Multiple sequence alignment - TraesCS2D01G554900

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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 TraesCS2D01G554900 chr2D 100.000 4284 0 0 1 4284 629206074 629201791 0.000000e+00 7912.0
1 TraesCS2D01G554900 chr2A 95.235 2875 70 21 1250 4071 758924898 758922038 0.000000e+00 4488.0
2 TraesCS2D01G554900 chr2A 87.899 595 21 15 613 1179 758925728 758925157 0.000000e+00 652.0
3 TraesCS2D01G554900 chr2A 94.048 168 7 1 4115 4282 758922044 758921880 7.110000e-63 252.0
4 TraesCS2D01G554900 chr2A 86.986 146 19 0 165 310 758926759 758926614 9.530000e-37 165.0
5 TraesCS2D01G554900 chr2A 92.222 90 7 0 1177 1266 758925130 758925041 1.250000e-25 128.0
6 TraesCS2D01G554900 chr2B 92.763 3026 117 37 1249 4184 772050237 772053250 0.000000e+00 4281.0
7 TraesCS2D01G554900 chr2B 78.330 563 68 29 745 1260 772049512 772050067 8.940000e-82 315.0
8 TraesCS2D01G554900 chr2B 97.059 102 3 0 4181 4282 772053320 772053421 5.700000e-39 172.0
9 TraesCS2D01G554900 chr6A 93.697 587 14 3 3506 4071 527457292 527456708 0.000000e+00 857.0
10 TraesCS2D01G554900 chr6A 93.356 587 16 3 3506 4071 527380495 527379911 0.000000e+00 846.0
11 TraesCS2D01G554900 chr6A 94.083 169 6 2 4115 4282 527379917 527379752 1.980000e-63 254.0
12 TraesCS2D01G554900 chr6A 91.908 173 6 2 4115 4282 527456714 527456545 7.160000e-58 235.0
13 TraesCS2D01G554900 chr4A 88.927 289 27 4 3742 4026 398499597 398499310 6.820000e-93 351.0
14 TraesCS2D01G554900 chr4A 88.148 135 15 1 4148 4282 398491767 398491634 4.430000e-35 159.0
15 TraesCS2D01G554900 chr7B 78.226 124 16 7 432 552 686893203 686893318 7.690000e-08 69.4


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 TraesCS2D01G554900 chr2D 629201791 629206074 4283 True 7912.000000 7912 100.0000 1 4284 1 chr2D.!!$R1 4283
1 TraesCS2D01G554900 chr2A 758921880 758926759 4879 True 1137.000000 4488 91.2780 165 4282 5 chr2A.!!$R1 4117
2 TraesCS2D01G554900 chr2B 772049512 772053421 3909 False 1589.333333 4281 89.3840 745 4282 3 chr2B.!!$F1 3537
3 TraesCS2D01G554900 chr6A 527379752 527380495 743 True 550.000000 846 93.7195 3506 4282 2 chr6A.!!$R1 776
4 TraesCS2D01G554900 chr6A 527456545 527457292 747 True 546.000000 857 92.8025 3506 4282 2 chr6A.!!$R2 776

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
106 107 0.037697 CATGGTCGACGAGGGAAACA 60.038 55.0 9.92 0.00 0.00 2.83 F
443 444 0.242555 ACTAAAATTTGGGTGCGGCG 59.757 50.0 0.51 0.51 0.00 6.46 F
1214 1925 0.392595 CCCCCTTCTGCTCCGTTTAC 60.393 60.0 0.00 0.00 0.00 2.01 F
2863 3831 0.528017 TCATCTCTGTGGTCACGAGC 59.472 55.0 13.81 0.00 34.42 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1337 2240 0.887387 TTGGTAGCCAAACCGTGAGC 60.887 55.0 0.0 0.0 40.92 4.26 R
1915 2852 1.434622 CCATAGCACGCAGGCTTGAG 61.435 60.0 0.0 0.0 42.71 3.02 R
2903 3871 2.728013 ACTCTAGAGGGGGCCATATACA 59.272 50.0 23.5 0.0 0.00 2.29 R
4116 5166 0.039472 TGGCTATTGGGCAGCAGAAA 59.961 50.0 0.0 0.0 45.79 2.52 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
24 25 5.401531 AGCTTTTGACATCATTGCAATCT 57.598 34.783 9.53 0.00 0.00 2.40
25 26 5.790593 AGCTTTTGACATCATTGCAATCTT 58.209 33.333 9.53 0.00 0.00 2.40
26 27 6.228258 AGCTTTTGACATCATTGCAATCTTT 58.772 32.000 9.53 0.00 0.00 2.52
27 28 6.367969 AGCTTTTGACATCATTGCAATCTTTC 59.632 34.615 9.53 4.57 0.00 2.62
28 29 6.367969 GCTTTTGACATCATTGCAATCTTTCT 59.632 34.615 9.53 0.00 0.00 2.52
29 30 7.411588 GCTTTTGACATCATTGCAATCTTTCTC 60.412 37.037 9.53 1.66 0.00 2.87
30 31 6.578163 TTGACATCATTGCAATCTTTCTCA 57.422 33.333 9.53 4.28 0.00 3.27
31 32 6.578163 TGACATCATTGCAATCTTTCTCAA 57.422 33.333 9.53 0.00 0.00 3.02
32 33 6.617879 TGACATCATTGCAATCTTTCTCAAG 58.382 36.000 9.53 0.00 0.00 3.02
33 34 6.431852 TGACATCATTGCAATCTTTCTCAAGA 59.568 34.615 9.53 0.63 43.45 3.02
34 35 6.853720 ACATCATTGCAATCTTTCTCAAGAG 58.146 36.000 9.53 0.00 42.53 2.85
35 36 5.892160 TCATTGCAATCTTTCTCAAGAGG 57.108 39.130 9.53 0.00 42.53 3.69
36 37 5.563592 TCATTGCAATCTTTCTCAAGAGGA 58.436 37.500 9.53 0.00 42.53 3.71
37 38 5.413833 TCATTGCAATCTTTCTCAAGAGGAC 59.586 40.000 9.53 0.00 42.53 3.85
38 39 4.356405 TGCAATCTTTCTCAAGAGGACA 57.644 40.909 0.00 0.00 42.53 4.02
39 40 4.321718 TGCAATCTTTCTCAAGAGGACAG 58.678 43.478 0.00 0.00 42.53 3.51
40 41 4.040829 TGCAATCTTTCTCAAGAGGACAGA 59.959 41.667 0.00 0.00 42.53 3.41
41 42 4.391523 GCAATCTTTCTCAAGAGGACAGAC 59.608 45.833 0.00 0.00 42.53 3.51
42 43 4.817318 ATCTTTCTCAAGAGGACAGACC 57.183 45.455 0.00 0.00 42.53 3.85
43 44 3.576861 TCTTTCTCAAGAGGACAGACCA 58.423 45.455 0.00 0.00 42.04 4.02
44 45 4.163427 TCTTTCTCAAGAGGACAGACCAT 58.837 43.478 0.00 0.00 42.04 3.55
45 46 4.221703 TCTTTCTCAAGAGGACAGACCATC 59.778 45.833 0.00 0.00 42.04 3.51
46 47 3.175438 TCTCAAGAGGACAGACCATCA 57.825 47.619 0.00 0.00 42.04 3.07
47 48 3.095332 TCTCAAGAGGACAGACCATCAG 58.905 50.000 0.00 0.00 42.04 2.90
48 49 2.830923 CTCAAGAGGACAGACCATCAGT 59.169 50.000 0.00 0.00 42.04 3.41
49 50 4.019858 CTCAAGAGGACAGACCATCAGTA 58.980 47.826 0.00 0.00 42.04 2.74
50 51 4.614475 TCAAGAGGACAGACCATCAGTAT 58.386 43.478 0.00 0.00 42.04 2.12
51 52 4.403752 TCAAGAGGACAGACCATCAGTATG 59.596 45.833 0.00 0.00 43.59 2.39
52 53 4.256983 AGAGGACAGACCATCAGTATGA 57.743 45.455 0.00 0.00 40.27 2.15
