Multiple sequence alignment - TraesCS3A01G398900

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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 TraesCS3A01G398900 chr3A 100.000 5764 0 0 1 5764 645642269 645636506 0.000000e+00 10645.0
1 TraesCS3A01G398900 chr3A 86.457 731 63 13 5070 5764 477707461 477706731 0.000000e+00 769.0
2 TraesCS3A01G398900 chr3A 81.137 721 94 25 5069 5764 405939502 405940205 1.830000e-149 540.0
3 TraesCS3A01G398900 chr3A 88.679 53 4 2 1750 1801 160673041 160672990 4.820000e-06 63.9
4 TraesCS3A01G398900 chr3D 90.129 3171 145 61 1807 4877 508082853 508079751 0.000000e+00 3967.0
5 TraesCS3A01G398900 chr3D 90.533 1257 74 27 1 1244 508084639 508083415 0.000000e+00 1620.0
6 TraesCS3A01G398900 chr3D 90.581 499 39 3 1272 1766 508083349 508082855 0.000000e+00 654.0
7 TraesCS3A01G398900 chr3B 91.224 1732 101 28 1799 3508 670026097 670024395 0.000000e+00 2309.0
8 TraesCS3A01G398900 chr3B 93.660 1388 58 9 3594 4964 670024353 670022979 0.000000e+00 2049.0
9 TraesCS3A01G398900 chr3B 88.046 1054 57 35 156 1174 670027721 670026702 0.000000e+00 1184.0
10 TraesCS3A01G398900 chr3B 90.086 464 39 3 1305 1763 670026561 670026100 3.840000e-166 595.0
11 TraesCS3A01G398900 chr3B 92.708 96 7 0 4 99 670027822 670027727 7.790000e-29 139.0
12 TraesCS3A01G398900 chr4D 86.889 839 74 17 4961 5764 488180819 488179982 0.000000e+00 907.0
13 TraesCS3A01G398900 chr4D 81.373 102 14 4 4963 5062 131037050 131037148 1.720000e-10 78.7
14 TraesCS3A01G398900 chr5D 89.554 718 54 8 5067 5764 404490923 404491639 0.000000e+00 891.0
15 TraesCS3A01G398900 chr5D 84.803 862 74 26 4960 5764 397229894 397229033 0.000000e+00 813.0
16 TraesCS3A01G398900 chr5D 77.255 255 21 14 4963 5182 105097028 105096776 1.310000e-21 115.0
17 TraesCS3A01G398900 chr7A 89.710 690 58 7 5071 5748 54819473 54820161 0.000000e+00 869.0
18 TraesCS3A01G398900 chr7A 84.314 102 15 1 4961 5062 118333671 118333771 1.320000e-16 99.0
19 TraesCS3A01G398900 chr7A 93.333 45 3 0 1757 1801 19955415 19955459 3.730000e-07 67.6
20 TraesCS3A01G398900 chr6D 85.325 845 85 20 4956 5764 467017654 467016813 0.000000e+00 837.0
21 TraesCS3A01G398900 chr6D 86.027 730 65 12 5070 5764 355864955 355864228 0.000000e+00 749.0
22 TraesCS3A01G398900 chr6D 84.511 736 75 13 5067 5764 443750189 443749455 0.000000e+00 691.0
23 TraesCS3A01G398900 chr7D 85.134 861 71 20 4961 5764 552266874 552267734 0.000000e+00 828.0
24 TraesCS3A01G398900 chr7D 79.646 113 20 2 4963 5075 44707338 44707447 1.720000e-10 78.7
25 TraesCS3A01G398900 chr2A 87.465 710 73 9 5070 5764 594993892 594993184 0.000000e+00 804.0
26 TraesCS3A01G398900 chr2A 80.180 111 18 2 4963 5073 680553829 680553723 4.790000e-11 80.5
27 TraesCS3A01G398900 chr2D 82.361 703 61 28 5067 5732 633597103 633596427 2.350000e-153 553.0
28 TraesCS3A01G398900 chr2D 89.091 110 10 2 5070 5177 14633468 14633577 1.010000e-27 135.0
29 TraesCS3A01G398900 chr4B 80.000 720 100 27 5067 5744 468002951 468003668 5.190000e-135 492.0
30 TraesCS3A01G398900 chr1D 79.804 713 106 21 5070 5747 362783814 362783105 8.680000e-133 484.0
31 TraesCS3A01G398900 chr2B 79.146 609 94 15 5070 5646 730560132 730559525 1.950000e-104 390.0
32 TraesCS3A01G398900 chr5B 92.857 70 4 1 5070 5139 262277349 262277281 3.680000e-17 100.0
33 TraesCS3A01G398900 chr7B 95.455 44 2 0 1758 1801 544587755 544587798 2.880000e-08 71.3
34 TraesCS3A01G398900 chr7B 95.455 44 1 1 1759 1801 187166080 187166037 1.040000e-07 69.4
35 TraesCS3A01G398900 chr7B 95.455 44 1 1 1759 1801 621709385 621709428 1.040000e-07 69.4
36 TraesCS3A01G398900 chr1B 97.619 42 0 1 1760 1801 42056490 42056530 2.880000e-08 71.3
37 TraesCS3A01G398900 chr6B 95.455 44 1 1 1759 1801 545118990 545119033 1.040000e-07 69.4
38 TraesCS3A01G398900 chr5A 90.385 52 2 3 1756 1806 644112500 644112451 1.340000e-06 65.8
39 TraesCS3A01G398900 chr4A 94.872 39 0 2 1758 1796 626547382 626547346 6.240000e-05 60.2


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 TraesCS3A01G398900 chr3A 645636506 645642269 5763 True 10645.000000 10645 100.000000 1 5764 1 chr3A.!!$R3 5763
1 TraesCS3A01G398900 chr3A 477706731 477707461 730 True 769.000000 769 86.457000 5070 5764 1 chr3A.!!$R2 694
2 TraesCS3A01G398900 chr3A 405939502 405940205 703 False 540.000000 540 81.137000 5069 5764 1 chr3A.!!$F1 695
3 TraesCS3A01G398900 chr3D 508079751 508084639 4888 True 2080.333333 3967 90.414333 1 4877 3 chr3D.!!$R1 4876
4 TraesCS3A01G398900 chr3B 670022979 670027822 4843 True 1255.200000 2309 91.144800 4 4964 5 chr3B.!!$R1 4960
5 TraesCS3A01G398900 chr4D 488179982 488180819 837 True 907.000000 907 86.889000 4961 5764 1 chr4D.!!$R1 803
6 TraesCS3A01G398900 chr5D 404490923 404491639 716 False 891.000000 891 89.554000 5067 5764 1 chr5D.!!$F1 697
7 TraesCS3A01G398900 chr5D 397229033 397229894 861 True 813.000000 813 84.803000 4960 5764 1 chr5D.!!$R2 804
