Multiple sequence alignment - TraesCS6D01G336000

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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 TraesCS6D01G336000 chr6D 100.000 4080 0 0 1 4080 437162517 437166596 0.000000e+00 7535
1 TraesCS6D01G336000 chr6B 93.612 2395 104 30 1703 4080 661338723 661341085 0.000000e+00 3530
2 TraesCS6D01G336000 chr6B 90.124 1367 95 17 204 1558 661337322 661338660 0.000000e+00 1740
3 TraesCS6D01G336000 chr6B 88.732 213 12 6 1294 1503 464518008 464518211 2.430000e-62 250
4 TraesCS6D01G336000 chr6A 93.028 2381 107 32 1739 4080 585427764 585430124 0.000000e+00 3422
5 TraesCS6D01G336000 chr6A 90.438 753 34 15 826 1556 585426784 585427520 0.000000e+00 957
6 TraesCS6D01G336000 chr6A 84.383 397 27 19 9 381 585424503 585424888 1.390000e-94 357
7 TraesCS6D01G336000 chr6A 88.095 210 16 4 1294 1503 1327075 1327275 1.470000e-59 241
8 TraesCS6D01G336000 chr4B 94.029 1189 39 9 1758 2946 429268965 429270121 0.000000e+00 1773
9 TraesCS6D01G336000 chr3A 94.995 999 44 3 1948 2946 681625860 681626852 0.000000e+00 1563
10 TraesCS6D01G336000 chr3A 80.783 281 18 10 1229 1503 189304022 189304272 1.940000e-43 187
11 TraesCS6D01G336000 chr7A 92.164 804 30 13 1758 2561 130189204 130189974 0.000000e+00 1105
12 TraesCS6D01G336000 chr7A 96.377 276 10 0 2597 2872 130189973 130190248 4.810000e-124 455
13 TraesCS6D01G336000 chr7A 92.994 157 8 1 2716 2872 130190395 130190548 4.100000e-55 226
14 TraesCS6D01G336000 chr4A 94.464 289 16 0 2655 2943 589150266 589150554 2.890000e-121 446
15 TraesCS6D01G336000 chr3D 86.167 347 27 11 1165 1503 3897080 3896747 5.020000e-94 355
16 TraesCS6D01G336000 chr3D 88.034 117 11 3 1769 1884 139731815 139731929 7.110000e-28 135
17 TraesCS6D01G336000 chr1B 88.256 281 18 7 1229 1503 683657198 683657469 5.090000e-84 322
18 TraesCS6D01G336000 chr1B 88.448 277 17 7 1233 1503 143667532 143667265 1.830000e-83 320
19 TraesCS6D01G336000 chr5B 89.048 210 14 4 1294 1503 676286805 676286605 6.770000e-63 252
20 TraesCS6D01G336000 chr5B 81.106 217 11 8 1287 1503 699305032 699304846 3.290000e-31 147
21 TraesCS6D01G336000 chr5B 87.179 117 12 3 1769 1884 548545638 548545524 3.310000e-26 130
22 TraesCS6D01G336000 chr1D 84.528 265 23 10 1163 1421 82790000 82789748 3.150000e-61 246
23 TraesCS6D01G336000 chr2B 86.486 148 14 5 1769 1915 632573621 632573479 1.520000e-34 158
24 TraesCS6D01G336000 chr1A 88.393 112 11 2 1773 1884 300591178 300591069 2.560000e-27 134
25 TraesCS6D01G336000 chr7B 87.179 117 12 3 1769 1884 681948919 681949033 3.310000e-26 130


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 TraesCS6D01G336000 chr6D 437162517 437166596 4079 False 7535.000000 7535 100.000 1 4080 1 chr6D.!!$F1 4079
1 TraesCS6D01G336000 chr6B 661337322 661341085 3763 False 2635.000000 3530 91.868 204 4080 2 chr6B.!!$F2 3876
2 TraesCS6D01G336000 chr6A 585424503 585430124 5621 False 1578.666667 3422 89.283 9 4080 3 chr6A.!!$F2 4071
3 TraesCS6D01G336000 chr4B 429268965 429270121 1156 False 1773.000000 1773 94.029 1758 2946 1 chr4B.!!$F1 1188
4 TraesCS6D01G336000 chr3A 681625860 681626852 992 False 1563.000000 1563 94.995 1948 2946 1 chr3A.!!$F2 998
5 TraesCS6D01G336000 chr7A 130189204 130190548 1344 False 595.333333 1105 93.845 1758 2872 3 chr7A.!!$F1 1114

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
34 35 0.034896 GTCACACCACCGTGGATTCT 59.965 55.0 24.8 0.0 44.86 2.40 F
183 205 0.036952 ACCCGTGTTGATGCTCTCAG 60.037 55.0 0.0 0.0 34.68 3.35 F
490 521 0.112218 ATGTAGTTGGGTGCCAGCAA 59.888 50.0 0.0 0.0 37.20 3.91 F
957 2521 0.235926 GAACTCACTCGCCAGTTTGC 59.764 55.0 0.0 0.0 32.83 3.68 F
1568 3160 0.314302 GCACAGGTAGACGAGTGTGT 59.686 55.0 0.0 0.0 41.94 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1843 3565 0.389166 CAGGACGAGACAAGACCTGC 60.389 60.000 0.00 0.00 42.49 4.85 R
1855 3577 0.671796 TCGAAAGAAGTGCAGGACGA 59.328 50.000 0.00 0.00 37.03 4.20 R
1856 3578 1.497991 TTCGAAAGAAGTGCAGGACG 58.502 50.000 0.00 0.00 46.92 4.79 R
1928 3650 2.159226 TGCATGCGCATCAATCAAATCA 60.159 40.909 22.51 4.52 45.36 2.57 R
3483 5366 0.244721 TGTCGAGTCTGGTCTGCATG 59.755 55.000 0.00 0.00 0.00 4.06 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 0.669625 GGCGGAACTAGTCACACCAC 60.670 60.000 0.00 0.00 0.00 4.16