53 54 4.614475 AGAGGACAGACCATCAGTATGAA 58.386 43.478 0.00 0.00 42.69 2.57
54 55 5.215069 AGAGGACAGACCATCAGTATGAAT 58.785 41.667 0.00 0.00 42.69 2.57
55 56 5.304101 AGAGGACAGACCATCAGTATGAATC 59.696 44.000 0.00 0.00 42.69 2.52
56 57 5.215069 AGGACAGACCATCAGTATGAATCT 58.785 41.667 0.00 0.00 42.69 2.40
57 58 5.664908 AGGACAGACCATCAGTATGAATCTT 59.335 40.000 0.00 0.00 42.69 2.40
58 59 6.841229 AGGACAGACCATCAGTATGAATCTTA 59.159 38.462 0.00 0.00 42.69 2.10
59 60 7.512058 AGGACAGACCATCAGTATGAATCTTAT 59.488 37.037 0.00 0.00 42.69 1.73
86 87 9.935241 ATGTTTATCGCATAGAAGATTCATAGT 57.065 29.630 0.00 0.00 0.00 2.12
87 88 9.411801 TGTTTATCGCATAGAAGATTCATAGTC 57.588 33.333 0.00 0.00 0.00 2.59
88 89 9.411801 GTTTATCGCATAGAAGATTCATAGTCA 57.588 33.333 0.00 0.00 0.00 3.41
90 91 9.578439 TTATCGCATAGAAGATTCATAGTCATG 57.422 33.333 0.00 0.00 0.00 3.07
91 92 6.393171 TCGCATAGAAGATTCATAGTCATGG 58.607 40.000 0.00 0.00 32.61 3.66
92 93 6.015095 TCGCATAGAAGATTCATAGTCATGGT 60.015 38.462 0.00 0.00 32.61 3.55
93 94 6.309980 CGCATAGAAGATTCATAGTCATGGTC 59.690 42.308 0.00 0.00 32.61 4.02
94 95 6.309980 GCATAGAAGATTCATAGTCATGGTCG 59.690 42.308 0.00 0.00 32.61 4.79
95 96 7.597386 CATAGAAGATTCATAGTCATGGTCGA 58.403 38.462 0.00 0.00 32.61 4.20
96 97 5.837437 AGAAGATTCATAGTCATGGTCGAC 58.163 41.667 7.13 7.13 36.08 4.20
97 98 4.230314 AGATTCATAGTCATGGTCGACG 57.770 45.455 9.92 0.00 40.98 5.12
98 99 3.883489 AGATTCATAGTCATGGTCGACGA 59.117 43.478 9.92 5.99 40.98 4.20
99 100 3.692791 TTCATAGTCATGGTCGACGAG 57.307 47.619 9.92 1.67 40.98 4.18
100 101 1.947456 TCATAGTCATGGTCGACGAGG 59.053 52.381 9.92 7.81 40.98 4.63
101 102 1.001268 CATAGTCATGGTCGACGAGGG 60.001 57.143 12.26 4.20 40.98 4.30
102 103 0.253894 TAGTCATGGTCGACGAGGGA 59.746 55.000 12.26 6.51 40.98 4.20
103 104 0.611062 AGTCATGGTCGACGAGGGAA 60.611 55.000 12.26 0.00 40.98 3.97
104 105 0.245539 GTCATGGTCGACGAGGGAAA 59.754 55.000 12.26 0.00 0.00 3.13
105 106 0.245539 TCATGGTCGACGAGGGAAAC 59.754 55.000 12.26 0.00 0.00 2.78
106 107 0.037697 CATGGTCGACGAGGGAAACA 60.038 55.000 9.92 0.00 0.00 2.83
107 108 0.902531 ATGGTCGACGAGGGAAACAT 59.097 50.000 9.92 1.61 0.00 2.71
108 109 0.682852 TGGTCGACGAGGGAAACATT 59.317 50.000 9.92 0.00 0.00 2.71
109 110 1.337447 TGGTCGACGAGGGAAACATTC 60.337 52.381 9.92 0.00 0.00 2.67
110 111 1.337447 GGTCGACGAGGGAAACATTCA 60.337 52.381 9.92 0.00 0.00 2.57
111 112 1.725164 GTCGACGAGGGAAACATTCAC 59.275 52.381 0.00 0.00 0.00 3.18
112 113 1.341852 TCGACGAGGGAAACATTCACA 59.658 47.619 0.00 0.00 34.83 3.58
113 114 2.028476 TCGACGAGGGAAACATTCACAT 60.028 45.455 0.00 0.00 34.83 3.21
114 115 2.348666 CGACGAGGGAAACATTCACATC 59.651 50.000 0.00 0.00 34.83 3.06
115 116 3.334691 GACGAGGGAAACATTCACATCA 58.665 45.455 0.00 0.00 34.83 3.07
116 117 3.338249 ACGAGGGAAACATTCACATCAG 58.662 45.455 0.00 0.00 34.83 2.90
117 118 3.244561 ACGAGGGAAACATTCACATCAGT 60.245 43.478 0.00 0.00 34.83 3.41
118 119 4.020573 ACGAGGGAAACATTCACATCAGTA 60.021 41.667 0.00 0.00 34.83 2.74
119 120 5.118990 CGAGGGAAACATTCACATCAGTAT 58.881 41.667 0.00 0.00 34.83 2.12
120 121 5.586243 CGAGGGAAACATTCACATCAGTATT 59.414 40.000 0.00 0.00 34.83 1.89
121 122 6.457392 CGAGGGAAACATTCACATCAGTATTG 60.457 42.308 0.00 0.00 34.83 1.90
122 123 6.248433 AGGGAAACATTCACATCAGTATTGT 58.752 36.000 0.00 0.00 34.83 2.71
123 124 6.721208 AGGGAAACATTCACATCAGTATTGTT 59.279 34.615 0.00 0.00 34.83 2.83
124 125 7.233348 AGGGAAACATTCACATCAGTATTGTTT 59.767 33.333 0.00 0.00 36.65 2.83
125 126 7.872483 GGGAAACATTCACATCAGTATTGTTTT 59.128 33.333 0.00 0.00 35.35 2.43
126 127 9.260002 GGAAACATTCACATCAGTATTGTTTTT 57.740 29.630 0.00 0.00 35.35 1.94
147 148 9.993881 GTTTTTCTTTTGAATCATAATGTGTCG 57.006 29.630 0.00 0.00 38.37 4.35
148 149 9.958234 TTTTTCTTTTGAATCATAATGTGTCGA 57.042 25.926 0.00 0.00 38.37 4.20
157 158 9.423061 TGAATCATAATGTGTCGATATAACTGG 57.577 33.333 0.00 0.00 0.00 4.00
158 159 9.639601 GAATCATAATGTGTCGATATAACTGGA 57.360 33.333 0.00 0.00 0.00 3.86
160 161 8.986477 TCATAATGTGTCGATATAACTGGATG 57.014 34.615 0.00 0.00 0.00 3.51
161 162 8.802267 TCATAATGTGTCGATATAACTGGATGA 58.198 33.333 0.00 0.00 0.00 2.92
162 163 9.423061 CATAATGTGTCGATATAACTGGATGAA 57.577 33.333 0.00 0.00 0.00 2.57
163 164 7.953158 AATGTGTCGATATAACTGGATGAAG 57.047 36.000 0.00 0.00 0.00 3.02
202 203 6.438259 TGTCACTGTAGTAAGAGTATCAGC 57.562 41.667 0.00 0.00 37.82 4.26
219 220 4.744136 TCAGCATATACTAACGAGACGG 57.256 45.455 0.00 0.00 0.00 4.79
237 238 2.254459 CGGACTTGACACTCGATGAAG 58.746 52.381 0.00 0.00 0.00 3.02
239 240 3.611766 CGGACTTGACACTCGATGAAGAA 60.612 47.826 0.00 0.00 0.00 2.52
242 243 5.139435 ACTTGACACTCGATGAAGAATCA 57.861 39.130 0.00 0.00 40.57 2.57
281 282 7.175347 TGCAATCTAGTGTCAAGTTATCTCT 57.825 36.000 0.00 0.00 0.00 3.10
285 286 8.802856 CAATCTAGTGTCAAGTTATCTCTTTCG 58.197 37.037 0.00 0.00 0.00 3.46
287 288 4.883083 AGTGTCAAGTTATCTCTTTCGCA 58.117 39.130 0.00 0.00 0.00 5.10
290 291 4.686091 TGTCAAGTTATCTCTTTCGCACAG 59.314 41.667 0.00 0.00 0.00 3.66
291 292 3.679980 TCAAGTTATCTCTTTCGCACAGC 59.320 43.478 0.00 0.00 0.00 4.40
305 306 3.687572 GCACAGCGAGAATTGATTGAT 57.312 42.857 0.00 0.00 0.00 2.57
306 307 3.615614 GCACAGCGAGAATTGATTGATC 58.384 45.455 0.00 0.00 0.00 2.92
307 308 3.311871 GCACAGCGAGAATTGATTGATCT 59.688 43.478 0.00 0.00 0.00 2.75
