Multiple sequence alignment - TraesCS2D01G412500

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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 TraesCS2D01G412500 chr2D 100.000 3587 0 0 1 3587 527309353 527305767 0.000000e+00 6625.0
1 TraesCS2D01G412500 chr2D 80.214 187 17 6 61 247 458487621 458487787 4.860000e-24 122.0
2 TraesCS2D01G412500 chr2D 81.308 107 13 6 146 250 567039588 567039487 2.970000e-11 80.5
3 TraesCS2D01G412500 chr2B 90.473 3401 206 48 107 3462 624405330 624402003 0.000000e+00 4377.0
4 TraesCS2D01G412500 chr2A 88.123 2046 151 63 1508 3514 672338370 672336378 0.000000e+00 2348.0
5 TraesCS2D01G412500 chr2A 90.093 1403 78 30 131 1510 672339891 672338527 0.000000e+00 1764.0
6 TraesCS2D01G412500 chr2A 84.282 439 50 13 3160 3587 672335376 672334946 9.270000e-111 411.0
7 TraesCS2D01G412500 chr7D 88.827 179 20 0 1063 1241 220989878 220990056 1.680000e-53 220.0
8 TraesCS2D01G412500 chr7A 88.827 179 20 0 1063 1241 235473534 235473712 1.680000e-53 220.0
9 TraesCS2D01G412500 chr7B 84.615 208 28 4 1063 1267 175992982 175992776 1.690000e-48 204.0
10 TraesCS2D01G412500 chr5D 82.237 152 17 5 103 252 528586577 528586434 4.860000e-24 122.0
11 TraesCS2D01G412500 chr3B 82.727 110 12 3 60 169 757972530 757972632 1.370000e-14 91.6
12 TraesCS2D01G412500 chr3B 94.872 39 2 0 1788 1826 478322771 478322733 1.080000e-05 62.1
13 TraesCS2D01G412500 chr3D 94.872 39 2 0 1788 1826 367236346 367236308 1.080000e-05 62.1
14 TraesCS2D01G412500 chr3A 94.872 39 2 0 1788 1826 489311323 489311285 1.080000e-05 62.1
15 TraesCS2D01G412500 chr3A 87.234 47 6 0 3015 3061 454158566 454158520 2.000000e-03 54.7
16 TraesCS2D01G412500 chr6B 100.000 28 0 0 3210 3237 648464602 648464629 6.000000e-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 TraesCS2D01G412500 chr2D 527305767 527309353 3586 True 6625.000000 6625 100.000000 1 3587 1 chr2D.!!$R1 3586
1 TraesCS2D01G412500 chr2B 624402003 624405330 3327 True 4377.000000 4377 90.473000 107 3462 1 chr2B.!!$R1 3355
2 TraesCS2D01G412500 chr2A 672334946 672339891 4945 True 1507.666667 2348 87.499333 131 3587 3 chr2A.!!$R1 3456

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
21 22 0.250295 CCCAGTCTTCGAAGGTTGCA 60.250 55.0 24.37 2.14 0.00 4.08 F
46 47 0.297820 GGTTAGCGTTTCGAGCGATG 59.702 55.0 14.22 0.00 40.04 3.84 F
47 48 0.297820 GTTAGCGTTTCGAGCGATGG 59.702 55.0 14.22 0.00 40.04 3.51 F
1600 1790 0.451628 CGACAGTGATGTGCAAAGCG 60.452 55.0 0.00 0.00 0.00 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 1874 0.183492 ACTTGCAGCCACTTCAGGAA 59.817 50.0 0.00 0.00 0.0 3.36 R
1685 1875 0.183492 AACTTGCAGCCACTTCAGGA 59.817 50.0 0.00 0.00 0.0 3.86 R
1686 1876 0.595095 GAACTTGCAGCCACTTCAGG 59.405 55.0 0.00 0.00 0.0 3.86 R
3257 3549 0.727398 GTGATTTGACGCCTAGGTGC 59.273 55.0 22.51 14.95 0.0 5.01 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
19 20 2.256117 AACCCAGTCTTCGAAGGTTG 57.744 50.000 24.37 20.39 39.32 3.77
20 21 0.250338 ACCCAGTCTTCGAAGGTTGC 60.250 55.000 24.37 12.38 0.00 4.17
21 22 0.250295 CCCAGTCTTCGAAGGTTGCA 60.250 55.000 24.37 2.14 0.00 4.08
22 23 0.868406 CCAGTCTTCGAAGGTTGCAC 59.132 55.000 24.37 14.63 0.00 4.57
23 24 1.541233 CCAGTCTTCGAAGGTTGCACT 60.541 52.381 24.37 16.59 0.00 4.40
24 25 1.528586 CAGTCTTCGAAGGTTGCACTG 59.471 52.381 24.37 23.05 0.00 3.66
25 26 0.868406 GTCTTCGAAGGTTGCACTGG 59.132 55.000 24.37 0.00 0.00 4.00
26 27 0.884704 TCTTCGAAGGTTGCACTGGC 60.885 55.000 24.37 0.00 41.68 4.85
27 28 2.175184 CTTCGAAGGTTGCACTGGCG 62.175 60.000 17.70 0.00 45.35 5.69
28 29 3.726517 CGAAGGTTGCACTGGCGG 61.727 66.667 0.00 0.00 45.35 6.13
29 30 2.594592 GAAGGTTGCACTGGCGGT 60.595 61.111 0.00 0.00 45.35 5.68
30 31 2.123897 AAGGTTGCACTGGCGGTT 60.124 55.556 0.00 0.00 45.35 4.44
31 32 0.887387 GAAGGTTGCACTGGCGGTTA 60.887 55.000 0.00 0.00 45.35 2.85
32 33 0.889186 AAGGTTGCACTGGCGGTTAG 60.889 55.000 0.00 0.00 45.35 2.34
33 34 2.561373 GTTGCACTGGCGGTTAGC 59.439 61.111 0.00 0.00 45.35 3.09
42 43 2.394524 GCGGTTAGCGTTTCGAGC 59.605 61.111 5.55 0.00 35.41 5.03
43 44 2.687436 CGGTTAGCGTTTCGAGCG 59.313 61.111 7.04 7.04 40.04 5.03
