Multiple sequence alignment - TraesCS1B01G010700

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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 TraesCS1B01G010700 chr1B 100.000 2454 0 0 1 2454 5056629 5059082 0.000000e+00 4532
1 TraesCS1B01G010700 chr1B 93.096 1347 47 11 1 1347 5099009 5100309 0.000000e+00 1930
2 TraesCS1B01G010700 chr1B 95.383 758 35 0 1321 2078 5100315 5101072 0.000000e+00 1206
3 TraesCS1B01G010700 chr1B 87.931 986 113 6 1091 2075 5137830 5138810 0.000000e+00 1157
4 TraesCS1B01G010700 chr1B 87.657 794 75 9 1 781 5136773 5137556 0.000000e+00 902
5 TraesCS1B01G010700 chr1B 87.050 695 67 14 1 686 5141742 5142422 0.000000e+00 763
6 TraesCS1B01G010700 chr1B 85.271 645 65 11 518 1147 5137212 5137841 2.660000e-179 638
7 TraesCS1B01G010700 chr1B 86.010 579 77 3 1202 1779 4991918 4991343 3.470000e-173 617
8 TraesCS1B01G010700 chr1B 83.956 642 69 22 473 1112 4965763 4966372 3.520000e-163 584
9 TraesCS1B01G010700 chr1B 83.106 586 60 11 526 1111 5142145 5142691 4.710000e-137 497
10 TraesCS1B01G010700 chr1D 88.931 1590 123 20 518 2083 322758 321198 0.000000e+00 1912
11 TraesCS1B01G010700 chr1D 89.116 928 99 2 1133 2058 259896 258969 0.000000e+00 1153
12 TraesCS1B01G010700 chr1D 93.856 765 37 5 4 761 323195 322434 0.000000e+00 1144
13 TraesCS1B01G010700 chr1D 87.306 772 91 5 1202 1969 381106 380338 0.000000e+00 876
14 TraesCS1B01G010700 chr1D 87.717 749 69 13 4 745 260845 260113 0.000000e+00 852
15 TraesCS1B01G010700 chr1D 86.874 739 77 11 4 734 251662 250936 0.000000e+00 809
16 TraesCS1B01G010700 chr1D 86.792 583 59 10 526 1108 260446 259882 3.440000e-178 634
17 TraesCS1B01G010700 chr1D 86.348 586 62 10 526 1111 251261 250694 7.450000e-175 623
18 TraesCS1B01G010700 chr1D 87.623 509 58 4 1124 1628 250711 250204 9.780000e-164 586
19 TraesCS1B01G010700 chr1D 88.889 387 43 0 717 1103 381528 381142 6.140000e-131 477
20 TraesCS1B01G010700 chr1A 83.550 1386 173 26 679 2060 3846428 3845094 0.000000e+00 1245
21 TraesCS1B01G010700 chr1A 84.707 837 123 5 1202 2036 4034026 4034859 0.000000e+00 832
22 TraesCS1B01G010700 chr1A 84.468 837 125 5 1202 2036 4042011 4042844 0.000000e+00 821
23 TraesCS1B01G010700 chr1A 83.584 865 124 5 1202 2060 3911098 3911950 0.000000e+00 795
24 TraesCS1B01G010700 chr1A 86.022 744 78 14 1 737 4033035 4033759 0.000000e+00 774
25 TraesCS1B01G010700 chr1A 86.022 744 78 14 1 737 4041020 4041744 0.000000e+00 774
26 TraesCS1B01G010700 chr1A 83.158 760 90 20 1 737 3910090 3910834 0.000000e+00 660
27 TraesCS1B01G010700 chr1A 83.193 595 79 11 520 1106 3910487 3911068 2.160000e-145 525
28 TraesCS1B01G010700 chr2D 94.102 373 21 1 2083 2454 202095394 202095766 1.270000e-157 566
29 TraesCS1B01G010700 chr2D 93.122 378 26 0 2077 2454 580135634 580136011 2.760000e-154 555
30 TraesCS1B01G010700 chrUn 93.583 374 22 2 2082 2454 154565555 154565183 7.670000e-155 556
31 TraesCS1B01G010700 chr4D 93.369 377 24 1 2079 2454 40409553 40409929 7.670000e-155 556
32 TraesCS1B01G010700 chr6D 93.548 372 24 0 2083 2454 154108443 154108072 2.760000e-154 555
33 TraesCS1B01G010700 chr5D 93.548 372 24 0 2083 2454 459396254 459395883 2.760000e-154 555
34 TraesCS1B01G010700 chr3D 93.566 373 23 1 2083 2454 32289900 32290272 2.760000e-154 555
35 TraesCS1B01G010700 chr3D 93.316 374 25 0 2081 2454 323479067 323479440 9.920000e-154 553
36 TraesCS1B01G010700 chr7D 93.333 375 24 1 2081 2454 185109630 185109256 9.920000e-154 553


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 TraesCS1B01G010700 chr1B 5056629 5059082 2453 False 4532.000000 4532 100.000000 1 2454 1 chr1B.!!$F2 2453
1 TraesCS1B01G010700 chr1B 5099009 5101072 2063 False 1568.000000 1930 94.239500 1 2078 2 chr1B.!!$F3 2077
2 TraesCS1B01G010700 chr1B 5136773 5142691 5918 False 791.400000 1157 86.203000 1 2075 5 chr1B.!!$F4 2074
3 TraesCS1B01G010700 chr1B 4991343 4991918 575 True 617.000000 617 86.010000 1202 1779 1 chr1B.!!$R1 577
4 TraesCS1B01G010700 chr1B 4965763 4966372 609 False 584.000000 584 83.956000 473 1112 1 chr1B.!!$F1 639
5 TraesCS1B01G010700 chr1D 321198 323195 1997 True 1528.000000 1912 91.393500 4 2083 2 chr1D.!!$R3 2079
6 TraesCS1B01G010700 chr1D 258969 260845 1876 True 879.666667 1153 87.875000 4 2058 3 chr1D.!!$R2 2054
7 TraesCS1B01G010700 chr1D 380338 381528 1190 True 676.500000 876 88.097500 717 1969 2 chr1D.!!$R4 1252
8 TraesCS1B01G010700 chr1D 250204 251662 1458 True 672.666667 809 86.948333 4 1628 3 chr1D.!!$R1 1624
9 TraesCS1B01G010700 chr1A 3845094 3846428 1334 True 1245.000000 1245 83.550000 679 2060 1 chr1A.!!$R1 1381
10 TraesCS1B01G010700 chr1A 4033035 4034859 1824 False 803.000000 832 85.364500 1 2036 2 chr1A.!!$F2 2035
11 TraesCS1B01G010700 chr1A 4041020 4042844 1824 False 797.500000 821 85.245000 1 2036 2 chr1A.!!$F3 2035
12 TraesCS1B01G010700 chr1A 3910090 3911950 1860 False 660.000000 795 83.311667 1 2060 3 chr1A.!!$F1 2059

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
670 702 0.034756 GCCACAACAACCATTTCCCC 59.965 55.0 0.0 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2298 2937 0.038618 CGTGAGTTCATGGGACGTCA 60.039 55.0 18.91 0.0 0.0 4.35 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
194 199 9.860898 AGCAATAATGAAAAGAAATCTAACCAC 57.139 29.630 0.00 0.00 0.00 4.16
