Multiple sequence alignment - TraesCS5A01G289400

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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 TraesCS5A01G289400 chr5A 100.000 3025 0 0 1 3025 496136465 496133441 0.000000e+00 5587.0
1 TraesCS5A01G289400 chr5A 100.000 63 0 0 2963 3025 496106346 496106284 1.910000e-22 117.0
2 TraesCS5A01G289400 chr5D 86.882 1052 67 37 1 1028 394164488 394163484 0.000000e+00 1112.0
3 TraesCS5A01G289400 chr5D 88.331 797 46 26 1116 1894 394163446 394162679 0.000000e+00 913.0
4 TraesCS5A01G289400 chr5D 90.385 208 8 4 2830 3025 394145966 394145759 2.310000e-66 263.0
5 TraesCS5A01G289400 chr5D 82.609 207 17 7 2266 2454 394161715 394161510 6.710000e-37 165.0
6 TraesCS5A01G289400 chr5D 77.439 328 27 16 2510 2809 394146263 394145955 5.220000e-33 152.0
7 TraesCS5A01G289400 chr5D 88.119 101 12 0 1532 1632 394280610 394280510 1.470000e-23 121.0
8 TraesCS5A01G289400 chr5D 93.023 43 2 1 998 1040 394559721 394559680 9.060000e-06 62.1
9 TraesCS5A01G289400 chr5D 93.023 43 2 1 998 1040 394563136 394563095 9.060000e-06 62.1
10 TraesCS5A01G289400 chr5D 100.000 32 0 0 998 1029 394549026 394548995 3.260000e-05 60.2
11 TraesCS5A01G289400 chr5D 100.000 32 0 0 998 1029 394551039 394551008 3.260000e-05 60.2
12 TraesCS5A01G289400 chr5B 91.892 703 39 14 1130 1831 474048071 474047386 0.000000e+00 966.0
13 TraesCS5A01G289400 chr5B 85.882 595 31 20 518 1108 474048605 474048060 4.350000e-163 584.0
14 TraesCS5A01G289400 chr5B 88.108 370 33 5 2025 2385 474047156 474046789 2.150000e-116 429.0
15 TraesCS5A01G289400 chr5B 91.386 267 11 9 245 508 474049061 474048804 3.710000e-94 355.0
16 TraesCS5A01G289400 chr5B 88.406 207 10 4 2830 3025 474044621 474044418 1.400000e-58 237.0
17 TraesCS5A01G289400 chr5B 82.877 146 14 5 2673 2809 474044753 474044610 1.470000e-23 121.0
18 TraesCS5A01G289400 chr4A 84.559 272 28 9 2397 2667 198399393 198399135 1.080000e-64 257.0
19 TraesCS5A01G289400 chr4A 76.240 383 39 33 1271 1618 30286895 30287260 4.040000e-34 156.0
20 TraesCS5A01G289400 chrUn 89.706 204 13 5 2744 2947 323279682 323279877 1.390000e-63 254.0
21 TraesCS5A01G289400 chrUn 85.276 163 4 10 2507 2667 323278184 323278328 1.880000e-32 150.0
22 TraesCS5A01G289400 chrUn 100.000 63 0 0 2963 3025 296930422 296930360 1.910000e-22 117.0
23 TraesCS5A01G289400 chrUn 93.023 43 2 1 998 1040 211147316 211147275 9.060000e-06 62.1
24 TraesCS5A01G289400 chrUn 100.000 32 0 0 998 1029 332176568 332176537 3.260000e-05 60.2
25 TraesCS5A01G289400 chr7D 78.492 358 44 25 1260 1611 489299590 489299920 1.420000e-48 204.0
26 TraesCS5A01G289400 chr7D 76.945 347 44 27 1260 1602 484068735 484069049 6.710000e-37 165.0
27 TraesCS5A01G289400 chr7B 87.059 170 18 2 1260 1429 509732850 509733015 3.980000e-44 189.0
28 TraesCS5A01G289400 chr7A 77.654 358 47 24 1260 1611 551540221 551540551 1.430000e-43 187.0
29 TraesCS5A01G289400 chr4D 75.401 374 47 26 1270 1611 437818854 437818494 4.070000e-29 139.0
30 TraesCS5A01G289400 chr4B 75.202 371 42 31 1271 1607 540726444 540726090 2.450000e-26 130.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G289400 chr5A 496133441 496136465 3024 True 5587.000000 5587 100.000000 1 3025 1 chr5A.!!$R2 3024
1 TraesCS5A01G289400 chr5D 394161510 394164488 2978 True 730.000000 1112 85.940667 1 2454 3 chr5D.!!$R3 2453
2 TraesCS5A01G289400 chr5D 394145759 394146263 504 True 207.500000 263 83.912000 2510 3025 2 chr5D.!!$R2 515
3 TraesCS5A01G289400 chr5B 474044418 474049061 4643 True 448.666667 966 88.091833 245 3025 6 chr5B.!!$R1 2780
4 TraesCS5A01G289400 chrUn 323278184 323279877 1693 False 202.000000 254 87.491000 2507 2947 2 chrUn.!!$F1 440

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
825 1043 0.032217 CTCCCTCTCTCTCCCTTGCT 60.032 60.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2503 3464 0.108424 CCCTTTGACCTCGCTCAGAG 60.108 60.0 0.0 0.0 46.44 3.35 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
35 38 9.936759 TGTTTTTGAAATCAAGTTTTTCTAGGT 57.063 25.926 0.00 0.00 37.15 3.08
43 46 4.741676 TCAAGTTTTTCTAGGTCGTTCGTC 59.258 41.667 0.00 0.00 0.00 4.20
50 53 2.555325 TCTAGGTCGTTCGTCAATGTGT 59.445 45.455 0.00 0.00 0.00 3.72
81 84 8.928733 CCATGAAACTTTGAATACTGATTTTGG 58.071 33.333 0.00 0.00 0.00 3.28
97 100 8.090831 ACTGATTTTGGGAAGAGAAAAATAAGC 58.909 33.333 4.93 0.00 36.08 3.09
98 101 7.961351 TGATTTTGGGAAGAGAAAAATAAGCA 58.039 30.769 0.00 0.00 34.51 3.91
99 102 8.596293 TGATTTTGGGAAGAGAAAAATAAGCAT 58.404 29.630 0.00 0.00 34.51 3.79
100 103 8.782339 ATTTTGGGAAGAGAAAAATAAGCATG 57.218 30.769 0.00 0.00 33.02 4.06
101 104 5.329035 TGGGAAGAGAAAAATAAGCATGC 57.671 39.130 10.51 10.51 0.00 4.06
102 105 4.142403 TGGGAAGAGAAAAATAAGCATGCG 60.142 41.667 13.01 0.00 0.00 4.73
103 106 3.793492 GGAAGAGAAAAATAAGCATGCGC 59.207 43.478 13.01 0.00 38.99 6.09
104 107 3.056952 AGAGAAAAATAAGCATGCGCG 57.943 42.857 13.01 0.00 45.49 6.86
105 108 1.514402 GAGAAAAATAAGCATGCGCGC 59.486 47.619 27.26 27.26 45.49 6.86
144 147 1.087501 GGCATTTCTTCGGTCTGTCC 58.912 55.000 0.00 0.00 0.00 4.02
148 151 1.878953 TTTCTTCGGTCTGTCCTTGC 58.121 50.000 0.00 0.00 0.00 4.01
153 156 2.450609 TCGGTCTGTCCTTGCTAAAC 57.549 50.000 0.00 0.00 0.00 2.01
