Multiple sequence alignment - TraesCS3A01G537900

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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 TraesCS3A01G537900 chr3A 100.000 2766 0 0 1 2766 749330844 749328079 0.000000e+00 5108.0
1 TraesCS3A01G537900 chr3A 100.000 120 0 0 3114 3233 749327731 749327612 4.200000e-54 222.0
2 TraesCS3A01G537900 chr3B 93.266 1485 62 23 972 2440 822881045 822879583 0.000000e+00 2154.0
3 TraesCS3A01G537900 chr3B 87.833 600 35 19 174 747 822881994 822881407 0.000000e+00 669.0
4 TraesCS3A01G537900 chr3B 91.139 158 5 4 746 895 822881294 822881138 4.230000e-49 206.0
5 TraesCS3A01G537900 chr3B 100.000 66 0 0 2698 2763 519763935 519764000 4.380000e-24 122.0
6 TraesCS3A01G537900 chr3B 98.485 66 1 0 2698 2763 141604295 141604360 2.040000e-22 117.0
7 TraesCS3A01G537900 chr3B 97.826 46 1 0 3114 3159 519764068 519764113 2.670000e-11 80.5
8 TraesCS3A01G537900 chr3D 93.033 1507 50 17 972 2466 613693437 613691974 0.000000e+00 2150.0
9 TraesCS3A01G537900 chr3D 85.378 595 39 22 9 576 613694431 613693858 1.010000e-159 573.0
10 TraesCS3A01G537900 chr3D 86.813 182 17 4 2468 2642 613688854 613688673 2.540000e-46 196.0
11 TraesCS3A01G537900 chr4D 73.665 824 146 44 1275 2082 464638 463870 1.490000e-63 254.0
12 TraesCS3A01G537900 chr6D 74.485 631 115 34 1330 1942 473102661 473103263 6.980000e-57 231.0
13 TraesCS3A01G537900 chr6D 96.875 64 2 0 2697 2760 163348771 163348834 1.230000e-19 108.0
14 TraesCS3A01G537900 chr6D 89.655 58 6 0 1856 1913 308330432 308330375 1.240000e-09 75.0
15 TraesCS3A01G537900 chr4B 80.519 308 54 6 1214 1518 234806 234502 6.980000e-57 231.0
16 TraesCS3A01G537900 chr4A 80.195 308 55 6 1214 1518 194145 193841 3.250000e-55 226.0
17 TraesCS3A01G537900 chr4A 98.571 70 1 0 2697 2766 56146285 56146216 1.220000e-24 124.0
18 TraesCS3A01G537900 chr4A 98.551 69 1 0 2698 2766 56146643 56146575 4.380000e-24 122.0
19 TraesCS3A01G537900 chr4A 97.826 46 1 0 3114 3159 56146149 56146104 2.670000e-11 80.5
20 TraesCS3A01G537900 chr4A 100.000 39 0 0 3121 3159 56146334 56146296 4.470000e-09 73.1
21 TraesCS3A01G537900 chr6B 73.980 588 102 34 1333 1914 718475689 718476231 1.180000e-44 191.0
22 TraesCS3A01G537900 chr1B 100.000 66 0 0 2698 2763 640058502 640058567 4.380000e-24 122.0
23 TraesCS3A01G537900 chr1B 97.826 46 1 0 3114 3159 640058638 640058683 2.670000e-11 80.5
24 TraesCS3A01G537900 chr1D 98.529 68 1 0 2699 2766 194737943 194737876 1.580000e-23 121.0
25 TraesCS3A01G537900 chr2A 95.714 70 3 0 2697 2766 607547293 607547224 2.640000e-21 113.0
26 TraesCS3A01G537900 chr2A 95.652 46 2 0 3114 3159 607547159 607547114 1.240000e-09 75.0
27 TraesCS3A01G537900 chr6A 95.455 66 3 0 2698 2763 36247121 36247186 4.410000e-19 106.0
28 TraesCS3A01G537900 chr2B 86.957 92 11 1 1648 1738 78072099 78072190 5.710000e-18 102.0
29 TraesCS3A01G537900 chr2B 97.872 47 1 0 3114 3160 64064344 64064390 7.430000e-12 82.4
30 TraesCS3A01G537900 chr5D 90.244 41 4 0 1857 1897 432041665 432041625 2.000000e-03 54.7
31 TraesCS3A01G537900 chr5B 88.636 44 5 0 1851 1894 523908267 523908310 2.000000e-03 54.7
32 TraesCS3A01G537900 chr5B 88.636 44 5 0 1851 1894 523908395 523908438 2.000000e-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 TraesCS3A01G537900 chr3A 749327612 749330844 3232 True 2665.000000 5108 100.000 1 3233 2 chr3A.!!$R1 3232
1 TraesCS3A01G537900 chr3B 822879583 822881994 2411 True 1009.666667 2154 90.746 174 2440 3 chr3B.!!$R1 2266
2 TraesCS3A01G537900 chr3D 613688673 613694431 5758 True 973.000000 2150 88.408 9 2642 3 chr3D.!!$R1 2633
3 TraesCS3A01G537900 chr4D 463870 464638 768 True 254.000000 254 73.665 1275 2082 1 chr4D.!!$R1 807
4 TraesCS3A01G537900 chr6D 473102661 473103263 602 False 231.000000 231 74.485 1330 1942 1 chr6D.!!$F2 612

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
959 1191 0.110823 GTAACAGACAGCAAACGCCG 60.111 55.0 0.0 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2529 5958 0.029577 ATCTTTCCCCCTCCTCCTCC 60.03 60.0 0.0 0.0 0.0 4.3 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
32 33 6.660887 ATTGTGGTTTTTGTTGATTCACAC 57.339 33.333 0.00 0.00 34.08 3.82
37 38 4.979197 GGTTTTTGTTGATTCACACGCATA 59.021 37.500 0.00 0.00 0.00 3.14
40 41 7.327275 GGTTTTTGTTGATTCACACGCATAATA 59.673 33.333 0.00 0.00 0.00 0.98
100 101 6.544931 TGAGAGATTCCAAAATAGGCATCTTG 59.455 38.462 0.00 0.00 40.93 3.02
103 104 6.870769 AGATTCCAAAATAGGCATCTTGTTG 58.129 36.000 0.00 0.00 38.28 3.33
106 107 4.282957 TCCAAAATAGGCATCTTGTTGCAA 59.717 37.500 0.00 0.00 44.59 4.08
109 110 5.664294 AAATAGGCATCTTGTTGCAATGA 57.336 34.783 0.59 2.12 44.59 2.57
110 111 5.864418 AATAGGCATCTTGTTGCAATGAT 57.136 34.783 0.59 4.60 44.59 2.45
111 112 6.964807 AATAGGCATCTTGTTGCAATGATA 57.035 33.333 0.59 0.00 44.59 2.15
112 113 7.534723 AATAGGCATCTTGTTGCAATGATAT 57.465 32.000 0.59 0.00 44.59 1.63
