Multiple sequence alignment - TraesCS7A01G270700

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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 TraesCS7A01G270700 chr7A 100.000 3785 0 0 1 3785 280072818 280069034 0.000000e+00 6990
1 TraesCS7A01G270700 chr7A 82.850 379 53 6 3293 3661 706281044 706280668 2.820000e-86 329
2 TraesCS7A01G270700 chr7B 88.934 2702 165 52 809 3449 237509884 237507256 0.000000e+00 3210
3 TraesCS7A01G270700 chr7B 89.397 547 40 9 3 533 237514627 237514083 0.000000e+00 673
4 TraesCS7A01G270700 chr7B 91.489 282 24 0 3462 3743 237505299 237505018 4.580000e-104 388
5 TraesCS7A01G270700 chr7D 93.900 1295 45 7 817 2094 258238438 258237161 0.000000e+00 1923
6 TraesCS7A01G270700 chr7D 88.710 1240 79 35 2109 3324 258237176 258235974 0.000000e+00 1458
7 TraesCS7A01G270700 chr7D 86.314 548 49 12 3 538 258238992 258238459 1.180000e-159 573
8 TraesCS7A01G270700 chr7D 88.889 198 21 1 3460 3657 614243849 614243653 3.780000e-60 243
9 TraesCS7A01G270700 chr7D 85.294 136 12 3 3100 3227 614245490 614245355 2.370000e-27 134
10 TraesCS7A01G270700 chr5D 78.856 804 142 19 1224 2014 414810641 414809853 5.600000e-143 518
11 TraesCS7A01G270700 chr5D 75.279 627 129 17 2130 2753 414809776 414809173 3.720000e-70 276
12 TraesCS7A01G270700 chr5B 78.624 814 138 24 1217 2014 500530025 500529232 1.210000e-139 507
13 TraesCS7A01G270700 chr5B 75.719 626 128 15 2130 2753 500529156 500528553 3.700000e-75 292
14 TraesCS7A01G270700 chr5A 78.580 803 146 17 1224 2014 527491341 527490553 1.210000e-139 507
15 TraesCS7A01G270700 chr1B 83.288 371 51 7 3298 3660 653814745 653814378 7.840000e-87 331
16 TraesCS7A01G270700 chr4A 83.537 164 23 4 3099 3262 640093136 640093295 2.360000e-32 150
17 TraesCS7A01G270700 chr4A 78.981 157 28 5 582 737 552691191 552691343 6.690000e-18 102


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 TraesCS7A01G270700 chr7A 280069034 280072818 3784 True 6990.0 6990 100.000000 1 3785 1 chr7A.!!$R1 3784
1 TraesCS7A01G270700 chr7B 237505018 237509884 4866 True 1799.0 3210 90.211500 809 3743 2 chr7B.!!$R2 2934
2 TraesCS7A01G270700 chr7B 237514083 237514627 544 True 673.0 673 89.397000 3 533 1 chr7B.!!$R1 530
3 TraesCS7A01G270700 chr7D 258235974 258238992 3018 True 1318.0 1923 89.641333 3 3324 3 chr7D.!!$R1 3321
4 TraesCS7A01G270700 chr5D 414809173 414810641 1468 True 397.0 518 77.067500 1224 2753 2 chr5D.!!$R1 1529
5 TraesCS7A01G270700 chr5B 500528553 500530025 1472 True 399.5 507 77.171500 1217 2753 2 chr5B.!!$R1 1536
6 TraesCS7A01G270700 chr5A 527490553 527491341 788 True 507.0 507 78.580000 1224 2014 1 chr5A.!!$R1 790

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
320 333 1.155889 CACGGCAAGCACACATTAGA 58.844 50.0 0.0 0.0 0.0 2.10 F
1191 1207 0.179081 GGAGGTATTGGTGGACGAGC 60.179 60.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2288 2355 0.800300 CTGGAGAAAGACGAGCGAGC 60.800 60.000 0.0 0.0 0.0 5.03 R
2808 2875 1.066918 GCCCATGTACGTCTACCCG 59.933 63.158 0.0 0.0 0.0 5.28 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
201 214 2.811317 GTCAAGCTGCTCGACCGG 60.811 66.667 9.57 0.00 0.00 5.28
256 269 7.038154 TCTTTTCGAGTCAATTTTGAACCAT 57.962 32.000 0.00 0.00 39.21 3.55
258 271 7.978975 TCTTTTCGAGTCAATTTTGAACCATTT 59.021 29.630 0.00 0.00 39.21 2.32
303 316 1.512926 CCTTAGCCACACAGACACAC 58.487 55.000 0.00 0.00 0.00 3.82
320 333 1.155889 CACGGCAAGCACACATTAGA 58.844 50.000 0.00 0.00 0.00 2.10
559 574 7.906199 TCAATATATGGGTGGGGTTTAAAAG 57.094 36.000 0.00 0.00 0.00 2.27
562 577 8.763601 CAATATATGGGTGGGGTTTAAAAGAAA 58.236 33.333 0.00 0.00 0.00 2.52
563 578 6.867519 ATATGGGTGGGGTTTAAAAGAAAG 57.132 37.500 0.00 0.00 0.00 2.62
565 580 4.621769 TGGGTGGGGTTTAAAAGAAAGAA 58.378 39.130 0.00 0.00 0.00 2.52
567 582 5.305902 TGGGTGGGGTTTAAAAGAAAGAATC 59.694 40.000 0.00 0.00 0.00 2.52
568 583 5.305902 GGGTGGGGTTTAAAAGAAAGAATCA 59.694 40.000 0.00 0.00 0.00 2.57
569 584 6.013725 GGGTGGGGTTTAAAAGAAAGAATCAT 60.014 38.462 0.00 0.00 0.00 2.45
570 585 7.450074 GGTGGGGTTTAAAAGAAAGAATCATT 58.550 34.615 0.00 0.00 0.00 2.57
571 586 7.936847 GGTGGGGTTTAAAAGAAAGAATCATTT 59.063 33.333 0.00 0.00 33.76 2.32
572 587 9.990360 GTGGGGTTTAAAAGAAAGAATCATTTA 57.010 29.630 0.00 0.00 31.78 1.40
647 662 9.956640 TGCCAATTAAGGAATTTTAATGAATGT 57.043 25.926 0.00 0.00 34.39 2.71
741 756 9.392259 TGCTACTACATGATACTAATATACGCT 57.608 33.333 0.00 0.00 0.00 5.07
745 760 9.676861 ACTACATGATACTAATATACGCTACCA 57.323 33.333 0.00 0.00 0.00 3.25
748 763 7.921214 ACATGATACTAATATACGCTACCATGC 59.079 37.037 0.00 0.00 32.29 4.06