8 TraesCS3A01G398900 chr7A 54819473 54820161 688 False 869.000000 869 89.710000 5071 5748 1 chr7A.!!$F2 677
9 TraesCS3A01G398900 chr6D 467016813 467017654 841 True 837.000000 837 85.325000 4956 5764 1 chr6D.!!$R3 808
10 TraesCS3A01G398900 chr6D 355864228 355864955 727 True 749.000000 749 86.027000 5070 5764 1 chr6D.!!$R1 694
11 TraesCS3A01G398900 chr6D 443749455 443750189 734 True 691.000000 691 84.511000 5067 5764 1 chr6D.!!$R2 697
12 TraesCS3A01G398900 chr7D 552266874 552267734 860 False 828.000000 828 85.134000 4961 5764 1 chr7D.!!$F2 803
13 TraesCS3A01G398900 chr2A 594993184 594993892 708 True 804.000000 804 87.465000 5070 5764 1 chr2A.!!$R1 694
14 TraesCS3A01G398900 chr2D 633596427 633597103 676 True 553.000000 553 82.361000 5067 5732 1 chr2D.!!$R1 665
15 TraesCS3A01G398900 chr4B 468002951 468003668 717 False 492.000000 492 80.000000 5067 5744 1 chr4B.!!$F1 677
16 TraesCS3A01G398900 chr1D 362783105 362783814 709 True 484.000000 484 79.804000 5070 5747 1 chr1D.!!$R1 677
17 TraesCS3A01G398900 chr2B 730559525 730560132 607 True 390.000000 390 79.146000 5070 5646 1 chr2B.!!$R1 576

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
469 488 0.036010 ACTGAATCACCAGCTTCCCG 60.036 55.0 0.00 0.00 37.68 5.14 F
763 796 0.106708 ACACATGGATTCGGATCGGG 59.893 55.0 0.00 0.00 32.84 5.14 F
767 800 0.178932 ATGGATTCGGATCGGGGAGA 60.179 55.0 0.00 0.00 32.84 3.71 F
1427 1564 0.250295 TCAAGAAGGCCTTCACCACG 60.250 55.0 39.84 24.71 41.84 4.94 F
2993 3180 0.248094 GCACGATCGATCACGTCTGA 60.248 55.0 24.34 0.00 40.76 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1530 1671 0.107410 TTTCTCCAACACACGTGCCT 60.107 50.0 17.22 0.0 0.00 4.75 R
2740 2895 0.106149 AACGGAAAGACGAGCCAAGT 59.894 50.0 0.00 0.0 37.61 3.16 R
2757 2912 0.884704 ATGCACGGGTGAGTGTCAAC 60.885 55.0 2.38 0.0 43.61 3.18 R
3116 3303 0.034380 TACTGGTCTCTGTCGGGAGG 60.034 60.0 0.00 0.0 34.39 4.30 R
4947 5218 0.026803 GCTCTTATCGTTGCGCCTTG 59.973 55.0 4.18 0.0 0.00 3.61 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
35 37 2.123939 TGGGCCACACCAGTGTTG 60.124 61.111 0.00 0.00 44.39 3.33
70 72 6.861065 TTTAGTTGGTTTTGAGAGCTACTG 57.139 37.500 0.00 0.00 35.40 2.74
88 90 6.490040 AGCTACTGAAAAAGGCTGATAAACAA 59.510 34.615 0.00 0.00 31.68 2.83
135 138 1.747444 TTCAGGAGGGCTTCTTTCCT 58.253 50.000 0.00 0.00 41.97 3.36
137 140 1.688211 AGGAGGGCTTCTTTCCTGC 59.312 57.895 0.00 0.00 39.80 4.85
138 141 1.379176 GGAGGGCTTCTTTCCTGCC 60.379 63.158 0.00 0.00 45.42 4.85
198 201 3.067040 GGTAAACTTGTTGCCGGAAGAAA 59.933 43.478 5.05 0.00 0.00 2.52
202 205 0.316841 TTGTTGCCGGAAGAAATGCC 59.683 50.000 5.05 0.00 0.00 4.40
215 218 4.931661 AGAAATGCCAACCATGATCATC 57.068 40.909 4.86 0.00 33.49 2.92
294 297 1.755161 GCATGAGCATTTGAGCGATG 58.245 50.000 0.00 0.00 41.58 3.84
295 298 1.332686 GCATGAGCATTTGAGCGATGA 59.667 47.619 0.00 0.00 41.58 2.92
320 338 3.751175 TGCACATGAAGCTAGTTACCAAC 59.249 43.478 14.16 0.00 0.00 3.77
404 422 1.450848 CCACCAGCACGAGCATGAT 60.451 57.895 7.77 0.00 45.49 2.45
423 442 0.327924 TCGGAATCATTGCCCACTGT 59.672 50.000 0.00 0.00 0.00 3.55
445 464 0.543749 AACCCCTCAGATGCTACTGC 59.456 55.000 5.98 0.00 37.75 4.40
459 478 3.253188 TGCTACTGCCAAAACTGAATCAC 59.747 43.478 0.00 0.00 38.71 3.06
469 488 0.036010 ACTGAATCACCAGCTTCCCG 60.036 55.000 0.00 0.00 37.68 5.14
566 585 0.456824 CCATATCTGCCCGATCGACG 60.457 60.000 18.66 7.27 42.18 5.12
613 632 0.893727 CACGCCAGCTAAAACCCCTT 60.894 55.000 0.00 0.00 0.00 3.95
615 634 1.283905 ACGCCAGCTAAAACCCCTTAT 59.716 47.619 0.00 0.00 0.00 1.73
616 635 1.676006 CGCCAGCTAAAACCCCTTATG 59.324 52.381 0.00 0.00 0.00 1.90
617 636 2.735151 GCCAGCTAAAACCCCTTATGT 58.265 47.619 0.00 0.00 0.00 2.29
618 637 2.688446 GCCAGCTAAAACCCCTTATGTC 59.312 50.000 0.00 0.00 0.00 3.06
619 638 3.624959 GCCAGCTAAAACCCCTTATGTCT 60.625 47.826 0.00 0.00 0.00 3.41
649 668 1.535833 CTGTGGACTCCTCGTGTAGT 58.464 55.000 0.00 0.00 0.00 2.73
656 675 4.141892 TGGACTCCTCGTGTAGTTTTCAAA 60.142 41.667 0.00 0.00 0.00 2.69
658 677 5.469084 GGACTCCTCGTGTAGTTTTCAAATT 59.531 40.000 0.00 0.00 0.00 1.82
664 697 9.887406 TCCTCGTGTAGTTTTCAAATTTATTTC 57.113 29.630 0.00 0.00 0.00 2.17
699 732 2.870372 GCCGCAGCCTTACAGTTG 59.130 61.111 0.00 0.00 0.00 3.16
711 744 0.579630 TACAGTTGAGTTTGTGCGCG 59.420 50.000 0.00 0.00 0.00 6.86
759 792 3.208594 CACATCACACATGGATTCGGAT 58.791 45.455 0.00 0.00 0.00 4.18
760 793 3.249320 CACATCACACATGGATTCGGATC 59.751 47.826 0.00 0.00 0.00 3.36
761 794 2.223537 TCACACATGGATTCGGATCG 57.776 50.000 0.00 0.00 32.84 3.69
762 795 1.202521 TCACACATGGATTCGGATCGG 60.203 52.381 0.00 0.00 32.84 4.18
763 796 0.106708 ACACATGGATTCGGATCGGG 59.893 55.000 0.00 0.00 32.84 5.14
767 800 0.178932 ATGGATTCGGATCGGGGAGA 60.179 55.000 0.00 0.00 32.84 3.71
779 812 1.490490 TCGGGGAGATCCAATTCCAAG 59.510 52.381 0.47 0.00 37.91 3.61
