Multiple sequence alignment - TraesCS5D01G524800

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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 TraesCS5D01G524800 chr5D 100.000 5395 0 0 1 5395 543613338 543607944 0.000000e+00 9963.0
1 TraesCS5D01G524800 chr5D 97.872 376 6 1 4535 4910 543575300 543575673 0.000000e+00 649.0
2 TraesCS5D01G524800 chr5D 99.371 159 1 0 4989 5147 543608297 543608139 6.840000e-74 289.0
3 TraesCS5D01G524800 chr5D 99.371 159 1 0 5042 5200 543608350 543608192 6.840000e-74 289.0
4 TraesCS5D01G524800 chr5D 99.057 106 1 0 4989 5094 543608244 543608139 1.980000e-44 191.0
5 TraesCS5D01G524800 chr5D 99.057 106 1 0 5095 5200 543608350 543608245 1.980000e-44 191.0
6 TraesCS5D01G524800 chr5D 77.500 280 57 5 3317 3593 447141887 447141611 4.320000e-36 163.0
7 TraesCS5D01G524800 chr5D 71.672 646 162 18 3317 3954 447192648 447192016 5.590000e-35 159.0
8 TraesCS5D01G524800 chr5D 98.113 53 1 0 4989 5041 543608191 543608139 5.750000e-15 93.5
9 TraesCS5D01G524800 chr5D 98.113 53 1 0 5148 5200 543608350 543608298 5.750000e-15 93.5
10 TraesCS5D01G524800 chr5D 90.141 71 5 1 349 419 543612846 543612778 2.070000e-14 91.6
11 TraesCS5D01G524800 chr5D 90.141 71 5 1 493 561 543612990 543612920 2.070000e-14 91.6
12 TraesCS5D01G524800 chr5B 91.667 2136 114 34 2820 4943 685567405 685565322 0.000000e+00 2900.0
13 TraesCS5D01G524800 chr5B 92.590 1660 84 12 344 1981 685569943 685568301 0.000000e+00 2348.0
14 TraesCS5D01G524800 chr5B 94.088 795 40 5 1979 2772 685568196 685567408 0.000000e+00 1201.0
15 TraesCS5D01G524800 chr5B 90.173 692 48 16 4357 5035 685425219 685425903 0.000000e+00 883.0
16 TraesCS5D01G524800 chr5B 92.532 308 14 6 4357 4661 685441991 685441690 2.980000e-117 433.0
17 TraesCS5D01G524800 chr5B 91.440 257 12 4 5148 5395 685425858 685426113 1.440000e-90 344.0
18 TraesCS5D01G524800 chr5B 87.500 224 28 0 4156 4379 685424071 685424294 5.360000e-65 259.0
19 TraesCS5D01G524800 chr5B 85.448 268 18 5 4663 4923 685441583 685441330 5.360000e-65 259.0
20 TraesCS5D01G524800 chr5B 83.838 297 18 4 1 284 685570490 685570211 6.930000e-64 255.0
21 TraesCS5D01G524800 chr5B 95.745 47 1 1 5042 5088 685425858 685425903 2.080000e-09 75.0
22 TraesCS5D01G524800 chr5B 95.745 47 1 1 5095 5141 685425858 685425903 2.080000e-09 75.0
23 TraesCS5D01G524800 chr4A 92.222 1800 90 25 2820 4598 625487021 625488791 0.000000e+00 2503.0
24 TraesCS5D01G524800 chr4A 92.386 788 45 5 1985 2771 625486244 625487017 0.000000e+00 1109.0
25 TraesCS5D01G524800 chr4A 94.295 631 23 7 349 975 625484933 625485554 0.000000e+00 953.0
26 TraesCS5D01G524800 chr4A 94.444 594 23 3 1386 1977 625485548 625486133 0.000000e+00 905.0
27 TraesCS5D01G524800 chr4A 86.770 582 40 22 4357 4917 625540507 625539942 9.930000e-172 614.0
28 TraesCS5D01G524800 chr4A 85.503 338 38 7 4583 4916 625489590 625489920 5.170000e-90 342.0
29 TraesCS5D01G524800 chr4A 90.870 230 14 5 4357 4583 625488780 625489005 8.780000e-78 302.0
30 TraesCS5D01G524800 chr4A 91.525 118 7 2 4823 4937 625547193 625547076 5.590000e-35 159.0
31 TraesCS5D01G524800 chr4A 96.000 75 3 0 5321 5395 625489946 625490020 7.340000e-24 122.0
32 TraesCS5D01G524800 chr4A 91.304 69 6 0 493 561 625484933 625485001 1.600000e-15 95.3
33 TraesCS5D01G524800 chr4A 84.932 73 8 3 3850 3920 668094170 668094099 2.700000e-08 71.3
34 TraesCS5D01G524800 chr4A 83.562 73 11 1 3850 3921 175856736 175856808 3.490000e-07 67.6
35 TraesCS5D01G524800 chr3B 83.871 310 28 10 4438 4746 173620826 173620538 5.320000e-70 276.0
36 TraesCS5D01G524800 chr3B 83.562 73 11 1 3850 3921 76433112 76433040 3.490000e-07 67.6
37 TraesCS5D01G524800 chr3B 81.944 72 12 1 3850 3920 584551249 584551320 5.840000e-05 60.2
38 TraesCS5D01G524800 chr2B 89.503 181 15 4 4567 4746 346306949 346306772 5.440000e-55 226.0
39 TraesCS5D01G524800 chr2B 84.810 158 6 8 4438 4595 346307035 346306896 5.630000e-30 143.0
40 TraesCS5D01G524800 chr7B 88.298 188 18 4 4560 4746 493507301 493507485 7.030000e-54 222.0
41 TraesCS5D01G524800 chr7B 85.443 158 5 9 4438 4595 493507222 493507361 1.210000e-31 148.0
42 TraesCS5D01G524800 chr7B 84.810 158 6 6 4438 4595 173305502 173305641 5.630000e-30 143.0
43 TraesCS5D01G524800 chr1A 88.298 188 18 4 4560 4746 509240107 509240291 7.030000e-54 222.0
44 TraesCS5D01G524800 chr1A 96.078 102 2 2 4823 4922 558194443 558194544 1.200000e-36 165.0
45 TraesCS5D01G524800 chr1A 84.177 158 7 7 4438 4595 99535777 99535916 2.620000e-28 137.0
46 TraesCS5D01G524800 chr1A 83.544 158 8 6 4438 4595 509240028 509240167 1.220000e-26 132.0
47 TraesCS5D01G524800 chr5A 73.011 641 150 21 3317 3947 565417098 565417725 2.550000e-48 204.0
48 TraesCS5D01G524800 chr5A 77.241 290 61 5 3317 3602 565489759 565490047 1.200000e-36 165.0