749 764 7.399245 TGATACTAATATACGCTACCATGCA 57.601 36.000 0.00 0.00 0.00 3.96
750 765 7.832769 TGATACTAATATACGCTACCATGCAA 58.167 34.615 0.00 0.00 0.00 4.08
751 766 8.474831 TGATACTAATATACGCTACCATGCAAT 58.525 33.333 0.00 0.00 0.00 3.56
752 767 9.961265 GATACTAATATACGCTACCATGCAATA 57.039 33.333 0.00 0.00 0.00 1.90
753 768 9.967346 ATACTAATATACGCTACCATGCAATAG 57.033 33.333 0.00 0.00 0.00 1.73
754 769 8.063200 ACTAATATACGCTACCATGCAATAGA 57.937 34.615 0.00 0.00 0.00 1.98
755 770 8.528643 ACTAATATACGCTACCATGCAATAGAA 58.471 33.333 0.00 0.00 0.00 2.10
756 771 9.366216 CTAATATACGCTACCATGCAATAGAAA 57.634 33.333 0.00 0.00 0.00 2.52
757 772 7.834068 ATATACGCTACCATGCAATAGAAAG 57.166 36.000 0.00 0.00 0.00 2.62
758 773 4.137116 ACGCTACCATGCAATAGAAAGA 57.863 40.909 0.00 0.00 0.00 2.52
759 774 4.708177 ACGCTACCATGCAATAGAAAGAT 58.292 39.130 0.00 0.00 0.00 2.40
760 775 5.853936 ACGCTACCATGCAATAGAAAGATA 58.146 37.500 0.00 0.00 0.00 1.98
761 776 6.467677 ACGCTACCATGCAATAGAAAGATAT 58.532 36.000 0.00 0.00 0.00 1.63
762 777 7.611770 ACGCTACCATGCAATAGAAAGATATA 58.388 34.615 0.00 0.00 0.00 0.86
763 778 8.260818 ACGCTACCATGCAATAGAAAGATATAT 58.739 33.333 0.00 0.00 0.00 0.86
764 779 8.546244 CGCTACCATGCAATAGAAAGATATATG 58.454 37.037 0.00 0.00 0.00 1.78
765 780 9.605275 GCTACCATGCAATAGAAAGATATATGA 57.395 33.333 0.00 0.00 0.00 2.15
768 783 9.224267 ACCATGCAATAGAAAGATATATGACAC 57.776 33.333 0.00 0.00 0.00 3.67
769 784 9.445878 CCATGCAATAGAAAGATATATGACACT 57.554 33.333 0.00 0.00 0.00 3.55
795 810 8.736097 AGTATATGATACTTCCATTACCACCA 57.264 34.615 0.00 0.00 0.00 4.17
796 811 8.816894 AGTATATGATACTTCCATTACCACCAG 58.183 37.037 0.00 0.00 0.00 4.00
797 812 7.872061 ATATGATACTTCCATTACCACCAGA 57.128 36.000 0.00 0.00 0.00 3.86
798 813 5.353394 TGATACTTCCATTACCACCAGAC 57.647 43.478 0.00 0.00 0.00 3.51
799 814 5.030147 TGATACTTCCATTACCACCAGACT 58.970 41.667 0.00 0.00 0.00 3.24
800 815 5.487488 TGATACTTCCATTACCACCAGACTT 59.513 40.000 0.00 0.00 0.00 3.01
801 816 6.670464 TGATACTTCCATTACCACCAGACTTA 59.330 38.462 0.00 0.00 0.00 2.24
802 817 5.422214 ACTTCCATTACCACCAGACTTAG 57.578 43.478 0.00 0.00 0.00 2.18
803 818 5.091552 ACTTCCATTACCACCAGACTTAGA 58.908 41.667 0.00 0.00 0.00 2.10
804 819 5.046520 ACTTCCATTACCACCAGACTTAGAC 60.047 44.000 0.00 0.00 0.00 2.59
805 820 4.422057 TCCATTACCACCAGACTTAGACA 58.578 43.478 0.00 0.00 0.00 3.41
806 821 4.222145 TCCATTACCACCAGACTTAGACAC 59.778 45.833 0.00 0.00 0.00 3.67
807 822 4.223032 CCATTACCACCAGACTTAGACACT 59.777 45.833 0.00 0.00 0.00 3.55
814 829 5.163602 CCACCAGACTTAGACACTGAGATAC 60.164 48.000 0.00 0.00 34.07 2.24
828 843 7.624549 ACACTGAGATACCATCACTTTACATT 58.375 34.615 0.00 0.00 0.00 2.71
834 849 6.980978 AGATACCATCACTTTACATTGACTCG 59.019 38.462 0.00 0.00 0.00 4.18
931 947 2.825532 ACAATCCGTCCTTTCATTTGGG 59.174 45.455 0.00 0.00 0.00 4.12
979 995 1.562575 GCGCGAGAACGAGGGAAAAA 61.563 55.000 12.10 0.00 42.66 1.94
1110 1126 4.633980 GGCTTTGTTGCCGTTCTG 57.366 55.556 0.00 0.00 43.74 3.02
1122 1138 2.720758 CGTTCTGCTCGCCGTCTTG 61.721 63.158 0.00 0.00 0.00 3.02
1191 1207 0.179081 GGAGGTATTGGTGGACGAGC 60.179 60.000 0.00 0.00 0.00 5.03
1440 1459 3.691342 CCGGTCAAGGAGTCCGCA 61.691 66.667 2.76 0.00 45.75 5.69
1533 1552 1.309499 CGTCCTCGCACCTCTTCTCT 61.309 60.000 0.00 0.00 0.00 3.10
1689 1708 1.670791 ACGTGATGTGGTCCGTTTTT 58.329 45.000 0.00 0.00 32.33 1.94
1696 1715 3.676605 GGTCCGTTTTTGGCCGGG 61.677 66.667 2.18 0.00 44.32 5.73
1941 1972 1.000938 GTGGTAGACTTCACCGACGTT 60.001 52.381 0.00 0.00 39.04 3.99
1968 1999 4.697756 CTCCAGGGCGGCGACAAA 62.698 66.667 17.61 0.00 33.14 2.83
2011 2042 2.618053 CCGTTCTCTGGGTATGTTCAC 58.382 52.381 0.00 0.00 0.00 3.18
2014 2050 1.933021 TCTCTGGGTATGTTCACCGT 58.067 50.000 0.00 0.00 39.69 4.83
2029 2065 6.574350 TGTTCACCGTTTAAATGGAAAACAT 58.426 32.000 29.26 6.34 43.07 2.71
2038 2074 7.148656 CGTTTAAATGGAAAACATGAATGGACC 60.149 37.037 0.00 0.00 40.44 4.46
2082 2149 6.183360 CGGATAATTAGCTTGCTCATAACGAG 60.183 42.308 0.00 0.00 45.37 4.18
2083 2150 6.868864 GGATAATTAGCTTGCTCATAACGAGA 59.131 38.462 0.00 0.00 45.45 4.04
2084 2151 7.385205 GGATAATTAGCTTGCTCATAACGAGAA 59.615 37.037 0.00 0.00 45.45 2.87
2085 2152 6.985188 AATTAGCTTGCTCATAACGAGAAA 57.015 33.333 0.00 0.00 45.45 2.52
2086 2153 7.559590 AATTAGCTTGCTCATAACGAGAAAT 57.440 32.000 0.00 0.00 45.45 2.17
2087 2154 4.871993 AGCTTGCTCATAACGAGAAATG 57.128 40.909 0.00 0.00 45.45 2.32
2088 2155 4.256920 AGCTTGCTCATAACGAGAAATGT 58.743 39.130 0.00 0.00 45.45 2.71
2089 2156 4.697352 AGCTTGCTCATAACGAGAAATGTT 59.303 37.500 0.00 0.00 45.45 2.71
2090 2157 5.182001 AGCTTGCTCATAACGAGAAATGTTT 59.818 36.000 0.00 0.00 45.45 2.83
