Multiple sequence alignment - TraesCS2D01G432500

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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 TraesCS2D01G432500 chr2D 100.000 3346 0 0 1 3346 544658991 544662336 0.000000e+00 6180.0
1 TraesCS2D01G432500 chr2D 86.680 488 63 1 1159 1646 447321422 447321907 1.060000e-149 540.0
2 TraesCS2D01G432500 chr2D 84.241 514 73 5 1798 2307 447321994 447322503 8.340000e-136 494.0
3 TraesCS2D01G432500 chr2B 92.584 1335 46 20 342 1674 650352707 650353990 0.000000e+00 1868.0
4 TraesCS2D01G432500 chr2B 94.980 737 32 5 1708 2443 650353994 650354726 0.000000e+00 1151.0
5 TraesCS2D01G432500 chr2B 86.680 488 63 1 1159 1646 526970020 526970505 1.060000e-149 540.0
6 TraesCS2D01G432500 chr2B 87.037 432 38 11 2919 3346 650355629 650356046 3.910000e-129 472.0
7 TraesCS2D01G432500 chr2B 83.074 514 79 5 1798 2307 526970597 526971106 8.460000e-126 460.0
8 TraesCS2D01G432500 chr2B 80.147 272 48 6 1799 2067 526763965 526764233 7.320000e-47 198.0
9 TraesCS2D01G432500 chr2B 87.273 110 10 3 7 112 650352605 650352714 4.530000e-24 122.0
10 TraesCS2D01G432500 chr2B 80.000 180 21 9 2729 2906 650355208 650355374 5.860000e-23 119.0
11 TraesCS2D01G432500 chr2A 91.432 887 39 18 1758 2620 686867930 686868803 0.000000e+00 1182.0
12 TraesCS2D01G432500 chr2A 87.379 927 41 24 761 1684 686867064 686867917 0.000000e+00 994.0
13 TraesCS2D01G432500 chr2A 86.680 488 63 1 1159 1646 592091402 592091887 1.060000e-149 540.0
14 TraesCS2D01G432500 chr2A 91.795 390 17 10 342 720 686866683 686867068 2.290000e-146 529.0
15 TraesCS2D01G432500 chr2A 84.690 516 67 7 1798 2307 592091993 592092502 3.850000e-139 505.0
16 TraesCS2D01G432500 chr2A 80.620 516 95 5 1154 1667 591607980 591608492 8.700000e-106 394.0
17 TraesCS2D01G432500 chr2A 86.688 308 19 7 3017 3318 686873327 686873618 4.160000e-84 322.0
18 TraesCS2D01G432500 chr2A 80.000 290 56 2 1801 2089 676984959 676985247 2.620000e-51 213.0
19 TraesCS2D01G432500 chr2A 79.667 300 53 8 1799 2094 591265115 591265410 3.380000e-50 209.0
20 TraesCS2D01G432500 chr5D 79.344 518 88 14 1804 2307 463088064 463088576 2.470000e-91 346.0
21 TraesCS2D01G432500 chr1D 88.750 240 25 2 110 348 415392689 415392927 3.270000e-75 292.0
22 TraesCS2D01G432500 chr1D 87.500 240 29 1 109 347 465990795 465991034 3.290000e-70 276.0
23 TraesCS2D01G432500 chr1D 86.885 244 29 3 110 352 323916793 323916552 1.530000e-68 270.0
24 TraesCS2D01G432500 chr5B 77.413 518 98 14 1804 2307 569826153 569826665 1.170000e-74 291.0
25 TraesCS2D01G432500 chr7B 86.905 252 32 1 103 353 41291603 41291854 7.070000e-72 281.0
26 TraesCS2D01G432500 chr4B 87.295 244 29 2 105 347 330426927 330426685 9.140000e-71 278.0
27 TraesCS2D01G432500 chr4B 93.878 49 3 0 22 70 209190142 209190094 1.290000e-09 75.0
28 TraesCS2D01G432500 chr4D 87.500 240 29 1 109 347 177493991 177493752 3.290000e-70 276.0
29 TraesCS2D01G432500 chr6A 87.137 241 30 1 109 348 514704873 514705113 4.250000e-69 272.0
30 TraesCS2D01G432500 chr6D 86.531 245 29 4 103 346 200818476 200818717 1.980000e-67 267.0
31 TraesCS2D01G432500 chr6D 95.918 49 2 0 22 70 108510203 108510155 2.770000e-11 80.5
32 TraesCS2D01G432500 chr6D 93.878 49 3 0 22 70 57911113 57911065 1.290000e-09 75.0
33 TraesCS2D01G432500 chr3D 86.722 241 31 1 110 349 91705623 91705383 1.980000e-67 267.0
34 TraesCS2D01G432500 chr1A 93.750 48 3 0 22 69 68949783 68949736 4.630000e-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 TraesCS2D01G432500 chr2D 544658991 544662336 3345 False 6180.000000 6180 100.0000 1 3346 1 chr2D.!!$F1 3345
1 TraesCS2D01G432500 chr2D 447321422 447322503 1081 False 517.000000 540 85.4605 1159 2307 2 chr2D.!!$F2 1148
2 TraesCS2D01G432500 chr2B 650352605 650356046 3441 False 746.400000 1868 88.3748 7 3346 5 chr2B.!!$F3 3339
3 TraesCS2D01G432500 chr2B 526970020 526971106 1086 False 500.000000 540 84.8770 1159 2307 2 chr2B.!!$F2 1148
4 TraesCS2D01G432500 chr2A 686866683 686868803 2120 False 901.666667 1182 90.2020 342 2620 3 chr2A.!!$F6 2278
5 TraesCS2D01G432500 chr2A 592091402 592092502 1100 False 522.500000 540 85.6850 1159 2307 2 chr2A.!!$F5 1148
6 TraesCS2D01G432500 chr2A 591607980 591608492 512 False 394.000000 394 80.6200 1154 1667 1 chr2A.!!$F2 513
7 TraesCS2D01G432500 chr5D 463088064 463088576 512 False 346.000000 346 79.3440 1804 2307 1 chr5D.!!$F1 503
8 TraesCS2D01G432500 chr5B 569826153 569826665 512 False 291.000000 291 77.4130 1804 2307 1 chr5B.!!$F1 503

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
980 1001 1.001517 AGCAGAGCTCGAGAGACCA 60.002 57.895 18.75 0.0 30.62 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2797 3067 0.035458 CAAGGACCTGTGGAGTGACC 59.965 60.0 0.0 0.0 39.54 4.02 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
29 30 2.682352 GCCACAAGCCAAACAAACAAAT 59.318 40.909 0.00 0.00 34.35 2.32
31 32 4.024977 GCCACAAGCCAAACAAACAAATAG 60.025 41.667 0.00 0.00 34.35 1.73
