Multiple sequence alignment - TraesCS4B01G064000

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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 TraesCS4B01G064000 chr4B 100.000 4801 0 0 1 4801 56276583 56271783 0.000000e+00 8866
1 TraesCS4B01G064000 chr4B 87.614 549 49 7 2679 3223 64454854 64455387 1.900000e-173 619
2 TraesCS4B01G064000 chr4B 86.179 123 14 1 4299 4421 795681 795562 3.900000e-26 130
3 TraesCS4B01G064000 chr4A 94.418 2992 95 38 1259 4201 561370685 561367717 0.000000e+00 4534
4 TraesCS4B01G064000 chr4A 86.545 602 24 17 147 720 561372120 561371548 1.140000e-170 610
5 TraesCS4B01G064000 chr4A 88.395 517 22 20 744 1249 561371235 561370746 5.350000e-164 588
6 TraesCS4B01G064000 chr4A 80.791 531 50 18 2159 2682 708068040 708068525 7.590000e-98 368
7 TraesCS4B01G064000 chr4A 83.077 195 23 7 4417 4602 660701559 660701752 8.260000e-38 169
8 TraesCS4B01G064000 chr4A 86.179 123 14 2 4299 4421 731416220 731416101 3.900000e-26 130
9 TraesCS4B01G064000 chr4D 93.563 2905 105 36 1259 4119 38593914 38591048 0.000000e+00 4253
10 TraesCS4B01G064000 chr4D 86.883 1296 75 47 1 1249 38595221 38593974 0.000000e+00 1363
11 TraesCS4B01G064000 chr4D 87.209 172 18 4 4434 4601 54289286 54289115 4.900000e-45 193
12 TraesCS4B01G064000 chr4D 84.865 185 15 4 4424 4601 138318236 138318058 1.780000e-39 174
13 TraesCS4B01G064000 chr4D 81.900 221 9 12 4074 4291 38591047 38590855 1.790000e-34 158
14 TraesCS4B01G064000 chr4D 98.667 75 1 0 4719 4793 38590706 38590632 3.010000e-27 134
15 TraesCS4B01G064000 chr4D 85.366 123 15 1 4299 4421 314930327 314930446 1.810000e-24 124
16 TraesCS4B01G064000 chr2D 91.622 1313 78 12 2105 3397 154949281 154950581 0.000000e+00 1786
17 TraesCS4B01G064000 chr2D 91.394 1313 81 13 2105 3397 94715550 94714250 0.000000e+00 1770
18 TraesCS4B01G064000 chr2D 88.418 708 45 19 2526 3224 68786115 68786794 0.000000e+00 819
19 TraesCS4B01G064000 chr2D 89.655 522 32 4 3118 3639 488987903 488987404 0.000000e+00 645
20 TraesCS4B01G064000 chr2D 92.874 421 17 6 1426 1843 488989812 488989402 2.470000e-167 599
21 TraesCS4B01G064000 chr2D 92.637 421 18 6 1426 1843 94716169 94715759 1.150000e-165 593
22 TraesCS4B01G064000 chr2D 90.736 421 26 6 1426 1843 154948660 154949070 2.530000e-152 549
23 TraesCS4B01G064000 chr2D 95.109 184 9 0 2148 2331 488987904 488988087 1.690000e-74 291
24 TraesCS4B01G064000 chr2D 94.531 128 2 2 1982 2108 94715757 94715634 4.900000e-45 193
25 TraesCS4B01G064000 chr2D 93.750 128 3 2 1982 2108 154949072 154949195 2.280000e-43 187
26 TraesCS4B01G064000 chr2D 94.068 118 4 3 1982 2097 488989400 488989284 4.940000e-40 176
27 TraesCS4B01G064000 chr2D 86.992 123 13 1 4299 4421 299891690 299891571 8.380000e-28 135
28 TraesCS4B01G064000 chr2D 93.407 91 3 2 2327 2417 488989199 488989286 1.080000e-26 132
29 TraesCS4B01G064000 chr7A 87.645 688 42 22 2553 3224 108852968 108852308 0.000000e+00 760
30 TraesCS4B01G064000 chr5A 87.391 690 43 20 2553 3224 580276522 580275859 0.000000e+00 752
31 TraesCS4B01G064000 chr2B 92.784 485 20 3 2110 2581 577443327 577442845 0.000000e+00 688
32 TraesCS4B01G064000 chr2B 88.863 422 19 9 1425 1843 577443906 577443510 1.200000e-135 494
33 TraesCS4B01G064000 chr2B 93.077 130 5 1 1982 2111 577443508 577443383 2.280000e-43 187
34 TraesCS4B01G064000 chr2B 84.153 183 21 5 4427 4601 355137291 355137109 2.300000e-38 171
35 TraesCS4B01G064000 chr2B 98.485 66 1 0 3450 3515 577442248 577442183 3.040000e-22 117
36 TraesCS4B01G064000 chr7D 90.230 522 32 5 3118 3639 505332612 505333114 0.000000e+00 664
37 TraesCS4B01G064000 chr7D 88.889 549 42 8 2679 3223 346568220 346567687 0.000000e+00 658
38 TraesCS4B01G064000 chr7D 90.081 494 34 7 2733 3221 49472705 49472222 1.130000e-175 627
39 TraesCS4B01G064000 chr7D 87.424 493 33 8 2733 3221 49521739 49521272 1.520000e-149 540
40 TraesCS4B01G064000 chr7D 95.814 215 3 4 1630 1843 505330902 505331111 4.600000e-90 342
41 TraesCS4B01G064000 chr7D 94.565 184 9 1 2148 2331 505332611 505332429 2.830000e-72 283
42 TraesCS4B01G064000 chr7D 88.824 170 11 3 1426 1592 505330739 505330903 8.150000e-48 202
43 TraesCS4B01G064000 chr7D 94.068 118 4 3 1982 2097 505331113 505331229 4.940000e-40 176
44 TraesCS4B01G064000 chr7D 84.530 181 20 4 4426 4598 31996742 31996922 6.390000e-39 172
45 TraesCS4B01G064000 chr6D 87.571 177 16 4 4427 4601 473170551 473170379 2.930000e-47 200
46 TraesCS4B01G064000 chr6D 82.000 200 26 9 4407 4598 106946746 106946943 1.380000e-35 161
47 TraesCS4B01G064000 chr6D 86.179 123 13 4 4299 4421 147691271 147691153 3.900000e-26 130
48 TraesCS4B01G064000 chr1A 85.714 182 19 3 4427 4601 585655991 585655810 8.210000e-43 185
49 TraesCS4B01G064000 chr1A 84.916 179 18 5 4426 4595 44475870 44476048 6.390000e-39 172
50 TraesCS4B01G064000 chr3D 86.179 123 14 2 4299 4421 11442573 11442692 3.900000e-26 130
51 TraesCS4B01G064000 chr3A 86.777 121 11 3 4301 4421 26139821 26139936 3.900000e-26 130
52 TraesCS4B01G064000 chr1B 86.179 123 14 3 4299 4421 531122149 531122030 3.900000e-26 130
53 TraesCS4B01G064000 chr5B 85.271 129 14 3 4300 4426 316709120 316708995 1.400000e-25 128


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 TraesCS4B01G064000 chr4B 56271783 56276583 4800 True 8866.000000 8866 100.00000 1 4801 1 chr4B.!!$R2 4800
1 TraesCS4B01G064000 chr4B 64454854 64455387 533 False 619.000000 619 87.61400 2679 3223 1 chr4B.!!$F1 544