2091 2158 5.858581 GCTTGCTCATAACGAGAAATGTTTT 59.141 36.000 0.00 0.00 45.45 2.43
2092 2159 6.032880 GCTTGCTCATAACGAGAAATGTTTTC 59.967 38.462 0.00 0.00 45.45 2.29
2093 2160 6.801539 TGCTCATAACGAGAAATGTTTTCT 57.198 33.333 2.27 2.27 45.45 2.52
2094 2161 7.202016 TGCTCATAACGAGAAATGTTTTCTT 57.798 32.000 4.16 0.00 45.45 2.52
2095 2162 7.648142 TGCTCATAACGAGAAATGTTTTCTTT 58.352 30.769 4.16 0.00 45.45 2.52
2096 2163 8.134895 TGCTCATAACGAGAAATGTTTTCTTTT 58.865 29.630 4.16 4.25 45.45 2.27
2097 2164 8.968242 GCTCATAACGAGAAATGTTTTCTTTTT 58.032 29.630 4.16 3.97 45.45 1.94
2223 2290 4.624364 CACCAGGACGTGCAGGCA 62.624 66.667 18.45 0.00 0.00 4.75
2232 2299 2.036256 GTGCAGGCAAGGGTCCAT 59.964 61.111 0.00 0.00 0.00 3.41
2250 2317 3.003763 GAGGAGCTGGACCGGGTT 61.004 66.667 6.32 0.00 0.00 4.11
2326 2393 2.584391 GCCGTGGTCAAGGAGGTCT 61.584 63.158 7.11 0.00 31.21 3.85
2355 2422 3.329889 CCACCAGGCCCACTGCTA 61.330 66.667 0.00 0.00 46.14 3.49
2546 2613 2.348998 CGCAGGGGCTGAGTTCTT 59.651 61.111 0.00 0.00 38.10 2.52
2549 2616 1.246737 GCAGGGGCTGAGTTCTTTGG 61.247 60.000 0.00 0.00 36.96 3.28
2796 2863 1.904852 CTGTGTGATGACGTGGCTGC 61.905 60.000 0.00 0.00 0.00 5.25
2820 2887 3.892581 CGGGCCGGGTAGACGTAC 61.893 72.222 20.56 0.00 0.00 3.67
2821 2888 2.755469 GGGCCGGGTAGACGTACA 60.755 66.667 2.18 0.00 0.00 2.90
2822 2889 2.129785 GGGCCGGGTAGACGTACAT 61.130 63.158 2.18 0.00 0.00 2.29
2823 2890 1.066918 GGCCGGGTAGACGTACATG 59.933 63.158 2.18 0.00 0.00 3.21
2838 2917 2.503895 ACATGGGCCTCTTCTTCTTG 57.496 50.000 4.53 0.00 0.00 3.02
2839 2918 1.707427 ACATGGGCCTCTTCTTCTTGT 59.293 47.619 4.53 0.00 0.00 3.16
2840 2919 2.089980 CATGGGCCTCTTCTTCTTGTG 58.910 52.381 4.53 0.00 0.00 3.33
2857 2954 8.195436 TCTTCTTGTGTACTATGGTAATGTAGC 58.805 37.037 0.00 0.00 0.00 3.58
2936 3034 3.578716 TGCTGTCCTTACTGTTCTTAGCT 59.421 43.478 0.00 0.00 0.00 3.32
2955 3053 7.924412 TCTTAGCTGGGTAGATGTTTAATTACG 59.076 37.037 0.00 0.00 0.00 3.18
2956 3054 5.985911 AGCTGGGTAGATGTTTAATTACGT 58.014 37.500 0.00 0.00 0.00 3.57
2957 3055 7.116075 AGCTGGGTAGATGTTTAATTACGTA 57.884 36.000 0.00 0.00 0.00 3.57
2958 3056 7.208080 AGCTGGGTAGATGTTTAATTACGTAG 58.792 38.462 0.00 0.00 0.00 3.51
2960 3058 7.493645 GCTGGGTAGATGTTTAATTACGTAGTT 59.506 37.037 8.47 8.47 37.78 2.24
2961 3059 9.374838 CTGGGTAGATGTTTAATTACGTAGTTT 57.625 33.333 8.72 3.62 37.78 2.66
2962 3060 9.723601 TGGGTAGATGTTTAATTACGTAGTTTT 57.276 29.630 8.72 1.21 37.78 2.43
3032 3130 2.423538 AGTGTGACAGTTTTCTTGTGCC 59.576 45.455 0.00 0.00 0.00 5.01
3036 3134 2.092429 TGACAGTTTTCTTGTGCCTCCT 60.092 45.455 0.00 0.00 0.00 3.69
3059 3157 3.808466 TTGCTGCCTAGAGATGTACTG 57.192 47.619 0.00 0.00 0.00 2.74
3112 3220 9.725019 AAGTATCAGTTGTGTTAGAATTGATCA 57.275 29.630 0.00 0.00 33.35 2.92
3121 3229 6.037720 TGTGTTAGAATTGATCACACGTTGTT 59.962 34.615 0.00 0.00 37.63 2.83
3176 3284 0.178975 TTTGTGCTTTGATCGGGGGT 60.179 50.000 0.00 0.00 0.00 4.95
3178 3286 0.916086 TGTGCTTTGATCGGGGGTAT 59.084 50.000 0.00 0.00 0.00 2.73
3195 3303 3.502979 GGGTATGCCAAAACTAACGTTCA 59.497 43.478 2.82 0.00 36.17 3.18
3201 3309 4.156190 TGCCAAAACTAACGTTCAGTTTCA 59.844 37.500 23.63 18.15 43.62 2.69
3205 3313 5.729974 AAACTAACGTTCAGTTTCAGTCC 57.270 39.130 20.50 0.00 41.26 3.85
3208 3316 4.586001 ACTAACGTTCAGTTTCAGTCCCTA 59.414 41.667 2.82 0.00 43.86 3.53
3228 3336 1.503294 GCTCCTTAGCGCTATTCACC 58.497 55.000 19.60 3.61 39.39 4.02
3229 3337 1.772182 CTCCTTAGCGCTATTCACCG 58.228 55.000 19.60 2.50 0.00 4.94
3230 3338 1.067212 CTCCTTAGCGCTATTCACCGT 59.933 52.381 19.60 0.00 0.00 4.83
3231 3339 1.202371 TCCTTAGCGCTATTCACCGTG 60.202 52.381 19.60 1.24 0.00 4.94
3232 3340 0.577269 CTTAGCGCTATTCACCGTGC 59.423 55.000 19.60 0.00 36.93 5.34
3237 3345 1.719780 GCGCTATTCACCGTGCTATAC 59.280 52.381 0.00 0.00 34.05 1.47
3251 3359 4.263209 CGTGCTATACAAGAAGAGAACGTG 59.737 45.833 0.00 0.00 0.00 4.49
3255 3363 2.604046 ACAAGAAGAGAACGTGCACT 57.396 45.000 16.19 0.00 0.00 4.40
3276 3384 7.087409 CACTTTTGCATGGTTGAGATATACA 57.913 36.000 0.00 0.00 0.00 2.29
3287 3395 2.090775 TGAGATATACAGGCTGGACCCA 60.091 50.000 20.34 0.00 40.58 4.51
3289 3397 3.584848 GAGATATACAGGCTGGACCCAAT 59.415 47.826 20.34 2.35 40.58 3.16
3290 3398 4.763355 AGATATACAGGCTGGACCCAATA 58.237 43.478 20.34 0.00 40.58 1.90
3291 3399 5.353986 AGATATACAGGCTGGACCCAATAT 58.646 41.667 20.34 4.36 40.58 1.28
3292 3400 6.512120 AGATATACAGGCTGGACCCAATATA 58.488 40.000 20.34 9.94 40.58 0.86
3293 3401 7.142364 AGATATACAGGCTGGACCCAATATAT 58.858 38.462 20.34 14.01 40.58 0.86
3315 3423 1.136500 GACTCCTAACCACCGATCCAC 59.864 57.143 0.00 0.00 0.00 4.02