113 114 5.449107 AGGCATCTTGTTGCAATGATATC 57.551 39.130 0.59 0.00 44.59 1.63
114 115 4.891168 AGGCATCTTGTTGCAATGATATCA 59.109 37.500 8.10 8.10 44.59 2.15
115 116 5.538813 AGGCATCTTGTTGCAATGATATCAT 59.461 36.000 12.62 12.62 44.59 2.45
121 122 9.743581 ATCTTGTTGCAATGATATCATATGGTA 57.256 29.630 18.47 8.33 35.10 3.25
127 128 9.979578 TTGCAATGATATCATATGGTAAAAACC 57.020 29.630 18.47 5.28 35.10 3.27
134 135 3.949113 TCATATGGTAAAAACCGGGAAGC 59.051 43.478 6.32 0.00 0.00 3.86
149 150 5.897250 ACCGGGAAGCTTTATCCAATATTTT 59.103 36.000 6.32 0.00 38.80 1.82
152 159 7.865889 CCGGGAAGCTTTATCCAATATTTTTAC 59.134 37.037 0.00 0.00 38.80 2.01
235 254 4.213694 GGAGATTCAGCTAGTGATGCATTG 59.786 45.833 0.00 0.00 34.17 2.82
277 300 8.739039 TGATGAAGTGTAATTGATCGGAAAAAT 58.261 29.630 0.00 0.00 0.00 1.82
296 319 7.008266 GGAAAAATAATAATGCACTGACGTGTG 59.992 37.037 0.00 0.00 43.16 3.82
298 321 6.494893 AATAATAATGCACTGACGTGTGTT 57.505 33.333 7.73 0.00 43.16 3.32
301 324 1.378531 ATGCACTGACGTGTGTTTGT 58.621 45.000 7.73 0.00 43.16 2.83
302 325 0.445829 TGCACTGACGTGTGTTTGTG 59.554 50.000 7.73 2.37 43.16 3.33
303 326 0.446222 GCACTGACGTGTGTTTGTGT 59.554 50.000 7.73 0.00 43.16 3.72
369 395 3.366374 GCTTGATAGGTTTTGTGGCAGTC 60.366 47.826 0.00 0.00 0.00 3.51
370 396 3.788227 TGATAGGTTTTGTGGCAGTCT 57.212 42.857 0.00 0.00 0.00 3.24
371 397 3.411446 TGATAGGTTTTGTGGCAGTCTG 58.589 45.455 0.00 0.00 0.00 3.51
406 432 5.487433 TGTACATTTGACCACCAGACTATG 58.513 41.667 0.00 0.00 0.00 2.23
409 435 6.121776 ACATTTGACCACCAGACTATGTAA 57.878 37.500 0.00 0.00 0.00 2.41
512 541 3.254657 GGTTGGCTTGTGTGTTGCTAATA 59.745 43.478 0.00 0.00 30.55 0.98
513 542 4.082245 GGTTGGCTTGTGTGTTGCTAATAT 60.082 41.667 0.00 0.00 30.55 1.28
514 543 5.469479 GTTGGCTTGTGTGTTGCTAATATT 58.531 37.500 0.00 0.00 30.55 1.28
515 544 5.058149 TGGCTTGTGTGTTGCTAATATTG 57.942 39.130 0.00 0.00 0.00 1.90
516 545 4.764308 TGGCTTGTGTGTTGCTAATATTGA 59.236 37.500 0.00 0.00 0.00 2.57
517 546 5.106197 TGGCTTGTGTGTTGCTAATATTGAG 60.106 40.000 0.00 0.00 0.00 3.02
538 571 6.136857 TGAGTGAGATGCCCTAGTATACTTT 58.863 40.000 11.40 0.00 0.00 2.66
539 572 6.265649 TGAGTGAGATGCCCTAGTATACTTTC 59.734 42.308 11.40 0.00 0.00 2.62
620 668 7.503521 TCATGTTTCTTGTGTATGCTTGTTA 57.496 32.000 0.00 0.00 0.00 2.41
627 675 7.801716 TCTTGTGTATGCTTGTTACTCTTTT 57.198 32.000 0.00 0.00 0.00 2.27
629 677 6.554334 TGTGTATGCTTGTTACTCTTTTCC 57.446 37.500 0.00 0.00 0.00 3.13
638 686 6.143919 GCTTGTTACTCTTTTCCGGAATTTTG 59.856 38.462 19.62 11.51 0.00 2.44
682 741 2.070783 CCATGAACAACAAATGCAGGC 58.929 47.619 0.00 0.00 0.00 4.85
764 945 7.378461 ACTGTAAGCACGTGTGAAAAATAAATG 59.622 33.333 18.38 0.00 37.60 2.32
773 955 7.378461 ACGTGTGAAAAATAAATGTACTTGCTG 59.622 33.333 0.00 0.00 0.00 4.41
803 985 7.452813 TGTTGGTGTGCATCTATCTATCTATCT 59.547 37.037 0.00 0.00 0.00 1.98
804 986 7.637631 TGGTGTGCATCTATCTATCTATCTC 57.362 40.000 0.00 0.00 0.00 2.75
815 1005 3.996124 CTATCTCTGGCCGGCCGG 61.996 72.222 43.49 43.49 43.69 6.13
861 1051 0.535553 GCCTAACAACCACCGGAACA 60.536 55.000 9.46 0.00 0.00 3.18
895 1086 6.035368 TCCATAATTAAGCAAGCAAGCAAA 57.965 33.333 3.19 0.00 36.85 3.68
896 1087 6.462500 TCCATAATTAAGCAAGCAAGCAAAA 58.538 32.000 3.19 0.00 36.85 2.44
897 1088 6.368516 TCCATAATTAAGCAAGCAAGCAAAAC 59.631 34.615 3.19 0.00 36.85 2.43
898 1089 6.369615 CCATAATTAAGCAAGCAAGCAAAACT 59.630 34.615 3.19 0.00 36.85 2.66
900 1091 8.589629 CATAATTAAGCAAGCAAGCAAAACTAG 58.410 33.333 3.19 0.00 36.85 2.57
901 1092 5.766150 TTAAGCAAGCAAGCAAAACTAGA 57.234 34.783 0.00 0.00 36.85 2.43
923 1155 6.241645 AGACTAAATCTGGTTTCTTCCCTTG 58.758 40.000 0.00 0.00 35.81 3.61
926 1158 6.839134 ACTAAATCTGGTTTCTTCCCTTGTTT 59.161 34.615 0.00 0.00 0.00 2.83
950 1182 2.125673 CGGCCGGGTAACAGACAG 60.126 66.667 20.10 0.00 39.74 3.51
951 1183 2.436115 GGCCGGGTAACAGACAGC 60.436 66.667 2.18 0.00 39.74 4.40
952 1184 2.345991 GCCGGGTAACAGACAGCA 59.654 61.111 2.18 0.00 39.74 4.41
953 1185 1.302192 GCCGGGTAACAGACAGCAA 60.302 57.895 2.18 0.00 39.74 3.91
954 1186 0.887387 GCCGGGTAACAGACAGCAAA 60.887 55.000 2.18 0.00 39.74 3.68
955 1187 0.872388 CCGGGTAACAGACAGCAAAC 59.128 55.000 0.00 0.00 39.74 2.93
956 1188 0.511221 CGGGTAACAGACAGCAAACG 59.489 55.000 0.00 0.00 39.74 3.60
957 1189 0.237498 GGGTAACAGACAGCAAACGC 59.763 55.000 0.00 0.00 39.74 4.84
958 1190 0.237498 GGTAACAGACAGCAAACGCC 59.763 55.000 0.00 0.00 0.00 5.68
959 1191 0.110823 GTAACAGACAGCAAACGCCG 60.111 55.000 0.00 0.00 0.00 6.46
960 1192 0.531090 TAACAGACAGCAAACGCCGT 60.531 50.000 0.00 0.00 0.00 5.68
961 1193 0.531090 AACAGACAGCAAACGCCGTA 60.531 50.000 0.00 0.00 0.00 4.02
962 1194 1.219522 ACAGACAGCAAACGCCGTAC 61.220 55.000 0.00 0.00 0.00 3.67
1233 1474 1.226717 GCGCTCCTTCACCTACGAG 60.227 63.158 0.00 0.00 0.00 4.18
2214 2515 2.038269 GGCCGATGAAACCTTGCGA 61.038 57.895 0.00 0.00 0.00 5.10
2215 2516 1.134694 GCCGATGAAACCTTGCGAC 59.865 57.895 0.00 0.00 0.00 5.19
