Multiple sequence alignment - TraesCS2A01G441300

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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 TraesCS2A01G441300 chr2A 100.000 3920 0 0 1 3920 691235027 691238946 0.000000e+00 7239.0
1 TraesCS2A01G441300 chr2A 92.121 165 11 2 3124 3286 35896207 35896371 8.470000e-57 231.0
2 TraesCS2A01G441300 chr2A 77.953 127 24 4 235 358 587166339 587166464 4.200000e-10 76.8
3 TraesCS2A01G441300 chr2D 83.675 2977 281 97 237 3124 547613375 547610515 0.000000e+00 2615.0
4 TraesCS2A01G441300 chr2B 83.798 2222 172 74 1 2163 653917478 653915386 0.000000e+00 1936.0
5 TraesCS2A01G441300 chr2B 92.474 970 54 6 2161 3124 653915258 653914302 0.000000e+00 1369.0
6 TraesCS2A01G441300 chr6A 96.535 635 22 0 3286 3920 593296669 593296035 0.000000e+00 1051.0
7 TraesCS2A01G441300 chr6A 83.758 745 54 31 942 1673 54666097 54666787 0.000000e+00 643.0
8 TraesCS2A01G441300 chr6A 93.865 163 9 1 3125 3286 98465611 98465449 1.090000e-60 244.0
9 TraesCS2A01G441300 chr3D 96.123 619 18 5 3303 3920 105111763 105112376 0.000000e+00 1005.0
10 TraesCS2A01G441300 chr4A 94.219 640 29 7 3286 3920 468605903 468606539 0.000000e+00 970.0
11 TraesCS2A01G441300 chr4A 75.484 155 26 5 178 321 711243154 711243307 9.090000e-07 65.8
12 TraesCS2A01G441300 chr5A 93.157 643 34 5 3286 3920 548678439 548677799 0.000000e+00 935.0
13 TraesCS2A01G441300 chr5A 93.413 167 9 2 3121 3286 522127775 522127610 3.030000e-61 246.0
14 TraesCS2A01G441300 chr3B 93.355 617 33 7 3306 3920 817282535 817281925 0.000000e+00 905.0
15 TraesCS2A01G441300 chr6B 89.050 621 57 8 3303 3920 648180808 648181420 0.000000e+00 760.0
16 TraesCS2A01G441300 chr7B 88.960 625 51 14 3303 3920 697051587 697052200 0.000000e+00 756.0
17 TraesCS2A01G441300 chr1B 88.907 622 58 10 3303 3920 653263106 653262492 0.000000e+00 756.0
18 TraesCS2A01G441300 chr1B 88.585 622 60 9 3303 3920 473059574 473060188 0.000000e+00 745.0
19 TraesCS2A01G441300 chr1D 90.214 327 15 9 1336 1654 480516453 480516770 1.010000e-110 411.0
20 TraesCS2A01G441300 chr1D 86.713 143 8 4 1145 1287 480516213 480516344 8.780000e-32 148.0
21 TraesCS2A01G441300 chr4B 95.092 163 6 2 3125 3286 53569718 53569557 5.030000e-64 255.0
22 TraesCS2A01G441300 chr1A 95.092 163 6 2 3125 3286 500064854 500065015 5.030000e-64 255.0
23 TraesCS2A01G441300 chr7A 94.512 164 8 1 3124 3286 20510160 20509997 6.500000e-63 252.0
24 TraesCS2A01G441300 chr7D 94.479 163 8 1 3125 3286 36122740 36122902 2.340000e-62 250.0
25 TraesCS2A01G441300 chr5B 94.479 163 8 1 3125 3286 662567198 662567036 2.340000e-62 250.0
26 TraesCS2A01G441300 chr3A 92.771 166 11 1 3121 3285 582316639 582316474 5.060000e-59 239.0


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 TraesCS2A01G441300 chr2A 691235027 691238946 3919 False 7239.0 7239 100.0000 1 3920 1 chr2A.!!$F3 3919
1 TraesCS2A01G441300 chr2D 547610515 547613375 2860 True 2615.0 2615 83.6750 237 3124 1 chr2D.!!$R1 2887
2 TraesCS2A01G441300 chr2B 653914302 653917478 3176 True 1652.5 1936 88.1360 1 3124 2 chr2B.!!$R1 3123
3 TraesCS2A01G441300 chr6A 593296035 593296669 634 True 1051.0 1051 96.5350 3286 3920 1 chr6A.!!$R2 634
4 TraesCS2A01G441300 chr6A 54666097 54666787 690 False 643.0 643 83.7580 942 1673 1 chr6A.!!$F1 731
5 TraesCS2A01G441300 chr3D 105111763 105112376 613 False 1005.0 1005 96.1230 3303 3920 1 chr3D.!!$F1 617
6 TraesCS2A01G441300 chr4A 468605903 468606539 636 False 970.0 970 94.2190 3286 3920 1 chr4A.!!$F1 634
7 TraesCS2A01G441300 chr5A 548677799 548678439 640 True 935.0 935 93.1570 3286 3920 1 chr5A.!!$R2 634
8 TraesCS2A01G441300 chr3B 817281925 817282535 610 True 905.0 905 93.3550 3306 3920 1 chr3B.!!$R1 614
9 TraesCS2A01G441300 chr6B 648180808 648181420 612 False 760.0 760 89.0500 3303 3920 1 chr6B.!!$F1 617
10 TraesCS2A01G441300 chr7B 697051587 697052200 613 False 756.0 756 88.9600 3303 3920 1 chr7B.!!$F1 617
11 TraesCS2A01G441300 chr1B 653262492 653263106 614 True 756.0 756 88.9070 3303 3920 1 chr1B.!!$R1 617
12 TraesCS2A01G441300 chr1B 473059574 473060188 614 False 745.0 745 88.5850 3303 3920 1 chr1B.!!$F1 617
13 TraesCS2A01G441300 chr1D 480516213 480516770 557 False 279.5 411 88.4635 1145 1654 2 chr1D.!!$F1 509


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
973 1021 0.098376 CCTTGCTTGATCTTGCGAGC 59.902 55.0 17.00 0.0 44.02 5.03 F
1716 1844 0.604578 TCCAAGCTTGCCATCTTTGC 59.395 50.0 21.43 0.0 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2656 2974 0.247736 AAGTCCGTCAGCTGTGATCC 59.752 55.0 14.67 0.49 34.36 3.36 R
3658 4004 0.035439 AGAACATAGTTGGTGCGGGG 60.035 55.0 0.00 0.00 0.00 5.73 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
28 29 4.078516 GGCACCGCGACCTAGGTT 62.079 66.667 17.53 0.00 39.00 3.50
29 30 2.047560 GCACCGCGACCTAGGTTT 60.048 61.111 17.53 0.00 39.00 3.27