3332 3440 5.683743 CGATCCACAAAAAGAAACGCTAAAA 59.316 36.000 0.00 0.00 0.00 1.52
3335 3443 5.105675 TCCACAAAAAGAAACGCTAAAAGGT 60.106 36.000 0.00 0.00 0.00 3.50
3341 3449 9.078753 CAAAAAGAAACGCTAAAAGGTTAGAAA 57.921 29.630 0.00 0.00 39.36 2.52
3344 3452 4.761235 AACGCTAAAAGGTTAGAAAGCC 57.239 40.909 0.00 0.00 39.36 4.35
3350 3458 5.063186 GCTAAAAGGTTAGAAAGCCGTCTAC 59.937 44.000 0.00 0.00 39.36 2.59
3351 3459 3.606595 AAGGTTAGAAAGCCGTCTACC 57.393 47.619 0.00 0.00 29.70 3.18
3352 3460 2.532843 AGGTTAGAAAGCCGTCTACCA 58.467 47.619 0.00 0.00 29.70 3.25
3353 3461 2.233186 AGGTTAGAAAGCCGTCTACCAC 59.767 50.000 0.00 3.31 29.70 4.16
3354 3462 2.614779 GTTAGAAAGCCGTCTACCACC 58.385 52.381 0.00 0.00 29.70 4.61
3355 3463 1.927487 TAGAAAGCCGTCTACCACCA 58.073 50.000 0.00 0.00 0.00 4.17
3356 3464 0.320697 AGAAAGCCGTCTACCACCAC 59.679 55.000 0.00 0.00 0.00 4.16
3357 3465 0.672711 GAAAGCCGTCTACCACCACC 60.673 60.000 0.00 0.00 0.00 4.61
3358 3466 2.444700 AAAGCCGTCTACCACCACCG 62.445 60.000 0.00 0.00 0.00 4.94
3359 3467 4.446413 GCCGTCTACCACCACCGG 62.446 72.222 0.00 0.00 41.50 5.28
3362 3470 4.446413 GTCTACCACCACCGGCCG 62.446 72.222 21.04 21.04 0.00 6.13
3377 3485 4.720902 CCGCCACATCAGTGCCCA 62.721 66.667 0.00 0.00 44.53 5.36
3378 3486 2.438975 CGCCACATCAGTGCCCAT 60.439 61.111 0.00 0.00 44.53 4.00
3391 3499 2.353610 GCCCATGGCTTCCTGTTGG 61.354 63.158 6.09 0.00 46.69 3.77
3393 3501 2.703798 CCATGGCTTCCTGTTGGCG 61.704 63.158 0.00 0.00 0.00 5.69
3394 3502 2.361610 ATGGCTTCCTGTTGGCGG 60.362 61.111 0.00 0.00 0.00 6.13
3395 3503 3.944250 ATGGCTTCCTGTTGGCGGG 62.944 63.158 0.00 0.00 42.59 6.13
3399 3507 4.344865 TTCCTGTTGGCGGGCTCC 62.345 66.667 2.38 0.00 40.99 4.70
3406 3514 3.916438 TTGGCGGGCTCCTGGACTA 62.916 63.158 2.38 0.00 0.00 2.59
3407 3515 3.541713 GGCGGGCTCCTGGACTAG 61.542 72.222 0.00 0.00 0.00 2.57
3408 3516 2.760385 GCGGGCTCCTGGACTAGT 60.760 66.667 0.00 0.00 0.00 2.57
3419 3534 2.355513 CCTGGACTAGTTGCTGCATCTT 60.356 50.000 17.46 1.81 0.00 2.40
3469 5528 2.280457 GCGCTCCCTGCCATCTAC 60.280 66.667 0.00 0.00 38.78 2.59
3501 5560 4.803908 GCTGCCCTTCTTCCCCGG 62.804 72.222 0.00 0.00 0.00 5.73
3519 5578 1.375908 GCCATGTCTTCACTGCCGA 60.376 57.895 0.00 0.00 0.00 5.54
3527 5586 1.831652 CTTCACTGCCGAAGACCCCT 61.832 60.000 2.33 0.00 44.32 4.79
3529 5588 0.970937 TCACTGCCGAAGACCCCTAG 60.971 60.000 0.00 0.00 0.00 3.02
3560 5619 2.247635 TGGGCTATCTTCTACTGGTCCT 59.752 50.000 0.00 0.00 0.00 3.85
3572 5631 1.303236 TGGTCCTTGCCAATCACGG 60.303 57.895 0.00 0.00 35.25 4.94
3582 5641 1.732259 GCCAATCACGGTTAGTCACTG 59.268 52.381 0.00 0.00 37.84 3.66
3584 5643 1.732259 CAATCACGGTTAGTCACTGCC 59.268 52.381 0.00 0.00 34.68 4.85
3589 5648 2.552315 CACGGTTAGTCACTGCCATTTT 59.448 45.455 0.00 0.00 34.68 1.82
3596 5655 4.445452 AGTCACTGCCATTTTGCATAAG 57.555 40.909 0.00 0.00 41.16 1.73
3609 5668 8.253113 CCATTTTGCATAAGAGGTGTTCTAATT 58.747 33.333 0.00 0.00 34.14 1.40
3686 5745 7.504238 AGTTGAACCTACCACATGTTTTCAATA 59.496 33.333 0.00 0.00 34.36 1.90
3692 5751 8.357402 ACCTACCACATGTTTTCAATAAAAGAC 58.643 33.333 0.00 0.00 35.29 3.01
3718 5777 3.587797 TGAGTAACTAGGGAACGCTTG 57.412 47.619 0.00 0.00 0.00 4.01
3736 5795 5.472137 ACGCTTGTGTACATTCCTGTTTATT 59.528 36.000 0.00 0.00 36.79 1.40
3764 5823 9.124807 TCTTATTGTTTGTATATATGCGTCTCG 57.875 33.333 0.00 0.00 0.00 4.04
3765 5824 8.806177 TTATTGTTTGTATATATGCGTCTCGT 57.194 30.769 0.00 0.00 0.00 4.18
3766 5825 6.505039 TTGTTTGTATATATGCGTCTCGTG 57.495 37.500 0.00 0.00 0.00 4.35
3767 5826 5.823353 TGTTTGTATATATGCGTCTCGTGA 58.177 37.500 0.00 0.00 0.00 4.35
3768 5827 5.912955 TGTTTGTATATATGCGTCTCGTGAG 59.087 40.000 0.00 0.00 0.00 3.51
3769 5828 5.934935 TTGTATATATGCGTCTCGTGAGA 57.065 39.130 0.00 0.00 39.12 3.27
3770 5829 6.496338 TTGTATATATGCGTCTCGTGAGAT 57.504 37.500 2.42 0.00 39.97 2.75
3771 5830 7.605410 TTGTATATATGCGTCTCGTGAGATA 57.395 36.000 2.42 0.00 39.97 1.98
3772 5831 7.235430 TGTATATATGCGTCTCGTGAGATAG 57.765 40.000 2.42 2.34 39.97 2.08
3773 5832 2.971430 TATGCGTCTCGTGAGATAGC 57.029 50.000 17.64 17.64 39.97 2.97
3774 5833 2.477880 TGCGTCTCGTGAGATAGCA 58.522 52.632 21.07 21.07 44.99 3.49
3775 5834 0.098905 TGCGTCTCGTGAGATAGCAC 59.901 55.000 21.07 3.19 43.58 4.40
3776 5835 0.592754 GCGTCTCGTGAGATAGCACC 60.593 60.000 18.82 0.77 40.85 5.01
3777 5836 0.733150 CGTCTCGTGAGATAGCACCA 59.267 55.000 2.42 0.00 39.97 4.17
3778 5837 1.335182 CGTCTCGTGAGATAGCACCAT 59.665 52.381 2.42 0.00 39.97 3.55
3779 5838 2.603412 CGTCTCGTGAGATAGCACCATC 60.603 54.545 2.42 0.00 39.97 3.51
3780 5839 2.621055 GTCTCGTGAGATAGCACCATCT 59.379 50.000 2.42 0.00 39.97 2.90