44 45 1.798725 CGGTTAGCGTTTCGAGCGA 60.799 57.895 14.22 0.00 40.04 4.93
45 46 1.138047 CGGTTAGCGTTTCGAGCGAT 61.138 55.000 14.22 10.78 40.04 4.58
46 47 0.297820 GGTTAGCGTTTCGAGCGATG 59.702 55.000 14.22 0.00 40.04 3.84
47 48 0.297820 GTTAGCGTTTCGAGCGATGG 59.702 55.000 14.22 0.00 40.04 3.51
48 49 1.418342 TTAGCGTTTCGAGCGATGGC 61.418 55.000 14.22 0.00 40.04 4.40
49 50 2.551097 TAGCGTTTCGAGCGATGGCA 62.551 55.000 14.22 0.00 43.41 4.92
50 51 3.022401 GCGTTTCGAGCGATGGCAA 62.022 57.895 14.22 0.00 43.41 4.52
51 52 1.059369 CGTTTCGAGCGATGGCAAG 59.941 57.895 1.50 0.00 43.41 4.01
52 53 1.425428 GTTTCGAGCGATGGCAAGG 59.575 57.895 1.50 0.00 43.41 3.61
53 54 2.398554 TTTCGAGCGATGGCAAGGC 61.399 57.895 1.50 5.11 43.41 4.35
63 64 2.501610 GGCAAGGCCCGAGAGTAG 59.498 66.667 0.00 0.00 44.06 2.57
64 65 2.359967 GGCAAGGCCCGAGAGTAGT 61.360 63.158 0.00 0.00 44.06 2.73
65 66 1.153549 GCAAGGCCCGAGAGTAGTG 60.154 63.158 0.00 0.00 0.00 2.74
66 67 1.517832 CAAGGCCCGAGAGTAGTGG 59.482 63.158 0.00 0.00 0.00 4.00
67 68 2.359967 AAGGCCCGAGAGTAGTGGC 61.360 63.158 0.00 0.00 43.26 5.01
68 69 4.208686 GGCCCGAGAGTAGTGGCG 62.209 72.222 0.00 0.00 44.96 5.69
69 70 4.208686 GCCCGAGAGTAGTGGCGG 62.209 72.222 0.00 0.00 43.20 6.13
70 71 2.439701 CCCGAGAGTAGTGGCGGA 60.440 66.667 0.00 0.00 46.29 5.54
71 72 2.482333 CCCGAGAGTAGTGGCGGAG 61.482 68.421 0.00 0.00 46.29 4.63
86 87 2.802787 CGGAGCTTGATAGGAATCGT 57.197 50.000 0.00 0.00 34.60 3.73
87 88 2.667137 CGGAGCTTGATAGGAATCGTC 58.333 52.381 0.00 0.00 34.60 4.20
88 89 2.667137 GGAGCTTGATAGGAATCGTCG 58.333 52.381 0.00 0.00 34.60 5.12
89 90 2.608261 GGAGCTTGATAGGAATCGTCGG 60.608 54.545 0.00 0.00 34.60 4.79
90 91 1.341531 AGCTTGATAGGAATCGTCGGG 59.658 52.381 0.00 0.00 34.60 5.14
91 92 1.605712 GCTTGATAGGAATCGTCGGGG 60.606 57.143 0.00 0.00 34.60 5.73
92 93 1.000955 CTTGATAGGAATCGTCGGGGG 59.999 57.143 0.00 0.00 34.60 5.40
141 142 5.975988 ACTAGGAGGGCAAAGAATTGATA 57.024 39.130 0.00 0.00 38.94 2.15
171 172 6.591750 ACTTATCTAAGCCGTGCATAGTAT 57.408 37.500 0.00 4.45 36.79 2.12
207 208 3.028683 CCTAGAGCTGGGAGGGGA 58.971 66.667 0.00 0.00 32.26 4.81
208 209 1.458588 CCTAGAGCTGGGAGGGGAC 60.459 68.421 0.00 0.00 32.26 4.46
241 242 3.515901 CCCCTCAGACTTGTACTAAGCTT 59.484 47.826 3.48 3.48 0.00 3.74
253 254 2.803155 CTAAGCTTCGCCACTGCCCA 62.803 60.000 0.00 0.00 0.00 5.36
267 268 2.031120 CTGCCCAAGAACAAGGTTGAA 58.969 47.619 0.00 0.00 0.00 2.69
268 269 2.031120 TGCCCAAGAACAAGGTTGAAG 58.969 47.619 0.00 0.00 0.00 3.02
269 270 2.306847 GCCCAAGAACAAGGTTGAAGA 58.693 47.619 0.00 0.00 0.00 2.87
270 271 2.893489 GCCCAAGAACAAGGTTGAAGAT 59.107 45.455 0.00 0.00 0.00 2.40
271 272 3.321968 GCCCAAGAACAAGGTTGAAGATT 59.678 43.478 0.00 0.00 0.00 2.40
272 273 4.202253 GCCCAAGAACAAGGTTGAAGATTT 60.202 41.667 0.00 0.00 0.00 2.17
273 274 5.291971 CCCAAGAACAAGGTTGAAGATTTG 58.708 41.667 0.00 0.00 0.00 2.32
293 300 2.976185 TGAGGGTGGTGTCAATGTTAGA 59.024 45.455 0.00 0.00 0.00 2.10
321 329 2.761208 ACGGATTCGAGATTTGAGGAGT 59.239 45.455 0.00 0.00 40.11 3.85
323 331 4.585162 ACGGATTCGAGATTTGAGGAGTAT 59.415 41.667 0.00 0.00 40.11 2.12
350 358 5.247110 AGACGATCCTCACTTAATATGCCAT 59.753 40.000 0.00 0.00 0.00 4.40
403 412 1.284982 CTCGACTCACAAAGCCCACG 61.285 60.000 0.00 0.00 0.00 4.94
416 433 2.173669 CCCACGTGGCGATGATGTC 61.174 63.158 29.75 0.00 0.00 3.06
453 470 0.884704 GACAAGCGGCAAGGAAGACA 60.885 55.000 1.45 0.00 0.00 3.41
458 475 1.166531 GCGGCAAGGAAGACAGTTGT 61.167 55.000 0.00 0.00 0.00 3.32
459 476 1.876416 GCGGCAAGGAAGACAGTTGTA 60.876 52.381 0.00 0.00 0.00 2.41
496 513 6.475504 AGGGCTTTATTGCAGCTAAATTTTT 58.524 32.000 0.00 0.00 37.43 1.94
518 535 8.870160 TTTTCATGGTTCTTTCTACAAATGTG 57.130 30.769 0.00 0.00 0.00 3.21
558 575 4.070581 GTGATTTCCACGAGTCATGTTG 57.929 45.455 0.00 0.00 35.86 3.33
559 576 3.498397 GTGATTTCCACGAGTCATGTTGT 59.502 43.478 0.00 0.00 35.86 3.32
560 577 4.688879 GTGATTTCCACGAGTCATGTTGTA 59.311 41.667 0.00 0.00 35.86 2.41
561 578 4.688879 TGATTTCCACGAGTCATGTTGTAC 59.311 41.667 0.00 0.00 0.00 2.90
573 591 8.443160 CGAGTCATGTTGTACTTTGACATTTAT 58.557 33.333 15.40 1.31 32.01 1.40
