Multiple sequence alignment - TraesCS6B01G288500

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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 TraesCS6B01G288500 chr6B 100.000 4523 0 0 1 4523 519407681 519403159 0.000000e+00 8353.0
1 TraesCS6B01G288500 chr6D 94.483 2157 76 20 2119 4261 344178394 344176267 0.000000e+00 3284.0
2 TraesCS6B01G288500 chr6D 86.216 1081 59 35 3 1040 344180546 344179513 0.000000e+00 1088.0
3 TraesCS6B01G288500 chr6D 93.738 527 15 5 1138 1647 344179434 344178909 0.000000e+00 774.0
4 TraesCS6B01G288500 chr6D 96.413 446 12 2 1645 2086 344178838 344178393 0.000000e+00 732.0
5 TraesCS6B01G288500 chr6D 85.897 312 35 5 1645 1948 469309133 469309443 1.570000e-84 324.0
6 TraesCS6B01G288500 chr6D 91.617 167 7 2 4364 4523 344176259 344176093 1.640000e-54 224.0
7 TraesCS6B01G288500 chr6D 88.636 132 9 2 2321 2452 390489595 390489470 6.060000e-34 156.0
8 TraesCS6B01G288500 chr6A 93.550 1783 57 17 2778 4523 484568767 484567006 0.000000e+00 2603.0
9 TraesCS6B01G288500 chr6A 94.764 955 33 11 1138 2077 484570552 484569600 0.000000e+00 1471.0
10 TraesCS6B01G288500 chr6A 85.488 1075 79 45 3 1040 484571651 484570617 0.000000e+00 1050.0
11 TraesCS6B01G288500 chr6A 91.071 168 11 3 2090 2253 484569503 484569336 1.640000e-54 224.0
12 TraesCS6B01G288500 chr6A 92.063 63 5 0 2479 2541 106694459 106694397 6.230000e-14 89.8
13 TraesCS6B01G288500 chr5A 80.741 135 13 8 2319 2452 333413679 333413557 4.820000e-15 93.5
14 TraesCS6B01G288500 chr2D 93.651 63 3 1 2479 2541 201153027 201152966 4.820000e-15 93.5
15 TraesCS6B01G288500 chr3A 80.315 127 15 6 2327 2452 144450874 144450991 2.240000e-13 87.9
16 TraesCS6B01G288500 chr3A 100.000 28 0 0 2329 2356 605990774 605990747 8.000000e-03 52.8
17 TraesCS6B01G288500 chr4B 82.418 91 9 4 2329 2417 461624577 461624662 6.280000e-09 73.1


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 TraesCS6B01G288500 chr6B 519403159 519407681 4522 True 8353.0 8353 100.00000 1 4523 1 chr6B.!!$R1 4522
1 TraesCS6B01G288500 chr6D 344176093 344180546 4453 True 1220.4 3284 92.49340 3 4523 5 chr6D.!!$R2 4520
2 TraesCS6B01G288500 chr6A 484567006 484571651 4645 True 1337.0 2603 91.21825 3 4523 4 chr6A.!!$R2 4520

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
609 676 0.390340 GGCACATGAGAGCGAGTGAA 60.390 55.0 0.00 0.0 33.99 3.18 F
1085 1161 0.108709 CGTGGACGATCGGGGTTAAA 60.109 55.0 20.98 0.0 43.02 1.52 F
1110 1187 0.253044 AATGGCGCTGCTCTAGGAAA 59.747 50.0 7.64 0.0 0.00 3.13 F
2798 3401 0.321298 TCTGCTTTAACACCTCCGGC 60.321 55.0 0.00 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 1593 0.601841 GAAAGGGTGAGCGAACCGAA 60.602 55.000 4.96 0.0 41.52 4.30 R
2710 3313 0.615331 TTCACAGGGAGGATGTCTGC 59.385 55.000 0.00 0.0 32.19 4.26 R
2874 3477 1.765314 GCTGATCCTGTACATGACCCT 59.235 52.381 0.00 0.0 0.00 4.34 R
4351 4996 0.031111 AGCTCCCCTGTATGGCTGTA 60.031 55.000 0.00 0.0 31.68 2.74 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
57 62 3.616935 CGAAAGCGACGTCTATCCA 57.383 52.632 14.70 0.00 40.82 3.41
61 66 1.183549 AAGCGACGTCTATCCAACCT 58.816 50.000 14.70 0.00 0.00 3.50
220 226 4.293648 CCACCCGCACAGTCACGA 62.294 66.667 0.00 0.00 0.00 4.35
268 274 3.864789 ATCTCGTGGCTGGGATATTTT 57.135 42.857 0.00 0.00 0.00 1.82
283 289 5.163632 GGGATATTTTCGCGGGTTTTTCTTA 60.164 40.000 6.13 0.00 0.00 2.10
293 303 4.729595 CGGGTTTTTCTTAGGATTTTCCG 58.270 43.478 0.00 0.00 42.75 4.30
361 379 2.631160 TTTTCTTCCTCTTGTGGCGA 57.369 45.000 0.00 0.00 0.00 5.54
364 382 3.973206 TTCTTCCTCTTGTGGCGATAA 57.027 42.857 0.00 0.00 0.00 1.75
457 475 0.393808 TTAAGGCGGCCCTGTGATTC 60.394 55.000 17.02 0.00 41.90 2.52
458 476 1.271840 TAAGGCGGCCCTGTGATTCT 61.272 55.000 17.02 0.00 41.90 2.40
609 676 0.390340 GGCACATGAGAGCGAGTGAA 60.390 55.000 0.00 0.00 33.99 3.18
674 741 4.867608 CGCAGGGTTTGGGTTATATTTTTG 59.132 41.667 0.00 0.00 35.17 2.44
675 742 5.336849 CGCAGGGTTTGGGTTATATTTTTGA 60.337 40.000 0.00 0.00 35.17 2.69
788 855 4.151582 GCGCTGGGCCCTACGTAA 62.152 66.667 29.58 7.89 34.80 3.18