49 TraesCS5D01G524800 chr6D 73.770 549 121 16 3382 3920 24376415 24375880 1.530000e-45 195.0
50 TraesCS5D01G524800 chr1B 97.000 100 2 1 4823 4921 642734859 642734958 3.340000e-37 167.0
51 TraesCS5D01G524800 chr3A 85.443 158 5 9 4438 4595 740072399 740072538 1.210000e-31 148.0
52 TraesCS5D01G524800 chr6A 84.810 158 6 9 4438 4595 31467404 31467265 5.630000e-30 143.0
53 TraesCS5D01G524800 chr7A 82.911 158 9 9 4438 4595 480550328 480550189 5.670000e-25 126.0
54 TraesCS5D01G524800 chr4D 82.192 73 12 1 3850 3921 303518840 303518768 1.620000e-05 62.1
55 TraesCS5D01G524800 chr4B 82.192 73 12 1 3850 3921 377938638 377938566 1.620000e-05 62.1
56 TraesCS5D01G524800 chr3D 82.192 73 10 3 3850 3920 445638661 445638732 5.840000e-05 60.2


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 TraesCS5D01G524800 chr5D 543607944 543613338 5394 True 9963.0000 9963 100.00000 1 5395 1 chr5D.!!$R3 5394
1 TraesCS5D01G524800 chr5B 685565322 685570490 5168 True 1676.0000 2900 90.54575 1 4943 4 chr5B.!!$R2 4942
2 TraesCS5D01G524800 chr5B 685441330 685441991 661 True 346.0000 433 88.99000 4357 4923 2 chr5B.!!$R1 566
3 TraesCS5D01G524800 chr5B 685424071 685426113 2042 False 327.2000 883 92.12060 4156 5395 5 chr5B.!!$F1 1239
4 TraesCS5D01G524800 chr4A 625484933 625490020 5087 False 791.4125 2503 92.12800 349 5395 8 chr4A.!!$F2 5046
5 TraesCS5D01G524800 chr4A 625539942 625540507 565 True 614.0000 614 86.77000 4357 4917 1 chr4A.!!$R1 560
6 TraesCS5D01G524800 chr5A 565417098 565417725 627 False 204.0000 204 73.01100 3317 3947 1 chr5A.!!$F1 630

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
289 303 0.729116 CTCCCAACACATCACATCGC 59.271 55.000 0.00 0.00 0.00 4.58 F
568 810 1.006922 GCACAAGCTTGTTCCCTGC 60.007 57.895 29.23 23.64 39.91 4.85 F
1388 1648 0.459759 GCGACCTACAACTACCTGGC 60.460 60.000 0.00 0.00 0.00 4.85 F
1927 2187 1.939980 ACCTCCTTCCACACCTAGTC 58.060 55.000 0.00 0.00 0.00 2.59 F
2980 3358 0.108138 GTTGCCCTCACGCTACATCT 60.108 55.000 0.00 0.00 35.04 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1178 1438 0.107945 GCAGATGAGGTCGAAGCCTT 60.108 55.000 0.00 0.00 39.34 4.35 R
1758 2018 0.179111 CATCCGACCGAGCTTTAGCA 60.179 55.000 4.33 0.00 45.16 3.49 R
2886 3264 1.863454 GGCACTCGTCAATATCTGCAG 59.137 52.381 7.63 7.63 0.00 4.41 R
3621 4000 0.311790 CACGTCAGCAAGCATTTGGT 59.688 50.000 0.00 0.00 45.38 3.67 R
4427 5970 0.242555 ATAAACAAAACGGGGCGCAG 59.757 50.000 10.83 0.00 0.00 5.18 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
22 23 2.812178 CGTCCGGGTTAGCGGTTG 60.812 66.667 0.00 0.00 0.00 3.77
76 87 2.722201 CCCTCAGTCAGGCGGGTAC 61.722 68.421 0.00 0.00 41.80 3.34
77 88 2.490217 CTCAGTCAGGCGGGTACG 59.510 66.667 0.00 0.00 44.63 3.67
90 101 2.426425 GTACGGCTCGGCGTATCG 60.426 66.667 24.80 11.57 0.00 2.92
236 250 3.340814 ACGCATTCTTCTTGGATGACT 57.659 42.857 0.00 0.00 0.00 3.41
261 275 0.742281 CATCTTCTCCGCCACAGGTG 60.742 60.000 0.00 0.00 0.00 4.00
274 288 2.620627 CCACAGGTGGGTAATTTCTCCC 60.621 54.545 10.67 6.22 46.81 4.30
284 298 4.157840 GGGTAATTTCTCCCAACACATCAC 59.842 45.833 7.79 0.00 42.95 3.06
285 299 4.764823 GGTAATTTCTCCCAACACATCACA 59.235 41.667 0.00 0.00 0.00 3.58
286 300 5.418840 GGTAATTTCTCCCAACACATCACAT 59.581 40.000 0.00 0.00 0.00 3.21
287 301 5.649782 AATTTCTCCCAACACATCACATC 57.350 39.130 0.00 0.00 0.00 3.06
288 302 2.385013 TCTCCCAACACATCACATCG 57.615 50.000 0.00 0.00 0.00 3.84
289 303 0.729116 CTCCCAACACATCACATCGC 59.271 55.000 0.00 0.00 0.00 4.58
301 328 2.089201 TCACATCGCGTCTTCTTCCTA 58.911 47.619 5.77 0.00 0.00 2.94
305 332 5.041287 CACATCGCGTCTTCTTCCTAATAA 58.959 41.667 5.77 0.00 0.00 1.40
313 340 5.763698 CGTCTTCTTCCTAATAATTTCCCCC 59.236 44.000 0.00 0.00 0.00 5.40
314 341 6.634039 CGTCTTCTTCCTAATAATTTCCCCCA 60.634 42.308 0.00 0.00 0.00 4.96
315 342 7.298374 GTCTTCTTCCTAATAATTTCCCCCAT 58.702 38.462 0.00 0.00 0.00 4.00
316 343 7.231519 GTCTTCTTCCTAATAATTTCCCCCATG 59.768 40.741 0.00 0.00 0.00 3.66
317 344 6.606241 TCTTCCTAATAATTTCCCCCATGT 57.394 37.500 0.00 0.00 0.00 3.21
318 345 6.372931 TCTTCCTAATAATTTCCCCCATGTG 58.627 40.000 0.00 0.00 0.00 3.21
319 346 6.161348 TCTTCCTAATAATTTCCCCCATGTGA 59.839 38.462 0.00 0.00 0.00 3.58
320 347 6.348478 TCCTAATAATTTCCCCCATGTGAA 57.652 37.500 0.00 0.00 0.00 3.18
321 348 6.932753 TCCTAATAATTTCCCCCATGTGAAT 58.067 36.000 0.00 0.00 0.00 2.57
322 349 7.369434 TCCTAATAATTTCCCCCATGTGAATT 58.631 34.615 0.00 0.00 0.00 2.17
323 350 7.289782 TCCTAATAATTTCCCCCATGTGAATTG 59.710 37.037 0.00 0.00 0.00 2.32
324 351 6.889595 AATAATTTCCCCCATGTGAATTGT 57.110 33.333 0.00 0.00 0.00 2.71
325 352 4.556592 AATTTCCCCCATGTGAATTGTG 57.443 40.909 0.00 0.00 0.00 3.33
326 353 2.988636 TTCCCCCATGTGAATTGTGA 57.011 45.000 0.00 0.00 0.00 3.58
