Multiple sequence alignment - TraesCS3B01G124200

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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 TraesCS3B01G124200 chr3B 100.000 5376 0 0 1 5376 97733228 97738603 0.000000e+00 9928.0
1 TraesCS3B01G124200 chr3A 92.677 2103 91 27 2554 4609 69640828 69642914 0.000000e+00 2972.0
2 TraesCS3B01G124200 chr3A 84.282 1756 139 73 15 1692 69638103 69639799 0.000000e+00 1587.0
3 TraesCS3B01G124200 chr3A 89.189 888 57 15 1690 2553 69639843 69640715 0.000000e+00 1072.0
4 TraesCS3B01G124200 chr3A 92.357 314 9 9 4913 5212 69646598 69646910 2.970000e-117 433.0
5 TraesCS3B01G124200 chr3A 95.625 160 7 0 5217 5376 69646946 69647105 1.920000e-64 257.0
6 TraesCS3B01G124200 chr3A 97.059 34 1 0 4747 4780 562912888 562912855 2.090000e-04 58.4
7 TraesCS3B01G124200 chr3D 92.468 2111 61 43 2551 4616 61567127 61569184 0.000000e+00 2928.0
8 TraesCS3B01G124200 chr3D 86.667 2580 159 74 15 2505 61564451 61566934 0.000000e+00 2687.0
9 TraesCS3B01G124200 chr3D 91.633 502 22 9 4895 5376 61569275 61569776 0.000000e+00 676.0
10 TraesCS3B01G124200 chr6D 94.444 36 2 0 4744 4779 81654727 81654762 7.520000e-04 56.5
11 TraesCS3B01G124200 chr6D 100.000 28 0 0 4747 4774 112916707 112916680 1.000000e-02 52.8
12 TraesCS3B01G124200 chr5B 94.444 36 2 0 4744 4779 334071881 334071916 7.520000e-04 56.5
13 TraesCS3B01G124200 chr2B 96.970 33 1 0 4747 4779 16263085 16263053 7.520000e-04 56.5
14 TraesCS3B01G124200 chr2B 96.970 33 1 0 4747 4779 765556395 765556363 7.520000e-04 56.5
15 TraesCS3B01G124200 chr1B 94.444 36 2 0 4744 4779 652480925 652480960 7.520000e-04 56.5
16 TraesCS3B01G124200 chr6A 94.286 35 2 0 4744 4778 600811414 600811448 3.000000e-03 54.7


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 TraesCS3B01G124200 chr3B 97733228 97738603 5375 False 9928.0 9928 100.000 1 5376 1 chr3B.!!$F1 5375
1 TraesCS3B01G124200 chr3A 69638103 69647105 9002 False 1264.2 2972 90.826 15 5376 5 chr3A.!!$F1 5361
2 TraesCS3B01G124200 chr3D 61564451 61569776 5325 False 2097.0 2928 90.256 15 5376 3 chr3D.!!$F1 5361

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
97 98 0.166597 CACCACAGCACGCACAATAG 59.833 55.000 0.00 0.00 0.0 1.73 F
846 938 0.252513 ATAAAAGCCAACCCCCACCC 60.253 55.000 0.00 0.00 0.0 4.61 F
1940 2128 1.741770 CACTAGTGCCGGGCTGAAC 60.742 63.158 21.46 10.31 0.0 3.18 F
2336 2542 0.470833 TGGATGGTTGGTTGGTTGGG 60.471 55.000 0.00 0.00 0.0 4.12 F
3048 3457 0.251653 TCCGAACCCTACTGTGCTCT 60.252 55.000 0.00 0.00 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 2281 0.690411 TAATTGCCTGGCCAATGGGG 60.690 55.0 17.53 5.47 35.70 4.96 R
2261 2467 0.038166 AACGCACCATCCATCCAAGT 59.962 50.0 0.00 0.00 0.00 3.16 R
3035 3444 0.109086 CACACGAGAGCACAGTAGGG 60.109 60.0 0.00 0.00 0.00 3.53 R
3610 4025 0.456142 CGATGGACGCGAAGAAGACA 60.456 55.0 15.93 0.49 34.51 3.41 R
4740 8378 0.880278 GTTGACTGAGACCTTGCGCA 60.880 55.0 5.66 5.66 0.00 6.09 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
22 23 5.108385 AGTAGAAAAACAGCGGAACATTG 57.892 39.130 0.00 0.00 0.00 2.82
28 29 2.989422 ACAGCGGAACATTGTTAAGC 57.011 45.000 16.38 16.38 0.00 3.09
31 32 2.030363 CAGCGGAACATTGTTAAGCCAA 60.030 45.455 18.98 0.00 0.00 4.52
52 53 6.519761 GCCAAATATAATCGCAAGTGATTACG 59.480 38.462 15.86 5.43 42.04 3.18
83 84 5.411669 CCTGTAACTAACATTCTTCCACCAC 59.588 44.000 0.00 0.00 37.50 4.16
97 98 0.166597 CACCACAGCACGCACAATAG 59.833 55.000 0.00 0.00 0.00 1.73
130 131 8.205131 TGACAACAAATCATCAGTGATCATAG 57.795 34.615 1.56 0.00 44.20 2.23
221 227 0.732571 CAGCGGCAATAATTCCACGT 59.267 50.000 1.45 0.00 0.00 4.49
306 320 6.766467 TCCAAACACTTCTTCTTAGGTTTCTC 59.234 38.462 0.00 0.00 0.00 2.87
333 350 5.588648 GTGTACCATGTAGCACCACATAATT 59.411 40.000 0.00 0.00 37.02 1.40
369 390 1.531149 CGAAAGCACTGTAACCACCAG 59.469 52.381 0.00 0.00 36.01 4.00
370 391 2.572290 GAAAGCACTGTAACCACCAGT 58.428 47.619 0.00 0.00 43.76 4.00
371 392 3.735591 GAAAGCACTGTAACCACCAGTA 58.264 45.455 0.00 0.00 41.10 2.74
397 418 1.164411 CTCCACCAAAGCACGCATTA 58.836 50.000 0.00 0.00 0.00 1.90
415 443 7.239816 CGCATTACGCACAATAATAATTCAG 57.760 36.000 0.00 0.00 42.60 3.02
416 444 6.183359 CGCATTACGCACAATAATAATTCAGC 60.183 38.462 0.00 0.00 42.60 4.26
417 445 6.636447 GCATTACGCACAATAATAATTCAGCA 59.364 34.615 0.00 0.00 41.79 4.41
418 446 7.326789 GCATTACGCACAATAATAATTCAGCAT 59.673 33.333 0.00 0.00 41.79 3.79
419 447 8.632551 CATTACGCACAATAATAATTCAGCATG 58.367 33.333 0.00 0.00 37.54 4.06
517 547 3.053768 TCCCACCAACAGCATCAATGATA 60.054 43.478 0.00 0.00 0.00 2.15
540 570 4.021981 AGGAAAAGCCTCCAAAAGAAATCG 60.022 41.667 0.37 0.00 46.97 3.34
559 589 3.106738 CCAATCATGGGGAGAGCAC 57.893 57.895 0.00 0.00 43.51 4.40
562 592 2.449464 CAATCATGGGGAGAGCACAAA 58.551 47.619 0.00 0.00 0.00 2.83
564 594 2.673775 TCATGGGGAGAGCACAAAAA 57.326 45.000 0.00 0.00 0.00 1.94
591 621 4.537936 TTTTAACCAAAACAAATGCGCC 57.462 36.364 4.18 0.00 0.00 6.53
592 622 1.772182 TAACCAAAACAAATGCGCCG 58.228 45.000 4.18 0.00 0.00 6.46
593 623 0.878086 AACCAAAACAAATGCGCCGG 60.878 50.000 4.18 0.00 0.00 6.13
594 624 1.006805 CCAAAACAAATGCGCCGGA 60.007 52.632 5.05 0.00 0.00 5.14
