Multiple sequence alignment - TraesCS2B01G064800

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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 TraesCS2B01G064800 chr2B 100.000 3570 0 0 1 3570 31299908 31303477 0.000000e+00 6593.0
1 TraesCS2B01G064800 chr2B 90.549 1439 86 14 1058 2476 7776655 7778063 0.000000e+00 1858.0
2 TraesCS2B01G064800 chr2B 84.158 1395 194 15 1069 2457 11478 10105 0.000000e+00 1327.0
3 TraesCS2B01G064800 chr2B 83.477 1392 196 23 1070 2450 319420 318052 0.000000e+00 1266.0
4 TraesCS2B01G064800 chr2B 91.139 158 13 1 799 955 11347037 11347194 2.790000e-51 213.0
5 TraesCS2B01G064800 chr2D 91.365 1575 86 18 1027 2591 2613831 2615365 0.000000e+00 2109.0
6 TraesCS2B01G064800 chr2D 90.827 1112 66 8 1103 2207 2905018 2903936 0.000000e+00 1456.0
7 TraesCS2B01G064800 chr2D 87.043 602 53 11 1 592 2612800 2613386 0.000000e+00 656.0
8 TraesCS2B01G064800 chr2D 89.008 373 23 8 2200 2568 2903305 2902947 2.530000e-121 446.0
9 TraesCS2B01G064800 chr2D 87.413 143 15 1 2221 2363 2902628 2902489 1.030000e-35 161.0
10 TraesCS2B01G064800 chr2D 95.098 102 3 1 587 688 2613556 2613655 3.690000e-35 159.0
11 TraesCS2B01G064800 chr2D 82.258 124 22 0 1 124 220660368 220660245 1.360000e-19 108.0
12 TraesCS2B01G064800 chr6D 89.684 1580 107 14 1008 2575 18097939 18099474 0.000000e+00 1964.0
13 TraesCS2B01G064800 chr6D 84.211 323 32 6 368 688 18097369 18097674 2.690000e-76 296.0
14 TraesCS2B01G064800 chr6D 92.157 51 3 1 954 1003 471069897 471069847 1.780000e-08 71.3
15 TraesCS2B01G064800 chr2A 83.369 1395 210 15 1070 2457 1685670 1687049 0.000000e+00 1271.0
16 TraesCS2B01G064800 chr2A 92.903 155 10 1 799 952 739693742 739693588 1.290000e-54 224.0
17 TraesCS2B01G064800 chr2A 80.451 133 26 0 1519 1651 32265540 32265672 6.310000e-18 102.0
18 TraesCS2B01G064800 chr4D 88.830 949 99 6 2624 3568 80134438 80133493 0.000000e+00 1158.0
19 TraesCS2B01G064800 chr4D 97.436 39 1 0 954 992 416427837 416427875 2.300000e-07 67.6
20 TraesCS2B01G064800 chr7D 83.925 958 145 9 2616 3568 480820184 480819231 0.000000e+00 907.0
21 TraesCS2B01G064800 chr7D 82.143 196 27 4 172 361 503761695 503761888 1.030000e-35 161.0
22 TraesCS2B01G064800 chr3D 82.698 971 158 7 2604 3570 957252 958216 0.000000e+00 854.0
23 TraesCS2B01G064800 chr3D 93.478 46 3 0 954 999 508471343 508471298 6.400000e-08 69.4
24 TraesCS2B01G064800 chr4B 96.053 152 5 1 799 949 404121298 404121449 2.750000e-61 246.0
25 TraesCS2B01G064800 chr4B 95.455 154 7 0 799 952 603998720 603998873 2.750000e-61 246.0
26 TraesCS2B01G064800 chr4B 93.506 154 10 0 799 952 496461502 496461655 2.770000e-56 230.0
27 TraesCS2B01G064800 chr7B 94.156 154 9 0 799 952 742593012 742592859 5.960000e-58 235.0
28 TraesCS2B01G064800 chr7B 91.837 49 4 0 958 1006 397594898 397594850 6.400000e-08 69.4
29 TraesCS2B01G064800 chr3B 92.903 155 10 1 799 952 189100925 189100771 1.290000e-54 224.0
30 TraesCS2B01G064800 chr3B 78.226 124 25 2 1521 1643 20378968 20379090 1.060000e-10 78.7
31 TraesCS2B01G064800 chr3B 95.349 43 2 0 957 999 26779990 26780032 6.400000e-08 69.4
32 TraesCS2B01G064800 chr6A 80.769 286 48 5 1 281 32888769 32888486 2.160000e-52 217.0
33 TraesCS2B01G064800 chr6A 92.453 53 3 1 954 1006 615888583 615888532 1.370000e-09 75.0
34 TraesCS2B01G064800 chrUn 91.613 155 12 1 799 952 87036232 87036386 2.790000e-51 213.0
35 TraesCS2B01G064800 chr7A 90.625 160 13 2 799 957 83138917 83138759 1.000000e-50 211.0
36 TraesCS2B01G064800 chr7A 95.652 46 2 0 954 999 8523429 8523384 1.370000e-09 75.0
37 TraesCS2B01G064800 chr5B 95.349 43 2 0 958 1000 127744605 127744647 6.400000e-08 69.4
38 TraesCS2B01G064800 chr1B 90.566 53 3 1 954 1006 554241242 554241192 6.400000e-08 69.4
39 TraesCS2B01G064800 chr1B 100.000 30 0 0 3483 3512 69552694 69552723 4.980000e-04 56.5


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 TraesCS2B01G064800 chr2B 31299908 31303477 3569 False 6593.000000 6593 100.000000 1 3570 1 chr2B.!!$F3 3569
1 TraesCS2B01G064800 chr2B 7776655 7778063 1408 False 1858.000000 1858 90.549000 1058 2476 1 chr2B.!!$F1 1418
2 TraesCS2B01G064800 chr2B 10105 11478 1373 True 1327.000000 1327 84.158000 1069 2457 1 chr2B.!!$R1 1388
3 TraesCS2B01G064800 chr2B 318052 319420 1368 True 1266.000000 1266 83.477000 1070 2450 1 chr2B.!!$R2 1380
4 TraesCS2B01G064800 chr2D 2612800 2615365 2565 False 974.666667 2109 91.168667 1 2591 3 chr2D.!!$F1 2590
5 TraesCS2B01G064800 chr2D 2902489 2905018 2529 True 687.666667 1456 89.082667 1103 2568 3 chr2D.!!$R2 1465
6 TraesCS2B01G064800 chr6D 18097369 18099474 2105 False 1130.000000 1964 86.947500 368 2575 2 chr6D.!!$F1 2207
7 TraesCS2B01G064800 chr2A 1685670 1687049 1379 False 1271.000000 1271 83.369000 1070 2457 1 chr2A.!!$F1 1387
8 TraesCS2B01G064800 chr4D 80133493 80134438 945 True 1158.000000 1158 88.830000 2624 3568 1 chr4D.!!$R1 944
9 TraesCS2B01G064800 chr7D 480819231 480820184 953 True 907.000000 907 83.925000 2616 3568 1 chr7D.!!$R1 952
10 TraesCS2B01G064800 chr3D 957252 958216 964 False 854.000000 854 82.698000 2604 3570 1 chr3D.!!$F1 966