830 863 2.820767 AAGGCGTACGAGAGCAGTGC 62.821 60.000 21.65 7.13 34.54 4.40
831 864 2.179517 GCGTACGAGAGCAGTGCT 59.820 61.111 19.86 19.86 43.88 4.40
986 1020 1.117150 GTATAAGACGGCCACCTCCA 58.883 55.000 2.24 0.00 0.00 3.86
1029 1063 4.899239 CCGGAGAGCGGGTGCATC 62.899 72.222 0.00 0.00 46.23 3.91
1030 1064 3.842923 CGGAGAGCGGGTGCATCT 61.843 66.667 0.00 0.00 46.23 2.90
1077 1112 1.271379 TGAAGCATCAGCAAGGCTTTG 59.729 47.619 11.51 3.80 47.00 2.77
1081 1116 2.086869 GCATCAGCAAGGCTTTGTAGA 58.913 47.619 10.54 8.73 36.40 2.59
1082 1117 2.159462 GCATCAGCAAGGCTTTGTAGAC 60.159 50.000 10.54 0.00 36.40 2.59
1116 1151 3.157087 CAAACAAGGTATGGCTGGACTT 58.843 45.455 0.00 0.00 0.00 3.01
1117 1152 3.525800 AACAAGGTATGGCTGGACTTT 57.474 42.857 0.00 0.00 0.00 2.66
1118 1153 2.795329 ACAAGGTATGGCTGGACTTTG 58.205 47.619 7.10 7.10 38.30 2.77
1119 1154 1.474077 CAAGGTATGGCTGGACTTTGC 59.526 52.381 0.00 0.00 0.00 3.68
1120 1155 0.995024 AGGTATGGCTGGACTTTGCT 59.005 50.000 0.00 0.00 0.00 3.91
1121 1156 1.065126 AGGTATGGCTGGACTTTGCTC 60.065 52.381 0.00 0.00 0.00 4.26
1139 1174 4.234550 TGCTCCATGTATCTACCATCCTT 58.765 43.478 0.00 0.00 0.00 3.36
1143 1178 4.284490 TCCATGTATCTACCATCCTTCTGC 59.716 45.833 0.00 0.00 0.00 4.26
1146 1181 5.074746 TGTATCTACCATCCTTCTGCCTA 57.925 43.478 0.00 0.00 0.00 3.93
1151 1186 3.356529 ACCATCCTTCTGCCTAGTTTG 57.643 47.619 0.00 0.00 0.00 2.93
1166 1258 6.150474 TGCCTAGTTTGTATTAGGAAACAAGC 59.850 38.462 1.86 0.00 39.02 4.01
1171 1263 8.549338 AGTTTGTATTAGGAAACAAGCTAGTC 57.451 34.615 3.22 0.00 42.85 2.59
1179 1271 3.514309 GGAAACAAGCTAGTCCTGAGGTA 59.486 47.826 0.00 0.00 0.00 3.08
1184 1276 5.306394 ACAAGCTAGTCCTGAGGTAAAAAC 58.694 41.667 0.00 0.00 0.00 2.43
1218 1314 7.563188 CCCTTGTATAGAGTAGGCATCAGATAT 59.437 40.741 0.00 0.00 0.00 1.63
1229 1325 6.905067 AGGCATCAGATATATGATTTCCCT 57.095 37.500 18.06 16.05 37.84 4.20
1260 1356 8.771920 TTTGTGTATCAATAGTTCGATTCAGT 57.228 30.769 0.00 0.00 35.84 3.41
1261 1357 9.863845 TTTGTGTATCAATAGTTCGATTCAGTA 57.136 29.630 0.00 0.00 35.84 2.74
1262 1358 8.851960 TGTGTATCAATAGTTCGATTCAGTAC 57.148 34.615 0.00 0.00 0.00 2.73
1264 1360 7.919091 GTGTATCAATAGTTCGATTCAGTACCA 59.081 37.037 0.00 0.00 0.00 3.25
1265 1361 7.919091 TGTATCAATAGTTCGATTCAGTACCAC 59.081 37.037 0.00 0.00 0.00 4.16
1283 1417 5.097742 ACCACTACTTAGCATGCATGTTA 57.902 39.130 26.79 22.46 0.00 2.41
1293 1427 5.196341 AGCATGCATGTTATCCAATCTTG 57.804 39.130 26.79 0.00 0.00 3.02
1303 1437 6.841119 TGTTATCCAATCTTGTTCATGTTCG 58.159 36.000 0.00 0.00 0.00 3.95
1312 1446 5.224135 TCTTGTTCATGTTCGTTGATCGTA 58.776 37.500 0.00 0.00 40.80 3.43
1327 1461 6.355638 GTTGATCGTAGTTGAGTTCTTGTTG 58.644 40.000 0.00 0.00 0.00 3.33
1329 1463 6.046593 TGATCGTAGTTGAGTTCTTGTTGTT 58.953 36.000 0.00 0.00 0.00 2.83
1330 1464 5.961395 TCGTAGTTGAGTTCTTGTTGTTC 57.039 39.130 0.00 0.00 0.00 3.18
1340 1474 5.291971 AGTTCTTGTTGTTCATGGAATTGC 58.708 37.500 0.00 0.00 0.00 3.56
1353 1490 1.152483 AATTGCTGCAGGGGTGTGT 60.152 52.632 17.12 0.00 0.00 3.72
1354 1491 1.466025 AATTGCTGCAGGGGTGTGTG 61.466 55.000 17.12 0.00 0.00 3.82
1362 1499 1.385347 AGGGGTGTGTGTGGGAGAA 60.385 57.895 0.00 0.00 0.00 2.87
1406 1543 4.827087 AGCGGCTGGATCACTGCG 62.827 66.667 0.00 0.00 44.16 5.18
1427 1564 0.250295 TCAAGAAGGCCTTCACCACG 60.250 55.000 39.84 24.71 41.84 4.94
1429 1566 0.250338 AAGAAGGCCTTCACCACGAC 60.250 55.000 39.84 17.16 41.84 4.34
1502 1643 7.936496 AAAATGTGTTTTTCCCACTTGAAAT 57.064 28.000 0.00 0.00 33.89 2.17
1506 1647 5.175127 GTGTTTTTCCCACTTGAAATGTGT 58.825 37.500 0.00 0.00 40.09 3.72
1513 1654 4.825085 TCCCACTTGAAATGTGTAAAGGTC 59.175 41.667 0.00 0.00 40.09 3.85
1530 1671 9.621629 TGTAAAGGTCATCAGAGAAAACTAAAA 57.378 29.630 0.00 0.00 0.00 1.52
1584 1725 0.752658 ACCCAAACTCAAGCTTTGCC 59.247 50.000 0.00 0.00 0.00 4.52
1586 1727 0.752054 CCAAACTCAAGCTTTGCCCA 59.248 50.000 0.00 0.00 0.00 5.36
1643 1784 0.390340 ACAGGTGCAGCAGTATCGTG 60.390 55.000 19.63 8.08 0.00 4.35
1671 1813 4.367039 AATACACAGCCCTGTACAAAGT 57.633 40.909 0.00 0.00 42.83 2.66
1693 1835 6.231211 AGTCACTTTATCCTGTTCGTTGATT 58.769 36.000 0.00 0.00 0.00 2.57
1699 1841 1.262950 TCCTGTTCGTTGATTTGCACG 59.737 47.619 0.00 0.00 0.00 5.34
1703 1845 2.608090 TGTTCGTTGATTTGCACGTGTA 59.392 40.909 18.38 10.46 0.00 2.90
1706 1848 2.473609 TCGTTGATTTGCACGTGTAGTC 59.526 45.455 18.38 14.60 0.00 2.59
1753 1896 3.872182 TCACATTTTCCGTTCTTTCGTGA 59.128 39.130 0.00 0.00 0.00 4.35
1766 1909 6.561717 CGTTCTTTCGTGAAGTTTTCTACTCC 60.562 42.308 2.24 0.00 35.54 3.85
1767 1910 5.295152 TCTTTCGTGAAGTTTTCTACTCCC 58.705 41.667 2.24 0.00 35.54 4.30
1768 1911 4.950205 TTCGTGAAGTTTTCTACTCCCT 57.050 40.909 0.00 0.00 35.54 4.20
1769 1912 4.516365 TCGTGAAGTTTTCTACTCCCTC 57.484 45.455 0.00 0.00 35.54 4.30
1770 1913 3.257624 TCGTGAAGTTTTCTACTCCCTCC 59.742 47.826 0.00 0.00 35.54 4.30
1771 1914 3.006537 CGTGAAGTTTTCTACTCCCTCCA 59.993 47.826 0.00 0.00 35.54 3.86