308 309 4.509230 GCACAGCGAGAATTGATTGATCTA 59.491 41.667 0.00 0.00 0.00 1.98
309 310 5.178996 GCACAGCGAGAATTGATTGATCTAT 59.821 40.000 0.00 0.00 0.00 1.98
310 311 6.367149 GCACAGCGAGAATTGATTGATCTATA 59.633 38.462 0.00 0.00 0.00 1.31
311 312 7.064371 GCACAGCGAGAATTGATTGATCTATAT 59.936 37.037 0.00 0.00 0.00 0.86
312 313 9.578439 CACAGCGAGAATTGATTGATCTATATA 57.422 33.333 0.00 0.00 0.00 0.86
353 354 7.489113 GGAATTAATTGACCTATGCAACAACAG 59.511 37.037 5.17 0.00 0.00 3.16
355 356 7.517614 TTAATTGACCTATGCAACAACAGAA 57.482 32.000 0.00 0.00 0.00 3.02
362 363 5.163416 ACCTATGCAACAACAGAAAAGCTTT 60.163 36.000 5.69 5.69 0.00 3.51
365 366 2.030823 GCAACAACAGAAAAGCTTTGCC 59.969 45.455 13.54 8.06 32.86 4.52
439 440 3.243602 ACGTGGAACTAAAATTTGGGTGC 60.244 43.478 0.00 0.00 31.75 5.01
443 444 0.242555 ACTAAAATTTGGGTGCGGCG 59.757 50.000 0.51 0.51 0.00 6.46
452 453 2.279120 GGTGCGGCGATGAGAGAG 60.279 66.667 12.98 0.00 0.00 3.20
464 465 3.730215 CGATGAGAGAGAAATGAGCTTCG 59.270 47.826 0.00 0.00 0.00 3.79
470 471 1.021390 AGAAATGAGCTTCGGTGGCG 61.021 55.000 0.00 0.00 34.52 5.69
491 492 4.139234 GGTGGGACCGCTACGACC 62.139 72.222 1.50 0.00 0.00 4.79
493 494 3.066190 TGGGACCGCTACGACCTG 61.066 66.667 0.00 0.00 0.00 4.00
494 495 4.509737 GGGACCGCTACGACCTGC 62.510 72.222 0.00 0.00 0.00 4.85
495 496 3.755628 GGACCGCTACGACCTGCA 61.756 66.667 0.00 0.00 0.00 4.41
496 497 2.202623 GACCGCTACGACCTGCAG 60.203 66.667 6.78 6.78 0.00 4.41
497 498 4.436998 ACCGCTACGACCTGCAGC 62.437 66.667 8.66 0.00 0.00 5.25
500 501 3.775654 GCTACGACCTGCAGCCCT 61.776 66.667 8.66 0.00 0.00 5.19
501 502 2.185350 CTACGACCTGCAGCCCTG 59.815 66.667 8.66 0.00 0.00 4.45
519 520 4.778415 CAGTGAGGTCGGCGGACG 62.778 72.222 17.09 0.00 44.39 4.79
542 543 1.607251 CCCGAACGCCTTATATCCACC 60.607 57.143 0.00 0.00 0.00 4.61
547 548 4.082408 CGAACGCCTTATATCCACCTCATA 60.082 45.833 0.00 0.00 0.00 2.15
553 554 5.888161 GCCTTATATCCACCTCATATTTGGG 59.112 44.000 0.00 0.00 0.00 4.12
555 556 6.461577 TTATATCCACCTCATATTTGGGCA 57.538 37.500 0.00 0.00 0.00 5.36
557 558 2.204463 TCCACCTCATATTTGGGCAGA 58.796 47.619 0.00 0.00 0.00 4.26
561 562 4.520492 CCACCTCATATTTGGGCAGAATAC 59.480 45.833 0.00 0.00 0.00 1.89
562 563 5.132502 CACCTCATATTTGGGCAGAATACA 58.867 41.667 0.00 0.00 0.00 2.29
567 568 6.064060 TCATATTTGGGCAGAATACAAGAGG 58.936 40.000 0.00 0.00 0.00 3.69
568 569 3.806949 TTTGGGCAGAATACAAGAGGT 57.193 42.857 0.00 0.00 0.00 3.85
571 572 1.065126 GGGCAGAATACAAGAGGTGCT 60.065 52.381 0.00 0.00 0.00 4.40
573 574 2.012673 GCAGAATACAAGAGGTGCTGG 58.987 52.381 0.00 0.00 0.00 4.85
575 576 3.679389 CAGAATACAAGAGGTGCTGGTT 58.321 45.455 0.00 0.00 31.63 3.67
577 578 4.074970 AGAATACAAGAGGTGCTGGTTTG 58.925 43.478 0.00 0.00 31.63 2.93
578 579 3.788227 ATACAAGAGGTGCTGGTTTGA 57.212 42.857 0.00 0.00 31.63 2.69
579 580 1.680338 ACAAGAGGTGCTGGTTTGAC 58.320 50.000 0.00 0.00 0.00 3.18
580 581 0.954452 CAAGAGGTGCTGGTTTGACC 59.046 55.000 0.00 0.00 39.22 4.02
581 582 0.535102 AAGAGGTGCTGGTTTGACCG 60.535 55.000 0.00 0.00 42.58 4.79
584 585 2.112297 GTGCTGGTTTGACCGGGA 59.888 61.111 6.32 2.05 44.90 5.14
585 586 1.966451 GTGCTGGTTTGACCGGGAG 60.966 63.158 6.32 0.00 46.04 4.30
588 589 0.822121 GCTGGTTTGACCGGGAGTTT 60.822 55.000 6.32 0.00 44.90 2.66
591 592 1.072648 TGGTTTGACCGGGAGTTTAGG 59.927 52.381 6.32 0.00 42.58 2.69
599 600 1.303091 CGGGAGTTTAGGCGGGTTTG 61.303 60.000 0.00 0.00 0.00 2.93
601 602 0.963856 GGAGTTTAGGCGGGTTTGGG 60.964 60.000 0.00 0.00 0.00 4.12
602 603 0.963856 GAGTTTAGGCGGGTTTGGGG 60.964 60.000 0.00 0.00 0.00 4.96
604 605 4.726304 TTAGGCGGGTTTGGGGCG 62.726 66.667 0.00 0.00 0.00 6.13
659 1287 1.347707 TCAGACTGAAACCAGCCGAAT 59.652 47.619 1.64 0.00 35.09 3.34
660 1288 2.154462 CAGACTGAAACCAGCCGAATT 58.846 47.619 0.00 0.00 35.09 2.17
661 1289 2.554032 CAGACTGAAACCAGCCGAATTT 59.446 45.455 0.00 0.00 35.09 1.82
662 1290 2.814336 AGACTGAAACCAGCCGAATTTC 59.186 45.455 0.00 0.00 35.09 2.17
663 1291 2.814336 GACTGAAACCAGCCGAATTTCT 59.186 45.455 0.00 0.00 35.09 2.52
664 1292 3.222603 ACTGAAACCAGCCGAATTTCTT 58.777 40.909 0.00 0.00 35.09 2.52
676 1304 6.018669 CAGCCGAATTTCTTTCCTAGTCATAC 60.019 42.308 0.00 0.00 0.00 2.39
720 1348 4.143333 CCGCACCACCTAGACCGG 62.143 72.222 0.00 0.00 0.00 5.28
741 1369 1.658673 GACTTGTCGTCGTCCACCT 59.341 57.895 0.00 0.00 32.04 4.00
872 1520 2.956964 CGCTGGCGACGGAGATTC 60.957 66.667 0.00 0.00 42.83 2.52
937 1586 1.743252 GCTTCAGCCGAGTTCCCAG 60.743 63.158 0.00 0.00 34.31 4.45
940 1589 4.785453 CAGCCGAGTTCCCAGCCC 62.785 72.222 0.00 0.00 0.00 5.19
1161 1836 2.645394 CTATCCCCCGTCCCCGTGTA 62.645 65.000 0.00 0.00 0.00 2.90
1203 1914 4.109656 ATCTCCCGGCCCCCTTCT 62.110 66.667 0.00 0.00 0.00 2.85
1214 1925 0.392595 CCCCCTTCTGCTCCGTTTAC 60.393 60.000 0.00 0.00 0.00 2.01
1215 1926 0.613777 CCCCTTCTGCTCCGTTTACT 59.386 55.000 0.00 0.00 0.00 2.24
1267 1981 0.959372 ATGAGCAGAGCAGCACAACC 60.959 55.000 0.00 0.00 38.54 3.77
1268 1982 2.282040 AGCAGAGCAGCACAACCC 60.282 61.111 0.00 0.00 36.85 4.11
1330 2233 4.261801 TGCTGTAATTCTTTCCCTGCTAC 58.738 43.478 0.00 0.00 0.00 3.58
1337 2240 8.429641 TGTAATTCTTTCCCTGCTACTATTAGG 58.570 37.037 0.00 0.00 0.00 2.69
1393 2296 1.247567 CAGAATCGGGCTTTGGTGTT 58.752 50.000 0.00 0.00 0.00 3.32