172 182 6.578919 GCTAAACAAGTCTGAAACAATGTAGC 59.421 38.462 0.00 0.00 32.03 3.58
183 193 0.171007 CAATGTAGCTGCCCAAACCG 59.829 55.000 0.00 0.00 0.00 4.44
205 215 3.605486 GTGCAATTTTCGCTAGAGCAAAG 59.395 43.478 1.89 0.00 42.21 2.77
206 216 2.595977 GCAATTTTCGCTAGAGCAAAGC 59.404 45.455 1.89 0.00 42.21 3.51
217 234 4.443598 GCTAGAGCAAAGCCCTACAATACT 60.444 45.833 0.00 0.00 41.59 2.12
222 239 5.783111 AGCAAAGCCCTACAATACTTTTTG 58.217 37.500 0.00 0.00 30.16 2.44
223 240 4.929211 GCAAAGCCCTACAATACTTTTTGG 59.071 41.667 0.00 0.00 30.16 3.28
224 241 5.279256 GCAAAGCCCTACAATACTTTTTGGA 60.279 40.000 0.00 0.00 30.16 3.53
228 245 6.970191 AGCCCTACAATACTTTTTGGAGTAT 58.030 36.000 0.00 0.00 42.99 2.12
256 273 9.933723 CCATCTCCATTTTGAGAGTAAAATTTT 57.066 29.630 8.75 8.75 44.19 1.82
259 276 9.142014 TCTCCATTTTGAGAGTAAAATTTTCCA 57.858 29.630 6.72 0.00 37.97 3.53
260 277 9.933723 CTCCATTTTGAGAGTAAAATTTTCCAT 57.066 29.630 6.72 0.00 37.97 3.41
261 278 9.927668 TCCATTTTGAGAGTAAAATTTTCCATC 57.072 29.630 6.72 4.47 37.97 3.51
262 279 8.863049 CCATTTTGAGAGTAAAATTTTCCATCG 58.137 33.333 6.72 0.00 37.97 3.84
264 281 9.981114 ATTTTGAGAGTAAAATTTTCCATCGTT 57.019 25.926 6.72 0.00 37.02 3.85
265 282 9.810545 TTTTGAGAGTAAAATTTTCCATCGTTT 57.189 25.926 6.72 0.00 0.00 3.60
330 353 4.183865 TCATTTGAATGCTACCTCGAGTG 58.816 43.478 12.31 5.52 36.36 3.51
368 391 2.594962 GCCACACTTGTCGACACCG 61.595 63.158 19.90 14.83 37.07 4.94
391 414 6.128445 CCGGAGCAGAAGCAATAATAATACAG 60.128 42.308 0.00 0.00 45.49 2.74
393 416 7.598869 CGGAGCAGAAGCAATAATAATACAGTA 59.401 37.037 0.00 0.00 45.49 2.74
463 489 1.519455 CACCTCGGAGTCATTCGGC 60.519 63.158 4.02 0.00 0.00 5.54
536 751 1.062525 GCGATGATGCCGAAACACC 59.937 57.895 0.00 0.00 0.00 4.16
547 762 3.194272 GAAACACCACAGCACGGGC 62.194 63.158 0.00 0.00 41.61 6.13
717 935 2.279517 CTGCCCGTCGATGCCTAC 60.280 66.667 0.00 0.00 0.00 3.18
718 936 2.758327 TGCCCGTCGATGCCTACT 60.758 61.111 0.00 0.00 0.00 2.57
719 937 1.452953 CTGCCCGTCGATGCCTACTA 61.453 60.000 0.00 0.00 0.00 1.82
720 938 1.007618 GCCCGTCGATGCCTACTAC 60.008 63.158 0.00 0.00 0.00 2.73
721 939 1.453762 GCCCGTCGATGCCTACTACT 61.454 60.000 0.00 0.00 0.00 2.57
722 940 1.888215 CCCGTCGATGCCTACTACTA 58.112 55.000 0.00 0.00 0.00 1.82
723 941 1.805345 CCCGTCGATGCCTACTACTAG 59.195 57.143 0.00 0.00 0.00 2.57
724 942 1.197264 CCGTCGATGCCTACTACTAGC 59.803 57.143 0.00 0.00 0.00 3.42
725 943 2.144730 CGTCGATGCCTACTACTAGCT 58.855 52.381 0.00 0.00 0.00 3.32
726 944 2.158058 CGTCGATGCCTACTACTAGCTC 59.842 54.545 0.00 0.00 0.00 4.09
730 948 0.183014 TGCCTACTACTAGCTCGCCT 59.817 55.000 0.00 0.00 0.00 5.52
733 951 0.594110 CTACTACTAGCTCGCCTGCC 59.406 60.000 0.00 0.00 0.00 4.85
754 972 1.002274 AGGCTACAGTGGGCTAGCT 59.998 57.895 15.72 0.00 37.82 3.32
800 1018 2.203209 CGGCCTTCCATACTGCCC 60.203 66.667 0.00 0.00 40.87 5.36
809 1027 1.124477 CCATACTGCCCCCTCTCTCC 61.124 65.000 0.00 0.00 0.00 3.71
817 1035 0.998945 CCCCCTCTCTCCCTCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
818 1036 0.478507 CCCCTCTCTCCCTCTCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
819 1037 0.478507 CCCTCTCTCCCTCTCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
820 1038 0.478507 CCTCTCTCCCTCTCTCTCCC 59.521 65.000 0.00 0.00 0.00 4.30
821 1039 1.522900 CTCTCTCCCTCTCTCTCCCT 58.477 60.000 0.00 0.00 0.00 4.20
822 1040 1.852965 CTCTCTCCCTCTCTCTCCCTT 59.147 57.143 0.00 0.00 0.00 3.95
823 1041 1.568597 TCTCTCCCTCTCTCTCCCTTG 59.431 57.143 0.00 0.00 0.00 3.61
824 1042 0.032615 TCTCCCTCTCTCTCCCTTGC 60.033 60.000 0.00 0.00 0.00 4.01
825 1043 0.032217 CTCCCTCTCTCTCCCTTGCT 60.032 60.000 0.00 0.00 0.00 3.91
826 1044 0.032615 TCCCTCTCTCTCCCTTGCTC 60.033 60.000 0.00 0.00 0.00 4.26
842 1060 2.202492 TCGCTCGCTCGCTCTTTC 60.202 61.111 0.00 0.00 0.00 2.62
895 1113 3.777925 CCTCACTTCAACGCCGCG 61.778 66.667 12.14 12.14 0.00 6.46
979 1197 5.274718 CCGGCTCTCGCTATAAATATAGTG 58.725 45.833 12.67 12.67 44.25 2.74
980 1198 4.735822 CGGCTCTCGCTATAAATATAGTGC 59.264 45.833 13.65 8.50 43.19 4.40
983 1201 5.228220 GCTCTCGCTATAAATATAGTGCACG 59.772 44.000 12.01 7.25 43.19 5.34
986 1204 3.606777 CGCTATAAATATAGTGCACGCGT 59.393 43.478 5.58 5.58 39.18 6.01
996 1214 2.736995 GCACGCGTGTCCAGCTAA 60.737 61.111 36.80 0.00 0.00 3.09
1028 1246 1.342374 GCCATTGGAGGAGGTTCCATT 60.342 52.381 6.95 0.00 46.22 3.16
1032 1250 2.059756 TGGAGGAGGTTCCATTTCCT 57.940 50.000 0.00 0.00 42.24 3.36
1041 1259 5.066913 AGGTTCCATTTCCTCTCTGTTTT 57.933 39.130 0.00 0.00 0.00 2.43
1055 1273 5.597806 TCTCTGTTTTGCTCTAAACTTCGA 58.402 37.500 8.03 0.00 38.52 3.71
1056 1274 6.223852 TCTCTGTTTTGCTCTAAACTTCGAT 58.776 36.000 8.03 0.00 38.52 3.59
1061 1279 3.247006 TGCTCTAAACTTCGATCCACC 57.753 47.619 0.00 0.00 0.00 4.61
1063 1281 2.742204 GCTCTAAACTTCGATCCACCCC 60.742 54.545 0.00 0.00 0.00 4.95
1096 1314 4.379243 CCCAGCGTCGTTGCCTCT 62.379 66.667 3.21 0.00 34.65 3.69
1097 1315 2.811317 CCAGCGTCGTTGCCTCTC 60.811 66.667 3.21 0.00 34.65 3.20
1099 1317 1.373497 CAGCGTCGTTGCCTCTCTT 60.373 57.895 0.00 0.00 34.65 2.85
1100 1318 1.080434 AGCGTCGTTGCCTCTCTTC 60.080 57.895 0.00 0.00 34.65 2.87
1101 1319 2.095252 GCGTCGTTGCCTCTCTTCC 61.095 63.158 0.00 0.00 0.00 3.46