36 37 0.451783 GCGACCTAGGTTTGCATTGG 59.548 55.000 26.52 3.58 32.52 3.16
37 38 1.821216 CGACCTAGGTTTGCATTGGT 58.179 50.000 17.53 0.00 37.24 3.67
42 43 1.302383 TAGGTTTGCATTGGTCGCGG 61.302 55.000 6.13 0.00 0.00 6.46
66 67 2.523168 TCCACACGGCACAGGAGA 60.523 61.111 0.00 0.00 0.00 3.71
68 69 1.227823 CCACACGGCACAGGAGAAA 60.228 57.895 0.00 0.00 0.00 2.52
69 70 1.230635 CCACACGGCACAGGAGAAAG 61.231 60.000 0.00 0.00 0.00 2.62
70 71 1.598130 ACACGGCACAGGAGAAAGC 60.598 57.895 0.00 0.00 0.00 3.51
71 72 2.357517 ACGGCACAGGAGAAAGCG 60.358 61.111 0.00 0.00 0.00 4.68
72 73 3.121030 CGGCACAGGAGAAAGCGG 61.121 66.667 0.00 0.00 0.00 5.52
94 95 2.373707 GGCTCCTCCATGAGTGCCT 61.374 63.158 14.23 0.00 41.05 4.75
99 100 4.100084 TCCATGAGTGCCTGGCGG 62.100 66.667 14.98 7.96 32.30 6.13
146 147 2.587889 CCCTACGGCCGTTGGAAT 59.412 61.111 46.24 22.97 42.22 3.01
149 150 0.179056 CCTACGGCCGTTGGAATGAT 60.179 55.000 43.69 17.99 42.22 2.45
155 156 0.373716 GCCGTTGGAATGATGACGAC 59.626 55.000 0.00 0.00 37.69 4.34
160 161 2.223537 TGGAATGATGACGACGATGG 57.776 50.000 0.00 0.00 0.00 3.51
163 164 2.138320 GAATGATGACGACGATGGCAT 58.862 47.619 0.00 0.00 0.00 4.40
164 165 3.317150 GAATGATGACGACGATGGCATA 58.683 45.455 0.00 0.00 0.00 3.14
165 166 2.422276 TGATGACGACGATGGCATAG 57.578 50.000 0.00 2.16 0.00 2.23
166 167 1.953686 TGATGACGACGATGGCATAGA 59.046 47.619 14.76 0.00 0.00 1.98
167 168 2.287608 TGATGACGACGATGGCATAGAC 60.288 50.000 14.76 7.28 0.00 2.59
169 170 0.660595 GACGACGATGGCATAGACGG 60.661 60.000 27.86 15.04 0.00 4.79
170 171 2.016704 CGACGATGGCATAGACGGC 61.017 63.158 20.37 12.64 0.00 5.68
171 172 2.016704 GACGATGGCATAGACGGCG 61.017 63.158 14.76 4.80 0.00 6.46
172 173 2.335011 CGATGGCATAGACGGCGA 59.665 61.111 16.62 0.00 0.00 5.54
173 174 1.299850 CGATGGCATAGACGGCGAA 60.300 57.895 16.62 0.00 0.00 4.70
174 175 1.278172 CGATGGCATAGACGGCGAAG 61.278 60.000 16.62 0.00 0.00 3.79
175 176 0.946221 GATGGCATAGACGGCGAAGG 60.946 60.000 16.62 0.87 0.00 3.46
206 207 1.808390 CCAAGGCGGCTACGTGTAC 60.808 63.158 13.71 0.00 43.45 2.90
207 208 2.156446 CAAGGCGGCTACGTGTACG 61.156 63.158 13.71 2.43 43.45 3.67
227 228 1.513586 GGTCGTCGTCCGCTACAAG 60.514 63.158 0.00 0.00 36.19 3.16
232 233 1.135859 CGTCGTCCGCTACAAGTTAGT 60.136 52.381 0.00 0.00 0.00 2.24
235 236 2.417933 TCGTCCGCTACAAGTTAGTCTC 59.582 50.000 0.00 0.00 0.00 3.36
242 243 6.208204 TCCGCTACAAGTTAGTCTCTTTTAGT 59.792 38.462 0.00 0.00 31.67 2.24
258 259 7.497909 TCTCTTTTAGTTTTCAGTTGATCGGTT 59.502 33.333 0.00 0.00 0.00 4.44
266 267 8.023128 AGTTTTCAGTTGATCGGTTGAAATATG 58.977 33.333 14.91 0.00 38.77 1.78
267 268 6.435430 TTCAGTTGATCGGTTGAAATATGG 57.565 37.500 3.87 0.00 0.00 2.74
271 272 4.495690 TGATCGGTTGAAATATGGTCCA 57.504 40.909 0.00 0.00 0.00 4.02
325 326 7.963981 TGAAATCTGTCGTGTTTGATAAGATC 58.036 34.615 0.00 0.00 0.00 2.75
334 335 5.051441 CGTGTTTGATAAGATCTGTCCGATG 60.051 44.000 0.00 0.00 30.84 3.84
336 337 6.978659 GTGTTTGATAAGATCTGTCCGATGTA 59.021 38.462 0.00 0.00 30.84 2.29
385 386 4.966965 ATATGGTTAGATAGTCGGCTCG 57.033 45.455 0.00 0.00 0.00 5.03
386 387 2.336945 TGGTTAGATAGTCGGCTCGA 57.663 50.000 0.00 0.00 0.00 4.04
398 399 0.798776 CGGCTCGAGCATCACTTTTT 59.201 50.000 36.27 0.00 44.36 1.94
399 400 1.201965 CGGCTCGAGCATCACTTTTTC 60.202 52.381 36.27 15.34 44.36 2.29
402 403 1.394917 CTCGAGCATCACTTTTTCCGG 59.605 52.381 0.00 0.00 33.17 5.14
408 409 2.749621 GCATCACTTTTTCCGGACTGAT 59.250 45.455 1.83 2.74 0.00 2.90
423 424 2.582498 GATTCTCACCGGTCCGCG 60.582 66.667 2.59 0.00 0.00 6.46
457 458 2.036089 GTCCTATCCAGGGATCAACGTC 59.964 54.545 3.62 0.00 42.87 4.34
483 484 1.742880 CCATGAGTGGTGAGCGGTG 60.743 63.158 0.00 0.00 40.83 4.94
486 487 1.471829 ATGAGTGGTGAGCGGTGACA 61.472 55.000 6.53 0.00 0.00 3.58
507 516 2.304180 AGATGCTATGGGATGTGCTACC 59.696 50.000 0.00 0.00 0.00 3.18
508 517 1.806496 TGCTATGGGATGTGCTACCT 58.194 50.000 0.00 0.00 0.00 3.08
509 518 2.970987 TGCTATGGGATGTGCTACCTA 58.029 47.619 0.00 0.00 0.00 3.08
510 519 2.632996 TGCTATGGGATGTGCTACCTAC 59.367 50.000 0.00 0.00 0.00 3.18
511 520 2.352814 GCTATGGGATGTGCTACCTACG 60.353 54.545 0.00 0.00 0.00 3.51
512 521 2.082140 ATGGGATGTGCTACCTACGA 57.918 50.000 0.00 0.00 0.00 3.43
513 522 1.108776 TGGGATGTGCTACCTACGAC 58.891 55.000 0.00 0.00 0.00 4.34
549 558 0.110509 AGCGTCACACACTACGTACG 60.111 55.000 15.01 15.01 41.10 3.67
570 579 2.049433 GACGTACGCAGCCACAGT 60.049 61.111 16.72 0.00 0.00 3.55
571 580 1.663702 GACGTACGCAGCCACAGTT 60.664 57.895 16.72 0.00 0.00 3.16
572 581 1.886861 GACGTACGCAGCCACAGTTG 61.887 60.000 16.72 0.00 0.00 3.16
574 583 1.597027 GTACGCAGCCACAGTTGGT 60.597 57.895 0.00 0.00 45.98 3.67
575 584 1.147376 TACGCAGCCACAGTTGGTT 59.853 52.632 0.00 0.00 45.98 3.67
576 585 0.393448 TACGCAGCCACAGTTGGTTA 59.607 50.000 0.00 0.00 45.98 2.85
577 586 1.164041 ACGCAGCCACAGTTGGTTAC 61.164 55.000 0.00 0.00 45.98 2.50
766 799 2.026542 ACAGACACATGACATGATGCCT 60.027 45.455 22.19 10.87 0.00 4.75