2 TraesCS4B01G064000 chr4A 561367717 561372120 4403 True 1910.666667 4534 89.78600 147 4201 3 chr4A.!!$R2 4054
3 TraesCS4B01G064000 chr4D 38590632 38595221 4589 True 1477.000000 4253 90.25325 1 4793 4 chr4D.!!$R3 4792
4 TraesCS4B01G064000 chr2D 94714250 94716169 1919 True 852.000000 1770 92.85400 1426 3397 3 chr2D.!!$R2 1971
5 TraesCS4B01G064000 chr2D 154948660 154950581 1921 False 840.666667 1786 92.03600 1426 3397 3 chr2D.!!$F2 1971
6 TraesCS4B01G064000 chr2D 68786115 68786794 679 False 819.000000 819 88.41800 2526 3224 1 chr2D.!!$F1 698
7 TraesCS4B01G064000 chr2D 488987404 488989812 2408 True 473.333333 645 92.19900 1426 3639 3 chr2D.!!$R3 2213
8 TraesCS4B01G064000 chr2D 488987904 488989286 1382 False 211.500000 291 94.25800 2148 2417 2 chr2D.!!$F3 269
9 TraesCS4B01G064000 chr7A 108852308 108852968 660 True 760.000000 760 87.64500 2553 3224 1 chr7A.!!$R1 671
10 TraesCS4B01G064000 chr5A 580275859 580276522 663 True 752.000000 752 87.39100 2553 3224 1 chr5A.!!$R1 671
11 TraesCS4B01G064000 chr2B 577442183 577443906 1723 True 371.500000 688 93.30225 1425 3515 4 chr2B.!!$R2 2090
12 TraesCS4B01G064000 chr7D 346567687 346568220 533 True 658.000000 658 88.88900 2679 3223 1 chr7D.!!$R3 544
13 TraesCS4B01G064000 chr7D 505330739 505333114 2375 False 346.000000 664 92.23400 1426 3639 4 chr7D.!!$F2 2213

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
199 216 0.109458 CTCCGTTGCTGCACGTAGTA 60.109 55.0 18.25 0.00 41.61 1.82 F
200 217 0.109458 TCCGTTGCTGCACGTAGTAG 60.109 55.0 18.25 0.00 41.61 2.57 F
805 1152 0.251077 CAAAACCCTGCCTGCTCTCT 60.251 55.0 0.00 0.00 0.00 3.10 F
2599 4716 0.179145 GTGATGGAATGCTGCAGTGC 60.179 55.0 16.64 14.69 0.00 4.40 F
2821 4953 0.544697 ACGTTGGTTGAGACCCAAGT 59.455 50.0 0.00 0.00 45.92 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1257 1643 0.396060 GAAGGCCAGGATAGAGCAGG 59.604 60.000 5.01 0.0 0.00 4.85 R
2108 2708 1.275291 ACACGGTAGCATGTAAGCAGT 59.725 47.619 0.00 0.0 36.85 4.40 R
2757 4882 1.003580 AGGACCTAGTACGACCAACGA 59.996 52.381 0.00 0.0 45.77 3.85 R
3657 6357 1.025812 CCATAGTCCGAGAAGACGCT 58.974 55.000 0.00 0.0 41.83 5.07 R
4105 6862 1.082169 CCACGGCACAATGAACACG 60.082 57.895 0.00 0.0 0.00 4.49 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
30 34 0.441533 ACTGTAGCACGTACGTCTCG 59.558 55.000 19.94 9.02 33.87 4.04
90 94 0.598942 GCGGAATGGCGTTTTTGGTT 60.599 50.000 0.00 0.00 0.00 3.67
91 95 1.414378 CGGAATGGCGTTTTTGGTTC 58.586 50.000 0.00 0.00 0.00 3.62
98 102 1.812686 GCGTTTTTGGTTCCCCTCCC 61.813 60.000 0.00 0.00 0.00 4.30
99 103 0.468400 CGTTTTTGGTTCCCCTCCCA 60.468 55.000 0.00 0.00 0.00 4.37
100 104 1.796017 GTTTTTGGTTCCCCTCCCAA 58.204 50.000 0.00 0.00 38.92 4.12
112 128 1.679032 CCCTCCCAAACGAGTTCATCC 60.679 57.143 0.00 0.00 0.00 3.51
113 129 1.359848 CTCCCAAACGAGTTCATCCG 58.640 55.000 0.00 0.00 0.00 4.18
114 130 0.672401 TCCCAAACGAGTTCATCCGC 60.672 55.000 0.00 0.00 0.00 5.54
115 131 0.673644 CCCAAACGAGTTCATCCGCT 60.674 55.000 0.00 0.00 0.00 5.52
116 132 0.443869 CCAAACGAGTTCATCCGCTG 59.556 55.000 0.00 0.00 0.00 5.18
117 133 0.443869 CAAACGAGTTCATCCGCTGG 59.556 55.000 0.00 0.00 0.00 4.85
118 134 0.673644 AAACGAGTTCATCCGCTGGG 60.674 55.000 0.00 0.00 0.00 4.45
119 135 2.892425 CGAGTTCATCCGCTGGGC 60.892 66.667 0.00 0.00 0.00 5.36
120 136 2.586792 GAGTTCATCCGCTGGGCT 59.413 61.111 0.00 0.00 0.00 5.19
121 137 1.522580 GAGTTCATCCGCTGGGCTC 60.523 63.158 0.00 0.00 0.00 4.70
122 138 1.965754 GAGTTCATCCGCTGGGCTCT 61.966 60.000 0.00 0.00 0.00 4.09
123 139 1.817099 GTTCATCCGCTGGGCTCTG 60.817 63.158 0.00 0.00 0.00 3.35
124 140 3.035173 TTCATCCGCTGGGCTCTGG 62.035 63.158 0.00 0.00 0.00 3.86
125 141 4.559063 CATCCGCTGGGCTCTGGG 62.559 72.222 0.01 0.01 0.00 4.45
163 180 2.490903 ACTTACCGTAAGCACGTCTGAT 59.509 45.455 16.73 0.00 46.96 2.90
196 213 2.736995 GCTCCGTTGCTGCACGTA 60.737 61.111 18.25 6.75 38.57 3.57
197 214 2.730672 GCTCCGTTGCTGCACGTAG 61.731 63.158 18.25 14.61 38.57 3.51
199 216 0.109458 CTCCGTTGCTGCACGTAGTA 60.109 55.000 18.25 0.00 41.61 1.82
200 217 0.109458 TCCGTTGCTGCACGTAGTAG 60.109 55.000 18.25 0.00 41.61 2.57
213 239 7.402811 TGCACGTAGTAGCATGTAAATATTC 57.597 36.000 0.00 0.00 41.61 1.75
236 262 9.869757 ATTCTATTTTTAATAACTGGTTGGTGC 57.130 29.630 0.00 0.00 0.00 5.01
355 386 1.762460 ACATAGCCCCTGGACGGAG 60.762 63.158 0.00 0.00 33.16 4.63
480 523 2.747989 GCCTACAGATACGATCGATGGA 59.252 50.000 24.34 10.30 0.00 3.41
606 655 0.320946 AAGTTGCATTGCATGGTGGC 60.321 50.000 12.95 0.00 38.76 5.01
615 664 2.597340 CATGGTGGCAGGGGTAGG 59.403 66.667 0.00 0.00 0.00 3.18
617 666 1.694169 ATGGTGGCAGGGGTAGGAG 60.694 63.158 0.00 0.00 0.00 3.69
618 667 2.285442 GGTGGCAGGGGTAGGAGT 60.285 66.667 0.00 0.00 0.00 3.85
620 669 0.619543 GGTGGCAGGGGTAGGAGTAA 60.620 60.000 0.00 0.00 0.00 2.24
621 670 1.282382 GTGGCAGGGGTAGGAGTAAA 58.718 55.000 0.00 0.00 0.00 2.01
622 671 1.631898 GTGGCAGGGGTAGGAGTAAAA 59.368 52.381 0.00 0.00 0.00 1.52
623 672 1.913419 TGGCAGGGGTAGGAGTAAAAG 59.087 52.381 0.00 0.00 0.00 2.27
624 673 1.408405 GGCAGGGGTAGGAGTAAAAGC 60.408 57.143 0.00 0.00 0.00 3.51
625 674 1.408405 GCAGGGGTAGGAGTAAAAGCC 60.408 57.143 0.00 0.00 0.00 4.35
626 675 2.197465 CAGGGGTAGGAGTAAAAGCCT 58.803 52.381 0.00 0.00 38.31 4.58
627 676 2.170817 CAGGGGTAGGAGTAAAAGCCTC 59.829 54.545 0.00 0.00 35.73 4.70
725 1058 3.868200 AACCCCTTGAAGCGGCAGG 62.868 63.158 1.45 0.00 0.00 4.85
805 1152 0.251077 CAAAACCCTGCCTGCTCTCT 60.251 55.000 0.00 0.00 0.00 3.10