226 231 7.896383 ATAAAAAGGCCTGCAATATGTAGAA 57.104 32.000 5.69 0.00 31.36 2.10
319 324 4.394920 GCAAATCGACCATGAAGACCTTAA 59.605 41.667 0.00 0.00 0.00 1.85
391 396 2.998480 TCGACCCTAGCGGCCAAA 60.998 61.111 2.24 0.00 33.26 3.28
400 405 2.297701 CTAGCGGCCAAATACAATGGT 58.702 47.619 2.24 0.00 40.23 3.55
430 438 2.286121 TAGTCCCCCAGCCCCAAG 60.286 66.667 0.00 0.00 0.00 3.61
442 450 0.480252 GCCCCAAGAGCCATTATCCT 59.520 55.000 0.00 0.00 0.00 3.24
613 621 4.899502 TCAACAACCACAACAACCATTTT 58.100 34.783 0.00 0.00 0.00 1.82
636 668 2.419851 CCAGCAACCACAACAACCATTT 60.420 45.455 0.00 0.00 0.00 2.32
651 683 2.224867 ACCATTTCCCCAGACTCAACAG 60.225 50.000 0.00 0.00 0.00 3.16
654 686 1.059584 TTCCCCAGACTCAACAGCCA 61.060 55.000 0.00 0.00 0.00 4.75
655 687 1.302832 CCCCAGACTCAACAGCCAC 60.303 63.158 0.00 0.00 0.00 5.01
656 688 1.451504 CCCAGACTCAACAGCCACA 59.548 57.895 0.00 0.00 0.00 4.17
657 689 0.179020 CCCAGACTCAACAGCCACAA 60.179 55.000 0.00 0.00 0.00 3.33
658 690 0.947244 CCAGACTCAACAGCCACAAC 59.053 55.000 0.00 0.00 0.00 3.32
659 691 1.667236 CAGACTCAACAGCCACAACA 58.333 50.000 0.00 0.00 0.00 3.33
660 692 2.016318 CAGACTCAACAGCCACAACAA 58.984 47.619 0.00 0.00 0.00 2.83
661 693 2.017049 AGACTCAACAGCCACAACAAC 58.983 47.619 0.00 0.00 0.00 3.32
662 694 1.065551 GACTCAACAGCCACAACAACC 59.934 52.381 0.00 0.00 0.00 3.77
663 695 1.102154 CTCAACAGCCACAACAACCA 58.898 50.000 0.00 0.00 0.00 3.67
664 696 1.682854 CTCAACAGCCACAACAACCAT 59.317 47.619 0.00 0.00 0.00 3.55
665 697 2.101249 CTCAACAGCCACAACAACCATT 59.899 45.455 0.00 0.00 0.00 3.16
666 698 2.499289 TCAACAGCCACAACAACCATTT 59.501 40.909 0.00 0.00 0.00 2.32
667 699 2.865551 CAACAGCCACAACAACCATTTC 59.134 45.455 0.00 0.00 0.00 2.17
668 700 1.412343 ACAGCCACAACAACCATTTCC 59.588 47.619 0.00 0.00 0.00 3.13
669 701 1.047801 AGCCACAACAACCATTTCCC 58.952 50.000 0.00 0.00 0.00 3.97
670 702 0.034756 GCCACAACAACCATTTCCCC 59.965 55.000 0.00 0.00 0.00 4.81
671 703 1.418334 CCACAACAACCATTTCCCCA 58.582 50.000 0.00 0.00 0.00 4.96
672 704 1.344114 CCACAACAACCATTTCCCCAG 59.656 52.381 0.00 0.00 0.00 4.45
673 705 1.047801 ACAACAACCATTTCCCCAGC 58.952 50.000 0.00 0.00 0.00 4.85
674 706 1.047002 CAACAACCATTTCCCCAGCA 58.953 50.000 0.00 0.00 0.00 4.41
675 707 1.415659 CAACAACCATTTCCCCAGCAA 59.584 47.619 0.00 0.00 0.00 3.91
676 708 1.047801 ACAACCATTTCCCCAGCAAC 58.952 50.000 0.00 0.00 0.00 4.17
677 709 0.321346 CAACCATTTCCCCAGCAACC 59.679 55.000 0.00 0.00 0.00 3.77
690 722 3.305335 CCCAGCAACCACAACAACTATTC 60.305 47.826 0.00 0.00 0.00 1.75
697 729 2.041081 CCACAACAACTATTCCCCCAGA 59.959 50.000 0.00 0.00 0.00 3.86
699 731 2.986728 ACAACAACTATTCCCCCAGACT 59.013 45.455 0.00 0.00 0.00 3.24
848 917 4.639171 GCCCCAACAACCGCAACG 62.639 66.667 0.00 0.00 0.00 4.10
868 937 2.178580 GATCATTCCCCCAGCAACAAA 58.821 47.619 0.00 0.00 0.00 2.83
877 946 0.535102 CCAGCAACAAAGACCGTCCT 60.535 55.000 0.00 0.00 0.00 3.85
963 1032 2.291735 TGCATCATTGGTGTCATCCCTT 60.292 45.455 0.00 0.00 0.00 3.95
986 1055 3.013921 GGTCGATAATCTGGCCACAAAA 58.986 45.455 0.00 0.00 0.00 2.44
1099 1252 2.425668 TCCATCATCATGCAGCAACAAG 59.574 45.455 0.00 0.00 0.00 3.16
1110 1263 3.056962 TGCAGCAACAAGAACAAGAACAA 60.057 39.130 0.00 0.00 0.00 2.83
1111 1264 3.549070 GCAGCAACAAGAACAAGAACAAG 59.451 43.478 0.00 0.00 0.00 3.16
1143 1296 5.006165 ACAACAACAACAACAACAACAACAG 59.994 36.000 0.00 0.00 0.00 3.16
1162 1315 2.566952 GCAAGGCATGCGTATCTTTT 57.433 45.000 14.17 0.00 46.87 2.27
1185 1338 4.801330 TCCACTATCTCGACAACAACAT 57.199 40.909 0.00 0.00 0.00 2.71
1290 1443 3.642705 GTTGCAAACTCTTCCAACCATC 58.357 45.455 0.00 0.00 45.32 3.51
1296 1449 3.446442 ACTCTTCCAACCATCTGCAAT 57.554 42.857 0.00 0.00 0.00 3.56
1322 1475 1.461268 TCCCACCTGAGTGCTCCAA 60.461 57.895 0.00 0.00 43.09 3.53
1460 1657 4.419522 ACGATGACAAATAAAGTGGCAC 57.580 40.909 10.29 10.29 36.66 5.01
1462 1659 3.120338 CGATGACAAATAAAGTGGCACGT 60.120 43.478 12.71 6.02 36.66 4.49
1542 1740 2.694628 AGTTCTTGTTTGCCAGCATTGA 59.305 40.909 0.00 0.00 0.00 2.57
1573 1775 8.514594 CATTGTTCCATTCACTGTGTATTTAGT 58.485 33.333 7.79 0.00 0.00 2.24
1613 1815 5.220739 GCAGTTCTAGGCTTACACATCAATG 60.221 44.000 0.00 0.00 0.00 2.82
1618 1820 4.443978 AGGCTTACACATCAATGGCTAT 57.556 40.909 0.00 0.00 0.00 2.97
1655 1857 5.770417 CAGGTTCCTATGTAATCTACCGAC 58.230 45.833 0.00 0.00 0.00 4.79
1674 1876 3.391049 GACTAATGGTCGGCCTATTGAC 58.609 50.000 7.97 0.00 35.07 3.18
1880 2082 8.058667 TGTTCACCTAGATATTTCTACGTTGA 57.941 34.615 0.00 0.00 33.17 3.18
2060 2265 7.333528 TGCCATTAAACTCTTCATATGGTTC 57.666 36.000 2.13 0.00 35.94 3.62
2071 2276 2.499693 TCATATGGTTCCGTGCAGAGAA 59.500 45.455 2.13 0.00 0.00 2.87
2080 2285 0.250727 CGTGCAGAGAAGGGGGAAAA 60.251 55.000 0.00 0.00 0.00 2.29
2083 2288 2.232208 GTGCAGAGAAGGGGGAAAATTG 59.768 50.000 0.00 0.00 0.00 2.32
2084 2289 2.158325 TGCAGAGAAGGGGGAAAATTGT 60.158 45.455 0.00 0.00 0.00 2.71
2085 2290 2.899900 GCAGAGAAGGGGGAAAATTGTT 59.100 45.455 0.00 0.00 0.00 2.83
2087 2292 3.259123 CAGAGAAGGGGGAAAATTGTTGG 59.741 47.826 0.00 0.00 0.00 3.77
2088 2293 2.567169 GAGAAGGGGGAAAATTGTTGGG 59.433 50.000 0.00 0.00 0.00 4.12
2091 2296 1.224381 AGGGGGAAAATTGTTGGGGAA 59.776 47.619 0.00 0.00 0.00 3.97
2092 2297 1.349688 GGGGGAAAATTGTTGGGGAAC 59.650 52.381 0.00 0.00 0.00 3.62