1432 2345 3.021695 TCGCACTAGGCTGTATGTAACT 58.978 45.455 0.00 0.00 41.67 2.24
1445 2358 6.032956 TGTATGTAACTAAGGTCACCACTG 57.967 41.667 0.00 0.00 0.00 3.66
1464 2377 5.385617 CACTGCAAGATACTTACTGCAAAC 58.614 41.667 0.00 0.00 37.43 2.93
1486 2400 9.185192 CAAACTCAATGTAGACAGGAAATTTTC 57.815 33.333 0.24 0.24 0.00 2.29
1492 2406 5.492895 TGTAGACAGGAAATTTTCGGCATA 58.507 37.500 3.17 0.00 0.00 3.14
1574 2492 3.393278 AGGTTGCTACAAAGGGAGTAACA 59.607 43.478 9.56 0.00 39.29 2.41
1700 2627 2.072298 CAAGTGCACTAGTCTCTTGCC 58.928 52.381 22.01 0.00 35.26 4.52
1815 2742 9.549078 TCAAATTATTGTGCGTATGGATTACTA 57.451 29.630 0.00 0.00 37.79 1.82
1915 2852 4.201920 GGACAAACAACAACTCAGAACTCC 60.202 45.833 0.00 0.00 0.00 3.85
2032 2989 2.037902 ACAATGTGTCACGTCCATACCA 59.962 45.455 0.00 0.00 0.00 3.25
2110 3067 7.180408 AGTTATTCACCTGTCTATAAGTGTGGT 59.820 37.037 0.00 0.00 0.00 4.16
2225 3182 1.272781 GATTGTGCTCGTCCTCTTCG 58.727 55.000 0.00 0.00 0.00 3.79
2239 3196 3.192844 TCCTCTTCGTGCTCTTCGTTATT 59.807 43.478 0.00 0.00 0.00 1.40
2251 3208 8.160976 GTGCTCTTCGTTATTTGTAAGTTCTAC 58.839 37.037 0.00 0.00 0.00 2.59
2374 3340 2.359531 TGTTTCCTTTTCGCCGTTTCAT 59.640 40.909 0.00 0.00 0.00 2.57
2705 3671 8.472413 AGTTGGATAAATTTGACCAGAATGATG 58.528 33.333 14.56 0.00 39.69 3.07
2863 3831 0.528017 TCATCTCTGTGGTCACGAGC 59.472 55.000 13.81 0.00 34.42 5.03
2961 3929 6.998074 TCATCATATGGTCAAATGGGTTCTAC 59.002 38.462 2.13 0.00 0.00 2.59
3351 4319 5.739161 GTCGTTGTTTCATCCTTTCATATGC 59.261 40.000 0.00 0.00 0.00 3.14
3369 4337 0.811616 GCAGACCCGCTCTTGTATGG 60.812 60.000 0.00 0.00 0.00 2.74
3480 4449 8.669946 TTATCAAATGCACAGATTCGGTATTA 57.330 30.769 0.00 0.00 0.00 0.98
3645 4617 3.754965 TCTTTCAAGATTGGTGGTGGAG 58.245 45.455 0.00 0.00 0.00 3.86
3684 4656 3.879912 CTGTTTTGCCAGCCTTCAG 57.120 52.632 0.00 0.00 0.00 3.02
3843 4838 6.618287 TGAAGGTTTCATTGTGTGAGTTAG 57.382 37.500 0.00 0.00 38.29 2.34
3934 4929 5.141182 TGGAAGATGGAGCTAGTTAGTAGG 58.859 45.833 0.00 0.00 0.00 3.18
4071 5121 0.256752 ACATGCAGGCTCCATTGCTA 59.743 50.000 0.00 0.00 40.87 3.49
4072 5122 1.341285 ACATGCAGGCTCCATTGCTAA 60.341 47.619 0.00 0.00 40.87 3.09
4073 5123 1.961394 CATGCAGGCTCCATTGCTAAT 59.039 47.619 0.00 0.00 40.87 1.73
4074 5124 3.151554 CATGCAGGCTCCATTGCTAATA 58.848 45.455 0.00 0.00 40.87 0.98
4075 5125 3.513909 TGCAGGCTCCATTGCTAATAT 57.486 42.857 2.51 0.00 40.87 1.28
4076 5126 3.151554 TGCAGGCTCCATTGCTAATATG 58.848 45.455 2.51 0.00 40.87 1.78
4077 5127 3.152341 GCAGGCTCCATTGCTAATATGT 58.848 45.455 0.00 0.00 37.35 2.29
4078 5128 4.202451 TGCAGGCTCCATTGCTAATATGTA 60.202 41.667 2.51 0.00 40.87 2.29
4079 5129 4.154918 GCAGGCTCCATTGCTAATATGTAC 59.845 45.833 0.00 0.00 37.35 2.90
4080 5130 5.308014 CAGGCTCCATTGCTAATATGTACA 58.692 41.667 0.00 0.00 0.00 2.90
4081 5131 5.942236 CAGGCTCCATTGCTAATATGTACAT 59.058 40.000 13.93 13.93 0.00 2.29
4082 5132 6.432162 CAGGCTCCATTGCTAATATGTACATT 59.568 38.462 14.77 0.00 0.00 2.71
4083 5133 7.006509 AGGCTCCATTGCTAATATGTACATTT 58.993 34.615 14.77 10.48 0.00 2.32
4084 5134 7.175641 AGGCTCCATTGCTAATATGTACATTTC 59.824 37.037 14.77 0.16 0.00 2.17
4085 5135 7.040478 GGCTCCATTGCTAATATGTACATTTCA 60.040 37.037 14.77 0.00 0.00 2.69
4086 5136 7.805071 GCTCCATTGCTAATATGTACATTTCAC 59.195 37.037 14.77 1.43 0.00 3.18
4087 5137 8.165239 TCCATTGCTAATATGTACATTTCACC 57.835 34.615 14.77 1.45 0.00 4.02
4088 5138 7.777440 TCCATTGCTAATATGTACATTTCACCA 59.223 33.333 14.77 4.08 0.00 4.17
4089 5139 8.412456 CCATTGCTAATATGTACATTTCACCAA 58.588 33.333 14.77 12.35 0.00 3.67
4090 5140 9.970395 CATTGCTAATATGTACATTTCACCAAT 57.030 29.630 14.77 13.88 0.00 3.16
4092 5142 9.800433 TTGCTAATATGTACATTTCACCAATTG 57.200 29.630 14.77 0.00 0.00 2.32
4093 5143 9.183368 TGCTAATATGTACATTTCACCAATTGA 57.817 29.630 14.77 0.00 0.00 2.57
4094 5144 9.669353 GCTAATATGTACATTTCACCAATTGAG 57.331 33.333 14.77 0.00 34.94 3.02
4096 5146 5.920193 ATGTACATTTCACCAATTGAGGG 57.080 39.130 7.12 0.00 34.94 4.30
4097 5147 4.991776 TGTACATTTCACCAATTGAGGGA 58.008 39.130 7.12 0.51 34.94 4.20
4098 5148 5.389520 TGTACATTTCACCAATTGAGGGAA 58.610 37.500 7.12 7.24 34.94 3.97
4099 5149 5.476599 TGTACATTTCACCAATTGAGGGAAG 59.523 40.000 7.12 2.44 34.94 3.46
4100 5150 3.834231 ACATTTCACCAATTGAGGGAAGG 59.166 43.478 7.12 3.87 34.94 3.46
4101 5151 3.893753 TTTCACCAATTGAGGGAAGGA 57.106 42.857 7.12 0.00 34.94 3.36
4102 5152 4.402616 TTTCACCAATTGAGGGAAGGAT 57.597 40.909 7.12 0.00 34.94 3.24
4103 5153 3.370840 TCACCAATTGAGGGAAGGATG 57.629 47.619 7.12 0.00 0.00 3.51
4104 5154 2.649312 TCACCAATTGAGGGAAGGATGT 59.351 45.455 7.12 0.00 0.00 3.06
4105 5155 3.075882 TCACCAATTGAGGGAAGGATGTT 59.924 43.478 7.12 0.00 0.00 2.71
4106 5156 3.834231 CACCAATTGAGGGAAGGATGTTT 59.166 43.478 7.12 0.00 0.00 2.83
4107 5157 3.834231 ACCAATTGAGGGAAGGATGTTTG 59.166 43.478 7.12 0.00 0.00 2.93
4108 5158 4.088634 CCAATTGAGGGAAGGATGTTTGA 58.911 43.478 7.12 0.00 0.00 2.69
4109 5159 4.713321 CCAATTGAGGGAAGGATGTTTGAT 59.287 41.667 7.12 0.00 0.00 2.57
4110 5160 5.188359 CCAATTGAGGGAAGGATGTTTGATT 59.812 40.000 7.12 0.00 0.00 2.57
4111 5161 6.335777 CAATTGAGGGAAGGATGTTTGATTC 58.664 40.000 0.00 0.00 0.00 2.52
4112 5162 4.934797 TGAGGGAAGGATGTTTGATTCT 57.065 40.909 0.00 0.00 0.00 2.40
4113 5163 4.592942 TGAGGGAAGGATGTTTGATTCTG 58.407 43.478 0.00 0.00 0.00 3.02
