Multiple sequence alignment - TraesCS4B01G254000

Loading Multiple Alignment...

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 TraesCS4B01G254000 chr4B 100.000 4067 0 0 128 4194 519408858 519404792 0.000000e+00 7511.0
1 TraesCS4B01G254000 chr4B 100.000 41 0 0 1 41 519408985 519408945 4.500000e-10 76.8
2 TraesCS4B01G254000 chr4D 92.222 2957 124 43 797 3655 422552788 422549840 0.000000e+00 4089.0
3 TraesCS4B01G254000 chr4D 94.737 418 22 0 3777 4194 422549840 422549423 0.000000e+00 651.0
4 TraesCS4B01G254000 chr4D 74.457 599 110 28 1779 2363 421925654 421925085 7.060000e-53 219.0
5 TraesCS4B01G254000 chr4D 93.056 144 8 2 3649 3791 497646531 497646673 4.250000e-50 209.0
6 TraesCS4B01G254000 chr4D 89.130 46 3 2 2406 2450 108968424 108968380 5.860000e-04 56.5
7 TraesCS4B01G254000 chr4D 89.130 46 3 2 2406 2450 129250401 129250357 5.860000e-04 56.5
8 TraesCS4B01G254000 chr4D 89.130 46 3 2 2406 2450 136301896 136301940 5.860000e-04 56.5
9 TraesCS4B01G254000 chr4A 91.118 2477 119 45 794 3205 41915621 41918061 0.000000e+00 3262.0
10 TraesCS4B01G254000 chr4A 92.363 419 31 1 3777 4194 41918946 41919364 2.790000e-166 595.0
11 TraesCS4B01G254000 chr4A 92.241 348 24 3 3310 3655 41918600 41918946 1.360000e-134 490.0
12 TraesCS4B01G254000 chr4A 97.297 74 2 0 727 800 54635515 54635588 4.400000e-25 126.0
13 TraesCS4B01G254000 chr5D 100.000 600 0 0 128 727 398371563 398370964 0.000000e+00 1109.0
14 TraesCS4B01G254000 chr5D 97.525 202 3 2 137 336 203062055 203061854 1.120000e-90 344.0
15 TraesCS4B01G254000 chr5D 92.537 201 11 4 129 327 517441243 517441045 6.860000e-73 285.0
16 TraesCS4B01G254000 chr5D 97.458 118 2 1 610 726 398370755 398370638 2.560000e-47 200.0
17 TraesCS4B01G254000 chr5D 100.000 41 0 0 1 41 398371821 398371781 4.500000e-10 76.8
18 TraesCS4B01G254000 chr5D 95.122 41 2 0 1 41 203062103 203062063 9.730000e-07 65.8
19 TraesCS4B01G254000 chr1D 100.000 600 0 0 128 727 339297300 339297899 0.000000e+00 1109.0
20 TraesCS4B01G254000 chr1D 100.000 41 0 0 1 41 339297023 339297063 4.500000e-10 76.8
21 TraesCS4B01G254000 chr7D 97.512 201 4 1 128 328 115084122 115084321 4.020000e-90 342.0
22 TraesCS4B01G254000 chr7D 94.712 208 7 2 128 332 119581823 119581617 1.880000e-83 320.0
23 TraesCS4B01G254000 chr7D 100.000 38 0 0 1 38 115084067 115084104 2.090000e-08 71.3
24 TraesCS4B01G254000 chr3D 95.215 209 5 3 128 333 495686446 495686652 4.040000e-85 326.0
25 TraesCS4B01G254000 chr3D 96.947 131 4 0 3652 3782 67064911 67064781 1.960000e-53 220.0
26 TraesCS4B01G254000 chr3D 97.561 41 1 0 1 41 209467050 209467010 2.090000e-08 71.3
27 TraesCS4B01G254000 chr2B 94.301 193 8 1 128 317 405483010 405482818 4.100000e-75 292.0
28 TraesCS4B01G254000 chr2B 93.023 86 4 2 727 812 782101441 782101358 1.580000e-24 124.0
29 TraesCS4B01G254000 chr3B 93.846 195 9 1 128 319 92114039 92113845 1.480000e-74 291.0
30 TraesCS4B01G254000 chr3B 97.333 75 2 0 727 801 216206686 216206760 1.220000e-25 128.0
31 TraesCS4B01G254000 chr3B 97.436 39 1 0 3 41 92114113 92114075 2.710000e-07 67.6
32 TraesCS4B01G254000 chr3B 89.362 47 3 2 2405 2450 300798051 300798096 1.630000e-04 58.4
33 TraesCS4B01G254000 chr3A 96.992 133 4 0 3646 3778 371626718 371626586 1.520000e-54 224.0
34 TraesCS4B01G254000 chr3A 98.630 73 1 0 727 799 81089254 81089182 3.400000e-26 130.0
35 TraesCS4B01G254000 chr3A 98.630 73 1 0 727 799 697558248 697558320 3.400000e-26 130.0
36 TraesCS4B01G254000 chr1B 96.947 131 4 0 3651 3781 56893235 56893365 1.960000e-53 220.0
37 TraesCS4B01G254000 chr6B 96.241 133 5 0 3649 3781 707499652 707499520 7.060000e-53 219.0
38 TraesCS4B01G254000 chr6B 96.241 133 4 1 3651 3783 277700186 277700317 2.540000e-52 217.0
39 TraesCS4B01G254000 chr5B 94.286 140 6 2 3646 3785 563340640 563340503 3.280000e-51 213.0
40 TraesCS4B01G254000 chr5B 92.105 152 9 3 3643 3792 252323646 252323496 1.180000e-50 211.0
41 TraesCS4B01G254000 chrUn 94.574 129 7 0 3649 3777 36530674 36530802 2.560000e-47 200.0
42 TraesCS4B01G254000 chrUn 97.260 73 2 0 727 799 249144799 249144871 1.580000e-24 124.0
43 TraesCS4B01G254000 chr6A 97.297 74 2 0 727 800 276453971 276453898 4.400000e-25 126.0
44 TraesCS4B01G254000 chr6A 88.235 51 4 2 2406 2455 181253259 181253308 4.530000e-05 60.2
45 TraesCS4B01G254000 chr2D 97.297 74 2 0 727 800 515227964 515228037 4.400000e-25 126.0
46 TraesCS4B01G254000 chr2D 91.304 46 2 2 2406 2450 408978507 408978463 1.260000e-05 62.1
47 TraesCS4B01G254000 chr6D 97.260 73 2 0 727 799 35627028 35627100 1.580000e-24 124.0
48 TraesCS4B01G254000 chr1A 91.304 46 2 2 2406 2450 388288654 388288698 1.260000e-05 62.1
49 TraesCS4B01G254000 chr7A 90.909 44 2 2 2406 2448 558806642 558806600 1.630000e-04 58.4


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 TraesCS4B01G254000 chr4B 519404792 519408985 4193 True 3793.900000 7511 100.000000 1 4194 2 chr4B.!!$R1 4193
1 TraesCS4B01G254000 chr4D 422549423 422552788 3365 True 2370.000000 4089 93.479500 797 4194 2 chr4D.!!$R4 3397
2 TraesCS4B01G254000 chr4D 421925085 421925654 569 True 219.000000 219 74.457000 1779 2363 1 chr4D.!!$R3 584
3 TraesCS4B01G254000 chr4A 41915621 41919364 3743 False 1449.000000 3262 91.907333 794 4194 3 chr4A.!!$F2 3400
