Multiple sequence alignment - TraesCS1A01G186700

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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 TraesCS1A01G186700 chr1A 100.000 2929 0 0 1 2929 337705179 337702251 0.000000e+00 5409.0
1 TraesCS1A01G186700 chr1A 82.295 305 54 0 1076 1380 337658527 337658223 6.220000e-67 265.0
2 TraesCS1A01G186700 chr1A 100.000 28 0 0 2797 2824 534970265 534970292 5.000000e-03 52.8
3 TraesCS1A01G186700 chr1B 92.025 2069 110 20 738 2792 349596476 349594449 0.000000e+00 2856.0
4 TraesCS1A01G186700 chr1B 88.804 393 27 9 100 487 349599502 349599122 1.590000e-127 466.0
5 TraesCS1A01G186700 chr1B 84.590 305 47 0 1076 1380 349547298 349546994 1.320000e-78 303.0
6 TraesCS1A01G186700 chr1B 84.762 105 13 2 853 955 349719454 349719351 5.160000e-18 102.0
7 TraesCS1A01G186700 chr1B 100.000 28 0 0 2797 2824 567468391 567468418 5.000000e-03 52.8
8 TraesCS1A01G186700 chr1D 93.235 1153 40 15 836 1970 262036051 262037183 0.000000e+00 1663.0
9 TraesCS1A01G186700 chr1D 84.783 460 38 9 56 514 262034519 262034947 1.610000e-117 433.0
10 TraesCS1A01G186700 chr1D 91.165 249 14 2 528 776 262034932 262035172 6.050000e-87 331.0
11 TraesCS1A01G186700 chr1D 82.623 305 53 0 1076 1380 262287840 262288144 1.340000e-68 270.0
12 TraesCS1A01G186700 chr1D 84.431 167 18 3 56 214 262032865 262033031 1.090000e-34 158.0
13 TraesCS1A01G186700 chr5D 85.531 311 42 2 1083 1390 25042331 25042641 3.640000e-84 322.0
14 TraesCS1A01G186700 chr5D 84.591 318 43 4 1079 1390 24974719 24974402 7.880000e-81 311.0
15 TraesCS1A01G186700 chr7D 83.143 350 51 6 1060 1402 22624675 22624327 2.190000e-81 313.0
16 TraesCS1A01G186700 chr7D 87.050 139 17 1 2792 2929 543585884 543586022 3.910000e-34 156.0
17 TraesCS1A01G186700 chr5B 84.395 314 43 4 1083 1390 17952369 17952682 1.320000e-78 303.0
18 TraesCS1A01G186700 chr4A 79.056 339 59 11 1495 1827 705544917 705544585 3.800000e-54 222.0
19 TraesCS1A01G186700 chr2B 82.203 236 31 7 2553 2780 567580652 567580420 2.980000e-45 193.0
20 TraesCS1A01G186700 chr2B 80.237 253 49 1 2527 2779 46722996 46722745 3.850000e-44 189.0
21 TraesCS1A01G186700 chr2A 86.286 175 23 1 2617 2791 625567485 625567312 3.850000e-44 189.0
22 TraesCS1A01G186700 chr2D 82.028 217 35 4 2566 2780 483069680 483069466 6.450000e-42 182.0
23 TraesCS1A01G186700 chr6B 80.408 245 40 8 2553 2792 93380862 93381103 2.320000e-41 180.0
24 TraesCS1A01G186700 chr6B 79.856 139 13 11 2792 2929 333269992 333270116 1.450000e-13 87.9
25 TraesCS1A01G186700 chr7B 80.349 229 42 3 2566 2792 264010732 264010505 1.400000e-38 171.0
26 TraesCS1A01G186700 chrUn 79.592 245 41 9 2553 2792 19495257 19495017 1.810000e-37 167.0
27 TraesCS1A01G186700 chrUn 85.417 144 18 3 2788 2929 10300401 10300543 2.350000e-31 147.0
28 TraesCS1A01G186700 chr3D 78.409 264 47 5 2536 2792 532771719 532771459 2.340000e-36 163.0
29 TraesCS1A01G186700 chr3B 84.058 138 21 1 2792 2929 795745316 795745452 6.590000e-27 132.0
30 TraesCS1A01G186700 chr3B 85.870 92 8 3 2792 2883 555065066 555065152 3.110000e-15 93.5
31 TraesCS1A01G186700 chr3B 86.538 52 3 3 1 50 390912429 390912380 1.000000e-03 54.7
32 TraesCS1A01G186700 chr6A 100.000 28 0 0 2797 2824 310254526 310254553 5.000000e-03 52.8


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 TraesCS1A01G186700 chr1A 337702251 337705179 2928 True 5409.00 5409 100.0000 1 2929 1 chr1A.!!$R2 2928
1 TraesCS1A01G186700 chr1B 349594449 349599502 5053 True 1661.00 2856 90.4145 100 2792 2 chr1B.!!$R3 2692
2 TraesCS1A01G186700 chr1D 262032865 262037183 4318 False 646.25 1663 88.4035 56 1970 4 chr1D.!!$F2 1914

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
358 1989 0.678048 CCTCTCCTCCCCGCAAAAAG 60.678 60.0 0.0 0.0 0.0 2.27 F
1038 5985 0.466189 AGCCACCAACCACACAAGAG 60.466 55.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1407 6354 1.127951 ACGAAACGAATCAACCGATGC 59.872 47.619 0.00 0.0 30.13 3.91 R
2867 7836 0.039472 TGCAGGTACGGGTACAGGTA 59.961 55.000 10.81 0.0 37.78 3.08 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
24 25 7.047460 AGATAAGGATGAACATGAAAATGCC 57.953 36.000 0.00 0.00 0.00 4.40
25 26 6.837568 AGATAAGGATGAACATGAAAATGCCT 59.162 34.615 0.00 0.00 0.00 4.75
26 27 5.750352 AAGGATGAACATGAAAATGCCTT 57.250 34.783 0.00 2.28 0.00 4.35
27 28 6.855763 AAGGATGAACATGAAAATGCCTTA 57.144 33.333 0.00 0.00 31.91 2.69
28 29 7.427989 AAGGATGAACATGAAAATGCCTTAT 57.572 32.000 0.00 0.00 31.91 1.73
29 30 7.047460 AGGATGAACATGAAAATGCCTTATC 57.953 36.000 0.00 0.00 0.00 1.75
30 31 6.837568 AGGATGAACATGAAAATGCCTTATCT 59.162 34.615 0.00 0.00 0.00 1.98
31 32 8.000709 AGGATGAACATGAAAATGCCTTATCTA 58.999 33.333 0.00 0.00 0.00 1.98
32 33 8.078596 GGATGAACATGAAAATGCCTTATCTAC 58.921 37.037 0.00 0.00 0.00 2.59
33 34 7.936496 TGAACATGAAAATGCCTTATCTACA 57.064 32.000 0.00 0.00 0.00 2.74
34 35 8.347004 TGAACATGAAAATGCCTTATCTACAA 57.653 30.769 0.00 0.00 0.00 2.41
35 36 8.801299 TGAACATGAAAATGCCTTATCTACAAA 58.199 29.630 0.00 0.00 0.00 2.83