327 354 2.988636 TCCCCCATGTGAATTGTGAA 57.011 45.000 0.00 0.00 0.00 3.18
328 355 3.251016 TCCCCCATGTGAATTGTGAAA 57.749 42.857 0.00 0.00 0.00 2.69
329 356 2.896685 TCCCCCATGTGAATTGTGAAAC 59.103 45.455 0.00 0.00 37.35 2.78
330 357 2.028203 CCCCCATGTGAATTGTGAAACC 60.028 50.000 0.00 0.00 34.36 3.27
410 650 2.874086 CACAAGTCACATGAGTCTTGCA 59.126 45.455 22.68 0.00 40.29 4.08
463 705 1.742831 TGCATCCACAATTTAGTCGCC 59.257 47.619 0.00 0.00 0.00 5.54
530 772 2.563179 ACCAGTGGCTGTCAACTACTAG 59.437 50.000 9.78 0.00 0.00 2.57
568 810 1.006922 GCACAAGCTTGTTCCCTGC 60.007 57.895 29.23 23.64 39.91 4.85
572 814 1.961277 AAGCTTGTTCCCTGCGTCG 60.961 57.895 0.00 0.00 0.00 5.12
619 876 7.255381 CCTCCTCCATTGATGAATTGTATGAAC 60.255 40.741 0.00 0.00 0.00 3.18
620 877 6.260714 TCCTCCATTGATGAATTGTATGAACG 59.739 38.462 0.00 0.00 0.00 3.95
639 896 5.779806 AACGTTGCTAGTTCACATATGAC 57.220 39.130 10.38 0.00 33.38 3.06
653 911 3.206150 CATATGACGGGGTTCCAAGAAG 58.794 50.000 0.00 0.00 0.00 2.85
784 1043 6.635030 ATTCCCTGTTCTACTTTTTGACAC 57.365 37.500 0.00 0.00 0.00 3.67
857 1117 2.309528 ATATGCGCGAAAGTCTTCCA 57.690 45.000 12.10 0.00 0.00 3.53
927 1187 5.682234 TCACATCTTTGATAGGCTTCTGA 57.318 39.130 0.00 0.00 0.00 3.27
930 1190 7.971201 TCACATCTTTGATAGGCTTCTGATAT 58.029 34.615 0.00 0.00 0.00 1.63
999 1259 5.600696 ACAAACAAAATTCTGTTAGCCAGG 58.399 37.500 0.00 0.00 41.83 4.45
1003 1263 5.324409 ACAAAATTCTGTTAGCCAGGATGA 58.676 37.500 0.00 0.00 38.55 2.92
1058 1318 1.252904 GCACCCACTGCCATGAACAT 61.253 55.000 0.00 0.00 40.42 2.71
1069 1329 1.203052 CCATGAACATCAAGGTGGCAC 59.797 52.381 9.70 9.70 31.05 5.01
1222 1482 2.677875 CCACCAAGCCTCCCAAGC 60.678 66.667 0.00 0.00 0.00 4.01
1368 1628 2.716424 TCCAGGGAGAAACCTCAACATT 59.284 45.455 0.00 0.00 39.34 2.71
1388 1648 0.459759 GCGACCTACAACTACCTGGC 60.460 60.000 0.00 0.00 0.00 4.85
1503 1763 2.341101 GCTCCTCGTGACGGAAGGA 61.341 63.158 13.75 13.75 0.00 3.36
1552 1812 3.124921 CCGTCACATTCCCCGTGC 61.125 66.667 0.00 0.00 34.27 5.34
1590 1850 3.074412 GGTGACCATCGTGAAGAACAAT 58.926 45.455 0.00 0.00 0.00 2.71
1758 2018 6.425735 TGTGATCACAGATAATCCCAATTGT 58.574 36.000 24.56 0.00 36.21 2.71
1908 2168 5.534278 TGATGATTGCAAACAAGGTACTCAA 59.466 36.000 13.75 0.00 38.49 3.02
1927 2187 1.939980 ACCTCCTTCCACACCTAGTC 58.060 55.000 0.00 0.00 0.00 2.59
1940 2203 6.605594 TCCACACCTAGTCTTTTTCATTTGTT 59.394 34.615 0.00 0.00 0.00 2.83
1947 2210 7.706179 CCTAGTCTTTTTCATTTGTTTGCTCAA 59.294 33.333 0.00 0.00 0.00 3.02
2037 2407 5.152623 TGATAGTCAGGGACTTGAACAAG 57.847 43.478 12.22 12.22 40.28 3.16
2116 2486 9.349713 TGTTTGGTTACTGATATTTCTTCACTT 57.650 29.630 0.00 0.00 0.00 3.16
2137 2508 9.656323 TCACTTAACAGAGTATAATCATACCCT 57.344 33.333 2.62 0.00 38.24 4.34
2652 3023 3.469008 TGTGTTCCTGTAGTTCAGTGG 57.531 47.619 0.00 0.00 42.19 4.00
2660 3031 4.220821 TCCTGTAGTTCAGTGGATTCTGTC 59.779 45.833 0.00 0.00 42.19 3.51
2672 3043 4.449068 GTGGATTCTGTCTTATGGTATGCG 59.551 45.833 0.00 0.00 0.00 4.73
2674 3045 2.526304 TCTGTCTTATGGTATGCGGC 57.474 50.000 0.00 0.00 0.00 6.53
2677 3048 2.942376 CTGTCTTATGGTATGCGGCAAA 59.058 45.455 6.82 0.00 0.00 3.68
2678 3049 2.680841 TGTCTTATGGTATGCGGCAAAC 59.319 45.455 6.82 0.43 0.00 2.93
2679 3050 2.680841 GTCTTATGGTATGCGGCAAACA 59.319 45.455 6.82 6.93 0.00 2.83
2682 3053 5.181245 GTCTTATGGTATGCGGCAAACATAT 59.819 40.000 18.65 9.24 32.87 1.78
2687 3058 2.346766 ATGCGGCAAACATATGGAGA 57.653 45.000 6.82 0.00 0.00 3.71
2697 3068 7.468494 CGGCAAACATATGGAGATTTAACATGA 60.468 37.037 7.80 0.00 0.00 3.07
2704 3075 9.616634 CATATGGAGATTTAACATGAAATTCCG 57.383 33.333 0.00 0.00 33.39 4.30
2706 3077 7.320443 TGGAGATTTAACATGAAATTCCGAG 57.680 36.000 0.00 0.00 33.39 4.63
2707 3078 7.109501 TGGAGATTTAACATGAAATTCCGAGA 58.890 34.615 0.00 0.00 33.39 4.04
2709 3080 8.458843 GGAGATTTAACATGAAATTCCGAGAAA 58.541 33.333 0.00 0.00 0.00 2.52
2719 3090 5.530915 TGAAATTCCGAGAAAAGTGACATGT 59.469 36.000 0.00 0.00 0.00 3.21
2724 3095 5.175859 TCCGAGAAAAGTGACATGTTATCC 58.824 41.667 0.00 0.00 0.00 2.59
2725 3096 4.935205 CCGAGAAAAGTGACATGTTATCCA 59.065 41.667 0.00 0.00 0.00 3.41
2739 3110 7.894376 CATGTTATCCATGGAATTTTATGGC 57.106 36.000 20.67 2.64 46.03 4.40
2751 3122 5.180868 GGAATTTTATGGCATGTTGTTTGCA 59.819 36.000 10.98 0.00 41.95 4.08
2760 3131 6.331845 TGGCATGTTGTTTGCAGATATTAAG 58.668 36.000 0.00 0.00 41.95 1.85
2772 3143 9.515226 TTTGCAGATATTAAGGAGTGTTTAGTT 57.485 29.630 0.00 0.00 0.00 2.24
2774 3145 9.817809 TGCAGATATTAAGGAGTGTTTAGTTAG 57.182 33.333 0.00 0.00 0.00 2.34
2775 3146 9.819267 GCAGATATTAAGGAGTGTTTAGTTAGT 57.181 33.333 0.00 0.00 0.00 2.24
2784 3155 5.963594 GAGTGTTTAGTTAGTACTCCCCTG 58.036 45.833 0.00 0.00 35.78 4.45