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
851 1125 0.03254 CCAGTTTCCTTTGCTGCACC 59.967 55.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2588 3572 0.106769 TGCTTCAGGGAACTTGCACA 60.107 50.0 0.0 0.0 40.21 4.57 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
99 100 4.346734 AATTCAACAACAGCGCTATCTG 57.653 40.909 10.99 10.45 39.86 2.90
111 112 5.212934 CAGCGCTATCTGTTTTATCGTCTA 58.787 41.667 10.99 0.00 0.00 2.59
123 124 7.981142 TGTTTTATCGTCTAATGAATTGGACC 58.019 34.615 12.30 0.00 42.95 4.46
127 128 3.517901 TCGTCTAATGAATTGGACCAGGT 59.482 43.478 12.30 0.00 42.95 4.00
136 137 0.331278 TTGGACCAGGTGGCTTATGG 59.669 55.000 0.00 1.64 39.32 2.74
152 153 4.934602 GCTTATGGGCATCTCATCTTAGAC 59.065 45.833 0.00 0.00 0.00 2.59
161 162 5.695816 GCATCTCATCTTAGACATCAAGGAC 59.304 44.000 0.00 0.00 0.00 3.85
249 250 5.530915 TGGCAAATTAGGGTAGAATTGATCG 59.469 40.000 0.00 0.00 0.00 3.69
255 256 6.665992 TTAGGGTAGAATTGATCGTAGCAT 57.334 37.500 0.00 0.00 0.00 3.79
257 258 3.997021 GGGTAGAATTGATCGTAGCATGG 59.003 47.826 0.00 0.00 0.00 3.66
261 262 3.562973 AGAATTGATCGTAGCATGGCTTG 59.437 43.478 0.00 0.00 40.44 4.01
266 267 0.323302 TCGTAGCATGGCTTGTTGGA 59.677 50.000 0.00 0.00 40.44 3.53
269 270 2.287915 CGTAGCATGGCTTGTTGGATAC 59.712 50.000 0.00 0.00 40.44 2.24
280 281 1.837439 TGTTGGATACGAAGAGGCCAT 59.163 47.619 5.01 0.00 42.51 4.40
282 283 1.048601 TGGATACGAAGAGGCCATCC 58.951 55.000 5.01 7.35 42.51 3.51
283 284 1.048601 GGATACGAAGAGGCCATCCA 58.951 55.000 5.01 0.00 36.09 3.41
290 291 3.646162 ACGAAGAGGCCATCCATGTATTA 59.354 43.478 5.01 0.00 33.74 0.98
300 301 6.096846 GGCCATCCATGTATTACTGAACTTTT 59.903 38.462 0.00 0.00 0.00 2.27
304 305 8.729756 CATCCATGTATTACTGAACTTTTGTCA 58.270 33.333 0.00 0.00 0.00 3.58
308 309 7.189693 TGTATTACTGAACTTTTGTCAGCAG 57.810 36.000 1.41 0.00 33.75 4.24
310 311 5.734855 TTACTGAACTTTTGTCAGCAGAC 57.265 39.130 1.64 1.64 45.19 3.51
320 321 3.650070 TGTCAGCAGACTGTAACTCTG 57.350 47.619 10.83 2.68 45.20 3.35
338 339 2.825532 TCTGCACCTTTGGAATAAAGCC 59.174 45.455 0.00 0.00 0.00 4.35
342 343 3.701664 CACCTTTGGAATAAAGCCCTCT 58.298 45.455 0.00 0.00 0.00 3.69
382 393 5.718724 AAGAGGCAAAAGAGAGAAATTGG 57.281 39.130 0.00 0.00 0.00 3.16
390 401 7.093771 GGCAAAAGAGAGAAATTGGATTCCTAA 60.094 37.037 3.95 0.00 0.00 2.69
484 497 9.902684 TTAGGATTATAACAAAATACGGTTCCA 57.097 29.630 0.00 0.00 0.00 3.53
513 526 4.833390 CCTACCCCAAAACTCAGACTTAG 58.167 47.826 0.00 0.00 0.00 2.18
516 529 3.072622 ACCCCAAAACTCAGACTTAGTCC 59.927 47.826 8.96 0.00 32.18 3.85
523 536 7.172703 CCAAAACTCAGACTTAGTCCGTTAAAT 59.827 37.037 8.96 0.00 32.18 1.40
524 537 9.199982 CAAAACTCAGACTTAGTCCGTTAAATA 57.800 33.333 8.96 0.00 32.18 1.40
525 538 9.768662 AAAACTCAGACTTAGTCCGTTAAATAA 57.231 29.630 8.96 0.00 32.18 1.40
555 568 5.142061 TCGACTTAGTCCTATGCACAAAA 57.858 39.130 6.80 0.00 0.00 2.44
647 835 8.011106 ACATGCATGCTTTTTAAAAGAAAATCG 58.989 29.630 26.53 5.79 0.00 3.34
731 968 6.179504 ACATACTCCGCTTGTATATACTCG 57.820 41.667 13.89 13.08 0.00 4.18
739 1013 5.334646 CCGCTTGTATATACTCGCTCTGTAA 60.335 44.000 13.89 0.00 0.00 2.41
741 1015 6.086502 CGCTTGTATATACTCGCTCTGTAAAC 59.913 42.308 13.89 0.00 0.00 2.01
777 1051 8.757982 ATTTACAGAGAATTTGGCTATCATGT 57.242 30.769 0.00 0.00 0.00 3.21
778 1052 9.851686 ATTTACAGAGAATTTGGCTATCATGTA 57.148 29.630 0.00 0.00 0.00 2.29
779 1053 8.662781 TTACAGAGAATTTGGCTATCATGTAC 57.337 34.615 0.00 0.00 0.00 2.90
780 1054 6.058183 ACAGAGAATTTGGCTATCATGTACC 58.942 40.000 0.00 0.00 0.00 3.34
782 1056 6.543465 CAGAGAATTTGGCTATCATGTACCAA 59.457 38.462 7.19 7.19 40.34 3.67
783 1057 7.230108 CAGAGAATTTGGCTATCATGTACCAAT 59.770 37.037 10.66 0.68 41.59 3.16
784 1058 8.439971 AGAGAATTTGGCTATCATGTACCAATA 58.560 33.333 10.66 5.09 41.59 1.90
785 1059 8.396272 AGAATTTGGCTATCATGTACCAATAC 57.604 34.615 10.66 7.03 41.59 1.89
786 1060 7.998383 AGAATTTGGCTATCATGTACCAATACA 59.002 33.333 10.66 0.00 45.37 2.29
802 1076 8.996271 GTACCAATACATATTACTTTAGTGGGC 58.004 37.037 0.00 0.00 34.64 5.36
803 1077 7.002276 ACCAATACATATTACTTTAGTGGGCC 58.998 38.462 0.00 0.00 34.64 5.80
805 1079 7.724061 CCAATACATATTACTTTAGTGGGCCTT 59.276 37.037 4.53 0.00 0.00 4.35
806 1080 8.567948 CAATACATATTACTTTAGTGGGCCTTG 58.432 37.037 4.53 0.00 0.00 3.61
808 1082 6.490492 ACATATTACTTTAGTGGGCCTTGTT 58.510 36.000 4.53 0.00 0.00 2.83
810 1084 7.453439 ACATATTACTTTAGTGGGCCTTGTTTT 59.547 33.333 4.53 0.00 0.00 2.43
812 1086 9.709387 ATATTACTTTAGTGGGCCTTGTTTTAT 57.291 29.630 4.53 0.00 0.00 1.40
813 1087 7.842887 TTACTTTAGTGGGCCTTGTTTTATT 57.157 32.000 4.53 0.00 0.00 1.40
814 1088 6.740944 ACTTTAGTGGGCCTTGTTTTATTT 57.259 33.333 4.53 0.00 0.00 1.40
815 1089 7.131907 ACTTTAGTGGGCCTTGTTTTATTTT 57.868 32.000 4.53 0.00 0.00 1.82
816 1090 6.989759 ACTTTAGTGGGCCTTGTTTTATTTTG 59.010 34.615 4.53 0.00 0.00 2.44
817 1091 3.738982 AGTGGGCCTTGTTTTATTTTGC 58.261 40.909 4.53 0.00 0.00 3.68
819 1093 4.133820 GTGGGCCTTGTTTTATTTTGCTT 58.866 39.130 4.53 0.00 0.00 3.91
820 1094 4.024133 GTGGGCCTTGTTTTATTTTGCTTG 60.024 41.667 4.53 0.00 0.00 4.01