1102 1320 1.587054 CGTCGTTGCCTCTCTTCCT 59.413 57.895 0.00 0.00 0.00 3.36
1103 1321 0.456995 CGTCGTTGCCTCTCTTCCTC 60.457 60.000 0.00 0.00 0.00 3.71
1104 1322 0.892063 GTCGTTGCCTCTCTTCCTCT 59.108 55.000 0.00 0.00 0.00 3.69
1105 1323 1.273886 GTCGTTGCCTCTCTTCCTCTT 59.726 52.381 0.00 0.00 0.00 2.85
1106 1324 1.546476 TCGTTGCCTCTCTTCCTCTTC 59.454 52.381 0.00 0.00 0.00 2.87
1107 1325 1.548269 CGTTGCCTCTCTTCCTCTTCT 59.452 52.381 0.00 0.00 0.00 2.85
1108 1326 2.028567 CGTTGCCTCTCTTCCTCTTCTT 60.029 50.000 0.00 0.00 0.00 2.52
1109 1327 3.595173 GTTGCCTCTCTTCCTCTTCTTC 58.405 50.000 0.00 0.00 0.00 2.87
1110 1328 3.182887 TGCCTCTCTTCCTCTTCTTCT 57.817 47.619 0.00 0.00 0.00 2.85
1111 1329 3.515562 TGCCTCTCTTCCTCTTCTTCTT 58.484 45.455 0.00 0.00 0.00 2.52
1112 1330 3.513515 TGCCTCTCTTCCTCTTCTTCTTC 59.486 47.826 0.00 0.00 0.00 2.87
1113 1331 3.118775 GCCTCTCTTCCTCTTCTTCTTCC 60.119 52.174 0.00 0.00 0.00 3.46
1114 1332 4.352893 CCTCTCTTCCTCTTCTTCTTCCT 58.647 47.826 0.00 0.00 0.00 3.36
1115 1333 4.402474 CCTCTCTTCCTCTTCTTCTTCCTC 59.598 50.000 0.00 0.00 0.00 3.71
1116 1334 5.264395 CTCTCTTCCTCTTCTTCTTCCTCT 58.736 45.833 0.00 0.00 0.00 3.69
1117 1335 5.650283 TCTCTTCCTCTTCTTCTTCCTCTT 58.350 41.667 0.00 0.00 0.00 2.85
1118 1336 5.714806 TCTCTTCCTCTTCTTCTTCCTCTTC 59.285 44.000 0.00 0.00 0.00 2.87
1119 1337 5.650283 TCTTCCTCTTCTTCTTCCTCTTCT 58.350 41.667 0.00 0.00 0.00 2.85
1160 1378 3.936453 TCTTCTCTAGCTCGTTCTGTCTC 59.064 47.826 0.00 0.00 0.00 3.36
1202 1425 2.505672 TGGAGGTAAGGCATCCCATA 57.494 50.000 0.00 0.00 46.85 2.74
1214 1437 0.106519 ATCCCATACCAGTGCCAAGC 60.107 55.000 0.00 0.00 0.00 4.01
1217 1440 1.091771 CCATACCAGTGCCAAGCTCG 61.092 60.000 0.00 0.00 0.00 5.03
1263 1486 1.202604 TCCTTGTGGTCGGTCTGTTTC 60.203 52.381 0.00 0.00 34.23 2.78
1268 1491 0.105964 TGGTCGGTCTGTTTCTGGTG 59.894 55.000 0.00 0.00 0.00 4.17
1631 1860 2.580276 CGGCGGCCAGTTAAGGTA 59.420 61.111 20.71 0.00 0.00 3.08
1632 1861 1.520787 CGGCGGCCAGTTAAGGTAG 60.521 63.158 20.71 0.00 0.00 3.18
1633 1862 1.902556 GGCGGCCAGTTAAGGTAGA 59.097 57.895 15.62 0.00 0.00 2.59
1634 1863 0.179081 GGCGGCCAGTTAAGGTAGAG 60.179 60.000 15.62 0.00 0.00 2.43
1635 1864 0.810426 GCGGCCAGTTAAGGTAGAGC 60.810 60.000 2.24 0.00 0.00 4.09
1636 1865 0.535335 CGGCCAGTTAAGGTAGAGCA 59.465 55.000 2.24 0.00 0.00 4.26
1637 1866 1.739371 CGGCCAGTTAAGGTAGAGCAC 60.739 57.143 2.24 0.00 0.00 4.40
1638 1867 1.641577 GCCAGTTAAGGTAGAGCACG 58.358 55.000 0.00 0.00 0.00 5.34
1639 1868 1.641577 CCAGTTAAGGTAGAGCACGC 58.358 55.000 0.00 0.00 0.00 5.34
1661 1890 1.725164 CGTACGGCCTCAGAAAAGAAC 59.275 52.381 7.57 0.00 0.00 3.01
1695 1924 4.234574 GCTGGAACGGGTTTCTTTAATTG 58.765 43.478 0.00 0.00 34.26 2.32
1730 1959 5.172205 GGTTGGAACTTACTGACTGATCTC 58.828 45.833 0.00 0.00 0.00 2.75
1742 1976 4.644498 TGACTGATCTCTGTTTGAATGCA 58.356 39.130 0.00 0.00 0.00 3.96
1744 1978 4.008330 ACTGATCTCTGTTTGAATGCAGG 58.992 43.478 0.00 0.00 33.81 4.85
1748 1982 2.294233 TCTCTGTTTGAATGCAGGTTGC 59.706 45.455 0.00 0.00 45.29 4.17
1813 2047 1.899437 CGCCTGAAGCCCTCAACCTA 61.899 60.000 0.00 0.00 38.78 3.08
1832 2066 2.172483 ATCCCGTGCTGACCAGACAC 62.172 60.000 0.47 7.64 34.45 3.67
1834 2068 2.734723 CGTGCTGACCAGACACGG 60.735 66.667 24.92 14.44 45.69 4.94
1854 2118 0.950555 TCACTGGATGCTGCGTGTTC 60.951 55.000 0.00 0.00 0.00 3.18
1861 2125 0.391130 ATGCTGCGTGTTCATACCGT 60.391 50.000 0.00 0.00 0.00 4.83
1864 2128 0.921347 CTGCGTGTTCATACCGTAGC 59.079 55.000 0.00 0.00 29.69 3.58
1869 2133 3.360533 CGTGTTCATACCGTAGCAGTAG 58.639 50.000 0.00 0.00 0.00 2.57
1876 2140 8.131100 TGTTCATACCGTAGCAGTAGTATTTAC 58.869 37.037 0.00 0.00 0.00 2.01
1882 2146 8.782339 ACCGTAGCAGTAGTATTTACATTTTT 57.218 30.769 0.00 0.00 0.00 1.94
1885 2149 9.685005 CGTAGCAGTAGTATTTACATTTTTCAC 57.315 33.333 0.00 0.00 0.00 3.18
1906 2170 6.411376 TCACTTTCACTTTCTCTTGTTGGTA 58.589 36.000 0.00 0.00 0.00 3.25
1908 2172 6.316390 CACTTTCACTTTCTCTTGTTGGTAGT 59.684 38.462 0.00 0.00 0.00 2.73
1909 2173 7.494625 CACTTTCACTTTCTCTTGTTGGTAGTA 59.505 37.037 0.00 0.00 0.00 1.82
1910 2174 7.711339 ACTTTCACTTTCTCTTGTTGGTAGTAG 59.289 37.037 0.00 0.00 0.00 2.57
1911 2175 6.726490 TCACTTTCTCTTGTTGGTAGTAGT 57.274 37.500 0.00 0.00 0.00 2.73
1914 2178 8.044908 TCACTTTCTCTTGTTGGTAGTAGTTTT 58.955 33.333 0.00 0.00 0.00 2.43
1916 2180 9.895138 ACTTTCTCTTGTTGGTAGTAGTTTTTA 57.105 29.630 0.00 0.00 0.00 1.52
1918 2182 9.895138 TTTCTCTTGTTGGTAGTAGTTTTTACT 57.105 29.630 0.00 0.00 0.00 2.24
1921 2185 8.801715 TCTTGTTGGTAGTAGTTTTTACTACG 57.198 34.615 14.76 4.43 46.53 3.51
1968 2297 3.404224 TTGTGCGATGTGGGTAAACTA 57.596 42.857 0.00 0.00 0.00 2.24
1970 2299 2.277084 GTGCGATGTGGGTAAACTAGG 58.723 52.381 0.00 0.00 0.00 3.02
1971 2300 1.296727 GCGATGTGGGTAAACTAGGC 58.703 55.000 0.00 0.00 0.00 3.93
1974 2303 3.541632 CGATGTGGGTAAACTAGGCATT 58.458 45.455 0.00 0.00 0.00 3.56
1976 2305 5.120399 CGATGTGGGTAAACTAGGCATTAA 58.880 41.667 0.00 0.00 0.00 1.40
1985 2314 7.184779 GGTAAACTAGGCATTAACATTTCGAC 58.815 38.462 0.00 0.00 0.00 4.20
1993 2322 5.220796 GGCATTAACATTTCGACCTTCTACC 60.221 44.000 0.00 0.00 0.00 3.18
1996 2325 3.611766 ACATTTCGACCTTCTACCCTG 57.388 47.619 0.00 0.00 0.00 4.45
1998 2327 3.326880 ACATTTCGACCTTCTACCCTGTT 59.673 43.478 0.00 0.00 0.00 3.16