2216 2517 1.573829 GCCGATGAAACCTTGCGACA 61.574 55.000 0.00 0.00 0.00 4.35
2343 2654 3.934579 GCCATTGGTTTTGATGGATCAAC 59.065 43.478 4.26 0.00 45.63 3.18
2357 2668 8.255111 TGATGGATCAACTAGATGATACTTGT 57.745 34.615 21.94 10.93 40.66 3.16
2361 2672 9.367160 TGGATCAACTAGATGATACTTGTATGA 57.633 33.333 21.94 1.81 40.66 2.15
2366 2677 9.900710 CAACTAGATGATACTTGTATGAGTACC 57.099 37.037 0.00 0.00 35.12 3.34
2367 2678 9.869667 AACTAGATGATACTTGTATGAGTACCT 57.130 33.333 0.00 0.00 35.12 3.08
2448 2759 3.719268 TTTCAGTGCCACCTGTCATAT 57.281 42.857 0.00 0.00 34.02 1.78
2466 2777 6.761242 TGTCATATTAACTTTGATCAGACCGG 59.239 38.462 0.00 0.00 0.00 5.28
2471 5900 2.893637 ACTTTGATCAGACCGGAATCG 58.106 47.619 9.46 0.00 0.00 3.34
2479 5908 1.405463 CAGACCGGAATCGAGACATGA 59.595 52.381 9.46 0.00 39.00 3.07
2529 5958 2.432628 GGCCGACGTCTCAAGGTG 60.433 66.667 14.70 0.00 0.00 4.00
2537 5966 0.612174 CGTCTCAAGGTGGAGGAGGA 60.612 60.000 0.00 0.00 35.58 3.71
2540 5969 0.980231 CTCAAGGTGGAGGAGGAGGG 60.980 65.000 0.00 0.00 0.00 4.30
2541 5970 1.997874 CAAGGTGGAGGAGGAGGGG 60.998 68.421 0.00 0.00 0.00 4.79
2542 5971 3.274550 AAGGTGGAGGAGGAGGGGG 62.275 68.421 0.00 0.00 0.00 5.40
2543 5972 3.695825 GGTGGAGGAGGAGGGGGA 61.696 72.222 0.00 0.00 0.00 4.81
2545 5974 1.229853 GTGGAGGAGGAGGGGGAAA 60.230 63.158 0.00 0.00 0.00 3.13
2548 5984 0.029577 GGAGGAGGAGGGGGAAAGAT 60.030 60.000 0.00 0.00 0.00 2.40
2551 5987 1.135960 GGAGGAGGGGGAAAGATGAG 58.864 60.000 0.00 0.00 0.00 2.90
2579 6015 0.820891 CGATGGCATGAGGGAAAGGG 60.821 60.000 3.81 0.00 0.00 3.95
2585 6021 1.005924 GCATGAGGGAAAGGGAAGGAA 59.994 52.381 0.00 0.00 0.00 3.36
2627 6063 2.276732 TGAAAGAGAGGGCACAAAGG 57.723 50.000 0.00 0.00 0.00 3.11
2642 6078 3.503748 CACAAAGGTTGGTGGAGATTCTC 59.496 47.826 5.03 5.03 34.12 2.87
2643 6079 3.395941 ACAAAGGTTGGTGGAGATTCTCT 59.604 43.478 13.22 0.00 34.12 3.10
2644 6080 3.990959 AAGGTTGGTGGAGATTCTCTC 57.009 47.619 13.22 7.13 42.66 3.20
2645 6081 3.197927 AGGTTGGTGGAGATTCTCTCT 57.802 47.619 13.22 0.00 42.95 3.10
2646 6082 3.525862 AGGTTGGTGGAGATTCTCTCTT 58.474 45.455 13.22 0.00 42.95 2.85
2647 6083 3.913163 AGGTTGGTGGAGATTCTCTCTTT 59.087 43.478 13.22 0.00 42.95 2.52
2648 6084 4.352298 AGGTTGGTGGAGATTCTCTCTTTT 59.648 41.667 13.22 0.00 42.95 2.27
2649 6085 5.073428 GGTTGGTGGAGATTCTCTCTTTTT 58.927 41.667 13.22 0.00 42.95 1.94
2650 6086 5.182190 GGTTGGTGGAGATTCTCTCTTTTTC 59.818 44.000 13.22 0.00 42.95 2.29
2651 6087 4.911390 TGGTGGAGATTCTCTCTTTTTCC 58.089 43.478 13.22 6.52 42.95 3.13
2652 6088 4.263506 TGGTGGAGATTCTCTCTTTTTCCC 60.264 45.833 13.22 3.52 42.95 3.97
2653 6089 4.018870 GGTGGAGATTCTCTCTTTTTCCCT 60.019 45.833 13.22 0.00 42.95 4.20
2654 6090 5.189934 GGTGGAGATTCTCTCTTTTTCCCTA 59.810 44.000 13.22 0.00 42.95 3.53
2655 6091 6.110033 GTGGAGATTCTCTCTTTTTCCCTAC 58.890 44.000 13.22 0.00 42.95 3.18
2656 6092 5.189934 TGGAGATTCTCTCTTTTTCCCTACC 59.810 44.000 13.22 0.00 42.95 3.18
2657 6093 5.396996 GGAGATTCTCTCTTTTTCCCTACCC 60.397 48.000 13.22 0.00 42.95 3.69
2658 6094 5.101529 AGATTCTCTCTTTTTCCCTACCCA 58.898 41.667 0.00 0.00 0.00 4.51
2659 6095 5.733647 AGATTCTCTCTTTTTCCCTACCCAT 59.266 40.000 0.00 0.00 0.00 4.00
2660 6096 6.909158 AGATTCTCTCTTTTTCCCTACCCATA 59.091 38.462 0.00 0.00 0.00 2.74
2661 6097 5.952347 TCTCTCTTTTTCCCTACCCATAC 57.048 43.478 0.00 0.00 0.00 2.39
2662 6098 4.720273 TCTCTCTTTTTCCCTACCCATACC 59.280 45.833 0.00 0.00 0.00 2.73
2663 6099 3.453353 TCTCTTTTTCCCTACCCATACCG 59.547 47.826 0.00 0.00 0.00 4.02
2664 6100 3.452878 TCTTTTTCCCTACCCATACCGA 58.547 45.455 0.00 0.00 0.00 4.69
2665 6101 3.453353 TCTTTTTCCCTACCCATACCGAG 59.547 47.826 0.00 0.00 0.00 4.63
2666 6102 2.555732 TTTCCCTACCCATACCGAGT 57.444 50.000 0.00 0.00 0.00 4.18
2667 6103 2.555732 TTCCCTACCCATACCGAGTT 57.444 50.000 0.00 0.00 0.00 3.01
2668 6104 1.784358 TCCCTACCCATACCGAGTTG 58.216 55.000 0.00 0.00 0.00 3.16
2669 6105 0.106149 CCCTACCCATACCGAGTTGC 59.894 60.000 0.00 0.00 0.00 4.17
2670 6106 0.106149 CCTACCCATACCGAGTTGCC 59.894 60.000 0.00 0.00 0.00 4.52
2671 6107 0.106149 CTACCCATACCGAGTTGCCC 59.894 60.000 0.00 0.00 0.00 5.36
2672 6108 0.325860 TACCCATACCGAGTTGCCCT 60.326 55.000 0.00 0.00 0.00 5.19
2673 6109 1.146263 CCCATACCGAGTTGCCCTC 59.854 63.158 0.00 0.00 36.80 4.30
2706 6142 2.503869 AGGGATCCCTGAGTAATGCT 57.496 50.000 33.46 3.98 46.22 3.79
2707 6143 3.637821 AGGGATCCCTGAGTAATGCTA 57.362 47.619 33.46 0.00 46.22 3.49
2708 6144 3.243724 AGGGATCCCTGAGTAATGCTAC 58.756 50.000 33.46 0.00 46.22 3.58
2709 6145 2.972713 GGGATCCCTGAGTAATGCTACA 59.027 50.000 24.69 0.00 0.00 2.74
2710 6146 3.584848 GGGATCCCTGAGTAATGCTACAT 59.415 47.826 24.69 0.00 0.00 2.29
2711 6147 4.323104 GGGATCCCTGAGTAATGCTACATC 60.323 50.000 24.69 0.00 0.00 3.06
2712 6148 4.323104 GGATCCCTGAGTAATGCTACATCC 60.323 50.000 0.00 0.00 0.00 3.51
2713 6149 3.653164 TCCCTGAGTAATGCTACATCCA 58.347 45.455 0.00 0.00 0.00 3.41
2714 6150 3.388024 TCCCTGAGTAATGCTACATCCAC 59.612 47.826 0.00 0.00 0.00 4.02
