Multiple sequence alignment - TraesCS1D01G046300

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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 TraesCS1D01G046300 chr1D 100.000 2796 0 0 1 2796 25955796 25953001 0.000000e+00 5164.0
1 TraesCS1D01G046300 chr1D 100.000 538 0 0 3153 3690 25952644 25952107 0.000000e+00 994.0
2 TraesCS1D01G046300 chr1D 89.249 493 27 13 3200 3690 25817163 25816695 8.820000e-166 593.0
3 TraesCS1D01G046300 chr1D 89.862 217 15 4 2073 2288 2852882 2853092 4.700000e-69 272.0
4 TraesCS1D01G046300 chr1D 90.909 66 6 0 1 66 452347549 452347614 5.080000e-14 89.8
5 TraesCS1D01G046300 chr1D 90.000 60 6 0 2728 2787 25827942 25827883 1.100000e-10 78.7
6 TraesCS1D01G046300 chr1B 86.388 1102 56 34 1172 2207 41450165 41449092 0.000000e+00 1118.0
7 TraesCS1D01G046300 chr1B 90.542 719 46 10 1 709 41642198 41641492 0.000000e+00 931.0
8 TraesCS1D01G046300 chr1B 94.715 492 22 2 3200 3687 41444420 41443929 0.000000e+00 761.0
9 TraesCS1D01G046300 chr1B 88.843 484 36 9 2124 2604 41640478 41640010 2.470000e-161 579.0
10 TraesCS1D01G046300 chr1B 90.376 426 29 4 2215 2640 41446318 41445905 1.940000e-152 549.0
11 TraesCS1D01G046300 chr1B 92.350 366 23 3 1752 2114 632752171 632752534 1.960000e-142 516.0
12 TraesCS1D01G046300 chr1B 82.581 465 47 17 1329 1768 41641232 41640777 2.690000e-101 379.0
13 TraesCS1D01G046300 chr1B 89.803 304 8 3 1805 2085 41640782 41640479 5.820000e-98 368.0
14 TraesCS1D01G046300 chr1B 76.538 439 56 24 2379 2787 41597914 41597493 2.910000e-46 196.0
15 TraesCS1D01G046300 chr1B 92.000 75 6 0 2703 2777 41445885 41445811 5.040000e-19 106.0
16 TraesCS1D01G046300 chr1B 89.394 66 7 0 1 66 622180127 622180062 2.360000e-12 84.2
17 TraesCS1D01G046300 chr1B 90.741 54 5 0 1433 1486 41450184 41450131 5.110000e-09 73.1
18 TraesCS1D01G046300 chr1B 82.609 69 8 4 715 781 23632066 23632132 1.430000e-04 58.4
19 TraesCS1D01G046300 chr1A 91.751 497 34 3 3200 3690 27203215 27202720 0.000000e+00 684.0
20 TraesCS1D01G046300 chr1A 87.396 603 47 19 2207 2796 27204160 27203574 0.000000e+00 665.0
21 TraesCS1D01G046300 chr1A 85.149 606 63 19 2 593 27260352 27260944 2.450000e-166 595.0
22 TraesCS1D01G046300 chr1A 89.394 66 7 0 1 66 547276547 547276612 2.360000e-12 84.2
23 TraesCS1D01G046300 chr4B 88.364 550 43 10 1752 2288 342969126 342968585 3.110000e-180 641.0
24 TraesCS1D01G046300 chr3B 92.077 366 23 3 1752 2114 569597353 569597715 9.140000e-141 510.0
25 TraesCS1D01G046300 chr3B 86.059 373 37 9 710 1069 465714726 465714356 1.610000e-103 387.0
26 TraesCS1D01G046300 chr3B 83.436 326 22 7 717 1010 465727537 465727212 1.310000e-69 274.0
27 TraesCS1D01G046300 chr3A 90.591 372 30 3 1752 2120 295950609 295950240 4.280000e-134 488.0
28 TraesCS1D01G046300 chr3A 89.552 67 7 0 1 67 740078176 740078110 6.570000e-13 86.1
29 TraesCS1D01G046300 chr7A 89.891 366 32 3 1752 2114 690659631 690659994 2.010000e-127 466.0
30 TraesCS1D01G046300 chr7A 82.741 394 42 19 1 375 721586033 721585647 9.880000e-86 327.0
31 TraesCS1D01G046300 chr7A 82.741 394 42 19 1 375 721660687 721660301 9.880000e-86 327.0
32 TraesCS1D01G046300 chr2D 89.071 366 34 6 1752 2114 229311392 229311754 2.020000e-122 449.0
33 TraesCS1D01G046300 chr2D 86.735 294 9 11 709 972 2632492 2632785 2.150000e-77 300.0
34 TraesCS1D01G046300 chr2D 84.589 292 15 10 711 972 2626825 2627116 2.830000e-66 263.0
35 TraesCS1D01G046300 chr7B 80.328 610 74 26 1 592 725854735 725855316 1.580000e-113 420.0
36 TraesCS1D01G046300 chr7D 81.395 516 54 26 1 492 626050907 626050410 2.080000e-102 383.0
37 TraesCS1D01G046300 chr7D 88.168 262 24 4 2028 2288 292420101 292420356 4.630000e-79 305.0
38 TraesCS1D01G046300 chr6D 91.367 278 8 3 710 971 151945420 151945143 2.090000e-97 366.0
39 TraesCS1D01G046300 chr6D 91.450 269 7 3 719 971 151949505 151949237 4.530000e-94 355.0
40 TraesCS1D01G046300 chr6B 88.043 276 26 4 2014 2288 575574537 575574268 1.650000e-83 320.0
41 TraesCS1D01G046300 chr6B 80.263 304 31 15 3356 3652 37956809 37957090 6.250000e-48 202.0
42 TraesCS1D01G046300 chr3D 89.552 67 7 0 1 67 607666586 607666520 6.570000e-13 86.1
43 TraesCS1D01G046300 chr6A 83.099 71 11 1 718 788 615718790 615718721 3.080000e-06 63.9
44 TraesCS1D01G046300 chrUn 82.609 69 8 4 715 781 2722431 2722365 1.430000e-04 58.4
45 TraesCS1D01G046300 chrUn 82.609 69 8 4 715 781 2727726 2727660 1.430000e-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 TraesCS1D01G046300 chr1D 25952107 25955796 3689 True 3079.00 5164 100.00000 1 3690 2 chr1D.!!$R3 3689
1 TraesCS1D01G046300 chr1B 41640010 41642198 2188 True 564.25 931 87.94225 1 2604 4 chr1B.!!$R4 2603
2 TraesCS1D01G046300 chr1B 41443929 41450184 6255 True 521.42 1118 90.84400 1172 3687 5 chr1B.!!$R3 2515
3 TraesCS1D01G046300 chr1A 27202720 27204160 1440 True 674.50 684 89.57350 2207 3690 2 chr1A.!!$R1 1483