767 800 3.014623 CAGACACATGACATGATGCCTT 58.985 45.455 22.19 0.00 0.00 4.35
768 801 3.014623 AGACACATGACATGATGCCTTG 58.985 45.455 22.19 10.69 0.00 3.61
769 802 1.475280 ACACATGACATGATGCCTTGC 59.525 47.619 22.19 0.00 0.00 4.01
770 803 1.474879 CACATGACATGATGCCTTGCA 59.525 47.619 22.19 0.00 44.86 4.08
771 804 1.475280 ACATGACATGATGCCTTGCAC 59.525 47.619 22.19 0.00 43.04 4.57
772 805 1.108776 ATGACATGATGCCTTGCACC 58.891 50.000 0.00 0.00 43.04 5.01
801 842 2.822399 CCACCATCTCCGCTACCC 59.178 66.667 0.00 0.00 0.00 3.69
840 881 0.315568 CCGGATCGAACATCTCTCCC 59.684 60.000 0.00 0.00 0.00 4.30
872 913 1.529152 TTGTCCTCGCGTAGGCTTCA 61.529 55.000 16.74 13.00 46.10 3.02
888 929 2.599848 GCTTCACACTTGCACAACGTAG 60.600 50.000 0.00 0.00 0.00 3.51
925 966 1.701847 ACCACCTCAGTCAGCAAGATT 59.298 47.619 0.00 0.00 0.00 2.40
939 980 3.558505 GCAAGATTGCGTTATATGCTGG 58.441 45.455 1.16 0.00 45.11 4.85
942 983 5.277779 GCAAGATTGCGTTATATGCTGGTAA 60.278 40.000 1.16 0.00 45.11 2.85
954 1002 0.176910 GCTGGTAAGGAGGAGCTCAC 59.823 60.000 17.19 8.81 31.08 3.51
970 1018 1.129998 CTCACCTTGCTTGATCTTGCG 59.870 52.381 0.00 0.00 0.00 4.85
973 1021 0.098376 CCTTGCTTGATCTTGCGAGC 59.902 55.000 17.00 0.00 44.02 5.03
984 1032 4.680237 TGCGAGCACAGGGGAACG 62.680 66.667 0.00 0.00 0.00 3.95
1056 1104 4.586235 GGTGGTGCTGGTGCTGGT 62.586 66.667 0.00 0.00 40.48 4.00
1057 1105 3.289834 GTGGTGCTGGTGCTGGTG 61.290 66.667 0.00 0.00 40.48 4.17
1061 1109 4.960866 TGCTGGTGCTGGTGCTGG 62.961 66.667 0.00 0.00 40.48 4.85
1068 1116 4.962836 GCTGGTGCTGGTGCTGGT 62.963 66.667 0.00 0.00 40.48 4.00
1222 1270 2.041928 CTCCTCCTTCCCCCTGCT 59.958 66.667 0.00 0.00 0.00 4.24
1223 1271 2.041265 TCCTCCTTCCCCCTGCTC 59.959 66.667 0.00 0.00 0.00 4.26
1224 1272 3.474570 CCTCCTTCCCCCTGCTCG 61.475 72.222 0.00 0.00 0.00 5.03
1225 1273 2.685380 CTCCTTCCCCCTGCTCGT 60.685 66.667 0.00 0.00 0.00 4.18
1226 1274 2.683933 TCCTTCCCCCTGCTCGTC 60.684 66.667 0.00 0.00 0.00 4.20
1227 1275 3.003173 CCTTCCCCCTGCTCGTCA 61.003 66.667 0.00 0.00 0.00 4.35
1228 1276 2.581354 CTTCCCCCTGCTCGTCAG 59.419 66.667 1.40 1.40 42.49 3.51
1291 1347 7.785033 TGATTCATCAGCTCACTATCACTTTA 58.215 34.615 0.00 0.00 32.11 1.85
1474 1592 3.974912 TGCTCTTCGCTCATATCTCTTG 58.025 45.455 0.00 0.00 40.11 3.02
1475 1593 3.382865 TGCTCTTCGCTCATATCTCTTGT 59.617 43.478 0.00 0.00 40.11 3.16
1476 1594 3.980775 GCTCTTCGCTCATATCTCTTGTC 59.019 47.826 0.00 0.00 35.14 3.18
1477 1595 4.261572 GCTCTTCGCTCATATCTCTTGTCT 60.262 45.833 0.00 0.00 35.14 3.41
1478 1596 5.735922 GCTCTTCGCTCATATCTCTTGTCTT 60.736 44.000 0.00 0.00 35.14 3.01
1508 1626 1.419381 TTGCAGTCCAGTCCAGTGTA 58.581 50.000 0.00 0.00 0.00 2.90
1513 1631 3.154710 CAGTCCAGTCCAGTGTAGTACA 58.845 50.000 0.00 0.00 0.00 2.90
1514 1632 3.191581 CAGTCCAGTCCAGTGTAGTACAG 59.808 52.174 2.39 0.00 0.00 2.74
1515 1633 3.155501 GTCCAGTCCAGTGTAGTACAGT 58.844 50.000 2.39 3.65 30.48 3.55
1516 1634 4.042560 AGTCCAGTCCAGTGTAGTACAGTA 59.957 45.833 10.32 0.00 29.11 2.74
1517 1635 4.155644 GTCCAGTCCAGTGTAGTACAGTAC 59.844 50.000 10.32 2.05 29.11 2.73
1518 1636 3.442977 CCAGTCCAGTGTAGTACAGTACC 59.557 52.174 10.32 2.25 29.11 3.34
1525 1644 3.750130 AGTGTAGTACAGTACCACTCACG 59.250 47.826 8.95 0.00 32.69 4.35
1539 1658 1.459592 ACTCACGAATTAACACAGCGC 59.540 47.619 0.00 0.00 0.00 5.92
1605 1727 3.425162 AGAAATCCACAGACCTGGAAC 57.575 47.619 0.00 0.00 43.79 3.62
1634 1762 7.482654 CAACAATGGAGGTACACACATATAG 57.517 40.000 0.00 0.00 0.00 1.31
1702 1830 3.751698 CGTTTCCCCTTCTAAACTCCAAG 59.248 47.826 0.00 0.00 34.21 3.61
1708 1836 2.489722 CCTTCTAAACTCCAAGCTTGCC 59.510 50.000 21.43 0.00 0.00 4.52
1716 1844 0.604578 TCCAAGCTTGCCATCTTTGC 59.395 50.000 21.43 0.00 0.00 3.68
1760 1888 1.064654 GACATCAGCTTCCAAATCGGC 59.935 52.381 0.00 0.00 33.14 5.54
1822 1959 3.012274 AGACATTTCTCCTCTCCCTCTGA 59.988 47.826 0.00 0.00 0.00 3.27
1825 1962 3.260269 TTTCTCCTCTCCCTCTGAACA 57.740 47.619 0.00 0.00 0.00 3.18
1832 1969 4.168871 TCCTCTCCCTCTGAACATATCTGA 59.831 45.833 0.00 0.00 35.08 3.27
1849 1986 7.831193 ACATATCTGAGAGCAAAATACCTGTTT 59.169 33.333 0.00 0.00 0.00 2.83
1872 2009 6.494666 TTTTCTTTTGTCTACTGGGAGAGA 57.505 37.500 0.00 0.00 0.00 3.10
1888 2025 9.978044 ACTGGGAGAGATTAAAAATATACGTAC 57.022 33.333 0.00 0.00 0.00 3.67
1902 2039 9.823098 AAAATATACGTACTAGTCAATAGCGAG 57.177 33.333 0.00 0.00 34.56 5.03
1912 2049 8.223177 ACTAGTCAATAGCGAGTAACAGTATT 57.777 34.615 0.00 0.00 34.56 1.89
1920 2091 6.830114 AGCGAGTAACAGTATTTTATGAGC 57.170 37.500 0.00 0.00 0.00 4.26
1924 2095 8.979574 GCGAGTAACAGTATTTTATGAGCTTAT 58.020 33.333 0.00 0.00 0.00 1.73
1942 2113 3.918220 CTCGAAGATGCGCGCCAC 61.918 66.667 30.77 21.88 33.89 5.01
1973 2152 8.445275 TGCATTCTGTTTAGTCAACTAAAAGA 57.555 30.769 15.06 15.41 46.35 2.52
1990 2169 4.484537 AAAGACATCATGTGCTAGAGCT 57.515 40.909 0.00 0.00 42.66 4.09