36 37 9.807649 GAACATGAAAATGCCTTATCTACAAAT 57.192 29.630 0.00 0.00 0.00 2.32
37 38 9.590451 AACATGAAAATGCCTTATCTACAAATG 57.410 29.630 0.00 0.00 0.00 2.32
38 39 8.752187 ACATGAAAATGCCTTATCTACAAATGT 58.248 29.630 0.00 0.00 0.00 2.71
39 40 9.027129 CATGAAAATGCCTTATCTACAAATGTG 57.973 33.333 0.00 0.00 0.00 3.21
40 41 7.546358 TGAAAATGCCTTATCTACAAATGTGG 58.454 34.615 0.00 0.00 0.00 4.17
41 42 7.395772 TGAAAATGCCTTATCTACAAATGTGGA 59.604 33.333 1.96 1.96 39.83 4.02
42 43 6.949352 AATGCCTTATCTACAAATGTGGAG 57.051 37.500 5.83 0.00 38.91 3.86
50 51 4.569943 TCTACAAATGTGGAGAGAGTTGC 58.430 43.478 0.00 0.00 40.02 4.17
51 52 3.213206 ACAAATGTGGAGAGAGTTGCA 57.787 42.857 0.00 0.00 0.00 4.08
52 53 2.880890 ACAAATGTGGAGAGAGTTGCAC 59.119 45.455 0.00 0.00 39.55 4.57
59 60 3.194542 GTGGAGAGAGTTGCACATAGAGT 59.805 47.826 0.00 0.00 39.01 3.24
72 73 1.478510 CATAGAGTGCTGGGAAGTCGT 59.521 52.381 0.00 0.00 0.00 4.34
73 74 2.502142 TAGAGTGCTGGGAAGTCGTA 57.498 50.000 0.00 0.00 0.00 3.43
83 84 2.559668 TGGGAAGTCGTACCTTGTACTG 59.440 50.000 0.00 0.00 0.00 2.74
91 92 5.048434 AGTCGTACCTTGTACTGTCCTAAAC 60.048 44.000 0.00 0.00 0.00 2.01
173 182 5.881443 TGAACATCATGCATGTCACTAATCA 59.119 36.000 25.43 17.30 45.77 2.57
176 185 6.296803 ACATCATGCATGTCACTAATCAGAT 58.703 36.000 25.43 5.02 42.62 2.90
177 186 7.447594 ACATCATGCATGTCACTAATCAGATA 58.552 34.615 25.43 1.99 42.62 1.98
210 219 7.254137 CGTTATCTCCTCGAATGTGATATCAT 58.746 38.462 9.02 0.00 0.00 2.45
350 1981 1.382009 GGTCAGACCTCTCCTCCCC 60.382 68.421 12.94 0.00 34.73 4.81
356 1987 1.838073 GACCTCTCCTCCCCGCAAAA 61.838 60.000 0.00 0.00 0.00 2.44
357 1988 1.378762 CCTCTCCTCCCCGCAAAAA 59.621 57.895 0.00 0.00 0.00 1.94
358 1989 0.678048 CCTCTCCTCCCCGCAAAAAG 60.678 60.000 0.00 0.00 0.00 2.27
389 2020 2.043992 TCAAACCTCTCCTCCAAACGA 58.956 47.619 0.00 0.00 0.00 3.85
399 2030 4.158025 TCTCCTCCAAACGATGTTCTACTC 59.842 45.833 0.00 0.00 0.00 2.59
403 2034 5.107065 CCTCCAAACGATGTTCTACTCAAAC 60.107 44.000 0.00 0.00 0.00 2.93
506 2138 6.237313 CCTCTTAACGGAGGTAAAGTTTTG 57.763 41.667 0.00 0.00 45.65 2.44
507 2139 5.993441 CCTCTTAACGGAGGTAAAGTTTTGA 59.007 40.000 0.00 0.00 45.65 2.69
508 2140 6.147328 CCTCTTAACGGAGGTAAAGTTTTGAG 59.853 42.308 0.00 0.00 45.65 3.02
509 2141 5.993441 TCTTAACGGAGGTAAAGTTTTGAGG 59.007 40.000 0.00 0.00 0.00 3.86
510 2142 4.426736 AACGGAGGTAAAGTTTTGAGGA 57.573 40.909 0.00 0.00 0.00 3.71
511 2143 4.426736 ACGGAGGTAAAGTTTTGAGGAA 57.573 40.909 0.00 0.00 0.00 3.36
512 2144 4.981812 ACGGAGGTAAAGTTTTGAGGAAT 58.018 39.130 0.00 0.00 0.00 3.01
513 2145 6.117975 ACGGAGGTAAAGTTTTGAGGAATA 57.882 37.500 0.00 0.00 0.00 1.75
514 2146 6.718294 ACGGAGGTAAAGTTTTGAGGAATAT 58.282 36.000 0.00 0.00 0.00 1.28
515 2147 6.822170 ACGGAGGTAAAGTTTTGAGGAATATC 59.178 38.462 0.00 0.00 0.00 1.63
516 2148 6.821665 CGGAGGTAAAGTTTTGAGGAATATCA 59.178 38.462 0.00 0.00 0.00 2.15
517 2149 7.335924 CGGAGGTAAAGTTTTGAGGAATATCAA 59.664 37.037 0.00 0.00 37.41 2.57
518 2150 8.459635 GGAGGTAAAGTTTTGAGGAATATCAAC 58.540 37.037 0.00 0.00 38.87 3.18
519 2151 8.934023 AGGTAAAGTTTTGAGGAATATCAACA 57.066 30.769 0.00 0.00 38.87 3.33
520 2152 9.362151 AGGTAAAGTTTTGAGGAATATCAACAA 57.638 29.630 0.00 0.00 38.87 2.83
521 2153 9.406828 GGTAAAGTTTTGAGGAATATCAACAAC 57.593 33.333 0.00 0.00 38.87 3.32
522 2154 9.959749 GTAAAGTTTTGAGGAATATCAACAACA 57.040 29.630 0.00 0.00 38.87 3.33
524 2156 8.871686 AAGTTTTGAGGAATATCAACAACAAC 57.128 30.769 12.53 0.00 38.87 3.32
525 2157 8.006298 AGTTTTGAGGAATATCAACAACAACA 57.994 30.769 12.53 0.00 38.87 3.33
526 2158 8.474025 AGTTTTGAGGAATATCAACAACAACAA 58.526 29.630 12.53 0.00 38.87 2.83
657 2289 8.682128 TCTGTTTGATCCAAATTAATTAACGC 57.318 30.769 0.01 0.00 35.74 4.84
695 2346 8.703604 TGAATCGAAGAGAGTATTTAGTTTGG 57.296 34.615 0.00 0.00 43.63 3.28
716 2367 3.203716 GGTTATCTCCGGTCCATTTCAC 58.796 50.000 0.00 0.00 0.00 3.18
717 2368 3.118371 GGTTATCTCCGGTCCATTTCACT 60.118 47.826 0.00 0.00 0.00 3.41
718 2369 2.990066 ATCTCCGGTCCATTTCACTC 57.010 50.000 0.00 0.00 0.00 3.51
719 2370 1.938585 TCTCCGGTCCATTTCACTCT 58.061 50.000 0.00 0.00 0.00 3.24
720 2371 2.257207 TCTCCGGTCCATTTCACTCTT 58.743 47.619 0.00 0.00 0.00 2.85
721 2372 2.233922 TCTCCGGTCCATTTCACTCTTC 59.766 50.000 0.00 0.00 0.00 2.87
722 2373 1.974957 TCCGGTCCATTTCACTCTTCA 59.025 47.619 0.00 0.00 0.00 3.02
889 5835 3.552890 GGTTCCTGAATCAACTTGTTGCC 60.553 47.826 8.48 2.14 0.00 4.52
973 5920 4.683832 GCTTCTAGGCCATATATACACCG 58.316 47.826 5.01 0.00 0.00 4.94
974 5921 4.683832 CTTCTAGGCCATATATACACCGC 58.316 47.826 5.01 0.00 0.00 5.68
975 5922 3.977312 TCTAGGCCATATATACACCGCT 58.023 45.455 5.01 0.00 0.00 5.52
976 5923 3.952323 TCTAGGCCATATATACACCGCTC 59.048 47.826 5.01 0.00 0.00 5.03
977 5924 1.831736 AGGCCATATATACACCGCTCC 59.168 52.381 5.01 0.00 0.00 4.70
978 5925 1.134491 GGCCATATATACACCGCTCCC 60.134 57.143 0.00 0.00 0.00 4.30
979 5926 1.470979 GCCATATATACACCGCTCCCG 60.471 57.143 0.00 0.00 0.00 5.14
1038 5985 0.466189 AGCCACCAACCACACAAGAG 60.466 55.000 0.00 0.00 0.00 2.85