789 856 2.202837 CGCTGGGCCCTACGTAAC 60.203 66.667 25.70 3.23 0.00 2.50
790 857 2.202837 GCTGGGCCCTACGTAACG 60.203 66.667 25.70 2.07 0.00 3.18
791 858 3.010413 GCTGGGCCCTACGTAACGT 62.010 63.158 25.70 0.00 44.35 3.99
792 859 1.666209 GCTGGGCCCTACGTAACGTA 61.666 60.000 25.70 0.00 41.54 3.57
793 860 0.817013 CTGGGCCCTACGTAACGTAA 59.183 55.000 25.70 0.00 41.82 3.18
794 861 0.530288 TGGGCCCTACGTAACGTAAC 59.470 55.000 25.70 0.00 41.82 2.50
830 897 5.437946 TCTCTCTTTTATGCGACTCCTCTA 58.562 41.667 0.00 0.00 0.00 2.43
836 903 1.917872 ATGCGACTCCTCTATCCTCC 58.082 55.000 0.00 0.00 0.00 4.30
875 942 2.756025 CGTCTCTCGCCTCTTCGCT 61.756 63.158 0.00 0.00 0.00 4.93
878 945 1.226831 CTCTCGCCTCTTCGCTTCC 60.227 63.158 0.00 0.00 0.00 3.46
880 947 3.724914 CTCGCCTCTTCGCTTCCCC 62.725 68.421 0.00 0.00 0.00 4.81
885 952 1.681486 CCTCTTCGCTTCCCCTCTCC 61.681 65.000 0.00 0.00 0.00 3.71
887 954 0.972983 TCTTCGCTTCCCCTCTCCTG 60.973 60.000 0.00 0.00 0.00 3.86
888 955 0.972983 CTTCGCTTCCCCTCTCCTGA 60.973 60.000 0.00 0.00 0.00 3.86
892 964 0.907230 GCTTCCCCTCTCCTGACTGT 60.907 60.000 0.00 0.00 0.00 3.55
899 972 1.000771 TCTCCTGACTGTCCCTCCG 60.001 63.158 5.17 0.00 0.00 4.63
911 984 4.824515 CCTCCGTCCTCGCCCTCT 62.825 72.222 0.00 0.00 35.54 3.69
934 1007 0.946221 GACAACGAGCACCTGGTCTG 60.946 60.000 0.00 0.00 40.17 3.51
936 1009 3.537206 AACGAGCACCTGGTCTGGC 62.537 63.158 0.00 0.00 40.17 4.85
937 1010 4.767255 CGAGCACCTGGTCTGGCC 62.767 72.222 0.00 0.00 40.17 5.36
938 1011 3.325753 GAGCACCTGGTCTGGCCT 61.326 66.667 3.32 0.00 39.31 5.19
939 1012 3.618780 GAGCACCTGGTCTGGCCTG 62.619 68.421 3.32 2.92 39.31 4.85
944 1017 3.488423 CTGGTCTGGCCTGGTCTT 58.512 61.111 10.07 0.00 38.35 3.01
945 1018 1.002868 CTGGTCTGGCCTGGTCTTG 60.003 63.158 10.07 0.00 38.35 3.02
947 1020 1.352622 TGGTCTGGCCTGGTCTTGTT 61.353 55.000 10.07 0.00 38.35 2.83
948 1021 0.606673 GGTCTGGCCTGGTCTTGTTC 60.607 60.000 10.07 0.00 0.00 3.18
964 1040 1.593209 TTCTTGGTGTGGCGACGTC 60.593 57.895 5.18 5.18 0.00 4.34
979 1055 2.514013 CGTCGGGCAGTGCGATTAC 61.514 63.158 9.45 3.86 0.00 1.89
980 1056 1.153628 GTCGGGCAGTGCGATTACT 60.154 57.895 9.45 0.00 0.00 2.24
995 1071 2.543777 TTACTTTGTTCTCGCTGGCT 57.456 45.000 0.00 0.00 0.00 4.75
1027 1103 1.949525 GCACGCAGGTAATTCATCCAT 59.050 47.619 0.00 0.00 0.00 3.41
1028 1104 2.287188 GCACGCAGGTAATTCATCCATG 60.287 50.000 0.00 0.00 0.00 3.66
1036 1112 4.818546 AGGTAATTCATCCATGCTTCTTCG 59.181 41.667 0.00 0.00 0.00 3.79
1039 1115 0.911769 TCATCCATGCTTCTTCGGGT 59.088 50.000 0.00 0.00 0.00 5.28
1040 1116 1.134401 TCATCCATGCTTCTTCGGGTC 60.134 52.381 0.00 0.00 0.00 4.46
1041 1117 1.134280 CATCCATGCTTCTTCGGGTCT 60.134 52.381 0.00 0.00 0.00 3.85
1042 1118 0.984230 TCCATGCTTCTTCGGGTCTT 59.016 50.000 0.00 0.00 0.00 3.01
1043 1119 1.351017 TCCATGCTTCTTCGGGTCTTT 59.649 47.619 0.00 0.00 0.00 2.52
1044 1120 2.162681 CCATGCTTCTTCGGGTCTTTT 58.837 47.619 0.00 0.00 0.00 2.27
1045 1121 2.162408 CCATGCTTCTTCGGGTCTTTTC 59.838 50.000 0.00 0.00 0.00 2.29
1047 1123 1.166129 GCTTCTTCGGGTCTTTTCCC 58.834 55.000 0.00 0.00 43.78 3.97
1048 1124 1.271434 GCTTCTTCGGGTCTTTTCCCT 60.271 52.381 0.25 0.00 44.95 4.20
1050 1126 0.690762 TCTTCGGGTCTTTTCCCTGG 59.309 55.000 0.25 0.00 44.95 4.45
1051 1127 0.400594 CTTCGGGTCTTTTCCCTGGT 59.599 55.000 0.00 0.00 44.95 4.00
1052 1128 0.109723 TTCGGGTCTTTTCCCTGGTG 59.890 55.000 0.00 0.00 44.95 4.17
1053 1129 1.057851 TCGGGTCTTTTCCCTGGTGT 61.058 55.000 0.00 0.00 44.95 4.16
1054 1130 0.889186 CGGGTCTTTTCCCTGGTGTG 60.889 60.000 0.00 0.00 44.95 3.82
1055 1131 0.539669 GGGTCTTTTCCCTGGTGTGG 60.540 60.000 0.00 0.00 43.85 4.17
1056 1132 0.185175 GGTCTTTTCCCTGGTGTGGT 59.815 55.000 0.00 0.00 0.00 4.16
1057 1133 1.318576 GTCTTTTCCCTGGTGTGGTG 58.681 55.000 0.00 0.00 0.00 4.17
1058 1134 1.133915 GTCTTTTCCCTGGTGTGGTGA 60.134 52.381 0.00 0.00 0.00 4.02
1059 1135 1.142870 TCTTTTCCCTGGTGTGGTGAG 59.857 52.381 0.00 0.00 0.00 3.51
1060 1136 1.142870 CTTTTCCCTGGTGTGGTGAGA 59.857 52.381 0.00 0.00 0.00 3.27