4 TraesCS1D01G046300 chr1A 27260352 27260944 592 False 595.00 595 85.14900 2 593 1 chr1A.!!$F1 591
5 TraesCS1D01G046300 chr4B 342968585 342969126 541 True 641.00 641 88.36400 1752 2288 1 chr4B.!!$R1 536
6 TraesCS1D01G046300 chr7B 725854735 725855316 581 False 420.00 420 80.32800 1 592 1 chr7B.!!$F1 591
7 TraesCS1D01G046300 chr6D 151945143 151949505 4362 True 360.50 366 91.40850 710 971 2 chr6D.!!$R1 261

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
523 559 0.398696 AGTATGTTTGTGGTCGGCCA 59.601 50.0 3.51 3.51 43.73 5.36 F
1090 1146 0.112995 ACACCCACGTACACCTAGGA 59.887 55.0 17.98 0.00 0.00 2.94 F
1431 1641 0.178938 TTCATTTTGAGCAGGCCCCA 60.179 50.0 0.00 0.00 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 5802 0.179018 AGGACCCTGCACAACAAGAC 60.179 55.0 0.0 0.00 0.00 3.01 R
2565 8208 0.250234 TGGCCAGCGATATATGCTCC 59.750 55.0 0.0 7.09 41.72 4.70 R
2713 8404 0.531974 TGTGCTCGTGTTTCCTCCAC 60.532 55.0 0.0 0.00 0.00 4.02 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
54 55 2.544685 GAGTGGTTCTCCATCATCACG 58.455 52.381 0.00 0.00 46.20 4.35
67 68 2.193127 TCATCACGACCCCCAAGTAAT 58.807 47.619 0.00 0.00 0.00 1.89
68 69 2.574369 TCATCACGACCCCCAAGTAATT 59.426 45.455 0.00 0.00 0.00 1.40
71 72 4.411256 TCACGACCCCCAAGTAATTATC 57.589 45.455 0.00 0.00 0.00 1.75
74 75 4.101119 CACGACCCCCAAGTAATTATCTCT 59.899 45.833 0.00 0.00 0.00 3.10
75 76 4.101119 ACGACCCCCAAGTAATTATCTCTG 59.899 45.833 0.00 0.00 0.00 3.35
76 77 4.344102 CGACCCCCAAGTAATTATCTCTGA 59.656 45.833 0.00 0.00 0.00 3.27
78 79 6.631766 CGACCCCCAAGTAATTATCTCTGAAA 60.632 42.308 0.00 0.00 0.00 2.69
79 80 6.424032 ACCCCCAAGTAATTATCTCTGAAAC 58.576 40.000 0.00 0.00 0.00 2.78
80 81 5.828328 CCCCCAAGTAATTATCTCTGAAACC 59.172 44.000 0.00 0.00 0.00 3.27
81 82 5.527582 CCCCAAGTAATTATCTCTGAAACCG 59.472 44.000 0.00 0.00 0.00 4.44
82 83 6.113411 CCCAAGTAATTATCTCTGAAACCGT 58.887 40.000 0.00 0.00 0.00 4.83
83 84 6.598064 CCCAAGTAATTATCTCTGAAACCGTT 59.402 38.462 0.00 0.00 0.00 4.44
84 85 7.414098 CCCAAGTAATTATCTCTGAAACCGTTG 60.414 40.741 0.00 0.00 0.00 4.10
85 86 6.663944 AGTAATTATCTCTGAAACCGTTGC 57.336 37.500 0.00 0.00 0.00 4.17
87 88 1.355971 TATCTCTGAAACCGTTGCGC 58.644 50.000 0.00 0.00 0.00 6.09
97 103 2.125991 CGTTGCGCCCATTGCATT 60.126 55.556 4.18 0.00 42.84 3.56
284 313 4.136978 TCCAAGAGGCTGGACTCC 57.863 61.111 0.00 0.00 40.71 3.85
423 457 1.133513 AGCTGGTGGTGGTTTTCATCA 60.134 47.619 0.00 0.00 33.36 3.07
490 525 3.069016 TGTTAGTGTCAGGTCATCGTTGT 59.931 43.478 0.00 0.00 0.00 3.32
493 528 2.872245 AGTGTCAGGTCATCGTTGTTTG 59.128 45.455 0.00 0.00 0.00 2.93
499 535 3.431912 CAGGTCATCGTTGTTTGAATCGA 59.568 43.478 0.00 0.00 36.77 3.59
500 536 3.679980 AGGTCATCGTTGTTTGAATCGAG 59.320 43.478 0.00 0.00 35.85 4.04
501 537 3.432252 GGTCATCGTTGTTTGAATCGAGT 59.568 43.478 0.00 0.00 35.85 4.18
506 542 4.116961 TCGTTGTTTGAATCGAGTTGAGT 58.883 39.130 0.00 0.00 0.00 3.41
517 553 4.330944 TCGAGTTGAGTATGTTTGTGGT 57.669 40.909 0.00 0.00 0.00 4.16
523 559 0.398696 AGTATGTTTGTGGTCGGCCA 59.601 50.000 3.51 3.51 43.73 5.36
639 675 3.292423 GCGTGCTTCTTTTCTGTTTCTC 58.708 45.455 0.00 0.00 0.00 2.87
643 679 5.218139 GTGCTTCTTTTCTGTTTCTCCATG 58.782 41.667 0.00 0.00 0.00 3.66
662 698 5.306937 TCCATGACTTCCTCTTTTGTGACTA 59.693 40.000 0.00 0.00 0.00 2.59
663 699 5.409826 CCATGACTTCCTCTTTTGTGACTAC 59.590 44.000 0.00 0.00 0.00 2.73
664 700 5.871396 TGACTTCCTCTTTTGTGACTACT 57.129 39.130 0.00 0.00 0.00 2.57
688 724 9.136323 ACTATTTCTTCACTTCTGTTTTGGAAT 57.864 29.630 0.00 0.00 0.00 3.01
696 732 7.703328 TCACTTCTGTTTTGGAATACAGTTTC 58.297 34.615 9.05 0.00 41.87 2.78
698 734 7.645340 CACTTCTGTTTTGGAATACAGTTTCAG 59.355 37.037 9.05 0.00 41.87 3.02
705 741 9.406828 GTTTTGGAATACAGTTTCAGGATTTAC 57.593 33.333 0.00 0.00 0.00 2.01
706 742 8.698973 TTTGGAATACAGTTTCAGGATTTACA 57.301 30.769 0.00 0.00 0.00 2.41
707 743 8.698973 TTGGAATACAGTTTCAGGATTTACAA 57.301 30.769 0.00 0.00 0.00 2.41
708 744 8.698973 TGGAATACAGTTTCAGGATTTACAAA 57.301 30.769 0.00 0.00 0.00 2.83
709 745 8.792633 TGGAATACAGTTTCAGGATTTACAAAG 58.207 33.333 0.00 0.00 0.00 2.77
710 746 9.010029 GGAATACAGTTTCAGGATTTACAAAGA 57.990 33.333 0.00 0.00 0.00 2.52
714 750 8.336801 ACAGTTTCAGGATTTACAAAGATACC 57.663 34.615 0.00 0.00 0.00 2.73
715 751 7.942341 ACAGTTTCAGGATTTACAAAGATACCA 59.058 33.333 0.00 0.00 0.00 3.25
716 752 8.792633 CAGTTTCAGGATTTACAAAGATACCAA 58.207 33.333 0.00 0.00 0.00 3.67
717 753 9.533831 AGTTTCAGGATTTACAAAGATACCAAT 57.466 29.630 0.00 0.00 0.00 3.16
720 756 8.877864 TCAGGATTTACAAAGATACCAATTGT 57.122 30.769 4.43 0.00 40.22 2.71
721 757 9.308000 TCAGGATTTACAAAGATACCAATTGTT 57.692 29.630 4.43 0.00 38.22 2.83
722 758 9.357652 CAGGATTTACAAAGATACCAATTGTTG 57.642 33.333 4.43 3.84 38.22 3.33