2093 2298 1.001520 GGGGAAAATTGTTGGGGAACG 59.998 52.381 0.00 0.00 0.00 3.95
2094 2299 1.689813 GGGAAAATTGTTGGGGAACGT 59.310 47.619 0.00 0.00 0.00 3.99
2095 2300 2.892215 GGGAAAATTGTTGGGGAACGTA 59.108 45.455 0.00 0.00 0.00 3.57
2096 2301 3.057104 GGGAAAATTGTTGGGGAACGTAG 60.057 47.826 0.00 0.00 0.00 3.51
2098 2303 4.320714 GGAAAATTGTTGGGGAACGTAGTC 60.321 45.833 0.00 0.00 45.00 2.59
2100 2305 3.713826 ATTGTTGGGGAACGTAGTCAT 57.286 42.857 0.00 0.00 45.00 3.06
2126 2765 1.231221 AAAAATCCTACGCACACGCA 58.769 45.000 0.00 0.00 45.53 5.24
2127 2766 1.231221 AAAATCCTACGCACACGCAA 58.769 45.000 0.00 0.00 45.53 4.85
2128 2767 0.796312 AAATCCTACGCACACGCAAG 59.204 50.000 0.00 0.00 45.53 4.01
2129 2768 0.037697 AATCCTACGCACACGCAAGA 60.038 50.000 0.00 0.00 45.53 3.02
2130 2769 0.175760 ATCCTACGCACACGCAAGAT 59.824 50.000 0.00 0.00 45.53 2.40
2131 2770 0.457853 TCCTACGCACACGCAAGATC 60.458 55.000 0.00 0.00 45.53 2.75
2132 2771 0.735978 CCTACGCACACGCAAGATCA 60.736 55.000 0.00 0.00 45.53 2.92
2133 2772 1.280982 CTACGCACACGCAAGATCAT 58.719 50.000 0.00 0.00 45.53 2.45
2134 2773 0.998669 TACGCACACGCAAGATCATG 59.001 50.000 0.00 0.00 45.53 3.07
2135 2774 1.061411 CGCACACGCAAGATCATGG 59.939 57.895 0.00 0.00 43.62 3.66
2136 2775 1.638388 CGCACACGCAAGATCATGGT 61.638 55.000 0.00 0.00 43.62 3.55
2137 2776 0.179181 GCACACGCAAGATCATGGTG 60.179 55.000 14.17 14.17 43.62 4.17
2138 2777 1.441738 CACACGCAAGATCATGGTGA 58.558 50.000 19.56 0.00 43.62 4.02
2139 2778 2.011947 CACACGCAAGATCATGGTGAT 58.988 47.619 19.56 0.00 40.34 3.06
2140 2779 2.011947 ACACGCAAGATCATGGTGATG 58.988 47.619 19.56 8.58 37.20 3.07
2141 2780 1.019673 ACGCAAGATCATGGTGATGC 58.980 50.000 0.00 3.06 37.20 3.91
2142 2781 1.018910 CGCAAGATCATGGTGATGCA 58.981 50.000 11.83 0.00 37.20 3.96
2143 2782 1.607148 CGCAAGATCATGGTGATGCAT 59.393 47.619 0.00 0.00 37.20 3.96
2144 2783 2.809696 CGCAAGATCATGGTGATGCATA 59.190 45.455 0.00 0.00 37.20 3.14
2145 2784 3.120304 CGCAAGATCATGGTGATGCATAG 60.120 47.826 0.00 0.00 37.20 2.23
2146 2785 3.366070 GCAAGATCATGGTGATGCATAGC 60.366 47.826 0.00 0.00 37.20 2.97
2147 2786 3.782656 AGATCATGGTGATGCATAGCA 57.217 42.857 0.00 4.86 44.86 3.49
2148 2787 4.094830 AGATCATGGTGATGCATAGCAA 57.905 40.909 0.00 0.00 43.62 3.91
2149 2788 4.663334 AGATCATGGTGATGCATAGCAAT 58.337 39.130 0.00 0.00 43.62 3.56
2150 2789 4.459337 AGATCATGGTGATGCATAGCAATG 59.541 41.667 0.00 5.10 43.62 2.82
2151 2790 3.822940 TCATGGTGATGCATAGCAATGA 58.177 40.909 13.21 13.21 43.62 2.57
2152 2791 3.818773 TCATGGTGATGCATAGCAATGAG 59.181 43.478 13.21 5.62 43.62 2.90
2153 2792 3.564053 TGGTGATGCATAGCAATGAGA 57.436 42.857 0.00 0.00 43.62 3.27
2154 2793 3.473625 TGGTGATGCATAGCAATGAGAG 58.526 45.455 0.00 0.00 43.62 3.20
2155 2794 2.812591 GGTGATGCATAGCAATGAGAGG 59.187 50.000 0.00 0.00 43.62 3.69
2156 2795 2.812591 GTGATGCATAGCAATGAGAGGG 59.187 50.000 0.00 0.00 43.62 4.30
2157 2796 2.224695 TGATGCATAGCAATGAGAGGGG 60.225 50.000 0.00 0.00 43.62 4.79
2158 2797 1.510492 TGCATAGCAATGAGAGGGGA 58.490 50.000 0.00 0.00 34.76 4.81
2159 2798 1.419012 TGCATAGCAATGAGAGGGGAG 59.581 52.381 0.00 0.00 34.76 4.30
2160 2799 1.696336 GCATAGCAATGAGAGGGGAGA 59.304 52.381 0.00 0.00 34.84 3.71
2161 2800 2.289569 GCATAGCAATGAGAGGGGAGAG 60.290 54.545 0.00 0.00 34.84 3.20
2162 2801 1.418334 TAGCAATGAGAGGGGAGAGC 58.582 55.000 0.00 0.00 0.00 4.09
2163 2802 0.619832 AGCAATGAGAGGGGAGAGCA 60.620 55.000 0.00 0.00 0.00 4.26
2164 2803 0.473326 GCAATGAGAGGGGAGAGCAT 59.527 55.000 0.00 0.00 0.00 3.79
2165 2804 1.542987 GCAATGAGAGGGGAGAGCATC 60.543 57.143 0.00 0.00 0.00 3.91
2166 2805 1.047002 AATGAGAGGGGAGAGCATCG 58.953 55.000 0.00 0.00 42.67 3.84
2167 2806 0.105760 ATGAGAGGGGAGAGCATCGT 60.106 55.000 0.00 0.00 42.67 3.73
2168 2807 0.753479 TGAGAGGGGAGAGCATCGTC 60.753 60.000 0.00 0.00 42.67 4.20
2169 2808 1.456705 AGAGGGGAGAGCATCGTCC 60.457 63.158 0.00 0.00 42.67 4.79
2170 2809 1.758514 GAGGGGAGAGCATCGTCCA 60.759 63.158 0.00 0.00 42.67 4.02
2171 2810 2.022240 GAGGGGAGAGCATCGTCCAC 62.022 65.000 0.00 0.00 42.67 4.02
2172 2811 2.501610 GGGAGAGCATCGTCCACC 59.498 66.667 0.00 0.00 42.67 4.61
2173 2812 2.060980 GGGAGAGCATCGTCCACCT 61.061 63.158 0.00 0.00 42.67 4.00
2174 2813 0.755698 GGGAGAGCATCGTCCACCTA 60.756 60.000 0.00 0.00 42.67 3.08
2175 2814 0.386113 GGAGAGCATCGTCCACCTAC 59.614 60.000 0.00 0.00 42.67 3.18
2176 2815 0.386113 GAGAGCATCGTCCACCTACC 59.614 60.000 0.00 0.00 42.67 3.18
2177 2816 1.043673 AGAGCATCGTCCACCTACCC 61.044 60.000 0.00 0.00 42.67 3.69
2178 2817 1.001760 AGCATCGTCCACCTACCCT 59.998 57.895 0.00 0.00 0.00 4.34
2179 2818 1.043673 AGCATCGTCCACCTACCCTC 61.044 60.000 0.00 0.00 0.00 4.30
2180 2819 1.734137 CATCGTCCACCTACCCTCG 59.266 63.158 0.00 0.00 0.00 4.63
2181 2820 1.035932 CATCGTCCACCTACCCTCGT 61.036 60.000 0.00 0.00 0.00 4.18
2182 2821 0.548031 ATCGTCCACCTACCCTCGTA 59.452 55.000 0.00 0.00 0.00 3.43
2183 2822 0.107508 TCGTCCACCTACCCTCGTAG 60.108 60.000 0.00 0.00 41.55 3.51
2184 2823 0.107508 CGTCCACCTACCCTCGTAGA 60.108 60.000 0.00 0.00 44.18 2.59
2185 2824 1.387539 GTCCACCTACCCTCGTAGAC 58.612 60.000 0.00 0.00 44.18 2.59
2186 2825 0.257039 TCCACCTACCCTCGTAGACC 59.743 60.000 0.00 0.00 44.18 3.85
2187 2826 1.099879 CCACCTACCCTCGTAGACCG 61.100 65.000 0.00 0.00 44.18 4.79