595 625 1.008361 CCAAAACAAATGCGCCGGAG 61.008 55.000 5.05 1.55 0.00 4.63
619 649 1.875419 GAAAAACGTGCATGTGCGGC 61.875 55.000 13.39 0.00 45.83 6.53
621 651 2.348605 AAAACGTGCATGTGCGGCTT 62.349 50.000 13.39 0.00 45.83 4.35
636 696 4.189188 CTTCCCGCGTCGACCGAT 62.189 66.667 22.53 0.00 39.56 4.18
671 737 1.003331 CGCGTGATGAGTAGAGGAGTC 60.003 57.143 0.00 0.00 0.00 3.36
739 828 1.295423 CCCGTCCACGTCCAATCTT 59.705 57.895 0.00 0.00 37.74 2.40
740 829 0.739813 CCCGTCCACGTCCAATCTTC 60.740 60.000 0.00 0.00 37.74 2.87
741 830 0.739813 CCGTCCACGTCCAATCTTCC 60.740 60.000 0.00 0.00 37.74 3.46
742 831 0.739813 CGTCCACGTCCAATCTTCCC 60.740 60.000 0.00 0.00 34.11 3.97
743 832 0.739813 GTCCACGTCCAATCTTCCCG 60.740 60.000 0.00 0.00 0.00 5.14
744 833 1.449601 CCACGTCCAATCTTCCCGG 60.450 63.158 0.00 0.00 0.00 5.73
745 834 2.106683 CACGTCCAATCTTCCCGGC 61.107 63.158 0.00 0.00 0.00 6.13
746 835 2.267642 CGTCCAATCTTCCCGGCA 59.732 61.111 0.00 0.00 0.00 5.69
747 836 2.106683 CGTCCAATCTTCCCGGCAC 61.107 63.158 0.00 0.00 0.00 5.01
748 837 1.749258 GTCCAATCTTCCCGGCACC 60.749 63.158 0.00 0.00 0.00 5.01
749 838 2.227757 TCCAATCTTCCCGGCACCA 61.228 57.895 0.00 0.00 0.00 4.17
750 839 2.046285 CCAATCTTCCCGGCACCAC 61.046 63.158 0.00 0.00 0.00 4.16
751 840 2.046285 CAATCTTCCCGGCACCACC 61.046 63.158 0.00 0.00 0.00 4.61
846 938 0.252513 ATAAAAGCCAACCCCCACCC 60.253 55.000 0.00 0.00 0.00 4.61
929 1036 2.335011 CACAGACAGACGCGTCCA 59.665 61.111 34.08 0.00 36.52 4.02
968 1079 4.225340 CGACCGACGCTCGAGGAG 62.225 72.222 15.58 0.00 43.74 3.69
972 1083 3.578272 CGACGCTCGAGGAGGGAG 61.578 72.222 15.58 6.22 43.74 4.30
973 1084 2.124653 GACGCTCGAGGAGGGAGA 60.125 66.667 15.58 0.00 43.87 3.71
974 1085 2.124487 ACGCTCGAGGAGGGAGAG 60.124 66.667 15.58 0.00 43.87 3.20
975 1086 2.904866 CGCTCGAGGAGGGAGAGG 60.905 72.222 15.58 0.00 43.87 3.69
976 1087 3.223589 GCTCGAGGAGGGAGAGGC 61.224 72.222 15.58 0.00 33.27 4.70
977 1088 2.904866 CTCGAGGAGGGAGAGGCG 60.905 72.222 3.91 0.00 33.27 5.52
978 1089 4.507916 TCGAGGAGGGAGAGGCGG 62.508 72.222 0.00 0.00 0.00 6.13
979 1090 4.507916 CGAGGAGGGAGAGGCGGA 62.508 72.222 0.00 0.00 0.00 5.54
1152 1263 1.882167 GCTCTCGCAGATGCTCACC 60.882 63.158 2.95 0.00 39.32 4.02
1405 1516 7.770433 TGATTTTTACTCCATCAGATCAATCGT 59.230 33.333 0.00 0.00 0.00 3.73
1408 1519 4.582701 ACTCCATCAGATCAATCGTCTC 57.417 45.455 0.00 0.00 0.00 3.36
1414 1525 4.837896 TCAGATCAATCGTCTCGCTTAT 57.162 40.909 0.00 0.00 0.00 1.73
1415 1526 5.941948 TCAGATCAATCGTCTCGCTTATA 57.058 39.130 0.00 0.00 0.00 0.98
1416 1527 5.690816 TCAGATCAATCGTCTCGCTTATAC 58.309 41.667 0.00 0.00 0.00 1.47
1418 1529 5.792962 CAGATCAATCGTCTCGCTTATACTC 59.207 44.000 0.00 0.00 0.00 2.59
1419 1530 4.129878 TCAATCGTCTCGCTTATACTCG 57.870 45.455 0.00 0.00 0.00 4.18
1420 1531 3.805971 TCAATCGTCTCGCTTATACTCGA 59.194 43.478 0.00 0.00 0.00 4.04
1439 1553 5.467399 ACTCGAGAGTCCTCTAATACAATCG 59.533 44.000 21.68 0.00 40.61 3.34
1460 1574 3.305608 CGCTCCATTTTCTTTCCAAAGCT 60.306 43.478 0.00 0.00 35.99 3.74
1485 1601 6.939551 CAGTTTTTCCTGCACATTTCATAG 57.060 37.500 0.00 0.00 0.00 2.23
1486 1602 6.449698 CAGTTTTTCCTGCACATTTCATAGT 58.550 36.000 0.00 0.00 0.00 2.12
1498 1614 7.332182 TGCACATTTCATAGTAACACACGATTA 59.668 33.333 0.00 0.00 0.00 1.75
1499 1615 8.335356 GCACATTTCATAGTAACACACGATTAT 58.665 33.333 0.00 0.00 0.00 1.28
1507 1623 6.569228 AGTAACACACGATTATTGTCGATG 57.431 37.500 3.09 4.01 44.06 3.84
1510 1626 3.306973 ACACACGATTATTGTCGATGCTG 59.693 43.478 3.09 0.00 44.06 4.41
1511 1627 3.551485 CACACGATTATTGTCGATGCTGA 59.449 43.478 3.09 0.00 44.06 4.26
1515 1631 6.183360 ACACGATTATTGTCGATGCTGAAAAT 60.183 34.615 3.09 0.00 44.06 1.82
1540 1658 4.863131 ACACGATTGACGATTTCTACCTTC 59.137 41.667 0.00 0.00 45.77 3.46
1554 1672 3.693085 TCTACCTTCGCGACAGATTTACT 59.307 43.478 9.15 0.00 0.00 2.24
1556 1674 4.030134 ACCTTCGCGACAGATTTACTAG 57.970 45.455 9.15 0.00 0.00 2.57
1559 1677 5.298777 ACCTTCGCGACAGATTTACTAGTAT 59.701 40.000 9.15 0.00 0.00 2.12
1578 1696 9.517868 ACTAGTATGATAATTACTAGCTCCGTT 57.482 33.333 14.66 0.00 46.92 4.44
1581 1699 9.694137 AGTATGATAATTACTAGCTCCGTTTTC 57.306 33.333 0.00 0.00 0.00 2.29
1582 1700 9.472361 GTATGATAATTACTAGCTCCGTTTTCA 57.528 33.333 0.00 0.00 0.00 2.69
1584 1702 8.589335 TGATAATTACTAGCTCCGTTTTCATC 57.411 34.615 0.00 0.00 0.00 2.92
1585 1703 8.421784 TGATAATTACTAGCTCCGTTTTCATCT 58.578 33.333 0.00 0.00 0.00 2.90
1586 1704 9.909644 GATAATTACTAGCTCCGTTTTCATCTA 57.090 33.333 0.00 0.00 0.00 1.98
1587 1705 9.694137 ATAATTACTAGCTCCGTTTTCATCTAC 57.306 33.333 0.00 0.00 0.00 2.59
1588 1706 6.519679 TTACTAGCTCCGTTTTCATCTACA 57.480 37.500 0.00 0.00 0.00 2.74
1589 1707 5.000012 ACTAGCTCCGTTTTCATCTACAG 58.000 43.478 0.00 0.00 0.00 2.74
1590 1708 4.705507 ACTAGCTCCGTTTTCATCTACAGA 59.294 41.667 0.00 0.00 0.00 3.41
1604 1722 5.462068 TCATCTACAGACAGACAAACAAACG 59.538 40.000 0.00 0.00 0.00 3.60
1686 1811 5.226194 TGCTTTACCAATGCTTCCAAATT 57.774 34.783 0.00 0.00 33.15 1.82
1728 1899 9.143631 TCAATGATAGCGTTGATGATGTATTAG 57.856 33.333 11.50 0.00 43.26 1.73
1729 1900 8.929746 CAATGATAGCGTTGATGATGTATTAGT 58.070 33.333 7.14 0.00 42.38 2.24