575 593 9.507329 AGTCATGTTGTACTTTGACATTTATCT 57.493 29.630 15.40 5.75 32.01 1.98
588 606 7.984422 TGACATTTATCTAATAGCATGTGGG 57.016 36.000 0.00 0.00 0.00 4.61
918 949 3.871594 CCATAGAAGTTACAGAAAGGGCG 59.128 47.826 0.00 0.00 0.00 6.13
919 950 1.809684 AGAAGTTACAGAAAGGGCGC 58.190 50.000 0.00 0.00 0.00 6.53
920 951 0.803117 GAAGTTACAGAAAGGGCGCC 59.197 55.000 21.18 21.18 0.00 6.53
948 979 0.968901 TTCCGGGACACTACTCGCAT 60.969 55.000 0.00 0.00 31.89 4.73
1099 1130 2.444895 GGATGGCGGAGGAGGACT 60.445 66.667 0.00 0.00 0.00 3.85
1277 1308 3.055094 TCCTCCCCATTTCTTCTTCTTCG 60.055 47.826 0.00 0.00 0.00 3.79
1278 1309 3.307762 CCTCCCCATTTCTTCTTCTTCGT 60.308 47.826 0.00 0.00 0.00 3.85
1279 1310 3.935828 CTCCCCATTTCTTCTTCTTCGTC 59.064 47.826 0.00 0.00 0.00 4.20
1280 1311 2.673368 CCCCATTTCTTCTTCTTCGTCG 59.327 50.000 0.00 0.00 0.00 5.12
1281 1312 3.326747 CCCATTTCTTCTTCTTCGTCGT 58.673 45.455 0.00 0.00 0.00 4.34
1282 1313 3.368236 CCCATTTCTTCTTCTTCGTCGTC 59.632 47.826 0.00 0.00 0.00 4.20
1283 1314 3.059570 CCATTTCTTCTTCTTCGTCGTCG 59.940 47.826 0.00 0.00 38.55 5.12
1284 1315 3.344904 TTTCTTCTTCTTCGTCGTCGT 57.655 42.857 1.33 0.00 38.33 4.34
1285 1316 2.591066 TCTTCTTCTTCGTCGTCGTC 57.409 50.000 1.33 0.00 38.33 4.20
1286 1317 2.141517 TCTTCTTCTTCGTCGTCGTCT 58.858 47.619 1.33 0.00 38.33 4.18
1287 1318 2.547211 TCTTCTTCTTCGTCGTCGTCTT 59.453 45.455 1.33 0.00 38.33 3.01
1288 1319 2.591066 TCTTCTTCGTCGTCGTCTTC 57.409 50.000 1.33 0.00 38.33 2.87
1289 1320 2.141517 TCTTCTTCGTCGTCGTCTTCT 58.858 47.619 1.33 0.00 38.33 2.85
1290 1321 2.547211 TCTTCTTCGTCGTCGTCTTCTT 59.453 45.455 1.33 0.00 38.33 2.52
1291 1322 2.591066 TCTTCGTCGTCGTCTTCTTC 57.409 50.000 1.33 0.00 38.33 2.87
1292 1323 2.141517 TCTTCGTCGTCGTCTTCTTCT 58.858 47.619 1.33 0.00 38.33 2.85
1328 1359 2.483876 TCTTCTTCTTGGCACTGTTCG 58.516 47.619 0.00 0.00 0.00 3.95
1348 1379 2.510064 ATCGCGCTGGGTTTCGGTTA 62.510 55.000 5.56 0.00 0.00 2.85
1356 1387 3.565063 GCTGGGTTTCGGTTAAACTTGTA 59.435 43.478 0.00 0.00 45.70 2.41
1445 1476 2.276201 TCGCTGATTAACAATGACCCG 58.724 47.619 0.00 0.00 0.00 5.28
1509 1696 4.483476 AGTGCCAACGATTGTTTTCTAC 57.517 40.909 0.00 0.00 35.72 2.59
1510 1697 3.252458 AGTGCCAACGATTGTTTTCTACC 59.748 43.478 0.00 0.00 35.72 3.18
1535 1725 7.013559 CCAGAGATGATTACCAACAAATGCATA 59.986 37.037 0.00 0.00 0.00 3.14
1596 1786 1.597195 GACAACGACAGTGATGTGCAA 59.403 47.619 0.00 0.00 0.00 4.08
1600 1790 0.451628 CGACAGTGATGTGCAAAGCG 60.452 55.000 0.00 0.00 0.00 4.68
1618 1808 1.550065 CGTCGTGTTATCCTCTGCAG 58.450 55.000 7.63 7.63 0.00 4.41
1644 1834 2.559440 GCTATCAACCTTGGCTGAGAG 58.441 52.381 9.57 9.57 34.67 3.20
1771 1961 1.244019 GCAACAAGTGGGCGAGGATT 61.244 55.000 0.00 0.00 0.00 3.01
1907 2097 2.063541 GAGCAGCAACACCAAAGCGT 62.064 55.000 0.00 0.00 0.00 5.07
2091 2333 0.902531 AGGATCATGTTCCGTCCGTT 59.097 50.000 15.60 0.00 40.94 4.44
2092 2334 1.278127 AGGATCATGTTCCGTCCGTTT 59.722 47.619 15.60 0.00 40.94 3.60
2202 2444 2.202566 GGATTCCTAAGTTTCGAGCCG 58.797 52.381 0.00 0.00 0.00 5.52
2283 2528 3.997021 CAGCTTATTATCAGTTAGCCCCG 59.003 47.826 0.00 0.00 32.36 5.73
2350 2595 2.864378 CTTGCCGGAGAGATGCAGCA 62.864 60.000 5.05 0.00 36.21 4.41
2424 2669 2.203126 CTTCCGCCTCTGCATCCC 60.203 66.667 0.00 0.00 37.32 3.85
2538 2783 2.218075 GGACGTGTTCGACTCTTTTGAC 59.782 50.000 0.00 0.00 40.62 3.18
2601 2875 5.783360 TGAACTCTAAGTAAGGTTGGATGGA 59.217 40.000 0.00 0.00 0.00 3.41
2603 2877 4.159879 ACTCTAAGTAAGGTTGGATGGACG 59.840 45.833 0.00 0.00 0.00 4.79
2604 2878 4.346730 TCTAAGTAAGGTTGGATGGACGA 58.653 43.478 0.00 0.00 0.00 4.20
2605 2879 3.329929 AAGTAAGGTTGGATGGACGAC 57.670 47.619 0.00 0.00 0.00 4.34
2606 2880 1.553704 AGTAAGGTTGGATGGACGACC 59.446 52.381 0.00 0.00 43.95 4.79
2608 2882 2.660802 GGTTGGATGGACGACCGT 59.339 61.111 0.00 0.00 39.42 4.83
2619 2893 2.488355 CGACCGTCGTGGCTGTAT 59.512 61.111 12.91 0.00 43.94 2.29
2620 2894 1.153901 CGACCGTCGTGGCTGTATT 60.154 57.895 12.91 0.00 43.94 1.89
2621 2895 0.099259 CGACCGTCGTGGCTGTATTA 59.901 55.000 12.91 0.00 43.94 0.98
2622 2896 1.268896 CGACCGTCGTGGCTGTATTAT 60.269 52.381 12.91 0.00 43.94 1.28