823 1170 4.398319 TCTCTTTCTCATCACCAAAACCC 58.602 43.478 0.00 0.00 0.00 4.11
824 1171 3.496331 TCTTTCTCATCACCAAAACCCC 58.504 45.455 0.00 0.00 0.00 4.95
825 1172 3.117322 TCTTTCTCATCACCAAAACCCCA 60.117 43.478 0.00 0.00 0.00 4.96
826 1173 3.320610 TTCTCATCACCAAAACCCCAA 57.679 42.857 0.00 0.00 0.00 4.12
895 1249 2.130426 GCAGCGAGATCAGAGGGGA 61.130 63.158 0.00 0.00 0.00 4.81
941 1299 1.271597 GGAGAAGCAGAGCAAAAGGGA 60.272 52.381 0.00 0.00 0.00 4.20
951 1309 3.182996 AAAAGGGACGGCAGGGGT 61.183 61.111 0.00 0.00 0.00 4.95
1102 1479 4.102681 TCATTCAGCAGGTCATCTCATCAT 59.897 41.667 0.00 0.00 0.00 2.45
1188 1574 8.552296 ACTCTTATCTCTCTCTTTCTCTCTCTT 58.448 37.037 0.00 0.00 0.00 2.85
1224 1610 6.817765 TTGCTTCCGTATTCTTCTTCATTT 57.182 33.333 0.00 0.00 0.00 2.32
1225 1611 6.422776 TGCTTCCGTATTCTTCTTCATTTC 57.577 37.500 0.00 0.00 0.00 2.17
1226 1612 6.173339 TGCTTCCGTATTCTTCTTCATTTCT 58.827 36.000 0.00 0.00 0.00 2.52
1249 1635 6.656693 TCTTCTGGTTCTTGAATCATTTCTCC 59.343 38.462 0.00 0.00 32.78 3.71
1250 1636 4.937620 TCTGGTTCTTGAATCATTTCTCCG 59.062 41.667 0.00 0.00 32.78 4.63
1252 1638 5.070001 TGGTTCTTGAATCATTTCTCCGTT 58.930 37.500 0.00 0.00 32.78 4.44
1255 1641 6.594159 GGTTCTTGAATCATTTCTCCGTTCTA 59.406 38.462 0.00 0.00 32.78 2.10
1256 1642 7.413109 GGTTCTTGAATCATTTCTCCGTTCTAC 60.413 40.741 0.00 0.00 32.78 2.59
1257 1643 6.106673 TCTTGAATCATTTCTCCGTTCTACC 58.893 40.000 0.00 0.00 32.78 3.18
1267 1704 2.554893 CTCCGTTCTACCCTGCTCTATC 59.445 54.545 0.00 0.00 0.00 2.08
1279 1717 1.343377 TGCTCTATCCTGGCCTTCTCA 60.343 52.381 3.32 0.00 0.00 3.27
1280 1718 1.765314 GCTCTATCCTGGCCTTCTCAA 59.235 52.381 3.32 0.00 0.00 3.02
1477 1930 3.155167 CCCACCCTCCGGTCTAGC 61.155 72.222 0.00 0.00 42.04 3.42
1917 2411 4.879295 ATGTTTTCCCAGGGATATGTCA 57.121 40.909 9.80 5.48 0.00 3.58
1918 2412 4.666412 TGTTTTCCCAGGGATATGTCAA 57.334 40.909 9.80 0.00 0.00 3.18
1945 2440 9.343539 GGCATATCTTGGTAGAAAAAGATTAGT 57.656 33.333 3.47 0.00 41.97 2.24
2011 2506 3.335579 GTCCAAGTTCATGTGGGTAGTC 58.664 50.000 0.59 0.00 35.46 2.59
2108 2708 4.326826 CTTGTCCTTGCCTCTGTGATAAA 58.673 43.478 0.00 0.00 0.00 1.40
2171 2771 3.808618 GCTTGATAGGATAGGCTGTTGGG 60.809 52.174 0.00 0.00 0.00 4.12
2191 2791 7.180229 TGTTGGGAGTCAGATCTTTTGTATCTA 59.820 37.037 0.00 0.00 32.40 1.98
2260 3026 5.808540 ACATGATTGTGTTTTCATATGCTGC 59.191 36.000 0.00 0.00 33.85 5.25
2549 4666 6.901300 TGGTCTGATATCCTTGTAAACTACCT 59.099 38.462 0.00 0.00 0.00 3.08
2599 4716 0.179145 GTGATGGAATGCTGCAGTGC 60.179 55.000 16.64 14.69 0.00 4.40
2682 4801 9.686683 AGTGTTAGGAACAATTAGAATATGCTT 57.313 29.630 0.00 0.00 44.16 3.91
2712 4837 6.488683 CGTCTAATAGAGAGAGATTCAAGGGT 59.511 42.308 0.00 0.00 33.72 4.34
2757 4882 4.206375 TGTGTTCACAAATGACATCCACT 58.794 39.130 2.99 0.00 33.38 4.00
2758 4883 4.275689 TGTGTTCACAAATGACATCCACTC 59.724 41.667 2.99 0.00 33.38 3.51
2821 4953 0.544697 ACGTTGGTTGAGACCCAAGT 59.455 50.000 0.00 0.00 45.92 3.16
2822 4954 1.064979 ACGTTGGTTGAGACCCAAGTT 60.065 47.619 0.00 0.00 45.92 2.66
2823 4955 1.333619 CGTTGGTTGAGACCCAAGTTG 59.666 52.381 0.00 0.00 45.92 3.16
2824 4956 2.650322 GTTGGTTGAGACCCAAGTTGA 58.350 47.619 3.87 0.00 45.92 3.18
2825 4957 3.222603 GTTGGTTGAGACCCAAGTTGAT 58.777 45.455 3.87 0.00 45.92 2.57
2842 4974 8.081633 CCAAGTTGATTTGATTTGTGCTAGTTA 58.918 33.333 3.87 0.00 0.00 2.24
3096 5556 1.340405 ACTGCACAATCCTCCCACATC 60.340 52.381 0.00 0.00 0.00 3.06
3287 5843 1.474478 TCTCAGGTGAGTTCTCATCGC 59.526 52.381 6.87 0.00 42.60 4.58
3328 5970 7.913297 CGATTCTTGTTTTTCTGGAGTTGTTAA 59.087 33.333 0.00 0.00 0.00 2.01
3596 6293 1.302511 CACCGGGTTCAACCTCCTG 60.303 63.158 6.51 0.00 38.64 3.86
3657 6357 0.522626 CAACAGCATGATGAACGCCA 59.477 50.000 19.60 0.00 42.01 5.69
3674 6374 1.025812 CCAGCGTCTTCTCGGACTAT 58.974 55.000 0.00 0.00 34.38 2.12
3830 6530 2.962253 GTCGCTAGCACCGGCATC 60.962 66.667 16.45 0.00 44.61 3.91
3919 6627 2.257691 TGTTGCGTTGGCTAAGGTTA 57.742 45.000 4.39 0.00 40.82 2.85
4104 6861 4.774726 TCTTCTTCACATGCCTTCTCTAGT 59.225 41.667 0.00 0.00 0.00 2.57
4105 6862 4.727507 TCTTCACATGCCTTCTCTAGTC 57.272 45.455 0.00 0.00 0.00 2.59
4135 6892 2.170397 TGTGCCGTGGATCATGAGTTAT 59.830 45.455 0.09 0.00 0.00 1.89
4136 6893 3.386402 TGTGCCGTGGATCATGAGTTATA 59.614 43.478 0.09 0.00 0.00 0.98
4137 6894 3.990469 GTGCCGTGGATCATGAGTTATAG 59.010 47.826 0.09 0.00 0.00 1.31
4176 6943 3.659786 TCAACTCCGTTTCACCACTATG 58.340 45.455 0.00 0.00 0.00 2.23
4178 6945 3.594603 ACTCCGTTTCACCACTATGAG 57.405 47.619 0.00 0.00 0.00 2.90
4180 6947 1.621317 TCCGTTTCACCACTATGAGCA 59.379 47.619 0.00 0.00 0.00 4.26
4181 6948 2.037902 TCCGTTTCACCACTATGAGCAA 59.962 45.455 0.00 0.00 0.00 3.91
4182 6949 2.811431 CCGTTTCACCACTATGAGCAAA 59.189 45.455 0.00 0.00 0.00 3.68
4201 6968 8.400947 TGAGCAAAAGATCTTAATTATGACAGC 58.599 33.333 8.75 0.00 0.00 4.40
4202 6969 8.284945 AGCAAAAGATCTTAATTATGACAGCA 57.715 30.769 8.75 0.00 0.00 4.41
4203 6970 8.910944 AGCAAAAGATCTTAATTATGACAGCAT 58.089 29.630 8.75 0.00 38.54 3.79
4259 7026 1.904287 TGCATGTAAACCACCAGTCC 58.096 50.000 0.00 0.00 0.00 3.85
4260 7027 1.423541 TGCATGTAAACCACCAGTCCT 59.576 47.619 0.00 0.00 0.00 3.85
4265 7032 2.781174 TGTAAACCACCAGTCCTTCCTT 59.219 45.455 0.00 0.00 0.00 3.36
4278 7045 5.241506 CAGTCCTTCCTTAATGCTCACAAAA 59.758 40.000 0.00 0.00 0.00 2.44
4304 7071 8.622948 AAAAATATCACTCCGTTTCTCTTTCT 57.377 30.769 0.00 0.00 0.00 2.52
4306 7073 8.934507 AAATATCACTCCGTTTCTCTTTCTAG 57.065 34.615 0.00 0.00 0.00 2.43