2715 6151 3.384668 CCTGAGTAATGCTACATCCACG 58.615 50.000 0.00 0.00 0.00 4.94
2716 6152 3.181475 CCTGAGTAATGCTACATCCACGT 60.181 47.826 0.00 0.00 0.00 4.49
2717 6153 4.037565 CCTGAGTAATGCTACATCCACGTA 59.962 45.833 0.00 0.00 0.00 3.57
2718 6154 5.451381 CCTGAGTAATGCTACATCCACGTAA 60.451 44.000 0.00 0.00 0.00 3.18
2719 6155 5.968254 TGAGTAATGCTACATCCACGTAAA 58.032 37.500 0.00 0.00 0.00 2.01
2720 6156 6.040247 TGAGTAATGCTACATCCACGTAAAG 58.960 40.000 0.00 0.00 0.00 1.85
2721 6157 6.127563 TGAGTAATGCTACATCCACGTAAAGA 60.128 38.462 0.00 0.00 0.00 2.52
2722 6158 6.636705 AGTAATGCTACATCCACGTAAAGAA 58.363 36.000 0.00 0.00 0.00 2.52
2723 6159 7.272978 AGTAATGCTACATCCACGTAAAGAAT 58.727 34.615 0.00 0.00 0.00 2.40
2724 6160 7.769044 AGTAATGCTACATCCACGTAAAGAATT 59.231 33.333 0.00 0.00 0.00 2.17
2725 6161 7.391148 AATGCTACATCCACGTAAAGAATTT 57.609 32.000 0.00 0.00 43.42 1.82
2726 6162 6.811253 TGCTACATCCACGTAAAGAATTTT 57.189 33.333 0.00 0.00 40.09 1.82
2727 6163 7.908827 TGCTACATCCACGTAAAGAATTTTA 57.091 32.000 0.00 0.00 40.09 1.52
2728 6164 7.745015 TGCTACATCCACGTAAAGAATTTTAC 58.255 34.615 0.00 1.14 43.30 2.01
2749 6185 3.257745 GTGTTTTACGTAACCTGCCAC 57.742 47.619 7.70 6.84 0.00 5.01
2750 6186 2.613133 GTGTTTTACGTAACCTGCCACA 59.387 45.455 7.70 2.05 0.00 4.17
2751 6187 3.251487 GTGTTTTACGTAACCTGCCACAT 59.749 43.478 7.70 0.00 0.00 3.21
2752 6188 3.251245 TGTTTTACGTAACCTGCCACATG 59.749 43.478 7.70 0.00 0.00 3.21
2753 6189 2.102070 TTACGTAACCTGCCACATGG 57.898 50.000 3.29 0.00 38.53 3.66
2754 6190 1.268066 TACGTAACCTGCCACATGGA 58.732 50.000 0.87 0.00 37.39 3.41
2755 6191 0.321298 ACGTAACCTGCCACATGGAC 60.321 55.000 0.87 0.00 37.39 4.02
2756 6192 0.321210 CGTAACCTGCCACATGGACA 60.321 55.000 0.87 0.00 37.39 4.02
2757 6193 1.880221 CGTAACCTGCCACATGGACAA 60.880 52.381 0.87 0.00 37.39 3.18
2758 6194 2.446435 GTAACCTGCCACATGGACAAT 58.554 47.619 0.87 0.00 37.39 2.71
2759 6195 2.014010 AACCTGCCACATGGACAATT 57.986 45.000 0.87 0.00 37.39 2.32
2760 6196 1.259609 ACCTGCCACATGGACAATTG 58.740 50.000 3.24 3.24 37.39 2.32
2761 6197 1.259609 CCTGCCACATGGACAATTGT 58.740 50.000 11.78 11.78 37.39 2.71
2762 6198 1.067425 CCTGCCACATGGACAATTGTG 60.067 52.381 17.58 3.85 42.25 3.33
3136 6572 6.381465 GGTTAGGTAGAACGTTTCGTAAAG 57.619 41.667 0.46 0.00 39.99 1.85
3137 6573 5.164051 GGTTAGGTAGAACGTTTCGTAAAGC 60.164 44.000 0.46 0.00 39.99 3.51
3138 6574 4.248691 AGGTAGAACGTTTCGTAAAGCT 57.751 40.909 0.46 0.00 39.99 3.74
3139 6575 5.376854 AGGTAGAACGTTTCGTAAAGCTA 57.623 39.130 0.46 0.00 39.99 3.32
3140 6576 5.157067 AGGTAGAACGTTTCGTAAAGCTAC 58.843 41.667 0.46 6.61 39.99 3.58
3151 6587 3.945179 CGTAAAGCTACGTAGGTGTAGG 58.055 50.000 26.63 24.54 44.79 3.18
3152 6588 3.623060 CGTAAAGCTACGTAGGTGTAGGA 59.377 47.826 28.41 9.66 44.79 2.94
3153 6589 4.274459 CGTAAAGCTACGTAGGTGTAGGAT 59.726 45.833 28.41 12.32 44.79 3.24
3154 6590 5.220931 CGTAAAGCTACGTAGGTGTAGGATT 60.221 44.000 28.41 19.95 44.79 3.01
3155 6591 6.017934 CGTAAAGCTACGTAGGTGTAGGATTA 60.018 42.308 28.41 19.13 44.79 1.75
3156 6592 6.973460 AAAGCTACGTAGGTGTAGGATTAT 57.027 37.500 26.63 6.06 41.70 1.28
3157 6593 6.572167 AAGCTACGTAGGTGTAGGATTATC 57.428 41.667 26.63 4.15 41.70 1.75
3158 6594 4.694509 AGCTACGTAGGTGTAGGATTATCG 59.305 45.833 25.50 0.00 41.70 2.92
3159 6595 4.142730 GCTACGTAGGTGTAGGATTATCGG 60.143 50.000 23.47 0.00 41.70 4.18
3160 6596 3.152341 ACGTAGGTGTAGGATTATCGGG 58.848 50.000 0.00 0.00 0.00 5.14
3161 6597 2.490903 CGTAGGTGTAGGATTATCGGGG 59.509 54.545 0.00 0.00 0.00 5.73
3162 6598 3.771216 GTAGGTGTAGGATTATCGGGGA 58.229 50.000 0.00 0.00 0.00 4.81
3163 6599 3.562108 AGGTGTAGGATTATCGGGGAT 57.438 47.619 0.00 0.00 0.00 3.85
3164 6600 3.442076 AGGTGTAGGATTATCGGGGATC 58.558 50.000 0.00 0.00 0.00 3.36
3165 6601 2.500504 GGTGTAGGATTATCGGGGATCC 59.499 54.545 1.92 1.92 41.75 3.36
3166 6602 2.500504 GTGTAGGATTATCGGGGATCCC 59.499 54.545 23.95 23.95 42.28 3.85
3167 6603 2.385765 TGTAGGATTATCGGGGATCCCT 59.614 50.000 30.08 13.57 42.67 4.20
3168 6604 2.743131 AGGATTATCGGGGATCCCTT 57.257 50.000 30.08 17.21 42.67 3.95
3169 6605 2.269940 AGGATTATCGGGGATCCCTTG 58.730 52.381 30.08 21.95 42.67 3.61
3170 6606 1.340114 GGATTATCGGGGATCCCTTGC 60.340 57.143 30.08 13.01 42.67 4.01
3171 6607 0.698818 ATTATCGGGGATCCCTTGCC 59.301 55.000 30.08 12.63 42.67 4.52
3172 6608 0.696143 TTATCGGGGATCCCTTGCCA 60.696 55.000 30.08 9.46 42.67 4.92
3173 6609 0.475632 TATCGGGGATCCCTTGCCAT 60.476 55.000 30.08 16.08 42.67 4.40
3174 6610 1.783250 ATCGGGGATCCCTTGCCATC 61.783 60.000 30.08 10.72 42.67 3.51
3175 6611 2.756042 CGGGGATCCCTTGCCATCA 61.756 63.158 30.08 0.00 42.67 3.07
3176 6612 1.152673 GGGGATCCCTTGCCATCAC 60.153 63.158 30.08 6.44 41.34 3.06
3177 6613 1.152673 GGGATCCCTTGCCATCACC 60.153 63.158 24.69 0.00 35.48 4.02
3178 6614 1.526917 GGATCCCTTGCCATCACCG 60.527 63.158 0.00 0.00 0.00 4.94
3179 6615 1.224592 GATCCCTTGCCATCACCGT 59.775 57.895 0.00 0.00 0.00 4.83