1772 1915 4.322801 CGTGAAGTTTTCTACTCCCTCCAT 60.323 45.833 0.00 0.00 35.54 3.41
1773 1916 5.179533 GTGAAGTTTTCTACTCCCTCCATC 58.820 45.833 0.00 0.00 35.54 3.51
1774 1917 4.225267 TGAAGTTTTCTACTCCCTCCATCC 59.775 45.833 0.00 0.00 35.54 3.51
1775 1918 3.116174 AGTTTTCTACTCCCTCCATCCC 58.884 50.000 0.00 0.00 28.23 3.85
1776 1919 2.844348 GTTTTCTACTCCCTCCATCCCA 59.156 50.000 0.00 0.00 0.00 4.37
1777 1920 3.438131 TTTCTACTCCCTCCATCCCAT 57.562 47.619 0.00 0.00 0.00 4.00
1778 1921 4.569676 TTTCTACTCCCTCCATCCCATA 57.430 45.455 0.00 0.00 0.00 2.74
1779 1922 4.569676 TTCTACTCCCTCCATCCCATAA 57.430 45.455 0.00 0.00 0.00 1.90
1780 1923 4.785173 TCTACTCCCTCCATCCCATAAT 57.215 45.455 0.00 0.00 0.00 1.28
1781 1924 5.896530 TCTACTCCCTCCATCCCATAATA 57.103 43.478 0.00 0.00 0.00 0.98
1782 1925 6.438111 TCTACTCCCTCCATCCCATAATAT 57.562 41.667 0.00 0.00 0.00 1.28
1783 1926 7.554597 TCTACTCCCTCCATCCCATAATATA 57.445 40.000 0.00 0.00 0.00 0.86
1784 1927 7.961940 TCTACTCCCTCCATCCCATAATATAA 58.038 38.462 0.00 0.00 0.00 0.98
1785 1928 8.068110 TCTACTCCCTCCATCCCATAATATAAG 58.932 40.741 0.00 0.00 0.00 1.73
1786 1929 6.826727 ACTCCCTCCATCCCATAATATAAGA 58.173 40.000 0.00 0.00 0.00 2.10
1787 1930 7.263901 ACTCCCTCCATCCCATAATATAAGAA 58.736 38.462 0.00 0.00 0.00 2.52
1788 1931 7.914407 ACTCCCTCCATCCCATAATATAAGAAT 59.086 37.037 0.00 0.00 0.00 2.40
1789 1932 8.106017 TCCCTCCATCCCATAATATAAGAATG 57.894 38.462 0.00 0.00 0.00 2.67
1790 1933 7.688534 TCCCTCCATCCCATAATATAAGAATGT 59.311 37.037 0.00 0.00 0.00 2.71
1791 1934 8.339247 CCCTCCATCCCATAATATAAGAATGTT 58.661 37.037 0.00 0.00 0.00 2.71
1792 1935 9.401058 CCTCCATCCCATAATATAAGAATGTTC 57.599 37.037 0.00 0.00 0.00 3.18
1839 1982 7.168219 AGCAGTGGAAGAATTTTACATGTAGA 58.832 34.615 5.56 0.00 0.00 2.59
1947 2093 3.712907 GCAGCAGTACCGGGGGAA 61.713 66.667 6.32 0.00 0.00 3.97
2608 2763 2.509111 CGGTGCATGCAGACGCTA 60.509 61.111 23.41 0.00 39.64 4.26
2757 2912 1.901650 GCACTTGGCTCGTCTTTCCG 61.902 60.000 0.00 0.00 40.25 4.30
2762 2917 0.599204 TGGCTCGTCTTTCCGTTGAC 60.599 55.000 0.00 0.00 0.00 3.18
2763 2918 0.599204 GGCTCGTCTTTCCGTTGACA 60.599 55.000 0.00 0.00 33.18 3.58
2764 2919 0.507358 GCTCGTCTTTCCGTTGACAC 59.493 55.000 0.00 0.00 33.18 3.67
2766 2921 2.052157 CTCGTCTTTCCGTTGACACTC 58.948 52.381 0.00 0.00 33.18 3.51
2769 2930 1.865340 GTCTTTCCGTTGACACTCACC 59.135 52.381 0.00 0.00 33.75 4.02
2991 3178 0.248255 CAGCACGATCGATCACGTCT 60.248 55.000 24.34 13.68 40.76 4.18
2993 3180 0.248094 GCACGATCGATCACGTCTGA 60.248 55.000 24.34 0.00 40.76 3.27
3001 3188 4.639135 TCGATCACGTCTGAATCTGAAT 57.361 40.909 0.00 0.00 40.69 2.57
3025 3212 2.159114 TGAAACAAGCAAAAGGGACAGC 60.159 45.455 0.00 0.00 0.00 4.40
3073 3260 4.441079 GCGGGAGTAGTTACAGCAGATTAA 60.441 45.833 0.00 0.00 0.00 1.40
3074 3261 5.739358 GCGGGAGTAGTTACAGCAGATTAAT 60.739 44.000 0.00 0.00 0.00 1.40
3075 3262 6.516194 GCGGGAGTAGTTACAGCAGATTAATA 60.516 42.308 0.00 0.00 0.00 0.98
3076 3263 7.603651 CGGGAGTAGTTACAGCAGATTAATAT 58.396 38.462 0.00 0.00 0.00 1.28
3077 3264 8.088981 CGGGAGTAGTTACAGCAGATTAATATT 58.911 37.037 0.00 0.00 0.00 1.28
3114 3301 3.181462 CGAACATCTCTTCCATCCATCCA 60.181 47.826 0.00 0.00 0.00 3.41
3115 3302 4.504514 CGAACATCTCTTCCATCCATCCAT 60.505 45.833 0.00 0.00 0.00 3.41
3116 3303 4.637387 ACATCTCTTCCATCCATCCATC 57.363 45.455 0.00 0.00 0.00 3.51
3117 3304 3.330110 ACATCTCTTCCATCCATCCATCC 59.670 47.826 0.00 0.00 0.00 3.51
3195 3405 2.165845 AGTGAGCGAGCTACCGTATTTT 59.834 45.455 0.00 0.00 0.00 1.82
3251 3463 3.141398 GTTGGAATGTGTCTTCTCTGCA 58.859 45.455 0.00 0.00 0.00 4.41
3258 3470 1.342819 GTGTCTTCTCTGCACCTGTCT 59.657 52.381 0.00 0.00 0.00 3.41
3274 3486 3.733960 CTGGTCGGTCTCGCACGA 61.734 66.667 0.00 0.00 36.68 4.35
3283 3495 0.708918 GTCTCGCACGAGCTGTTTAC 59.291 55.000 15.04 3.61 41.71 2.01
3384 3597 7.138736 ACGTGTAGGTGATGAAAATTTTCTTG 58.861 34.615 26.73 11.21 38.02 3.02
3401 3614 0.726827 TTGTGCTTCGATTCGATGGC 59.273 50.000 19.65 19.97 35.23 4.40
3418 3631 1.883084 GCGTCGATGGGCCAACTAG 60.883 63.158 11.89 2.03 0.00 2.57
3420 3633 0.249073 CGTCGATGGGCCAACTAGAG 60.249 60.000 11.89 0.00 0.00 2.43
3421 3634 0.530870 GTCGATGGGCCAACTAGAGC 60.531 60.000 11.89 0.00 0.00 4.09
3455 3672 4.142687 ACGTTTTTCTTTGTCAGAGGTGTG 60.143 41.667 0.00 0.00 31.12 3.82
3462 3679 0.464036 TGTCAGAGGTGTGGTGTCAC 59.536 55.000 0.00 0.00 43.87 3.67
3470 3687 0.098728 GTGTGGTGTCACTGTGTTGC 59.901 55.000 7.79 0.76 43.94 4.17
3490 3707 3.194755 TGCTTATCTGAAACTAGGCGTGA 59.805 43.478 0.00 0.00 0.00 4.35
3522 3747 6.104665 GTCAGTAGGTACTTGGATGGTTTAC 58.895 44.000 0.00 0.00 41.75 2.01
3529 3754 7.336396 AGGTACTTGGATGGTTTACTATGTTC 58.664 38.462 0.00 0.00 27.25 3.18
3545 3770 1.421268 TGTTCTCCCTGCACTTGTCAT 59.579 47.619 0.00 0.00 0.00 3.06
3546 3771 2.637382 TGTTCTCCCTGCACTTGTCATA 59.363 45.455 0.00 0.00 0.00 2.15
3547 3772 3.072330 TGTTCTCCCTGCACTTGTCATAA 59.928 43.478 0.00 0.00 0.00 1.90