37 38 5.983540 AGCCAAACAAACAAATAGAAACCA 58.016 33.333 0.00 0.00 0.00 3.67
59 60 7.590279 ACCAAATTAATACCGAAGAACACAAG 58.410 34.615 0.00 0.00 0.00 3.16
60 61 7.229907 ACCAAATTAATACCGAAGAACACAAGT 59.770 33.333 0.00 0.00 0.00 3.16
61 62 8.079809 CCAAATTAATACCGAAGAACACAAGTT 58.920 33.333 0.00 0.00 41.64 2.66
119 120 9.209175 AGTTTAATATAGTACGTACTACCTCCG 57.791 37.037 32.09 0.00 41.18 4.63
120 121 8.989980 GTTTAATATAGTACGTACTACCTCCGT 58.010 37.037 32.09 19.88 41.18 4.69
121 122 8.758633 TTAATATAGTACGTACTACCTCCGTC 57.241 38.462 32.09 1.11 41.18 4.79
122 123 1.927895 AGTACGTACTACCTCCGTCG 58.072 55.000 26.36 0.00 36.12 5.12
123 124 1.204941 AGTACGTACTACCTCCGTCGT 59.795 52.381 26.36 0.00 36.12 4.34
124 125 1.324736 GTACGTACTACCTCCGTCGTG 59.675 57.143 18.47 0.00 36.12 4.35
125 126 1.021390 ACGTACTACCTCCGTCGTGG 61.021 60.000 0.00 0.00 40.09 4.94
126 127 1.021390 CGTACTACCTCCGTCGTGGT 61.021 60.000 11.14 11.14 39.25 4.16
127 128 1.168714 GTACTACCTCCGTCGTGGTT 58.831 55.000 11.54 0.00 37.13 3.67
128 129 1.541588 GTACTACCTCCGTCGTGGTTT 59.458 52.381 11.54 3.96 37.13 3.27
129 130 1.909700 ACTACCTCCGTCGTGGTTTA 58.090 50.000 11.54 0.00 37.13 2.01
130 131 2.450476 ACTACCTCCGTCGTGGTTTAT 58.550 47.619 11.54 0.00 37.13 1.40
131 132 2.827921 ACTACCTCCGTCGTGGTTTATT 59.172 45.455 11.54 0.00 37.13 1.40
132 133 2.088950 ACCTCCGTCGTGGTTTATTG 57.911 50.000 1.86 0.00 39.52 1.90
133 134 1.338389 ACCTCCGTCGTGGTTTATTGG 60.338 52.381 1.86 0.00 39.52 3.16
134 135 1.338389 CCTCCGTCGTGGTTTATTGGT 60.338 52.381 0.00 0.00 39.52 3.67
135 136 2.419667 CTCCGTCGTGGTTTATTGGTT 58.580 47.619 0.00 0.00 39.52 3.67
136 137 2.414138 CTCCGTCGTGGTTTATTGGTTC 59.586 50.000 0.00 0.00 39.52 3.62
137 138 1.465777 CCGTCGTGGTTTATTGGTTCC 59.534 52.381 0.00 0.00 0.00 3.62
138 139 1.465777 CGTCGTGGTTTATTGGTTCCC 59.534 52.381 0.00 0.00 0.00 3.97
139 140 2.786777 GTCGTGGTTTATTGGTTCCCT 58.213 47.619 0.00 0.00 0.00 4.20
140 141 3.151554 GTCGTGGTTTATTGGTTCCCTT 58.848 45.455 0.00 0.00 0.00 3.95
141 142 3.189910 GTCGTGGTTTATTGGTTCCCTTC 59.810 47.826 0.00 0.00 0.00 3.46
142 143 2.160813 CGTGGTTTATTGGTTCCCTTCG 59.839 50.000 0.00 0.00 0.00 3.79
143 144 2.094906 GTGGTTTATTGGTTCCCTTCGC 60.095 50.000 0.00 0.00 0.00 4.70
144 145 2.164338 GGTTTATTGGTTCCCTTCGCA 58.836 47.619 0.00 0.00 0.00 5.10
145 146 2.758423 GGTTTATTGGTTCCCTTCGCAT 59.242 45.455 0.00 0.00 0.00 4.73
146 147 3.194755 GGTTTATTGGTTCCCTTCGCATT 59.805 43.478 0.00 0.00 0.00 3.56
147 148 4.322424 GGTTTATTGGTTCCCTTCGCATTT 60.322 41.667 0.00 0.00 0.00 2.32
148 149 5.234752 GTTTATTGGTTCCCTTCGCATTTT 58.765 37.500 0.00 0.00 0.00 1.82
149 150 2.810439 TTGGTTCCCTTCGCATTTTG 57.190 45.000 0.00 0.00 0.00 2.44
150 151 1.698506 TGGTTCCCTTCGCATTTTGT 58.301 45.000 0.00 0.00 0.00 2.83
151 152 1.339610 TGGTTCCCTTCGCATTTTGTG 59.660 47.619 0.00 0.00 0.00 3.33
169 170 9.897744 CATTTTGTGCTAAGTTTTGATCTTAGA 57.102 29.630 14.32 0.00 43.88 2.10
200 201 9.973450 ACTAACAAAATGTTAATGCATGTAACA 57.027 25.926 24.01 24.01 41.70 2.41
319 320 8.410141 TCAAAGTTTGACACAAAATACTAAGGG 58.590 33.333 14.35 0.00 34.08 3.95
320 321 8.410141 CAAAGTTTGACACAAAATACTAAGGGA 58.590 33.333 10.19 0.00 0.00 4.20
321 322 8.528044 AAGTTTGACACAAAATACTAAGGGAA 57.472 30.769 0.00 0.00 0.00 3.97
322 323 8.528044 AGTTTGACACAAAATACTAAGGGAAA 57.472 30.769 0.00 0.00 0.00 3.13
323 324 9.143155 AGTTTGACACAAAATACTAAGGGAAAT 57.857 29.630 0.00 0.00 0.00 2.17
337 338 7.052248 ACTAAGGGAAATAATAAACCTGGACG 58.948 38.462 0.00 0.00 0.00 4.79
338 339 4.788679 AGGGAAATAATAAACCTGGACGG 58.211 43.478 0.00 0.00 39.35 4.79
339 340 4.475747 AGGGAAATAATAAACCTGGACGGA 59.524 41.667 0.00 0.00 36.31 4.69
340 341 4.820173 GGGAAATAATAAACCTGGACGGAG 59.180 45.833 0.00 0.00 36.31 4.63
341 342 4.820173 GGAAATAATAAACCTGGACGGAGG 59.180 45.833 0.00 0.00 39.28 4.30
343 344 6.408434 GGAAATAATAAACCTGGACGGAGGTA 60.408 42.308 0.00 0.00 46.29 3.08
352 353 3.434739 CCTGGACGGAGGTAGTACAGTAT 60.435 52.174 7.67 0.00 46.41 2.12
389 391 3.423154 CCGGTGAAGCGAGTTGGC 61.423 66.667 3.03 0.00 0.00 4.52
433 435 4.796038 AATGATCTTGGACAAGGCAAAG 57.204 40.909 11.76 0.00 38.88 2.77
510 514 2.607635 CGAACAATACCTTCATCGTGGG 59.392 50.000 0.00 0.00 0.00 4.61
945 966 4.198625 CAGCTCTGCTTTCCTCCG 57.801 61.111 0.00 0.00 36.40 4.63
948 969 1.066858 CAGCTCTGCTTTCCTCCGTTA 60.067 52.381 0.00 0.00 36.40 3.18
980 1001 1.001517 AGCAGAGCTCGAGAGACCA 60.002 57.895 18.75 0.00 30.62 4.02
989 1010 1.896465 CTCGAGAGACCAAAGGGAGTT 59.104 52.381 6.58 0.00 38.05 3.01
990 1011 1.618837 TCGAGAGACCAAAGGGAGTTG 59.381 52.381 0.00 0.00 38.05 3.16
1045 1066 0.317854 GTTCTTTGTGCTCGTTGCCC 60.318 55.000 1.30 0.00 42.00 5.36
1108 1132 3.998341 CTCGGAAACTTTATCCCACGAAA 59.002 43.478 0.00 0.00 33.13 3.46
1112 1136 5.647589 GGAAACTTTATCCCACGAAATTCC 58.352 41.667 0.00 0.00 0.00 3.01
1114 1138 5.897377 AACTTTATCCCACGAAATTCCAG 57.103 39.130 0.00 0.00 0.00 3.86
1115 1139 4.270008 ACTTTATCCCACGAAATTCCAGG 58.730 43.478 0.00 0.00 0.00 4.45
1116 1140 3.290948 TTATCCCACGAAATTCCAGGG 57.709 47.619 10.22 10.22 40.98 4.45