821 1095 3.058293 GGGCCTTGTTTTATTTTGCTTGC 60.058 43.478 0.84 0.00 0.00 4.01
822 1096 3.814842 GGCCTTGTTTTATTTTGCTTGCT 59.185 39.130 0.00 0.00 0.00 3.91
823 1097 4.083855 GGCCTTGTTTTATTTTGCTTGCTC 60.084 41.667 0.00 0.00 0.00 4.26
825 1099 5.333568 GCCTTGTTTTATTTTGCTTGCTCTG 60.334 40.000 0.00 0.00 0.00 3.35
826 1100 5.754890 CCTTGTTTTATTTTGCTTGCTCTGT 59.245 36.000 0.00 0.00 0.00 3.41
827 1101 6.292488 CCTTGTTTTATTTTGCTTGCTCTGTG 60.292 38.462 0.00 0.00 0.00 3.66
830 1104 5.512753 TTTATTTTGCTTGCTCTGTGTGA 57.487 34.783 0.00 0.00 0.00 3.58
840 1114 1.517242 CTCTGTGTGAGCCAGTTTCC 58.483 55.000 0.00 0.00 35.84 3.13
843 1117 2.092429 TCTGTGTGAGCCAGTTTCCTTT 60.092 45.455 0.00 0.00 0.00 3.11
844 1118 2.023673 TGTGTGAGCCAGTTTCCTTTG 58.976 47.619 0.00 0.00 0.00 2.77
845 1119 1.032014 TGTGAGCCAGTTTCCTTTGC 58.968 50.000 0.00 0.00 0.00 3.68
846 1120 1.322442 GTGAGCCAGTTTCCTTTGCT 58.678 50.000 0.00 0.00 34.40 3.91
848 1122 0.038801 GAGCCAGTTTCCTTTGCTGC 60.039 55.000 0.00 0.00 31.23 5.25
849 1123 0.756442 AGCCAGTTTCCTTTGCTGCA 60.756 50.000 0.00 0.00 0.00 4.41
850 1124 0.598419 GCCAGTTTCCTTTGCTGCAC 60.598 55.000 0.00 0.00 0.00 4.57
851 1125 0.032540 CCAGTTTCCTTTGCTGCACC 59.967 55.000 0.00 0.00 0.00 5.01
853 1127 0.746659 AGTTTCCTTTGCTGCACCAC 59.253 50.000 0.00 0.00 0.00 4.16
855 1129 1.136891 GTTTCCTTTGCTGCACCACTT 59.863 47.619 0.00 0.00 0.00 3.16
856 1130 1.484038 TTCCTTTGCTGCACCACTTT 58.516 45.000 0.00 0.00 0.00 2.66
857 1131 2.356665 TCCTTTGCTGCACCACTTTA 57.643 45.000 0.00 0.00 0.00 1.85
858 1132 1.953686 TCCTTTGCTGCACCACTTTAC 59.046 47.619 0.00 0.00 0.00 2.01
859 1133 1.680735 CCTTTGCTGCACCACTTTACA 59.319 47.619 0.00 0.00 0.00 2.41
860 1134 2.100584 CCTTTGCTGCACCACTTTACAA 59.899 45.455 0.00 0.00 0.00 2.41
861 1135 3.374745 CTTTGCTGCACCACTTTACAAG 58.625 45.455 0.00 0.00 0.00 3.16
862 1136 2.340210 TGCTGCACCACTTTACAAGA 57.660 45.000 0.00 0.00 0.00 3.02
863 1137 1.946768 TGCTGCACCACTTTACAAGAC 59.053 47.619 0.00 0.00 0.00 3.01
864 1138 1.946768 GCTGCACCACTTTACAAGACA 59.053 47.619 0.00 0.00 0.00 3.41
865 1139 2.554032 GCTGCACCACTTTACAAGACAT 59.446 45.455 0.00 0.00 0.00 3.06
866 1140 3.004734 GCTGCACCACTTTACAAGACATT 59.995 43.478 0.00 0.00 0.00 2.71
867 1141 4.787598 CTGCACCACTTTACAAGACATTC 58.212 43.478 0.00 0.00 0.00 2.67
868 1142 4.460263 TGCACCACTTTACAAGACATTCT 58.540 39.130 0.00 0.00 0.00 2.40
869 1143 4.887071 TGCACCACTTTACAAGACATTCTT 59.113 37.500 0.00 0.00 37.14 2.52
904 1178 8.980143 ATTTATTTATAAATGTGGCCGTATGC 57.020 30.769 18.98 0.00 40.42 3.14
905 1179 7.511959 TTATTTATAAATGTGGCCGTATGCA 57.488 32.000 18.98 0.00 43.89 3.96
906 1180 6.588719 ATTTATAAATGTGGCCGTATGCAT 57.411 33.333 9.93 3.79 43.89 3.96
907 1181 5.621197 TTATAAATGTGGCCGTATGCATC 57.379 39.130 0.19 0.00 43.89 3.91
908 1182 2.057137 AAATGTGGCCGTATGCATCT 57.943 45.000 0.19 0.00 43.89 2.90
909 1183 2.057137 AATGTGGCCGTATGCATCTT 57.943 45.000 0.19 0.00 43.89 2.40
910 1184 2.057137 ATGTGGCCGTATGCATCTTT 57.943 45.000 0.19 0.00 43.89 2.52
911 1185 1.378531 TGTGGCCGTATGCATCTTTC 58.621 50.000 0.19 0.00 43.89 2.62
912 1186 1.065491 TGTGGCCGTATGCATCTTTCT 60.065 47.619 0.19 0.00 43.89 2.52
913 1187 1.331756 GTGGCCGTATGCATCTTTCTG 59.668 52.381 0.19 0.00 43.89 3.02
914 1188 1.209261 TGGCCGTATGCATCTTTCTGA 59.791 47.619 0.19 0.00 43.89 3.27
915 1189 2.158769 TGGCCGTATGCATCTTTCTGAT 60.159 45.455 0.19 0.00 43.89 2.90
924 1198 1.948145 CATCTTTCTGATGCAGAGGCC 59.052 52.381 0.00 0.00 44.96 5.19
925 1199 0.986527 TCTTTCTGATGCAGAGGCCA 59.013 50.000 5.01 0.00 41.75 5.36
926 1200 1.065636 TCTTTCTGATGCAGAGGCCAG 60.066 52.381 5.01 0.00 41.75 4.85
927 1201 0.034767 TTTCTGATGCAGAGGCCAGG 60.035 55.000 5.01 0.00 41.75 4.45
928 1202 1.918467 TTCTGATGCAGAGGCCAGGG 61.918 60.000 5.01 0.00 41.75 4.45
929 1203 2.285592 TGATGCAGAGGCCAGGGA 60.286 61.111 5.01 0.00 40.13 4.20
930 1204 1.918467 CTGATGCAGAGGCCAGGGAA 61.918 60.000 5.01 0.00 40.13 3.97
931 1205 1.153005 GATGCAGAGGCCAGGGAAG 60.153 63.158 5.01 0.00 40.13 3.46
932 1206 3.355957 ATGCAGAGGCCAGGGAAGC 62.356 63.158 5.01 0.00 40.13 3.86
939 1213 2.685999 GCCAGGGAAGCCTCCATT 59.314 61.111 3.19 0.00 44.51 3.16
940 1214 1.000866 GCCAGGGAAGCCTCCATTT 59.999 57.895 3.19 0.00 44.51 2.32
941 1215 0.615827 GCCAGGGAAGCCTCCATTTT 60.616 55.000 3.19 0.00 44.51 1.82
942 1216 1.942776 CCAGGGAAGCCTCCATTTTT 58.057 50.000 3.19 0.00 44.51 1.94
943 1217 1.551883 CCAGGGAAGCCTCCATTTTTG 59.448 52.381 3.19 0.00 44.51 2.44
944 1218 2.528564 CAGGGAAGCCTCCATTTTTGA 58.471 47.619 3.19 0.00 44.51 2.69
945 1219 2.899256 CAGGGAAGCCTCCATTTTTGAA 59.101 45.455 3.19 0.00 44.51 2.69
946 1220 3.324556 CAGGGAAGCCTCCATTTTTGAAA 59.675 43.478 3.19 0.00 44.51 2.69
947 1221 3.973305 AGGGAAGCCTCCATTTTTGAAAA 59.027 39.130 3.19 0.00 44.51 2.29
948 1222 4.411869 AGGGAAGCCTCCATTTTTGAAAAA 59.588 37.500 5.47 5.47 44.51 1.94
1024 1302 8.844865 TGTATAAGTATGATAGCCATGATCCT 57.155 34.615 0.00 0.00 36.71 3.24
1025 1303 8.918116 TGTATAAGTATGATAGCCATGATCCTC 58.082 37.037 0.00 0.00 36.71 3.71
1026 1304 7.984859 ATAAGTATGATAGCCATGATCCTCA 57.015 36.000 0.00 0.00 36.71 3.86
