Multiple sequence alignment - TraesCS1D01G122400

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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 TraesCS1D01G122400 chr1D 100.000 2585 0 0 1 2585 122900714 122898130 0.000000e+00 4774
1 TraesCS1D01G122400 chr1D 95.190 499 24 0 2079 2577 101105754 101106252 0.000000e+00 789
2 TraesCS1D01G122400 chr1D 94.685 508 25 2 2079 2585 22302681 22302175 0.000000e+00 787
3 TraesCS1D01G122400 chr1D 94.477 507 28 0 2079 2585 494852983 494853489 0.000000e+00 782
4 TraesCS1D01G122400 chr1A 92.374 813 41 11 282 1084 135184254 135183453 0.000000e+00 1138
5 TraesCS1D01G122400 chr1A 91.687 806 49 10 1154 1946 135183031 135182231 0.000000e+00 1101
6 TraesCS1D01G122400 chr1A 95.238 63 1 1 1949 2009 135182145 135182083 5.890000e-17 99
7 TraesCS1D01G122400 chr7D 95.661 507 21 1 2079 2585 478767641 478768146 0.000000e+00 813
8 TraesCS1D01G122400 chr7D 94.477 507 27 1 2079 2585 87362907 87363412 0.000000e+00 780
9 TraesCS1D01G122400 chr2D 95.331 514 21 3 2072 2585 57199098 57199608 0.000000e+00 813
10 TraesCS1D01G122400 chr5B 95.069 507 25 0 2079 2585 707138375 707137869 0.000000e+00 798
11 TraesCS1D01G122400 chr1B 94.510 510 25 3 2079 2585 40019295 40019804 0.000000e+00 784
12 TraesCS1D01G122400 chr5D 94.325 511 24 2 2079 2585 276556226 276556735 0.000000e+00 778
13 TraesCS1D01G122400 chr3A 87.619 420 41 8 1596 2009 17565013 17565427 6.470000e-131 477
14 TraesCS1D01G122400 chr3D 87.619 420 37 9 1596 2009 51580039 51580449 8.370000e-130 473
15 TraesCS1D01G122400 chr5A 87.043 301 28 8 1714 2009 450227650 450227356 1.920000e-86 329
16 TraesCS1D01G122400 chr5A 91.129 124 11 0 1596 1719 450237370 450237247 4.420000e-38 169
17 TraesCS1D01G122400 chr3B 85.308 211 18 9 1803 2009 50158363 50158162 3.370000e-49 206
18 TraesCS1D01G122400 chr3B 93.878 49 3 0 1545 1593 23161547 23161595 9.920000e-10 75


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 TraesCS1D01G122400 chr1D 122898130 122900714 2584 True 4774.000000 4774 100.000000 1 2585 1 chr1D.!!$R2 2584
1 TraesCS1D01G122400 chr1D 22302175 22302681 506 True 787.000000 787 94.685000 2079 2585 1 chr1D.!!$R1 506
2 TraesCS1D01G122400 chr1D 494852983 494853489 506 False 782.000000 782 94.477000 2079 2585 1 chr1D.!!$F2 506
3 TraesCS1D01G122400 chr1A 135182083 135184254 2171 True 779.333333 1138 93.099667 282 2009 3 chr1A.!!$R1 1727
4 TraesCS1D01G122400 chr7D 478767641 478768146 505 False 813.000000 813 95.661000 2079 2585 1 chr7D.!!$F2 506
5 TraesCS1D01G122400 chr7D 87362907 87363412 505 False 780.000000 780 94.477000 2079 2585 1 chr7D.!!$F1 506
6 TraesCS1D01G122400 chr2D 57199098 57199608 510 False 813.000000 813 95.331000 2072 2585 1 chr2D.!!$F1 513
7 TraesCS1D01G122400 chr5B 707137869 707138375 506 True 798.000000 798 95.069000 2079 2585 1 chr5B.!!$R1 506
8 TraesCS1D01G122400 chr1B 40019295 40019804 509 False 784.000000 784 94.510000 2079 2585 1 chr1B.!!$F1 506
9 TraesCS1D01G122400 chr5D 276556226 276556735 509 False 778.000000 778 94.325000 2079 2585 1 chr5D.!!$F1 506

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
962 970 0.244721 AACCGGCGACCAACTAGTAC 59.755 55.0 9.3 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1763 2131 0.105039 CCCTCCACCTATTCGTGCTC 59.895 60.0 0.0 0.0 32.1 4.26 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
17 18 2.202756 GCGGGGAGCTTGTAGTCG 60.203 66.667 0.00 0.00 44.04 4.18
18 19 2.202756 CGGGGAGCTTGTAGTCGC 60.203 66.667 0.00 0.00 0.00 5.19
19 20 2.202756 GGGGAGCTTGTAGTCGCG 60.203 66.667 0.00 0.00 0.00 5.87
20 21 2.707849 GGGGAGCTTGTAGTCGCGA 61.708 63.158 3.71 3.71 0.00 5.87
21 22 1.516603 GGGAGCTTGTAGTCGCGAC 60.517 63.158 31.30 31.30 0.00 5.19
22 23 1.211969 GGAGCTTGTAGTCGCGACA 59.788 57.895 37.85 22.36 0.00 4.35
23 24 0.798771 GGAGCTTGTAGTCGCGACAG 60.799 60.000 37.85 27.10 0.00 3.51
24 25 0.798771 GAGCTTGTAGTCGCGACAGG 60.799 60.000 37.85 21.18 0.00 4.00
25 26 1.211969 GCTTGTAGTCGCGACAGGA 59.788 57.895 37.85 21.48 0.00 3.86
26 27 0.798771 GCTTGTAGTCGCGACAGGAG 60.799 60.000 37.85 27.82 0.00 3.69
27 28 0.798771 CTTGTAGTCGCGACAGGAGC 60.799 60.000 37.85 22.50 0.00 4.70
28 29 2.102553 GTAGTCGCGACAGGAGCC 59.897 66.667 37.85 16.27 0.00 4.70
29 30 2.360726 TAGTCGCGACAGGAGCCA 60.361 61.111 37.85 12.92 0.00 4.75
30 31 2.407428 TAGTCGCGACAGGAGCCAG 61.407 63.158 37.85 0.00 0.00 4.85
31 32 4.803426 GTCGCGACAGGAGCCAGG 62.803 72.222 33.09 0.00 0.00 4.45
34 35 4.767255 GCGACAGGAGCCAGGGTG 62.767 72.222 0.00 0.00 0.00 4.61
35 36 4.767255 CGACAGGAGCCAGGGTGC 62.767 72.222 0.94 0.94 0.00 5.01
36 37 4.767255 GACAGGAGCCAGGGTGCG 62.767 72.222 4.26 2.68 36.02 5.34