2000 2329 3.396260 TTCGACCTTCTACCCTGTTTG 57.604 47.619 0.00 0.00 0.00 2.93
2002 2331 2.036733 TCGACCTTCTACCCTGTTTGTG 59.963 50.000 0.00 0.00 0.00 3.33
2004 2333 3.006110 CGACCTTCTACCCTGTTTGTGTA 59.994 47.826 0.00 0.00 0.00 2.90
2005 2334 4.501915 CGACCTTCTACCCTGTTTGTGTAA 60.502 45.833 0.00 0.00 0.00 2.41
2006 2335 5.557866 GACCTTCTACCCTGTTTGTGTAAT 58.442 41.667 0.00 0.00 0.00 1.89
2007 2336 6.572898 CGACCTTCTACCCTGTTTGTGTAATA 60.573 42.308 0.00 0.00 0.00 0.98
2020 2368 3.577667 TGTGTAATACGGTGAGGTTTCG 58.422 45.455 0.00 0.00 0.00 3.46
2023 2371 3.989167 TGTAATACGGTGAGGTTTCGTTG 59.011 43.478 0.00 0.00 38.19 4.10
2043 2391 1.291184 TGAATGCAACGTCTCTGCGG 61.291 55.000 6.25 0.00 42.97 5.69
2063 2411 2.599659 GTAGCACGTTGGTACCACTAC 58.400 52.381 16.04 17.68 43.41 2.73
2064 2412 0.319405 AGCACGTTGGTACCACTACC 59.681 55.000 16.04 2.30 42.83 3.18
2074 2422 4.164981 TGGTACCACTACCACTCTTCATT 58.835 43.478 11.60 0.00 46.53 2.57
2079 2427 3.452627 CCACTACCACTCTTCATTAGCCT 59.547 47.826 0.00 0.00 0.00 4.58
2082 2430 4.777896 ACTACCACTCTTCATTAGCCTGAA 59.222 41.667 0.00 0.00 34.14 3.02
2083 2431 4.640771 ACCACTCTTCATTAGCCTGAAA 57.359 40.909 0.00 0.00 34.86 2.69
2090 2438 3.829886 TCATTAGCCTGAAAAAGCACG 57.170 42.857 0.00 0.00 0.00 5.34
2099 2447 3.997021 CCTGAAAAAGCACGATGTCTACT 59.003 43.478 0.00 0.00 0.00 2.57
2100 2448 4.452455 CCTGAAAAAGCACGATGTCTACTT 59.548 41.667 0.00 0.00 0.00 2.24
2104 2453 5.358298 AAAAGCACGATGTCTACTTTTCC 57.642 39.130 0.00 0.00 36.14 3.13
2124 2473 5.356882 TCCGATCAAGTTTAAGTTGCAAG 57.643 39.130 0.00 1.94 0.00 4.01
2137 2486 0.308684 TTGCAAGCAAACGAGCTCTG 59.691 50.000 12.85 8.06 45.89 3.35
2141 2490 1.194098 CAAGCAAACGAGCTCTGACAG 59.806 52.381 12.85 0.00 45.89 3.51
2179 2537 2.259439 ACGAGAAGACACGGCGACT 61.259 57.895 16.62 7.07 34.68 4.18
2244 2608 0.807667 CGCCAGTCCACTGTATCAGC 60.808 60.000 5.99 1.12 42.27 4.26
2264 2628 0.751643 GACCGCAATAGGCAATGGGT 60.752 55.000 0.00 0.00 45.17 4.51
2350 3267 1.076332 GATACGTGGTGCAGTTGGAC 58.924 55.000 0.00 0.00 35.50 4.02
2403 3364 4.409342 CGCAGCGCAGAGATAGTT 57.591 55.556 11.47 0.00 0.00 2.24
2404 3365 2.211675 CGCAGCGCAGAGATAGTTC 58.788 57.895 11.47 0.00 0.00 3.01
2409 3370 0.248661 GCGCAGAGATAGTTCGAGCA 60.249 55.000 0.30 0.00 0.00 4.26
2411 3372 2.049959 CGCAGAGATAGTTCGAGCATG 58.950 52.381 1.01 0.00 0.00 4.06
2414 3375 3.637432 CAGAGATAGTTCGAGCATGGTC 58.363 50.000 15.01 15.01 0.00 4.02
2416 3377 3.701542 AGAGATAGTTCGAGCATGGTCAA 59.298 43.478 23.68 14.06 0.00 3.18
2417 3378 4.160439 AGAGATAGTTCGAGCATGGTCAAA 59.840 41.667 23.68 10.06 0.00 2.69
2418 3379 4.184629 AGATAGTTCGAGCATGGTCAAAC 58.815 43.478 23.68 21.17 0.00 2.93
2419 3380 1.523758 AGTTCGAGCATGGTCAAACC 58.476 50.000 21.79 8.51 39.22 3.27
2420 3381 0.165944 GTTCGAGCATGGTCAAACCG 59.834 55.000 23.68 10.80 42.58 4.44
2421 3382 0.250124 TTCGAGCATGGTCAAACCGT 60.250 50.000 23.68 0.00 42.58 4.83
2422 3383 0.669318 TCGAGCATGGTCAAACCGTC 60.669 55.000 23.68 0.00 42.58 4.79
2423 3384 0.948623 CGAGCATGGTCAAACCGTCA 60.949 55.000 23.68 0.00 42.58 4.35
2424 3385 0.517316 GAGCATGGTCAAACCGTCAC 59.483 55.000 19.79 0.00 42.58 3.67
2425 3386 0.179032 AGCATGGTCAAACCGTCACA 60.179 50.000 0.00 0.00 42.58 3.58
2426 3387 0.238289 GCATGGTCAAACCGTCACAG 59.762 55.000 0.00 0.00 42.58 3.66
2427 3388 1.877637 CATGGTCAAACCGTCACAGA 58.122 50.000 0.00 0.00 42.58 3.41
2428 3389 1.531149 CATGGTCAAACCGTCACAGAC 59.469 52.381 0.00 0.00 42.58 3.51
2438 3399 3.588277 GTCACAGACGGAAAGCTCA 57.412 52.632 0.00 0.00 0.00 4.26
2439 3400 2.086054 GTCACAGACGGAAAGCTCAT 57.914 50.000 0.00 0.00 0.00 2.90
2440 3401 1.728971 GTCACAGACGGAAAGCTCATG 59.271 52.381 0.00 0.00 0.00 3.07
2441 3402 1.618343 TCACAGACGGAAAGCTCATGA 59.382 47.619 0.00 0.00 0.00 3.07
2442 3403 1.998315 CACAGACGGAAAGCTCATGAG 59.002 52.381 18.84 18.84 0.00 2.90
2452 3413 4.233635 CTCATGAGCTTGCGCGGC 62.234 66.667 10.38 15.77 42.32 6.53
2457 3418 4.543084 GAGCTTGCGCGGCCATTC 62.543 66.667 19.03 8.82 42.32 2.67
2460 3421 3.443045 CTTGCGCGGCCATTCCTT 61.443 61.111 8.83 0.00 0.00 3.36
2461 3422 3.401243 CTTGCGCGGCCATTCCTTC 62.401 63.158 8.83 0.00 0.00 3.46
2464 3425 3.204827 CGCGGCCATTCCTTCCTG 61.205 66.667 2.24 0.00 0.00 3.86
2465 3426 2.830370 GCGGCCATTCCTTCCTGG 60.830 66.667 2.24 0.00 35.53 4.45
2483 3444 2.051345 CTGCGTGCCCGTGTTTTC 60.051 61.111 0.00 0.00 36.15 2.29
2489 3450 2.251371 GCCCGTGTTTTCAGCGTC 59.749 61.111 0.00 0.00 0.00 5.19
2490 3451 2.539338 GCCCGTGTTTTCAGCGTCA 61.539 57.895 0.00 0.00 0.00 4.35
2492 3453 0.378962 CCCGTGTTTTCAGCGTCAAA 59.621 50.000 0.00 0.00 0.00 2.69
2494 3455 1.596954 CCGTGTTTTCAGCGTCAAAGG 60.597 52.381 0.00 0.00 0.00 3.11
2495 3456 1.596954 CGTGTTTTCAGCGTCAAAGGG 60.597 52.381 0.00 0.00 0.00 3.95
2498 3459 2.494073 TGTTTTCAGCGTCAAAGGGTTT 59.506 40.909 0.00 0.00 0.00 3.27
2499 3460 3.056465 TGTTTTCAGCGTCAAAGGGTTTT 60.056 39.130 0.00 0.00 0.00 2.43
2500 3461 2.861462 TTCAGCGTCAAAGGGTTTTG 57.139 45.000 0.00 0.00 44.03 2.44
2600 5309 0.302890 GGCGTGCGATTCAAGATGAG 59.697 55.000 0.00 0.00 0.00 2.90
2602 5311 0.302890 CGTGCGATTCAAGATGAGGC 59.697 55.000 0.00 0.00 0.00 4.70
2603 5312 0.302890 GTGCGATTCAAGATGAGGCG 59.697 55.000 0.00 0.00 0.00 5.52