1061 1137 1.444933 TTTCCCTGGTGTGGTGAGAT 58.555 50.000 0.00 0.00 0.00 2.75
1062 1138 1.444933 TTCCCTGGTGTGGTGAGATT 58.555 50.000 0.00 0.00 0.00 2.40
1063 1139 0.692476 TCCCTGGTGTGGTGAGATTG 59.308 55.000 0.00 0.00 0.00 2.67
1064 1140 0.401738 CCCTGGTGTGGTGAGATTGT 59.598 55.000 0.00 0.00 0.00 2.71
1065 1141 1.202927 CCCTGGTGTGGTGAGATTGTT 60.203 52.381 0.00 0.00 0.00 2.83
1066 1142 2.154462 CCTGGTGTGGTGAGATTGTTC 58.846 52.381 0.00 0.00 0.00 3.18
1067 1143 1.800586 CTGGTGTGGTGAGATTGTTCG 59.199 52.381 0.00 0.00 0.00 3.95
1068 1144 1.140052 TGGTGTGGTGAGATTGTTCGT 59.860 47.619 0.00 0.00 0.00 3.85
1069 1145 1.531149 GGTGTGGTGAGATTGTTCGTG 59.469 52.381 0.00 0.00 0.00 4.35
1070 1146 1.531149 GTGTGGTGAGATTGTTCGTGG 59.469 52.381 0.00 0.00 0.00 4.94
1071 1147 1.414550 TGTGGTGAGATTGTTCGTGGA 59.585 47.619 0.00 0.00 0.00 4.02
1072 1148 1.798813 GTGGTGAGATTGTTCGTGGAC 59.201 52.381 0.00 0.00 0.00 4.02
1073 1149 1.068474 GGTGAGATTGTTCGTGGACG 58.932 55.000 0.00 0.00 41.45 4.79
1082 1158 2.677524 TCGTGGACGATCGGGGTT 60.678 61.111 20.98 0.00 44.22 4.11
1083 1159 1.378382 TCGTGGACGATCGGGGTTA 60.378 57.895 20.98 0.00 44.22 2.85
1084 1160 0.964860 TCGTGGACGATCGGGGTTAA 60.965 55.000 20.98 0.00 44.22 2.01
1085 1161 0.108709 CGTGGACGATCGGGGTTAAA 60.109 55.000 20.98 0.00 43.02 1.52
1086 1162 1.672441 CGTGGACGATCGGGGTTAAAA 60.672 52.381 20.98 0.00 43.02 1.52
1096 1172 5.460748 CGATCGGGGTTAAAATTAAAATGGC 59.539 40.000 7.38 0.00 0.00 4.40
1100 1176 4.331443 GGGGTTAAAATTAAAATGGCGCTG 59.669 41.667 7.64 0.00 0.00 5.18
1101 1177 4.201773 GGGTTAAAATTAAAATGGCGCTGC 60.202 41.667 7.64 0.00 0.00 5.25
1102 1178 4.629634 GGTTAAAATTAAAATGGCGCTGCT 59.370 37.500 7.64 0.00 0.00 4.24
1103 1179 5.220397 GGTTAAAATTAAAATGGCGCTGCTC 60.220 40.000 7.64 0.00 0.00 4.26
1105 1182 4.981806 AAATTAAAATGGCGCTGCTCTA 57.018 36.364 7.64 0.00 0.00 2.43
1110 1187 0.253044 AATGGCGCTGCTCTAGGAAA 59.747 50.000 7.64 0.00 0.00 3.13
1112 1189 2.167861 GGCGCTGCTCTAGGAAACG 61.168 63.158 7.64 0.00 0.00 3.60
1118 1195 3.124560 GCTGCTCTAGGAAACGGATTAC 58.875 50.000 0.00 0.00 0.00 1.89
1132 1209 4.404507 CGGATTACGGATGCTTATTTGG 57.595 45.455 0.00 0.00 39.42 3.28
1134 1211 3.057526 GGATTACGGATGCTTATTTGGCC 60.058 47.826 0.00 0.00 0.00 5.36
1135 1212 1.975660 TACGGATGCTTATTTGGCCC 58.024 50.000 0.00 0.00 0.00 5.80
1136 1213 1.101049 ACGGATGCTTATTTGGCCCG 61.101 55.000 0.00 0.00 39.29 6.13
1282 1377 1.517475 AAAACCCGCGTGTTTGTGC 60.517 52.632 20.16 0.00 38.41 4.57
1477 1587 3.540617 GTGGAACAAGGCAACCAATTTT 58.459 40.909 0.00 0.00 44.16 1.82
1618 1733 2.571653 CCCTCACCATCTAACCAACTCA 59.428 50.000 0.00 0.00 0.00 3.41
2088 2284 5.668471 AGGTACCGTATTCTTTTCTAAGGC 58.332 41.667 6.18 0.00 32.02 4.35
2105 2385 9.598517 TTTCTAAGGCATTTTATATGGCAAAAG 57.401 29.630 11.17 5.82 45.66 2.27
2106 2386 7.725251 TCTAAGGCATTTTATATGGCAAAAGG 58.275 34.615 11.17 0.00 45.66 3.11
2109 2389 7.854166 AGGCATTTTATATGGCAAAAGGATA 57.146 32.000 11.17 0.00 45.66 2.59
2262 2856 7.110155 TCAATAGATCTAAAGGTGGTGGAAAC 58.890 38.462 6.52 0.00 0.00 2.78
2273 2867 3.937079 GGTGGTGGAAACTAACGGAATAG 59.063 47.826 0.00 0.00 0.00 1.73
2274 2868 3.373130 GTGGTGGAAACTAACGGAATAGC 59.627 47.826 0.00 0.00 0.00 2.97
2376 2970 5.104982 TGTGATGTGTCCTAGATATTGCACA 60.105 40.000 0.00 0.00 40.42 4.57
2389 2983 7.117285 AGATATTGCACATCTAAGTGACTCA 57.883 36.000 8.00 0.00 42.05 3.41
2390 2984 6.983307 AGATATTGCACATCTAAGTGACTCAC 59.017 38.462 8.00 0.38 42.05 3.51
2448 3042 0.721154 TGCTTGCACGAATCTTAGCG 59.279 50.000 0.00 0.00 0.00 4.26
2451 3045 2.347452 GCTTGCACGAATCTTAGCGTAA 59.653 45.455 0.00 0.00 38.92 3.18
2476 3071 5.979288 TTTTCGAGAGTAGCTTTAGGAGT 57.021 39.130 0.00 0.00 0.00 3.85
2477 3072 4.966965 TTCGAGAGTAGCTTTAGGAGTG 57.033 45.455 0.00 0.00 0.00 3.51
2486 3081 1.743996 CTTTAGGAGTGGAAGGCAGC 58.256 55.000 0.00 0.00 0.00 5.25
2504 3099 5.355350 AGGCAGCATATCAGTTACAAGAAAC 59.645 40.000 0.00 0.00 0.00 2.78
2512 3107 5.190992 TCAGTTACAAGAAACTACGCTCA 57.809 39.130 0.00 0.00 37.61 4.26
2517 3112 2.135139 CAAGAAACTACGCTCACTGCA 58.865 47.619 0.00 0.00 43.06 4.41