1027 1305 6.887886 AAGTATGATAGCCATGATCCTCAT 57.112 37.500 0.00 0.34 37.65 2.90
1030 1308 5.774102 ATGATAGCCATGATCCTCATCAA 57.226 39.130 0.00 0.00 42.53 2.57
1031 1309 5.161943 TGATAGCCATGATCCTCATCAAG 57.838 43.478 0.00 0.00 42.53 3.02
1042 1320 6.111382 TGATCCTCATCAAGATCAAGTTGAC 58.889 40.000 7.96 2.64 44.44 3.18
1074 1357 1.376543 TTAGACCACCGAGACTAGCG 58.623 55.000 0.00 0.00 0.00 4.26
1172 1464 2.682494 CCGGGGAAGACGAGGGAA 60.682 66.667 0.00 0.00 0.00 3.97
1238 1530 2.743718 CAGGTCACGGTGCTCCTT 59.256 61.111 17.52 0.00 0.00 3.36
1266 1558 4.329545 GCTCGGTTCACCAGCCCA 62.330 66.667 8.46 0.00 35.53 5.36
1355 1653 3.300765 ACCGCCGACGAAGAAGGT 61.301 61.111 0.00 0.00 43.93 3.50
1445 1746 2.143419 GGATCACGGGCTCCTGGAT 61.143 63.158 0.00 0.00 0.00 3.41
1769 2073 1.812922 GTCGCTGATGCTGGACCTG 60.813 63.158 0.00 0.00 36.97 4.00
1771 2075 2.827642 GCTGATGCTGGACCTGGC 60.828 66.667 0.00 2.01 36.03 4.85
1994 2316 2.489971 CTGGCCTTCTTTGTGAACGTA 58.510 47.619 3.32 0.00 0.00 3.57
2250 3220 1.153489 CTGATGGTGACGAGCTGGG 60.153 63.158 0.00 0.00 0.00 4.45
2271 3241 2.163818 GAACATCAGGTTCGACCACA 57.836 50.000 6.78 0.00 45.82 4.17
2357 3327 1.004560 CATGGCGTCACTGTCCTGT 60.005 57.895 0.00 0.00 0.00 4.00
2459 3432 2.713770 CAGCTCGCACATGCATCC 59.286 61.111 0.00 0.00 42.21 3.51
2501 3475 2.034939 TGAACTGAATTGTTGCTGGCAG 59.965 45.455 10.94 10.94 0.00 4.85
2504 3484 0.675083 TGAATTGTTGCTGGCAGGTG 59.325 50.000 17.64 0.00 0.00 4.00
2512 3492 1.290955 GCTGGCAGGTGTGTACGTA 59.709 57.895 17.64 0.00 0.00 3.57
2513 3493 1.012486 GCTGGCAGGTGTGTACGTAC 61.012 60.000 18.90 18.90 0.00 3.67
2514 3494 0.315886 CTGGCAGGTGTGTACGTACA 59.684 55.000 24.10 24.10 0.00 2.90
2575 3559 3.071479 TGAGTTGTTCCGGTGAATAAGC 58.929 45.455 0.00 0.00 33.01 3.09
2576 3560 3.071479 GAGTTGTTCCGGTGAATAAGCA 58.929 45.455 0.00 0.00 33.01 3.91
2577 3561 3.074412 AGTTGTTCCGGTGAATAAGCAG 58.926 45.455 0.00 0.00 33.01 4.24
2578 3562 2.107950 TGTTCCGGTGAATAAGCAGG 57.892 50.000 0.00 0.00 31.98 4.85
2579 3563 1.349688 TGTTCCGGTGAATAAGCAGGT 59.650 47.619 0.00 0.00 31.98 4.00
2580 3564 2.568062 TGTTCCGGTGAATAAGCAGGTA 59.432 45.455 0.00 0.00 31.98 3.08
2583 3567 1.474498 CCGGTGAATAAGCAGGTACCC 60.474 57.143 8.74 0.00 0.00 3.69
2585 3569 2.158813 CGGTGAATAAGCAGGTACCCAT 60.159 50.000 8.74 0.00 0.00 4.00
2586 3570 3.684413 CGGTGAATAAGCAGGTACCCATT 60.684 47.826 8.74 3.62 0.00 3.16
2587 3571 4.443739 CGGTGAATAAGCAGGTACCCATTA 60.444 45.833 8.74 5.92 0.00 1.90
2588 3572 5.631119 GGTGAATAAGCAGGTACCCATTAT 58.369 41.667 8.74 8.05 0.00 1.28
2589 3573 5.473504 GGTGAATAAGCAGGTACCCATTATG 59.526 44.000 8.74 0.32 0.00 1.90
2590 3574 6.062095 GTGAATAAGCAGGTACCCATTATGT 58.938 40.000 8.74 2.89 0.00 2.29
2591 3575 6.017109 GTGAATAAGCAGGTACCCATTATGTG 60.017 42.308 8.74 0.00 0.00 3.21
2594 3578 2.025416 AGCAGGTACCCATTATGTGCAA 60.025 45.455 18.85 0.00 31.75 4.08
2595 3579 2.358898 GCAGGTACCCATTATGTGCAAG 59.641 50.000 8.74 0.00 0.00 4.01
2596 3580 3.620488 CAGGTACCCATTATGTGCAAGT 58.380 45.455 8.74 0.00 0.00 3.16
2597 3581 4.016444 CAGGTACCCATTATGTGCAAGTT 58.984 43.478 8.74 0.00 0.00 2.66
2598 3582 4.096382 CAGGTACCCATTATGTGCAAGTTC 59.904 45.833 8.74 0.00 0.00 3.01
2599 3583 3.380320 GGTACCCATTATGTGCAAGTTCC 59.620 47.826 0.00 0.00 0.00 3.62
2600 3584 2.456577 ACCCATTATGTGCAAGTTCCC 58.543 47.619 0.00 0.00 0.00 3.97
2602 3586 2.428171 CCCATTATGTGCAAGTTCCCTG 59.572 50.000 0.00 0.00 0.00 4.45
2607 3591 0.106769 TGTGCAAGTTCCCTGAAGCA 60.107 50.000 0.00 0.00 0.00 3.91
2608 3592 1.251251 GTGCAAGTTCCCTGAAGCAT 58.749 50.000 0.00 0.00 34.24 3.79
2613 3597 2.624838 CAAGTTCCCTGAAGCATGTGTT 59.375 45.455 0.00 0.00 0.00 3.32
2614 3598 2.233271 AGTTCCCTGAAGCATGTGTTG 58.767 47.619 0.00 0.00 0.00 3.33
2620 3604 2.605338 CCTGAAGCATGTGTTGGTTTCG 60.605 50.000 0.00 0.00 45.76 3.46
2626 3610 1.066908 CATGTGTTGGTTTCGGTTGCT 59.933 47.619 0.00 0.00 0.00 3.91
2646 3631 1.235724 GGTGTGGTAAACTCCAGTGC 58.764 55.000 0.00 0.00 41.33 4.40
2664 3649 3.563808 AGTGCGATAAACAAGTCAAGCAA 59.436 39.130 0.00 0.00 35.05 3.91
2670 3655 6.402118 GCGATAAACAAGTCAAGCAATGTCTA 60.402 38.462 0.00 0.00 0.00 2.59
2674 3659 4.655963 ACAAGTCAAGCAATGTCTATGGT 58.344 39.130 0.00 0.00 0.00 3.55
2746 3821 5.163088 GGAACCTATGATGGAATACTTGGGT 60.163 44.000 0.00 0.00 0.00 4.51
2751 3826 4.879295 TGATGGAATACTTGGGTTGGAT 57.121 40.909 0.00 0.00 0.00 3.41
2762 3837 0.548510 GGGTTGGATTGGCTAGCTCT 59.451 55.000 15.72 0.00 0.00 4.09
2790 3865 2.366916 CCCTATGCAGGTTGACTAGGAG 59.633 54.545 8.56 0.00 40.79 3.69
2816 3892 2.368875 AGTGGTTGTCCTTCCAGTACAG 59.631 50.000 0.00 0.00 35.85 2.74
2829 3959 6.099269 CCTTCCAGTACAGGGCTAAAACTATA 59.901 42.308 4.24 0.00 0.00 1.31
2831 3961 7.685849 TCCAGTACAGGGCTAAAACTATAAT 57.314 36.000 4.24 0.00 0.00 1.28
2880 4010 3.618150 GTGCTTTCACAGTTGTTGCAATT 59.382 39.130 0.59 0.00 42.66 2.32
2903 4033 1.888512 TGCCACAGAAATTGAAGAGGC 59.111 47.619 0.00 0.00 41.15 4.70
2905 4035 2.094854 GCCACAGAAATTGAAGAGGCTG 60.095 50.000 0.00 0.00 37.89 4.85
2906 4036 3.152341 CCACAGAAATTGAAGAGGCTGT 58.848 45.455 0.00 0.00 37.09 4.40