2623 2897 2.797087 CGACCGTCGTGGCTGTATTATT 60.797 50.000 12.91 0.00 43.94 1.40
2624 2898 2.793232 GACCGTCGTGGCTGTATTATTC 59.207 50.000 0.00 0.00 43.94 1.75
2625 2899 2.429610 ACCGTCGTGGCTGTATTATTCT 59.570 45.455 0.00 0.00 43.94 2.40
2626 2900 3.118884 ACCGTCGTGGCTGTATTATTCTT 60.119 43.478 0.00 0.00 43.94 2.52
2627 2901 3.489785 CCGTCGTGGCTGTATTATTCTTC 59.510 47.826 0.00 0.00 0.00 2.87
2628 2902 4.360563 CGTCGTGGCTGTATTATTCTTCT 58.639 43.478 0.00 0.00 0.00 2.85
2629 2903 4.207224 CGTCGTGGCTGTATTATTCTTCTG 59.793 45.833 0.00 0.00 0.00 3.02
2630 2904 4.025647 GTCGTGGCTGTATTATTCTTCTGC 60.026 45.833 0.00 0.00 0.00 4.26
2631 2905 3.060272 CGTGGCTGTATTATTCTTCTGCG 60.060 47.826 0.00 0.00 0.00 5.18
2672 2946 3.081710 TGGCACAGCTGACTAGTAGTA 57.918 47.619 23.35 0.00 0.00 1.82
2709 2983 6.704493 TGAGTGTTGTAGTTTAGCCTAAGTTG 59.296 38.462 0.00 0.00 0.00 3.16
2714 2988 5.369833 TGTAGTTTAGCCTAAGTTGCAACA 58.630 37.500 30.11 10.80 0.00 3.33
2772 3046 4.156190 TGTTTTCGAAGTGTTGCCAAGTAA 59.844 37.500 0.00 0.00 0.00 2.24
2872 3146 3.211045 TGAACACTCTTTTTCTTCGGGG 58.789 45.455 0.00 0.00 0.00 5.73
2896 3170 3.411446 GATCATCATGGCCGGTAATTCA 58.589 45.455 1.90 0.00 0.00 2.57
2921 3197 3.704151 GCCCAGGCTCATTTGCTT 58.296 55.556 0.08 0.00 38.26 3.91
2923 3199 1.953231 GCCCAGGCTCATTTGCTTCC 61.953 60.000 0.08 0.00 38.26 3.46
2948 3224 9.889128 CCCATGGACAGTAAATTCAAATAAAAT 57.111 29.630 15.22 0.00 0.00 1.82
3012 3288 2.692557 AGATGCTCGAGTGCACTAGATT 59.307 45.455 26.87 16.10 46.33 2.40
3013 3289 3.131933 AGATGCTCGAGTGCACTAGATTT 59.868 43.478 26.87 15.78 46.33 2.17
3017 3293 3.579709 CTCGAGTGCACTAGATTTGTGT 58.420 45.455 26.87 0.00 37.70 3.72
3043 3319 8.879342 AAATTTTCGTGGTTAAATGACATTCA 57.121 26.923 0.05 0.00 0.00 2.57
3048 3324 5.765677 TCGTGGTTAAATGACATTCAAGGAA 59.234 36.000 0.05 0.00 0.00 3.36
3088 3369 9.905713 ACAAAATCAGGTCTAAATAATGCTCTA 57.094 29.630 0.00 0.00 0.00 2.43
3108 3389 8.131100 TGCTCTATTTGAAAACTTCTTTGACAG 58.869 33.333 0.00 0.00 0.00 3.51
3115 3399 6.463360 TGAAAACTTCTTTGACAGCCTTTTT 58.537 32.000 0.00 0.00 0.00 1.94
3152 3436 3.063997 CCTAGAATGTCATTTCACCACGC 59.936 47.826 0.00 0.00 0.00 5.34
3155 3439 2.925578 ATGTCATTTCACCACGCATG 57.074 45.000 0.00 0.00 0.00 4.06
3255 3547 2.034532 CTCATGGCCAGGTGCACA 59.965 61.111 18.43 0.00 43.89 4.57
3257 3549 1.663379 CTCATGGCCAGGTGCACATG 61.663 60.000 24.06 24.06 43.88 3.21
3258 3550 3.072468 ATGGCCAGGTGCACATGC 61.072 61.111 25.46 19.37 43.89 4.06
3268 3560 2.436646 GCACATGCACCTAGGCGT 60.437 61.111 9.30 0.00 41.59 5.68
3275 3567 0.323302 TGCACCTAGGCGTCAAATCA 59.677 50.000 9.30 0.00 36.28 2.57
3283 3575 1.225745 GCGTCAAATCACCGCTTCG 60.226 57.895 0.00 0.00 43.81 3.79
3298 3590 6.015504 CACCGCTTCGCATCATAATAATTAC 58.984 40.000 0.00 0.00 0.00 1.89
3301 3593 6.296605 CGCTTCGCATCATAATAATTACGTT 58.703 36.000 0.00 0.00 0.00 3.99
3303 3595 6.031417 GCTTCGCATCATAATAATTACGTTGC 59.969 38.462 0.00 0.00 0.00 4.17
3304 3596 6.779115 TCGCATCATAATAATTACGTTGCT 57.221 33.333 0.00 0.00 0.00 3.91
3336 3629 9.149225 GCTTAGAATCTGATAGGTACATTCATG 57.851 37.037 0.00 0.00 0.00 3.07
3342 3635 8.859236 ATCTGATAGGTACATTCATGGATTTG 57.141 34.615 0.00 0.00 0.00 2.32
3344 3637 7.933577 TCTGATAGGTACATTCATGGATTTGAC 59.066 37.037 0.00 0.00 0.00 3.18
3422 5069 9.999009 TGAATCTATGTATTTACCGATCGATAC 57.001 33.333 18.66 16.06 0.00 2.24
3476 5123 5.741011 TGTCCACATTCTTATAAGGGTGTC 58.259 41.667 20.95 16.40 0.00 3.67
3480 5127 4.809426 CACATTCTTATAAGGGTGTCGTCC 59.191 45.833 12.54 0.00 0.00 4.79
3485 5132 0.249398 ATAAGGGTGTCGTCCAGTGC 59.751 55.000 0.00 0.00 0.00 4.40
3488 5135 2.421739 GGTGTCGTCCAGTGCTGT 59.578 61.111 0.00 0.00 0.00 4.40
3505 5153 4.976116 GTGCTGTAAGGTTCAAAACATGAC 59.024 41.667 0.00 0.00 37.92 3.06
3509 5157 6.363357 GCTGTAAGGTTCAAAACATGACAATC 59.637 38.462 0.00 0.00 36.22 2.67
3519 5167 7.202526 TCAAAACATGACAATCTCCTGTTTTC 58.797 34.615 10.79 0.00 46.48 2.29
3520 5168 6.966534 AAACATGACAATCTCCTGTTTTCT 57.033 33.333 0.00 0.00 42.07 2.52
3523 5171 6.974965 ACATGACAATCTCCTGTTTTCTTTC 58.025 36.000 0.00 0.00 0.00 2.62
