Multiple sequence alignment - TraesCS4D01G065400

Loading Multiple Alignment...

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 TraesCS4D01G065400 chr4D 100.000 3640 0 0 1 3640 40570268 40566629 0.000000e+00 6722.0
1 TraesCS4D01G065400 chr4A 88.674 2693 146 68 283 2877 559070099 559067468 0.000000e+00 3136.0
2 TraesCS4D01G065400 chr4A 81.614 223 19 11 23 225 559070347 559070127 8.090000e-37 165.0
3 TraesCS4D01G065400 chr4B 91.452 1942 104 31 865 2761 59238008 59236084 0.000000e+00 2610.0
4 TraesCS4D01G065400 chr4B 88.160 701 39 20 2095 2778 59227317 59226644 0.000000e+00 795.0
5 TraesCS4D01G065400 chr4B 83.961 611 39 26 271 840 59238660 59238068 6.920000e-147 531.0
6 TraesCS4D01G065400 chr4B 77.390 544 88 15 3104 3640 59235746 59235231 1.280000e-74 291.0
7 TraesCS4D01G065400 chr4B 77.354 446 83 12 3090 3521 94828427 94827986 7.810000e-62 248.0
8 TraesCS4D01G065400 chr4B 91.026 78 7 0 2988 3065 59226180 59226103 4.970000e-19 106.0
9 TraesCS4D01G065400 chr2B 85.327 1622 212 13 1015 2635 454824055 454825651 0.000000e+00 1653.0
10 TraesCS4D01G065400 chr2B 79.597 397 60 15 3180 3564 614487334 614486947 7.750000e-67 265.0
11 TraesCS4D01G065400 chr2B 80.836 287 39 10 3287 3564 614381766 614381487 1.020000e-50 211.0
12 TraesCS4D01G065400 chr2B 82.468 154 25 2 3080 3232 377539958 377540110 2.280000e-27 134.0
13 TraesCS4D01G065400 chr2A 85.053 1619 200 15 1024 2633 6509747 6511332 0.000000e+00 1611.0
14 TraesCS4D01G065400 chr2A 82.129 526 77 14 2101 2617 6968592 6969109 5.580000e-118 435.0
15 TraesCS4D01G065400 chr2A 85.000 320 42 3 1652 1966 6968261 6968579 1.630000e-83 320.0
16 TraesCS4D01G065400 chr1B 82.906 468 74 5 2129 2591 223146108 223145642 2.020000e-112 416.0
17 TraesCS4D01G065400 chr1D 82.526 475 75 7 2123 2591 159905738 159906210 9.410000e-111 411.0
18 TraesCS4D01G065400 chr1D 80.342 117 19 4 3089 3203 487776632 487776518 6.480000e-13 86.1
19 TraesCS4D01G065400 chr1A 82.278 474 78 5 2123 2591 234798909 234799381 4.380000e-109 405.0
20 TraesCS4D01G065400 chr1A 77.907 172 30 8 3096 3263 444426382 444426215 2.310000e-17 100.0
21 TraesCS4D01G065400 chr5A 75.659 493 97 19 3137 3620 662959901 662959423 1.320000e-54 224.0
22 TraesCS4D01G065400 chr5D 75.551 454 85 16 3077 3518 507165179 507164740 2.220000e-47 200.0
23 TraesCS4D01G065400 chr6D 74.374 519 101 25 3122 3625 302151799 302151298 3.710000e-45 193.0
24 TraesCS4D01G065400 chr6D 83.636 110 16 2 3139 3247 81197568 81197676 6.430000e-18 102.0
25 TraesCS4D01G065400 chr3A 73.056 553 116 20 3099 3640 442293002 442292472 8.090000e-37 165.0
26 TraesCS4D01G065400 chr3A 77.632 304 37 8 3334 3628 54325203 54324922 4.870000e-34 156.0
27 TraesCS4D01G065400 chr7D 75.588 340 69 12 3105 3436 3104705 3105038 4.870000e-34 156.0
28 TraesCS4D01G065400 chr3B 86.111 144 20 0 1649 1792 47197603 47197746 4.870000e-34 156.0
29 TraesCS4D01G065400 chr3B 77.215 158 28 6 3367 3518 557104766 557104611 6.480000e-13 86.1
30 TraesCS4D01G065400 chr6A 79.191 173 33 3 3077 3247 497736411 497736240 2.300000e-22 117.0
31 TraesCS4D01G065400 chr6A 72.862 269 50 19 3070 3324 7701543 7701802 1.810000e-08 71.3


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 TraesCS4D01G065400 chr4D 40566629 40570268 3639 True 6722.0 6722 100.000000 1 3640 1 chr4D.!!$R1 3639
1 TraesCS4D01G065400 chr4A 559067468 559070347 2879 True 1650.5 3136 85.144000 23 2877 2 chr4A.!!$R1 2854
2 TraesCS4D01G065400 chr4B 59235231 59238660 3429 True 1144.0 2610 84.267667 271 3640 3 chr4B.!!$R3 3369
3 TraesCS4D01G065400 chr4B 59226103 59227317 1214 True 450.5 795 89.593000 2095 3065 2 chr4B.!!$R2 970
4 TraesCS4D01G065400 chr2B 454824055 454825651 1596 False 1653.0 1653 85.327000 1015 2635 1 chr2B.!!$F2 1620
5 TraesCS4D01G065400 chr2A 6509747 6511332 1585 False 1611.0 1611 85.053000 1024 2633 1 chr2A.!!$F1 1609
6 TraesCS4D01G065400 chr2A 6968261 6969109 848 False 377.5 435 83.564500 1652 2617 2 chr2A.!!$F2 965

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
944 1063 0.106708 GACAGAGACACACCAAGGCA 59.893 55.0 0.0 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2941 3473 0.179134 AGAGAATCGTGCTACGGTGC 60.179 55.0 8.46 1.05 42.81 5.01 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
38 39 0.798776 CTCACCGAAGAGCGCAAAAT 59.201 50.000 11.47 0.00 39.11 1.82
55 61 3.940209 AAATTGCTCGCTCCAATCAAA 57.060 38.095 0.00 0.00 32.07 2.69
63 69 3.734463 TCGCTCCAATCAAACAACTGTA 58.266 40.909 0.00 0.00 0.00 2.74
64 70 3.745975 TCGCTCCAATCAAACAACTGTAG 59.254 43.478 0.00 0.00 0.00 2.74
77 83 2.770164 ACTGTAGATGACTGTTGGGC 57.230 50.000 0.00 0.00 36.91 5.36
83 89 1.555075 AGATGACTGTTGGGCATACGT 59.445 47.619 0.00 0.00 45.06 3.57
84 90 2.764010 AGATGACTGTTGGGCATACGTA 59.236 45.455 0.00 0.00 45.06 3.57
89 95 4.189231 GACTGTTGGGCATACGTATTTCT 58.811 43.478 5.03 0.00 0.00 2.52
100 106 3.690475 ACGTATTTCTCGGTTCCCTTT 57.310 42.857 0.00 0.00 0.00 3.11
113 119 3.630769 GGTTCCCTTTCGAAGAACAAAGT 59.369 43.478 22.62 0.00 45.90 2.66
