Multiple sequence alignment - TraesCS2A01G017600

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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 TraesCS2A01G017600 chr2A 100.000 4464 0 0 1 4464 8183767 8179304 0.000000e+00 8244.0
1 TraesCS2A01G017600 chr2A 99.771 872 1 1 1 872 3596559 3595689 0.000000e+00 1598.0
2 TraesCS2A01G017600 chr2A 84.599 1383 160 30 1281 2638 7919425 7920779 0.000000e+00 1325.0
3 TraesCS2A01G017600 chr2A 77.209 1347 215 60 1278 2577 8314822 8313521 0.000000e+00 702.0
4 TraesCS2A01G017600 chr2A 99.660 294 1 0 1 294 3598064 3597771 5.080000e-149 538.0
5 TraesCS2A01G017600 chr2A 88.341 446 45 5 35 477 3625040 3624599 3.060000e-146 529.0
6 TraesCS2A01G017600 chr2A 82.334 617 66 22 2914 3513 7921542 7922132 3.100000e-136 496.0
7 TraesCS2A01G017600 chr2A 90.909 231 17 4 2717 2946 7921317 7921544 1.560000e-79 307.0
8 TraesCS2A01G017600 chr2A 81.449 345 49 8 491 821 3637680 3637337 7.360000e-68 268.0
9 TraesCS2A01G017600 chr2A 81.935 155 17 8 334 487 3628244 3628100 2.180000e-23 121.0
10 TraesCS2A01G017600 chr2A 83.636 110 9 4 2825 2925 7808496 7808605 1.320000e-15 95.3
11 TraesCS2A01G017600 chr2A 75.330 227 28 17 1012 1233 7919150 7919353 2.860000e-12 84.2
12 TraesCS2A01G017600 chr2A 92.857 56 3 1 2819 2873 8047005 8047060 3.700000e-11 80.5
13 TraesCS2A01G017600 chr2A 93.750 48 3 0 2745 2792 8046963 8047010 6.190000e-09 73.1
14 TraesCS2A01G017600 chr2B 97.311 1339 29 2 1211 2542 70882082 70880744 0.000000e+00 2266.0
15 TraesCS2A01G017600 chr2B 76.542 1232 196 45 1283 2472 12077535 12076355 4.970000e-164 588.0
16 TraesCS2A01G017600 chr2B 76.283 877 123 51 1020 1852 12027150 12026315 5.410000e-104 388.0
17 TraesCS2A01G017600 chr2B 90.411 219 19 2 2429 2647 70880562 70880346 2.030000e-73 287.0
18 TraesCS2A01G017600 chr2B 96.386 166 5 1 2684 2849 70880211 70880047 5.690000e-69 272.0
19 TraesCS2A01G017600 chr2B 85.401 137 1 7 994 1128 70882820 70882701 1.690000e-24 124.0
20 TraesCS2A01G017600 chr2B 89.474 95 9 1 35 129 6294195 6294288 7.840000e-23 119.0
21 TraesCS2A01G017600 chr2B 91.667 60 3 2 2819 2876 11986238 11986297 1.030000e-11 82.4
22 TraesCS2A01G017600 chr7A 97.243 1306 30 1 1357 2656 466508094 466509399 0.000000e+00 2207.0
23 TraesCS2A01G017600 chr7A 93.953 645 15 6 2684 3325 466509805 466510428 0.000000e+00 953.0
24 TraesCS2A01G017600 chr7A 96.231 398 11 1 4067 4464 466511140 466511533 0.000000e+00 649.0