2523 3118 1.597663 ACTACGCTCACTGCAAACAAC 59.402 47.619 0.00 0.00 43.06 3.32
2543 3138 4.785511 ACGAGAGTAGCACAAACACTAT 57.214 40.909 0.00 0.00 46.88 2.12
2601 3196 1.597742 GAGTTTGGCTTCACTCAGCA 58.402 50.000 6.46 0.00 42.10 4.41
2602 3197 1.949525 GAGTTTGGCTTCACTCAGCAA 59.050 47.619 6.46 0.00 42.10 3.91
2606 3201 0.601046 TGGCTTCACTCAGCAACTCG 60.601 55.000 0.00 0.00 42.10 4.18
2678 3281 7.913789 TGGGACATAAACAAGTAATACTGAGT 58.086 34.615 0.00 0.00 0.00 3.41
2679 3282 8.380099 TGGGACATAAACAAGTAATACTGAGTT 58.620 33.333 0.00 0.00 31.37 3.01
2680 3283 9.880157 GGGACATAAACAAGTAATACTGAGTTA 57.120 33.333 10.54 3.30 30.38 2.24
2710 3313 7.756722 ACATCACTTTGAGAAGAAAACAAACTG 59.243 33.333 0.00 0.00 36.69 3.16
2732 3335 3.118261 GCAGACATCCTCCCTGTGAATTA 60.118 47.826 0.00 0.00 0.00 1.40
2798 3401 0.321298 TCTGCTTTAACACCTCCGGC 60.321 55.000 0.00 0.00 0.00 6.13
2848 3451 4.356405 TGCCAATTTCAGACTTCAGAGA 57.644 40.909 0.00 0.00 0.00 3.10
2863 3466 4.824479 TCAGAGATCACTGCAAATGGTA 57.176 40.909 14.63 0.00 37.75 3.25
2874 3477 6.040278 TCACTGCAAATGGTAATGTCAAAGAA 59.960 34.615 0.00 0.00 0.00 2.52
2987 3590 2.568090 CAACCCGCAGAATGGTGC 59.432 61.111 0.00 0.00 40.29 5.01
3092 3695 1.453745 GGAATCCATGGCCGAGCAA 60.454 57.895 6.96 0.00 0.00 3.91
3294 3903 0.251297 CAGGATCAAACACTGGCCCA 60.251 55.000 0.00 0.00 0.00 5.36
3347 3956 0.042731 TCCCGAGGGAGAGGAAACAT 59.957 55.000 6.80 0.00 39.76 2.71
3390 3999 1.096386 TGCCGCGGTTAACAAAGTGT 61.096 50.000 28.70 0.00 0.00 3.55
3406 4015 1.957177 AGTGTGAGAGCTCTGTTTCGA 59.043 47.619 23.91 0.00 0.00 3.71
3495 4104 1.456705 GCCCAGAGAGGAGACCGAT 60.457 63.158 0.00 0.00 41.22 4.18
3529 4138 2.996444 CTGTGCTTGTGACAGCTGA 58.004 52.632 23.35 0.00 40.79 4.26
3541 4150 2.181205 GACAGCTGAGAAGATTCGACG 58.819 52.381 23.35 0.00 0.00 5.12
3624 4233 1.738099 CAGTGGGAAGAAGCGACCG 60.738 63.158 0.00 0.00 0.00 4.79
3727 4336 9.809096 CTGGTTCTTGCTCGTGAATATATATAT 57.191 33.333 0.00 0.00 0.00 0.86
3751 4363 5.615289 AGTTGGAATCTGTAGTATCCATGC 58.385 41.667 8.47 6.21 41.36 4.06
3892 4507 0.761802 AGCTAGGCAGGCTTGTATCC 59.238 55.000 0.00 0.00 36.56 2.59
3920 4535 6.423905 TCTGTAGTCTGCATTCTGTAAAACAC 59.576 38.462 0.00 0.00 0.00 3.32
4018 4635 3.423571 GTCTGCGCATTCATCTTCTTTG 58.576 45.455 12.24 0.00 0.00 2.77
4095 4736 6.073222 CCAGTTATGACGAGCTACTTGTTTTT 60.073 38.462 0.00 0.00 0.00 1.94
4258 4903 3.003763 GCCGAAGTGGGGAGGAGT 61.004 66.667 0.00 0.00 38.63 3.85
4259 4904 1.684734 GCCGAAGTGGGGAGGAGTA 60.685 63.158 0.00 0.00 38.63 2.59
4260 4905 1.677637 GCCGAAGTGGGGAGGAGTAG 61.678 65.000 0.00 0.00 38.63 2.57
4351 4996 3.813443 CCATTTCTACCTGTGCTAGCAT 58.187 45.455 22.51 7.30 0.00 3.79
4354 4999 5.359756 CATTTCTACCTGTGCTAGCATACA 58.640 41.667 22.51 14.17 0.00 2.29
4355 5000 4.655762 TTCTACCTGTGCTAGCATACAG 57.344 45.455 22.51 22.43 42.97 2.74
4356 5001 2.362397 TCTACCTGTGCTAGCATACAGC 59.638 50.000 22.51 8.08 42.21 4.40
4385 5030 0.238553 GAGCTTCAAAACCAGCCGTC 59.761 55.000 0.00 0.00 36.62 4.79
4425 5070 3.443681 TCGCACTATGTGACTCAGATCAA 59.556 43.478 1.52 0.00 35.23 2.57
4473 5118 6.645415 CACTACAAACTTACATCCGAGTTCTT 59.355 38.462 0.00 0.00 35.17 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.965539 CTCCTGGCCACAAGCTCGG 62.966 68.421 0.00 0.00 43.05 4.63
1 2 2.435586 CTCCTGGCCACAAGCTCG 60.436 66.667 0.00 0.00 43.05 5.03
50 55 1.138266 GCGGCAAGTAGGTTGGATAGA 59.862 52.381 0.00 0.00 36.56 1.98
57 62 0.321653 CTGGAAGCGGCAAGTAGGTT 60.322 55.000 1.45 0.00 0.00 3.50
61 66 1.079127 GCTCTGGAAGCGGCAAGTA 60.079 57.895 1.45 0.00 42.21 2.24
124 129 1.350193 CGCTTTATGACACGTCAGCT 58.650 50.000 6.01 0.00 43.61 4.24
237 243 0.893270 CCACGAGATTTGTTGGGGCA 60.893 55.000 0.00 0.00 0.00 5.36
268 274 2.773993 ATCCTAAGAAAAACCCGCGA 57.226 45.000 8.23 0.00 0.00 5.87
283 289 0.678048 GTGCTCCAGCGGAAAATCCT 60.678 55.000 0.00 0.00 45.83 3.24
293 303 2.749441 GCCTTCCTGTGCTCCAGC 60.749 66.667 0.00 0.00 40.06 4.85
306 316 0.899720 TTTAGACCATCGACGGCCTT 59.100 50.000 0.00 0.00 0.00 4.35