798 841 4.436584 GCTAGCAAGATAAACAGTGCACAG 60.437 45.833 21.04 14.44 39.50 3.66
896 948 1.781429 CGAACTCTCACACGAACACAG 59.219 52.381 0.00 0.00 0.00 3.66
911 963 1.005037 ACAGCGAAGGCACGAATCA 60.005 52.632 8.16 0.00 43.41 2.57
925 977 4.734402 GCACGAATCAATGTATTGCCACAT 60.734 41.667 0.00 0.00 40.90 3.21
934 986 0.463654 TATTGCCACATGCCCGTCTC 60.464 55.000 0.00 0.00 40.16 3.36
972 1028 5.649602 TTTATTGCTTTGCTTTTCGTTGG 57.350 34.783 0.00 0.00 0.00 3.77
977 1033 3.123050 GCTTTGCTTTTCGTTGGTGATT 58.877 40.909 0.00 0.00 0.00 2.57
979 1035 4.923281 GCTTTGCTTTTCGTTGGTGATTAT 59.077 37.500 0.00 0.00 0.00 1.28
980 1036 5.405269 GCTTTGCTTTTCGTTGGTGATTATT 59.595 36.000 0.00 0.00 0.00 1.40
982 1038 7.115663 GCTTTGCTTTTCGTTGGTGATTATTTA 59.884 33.333 0.00 0.00 0.00 1.40
983 1039 7.861176 TTGCTTTTCGTTGGTGATTATTTAC 57.139 32.000 0.00 0.00 0.00 2.01
984 1040 6.971602 TGCTTTTCGTTGGTGATTATTTACA 58.028 32.000 0.00 0.00 0.00 2.41
986 1042 7.593273 TGCTTTTCGTTGGTGATTATTTACAAG 59.407 33.333 0.00 0.00 0.00 3.16
990 1046 4.439563 CGTTGGTGATTATTTACAAGGGGC 60.440 45.833 0.00 0.00 0.00 5.80
992 1048 4.941713 TGGTGATTATTTACAAGGGGCTT 58.058 39.130 0.00 0.00 0.00 4.35
993 1049 5.337788 TGGTGATTATTTACAAGGGGCTTT 58.662 37.500 0.00 0.00 0.00 3.51
994 1050 6.494952 TGGTGATTATTTACAAGGGGCTTTA 58.505 36.000 0.00 0.00 0.00 1.85
999 1055 6.783708 TTATTTACAAGGGGCTTTACATGG 57.216 37.500 0.00 0.00 0.00 3.66
1000 1056 2.137810 TACAAGGGGCTTTACATGGC 57.862 50.000 0.00 0.00 0.00 4.40
1007 1063 6.011628 ACAAGGGGCTTTACATGGCTATATAT 60.012 38.462 0.00 0.00 0.00 0.86
1008 1064 7.183839 ACAAGGGGCTTTACATGGCTATATATA 59.816 37.037 0.00 0.00 0.00 0.86
1010 1066 8.350180 AGGGGCTTTACATGGCTATATATAAT 57.650 34.615 0.00 0.00 0.00 1.28
1011 1067 9.460413 AGGGGCTTTACATGGCTATATATAATA 57.540 33.333 0.00 0.00 0.00 0.98
1012 1068 9.726438 GGGGCTTTACATGGCTATATATAATAG 57.274 37.037 0.00 0.00 0.00 1.73
1013 1069 9.220767 GGGCTTTACATGGCTATATATAATAGC 57.779 37.037 8.22 8.22 44.56 2.97
1025 1081 9.482627 GCTATATATAATAGCCAGGATCAACAC 57.517 37.037 5.84 0.00 40.69 3.32
1028 1084 9.896645 ATATATAATAGCCAGGATCAACACAAG 57.103 33.333 0.00 0.00 0.00 3.16
1029 1085 2.113860 TAGCCAGGATCAACACAAGC 57.886 50.000 0.00 0.00 0.00 4.01
1030 1086 0.403271 AGCCAGGATCAACACAAGCT 59.597 50.000 0.00 0.00 0.00 3.74
1031 1087 1.630369 AGCCAGGATCAACACAAGCTA 59.370 47.619 0.00 0.00 0.00 3.32
1032 1088 2.012673 GCCAGGATCAACACAAGCTAG 58.987 52.381 0.00 0.00 0.00 3.42
1033 1089 2.012673 CCAGGATCAACACAAGCTAGC 58.987 52.381 6.62 6.62 0.00 3.42
1034 1090 2.012673 CAGGATCAACACAAGCTAGCC 58.987 52.381 12.13 0.00 0.00 3.93
1035 1091 1.009829 GGATCAACACAAGCTAGCCG 58.990 55.000 12.13 5.56 0.00 5.52
1036 1092 1.405526 GGATCAACACAAGCTAGCCGA 60.406 52.381 12.13 0.00 0.00 5.54
1037 1093 1.929836 GATCAACACAAGCTAGCCGAG 59.070 52.381 12.13 4.32 0.00 4.63
1039 1095 1.071605 CAACACAAGCTAGCCGAGTC 58.928 55.000 12.13 0.00 0.00 3.36
1040 1096 0.388649 AACACAAGCTAGCCGAGTCG 60.389 55.000 12.13 5.29 0.00 4.18
1051 1107 2.750815 CCGAGTCGGTGTCCAATTC 58.249 57.895 23.83 0.00 42.73 2.17
1052 1108 0.246635 CCGAGTCGGTGTCCAATTCT 59.753 55.000 23.83 0.00 42.73 2.40
1053 1109 1.475280 CCGAGTCGGTGTCCAATTCTA 59.525 52.381 23.83 0.00 42.73 2.10
1054 1110 2.479730 CCGAGTCGGTGTCCAATTCTAG 60.480 54.545 23.83 0.00 42.73 2.43
1057 1113 3.432378 AGTCGGTGTCCAATTCTAGTCT 58.568 45.455 0.00 0.00 0.00 3.24
1069 1125 5.520288 CCAATTCTAGTCTTACATGGACACG 59.480 44.000 0.00 0.00 36.29 4.49
1070 1126 4.713824 TTCTAGTCTTACATGGACACGG 57.286 45.455 0.00 0.00 36.29 4.94
1072 1128 3.693085 TCTAGTCTTACATGGACACGGAC 59.307 47.826 0.00 0.00 36.29 4.79
1075 1131 1.274167 TCTTACATGGACACGGACACC 59.726 52.381 0.00 0.00 0.00 4.16
1077 1133 0.832559 TACATGGACACGGACACCCA 60.833 55.000 0.00 0.00 0.00 4.51
1078 1134 1.671054 CATGGACACGGACACCCAC 60.671 63.158 0.00 0.00 0.00 4.61
1079 1135 3.234630 ATGGACACGGACACCCACG 62.235 63.158 0.00 0.00 0.00 4.94
1080 1136 3.920196 GGACACGGACACCCACGT 61.920 66.667 0.00 0.00 45.25 4.49
1083 1139 2.074230 GACACGGACACCCACGTACA 62.074 60.000 0.00 0.00 42.04 2.90
1084 1140 1.662446 CACGGACACCCACGTACAC 60.662 63.158 0.00 0.00 42.04 2.90
1085 1141 2.048877 CGGACACCCACGTACACC 60.049 66.667 0.00 0.00 0.00 4.16
1086 1142 2.567497 CGGACACCCACGTACACCT 61.567 63.158 0.00 0.00 0.00 4.00
1087 1143 1.243342 CGGACACCCACGTACACCTA 61.243 60.000 0.00 0.00 0.00 3.08
1088 1144 0.529378 GGACACCCACGTACACCTAG 59.471 60.000 0.00 0.00 0.00 3.02
1089 1145 0.529378 GACACCCACGTACACCTAGG 59.471 60.000 7.41 7.41 0.00 3.02
1090 1146 0.112995 ACACCCACGTACACCTAGGA 59.887 55.000 17.98 0.00 0.00 2.94
1091 1147 0.815734 CACCCACGTACACCTAGGAG 59.184 60.000 17.98 10.85 0.00 3.69
1093 1149 1.635487 ACCCACGTACACCTAGGAGTA 59.365 52.381 17.98 15.93 0.00 2.59
1094 1150 2.243221 ACCCACGTACACCTAGGAGTAT 59.757 50.000 20.23 4.69 0.00 2.12