1117 1141 0.258774 ATCCCACGAAATTCCAGGGG 59.741 55.000 14.86 10.22 40.02 4.79
1118 1142 2.052104 CCCACGAAATTCCAGGGGC 61.052 63.158 8.95 0.00 35.83 5.80
1119 1143 2.052104 CCACGAAATTCCAGGGGCC 61.052 63.158 0.00 0.00 0.00 5.80
1120 1144 1.304052 CACGAAATTCCAGGGGCCA 60.304 57.895 4.39 0.00 0.00 5.36
1121 1145 0.684153 CACGAAATTCCAGGGGCCAT 60.684 55.000 4.39 0.00 0.00 4.40
1122 1146 0.923358 ACGAAATTCCAGGGGCCATA 59.077 50.000 4.39 0.00 0.00 2.74
1123 1147 1.499007 ACGAAATTCCAGGGGCCATAT 59.501 47.619 4.39 0.00 0.00 1.78
1124 1148 2.714250 ACGAAATTCCAGGGGCCATATA 59.286 45.455 4.39 0.00 0.00 0.86
1125 1149 3.081804 CGAAATTCCAGGGGCCATATAC 58.918 50.000 4.39 0.00 0.00 1.47
1126 1150 3.244911 CGAAATTCCAGGGGCCATATACT 60.245 47.826 4.39 0.00 0.00 2.12
1127 1151 3.814504 AATTCCAGGGGCCATATACTG 57.185 47.619 4.39 2.37 0.00 2.74
1128 1152 2.206322 TTCCAGGGGCCATATACTGT 57.794 50.000 4.39 0.00 0.00 3.55
1129 1153 1.434188 TCCAGGGGCCATATACTGTG 58.566 55.000 4.39 0.00 0.00 3.66
1130 1154 1.061735 TCCAGGGGCCATATACTGTGA 60.062 52.381 4.39 0.18 0.00 3.58
1131 1155 1.988107 CCAGGGGCCATATACTGTGAT 59.012 52.381 4.39 0.00 0.00 3.06
1132 1156 2.026822 CCAGGGGCCATATACTGTGATC 60.027 54.545 4.39 0.00 0.00 2.92
1133 1157 2.909006 CAGGGGCCATATACTGTGATCT 59.091 50.000 4.39 0.00 0.00 2.75
1134 1158 3.328931 CAGGGGCCATATACTGTGATCTT 59.671 47.826 4.39 0.00 0.00 2.40
1135 1159 3.983410 AGGGGCCATATACTGTGATCTTT 59.017 43.478 4.39 0.00 0.00 2.52
1136 1160 4.416848 AGGGGCCATATACTGTGATCTTTT 59.583 41.667 4.39 0.00 0.00 2.27
1137 1161 4.762251 GGGGCCATATACTGTGATCTTTTC 59.238 45.833 4.39 0.00 0.00 2.29
1138 1162 5.456763 GGGGCCATATACTGTGATCTTTTCT 60.457 44.000 4.39 0.00 0.00 2.52
1139 1163 5.471456 GGGCCATATACTGTGATCTTTTCTG 59.529 44.000 4.39 0.00 0.00 3.02
1140 1164 6.291377 GGCCATATACTGTGATCTTTTCTGA 58.709 40.000 0.00 0.00 0.00 3.27
1141 1165 6.203723 GGCCATATACTGTGATCTTTTCTGAC 59.796 42.308 0.00 0.00 0.00 3.51
1142 1166 6.763135 GCCATATACTGTGATCTTTTCTGACA 59.237 38.462 0.00 0.00 0.00 3.58
1143 1167 7.280876 GCCATATACTGTGATCTTTTCTGACAA 59.719 37.037 0.00 0.00 0.00 3.18
1144 1168 8.824781 CCATATACTGTGATCTTTTCTGACAAG 58.175 37.037 0.00 0.00 0.00 3.16
1145 1169 9.376075 CATATACTGTGATCTTTTCTGACAAGT 57.624 33.333 3.70 0.00 0.00 3.16
1146 1170 5.998454 ACTGTGATCTTTTCTGACAAGTG 57.002 39.130 3.70 0.00 0.00 3.16
1147 1171 4.274459 ACTGTGATCTTTTCTGACAAGTGC 59.726 41.667 3.70 0.00 0.00 4.40
1151 1175 3.281727 TCTTTTCTGACAAGTGCACCT 57.718 42.857 14.63 0.00 0.00 4.00
1162 1186 1.658409 GTGCACCTTCTTGTTGCGC 60.658 57.895 5.22 0.00 0.00 6.09
1164 1188 1.065600 GCACCTTCTTGTTGCGCAA 59.934 52.632 21.02 21.02 35.50 4.85
1678 1702 1.345415 ACCAAGGGTTCGTCGTAACAT 59.655 47.619 8.93 0.00 27.29 2.71
1679 1703 2.562298 ACCAAGGGTTCGTCGTAACATA 59.438 45.455 8.93 0.00 27.29 2.29
1681 1705 4.402155 ACCAAGGGTTCGTCGTAACATATA 59.598 41.667 8.93 0.00 27.29 0.86
1683 1707 6.265196 ACCAAGGGTTCGTCGTAACATATATA 59.735 38.462 8.93 0.00 27.29 0.86
1685 1709 8.461222 CCAAGGGTTCGTCGTAACATATATATA 58.539 37.037 0.00 0.00 0.00 0.86
1741 1769 6.072112 CATGTCAAGATCATGCATGATTCA 57.928 37.500 36.12 27.61 46.84 2.57
1743 1771 5.886992 TGTCAAGATCATGCATGATTCAAC 58.113 37.500 36.12 28.99 46.84 3.18
1744 1772 4.968181 GTCAAGATCATGCATGATTCAACG 59.032 41.667 36.12 23.93 46.84 4.10
1745 1773 3.620929 AGATCATGCATGATTCAACGC 57.379 42.857 36.12 24.26 46.84 4.84
1756 1784 2.095466 TGATTCAACGCCATTCCGAAAC 60.095 45.455 0.00 0.00 0.00 2.78
2249 2315 1.067295 TGTTCCAGAGCTCCAACCAT 58.933 50.000 10.93 0.00 0.00 3.55
2407 2480 4.517815 GTACCGGCCGGCATTCGA 62.518 66.667 43.58 19.14 42.43 3.71
2479 2584 8.424918 ACACAATATATAACAGTCTCCCTGAAG 58.575 37.037 0.00 0.00 44.49 3.02
2543 2685 2.788786 AGTTGCTCGAAAATTTTGCACG 59.211 40.909 8.47 6.17 33.13 5.34
2544 2686 1.127701 TGCTCGAAAATTTTGCACGC 58.872 45.000 8.47 6.20 0.00 5.34
2548 2690 2.968006 CTCGAAAATTTTGCACGCGTAA 59.032 40.909 13.44 2.14 0.00 3.18
2559 2701 1.510007 CACGCGTAAGTCGATTTTGC 58.490 50.000 13.44 3.15 42.86 3.68
2560 2702 1.136474 CACGCGTAAGTCGATTTTGCA 60.136 47.619 13.44 0.00 42.86 4.08
2561 2703 1.136446 ACGCGTAAGTCGATTTTGCAC 60.136 47.619 11.67 1.43 42.86 4.57
2562 2704 1.136474 CGCGTAAGTCGATTTTGCACA 60.136 47.619 14.69 0.00 42.86 4.57
2563 2705 2.495939 GCGTAAGTCGATTTTGCACAG 58.504 47.619 11.10 0.00 42.86 3.66
2625 2848 2.636412 CGAGGACGCTGGAGGTTGA 61.636 63.158 0.00 0.00 0.00 3.18
2637 2860 1.157585 GAGGTTGAAGGAAACGGCTC 58.842 55.000 0.00 0.00 0.00 4.70
2644 2867 2.028839 TGAAGGAAACGGCTCGATGTAA 60.029 45.455 1.50 0.00 0.00 2.41
2657 2880 4.153117 GCTCGATGTAAAAGATGCATAGGG 59.847 45.833 0.00 0.00 34.17 3.53
2664 2887 1.833187 AAGATGCATAGGGGCCCTTA 58.167 50.000 33.98 20.74 34.61 2.69
2668 2891 1.833187 TGCATAGGGGCCCTTAGATT 58.167 50.000 33.98 7.89 34.61 2.40
2679 2902 4.457466 GGCCCTTAGATTTAAATCGGACA 58.543 43.478 19.86 6.64 40.35 4.02
2683 2906 5.467063 CCCTTAGATTTAAATCGGACAGCTC 59.533 44.000 19.86 0.00 40.35 4.09
