38.76 1.90
3350 3839 7.048512 ACTGTTACAAGAACAAGAAGTTAGCT 58.951 34.615 0.00 0.00 41.51 3.32
3387 3880 9.733556 ACATTATCAAAAGGTACATGTGACTAA 57.266 29.630 9.11 0.00 0.00 2.24
3469 3962 7.103641 TCGTAGAGAAAAATGGCTGATACTTT 58.896 34.615 0.00 0.00 0.00 2.66
3729 4223 3.321968 GTCTGGTTCAAATTGCCTTTCCT 59.678 43.478 0.00 0.00 0.00 3.36
3765 4259 2.584835 TTTGGCCAGCAACTCTACAT 57.415 45.000 5.11 0.00 0.00 2.29
3829 4323 7.617225 ACTTATACTGCTGTATGTTGGTGTTA 58.383 34.615 22.42 0.68 39.49 2.41
3842 4336 4.186159 GTTGGTGTTATACATGCGTACCT 58.814 43.478 0.00 0.00 0.00 3.08
3846 4340 5.127519 TGGTGTTATACATGCGTACCTTAGT 59.872 40.000 0.00 0.00 0.00 2.24
4067 4561 2.525877 GGCGCTCCACCCCCTATA 60.526 66.667 7.64 0.00 0.00 1.31
4142 4636 4.829872 ACCGATATCAAACTTGGGTGTA 57.170 40.909 3.12 0.00 0.00 2.90
4167 4661 6.817396 CGATCTACTTTCGTGTGAAATTTCA 58.183 36.000 16.91 16.91 42.90 2.69
4259 4755 3.505680 TGGATGGATTTTTGTTCGGACAG 59.494 43.478 0.00 0.00 37.04 3.51
4260 4756 3.506067 GGATGGATTTTTGTTCGGACAGT 59.494 43.478 0.00 0.00 37.04 3.55
4261 4757 4.698304 GGATGGATTTTTGTTCGGACAGTA 59.302 41.667 0.00 0.00 37.04 2.74
4262 4758 5.357032 GGATGGATTTTTGTTCGGACAGTAT 59.643 40.000 0.00 0.00 37.04 2.12
4263 4759 6.127730 GGATGGATTTTTGTTCGGACAGTATT 60.128 38.462 0.00 0.00 37.04 1.89
4264 4760 6.642707 TGGATTTTTGTTCGGACAGTATTT 57.357 33.333 0.00 0.00 37.04 1.40
4265 4761 6.674066 TGGATTTTTGTTCGGACAGTATTTC 58.326 36.000 0.00 0.00 37.04 2.17
4266 4762 6.090783 GGATTTTTGTTCGGACAGTATTTCC 58.909 40.000 0.00 0.00 37.04 3.13
4267 4763 6.072119 GGATTTTTGTTCGGACAGTATTTCCT 60.072 38.462 0.00 0.00 37.04 3.36
4268 4764 6.702716 TTTTTGTTCGGACAGTATTTCCTT 57.297 33.333 0.00 0.00 37.04 3.36
4269 4765 5.934935 TTTGTTCGGACAGTATTTCCTTC 57.065 39.130 0.00 0.00 37.04 3.46
4270 4766 4.610605 TGTTCGGACAGTATTTCCTTCA 57.389 40.909 0.00 0.00 0.00 3.02
4271 4767 4.312443 TGTTCGGACAGTATTTCCTTCAC 58.688 43.478 0.00 0.00 0.00 3.18
4272 4768 3.604875 TCGGACAGTATTTCCTTCACC 57.395 47.619 0.00 0.00 0.00 4.02
4273 4769 2.901192 TCGGACAGTATTTCCTTCACCA 59.099 45.455 0.00 0.00 0.00 4.17
4317 4813 1.292061 TTCACGAAACTTCACACGGG 58.708 50.000 0.00 0.00 0.00 5.28
4358 4854 6.380846 CAGGTTTGATATCCCCAAATTTCAGA 59.619 38.462 0.00 0.00 36.14 3.27
4359 4855 7.070322 CAGGTTTGATATCCCCAAATTTCAGAT 59.930 37.037 0.00 0.00 36.14 2.90
4532 5036 3.209410 CTGAAGCTCATCCCCACAATAC 58.791 50.000 0.00 0.00 0.00 1.89
4579 5093 4.252878 TGAGCATTCACTAAGCGATTTGA 58.747 39.130 1.04 0.00 0.00 2.69
4580 5094 4.694982 TGAGCATTCACTAAGCGATTTGAA 59.305 37.500 1.04 2.28 32.71 2.69
4581 5095 5.163824 TGAGCATTCACTAAGCGATTTGAAG 60.164 40.000 1.04 0.00 31.72 3.02
4584 5098 6.371548 AGCATTCACTAAGCGATTTGAAGTAA 59.628 34.615 1.04 0.00 31.72 2.24
4748 5262 1.712018 CTCACACAGGATGCATGCGG 61.712 60.000 16.30 16.30 42.53 5.69