1122 6069 4.736896 AGCCCGTTCGTCCTTCGC 62.737 66.667 0.00 0.00 39.67 4.70
1126 6073 3.170585 CGTTCGTCCTTCGCGTCC 61.171 66.667 5.77 0.00 39.67 4.79
1284 6231 1.517257 GTCGTCGGTCATCCTGCAG 60.517 63.158 6.78 6.78 0.00 4.41
1403 6350 4.365723 GGCACGGTATTATATACATCCCG 58.634 47.826 0.00 0.00 39.75 5.14
1404 6351 4.365723 GCACGGTATTATATACATCCCGG 58.634 47.826 0.00 0.00 38.27 5.73
1405 6352 4.365723 CACGGTATTATATACATCCCGGC 58.634 47.826 0.00 0.00 38.27 6.13
1406 6353 3.385755 ACGGTATTATATACATCCCGGCC 59.614 47.826 0.00 0.00 38.27 6.13
1407 6354 3.551454 CGGTATTATATACATCCCGGCCG 60.551 52.174 21.04 21.04 0.00 6.13
1434 6381 3.966218 GGTTGATTCGTTTCGTTTGAGTG 59.034 43.478 0.00 0.00 0.00 3.51
1482 6430 0.931702 CCGCGCGGTTTTGTGATATA 59.068 50.000 39.71 0.00 0.00 0.86
1516 6464 2.049802 TCGTGAAAGCGTCGTCCC 60.050 61.111 0.00 0.00 0.00 4.46
1570 6518 1.544825 CGAGGGGAAGAAGCAGGTGA 61.545 60.000 0.00 0.00 0.00 4.02
1620 6568 1.142097 GAGGGACTGCTCTAACGGC 59.858 63.158 0.00 0.00 41.55 5.68
1635 6583 2.962569 GGCAAACCCTTCTTCGGC 59.037 61.111 0.00 0.00 0.00 5.54
1716 6664 1.140816 GCGATAAGATGAAGGGCGTC 58.859 55.000 0.00 0.00 0.00 5.19
1728 6676 4.913126 GGCGTCAAGACCTTCGAT 57.087 55.556 0.00 0.00 0.00 3.59
1896 6861 6.842437 AGAGACGTGCCTACAATCATATAT 57.158 37.500 0.00 0.00 0.00 0.86
2026 6991 9.709495 TTTCATGTTTGAAGATATTTTGAAGGG 57.291 29.630 0.00 0.00 42.60 3.95
2047 7012 2.392933 TTTGTCAAATTCGTCGTGCC 57.607 45.000 0.00 0.00 0.00 5.01
2061 7026 1.418342 CGTGCCCGGTCGATAGTTTG 61.418 60.000 0.00 0.00 37.40 2.93
2071 7036 4.267928 CGGTCGATAGTTTGAAATGTCCTC 59.732 45.833 0.00 0.00 37.40 3.71
2074 7039 5.292101 GTCGATAGTTTGAAATGTCCTCTGG 59.708 44.000 0.00 0.00 37.40 3.86
2092 7057 0.871057 GGCCATTAGCTTCATCTCGC 59.129 55.000 0.00 0.00 43.05 5.03
2104 7069 1.000717 TCATCTCGCAGTTTCACACGA 60.001 47.619 0.00 0.00 0.00 4.35
2108 7073 2.475111 TCTCGCAGTTTCACACGATTTC 59.525 45.455 0.00 0.00 33.53 2.17
2118 7083 2.819019 TCACACGATTTCCATGTTGCAT 59.181 40.909 0.00 0.00 0.00 3.96
2131 7096 6.092092 TCCATGTTGCATATTTTCTGTTTCG 58.908 36.000 0.00 0.00 0.00 3.46
2132 7097 6.072230 TCCATGTTGCATATTTTCTGTTTCGA 60.072 34.615 0.00 0.00 0.00 3.71
2137 7102 5.795766 TGCATATTTTCTGTTTCGACGATC 58.204 37.500 0.00 0.00 0.00 3.69
2151 7116 2.285718 CGACGATCCAAGACGAGTAGAC 60.286 54.545 0.00 0.00 0.00 2.59
2169 7134 5.600484 AGTAGACCTACATCTTCTTCATGGG 59.400 44.000 9.56 0.00 38.48 4.00
2206 7173 4.804608 TGTGTGGTCTGTTTTAATGACG 57.195 40.909 0.00 0.00 0.00 4.35
2244 7211 5.755409 TGCCTAGTCCTTTCTGATGTTTA 57.245 39.130 0.00 0.00 0.00 2.01
2250 7217 6.926630 AGTCCTTTCTGATGTTTACTCTCT 57.073 37.500 0.00 0.00 0.00 3.10
2274 7241 0.456221 CTGGCGTCCTACTACACTGG 59.544 60.000 0.00 0.00 0.00 4.00
2275 7242 1.141234 GGCGTCCTACTACACTGGC 59.859 63.158 0.00 0.00 0.00 4.85
2316 7285 0.322636 TTCGGCCTTCTCTCTCGTCT 60.323 55.000 0.00 0.00 0.00 4.18
2323 7292 3.001533 GCCTTCTCTCTCGTCTTACTACG 59.998 52.174 0.00 0.00 44.19 3.51
2325 7294 3.523606 TCTCTCTCGTCTTACTACGCT 57.476 47.619 0.00 0.00 42.56 5.07
2330 7299 0.723414 TCGTCTTACTACGCTCACGG 59.277 55.000 0.00 0.00 46.04 4.94
2331 7300 0.445436 CGTCTTACTACGCTCACGGT 59.555 55.000 0.00 0.00 46.04 4.83
2333 7302 2.285486 CGTCTTACTACGCTCACGGTAG 60.285 54.545 0.00 0.00 46.04 3.18
2339 7308 2.622903 TACGCTCACGGTAGCATGGC 62.623 60.000 11.22 0.00 46.04 4.40
2361 7330 1.808945 CACACACTGCATTTCTCCTCC 59.191 52.381 0.00 0.00 0.00 4.30
2366 7335 1.280421 ACTGCATTTCTCCTCCCTGAC 59.720 52.381 0.00 0.00 0.00 3.51
2370 7339 2.476199 CATTTCTCCTCCCTGACCTCT 58.524 52.381 0.00 0.00 0.00 3.69
2372 7341 0.787084 TTCTCCTCCCTGACCTCTGT 59.213 55.000 0.00 0.00 0.00 3.41
2402 7371 3.024547 CTCCTATTCGTCTCTTCCCACA 58.975 50.000 0.00 0.00 0.00 4.17
2403 7372 3.024547 TCCTATTCGTCTCTTCCCACAG 58.975 50.000 0.00 0.00 0.00 3.66
2411 7380 3.612955 CGTCTCTTCCCACAGACTTTCTC 60.613 52.174 0.00 0.00 37.49 2.87
2414 7383 3.251484 TCTTCCCACAGACTTTCTCCAT 58.749 45.455 0.00 0.00 0.00 3.41
2416 7385 2.338809 TCCCACAGACTTTCTCCATGT 58.661 47.619 0.00 0.00 0.00 3.21
2423 7392 1.464997 GACTTTCTCCATGTTGGCGAC 59.535 52.381 0.00 0.00 37.47 5.19
2424 7393 1.202758 ACTTTCTCCATGTTGGCGACA 60.203 47.619 10.57 10.57 43.71 4.35
2436 7405 1.541379 TGGCGACACTAGCAACTAGA 58.459 50.000 8.57 0.00 37.49 2.43
2441 7410 3.696898 CGACACTAGCAACTAGATCACC 58.303 50.000 8.57 0.00 37.49 4.02
2442 7411 3.128764 CGACACTAGCAACTAGATCACCA 59.871 47.826 8.57 0.00 37.49 4.17
2445 7414 3.090037 ACTAGCAACTAGATCACCACGT 58.910 45.455 8.57 0.00 37.49 4.49
2550 7519 4.400884 AGACACTCTGTTCTCGCTAATCAT 59.599 41.667 0.00 0.00 0.00 2.45
2555 7524 3.377172 TCTGTTCTCGCTAATCATCGTCA 59.623 43.478 0.00 0.00 0.00 4.35
2579 7548 3.487202 CCGGATGGACGCACGTTG 61.487 66.667 0.00 0.00 37.49 4.10
2580 7549 2.736995 CGGATGGACGCACGTTGT 60.737 61.111 0.00 0.00 0.00 3.32
2581 7550 2.860293 GGATGGACGCACGTTGTG 59.140 61.111 0.00 0.00 36.51 3.33
2603 7572 4.961511 GCACCACTGTCGCCGTCA 62.962 66.667 0.00 0.00 0.00 4.35