125 126 3.966543 GGGGTGGTGGTGGTGGAG 61.967 72.222 0.00 0.00 0.00 3.86
126 127 4.660938 GGGTGGTGGTGGTGGAGC 62.661 72.222 0.00 0.00 0.00 4.70
127 128 3.884774 GGTGGTGGTGGTGGAGCA 61.885 66.667 0.00 0.00 0.00 4.26
131 132 4.626081 GTGGTGGTGGAGCACGCT 62.626 66.667 3.05 0.00 42.93 5.07
132 133 2.920384 TGGTGGTGGAGCACGCTA 60.920 61.111 3.05 0.00 34.83 4.26
133 134 2.125512 GGTGGTGGAGCACGCTAG 60.126 66.667 3.05 0.00 34.83 3.42
134 135 2.657237 GTGGTGGAGCACGCTAGT 59.343 61.111 0.00 0.00 34.83 2.57
143 144 2.683933 CACGCTAGTGGAGGGGGT 60.684 66.667 8.42 0.00 44.34 4.95
144 145 2.363925 ACGCTAGTGGAGGGGGTC 60.364 66.667 8.42 0.00 42.42 4.46
145 146 2.363795 CGCTAGTGGAGGGGGTCA 60.364 66.667 0.00 0.00 34.46 4.02
146 147 2.427245 CGCTAGTGGAGGGGGTCAG 61.427 68.421 0.00 0.00 34.46 3.51
147 148 1.001760 GCTAGTGGAGGGGGTCAGA 59.998 63.158 0.00 0.00 0.00 3.27
148 149 0.399233 GCTAGTGGAGGGGGTCAGAT 60.399 60.000 0.00 0.00 0.00 2.90
149 150 1.710816 CTAGTGGAGGGGGTCAGATC 58.289 60.000 0.00 0.00 0.00 2.75
150 151 0.264955 TAGTGGAGGGGGTCAGATCC 59.735 60.000 0.00 0.00 0.00 3.36
151 152 2.041922 TGGAGGGGGTCAGATCCG 60.042 66.667 0.00 0.00 34.39 4.18
152 153 3.551407 GGAGGGGGTCAGATCCGC 61.551 72.222 8.83 8.83 39.30 5.54
157 158 4.176752 GGGTCAGATCCGCCCCAC 62.177 72.222 6.35 0.00 37.09 4.61
158 159 3.083997 GGTCAGATCCGCCCCACT 61.084 66.667 0.00 0.00 0.00 4.00
159 160 2.187946 GTCAGATCCGCCCCACTG 59.812 66.667 0.00 0.00 0.00 3.66
160 161 3.785859 TCAGATCCGCCCCACTGC 61.786 66.667 0.00 0.00 0.00 4.40
161 162 4.864334 CAGATCCGCCCCACTGCC 62.864 72.222 0.00 0.00 0.00 4.85
292 293 3.083997 AGAGGTTAGGCAGGGGCG 61.084 66.667 0.00 0.00 42.47 6.13
310 311 0.521242 CGTGCGTGCCTATTTGCTTC 60.521 55.000 0.00 0.00 0.00 3.86
365 366 8.799367 GTTATGTCTGTTTATTTGTTTAGGGGT 58.201 33.333 0.00 0.00 0.00 4.95
388 389 7.436970 GGGTGTTGAATTGTTAAGGTTAACTTG 59.563 37.037 12.61 0.00 42.61 3.16
389 390 7.436970 GGTGTTGAATTGTTAAGGTTAACTTGG 59.563 37.037 12.61 0.00 42.61 3.61
403 404 5.300792 GGTTAACTTGGTGAATCTTGGTTCA 59.699 40.000 5.42 0.00 35.84 3.18
406 407 5.458041 ACTTGGTGAATCTTGGTTCATTG 57.542 39.130 0.00 0.00 39.99 2.82
409 410 4.468713 TGGTGAATCTTGGTTCATTGTCA 58.531 39.130 0.00 0.00 39.99 3.58
424 425 6.899393 TCATTGTCAGTTGGCTTTATCTTT 57.101 33.333 0.00 0.00 0.00 2.52
427 428 7.867403 TCATTGTCAGTTGGCTTTATCTTTTTC 59.133 33.333 0.00 0.00 0.00 2.29
440 441 9.864034 GCTTTATCTTTTTCTTTTTGGCTTTAC 57.136 29.630 0.00 0.00 0.00 2.01
498 499 7.855784 AATGTTTAGAGGAGGAAAAACCAAT 57.144 32.000 0.00 0.00 42.04 3.16
501 502 8.770010 TGTTTAGAGGAGGAAAAACCAATTTA 57.230 30.769 0.00 0.00 42.04 1.40
502 503 9.374711 TGTTTAGAGGAGGAAAAACCAATTTAT 57.625 29.630 0.00 0.00 42.04 1.40
505 506 9.822727 TTAGAGGAGGAAAAACCAATTTATTCT 57.177 29.630 0.00 0.00 42.04 2.40
533 536 8.871629 TTAACACATTTTAGGGAATCAGCTAA 57.128 30.769 0.00 0.00 0.00 3.09
549 553 9.959721 GAATCAGCTAAAAATGATATAGGGGTA 57.040 33.333 0.00 0.00 35.11 3.69
568 572 3.436180 GGTAATAGGTCGAGAGAAGGGGA 60.436 52.174 0.00 0.00 45.01 4.81
573 577 1.900486 GGTCGAGAGAAGGGGAAAAGA 59.100 52.381 0.00 0.00 45.01 2.52
595 601 4.019174 AGGTAATAGCATTTGCACAAGCT 58.981 39.130 7.80 7.80 45.16 3.74
625 632 2.721797 CGCTGAAATGACCGAAAGAACG 60.722 50.000 0.00 0.00 0.00 3.95
644 651 1.009829 GCTGAACCGCGAATCAATCT 58.990 50.000 8.23 0.00 0.00 2.40
666 673 9.708092 AATCTCGCTTATTTAATTAGTACTCCC 57.292 33.333 0.00 0.00 0.00 4.30
710 718 2.918712 ACGCCAAGCTGCTATTAGAT 57.081 45.000 0.90 0.00 0.00 1.98
854 862 2.108075 TCAGCTTTGGGAAACATCCTGA 59.892 45.455 0.00 0.00 0.00 3.86
918 926 6.620678 AGCTTGCACGACACAATATTTATTT 58.379 32.000 0.00 0.00 0.00 1.40
946 954 2.162681 AGCCAATCTACACAAGCAACC 58.837 47.619 0.00 0.00 0.00 3.77
962 970 0.244721 AACCGGCGACCAACTAGTAC 59.755 55.000 9.30 0.00 0.00 2.73
964 972 1.340017 ACCGGCGACCAACTAGTACTA 60.340 52.381 9.30 1.89 0.00 1.82
965 973 1.332997 CCGGCGACCAACTAGTACTAG 59.667 57.143 25.30 25.30 39.04 2.57
966 974 1.268437 CGGCGACCAACTAGTACTAGC 60.268 57.143 26.54 13.45 36.66 3.42
967 975 2.022934 GGCGACCAACTAGTACTAGCT 58.977 52.381 26.54 14.42 36.66 3.32
980 988 7.401246 ACTAGTACTAGCTTAGTGGTGTAACT 58.599 38.462 26.54 1.76 39.81 2.24
981 989 7.887495 ACTAGTACTAGCTTAGTGGTGTAACTT 59.113 37.037 26.54 1.40 39.81 2.66
982 990 7.155655 AGTACTAGCTTAGTGGTGTAACTTC 57.844 40.000 0.00 0.00 39.81 3.01
983 991 6.718454 AGTACTAGCTTAGTGGTGTAACTTCA 59.282 38.462 0.00 0.00 39.81 3.02
985 993 6.456501 ACTAGCTTAGTGGTGTAACTTCAAG 58.543 40.000 0.00 0.00 37.69 3.02
1049 1057 0.107654 GGTGTATTCAGCTCCGCCTT 60.108 55.000 0.00 0.00 38.80 4.35
1062 1070 3.706373 GCCTTCGCCCACTCCTCA 61.706 66.667 0.00 0.00 0.00 3.86