2907 4037 4.156664 CACAGAAATTGAAGAGGCTGTG 57.843 45.455 0.00 0.00 44.60 3.66
2908 4038 3.057736 CACAGAAATTGAAGAGGCTGTGG 60.058 47.826 0.00 0.00 45.60 4.17
2909 4039 3.152341 CAGAAATTGAAGAGGCTGTGGT 58.848 45.455 0.00 0.00 0.00 4.16
2911 4041 4.154918 CAGAAATTGAAGAGGCTGTGGTAC 59.845 45.833 0.00 0.00 0.00 3.34
2928 4058 5.147330 TGGTACACAGACCTGAAATACAG 57.853 43.478 3.76 0.00 45.36 2.74
2946 4076 2.558359 ACAGGCTTTGCTGGACAAATAC 59.442 45.455 0.00 0.00 46.90 1.89
2973 4103 1.604278 GTGTTCTCTGAACCTGTTGGC 59.396 52.381 7.81 0.00 36.63 4.52
3000 4130 5.455899 GCCACCTAGGAGAGAATTTGATCAT 60.456 44.000 17.98 0.00 41.22 2.45
3027 4157 1.304547 ACTAGTGCCAGGAGCTCGT 60.305 57.895 7.83 5.12 44.23 4.18
3049 4179 5.625886 CGTCCAGTTTCCATTAGACCATACA 60.626 44.000 0.00 0.00 0.00 2.29
3057 4187 5.376625 TCCATTAGACCATACAGAATTGCC 58.623 41.667 0.00 0.00 0.00 4.52
3100 4230 4.892934 TGGAAAAACAAGTGGCTGAACTAT 59.107 37.500 0.00 0.00 0.00 2.12
3171 4301 4.704057 GCTCTCATGGTCAAAAAGAAGGAT 59.296 41.667 0.00 0.00 0.00 3.24
3178 4308 3.366374 GGTCAAAAAGAAGGATGAAGGCG 60.366 47.826 0.00 0.00 0.00 5.52
3189 4319 0.326264 ATGAAGGCGCTTGGAGACTT 59.674 50.000 7.64 0.00 0.00 3.01
3203 4333 7.225538 CGCTTGGAGACTTGTAATAGATTTCAT 59.774 37.037 0.00 0.00 0.00 2.57
3249 4379 5.402054 AGGGCAAATATCCAATTCCAGTA 57.598 39.130 0.00 0.00 0.00 2.74
3270 4400 8.887717 CCAGTAATTGAAGAATTGTTAGAGGAG 58.112 37.037 0.00 0.00 33.63 3.69
3275 4405 6.097915 TGAAGAATTGTTAGAGGAGTTCGT 57.902 37.500 0.00 0.00 0.00 3.85
3298 4428 6.224584 GTTGGAGCTCACTAGTTTTCTAAGT 58.775 40.000 17.19 0.00 31.45 2.24
3370 4500 3.297134 TCAAGACTGCCTTCCAAACTT 57.703 42.857 0.00 0.00 31.42 2.66
3387 4517 4.634012 AACTTACTGTGGCCACTATGAA 57.366 40.909 34.75 21.37 0.00 2.57
3396 4526 3.378427 GTGGCCACTATGAATTCCTTGTC 59.622 47.826 29.12 0.00 0.00 3.18
3397 4527 2.952310 GGCCACTATGAATTCCTTGTCC 59.048 50.000 0.00 0.00 0.00 4.02
3398 4528 3.620488 GCCACTATGAATTCCTTGTCCA 58.380 45.455 2.27 0.00 0.00 4.02
3407 4537 0.827507 TTCCTTGTCCAGGCCTTTGC 60.828 55.000 0.00 0.00 43.55 3.68
3414 4544 1.272490 GTCCAGGCCTTTGCTTTAACC 59.728 52.381 0.00 0.00 37.74 2.85
3420 4550 0.601057 CCTTTGCTTTAACCGGTGGG 59.399 55.000 8.52 0.00 40.11 4.61
3432 4562 1.190643 CCGGTGGGCCAAATACATTT 58.809 50.000 8.40 0.00 34.09 2.32
3433 4563 1.552792 CCGGTGGGCCAAATACATTTT 59.447 47.619 8.40 0.00 34.09 1.82
3457 4587 4.922206 AGGAGCCATGAACAGTGATTTAA 58.078 39.130 0.00 0.00 0.00 1.52
3465 4595 4.798882 TGAACAGTGATTTAACCCCAGTT 58.201 39.130 0.00 0.00 40.15 3.16
3471 4601 4.105697 AGTGATTTAACCCCAGTTTCCAGA 59.894 41.667 0.00 0.00 37.42 3.86
3476 4606 3.441500 AACCCCAGTTTCCAGAGAATC 57.558 47.619 0.00 0.00 29.61 2.52
3537 4667 4.598036 AACATTCCTGGATCACCTGAAT 57.402 40.909 0.00 0.00 38.16 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 4.564406 CCATGGGAAGAGGAGAATATTCGG 60.564 50.000 2.85 0.00 0.00 4.30
49 50 2.922283 ACAACCATGGGAAGAGGAGAAT 59.078 45.455 18.09 0.00 0.00 2.40
88 89 4.045104 AGACGATAAAACAGATAGCGCTG 58.955 43.478 22.90 6.48 41.63 5.18
89 90 4.308899 AGACGATAAAACAGATAGCGCT 57.691 40.909 17.26 17.26 35.71 5.92
90 91 6.362551 TCATTAGACGATAAAACAGATAGCGC 59.637 38.462 0.00 0.00 35.71 5.92
99 100 7.981142 TGGTCCAATTCATTAGACGATAAAAC 58.019 34.615 0.00 0.00 30.66 2.43
100 101 7.282224 CCTGGTCCAATTCATTAGACGATAAAA 59.718 37.037 0.00 0.00 30.66 1.52
107 108 3.947834 CCACCTGGTCCAATTCATTAGAC 59.052 47.826 0.00 0.00 0.00 2.59
111 112 1.077663 AGCCACCTGGTCCAATTCATT 59.922 47.619 0.00 0.00 37.57 2.57
123 124 0.184451 AGATGCCCATAAGCCACCTG 59.816 55.000 0.00 0.00 0.00 4.00
127 128 2.060275 AGATGAGATGCCCATAAGCCA 58.940 47.619 0.00 0.00 0.00 4.75
136 137 4.996122 CCTTGATGTCTAAGATGAGATGCC 59.004 45.833 0.00 0.00 0.00 4.40
161 162 1.584724 ACTCCCTACCAACCATCAGG 58.415 55.000 0.00 0.00 42.21 3.86
202 203 7.363968 GCCAGACTACTACTCTATTTTGTTCCT 60.364 40.741 0.00 0.00 0.00 3.36
216 217 5.354842 ACCCTAATTTGCCAGACTACTAC 57.645 43.478 0.00 0.00 0.00 2.73
235 236 3.997021 CCATGCTACGATCAATTCTACCC 59.003 47.826 0.00 0.00 0.00 3.69
249 250 2.287915 CGTATCCAACAAGCCATGCTAC 59.712 50.000 0.00 0.00 38.25 3.58
255 256 2.354704 CCTCTTCGTATCCAACAAGCCA 60.355 50.000 0.00 0.00 0.00 4.75
257 258 1.666189 GCCTCTTCGTATCCAACAAGC 59.334 52.381 0.00 0.00 0.00 4.01
261 262 2.484889 GATGGCCTCTTCGTATCCAAC 58.515 52.381 3.32 0.00 0.00 3.77
266 267 2.050144 ACATGGATGGCCTCTTCGTAT 58.950 47.619 3.32 0.00 34.31 3.06
269 270 2.847327 ATACATGGATGGCCTCTTCG 57.153 50.000 3.32 0.00 34.31 3.79
280 281 7.094805 GCTGACAAAAGTTCAGTAATACATGGA 60.095 37.037 0.00 0.00 42.26 3.41
282 283 7.584108 TGCTGACAAAAGTTCAGTAATACATG 58.416 34.615 0.00 0.00 42.26 3.21
283 284 7.661437 TCTGCTGACAAAAGTTCAGTAATACAT 59.339 33.333 1.59 0.00 42.26 2.29
290 291 3.624861 CAGTCTGCTGACAAAAGTTCAGT 59.375 43.478 23.61 0.00 45.28 3.41
300 301 3.650070 CAGAGTTACAGTCTGCTGACA 57.350 47.619 23.61 2.51 45.28 3.58
308 309 2.808543 CCAAAGGTGCAGAGTTACAGTC 59.191 50.000 0.00 0.00 0.00 3.51
310 311 3.126001 TCCAAAGGTGCAGAGTTACAG 57.874 47.619 0.00 0.00 0.00 2.74
320 321 2.166459 GAGGGCTTTATTCCAAAGGTGC 59.834 50.000 0.00 0.00 0.00 5.01