2014 2193 5.857471 AACTTCTCAGAGATCATCAGGAG 57.143 43.478 0.00 0.00 34.57 3.69
2018 2197 4.463070 TCTCAGAGATCATCAGGAGTCTG 58.537 47.826 0.00 0.00 39.93 3.51
2048 2227 4.581868 AGCATTATTGTTTTTGCCTGCAT 58.418 34.783 0.00 0.00 35.71 3.96
2049 2228 4.632688 AGCATTATTGTTTTTGCCTGCATC 59.367 37.500 0.00 0.00 35.71 3.91
2050 2229 4.392445 GCATTATTGTTTTTGCCTGCATCA 59.608 37.500 0.00 0.00 0.00 3.07
2089 2268 8.443937 GTGAAAGTATGGATAGAACAAACTCAC 58.556 37.037 0.00 0.00 0.00 3.51
2119 2298 7.844779 AGAAATTGGGACCAGATAGTCTAGTAA 59.155 37.037 0.00 0.00 36.95 2.24
2120 2299 7.604657 AATTGGGACCAGATAGTCTAGTAAG 57.395 40.000 0.00 0.00 36.95 2.34
2121 2300 5.728937 TGGGACCAGATAGTCTAGTAAGT 57.271 43.478 0.00 0.00 36.95 2.24
2122 2301 6.836714 TGGGACCAGATAGTCTAGTAAGTA 57.163 41.667 0.00 0.00 36.95 2.24
2153 2332 9.025041 TGAAAAGTGAGATCTGATCAGTAGTTA 57.975 33.333 21.92 2.94 30.14 2.24
2189 2498 4.378874 GCAAGTACTAGCTTTTCTTGGCTG 60.379 45.833 16.39 0.00 39.31 4.85
2254 2563 7.483580 AGTTTCTTATACAGAGGCACTAAGT 57.516 36.000 0.00 0.00 41.55 2.24
2265 2574 6.069963 ACAGAGGCACTAAGTTGAAATCCTAT 60.070 38.462 0.00 0.00 41.55 2.57
2314 2626 6.073765 GCGTCTTCTATGTGTCTTTTTCTTCA 60.074 38.462 0.00 0.00 0.00 3.02
2319 2631 7.496529 TCTATGTGTCTTTTTCTTCAGTTGG 57.503 36.000 0.00 0.00 0.00 3.77
2336 2648 7.337480 TCAGTTGGGATTGTATGATGATTTG 57.663 36.000 0.00 0.00 0.00 2.32
2369 2681 9.993881 CATTTCGAAAACATTTCTTATGTGAAC 57.006 29.630 15.66 0.00 31.80 3.18
2430 2742 3.199880 CAGGTCCAAAGAGAACTGTGT 57.800 47.619 0.00 0.00 44.95 3.72
2487 2799 8.634444 CACTGCTTATACTCCTAAACTCTGTAT 58.366 37.037 0.00 0.00 0.00 2.29
2656 2974 2.158957 TCTGCTGGCCTAGAAAATACCG 60.159 50.000 3.32 0.00 0.00 4.02
2667 2985 3.535561 AGAAAATACCGGATCACAGCTG 58.464 45.455 13.48 13.48 0.00 4.24
2676 2994 1.338200 GGATCACAGCTGACGGACTTT 60.338 52.381 23.35 0.00 0.00 2.66
2682 3000 2.069273 CAGCTGACGGACTTTAACCTG 58.931 52.381 8.42 0.00 0.00 4.00
2731 3049 4.085357 ACACAGGTGTATGAAGAAAGCA 57.915 40.909 2.68 0.00 42.90 3.91
2841 3159 0.478072 AGAGTGTCAAATGCACCCCA 59.522 50.000 0.00 0.00 37.56 4.96
2942 3261 8.669243 GTGAGTTAAATCTGAAGATTAACCAGG 58.331 37.037 5.99 0.00 43.41 4.45
2958 3277 5.885449 AACCAGGAGAGGAAATAGAGATG 57.115 43.478 0.00 0.00 0.00 2.90
3018 3338 8.088365 ACTGTTTGCTATTAGAATTTGTTTCCC 58.912 33.333 0.00 0.00 34.67 3.97
3019 3339 7.382898 TGTTTGCTATTAGAATTTGTTTCCCC 58.617 34.615 0.00 0.00 34.67 4.81
3034 3354 2.662596 CCCGTGGCAGTGCTTAGA 59.337 61.111 16.11 0.00 0.00 2.10
3044 3364 3.009723 GCAGTGCTTAGAATGCTTGGTA 58.990 45.455 8.18 0.00 35.78 3.25
3066 3386 6.262273 GGTAACAAGTTTGAATTCCTCTGTGA 59.738 38.462 2.27 0.00 0.00 3.58
3111 3431 0.169672 CATGAACGCTTGAAGCCTGG 59.830 55.000 12.13 0.00 38.18 4.45
3124 3444 5.152623 TGAAGCCTGGTAGTATATGCATC 57.847 43.478 0.19 0.00 0.00 3.91
3125 3445 4.592778 TGAAGCCTGGTAGTATATGCATCA 59.407 41.667 0.19 0.00 0.00 3.07
3126 3446 4.815533 AGCCTGGTAGTATATGCATCAG 57.184 45.455 0.19 2.04 0.00 2.90
3127 3447 3.517100 AGCCTGGTAGTATATGCATCAGG 59.483 47.826 19.17 19.17 42.13 3.86
3128 3448 3.369892 GCCTGGTAGTATATGCATCAGGG 60.370 52.174 22.76 10.20 40.25 4.45
3129 3449 3.369892 CCTGGTAGTATATGCATCAGGGC 60.370 52.174 16.79 0.80 37.30 5.19
3130 3450 2.571653 TGGTAGTATATGCATCAGGGCC 59.428 50.000 0.19 0.00 0.00 5.80
3131 3451 2.418746 GGTAGTATATGCATCAGGGCCG 60.419 54.545 0.19 0.00 0.00 6.13
3132 3452 1.352083 AGTATATGCATCAGGGCCGT 58.648 50.000 0.19 0.00 0.00 5.68
3133 3453 1.699634 AGTATATGCATCAGGGCCGTT 59.300 47.619 0.19 0.00 0.00 4.44
3134 3454 2.076863 GTATATGCATCAGGGCCGTTC 58.923 52.381 0.19 0.00 0.00 3.95
3135 3455 0.250901 ATATGCATCAGGGCCGTTCC 60.251 55.000 0.19 0.00 0.00 3.62
3136 3456 1.344953 TATGCATCAGGGCCGTTCCT 61.345 55.000 0.19 0.00 37.71 3.36
3144 3464 2.640316 AGGGCCGTTCCTGATATTTC 57.360 50.000 0.00 0.00 35.47 2.17
3145 3465 1.202651 AGGGCCGTTCCTGATATTTCG 60.203 52.381 0.00 0.00 35.47 3.46
3146 3466 1.226746 GGCCGTTCCTGATATTTCGG 58.773 55.000 0.00 0.00 40.72 4.30
3148 3468 1.878953 CCGTTCCTGATATTTCGGGG 58.121 55.000 10.75 0.73 46.93 5.73
3149 3469 1.542547 CCGTTCCTGATATTTCGGGGG 60.543 57.143 10.75 1.52 46.93 5.40
3150 3470 1.605753 GTTCCTGATATTTCGGGGGC 58.394 55.000 10.75 1.58 46.93 5.80
3151 3471 0.476771 TTCCTGATATTTCGGGGGCC 59.523 55.000 10.75 0.00 46.93 5.80
3152 3472 1.074951 CCTGATATTTCGGGGGCCC 59.925 63.158 15.76 15.76 43.74 5.80
3153 3473 1.715019 CCTGATATTTCGGGGGCCCA 61.715 60.000 26.86 3.15 43.74 5.36
3154 3474 0.250901 CTGATATTTCGGGGGCCCAG 60.251 60.000 26.86 22.31 35.37 4.45
3155 3475 1.074951 GATATTTCGGGGGCCCAGG 59.925 63.158 26.86 16.13 35.37 4.45
3156 3476 2.426305 GATATTTCGGGGGCCCAGGG 62.426 65.000 26.86 13.27 35.37 4.45
3166 3486 4.329831 GCCCAGGGCGAAATTACA 57.670 55.556 17.05 0.00 39.62 2.41
3167 3487 2.573920 GCCCAGGGCGAAATTACAA 58.426 52.632 17.05 0.00 39.62 2.41
3168 3488 0.172578 GCCCAGGGCGAAATTACAAC 59.827 55.000 17.05 0.00 39.62 3.32
