Multiple sequence alignment - TraesCS7D01G046000

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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 TraesCS7D01G046000 chr7D 100.000 3325 0 0 1 3325 23494932 23498256 0.000000e+00 6141.0
1 TraesCS7D01G046000 chr7D 85.437 412 58 2 2829 3239 348188574 348188164 8.520000e-116 427.0
2 TraesCS7D01G046000 chr7D 98.795 166 2 0 2663 2828 312574292 312574127 2.510000e-76 296.0
3 TraesCS7D01G046000 chr7D 97.576 165 4 0 2663 2827 56399642 56399806 1.950000e-72 283.0
4 TraesCS7D01G046000 chr4A 91.985 1335 73 19 939 2259 708322568 708321254 0.000000e+00 1842.0
5 TraesCS7D01G046000 chr4A 90.295 814 48 15 2 799 708323660 708322862 0.000000e+00 1037.0
6 TraesCS7D01G046000 chr4A 84.615 312 42 6 98 406 706206057 706205749 4.170000e-79 305.0
7 TraesCS7D01G046000 chr4A 95.055 182 8 1 2654 2835 428284292 428284112 5.430000e-73 285.0
8 TraesCS7D01G046000 chr4A 84.932 219 31 2 2447 2664 15636663 15636880 1.550000e-53 220.0
9 TraesCS7D01G046000 chr4A 91.525 59 5 0 3261 3319 639194250 639194308 7.650000e-12 82.4
10 TraesCS7D01G046000 chr7A 90.386 1373 101 18 985 2347 24592150 24593501 0.000000e+00 1775.0
11 TraesCS7D01G046000 chr7A 93.218 811 31 7 1 799 24591018 24591816 0.000000e+00 1171.0
12 TraesCS7D01G046000 chr7A 82.727 110 18 1 2388 2497 1751118 1751010 2.730000e-16 97.1
13 TraesCS7D01G046000 chr2B 83.897 503 78 3 2826 3325 583918722 583919224 8.350000e-131 477.0
14 TraesCS7D01G046000 chr2B 83.614 415 67 1 2826 3239 20667436 20667850 4.020000e-104 388.0
15 TraesCS7D01G046000 chr2B 80.756 291 46 7 2380 2664 583918437 583918723 5.590000e-53 219.0
16 TraesCS7D01G046000 chr2B 82.143 112 18 1 2388 2497 789676491 789676380 9.820000e-16 95.3
17 TraesCS7D01G046000 chr1B 84.388 474 52 10 2829 3300 632661378 632660925 2.350000e-121 446.0
18 TraesCS7D01G046000 chr3A 83.855 415 65 2 2826 3239 123902019 123902432 8.650000e-106 394.0
19 TraesCS7D01G046000 chr3A 83.600 250 41 0 2412 2661 707082120 707081871 5.550000e-58 235.0
20 TraesCS7D01G046000 chr1D 83.693 417 67 1 2824 3239 372566581 372566165 3.110000e-105 392.0
21 TraesCS7D01G046000 chr1D 83.500 400 65 1 2826 3224 33633408 33633807 4.050000e-99 372.0
22 TraesCS7D01G046000 chr4B 83.455 411 67 1 2829 3238 452737426 452737016 6.730000e-102 381.0
23 TraesCS7D01G046000 chr4B 82.310 277 46 2 2391 2665 484081474 484081199 1.540000e-58 237.0
24 TraesCS7D01G046000 chr4B 82.079 279 46 3 2388 2663 470292997 470292720 5.550000e-58 235.0
25 TraesCS7D01G046000 chr4D 82.567 413 69 3 2829 3239 49517457 49517046 8.770000e-96 361.0
26 TraesCS7D01G046000 chr4D 86.283 226 31 0 2445 2670 502369102 502368877 2.560000e-61 246.0
27 TraesCS7D01G046000 chr4D 86.239 218 30 0 2453 2670 451301484 451301267 1.540000e-58 237.0
28 TraesCS7D01G046000 chr4D 79.577 284 49 5 2388 2670 49517728 49517453 9.410000e-46 195.0
29 TraesCS7D01G046000 chr4D 78.680 197 35 5 2382 2573 337426006 337426200 1.250000e-24 124.0
30 TraesCS7D01G046000 chr6B 80.529 416 51 14 879 1285 643395425 643395031 3.240000e-75 292.0
31 TraesCS7D01G046000 chr2A 97.093 172 5 0 2659 2830 469790204 469790033 1.170000e-74 291.0
32 TraesCS7D01G046000 chr5D 97.576 165 4 0 2663 2827 42949724 42949560 1.950000e-72 283.0
33 TraesCS7D01G046000 chr5D 82.332 283 50 0 2388 2670 424942012 424941730 2.560000e-61 246.0
34 TraesCS7D01G046000 chr5D 83.636 110 18 0 2388 2497 56804010 56803901 1.630000e-18 104.0
35 TraesCS7D01G046000 chr2D 95.954 173 5 2 2655 2827 609886785 609886955 2.530000e-71 279.0
36 TraesCS7D01G046000 chr5A 95.402 174 8 0 2662 2835 367790076 367790249 9.090000e-71 278.0
37 TraesCS7D01G046000 chr5A 95.402 174 7 1 2658 2831 526657959 526657787 3.270000e-70 276.0
38 TraesCS7D01G046000 chr6A 95.402 174 7 1 2663 2835 33260027 33259854 3.270000e-70 276.0


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 TraesCS7D01G046000 chr7D 23494932 23498256 3324 False 6141.0 6141 100.0000 1 3325 1 chr7D.!!$F1 3324
1 TraesCS7D01G046000 chr4A 708321254 708323660 2406 True 1439.5 1842 91.1400 2 2259 2 chr4A.!!$R3 2257
2 TraesCS7D01G046000 chr7A 24591018 24593501 2483 False 1473.0 1775 91.8020 1 2347 2 chr7A.!!$F1 2346
3 TraesCS7D01G046000 chr2B 583918437 583919224 787 False 348.0 477 82.3265 2380 3325 2 chr2B.!!$F2 945
4 TraesCS7D01G046000 chr4D 49517046 49517728 682 True 278.0 361 81.0720 2388 3239 2 chr4D.!!$R3 851

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
620 635 0.035725 CCAAGAGTGAGGCATGAGCA 60.036 55.0 0.0 0.0 44.61 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2400 2645 0.114364 GGAGGAAATGTGGGGGTTGT 59.886 55.0 0.0 0.0 0.0 3.32 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
476 488 1.210478 GAGTAGGATGCTGCCTGGAAA 59.790 52.381 0.00 0.00 39.08 3.13
478 490 2.243221 AGTAGGATGCTGCCTGGAAATT 59.757 45.455 0.00 0.00 39.08 1.82
479 491 2.242882 AGGATGCTGCCTGGAAATTT 57.757 45.000 0.00 0.00 36.76 1.82
480 492 1.829222 AGGATGCTGCCTGGAAATTTG 59.171 47.619 0.00 0.00 36.76 2.32
618 633 0.907486 TCCCAAGAGTGAGGCATGAG 59.093 55.000 0.00 0.00 0.00 2.90
619 634 0.747283 CCCAAGAGTGAGGCATGAGC 60.747 60.000 0.00 0.00 41.10 4.26