345 355 3.096852 TCTTATCGCCACAAGAGGAAGA 58.903 45.455 0.00 0.00 0.00 2.87
347 357 3.096852 TCTCTTATCGCCACAAGAGGAA 58.903 45.455 13.11 0.00 45.16 3.36
361 379 3.129638 GGACACGCTCACTTCTCTCTTAT 59.870 47.826 0.00 0.00 0.00 1.73
364 382 0.885196 GGACACGCTCACTTCTCTCT 59.115 55.000 0.00 0.00 0.00 3.10
497 526 3.367743 CCTGCCTGCATGCAACGT 61.368 61.111 22.88 0.00 41.51 3.99
599 666 2.202676 CCTCCGCTTCACTCGCTC 60.203 66.667 0.00 0.00 0.00 5.03
609 676 4.704103 TGTGGCTCCTCCTCCGCT 62.704 66.667 0.00 0.00 34.14 5.52
661 728 7.043656 CGCGGAGAAAAATCAAAAATATAACCC 60.044 37.037 0.00 0.00 0.00 4.11
662 729 7.698970 TCGCGGAGAAAAATCAAAAATATAACC 59.301 33.333 6.13 0.00 0.00 2.85
663 730 8.609478 TCGCGGAGAAAAATCAAAAATATAAC 57.391 30.769 6.13 0.00 0.00 1.89
666 733 6.265577 CCTCGCGGAGAAAAATCAAAAATAT 58.734 36.000 6.13 0.00 0.00 1.28
668 735 4.485163 CCTCGCGGAGAAAAATCAAAAAT 58.515 39.130 6.13 0.00 0.00 1.82
669 736 3.305064 CCCTCGCGGAGAAAAATCAAAAA 60.305 43.478 6.13 0.00 0.00 1.94
674 741 1.722082 GCCCTCGCGGAGAAAAATC 59.278 57.895 6.13 0.00 0.00 2.17
675 742 3.905249 GCCCTCGCGGAGAAAAAT 58.095 55.556 6.13 0.00 0.00 1.82
697 764 2.159296 GGACGGGATTTTTCCATTTCCG 60.159 50.000 0.00 0.00 41.45 4.30
699 766 2.750712 TCGGACGGGATTTTTCCATTTC 59.249 45.455 0.00 0.00 0.00 2.17
789 856 1.737793 AGAGGGGTACGTTACGTTACG 59.262 52.381 23.86 23.86 46.52 3.18
790 857 3.010420 AGAGAGGGGTACGTTACGTTAC 58.990 50.000 17.42 11.71 41.54 2.50
791 858 3.055094 AGAGAGAGGGGTACGTTACGTTA 60.055 47.826 17.42 0.00 41.54 3.18
792 859 2.087646 GAGAGAGGGGTACGTTACGTT 58.912 52.381 17.42 0.00 41.54 3.99
793 860 1.280421 AGAGAGAGGGGTACGTTACGT 59.720 52.381 16.31 16.31 44.35 3.57
794 861 2.035530 AGAGAGAGGGGTACGTTACG 57.964 55.000 2.19 2.19 0.00 3.18
795 862 4.797800 AAAAGAGAGAGGGGTACGTTAC 57.202 45.455 0.00 0.00 0.00 2.50
796 863 5.163478 GCATAAAAGAGAGAGGGGTACGTTA 60.163 44.000 0.00 0.00 0.00 3.18
797 864 4.382793 GCATAAAAGAGAGAGGGGTACGTT 60.383 45.833 0.00 0.00 0.00 3.99
798 865 3.132467 GCATAAAAGAGAGAGGGGTACGT 59.868 47.826 0.00 0.00 0.00 3.57
799 866 3.718815 GCATAAAAGAGAGAGGGGTACG 58.281 50.000 0.00 0.00 0.00 3.67
800 867 3.383825 TCGCATAAAAGAGAGAGGGGTAC 59.616 47.826 0.00 0.00 0.00 3.34
801 868 3.383825 GTCGCATAAAAGAGAGAGGGGTA 59.616 47.826 0.00 0.00 0.00 3.69
802 869 2.168728 GTCGCATAAAAGAGAGAGGGGT 59.831 50.000 0.00 0.00 0.00 4.95
803 870 2.432510 AGTCGCATAAAAGAGAGAGGGG 59.567 50.000 0.00 0.00 0.00 4.79
804 871 3.491792 GGAGTCGCATAAAAGAGAGAGGG 60.492 52.174 0.00 0.00 0.00 4.30
807 874 4.274147 AGAGGAGTCGCATAAAAGAGAGA 58.726 43.478 0.00 0.00 0.00 3.10
830 897 0.631998 TCAGGAGAGGGGAGGAGGAT 60.632 60.000 0.00 0.00 0.00 3.24
836 903 0.106217 GAGGAGTCAGGAGAGGGGAG 60.106 65.000 0.00 0.00 0.00 4.30
875 942 0.252284 GGACAGTCAGGAGAGGGGAA 60.252 60.000 2.17 0.00 0.00 3.97
878 945 0.686112 GAGGGACAGTCAGGAGAGGG 60.686 65.000 2.17 0.00 0.00 4.30
880 947 1.034838 CGGAGGGACAGTCAGGAGAG 61.035 65.000 2.17 0.00 0.00 3.20
885 952 1.304547 AGGACGGAGGGACAGTCAG 60.305 63.158 2.17 0.00 43.53 3.51
887 954 2.408241 CGAGGACGGAGGGACAGTC 61.408 68.421 0.00 0.00 41.63 3.51
888 955 2.361357 CGAGGACGGAGGGACAGT 60.361 66.667 0.00 0.00 35.72 3.55
899 972 4.477413 TCGATAGAGGGCGAGGAC 57.523 61.111 0.00 0.00 42.67 3.85
911 984 0.172578 CCAGGTGCTCGTTGTCGATA 59.827 55.000 0.00 0.00 45.21 2.92
929 1002 0.606673 GAACAAGACCAGGCCAGACC 60.607 60.000 5.01 0.00 39.61 3.85
934 1007 0.178990 ACCAAGAACAAGACCAGGCC 60.179 55.000 0.00 0.00 0.00 5.19
936 1009 1.949525 CACACCAAGAACAAGACCAGG 59.050 52.381 0.00 0.00 0.00 4.45
937 1010 1.949525 CCACACCAAGAACAAGACCAG 59.050 52.381 0.00 0.00 0.00 4.00
938 1011 2.021723 GCCACACCAAGAACAAGACCA 61.022 52.381 0.00 0.00 0.00 4.02
939 1012 0.668535 GCCACACCAAGAACAAGACC 59.331 55.000 0.00 0.00 0.00 3.85
940 1013 0.307760 CGCCACACCAAGAACAAGAC 59.692 55.000 0.00 0.00 0.00 3.01
941 1014 0.179234 TCGCCACACCAAGAACAAGA 59.821 50.000 0.00 0.00 0.00 3.02
942 1015 0.307760 GTCGCCACACCAAGAACAAG 59.692 55.000 0.00 0.00 0.00 3.16
944 1017 1.885388 CGTCGCCACACCAAGAACA 60.885 57.895 0.00 0.00 0.00 3.18