34 35 0.034896 GTCACACCACCGTGGATTCT 59.965 55.000 24.80 0.00 44.86 2.40
52 53 5.298527 GGATTCTTCTAAAATAACCGGTGGG 59.701 44.000 8.52 0.00 40.11 4.61
69 70 4.814771 CGGTGGGGTATCTTTTGTAAGATC 59.185 45.833 3.82 0.00 45.82 2.75
73 74 5.131067 GGGGTATCTTTTGTAAGATCCACC 58.869 45.833 3.82 7.29 45.82 4.61
74 75 5.339695 GGGGTATCTTTTGTAAGATCCACCA 60.340 44.000 16.09 0.00 45.18 4.17
131 132 3.129988 ACCTACATTCCGACCTTAACTCG 59.870 47.826 0.00 0.00 0.00 4.18
146 147 3.627395 AACTCGATGGAGCCAACAATA 57.373 42.857 4.41 0.00 44.48 1.90
147 148 3.627395 ACTCGATGGAGCCAACAATAA 57.373 42.857 4.41 0.00 44.48 1.40
148 149 4.156455 ACTCGATGGAGCCAACAATAAT 57.844 40.909 4.41 0.00 44.48 1.28
153 154 6.038161 CTCGATGGAGCCAACAATAATGTTAA 59.962 38.462 0.00 0.00 39.49 2.01
183 205 0.036952 ACCCGTGTTGATGCTCTCAG 60.037 55.000 0.00 0.00 34.68 3.35
223 248 9.973661 TTGACATTAGGATGAAAAGGATAAAGA 57.026 29.630 0.00 0.00 36.73 2.52
265 290 6.930731 TGATTGGTTTAGCTAAATTTCACCC 58.069 36.000 21.28 16.18 0.00 4.61
325 356 8.669946 TTTCCTTTTTCTTGTCTTTGTGTTTT 57.330 26.923 0.00 0.00 0.00 2.43
326 357 7.883229 TCCTTTTTCTTGTCTTTGTGTTTTC 57.117 32.000 0.00 0.00 0.00 2.29
327 358 7.666623 TCCTTTTTCTTGTCTTTGTGTTTTCT 58.333 30.769 0.00 0.00 0.00 2.52
328 359 8.798402 TCCTTTTTCTTGTCTTTGTGTTTTCTA 58.202 29.630 0.00 0.00 0.00 2.10
335 366 9.052759 TCTTGTCTTTGTGTTTTCTATACTTCC 57.947 33.333 0.00 0.00 0.00 3.46
352 383 0.511221 TCCTTTTCTTCTTTCGCGCG 59.489 50.000 26.76 26.76 0.00 6.86
357 388 0.596600 TTCTTCTTTCGCGCGTGTCT 60.597 50.000 30.98 0.00 0.00 3.41
381 412 1.656587 AGGGATGTGCAACTGTAGGA 58.343 50.000 0.00 0.00 38.04 2.94
382 413 2.200081 AGGGATGTGCAACTGTAGGAT 58.800 47.619 0.00 0.00 38.04 3.24
391 422 2.738846 GCAACTGTAGGATGTGTGACTG 59.261 50.000 0.00 0.00 0.00 3.51
392 423 2.738846 CAACTGTAGGATGTGTGACTGC 59.261 50.000 0.00 0.00 0.00 4.40
401 432 5.143369 AGGATGTGTGACTGCTGAGATATA 58.857 41.667 0.00 0.00 0.00 0.86
407 438 7.955918 TGTGTGACTGCTGAGATATATGTAAT 58.044 34.615 0.00 0.00 0.00 1.89
422 453 2.853705 TGTAATTATAGTTGCCCGGCC 58.146 47.619 7.03 0.00 0.00 6.13
447 478 5.428253 ACCGAGATATGCAATTGTAGTTGT 58.572 37.500 7.40 0.00 0.00 3.32
458 489 1.735559 GTAGTTGTGCCCGTCCGAC 60.736 63.158 0.00 0.00 0.00 4.79
490 521 0.112218 ATGTAGTTGGGTGCCAGCAA 59.888 50.000 0.00 0.00 37.20 3.91
519 550 5.885912 ACTTGAGTGGAAAAGAGCAAAACTA 59.114 36.000 0.00 0.00 0.00 2.24
528 559 6.693113 GGAAAAGAGCAAAACTAGAACACAAG 59.307 38.462 0.00 0.00 0.00 3.16
573 604 9.995003 AAAAGGTGCACTATGAAATGATAAAAA 57.005 25.926 17.98 0.00 0.00 1.94
575 606 7.260603 AGGTGCACTATGAAATGATAAAAAGC 58.739 34.615 17.98 0.00 0.00 3.51
636 667 9.825972 AAATTGACGAGTGTAATGTTAATCAAG 57.174 29.630 0.00 0.00 0.00 3.02
786 2262 6.263168 CACCAAGAGTACAAGAAACCTCAAAT 59.737 38.462 0.00 0.00 0.00 2.32
788 2264 7.444487 ACCAAGAGTACAAGAAACCTCAAATAC 59.556 37.037 0.00 0.00 0.00 1.89
815 2291 6.603095 ACGTTTATCTCAAAAGAATGCTGAC 58.397 36.000 0.00 0.00 34.49 3.51
819 2295 7.984422 TTATCTCAAAAGAATGCTGACTTGA 57.016 32.000 0.00 0.00 34.49 3.02
822 2386 3.569701 TCAAAAGAATGCTGACTTGACCC 59.430 43.478 0.00 0.00 0.00 4.46
824 2388 2.486472 AGAATGCTGACTTGACCCTG 57.514 50.000 0.00 0.00 0.00 4.45
844 2408 5.507985 CCCTGAATGTTTTGGTCACTTTCTC 60.508 44.000 0.00 0.00 32.25 2.87
870 2434 3.243401 GGTCGCTCTTTGTTTGGTCATTT 60.243 43.478 0.00 0.00 0.00 2.32
876 2440 7.389330 TCGCTCTTTGTTTGGTCATTTATCTAA 59.611 33.333 0.00 0.00 0.00 2.10
883 2447 8.196802 TGTTTGGTCATTTATCTAATCTGTCG 57.803 34.615 0.00 0.00 0.00 4.35
921 2485 7.144661 TGAACTTGTCGCATAATGTCAAATTT 58.855 30.769 0.00 0.00 0.00 1.82
938 2502 3.892740 TTGTCCCGGATGCGTGTGG 62.893 63.158 0.73 0.00 0.00 4.17
957 2521 0.235926 GAACTCACTCGCCAGTTTGC 59.764 55.000 0.00 0.00 32.83 3.68
974 2538 2.357517 CACGACAGGGACACAGGC 60.358 66.667 0.00 0.00 0.00 4.85
975 2539 3.991051 ACGACAGGGACACAGGCG 61.991 66.667 0.00 0.00 0.00 5.52
992 2556 2.478989 CGACTCGCCAGAACCTCTA 58.521 57.895 0.00 0.00 0.00 2.43
994 2558 1.405821 CGACTCGCCAGAACCTCTATT 59.594 52.381 0.00 0.00 0.00 1.73
1002 2566 3.449018 GCCAGAACCTCTATTGAGTCTCA 59.551 47.826 0.00 0.00 38.61 3.27
1003 2567 4.100808 GCCAGAACCTCTATTGAGTCTCAT 59.899 45.833 2.68 0.00 38.61 2.90
1004 2568 5.303078 GCCAGAACCTCTATTGAGTCTCATA 59.697 44.000 2.68 0.00 38.61 2.15