2687 2910 6.817765 AGATTTAAATCGGACAGCTCAAAA 57.182 33.333 19.86 0.00 40.35 2.44
2688 2911 7.396540 AGATTTAAATCGGACAGCTCAAAAT 57.603 32.000 19.86 0.00 40.35 1.82
2690 2913 9.125026 AGATTTAAATCGGACAGCTCAAAATAT 57.875 29.630 19.86 0.00 40.35 1.28
2692 2915 7.857734 TTAAATCGGACAGCTCAAAATATCA 57.142 32.000 0.00 0.00 0.00 2.15
2695 2918 3.938963 TCGGACAGCTCAAAATATCAACC 59.061 43.478 0.00 0.00 0.00 3.77
2697 2920 4.155826 CGGACAGCTCAAAATATCAACCAA 59.844 41.667 0.00 0.00 0.00 3.67
2698 2921 5.402398 GGACAGCTCAAAATATCAACCAAC 58.598 41.667 0.00 0.00 0.00 3.77
2699 2922 5.048083 GGACAGCTCAAAATATCAACCAACA 60.048 40.000 0.00 0.00 0.00 3.33
2700 2923 5.772521 ACAGCTCAAAATATCAACCAACAC 58.227 37.500 0.00 0.00 0.00 3.32
2745 3015 4.684265 CATCAAGCATGCGCACTC 57.316 55.556 14.90 7.56 42.27 3.51
2746 3016 2.095750 CATCAAGCATGCGCACTCT 58.904 52.632 14.90 10.27 42.27 3.24
2747 3017 0.450583 CATCAAGCATGCGCACTCTT 59.549 50.000 14.90 16.42 42.27 2.85
2748 3018 1.667212 CATCAAGCATGCGCACTCTTA 59.333 47.619 14.90 8.39 42.27 2.10
2783 3053 8.915871 AATGTAACATATTTGCATCAACAGAC 57.084 30.769 0.00 0.00 0.00 3.51
2792 3062 1.135859 GCATCAACAGACGAAAGCCAG 60.136 52.381 0.00 0.00 0.00 4.85
2796 3066 0.320771 AACAGACGAAAGCCAGCGAT 60.321 50.000 0.00 0.00 0.00 4.58
2797 3067 1.016130 ACAGACGAAAGCCAGCGATG 61.016 55.000 0.00 0.00 0.00 3.84
2804 3074 0.674895 AAAGCCAGCGATGGTCACTC 60.675 55.000 22.68 3.58 0.00 3.51
2821 3091 0.397941 CTCCACAGGTCCTTGCTTGA 59.602 55.000 0.00 0.00 0.00 3.02
2822 3092 0.108585 TCCACAGGTCCTTGCTTGAC 59.891 55.000 0.00 0.00 0.00 3.18
2823 3093 0.109342 CCACAGGTCCTTGCTTGACT 59.891 55.000 0.00 0.00 33.22 3.41
2824 3094 1.347707 CCACAGGTCCTTGCTTGACTA 59.652 52.381 0.00 0.00 33.22 2.59
2825 3095 2.417719 CACAGGTCCTTGCTTGACTAC 58.582 52.381 0.00 0.00 33.22 2.73
2826 3096 2.047061 ACAGGTCCTTGCTTGACTACA 58.953 47.619 0.00 0.00 33.22 2.74
2827 3097 2.224305 ACAGGTCCTTGCTTGACTACAC 60.224 50.000 0.00 0.00 33.22 2.90
2828 3098 2.047061 AGGTCCTTGCTTGACTACACA 58.953 47.619 0.00 0.00 33.22 3.72
2829 3099 2.639839 AGGTCCTTGCTTGACTACACAT 59.360 45.455 0.00 0.00 33.22 3.21
2832 3102 3.187227 GTCCTTGCTTGACTACACATGTG 59.813 47.826 24.25 24.25 0.00 3.21
2848 3118 5.739752 ACATGTGTGACATATATGTGCAC 57.260 39.130 26.99 26.99 41.95 4.57
2851 3121 4.249661 TGTGTGACATATATGTGCACGTT 58.750 39.130 27.34 7.14 41.80 3.99
2852 3122 4.328712 TGTGTGACATATATGTGCACGTTC 59.671 41.667 27.34 22.13 41.80 3.95
2869 3139 1.339929 GTTCCAGCACCGGTTTGAAAT 59.660 47.619 2.97 0.00 0.00 2.17
2872 3142 1.068333 CCAGCACCGGTTTGAAATCAG 60.068 52.381 2.97 0.00 0.00 2.90
2875 3145 1.068541 GCACCGGTTTGAAATCAGTCC 60.069 52.381 2.97 0.00 0.00 3.85
2880 3150 4.202111 ACCGGTTTGAAATCAGTCCAAAAG 60.202 41.667 0.00 0.00 32.44 2.27
2883 3153 5.687285 CGGTTTGAAATCAGTCCAAAAGAAG 59.313 40.000 0.00 0.00 32.44 2.85
2887 3157 6.076981 TGAAATCAGTCCAAAAGAAGCTTC 57.923 37.500 19.11 19.11 0.00 3.86
2906 3176 7.633018 AGCTTCCCATAGAAATAATACCTGA 57.367 36.000 0.00 0.00 32.88 3.86
2907 3177 8.224620 AGCTTCCCATAGAAATAATACCTGAT 57.775 34.615 0.00 0.00 32.88 2.90
2908 3178 8.105829 AGCTTCCCATAGAAATAATACCTGATG 58.894 37.037 0.00 0.00 32.88 3.07
2909 3179 7.337942 GCTTCCCATAGAAATAATACCTGATGG 59.662 40.741 0.00 0.00 32.88 3.51
2919 3189 4.838152 CCTGATGGGTGGCGTCCG 62.838 72.222 0.00 0.00 0.00 4.79
2943 3455 0.391793 CCTCGTCAAGAAGCTTCCCC 60.392 60.000 22.81 7.43 0.00 4.81
2957 3469 2.449464 CTTCCCCTTGCATGATTGACA 58.551 47.619 0.00 0.00 0.00 3.58
2962 3474 2.031420 CCCTTGCATGATTGACATAGCG 60.031 50.000 0.00 0.00 37.46 4.26
2964 3476 3.065786 CCTTGCATGATTGACATAGCGTT 59.934 43.478 0.00 0.00 37.46 4.84
2966 3478 2.355444 TGCATGATTGACATAGCGTTGG 59.645 45.455 0.00 0.00 37.46 3.77
2975 3487 0.816825 CATAGCGTTGGCAGGCTGAT 60.817 55.000 20.86 10.40 44.03 2.90
2976 3488 0.533755 ATAGCGTTGGCAGGCTGATC 60.534 55.000 20.86 10.03 44.03 2.92
2977 3489 2.906182 TAGCGTTGGCAGGCTGATCG 62.906 60.000 20.86 16.19 44.03 3.69
2978 3490 2.125552 CGTTGGCAGGCTGATCGA 60.126 61.111 20.86 6.40 0.00 3.59
2979 3491 2.456119 CGTTGGCAGGCTGATCGAC 61.456 63.158 20.86 16.99 0.00 4.20
2980 3492 2.125552 TTGGCAGGCTGATCGACG 60.126 61.111 20.86 0.00 0.00 5.12
2981 3493 2.645192 TTGGCAGGCTGATCGACGA 61.645 57.895 20.86 0.00 0.00 4.20
2982 3494 2.583593 GGCAGGCTGATCGACGAC 60.584 66.667 20.86 0.00 0.00 4.34
2983 3495 2.181777 GCAGGCTGATCGACGACA 59.818 61.111 20.86 0.00 0.00 4.35
2984 3496 1.227089 GCAGGCTGATCGACGACAT 60.227 57.895 20.86 0.00 0.00 3.06
2985 3497 0.807667 GCAGGCTGATCGACGACATT 60.808 55.000 20.86 0.00 0.00 2.71
2986 3498 0.926155 CAGGCTGATCGACGACATTG 59.074 55.000 9.42 0.00 0.00 2.82
2987 3499 0.179100 AGGCTGATCGACGACATTGG 60.179 55.000 0.00 0.00 0.00 3.16
2988 3500 1.638467 GCTGATCGACGACATTGGC 59.362 57.895 0.00 0.00 0.00 4.52
2989 3501 0.807667 GCTGATCGACGACATTGGCT 60.808 55.000 0.00 0.00 0.00 4.75
2990 3502 0.926155 CTGATCGACGACATTGGCTG 59.074 55.000 0.00 0.00 0.00 4.85