620 635 0.035725 CCAAGAGTGAGGCATGAGCA 60.036 55.000 0.00 0.00 44.61 4.26
621 636 1.408405 CCAAGAGTGAGGCATGAGCAT 60.408 52.381 0.00 0.00 44.61 3.79
622 637 1.671328 CAAGAGTGAGGCATGAGCATG 59.329 52.381 6.11 6.11 44.61 4.06
623 638 1.201424 AGAGTGAGGCATGAGCATGA 58.799 50.000 14.27 0.00 44.61 3.07
656 671 8.023128 GCGGCATCTTGTATTGTATAATTGATT 58.977 33.333 0.00 0.00 0.00 2.57
657 672 9.333497 CGGCATCTTGTATTGTATAATTGATTG 57.667 33.333 0.00 0.00 0.00 2.67
721 737 2.120232 GTCTATTCATGTCGCTGGTCG 58.880 52.381 0.00 0.00 40.15 4.79
723 739 0.104120 TATTCATGTCGCTGGTCGGG 59.896 55.000 0.00 0.00 39.05 5.14
730 746 2.432628 CGCTGGTCGGGACACTTC 60.433 66.667 0.75 0.00 33.78 3.01
731 747 2.047179 GCTGGTCGGGACACTTCC 60.047 66.667 0.75 0.00 41.95 3.46
737 753 1.079405 TCGGGACACTTCCGCATTC 60.079 57.895 0.00 0.00 46.43 2.67
754 770 3.425193 GCATTCGAAACAATTTTGCTCGT 59.575 39.130 0.00 0.00 37.78 4.18
765 781 3.338818 TTTTGCTCGTTCTGCTTTCAG 57.661 42.857 0.00 0.00 41.67 3.02
772 788 2.612212 TCGTTCTGCTTTCAGTGGTTTC 59.388 45.455 0.00 0.00 41.10 2.78
773 789 2.354510 CGTTCTGCTTTCAGTGGTTTCA 59.645 45.455 0.00 0.00 41.10 2.69
799 816 5.427378 AGTTTGGATTTGGACAGTTTTTGG 58.573 37.500 0.00 0.00 0.00 3.28
800 817 5.188751 AGTTTGGATTTGGACAGTTTTTGGA 59.811 36.000 0.00 0.00 0.00 3.53
801 818 5.885449 TTGGATTTGGACAGTTTTTGGAT 57.115 34.783 0.00 0.00 0.00 3.41
803 820 4.653341 TGGATTTGGACAGTTTTTGGATGT 59.347 37.500 0.00 0.00 0.00 3.06
804 821 4.990426 GGATTTGGACAGTTTTTGGATGTG 59.010 41.667 0.00 0.00 0.00 3.21
805 822 4.399004 TTTGGACAGTTTTTGGATGTGG 57.601 40.909 0.00 0.00 0.00 4.17
806 823 3.025322 TGGACAGTTTTTGGATGTGGT 57.975 42.857 0.00 0.00 0.00 4.16
807 824 2.955660 TGGACAGTTTTTGGATGTGGTC 59.044 45.455 0.00 0.00 0.00 4.02
809 826 3.573967 GGACAGTTTTTGGATGTGGTCAT 59.426 43.478 0.00 0.00 36.95 3.06
820 855 1.979855 TGTGGTCATCCTTGTGGTTG 58.020 50.000 0.00 0.00 35.04 3.77
824 859 1.880027 GGTCATCCTTGTGGTTGTGTC 59.120 52.381 0.00 0.00 35.22 3.67
825 860 2.487265 GGTCATCCTTGTGGTTGTGTCT 60.487 50.000 0.00 0.00 35.22 3.41
839 874 2.997980 TGTGTCTTTCTGGAACTTGCA 58.002 42.857 0.00 0.00 0.00 4.08
844 879 3.319122 GTCTTTCTGGAACTTGCATGGTT 59.681 43.478 4.44 4.99 0.00 3.67
848 883 3.295093 TCTGGAACTTGCATGGTTTTCA 58.705 40.909 4.44 7.06 0.00 2.69
850 885 2.224018 TGGAACTTGCATGGTTTTCAGC 60.224 45.455 4.44 0.00 0.00 4.26
854 889 3.197265 ACTTGCATGGTTTTCAGCAAAC 58.803 40.909 4.44 0.00 45.18 2.93
861 1094 5.782047 CATGGTTTTCAGCAAACTCCAATA 58.218 37.500 0.00 0.00 43.95 1.90
862 1095 6.400568 CATGGTTTTCAGCAAACTCCAATAT 58.599 36.000 0.00 0.00 43.95 1.28
875 1108 6.469782 AACTCCAATATTTGTAATGGCTGG 57.530 37.500 0.00 0.00 32.87 4.85
882 1115 6.808008 ATATTTGTAATGGCTGGATTCTCG 57.192 37.500 0.00 0.00 0.00 4.04
890 1123 2.300152 TGGCTGGATTCTCGTGGATATC 59.700 50.000 0.00 0.00 0.00 1.63
895 1128 3.826729 TGGATTCTCGTGGATATCGATGT 59.173 43.478 8.54 0.00 36.73 3.06
928 1161 9.490663 CTGGAAGTTTTTGTAATTCATATCGAC 57.509 33.333 0.00 0.00 0.00 4.20
929 1162 9.004717 TGGAAGTTTTTGTAATTCATATCGACA 57.995 29.630 0.00 0.00 0.00 4.35
930 1163 9.274065 GGAAGTTTTTGTAATTCATATCGACAC 57.726 33.333 0.00 0.00 0.00 3.67
931 1164 8.874745 AAGTTTTTGTAATTCATATCGACACG 57.125 30.769 0.00 0.00 0.00 4.49
932 1165 7.461107 AGTTTTTGTAATTCATATCGACACGG 58.539 34.615 0.00 0.00 0.00 4.94
933 1166 5.398176 TTTGTAATTCATATCGACACGGC 57.602 39.130 0.00 0.00 0.00 5.68
934 1167 4.048241 TGTAATTCATATCGACACGGCA 57.952 40.909 0.00 0.00 0.00 5.69
935 1168 3.799963 TGTAATTCATATCGACACGGCAC 59.200 43.478 0.00 0.00 0.00 5.01
936 1169 2.595124 ATTCATATCGACACGGCACA 57.405 45.000 0.00 0.00 0.00 4.57
937 1170 2.371910 TTCATATCGACACGGCACAA 57.628 45.000 0.00 0.00 0.00 3.33
963 1196 6.703165 AGAACATTTGAGCAATTTTGAGAACC 59.297 34.615 0.00 0.00 0.00 3.62
965 1198 6.347696 ACATTTGAGCAATTTTGAGAACCAA 58.652 32.000 0.00 0.00 0.00 3.67
966 1199 6.480981 ACATTTGAGCAATTTTGAGAACCAAG 59.519 34.615 0.00 0.00 35.94 3.61
967 1200 5.596836 TTGAGCAATTTTGAGAACCAAGT 57.403 34.783 0.00 0.00 35.94 3.16
968 1201 5.596836 TGAGCAATTTTGAGAACCAAGTT 57.403 34.783 0.00 0.00 35.94 2.66
969 1202 5.591099 TGAGCAATTTTGAGAACCAAGTTC 58.409 37.500 0.00 0.00 42.25 3.01
971 1204 4.651045 AGCAATTTTGAGAACCAAGTTCCT 59.349 37.500 3.91 0.00 42.85 3.36
972 1205 4.984785 GCAATTTTGAGAACCAAGTTCCTC 59.015 41.667 3.91 2.85 42.85 3.71
973 1206 5.221322 GCAATTTTGAGAACCAAGTTCCTCT 60.221 40.000 3.91 0.00 42.85 3.69
974 1207 6.211515 CAATTTTGAGAACCAAGTTCCTCTG 58.788 40.000 3.91 0.00 42.85 3.35
975 1208 4.771114 TTTGAGAACCAAGTTCCTCTGA 57.229 40.909 3.91 0.00 42.85 3.27
976 1209 4.771114 TTGAGAACCAAGTTCCTCTGAA 57.229 40.909 3.91 0.00 42.85 3.02
990 1223 3.172229 CTCTGAACGGAGGAAGAATCC 57.828 52.381 2.99 0.00 46.98 3.01
1007 1240 2.559785 CCATTGTGTGGCTGAGACC 58.440 57.895 0.00 0.00 42.12 3.85
1008 1241 0.037303 CCATTGTGTGGCTGAGACCT 59.963 55.000 0.00 0.00 42.12 3.85
1019 1252 0.671781 CTGAGACCTTGGACGCTTGG 60.672 60.000 0.00 0.00 0.00 3.61
1022 1255 1.371558 GACCTTGGACGCTTGGTCT 59.628 57.895 0.00 0.00 45.35 3.85
1024 1257 1.122019 ACCTTGGACGCTTGGTCTCT 61.122 55.000 0.00 0.00 45.35 3.10
1040 1273 0.177604 CTCTTCTCTCGCTGCCCAAT 59.822 55.000 0.00 0.00 0.00 3.16