1095 1151 3.294214 CCCACGTACACCTAGGAGTATT 58.706 50.000 20.23 9.39 0.00 1.89
1097 1153 4.518211 CCCACGTACACCTAGGAGTATTAG 59.482 50.000 20.23 16.39 0.00 1.73
1098 1154 4.023365 CCACGTACACCTAGGAGTATTAGC 60.023 50.000 20.23 8.16 0.00 3.09
1099 1155 4.820716 CACGTACACCTAGGAGTATTAGCT 59.179 45.833 20.23 0.00 0.00 3.32
1101 1157 6.147492 CACGTACACCTAGGAGTATTAGCTAG 59.853 46.154 20.23 9.68 0.00 3.42
1104 1160 3.440872 CACCTAGGAGTATTAGCTAGCCG 59.559 52.174 17.98 0.00 0.00 5.52
1105 1161 3.074242 ACCTAGGAGTATTAGCTAGCCGT 59.926 47.826 17.98 0.00 0.00 5.68
1106 1162 3.440872 CCTAGGAGTATTAGCTAGCCGTG 59.559 52.174 12.13 0.00 0.00 4.94
1107 1163 2.946785 AGGAGTATTAGCTAGCCGTGT 58.053 47.619 12.13 0.00 0.00 4.49
1108 1164 2.885894 AGGAGTATTAGCTAGCCGTGTC 59.114 50.000 12.13 0.96 0.00 3.67
1109 1165 2.030096 GGAGTATTAGCTAGCCGTGTCC 60.030 54.545 12.13 6.89 0.00 4.02
1110 1166 2.885894 GAGTATTAGCTAGCCGTGTCCT 59.114 50.000 12.13 0.25 0.00 3.85
1111 1167 3.297736 AGTATTAGCTAGCCGTGTCCTT 58.702 45.455 12.13 0.00 0.00 3.36
1112 1168 3.705072 AGTATTAGCTAGCCGTGTCCTTT 59.295 43.478 12.13 0.00 0.00 3.11
1113 1169 3.629142 ATTAGCTAGCCGTGTCCTTTT 57.371 42.857 12.13 0.00 0.00 2.27
1114 1170 3.412237 TTAGCTAGCCGTGTCCTTTTT 57.588 42.857 12.13 0.00 0.00 1.94
1138 1194 9.651913 TTTTGAGATTTACACAAAAAGCTTTCT 57.348 25.926 13.10 0.00 42.60 2.52
1152 1208 7.914537 AAAAGCTTTCTGTTTACAATCTTCG 57.085 32.000 13.10 0.00 0.00 3.79
1161 1217 8.094798 TCTGTTTACAATCTTCGTAGCAATTT 57.905 30.769 0.00 0.00 0.00 1.82
1163 1219 8.722342 TGTTTACAATCTTCGTAGCAATTTTC 57.278 30.769 0.00 0.00 0.00 2.29
1164 1220 8.346300 TGTTTACAATCTTCGTAGCAATTTTCA 58.654 29.630 0.00 0.00 0.00 2.69
1165 1221 9.341899 GTTTACAATCTTCGTAGCAATTTTCAT 57.658 29.630 0.00 0.00 0.00 2.57
1169 1225 8.915654 ACAATCTTCGTAGCAATTTTCATTTTC 58.084 29.630 0.00 0.00 0.00 2.29
1170 1226 8.914654 CAATCTTCGTAGCAATTTTCATTTTCA 58.085 29.630 0.00 0.00 0.00 2.69
1177 1233 9.519905 CGTAGCAATTTTCATTTTCATTTTCTG 57.480 29.630 0.00 0.00 0.00 3.02
1231 1416 9.496873 TGAGAAAGGAAAAACACTTCGATATTA 57.503 29.630 0.00 0.00 0.00 0.98
1259 1445 4.035441 TCTGTTTTACAAAACTACGCCCAC 59.965 41.667 16.24 0.00 46.37 4.61
1289 1477 5.799827 TTAATTACCTTGTTTGCTTGGCT 57.200 34.783 0.00 0.00 0.00 4.75
1345 1552 9.337396 TCTTTTACAACTATTTCTTCAGAAGCA 57.663 29.630 5.15 0.00 35.21 3.91
1351 1558 8.940952 ACAACTATTTCTTCAGAAGCATCTAAC 58.059 33.333 5.15 0.00 35.21 2.34
1381 1591 2.966708 CACTTTTCGTGATGTCTTTGCG 59.033 45.455 0.00 0.00 46.81 4.85
1431 1641 0.178938 TTCATTTTGAGCAGGCCCCA 60.179 50.000 0.00 0.00 0.00 4.96
1490 1707 8.716909 CAGTACCTCTTCTTTCTGATTCTTTTC 58.283 37.037 0.00 0.00 0.00 2.29
1584 1829 3.692257 AAGTGTTCACATCAGAGGGAG 57.308 47.619 5.74 0.00 0.00 4.30
1739 1985 1.199327 TCGTTGCTCCTAGAGTTGTCG 59.801 52.381 0.00 0.00 31.39 4.35
1743 1989 1.099689 GCTCCTAGAGTTGTCGCTCT 58.900 55.000 0.00 1.16 46.49 4.09
1747 1993 1.133407 CCTAGAGTTGTCGCTCTGGTC 59.867 57.143 5.92 0.00 44.71 4.02
1749 1995 1.444553 GAGTTGTCGCTCTGGTCGG 60.445 63.158 0.00 0.00 32.99 4.79
1750 1996 2.143594 GAGTTGTCGCTCTGGTCGGT 62.144 60.000 0.00 0.00 32.99 4.69
1882 2664 7.439157 AGATCGAACACAATTCTCATTTCAA 57.561 32.000 0.00 0.00 0.00 2.69
1885 2667 6.969366 TCGAACACAATTCTCATTTCAACAT 58.031 32.000 0.00 0.00 0.00 2.71
1910 2692 3.067320 CGATCCATCTGTGCTAACTGAGA 59.933 47.826 0.00 0.00 37.64 3.27
2310 5891 2.841988 GAGGAGGCGCCCATCTCT 60.842 66.667 26.15 14.03 37.37 3.10
2500 8140 1.431488 CGGCGGTGCGAGTAGTACTA 61.431 60.000 1.88 0.00 35.67 1.82
2524 8167 2.436292 GGCAGCAGCAGAGTCAGG 60.436 66.667 2.65 0.00 44.61 3.86
2540 8183 4.160329 AGTCAGGTTCAGACTAATGGACA 58.840 43.478 0.00 0.00 44.10 4.02
2543 8186 5.026121 TCAGGTTCAGACTAATGGACAGAT 58.974 41.667 0.00 0.00 29.46 2.90
2565 8208 2.892425 GGTGCGGATCAGGAAGCG 60.892 66.667 0.00 0.00 0.00 4.68
2599 8242 2.637025 CCACCGCGGTTTGAACAG 59.363 61.111 32.11 15.83 0.00 3.16
2600 8243 1.890041 CCACCGCGGTTTGAACAGA 60.890 57.895 32.11 0.00 0.00 3.41
2601 8244 1.569493 CACCGCGGTTTGAACAGAG 59.431 57.895 32.11 10.47 0.00 3.35
2602 8245 1.145377 ACCGCGGTTTGAACAGAGT 59.855 52.632 28.70 0.00 0.00 3.24
2603 8246 0.463116 ACCGCGGTTTGAACAGAGTT 60.463 50.000 28.70 0.00 0.00 3.01
2604 8247 0.041312 CCGCGGTTTGAACAGAGTTG 60.041 55.000 19.50 0.00 0.00 3.16
2605 8248 0.041312 CGCGGTTTGAACAGAGTTGG 60.041 55.000 0.00 0.00 0.00 3.77
2608 8251 1.602377 CGGTTTGAACAGAGTTGGGAC 59.398 52.381 0.00 0.00 0.00 4.46
2640 8283 4.317671 ACTGTACTTTCAGCGTGTACTT 57.682 40.909 0.00 0.00 38.84 2.24
2641 8284 4.049186 ACTGTACTTTCAGCGTGTACTTG 58.951 43.478 0.00 0.00 38.84 3.16
2643 8286 4.684877 TGTACTTTCAGCGTGTACTTGAA 58.315 39.130 0.00 0.00 37.85 2.69
2648 8291 1.864711 TCAGCGTGTACTTGAAAGTGC 59.135 47.619 5.95 5.21 40.07 4.40
2649 8292 1.597195 CAGCGTGTACTTGAAAGTGCA 59.403 47.619 9.54 9.54 46.92 4.57