3180 6616 0.815615 GATCCCTTGCCATCACCGTC 60.816 60.000 0.00 0.00 0.00 4.79
3181 6617 1.561769 ATCCCTTGCCATCACCGTCA 61.562 55.000 0.00 0.00 0.00 4.35
3182 6618 1.077501 CCCTTGCCATCACCGTCAT 60.078 57.895 0.00 0.00 0.00 3.06
3183 6619 1.097547 CCCTTGCCATCACCGTCATC 61.098 60.000 0.00 0.00 0.00 2.92
3184 6620 1.097547 CCTTGCCATCACCGTCATCC 61.098 60.000 0.00 0.00 0.00 3.51
3185 6621 1.077787 TTGCCATCACCGTCATCCC 60.078 57.895 0.00 0.00 0.00 3.85
3186 6622 2.203209 GCCATCACCGTCATCCCC 60.203 66.667 0.00 0.00 0.00 4.81
3187 6623 2.510906 CCATCACCGTCATCCCCC 59.489 66.667 0.00 0.00 0.00 5.40
3204 6640 2.935481 CCCCCTTCTGCCACTCCA 60.935 66.667 0.00 0.00 0.00 3.86
3205 6641 2.352805 CCCCTTCTGCCACTCCAC 59.647 66.667 0.00 0.00 0.00 4.02
3206 6642 2.352805 CCCTTCTGCCACTCCACC 59.647 66.667 0.00 0.00 0.00 4.61
3207 6643 2.352805 CCTTCTGCCACTCCACCC 59.647 66.667 0.00 0.00 0.00 4.61
3208 6644 2.352805 CTTCTGCCACTCCACCCC 59.647 66.667 0.00 0.00 0.00 4.95
3209 6645 2.121963 TTCTGCCACTCCACCCCT 60.122 61.111 0.00 0.00 0.00 4.79
3210 6646 2.190488 CTTCTGCCACTCCACCCCTC 62.190 65.000 0.00 0.00 0.00 4.30
3211 6647 3.721706 CTGCCACTCCACCCCTCC 61.722 72.222 0.00 0.00 0.00 4.30
3212 6648 4.270153 TGCCACTCCACCCCTCCT 62.270 66.667 0.00 0.00 0.00 3.69
3213 6649 3.403558 GCCACTCCACCCCTCCTC 61.404 72.222 0.00 0.00 0.00 3.71
3214 6650 2.122729 CCACTCCACCCCTCCTCA 59.877 66.667 0.00 0.00 0.00 3.86
3215 6651 2.294078 CCACTCCACCCCTCCTCAC 61.294 68.421 0.00 0.00 0.00 3.51
3216 6652 2.122954 ACTCCACCCCTCCTCACC 59.877 66.667 0.00 0.00 0.00 4.02
3217 6653 2.689034 CTCCACCCCTCCTCACCC 60.689 72.222 0.00 0.00 0.00 4.61
3218 6654 3.537506 TCCACCCCTCCTCACCCA 61.538 66.667 0.00 0.00 0.00 4.51
3219 6655 2.286425 CCACCCCTCCTCACCCAT 60.286 66.667 0.00 0.00 0.00 4.00
3220 6656 2.683465 CCACCCCTCCTCACCCATG 61.683 68.421 0.00 0.00 0.00 3.66
3221 6657 1.616327 CACCCCTCCTCACCCATGA 60.616 63.158 0.00 0.00 0.00 3.07
3222 6658 0.990282 CACCCCTCCTCACCCATGAT 60.990 60.000 0.00 0.00 33.22 2.45
3223 6659 0.990282 ACCCCTCCTCACCCATGATG 60.990 60.000 0.00 0.00 33.22 3.07
3224 6660 0.695462 CCCCTCCTCACCCATGATGA 60.695 60.000 0.00 0.00 33.22 2.92
3225 6661 0.471617 CCCTCCTCACCCATGATGAC 59.528 60.000 0.00 0.00 33.22 3.06
3226 6662 0.471617 CCTCCTCACCCATGATGACC 59.528 60.000 0.00 0.00 33.22 4.02
3227 6663 0.471617 CTCCTCACCCATGATGACCC 59.528 60.000 0.00 0.00 33.22 4.46
3228 6664 0.253113 TCCTCACCCATGATGACCCA 60.253 55.000 0.00 0.00 33.22 4.51
3229 6665 0.107017 CCTCACCCATGATGACCCAC 60.107 60.000 0.00 0.00 33.22 4.61
3230 6666 0.620030 CTCACCCATGATGACCCACA 59.380 55.000 0.00 0.00 33.22 4.17
3231 6667 1.004628 CTCACCCATGATGACCCACAA 59.995 52.381 0.00 0.00 33.22 3.33
3232 6668 1.004628 TCACCCATGATGACCCACAAG 59.995 52.381 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.877003 TCAACAAAAACCACAATACGTATGAT 58.123 30.769 9.24 0.00 0.00 2.45
1 2 7.260558 TCAACAAAAACCACAATACGTATGA 57.739 32.000 9.24 0.00 0.00 2.15
3 4 8.353684 TGAATCAACAAAAACCACAATACGTAT 58.646 29.630 1.14 1.14 0.00 3.06
4 5 7.644551 GTGAATCAACAAAAACCACAATACGTA 59.355 33.333 0.00 0.00 0.00 3.57
6 7 6.473778 TGTGAATCAACAAAAACCACAATACG 59.526 34.615 0.00 0.00 31.21 3.06
7 8 7.514435 CGTGTGAATCAACAAAAACCACAATAC 60.514 37.037 0.00 0.00 35.26 1.89
63 64 8.924511 TTTGGAATCTCTCAACTTCATAAACT 57.075 30.769 0.00 0.00 0.00 2.66
70 71 6.375455 TGCCTATTTTGGAATCTCTCAACTTC 59.625 38.462 0.00 0.00 0.00 3.01
74 75 6.666678 AGATGCCTATTTTGGAATCTCTCAA 58.333 36.000 0.00 0.00 46.92 3.02
103 104 7.754924 CCGGTTTTTACCATATGATATCATTGC 59.245 37.037 22.84 7.03 37.76 3.56
106 107 7.695055 TCCCGGTTTTTACCATATGATATCAT 58.305 34.615 21.50 21.50 40.22 2.45
109 110 6.433093 GCTTCCCGGTTTTTACCATATGATAT 59.567 38.462 3.65 0.00 0.00 1.63
110 111 5.766174 GCTTCCCGGTTTTTACCATATGATA 59.234 40.000 3.65 0.00 0.00 2.15
111 112 4.583073 GCTTCCCGGTTTTTACCATATGAT 59.417 41.667 3.65 0.00 0.00 2.45
112 113 3.949113 GCTTCCCGGTTTTTACCATATGA 59.051 43.478 3.65 0.00 0.00 2.15
113 114 3.951680 AGCTTCCCGGTTTTTACCATATG 59.048 43.478 0.00 0.00 0.00 1.78
114 115 4.245251 AGCTTCCCGGTTTTTACCATAT 57.755 40.909 0.00 0.00 0.00 1.78
115 116 3.724732 AGCTTCCCGGTTTTTACCATA 57.275 42.857 0.00 0.00 0.00 2.74
121 122 3.502356 TGGATAAAGCTTCCCGGTTTTT 58.498 40.909 0.00 0.00 42.78 1.94
127 128 8.410141 TGTAAAAATATTGGATAAAGCTTCCCG 58.590 33.333 0.00 0.00 31.87 5.14
160 167 2.161855 TGATGTGCCAGGCTTAAACAG 58.838 47.619 14.15 0.00 0.00 3.16
161 168 2.284754 TGATGTGCCAGGCTTAAACA 57.715 45.000 14.15 9.03 0.00 2.83
170 177 3.562973 GGACTACATGAATGATGTGCCAG 59.437 47.826 0.00 0.00 45.43 4.85
206 223 0.596083 CTAGCTGAATCTCCACGCGG 60.596 60.000 12.47 0.00 0.00 6.46
210 229 3.129871 GCATCACTAGCTGAATCTCCAC 58.870 50.000 0.00 0.00 30.60 4.02
235 254 6.863126 CACTTCATCACCTGGTAAACAATTTC 59.137 38.462 0.00 0.00 0.00 2.17
296 319 5.085390 GCACCAATGTTGAAAAACACAAAC 58.915 37.500 0.00 0.00 35.22 2.93