945 1018 1.828331 GACGTCGCCACACCAAGAAC 61.828 60.000 0.00 0.00 0.00 3.01
947 1020 2.028484 GACGTCGCCACACCAAGA 59.972 61.111 0.00 0.00 0.00 3.02
948 1021 3.403057 CGACGTCGCCACACCAAG 61.403 66.667 26.59 0.00 0.00 3.61
964 1040 0.096976 CAAAGTAATCGCACTGCCCG 59.903 55.000 0.00 0.00 0.00 6.13
968 1044 3.978759 CGAGAACAAAGTAATCGCACTG 58.021 45.455 0.00 0.00 0.00 3.66
973 1049 2.222819 GCCAGCGAGAACAAAGTAATCG 60.223 50.000 0.00 0.00 36.51 3.34
979 1055 0.603707 TCCAGCCAGCGAGAACAAAG 60.604 55.000 0.00 0.00 0.00 2.77
980 1056 0.603707 CTCCAGCCAGCGAGAACAAA 60.604 55.000 0.00 0.00 0.00 2.83
995 1071 4.783621 GCGTGCAGGCCATCTCCA 62.784 66.667 20.50 0.00 0.00 3.86
1008 1084 2.287188 GCATGGATGAATTACCTGCGTG 60.287 50.000 0.00 0.00 0.00 5.34
1027 1103 1.544759 GGGAAAAGACCCGAAGAAGCA 60.545 52.381 0.00 0.00 40.49 3.91
1028 1104 1.166129 GGGAAAAGACCCGAAGAAGC 58.834 55.000 0.00 0.00 40.49 3.86
1039 1115 1.142870 CTCACCACACCAGGGAAAAGA 59.857 52.381 0.00 0.00 0.00 2.52
1040 1116 1.142870 TCTCACCACACCAGGGAAAAG 59.857 52.381 0.00 0.00 0.00 2.27
1041 1117 1.217916 TCTCACCACACCAGGGAAAA 58.782 50.000 0.00 0.00 0.00 2.29
1042 1118 1.444933 ATCTCACCACACCAGGGAAA 58.555 50.000 0.00 0.00 0.00 3.13
1043 1119 1.073763 CAATCTCACCACACCAGGGAA 59.926 52.381 0.00 0.00 0.00 3.97
1044 1120 0.692476 CAATCTCACCACACCAGGGA 59.308 55.000 0.00 0.00 0.00 4.20
1045 1121 0.401738 ACAATCTCACCACACCAGGG 59.598 55.000 0.00 0.00 0.00 4.45
1047 1123 1.800586 CGAACAATCTCACCACACCAG 59.199 52.381 0.00 0.00 0.00 4.00
1048 1124 1.140052 ACGAACAATCTCACCACACCA 59.860 47.619 0.00 0.00 0.00 4.17
1050 1126 1.531149 CCACGAACAATCTCACCACAC 59.469 52.381 0.00 0.00 0.00 3.82
1051 1127 1.414550 TCCACGAACAATCTCACCACA 59.585 47.619 0.00 0.00 0.00 4.17
1052 1128 1.798813 GTCCACGAACAATCTCACCAC 59.201 52.381 0.00 0.00 0.00 4.16
1053 1129 1.604438 CGTCCACGAACAATCTCACCA 60.604 52.381 0.00 0.00 43.02 4.17
1054 1130 1.068474 CGTCCACGAACAATCTCACC 58.932 55.000 0.00 0.00 43.02 4.02
1055 1131 2.060326 TCGTCCACGAACAATCTCAC 57.940 50.000 0.00 0.00 46.30 3.51
1066 1142 0.108709 TTTAACCCCGATCGTCCACG 60.109 55.000 15.09 0.00 41.45 4.94
1067 1143 2.097680 TTTTAACCCCGATCGTCCAC 57.902 50.000 15.09 0.00 0.00 4.02
1068 1144 3.353370 AATTTTAACCCCGATCGTCCA 57.647 42.857 15.09 0.00 0.00 4.02
1069 1145 5.816449 TTTAATTTTAACCCCGATCGTCC 57.184 39.130 15.09 0.00 0.00 4.79
1070 1146 6.693978 CCATTTTAATTTTAACCCCGATCGTC 59.306 38.462 15.09 0.00 0.00 4.20
1071 1147 6.566141 CCATTTTAATTTTAACCCCGATCGT 58.434 36.000 15.09 0.00 0.00 3.73
1072 1148 5.460748 GCCATTTTAATTTTAACCCCGATCG 59.539 40.000 8.51 8.51 0.00 3.69
1073 1149 5.460748 CGCCATTTTAATTTTAACCCCGATC 59.539 40.000 0.00 0.00 0.00 3.69
1074 1150 5.353111 CGCCATTTTAATTTTAACCCCGAT 58.647 37.500 0.00 0.00 0.00 4.18
1075 1151 4.745649 CGCCATTTTAATTTTAACCCCGA 58.254 39.130 0.00 0.00 0.00 5.14
1076 1152 3.307512 GCGCCATTTTAATTTTAACCCCG 59.692 43.478 0.00 0.00 0.00 5.73
1077 1153 4.331443 CAGCGCCATTTTAATTTTAACCCC 59.669 41.667 2.29 0.00 0.00 4.95
1078 1154 4.201773 GCAGCGCCATTTTAATTTTAACCC 60.202 41.667 2.29 0.00 0.00 4.11
1079 1155 4.629634 AGCAGCGCCATTTTAATTTTAACC 59.370 37.500 2.29 0.00 0.00 2.85
1080 1156 5.576774 AGAGCAGCGCCATTTTAATTTTAAC 59.423 36.000 2.29 0.00 0.00 2.01
1081 1157 5.719173 AGAGCAGCGCCATTTTAATTTTAA 58.281 33.333 2.29 0.00 0.00 1.52
1082 1158 5.323371 AGAGCAGCGCCATTTTAATTTTA 57.677 34.783 2.29 0.00 0.00 1.52
1083 1159 4.192429 AGAGCAGCGCCATTTTAATTTT 57.808 36.364 2.29 0.00 0.00 1.82
1084 1160 3.874392 AGAGCAGCGCCATTTTAATTT 57.126 38.095 2.29 0.00 0.00 1.82
1085 1161 3.316308 CCTAGAGCAGCGCCATTTTAATT 59.684 43.478 2.29 0.00 0.00 1.40
1086 1162 2.880890 CCTAGAGCAGCGCCATTTTAAT 59.119 45.455 2.29 0.00 0.00 1.40
1096 1172 0.103208 ATCCGTTTCCTAGAGCAGCG 59.897 55.000 0.00 0.00 0.00 5.18
1100 1176 2.360165 TCCGTAATCCGTTTCCTAGAGC 59.640 50.000 0.00 0.00 33.66 4.09
1101 1177 4.547532 CATCCGTAATCCGTTTCCTAGAG 58.452 47.826 0.00 0.00 33.66 2.43
1102 1178 3.243636 GCATCCGTAATCCGTTTCCTAGA 60.244 47.826 0.00 0.00 33.66 2.43