25 TraesCS2A01G017600 chr7A 88.190 525 29 15 959 1471 466507590 466508093 2.970000e-166 595.0
26 TraesCS2A01G017600 chr7A 97.692 260 4 2 3811 4070 466510701 466510958 3.170000e-121 446.0
27 TraesCS2A01G017600 chr7A 89.498 219 21 2 2429 2647 466509383 466509599 4.400000e-70 276.0
28 TraesCS2A01G017600 chr7A 91.241 137 9 2 3579 3712 466510511 466510647 2.740000e-42 183.0
29 TraesCS2A01G017600 chr3D 82.908 1685 193 53 1012 2638 563859403 563861050 0.000000e+00 1428.0
30 TraesCS2A01G017600 chr3D 76.323 1115 175 50 1276 2355 564005892 564004832 8.560000e-142 514.0
31 TraesCS2A01G017600 chr3D 81.715 618 71 22 2914 3513 563861816 563862409 1.120000e-130 477.0
32 TraesCS2A01G017600 chr3D 90.909 231 17 4 2717 2946 563861591 563861818 1.560000e-79 307.0
33 TraesCS2A01G017600 chr2D 98.438 704 11 0 1953 2656 8928474 8929177 0.000000e+00 1240.0
34 TraesCS2A01G017600 chr2D 90.712 969 24 16 1014 1961 8920099 8921022 0.000000e+00 1230.0
35 TraesCS2A01G017600 chr2D 94.634 615 10 6 2684 3297 8929512 8930104 0.000000e+00 931.0
36 TraesCS2A01G017600 chr2D 78.627 1413 229 48 1269 2648 8889081 8890453 0.000000e+00 869.0
37 TraesCS2A01G017600 chr2D 93.500 400 11 4 4067 4464 8931084 8931470 8.320000e-162 580.0
38 TraesCS2A01G017600 chr2D 75.722 1351 191 74 1276 2566 8983000 8981727 6.530000e-153 551.0
39 TraesCS2A01G017600 chr2D 97.398 269 6 1 3802 4070 8930673 8930940 1.460000e-124 457.0
40 TraesCS2A01G017600 chr2D 81.703 552 74 10 2090 2635 8717114 8717644 6.860000e-118 435.0
41 TraesCS2A01G017600 chr2D 75.726 861 139 41 1020 1852 8715998 8716816 7.050000e-98 368.0
42 TraesCS2A01G017600 chr2D 89.862 217 20 2 2429 2645 8929161 8929375 1.220000e-70 278.0
43 TraesCS2A01G017600 chr2D 92.105 152 11 1 3577 3728 8930473 8930623 3.500000e-51 213.0
44 TraesCS2A01G017600 chr2D 79.360 344 36 15 491 821 5197978 5198299 4.520000e-50 209.0
45 TraesCS2A01G017600 chr2D 93.578 109 7 0 3419 3527 8930347 8930455 3.570000e-36 163.0
46 TraesCS2A01G017600 chr2D 97.403 77 2 0 3322 3398 8930281 8930357 1.010000e-26 132.0
47 TraesCS2A01G017600 chr2D 78.626 131 15 8 988 1116 8888782 8888901 1.720000e-09 75.0
48 TraesCS2A01G017600 chr4A 76.642 137 22 7 1413 1548 46416883 46417010 2.880000e-07 67.6
49 TraesCS2A01G017600 chr4B 91.489 47 3 1 1413 1458 515122472 515122518 3.730000e-06 63.9
50 TraesCS2A01G017600 chr7B 94.872 39 1 1 1071 1108 241369687 241369649 4.820000e-05 60.2