298 321 4.318332 TGCACCAATGTTGAAAAACACAA 58.682 34.783 0.00 0.00 35.22 3.33
301 324 4.180057 GTCTGCACCAATGTTGAAAAACA 58.820 39.130 0.00 0.00 37.05 2.83
302 325 4.180057 TGTCTGCACCAATGTTGAAAAAC 58.820 39.130 0.00 0.00 0.00 2.43
303 326 4.462508 TGTCTGCACCAATGTTGAAAAA 57.537 36.364 0.00 0.00 0.00 1.94
371 397 4.736793 GTCAAATGTACAATATGCTGCAGC 59.263 41.667 31.89 31.89 42.50 5.25
406 432 9.672086 TTCGGCAAAGCACATATATATTTTTAC 57.328 29.630 0.00 0.00 0.00 2.01
409 435 9.195411 CATTTCGGCAAAGCACATATATATTTT 57.805 29.630 0.00 0.00 0.00 1.82
512 541 6.318913 AGTATACTAGGGCATCTCACTCAAT 58.681 40.000 2.75 0.00 0.00 2.57
513 542 5.706447 AGTATACTAGGGCATCTCACTCAA 58.294 41.667 2.75 0.00 0.00 3.02
514 543 5.326283 AGTATACTAGGGCATCTCACTCA 57.674 43.478 2.75 0.00 0.00 3.41
515 544 6.492087 AGAAAGTATACTAGGGCATCTCACTC 59.508 42.308 5.65 0.00 0.00 3.51
516 545 6.377912 AGAAAGTATACTAGGGCATCTCACT 58.622 40.000 5.65 0.00 0.00 3.41
517 546 6.658188 AGAAAGTATACTAGGGCATCTCAC 57.342 41.667 5.65 0.00 0.00 3.51
613 661 5.372547 AATTCCGGAAAAGAGTAACAAGC 57.627 39.130 23.08 0.00 0.00 4.01
620 668 5.845391 TGAACAAAATTCCGGAAAAGAGT 57.155 34.783 23.08 14.78 0.00 3.24
669 728 0.320073 CACCTGGCCTGCATTTGTTG 60.320 55.000 3.32 0.00 0.00 3.33
741 801 7.617533 ACATTTATTTTTCACACGTGCTTAC 57.382 32.000 17.22 0.00 0.00 2.34
764 945 2.034558 ACACCAACAATGCAGCAAGTAC 59.965 45.455 0.00 0.00 0.00 2.73
773 955 3.379372 AGATAGATGCACACCAACAATGC 59.621 43.478 0.00 0.00 39.88 3.56
815 1005 3.930634 ACTATAATTAGGACGGACGGC 57.069 47.619 0.00 0.00 0.00 5.68
861 1051 6.554784 TGCTTAATTATGGATGGATGGATGT 58.445 36.000 1.00 0.00 0.00 3.06
895 1086 7.237887 AGGGAAGAAACCAGATTTAGTCTAGTT 59.762 37.037 0.00 0.00 39.94 2.24
896 1087 6.731448 AGGGAAGAAACCAGATTTAGTCTAGT 59.269 38.462 0.00 0.00 34.69 2.57
897 1088 7.189079 AGGGAAGAAACCAGATTTAGTCTAG 57.811 40.000 0.00 0.00 34.69 2.43
898 1089 7.017254 ACAAGGGAAGAAACCAGATTTAGTCTA 59.983 37.037 0.00 0.00 34.69 2.59
900 1091 6.004574 ACAAGGGAAGAAACCAGATTTAGTC 58.995 40.000 0.00 0.00 0.00 2.59
901 1092 5.953571 ACAAGGGAAGAAACCAGATTTAGT 58.046 37.500 0.00 0.00 0.00 2.24
918 1150 2.746277 CCGGCGAGGAAACAAGGG 60.746 66.667 9.30 0.00 45.00 3.95
958 1190 1.201640 CGATCGATCCGAGTACGTACG 60.202 57.143 19.51 15.01 39.91 3.67
959 1191 2.054363 TCGATCGATCCGAGTACGTAC 58.946 52.381 19.51 18.10 39.91 3.67
960 1192 2.422276 TCGATCGATCCGAGTACGTA 57.578 50.000 19.51 0.00 39.91 3.57
961 1193 1.725706 GATCGATCGATCCGAGTACGT 59.274 52.381 36.97 12.98 43.71 3.57
962 1194 2.422773 GATCGATCGATCCGAGTACG 57.577 55.000 36.97 6.94 43.71 3.67
1219 1460 0.612174 AGCTGCTCGTAGGTGAAGGA 60.612 55.000 0.00 0.00 0.00 3.36
2094 2395 4.819761 TCGCTCATGCACGGCCTC 62.820 66.667 0.00 0.00 39.64 4.70
2214 2515 5.719085 TCTCATCTAGGCTTCTTCTTCTTGT 59.281 40.000 0.00 0.00 0.00 3.16
2215 2516 6.219417 TCTCATCTAGGCTTCTTCTTCTTG 57.781 41.667 0.00 0.00 0.00 3.02
2216 2517 7.255942 GCTATCTCATCTAGGCTTCTTCTTCTT 60.256 40.741 0.00 0.00 0.00 2.52
2343 2654 9.508642 TCAGGTACTCATACAAGTATCATCTAG 57.491 37.037 0.00 0.00 35.66 2.43
2357 2668 5.363580 TGCAACTCATCATCAGGTACTCATA 59.636 40.000 0.00 0.00 34.60 2.15
2359 2670 3.515104 TGCAACTCATCATCAGGTACTCA 59.485 43.478 0.00 0.00 34.60 3.41
2360 2671 4.128925 TGCAACTCATCATCAGGTACTC 57.871 45.455 0.00 0.00 34.60 2.59
2361 2672 4.767578 ATGCAACTCATCATCAGGTACT 57.232 40.909 0.00 0.00 43.88 2.73
2363 2674 4.080413 TCCAATGCAACTCATCATCAGGTA 60.080 41.667 0.00 0.00 33.40 3.08
2364 2675 3.021695 CCAATGCAACTCATCATCAGGT 58.978 45.455 0.00 0.00 33.40 4.00
2365 2676 3.284617 TCCAATGCAACTCATCATCAGG 58.715 45.455 0.00 0.00 33.40 3.86
2366 2677 4.976224 TTCCAATGCAACTCATCATCAG 57.024 40.909 0.00 0.00 33.40 2.90
2367 2678 5.011586 TCTTTCCAATGCAACTCATCATCA 58.988 37.500 0.00 0.00 33.40 3.07
2433 2744 5.414454 TCAAAGTTAATATGACAGGTGGCAC 59.586 40.000 9.70 9.70 34.80 5.01
2440 2751 7.042456 CCGGTCTGATCAAAGTTAATATGACAG 60.042 40.741 0.00 0.00 0.00 3.51
2448 2759 4.868171 CGATTCCGGTCTGATCAAAGTTAA 59.132 41.667 0.00 0.00 0.00 2.01
2466 2777 2.097685 CGAATGCGTCATGTCTCGATTC 60.098 50.000 10.57 12.78 0.00 2.52
2489 5918 2.917296 GCTGTCGACTATTAGCCGTAGC 60.917 54.545 17.92 9.18 40.32 3.58
2493 5922 0.660595 CCGCTGTCGACTATTAGCCG 60.661 60.000 17.92 12.37 38.10 5.52
2495 5924 0.940047 GCCCGCTGTCGACTATTAGC 60.940 60.000 17.92 15.67 38.10 3.09
2520 5949 0.041833 CCTCCTCCTCCACCTTGAGA 59.958 60.000 0.00 0.00 34.11 3.27
2529 5958 0.029577 ATCTTTCCCCCTCCTCCTCC 60.030 60.000 0.00 0.00 0.00 4.30
2537 5966 2.294127 ACATCTCCTCATCTTTCCCCCT 60.294 50.000 0.00 0.00 0.00 4.79
2540 5969 2.570135 GCACATCTCCTCATCTTTCCC 58.430 52.381 0.00 0.00 0.00 3.97
2541 5970 2.159043 TCGCACATCTCCTCATCTTTCC 60.159 50.000 0.00 0.00 0.00 3.13
2542 5971 3.170791 TCGCACATCTCCTCATCTTTC 57.829 47.619 0.00 0.00 0.00 2.62
2543 5972 3.464907 CATCGCACATCTCCTCATCTTT 58.535 45.455 0.00 0.00 0.00 2.52