1073 1081 0.326264 CACTCCTCACCTTTCCTGGG 59.674 60.000 0.00 0.00 0.00 4.45
1078 1086 0.462759 CTCACCTTTCCTGGGCGATC 60.463 60.000 0.00 0.00 0.00 3.69
1084 1092 0.174845 TTTCCTGGGCGATCACTACG 59.825 55.000 0.00 0.00 0.00 3.51
1091 1099 2.954868 CGATCACTACGCACCGCC 60.955 66.667 0.00 0.00 0.00 6.13
1092 1100 2.494918 GATCACTACGCACCGCCT 59.505 61.111 0.00 0.00 0.00 5.52
1093 1101 1.878522 GATCACTACGCACCGCCTG 60.879 63.158 0.00 0.00 0.00 4.85
1094 1102 4.735132 TCACTACGCACCGCCTGC 62.735 66.667 0.00 0.00 43.21 4.85
1112 1120 4.847516 CCGCGCCTTCATCGACGA 62.848 66.667 0.00 0.00 0.00 4.20
1113 1121 3.607987 CGCGCCTTCATCGACGAC 61.608 66.667 0.00 0.00 0.00 4.34
1114 1122 2.506217 GCGCCTTCATCGACGACA 60.506 61.111 0.00 0.00 0.00 4.35
1115 1123 2.508891 GCGCCTTCATCGACGACAG 61.509 63.158 0.00 0.00 0.00 3.51
1116 1124 1.154016 CGCCTTCATCGACGACAGT 60.154 57.895 0.00 0.00 0.00 3.55
1117 1125 1.406219 CGCCTTCATCGACGACAGTG 61.406 60.000 0.00 0.00 0.00 3.66
1118 1126 0.109272 GCCTTCATCGACGACAGTGA 60.109 55.000 0.00 0.00 0.00 3.41
1119 1127 1.469940 GCCTTCATCGACGACAGTGAT 60.470 52.381 0.00 0.00 0.00 3.06
1120 1128 2.881074 CCTTCATCGACGACAGTGATT 58.119 47.619 0.00 0.00 0.00 2.57
1121 1129 3.733988 GCCTTCATCGACGACAGTGATTA 60.734 47.826 0.00 0.00 0.00 1.75
1122 1130 3.791887 CCTTCATCGACGACAGTGATTAC 59.208 47.826 0.00 0.00 0.00 1.89
1123 1131 3.047613 TCATCGACGACAGTGATTACG 57.952 47.619 0.00 0.00 0.00 3.18
1124 1132 1.513178 CATCGACGACAGTGATTACGC 59.487 52.381 0.00 0.00 0.00 4.42
1125 1133 0.519792 TCGACGACAGTGATTACGCG 60.520 55.000 3.53 3.53 0.00 6.01
1126 1134 1.461317 CGACGACAGTGATTACGCGG 61.461 60.000 12.47 0.00 0.00 6.46
1127 1135 1.740043 GACGACAGTGATTACGCGGC 61.740 60.000 12.47 0.00 0.00 6.53
1128 1136 1.516386 CGACAGTGATTACGCGGCT 60.516 57.895 12.47 0.00 0.00 5.52
1129 1137 1.472276 CGACAGTGATTACGCGGCTC 61.472 60.000 12.47 4.31 0.00 4.70
1130 1138 0.457853 GACAGTGATTACGCGGCTCA 60.458 55.000 12.47 7.28 0.00 4.26
1131 1139 0.458543 ACAGTGATTACGCGGCTCAG 60.459 55.000 12.47 2.06 0.00 3.35
1132 1140 1.519455 AGTGATTACGCGGCTCAGC 60.519 57.895 12.47 0.00 0.00 4.26
1133 1141 1.519455 GTGATTACGCGGCTCAGCT 60.519 57.895 12.47 0.00 34.40 4.24
1134 1142 1.226974 TGATTACGCGGCTCAGCTC 60.227 57.895 12.47 0.00 34.40 4.09
1135 1143 1.951631 GATTACGCGGCTCAGCTCC 60.952 63.158 12.47 0.00 34.40 4.70
1136 1144 2.629050 GATTACGCGGCTCAGCTCCA 62.629 60.000 12.47 0.00 34.40 3.86
1137 1145 2.907897 ATTACGCGGCTCAGCTCCAC 62.908 60.000 12.47 0.00 34.40 4.02
1140 1148 4.828925 GCGGCTCAGCTCCACCTC 62.829 72.222 0.00 0.00 0.00 3.85
1141 1149 4.154347 CGGCTCAGCTCCACCTCC 62.154 72.222 0.00 0.00 0.00 4.30
1142 1150 3.005539 GGCTCAGCTCCACCTCCA 61.006 66.667 0.00 0.00 0.00 3.86
1143 1151 2.267324 GCTCAGCTCCACCTCCAC 59.733 66.667 0.00 0.00 0.00 4.02
1144 1152 2.575993 CTCAGCTCCACCTCCACG 59.424 66.667 0.00 0.00 0.00 4.94
1145 1153 1.979155 CTCAGCTCCACCTCCACGA 60.979 63.158 0.00 0.00 0.00 4.35
1146 1154 2.219325 CTCAGCTCCACCTCCACGAC 62.219 65.000 0.00 0.00 0.00 4.34
1147 1155 3.374402 AGCTCCACCTCCACGACG 61.374 66.667 0.00 0.00 0.00 5.12
1148 1156 3.371063 GCTCCACCTCCACGACGA 61.371 66.667 0.00 0.00 0.00 4.20
1149 1157 2.711922 GCTCCACCTCCACGACGAT 61.712 63.158 0.00 0.00 0.00 3.73
1150 1158 1.433879 CTCCACCTCCACGACGATC 59.566 63.158 0.00 0.00 0.00 3.69
1151 1159 1.303806 TCCACCTCCACGACGATCA 60.304 57.895 0.00 0.00 0.00 2.92
1152 1160 0.683179 TCCACCTCCACGACGATCAT 60.683 55.000 0.00 0.00 0.00 2.45
1159 1519 0.179127 CCACGACGATCATCAGCACT 60.179 55.000 0.00 0.00 0.00 4.40
1173 1533 2.565391 TCAGCACTACCCTTTCGATCAA 59.435 45.455 0.00 0.00 0.00 2.57
1193 1553 3.950254 CGAGTACTCGCCGCCGAT 61.950 66.667 30.44 0.00 46.50 4.18
1215 1581 2.815647 CAGGTCTCTTTCGCCGGC 60.816 66.667 19.07 19.07 0.00 6.13
1247 1613 1.071605 AAACATCGCAGCGAGAAGAC 58.928 50.000 24.08 0.00 39.91 3.01
1254 1620 1.350193 GCAGCGAGAAGACGATCAAA 58.650 50.000 0.00 0.00 35.09 2.69
1273 1639 2.842394 AATCAGTGCGAGGGTGAGCG 62.842 60.000 0.00 0.00 35.87 5.03
1471 1837 1.159285 CTACGTCGTCACCACCTACA 58.841 55.000 0.00 0.00 0.00 2.74
1613 1979 1.134371 AGCTAATTCCGTTCTGCTCCC 60.134 52.381 0.00 0.00 0.00 4.30
1629 1995 3.019564 GCTCCCCGTACAGTAGAAACTA 58.980 50.000 0.00 0.00 33.48 2.24
1662 2029 2.480419 ACTTCTGTTTTTGCCGATCGAG 59.520 45.455 18.66 8.00 0.00 4.04
1686 2053 1.056994 GTCGTCGTCGGTTCGAGTTC 61.057 60.000 1.55 0.00 40.52 3.01
1689 2056 1.050767 GTCGTCGGTTCGAGTTCTTG 58.949 55.000 0.00 0.00 40.52 3.02
1696 2063 4.792189 GTCGGTTCGAGTTCTTGTATACAG 59.208 45.833 5.56 1.19 36.23 2.74
1775 2143 5.530915 TCCAAAATTATGGAGCACGAATAGG 59.469 40.000 0.00 0.00 44.52 2.57