2604 5313 0.175531 TGCGATTCAAGATGAGGCGA 59.824 50.000 7.72 0.00 30.06 5.54
2605 5314 0.857935 GCGATTCAAGATGAGGCGAG 59.142 55.000 7.72 0.00 30.06 5.03
2606 5315 1.495878 CGATTCAAGATGAGGCGAGG 58.504 55.000 0.00 0.00 30.06 4.63
2607 5316 1.871408 CGATTCAAGATGAGGCGAGGG 60.871 57.143 0.00 0.00 30.06 4.30
2608 5317 0.471617 ATTCAAGATGAGGCGAGGGG 59.528 55.000 0.00 0.00 0.00 4.79
2609 5318 0.909610 TTCAAGATGAGGCGAGGGGT 60.910 55.000 0.00 0.00 0.00 4.95
2610 5319 0.909610 TCAAGATGAGGCGAGGGGTT 60.910 55.000 0.00 0.00 0.00 4.11
2611 5320 0.462759 CAAGATGAGGCGAGGGGTTC 60.463 60.000 0.00 0.00 0.00 3.62
2612 5321 0.909610 AAGATGAGGCGAGGGGTTCA 60.910 55.000 0.00 0.00 0.00 3.18
2670 5392 2.824489 TCGAGAGATGAGCGCCGT 60.824 61.111 2.29 0.00 33.31 5.68
2671 5393 2.103143 CGAGAGATGAGCGCCGTT 59.897 61.111 2.29 0.00 0.00 4.44
2672 5394 2.226896 CGAGAGATGAGCGCCGTTG 61.227 63.158 2.29 0.00 0.00 4.10
2724 5481 1.527696 GAAGCGTTCACATGATTGCG 58.472 50.000 0.00 0.00 32.14 4.85
2725 5482 1.128507 GAAGCGTTCACATGATTGCGA 59.871 47.619 0.00 0.00 32.14 5.10
2741 5498 1.575922 CGACGGTGACTTGGACGTA 59.424 57.895 0.00 0.00 39.95 3.57
2743 5500 0.311790 GACGGTGACTTGGACGTACA 59.688 55.000 0.00 0.00 39.95 2.90
2825 6842 9.231297 TCTTTGGATCGAAGTTCAAGAAAATAT 57.769 29.630 3.32 0.00 0.00 1.28
2905 6924 2.115266 CTGTTGCCCTCCGGGTTT 59.885 61.111 0.00 0.00 46.51 3.27
2906 6925 1.530655 CTGTTGCCCTCCGGGTTTT 60.531 57.895 0.00 0.00 46.51 2.43
2907 6926 1.524008 CTGTTGCCCTCCGGGTTTTC 61.524 60.000 0.00 0.00 46.51 2.29
2960 6994 4.819761 GGACGCTCGCATCCTGCA 62.820 66.667 0.00 0.00 45.36 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.685924 TGACGAACGACCTAGAAAAACTT 58.314 39.130 0.14 0.00 0.00 2.66
23 24 4.311816 TGACGAACGACCTAGAAAAACT 57.688 40.909 0.14 0.00 0.00 2.66
30 33 2.942710 ACACATTGACGAACGACCTAG 58.057 47.619 0.14 0.00 0.00 3.02
32 35 2.234300 AACACATTGACGAACGACCT 57.766 45.000 0.14 0.00 0.00 3.85
33 36 2.285756 TGAAACACATTGACGAACGACC 59.714 45.455 0.14 0.00 0.00 4.79
35 38 2.285756 GGTGAAACACATTGACGAACGA 59.714 45.455 0.14 0.00 39.98 3.85
36 39 2.031068 TGGTGAAACACATTGACGAACG 59.969 45.455 0.00 0.00 39.98 3.95
50 53 8.231692 TCAGTATTCAAAGTTTCATGGTGAAA 57.768 30.769 1.24 1.24 43.37 2.69
71 74 8.090831 GCTTATTTTTCTCTTCCCAAAATCAGT 58.909 33.333 0.00 0.00 33.28 3.41
81 84 3.793492 GCGCATGCTTATTTTTCTCTTCC 59.207 43.478 17.13 0.00 38.39 3.46
104 107 2.012902 TTTAGTCCTCCGGCGCTAGC 62.013 60.000 7.64 4.06 44.18 3.42
105 108 0.458669 TTTTAGTCCTCCGGCGCTAG 59.541 55.000 7.64 1.17 0.00 3.42
117 120 4.695928 AGACCGAAGAAATGCCTTTTAGTC 59.304 41.667 0.00 0.00 0.00 2.59
148 151 7.800380 CAGCTACATTGTTTCAGACTTGTTTAG 59.200 37.037 0.00 0.00 31.08 1.85
153 156 4.470462 GCAGCTACATTGTTTCAGACTTG 58.530 43.478 0.00 0.00 0.00 3.16
159 162 2.284754 TGGGCAGCTACATTGTTTCA 57.715 45.000 0.00 0.00 0.00 2.69
163 166 1.256812 GGTTTGGGCAGCTACATTGT 58.743 50.000 0.00 0.00 0.00 2.71
164 167 0.171007 CGGTTTGGGCAGCTACATTG 59.829 55.000 0.00 0.00 0.00 2.82
165 168 0.251165 ACGGTTTGGGCAGCTACATT 60.251 50.000 0.00 0.00 0.00 2.71
166 169 0.960364 CACGGTTTGGGCAGCTACAT 60.960 55.000 0.00 0.00 0.00 2.29
167 170 1.599518 CACGGTTTGGGCAGCTACA 60.600 57.895 0.00 0.00 0.00 2.74
168 171 2.978018 GCACGGTTTGGGCAGCTAC 61.978 63.158 0.00 0.00 0.00 3.58
172 182 0.249826 AAATTGCACGGTTTGGGCAG 60.250 50.000 0.00 0.00 38.97 4.85
183 193 2.900122 TGCTCTAGCGAAAATTGCAC 57.100 45.000 0.00 0.00 45.83 4.57
205 215 7.640597 AATACTCCAAAAAGTATTGTAGGGC 57.359 36.000 8.15 0.00 45.99 5.19
223 240 7.278875 ACTCTCAAAATGGAGATGGAATACTC 58.721 38.462 0.00 0.00 42.69 2.59
224 241 7.205515 ACTCTCAAAATGGAGATGGAATACT 57.794 36.000 0.00 0.00 42.69 2.12
228 245 8.884124 ATTTTACTCTCAAAATGGAGATGGAA 57.116 30.769 0.00 0.00 42.69 3.53
234 251 9.933723 ATGGAAAATTTTACTCTCAAAATGGAG 57.066 29.630 14.21 0.00 37.97 3.86
236 253 8.863049 CGATGGAAAATTTTACTCTCAAAATGG 58.137 33.333 14.21 0.00 37.97 3.16
256 273 7.342769 TGCTCTTAACTCTATAAACGATGGA 57.657 36.000 0.00 0.00 0.00 3.41
258 275 7.867909 TGGATGCTCTTAACTCTATAAACGATG 59.132 37.037 0.00 0.00 0.00 3.84
259 276 7.952671 TGGATGCTCTTAACTCTATAAACGAT 58.047 34.615 0.00 0.00 0.00 3.73
260 277 7.342769 TGGATGCTCTTAACTCTATAAACGA 57.657 36.000 0.00 0.00 0.00 3.85
261 278 7.306051 CGTTGGATGCTCTTAACTCTATAAACG 60.306 40.741 0.00 0.00 0.00 3.60
262 279 7.491696 ACGTTGGATGCTCTTAACTCTATAAAC 59.508 37.037 0.00 0.00 0.00 2.01
264 281 7.108841 ACGTTGGATGCTCTTAACTCTATAA 57.891 36.000 0.00 0.00 0.00 0.98
265 282 6.710597 ACGTTGGATGCTCTTAACTCTATA 57.289 37.500 0.00 0.00 0.00 1.31
266 283 5.599999 ACGTTGGATGCTCTTAACTCTAT 57.400 39.130 0.00 0.00 0.00 1.98
330 353 2.464865 CTCGGAATCTCGGATTGTGTC 58.535 52.381 4.18 0.00 0.00 3.67
368 391 7.736447 ACTGTATTATTATTGCTTCTGCTCC 57.264 36.000 0.00 0.00 40.48 4.70
391 414 3.582780 ACCGCAAGCTTTGTACTACTAC 58.417 45.455 0.00 0.00 0.00 2.73
393 416 2.833631 ACCGCAAGCTTTGTACTACT 57.166 45.000 0.00 0.00 0.00 2.57
443 466 0.458543 CCGAATGACTCCGAGGTGTG 60.459 60.000 1.17 0.00 0.00 3.82
682 899 1.375268 GAGCAGTGCCTGTCTGTCC 60.375 63.158 12.58 0.00 35.60 4.02
684 901 1.370437 CAGAGCAGTGCCTGTCTGT 59.630 57.895 19.63 0.00 36.20 3.41