1738 1909 9.608617 CGTTGATGATGTATTAGTATTACGTCT 57.391 33.333 18.49 9.32 32.56 4.18
1775 1946 3.058016 CGTGGACAGCATTTCTTGTGAAT 60.058 43.478 0.00 0.00 31.56 2.57
1795 1974 2.811317 CAAGCCTGAGACGACCGC 60.811 66.667 0.00 0.00 0.00 5.68
1939 2127 2.662596 CACTAGTGCCGGGCTGAA 59.337 61.111 21.46 4.09 0.00 3.02
1940 2128 1.741770 CACTAGTGCCGGGCTGAAC 60.742 63.158 21.46 10.31 0.00 3.18
2112 2315 5.050159 CAGGCAATTAAGTTTGACTTTTGGC 60.050 40.000 17.19 17.19 42.40 4.52
2113 2316 5.056480 GGCAATTAAGTTTGACTTTTGGCT 58.944 37.500 17.44 0.00 42.89 4.75
2114 2317 6.220201 GGCAATTAAGTTTGACTTTTGGCTA 58.780 36.000 17.44 0.00 42.89 3.93
2128 2331 7.231722 TGACTTTTGGCTATTAGGCTTTTGTTA 59.768 33.333 17.14 6.61 41.96 2.41
2255 2461 7.094377 ACGTTAAAGATGCATTTGGTTGATAGT 60.094 33.333 0.00 0.00 0.00 2.12
2256 2462 7.754924 CGTTAAAGATGCATTTGGTTGATAGTT 59.245 33.333 0.00 0.00 0.00 2.24
2257 2463 8.863049 GTTAAAGATGCATTTGGTTGATAGTTG 58.137 33.333 0.00 0.00 0.00 3.16
2258 2464 5.587388 AGATGCATTTGGTTGATAGTTGG 57.413 39.130 0.00 0.00 0.00 3.77
2259 2465 5.263599 AGATGCATTTGGTTGATAGTTGGA 58.736 37.500 0.00 0.00 0.00 3.53
2260 2466 5.895534 AGATGCATTTGGTTGATAGTTGGAT 59.104 36.000 0.00 0.00 0.00 3.41
2261 2467 7.062322 AGATGCATTTGGTTGATAGTTGGATA 58.938 34.615 0.00 0.00 0.00 2.59
2262 2468 6.449635 TGCATTTGGTTGATAGTTGGATAC 57.550 37.500 0.00 0.00 0.00 2.24
2281 2487 1.280710 ACTTGGATGGATGGTGCGTTA 59.719 47.619 0.00 0.00 0.00 3.18
2286 2492 3.118223 TGGATGGATGGTGCGTTATGTTA 60.118 43.478 0.00 0.00 0.00 2.41
2312 2518 1.440145 TTTCGGCGTTGATGTGTGCA 61.440 50.000 6.85 0.00 0.00 4.57
2336 2542 0.470833 TGGATGGTTGGTTGGTTGGG 60.471 55.000 0.00 0.00 0.00 4.12
2441 2653 9.319143 CAACAGTAATCAGTTAATCTCCCTTAG 57.681 37.037 0.00 0.00 0.00 2.18
2565 2936 4.327680 GCAGAGGAACCATGAAACTTACT 58.672 43.478 0.00 0.00 0.00 2.24
2606 2977 2.983229 TCAAGGCATCTCTGCTTTCTC 58.017 47.619 0.00 0.00 43.51 2.87
2634 3005 4.365723 GTCGTATTCATTCCCGTGTGTAT 58.634 43.478 0.00 0.00 0.00 2.29
2639 3010 6.128929 CGTATTCATTCCCGTGTGTATGTATG 60.129 42.308 0.00 0.00 0.00 2.39
2660 3031 1.112315 TGCGTGGGCTTTTGGTCATT 61.112 50.000 0.00 0.00 40.82 2.57
2887 3267 3.175710 AAGGACGGGTGGGCAAGT 61.176 61.111 0.00 0.00 0.00 3.16
2915 3295 2.632377 TGCTCTATGTAAGCAACCAGC 58.368 47.619 0.00 0.00 46.29 4.85
2928 3311 3.077359 GCAACCAGCATATACATCCTCC 58.923 50.000 0.00 0.00 44.79 4.30
2942 3325 3.457749 ACATCCTCCCTCTCCTTTGATTC 59.542 47.826 0.00 0.00 0.00 2.52
2946 3329 3.203934 CCTCCCTCTCCTTTGATTCCATT 59.796 47.826 0.00 0.00 0.00 3.16
2978 3380 6.055231 TCTCCAATTGTTTACGAGTTTGTG 57.945 37.500 4.43 0.00 0.00 3.33
2980 3382 5.812652 TCCAATTGTTTACGAGTTTGTGTC 58.187 37.500 4.43 0.00 0.00 3.67
2981 3383 4.668837 CCAATTGTTTACGAGTTTGTGTCG 59.331 41.667 4.43 0.00 43.25 4.35
2993 3395 3.310501 AGTTTGTGTCGGTTTAGGTTTCG 59.689 43.478 0.00 0.00 0.00 3.46
3035 3444 2.725221 TCTAGGGTAGGAGTCCGAAC 57.275 55.000 2.76 0.00 0.00 3.95
3048 3457 0.251653 TCCGAACCCTACTGTGCTCT 60.252 55.000 0.00 0.00 0.00 4.09
3055 3464 0.734253 CCTACTGTGCTCTCGTGTGC 60.734 60.000 4.67 4.67 0.00 4.57
3066 3475 0.882042 CTCGTGTGCTCTGGCTTGTT 60.882 55.000 0.00 0.00 39.59 2.83
3067 3476 0.391228 TCGTGTGCTCTGGCTTGTTA 59.609 50.000 0.00 0.00 39.59 2.41
3068 3477 1.001974 TCGTGTGCTCTGGCTTGTTAT 59.998 47.619 0.00 0.00 39.59 1.89
3069 3478 2.232696 TCGTGTGCTCTGGCTTGTTATA 59.767 45.455 0.00 0.00 39.59 0.98
3070 3479 3.000041 CGTGTGCTCTGGCTTGTTATAA 59.000 45.455 0.00 0.00 39.59 0.98
3071 3480 3.435327 CGTGTGCTCTGGCTTGTTATAAA 59.565 43.478 0.00 0.00 39.59 1.40
3072 3481 4.094887 CGTGTGCTCTGGCTTGTTATAAAT 59.905 41.667 0.00 0.00 39.59 1.40
3073 3482 5.391950 CGTGTGCTCTGGCTTGTTATAAATT 60.392 40.000 0.00 0.00 39.59 1.82
3074 3483 6.030228 GTGTGCTCTGGCTTGTTATAAATTC 58.970 40.000 0.00 0.00 39.59 2.17
3075 3484 5.709631 TGTGCTCTGGCTTGTTATAAATTCA 59.290 36.000 0.00 0.00 39.59 2.57
3090 3499 8.408601 GTTATAAATTCAGTGCATCAATGGAGT 58.591 33.333 0.00 0.00 29.97 3.85
3097 3506 1.065199 TGCATCAATGGAGTCCTGGTC 60.065 52.381 11.33 0.00 0.00 4.02
3098 3507 1.748591 GCATCAATGGAGTCCTGGTCC 60.749 57.143 11.33 0.00 34.31 4.46
3105 3514 1.064825 GGAGTCCTGGTCCCTGAAAA 58.935 55.000 0.41 0.00 0.00 2.29
3107 3516 2.356227 GGAGTCCTGGTCCCTGAAAATC 60.356 54.545 0.41 0.00 0.00 2.17
3116 3525 1.879380 TCCCTGAAAATCGTGTGCTTG 59.121 47.619 0.00 0.00 0.00 4.01
3117 3526 1.608590 CCCTGAAAATCGTGTGCTTGT 59.391 47.619 0.00 0.00 0.00 3.16
3118 3527 2.605338 CCCTGAAAATCGTGTGCTTGTG 60.605 50.000 0.00 0.00 0.00 3.33
3119 3528 2.046313 CTGAAAATCGTGTGCTTGTGC 58.954 47.619 0.00 0.00 40.20 4.57
3256 3665 2.447714 GGAGATCCACAGGGGCTCC 61.448 68.421 0.00 0.00 43.80 4.70
3259 3668 3.017581 ATCCACAGGGGCTCCACC 61.018 66.667 4.79 0.00 36.21 4.61
3525 3937 4.899239 CCAGGAGATGCCCGTCGC 62.899 72.222 0.00 0.00 37.37 5.19
4048 4469 0.946221 ACTTCTTCGTGCTCAAGGCG 60.946 55.000 0.00 0.00 45.43 5.52
4547 4985 6.770785 GGCACAGGGAATACAGAATATGTTTA 59.229 38.462 0.00 0.00 39.96 2.01
4548 4986 7.255139 GGCACAGGGAATACAGAATATGTTTAC 60.255 40.741 0.00 0.00 39.96 2.01
