Multiple sequence alignment - TraesCS3D01G077700

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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 TraesCS3D01G077700 chr3D 100.000 2415 0 0 1 2415 38375124 38372710 0.000000e+00 4460.0
1 TraesCS3D01G077700 chr3D 91.255 263 22 1 734 996 447584884 447585145 8.210000e-95 357.0
2 TraesCS3D01G077700 chr3D 89.286 280 28 2 727 1006 330370424 330370701 1.370000e-92 350.0
3 TraesCS3D01G077700 chr3D 79.070 172 31 4 1351 1520 38364327 38364159 1.960000e-21 113.0
4 TraesCS3D01G077700 chr3D 78.378 185 14 12 306 478 38603613 38603443 1.980000e-16 97.1
5 TraesCS3D01G077700 chr3D 97.778 45 1 0 1621 1665 38373366 38373322 7.160000e-11 78.7
6 TraesCS3D01G077700 chr3D 97.778 45 1 0 1759 1803 38373504 38373460 7.160000e-11 78.7
7 TraesCS3D01G077700 chr3A 92.722 687 47 3 167 852 49610264 49609580 0.000000e+00 989.0
8 TraesCS3D01G077700 chr3A 91.518 672 56 1 1741 2412 49601326 49600656 0.000000e+00 924.0
9 TraesCS3D01G077700 chr3A 88.393 784 51 20 851 1624 49604198 49603445 0.000000e+00 907.0
10 TraesCS3D01G077700 chr3A 97.015 134 4 0 32 165 49622811 49622678 2.420000e-55 226.0
11 TraesCS3D01G077700 chr3A 93.333 45 3 0 1621 1665 49601308 49601264 1.550000e-07 67.6
12 TraesCS3D01G077700 chr2A 82.754 748 121 6 1664 2407 757365094 757364351 0.000000e+00 660.0
13 TraesCS3D01G077700 chr2A 82.620 748 122 6 1664 2407 757334530 757335273 0.000000e+00 654.0
14 TraesCS3D01G077700 chr2A 80.603 232 34 10 2187 2412 764328957 764328731 4.130000e-38 169.0
15 TraesCS3D01G077700 chr6B 82.667 750 120 8 1664 2407 75280169 75279424 0.000000e+00 656.0
16 TraesCS3D01G077700 chr7A 82.503 743 118 10 1664 2401 518810222 518810957 2.020000e-180 641.0
17 TraesCS3D01G077700 chr7A 92.453 265 20 0 730 994 202997242 202996978 1.750000e-101 379.0
18 TraesCS3D01G077700 chr2D 82.082 759 106 19 1664 2412 638817196 638816458 2.640000e-174 621.0
19 TraesCS3D01G077700 chr2B 79.973 754 110 23 1664 2412 798141820 798141103 3.560000e-143 518.0
20 TraesCS3D01G077700 chr2B 91.255 263 22 1 733 995 22013616 22013355 8.210000e-95 357.0
21 TraesCS3D01G077700 chr2B 90.530 264 25 0 732 995 245947961 245948224 1.370000e-92 350.0
22 TraesCS3D01G077700 chr2B 94.872 39 2 0 2340 2378 46681121 46681159 7.210000e-06 62.1
23 TraesCS3D01G077700 chr2B 94.872 39 2 0 2340 2378 161921639 161921677 7.210000e-06 62.1
24 TraesCS3D01G077700 chr6A 84.675 385 55 3 2024 2407 420408352 420407971 4.870000e-102 381.0
25 TraesCS3D01G077700 chr1B 92.075 265 21 0 734 998 610020269 610020005 8.150000e-100 374.0
26 TraesCS3D01G077700 chr1B 91.221 262 23 0 733 994 211479120 211478859 8.210000e-95 357.0
27 TraesCS3D01G077700 chr7B 90.706 269 23 2 734 1001 514515240 514515507 8.210000e-95 357.0
28 TraesCS3D01G077700 chr5D 90.943 265 21 3 732 995 371848569 371848307 1.060000e-93 353.0
29 TraesCS3D01G077700 chr3B 85.315 143 17 4 15 157 61050368 61050230 6.960000e-31 145.0
30 TraesCS3D01G077700 chr3B 81.457 151 22 5 12 162 61047991 61047847 4.220000e-23 119.0
31 TraesCS3D01G077700 chr3B 86.905 84 11 0 350 433 61533025 61532942 7.110000e-16 95.3
32 TraesCS3D01G077700 chr3B 83.696 92 7 4 15 98 60869385 60869294 1.990000e-11 80.5
33 TraesCS3D01G077700 chrUn 94.872 39 2 0 2340 2378 247061189 247061227 7.210000e-06 62.1


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 TraesCS3D01G077700 chr3D 38372710 38375124 2414 True 1539.133333 4460 98.518667 1 2415 3 chr3D.!!$R3 2414
1 TraesCS3D01G077700 chr3A 49609580 49610264 684 True 989.000000 989 92.722000 167 852 1 chr3A.!!$R1 685
2 TraesCS3D01G077700 chr3A 49600656 49604198 3542 True 632.866667 924 91.081333 851 2412 3 chr3A.!!$R3 1561
3 TraesCS3D01G077700 chr2A 757364351 757365094 743 True 660.000000 660 82.754000 1664 2407 1 chr2A.!!$R1 743
4 TraesCS3D01G077700 chr2A 757334530 757335273 743 False 654.000000 654 82.620000 1664 2407 1 chr2A.!!$F1 743
5 TraesCS3D01G077700 chr6B 75279424 75280169 745 True 656.000000 656 82.667000 1664 2407 1 chr6B.!!$R1 743
6 TraesCS3D01G077700 chr7A 518810222 518810957 735 False 641.000000 641 82.503000 1664 2401 1 chr7A.!!$F1 737
7 TraesCS3D01G077700 chr2D 638816458 638817196 738 True 621.000000 621 82.082000 1664 2412 1 chr2D.!!$R1 748
8 TraesCS3D01G077700 chr2B 798141103 798141820 717 True 518.000000 518 79.973000 1664 2412 1 chr2B.!!$R2 748

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
29 30 0.179076 TGATGATGCGCCTGTTCGAT 60.179 50.0 4.18 0.0 0.0 3.59 F
30 31 0.234106 GATGATGCGCCTGTTCGATG 59.766 55.0 4.18 0.0 0.0 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1302 1304 0.677731 AATGACCATGTCAGGCACGG 60.678 55.0 3.11 0.00 46.04 4.94 R
1912 3954 0.798776 CACGAAGTCCAGGACATTGC 59.201 55.0 22.31 6.65 41.61 3.56 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