3524 5172 6.774656 ACATGACAATCTCCTGTTTTCTTTCT 59.225 34.615 0.00 0.00 0.00 2.52
3527 5175 8.746052 TGACAATCTCCTGTTTTCTTTCTTTA 57.254 30.769 0.00 0.00 0.00 1.85
3528 5176 9.354673 TGACAATCTCCTGTTTTCTTTCTTTAT 57.645 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.814248 GCAACCTTCGAAGACTGGGTT 60.814 52.381 26.61 18.47 42.02 4.11
1 2 0.250338 GCAACCTTCGAAGACTGGGT 60.250 55.000 26.61 13.34 36.08 4.51
2 3 0.250295 TGCAACCTTCGAAGACTGGG 60.250 55.000 26.61 12.65 35.17 4.45
3 4 0.868406 GTGCAACCTTCGAAGACTGG 59.132 55.000 26.61 13.04 34.32 4.00
4 5 1.528586 CAGTGCAACCTTCGAAGACTG 59.471 52.381 26.61 23.93 37.80 3.51
5 6 1.541233 CCAGTGCAACCTTCGAAGACT 60.541 52.381 26.61 17.44 37.80 3.24
6 7 0.868406 CCAGTGCAACCTTCGAAGAC 59.132 55.000 26.61 15.45 37.80 3.01
7 8 0.884704 GCCAGTGCAACCTTCGAAGA 60.885 55.000 26.61 2.79 37.80 2.87
8 9 1.576421 GCCAGTGCAACCTTCGAAG 59.424 57.895 18.51 18.51 37.80 3.79
9 10 2.250939 CGCCAGTGCAACCTTCGAA 61.251 57.895 0.00 0.00 37.80 3.71
10 11 2.664851 CGCCAGTGCAACCTTCGA 60.665 61.111 0.00 0.00 37.80 3.71
11 12 3.726517 CCGCCAGTGCAACCTTCG 61.727 66.667 0.00 0.00 37.80 3.79
12 13 0.887387 TAACCGCCAGTGCAACCTTC 60.887 55.000 0.00 0.00 37.80 3.46
13 14 0.889186 CTAACCGCCAGTGCAACCTT 60.889 55.000 0.00 0.00 37.80 3.50
14 15 1.302511 CTAACCGCCAGTGCAACCT 60.303 57.895 0.00 0.00 37.80 3.50
15 16 2.978018 GCTAACCGCCAGTGCAACC 61.978 63.158 0.00 0.00 37.80 3.77
16 17 2.561373 GCTAACCGCCAGTGCAAC 59.439 61.111 0.00 0.00 37.32 4.17
17 18 3.047280 CGCTAACCGCCAGTGCAA 61.047 61.111 0.00 0.00 37.32 4.08
18 19 3.818121 AACGCTAACCGCCAGTGCA 62.818 57.895 0.00 0.00 41.76 4.57
19 20 2.508755 GAAACGCTAACCGCCAGTGC 62.509 60.000 0.00 0.00 41.76 4.40
20 21 1.495951 GAAACGCTAACCGCCAGTG 59.504 57.895 0.00 0.00 41.76 3.66
21 22 2.025418 CGAAACGCTAACCGCCAGT 61.025 57.895 0.00 0.00 41.76 4.00
22 23 1.683790 CTCGAAACGCTAACCGCCAG 61.684 60.000 0.00 0.00 41.76 4.85
23 24 1.735198 CTCGAAACGCTAACCGCCA 60.735 57.895 0.00 0.00 41.76 5.69
24 25 3.078560 CTCGAAACGCTAACCGCC 58.921 61.111 0.00 0.00 41.76 6.13
25 26 2.394524 GCTCGAAACGCTAACCGC 59.605 61.111 0.00 0.00 41.76 5.68
26 27 1.138047 ATCGCTCGAAACGCTAACCG 61.138 55.000 2.77 0.00 44.21 4.44
27 28 0.297820 CATCGCTCGAAACGCTAACC 59.702 55.000 2.77 0.00 0.00 2.85
28 29 0.297820 CCATCGCTCGAAACGCTAAC 59.702 55.000 2.77 0.00 0.00 2.34
29 30 1.418342 GCCATCGCTCGAAACGCTAA 61.418 55.000 2.77 0.00 0.00 3.09
30 31 1.876714 GCCATCGCTCGAAACGCTA 60.877 57.895 2.77 0.00 0.00 4.26
31 32 3.188786 GCCATCGCTCGAAACGCT 61.189 61.111 2.77 0.00 0.00 5.07
32 33 2.886512 CTTGCCATCGCTCGAAACGC 62.887 60.000 2.77 0.00 35.36 4.84
33 34 1.059369 CTTGCCATCGCTCGAAACG 59.941 57.895 1.24 1.24 35.36 3.60
34 35 1.425428 CCTTGCCATCGCTCGAAAC 59.575 57.895 0.00 0.00 35.36 2.78
35 36 2.398554 GCCTTGCCATCGCTCGAAA 61.399 57.895 0.00 0.00 35.36 3.46
36 37 2.819595 GCCTTGCCATCGCTCGAA 60.820 61.111 0.00 0.00 35.36 3.71
47 48 1.153549 CACTACTCTCGGGCCTTGC 60.154 63.158 0.84 0.00 0.00 4.01
48 49 1.517832 CCACTACTCTCGGGCCTTG 59.482 63.158 0.84 0.00 0.00 3.61
49 50 2.359967 GCCACTACTCTCGGGCCTT 61.360 63.158 0.84 0.00 40.55 4.35
50 51 2.760385 GCCACTACTCTCGGGCCT 60.760 66.667 0.84 0.00 40.55 5.19
51 52 4.208686 CGCCACTACTCTCGGGCC 62.209 72.222 0.00 0.00 43.50 5.80
52 53 4.208686 CCGCCACTACTCTCGGGC 62.209 72.222 0.00 0.00 42.98 6.13
53 54 2.439701 TCCGCCACTACTCTCGGG 60.440 66.667 0.00 0.00 41.98 5.14
54 55 3.111939 CTCCGCCACTACTCTCGG 58.888 66.667 0.00 0.00 42.96 4.63
55 56 1.658686 AAGCTCCGCCACTACTCTCG 61.659 60.000 0.00 0.00 0.00 4.04
56 57 0.179124 CAAGCTCCGCCACTACTCTC 60.179 60.000 0.00 0.00 0.00 3.20
57 58 0.612174 TCAAGCTCCGCCACTACTCT 60.612 55.000 0.00 0.00 0.00 3.24
58 59 0.461961 ATCAAGCTCCGCCACTACTC 59.538 55.000 0.00 0.00 0.00 2.59
59 60 1.683917 CTATCAAGCTCCGCCACTACT 59.316 52.381 0.00 0.00 0.00 2.57
60 61 1.269831 CCTATCAAGCTCCGCCACTAC 60.270 57.143 0.00 0.00 0.00 2.73
61 62 1.040646 CCTATCAAGCTCCGCCACTA 58.959 55.000 0.00 0.00 0.00 2.74
62 63 0.687757 TCCTATCAAGCTCCGCCACT 60.688 55.000 0.00 0.00 0.00 4.00
63 64 0.178068 TTCCTATCAAGCTCCGCCAC 59.822 55.000 0.00 0.00 0.00 5.01