2604 7573 3.036084 CACCACTGTCGCCGTCAC 61.036 66.667 0.00 0.00 0.00 3.67
2605 7574 4.295119 ACCACTGTCGCCGTCACC 62.295 66.667 0.00 0.00 0.00 4.02
2642 7611 0.319083 CACGGCCTACACTAACACCA 59.681 55.000 0.00 0.00 0.00 4.17
2648 7617 3.206150 GCCTACACTAACACCATCATGG 58.794 50.000 0.54 0.54 45.02 3.66
2655 7624 1.308069 AACACCATCATGGCGAGCAC 61.308 55.000 2.52 0.00 42.67 4.40
2659 7628 1.712018 CCATCATGGCGAGCACACTG 61.712 60.000 0.00 0.00 0.00 3.66
2669 7638 2.205074 CGAGCACACTGTCAAGAAACT 58.795 47.619 0.00 0.00 0.00 2.66
2681 7650 9.562583 CACTGTCAAGAAACTCTACTATAACTC 57.437 37.037 0.00 0.00 0.00 3.01
2792 7761 3.547649 ACCAAACGCGAGGTAAAAATC 57.452 42.857 15.93 0.00 36.07 2.17
2793 7762 2.879646 ACCAAACGCGAGGTAAAAATCA 59.120 40.909 15.93 0.00 36.07 2.57
2794 7763 3.315749 ACCAAACGCGAGGTAAAAATCAA 59.684 39.130 15.93 0.00 36.07 2.57
2795 7764 3.666797 CCAAACGCGAGGTAAAAATCAAC 59.333 43.478 15.93 0.00 0.00 3.18
2796 7765 4.283678 CAAACGCGAGGTAAAAATCAACA 58.716 39.130 15.93 0.00 0.00 3.33
2797 7766 4.759516 AACGCGAGGTAAAAATCAACAT 57.240 36.364 15.93 0.00 0.00 2.71
2798 7767 4.078363 ACGCGAGGTAAAAATCAACATG 57.922 40.909 15.93 0.00 0.00 3.21
2799 7768 3.119990 ACGCGAGGTAAAAATCAACATGG 60.120 43.478 15.93 0.00 0.00 3.66
2800 7769 3.179048 GCGAGGTAAAAATCAACATGGC 58.821 45.455 0.00 0.00 0.00 4.40
2801 7770 3.366883 GCGAGGTAAAAATCAACATGGCA 60.367 43.478 0.00 0.00 32.45 4.92
2802 7771 4.165779 CGAGGTAAAAATCAACATGGCAC 58.834 43.478 0.00 0.00 0.00 5.01
2803 7772 4.494484 GAGGTAAAAATCAACATGGCACC 58.506 43.478 0.00 0.00 0.00 5.01
2804 7773 3.260632 AGGTAAAAATCAACATGGCACCC 59.739 43.478 0.00 0.00 0.00 4.61
2805 7774 2.453983 AAAAATCAACATGGCACCCG 57.546 45.000 0.00 0.00 0.00 5.28
2806 7775 1.337118 AAAATCAACATGGCACCCGT 58.663 45.000 0.00 0.00 0.00 5.28
2807 7776 2.208132 AAATCAACATGGCACCCGTA 57.792 45.000 0.00 0.00 0.00 4.02
2808 7777 1.750193 AATCAACATGGCACCCGTAG 58.250 50.000 0.00 0.00 0.00 3.51
2822 7791 3.792712 CGTAGGGTTTGGGTATGGG 57.207 57.895 0.00 0.00 0.00 4.00
2823 7792 0.913924 CGTAGGGTTTGGGTATGGGT 59.086 55.000 0.00 0.00 0.00 4.51
2824 7793 2.117865 CGTAGGGTTTGGGTATGGGTA 58.882 52.381 0.00 0.00 0.00 3.69
2825 7794 2.707257 CGTAGGGTTTGGGTATGGGTAT 59.293 50.000 0.00 0.00 0.00 2.73
2826 7795 3.136992 CGTAGGGTTTGGGTATGGGTATT 59.863 47.826 0.00 0.00 0.00 1.89
2827 7796 4.347583 CGTAGGGTTTGGGTATGGGTATTA 59.652 45.833 0.00 0.00 0.00 0.98
2828 7797 5.511888 CGTAGGGTTTGGGTATGGGTATTAG 60.512 48.000 0.00 0.00 0.00 1.73
2829 7798 3.725267 AGGGTTTGGGTATGGGTATTAGG 59.275 47.826 0.00 0.00 0.00 2.69
2830 7799 3.464456 GGGTTTGGGTATGGGTATTAGGT 59.536 47.826 0.00 0.00 0.00 3.08
2831 7800 4.466827 GGTTTGGGTATGGGTATTAGGTG 58.533 47.826 0.00 0.00 0.00 4.00
2832 7801 3.868619 TTGGGTATGGGTATTAGGTGC 57.131 47.619 0.00 0.00 0.00 5.01
2833 7802 2.059490 TGGGTATGGGTATTAGGTGCC 58.941 52.381 0.00 0.00 0.00 5.01
2840 7809 2.873094 GGTATTAGGTGCCCATACCC 57.127 55.000 12.83 0.00 41.83 3.69
2841 7810 2.059490 GGTATTAGGTGCCCATACCCA 58.941 52.381 12.83 0.00 41.83 4.51
2842 7811 2.224695 GGTATTAGGTGCCCATACCCAC 60.225 54.545 12.83 0.00 41.83 4.61
2843 7812 1.602440 ATTAGGTGCCCATACCCACA 58.398 50.000 0.00 0.00 41.83 4.17
2844 7813 0.621609 TTAGGTGCCCATACCCACAC 59.378 55.000 0.00 0.00 41.83 3.82
2845 7814 2.044352 GGTGCCCATACCCACACC 60.044 66.667 0.00 0.00 45.22 4.16
2846 7815 2.044352 GTGCCCATACCCACACCC 60.044 66.667 0.00 0.00 32.37 4.61
2847 7816 2.532974 TGCCCATACCCACACCCA 60.533 61.111 0.00 0.00 0.00 4.51
2848 7817 1.933284 TGCCCATACCCACACCCAT 60.933 57.895 0.00 0.00 0.00 4.00
2849 7818 1.152756 GCCCATACCCACACCCATC 60.153 63.158 0.00 0.00 0.00 3.51
2850 7819 1.645402 GCCCATACCCACACCCATCT 61.645 60.000 0.00 0.00 0.00 2.90
2851 7820 0.474184 CCCATACCCACACCCATCTC 59.526 60.000 0.00 0.00 0.00 2.75
2852 7821 1.212375 CCATACCCACACCCATCTCA 58.788 55.000 0.00 0.00 0.00 3.27
2853 7822 1.563879 CCATACCCACACCCATCTCAA 59.436 52.381 0.00 0.00 0.00 3.02
2854 7823 2.025416 CCATACCCACACCCATCTCAAA 60.025 50.000 0.00 0.00 0.00 2.69
2855 7824 3.563261 CCATACCCACACCCATCTCAAAA 60.563 47.826 0.00 0.00 0.00 2.44
2856 7825 2.292828 ACCCACACCCATCTCAAAAG 57.707 50.000 0.00 0.00 0.00 2.27
2857 7826 1.780309 ACCCACACCCATCTCAAAAGA 59.220 47.619 0.00 0.00 35.54 2.52
2858 7827 2.176798 ACCCACACCCATCTCAAAAGAA 59.823 45.455 0.00 0.00 34.49 2.52
2859 7828 3.181418 ACCCACACCCATCTCAAAAGAAT 60.181 43.478 0.00 0.00 34.49 2.40
2860 7829 3.834231 CCCACACCCATCTCAAAAGAATT 59.166 43.478 0.00 0.00 34.49 2.17
2861 7830 4.322198 CCCACACCCATCTCAAAAGAATTG 60.322 45.833 0.00 0.00 34.49 2.32
2862 7831 4.322198 CCACACCCATCTCAAAAGAATTGG 60.322 45.833 0.00 0.00 34.49 3.16
2863 7832 4.281688 CACACCCATCTCAAAAGAATTGGT 59.718 41.667 0.00 0.00 32.02 3.67
2864 7833 4.524328 ACACCCATCTCAAAAGAATTGGTC 59.476 41.667 0.00 0.00 32.02 4.02
2865 7834 4.082026 CACCCATCTCAAAAGAATTGGTCC 60.082 45.833 0.00 0.00 32.02 4.46
2866 7835 4.088634 CCCATCTCAAAAGAATTGGTCCA 58.911 43.478 0.00 0.00 32.02 4.02
2867 7836 4.713321 CCCATCTCAAAAGAATTGGTCCAT 59.287 41.667 0.00 0.00 32.02 3.41