2991 3503 0.530288 TGATCGACGACATTGGCTGA 59.470 50.000 0.00 0.00 0.00 4.26
2992 3504 1.136891 TGATCGACGACATTGGCTGAT 59.863 47.619 0.00 0.00 0.00 2.90
3006 3518 1.865788 GCTGATTGGCAACGCTCCAA 61.866 55.000 0.00 6.16 46.44 3.53
3011 3523 0.316841 TTGGCAACGCTCCAATTTCC 59.683 50.000 0.00 0.00 38.57 3.13
3027 3539 5.922544 CCAATTTCCTGTTGAAGCTAAAGTG 59.077 40.000 0.00 0.00 33.63 3.16
3036 3548 3.517612 TGAAGCTAAAGTGGTACCCTCT 58.482 45.455 10.07 5.12 0.00 3.69
3043 3555 6.387220 AGCTAAAGTGGTACCCTCTATGAAAT 59.613 38.462 10.07 0.00 0.00 2.17
3056 3568 5.041951 TCTATGAAATTGCAACCGTCAAC 57.958 39.130 0.00 0.00 0.00 3.18
3057 3569 3.724508 ATGAAATTGCAACCGTCAACA 57.275 38.095 0.00 0.00 0.00 3.33
3058 3570 2.803451 TGAAATTGCAACCGTCAACAC 58.197 42.857 0.00 0.00 0.00 3.32
3069 3581 0.508641 CGTCAACACTTCGCCTCTTG 59.491 55.000 0.00 0.00 0.00 3.02
3080 3592 0.528684 CGCCTCTTGGACGATCTTCC 60.529 60.000 11.29 11.29 35.80 3.46
3097 3609 3.315470 TCTTCCTCACAATATCGTCGAGG 59.685 47.826 0.00 0.00 43.88 4.63
3107 3619 1.988293 ATCGTCGAGGGTGATCATCT 58.012 50.000 5.82 3.55 0.00 2.90
3152 3665 5.452496 CGTAAATGAGTGAGTGGATCCATCT 60.452 44.000 19.62 16.49 0.00 2.90
3155 3668 0.835941 AGTGAGTGGATCCATCTGCC 59.164 55.000 19.62 4.23 0.00 4.85
3157 3670 1.070445 GAGTGGATCCATCTGCCGG 59.930 63.158 19.62 0.00 0.00 6.13
3165 3678 2.729479 CCATCTGCCGGAGTCAGCT 61.729 63.158 5.05 0.00 31.25 4.24
3168 3681 4.383861 CTGCCGGAGTCAGCTGCA 62.384 66.667 9.47 0.00 32.11 4.41
3171 3684 2.970974 GCCGGAGTCAGCTGCAAAC 61.971 63.158 9.47 1.80 32.11 2.93
3173 3686 0.037326 CCGGAGTCAGCTGCAAACTA 60.037 55.000 9.47 0.00 32.11 2.24
3193 3706 0.110688 CACACCAACATCTGCGTTCG 60.111 55.000 0.00 0.00 0.00 3.95
3207 3720 1.227999 CGTTCGTGCACAGGTTGGAT 61.228 55.000 18.64 0.00 0.00 3.41
3209 3722 0.888736 TTCGTGCACAGGTTGGATGG 60.889 55.000 18.64 0.00 33.41 3.51
3212 3725 2.036256 GCACAGGTTGGATGGGCT 59.964 61.111 0.00 0.00 43.90 5.19
3213 3726 2.048603 GCACAGGTTGGATGGGCTC 61.049 63.158 0.00 0.00 43.90 4.70
3259 3772 1.921869 AACCGAGGGCCATGTAAGGG 61.922 60.000 6.18 0.00 43.76 3.95
3260 3773 2.375345 CCGAGGGCCATGTAAGGGT 61.375 63.158 6.18 0.00 42.11 4.34
3279 3794 6.426646 AGGGTACTGATCATGTTAGAATCC 57.573 41.667 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.731720 TTGTTTGTTTGGCTTGTGGC 58.268 45.000 0.00 0.00 40.90 5.01
9 10 5.355596 TCTATTTGTTTGTTTGGCTTGTGG 58.644 37.500 0.00 0.00 0.00 4.17
11 12 6.315144 GGTTTCTATTTGTTTGTTTGGCTTGT 59.685 34.615 0.00 0.00 0.00 3.16
14 15 5.983540 TGGTTTCTATTTGTTTGTTTGGCT 58.016 33.333 0.00 0.00 0.00 4.75
15 16 6.670077 TTGGTTTCTATTTGTTTGTTTGGC 57.330 33.333 0.00 0.00 0.00 4.52
29 30 9.504708 TGTTCTTCGGTATTAATTTGGTTTCTA 57.495 29.630 0.00 0.00 0.00 2.10
31 32 8.077386 TGTGTTCTTCGGTATTAATTTGGTTTC 58.923 33.333 0.00 0.00 0.00 2.78
37 38 8.626526 ACAACTTGTGTTCTTCGGTATTAATTT 58.373 29.630 0.00 0.00 37.01 1.82
59 60 1.942223 GTCAAAACCGGCGCACAAC 60.942 57.895 10.83 0.00 0.00 3.32
60 61 2.409651 GTCAAAACCGGCGCACAA 59.590 55.556 10.83 0.00 0.00 3.33
61 62 3.587933 GGTCAAAACCGGCGCACA 61.588 61.111 10.83 0.00 35.36 4.57
108 109 1.168714 AACCACGACGGAGGTAGTAC 58.831 55.000 13.61 0.00 35.96 2.73
109 110 1.909700 AAACCACGACGGAGGTAGTA 58.090 50.000 13.61 0.00 35.96 1.82
110 111 1.909700 TAAACCACGACGGAGGTAGT 58.090 50.000 13.61 8.35 35.96 2.73
111 112 3.184541 CAATAAACCACGACGGAGGTAG 58.815 50.000 13.61 0.91 35.96 3.18
112 113 2.094078 CCAATAAACCACGACGGAGGTA 60.094 50.000 13.61 1.41 35.96 3.08
113 114 1.338389 CCAATAAACCACGACGGAGGT 60.338 52.381 8.26 8.26 38.94 3.85
114 115 1.338389 ACCAATAAACCACGACGGAGG 60.338 52.381 0.00 3.16 38.63 4.30
115 116 2.088950 ACCAATAAACCACGACGGAG 57.911 50.000 0.00 0.00 38.63 4.63
116 117 2.415776 GAACCAATAAACCACGACGGA 58.584 47.619 0.00 0.00 38.63 4.69
117 118 1.465777 GGAACCAATAAACCACGACGG 59.534 52.381 0.00 0.00 42.50 4.79
118 119 2.886587 GGAACCAATAAACCACGACG 57.113 50.000 0.00 0.00 0.00 5.12
133 134 1.418373 GCACAAAATGCGAAGGGAAC 58.582 50.000 0.00 0.00 46.55 3.62
134 135 3.883997 GCACAAAATGCGAAGGGAA 57.116 47.368 0.00 0.00 46.55 3.97
143 144 9.897744 TCTAAGATCAAAACTTAGCACAAAATG 57.102 29.630 0.00 0.00 43.47 2.32
174 175 9.973450 TGTTACATGCATTAACATTTTGTTAGT 57.027 25.926 20.77 6.21 42.93 2.24
293 294 8.410141 CCCTTAGTATTTTGTGTCAAACTTTGA 58.590 33.333 0.00 0.00 37.33 2.69
294 295 8.410141 TCCCTTAGTATTTTGTGTCAAACTTTG 58.590 33.333 0.00 0.00 0.00 2.77
295 296 8.528044 TCCCTTAGTATTTTGTGTCAAACTTT 57.472 30.769 0.00 0.00 0.00 2.66
296 297 8.528044 TTCCCTTAGTATTTTGTGTCAAACTT 57.472 30.769 0.00 0.00 0.00 2.66
297 298 8.528044 TTTCCCTTAGTATTTTGTGTCAAACT 57.472 30.769 0.00 0.00 0.00 2.66
311 312 8.206189 CGTCCAGGTTTATTATTTCCCTTAGTA 58.794 37.037 0.00 0.00 0.00 1.82
312 313 7.052248 CGTCCAGGTTTATTATTTCCCTTAGT 58.948 38.462 0.00 0.00 0.00 2.24
313 314 6.485648 CCGTCCAGGTTTATTATTTCCCTTAG 59.514 42.308 0.00 0.00 34.51 2.18
314 315 6.158344 TCCGTCCAGGTTTATTATTTCCCTTA 59.842 38.462 0.00 0.00 41.99 2.69