3781 5840 2.620585 TCTCGTGAGATAGCACCATCTG 59.379 50.000 0.00 0.00 40.84 2.90
3782 5841 2.620585 CTCGTGAGATAGCACCATCTGA 59.379 50.000 0.72 0.00 40.84 3.27
3783 5842 2.359214 TCGTGAGATAGCACCATCTGAC 59.641 50.000 0.72 2.29 36.25 3.51
3784 5843 2.360483 CGTGAGATAGCACCATCTGACT 59.640 50.000 9.61 0.00 37.11 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.606965 GCTTTAATAGCCGTGTGTTAAAAC 57.393 37.500 0.00 0.00 44.48 2.43
40 41 6.467677 TCTACTAGCAGAACATGAAAGCTTT 58.532 36.000 12.53 12.53 36.80 3.51
155 159 3.700538 TGGCTTGCTTGATACCTTGATT 58.299 40.909 0.00 0.00 0.00 2.57
167 171 0.318955 GACGCAACATTGGCTTGCTT 60.319 50.000 9.48 1.65 41.64 3.91
190 194 1.452953 TATGTAGCCCGGTCGAGCAG 61.453 60.000 15.89 2.64 0.00 4.24
192 196 1.132643 CTATATGTAGCCCGGTCGAGC 59.867 57.143 4.06 4.06 0.00 5.03
217 230 6.993902 ACTCGAAAAGAAATAAACAGTGGGTA 59.006 34.615 0.00 0.00 0.00 3.69
219 232 6.017440 TGACTCGAAAAGAAATAAACAGTGGG 60.017 38.462 0.00 0.00 0.00 4.61
228 241 9.458374 GGTTCAAAATTGACTCGAAAAGAAATA 57.542 29.630 0.00 0.00 36.83 1.40
272 285 2.035832 GTGGCTAAGGCTGCAAGAAAAA 59.964 45.455 0.50 0.00 38.73 1.94
303 316 1.155889 TGTCTAATGTGTGCTTGCCG 58.844 50.000 0.00 0.00 0.00 5.69
475 490 9.160496 GCATGTCCTATCTTAATTAAGAGATGG 57.840 37.037 27.18 25.25 44.67 3.51
533 548 8.862091 TTTTAAACCCCACCCATATATTGATT 57.138 30.769 0.00 0.00 0.00 2.57
538 553 8.348354 TCTTTCTTTTAAACCCCACCCATATAT 58.652 33.333 0.00 0.00 0.00 0.86
539 554 7.710579 TCTTTCTTTTAAACCCCACCCATATA 58.289 34.615 0.00 0.00 0.00 0.86
540 555 6.566914 TCTTTCTTTTAAACCCCACCCATAT 58.433 36.000 0.00 0.00 0.00 1.78
541 556 5.966684 TCTTTCTTTTAAACCCCACCCATA 58.033 37.500 0.00 0.00 0.00 2.74
542 557 4.821940 TCTTTCTTTTAAACCCCACCCAT 58.178 39.130 0.00 0.00 0.00 4.00
543 558 4.267341 TCTTTCTTTTAAACCCCACCCA 57.733 40.909 0.00 0.00 0.00 4.51
544 559 5.305902 TGATTCTTTCTTTTAAACCCCACCC 59.694 40.000 0.00 0.00 0.00 4.61
545 560 6.413783 TGATTCTTTCTTTTAAACCCCACC 57.586 37.500 0.00 0.00 0.00 4.61
546 561 8.902540 AAATGATTCTTTCTTTTAAACCCCAC 57.097 30.769 0.00 0.00 31.80 4.61
621 636 9.956640 ACATTCATTAAAATTCCTTAATTGGCA 57.043 25.926 0.00 0.00 35.46 4.92
715 730 9.392259 AGCGTATATTAGTATCATGTAGTAGCA 57.608 33.333 0.00 0.00 0.00 3.49
719 734 9.676861 TGGTAGCGTATATTAGTATCATGTAGT 57.323 33.333 0.00 0.00 0.00 2.73
722 737 7.921214 GCATGGTAGCGTATATTAGTATCATGT 59.079 37.037 0.00 0.00 32.37 3.21
723 738 7.920682 TGCATGGTAGCGTATATTAGTATCATG 59.079 37.037 0.00 0.00 37.31 3.07
724 739 8.007405 TGCATGGTAGCGTATATTAGTATCAT 57.993 34.615 0.00 0.00 37.31 2.45
725 740 7.399245 TGCATGGTAGCGTATATTAGTATCA 57.601 36.000 0.00 0.00 37.31 2.15
726 741 8.873215 ATTGCATGGTAGCGTATATTAGTATC 57.127 34.615 0.00 0.00 37.31 2.24
727 742 9.967346 CTATTGCATGGTAGCGTATATTAGTAT 57.033 33.333 0.00 0.00 37.31 2.12
728 743 9.181061 TCTATTGCATGGTAGCGTATATTAGTA 57.819 33.333 0.00 0.00 37.31 1.82
729 744 8.063200 TCTATTGCATGGTAGCGTATATTAGT 57.937 34.615 0.00 0.00 37.31 2.24
730 745 8.926715 TTCTATTGCATGGTAGCGTATATTAG 57.073 34.615 0.00 0.00 37.31 1.73
731 746 9.366216 CTTTCTATTGCATGGTAGCGTATATTA 57.634 33.333 0.00 0.00 37.31 0.98
732 747 8.094548 TCTTTCTATTGCATGGTAGCGTATATT 58.905 33.333 0.00 0.00 37.31 1.28
733 748 7.611770 TCTTTCTATTGCATGGTAGCGTATAT 58.388 34.615 0.00 0.00 37.31 0.86
734 749 6.988522 TCTTTCTATTGCATGGTAGCGTATA 58.011 36.000 0.00 0.00 37.31 1.47
735 750 5.853936 TCTTTCTATTGCATGGTAGCGTAT 58.146 37.500 0.00 0.00 37.31 3.06
736 751 5.270893 TCTTTCTATTGCATGGTAGCGTA 57.729 39.130 0.00 0.00 37.31 4.42
737 752 4.137116 TCTTTCTATTGCATGGTAGCGT 57.863 40.909 0.00 0.00 37.31 5.07
738 753 6.974932 ATATCTTTCTATTGCATGGTAGCG 57.025 37.500 0.00 0.00 37.31 4.26
739 754 9.605275 TCATATATCTTTCTATTGCATGGTAGC 57.395 33.333 0.00 0.00 0.00 3.58
742 757 9.224267 GTGTCATATATCTTTCTATTGCATGGT 57.776 33.333 0.00 0.00 0.00 3.55
743 758 9.445878 AGTGTCATATATCTTTCTATTGCATGG 57.554 33.333 0.00 0.00 0.00 3.66
769 784 9.831682 TGGTGGTAATGGAAGTATCATATACTA 57.168 33.333 0.21 0.00 26.62 1.82
770 785 8.736097 TGGTGGTAATGGAAGTATCATATACT 57.264 34.615 0.00 0.00 26.62 2.12
771 786 8.812972 TCTGGTGGTAATGGAAGTATCATATAC 58.187 37.037 0.00 0.00 26.62 1.47
772 787 8.812972 GTCTGGTGGTAATGGAAGTATCATATA 58.187 37.037 0.00 0.00 26.62 0.86
773 788 7.514127 AGTCTGGTGGTAATGGAAGTATCATAT 59.486 37.037 0.00 0.00 26.62 1.78
774 789 6.844388 AGTCTGGTGGTAATGGAAGTATCATA 59.156 38.462 0.00 0.00 26.62 2.15
775 790 5.667626 AGTCTGGTGGTAATGGAAGTATCAT 59.332 40.000 0.00 0.00 26.62 2.45
776 791 5.030147 AGTCTGGTGGTAATGGAAGTATCA 58.970 41.667 0.00 0.00 0.00 2.15
