Multiple sequence alignment - TraesCS4A01G018000

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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 TraesCS4A01G018000 chr4A 100.000 4990 0 0 1 4990 11807307 11812296 0.000000e+00 9215
1 TraesCS4A01G018000 chr4D 94.675 2742 115 16 1591 4322 455748560 455745840 0.000000e+00 4226
2 TraesCS4A01G018000 chr4D 94.848 660 25 4 4338 4990 455745858 455745201 0.000000e+00 1022
3 TraesCS4A01G018000 chr4D 92.557 618 40 2 1 617 488494346 488494958 0.000000e+00 881
4 TraesCS4A01G018000 chr4D 92.557 618 37 6 1 615 85888283 85888894 0.000000e+00 878
5 TraesCS4A01G018000 chr4D 90.453 618 32 14 636 1239 455749368 455748764 0.000000e+00 789
6 TraesCS4A01G018000 chr4D 84.861 251 14 8 1245 1489 455748796 455748564 1.080000e-56 231
7 TraesCS4A01G018000 chr4B 94.280 2133 92 13 2192 4319 569632550 569630443 0.000000e+00 3236
8 TraesCS4A01G018000 chr4B 94.697 660 26 4 4338 4990 569630458 569629801 0.000000e+00 1016
9 TraesCS4A01G018000 chr4B 90.758 660 32 13 1547 2198 569633589 569632951 0.000000e+00 854
10 TraesCS4A01G018000 chr4B 87.407 675 44 16 821 1491 569634243 569633606 0.000000e+00 737
11 TraesCS4A01G018000 chr4B 86.364 154 11 6 683 834 569634407 569634262 5.170000e-35 159
12 TraesCS4A01G018000 chr2D 93.098 623 41 2 1 622 511531754 511532375 0.000000e+00 911
13 TraesCS4A01G018000 chr2D 93.193 617 38 3 1 617 201456003 201456615 0.000000e+00 904
14 TraesCS4A01G018000 chr2D 92.857 616 43 1 1 615 429202353 429202968 0.000000e+00 893
15 TraesCS4A01G018000 chr5A 92.880 618 42 2 1 616 584710059 584710676 0.000000e+00 896
16 TraesCS4A01G018000 chr5A 92.880 618 40 3 1 617 631062910 631062296 0.000000e+00 894
17 TraesCS4A01G018000 chr7A 92.407 619 41 4 3 618 685449090 685448475 0.000000e+00 878
18 TraesCS4A01G018000 chr1A 92.084 619 48 1 1 618 547024225 547023607 0.000000e+00 870


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 TraesCS4A01G018000 chr4A 11807307 11812296 4989 False 9215.0 9215 100.00000 1 4990 1 chr4A.!!$F1 4989
1 TraesCS4A01G018000 chr4D 455745201 455749368 4167 True 1567.0 4226 91.20925 636 4990 4 chr4D.!!$R1 4354
2 TraesCS4A01G018000 chr4D 488494346 488494958 612 False 881.0 881 92.55700 1 617 1 chr4D.!!$F2 616
3 TraesCS4A01G018000 chr4D 85888283 85888894 611 False 878.0 878 92.55700 1 615 1 chr4D.!!$F1 614
4 TraesCS4A01G018000 chr4B 569629801 569634407 4606 True 1200.4 3236 90.70120 683 4990 5 chr4B.!!$R1 4307
5 TraesCS4A01G018000 chr2D 511531754 511532375 621 False 911.0 911 93.09800 1 622 1 chr2D.!!$F3 621
6 TraesCS4A01G018000 chr2D 201456003 201456615 612 False 904.0 904 93.19300 1 617 1 chr2D.!!$F1 616
7 TraesCS4A01G018000 chr2D 429202353 429202968 615 False 893.0 893 92.85700 1 615 1 chr2D.!!$F2 614
8 TraesCS4A01G018000 chr5A 584710059 584710676 617 False 896.0 896 92.88000 1 616 1 chr5A.!!$F1 615
9 TraesCS4A01G018000 chr5A 631062296 631062910 614 True 894.0 894 92.88000 1 617 1 chr5A.!!$R1 616
10 TraesCS4A01G018000 chr7A 685448475 685449090 615 True 878.0 878 92.40700 3 618 1 chr7A.!!$R1 615
11 TraesCS4A01G018000 chr1A 547023607 547024225 618 True 870.0 870 92.08400 1 618 1 chr1A.!!$R1 617

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
572 584 0.040425 CCAGACGAACAAAAAGCGGG 60.040 55.0 0.00 0.00 0.00 6.13 F
841 890 0.179166 CTCTCTCTCTCTGTGTGCGC 60.179 60.0 0.00 0.00 0.00 6.09 F
1526 1594 0.321671 ATTGATATCTCGGTGGGCGG 59.678 55.0 3.98 0.00 0.00 6.13 F
2115 2192 0.035317 TGGACATGTCACCTGTGAGC 59.965 55.0 26.47 7.06 40.75 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2094 2171 0.035317 TCACAGGTGACATGTCCAGC 59.965 55.000 22.85 18.43 34.14 4.85 R
2097 2174 0.322975 AGCTCACAGGTGACATGTCC 59.677 55.000 22.85 13.66 35.46 4.02 R
3450 3944 1.627329 AGTGCAGCCATCTGAGAAGAA 59.373 47.619 0.00 0.00 42.95 2.52 R
4027 4521 0.936764 CTTCAGTCCGCGGATCATCG 60.937 60.000 33.58 17.55 0.00 3.84 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
20 21 2.041922 AGGAGCCGGCCTACATCA 60.042 61.111 26.15 0.00 36.22 3.07
41 42 2.050350 CGCTACTCCTGGACCGGAA 61.050 63.158 9.46 0.00 31.44 4.30
392 394 3.740044 AATGTAATGTGGACTTTCGCG 57.260 42.857 0.00 0.00 0.00 5.87