1005 2569 6.014669 GCCAGAACCTCTATTGAGTCTCATAT 60.015 42.308 2.68 3.45 38.61 1.78
1006 2570 7.177568 GCCAGAACCTCTATTGAGTCTCATATA 59.822 40.741 2.68 4.38 38.61 0.86
1007 2571 9.253832 CCAGAACCTCTATTGAGTCTCATATAT 57.746 37.037 2.68 0.00 38.61 0.86
1156 2733 1.448540 CAGACCAGACATGACGCCC 60.449 63.158 0.00 0.00 0.00 6.13
1228 2808 2.964389 GCCGCGCTCAAGATCTCC 60.964 66.667 5.56 0.00 0.00 3.71
1558 3150 2.586079 CGATGCCCGCACAGGTAG 60.586 66.667 0.00 0.00 38.74 3.18
1561 3153 3.371097 ATGCCCGCACAGGTAGACG 62.371 63.158 0.00 0.00 38.74 4.18
1563 3155 2.490217 CCCGCACAGGTAGACGAG 59.510 66.667 0.00 0.00 38.74 4.18
1564 3156 2.341101 CCCGCACAGGTAGACGAGT 61.341 63.158 0.00 0.00 38.74 4.18
1565 3157 1.154016 CCGCACAGGTAGACGAGTG 60.154 63.158 0.00 0.00 34.51 3.51
1567 3159 0.729478 CGCACAGGTAGACGAGTGTG 60.729 60.000 0.00 0.00 42.66 3.82
1568 3160 0.314302 GCACAGGTAGACGAGTGTGT 59.686 55.000 0.00 0.00 41.94 3.72
1570 3162 1.607148 CACAGGTAGACGAGTGTGTCA 59.393 52.381 0.00 0.00 41.41 3.58
1571 3163 1.880675 ACAGGTAGACGAGTGTGTCAG 59.119 52.381 0.00 0.00 41.41 3.51
1576 3168 3.501445 GGTAGACGAGTGTGTCAGTACTT 59.499 47.826 0.00 0.00 41.41 2.24
1589 3306 6.016527 TGTGTCAGTACTTATCTCGTTTCAGT 60.017 38.462 0.00 0.00 0.00 3.41
1600 3317 9.542462 CTTATCTCGTTTCAGTATAAAATCCCA 57.458 33.333 0.00 0.00 0.00 4.37
1601 3318 9.893634 TTATCTCGTTTCAGTATAAAATCCCAA 57.106 29.630 0.00 0.00 0.00 4.12
1602 3319 8.980481 ATCTCGTTTCAGTATAAAATCCCAAT 57.020 30.769 0.00 0.00 0.00 3.16
1603 3320 8.801882 TCTCGTTTCAGTATAAAATCCCAATT 57.198 30.769 0.00 0.00 0.00 2.32
1604 3321 8.889717 TCTCGTTTCAGTATAAAATCCCAATTC 58.110 33.333 0.00 0.00 0.00 2.17
1605 3322 7.690228 TCGTTTCAGTATAAAATCCCAATTCG 58.310 34.615 0.00 0.00 0.00 3.34
1606 3323 7.334921 TCGTTTCAGTATAAAATCCCAATTCGT 59.665 33.333 0.00 0.00 0.00 3.85
1607 3324 7.428183 CGTTTCAGTATAAAATCCCAATTCGTG 59.572 37.037 0.00 0.00 0.00 4.35
1608 3325 6.371809 TCAGTATAAAATCCCAATTCGTGC 57.628 37.500 0.00 0.00 0.00 5.34
1609 3326 5.883115 TCAGTATAAAATCCCAATTCGTGCA 59.117 36.000 0.00 0.00 0.00 4.57
1612 3329 6.772716 AGTATAAAATCCCAATTCGTGCATCT 59.227 34.615 0.00 0.00 0.00 2.90
1614 3331 5.913137 AAAATCCCAATTCGTGCATCTAA 57.087 34.783 0.00 0.00 0.00 2.10
1615 3332 5.913137 AAATCCCAATTCGTGCATCTAAA 57.087 34.783 0.00 0.00 0.00 1.85
1616 3333 4.900635 ATCCCAATTCGTGCATCTAAAC 57.099 40.909 0.00 0.00 0.00 2.01
1617 3334 3.950397 TCCCAATTCGTGCATCTAAACT 58.050 40.909 0.00 0.00 0.00 2.66
1618 3335 4.331968 TCCCAATTCGTGCATCTAAACTT 58.668 39.130 0.00 0.00 0.00 2.66
1622 3339 6.093495 CCCAATTCGTGCATCTAAACTTAGAA 59.907 38.462 3.39 0.00 42.55 2.10
1623 3340 7.361713 CCCAATTCGTGCATCTAAACTTAGAAA 60.362 37.037 3.39 0.00 42.55 2.52
1624 3341 8.184192 CCAATTCGTGCATCTAAACTTAGAAAT 58.816 33.333 3.39 0.00 42.55 2.17
1625 3342 9.214953 CAATTCGTGCATCTAAACTTAGAAATC 57.785 33.333 3.39 0.00 42.55 2.17
1627 3344 6.403049 TCGTGCATCTAAACTTAGAAATCCA 58.597 36.000 3.39 0.00 42.55 3.41
1628 3345 7.047891 TCGTGCATCTAAACTTAGAAATCCAT 58.952 34.615 3.39 0.00 42.55 3.41
1629 3346 7.224753 TCGTGCATCTAAACTTAGAAATCCATC 59.775 37.037 3.39 0.00 42.55 3.51
1630 3347 7.225538 CGTGCATCTAAACTTAGAAATCCATCT 59.774 37.037 3.39 0.00 42.55 2.90
1631 3348 8.897752 GTGCATCTAAACTTAGAAATCCATCTT 58.102 33.333 3.39 0.00 42.55 2.40
1632 3349 9.113838 TGCATCTAAACTTAGAAATCCATCTTC 57.886 33.333 3.39 0.00 42.55 2.87
1633 3350 9.113838 GCATCTAAACTTAGAAATCCATCTTCA 57.886 33.333 3.39 0.00 42.55 3.02
1638 3355 8.792830 AAACTTAGAAATCCATCTTCATTCGA 57.207 30.769 0.00 0.00 0.00 3.71
1639 3356 8.430801 AACTTAGAAATCCATCTTCATTCGAG 57.569 34.615 0.00 0.00 0.00 4.04
1640 3357 6.481644 ACTTAGAAATCCATCTTCATTCGAGC 59.518 38.462 0.00 0.00 0.00 5.03
1641 3358 4.774124 AGAAATCCATCTTCATTCGAGCA 58.226 39.130 0.00 0.00 0.00 4.26
1643 3360 4.412796 AATCCATCTTCATTCGAGCAGA 57.587 40.909 0.00 0.00 0.00 4.26
1644 3361 4.620589 ATCCATCTTCATTCGAGCAGAT 57.379 40.909 0.00 0.00 0.00 2.90
1645 3362 3.725490 TCCATCTTCATTCGAGCAGATG 58.275 45.455 13.99 13.99 41.58 2.90
1646 3363 3.385755 TCCATCTTCATTCGAGCAGATGA 59.614 43.478 19.15 9.31 43.68 2.92
1647 3364 4.124970 CCATCTTCATTCGAGCAGATGAA 58.875 43.478 19.15 14.79 43.68 2.57
1648 3365 4.573607 CCATCTTCATTCGAGCAGATGAAA 59.426 41.667 19.15 9.30 43.68 2.69