2545 5974 1.343789 CCATCGCACATCTCCTCATCT 59.656 52.381 0.00 0.00 0.00 2.90
2548 5984 1.144716 GCCATCGCACATCTCCTCA 59.855 57.895 0.00 0.00 34.03 3.86
2579 6015 2.357257 GGATGTCCCTTCCCTTTCCTTC 60.357 54.545 0.00 0.00 0.00 3.46
2585 6021 1.497309 TTGCGGATGTCCCTTCCCTT 61.497 55.000 0.00 0.00 0.00 3.95
2642 6078 3.453353 TCGGTATGGGTAGGGAAAAAGAG 59.547 47.826 0.00 0.00 0.00 2.85
2643 6079 3.452878 TCGGTATGGGTAGGGAAAAAGA 58.547 45.455 0.00 0.00 0.00 2.52
2644 6080 3.199289 ACTCGGTATGGGTAGGGAAAAAG 59.801 47.826 0.00 0.00 0.00 2.27
2645 6081 3.183801 ACTCGGTATGGGTAGGGAAAAA 58.816 45.455 0.00 0.00 0.00 1.94
2646 6082 2.836667 ACTCGGTATGGGTAGGGAAAA 58.163 47.619 0.00 0.00 0.00 2.29
2647 6083 2.502538 CAACTCGGTATGGGTAGGGAAA 59.497 50.000 0.00 0.00 0.00 3.13
2648 6084 2.112998 CAACTCGGTATGGGTAGGGAA 58.887 52.381 0.00 0.00 0.00 3.97
2649 6085 1.784358 CAACTCGGTATGGGTAGGGA 58.216 55.000 0.00 0.00 0.00 4.20
2650 6086 0.106149 GCAACTCGGTATGGGTAGGG 59.894 60.000 0.00 0.00 0.00 3.53
2651 6087 0.106149 GGCAACTCGGTATGGGTAGG 59.894 60.000 0.00 0.00 0.00 3.18
2652 6088 0.106149 GGGCAACTCGGTATGGGTAG 59.894 60.000 0.00 0.00 0.00 3.18
2653 6089 0.325860 AGGGCAACTCGGTATGGGTA 60.326 55.000 0.00 0.00 0.00 3.69
2654 6090 1.615424 AGGGCAACTCGGTATGGGT 60.615 57.895 0.00 0.00 0.00 4.51
2655 6091 1.146263 GAGGGCAACTCGGTATGGG 59.854 63.158 0.00 0.00 36.29 4.00
2656 6092 4.857251 GAGGGCAACTCGGTATGG 57.143 61.111 0.00 0.00 36.29 2.74
2676 6112 4.554036 GATCCCTCCCGGCTGCAC 62.554 72.222 0.50 0.00 0.00 4.57
2685 6121 1.349357 GCATTACTCAGGGATCCCTCC 59.651 57.143 31.71 4.04 46.28 4.30
2686 6122 2.334023 AGCATTACTCAGGGATCCCTC 58.666 52.381 31.71 16.66 46.28 4.30
2688 6124 2.972713 TGTAGCATTACTCAGGGATCCC 59.027 50.000 24.59 24.59 0.00 3.85
2689 6125 4.323104 GGATGTAGCATTACTCAGGGATCC 60.323 50.000 1.92 1.92 0.00 3.36
2690 6126 4.284490 TGGATGTAGCATTACTCAGGGATC 59.716 45.833 0.00 0.00 0.00 3.36
2691 6127 4.040952 GTGGATGTAGCATTACTCAGGGAT 59.959 45.833 0.00 0.00 0.00 3.85
2692 6128 3.388024 GTGGATGTAGCATTACTCAGGGA 59.612 47.826 0.00 0.00 0.00 4.20
2693 6129 3.733337 GTGGATGTAGCATTACTCAGGG 58.267 50.000 0.00 0.00 0.00 4.45
2694 6130 3.181475 ACGTGGATGTAGCATTACTCAGG 60.181 47.826 0.00 0.00 0.00 3.86
2695 6131 4.046938 ACGTGGATGTAGCATTACTCAG 57.953 45.455 0.00 0.00 0.00 3.35
2696 6132 5.585820 TTACGTGGATGTAGCATTACTCA 57.414 39.130 0.00 0.00 0.00 3.41
2697 6133 6.270815 TCTTTACGTGGATGTAGCATTACTC 58.729 40.000 0.00 0.00 0.00 2.59
2698 6134 6.216801 TCTTTACGTGGATGTAGCATTACT 57.783 37.500 0.00 0.00 0.00 2.24
2699 6135 6.897259 TTCTTTACGTGGATGTAGCATTAC 57.103 37.500 0.00 0.00 0.00 1.89
2700 6136 8.500753 AAATTCTTTACGTGGATGTAGCATTA 57.499 30.769 0.00 0.00 0.00 1.90
2701 6137 7.391148 AAATTCTTTACGTGGATGTAGCATT 57.609 32.000 0.00 0.00 0.00 3.56
2702 6138 7.391148 AAAATTCTTTACGTGGATGTAGCAT 57.609 32.000 0.00 0.00 0.00 3.79
2703 6139 6.811253 AAAATTCTTTACGTGGATGTAGCA 57.189 33.333 0.00 0.00 0.00 3.49
2729 6165 2.613133 TGTGGCAGGTTACGTAAAACAC 59.387 45.455 10.11 13.96 0.00 3.32
2730 6166 2.915349 TGTGGCAGGTTACGTAAAACA 58.085 42.857 10.11 5.52 0.00 2.83
2731 6167 3.365565 CCATGTGGCAGGTTACGTAAAAC 60.366 47.826 10.11 6.38 0.00 2.43
2732 6168 2.814919 CCATGTGGCAGGTTACGTAAAA 59.185 45.455 10.11 0.00 0.00 1.52
2733 6169 2.038689 TCCATGTGGCAGGTTACGTAAA 59.961 45.455 10.11 0.00 34.44 2.01
2734 6170 1.624312 TCCATGTGGCAGGTTACGTAA 59.376 47.619 3.29 3.29 34.44 3.18
2735 6171 1.066716 GTCCATGTGGCAGGTTACGTA 60.067 52.381 0.00 0.00 34.44 3.57
2736 6172 0.321298 GTCCATGTGGCAGGTTACGT 60.321 55.000 0.00 0.00 34.44 3.57
2737 6173 0.321210 TGTCCATGTGGCAGGTTACG 60.321 55.000 0.00 0.00 34.44 3.18
2738 6174 1.904287 TTGTCCATGTGGCAGGTTAC 58.096 50.000 0.00 0.00 34.44 2.50
2739 6175 2.824936 CAATTGTCCATGTGGCAGGTTA 59.175 45.455 0.00 0.00 34.44 2.85
2740 6176 1.619827 CAATTGTCCATGTGGCAGGTT 59.380 47.619 0.00 0.00 34.44 3.50
2741 6177 1.259609 CAATTGTCCATGTGGCAGGT 58.740 50.000 0.00 0.00 34.44 4.00
2742 6178 1.067425 CACAATTGTCCATGTGGCAGG 60.067 52.381 8.48 0.00 42.46 4.85
2743 6179 2.357327 CACAATTGTCCATGTGGCAG 57.643 50.000 8.48 0.00 42.46 4.85
3113 6549 5.164051 GCTTTACGAAACGTTCTACCTAACC 60.164 44.000 0.00 0.00 41.54 2.85
3114 6550 5.631096 AGCTTTACGAAACGTTCTACCTAAC 59.369 40.000 0.00 0.00 41.54 2.34
3115 6551 5.772521 AGCTTTACGAAACGTTCTACCTAA 58.227 37.500 0.00 0.00 41.54 2.69
3116 6552 5.376854 AGCTTTACGAAACGTTCTACCTA 57.623 39.130 0.00 0.00 41.54 3.08
3117 6553 4.248691 AGCTTTACGAAACGTTCTACCT 57.751 40.909 0.00 0.00 41.54 3.08
3118 6554 4.029529 CGTAGCTTTACGAAACGTTCTACC 59.970 45.833 0.00 0.00 45.45 3.18
3119 6555 4.613031 ACGTAGCTTTACGAAACGTTCTAC 59.387 41.667 15.63 5.41 43.63 2.59
3120 6556 4.783242 ACGTAGCTTTACGAAACGTTCTA 58.217 39.130 15.63 0.00 43.63 2.10
3121 6557 3.632189 ACGTAGCTTTACGAAACGTTCT 58.368 40.909 15.63 0.00 43.63 3.01
3122 6558 4.029529 CCTACGTAGCTTTACGAAACGTTC 59.970 45.833 17.41 0.00 43.63 3.95