399 401 3.431725 GGACTTTCGCGGGCCTTG 61.432 66.667 6.13 0.00 0.00 3.61
423 425 4.565166 GTGGCCGGCTTTTATGTTTAATTC 59.435 41.667 28.56 3.57 0.00 2.17
523 534 3.587933 GCGCCGACCCAAACACAA 61.588 61.111 0.00 0.00 0.00 3.33
528 539 2.473760 CGACCCAAACACAACGCCA 61.474 57.895 0.00 0.00 0.00 5.69
532 543 1.380403 CCCAAACACAACGCCAGACA 61.380 55.000 0.00 0.00 0.00 3.41
560 572 4.334118 TCGGACCGACCCAGACGA 62.334 66.667 13.88 0.00 34.64 4.20
572 584 0.040425 CCAGACGAACAAAAAGCGGG 60.040 55.000 0.00 0.00 0.00 6.13
596 608 4.973055 CGCCGTCCGTTTGGGTCA 62.973 66.667 0.00 0.00 37.00 4.02
598 610 2.424302 CCGTCCGTTTGGGTCAGT 59.576 61.111 0.00 0.00 37.00 3.41
600 612 1.366366 CGTCCGTTTGGGTCAGTCT 59.634 57.895 0.00 0.00 37.00 3.24
618 630 5.480422 TCAGTCTGTTGGAGTTGCTCTTATA 59.520 40.000 0.00 0.00 0.00 0.98
620 632 6.820656 CAGTCTGTTGGAGTTGCTCTTATATT 59.179 38.462 0.00 0.00 0.00 1.28
621 633 7.981789 CAGTCTGTTGGAGTTGCTCTTATATTA 59.018 37.037 0.00 0.00 0.00 0.98
622 634 7.982354 AGTCTGTTGGAGTTGCTCTTATATTAC 59.018 37.037 0.00 0.00 0.00 1.89
623 635 7.764443 GTCTGTTGGAGTTGCTCTTATATTACA 59.236 37.037 0.00 0.00 0.00 2.41
624 636 8.318412 TCTGTTGGAGTTGCTCTTATATTACAA 58.682 33.333 0.00 0.00 0.00 2.41
625 637 8.492673 TGTTGGAGTTGCTCTTATATTACAAG 57.507 34.615 0.00 0.00 0.00 3.16
626 638 8.318412 TGTTGGAGTTGCTCTTATATTACAAGA 58.682 33.333 0.00 0.00 0.00 3.02
627 639 9.331282 GTTGGAGTTGCTCTTATATTACAAGAT 57.669 33.333 0.00 0.00 31.82 2.40
628 640 9.905713 TTGGAGTTGCTCTTATATTACAAGATT 57.094 29.630 0.00 0.00 31.82 2.40
629 641 9.905713 TGGAGTTGCTCTTATATTACAAGATTT 57.094 29.630 0.00 0.00 31.82 2.17
632 644 9.125026 AGTTGCTCTTATATTACAAGATTTGGG 57.875 33.333 0.00 0.00 31.82 4.12
633 645 8.352942 GTTGCTCTTATATTACAAGATTTGGGG 58.647 37.037 0.00 0.00 31.82 4.96
634 646 7.811282 TGCTCTTATATTACAAGATTTGGGGA 58.189 34.615 0.00 0.00 31.82 4.81
635 647 7.939039 TGCTCTTATATTACAAGATTTGGGGAG 59.061 37.037 0.00 0.00 31.82 4.30
636 648 7.939588 GCTCTTATATTACAAGATTTGGGGAGT 59.060 37.037 0.00 0.00 31.82 3.85
658 670 0.885879 TACTCCACCAGTGTAGTGCG 59.114 55.000 6.30 0.00 36.43 5.34
699 711 3.972227 GTGATCACACGCTTGGCT 58.028 55.556 21.07 0.00 37.28 4.75
707 719 2.159099 TCACACGCTTGGCTAAGGATAG 60.159 50.000 12.16 1.63 34.40 2.08
714 726 3.406764 CTTGGCTAAGGATAGTCCATGC 58.593 50.000 1.05 0.00 39.61 4.06
715 727 1.699634 TGGCTAAGGATAGTCCATGCC 59.300 52.381 15.24 15.24 43.60 4.40
716 728 1.699634 GGCTAAGGATAGTCCATGCCA 59.300 52.381 16.43 0.00 43.16 4.92
717 729 2.106511 GGCTAAGGATAGTCCATGCCAA 59.893 50.000 16.43 0.00 43.16 4.52
718 730 3.406764 GCTAAGGATAGTCCATGCCAAG 58.593 50.000 0.00 0.00 39.61 3.61
719 731 2.355010 AAGGATAGTCCATGCCAAGC 57.645 50.000 0.00 0.00 39.61 4.01
792 805 1.394697 CACAAAAGCCAAACGCGTAG 58.605 50.000 14.46 8.64 44.76 3.51
834 851 3.189080 CACACACACTCTCTCTCTCTCTG 59.811 52.174 0.00 0.00 0.00 3.35
836 853 3.189080 CACACACTCTCTCTCTCTCTGTG 59.811 52.174 0.00 0.00 34.90 3.66
839 888 2.162208 CACTCTCTCTCTCTCTGTGTGC 59.838 54.545 0.00 0.00 0.00 4.57
841 890 0.179166 CTCTCTCTCTCTGTGTGCGC 60.179 60.000 0.00 0.00 0.00 6.09
842 891 1.153862 CTCTCTCTCTGTGTGCGCC 60.154 63.158 4.18 0.00 0.00 6.53
845 894 3.117171 CTCTCTGTGTGCGCCTGC 61.117 66.667 4.18 0.00 43.20 4.85
895 944 0.533085 GATCTTAGCTCCCAACGGGC 60.533 60.000 0.00 0.00 43.94 6.13
1208 1263 5.165676 CCTTTCCGCCTAATTTTTGTTACC 58.834 41.667 0.00 0.00 0.00 2.85
1248 1303 9.817809 TTTTATCGATTAGTTCTTGCATCTACT 57.182 29.630 1.71 0.00 0.00 2.57
1249 1304 8.803201 TTATCGATTAGTTCTTGCATCTACTG 57.197 34.615 1.71 0.00 0.00 2.74
1250 1305 5.592054 TCGATTAGTTCTTGCATCTACTGG 58.408 41.667 0.00 0.00 0.00 4.00
1251 1306 4.210120 CGATTAGTTCTTGCATCTACTGGC 59.790 45.833 0.00 0.00 0.00 4.85
1252 1307 4.826274 TTAGTTCTTGCATCTACTGGCT 57.174 40.909 0.00 0.00 0.00 4.75
1253 1308 5.932619 TTAGTTCTTGCATCTACTGGCTA 57.067 39.130 0.00 0.00 0.00 3.93
1254 1309 4.826274 AGTTCTTGCATCTACTGGCTAA 57.174 40.909 0.00 0.00 0.00 3.09
1255 1310 5.165961 AGTTCTTGCATCTACTGGCTAAA 57.834 39.130 0.00 0.00 0.00 1.85
1256 1311 5.749462 AGTTCTTGCATCTACTGGCTAAAT 58.251 37.500 0.00 0.00 0.00 1.40