4307 7074 7.883391 ATATCACTCCGTTTCTCTTTCTAGA 57.117 36.000 0.00 0.00 0.00 2.43
4333 7100 9.784531 AGATTTCAATATGGACTACATACAAGG 57.215 33.333 0.00 0.00 44.41 3.61
4334 7101 7.801716 TTTCAATATGGACTACATACAAGGC 57.198 36.000 0.00 0.00 44.41 4.35
4335 7102 6.493189 TCAATATGGACTACATACAAGGCA 57.507 37.500 0.00 0.00 44.41 4.75
4336 7103 6.894682 TCAATATGGACTACATACAAGGCAA 58.105 36.000 0.00 0.00 44.41 4.52
4337 7104 7.342581 TCAATATGGACTACATACAAGGCAAA 58.657 34.615 0.00 0.00 44.41 3.68
4338 7105 7.831690 TCAATATGGACTACATACAAGGCAAAA 59.168 33.333 0.00 0.00 44.41 2.44
4339 7106 8.632679 CAATATGGACTACATACAAGGCAAAAT 58.367 33.333 0.00 0.00 44.41 1.82
4340 7107 5.895636 TGGACTACATACAAGGCAAAATG 57.104 39.130 0.00 0.00 0.00 2.32
4341 7108 5.565509 TGGACTACATACAAGGCAAAATGA 58.434 37.500 0.00 0.00 0.00 2.57
4342 7109 5.647658 TGGACTACATACAAGGCAAAATGAG 59.352 40.000 0.00 0.00 0.00 2.90
4343 7110 5.648092 GGACTACATACAAGGCAAAATGAGT 59.352 40.000 0.00 0.00 0.00 3.41
4344 7111 6.403636 GGACTACATACAAGGCAAAATGAGTG 60.404 42.308 0.00 0.00 0.00 3.51
4345 7112 6.237901 ACTACATACAAGGCAAAATGAGTGA 58.762 36.000 0.00 0.00 0.00 3.41
4346 7113 6.714810 ACTACATACAAGGCAAAATGAGTGAA 59.285 34.615 0.00 0.00 0.00 3.18
4347 7114 6.594788 ACATACAAGGCAAAATGAGTGAAT 57.405 33.333 0.00 0.00 0.00 2.57
4348 7115 6.624423 ACATACAAGGCAAAATGAGTGAATC 58.376 36.000 0.00 0.00 0.00 2.52
4349 7116 6.209192 ACATACAAGGCAAAATGAGTGAATCA 59.791 34.615 0.00 0.00 43.70 2.57
4350 7117 5.534207 ACAAGGCAAAATGAGTGAATCAA 57.466 34.783 0.00 0.00 42.53 2.57
4351 7118 5.916318 ACAAGGCAAAATGAGTGAATCAAA 58.084 33.333 0.00 0.00 42.53 2.69
4352 7119 6.347696 ACAAGGCAAAATGAGTGAATCAAAA 58.652 32.000 0.00 0.00 42.53 2.44
4353 7120 6.258507 ACAAGGCAAAATGAGTGAATCAAAAC 59.741 34.615 0.00 0.00 42.53 2.43
4354 7121 6.165700 AGGCAAAATGAGTGAATCAAAACT 57.834 33.333 0.00 0.00 42.53 2.66
4355 7122 6.218746 AGGCAAAATGAGTGAATCAAAACTC 58.781 36.000 0.00 0.00 42.53 3.01
4356 7123 6.041296 AGGCAAAATGAGTGAATCAAAACTCT 59.959 34.615 4.62 0.00 42.53 3.24
4357 7124 7.231317 AGGCAAAATGAGTGAATCAAAACTCTA 59.769 33.333 4.62 0.00 42.53 2.43
4358 7125 7.327032 GGCAAAATGAGTGAATCAAAACTCTAC 59.673 37.037 4.62 0.00 42.53 2.59
4359 7126 7.862372 GCAAAATGAGTGAATCAAAACTCTACA 59.138 33.333 4.62 0.00 42.53 2.74
4360 7127 9.734620 CAAAATGAGTGAATCAAAACTCTACAA 57.265 29.630 4.62 0.00 42.53 2.41
4364 7131 8.239681 TGAGTGAATCAAAACTCTACAATACG 57.760 34.615 4.62 0.00 42.72 3.06
4365 7132 7.870954 TGAGTGAATCAAAACTCTACAATACGT 59.129 33.333 0.00 0.00 42.72 3.57
4366 7133 8.240883 AGTGAATCAAAACTCTACAATACGTC 57.759 34.615 0.00 0.00 0.00 4.34
4367 7134 8.088981 AGTGAATCAAAACTCTACAATACGTCT 58.911 33.333 0.00 0.00 0.00 4.18
4368 7135 9.350357 GTGAATCAAAACTCTACAATACGTCTA 57.650 33.333 0.00 0.00 0.00 2.59
4433 7200 9.476202 AAAAGACTTATATTGAAACAGTTTGGC 57.524 29.630 2.34 0.00 0.00 4.52
4434 7201 8.409358 AAGACTTATATTGAAACAGTTTGGCT 57.591 30.769 2.34 0.00 0.00 4.75
4435 7202 9.515226 AAGACTTATATTGAAACAGTTTGGCTA 57.485 29.630 2.34 0.00 0.00 3.93
4436 7203 9.515226 AGACTTATATTGAAACAGTTTGGCTAA 57.485 29.630 2.34 0.00 0.00 3.09
4441 7208 8.986477 ATATTGAAACAGTTTGGCTAATTCAC 57.014 30.769 2.34 0.00 33.50 3.18
4442 7209 5.843673 TGAAACAGTTTGGCTAATTCACA 57.156 34.783 2.34 0.00 30.73 3.58
4443 7210 6.403866 TGAAACAGTTTGGCTAATTCACAT 57.596 33.333 2.34 0.00 30.73 3.21
4444 7211 6.815089 TGAAACAGTTTGGCTAATTCACATT 58.185 32.000 2.34 0.00 30.73 2.71
4445 7212 7.271511 TGAAACAGTTTGGCTAATTCACATTT 58.728 30.769 2.34 0.00 30.73 2.32
4446 7213 8.417106 TGAAACAGTTTGGCTAATTCACATTTA 58.583 29.630 2.34 0.00 30.73 1.40
4447 7214 8.816640 AAACAGTTTGGCTAATTCACATTTAG 57.183 30.769 0.00 0.00 0.00 1.85
4448 7215 7.759489 ACAGTTTGGCTAATTCACATTTAGA 57.241 32.000 0.00 0.00 0.00 2.10
4449 7216 8.353423 ACAGTTTGGCTAATTCACATTTAGAT 57.647 30.769 0.00 0.00 0.00 1.98
4450 7217 8.246180 ACAGTTTGGCTAATTCACATTTAGATG 58.754 33.333 0.00 0.00 39.25 2.90
4452 7219 8.806146 AGTTTGGCTAATTCACATTTAGATGTT 58.194 29.630 0.00 0.00 43.92 2.71
4453 7220 9.423061 GTTTGGCTAATTCACATTTAGATGTTT 57.577 29.630 0.00 0.00 43.92 2.83
4454 7221 9.995003 TTTGGCTAATTCACATTTAGATGTTTT 57.005 25.926 0.00 0.00 43.92 2.43
4455 7222 9.995003 TTGGCTAATTCACATTTAGATGTTTTT 57.005 25.926 0.00 0.00 43.92 1.94
4480 7247 8.972662 TTAAGGATGTCATATCTAATCTCCCA 57.027 34.615 0.00 0.00 0.00 4.37
4481 7248 9.566331 TTAAGGATGTCATATCTAATCTCCCAT 57.434 33.333 0.00 0.00 0.00 4.00
4483 7250 9.566331 AAGGATGTCATATCTAATCTCCCATAA 57.434 33.333 0.00 0.00 0.00 1.90
4484 7251 9.566331 AGGATGTCATATCTAATCTCCCATAAA 57.434 33.333 0.00 0.00 0.00 1.40
4493 7260 8.854614 ATCTAATCTCCCATAAATAACACAGC 57.145 34.615 0.00 0.00 0.00 4.40
4494 7261 7.801104 TCTAATCTCCCATAAATAACACAGCA 58.199 34.615 0.00 0.00 0.00 4.41
4495 7262 8.271458 TCTAATCTCCCATAAATAACACAGCAA 58.729 33.333 0.00 0.00 0.00 3.91
4496 7263 6.699575 ATCTCCCATAAATAACACAGCAAC 57.300 37.500 0.00 0.00 0.00 4.17
4497 7264 5.565509 TCTCCCATAAATAACACAGCAACA 58.434 37.500 0.00 0.00 0.00 3.33
4498 7265 6.007076 TCTCCCATAAATAACACAGCAACAA 58.993 36.000 0.00 0.00 0.00 2.83
4499 7266 6.150976 TCTCCCATAAATAACACAGCAACAAG 59.849 38.462 0.00 0.00 0.00 3.16
4500 7267 5.184864 TCCCATAAATAACACAGCAACAAGG 59.815 40.000 0.00 0.00 0.00 3.61
4501 7268 5.184864 CCCATAAATAACACAGCAACAAGGA 59.815 40.000 0.00 0.00 0.00 3.36
4502 7269 6.295011 CCCATAAATAACACAGCAACAAGGAA 60.295 38.462 0.00 0.00 0.00 3.36