20 21 2.830772 TTAGCAGTTTGATGATGCGC 57.169 45.000 0.00 0.00 44.64 6.09
21 22 1.016627 TAGCAGTTTGATGATGCGCC 58.983 50.000 4.18 0.00 44.64 6.53
22 23 0.679002 AGCAGTTTGATGATGCGCCT 60.679 50.000 4.18 0.00 44.64 5.52
23 24 0.524816 GCAGTTTGATGATGCGCCTG 60.525 55.000 4.18 2.13 0.00 4.85
24 25 0.806868 CAGTTTGATGATGCGCCTGT 59.193 50.000 4.18 0.00 0.00 4.00
25 26 1.200716 CAGTTTGATGATGCGCCTGTT 59.799 47.619 4.18 0.00 0.00 3.16
26 27 1.470098 AGTTTGATGATGCGCCTGTTC 59.530 47.619 4.18 0.00 0.00 3.18
27 28 0.447406 TTTGATGATGCGCCTGTTCG 59.553 50.000 4.18 0.00 0.00 3.95
28 29 0.390998 TTGATGATGCGCCTGTTCGA 60.391 50.000 4.18 0.00 0.00 3.71
29 30 0.179076 TGATGATGCGCCTGTTCGAT 60.179 50.000 4.18 0.00 0.00 3.59
30 31 0.234106 GATGATGCGCCTGTTCGATG 59.766 55.000 4.18 0.00 0.00 3.84
31 32 0.462581 ATGATGCGCCTGTTCGATGT 60.463 50.000 4.18 0.00 0.00 3.06
32 33 1.349627 GATGCGCCTGTTCGATGTG 59.650 57.895 4.18 0.00 0.00 3.21
33 34 1.361668 GATGCGCCTGTTCGATGTGT 61.362 55.000 4.18 0.00 0.00 3.72
34 35 1.638388 ATGCGCCTGTTCGATGTGTG 61.638 55.000 4.18 0.00 0.00 3.82
35 36 2.317609 GCGCCTGTTCGATGTGTGT 61.318 57.895 0.00 0.00 0.00 3.72
36 37 1.011968 GCGCCTGTTCGATGTGTGTA 61.012 55.000 0.00 0.00 0.00 2.90
37 38 0.992072 CGCCTGTTCGATGTGTGTAG 59.008 55.000 0.00 0.00 0.00 2.74
38 39 0.721718 GCCTGTTCGATGTGTGTAGC 59.278 55.000 0.00 0.00 0.00 3.58
39 40 1.359848 CCTGTTCGATGTGTGTAGCC 58.640 55.000 0.00 0.00 0.00 3.93
40 41 1.066858 CCTGTTCGATGTGTGTAGCCT 60.067 52.381 0.00 0.00 0.00 4.58
41 42 2.612972 CCTGTTCGATGTGTGTAGCCTT 60.613 50.000 0.00 0.00 0.00 4.35
42 43 2.412870 TGTTCGATGTGTGTAGCCTTG 58.587 47.619 0.00 0.00 0.00 3.61
43 44 1.732259 GTTCGATGTGTGTAGCCTTGG 59.268 52.381 0.00 0.00 0.00 3.61
44 45 0.391130 TCGATGTGTGTAGCCTTGGC 60.391 55.000 2.97 2.97 0.00 4.52
45 46 0.673333 CGATGTGTGTAGCCTTGGCA 60.673 55.000 14.54 0.00 0.00 4.92
46 47 1.755179 GATGTGTGTAGCCTTGGCAT 58.245 50.000 14.54 1.97 0.00 4.40
47 48 1.402968 GATGTGTGTAGCCTTGGCATG 59.597 52.381 14.54 0.00 0.00 4.06
48 49 0.399833 TGTGTGTAGCCTTGGCATGA 59.600 50.000 14.54 0.00 0.00 3.07
49 50 1.004628 TGTGTGTAGCCTTGGCATGAT 59.995 47.619 14.54 0.00 0.00 2.45
50 51 1.402968 GTGTGTAGCCTTGGCATGATG 59.597 52.381 14.54 0.00 0.00 3.07
51 52 1.027357 GTGTAGCCTTGGCATGATGG 58.973 55.000 14.54 0.00 0.00 3.51
52 53 0.918258 TGTAGCCTTGGCATGATGGA 59.082 50.000 14.54 0.00 0.00 3.41
53 54 1.496001 TGTAGCCTTGGCATGATGGAT 59.504 47.619 14.54 0.00 0.00 3.41
54 55 1.884579 GTAGCCTTGGCATGATGGATG 59.115 52.381 14.54 0.00 34.84 3.51
68 69 7.741027 CATGATGGATGCTTGTACTAATCTT 57.259 36.000 0.00 0.00 0.00 2.40
69 70 8.837788 CATGATGGATGCTTGTACTAATCTTA 57.162 34.615 0.00 0.00 0.00 2.10
70 71 8.933807 CATGATGGATGCTTGTACTAATCTTAG 58.066 37.037 0.00 0.00 36.82 2.18
71 72 8.250143 TGATGGATGCTTGTACTAATCTTAGA 57.750 34.615 4.03 0.00 34.84 2.10
72 73 8.704668 TGATGGATGCTTGTACTAATCTTAGAA 58.295 33.333 4.03 0.00 34.84 2.10
73 74 9.717942 GATGGATGCTTGTACTAATCTTAGAAT 57.282 33.333 4.03 0.00 34.84 2.40
74 75 8.893219 TGGATGCTTGTACTAATCTTAGAATG 57.107 34.615 4.03 0.00 34.84 2.67
75 76 8.486210 TGGATGCTTGTACTAATCTTAGAATGT 58.514 33.333 4.03 0.00 34.84 2.71
76 77 9.982651 GGATGCTTGTACTAATCTTAGAATGTA 57.017 33.333 4.03 0.00 34.84 2.29
91 92 9.555727 TCTTAGAATGTATTTTGTATGTAGCCC 57.444 33.333 0.00 0.00 0.00 5.19
92 93 9.561069 CTTAGAATGTATTTTGTATGTAGCCCT 57.439 33.333 0.00 0.00 0.00 5.19
93 94 7.807977 AGAATGTATTTTGTATGTAGCCCTG 57.192 36.000 0.00 0.00 0.00 4.45
94 95 6.772716 AGAATGTATTTTGTATGTAGCCCTGG 59.227 38.462 0.00 0.00 0.00 4.45
95 96 4.204012 TGTATTTTGTATGTAGCCCTGGC 58.796 43.478 0.00 0.00 42.33 4.85
96 97 2.889170 TTTTGTATGTAGCCCTGGCA 57.111 45.000 11.38 0.00 44.88 4.92
97 98 3.380471 TTTTGTATGTAGCCCTGGCAT 57.620 42.857 11.38 0.00 44.88 4.40
98 99 4.511786 TTTTGTATGTAGCCCTGGCATA 57.488 40.909 11.38 0.00 44.88 3.14
99 100 3.769739 TTGTATGTAGCCCTGGCATAG 57.230 47.619 11.38 0.00 44.88 2.23
100 101 2.970987 TGTATGTAGCCCTGGCATAGA 58.029 47.619 11.38 0.00 44.88 1.98
101 102 3.520696 TGTATGTAGCCCTGGCATAGAT 58.479 45.455 11.38 6.71 44.88 1.98
102 103 3.261643 TGTATGTAGCCCTGGCATAGATG 59.738 47.826 11.38 0.00 44.88 2.90
118 119 6.756299 CATAGATGCTAGTGCTGATCTAGA 57.244 41.667 0.00 0.00 37.50 2.43
119 120 6.788243 CATAGATGCTAGTGCTGATCTAGAG 58.212 44.000 0.00 0.00 37.50 2.43
120 121 4.728772 AGATGCTAGTGCTGATCTAGAGT 58.271 43.478 0.00 0.00 37.62 3.24
121 122 5.875224 AGATGCTAGTGCTGATCTAGAGTA 58.125 41.667 0.00 0.00 37.62 2.59
122 123 6.484288 AGATGCTAGTGCTGATCTAGAGTAT 58.516 40.000 0.00 0.00 37.62 2.12
123 124 7.629157 AGATGCTAGTGCTGATCTAGAGTATA 58.371 38.462 0.00 0.00 37.62 1.47
124 125 8.274322 AGATGCTAGTGCTGATCTAGAGTATAT 58.726 37.037 0.00 0.00 37.62 0.86
125 126 9.554395 GATGCTAGTGCTGATCTAGAGTATATA 57.446 37.037 0.00 0.00 37.62 0.86
127 128 9.913310 TGCTAGTGCTGATCTAGAGTATATATT 57.087 33.333 0.00 0.00 37.62 1.28