1257 1312 6.183347 AGTTCTTGCATCTACTGGCTAAATT 58.817 36.000 0.00 0.00 0.00 1.82
1258 1313 6.660949 AGTTCTTGCATCTACTGGCTAAATTT 59.339 34.615 0.00 0.00 0.00 1.82
1259 1314 7.177392 AGTTCTTGCATCTACTGGCTAAATTTT 59.823 33.333 0.00 0.00 0.00 1.82
1260 1315 8.458843 GTTCTTGCATCTACTGGCTAAATTTTA 58.541 33.333 0.00 0.00 0.00 1.52
1261 1316 8.752005 TCTTGCATCTACTGGCTAAATTTTAT 57.248 30.769 0.00 0.00 0.00 1.40
1262 1317 8.840321 TCTTGCATCTACTGGCTAAATTTTATC 58.160 33.333 0.00 0.00 0.00 1.75
1263 1318 7.189693 TGCATCTACTGGCTAAATTTTATCG 57.810 36.000 0.00 0.00 0.00 2.92
1264 1319 6.204688 TGCATCTACTGGCTAAATTTTATCGG 59.795 38.462 0.00 0.00 0.00 4.18
1265 1320 6.204882 GCATCTACTGGCTAAATTTTATCGGT 59.795 38.462 0.00 0.47 0.00 4.69
1266 1321 7.571428 GCATCTACTGGCTAAATTTTATCGGTC 60.571 40.741 0.00 0.00 0.00 4.79
1267 1322 6.880484 TCTACTGGCTAAATTTTATCGGTCA 58.120 36.000 0.00 0.00 0.00 4.02
1268 1323 6.984474 TCTACTGGCTAAATTTTATCGGTCAG 59.016 38.462 0.00 6.85 0.00 3.51
1269 1324 5.497474 ACTGGCTAAATTTTATCGGTCAGT 58.503 37.500 7.82 7.82 0.00 3.41
1270 1325 6.646267 ACTGGCTAAATTTTATCGGTCAGTA 58.354 36.000 10.64 0.00 31.13 2.74
1271 1326 7.280356 ACTGGCTAAATTTTATCGGTCAGTAT 58.720 34.615 10.64 0.00 31.13 2.12
1272 1327 7.773690 ACTGGCTAAATTTTATCGGTCAGTATT 59.226 33.333 10.64 0.00 31.13 1.89
1296 1358 7.930513 TGTATCTACGAGCAAATAAGTGATG 57.069 36.000 0.00 0.00 0.00 3.07
1356 1421 3.989817 GTGCATTTTTGTGATCACCCTTC 59.010 43.478 22.85 6.50 0.00 3.46
1380 1445 7.192628 TCCCCAAATTCATACCAATTTTCCTA 58.807 34.615 0.00 0.00 34.37 2.94
1426 1494 4.832823 CCAAATTTGTGAAGTTAGAGGGGT 59.167 41.667 16.73 0.00 0.00 4.95
1491 1559 1.541147 CGCTCTGGAAGGCATGAAAAA 59.459 47.619 0.00 0.00 31.60 1.94
1492 1560 2.165030 CGCTCTGGAAGGCATGAAAAAT 59.835 45.455 0.00 0.00 31.60 1.82
1493 1561 3.518590 GCTCTGGAAGGCATGAAAAATG 58.481 45.455 0.00 0.00 31.60 2.32
1495 1563 2.833338 TCTGGAAGGCATGAAAAATGGG 59.167 45.455 0.00 0.00 0.00 4.00
1498 1566 3.649981 TGGAAGGCATGAAAAATGGGAAA 59.350 39.130 0.00 0.00 0.00 3.13
1499 1567 4.103785 TGGAAGGCATGAAAAATGGGAAAA 59.896 37.500 0.00 0.00 0.00 2.29
1500 1568 5.222089 TGGAAGGCATGAAAAATGGGAAAAT 60.222 36.000 0.00 0.00 0.00 1.82
1501 1569 5.711506 GGAAGGCATGAAAAATGGGAAAATT 59.288 36.000 0.00 0.00 0.00 1.82
1503 1571 7.392953 GGAAGGCATGAAAAATGGGAAAATTAA 59.607 33.333 0.00 0.00 0.00 1.40
1506 1574 7.391275 AGGCATGAAAAATGGGAAAATTAACTG 59.609 33.333 0.00 0.00 0.00 3.16
1507 1575 7.390162 GGCATGAAAAATGGGAAAATTAACTGA 59.610 33.333 0.00 0.00 0.00 3.41
1508 1576 8.949177 GCATGAAAAATGGGAAAATTAACTGAT 58.051 29.630 0.00 0.00 0.00 2.90
1518 1586 9.056005 TGGGAAAATTAACTGATTGATATCTCG 57.944 33.333 3.98 0.00 0.00 4.04
1519 1587 8.507249 GGGAAAATTAACTGATTGATATCTCGG 58.493 37.037 3.98 1.92 0.00 4.63
1520 1588 9.057089 GGAAAATTAACTGATTGATATCTCGGT 57.943 33.333 3.98 2.57 32.37 4.69
1521 1589 9.869844 GAAAATTAACTGATTGATATCTCGGTG 57.130 33.333 3.98 0.00 31.45 4.94
1522 1590 7.969536 AATTAACTGATTGATATCTCGGTGG 57.030 36.000 3.98 0.00 31.45 4.61
1523 1591 4.342862 AACTGATTGATATCTCGGTGGG 57.657 45.455 3.98 0.00 31.45 4.61
1524 1592 2.037772 ACTGATTGATATCTCGGTGGGC 59.962 50.000 3.98 0.00 29.89 5.36
1525 1593 1.000843 TGATTGATATCTCGGTGGGCG 59.999 52.381 3.98 0.00 0.00 6.13
1526 1594 0.321671 ATTGATATCTCGGTGGGCGG 59.678 55.000 3.98 0.00 0.00 6.13
1527 1595 1.754380 TTGATATCTCGGTGGGCGGG 61.754 60.000 3.98 0.00 0.00 6.13
1528 1596 2.923035 ATATCTCGGTGGGCGGGG 60.923 66.667 0.00 0.00 0.00 5.73
1543 1611 2.915869 GGGGGAATAGAAGCCGCA 59.084 61.111 0.00 0.00 38.73 5.69
1544 1612 1.227973 GGGGGAATAGAAGCCGCAG 60.228 63.158 0.00 0.00 38.73 5.18
1545 1613 1.527370 GGGGAATAGAAGCCGCAGT 59.473 57.895 0.00 0.00 37.11 4.40
1622 1695 7.470289 AGATGTTACTATTTCAGTCAATCGC 57.530 36.000 0.00 0.00 38.80 4.58
1623 1696 6.480320 AGATGTTACTATTTCAGTCAATCGCC 59.520 38.462 0.00 0.00 38.80 5.54
1624 1697 5.483811 TGTTACTATTTCAGTCAATCGCCA 58.516 37.500 0.00 0.00 38.80 5.69
1625 1698 5.580691 TGTTACTATTTCAGTCAATCGCCAG 59.419 40.000 0.00 0.00 38.80 4.85
1626 1699 4.207891 ACTATTTCAGTCAATCGCCAGT 57.792 40.909 0.00 0.00 28.33 4.00