4 TraesCS4B01G254000 chr5D 398370638 398371821 1183 True 461.933333 1109 99.152667 1 727 3 chr5D.!!$R3 726
5 TraesCS4B01G254000 chr1D 339297023 339297899 876 False 592.900000 1109 100.000000 1 727 2 chr1D.!!$F1 726

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
991 1337 0.233848 CGAAACCCAAAACTCGACGG 59.766 55.0 0.0 0.0 33.13 4.79 F
1403 1761 0.447801 GACAATGCGTGCGGAAATCT 59.552 50.0 0.0 0.0 0.00 2.40 F
2423 2830 0.406750 TCAAGTACTCCCTCCGTCCA 59.593 55.0 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 2215 0.462047 CCCCTCATAGTGGCGTTGAC 60.462 60.0 0.00 0.0 0.00 3.18 R
3163 3576 1.107114 GGTCTTCGAGGAGAGATGCA 58.893 55.0 0.00 0.0 0.00 3.96 R
3755 4604 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 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
727 1060 1.610624 GGGCATGTGGACTTCTTTCGA 60.611 52.381 0.00 0.00 0.00 3.71
728 1061 1.464997 GGCATGTGGACTTCTTTCGAC 59.535 52.381 0.00 0.00 0.00 4.20
729 1062 2.417719 GCATGTGGACTTCTTTCGACT 58.582 47.619 0.00 0.00 0.00 4.18
730 1063 2.808543 GCATGTGGACTTCTTTCGACTT 59.191 45.455 0.00 0.00 0.00 3.01
731 1064 3.364366 GCATGTGGACTTCTTTCGACTTG 60.364 47.826 0.00 0.00 34.48 3.16
732 1065 3.536956 TGTGGACTTCTTTCGACTTGT 57.463 42.857 0.00 0.00 0.00 3.16
733 1066 4.659111 TGTGGACTTCTTTCGACTTGTA 57.341 40.909 0.00 0.00 0.00 2.41
734 1067 5.209818 TGTGGACTTCTTTCGACTTGTAT 57.790 39.130 0.00 0.00 0.00 2.29
735 1068 5.607477 TGTGGACTTCTTTCGACTTGTATT 58.393 37.500 0.00 0.00 0.00 1.89
736 1069 6.751157 TGTGGACTTCTTTCGACTTGTATTA 58.249 36.000 0.00 0.00 0.00 0.98
737 1070 6.866770 TGTGGACTTCTTTCGACTTGTATTAG 59.133 38.462 0.00 0.00 0.00 1.73
738 1071 6.310711 GTGGACTTCTTTCGACTTGTATTAGG 59.689 42.308 0.00 0.00 0.00 2.69
739 1072 6.014840 TGGACTTCTTTCGACTTGTATTAGGT 60.015 38.462 0.00 0.00 0.00 3.08
740 1073 6.872547 GGACTTCTTTCGACTTGTATTAGGTT 59.127 38.462 0.00 0.00 0.00 3.50
741 1074 7.148623 GGACTTCTTTCGACTTGTATTAGGTTG 60.149 40.741 0.00 0.00 0.00 3.77
742 1075 6.649557 ACTTCTTTCGACTTGTATTAGGTTGG 59.350 38.462 0.00 0.00 0.00 3.77
743 1076 6.105397 TCTTTCGACTTGTATTAGGTTGGT 57.895 37.500 0.00 0.00 0.00 3.67
744 1077 6.527423 TCTTTCGACTTGTATTAGGTTGGTT 58.473 36.000 0.00 0.00 0.00 3.67
745 1078 7.669427 TCTTTCGACTTGTATTAGGTTGGTTA 58.331 34.615 0.00 0.00 0.00 2.85
746 1079 8.149647 TCTTTCGACTTGTATTAGGTTGGTTAA 58.850 33.333 0.00 0.00 0.00 2.01
747 1080 8.674263 TTTCGACTTGTATTAGGTTGGTTAAA 57.326 30.769 0.00 0.00 0.00 1.52
748 1081 8.851541 TTCGACTTGTATTAGGTTGGTTAAAT 57.148 30.769 0.00 0.00 0.00 1.40
749 1082 8.851541 TCGACTTGTATTAGGTTGGTTAAATT 57.148 30.769 0.00 0.00 0.00 1.82
750 1083 8.723311 TCGACTTGTATTAGGTTGGTTAAATTG 58.277 33.333 0.00 0.00 0.00 2.32
751 1084 8.723311 CGACTTGTATTAGGTTGGTTAAATTGA 58.277 33.333 0.00 0.00 0.00 2.57
752 1085 9.836076 GACTTGTATTAGGTTGGTTAAATTGAC 57.164 33.333 0.00 0.00 0.00 3.18
753 1086 8.508875 ACTTGTATTAGGTTGGTTAAATTGACG 58.491 33.333 0.00 0.00 0.00 4.35
754 1087 8.618702 TTGTATTAGGTTGGTTAAATTGACGA 57.381 30.769 0.00 0.00 0.00 4.20
755 1088 8.031848 TGTATTAGGTTGGTTAAATTGACGAC 57.968 34.615 0.00 0.00 0.00 4.34
756 1089 5.945466 TTAGGTTGGTTAAATTGACGACC 57.055 39.130 0.00 4.64 0.00 4.79
757 1090 4.094830 AGGTTGGTTAAATTGACGACCT 57.905 40.909 8.18 8.18 32.66 3.85
758 1091 5.231702 AGGTTGGTTAAATTGACGACCTA 57.768 39.130 11.08 0.91 34.50 3.08
759 1092 5.243207 AGGTTGGTTAAATTGACGACCTAG 58.757 41.667 11.08 0.00 34.50 3.02
760 1093 4.393990 GGTTGGTTAAATTGACGACCTAGG 59.606 45.833 7.41 7.41 33.33 3.02
761 1094 5.240121 GTTGGTTAAATTGACGACCTAGGA 58.760 41.667 17.98 0.00 33.33 2.94
762 1095 5.080969 TGGTTAAATTGACGACCTAGGAG 57.919 43.478 17.98 11.62 33.33 3.69
763 1096 4.529377 TGGTTAAATTGACGACCTAGGAGT 59.471 41.667 17.98 15.04 33.33 3.85
764 1097 5.716228 TGGTTAAATTGACGACCTAGGAGTA 59.284 40.000 17.98 1.50 33.33 2.59
765 1098 6.038985 GGTTAAATTGACGACCTAGGAGTAC 58.961 44.000 17.98 7.89 0.00 2.73
766 1099 4.367386 AAATTGACGACCTAGGAGTACG 57.633 45.455 17.98 16.64 0.00 3.67
767 1100 1.089920 TTGACGACCTAGGAGTACGC 58.910 55.000 17.98 11.35 0.00 4.42
768 1101 1.086067 TGACGACCTAGGAGTACGCG 61.086 60.000 17.98 3.53 0.00 6.01
769 1102 2.327244 CGACCTAGGAGTACGCGC 59.673 66.667 17.98 0.00 0.00 6.86
770 1103 2.466982 CGACCTAGGAGTACGCGCA 61.467 63.158 17.98 0.00 0.00 6.09
771 1104 1.063811 GACCTAGGAGTACGCGCAC 59.936 63.158 17.98 2.54 0.00 5.34
773 1106 2.651232 CTAGGAGTACGCGCACGC 60.651 66.667 5.73 4.99 45.53 5.34
774 1107 4.183686 TAGGAGTACGCGCACGCC 62.184 66.667 22.99 22.99 45.53 5.68
779 1112 4.781959 GTACGCGCACGCCCTGTA 62.782 66.667 5.73 3.39 45.53 2.74
780 1113 4.053526 TACGCGCACGCCCTGTAA 62.054 61.111 5.73 0.00 45.53 2.41
781 1114 3.570621 TACGCGCACGCCCTGTAAA 62.571 57.895 5.73 0.00 45.53 2.01
782 1115 4.439472 CGCGCACGCCCTGTAAAC 62.439 66.667 8.75 0.00 37.98 2.01
783 1116 3.047877 GCGCACGCCCTGTAAACT 61.048 61.111 0.30 0.00 34.56 2.66
784 1117 2.860293 CGCACGCCCTGTAAACTG 59.140 61.111 0.00 0.00 0.00 3.16
785 1118 1.666553 CGCACGCCCTGTAAACTGA 60.667 57.895 0.00 0.00 0.00 3.41
786 1119 1.626654 CGCACGCCCTGTAAACTGAG 61.627 60.000 0.00 0.00 0.00 3.35
787 1120 0.320421 GCACGCCCTGTAAACTGAGA 60.320 55.000 0.00 0.00 0.00 3.27
788 1121 1.714794 CACGCCCTGTAAACTGAGAG 58.285 55.000 0.00 0.00 0.00 3.20
789 1122 1.272490 CACGCCCTGTAAACTGAGAGA 59.728 52.381 0.00 0.00 0.00 3.10