3169 3489 0.815095 CCCAGGGCGAAATTACAACC 59.185 55.000 0.00 0.00 0.00 3.77
3170 3490 0.815095 CCAGGGCGAAATTACAACCC 59.185 55.000 0.00 0.00 41.17 4.11
3171 3491 1.540267 CAGGGCGAAATTACAACCCA 58.460 50.000 8.10 0.00 43.47 4.51
3172 3492 1.472480 CAGGGCGAAATTACAACCCAG 59.528 52.381 8.10 0.00 43.47 4.45
3173 3493 0.815095 GGGCGAAATTACAACCCAGG 59.185 55.000 0.00 0.00 40.52 4.45
3174 3494 0.815095 GGCGAAATTACAACCCAGGG 59.185 55.000 2.85 2.85 0.00 4.45
3175 3495 0.172578 GCGAAATTACAACCCAGGGC 59.827 55.000 4.91 0.00 0.00 5.19
3176 3496 0.815095 CGAAATTACAACCCAGGGCC 59.185 55.000 4.91 0.00 0.00 5.80
3177 3497 1.191535 GAAATTACAACCCAGGGCCC 58.808 55.000 16.46 16.46 0.00 5.80
3178 3498 0.252513 AAATTACAACCCAGGGCCCC 60.253 55.000 21.43 0.00 0.00 5.80
3179 3499 1.153041 AATTACAACCCAGGGCCCCT 61.153 55.000 21.43 0.00 0.00 4.79
3180 3500 0.253915 ATTACAACCCAGGGCCCCTA 60.254 55.000 21.43 0.00 29.64 3.53
3181 3501 1.209523 TTACAACCCAGGGCCCCTAC 61.210 60.000 21.43 0.00 29.64 3.18
3182 3502 2.127685 TACAACCCAGGGCCCCTACT 62.128 60.000 21.43 0.00 29.64 2.57
3183 3503 1.307517 CAACCCAGGGCCCCTACTA 60.308 63.158 21.43 0.00 29.64 1.82
3184 3504 0.697854 CAACCCAGGGCCCCTACTAT 60.698 60.000 21.43 0.00 29.64 2.12
3185 3505 0.954203 AACCCAGGGCCCCTACTATA 59.046 55.000 21.43 0.00 29.64 1.31
3186 3506 0.954203 ACCCAGGGCCCCTACTATAA 59.046 55.000 21.43 0.00 29.64 0.98
3187 3507 1.299005 ACCCAGGGCCCCTACTATAAA 59.701 52.381 21.43 0.00 29.64 1.40
3188 3508 1.985895 CCCAGGGCCCCTACTATAAAG 59.014 57.143 21.43 0.00 29.64 1.85
3189 3509 2.428783 CCCAGGGCCCCTACTATAAAGA 60.429 54.545 21.43 0.00 29.64 2.52
3190 3510 3.532102 CCAGGGCCCCTACTATAAAGAT 58.468 50.000 21.43 0.00 29.64 2.40
3191 3511 4.514050 CCCAGGGCCCCTACTATAAAGATA 60.514 50.000 21.43 0.00 29.64 1.98
3192 3512 5.098663 CCAGGGCCCCTACTATAAAGATAA 58.901 45.833 21.43 0.00 29.64 1.75
3193 3513 5.550403 CCAGGGCCCCTACTATAAAGATAAA 59.450 44.000 21.43 0.00 29.64 1.40
3194 3514 6.045106 CCAGGGCCCCTACTATAAAGATAAAA 59.955 42.308 21.43 0.00 29.64 1.52
3195 3515 7.422089 CCAGGGCCCCTACTATAAAGATAAAAA 60.422 40.741 21.43 0.00 29.64 1.94
3196 3516 8.170730 CAGGGCCCCTACTATAAAGATAAAAAT 58.829 37.037 21.43 0.00 29.64 1.82
3197 3517 9.414449 AGGGCCCCTACTATAAAGATAAAAATA 57.586 33.333 21.43 0.00 28.47 1.40
3534 3878 2.143122 CGCCTTTCGCACATGGTATAT 58.857 47.619 0.00 0.00 37.30 0.86
3569 3913 4.393990 TCTTCATCACGTCTAGTTCGCTAA 59.606 41.667 9.22 0.00 0.00 3.09
3613 3959 3.036429 GCCGCCATGTCCTCCTCTT 62.036 63.158 0.00 0.00 0.00 2.85
3615 3961 1.333636 CCGCCATGTCCTCCTCTTCT 61.334 60.000 0.00 0.00 0.00 2.85
3618 3964 0.179089 CCATGTCCTCCTCTTCTGCG 60.179 60.000 0.00 0.00 0.00 5.18
3658 4004 3.509740 GGTCAAGTTACCGAGAAGCTAC 58.490 50.000 0.00 0.00 0.00 3.58
3775 4121 1.143183 AAGCACGTCGTCACCAAGT 59.857 52.632 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.388232 GCAAACCTAGGTCGCGGTG 61.388 63.158 16.64 9.67 32.86 4.94
18 19 1.737793 GACCAATGCAAACCTAGGTCG 59.262 52.381 16.64 10.95 36.55 4.79
19 20 1.737793 CGACCAATGCAAACCTAGGTC 59.262 52.381 16.64 3.16 41.53 3.85
20 21 1.821216 CGACCAATGCAAACCTAGGT 58.179 50.000 9.21 9.21 0.00 3.08
23 24 1.302383 CCGCGACCAATGCAAACCTA 61.302 55.000 8.23 0.00 0.00 3.08
24 25 2.625823 CCGCGACCAATGCAAACCT 61.626 57.895 8.23 0.00 0.00 3.50
48 49 2.357517 CTCCTGTGCCGTGTGGAC 60.358 66.667 0.00 0.00 37.49 4.02
49 50 1.691195 TTTCTCCTGTGCCGTGTGGA 61.691 55.000 0.00 0.00 37.49 4.02
50 51 1.227823 TTTCTCCTGTGCCGTGTGG 60.228 57.895 0.00 0.00 38.77 4.17
52 53 1.598130 GCTTTCTCCTGTGCCGTGT 60.598 57.895 0.00 0.00 0.00 4.49
58 59 1.089920 CCATTCCGCTTTCTCCTGTG 58.910 55.000 0.00 0.00 0.00 3.66
59 60 0.678048 GCCATTCCGCTTTCTCCTGT 60.678 55.000 0.00 0.00 0.00 4.00
60 61 0.393537 AGCCATTCCGCTTTCTCCTG 60.394 55.000 0.00 0.00 34.73 3.86
133 134 1.024579 GTCATCATTCCAACGGCCGT 61.025 55.000 28.70 28.70 0.00 5.68
137 138 0.645355 CGTCGTCATCATTCCAACGG 59.355 55.000 0.00 0.00 35.89 4.44
140 141 2.549926 CCATCGTCGTCATCATTCCAA 58.450 47.619 0.00 0.00 0.00 3.53
146 147 1.953686 TCTATGCCATCGTCGTCATCA 59.046 47.619 0.00 0.00 0.00 3.07
149 150 0.028902 CGTCTATGCCATCGTCGTCA 59.971 55.000 0.00 0.00 0.00 4.35
155 156 1.278172 CTTCGCCGTCTATGCCATCG 61.278 60.000 0.00 0.00 0.00 3.84
160 161 3.330853 CGCCTTCGCCGTCTATGC 61.331 66.667 0.00 0.00 0.00 3.14
163 164 4.124351 CACCGCCTTCGCCGTCTA 62.124 66.667 0.00 0.00 0.00 2.59
188 189 1.808390 GTACACGTAGCCGCCTTGG 60.808 63.158 0.00 0.00 42.50 3.61
189 190 2.156446 CGTACACGTAGCCGCCTTG 61.156 63.158 0.00 0.00 37.70 3.61
190 191 2.180017 CGTACACGTAGCCGCCTT 59.820 61.111 0.00 0.00 37.70 4.35
191 192 2.747460 TCGTACACGTAGCCGCCT 60.747 61.111 1.19 0.00 40.80 5.52
219 220 7.870588 AACTAAAAGAGACTAACTTGTAGCG 57.129 36.000 0.00 0.00 38.20 4.26
232 233 6.990349 ACCGATCAACTGAAAACTAAAAGAGA 59.010 34.615 0.00 0.00 0.00 3.10