4114 5164 3.359950 AGGGAAGGATGTTTGATTCTGC 58.640 45.455 0.00 0.00 0.00 4.26
4115 5165 3.091545 GGGAAGGATGTTTGATTCTGCA 58.908 45.455 0.00 0.00 0.00 4.41
4116 5166 3.703052 GGGAAGGATGTTTGATTCTGCAT 59.297 43.478 0.00 0.00 0.00 3.96
4117 5167 4.161001 GGGAAGGATGTTTGATTCTGCATT 59.839 41.667 0.00 0.00 0.00 3.56
4118 5168 5.337813 GGGAAGGATGTTTGATTCTGCATTT 60.338 40.000 0.00 0.00 0.00 2.32
4119 5169 5.809051 GGAAGGATGTTTGATTCTGCATTTC 59.191 40.000 0.00 0.00 0.00 2.17
4120 5170 6.350780 GGAAGGATGTTTGATTCTGCATTTCT 60.351 38.462 0.00 0.00 0.00 2.52
4137 5187 0.680921 TCTGCTGCCCAATAGCCAAC 60.681 55.000 0.00 0.00 40.42 3.77
4179 5229 5.447818 GCTGGTGATGTAAAATAGCAGTGAC 60.448 44.000 0.00 0.00 39.94 3.67
4282 5410 3.996614 GGTGGATGTTTCACCGGG 58.003 61.111 6.32 0.00 44.16 5.73
4283 5411 1.677633 GGTGGATGTTTCACCGGGG 60.678 63.158 6.32 0.00 44.16 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.927416 AGATTGCAATGATGTCAAAAGCTTA 58.073 32.000 18.59 0.00 0.00 3.09
1 2 5.790593 AGATTGCAATGATGTCAAAAGCTT 58.209 33.333 18.59 0.00 0.00 3.74
2 3 5.401531 AGATTGCAATGATGTCAAAAGCT 57.598 34.783 18.59 0.00 0.00 3.74
3 4 6.367969 AGAAAGATTGCAATGATGTCAAAAGC 59.632 34.615 18.59 0.00 0.00 3.51
4 5 7.597369 TGAGAAAGATTGCAATGATGTCAAAAG 59.403 33.333 18.59 0.00 0.00 2.27
5 6 7.435305 TGAGAAAGATTGCAATGATGTCAAAA 58.565 30.769 18.59 0.00 0.00 2.44
6 7 6.983984 TGAGAAAGATTGCAATGATGTCAAA 58.016 32.000 18.59 0.00 0.00 2.69
7 8 6.578163 TGAGAAAGATTGCAATGATGTCAA 57.422 33.333 18.59 0.34 0.00 3.18
8 9 6.431852 TCTTGAGAAAGATTGCAATGATGTCA 59.568 34.615 18.59 13.10 0.00 3.58
9 10 6.849502 TCTTGAGAAAGATTGCAATGATGTC 58.150 36.000 18.59 9.81 0.00 3.06
10 11 6.127703 CCTCTTGAGAAAGATTGCAATGATGT 60.128 38.462 18.59 0.00 0.00 3.06
11 12 6.095021 TCCTCTTGAGAAAGATTGCAATGATG 59.905 38.462 18.59 1.93 0.00 3.07
12 13 6.095160 GTCCTCTTGAGAAAGATTGCAATGAT 59.905 38.462 18.59 1.84 0.00 2.45
13 14 5.413833 GTCCTCTTGAGAAAGATTGCAATGA 59.586 40.000 18.59 3.40 0.00 2.57
14 15 5.182570 TGTCCTCTTGAGAAAGATTGCAATG 59.817 40.000 18.59 0.00 0.00 2.82
15 16 5.319453 TGTCCTCTTGAGAAAGATTGCAAT 58.681 37.500 12.83 12.83 0.00 3.56
16 17 4.717877 TGTCCTCTTGAGAAAGATTGCAA 58.282 39.130 0.00 0.00 0.00 4.08
17 18 4.040829 TCTGTCCTCTTGAGAAAGATTGCA 59.959 41.667 0.00 0.00 0.00 4.08
18 19 4.391523 GTCTGTCCTCTTGAGAAAGATTGC 59.608 45.833 0.00 0.00 0.00 3.56
19 20 4.934602 GGTCTGTCCTCTTGAGAAAGATTG 59.065 45.833 0.00 0.00 0.00 2.67
20 21 4.594920 TGGTCTGTCCTCTTGAGAAAGATT 59.405 41.667 0.00 0.00 37.07 2.40
21 22 4.163427 TGGTCTGTCCTCTTGAGAAAGAT 58.837 43.478 0.00 0.00 37.07 2.40
22 23 3.576861 TGGTCTGTCCTCTTGAGAAAGA 58.423 45.455 0.00 0.00 37.07 2.52
23 24 4.020751 TGATGGTCTGTCCTCTTGAGAAAG 60.021 45.833 0.00 0.00 37.07 2.62
24 25 3.903714 TGATGGTCTGTCCTCTTGAGAAA 59.096 43.478 0.00 0.00 37.07 2.52
25 26 3.510459 TGATGGTCTGTCCTCTTGAGAA 58.490 45.455 0.00 0.00 37.07 2.87
26 27 3.095332 CTGATGGTCTGTCCTCTTGAGA 58.905 50.000 0.00 0.00 37.07 3.27
27 28 2.830923 ACTGATGGTCTGTCCTCTTGAG 59.169 50.000 0.00 0.00 37.07 3.02
28 29 2.894731 ACTGATGGTCTGTCCTCTTGA 58.105 47.619 0.00 0.00 37.07 3.02
29 30 4.403752 TCATACTGATGGTCTGTCCTCTTG 59.596 45.833 0.00 0.00 37.07 3.02
30 31 4.614475 TCATACTGATGGTCTGTCCTCTT 58.386 43.478 0.00 0.00 37.07 2.85
31 32 4.256983 TCATACTGATGGTCTGTCCTCT 57.743 45.455 0.00 0.00 37.07 3.69
32 33 5.304101 AGATTCATACTGATGGTCTGTCCTC 59.696 44.000 0.00 0.00 37.07 3.71
33 34 5.215069 AGATTCATACTGATGGTCTGTCCT 58.785 41.667 0.00 0.00 37.07 3.85
34 35 5.543507 AGATTCATACTGATGGTCTGTCC 57.456 43.478 0.00 0.00 33.49 4.02
60 61 9.935241 ACTATGAATCTTCTATGCGATAAACAT 57.065 29.630 0.00 0.00 0.00 2.71
61 62 9.411801 GACTATGAATCTTCTATGCGATAAACA 57.588 33.333 0.00 0.00 0.00 2.83
62 63 9.411801 TGACTATGAATCTTCTATGCGATAAAC 57.588 33.333 0.00 0.00 0.00 2.01
64 65 9.578439 CATGACTATGAATCTTCTATGCGATAA 57.422 33.333 0.00 0.00 36.36 1.75
65 66 8.193438 CCATGACTATGAATCTTCTATGCGATA 58.807 37.037 0.00 0.00 36.36 2.92
66 67 7.040494 CCATGACTATGAATCTTCTATGCGAT 58.960 38.462 0.00 0.00 36.36 4.58
67 68 6.015095 ACCATGACTATGAATCTTCTATGCGA 60.015 38.462 0.00 0.00 36.36 5.10
68 69 6.162079 ACCATGACTATGAATCTTCTATGCG 58.838 40.000 0.00 0.00 36.36 4.73
69 70 6.309980 CGACCATGACTATGAATCTTCTATGC 59.690 42.308 0.00 0.00 36.36 3.14
70 71 7.540400 GTCGACCATGACTATGAATCTTCTATG 59.460 40.741 3.51 0.00 36.36 2.23
71 72 7.574030 CGTCGACCATGACTATGAATCTTCTAT 60.574 40.741 10.58 0.00 36.36 1.98
72 73 6.293462 CGTCGACCATGACTATGAATCTTCTA 60.293 42.308 10.58 0.00 36.36 2.10
73 74 5.506483 CGTCGACCATGACTATGAATCTTCT 60.506 44.000 10.58 0.00 36.36 2.85
74 75 4.677378 CGTCGACCATGACTATGAATCTTC 59.323 45.833 10.58 0.00 36.36 2.87
75 76 4.338400 TCGTCGACCATGACTATGAATCTT 59.662 41.667 10.58 0.00 36.36 2.40
76 77 3.883489 TCGTCGACCATGACTATGAATCT 59.117 43.478 10.58 0.00 36.36 2.40
77 78 4.222886 CTCGTCGACCATGACTATGAATC 58.777 47.826 10.58 0.00 36.36 2.52
78 79 3.004839 CCTCGTCGACCATGACTATGAAT 59.995 47.826 10.58 0.00 36.36 2.57
79 80 2.357952 CCTCGTCGACCATGACTATGAA 59.642 50.000 10.58 0.00 36.36 2.57
80 81 1.947456 CCTCGTCGACCATGACTATGA 59.053 52.381 10.58 0.00 36.36 2.15
81 82 1.001268 CCCTCGTCGACCATGACTATG 60.001 57.143 10.58 0.00 36.71 2.23