151 152 9.853177 ATTTAATTAGGTATCCTCTTTGGTCTG 57.147 33.333 0.00 0.00 34.61 3.51
152 153 8.618240 TTAATTAGGTATCCTCTTTGGTCTGA 57.382 34.615 0.00 0.00 34.61 3.27
153 154 6.739331 ATTAGGTATCCTCTTTGGTCTGAG 57.261 41.667 0.00 0.00 34.61 3.35
154 155 4.067944 AGGTATCCTCTTTGGTCTGAGT 57.932 45.455 0.00 0.00 37.07 3.41
155 156 3.772025 AGGTATCCTCTTTGGTCTGAGTG 59.228 47.826 0.00 0.00 37.07 3.51
156 157 3.515901 GGTATCCTCTTTGGTCTGAGTGT 59.484 47.826 0.00 0.00 37.07 3.55
157 158 4.020128 GGTATCCTCTTTGGTCTGAGTGTT 60.020 45.833 0.00 0.00 37.07 3.32
158 159 3.753294 TCCTCTTTGGTCTGAGTGTTC 57.247 47.619 0.00 0.00 37.07 3.18
159 160 3.038280 TCCTCTTTGGTCTGAGTGTTCA 58.962 45.455 0.00 0.00 37.07 3.18
160 161 3.648067 TCCTCTTTGGTCTGAGTGTTCAT 59.352 43.478 0.00 0.00 37.07 2.57
161 162 4.103153 TCCTCTTTGGTCTGAGTGTTCATT 59.897 41.667 0.00 0.00 37.07 2.57
162 163 4.453819 CCTCTTTGGTCTGAGTGTTCATTC 59.546 45.833 0.00 0.00 31.68 2.67
163 164 5.296151 TCTTTGGTCTGAGTGTTCATTCT 57.704 39.130 0.00 0.00 31.68 2.40
164 165 5.059161 TCTTTGGTCTGAGTGTTCATTCTG 58.941 41.667 0.00 0.00 31.68 3.02
165 166 2.771089 TGGTCTGAGTGTTCATTCTGC 58.229 47.619 0.00 0.00 31.68 4.26
175 176 4.754618 AGTGTTCATTCTGCGTGTAAATGA 59.245 37.500 0.00 0.00 37.57 2.57
178 179 5.163764 TGTTCATTCTGCGTGTAAATGATCC 60.164 40.000 0.00 0.00 38.72 3.36
191 192 2.832643 ATGATCCCTTGTGCCAATGA 57.167 45.000 0.00 0.00 0.00 2.57
239 240 8.169268 GCAACAAATCTACTGTGTTATAGTGAC 58.831 37.037 0.00 0.00 33.80 3.67
248 249 7.228314 ACTGTGTTATAGTGACAGCTTTAGA 57.772 36.000 0.00 0.00 40.71 2.10
312 313 6.420913 AATCTACTGTGTTATAGGCGGATT 57.579 37.500 0.00 0.00 0.00 3.01
351 352 5.278463 GCACTGCAGTTTCTCTATTTGGAAA 60.278 40.000 18.94 0.00 0.00 3.13
364 365 4.961438 ATTTGGAAACTGGAAACTGCAT 57.039 36.364 0.00 0.00 0.00 3.96
434 435 0.952984 GTGCCACCTGCTCTGTTCTC 60.953 60.000 0.00 0.00 42.00 2.87
435 436 1.123861 TGCCACCTGCTCTGTTCTCT 61.124 55.000 0.00 0.00 42.00 3.10
436 437 0.673022 GCCACCTGCTCTGTTCTCTG 60.673 60.000 0.00 0.00 36.87 3.35
437 438 0.972134 CCACCTGCTCTGTTCTCTGA 59.028 55.000 0.00 0.00 0.00 3.27
469 470 2.494073 TCTTCCACCCAAACACACAAAC 59.506 45.455 0.00 0.00 0.00 2.93
506 507 6.533367 CACTATACAGCAAGAAGAAACCTCTC 59.467 42.308 0.00 0.00 0.00 3.20
509 510 2.483491 CAGCAAGAAGAAACCTCTCTGC 59.517 50.000 0.00 0.00 34.32 4.26
560 561 5.692814 CGTGCAGATTTTCATGAAGAAAGA 58.307 37.500 8.41 0.00 46.24 2.52
571 572 7.718272 TTCATGAAGAAAGAAGCATTTTTGG 57.282 32.000 3.38 0.00 32.05 3.28
573 574 7.499292 TCATGAAGAAAGAAGCATTTTTGGAA 58.501 30.769 0.00 0.00 0.00 3.53
616 617 5.648178 TTGCATGCATGTTCAGAATTAGT 57.352 34.783 26.79 0.00 0.00 2.24
630 631 8.352942 GTTCAGAATTAGTCAATGTTTGTTCCT 58.647 33.333 0.00 0.00 0.00 3.36
633 634 9.612620 CAGAATTAGTCAATGTTTGTTCCTAAC 57.387 33.333 0.00 0.00 0.00 2.34
644 645 7.504924 TGTTTGTTCCTAACGAAATTCAGAT 57.495 32.000 0.00 0.00 36.57 2.90
718 720 1.226717 CTCGCGAGCAGAAGGGTAC 60.227 63.158 25.07 0.00 0.00 3.34
726 728 1.348036 AGCAGAAGGGTACTTTCGCTT 59.652 47.619 16.01 0.00 39.83 4.68
729 731 3.556365 GCAGAAGGGTACTTTCGCTTATC 59.444 47.826 13.89 0.00 39.92 1.75
735 737 5.658468 AGGGTACTTTCGCTTATCAAGTAC 58.342 41.667 11.38 11.38 46.56 2.73
737 739 5.747675 GGGTACTTTCGCTTATCAAGTACTC 59.252 44.000 16.85 11.79 46.52 2.59
738 740 5.747675 GGTACTTTCGCTTATCAAGTACTCC 59.252 44.000 16.85 3.01 46.52 3.85
741 743 4.650754 TTCGCTTATCAAGTACTCCCTC 57.349 45.455 0.00 0.00 0.00 4.30
742 744 2.957006 TCGCTTATCAAGTACTCCCTCC 59.043 50.000 0.00 0.00 0.00 4.30
743 745 2.693591 CGCTTATCAAGTACTCCCTCCA 59.306 50.000 0.00 0.00 0.00 3.86
756 758 7.395617 AGTACTCCCTCCATTTCTTTTTAGTC 58.604 38.462 0.00 0.00 0.00 2.59
761 763 5.243730 CCCTCCATTTCTTTTTAGTCTGCAA 59.756 40.000 0.00 0.00 0.00 4.08
928 930 9.262358 GTTGATATCTTTTCCTATAAAGCTCGT 57.738 33.333 3.98 0.00 35.56 4.18
929 931 9.477484 TTGATATCTTTTCCTATAAAGCTCGTC 57.523 33.333 3.98 0.00 35.56 4.20
930 932 8.638873 TGATATCTTTTCCTATAAAGCTCGTCA 58.361 33.333 3.98 0.00 35.56 4.35
931 933 9.477484 GATATCTTTTCCTATAAAGCTCGTCAA 57.523 33.333 0.00 0.00 35.56 3.18
932 934 9.832445 ATATCTTTTCCTATAAAGCTCGTCAAA 57.168 29.630 0.00 0.00 35.56 2.69
933 935 7.360575 TCTTTTCCTATAAAGCTCGTCAAAC 57.639 36.000 0.00 0.00 35.56 2.93
934 936 7.159372 TCTTTTCCTATAAAGCTCGTCAAACT 58.841 34.615 0.00 0.00 35.56 2.66
935 937 7.660208 TCTTTTCCTATAAAGCTCGTCAAACTT 59.340 33.333 0.00 0.00 35.56 2.66
936 938 7.739498 TTTCCTATAAAGCTCGTCAAACTTT 57.261 32.000 0.00 0.00 37.40 2.66
937 939 8.836268 TTTCCTATAAAGCTCGTCAAACTTTA 57.164 30.769 0.00 0.00 39.47 1.85
1061 1063 1.811679 GCCTGCTGGTTCTCTACGC 60.812 63.158 11.69 0.00 35.27 4.42
1068 1070 1.445582 GGTTCTCTACGCCACCACG 60.446 63.158 0.00 0.00 39.50 4.94
1093 1095 2.046988 CAGTCGCTGCCATGTCCA 60.047 61.111 0.00 0.00 0.00 4.02
1139 1141 1.758440 GATCGCCTATGTCTGGGGCA 61.758 60.000 0.00 0.00 45.50 5.36