4802 5316 3.506067 CGGAAATTAGCAGGTCTGGTTTT 59.494 43.478 8.01 4.10 41.96 2.43
4819 5333 3.234386 GTTTTCTAACACATGCTTCCGC 58.766 45.455 0.00 0.00 34.31 5.54
4899 5423 6.573664 TGAGTAATAAAATGTGTGCTGCTT 57.426 33.333 0.00 0.00 0.00 3.91
4961 5485 0.247736 AGCGAGCAGAAGGTACAAGG 59.752 55.000 0.00 0.00 0.00 3.61
5259 5793 2.716424 TGTTTTCTGATCTTCCAGGGGT 59.284 45.455 0.00 0.00 34.99 4.95
5306 6537 7.096885 CGACAGATTTCAGTTTTGTTTTAGCTG 60.097 37.037 0.00 0.00 0.00 4.24
5340 6571 4.618920 CCAAGTGGGTAAGTAGTGTCTT 57.381 45.455 0.00 0.00 0.00 3.01
5341 6572 4.969484 CCAAGTGGGTAAGTAGTGTCTTT 58.031 43.478 0.00 0.00 0.00 2.52
5343 6574 5.826208 CCAAGTGGGTAAGTAGTGTCTTTTT 59.174 40.000 0.00 0.00 0.00 1.94
5404 6635 5.979517 GGGTTCATCAAAATGCTAGTATTGC 59.020 40.000 6.84 0.00 32.58 3.56
5467 6698 2.001269 GGGTGCCATAGGGGTGAGT 61.001 63.158 0.00 0.00 39.65 3.41
5515 6746 2.106511 TCAGGAGCTATTGGTATTGGGC 59.893 50.000 0.00 0.00 0.00 5.36
5562 6794 2.230940 CGATAGTGGCGCCAACGAG 61.231 63.158 34.66 17.93 43.93 4.18
5617 6849 5.221244 GCTTGTGGCTCCTTTTTCTTTTCTA 60.221 40.000 0.00 0.00 38.06 2.10
5639 6871 3.733443 ACACACCAAGCTCCATTTTTC 57.267 42.857 0.00 0.00 0.00 2.29
5663 6895 1.949465 GTGAAAACCACACGAGGAGT 58.051 50.000 0.00 0.00 45.03 3.85
5685 6917 6.779117 AGTGTGCGATAATCTGAATTGAAAG 58.221 36.000 0.00 0.00 0.00 2.62
5686 6918 5.967674 GTGTGCGATAATCTGAATTGAAAGG 59.032 40.000 0.00 0.00 0.00 3.11
5760 6993 1.032014 ACCAGCGTGTTTCAGCAATT 58.968 45.000 0.00 0.00 35.48 2.32
5900 7143 1.471327 GCTTTTTGGTGTGAGCTGCAA 60.471 47.619 1.02 0.00 32.54 4.08
6041 7285 9.176181 TCGACTTTTGCACTTTTGAAAATATAC 57.824 29.630 0.00 0.00 0.00 1.47
6043 7287 9.255304 GACTTTTGCACTTTTGAAAATATACCA 57.745 29.630 0.00 0.00 0.00 3.25
6089 7333 6.641169 AAGGTTCTCATTTCACCTTTCTTC 57.359 37.500 0.00 0.00 46.85 2.87
6124 7368 9.123902 CTTTCATCCAACCTTTCATGTATATGA 57.876 33.333 0.00 0.00 41.44 2.15
6161 7405 6.198650 TCATTTACGTATCTTCTGAACCGA 57.801 37.500 0.00 0.00 0.00 4.69
6164 7408 7.434307 TCATTTACGTATCTTCTGAACCGATTC 59.566 37.037 0.00 0.00 35.18 2.52
6170 7414 3.926616 TCTTCTGAACCGATTCCACTTC 58.073 45.455 0.00 0.00 33.49 3.01
6231 7475 2.487762 TCACGGCCAGAATTTGATGAAC 59.512 45.455 2.24 0.00 0.00 3.18
6268 7512 8.898761 ACAATCGCATTATTATTGACAGGTAAA 58.101 29.630 0.00 0.00 35.18 2.01
6280 7524 5.142061 TGACAGGTAAATCACGAGCTAAA 57.858 39.130 0.00 0.00 0.00 1.85
6281 7525 5.168569 TGACAGGTAAATCACGAGCTAAAG 58.831 41.667 0.00 0.00 0.00 1.85
6282 7526 5.148651 ACAGGTAAATCACGAGCTAAAGT 57.851 39.130 0.00 0.00 0.00 2.66
6283 7527 6.071784 TGACAGGTAAATCACGAGCTAAAGTA 60.072 38.462 0.00 0.00 0.00 2.24
6284 7528 6.875076 ACAGGTAAATCACGAGCTAAAGTAT 58.125 36.000 0.00 0.00 0.00 2.12
6346 7591 8.826710 TGTTCTAGTGTCTCTAAAAACACATTG 58.173 33.333 8.20 0.00 46.47 2.82