118 124 7.576861 TCCCTTTCGAAGAACAAAGTATTTT 57.423 32.000 0.00 0.00 45.90 1.82
119 125 7.645402 TCCCTTTCGAAGAACAAAGTATTTTC 58.355 34.615 0.00 0.00 45.90 2.29
122 128 5.600908 TCGAAGAACAAAGTATTTTCGGG 57.399 39.130 4.85 0.00 35.03 5.14
123 129 4.083696 TCGAAGAACAAAGTATTTTCGGGC 60.084 41.667 4.85 0.00 35.03 6.13
166 180 4.465512 CGCGTGTGCCAAGCCATC 62.466 66.667 0.00 0.00 35.58 3.51
167 181 3.058160 GCGTGTGCCAAGCCATCT 61.058 61.111 2.56 0.00 33.06 2.90
168 182 2.629656 GCGTGTGCCAAGCCATCTT 61.630 57.895 2.56 0.00 33.06 2.40
170 184 1.236616 CGTGTGCCAAGCCATCTTCA 61.237 55.000 0.00 0.00 0.00 3.02
173 187 0.108945 GTGCCAAGCCATCTTCAAGC 60.109 55.000 0.00 0.00 0.00 4.01
174 188 1.252904 TGCCAAGCCATCTTCAAGCC 61.253 55.000 0.00 0.00 0.00 4.35
176 190 0.324091 CCAAGCCATCTTCAAGCCCT 60.324 55.000 0.00 0.00 0.00 5.19
244 270 2.797177 GAGCCTGACTCCTCCATTTT 57.203 50.000 0.00 0.00 39.75 1.82
245 271 3.914426 GAGCCTGACTCCTCCATTTTA 57.086 47.619 0.00 0.00 39.75 1.52
246 272 3.536570 GAGCCTGACTCCTCCATTTTAC 58.463 50.000 0.00 0.00 39.75 2.01
247 273 3.185455 AGCCTGACTCCTCCATTTTACT 58.815 45.455 0.00 0.00 0.00 2.24
248 274 3.589288 AGCCTGACTCCTCCATTTTACTT 59.411 43.478 0.00 0.00 0.00 2.24
249 275 4.043435 AGCCTGACTCCTCCATTTTACTTT 59.957 41.667 0.00 0.00 0.00 2.66
250 276 5.250774 AGCCTGACTCCTCCATTTTACTTTA 59.749 40.000 0.00 0.00 0.00 1.85
251 277 6.069381 AGCCTGACTCCTCCATTTTACTTTAT 60.069 38.462 0.00 0.00 0.00 1.40
252 278 6.603599 GCCTGACTCCTCCATTTTACTTTATT 59.396 38.462 0.00 0.00 0.00 1.40
253 279 7.122799 GCCTGACTCCTCCATTTTACTTTATTT 59.877 37.037 0.00 0.00 0.00 1.40
254 280 9.025041 CCTGACTCCTCCATTTTACTTTATTTT 57.975 33.333 0.00 0.00 0.00 1.82
354 384 1.614317 CCTGTGCCCACTCCCTAAAAG 60.614 57.143 0.00 0.00 0.00 2.27
355 385 1.351017 CTGTGCCCACTCCCTAAAAGA 59.649 52.381 0.00 0.00 0.00 2.52
383 413 0.261109 TATGTGCCCATCAATGCCCA 59.739 50.000 0.00 0.00 32.29 5.36
390 420 1.456331 CATCAATGCCCACCTCCCC 60.456 63.158 0.00 0.00 0.00 4.81
411 441 3.677527 CCCAAGAGGCAGCTGTTG 58.322 61.111 16.64 11.47 0.00 3.33
412 442 1.228367 CCCAAGAGGCAGCTGTTGT 60.228 57.895 16.64 0.00 0.00 3.32
416 475 0.475906 AAGAGGCAGCTGTTGTTCCT 59.524 50.000 16.64 12.65 0.00 3.36
418 477 0.957888 GAGGCAGCTGTTGTTCCTCC 60.958 60.000 20.75 9.71 37.85 4.30
442 501 1.596603 TACGCCTCGAATATCGACCA 58.403 50.000 0.00 0.00 44.82 4.02
447 506 1.068588 CCTCGAATATCGACCAAGGCA 59.931 52.381 0.00 0.00 44.82 4.75
448 507 2.398498 CTCGAATATCGACCAAGGCAG 58.602 52.381 0.00 0.00 44.82 4.85
465 524 1.231221 CAGAGGAGTAGGATCGACCG 58.769 60.000 0.00 0.00 44.74 4.79
566 634 3.602483 TGAAATAAACTACCTGTCGCCC 58.398 45.455 0.00 0.00 0.00 6.13
587 659 2.356553 TCCGGGCGAACAAGAACG 60.357 61.111 0.00 0.00 0.00 3.95
588 660 2.356553 CCGGGCGAACAAGAACGA 60.357 61.111 0.00 0.00 0.00 3.85
589 661 2.380410 CCGGGCGAACAAGAACGAG 61.380 63.158 0.00 0.00 0.00 4.18
591 663 0.942410 CGGGCGAACAAGAACGAGAA 60.942 55.000 0.00 0.00 0.00 2.87
592 664 0.511653 GGGCGAACAAGAACGAGAAC 59.488 55.000 0.00 0.00 0.00 3.01
593 665 1.499049 GGCGAACAAGAACGAGAACT 58.501 50.000 0.00 0.00 0.00 3.01
594 666 1.456165 GGCGAACAAGAACGAGAACTC 59.544 52.381 0.00 0.00 0.00 3.01
595 667 1.456165 GCGAACAAGAACGAGAACTCC 59.544 52.381 0.00 0.00 0.00 3.85
596 668 2.739292 CGAACAAGAACGAGAACTCCA 58.261 47.619 0.00 0.00 0.00 3.86
597 669 3.318017 CGAACAAGAACGAGAACTCCAT 58.682 45.455 0.00 0.00 0.00 3.41
598 670 3.365220 CGAACAAGAACGAGAACTCCATC 59.635 47.826 0.00 0.00 0.00 3.51
599 671 4.561105 GAACAAGAACGAGAACTCCATCT 58.439 43.478 0.00 0.00 0.00 2.90
600 672 4.181309 ACAAGAACGAGAACTCCATCTC 57.819 45.455 0.00 0.00 41.99 2.75
603 675 3.963129 AGAACGAGAACTCCATCTCTCT 58.037 45.455 0.00 0.00 43.00 3.10
609 681 4.554526 CGAGAACTCCATCTCTCTCAATCG 60.555 50.000 3.15 0.00 43.00 3.34
631 704 5.522460 TCGAAAGAAAGACAACAAGAACGAT 59.478 36.000 0.00 0.00 37.03 3.73
854 941 1.397441 GCACGCGTCGTAAACAATTCA 60.397 47.619 9.86 0.00 38.32 2.57
859 946 4.377445 ACGCGTCGTAAACAATTCATTTTG 59.623 37.500 5.58 0.00 38.73 2.44
863 982 6.140110 CGTCGTAAACAATTCATTTTGGTCT 58.860 36.000 0.00 0.00 0.00 3.85
887 1006 4.332268 TGTATATAAACGGCCACGGAAAAC 59.668 41.667 2.24 0.00 46.48 2.43
923 1042 3.244215 TGCAGAGTTCTACACTTGGAAGG 60.244 47.826 0.00 0.00 35.01 3.46
929 1048 4.282195 AGTTCTACACTTGGAAGGAGACAG 59.718 45.833 0.00 0.00 27.32 3.51
933 1052 2.630580 ACACTTGGAAGGAGACAGAGAC 59.369 50.000 0.00 0.00 0.00 3.36
936 1055 2.381752 TGGAAGGAGACAGAGACACA 57.618 50.000 0.00 0.00 0.00 3.72
938 1057 1.273886 GGAAGGAGACAGAGACACACC 59.726 57.143 0.00 0.00 0.00 4.16
939 1058 1.964223 GAAGGAGACAGAGACACACCA 59.036 52.381 0.00 0.00 0.00 4.17
940 1059 2.088104 AGGAGACAGAGACACACCAA 57.912 50.000 0.00 0.00 0.00 3.67
943 1062 0.394565 AGACAGAGACACACCAAGGC 59.605 55.000 0.00 0.00 0.00 4.35
944 1063 0.106708 GACAGAGACACACCAAGGCA 59.893 55.000 0.00 0.00 0.00 4.75
961 1089 3.782046 AGGCACTTACTACATTGTAGCG 58.218 45.455 21.12 13.21 27.25 4.26
964 1092 3.306166 GCACTTACTACATTGTAGCGTGG 59.694 47.826 25.98 16.92 31.96 4.94