51 TraesCS2A01G017600 chr3B 92.308 39 1 1 1079 1117 273765043 273765079 2.000000e-03 54.7
52 TraesCS2A01G017600 chr3A 96.774 31 1 0 1078 1108 451791306 451791276 8.000000e-03 52.8
53 TraesCS2A01G017600 chr1A 91.892 37 3 0 1072 1108 106679749 106679713 8.000000e-03 52.8


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 TraesCS2A01G017600 chr2A 8179304 8183767 4463 True 8244.000000 8244 100.000000 1 4464 1 chr2A.!!$R2 4463
1 TraesCS2A01G017600 chr2A 3595689 3598064 2375 True 1068.000000 1598 99.715500 1 872 2 chr2A.!!$R4 871
2 TraesCS2A01G017600 chr2A 8313521 8314822 1301 True 702.000000 702 77.209000 1278 2577 1 chr2A.!!$R3 1299
3 TraesCS2A01G017600 chr2A 7919150 7922132 2982 False 553.050000 1325 83.293000 1012 3513 4 chr2A.!!$F2 2501
4 TraesCS2A01G017600 chr2A 3624599 3628244 3645 True 325.000000 529 85.138000 35 487 2 chr2A.!!$R5 452
5 TraesCS2A01G017600 chr2B 70880047 70882820 2773 True 737.250000 2266 92.377250 994 2849 4 chr2B.!!$R3 1855
6 TraesCS2A01G017600 chr2B 12076355 12077535 1180 True 588.000000 588 76.542000 1283 2472 1 chr2B.!!$R2 1189
7 TraesCS2A01G017600 chr2B 12026315 12027150 835 True 388.000000 388 76.283000 1020 1852 1 chr2B.!!$R1 832
8 TraesCS2A01G017600 chr7A 466507590 466511533 3943 False 758.428571 2207 93.435429 959 4464 7 chr7A.!!$F1 3505
9 TraesCS2A01G017600 chr3D 563859403 563862409 3006 False 737.333333 1428 85.177333 1012 3513 3 chr3D.!!$F1 2501
10 TraesCS2A01G017600 chr3D 564004832 564005892 1060 True 514.000000 514 76.323000 1276 2355 1 chr3D.!!$R1 1079
11 TraesCS2A01G017600 chr2D 8920099 8921022 923 False 1230.000000 1230 90.712000 1014 1961 1 chr2D.!!$F2 947
12 TraesCS2A01G017600 chr2D 8981727 8983000 1273 True 551.000000 551 75.722000 1276 2566 1 chr2D.!!$R1 1290
13 TraesCS2A01G017600 chr2D 8928474 8931470 2996 False 499.250000 1240 94.614750 1953 4464 8 chr2D.!!$F5 2511
14 TraesCS2A01G017600 chr2D 8888782 8890453 1671 False 472.000000 869 78.626500 988 2648 2 chr2D.!!$F4 1660
15 TraesCS2A01G017600 chr2D 8715998 8717644 1646 False 401.500000 435 78.714500 1020 2635 2 chr2D.!!$F3 1615

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
877 2383 0.037232 CTTATGCTACTAGGCCGGCC 60.037 60.000 39.29 39.29 0.00 6.13 F
895 2401 0.037975 CCCGTGTACTTAACGTGCCT 60.038 55.000 0.00 0.00 39.38 4.75 F
899 2405 0.320946 TGTACTTAACGTGCCTGGCC 60.321 55.000 17.53 6.66 0.00 5.36 F
1052 2558 0.550914 CTCGATCCCCAAATCCCCAA 59.449 55.000 0.00 0.00 0.00 4.12 F