3550 3775 3.776969 TCTCCCTGCACTTGTCATAATCT 59.223 43.478 0.00 0.00 0.00 2.40
3551 3776 4.962362 TCTCCCTGCACTTGTCATAATCTA 59.038 41.667 0.00 0.00 0.00 1.98
3553 3778 4.716784 TCCCTGCACTTGTCATAATCTAGT 59.283 41.667 0.00 0.00 0.00 2.57
3555 3780 5.525378 CCCTGCACTTGTCATAATCTAGTTC 59.475 44.000 0.00 0.00 0.00 3.01
3557 3782 6.820656 CCTGCACTTGTCATAATCTAGTTCTT 59.179 38.462 0.00 0.00 0.00 2.52
3559 3784 8.621532 TGCACTTGTCATAATCTAGTTCTTTT 57.378 30.769 0.00 0.00 0.00 2.27
3626 3867 4.549458 CCTGATTTGTTCATGTTGGTGTC 58.451 43.478 0.00 0.00 32.72 3.67
3837 4078 2.298629 CGCGAGATGACCATGAGCG 61.299 63.158 0.00 8.22 40.14 5.03
3976 4217 3.503363 GCACCGCCAGATGAGCAC 61.503 66.667 0.00 0.00 0.00 4.40
4046 4287 1.521681 GGCCTACTACAAGCAGCCG 60.522 63.158 0.00 0.00 0.00 5.52
4604 4862 1.851053 CTCTGTCGATCTTGCATGTCG 59.149 52.381 14.16 14.16 36.75 4.35
4675 4933 1.581447 CTGCTGGTTTCCCTTTCGC 59.419 57.895 0.00 0.00 0.00 4.70
4767 5028 6.000891 ACATACTGTAGTTTGTGTGCATTG 57.999 37.500 7.21 0.00 38.46 2.82
4806 5067 2.535984 CGTGTCCTTGTCATAAGATCGC 59.464 50.000 0.00 0.00 0.00 4.58
4828 5089 2.224475 CCATGGTGGAAAATTTGTGCCA 60.224 45.455 2.57 0.00 40.96 4.92
4829 5090 3.559597 CCATGGTGGAAAATTTGTGCCAT 60.560 43.478 2.57 9.75 40.96 4.40
4831 5092 2.437281 TGGTGGAAAATTTGTGCCATGT 59.563 40.909 9.93 0.00 32.26 3.21
4853 5114 1.710013 TCGCCTGTCTCGACAAAATC 58.290 50.000 1.02 0.00 41.33 2.17
4871 5132 1.464734 TCTCATCAGACGTCTCACCC 58.535 55.000 16.96 0.00 0.00 4.61
4878 5139 1.070786 GACGTCTCACCCTTTGCCA 59.929 57.895 8.70 0.00 0.00 4.92
4890 5151 2.038659 CCTTTGCCAACCCTCTTTCAA 58.961 47.619 0.00 0.00 0.00 2.69
4906 5172 5.424757 TCTTTCAAGTTGTTCTTCCGAGAA 58.575 37.500 2.11 0.00 39.54 2.87
4926 5197 1.200716 ACAATGTCAGCAATCAAGGCG 59.799 47.619 0.00 0.00 36.08 5.52
4931 5202 2.358615 AGCAATCAAGGCGCGACA 60.359 55.556 17.71 0.00 36.08 4.35
4932 5203 1.746615 AGCAATCAAGGCGCGACAT 60.747 52.632 17.71 0.00 36.08 3.06
4948 5219 3.157727 CATCGGCTGATGGTGAACA 57.842 52.632 25.35 0.00 46.76 3.18
4989 5260 2.279120 CAACAGCGGCGCCAAAAA 60.279 55.556 30.40 0.00 0.00 1.94
5021 5293 3.805971 GCGGTAAACTGTCACTTTAGTGT 59.194 43.478 9.53 0.00 45.76 3.55
5024 5296 4.573201 GGTAAACTGTCACTTTAGTGTGCA 59.427 41.667 9.53 9.00 45.76 4.57
5062 5334 2.252260 CAGCGGTGGCAGAAAACG 59.748 61.111 6.74 0.00 43.41 3.60
5064 5336 1.302511 AGCGGTGGCAGAAAACGAT 60.303 52.632 0.00 0.00 43.41 3.73
5065 5337 0.889186 AGCGGTGGCAGAAAACGATT 60.889 50.000 0.00 0.00 43.41 3.34
5507 5880 0.397675 ATCACCGAGGAGGATGAGCA 60.398 55.000 0.00 0.00 45.00 4.26
5748 6130 2.371179 ACCAGCGAGGATGATGATGATT 59.629 45.455 5.19 0.00 41.22 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 72 5.572896 CGGATGTTGTTTATCAGCCTTTTTC 59.427 40.000 0.00 0.00 37.89 2.29
198 201 2.353357 ACGATGATCATGGTTGGCAT 57.647 45.000 16.73 0.00 0.00 4.40
215 218 3.073678 TGATGATGGTTCACTTCCAACG 58.926 45.455 0.00 0.00 38.52 4.10
286 289 1.011333 CATGTGCATGTCATCGCTCA 58.989 50.000 11.64 11.64 36.22 4.26
287 290 1.292992 TCATGTGCATGTCATCGCTC 58.707 50.000 11.38 5.89 39.72 5.03
288 291 1.669265 CTTCATGTGCATGTCATCGCT 59.331 47.619 11.38 0.00 39.72 4.93
289 292 1.858798 GCTTCATGTGCATGTCATCGC 60.859 52.381 11.38 5.51 39.72 4.58
290 293 1.669265 AGCTTCATGTGCATGTCATCG 59.331 47.619 11.38 0.00 39.72 3.84
291 294 3.875727 ACTAGCTTCATGTGCATGTCATC 59.124 43.478 11.38 1.69 39.72 2.92
292 295 3.882444 ACTAGCTTCATGTGCATGTCAT 58.118 40.909 11.38 0.00 39.72 3.06
293 296 3.339253 ACTAGCTTCATGTGCATGTCA 57.661 42.857 11.38 0.00 39.72 3.58
294 297 4.034510 GGTAACTAGCTTCATGTGCATGTC 59.965 45.833 11.38 3.73 39.72 3.06
295 298 3.941483 GGTAACTAGCTTCATGTGCATGT 59.059 43.478 11.38 9.55 39.72 3.21
357 375 1.382522 TCCGAAGCCTGATCATTTGC 58.617 50.000 0.00 0.00 0.00 3.68
404 422 0.327924 ACAGTGGGCAATGATTCCGA 59.672 50.000 0.00 0.00 0.00 4.55
423 442 2.237143 CAGTAGCATCTGAGGGGTTTCA 59.763 50.000 2.61 0.00 37.61 2.69
445 464 3.305608 GGAAGCTGGTGATTCAGTTTTGG 60.306 47.826 0.00 0.00 40.08 3.28
459 478 0.529992 GTAACGATCCGGGAAGCTGG 60.530 60.000 0.00 0.00 0.00 4.85
575 594 0.908198 GAGAGTGAGGGTTCAGGCAT 59.092 55.000 0.00 0.00 32.98 4.40
613 632 3.402110 CACAGGAAGTTGTGCAGACATA 58.598 45.455 0.00 0.00 41.65 2.29
615 634 1.667236 CACAGGAAGTTGTGCAGACA 58.333 50.000 0.00 0.00 41.65 3.41
616 635 0.947244 CCACAGGAAGTTGTGCAGAC 59.053 55.000 0.00 0.00 45.52 3.51
617 636 0.836606 TCCACAGGAAGTTGTGCAGA 59.163 50.000 0.00 0.00 45.52 4.26
618 637 0.947244 GTCCACAGGAAGTTGTGCAG 59.053 55.000 0.00 0.00 45.52 4.41
619 638 0.546122 AGTCCACAGGAAGTTGTGCA 59.454 50.000 0.76 0.00 45.52 4.57
649 668 8.083462 GGTCGGTACAGGAAATAAATTTGAAAA 58.917 33.333 0.00 0.00 0.00 2.29
656 675 4.945543 GGTTGGTCGGTACAGGAAATAAAT 59.054 41.667 0.00 0.00 0.00 1.40
658 677 3.617045 CGGTTGGTCGGTACAGGAAATAA 60.617 47.826 0.00 0.00 0.00 1.40