4627 6462 4.682778 TGGGTAGGCAGTGAACATATAC 57.317 45.455 0.00 0.00 0.00 1.47
4632 6467 6.239487 GGGTAGGCAGTGAACATATACATACA 60.239 42.308 0.00 0.00 0.00 2.29
4633 6468 7.386851 GGTAGGCAGTGAACATATACATACAT 58.613 38.462 0.00 0.00 0.00 2.29
4635 6470 9.355215 GTAGGCAGTGAACATATACATACATAC 57.645 37.037 0.00 0.00 0.00 2.39
4636 6471 7.090808 AGGCAGTGAACATATACATACATACG 58.909 38.462 0.00 0.00 0.00 3.06
4660 8298 6.347725 CGGAGTCCTTGAGTTTTCTTATGTTG 60.348 42.308 7.77 0.00 0.00 3.33
4665 8303 6.040391 TCCTTGAGTTTTCTTATGTTGTTGGG 59.960 38.462 0.00 0.00 0.00 4.12
4666 8304 6.183360 CCTTGAGTTTTCTTATGTTGTTGGGT 60.183 38.462 0.00 0.00 0.00 4.51
4667 8305 7.013846 CCTTGAGTTTTCTTATGTTGTTGGGTA 59.986 37.037 0.00 0.00 0.00 3.69
4668 8306 7.266922 TGAGTTTTCTTATGTTGTTGGGTAC 57.733 36.000 0.00 0.00 0.00 3.34
4669 8307 6.017770 TGAGTTTTCTTATGTTGTTGGGTACG 60.018 38.462 0.00 0.00 0.00 3.67
4670 8308 6.056884 AGTTTTCTTATGTTGTTGGGTACGA 58.943 36.000 0.00 0.00 0.00 3.43
4671 8309 5.927954 TTTCTTATGTTGTTGGGTACGAC 57.072 39.130 0.00 0.00 40.93 4.34
4673 8311 2.367030 TATGTTGTTGGGTACGACGG 57.633 50.000 0.00 0.00 43.08 4.79
4674 8312 0.680618 ATGTTGTTGGGTACGACGGA 59.319 50.000 0.00 0.00 43.08 4.69
4682 8320 2.292267 TGGGTACGACGGATACTTCTC 58.708 52.381 0.00 0.00 31.42 2.87
4693 8331 3.366883 CGGATACTTCTCTGGATAGCTGC 60.367 52.174 0.00 0.00 0.00 5.25
4695 8333 0.103937 ACTTCTCTGGATAGCTGCGC 59.896 55.000 0.00 0.00 0.00 6.09
4720 8358 5.912892 TGTCACTCTGAATTTCAGTACACA 58.087 37.500 22.44 17.53 44.58 3.72
4721 8359 5.753438 TGTCACTCTGAATTTCAGTACACAC 59.247 40.000 22.44 14.92 44.58 3.82
4722 8360 5.753438 GTCACTCTGAATTTCAGTACACACA 59.247 40.000 22.44 4.35 44.58 3.72
4740 8378 5.474532 ACACACAATACACTGAGATGCAATT 59.525 36.000 0.00 0.00 0.00 2.32
4742 8380 4.796830 CACAATACACTGAGATGCAATTGC 59.203 41.667 23.69 23.69 42.50 3.56
4752 8401 0.171903 ATGCAATTGCGCAAGGTCTC 59.828 50.000 28.62 14.89 46.87 3.36
4754 8403 0.455633 GCAATTGCGCAAGGTCTCAG 60.456 55.000 28.62 12.81 38.28 3.35
4761 8410 1.143305 CGCAAGGTCTCAGTCAACTG 58.857 55.000 3.69 3.69 45.08 3.16
4785 8611 6.590292 TGAGATTTAACCAATTCTCGAGACAC 59.410 38.462 16.36 0.00 41.18 3.67
4798 8624 4.462834 TCTCGAGACACCATCATGTTTAGT 59.537 41.667 12.08 0.00 31.24 2.24
4848 8674 8.693542 AGAAAAGAACTTGAAAAATCACACAG 57.306 30.769 0.00 0.00 0.00 3.66
4849 8675 7.761249 AGAAAAGAACTTGAAAAATCACACAGG 59.239 33.333 0.00 0.00 0.00 4.00
4850 8676 6.530019 AAGAACTTGAAAAATCACACAGGT 57.470 33.333 0.00 0.00 0.00 4.00
4851 8677 6.136541 AGAACTTGAAAAATCACACAGGTC 57.863 37.500 0.00 0.00 0.00 3.85
4852 8678 5.888161 AGAACTTGAAAAATCACACAGGTCT 59.112 36.000 0.00 0.00 0.00 3.85
4853 8679 5.757850 ACTTGAAAAATCACACAGGTCTC 57.242 39.130 0.00 0.00 0.00 3.36
4854 8680 5.440610 ACTTGAAAAATCACACAGGTCTCT 58.559 37.500 0.00 0.00 0.00 3.10
4855 8681 5.297776 ACTTGAAAAATCACACAGGTCTCTG 59.702 40.000 0.00 0.00 46.10 3.35
4874 8700 5.065704 TCTGTGTAAGATCTCAAGACAGC 57.934 43.478 21.46 9.60 31.42 4.40
4876 8702 3.578282 TGTGTAAGATCTCAAGACAGCCA 59.422 43.478 0.00 0.00 0.00 4.75
4879 8705 4.284490 TGTAAGATCTCAAGACAGCCAACT 59.716 41.667 0.00 0.00 0.00 3.16
4880 8706 5.480422 TGTAAGATCTCAAGACAGCCAACTA 59.520 40.000 0.00 0.00 0.00 2.24
4881 8707 4.464069 AGATCTCAAGACAGCCAACTAC 57.536 45.455 0.00 0.00 0.00 2.73
4882 8708 2.724977 TCTCAAGACAGCCAACTACG 57.275 50.000 0.00 0.00 0.00 3.51
4883 8709 1.961394 TCTCAAGACAGCCAACTACGT 59.039 47.619 0.00 0.00 0.00 3.57
4884 8710 3.151554 TCTCAAGACAGCCAACTACGTA 58.848 45.455 0.00 0.00 0.00 3.57
4885 8711 3.057736 TCTCAAGACAGCCAACTACGTAC 60.058 47.826 0.00 0.00 0.00 3.67
4887 8713 2.987149 CAAGACAGCCAACTACGTACTG 59.013 50.000 8.21 8.21 0.00 2.74
4889 8715 2.030185 AGACAGCCAACTACGTACTGTG 60.030 50.000 17.50 4.84 41.45 3.66
4890 8716 1.958579 ACAGCCAACTACGTACTGTGA 59.041 47.619 13.24 0.00 39.97 3.58
4891 8717 2.030185 ACAGCCAACTACGTACTGTGAG 60.030 50.000 13.24 0.00 39.97 3.51
4892 8718 2.030185 CAGCCAACTACGTACTGTGAGT 60.030 50.000 0.00 0.00 0.00 3.41
4893 8719 2.030185 AGCCAACTACGTACTGTGAGTG 60.030 50.000 0.00 0.00 0.00 3.51
4905 8731 3.412386 ACTGTGAGTGGGATTTAGCAAC 58.588 45.455 0.00 0.00 0.00 4.17
4911 8760 1.467342 GTGGGATTTAGCAACACCGTC 59.533 52.381 0.00 0.00 0.00 4.79
4944 8793 2.014128 AGCCGTCCGAATTTGTATTGG 58.986 47.619 0.00 0.00 0.00 3.16
4945 8794 1.741145 GCCGTCCGAATTTGTATTGGT 59.259 47.619 0.00 0.00 0.00 3.67
5106 8969 7.391786 CAACACATCTATGCTACGTTTTCTAC 58.608 38.462 0.00 0.00 0.00 2.59
5212 9075 4.715534 TGGTAAAGTCACCCAGAATCAA 57.284 40.909 0.00 0.00 37.84 2.57
5213 9076 5.255397 TGGTAAAGTCACCCAGAATCAAT 57.745 39.130 0.00 0.00 37.84 2.57
5214 9077 5.253330 TGGTAAAGTCACCCAGAATCAATC 58.747 41.667 0.00 0.00 37.84 2.67
5218 9112 2.009774 GTCACCCAGAATCAATCACCG 58.990 52.381 0.00 0.00 0.00 4.94
5222 9116 1.486310 CCCAGAATCAATCACCGAGGA 59.514 52.381 0.00 0.00 0.00 3.71
5225 9119 2.093500 CAGAATCAATCACCGAGGACCA 60.093 50.000 0.00 0.00 0.00 4.02
5228 9122 1.183030 TCAATCACCGAGGACCACGT 61.183 55.000 10.51 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.578928 ACAATGTTCCGCTGTTTTTCTACT 59.421 37.500 0.00 0.00 0.00 2.57