6347 7592 8.827677 GTTCTAGTGTCTCTAAAAACACATTGT 58.172 33.333 8.20 0.00 46.47 2.71
6348 7593 8.958119 TCTAGTGTCTCTAAAAACACATTGTT 57.042 30.769 8.20 0.00 46.47 2.83
6349 7594 9.042008 TCTAGTGTCTCTAAAAACACATTGTTC 57.958 33.333 8.20 0.00 46.47 3.18
6350 7595 7.865706 AGTGTCTCTAAAAACACATTGTTCT 57.134 32.000 8.20 0.00 46.47 3.01
6351 7596 8.958119 AGTGTCTCTAAAAACACATTGTTCTA 57.042 30.769 8.20 0.00 46.47 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
336 340 2.045536 GCTTGCCTGCTAGCACCT 60.046 61.111 14.93 0.00 43.97 4.00
365 369 4.736759 GCTTACCACTCGCTAGCTATCAAA 60.737 45.833 13.93 0.00 0.00 2.69
367 371 2.293677 GCTTACCACTCGCTAGCTATCA 59.706 50.000 13.93 0.00 0.00 2.15
368 372 2.554893 AGCTTACCACTCGCTAGCTATC 59.445 50.000 13.93 0.00 40.19 2.08
383 387 4.402793 TGGACCACTCTCTCATTAGCTTAC 59.597 45.833 0.00 0.00 0.00 2.34
414 418 5.103813 ACATTACCATTACCTTCTTACCCCC 60.104 44.000 0.00 0.00 0.00 5.40
416 420 7.114095 TGAACATTACCATTACCTTCTTACCC 58.886 38.462 0.00 0.00 0.00 3.69
444 467 6.656693 CACCCTCATGATCCAATTCTTATACC 59.343 42.308 0.00 0.00 0.00 2.73
448 471 5.397899 GGTCACCCTCATGATCCAATTCTTA 60.398 44.000 0.00 0.00 0.00 2.10
487 510 6.038714 GCATGCTAATATGTTAGGAATAGGCC 59.961 42.308 11.37 0.00 40.89 5.19
493 516 7.223584 TGCTAAGCATGCTAATATGTTAGGAA 58.776 34.615 23.00 0.00 40.89 3.36
494 517 6.768483 TGCTAAGCATGCTAATATGTTAGGA 58.232 36.000 23.00 15.01 41.61 2.94
537 560 3.644884 ACACGAGTGTAGGAACTTCAG 57.355 47.619 7.14 0.00 42.90 3.02
546 569 6.530181 TCTTGCAATTATGTACACGAGTGTAG 59.470 38.462 15.49 4.65 45.61 2.74
547 570 6.309494 GTCTTGCAATTATGTACACGAGTGTA 59.691 38.462 11.61 11.61 44.42 2.90
548 571 5.120208 GTCTTGCAATTATGTACACGAGTGT 59.880 40.000 13.68 13.68 46.87 3.55
599 622 3.057245 GGCCAGAAGATTGGTTTTGAGTC 60.057 47.826 0.00 0.00 40.49 3.36
617 640 1.918467 CTCAGGGAGATTGCAGGCCA 61.918 60.000 5.01 0.00 0.00 5.36
621 644 0.747283 GGTGCTCAGGGAGATTGCAG 60.747 60.000 0.00 0.00 34.15 4.41
625 648 2.441001 CCTTATGGTGCTCAGGGAGATT 59.559 50.000 0.00 0.00 0.00 2.40
626 649 2.053244 CCTTATGGTGCTCAGGGAGAT 58.947 52.381 0.00 0.00 0.00 2.75
680 703 1.079888 CGGTTCCAATTGCAAGGGC 60.080 57.895 13.67 4.05 41.68 5.19
691 714 1.600023 GAACATTCACACCGGTTCCA 58.400 50.000 2.97 0.00 34.92 3.53
693 716 1.804748 GAGGAACATTCACACCGGTTC 59.195 52.381 2.97 0.00 39.04 3.62
694 717 1.142060 TGAGGAACATTCACACCGGTT 59.858 47.619 2.97 0.00 0.00 4.44
695 718 0.762418 TGAGGAACATTCACACCGGT 59.238 50.000 0.00 0.00 0.00 5.28
696 719 1.442769 CTGAGGAACATTCACACCGG 58.557 55.000 0.00 0.00 0.00 5.28
697 720 1.442769 CCTGAGGAACATTCACACCG 58.557 55.000 0.00 0.00 0.00 4.94
698 721 1.168714 GCCTGAGGAACATTCACACC 58.831 55.000 0.65 0.00 0.00 4.16
699 722 1.168714 GGCCTGAGGAACATTCACAC 58.831 55.000 0.65 0.00 0.00 3.82