1051 1284 1.619654 CTGCCCAATTCTGTCCACAA 58.380 50.000 0.00 0.00 0.00 3.33
1062 1295 2.303022 TCTGTCCACAACCTCATCTTCC 59.697 50.000 0.00 0.00 0.00 3.46
1063 1296 2.304180 CTGTCCACAACCTCATCTTCCT 59.696 50.000 0.00 0.00 0.00 3.36
1080 1313 5.017490 TCTTCCTCTCCTTGTACGAGAATT 58.983 41.667 12.02 0.00 35.98 2.17
1081 1314 5.480772 TCTTCCTCTCCTTGTACGAGAATTT 59.519 40.000 12.02 0.00 35.98 1.82
1083 1316 5.721232 TCCTCTCCTTGTACGAGAATTTTC 58.279 41.667 12.02 0.00 35.98 2.29
1085 1318 5.578727 CCTCTCCTTGTACGAGAATTTTCTG 59.421 44.000 12.02 0.00 37.73 3.02
1086 1319 6.097915 TCTCCTTGTACGAGAATTTTCTGT 57.902 37.500 12.02 0.10 37.73 3.41
1087 1320 6.522054 TCTCCTTGTACGAGAATTTTCTGTT 58.478 36.000 12.02 0.00 37.73 3.16
1111 1348 1.786937 TTGGTTGGTGGTTGCATCTT 58.213 45.000 0.00 0.00 0.00 2.40
1124 1361 4.181010 ATCTTGGATGCGGCGGCT 62.181 61.111 17.76 2.89 40.82 5.52
1394 1631 4.227134 CTCGGGGCCATCGACCTG 62.227 72.222 15.09 4.17 32.86 4.00
1547 1784 2.907042 CCAAGGTAAACCAGTCTCCTCT 59.093 50.000 1.26 0.00 38.89 3.69
1550 1787 3.588569 AGGTAAACCAGTCTCCTCTGTT 58.411 45.455 1.26 0.00 38.89 3.16
1554 1791 4.779993 AAACCAGTCTCCTCTGTTTCTT 57.220 40.909 0.00 0.00 34.02 2.52
1563 1800 5.235401 GTCTCCTCTGTTTCTTGTTCTTGTC 59.765 44.000 0.00 0.00 0.00 3.18
1569 1806 3.296854 GTTTCTTGTTCTTGTCCCCCTT 58.703 45.455 0.00 0.00 0.00 3.95
1613 1855 4.657824 ACGTTCAGACCCGTGCGG 62.658 66.667 3.25 3.25 35.69 5.69
1711 1953 1.451028 GGCAGCTGGGCTACTTCAG 60.451 63.158 17.12 0.00 36.40 3.02
1723 1965 1.552337 CTACTTCAGGCCTCAGAGCAA 59.448 52.381 14.49 0.15 0.00 3.91
2163 2405 2.119801 TCAGGCTGAGGCTTGATTTC 57.880 50.000 14.43 0.00 46.99 2.17
2172 2414 1.216427 AGGCTTGATTTCATCTCCCCC 59.784 52.381 0.00 0.00 0.00 5.40
2175 2417 3.369175 GCTTGATTTCATCTCCCCCTTT 58.631 45.455 0.00 0.00 0.00 3.11
2180 2422 5.154418 TGATTTCATCTCCCCCTTTTGTTT 58.846 37.500 0.00 0.00 0.00 2.83
2181 2423 5.245977 TGATTTCATCTCCCCCTTTTGTTTC 59.754 40.000 0.00 0.00 0.00 2.78
2209 2453 3.793129 GCACAGTGGCATTATGGATTTCG 60.793 47.826 1.84 0.00 0.00 3.46
2220 2464 6.033831 GCATTATGGATTTCGTGTTTGTTGAG 59.966 38.462 0.00 0.00 0.00 3.02
2227 2471 8.447833 TGGATTTCGTGTTTGTTGAGATATAAC 58.552 33.333 0.00 0.00 0.00 1.89
2279 2523 4.642445 TTATCATGTGGAGCAAATGCAG 57.358 40.909 8.28 0.00 45.16 4.41
2282 2526 0.245539 ATGTGGAGCAAATGCAGTGC 59.754 50.000 15.57 15.57 45.16 4.40
2285 2529 1.108132 TGGAGCAAATGCAGTGCACA 61.108 50.000 22.44 18.40 43.04 4.57
2286 2530 0.032403 GGAGCAAATGCAGTGCACAA 59.968 50.000 22.44 4.31 43.04 3.33
2302 2546 3.263602 CACAATATGCATTCTGGAGCG 57.736 47.619 3.54 0.00 0.00 5.03
2325 2569 2.040412 AGTTTGTCTTCTCCATGTCCCC 59.960 50.000 0.00 0.00 0.00 4.81
2328 2572 0.833949 GTCTTCTCCATGTCCCCTCC 59.166 60.000 0.00 0.00 0.00 4.30
2336 2581 3.254035 ATGTCCCCTCCTGACCCGT 62.254 63.158 0.00 0.00 31.60 5.28
2380 2625 8.982925 AAAATAGCGTCGTACTAAAATTATGC 57.017 30.769 0.00 0.00 0.00 3.14
2381 2626 7.941795 AATAGCGTCGTACTAAAATTATGCT 57.058 32.000 0.00 0.00 0.00 3.79
2382 2627 9.467258 AAATAGCGTCGTACTAAAATTATGCTA 57.533 29.630 0.00 0.00 35.88 3.49
2383 2628 6.744550 AGCGTCGTACTAAAATTATGCTAC 57.255 37.500 0.00 0.00 0.00 3.58
2384 2629 6.501781 AGCGTCGTACTAAAATTATGCTACT 58.498 36.000 0.00 0.00 0.00 2.57
2385 2630 7.642669 AGCGTCGTACTAAAATTATGCTACTA 58.357 34.615 0.00 0.00 0.00 1.82
2386 2631 8.295288 AGCGTCGTACTAAAATTATGCTACTAT 58.705 33.333 0.00 0.00 0.00 2.12
2410 2655 1.599797 CTCCAACGACAACCCCCAC 60.600 63.158 0.00 0.00 0.00 4.61
2426 2671 0.107017 CCACATTTCCTCCCGCATCT 60.107 55.000 0.00 0.00 0.00 2.90
2429 2674 1.837439 ACATTTCCTCCCGCATCTGTA 59.163 47.619 0.00 0.00 0.00 2.74
2430 2675 2.238646 ACATTTCCTCCCGCATCTGTAA 59.761 45.455 0.00 0.00 0.00 2.41
2438 2683 1.645034 CCGCATCTGTAAGTGGACAG 58.355 55.000 0.00 0.00 46.90 3.51
2481 2728 1.153168 CGGGAGGACGCCATTCAAT 60.153 57.895 0.00 0.00 0.00 2.57
2482 2729 0.748005 CGGGAGGACGCCATTCAATT 60.748 55.000 0.00 0.00 0.00 2.32
2505 2753 3.932545 AGCCGCATACATTTTCACAAA 57.067 38.095 0.00 0.00 0.00 2.83
2514 2762 7.148983 CGCATACATTTTCACAAAAACTCGAAT 60.149 33.333 0.00 0.00 37.20 3.34
2518 2766 8.647143 ACATTTTCACAAAAACTCGAATCAAT 57.353 26.923 0.00 0.00 37.20 2.57
2563 2811 4.522405 TGGCCGGATTTCATATAAACATGG 59.478 41.667 5.05 0.00 0.00 3.66
2573 2821 6.312399 TCATATAAACATGGCGGATTTCAC 57.688 37.500 0.00 0.00 0.00 3.18
2645 2893 4.021368 ACATCAACTAAACGGTGCTAGTCT 60.021 41.667 4.24 0.00 0.00 3.24
2655 2903 1.118838 GTGCTAGTCTGGCTCTGGAT 58.881 55.000 9.82 0.00 0.00 3.41
2664 2912 6.597832 AGTCTGGCTCTGGATGTATAATAC 57.402 41.667 0.00 0.00 0.00 1.89
2665 2913 6.318913 AGTCTGGCTCTGGATGTATAATACT 58.681 40.000 0.00 0.00 0.00 2.12
2666 2914 6.435904 AGTCTGGCTCTGGATGTATAATACTC 59.564 42.308 0.00 0.00 0.00 2.59
2667 2915 5.717178 TCTGGCTCTGGATGTATAATACTCC 59.283 44.000 0.00 0.00 0.00 3.85
2668 2916 4.777896 TGGCTCTGGATGTATAATACTCCC 59.222 45.833 0.00 0.00 0.00 4.30
2669 2917 5.026790 GGCTCTGGATGTATAATACTCCCT 58.973 45.833 0.00 0.00 0.00 4.20
2670 2918 5.128008 GGCTCTGGATGTATAATACTCCCTC 59.872 48.000 0.00 0.00 0.00 4.30
2671 2919 5.128008 GCTCTGGATGTATAATACTCCCTCC 59.872 48.000 0.00 0.00 0.00 4.30