1627 1700 4.579869 ACTATTTCAGTCAATCGCCAGTT 58.420 39.130 0.00 0.00 28.33 3.16
1628 1701 4.631813 ACTATTTCAGTCAATCGCCAGTTC 59.368 41.667 0.00 0.00 28.33 3.01
1629 1702 1.428448 TTCAGTCAATCGCCAGTTCG 58.572 50.000 0.00 0.00 0.00 3.95
1680 1753 4.427312 CAGGAATCTACAAAAGCAATGGC 58.573 43.478 0.00 0.00 41.61 4.40
1740 1813 2.398498 CGTTCAGAGGTCAGTTGTCTG 58.602 52.381 0.00 0.00 42.54 3.51
1750 1823 3.248602 GGTCAGTTGTCTGTGCTTACTTG 59.751 47.826 0.00 0.00 41.91 3.16
1782 1855 4.772886 TCCTAGCTTTCCCATTCTAACC 57.227 45.455 0.00 0.00 0.00 2.85
1787 1860 3.593780 AGCTTTCCCATTCTAACCCTTCT 59.406 43.478 0.00 0.00 0.00 2.85
1789 1862 4.567747 GCTTTCCCATTCTAACCCTTCTCA 60.568 45.833 0.00 0.00 0.00 3.27
1795 1871 5.951747 CCCATTCTAACCCTTCTCATTTTGA 59.048 40.000 0.00 0.00 0.00 2.69
1802 1878 8.043710 TCTAACCCTTCTCATTTTGAATCTCTC 58.956 37.037 0.00 0.00 0.00 3.20
1807 1883 9.406113 CCCTTCTCATTTTGAATCTCTCTTATT 57.594 33.333 0.00 0.00 0.00 1.40
1959 2036 4.073293 ACCAGGTTGATATCTTAAGCGG 57.927 45.455 3.98 8.65 0.00 5.52
2086 2163 3.490348 AGGTTTGGTCCAACAGATTCAG 58.510 45.455 2.98 0.00 0.00 3.02
2090 2167 1.355381 TGGTCCAACAGATTCAGGCAT 59.645 47.619 0.00 0.00 0.00 4.40
2091 2168 2.019984 GGTCCAACAGATTCAGGCATC 58.980 52.381 0.00 0.00 0.00 3.91
2093 2170 3.285484 GTCCAACAGATTCAGGCATCAT 58.715 45.455 0.00 0.00 0.00 2.45
2094 2171 3.066342 GTCCAACAGATTCAGGCATCATG 59.934 47.826 0.00 0.00 0.00 3.07
2097 2174 2.298610 ACAGATTCAGGCATCATGCTG 58.701 47.619 10.11 6.18 44.28 4.41
2115 2192 0.035317 TGGACATGTCACCTGTGAGC 59.965 55.000 26.47 7.06 40.75 4.26
2133 2210 4.808364 GTGAGCTGGTCAGATGAGAAATAC 59.192 45.833 10.21 0.00 35.13 1.89
2170 2247 3.321039 TGTCAGCTTATCTGGGATCCAT 58.679 45.455 15.23 0.66 43.06 3.41
2171 2248 3.326006 TGTCAGCTTATCTGGGATCCATC 59.674 47.826 15.23 0.00 43.06 3.51
2180 2257 3.122480 TCTGGGATCCATCCTTGCTTTA 58.878 45.455 15.23 0.00 46.35 1.85
2181 2258 3.723681 TCTGGGATCCATCCTTGCTTTAT 59.276 43.478 15.23 0.00 46.35 1.40
2182 2259 3.825014 CTGGGATCCATCCTTGCTTTATG 59.175 47.826 15.23 0.00 46.35 1.90
2184 2261 3.437052 GGGATCCATCCTTGCTTTATGGT 60.437 47.826 15.23 0.00 46.35 3.55
2185 2262 4.202567 GGGATCCATCCTTGCTTTATGGTA 60.203 45.833 15.23 0.00 46.35 3.25
2186 2263 4.762251 GGATCCATCCTTGCTTTATGGTAC 59.238 45.833 6.95 0.00 43.73 3.34
2187 2264 5.690097 GGATCCATCCTTGCTTTATGGTACA 60.690 44.000 6.95 0.00 43.73 2.90
2188 2265 6.973651 GGATCCATCCTTGCTTTATGGTACAT 60.974 42.308 6.95 0.00 43.63 2.29
2189 2266 8.920108 GGATCCATCCTTGCTTTATGGTACATG 61.920 44.444 6.95 0.00 43.63 3.21
2343 2828 5.623335 TGTTAGATGCCGTGTTAATTTTCG 58.377 37.500 0.00 0.00 0.00 3.46
2455 2940 4.185467 ACGATATGAGATGGACATGCTC 57.815 45.455 0.00 0.00 0.00 4.26
2497 2982 2.302260 GGCCTTAATCCTGAAGAAGCC 58.698 52.381 0.00 0.00 0.00 4.35
2530 3015 7.367285 TCAAAAGAATGAGGTACAATTTTCGG 58.633 34.615 0.00 0.00 0.00 4.30
2576 3061 9.754382 CATCAATAAATACATAGCAGCCTTTTT 57.246 29.630 0.00 0.00 0.00 1.94
2652 3137 9.952188 TTGATTCTTGACTTATCTACAGATACG 57.048 33.333 0.00 0.43 36.81 3.06
2662 3147 5.537300 ATCTACAGATACGAGCAATGGTT 57.463 39.130 0.00 0.00 32.01 3.67
2698 3184 8.671384 TGTATATATTAGTTTGTTCCTGTGGC 57.329 34.615 0.00 0.00 0.00 5.01
2756 3242 0.391130 GAGCCGGATGCAGTGTAACA 60.391 55.000 5.05 0.00 44.83 2.41
2757 3243 0.253044 AGCCGGATGCAGTGTAACAT 59.747 50.000 5.05 0.00 44.83 2.71
2758 3244 0.657840 GCCGGATGCAGTGTAACATC 59.342 55.000 5.05 0.00 41.43 3.06
2759 3245 2.011548 GCCGGATGCAGTGTAACATCA 61.012 52.381 5.05 0.00 43.64 3.07
2760 3246 1.935873 CCGGATGCAGTGTAACATCAG 59.064 52.381 0.00 6.87 43.64 2.90
2761 3247 2.621338 CGGATGCAGTGTAACATCAGT 58.379 47.619 10.27 0.00 43.64 3.41
3296 3790 0.890542 TTGCTCGTTTCTGCCAGCAT 60.891 50.000 0.00 0.00 41.44 3.79
3302 3796 1.199789 CGTTTCTGCCAGCATTGCTTA 59.800 47.619 8.83 0.00 36.40 3.09
3331 3825 0.700564 ACCTTCCATGCCATGTGTCT 59.299 50.000 3.63 0.00 0.00 3.41
3333 3827 2.092753 ACCTTCCATGCCATGTGTCTAG 60.093 50.000 3.63 0.00 0.00 2.43
3450 3944 0.749649 TGCGCCAGTTTCAAAACCAT 59.250 45.000 4.18 0.00 39.71 3.55
3513 4007 3.983044 AGTGATGTGTTCCTTCCTACC 57.017 47.619 0.00 0.00 0.00 3.18
3515 4009 4.684724 AGTGATGTGTTCCTTCCTACCTA 58.315 43.478 0.00 0.00 0.00 3.08