1053 2559 1.003646 TCGATCCCCAAATCCCCAAA 58.996 50.000 0.00 0.00 0.00 3.28 F
1746 5566 1.143329 TGCCCCTTCCACCCAACATA 61.143 55.000 0.00 0.00 0.00 2.29 F
1857 5686 1.300388 GCACCAAGGCTGCAAGTTG 60.300 57.895 0.50 0.00 35.30 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 5686 0.813821 GGGGCAACTCAATGAAGCTC 59.186 55.000 0.00 0.00 36.63 4.09 R
2672 7203 2.517650 TGACAACACATACGCTGACA 57.482 45.000 0.00 0.00 0.00 3.58 R
2675 7206 3.618594 AGCTAATGACAACACATACGCTG 59.381 43.478 0.00 0.00 35.87 5.18 R
2676 7207 3.861840 AGCTAATGACAACACATACGCT 58.138 40.909 0.00 0.00 33.97 5.07 R
2677 7208 4.092821 TGAAGCTAATGACAACACATACGC 59.907 41.667 0.00 0.00 0.00 4.42 R
3125 8743 0.239347 CTTCTTTCCACTTGCGCCAG 59.761 55.000 4.18 5.76 0.00 4.85 R
3774 9573 0.173029 CAGCCATGCCGCATAAACAA 59.827 50.000 5.31 0.00 0.00 2.83 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
658 2164 6.635030 AATTTGGGACACTTTTCTGTACTC 57.365 37.500 0.00 0.00 39.29 2.59
872 2378 4.576463 ACATGCAAACTTATGCTACTAGGC 59.424 41.667 0.00 0.00 46.54 3.93
873 2379 3.541632 TGCAAACTTATGCTACTAGGCC 58.458 45.455 0.00 0.00 46.54 5.19
874 2380 2.544267 GCAAACTTATGCTACTAGGCCG 59.456 50.000 0.00 0.00 43.06 6.13
875 2381 3.131396 CAAACTTATGCTACTAGGCCGG 58.869 50.000 0.00 0.00 0.00 6.13
876 2382 0.680061 ACTTATGCTACTAGGCCGGC 59.320 55.000 21.18 21.18 0.00 6.13
877 2383 0.037232 CTTATGCTACTAGGCCGGCC 60.037 60.000 39.29 39.29 0.00 6.13
878 2384 1.477685 TTATGCTACTAGGCCGGCCC 61.478 60.000 41.72 25.30 36.58 5.80
881 2387 3.912907 CTACTAGGCCGGCCCGTG 61.913 72.222 41.72 31.18 39.21 4.94
882 2388 4.764771 TACTAGGCCGGCCCGTGT 62.765 66.667 41.72 34.58 39.21 4.49
883 2389 3.357444 TACTAGGCCGGCCCGTGTA 62.357 63.158 41.72 33.55 39.21 2.90
884 2390 4.217159 CTAGGCCGGCCCGTGTAC 62.217 72.222 41.72 15.73 39.21 2.90
885 2391 4.764771 TAGGCCGGCCCGTGTACT 62.765 66.667 41.72 23.95 39.21 2.73
887 2393 2.852563 TAGGCCGGCCCGTGTACTTA 62.853 60.000 41.72 21.96 39.21 2.24
888 2394 2.265424 GCCGGCCCGTGTACTTAA 59.735 61.111 18.11 0.00 0.00 1.85
889 2395 2.102438 GCCGGCCCGTGTACTTAAC 61.102 63.158 18.11 0.00 0.00 2.01
890 2396 1.806758 CCGGCCCGTGTACTTAACG 60.807 63.158 0.85 0.00 40.70 3.18
891 2397 1.080569 CGGCCCGTGTACTTAACGT 60.081 57.895 0.00 0.00 39.38 3.99
892 2398 1.346378 CGGCCCGTGTACTTAACGTG 61.346 60.000 0.00 0.00 39.38 4.49
893 2399 1.629345 GGCCCGTGTACTTAACGTGC 61.629 60.000 3.62 3.62 42.57 5.34