777 792 5.615925 AGTCTGGTGGTAATGGAAGTATC 57.384 43.478 0.00 0.00 0.00 2.24
778 793 6.901300 TCTAAGTCTGGTGGTAATGGAAGTAT 59.099 38.462 0.00 0.00 0.00 2.12
779 794 6.154021 GTCTAAGTCTGGTGGTAATGGAAGTA 59.846 42.308 0.00 0.00 0.00 2.24
780 795 5.046520 GTCTAAGTCTGGTGGTAATGGAAGT 60.047 44.000 0.00 0.00 0.00 3.01
781 796 5.046591 TGTCTAAGTCTGGTGGTAATGGAAG 60.047 44.000 0.00 0.00 0.00 3.46
782 797 4.841813 TGTCTAAGTCTGGTGGTAATGGAA 59.158 41.667 0.00 0.00 0.00 3.53
783 798 4.222145 GTGTCTAAGTCTGGTGGTAATGGA 59.778 45.833 0.00 0.00 0.00 3.41
784 799 4.223032 AGTGTCTAAGTCTGGTGGTAATGG 59.777 45.833 0.00 0.00 0.00 3.16
785 800 5.047306 TCAGTGTCTAAGTCTGGTGGTAATG 60.047 44.000 0.00 0.00 0.00 1.90
786 801 5.084519 TCAGTGTCTAAGTCTGGTGGTAAT 58.915 41.667 0.00 0.00 0.00 1.89
787 802 4.476297 TCAGTGTCTAAGTCTGGTGGTAA 58.524 43.478 0.00 0.00 0.00 2.85
788 803 4.079970 CTCAGTGTCTAAGTCTGGTGGTA 58.920 47.826 0.00 0.00 0.00 3.25
789 804 2.894126 CTCAGTGTCTAAGTCTGGTGGT 59.106 50.000 0.00 0.00 0.00 4.16
790 805 3.157881 TCTCAGTGTCTAAGTCTGGTGG 58.842 50.000 0.00 0.00 0.00 4.61
791 806 5.163602 GGTATCTCAGTGTCTAAGTCTGGTG 60.164 48.000 0.00 0.00 0.00 4.17
792 807 4.951094 GGTATCTCAGTGTCTAAGTCTGGT 59.049 45.833 0.00 0.00 0.00 4.00
793 808 4.950475 TGGTATCTCAGTGTCTAAGTCTGG 59.050 45.833 0.00 0.00 0.00 3.86
794 809 6.319911 TGATGGTATCTCAGTGTCTAAGTCTG 59.680 42.308 0.00 0.00 0.00 3.51
795 810 6.320164 GTGATGGTATCTCAGTGTCTAAGTCT 59.680 42.308 0.00 0.00 0.00 3.24
796 811 6.320164 AGTGATGGTATCTCAGTGTCTAAGTC 59.680 42.308 0.00 0.00 0.00 3.01
797 812 6.191315 AGTGATGGTATCTCAGTGTCTAAGT 58.809 40.000 0.00 0.00 0.00 2.24
798 813 6.707440 AGTGATGGTATCTCAGTGTCTAAG 57.293 41.667 0.00 0.00 0.00 2.18
799 814 7.482169 AAAGTGATGGTATCTCAGTGTCTAA 57.518 36.000 0.00 0.00 0.00 2.10
800 815 7.614192 TGTAAAGTGATGGTATCTCAGTGTCTA 59.386 37.037 0.00 0.00 0.00 2.59
801 816 6.437477 TGTAAAGTGATGGTATCTCAGTGTCT 59.563 38.462 0.00 0.00 0.00 3.41
802 817 6.631016 TGTAAAGTGATGGTATCTCAGTGTC 58.369 40.000 0.00 0.00 0.00 3.67
803 818 6.605471 TGTAAAGTGATGGTATCTCAGTGT 57.395 37.500 0.00 0.00 0.00 3.55
804 819 7.765819 TCAATGTAAAGTGATGGTATCTCAGTG 59.234 37.037 0.00 0.00 0.00 3.66
805 820 7.766278 GTCAATGTAAAGTGATGGTATCTCAGT 59.234 37.037 0.00 0.00 0.00 3.41
806 821 7.984050 AGTCAATGTAAAGTGATGGTATCTCAG 59.016 37.037 0.00 0.00 0.00 3.35
807 822 7.851228 AGTCAATGTAAAGTGATGGTATCTCA 58.149 34.615 0.00 0.00 0.00 3.27
814 829 3.063997 GCCGAGTCAATGTAAAGTGATGG 59.936 47.826 0.00 0.00 0.00 3.51
828 843 1.202486 CCTTTTATAGCGGCCGAGTCA 60.202 52.381 33.48 10.42 0.00 3.41
931 947 3.536570 GAATGGGAAGAACACTAGGAGC 58.463 50.000 0.00 0.00 0.00 4.70
1110 1126 4.719369 ACGACCAAGACGGCGAGC 62.719 66.667 16.62 4.95 39.03 5.03
1118 1134 2.050714 GCGACGTGACGACCAAGA 60.051 61.111 13.70 0.00 35.09 3.02
1122 1138 3.735029 AGGAGCGACGTGACGACC 61.735 66.667 13.70 6.88 35.09 4.79
1191 1207 2.353610 GCCAATGCCCAGACCCTTG 61.354 63.158 0.00 0.00 0.00 3.61
1696 1715 2.772691 CCTCGTCCAGCTCGTACCC 61.773 68.421 0.00 0.00 0.00 3.69
1731 1753 3.322318 AAGGCTCTTCAGCTCCGCC 62.322 63.158 0.00 0.00 46.03 6.13
1749 1771 3.970721 TCGTAGCCTTCGTCGACA 58.029 55.556 17.16 0.00 0.00 4.35
1968 1999 2.750637 ATGTCGGCGTCGGAGAGT 60.751 61.111 10.62 0.00 36.95 3.24
1995 2026 1.933021 ACGGTGAACATACCCAGAGA 58.067 50.000 0.00 0.00 37.44 3.10
2011 2042 6.870965 TCCATTCATGTTTTCCATTTAAACGG 59.129 34.615 0.00 0.00 38.11 4.44
2014 2050 7.017056 AGGGTCCATTCATGTTTTCCATTTAAA 59.983 33.333 0.00 0.00 0.00 1.52
2056 2123 5.163953 CGTTATGAGCAAGCTAATTATCCGG 60.164 44.000 0.00 0.00 0.00 5.14
2097 2164 9.364989 AGAAAACATTTCTCGTCATTTCAAAAA 57.635 25.926 0.00 0.00 0.00 1.94
2098 2165 8.806634 CAGAAAACATTTCTCGTCATTTCAAAA 58.193 29.630 2.47 0.00 0.00 2.44
2099 2166 7.973388 ACAGAAAACATTTCTCGTCATTTCAAA 59.027 29.630 2.47 0.00 0.00 2.69
2100 2167 7.431960 CACAGAAAACATTTCTCGTCATTTCAA 59.568 33.333 2.47 0.00 0.00 2.69
2101 2168 6.912051 CACAGAAAACATTTCTCGTCATTTCA 59.088 34.615 2.47 0.00 0.00 2.69
2102 2169 6.912591 ACACAGAAAACATTTCTCGTCATTTC 59.087 34.615 2.47 0.00 0.00 2.17
2103 2170 6.692681 CACACAGAAAACATTTCTCGTCATTT 59.307 34.615 2.47 0.00 0.00 2.32
2104 2171 6.201517 CACACAGAAAACATTTCTCGTCATT 58.798 36.000 2.47 0.00 0.00 2.57
2105 2172 5.277974 CCACACAGAAAACATTTCTCGTCAT 60.278 40.000 2.47 0.00 0.00 3.06
2106 2173 4.035091 CCACACAGAAAACATTTCTCGTCA 59.965 41.667 2.47 0.00 0.00 4.35
2107 2174 4.527564 CCACACAGAAAACATTTCTCGTC 58.472 43.478 2.47 0.00 0.00 4.20
2108 2175 3.315191 CCCACACAGAAAACATTTCTCGT 59.685 43.478 2.47 1.50 0.00 4.18