2672 2920 5.262009 TCTGGATGTATAATACTCCCTCCG 58.738 45.833 0.00 0.00 0.00 4.63
2673 2921 5.006896 TGGATGTATAATACTCCCTCCGT 57.993 43.478 0.00 0.00 0.00 4.69
2674 2922 5.399991 TGGATGTATAATACTCCCTCCGTT 58.600 41.667 0.00 0.00 0.00 4.44
2675 2923 5.479375 TGGATGTATAATACTCCCTCCGTTC 59.521 44.000 0.00 0.00 0.00 3.95
2676 2924 5.105432 GGATGTATAATACTCCCTCCGTTCC 60.105 48.000 0.00 0.00 0.00 3.62
2677 2925 4.154942 TGTATAATACTCCCTCCGTTCCC 58.845 47.826 0.00 0.00 0.00 3.97
2678 2926 2.852714 TAATACTCCCTCCGTTCCCA 57.147 50.000 0.00 0.00 0.00 4.37
2679 2927 1.961133 AATACTCCCTCCGTTCCCAA 58.039 50.000 0.00 0.00 0.00 4.12
2680 2928 1.961133 ATACTCCCTCCGTTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
2681 2929 1.961133 TACTCCCTCCGTTCCCAAAT 58.039 50.000 0.00 0.00 0.00 2.32
2682 2930 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2683 2931 2.488836 ACTCCCTCCGTTCCCAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
2684 2932 3.660959 ACTCCCTCCGTTCCCAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
2685 2933 4.042174 ACTCCCTCCGTTCCCAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
2686 2934 4.102681 ACTCCCTCCGTTCCCAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
2687 2935 4.042174 TCCCTCCGTTCCCAAATATAAGT 58.958 43.478 0.00 0.00 0.00 2.24
2688 2936 4.102054 TCCCTCCGTTCCCAAATATAAGTC 59.898 45.833 0.00 0.00 0.00 3.01
2689 2937 4.102681 CCCTCCGTTCCCAAATATAAGTCT 59.897 45.833 0.00 0.00 0.00 3.24
2690 2938 5.397559 CCCTCCGTTCCCAAATATAAGTCTT 60.398 44.000 0.00 0.00 0.00 3.01
2691 2939 6.120220 CCTCCGTTCCCAAATATAAGTCTTT 58.880 40.000 0.00 0.00 0.00 2.52
2692 2940 6.602009 CCTCCGTTCCCAAATATAAGTCTTTT 59.398 38.462 0.00 0.00 0.00 2.27
2693 2941 7.122204 CCTCCGTTCCCAAATATAAGTCTTTTT 59.878 37.037 0.00 0.00 0.00 1.94
2694 2942 9.169592 CTCCGTTCCCAAATATAAGTCTTTTTA 57.830 33.333 0.00 0.00 0.00 1.52
2695 2943 9.169592 TCCGTTCCCAAATATAAGTCTTTTTAG 57.830 33.333 0.00 0.00 0.00 1.85
2696 2944 9.169592 CCGTTCCCAAATATAAGTCTTTTTAGA 57.830 33.333 0.00 0.00 0.00 2.10
2720 2968 8.643324 AGAGATTCCAATAAGTGACTACATACC 58.357 37.037 0.00 0.00 0.00 2.73
2721 2969 7.434492 AGATTCCAATAAGTGACTACATACCG 58.566 38.462 0.00 0.00 0.00 4.02
2722 2970 6.778834 TTCCAATAAGTGACTACATACCGA 57.221 37.500 0.00 0.00 0.00 4.69
2723 2971 6.387041 TCCAATAAGTGACTACATACCGAG 57.613 41.667 0.00 0.00 0.00 4.63
2724 2972 4.982916 CCAATAAGTGACTACATACCGAGC 59.017 45.833 0.00 0.00 0.00 5.03
2725 2973 5.451381 CCAATAAGTGACTACATACCGAGCA 60.451 44.000 0.00 0.00 0.00 4.26
2726 2974 5.847111 ATAAGTGACTACATACCGAGCAA 57.153 39.130 0.00 0.00 0.00 3.91
2727 2975 4.530710 AAGTGACTACATACCGAGCAAA 57.469 40.909 0.00 0.00 0.00 3.68
2728 2976 4.530710 AGTGACTACATACCGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2729 2977 5.086104 AGTGACTACATACCGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
2730 2978 4.870426 AGTGACTACATACCGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
2731 2979 4.868171 GTGACTACATACCGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
2732 2980 5.005779 GTGACTACATACCGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
2733 2981 5.086104 ACTACATACCGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2734 2982 4.870426 ACTACATACCGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2735 2983 3.937814 ACATACCGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2736 2984 4.323417 ACATACCGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2737 2985 4.943705 ACATACCGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2738 2986 5.065218 ACATACCGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2739 2987 3.679389 ACCGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2740 2988 4.832248 ACCGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2741 2989 4.631813 ACCGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2742 2990 4.631377 CCGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2743 2991 5.446473 CCGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2783 3031 7.905604 CATACATCCGTATGTTGTAATCCAT 57.094 36.000 0.00 0.00 46.70 3.41
2784 3032 8.322906 CATACATCCGTATGTTGTAATCCATT 57.677 34.615 0.00 0.00 46.70 3.16
2785 3033 8.783093 CATACATCCGTATGTTGTAATCCATTT 58.217 33.333 0.00 0.00 46.70 2.32
2786 3034 7.026631 ACATCCGTATGTTGTAATCCATTTG 57.973 36.000 0.00 0.00 44.07 2.32
2787 3035 6.826231 ACATCCGTATGTTGTAATCCATTTGA 59.174 34.615 0.00 0.00 44.07 2.69
2788 3036 7.338196 ACATCCGTATGTTGTAATCCATTTGAA 59.662 33.333 0.00 0.00 44.07 2.69
2789 3037 7.689446 TCCGTATGTTGTAATCCATTTGAAA 57.311 32.000 0.00 0.00 0.00 2.69
2790 3038 8.287439 TCCGTATGTTGTAATCCATTTGAAAT 57.713 30.769 0.00 0.00 0.00 2.17
2791 3039 8.187480 TCCGTATGTTGTAATCCATTTGAAATG 58.813 33.333 10.84 10.84 0.00 2.32
2792 3040 7.973388 CCGTATGTTGTAATCCATTTGAAATGT 59.027 33.333 15.93 1.43 0.00 2.71
2793 3041 9.009327 CGTATGTTGTAATCCATTTGAAATGTC 57.991 33.333 15.93 3.21 0.00 3.06
2821 3069 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
2822 3070 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2823 3071 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2824 3072 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2825 3073 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