2188 2827 0.393537 CACCTACCCTCGTAGACCGT 60.394 60.000 0.00 0.00 44.18 4.83
2189 2828 1.134401 CACCTACCCTCGTAGACCGTA 60.134 57.143 0.00 0.00 44.18 4.02
2190 2829 1.559682 ACCTACCCTCGTAGACCGTAA 59.440 52.381 0.00 0.00 44.18 3.18
2191 2830 2.216898 CCTACCCTCGTAGACCGTAAG 58.783 57.143 0.00 0.00 44.18 2.34
2192 2831 1.601430 CTACCCTCGTAGACCGTAAGC 59.399 57.143 0.00 0.00 44.18 3.09
2193 2832 1.354506 CCCTCGTAGACCGTAAGCG 59.645 63.158 0.00 0.00 37.94 4.68
2210 2849 3.850207 CGGAAGCGTTATGACAACG 57.150 52.632 5.22 5.22 45.56 4.10
2217 2856 0.785378 CGTTATGACAACGCGGTTGA 59.215 50.000 22.26 6.79 45.28 3.18
2218 2857 1.392168 CGTTATGACAACGCGGTTGAT 59.608 47.619 22.26 12.10 45.28 2.57
2219 2858 2.769376 GTTATGACAACGCGGTTGATG 58.231 47.619 22.26 11.18 45.28 3.07
2220 2859 2.087501 TATGACAACGCGGTTGATGT 57.912 45.000 22.26 13.84 45.28 3.06
2221 2860 2.087501 ATGACAACGCGGTTGATGTA 57.912 45.000 22.26 9.68 45.28 2.29
2222 2861 1.424403 TGACAACGCGGTTGATGTAG 58.576 50.000 22.26 1.41 45.28 2.74
2223 2862 1.269883 TGACAACGCGGTTGATGTAGT 60.270 47.619 22.26 4.69 45.28 2.73
2224 2863 1.389106 GACAACGCGGTTGATGTAGTC 59.611 52.381 22.26 10.01 45.28 2.59
2225 2864 0.365523 CAACGCGGTTGATGTAGTCG 59.634 55.000 12.47 0.00 45.28 4.18
2226 2865 0.038892 AACGCGGTTGATGTAGTCGT 60.039 50.000 12.47 0.00 0.00 4.34
2227 2866 0.804364 ACGCGGTTGATGTAGTCGTA 59.196 50.000 12.47 0.00 0.00 3.43
2228 2867 1.186030 CGCGGTTGATGTAGTCGTAC 58.814 55.000 0.00 0.00 0.00 3.67
2229 2868 1.466192 CGCGGTTGATGTAGTCGTACA 60.466 52.381 0.00 0.00 43.43 2.90
2242 2881 8.943909 ATGTAGTCGTACATCTATATGATCGA 57.056 34.615 0.00 0.00 45.20 3.59
2243 2882 8.819015 ATGTAGTCGTACATCTATATGATCGAC 58.181 37.037 21.53 21.53 45.20 4.20
2245 2884 5.491092 GTCGTACATCTATATGATCGACCG 58.509 45.833 20.01 0.00 45.16 4.79
2246 2885 5.290400 GTCGTACATCTATATGATCGACCGA 59.710 44.000 20.01 0.00 45.16 4.69
2247 2886 6.018913 GTCGTACATCTATATGATCGACCGAT 60.019 42.308 20.01 4.42 45.16 4.18
2257 2896 1.731160 GATCGACCGATCCTAGTACCG 59.269 57.143 18.61 0.00 43.71 4.02
2258 2897 0.752658 TCGACCGATCCTAGTACCGA 59.247 55.000 0.00 0.00 0.00 4.69
2259 2898 1.138859 TCGACCGATCCTAGTACCGAA 59.861 52.381 0.00 0.00 0.00 4.30
2260 2899 1.262683 CGACCGATCCTAGTACCGAAC 59.737 57.143 0.00 0.00 0.00 3.95
2261 2900 1.262683 GACCGATCCTAGTACCGAACG 59.737 57.143 0.00 0.00 0.00 3.95
2262 2901 1.303309 CCGATCCTAGTACCGAACGT 58.697 55.000 0.00 0.00 0.00 3.99
2263 2902 2.158957 ACCGATCCTAGTACCGAACGTA 60.159 50.000 0.00 0.00 0.00 3.57
2264 2903 2.221981 CCGATCCTAGTACCGAACGTAC 59.778 54.545 0.00 0.00 46.69 3.67
2272 2911 2.505557 CCGAACGTACGGCACCTC 60.506 66.667 21.06 6.84 46.20 3.85
2273 2912 2.505557 CGAACGTACGGCACCTCC 60.506 66.667 21.06 0.00 0.00 4.30
2282 2921 3.512516 GGCACCTCCGCAATCTGC 61.513 66.667 0.00 0.00 40.69 4.26
2283 2922 2.747460 GCACCTCCGCAATCTGCA 60.747 61.111 0.00 0.00 45.36 4.41
2284 2923 3.044059 GCACCTCCGCAATCTGCAC 62.044 63.158 0.00 0.00 45.36 4.57
2285 2924 1.672030 CACCTCCGCAATCTGCACA 60.672 57.895 0.00 0.00 45.36 4.57
2286 2925 1.672356 ACCTCCGCAATCTGCACAC 60.672 57.895 0.00 0.00 45.36 3.82
2287 2926 2.743752 CCTCCGCAATCTGCACACG 61.744 63.158 0.00 0.00 45.36 4.49
2288 2927 2.029288 CTCCGCAATCTGCACACGT 61.029 57.895 0.00 0.00 45.36 4.49
2289 2928 1.568612 CTCCGCAATCTGCACACGTT 61.569 55.000 0.00 0.00 45.36 3.99
2290 2929 1.154413 CCGCAATCTGCACACGTTC 60.154 57.895 0.00 0.00 45.36 3.95
2291 2930 1.569003 CGCAATCTGCACACGTTCA 59.431 52.632 0.00 0.00 45.36 3.18
2292 2931 0.451628 CGCAATCTGCACACGTTCAG 60.452 55.000 0.00 0.00 45.36 3.02
2293 2932 0.727122 GCAATCTGCACACGTTCAGC 60.727 55.000 4.78 1.26 44.26 4.26
2294 2933 0.870393 CAATCTGCACACGTTCAGCT 59.130 50.000 5.40 0.00 0.00 4.24
2295 2934 1.136141 CAATCTGCACACGTTCAGCTC 60.136 52.381 5.40 0.00 0.00 4.09
2296 2935 1.010935 ATCTGCACACGTTCAGCTCG 61.011 55.000 5.40 0.00 0.00 5.03
2297 2936 2.661537 TGCACACGTTCAGCTCGG 60.662 61.111 5.40 0.00 0.00 4.63
2298 2937 2.661866 GCACACGTTCAGCTCGGT 60.662 61.111 0.00 0.00 0.00 4.69
2299 2938 2.943345 GCACACGTTCAGCTCGGTG 61.943 63.158 9.18 9.18 34.88 4.94
2300 2939 1.299850 CACACGTTCAGCTCGGTGA 60.300 57.895 9.25 0.00 34.24 4.02
2301 2940 1.299926 ACACGTTCAGCTCGGTGAC 60.300 57.895 9.25 0.00 0.00 3.67
2316 2955 1.429463 GTGACGTCCCATGAACTCAC 58.571 55.000 14.12 5.00 0.00 3.51
2317 2956 0.038618 TGACGTCCCATGAACTCACG 60.039 55.000 14.12 0.00 36.54 4.35
2318 2957 0.242825 GACGTCCCATGAACTCACGA 59.757 55.000 3.51 0.00 34.55 4.35
2319 2958 0.895530 ACGTCCCATGAACTCACGAT 59.104 50.000 0.00 0.00 34.55 3.73
2320 2959 1.135083 ACGTCCCATGAACTCACGATC 60.135 52.381 0.00 0.00 34.55 3.69
2321 2960 1.560923 GTCCCATGAACTCACGATCG 58.439 55.000 14.88 14.88 0.00 3.69
2328 2967 4.023622 CCATGAACTCACGATCGAGTAGAT 60.024 45.833 24.34 10.09 45.56 1.98
2342 2981 4.080243 TCGAGTAGATCTTCAAGGGAGAGT 60.080 45.833 0.00 0.00 0.00 3.24
2343 2982 4.642885 CGAGTAGATCTTCAAGGGAGAGTT 59.357 45.833 0.00 0.00 0.00 3.01
2344 2983 5.220970 CGAGTAGATCTTCAAGGGAGAGTTC 60.221 48.000 0.00 0.00 0.00 3.01
2345 2984 4.959839 AGTAGATCTTCAAGGGAGAGTTCC 59.040 45.833 0.00 0.00 43.23 3.62
2346 2985 2.763448 AGATCTTCAAGGGAGAGTTCCG 59.237 50.000 0.00 0.00 45.04 4.30
2348 2987 1.893801 TCTTCAAGGGAGAGTTCCGTC 59.106 52.381 0.00 0.00 45.04 4.79
2351 2990 0.390472 CAAGGGAGAGTTCCGTCAGC 60.390 60.000 0.00 0.00 45.04 4.26