686 903 2.346739 GCAGAGCAGTGCCTGTCT 59.653 61.111 25.04 15.03 37.49 3.41
696 914 4.819761 GCATCGACGGGCAGAGCA 62.820 66.667 7.41 0.00 0.00 4.26
717 935 2.333225 CGGCAGGCGAGCTAGTAG 59.667 66.667 11.78 0.00 34.17 2.57
718 936 3.900892 GCGGCAGGCGAGCTAGTA 61.901 66.667 22.52 0.00 34.17 1.82
733 951 2.635229 CTAGCCCACTGTAGCCTGCG 62.635 65.000 0.00 0.00 0.00 5.18
747 965 1.680522 TAGGAGCACTGCAGCTAGCC 61.681 60.000 15.27 10.84 46.75 3.93
748 966 0.529555 GTAGGAGCACTGCAGCTAGC 60.530 60.000 15.27 15.75 46.75 3.42
754 972 3.390521 CGGGGTAGGAGCACTGCA 61.391 66.667 3.30 0.00 32.86 4.41
800 1018 0.478507 GGAGAGAGAGGGAGAGAGGG 59.521 65.000 0.00 0.00 0.00 4.30
809 1027 2.015227 GCGAGCAAGGGAGAGAGAGG 62.015 65.000 0.00 0.00 0.00 3.69
817 1035 4.135153 GAGCGAGCGAGCAAGGGA 62.135 66.667 9.01 0.00 40.15 4.20
823 1041 4.845705 AAGAGCGAGCGAGCGAGC 62.846 66.667 9.12 9.12 43.00 5.03
824 1042 2.202544 AAAGAGCGAGCGAGCGAG 60.203 61.111 1.41 0.00 43.00 5.03
825 1043 2.202492 GAAAGAGCGAGCGAGCGA 60.202 61.111 1.41 0.00 43.00 4.93
826 1044 2.202544 AGAAAGAGCGAGCGAGCG 60.203 61.111 0.00 0.00 43.00 5.03
919 1137 4.742201 CCACGCCGGTCAGAGTGG 62.742 72.222 16.30 16.30 46.52 4.00
960 1178 5.228220 GCGTGCACTATATTTATAGCGAGAG 59.772 44.000 16.19 0.00 39.36 3.20
979 1197 2.736995 TTAGCTGGACACGCGTGC 60.737 61.111 37.35 28.01 0.00 5.34
980 1198 2.380410 GGTTAGCTGGACACGCGTG 61.380 63.158 35.99 35.99 0.00 5.34
983 1201 2.391389 GCTGGTTAGCTGGACACGC 61.391 63.158 0.00 0.00 46.57 5.34
996 1214 3.988678 AATGGCTGGCTGGCTGGT 61.989 61.111 18.27 2.84 42.34 4.00
1028 1246 5.930135 AGTTTAGAGCAAAACAGAGAGGAA 58.070 37.500 10.67 0.00 40.97 3.36
1032 1250 5.597806 TCGAAGTTTAGAGCAAAACAGAGA 58.402 37.500 10.67 5.08 40.97 3.10
1041 1259 2.093658 GGGTGGATCGAAGTTTAGAGCA 60.094 50.000 0.00 0.00 0.00 4.26
1085 1303 0.892063 AGAGGAAGAGAGGCAACGAC 59.108 55.000 0.00 0.00 46.39 4.34
1087 1305 1.548269 AGAAGAGGAAGAGAGGCAACG 59.452 52.381 0.00 0.00 46.39 4.10
1088 1306 3.260632 AGAAGAAGAGGAAGAGAGGCAAC 59.739 47.826 0.00 0.00 0.00 4.17
1096 1314 5.650283 AGAAGAGGAAGAAGAAGAGGAAGA 58.350 41.667 0.00 0.00 0.00 2.87
1097 1315 6.211384 AGAAGAAGAGGAAGAAGAAGAGGAAG 59.789 42.308 0.00 0.00 0.00 3.46
1099 1317 5.650283 AGAAGAAGAGGAAGAAGAAGAGGA 58.350 41.667 0.00 0.00 0.00 3.71
1100 1318 6.211384 AGAAGAAGAAGAGGAAGAAGAAGAGG 59.789 42.308 0.00 0.00 0.00 3.69
1101 1319 7.232118 AGAAGAAGAAGAGGAAGAAGAAGAG 57.768 40.000 0.00 0.00 0.00 2.85
1102 1320 7.508977 AGAAGAAGAAGAAGAGGAAGAAGAAGA 59.491 37.037 0.00 0.00 0.00 2.87
1103 1321 7.670364 AGAAGAAGAAGAAGAGGAAGAAGAAG 58.330 38.462 0.00 0.00 0.00 2.85
1104 1322 7.610580 AGAAGAAGAAGAAGAGGAAGAAGAA 57.389 36.000 0.00 0.00 0.00 2.52
1105 1323 7.508977 AGAAGAAGAAGAAGAAGAGGAAGAAGA 59.491 37.037 0.00 0.00 0.00 2.87
1106 1324 7.670364 AGAAGAAGAAGAAGAAGAGGAAGAAG 58.330 38.462 0.00 0.00 0.00 2.85
1107 1325 7.610580 AGAAGAAGAAGAAGAAGAGGAAGAA 57.389 36.000 0.00 0.00 0.00 2.52
1108 1326 7.508977 AGAAGAAGAAGAAGAAGAAGAGGAAGA 59.491 37.037 0.00 0.00 0.00 2.87
1109 1327 7.670364 AGAAGAAGAAGAAGAAGAAGAGGAAG 58.330 38.462 0.00 0.00 0.00 3.46
1110 1328 7.610580 AGAAGAAGAAGAAGAAGAAGAGGAA 57.389 36.000 0.00 0.00 0.00 3.36
1111 1329 7.508977 AGAAGAAGAAGAAGAAGAAGAAGAGGA 59.491 37.037 0.00 0.00 0.00 3.71
1112 1330 7.670364 AGAAGAAGAAGAAGAAGAAGAAGAGG 58.330 38.462 0.00 0.00 0.00 3.69
1113 1331 9.196552 GAAGAAGAAGAAGAAGAAGAAGAAGAG 57.803 37.037 0.00 0.00 0.00 2.85
1114 1332 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
1115 1333 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
1116 1334 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
1117 1335 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
1118 1336 9.196552 GAGAAGAAGAAGAAGAAGAAGAAGAAG 57.803 37.037 0.00 0.00 0.00 2.85
1119 1337 8.923270 AGAGAAGAAGAAGAAGAAGAAGAAGAA 58.077 33.333 0.00 0.00 0.00 2.52
1202 1425 2.031163 GACGAGCTTGGCACTGGT 59.969 61.111 0.32 0.00 0.00 4.00
1214 1437 0.031314 CACCCATGATCCTCGACGAG 59.969 60.000 18.08 18.08 0.00 4.18
1217 1440 0.179073 CCACACCCATGATCCTCGAC 60.179 60.000 0.00 0.00 0.00 4.20
1263 1486 1.572085 CTCGCCTTCTGCAACACCAG 61.572 60.000 0.00 0.00 41.33 4.00
1268 1491 1.743252 CCTCCTCGCCTTCTGCAAC 60.743 63.158 0.00 0.00 41.33 4.17
1623 1852 0.989890 CGTGCGTGCTCTACCTTAAC 59.010 55.000 0.00 0.00 0.00 2.01
1624 1853 0.599558 ACGTGCGTGCTCTACCTTAA 59.400 50.000 0.00 0.00 0.00 1.85
1625 1854 1.131126 GTACGTGCGTGCTCTACCTTA 59.869 52.381 7.55 0.00 0.00 2.69
1635 1864 4.710695 TGAGGCCGTACGTGCGTG 62.711 66.667 24.09 16.18 0.00 5.34
1636 1865 4.415332 CTGAGGCCGTACGTGCGT 62.415 66.667 24.09 19.05 0.00 5.24
1637 1866 3.620300 TTCTGAGGCCGTACGTGCG 62.620 63.158 19.61 19.61 0.00 5.34
1638 1867 0.947180 TTTTCTGAGGCCGTACGTGC 60.947 55.000 15.21 16.33 0.00 5.34
1639 1868 1.068474 CTTTTCTGAGGCCGTACGTG 58.932 55.000 15.21 6.95 0.00 4.49
1650 1879 6.704493 AGCAGTAATTACACGTTCTTTTCTGA 59.296 34.615 17.65 0.00 0.00 3.27
1661 1890 2.347452 CCGTTCCAGCAGTAATTACACG 59.653 50.000 17.65 14.86 0.00 4.49
1695 1924 4.823790 AGTTCCAACCATTACGACAAAC 57.176 40.909 0.00 0.00 0.00 2.93
1730 1959 1.411394 CGCAACCTGCATTCAAACAG 58.589 50.000 0.00 0.00 45.36 3.16
1742 1976 3.602513 CTCCTCTGCTGCGCAACCT 62.603 63.158 13.05 0.00 38.41 3.50