894 2400 1.629345 GCCCGTGTACTTAACGTGCC 61.629 60.000 1.14 0.00 38.28 5.01
895 2401 0.037975 CCCGTGTACTTAACGTGCCT 60.038 55.000 0.00 0.00 39.38 4.75
896 2402 1.065358 CCGTGTACTTAACGTGCCTG 58.935 55.000 0.00 0.00 39.38 4.85
897 2403 1.065358 CGTGTACTTAACGTGCCTGG 58.935 55.000 0.00 0.00 36.31 4.45
898 2404 0.794473 GTGTACTTAACGTGCCTGGC 59.206 55.000 12.87 12.87 0.00 4.85
899 2405 0.320946 TGTACTTAACGTGCCTGGCC 60.321 55.000 17.53 6.66 0.00 5.36
900 2406 1.079681 TACTTAACGTGCCTGGCCG 60.080 57.895 22.29 22.29 0.00 6.13
901 2407 2.510064 TACTTAACGTGCCTGGCCGG 62.510 60.000 25.72 16.70 0.00 6.13
902 2408 4.708386 TTAACGTGCCTGGCCGGG 62.708 66.667 27.88 27.88 0.00 5.73
925 2431 4.708386 CCGTGCCTGGCCCGTTTA 62.708 66.667 21.55 0.00 0.00 2.01
926 2432 2.670251 CGTGCCTGGCCCGTTTAA 60.670 61.111 17.53 0.00 0.00 1.52
927 2433 2.959372 GTGCCTGGCCCGTTTAAC 59.041 61.111 17.53 1.30 0.00 2.01
928 2434 2.282603 TGCCTGGCCCGTTTAACC 60.283 61.111 17.53 0.00 0.00 2.85
929 2435 3.066190 GCCTGGCCCGTTTAACCC 61.066 66.667 7.66 0.00 0.00 4.11
930 2436 2.761160 CCTGGCCCGTTTAACCCT 59.239 61.111 0.00 0.00 0.00 4.34
931 2437 1.677633 CCTGGCCCGTTTAACCCTG 60.678 63.158 0.00 0.00 0.00 4.45
932 2438 1.677633 CTGGCCCGTTTAACCCTGG 60.678 63.158 0.00 0.00 0.00 4.45
933 2439 3.066190 GGCCCGTTTAACCCTGGC 61.066 66.667 8.77 8.77 41.42 4.85
934 2440 3.066190 GCCCGTTTAACCCTGGCC 61.066 66.667 0.00 0.00 36.07 5.36
935 2441 2.748647 CCCGTTTAACCCTGGCCG 60.749 66.667 0.00 0.00 0.00 6.13
936 2442 2.748647 CCGTTTAACCCTGGCCGG 60.749 66.667 3.88 3.88 0.00 6.13
979 2485 4.697756 CGCCGGTTTCCCTGCTGA 62.698 66.667 1.90 0.00 38.71 4.26
982 2488 1.002134 CCGGTTTCCCTGCTGATGT 60.002 57.895 0.00 0.00 0.00 3.06
990 2496 6.183360 CGGTTTCCCTGCTGATGTATTTTATT 60.183 38.462 0.00 0.00 0.00 1.40
1048 2554 0.601311 CTCGCTCGATCCCCAAATCC 60.601 60.000 0.00 0.00 0.00 3.01
1050 2556 1.228276 GCTCGATCCCCAAATCCCC 60.228 63.158 0.00 0.00 0.00 4.81
1051 2557 1.994885 GCTCGATCCCCAAATCCCCA 61.995 60.000 0.00 0.00 0.00 4.96
1052 2558 0.550914 CTCGATCCCCAAATCCCCAA 59.449 55.000 0.00 0.00 0.00 4.12
1053 2559 1.003646 TCGATCCCCAAATCCCCAAA 58.996 50.000 0.00 0.00 0.00 3.28
1054 2560 1.573376 TCGATCCCCAAATCCCCAAAT 59.427 47.619 0.00 0.00 0.00 2.32
1055 2561 1.963515 CGATCCCCAAATCCCCAAATC 59.036 52.381 0.00 0.00 0.00 2.17
1056 2562 2.689421 CGATCCCCAAATCCCCAAATCA 60.689 50.000 0.00 0.00 0.00 2.57
1057 2563 3.383223 GATCCCCAAATCCCCAAATCAA 58.617 45.455 0.00 0.00 0.00 2.57