1776 2144 5.299279 CCAAAATTATGGAGCACGAATAGGT 59.701 40.000 0.00 0.00 43.54 3.08
1824 2192 2.099756 ACTTCTGGTTTGCTTGCTTGTC 59.900 45.455 0.00 0.00 0.00 3.18
1836 2204 4.907879 CTTGCTTGTCAAGTTTCTCCTT 57.092 40.909 14.03 0.00 45.48 3.36
1837 2205 4.604976 CTTGCTTGTCAAGTTTCTCCTTG 58.395 43.478 14.03 0.00 45.48 3.61
1838 2206 3.620488 TGCTTGTCAAGTTTCTCCTTGT 58.380 40.909 14.03 0.00 42.01 3.16
1839 2207 4.776349 TGCTTGTCAAGTTTCTCCTTGTA 58.224 39.130 14.03 0.00 42.01 2.41
1840 2208 5.376625 TGCTTGTCAAGTTTCTCCTTGTAT 58.623 37.500 14.03 0.00 42.01 2.29
1841 2209 5.470098 TGCTTGTCAAGTTTCTCCTTGTATC 59.530 40.000 14.03 0.00 42.01 2.24
1842 2210 5.470098 GCTTGTCAAGTTTCTCCTTGTATCA 59.530 40.000 14.03 0.00 42.01 2.15
1845 2213 5.071788 TGTCAAGTTTCTCCTTGTATCACCT 59.928 40.000 0.00 0.00 42.01 4.00
1846 2214 5.409826 GTCAAGTTTCTCCTTGTATCACCTG 59.590 44.000 0.00 0.00 42.01 4.00
1847 2215 5.306937 TCAAGTTTCTCCTTGTATCACCTGA 59.693 40.000 0.00 0.00 42.01 3.86
1851 2228 6.486993 AGTTTCTCCTTGTATCACCTGAAAAC 59.513 38.462 0.00 0.00 0.00 2.43
1852 2229 5.560722 TCTCCTTGTATCACCTGAAAACA 57.439 39.130 0.00 0.00 0.00 2.83
1856 2233 7.013274 TCTCCTTGTATCACCTGAAAACAAAAG 59.987 37.037 7.57 7.91 35.22 2.27
1858 2235 7.340743 TCCTTGTATCACCTGAAAACAAAAGAA 59.659 33.333 7.57 0.00 35.22 2.52
1862 2239 8.188139 TGTATCACCTGAAAACAAAAGAAGTTC 58.812 33.333 0.00 0.00 0.00 3.01
1869 2246 7.068226 CCTGAAAACAAAAGAAGTTCCTCCTTA 59.932 37.037 0.00 0.00 0.00 2.69
1870 2247 8.356000 TGAAAACAAAAGAAGTTCCTCCTTAA 57.644 30.769 0.00 0.00 0.00 1.85
1871 2248 8.977412 TGAAAACAAAAGAAGTTCCTCCTTAAT 58.023 29.630 0.00 0.00 0.00 1.40
1874 2251 9.642343 AAACAAAAGAAGTTCCTCCTTAATAGT 57.358 29.630 0.00 0.00 0.00 2.12
1876 2253 9.945904 ACAAAAGAAGTTCCTCCTTAATAGTAG 57.054 33.333 0.00 0.00 0.00 2.57
1877 2254 9.945904 CAAAAGAAGTTCCTCCTTAATAGTAGT 57.054 33.333 0.00 0.00 0.00 2.73
1906 2283 5.545658 TTAGGCGCTTCTTGACTTAATTG 57.454 39.130 7.64 0.00 0.00 2.32
1917 2294 0.802494 ACTTAATTGAACGGCCTGCG 59.198 50.000 0.00 0.00 0.00 5.18
1946 2323 5.424757 TCCATCAGTCAAATAAACGGGTAG 58.575 41.667 0.00 0.00 0.00 3.18
1947 2324 4.035208 CCATCAGTCAAATAAACGGGTAGC 59.965 45.833 0.00 0.00 0.00 3.58
2002 2462 8.520835 TGAATGCTCAATCGTGTAATCTATAC 57.479 34.615 0.00 0.00 0.00 1.47
2003 2463 8.141268 TGAATGCTCAATCGTGTAATCTATACA 58.859 33.333 0.00 0.00 0.00 2.29
2004 2464 8.887036 AATGCTCAATCGTGTAATCTATACAA 57.113 30.769 0.00 0.00 0.00 2.41
2005 2465 9.494271 AATGCTCAATCGTGTAATCTATACAAT 57.506 29.630 0.00 0.00 0.00 2.71
2006 2466 8.298030 TGCTCAATCGTGTAATCTATACAATG 57.702 34.615 0.00 0.00 0.00 2.82
2007 2467 7.926018 TGCTCAATCGTGTAATCTATACAATGT 59.074 33.333 0.00 0.00 0.00 2.71
2008 2468 8.765219 GCTCAATCGTGTAATCTATACAATGTT 58.235 33.333 0.00 0.00 0.00 2.71
2034 2494 7.979444 TTTTATATAGCTTACCACTCATGCC 57.021 36.000 0.00 0.00 0.00 4.40
2035 2495 6.680148 TTATATAGCTTACCACTCATGCCA 57.320 37.500 0.00 0.00 0.00 4.92
2036 2496 3.931907 ATAGCTTACCACTCATGCCAA 57.068 42.857 0.00 0.00 0.00 4.52
2037 2497 1.826385 AGCTTACCACTCATGCCAAC 58.174 50.000 0.00 0.00 0.00 3.77
2038 2498 1.352352 AGCTTACCACTCATGCCAACT 59.648 47.619 0.00 0.00 0.00 3.16
2039 2499 1.470098 GCTTACCACTCATGCCAACTG 59.530 52.381 0.00 0.00 0.00 3.16
2040 2500 2.086869 CTTACCACTCATGCCAACTGG 58.913 52.381 0.00 0.00 38.53 4.00
2041 2501 1.064003 TACCACTCATGCCAACTGGT 58.936 50.000 0.00 0.00 38.75 4.00
2042 2502 0.185901 ACCACTCATGCCAACTGGTT 59.814 50.000 0.00 0.00 37.57 3.67
2043 2503 1.423541 ACCACTCATGCCAACTGGTTA 59.576 47.619 0.00 0.00 37.57 2.85
2044 2504 2.041620 ACCACTCATGCCAACTGGTTAT 59.958 45.455 0.00 0.00 37.57 1.89
2045 2505 3.265737 ACCACTCATGCCAACTGGTTATA 59.734 43.478 0.00 0.00 37.57 0.98
2046 2506 3.627577 CCACTCATGCCAACTGGTTATAC 59.372 47.826 0.00 0.00 37.57 1.47
2047 2507 4.260985 CACTCATGCCAACTGGTTATACA 58.739 43.478 0.00 0.00 37.57 2.29
2048 2508 4.699735 CACTCATGCCAACTGGTTATACAA 59.300 41.667 0.00 0.00 37.57 2.41
2049 2509 5.357878 CACTCATGCCAACTGGTTATACAAT 59.642 40.000 0.00 0.00 37.57 2.71
2050 2510 5.357878 ACTCATGCCAACTGGTTATACAATG 59.642 40.000 0.00 0.00 37.57 2.82
2051 2511 5.260424 TCATGCCAACTGGTTATACAATGT 58.740 37.500 0.00 0.00 37.57 2.71
2052 2512 5.714333 TCATGCCAACTGGTTATACAATGTT 59.286 36.000 0.00 0.00 37.57 2.71
2053 2513 6.210385 TCATGCCAACTGGTTATACAATGTTT 59.790 34.615 0.00 0.00 37.57 2.83
2054 2514 6.412362 TGCCAACTGGTTATACAATGTTTT 57.588 33.333 0.00 0.00 37.57 2.43
2055 2515 6.821388 TGCCAACTGGTTATACAATGTTTTT 58.179 32.000 0.00 0.00 37.57 1.94
2155 2622 5.356190 CAGCAGACATACAATGAAATCAGGT 59.644 40.000 0.00 0.00 0.00 4.00
2266 2733 5.677567 TCAATAGTAAACCTCCCGAAATCC 58.322 41.667 0.00 0.00 0.00 3.01