1744 1978 3.123620 CCTCCTCTGCTGCGCAAC 61.124 66.667 13.05 7.98 38.41 4.17
1748 1982 4.527583 GGCTCCTCCTCTGCTGCG 62.528 72.222 0.00 0.00 0.00 5.18
1813 2047 1.913262 TGTCTGGTCAGCACGGGAT 60.913 57.895 0.00 0.00 0.00 3.85
1832 2066 3.190849 CGCAGCATCCAGTGACCG 61.191 66.667 0.00 0.00 0.00 4.79
1834 2068 1.230635 AACACGCAGCATCCAGTGAC 61.231 55.000 4.57 0.00 37.95 3.67
1836 2070 1.229975 TGAACACGCAGCATCCAGTG 61.230 55.000 0.00 0.00 40.17 3.66
1837 2071 0.321919 ATGAACACGCAGCATCCAGT 60.322 50.000 0.00 0.00 0.00 4.00
1838 2072 1.328680 GTATGAACACGCAGCATCCAG 59.671 52.381 0.00 0.00 0.00 3.86
1839 2073 1.368641 GTATGAACACGCAGCATCCA 58.631 50.000 0.00 0.00 0.00 3.41
1854 2118 9.472361 AAATGTAAATACTACTGCTACGGTATG 57.528 33.333 0.00 0.00 0.00 2.39
1876 2140 8.693542 ACAAGAGAAAGTGAAAGTGAAAAATG 57.306 30.769 0.00 0.00 0.00 2.32
1882 2146 5.253330 ACCAACAAGAGAAAGTGAAAGTGA 58.747 37.500 0.00 0.00 0.00 3.41
1885 2149 6.927294 ACTACCAACAAGAGAAAGTGAAAG 57.073 37.500 0.00 0.00 0.00 2.62
1906 2170 8.534778 CAACTCGAAAACGTAGTAAAAACTACT 58.465 33.333 12.45 0.00 45.00 2.57
1908 2172 7.704472 TCCAACTCGAAAACGTAGTAAAAACTA 59.296 33.333 0.00 0.00 45.00 2.24
1909 2173 6.534793 TCCAACTCGAAAACGTAGTAAAAACT 59.465 34.615 0.00 0.00 45.00 2.66
1910 2174 6.704819 TCCAACTCGAAAACGTAGTAAAAAC 58.295 36.000 0.00 0.00 45.00 2.43
1911 2175 6.534793 ACTCCAACTCGAAAACGTAGTAAAAA 59.465 34.615 0.00 0.00 45.00 1.94
1914 2178 5.186996 ACTCCAACTCGAAAACGTAGTAA 57.813 39.130 0.00 0.00 45.00 2.24
1917 2181 5.399604 AAAACTCCAACTCGAAAACGTAG 57.600 39.130 0.00 0.00 0.00 3.51
1918 2182 5.799681 AAAAACTCCAACTCGAAAACGTA 57.200 34.783 0.00 0.00 0.00 3.57
1919 2183 4.690184 AAAAACTCCAACTCGAAAACGT 57.310 36.364 0.00 0.00 0.00 3.99
1921 2185 8.851960 AAAGATAAAAACTCCAACTCGAAAAC 57.148 30.769 0.00 0.00 0.00 2.43
1953 2276 2.684001 TGCCTAGTTTACCCACATCG 57.316 50.000 0.00 0.00 0.00 3.84
1961 2284 7.065443 AGGTCGAAATGTTAATGCCTAGTTTAC 59.935 37.037 0.00 0.00 0.00 2.01
1962 2285 7.107542 AGGTCGAAATGTTAATGCCTAGTTTA 58.892 34.615 0.00 0.00 0.00 2.01
1964 2293 5.497474 AGGTCGAAATGTTAATGCCTAGTT 58.503 37.500 0.00 0.00 0.00 2.24
1968 2297 4.589908 AGAAGGTCGAAATGTTAATGCCT 58.410 39.130 0.00 0.00 0.00 4.75
1970 2299 5.220796 GGGTAGAAGGTCGAAATGTTAATGC 60.221 44.000 0.00 0.00 0.00 3.56
1971 2300 6.037172 CAGGGTAGAAGGTCGAAATGTTAATG 59.963 42.308 0.00 0.00 0.00 1.90
1974 2303 4.529377 ACAGGGTAGAAGGTCGAAATGTTA 59.471 41.667 0.00 0.00 0.00 2.41
1976 2305 2.904434 ACAGGGTAGAAGGTCGAAATGT 59.096 45.455 0.00 0.00 0.00 2.71
1985 2314 5.579511 CGTATTACACAAACAGGGTAGAAGG 59.420 44.000 0.00 0.00 37.43 3.46
1993 2322 3.682858 CCTCACCGTATTACACAAACAGG 59.317 47.826 0.00 0.00 0.00 4.00
1996 2325 5.613142 CGAAACCTCACCGTATTACACAAAC 60.613 44.000 0.00 0.00 0.00 2.93
1998 2327 3.989167 CGAAACCTCACCGTATTACACAA 59.011 43.478 0.00 0.00 0.00 3.33
2000 2329 3.578688 ACGAAACCTCACCGTATTACAC 58.421 45.455 0.00 0.00 34.52 2.90
2002 2331 3.989817 ACAACGAAACCTCACCGTATTAC 59.010 43.478 0.00 0.00 35.28 1.89
2004 2333 2.803956 CACAACGAAACCTCACCGTATT 59.196 45.455 0.00 0.00 35.28 1.89
2005 2334 2.036217 TCACAACGAAACCTCACCGTAT 59.964 45.455 0.00 0.00 35.28 3.06
2006 2335 1.408340 TCACAACGAAACCTCACCGTA 59.592 47.619 0.00 0.00 35.28 4.02
2007 2336 0.176219 TCACAACGAAACCTCACCGT 59.824 50.000 0.00 0.00 38.24 4.83
2020 2368 2.908634 CAGAGACGTTGCATTCACAAC 58.091 47.619 0.00 0.00 45.19 3.32
2023 2371 0.179240 CGCAGAGACGTTGCATTCAC 60.179 55.000 11.01 0.00 41.59 3.18
2043 2391 2.599659 GTAGTGGTACCAACGTGCTAC 58.400 52.381 18.31 18.49 36.52 3.58
2056 2404 3.197983 GGCTAATGAAGAGTGGTAGTGGT 59.802 47.826 0.00 0.00 0.00 4.16
2063 2411 5.620879 GCTTTTTCAGGCTAATGAAGAGTGG 60.621 44.000 0.00 0.00 40.16 4.00
2064 2412 5.048504 TGCTTTTTCAGGCTAATGAAGAGTG 60.049 40.000 0.00 0.00 40.16 3.51
2065 2413 5.048434 GTGCTTTTTCAGGCTAATGAAGAGT 60.048 40.000 0.00 0.00 40.16 3.24
2067 2415 4.083324 CGTGCTTTTTCAGGCTAATGAAGA 60.083 41.667 0.00 0.00 40.16 2.87
2068 2416 4.083324 TCGTGCTTTTTCAGGCTAATGAAG 60.083 41.667 0.00 0.00 40.16 3.02
2074 2422 2.742053 GACATCGTGCTTTTTCAGGCTA 59.258 45.455 0.00 0.00 0.00 3.93
2079 2427 6.371809 AAAAGTAGACATCGTGCTTTTTCA 57.628 33.333 0.00 0.00 36.38 2.69
2082 2430 4.084013 CGGAAAAGTAGACATCGTGCTTTT 60.084 41.667 0.00 0.00 40.63 2.27
2083 2431 3.432252 CGGAAAAGTAGACATCGTGCTTT 59.568 43.478 0.00 0.00 0.00 3.51
2090 2438 6.969828 AACTTGATCGGAAAAGTAGACATC 57.030 37.500 9.14 0.00 35.60 3.06
2099 2447 6.137794 TGCAACTTAAACTTGATCGGAAAA 57.862 33.333 0.00 0.00 0.00 2.29
2100 2448 5.759506 TGCAACTTAAACTTGATCGGAAA 57.240 34.783 0.00 0.00 0.00 3.13
2104 2453 4.536065 TGCTTGCAACTTAAACTTGATCG 58.464 39.130 0.00 0.00 0.00 3.69
2124 2473 1.495069 GCTGTCAGAGCTCGTTTGC 59.505 57.895 8.37 7.02 45.21 3.68
2137 2486 1.065358 GTGCAATGCAATGTGCTGTC 58.935 50.000 10.44 0.00 45.31 3.51
2141 2490 0.165079 GCAAGTGCAATGCAATGTGC 59.835 50.000 19.97 19.97 41.47 4.57
2167 2525 1.597027 CCCAAAAGTCGCCGTGTCT 60.597 57.895 0.00 0.00 0.00 3.41
2179 2537 2.203567 CCAAGCCCGGACCCAAAA 60.204 61.111 0.73 0.00 0.00 2.44
2244 2608 1.648720 CCATTGCCTATTGCGGTCG 59.351 57.895 0.00 0.00 45.60 4.79
2306 3223 1.832912 GGTACCAGGCCTCATCAGG 59.167 63.158 0.00 2.58 43.82 3.86