1649 3366 5.499935 CATCTTCATTCGAGCAGATGAAAC 58.500 41.667 15.11 0.00 43.68 2.78
1650 3367 4.825422 TCTTCATTCGAGCAGATGAAACT 58.175 39.130 10.56 0.00 33.32 2.66
1651 3368 5.965922 TCTTCATTCGAGCAGATGAAACTA 58.034 37.500 10.56 0.00 33.32 2.24
1652 3369 6.038985 TCTTCATTCGAGCAGATGAAACTAG 58.961 40.000 10.56 1.33 33.32 2.57
1653 3370 5.582689 TCATTCGAGCAGATGAAACTAGA 57.417 39.130 0.00 0.00 0.00 2.43
1654 3371 6.154203 TCATTCGAGCAGATGAAACTAGAT 57.846 37.500 0.00 0.00 0.00 1.98
1655 3372 6.212235 TCATTCGAGCAGATGAAACTAGATC 58.788 40.000 0.00 0.00 0.00 2.75
1656 3373 4.216366 TCGAGCAGATGAAACTAGATCG 57.784 45.455 0.00 0.00 0.00 3.69
1657 3374 2.723658 CGAGCAGATGAAACTAGATCGC 59.276 50.000 0.00 0.00 0.00 4.58
1658 3375 3.056304 GAGCAGATGAAACTAGATCGCC 58.944 50.000 0.00 0.00 0.00 5.54
1659 3376 2.432146 AGCAGATGAAACTAGATCGCCA 59.568 45.455 0.00 0.00 0.00 5.69
1660 3377 3.070734 AGCAGATGAAACTAGATCGCCAT 59.929 43.478 0.00 0.00 0.00 4.40
1661 3378 3.186001 GCAGATGAAACTAGATCGCCATG 59.814 47.826 0.00 0.00 0.00 3.66
1662 3379 4.625028 CAGATGAAACTAGATCGCCATGA 58.375 43.478 0.00 0.00 0.00 3.07
1663 3380 5.236282 CAGATGAAACTAGATCGCCATGAT 58.764 41.667 0.00 0.00 41.06 2.45
1664 3381 5.699915 CAGATGAAACTAGATCGCCATGATT 59.300 40.000 0.00 0.00 37.47 2.57
1665 3382 5.699915 AGATGAAACTAGATCGCCATGATTG 59.300 40.000 0.00 0.00 37.47 2.67
1666 3383 5.022282 TGAAACTAGATCGCCATGATTGA 57.978 39.130 0.00 0.00 37.47 2.57
1667 3384 5.614308 TGAAACTAGATCGCCATGATTGAT 58.386 37.500 0.00 0.00 37.47 2.57
1668 3385 6.758254 TGAAACTAGATCGCCATGATTGATA 58.242 36.000 0.00 0.00 37.47 2.15
1669 3386 7.216494 TGAAACTAGATCGCCATGATTGATAA 58.784 34.615 0.00 0.00 37.47 1.75
1670 3387 7.171508 TGAAACTAGATCGCCATGATTGATAAC 59.828 37.037 0.00 0.00 37.47 1.89
1671 3388 6.352016 ACTAGATCGCCATGATTGATAACT 57.648 37.500 0.00 0.00 37.47 2.24
1672 3389 6.162079 ACTAGATCGCCATGATTGATAACTG 58.838 40.000 0.00 0.00 37.47 3.16
1673 3390 5.219343 AGATCGCCATGATTGATAACTGA 57.781 39.130 0.00 0.00 37.47 3.41
1674 3391 5.614308 AGATCGCCATGATTGATAACTGAA 58.386 37.500 0.00 0.00 37.47 3.02
1675 3392 5.699915 AGATCGCCATGATTGATAACTGAAG 59.300 40.000 0.00 0.00 37.47 3.02
1676 3393 4.769688 TCGCCATGATTGATAACTGAAGT 58.230 39.130 0.00 0.00 0.00 3.01
1677 3394 5.185454 TCGCCATGATTGATAACTGAAGTT 58.815 37.500 0.00 0.71 41.73 2.66
1678 3395 6.345298 TCGCCATGATTGATAACTGAAGTTA 58.655 36.000 5.43 5.43 43.71 2.24
1679 3396 7.663081 ATCGCCATGATTGATAACTGAAGTTAT 59.337 33.333 14.13 14.13 42.78 1.89
1696 3413 7.423199 TGAAGTTATAATACTGTGTAGCTCCG 58.577 38.462 0.00 0.00 0.00 4.63
1699 3416 7.818642 AGTTATAATACTGTGTAGCTCCGATC 58.181 38.462 0.00 0.00 0.00 3.69
1734 3456 2.142356 TGATCCAAACATGGCCGATT 57.858 45.000 0.00 0.00 0.00 3.34
1736 3458 0.461135 ATCCAAACATGGCCGATTGC 59.539 50.000 0.00 0.00 40.16 3.56
1737 3459 0.897401 TCCAAACATGGCCGATTGCA 60.897 50.000 0.00 0.00 43.89 4.08
1843 3565 1.970917 GCAAGTGCGTCAAGATCCCG 61.971 60.000 0.00 0.00 0.00 5.14
1859 3581 4.154613 CGCAGGTCTTGTCTCGTC 57.845 61.111 0.00 0.00 0.00 4.20
1860 3582 1.444553 CGCAGGTCTTGTCTCGTCC 60.445 63.158 0.00 0.00 0.00 4.79
1861 3583 1.867919 CGCAGGTCTTGTCTCGTCCT 61.868 60.000 0.00 0.00 0.00 3.85
1862 3584 0.389166 GCAGGTCTTGTCTCGTCCTG 60.389 60.000 0.00 0.00 45.68 3.86
1863 3585 0.389166 CAGGTCTTGTCTCGTCCTGC 60.389 60.000 0.00 0.00 39.02 4.85
1864 3586 0.827925 AGGTCTTGTCTCGTCCTGCA 60.828 55.000 0.00 0.00 0.00 4.41
1865 3587 0.667792 GGTCTTGTCTCGTCCTGCAC 60.668 60.000 0.00 0.00 0.00 4.57
1866 3588 0.315568 GTCTTGTCTCGTCCTGCACT 59.684 55.000 0.00 0.00 0.00 4.40
1867 3589 1.040646 TCTTGTCTCGTCCTGCACTT 58.959 50.000 0.00 0.00 0.00 3.16
1868 3590 1.000163 TCTTGTCTCGTCCTGCACTTC 60.000 52.381 0.00 0.00 0.00 3.01
1869 3591 1.000283 CTTGTCTCGTCCTGCACTTCT 60.000 52.381 0.00 0.00 0.00 2.85
1870 3592 1.040646 TGTCTCGTCCTGCACTTCTT 58.959 50.000 0.00 0.00 0.00 2.52
1888 3610 7.355017 CACTTCTTTCGAATCAAGTTCATTCA 58.645 34.615 15.98 0.00 36.60 2.57
1898 3620 7.225341 CGAATCAAGTTCATTCATGGATCAGTA 59.775 37.037 0.22 0.00 36.60 2.74
1900 3622 6.950842 TCAAGTTCATTCATGGATCAGTACT 58.049 36.000 0.00 0.00 0.00 2.73
1901 3623 8.078060 TCAAGTTCATTCATGGATCAGTACTA 57.922 34.615 0.00 0.00 0.00 1.82
1902 3624 7.981789 TCAAGTTCATTCATGGATCAGTACTAC 59.018 37.037 0.00 0.00 0.00 2.73