2352 2991 0.832135 AAGGGAGAGTTCCGTCAGCA 60.832 55.000 0.00 0.00 45.04 4.41
2378 3272 1.708822 CGTGATGACGGTGTTGATGA 58.291 50.000 0.00 0.00 42.18 2.92
2381 3275 2.076100 TGATGACGGTGTTGATGAAGC 58.924 47.619 0.00 0.00 0.00 3.86
2384 3278 2.683968 TGACGGTGTTGATGAAGCTAC 58.316 47.619 0.00 0.00 0.00 3.58
2388 3282 2.000447 GGTGTTGATGAAGCTACCGAC 59.000 52.381 0.00 0.00 0.00 4.79
2391 3285 0.245266 TTGATGAAGCTACCGACGCA 59.755 50.000 0.00 0.00 0.00 5.24
2392 3286 0.179137 TGATGAAGCTACCGACGCAG 60.179 55.000 0.00 0.00 0.00 5.18
2393 3287 0.872021 GATGAAGCTACCGACGCAGG 60.872 60.000 0.00 0.00 37.30 4.85
2394 3288 2.202756 GAAGCTACCGACGCAGGG 60.203 66.667 1.73 0.00 35.02 4.45
2395 3289 4.452733 AAGCTACCGACGCAGGGC 62.453 66.667 1.73 0.00 35.02 5.19
2398 3292 2.202756 CTACCGACGCAGGGCTTC 60.203 66.667 1.73 0.00 35.02 3.86
2399 3293 4.124351 TACCGACGCAGGGCTTCG 62.124 66.667 9.73 9.73 47.00 3.79
2403 3297 2.125673 GACGCAGGGCTTCGCTTA 60.126 61.111 0.00 0.00 0.00 3.09
2406 3300 2.718107 GCAGGGCTTCGCTTATGC 59.282 61.111 0.00 0.00 0.00 3.14
2407 3301 2.114670 GCAGGGCTTCGCTTATGCA 61.115 57.895 1.16 0.00 39.64 3.96
2409 3303 0.745845 CAGGGCTTCGCTTATGCACT 60.746 55.000 0.00 0.00 42.49 4.40
2410 3304 0.830648 AGGGCTTCGCTTATGCACTA 59.169 50.000 0.00 0.00 40.08 2.74
2412 3306 1.473434 GGGCTTCGCTTATGCACTACT 60.473 52.381 0.00 0.00 39.64 2.57
2413 3307 2.223971 GGGCTTCGCTTATGCACTACTA 60.224 50.000 0.00 0.00 39.64 1.82
2414 3308 3.555168 GGGCTTCGCTTATGCACTACTAT 60.555 47.826 0.00 0.00 39.64 2.12
2415 3309 3.430218 GGCTTCGCTTATGCACTACTATG 59.570 47.826 0.00 0.00 39.64 2.23
2416 3310 4.299155 GCTTCGCTTATGCACTACTATGA 58.701 43.478 0.00 0.00 39.64 2.15
2417 3311 4.926238 GCTTCGCTTATGCACTACTATGAT 59.074 41.667 0.00 0.00 39.64 2.45
2418 3312 6.093404 GCTTCGCTTATGCACTACTATGATA 58.907 40.000 0.00 0.00 39.64 2.15
2419 3313 6.754209 GCTTCGCTTATGCACTACTATGATAT 59.246 38.462 0.00 0.00 39.64 1.63
2421 3315 7.391148 TCGCTTATGCACTACTATGATATGA 57.609 36.000 0.00 0.00 39.64 2.15
2422 3316 7.251281 TCGCTTATGCACTACTATGATATGAC 58.749 38.462 0.00 0.00 39.64 3.06
2423 3317 6.473778 CGCTTATGCACTACTATGATATGACC 59.526 42.308 0.00 0.00 39.64 4.02
2424 3318 6.473778 GCTTATGCACTACTATGATATGACCG 59.526 42.308 0.00 0.00 39.41 4.79
2425 3319 7.628580 GCTTATGCACTACTATGATATGACCGA 60.629 40.741 0.00 0.00 39.41 4.69
2426 3320 5.629079 TGCACTACTATGATATGACCGAG 57.371 43.478 0.00 0.00 0.00 4.63
2427 3321 4.459337 TGCACTACTATGATATGACCGAGG 59.541 45.833 0.00 0.00 0.00 4.63
2428 3322 4.459685 GCACTACTATGATATGACCGAGGT 59.540 45.833 0.00 0.00 0.00 3.85
2429 3323 5.620205 GCACTACTATGATATGACCGAGGTG 60.620 48.000 0.00 0.00 0.00 4.00
2430 3324 5.010933 ACTACTATGATATGACCGAGGTGG 58.989 45.833 0.00 0.00 46.41 4.61
2435 3329 6.897966 ACTATGATATGACCGAGGTGGATTAT 59.102 38.462 0.00 0.00 42.00 1.28
2436 3330 5.405935 TGATATGACCGAGGTGGATTATG 57.594 43.478 0.00 0.00 42.00 1.90
2441 3335 1.128200 CCGAGGTGGATTATGGTGGA 58.872 55.000 0.00 0.00 42.00 4.02
2443 3337 1.070758 CGAGGTGGATTATGGTGGAGG 59.929 57.143 0.00 0.00 0.00 4.30
2445 3339 0.478507 GGTGGATTATGGTGGAGGGG 59.521 60.000 0.00 0.00 0.00 4.79
2447 3341 1.360393 TGGATTATGGTGGAGGGGGC 61.360 60.000 0.00 0.00 0.00 5.80
2449 3343 0.178990 GATTATGGTGGAGGGGGCAC 60.179 60.000 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.040166 ACTTGATAATTGGCATTGACTCATCC 59.960 38.462 0.00 0.00 0.00 3.51
186 191 6.927381 GCCTTTTTATAGCTATCGTGGTTAGA 59.073 38.462 10.16 0.00 0.00 2.10
194 199 4.065088 TGCAGGCCTTTTTATAGCTATCG 58.935 43.478 10.16 0.00 0.00 2.92
226 231 4.853856 TGAAGGATGGATGATGGTATGGAT 59.146 41.667 0.00 0.00 0.00 3.41
319 324 3.597855 TCGCAAGGATCGTCAGGATGAT 61.598 50.000 3.72 3.72 44.09 2.45
391 396 6.770785 ACTAGTTGTTGTTGTGACCATTGTAT 59.229 34.615 0.00 0.00 0.00 2.29
400 405 2.158726 GGGGGACTAGTTGTTGTTGTGA 60.159 50.000 0.00 0.00 0.00 3.58
430 438 3.142174 GTGGTTGCTAGGATAATGGCTC 58.858 50.000 0.00 0.00 0.00 4.70
442 450 3.243704 GGAAATGCTTGTTGTGGTTGCTA 60.244 43.478 0.00 0.00 0.00 3.49
613 621 1.040339 GGTTGTTGTGGTTGCTGGGA 61.040 55.000 0.00 0.00 0.00 4.37
636 668 1.461268 TGGCTGTTGAGTCTGGGGA 60.461 57.895 0.00 0.00 0.00 4.81
651 683 0.034756 GGGGAAATGGTTGTTGTGGC 59.965 55.000 0.00 0.00 0.00 5.01
654 686 1.047801 GCTGGGGAAATGGTTGTTGT 58.952 50.000 0.00 0.00 0.00 3.32
655 687 1.047002 TGCTGGGGAAATGGTTGTTG 58.953 50.000 0.00 0.00 0.00 3.33
656 688 1.416030 GTTGCTGGGGAAATGGTTGTT 59.584 47.619 0.00 0.00 0.00 2.83
657 689 1.047801 GTTGCTGGGGAAATGGTTGT 58.952 50.000 0.00 0.00 0.00 3.32
658 690 0.321346 GGTTGCTGGGGAAATGGTTG 59.679 55.000 0.00 0.00 0.00 3.77
659 691 0.105246 TGGTTGCTGGGGAAATGGTT 60.105 50.000 0.00 0.00 0.00 3.67
660 692 0.831711 GTGGTTGCTGGGGAAATGGT 60.832 55.000 0.00 0.00 0.00 3.55
661 693 0.831288 TGTGGTTGCTGGGGAAATGG 60.831 55.000 0.00 0.00 0.00 3.16
662 694 1.047002 TTGTGGTTGCTGGGGAAATG 58.953 50.000 0.00 0.00 0.00 2.32
663 695 1.047801 GTTGTGGTTGCTGGGGAAAT 58.952 50.000 0.00 0.00 0.00 2.17
664 696 0.324738 TGTTGTGGTTGCTGGGGAAA 60.325 50.000 0.00 0.00 0.00 3.13
665 697 0.324738 TTGTTGTGGTTGCTGGGGAA 60.325 50.000 0.00 0.00 0.00 3.97
666 698 1.040339 GTTGTTGTGGTTGCTGGGGA 61.040 55.000 0.00 0.00 0.00 4.81
667 699 1.042559 AGTTGTTGTGGTTGCTGGGG 61.043 55.000 0.00 0.00 0.00 4.96