3639 4133 6.098679 GTGTAGATATAGCCATCTTCTGCAG 58.901 44.000 7.63 7.63 36.63 4.41
3647 4141 2.165845 GCCATCTTCTGCAGCAAGATTT 59.834 45.455 25.81 13.55 38.33 2.17
3826 4320 9.358872 GACAATTTCTTGGGAGAATTTTACATC 57.641 33.333 0.00 0.00 41.35 3.06
4027 4521 5.582225 TGCCTGTGCAAGTTACTGTTTGC 62.582 47.826 8.38 8.38 46.66 3.68
4077 4572 0.318275 GCAGAGTCCCGATGATCGTC 60.318 60.000 14.27 4.73 38.40 4.20
4110 4605 4.164981 TCCCAGTGTTCTGTTGTATAGGT 58.835 43.478 0.00 0.00 39.82 3.08
4166 4663 6.455913 CCATTCATTTATTTTGAAGCTTGCCG 60.456 38.462 2.10 0.00 36.60 5.69
4174 4671 2.489938 TGAAGCTTGCCGAAATAGGT 57.510 45.000 2.10 0.00 0.00 3.08
4210 4707 5.869888 TGTAAATTTTTGTTGGTCGTTTGCT 59.130 32.000 0.00 0.00 0.00 3.91
4213 4710 3.414549 TTTTGTTGGTCGTTTGCTCTC 57.585 42.857 0.00 0.00 0.00 3.20
4230 4727 4.883585 TGCTCTCTTGTTCACTGTTGATTT 59.116 37.500 0.00 0.00 0.00 2.17
4232 4729 6.712095 TGCTCTCTTGTTCACTGTTGATTTAT 59.288 34.615 0.00 0.00 0.00 1.40
4234 4731 7.748241 GCTCTCTTGTTCACTGTTGATTTATTC 59.252 37.037 0.00 0.00 0.00 1.75
4235 4732 8.675705 TCTCTTGTTCACTGTTGATTTATTCA 57.324 30.769 0.00 0.00 0.00 2.57
4236 4733 9.288576 TCTCTTGTTCACTGTTGATTTATTCAT 57.711 29.630 0.00 0.00 33.34 2.57
4237 4734 9.338291 CTCTTGTTCACTGTTGATTTATTCATG 57.662 33.333 0.00 0.00 33.34 3.07
4250 4747 8.836268 TGATTTATTCATGATGATGATGTCGA 57.164 30.769 0.00 0.00 38.43 4.20
4270 4767 5.473504 GTCGAAAGGGATATACAATTGCCAT 59.526 40.000 5.05 1.78 0.00 4.40
4287 4784 2.372264 CCATGGTGACCAATTGAGAGG 58.628 52.381 9.06 0.00 36.95 3.69
4307 4804 4.886579 AGGCATTTTGGTTTCATCAAGTC 58.113 39.130 0.00 0.00 0.00 3.01
4362 4859 7.333528 AGTGTTGTTATTTTTCTTGAGCTCA 57.666 32.000 13.74 13.74 0.00 4.26
4387 4884 8.635328 CATCATTTCCTTTCATTATCCATGTGA 58.365 33.333 0.00 0.00 34.06 3.58
4388 4885 8.592529 TCATTTCCTTTCATTATCCATGTGAA 57.407 30.769 0.00 0.00 34.06 3.18
4401 4898 9.638176 ATTATCCATGTGAAAAGCTTTCTCTAT 57.362 29.630 13.10 2.87 0.00 1.98
4409 4906 6.708502 GTGAAAAGCTTTCTCTATCTATCCCC 59.291 42.308 13.10 0.00 0.00 4.81
4418 4915 4.597507 TCTCTATCTATCCCCGCCAAAAAT 59.402 41.667 0.00 0.00 0.00 1.82
4419 4916 5.073144 TCTCTATCTATCCCCGCCAAAAATT 59.927 40.000 0.00 0.00 0.00 1.82
4462 4966 0.108138 AGCCACGCTAAGCTACAAGG 60.108 55.000 0.00 0.00 36.99 3.61
4469 4973 1.404315 GCTAAGCTACAAGGTCAGCGT 60.404 52.381 0.00 0.00 42.74 5.07
4547 5051 2.817396 GAGAGCTGCCTGGCGAAC 60.817 66.667 14.98 5.72 37.29 3.95
4685 5189 4.015406 ATGTTCTCGGGCGTGGCA 62.015 61.111 0.00 0.00 0.00 4.92
4741 5245 0.755698 TCCTGGATGCGGAGGTAGTC 60.756 60.000 0.00 0.00 0.00 2.59
4847 5351 4.440127 GCCATGCCCTTGTTGCGG 62.440 66.667 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.711922 CGGTCCAGGAGTAGCGCTT 61.712 63.158 18.68 0.00 0.00 4.68
41 42 0.389391 CTGACCCATTCGCGGACTAT 59.611 55.000 6.13 0.00 0.00 2.12
399 401 0.606096 AAACATAAAAGCCGGCCACC 59.394 50.000 26.15 0.00 0.00 4.61
556 568 0.248702 TTGCCCGCTTTTTGTTCGTC 60.249 50.000 0.00 0.00 0.00 4.20
560 572 1.395262 CGTTTTTGCCCGCTTTTTGTT 59.605 42.857 0.00 0.00 0.00 2.83
572 584 1.586826 AAACGGACGGCGTTTTTGC 60.587 52.632 16.19 0.00 36.32 3.68
596 608 4.899352 ATAAGAGCAACTCCAACAGACT 57.101 40.909 0.00 0.00 0.00 3.24
598 610 7.847096 TGTAATATAAGAGCAACTCCAACAGA 58.153 34.615 0.00 0.00 0.00 3.41
600 612 8.318412 TCTTGTAATATAAGAGCAACTCCAACA 58.682 33.333 0.00 0.00 31.04 3.33
618 630 7.750947 AGTAGTACTCCCCAAATCTTGTAAT 57.249 36.000 0.00 0.00 0.00 1.89
620 632 6.786967 GAGTAGTACTCCCCAAATCTTGTA 57.213 41.667 18.10 0.00 39.28 2.41
621 633 5.678955 GAGTAGTACTCCCCAAATCTTGT 57.321 43.478 18.10 0.00 39.28 3.16
652 664 1.445410 CGCTTAGCACACCGCACTA 60.445 57.895 4.70 0.00 46.13 2.74
681 693 0.608130 TAGCCAAGCGTGTGATCACT 59.392 50.000 25.55 3.34 41.89 3.41
692 704 3.406764 CATGGACTATCCTTAGCCAAGC 58.593 50.000 0.00 0.00 37.46 4.01
699 711 2.106511 GGCTTGGCATGGACTATCCTTA 59.893 50.000 2.33 0.00 37.46 2.69
707 719 2.575461 GCTTGGCTTGGCATGGAC 59.425 61.111 10.95 0.00 0.00 4.02
714 726 4.060038 CGGCTTGGCTTGGCTTGG 62.060 66.667 0.00 0.00 0.00 3.61
715 727 4.729856 GCGGCTTGGCTTGGCTTG 62.730 66.667 0.00 0.00 0.00 4.01