2654 8297 3.552132 TGTACTTGAAAGTGCACTCCA 57.448 42.857 21.95 18.02 44.81 3.86
2656 8299 3.369997 TGTACTTGAAAGTGCACTCCACA 60.370 43.478 21.95 16.94 44.81 4.17
2657 8300 5.215809 TGTACTTGAAAGTGCACTCCACAG 61.216 45.833 21.95 19.49 44.81 3.66
2667 8310 2.403252 CACTCCACAGTGGTAATCCC 57.597 55.000 19.65 0.00 45.75 3.85
2668 8311 1.909302 CACTCCACAGTGGTAATCCCT 59.091 52.381 19.65 0.00 45.75 4.20
2669 8312 3.104512 CACTCCACAGTGGTAATCCCTA 58.895 50.000 19.65 0.00 45.75 3.53
2670 8313 3.711704 CACTCCACAGTGGTAATCCCTAT 59.288 47.826 19.65 0.00 45.75 2.57
2671 8314 4.164221 CACTCCACAGTGGTAATCCCTATT 59.836 45.833 19.65 0.00 45.75 1.73
2672 8315 4.788617 ACTCCACAGTGGTAATCCCTATTT 59.211 41.667 19.65 0.00 39.03 1.40
2673 8316 5.110814 TCCACAGTGGTAATCCCTATTTG 57.889 43.478 19.65 0.00 39.03 2.32
2674 8317 4.538490 TCCACAGTGGTAATCCCTATTTGT 59.462 41.667 19.65 0.00 39.03 2.83
2675 8318 5.727279 TCCACAGTGGTAATCCCTATTTGTA 59.273 40.000 19.65 0.00 39.03 2.41
2676 8319 6.215841 TCCACAGTGGTAATCCCTATTTGTAA 59.784 38.462 19.65 0.00 39.03 2.41
2677 8320 6.887545 CCACAGTGGTAATCCCTATTTGTAAA 59.112 38.462 11.99 0.00 31.35 2.01
2678 8321 7.067008 CCACAGTGGTAATCCCTATTTGTAAAG 59.933 40.741 11.99 0.00 31.35 1.85
2679 8322 7.610305 CACAGTGGTAATCCCTATTTGTAAAGT 59.390 37.037 0.00 0.00 0.00 2.66
2680 8323 8.828751 ACAGTGGTAATCCCTATTTGTAAAGTA 58.171 33.333 0.00 0.00 0.00 2.24
2681 8324 9.675464 CAGTGGTAATCCCTATTTGTAAAGTAA 57.325 33.333 0.00 0.00 0.00 2.24
2688 8331 9.774413 AATCCCTATTTGTAAAGTAATACTCCG 57.226 33.333 0.00 0.00 0.00 4.63
2689 8332 8.310122 TCCCTATTTGTAAAGTAATACTCCGT 57.690 34.615 0.00 0.00 0.00 4.69
2690 8333 9.420118 TCCCTATTTGTAAAGTAATACTCCGTA 57.580 33.333 0.00 0.00 0.00 4.02
2730 8421 1.070786 GGTGGAGGAAACACGAGCA 59.929 57.895 0.00 0.00 39.69 4.26
2769 8460 0.968405 GGCCACTCCAATGAAGCAAA 59.032 50.000 0.00 0.00 34.01 3.68
2770 8461 1.551883 GGCCACTCCAATGAAGCAAAT 59.448 47.619 0.00 0.00 34.01 2.32
2777 8468 6.319658 CCACTCCAATGAAGCAAATATGTAGT 59.680 38.462 0.00 0.00 0.00 2.73
2778 8469 7.191551 CACTCCAATGAAGCAAATATGTAGTG 58.808 38.462 0.00 0.00 0.00 2.74
2779 8470 6.319658 ACTCCAATGAAGCAAATATGTAGTGG 59.680 38.462 0.00 0.00 0.00 4.00
2784 8475 3.194005 AGCAAATATGTAGTGGGTCGG 57.806 47.619 0.00 0.00 0.00 4.79
2786 8477 3.199071 AGCAAATATGTAGTGGGTCGGAA 59.801 43.478 0.00 0.00 0.00 4.30
3184 9738 2.280524 CGAGTCGTGGGGCACAAA 60.281 61.111 3.82 0.00 33.40 2.83
3189 9743 0.386731 GTCGTGGGGCACAAATTTCG 60.387 55.000 0.00 0.00 33.40 3.46
3198 9752 3.389221 GGCACAAATTTCGGTCACATTT 58.611 40.909 0.00 0.00 0.00 2.32
3285 9990 7.168219 ACAATAGTAGCCAAATTCTCAACTCA 58.832 34.615 0.00 0.00 0.00 3.41
3287 9992 4.327680 AGTAGCCAAATTCTCAACTCACC 58.672 43.478 0.00 0.00 0.00 4.02
3351 10058 5.215903 CACATGTAGCTACACCTTCTATCG 58.784 45.833 28.28 10.63 39.30 2.92
3400 10107 8.918202 TCGTGCCATCCTTATATAGAAATTTT 57.082 30.769 0.00 0.00 0.00 1.82
3443 10150 5.474876 AGCAAGAGGACATTTAACCTTGAAG 59.525 40.000 0.00 0.00 36.57 3.02
3466 10173 7.653767 AGCTTTGTAGACAACTATACACAAC 57.346 36.000 0.00 0.00 35.28 3.32
3483 10190 4.986659 ACACAACCGACACTCTTTGTATAC 59.013 41.667 0.00 0.00 39.17 1.47
3653 10906 8.507470 AGTTTCGAGCTCAAATGTTATTTTTC 57.493 30.769 15.40 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 5.888982 TCAGAGATAATTACTTGGGGGTC 57.111 43.478 0.00 0.00 0.00 4.46
67 68 1.730064 GCGCAACGGTTTCAGAGATAA 59.270 47.619 0.30 0.00 0.00 1.75
68 69 1.355971 GCGCAACGGTTTCAGAGATA 58.644 50.000 0.30 0.00 0.00 1.98
71 72 2.556287 GGCGCAACGGTTTCAGAG 59.444 61.111 10.83 0.00 0.00 3.35
74 75 2.196925 AATGGGCGCAACGGTTTCA 61.197 52.632 10.83 0.00 0.00 2.69
75 76 1.732683 CAATGGGCGCAACGGTTTC 60.733 57.895 10.83 0.00 0.00 2.78
76 77 2.338257 CAATGGGCGCAACGGTTT 59.662 55.556 10.83 0.00 0.00 3.27
87 88 6.698008 TGAAATACAGAGTAATGCAATGGG 57.302 37.500 0.00 0.00 0.00 4.00
130 153 4.398044 ACACACAAAACGGTTTCAGAGATT 59.602 37.500 6.57 0.00 0.00 2.40
135 158 1.917303 GCACACACAAAACGGTTTCAG 59.083 47.619 6.57 5.61 0.00 3.02
141 164 1.588667 GGCTGCACACACAAAACGG 60.589 57.895 0.50 0.00 0.00 4.44
284 313 0.392461 TGGGGGCGAAGAAAATCTCG 60.392 55.000 0.00 0.00 0.00 4.04
423 457 5.543507 AAGATAGATTCGCAGAGGTGATT 57.456 39.130 0.00 0.00 38.43 2.57
463 498 4.800993 CGATGACCTGACACTAACATTCTC 59.199 45.833 0.00 0.00 0.00 2.87
490 525 7.351981 CACAAACATACTCAACTCGATTCAAA 58.648 34.615 0.00 0.00 0.00 2.69
493 528 5.408604 ACCACAAACATACTCAACTCGATTC 59.591 40.000 0.00 0.00 0.00 2.52
499 535 3.399330 CCGACCACAAACATACTCAACT 58.601 45.455 0.00 0.00 0.00 3.16
500 536 2.095919 GCCGACCACAAACATACTCAAC 60.096 50.000 0.00 0.00 0.00 3.18
501 537 2.147958 GCCGACCACAAACATACTCAA 58.852 47.619 0.00 0.00 0.00 3.02
517 553 3.767673 AGTTCTCATACTAGTTTGGCCGA 59.232 43.478 12.61 0.00 0.00 5.54