2868 7837 5.893255 CCCATCTCAAAAGAATTGGTCCATA 59.107 40.000 0.00 0.00 32.02 2.74
2869 7838 6.183360 CCCATCTCAAAAGAATTGGTCCATAC 60.183 42.308 0.00 0.00 32.02 2.39
2870 7839 6.183360 CCATCTCAAAAGAATTGGTCCATACC 60.183 42.308 0.00 0.00 39.70 2.73
2871 7840 6.139679 TCTCAAAAGAATTGGTCCATACCT 57.860 37.500 0.00 0.00 46.91 3.08
2872 7841 5.945784 TCTCAAAAGAATTGGTCCATACCTG 59.054 40.000 0.00 0.00 46.91 4.00
2873 7842 5.640147 TCAAAAGAATTGGTCCATACCTGT 58.360 37.500 0.00 0.00 46.91 4.00
2874 7843 6.785076 TCAAAAGAATTGGTCCATACCTGTA 58.215 36.000 0.00 0.00 46.91 2.74
2875 7844 6.657541 TCAAAAGAATTGGTCCATACCTGTAC 59.342 38.462 0.00 0.00 46.91 2.90
2876 7845 4.772886 AGAATTGGTCCATACCTGTACC 57.227 45.455 0.00 0.00 46.91 3.34
2877 7846 3.458487 AGAATTGGTCCATACCTGTACCC 59.542 47.826 0.00 0.00 46.91 3.69
2878 7847 1.196911 TTGGTCCATACCTGTACCCG 58.803 55.000 0.00 0.00 46.91 5.28
2879 7848 0.041535 TGGTCCATACCTGTACCCGT 59.958 55.000 0.00 0.00 46.91 5.28
2880 7849 1.287442 TGGTCCATACCTGTACCCGTA 59.713 52.381 0.00 0.00 46.91 4.02
2881 7850 1.683385 GGTCCATACCTGTACCCGTAC 59.317 57.143 0.00 0.00 43.08 3.67
2882 7851 1.683385 GTCCATACCTGTACCCGTACC 59.317 57.143 2.66 0.00 35.26 3.34
2883 7852 1.570501 TCCATACCTGTACCCGTACCT 59.429 52.381 2.66 0.00 35.26 3.08
2884 7853 1.684983 CCATACCTGTACCCGTACCTG 59.315 57.143 2.66 0.00 35.26 4.00
2885 7854 1.068127 CATACCTGTACCCGTACCTGC 59.932 57.143 2.66 0.00 35.26 4.85
2886 7855 0.039472 TACCTGTACCCGTACCTGCA 59.961 55.000 2.66 0.00 35.26 4.41
2887 7856 0.616679 ACCTGTACCCGTACCTGCAT 60.617 55.000 2.66 0.00 35.26 3.96
2888 7857 0.104304 CCTGTACCCGTACCTGCATC 59.896 60.000 2.66 0.00 35.26 3.91
2889 7858 0.104304 CTGTACCCGTACCTGCATCC 59.896 60.000 2.66 0.00 35.26 3.51
2890 7859 1.332144 TGTACCCGTACCTGCATCCC 61.332 60.000 2.66 0.00 35.26 3.85
2891 7860 2.129146 TACCCGTACCTGCATCCCG 61.129 63.158 0.00 0.00 0.00 5.14
2892 7861 4.235762 CCCGTACCTGCATCCCGG 62.236 72.222 0.00 0.00 38.39 5.73
2893 7862 4.235762 CCGTACCTGCATCCCGGG 62.236 72.222 16.85 16.85 46.17 5.73
2898 7867 2.354729 CCTGCATCCCGGGTTTCA 59.645 61.111 22.86 12.45 35.07 2.69
2899 7868 1.304052 CCTGCATCCCGGGTTTCAA 60.304 57.895 22.86 0.00 35.07 2.69
2900 7869 0.897863 CCTGCATCCCGGGTTTCAAA 60.898 55.000 22.86 0.00 35.07 2.69
2901 7870 0.243636 CTGCATCCCGGGTTTCAAAC 59.756 55.000 22.86 4.94 0.00 2.93
2913 7882 3.671716 GGTTTCAAACCGTCTCATACCT 58.328 45.455 2.78 0.00 42.62 3.08
2914 7883 4.824289 GGTTTCAAACCGTCTCATACCTA 58.176 43.478 2.78 0.00 42.62 3.08
2915 7884 5.425630 GGTTTCAAACCGTCTCATACCTAT 58.574 41.667 2.78 0.00 42.62 2.57
2916 7885 6.576185 GGTTTCAAACCGTCTCATACCTATA 58.424 40.000 2.78 0.00 42.62 1.31
2917 7886 6.478016 GGTTTCAAACCGTCTCATACCTATAC 59.522 42.308 2.78 0.00 42.62 1.47
2918 7887 5.779529 TCAAACCGTCTCATACCTATACC 57.220 43.478 0.00 0.00 0.00 2.73
2919 7888 4.586001 TCAAACCGTCTCATACCTATACCC 59.414 45.833 0.00 0.00 0.00 3.69
2920 7889 2.787994 ACCGTCTCATACCTATACCCG 58.212 52.381 0.00 0.00 0.00 5.28
2921 7890 2.089980 CCGTCTCATACCTATACCCGG 58.910 57.143 0.00 0.00 0.00 5.73
2922 7891 1.471684 CGTCTCATACCTATACCCGGC 59.528 57.143 0.00 0.00 0.00 6.13
2923 7892 2.805194 GTCTCATACCTATACCCGGCT 58.195 52.381 0.00 0.00 0.00 5.52
2924 7893 2.492484 GTCTCATACCTATACCCGGCTG 59.508 54.545 0.00 0.00 0.00 4.85
2925 7894 1.825474 CTCATACCTATACCCGGCTGG 59.175 57.143 3.88 3.88 41.37 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.837568 AGGCATTTTCATGTTCATCCTTATCT 59.162 34.615 0.00 0.00 32.28 1.98
1 2 7.047460 AGGCATTTTCATGTTCATCCTTATC 57.953 36.000 0.00 0.00 32.28 1.75
2 3 7.427989 AAGGCATTTTCATGTTCATCCTTAT 57.572 32.000 0.00 0.00 30.28 1.73
3 4 6.855763 AAGGCATTTTCATGTTCATCCTTA 57.144 33.333 0.00 0.00 30.28 2.69
4 5 5.750352 AAGGCATTTTCATGTTCATCCTT 57.250 34.783 0.00 0.00 32.28 3.36
5 6 6.837568 AGATAAGGCATTTTCATGTTCATCCT 59.162 34.615 4.43 0.00 32.28 3.24
6 7 7.047460 AGATAAGGCATTTTCATGTTCATCC 57.953 36.000 4.43 0.00 32.28 3.51
7 8 8.623903 TGTAGATAAGGCATTTTCATGTTCATC 58.376 33.333 4.43 0.00 32.28 2.92
8 9 8.523915 TGTAGATAAGGCATTTTCATGTTCAT 57.476 30.769 4.43 0.00 32.28 2.57
9 10 7.936496 TGTAGATAAGGCATTTTCATGTTCA 57.064 32.000 4.43 0.00 32.28 3.18
10 11 9.807649 ATTTGTAGATAAGGCATTTTCATGTTC 57.192 29.630 4.43 0.00 32.28 3.18
11 12 9.590451 CATTTGTAGATAAGGCATTTTCATGTT 57.410 29.630 4.43 0.00 32.28 2.71
12 13 8.752187 ACATTTGTAGATAAGGCATTTTCATGT 58.248 29.630 4.43 2.38 32.28 3.21
13 14 9.027129 CACATTTGTAGATAAGGCATTTTCATG 57.973 33.333 4.43 1.83 0.00 3.07
14 15 8.199449 CCACATTTGTAGATAAGGCATTTTCAT 58.801 33.333 4.43 0.00 0.00 2.57
15 16 7.395772 TCCACATTTGTAGATAAGGCATTTTCA 59.604 33.333 4.43 0.00 0.00 2.69
16 17 7.771183 TCCACATTTGTAGATAAGGCATTTTC 58.229 34.615 0.00 0.00 0.00 2.29
17 18 7.615365 TCTCCACATTTGTAGATAAGGCATTTT 59.385 33.333 0.00 0.00 0.00 1.82
18 19 7.118723 TCTCCACATTTGTAGATAAGGCATTT 58.881 34.615 0.00 0.00 0.00 2.32
19 20 6.662755 TCTCCACATTTGTAGATAAGGCATT 58.337 36.000 0.00 0.00 0.00 3.56