82 83 1.133884 TCCCTCGTCGACCATGACTAT 60.134 52.381 10.58 0.00 36.71 2.12
83 84 0.253894 TCCCTCGTCGACCATGACTA 59.746 55.000 10.58 0.00 36.71 2.59
84 85 0.611062 TTCCCTCGTCGACCATGACT 60.611 55.000 10.58 0.00 36.71 3.41
85 86 0.245539 TTTCCCTCGTCGACCATGAC 59.754 55.000 10.58 0.00 35.49 3.06
86 87 0.245539 GTTTCCCTCGTCGACCATGA 59.754 55.000 10.58 0.30 0.00 3.07
87 88 0.037697 TGTTTCCCTCGTCGACCATG 60.038 55.000 10.58 0.00 0.00 3.66
88 89 0.902531 ATGTTTCCCTCGTCGACCAT 59.097 50.000 10.58 1.83 0.00 3.55
89 90 0.682852 AATGTTTCCCTCGTCGACCA 59.317 50.000 10.58 0.00 0.00 4.02
90 91 1.337447 TGAATGTTTCCCTCGTCGACC 60.337 52.381 10.58 0.00 0.00 4.79
91 92 1.725164 GTGAATGTTTCCCTCGTCGAC 59.275 52.381 5.18 5.18 0.00 4.20
92 93 1.341852 TGTGAATGTTTCCCTCGTCGA 59.658 47.619 0.00 0.00 0.00 4.20
93 94 1.790755 TGTGAATGTTTCCCTCGTCG 58.209 50.000 0.00 0.00 0.00 5.12
94 95 3.334691 TGATGTGAATGTTTCCCTCGTC 58.665 45.455 0.00 0.00 0.00 4.20
95 96 3.244561 ACTGATGTGAATGTTTCCCTCGT 60.245 43.478 0.00 0.00 0.00 4.18
96 97 3.338249 ACTGATGTGAATGTTTCCCTCG 58.662 45.455 0.00 0.00 0.00 4.63
97 98 6.375455 ACAATACTGATGTGAATGTTTCCCTC 59.625 38.462 0.00 0.00 0.00 4.30
98 99 6.248433 ACAATACTGATGTGAATGTTTCCCT 58.752 36.000 0.00 0.00 0.00 4.20
99 100 6.515272 ACAATACTGATGTGAATGTTTCCC 57.485 37.500 0.00 0.00 0.00 3.97
100 101 8.816640 AAAACAATACTGATGTGAATGTTTCC 57.183 30.769 0.00 0.00 36.97 3.13
121 122 9.993881 CGACACATTATGATTCAAAAGAAAAAC 57.006 29.630 0.00 0.00 0.00 2.43
122 123 9.958234 TCGACACATTATGATTCAAAAGAAAAA 57.042 25.926 0.00 0.00 0.00 1.94
131 132 9.423061 CCAGTTATATCGACACATTATGATTCA 57.577 33.333 0.00 0.00 0.00 2.57
132 133 9.639601 TCCAGTTATATCGACACATTATGATTC 57.360 33.333 0.00 0.00 0.00 2.52
134 135 9.591792 CATCCAGTTATATCGACACATTATGAT 57.408 33.333 0.00 0.00 0.00 2.45
135 136 8.802267 TCATCCAGTTATATCGACACATTATGA 58.198 33.333 0.00 0.00 0.00 2.15
136 137 8.986477 TCATCCAGTTATATCGACACATTATG 57.014 34.615 0.00 0.00 0.00 1.90
137 138 9.645059 CTTCATCCAGTTATATCGACACATTAT 57.355 33.333 0.00 0.00 0.00 1.28
138 139 8.856103 TCTTCATCCAGTTATATCGACACATTA 58.144 33.333 0.00 0.00 0.00 1.90
139 140 7.726216 TCTTCATCCAGTTATATCGACACATT 58.274 34.615 0.00 0.00 0.00 2.71
140 141 7.290110 TCTTCATCCAGTTATATCGACACAT 57.710 36.000 0.00 0.00 0.00 3.21
141 142 6.709018 TCTTCATCCAGTTATATCGACACA 57.291 37.500 0.00 0.00 0.00 3.72
142 143 8.420374 TTTTCTTCATCCAGTTATATCGACAC 57.580 34.615 0.00 0.00 0.00 3.67
180 181 6.438259 TGCTGATACTCTTACTACAGTGAC 57.562 41.667 0.00 0.00 0.00 3.67
194 195 6.092396 CCGTCTCGTTAGTATATGCTGATACT 59.908 42.308 13.43 13.43 43.52 2.12
201 202 4.745837 AGTCCGTCTCGTTAGTATATGC 57.254 45.455 0.00 0.00 0.00 3.14
202 203 6.134730 GTCAAGTCCGTCTCGTTAGTATATG 58.865 44.000 0.00 0.00 0.00 1.78
212 213 0.452950 CGAGTGTCAAGTCCGTCTCG 60.453 60.000 0.00 0.00 38.63 4.04
219 220 5.164233 TGATTCTTCATCGAGTGTCAAGTC 58.836 41.667 0.00 0.00 34.08 3.01
237 238 7.754069 TTGCATTTTCATTAACCGATGATTC 57.246 32.000 0.00 0.00 36.05 2.52
239 240 7.719483 AGATTGCATTTTCATTAACCGATGAT 58.281 30.769 0.00 0.00 36.05 2.45
242 243 8.131100 CACTAGATTGCATTTTCATTAACCGAT 58.869 33.333 0.00 0.00 0.00 4.18
246 247 9.624697 TTGACACTAGATTGCATTTTCATTAAC 57.375 29.630 0.00 0.00 0.00 2.01
248 249 9.013229 ACTTGACACTAGATTGCATTTTCATTA 57.987 29.630 0.00 0.00 0.00 1.90
285 286 3.311871 AGATCAATCAATTCTCGCTGTGC 59.688 43.478 0.00 0.00 0.00 4.57
315 316 6.370166 GGTCAATTAATTCCAATCCGCAAAAA 59.630 34.615 0.00 0.00 0.00 1.94
316 317 5.872070 GGTCAATTAATTCCAATCCGCAAAA 59.128 36.000 0.00 0.00 0.00 2.44
317 318 5.186797 AGGTCAATTAATTCCAATCCGCAAA 59.813 36.000 8.26 0.00 0.00 3.68
318 319 4.709397 AGGTCAATTAATTCCAATCCGCAA 59.291 37.500 8.26 0.00 0.00 4.85
319 320 4.277476 AGGTCAATTAATTCCAATCCGCA 58.723 39.130 8.26 0.00 0.00 5.69
320 321 4.918810 AGGTCAATTAATTCCAATCCGC 57.081 40.909 8.26 0.00 0.00 5.54
321 322 6.016360 TGCATAGGTCAATTAATTCCAATCCG 60.016 38.462 8.26 0.00 0.00 4.18
322 323 7.288810 TGCATAGGTCAATTAATTCCAATCC 57.711 36.000 8.26 3.28 0.00 3.01
323 324 8.196771 TGTTGCATAGGTCAATTAATTCCAATC 58.803 33.333 8.26 0.00 0.00 2.67
324 325 8.076910 TGTTGCATAGGTCAATTAATTCCAAT 57.923 30.769 8.26 0.00 0.00 3.16
325 326 7.473735 TGTTGCATAGGTCAATTAATTCCAA 57.526 32.000 8.26 0.00 0.00 3.53
326 327 7.039434 TGTTGTTGCATAGGTCAATTAATTCCA 60.039 33.333 8.26 0.00 0.00 3.53
327 328 7.319646 TGTTGTTGCATAGGTCAATTAATTCC 58.680 34.615 0.00 0.00 0.00 3.01
333 334 6.403866 TTTCTGTTGTTGCATAGGTCAATT 57.596 33.333 0.00 0.00 0.00 2.32
353 354 1.729149 CGGATGACGGCAAAGCTTTTC 60.729 52.381 9.53 4.29 39.42 2.29
355 356 1.875963 CGGATGACGGCAAAGCTTT 59.124 52.632 5.69 5.69 39.42 3.51
419 420 3.313690 CGCACCCAAATTTTAGTTCCAC 58.686 45.455 0.00 0.00 0.00 4.02
422 423 2.333926 GCCGCACCCAAATTTTAGTTC 58.666 47.619 0.00 0.00 0.00 3.01
439 440 2.392821 CTCATTTCTCTCTCATCGCCG 58.607 52.381 0.00 0.00 0.00 6.46
443 444 4.050553 CCGAAGCTCATTTCTCTCTCATC 58.949 47.826 0.00 0.00 0.00 2.92
452 453 1.425428 CGCCACCGAAGCTCATTTC 59.575 57.895 0.00 0.00 36.29 2.17
470 471 4.468689 GTAGCGGTCCCACCTGCC 62.469 72.222 0.00 0.00 38.12 4.85
472 473 3.066190 TCGTAGCGGTCCCACCTG 61.066 66.667 0.00 0.00 35.66 4.00
494 495 2.046507 GACCTCACTGCAGGGCTG 60.047 66.667 19.93 10.84 38.78 4.85