668 700 1.686355 TAGTTGTTGTGGTTGCTGGG 58.314 50.000 0.00 0.00 0.00 4.45
669 701 3.305335 GGAATAGTTGTTGTGGTTGCTGG 60.305 47.826 0.00 0.00 0.00 4.85
670 702 3.305335 GGGAATAGTTGTTGTGGTTGCTG 60.305 47.826 0.00 0.00 0.00 4.41
671 703 2.890945 GGGAATAGTTGTTGTGGTTGCT 59.109 45.455 0.00 0.00 0.00 3.91
672 704 2.029380 GGGGAATAGTTGTTGTGGTTGC 60.029 50.000 0.00 0.00 0.00 4.17
673 705 2.560981 GGGGGAATAGTTGTTGTGGTTG 59.439 50.000 0.00 0.00 0.00 3.77
674 706 2.178106 TGGGGGAATAGTTGTTGTGGTT 59.822 45.455 0.00 0.00 0.00 3.67
675 707 1.783979 TGGGGGAATAGTTGTTGTGGT 59.216 47.619 0.00 0.00 0.00 4.16
676 708 2.041081 TCTGGGGGAATAGTTGTTGTGG 59.959 50.000 0.00 0.00 0.00 4.17
677 709 3.081804 GTCTGGGGGAATAGTTGTTGTG 58.918 50.000 0.00 0.00 0.00 3.33
690 722 0.537371 GTGGTTGTTGAGTCTGGGGG 60.537 60.000 0.00 0.00 0.00 5.40
697 729 2.520069 TGGTTGTTGTGGTTGTTGAGT 58.480 42.857 0.00 0.00 0.00 3.41
699 731 4.499183 GAAATGGTTGTTGTGGTTGTTGA 58.501 39.130 0.00 0.00 0.00 3.18
848 917 1.851304 TTGTTGCTGGGGGAATGATC 58.149 50.000 0.00 0.00 0.00 2.92
868 937 0.250513 GATGGCTGAAAGGACGGTCT 59.749 55.000 8.23 0.00 0.00 3.85
877 946 3.745975 CGTTGTTGTAGAGATGGCTGAAA 59.254 43.478 0.00 0.00 0.00 2.69
945 1014 3.245730 ACCAAAGGGATGACACCAATGAT 60.246 43.478 0.00 0.00 38.05 2.45
963 1032 1.557371 TGTGGCCAGATTATCGACCAA 59.443 47.619 5.11 0.00 0.00 3.67
986 1055 1.136305 GCTGCATCACTTGGCAATCAT 59.864 47.619 0.00 0.00 39.93 2.45
1099 1252 6.419413 TGTTGTTGTTGTTCTTGTTCTTGTTC 59.581 34.615 0.00 0.00 0.00 3.18
1110 1263 5.352284 TGTTGTTGTTGTTGTTGTTGTTCT 58.648 33.333 0.00 0.00 0.00 3.01
1111 1264 5.643339 TGTTGTTGTTGTTGTTGTTGTTC 57.357 34.783 0.00 0.00 0.00 3.18
1162 1315 4.951254 TGTTGTTGTCGAGATAGTGGAAA 58.049 39.130 0.00 0.00 0.00 3.13
1164 1317 4.021456 ACATGTTGTTGTCGAGATAGTGGA 60.021 41.667 0.00 0.00 0.00 4.02
1175 1328 2.034558 CCTTGACCCACATGTTGTTGTC 59.965 50.000 0.00 1.23 32.91 3.18
1185 1338 1.254026 CGAGAGTACCTTGACCCACA 58.746 55.000 0.00 0.00 0.00 4.17
1290 1443 1.745087 GGTGGGACATACACATTGCAG 59.255 52.381 0.00 0.00 44.52 4.41
1296 1449 1.623311 CACTCAGGTGGGACATACACA 59.377 52.381 0.00 0.00 44.52 3.72
1407 1603 1.061711 GTGCATCTGCTAAGCAACGAG 59.938 52.381 3.53 0.00 40.35 4.18
1460 1657 1.651987 GGGTCACACATGATGGTACG 58.348 55.000 0.00 0.00 37.14 3.67
1462 1659 0.539518 CGGGGTCACACATGATGGTA 59.460 55.000 0.00 0.00 37.14 3.25
1573 1775 1.349688 ACTGCGGTTAGGGATGAACAA 59.650 47.619 0.00 0.00 0.00 2.83
1674 1876 3.485463 TCAATCGGCCTATAAACTGGG 57.515 47.619 0.00 0.00 0.00 4.45
1872 2074 6.252015 CCAATCTCAAAATTGCATCAACGTAG 59.748 38.462 0.00 0.00 35.68 3.51
1874 2076 4.925054 CCAATCTCAAAATTGCATCAACGT 59.075 37.500 0.00 0.00 35.68 3.99
1880 2082 3.008157 TGCCACCAATCTCAAAATTGCAT 59.992 39.130 0.00 0.00 35.68 3.96
2060 2265 2.124507 TTTCCCCCTTCTCTGCACGG 62.125 60.000 0.00 0.00 0.00 4.94
2071 2276 0.871024 TCCCCAACAATTTTCCCCCT 59.129 50.000 0.00 0.00 0.00 4.79
2080 2285 3.713826 ATGACTACGTTCCCCAACAAT 57.286 42.857 0.00 0.00 32.14 2.71
2083 2288 3.404899 TGAAATGACTACGTTCCCCAAC 58.595 45.455 0.00 0.00 0.00 3.77
2084 2289 3.773418 TGAAATGACTACGTTCCCCAA 57.227 42.857 0.00 0.00 0.00 4.12
2085 2290 3.773418 TTGAAATGACTACGTTCCCCA 57.227 42.857 0.00 0.00 0.00 4.96
2118 2757 0.179181 CACCATGATCTTGCGTGTGC 60.179 55.000 15.81 0.00 43.20 4.57
2121 2760 1.268386 GCATCACCATGATCTTGCGTG 60.268 52.381 17.02 17.02 34.28 5.34
2123 2762 1.018910 TGCATCACCATGATCTTGCG 58.981 50.000 3.07 0.30 34.28 4.85
2124 2763 3.366070 GCTATGCATCACCATGATCTTGC 60.366 47.826 0.19 0.00 34.28 4.01
2125 2764 3.818773 TGCTATGCATCACCATGATCTTG 59.181 43.478 0.19 1.60 34.28 3.02
2126 2765 4.094830 TGCTATGCATCACCATGATCTT 57.905 40.909 0.19 0.00 34.28 2.40
2127 2766 3.782656 TGCTATGCATCACCATGATCT 57.217 42.857 0.19 0.00 34.28 2.75
2128 2767 4.457949 TCATTGCTATGCATCACCATGATC 59.542 41.667 0.19 0.00 38.76 2.92
2129 2768 4.403734 TCATTGCTATGCATCACCATGAT 58.596 39.130 0.19 0.00 38.76 2.45
2130 2769 3.818773 CTCATTGCTATGCATCACCATGA 59.181 43.478 0.19 8.77 38.76 3.07
2131 2770 3.818773 TCTCATTGCTATGCATCACCATG 59.181 43.478 0.19 4.57 38.76 3.66
2132 2771 4.072839 CTCTCATTGCTATGCATCACCAT 58.927 43.478 0.19 0.00 38.76 3.55
2133 2772 3.473625 CTCTCATTGCTATGCATCACCA 58.526 45.455 0.19 0.00 38.76 4.17
2134 2773 2.812591 CCTCTCATTGCTATGCATCACC 59.187 50.000 0.19 0.00 38.76 4.02
2135 2774 2.812591 CCCTCTCATTGCTATGCATCAC 59.187 50.000 0.19 0.00 38.76 3.06
2136 2775 2.224695 CCCCTCTCATTGCTATGCATCA 60.225 50.000 0.19 0.00 38.76 3.07
2137 2776 2.039480 TCCCCTCTCATTGCTATGCATC 59.961 50.000 0.19 0.00 38.76 3.91
2138 2777 2.040012 CTCCCCTCTCATTGCTATGCAT 59.960 50.000 3.79 3.79 38.76 3.96
2139 2778 1.419012 CTCCCCTCTCATTGCTATGCA 59.581 52.381 3.00 0.00 36.47 3.96
2140 2779 1.696336 TCTCCCCTCTCATTGCTATGC 59.304 52.381 3.00 0.00 0.00 3.14
2141 2780 2.289569 GCTCTCCCCTCTCATTGCTATG 60.290 54.545 1.30 1.30 0.00 2.23
2142 2781 1.977129 GCTCTCCCCTCTCATTGCTAT 59.023 52.381 0.00 0.00 0.00 2.97
2143 2782 1.343377 TGCTCTCCCCTCTCATTGCTA 60.343 52.381 0.00 0.00 0.00 3.49
2144 2783 0.619832 TGCTCTCCCCTCTCATTGCT 60.620 55.000 0.00 0.00 0.00 3.91
2145 2784 0.473326 ATGCTCTCCCCTCTCATTGC 59.527 55.000 0.00 0.00 0.00 3.56
2146 2785 1.270199 CGATGCTCTCCCCTCTCATTG 60.270 57.143 0.00 0.00 0.00 2.82