315 316 5.044698 TCCGTCCAGGTTTATTATTTCCCTT 60.045 40.000 0.00 0.00 41.99 3.95
316 317 4.475747 TCCGTCCAGGTTTATTATTTCCCT 59.524 41.667 0.00 0.00 41.99 4.20
317 318 4.784177 TCCGTCCAGGTTTATTATTTCCC 58.216 43.478 0.00 0.00 41.99 3.97
318 319 4.820173 CCTCCGTCCAGGTTTATTATTTCC 59.180 45.833 0.00 0.00 41.99 3.13
319 320 5.434408 ACCTCCGTCCAGGTTTATTATTTC 58.566 41.667 0.00 0.00 45.24 2.17
320 321 5.446260 ACCTCCGTCCAGGTTTATTATTT 57.554 39.130 0.00 0.00 45.24 1.40
321 322 5.664457 ACTACCTCCGTCCAGGTTTATTATT 59.336 40.000 3.48 0.00 45.24 1.40
322 323 5.214293 ACTACCTCCGTCCAGGTTTATTAT 58.786 41.667 3.48 0.00 45.24 1.28
323 324 4.613437 ACTACCTCCGTCCAGGTTTATTA 58.387 43.478 3.48 0.00 45.24 0.98
324 325 3.447950 ACTACCTCCGTCCAGGTTTATT 58.552 45.455 3.48 0.00 45.24 1.40
325 326 3.111741 ACTACCTCCGTCCAGGTTTAT 57.888 47.619 3.48 0.00 45.24 1.40
326 327 2.610438 ACTACCTCCGTCCAGGTTTA 57.390 50.000 3.48 0.00 45.24 2.01
327 328 2.174360 GTACTACCTCCGTCCAGGTTT 58.826 52.381 3.48 0.00 45.24 3.27
328 329 1.076024 TGTACTACCTCCGTCCAGGTT 59.924 52.381 3.48 0.00 45.24 3.50
330 331 1.340795 ACTGTACTACCTCCGTCCAGG 60.341 57.143 0.00 0.00 42.97 4.45
331 332 2.125773 ACTGTACTACCTCCGTCCAG 57.874 55.000 0.00 0.00 0.00 3.86
332 333 3.939740 ATACTGTACTACCTCCGTCCA 57.060 47.619 0.00 0.00 0.00 4.02
333 334 6.070538 TCCTATATACTGTACTACCTCCGTCC 60.071 46.154 0.00 0.00 0.00 4.79
334 335 6.940739 TCCTATATACTGTACTACCTCCGTC 58.059 44.000 0.00 0.00 0.00 4.79
335 336 6.728164 TCTCCTATATACTGTACTACCTCCGT 59.272 42.308 0.00 0.00 0.00 4.69
336 337 7.180322 TCTCCTATATACTGTACTACCTCCG 57.820 44.000 0.00 0.00 0.00 4.63
337 338 8.770322 TCATCTCCTATATACTGTACTACCTCC 58.230 40.741 0.00 0.00 0.00 4.30
338 339 9.826574 CTCATCTCCTATATACTGTACTACCTC 57.173 40.741 0.00 0.00 0.00 3.85
339 340 8.774183 CCTCATCTCCTATATACTGTACTACCT 58.226 40.741 0.00 0.00 0.00 3.08
340 341 8.770322 TCCTCATCTCCTATATACTGTACTACC 58.230 40.741 0.00 0.00 0.00 3.18
341 342 9.826574 CTCCTCATCTCCTATATACTGTACTAC 57.173 40.741 0.00 0.00 0.00 2.73
342 343 9.785854 TCTCCTCATCTCCTATATACTGTACTA 57.214 37.037 0.00 0.00 0.00 1.82
343 344 8.545472 GTCTCCTCATCTCCTATATACTGTACT 58.455 40.741 0.00 0.00 0.00 2.73
352 353 4.263550 CCGGAAGTCTCCTCATCTCCTATA 60.264 50.000 0.00 0.00 39.93 1.31
433 435 3.568430 ACCGACCATTTTTCCTCTTGTTC 59.432 43.478 0.00 0.00 0.00 3.18
510 514 2.239341 TTAGCGTCGCACAATGCTGC 62.239 55.000 21.09 0.00 42.25 5.25
898 909 1.149361 TTTATAAGCAGTCCCGCGCG 61.149 55.000 25.67 25.67 36.85 6.86
899 910 0.582005 CTTTATAAGCAGTCCCGCGC 59.418 55.000 0.00 0.00 36.85 6.86
934 955 0.611714 GGAGGTAACGGAGGAAAGCA 59.388 55.000 0.00 0.00 46.39 3.91
945 966 1.911702 GCTGGGGTGGAGGAGGTAAC 61.912 65.000 0.00 0.00 0.00 2.50
948 969 4.270153 TGCTGGGGTGGAGGAGGT 62.270 66.667 0.00 0.00 0.00 3.85
980 1001 1.299939 GATCTCCCCCAACTCCCTTT 58.700 55.000 0.00 0.00 0.00 3.11
989 1010 2.040988 TCGCCATGATCTCCCCCA 60.041 61.111 0.00 0.00 0.00 4.96
990 1011 2.746359 CTCGCCATGATCTCCCCC 59.254 66.667 0.00 0.00 0.00 5.40
991 1012 1.825281 CTCCTCGCCATGATCTCCCC 61.825 65.000 0.00 0.00 0.00 4.81
1085 1109 2.827322 TCGTGGGATAAAGTTTCCGAGA 59.173 45.455 0.00 0.00 33.82 4.04
1108 1132 2.376518 CACAGTATATGGCCCCTGGAAT 59.623 50.000 0.00 0.00 0.00 3.01
1112 1136 2.909006 AGATCACAGTATATGGCCCCTG 59.091 50.000 0.00 0.86 0.00 4.45
1114 1138 4.373156 AAAGATCACAGTATATGGCCCC 57.627 45.455 0.00 0.00 0.00 5.80
1115 1139 5.471456 CAGAAAAGATCACAGTATATGGCCC 59.529 44.000 0.00 0.00 0.00 5.80
1116 1140 6.203723 GTCAGAAAAGATCACAGTATATGGCC 59.796 42.308 0.00 0.00 0.00 5.36
1117 1141 6.763135 TGTCAGAAAAGATCACAGTATATGGC 59.237 38.462 0.00 0.00 0.00 4.40
1118 1142 8.722480 TTGTCAGAAAAGATCACAGTATATGG 57.278 34.615 0.00 0.00 0.00 2.74
1119 1143 9.376075 ACTTGTCAGAAAAGATCACAGTATATG 57.624 33.333 7.40 0.00 0.00 1.78
1120 1144 9.376075 CACTTGTCAGAAAAGATCACAGTATAT 57.624 33.333 7.40 0.00 0.00 0.86
1121 1145 7.331934 GCACTTGTCAGAAAAGATCACAGTATA 59.668 37.037 7.40 0.00 0.00 1.47
1122 1146 6.148480 GCACTTGTCAGAAAAGATCACAGTAT 59.852 38.462 7.40 0.00 0.00 2.12
1123 1147 5.466728 GCACTTGTCAGAAAAGATCACAGTA 59.533 40.000 7.40 0.00 0.00 2.74
1124 1148 4.274459 GCACTTGTCAGAAAAGATCACAGT 59.726 41.667 7.40 0.00 0.00 3.55
1125 1149 4.274214 TGCACTTGTCAGAAAAGATCACAG 59.726 41.667 7.40 0.00 0.00 3.66
1126 1150 4.035558 GTGCACTTGTCAGAAAAGATCACA 59.964 41.667 10.32 0.00 34.16 3.58
1127 1151 4.531332 GTGCACTTGTCAGAAAAGATCAC 58.469 43.478 10.32 9.88 0.00 3.06
1128 1152 3.565482 GGTGCACTTGTCAGAAAAGATCA 59.435 43.478 17.98 1.81 0.00 2.92
1129 1153 3.817647 AGGTGCACTTGTCAGAAAAGATC 59.182 43.478 17.98 0.00 0.00 2.75
1130 1154 3.825328 AGGTGCACTTGTCAGAAAAGAT 58.175 40.909 17.98 0.00 0.00 2.40
1131 1155 3.281727 AGGTGCACTTGTCAGAAAAGA 57.718 42.857 17.98 0.00 0.00 2.52
1132 1156 3.629398 AGAAGGTGCACTTGTCAGAAAAG 59.371 43.478 17.98 0.00 40.21 2.27
1133 1157 3.620488 AGAAGGTGCACTTGTCAGAAAA 58.380 40.909 17.98 0.00 40.21 2.29
1134 1158 3.281727 AGAAGGTGCACTTGTCAGAAA 57.718 42.857 17.98 0.00 40.21 2.52