2109 2176 3.315191 ACCCACACAGAAAACATTTCTCG 59.685 43.478 2.47 0.95 0.00 4.04
2110 2177 4.918810 ACCCACACAGAAAACATTTCTC 57.081 40.909 2.47 0.00 0.00 2.87
2111 2178 4.680440 GCAACCCACACAGAAAACATTTCT 60.680 41.667 0.00 0.00 0.00 2.52
2223 2290 1.277580 CCAGCTCCTCATGGACCCTT 61.278 60.000 0.00 0.00 39.02 3.95
2232 2299 3.846405 AACCCGGTCCAGCTCCTCA 62.846 63.158 0.00 0.00 0.00 3.86
2288 2355 0.800300 CTGGAGAAAGACGAGCGAGC 60.800 60.000 0.00 0.00 0.00 5.03
2326 2393 4.196778 TGGTGGGTGAAGGCGCAA 62.197 61.111 10.83 0.00 33.14 4.85
2480 2547 1.305201 GAACCGTTCTGGCTTGAACA 58.695 50.000 18.51 0.00 44.59 3.18
2532 2599 1.149101 TTCCAAAGAACTCAGCCCCT 58.851 50.000 0.00 0.00 0.00 4.79
2808 2875 1.066918 GCCCATGTACGTCTACCCG 59.933 63.158 0.00 0.00 0.00 5.28
2819 2886 1.707427 ACAAGAAGAAGAGGCCCATGT 59.293 47.619 0.00 0.00 0.00 3.21
2820 2887 2.089980 CACAAGAAGAAGAGGCCCATG 58.910 52.381 0.00 0.00 0.00 3.66
2821 2888 1.707427 ACACAAGAAGAAGAGGCCCAT 59.293 47.619 0.00 0.00 0.00 4.00
2822 2889 1.140312 ACACAAGAAGAAGAGGCCCA 58.860 50.000 0.00 0.00 0.00 5.36
2823 2890 2.303311 AGTACACAAGAAGAAGAGGCCC 59.697 50.000 0.00 0.00 0.00 5.80
2838 2917 5.218139 GGACGCTACATTACCATAGTACAC 58.782 45.833 0.00 0.00 0.00 2.90
2839 2918 4.279169 GGGACGCTACATTACCATAGTACA 59.721 45.833 0.00 0.00 0.00 2.90
2840 2919 4.802999 GGGACGCTACATTACCATAGTAC 58.197 47.826 0.00 0.00 0.00 2.73
2936 3034 9.723601 AAAACTACGTAATTAAACATCTACCCA 57.276 29.630 0.00 0.00 0.00 4.51
2962 3060 8.497554 ACTACTCGTAATTAAACATCGCAAAAA 58.502 29.630 0.00 0.00 0.00 1.94
2963 3061 8.020861 ACTACTCGTAATTAAACATCGCAAAA 57.979 30.769 0.00 0.00 0.00 2.44
2964 3062 7.585286 ACTACTCGTAATTAAACATCGCAAA 57.415 32.000 0.00 0.00 0.00 3.68
2965 3063 7.585286 AACTACTCGTAATTAAACATCGCAA 57.415 32.000 0.00 0.00 0.00 4.85
2966 3064 8.748582 CATAACTACTCGTAATTAAACATCGCA 58.251 33.333 0.00 0.00 0.00 5.10
2967 3065 8.961092 TCATAACTACTCGTAATTAAACATCGC 58.039 33.333 0.00 0.00 0.00 4.58
3007 3105 3.689649 ACAAGAAAACTGTCACACTCACC 59.310 43.478 0.00 0.00 0.00 4.02
3032 3130 1.552337 TCTCTAGGCAGCAAACAGGAG 59.448 52.381 0.00 0.00 0.00 3.69
3036 3134 3.515502 AGTACATCTCTAGGCAGCAAACA 59.484 43.478 0.00 0.00 0.00 2.83
3076 3183 5.874810 ACACAACTGATACTTGCATTACGAT 59.125 36.000 0.00 0.00 0.00 3.73
3077 3184 5.234752 ACACAACTGATACTTGCATTACGA 58.765 37.500 0.00 0.00 0.00 3.43
3078 3185 5.530519 ACACAACTGATACTTGCATTACG 57.469 39.130 0.00 0.00 0.00 3.18
3079 3186 8.251750 TCTAACACAACTGATACTTGCATTAC 57.748 34.615 0.00 0.00 0.00 1.89
3112 3220 3.005050 TCTCTCGGTCAATAACAACGTGT 59.995 43.478 0.00 0.00 0.00 4.49
3121 3229 3.141460 TCCCCCTATTCTCTCGGTCAATA 59.859 47.826 0.00 0.00 0.00 1.90
3155 3263 1.067635 CCCCCGATCAAAGCACAAAAG 60.068 52.381 0.00 0.00 0.00 2.27
3176 3284 6.038382 TGAAACTGAACGTTAGTTTTGGCATA 59.962 34.615 23.96 12.24 45.52 3.14
3178 3286 4.156190 TGAAACTGAACGTTAGTTTTGGCA 59.844 37.500 23.96 18.34 45.52 4.92
3195 3303 2.632763 AGGAGCTAGGGACTGAAACT 57.367 50.000 0.00 0.00 41.52 2.66
3201 3309 3.494815 AGCGCTAAGGAGCTAGGGACT 62.495 57.143 8.99 0.00 46.23 3.85
3219 3327 4.617959 TCTTGTATAGCACGGTGAATAGC 58.382 43.478 13.29 0.00 0.00 2.97
3228 3336 4.263209 CACGTTCTCTTCTTGTATAGCACG 59.737 45.833 0.00 0.00 0.00 5.34
3229 3337 4.031878 GCACGTTCTCTTCTTGTATAGCAC 59.968 45.833 0.00 0.00 0.00 4.40
3230 3338 4.174009 GCACGTTCTCTTCTTGTATAGCA 58.826 43.478 0.00 0.00 0.00 3.49
3231 3339 4.031878 GTGCACGTTCTCTTCTTGTATAGC 59.968 45.833 0.00 0.00 0.00 2.97
3232 3340 5.403246 AGTGCACGTTCTCTTCTTGTATAG 58.597 41.667 12.01 0.00 0.00 1.31
3237 3345 3.951979 AAAGTGCACGTTCTCTTCTTG 57.048 42.857 12.50 0.00 0.00 3.02
3255 3363 5.067674 GCCTGTATATCTCAACCATGCAAAA 59.932 40.000 0.00 0.00 0.00 2.44
3263 3371 3.244249 GGTCCAGCCTGTATATCTCAACC 60.244 52.174 0.00 0.00 0.00 3.77
3265 3373 2.972713 GGGTCCAGCCTGTATATCTCAA 59.027 50.000 0.00 0.00 37.43 3.02
3276 3384 5.026790 GAGTCTATATATTGGGTCCAGCCT 58.973 45.833 0.00 0.00 37.43 4.58
3287 3395 7.560626 GGATCGGTGGTTAGGAGTCTATATATT 59.439 40.741 0.00 0.00 0.00 1.28
3289 3397 6.012245 TGGATCGGTGGTTAGGAGTCTATATA 60.012 42.308 0.00 0.00 0.00 0.86
3290 3398 5.222275 TGGATCGGTGGTTAGGAGTCTATAT 60.222 44.000 0.00 0.00 0.00 0.86
3291 3399 4.105217 TGGATCGGTGGTTAGGAGTCTATA 59.895 45.833 0.00 0.00 0.00 1.31
3292 3400 3.117246 TGGATCGGTGGTTAGGAGTCTAT 60.117 47.826 0.00 0.00 0.00 1.98
3293 3401 2.242965 TGGATCGGTGGTTAGGAGTCTA 59.757 50.000 0.00 0.00 0.00 2.59
3315 3423 8.623310 TTCTAACCTTTTAGCGTTTCTTTTTG 57.377 30.769 0.00 0.00 35.53 2.44
3332 3440 2.233186 GTGGTAGACGGCTTTCTAACCT 59.767 50.000 8.60 0.00 35.23 3.50