2826 3074 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
2827 3075 7.450944 ACTTATATTTAGGAACGGAGGGAGTAG 59.549 40.741 0.00 0.00 0.00 2.57
2848 3096 2.271944 ACCTAATCTAAATGGCCGCC 57.728 50.000 1.04 1.04 0.00 6.13
2883 3131 2.249413 CTTCCTCATGTCCGGCAGCT 62.249 60.000 0.00 0.00 0.00 4.24
2919 3167 1.006758 CGGGAGCCCCTGAGGTATATA 59.993 57.143 0.00 0.00 42.67 0.86
2920 3168 2.559026 CGGGAGCCCCTGAGGTATATAA 60.559 54.545 0.00 0.00 42.67 0.98
2925 3173 5.250774 GGAGCCCCTGAGGTATATAATTCAA 59.749 44.000 0.00 0.00 38.26 2.69
2935 3183 7.936847 TGAGGTATATAATTCAACGCAAAGGAT 59.063 33.333 0.00 0.00 0.00 3.24
2945 3193 1.089481 CGCAAAGGATGGCTCGCTTA 61.089 55.000 0.00 0.00 0.00 3.09
2985 3234 2.045045 CCCCGGCTGATGCTTCAA 60.045 61.111 0.00 0.00 39.59 2.69
2997 3246 1.377333 GCTTCAACGGGAGGGGAAG 60.377 63.158 0.00 0.00 42.95 3.46
3024 3273 3.121030 CCGCTTCTGTGAAGCCCG 61.121 66.667 21.72 11.71 40.02 6.13
3040 3289 2.202570 CGTGTGGGATCGACGGAC 60.203 66.667 0.00 0.00 0.00 4.79
3064 3313 2.665603 GCAAGAGAAGAGCCGGGT 59.334 61.111 5.45 5.45 0.00 5.28
3097 3346 2.034532 TACACCGGAGTCGCCTCA 59.965 61.111 9.46 0.00 39.64 3.86
3099 3348 4.803426 CACCGGAGTCGCCTCAGC 62.803 72.222 9.46 0.00 39.64 4.26
3148 3397 0.391263 GGCCTCCCGTGTTCTACTTG 60.391 60.000 0.00 0.00 0.00 3.16
3156 3405 2.030540 CCGTGTTCTACTTGTCCTCGAA 60.031 50.000 0.00 0.00 0.00 3.71
3205 3454 1.374125 CACCTCGTCAACATCCGCA 60.374 57.895 0.00 0.00 0.00 5.69
3211 3460 1.018752 CGTCAACATCCGCACATCCA 61.019 55.000 0.00 0.00 0.00 3.41
3212 3461 1.382522 GTCAACATCCGCACATCCAT 58.617 50.000 0.00 0.00 0.00 3.41
3229 3478 2.300152 TCCATCTTCTTTCTCTGCGTGT 59.700 45.455 0.00 0.00 0.00 4.49
3263 3512 2.961721 CGTGATGACGGCCGATGG 60.962 66.667 35.90 9.41 42.18 3.51
3312 3561 3.110178 CGAGCCGTCGTGTTTCCC 61.110 66.667 0.00 0.00 41.57 3.97
3319 3568 4.224274 TCGTGTTTCCCGCCGTGT 62.224 61.111 0.00 0.00 0.00 4.49
3320 3569 3.708734 CGTGTTTCCCGCCGTGTC 61.709 66.667 0.00 0.00 0.00 3.67
3321 3570 3.708734 GTGTTTCCCGCCGTGTCG 61.709 66.667 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 103 6.628844 GCAAAAGGGAATGCATCAGTTATTCT 60.629 38.462 0.00 0.00 42.12 2.40
619 634 3.112126 GATGCCGCCAACCGTCATG 62.112 63.158 0.00 0.00 35.41 3.07
620 635 2.819984 AAGATGCCGCCAACCGTCAT 62.820 55.000 0.00 0.00 38.37 3.06
621 636 3.545124 AAGATGCCGCCAACCGTCA 62.545 57.895 0.00 0.00 34.38 4.35
622 637 2.746277 AAGATGCCGCCAACCGTC 60.746 61.111 0.00 0.00 34.38 4.79
623 638 2.457743 TACAAGATGCCGCCAACCGT 62.458 55.000 0.00 0.00 34.38 4.83
656 671 8.988934 GTGTGTCTCTAAAACATAACAAGATCA 58.011 33.333 0.00 0.00 0.00 2.92
657 672 9.209175 AGTGTGTCTCTAAAACATAACAAGATC 57.791 33.333 0.00 0.00 0.00 2.75
658 673 8.993121 CAGTGTGTCTCTAAAACATAACAAGAT 58.007 33.333 0.00 0.00 0.00 2.40
659 674 8.201464 TCAGTGTGTCTCTAAAACATAACAAGA 58.799 33.333 0.00 0.00 0.00 3.02
721 737 0.672401 TTCGAATGCGGAAGTGTCCC 60.672 55.000 0.00 0.00 41.44 4.46
723 739 1.529438 TGTTTCGAATGCGGAAGTGTC 59.471 47.619 0.00 0.00 35.26 3.67
725 741 2.679355 TTGTTTCGAATGCGGAAGTG 57.321 45.000 0.00 0.00 35.26 3.16
727 743 4.663889 GCAAAATTGTTTCGAATGCGGAAG 60.664 41.667 0.00 0.00 35.26 3.46
730 746 2.730928 AGCAAAATTGTTTCGAATGCGG 59.269 40.909 10.90 0.00 37.40 5.69
731 747 3.478598 CGAGCAAAATTGTTTCGAATGCG 60.479 43.478 10.90 0.00 38.63 4.73
737 753 3.121696 GCAGAACGAGCAAAATTGTTTCG 60.122 43.478 15.54 15.54 40.55 3.46
754 770 4.269183 TCTTGAAACCACTGAAAGCAGAA 58.731 39.130 0.00 0.00 45.17 3.02
765 781 5.049828 CCAAATCCAAACTCTTGAAACCAC 58.950 41.667 0.00 0.00 34.14 4.16
772 788 5.520376 AACTGTCCAAATCCAAACTCTTG 57.480 39.130 0.00 0.00 0.00 3.02
773 789 6.544928 AAAACTGTCCAAATCCAAACTCTT 57.455 33.333 0.00 0.00 0.00 2.85
800 817 2.158475 ACAACCACAAGGATGACCACAT 60.158 45.455 0.00 0.00 39.92 3.21
801 818 1.214175 ACAACCACAAGGATGACCACA 59.786 47.619 0.00 0.00 39.92 4.17
803 820 1.214175 ACACAACCACAAGGATGACCA 59.786 47.619 0.00 0.00 39.92 4.02
804 821 1.880027 GACACAACCACAAGGATGACC 59.120 52.381 0.00 0.00 39.92 4.02
805 822 2.851195 AGACACAACCACAAGGATGAC 58.149 47.619 0.00 0.00 39.92 3.06
806 823 3.576078 AAGACACAACCACAAGGATGA 57.424 42.857 0.00 0.00 39.92 2.92
807 824 3.885297 AGAAAGACACAACCACAAGGATG 59.115 43.478 0.00 0.00 42.95 3.51
809 826 3.278574 CAGAAAGACACAACCACAAGGA 58.721 45.455 0.00 0.00 38.69 3.36
814 849 3.279434 AGTTCCAGAAAGACACAACCAC 58.721 45.455 0.00 0.00 0.00 4.16
820 855 3.304928 CCATGCAAGTTCCAGAAAGACAC 60.305 47.826 0.00 0.00 0.00 3.67
824 859 4.326504 AAACCATGCAAGTTCCAGAAAG 57.673 40.909 6.00 0.00 0.00 2.62
825 860 4.161189 TGAAAACCATGCAAGTTCCAGAAA 59.839 37.500 6.00 0.00 0.00 2.52
844 879 9.421806 CATTACAAATATTGGAGTTTGCTGAAA 57.578 29.630 0.00 0.00 38.54 2.69
848 883 6.155049 AGCCATTACAAATATTGGAGTTTGCT 59.845 34.615 0.00 0.00 38.54 3.91
850 885 6.757947 CCAGCCATTACAAATATTGGAGTTTG 59.242 38.462 0.00 0.00 40.29 2.93
854 889 6.906157 ATCCAGCCATTACAAATATTGGAG 57.094 37.500 0.00 0.00 36.95 3.86
861 1094 4.336433 CACGAGAATCCAGCCATTACAAAT 59.664 41.667 0.00 0.00 0.00 2.32
862 1095 3.689161 CACGAGAATCCAGCCATTACAAA 59.311 43.478 0.00 0.00 0.00 2.83