323 324 5.245977 TGAAAAGAGGGCTTTATTCCAAAGG 59.754 40.000 0.00 0.00 43.32 3.11
358 359 6.324770 TCCAATTTCTCTCTTTTGCCTCTTTT 59.675 34.615 0.00 0.00 0.00 2.27
363 364 5.186603 GGAATCCAATTTCTCTCTTTTGCCT 59.813 40.000 0.00 0.00 0.00 4.75
364 365 5.186603 AGGAATCCAATTTCTCTCTTTTGCC 59.813 40.000 0.61 0.00 0.00 4.52
365 366 6.278172 AGGAATCCAATTTCTCTCTTTTGC 57.722 37.500 0.61 0.00 0.00 3.68
366 367 8.465201 CCTTAGGAATCCAATTTCTCTCTTTTG 58.535 37.037 0.61 0.00 29.03 2.44
479 492 0.179065 GGGGTAGGCATACGTGGAAC 60.179 60.000 0.00 0.00 32.24 3.62
481 494 0.618107 TTGGGGTAGGCATACGTGGA 60.618 55.000 0.00 0.00 32.24 4.02
483 496 1.741145 GTTTTGGGGTAGGCATACGTG 59.259 52.381 0.00 0.00 32.24 4.49
484 497 1.631898 AGTTTTGGGGTAGGCATACGT 59.368 47.619 1.93 0.00 32.24 3.57
555 568 1.987080 ATCAACTAGGGGAGGCCTTT 58.013 50.000 6.77 0.00 0.00 3.11
566 579 5.728351 TTTTAATCCCGCGAATCAACTAG 57.272 39.130 8.23 0.00 0.00 2.57
616 804 8.830201 TCTTTTAAAAAGCATGCATGTGTTAT 57.170 26.923 26.79 13.70 0.00 1.89
617 805 8.654230 TTCTTTTAAAAAGCATGCATGTGTTA 57.346 26.923 26.79 16.19 0.00 2.41
647 835 7.698836 AATTTGTCACACTTGAAATGCTTAC 57.301 32.000 0.00 0.00 31.90 2.34
688 876 2.866872 TTGGCGCTGTCCCAATTAG 58.133 52.632 7.64 0.00 37.43 1.73
692 904 0.034574 ATGTATTGGCGCTGTCCCAA 60.035 50.000 7.64 2.35 45.63 4.12
695 907 2.135933 GAGTATGTATTGGCGCTGTCC 58.864 52.381 7.64 0.00 0.00 4.02
761 1035 8.165239 TGTATTGGTACATGATAGCCAAATTC 57.835 34.615 0.00 4.45 43.19 2.17
776 1050 8.996271 GCCCACTAAAGTAATATGTATTGGTAC 58.004 37.037 0.00 0.00 0.00 3.34
777 1051 8.158789 GGCCCACTAAAGTAATATGTATTGGTA 58.841 37.037 0.00 0.00 0.00 3.25
778 1052 7.002276 GGCCCACTAAAGTAATATGTATTGGT 58.998 38.462 0.00 0.00 0.00 3.67
779 1053 7.231467 AGGCCCACTAAAGTAATATGTATTGG 58.769 38.462 0.00 0.00 0.00 3.16
780 1054 8.567948 CAAGGCCCACTAAAGTAATATGTATTG 58.432 37.037 0.00 0.00 0.00 1.90
782 1056 7.812306 ACAAGGCCCACTAAAGTAATATGTAT 58.188 34.615 0.00 0.00 0.00 2.29
783 1057 7.202972 ACAAGGCCCACTAAAGTAATATGTA 57.797 36.000 0.00 0.00 0.00 2.29
784 1058 6.074698 ACAAGGCCCACTAAAGTAATATGT 57.925 37.500 0.00 0.00 0.00 2.29
785 1059 7.404671 AAACAAGGCCCACTAAAGTAATATG 57.595 36.000 0.00 0.00 0.00 1.78
786 1060 9.709387 ATAAAACAAGGCCCACTAAAGTAATAT 57.291 29.630 0.00 0.00 0.00 1.28
787 1061 9.536510 AATAAAACAAGGCCCACTAAAGTAATA 57.463 29.630 0.00 0.00 0.00 0.98
789 1063 7.842887 AATAAAACAAGGCCCACTAAAGTAA 57.157 32.000 0.00 0.00 0.00 2.24
790 1064 7.842887 AAATAAAACAAGGCCCACTAAAGTA 57.157 32.000 0.00 0.00 0.00 2.24
792 1066 6.073276 GCAAAATAAAACAAGGCCCACTAAAG 60.073 38.462 0.00 0.00 0.00 1.85
793 1067 5.760743 GCAAAATAAAACAAGGCCCACTAAA 59.239 36.000 0.00 0.00 0.00 1.85
794 1068 5.071115 AGCAAAATAAAACAAGGCCCACTAA 59.929 36.000 0.00 0.00 0.00 2.24
795 1069 4.591072 AGCAAAATAAAACAAGGCCCACTA 59.409 37.500 0.00 0.00 0.00 2.74
796 1070 3.390967 AGCAAAATAAAACAAGGCCCACT 59.609 39.130 0.00 0.00 0.00 4.00
798 1072 4.133078 CAAGCAAAATAAAACAAGGCCCA 58.867 39.130 0.00 0.00 0.00 5.36
799 1073 3.058293 GCAAGCAAAATAAAACAAGGCCC 60.058 43.478 0.00 0.00 0.00 5.80
800 1074 3.814842 AGCAAGCAAAATAAAACAAGGCC 59.185 39.130 0.00 0.00 0.00 5.19
801 1075 4.751600 AGAGCAAGCAAAATAAAACAAGGC 59.248 37.500 0.00 0.00 0.00 4.35
802 1076 5.754890 ACAGAGCAAGCAAAATAAAACAAGG 59.245 36.000 0.00 0.00 0.00 3.61
803 1077 6.256321 ACACAGAGCAAGCAAAATAAAACAAG 59.744 34.615 0.00 0.00 0.00 3.16
805 1079 5.519566 CACACAGAGCAAGCAAAATAAAACA 59.480 36.000 0.00 0.00 0.00 2.83
806 1080 5.748152 TCACACAGAGCAAGCAAAATAAAAC 59.252 36.000 0.00 0.00 0.00 2.43
808 1082 5.512753 TCACACAGAGCAAGCAAAATAAA 57.487 34.783 0.00 0.00 0.00 1.40
810 1084 4.754372 CTCACACAGAGCAAGCAAAATA 57.246 40.909 0.00 0.00 37.59 1.40
821 1095 1.071385 AGGAAACTGGCTCACACAGAG 59.929 52.381 0.00 0.00 43.60 3.35
822 1096 1.131638 AGGAAACTGGCTCACACAGA 58.868 50.000 0.00 0.00 41.13 3.41
823 1097 1.972872 AAGGAAACTGGCTCACACAG 58.027 50.000 0.00 0.00 42.68 3.66
825 1099 1.269257 GCAAAGGAAACTGGCTCACAC 60.269 52.381 0.00 0.00 42.68 3.82
826 1100 1.032014 GCAAAGGAAACTGGCTCACA 58.968 50.000 0.00 0.00 42.68 3.58
827 1101 1.000938 CAGCAAAGGAAACTGGCTCAC 60.001 52.381 0.00 0.00 45.62 3.51
832 1106 0.032540 GGTGCAGCAAAGGAAACTGG 59.967 55.000 11.86 0.00 42.68 4.00
833 1107 0.746063 TGGTGCAGCAAAGGAAACTG 59.254 50.000 17.80 0.00 42.68 3.16
837 1111 1.484038 AAAGTGGTGCAGCAAAGGAA 58.516 45.000 22.04 0.00 0.00 3.36
838 1112 1.953686 GTAAAGTGGTGCAGCAAAGGA 59.046 47.619 22.04 3.85 0.00 3.36
839 1113 1.680735 TGTAAAGTGGTGCAGCAAAGG 59.319 47.619 22.04 0.00 0.00 3.11
840 1114 3.066621 TCTTGTAAAGTGGTGCAGCAAAG 59.933 43.478 22.04 18.42 46.34 2.77
843 1117 1.946768 GTCTTGTAAAGTGGTGCAGCA 59.053 47.619 15.99 15.99 46.34 4.41
844 1118 1.946768 TGTCTTGTAAAGTGGTGCAGC 59.053 47.619 9.47 9.47 46.34 5.25
845 1119 4.516698 AGAATGTCTTGTAAAGTGGTGCAG 59.483 41.667 0.00 0.00 46.34 4.41
846 1120 4.460263 AGAATGTCTTGTAAAGTGGTGCA 58.540 39.130 0.00 0.00 46.34 4.57
880 1154 7.941919 TGCATACGGCCACATTTATAAATAAA 58.058 30.769 10.34 0.00 43.89 1.40