854 903 2.602676 TTGGCCTAGCTGTGGGGAC 61.603 63.158 3.32 0.00 0.00 4.46
954 1003 4.313675 GATCGGCGCCGGCATTTC 62.314 66.667 44.95 28.70 42.47 2.17
1239 1294 6.204688 CCGATAAAATTTAGCCAGTAGATGCA 59.795 38.462 0.00 0.00 0.00 3.96
1240 1295 6.204882 ACCGATAAAATTTAGCCAGTAGATGC 59.795 38.462 0.00 0.00 0.00 3.91
1241 1296 7.441157 TGACCGATAAAATTTAGCCAGTAGATG 59.559 37.037 0.00 0.00 0.00 2.90
1242 1297 7.506114 TGACCGATAAAATTTAGCCAGTAGAT 58.494 34.615 0.00 0.00 0.00 1.98
1243 1298 6.880484 TGACCGATAAAATTTAGCCAGTAGA 58.120 36.000 0.00 0.00 0.00 2.59
1244 1299 6.761714 ACTGACCGATAAAATTTAGCCAGTAG 59.238 38.462 8.77 1.11 30.48 2.57
1245 1300 6.646267 ACTGACCGATAAAATTTAGCCAGTA 58.354 36.000 8.77 0.00 30.48 2.74
1246 1301 5.497474 ACTGACCGATAAAATTTAGCCAGT 58.503 37.500 5.86 5.86 0.00 4.00
1247 1302 7.730364 ATACTGACCGATAAAATTTAGCCAG 57.270 36.000 0.00 4.88 0.00 4.85
1248 1303 7.554835 ACAATACTGACCGATAAAATTTAGCCA 59.445 33.333 0.00 0.00 0.00 4.75
1249 1304 7.927048 ACAATACTGACCGATAAAATTTAGCC 58.073 34.615 0.00 0.00 0.00 3.93
1255 1310 9.622004 CGTAGATACAATACTGACCGATAAAAT 57.378 33.333 0.00 0.00 0.00 1.82
1256 1311 8.839343 TCGTAGATACAATACTGACCGATAAAA 58.161 33.333 0.00 0.00 0.00 1.52
1257 1312 8.382030 TCGTAGATACAATACTGACCGATAAA 57.618 34.615 0.00 0.00 0.00 1.40
1258 1313 7.360691 GCTCGTAGATACAATACTGACCGATAA 60.361 40.741 0.00 0.00 33.89 1.75
1259 1314 6.091849 GCTCGTAGATACAATACTGACCGATA 59.908 42.308 0.00 0.00 33.89 2.92
1260 1315 5.106634 GCTCGTAGATACAATACTGACCGAT 60.107 44.000 0.00 0.00 33.89 4.18
1261 1316 4.212847 GCTCGTAGATACAATACTGACCGA 59.787 45.833 0.00 0.00 33.89 4.69
1262 1317 4.024302 TGCTCGTAGATACAATACTGACCG 60.024 45.833 0.00 0.00 33.89 4.79
1263 1318 5.434352 TGCTCGTAGATACAATACTGACC 57.566 43.478 0.00 0.00 33.89 4.02
1264 1319 7.932120 ATTTGCTCGTAGATACAATACTGAC 57.068 36.000 0.00 0.00 33.53 3.51
1265 1320 9.678941 CTTATTTGCTCGTAGATACAATACTGA 57.321 33.333 0.00 0.00 33.53 3.41
1266 1321 9.464714 ACTTATTTGCTCGTAGATACAATACTG 57.535 33.333 0.00 0.00 33.53 2.74
1267 1322 9.464714 CACTTATTTGCTCGTAGATACAATACT 57.535 33.333 0.00 0.00 33.53 2.12
1268 1323 9.459640 TCACTTATTTGCTCGTAGATACAATAC 57.540 33.333 0.00 0.00 33.53 1.89
1270 1325 8.982685 CATCACTTATTTGCTCGTAGATACAAT 58.017 33.333 0.00 0.00 33.53 2.71
1271 1326 8.194769 TCATCACTTATTTGCTCGTAGATACAA 58.805 33.333 0.00 0.00 33.89 2.41
1272 1327 7.712797 TCATCACTTATTTGCTCGTAGATACA 58.287 34.615 0.00 0.00 33.89 2.29
1356 1421 6.312141 AGGAAAATTGGTATGAATTTGGGG 57.688 37.500 0.00 0.00 36.01 4.96
1397 1462 9.449719 CCTCTAACTTCACAAATTTGGTACTAT 57.550 33.333 21.74 6.99 0.00 2.12
1426 1494 1.538512 CAGCTAAGCTTTCAGCAGCAA 59.461 47.619 20.52 0.00 45.56 3.91
1492 1560 9.056005 CGAGATATCAATCAGTTAATTTTCCCA 57.944 33.333 5.32 0.00 34.28 4.37
1493 1561 8.507249 CCGAGATATCAATCAGTTAATTTTCCC 58.493 37.037 5.32 0.00 34.28 3.97
1495 1563 9.869844 CACCGAGATATCAATCAGTTAATTTTC 57.130 33.333 5.32 0.00 34.28 2.29
1498 1566 6.936900 CCCACCGAGATATCAATCAGTTAATT 59.063 38.462 5.32 0.00 34.28 1.40
1499 1567 6.467677 CCCACCGAGATATCAATCAGTTAAT 58.532 40.000 5.32 0.00 34.28 1.40
1500 1568 5.741964 GCCCACCGAGATATCAATCAGTTAA 60.742 44.000 5.32 0.00 34.28 2.01
1501 1569 4.262463 GCCCACCGAGATATCAATCAGTTA 60.262 45.833 5.32 0.00 34.28 2.24
1503 1571 2.037772 GCCCACCGAGATATCAATCAGT 59.962 50.000 5.32 0.00 34.28 3.41
1506 1574 1.673033 CCGCCCACCGAGATATCAATC 60.673 57.143 5.32 0.00 40.02 2.67
1507 1575 0.321671 CCGCCCACCGAGATATCAAT 59.678 55.000 5.32 0.00 40.02 2.57
1508 1576 1.745890 CCGCCCACCGAGATATCAA 59.254 57.895 5.32 0.00 40.02 2.57
1509 1577 2.207229 CCCGCCCACCGAGATATCA 61.207 63.158 5.32 0.00 40.02 2.15
1510 1578 2.657237 CCCGCCCACCGAGATATC 59.343 66.667 0.00 0.00 40.02 1.63
1511 1579 2.923035 CCCCGCCCACCGAGATAT 60.923 66.667 0.00 0.00 40.02 1.63
1526 1594 1.227973 CTGCGGCTTCTATTCCCCC 60.228 63.158 0.00 0.00 0.00 5.40
1527 1595 0.107165 AACTGCGGCTTCTATTCCCC 60.107 55.000 0.00 0.00 0.00 4.81
1528 1596 2.210961 GTAACTGCGGCTTCTATTCCC 58.789 52.381 0.00 0.00 0.00 3.97
1529 1597 2.210961 GGTAACTGCGGCTTCTATTCC 58.789 52.381 0.00 0.00 0.00 3.01