235 236 7.414436 TCAACCGATCAACTGAAAACTAAAAG 58.586 34.615 0.00 0.00 0.00 2.27
242 243 7.040062 ACCATATTTCAACCGATCAACTGAAAA 60.040 33.333 13.82 7.13 40.21 2.29
246 247 5.220854 GGACCATATTTCAACCGATCAACTG 60.221 44.000 0.00 0.00 0.00 3.16
253 254 7.340743 ACATAAAATGGACCATATTTCAACCGA 59.659 33.333 7.59 0.00 33.60 4.69
287 288 6.128445 ACGACAGATTTCAGCATAGTTTGAAG 60.128 38.462 0.00 0.00 35.01 3.02
307 308 5.168569 GGACAGATCTTATCAAACACGACA 58.831 41.667 0.00 0.00 0.00 4.35
358 359 5.749109 GCCGACTATCTAACCATATATGCAC 59.251 44.000 7.24 0.00 0.00 4.57
360 361 6.150396 AGCCGACTATCTAACCATATATGC 57.850 41.667 7.24 0.00 0.00 3.14
363 364 5.737860 TCGAGCCGACTATCTAACCATATA 58.262 41.667 0.00 0.00 0.00 0.86
365 366 4.001652 CTCGAGCCGACTATCTAACCATA 58.998 47.826 0.00 0.00 0.00 2.74
367 368 2.219458 CTCGAGCCGACTATCTAACCA 58.781 52.381 0.00 0.00 0.00 3.67
372 373 0.878416 GATGCTCGAGCCGACTATCT 59.122 55.000 33.23 8.54 41.18 1.98
376 377 1.599606 AAGTGATGCTCGAGCCGACT 61.600 55.000 33.23 26.33 41.18 4.18
385 386 2.160417 CAGTCCGGAAAAAGTGATGCTC 59.840 50.000 5.23 0.00 0.00 4.26
386 387 2.154462 CAGTCCGGAAAAAGTGATGCT 58.846 47.619 5.23 0.00 0.00 3.79
443 444 1.141881 CTCCGACGTTGATCCCTGG 59.858 63.158 3.74 0.00 0.00 4.45
444 445 0.747255 ATCTCCGACGTTGATCCCTG 59.253 55.000 3.74 0.00 0.00 4.45
457 458 4.451241 CCACTCATGGCATCTCCG 57.549 61.111 0.00 0.00 39.82 4.63
483 484 2.149578 GCACATCCCATAGCATCTGTC 58.850 52.381 0.00 0.00 0.00 3.51
486 487 2.304180 GGTAGCACATCCCATAGCATCT 59.696 50.000 0.00 0.00 0.00 2.90
507 516 1.400846 ACACATGCCTCGTAGTCGTAG 59.599 52.381 0.00 0.00 38.33 3.51
508 517 1.131693 CACACATGCCTCGTAGTCGTA 59.868 52.381 0.00 0.00 38.33 3.43
509 518 0.109272 CACACATGCCTCGTAGTCGT 60.109 55.000 0.00 0.00 38.33 4.34
510 519 1.413767 GCACACATGCCTCGTAGTCG 61.414 60.000 0.00 0.00 46.97 4.18
511 520 2.373938 GCACACATGCCTCGTAGTC 58.626 57.895 0.00 0.00 46.97 2.59
512 521 4.598257 GCACACATGCCTCGTAGT 57.402 55.556 0.00 0.00 46.97 2.73
549 558 1.515736 GTGGCTGCGTACGTCCTAC 60.516 63.158 17.90 9.53 0.00 3.18
552 561 2.809601 CTGTGGCTGCGTACGTCC 60.810 66.667 17.90 15.46 0.00 4.79
553 562 1.663702 AACTGTGGCTGCGTACGTC 60.664 57.895 17.90 9.82 0.00 4.34
840 881 2.359967 GGACAAGGAGACGGGAGGG 61.360 68.421 0.00 0.00 0.00 4.30
872 913 1.663695 AAGCTACGTTGTGCAAGTGT 58.336 45.000 0.00 0.00 0.00 3.55
888 929 1.527433 GGTGGTGCTGGGAGAAAAGC 61.527 60.000 0.00 0.00 39.96 3.51
925 966 3.244078 CCTCCTTACCAGCATATAACGCA 60.244 47.826 0.89 0.00 0.00 5.24
936 977 0.827368 GGTGAGCTCCTCCTTACCAG 59.173 60.000 12.15 0.00 40.26 4.00
939 980 1.406205 GCAAGGTGAGCTCCTCCTTAC 60.406 57.143 28.10 22.51 44.50 2.34
942 983 0.839853 AAGCAAGGTGAGCTCCTCCT 60.840 55.000 18.17 18.17 42.53 3.69
973 1021 4.096003 ATCGGCCGTTCCCCTGTG 62.096 66.667 27.15 0.00 0.00 3.66
984 1032 1.595382 CATCTTGACCCGATCGGCC 60.595 63.158 29.12 21.23 33.26 6.13
1039 1087 4.586235 ACCAGCACCAGCACCACC 62.586 66.667 0.00 0.00 45.49 4.61
1040 1088 3.289834 CACCAGCACCAGCACCAC 61.290 66.667 0.00 0.00 45.49 4.16
1042 1090 4.962836 AGCACCAGCACCAGCACC 62.963 66.667 0.00 0.00 45.49 5.01
1043 1091 3.667282 CAGCACCAGCACCAGCAC 61.667 66.667 0.00 0.00 45.49 4.40
1044 1092 4.960866 CCAGCACCAGCACCAGCA 62.961 66.667 0.00 0.00 45.49 4.41
1045 1093 4.962836 ACCAGCACCAGCACCAGC 62.963 66.667 0.00 0.00 45.49 4.85
1046 1094 2.981909 CACCAGCACCAGCACCAG 60.982 66.667 0.00 0.00 45.49 4.00
1048 1096 4.962836 AGCACCAGCACCAGCACC 62.963 66.667 0.00 0.00 45.49 5.01
1049 1097 3.667282 CAGCACCAGCACCAGCAC 61.667 66.667 0.00 0.00 45.49 4.40
1050 1098 4.960866 CCAGCACCAGCACCAGCA 62.961 66.667 0.00 0.00 45.49 4.41
1051 1099 4.962836 ACCAGCACCAGCACCAGC 62.963 66.667 0.00 0.00 45.49 4.85
1052 1100 2.981909 CACCAGCACCAGCACCAG 60.982 66.667 0.00 0.00 45.49 4.00
1054 1102 4.962836 AGCACCAGCACCAGCACC 62.963 66.667 0.00 0.00 45.49 5.01
1055 1103 3.667282 CAGCACCAGCACCAGCAC 61.667 66.667 0.00 0.00 45.49 4.40
1056 1104 4.960866 CCAGCACCAGCACCAGCA 62.961 66.667 0.00 0.00 45.49 4.41
1222 1270 3.281395 TGGCGTGACGACTGACGA 61.281 61.111 13.72 0.00 45.77 4.20
1224 1272 2.016704 CTGTGGCGTGACGACTGAC 61.017 63.158 13.72 2.84 35.04 3.51
1225 1273 2.335011 CTGTGGCGTGACGACTGA 59.665 61.111 13.72 0.00 35.04 3.41
1226 1274 2.027605 ACTGTGGCGTGACGACTG 59.972 61.111 13.72 7.26 35.04 3.51
1227 1275 2.027605 CACTGTGGCGTGACGACT 59.972 61.111 13.72 0.00 35.04 4.18
1228 1276 3.702555 GCACTGTGGCGTGACGAC 61.703 66.667 10.10 6.49 37.06 4.34
1283 1331 5.942236 TGATGCTCAAAGAAGCTAAAGTGAT 59.058 36.000 0.00 0.00 42.94 3.06
1386 1497 1.597461 GTGGTACAGAGTGAGGCCC 59.403 63.158 0.00 0.00 41.80 5.80
1428 1545 2.682856 GTGGAGCAGAGTTGTTGAACAA 59.317 45.455 6.66 6.66 35.42 2.83
1474 1592 3.481453 ACTGCAAAAGGGAAGAGAAGAC 58.519 45.455 0.00 0.00 0.00 3.01
1475 1593 3.496870 GGACTGCAAAAGGGAAGAGAAGA 60.497 47.826 0.00 0.00 0.00 2.87