64 65 1.070758 GATTCCTATCAAGCTCCGCCA 59.929 52.381 0.00 0.00 0.00 5.69
65 66 1.802069 GATTCCTATCAAGCTCCGCC 58.198 55.000 0.00 0.00 0.00 6.13
66 67 1.269831 ACGATTCCTATCAAGCTCCGC 60.270 52.381 0.00 0.00 0.00 5.54
67 68 2.667137 GACGATTCCTATCAAGCTCCG 58.333 52.381 0.00 0.00 0.00 4.63
68 69 2.608261 CCGACGATTCCTATCAAGCTCC 60.608 54.545 0.00 0.00 0.00 4.70
69 70 2.608261 CCCGACGATTCCTATCAAGCTC 60.608 54.545 0.00 0.00 0.00 4.09
70 71 1.341531 CCCGACGATTCCTATCAAGCT 59.658 52.381 0.00 0.00 0.00 3.74
71 72 1.605712 CCCCGACGATTCCTATCAAGC 60.606 57.143 0.00 0.00 0.00 4.01
72 73 1.000955 CCCCCGACGATTCCTATCAAG 59.999 57.143 0.00 0.00 0.00 3.02
73 74 1.045407 CCCCCGACGATTCCTATCAA 58.955 55.000 0.00 0.00 0.00 2.57
74 75 2.741433 CCCCCGACGATTCCTATCA 58.259 57.895 0.00 0.00 0.00 2.15
95 96 1.754226 TCATATTTTCGCTTTGCCCCC 59.246 47.619 0.00 0.00 0.00 5.40
96 97 3.186909 GTTCATATTTTCGCTTTGCCCC 58.813 45.455 0.00 0.00 0.00 5.80
97 98 3.843999 TGTTCATATTTTCGCTTTGCCC 58.156 40.909 0.00 0.00 0.00 5.36
98 99 4.923281 AGTTGTTCATATTTTCGCTTTGCC 59.077 37.500 0.00 0.00 0.00 4.52
99 100 6.251376 CCTAGTTGTTCATATTTTCGCTTTGC 59.749 38.462 0.00 0.00 0.00 3.68
100 101 7.526608 TCCTAGTTGTTCATATTTTCGCTTTG 58.473 34.615 0.00 0.00 0.00 2.77
101 102 7.148239 CCTCCTAGTTGTTCATATTTTCGCTTT 60.148 37.037 0.00 0.00 0.00 3.51
102 103 6.316390 CCTCCTAGTTGTTCATATTTTCGCTT 59.684 38.462 0.00 0.00 0.00 4.68
103 104 5.817816 CCTCCTAGTTGTTCATATTTTCGCT 59.182 40.000 0.00 0.00 0.00 4.93
104 105 5.007724 CCCTCCTAGTTGTTCATATTTTCGC 59.992 44.000 0.00 0.00 0.00 4.70
105 106 5.007724 GCCCTCCTAGTTGTTCATATTTTCG 59.992 44.000 0.00 0.00 0.00 3.46
171 172 8.028938 GCTCTAGGCAAAACAATGAAGAAAATA 58.971 33.333 0.00 0.00 41.35 1.40
215 216 1.159905 TACAAGTCTGAGGGGGCCA 59.840 57.895 4.39 0.00 0.00 5.36
241 242 2.281484 GTTCTTGGGCAGTGGCGA 60.281 61.111 10.99 3.46 42.47 5.54
253 254 5.302823 CCCTCAAATCTTCAACCTTGTTCTT 59.697 40.000 0.00 0.00 0.00 2.52
267 268 3.181429 ACATTGACACCACCCTCAAATCT 60.181 43.478 0.00 0.00 30.32 2.40
268 269 3.157087 ACATTGACACCACCCTCAAATC 58.843 45.455 0.00 0.00 30.32 2.17
269 270 3.243359 ACATTGACACCACCCTCAAAT 57.757 42.857 0.00 0.00 30.32 2.32
270 271 2.746279 ACATTGACACCACCCTCAAA 57.254 45.000 0.00 0.00 30.32 2.69
271 272 2.746279 AACATTGACACCACCCTCAA 57.254 45.000 0.00 0.00 0.00 3.02
272 273 2.976185 TCTAACATTGACACCACCCTCA 59.024 45.455 0.00 0.00 0.00 3.86
273 274 3.244422 TGTCTAACATTGACACCACCCTC 60.244 47.826 0.00 0.00 39.23 4.30
293 300 2.315925 ATCTCGAATCCGTTGCATGT 57.684 45.000 0.00 0.00 37.05 3.21
366 374 2.038975 AAGAGGCCCACCGCTAGA 59.961 61.111 0.00 0.00 46.72 2.43
371 379 3.068691 TCGAGAAGAGGCCCACCG 61.069 66.667 0.00 0.00 42.76 4.94
403 412 1.097547 CCAAGGGACATCATCGCCAC 61.098 60.000 0.00 0.00 41.22 5.01
416 433 1.447838 CGTCATCGGACACCAAGGG 60.448 63.158 0.00 0.00 44.54 3.95
480 497 7.163441 AGAACCATGAAAAATTTAGCTGCAAT 58.837 30.769 1.02 0.00 0.00 3.56
496 513 6.068010 ACCACATTTGTAGAAAGAACCATGA 58.932 36.000 0.00 0.00 0.00 3.07
518 535 1.395826 CGAGACATGGAGGGAGGACC 61.396 65.000 0.00 0.00 40.67 4.46
561 578 9.888878 CCACATGCTATTAGATAAATGTCAAAG 57.111 33.333 0.00 0.00 0.00 2.77
573 591 9.693739 TTAAAGAAATTCCCACATGCTATTAGA 57.306 29.630 0.00 0.00 0.00 2.10
635 655 0.673644 GAGAAAGTAGCCGCCTTGCA 60.674 55.000 0.00 0.00 0.00 4.08
637 657 2.003301 GAAGAGAAAGTAGCCGCCTTG 58.997 52.381 0.00 0.00 0.00 3.61
716 744 1.482954 CCTGGATGCTCTCTCTGTCA 58.517 55.000 0.00 0.00 0.00 3.58
891 922 2.888594 TCTGTAACTTCTATGGCGTGC 58.111 47.619 0.00 0.00 0.00 5.34
895 926 3.628032 GCCCTTTCTGTAACTTCTATGGC 59.372 47.826 0.00 0.00 0.00 4.40
1277 1308 4.086199 AGATGAAGAAGAAGACGACGAC 57.914 45.455 0.00 0.00 0.00 4.34
1278 1309 4.456222 AGAAGATGAAGAAGAAGACGACGA 59.544 41.667 0.00 0.00 0.00 4.20
1279 1310 4.728534 AGAAGATGAAGAAGAAGACGACG 58.271 43.478 0.00 0.00 0.00 5.12
1280 1311 6.386654 AGAAGAAGATGAAGAAGAAGACGAC 58.613 40.000 0.00 0.00 0.00 4.34
1281 1312 6.349777 GGAGAAGAAGATGAAGAAGAAGACGA 60.350 42.308 0.00 0.00 0.00 4.20
1282 1313 5.804979 GGAGAAGAAGATGAAGAAGAAGACG 59.195 44.000 0.00 0.00 0.00 4.18