790 1123 1.546476 ACGCCCTGTAAACTGAGAGAG 59.454 52.381 0.00 0.00 0.00 3.20
791 1124 1.819288 CGCCCTGTAAACTGAGAGAGA 59.181 52.381 0.00 0.00 0.00 3.10
792 1125 2.159310 CGCCCTGTAAACTGAGAGAGAG 60.159 54.545 0.00 0.00 0.00 3.20
795 1128 4.601084 CCCTGTAAACTGAGAGAGAGGTA 58.399 47.826 0.00 0.00 0.00 3.08
893 1236 2.493501 GACCGCGTACCCTTCTCC 59.506 66.667 4.92 0.00 0.00 3.71
927 1270 4.918201 CGCCGCCTCCTTCCATCC 62.918 72.222 0.00 0.00 0.00 3.51
976 1322 2.716833 AAACCCCCGGCCAATCGAAA 62.717 55.000 2.24 0.00 0.00 3.46
991 1337 0.233848 CGAAACCCAAAACTCGACGG 59.766 55.000 0.00 0.00 33.13 4.79
1335 1693 2.635899 GTCGCGGATATCGACGGT 59.364 61.111 6.13 0.00 45.19 4.83
1403 1761 0.447801 GACAATGCGTGCGGAAATCT 59.552 50.000 0.00 0.00 0.00 2.40
1435 1794 2.754254 GGCGGCTTGTTTAGGGGG 60.754 66.667 0.00 0.00 0.00 5.40
1484 1843 1.274167 TCGGTCCTGTTGGTATGTCAC 59.726 52.381 0.00 0.00 34.23 3.67
1517 1877 4.712337 TGGTACACACATTTGGGAGTTTTT 59.288 37.500 0.00 0.00 0.00 1.94
1521 1881 2.437651 ACACATTTGGGAGTTTTTGGGG 59.562 45.455 0.00 0.00 0.00 4.96
1523 1883 1.064003 ATTTGGGAGTTTTTGGGGGC 58.936 50.000 0.00 0.00 0.00 5.80
1524 1884 1.403687 TTTGGGAGTTTTTGGGGGCG 61.404 55.000 0.00 0.00 0.00 6.13
1525 1885 2.203582 GGGAGTTTTTGGGGGCGT 60.204 61.111 0.00 0.00 0.00 5.68
1527 1887 1.404479 GGGAGTTTTTGGGGGCGTTT 61.404 55.000 0.00 0.00 0.00 3.60
1528 1888 1.330234 GGAGTTTTTGGGGGCGTTTA 58.670 50.000 0.00 0.00 0.00 2.01
1529 1889 1.000060 GGAGTTTTTGGGGGCGTTTAC 60.000 52.381 0.00 0.00 0.00 2.01
1530 1890 1.958579 GAGTTTTTGGGGGCGTTTACT 59.041 47.619 0.00 0.00 0.00 2.24
1533 1920 0.828343 TTTTGGGGGCGTTTACTGGG 60.828 55.000 0.00 0.00 0.00 4.45
1556 1944 2.111613 TGGATTGAGTTGGGGGTGAATT 59.888 45.455 0.00 0.00 0.00 2.17
1562 1950 5.205517 TGAGTTGGGGGTGAATTAATCAT 57.794 39.130 0.00 0.00 40.97 2.45
1595 1983 7.016153 TGTTAGATTGGGACATTTCTAGTGT 57.984 36.000 0.00 0.00 39.30 3.55
1673 2067 6.841229 TCATCCTGATTGTCTGAAGGTACTAT 59.159 38.462 0.00 0.00 38.49 2.12
1686 2080 8.350722 TCTGAAGGTACTATCATTACGATGAAC 58.649 37.037 0.00 0.00 41.75 3.18
1688 2082 6.010294 AGGTACTATCATTACGATGAACGG 57.990 41.667 0.00 0.00 44.96 4.44
1703 2097 4.085357 TGAACGGAATGCAATATAGCCT 57.915 40.909 0.00 0.00 0.00 4.58
1750 2144 6.400940 GGGACATTATTTGTGATTTTGTTGCG 60.401 38.462 0.00 0.00 39.18 4.85
1821 2215 1.503542 GTGGCCATGCAGAAAGACG 59.496 57.895 9.72 0.00 0.00 4.18
1845 2239 0.833834 CGCCACTATGAGGGGGATCT 60.834 60.000 0.00 0.00 39.88 2.75
1905 2299 3.625764 GCTTCTGGTTGACACACTTTACA 59.374 43.478 0.00 0.00 0.00 2.41
2031 2426 7.417570 CGCCTAAACTTTCCTCTATCTCCTTTA 60.418 40.741 0.00 0.00 0.00 1.85
2048 2443 6.384015 TCTCCTTTATGCCTCTCTTTGTCATA 59.616 38.462 0.00 0.00 0.00 2.15
2125 2523 6.287589 ACGAAGAGATTCATGTTCCTAAGT 57.712 37.500 0.00 0.00 0.00 2.24
2219 2622 8.088365 ACATTTTTGGTAAATTTCCTAGCACTC 58.912 33.333 0.00 0.00 0.00 3.51
2369 2776 5.357878 TGCTCTATCTGAAATTTCCGCATTT 59.642 36.000 15.48 0.00 0.00 2.32
2399 2806 6.015434 TGCACATACCTATCAACTATCATCGT 60.015 38.462 0.00 0.00 0.00 3.73
2400 2807 6.309009 GCACATACCTATCAACTATCATCGTG 59.691 42.308 0.00 0.00 0.00 4.35
2423 2830 0.406750 TCAAGTACTCCCTCCGTCCA 59.593 55.000 0.00 0.00 0.00 4.02
2444 2851 2.159627 AGAATTACTTGCCGCTCAAACG 59.840 45.455 0.00 0.00 33.65 3.60
2458 2865 5.806286 CGCTCAAACGGATGTATGTAATTT 58.194 37.500 0.00 0.00 0.00 1.82
2463 2870 6.764085 TCAAACGGATGTATGTAATTTCGGAT 59.236 34.615 0.00 0.00 0.00 4.18
2710 3123 3.942130 AAAAGGTTGGAGCTTATGTGC 57.058 42.857 0.00 0.00 34.42 4.57
2786 3199 2.027285 TCAGTTATTGCTGCTGCCTGTA 60.027 45.455 13.47 0.69 38.71 2.74
2847 3260 8.487848 TCGTCCTTGGGTAAGATTAATCAAATA 58.512 33.333 17.56 5.11 35.92 1.40
2878 3291 8.849168 TGAATTATCGAATCCACATTATGCTTT 58.151 29.630 0.00 0.00 0.00 3.51
2881 3294 3.066621 TCGAATCCACATTATGCTTTGCC 59.933 43.478 0.00 0.00 0.00 4.52
2963 3376 2.071778 AGGTCTCTGATCTCAGGAGC 57.928 55.000 7.33 11.79 43.91 4.70
3148 3561 1.141665 CGTGTCGATGATGGCCTCA 59.858 57.895 3.32 5.76 38.53 3.86
3151 3564 0.977627 TGTCGATGATGGCCTCACCT 60.978 55.000 3.32 0.00 40.22 4.00
3153 3566 0.977627 TCGATGATGGCCTCACCTGT 60.978 55.000 3.32 0.00 40.22 4.00
3163 3576 2.239907 GGCCTCACCTGTAGAAATTCCT 59.760 50.000 0.00 0.00 34.51 3.36
3176 3589 2.906691 AATTCCTGCATCTCTCCTCG 57.093 50.000 0.00 0.00 0.00 4.63
3241 3670 3.990318 GGAGCGGATCCCTTATTTTTG 57.010 47.619 6.06 0.00 43.01 2.44
3243 3672 3.288092 GAGCGGATCCCTTATTTTTGGT 58.712 45.455 6.06 0.00 0.00 3.67
3245 3674 2.481276 GCGGATCCCTTATTTTTGGTGC 60.481 50.000 6.06 0.00 0.00 5.01
3249 3678 5.178061 GGATCCCTTATTTTTGGTGCAAAG 58.822 41.667 0.00 0.00 34.72 2.77
3253 3682 3.558958 CCTTATTTTTGGTGCAAAGGGGG 60.559 47.826 2.19 0.00 34.72 5.40
3260 3689 2.695585 TGGTGCAAAGGGGGTTAAAAT 58.304 42.857 0.00 0.00 0.00 1.82
3273 4095 4.322650 GGGGTTAAAATGCTGATTTGCTCA 60.323 41.667 0.00 0.00 31.83 4.26
3274 4096 5.422145 GGGTTAAAATGCTGATTTGCTCAT 58.578 37.500 0.00 0.00 31.83 2.90
3276 4098 5.220529 GGTTAAAATGCTGATTTGCTCATGC 60.221 40.000 0.00 0.00 40.20 4.06
3308 4134 2.757314 GCAGGCTAAGGCAGAAAATTCT 59.243 45.455 0.00 0.00 40.87 2.40
3360 4207 4.281898 AGGTAGTTAGTCGTGCCATTTT 57.718 40.909 0.00 0.00 0.00 1.82
3372 4219 3.683822 CGTGCCATTTTGGTTGCATTTAT 59.316 39.130 0.00 0.00 40.46 1.40