875 1108 4.859798 GGAACATCGATATCCACGAGAATC 59.140 45.833 19.48 2.42 42.81 2.52
882 1115 5.010719 TCCAGTTAGGAACATCGATATCCAC 59.989 44.000 23.92 16.73 45.65 4.02
907 1140 7.461107 CCGTGTCGATATGAATTACAAAAACT 58.539 34.615 2.52 0.00 0.00 2.66
911 1144 4.870991 TGCCGTGTCGATATGAATTACAAA 59.129 37.500 2.52 0.00 0.00 2.83
922 1155 2.063266 GTTCTTTGTGCCGTGTCGATA 58.937 47.619 0.00 0.00 0.00 2.92
923 1156 0.865769 GTTCTTTGTGCCGTGTCGAT 59.134 50.000 0.00 0.00 0.00 3.59
924 1157 0.460459 TGTTCTTTGTGCCGTGTCGA 60.460 50.000 0.00 0.00 0.00 4.20
925 1158 0.586319 ATGTTCTTTGTGCCGTGTCG 59.414 50.000 0.00 0.00 0.00 4.35
926 1159 2.774439 AATGTTCTTTGTGCCGTGTC 57.226 45.000 0.00 0.00 0.00 3.67
927 1160 2.425312 TCAAATGTTCTTTGTGCCGTGT 59.575 40.909 0.00 0.00 0.00 4.49
928 1161 3.044986 CTCAAATGTTCTTTGTGCCGTG 58.955 45.455 0.00 0.00 0.00 4.94
929 1162 2.543653 GCTCAAATGTTCTTTGTGCCGT 60.544 45.455 11.62 0.00 40.78 5.68
930 1163 2.053627 GCTCAAATGTTCTTTGTGCCG 58.946 47.619 11.62 0.00 40.78 5.69
931 1164 3.096489 TGCTCAAATGTTCTTTGTGCC 57.904 42.857 17.14 5.39 43.92 5.01
932 1165 5.662211 AATTGCTCAAATGTTCTTTGTGC 57.338 34.783 14.45 14.45 44.45 4.57
933 1166 7.686519 TCAAAATTGCTCAAATGTTCTTTGTG 58.313 30.769 0.00 0.00 29.87 3.33
934 1167 7.765360 TCTCAAAATTGCTCAAATGTTCTTTGT 59.235 29.630 0.00 0.00 29.87 2.83
935 1168 8.133754 TCTCAAAATTGCTCAAATGTTCTTTG 57.866 30.769 0.00 0.00 0.00 2.77
936 1169 8.606602 GTTCTCAAAATTGCTCAAATGTTCTTT 58.393 29.630 0.00 0.00 0.00 2.52
937 1170 7.225341 GGTTCTCAAAATTGCTCAAATGTTCTT 59.775 33.333 0.00 0.00 0.00 2.52
971 1204 2.536066 TGGATTCTTCCTCCGTTCAGA 58.464 47.619 0.00 0.00 43.07 3.27
972 1205 3.550437 ATGGATTCTTCCTCCGTTCAG 57.450 47.619 0.00 0.00 43.07 3.02
973 1206 3.009033 ACAATGGATTCTTCCTCCGTTCA 59.991 43.478 0.00 0.00 43.07 3.18
974 1207 3.375299 CACAATGGATTCTTCCTCCGTTC 59.625 47.826 0.00 0.00 43.07 3.95
975 1208 3.244911 ACACAATGGATTCTTCCTCCGTT 60.245 43.478 0.00 0.00 43.07 4.44
976 1209 2.305927 ACACAATGGATTCTTCCTCCGT 59.694 45.455 0.00 0.00 43.07 4.69
977 1210 2.679837 CACACAATGGATTCTTCCTCCG 59.320 50.000 0.00 0.00 43.07 4.63
990 1223 1.538512 CAAGGTCTCAGCCACACAATG 59.461 52.381 0.00 0.00 0.00 2.82
994 1227 0.603975 GTCCAAGGTCTCAGCCACAC 60.604 60.000 0.00 0.00 0.00 3.82
1003 1236 1.371558 GACCAAGCGTCCAAGGTCT 59.628 57.895 0.00 0.00 45.46 3.85
1007 1240 1.001406 AGAAGAGACCAAGCGTCCAAG 59.999 52.381 0.00 0.00 43.08 3.61
1008 1241 1.000955 GAGAAGAGACCAAGCGTCCAA 59.999 52.381 0.00 0.00 43.08 3.53
1019 1252 1.140804 GGGCAGCGAGAGAAGAGAC 59.859 63.158 0.00 0.00 0.00 3.36
1022 1255 0.615331 AATTGGGCAGCGAGAGAAGA 59.385 50.000 0.00 0.00 0.00 2.87
1024 1257 0.615331 AGAATTGGGCAGCGAGAGAA 59.385 50.000 0.00 0.00 0.00 2.87
1040 1273 3.244561 GGAAGATGAGGTTGTGGACAGAA 60.245 47.826 0.00 0.00 0.00 3.02
1051 1284 3.197927 ACAAGGAGAGGAAGATGAGGT 57.802 47.619 0.00 0.00 0.00 3.85
1062 1295 6.159988 ACAGAAAATTCTCGTACAAGGAGAG 58.840 40.000 0.00 0.00 39.85 3.20
1063 1296 6.097915 ACAGAAAATTCTCGTACAAGGAGA 57.902 37.500 0.00 0.00 37.35 3.71
1080 1313 4.284746 ACCACCAACCAAAAAGAACAGAAA 59.715 37.500 0.00 0.00 0.00 2.52
1081 1314 3.835395 ACCACCAACCAAAAAGAACAGAA 59.165 39.130 0.00 0.00 0.00 3.02
1083 1316 3.885724 ACCACCAACCAAAAAGAACAG 57.114 42.857 0.00 0.00 0.00 3.16
1085 1318 2.675844 GCAACCACCAACCAAAAAGAAC 59.324 45.455 0.00 0.00 0.00 3.01
1086 1319 2.303022 TGCAACCACCAACCAAAAAGAA 59.697 40.909 0.00 0.00 0.00 2.52
1087 1320 1.902508 TGCAACCACCAACCAAAAAGA 59.097 42.857 0.00 0.00 0.00 2.52
1124 1361 0.318441 GCATCCTGCTCCTATACGCA 59.682 55.000 0.00 0.00 40.96 5.24
1136 1373 1.597302 CATCGGCCTCAGCATCCTG 60.597 63.158 0.00 0.00 42.56 3.86
1253 1490 1.593209 GTCGGCGAAGGTGTTGACA 60.593 57.895 12.92 0.00 0.00 3.58
1528 1765 3.588569 ACAGAGGAGACTGGTTTACCTT 58.411 45.455 0.00 0.00 44.43 3.50
1547 1784 2.243736 AGGGGGACAAGAACAAGAAACA 59.756 45.455 0.00 0.00 0.00 2.83
1550 1787 3.295973 CAAAGGGGGACAAGAACAAGAA 58.704 45.455 0.00 0.00 0.00 2.52
1554 1791 0.555769 AGCAAAGGGGGACAAGAACA 59.444 50.000 0.00 0.00 0.00 3.18
1563 1800 2.203684 AGTGGCAAGCAAAGGGGG 60.204 61.111 0.00 0.00 0.00 5.40
1628 1870 3.984200 GAGGTACGTCGGCACTGCC 62.984 68.421 10.35 10.35 46.75 4.85
1715 1957 2.049156 CACTCGGCGTTGCTCTGA 60.049 61.111 6.85 0.00 0.00 3.27
2163 2405 5.551305 AAAAGAAACAAAAGGGGGAGATG 57.449 39.130 0.00 0.00 0.00 2.90
2172 2414 5.005682 GCCACTGTGCTAAAAGAAACAAAAG 59.994 40.000 1.29 0.00 0.00 2.27
2175 2417 3.445450 TGCCACTGTGCTAAAAGAAACAA 59.555 39.130 1.29 0.00 0.00 2.83
2180 2422 4.398988 CCATAATGCCACTGTGCTAAAAGA 59.601 41.667 1.29 0.00 0.00 2.52
2181 2423 4.398988 TCCATAATGCCACTGTGCTAAAAG 59.601 41.667 1.29 0.00 0.00 2.27
2209 2453 8.592998 CGGTTAGAGTTATATCTCAACAAACAC 58.407 37.037 12.31 5.74 36.97 3.32
2260 2504 2.165641 CACTGCATTTGCTCCACATGAT 59.834 45.455 0.00 0.00 42.66 2.45
2268 2512 2.074547 ATTGTGCACTGCATTTGCTC 57.925 45.000 19.41 15.64 41.91 4.26
2282 2526 2.031420 CCGCTCCAGAATGCATATTGTG 60.031 50.000 0.00 0.00 37.33 3.33
2285 2529 2.105477 ACTCCGCTCCAGAATGCATATT 59.895 45.455 0.00 0.00 31.97 1.28
2286 2530 1.696336 ACTCCGCTCCAGAATGCATAT 59.304 47.619 0.00 0.00 31.97 1.78