700 723 0.770499 TGGCCTGAGGAACATTCACA 59.230 50.000 0.65 0.00 0.00 3.58
701 724 1.541588 GTTGGCCTGAGGAACATTCAC 59.458 52.381 0.65 0.00 0.00 3.18
702 725 1.144708 TGTTGGCCTGAGGAACATTCA 59.855 47.619 0.65 0.69 0.00 2.57
703 726 1.909700 TGTTGGCCTGAGGAACATTC 58.090 50.000 0.65 0.00 0.00 2.67
704 727 2.450476 GATGTTGGCCTGAGGAACATT 58.550 47.619 16.73 4.56 39.77 2.71
705 728 1.679944 CGATGTTGGCCTGAGGAACAT 60.680 52.381 15.90 15.90 41.82 2.71
706 729 0.321564 CGATGTTGGCCTGAGGAACA 60.322 55.000 0.65 5.31 34.25 3.18
707 730 0.321653 ACGATGTTGGCCTGAGGAAC 60.322 55.000 0.65 0.00 0.00 3.62
708 731 0.036388 GACGATGTTGGCCTGAGGAA 60.036 55.000 0.65 0.00 0.00 3.36
709 732 1.191489 TGACGATGTTGGCCTGAGGA 61.191 55.000 0.65 0.00 0.00 3.71
710 733 0.742281 CTGACGATGTTGGCCTGAGG 60.742 60.000 3.32 0.00 0.00 3.86
711 734 1.364626 GCTGACGATGTTGGCCTGAG 61.365 60.000 3.32 0.00 0.00 3.35
712 735 1.375908 GCTGACGATGTTGGCCTGA 60.376 57.895 3.32 0.00 0.00 3.86
713 736 2.743752 CGCTGACGATGTTGGCCTG 61.744 63.158 3.32 0.00 43.93 4.85
714 737 2.434884 CGCTGACGATGTTGGCCT 60.435 61.111 3.32 0.00 43.93 5.19
715 738 2.434185 TCGCTGACGATGTTGGCC 60.434 61.111 0.00 0.00 45.12 5.36
739 762 2.006169 GCTCTTGCTTGTAGGAAGCTC 58.994 52.381 7.84 0.00 42.50 4.09
783 1181 9.936759 ACTCTAGTCCTCTTCTCAAAATAAAAG 57.063 33.333 0.00 0.00 0.00 2.27
786 1184 9.756571 ACTACTCTAGTCCTCTTCTCAAAATAA 57.243 33.333 0.00 0.00 32.47 1.40
787 1185 9.756571 AACTACTCTAGTCCTCTTCTCAAAATA 57.243 33.333 0.00 0.00 38.26 1.40
789 1187 8.480133 AAACTACTCTAGTCCTCTTCTCAAAA 57.520 34.615 0.00 0.00 38.26 2.44
816 1214 3.391296 ACTCTAGTCCTGCCTGTCAAAAA 59.609 43.478 0.00 0.00 0.00 1.94
817 1215 2.972713 ACTCTAGTCCTGCCTGTCAAAA 59.027 45.455 0.00 0.00 0.00 2.44
818 1216 2.609747 ACTCTAGTCCTGCCTGTCAAA 58.390 47.619 0.00 0.00 0.00 2.69
819 1217 2.310779 ACTCTAGTCCTGCCTGTCAA 57.689 50.000 0.00 0.00 0.00 3.18
820 1218 2.309162 ACTACTCTAGTCCTGCCTGTCA 59.691 50.000 0.00 0.00 32.47 3.58
821 1219 3.007473 ACTACTCTAGTCCTGCCTGTC 57.993 52.381 0.00 0.00 32.47 3.51
822 1220 3.459710 AACTACTCTAGTCCTGCCTGT 57.540 47.619 0.00 0.00 38.26 4.00
823 1221 4.810191 AAAACTACTCTAGTCCTGCCTG 57.190 45.455 0.00 0.00 38.26 4.85
824 1222 5.088026 AGAAAAACTACTCTAGTCCTGCCT 58.912 41.667 0.00 0.00 38.26 4.75
825 1223 5.408880 AGAAAAACTACTCTAGTCCTGCC 57.591 43.478 0.00 0.00 38.26 4.85
826 1224 7.731882 AAAAGAAAAACTACTCTAGTCCTGC 57.268 36.000 0.00 0.00 38.26 4.85
827 1225 9.326413 TCAAAAAGAAAAACTACTCTAGTCCTG 57.674 33.333 0.00 0.00 38.26 3.86
828 1226 9.327628 GTCAAAAAGAAAAACTACTCTAGTCCT 57.672 33.333 0.00 0.00 38.26 3.85
829 1227 9.106070 TGTCAAAAAGAAAAACTACTCTAGTCC 57.894 33.333 0.00 0.00 38.26 3.85
831 1229 9.110502 CCTGTCAAAAAGAAAAACTACTCTAGT 57.889 33.333 0.00 0.00 41.73 2.57