20 21 6.100279 TCTCTCCACATTTGTAGATAAGGCAT 59.900 38.462 0.00 0.00 0.00 4.40
21 22 5.425217 TCTCTCCACATTTGTAGATAAGGCA 59.575 40.000 0.00 0.00 0.00 4.75
22 23 5.918608 TCTCTCCACATTTGTAGATAAGGC 58.081 41.667 0.00 0.00 0.00 4.35
23 24 7.118496 ACTCTCTCCACATTTGTAGATAAGG 57.882 40.000 0.00 0.00 0.00 2.69
24 25 7.010923 GCAACTCTCTCCACATTTGTAGATAAG 59.989 40.741 0.00 0.00 0.00 1.73
25 26 6.818644 GCAACTCTCTCCACATTTGTAGATAA 59.181 38.462 0.00 0.00 0.00 1.75
26 27 6.070824 TGCAACTCTCTCCACATTTGTAGATA 60.071 38.462 0.00 0.00 0.00 1.98
27 28 5.181748 GCAACTCTCTCCACATTTGTAGAT 58.818 41.667 0.00 0.00 0.00 1.98
28 29 4.040339 TGCAACTCTCTCCACATTTGTAGA 59.960 41.667 0.00 0.00 0.00 2.59
29 30 4.153117 GTGCAACTCTCTCCACATTTGTAG 59.847 45.833 0.00 0.00 0.00 2.74
30 31 4.065088 GTGCAACTCTCTCCACATTTGTA 58.935 43.478 0.00 0.00 0.00 2.41
31 32 2.880890 GTGCAACTCTCTCCACATTTGT 59.119 45.455 0.00 0.00 0.00 2.83
32 33 2.880268 TGTGCAACTCTCTCCACATTTG 59.120 45.455 0.00 0.00 38.04 2.32
33 34 3.213206 TGTGCAACTCTCTCCACATTT 57.787 42.857 0.00 0.00 38.04 2.32
34 35 2.936919 TGTGCAACTCTCTCCACATT 57.063 45.000 0.00 0.00 38.04 2.71
35 36 3.771479 TCTATGTGCAACTCTCTCCACAT 59.229 43.478 9.64 9.64 46.91 3.21
36 37 3.165071 TCTATGTGCAACTCTCTCCACA 58.835 45.455 0.00 0.00 41.77 4.17
37 38 3.194542 ACTCTATGTGCAACTCTCTCCAC 59.805 47.826 0.00 0.00 38.04 4.02
38 39 3.194329 CACTCTATGTGCAACTCTCTCCA 59.806 47.826 0.00 0.00 40.06 3.86
39 40 3.779759 CACTCTATGTGCAACTCTCTCC 58.220 50.000 0.00 0.00 40.06 3.71
51 52 1.478510 CGACTTCCCAGCACTCTATGT 59.521 52.381 0.00 0.00 0.00 2.29
52 53 1.478510 ACGACTTCCCAGCACTCTATG 59.521 52.381 0.00 0.00 0.00 2.23
53 54 1.853963 ACGACTTCCCAGCACTCTAT 58.146 50.000 0.00 0.00 0.00 1.98
54 55 2.089980 GTACGACTTCCCAGCACTCTA 58.910 52.381 0.00 0.00 0.00 2.43
59 60 0.320374 CAAGGTACGACTTCCCAGCA 59.680 55.000 0.00 0.00 0.00 4.41
65 66 3.505293 AGGACAGTACAAGGTACGACTTC 59.495 47.826 0.00 0.00 0.00 3.01
73 74 8.983702 TTTATTTGTTTAGGACAGTACAAGGT 57.016 30.769 0.00 0.00 39.94 3.50
137 146 5.055642 CATGATGTTCATGTCAAGTTGCT 57.944 39.130 8.92 0.00 46.80 3.91
173 182 5.455056 AGGAGATAACGCGTGAATTATCT 57.545 39.130 24.10 24.10 46.20 1.98
176 185 3.313249 TCGAGGAGATAACGCGTGAATTA 59.687 43.478 14.98 0.40 0.00 1.40
177 186 2.098607 TCGAGGAGATAACGCGTGAATT 59.901 45.455 14.98 0.00 0.00 2.17
337 1968 1.838073 TTTTGCGGGGAGGAGAGGTC 61.838 60.000 0.00 0.00 0.00 3.85
350 1981 4.552166 TGACCTTCTTCTTCTTTTTGCG 57.448 40.909 0.00 0.00 0.00 4.85
389 2020 7.095187 CCTCGCTTTTTAGTTTGAGTAGAACAT 60.095 37.037 0.00 0.00 0.00 2.71
430 2062 4.398319 TGATCAACTCCTCAAACCCTTTC 58.602 43.478 0.00 0.00 0.00 2.62
492 2124 8.459635 GTTGATATTCCTCAAAACTTTACCTCC 58.540 37.037 0.00 0.00 36.92 4.30
493 2125 9.010029 TGTTGATATTCCTCAAAACTTTACCTC 57.990 33.333 0.00 0.00 36.92 3.85
498 2130 9.313118 GTTGTTGTTGATATTCCTCAAAACTTT 57.687 29.630 0.00 0.00 36.92 2.66
499 2131 8.474025 TGTTGTTGTTGATATTCCTCAAAACTT 58.526 29.630 0.00 0.00 36.92 2.66
500 2132 8.006298 TGTTGTTGTTGATATTCCTCAAAACT 57.994 30.769 0.00 0.00 36.92 2.66
501 2133 8.641499 TTGTTGTTGTTGATATTCCTCAAAAC 57.359 30.769 0.00 0.00 36.92 2.43
502 2134 9.658799 TTTTGTTGTTGTTGATATTCCTCAAAA 57.341 25.926 0.00 0.00 36.92 2.44
503 2135 9.658799 TTTTTGTTGTTGTTGATATTCCTCAAA 57.341 25.926 0.00 0.00 36.92 2.69
504 2136 9.311916 CTTTTTGTTGTTGTTGATATTCCTCAA 57.688 29.630 0.00 0.00 32.84 3.02
505 2137 8.474025 ACTTTTTGTTGTTGTTGATATTCCTCA 58.526 29.630 0.00 0.00 0.00 3.86
506 2138 8.871686 ACTTTTTGTTGTTGTTGATATTCCTC 57.128 30.769 0.00 0.00 0.00 3.71
522 2154 6.833933 AGAGTTATCCCTCACAACTTTTTGTT 59.166 34.615 0.00 0.00 43.89 2.83
524 2156 6.884280 AGAGTTATCCCTCACAACTTTTTG 57.116 37.500 0.00 0.00 38.83 2.44
525 2157 7.746703 AGTAGAGTTATCCCTCACAACTTTTT 58.253 34.615 0.00 0.00 32.79 1.94
526 2158 7.317722 AGTAGAGTTATCCCTCACAACTTTT 57.682 36.000 0.00 0.00 32.79 2.27
596 2228 9.616156 TTTCTAGTGAATACAACCTTTTGTGTA 57.384 29.630 0.21 0.00 45.91 2.90
638 2270 7.151999 AGTGTGCGTTAATTAATTTGGATCA 57.848 32.000 5.91 0.00 0.00 2.92
657 2289 8.634475 TCTCTTCGATTCATGTATTAAGTGTG 57.366 34.615 0.00 0.00 0.00 3.82
695 2346 3.118371 AGTGAAATGGACCGGAGATAACC 60.118 47.826 9.46 1.94 0.00 2.85
716 2367 9.869844 CCTTAATCGCATATTTAAACTGAAGAG 57.130 33.333 4.25 0.00 0.00 2.85
717 2368 9.607988 TCCTTAATCGCATATTTAAACTGAAGA 57.392 29.630 4.25 3.44 0.00 2.87
719 2370 9.997482 GTTCCTTAATCGCATATTTAAACTGAA 57.003 29.630 4.25 0.00 0.00 3.02
720 2371 9.168451 TGTTCCTTAATCGCATATTTAAACTGA 57.832 29.630 4.25 0.00 0.00 3.41
721 2372 9.950680 ATGTTCCTTAATCGCATATTTAAACTG 57.049 29.630 0.00 0.00 0.00 3.16
889 5835 7.518161 TGTAGTGCGTTTTCTGATTATCTTTG 58.482 34.615 0.00 0.00 0.00 2.77
977 5924 4.888325 ATGGAGGGGAGGAGCCGG 62.888 72.222 0.00 0.00 37.63 6.13
978 5925 3.237741 GATGGAGGGGAGGAGCCG 61.238 72.222 0.00 0.00 37.63 5.52
979 5926 1.841103 GAGATGGAGGGGAGGAGCC 60.841 68.421 0.00 0.00 0.00 4.70
1038 5985 0.955428 TTGCTGGTGTCTTGATCGGC 60.955 55.000 0.00 0.00 0.00 5.54