523 559 8.043113 TGCATTCATCAGTTCTCATACTAGTTT 58.957 33.333 0.00 0.00 0.00 2.66
525 561 7.117285 TGCATTCATCAGTTCTCATACTAGT 57.883 36.000 0.00 0.00 0.00 2.57
528 564 6.202379 CGATTGCATTCATCAGTTCTCATACT 59.798 38.462 9.14 0.00 0.00 2.12
531 567 5.121105 TCGATTGCATTCATCAGTTCTCAT 58.879 37.500 9.14 0.00 0.00 2.90
613 649 2.287788 ACAGAAAAGAAGCACGCCAATG 60.288 45.455 0.00 0.00 0.00 2.82
639 675 4.392940 AGTCACAAAAGAGGAAGTCATGG 58.607 43.478 0.00 0.00 0.00 3.66
643 679 8.834749 AAATAGTAGTCACAAAAGAGGAAGTC 57.165 34.615 0.00 0.00 0.00 3.01
662 698 8.519799 TTCCAAAACAGAAGTGAAGAAATAGT 57.480 30.769 0.00 0.00 0.00 2.12
688 724 9.444600 GGTATCTTTGTAAATCCTGAAACTGTA 57.555 33.333 0.00 0.00 0.00 2.74
696 732 9.357652 CAACAATTGGTATCTTTGTAAATCCTG 57.642 33.333 10.83 0.00 33.44 3.86
698 734 8.702163 CCAACAATTGGTATCTTTGTAAATCC 57.298 34.615 10.83 0.00 45.93 3.01
714 750 3.319755 AGCGATCAAAAGCCAACAATTG 58.680 40.909 3.24 3.24 0.00 2.32
715 751 3.665745 AGCGATCAAAAGCCAACAATT 57.334 38.095 0.00 0.00 0.00 2.32
716 752 4.009675 TCTAGCGATCAAAAGCCAACAAT 58.990 39.130 0.00 0.00 0.00 2.71
717 753 3.188460 GTCTAGCGATCAAAAGCCAACAA 59.812 43.478 0.00 0.00 0.00 2.83
718 754 2.742053 GTCTAGCGATCAAAAGCCAACA 59.258 45.455 0.00 0.00 0.00 3.33
719 755 2.096013 GGTCTAGCGATCAAAAGCCAAC 59.904 50.000 0.00 0.00 0.00 3.77
720 756 2.290008 TGGTCTAGCGATCAAAAGCCAA 60.290 45.455 0.00 0.00 0.00 4.52
721 757 1.277842 TGGTCTAGCGATCAAAAGCCA 59.722 47.619 0.00 0.00 0.00 4.75
722 758 2.024176 TGGTCTAGCGATCAAAAGCC 57.976 50.000 0.00 0.00 0.00 4.35
760 796 3.200483 TGCTAGCTTGCACATACATCTG 58.800 45.455 19.10 0.00 38.12 2.90
764 800 3.333029 TCTTGCTAGCTTGCACATACA 57.667 42.857 22.57 6.82 43.20 2.29
782 818 2.566833 TGCCTGTGCACTGTTTATCT 57.433 45.000 19.41 0.00 44.23 1.98
798 841 1.007038 TGAAGTACCGTGACGTGCC 60.007 57.895 3.64 0.00 0.00 5.01
896 948 0.447801 ACATTGATTCGTGCCTTCGC 59.552 50.000 0.00 0.00 0.00 4.70
972 1028 7.399245 TGTAAAGCCCCTTGTAAATAATCAC 57.601 36.000 0.00 0.00 0.00 3.06
977 1033 4.647399 GCCATGTAAAGCCCCTTGTAAATA 59.353 41.667 0.00 0.00 0.00 1.40
979 1035 2.829120 GCCATGTAAAGCCCCTTGTAAA 59.171 45.455 0.00 0.00 0.00 2.01
980 1036 2.042433 AGCCATGTAAAGCCCCTTGTAA 59.958 45.455 0.00 0.00 0.00 2.41
982 1038 0.409484 AGCCATGTAAAGCCCCTTGT 59.591 50.000 0.00 0.00 0.00 3.16
983 1039 2.435372 TAGCCATGTAAAGCCCCTTG 57.565 50.000 0.00 0.00 0.00 3.61
984 1040 6.658555 ATATATAGCCATGTAAAGCCCCTT 57.341 37.500 0.00 0.00 0.00 3.95
986 1042 9.726438 CTATTATATATAGCCATGTAAAGCCCC 57.274 37.037 0.00 0.00 0.00 5.80
999 1055 9.482627 GTGTTGATCCTGGCTATTATATATAGC 57.517 37.037 13.92 13.92 44.56 2.97
1007 1063 4.080356 AGCTTGTGTTGATCCTGGCTATTA 60.080 41.667 0.00 0.00 0.00 0.98
1008 1064 3.019564 GCTTGTGTTGATCCTGGCTATT 58.980 45.455 0.00 0.00 0.00 1.73
1010 1066 1.630369 AGCTTGTGTTGATCCTGGCTA 59.370 47.619 0.00 0.00 0.00 3.93
1011 1067 0.403271 AGCTTGTGTTGATCCTGGCT 59.597 50.000 0.00 0.00 0.00 4.75
1012 1068 2.012673 CTAGCTTGTGTTGATCCTGGC 58.987 52.381 0.00 0.00 0.00 4.85
1013 1069 2.012673 GCTAGCTTGTGTTGATCCTGG 58.987 52.381 7.70 0.00 0.00 4.45
1014 1070 2.012673 GGCTAGCTTGTGTTGATCCTG 58.987 52.381 15.72 0.00 0.00 3.86
1015 1071 1.406069 CGGCTAGCTTGTGTTGATCCT 60.406 52.381 15.72 0.00 0.00 3.24
1016 1072 1.009829 CGGCTAGCTTGTGTTGATCC 58.990 55.000 15.72 0.00 0.00 3.36
1017 1073 1.929836 CTCGGCTAGCTTGTGTTGATC 59.070 52.381 15.72 0.00 0.00 2.92
1018 1074 1.276421 ACTCGGCTAGCTTGTGTTGAT 59.724 47.619 15.72 0.00 0.00 2.57
1019 1075 0.679505 ACTCGGCTAGCTTGTGTTGA 59.320 50.000 15.72 1.11 0.00 3.18
1022 1078 1.213013 CGACTCGGCTAGCTTGTGT 59.787 57.895 15.72 13.89 0.00 3.72
1023 1079 1.517257 CCGACTCGGCTAGCTTGTG 60.517 63.158 15.72 10.84 41.17 3.33
1034 1090 2.163815 ACTAGAATTGGACACCGACTCG 59.836 50.000 0.00 0.00 0.00 4.18
1035 1091 3.444388 AGACTAGAATTGGACACCGACTC 59.556 47.826 0.00 0.00 0.00 3.36
1036 1092 3.432378 AGACTAGAATTGGACACCGACT 58.568 45.455 0.00 0.00 0.00 4.18
1037 1093 3.870633 AGACTAGAATTGGACACCGAC 57.129 47.619 0.00 0.00 0.00 4.79
1039 1095 5.068234 TGTAAGACTAGAATTGGACACCG 57.932 43.478 0.00 0.00 0.00 4.94
1040 1096 5.817816 CCATGTAAGACTAGAATTGGACACC 59.182 44.000 0.00 0.00 0.00 4.16
1041 1097 6.640518 TCCATGTAAGACTAGAATTGGACAC 58.359 40.000 0.00 0.00 0.00 3.67
1044 1100 6.627287 CGTGTCCATGTAAGACTAGAATTGGA 60.627 42.308 0.00 0.00 35.21 3.53
1045 1101 5.520288 CGTGTCCATGTAAGACTAGAATTGG 59.480 44.000 0.00 0.00 35.21 3.16
1046 1102 5.520288 CCGTGTCCATGTAAGACTAGAATTG 59.480 44.000 0.00 0.00 35.21 2.32
1048 1104 4.954202 TCCGTGTCCATGTAAGACTAGAAT 59.046 41.667 0.00 0.00 35.21 2.40
1049 1105 4.157289 GTCCGTGTCCATGTAAGACTAGAA 59.843 45.833 0.00 0.00 35.21 2.10
1050 1106 3.693085 GTCCGTGTCCATGTAAGACTAGA 59.307 47.826 0.00 0.00 35.21 2.43
1051 1107 3.442625 TGTCCGTGTCCATGTAAGACTAG 59.557 47.826 2.85 0.00 35.21 2.57