2 3 5.508200 AACAATGTTCCGCTGTTTTTCTA 57.492 34.783 0.00 0.00 28.99 2.10
4 5 5.332280 GCTTAACAATGTTCCGCTGTTTTTC 60.332 40.000 0.22 0.00 35.09 2.29
6 7 4.048504 GCTTAACAATGTTCCGCTGTTTT 58.951 39.130 0.22 0.00 35.09 2.43
7 8 3.552068 GGCTTAACAATGTTCCGCTGTTT 60.552 43.478 15.62 0.00 35.09 2.83
9 10 1.539827 GGCTTAACAATGTTCCGCTGT 59.460 47.619 15.62 0.00 0.00 4.40
10 11 1.539388 TGGCTTAACAATGTTCCGCTG 59.461 47.619 15.62 1.22 0.00 5.18
11 12 1.904287 TGGCTTAACAATGTTCCGCT 58.096 45.000 15.62 0.00 0.00 5.52
12 13 2.715737 TTGGCTTAACAATGTTCCGC 57.284 45.000 0.22 6.46 0.00 5.54
13 14 9.180678 GATTATATTTGGCTTAACAATGTTCCG 57.819 33.333 0.22 0.00 0.00 4.30
22 23 7.414436 TCACTTGCGATTATATTTGGCTTAAC 58.586 34.615 0.00 0.00 0.00 2.01
28 29 7.015289 CCGTAATCACTTGCGATTATATTTGG 58.985 38.462 0.00 0.00 42.24 3.28
31 32 6.090898 GCTCCGTAATCACTTGCGATTATATT 59.909 38.462 0.00 0.00 42.24 1.28
52 53 6.223351 AGAATGTTAGTTACAGGTAGCTCC 57.777 41.667 0.00 0.00 40.83 4.70
83 84 4.140518 TGTTAAACTATTGTGCGTGCTG 57.859 40.909 0.00 0.00 0.00 4.41
97 98 8.693504 CACTGATGATTTGTTGTCATGTTAAAC 58.306 33.333 0.00 0.00 36.49 2.01
177 178 3.735237 ATCTACAGCTATTCCACGTGG 57.265 47.619 29.26 29.26 0.00 4.94
221 227 3.264104 GGTAGTGCGCAGGTTATGTTTA 58.736 45.455 12.22 0.00 0.00 2.01
282 288 6.542370 TGAGAAACCTAAGAAGAAGTGTTTGG 59.458 38.462 0.00 0.00 32.57 3.28
283 289 7.553881 TGAGAAACCTAAGAAGAAGTGTTTG 57.446 36.000 0.00 0.00 0.00 2.93
284 290 7.829706 ACTTGAGAAACCTAAGAAGAAGTGTTT 59.170 33.333 0.00 0.00 0.00 2.83
287 293 6.763610 ACACTTGAGAAACCTAAGAAGAAGTG 59.236 38.462 0.00 0.00 42.14 3.16
289 295 7.385478 GGTACACTTGAGAAACCTAAGAAGAAG 59.615 40.741 0.00 0.00 0.00 2.85
291 297 6.325545 TGGTACACTTGAGAAACCTAAGAAGA 59.674 38.462 0.00 0.00 0.00 2.87
349 370 1.531149 CTGGTGGTTACAGTGCTTTCG 59.469 52.381 0.00 0.00 0.00 3.46
351 372 2.729028 ACTGGTGGTTACAGTGCTTT 57.271 45.000 0.00 0.00 46.67 3.51
369 390 2.092323 GCTTTGGTGGAGGAATGGTAC 58.908 52.381 0.00 0.00 0.00 3.34
370 391 1.707989 TGCTTTGGTGGAGGAATGGTA 59.292 47.619 0.00 0.00 0.00 3.25
371 392 0.482446 TGCTTTGGTGGAGGAATGGT 59.518 50.000 0.00 0.00 0.00 3.55
397 418 6.375945 TCATGCTGAATTATTATTGTGCGT 57.624 33.333 0.00 0.00 0.00 5.24
416 444 2.426261 CGCGCCGCATCATTCATG 60.426 61.111 10.75 0.00 35.29 3.07
417 445 3.653009 CCGCGCCGCATCATTCAT 61.653 61.111 10.75 0.00 0.00 2.57
540 570 1.105759 GTGCTCTCCCCATGATTGGC 61.106 60.000 0.00 0.00 42.15 4.52
569 599 4.494199 CGGCGCATTTGTTTTGGTTAAAAA 60.494 37.500 10.83 0.00 37.51 1.94
570 600 3.001330 CGGCGCATTTGTTTTGGTTAAAA 59.999 39.130 10.83 0.00 33.57 1.52
571 601 2.540101 CGGCGCATTTGTTTTGGTTAAA 59.460 40.909 10.83 0.00 0.00 1.52
573 603 1.603172 CCGGCGCATTTGTTTTGGTTA 60.603 47.619 10.83 0.00 0.00 2.85
574 604 0.878086 CCGGCGCATTTGTTTTGGTT 60.878 50.000 10.83 0.00 0.00 3.67
575 605 1.300542 CCGGCGCATTTGTTTTGGT 60.301 52.632 10.83 0.00 0.00 3.67
576 606 1.006805 TCCGGCGCATTTGTTTTGG 60.007 52.632 10.83 0.00 0.00 3.28
577 607 1.008361 CCTCCGGCGCATTTGTTTTG 61.008 55.000 10.83 0.00 0.00 2.44
578 608 1.288752 CCTCCGGCGCATTTGTTTT 59.711 52.632 10.83 0.00 0.00 2.43
579 609 2.635443 CCCTCCGGCGCATTTGTTT 61.635 57.895 10.83 0.00 0.00 2.83
580 610 3.061848 CCCTCCGGCGCATTTGTT 61.062 61.111 10.83 0.00 0.00 2.83
581 611 3.976701 CTCCCTCCGGCGCATTTGT 62.977 63.158 10.83 0.00 0.00 2.83
588 618 2.038837 GTTTTTCCTCCCTCCGGCG 61.039 63.158 0.00 0.00 0.00 6.46
589 619 2.038837 CGTTTTTCCTCCCTCCGGC 61.039 63.158 0.00 0.00 0.00 6.13
590 620 0.953960 CACGTTTTTCCTCCCTCCGG 60.954 60.000 0.00 0.00 0.00 5.14
591 621 1.574702 GCACGTTTTTCCTCCCTCCG 61.575 60.000 0.00 0.00 0.00 4.63
592 622 0.536460 TGCACGTTTTTCCTCCCTCC 60.536 55.000 0.00 0.00 0.00 4.30
593 623 1.200020 CATGCACGTTTTTCCTCCCTC 59.800 52.381 0.00 0.00 0.00 4.30
594 624 1.247567 CATGCACGTTTTTCCTCCCT 58.752 50.000 0.00 0.00 0.00 4.20
595 625 0.958822 ACATGCACGTTTTTCCTCCC 59.041 50.000 0.00 0.00 0.00 4.30
596 626 1.930371 GCACATGCACGTTTTTCCTCC 60.930 52.381 0.00 0.00 41.59 4.30
597 627 1.408422 GCACATGCACGTTTTTCCTC 58.592 50.000 0.00 0.00 41.59 3.71
598 628 0.317770 CGCACATGCACGTTTTTCCT 60.318 50.000 4.49 0.00 42.21 3.36
599 629 1.274798 CCGCACATGCACGTTTTTCC 61.275 55.000 4.49 0.00 42.21 3.13
600 630 1.875419 GCCGCACATGCACGTTTTTC 61.875 55.000 4.49 0.00 42.21 2.29
619 649 4.189188 ATCGGTCGACGCGGGAAG 62.189 66.667 20.97 5.51 43.86 3.46
720 786 2.125269 GATTGGACGTGGACGGGG 60.125 66.667 0.00 0.00 44.95 5.73
823 915 2.764010 GTGGGGGTTGGCTTTTATTAGG 59.236 50.000 0.00 0.00 0.00 2.69
967 1078 4.824515 CTCCGTCCGCCTCTCCCT 62.825 72.222 0.00 0.00 0.00 4.20
970 1081 3.827898 CACCTCCGTCCGCCTCTC 61.828 72.222 0.00 0.00 0.00 3.20
1408 1519 3.395639 AGAGGACTCTCGAGTATAAGCG 58.604 50.000 13.13 0.00 44.47 4.68
1414 1525 6.645827 CGATTGTATTAGAGGACTCTCGAGTA 59.354 42.308 13.13 0.00 44.47 2.59
1415 1526 5.467399 CGATTGTATTAGAGGACTCTCGAGT 59.533 44.000 13.13 0.00 44.47 4.18
1416 1527 5.615984 GCGATTGTATTAGAGGACTCTCGAG 60.616 48.000 5.93 5.93 44.47 4.04
1418 1529 4.214545 AGCGATTGTATTAGAGGACTCTCG 59.785 45.833 4.90 2.42 44.47 4.04
1419 1530 5.335348 GGAGCGATTGTATTAGAGGACTCTC 60.335 48.000 4.90 0.00 40.93 3.20