832 1230 8.070769 GCCTGTCAAAAAGAAAAACTACTCTAG 58.929 37.037 0.00 0.00 0.00 2.43
833 1231 7.554835 TGCCTGTCAAAAAGAAAAACTACTCTA 59.445 33.333 0.00 0.00 0.00 2.43
834 1232 6.377146 TGCCTGTCAAAAAGAAAAACTACTCT 59.623 34.615 0.00 0.00 0.00 3.24
835 1233 6.560711 TGCCTGTCAAAAAGAAAAACTACTC 58.439 36.000 0.00 0.00 0.00 2.59
836 1234 6.405842 CCTGCCTGTCAAAAAGAAAAACTACT 60.406 38.462 0.00 0.00 0.00 2.57
837 1235 5.748630 CCTGCCTGTCAAAAAGAAAAACTAC 59.251 40.000 0.00 0.00 0.00 2.73
838 1236 5.654650 TCCTGCCTGTCAAAAAGAAAAACTA 59.345 36.000 0.00 0.00 0.00 2.24
839 1237 4.466015 TCCTGCCTGTCAAAAAGAAAAACT 59.534 37.500 0.00 0.00 0.00 2.66
840 1238 4.566759 GTCCTGCCTGTCAAAAAGAAAAAC 59.433 41.667 0.00 0.00 0.00 2.43
841 1239 4.466015 AGTCCTGCCTGTCAAAAAGAAAAA 59.534 37.500 0.00 0.00 0.00 1.94
842 1240 4.023291 AGTCCTGCCTGTCAAAAAGAAAA 58.977 39.130 0.00 0.00 0.00 2.29
843 1241 3.631250 AGTCCTGCCTGTCAAAAAGAAA 58.369 40.909 0.00 0.00 0.00 2.52
844 1242 3.297134 AGTCCTGCCTGTCAAAAAGAA 57.703 42.857 0.00 0.00 0.00 2.52
845 1243 3.646162 TCTAGTCCTGCCTGTCAAAAAGA 59.354 43.478 0.00 0.00 0.00 2.52
846 1244 3.999663 CTCTAGTCCTGCCTGTCAAAAAG 59.000 47.826 0.00 0.00 0.00 2.27
1009 1407 1.264295 GGAGTGAGGAACCCTAACGT 58.736 55.000 0.00 0.00 39.93 3.99
1062 1460 3.319198 GAAGGGACTCCGGTGGCA 61.319 66.667 12.27 0.00 38.49 4.92
1273 1677 3.575351 GACAGCAAGGCGGACGTCT 62.575 63.158 16.46 0.00 0.00 4.18
1348 1752 1.217882 GGAACATCGCAATACCGAGG 58.782 55.000 0.00 0.00 43.78 4.63
1364 1768 1.216977 CACTGGGATACGCACGGAA 59.783 57.895 0.00 0.00 37.60 4.30
1365 1769 0.680601 TACACTGGGATACGCACGGA 60.681 55.000 0.00 0.00 37.60 4.69
1374 1778 0.036164 TTGCAACGCTACACTGGGAT 59.964 50.000 0.00 0.00 0.00 3.85
1420 1824 6.423182 CCCCATCAAATTTACACCTCTCTAA 58.577 40.000 0.00 0.00 0.00 2.10
1440 1844 1.379916 CTCACATGCTGTTCCCCCA 59.620 57.895 0.00 0.00 0.00 4.96
1458 1862 1.102978 ACGCCCATTATCCAAGTTGC 58.897 50.000 0.00 0.00 0.00 4.17
1476 1880 4.033358 CGATCTTCATACCTGAACAGCAAC 59.967 45.833 0.00 0.00 36.46 4.17
1556 1960 2.287009 CCGTCAACTTTTCTGTCTTGGC 60.287 50.000 0.00 0.00 0.00 4.52
1589 1993 4.383010 CCAGGATTTTGGCTTTGATAACCC 60.383 45.833 0.00 0.00 0.00 4.11
1599 2003 1.642762 AGACCATCCAGGATTTTGGCT 59.357 47.619 7.43 0.64 41.22 4.75
1654 2058 0.112995 TGGGGAGAAAACAGCAGCAT 59.887 50.000 0.00 0.00 0.00 3.79
1749 2153 2.524034 CGCACGATCTCATATAGCTGG 58.476 52.381 0.00 0.00 0.00 4.85
1781 2185 2.881352 GCACTGACGCGCTCTACC 60.881 66.667 5.73 0.00 0.00 3.18
1845 2249 6.723977 TGGCAGTGTCTATAAATTTCCCTTTT 59.276 34.615 0.00 0.00 0.00 2.27
1931 2335 3.570540 AGCTGAGACTAGTGGCATATCA 58.429 45.455 0.00 0.00 0.00 2.15
1932 2336 3.571828 TGAGCTGAGACTAGTGGCATATC 59.428 47.826 0.00 0.35 0.00 1.63
1933 2337 3.570540 TGAGCTGAGACTAGTGGCATAT 58.429 45.455 0.00 0.00 0.00 1.78