2278 2745 5.509840 CCTCCCGAAATCCACTAGATAACTG 60.510 48.000 0.00 0.00 33.66 3.16
2287 2754 4.645136 TCCACTAGATAACTGCGACATTCT 59.355 41.667 0.00 0.00 0.00 2.40
2289 2756 5.233050 CCACTAGATAACTGCGACATTCTTG 59.767 44.000 0.00 0.00 0.00 3.02
2298 2765 2.066262 GCGACATTCTTGAAGAACCGA 58.934 47.619 21.74 0.00 37.00 4.69
2370 2837 5.336451 CCGTGATATTATCCGATCTCACCAA 60.336 44.000 13.00 0.00 32.52 3.67
2473 2940 3.953712 TGTTCTAATCTCGCTGTGGAA 57.046 42.857 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.202756 CGACTACAAGCTCCCCGC 60.203 66.667 0.00 0.00 39.57 6.13
1 2 2.202756 GCGACTACAAGCTCCCCG 60.203 66.667 0.00 0.00 0.00 5.73
2 3 2.202756 CGCGACTACAAGCTCCCC 60.203 66.667 0.00 0.00 0.00 4.81
3 4 1.516603 GTCGCGACTACAAGCTCCC 60.517 63.158 31.12 0.00 0.00 4.30
4 5 0.798771 CTGTCGCGACTACAAGCTCC 60.799 60.000 36.27 9.87 0.00 4.70
5 6 0.798771 CCTGTCGCGACTACAAGCTC 60.799 60.000 36.27 10.63 0.00 4.09
6 7 1.213013 CCTGTCGCGACTACAAGCT 59.787 57.895 36.27 0.00 0.00 3.74
7 8 0.798771 CTCCTGTCGCGACTACAAGC 60.799 60.000 36.27 12.16 0.00 4.01
8 9 0.798771 GCTCCTGTCGCGACTACAAG 60.799 60.000 36.27 26.83 0.00 3.16
9 10 1.211969 GCTCCTGTCGCGACTACAA 59.788 57.895 36.27 17.98 0.00 2.41
10 11 2.697761 GGCTCCTGTCGCGACTACA 61.698 63.158 36.27 18.95 0.00 2.74
11 12 2.102553 GGCTCCTGTCGCGACTAC 59.897 66.667 36.27 21.17 0.00 2.73
12 13 2.360726 TGGCTCCTGTCGCGACTA 60.361 61.111 36.27 22.64 0.00 2.59
13 14 3.753434 CTGGCTCCTGTCGCGACT 61.753 66.667 36.27 0.00 0.00 4.18
14 15 4.803426 CCTGGCTCCTGTCGCGAC 62.803 72.222 31.66 31.66 0.00 5.19
17 18 4.767255 CACCCTGGCTCCTGTCGC 62.767 72.222 0.00 0.00 0.00 5.19
18 19 4.767255 GCACCCTGGCTCCTGTCG 62.767 72.222 0.00 0.00 0.00 4.35
19 20 4.767255 CGCACCCTGGCTCCTGTC 62.767 72.222 0.00 0.00 0.00 3.51
108 109 3.966543 CTCCACCACCACCACCCC 61.967 72.222 0.00 0.00 0.00 4.95
109 110 4.660938 GCTCCACCACCACCACCC 62.661 72.222 0.00 0.00 0.00 4.61
110 111 3.884774 TGCTCCACCACCACCACC 61.885 66.667 0.00 0.00 0.00 4.61
111 112 2.594592 GTGCTCCACCACCACCAC 60.595 66.667 0.00 0.00 0.00 4.16
112 113 4.248842 CGTGCTCCACCACCACCA 62.249 66.667 0.00 0.00 32.10 4.17
114 115 3.234630 TAGCGTGCTCCACCACCAC 62.235 63.158 0.00 0.00 32.10 4.16
115 116 2.920384 TAGCGTGCTCCACCACCA 60.920 61.111 0.00 0.00 32.10 4.17
116 117 2.125512 CTAGCGTGCTCCACCACC 60.126 66.667 0.00 0.00 32.10 4.61
117 118 1.738099 CACTAGCGTGCTCCACCAC 60.738 63.158 0.00 0.00 33.82 4.16
118 119 2.656646 CACTAGCGTGCTCCACCA 59.343 61.111 0.00 0.00 33.82 4.17
119 120 2.125512 CCACTAGCGTGCTCCACC 60.126 66.667 0.00 0.00 39.86 4.61
120 121 1.153745 CTCCACTAGCGTGCTCCAC 60.154 63.158 0.00 0.00 39.86 4.02
121 122 2.351244 CCTCCACTAGCGTGCTCCA 61.351 63.158 0.00 0.00 39.86 3.86
122 123 2.496817 CCTCCACTAGCGTGCTCC 59.503 66.667 0.00 0.00 39.86 4.70
123 124 2.496817 CCCTCCACTAGCGTGCTC 59.503 66.667 0.00 0.00 39.86 4.26
124 125 3.077556 CCCCTCCACTAGCGTGCT 61.078 66.667 0.00 0.00 39.86 4.40
125 126 4.162690 CCCCCTCCACTAGCGTGC 62.163 72.222 0.00 0.00 39.86 5.34
126 127 2.683933 ACCCCCTCCACTAGCGTG 60.684 66.667 0.00 0.00 40.89 5.34
127 128 2.363925 GACCCCCTCCACTAGCGT 60.364 66.667 0.00 0.00 0.00 5.07
128 129 2.363795 TGACCCCCTCCACTAGCG 60.364 66.667 0.00 0.00 0.00 4.26
129 130 0.399233 ATCTGACCCCCTCCACTAGC 60.399 60.000 0.00 0.00 0.00 3.42
130 131 1.710816 GATCTGACCCCCTCCACTAG 58.289 60.000 0.00 0.00 0.00 2.57
131 132 0.264955 GGATCTGACCCCCTCCACTA 59.735 60.000 0.00 0.00 0.00 2.74
132 133 1.003573 GGATCTGACCCCCTCCACT 59.996 63.158 0.00 0.00 0.00 4.00
133 134 2.435693 CGGATCTGACCCCCTCCAC 61.436 68.421 0.00 0.00 0.00 4.02
134 135 2.041922 CGGATCTGACCCCCTCCA 60.042 66.667 0.00 0.00 0.00 3.86
135 136 3.551407 GCGGATCTGACCCCCTCC 61.551 72.222 5.48 0.00 0.00 4.30
136 137 3.551407 GGCGGATCTGACCCCCTC 61.551 72.222 5.48 0.00 0.00 4.30
141 142 3.083997 AGTGGGGCGGATCTGACC 61.084 66.667 19.32 19.32 35.71 4.02
142 143 2.187946 CAGTGGGGCGGATCTGAC 59.812 66.667 5.48 0.83 0.00 3.51
143 144 3.785859 GCAGTGGGGCGGATCTGA 61.786 66.667 5.48 0.00 0.00 3.27
144 145 4.864334 GGCAGTGGGGCGGATCTG 62.864 72.222 0.00 0.00 33.57 2.90
265 266 3.072468 TAACCTCTGGCGACCCGG 61.072 66.667 0.00 0.00 38.98 5.73
266 267 2.494918 CTAACCTCTGGCGACCCG 59.505 66.667 0.00 0.00 0.00 5.28
267 268 2.901042 CCTAACCTCTGGCGACCC 59.099 66.667 0.00 0.00 0.00 4.46
268 269 2.187163 GCCTAACCTCTGGCGACC 59.813 66.667 0.00 0.00 39.71 4.79
273 274 3.049080 GCCCCTGCCTAACCTCTGG 62.049 68.421 0.00 0.00 0.00 3.86
274 275 2.592308 GCCCCTGCCTAACCTCTG 59.408 66.667 0.00 0.00 0.00 3.35
275 276 3.083997 CGCCCCTGCCTAACCTCT 61.084 66.667 0.00 0.00 0.00 3.69