664 697 2.263540 CCGGTTGGTCGGTACAGG 59.736 66.667 0.00 0.00 44.60 4.00
683 716 0.320771 ACTCAACTGTAAGGCTGCGG 60.321 55.000 0.00 0.00 39.30 5.69
699 732 2.427410 CTTGCCGCGCACAAACTC 60.427 61.111 8.75 0.00 38.71 3.01
759 792 1.490490 CTTGGAATTGGATCTCCCCGA 59.510 52.381 0.00 0.00 34.29 5.14
760 793 1.477558 CCTTGGAATTGGATCTCCCCG 60.478 57.143 0.00 0.00 34.29 5.73
761 794 1.852965 TCCTTGGAATTGGATCTCCCC 59.147 52.381 0.00 0.00 34.29 4.81
762 795 3.139025 TCATCCTTGGAATTGGATCTCCC 59.861 47.826 0.00 0.00 40.76 4.30
763 796 4.443978 TCATCCTTGGAATTGGATCTCC 57.556 45.455 0.00 0.00 40.76 3.71
767 800 7.071273 ACATACATTCATCCTTGGAATTGGAT 58.929 34.615 0.00 0.00 43.23 3.41
779 812 7.148255 TGCTGTACTTCAAACATACATTCATCC 60.148 37.037 0.00 0.00 0.00 3.51
830 863 0.829990 GCTTTCAGGAGGAGGAGGAG 59.170 60.000 0.00 0.00 0.00 3.69
831 864 0.618968 GGCTTTCAGGAGGAGGAGGA 60.619 60.000 0.00 0.00 0.00 3.71
832 865 1.911471 GGCTTTCAGGAGGAGGAGG 59.089 63.158 0.00 0.00 0.00 4.30
833 866 1.261238 ACGGCTTTCAGGAGGAGGAG 61.261 60.000 0.00 0.00 0.00 3.69
834 867 1.229209 ACGGCTTTCAGGAGGAGGA 60.229 57.895 0.00 0.00 0.00 3.71
835 868 1.078848 CACGGCTTTCAGGAGGAGG 60.079 63.158 0.00 0.00 0.00 4.30
986 1020 1.551452 CAACTCTCTCTTCCTCCGGT 58.449 55.000 0.00 0.00 0.00 5.28
992 1026 2.235155 GGTCCTTCCAACTCTCTCTTCC 59.765 54.545 0.00 0.00 35.97 3.46
1028 1062 1.475280 GCATCTCATGGCAGCAAAAGA 59.525 47.619 0.00 0.00 0.00 2.52
1029 1063 1.476891 AGCATCTCATGGCAGCAAAAG 59.523 47.619 0.00 0.00 0.00 2.27
1030 1064 1.552578 AGCATCTCATGGCAGCAAAA 58.447 45.000 0.00 0.00 0.00 2.44
1073 1108 1.726853 CTTCCCCTGCGTCTACAAAG 58.273 55.000 0.00 0.00 0.00 2.77
1077 1112 1.142097 GAGCTTCCCCTGCGTCTAC 59.858 63.158 0.00 0.00 35.28 2.59
1081 1116 1.600916 GTTTGAGCTTCCCCTGCGT 60.601 57.895 0.00 0.00 35.28 5.24
1082 1117 1.172180 TTGTTTGAGCTTCCCCTGCG 61.172 55.000 0.00 0.00 35.28 5.18
1116 1151 4.234550 AGGATGGTAGATACATGGAGCAA 58.765 43.478 0.00 0.00 0.00 3.91
1117 1152 3.861846 AGGATGGTAGATACATGGAGCA 58.138 45.455 0.00 0.00 0.00 4.26
1118 1153 4.530161 AGAAGGATGGTAGATACATGGAGC 59.470 45.833 0.00 0.00 0.00 4.70
1119 1154 5.568423 GCAGAAGGATGGTAGATACATGGAG 60.568 48.000 0.00 0.00 0.00 3.86
1120 1155 4.284490 GCAGAAGGATGGTAGATACATGGA 59.716 45.833 0.00 0.00 0.00 3.41
1121 1156 4.564406 GGCAGAAGGATGGTAGATACATGG 60.564 50.000 0.00 0.00 0.00 3.66
1139 1174 7.011499 TGTTTCCTAATACAAACTAGGCAGA 57.989 36.000 0.00 0.00 35.57 4.26
1143 1178 7.923414 AGCTTGTTTCCTAATACAAACTAGG 57.077 36.000 0.00 0.00 36.47 3.02
1146 1181 7.606839 GGACTAGCTTGTTTCCTAATACAAACT 59.393 37.037 1.43 0.00 35.52 2.66
1151 1186 6.875076 TCAGGACTAGCTTGTTTCCTAATAC 58.125 40.000 7.97 0.00 36.26 1.89
1166 1258 4.695928 GCCAAGTTTTTACCTCAGGACTAG 59.304 45.833 0.00 0.00 0.00 2.57
1171 1263 2.296190 GTGGCCAAGTTTTTACCTCAGG 59.704 50.000 7.24 0.00 0.00 3.86
1179 1271 1.578897 ACAAGGGTGGCCAAGTTTTT 58.421 45.000 7.24 0.00 0.00 1.94
1184 1276 2.505819 ACTCTATACAAGGGTGGCCAAG 59.494 50.000 7.24 0.00 37.60 3.61
1244 1340 7.481642 AGTAGTGGTACTGAATCGAACTATTG 58.518 38.462 0.00 0.00 38.14 1.90
1245 1341 7.642082 AGTAGTGGTACTGAATCGAACTATT 57.358 36.000 0.00 0.00 38.14 1.73
1248 1344 5.979288 AAGTAGTGGTACTGAATCGAACT 57.021 39.130 0.00 0.00 39.60 3.01
1249 1345 5.742926 GCTAAGTAGTGGTACTGAATCGAAC 59.257 44.000 0.00 0.00 39.60 3.95
1250 1346 5.416639 TGCTAAGTAGTGGTACTGAATCGAA 59.583 40.000 0.00 0.00 39.60 3.71
1252 1348 5.244785 TGCTAAGTAGTGGTACTGAATCG 57.755 43.478 0.00 0.00 39.60 3.34
1253 1349 5.463724 GCATGCTAAGTAGTGGTACTGAATC 59.536 44.000 11.37 0.00 39.60 2.52
1254 1350 5.104941 TGCATGCTAAGTAGTGGTACTGAAT 60.105 40.000 20.33 0.00 39.60 2.57
1255 1351 4.221924 TGCATGCTAAGTAGTGGTACTGAA 59.778 41.667 20.33 0.00 39.60 3.02
1256 1352 3.767131 TGCATGCTAAGTAGTGGTACTGA 59.233 43.478 20.33 0.00 39.60 3.41
1257 1353 4.123497 TGCATGCTAAGTAGTGGTACTG 57.877 45.455 20.33 0.00 39.60 2.74
1258 1354 4.162320 ACATGCATGCTAAGTAGTGGTACT 59.838 41.667 26.53 0.00 41.61 2.73
1260 1356 4.753516 ACATGCATGCTAAGTAGTGGTA 57.246 40.909 26.53 0.00 0.00 3.25
1261 1357 3.634397 ACATGCATGCTAAGTAGTGGT 57.366 42.857 26.53 0.00 0.00 4.16
1262 1358 5.180117 GGATAACATGCATGCTAAGTAGTGG 59.820 44.000 26.53 0.00 0.00 4.00
1264 1360 5.928976 TGGATAACATGCATGCTAAGTAGT 58.071 37.500 26.53 3.20 0.00 2.73
1265 1361 6.866010 TTGGATAACATGCATGCTAAGTAG 57.134 37.500 26.53 0.29 0.00 2.57
1283 1417 5.473162 TCAACGAACATGAACAAGATTGGAT 59.527 36.000 0.00 0.00 0.00 3.41
1293 1427 5.118050 TCAACTACGATCAACGAACATGAAC 59.882 40.000 0.00 0.00 45.77 3.18
1303 1437 6.018994 ACAACAAGAACTCAACTACGATCAAC 60.019 38.462 0.00 0.00 0.00 3.18
1312 1446 5.192927 TCCATGAACAACAAGAACTCAACT 58.807 37.500 0.00 0.00 0.00 3.16
1327 1461 1.134907 CCCTGCAGCAATTCCATGAAC 60.135 52.381 8.66 0.00 0.00 3.18
1329 1463 0.685131 CCCCTGCAGCAATTCCATGA 60.685 55.000 8.66 0.00 0.00 3.07