1174 1176 4.020617 CTCACCAAGGCGAGCCCA 62.021 66.667 10.95 0.00 36.58 5.36
1175 1177 3.965539 CTCACCAAGGCGAGCCCAG 62.966 68.421 10.95 3.45 36.58 4.45
1233 1235 3.195002 CGGCTGCCGTATGTGTGG 61.195 66.667 31.72 1.11 42.73 4.17
1234 1236 2.046314 GGCTGCCGTATGTGTGGT 60.046 61.111 1.35 0.00 0.00 4.16
1235 1237 2.398554 GGCTGCCGTATGTGTGGTG 61.399 63.158 1.35 0.00 0.00 4.17
1236 1238 1.671054 GCTGCCGTATGTGTGGTGT 60.671 57.895 0.00 0.00 0.00 4.16
1237 1239 1.911293 GCTGCCGTATGTGTGGTGTG 61.911 60.000 0.00 0.00 0.00 3.82
1238 1240 1.911293 CTGCCGTATGTGTGGTGTGC 61.911 60.000 0.00 0.00 0.00 4.57
1240 1242 1.635663 GCCGTATGTGTGGTGTGCTC 61.636 60.000 0.00 0.00 0.00 4.26
1241 1243 1.351430 CCGTATGTGTGGTGTGCTCG 61.351 60.000 0.00 0.00 0.00 5.03
1244 1246 0.670239 TATGTGTGGTGTGCTCGCTG 60.670 55.000 0.00 0.00 0.00 5.18
1246 1248 2.280119 TGTGGTGTGCTCGCTGTC 60.280 61.111 0.00 0.00 0.00 3.51
1248 1250 3.233980 TGGTGTGCTCGCTGTCCT 61.234 61.111 0.00 0.00 0.00 3.85
1249 1251 2.433318 GGTGTGCTCGCTGTCCTC 60.433 66.667 0.00 0.00 0.00 3.71
1250 1252 2.653702 GTGTGCTCGCTGTCCTCT 59.346 61.111 0.00 0.00 0.00 3.69
1251 1253 1.005630 GTGTGCTCGCTGTCCTCTT 60.006 57.895 0.00 0.00 0.00 2.85
1252 1254 1.011451 GTGTGCTCGCTGTCCTCTTC 61.011 60.000 0.00 0.00 0.00 2.87
1270 1272 2.662596 GTCGGACCATGCCTGACA 59.337 61.111 15.98 0.00 34.14 3.58
1280 1282 0.392998 ATGCCTGACATGGTCGTTCC 60.393 55.000 0.00 0.00 37.70 3.62
1293 1295 2.032681 GTTCCGTGCTGGCCTCTT 59.967 61.111 3.32 0.00 37.80 2.85
1297 1299 3.123620 CGTGCTGGCCTCTTCTGC 61.124 66.667 3.32 0.00 0.00 4.26
1334 1336 2.073056 TGGTCATTCCGTTCATGTTCG 58.927 47.619 0.00 0.00 39.52 3.95
1340 1342 1.006825 TCCGTTCATGTTCGCTGTCG 61.007 55.000 0.00 0.00 0.00 4.35
1404 1406 0.544357 TGGGAGGACGACAATGAGGT 60.544 55.000 0.00 0.00 0.00 3.85
1405 1407 1.272816 TGGGAGGACGACAATGAGGTA 60.273 52.381 0.00 0.00 0.00 3.08
1406 1408 2.040178 GGGAGGACGACAATGAGGTAT 58.960 52.381 0.00 0.00 0.00 2.73
1419 1428 5.878406 AATGAGGTATTGAGGTAGGACAG 57.122 43.478 0.00 0.00 0.00 3.51
1427 1436 1.714787 TGAGGTAGGACAGGTGTAGGT 59.285 52.381 0.00 0.00 0.00 3.08
1433 1442 1.838077 AGGACAGGTGTAGGTTATGCC 59.162 52.381 0.00 0.00 37.58 4.40
1507 1517 5.766670 ACAATGCAGAGTCAAATCTTTCTGA 59.233 36.000 4.65 0.00 39.46 3.27
1514 1524 7.571059 GCAGAGTCAAATCTTTCTGAACTTCTC 60.571 40.741 4.65 0.00 39.46 2.87
1550 1560 2.229062 CTGAAAGCAGGACGACTACTGA 59.771 50.000 0.00 0.00 38.51 3.41
1551 1561 2.826128 TGAAAGCAGGACGACTACTGAT 59.174 45.455 0.00 0.00 36.86 2.90
1552 1562 4.014406 TGAAAGCAGGACGACTACTGATA 58.986 43.478 0.00 0.00 36.86 2.15
1574 1584 9.803507 TGATAGCTTCAATCAATAATCCAATCT 57.196 29.630 0.00 0.00 30.52 2.40
1594 1604 7.337718 CAATCTGAAACGACCGACAAATATAG 58.662 38.462 0.00 0.00 0.00 1.31
1619 1629 1.561643 TTGGCAAACAACAACCCTCA 58.438 45.000 0.00 0.00 33.18 3.86
1624 1634 2.935849 GCAAACAACAACCCTCAAAAGG 59.064 45.455 0.00 0.00 42.95 3.11
1625 1635 3.368948 GCAAACAACAACCCTCAAAAGGA 60.369 43.478 0.00 0.00 46.67 3.36
1626 1636 4.826556 CAAACAACAACCCTCAAAAGGAA 58.173 39.130 0.00 0.00 46.67 3.36
1630 1640 5.265989 ACAACAACCCTCAAAAGGAAGTTA 58.734 37.500 0.00 0.00 46.67 2.24
1631 1641 5.897250 ACAACAACCCTCAAAAGGAAGTTAT 59.103 36.000 0.00 0.00 46.67 1.89
1634 1644 6.246163 ACAACCCTCAAAAGGAAGTTATAGG 58.754 40.000 0.00 0.00 46.67 2.57
1637 1647 7.196637 ACCCTCAAAAGGAAGTTATAGGTAG 57.803 40.000 0.00 0.00 46.67 3.18
1638 1648 6.964086 ACCCTCAAAAGGAAGTTATAGGTAGA 59.036 38.462 0.00 0.00 46.67 2.59
1640 1650 7.988028 CCCTCAAAAGGAAGTTATAGGTAGAAG 59.012 40.741 0.00 0.00 46.67 2.85
1641 1651 7.988028 CCTCAAAAGGAAGTTATAGGTAGAAGG 59.012 40.741 0.00 0.00 46.67 3.46
1642 1652 8.674925 TCAAAAGGAAGTTATAGGTAGAAGGA 57.325 34.615 0.00 0.00 0.00 3.36
1643 1653 8.759782 TCAAAAGGAAGTTATAGGTAGAAGGAG 58.240 37.037 0.00 0.00 0.00 3.69
1644 1654 8.759782 CAAAAGGAAGTTATAGGTAGAAGGAGA 58.240 37.037 0.00 0.00 0.00 3.71
1645 1655 9.508721 AAAAGGAAGTTATAGGTAGAAGGAGAT 57.491 33.333 0.00 0.00 0.00 2.75
1646 1656 9.508721 AAAGGAAGTTATAGGTAGAAGGAGATT 57.491 33.333 0.00 0.00 0.00 2.40
1647 1657 9.508721 AAGGAAGTTATAGGTAGAAGGAGATTT 57.491 33.333 0.00 0.00 0.00 2.17
1658 1668 9.362151 AGGTAGAAGGAGATTTAGAAGAGTATG 57.638 37.037 0.00 0.00 0.00 2.39
1659 1669 8.085909 GGTAGAAGGAGATTTAGAAGAGTATGC 58.914 40.741 0.00 0.00 0.00 3.14
1660 1670 7.061566 AGAAGGAGATTTAGAAGAGTATGCC 57.938 40.000 0.00 0.00 0.00 4.40
1661 1671 5.816955 AGGAGATTTAGAAGAGTATGCCC 57.183 43.478 0.00 0.00 0.00 5.36
1662 1672 5.472347 AGGAGATTTAGAAGAGTATGCCCT 58.528 41.667 0.00 0.00 0.00 5.19
1694 1886 5.510520 CCAAGGGAATGTACAGAGATCTAGC 60.511 48.000 0.33 0.00 0.00 3.42
1712 1904 4.957327 TCTAGCTCCCTCTAGGAAAAGAAC 59.043 45.833 0.00 0.00 46.94 3.01
1724 1916 2.698274 GGAAAAGAACTGGCCTCCAAAA 59.302 45.455 3.32 0.00 30.80 2.44