966 1094 2.589798 TACTACATTGTAGCGTGGGC 57.410 50.000 21.12 0.00 40.37 5.36
989 1117 2.366435 GAGGGATCGGGTTGGGGA 60.366 66.667 0.00 0.00 0.00 4.81
990 1118 2.691252 AGGGATCGGGTTGGGGAC 60.691 66.667 0.00 0.00 0.00 4.46
997 1125 2.612493 CGGGTTGGGGACTTGGGAT 61.612 63.158 0.00 0.00 0.00 3.85
1010 1138 4.996434 GGGATCGATGGCGGGCAG 62.996 72.222 10.83 0.00 38.28 4.85
2047 2194 4.093408 CGCAGTACATATGCAACTTCTGTT 59.907 41.667 1.58 0.00 44.05 3.16
2058 2205 3.608008 GCAACTTCTGTTTAGCAGTCAGC 60.608 47.826 0.00 0.00 45.23 4.26
2060 2207 3.433598 AACTTCTGTTTAGCAGTCAGCCA 60.434 43.478 0.00 0.00 45.23 4.75
2061 2208 5.278577 AACTTCTGTTTAGCAGTCAGCCAG 61.279 45.833 0.00 0.00 45.23 4.85
2062 2209 7.662526 AACTTCTGTTTAGCAGTCAGCCAGT 62.663 44.000 0.00 0.00 45.23 4.00
2069 2216 1.665916 CAGTCAGCCAGTCACCACG 60.666 63.158 0.00 0.00 0.00 4.94
2071 2218 2.842462 TCAGCCAGTCACCACGGT 60.842 61.111 0.00 0.00 0.00 4.83
2084 2231 2.672996 ACGGTGCACTCCATTGGC 60.673 61.111 17.98 0.00 0.00 4.52
2092 2248 2.672651 CTCCATTGGCCACGTGCA 60.673 61.111 3.88 0.00 43.89 4.57
2612 2780 1.880027 GTCGTCTCCAAGCCAAACATT 59.120 47.619 0.00 0.00 0.00 2.71
2641 2812 4.429854 AGAAGTTCATGGGCTCCTAATC 57.570 45.455 5.50 0.00 0.00 1.75
2643 2814 4.228210 AGAAGTTCATGGGCTCCTAATCAA 59.772 41.667 5.50 0.00 0.00 2.57
2644 2815 4.591321 AGTTCATGGGCTCCTAATCAAA 57.409 40.909 0.00 0.00 0.00 2.69
2770 2979 3.368739 GCTGCTGGATTAATGCACCTTTT 60.369 43.478 5.43 0.00 32.91 2.27
2771 2980 4.427312 CTGCTGGATTAATGCACCTTTTC 58.573 43.478 5.43 0.00 32.91 2.29
2774 2983 5.714333 TGCTGGATTAATGCACCTTTTCTTA 59.286 36.000 5.43 0.00 0.00 2.10
2775 2984 6.036470 GCTGGATTAATGCACCTTTTCTTAC 58.964 40.000 5.43 0.00 0.00 2.34
2776 2985 6.127619 GCTGGATTAATGCACCTTTTCTTACT 60.128 38.462 5.43 0.00 0.00 2.24
2777 2986 7.067008 GCTGGATTAATGCACCTTTTCTTACTA 59.933 37.037 5.43 0.00 0.00 1.82
2778 2987 8.871629 TGGATTAATGCACCTTTTCTTACTAA 57.128 30.769 5.43 0.00 0.00 2.24
2807 3322 3.412386 AGAGCAATTGTTCTACACCCAC 58.588 45.455 21.72 0.00 33.74 4.61
2823 3338 1.597027 CACCTGGACGTCACCAACC 60.597 63.158 18.91 0.00 39.59 3.77
2824 3339 2.067605 ACCTGGACGTCACCAACCA 61.068 57.895 18.91 4.42 39.59 3.67
2825 3340 1.374947 CCTGGACGTCACCAACCAT 59.625 57.895 18.91 0.00 39.59 3.55
2826 3341 0.673644 CCTGGACGTCACCAACCATC 60.674 60.000 18.91 0.00 39.59 3.51
2827 3342 0.673644 CTGGACGTCACCAACCATCC 60.674 60.000 18.91 0.00 39.59 3.51
2862 3377 4.500887 CCATTCTGCATCCAATGGTTGATC 60.501 45.833 14.11 0.00 42.90 2.92
2903 3435 1.399440 CGACCTGCAATGGTTGATGAG 59.601 52.381 6.53 0.00 42.68 2.90
2918 3450 1.865970 GATGAGAGAGCTTTGCATCCG 59.134 52.381 5.74 0.00 31.54 4.18
2961 3493 1.550065 CACCGTAGCACGATTCTCTG 58.450 55.000 9.75 0.00 46.05 3.35
2978 3510 4.937431 GGTGCCATAGCTCCCGCC 62.937 72.222 0.00 0.00 45.20 6.13
3045 3579 0.910088 AGTGGTGTAGGCCTCTTCCC 60.910 60.000 9.68 6.08 0.00 3.97
3048 3582 1.615424 GTGTAGGCCTCTTCCCCCA 60.615 63.158 9.68 0.00 0.00 4.96
3049 3583 0.988678 GTGTAGGCCTCTTCCCCCAT 60.989 60.000 9.68 0.00 0.00 4.00
3065 3599 2.568509 CCCCATGGCTGAAAAATCTTGT 59.431 45.455 6.09 0.00 0.00 3.16
3066 3600 3.368739 CCCCATGGCTGAAAAATCTTGTC 60.369 47.826 6.09 0.00 0.00 3.18
3069 3603 4.240096 CATGGCTGAAAAATCTTGTCCAC 58.760 43.478 0.00 0.00 0.00 4.02
3070 3604 2.293122 TGGCTGAAAAATCTTGTCCACG 59.707 45.455 0.00 0.00 0.00 4.94
3072 3606 3.500680 GGCTGAAAAATCTTGTCCACGTA 59.499 43.478 0.00 0.00 0.00 3.57
3075 3609 5.334879 GCTGAAAAATCTTGTCCACGTACAT 60.335 40.000 0.00 0.00 0.00 2.29
3080 3641 2.679450 TCTTGTCCACGTACATTTCGG 58.321 47.619 0.00 0.00 0.00 4.30
3082 3643 3.056393 TCTTGTCCACGTACATTTCGGAT 60.056 43.478 0.00 0.00 0.00 4.18
3085 3646 1.473677 TCCACGTACATTTCGGATCGT 59.526 47.619 0.00 0.00 0.00 3.73
3092 3653 0.652592 CATTTCGGATCGTGCTGTCC 59.347 55.000 0.00 0.00 0.00 4.02
3098 3659 4.129737 ATCGTGCTGTCCGGACCG 62.130 66.667 31.19 25.82 0.00 4.79
3119 3682 3.683587 GAAGCCATTCAACGCGGGC 62.684 63.158 12.47 12.84 46.77 6.13
3127 3690 0.391793 TTCAACGCGGGCATGTATCA 60.392 50.000 12.47 0.00 0.00 2.15
3128 3691 0.391793 TCAACGCGGGCATGTATCAA 60.392 50.000 12.47 0.00 0.00 2.57
3130 3693 1.065401 CAACGCGGGCATGTATCAATT 59.935 47.619 12.47 0.00 0.00 2.32
3135 3698 1.333308 CGGGCATGTATCAATTCGCAA 59.667 47.619 0.00 0.00 0.00 4.85
3137 3700 2.287788 GGGCATGTATCAATTCGCAAGG 60.288 50.000 0.00 0.00 38.47 3.61
3138 3701 2.388121 GCATGTATCAATTCGCAAGGC 58.612 47.619 0.00 0.00 38.47 4.35
3158 3721 1.202382 CGGTCCGGATGTACTTTCTCC 60.202 57.143 7.81 0.00 0.00 3.71
3159 3722 1.138464 GGTCCGGATGTACTTTCTCCC 59.862 57.143 7.81 0.00 0.00 4.30
3161 3724 0.529992 CCGGATGTACTTTCTCCCGC 60.530 60.000 0.00 0.00 36.01 6.13
3166 3729 1.886886 TGTACTTTCTCCCGCAAACC 58.113 50.000 0.00 0.00 0.00 3.27
3167 3730 0.794473 GTACTTTCTCCCGCAAACCG 59.206 55.000 0.00 0.00 0.00 4.44
3168 3731 0.680618 TACTTTCTCCCGCAAACCGA 59.319 50.000 0.00 0.00 40.02 4.69
3170 3733 0.948678 CTTTCTCCCGCAAACCGAAA 59.051 50.000 0.00 0.00 40.02 3.46
3172 3735 1.611519 TTCTCCCGCAAACCGAAAAT 58.388 45.000 0.00 0.00 40.02 1.82