495 496 3.699894 CGACCTCACTGCAGGGCT 61.700 66.667 19.93 0.00 39.89 5.19
496 497 4.767255 CCGACCTCACTGCAGGGC 62.767 72.222 19.93 1.23 38.40 5.19
497 498 4.767255 GCCGACCTCACTGCAGGG 62.767 72.222 19.93 15.69 37.96 4.45
522 523 1.607251 GGTGGATATAAGGCGTTCGGG 60.607 57.143 0.00 0.00 0.00 5.14
523 524 1.343465 AGGTGGATATAAGGCGTTCGG 59.657 52.381 0.00 0.00 0.00 4.30
525 526 3.746045 TGAGGTGGATATAAGGCGTTC 57.254 47.619 0.00 0.00 0.00 3.95
526 527 6.374417 AATATGAGGTGGATATAAGGCGTT 57.626 37.500 0.00 0.00 0.00 4.84
529 530 5.888161 CCCAAATATGAGGTGGATATAAGGC 59.112 44.000 0.00 0.00 34.05 4.35
532 533 6.274436 TCTGCCCAAATATGAGGTGGATATAA 59.726 38.462 0.00 0.00 34.05 0.98
533 534 5.790096 TCTGCCCAAATATGAGGTGGATATA 59.210 40.000 0.00 0.00 34.05 0.86
542 543 6.206243 CCTCTTGTATTCTGCCCAAATATGAG 59.794 42.308 0.00 0.00 0.00 2.90
547 548 4.019174 CACCTCTTGTATTCTGCCCAAAT 58.981 43.478 0.00 0.00 0.00 2.32
553 554 2.012673 CCAGCACCTCTTGTATTCTGC 58.987 52.381 0.00 0.00 0.00 4.26
555 556 4.074970 CAAACCAGCACCTCTTGTATTCT 58.925 43.478 0.00 0.00 0.00 2.40
557 558 3.821033 GTCAAACCAGCACCTCTTGTATT 59.179 43.478 0.00 0.00 0.00 1.89
561 562 0.954452 GGTCAAACCAGCACCTCTTG 59.046 55.000 0.00 0.00 38.42 3.02
562 563 0.535102 CGGTCAAACCAGCACCTCTT 60.535 55.000 0.00 0.00 38.47 2.85
567 568 1.966451 CTCCCGGTCAAACCAGCAC 60.966 63.158 0.00 0.00 38.47 4.40
568 569 1.990160 AACTCCCGGTCAAACCAGCA 61.990 55.000 0.00 0.00 38.47 4.41
571 572 1.072648 CCTAAACTCCCGGTCAAACCA 59.927 52.381 0.00 0.00 38.47 3.67
573 574 1.162698 GCCTAAACTCCCGGTCAAAC 58.837 55.000 0.00 0.00 0.00 2.93
575 576 1.294138 CGCCTAAACTCCCGGTCAA 59.706 57.895 0.00 0.00 0.00 3.18
577 578 2.186125 CCGCCTAAACTCCCGGTC 59.814 66.667 0.00 0.00 36.18 4.79
578 579 3.396570 CCCGCCTAAACTCCCGGT 61.397 66.667 0.00 0.00 39.12 5.28
579 580 2.473891 AAACCCGCCTAAACTCCCGG 62.474 60.000 0.00 0.00 40.39 5.73
580 581 1.002990 AAACCCGCCTAAACTCCCG 60.003 57.895 0.00 0.00 0.00 5.14
581 582 0.963856 CCAAACCCGCCTAAACTCCC 60.964 60.000 0.00 0.00 0.00 4.30
582 583 0.963856 CCCAAACCCGCCTAAACTCC 60.964 60.000 0.00 0.00 0.00 3.85
584 585 1.076014 CCCCAAACCCGCCTAAACT 59.924 57.895 0.00 0.00 0.00 2.66
585 586 2.642254 GCCCCAAACCCGCCTAAAC 61.642 63.158 0.00 0.00 0.00 2.01
608 609 1.005097 TCATCCATGCTTCCAACAGCT 59.995 47.619 0.00 0.00 40.79 4.24
611 612 1.820519 GCTTCATCCATGCTTCCAACA 59.179 47.619 0.00 0.00 0.00 3.33
613 614 2.519771 AGCTTCATCCATGCTTCCAA 57.480 45.000 0.00 0.00 31.35 3.53
616 617 5.573337 AAAGTTAGCTTCATCCATGCTTC 57.427 39.130 0.00 0.00 36.84 3.86
617 618 5.477984 TGAAAAGTTAGCTTCATCCATGCTT 59.522 36.000 0.00 0.00 36.84 3.91
618 619 5.012239 TGAAAAGTTAGCTTCATCCATGCT 58.988 37.500 0.00 0.00 38.93 3.79
619 620 5.124457 TCTGAAAAGTTAGCTTCATCCATGC 59.876 40.000 0.00 0.00 33.01 4.06
620 621 6.373774 AGTCTGAAAAGTTAGCTTCATCCATG 59.626 38.462 0.00 0.00 33.01 3.66
659 1287 5.988310 TGGTCGTATGACTAGGAAAGAAA 57.012 39.130 14.61 0.00 44.83 2.52
660 1288 5.988310 TTGGTCGTATGACTAGGAAAGAA 57.012 39.130 14.61 0.00 44.83 2.52
661 1289 5.337009 GGTTTGGTCGTATGACTAGGAAAGA 60.337 44.000 14.61 0.00 44.83 2.52
662 1290 4.868734 GGTTTGGTCGTATGACTAGGAAAG 59.131 45.833 14.61 0.00 44.83 2.62
663 1291 4.618927 CGGTTTGGTCGTATGACTAGGAAA 60.619 45.833 14.61 6.55 44.83 3.13
664 1292 3.119388 CGGTTTGGTCGTATGACTAGGAA 60.119 47.826 14.61 0.00 44.83 3.36
775 1403 4.796231 GAAAGCGAGGCGGCGAGA 62.796 66.667 12.98 0.00 38.18 4.04
782 1412 1.154814 GGATTCGAGGAAAGCGAGGC 61.155 60.000 0.00 0.00 39.14 4.70
785 1415 2.295253 GAAGGATTCGAGGAAAGCGA 57.705 50.000 0.00 0.00 34.17 4.93
811 1449 0.243095 GAGTAGTTCCGCCACGACTT 59.757 55.000 0.00 0.00 33.25 3.01
889 1537 1.686110 GAAGGGGCGAGGAAGAGGA 60.686 63.158 0.00 0.00 0.00 3.71
940 1589 4.292178 GAGATCGGAGGCGGCTGG 62.292 72.222 19.63 8.46 0.00 4.85
942 1591 2.909965 GAGAGATCGGAGGCGGCT 60.910 66.667 13.09 13.09 0.00 5.52
1203 1914 1.346395 ACCATGTCAGTAAACGGAGCA 59.654 47.619 0.00 0.00 0.00 4.26
1214 1925 3.055167 TGTGTTCATCCCTACCATGTCAG 60.055 47.826 0.00 0.00 0.00 3.51
1215 1926 2.909662 TGTGTTCATCCCTACCATGTCA 59.090 45.455 0.00 0.00 0.00 3.58
1286 2187 4.678287 CAGCACTGTTTGTTTCATCACATC 59.322 41.667 0.00 0.00 0.00 3.06
1287 2188 4.613944 CAGCACTGTTTGTTTCATCACAT 58.386 39.130 0.00 0.00 0.00 3.21
1288 2189 3.734597 GCAGCACTGTTTGTTTCATCACA 60.735 43.478 0.00 0.00 0.00 3.58
1289 2190 2.791004 GCAGCACTGTTTGTTTCATCAC 59.209 45.455 0.00 0.00 0.00 3.06
1290 2191 2.689471 AGCAGCACTGTTTGTTTCATCA 59.311 40.909 0.00 0.00 0.00 3.07
1291 2192 3.047796 CAGCAGCACTGTTTGTTTCATC 58.952 45.455 0.00 0.00 41.86 2.92
1330 2233 1.940613 GCCAAACCGTGAGCCTAATAG 59.059 52.381 0.00 0.00 0.00 1.73
1337 2240 0.887387 TTGGTAGCCAAACCGTGAGC 60.887 55.000 0.00 0.00 40.92 4.26
1371 2274 1.745115 CCAAAGCCCGATTCTGCGA 60.745 57.895 0.00 0.00 0.00 5.10
1393 2296 2.270923 CGATCTCGAGCCAAATTGACA 58.729 47.619 7.81 0.00 43.02 3.58
1432 2345 3.838317 AGTATCTTGCAGTGGTGACCTTA 59.162 43.478 2.11 0.00 0.00 2.69
1445 2358 5.862924 TGAGTTTGCAGTAAGTATCTTGC 57.137 39.130 0.00 0.00 0.00 4.01
1464 2377 6.546395 CCGAAAATTTCCTGTCTACATTGAG 58.454 40.000 0.00 0.00 0.00 3.02
1528 2443 8.473219 CCTGCTGCATATCTGAAGAAGTATATA 58.527 37.037 1.31 0.00 32.03 0.86
1529 2444 7.038445 ACCTGCTGCATATCTGAAGAAGTATAT 60.038 37.037 1.31 0.00 32.03 0.86