276 277 3.400054 ACGCCCCTGCCTAACCTC 61.400 66.667 0.00 0.00 0.00 3.85
277 278 3.717294 CACGCCCCTGCCTAACCT 61.717 66.667 0.00 0.00 0.00 3.50
292 293 0.804989 AGAAGCAAATAGGCACGCAC 59.195 50.000 0.00 0.00 35.83 5.34
295 296 1.089920 AGCAGAAGCAAATAGGCACG 58.910 50.000 0.00 0.00 45.49 5.34
299 300 2.286294 CGCAGTAGCAGAAGCAAATAGG 59.714 50.000 0.00 0.00 45.49 2.57
365 366 7.976734 CACCAAGTTAACCTTAACAATTCAACA 59.023 33.333 0.88 0.00 44.14 3.33
388 389 4.520492 ACTGACAATGAACCAAGATTCACC 59.480 41.667 0.00 0.00 41.29 4.02
389 390 5.695851 ACTGACAATGAACCAAGATTCAC 57.304 39.130 0.00 0.00 41.29 3.18
403 404 7.955918 AGAAAAAGATAAAGCCAACTGACAAT 58.044 30.769 0.00 0.00 0.00 2.71
406 407 8.648557 AAAAGAAAAAGATAAAGCCAACTGAC 57.351 30.769 0.00 0.00 0.00 3.51
409 410 7.012327 GCCAAAAAGAAAAAGATAAAGCCAACT 59.988 33.333 0.00 0.00 0.00 3.16
440 441 8.213518 TGAAAGACATTTGCTAGCTTTATAGG 57.786 34.615 17.23 1.78 0.00 2.57
504 505 8.925700 GCTGATTCCCTAAAATGTGTTAAAAAG 58.074 33.333 0.00 0.00 0.00 2.27
505 506 8.646900 AGCTGATTCCCTAAAATGTGTTAAAAA 58.353 29.630 0.00 0.00 0.00 1.94
513 516 9.034800 TCATTTTTAGCTGATTCCCTAAAATGT 57.965 29.630 14.74 8.38 40.89 2.71
533 536 8.674925 TCGACCTATTACCCCTATATCATTTT 57.325 34.615 0.00 0.00 0.00 1.82
549 553 3.399952 TTCCCCTTCTCTCGACCTATT 57.600 47.619 0.00 0.00 0.00 1.73
555 559 2.180276 CCTCTTTTCCCCTTCTCTCGA 58.820 52.381 0.00 0.00 0.00 4.04
568 572 6.588719 TGTGCAAATGCTATTACCTCTTTT 57.411 33.333 6.97 0.00 42.66 2.27
573 577 4.019174 AGCTTGTGCAAATGCTATTACCT 58.981 39.130 15.31 0.00 42.74 3.08
595 601 2.677836 GGTCATTTCAGCGCTTGTGATA 59.322 45.455 7.50 0.00 0.00 2.15
625 632 1.004504 GAGATTGATTCGCGGTTCAGC 60.005 52.381 6.13 6.21 0.00 4.26
641 648 9.091220 AGGGAGTACTAATTAAATAAGCGAGAT 57.909 33.333 0.00 0.00 0.00 2.75
660 667 9.947433 TTTTGTTTCGAAAAGATATAGGGAGTA 57.053 29.630 13.10 0.00 0.00 2.59
661 668 8.857694 TTTTGTTTCGAAAAGATATAGGGAGT 57.142 30.769 13.10 0.00 0.00 3.85
750 758 7.712639 AGATATGTCACATGTCAATTCTACCAC 59.287 37.037 16.14 0.00 0.00 4.16
854 862 0.322456 TCTACGGCCAAGCATGCTTT 60.322 50.000 30.07 17.68 33.42 3.51
940 948 2.781595 CTAGTTGGTCGCCGGTTGCT 62.782 60.000 1.90 0.00 38.05 3.91
946 954 1.268437 GCTAGTACTAGTTGGTCGCCG 60.268 57.143 26.76 3.37 35.65 6.46
957 965 7.884877 TGAAGTTACACCACTAAGCTAGTACTA 59.115 37.037 1.89 1.89 37.23 1.82
962 970 6.456501 ACTTGAAGTTACACCACTAAGCTAG 58.543 40.000 0.00 0.00 0.00 3.42
964 972 5.291905 ACTTGAAGTTACACCACTAAGCT 57.708 39.130 0.00 0.00 0.00 3.74
965 973 5.120363 GCTACTTGAAGTTACACCACTAAGC 59.880 44.000 1.97 0.00 0.00 3.09
966 974 6.456501 AGCTACTTGAAGTTACACCACTAAG 58.543 40.000 1.97 0.00 0.00 2.18
967 975 6.415206 AGCTACTTGAAGTTACACCACTAA 57.585 37.500 1.97 0.00 0.00 2.24
980 988 6.570692 GCCATTACTGTACTAGCTACTTGAA 58.429 40.000 0.00 0.00 0.00 2.69
981 989 5.220989 CGCCATTACTGTACTAGCTACTTGA 60.221 44.000 0.00 0.00 0.00 3.02
982 990 4.976731 CGCCATTACTGTACTAGCTACTTG 59.023 45.833 0.00 0.00 0.00 3.16
983 991 4.037684 CCGCCATTACTGTACTAGCTACTT 59.962 45.833 0.00 0.00 0.00 2.24
985 993 3.856267 GCCGCCATTACTGTACTAGCTAC 60.856 52.174 0.00 0.00 0.00 3.58
1049 1057 1.827399 GAAAGGTGAGGAGTGGGCGA 61.827 60.000 0.00 0.00 0.00 5.54
1054 1062 0.326264 CCCAGGAAAGGTGAGGAGTG 59.674 60.000 0.00 0.00 0.00 3.51
1062 1070 1.201429 AGTGATCGCCCAGGAAAGGT 61.201 55.000 1.76 0.00 0.00 3.50
1095 1103 4.847516 TCGTCGATGAAGGCGCGG 62.848 66.667 8.83 0.00 39.34 6.46
1096 1104 3.607987 GTCGTCGATGAAGGCGCG 61.608 66.667 9.35 0.00 39.34 6.86
1097 1105 2.506217 TGTCGTCGATGAAGGCGC 60.506 61.111 9.35 0.00 39.34 6.53
1098 1106 1.154016 ACTGTCGTCGATGAAGGCG 60.154 57.895 9.35 0.00 41.09 5.52
1099 1107 0.109272 TCACTGTCGTCGATGAAGGC 60.109 55.000 9.35 0.00 0.00 4.35
1100 1108 2.568696 ATCACTGTCGTCGATGAAGG 57.431 50.000 9.35 7.66 0.00 3.46
1101 1109 3.478874 CGTAATCACTGTCGTCGATGAAG 59.521 47.826 9.35 11.32 0.00 3.02
1102 1110 3.422655 CGTAATCACTGTCGTCGATGAA 58.577 45.455 9.35 0.00 0.00 2.57
1103 1111 2.790123 GCGTAATCACTGTCGTCGATGA 60.790 50.000 2.39 2.39 0.00 2.92
1104 1112 1.513178 GCGTAATCACTGTCGTCGATG 59.487 52.381 0.00 0.00 0.00 3.84
1105 1113 1.823828 GCGTAATCACTGTCGTCGAT 58.176 50.000 0.00 0.00 0.00 3.59
1106 1114 0.519792 CGCGTAATCACTGTCGTCGA 60.520 55.000 0.00 0.00 0.00 4.20
1107 1115 1.461317 CCGCGTAATCACTGTCGTCG 61.461 60.000 4.92 0.00 0.00 5.12
1108 1116 1.740043 GCCGCGTAATCACTGTCGTC 61.740 60.000 4.92 0.00 0.00 4.20
1109 1117 1.804326 GCCGCGTAATCACTGTCGT 60.804 57.895 4.92 0.00 0.00 4.34
1110 1118 1.472276 GAGCCGCGTAATCACTGTCG 61.472 60.000 4.92 0.00 0.00 4.35
1111 1119 0.457853 TGAGCCGCGTAATCACTGTC 60.458 55.000 4.92 0.00 0.00 3.51