4503 7270 7.151308 CCATAAATAACACAGCAACAAGGAAA 58.849 34.615 0.00 0.00 0.00 3.13
4504 7271 7.655328 CCATAAATAACACAGCAACAAGGAAAA 59.345 33.333 0.00 0.00 0.00 2.29
4505 7272 9.039870 CATAAATAACACAGCAACAAGGAAAAA 57.960 29.630 0.00 0.00 0.00 1.94
4548 7315 2.349580 CACAAGCATAGTGGACATGACG 59.650 50.000 0.00 0.00 33.43 4.35
4549 7316 2.028112 ACAAGCATAGTGGACATGACGT 60.028 45.455 0.00 0.00 0.00 4.34
4550 7317 3.002791 CAAGCATAGTGGACATGACGTT 58.997 45.455 0.00 0.00 0.00 3.99
4551 7318 4.180817 CAAGCATAGTGGACATGACGTTA 58.819 43.478 0.00 0.00 0.00 3.18
4552 7319 4.046938 AGCATAGTGGACATGACGTTAG 57.953 45.455 0.00 0.00 0.00 2.34
4553 7320 3.699538 AGCATAGTGGACATGACGTTAGA 59.300 43.478 0.00 0.00 0.00 2.10
4554 7321 4.342378 AGCATAGTGGACATGACGTTAGAT 59.658 41.667 0.00 0.00 0.00 1.98
4555 7322 4.445718 GCATAGTGGACATGACGTTAGATG 59.554 45.833 0.00 0.00 0.00 2.90
4556 7323 5.592054 CATAGTGGACATGACGTTAGATGT 58.408 41.667 0.00 8.13 35.46 3.06
4557 7324 3.849911 AGTGGACATGACGTTAGATGTG 58.150 45.455 12.04 0.00 32.85 3.21
4558 7325 3.509967 AGTGGACATGACGTTAGATGTGA 59.490 43.478 12.04 0.00 32.85 3.58
4559 7326 3.612860 GTGGACATGACGTTAGATGTGAC 59.387 47.826 12.04 6.47 32.85 3.67
4560 7327 3.257127 TGGACATGACGTTAGATGTGACA 59.743 43.478 12.04 8.83 32.85 3.58
4561 7328 4.081697 TGGACATGACGTTAGATGTGACAT 60.082 41.667 12.04 0.00 32.85 3.06
4562 7329 5.126384 TGGACATGACGTTAGATGTGACATA 59.874 40.000 12.04 0.00 32.85 2.29
4563 7330 6.040247 GGACATGACGTTAGATGTGACATAA 58.960 40.000 12.04 0.00 32.85 1.90
4564 7331 6.019801 GGACATGACGTTAGATGTGACATAAC 60.020 42.308 12.04 0.00 32.85 1.89
4583 7350 8.357796 ACATAACGATGTCAAATCTAGATGTG 57.642 34.615 15.84 15.84 43.01 3.21
4584 7351 7.981789 ACATAACGATGTCAAATCTAGATGTGT 59.018 33.333 20.21 3.74 43.01 3.72
4585 7352 6.893958 AACGATGTCAAATCTAGATGTGTC 57.106 37.500 20.21 15.94 0.00 3.67
4586 7353 5.352284 ACGATGTCAAATCTAGATGTGTCC 58.648 41.667 20.21 13.41 0.00 4.02
4587 7354 5.127845 ACGATGTCAAATCTAGATGTGTCCT 59.872 40.000 20.21 9.64 0.00 3.85
4588 7355 6.321435 ACGATGTCAAATCTAGATGTGTCCTA 59.679 38.462 20.21 7.84 0.00 2.94
4589 7356 6.860539 CGATGTCAAATCTAGATGTGTCCTAG 59.139 42.308 20.21 6.89 35.97 3.02
4590 7357 7.255277 CGATGTCAAATCTAGATGTGTCCTAGA 60.255 40.741 20.21 2.74 44.50 2.43
4591 7358 7.101652 TGTCAAATCTAGATGTGTCCTAGAC 57.898 40.000 20.21 11.66 43.57 2.59
4592 7359 6.663523 TGTCAAATCTAGATGTGTCCTAGACA 59.336 38.462 20.21 13.79 43.57 3.41
4593 7360 7.148000 TGTCAAATCTAGATGTGTCCTAGACAG 60.148 40.741 20.21 0.00 43.57 3.51
4594 7361 7.067615 GTCAAATCTAGATGTGTCCTAGACAGA 59.932 40.741 20.21 0.00 43.57 3.41
4595 7362 6.952773 AATCTAGATGTGTCCTAGACAGAC 57.047 41.667 5.86 0.00 43.57 3.51
4596 7363 4.783055 TCTAGATGTGTCCTAGACAGACC 58.217 47.826 0.00 0.00 43.57 3.85
4597 7364 2.741145 AGATGTGTCCTAGACAGACCC 58.259 52.381 0.00 0.00 43.57 4.46
4598 7365 2.043115 AGATGTGTCCTAGACAGACCCA 59.957 50.000 0.00 0.00 43.57 4.51
4599 7366 2.623418 TGTGTCCTAGACAGACCCAT 57.377 50.000 0.00 0.00 43.57 4.00
4600 7367 3.750501 TGTGTCCTAGACAGACCCATA 57.249 47.619 0.00 0.00 43.57 2.74
4601 7368 4.265856 TGTGTCCTAGACAGACCCATAT 57.734 45.455 0.00 0.00 43.57 1.78
4602 7369 4.620723 TGTGTCCTAGACAGACCCATATT 58.379 43.478 0.00 0.00 43.57 1.28
4603 7370 4.405680 TGTGTCCTAGACAGACCCATATTG 59.594 45.833 0.00 0.00 43.57 1.90
4604 7371 4.649674 GTGTCCTAGACAGACCCATATTGA 59.350 45.833 0.00 0.00 43.57 2.57
4605 7372 5.128827 GTGTCCTAGACAGACCCATATTGAA 59.871 44.000 0.00 0.00 43.57 2.69
4606 7373 5.724370 TGTCCTAGACAGACCCATATTGAAA 59.276 40.000 0.00 0.00 37.67 2.69
4607 7374 6.386927 TGTCCTAGACAGACCCATATTGAAAT 59.613 38.462 0.00 0.00 37.67 2.17
4608 7375 6.931840 GTCCTAGACAGACCCATATTGAAATC 59.068 42.308 0.00 0.00 32.09 2.17
4609 7376 6.846505 TCCTAGACAGACCCATATTGAAATCT 59.153 38.462 0.00 0.00 0.00 2.40
4610 7377 7.015682 TCCTAGACAGACCCATATTGAAATCTC 59.984 40.741 0.00 0.00 0.00 2.75
4611 7378 6.821616 AGACAGACCCATATTGAAATCTCT 57.178 37.500 0.00 0.00 0.00 3.10
4661 7428 3.438216 TGCACCATTGATTTCTCCTCA 57.562 42.857 0.00 0.00 0.00 3.86
4663 7430 3.009363 TGCACCATTGATTTCTCCTCAGA 59.991 43.478 0.00 0.00 0.00 3.27
4664 7431 3.626670 GCACCATTGATTTCTCCTCAGAG 59.373 47.826 0.00 0.00 41.93 3.35
4701 7468 0.823356 GGGCTGTTTTGTGAGCTGGA 60.823 55.000 0.00 0.00 35.42 3.86
4795 7590 8.939201 TCTTTATGTTTTTCTGTTTTGATGCA 57.061 26.923 0.00 0.00 0.00 3.96
4796 7591 9.545105 TCTTTATGTTTTTCTGTTTTGATGCAT 57.455 25.926 0.00 0.00 0.00 3.96
4800 7595 7.846644 TGTTTTTCTGTTTTGATGCATTTCT 57.153 28.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 51 4.200283 GACTGAGCGGCGGAGAGG 62.200 72.222 9.78 0.00 0.00 3.69
48 52 4.544689 CGACTGAGCGGCGGAGAG 62.545 72.222 9.78 0.00 0.00 3.20
90 94 0.765135 TGAACTCGTTTGGGAGGGGA 60.765 55.000 0.00 0.00 38.39 4.81
91 95 0.328258 ATGAACTCGTTTGGGAGGGG 59.672 55.000 0.00 0.00 38.39 4.79
98 102 0.443869 CCAGCGGATGAACTCGTTTG 59.556 55.000 0.00 0.00 0.00 2.93
99 103 0.673644 CCCAGCGGATGAACTCGTTT 60.674 55.000 0.00 0.00 0.00 3.60
100 104 1.079127 CCCAGCGGATGAACTCGTT 60.079 57.895 0.00 0.00 0.00 3.85
116 132 4.437587 ATGCTGTGCCCAGAGCCC 62.438 66.667 13.88 0.00 45.99 5.19
117 133 3.138798 CATGCTGTGCCCAGAGCC 61.139 66.667 13.88 0.00 45.99 4.70
126 142 4.414852 GGTAAGTAATGTTGCATGCTGTG 58.585 43.478 20.33 0.00 0.00 3.66
127 143 3.126858 CGGTAAGTAATGTTGCATGCTGT 59.873 43.478 20.33 1.93 0.00 4.40