1052 1108 3.192001 GTGTCCGTGTCCATGTAAGACTA 59.808 47.826 2.85 0.00 35.21 2.59
1053 1109 2.029290 GTGTCCGTGTCCATGTAAGACT 60.029 50.000 2.85 0.00 35.21 3.24
1054 1110 2.334838 GTGTCCGTGTCCATGTAAGAC 58.665 52.381 0.00 0.00 34.72 3.01
1057 1113 0.322322 GGGTGTCCGTGTCCATGTAA 59.678 55.000 0.00 0.00 0.00 2.41
1066 1122 1.662446 GTGTACGTGGGTGTCCGTG 60.662 63.158 0.00 0.00 37.91 4.94
1069 1125 0.529378 CTAGGTGTACGTGGGTGTCC 59.471 60.000 0.00 0.00 0.00 4.02
1070 1126 0.529378 CCTAGGTGTACGTGGGTGTC 59.471 60.000 0.00 0.00 0.00 3.67
1072 1128 0.815734 CTCCTAGGTGTACGTGGGTG 59.184 60.000 9.08 1.84 34.54 4.61
1075 1131 4.023365 GCTAATACTCCTAGGTGTACGTGG 60.023 50.000 22.72 16.69 0.00 4.94
1077 1133 5.046288 AGCTAATACTCCTAGGTGTACGT 57.954 43.478 22.72 16.58 0.00 3.57
1078 1134 5.122082 GCTAGCTAATACTCCTAGGTGTACG 59.878 48.000 22.72 15.63 31.46 3.67
1079 1135 5.415389 GGCTAGCTAATACTCCTAGGTGTAC 59.585 48.000 22.72 12.08 31.46 2.90
1080 1136 5.568392 GGCTAGCTAATACTCCTAGGTGTA 58.432 45.833 22.55 22.55 31.46 2.90
1083 1139 3.074242 ACGGCTAGCTAATACTCCTAGGT 59.926 47.826 15.72 0.00 31.46 3.08
1084 1140 3.440872 CACGGCTAGCTAATACTCCTAGG 59.559 52.174 15.72 0.82 31.46 3.02
1085 1141 4.073549 ACACGGCTAGCTAATACTCCTAG 58.926 47.826 15.72 0.00 33.41 3.02
1086 1142 4.070716 GACACGGCTAGCTAATACTCCTA 58.929 47.826 15.72 0.00 0.00 2.94
1087 1143 2.885894 GACACGGCTAGCTAATACTCCT 59.114 50.000 15.72 0.00 0.00 3.69
1088 1144 2.030096 GGACACGGCTAGCTAATACTCC 60.030 54.545 15.72 7.69 0.00 3.85
1089 1145 2.885894 AGGACACGGCTAGCTAATACTC 59.114 50.000 15.72 2.24 0.00 2.59
1090 1146 2.946785 AGGACACGGCTAGCTAATACT 58.053 47.619 15.72 1.15 0.00 2.12
1091 1147 3.729862 AAGGACACGGCTAGCTAATAC 57.270 47.619 15.72 4.11 0.00 1.89
1093 1149 3.629142 AAAAGGACACGGCTAGCTAAT 57.371 42.857 15.72 0.00 0.00 1.73
1094 1150 3.412237 AAAAAGGACACGGCTAGCTAA 57.588 42.857 15.72 0.00 0.00 3.09
1112 1168 9.651913 AGAAAGCTTTTTGTGTAAATCTCAAAA 57.348 25.926 14.05 0.00 43.23 2.44
1113 1169 9.086336 CAGAAAGCTTTTTGTGTAAATCTCAAA 57.914 29.630 19.00 0.00 37.62 2.69
1114 1170 8.250332 ACAGAAAGCTTTTTGTGTAAATCTCAA 58.750 29.630 28.75 0.00 36.77 3.02
1115 1171 7.771183 ACAGAAAGCTTTTTGTGTAAATCTCA 58.229 30.769 28.75 0.00 36.77 3.27
1116 1172 8.634475 AACAGAAAGCTTTTTGTGTAAATCTC 57.366 30.769 29.64 6.94 37.43 2.75
1119 1175 9.646427 TGTAAACAGAAAGCTTTTTGTGTAAAT 57.354 25.926 29.64 15.07 37.43 1.40
1120 1176 9.477484 TTGTAAACAGAAAGCTTTTTGTGTAAA 57.523 25.926 29.64 22.51 37.43 2.01
1121 1177 9.646427 ATTGTAAACAGAAAGCTTTTTGTGTAA 57.354 25.926 29.64 21.91 37.43 2.41
1122 1178 9.296400 GATTGTAAACAGAAAGCTTTTTGTGTA 57.704 29.630 29.64 25.98 37.43 2.90
1123 1179 8.034804 AGATTGTAAACAGAAAGCTTTTTGTGT 58.965 29.630 29.64 26.90 39.66 3.72
1124 1180 8.411318 AGATTGTAAACAGAAAGCTTTTTGTG 57.589 30.769 29.64 20.87 35.90 3.33
1125 1181 9.087424 GAAGATTGTAAACAGAAAGCTTTTTGT 57.913 29.630 25.22 25.22 37.12 2.83
1126 1182 8.261908 CGAAGATTGTAAACAGAAAGCTTTTTG 58.738 33.333 24.00 24.00 30.22 2.44
1132 1188 6.016111 GCTACGAAGATTGTAAACAGAAAGC 58.984 40.000 0.00 0.00 0.00 3.51
1137 1193 8.728088 AAAATTGCTACGAAGATTGTAAACAG 57.272 30.769 0.00 0.00 0.00 3.16
1138 1194 8.346300 TGAAAATTGCTACGAAGATTGTAAACA 58.654 29.630 0.00 0.00 0.00 2.83
1174 1230 9.799106 AAAAGGAAGAGATAATGAAGAAACAGA 57.201 29.630 0.00 0.00 0.00 3.41
1201 1386 8.215926 TCGAAGTGTTTTTCCTTTCTCAAATA 57.784 30.769 0.00 0.00 0.00 1.40
1205 1390 7.979444 ATATCGAAGTGTTTTTCCTTTCTCA 57.021 32.000 0.00 0.00 0.00 3.27
1242 1428 2.226912 GCATGTGGGCGTAGTTTTGTAA 59.773 45.455 0.00 0.00 0.00 2.41
1259 1445 6.646240 AGCAAACAAGGTAATTAAACAGCATG 59.354 34.615 0.00 0.00 46.00 4.06
1319 1507 9.337396 TGCTTCTGAAGAAATAGTTGTAAAAGA 57.663 29.630 21.06 0.00 33.07 2.52
1325 1513 8.940952 GTTAGATGCTTCTGAAGAAATAGTTGT 58.059 33.333 21.06 0.00 33.07 3.32
1326 1514 9.160496 AGTTAGATGCTTCTGAAGAAATAGTTG 57.840 33.333 21.06 0.00 33.07 3.16
1343 1550 8.068380 ACGAAAAGTGTTTTCTAAGTTAGATGC 58.932 33.333 13.34 7.48 45.23 3.91
1344 1551 9.370126 CACGAAAAGTGTTTTCTAAGTTAGATG 57.630 33.333 13.34 0.86 45.23 2.90
1381 1591 1.806247 GCCCAACAAAAGTGAAGCCAC 60.806 52.381 0.00 0.00 43.50 5.01
1530 1763 6.446318 CAAAACAAGCAACTGGAAGCTATAA 58.554 36.000 0.00 0.00 40.90 0.98
1566 1799 1.902508 TCCTCCCTCTGATGTGAACAC 59.097 52.381 0.00 0.00 0.00 3.32
1584 1829 1.602377 GCATGTGGGCGTAGTTTATCC 59.398 52.381 0.00 0.00 0.00 2.59
1687 1933 6.401153 CGAGGAAACAAGCATAGAGTGTTTAC 60.401 42.308 3.09 3.09 43.60 2.01
1691 1937 3.589988 CGAGGAAACAAGCATAGAGTGT 58.410 45.455 0.00 0.00 0.00 3.55
1692 1938 2.349886 GCGAGGAAACAAGCATAGAGTG 59.650 50.000 0.00 0.00 35.48 3.51
1693 1939 2.622436 GCGAGGAAACAAGCATAGAGT 58.378 47.619 0.00 0.00 35.48 3.24
1694 1940 1.936547 GGCGAGGAAACAAGCATAGAG 59.063 52.381 0.00 0.00 36.83 2.43