1829 3866 5.961396 AAGATTATGAGCCATCAGATTGC 57.039 39.130 0.00 0.00 39.29 3.56
1869 3907 3.846588 TCAATCCTCTAAGAACCAAGCCT 59.153 43.478 0.00 0.00 0.00 4.58
1876 3914 5.046231 CCTCTAAGAACCAAGCCTAGAAACT 60.046 44.000 0.00 0.00 0.00 2.66
1896 3934 7.604164 AGAAACTAGATTGAAGAAATCAGCGAA 59.396 33.333 0.00 0.00 46.21 4.70
1897 3935 7.856145 AACTAGATTGAAGAAATCAGCGAAT 57.144 32.000 0.00 0.00 46.21 3.34
1912 3954 5.168569 TCAGCGAATGTAGGTCTTAAGTTG 58.831 41.667 1.63 0.00 0.00 3.16
1931 3973 0.798776 GCAATGTCCTGGACTTCGTG 59.201 55.000 26.03 16.64 33.15 4.35
1934 3976 0.243907 ATGTCCTGGACTTCGTGTCG 59.756 55.000 26.03 0.00 46.24 4.35
1959 4001 1.734465 CTTAGCTTTCACCGCTTCCAG 59.266 52.381 0.00 0.00 38.86 3.86
1963 4005 0.040067 CTTTCACCGCTTCCAGCAAC 60.040 55.000 0.00 0.00 42.58 4.17
2022 4064 5.947228 TTCAAGTATTTGACAGCCTCAAG 57.053 39.130 0.00 0.00 42.79 3.02
2073 4115 5.195001 TGCTAAACAGAACAAACATTCCC 57.805 39.130 0.00 0.00 0.00 3.97
2074 4116 4.038642 TGCTAAACAGAACAAACATTCCCC 59.961 41.667 0.00 0.00 0.00 4.81
2075 4117 4.560716 GCTAAACAGAACAAACATTCCCCC 60.561 45.833 0.00 0.00 0.00 5.40
2121 4163 5.429681 TGATTCCTTGATTCGTCCCTTAA 57.570 39.130 0.00 0.00 0.00 1.85
2174 4216 5.376854 AACTACAGGATTGAATGTTGCAC 57.623 39.130 0.00 0.00 0.00 4.57
2229 4272 5.614324 TTCAGACCCCTGTCAATAGTATG 57.386 43.478 0.00 0.00 44.33 2.39
2230 4273 4.620723 TCAGACCCCTGTCAATAGTATGT 58.379 43.478 0.00 0.00 44.33 2.29
2235 4278 5.990668 ACCCCTGTCAATAGTATGTCTTTC 58.009 41.667 0.00 0.00 0.00 2.62
2334 4379 5.487433 CGTATATTACCTGCATTGGATCCA 58.513 41.667 11.44 11.44 0.00 3.41
2335 4380 5.937540 CGTATATTACCTGCATTGGATCCAA 59.062 40.000 28.92 28.92 40.47 3.53
2338 4383 7.673641 ATATTACCTGCATTGGATCCAAAAA 57.326 32.000 30.28 17.21 39.55 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.159393 GGCGCATCATCAAACTGCTAAA 60.159 45.455 10.83 0.00 33.75 1.85
1 2 1.401552 GGCGCATCATCAAACTGCTAA 59.598 47.619 10.83 0.00 33.75 3.09
2 3 1.016627 GGCGCATCATCAAACTGCTA 58.983 50.000 10.83 0.00 33.75 3.49
3 4 0.679002 AGGCGCATCATCAAACTGCT 60.679 50.000 10.83 0.00 33.75 4.24
4 5 0.524816 CAGGCGCATCATCAAACTGC 60.525 55.000 10.83 0.00 0.00 4.40
5 6 0.806868 ACAGGCGCATCATCAAACTG 59.193 50.000 10.83 6.34 0.00 3.16
6 7 1.470098 GAACAGGCGCATCATCAAACT 59.530 47.619 10.83 0.00 0.00 2.66
7 8 1.791555 CGAACAGGCGCATCATCAAAC 60.792 52.381 10.83 0.00 0.00 2.93
8 9 0.447406 CGAACAGGCGCATCATCAAA 59.553 50.000 10.83 0.00 0.00 2.69
9 10 0.390998 TCGAACAGGCGCATCATCAA 60.391 50.000 10.83 0.00 0.00 2.57
10 11 0.179076 ATCGAACAGGCGCATCATCA 60.179 50.000 10.83 0.00 0.00 3.07
11 12 0.234106 CATCGAACAGGCGCATCATC 59.766 55.000 10.83 0.99 0.00 2.92
12 13 0.462581 ACATCGAACAGGCGCATCAT 60.463 50.000 10.83 0.00 0.00 2.45
13 14 1.079197 ACATCGAACAGGCGCATCA 60.079 52.632 10.83 0.00 0.00 3.07
14 15 1.349627 CACATCGAACAGGCGCATC 59.650 57.895 10.83 0.15 0.00 3.91
15 16 1.375908 ACACATCGAACAGGCGCAT 60.376 52.632 10.83 0.00 0.00 4.73
16 17 2.030412 ACACATCGAACAGGCGCA 59.970 55.556 10.83 0.00 0.00 6.09
17 18 1.011968 TACACACATCGAACAGGCGC 61.012 55.000 0.00 0.00 0.00 6.53
18 19 0.992072 CTACACACATCGAACAGGCG 59.008 55.000 0.00 0.00 0.00 5.52
19 20 0.721718 GCTACACACATCGAACAGGC 59.278 55.000 0.00 0.00 0.00 4.85
20 21 1.066858 AGGCTACACACATCGAACAGG 60.067 52.381 0.00 0.00 0.00 4.00
21 22 2.370281 AGGCTACACACATCGAACAG 57.630 50.000 0.00 0.00 0.00 3.16
22 23 2.412870 CAAGGCTACACACATCGAACA 58.587 47.619 0.00 0.00 0.00 3.18
23 24 1.732259 CCAAGGCTACACACATCGAAC 59.268 52.381 0.00 0.00 0.00 3.95
24 25 1.943968 GCCAAGGCTACACACATCGAA 60.944 52.381 3.29 0.00 38.26 3.71
25 26 0.391130 GCCAAGGCTACACACATCGA 60.391 55.000 3.29 0.00 38.26 3.59
26 27 0.673333 TGCCAAGGCTACACACATCG 60.673 55.000 12.96 0.00 42.51 3.84
27 28 1.402968 CATGCCAAGGCTACACACATC 59.597 52.381 12.96 0.00 42.51 3.06
28 29 1.004628 TCATGCCAAGGCTACACACAT 59.995 47.619 12.96 0.00 42.51 3.21
29 30 0.399833 TCATGCCAAGGCTACACACA 59.600 50.000 12.96 0.00 42.51 3.72
30 31 1.402968 CATCATGCCAAGGCTACACAC 59.597 52.381 12.96 0.00 42.51 3.82
31 32 1.682702 CCATCATGCCAAGGCTACACA 60.683 52.381 12.96 0.00 42.51 3.72
32 33 1.027357 CCATCATGCCAAGGCTACAC 58.973 55.000 12.96 0.00 42.51 2.90
33 34 0.918258 TCCATCATGCCAAGGCTACA 59.082 50.000 12.96 0.00 42.51 2.74
34 35 1.884579 CATCCATCATGCCAAGGCTAC 59.115 52.381 12.96 0.00 42.51 3.58
35 36 2.281539 CATCCATCATGCCAAGGCTA 57.718 50.000 12.96 0.00 42.51 3.93
36 37 3.127099 CATCCATCATGCCAAGGCT 57.873 52.632 12.96 0.00 42.51 4.58
44 45 7.741027 AAGATTAGTACAAGCATCCATCATG 57.259 36.000 0.00 0.00 35.29 3.07
45 46 8.874156 TCTAAGATTAGTACAAGCATCCATCAT 58.126 33.333 0.00 0.00 32.61 2.45
46 47 8.250143 TCTAAGATTAGTACAAGCATCCATCA 57.750 34.615 0.00 0.00 32.61 3.07
47 48 9.717942 ATTCTAAGATTAGTACAAGCATCCATC 57.282 33.333 0.00 0.00 32.61 3.51
48 49 9.499479 CATTCTAAGATTAGTACAAGCATCCAT 57.501 33.333 0.00 0.00 32.61 3.41