3123 6559 3.914364 CCTACGTAGCTTTACGAAACGTT 59.086 43.478 17.41 0.00 43.63 3.99
3125 6561 3.299020 CACCTACGTAGCTTTACGAAACG 59.701 47.826 17.41 8.63 45.45 3.60
3126 6562 4.229876 ACACCTACGTAGCTTTACGAAAC 58.770 43.478 17.41 0.00 45.45 2.78
3127 6563 4.503741 ACACCTACGTAGCTTTACGAAA 57.496 40.909 17.41 2.92 45.45 3.46
3128 6564 4.094887 CCTACACCTACGTAGCTTTACGAA 59.905 45.833 17.41 0.00 45.45 3.85
3129 6565 3.623060 CCTACACCTACGTAGCTTTACGA 59.377 47.826 17.41 0.00 45.45 3.43
3131 6567 5.764487 ATCCTACACCTACGTAGCTTTAC 57.236 43.478 17.41 0.00 38.03 2.01
3132 6568 7.095060 CGATAATCCTACACCTACGTAGCTTTA 60.095 40.741 17.41 6.15 38.03 1.85
3133 6569 6.293845 CGATAATCCTACACCTACGTAGCTTT 60.294 42.308 17.41 5.29 38.03 3.51
3134 6570 5.180868 CGATAATCCTACACCTACGTAGCTT 59.819 44.000 17.41 3.05 38.03 3.74
3135 6571 4.694509 CGATAATCCTACACCTACGTAGCT 59.305 45.833 17.41 0.00 38.03 3.32
3136 6572 4.142730 CCGATAATCCTACACCTACGTAGC 60.143 50.000 17.41 0.00 38.03 3.58
3137 6573 4.394300 CCCGATAATCCTACACCTACGTAG 59.606 50.000 15.92 15.92 38.90 3.51
3138 6574 4.326826 CCCGATAATCCTACACCTACGTA 58.673 47.826 0.00 0.00 0.00 3.57
3139 6575 3.152341 CCCGATAATCCTACACCTACGT 58.848 50.000 0.00 0.00 0.00 3.57
3140 6576 2.490903 CCCCGATAATCCTACACCTACG 59.509 54.545 0.00 0.00 0.00 3.51
3141 6577 3.771216 TCCCCGATAATCCTACACCTAC 58.229 50.000 0.00 0.00 0.00 3.18
3142 6578 4.571362 GGATCCCCGATAATCCTACACCTA 60.571 50.000 0.00 0.00 38.74 3.08
3143 6579 3.442076 GATCCCCGATAATCCTACACCT 58.558 50.000 0.00 0.00 0.00 4.00
3144 6580 2.500504 GGATCCCCGATAATCCTACACC 59.499 54.545 0.00 0.00 38.74 4.16
3145 6581 2.500504 GGGATCCCCGATAATCCTACAC 59.499 54.545 21.42 0.00 41.10 2.90
3146 6582 2.829023 GGGATCCCCGATAATCCTACA 58.171 52.381 21.42 0.00 41.10 2.74
3158 6594 1.152673 GTGATGGCAAGGGATCCCC 60.153 63.158 28.11 12.57 45.90 4.81
3159 6595 1.152673 GGTGATGGCAAGGGATCCC 60.153 63.158 24.59 24.59 0.00 3.85
3160 6596 1.526917 CGGTGATGGCAAGGGATCC 60.527 63.158 1.92 1.92 0.00 3.36
3161 6597 0.815615 GACGGTGATGGCAAGGGATC 60.816 60.000 0.00 0.00 0.00 3.36
3162 6598 1.224592 GACGGTGATGGCAAGGGAT 59.775 57.895 0.00 0.00 0.00 3.85
3163 6599 1.561769 ATGACGGTGATGGCAAGGGA 61.562 55.000 0.00 0.00 0.00 4.20
3164 6600 1.077501 ATGACGGTGATGGCAAGGG 60.078 57.895 0.00 0.00 0.00 3.95
3165 6601 1.097547 GGATGACGGTGATGGCAAGG 61.098 60.000 0.00 0.00 0.00 3.61
3166 6602 1.097547 GGGATGACGGTGATGGCAAG 61.098 60.000 0.00 0.00 0.00 4.01
3167 6603 1.077787 GGGATGACGGTGATGGCAA 60.078 57.895 0.00 0.00 0.00 4.52
3168 6604 2.589540 GGGATGACGGTGATGGCA 59.410 61.111 0.00 0.00 0.00 4.92
3169 6605 2.203209 GGGGATGACGGTGATGGC 60.203 66.667 0.00 0.00 0.00 4.40
3170 6606 2.510906 GGGGGATGACGGTGATGG 59.489 66.667 0.00 0.00 0.00 3.51
3187 6623 2.935481 TGGAGTGGCAGAAGGGGG 60.935 66.667 0.00 0.00 0.00 5.40
3188 6624 2.352805 GTGGAGTGGCAGAAGGGG 59.647 66.667 0.00 0.00 0.00 4.79
3189 6625 2.352805 GGTGGAGTGGCAGAAGGG 59.647 66.667 0.00 0.00 0.00 3.95
3190 6626 2.352805 GGGTGGAGTGGCAGAAGG 59.647 66.667 0.00 0.00 0.00 3.46
3191 6627 2.190488 GAGGGGTGGAGTGGCAGAAG 62.190 65.000 0.00 0.00 0.00 2.85
3192 6628 2.121963 AGGGGTGGAGTGGCAGAA 60.122 61.111 0.00 0.00 0.00 3.02
3193 6629 2.607750 GAGGGGTGGAGTGGCAGA 60.608 66.667 0.00 0.00 0.00 4.26
3194 6630 3.721706 GGAGGGGTGGAGTGGCAG 61.722 72.222 0.00 0.00 0.00 4.85
3195 6631 4.270153 AGGAGGGGTGGAGTGGCA 62.270 66.667 0.00 0.00 0.00 4.92
3196 6632 3.403558 GAGGAGGGGTGGAGTGGC 61.404 72.222 0.00 0.00 0.00 5.01
3197 6633 2.122729 TGAGGAGGGGTGGAGTGG 59.877 66.667 0.00 0.00 0.00 4.00
3198 6634 2.294078 GGTGAGGAGGGGTGGAGTG 61.294 68.421 0.00 0.00 0.00 3.51
3199 6635 2.122954 GGTGAGGAGGGGTGGAGT 59.877 66.667 0.00 0.00 0.00 3.85
3200 6636 2.689034 GGGTGAGGAGGGGTGGAG 60.689 72.222 0.00 0.00 0.00 3.86
3201 6637 2.892702 ATGGGTGAGGAGGGGTGGA 61.893 63.158 0.00 0.00 0.00 4.02
3202 6638 2.286425 ATGGGTGAGGAGGGGTGG 60.286 66.667 0.00 0.00 0.00 4.61
3203 6639 0.990282 ATCATGGGTGAGGAGGGGTG 60.990 60.000 0.00 0.00 37.87 4.61
3204 6640 0.990282 CATCATGGGTGAGGAGGGGT 60.990 60.000 0.00 0.00 38.38 4.95
3205 6641 0.695462 TCATCATGGGTGAGGAGGGG 60.695 60.000 0.00 0.00 39.98 4.79
3206 6642 0.471617 GTCATCATGGGTGAGGAGGG 59.528 60.000 0.00 0.00 44.88 4.30
3207 6643 0.471617 GGTCATCATGGGTGAGGAGG 59.528 60.000 0.00 0.00 44.88 4.30
3208 6644 0.471617 GGGTCATCATGGGTGAGGAG 59.528 60.000 0.00 0.00 44.88 3.69
3209 6645 0.253113 TGGGTCATCATGGGTGAGGA 60.253 55.000 0.00 0.00 42.36 3.71
3210 6646 0.107017 GTGGGTCATCATGGGTGAGG 60.107 60.000 0.00 0.00 37.87 3.86
3211 6647 0.620030 TGTGGGTCATCATGGGTGAG 59.380 55.000 0.00 0.00 37.87 3.51
3212 6648 1.004628 CTTGTGGGTCATCATGGGTGA 59.995 52.381 0.00 0.00 39.04 4.02
3213 6649 1.466856 CTTGTGGGTCATCATGGGTG 58.533 55.000 0.00 0.00 0.00 4.61
3214 6650 3.985410 CTTGTGGGTCATCATGGGT 57.015 52.632 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.