1330 1464 0.974010 ACCCCTGCAGCAATTCCATG 60.974 55.000 8.66 0.00 0.00 3.66
1340 1474 2.595463 CCACACACACCCCTGCAG 60.595 66.667 6.78 6.78 0.00 4.41
1353 1490 5.500234 CATCTCCTTAACATTTCTCCCACA 58.500 41.667 0.00 0.00 0.00 4.17
1354 1491 4.884164 CCATCTCCTTAACATTTCTCCCAC 59.116 45.833 0.00 0.00 0.00 4.61
1362 1499 4.591321 TCTTGCCCATCTCCTTAACATT 57.409 40.909 0.00 0.00 0.00 2.71
1406 1543 0.250901 TGGTGAAGGCCTTCTTGAGC 60.251 55.000 38.38 29.22 40.14 4.26
1427 1564 2.035783 GGCTTGTCCTTGGGGGTC 59.964 66.667 0.00 0.00 36.25 4.46
1429 1566 1.908299 GTTGGCTTGTCCTTGGGGG 60.908 63.158 0.00 0.00 35.26 5.40
1502 1643 6.591935 AGTTTTCTCTGATGACCTTTACACA 58.408 36.000 0.00 0.00 0.00 3.72
1506 1647 9.284968 CCTTTTAGTTTTCTCTGATGACCTTTA 57.715 33.333 0.00 0.00 0.00 1.85
1513 1654 5.049405 ACGTGCCTTTTAGTTTTCTCTGATG 60.049 40.000 0.00 0.00 0.00 3.07
1530 1671 0.107410 TTTCTCCAACACACGTGCCT 60.107 50.000 17.22 0.00 0.00 4.75
1643 1784 0.676782 AGGGCTGTGTATTTGTCGCC 60.677 55.000 0.00 0.00 36.83 5.54
1671 1813 6.567701 GCAAATCAACGAACAGGATAAAGTGA 60.568 38.462 0.00 0.00 0.00 3.41
1693 1835 5.994887 AAAAATACAGACTACACGTGCAA 57.005 34.783 17.22 2.85 0.00 4.08
1753 1896 3.523972 GGGATGGAGGGAGTAGAAAACTT 59.476 47.826 0.00 0.00 39.07 2.66
1766 1909 9.401058 GAACATTCTTATATTATGGGATGGAGG 57.599 37.037 0.00 0.00 0.00 4.30
1795 1938 8.995220 CCACTGCTAAAACTTGTATTAAGTGTA 58.005 33.333 0.00 0.00 31.58 2.90
1796 1939 7.717875 TCCACTGCTAAAACTTGTATTAAGTGT 59.282 33.333 0.00 0.00 31.58 3.55
1797 1940 8.094798 TCCACTGCTAAAACTTGTATTAAGTG 57.905 34.615 0.00 0.00 0.00 3.16
1803 1946 8.409358 AATTCTTCCACTGCTAAAACTTGTAT 57.591 30.769 0.00 0.00 0.00 2.29
1839 1982 4.332819 CGCTCAGTTATCTTCCCGAAAATT 59.667 41.667 0.00 0.00 0.00 1.82
1947 2093 2.048127 GCTTCTTGTCCCTCGCGT 60.048 61.111 5.77 0.00 0.00 6.01
2038 2184 1.500108 GGATCTTCTCGATGCTGCTG 58.500 55.000 0.00 0.00 37.48 4.41
2233 2385 4.933563 TGCCGCTGCTGCTTGTCA 62.934 61.111 16.81 3.34 38.71 3.58
2401 2556 1.369091 CCCGTGTTCTGGTATGCTGC 61.369 60.000 0.00 0.00 0.00 5.25
2402 2557 1.369091 GCCCGTGTTCTGGTATGCTG 61.369 60.000 0.00 0.00 0.00 4.41
2403 2558 1.078426 GCCCGTGTTCTGGTATGCT 60.078 57.895 0.00 0.00 0.00 3.79
2735 2890 0.886490 AAAGACGAGCCAAGTGCCTG 60.886 55.000 0.00 0.00 42.71 4.85
2738 2893 1.869690 GGAAAGACGAGCCAAGTGC 59.130 57.895 0.00 0.00 41.71 4.40
2739 2894 0.600255 ACGGAAAGACGAGCCAAGTG 60.600 55.000 0.00 0.00 37.61 3.16
2740 2895 0.106149 AACGGAAAGACGAGCCAAGT 59.894 50.000 0.00 0.00 37.61 3.16
2746 2901 2.052157 GAGTGTCAACGGAAAGACGAG 58.948 52.381 0.00 0.00 37.58 4.18
2757 2912 0.884704 ATGCACGGGTGAGTGTCAAC 60.885 55.000 2.38 0.00 43.61 3.18
2762 2917 2.042259 ATGCATGCACGGGTGAGTG 61.042 57.895 25.37 1.63 44.47 3.51
2763 2918 2.042259 CATGCATGCACGGGTGAGT 61.042 57.895 25.37 0.38 0.00 3.41
2764 2919 2.042259 ACATGCATGCACGGGTGAG 61.042 57.895 25.37 9.38 0.00 3.51
2766 2921 2.179767 CACATGCATGCACGGGTG 59.820 61.111 25.37 25.28 0.00 4.61
2769 2930 1.910216 TTCGTCACATGCATGCACGG 61.910 55.000 34.09 20.51 37.73 4.94
2813 2992 2.357517 CAGGCTGTCGTCCCACAC 60.358 66.667 6.28 0.00 0.00 3.82
2847 3026 4.117661 GCTTCGTCCTCGCGTCCT 62.118 66.667 5.77 0.00 36.96 3.85
2960 3147 4.514066 TCGATCGTGCTGTGTGTATACTAT 59.486 41.667 15.94 0.00 0.00 2.12
2963 3150 3.060978 TCGATCGTGCTGTGTGTATAC 57.939 47.619 15.94 0.00 0.00 1.47
2991 3178 6.638096 TGCTTGTTTCAGAATTCAGATTCA 57.362 33.333 8.44 5.03 43.35 2.57
2993 3180 7.440255 CCTTTTGCTTGTTTCAGAATTCAGATT 59.560 33.333 8.44 0.00 0.00 2.40
3001 3188 3.766591 TGTCCCTTTTGCTTGTTTCAGAA 59.233 39.130 0.00 0.00 0.00 3.02
3025 3212 4.093556 GCTTGACTGACGGAAGGAATTAAG 59.906 45.833 0.00 0.00 0.00 1.85
3027 3214 3.007506 TGCTTGACTGACGGAAGGAATTA 59.992 43.478 0.00 0.00 0.00 1.40
3073 3260 1.887198 CGGTCACCCTCTCGCTAATAT 59.113 52.381 0.00 0.00 0.00 1.28
3074 3261 1.134007 TCGGTCACCCTCTCGCTAATA 60.134 52.381 0.00 0.00 0.00 0.98
3075 3262 0.395311 TCGGTCACCCTCTCGCTAAT 60.395 55.000 0.00 0.00 0.00 1.73
3076 3263 0.609957 TTCGGTCACCCTCTCGCTAA 60.610 55.000 0.00 0.00 0.00 3.09
3077 3264 1.001764 TTCGGTCACCCTCTCGCTA 60.002 57.895 0.00 0.00 0.00 4.26
3078 3265 2.282958 TTCGGTCACCCTCTCGCT 60.283 61.111 0.00 0.00 0.00 4.93
3093 3280 4.428294 TGGATGGATGGAAGAGATGTTC 57.572 45.455 0.00 0.00 0.00 3.18
3114 3301 0.396417 CTGGTCTCTGTCGGGAGGAT 60.396 60.000 0.00 0.00 34.39 3.24
3115 3302 1.000771 CTGGTCTCTGTCGGGAGGA 60.001 63.158 0.00 0.00 34.39 3.71
3116 3303 0.034380 TACTGGTCTCTGTCGGGAGG 60.034 60.000 0.00 0.00 34.39 4.30
3117 3304 1.384525 CTACTGGTCTCTGTCGGGAG 58.615 60.000 0.00 0.00 34.88 4.30
3166 3376 2.003196 AGCTCGCTCACTAGCTTTTC 57.997 50.000 0.00 0.00 46.82 2.29
3176 3386 2.953466 AAAATACGGTAGCTCGCTCA 57.047 45.000 0.00 0.00 0.00 4.26
3204 3414 2.260844 ACAATGACACCACACCTCTG 57.739 50.000 0.00 0.00 0.00 3.35
3206 3416 1.608590 CCAACAATGACACCACACCTC 59.391 52.381 0.00 0.00 0.00 3.85