2147 2786 1.047002 CGATGCTCTCCCCTCTCATT 58.953 55.000 0.00 0.00 0.00 2.57
2148 2787 0.105760 ACGATGCTCTCCCCTCTCAT 60.106 55.000 0.00 0.00 0.00 2.90
2149 2788 0.753479 GACGATGCTCTCCCCTCTCA 60.753 60.000 0.00 0.00 0.00 3.27
2150 2789 1.460273 GGACGATGCTCTCCCCTCTC 61.460 65.000 0.00 0.00 0.00 3.20
2151 2790 1.456705 GGACGATGCTCTCCCCTCT 60.457 63.158 0.00 0.00 0.00 3.69
2152 2791 1.758514 TGGACGATGCTCTCCCCTC 60.759 63.158 0.00 0.00 0.00 4.30
2153 2792 2.060980 GTGGACGATGCTCTCCCCT 61.061 63.158 0.00 0.00 0.00 4.79
2154 2793 2.501610 GTGGACGATGCTCTCCCC 59.498 66.667 0.00 0.00 0.00 4.81
2155 2794 0.755698 TAGGTGGACGATGCTCTCCC 60.756 60.000 0.00 0.00 0.00 4.30
2156 2795 0.386113 GTAGGTGGACGATGCTCTCC 59.614 60.000 0.00 0.00 0.00 3.71
2157 2796 0.386113 GGTAGGTGGACGATGCTCTC 59.614 60.000 0.00 0.00 0.00 3.20
2158 2797 1.043673 GGGTAGGTGGACGATGCTCT 61.044 60.000 0.00 0.00 0.00 4.09
2159 2798 1.043673 AGGGTAGGTGGACGATGCTC 61.044 60.000 0.00 0.00 0.00 4.26
2160 2799 1.001760 AGGGTAGGTGGACGATGCT 59.998 57.895 0.00 0.00 0.00 3.79
2161 2800 1.442148 GAGGGTAGGTGGACGATGC 59.558 63.158 0.00 0.00 0.00 3.91
2162 2801 1.035932 ACGAGGGTAGGTGGACGATG 61.036 60.000 0.00 0.00 0.00 3.84
2163 2802 0.548031 TACGAGGGTAGGTGGACGAT 59.452 55.000 0.00 0.00 0.00 3.73
2164 2803 0.107508 CTACGAGGGTAGGTGGACGA 60.108 60.000 0.00 0.00 42.02 4.20
2165 2804 0.107508 TCTACGAGGGTAGGTGGACG 60.108 60.000 0.00 0.00 45.10 4.79
2166 2805 1.387539 GTCTACGAGGGTAGGTGGAC 58.612 60.000 0.00 0.00 45.10 4.02
2167 2806 0.257039 GGTCTACGAGGGTAGGTGGA 59.743 60.000 0.00 0.00 45.10 4.02
2168 2807 2.804549 GGTCTACGAGGGTAGGTGG 58.195 63.158 0.00 0.00 45.10 4.61
2186 2825 1.254570 GTCATAACGCTTCCGCTTACG 59.745 52.381 0.00 0.00 38.22 3.18
2187 2826 2.264813 TGTCATAACGCTTCCGCTTAC 58.735 47.619 0.00 0.00 38.22 2.34
2188 2827 2.658373 TGTCATAACGCTTCCGCTTA 57.342 45.000 0.00 0.00 38.22 3.09
2189 2828 1.463444 GTTGTCATAACGCTTCCGCTT 59.537 47.619 0.00 0.00 38.22 4.68
2190 2829 1.076332 GTTGTCATAACGCTTCCGCT 58.924 50.000 0.00 0.00 38.22 5.52
2191 2830 0.247145 CGTTGTCATAACGCTTCCGC 60.247 55.000 0.00 0.00 36.82 5.54
2192 2831 3.850207 CGTTGTCATAACGCTTCCG 57.150 52.632 0.00 0.00 36.82 4.30
2198 2837 0.785378 TCAACCGCGTTGTCATAACG 59.215 50.000 16.97 1.71 43.23 3.18
2199 2838 2.158841 ACATCAACCGCGTTGTCATAAC 59.841 45.455 16.97 0.00 43.23 1.89
2200 2839 2.418692 ACATCAACCGCGTTGTCATAA 58.581 42.857 16.97 2.99 43.23 1.90
2201 2840 2.087501 ACATCAACCGCGTTGTCATA 57.912 45.000 16.97 3.28 43.23 2.15
2202 2841 1.999735 CTACATCAACCGCGTTGTCAT 59.000 47.619 16.97 5.85 43.23 3.06
2203 2842 1.269883 ACTACATCAACCGCGTTGTCA 60.270 47.619 16.97 4.13 43.23 3.58
2204 2843 1.389106 GACTACATCAACCGCGTTGTC 59.611 52.381 16.97 5.64 43.23 3.18
2205 2844 1.425412 GACTACATCAACCGCGTTGT 58.575 50.000 16.97 9.99 43.23 3.32
2206 2845 0.365523 CGACTACATCAACCGCGTTG 59.634 55.000 4.92 10.14 43.99 4.10
2207 2846 0.038892 ACGACTACATCAACCGCGTT 60.039 50.000 4.92 0.00 0.00 4.84
2208 2847 0.804364 TACGACTACATCAACCGCGT 59.196 50.000 4.92 0.00 0.00 6.01
2209 2848 1.186030 GTACGACTACATCAACCGCG 58.814 55.000 0.00 0.00 0.00 6.46
2210 2849 2.267188 TGTACGACTACATCAACCGC 57.733 50.000 0.00 0.00 0.00 5.68
2217 2856 8.819015 GTCGATCATATAGATGTACGACTACAT 58.181 37.037 26.80 0.00 46.09 2.29
2218 2857 8.182658 GTCGATCATATAGATGTACGACTACA 57.817 38.462 26.80 0.00 46.09 2.74
2223 2862 5.413499 TCGGTCGATCATATAGATGTACGA 58.587 41.667 13.83 13.83 37.00 3.43
2224 2863 5.713822 TCGGTCGATCATATAGATGTACG 57.286 43.478 0.00 10.68 37.00 3.67
2238 2877 1.345741 TCGGTACTAGGATCGGTCGAT 59.654 52.381 8.01 5.49 37.59 3.59
2239 2878 0.752658 TCGGTACTAGGATCGGTCGA 59.247 55.000 8.01 0.00 0.00 4.20
2240 2879 1.262683 GTTCGGTACTAGGATCGGTCG 59.737 57.143 8.01 0.00 0.00 4.79
2241 2880 1.262683 CGTTCGGTACTAGGATCGGTC 59.737 57.143 8.01 0.36 0.00 4.79
2242 2881 1.303309 CGTTCGGTACTAGGATCGGT 58.697 55.000 8.01 0.00 0.00 4.69
2243 2882 1.303309 ACGTTCGGTACTAGGATCGG 58.697 55.000 8.01 0.00 31.53 4.18
2244 2883 3.511856 GTACGTTCGGTACTAGGATCG 57.488 52.381 0.00 0.00 46.50 3.69
2256 2895 2.505557 GGAGGTGCCGTACGTTCG 60.506 66.667 15.21 7.68 0.00 3.95
2265 2904 3.512516 GCAGATTGCGGAGGTGCC 61.513 66.667 0.00 0.00 31.71 5.01
2274 2913 0.727122 GCTGAACGTGTGCAGATTGC 60.727 55.000 12.25 0.00 45.29 3.56
2275 2914 0.870393 AGCTGAACGTGTGCAGATTG 59.130 50.000 12.25 0.00 34.06 2.67
2276 2915 1.151668 GAGCTGAACGTGTGCAGATT 58.848 50.000 12.25 0.00 34.06 2.40
2277 2916 1.010935 CGAGCTGAACGTGTGCAGAT 61.011 55.000 12.25 5.18 34.06 2.90
2278 2917 1.661509 CGAGCTGAACGTGTGCAGA 60.662 57.895 12.25 0.00 34.06 4.26
2279 2918 2.661566 CCGAGCTGAACGTGTGCAG 61.662 63.158 3.48 3.48 35.28 4.41
2280 2919 2.661537 CCGAGCTGAACGTGTGCA 60.662 61.111 0.00 0.00 0.00 4.57
2281 2920 2.661866 ACCGAGCTGAACGTGTGC 60.662 61.111 0.00 0.00 0.00 4.57
2282 2921 1.299850 TCACCGAGCTGAACGTGTG 60.300 57.895 0.00 0.00 35.24 3.82
2283 2922 1.299926 GTCACCGAGCTGAACGTGT 60.300 57.895 0.00 0.00 0.00 4.49
2284 2923 2.365068 CGTCACCGAGCTGAACGTG 61.365 63.158 0.00 0.00 35.63 4.49
2285 2924 2.050351 CGTCACCGAGCTGAACGT 60.050 61.111 0.00 0.00 35.63 3.99
2286 2925 2.050351 ACGTCACCGAGCTGAACG 60.050 61.111 0.00 0.00 37.88 3.95
2287 2926 1.733399 GGACGTCACCGAGCTGAAC 60.733 63.158 18.91 0.00 37.88 3.18