2785 3156 4.776308 AGTGTTTAGTTAGTACTCCCCTGG 59.224 45.833 0.00 0.00 35.78 4.45
2786 3157 4.529769 GTGTTTAGTTAGTACTCCCCTGGT 59.470 45.833 0.00 0.00 35.78 4.00
2787 3158 4.774200 TGTTTAGTTAGTACTCCCCTGGTC 59.226 45.833 0.00 0.00 35.78 4.02
2788 3159 4.961440 TTAGTTAGTACTCCCCTGGTCT 57.039 45.455 0.00 0.00 35.78 3.85
2789 3160 3.385314 AGTTAGTACTCCCCTGGTCTC 57.615 52.381 0.00 0.00 0.00 3.36
2790 3161 2.653366 AGTTAGTACTCCCCTGGTCTCA 59.347 50.000 0.00 0.00 0.00 3.27
2791 3162 3.272551 AGTTAGTACTCCCCTGGTCTCAT 59.727 47.826 0.00 0.00 0.00 2.90
2792 3163 4.481280 AGTTAGTACTCCCCTGGTCTCATA 59.519 45.833 0.00 0.00 0.00 2.15
2793 3164 5.043582 AGTTAGTACTCCCCTGGTCTCATAA 60.044 44.000 0.00 0.00 0.00 1.90
2794 3165 4.561254 AGTACTCCCCTGGTCTCATAAT 57.439 45.455 0.00 0.00 0.00 1.28
2795 3166 5.681494 AGTACTCCCCTGGTCTCATAATA 57.319 43.478 0.00 0.00 0.00 0.98
2796 3167 6.234404 AGTACTCCCCTGGTCTCATAATAT 57.766 41.667 0.00 0.00 0.00 1.28
2797 3168 7.358255 AGTACTCCCCTGGTCTCATAATATA 57.642 40.000 0.00 0.00 0.00 0.86
2798 3169 7.776745 AGTACTCCCCTGGTCTCATAATATAA 58.223 38.462 0.00 0.00 0.00 0.98
2799 3170 7.896496 AGTACTCCCCTGGTCTCATAATATAAG 59.104 40.741 0.00 0.00 0.00 1.73
2800 3171 6.875469 ACTCCCCTGGTCTCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
2801 3172 7.313731 ACTCCCCTGGTCTCATAATATAAGAA 58.686 38.462 0.00 0.00 0.00 2.52
2802 3173 7.964293 ACTCCCCTGGTCTCATAATATAAGAAT 59.036 37.037 0.00 0.00 0.00 2.40
2803 3174 8.757307 TCCCCTGGTCTCATAATATAAGAATT 57.243 34.615 0.00 0.00 0.00 2.17
2804 3175 9.182642 TCCCCTGGTCTCATAATATAAGAATTT 57.817 33.333 0.00 0.00 0.00 1.82
2805 3176 9.813826 CCCCTGGTCTCATAATATAAGAATTTT 57.186 33.333 0.00 0.00 0.00 1.82
2834 3205 7.981789 TGACACTATCAGTAGAAAGCAAATAGG 59.018 37.037 0.00 0.00 31.91 2.57
2836 3207 7.982354 ACACTATCAGTAGAAAGCAAATAGGAC 59.018 37.037 0.00 0.00 0.00 3.85
2837 3208 7.439655 CACTATCAGTAGAAAGCAAATAGGACC 59.560 40.741 0.00 0.00 0.00 4.46
2844 3215 6.478512 AGAAAGCAAATAGGACCACAAAAA 57.521 33.333 0.00 0.00 0.00 1.94
2845 3216 7.066307 AGAAAGCAAATAGGACCACAAAAAT 57.934 32.000 0.00 0.00 0.00 1.82
2846 3217 6.930722 AGAAAGCAAATAGGACCACAAAAATG 59.069 34.615 0.00 0.00 0.00 2.32
2847 3218 6.418057 AAGCAAATAGGACCACAAAAATGA 57.582 33.333 0.00 0.00 0.00 2.57
2848 3219 6.610075 AGCAAATAGGACCACAAAAATGAT 57.390 33.333 0.00 0.00 0.00 2.45
2849 3220 7.716799 AGCAAATAGGACCACAAAAATGATA 57.283 32.000 0.00 0.00 0.00 2.15
2884 3262 7.708322 CACTCAAGCTTACATCTTAGCATTCTA 59.292 37.037 0.00 0.00 39.85 2.10
2885 3263 8.428063 ACTCAAGCTTACATCTTAGCATTCTAT 58.572 33.333 0.00 0.00 39.85 1.98
2886 3264 8.824159 TCAAGCTTACATCTTAGCATTCTATC 57.176 34.615 0.00 0.00 39.85 2.08
2971 3349 1.949257 CTTCCGTTGTTGCCCTCAC 59.051 57.895 0.00 0.00 0.00 3.51
2973 3351 4.025401 CCGTTGTTGCCCTCACGC 62.025 66.667 0.00 0.00 0.00 5.34
2974 3352 2.972505 CGTTGTTGCCCTCACGCT 60.973 61.111 0.00 0.00 0.00 5.07
2976 3354 1.866925 GTTGTTGCCCTCACGCTAC 59.133 57.895 0.00 0.00 35.42 3.58
2977 3355 0.882927 GTTGTTGCCCTCACGCTACA 60.883 55.000 0.00 0.00 41.63 2.74
2979 3357 0.391130 TGTTGCCCTCACGCTACATC 60.391 55.000 0.00 0.00 39.12 3.06
2980 3358 0.108138 GTTGCCCTCACGCTACATCT 60.108 55.000 0.00 0.00 35.04 2.90
2989 3367 4.437239 CTCACGCTACATCTTTTGATCCT 58.563 43.478 0.00 0.00 36.97 3.24
3010 3388 2.171659 TGTAGGAAAACAGTGCACTCCA 59.828 45.455 18.64 3.48 0.00 3.86
3175 3554 0.322975 CTAGCTCTTGCACTGGGTGT 59.677 55.000 0.00 0.00 42.74 4.16
3345 3724 2.413453 GAGCTAGAGAAAGCAACCAACG 59.587 50.000 0.00 0.00 45.30 4.10
3365 3744 2.654912 CTTTGACCCGACGCGTGTC 61.655 63.158 20.70 19.16 41.91 3.67
3749 4128 5.220931 GGATGTGAAATCTGCCAACATACTC 60.221 44.000 0.00 0.00 0.00 2.59
3758 4137 4.019411 TCTGCCAACATACTCTTGGATGAA 60.019 41.667 1.24 0.00 40.76 2.57
3760 4139 5.076182 TGCCAACATACTCTTGGATGAAAA 58.924 37.500 1.24 0.00 40.76 2.29
3845 4224 4.082523 ACCATCGTGCAGGGGACG 62.083 66.667 6.56 3.81 38.20 4.79
4013 4392 2.280628 CATTACTTCCTTGGACGGCTC 58.719 52.381 0.00 0.00 0.00 4.70
4028 4407 0.234884 GGCTCAAAGACGAAACCGTG 59.765 55.000 0.00 0.00 40.80 4.94
4040 4419 6.522054 AGACGAAACCGTGATGGATATTATT 58.478 36.000 0.00 0.00 42.00 1.40
4127 4506 1.038130 GCTTGAGGACTAGAGGCGGA 61.038 60.000 0.00 0.00 0.00 5.54
4130 4509 0.039180 TGAGGACTAGAGGCGGACAA 59.961 55.000 0.00 0.00 0.00 3.18
4254 4633 2.233271 AGCCATTGTTGTCAACTCCAG 58.767 47.619 16.45 4.95 36.33 3.86
4260 4639 2.288666 TGTTGTCAACTCCAGTGAAGC 58.711 47.619 16.45 0.00 0.00 3.86
4359 5685 0.755686 GAGGTGCTACTCCATGGAGG 59.244 60.000 38.54 25.65 45.88 4.30
4540 6118 7.285858 GTGACTAGTGGTAGATAGTGGAAGAAT 59.714 40.741 0.00 0.00 32.43 2.40
4541 6119 7.285629 TGACTAGTGGTAGATAGTGGAAGAATG 59.714 40.741 0.00 0.00 32.43 2.67
4542 6120 7.126733 ACTAGTGGTAGATAGTGGAAGAATGT 58.873 38.462 0.00 0.00 31.09 2.71