1112 1120 0.458543 CTGAGCCGCGTAATCACTGT 60.459 55.000 4.92 0.00 0.00 3.55
1113 1121 1.756375 GCTGAGCCGCGTAATCACTG 61.756 60.000 4.92 0.00 0.00 3.66
1114 1122 1.519455 GCTGAGCCGCGTAATCACT 60.519 57.895 4.92 0.00 0.00 3.41
1115 1123 1.483424 GAGCTGAGCCGCGTAATCAC 61.483 60.000 4.92 1.81 34.40 3.06
1116 1124 1.226974 GAGCTGAGCCGCGTAATCA 60.227 57.895 4.92 5.12 34.40 2.57
1117 1125 1.951631 GGAGCTGAGCCGCGTAATC 60.952 63.158 4.92 0.00 34.40 1.75
1118 1126 2.107141 GGAGCTGAGCCGCGTAAT 59.893 61.111 4.92 0.00 34.40 1.89
1119 1127 3.378602 TGGAGCTGAGCCGCGTAA 61.379 61.111 4.92 0.00 34.40 3.18
1120 1128 4.129737 GTGGAGCTGAGCCGCGTA 62.130 66.667 4.92 0.00 34.40 4.42
1123 1131 4.828925 GAGGTGGAGCTGAGCCGC 62.829 72.222 0.00 0.00 35.19 6.53
1124 1132 4.154347 GGAGGTGGAGCTGAGCCG 62.154 72.222 0.00 0.00 0.00 5.52
1125 1133 3.005539 TGGAGGTGGAGCTGAGCC 61.006 66.667 0.00 0.00 0.00 4.70
1126 1134 2.267324 GTGGAGGTGGAGCTGAGC 59.733 66.667 0.00 0.00 0.00 4.26
1127 1135 1.979155 TCGTGGAGGTGGAGCTGAG 60.979 63.158 0.00 0.00 0.00 3.35
1128 1136 2.117423 TCGTGGAGGTGGAGCTGA 59.883 61.111 0.00 0.00 0.00 4.26
1129 1137 2.262915 GTCGTGGAGGTGGAGCTG 59.737 66.667 0.00 0.00 0.00 4.24
1130 1138 3.374402 CGTCGTGGAGGTGGAGCT 61.374 66.667 0.00 0.00 0.00 4.09
1131 1139 2.615262 GATCGTCGTGGAGGTGGAGC 62.615 65.000 0.00 0.00 0.00 4.70
1132 1140 1.313091 TGATCGTCGTGGAGGTGGAG 61.313 60.000 0.00 0.00 0.00 3.86
1133 1141 0.683179 ATGATCGTCGTGGAGGTGGA 60.683 55.000 0.00 0.00 0.00 4.02
1134 1142 0.249073 GATGATCGTCGTGGAGGTGG 60.249 60.000 0.00 0.00 0.00 4.61
1135 1143 0.455815 TGATGATCGTCGTGGAGGTG 59.544 55.000 10.32 0.00 0.00 4.00
1136 1144 0.741326 CTGATGATCGTCGTGGAGGT 59.259 55.000 10.32 0.00 0.00 3.85
1137 1145 0.596083 GCTGATGATCGTCGTGGAGG 60.596 60.000 10.32 0.00 0.00 4.30
1138 1146 0.101219 TGCTGATGATCGTCGTGGAG 59.899 55.000 10.32 3.36 0.00 3.86
1139 1147 0.179137 GTGCTGATGATCGTCGTGGA 60.179 55.000 10.32 4.41 0.00 4.02
1140 1148 0.179127 AGTGCTGATGATCGTCGTGG 60.179 55.000 10.32 4.57 0.00 4.94
1141 1149 2.112522 GTAGTGCTGATGATCGTCGTG 58.887 52.381 10.32 6.87 0.00 4.35
1142 1150 1.065701 GGTAGTGCTGATGATCGTCGT 59.934 52.381 10.32 0.00 0.00 4.34
1143 1151 1.600663 GGGTAGTGCTGATGATCGTCG 60.601 57.143 10.32 6.45 0.00 5.12
1144 1152 1.683917 AGGGTAGTGCTGATGATCGTC 59.316 52.381 8.06 8.06 0.00 4.20
1145 1153 1.781786 AGGGTAGTGCTGATGATCGT 58.218 50.000 0.00 0.00 0.00 3.73
1146 1154 2.898729 AAGGGTAGTGCTGATGATCG 57.101 50.000 0.00 0.00 0.00 3.69
1147 1155 3.126831 CGAAAGGGTAGTGCTGATGATC 58.873 50.000 0.00 0.00 0.00 2.92
1148 1156 2.766263 TCGAAAGGGTAGTGCTGATGAT 59.234 45.455 0.00 0.00 0.00 2.45
1149 1157 2.176045 TCGAAAGGGTAGTGCTGATGA 58.824 47.619 0.00 0.00 0.00 2.92
1150 1158 2.672961 TCGAAAGGGTAGTGCTGATG 57.327 50.000 0.00 0.00 0.00 3.07
1151 1159 2.766263 TGATCGAAAGGGTAGTGCTGAT 59.234 45.455 0.00 0.00 0.00 2.90
1152 1160 2.176045 TGATCGAAAGGGTAGTGCTGA 58.824 47.619 0.00 0.00 0.00 4.26
1193 1553 1.301716 GCGAAAGAGACCTGTGCCA 60.302 57.895 0.00 0.00 0.00 4.92
1215 1581 1.714899 GATGTTTGTCATCCCCGGCG 61.715 60.000 0.00 0.00 45.05 6.46
1228 1594 1.071605 GTCTTCTCGCTGCGATGTTT 58.928 50.000 26.15 0.00 34.61 2.83
1237 1603 3.849911 TGATTTTGATCGTCTTCTCGCT 58.150 40.909 0.00 0.00 0.00 4.93
1247 1613 1.328680 CCCTCGCACTGATTTTGATCG 59.671 52.381 0.00 0.00 0.00 3.69
1254 1620 1.078848 GCTCACCCTCGCACTGATT 60.079 57.895 0.00 0.00 0.00 2.57
1273 1639 2.317149 CTGAACCCGATCCTCCCTGC 62.317 65.000 0.00 0.00 0.00 4.85
1414 1780 0.459237 CTCTCCACGCGCTTCTTGAT 60.459 55.000 5.73 0.00 0.00 2.57
1471 1837 2.898343 GTGGTTGTGGACGCCGTT 60.898 61.111 0.00 0.00 0.00 4.44
1613 1979 5.952033 AGCTTTCTAGTTTCTACTGTACGG 58.048 41.667 0.00 0.00 35.78 4.02
1662 2029 1.515736 GAACCGACGACGACATCCC 60.516 63.158 9.28 0.00 42.66 3.85
1686 2053 9.631452 CTACATACATCATGTCCTGTATACAAG 57.369 37.037 7.06 0.53 44.99 3.16
1689 2056 7.831753 AGCTACATACATCATGTCCTGTATAC 58.168 38.462 11.61 0.00 44.99 1.47
1696 2063 8.715998 CAATTCTAAGCTACATACATCATGTCC 58.284 37.037 0.00 0.00 44.99 4.02
1713 2080 5.472148 TGGCTGCAATTGAACAATTCTAAG 58.528 37.500 10.34 8.60 38.84 2.18
1718 2085 4.546829 ATCTGGCTGCAATTGAACAATT 57.453 36.364 10.34 6.91 41.33 2.32
1762 2130 0.105039 CCTCCACCTATTCGTGCTCC 59.895 60.000 0.00 0.00 32.10 4.70
1763 2131 0.105039 CCCTCCACCTATTCGTGCTC 59.895 60.000 0.00 0.00 32.10 4.26
1775 2143 3.697166 TCCAAATTTTAGAGCCCTCCAC 58.303 45.455 0.00 0.00 0.00 4.02
1776 2144 4.536765 GATCCAAATTTTAGAGCCCTCCA 58.463 43.478 0.00 0.00 0.00 3.86
1833 2201 7.038154 TCTTTTGTTTTCAGGTGATACAAGG 57.962 36.000 7.71 6.39 33.54 3.61
1834 2202 8.190784 ACTTCTTTTGTTTTCAGGTGATACAAG 58.809 33.333 7.71 0.00 33.54 3.16