3436 4284 4.035792 TGTGACCGGAATGTTTTTGTACAG 59.964 41.667 9.46 0.00 0.00 2.74
3454 4302 1.470098 CAGAGGTTAGCATGTTGGTGC 59.530 52.381 0.00 0.00 45.38 5.01
3478 4326 4.460731 TGCCGTGGTCAATGATAAAATTCA 59.539 37.500 0.00 0.00 0.00 2.57
3526 4374 5.559427 TTGTTGCATACATCGTGCTTAAT 57.441 34.783 0.00 0.00 42.92 1.40
3527 4375 6.670077 TTGTTGCATACATCGTGCTTAATA 57.330 33.333 0.00 0.00 42.92 0.98
3531 4379 7.483375 TGTTGCATACATCGTGCTTAATAAAAC 59.517 33.333 0.00 0.00 42.92 2.43
3537 4385 5.106317 ACATCGTGCTTAATAAAACCACTGG 60.106 40.000 0.00 0.00 0.00 4.00
3654 4503 1.466856 TCAGCCGGTAATGTCGTACT 58.533 50.000 1.90 0.00 0.00 2.73
3655 4504 1.402968 TCAGCCGGTAATGTCGTACTC 59.597 52.381 1.90 0.00 0.00 2.59
3656 4505 0.743097 AGCCGGTAATGTCGTACTCC 59.257 55.000 1.90 0.00 0.00 3.85
3657 4506 0.249197 GCCGGTAATGTCGTACTCCC 60.249 60.000 1.90 0.00 0.00 4.30
3658 4507 1.396653 CCGGTAATGTCGTACTCCCT 58.603 55.000 0.00 0.00 0.00 4.20
3659 4508 1.336125 CCGGTAATGTCGTACTCCCTC 59.664 57.143 0.00 0.00 0.00 4.30
3660 4509 2.295885 CGGTAATGTCGTACTCCCTCT 58.704 52.381 0.00 0.00 0.00 3.69
3661 4510 2.033049 CGGTAATGTCGTACTCCCTCTG 59.967 54.545 0.00 0.00 0.00 3.35
3662 4511 3.022406 GGTAATGTCGTACTCCCTCTGT 58.978 50.000 0.00 0.00 0.00 3.41
3663 4512 3.066481 GGTAATGTCGTACTCCCTCTGTC 59.934 52.174 0.00 0.00 0.00 3.51
3664 4513 1.765230 ATGTCGTACTCCCTCTGTCC 58.235 55.000 0.00 0.00 0.00 4.02
3665 4514 0.675837 TGTCGTACTCCCTCTGTCCG 60.676 60.000 0.00 0.00 0.00 4.79
3666 4515 0.392193 GTCGTACTCCCTCTGTCCGA 60.392 60.000 0.00 0.00 0.00 4.55
3667 4516 0.325933 TCGTACTCCCTCTGTCCGAA 59.674 55.000 0.00 0.00 0.00 4.30
3668 4517 1.171308 CGTACTCCCTCTGTCCGAAA 58.829 55.000 0.00 0.00 0.00 3.46
3669 4518 1.542915 CGTACTCCCTCTGTCCGAAAA 59.457 52.381 0.00 0.00 0.00 2.29
3670 4519 2.165845 CGTACTCCCTCTGTCCGAAAAT 59.834 50.000 0.00 0.00 0.00 1.82
3671 4520 3.379372 CGTACTCCCTCTGTCCGAAAATA 59.621 47.826 0.00 0.00 0.00 1.40
3672 4521 3.889520 ACTCCCTCTGTCCGAAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
3673 4522 3.442076 ACTCCCTCTGTCCGAAAATACT 58.558 45.455 0.00 0.00 0.00 2.12
3674 4523 3.838903 ACTCCCTCTGTCCGAAAATACTT 59.161 43.478 0.00 0.00 0.00 2.24
3675 4524 4.184629 CTCCCTCTGTCCGAAAATACTTG 58.815 47.826 0.00 0.00 0.00 3.16
3676 4525 3.581332 TCCCTCTGTCCGAAAATACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
3677 4526 3.933332 CCCTCTGTCCGAAAATACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
3678 4527 4.562757 CCCTCTGTCCGAAAATACTTGTCA 60.563 45.833 0.00 0.00 0.00 3.58
3679 4528 5.178797 CCTCTGTCCGAAAATACTTGTCAT 58.821 41.667 0.00 0.00 0.00 3.06
3680 4529 5.292101 CCTCTGTCCGAAAATACTTGTCATC 59.708 44.000 0.00 0.00 0.00 2.92
3681 4530 5.789521 TCTGTCCGAAAATACTTGTCATCA 58.210 37.500 0.00 0.00 0.00 3.07
3682 4531 6.227522 TCTGTCCGAAAATACTTGTCATCAA 58.772 36.000 0.00 0.00 0.00 2.57
3683 4532 6.708502 TCTGTCCGAAAATACTTGTCATCAAA 59.291 34.615 0.00 0.00 32.87 2.69
3684 4533 7.227711 TCTGTCCGAAAATACTTGTCATCAAAA 59.772 33.333 0.00 0.00 32.87 2.44
3685 4534 7.881142 TGTCCGAAAATACTTGTCATCAAAAT 58.119 30.769 0.00 0.00 32.87 1.82
3686 4535 7.807433 TGTCCGAAAATACTTGTCATCAAAATG 59.193 33.333 0.00 0.00 32.87 2.32
3687 4536 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
3688 4537 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
3689 4538 7.273381 CCGAAAATACTTGTCATCAAAATGGAC 59.727 37.037 0.00 0.00 33.42 4.02
3690 4539 7.807433 CGAAAATACTTGTCATCAAAATGGACA 59.193 33.333 0.00 0.00 33.42 4.02
3691 4540 9.474920 GAAAATACTTGTCATCAAAATGGACAA 57.525 29.630 0.00 0.00 34.59 3.18
3692 4541 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
3693 4542 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
3694 4543 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
3695 4544 7.775397 ACTTGTCATCAAAATGGACAAAAAG 57.225 32.000 7.70 0.11 34.98 2.27
3696 4545 6.762661 ACTTGTCATCAAAATGGACAAAAAGG 59.237 34.615 7.70 0.11 34.98 3.11
3697 4546 5.609423 TGTCATCAAAATGGACAAAAAGGG 58.391 37.500 0.00 0.00 33.42 3.95
3698 4547 5.365025 TGTCATCAAAATGGACAAAAAGGGA 59.635 36.000 0.00 0.00 33.42 4.20
3699 4548 6.043012 TGTCATCAAAATGGACAAAAAGGGAT 59.957 34.615 0.00 0.00 33.42 3.85
3700 4549 6.369615 GTCATCAAAATGGACAAAAAGGGATG 59.630 38.462 0.00 0.00 33.42 3.51
3701 4550 5.885449 TCAAAATGGACAAAAAGGGATGT 57.115 34.783 0.00 0.00 0.00 3.06
3702 4551 6.985653 TCAAAATGGACAAAAAGGGATGTA 57.014 33.333 0.00 0.00 0.00 2.29
3703 4552 7.552050 TCAAAATGGACAAAAAGGGATGTAT 57.448 32.000 0.00 0.00 0.00 2.29
3704 4553 7.610865 TCAAAATGGACAAAAAGGGATGTATC 58.389 34.615 0.00 0.00 0.00 2.24
3705 4554 7.454380 TCAAAATGGACAAAAAGGGATGTATCT 59.546 33.333 0.00 0.00 0.00 1.98
3706 4555 8.748412 CAAAATGGACAAAAAGGGATGTATCTA 58.252 33.333 0.00 0.00 0.00 1.98
3707 4556 8.525290 AAATGGACAAAAAGGGATGTATCTAG 57.475 34.615 0.00 0.00 0.00 2.43
3708 4557 6.884472 TGGACAAAAAGGGATGTATCTAGA 57.116 37.500 0.00 0.00 0.00 2.43
3709 4558 7.265599 TGGACAAAAAGGGATGTATCTAGAA 57.734 36.000 0.00 0.00 0.00 2.10
3710 4559 7.110155 TGGACAAAAAGGGATGTATCTAGAAC 58.890 38.462 0.00 0.00 0.00 3.01
3711 4560 7.037586 TGGACAAAAAGGGATGTATCTAGAACT 60.038 37.037 0.00 0.00 0.00 3.01
3712 4561 8.483758 GGACAAAAAGGGATGTATCTAGAACTA 58.516 37.037 0.00 0.00 0.00 2.24
3713 4562 9.886132 GACAAAAAGGGATGTATCTAGAACTAA 57.114 33.333 0.00 0.00 0.00 2.24