2295 2539 1.001406 AGAAGACAAACTCCGCTCCAG 59.999 52.381 0.00 0.00 0.00 3.86
2297 2541 1.673329 GGAGAAGACAAACTCCGCTCC 60.673 57.143 0.00 0.00 42.25 4.70
2298 2542 1.715993 GGAGAAGACAAACTCCGCTC 58.284 55.000 0.00 0.00 42.25 5.03
2325 2569 0.523072 CAAAATGCACGGGTCAGGAG 59.477 55.000 0.00 0.00 0.00 3.69
2328 2572 3.477504 CACAAAATGCACGGGTCAG 57.522 52.632 0.00 0.00 0.00 3.51
2354 2599 9.429600 GCATAATTTTAGTACGACGCTATTTTT 57.570 29.630 0.00 0.00 0.00 1.94
2355 2600 8.823818 AGCATAATTTTAGTACGACGCTATTTT 58.176 29.630 0.00 0.00 0.00 1.82
2356 2601 8.361592 AGCATAATTTTAGTACGACGCTATTT 57.638 30.769 0.00 0.00 0.00 1.40
2357 2602 7.941795 AGCATAATTTTAGTACGACGCTATT 57.058 32.000 0.00 0.00 0.00 1.73
2358 2603 8.295288 AGTAGCATAATTTTAGTACGACGCTAT 58.705 33.333 0.00 0.00 31.60 2.97
2359 2604 7.642669 AGTAGCATAATTTTAGTACGACGCTA 58.357 34.615 0.00 0.00 0.00 4.26
2360 2605 6.501781 AGTAGCATAATTTTAGTACGACGCT 58.498 36.000 0.00 0.00 0.00 5.07
2361 2606 6.744550 AGTAGCATAATTTTAGTACGACGC 57.255 37.500 0.00 0.00 0.00 5.19
2362 2607 8.847567 CCATAGTAGCATAATTTTAGTACGACG 58.152 37.037 0.00 0.00 0.00 5.12
2363 2608 8.645487 GCCATAGTAGCATAATTTTAGTACGAC 58.355 37.037 0.00 0.00 0.00 4.34
2364 2609 8.361889 TGCCATAGTAGCATAATTTTAGTACGA 58.638 33.333 0.00 0.00 34.69 3.43
2365 2610 8.528917 TGCCATAGTAGCATAATTTTAGTACG 57.471 34.615 0.00 0.00 34.69 3.67
2400 2645 0.114364 GGAGGAAATGTGGGGGTTGT 59.886 55.000 0.00 0.00 0.00 3.32
2410 2655 2.620251 TACAGATGCGGGAGGAAATG 57.380 50.000 0.00 0.00 0.00 2.32
2426 2671 4.448210 GACTGGTTTTCTGTCCACTTACA 58.552 43.478 0.00 0.00 38.08 2.41
2438 2683 1.595929 TGTCCGCGGACTGGTTTTC 60.596 57.895 46.72 26.65 44.80 2.29
2439 2684 1.890510 GTGTCCGCGGACTGGTTTT 60.891 57.895 46.72 0.00 44.80 2.43
2440 2685 2.280592 GTGTCCGCGGACTGGTTT 60.281 61.111 46.72 0.00 44.80 3.27
2441 2686 4.657824 CGTGTCCGCGGACTGGTT 62.658 66.667 46.72 0.00 44.80 3.67
2477 2724 5.124617 TGAAAATGTATGCGGCTACAATTGA 59.875 36.000 13.59 0.00 35.37 2.57
2481 2728 3.753797 TGTGAAAATGTATGCGGCTACAA 59.246 39.130 13.54 0.00 35.37 2.41
2482 2729 3.339141 TGTGAAAATGTATGCGGCTACA 58.661 40.909 12.42 12.42 36.14 2.74
2505 2753 9.695884 CGAATTTCGTCCGATTGATTCGAGTTT 62.696 40.741 23.60 1.58 41.82 2.66
2523 2771 4.208355 CGGCCATGTTTATACGAATTTCG 58.792 43.478 16.84 16.84 46.93 3.46
2533 2781 8.303876 GTTTATATGAAATCCGGCCATGTTTAT 58.696 33.333 2.24 0.00 0.00 1.40
2534 2782 7.285629 TGTTTATATGAAATCCGGCCATGTTTA 59.714 33.333 2.24 0.00 0.00 2.01
2540 2788 4.522405 CCATGTTTATATGAAATCCGGCCA 59.478 41.667 2.24 0.00 0.00 5.36
2563 2811 3.242712 CGGCATTTTTATGTGAAATCCGC 59.757 43.478 0.00 0.00 34.15 5.54
2617 2865 8.036575 ACTAGCACCGTTTAGTTGATGTAAATA 58.963 33.333 0.00 0.00 0.00 1.40
2645 2893 4.777896 GGGAGTATTATACATCCAGAGCCA 59.222 45.833 16.69 0.00 33.24 4.75
2655 2903 4.154942 GGGAACGGAGGGAGTATTATACA 58.845 47.826 5.11 0.00 0.00 2.29
2664 2912 4.102681 ACTTATATTTGGGAACGGAGGGAG 59.897 45.833 0.00 0.00 0.00 4.30
2665 2913 4.042174 ACTTATATTTGGGAACGGAGGGA 58.958 43.478 0.00 0.00 0.00 4.20
2666 2914 4.102681 AGACTTATATTTGGGAACGGAGGG 59.897 45.833 0.00 0.00 0.00 4.30
2667 2915 5.291905 AGACTTATATTTGGGAACGGAGG 57.708 43.478 0.00 0.00 0.00 4.30
2668 2916 7.625828 AAAAGACTTATATTTGGGAACGGAG 57.374 36.000 0.00 0.00 0.00 4.63
2669 2917 9.169592 CTAAAAAGACTTATATTTGGGAACGGA 57.830 33.333 0.00 0.00 0.00 4.69
2670 2918 9.169592 TCTAAAAAGACTTATATTTGGGAACGG 57.830 33.333 0.00 0.00 0.00 4.44
2694 2942 8.643324 GGTATGTAGTCACTTATTGGAATCTCT 58.357 37.037 0.00 0.00 0.00 3.10
2695 2943 7.595502 CGGTATGTAGTCACTTATTGGAATCTC 59.404 40.741 0.00 0.00 0.00 2.75
2696 2944 7.287005 TCGGTATGTAGTCACTTATTGGAATCT 59.713 37.037 0.00 0.00 0.00 2.40
2697 2945 7.431249 TCGGTATGTAGTCACTTATTGGAATC 58.569 38.462 0.00 0.00 0.00 2.52
2698 2946 7.356089 TCGGTATGTAGTCACTTATTGGAAT 57.644 36.000 0.00 0.00 0.00 3.01
2699 2947 6.682113 GCTCGGTATGTAGTCACTTATTGGAA 60.682 42.308 0.00 0.00 0.00 3.53
2700 2948 5.221185 GCTCGGTATGTAGTCACTTATTGGA 60.221 44.000 0.00 0.00 0.00 3.53
2701 2949 4.982916 GCTCGGTATGTAGTCACTTATTGG 59.017 45.833 0.00 0.00 0.00 3.16
2702 2950 5.588240 TGCTCGGTATGTAGTCACTTATTG 58.412 41.667 0.00 0.00 0.00 1.90
2703 2951 5.847111 TGCTCGGTATGTAGTCACTTATT 57.153 39.130 0.00 0.00 0.00 1.40
2704 2952 5.847111 TTGCTCGGTATGTAGTCACTTAT 57.153 39.130 0.00 0.00 0.00 1.73
2705 2953 5.648178 TTTGCTCGGTATGTAGTCACTTA 57.352 39.130 0.00 0.00 0.00 2.24
2706 2954 4.530710 TTTGCTCGGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
2707 2955 4.530710 TTTTGCTCGGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
2708 2956 4.868171 TCATTTTGCTCGGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
2709 2957 5.079689 TCATTTTGCTCGGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
2710 2958 5.005779 CACTCATTTTGCTCGGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2711 2959 4.870426 CACTCATTTTGCTCGGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2712 2960 5.109210 TCACTCATTTTGCTCGGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2713 2961 5.079689 TCACTCATTTTGCTCGGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2714 2962 3.937814 TCACTCATTTTGCTCGGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2715 2963 4.944962 TTCACTCATTTTGCTCGGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2716 2964 5.431765 AGATTCACTCATTTTGCTCGGTAT 58.568 37.500 0.00 0.00 0.00 2.73