4543 6121 6.227298 AGTGGTAGATAGTGGAAGAATGTG 57.773 41.667 0.00 0.00 0.00 3.21
4544 6122 5.721960 AGTGGTAGATAGTGGAAGAATGTGT 59.278 40.000 0.00 0.00 0.00 3.72
4545 6123 6.213600 AGTGGTAGATAGTGGAAGAATGTGTT 59.786 38.462 0.00 0.00 0.00 3.32
4546 6124 6.313905 GTGGTAGATAGTGGAAGAATGTGTTG 59.686 42.308 0.00 0.00 0.00 3.33
4547 6125 6.212589 TGGTAGATAGTGGAAGAATGTGTTGA 59.787 38.462 0.00 0.00 0.00 3.18
4623 6791 5.300752 CACACCAGATTCAGTGTAAGAGTT 58.699 41.667 10.93 0.00 45.20 3.01
4632 6800 7.665559 AGATTCAGTGTAAGAGTTTTATTGCCA 59.334 33.333 0.00 0.00 0.00 4.92
4784 7068 3.104512 CCCAGTGTGGATGTAAGTCCTA 58.895 50.000 0.00 0.00 40.96 2.94
4816 7100 4.265073 AGATTAGTTTCCACAGATGGCAC 58.735 43.478 0.00 0.00 46.80 5.01
4821 7106 2.299867 GTTTCCACAGATGGCACCAAAT 59.700 45.455 0.00 0.00 46.80 2.32
4960 7262 7.603651 TCTTACTCCAGAAGATCACTACAAAC 58.396 38.462 0.00 0.00 0.00 2.93
5018 7320 9.715121 TCTAGCCTTCTTTTATTTCTTCGTAAA 57.285 29.630 0.00 0.00 0.00 2.01
5051 7353 8.888579 TGCTATTTCAGTAGTATTTTCTAGCC 57.111 34.615 0.00 0.00 0.00 3.93
5052 7354 8.705594 TGCTATTTCAGTAGTATTTTCTAGCCT 58.294 33.333 0.00 0.00 0.00 4.58
5053 7355 9.549078 GCTATTTCAGTAGTATTTTCTAGCCTT 57.451 33.333 0.00 0.00 0.00 4.35
5068 7370 8.617290 TTTCTAGCCTTCTTTTATTTCTTCGT 57.383 30.769 0.00 0.00 0.00 3.85
5069 7371 9.715121 TTTCTAGCCTTCTTTTATTTCTTCGTA 57.285 29.630 0.00 0.00 0.00 3.43
5070 7372 9.715121 TTCTAGCCTTCTTTTATTTCTTCGTAA 57.285 29.630 0.00 0.00 0.00 3.18
5071 7373 9.715121 TCTAGCCTTCTTTTATTTCTTCGTAAA 57.285 29.630 0.00 0.00 0.00 2.01
5104 7406 8.888579 TGCTATTTCAGTAGTATTTTCTAGCC 57.111 34.615 0.00 0.00 0.00 3.93
5105 7407 8.705594 TGCTATTTCAGTAGTATTTTCTAGCCT 58.294 33.333 0.00 0.00 0.00 4.58
5106 7408 9.549078 GCTATTTCAGTAGTATTTTCTAGCCTT 57.451 33.333 0.00 0.00 0.00 4.35
5121 7423 8.617290 TTTCTAGCCTTCTTTTATTTCTTCGT 57.383 30.769 0.00 0.00 0.00 3.85
5122 7424 9.715121 TTTCTAGCCTTCTTTTATTTCTTCGTA 57.285 29.630 0.00 0.00 0.00 3.43
5123 7425 9.715121 TTCTAGCCTTCTTTTATTTCTTCGTAA 57.285 29.630 0.00 0.00 0.00 3.18
5124 7426 9.715121 TCTAGCCTTCTTTTATTTCTTCGTAAA 57.285 29.630 0.00 0.00 0.00 2.01
5157 7459 8.888579 TGCTATTTCAGTAGTATTTTCTAGCC 57.111 34.615 0.00 0.00 0.00 3.93
5158 7460 8.705594 TGCTATTTCAGTAGTATTTTCTAGCCT 58.294 33.333 0.00 0.00 0.00 4.58
5159 7461 9.549078 GCTATTTCAGTAGTATTTTCTAGCCTT 57.451 33.333 0.00 0.00 0.00 4.35
5174 7476 8.617290 TTTCTAGCCTTCTTTTATTTCTTCGT 57.383 30.769 0.00 0.00 0.00 3.85
5175 7477 9.715121 TTTCTAGCCTTCTTTTATTTCTTCGTA 57.285 29.630 0.00 0.00 0.00 3.43
5176 7478 9.715121 TTCTAGCCTTCTTTTATTTCTTCGTAA 57.285 29.630 0.00 0.00 0.00 3.18
5177 7479 9.715121 TCTAGCCTTCTTTTATTTCTTCGTAAA 57.285 29.630 0.00 0.00 0.00 2.01
5217 7519 8.523915 TCGGTAGTTTCCTGTAGTTCATAATA 57.476 34.615 0.00 0.00 0.00 0.98
5222 7524 8.668510 AGTTTCCTGTAGTTCATAATATGCTG 57.331 34.615 0.00 0.00 0.00 4.41
5257 7566 9.806203 CTTCTTTCATAATTTGCCATATCAACA 57.194 29.630 0.00 0.00 0.00 3.33
5259 7568 7.922278 TCTTTCATAATTTGCCATATCAACAGC 59.078 33.333 0.00 0.00 0.00 4.40
5281 7591 7.147637 ACAGCTTTATTTTGTTCCCACCTAAAA 60.148 33.333 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.722535 AGCGGGAGAGGAGGCCAA 62.723 66.667 5.01 0.00 0.00 4.52
201 212 4.389576 CGTTGGTCGCTGCTTGCC 62.390 66.667 0.00 0.00 38.78 4.52
236 250 1.112916 TGGCGGAGAAGATGCGGATA 61.113 55.000 0.00 0.00 43.95 2.59
261 275 4.157840 GTGATGTGTTGGGAGAAATTACCC 59.842 45.833 7.95 7.95 45.74 3.69
262 276 4.764823 TGTGATGTGTTGGGAGAAATTACC 59.235 41.667 0.00 0.00 0.00 2.85
263 277 5.957842 TGTGATGTGTTGGGAGAAATTAC 57.042 39.130 0.00 0.00 0.00 1.89
264 278 5.353956 CGATGTGATGTGTTGGGAGAAATTA 59.646 40.000 0.00 0.00 0.00 1.40
274 288 1.070821 AGACGCGATGTGATGTGTTG 58.929 50.000 15.93 0.00 0.00 3.33
284 298 6.771188 AATTATTAGGAAGAAGACGCGATG 57.229 37.500 15.93 0.00 0.00 3.84
285 299 6.424207 GGAAATTATTAGGAAGAAGACGCGAT 59.576 38.462 15.93 0.00 0.00 4.58
286 300 5.751990 GGAAATTATTAGGAAGAAGACGCGA 59.248 40.000 15.93 0.00 0.00 5.87
287 301 5.050295 GGGAAATTATTAGGAAGAAGACGCG 60.050 44.000 3.53 3.53 0.00 6.01
288 302 5.238868 GGGGAAATTATTAGGAAGAAGACGC 59.761 44.000 0.00 0.00 0.00 5.19
289 303 5.763698 GGGGGAAATTATTAGGAAGAAGACG 59.236 44.000 0.00 0.00 0.00 4.18
301 328 6.443206 TCACAATTCACATGGGGGAAATTATT 59.557 34.615 0.00 0.00 0.00 1.40
305 332 3.788933 TCACAATTCACATGGGGGAAAT 58.211 40.909 0.00 0.00 0.00 2.17
313 340 5.568677 CACATACGGTTTCACAATTCACATG 59.431 40.000 0.00 0.00 0.00 3.21
314 341 5.240623 ACACATACGGTTTCACAATTCACAT 59.759 36.000 0.00 0.00 0.00 3.21
315 342 4.576873 ACACATACGGTTTCACAATTCACA 59.423 37.500 0.00 0.00 0.00 3.58
316 343 4.909305 CACACATACGGTTTCACAATTCAC 59.091 41.667 0.00 0.00 0.00 3.18