3735 4584 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
3737 4586 6.552445 AATACATCTAGATACATCCCCTGC 57.448 41.667 4.54 0.00 0.00 4.85
3738 4587 4.139162 ACATCTAGATACATCCCCTGCT 57.861 45.455 4.54 0.00 0.00 4.24
3739 4588 5.276694 ACATCTAGATACATCCCCTGCTA 57.723 43.478 4.54 0.00 0.00 3.49
3740 4589 5.848004 ACATCTAGATACATCCCCTGCTAT 58.152 41.667 4.54 0.00 0.00 2.97
3741 4590 6.267635 ACATCTAGATACATCCCCTGCTATT 58.732 40.000 4.54 0.00 0.00 1.73
3742 4591 6.382570 ACATCTAGATACATCCCCTGCTATTC 59.617 42.308 4.54 0.00 0.00 1.75
3743 4592 5.903923 TCTAGATACATCCCCTGCTATTCA 58.096 41.667 0.00 0.00 0.00 2.57
3744 4593 6.506661 TCTAGATACATCCCCTGCTATTCAT 58.493 40.000 0.00 0.00 0.00 2.57
3745 4594 6.962311 TCTAGATACATCCCCTGCTATTCATT 59.038 38.462 0.00 0.00 0.00 2.57
3746 4595 6.460103 AGATACATCCCCTGCTATTCATTT 57.540 37.500 0.00 0.00 0.00 2.32
3747 4596 6.856757 AGATACATCCCCTGCTATTCATTTT 58.143 36.000 0.00 0.00 0.00 1.82
3748 4597 6.718454 AGATACATCCCCTGCTATTCATTTTG 59.282 38.462 0.00 0.00 0.00 2.44
3749 4598 4.870636 ACATCCCCTGCTATTCATTTTGA 58.129 39.130 0.00 0.00 0.00 2.69
3750 4599 5.461327 ACATCCCCTGCTATTCATTTTGAT 58.539 37.500 0.00 0.00 0.00 2.57
3751 4600 5.303589 ACATCCCCTGCTATTCATTTTGATG 59.696 40.000 0.00 0.00 33.80 3.07
3752 4601 5.128033 TCCCCTGCTATTCATTTTGATGA 57.872 39.130 0.00 0.00 0.00 2.92
3753 4602 4.889409 TCCCCTGCTATTCATTTTGATGAC 59.111 41.667 0.00 0.00 0.00 3.06
3754 4603 4.646040 CCCCTGCTATTCATTTTGATGACA 59.354 41.667 0.00 0.00 0.00 3.58
3755 4604 5.127519 CCCCTGCTATTCATTTTGATGACAA 59.872 40.000 0.00 0.00 0.00 3.18
3756 4605 6.270815 CCCTGCTATTCATTTTGATGACAAG 58.729 40.000 0.00 0.00 37.32 3.16
3757 4606 6.127535 CCCTGCTATTCATTTTGATGACAAGT 60.128 38.462 0.00 0.00 37.32 3.16
3758 4607 7.067372 CCCTGCTATTCATTTTGATGACAAGTA 59.933 37.037 0.00 0.00 37.32 2.24
3759 4608 8.627403 CCTGCTATTCATTTTGATGACAAGTAT 58.373 33.333 0.00 0.00 37.32 2.12
3764 4613 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
3765 4614 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
3766 4615 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
3767 4616 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
3768 4617 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
3769 4618 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
3770 4619 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
3771 4620 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
3772 4621 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3773 4622 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3774 4623 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
3775 4624 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
3783 4632 1.607628 CGGACGGAGGGAGTAGTAATG 59.392 57.143 0.00 0.00 0.00 1.90
3864 4713 3.549794 AGCAATAGGACTTCAGAATGGC 58.450 45.455 0.00 0.00 36.16 4.40
3870 4719 1.005037 ACTTCAGAATGGCGTCGCA 60.005 52.632 20.50 5.66 36.16 5.10
3918 4767 1.457346 GGCTTCAGAATGGTGTGGAG 58.543 55.000 0.00 0.00 36.16 3.86
3922 4771 2.455674 TCAGAATGGTGTGGAGAACG 57.544 50.000 0.00 0.00 36.16 3.95
3983 4833 1.404391 ACTTACGAACGGCGATCATCT 59.596 47.619 16.62 0.00 44.57 2.90
4123 4973 3.567797 GAGCTCGTCAATGGCGCC 61.568 66.667 22.73 22.73 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
727 1060 8.508875 CGTCAATTTAACCAACCTAATACAAGT 58.491 33.333 0.00 0.00 0.00 3.16
728 1061 8.723311 TCGTCAATTTAACCAACCTAATACAAG 58.277 33.333 0.00 0.00 0.00 3.16
729 1062 8.505625 GTCGTCAATTTAACCAACCTAATACAA 58.494 33.333 0.00 0.00 0.00 2.41
730 1063 7.119553 GGTCGTCAATTTAACCAACCTAATACA 59.880 37.037 0.00 0.00 0.00 2.29
731 1064 7.335171 AGGTCGTCAATTTAACCAACCTAATAC 59.665 37.037 7.30 0.00 34.22 1.89
732 1065 7.396418 AGGTCGTCAATTTAACCAACCTAATA 58.604 34.615 7.30 0.00 34.22 0.98
733 1066 6.243148 AGGTCGTCAATTTAACCAACCTAAT 58.757 36.000 7.30 0.00 34.22 1.73
734 1067 5.623169 AGGTCGTCAATTTAACCAACCTAA 58.377 37.500 7.30 0.00 34.22 2.69
735 1068 5.231702 AGGTCGTCAATTTAACCAACCTA 57.768 39.130 7.30 0.00 34.22 3.08
736 1069 4.094830 AGGTCGTCAATTTAACCAACCT 57.905 40.909 0.00 0.00 34.09 3.50
737 1070 4.393990 CCTAGGTCGTCAATTTAACCAACC 59.606 45.833 0.00 0.00 34.09 3.77
738 1071 5.240121 TCCTAGGTCGTCAATTTAACCAAC 58.760 41.667 9.08 0.00 34.09 3.77
739 1072 5.012354 ACTCCTAGGTCGTCAATTTAACCAA 59.988 40.000 9.08 0.00 34.09 3.67
740 1073 4.529377 ACTCCTAGGTCGTCAATTTAACCA 59.471 41.667 9.08 0.00 34.09 3.67
741 1074 5.082251 ACTCCTAGGTCGTCAATTTAACC 57.918 43.478 9.08 0.00 0.00 2.85
742 1075 5.741040 CGTACTCCTAGGTCGTCAATTTAAC 59.259 44.000 9.08 0.63 0.00 2.01
743 1076 5.677091 GCGTACTCCTAGGTCGTCAATTTAA 60.677 44.000 9.08 0.00 0.00 1.52
744 1077 4.201950 GCGTACTCCTAGGTCGTCAATTTA 60.202 45.833 9.08 0.00 0.00 1.40
745 1078 3.428589 GCGTACTCCTAGGTCGTCAATTT 60.429 47.826 9.08 0.00 0.00 1.82
746 1079 2.098770 GCGTACTCCTAGGTCGTCAATT 59.901 50.000 9.08 0.00 0.00 2.32
747 1080 1.674962 GCGTACTCCTAGGTCGTCAAT 59.325 52.381 9.08 0.00 0.00 2.57
748 1081 1.089920 GCGTACTCCTAGGTCGTCAA 58.910 55.000 9.08 0.00 0.00 3.18
749 1082 1.086067 CGCGTACTCCTAGGTCGTCA 61.086 60.000 9.08 0.00 0.00 4.35
750 1083 1.640604 CGCGTACTCCTAGGTCGTC 59.359 63.158 9.08 5.93 0.00 4.20
751 1084 2.467826 GCGCGTACTCCTAGGTCGT 61.468 63.158 8.43 9.96 0.00 4.34