1574 2492 9.453572 TTGAGATGAATTTCTGCATACTTTACT 57.546 29.630 0.00 0.00 0.00 2.24
1815 2742 2.390225 TTATTGGTGGCCTTGGTGTT 57.610 45.000 3.32 0.00 0.00 3.32
1816 2743 2.566724 CAATTATTGGTGGCCTTGGTGT 59.433 45.455 3.32 0.00 0.00 4.16
1817 2744 2.566724 ACAATTATTGGTGGCCTTGGTG 59.433 45.455 3.32 0.00 34.12 4.17
1915 2852 1.434622 CCATAGCACGCAGGCTTGAG 61.435 60.000 0.00 0.00 42.71 3.02
2032 2989 3.015327 GCAAGTGGCTTCATGATCTTCT 58.985 45.455 0.00 0.00 40.25 2.85
2110 3067 4.876701 GTGACTGCTCCACACCAA 57.123 55.556 0.00 0.00 34.81 3.67
2225 3182 7.118422 AGAACTTACAAATAACGAAGAGCAC 57.882 36.000 0.00 0.00 0.00 4.40
2239 3196 9.020731 TGACAGTGAGATATGTAGAACTTACAA 57.979 33.333 0.00 0.00 0.00 2.41
2903 3871 2.728013 ACTCTAGAGGGGGCCATATACA 59.272 50.000 23.50 0.00 0.00 2.29
3211 4179 5.763876 AGCCCAACAATAGTCTAGAAAGT 57.236 39.130 0.00 0.00 0.00 2.66
3351 4319 0.824109 TCCATACAAGAGCGGGTCTG 59.176 55.000 10.92 7.65 34.84 3.51
3369 4337 9.399403 GACAACTGAAAGGAAATTTATCTTGTC 57.601 33.333 6.93 8.46 39.30 3.18
3480 4449 3.897505 GGCCTTTGAAGCCCATAATGTAT 59.102 43.478 0.00 0.00 45.16 2.29
3645 4617 3.322254 AGCCTATAGTGCATACTGGTGTC 59.678 47.826 13.52 0.00 37.78 3.67
4071 5121 7.838696 TCCCTCAATTGGTGAAATGTACATATT 59.161 33.333 9.21 5.93 35.22 1.28
4072 5122 7.353525 TCCCTCAATTGGTGAAATGTACATAT 58.646 34.615 9.21 0.00 35.22 1.78
4073 5123 6.726379 TCCCTCAATTGGTGAAATGTACATA 58.274 36.000 9.21 0.00 35.22 2.29
4074 5124 5.579047 TCCCTCAATTGGTGAAATGTACAT 58.421 37.500 1.41 1.41 35.22 2.29
4075 5125 4.991776 TCCCTCAATTGGTGAAATGTACA 58.008 39.130 5.42 0.00 35.22 2.90
4076 5126 5.105756 CCTTCCCTCAATTGGTGAAATGTAC 60.106 44.000 5.42 0.00 35.22 2.90
4077 5127 5.016173 CCTTCCCTCAATTGGTGAAATGTA 58.984 41.667 5.42 0.00 35.22 2.29
4078 5128 3.834231 CCTTCCCTCAATTGGTGAAATGT 59.166 43.478 5.42 0.00 35.22 2.71
4079 5129 4.088634 TCCTTCCCTCAATTGGTGAAATG 58.911 43.478 5.42 1.74 35.22 2.32
4080 5130 4.402616 TCCTTCCCTCAATTGGTGAAAT 57.597 40.909 5.42 0.00 35.22 2.17
4081 5131 3.893753 TCCTTCCCTCAATTGGTGAAA 57.106 42.857 5.42 0.00 35.22 2.69
4082 5132 3.075882 ACATCCTTCCCTCAATTGGTGAA 59.924 43.478 5.42 5.47 35.22 3.18
4083 5133 2.649312 ACATCCTTCCCTCAATTGGTGA 59.351 45.455 5.42 0.00 34.17 4.02
4084 5134 3.091633 ACATCCTTCCCTCAATTGGTG 57.908 47.619 5.42 0.00 0.00 4.17
4085 5135 3.833559 AACATCCTTCCCTCAATTGGT 57.166 42.857 5.42 0.00 0.00 3.67
4086 5136 4.088634 TCAAACATCCTTCCCTCAATTGG 58.911 43.478 5.42 0.00 0.00 3.16
4087 5137 5.927281 ATCAAACATCCTTCCCTCAATTG 57.073 39.130 0.00 0.00 0.00 2.32
4088 5138 6.154021 CAGAATCAAACATCCTTCCCTCAATT 59.846 38.462 0.00 0.00 0.00 2.32
4089 5139 5.655532 CAGAATCAAACATCCTTCCCTCAAT 59.344 40.000 0.00 0.00 0.00 2.57
4090 5140 5.012239 CAGAATCAAACATCCTTCCCTCAA 58.988 41.667 0.00 0.00 0.00 3.02
4091 5141 4.592942 CAGAATCAAACATCCTTCCCTCA 58.407 43.478 0.00 0.00 0.00 3.86
4092 5142 3.379688 GCAGAATCAAACATCCTTCCCTC 59.620 47.826 0.00 0.00 0.00 4.30
4093 5143 3.245371 TGCAGAATCAAACATCCTTCCCT 60.245 43.478 0.00 0.00 0.00 4.20
4094 5144 3.091545 TGCAGAATCAAACATCCTTCCC 58.908 45.455 0.00 0.00 0.00 3.97
4095 5145 4.996788 ATGCAGAATCAAACATCCTTCC 57.003 40.909 0.00 0.00 0.00 3.46
4096 5146 6.530534 CAGAAATGCAGAATCAAACATCCTTC 59.469 38.462 0.00 0.00 0.00 3.46
4097 5147 6.395629 CAGAAATGCAGAATCAAACATCCTT 58.604 36.000 0.00 0.00 0.00 3.36
4098 5148 5.623824 GCAGAAATGCAGAATCAAACATCCT 60.624 40.000 0.00 0.00 34.41 3.24
4099 5149 4.565564 GCAGAAATGCAGAATCAAACATCC 59.434 41.667 0.00 0.00 34.41 3.51
4100 5150 5.288712 CAGCAGAAATGCAGAATCAAACATC 59.711 40.000 2.73 0.00 37.25 3.06
4101 5151 5.168569 CAGCAGAAATGCAGAATCAAACAT 58.831 37.500 2.73 0.00 37.25 2.71
4102 5152 4.552355 CAGCAGAAATGCAGAATCAAACA 58.448 39.130 2.73 0.00 37.25 2.83
4103 5153 3.367025 GCAGCAGAAATGCAGAATCAAAC 59.633 43.478 2.73 0.00 43.31 2.93
4104 5154 3.581755 GCAGCAGAAATGCAGAATCAAA 58.418 40.909 2.73 0.00 43.31 2.69
4105 5155 2.094390 GGCAGCAGAAATGCAGAATCAA 60.094 45.455 2.73 0.00 45.68 2.57
4106 5156 1.475280 GGCAGCAGAAATGCAGAATCA 59.525 47.619 2.73 0.00 45.68 2.57
4107 5157 1.202382 GGGCAGCAGAAATGCAGAATC 60.202 52.381 2.73 0.00 45.68 2.52
4108 5158 0.822164 GGGCAGCAGAAATGCAGAAT 59.178 50.000 2.73 0.00 45.68 2.40
4109 5159 0.540133 TGGGCAGCAGAAATGCAGAA 60.540 50.000 2.73 0.00 45.68 3.02
4110 5160 0.540133 TTGGGCAGCAGAAATGCAGA 60.540 50.000 2.73 0.00 45.68 4.26
4111 5161 0.535335 ATTGGGCAGCAGAAATGCAG 59.465 50.000 2.73 0.00 45.68 4.41
4112 5162 1.752498 CTATTGGGCAGCAGAAATGCA 59.248 47.619 2.73 0.00 45.68 3.96
4113 5163 1.537562 GCTATTGGGCAGCAGAAATGC 60.538 52.381 0.00 0.00 43.09 3.56
4114 5164 1.068127 GGCTATTGGGCAGCAGAAATG 59.932 52.381 0.00 0.00 40.95 2.32
4115 5165 1.342275 TGGCTATTGGGCAGCAGAAAT 60.342 47.619 0.00 0.00 45.79 2.17
4116 5166 0.039472 TGGCTATTGGGCAGCAGAAA 59.961 50.000 0.00 0.00 45.79 2.52
4117 5167 1.690616 TGGCTATTGGGCAGCAGAA 59.309 52.632 0.00 0.00 45.79 3.02
4118 5168 3.414022 TGGCTATTGGGCAGCAGA 58.586 55.556 0.00 0.00 45.79 4.26
4137 5187 4.021894 ACCAGCTTCAGTTGTACAGACTAG 60.022 45.833 9.43 6.87 0.00 2.57
4208 5336 8.663911 CAAAAGAAAATCTTTGTAACAAAGCCA 58.336 29.630 0.00 0.00 45.19 4.75


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

AutoCloner maintained by Alex Coulton.