317 344 4.555708 GCACACATACGGTTTCACAATTCA 60.556 41.667 0.00 0.00 0.00 2.57
318 345 3.911964 GCACACATACGGTTTCACAATTC 59.088 43.478 0.00 0.00 0.00 2.17
319 346 3.316588 TGCACACATACGGTTTCACAATT 59.683 39.130 0.00 0.00 0.00 2.32
320 347 2.881513 TGCACACATACGGTTTCACAAT 59.118 40.909 0.00 0.00 0.00 2.71
321 348 2.289565 TGCACACATACGGTTTCACAA 58.710 42.857 0.00 0.00 0.00 3.33
322 349 1.954927 TGCACACATACGGTTTCACA 58.045 45.000 0.00 0.00 0.00 3.58
323 350 3.233578 CATTGCACACATACGGTTTCAC 58.766 45.455 0.00 0.00 0.00 3.18
324 351 2.881513 ACATTGCACACATACGGTTTCA 59.118 40.909 0.00 0.00 0.00 2.69
325 352 3.552604 ACATTGCACACATACGGTTTC 57.447 42.857 0.00 0.00 0.00 2.78
326 353 5.440234 TTTACATTGCACACATACGGTTT 57.560 34.783 0.00 0.00 0.00 3.27
327 354 5.414454 AGATTTACATTGCACACATACGGTT 59.586 36.000 0.00 0.00 0.00 4.44
328 355 4.941263 AGATTTACATTGCACACATACGGT 59.059 37.500 0.00 0.00 0.00 4.83
329 356 5.484173 AGATTTACATTGCACACATACGG 57.516 39.130 0.00 0.00 0.00 4.02
330 357 6.779385 CAAGATTTACATTGCACACATACG 57.221 37.500 0.00 0.00 0.00 3.06
410 650 0.178953 ATGAAGGTGCCCAAGCTTGT 60.179 50.000 24.35 4.38 46.56 3.16
463 705 1.683790 GGACGACGCCGATTGTGAAG 61.684 60.000 0.00 0.00 39.50 3.02
568 810 2.434884 ATCTGTGCTTGGGCGACG 60.435 61.111 0.00 0.00 42.25 5.12
572 814 3.818787 CGCCATCTGTGCTTGGGC 61.819 66.667 0.00 0.00 41.20 5.36
619 876 3.242944 CCGTCATATGTGAACTAGCAACG 59.757 47.826 1.90 1.21 35.80 4.10
620 877 3.555956 CCCGTCATATGTGAACTAGCAAC 59.444 47.826 1.90 0.00 35.80 4.17
639 896 1.880027 CTGTTTCTTCTTGGAACCCCG 59.120 52.381 0.00 0.00 34.29 5.73
653 911 3.118905 AGACTTGCTGACCTCTGTTTC 57.881 47.619 0.00 0.00 0.00 2.78
740 999 2.170166 TCCACTTGGTCATGAATTGGC 58.830 47.619 0.00 0.00 36.34 4.52
784 1043 0.378257 GAAGCACGCCACCATACATG 59.622 55.000 0.00 0.00 0.00 3.21
857 1117 1.305381 CCTCTCCCGTGGGAACTCT 60.305 63.158 9.34 0.00 44.66 3.24
895 1155 6.541278 CCTATCAAAGATGTGATTTGCAGAGA 59.459 38.462 0.00 0.00 39.07 3.10
927 1187 3.527665 AGCACCCTCCCTGTTTTGTATAT 59.472 43.478 0.00 0.00 0.00 0.86
930 1190 1.073284 GAGCACCCTCCCTGTTTTGTA 59.927 52.381 0.00 0.00 31.68 2.41
935 1195 1.062488 AACAGAGCACCCTCCCTGTT 61.062 55.000 0.00 0.00 38.96 3.16
999 1259 2.045926 AACAGCACCGGCCTCATC 60.046 61.111 0.00 0.00 42.56 2.92
1003 1263 2.906897 CAACAACAGCACCGGCCT 60.907 61.111 0.00 0.00 42.56 5.19
1007 1267 1.063972 CACACCAACAACAGCACCG 59.936 57.895 0.00 0.00 0.00 4.94
1076 1336 0.765903 GGCAGATGGAGGATCAGGGA 60.766 60.000 0.00 0.00 36.25 4.20
1178 1438 0.107945 GCAGATGAGGTCGAAGCCTT 60.108 55.000 0.00 0.00 39.34 4.35
1179 1439 1.519719 GCAGATGAGGTCGAAGCCT 59.480 57.895 0.00 0.00 42.53 4.58
1222 1482 1.339151 GGTGGTGTTGCCTAGGAAGAG 60.339 57.143 14.75 0.00 38.35 2.85
1356 1616 1.981256 AGGTCGCAATGTTGAGGTTT 58.019 45.000 0.00 0.00 0.00 3.27
1368 1628 0.892755 CCAGGTAGTTGTAGGTCGCA 59.107 55.000 0.00 0.00 0.00 5.10
1440 1700 4.357947 GTGCAGTGGCCGACGAGA 62.358 66.667 0.00 0.00 40.13 4.04
1459 1719 2.098293 CCATGGAGGCGCACTTAAC 58.902 57.895 10.83 0.00 0.00 2.01
1483 1743 1.513158 CTTCCGTCACGAGGAGCAT 59.487 57.895 0.00 0.00 39.22 3.79
1503 1763 3.036429 GCCGTTGCAGATCCCTCCT 62.036 63.158 0.00 0.00 37.47 3.69
1590 1850 1.185618 AAGGCTGCGGTACTGTCTCA 61.186 55.000 3.10 0.00 29.75 3.27
1710 1970 1.034838 AGAGGTACGCAGCAGAGGAG 61.035 60.000 0.00 0.00 0.00 3.69
1749 2009 2.083774 CGAGCTTTAGCACAATTGGGA 58.916 47.619 13.13 0.00 45.16 4.37
1758 2018 0.179111 CATCCGACCGAGCTTTAGCA 60.179 55.000 4.33 0.00 45.16 3.49
1908 2168 1.433592 AGACTAGGTGTGGAAGGAGGT 59.566 52.381 0.00 0.00 0.00 3.85
1927 2187 6.419980 TGGTTGAGCAAACAAATGAAAAAG 57.580 33.333 0.00 0.00 40.86 2.27
2037 2407 8.863049 CAAATGAAGCACTTTATACACCATTTC 58.137 33.333 0.00 0.00 31.74 2.17
2137 2508 8.724229 CACATGATCTAGAACAGTTCATTTTGA 58.276 33.333 15.85 6.20 40.30 2.69
2644 3015 5.491982 ACCATAAGACAGAATCCACTGAAC 58.508 41.667 0.00 0.00 40.63 3.18
2647 3018 5.468072 GCATACCATAAGACAGAATCCACTG 59.532 44.000 0.00 0.00 42.78 3.66
2652 3023 3.433615 GCCGCATACCATAAGACAGAATC 59.566 47.826 0.00 0.00 0.00 2.52
2660 3031 3.988379 ATGTTTGCCGCATACCATAAG 57.012 42.857 10.91 0.00 0.00 1.73
2672 3043 7.715657 TCATGTTAAATCTCCATATGTTTGCC 58.284 34.615 1.24 0.00 0.00 4.52
2678 3049 9.616634 CGGAATTTCATGTTAAATCTCCATATG 57.383 33.333 0.00 0.00 31.98 1.78
2679 3050 9.573166 TCGGAATTTCATGTTAAATCTCCATAT 57.427 29.630 14.37 0.00 31.98 1.78
2682 3053 7.109501 TCTCGGAATTTCATGTTAAATCTCCA 58.890 34.615 14.37 0.00 31.98 3.86
2687 3058 9.410556 CACTTTTCTCGGAATTTCATGTTAAAT 57.589 29.630 0.00 0.00 0.00 1.40
2697 3068 6.391227 AACATGTCACTTTTCTCGGAATTT 57.609 33.333 0.00 0.00 0.00 1.82
2702 3073 4.935205 TGGATAACATGTCACTTTTCTCGG 59.065 41.667 0.00 0.00 0.00 4.63
2703 3074 6.668541 ATGGATAACATGTCACTTTTCTCG 57.331 37.500 0.00 0.00 38.70 4.04