3176 3739 3.058085 TCTCCCGCAAACCGAAAATAAAC 60.058 43.478 0.00 0.00 40.02 2.01
3177 3740 2.621998 TCCCGCAAACCGAAAATAAACA 59.378 40.909 0.00 0.00 40.02 2.83
3179 3742 3.366422 CCCGCAAACCGAAAATAAACATG 59.634 43.478 0.00 0.00 40.02 3.21
3181 3744 3.366422 CGCAAACCGAAAATAAACATGGG 59.634 43.478 0.00 0.00 40.02 4.00
3184 3747 1.828595 ACCGAAAATAAACATGGGGGC 59.171 47.619 0.00 0.00 0.00 5.80
3185 3748 2.107366 CCGAAAATAAACATGGGGGCT 58.893 47.619 0.00 0.00 0.00 5.19
3188 3751 3.932089 CGAAAATAAACATGGGGGCTTTG 59.068 43.478 0.00 0.00 0.00 2.77
3189 3752 3.348647 AAATAAACATGGGGGCTTTGC 57.651 42.857 0.00 0.00 0.00 3.68
3190 3753 0.823460 ATAAACATGGGGGCTTTGCG 59.177 50.000 0.00 0.00 0.00 4.85
3232 3795 2.636412 CCGCTTCTGACCGTCCTGA 61.636 63.158 0.00 0.00 0.00 3.86
3234 3797 1.079750 GCTTCTGACCGTCCTGACC 60.080 63.158 0.00 0.00 0.00 4.02
3236 3799 1.152419 TTCTGACCGTCCTGACCCA 60.152 57.895 0.00 0.00 0.00 4.51
3242 3805 2.824880 CCGTCCTGACCCACCCAAA 61.825 63.158 0.00 0.00 0.00 3.28
3244 3807 1.228459 GTCCTGACCCACCCAAACC 60.228 63.158 0.00 0.00 0.00 3.27
3245 3808 2.117423 CCTGACCCACCCAAACCC 59.883 66.667 0.00 0.00 0.00 4.11
3246 3809 2.117423 CTGACCCACCCAAACCCC 59.883 66.667 0.00 0.00 0.00 4.95
3247 3810 3.513566 TGACCCACCCAAACCCCC 61.514 66.667 0.00 0.00 0.00 5.40
3248 3811 3.513566 GACCCACCCAAACCCCCA 61.514 66.667 0.00 0.00 0.00 4.96
3249 3812 2.789920 ACCCACCCAAACCCCCAT 60.790 61.111 0.00 0.00 0.00 4.00
3250 3813 2.038813 CCCACCCAAACCCCCATC 59.961 66.667 0.00 0.00 0.00 3.51
3251 3814 2.362375 CCACCCAAACCCCCATCG 60.362 66.667 0.00 0.00 0.00 3.84
3252 3815 3.068064 CACCCAAACCCCCATCGC 61.068 66.667 0.00 0.00 0.00 4.58
3253 3816 4.376170 ACCCAAACCCCCATCGCC 62.376 66.667 0.00 0.00 0.00 5.54
3255 3818 4.060667 CCAAACCCCCATCGCCCT 62.061 66.667 0.00 0.00 0.00 5.19
3256 3819 2.037208 CAAACCCCCATCGCCCTT 59.963 61.111 0.00 0.00 0.00 3.95
3257 3820 1.609210 CAAACCCCCATCGCCCTTT 60.609 57.895 0.00 0.00 0.00 3.11
3258 3821 1.304962 AAACCCCCATCGCCCTTTC 60.305 57.895 0.00 0.00 0.00 2.62
3259 3822 2.798445 AAACCCCCATCGCCCTTTCC 62.798 60.000 0.00 0.00 0.00 3.13
3260 3823 4.875713 CCCCCATCGCCCTTTCCG 62.876 72.222 0.00 0.00 0.00 4.30
3261 3824 4.109675 CCCCATCGCCCTTTCCGT 62.110 66.667 0.00 0.00 0.00 4.69
3262 3825 2.824041 CCCATCGCCCTTTCCGTG 60.824 66.667 0.00 0.00 0.00 4.94
3263 3826 2.046314 CCATCGCCCTTTCCGTGT 60.046 61.111 0.00 0.00 0.00 4.49
3264 3827 1.219664 CCATCGCCCTTTCCGTGTA 59.780 57.895 0.00 0.00 0.00 2.90
3267 3830 2.014128 CATCGCCCTTTCCGTGTATTT 58.986 47.619 0.00 0.00 0.00 1.40
3272 3835 2.422479 GCCCTTTCCGTGTATTTCTTCC 59.578 50.000 0.00 0.00 0.00 3.46
3274 3837 3.332034 CCTTTCCGTGTATTTCTTCCGT 58.668 45.455 0.00 0.00 0.00 4.69
3279 3842 2.418628 CCGTGTATTTCTTCCGTTGCAT 59.581 45.455 0.00 0.00 0.00 3.96
3282 3845 2.159585 TGTATTTCTTCCGTTGCATGCG 60.160 45.455 14.09 0.00 0.00 4.73
3285 3848 3.736100 CTTCCGTTGCATGCGCCA 61.736 61.111 14.09 0.00 37.32 5.69
3298 3861 3.089784 CGCCACTTACCGCATGAC 58.910 61.111 0.00 0.00 0.00 3.06
3314 3877 0.681887 TGACATTCATGCTGGCCCAG 60.682 55.000 6.32 6.32 34.12 4.45
3323 3886 2.185350 CTGGCCCAGAGCACGTAG 59.815 66.667 4.15 0.00 46.50 3.51
3338 3901 4.728102 TAGCGGCCGGTGTTGACG 62.728 66.667 38.34 4.26 0.00 4.35
3351 3915 1.666553 TTGACGCCGCGATTTGACT 60.667 52.632 21.79 0.00 0.00 3.41
3355 3919 2.785258 GCCGCGATTTGACTGGAC 59.215 61.111 8.23 0.00 0.00 4.02
3360 3924 0.462047 GCGATTTGACTGGACGGGAT 60.462 55.000 0.00 0.00 0.00 3.85
3362 3926 1.134818 CGATTTGACTGGACGGGATGA 60.135 52.381 0.00 0.00 0.00 2.92
3365 3929 0.896479 TTGACTGGACGGGATGACGA 60.896 55.000 0.00 0.00 37.61 4.20
3387 3951 4.517703 GACGGACGCGACCTCTCG 62.518 72.222 24.38 13.80 43.28 4.04
3435 3999 0.685097 TTCCTGAGGAACCAACTCCG 59.315 55.000 10.46 0.00 40.75 4.63
3436 4000 0.471211 TCCTGAGGAACCAACTCCGT 60.471 55.000 0.00 0.00 40.75 4.69
3440 4004 1.813728 GAGGAACCAACTCCGTCCGT 61.814 60.000 0.00 0.00 40.75 4.69
3504 4072 2.550978 GACTATTTAAGCAGCGCTCCA 58.449 47.619 7.13 0.00 38.25 3.86
3505 4073 2.541762 GACTATTTAAGCAGCGCTCCAG 59.458 50.000 7.13 0.00 38.25 3.86
3518 4086 3.958147 CTCCAGCGCCGTCCACATT 62.958 63.158 2.29 0.00 0.00 2.71
3527 4095 1.949525 GCCGTCCACATTGCAATCTAT 59.050 47.619 9.53 0.00 0.00 1.98
3528 4096 2.031682 GCCGTCCACATTGCAATCTATC 60.032 50.000 9.53 0.00 0.00 2.08
3529 4097 3.470709 CCGTCCACATTGCAATCTATCT 58.529 45.455 9.53 0.00 0.00 1.98
3530 4098 3.249320 CCGTCCACATTGCAATCTATCTG 59.751 47.826 9.53 0.90 0.00 2.90
3531 4099 3.303593 CGTCCACATTGCAATCTATCTGC 60.304 47.826 9.53 0.00 40.35 4.26
3533 4101 4.024218 GTCCACATTGCAATCTATCTGCTC 60.024 45.833 9.53 0.00 40.59 4.26
3535 4103 4.579340 CCACATTGCAATCTATCTGCTCTT 59.421 41.667 9.53 0.00 40.59 2.85
3538 4106 4.767578 TTGCAATCTATCTGCTCTTCCT 57.232 40.909 0.00 0.00 40.59 3.36
3539 4107 4.333913 TGCAATCTATCTGCTCTTCCTC 57.666 45.455 0.00 0.00 40.59 3.71
3540 4108 3.070734 TGCAATCTATCTGCTCTTCCTCC 59.929 47.826 0.00 0.00 40.59 4.30