1903 3625 6.507900 AGTTCATTCATGGATCAGTACTACG 58.492 40.000 0.00 0.00 0.00 3.51
1922 3644 4.685169 ACGAACGCATGAGAAAATTCAT 57.315 36.364 2.50 0.00 38.30 2.57
1934 3656 9.805966 CATGAGAAAATTCATGTGTTTGATTTG 57.194 29.630 7.63 0.00 45.95 2.32
1935 3657 9.767228 ATGAGAAAATTCATGTGTTTGATTTGA 57.233 25.926 0.00 0.00 36.48 2.69
2619 4366 0.039180 TCTACCTCAACCTCCGCTCA 59.961 55.000 0.00 0.00 0.00 4.26
2634 4381 1.517832 CTCATCGGACACCTGGGTC 59.482 63.158 0.00 2.67 37.06 4.46
2976 4852 4.351054 AAGGCCGTCTTGCTGGGG 62.351 66.667 0.00 0.00 33.76 4.96
3018 4894 1.153823 GTCGTATGCGTGTGGCTCT 60.154 57.895 2.37 0.00 44.05 4.09
3048 4924 6.317789 TCTTTGATCACAACCAACTTCATC 57.682 37.500 0.00 0.00 35.63 2.92
3225 5101 3.424962 GCAAGACAAGTTCATAAGCCGAC 60.425 47.826 0.00 0.00 0.00 4.79
3242 5118 5.519722 AGCCGACACTGAATTTTTAACTTG 58.480 37.500 0.00 0.00 0.00 3.16
3322 5205 5.184096 AGAAATAGAGCGAGTCTGTTCAGAA 59.816 40.000 3.99 0.00 35.66 3.02
3323 5206 5.392767 AATAGAGCGAGTCTGTTCAGAAA 57.607 39.130 3.99 0.00 31.19 2.52
3333 5216 6.090898 CGAGTCTGTTCAGAAATACCGAAATT 59.909 38.462 3.99 0.00 0.00 1.82
3352 5235 9.729023 CCGAAATTATGAAAATAACATACAGCA 57.271 29.630 0.00 0.00 31.26 4.41
3378 5261 5.707931 TGCATTTCATTCATTCGCACTTAA 58.292 33.333 0.00 0.00 0.00 1.85
3393 5276 3.052036 CACTTAAGCAACACACCAATGC 58.948 45.455 1.29 0.00 40.34 3.56
3396 5279 2.228138 AAGCAACACACCAATGCAAG 57.772 45.000 0.00 0.00 42.45 4.01
3397 5280 1.113788 AGCAACACACCAATGCAAGT 58.886 45.000 0.00 0.00 42.45 3.16
3483 5366 3.347216 ACAATGCCTTAGGTCACACATC 58.653 45.455 0.00 0.00 0.00 3.06
3779 5682 0.670546 ACCCGACATCGACAAGCTTG 60.671 55.000 24.84 24.84 43.02 4.01
3836 5739 1.552348 GCATCGCCGAGTACATGCTC 61.552 60.000 2.58 0.00 38.89 4.26
3914 5817 2.305927 GTCCTTGGTTTCCTCCTCATCA 59.694 50.000 0.00 0.00 0.00 3.07
3963 5866 0.035739 GGAACCTACAGGAAACGCCA 59.964 55.000 1.29 0.00 40.02 5.69
3991 5894 3.415237 GCAAGTTGCAACACACACA 57.585 47.368 30.11 0.00 44.26 3.72
3994 5897 2.670479 CAAGTTGCAACACACACACAA 58.330 42.857 30.11 0.00 0.00 3.33
4005 5914 8.020244 TGCAACACACACACAATACATAATTAG 58.980 33.333 0.00 0.00 0.00 1.73
4042 5951 2.293399 GAGAACAAAATCCAACCAGCGT 59.707 45.455 0.00 0.00 0.00 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.426024 GTGTGACTAGTTCCGCCATAGA 59.574 50.000 0.00 0.00 0.00 1.98
1 2 2.481449 GGTGTGACTAGTTCCGCCATAG 60.481 54.545 16.31 0.00 0.00 2.23
2 3 1.479323 GGTGTGACTAGTTCCGCCATA 59.521 52.381 16.31 0.00 0.00 2.74
3 4 0.249398 GGTGTGACTAGTTCCGCCAT 59.751 55.000 16.31 0.00 0.00 4.40
4 5 1.116536 TGGTGTGACTAGTTCCGCCA 61.117 55.000 18.75 18.75 34.50 5.69
5 6 0.669625 GTGGTGTGACTAGTTCCGCC 60.670 60.000 14.99 14.99 0.00 6.13
6 7 0.669625 GGTGGTGTGACTAGTTCCGC 60.670 60.000 0.00 4.78 0.00 5.54
7 8 0.388134 CGGTGGTGTGACTAGTTCCG 60.388 60.000 0.00 0.18 0.00 4.30
10 11 0.391597 CCACGGTGGTGTGACTAGTT 59.608 55.000 19.15 0.00 42.80 2.24
24 25 5.007332 CCGGTTATTTTAGAAGAATCCACGG 59.993 44.000 0.00 0.00 0.00 4.94
34 35 5.429435 AGATACCCCACCGGTTATTTTAGAA 59.571 40.000 2.97 0.00 45.36 2.10
59 60 7.831691 TTTTCTTGATGGTGGATCTTACAAA 57.168 32.000 0.00 0.00 31.55 2.83
69 70 6.095860 TGCTCTATTCATTTTCTTGATGGTGG 59.904 38.462 0.00 0.00 0.00 4.61
73 74 6.971184 GTGGTGCTCTATTCATTTTCTTGATG 59.029 38.462 0.00 0.00 0.00 3.07
74 75 6.888632 AGTGGTGCTCTATTCATTTTCTTGAT 59.111 34.615 0.00 0.00 0.00 2.57
107 108 5.082251 AGTTAAGGTCGGAATGTAGGTTC 57.918 43.478 0.00 0.00 0.00 3.62
126 127 2.496899 ATTGTTGGCTCCATCGAGTT 57.503 45.000 0.00 0.00 38.49 3.01
131 132 8.947055 AAATTAACATTATTGTTGGCTCCATC 57.053 30.769 12.20 0.00 45.56 3.51
146 147 5.751028 CACGGGTCAACACAAAATTAACATT 59.249 36.000 0.00 0.00 0.00 2.71
147 148 5.163499 ACACGGGTCAACACAAAATTAACAT 60.163 36.000 0.00 0.00 0.00 2.71
148 149 4.158025 ACACGGGTCAACACAAAATTAACA 59.842 37.500 0.00 0.00 0.00 2.41
153 154 2.755655 TCAACACGGGTCAACACAAAAT 59.244 40.909 0.00 0.00 0.00 1.82
164 165 0.036952 CTGAGAGCATCAACACGGGT 60.037 55.000 0.00 0.00 37.52 5.28
183 205 8.062065 TCCTAATGTCAAATCCAACCAATAAC 57.938 34.615 0.00 0.00 0.00 1.89
221 246 4.285020 TCAACTGAGATCTAGCCACATCT 58.715 43.478 0.00 0.00 31.70 2.90
223 248 5.366460 CAATCAACTGAGATCTAGCCACAT 58.634 41.667 0.00 0.00 0.00 3.21