881 1155 7.511959 TGCATACGGCCACATTTATAAATAA 57.488 32.000 10.34 0.00 43.89 1.40
885 1159 5.312895 AGATGCATACGGCCACATTTATAA 58.687 37.500 2.24 0.00 43.89 0.98
890 1164 2.057137 AAGATGCATACGGCCACATT 57.943 45.000 2.24 0.00 43.89 2.71
893 1167 1.331756 CAGAAAGATGCATACGGCCAC 59.668 52.381 2.24 0.00 43.89 5.01
896 1170 3.532892 CATCAGAAAGATGCATACGGC 57.467 47.619 0.00 0.00 46.90 5.68
905 1179 1.562942 TGGCCTCTGCATCAGAAAGAT 59.437 47.619 3.32 0.00 40.18 2.40
906 1180 0.986527 TGGCCTCTGCATCAGAAAGA 59.013 50.000 3.32 0.00 40.18 2.52
907 1181 1.380524 CTGGCCTCTGCATCAGAAAG 58.619 55.000 3.32 0.00 40.18 2.62
908 1182 0.034767 CCTGGCCTCTGCATCAGAAA 60.035 55.000 3.32 0.00 40.18 2.52
909 1183 1.605992 CCTGGCCTCTGCATCAGAA 59.394 57.895 3.32 0.00 40.18 3.02
910 1184 2.372890 CCCTGGCCTCTGCATCAGA 61.373 63.158 3.32 0.00 38.25 3.27
911 1185 1.918467 TTCCCTGGCCTCTGCATCAG 61.918 60.000 3.32 0.00 40.13 2.90
912 1186 1.918467 CTTCCCTGGCCTCTGCATCA 61.918 60.000 3.32 0.00 40.13 3.07
913 1187 1.153005 CTTCCCTGGCCTCTGCATC 60.153 63.158 3.32 0.00 40.13 3.91
914 1188 3.004951 CTTCCCTGGCCTCTGCAT 58.995 61.111 3.32 0.00 40.13 3.96
915 1189 4.039092 GCTTCCCTGGCCTCTGCA 62.039 66.667 3.32 0.00 40.13 4.41
916 1190 4.811364 GGCTTCCCTGGCCTCTGC 62.811 72.222 3.32 0.00 45.57 4.26
922 1196 0.615827 AAAATGGAGGCTTCCCTGGC 60.616 55.000 13.07 0.00 43.12 4.85
923 1197 1.551883 CAAAAATGGAGGCTTCCCTGG 59.448 52.381 13.07 0.00 43.12 4.45
924 1198 2.528564 TCAAAAATGGAGGCTTCCCTG 58.471 47.619 13.07 2.39 43.12 4.45
925 1199 2.999185 TCAAAAATGGAGGCTTCCCT 57.001 45.000 13.07 0.00 46.74 4.20
926 1200 4.350368 TTTTCAAAAATGGAGGCTTCCC 57.650 40.909 13.07 0.00 43.33 3.97
998 1272 8.922237 AGGATCATGGCTATCATACTTATACAG 58.078 37.037 0.00 0.00 34.12 2.74
999 1273 8.844865 AGGATCATGGCTATCATACTTATACA 57.155 34.615 0.00 0.00 34.12 2.29
1000 1274 8.918116 TGAGGATCATGGCTATCATACTTATAC 58.082 37.037 0.00 0.00 42.56 1.47
1002 1276 7.984859 TGAGGATCATGGCTATCATACTTAT 57.015 36.000 0.00 0.00 42.56 1.73
1024 1302 4.533707 AGAGGGTCAACTTGATCTTGATGA 59.466 41.667 2.04 0.00 30.46 2.92
1025 1303 4.634883 CAGAGGGTCAACTTGATCTTGATG 59.365 45.833 2.04 0.00 30.46 3.07
1026 1304 4.288105 ACAGAGGGTCAACTTGATCTTGAT 59.712 41.667 2.04 0.00 30.46 2.57
1027 1305 3.648067 ACAGAGGGTCAACTTGATCTTGA 59.352 43.478 2.04 0.00 0.00 3.02
1030 1308 3.971245 GACAGAGGGTCAACTTGATCT 57.029 47.619 2.04 0.47 46.19 2.75
1074 1357 1.791785 GCTCATCGTGATTGCTAGCTC 59.208 52.381 17.23 6.65 0.00 4.09
1352 1650 2.524394 ACGTGGAGGAGCACACCT 60.524 61.111 0.00 0.00 43.64 4.00
1355 1653 4.357947 GCGACGTGGAGGAGCACA 62.358 66.667 0.11 0.00 0.00 4.57
1445 1746 4.717629 CTCGTCGTGAAGGGCGCA 62.718 66.667 10.83 0.00 0.00 6.09
1569 1873 3.041940 GTTCCACGTCACGCCCAG 61.042 66.667 0.00 0.00 0.00 4.45
1786 2090 2.229302 GGGACGATGATGTCTAGGTAGC 59.771 54.545 0.00 0.00 38.91 3.58
1857 2179 4.452733 GCAGTACCCGGCTTCGCT 62.453 66.667 0.00 0.00 0.00 4.93
1858 2180 4.752879 TGCAGTACCCGGCTTCGC 62.753 66.667 0.00 0.00 32.50 4.70
1859 2181 2.813908 GTGCAGTACCCGGCTTCG 60.814 66.667 0.00 0.00 32.50 3.79
1862 2184 2.032071 GTTGTGCAGTACCCGGCT 59.968 61.111 0.00 0.00 32.50 5.52
1985 2307 1.813212 CGTGCTTGCGTACGTTCACA 61.813 55.000 17.90 8.03 43.03 3.58
2096 2424 0.893727 GGTCCACCAAGCCGTTCATT 60.894 55.000 0.00 0.00 35.64 2.57
2335 3305 3.015293 GACAGTGACGCCATGCACG 62.015 63.158 0.00 4.98 39.88 5.34
2459 3432 5.289595 TCATAATTAGTTACTCAGGCGCAG 58.710 41.667 10.83 0.00 0.00 5.18
2512 3492 3.257375 ACACCACACATAGACATACGTGT 59.743 43.478 0.00 0.00 43.12 4.49
2513 3493 3.612423 CACACCACACATAGACATACGTG 59.388 47.826 0.00 0.00 35.48 4.49
2514 3494 3.368013 CCACACCACACATAGACATACGT 60.368 47.826 0.00 0.00 0.00 3.57
2515 3495 3.186909 CCACACCACACATAGACATACG 58.813 50.000 0.00 0.00 0.00 3.06
2517 3497 3.055458 CCACCACACCACACATAGACATA 60.055 47.826 0.00 0.00 0.00 2.29
2518 3498 2.290260 CCACCACACCACACATAGACAT 60.290 50.000 0.00 0.00 0.00 3.06
2519 3499 1.071542 CCACCACACCACACATAGACA 59.928 52.381 0.00 0.00 0.00 3.41
2520 3500 1.071699 ACCACCACACCACACATAGAC 59.928 52.381 0.00 0.00 0.00 2.59
2521 3501 1.071542 CACCACCACACCACACATAGA 59.928 52.381 0.00 0.00 0.00 1.98
2522 3502 1.202758 ACACCACCACACCACACATAG 60.203 52.381 0.00 0.00 0.00 2.23
2578 3562 3.380320 GGGAACTTGCACATAATGGGTAC 59.620 47.826 0.00 0.00 0.00 3.34
2579 3563 3.268334 AGGGAACTTGCACATAATGGGTA 59.732 43.478 0.00 0.00 37.44 3.69
2580 3564 2.042979 AGGGAACTTGCACATAATGGGT 59.957 45.455 0.00 0.00 37.44 4.51
2583 3567 4.676196 GCTTCAGGGAACTTGCACATAATG 60.676 45.833 0.00 0.00 40.21 1.90
2585 3569 2.819608 GCTTCAGGGAACTTGCACATAA 59.180 45.455 0.00 0.00 40.21 1.90
2586 3570 2.224744 TGCTTCAGGGAACTTGCACATA 60.225 45.455 0.00 0.00 40.21 2.29
2587 3571 1.251251 GCTTCAGGGAACTTGCACAT 58.749 50.000 0.00 0.00 40.21 3.21
2588 3572 0.106769 TGCTTCAGGGAACTTGCACA 60.107 50.000 0.00 0.00 40.21 4.57
2589 3573 1.068055 CATGCTTCAGGGAACTTGCAC 60.068 52.381 0.00 0.00 40.02 4.57
2590 3574 1.250328 CATGCTTCAGGGAACTTGCA 58.750 50.000 0.00 0.00 40.21 4.08
2591 3575 1.068055 CACATGCTTCAGGGAACTTGC 60.068 52.381 0.00 0.00 40.21 4.01