3541 4109 3.324556 GCAATCTATCTGCTCTTCCTCCT 59.675 47.826 0.00 0.00 36.84 3.69
3542 4110 4.561326 GCAATCTATCTGCTCTTCCTCCTC 60.561 50.000 0.00 0.00 36.84 3.71
3543 4111 3.237268 TCTATCTGCTCTTCCTCCTCC 57.763 52.381 0.00 0.00 0.00 4.30
3544 4112 2.788807 TCTATCTGCTCTTCCTCCTCCT 59.211 50.000 0.00 0.00 0.00 3.69
3549 4117 0.261696 GCTCTTCCTCCTCCTCCTCT 59.738 60.000 0.00 0.00 0.00 3.69
3556 4124 0.105709 CTCCTCCTCCTCTTCCTCCC 60.106 65.000 0.00 0.00 0.00 4.30
3565 4133 2.444895 CTTCCTCCCCTCTCCCCG 60.445 72.222 0.00 0.00 0.00 5.73
3575 4143 4.880426 TCTCCCCGCCCATCTCCC 62.880 72.222 0.00 0.00 0.00 4.30
3584 4152 1.566298 GCCCATCTCCCTCCACAACT 61.566 60.000 0.00 0.00 0.00 3.16
3586 4154 0.543749 CCATCTCCCTCCACAACTCC 59.456 60.000 0.00 0.00 0.00 3.85
3587 4155 1.279496 CATCTCCCTCCACAACTCCA 58.721 55.000 0.00 0.00 0.00 3.86
3588 4156 1.209019 CATCTCCCTCCACAACTCCAG 59.791 57.143 0.00 0.00 0.00 3.86
3592 4160 1.599047 CCTCCACAACTCCAGCGAT 59.401 57.895 0.00 0.00 0.00 4.58
3596 4164 2.045926 ACAACTCCAGCGATGGGC 60.046 61.111 21.53 0.00 44.05 5.36
3610 4178 2.757099 GGGCAAGTCATGGGCCTG 60.757 66.667 4.53 0.24 46.87 4.85
3611 4179 2.757099 GGCAAGTCATGGGCCTGG 60.757 66.667 4.53 0.00 44.32 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.095160 CGGTGAGTAGTACTTCCTCTGTAAAT 59.905 42.308 17.97 0.00 0.00 1.40
1 2 5.413833 CGGTGAGTAGTACTTCCTCTGTAAA 59.586 44.000 17.97 1.44 0.00 2.01
2 3 4.940046 CGGTGAGTAGTACTTCCTCTGTAA 59.060 45.833 17.97 1.71 0.00 2.41
3 4 4.223700 TCGGTGAGTAGTACTTCCTCTGTA 59.776 45.833 17.97 1.99 0.00 2.74
6 7 3.996921 TCGGTGAGTAGTACTTCCTCT 57.003 47.619 17.97 6.56 0.00 3.69
7 8 4.260170 TCTTCGGTGAGTAGTACTTCCTC 58.740 47.826 17.48 7.96 0.00 3.71
9 10 3.181498 GCTCTTCGGTGAGTAGTACTTCC 60.181 52.174 0.00 9.40 36.51 3.46
10 11 3.485546 CGCTCTTCGGTGAGTAGTACTTC 60.486 52.174 0.00 0.00 36.51 3.01
11 12 2.419324 CGCTCTTCGGTGAGTAGTACTT 59.581 50.000 0.00 0.00 36.51 2.24
12 13 2.008329 CGCTCTTCGGTGAGTAGTACT 58.992 52.381 1.37 1.37 36.51 2.73
13 14 1.531470 GCGCTCTTCGGTGAGTAGTAC 60.531 57.143 0.00 0.00 38.94 2.73
14 15 0.731417 GCGCTCTTCGGTGAGTAGTA 59.269 55.000 0.00 0.00 38.94 1.82
15 16 1.241990 TGCGCTCTTCGGTGAGTAGT 61.242 55.000 9.73 0.00 38.94 2.73
16 17 0.109272 TTGCGCTCTTCGGTGAGTAG 60.109 55.000 9.73 4.16 38.94 2.57
17 18 0.315886 TTTGCGCTCTTCGGTGAGTA 59.684 50.000 9.73 0.00 38.94 2.59
18 19 0.531974 TTTTGCGCTCTTCGGTGAGT 60.532 50.000 9.73 0.00 38.94 3.41
19 20 0.798776 ATTTTGCGCTCTTCGGTGAG 59.201 50.000 9.73 2.02 38.94 3.51
20 21 1.069296 CAATTTTGCGCTCTTCGGTGA 60.069 47.619 9.73 0.00 38.94 4.02
21 22 1.330306 CAATTTTGCGCTCTTCGGTG 58.670 50.000 9.73 0.00 38.94 4.94
38 39 1.603456 TGTTTGATTGGAGCGAGCAA 58.397 45.000 0.00 0.00 0.00 3.91
44 50 5.412594 TCATCTACAGTTGTTTGATTGGAGC 59.587 40.000 0.00 0.00 0.00 4.70
49 55 7.642669 CAACAGTCATCTACAGTTGTTTGATT 58.357 34.615 5.54 0.00 45.56 2.57
63 69 1.555075 ACGTATGCCCAACAGTCATCT 59.445 47.619 0.00 0.00 0.00 2.90
64 70 2.024176 ACGTATGCCCAACAGTCATC 57.976 50.000 0.00 0.00 0.00 2.92
100 106 4.083696 GCCCGAAAATACTTTGTTCTTCGA 60.084 41.667 3.76 0.00 38.27 3.71
123 129 4.424430 CTTTTCGCGCCGGTGTCG 62.424 66.667 17.91 19.64 0.00 4.35
135 148 4.801221 CGCGGCGCTGCTCTTTTC 62.801 66.667 36.09 8.66 0.00 2.29
160 174 1.379576 GCAGGGCTTGAAGATGGCT 60.380 57.895 0.00 0.00 0.00 4.75
164 178 2.439156 GGCGCAGGGCTTGAAGAT 60.439 61.111 10.83 0.00 42.94 2.40
259 285 1.202698 CCCGATGGAGGAGTCATTTCC 60.203 57.143 0.00 0.00 37.52 3.13
260 286 1.811941 GCCCGATGGAGGAGTCATTTC 60.812 57.143 0.00 0.00 0.00 2.17
261 287 0.181350 GCCCGATGGAGGAGTCATTT 59.819 55.000 0.00 0.00 0.00 2.32
262 288 1.832912 GCCCGATGGAGGAGTCATT 59.167 57.895 0.00 0.00 0.00 2.57
263 289 2.502492 CGCCCGATGGAGGAGTCAT 61.502 63.158 0.00 0.00 0.00 3.06
264 290 3.147595 CGCCCGATGGAGGAGTCA 61.148 66.667 0.00 0.00 0.00 3.41
265 291 4.593864 GCGCCCGATGGAGGAGTC 62.594 72.222 0.00 0.00 31.02 3.36
354 384 3.953612 TGATGGGCACATAATTGTTCCTC 59.046 43.478 0.00 0.00 38.96 3.71
355 385 3.979911 TGATGGGCACATAATTGTTCCT 58.020 40.909 0.00 0.00 38.96 3.36
383 413 4.974438 TCTTGGGCACGGGGAGGT 62.974 66.667 0.00 0.00 0.00 3.85
405 435 3.002348 GCGTATTATGGAGGAACAACAGC 59.998 47.826 0.00 0.00 0.00 4.40
407 437 3.199071 AGGCGTATTATGGAGGAACAACA 59.801 43.478 0.00 0.00 0.00 3.33
408 438 3.805207 AGGCGTATTATGGAGGAACAAC 58.195 45.455 0.00 0.00 0.00 3.32
410 440 2.035449 CGAGGCGTATTATGGAGGAACA 59.965 50.000 0.00 0.00 0.00 3.18
411 441 2.295349 TCGAGGCGTATTATGGAGGAAC 59.705 50.000 0.00 0.00 0.00 3.62
412 442 2.589720 TCGAGGCGTATTATGGAGGAA 58.410 47.619 0.00 0.00 0.00 3.36
416 475 4.637091 TCGATATTCGAGGCGTATTATGGA 59.363 41.667 0.00 0.00 44.82 3.41
442 501 1.215673 TCGATCCTACTCCTCTGCCTT 59.784 52.381 0.00 0.00 0.00 4.35
447 506 0.108963 CCGGTCGATCCTACTCCTCT 59.891 60.000 0.00 0.00 0.00 3.69
448 507 0.890090 CCCGGTCGATCCTACTCCTC 60.890 65.000 0.00 0.00 0.00 3.71
475 534 0.804544 TGGTACGTAGCTTGCGATGC 60.805 55.000 23.89 6.32 0.00 3.91
477 536 1.636988 GTTGGTACGTAGCTTGCGAT 58.363 50.000 23.89 4.65 0.00 4.58