2717 2965 4.832248 AGATTCACTCATTTTGCTCGGTA 58.168 39.130 0.00 0.00 0.00 4.02
2718 2966 3.679389 AGATTCACTCATTTTGCTCGGT 58.321 40.909 0.00 0.00 0.00 4.69
2719 2967 4.631377 TGTAGATTCACTCATTTTGCTCGG 59.369 41.667 0.00 0.00 0.00 4.63
2720 2968 5.349817 AGTGTAGATTCACTCATTTTGCTCG 59.650 40.000 0.00 0.00 44.07 5.03
2721 2969 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2760 3008 8.783093 CAAATGGATTACAACATACGGATGTAT 58.217 33.333 15.10 8.21 45.93 2.29
2761 3009 7.988028 TCAAATGGATTACAACATACGGATGTA 59.012 33.333 15.10 0.00 45.93 2.29
2763 3011 7.258022 TCAAATGGATTACAACATACGGATG 57.742 36.000 5.94 5.94 39.16 3.51
2764 3012 7.873719 TTCAAATGGATTACAACATACGGAT 57.126 32.000 0.00 0.00 0.00 4.18
2765 3013 7.689446 TTTCAAATGGATTACAACATACGGA 57.311 32.000 0.00 0.00 0.00 4.69
2766 3014 7.973388 ACATTTCAAATGGATTACAACATACGG 59.027 33.333 14.70 0.00 0.00 4.02
2767 3015 8.909708 ACATTTCAAATGGATTACAACATACG 57.090 30.769 14.70 0.00 0.00 3.06
2795 3043 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
2796 3044 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
2797 3045 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2798 3046 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2799 3047 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2800 3048 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2801 3049 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2802 3050 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2803 3051 7.300658 ACTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
2804 3052 6.856757 ACTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
2805 3053 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2806 3054 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2807 3055 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2808 3056 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2809 3057 3.372025 GGTACTACTCCCTCCGTTCCTAA 60.372 52.174 0.00 0.00 0.00 2.69
2810 3058 2.173569 GGTACTACTCCCTCCGTTCCTA 59.826 54.545 0.00 0.00 0.00 2.94
2811 3059 1.064091 GGTACTACTCCCTCCGTTCCT 60.064 57.143 0.00 0.00 0.00 3.36
2812 3060 1.064091 AGGTACTACTCCCTCCGTTCC 60.064 57.143 0.00 0.00 36.02 3.62
2813 3061 2.433662 AGGTACTACTCCCTCCGTTC 57.566 55.000 0.00 0.00 36.02 3.95
2814 3062 4.167697 AGATTAGGTACTACTCCCTCCGTT 59.832 45.833 0.00 0.00 42.67 4.44
2815 3063 3.721050 AGATTAGGTACTACTCCCTCCGT 59.279 47.826 0.00 0.00 42.67 4.69
2816 3064 4.370094 AGATTAGGTACTACTCCCTCCG 57.630 50.000 0.00 0.00 42.67 4.63
2817 3065 7.178805 CCATTTAGATTAGGTACTACTCCCTCC 59.821 44.444 0.00 0.00 42.67 4.30
2818 3066 7.309928 GCCATTTAGATTAGGTACTACTCCCTC 60.310 44.444 0.00 0.00 42.67 4.30
2819 3067 6.497606 GCCATTTAGATTAGGTACTACTCCCT 59.502 42.308 0.00 0.00 42.67 4.20
2820 3068 6.295745 GGCCATTTAGATTAGGTACTACTCCC 60.296 46.154 0.00 0.00 42.67 4.30
2821 3069 6.571925 CGGCCATTTAGATTAGGTACTACTCC 60.572 46.154 2.24 0.00 42.67 3.85
2822 3070 6.388278 CGGCCATTTAGATTAGGTACTACTC 58.612 44.000 2.24 0.00 42.67 2.59
2823 3071 5.279356 GCGGCCATTTAGATTAGGTACTACT 60.279 44.000 2.24 0.00 42.67 2.57
2824 3072 4.928020 GCGGCCATTTAGATTAGGTACTAC 59.072 45.833 2.24 0.00 42.67 2.73
2825 3073 4.020839 GGCGGCCATTTAGATTAGGTACTA 60.021 45.833 15.62 0.00 41.75 1.82
2826 3074 3.244457 GGCGGCCATTTAGATTAGGTACT 60.244 47.826 15.62 0.00 46.37 2.73
2827 3075 3.072211 GGCGGCCATTTAGATTAGGTAC 58.928 50.000 15.62 0.00 0.00 3.34
2848 3096 2.356818 GAAGACAGAGGGATCGGCGG 62.357 65.000 7.21 0.00 0.00 6.13
2852 3100 1.769026 TGAGGAAGACAGAGGGATCG 58.231 55.000 0.00 0.00 0.00 3.69
2909 3157 7.276658 TCCTTTGCGTTGAATTATATACCTCA 58.723 34.615 0.00 0.00 0.00 3.86
2919 3167 1.895131 AGCCATCCTTTGCGTTGAATT 59.105 42.857 0.00 0.00 0.00 2.17
2920 3168 1.474077 GAGCCATCCTTTGCGTTGAAT 59.526 47.619 0.00 0.00 0.00 2.57
2925 3173 3.127533 GCGAGCCATCCTTTGCGT 61.128 61.111 0.00 0.00 0.00 5.24
2945 3193 3.314331 CTCTGGTGAGCGGTGGGT 61.314 66.667 0.00 0.00 33.12 4.51
3024 3273 2.202570 CGTCCGTCGATCCCACAC 60.203 66.667 0.00 0.00 42.86 3.82
3040 3289 0.800300 GCTCTTCTCTTGCGAGGACG 60.800 60.000 0.00 0.00 37.86 4.79
3076 3325 2.646719 GCGACTCCGGTGTACACA 59.353 61.111 26.51 6.34 36.06 3.72
3097 3346 4.431131 CCCATGAAGGCCACCGCT 62.431 66.667 5.01 0.00 35.39 5.52
3099 3348 2.438434 GTCCCATGAAGGCCACCG 60.438 66.667 5.01 0.00 35.39 4.94
3136 3385 2.983402 TCGAGGACAAGTAGAACACG 57.017 50.000 0.00 0.00 0.00 4.49
3148 3397 2.586357 GCCGCCATCTTCGAGGAC 60.586 66.667 0.00 0.00 0.00 3.85
3196 3445 2.092753 AGAAGATGGATGTGCGGATGTT 60.093 45.455 0.00 0.00 0.00 2.71
3205 3454 3.055530 ACGCAGAGAAAGAAGATGGATGT 60.056 43.478 0.00 0.00 0.00 3.06
3211 3460 4.437239 CCATACACGCAGAGAAAGAAGAT 58.563 43.478 0.00 0.00 0.00 2.40
3212 3461 3.849911 CCATACACGCAGAGAAAGAAGA 58.150 45.455 0.00 0.00 0.00 2.87
3247 3496 3.272334 GCCATCGGCCGTCATCAC 61.272 66.667 27.15 7.47 44.06 3.06
3296 3545 3.110178 CGGGAAACACGACGGCTC 61.110 66.667 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.