1420 1531 4.521256 GGAGCGATTGTATTAGAGGACTCT 59.479 45.833 7.08 7.08 43.40 3.24
1421 1532 4.278669 TGGAGCGATTGTATTAGAGGACTC 59.721 45.833 0.00 0.00 0.00 3.36
1439 1553 3.992427 CAGCTTTGGAAAGAAAATGGAGC 59.008 43.478 3.23 0.00 38.28 4.70
1485 1601 5.005394 AGCATCGACAATAATCGTGTGTTAC 59.995 40.000 0.00 0.00 42.80 2.50
1486 1602 5.005299 CAGCATCGACAATAATCGTGTGTTA 59.995 40.000 0.00 0.00 42.80 2.41
1498 1614 5.121611 TCGTGTTATTTTCAGCATCGACAAT 59.878 36.000 0.00 0.00 0.00 2.71
1499 1615 4.449405 TCGTGTTATTTTCAGCATCGACAA 59.551 37.500 0.00 0.00 0.00 3.18
1500 1616 3.991121 TCGTGTTATTTTCAGCATCGACA 59.009 39.130 0.00 0.00 0.00 4.35
1502 1618 5.350091 TCAATCGTGTTATTTTCAGCATCGA 59.650 36.000 0.00 0.00 0.00 3.59
1507 1623 4.953269 TCGTCAATCGTGTTATTTTCAGC 58.047 39.130 0.00 0.00 40.80 4.26
1510 1626 9.195831 GTAGAAATCGTCAATCGTGTTATTTTC 57.804 33.333 0.00 0.00 40.80 2.29
1511 1627 8.173130 GGTAGAAATCGTCAATCGTGTTATTTT 58.827 33.333 0.00 0.00 40.80 1.82
1515 1631 5.957798 AGGTAGAAATCGTCAATCGTGTTA 58.042 37.500 0.00 0.00 40.80 2.41
1540 1658 8.897457 ATTATCATACTAGTAAATCTGTCGCG 57.103 34.615 6.70 0.00 0.00 5.87
1556 1674 9.472361 TGAAAACGGAGCTAGTAATTATCATAC 57.528 33.333 0.00 0.00 0.00 2.39
1559 1677 8.421784 AGATGAAAACGGAGCTAGTAATTATCA 58.578 33.333 0.00 0.00 0.00 2.15
1571 1689 3.585862 TGTCTGTAGATGAAAACGGAGC 58.414 45.455 0.00 0.00 31.78 4.70
1572 1690 4.859798 GTCTGTCTGTAGATGAAAACGGAG 59.140 45.833 0.00 0.00 31.78 4.63
1573 1691 4.279922 TGTCTGTCTGTAGATGAAAACGGA 59.720 41.667 0.00 0.00 0.00 4.69
1575 1693 6.019075 TGTTTGTCTGTCTGTAGATGAAAACG 60.019 38.462 0.00 0.00 0.00 3.60
1576 1694 7.246674 TGTTTGTCTGTCTGTAGATGAAAAC 57.753 36.000 0.00 0.00 0.00 2.43
1578 1696 7.465379 CGTTTGTTTGTCTGTCTGTAGATGAAA 60.465 37.037 0.00 0.00 0.00 2.69
1581 1699 5.462068 TCGTTTGTTTGTCTGTCTGTAGATG 59.538 40.000 0.00 0.00 0.00 2.90
1582 1700 5.597806 TCGTTTGTTTGTCTGTCTGTAGAT 58.402 37.500 0.00 0.00 0.00 1.98
1583 1701 5.001237 TCGTTTGTTTGTCTGTCTGTAGA 57.999 39.130 0.00 0.00 0.00 2.59
1584 1702 5.490213 GTTCGTTTGTTTGTCTGTCTGTAG 58.510 41.667 0.00 0.00 0.00 2.74
1585 1703 4.031991 CGTTCGTTTGTTTGTCTGTCTGTA 59.968 41.667 0.00 0.00 0.00 2.74
1586 1704 3.181524 CGTTCGTTTGTTTGTCTGTCTGT 60.182 43.478 0.00 0.00 0.00 3.41
1587 1705 3.061563 TCGTTCGTTTGTTTGTCTGTCTG 59.938 43.478 0.00 0.00 0.00 3.51
1588 1706 3.255725 TCGTTCGTTTGTTTGTCTGTCT 58.744 40.909 0.00 0.00 0.00 3.41
1589 1707 3.644805 TCGTTCGTTTGTTTGTCTGTC 57.355 42.857 0.00 0.00 0.00 3.51
1590 1708 3.186817 TGTTCGTTCGTTTGTTTGTCTGT 59.813 39.130 0.00 0.00 0.00 3.41
1648 1769 8.083462 TGGTAAAGCATGTTTATAATAGAGCG 57.917 34.615 0.00 0.00 0.00 5.03
1654 1775 9.533253 GAAGCATTGGTAAAGCATGTTTATAAT 57.467 29.630 0.00 2.66 0.00 1.28
1656 1777 7.123397 TGGAAGCATTGGTAAAGCATGTTTATA 59.877 33.333 0.00 0.00 0.00 0.98
1664 1785 4.888326 ATTTGGAAGCATTGGTAAAGCA 57.112 36.364 0.00 0.00 0.00 3.91
1678 1803 9.347240 TGAGGAAAAATAATGCAAAATTTGGAA 57.653 25.926 3.64 0.00 33.68 3.53
1686 1811 9.316730 GCTATCATTGAGGAAAAATAATGCAAA 57.683 29.630 0.00 0.00 32.14 3.68
1728 1899 7.008086 CGCATTAGGCTTACATAGACGTAATAC 59.992 40.741 0.00 0.00 41.67 1.89
1729 1900 7.025365 CGCATTAGGCTTACATAGACGTAATA 58.975 38.462 0.00 0.00 41.67 0.98
1738 1909 3.133183 TGTCCACGCATTAGGCTTACATA 59.867 43.478 0.00 0.00 41.67 2.29
1740 1911 1.276705 TGTCCACGCATTAGGCTTACA 59.723 47.619 0.00 0.00 41.67 2.41
1742 1913 1.742411 GCTGTCCACGCATTAGGCTTA 60.742 52.381 0.00 0.00 41.67 3.09
1755 1926 3.189080 CGATTCACAAGAAATGCTGTCCA 59.811 43.478 0.00 0.00 37.29 4.02
1775 1946 2.258591 GTCGTCTCAGGCTTGCGA 59.741 61.111 0.00 0.00 0.00 5.10
1795 1974 1.798813 GACCTGAGGCGTTGTAAACTG 59.201 52.381 0.00 0.00 46.99 3.16
1931 2119 3.121030 CGCTTCCTGTTCAGCCCG 61.121 66.667 0.00 0.00 31.82 6.13
1934 2122 0.793250 GAGAACGCTTCCTGTTCAGC 59.207 55.000 8.38 0.00 46.34 4.26
1935 2123 1.001406 AGGAGAACGCTTCCTGTTCAG 59.999 52.381 8.38 0.00 46.34 3.02
1936 2124 1.000955 GAGGAGAACGCTTCCTGTTCA 59.999 52.381 7.60 0.00 46.34 3.18
1937 2125 1.273886 AGAGGAGAACGCTTCCTGTTC 59.726 52.381 7.60 0.00 44.72 3.18
1938 2126 1.273886 GAGAGGAGAACGCTTCCTGTT 59.726 52.381 7.60 0.00 33.37 3.16
1939 2127 0.892063 GAGAGGAGAACGCTTCCTGT 59.108 55.000 7.60 4.02 33.37 4.00
1940 2128 1.181786 AGAGAGGAGAACGCTTCCTG 58.818 55.000 7.60 0.00 33.37 3.86
2019 2217 4.004314 TCGTTTCACAGTTTCAAACCTCA 58.996 39.130 0.00 0.00 0.00 3.86
2078 2281 0.690411 TAATTGCCTGGCCAATGGGG 60.690 55.000 17.53 5.47 35.70 4.96
2081 2284 3.615224 AACTTAATTGCCTGGCCAATG 57.385 42.857 17.53 1.44 35.70 2.82
2112 2315 9.555727 TGCTACCTAATAACAAAAGCCTAATAG 57.444 33.333 0.00 0.00 0.00 1.73
2114 2317 8.996651 ATGCTACCTAATAACAAAAGCCTAAT 57.003 30.769 0.00 0.00 0.00 1.73
2128 2331 8.420222 GTCATAGATCATGCTATGCTACCTAAT 58.580 37.037 12.89 0.00 44.65 1.73
2255 2461 3.688126 GCACCATCCATCCAAGTATCCAA 60.688 47.826 0.00 0.00 0.00 3.53
2256 2462 2.158623 GCACCATCCATCCAAGTATCCA 60.159 50.000 0.00 0.00 0.00 3.41
2257 2463 2.508526 GCACCATCCATCCAAGTATCC 58.491 52.381 0.00 0.00 0.00 2.59
2258 2464 2.146342 CGCACCATCCATCCAAGTATC 58.854 52.381 0.00 0.00 0.00 2.24