1934 2338 3.018423 TGAGCTGAGACTAGTGGCATA 57.982 47.619 0.00 0.00 0.00 3.14
1935 2339 1.857965 TGAGCTGAGACTAGTGGCAT 58.142 50.000 0.00 0.00 0.00 4.40
1936 2340 1.632589 TTGAGCTGAGACTAGTGGCA 58.367 50.000 0.00 0.00 0.00 4.92
1937 2341 2.615869 CTTTGAGCTGAGACTAGTGGC 58.384 52.381 0.00 0.00 0.00 5.01
2150 2554 6.299805 TCCATTAGAATAACAGCTGTGACT 57.700 37.500 22.49 18.12 0.00 3.41
2151 2555 6.017605 CCATCCATTAGAATAACAGCTGTGAC 60.018 42.308 22.49 11.95 0.00 3.67
2152 2556 6.057533 CCATCCATTAGAATAACAGCTGTGA 58.942 40.000 22.49 14.63 0.00 3.58
2153 2557 6.057533 TCCATCCATTAGAATAACAGCTGTG 58.942 40.000 22.49 4.01 0.00 3.66
2373 2829 3.953612 ACAAGGAAACTGATTCTGCAACA 59.046 39.130 0.00 0.00 42.68 3.33
2579 3064 6.969993 TGTTTTCTATAAACTTGGCCAACT 57.030 33.333 16.05 2.20 0.00 3.16
2863 3349 4.822685 ACATCTCAGGGATATCATCTGC 57.177 45.455 16.11 0.00 32.64 4.26
2882 3368 9.130661 TGGATCTTACTCTTTTGAATTTGAACA 57.869 29.630 0.00 0.00 0.00 3.18
3013 3500 8.954950 ATTGATAGTCAATTACTGAGACTTGG 57.045 34.615 0.00 0.00 44.03 3.61
3138 3625 4.214971 AGCGAATCTGAATGGTTATGCATC 59.785 41.667 0.19 0.00 0.00 3.91
3146 3633 4.184629 GAGTACAAGCGAATCTGAATGGT 58.815 43.478 0.00 0.00 0.00 3.55
3350 3839 6.493115 ACCTTTTGATAATGTGAACACCATCA 59.507 34.615 2.46 6.28 31.49 3.07
3387 3880 8.483758 TGGTGTTTACTTTCTTTAGAGACTTCT 58.516 33.333 0.00 0.00 37.46 2.85
3469 3962 3.201353 TCACGAACCCATTCAAGTTGA 57.799 42.857 0.08 0.08 34.14 3.18
3729 4223 5.072329 TGGCCAAATTGGAAATAAAACTCCA 59.928 36.000 17.47 6.40 40.96 3.86
3799 4293 7.548075 ACCAACATACAGCAGTATAAGTAACAC 59.452 37.037 0.95 0.00 38.88 3.32
3862 4356 1.600638 CTCATCAGCACAGCAGGGA 59.399 57.895 0.00 0.00 0.00 4.20
3863 4357 1.451567 CCTCATCAGCACAGCAGGG 60.452 63.158 0.00 0.00 0.00 4.45
3942 4436 5.304686 TCTTGTACACCATCAAACTCCTT 57.695 39.130 0.00 0.00 0.00 3.36
4142 4636 6.422701 TGAAATTTCACACGAAAGTAGATCGT 59.577 34.615 16.91 0.00 44.15 3.73
4167 4661 6.320418 GGATACGTTTCCTGGTATTTTTCCAT 59.680 38.462 16.81 0.00 34.26 3.41
4232 4728 4.685628 CCGAACAAAAATCCATCCAAACTG 59.314 41.667 0.00 0.00 0.00 3.16
4233 4729 4.586841 TCCGAACAAAAATCCATCCAAACT 59.413 37.500 0.00 0.00 0.00 2.66
4259 4755 5.941788 AGGTATCCATGGTGAAGGAAATAC 58.058 41.667 12.58 9.27 37.48 1.89
4260 4756 6.590656 AAGGTATCCATGGTGAAGGAAATA 57.409 37.500 12.58 0.00 37.48 1.40
4261 4757 5.472301 AAGGTATCCATGGTGAAGGAAAT 57.528 39.130 12.58 0.00 37.48 2.17
4262 4758 4.946160 AAGGTATCCATGGTGAAGGAAA 57.054 40.909 12.58 0.00 37.48 3.13
4263 4759 4.325030 GGAAAGGTATCCATGGTGAAGGAA 60.325 45.833 12.58 0.00 39.42 3.36
4264 4760 3.202151 GGAAAGGTATCCATGGTGAAGGA 59.798 47.826 12.58 0.00 39.42 3.36
4265 4761 3.555966 GGAAAGGTATCCATGGTGAAGG 58.444 50.000 12.58 0.00 39.42 3.46
4266 4762 3.206150 CGGAAAGGTATCCATGGTGAAG 58.794 50.000 12.58 0.00 39.61 3.02