1258 6205 2.797866 ATGACCGACGACTCGCACAC 62.798 60.000 0.00 0.00 38.70 3.82
1260 6207 1.868251 GATGACCGACGACTCGCAC 60.868 63.158 0.00 0.00 38.70 5.34
1284 6231 1.189403 CGAAAGCCTCGTCGATGTAC 58.811 55.000 4.21 0.00 42.89 2.90
1407 6354 1.127951 ACGAAACGAATCAACCGATGC 59.872 47.619 0.00 0.00 30.13 3.91
1453 6401 4.084888 CCGCGCGGAAGAAACCAC 62.085 66.667 44.86 0.00 37.50 4.16
1482 6430 2.224079 CACGAGCTGCACAATTACAACT 59.776 45.455 1.02 0.00 0.00 3.16
1620 6568 2.978018 GCCGCCGAAGAAGGGTTTG 61.978 63.158 0.00 0.00 0.00 2.93
1697 6645 1.140816 GACGCCCTTCATCTTATCGC 58.859 55.000 0.00 0.00 0.00 4.58
1716 6664 1.521681 GGCGGGATCGAAGGTCTTG 60.522 63.158 0.00 0.00 39.00 3.02
1810 6758 1.576421 CAAACTCGACCAGCTTGCC 59.424 57.895 0.00 0.00 0.00 4.52
1859 6816 3.364023 CACGTCTCTTTAGTTTGTAGCGG 59.636 47.826 0.00 0.00 0.00 5.52
1921 6886 2.821969 GGCACACAAATTCCACAGAGAT 59.178 45.455 0.00 0.00 0.00 2.75
2026 6991 2.466205 GGCACGACGAATTTGACAAAAC 59.534 45.455 4.41 1.96 0.00 2.43
2039 7004 3.802008 CTATCGACCGGGCACGACG 62.802 68.421 11.66 16.17 44.60 5.12
2047 7012 3.308866 GGACATTTCAAACTATCGACCGG 59.691 47.826 0.00 0.00 0.00 5.28
2071 7036 2.141517 CGAGATGAAGCTAATGGCCAG 58.858 52.381 13.05 0.00 43.05 4.85
2074 7039 1.530293 CTGCGAGATGAAGCTAATGGC 59.470 52.381 0.00 0.00 42.19 4.40
2092 7057 4.488126 ACATGGAAATCGTGTGAAACTG 57.512 40.909 0.00 0.00 43.44 3.16
2104 7069 8.851541 AAACAGAAAATATGCAACATGGAAAT 57.148 26.923 0.00 0.00 0.00 2.17
2108 7073 6.033831 GTCGAAACAGAAAATATGCAACATGG 59.966 38.462 0.00 0.00 0.00 3.66
2118 7083 6.090358 GTCTTGGATCGTCGAAACAGAAAATA 59.910 38.462 0.00 0.00 0.00 1.40
2131 7096 2.031930 GGTCTACTCGTCTTGGATCGTC 59.968 54.545 0.00 0.00 0.00 4.20
2132 7097 2.015587 GGTCTACTCGTCTTGGATCGT 58.984 52.381 0.00 0.00 0.00 3.73
2137 7102 4.200874 AGATGTAGGTCTACTCGTCTTGG 58.799 47.826 9.24 0.00 37.00 3.61
2151 7116 3.853355 AGCCCATGAAGAAGATGTAGG 57.147 47.619 0.00 0.00 0.00 3.18
2186 7153 3.250040 AGCGTCATTAAAACAGACCACAC 59.750 43.478 0.00 0.00 0.00 3.82
2193 7160 7.308782 AGATTAAGGAGCGTCATTAAAACAG 57.691 36.000 8.24 0.00 36.42 3.16
2206 7173 3.289407 AGGCAAAGGAGATTAAGGAGC 57.711 47.619 0.00 0.00 0.00 4.70
2316 7285 1.452110 TGCTACCGTGAGCGTAGTAA 58.548 50.000 1.82 0.00 45.99 2.24
2323 7292 3.264897 CGCCATGCTACCGTGAGC 61.265 66.667 0.00 0.00 43.16 4.26
2325 7294 4.075854 TGCGCCATGCTACCGTGA 62.076 61.111 4.18 0.00 46.63 4.35
2330 7299 2.034879 AGTGTGTGCGCCATGCTAC 61.035 57.895 4.18 0.00 46.63 3.58
2331 7300 2.034317 CAGTGTGTGCGCCATGCTA 61.034 57.895 4.18 0.00 46.63 3.49
2350 7319 2.170187 CAGAGGTCAGGGAGGAGAAATG 59.830 54.545 0.00 0.00 0.00 2.32
2361 7330 0.736053 GACGCTAGACAGAGGTCAGG 59.264 60.000 0.00 0.00 46.80 3.86
2366 7335 0.106918 AGGAGGACGCTAGACAGAGG 60.107 60.000 0.00 0.00 0.00 3.69
2370 7339 2.219458 CGAATAGGAGGACGCTAGACA 58.781 52.381 0.00 0.00 0.00 3.41
2372 7341 2.104451 AGACGAATAGGAGGACGCTAGA 59.896 50.000 0.00 0.00 0.00 2.43
2402 7371 1.347707 TCGCCAACATGGAGAAAGTCT 59.652 47.619 0.00 0.00 43.39 3.24
2403 7372 1.808411 TCGCCAACATGGAGAAAGTC 58.192 50.000 0.00 0.00 43.39 3.01
2411 7380 0.673333 TGCTAGTGTCGCCAACATGG 60.673 55.000 0.00 0.00 40.80 3.66
2414 7383 0.105964 AGTTGCTAGTGTCGCCAACA 59.894 50.000 10.13 0.00 34.78 3.33
2416 7385 1.890489 TCTAGTTGCTAGTGTCGCCAA 59.110 47.619 3.48 0.00 35.72 4.52
2423 7392 3.119459 ACGTGGTGATCTAGTTGCTAGTG 60.119 47.826 0.00 0.00 35.72 2.74
2424 7393 3.090037 ACGTGGTGATCTAGTTGCTAGT 58.910 45.455 0.00 0.00 35.72 2.57
2550 7519 1.672854 CCATCCGGCTAGGTTGACGA 61.673 60.000 0.00 0.00 41.74 4.20
2555 7524 3.090219 GCGTCCATCCGGCTAGGTT 62.090 63.158 0.00 0.00 41.99 3.50
2586 7555 4.961511 TGACGGCGACAGTGGTGC 62.962 66.667 16.62 0.00 0.00 5.01
2587 7556 3.036084 GTGACGGCGACAGTGGTG 61.036 66.667 16.62 0.00 0.00 4.17
2588 7557 4.295119 GGTGACGGCGACAGTGGT 62.295 66.667 16.62 0.00 0.00 4.16
2599 7568 3.834799 GAGGCCTACCGGGTGACG 61.835 72.222 4.42 0.00 42.76 4.35
2600 7569 3.468140 GGAGGCCTACCGGGTGAC 61.468 72.222 4.42 0.00 42.76 3.67
2601 7570 3.674050 GAGGAGGCCTACCGGGTGA 62.674 68.421 12.85 0.00 42.76 4.02
2602 7571 3.155167 GAGGAGGCCTACCGGGTG 61.155 72.222 12.85 0.00 42.76 4.61
2603 7572 4.835891 CGAGGAGGCCTACCGGGT 62.836 72.222 12.85 4.46 42.76 5.28
2624 7593 1.206371 GATGGTGTTAGTGTAGGCCGT 59.794 52.381 0.00 0.00 0.00 5.68
2642 7611 0.742281 GACAGTGTGCTCGCCATGAT 60.742 55.000 0.00 0.00 0.00 2.45
2648 7617 0.937304 TTTCTTGACAGTGTGCTCGC 59.063 50.000 0.00 0.00 0.00 5.03
2655 7624 9.562583 GAGTTATAGTAGAGTTTCTTGACAGTG 57.437 37.037 0.00 0.00 0.00 3.66
2781 7750 4.494484 GGTGCCATGTTGATTTTTACCTC 58.506 43.478 0.00 0.00 0.00 3.85
2792 7761 1.748879 CCCTACGGGTGCCATGTTG 60.749 63.158 0.00 0.00 38.25 3.33
2793 7762 2.674754 CCCTACGGGTGCCATGTT 59.325 61.111 0.00 0.00 38.25 2.71
2803 7772 0.181824 CCCATACCCAAACCCTACGG 59.818 60.000 0.00 0.00 0.00 4.02
2804 7773 0.913924 ACCCATACCCAAACCCTACG 59.086 55.000 0.00 0.00 0.00 3.51
2805 7774 4.801521 AATACCCATACCCAAACCCTAC 57.198 45.455 0.00 0.00 0.00 3.18