2259 2465 1.490490 ACGCACCATCCATCCAAGTAT 59.510 47.619 0.00 0.00 0.00 2.12
2260 2466 0.908910 ACGCACCATCCATCCAAGTA 59.091 50.000 0.00 0.00 0.00 2.24
2261 2467 0.038166 AACGCACCATCCATCCAAGT 59.962 50.000 0.00 0.00 0.00 3.16
2262 2468 2.036958 TAACGCACCATCCATCCAAG 57.963 50.000 0.00 0.00 0.00 3.61
2281 2487 5.113383 TCAACGCCGAAAGATACATAACAT 58.887 37.500 0.00 0.00 0.00 2.71
2286 2492 3.309682 CACATCAACGCCGAAAGATACAT 59.690 43.478 0.00 0.00 0.00 2.29
2312 2518 0.615544 CCAACCAACCATCCAGGCAT 60.616 55.000 0.00 0.00 43.14 4.40
2336 2542 4.385358 AAAAGGTGACACCACATTGAAC 57.615 40.909 26.30 0.00 45.28 3.18
2415 2627 9.319143 CTAAGGGAGATTAACTGATTACTGTTG 57.681 37.037 0.00 0.00 38.33 3.33
2425 2637 6.472686 AGTACAGCTAAGGGAGATTAACTG 57.527 41.667 0.00 0.00 35.77 3.16
2532 2791 2.292292 GGTTCCTCTGCGTTTTTGCTTA 59.708 45.455 0.00 0.00 35.36 3.09
2546 2805 3.125316 CGCAGTAAGTTTCATGGTTCCTC 59.875 47.826 0.00 0.00 0.00 3.71
2565 2936 2.405805 CGGTGCCATTGATTCCGCA 61.406 57.895 0.00 0.00 35.01 5.69
2606 2977 2.029290 CGGGAATGAATACGACCCCTAG 60.029 54.545 0.00 0.00 37.49 3.02
2634 3005 1.472082 CAAAAGCCCACGCATCATACA 59.528 47.619 0.00 0.00 37.52 2.29
2639 3010 1.212751 GACCAAAAGCCCACGCATC 59.787 57.895 0.00 0.00 37.52 3.91
2660 3031 1.485124 TAGAGATTTGCCAGCTCCGA 58.515 50.000 0.00 0.00 0.00 4.55
2887 3267 3.181452 TGCTTACATAGAGCATGGCATCA 60.181 43.478 0.00 0.00 44.63 3.07
2914 3294 3.718723 AGGAGAGGGAGGATGTATATGC 58.281 50.000 0.00 0.00 0.00 3.14
2915 3295 5.782331 TCAAAGGAGAGGGAGGATGTATATG 59.218 44.000 0.00 0.00 0.00 1.78
2923 3303 2.225882 TGGAATCAAAGGAGAGGGAGGA 60.226 50.000 0.00 0.00 0.00 3.71
2924 3304 2.200081 TGGAATCAAAGGAGAGGGAGG 58.800 52.381 0.00 0.00 0.00 4.30
2928 3311 3.129988 GTGCAATGGAATCAAAGGAGAGG 59.870 47.826 0.00 0.00 0.00 3.69
2942 3325 2.133281 TTGGAGAGGATGTGCAATGG 57.867 50.000 0.00 0.00 34.09 3.16
2946 3329 2.885135 ACAATTGGAGAGGATGTGCA 57.115 45.000 10.83 0.00 0.00 4.57
2978 3380 5.351458 ACATATACCGAAACCTAAACCGAC 58.649 41.667 0.00 0.00 0.00 4.79
2980 3382 5.350633 TGACATATACCGAAACCTAAACCG 58.649 41.667 0.00 0.00 0.00 4.44
2981 3383 6.293244 GCATGACATATACCGAAACCTAAACC 60.293 42.308 0.00 0.00 0.00 3.27
2993 3395 3.067106 CGGAACCAGCATGACATATACC 58.933 50.000 0.00 0.00 39.69 2.73
3035 3444 0.109086 CACACGAGAGCACAGTAGGG 60.109 60.000 0.00 0.00 0.00 3.53
3048 3457 0.391228 TAACAAGCCAGAGCACACGA 59.609 50.000 0.00 0.00 43.56 4.35
3055 3464 6.127925 TGCACTGAATTTATAACAAGCCAGAG 60.128 38.462 0.00 0.00 0.00 3.35
3066 3475 7.229306 GGACTCCATTGATGCACTGAATTTATA 59.771 37.037 0.00 0.00 0.00 0.98
3067 3476 6.040166 GGACTCCATTGATGCACTGAATTTAT 59.960 38.462 0.00 0.00 0.00 1.40
3068 3477 5.357878 GGACTCCATTGATGCACTGAATTTA 59.642 40.000 0.00 0.00 0.00 1.40
3069 3478 4.159135 GGACTCCATTGATGCACTGAATTT 59.841 41.667 0.00 0.00 0.00 1.82
3070 3479 3.698040 GGACTCCATTGATGCACTGAATT 59.302 43.478 0.00 0.00 0.00 2.17
3071 3480 3.053842 AGGACTCCATTGATGCACTGAAT 60.054 43.478 0.00 0.00 0.00 2.57
3072 3481 2.306805 AGGACTCCATTGATGCACTGAA 59.693 45.455 0.00 0.00 0.00 3.02
3073 3482 1.911357 AGGACTCCATTGATGCACTGA 59.089 47.619 0.00 0.00 0.00 3.41
3074 3483 2.014857 CAGGACTCCATTGATGCACTG 58.985 52.381 0.00 0.00 0.00 3.66
3075 3484 1.064906 CCAGGACTCCATTGATGCACT 60.065 52.381 0.00 0.00 0.00 4.40
3090 3499 1.003118 CACGATTTTCAGGGACCAGGA 59.997 52.381 0.00 0.00 0.00 3.86
3097 3506 1.608590 ACAAGCACACGATTTTCAGGG 59.391 47.619 0.00 0.00 0.00 4.45
3098 3507 2.653890 CACAAGCACACGATTTTCAGG 58.346 47.619 0.00 0.00 0.00 3.86
3105 3514 0.588252 GTCAAGCACAAGCACACGAT 59.412 50.000 0.00 0.00 45.49 3.73
3107 3516 1.368019 CGTCAAGCACAAGCACACG 60.368 57.895 0.00 0.00 45.49 4.49
3116 3525 2.551270 CTGCCGTTCGTCAAGCAC 59.449 61.111 0.00 0.00 0.00 4.40
3117 3526 2.664851 CCTGCCGTTCGTCAAGCA 60.665 61.111 0.00 0.00 0.00 3.91
3118 3527 2.665185 ACCTGCCGTTCGTCAAGC 60.665 61.111 0.00 0.00 0.00 4.01
3119 3528 0.878523 TTCACCTGCCGTTCGTCAAG 60.879 55.000 0.00 0.00 0.00 3.02
3370 3779 2.750237 CTGCTGCTGCTCATGCCA 60.750 61.111 17.00 0.00 40.48 4.92
3525 3937 3.762247 CCCCCACGCAGCATTTGG 61.762 66.667 0.00 0.00 0.00 3.28
3610 4025 0.456142 CGATGGACGCGAAGAAGACA 60.456 55.000 15.93 0.49 34.51 3.41
3766 4181 4.154347 CAGAGCCGCCTCCACTCC 62.154 72.222 0.00 0.00 38.96 3.85
4179 4612 3.760035 CGACCACCACCTCCTCCG 61.760 72.222 0.00 0.00 0.00 4.63
4409 4842 7.336427 TGAATGTACATTGATCATGTTAGTGCA 59.664 33.333 25.42 8.97 44.40 4.57
4439 4872 7.105588 TGTTTCTATTCATCTGTGCTGTATGT 58.894 34.615 0.00 0.00 0.00 2.29
4440 4873 7.543947 TGTTTCTATTCATCTGTGCTGTATG 57.456 36.000 0.00 0.00 0.00 2.39
4482 4915 6.610075 ATCCAAAATCTTGCAACTGGTAAT 57.390 33.333 0.00 0.00 0.00 1.89
4547 4985 5.187772 TCTGTCTGCCTAATTCACTGTATGT 59.812 40.000 0.00 0.00 0.00 2.29
4548 4986 5.664457 TCTGTCTGCCTAATTCACTGTATG 58.336 41.667 0.00 0.00 0.00 2.39
4627 6462 4.920640 ACTCAAGGACTCCGTATGTATG 57.079 45.455 0.00 0.00 0.00 2.39
4632 6467 5.485209 AAGAAAACTCAAGGACTCCGTAT 57.515 39.130 0.00 0.00 0.00 3.06
4633 6468 4.950205 AAGAAAACTCAAGGACTCCGTA 57.050 40.909 0.00 0.00 0.00 4.02