1476 1594 2.816672 GGACTGCAAAAGGGAAGAGAAG 59.183 50.000 0.00 0.00 0.00 2.85
1477 1595 2.174639 TGGACTGCAAAAGGGAAGAGAA 59.825 45.455 0.00 0.00 0.00 2.87
1478 1596 1.774254 TGGACTGCAAAAGGGAAGAGA 59.226 47.619 0.00 0.00 0.00 3.10
1508 1626 6.016024 TGTTAATTCGTGAGTGGTACTGTACT 60.016 38.462 16.79 0.00 0.00 2.73
1513 1631 5.204409 TGTGTTAATTCGTGAGTGGTACT 57.796 39.130 0.00 0.00 0.00 2.73
1514 1632 4.143179 GCTGTGTTAATTCGTGAGTGGTAC 60.143 45.833 0.00 0.00 0.00 3.34
1515 1633 3.991773 GCTGTGTTAATTCGTGAGTGGTA 59.008 43.478 0.00 0.00 0.00 3.25
1516 1634 2.806244 GCTGTGTTAATTCGTGAGTGGT 59.194 45.455 0.00 0.00 0.00 4.16
1517 1635 2.159841 CGCTGTGTTAATTCGTGAGTGG 60.160 50.000 0.00 0.00 0.00 4.00
1518 1636 2.721797 GCGCTGTGTTAATTCGTGAGTG 60.722 50.000 0.00 0.00 0.00 3.51
1525 1644 3.628017 ACAAACAGCGCTGTGTTAATTC 58.372 40.909 41.21 0.00 44.13 2.17
1605 1727 3.270877 GTGTACCTCCATTGTTGGCTAG 58.729 50.000 0.00 0.00 43.29 3.42
1632 1760 3.616560 GCTGTAGCAGTTGCAAGGTACTA 60.617 47.826 21.47 10.50 45.16 1.82
1633 1761 2.872038 GCTGTAGCAGTTGCAAGGTACT 60.872 50.000 21.47 11.30 45.16 2.73
1634 1762 1.464997 GCTGTAGCAGTTGCAAGGTAC 59.535 52.381 16.81 16.81 45.16 3.34
1702 1830 2.995939 GGTAAAAGCAAAGATGGCAAGC 59.004 45.455 0.00 0.00 0.00 4.01
1708 1836 7.040409 AGGTAAACTCTGGTAAAAGCAAAGATG 60.040 37.037 0.00 0.00 0.00 2.90
1716 1844 4.312443 TGCGAGGTAAACTCTGGTAAAAG 58.688 43.478 0.00 0.00 44.33 2.27
1822 1959 7.341805 ACAGGTATTTTGCTCTCAGATATGTT 58.658 34.615 0.00 0.00 0.00 2.71
1825 1962 8.814038 AAAACAGGTATTTTGCTCTCAGATAT 57.186 30.769 0.00 0.00 30.56 1.63
1849 1986 6.494666 TCTCTCCCAGTAGACAAAAGAAAA 57.505 37.500 0.00 0.00 0.00 2.29
1853 1990 8.848474 TTTTAATCTCTCCCAGTAGACAAAAG 57.152 34.615 0.00 0.00 0.00 2.27
1883 2020 5.582269 TGTTACTCGCTATTGACTAGTACGT 59.418 40.000 0.00 0.00 0.00 3.57
1884 2021 6.040962 TGTTACTCGCTATTGACTAGTACG 57.959 41.667 0.00 0.00 0.00 3.67
1885 2022 7.014092 ACTGTTACTCGCTATTGACTAGTAC 57.986 40.000 0.00 0.00 0.00 2.73
1886 2023 8.899427 ATACTGTTACTCGCTATTGACTAGTA 57.101 34.615 0.00 0.00 0.00 1.82
1887 2024 7.804843 ATACTGTTACTCGCTATTGACTAGT 57.195 36.000 0.00 0.00 0.00 2.57
1888 2025 9.517609 AAAATACTGTTACTCGCTATTGACTAG 57.482 33.333 0.00 0.00 0.00 2.57
1912 2049 5.631096 CGCATCTTCGAGATAAGCTCATAAA 59.369 40.000 0.00 0.00 44.15 1.40
1920 2091 0.432738 GCGCGCATCTTCGAGATAAG 59.567 55.000 29.10 0.00 32.12 1.73
1924 2095 4.128388 TGGCGCGCATCTTCGAGA 62.128 61.111 34.42 1.02 0.00 4.04
1942 2113 0.734889 CTAAACAGAATGCAGCGGGG 59.265 55.000 0.00 0.00 42.53 5.73
1973 2152 5.350504 AGTTAAGCTCTAGCACATGATGT 57.649 39.130 0.00 0.00 45.16 3.06
1990 2169 6.894654 ACTCCTGATGATCTCTGAGAAGTTAA 59.105 38.462 12.00 0.00 31.69 2.01
2014 2193 5.841957 ACAATAATGCTCCATTTCCAGAC 57.158 39.130 0.00 0.00 35.54 3.51
2018 2197 6.403527 GGCAAAAACAATAATGCTCCATTTCC 60.404 38.462 0.00 0.00 38.79 3.13
2048 2227 0.764271 TTCACAGTCCCATGCAGTGA 59.236 50.000 0.00 0.00 37.43 3.41
2049 2228 1.538512 CTTTCACAGTCCCATGCAGTG 59.461 52.381 0.00 0.00 0.00 3.66
2050 2229 1.143684 ACTTTCACAGTCCCATGCAGT 59.856 47.619 0.00 0.00 0.00 4.40
2089 2268 2.584835 TCTGGTCCCAATTTCTGGTG 57.415 50.000 0.00 0.00 44.76 4.17
2120 2299 9.809096 TGATCAGATCTCACTTTTCAGTTATAC 57.191 33.333 11.83 0.00 0.00 1.47
2122 2301 8.538701 ACTGATCAGATCTCACTTTTCAGTTAT 58.461 33.333 29.27 0.00 36.77 1.89
2153 2332 7.612677 AGCTAGTACTTGCTATTAACTTGTGT 58.387 34.615 27.05 1.94 39.72 3.72
2265 2574 7.321153 GCTTGACAGTAAGTAATCAGTAGGAA 58.679 38.462 0.00 0.00 0.00 3.36
2288 2600 5.542779 AGAAAAAGACACATAGAAGACGCT 58.457 37.500 0.00 0.00 0.00 5.07
2314 2626 7.121382 AGTCAAATCATCATACAATCCCAACT 58.879 34.615 0.00 0.00 0.00 3.16
2319 2631 8.450578 TGGTTAGTCAAATCATCATACAATCC 57.549 34.615 0.00 0.00 0.00 3.01
2336 2648 8.797266 AAGAAATGTTTTCGAAATGGTTAGTC 57.203 30.769 12.12 4.25 0.00 2.59
2369 2681 0.731417 CTCAAGCGGCATTTCTCTGG 59.269 55.000 1.45 0.00 0.00 3.86
2430 2742 4.380531 CTTGTCTAACCTCAAGCTGTTCA 58.619 43.478 0.00 0.00 35.42 3.18
2453 2765 4.039004 AGGAGTATAAGCAGTGATGCAGAG 59.961 45.833 2.73 0.00 37.25 3.35
2517 2835 9.847224 TTCTGCACCTGATCGTAGATATATATA 57.153 33.333 0.00 0.00 45.12 0.86
2518 2836 8.753497 TTCTGCACCTGATCGTAGATATATAT 57.247 34.615 0.00 0.00 45.12 0.86
2519 2837 8.047310 TCTTCTGCACCTGATCGTAGATATATA 58.953 37.037 0.00 0.00 45.12 0.86
2520 2838 6.887002 TCTTCTGCACCTGATCGTAGATATAT 59.113 38.462 0.00 0.00 45.12 0.86
2528 2846 1.674221 GCTTCTTCTGCACCTGATCGT 60.674 52.381 0.00 0.00 0.00 3.73
2550 2868 0.952984 GGGCCTCTATTCGCATCTGC 60.953 60.000 0.84 0.00 37.78 4.26
2656 2974 0.247736 AAGTCCGTCAGCTGTGATCC 59.752 55.000 14.67 0.49 34.36 3.36
2667 2985 1.275573 AGAGCCAGGTTAAAGTCCGTC 59.724 52.381 0.00 0.00 0.00 4.79
2676 2994 2.666098 GCCCGGAAGAGCCAGGTTA 61.666 63.158 0.73 0.00 36.50 2.85
2682 3000 2.436824 GACAAGCCCGGAAGAGCC 60.437 66.667 0.73 0.00 0.00 4.70