752 1085 2.327244 GCGCGTACTCCTAGGTCG 59.673 66.667 8.43 10.72 0.00 4.79
753 1086 1.063811 GTGCGCGTACTCCTAGGTC 59.936 63.158 20.55 0.00 0.00 3.85
754 1087 2.758089 CGTGCGCGTACTCCTAGGT 61.758 63.158 24.56 0.00 0.00 3.08
755 1088 2.024305 CGTGCGCGTACTCCTAGG 59.976 66.667 24.56 0.82 0.00 3.02
756 1089 2.651232 GCGTGCGCGTACTCCTAG 60.651 66.667 24.56 10.08 40.81 3.02
757 1090 4.183686 GGCGTGCGCGTACTCCTA 62.184 66.667 26.13 0.00 43.06 2.94
762 1095 4.781959 TACAGGGCGTGCGCGTAC 62.782 66.667 22.18 17.94 43.06 3.67
763 1096 3.570621 TTTACAGGGCGTGCGCGTA 62.571 57.895 22.18 0.00 43.06 4.42
764 1097 4.973055 TTTACAGGGCGTGCGCGT 62.973 61.111 22.18 2.94 43.06 6.01
765 1098 4.439472 GTTTACAGGGCGTGCGCG 62.439 66.667 16.86 16.86 43.06 6.86
766 1099 3.047877 AGTTTACAGGGCGTGCGC 61.048 61.111 7.17 8.17 41.06 6.09
767 1100 1.626654 CTCAGTTTACAGGGCGTGCG 61.627 60.000 7.17 0.00 0.00 5.34
768 1101 0.320421 TCTCAGTTTACAGGGCGTGC 60.320 55.000 7.17 0.00 0.00 5.34
769 1102 1.272490 TCTCTCAGTTTACAGGGCGTG 59.728 52.381 5.50 5.50 0.00 5.34
770 1103 1.546476 CTCTCTCAGTTTACAGGGCGT 59.454 52.381 0.00 0.00 0.00 5.68
771 1104 1.819288 TCTCTCTCAGTTTACAGGGCG 59.181 52.381 0.00 0.00 0.00 6.13
772 1105 2.167487 CCTCTCTCTCAGTTTACAGGGC 59.833 54.545 0.00 0.00 0.00 5.19
773 1106 3.436243 ACCTCTCTCTCAGTTTACAGGG 58.564 50.000 0.00 0.00 0.00 4.45
774 1107 5.258051 ACTACCTCTCTCTCAGTTTACAGG 58.742 45.833 0.00 0.00 0.00 4.00
775 1108 7.413219 CGTTACTACCTCTCTCTCAGTTTACAG 60.413 44.444 0.00 0.00 0.00 2.74
776 1109 6.370994 CGTTACTACCTCTCTCTCAGTTTACA 59.629 42.308 0.00 0.00 0.00 2.41
777 1110 6.675244 GCGTTACTACCTCTCTCTCAGTTTAC 60.675 46.154 0.00 0.00 0.00 2.01
778 1111 5.353678 GCGTTACTACCTCTCTCTCAGTTTA 59.646 44.000 0.00 0.00 0.00 2.01
779 1112 4.156373 GCGTTACTACCTCTCTCTCAGTTT 59.844 45.833 0.00 0.00 0.00 2.66
780 1113 3.690628 GCGTTACTACCTCTCTCTCAGTT 59.309 47.826 0.00 0.00 0.00 3.16
781 1114 3.272581 GCGTTACTACCTCTCTCTCAGT 58.727 50.000 0.00 0.00 0.00 3.41
782 1115 2.614983 GGCGTTACTACCTCTCTCTCAG 59.385 54.545 0.00 0.00 0.00 3.35
783 1116 2.239150 AGGCGTTACTACCTCTCTCTCA 59.761 50.000 0.00 0.00 0.00 3.27
784 1117 2.921821 AGGCGTTACTACCTCTCTCTC 58.078 52.381 0.00 0.00 0.00 3.20
792 1125 1.034292 ACGAGGGAGGCGTTACTACC 61.034 60.000 0.00 0.00 42.18 3.18
795 1128 3.003113 GCACGAGGGAGGCGTTACT 62.003 63.158 0.00 0.00 40.44 2.24
946 1292 2.035155 GGGGTTTGGGAGGGTTCG 59.965 66.667 0.00 0.00 0.00 3.95
976 1322 2.281276 GGCCGTCGAGTTTTGGGT 60.281 61.111 0.00 0.00 0.00 4.51
991 1337 3.372730 TGGCTCCATTGCGTTGGC 61.373 61.111 0.00 0.00 36.66 4.52
1403 1761 1.406887 GCCGCCCTCTAAAATGACTCA 60.407 52.381 0.00 0.00 0.00 3.41
1435 1794 1.275657 CACACCACGAACTTCGCAC 59.724 57.895 11.15 0.00 45.12 5.34
1484 1843 5.811399 AATGTGTGTACCATTTATCACCG 57.189 39.130 0.00 0.00 0.00 4.94
1508 1868 1.404479 AAACGCCCCCAAAAACTCCC 61.404 55.000 0.00 0.00 0.00 4.30
1512 1872 1.269883 CCAGTAAACGCCCCCAAAAAC 60.270 52.381 0.00 0.00 0.00 2.43
1517 1877 2.462626 AACCCAGTAAACGCCCCCA 61.463 57.895 0.00 0.00 0.00 4.96
1521 1881 1.201414 CAATCCAACCCAGTAAACGCC 59.799 52.381 0.00 0.00 0.00 5.68
1523 1883 3.408634 ACTCAATCCAACCCAGTAAACG 58.591 45.455 0.00 0.00 0.00 3.60
1524 1884 4.022329 CCAACTCAATCCAACCCAGTAAAC 60.022 45.833 0.00 0.00 0.00 2.01
1525 1885 4.148838 CCAACTCAATCCAACCCAGTAAA 58.851 43.478 0.00 0.00 0.00 2.01
1527 1887 2.041081 CCCAACTCAATCCAACCCAGTA 59.959 50.000 0.00 0.00 0.00 2.74
1528 1888 1.203050 CCCAACTCAATCCAACCCAGT 60.203 52.381 0.00 0.00 0.00 4.00
1529 1889 1.549203 CCCAACTCAATCCAACCCAG 58.451 55.000 0.00 0.00 0.00 4.45
1530 1890 0.114168 CCCCAACTCAATCCAACCCA 59.886 55.000 0.00 0.00 0.00 4.51
1533 1920 1.203001 TCACCCCCAACTCAATCCAAC 60.203 52.381 0.00 0.00 0.00 3.77
1595 1983 4.431416 TCTGCTAGTGAAGGTGGAAAAA 57.569 40.909 0.00 0.00 0.00 1.94
1655 2049 8.350722 TCGTAATGATAGTACCTTCAGACAATC 58.649 37.037 2.29 0.00 0.00 2.67
1673 2067 3.526534 TGCATTCCGTTCATCGTAATGA 58.473 40.909 9.06 0.00 44.65 2.57
1686 2080 2.485426 CACCAGGCTATATTGCATTCCG 59.515 50.000 11.27 0.00 34.04 4.30
1688 2082 2.886523 TGCACCAGGCTATATTGCATTC 59.113 45.455 11.27 0.00 45.15 2.67
1703 2097 1.680522 ATTTTTGCCACGGTGCACCA 61.681 50.000 34.16 12.97 41.88 4.17
1750 2144 6.326375 TGTTCAACCTGTAATGTCACAAAAC 58.674 36.000 0.00 0.00 0.00 2.43
1821 2215 0.462047 CCCCTCATAGTGGCGTTGAC 60.462 60.000 0.00 0.00 0.00 3.18
1845 2239 5.496556 CACATCCACCAACCAATCTACTAA 58.503 41.667 0.00 0.00 0.00 2.24
1905 2299 5.356882 CGGTCAATATATGAAACCGCAAT 57.643 39.130 16.33 0.00 40.96 3.56
2031 2426 6.100279 TGGTAAGATATGACAAAGAGAGGCAT 59.900 38.462 0.00 0.00 0.00 4.40
2219 2622 7.549839 ACAAATTTATCTCCACCATTCACATG 58.450 34.615 0.00 0.00 0.00 3.21
2399 2806 2.100197 CGGAGGGAGTACTTGACATCA 58.900 52.381 0.00 0.00 0.00 3.07
2400 2807 2.099427 GACGGAGGGAGTACTTGACATC 59.901 54.545 0.00 0.00 0.00 3.06
2423 2830 2.159627 CGTTTGAGCGGCAAGTAATTCT 59.840 45.455 1.45 0.00 37.87 2.40
2444 2851 5.643777 CCTCCATCCGAAATTACATACATCC 59.356 44.000 0.00 0.00 0.00 3.51
2458 2865 3.236896 GGTAACTATTCCCTCCATCCGA 58.763 50.000 0.00 0.00 0.00 4.55
2463 2870 5.789574 AAACATGGTAACTATTCCCTCCA 57.210 39.130 0.00 0.00 37.61 3.86
2639 3046 7.769507 GGGGGAAACATGTTACAAAAGTTTAAA 59.230 33.333 12.39 0.00 33.04 1.52