1544 1612 8.784043 AGTATCTCAACAAAACATCAAGGTAAC 58.216 33.333 0.00 0.00 0.00 2.50
1545 1613 8.918202 AGTATCTCAACAAAACATCAAGGTAA 57.082 30.769 0.00 0.00 0.00 2.85
1575 1647 3.626670 TGACAAAATTTTGCAAGCCCTTG 59.373 39.130 26.94 5.64 41.79 3.61
1622 1695 0.250124 TACTGTTGGTGGCGAACTGG 60.250 55.000 0.00 0.00 0.00 4.00
1623 1696 1.588674 TTACTGTTGGTGGCGAACTG 58.411 50.000 0.00 0.00 0.00 3.16
1624 1697 2.552315 CAATTACTGTTGGTGGCGAACT 59.448 45.455 0.00 0.00 0.00 3.01
1625 1698 2.920647 GCAATTACTGTTGGTGGCGAAC 60.921 50.000 0.00 0.00 0.00 3.95
1626 1699 1.268352 GCAATTACTGTTGGTGGCGAA 59.732 47.619 0.00 0.00 0.00 4.70
1627 1700 0.878416 GCAATTACTGTTGGTGGCGA 59.122 50.000 0.00 0.00 0.00 5.54
1628 1701 0.454285 CGCAATTACTGTTGGTGGCG 60.454 55.000 0.00 0.00 37.17 5.69
1629 1702 0.878416 TCGCAATTACTGTTGGTGGC 59.122 50.000 0.00 0.00 0.00 5.01
1680 1753 6.114089 CCCATTGCAGGATATCTTCAGATAG 58.886 44.000 2.05 0.00 40.04 2.08
1740 1813 2.399396 TGAAAAGCGCAAGTAAGCAC 57.601 45.000 11.47 0.00 41.68 4.40
1750 1823 3.430008 GAAAGCTAGGATTGAAAAGCGC 58.570 45.455 0.00 0.00 39.94 5.92
1802 1878 7.445096 TGCCACCATGTCACATATCTTAATAAG 59.555 37.037 0.00 0.00 0.00 1.73
1807 1883 4.164030 ACTGCCACCATGTCACATATCTTA 59.836 41.667 0.00 0.00 0.00 2.10
1959 2036 5.672321 GCTGAAAAGCATACAGAACACTAGC 60.672 44.000 0.00 0.00 34.07 3.42
2093 2170 0.250424 CACAGGTGACATGTCCAGCA 60.250 55.000 22.85 1.81 34.73 4.41
2094 2171 0.035317 TCACAGGTGACATGTCCAGC 59.965 55.000 22.85 18.43 34.14 4.85
2097 2174 0.322975 AGCTCACAGGTGACATGTCC 59.677 55.000 22.85 13.66 35.46 4.02
2115 2192 6.478344 GCAAGTAGTATTTCTCATCTGACCAG 59.522 42.308 0.00 0.00 0.00 4.00
2133 2210 2.549754 CTGACAAACCTGGTGCAAGTAG 59.450 50.000 0.00 0.00 0.00 2.57
2170 2247 6.039270 GCAATACATGTACCATAAAGCAAGGA 59.961 38.462 7.96 0.00 0.00 3.36
2171 2248 6.039717 AGCAATACATGTACCATAAAGCAAGG 59.960 38.462 7.96 0.00 0.00 3.61
2180 2257 5.947228 GCACATAGCAATACATGTACCAT 57.053 39.130 7.96 0.00 44.79 3.55
2194 2679 5.009510 TGAGAGACTATGAAGAGCACATAGC 59.990 44.000 12.78 7.60 46.20 2.97
2293 2778 2.915349 AGCTCAGTACTGATGCCATTG 58.085 47.619 28.50 17.69 39.13 2.82
2343 2828 2.038557 TGAGGGGTAAACTTCAGAGCAC 59.961 50.000 0.00 0.00 0.00 4.40
2455 2940 2.674954 TGATTGCAACCAGAAAATGCG 58.325 42.857 0.00 0.00 42.91 4.73
2497 2982 4.319177 ACCTCATTCTTTTGAGTTCCTCG 58.681 43.478 1.24 0.00 41.30 4.63
2530 3015 6.220930 TGATGTTAGGTGAAAGACTGTACAC 58.779 40.000 0.00 0.00 0.00 2.90
2576 3061 8.981659 TCTGAGGAATTACTTGATTCAGTATCA 58.018 33.333 0.00 0.00 41.50 2.15
2581 3066 8.256605 TCTTCTCTGAGGAATTACTTGATTCAG 58.743 37.037 4.59 0.00 37.69 3.02
2652 3137 6.683974 ACAACATCTATGTAACCATTGCTC 57.316 37.500 0.00 0.00 40.80 4.26
2698 3184 5.649782 AAACTTGAGAAATGTATGCAGGG 57.350 39.130 0.00 0.00 0.00 4.45
2729 3215 2.292267 CTGCATCCGGCTCTAAACATT 58.708 47.619 0.00 0.00 45.15 2.71
2756 3242 5.587844 GCCATTTGTTGAGACTGATACTGAT 59.412 40.000 0.00 0.00 0.00 2.90
2757 3243 4.937620 GCCATTTGTTGAGACTGATACTGA 59.062 41.667 0.00 0.00 0.00 3.41
2758 3244 4.201753 CGCCATTTGTTGAGACTGATACTG 60.202 45.833 0.00 0.00 0.00 2.74
2759 3245 3.935203 CGCCATTTGTTGAGACTGATACT 59.065 43.478 0.00 0.00 0.00 2.12
2760 3246 3.485877 GCGCCATTTGTTGAGACTGATAC 60.486 47.826 0.00 0.00 0.00 2.24
2761 3247 2.677836 GCGCCATTTGTTGAGACTGATA 59.322 45.455 0.00 0.00 0.00 2.15
3248 3741 5.645067 TCACTTGCAATTGAATAGTCAGGAG 59.355 40.000 16.30 0.00 34.49 3.69
3296 3790 4.134563 GGAAGGTCAGAAACTGTAAGCAA 58.865 43.478 0.00 0.00 37.60 3.91
3302 3796 2.508526 GCATGGAAGGTCAGAAACTGT 58.491 47.619 0.00 0.00 32.61 3.55
3450 3944 1.627329 AGTGCAGCCATCTGAGAAGAA 59.373 47.619 0.00 0.00 42.95 2.52
3501 3995 6.099269 TGTTACCATCATAGGTAGGAAGGAAC 59.901 42.308 0.25 2.22 44.48 3.62
3513 4007 4.816385 AGTTTCGCCATGTTACCATCATAG 59.184 41.667 0.00 0.00 0.00 2.23
3515 4009 3.620488 AGTTTCGCCATGTTACCATCAT 58.380 40.909 0.00 0.00 0.00 2.45
3761 4255 8.120140 AGTCTATAAGTTCAACTAGTTTCCGT 57.880 34.615 5.07 0.00 0.00 4.69
3809 4303 6.659242 GGACAGAAGATGTAAAATTCTCCCAA 59.341 38.462 0.00 0.00 44.17 4.12
4027 4521 0.936764 CTTCAGTCCGCGGATCATCG 60.937 60.000 33.58 17.55 0.00 3.84