128 144 3.126858 ACGGTAAGTAATGTTGCATGCTG 59.873 43.478 20.33 0.00 0.00 4.41
129 145 3.343617 ACGGTAAGTAATGTTGCATGCT 58.656 40.909 20.33 0.00 0.00 3.79
130 146 3.757745 ACGGTAAGTAATGTTGCATGC 57.242 42.857 11.82 11.82 0.00 4.06
131 147 5.163804 TGCTTACGGTAAGTAATGTTGCATG 60.164 40.000 24.45 0.00 43.64 4.06
132 148 4.938832 TGCTTACGGTAAGTAATGTTGCAT 59.061 37.500 24.45 0.00 43.64 3.96
137 153 4.082571 AGACGTGCTTACGGTAAGTAATGT 60.083 41.667 24.45 22.33 43.64 2.71
139 155 4.156556 TCAGACGTGCTTACGGTAAGTAAT 59.843 41.667 24.45 14.36 43.64 1.89
143 159 2.624316 TCAGACGTGCTTACGGTAAG 57.376 50.000 20.87 20.87 38.80 2.34
213 239 7.759433 CCTGCACCAACCAGTTATTAAAAATAG 59.241 37.037 0.00 0.00 0.00 1.73
219 245 3.426615 CCCTGCACCAACCAGTTATTAA 58.573 45.455 0.00 0.00 0.00 1.40
236 262 2.603473 TCACCCGTCACTCCCCTG 60.603 66.667 0.00 0.00 0.00 4.45
355 386 0.615331 TTGATGTCCAGTCTGGCCTC 59.385 55.000 14.64 11.67 37.47 4.70
371 406 1.873591 GGCGAGTTTTCTTGAGCTTGA 59.126 47.619 0.00 0.00 33.28 3.02
606 655 2.170817 GAGGCTTTTACTCCTACCCCTG 59.829 54.545 0.00 0.00 31.71 4.45
615 664 3.762674 CCGAGGGAGGCTTTTACTC 57.237 57.895 0.00 0.00 0.00 2.59
624 673 0.748367 GCTTTAAAGGCCGAGGGAGG 60.748 60.000 16.78 0.00 0.00 4.30
625 674 0.253327 AGCTTTAAAGGCCGAGGGAG 59.747 55.000 16.78 0.00 0.00 4.30
626 675 0.252197 GAGCTTTAAAGGCCGAGGGA 59.748 55.000 16.78 0.00 0.00 4.20
627 676 1.090052 CGAGCTTTAAAGGCCGAGGG 61.090 60.000 16.78 0.00 0.00 4.30
628 677 0.391263 ACGAGCTTTAAAGGCCGAGG 60.391 55.000 16.78 2.59 0.00 4.63
700 758 2.102420 CCGCTTCAAGGGGTTTCTTTTT 59.898 45.455 12.50 0.00 42.78 1.94
805 1152 3.320610 TGGGGTTTTGGTGATGAGAAA 57.679 42.857 0.00 0.00 0.00 2.52
823 1170 2.623416 GGTCTGAAGGTTTCTTGGTTGG 59.377 50.000 0.00 0.00 32.52 3.77
824 1171 3.555966 AGGTCTGAAGGTTTCTTGGTTG 58.444 45.455 0.00 0.00 32.52 3.77
825 1172 3.459969 AGAGGTCTGAAGGTTTCTTGGTT 59.540 43.478 0.00 0.00 32.52 3.67
826 1173 3.049344 AGAGGTCTGAAGGTTTCTTGGT 58.951 45.455 0.00 0.00 32.52 3.67
951 1309 1.705002 CCCTCCACACAAGACCACCA 61.705 60.000 0.00 0.00 0.00 4.17
1114 1491 3.596046 AGAGAGGGGAAAAGAGAGAGAGA 59.404 47.826 0.00 0.00 0.00 3.10
1116 1493 4.045334 AGAAGAGAGGGGAAAAGAGAGAGA 59.955 45.833 0.00 0.00 0.00 3.10
1161 1547 9.213777 AGAGAGAGAAAGAGAGAGATAAGAGTA 57.786 37.037 0.00 0.00 0.00 2.59
1162 1548 8.095452 AGAGAGAGAAAGAGAGAGATAAGAGT 57.905 38.462 0.00 0.00 0.00 3.24
1163 1549 8.970859 AAGAGAGAGAAAGAGAGAGATAAGAG 57.029 38.462 0.00 0.00 0.00 2.85
1198 1584 7.721286 ATGAAGAAGAATACGGAAGCAATAG 57.279 36.000 0.00 0.00 0.00 1.73
1203 1589 6.670077 AGAAATGAAGAAGAATACGGAAGC 57.330 37.500 0.00 0.00 0.00 3.86
1224 1610 6.656693 GGAGAAATGATTCAAGAACCAGAAGA 59.343 38.462 0.00 0.00 38.06 2.87
1225 1611 6.402983 CGGAGAAATGATTCAAGAACCAGAAG 60.403 42.308 0.00 0.00 38.06 2.85
1226 1612 5.412594 CGGAGAAATGATTCAAGAACCAGAA 59.587 40.000 0.00 0.00 38.06 3.02
1249 1635 2.294791 CAGGATAGAGCAGGGTAGAACG 59.705 54.545 0.00 0.00 0.00 3.95
1250 1636 2.630580 CCAGGATAGAGCAGGGTAGAAC 59.369 54.545 0.00 0.00 0.00 3.01
1252 1638 1.481428 GCCAGGATAGAGCAGGGTAGA 60.481 57.143 0.00 0.00 0.00 2.59
1255 1641 1.768077 GGCCAGGATAGAGCAGGGT 60.768 63.158 0.00 0.00 0.00 4.34
1256 1642 1.059006 AAGGCCAGGATAGAGCAGGG 61.059 60.000 5.01 0.00 0.00 4.45
1257 1643 0.396060 GAAGGCCAGGATAGAGCAGG 59.604 60.000 5.01 0.00 0.00 4.85
1267 1704 2.575805 AAGAAGTTGAGAAGGCCAGG 57.424 50.000 5.01 0.00 0.00 4.45
1477 1930 8.980481 AAAAATACACATGAAGGGTATCTAGG 57.020 34.615 0.00 0.00 46.07 3.02
1720 2173 2.442413 GGCATGGTTACTACTTTGCCA 58.558 47.619 6.90 0.00 44.52 4.92
1917 2411 8.829373 AATCTTTTTCTACCAAGATATGCCTT 57.171 30.769 0.00 0.00 38.55 4.35
1918 2412 9.566432 CTAATCTTTTTCTACCAAGATATGCCT 57.434 33.333 0.00 0.00 38.55 4.75
1945 2440 1.281867 CCAATAAGGCCACTCTGACCA 59.718 52.381 5.01 0.00 0.00 4.02
2011 2506 1.393539 CACAAGCGAACCTACATTCCG 59.606 52.381 0.00 0.00 0.00 4.30
2108 2708 1.275291 ACACGGTAGCATGTAAGCAGT 59.725 47.619 0.00 0.00 36.85 4.40
2171 2771 8.710551 CATGCATAGATACAAAAGATCTGACTC 58.289 37.037 0.00 0.00 35.30 3.36
2191 2791 2.954318 GAGATTAGGGTGTTGCATGCAT 59.046 45.455 23.37 7.94 0.00 3.96
2237 2978 5.051973 CGCAGCATATGAAAACACAATCATG 60.052 40.000 6.97 0.00 36.93 3.07
2260 3026 2.101415 TCCCATATCAGTCAGTCAAGCG 59.899 50.000 0.00 0.00 0.00 4.68
2682 4801 7.054751 TGAATCTCTCTCTATTAGACGACCAA 58.945 38.462 0.00 0.00 0.00 3.67
2712 4837 3.874383 TGATTGTCCAAACTGGGAAGA 57.126 42.857 0.00 0.00 39.05 2.87
2757 4882 1.003580 AGGACCTAGTACGACCAACGA 59.996 52.381 0.00 0.00 45.77 3.85
2758 4883 7.442090 CCATTAGGACCTAGTACGACCAACG 62.442 52.000 0.48 0.00 42.38 4.10
2821 4953 8.405531 GCCTATAACTAGCACAAATCAAATCAA 58.594 33.333 0.00 0.00 0.00 2.57
2822 4954 7.775093 AGCCTATAACTAGCACAAATCAAATCA 59.225 33.333 0.00 0.00 0.00 2.57
2823 4955 8.072567 CAGCCTATAACTAGCACAAATCAAATC 58.927 37.037 0.00 0.00 0.00 2.17
2824 4956 7.775093 TCAGCCTATAACTAGCACAAATCAAAT 59.225 33.333 0.00 0.00 0.00 2.32
2825 4957 7.109501 TCAGCCTATAACTAGCACAAATCAAA 58.890 34.615 0.00 0.00 0.00 2.69
3096 5556 7.293018 GGCAATGAACATTAAGCAAAGAAAAG 58.707 34.615 10.42 0.00 0.00 2.27
3140 5606 0.662619 CAAAACAAGGCTCAGCGTGA 59.337 50.000 5.99 0.00 0.00 4.35
3297 5938 3.421888 CCAGAAAAACAAGAATCGCAACG 59.578 43.478 0.00 0.00 0.00 4.10
3328 5970 5.815233 TCAAGAAGTTCATTCAGTCCTCT 57.185 39.130 5.50 0.00 40.67 3.69
3657 6357 1.025812 CCATAGTCCGAGAAGACGCT 58.974 55.000 0.00 0.00 41.83 5.07
3841 6544 2.028130 CACTACCTGCTACTCCTCCTG 58.972 57.143 0.00 0.00 0.00 3.86