4267 4763 2.092646 CCGGAAAGGTATCCATGGTGAA 60.093 50.000 12.58 0.00 39.61 3.18
4268 4764 1.488812 CCGGAAAGGTATCCATGGTGA 59.511 52.381 12.58 0.00 39.61 4.02
4269 4765 1.476833 CCCGGAAAGGTATCCATGGTG 60.477 57.143 12.58 0.00 39.61 4.17
4270 4766 0.843984 CCCGGAAAGGTATCCATGGT 59.156 55.000 12.58 1.59 39.61 3.55
4271 4767 0.843984 ACCCGGAAAGGTATCCATGG 59.156 55.000 4.97 4.97 38.79 3.66
4299 4795 0.460722 TCCCGTGTGAAGTTTCGTGA 59.539 50.000 0.00 0.00 0.00 4.35
4300 4796 0.859232 CTCCCGTGTGAAGTTTCGTG 59.141 55.000 0.00 0.00 0.00 4.35
4301 4797 0.462789 ACTCCCGTGTGAAGTTTCGT 59.537 50.000 0.00 0.00 0.00 3.85
4302 4798 2.030540 TCTACTCCCGTGTGAAGTTTCG 60.031 50.000 0.00 0.00 0.00 3.46
4317 4813 2.197465 ACCTGGGTTCCCAATCTACTC 58.803 52.381 11.94 0.00 35.46 2.59
4381 4885 7.147284 TGCTCCACACCCCTATACAAATATTAA 60.147 37.037 0.00 0.00 0.00 1.40
4532 5036 2.747989 AGTTCTCACATGCAGCTCAATG 59.252 45.455 0.00 4.00 0.00 2.82
4636 5150 5.185056 AGGCACATGGTTAGTTTATTTGACC 59.815 40.000 0.00 0.00 0.00 4.02
4748 5262 3.744942 CAGCATCATGTACTGATAGCCAC 59.255 47.826 16.38 0.00 42.91 5.01
4899 5423 7.269316 GTTTCCTTTTACCACTGGAAATTTCA 58.731 34.615 19.49 5.50 46.16 2.69
5070 5597 3.607741 AGATTGCAAGTGAGTCCATGAG 58.392 45.455 4.94 0.00 0.00 2.90
5101 5633 4.696455 AGCAAAACCATGTTTCCAGAAAG 58.304 39.130 0.00 0.00 0.00 2.62
5259 5793 6.371271 TGTCGATTTGCTCATAAACAAGATCA 59.629 34.615 0.00 0.00 0.00 2.92
5306 6537 2.565841 CCACTTGGTATAGAAGCTGGC 58.434 52.381 0.00 0.00 0.00 4.85
5341 6572 4.007659 GGAAGGTCGCTTCCTGATAAAAA 58.992 43.478 12.97 0.00 46.92 1.94
5343 6574 3.261981 GGAAGGTCGCTTCCTGATAAA 57.738 47.619 12.97 0.00 46.92 1.40
5344 6575 2.981859 GGAAGGTCGCTTCCTGATAA 57.018 50.000 12.97 0.00 46.92 1.75
5351 6582 1.376037 CACCAGGGAAGGTCGCTTC 60.376 63.158 0.00 0.00 40.77 3.86
5352 6583 2.750350 CACCAGGGAAGGTCGCTT 59.250 61.111 0.00 0.00 40.77 4.68
5353 6584 4.021925 GCACCAGGGAAGGTCGCT 62.022 66.667 0.00 0.00 40.77 4.93
5355 6586 3.322466 AGGCACCAGGGAAGGTCG 61.322 66.667 0.00 0.00 40.77 4.79
5356 6587 2.352805 CAGGCACCAGGGAAGGTC 59.647 66.667 0.00 0.00 40.77 3.85
5357 6588 3.971702 GCAGGCACCAGGGAAGGT 61.972 66.667 0.00 0.00 44.48 3.50
5358 6589 1.925285 TATGCAGGCACCAGGGAAGG 61.925 60.000 0.00 0.00 0.00 3.46
5359 6590 0.034186 TTATGCAGGCACCAGGGAAG 60.034 55.000 0.00 0.00 0.00 3.46
5360 6591 0.407528 TTTATGCAGGCACCAGGGAA 59.592 50.000 0.00 0.00 0.00 3.97
5361 6592 0.034186 CTTTATGCAGGCACCAGGGA 60.034 55.000 0.00 0.00 0.00 4.20
5362 6593 1.039233 CCTTTATGCAGGCACCAGGG 61.039 60.000 0.00 0.00 0.00 4.45
5363 6594 1.039233 CCCTTTATGCAGGCACCAGG 61.039 60.000 0.00 2.28 31.69 4.45
5364 6595 0.323725 ACCCTTTATGCAGGCACCAG 60.324 55.000 0.00 0.00 31.69 4.00
5404 6635 0.819582 CCCTTTATGCAGGCACCAAG 59.180 55.000 0.00 1.81 31.69 3.61