298 325 8.669946 AACACAAAGACAAGAAAAAGGAAAAA 57.330 26.923 0.00 0.00 0.00 1.94
299 326 8.669946 AAACACAAAGACAAGAAAAAGGAAAA 57.330 26.923 0.00 0.00 0.00 2.29
300 327 8.669946 AAAACACAAAGACAAGAAAAAGGAAA 57.330 26.923 0.00 0.00 0.00 3.13
301 328 8.147704 AGAAAACACAAAGACAAGAAAAAGGAA 58.852 29.630 0.00 0.00 0.00 3.36
302 329 7.666623 AGAAAACACAAAGACAAGAAAAAGGA 58.333 30.769 0.00 0.00 0.00 3.36
303 330 7.889589 AGAAAACACAAAGACAAGAAAAAGG 57.110 32.000 0.00 0.00 0.00 3.11
325 356 6.530534 CGCGAAAGAAGAAAAGGAAGTATAGA 59.469 38.462 0.00 0.00 0.00 1.98
326 357 6.697152 CGCGAAAGAAGAAAAGGAAGTATAG 58.303 40.000 0.00 0.00 0.00 1.31
327 358 5.063060 GCGCGAAAGAAGAAAAGGAAGTATA 59.937 40.000 12.10 0.00 0.00 1.47
328 359 4.142881 GCGCGAAAGAAGAAAAGGAAGTAT 60.143 41.667 12.10 0.00 0.00 2.12
335 366 1.309108 CACGCGCGAAAGAAGAAAAG 58.691 50.000 39.36 1.99 0.00 2.27
348 379 0.739813 ATCCCTTGTTAGACACGCGC 60.740 55.000 5.73 0.00 0.00 6.86
352 383 2.778299 TGCACATCCCTTGTTAGACAC 58.222 47.619 0.00 0.00 36.00 3.67
357 388 3.222173 ACAGTTGCACATCCCTTGTTA 57.778 42.857 0.00 0.00 36.00 2.41
381 412 6.416631 ACATATATCTCAGCAGTCACACAT 57.583 37.500 0.00 0.00 0.00 3.21
382 413 5.859205 ACATATATCTCAGCAGTCACACA 57.141 39.130 0.00 0.00 0.00 3.72
401 432 3.418047 GGCCGGGCAACTATAATTACAT 58.582 45.455 25.33 0.00 0.00 2.29
407 438 1.144496 GTCGGCCGGGCAACTATAA 59.856 57.895 29.19 0.00 0.00 0.98
422 453 4.299155 ACTACAATTGCATATCTCGGTCG 58.701 43.478 5.05 0.00 0.00 4.79
447 478 1.046472 ATATCCTTGTCGGACGGGCA 61.046 55.000 13.01 6.05 46.80 5.36
458 489 5.360714 ACCCAACTACATTTGCATATCCTTG 59.639 40.000 0.00 0.00 0.00 3.61
490 521 4.141711 TGCTCTTTTCCACTCAAGTACAGT 60.142 41.667 0.00 0.00 0.00 3.55
519 550 7.803189 CGCTGTTTTTAATACATCTTGTGTTCT 59.197 33.333 0.00 0.00 42.29 3.01
528 559 8.846607 CACCTTTTACGCTGTTTTTAATACATC 58.153 33.333 0.00 0.00 0.00 3.06
613 644 8.771920 ATCTTGATTAACATTACACTCGTCAA 57.228 30.769 0.00 0.00 0.00 3.18
652 683 6.712998 TCTTGGATTTGTTGGTTCTTAATCGA 59.287 34.615 0.00 0.00 0.00 3.59
654 685 7.176690 TCCTCTTGGATTTGTTGGTTCTTAATC 59.823 37.037 0.00 0.00 37.46 1.75
666 697 6.156083 TGGTTTTCTTTTCCTCTTGGATTTGT 59.844 34.615 0.00 0.00 42.81 2.83
687 718 1.064758 TCCTTGCGCCTGAATATGGTT 60.065 47.619 4.18 0.00 0.00 3.67
757 788 5.998363 AGGTTTCTTGTACTCTTGGTGAATC 59.002 40.000 0.00 0.00 0.00 2.52
776 2252 7.876068 TGAGATAAACGTCTGTATTTGAGGTTT 59.124 33.333 15.39 15.39 46.84 3.27
777 2253 7.383687 TGAGATAAACGTCTGTATTTGAGGTT 58.616 34.615 0.00 0.00 42.08 3.50
786 2262 7.602644 AGCATTCTTTTGAGATAAACGTCTGTA 59.397 33.333 0.00 0.00 0.00 2.74
788 2264 6.740002 CAGCATTCTTTTGAGATAAACGTCTG 59.260 38.462 0.00 0.00 0.00 3.51
815 2291 4.243007 GACCAAAACATTCAGGGTCAAG 57.757 45.455 0.00 0.00 45.70 3.02
819 2295 3.312736 AGTGACCAAAACATTCAGGGT 57.687 42.857 0.00 0.00 33.78 4.34
822 2386 6.135290 TGAGAAAGTGACCAAAACATTCAG 57.865 37.500 0.00 0.00 29.78 3.02
824 2388 7.040409 ACCTATGAGAAAGTGACCAAAACATTC 60.040 37.037 0.00 0.00 0.00 2.67
844 2408 3.074412 ACCAAACAAAGAGCGACCTATG 58.926 45.455 0.00 0.00 0.00 2.23
876 2440 9.449719 AAGTTCAAAAATATTCTACCGACAGAT 57.550 29.630 0.00 0.00 0.00 2.90
883 2447 7.302524 TGCGACAAGTTCAAAAATATTCTACC 58.697 34.615 0.00 0.00 0.00 3.18
921 2485 4.386951 CCACACGCATCCGGGACA 62.387 66.667 0.00 0.00 41.39 4.02
938 2502 0.235926 GCAAACTGGCGAGTGAGTTC 59.764 55.000 0.71 0.00 31.02 3.01
957 2521 2.357517 GCCTGTGTCCCTGTCGTG 60.358 66.667 0.00 0.00 0.00 4.35
974 2538 1.025812 ATAGAGGTTCTGGCGAGTCG 58.974 55.000 8.54 8.54 0.00 4.18
975 2539 2.427453 TCAATAGAGGTTCTGGCGAGTC 59.573 50.000 0.00 0.00 0.00 3.36
992 2556 8.320396 ACACGTACGTATATATGAGACTCAAT 57.680 34.615 22.34 7.22 0.00 2.57
994 2558 8.703336 GTTACACGTACGTATATATGAGACTCA 58.297 37.037 22.34 7.80 0.00 3.41
1558 3150 5.548706 AGATAAGTACTGACACACTCGTC 57.451 43.478 0.00 0.00 36.40 4.20
1561 3153 5.548706 ACGAGATAAGTACTGACACACTC 57.451 43.478 0.00 0.00 0.00 3.51
1563 3155 6.147581 TGAAACGAGATAAGTACTGACACAC 58.852 40.000 0.00 0.00 0.00 3.82
1564 3156 6.016527 ACTGAAACGAGATAAGTACTGACACA 60.017 38.462 0.00 0.00 0.00 3.72
1565 3157 6.380190 ACTGAAACGAGATAAGTACTGACAC 58.620 40.000 0.00 0.00 0.00 3.67
1589 3306 8.684386 TTAGATGCACGAATTGGGATTTTATA 57.316 30.769 0.00 0.00 0.00 0.98