49 50 8.486210 ACATTCTAAGATTAGTACAAGCATCCA 58.514 33.333 0.00 0.00 32.61 3.41
50 51 8.894768 ACATTCTAAGATTAGTACAAGCATCC 57.105 34.615 0.00 0.00 32.61 3.51
65 66 9.555727 GGGCTACATACAAAATACATTCTAAGA 57.444 33.333 0.00 0.00 0.00 2.10
66 67 9.561069 AGGGCTACATACAAAATACATTCTAAG 57.439 33.333 0.00 0.00 0.00 2.18
67 68 9.337396 CAGGGCTACATACAAAATACATTCTAA 57.663 33.333 0.00 0.00 0.00 2.10
68 69 7.936847 CCAGGGCTACATACAAAATACATTCTA 59.063 37.037 0.00 0.00 0.00 2.10
69 70 6.772716 CCAGGGCTACATACAAAATACATTCT 59.227 38.462 0.00 0.00 0.00 2.40
70 71 6.515035 GCCAGGGCTACATACAAAATACATTC 60.515 42.308 2.30 0.00 38.26 2.67
71 72 5.301805 GCCAGGGCTACATACAAAATACATT 59.698 40.000 2.30 0.00 38.26 2.71
72 73 4.827284 GCCAGGGCTACATACAAAATACAT 59.173 41.667 2.30 0.00 38.26 2.29
73 74 4.204012 GCCAGGGCTACATACAAAATACA 58.796 43.478 2.30 0.00 38.26 2.29
74 75 4.204012 TGCCAGGGCTACATACAAAATAC 58.796 43.478 12.19 0.00 42.51 1.89
75 76 4.511786 TGCCAGGGCTACATACAAAATA 57.488 40.909 12.19 0.00 42.51 1.40
76 77 3.380471 TGCCAGGGCTACATACAAAAT 57.620 42.857 12.19 0.00 42.51 1.82
77 78 2.889170 TGCCAGGGCTACATACAAAA 57.111 45.000 12.19 0.00 42.51 2.44
78 79 3.714280 TCTATGCCAGGGCTACATACAAA 59.286 43.478 12.19 0.00 42.51 2.83
79 80 3.313791 TCTATGCCAGGGCTACATACAA 58.686 45.455 12.19 0.00 42.51 2.41
80 81 2.970987 TCTATGCCAGGGCTACATACA 58.029 47.619 12.19 0.00 42.51 2.29
81 82 3.866651 CATCTATGCCAGGGCTACATAC 58.133 50.000 12.19 0.00 42.51 2.39
95 96 6.375174 ACTCTAGATCAGCACTAGCATCTATG 59.625 42.308 0.00 0.00 45.49 2.23
96 97 6.484288 ACTCTAGATCAGCACTAGCATCTAT 58.516 40.000 0.00 0.00 45.49 1.98
97 98 5.875224 ACTCTAGATCAGCACTAGCATCTA 58.125 41.667 0.00 0.00 45.49 1.98
98 99 4.728772 ACTCTAGATCAGCACTAGCATCT 58.271 43.478 0.00 0.00 45.49 2.90
99 100 6.757897 ATACTCTAGATCAGCACTAGCATC 57.242 41.667 0.00 0.00 45.49 3.91
101 102 9.913310 AATATATACTCTAGATCAGCACTAGCA 57.087 33.333 0.00 0.00 45.49 3.49
125 126 9.853177 CAGACCAAAGAGGATACCTAATTAAAT 57.147 33.333 0.00 0.00 41.22 1.40
126 127 9.053472 TCAGACCAAAGAGGATACCTAATTAAA 57.947 33.333 0.00 0.00 41.22 1.52
127 128 8.618240 TCAGACCAAAGAGGATACCTAATTAA 57.382 34.615 0.00 0.00 41.22 1.40
128 129 7.844779 ACTCAGACCAAAGAGGATACCTAATTA 59.155 37.037 0.00 0.00 41.22 1.40
129 130 6.674419 ACTCAGACCAAAGAGGATACCTAATT 59.326 38.462 0.00 0.00 41.22 1.40
130 131 6.098982 CACTCAGACCAAAGAGGATACCTAAT 59.901 42.308 0.00 0.00 41.22 1.73
131 132 5.422331 CACTCAGACCAAAGAGGATACCTAA 59.578 44.000 0.00 0.00 41.22 2.69
132 133 4.956700 CACTCAGACCAAAGAGGATACCTA 59.043 45.833 0.00 0.00 41.22 3.08
133 134 3.772025 CACTCAGACCAAAGAGGATACCT 59.228 47.826 0.00 0.00 41.22 3.08
134 135 3.515901 ACACTCAGACCAAAGAGGATACC 59.484 47.826 0.00 0.00 41.22 2.73
135 136 4.810191 ACACTCAGACCAAAGAGGATAC 57.190 45.455 0.00 0.00 41.22 2.24
136 137 4.838423 TGAACACTCAGACCAAAGAGGATA 59.162 41.667 0.00 0.00 41.22 2.59
137 138 3.648067 TGAACACTCAGACCAAAGAGGAT 59.352 43.478 0.00 0.00 41.22 3.24
138 139 3.038280 TGAACACTCAGACCAAAGAGGA 58.962 45.455 0.00 0.00 41.22 3.71
139 140 3.475566 TGAACACTCAGACCAAAGAGG 57.524 47.619 0.00 0.00 45.67 3.69
140 141 5.178996 CAGAATGAACACTCAGACCAAAGAG 59.821 44.000 0.00 0.00 39.69 2.85
141 142 5.059161 CAGAATGAACACTCAGACCAAAGA 58.941 41.667 0.00 0.00 39.69 2.52
142 143 4.320057 GCAGAATGAACACTCAGACCAAAG 60.320 45.833 0.00 0.00 39.69 2.77
143 144 3.565482 GCAGAATGAACACTCAGACCAAA 59.435 43.478 0.00 0.00 39.69 3.28
144 145 3.141398 GCAGAATGAACACTCAGACCAA 58.859 45.455 0.00 0.00 39.69 3.67
145 146 2.771089 GCAGAATGAACACTCAGACCA 58.229 47.619 0.00 0.00 39.69 4.02
146 147 1.728971 CGCAGAATGAACACTCAGACC 59.271 52.381 0.00 0.00 39.69 3.85
147 148 2.156504 CACGCAGAATGAACACTCAGAC 59.843 50.000 0.00 0.00 39.69 3.51
148 149 2.224042 ACACGCAGAATGAACACTCAGA 60.224 45.455 0.00 0.00 39.69 3.27
149 150 2.138320 ACACGCAGAATGAACACTCAG 58.862 47.619 0.00 0.00 39.69 3.35
150 151 2.238942 ACACGCAGAATGAACACTCA 57.761 45.000 0.00 0.00 39.69 3.41
151 152 4.725556 TTTACACGCAGAATGAACACTC 57.274 40.909 0.00 0.00 39.69 3.51
152 153 4.754618 TCATTTACACGCAGAATGAACACT 59.245 37.500 0.00 0.00 39.69 3.55
153 154 5.029650 TCATTTACACGCAGAATGAACAC 57.970 39.130 0.00 0.00 39.69 3.32
154 155 5.163764 GGATCATTTACACGCAGAATGAACA 60.164 40.000 0.00 0.00 41.51 3.18
155 156 5.266242 GGATCATTTACACGCAGAATGAAC 58.734 41.667 0.00 5.94 41.51 3.18
156 157 4.335315 GGGATCATTTACACGCAGAATGAA 59.665 41.667 0.00 0.00 41.51 2.57
157 158 3.876914 GGGATCATTTACACGCAGAATGA 59.123 43.478 0.00 6.57 42.14 2.57
158 159 3.879295 AGGGATCATTTACACGCAGAATG 59.121 43.478 0.00 0.00 40.87 2.67
159 160 4.156455 AGGGATCATTTACACGCAGAAT 57.844 40.909 0.00 0.00 0.00 2.40
160 161 3.627395 AGGGATCATTTACACGCAGAA 57.373 42.857 0.00 0.00 0.00 3.02
161 162 3.270027 CAAGGGATCATTTACACGCAGA 58.730 45.455 0.00 0.00 0.00 4.26