3919 6627 1.203050 CCATGGAAACTCACCCACCTT 60.203 52.381 5.56 0.00 34.92 3.50
4104 6861 1.502990 CCACGGCACAATGAACACGA 61.503 55.000 0.00 0.00 0.00 4.35
4105 6862 1.082169 CCACGGCACAATGAACACG 60.082 57.895 0.00 0.00 0.00 4.49
4135 6892 6.602406 AGTTGAGCTACTCTTCCGATTTACTA 59.398 38.462 0.00 0.00 0.00 1.82
4136 6893 5.419471 AGTTGAGCTACTCTTCCGATTTACT 59.581 40.000 0.00 0.00 0.00 2.24
4137 6894 5.652518 AGTTGAGCTACTCTTCCGATTTAC 58.347 41.667 0.00 0.00 0.00 2.01
4176 6943 8.400947 TGCTGTCATAATTAAGATCTTTTGCTC 58.599 33.333 14.36 0.00 0.00 4.26
4178 6945 9.525409 AATGCTGTCATAATTAAGATCTTTTGC 57.475 29.630 14.36 2.46 31.46 3.68
4182 6949 9.525409 GCAAAATGCTGTCATAATTAAGATCTT 57.475 29.630 13.56 13.56 40.96 2.40
4225 6992 7.411804 GGTTTACATGCATGCATTTGAGTAAAC 60.412 37.037 38.94 38.94 42.87 2.01
4229 6996 4.021280 TGGTTTACATGCATGCATTTGAGT 60.021 37.500 30.32 24.88 33.90 3.41
4307 7074 9.784531 CCTTGTATGTAGTCCATATTGAAATCT 57.215 33.333 0.00 0.00 38.29 2.40
4308 7075 8.507249 GCCTTGTATGTAGTCCATATTGAAATC 58.493 37.037 0.00 0.00 38.29 2.17
4309 7076 7.998383 TGCCTTGTATGTAGTCCATATTGAAAT 59.002 33.333 0.00 0.00 38.29 2.17
4310 7077 7.342581 TGCCTTGTATGTAGTCCATATTGAAA 58.657 34.615 0.00 0.00 38.29 2.69
4311 7078 6.894682 TGCCTTGTATGTAGTCCATATTGAA 58.105 36.000 0.00 0.00 38.29 2.69
4312 7079 6.493189 TGCCTTGTATGTAGTCCATATTGA 57.507 37.500 0.00 0.00 38.29 2.57
4313 7080 7.566760 TTTGCCTTGTATGTAGTCCATATTG 57.433 36.000 0.00 0.00 38.29 1.90
4314 7081 8.632679 CATTTTGCCTTGTATGTAGTCCATATT 58.367 33.333 0.00 0.00 38.29 1.28
4315 7082 7.998383 TCATTTTGCCTTGTATGTAGTCCATAT 59.002 33.333 0.00 0.00 38.29 1.78
4316 7083 7.342581 TCATTTTGCCTTGTATGTAGTCCATA 58.657 34.615 0.00 0.00 34.86 2.74
4317 7084 6.186957 TCATTTTGCCTTGTATGTAGTCCAT 58.813 36.000 0.00 0.00 37.58 3.41
4318 7085 5.565509 TCATTTTGCCTTGTATGTAGTCCA 58.434 37.500 0.00 0.00 0.00 4.02
4319 7086 5.648092 ACTCATTTTGCCTTGTATGTAGTCC 59.352 40.000 0.00 0.00 0.00 3.85
4320 7087 6.371548 TCACTCATTTTGCCTTGTATGTAGTC 59.628 38.462 0.00 0.00 0.00 2.59
4321 7088 6.237901 TCACTCATTTTGCCTTGTATGTAGT 58.762 36.000 0.00 0.00 0.00 2.73
4322 7089 6.741992 TCACTCATTTTGCCTTGTATGTAG 57.258 37.500 0.00 0.00 0.00 2.74
4323 7090 7.392953 TGATTCACTCATTTTGCCTTGTATGTA 59.607 33.333 0.00 0.00 0.00 2.29
4324 7091 6.209192 TGATTCACTCATTTTGCCTTGTATGT 59.791 34.615 0.00 0.00 0.00 2.29
4325 7092 6.623486 TGATTCACTCATTTTGCCTTGTATG 58.377 36.000 0.00 0.00 0.00 2.39
4326 7093 6.839124 TGATTCACTCATTTTGCCTTGTAT 57.161 33.333 0.00 0.00 0.00 2.29
4327 7094 6.647334 TTGATTCACTCATTTTGCCTTGTA 57.353 33.333 0.00 0.00 32.72 2.41
4328 7095 5.534207 TTGATTCACTCATTTTGCCTTGT 57.466 34.783 0.00 0.00 32.72 3.16
4329 7096 6.480981 AGTTTTGATTCACTCATTTTGCCTTG 59.519 34.615 0.00 0.00 32.72 3.61
4330 7097 6.585416 AGTTTTGATTCACTCATTTTGCCTT 58.415 32.000 0.00 0.00 32.72 4.35
4331 7098 6.041296 AGAGTTTTGATTCACTCATTTTGCCT 59.959 34.615 2.36 0.00 41.77 4.75
4332 7099 6.218746 AGAGTTTTGATTCACTCATTTTGCC 58.781 36.000 2.36 0.00 41.77 4.52
4333 7100 7.862372 TGTAGAGTTTTGATTCACTCATTTTGC 59.138 33.333 2.36 0.00 41.77 3.68
4334 7101 9.734620 TTGTAGAGTTTTGATTCACTCATTTTG 57.265 29.630 2.36 0.00 41.77 2.44
4338 7105 8.873830 CGTATTGTAGAGTTTTGATTCACTCAT 58.126 33.333 2.36 0.00 41.77 2.90
4339 7106 7.870954 ACGTATTGTAGAGTTTTGATTCACTCA 59.129 33.333 2.36 0.00 41.77 3.41
4340 7107 8.240883 ACGTATTGTAGAGTTTTGATTCACTC 57.759 34.615 0.00 0.00 39.92 3.51
4341 7108 8.088981 AGACGTATTGTAGAGTTTTGATTCACT 58.911 33.333 0.00 0.00 0.00 3.41
4342 7109 8.240883 AGACGTATTGTAGAGTTTTGATTCAC 57.759 34.615 0.00 0.00 0.00 3.18
4407 7174 9.476202 GCCAAACTGTTTCAATATAAGTCTTTT 57.524 29.630 2.13 0.00 0.00 2.27
4408 7175 8.860088 AGCCAAACTGTTTCAATATAAGTCTTT 58.140 29.630 2.13 0.00 0.00 2.52
4409 7176 8.409358 AGCCAAACTGTTTCAATATAAGTCTT 57.591 30.769 2.13 0.00 0.00 3.01
4410 7177 9.515226 TTAGCCAAACTGTTTCAATATAAGTCT 57.485 29.630 2.13 0.00 0.00 3.24
4416 7183 8.584157 TGTGAATTAGCCAAACTGTTTCAATAT 58.416 29.630 2.13 0.00 34.39 1.28
4417 7184 7.946207 TGTGAATTAGCCAAACTGTTTCAATA 58.054 30.769 2.13 0.00 34.39 1.90
4418 7185 6.815089 TGTGAATTAGCCAAACTGTTTCAAT 58.185 32.000 2.13 0.00 34.39 2.57
4419 7186 6.214191 TGTGAATTAGCCAAACTGTTTCAA 57.786 33.333 2.13 0.00 34.39 2.69
4420 7187 5.843673 TGTGAATTAGCCAAACTGTTTCA 57.156 34.783 2.13 0.00 31.76 2.69
4421 7188 7.713764 AAATGTGAATTAGCCAAACTGTTTC 57.286 32.000 2.13 0.00 0.00 2.78
4422 7189 8.637986 TCTAAATGTGAATTAGCCAAACTGTTT 58.362 29.630 0.00 0.00 31.77 2.83
4423 7190 8.177119 TCTAAATGTGAATTAGCCAAACTGTT 57.823 30.769 0.00 0.00 31.77 3.16
4424 7191 7.759489 TCTAAATGTGAATTAGCCAAACTGT 57.241 32.000 0.00 0.00 31.77 3.55
4425 7192 8.246180 ACATCTAAATGTGAATTAGCCAAACTG 58.754 33.333 0.00 0.00 44.51 3.16
4426 7193 8.353423 ACATCTAAATGTGAATTAGCCAAACT 57.647 30.769 0.00 0.00 44.51 2.66
4427 7194 8.986477 AACATCTAAATGTGAATTAGCCAAAC 57.014 30.769 0.00 0.00 45.48 2.93
4428 7195 9.995003 AAAACATCTAAATGTGAATTAGCCAAA 57.005 25.926 0.00 0.00 45.48 3.28
4429 7196 9.995003 AAAAACATCTAAATGTGAATTAGCCAA 57.005 25.926 0.00 0.00 45.48 4.52
4454 7221 9.392506 TGGGAGATTAGATATGACATCCTTAAA 57.607 33.333 0.00 0.00 0.00 1.52
4455 7222 8.972662 TGGGAGATTAGATATGACATCCTTAA 57.027 34.615 0.00 0.00 0.00 1.85
4457 7224 9.566331 TTATGGGAGATTAGATATGACATCCTT 57.434 33.333 0.00 0.00 0.00 3.36
4458 7225 9.566331 TTTATGGGAGATTAGATATGACATCCT 57.434 33.333 0.00 0.00 0.00 3.24