2641 3048 6.612049 AGGGGGAAACATGTTACAAAAGTTTA 59.388 34.615 12.39 0.00 33.04 2.01
2642 3049 5.427157 AGGGGGAAACATGTTACAAAAGTTT 59.573 36.000 12.39 11.63 35.33 2.66
2643 3050 4.966168 AGGGGGAAACATGTTACAAAAGTT 59.034 37.500 12.39 0.00 0.00 2.66
2645 3052 5.069781 TGAAGGGGGAAACATGTTACAAAAG 59.930 40.000 12.39 0.00 0.00 2.27
2710 3123 2.057316 CTCAATTCCGCGAGATAGCAG 58.943 52.381 8.23 0.00 36.85 4.24
2786 3199 3.788227 TGTGAACCTGGCTAAGAACAT 57.212 42.857 0.00 0.00 0.00 2.71
2847 3260 6.889301 ATGTGGATTCGATAATTCAGCAAT 57.111 33.333 0.00 0.00 30.91 3.56
2857 3270 5.048782 GGCAAAGCATAATGTGGATTCGATA 60.049 40.000 0.00 0.00 0.00 2.92
2860 3273 3.067180 AGGCAAAGCATAATGTGGATTCG 59.933 43.478 0.00 0.00 0.00 3.34
2878 3291 2.441410 TGTCAGAACAAACACAAGGCA 58.559 42.857 0.00 0.00 30.70 4.75
2881 3294 6.255215 ACGTAAATGTCAGAACAAACACAAG 58.745 36.000 0.00 0.00 39.30 3.16
3148 3561 4.472833 AGAGATGCAGGAATTTCTACAGGT 59.527 41.667 0.00 0.00 0.00 4.00
3151 3564 4.718774 AGGAGAGATGCAGGAATTTCTACA 59.281 41.667 0.00 0.00 26.38 2.74
3153 3566 4.038522 CGAGGAGAGATGCAGGAATTTCTA 59.961 45.833 0.00 0.00 0.00 2.10
3163 3576 1.107114 GGTCTTCGAGGAGAGATGCA 58.893 55.000 0.00 0.00 0.00 3.96
3176 3589 3.866327 GCCTTTCACTTATCGAGGTCTTC 59.134 47.826 0.00 0.00 0.00 2.87
3240 3669 2.176247 TTTTAACCCCCTTTGCACCA 57.824 45.000 0.00 0.00 0.00 4.17
3241 3670 2.874052 GCATTTTAACCCCCTTTGCACC 60.874 50.000 0.00 0.00 0.00 5.01
3243 3672 2.038295 CAGCATTTTAACCCCCTTTGCA 59.962 45.455 0.00 0.00 0.00 4.08
3245 3674 4.824479 ATCAGCATTTTAACCCCCTTTG 57.176 40.909 0.00 0.00 0.00 2.77
3249 3678 3.055167 AGCAAATCAGCATTTTAACCCCC 60.055 43.478 0.00 0.00 36.85 5.40
3253 3682 5.792631 GCATGAGCAAATCAGCATTTTAAC 58.207 37.500 0.00 0.00 42.53 2.01
3280 4102 2.097825 CTGCCTTAGCCTGCAAAAGAT 58.902 47.619 5.99 0.00 36.98 2.40
3308 4134 6.606796 TGGCCATGAAAAATTCTTGCTAGATA 59.393 34.615 0.00 0.00 34.51 1.98
3322 4169 2.214376 CCTACAGGTGGCCATGAAAA 57.786 50.000 9.72 0.00 0.00 2.29
3372 4219 2.600439 AGCTAGATGGCTGCACTGA 58.400 52.632 0.50 0.00 41.43 3.41
3392 4239 8.414003 GTCACACTTGATACCAGATTACAGATA 58.586 37.037 0.00 0.00 33.11 1.98
3454 4302 4.637483 ATTTTATCATTGACCACGGCAG 57.363 40.909 0.00 0.00 0.00 4.85
3526 4374 5.042463 TCATCACTTCACCAGTGGTTTTA 57.958 39.130 13.62 0.00 45.46 1.52
3527 4375 3.885297 CTCATCACTTCACCAGTGGTTTT 59.115 43.478 13.62 0.00 45.46 2.43
3537 4385 6.915544 TTGAGAATATGCTCATCACTTCAC 57.084 37.500 14.45 0.00 43.84 3.18
3547 4395 6.976925 CCCATTTCAACTTTGAGAATATGCTC 59.023 38.462 3.43 3.43 38.61 4.26
3654 4503 3.581332 ACAAGTATTTTCGGACAGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
3655 4504 3.933332 GACAAGTATTTTCGGACAGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
3656 4505 4.566004 TGACAAGTATTTTCGGACAGAGG 58.434 43.478 0.00 0.00 0.00 3.69
3657 4506 5.869344 TGATGACAAGTATTTTCGGACAGAG 59.131 40.000 0.00 0.00 0.00 3.35
3658 4507 5.789521 TGATGACAAGTATTTTCGGACAGA 58.210 37.500 0.00 0.00 0.00 3.41
3659 4508 6.480524 TTGATGACAAGTATTTTCGGACAG 57.519 37.500 0.00 0.00 0.00 3.51
3660 4509 6.869315 TTTGATGACAAGTATTTTCGGACA 57.131 33.333 0.00 0.00 37.32 4.02
3661 4510 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
3662 4511 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
3663 4512 7.273381 GTCCATTTTGATGACAAGTATTTTCGG 59.727 37.037 0.00 0.00 37.32 4.30
3664 4513 7.807433 TGTCCATTTTGATGACAAGTATTTTCG 59.193 33.333 0.00 0.00 37.32 3.46
3665 4514 9.474920 TTGTCCATTTTGATGACAAGTATTTTC 57.525 29.630 0.00 0.00 37.32 2.29
3666 4515 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
3667 4516 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
3668 4517 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
3669 4518 9.480053 CTTTTTGTCCATTTTGATGACAAGTAT 57.520 29.630 0.00 0.00 37.13 2.12
3670 4519 7.925483 CCTTTTTGTCCATTTTGATGACAAGTA 59.075 33.333 0.00 0.00 37.13 2.24
3671 4520 6.762661 CCTTTTTGTCCATTTTGATGACAAGT 59.237 34.615 0.00 0.00 37.13 3.16
3672 4521 6.203338 CCCTTTTTGTCCATTTTGATGACAAG 59.797 38.462 0.00 0.00 37.13 3.16
3673 4522 6.054295 CCCTTTTTGTCCATTTTGATGACAA 58.946 36.000 0.00 0.00 34.47 3.18
3674 4523 5.365025 TCCCTTTTTGTCCATTTTGATGACA 59.635 36.000 0.00 0.00 0.00 3.58
3675 4524 5.852827 TCCCTTTTTGTCCATTTTGATGAC 58.147 37.500 0.00 0.00 0.00 3.06
3676 4525 6.043012 ACATCCCTTTTTGTCCATTTTGATGA 59.957 34.615 0.00 0.00 32.39 2.92
3677 4526 6.232692 ACATCCCTTTTTGTCCATTTTGATG 58.767 36.000 0.00 0.00 33.80 3.07
3678 4527 6.438186 ACATCCCTTTTTGTCCATTTTGAT 57.562 33.333 0.00 0.00 0.00 2.57
3679 4528 5.885449 ACATCCCTTTTTGTCCATTTTGA 57.115 34.783 0.00 0.00 0.00 2.69
3680 4529 7.614494 AGATACATCCCTTTTTGTCCATTTTG 58.386 34.615 0.00 0.00 0.00 2.44
3681 4530 7.797121 AGATACATCCCTTTTTGTCCATTTT 57.203 32.000 0.00 0.00 0.00 1.82
3682 4531 8.336235 TCTAGATACATCCCTTTTTGTCCATTT 58.664 33.333 0.00 0.00 0.00 2.32
3683 4532 7.872138 TCTAGATACATCCCTTTTTGTCCATT 58.128 34.615 0.00 0.00 0.00 3.16
3684 4533 7.451731 TCTAGATACATCCCTTTTTGTCCAT 57.548 36.000 0.00 0.00 0.00 3.41
3685 4534 6.884472 TCTAGATACATCCCTTTTTGTCCA 57.116 37.500 0.00 0.00 0.00 4.02
3686 4535 7.339482 AGTTCTAGATACATCCCTTTTTGTCC 58.661 38.462 0.00 0.00 0.00 4.02
3687 4536 9.886132 TTAGTTCTAGATACATCCCTTTTTGTC 57.114 33.333 0.00 0.00 0.00 3.18