1103 1179 3.057734 GCATCCGTAATCCGTTTCCTAG 58.942 50.000 0.00 0.00 33.66 3.02
1105 1182 1.485066 AGCATCCGTAATCCGTTTCCT 59.515 47.619 0.00 0.00 33.66 3.36
1110 1187 3.813166 CCAAATAAGCATCCGTAATCCGT 59.187 43.478 0.00 0.00 33.66 4.69
1112 1189 3.057526 GGCCAAATAAGCATCCGTAATCC 60.058 47.826 0.00 0.00 0.00 3.01
1118 1195 1.101049 ACGGGCCAAATAAGCATCCG 61.101 55.000 4.39 0.00 39.85 4.18
1132 1209 4.704833 TCTCCTGCAAGCACGGGC 62.705 66.667 0.00 0.00 41.61 6.13
1134 1211 2.671177 CGTTCTCCTGCAAGCACGG 61.671 63.158 3.09 0.00 0.00 4.94
1135 1212 2.856032 CGTTCTCCTGCAAGCACG 59.144 61.111 0.00 0.00 0.00 5.34
1136 1213 2.558313 GCGTTCTCCTGCAAGCAC 59.442 61.111 0.00 0.00 0.00 4.40
1188 1283 1.678300 GGGAACTCGGACGACTCCT 60.678 63.158 14.33 0.00 33.79 3.69
1374 1481 4.787871 AAGCGCTTGTGCTCTTCT 57.212 50.000 24.40 0.00 46.60 2.85
1455 1562 1.786937 ATTGGTTGCCTTGTTCCACA 58.213 45.000 0.00 0.00 0.00 4.17
1458 1568 2.290367 GCAAAATTGGTTGCCTTGTTCC 59.710 45.455 3.85 0.00 46.69 3.62
1477 1587 3.033764 GAGCGAACCGAACGTGCA 61.034 61.111 0.00 0.00 0.00 4.57
1483 1593 0.601841 GAAAGGGTGAGCGAACCGAA 60.602 55.000 4.96 0.00 41.52 4.30
1532 1647 2.661840 TTTGCACCGCCGTCTTGGTA 62.662 55.000 0.00 0.00 41.21 3.25
1618 1733 1.714541 ATCATGGCCGAGAGATGAGT 58.285 50.000 8.51 0.00 29.85 3.41
1643 1763 1.743394 GGAAAACCCGTGGCTGATAAG 59.257 52.381 0.00 0.00 0.00 1.73
2006 2199 2.442272 GAGCCGTAGAGGGAGCCA 60.442 66.667 0.00 0.00 41.48 4.75
2082 2278 7.725251 TCCTTTTGCCATATAAAATGCCTTAG 58.275 34.615 0.00 0.00 0.00 2.18
2083 2279 7.667575 TCCTTTTGCCATATAAAATGCCTTA 57.332 32.000 0.00 0.00 0.00 2.69
2084 2280 6.558488 TCCTTTTGCCATATAAAATGCCTT 57.442 33.333 0.00 0.00 0.00 4.35
2086 2282 7.118245 GCTTATCCTTTTGCCATATAAAATGCC 59.882 37.037 0.00 0.00 0.00 4.40
2088 2284 8.538409 GGCTTATCCTTTTGCCATATAAAATG 57.462 34.615 0.00 0.00 44.34 2.32
2106 2386 6.830324 TGCTATTGGATATTGGATGGCTTATC 59.170 38.462 0.00 0.00 34.93 1.75
2109 2389 5.001833 TGCTATTGGATATTGGATGGCTT 57.998 39.130 0.00 0.00 0.00 4.35
2186 2470 6.404074 GGCAAACTGAAGTCTAAGATGATTGG 60.404 42.308 0.00 0.00 0.00 3.16
2273 2867 5.314923 TCTATGCAACTGGAATTTTCTGC 57.685 39.130 0.00 0.00 0.00 4.26
2328 2922 1.282157 AGATGTGCCCTAAACAGACCC 59.718 52.381 0.00 0.00 0.00 4.46
2356 2950 6.430962 AGATGTGCAATATCTAGGACACAT 57.569 37.500 11.83 6.16 43.45 3.21
2357 2951 5.876651 AGATGTGCAATATCTAGGACACA 57.123 39.130 11.83 0.00 43.45 3.72
2358 2952 7.383572 CACTTAGATGTGCAATATCTAGGACAC 59.616 40.741 25.35 0.00 45.79 3.67
2359 2953 7.287696 TCACTTAGATGTGCAATATCTAGGACA 59.712 37.037 25.35 14.72 45.79 4.02
2431 3025 4.778842 ATTACGCTAAGATTCGTGCAAG 57.221 40.909 0.00 0.00 39.46 4.01
2459 3054 4.098807 CCTTCCACTCCTAAAGCTACTCTC 59.901 50.000 0.00 0.00 0.00 3.20
2472 3067 1.141657 TGATATGCTGCCTTCCACTCC 59.858 52.381 0.00 0.00 0.00 3.85
2473 3068 2.158842 ACTGATATGCTGCCTTCCACTC 60.159 50.000 0.00 0.00 0.00 3.51
2474 3069 1.842562 ACTGATATGCTGCCTTCCACT 59.157 47.619 0.00 0.00 0.00 4.00
2475 3070 2.338577 ACTGATATGCTGCCTTCCAC 57.661 50.000 0.00 0.00 0.00 4.02
2476 3071 3.199727 TGTAACTGATATGCTGCCTTCCA 59.800 43.478 0.00 0.00 0.00 3.53
2477 3072 3.808728 TGTAACTGATATGCTGCCTTCC 58.191 45.455 0.00 0.00 0.00 3.46
2486 3081 7.488150 TGAGCGTAGTTTCTTGTAACTGATATG 59.512 37.037 0.00 0.00 38.72 1.78
2512 3107 2.135933 GCTACTCTCGTTGTTTGCAGT 58.864 47.619 0.00 0.00 0.00 4.40
2517 3112 3.936453 TGTTTGTGCTACTCTCGTTGTTT 59.064 39.130 0.00 0.00 0.00 2.83
2523 3118 8.343366 TCTAATATAGTGTTTGTGCTACTCTCG 58.657 37.037 0.00 0.00 0.00 4.04
2601 3196 5.934402 AACCACTCATCCTTATACGAGTT 57.066 39.130 0.00 0.00 36.60 3.01
2602 3197 5.934402 AAACCACTCATCCTTATACGAGT 57.066 39.130 0.00 0.00 39.26 4.18
2677 3280 7.715265 TTCTTCTCAAAGTGATGTCAGTAAC 57.285 36.000 0.00 0.00 33.95 2.50
2678 3281 8.612619 GTTTTCTTCTCAAAGTGATGTCAGTAA 58.387 33.333 0.00 0.00 33.95 2.24
2679 3282 7.768582 TGTTTTCTTCTCAAAGTGATGTCAGTA 59.231 33.333 0.00 0.00 33.95 2.74
2680 3283 6.599244 TGTTTTCTTCTCAAAGTGATGTCAGT 59.401 34.615 0.00 0.00 33.95 3.41