162 163 3.009723 ACAAGGGATCATTTACACGCAG 58.990 45.455 0.00 0.00 0.00 5.18
163 164 2.746904 CACAAGGGATCATTTACACGCA 59.253 45.455 0.00 0.00 0.00 5.24
164 165 2.477863 GCACAAGGGATCATTTACACGC 60.478 50.000 0.00 0.00 0.00 5.34
165 166 2.097466 GGCACAAGGGATCATTTACACG 59.903 50.000 0.00 0.00 0.00 4.49
191 192 0.180406 AGAAAAGCAGGACACACCGT 59.820 50.000 0.00 0.00 44.74 4.83
248 249 1.484240 GTCCATGAGGCAGTTCTAGCT 59.516 52.381 0.00 0.00 33.74 3.32
306 307 3.063588 GCAGGTACAAGAACTAAATCCGC 59.936 47.826 0.00 0.00 0.00 5.54
312 313 3.181459 TGCAGTGCAGGTACAAGAACTAA 60.181 43.478 15.37 0.00 33.32 2.24
339 340 5.241506 TGCAGTTTCCAGTTTCCAAATAGAG 59.758 40.000 0.00 0.00 0.00 2.43
351 352 1.630369 TGCTCCTATGCAGTTTCCAGT 59.370 47.619 0.00 0.00 38.12 4.00
383 384 5.745227 TGTCAAATTTGATCTACTCCCCTC 58.255 41.667 23.05 7.05 39.73 4.30
436 437 1.646189 GTGGAAGATTGGCGAGAGTC 58.354 55.000 0.00 0.00 0.00 3.36
437 438 0.250513 GGTGGAAGATTGGCGAGAGT 59.749 55.000 0.00 0.00 0.00 3.24
469 470 4.189231 GCTGTATAGTGTAGTTGTTGGGG 58.811 47.826 0.00 0.00 0.00 4.96
506 507 3.482598 CGAGCGTAAACTTGATTGAGCAG 60.483 47.826 0.00 0.00 0.00 4.24
509 510 2.532973 CGCGAGCGTAAACTTGATTGAG 60.533 50.000 0.00 0.00 34.35 3.02
535 536 2.813172 TCTTCATGAAAATCTGCACGCA 59.187 40.909 9.88 0.00 0.00 5.24
545 546 8.614346 CCAAAAATGCTTCTTTCTTCATGAAAA 58.386 29.630 9.88 0.94 43.25 2.29
560 561 6.458615 GCAGAAACAACATTCCAAAAATGCTT 60.459 34.615 0.00 0.00 0.00 3.91
571 572 7.112426 GCAAATTTTCATGCAGAAACAACATTC 59.888 33.333 9.83 0.00 45.48 2.67
573 574 6.038382 TGCAAATTTTCATGCAGAAACAACAT 59.962 30.769 9.83 1.30 46.87 2.71
616 617 7.708051 TGAATTTCGTTAGGAACAAACATTGA 58.292 30.769 0.00 0.00 33.42 2.57
679 681 3.690139 AGCTCAAATGCACTCTCATGAAG 59.310 43.478 0.00 0.14 34.99 3.02
682 684 2.030579 CGAGCTCAAATGCACTCTCATG 59.969 50.000 15.40 0.00 34.99 3.07
718 720 5.012328 AGGGAGTACTTGATAAGCGAAAG 57.988 43.478 0.00 0.00 0.00 2.62
726 728 7.510675 AAAGAAATGGAGGGAGTACTTGATA 57.489 36.000 0.00 0.00 0.00 2.15
729 731 6.901081 AAAAAGAAATGGAGGGAGTACTTG 57.099 37.500 0.00 0.00 0.00 3.16
735 737 5.124617 GCAGACTAAAAAGAAATGGAGGGAG 59.875 44.000 0.00 0.00 0.00 4.30
737 739 4.766891 TGCAGACTAAAAAGAAATGGAGGG 59.233 41.667 0.00 0.00 0.00 4.30
738 740 5.964958 TGCAGACTAAAAAGAAATGGAGG 57.035 39.130 0.00 0.00 0.00 4.30
741 743 9.912634 TCTTATTTGCAGACTAAAAAGAAATGG 57.087 29.630 0.00 0.00 0.00 3.16
756 758 9.897744 TTGACTTTGACTAAATCTTATTTGCAG 57.102 29.630 0.00 0.00 0.00 4.41
908 910 7.824779 AGTTTGACGAGCTTTATAGGAAAAGAT 59.175 33.333 0.00 0.00 38.50 2.40
910 912 7.365840 AGTTTGACGAGCTTTATAGGAAAAG 57.634 36.000 0.00 0.00 39.10 2.27
982 984 5.148502 CACCATTGTAGGTACTCCCTCTAT 58.851 45.833 0.00 0.00 44.81 1.98
983 985 4.016851 ACACCATTGTAGGTACTCCCTCTA 60.017 45.833 0.00 0.00 44.81 2.43
985 987 3.105283 ACACCATTGTAGGTACTCCCTC 58.895 50.000 0.00 0.00 44.81 4.30
987 989 2.169978 GGACACCATTGTAGGTACTCCC 59.830 54.545 0.00 0.00 40.77 4.30
988 990 2.169978 GGGACACCATTGTAGGTACTCC 59.830 54.545 0.00 0.00 40.77 3.85
989 991 2.835764 TGGGACACCATTGTAGGTACTC 59.164 50.000 0.00 0.00 43.37 2.59
1040 1042 3.019003 TAGAGAACCAGCAGGCGGC 62.019 63.158 0.00 0.00 45.30 6.53
1053 1055 2.959372 CACGTGGTGGCGTAGAGA 59.041 61.111 7.95 0.00 43.83 3.10
1092 1094 1.148157 CGAGAGCCGTAACAGCCATG 61.148 60.000 0.00 0.00 0.00 3.66
1093 1095 1.141881 CGAGAGCCGTAACAGCCAT 59.858 57.895 0.00 0.00 0.00 4.40
1121 1123 3.151906 GCCCCAGACATAGGCGAT 58.848 61.111 0.00 0.00 36.84 4.58
1147 1149 2.281484 TTGGTGAGCAGCGAACCC 60.281 61.111 14.91 2.45 32.70 4.11
1153 1155 3.123620 CTCGCCTTGGTGAGCAGC 61.124 66.667 16.03 0.00 0.00 5.25
1220 1222 1.963855 GCACACCACACATACGGCA 60.964 57.895 0.00 0.00 0.00 5.69
1222 1224 1.351430 CGAGCACACCACACATACGG 61.351 60.000 0.00 0.00 0.00 4.02
1233 1235 1.005630 AAGAGGACAGCGAGCACAC 60.006 57.895 0.00 0.00 0.00 3.82
1234 1236 1.290324 GAAGAGGACAGCGAGCACA 59.710 57.895 0.00 0.00 0.00 4.57
1235 1237 1.803519 CGAAGAGGACAGCGAGCAC 60.804 63.158 0.00 0.00 0.00 4.40
1236 1238 2.201436 GACGAAGAGGACAGCGAGCA 62.201 60.000 0.00 0.00 0.00 4.26
1237 1239 1.515304 GACGAAGAGGACAGCGAGC 60.515 63.158 0.00 0.00 0.00 5.03
1238 1240 1.226156 CGACGAAGAGGACAGCGAG 60.226 63.158 0.00 0.00 0.00 5.03
1240 1242 2.202492 CCGACGAAGAGGACAGCG 60.202 66.667 0.00 0.00 0.00 5.18
1241 1243 3.275088 TCCGACGAAGAGGACAGC 58.725 61.111 0.00 0.00 33.74 4.40
1246 1248 1.519455 GCATGGTCCGACGAAGAGG 60.519 63.158 0.00 0.00 0.00 3.69
1248 1250 1.982395 AGGCATGGTCCGACGAAGA 60.982 57.895 0.00 0.00 0.00 2.87
1249 1251 1.811266 CAGGCATGGTCCGACGAAG 60.811 63.158 0.00 0.00 0.00 3.79
1250 1252 2.264480 CAGGCATGGTCCGACGAA 59.736 61.111 0.00 0.00 0.00 3.85
1251 1253 2.678580 TCAGGCATGGTCCGACGA 60.679 61.111 0.00 0.00 0.00 4.20
1252 1254 2.509336 GTCAGGCATGGTCCGACG 60.509 66.667 0.00 0.00 0.00 5.12