2288 2927 2.649034 GGACGTCACCGAGCTGAA 59.351 61.111 18.91 0.00 37.88 3.02
2289 2928 3.371063 GGGACGTCACCGAGCTGA 61.371 66.667 18.91 0.00 37.88 4.26
2290 2929 3.006756 ATGGGACGTCACCGAGCTG 62.007 63.158 16.75 0.00 37.88 4.24
2291 2930 2.680352 ATGGGACGTCACCGAGCT 60.680 61.111 16.75 0.00 37.88 4.09
2292 2931 2.501223 TTCATGGGACGTCACCGAGC 62.501 60.000 16.75 0.00 37.88 5.03
2293 2932 0.736325 GTTCATGGGACGTCACCGAG 60.736 60.000 16.75 10.99 37.88 4.63
2294 2933 1.183030 AGTTCATGGGACGTCACCGA 61.183 55.000 16.75 9.27 37.88 4.69
2295 2934 0.736325 GAGTTCATGGGACGTCACCG 60.736 60.000 16.75 6.68 40.83 4.94
2296 2935 0.320374 TGAGTTCATGGGACGTCACC 59.680 55.000 16.75 15.21 0.00 4.02
2297 2936 1.429463 GTGAGTTCATGGGACGTCAC 58.571 55.000 18.91 15.66 0.00 3.67
2298 2937 0.038618 CGTGAGTTCATGGGACGTCA 60.039 55.000 18.91 0.00 0.00 4.35
2299 2938 0.242825 TCGTGAGTTCATGGGACGTC 59.757 55.000 7.13 7.13 33.80 4.34
2300 2939 0.895530 ATCGTGAGTTCATGGGACGT 59.104 50.000 0.00 0.00 33.80 4.34
2301 2940 1.560923 GATCGTGAGTTCATGGGACG 58.439 55.000 0.00 0.00 33.80 4.79
2302 2941 1.134367 TCGATCGTGAGTTCATGGGAC 59.866 52.381 15.94 0.00 33.80 4.46
2303 2942 1.405463 CTCGATCGTGAGTTCATGGGA 59.595 52.381 15.94 0.00 33.80 4.37
2304 2943 1.135139 ACTCGATCGTGAGTTCATGGG 59.865 52.381 22.80 0.00 46.85 4.00
2307 2946 5.351233 GATCTACTCGATCGTGAGTTCAT 57.649 43.478 22.80 10.99 46.85 2.57
2318 2957 5.055265 TCTCCCTTGAAGATCTACTCGAT 57.945 43.478 0.00 0.00 34.25 3.59
2319 2958 4.080243 ACTCTCCCTTGAAGATCTACTCGA 60.080 45.833 0.00 0.00 0.00 4.04
2320 2959 4.204012 ACTCTCCCTTGAAGATCTACTCG 58.796 47.826 0.00 0.00 0.00 4.18
2321 2960 5.068591 GGAACTCTCCCTTGAAGATCTACTC 59.931 48.000 0.00 0.00 35.42 2.59
2324 2963 3.954904 CGGAACTCTCCCTTGAAGATCTA 59.045 47.826 0.00 0.00 38.71 1.98
2328 2967 1.893801 GACGGAACTCTCCCTTGAAGA 59.106 52.381 0.00 0.00 38.71 2.87
2335 2974 1.079750 GTGCTGACGGAACTCTCCC 60.080 63.158 0.00 0.00 38.71 4.30
2336 2975 1.444553 CGTGCTGACGGAACTCTCC 60.445 63.158 0.00 0.00 42.18 3.71
2339 2978 3.843985 GTCGTGCTGACGGAACTC 58.156 61.111 0.00 0.00 46.11 3.01
2356 2995 2.736995 AACACCGTCATCACGCCG 60.737 61.111 0.00 0.00 45.29 6.46
2357 2996 1.019278 ATCAACACCGTCATCACGCC 61.019 55.000 0.00 0.00 45.29 5.68
2358 2997 0.095245 CATCAACACCGTCATCACGC 59.905 55.000 0.00 0.00 45.29 5.34
2359 2998 1.708822 TCATCAACACCGTCATCACG 58.291 50.000 0.00 0.00 46.29 4.35
2360 2999 2.159653 GCTTCATCAACACCGTCATCAC 60.160 50.000 0.00 0.00 0.00 3.06
2362 3256 2.350522 AGCTTCATCAACACCGTCATC 58.649 47.619 0.00 0.00 0.00 2.92
2368 3262 2.000447 GTCGGTAGCTTCATCAACACC 59.000 52.381 0.00 0.00 0.00 4.16
2369 3263 1.654105 CGTCGGTAGCTTCATCAACAC 59.346 52.381 0.00 0.00 0.00 3.32
2370 3264 1.990799 CGTCGGTAGCTTCATCAACA 58.009 50.000 0.00 0.00 0.00 3.33
2373 3267 0.179137 CTGCGTCGGTAGCTTCATCA 60.179 55.000 0.00 0.00 35.28 3.07
2378 3272 4.452733 GCCCTGCGTCGGTAGCTT 62.453 66.667 0.00 0.00 35.28 3.74
2381 3275 2.202756 GAAGCCCTGCGTCGGTAG 60.203 66.667 0.00 0.00 0.00 3.18
2395 3289 7.970614 TCATATCATAGTAGTGCATAAGCGAAG 59.029 37.037 0.00 0.00 46.23 3.79
2398 3292 6.473778 GGTCATATCATAGTAGTGCATAAGCG 59.526 42.308 0.00 0.00 46.23 4.68
2399 3293 6.473778 CGGTCATATCATAGTAGTGCATAAGC 59.526 42.308 0.00 0.00 42.57 3.09
2400 3294 7.762382 TCGGTCATATCATAGTAGTGCATAAG 58.238 38.462 0.00 0.00 0.00 1.73
2402 3296 6.318900 CCTCGGTCATATCATAGTAGTGCATA 59.681 42.308 0.00 0.00 0.00 3.14
2403 3297 5.126222 CCTCGGTCATATCATAGTAGTGCAT 59.874 44.000 0.00 0.00 0.00 3.96
2406 3300 5.106118 CCACCTCGGTCATATCATAGTAGTG 60.106 48.000 0.00 0.00 0.00 2.74
2407 3301 5.010933 CCACCTCGGTCATATCATAGTAGT 58.989 45.833 0.00 0.00 0.00 2.73
2409 3303 5.251182 TCCACCTCGGTCATATCATAGTA 57.749 43.478 0.00 0.00 35.57 1.82
2410 3304 4.114015 TCCACCTCGGTCATATCATAGT 57.886 45.455 0.00 0.00 35.57 2.12
2412 3306 6.098266 CCATAATCCACCTCGGTCATATCATA 59.902 42.308 0.00 0.00 35.57 2.15
2413 3307 5.104776 CCATAATCCACCTCGGTCATATCAT 60.105 44.000 0.00 0.00 35.57 2.45
2414 3308 4.222810 CCATAATCCACCTCGGTCATATCA 59.777 45.833 0.00 0.00 35.57 2.15
2415 3309 4.223032 ACCATAATCCACCTCGGTCATATC 59.777 45.833 0.00 0.00 35.57 1.63
2416 3310 4.020218 CACCATAATCCACCTCGGTCATAT 60.020 45.833 0.00 0.00 35.57 1.78
2417 3311 3.323691 CACCATAATCCACCTCGGTCATA 59.676 47.826 0.00 0.00 35.57 2.15
2418 3312 2.104792 CACCATAATCCACCTCGGTCAT 59.895 50.000 0.00 0.00 35.57 3.06
2419 3313 1.484653 CACCATAATCCACCTCGGTCA 59.515 52.381 0.00 0.00 35.57 4.02
2421 3315 0.837272 CCACCATAATCCACCTCGGT 59.163 55.000 0.00 0.00 35.57 4.69
2422 3316 1.070758 CTCCACCATAATCCACCTCGG 59.929 57.143 0.00 0.00 0.00 4.63
2423 3317 1.070758 CCTCCACCATAATCCACCTCG 59.929 57.143 0.00 0.00 0.00 4.63
2424 3318 1.421646 CCCTCCACCATAATCCACCTC 59.578 57.143 0.00 0.00 0.00 3.85
2425 3319 1.522900 CCCTCCACCATAATCCACCT 58.477 55.000 0.00 0.00 0.00 4.00
2426 3320 0.478507 CCCCTCCACCATAATCCACC 59.521 60.000 0.00 0.00 0.00 4.61
2427 3321 0.478507 CCCCCTCCACCATAATCCAC 59.521 60.000 0.00 0.00 0.00 4.02
2428 3322 1.360393 GCCCCCTCCACCATAATCCA 61.360 60.000 0.00 0.00 0.00 3.41
2429 3323 1.360393 TGCCCCCTCCACCATAATCC 61.360 60.000 0.00 0.00 0.00 3.01
2430 3324 0.178990 GTGCCCCCTCCACCATAATC 60.179 60.000 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.