2719 3090 7.615039 ACATGCCATAAAATTCCATGGATAA 57.385 32.000 17.06 0.89 43.80 1.75
2724 3095 6.988622 AACAACATGCCATAAAATTCCATG 57.011 33.333 0.00 0.00 39.23 3.66
2725 3096 6.127952 GCAAACAACATGCCATAAAATTCCAT 60.128 34.615 0.00 0.00 37.85 3.41
2727 3098 5.180868 TGCAAACAACATGCCATAAAATTCC 59.819 36.000 0.00 0.00 43.16 3.01
2728 3099 6.147492 TCTGCAAACAACATGCCATAAAATTC 59.853 34.615 0.00 0.00 43.16 2.17
2737 3108 5.750067 CCTTAATATCTGCAAACAACATGCC 59.250 40.000 0.00 0.00 43.16 4.40
2738 3109 6.563422 TCCTTAATATCTGCAAACAACATGC 58.437 36.000 0.00 0.00 44.08 4.06
2739 3110 7.699391 CACTCCTTAATATCTGCAAACAACATG 59.301 37.037 0.00 0.00 0.00 3.21
2772 3143 5.681494 ATTATGAGACCAGGGGAGTACTA 57.319 43.478 0.00 0.00 0.00 1.82
2773 3144 4.561254 ATTATGAGACCAGGGGAGTACT 57.439 45.455 0.00 0.00 0.00 2.73
2774 3145 7.894364 TCTTATATTATGAGACCAGGGGAGTAC 59.106 40.741 0.00 0.00 0.00 2.73
2775 3146 8.008104 TCTTATATTATGAGACCAGGGGAGTA 57.992 38.462 0.00 0.00 0.00 2.59
2776 3147 6.875469 TCTTATATTATGAGACCAGGGGAGT 58.125 40.000 0.00 0.00 0.00 3.85
2777 3148 7.798710 TTCTTATATTATGAGACCAGGGGAG 57.201 40.000 0.00 0.00 0.00 4.30
2778 3149 8.757307 AATTCTTATATTATGAGACCAGGGGA 57.243 34.615 0.00 0.00 0.00 4.81
2779 3150 9.813826 AAAATTCTTATATTATGAGACCAGGGG 57.186 33.333 0.00 0.00 0.00 4.79
2804 3175 8.445275 TTGCTTTCTACTGATAGTGTCAAAAA 57.555 30.769 0.00 0.00 36.14 1.94
2805 3176 8.445275 TTTGCTTTCTACTGATAGTGTCAAAA 57.555 30.769 0.00 0.00 36.14 2.44
2806 3177 8.621532 ATTTGCTTTCTACTGATAGTGTCAAA 57.378 30.769 0.00 0.00 36.14 2.69
2807 3178 9.371136 CTATTTGCTTTCTACTGATAGTGTCAA 57.629 33.333 0.00 0.00 36.14 3.18
2808 3179 7.981789 CCTATTTGCTTTCTACTGATAGTGTCA 59.018 37.037 0.00 0.00 35.05 3.58
2809 3180 8.198109 TCCTATTTGCTTTCTACTGATAGTGTC 58.802 37.037 0.00 0.00 0.00 3.67
2810 3181 7.982354 GTCCTATTTGCTTTCTACTGATAGTGT 59.018 37.037 0.00 0.00 0.00 3.55
2811 3182 7.439655 GGTCCTATTTGCTTTCTACTGATAGTG 59.560 40.741 0.00 0.00 0.00 2.74
2812 3183 7.125811 TGGTCCTATTTGCTTTCTACTGATAGT 59.874 37.037 0.00 0.00 0.00 2.12
2813 3184 7.439655 GTGGTCCTATTTGCTTTCTACTGATAG 59.560 40.741 0.00 0.00 0.00 2.08
2814 3185 7.093068 TGTGGTCCTATTTGCTTTCTACTGATA 60.093 37.037 0.00 0.00 0.00 2.15
2815 3186 6.116126 GTGGTCCTATTTGCTTTCTACTGAT 58.884 40.000 0.00 0.00 0.00 2.90
2816 3187 5.012664 TGTGGTCCTATTTGCTTTCTACTGA 59.987 40.000 0.00 0.00 0.00 3.41
2817 3188 5.245531 TGTGGTCCTATTTGCTTTCTACTG 58.754 41.667 0.00 0.00 0.00 2.74
2818 3189 5.499004 TGTGGTCCTATTTGCTTTCTACT 57.501 39.130 0.00 0.00 0.00 2.57
2854 3225 6.098266 TGCTAAGATGTAAGCTTGAGTGGATA 59.902 38.462 9.86 0.00 45.56 2.59
2863 3234 7.387397 GCAGATAGAATGCTAAGATGTAAGCTT 59.613 37.037 3.48 3.48 39.14 3.74
2866 3237 8.087136 TCTGCAGATAGAATGCTAAGATGTAAG 58.913 37.037 13.74 0.00 44.17 2.34
2873 3244 8.871862 GTCAATATCTGCAGATAGAATGCTAAG 58.128 37.037 33.44 17.99 44.17 2.18
2884 3262 3.388308 GCACTCGTCAATATCTGCAGAT 58.612 45.455 30.85 30.85 38.51 2.90
2885 3263 2.481969 GGCACTCGTCAATATCTGCAGA 60.482 50.000 20.79 20.79 0.00 4.26
2886 3264 1.863454 GGCACTCGTCAATATCTGCAG 59.137 52.381 7.63 7.63 0.00 4.41
2930 3308 4.261363 GCTTCCTTTCAGGTTATAGCATGC 60.261 45.833 10.51 10.51 36.53 4.06
2971 3349 4.747108 CCTACAGGATCAAAAGATGTAGCG 59.253 45.833 5.37 0.00 41.16 4.26
2973 3351 8.669243 GTTTTCCTACAGGATCAAAAGATGTAG 58.331 37.037 0.00 4.14 44.98 2.74
2974 3352 8.160765 TGTTTTCCTACAGGATCAAAAGATGTA 58.839 33.333 0.00 0.00 44.98 2.29
2976 3354 7.452880 TGTTTTCCTACAGGATCAAAAGATG 57.547 36.000 0.00 0.00 44.98 2.90
2977 3355 7.693969 CTGTTTTCCTACAGGATCAAAAGAT 57.306 36.000 0.00 0.00 44.98 2.40
2989 3367 2.171659 TGGAGTGCACTGTTTTCCTACA 59.828 45.455 27.27 0.78 0.00 2.74
3010 3388 6.980397 CCAAAATAAGATTTTGCCGCTTATCT 59.020 34.615 15.93 0.00 37.89 1.98
3100 3479 4.889409 CCCCTACATGAGTAATTGCAACAT 59.111 41.667 0.00 0.00 0.00 2.71
3175 3554 9.868160 TCTTCAATCTCCTCACTAGTATAATCA 57.132 33.333 0.00 0.00 0.00 2.57
3345 3724 2.355481 ACGCGTCGGGTCAAAGTC 60.355 61.111 5.58 0.00 0.00 3.01
3621 4000 0.311790 CACGTCAGCAAGCATTTGGT 59.688 50.000 0.00 0.00 45.38 3.67
3749 4128 5.212532 TGGTGGTGAAATTTTCATCCAAG 57.787 39.130 23.26 0.00 40.09 3.61
3928 4307 1.743958 TCTTCCTCGTTAAGAGCTCGG 59.256 52.381 8.37 1.30 45.54 4.63
4127 4506 5.474876 CACTTCTTTCATCTTAGGCCTTTGT 59.525 40.000 12.58 0.00 0.00 2.83
4130 4509 4.289672 TCCACTTCTTTCATCTTAGGCCTT 59.710 41.667 12.58 0.00 0.00 4.35
4166 4545 2.422231 CCTCCTAGCTCGCAGCAGT 61.422 63.158 10.16 0.00 45.56 4.40
4254 4633 3.791245 CAGAAGTAGATCTGGGCTTCAC 58.209 50.000 24.91 9.39 42.52 3.18
4359 5685 2.873472 CTGATGAAGCTGCCATCTCTTC 59.127 50.000 22.30 9.34 40.65 2.87
4427 5970 0.242555 ATAAACAAAACGGGGCGCAG 59.757 50.000 10.83 0.00 0.00 5.18