2731 3049 5.827797 ACATATGTTTCACCAACTGTTCACT 59.172 36.000 1.41 0.00 36.21 3.41
2841 3159 2.278332 GGAGCAGGTCCTCAGTTTTT 57.722 50.000 11.76 0.00 42.99 1.94
2942 3261 6.257630 GCTGAAACACATCTCTATTTCCTCTC 59.742 42.308 0.00 0.00 31.39 3.20
3018 3338 0.729116 CATTCTAAGCACTGCCACGG 59.271 55.000 0.00 0.00 0.00 4.94
3019 3339 0.097674 GCATTCTAAGCACTGCCACG 59.902 55.000 0.00 0.00 0.00 4.94
3044 3364 6.966534 ATCACAGAGGAATTCAAACTTGTT 57.033 33.333 7.93 0.00 0.00 2.83
3055 3375 9.807649 GCAAATTTAACATTATCACAGAGGAAT 57.192 29.630 0.00 0.00 0.00 3.01
3058 3378 8.461222 TCAGCAAATTTAACATTATCACAGAGG 58.539 33.333 0.00 0.00 0.00 3.69
3111 3431 2.233922 ACGGCCCTGATGCATATACTAC 59.766 50.000 0.00 0.00 0.00 2.73
3125 3445 1.202651 CGAAATATCAGGAACGGCCCT 60.203 52.381 0.00 0.00 37.37 5.19
3126 3446 1.226746 CGAAATATCAGGAACGGCCC 58.773 55.000 0.00 0.00 37.37 5.80
3127 3447 1.226746 CCGAAATATCAGGAACGGCC 58.773 55.000 0.00 0.00 34.36 6.13
3128 3448 1.226746 CCCGAAATATCAGGAACGGC 58.773 55.000 0.00 0.00 39.19 5.68
3129 3449 1.542547 CCCCCGAAATATCAGGAACGG 60.543 57.143 0.00 0.00 40.03 4.44
3130 3450 1.878953 CCCCCGAAATATCAGGAACG 58.121 55.000 0.00 0.00 0.00 3.95
3131 3451 1.605753 GCCCCCGAAATATCAGGAAC 58.394 55.000 0.00 0.00 0.00 3.62
3132 3452 0.476771 GGCCCCCGAAATATCAGGAA 59.523 55.000 0.00 0.00 0.00 3.36
3133 3453 1.423794 GGGCCCCCGAAATATCAGGA 61.424 60.000 12.23 0.00 0.00 3.86
3134 3454 1.074951 GGGCCCCCGAAATATCAGG 59.925 63.158 12.23 0.00 0.00 3.86
3135 3455 0.250901 CTGGGCCCCCGAAATATCAG 60.251 60.000 22.27 0.79 39.42 2.90
3136 3456 1.715019 CCTGGGCCCCCGAAATATCA 61.715 60.000 22.27 0.00 39.42 2.15
3137 3457 1.074951 CCTGGGCCCCCGAAATATC 59.925 63.158 22.27 0.00 39.42 1.63
3138 3458 2.469765 CCCTGGGCCCCCGAAATAT 61.470 63.158 22.27 0.00 39.42 1.28
3139 3459 3.100514 CCCTGGGCCCCCGAAATA 61.101 66.667 22.27 0.00 39.42 1.40
3149 3469 0.172578 GTTGTAATTTCGCCCTGGGC 59.827 55.000 28.17 28.17 46.75 5.36
3150 3470 0.815095 GGTTGTAATTTCGCCCTGGG 59.185 55.000 8.86 8.86 0.00 4.45
3151 3471 0.815095 GGGTTGTAATTTCGCCCTGG 59.185 55.000 7.11 0.00 36.49 4.45
3152 3472 1.472480 CTGGGTTGTAATTTCGCCCTG 59.528 52.381 13.11 9.97 39.97 4.45
3153 3473 1.615919 CCTGGGTTGTAATTTCGCCCT 60.616 52.381 13.11 0.00 39.97 5.19
3154 3474 0.815095 CCTGGGTTGTAATTTCGCCC 59.185 55.000 7.34 7.34 39.73 6.13
3155 3475 0.815095 CCCTGGGTTGTAATTTCGCC 59.185 55.000 3.97 0.00 0.00 5.54
3156 3476 0.172578 GCCCTGGGTTGTAATTTCGC 59.827 55.000 15.56 0.00 0.00 4.70
3157 3477 0.815095 GGCCCTGGGTTGTAATTTCG 59.185 55.000 15.56 0.00 0.00 3.46
3158 3478 1.191535 GGGCCCTGGGTTGTAATTTC 58.808 55.000 17.04 0.00 0.00 2.17
3159 3479 0.252513 GGGGCCCTGGGTTGTAATTT 60.253 55.000 24.38 0.00 0.00 1.82
3160 3480 1.153041 AGGGGCCCTGGGTTGTAATT 61.153 55.000 28.21 0.00 29.57 1.40
3161 3481 0.253915 TAGGGGCCCTGGGTTGTAAT 60.254 55.000 35.70 7.15 34.61 1.89
3162 3482 1.163801 TAGGGGCCCTGGGTTGTAA 59.836 57.895 35.70 9.68 34.61 2.41
3163 3483 1.617233 GTAGGGGCCCTGGGTTGTA 60.617 63.158 35.70 10.57 34.61 2.41
3164 3484 2.127685 TAGTAGGGGCCCTGGGTTGT 62.128 60.000 35.70 14.50 34.61 3.32
3165 3485 0.697854 ATAGTAGGGGCCCTGGGTTG 60.698 60.000 35.70 0.00 34.61 3.77
3166 3486 0.954203 TATAGTAGGGGCCCTGGGTT 59.046 55.000 35.70 18.87 34.61 4.11
3167 3487 0.954203 TTATAGTAGGGGCCCTGGGT 59.046 55.000 35.70 20.64 34.61 4.51
3168 3488 1.985895 CTTTATAGTAGGGGCCCTGGG 59.014 57.143 35.70 8.86 34.61 4.45
3169 3489 2.986050 TCTTTATAGTAGGGGCCCTGG 58.014 52.381 35.70 13.54 34.61 4.45
3170 3490 6.697641 TTTATCTTTATAGTAGGGGCCCTG 57.302 41.667 35.70 15.73 34.61 4.45
3171 3491 7.716832 TTTTTATCTTTATAGTAGGGGCCCT 57.283 36.000 31.38 31.38 37.71 5.19
3278 3598 9.883142 TGACATGATGATGTTTAACATACACTA 57.117 29.630 10.82 4.84 43.22 2.74
3279 3599 8.791327 TGACATGATGATGTTTAACATACACT 57.209 30.769 10.82 2.07 43.22 3.55
3280 3600 8.668353 ACTGACATGATGATGTTTAACATACAC 58.332 33.333 10.82 5.88 43.22 2.90
3281 3601 8.791327 ACTGACATGATGATGTTTAACATACA 57.209 30.769 10.82 11.46 43.22 2.29
3282 3602 8.882736 TGACTGACATGATGATGTTTAACATAC 58.117 33.333 10.82 6.52 43.22 2.39
3283 3603 8.882736 GTGACTGACATGATGATGTTTAACATA 58.117 33.333 10.82 0.00 43.22 2.29
3284 3604 7.413328 CGTGACTGACATGATGATGTTTAACAT 60.413 37.037 10.64 10.64 43.22 2.71
3367 3710 5.844004 AGAGATAAGTACATGCGGTTTAGG 58.156 41.667 0.00 0.00 0.00 2.69
3534 3878 3.369471 CGTGATGAAGAAAAGGGGCTCTA 60.369 47.826 0.00 0.00 0.00 2.43
3613 3959 2.281484 GTTGGAGTTGGCCGCAGA 60.281 61.111 0.00 0.00 0.00 4.26
3615 3961 3.842925 GAGGTTGGAGTTGGCCGCA 62.843 63.158 0.00 0.00 0.00 5.69
3618 3964 1.002011 GGAGAGGTTGGAGTTGGCC 60.002 63.158 0.00 0.00 0.00 5.36
3658 4004 0.035439 AGAACATAGTTGGTGCGGGG 60.035 55.000 0.00 0.00 0.00 5.73
3775 4121 5.001232 CGTTTCTTCTTTCCCATCCTTGTA 58.999 41.667 0.00 0.00 0.00 2.41



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

AutoCloner maintained by Alex Coulton.