4635 6470 5.238583 ACATAAGAAAACTCAAGGACTCCG 58.761 41.667 0.00 0.00 0.00 4.63
4636 6471 6.486993 ACAACATAAGAAAACTCAAGGACTCC 59.513 38.462 0.00 0.00 0.00 3.85
4660 8298 2.424956 AGAAGTATCCGTCGTACCCAAC 59.575 50.000 0.00 0.00 0.00 3.77
4665 8303 3.201290 TCCAGAGAAGTATCCGTCGTAC 58.799 50.000 0.00 0.00 0.00 3.67
4666 8304 3.548745 TCCAGAGAAGTATCCGTCGTA 57.451 47.619 0.00 0.00 0.00 3.43
4667 8305 2.414994 TCCAGAGAAGTATCCGTCGT 57.585 50.000 0.00 0.00 0.00 4.34
4668 8306 3.120130 GCTATCCAGAGAAGTATCCGTCG 60.120 52.174 0.00 0.00 0.00 5.12
4669 8307 4.076394 AGCTATCCAGAGAAGTATCCGTC 58.924 47.826 0.00 0.00 0.00 4.79
4670 8308 3.823873 CAGCTATCCAGAGAAGTATCCGT 59.176 47.826 0.00 0.00 0.00 4.69
4671 8309 3.366883 GCAGCTATCCAGAGAAGTATCCG 60.367 52.174 0.00 0.00 0.00 4.18
4673 8311 3.832276 CGCAGCTATCCAGAGAAGTATC 58.168 50.000 0.00 0.00 0.00 2.24
4674 8312 3.932545 CGCAGCTATCCAGAGAAGTAT 57.067 47.619 0.00 0.00 0.00 2.12
4720 8358 4.437794 CGCAATTGCATCTCAGTGTATTGT 60.438 41.667 28.77 0.00 42.21 2.71
4721 8359 4.033019 CGCAATTGCATCTCAGTGTATTG 58.967 43.478 28.77 4.63 42.21 1.90
4722 8360 3.488047 GCGCAATTGCATCTCAGTGTATT 60.488 43.478 28.77 0.00 42.21 1.89
4740 8378 0.880278 GTTGACTGAGACCTTGCGCA 60.880 55.000 5.66 5.66 0.00 6.09
4742 8380 1.143305 CAGTTGACTGAGACCTTGCG 58.857 55.000 5.19 0.00 46.59 4.85
4752 8401 8.103948 AGAATTGGTTAAATCTCAGTTGACTG 57.896 34.615 4.77 4.77 45.08 3.51
4754 8403 7.117812 TCGAGAATTGGTTAAATCTCAGTTGAC 59.882 37.037 6.08 0.00 0.00 3.18
4761 8410 6.036191 GGTGTCTCGAGAATTGGTTAAATCTC 59.964 42.308 18.55 0.00 0.00 2.75
4774 8423 3.961480 AACATGATGGTGTCTCGAGAA 57.039 42.857 18.55 0.99 0.00 2.87
4824 8650 7.545615 ACCTGTGTGATTTTTCAAGTTCTTTTC 59.454 33.333 0.00 0.00 0.00 2.29
4826 8652 6.935167 ACCTGTGTGATTTTTCAAGTTCTTT 58.065 32.000 0.00 0.00 0.00 2.52
4827 8653 6.378280 AGACCTGTGTGATTTTTCAAGTTCTT 59.622 34.615 0.00 0.00 0.00 2.52
4828 8654 5.888161 AGACCTGTGTGATTTTTCAAGTTCT 59.112 36.000 0.00 0.00 0.00 3.01
4829 8655 6.038714 AGAGACCTGTGTGATTTTTCAAGTTC 59.961 38.462 0.00 0.00 0.00 3.01
4832 8658 5.755813 CAGAGACCTGTGTGATTTTTCAAG 58.244 41.667 0.00 0.00 35.70 3.02
4833 8659 5.756195 CAGAGACCTGTGTGATTTTTCAA 57.244 39.130 0.00 0.00 35.70 2.69
4846 8672 5.417266 TCTTGAGATCTTACACAGAGACCTG 59.583 44.000 0.00 0.00 45.76 4.00
4847 8673 5.417580 GTCTTGAGATCTTACACAGAGACCT 59.582 44.000 0.00 0.00 33.87 3.85
4848 8674 5.184096 TGTCTTGAGATCTTACACAGAGACC 59.816 44.000 11.62 0.00 33.87 3.85
4849 8675 6.260870 TGTCTTGAGATCTTACACAGAGAC 57.739 41.667 0.00 3.09 33.87 3.36
4850 8676 5.105957 GCTGTCTTGAGATCTTACACAGAGA 60.106 44.000 21.54 6.02 33.87 3.10
4851 8677 5.101628 GCTGTCTTGAGATCTTACACAGAG 58.898 45.833 21.54 4.06 33.87 3.35
4852 8678 4.081972 GGCTGTCTTGAGATCTTACACAGA 60.082 45.833 21.54 6.62 35.33 3.41
4853 8679 4.180057 GGCTGTCTTGAGATCTTACACAG 58.820 47.826 16.28 16.28 0.00 3.66
4854 8680 3.578282 TGGCTGTCTTGAGATCTTACACA 59.422 43.478 0.00 0.00 0.00 3.72
4855 8681 4.193826 TGGCTGTCTTGAGATCTTACAC 57.806 45.455 0.00 0.00 0.00 2.90
4874 8700 2.352421 CCCACTCACAGTACGTAGTTGG 60.352 54.545 10.06 10.06 37.78 3.77
4876 8702 2.867624 TCCCACTCACAGTACGTAGTT 58.132 47.619 0.00 0.00 37.78 2.24
4879 8705 4.142315 GCTAAATCCCACTCACAGTACGTA 60.142 45.833 0.00 0.00 0.00 3.57
4880 8706 3.368116 GCTAAATCCCACTCACAGTACGT 60.368 47.826 0.00 0.00 0.00 3.57
4881 8707 3.187700 GCTAAATCCCACTCACAGTACG 58.812 50.000 0.00 0.00 0.00 3.67
4882 8708 4.202245 TGCTAAATCCCACTCACAGTAC 57.798 45.455 0.00 0.00 0.00 2.73
4883 8709 4.041075 TGTTGCTAAATCCCACTCACAGTA 59.959 41.667 0.00 0.00 0.00 2.74
4884 8710 3.181445 TGTTGCTAAATCCCACTCACAGT 60.181 43.478 0.00 0.00 0.00 3.55
4885 8711 3.189287 GTGTTGCTAAATCCCACTCACAG 59.811 47.826 0.00 0.00 0.00 3.66
4887 8713 2.488153 GGTGTTGCTAAATCCCACTCAC 59.512 50.000 0.00 0.00 0.00 3.51
4889 8715 1.737793 CGGTGTTGCTAAATCCCACTC 59.262 52.381 0.00 0.00 0.00 3.51
4890 8716 1.073284 ACGGTGTTGCTAAATCCCACT 59.927 47.619 0.00 0.00 0.00 4.00
4891 8717 1.467342 GACGGTGTTGCTAAATCCCAC 59.533 52.381 0.00 0.00 0.00 4.61
4892 8718 1.072489 TGACGGTGTTGCTAAATCCCA 59.928 47.619 0.00 0.00 0.00 4.37
4893 8719 1.816074 TGACGGTGTTGCTAAATCCC 58.184 50.000 0.00 0.00 0.00 3.85
4905 8731 4.165779 GGCTGAATTTTGTTATGACGGTG 58.834 43.478 0.00 0.00 0.00 4.94
4911 8760 3.126171 TCGGACGGCTGAATTTTGTTATG 59.874 43.478 0.00 0.00 0.00 1.90
4964 8825 7.482169 ACTCACAGGAACAATAAGAGATACA 57.518 36.000 0.00 0.00 0.00 2.29
5106 8969 3.605486 GCTTAGAAATGCAGCGTTTTGAG 59.395 43.478 13.93 12.29 0.00 3.02
5212 9075 2.697761 CGACGTGGTCCTCGGTGAT 61.698 63.158 17.11 0.00 0.00 3.06
5213 9076 3.359523 CGACGTGGTCCTCGGTGA 61.360 66.667 17.11 0.00 0.00 4.02
5214 9077 4.415332 CCGACGTGGTCCTCGGTG 62.415 72.222 17.11 8.79 43.79 4.94
5218 9112 2.360852 TCCTCCGACGTGGTCCTC 60.361 66.667 0.00 0.00 39.52 3.71
5222 9116 4.296729 AGGGTCCTCCGACGTGGT 62.297 66.667 0.00 0.00 40.17 4.16
5228 9122 3.923645 ACACCCAGGGTCCTCCGA 61.924 66.667 8.79 0.00 41.52 4.55
5256 9151 2.481441 TCTGGCAATGTAGTCCCAGAT 58.519 47.619 4.23 0.00 46.50 2.90


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

AutoCloner maintained by Alex Coulton.