3213 3425 2.554032 CCAACTCTCCAACAATGACACC 59.446 50.000 0.00 0.00 0.00 4.16
3258 3470 3.733960 CTCGTGCGAGACCGACCA 61.734 66.667 15.65 0.00 44.53 4.02
3329 3541 0.911769 TGATTCGTCCAAGCATCCCT 59.088 50.000 0.00 0.00 0.00 4.20
3330 3542 1.972872 ATGATTCGTCCAAGCATCCC 58.027 50.000 0.00 0.00 36.28 3.85
3384 3597 1.273887 CGCCATCGAATCGAAGCAC 59.726 57.895 23.89 9.54 39.99 4.40
3401 3614 0.249073 CTCTAGTTGGCCCATCGACG 60.249 60.000 0.00 0.00 0.00 5.12
3416 3629 1.037493 ACGTTGACAGTGTGGCTCTA 58.963 50.000 0.00 0.00 0.00 2.43
3418 3631 1.014352 AAACGTTGACAGTGTGGCTC 58.986 50.000 0.00 0.00 0.00 4.70
3420 3633 2.159435 AGAAAAACGTTGACAGTGTGGC 60.159 45.455 0.00 0.00 0.00 5.01
3421 3634 3.757745 AGAAAAACGTTGACAGTGTGG 57.242 42.857 0.00 0.00 0.00 4.17
3455 3672 3.187227 CAGATAAGCAACACAGTGACACC 59.813 47.826 7.81 0.00 0.00 4.16
3462 3679 5.163814 GCCTAGTTTCAGATAAGCAACACAG 60.164 44.000 0.00 0.00 0.00 3.66
3470 3687 5.352284 ACATCACGCCTAGTTTCAGATAAG 58.648 41.667 0.00 0.00 0.00 1.73
3490 3707 4.321750 CCAAGTACCTACTGACAACGACAT 60.322 45.833 0.00 0.00 36.50 3.06
3522 3747 3.265791 GACAAGTGCAGGGAGAACATAG 58.734 50.000 0.00 0.00 0.00 2.23
3529 3754 4.148128 AGATTATGACAAGTGCAGGGAG 57.852 45.455 0.00 0.00 0.00 4.30
3607 3848 4.520492 AGAGGACACCAACATGAACAAATC 59.480 41.667 0.00 0.00 0.00 2.17
3626 3867 1.746615 CCATCCACGTGCCAAGAGG 60.747 63.158 10.91 3.51 38.23 3.69
3837 4078 1.153647 TGGACATCGGCGTCATCAC 60.154 57.895 6.85 0.00 37.66 3.06
4024 4265 0.525668 CTGCTTGTAGTAGGCCGACG 60.526 60.000 10.60 0.00 0.00 5.12
4604 4862 4.419522 ACCACTATCGTCAAACAAATGC 57.580 40.909 0.00 0.00 0.00 3.56
4609 4867 5.394224 TCACATACCACTATCGTCAAACA 57.606 39.130 0.00 0.00 0.00 2.83
4616 4874 5.041287 ACAACGAATCACATACCACTATCG 58.959 41.667 0.00 0.00 35.36 2.92
4622 4880 3.052455 AGCACAACGAATCACATACCA 57.948 42.857 0.00 0.00 0.00 3.25
4623 4881 3.426159 CCAAGCACAACGAATCACATACC 60.426 47.826 0.00 0.00 0.00 2.73
4626 4884 2.229792 ACCAAGCACAACGAATCACAT 58.770 42.857 0.00 0.00 0.00 3.21
4629 4887 3.003897 GGTAAACCAAGCACAACGAATCA 59.996 43.478 0.00 0.00 35.64 2.57
4630 4888 3.561503 GGTAAACCAAGCACAACGAATC 58.438 45.455 0.00 0.00 35.64 2.52
4675 4933 3.189010 AAAAACGGAAGGCCACGCG 62.189 57.895 5.01 3.53 0.00 6.01
4749 5010 3.988379 ACCAATGCACACAAACTACAG 57.012 42.857 0.00 0.00 0.00 2.74
4750 5011 4.824537 ACATACCAATGCACACAAACTACA 59.175 37.500 0.00 0.00 36.50 2.74
4751 5012 5.153513 CACATACCAATGCACACAAACTAC 58.846 41.667 0.00 0.00 36.50 2.73
4752 5013 4.824537 ACACATACCAATGCACACAAACTA 59.175 37.500 0.00 0.00 36.50 2.24
4753 5014 3.636300 ACACATACCAATGCACACAAACT 59.364 39.130 0.00 0.00 36.50 2.66
4767 5028 0.167251 CGCAAACCGGAACACATACC 59.833 55.000 9.46 0.00 0.00 2.73
4806 5067 2.425539 GCACAAATTTTCCACCATGGG 58.574 47.619 18.09 4.89 38.32 4.00
4828 5089 0.101399 GTCGAGACAGGCGATCACAT 59.899 55.000 0.00 0.00 40.19 3.21
4829 5090 1.241315 TGTCGAGACAGGCGATCACA 61.241 55.000 1.24 0.00 40.19 3.58
4831 5092 0.601057 TTTGTCGAGACAGGCGATCA 59.399 50.000 6.03 0.00 42.94 2.92
4853 5114 1.468985 AGGGTGAGACGTCTGATGAG 58.531 55.000 25.58 0.00 0.00 2.90
4871 5132 2.695147 ACTTGAAAGAGGGTTGGCAAAG 59.305 45.455 0.00 0.00 0.00 2.77
4878 5139 4.645136 GGAAGAACAACTTGAAAGAGGGTT 59.355 41.667 0.00 0.00 39.13 4.11
4906 5172 1.200716 CGCCTTGATTGCTGACATTGT 59.799 47.619 0.00 0.00 0.00 2.71
4907 5173 1.904144 CGCCTTGATTGCTGACATTG 58.096 50.000 0.00 0.00 0.00 2.82
4909 5175 1.805254 GCGCCTTGATTGCTGACAT 59.195 52.632 0.00 0.00 0.00 3.06
4910 5176 2.679934 CGCGCCTTGATTGCTGACA 61.680 57.895 0.00 0.00 0.00 3.58
4911 5177 2.099062 CGCGCCTTGATTGCTGAC 59.901 61.111 0.00 0.00 0.00 3.51
4912 5178 2.047370 TCGCGCCTTGATTGCTGA 60.047 55.556 0.00 0.00 0.00 4.26
4926 5197 2.202932 ACCATCAGCCGATGTCGC 60.203 61.111 9.05 0.00 46.54 5.19
4931 5202 1.679944 CCTTGTTCACCATCAGCCGAT 60.680 52.381 0.00 0.00 0.00 4.18
4932 5203 0.321564 CCTTGTTCACCATCAGCCGA 60.322 55.000 0.00 0.00 0.00 5.54
4945 5216 1.732259 CTCTTATCGTTGCGCCTTGTT 59.268 47.619 4.18 0.00 0.00 2.83
4946 5217 1.359848 CTCTTATCGTTGCGCCTTGT 58.640 50.000 4.18 0.00 0.00 3.16
4947 5218 0.026803 GCTCTTATCGTTGCGCCTTG 59.973 55.000 4.18 0.00 0.00 3.61
4948 5219 0.391130 TGCTCTTATCGTTGCGCCTT 60.391 50.000 4.18 0.00 0.00 4.35
4971 5242 2.775856 TTTTTGGCGCCGCTGTTGA 61.776 52.632 23.90 0.00 0.00 3.18
4995 5266 2.357760 TGACAGTTTACCGCGGCC 60.358 61.111 28.58 11.09 0.00 6.13
5021 5293 2.526993 CGTGAAAACGTCCCGTGCA 61.527 57.895 0.00 0.00 39.99 4.57
5024 5296 3.332409 CGCGTGAAAACGTCCCGT 61.332 61.111 0.00 0.00 43.97 5.28
5055 5327 2.202171 CGCGCGCAATCGTTTTCT 60.202 55.556 32.61 0.00 38.14 2.52
5398 5771 4.341783 GGCCTGCACCTGCTCACT 62.342 66.667 0.00 0.00 42.66 3.41
5422 5795 1.063616 CGTGATAAGACGAGGCGAAGA 59.936 52.381 0.00 0.00 42.10 2.87
5560 5935 1.601419 CGTCCTTTCCGCCCAGTAGA 61.601 60.000 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.