1594 3311 4.949856 AGTTTAGATGCACGAATTGGGATT 59.050 37.500 0.00 0.00 0.00 3.01
1597 3314 4.701956 AAGTTTAGATGCACGAATTGGG 57.298 40.909 0.00 0.00 0.00 4.12
1598 3315 6.662414 TCTAAGTTTAGATGCACGAATTGG 57.338 37.500 0.00 0.00 34.99 3.16
1600 3317 8.398665 GGATTTCTAAGTTTAGATGCACGAATT 58.601 33.333 2.65 0.00 39.36 2.17
1601 3318 7.552687 TGGATTTCTAAGTTTAGATGCACGAAT 59.447 33.333 2.65 0.00 39.36 3.34
1602 3319 6.876789 TGGATTTCTAAGTTTAGATGCACGAA 59.123 34.615 2.65 0.00 39.36 3.85
1603 3320 6.403049 TGGATTTCTAAGTTTAGATGCACGA 58.597 36.000 2.65 0.00 39.36 4.35
1604 3321 6.662414 TGGATTTCTAAGTTTAGATGCACG 57.338 37.500 2.65 0.00 39.36 5.34
1605 3322 8.443953 AGATGGATTTCTAAGTTTAGATGCAC 57.556 34.615 2.65 0.00 39.36 4.57
1606 3323 9.113838 GAAGATGGATTTCTAAGTTTAGATGCA 57.886 33.333 2.65 0.00 39.36 3.96
1607 3324 9.113838 TGAAGATGGATTTCTAAGTTTAGATGC 57.886 33.333 2.65 0.00 39.36 3.91
1612 3329 9.884636 TCGAATGAAGATGGATTTCTAAGTTTA 57.115 29.630 0.00 0.00 0.00 2.01
1614 3331 7.011857 GCTCGAATGAAGATGGATTTCTAAGTT 59.988 37.037 0.00 0.00 0.00 2.66
1615 3332 6.481644 GCTCGAATGAAGATGGATTTCTAAGT 59.518 38.462 0.00 0.00 0.00 2.24
1616 3333 6.481313 TGCTCGAATGAAGATGGATTTCTAAG 59.519 38.462 0.00 0.00 0.00 2.18
1617 3334 6.348498 TGCTCGAATGAAGATGGATTTCTAA 58.652 36.000 0.00 0.00 0.00 2.10
1618 3335 5.917462 TGCTCGAATGAAGATGGATTTCTA 58.083 37.500 0.00 0.00 0.00 2.10
1622 3339 4.412796 TCTGCTCGAATGAAGATGGATT 57.587 40.909 0.00 0.00 0.00 3.01
1623 3340 4.040095 TCATCTGCTCGAATGAAGATGGAT 59.960 41.667 18.11 0.00 44.00 3.41
1624 3341 3.385755 TCATCTGCTCGAATGAAGATGGA 59.614 43.478 18.11 6.71 44.00 3.41
1625 3342 3.725490 TCATCTGCTCGAATGAAGATGG 58.275 45.455 18.11 4.96 44.00 3.51
1627 3344 5.426504 AGTTTCATCTGCTCGAATGAAGAT 58.573 37.500 9.52 0.59 34.92 2.40
1628 3345 4.825422 AGTTTCATCTGCTCGAATGAAGA 58.175 39.130 9.52 0.00 34.92 2.87
1629 3346 6.038985 TCTAGTTTCATCTGCTCGAATGAAG 58.961 40.000 9.52 0.79 34.92 3.02
1630 3347 5.965922 TCTAGTTTCATCTGCTCGAATGAA 58.034 37.500 6.22 6.22 0.00 2.57
1631 3348 5.582689 TCTAGTTTCATCTGCTCGAATGA 57.417 39.130 0.00 0.00 0.00 2.57
1632 3349 5.116831 CGATCTAGTTTCATCTGCTCGAATG 59.883 44.000 0.00 0.00 0.00 2.67
1633 3350 5.218885 CGATCTAGTTTCATCTGCTCGAAT 58.781 41.667 0.00 0.00 0.00 3.34
1634 3351 4.602006 CGATCTAGTTTCATCTGCTCGAA 58.398 43.478 0.00 0.00 0.00 3.71
1635 3352 3.549019 GCGATCTAGTTTCATCTGCTCGA 60.549 47.826 0.00 0.00 0.00 4.04
1636 3353 2.723658 GCGATCTAGTTTCATCTGCTCG 59.276 50.000 0.00 0.00 0.00 5.03
1637 3354 3.056304 GGCGATCTAGTTTCATCTGCTC 58.944 50.000 0.00 0.00 0.00 4.26
1638 3355 2.432146 TGGCGATCTAGTTTCATCTGCT 59.568 45.455 0.00 0.00 0.00 4.24
1639 3356 2.826428 TGGCGATCTAGTTTCATCTGC 58.174 47.619 0.00 0.00 0.00 4.26
1640 3357 4.625028 TCATGGCGATCTAGTTTCATCTG 58.375 43.478 0.00 0.00 0.00 2.90
1641 3358 4.944619 TCATGGCGATCTAGTTTCATCT 57.055 40.909 0.00 0.00 0.00 2.90
1643 3360 5.614308 TCAATCATGGCGATCTAGTTTCAT 58.386 37.500 0.00 0.00 31.11 2.57
1644 3361 5.022282 TCAATCATGGCGATCTAGTTTCA 57.978 39.130 0.00 0.00 31.11 2.69
1645 3362 7.386299 AGTTATCAATCATGGCGATCTAGTTTC 59.614 37.037 0.00 0.00 31.11 2.78
1646 3363 7.172190 CAGTTATCAATCATGGCGATCTAGTTT 59.828 37.037 0.00 0.00 31.11 2.66
1647 3364 6.648310 CAGTTATCAATCATGGCGATCTAGTT 59.352 38.462 0.00 0.00 31.11 2.24
1648 3365 6.015095 TCAGTTATCAATCATGGCGATCTAGT 60.015 38.462 0.00 0.00 31.11 2.57
1649 3366 6.393171 TCAGTTATCAATCATGGCGATCTAG 58.607 40.000 0.00 0.00 31.11 2.43
1650 3367 6.345096 TCAGTTATCAATCATGGCGATCTA 57.655 37.500 0.00 0.00 31.11 1.98
1651 3368 5.219343 TCAGTTATCAATCATGGCGATCT 57.781 39.130 0.00 0.00 31.11 2.75
1652 3369 5.468072 ACTTCAGTTATCAATCATGGCGATC 59.532 40.000 0.00 0.00 31.11 3.69
1653 3370 5.371526 ACTTCAGTTATCAATCATGGCGAT 58.628 37.500 0.00 0.00 35.12 4.58
1654 3371 4.769688 ACTTCAGTTATCAATCATGGCGA 58.230 39.130 0.00 0.00 0.00 5.54
1655 3372 5.490139 AACTTCAGTTATCAATCATGGCG 57.510 39.130 0.00 0.00 36.32 5.69
1668 3385 9.804758 GAGCTACACAGTATTATAACTTCAGTT 57.195 33.333 0.00 0.00 41.73 3.16
1669 3386 8.414778 GGAGCTACACAGTATTATAACTTCAGT 58.585 37.037 0.00 0.00 0.00 3.41
1670 3387 7.591795 CGGAGCTACACAGTATTATAACTTCAG 59.408 40.741 0.00 0.00 0.00 3.02
1671 3388 7.283807 TCGGAGCTACACAGTATTATAACTTCA 59.716 37.037 0.00 0.00 0.00 3.02