3335 3443 2.028748 GTGGTGGTAGACGGCTTTCTAA 60.029 50.000 0.00 0.00 29.70 2.10
3341 3449 3.379445 CGGTGGTGGTAGACGGCT 61.379 66.667 0.00 0.00 0.00 5.52
3344 3452 4.446413 GGCCGGTGGTGGTAGACG 62.446 72.222 1.90 0.00 0.00 4.18
3376 3484 2.703798 CCGCCAACAGGAAGCCATG 61.704 63.158 0.00 0.00 0.00 3.66
3377 3485 2.361610 CCGCCAACAGGAAGCCAT 60.362 61.111 0.00 0.00 0.00 4.40
3378 3486 4.659172 CCCGCCAACAGGAAGCCA 62.659 66.667 0.00 0.00 0.00 4.75
3388 3496 3.916438 TAGTCCAGGAGCCCGCCAA 62.916 63.158 0.00 0.00 0.00 4.52
3391 3499 2.359967 AACTAGTCCAGGAGCCCGC 61.360 63.158 0.00 0.00 0.00 6.13
3393 3501 1.222113 GCAACTAGTCCAGGAGCCC 59.778 63.158 0.00 0.00 0.00 5.19
3394 3502 0.107945 CAGCAACTAGTCCAGGAGCC 60.108 60.000 0.00 0.00 0.00 4.70
3395 3503 0.742635 GCAGCAACTAGTCCAGGAGC 60.743 60.000 0.00 0.00 0.00 4.70
3396 3504 0.610174 TGCAGCAACTAGTCCAGGAG 59.390 55.000 0.00 0.00 0.00 3.69
3397 3505 1.208052 GATGCAGCAACTAGTCCAGGA 59.792 52.381 0.00 0.00 0.00 3.86
3399 3507 2.687700 AGATGCAGCAACTAGTCCAG 57.312 50.000 4.07 0.00 0.00 3.86
3400 3508 2.302733 TGAAGATGCAGCAACTAGTCCA 59.697 45.455 5.47 0.00 0.00 4.02
3403 3511 2.038952 TGGTGAAGATGCAGCAACTAGT 59.961 45.455 5.47 0.00 42.63 2.57
3404 3512 2.703416 TGGTGAAGATGCAGCAACTAG 58.297 47.619 5.47 0.00 42.63 2.57
3405 3513 2.857186 TGGTGAAGATGCAGCAACTA 57.143 45.000 5.47 0.00 42.63 2.24
3406 3514 3.731716 TGGTGAAGATGCAGCAACT 57.268 47.368 4.07 0.00 42.63 3.16
3456 3571 1.040646 GATGACGTAGATGGCAGGGA 58.959 55.000 0.00 0.00 0.00 4.20
3457 3572 0.034059 GGATGACGTAGATGGCAGGG 59.966 60.000 0.00 0.00 0.00 4.45
3459 3574 1.269988 CCTGGATGACGTAGATGGCAG 60.270 57.143 0.00 0.00 0.00 4.85
3460 3575 0.752658 CCTGGATGACGTAGATGGCA 59.247 55.000 0.00 0.00 0.00 4.92
3469 5528 1.742880 CAGCACCACCTGGATGACG 60.743 63.158 0.00 0.00 38.94 4.35
3501 5560 0.955428 TTCGGCAGTGAAGACATGGC 60.955 55.000 0.00 0.00 36.25 4.40
3519 5578 2.301738 GGCTGCACCTAGGGGTCTT 61.302 63.158 13.95 0.00 45.41 3.01
3524 5583 2.194056 CCATGGCTGCACCTAGGG 59.806 66.667 14.81 3.13 40.22 3.53
3554 5613 4.395519 CGTGATTGGCAAGGACCA 57.604 55.556 5.96 0.00 38.16 4.02
3560 5619 2.147958 GTGACTAACCGTGATTGGCAA 58.852 47.619 0.68 0.68 0.00 4.52
3572 5631 3.641437 TGCAAAATGGCAGTGACTAAC 57.359 42.857 0.00 0.00 39.25 2.34
3582 5641 3.874392 ACACCTCTTATGCAAAATGGC 57.126 42.857 0.00 0.00 0.00 4.40
3589 5648 8.704668 TCTCATAATTAGAACACCTCTTATGCA 58.295 33.333 0.00 0.00 34.21 3.96
3648 5707 9.530633 GTGGTAGGTTCAACTTGTTAGATATAG 57.469 37.037 0.00 0.00 0.00 1.31
3660 5719 5.197451 TGAAAACATGTGGTAGGTTCAACT 58.803 37.500 0.00 0.00 30.95 3.16
3665 5724 8.919145 TCTTTTATTGAAAACATGTGGTAGGTT 58.081 29.630 0.00 0.00 34.19 3.50
3686 5745 6.099269 TCCCTAGTTACTCAACACTGTCTTTT 59.901 38.462 0.00 0.00 37.10 2.27
3692 5751 4.235360 CGTTCCCTAGTTACTCAACACTG 58.765 47.826 0.00 0.00 37.10 3.66
3743 5802 6.267070 TCACGAGACGCATATATACAAACAA 58.733 36.000 0.00 0.00 0.00 2.83
3744 5803 5.823353 TCACGAGACGCATATATACAAACA 58.177 37.500 0.00 0.00 0.00 2.83
3745 5804 6.140786 TCTCACGAGACGCATATATACAAAC 58.859 40.000 0.00 0.00 31.41 2.93
3746 5805 6.308371 TCTCACGAGACGCATATATACAAA 57.692 37.500 0.00 0.00 31.41 2.83
3747 5806 5.934935 TCTCACGAGACGCATATATACAA 57.065 39.130 0.00 0.00 31.41 2.41
3748 5807 6.238130 GCTATCTCACGAGACGCATATATACA 60.238 42.308 12.70 0.00 40.75 2.29
3749 5808 6.130723 GCTATCTCACGAGACGCATATATAC 58.869 44.000 12.70 0.00 40.75 1.47
3750 5809 5.815740 TGCTATCTCACGAGACGCATATATA 59.184 40.000 15.14 0.00 40.19 0.86
3751 5810 4.636206 TGCTATCTCACGAGACGCATATAT 59.364 41.667 15.14 0.00 40.19 0.86
3752 5811 4.000988 TGCTATCTCACGAGACGCATATA 58.999 43.478 15.14 0.00 40.19 0.86
3753 5812 2.814336 TGCTATCTCACGAGACGCATAT 59.186 45.455 15.14 0.00 40.19 1.78
3754 5813 2.031944 GTGCTATCTCACGAGACGCATA 60.032 50.000 19.58 1.88 43.90 3.14
3755 5814 1.025041 TGCTATCTCACGAGACGCAT 58.975 50.000 15.14 0.00 40.19 4.73
3756 5815 0.098905 GTGCTATCTCACGAGACGCA 59.901 55.000 15.14 15.14 41.69 5.24
3757 5816 0.592754 GGTGCTATCTCACGAGACGC 60.593 60.000 11.32 11.32 40.75 5.19
3758 5817 0.733150 TGGTGCTATCTCACGAGACG 59.267 55.000 0.00 0.00 40.75 4.18
3759 5818 2.621055 AGATGGTGCTATCTCACGAGAC 59.379 50.000 0.00 0.00 40.75 3.36
3760 5819 2.620585 CAGATGGTGCTATCTCACGAGA 59.379 50.000 0.00 0.00 42.37 4.04
3761 5820 2.620585 TCAGATGGTGCTATCTCACGAG 59.379 50.000 0.00 0.00 35.28 4.18
3762 5821 2.359214 GTCAGATGGTGCTATCTCACGA 59.641 50.000 0.00 0.00 35.28 4.35
3763 5822 2.360483 AGTCAGATGGTGCTATCTCACG 59.640 50.000 0.00 0.00 33.92 4.35


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

AutoCloner maintained by Alex Coulton.