2350 3267 4.445545 GAGCCGGCTTCGCAAACG 62.446 66.667 33.34 0.00 42.01 3.60
2399 3360 2.695359 GGTTTGACCATGCTCGAACTA 58.305 47.619 17.07 0.00 38.42 2.24
2400 3361 1.523758 GGTTTGACCATGCTCGAACT 58.476 50.000 17.07 0.00 38.42 3.01
2401 3362 0.165944 CGGTTTGACCATGCTCGAAC 59.834 55.000 11.36 11.36 38.47 3.95
2402 3363 0.250124 ACGGTTTGACCATGCTCGAA 60.250 50.000 0.00 0.00 38.47 3.71
2403 3364 0.669318 GACGGTTTGACCATGCTCGA 60.669 55.000 0.00 0.00 38.47 4.04
2404 3365 0.948623 TGACGGTTTGACCATGCTCG 60.949 55.000 0.00 0.00 38.47 5.03
2409 3370 1.878953 GTCTGTGACGGTTTGACCAT 58.121 50.000 0.00 0.00 38.47 3.55
2420 3381 1.728971 CATGAGCTTTCCGTCTGTGAC 59.271 52.381 0.00 0.00 0.00 3.67
2421 3382 1.618343 TCATGAGCTTTCCGTCTGTGA 59.382 47.619 0.00 0.00 0.00 3.58
2422 3383 1.998315 CTCATGAGCTTTCCGTCTGTG 59.002 52.381 10.38 0.00 0.00 3.66
2423 3384 2.376808 CTCATGAGCTTTCCGTCTGT 57.623 50.000 10.38 0.00 0.00 3.41
2443 3404 3.401243 GAAGGAATGGCCGCGCAAG 62.401 63.158 8.75 0.00 43.43 4.01
2444 3405 3.439540 GAAGGAATGGCCGCGCAA 61.440 61.111 8.75 0.00 43.43 4.85
2447 3408 3.204827 CAGGAAGGAATGGCCGCG 61.205 66.667 0.00 0.00 43.43 6.46
2448 3409 2.830370 CCAGGAAGGAATGGCCGC 60.830 66.667 0.00 0.00 43.43 6.53
2452 3413 2.117156 CGCAGCCAGGAAGGAATGG 61.117 63.158 0.00 0.00 41.22 3.16
2453 3414 1.377725 ACGCAGCCAGGAAGGAATG 60.378 57.895 0.00 0.00 41.22 2.67
2454 3415 1.377725 CACGCAGCCAGGAAGGAAT 60.378 57.895 0.00 0.00 41.22 3.01
2455 3416 2.032528 CACGCAGCCAGGAAGGAA 59.967 61.111 0.00 0.00 41.22 3.36
2456 3417 4.704833 GCACGCAGCCAGGAAGGA 62.705 66.667 0.00 0.00 41.22 3.36
2465 3426 4.264638 AAAACACGGGCACGCAGC 62.265 61.111 9.12 0.00 46.04 5.25
2466 3427 2.051345 GAAAACACGGGCACGCAG 60.051 61.111 9.12 3.38 46.04 5.18
2467 3428 2.824489 TGAAAACACGGGCACGCA 60.824 55.556 9.12 0.00 46.04 5.24
2475 3436 1.596954 CCCTTTGACGCTGAAAACACG 60.597 52.381 0.00 0.00 0.00 4.49
2483 3444 1.600413 GCTCAAAACCCTTTGACGCTG 60.600 52.381 11.44 0.33 44.76 5.18
2489 3450 2.030451 GCTCAGAGCTCAAAACCCTTTG 60.030 50.000 17.77 1.73 42.88 2.77
2490 3451 2.234143 GCTCAGAGCTCAAAACCCTTT 58.766 47.619 17.77 0.00 38.45 3.11
2492 3453 0.321122 CGCTCAGAGCTCAAAACCCT 60.321 55.000 20.39 0.00 39.60 4.34
2494 3455 1.074752 CTCGCTCAGAGCTCAAAACC 58.925 55.000 20.39 0.00 40.54 3.27
2495 3456 1.074752 CCTCGCTCAGAGCTCAAAAC 58.925 55.000 20.39 1.46 45.54 2.43
2498 3459 0.895559 TGACCTCGCTCAGAGCTCAA 60.896 55.000 20.39 2.24 45.54 3.02
2499 3460 0.895559 TTGACCTCGCTCAGAGCTCA 60.896 55.000 20.39 13.68 45.54 4.26
2500 3461 0.244994 TTTGACCTCGCTCAGAGCTC 59.755 55.000 20.39 5.27 45.54 4.09
2501 3462 0.246086 CTTTGACCTCGCTCAGAGCT 59.754 55.000 20.39 0.72 45.54 4.09
2502 3463 0.739112 CCTTTGACCTCGCTCAGAGC 60.739 60.000 12.94 12.94 45.54 4.09
2503 3464 0.108424 CCCTTTGACCTCGCTCAGAG 60.108 60.000 0.00 0.00 46.44 3.35
2505 3466 0.390472 GACCCTTTGACCTCGCTCAG 60.390 60.000 0.00 0.00 0.00 3.35
2545 5248 2.025767 AATGGCCGCACAACAAGCAA 62.026 50.000 0.00 0.00 0.00 3.91
2546 5249 2.419057 GAATGGCCGCACAACAAGCA 62.419 55.000 0.00 0.00 0.00 3.91
2547 5250 1.734117 GAATGGCCGCACAACAAGC 60.734 57.895 0.00 0.00 0.00 4.01
2548 5251 1.080569 GGAATGGCCGCACAACAAG 60.081 57.895 0.00 0.00 0.00 3.16
2600 5309 2.046217 GAACCTGAACCCCTCGCC 60.046 66.667 0.00 0.00 0.00 5.54
2602 5311 0.324943 ATGTGAACCTGAACCCCTCG 59.675 55.000 0.00 0.00 0.00 4.63
2603 5312 1.630878 AGATGTGAACCTGAACCCCTC 59.369 52.381 0.00 0.00 0.00 4.30
2604 5313 1.352352 CAGATGTGAACCTGAACCCCT 59.648 52.381 0.00 0.00 32.37 4.79
2605 5314 1.351017 TCAGATGTGAACCTGAACCCC 59.649 52.381 0.00 0.00 36.58 4.95
2606 5315 2.704572 CTCAGATGTGAACCTGAACCC 58.295 52.381 0.00 0.00 38.75 4.11
2607 5316 2.079925 GCTCAGATGTGAACCTGAACC 58.920 52.381 0.00 0.00 38.75 3.62
2608 5317 1.728971 CGCTCAGATGTGAACCTGAAC 59.271 52.381 0.00 0.00 38.75 3.18
2609 5318 1.618343 TCGCTCAGATGTGAACCTGAA 59.382 47.619 0.00 0.00 38.75 3.02
2610 5319 1.203287 CTCGCTCAGATGTGAACCTGA 59.797 52.381 0.00 0.00 37.77 3.86
2611 5320 1.638133 CTCGCTCAGATGTGAACCTG 58.362 55.000 0.00 0.00 30.14 4.00
2612 5321 0.534412 CCTCGCTCAGATGTGAACCT 59.466 55.000 0.00 0.00 30.14 3.50
2667 5389 2.721231 CACACCAACAGGCAACGG 59.279 61.111 0.00 0.00 46.39 4.44
2670 5392 3.898509 GCGCACACCAACAGGCAA 61.899 61.111 0.30 0.00 0.00 4.52
2671 5393 4.873810 AGCGCACACCAACAGGCA 62.874 61.111 11.47 0.00 0.00 4.75
2672 5394 4.332637 CAGCGCACACCAACAGGC 62.333 66.667 11.47 0.00 0.00 4.85
2708 5464 0.853224 CGTCGCAATCATGTGAACGC 60.853 55.000 0.00 0.00 46.93 4.84
2724 5481 0.311790 TGTACGTCCAAGTCACCGTC 59.688 55.000 0.00 0.00 34.95 4.79
2725 5482 0.313043 CTGTACGTCCAAGTCACCGT 59.687 55.000 0.00 0.00 37.33 4.83
2759 6776 3.740832 CGGAAAATGCATATAGCTCGTCA 59.259 43.478 0.00 0.00 45.94 4.35
2825 6842 5.302059 CCGGTCTCTGATCCAAAGATTAGTA 59.698 44.000 0.00 0.00 37.39 1.82
2826 6843 4.100189 CCGGTCTCTGATCCAAAGATTAGT 59.900 45.833 0.00 0.00 37.39 2.24
2827 6844 4.342378 TCCGGTCTCTGATCCAAAGATTAG 59.658 45.833 0.00 0.00 37.44 1.73
2877 6896 3.372730 GCAACAGCATTCCCCGCA 61.373 61.111 0.00 0.00 0.00 5.69
2960 6994 2.300152 TCGTTGAGAAGAGCAGTTGGAT 59.700 45.455 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.