1836 2204 7.639113 ACTTCTTTTGTTTTCAGGTGATACA 57.361 32.000 0.00 0.00 0.00 2.29
1837 2205 7.648112 GGAACTTCTTTTGTTTTCAGGTGATAC 59.352 37.037 0.00 0.00 0.00 2.24
1838 2206 7.559897 AGGAACTTCTTTTGTTTTCAGGTGATA 59.440 33.333 0.00 0.00 27.25 2.15
1839 2207 6.381133 AGGAACTTCTTTTGTTTTCAGGTGAT 59.619 34.615 0.00 0.00 27.25 3.06
1840 2208 5.714806 AGGAACTTCTTTTGTTTTCAGGTGA 59.285 36.000 0.00 0.00 27.25 4.02
1841 2209 5.965922 AGGAACTTCTTTTGTTTTCAGGTG 58.034 37.500 0.00 0.00 27.25 4.00
1842 2210 5.127194 GGAGGAACTTCTTTTGTTTTCAGGT 59.873 40.000 0.00 0.00 41.55 4.00
1869 2246 9.191479 AGAAGCGCCTAATCATATACTACTATT 57.809 33.333 2.29 0.00 0.00 1.73
1870 2247 8.754991 AGAAGCGCCTAATCATATACTACTAT 57.245 34.615 2.29 0.00 0.00 2.12
1871 2248 8.459635 CAAGAAGCGCCTAATCATATACTACTA 58.540 37.037 2.29 0.00 0.00 1.82
1872 2249 7.176865 TCAAGAAGCGCCTAATCATATACTACT 59.823 37.037 2.29 0.00 0.00 2.57
1873 2250 7.273815 GTCAAGAAGCGCCTAATCATATACTAC 59.726 40.741 2.29 0.00 0.00 2.73
1874 2251 7.176865 AGTCAAGAAGCGCCTAATCATATACTA 59.823 37.037 2.29 0.00 0.00 1.82
1875 2252 6.015010 AGTCAAGAAGCGCCTAATCATATACT 60.015 38.462 2.29 0.00 0.00 2.12
1876 2253 6.159988 AGTCAAGAAGCGCCTAATCATATAC 58.840 40.000 2.29 0.00 0.00 1.47
1877 2254 6.346477 AGTCAAGAAGCGCCTAATCATATA 57.654 37.500 2.29 0.00 0.00 0.86
1878 2255 5.220710 AGTCAAGAAGCGCCTAATCATAT 57.779 39.130 2.29 0.00 0.00 1.78
1879 2256 4.672587 AGTCAAGAAGCGCCTAATCATA 57.327 40.909 2.29 0.00 0.00 2.15
1917 2294 6.801862 CCGTTTATTTGACTGATGGAGAAAAC 59.198 38.462 0.00 0.00 0.00 2.43
1946 2323 3.005155 GCTGAATGGGGATTCAAGTATGC 59.995 47.826 0.00 0.00 39.73 3.14
1947 2324 4.209538 TGCTGAATGGGGATTCAAGTATG 58.790 43.478 0.00 0.00 39.73 2.39
1969 2429 2.029623 GATTGAGCATTCAGGTGGCAT 58.970 47.619 0.00 0.00 34.15 4.40
2009 2469 7.996066 TGGCATGAGTGGTAAGCTATATAAAAA 59.004 33.333 0.00 0.00 0.00 1.94
2010 2470 7.513856 TGGCATGAGTGGTAAGCTATATAAAA 58.486 34.615 0.00 0.00 0.00 1.52
2011 2471 7.073457 TGGCATGAGTGGTAAGCTATATAAA 57.927 36.000 0.00 0.00 0.00 1.40
2012 2472 6.680148 TGGCATGAGTGGTAAGCTATATAA 57.320 37.500 0.00 0.00 0.00 0.98
2013 2473 6.270000 AGTTGGCATGAGTGGTAAGCTATATA 59.730 38.462 0.00 0.00 0.00 0.86
2014 2474 5.072329 AGTTGGCATGAGTGGTAAGCTATAT 59.928 40.000 0.00 0.00 0.00 0.86
2015 2475 4.408921 AGTTGGCATGAGTGGTAAGCTATA 59.591 41.667 0.00 0.00 0.00 1.31
2016 2476 3.200825 AGTTGGCATGAGTGGTAAGCTAT 59.799 43.478 0.00 0.00 0.00 2.97
2017 2477 2.571653 AGTTGGCATGAGTGGTAAGCTA 59.428 45.455 0.00 0.00 0.00 3.32
2018 2478 1.352352 AGTTGGCATGAGTGGTAAGCT 59.648 47.619 0.00 0.00 0.00 3.74
2019 2479 1.470098 CAGTTGGCATGAGTGGTAAGC 59.530 52.381 0.00 0.00 0.00 3.09
2020 2480 2.086869 CCAGTTGGCATGAGTGGTAAG 58.913 52.381 0.00 0.00 33.74 2.34
2021 2481 1.423541 ACCAGTTGGCATGAGTGGTAA 59.576 47.619 15.46 0.00 46.38 2.85
2022 2482 1.064003 ACCAGTTGGCATGAGTGGTA 58.936 50.000 15.46 0.00 46.38 3.25
2023 2483 1.846261 ACCAGTTGGCATGAGTGGT 59.154 52.632 12.02 12.02 44.12 4.16
2024 2484 2.198827 TAACCAGTTGGCATGAGTGG 57.801 50.000 10.81 10.81 42.22 4.00
2025 2485 4.260985 TGTATAACCAGTTGGCATGAGTG 58.739 43.478 0.00 0.00 39.32 3.51
2026 2486 4.568072 TGTATAACCAGTTGGCATGAGT 57.432 40.909 0.00 0.00 39.32 3.41
2027 2487 5.357878 ACATTGTATAACCAGTTGGCATGAG 59.642 40.000 0.00 0.00 39.32 2.90
2028 2488 5.260424 ACATTGTATAACCAGTTGGCATGA 58.740 37.500 0.00 0.00 39.32 3.07
2029 2489 5.581126 ACATTGTATAACCAGTTGGCATG 57.419 39.130 0.00 0.00 39.32 4.06
2030 2490 6.603940 AAACATTGTATAACCAGTTGGCAT 57.396 33.333 0.00 0.00 39.32 4.40
2031 2491 6.412362 AAAACATTGTATAACCAGTTGGCA 57.588 33.333 0.00 0.00 39.32 4.92
2139 2606 3.299503 GCCCCACCTGATTTCATTGTAT 58.700 45.455 0.00 0.00 0.00 2.29
2140 2607 2.042297 TGCCCCACCTGATTTCATTGTA 59.958 45.455 0.00 0.00 0.00 2.41
2155 2622 1.076841 TCTTGTTGGATTGATGCCCCA 59.923 47.619 0.00 0.00 0.00 4.96
2266 2733 6.036470 TCAAGAATGTCGCAGTTATCTAGTG 58.964 40.000 0.00 0.00 0.00 2.74
2278 2745 2.066262 TCGGTTCTTCAAGAATGTCGC 58.934 47.619 2.39 0.00 36.50 5.19
2287 2754 1.959226 GGCAGCGTCGGTTCTTCAA 60.959 57.895 0.00 0.00 0.00 2.69
2289 2756 2.357034 TGGCAGCGTCGGTTCTTC 60.357 61.111 0.00 0.00 0.00 2.87
2298 2765 2.561569 GTTATTCTATGGTGGCAGCGT 58.438 47.619 16.46 16.46 0.00 5.07
2370 2837 5.036117 AGATACGGGATGCAATAACTTGT 57.964 39.130 0.00 0.00 34.69 3.16
2432 2899 1.343142 TGTAGCTGATGTGTTCACGGT 59.657 47.619 0.00 0.00 0.00 4.83
2473 2940 1.152881 GGGATCTTTCATGCCGGCT 60.153 57.895 29.70 10.60 0.00 5.52
2478 2945 0.107214 TCACCGGGGATCTTTCATGC 60.107 55.000 0.00 0.00 0.00 4.06


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

AutoCloner maintained by Alex Coulton.