1672 3389 7.646314 TCGGAGCTACACAGTATTATAACTTC 58.354 38.462 0.00 0.00 0.00 3.01
1673 3390 7.578310 TCGGAGCTACACAGTATTATAACTT 57.422 36.000 0.00 0.00 0.00 2.66
1674 3391 7.094291 GGATCGGAGCTACACAGTATTATAACT 60.094 40.741 0.00 0.00 0.00 2.24
1675 3392 7.028361 GGATCGGAGCTACACAGTATTATAAC 58.972 42.308 0.00 0.00 0.00 1.89
1676 3393 6.946583 AGGATCGGAGCTACACAGTATTATAA 59.053 38.462 0.00 0.00 0.00 0.98
1677 3394 6.482524 AGGATCGGAGCTACACAGTATTATA 58.517 40.000 0.00 0.00 0.00 0.98
1678 3395 5.326069 AGGATCGGAGCTACACAGTATTAT 58.674 41.667 0.00 0.00 0.00 1.28
1679 3396 4.726583 AGGATCGGAGCTACACAGTATTA 58.273 43.478 0.00 0.00 0.00 0.98
1680 3397 3.567397 AGGATCGGAGCTACACAGTATT 58.433 45.455 0.00 0.00 0.00 1.89
1681 3398 3.150767 GAGGATCGGAGCTACACAGTAT 58.849 50.000 0.00 0.00 0.00 2.12
1682 3399 2.172930 AGAGGATCGGAGCTACACAGTA 59.827 50.000 0.00 0.00 42.67 2.74
1683 3400 1.064314 AGAGGATCGGAGCTACACAGT 60.064 52.381 0.00 0.00 42.67 3.55
1696 3413 4.511617 TCATGCGATCAGTTAGAGGATC 57.488 45.455 0.00 0.00 37.22 3.36
1734 3456 0.890542 CTTGGCTAACCTGCAGTGCA 60.891 55.000 18.58 18.58 36.63 4.57
1736 3458 0.607489 AGCTTGGCTAACCTGCAGTG 60.607 55.000 13.81 6.81 36.99 3.66
1737 3459 0.607489 CAGCTTGGCTAACCTGCAGT 60.607 55.000 13.81 0.00 36.40 4.40
1843 3565 0.389166 CAGGACGAGACAAGACCTGC 60.389 60.000 0.00 0.00 42.49 4.85
1849 3571 1.000283 AGAAGTGCAGGACGAGACAAG 60.000 52.381 0.00 0.00 0.00 3.16
1850 3572 1.040646 AGAAGTGCAGGACGAGACAA 58.959 50.000 0.00 0.00 0.00 3.18
1851 3573 1.040646 AAGAAGTGCAGGACGAGACA 58.959 50.000 0.00 0.00 0.00 3.41
1852 3574 2.062519 GAAAGAAGTGCAGGACGAGAC 58.937 52.381 0.00 0.00 0.00 3.36
1853 3575 1.335964 CGAAAGAAGTGCAGGACGAGA 60.336 52.381 0.00 0.00 0.00 4.04
1854 3576 1.063806 CGAAAGAAGTGCAGGACGAG 58.936 55.000 0.00 0.00 0.00 4.18
1855 3577 0.671796 TCGAAAGAAGTGCAGGACGA 59.328 50.000 0.00 0.00 37.03 4.20
1856 3578 1.497991 TTCGAAAGAAGTGCAGGACG 58.502 50.000 0.00 0.00 46.92 4.79
1867 3589 6.654582 TCCATGAATGAACTTGATTCGAAAGA 59.345 34.615 0.00 0.00 40.56 2.52
1868 3590 6.845302 TCCATGAATGAACTTGATTCGAAAG 58.155 36.000 0.00 0.00 40.56 2.62
1869 3591 6.816134 TCCATGAATGAACTTGATTCGAAA 57.184 33.333 0.00 0.00 40.56 3.46
1870 3592 6.598850 TGATCCATGAATGAACTTGATTCGAA 59.401 34.615 0.00 0.00 40.56 3.71
1888 3610 2.686405 TGCGTTCGTAGTACTGATCCAT 59.314 45.455 5.39 0.00 0.00 3.41
1898 3620 4.688879 TGAATTTTCTCATGCGTTCGTAGT 59.311 37.500 0.00 0.00 0.00 2.73
1900 3622 5.559227 CATGAATTTTCTCATGCGTTCGTA 58.441 37.500 0.95 0.00 44.54 3.43
1901 3623 4.406069 CATGAATTTTCTCATGCGTTCGT 58.594 39.130 0.95 0.00 44.54 3.85
1902 3624 4.986364 CATGAATTTTCTCATGCGTTCG 57.014 40.909 0.95 0.00 44.54 3.95
1922 3644 3.674281 GCGCATCAATCAAATCAAACACA 59.326 39.130 0.30 0.00 0.00 3.72
1925 3647 4.780946 GCATGCGCATCAATCAAATCAAAC 60.781 41.667 22.51 0.00 38.36 2.93
1928 3650 2.159226 TGCATGCGCATCAATCAAATCA 60.159 40.909 22.51 4.52 45.36 2.57
1929 3651 2.465855 TGCATGCGCATCAATCAAATC 58.534 42.857 22.51 1.94 45.36 2.17
1930 3652 2.588027 TGCATGCGCATCAATCAAAT 57.412 40.000 22.51 0.00 45.36 2.32
2421 4168 3.470888 ATCGACTTCCCCTGCCCG 61.471 66.667 0.00 0.00 0.00 6.13
2619 4366 3.771160 GCGACCCAGGTGTCCGAT 61.771 66.667 0.00 0.00 31.35 4.18
3018 4894 4.019858 TGGTTGTGATCAAAGAAACCACA 58.980 39.130 21.01 7.62 44.00 4.17
3048 4924 6.808008 ATTTACAATCTTCTGTGTGTCCTG 57.192 37.500 0.00 0.00 0.00 3.86
3333 5216 7.994194 TGCATGTGCTGTATGTTATTTTCATA 58.006 30.769 6.55 0.00 42.66 2.15
3352 5235 3.861113 GTGCGAATGAATGAAATGCATGT 59.139 39.130 0.00 0.00 43.54 3.21
3378 5261 1.113788 ACTTGCATTGGTGTGTTGCT 58.886 45.000 0.00 0.00 37.28 3.91
3436 5319 7.112122 TGCCAGTATTTCAACAGTGAAGATAT 58.888 34.615 0.00 0.00 44.49 1.63
3483 5366 0.244721 TGTCGAGTCTGGTCTGCATG 59.755 55.000 0.00 0.00 0.00 4.06
3836 5739 1.333636 ACCTCATCTTCTCCCTGGCG 61.334 60.000 0.00 0.00 0.00 5.69
3946 5849 0.605589 GCTGGCGTTTCCTGTAGGTT 60.606 55.000 0.00 0.00 36.29 3.50
3963 5866 3.243367 TGTTGCAACTTGCTAAATTCGCT 60.243 39.130 28.61 0.00 45.31 4.93
3994 5897 9.860650 TGGCCACTGAATTAACTAATTATGTAT 57.139 29.630 0.00 0.00 36.13 2.29
4005 5914 4.072131 TGTTCTCTGGCCACTGAATTAAC 58.928 43.478 15.98 11.19 0.00 2.01
4042 5951 1.048160 TCAGCACCAGACTCACCACA 61.048 55.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.