1058 2564 3.282135 TCCCCAAATCCCCAAATCAAA 57.718 42.857 0.00 0.00 0.00 2.69
1060 2566 3.779738 TCCCCAAATCCCCAAATCAAATC 59.220 43.478 0.00 0.00 0.00 2.17
1064 2573 3.806625 AATCCCCAAATCAAATCGCTG 57.193 42.857 0.00 0.00 0.00 5.18
1746 5566 1.143329 TGCCCCTTCCACCCAACATA 61.143 55.000 0.00 0.00 0.00 2.29
1857 5686 1.300388 GCACCAAGGCTGCAAGTTG 60.300 57.895 0.50 0.00 35.30 3.16
2050 5963 1.476477 GACTCTCTACCCTGACCACC 58.524 60.000 0.00 0.00 0.00 4.61
2656 7187 3.483808 TTGTCACTACCTGAACATGCA 57.516 42.857 0.00 0.00 0.00 3.96
2657 7188 3.483808 TGTCACTACCTGAACATGCAA 57.516 42.857 0.00 0.00 0.00 4.08
2658 7189 3.814625 TGTCACTACCTGAACATGCAAA 58.185 40.909 0.00 0.00 0.00 3.68
2659 7190 3.814842 TGTCACTACCTGAACATGCAAAG 59.185 43.478 0.00 0.00 0.00 2.77
2660 7191 3.815401 GTCACTACCTGAACATGCAAAGT 59.185 43.478 0.00 0.00 0.00 2.66
2661 7192 4.065088 TCACTACCTGAACATGCAAAGTC 58.935 43.478 0.00 0.00 0.00 3.01
2662 7193 3.189287 CACTACCTGAACATGCAAAGTCC 59.811 47.826 0.00 0.00 0.00 3.85
2663 7194 2.363306 ACCTGAACATGCAAAGTCCA 57.637 45.000 0.00 0.00 0.00 4.02
2664 7195 2.880443 ACCTGAACATGCAAAGTCCAT 58.120 42.857 0.00 0.00 0.00 3.41
2665 7196 3.233507 ACCTGAACATGCAAAGTCCATT 58.766 40.909 0.00 0.00 0.00 3.16
2666 7197 3.256631 ACCTGAACATGCAAAGTCCATTC 59.743 43.478 0.00 0.00 0.00 2.67
2667 7198 3.256383 CCTGAACATGCAAAGTCCATTCA 59.744 43.478 0.00 0.00 0.00 2.57
2668 7199 4.262121 CCTGAACATGCAAAGTCCATTCAA 60.262 41.667 0.00 0.00 0.00 2.69
2669 7200 5.273674 TGAACATGCAAAGTCCATTCAAA 57.726 34.783 0.00 0.00 0.00 2.69
2671 7202 5.068855 TGAACATGCAAAGTCCATTCAAAGA 59.931 36.000 0.00 0.00 0.00 2.52
2672 7203 5.733620 ACATGCAAAGTCCATTCAAAGAT 57.266 34.783 0.00 0.00 0.00 2.40
2673 7204 5.475719 ACATGCAAAGTCCATTCAAAGATG 58.524 37.500 0.00 0.00 0.00 2.90
2675 7206 5.125100 TGCAAAGTCCATTCAAAGATGTC 57.875 39.130 0.00 0.00 0.00 3.06
2676 7207 4.583907 TGCAAAGTCCATTCAAAGATGTCA 59.416 37.500 0.00 0.00 0.00 3.58
2677 7208 5.159209 GCAAAGTCCATTCAAAGATGTCAG 58.841 41.667 0.00 0.00 0.00 3.51
2678 7209 5.159209 CAAAGTCCATTCAAAGATGTCAGC 58.841 41.667 0.00 0.00 0.00 4.26
2679 7210 3.005554 AGTCCATTCAAAGATGTCAGCG 58.994 45.455 0.00 0.00 0.00 5.18
2680 7211 2.744202 GTCCATTCAAAGATGTCAGCGT 59.256 45.455 0.00 0.00 0.00 5.07
3000 7956 3.125146 CGCATGTTTACTCTAGCTTGCAA 59.875 43.478 0.00 0.00 33.44 4.08
3071 8689 8.330466 TGGTCACACTAAAGGTATTATGTTTG 57.670 34.615 0.00 0.00 0.00 2.93