546 614 3.869832 GAGGGCGACAGGTAGTTTATTTC 59.130 47.826 0.00 0.00 0.00 2.17
566 634 2.758770 TTCTTGTTCGCCCGGACGAG 62.759 60.000 13.88 7.44 44.00 4.18
587 659 4.578516 TCGATTGAGAGAGATGGAGTTCTC 59.421 45.833 0.00 0.00 42.08 2.87
588 660 4.531854 TCGATTGAGAGAGATGGAGTTCT 58.468 43.478 0.00 0.00 0.00 3.01
589 661 4.909696 TCGATTGAGAGAGATGGAGTTC 57.090 45.455 0.00 0.00 0.00 3.01
591 663 4.952957 TCTTTCGATTGAGAGAGATGGAGT 59.047 41.667 0.00 0.00 30.89 3.85
592 664 5.512753 TCTTTCGATTGAGAGAGATGGAG 57.487 43.478 0.00 0.00 30.89 3.86
593 665 5.921962 TTCTTTCGATTGAGAGAGATGGA 57.078 39.130 3.56 0.00 36.76 3.41
594 666 6.255453 GTCTTTCTTTCGATTGAGAGAGATGG 59.745 42.308 13.56 0.00 36.76 3.51
595 667 6.810676 TGTCTTTCTTTCGATTGAGAGAGATG 59.189 38.462 13.56 0.02 36.76 2.90
596 668 6.929625 TGTCTTTCTTTCGATTGAGAGAGAT 58.070 36.000 13.56 0.00 36.76 2.75
597 669 6.332735 TGTCTTTCTTTCGATTGAGAGAGA 57.667 37.500 3.56 8.56 36.76 3.10
598 670 6.422100 TGTTGTCTTTCTTTCGATTGAGAGAG 59.578 38.462 3.56 6.83 36.76 3.20
599 671 6.280643 TGTTGTCTTTCTTTCGATTGAGAGA 58.719 36.000 0.00 0.00 33.82 3.10
600 672 6.530913 TGTTGTCTTTCTTTCGATTGAGAG 57.469 37.500 0.00 0.00 0.00 3.20
603 675 6.918892 TCTTGTTGTCTTTCTTTCGATTGA 57.081 33.333 0.00 0.00 0.00 2.57
609 681 8.336080 AGTTATCGTTCTTGTTGTCTTTCTTTC 58.664 33.333 0.00 0.00 0.00 2.62
619 692 4.377431 GGCAGTGAGTTATCGTTCTTGTTG 60.377 45.833 0.00 0.00 0.00 3.33
628 701 0.174845 TTCGGGGCAGTGAGTTATCG 59.825 55.000 0.00 0.00 0.00 2.92
631 704 1.349688 ACAATTCGGGGCAGTGAGTTA 59.650 47.619 0.00 0.00 0.00 2.24
690 763 2.231235 CCTTGTTTTACATGTCCCCAGC 59.769 50.000 0.00 0.00 0.00 4.85
697 770 0.601057 GCGGGCCTTGTTTTACATGT 59.399 50.000 0.84 2.69 0.00 3.21
736 809 0.960364 GGCAATGCTCCAAGAACCGA 60.960 55.000 4.82 0.00 0.00 4.69
761 834 0.774098 CGTCGTCGTTAGGTGTTGTG 59.226 55.000 0.00 0.00 0.00 3.33
786 859 5.877012 AGATTACAAGGAGCACAAGTACATG 59.123 40.000 0.00 0.00 0.00 3.21
842 929 7.692908 ACAAGACCAAAATGAATTGTTTACG 57.307 32.000 0.00 0.00 0.00 3.18
854 941 6.603997 TGGCCGTTTATATACAAGACCAAAAT 59.396 34.615 0.00 0.00 0.00 1.82
859 946 3.492011 CGTGGCCGTTTATATACAAGACC 59.508 47.826 0.00 0.00 0.00 3.85
863 982 3.815856 TCCGTGGCCGTTTATATACAA 57.184 42.857 0.00 0.00 0.00 2.41
873 992 3.284449 GCAGTTTTCCGTGGCCGT 61.284 61.111 0.00 0.00 0.00 5.68
887 1006 0.455005 TCTGCATGAGAGTCTCGCAG 59.545 55.000 29.75 29.75 42.26 5.18
923 1042 1.606737 GCCTTGGTGTGTCTCTGTCTC 60.607 57.143 0.00 0.00 0.00 3.36
929 1048 2.143925 GTAAGTGCCTTGGTGTGTCTC 58.856 52.381 0.00 0.00 0.00 3.36
933 1052 3.120321 TGTAGTAAGTGCCTTGGTGTG 57.880 47.619 0.00 0.00 0.00 3.82
936 1055 4.367039 ACAATGTAGTAAGTGCCTTGGT 57.633 40.909 0.00 0.00 0.00 3.67
938 1057 4.032900 CGCTACAATGTAGTAAGTGCCTTG 59.967 45.833 20.14 0.00 0.00 3.61
939 1058 4.181578 CGCTACAATGTAGTAAGTGCCTT 58.818 43.478 20.14 0.00 0.00 4.35
940 1059 3.194968 ACGCTACAATGTAGTAAGTGCCT 59.805 43.478 20.14 0.00 0.00 4.75
943 1062 3.863424 CCCACGCTACAATGTAGTAAGTG 59.137 47.826 24.34 24.34 34.87 3.16
944 1063 3.677976 GCCCACGCTACAATGTAGTAAGT 60.678 47.826 20.14 14.86 0.00 2.24
946 1065 2.736081 CGCCCACGCTACAATGTAGTAA 60.736 50.000 20.14 0.00 0.00 2.24
948 1067 0.459585 CGCCCACGCTACAATGTAGT 60.460 55.000 20.14 1.07 0.00 2.73
975 1103 1.077716 CAAGTCCCCAACCCGATCC 60.078 63.158 0.00 0.00 0.00 3.36
989 1117 2.505982 CCGCCATCGATCCCAAGT 59.494 61.111 0.00 0.00 38.10 3.16
990 1118 2.281070 CCCGCCATCGATCCCAAG 60.281 66.667 0.00 0.00 38.10 3.61
1010 1138 2.202260 TCATCGTCGTCGTCGTGC 60.202 61.111 11.41 0.00 38.33 5.34
1011 1139 2.200073 CGTCATCGTCGTCGTCGTG 61.200 63.158 11.41 9.24 38.33 4.35
1014 1142 2.943034 GCCGTCATCGTCGTCGTC 60.943 66.667 1.33 0.00 38.33 4.20
1590 1726 2.963371 GTCTTCCTGTCGCCGAGT 59.037 61.111 0.00 0.00 0.00 4.18
2027 2168 6.878923 TGCTAAACAGAAGTTGCATATGTACT 59.121 34.615 4.29 5.76 38.17 2.73
2047 2194 0.321671 GGTGACTGGCTGACTGCTAA 59.678 55.000 4.20 0.00 42.39 3.09
2065 2212 2.334946 CCAATGGAGTGCACCGTGG 61.335 63.158 14.63 10.14 33.52 4.94
2069 2216 2.283101 TGGCCAATGGAGTGCACC 60.283 61.111 14.63 4.90 0.00 5.01
2071 2218 2.672651 CGTGGCCAATGGAGTGCA 60.673 61.111 7.24 0.00 0.00 4.57
2092 2248 2.073816 CCCGTTTTTATCAGCACGTCT 58.926 47.619 0.00 0.00 0.00 4.18
2106 2263 1.337447 CGACACCTGTACATCCCGTTT 60.337 52.381 0.00 0.00 0.00 3.60
2215 2381 3.660092 ATCACCAGGTCCCCCTCCC 62.660 68.421 0.00 0.00 39.89 4.30
2378 2544 2.146920 AGAAGTAGAAGGGGTCGAGG 57.853 55.000 0.00 0.00 0.00 4.63
2588 2756 0.976641 TTGGCTTGGAGACGACAGAT 59.023 50.000 0.00 0.00 0.00 2.90
2591 2759 0.179234 TGTTTGGCTTGGAGACGACA 59.821 50.000 0.00 0.00 0.00 4.35
2612 2780 3.149196 GCCCATGAACTTCTTCTTGTCA 58.851 45.455 0.00 0.00 32.17 3.58
2685 2873 4.447138 TTGAGTTTGTCCCCTGTTACAT 57.553 40.909 0.00 0.00 0.00 2.29
2770 2979 9.120538 ACAATTGCTCTTGTTTCTTTAGTAAGA 57.879 29.630 5.05 0.00 35.90 2.10
2771 2980 9.736023 AACAATTGCTCTTGTTTCTTTAGTAAG 57.264 29.630 5.05 0.00 44.76 2.34
2774 2983 8.000780 AGAACAATTGCTCTTGTTTCTTTAGT 57.999 30.769 15.28 0.00 46.50 2.24