2806 7775 4.915194 CCTAATACCCATACCCAAACCCTA 59.085 45.833 0.00 0.00 0.00 3.53
2807 7776 3.725267 CCTAATACCCATACCCAAACCCT 59.275 47.826 0.00 0.00 0.00 4.34
2808 7777 3.464456 ACCTAATACCCATACCCAAACCC 59.536 47.826 0.00 0.00 0.00 4.11
2809 7778 4.466827 CACCTAATACCCATACCCAAACC 58.533 47.826 0.00 0.00 0.00 3.27
2810 7779 3.887110 GCACCTAATACCCATACCCAAAC 59.113 47.826 0.00 0.00 0.00 2.93
2811 7780 3.117436 GGCACCTAATACCCATACCCAAA 60.117 47.826 0.00 0.00 0.00 3.28
2812 7781 2.444010 GGCACCTAATACCCATACCCAA 59.556 50.000 0.00 0.00 0.00 4.12
2813 7782 2.059490 GGCACCTAATACCCATACCCA 58.941 52.381 0.00 0.00 0.00 4.51
2814 7783 2.873094 GGCACCTAATACCCATACCC 57.127 55.000 0.00 0.00 0.00 3.69
2829 7798 2.044352 GGGTGTGGGTATGGGCAC 60.044 66.667 0.00 0.00 0.00 5.01
2830 7799 1.932156 GATGGGTGTGGGTATGGGCA 61.932 60.000 0.00 0.00 0.00 5.36
2831 7800 1.152756 GATGGGTGTGGGTATGGGC 60.153 63.158 0.00 0.00 0.00 5.36
2832 7801 0.474184 GAGATGGGTGTGGGTATGGG 59.526 60.000 0.00 0.00 0.00 4.00
2833 7802 1.212375 TGAGATGGGTGTGGGTATGG 58.788 55.000 0.00 0.00 0.00 2.74
2834 7803 3.364460 TTTGAGATGGGTGTGGGTATG 57.636 47.619 0.00 0.00 0.00 2.39
2835 7804 3.591527 TCTTTTGAGATGGGTGTGGGTAT 59.408 43.478 0.00 0.00 0.00 2.73
2836 7805 2.983192 TCTTTTGAGATGGGTGTGGGTA 59.017 45.455 0.00 0.00 0.00 3.69
2837 7806 1.780309 TCTTTTGAGATGGGTGTGGGT 59.220 47.619 0.00 0.00 0.00 4.51
2838 7807 2.584835 TCTTTTGAGATGGGTGTGGG 57.415 50.000 0.00 0.00 0.00 4.61
2839 7808 4.322198 CCAATTCTTTTGAGATGGGTGTGG 60.322 45.833 0.00 0.00 34.39 4.17
2840 7809 4.281688 ACCAATTCTTTTGAGATGGGTGTG 59.718 41.667 0.00 0.00 39.11 3.82
2841 7810 4.482990 ACCAATTCTTTTGAGATGGGTGT 58.517 39.130 0.00 0.00 39.11 4.16
2842 7811 4.082026 GGACCAATTCTTTTGAGATGGGTG 60.082 45.833 0.00 0.00 39.11 4.61
2843 7812 4.089361 GGACCAATTCTTTTGAGATGGGT 58.911 43.478 0.00 0.00 39.11 4.51
2844 7813 4.088634 TGGACCAATTCTTTTGAGATGGG 58.911 43.478 0.00 0.00 39.11 4.00
2845 7814 5.927281 ATGGACCAATTCTTTTGAGATGG 57.073 39.130 0.00 0.00 40.03 3.51
2846 7815 6.799512 GGTATGGACCAATTCTTTTGAGATG 58.200 40.000 0.00 0.00 46.12 2.90
2862 7831 1.683385 GGTACGGGTACAGGTATGGAC 59.317 57.143 10.81 0.00 39.83 4.02
2863 7832 1.570501 AGGTACGGGTACAGGTATGGA 59.429 52.381 10.81 0.00 37.78 3.41
2864 7833 1.684983 CAGGTACGGGTACAGGTATGG 59.315 57.143 10.81 0.00 37.78 2.74
2865 7834 1.068127 GCAGGTACGGGTACAGGTATG 59.932 57.143 10.81 3.20 37.78 2.39
2866 7835 1.342275 TGCAGGTACGGGTACAGGTAT 60.342 52.381 10.81 0.00 37.78 2.73
2867 7836 0.039472 TGCAGGTACGGGTACAGGTA 59.961 55.000 10.81 0.00 37.78 3.08
2868 7837 0.616679 ATGCAGGTACGGGTACAGGT 60.617 55.000 10.81 0.00 37.78 4.00
2869 7838 0.104304 GATGCAGGTACGGGTACAGG 59.896 60.000 10.81 3.62 37.78 4.00
2870 7839 0.104304 GGATGCAGGTACGGGTACAG 59.896 60.000 10.81 4.27 37.78 2.74
2871 7840 1.332144 GGGATGCAGGTACGGGTACA 61.332 60.000 10.81 0.00 37.78 2.90
2872 7841 1.444672 GGGATGCAGGTACGGGTAC 59.555 63.158 0.00 0.30 35.40 3.34
2873 7842 2.129146 CGGGATGCAGGTACGGGTA 61.129 63.158 0.00 0.00 0.00 3.69
2874 7843 3.467226 CGGGATGCAGGTACGGGT 61.467 66.667 0.00 0.00 0.00 5.28
2875 7844 4.235762 CCGGGATGCAGGTACGGG 62.236 72.222 12.42 0.00 40.79 5.28
2876 7845 4.235762 CCCGGGATGCAGGTACGG 62.236 72.222 18.48 13.08 43.89 4.02
2877 7846 2.530958 AAACCCGGGATGCAGGTACG 62.531 60.000 32.02 0.00 32.21 3.67
2878 7847 0.746923 GAAACCCGGGATGCAGGTAC 60.747 60.000 32.02 3.78 32.21 3.34
2879 7848 1.202099 TGAAACCCGGGATGCAGGTA 61.202 55.000 32.02 0.00 32.21 3.08
2880 7849 2.075355 TTGAAACCCGGGATGCAGGT 62.075 55.000 32.02 0.00 34.60 4.00
2881 7850 0.897863 TTTGAAACCCGGGATGCAGG 60.898 55.000 32.02 0.00 0.00 4.85
2882 7851 0.243636 GTTTGAAACCCGGGATGCAG 59.756 55.000 32.02 0.00 0.00 4.41
2883 7852 1.182385 GGTTTGAAACCCGGGATGCA 61.182 55.000 32.02 19.86 46.12 3.96
2884 7853 1.589630 GGTTTGAAACCCGGGATGC 59.410 57.895 32.02 16.60 46.12 3.91
2893 7862 6.478016 GGTATAGGTATGAGACGGTTTGAAAC 59.522 42.308 0.00 0.00 0.00 2.78
2894 7863 6.407299 GGGTATAGGTATGAGACGGTTTGAAA 60.407 42.308 0.00 0.00 0.00 2.69
2895 7864 5.069516 GGGTATAGGTATGAGACGGTTTGAA 59.930 44.000 0.00 0.00 0.00 2.69
2896 7865 4.586001 GGGTATAGGTATGAGACGGTTTGA 59.414 45.833 0.00 0.00 0.00 2.69
2897 7866 4.558095 CGGGTATAGGTATGAGACGGTTTG 60.558 50.000 0.00 0.00 0.00 2.93
2898 7867 3.571401 CGGGTATAGGTATGAGACGGTTT 59.429 47.826 0.00 0.00 0.00 3.27
2899 7868 3.152341 CGGGTATAGGTATGAGACGGTT 58.848 50.000 0.00 0.00 0.00 4.44
2900 7869 2.553904 CCGGGTATAGGTATGAGACGGT 60.554 54.545 0.00 0.00 34.54 4.83
2901 7870 2.089980 CCGGGTATAGGTATGAGACGG 58.910 57.143 0.00 0.00 0.00 4.79
2902 7871 1.471684 GCCGGGTATAGGTATGAGACG 59.528 57.143 2.18 0.00 0.00 4.18
2903 7872 2.492484 CAGCCGGGTATAGGTATGAGAC 59.508 54.545 5.47 0.00 0.00 3.36
2904 7873 2.556782 CCAGCCGGGTATAGGTATGAGA 60.557 54.545 5.47 0.00 0.00 3.27
2905 7874 1.825474 CCAGCCGGGTATAGGTATGAG 59.175 57.143 5.47 0.00 0.00 2.90
2906 7875 1.933021 CCAGCCGGGTATAGGTATGA 58.067 55.000 5.47 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.