5515 6746 1.102154 TGCGCCCTGAATTTACATGG 58.898 50.000 4.18 0.00 0.00 3.66
5562 6794 0.831307 ATCCTTCCACTAACGCCTCC 59.169 55.000 0.00 0.00 0.00 4.30
5617 6849 4.441792 GAAAAATGGAGCTTGGTGTGTTT 58.558 39.130 0.00 0.00 0.00 2.83
5663 6895 5.449041 GCCTTTCAATTCAGATTATCGCACA 60.449 40.000 0.00 0.00 0.00 4.57
5665 6897 4.883585 AGCCTTTCAATTCAGATTATCGCA 59.116 37.500 0.00 0.00 0.00 5.10
5685 6917 2.429610 TCTATTCTTACACGGACCAGCC 59.570 50.000 0.00 0.00 0.00 4.85
5686 6918 3.795623 TCTATTCTTACACGGACCAGC 57.204 47.619 0.00 0.00 0.00 4.85
5760 6993 0.740868 CGGGAGCAAGAAATCGAGCA 60.741 55.000 0.00 0.00 0.00 4.26
6061 7305 4.969484 AGGTGAAATGAGAACCTTACGTT 58.031 39.130 0.00 0.00 41.65 3.99
6062 7306 4.618920 AGGTGAAATGAGAACCTTACGT 57.381 40.909 0.00 0.00 41.65 3.57
6067 7311 5.073428 GGAAGAAAGGTGAAATGAGAACCT 58.927 41.667 0.00 0.00 46.40 3.50
6068 7312 4.218635 GGGAAGAAAGGTGAAATGAGAACC 59.781 45.833 0.00 0.00 0.00 3.62
6069 7313 4.827284 TGGGAAGAAAGGTGAAATGAGAAC 59.173 41.667 0.00 0.00 0.00 3.01
6070 7314 4.827284 GTGGGAAGAAAGGTGAAATGAGAA 59.173 41.667 0.00 0.00 0.00 2.87
6071 7315 4.398319 GTGGGAAGAAAGGTGAAATGAGA 58.602 43.478 0.00 0.00 0.00 3.27
6072 7316 3.507622 GGTGGGAAGAAAGGTGAAATGAG 59.492 47.826 0.00 0.00 0.00 2.90
6073 7317 3.117322 TGGTGGGAAGAAAGGTGAAATGA 60.117 43.478 0.00 0.00 0.00 2.57
6074 7318 3.005791 GTGGTGGGAAGAAAGGTGAAATG 59.994 47.826 0.00 0.00 0.00 2.32
6075 7319 3.230976 GTGGTGGGAAGAAAGGTGAAAT 58.769 45.455 0.00 0.00 0.00 2.17
6076 7320 2.661718 GTGGTGGGAAGAAAGGTGAAA 58.338 47.619 0.00 0.00 0.00 2.69
6077 7321 1.133606 GGTGGTGGGAAGAAAGGTGAA 60.134 52.381 0.00 0.00 0.00 3.18
6078 7322 0.476771 GGTGGTGGGAAGAAAGGTGA 59.523 55.000 0.00 0.00 0.00 4.02
6079 7323 0.539669 GGGTGGTGGGAAGAAAGGTG 60.540 60.000 0.00 0.00 0.00 4.00
6080 7324 0.701310 AGGGTGGTGGGAAGAAAGGT 60.701 55.000 0.00 0.00 0.00 3.50
6081 7325 0.482887 AAGGGTGGTGGGAAGAAAGG 59.517 55.000 0.00 0.00 0.00 3.11
6082 7326 2.239400 GAAAGGGTGGTGGGAAGAAAG 58.761 52.381 0.00 0.00 0.00 2.62
6089 7333 0.114168 TTGGATGAAAGGGTGGTGGG 59.886 55.000 0.00 0.00 0.00 4.61
6129 7373 8.883731 CAGAAGATACGTAAATGAAGGTGATTT 58.116 33.333 0.00 0.00 0.00 2.17
6135 7379 6.019801 CGGTTCAGAAGATACGTAAATGAAGG 60.020 42.308 0.00 0.00 0.00 3.46
6139 7383 7.306632 GGAATCGGTTCAGAAGATACGTAAATG 60.307 40.741 11.19 0.00 36.01 2.32
6146 7390 5.012328 AGTGGAATCGGTTCAGAAGATAC 57.988 43.478 11.19 0.00 36.01 2.24
6149 7393 3.323691 TGAAGTGGAATCGGTTCAGAAGA 59.676 43.478 11.19 0.00 36.01 2.87
6194 7438 7.012894 TCTGGCCGTGAATTACCTTATATTTTG 59.987 37.037 0.00 0.00 0.00 2.44
6195 7439 7.057894 TCTGGCCGTGAATTACCTTATATTTT 58.942 34.615 0.00 0.00 0.00 1.82
6261 7505 7.772332 AATACTTTAGCTCGTGATTTACCTG 57.228 36.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.