1283 1314 6.935167 AGGAGAAGAAGATGAAGAAGAAGAC 58.065 40.000 0.00 0.00 0.00 3.01
1284 1315 7.454380 AGAAGGAGAAGAAGATGAAGAAGAAGA 59.546 37.037 0.00 0.00 0.00 2.87
1285 1316 7.614494 AGAAGGAGAAGAAGATGAAGAAGAAG 58.386 38.462 0.00 0.00 0.00 2.85
1286 1317 7.552050 AGAAGGAGAAGAAGATGAAGAAGAA 57.448 36.000 0.00 0.00 0.00 2.52
1287 1318 7.454380 AGAAGAAGGAGAAGAAGATGAAGAAGA 59.546 37.037 0.00 0.00 0.00 2.87
1288 1319 7.614494 AGAAGAAGGAGAAGAAGATGAAGAAG 58.386 38.462 0.00 0.00 0.00 2.85
1289 1320 7.552050 AGAAGAAGGAGAAGAAGATGAAGAA 57.448 36.000 0.00 0.00 0.00 2.52
1290 1321 7.454380 AGAAGAAGAAGGAGAAGAAGATGAAGA 59.546 37.037 0.00 0.00 0.00 2.87
1291 1322 7.614494 AGAAGAAGAAGGAGAAGAAGATGAAG 58.386 38.462 0.00 0.00 0.00 3.02
1292 1323 7.552050 AGAAGAAGAAGGAGAAGAAGATGAA 57.448 36.000 0.00 0.00 0.00 2.57
1328 1359 3.564027 CCGAAACCCAGCGCGATC 61.564 66.667 12.10 0.00 0.00 3.69
1348 1379 2.739913 ACGTGCGCACATATACAAGTTT 59.260 40.909 37.03 3.42 0.00 2.66
1356 1387 3.159353 TCTTAGAACGTGCGCACATAT 57.841 42.857 37.03 24.94 0.00 1.78
1509 1696 5.125900 TGCATTTGTTGGTAATCATCTCTGG 59.874 40.000 0.00 0.00 0.00 3.86
1510 1697 6.198650 TGCATTTGTTGGTAATCATCTCTG 57.801 37.500 0.00 0.00 0.00 3.35
1596 1786 1.736032 GCAGAGGATAACACGACGCTT 60.736 52.381 0.00 0.00 0.00 4.68
1600 1790 2.656560 ACTGCAGAGGATAACACGAC 57.343 50.000 23.35 0.00 0.00 4.34
1618 1808 1.732405 GCCAAGGTTGATAGCGCAAAC 60.732 52.381 11.47 8.45 35.72 2.93
1644 1834 1.782044 ATTGCATTGCCGTTGTGAAC 58.218 45.000 6.12 0.00 0.00 3.18
1684 1874 0.183492 ACTTGCAGCCACTTCAGGAA 59.817 50.000 0.00 0.00 0.00 3.36
1685 1875 0.183492 AACTTGCAGCCACTTCAGGA 59.817 50.000 0.00 0.00 0.00 3.86
1686 1876 0.595095 GAACTTGCAGCCACTTCAGG 59.405 55.000 0.00 0.00 0.00 3.86
1962 2152 4.204573 CGAACGAATACTGAAGAACGGATC 59.795 45.833 0.00 0.00 0.00 3.36
2091 2333 2.668212 CCGCCGGAAGAGTTGCAA 60.668 61.111 5.05 0.00 0.00 4.08
2155 2397 4.308265 CACATCTGATCATGCGAGATTCT 58.692 43.478 0.00 0.00 0.00 2.40
2190 2432 3.340789 GGCAACGGCTCGAAACTT 58.659 55.556 1.50 0.00 40.87 2.66
2231 2473 2.048222 TCGCTTCGCCTTCAGTGG 60.048 61.111 0.00 0.00 0.00 4.00
2232 2474 2.734673 GCTCGCTTCGCCTTCAGTG 61.735 63.158 0.00 0.00 0.00 3.66
2233 2475 2.433318 GCTCGCTTCGCCTTCAGT 60.433 61.111 0.00 0.00 0.00 3.41
2283 2528 5.107065 GGGATGATGATAAAACGACGATTCC 60.107 44.000 0.00 0.00 0.00 3.01
2350 2595 2.842256 CGACGAACCCGGGATCGAT 61.842 63.158 46.99 34.00 41.82 3.59
2424 2669 4.081030 GGCATCATCATCGGCGCG 62.081 66.667 0.00 0.00 0.00 6.86
2603 2877 2.503920 ATAATACAGCCACGACGGTC 57.496 50.000 0.00 0.00 36.97 4.79
2604 2878 2.429610 AGAATAATACAGCCACGACGGT 59.570 45.455 0.00 0.00 36.97 4.83
2605 2879 3.093717 AGAATAATACAGCCACGACGG 57.906 47.619 0.00 0.00 38.11 4.79
2606 2880 4.207224 CAGAAGAATAATACAGCCACGACG 59.793 45.833 0.00 0.00 0.00 5.12
2607 2881 4.025647 GCAGAAGAATAATACAGCCACGAC 60.026 45.833 0.00 0.00 0.00 4.34
2608 2882 4.119862 GCAGAAGAATAATACAGCCACGA 58.880 43.478 0.00 0.00 0.00 4.35
2609 2883 3.060272 CGCAGAAGAATAATACAGCCACG 60.060 47.826 0.00 0.00 0.00 4.94
2610 2884 3.871594 ACGCAGAAGAATAATACAGCCAC 59.128 43.478 0.00 0.00 0.00 5.01
2611 2885 4.119862 GACGCAGAAGAATAATACAGCCA 58.880 43.478 0.00 0.00 0.00 4.75
2612 2886 4.372656 AGACGCAGAAGAATAATACAGCC 58.627 43.478 0.00 0.00 0.00 4.85
2613 2887 7.644986 ATTAGACGCAGAAGAATAATACAGC 57.355 36.000 0.00 0.00 0.00 4.40
2614 2888 8.491152 CCAATTAGACGCAGAAGAATAATACAG 58.509 37.037 0.00 0.00 0.00 2.74
2615 2889 8.201464 TCCAATTAGACGCAGAAGAATAATACA 58.799 33.333 0.00 0.00 0.00 2.29
2616 2890 8.488764 GTCCAATTAGACGCAGAAGAATAATAC 58.511 37.037 0.00 0.00 0.00 1.89
2617 2891 8.421784 AGTCCAATTAGACGCAGAAGAATAATA 58.578 33.333 0.00 0.00 41.83 0.98
2618 2892 7.275920 AGTCCAATTAGACGCAGAAGAATAAT 58.724 34.615 0.00 0.00 41.83 1.28
2619 2893 6.640518 AGTCCAATTAGACGCAGAAGAATAA 58.359 36.000 0.00 0.00 41.83 1.40
2620 2894 6.222038 AGTCCAATTAGACGCAGAAGAATA 57.778 37.500 0.00 0.00 41.83 1.75
2621 2895 5.091261 AGTCCAATTAGACGCAGAAGAAT 57.909 39.130 0.00 0.00 41.83 2.40