1135 1159 2.945008 CAAGAAGGTGCACTTGTCAGAA 59.055 45.455 17.98 0.00 40.21 3.02
1136 1160 2.564771 CAAGAAGGTGCACTTGTCAGA 58.435 47.619 17.98 0.00 40.21 3.27
1147 1171 1.480205 CTTTGCGCAACAAGAAGGTG 58.520 50.000 24.99 0.94 40.06 4.00
1151 1175 1.067250 GCCCTTTGCGCAACAAGAA 59.933 52.632 24.99 6.83 40.06 2.52
1700 1724 9.671279 CTTGACATGCTGGGAATTATATATGTA 57.329 33.333 0.00 0.00 0.00 2.29
1701 1725 8.385491 TCTTGACATGCTGGGAATTATATATGT 58.615 33.333 0.00 0.00 0.00 2.29
1702 1726 8.797350 TCTTGACATGCTGGGAATTATATATG 57.203 34.615 0.00 0.00 0.00 1.78
1703 1727 9.624373 GATCTTGACATGCTGGGAATTATATAT 57.376 33.333 0.00 0.00 0.00 0.86
1704 1728 8.605065 TGATCTTGACATGCTGGGAATTATATA 58.395 33.333 0.00 0.00 0.00 0.86
1705 1729 7.464273 TGATCTTGACATGCTGGGAATTATAT 58.536 34.615 0.00 0.00 0.00 0.86
1706 1730 6.840527 TGATCTTGACATGCTGGGAATTATA 58.159 36.000 0.00 0.00 0.00 0.98
1738 1766 1.533731 GAGTTTCGGAATGGCGTTGAA 59.466 47.619 0.00 0.00 0.00 2.69
1740 1768 0.871722 TGAGTTTCGGAATGGCGTTG 59.128 50.000 0.00 0.00 0.00 4.10
1741 1769 0.872388 GTGAGTTTCGGAATGGCGTT 59.128 50.000 0.00 0.00 0.00 4.84
1743 1771 0.953471 TGGTGAGTTTCGGAATGGCG 60.953 55.000 0.00 0.00 0.00 5.69
1744 1772 1.133025 CATGGTGAGTTTCGGAATGGC 59.867 52.381 0.00 0.00 0.00 4.40
1745 1773 2.710377 TCATGGTGAGTTTCGGAATGG 58.290 47.619 0.00 0.00 0.00 3.16
1756 1784 2.704464 TCCAAGCTGATCATGGTGAG 57.296 50.000 12.50 0.00 35.17 3.51
2055 2118 1.805945 CGAAGGACAGCCTGTACGC 60.806 63.158 0.34 0.00 46.28 4.42
2249 2315 1.248101 TGGCGTCGGACTTCATGAGA 61.248 55.000 6.57 0.00 0.00 3.27
2373 2446 4.050553 CGGTACAAACGTAAGAAACTCCA 58.949 43.478 0.00 0.00 43.62 3.86
2380 2453 0.388391 CGGCCGGTACAAACGTAAGA 60.388 55.000 20.10 0.00 43.62 2.10
2407 2480 1.450312 GCTCAACACTAGGGCGCAT 60.450 57.895 10.83 0.00 0.00 4.73
2443 2517 7.494298 ACTGTTATATATTGTGTCGTTGATGCA 59.506 33.333 0.00 0.00 0.00 3.96
2451 2556 6.863645 CAGGGAGACTGTTATATATTGTGTCG 59.136 42.308 0.00 0.00 42.42 4.35
2479 2584 1.155424 TTGCGTCGTTGAAGTGTCCC 61.155 55.000 0.00 0.00 0.00 4.46
2483 2588 2.363220 GAGTTTTGCGTCGTTGAAGTG 58.637 47.619 0.00 0.00 0.00 3.16
2518 2623 4.742659 TGCAAAATTTTCGAGCAACTTACC 59.257 37.500 10.91 0.00 31.42 2.85
2543 2685 2.156891 TCTGTGCAAAATCGACTTACGC 59.843 45.455 0.00 0.00 42.26 4.42
2544 2686 3.673338 TCTCTGTGCAAAATCGACTTACG 59.327 43.478 0.00 0.00 44.09 3.18
2548 2690 3.995199 TCTTCTCTGTGCAAAATCGACT 58.005 40.909 0.00 0.00 0.00 4.18
2559 2701 1.345741 TCTGCCCACTTCTTCTCTGTG 59.654 52.381 0.00 0.00 0.00 3.66
2560 2702 1.622811 CTCTGCCCACTTCTTCTCTGT 59.377 52.381 0.00 0.00 0.00 3.41
2561 2703 1.066286 CCTCTGCCCACTTCTTCTCTG 60.066 57.143 0.00 0.00 0.00 3.35
2562 2704 1.274712 CCTCTGCCCACTTCTTCTCT 58.725 55.000 0.00 0.00 0.00 3.10
2563 2705 0.392327 GCCTCTGCCCACTTCTTCTC 60.392 60.000 0.00 0.00 0.00 2.87
2620 2767 0.601841 TCGAGCCGTTTCCTTCAACC 60.602 55.000 0.00 0.00 0.00 3.77
2625 2848 2.754946 TTACATCGAGCCGTTTCCTT 57.245 45.000 0.00 0.00 0.00 3.36
2637 2860 3.189287 GCCCCTATGCATCTTTTACATCG 59.811 47.826 0.19 0.00 0.00 3.84
2644 2867 0.936691 AAGGGCCCCTATGCATCTTT 59.063 50.000 21.43 0.00 31.13 2.52
2657 2880 4.457466 TGTCCGATTTAAATCTAAGGGCC 58.543 43.478 22.52 9.53 33.24 5.80
2664 2887 6.817765 TTTTGAGCTGTCCGATTTAAATCT 57.182 33.333 22.52 5.29 33.24 2.40
2668 2891 7.857734 TGATATTTTGAGCTGTCCGATTTAA 57.142 32.000 0.00 0.00 0.00 1.52
2679 2902 4.832266 TGGTGTTGGTTGATATTTTGAGCT 59.168 37.500 0.00 0.00 0.00 4.09
2734 3004 4.675190 AATCATATAAGAGTGCGCATGC 57.325 40.909 15.91 7.91 43.20 4.06
2797 3067 0.035458 CAAGGACCTGTGGAGTGACC 59.965 60.000 0.00 0.00 39.54 4.02
2804 3074 0.109342 AGTCAAGCAAGGACCTGTGG 59.891 55.000 0.00 0.00 35.89 4.17
2809 3079 2.543777 TGTGTAGTCAAGCAAGGACC 57.456 50.000 0.00 0.00 35.89 4.46
2812 3082 3.058708 CACACATGTGTAGTCAAGCAAGG 60.059 47.826 30.11 10.34 42.83 3.61
2821 3091 6.479990 GCACATATATGTCACACATGTGTAGT 59.520 38.462 30.11 17.80 45.22 2.73
2822 3092 6.479660 TGCACATATATGTCACACATGTGTAG 59.520 38.462 30.11 22.64 45.22 2.74
2823 3093 6.257630 GTGCACATATATGTCACACATGTGTA 59.742 38.462 30.11 16.40 45.22 2.90
2824 3094 5.065090 GTGCACATATATGTCACACATGTGT 59.935 40.000 28.02 25.76 45.22 3.72
2825 3095 5.504392 GTGCACATATATGTCACACATGTG 58.496 41.667 28.02 24.25 45.86 3.21
2826 3096 4.270808 CGTGCACATATATGTCACACATGT 59.729 41.667 29.95 0.00 41.46 3.21
2827 3097 4.270808 ACGTGCACATATATGTCACACATG 59.729 41.667 29.95 23.77 41.46 3.21
2828 3098 4.441792 ACGTGCACATATATGTCACACAT 58.558 39.130 29.95 21.37 41.46 3.21
2829 3099 3.855858 ACGTGCACATATATGTCACACA 58.144 40.909 29.95 18.91 41.46 3.72
2832 3102 3.868661 TGGAACGTGCACATATATGTCAC 59.131 43.478 24.04 24.04 39.39 3.67
2834 3104 3.059597 GCTGGAACGTGCACATATATGTC 60.060 47.826 18.64 10.96 39.39 3.06
2838 3108 2.682155 TGCTGGAACGTGCACATATA 57.318 45.000 18.64 0.00 35.72 0.86
2846 3116 2.184167 AAACCGGTGCTGGAACGTG 61.184 57.895 8.52 0.00 0.00 4.49