1695 1941 1.739035 CGGCGAGGAAACAAGCATAGA 60.739 52.381 0.00 0.00 36.83 1.98
1696 1942 0.652592 CGGCGAGGAAACAAGCATAG 59.347 55.000 0.00 0.00 36.83 2.23
1697 1943 0.742990 CCGGCGAGGAAACAAGCATA 60.743 55.000 9.30 0.00 45.00 3.14
1698 1944 2.040544 CCGGCGAGGAAACAAGCAT 61.041 57.895 9.30 0.00 45.00 3.79
1739 1985 1.112113 TTCTCCATACCGACCAGAGC 58.888 55.000 0.00 0.00 0.00 4.09
1743 1989 1.475280 CGTCTTTCTCCATACCGACCA 59.525 52.381 0.00 0.00 0.00 4.02
1747 1993 0.870307 CCGCGTCTTTCTCCATACCG 60.870 60.000 4.92 0.00 0.00 4.02
1749 1995 1.278238 CACCGCGTCTTTCTCCATAC 58.722 55.000 4.92 0.00 0.00 2.39
1750 1996 0.459585 GCACCGCGTCTTTCTCCATA 60.460 55.000 4.92 0.00 0.00 2.74
1783 2029 4.847444 GAGCCGAGGAAGCCCAGC 62.847 72.222 0.00 0.00 33.88 4.85
1882 2664 3.272574 AGCACAGATGGATCGAAATGT 57.727 42.857 0.00 0.00 0.00 2.71
1885 2667 4.081697 TCAGTTAGCACAGATGGATCGAAA 60.082 41.667 0.00 0.00 0.00 3.46
1910 2692 0.901827 TCCACGGACTGCACATACAT 59.098 50.000 0.00 0.00 0.00 2.29
2221 5802 0.179018 AGGACCCTGCACAACAAGAC 60.179 55.000 0.00 0.00 0.00 3.01
2310 5891 0.525761 CGTACGAGGTCGGGGTTTTA 59.474 55.000 10.44 0.00 44.95 1.52
2500 8140 4.087892 CTGCTGCTGCCCCGTACT 62.088 66.667 13.47 0.00 38.71 2.73
2524 8167 3.873952 GCCATCTGTCCATTAGTCTGAAC 59.126 47.826 0.00 0.00 0.00 3.18
2565 8208 0.250234 TGGCCAGCGATATATGCTCC 59.750 55.000 0.00 7.09 41.72 4.70
2599 8242 6.407202 ACAGTACTGAATATTGTCCCAACTC 58.593 40.000 29.30 0.00 27.85 3.01
2600 8243 6.374417 ACAGTACTGAATATTGTCCCAACT 57.626 37.500 29.30 0.00 27.85 3.16
2601 8244 7.328737 AGTACAGTACTGAATATTGTCCCAAC 58.671 38.462 29.30 1.29 37.69 3.77
2602 8245 7.490657 AGTACAGTACTGAATATTGTCCCAA 57.509 36.000 29.30 0.00 37.69 4.12
2603 8246 7.490657 AAGTACAGTACTGAATATTGTCCCA 57.509 36.000 29.30 0.00 39.39 4.37
2604 8247 8.038944 TGAAAGTACAGTACTGAATATTGTCCC 58.961 37.037 29.30 8.42 39.39 4.46
2605 8248 8.997621 TGAAAGTACAGTACTGAATATTGTCC 57.002 34.615 29.30 9.65 39.39 4.02
2608 8251 7.275779 ACGCTGAAAGTACAGTACTGAATATTG 59.724 37.037 29.30 12.15 39.39 1.90
2640 8283 1.667236 CACTGTGGAGTGCACTTTCA 58.333 50.000 22.65 19.01 43.24 2.69
2649 8292 2.344093 AGGGATTACCACTGTGGAGT 57.656 50.000 32.30 16.96 40.96 3.85
2650 8293 5.126067 CAAATAGGGATTACCACTGTGGAG 58.874 45.833 32.30 8.17 40.96 3.86
2651 8294 4.538490 ACAAATAGGGATTACCACTGTGGA 59.462 41.667 32.30 12.33 40.96 4.02
2652 8295 4.855340 ACAAATAGGGATTACCACTGTGG 58.145 43.478 24.80 24.80 45.02 4.17
2654 8297 7.696017 ACTTTACAAATAGGGATTACCACTGT 58.304 34.615 0.00 0.00 43.89 3.55
2662 8305 9.774413 CGGAGTATTACTTTACAAATAGGGATT 57.226 33.333 0.00 0.00 0.00 3.01
2663 8306 8.931568 ACGGAGTATTACTTTACAAATAGGGAT 58.068 33.333 0.00 0.00 41.94 3.85
2664 8307 8.310122 ACGGAGTATTACTTTACAAATAGGGA 57.690 34.615 0.00 0.00 41.94 4.20
2691 8334 9.979897 TCCACCTATAGTCTACTAACAGTTTTA 57.020 33.333 0.00 0.00 31.39 1.52
2692 8335 8.890410 TCCACCTATAGTCTACTAACAGTTTT 57.110 34.615 0.00 0.00 31.39 2.43
2693 8336 7.560626 CCTCCACCTATAGTCTACTAACAGTTT 59.439 40.741 0.00 0.00 31.39 2.66
2694 8337 7.061688 CCTCCACCTATAGTCTACTAACAGTT 58.938 42.308 0.00 0.00 31.39 3.16
2695 8338 6.389278 TCCTCCACCTATAGTCTACTAACAGT 59.611 42.308 0.00 0.00 31.39 3.55
2696 8339 6.839454 TCCTCCACCTATAGTCTACTAACAG 58.161 44.000 0.00 0.00 31.39 3.16
2697 8340 6.836714 TCCTCCACCTATAGTCTACTAACA 57.163 41.667 0.00 0.00 31.39 2.41
2698 8341 7.559170 TGTTTCCTCCACCTATAGTCTACTAAC 59.441 40.741 0.00 0.00 31.39 2.34
2699 8342 7.559170 GTGTTTCCTCCACCTATAGTCTACTAA 59.441 40.741 0.00 0.00 31.39 2.24
2700 8343 7.059156 GTGTTTCCTCCACCTATAGTCTACTA 58.941 42.308 0.00 0.00 0.00 1.82
2701 8344 5.892686 GTGTTTCCTCCACCTATAGTCTACT 59.107 44.000 0.00 0.00 0.00 2.57
2713 8404 0.531974 TGTGCTCGTGTTTCCTCCAC 60.532 55.000 0.00 0.00 0.00 4.02
2715 8406 0.868406 CTTGTGCTCGTGTTTCCTCC 59.132 55.000 0.00 0.00 0.00 4.30
2730 8421 3.947834 GCCAATATTACAGTGCTCCTTGT 59.052 43.478 0.00 0.00 0.00 3.16
2769 8460 5.888982 ATTTCTTCCGACCCACTACATAT 57.111 39.130 0.00 0.00 0.00 1.78
2770 8461 5.687166 AATTTCTTCCGACCCACTACATA 57.313 39.130 0.00 0.00 0.00 2.29
3172 9726 1.080839 CCGAAATTTGTGCCCCACG 60.081 57.895 0.00 0.00 37.14 4.94
3263 9968 6.116126 GGTGAGTTGAGAATTTGGCTACTAT 58.884 40.000 0.00 0.00 0.00 2.12
3268 9973 2.154462 CGGTGAGTTGAGAATTTGGCT 58.846 47.619 0.00 0.00 0.00 4.75
3285 9990 0.965363 GGGTGTTGATTGATGCCGGT 60.965 55.000 1.90 0.00 0.00 5.28
3287 9992 0.887247 TTGGGTGTTGATTGATGCCG 59.113 50.000 0.00 0.00 0.00 5.69
3351 10058 3.494626 TCTTGACGCAAACTGAATGTCTC 59.505 43.478 0.00 0.00 0.00 3.36
3443 10150 6.400727 CGGTTGTGTATAGTTGTCTACAAAGC 60.401 42.308 0.00 0.00 37.63 3.51
3466 10173 6.721571 AACATTGTATACAAAGAGTGTCGG 57.278 37.500 23.67 8.29 41.98 4.79
3596 10303 7.234661 TCAACATCACAAGTACTACCATGTA 57.765 36.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.