4467 7234 9.944376 GCTGTGTTATTTATGGGAGATTAGATA 57.056 33.333 0.00 0.00 0.00 1.98
4468 7235 8.439971 TGCTGTGTTATTTATGGGAGATTAGAT 58.560 33.333 0.00 0.00 0.00 1.98
4469 7236 7.801104 TGCTGTGTTATTTATGGGAGATTAGA 58.199 34.615 0.00 0.00 0.00 2.10
4470 7237 8.345565 GTTGCTGTGTTATTTATGGGAGATTAG 58.654 37.037 0.00 0.00 0.00 1.73
4471 7238 7.831690 TGTTGCTGTGTTATTTATGGGAGATTA 59.168 33.333 0.00 0.00 0.00 1.75
4472 7239 6.663093 TGTTGCTGTGTTATTTATGGGAGATT 59.337 34.615 0.00 0.00 0.00 2.40
4473 7240 6.186957 TGTTGCTGTGTTATTTATGGGAGAT 58.813 36.000 0.00 0.00 0.00 2.75
4474 7241 5.565509 TGTTGCTGTGTTATTTATGGGAGA 58.434 37.500 0.00 0.00 0.00 3.71
4475 7242 5.895636 TGTTGCTGTGTTATTTATGGGAG 57.104 39.130 0.00 0.00 0.00 4.30
4476 7243 5.184864 CCTTGTTGCTGTGTTATTTATGGGA 59.815 40.000 0.00 0.00 0.00 4.37
4477 7244 5.184864 TCCTTGTTGCTGTGTTATTTATGGG 59.815 40.000 0.00 0.00 0.00 4.00
4478 7245 6.266168 TCCTTGTTGCTGTGTTATTTATGG 57.734 37.500 0.00 0.00 0.00 2.74
4479 7246 8.586570 TTTTCCTTGTTGCTGTGTTATTTATG 57.413 30.769 0.00 0.00 0.00 1.90
4527 7294 2.349580 CGTCATGTCCACTATGCTTGTG 59.650 50.000 0.00 0.00 35.39 3.33
4528 7295 2.028112 ACGTCATGTCCACTATGCTTGT 60.028 45.455 0.00 0.00 0.00 3.16
4529 7296 2.621338 ACGTCATGTCCACTATGCTTG 58.379 47.619 0.00 0.00 0.00 4.01
4530 7297 3.334583 AACGTCATGTCCACTATGCTT 57.665 42.857 0.00 0.00 0.00 3.91
4531 7298 3.699538 TCTAACGTCATGTCCACTATGCT 59.300 43.478 0.00 0.00 0.00 3.79
4532 7299 4.041740 TCTAACGTCATGTCCACTATGC 57.958 45.455 0.00 0.00 0.00 3.14
4533 7300 5.460091 CACATCTAACGTCATGTCCACTATG 59.540 44.000 5.08 0.00 30.48 2.23
4534 7301 5.359860 TCACATCTAACGTCATGTCCACTAT 59.640 40.000 5.08 0.00 30.48 2.12
4535 7302 4.703093 TCACATCTAACGTCATGTCCACTA 59.297 41.667 5.08 0.00 30.48 2.74
4536 7303 3.509967 TCACATCTAACGTCATGTCCACT 59.490 43.478 5.08 0.00 30.48 4.00
4537 7304 3.612860 GTCACATCTAACGTCATGTCCAC 59.387 47.826 5.08 2.88 30.48 4.02
4538 7305 3.257127 TGTCACATCTAACGTCATGTCCA 59.743 43.478 5.08 3.58 30.48 4.02
4539 7306 3.845178 TGTCACATCTAACGTCATGTCC 58.155 45.455 5.08 1.54 30.48 4.02
4540 7307 6.291112 CGTTATGTCACATCTAACGTCATGTC 60.291 42.308 15.00 0.00 41.51 3.06
4541 7308 5.515270 CGTTATGTCACATCTAACGTCATGT 59.485 40.000 15.00 0.00 41.51 3.21
4542 7309 5.741982 TCGTTATGTCACATCTAACGTCATG 59.258 40.000 20.17 0.00 44.79 3.07
4543 7310 5.886992 TCGTTATGTCACATCTAACGTCAT 58.113 37.500 20.17 0.00 44.79 3.06
4544 7311 5.299582 TCGTTATGTCACATCTAACGTCA 57.700 39.130 20.17 4.92 44.79 4.35
4545 7312 5.742453 ACATCGTTATGTCACATCTAACGTC 59.258 40.000 20.17 0.00 42.92 4.34
4546 7313 5.647589 ACATCGTTATGTCACATCTAACGT 58.352 37.500 20.17 9.26 42.92 3.99
4559 7326 8.357796 ACACATCTAGATTTGACATCGTTATG 57.642 34.615 22.67 2.68 39.17 1.90
4560 7327 7.653713 GGACACATCTAGATTTGACATCGTTAT 59.346 37.037 22.67 0.00 0.00 1.89
4561 7328 6.978659 GGACACATCTAGATTTGACATCGTTA 59.021 38.462 22.67 0.00 0.00 3.18
4562 7329 5.812642 GGACACATCTAGATTTGACATCGTT 59.187 40.000 22.67 1.34 0.00 3.85
4563 7330 5.127845 AGGACACATCTAGATTTGACATCGT 59.872 40.000 22.67 10.45 0.00 3.73
4564 7331 5.595885 AGGACACATCTAGATTTGACATCG 58.404 41.667 22.67 3.71 0.00 3.84
4565 7332 7.865385 GTCTAGGACACATCTAGATTTGACATC 59.135 40.741 22.67 11.37 43.25 3.06
4566 7333 7.343057 TGTCTAGGACACATCTAGATTTGACAT 59.657 37.037 22.67 16.96 43.25 3.06
4567 7334 6.663523 TGTCTAGGACACATCTAGATTTGACA 59.336 38.462 22.67 16.15 43.25 3.58
4568 7335 7.067615 TCTGTCTAGGACACATCTAGATTTGAC 59.932 40.741 22.67 16.85 43.25 3.18
4569 7336 7.067615 GTCTGTCTAGGACACATCTAGATTTGA 59.932 40.741 22.67 3.37 43.25 2.69
4570 7337 7.199766 GTCTGTCTAGGACACATCTAGATTTG 58.800 42.308 15.80 15.80 43.25 2.32
4571 7338 6.322712 GGTCTGTCTAGGACACATCTAGATTT 59.677 42.308 1.33 0.00 43.25 2.17
4572 7339 5.830991 GGTCTGTCTAGGACACATCTAGATT 59.169 44.000 1.33 0.00 43.25 2.40
4573 7340 5.381757 GGTCTGTCTAGGACACATCTAGAT 58.618 45.833 0.00 0.00 43.25 1.98
4574 7341 4.385421 GGGTCTGTCTAGGACACATCTAGA 60.385 50.000 0.00 0.00 37.67 2.43
4575 7342 3.886505 GGGTCTGTCTAGGACACATCTAG 59.113 52.174 0.00 0.00 37.67 2.43
4576 7343 3.268595 TGGGTCTGTCTAGGACACATCTA 59.731 47.826 0.00 0.00 41.46 1.98
4577 7344 2.043115 TGGGTCTGTCTAGGACACATCT 59.957 50.000 0.00 0.00 41.46 2.90
4578 7345 2.457598 TGGGTCTGTCTAGGACACATC 58.542 52.381 0.00 0.00 41.46 3.06
4579 7346 2.623418 TGGGTCTGTCTAGGACACAT 57.377 50.000 0.00 0.00 41.46 3.21
4581 7348 4.649674 TCAATATGGGTCTGTCTAGGACAC 59.350 45.833 0.00 0.00 37.67 3.67
4582 7349 4.878968 TCAATATGGGTCTGTCTAGGACA 58.121 43.478 0.43 0.43 40.50 4.02
4583 7350 5.871396 TTCAATATGGGTCTGTCTAGGAC 57.129 43.478 0.00 0.00 0.00 3.85
4584 7351 6.846505 AGATTTCAATATGGGTCTGTCTAGGA 59.153 38.462 0.00 0.00 0.00 2.94
4585 7352 7.016072 AGAGATTTCAATATGGGTCTGTCTAGG 59.984 40.741 0.00 0.00 0.00 3.02
4586 7353 7.961351 AGAGATTTCAATATGGGTCTGTCTAG 58.039 38.462 0.00 0.00 0.00 2.43
4587 7354 7.921041 AGAGATTTCAATATGGGTCTGTCTA 57.079 36.000 0.00 0.00 0.00 2.59
4588 7355 6.821616 AGAGATTTCAATATGGGTCTGTCT 57.178 37.500 0.00 0.00 0.00 3.41
4589 7356 8.964476 TTTAGAGATTTCAATATGGGTCTGTC 57.036 34.615 0.00 0.00 0.00 3.51
4590 7357 9.927081 ATTTTAGAGATTTCAATATGGGTCTGT 57.073 29.630 0.00 0.00 0.00 3.41
4717 7484 6.771267 AGTATAGTTAATGGGCTTTAACCAGC 59.229 38.462 15.28 0.00 41.09 4.85
4722 7517 6.066032 GGGCAGTATAGTTAATGGGCTTTAA 58.934 40.000 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.