2775 2984 9.387123 GTAGAACAATTGCTCTTGTTTCTTTAG 57.613 33.333 16.13 0.00 46.50 1.85
2776 2985 8.898761 TGTAGAACAATTGCTCTTGTTTCTTTA 58.101 29.630 16.13 1.88 46.50 1.85
2777 2986 7.702348 GTGTAGAACAATTGCTCTTGTTTCTTT 59.298 33.333 16.13 0.00 46.50 2.52
2778 2987 7.196331 GTGTAGAACAATTGCTCTTGTTTCTT 58.804 34.615 16.13 9.15 46.50 2.52
2781 2990 5.221244 GGGTGTAGAACAATTGCTCTTGTTT 60.221 40.000 16.13 0.00 46.50 2.83
2807 3322 0.673644 GATGGTTGGTGACGTCCAGG 60.674 60.000 14.12 0.00 38.66 4.45
2823 3338 2.556144 ATGGATGGACACGATGGATG 57.444 50.000 0.00 0.00 0.00 3.51
2824 3339 2.707791 AGAATGGATGGACACGATGGAT 59.292 45.455 0.00 0.00 0.00 3.41
2825 3340 2.118679 AGAATGGATGGACACGATGGA 58.881 47.619 0.00 0.00 0.00 3.41
2826 3341 2.216046 CAGAATGGATGGACACGATGG 58.784 52.381 0.00 0.00 0.00 3.51
2827 3342 1.600957 GCAGAATGGATGGACACGATG 59.399 52.381 0.00 0.00 35.86 3.84
2903 3435 2.002127 CGACGGATGCAAAGCTCTC 58.998 57.895 0.00 0.00 0.00 3.20
2936 3468 0.179145 ATCGTGCTACGGTGCTACAC 60.179 55.000 8.46 0.00 42.81 2.90
2938 3470 1.197910 GAATCGTGCTACGGTGCTAC 58.802 55.000 8.46 0.59 42.81 3.58
2941 3473 0.179134 AGAGAATCGTGCTACGGTGC 60.179 55.000 8.46 1.05 42.81 5.01
2945 3477 1.550065 CACCAGAGAATCGTGCTACG 58.450 55.000 2.79 2.79 42.67 3.51
2948 3480 1.078848 GGCACCAGAGAATCGTGCT 60.079 57.895 10.82 0.00 46.95 4.40
2950 3482 2.477825 CTATGGCACCAGAGAATCGTG 58.522 52.381 5.34 0.00 42.67 4.35
2978 3510 3.423154 GTGTCAAAGCGCGGGAGG 61.423 66.667 8.83 0.00 0.00 4.30
3033 3567 1.385915 CCATGGGGGAAGAGGCCTA 60.386 63.158 4.42 0.00 40.01 3.93
3045 3579 3.368739 GGACAAGATTTTTCAGCCATGGG 60.369 47.826 15.13 0.00 0.00 4.00
3048 3582 3.057315 CGTGGACAAGATTTTTCAGCCAT 60.057 43.478 0.00 0.00 0.00 4.40
3049 3583 2.293122 CGTGGACAAGATTTTTCAGCCA 59.707 45.455 0.00 0.00 0.00 4.75
3065 3599 1.473677 ACGATCCGAAATGTACGTGGA 59.526 47.619 0.00 0.00 32.93 4.02
3066 3600 1.586578 CACGATCCGAAATGTACGTGG 59.413 52.381 0.00 0.00 44.29 4.94
3069 3603 1.255342 CAGCACGATCCGAAATGTACG 59.745 52.381 0.00 0.00 0.00 3.67
3070 3604 2.268298 ACAGCACGATCCGAAATGTAC 58.732 47.619 0.00 0.00 0.00 2.90
3072 3606 1.359848 GACAGCACGATCCGAAATGT 58.640 50.000 0.00 0.00 0.00 2.71
3075 3609 4.590487 GGACAGCACGATCCGAAA 57.410 55.556 0.00 0.00 0.00 3.46
3080 3641 2.202756 GGTCCGGACAGCACGATC 60.203 66.667 34.40 12.03 0.00 3.69
3094 3655 2.038269 TTGAATGGCTTCCGCGGTC 61.038 57.895 27.15 14.06 36.88 4.79
3098 3659 2.202479 GCGTTGAATGGCTTCCGC 60.202 61.111 0.00 0.00 35.79 5.54
3099 3660 2.098298 CGCGTTGAATGGCTTCCG 59.902 61.111 0.00 0.00 0.00 4.30
3101 3662 2.485122 CCCGCGTTGAATGGCTTC 59.515 61.111 4.92 0.00 0.00 3.86
3102 3663 3.747976 GCCCGCGTTGAATGGCTT 61.748 61.111 13.62 0.00 40.77 4.35
3114 3677 0.385974 GCGAATTGATACATGCCCGC 60.386 55.000 0.00 0.00 34.71 6.13
3115 3678 0.943673 TGCGAATTGATACATGCCCG 59.056 50.000 0.00 0.00 0.00 6.13
3135 3698 1.262640 AAAGTACATCCGGACCGCCT 61.263 55.000 6.12 0.00 0.00 5.52
3137 3700 0.175073 AGAAAGTACATCCGGACCGC 59.825 55.000 6.12 0.00 0.00 5.68
3138 3701 1.202382 GGAGAAAGTACATCCGGACCG 60.202 57.143 6.12 6.99 0.00 4.79
3147 3710 1.874739 CGGTTTGCGGGAGAAAGTACA 60.875 52.381 0.00 0.00 0.00 2.90
3158 3721 3.366422 CCATGTTTATTTTCGGTTTGCGG 59.634 43.478 0.00 0.00 0.00 5.69
3159 3722 3.366422 CCCATGTTTATTTTCGGTTTGCG 59.634 43.478 0.00 0.00 0.00 4.85
3161 3724 4.249661 CCCCCATGTTTATTTTCGGTTTG 58.750 43.478 0.00 0.00 0.00 2.93
3166 3729 3.885724 AAGCCCCCATGTTTATTTTCG 57.114 42.857 0.00 0.00 0.00 3.46
3167 3730 3.689161 GCAAAGCCCCCATGTTTATTTTC 59.311 43.478 0.00 0.00 0.00 2.29
3168 3731 3.684908 GCAAAGCCCCCATGTTTATTTT 58.315 40.909 0.00 0.00 0.00 1.82
3170 3733 1.206849 CGCAAAGCCCCCATGTTTATT 59.793 47.619 0.00 0.00 0.00 1.40
3172 3735 1.254284 CCGCAAAGCCCCCATGTTTA 61.254 55.000 0.00 0.00 0.00 2.01
3176 3739 4.757355 TCCCGCAAAGCCCCCATG 62.757 66.667 0.00 0.00 0.00 3.66
3177 3740 4.759205 GTCCCGCAAAGCCCCCAT 62.759 66.667 0.00 0.00 0.00 4.00
3217 3780 1.185618 TGGGTCAGGACGGTCAGAAG 61.186 60.000 10.76 0.00 0.00 2.85
3218 3781 1.152419 TGGGTCAGGACGGTCAGAA 60.152 57.895 10.76 0.00 0.00 3.02
3232 3795 2.789920 ATGGGGGTTTGGGTGGGT 60.790 61.111 0.00 0.00 0.00 4.51
3234 3797 2.362375 CGATGGGGGTTTGGGTGG 60.362 66.667 0.00 0.00 0.00 4.61
3236 3799 4.376170 GGCGATGGGGGTTTGGGT 62.376 66.667 0.00 0.00 0.00 4.51
3242 3805 3.739613 GGAAAGGGCGATGGGGGT 61.740 66.667 0.00 0.00 0.00 4.95
3244 3807 4.109675 ACGGAAAGGGCGATGGGG 62.110 66.667 0.00 0.00 0.00 4.96
3245 3808 2.246761 TACACGGAAAGGGCGATGGG 62.247 60.000 0.00 0.00 0.00 4.00
3246 3809 0.179056 ATACACGGAAAGGGCGATGG 60.179 55.000 0.00 0.00 0.00 3.51
3247 3810 1.663695 AATACACGGAAAGGGCGATG 58.336 50.000 0.00 0.00 0.00 3.84
3248 3811 2.093128 AGAAATACACGGAAAGGGCGAT 60.093 45.455 0.00 0.00 0.00 4.58
3249 3812 1.276989 AGAAATACACGGAAAGGGCGA 59.723 47.619 0.00 0.00 0.00 5.54
3250 3813 1.734163 AGAAATACACGGAAAGGGCG 58.266 50.000 0.00 0.00 0.00 6.13
3251 3814 2.422479 GGAAGAAATACACGGAAAGGGC 59.578 50.000 0.00 0.00 0.00 5.19