2848 3118 1.440938 TTCAAACCGGTGCTGGAACG 61.441 55.000 8.52 0.00 0.00 3.95
2851 3121 1.243902 GATTTCAAACCGGTGCTGGA 58.756 50.000 8.52 0.00 0.00 3.86
2852 3122 0.958091 TGATTTCAAACCGGTGCTGG 59.042 50.000 8.52 0.00 0.00 4.85
2858 3128 4.037446 TCTTTTGGACTGATTTCAAACCGG 59.963 41.667 0.00 0.00 31.21 5.28
2869 3139 2.174639 TGGGAAGCTTCTTTTGGACTGA 59.825 45.455 25.05 0.00 0.00 3.41
2872 3142 4.589908 TCTATGGGAAGCTTCTTTTGGAC 58.410 43.478 25.05 7.21 0.00 4.02
2880 3150 8.157476 TCAGGTATTATTTCTATGGGAAGCTTC 58.843 37.037 18.54 18.54 35.16 3.86
2883 3153 7.337942 CCATCAGGTATTATTTCTATGGGAAGC 59.662 40.741 0.00 0.00 35.16 3.86
2902 3172 4.838152 CGGACGCCACCCATCAGG 62.838 72.222 0.00 0.00 43.78 3.86
2918 3188 4.735132 TTCTTGACGAGGCGGGCG 62.735 66.667 0.00 0.00 0.00 6.13
2919 3189 2.815647 CTTCTTGACGAGGCGGGC 60.816 66.667 0.00 0.00 0.00 6.13
2920 3190 2.815647 GCTTCTTGACGAGGCGGG 60.816 66.667 0.00 0.00 34.89 6.13
2928 3440 0.884514 GCAAGGGGAAGCTTCTTGAC 59.115 55.000 25.05 13.64 39.97 3.18
2943 3455 3.957671 ACGCTATGTCAATCATGCAAG 57.042 42.857 0.00 0.00 37.91 4.01
2957 3469 0.533755 GATCAGCCTGCCAACGCTAT 60.534 55.000 0.00 0.00 32.92 2.97
2962 3474 2.456119 CGTCGATCAGCCTGCCAAC 61.456 63.158 0.00 0.00 0.00 3.77
2964 3476 3.068064 TCGTCGATCAGCCTGCCA 61.068 61.111 0.00 0.00 0.00 4.92
2966 3478 0.807667 AATGTCGTCGATCAGCCTGC 60.808 55.000 0.00 0.00 0.00 4.85
2975 3487 1.358877 CAATCAGCCAATGTCGTCGA 58.641 50.000 0.00 0.00 0.00 4.20
2976 3488 0.374758 CCAATCAGCCAATGTCGTCG 59.625 55.000 0.00 0.00 0.00 5.12
2977 3489 0.099436 GCCAATCAGCCAATGTCGTC 59.901 55.000 0.00 0.00 0.00 4.20
2978 3490 0.608856 TGCCAATCAGCCAATGTCGT 60.609 50.000 0.00 0.00 0.00 4.34
2979 3491 0.527113 TTGCCAATCAGCCAATGTCG 59.473 50.000 0.00 0.00 0.00 4.35
2980 3492 1.733389 CGTTGCCAATCAGCCAATGTC 60.733 52.381 0.00 0.00 0.00 3.06
2981 3493 0.244450 CGTTGCCAATCAGCCAATGT 59.756 50.000 0.00 0.00 0.00 2.71
2982 3494 1.079875 GCGTTGCCAATCAGCCAATG 61.080 55.000 0.00 0.00 0.00 2.82
2983 3495 1.216178 GCGTTGCCAATCAGCCAAT 59.784 52.632 0.00 0.00 0.00 3.16
2984 3496 1.865788 GAGCGTTGCCAATCAGCCAA 61.866 55.000 0.11 0.00 0.00 4.52
2985 3497 2.282391 AGCGTTGCCAATCAGCCA 60.282 55.556 0.11 0.00 0.00 4.75
2986 3498 2.486966 GAGCGTTGCCAATCAGCC 59.513 61.111 0.11 0.00 0.00 4.85
2987 3499 1.865788 TTGGAGCGTTGCCAATCAGC 61.866 55.000 0.00 0.00 40.32 4.26
2988 3500 2.256391 TTGGAGCGTTGCCAATCAG 58.744 52.632 0.00 0.00 40.32 2.90
2989 3501 4.490696 TTGGAGCGTTGCCAATCA 57.509 50.000 0.00 0.00 40.32 2.57
3001 3513 5.964958 TTAGCTTCAACAGGAAATTGGAG 57.035 39.130 0.00 0.00 35.97 3.86
3006 3518 5.140454 ACCACTTTAGCTTCAACAGGAAAT 58.860 37.500 0.00 0.00 34.44 2.17
3036 3548 4.277174 AGTGTTGACGGTTGCAATTTCATA 59.723 37.500 0.59 0.00 0.00 2.15
3043 3555 0.375454 CGAAGTGTTGACGGTTGCAA 59.625 50.000 0.00 0.00 0.00 4.08
3056 3568 0.108615 ATCGTCCAAGAGGCGAAGTG 60.109 55.000 0.00 0.00 43.20 3.16
3057 3569 0.173708 GATCGTCCAAGAGGCGAAGT 59.826 55.000 0.00 0.00 43.20 3.01
3058 3570 0.457851 AGATCGTCCAAGAGGCGAAG 59.542 55.000 0.00 0.00 43.20 3.79
3069 3581 4.230657 CGATATTGTGAGGAAGATCGTCC 58.769 47.826 18.96 18.96 40.50 4.79
3080 3592 2.357952 TCACCCTCGACGATATTGTGAG 59.642 50.000 0.00 7.74 0.00 3.51
3097 3609 3.054802 ACAAAGAGTGGGAGATGATCACC 60.055 47.826 0.00 0.00 32.29 4.02
3107 3619 3.554960 CGTCTCAATGACAAAGAGTGGGA 60.555 47.826 7.22 0.00 45.60 4.37
3111 3623 6.929049 TCATTTACGTCTCAATGACAAAGAGT 59.071 34.615 11.70 0.00 45.60 3.24
3130 3643 5.685861 GCAGATGGATCCACTCACTCATTTA 60.686 44.000 18.99 0.00 0.00 1.40
3137 3650 0.531532 CGGCAGATGGATCCACTCAC 60.532 60.000 18.99 9.16 0.00 3.51
3155 3668 1.071605 GTAGTTTGCAGCTGACTCCG 58.928 55.000 20.43 0.00 0.00 4.63
3157 3670 2.221981 GTGTGTAGTTTGCAGCTGACTC 59.778 50.000 20.43 6.99 0.00 3.36
3165 3678 3.314913 CAGATGTTGGTGTGTAGTTTGCA 59.685 43.478 0.00 0.00 0.00 4.08
3168 3681 2.548057 CGCAGATGTTGGTGTGTAGTTT 59.452 45.455 0.00 0.00 0.00 2.66
3171 3684 1.795768 ACGCAGATGTTGGTGTGTAG 58.204 50.000 0.00 0.00 35.66 2.74
3173 3686 0.944386 GAACGCAGATGTTGGTGTGT 59.056 50.000 0.00 0.00 39.06 3.72
3193 3706 2.639327 GCCCATCCAACCTGTGCAC 61.639 63.158 10.75 10.75 0.00 4.57
3207 3720 1.252904 GCTTTTCTGCATGGAGCCCA 61.253 55.000 9.76 0.00 44.83 5.36
3209 3722 1.514553 GGCTTTTCTGCATGGAGCC 59.485 57.895 9.76 12.77 45.21 4.70
3211 3724 2.015587 GAGAGGCTTTTCTGCATGGAG 58.984 52.381 8.12 8.12 34.04 3.86
3212 3725 1.340405 GGAGAGGCTTTTCTGCATGGA 60.340 52.381 0.00 0.00 35.79 3.41
3213 3726 1.101331 GGAGAGGCTTTTCTGCATGG 58.899 55.000 0.00 0.00 35.79 3.66
3259 3772 6.426646 AGGGGATTCTAACATGATCAGTAC 57.573 41.667 0.00 0.00 0.00 2.73
3260 3773 6.846505 AGAAGGGGATTCTAACATGATCAGTA 59.153 38.462 0.00 0.00 46.75 2.74
3279 3794 5.593679 TCAAGATCTAACGGTTAGAAGGG 57.406 43.478 28.59 19.41 44.75 3.95
3293 3808 3.679980 CGTGACCAAATCGTTCAAGATCT 59.320 43.478 0.00 0.00 0.00 2.75
3307 3822 2.431771 CGGATGCGACGTGACCAA 60.432 61.111 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.