2681 3284 7.019774 TGTTTTCTTCTCAAAGTGATGTCAG 57.980 36.000 0.00 0.00 33.95 3.51
2682 3285 7.389803 TTGTTTTCTTCTCAAAGTGATGTCA 57.610 32.000 0.00 0.00 33.95 3.58
2683 3286 7.970614 AGTTTGTTTTCTTCTCAAAGTGATGTC 59.029 33.333 0.00 0.00 34.70 3.06
2684 3287 7.756722 CAGTTTGTTTTCTTCTCAAAGTGATGT 59.243 33.333 15.22 0.00 46.50 3.06
2710 3313 0.615331 TTCACAGGGAGGATGTCTGC 59.385 55.000 0.00 0.00 32.19 4.26
2798 3401 6.306356 CAGAAATGCGTTAGAATTGAAAGGTG 59.694 38.462 0.00 0.00 0.00 4.00
2839 3442 4.008330 CCATTTGCAGTGATCTCTGAAGT 58.992 43.478 25.18 12.00 37.61 3.01
2848 3451 5.981088 TTGACATTACCATTTGCAGTGAT 57.019 34.783 0.00 0.00 0.00 3.06
2863 3466 5.630121 TGTACATGACCCTTCTTTGACATT 58.370 37.500 0.00 0.00 0.00 2.71
2874 3477 1.765314 GCTGATCCTGTACATGACCCT 59.235 52.381 0.00 0.00 0.00 4.34
2987 3590 2.087009 GCTTCAGTTCCGACGTCCG 61.087 63.158 10.58 3.37 38.18 4.79
3092 3695 4.589216 AAATACACAAACTGCTGCATGT 57.411 36.364 1.31 6.94 0.00 3.21
3347 3956 1.275471 CGTTTTGTCGCTCTCGCTGA 61.275 55.000 0.00 0.00 35.26 4.26
3390 3999 2.416566 GCTGATCGAAACAGAGCTCTCA 60.417 50.000 14.96 5.54 37.54 3.27
3406 4015 2.165998 GAAACCTCTTTGCAGGCTGAT 58.834 47.619 20.86 0.00 36.98 2.90
3495 4104 1.367471 CAGCCTCGTCAACTCACCA 59.633 57.895 0.00 0.00 0.00 4.17
3527 4136 0.523546 GAGCGCGTCGAATCTTCTCA 60.524 55.000 8.43 0.00 0.00 3.27
3528 4137 0.248296 AGAGCGCGTCGAATCTTCTC 60.248 55.000 8.43 1.87 0.00 2.87
3529 4138 0.171455 AAGAGCGCGTCGAATCTTCT 59.829 50.000 8.43 0.00 32.08 2.85
3541 4150 2.996621 ACATCTAAACTGTGAAGAGCGC 59.003 45.455 0.00 0.00 0.00 5.92
3624 4233 0.108945 GCAAAACCAGCAGGATGAGC 60.109 55.000 0.35 0.00 39.69 4.26
3727 4336 6.554982 AGCATGGATACTACAGATTCCAACTA 59.445 38.462 0.00 0.00 41.36 2.24
3728 4337 5.367937 AGCATGGATACTACAGATTCCAACT 59.632 40.000 0.00 6.95 41.36 3.16
3751 4363 5.176590 GCAGACACTCTGTAGAGAACAAAAG 59.823 44.000 15.40 0.00 45.94 2.27
3892 4507 4.185467 ACAGAATGCAGACTACAGAGTG 57.815 45.455 0.00 0.00 42.53 3.51
3920 4535 1.667724 GTTCGTCTTCTGCCCATCATG 59.332 52.381 0.00 0.00 0.00 3.07
3976 4593 6.043243 CAGACCCAAGTCCAGGTATATTATGT 59.957 42.308 0.00 0.00 44.72 2.29
3977 4594 6.467677 CAGACCCAAGTCCAGGTATATTATG 58.532 44.000 0.00 0.00 44.72 1.90
3978 4595 5.013183 GCAGACCCAAGTCCAGGTATATTAT 59.987 44.000 0.00 0.00 44.72 1.28
4018 4635 8.934825 TGCAATTTATCTAAAAACATTTCCTGC 58.065 29.630 0.00 0.00 0.00 4.85
4210 4853 2.124403 TACGCCTCCCTCTCCGTC 60.124 66.667 0.00 0.00 35.36 4.79
4212 4855 3.597728 GCTACGCCTCCCTCTCCG 61.598 72.222 0.00 0.00 0.00 4.63
4213 4856 3.228017 GGCTACGCCTCCCTCTCC 61.228 72.222 0.00 0.00 46.69 3.71
4248 4893 0.790993 AGTTGTCCTACTCCTCCCCA 59.209 55.000 0.00 0.00 0.00 4.96
4258 4903 1.229082 ACCCGCCTCAGTTGTCCTA 60.229 57.895 0.00 0.00 0.00 2.94
4259 4904 2.526873 ACCCGCCTCAGTTGTCCT 60.527 61.111 0.00 0.00 0.00 3.85
4260 4905 2.047179 GACCCGCCTCAGTTGTCC 60.047 66.667 0.00 0.00 0.00 4.02
4291 4936 1.605712 GGTTCTCACTGAAGGTGTCCG 60.606 57.143 0.00 0.00 45.50 4.79
4351 4996 0.031111 AGCTCCCCTGTATGGCTGTA 60.031 55.000 0.00 0.00 31.68 2.74
4354 4999 0.621571 TGAAGCTCCCCTGTATGGCT 60.622 55.000 0.00 0.00 34.52 4.75
4355 5000 0.255890 TTGAAGCTCCCCTGTATGGC 59.744 55.000 0.00 0.00 0.00 4.40
4356 5001 2.755103 GTTTTGAAGCTCCCCTGTATGG 59.245 50.000 0.00 0.00 0.00 2.74
4357 5002 2.755103 GGTTTTGAAGCTCCCCTGTATG 59.245 50.000 0.00 0.00 0.00 2.39
4358 5003 2.378547 TGGTTTTGAAGCTCCCCTGTAT 59.621 45.455 0.00 0.00 0.00 2.29
4359 5004 1.777878 TGGTTTTGAAGCTCCCCTGTA 59.222 47.619 0.00 0.00 0.00 2.74
4360 5005 0.555769 TGGTTTTGAAGCTCCCCTGT 59.444 50.000 0.00 0.00 0.00 4.00
4361 5006 1.251251 CTGGTTTTGAAGCTCCCCTG 58.749 55.000 0.00 0.00 0.00 4.45
4362 5007 0.540597 GCTGGTTTTGAAGCTCCCCT 60.541 55.000 0.00 0.00 0.00 4.79
4385 5030 0.458025 GAGAGCAAAGACGTACCGGG 60.458 60.000 6.32 0.00 0.00 5.73
4473 5118 5.140454 TCCTCTTGAGTGATCCGATCATTA 58.860 41.667 14.15 1.85 42.04 1.90


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

AutoCloner maintained by Alex Coulton.