3252 3815 2.676342 CGGAAGAAATACACGGAAAGGG 59.324 50.000 0.00 0.00 0.00 3.95
3253 3816 3.332034 ACGGAAGAAATACACGGAAAGG 58.668 45.455 0.00 0.00 0.00 3.11
3254 3817 4.708601 CAACGGAAGAAATACACGGAAAG 58.291 43.478 0.00 0.00 0.00 2.62
3255 3818 3.058777 GCAACGGAAGAAATACACGGAAA 60.059 43.478 0.00 0.00 0.00 3.13
3256 3819 2.481185 GCAACGGAAGAAATACACGGAA 59.519 45.455 0.00 0.00 0.00 4.30
3257 3820 2.070783 GCAACGGAAGAAATACACGGA 58.929 47.619 0.00 0.00 0.00 4.69
3258 3821 1.801771 TGCAACGGAAGAAATACACGG 59.198 47.619 0.00 0.00 0.00 4.94
3259 3822 3.416277 CATGCAACGGAAGAAATACACG 58.584 45.455 0.00 0.00 0.00 4.49
3260 3823 3.171277 GCATGCAACGGAAGAAATACAC 58.829 45.455 14.21 0.00 0.00 2.90
3261 3824 2.159585 CGCATGCAACGGAAGAAATACA 60.160 45.455 19.57 0.00 0.00 2.29
3262 3825 2.440501 CGCATGCAACGGAAGAAATAC 58.559 47.619 19.57 0.00 0.00 1.89
3263 3826 1.202132 GCGCATGCAACGGAAGAAATA 60.202 47.619 19.57 0.00 42.15 1.40
3264 3827 0.456653 GCGCATGCAACGGAAGAAAT 60.457 50.000 19.57 0.00 42.15 2.17
3267 3830 3.430862 GGCGCATGCAACGGAAGA 61.431 61.111 19.57 0.00 45.35 2.87
3274 3837 2.685829 CGGTAAGTGGCGCATGCAA 61.686 57.895 19.57 0.00 45.35 4.08
3279 3842 3.124270 CATGCGGTAAGTGGCGCA 61.124 61.111 10.83 0.00 41.64 6.09
3282 3845 1.064060 GAATGTCATGCGGTAAGTGGC 59.936 52.381 0.00 0.00 0.00 5.01
3294 3857 0.032912 TGGGCCAGCATGAATGTCAT 60.033 50.000 0.00 0.00 39.69 3.06
3298 3861 1.735376 GCTCTGGGCCAGCATGAATG 61.735 60.000 29.02 12.30 39.69 2.67
3307 3870 4.082523 GCTACGTGCTCTGGGCCA 62.083 66.667 5.85 5.85 40.92 5.36
3319 3882 4.728102 TCAACACCGGCCGCTACG 62.728 66.667 22.85 8.91 0.00 3.51
3321 3884 4.728102 CGTCAACACCGGCCGCTA 62.728 66.667 22.85 0.00 0.00 4.26
3331 3894 1.956678 TCAAATCGCGGCGTCAACA 60.957 52.632 22.90 2.20 0.00 3.33
3332 3895 1.509162 GTCAAATCGCGGCGTCAAC 60.509 57.895 22.90 10.70 0.00 3.18
3338 3901 2.785258 GTCCAGTCAAATCGCGGC 59.215 61.111 6.13 0.00 0.00 6.53
3340 3903 2.452813 CCCGTCCAGTCAAATCGCG 61.453 63.158 0.00 0.00 0.00 5.87
3351 3915 4.124351 GCGTCGTCATCCCGTCCA 62.124 66.667 0.00 0.00 0.00 4.02
3355 3919 2.579787 GTCTGCGTCGTCATCCCG 60.580 66.667 0.00 0.00 0.00 5.14
3360 3924 4.379143 CGTCCGTCTGCGTCGTCA 62.379 66.667 0.00 0.00 36.15 4.35
3407 3971 0.034896 TTCCTCAGGAAGTTGCGTCC 59.965 55.000 0.34 0.00 36.71 4.79
3414 3978 1.700186 GGAGTTGGTTCCTCAGGAAGT 59.300 52.381 6.31 0.00 42.88 3.01
3435 3999 0.238817 TTTAATGTGGCGCAACGGAC 59.761 50.000 11.00 0.00 0.00 4.79
3436 4000 0.519519 CTTTAATGTGGCGCAACGGA 59.480 50.000 11.00 0.00 0.00 4.69
3440 4004 1.211449 CCGCTTTAATGTGGCGCAA 59.789 52.632 10.83 0.00 46.29 4.85
3474 4038 1.003866 CTTAAATAGTCGCGGCCAAGC 60.004 52.381 7.31 0.00 0.00 4.01
3475 4039 1.003866 GCTTAAATAGTCGCGGCCAAG 60.004 52.381 7.31 4.66 0.00 3.61
3477 4041 0.108089 TGCTTAAATAGTCGCGGCCA 60.108 50.000 7.31 0.00 0.00 5.36
3505 4073 3.340953 ATTGCAATGTGGACGGCGC 62.341 57.895 12.09 0.00 0.00 6.53
3516 4084 5.307204 GAGGAAGAGCAGATAGATTGCAAT 58.693 41.667 12.83 12.83 43.92 3.56
3518 4086 3.070734 GGAGGAAGAGCAGATAGATTGCA 59.929 47.826 0.00 0.00 43.92 4.08
3527 4095 0.032615 GGAGGAGGAGGAAGAGCAGA 60.033 60.000 0.00 0.00 0.00 4.26
3528 4096 0.032217 AGGAGGAGGAGGAAGAGCAG 60.032 60.000 0.00 0.00 0.00 4.24
3529 4097 0.032615 GAGGAGGAGGAGGAAGAGCA 60.033 60.000 0.00 0.00 0.00 4.26
3530 4098 0.261696 AGAGGAGGAGGAGGAAGAGC 59.738 60.000 0.00 0.00 0.00 4.09
3531 4099 2.666317 GAAGAGGAGGAGGAGGAAGAG 58.334 57.143 0.00 0.00 0.00 2.85
3533 4101 1.290732 AGGAAGAGGAGGAGGAGGAAG 59.709 57.143 0.00 0.00 0.00 3.46
3535 4103 0.930726 GAGGAAGAGGAGGAGGAGGA 59.069 60.000 0.00 0.00 0.00 3.71
3538 4106 1.595058 GGGGAGGAAGAGGAGGAGGA 61.595 65.000 0.00 0.00 0.00 3.71
3539 4107 1.074850 GGGGAGGAAGAGGAGGAGG 60.075 68.421 0.00 0.00 0.00 4.30
3540 4108 0.105709 GAGGGGAGGAAGAGGAGGAG 60.106 65.000 0.00 0.00 0.00 3.69
3541 4109 0.556380 AGAGGGGAGGAAGAGGAGGA 60.556 60.000 0.00 0.00 0.00 3.71
3542 4110 0.105709 GAGAGGGGAGGAAGAGGAGG 60.106 65.000 0.00 0.00 0.00 4.30
3543 4111 0.105709 GGAGAGGGGAGGAAGAGGAG 60.106 65.000 0.00 0.00 0.00 3.69
3544 4112 1.595058 GGGAGAGGGGAGGAAGAGGA 61.595 65.000 0.00 0.00 0.00 3.71
3549 4117 4.798682 GCGGGGAGAGGGGAGGAA 62.799 72.222 0.00 0.00 0.00 3.36
3556 4124 3.237741 GAGATGGGCGGGGAGAGG 61.238 72.222 0.00 0.00 0.00 3.69
3565 4133 1.077429 GTTGTGGAGGGAGATGGGC 60.077 63.158 0.00 0.00 0.00 5.36
3575 4143 0.742281 CCATCGCTGGAGTTGTGGAG 60.742 60.000 0.00 0.00 46.37 3.86
3584 4152 1.913951 ATGACTTGCCCATCGCTGGA 61.914 55.000 6.92 0.00 46.37 3.86
3586 4154 1.721664 CCATGACTTGCCCATCGCTG 61.722 60.000 0.00 0.00 38.78 5.18
3587 4155 1.452651 CCATGACTTGCCCATCGCT 60.453 57.895 0.00 0.00 38.78 4.93
3588 4156 2.484062 CCCATGACTTGCCCATCGC 61.484 63.158 0.00 0.00 38.31 4.58
3592 4160 3.267233 AGGCCCATGACTTGCCCA 61.267 61.111 0.00 0.00 46.55 5.36
3596 4164 2.757099 GCCCAGGCCCATGACTTG 60.757 66.667 0.00 0.00 34.56 3.16


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

AutoCloner maintained by Alex Coulton.