2594 3578 2.233271 CAACACATGCTTCAGGGAACT 58.767 47.619 0.00 0.00 46.44 3.01
2595 3579 1.270550 CCAACACATGCTTCAGGGAAC 59.729 52.381 0.00 0.00 0.00 3.62
2596 3580 1.133513 ACCAACACATGCTTCAGGGAA 60.134 47.619 0.00 0.00 0.00 3.97
2597 3581 0.478072 ACCAACACATGCTTCAGGGA 59.522 50.000 0.00 0.00 0.00 4.20
2598 3582 1.331214 AACCAACACATGCTTCAGGG 58.669 50.000 0.00 0.00 0.00 4.45
2599 3583 2.605338 CGAAACCAACACATGCTTCAGG 60.605 50.000 0.00 0.00 0.00 3.86
2600 3584 2.605338 CCGAAACCAACACATGCTTCAG 60.605 50.000 0.00 0.00 0.00 3.02
2602 3586 1.336755 ACCGAAACCAACACATGCTTC 59.663 47.619 0.00 0.00 0.00 3.86
2607 3591 1.066908 CAGCAACCGAAACCAACACAT 59.933 47.619 0.00 0.00 0.00 3.21
2608 3592 0.453793 CAGCAACCGAAACCAACACA 59.546 50.000 0.00 0.00 0.00 3.72
2613 3597 1.077357 ACACCAGCAACCGAAACCA 60.077 52.632 0.00 0.00 0.00 3.67
2614 3598 1.358759 CACACCAGCAACCGAAACC 59.641 57.895 0.00 0.00 0.00 3.27
2620 3604 1.607148 GAGTTTACCACACCAGCAACC 59.393 52.381 0.00 0.00 0.00 3.77
2626 3610 1.476110 GCACTGGAGTTTACCACACCA 60.476 52.381 0.00 0.00 43.36 4.17
2646 3631 5.931532 AGACATTGCTTGACTTGTTTATCG 58.068 37.500 0.00 0.00 0.00 2.92
2674 3659 2.912956 AGAACTCATTTCCCTGGCAGTA 59.087 45.455 14.43 0.00 34.32 2.74
2685 3670 9.574516 AACCTAAAATCAGTGTAGAACTCATTT 57.425 29.630 0.00 0.00 40.92 2.32
2746 3821 1.210478 GTGGAGAGCTAGCCAATCCAA 59.790 52.381 26.20 13.41 41.52 3.53
2751 3826 1.599047 GCTGTGGAGAGCTAGCCAA 59.401 57.895 12.13 0.00 35.63 4.52
2762 3837 3.323622 CCTGCATAGGGCTGTGGA 58.676 61.111 0.00 0.00 45.15 4.02
2790 3865 1.754226 TGGAAGGACAACCACTTTTGC 59.246 47.619 0.00 0.00 38.94 3.68
2816 3892 5.241728 CCTTGCAGGATTATAGTTTTAGCCC 59.758 44.000 0.00 0.00 37.67 5.19
2829 3959 1.272704 GGAAGTTCCCCTTGCAGGATT 60.273 52.381 11.17 0.00 40.92 3.01
2831 3961 1.065410 TGGAAGTTCCCCTTGCAGGA 61.065 55.000 19.42 0.00 45.37 3.86
2880 4010 4.158394 GCCTCTTCAATTTCTGTGGCATAA 59.842 41.667 0.00 0.00 38.99 1.90
2894 4024 1.765904 TGTGTACCACAGCCTCTTCAA 59.234 47.619 0.00 0.00 39.62 2.69
2905 4035 4.890088 TGTATTTCAGGTCTGTGTACCAC 58.110 43.478 0.00 0.00 42.40 4.16
2906 4036 5.147330 CTGTATTTCAGGTCTGTGTACCA 57.853 43.478 0.00 0.00 42.40 3.25
2934 4064 2.941415 CACCTCCTGGTATTTGTCCAGC 60.941 54.545 6.46 0.00 46.60 4.85
2935 4065 2.305927 ACACCTCCTGGTATTTGTCCAG 59.694 50.000 5.13 5.13 46.60 3.86
2946 4076 1.002544 GGTTCAGAGAACACCTCCTGG 59.997 57.143 11.51 0.00 42.97 4.45
2973 4103 1.799933 ATTCTCTCCTAGGTGGCAGG 58.200 55.000 9.08 0.00 35.26 4.85
3000 4130 2.642311 TCCTGGCACTAGTGGAATTGAA 59.358 45.455 23.95 0.00 0.00 2.69
3027 4157 5.724370 TCTGTATGGTCTAATGGAAACTGGA 59.276 40.000 0.00 0.00 0.00 3.86
3049 4179 2.905415 TTCAGATGTGGGGCAATTCT 57.095 45.000 0.00 0.00 0.00 2.40
3057 4187 3.693085 CCATCTCAGTTTTCAGATGTGGG 59.307 47.826 7.87 0.00 43.14 4.61
3100 4230 6.730447 TGGGTCTAATCATTCCATTCTTCAA 58.270 36.000 0.00 0.00 0.00 2.69
3171 4301 0.603707 CAAGTCTCCAAGCGCCTTCA 60.604 55.000 2.29 0.00 0.00 3.02
3178 4308 7.849804 TGAAATCTATTACAAGTCTCCAAGC 57.150 36.000 0.00 0.00 0.00 4.01
3203 4333 8.458052 CCTTAACAGTTAATGCATTCACATGTA 58.542 33.333 22.32 10.14 32.28 2.29
3249 4379 7.661847 ACGAACTCCTCTAACAATTCTTCAATT 59.338 33.333 0.00 0.00 31.91 2.32
3270 4400 2.726832 ACTAGTGAGCTCCAACGAAC 57.273 50.000 12.15 0.88 0.00 3.95
3273 4403 3.654414 AGAAAACTAGTGAGCTCCAACG 58.346 45.455 12.15 0.00 0.00 4.10
3275 4405 6.420913 ACTTAGAAAACTAGTGAGCTCCAA 57.579 37.500 12.15 0.00 0.00 3.53
3287 4417 7.821846 CAGCCTTGAGATCTAACTTAGAAAACT 59.178 37.037 0.00 3.63 38.50 2.66
3298 4428 5.163301 GGTGATAACCAGCCTTGAGATCTAA 60.163 44.000 0.00 0.00 37.30 2.10
3324 4454 1.298014 CCCAGGAGCCAGTCTGTTC 59.702 63.158 0.00 0.00 0.00 3.18
3326 4456 2.608988 CCCCAGGAGCCAGTCTGT 60.609 66.667 0.00 0.00 0.00 3.41
3354 4484 3.251004 CACAGTAAGTTTGGAAGGCAGTC 59.749 47.826 0.00 0.00 0.00 3.51
3370 4500 3.780294 AGGAATTCATAGTGGCCACAGTA 59.220 43.478 36.39 21.87 36.96 2.74
3396 4526 0.243636 CGGTTAAAGCAAAGGCCTGG 59.756 55.000 5.69 2.38 42.56 4.45
3397 4527 0.243636 CCGGTTAAAGCAAAGGCCTG 59.756 55.000 5.69 0.00 42.56 4.85
3398 4528 0.178973 ACCGGTTAAAGCAAAGGCCT 60.179 50.000 0.00 0.00 42.56 5.19
3407 4537 1.262417 ATTTGGCCCACCGGTTAAAG 58.738 50.000 2.97 0.00 39.70 1.85
3414 4544 4.429108 CTTAAAATGTATTTGGCCCACCG 58.571 43.478 0.00 0.00 39.70 4.94
3420 4550 5.337578 TGGCTCCTTAAAATGTATTTGGC 57.662 39.130 0.00 0.00 0.00 4.52
3432 4562 4.574674 ATCACTGTTCATGGCTCCTTAA 57.425 40.909 0.00 0.00 0.00 1.85
3433 4563 4.574674 AATCACTGTTCATGGCTCCTTA 57.425 40.909 0.00 0.00 0.00 2.69
3457 4587 2.307098 CAGATTCTCTGGAAACTGGGGT 59.693 50.000 7.74 0.00 43.82 4.95
3465 4595 1.980765 ACCACTGCAGATTCTCTGGAA 59.019 47.619 23.35 0.00 44.20 3.53
3471 4601 5.809001 TCAAAGAATACCACTGCAGATTCT 58.191 37.500 23.35 20.07 39.71 2.40
3476 4606 7.660617 AGATATCATCAAAGAATACCACTGCAG 59.339 37.037 13.48 13.48 0.00 4.41
3512 4642 4.081406 CAGGTGATCCAGGAATGTTTTGA 58.919 43.478 0.00 0.00 35.89 2.69
3537 4667 4.090761 ACTCAGAACTTGCTCCAAATGA 57.909 40.909 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.