4530 6108 3.254166 GTGCATCAACACATTCTTCCACT 59.746 43.478 0.00 0.00 40.40 4.00
4541 6119 4.362279 ACACTGAATTTGTGCATCAACAC 58.638 39.130 11.01 0.00 38.86 3.32
4542 6120 4.652421 ACACTGAATTTGTGCATCAACA 57.348 36.364 11.01 0.00 38.86 3.33
4543 6121 5.048782 TCCTACACTGAATTTGTGCATCAAC 60.049 40.000 11.01 0.00 38.86 3.18
4544 6122 5.069318 TCCTACACTGAATTTGTGCATCAA 58.931 37.500 11.01 0.00 38.86 2.57
4545 6123 4.650734 TCCTACACTGAATTTGTGCATCA 58.349 39.130 11.01 0.00 38.86 3.07
4546 6124 5.627499 TTCCTACACTGAATTTGTGCATC 57.373 39.130 11.01 0.00 38.86 3.91
4547 6125 5.477984 ACATTCCTACACTGAATTTGTGCAT 59.522 36.000 11.01 0.00 38.86 3.96
4816 7100 3.490896 CACTCGGACATATCGACATTTGG 59.509 47.826 0.00 0.00 32.86 3.28
4821 7106 1.758936 ACCACTCGGACATATCGACA 58.241 50.000 0.00 0.00 35.59 4.35
4936 7238 6.528423 CGTTTGTAGTGATCTTCTGGAGTAAG 59.472 42.308 0.00 0.00 0.00 2.34
4980 7282 8.427902 AAAAGAAGGCTAGAAAATTCAGGATT 57.572 30.769 0.00 0.00 0.00 3.01
5042 7344 9.063615 ACGAAGAAATAAAAGAAGGCTAGAAAA 57.936 29.630 0.00 0.00 0.00 2.29
5043 7345 8.617290 ACGAAGAAATAAAAGAAGGCTAGAAA 57.383 30.769 0.00 0.00 0.00 2.52
5044 7346 9.715121 TTACGAAGAAATAAAAGAAGGCTAGAA 57.285 29.630 0.00 0.00 0.00 2.10
5045 7347 9.715121 TTTACGAAGAAATAAAAGAAGGCTAGA 57.285 29.630 0.00 0.00 0.00 2.43
5078 7380 9.326413 GGCTAGAAAATACTACTGAAATAGCAA 57.674 33.333 0.00 0.00 34.92 3.91
5079 7381 8.705594 AGGCTAGAAAATACTACTGAAATAGCA 58.294 33.333 0.00 0.00 34.92 3.49
5080 7382 9.549078 AAGGCTAGAAAATACTACTGAAATAGC 57.451 33.333 0.00 0.00 33.00 2.97
5095 7397 9.063615 ACGAAGAAATAAAAGAAGGCTAGAAAA 57.936 29.630 0.00 0.00 0.00 2.29
5096 7398 8.617290 ACGAAGAAATAAAAGAAGGCTAGAAA 57.383 30.769 0.00 0.00 0.00 2.52
5097 7399 9.715121 TTACGAAGAAATAAAAGAAGGCTAGAA 57.285 29.630 0.00 0.00 0.00 2.10
5098 7400 9.715121 TTTACGAAGAAATAAAAGAAGGCTAGA 57.285 29.630 0.00 0.00 0.00 2.43
5131 7433 9.326413 GGCTAGAAAATACTACTGAAATAGCAA 57.674 33.333 0.00 0.00 34.92 3.91
5132 7434 8.705594 AGGCTAGAAAATACTACTGAAATAGCA 58.294 33.333 0.00 0.00 34.92 3.49
5133 7435 9.549078 AAGGCTAGAAAATACTACTGAAATAGC 57.451 33.333 0.00 0.00 33.00 2.97
5148 7450 9.063615 ACGAAGAAATAAAAGAAGGCTAGAAAA 57.936 29.630 0.00 0.00 0.00 2.29
5149 7451 8.617290 ACGAAGAAATAAAAGAAGGCTAGAAA 57.383 30.769 0.00 0.00 0.00 2.52
5150 7452 9.715121 TTACGAAGAAATAAAAGAAGGCTAGAA 57.285 29.630 0.00 0.00 0.00 2.10
5151 7453 9.715121 TTTACGAAGAAATAAAAGAAGGCTAGA 57.285 29.630 0.00 0.00 0.00 2.43
5170 7472 9.843334 ACCGAAATAGCAAATTTATTTTACGAA 57.157 25.926 0.00 0.00 32.42 3.85
5177 7479 9.797556 GGAAACTACCGAAATAGCAAATTTATT 57.202 29.630 0.00 0.00 0.00 1.40
5178 7480 9.185680 AGGAAACTACCGAAATAGCAAATTTAT 57.814 29.630 0.00 0.00 40.61 1.40
5179 7481 8.455682 CAGGAAACTACCGAAATAGCAAATTTA 58.544 33.333 0.00 0.00 40.21 1.40
5180 7482 7.039993 ACAGGAAACTACCGAAATAGCAAATTT 60.040 33.333 0.00 0.00 40.21 1.82
5181 7483 6.433093 ACAGGAAACTACCGAAATAGCAAATT 59.567 34.615 0.00 0.00 40.21 1.82
5182 7484 5.944007 ACAGGAAACTACCGAAATAGCAAAT 59.056 36.000 0.00 0.00 40.21 2.32
5183 7485 5.310451 ACAGGAAACTACCGAAATAGCAAA 58.690 37.500 0.00 0.00 40.21 3.68
5184 7486 4.901868 ACAGGAAACTACCGAAATAGCAA 58.098 39.130 0.00 0.00 40.21 3.91
5185 7487 4.546829 ACAGGAAACTACCGAAATAGCA 57.453 40.909 0.00 0.00 40.21 3.49
5186 7488 5.658468 ACTACAGGAAACTACCGAAATAGC 58.342 41.667 0.00 0.00 40.21 2.97
5187 7489 7.318141 TGAACTACAGGAAACTACCGAAATAG 58.682 38.462 0.00 0.00 40.21 1.73
5188 7490 7.230849 TGAACTACAGGAAACTACCGAAATA 57.769 36.000 0.00 0.00 40.21 1.40
5189 7491 6.105397 TGAACTACAGGAAACTACCGAAAT 57.895 37.500 0.00 0.00 40.21 2.17
5190 7492 5.534207 TGAACTACAGGAAACTACCGAAA 57.466 39.130 0.00 0.00 40.21 3.46
5191 7493 5.733620 ATGAACTACAGGAAACTACCGAA 57.266 39.130 0.00 0.00 40.21 4.30
5192 7494 6.839124 TTATGAACTACAGGAAACTACCGA 57.161 37.500 0.00 0.00 40.21 4.69
5193 7495 9.193133 CATATTATGAACTACAGGAAACTACCG 57.807 37.037 0.00 0.00 40.21 4.02
5194 7496 8.989980 GCATATTATGAACTACAGGAAACTACC 58.010 37.037 7.87 0.00 40.21 3.18
5195 7497 9.765795 AGCATATTATGAACTACAGGAAACTAC 57.234 33.333 7.87 0.00 40.21 2.73
5248 7557 8.034215 TGGGAACAAAATAAAGCTGTTGATATG 58.966 33.333 0.00 0.00 37.44 1.78
5251 7560 6.223120 GTGGGAACAAAATAAAGCTGTTGAT 58.777 36.000 0.00 0.00 46.06 2.57
5253 7562 4.749598 GGTGGGAACAAAATAAAGCTGTTG 59.250 41.667 0.00 0.00 46.06 3.33
5254 7563 4.653801 AGGTGGGAACAAAATAAAGCTGTT 59.346 37.500 0.00 0.00 46.06 3.16
5257 7566 6.987403 TTTAGGTGGGAACAAAATAAAGCT 57.013 33.333 0.00 0.00 46.06 3.74
5281 7591 9.316730 AGCATGACGAATATAAAAATGCATTTT 57.683 25.926 27.73 27.73 43.52 1.82
5305 7615 8.912658 GCAGGTACAAAACTTTTATTTAGAAGC 58.087 33.333 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.