1280 1282 3.123620 GCAGAAGAGGCCAGCACG 61.124 66.667 5.01 0.00 0.00 5.34
1302 1304 0.677731 AATGACCATGTCAGGCACGG 60.678 55.000 3.11 0.00 46.04 4.94
1304 1306 1.098050 GGAATGACCATGTCAGGCAC 58.902 55.000 3.11 0.00 46.04 5.01
1307 1309 2.009774 GAACGGAATGACCATGTCAGG 58.990 52.381 3.11 0.00 46.04 3.86
1313 1315 2.677836 CGAACATGAACGGAATGACCAT 59.322 45.455 0.00 0.00 38.90 3.55
1376 1378 4.083862 GTCCTCCCAGACGCCCAC 62.084 72.222 0.00 0.00 0.00 4.61
1404 1406 4.016851 ACCTACACCTGTCCTACCTCAATA 60.017 45.833 0.00 0.00 0.00 1.90
1405 1407 3.246021 ACCTACACCTGTCCTACCTCAAT 60.246 47.826 0.00 0.00 0.00 2.57
1406 1408 2.111255 ACCTACACCTGTCCTACCTCAA 59.889 50.000 0.00 0.00 0.00 3.02
1419 1428 1.137479 TGTAGCGGCATAACCTACACC 59.863 52.381 1.45 0.00 37.21 4.16
1427 1436 3.132111 TCTTGACTGATGTAGCGGCATAA 59.868 43.478 1.45 0.00 0.00 1.90
1459 1468 4.025061 TGCCGCTGACAAATTTCAAAAATG 60.025 37.500 0.00 0.00 0.00 2.32
1461 1470 3.525537 TGCCGCTGACAAATTTCAAAAA 58.474 36.364 0.00 0.00 0.00 1.94
1491 1501 7.721286 TGAGAAGTTCAGAAAGATTTGACTC 57.279 36.000 5.50 0.00 0.00 3.36
1526 1536 3.511934 AGTAGTCGTCCTGCTTTCAGATT 59.488 43.478 0.00 0.00 42.95 2.40
1541 1551 8.803201 TTATTGATTGAAGCTATCAGTAGTCG 57.197 34.615 0.00 0.00 39.77 4.18
1550 1560 9.803507 TCAGATTGGATTATTGATTGAAGCTAT 57.196 29.630 0.00 0.00 0.00 2.97
1551 1561 9.631257 TTCAGATTGGATTATTGATTGAAGCTA 57.369 29.630 0.00 0.00 0.00 3.32
1552 1562 8.529424 TTCAGATTGGATTATTGATTGAAGCT 57.471 30.769 0.00 0.00 0.00 3.74
1574 1584 7.424227 AAAACTATATTTGTCGGTCGTTTCA 57.576 32.000 0.00 0.00 0.00 2.69
1619 1629 8.912614 TCTCCTTCTACCTATAACTTCCTTTT 57.087 34.615 0.00 0.00 0.00 2.27
1634 1644 8.085909 GGCATACTCTTCTAAATCTCCTTCTAC 58.914 40.741 0.00 0.00 0.00 2.59
1637 1647 6.042666 AGGGCATACTCTTCTAAATCTCCTTC 59.957 42.308 0.00 0.00 0.00 3.46
1638 1648 5.908247 AGGGCATACTCTTCTAAATCTCCTT 59.092 40.000 0.00 0.00 0.00 3.36
1640 1650 5.816955 AGGGCATACTCTTCTAAATCTCC 57.183 43.478 0.00 0.00 0.00 3.71
1641 1651 7.386573 GCTAAAGGGCATACTCTTCTAAATCTC 59.613 40.741 0.00 0.00 0.00 2.75
1642 1652 7.147479 TGCTAAAGGGCATACTCTTCTAAATCT 60.147 37.037 0.00 0.00 37.29 2.40
1643 1653 6.992715 TGCTAAAGGGCATACTCTTCTAAATC 59.007 38.462 0.00 0.00 37.29 2.17
1644 1654 6.900194 TGCTAAAGGGCATACTCTTCTAAAT 58.100 36.000 0.00 0.00 37.29 1.40
1645 1655 6.308015 TGCTAAAGGGCATACTCTTCTAAA 57.692 37.500 0.00 0.00 37.29 1.85
1646 1656 5.950544 TGCTAAAGGGCATACTCTTCTAA 57.049 39.130 0.00 0.00 37.29 2.10
1657 1667 3.594453 CCTTGGATGCTAAAGGGCA 57.406 52.632 0.00 0.00 46.63 5.36
1660 1670 3.635591 ACATTCCCTTGGATGCTAAAGG 58.364 45.455 0.00 0.00 42.29 3.11
1661 1671 5.192927 TGTACATTCCCTTGGATGCTAAAG 58.807 41.667 0.00 0.00 0.00 1.85
1662 1672 5.045213 TCTGTACATTCCCTTGGATGCTAAA 60.045 40.000 0.00 0.00 0.00 1.85
1694 1886 3.369997 GCCAGTTCTTTTCCTAGAGGGAG 60.370 52.174 0.00 0.00 46.01 4.30
1712 1904 4.824479 ATAAAATGGTTTTGGAGGCCAG 57.176 40.909 5.01 0.00 35.56 4.85
1724 1916 9.160412 AGGAGCTAGATGTAACTATAAAATGGT 57.840 33.333 0.00 0.00 0.00 3.55
1829 3866 5.300286 GGATTGACCACATTCCAAGGATTAG 59.700 44.000 0.00 0.00 42.62 1.73
1869 3907 8.251026 TCGCTGATTTCTTCAATCTAGTTTCTA 58.749 33.333 0.00 0.00 41.91 2.10
1876 3914 7.439356 CCTACATTCGCTGATTTCTTCAATCTA 59.561 37.037 0.00 0.00 41.91 1.98
1896 3934 5.648092 GGACATTGCAACTTAAGACCTACAT 59.352 40.000 10.09 0.00 0.00 2.29
1897 3935 5.001232 GGACATTGCAACTTAAGACCTACA 58.999 41.667 10.09 0.00 0.00 2.74
1912 3954 0.798776 CACGAAGTCCAGGACATTGC 59.201 55.000 22.31 6.65 41.61 3.56
1931 3973 2.552031 GGTGAAAGCTAAGGATCCGAC 58.448 52.381 5.98 0.00 0.00 4.79
1934 3976 1.134371 AGCGGTGAAAGCTAAGGATCC 60.134 52.381 2.48 2.48 44.05 3.36
1959 4001 1.089920 ATCTGATTGCAGGACGTTGC 58.910 50.000 5.26 5.26 42.53 4.17
1963 4005 5.998454 ATTTCTTATCTGATTGCAGGACG 57.002 39.130 0.00 0.00 42.53 4.79
2022 4064 1.996191 CACTTGGACTTCTTCTAGCGC 59.004 52.381 0.00 0.00 0.00 5.92
2073 4115 7.111247 TCCATATTTATTCAAGCTGTTTGGG 57.889 36.000 4.39 0.00 37.39 4.12
2074 4116 9.037737 CATTCCATATTTATTCAAGCTGTTTGG 57.962 33.333 4.39 0.00 37.39 3.28
2075 4117 9.806203 TCATTCCATATTTATTCAAGCTGTTTG 57.194 29.630 0.00 0.00 38.17 2.93
2121 4163 7.339482 AGATAAAGCCTCTTTCGGAGTATTTT 58.661 34.615 0.00 0.00 40.30 1.82
2174 4216 3.248602 GCAGGTTTCTTAGCATATGTCGG 59.751 47.826 4.29 0.00 0.00 4.79
2229 4272 7.821846 ACTCTCCAGTGATTTAATCAGAAAGAC 59.178 37.037 8.00 0.00 40.53 3.01
2230 4273 7.911651 ACTCTCCAGTGATTTAATCAGAAAGA 58.088 34.615 8.00 8.10 40.53 2.52
2235 4278 8.558973 AAAAGACTCTCCAGTGATTTAATCAG 57.441 34.615 8.00 0.00 40.53 2.90
2241 4284 8.601546 AGAAGATAAAAGACTCTCCAGTGATTT 58.398 33.333 0.00 0.00 30.63 2.17
2242 4285 8.144862 AGAAGATAAAAGACTCTCCAGTGATT 57.855 34.615 0.00 0.00 30.63 2.57
2357 4406 9.538508 GCAATATTTGGAAAGCTAGAAATGATT 57.461 29.630 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.