2622 2896 4.537135 AGTCCAATTAGACGCAGAAGAA 57.463 40.909 0.00 0.00 41.83 2.52
2623 2897 4.142227 GGTAGTCCAATTAGACGCAGAAGA 60.142 45.833 0.00 0.00 41.83 2.87
2624 2898 4.113354 GGTAGTCCAATTAGACGCAGAAG 58.887 47.826 0.00 0.00 41.83 2.85
2625 2899 3.767673 AGGTAGTCCAATTAGACGCAGAA 59.232 43.478 0.00 0.00 41.83 3.02
2626 2900 3.130516 CAGGTAGTCCAATTAGACGCAGA 59.869 47.826 0.00 0.00 41.83 4.26
2627 2901 3.119101 ACAGGTAGTCCAATTAGACGCAG 60.119 47.826 0.00 0.00 41.83 5.18
2628 2902 2.829720 ACAGGTAGTCCAATTAGACGCA 59.170 45.455 0.00 0.00 41.83 5.24
2629 2903 3.521947 ACAGGTAGTCCAATTAGACGC 57.478 47.619 0.00 0.00 41.83 5.19
2630 2904 5.103000 CAGAACAGGTAGTCCAATTAGACG 58.897 45.833 0.00 0.00 41.83 4.18
2631 2905 5.420409 CCAGAACAGGTAGTCCAATTAGAC 58.580 45.833 0.00 0.00 37.01 2.59
2672 2946 9.959721 AAACTACAACACTCATCAATAGGTAAT 57.040 29.630 0.00 0.00 0.00 1.89
2772 3046 6.371548 CACTTACACACCATACTAACTGCATT 59.628 38.462 0.00 0.00 0.00 3.56
2872 3146 0.976641 TACCGGCCATGATGATCCTC 59.023 55.000 0.00 0.00 0.00 3.71
2921 3197 8.657387 TTTATTTGAATTTACTGTCCATGGGA 57.343 30.769 13.02 0.00 0.00 4.37
2973 3249 8.671921 CGAGCATCTTTGATGCCTAATAATAAT 58.328 33.333 23.59 6.21 45.59 1.28
2974 3250 7.877612 TCGAGCATCTTTGATGCCTAATAATAA 59.122 33.333 23.59 2.97 45.59 1.40
2975 3251 7.386059 TCGAGCATCTTTGATGCCTAATAATA 58.614 34.615 23.59 4.22 45.59 0.98
2976 3252 6.233434 TCGAGCATCTTTGATGCCTAATAAT 58.767 36.000 23.59 8.06 45.59 1.28
2977 3253 5.610398 TCGAGCATCTTTGATGCCTAATAA 58.390 37.500 23.59 6.33 45.59 1.40
2978 3254 5.213891 TCGAGCATCTTTGATGCCTAATA 57.786 39.130 23.59 7.45 45.59 0.98
2979 3255 4.063689 CTCGAGCATCTTTGATGCCTAAT 58.936 43.478 23.59 9.61 45.59 1.73
2980 3256 3.118629 ACTCGAGCATCTTTGATGCCTAA 60.119 43.478 23.59 11.62 45.59 2.69
2981 3257 2.432146 ACTCGAGCATCTTTGATGCCTA 59.568 45.455 23.59 11.90 45.59 3.93
2982 3258 1.209019 ACTCGAGCATCTTTGATGCCT 59.791 47.619 23.59 13.91 45.59 4.75
3012 3288 9.021863 GTCATTTAACCACGAAAATTTACACAA 57.978 29.630 0.00 0.00 0.00 3.33
3013 3289 8.188799 TGTCATTTAACCACGAAAATTTACACA 58.811 29.630 0.00 0.00 0.00 3.72
3017 3293 9.967346 TGAATGTCATTTAACCACGAAAATTTA 57.033 25.926 0.00 0.00 0.00 1.40
3088 3369 6.225981 AGGCTGTCAAAGAAGTTTTCAAAT 57.774 33.333 0.00 0.00 0.00 2.32
3092 3373 6.968131 AAAAAGGCTGTCAAAGAAGTTTTC 57.032 33.333 0.00 0.00 0.00 2.29
3115 3399 1.899814 TCTAGGAGCTCTCGGCAAAAA 59.100 47.619 14.64 0.00 44.79 1.94
3131 3415 3.684305 TGCGTGGTGAAATGACATTCTAG 59.316 43.478 0.05 0.00 0.00 2.43
3133 3417 2.503331 TGCGTGGTGAAATGACATTCT 58.497 42.857 0.05 0.00 0.00 2.40
3255 3547 1.065491 TGATTTGACGCCTAGGTGCAT 60.065 47.619 22.51 9.21 0.00 3.96
3257 3549 0.727398 GTGATTTGACGCCTAGGTGC 59.273 55.000 22.51 14.95 0.00 5.01
3258 3550 1.369625 GGTGATTTGACGCCTAGGTG 58.630 55.000 21.04 21.04 37.45 4.00
3261 3553 2.006772 GCGGTGATTTGACGCCTAG 58.993 57.895 0.00 0.00 46.92 3.02
3262 3554 4.195308 GCGGTGATTTGACGCCTA 57.805 55.556 0.00 0.00 46.92 3.93
3304 3596 9.588096 TGTACCTATCAGATTCTAAGCTTATGA 57.412 33.333 6.64 7.87 0.00 2.15
3311 3603 9.650539 CCATGAATGTACCTATCAGATTCTAAG 57.349 37.037 0.00 0.00 0.00 2.18
3313 3605 8.956446 TCCATGAATGTACCTATCAGATTCTA 57.044 34.615 0.00 0.00 0.00 2.10
3336 3629 6.581171 AATGACCAGAGAAAAGTCAAATCC 57.419 37.500 0.00 0.00 43.29 3.01
3342 3635 7.849804 TTATGCTAATGACCAGAGAAAAGTC 57.150 36.000 0.00 0.00 0.00 3.01
3412 5059 8.406297 TCTCTAAAATCATATGGTATCGATCGG 58.594 37.037 16.41 0.00 0.00 4.18
3416 5063 8.462811 GCTCTCTCTAAAATCATATGGTATCGA 58.537 37.037 2.13 0.00 0.00 3.59
3422 5069 9.941325 AAGTATGCTCTCTCTAAAATCATATGG 57.059 33.333 2.13 0.00 0.00 2.74
3449 5096 6.603201 CACCCTTATAAGAATGTGGACATTGT 59.397 38.462 14.28 3.07 45.72 2.71
3476 5123 1.270094 TGAACCTTACAGCACTGGACG 60.270 52.381 2.21 0.00 34.19 4.79
3480 5127 4.630894 TGTTTTGAACCTTACAGCACTG 57.369 40.909 0.00 0.00 0.00 3.66
3485 5132 7.651808 AGATTGTCATGTTTTGAACCTTACAG 58.348 34.615 0.00 0.00 35.70 2.74
3488 5135 7.004086 AGGAGATTGTCATGTTTTGAACCTTA 58.996 34.615 0.00 0.00 35.70 2.69


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

AutoCloner maintained by Alex Coulton.