3709 4558 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
3711 4560 8.540388 GCAGGGGATGTATCTAGATGTATTTTA 58.460 37.037 15.79 0.00 0.00 1.52
3712 4561 7.238514 AGCAGGGGATGTATCTAGATGTATTTT 59.761 37.037 15.79 0.00 0.00 1.82
3713 4562 6.732862 AGCAGGGGATGTATCTAGATGTATTT 59.267 38.462 15.79 0.00 0.00 1.40
3714 4563 6.267635 AGCAGGGGATGTATCTAGATGTATT 58.732 40.000 15.79 0.00 0.00 1.89
3715 4564 5.848004 AGCAGGGGATGTATCTAGATGTAT 58.152 41.667 15.79 9.11 0.00 2.29
3716 4565 5.276694 AGCAGGGGATGTATCTAGATGTA 57.723 43.478 15.79 4.44 0.00 2.29
3717 4566 4.139162 AGCAGGGGATGTATCTAGATGT 57.861 45.455 15.79 1.25 0.00 3.06
3718 4567 6.382282 TGAATAGCAGGGGATGTATCTAGATG 59.618 42.308 15.79 0.00 0.00 2.90
3719 4568 6.506661 TGAATAGCAGGGGATGTATCTAGAT 58.493 40.000 10.73 10.73 0.00 1.98
3720 4569 5.903923 TGAATAGCAGGGGATGTATCTAGA 58.096 41.667 0.00 0.00 0.00 2.43
3721 4570 6.805016 ATGAATAGCAGGGGATGTATCTAG 57.195 41.667 0.00 0.00 0.00 2.43
3722 4571 7.574021 AAATGAATAGCAGGGGATGTATCTA 57.426 36.000 0.00 0.00 0.00 1.98
3723 4572 6.460103 AAATGAATAGCAGGGGATGTATCT 57.540 37.500 0.00 0.00 0.00 1.98
3724 4573 6.716628 TCAAAATGAATAGCAGGGGATGTATC 59.283 38.462 0.00 0.00 0.00 2.24
3725 4574 6.613699 TCAAAATGAATAGCAGGGGATGTAT 58.386 36.000 0.00 0.00 0.00 2.29
3726 4575 6.012337 TCAAAATGAATAGCAGGGGATGTA 57.988 37.500 0.00 0.00 0.00 2.29
3727 4576 4.870636 TCAAAATGAATAGCAGGGGATGT 58.129 39.130 0.00 0.00 0.00 3.06
3728 4577 5.537295 TCATCAAAATGAATAGCAGGGGATG 59.463 40.000 0.00 0.00 38.97 3.51
3729 4578 5.537674 GTCATCAAAATGAATAGCAGGGGAT 59.462 40.000 0.00 0.00 43.42 3.85
3730 4579 4.889409 GTCATCAAAATGAATAGCAGGGGA 59.111 41.667 0.00 0.00 43.42 4.81
3731 4580 4.646040 TGTCATCAAAATGAATAGCAGGGG 59.354 41.667 0.00 0.00 43.42 4.79
3732 4581 5.840243 TGTCATCAAAATGAATAGCAGGG 57.160 39.130 0.00 0.00 43.42 4.45
3733 4582 6.860080 ACTTGTCATCAAAATGAATAGCAGG 58.140 36.000 0.00 0.00 43.42 4.85
3739 4588 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
3740 4589 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
3741 4590 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
3742 4591 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
3743 4592 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
3744 4593 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
3745 4594 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
3746 4595 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
3747 4596 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
3748 4597 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
3749 4598 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
3750 4599 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
3751 4600 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3752 4601 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3753 4602 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3754 4603 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
3755 4604 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
3756 4605 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3757 4606 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3758 4607 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3759 4608 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
3760 4609 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
3761 4610 0.982852 TACTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
3762 4611 0.107017 TTACTACTCCCTCCGTCCGG 60.107 60.000 0.00 0.00 0.00 5.14
3763 4612 1.607628 CATTACTACTCCCTCCGTCCG 59.392 57.143 0.00 0.00 0.00 4.79
3764 4613 2.941480 TCATTACTACTCCCTCCGTCC 58.059 52.381 0.00 0.00 0.00 4.79
3765 4614 4.142790 TGATCATTACTACTCCCTCCGTC 58.857 47.826 0.00 0.00 0.00 4.79
3766 4615 4.180377 TGATCATTACTACTCCCTCCGT 57.820 45.455 0.00 0.00 0.00 4.69
3767 4616 4.158764 GGATGATCATTACTACTCCCTCCG 59.841 50.000 10.14 0.00 0.00 4.63
3768 4617 5.046950 GTGGATGATCATTACTACTCCCTCC 60.047 48.000 10.14 3.16 0.00 4.30
3769 4618 5.540337 TGTGGATGATCATTACTACTCCCTC 59.460 44.000 10.14 5.43 0.00 4.30
3770 4619 5.467738 TGTGGATGATCATTACTACTCCCT 58.532 41.667 10.14 0.00 0.00 4.20
3771 4620 5.808366 TGTGGATGATCATTACTACTCCC 57.192 43.478 10.14 4.30 0.00 4.30
3772 4621 7.225538 CACTTTGTGGATGATCATTACTACTCC 59.774 40.741 10.14 5.98 0.00 3.85
3773 4622 7.254590 GCACTTTGTGGATGATCATTACTACTC 60.255 40.741 10.14 0.00 33.64 2.59
3774 4623 6.540189 GCACTTTGTGGATGATCATTACTACT 59.460 38.462 10.14 0.00 33.64 2.57
3775 4624 6.540189 AGCACTTTGTGGATGATCATTACTAC 59.460 38.462 10.14 6.79 33.64 2.73
3783 4632 5.294306 TCGATTAAGCACTTTGTGGATGATC 59.706 40.000 0.00 0.00 33.64 2.92
3896 4745 0.798776 CACACCATTCTGAAGCCGAC 59.201 55.000 0.00 0.00 0.00 4.79
3897 4746 0.321564 CCACACCATTCTGAAGCCGA 60.322 55.000 0.00 0.00 0.00 5.54
3918 4767 1.061485 GAAGTCGTCAAGCTCCGTTC 58.939 55.000 0.00 0.00 0.00 3.95
3922 4771 2.440539 TTCTGAAGTCGTCAAGCTCC 57.559 50.000 0.00 0.00 35.22 4.70
3983 4833 0.771127 CCTTCTGTGGGGTGGAGAAA 59.229 55.000 0.00 0.00 0.00 2.52
4052 4902 1.300311 CACCAACGACGGCTACACA 60.300 57.895 0.00 0.00 0.00 3.72
4115 4965 2.044946 GTCCTTCTGGGCGCCATT 60.045 61.111 30.85 0.00 30.82 3.16


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

AutoCloner maintained by Alex Coulton.