4077 4572 2.762535 ACACTGGGAACATCGGTTAG 57.237 50.000 0.00 0.00 41.51 2.34
4110 4605 8.137437 CAGCATAGAAAGAAAAGAAAAACCTGA 58.863 33.333 0.00 0.00 0.00 3.86
4166 4663 4.844884 ACACAAAGCCTCCTACCTATTTC 58.155 43.478 0.00 0.00 0.00 2.17
4174 4671 7.354751 ACAAAAATTTACACAAAGCCTCCTA 57.645 32.000 0.00 0.00 0.00 2.94
4210 4707 8.675705 TGAATAAATCAACAGTGAACAAGAGA 57.324 30.769 0.00 0.00 37.30 3.10
4213 4710 9.850628 ATCATGAATAAATCAACAGTGAACAAG 57.149 29.630 0.00 0.00 42.54 3.16
4230 4727 6.652062 CCCTTTCGACATCATCATCATGAATA 59.348 38.462 0.00 0.00 42.53 1.75
4232 4729 4.818005 CCCTTTCGACATCATCATCATGAA 59.182 41.667 0.00 0.00 42.53 2.57
4234 4731 4.383173 TCCCTTTCGACATCATCATCATG 58.617 43.478 0.00 0.00 0.00 3.07
4235 4732 4.694760 TCCCTTTCGACATCATCATCAT 57.305 40.909 0.00 0.00 0.00 2.45
4236 4733 4.694760 ATCCCTTTCGACATCATCATCA 57.305 40.909 0.00 0.00 0.00 3.07
4237 4734 7.323420 TGTATATCCCTTTCGACATCATCATC 58.677 38.462 0.00 0.00 0.00 2.92
4246 4743 4.819630 TGGCAATTGTATATCCCTTTCGAC 59.180 41.667 7.40 0.00 0.00 4.20
4250 4747 5.305128 CACCATGGCAATTGTATATCCCTTT 59.695 40.000 13.04 0.00 0.00 3.11
4270 4767 0.770499 TGCCTCTCAATTGGTCACCA 59.230 50.000 5.42 0.00 0.00 4.17
4287 4784 5.754890 ACAAGACTTGATGAAACCAAAATGC 59.245 36.000 21.95 0.00 0.00 3.56
4334 4831 9.435688 AGCTCAAGAAAAATAACAACACTTTTT 57.564 25.926 0.00 0.00 35.42 1.94
4335 4832 9.087424 GAGCTCAAGAAAAATAACAACACTTTT 57.913 29.630 9.40 0.00 0.00 2.27
4336 4833 8.250332 TGAGCTCAAGAAAAATAACAACACTTT 58.750 29.630 15.67 0.00 0.00 2.66
4337 4834 7.771183 TGAGCTCAAGAAAAATAACAACACTT 58.229 30.769 15.67 0.00 0.00 3.16
4338 4835 7.333528 TGAGCTCAAGAAAAATAACAACACT 57.666 32.000 15.67 0.00 0.00 3.55
4339 4836 7.862372 TGATGAGCTCAAGAAAAATAACAACAC 59.138 33.333 22.50 0.00 0.00 3.32
4340 4837 7.939782 TGATGAGCTCAAGAAAAATAACAACA 58.060 30.769 22.50 0.00 0.00 3.33
4341 4838 8.976986 ATGATGAGCTCAAGAAAAATAACAAC 57.023 30.769 22.50 0.00 37.44 3.32
4342 4839 9.985730 AAATGATGAGCTCAAGAAAAATAACAA 57.014 25.926 22.50 0.00 37.44 2.83
4343 4840 9.630098 GAAATGATGAGCTCAAGAAAAATAACA 57.370 29.630 22.50 8.38 37.44 2.41
4344 4841 9.080915 GGAAATGATGAGCTCAAGAAAAATAAC 57.919 33.333 22.50 5.64 37.44 1.89
4345 4842 9.028284 AGGAAATGATGAGCTCAAGAAAAATAA 57.972 29.630 22.50 0.00 37.44 1.40
4346 4843 8.585471 AGGAAATGATGAGCTCAAGAAAAATA 57.415 30.769 22.50 1.48 37.44 1.40
4347 4844 7.477945 AGGAAATGATGAGCTCAAGAAAAAT 57.522 32.000 22.50 1.08 37.44 1.82
4348 4845 6.906157 AGGAAATGATGAGCTCAAGAAAAA 57.094 33.333 22.50 3.20 37.44 1.94
4349 4846 6.906157 AAGGAAATGATGAGCTCAAGAAAA 57.094 33.333 22.50 5.07 37.44 2.29
4350 4847 6.491062 TGAAAGGAAATGATGAGCTCAAGAAA 59.509 34.615 22.50 6.98 37.44 2.52
4351 4848 6.005823 TGAAAGGAAATGATGAGCTCAAGAA 58.994 36.000 22.50 9.69 37.44 2.52
4352 4849 5.563592 TGAAAGGAAATGATGAGCTCAAGA 58.436 37.500 22.50 10.64 37.44 3.02
4353 4850 5.892160 TGAAAGGAAATGATGAGCTCAAG 57.108 39.130 22.50 0.00 37.44 3.02
4354 4851 6.845758 AATGAAAGGAAATGATGAGCTCAA 57.154 33.333 22.50 5.35 37.44 3.02
4355 4852 7.230108 GGATAATGAAAGGAAATGATGAGCTCA 59.770 37.037 20.79 20.79 38.53 4.26
4358 4855 7.281040 TGGATAATGAAAGGAAATGATGAGC 57.719 36.000 0.00 0.00 0.00 4.26
4362 4859 8.771521 TCACATGGATAATGAAAGGAAATGAT 57.228 30.769 0.00 0.00 38.72 2.45
4387 4884 5.743422 GCGGGGATAGATAGAGAAAGCTTTT 60.743 44.000 14.05 3.35 0.00 2.27
4388 4885 4.262678 GCGGGGATAGATAGAGAAAGCTTT 60.263 45.833 12.53 12.53 0.00 3.51
4401 4898 8.607713 TCTATATAAATTTTTGGCGGGGATAGA 58.392 33.333 0.00 0.00 0.00 1.98
4449 4953 1.281899 CGCTGACCTTGTAGCTTAGC 58.718 55.000 0.00 0.00 37.78 3.09
4462 4966 2.370281 TCTGAAATCCAGACGCTGAC 57.630 50.000 8.20 0.00 46.38 3.51
4506 5010 0.681564 GAGAGGAGGACAAGGCTCGA 60.682 60.000 0.00 0.00 0.00 4.04
4805 5309 2.985957 TCATCGACATCTTCATGGCA 57.014 45.000 0.00 0.00 38.04 4.92
4847 5351 1.897615 GGGCATCATCAGCTGGCTC 60.898 63.158 15.13 4.77 36.74 4.70
4919 5423 2.509336 CTGGTGATGTCCGTCGGC 60.509 66.667 6.34 2.31 0.00 5.54
4930 5434 2.281484 GCGGCAAGTTCCTGGTGA 60.281 61.111 0.00 0.00 0.00 4.02
4960 5464 1.681327 GAGGAGCTGTACCCGGTGA 60.681 63.158 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.