3072 8690 8.158132 TGGTCACACTAAAGGTATTATGTTTGA 58.842 33.333 0.00 0.00 0.00 2.69
3073 8691 8.448615 GGTCACACTAAAGGTATTATGTTTGAC 58.551 37.037 0.00 0.00 34.37 3.18
3074 8692 8.995220 GTCACACTAAAGGTATTATGTTTGACA 58.005 33.333 0.00 0.00 34.77 3.58
3075 8693 9.562408 TCACACTAAAGGTATTATGTTTGACAA 57.438 29.630 0.00 0.00 0.00 3.18
3115 8733 2.957680 TGCCAGAGAGAGATAGAAGCAG 59.042 50.000 0.00 0.00 0.00 4.24
3116 8734 2.288395 GCCAGAGAGAGATAGAAGCAGC 60.288 54.545 0.00 0.00 0.00 5.25
3117 8735 2.957680 CCAGAGAGAGATAGAAGCAGCA 59.042 50.000 0.00 0.00 0.00 4.41
3129 8747 3.797546 GCAGCAAGCGAGTCTGGC 61.798 66.667 0.00 0.00 42.27 4.85
3205 8824 3.884895 TGGACCGCATCATTATCACTTT 58.115 40.909 0.00 0.00 0.00 2.66
3234 8856 0.967380 GGGTCCACTGGAGGCATTTG 60.967 60.000 0.00 0.00 29.39 2.32
3321 9107 4.541705 AGTCATGGCTCTATGTCTAGTGT 58.458 43.478 0.00 0.00 0.00 3.55
3322 9108 5.696030 AGTCATGGCTCTATGTCTAGTGTA 58.304 41.667 0.00 0.00 0.00 2.90
3323 9109 6.310941 AGTCATGGCTCTATGTCTAGTGTAT 58.689 40.000 0.00 0.00 0.00 2.29
3324 9110 6.208402 AGTCATGGCTCTATGTCTAGTGTATG 59.792 42.308 0.00 0.00 0.00 2.39
3325 9111 6.015856 GTCATGGCTCTATGTCTAGTGTATGT 60.016 42.308 0.00 0.00 0.00 2.29
3326 9112 6.207614 TCATGGCTCTATGTCTAGTGTATGTC 59.792 42.308 0.00 0.00 0.00 3.06
3327 9113 5.696030 TGGCTCTATGTCTAGTGTATGTCT 58.304 41.667 0.00 0.00 0.00 3.41
3328 9114 6.838382 TGGCTCTATGTCTAGTGTATGTCTA 58.162 40.000 0.00 0.00 0.00 2.59
3329 9115 6.937465 TGGCTCTATGTCTAGTGTATGTCTAG 59.063 42.308 0.00 0.00 36.99 2.43
3330 9116 6.938030 GGCTCTATGTCTAGTGTATGTCTAGT 59.062 42.308 0.00 0.00 36.99 2.57
3331 9117 7.094975 GGCTCTATGTCTAGTGTATGTCTAGTG 60.095 44.444 0.00 0.00 36.99 2.74
3495 9291 9.883142 TTGACAGACCAAAAACAAGATAAATTT 57.117 25.926 0.00 0.00 0.00 1.82
3531 9327 6.842163 AGGAATCAATTTGTTAACTAGCGTG 58.158 36.000 7.22 0.00 0.00 5.34
3532 9328 6.653320 AGGAATCAATTTGTTAACTAGCGTGA 59.347 34.615 7.22 4.85 0.00 4.35
3533 9329 7.336931 AGGAATCAATTTGTTAACTAGCGTGAT 59.663 33.333 7.22 6.81 0.00 3.06
3536 9332 9.691362 AATCAATTTGTTAACTAGCGTGATTTT 57.309 25.926 7.22 0.00 31.00 1.82
3538 9334 8.346300 TCAATTTGTTAACTAGCGTGATTTTCA 58.654 29.630 7.22 0.00 0.00 2.69
3539 9335 9.128107 CAATTTGTTAACTAGCGTGATTTTCAT 57.872 29.630 7.22 0.00 0.00 2.57
3541 9337 9.769093 ATTTGTTAACTAGCGTGATTTTCATAC 57.231 29.630 7.22 0.00 0.00 2.39
3542 9338 8.542497 TTGTTAACTAGCGTGATTTTCATACT 57.458 30.769 7.22 0.00 0.00 2.12
3543 9339 8.542497 TGTTAACTAGCGTGATTTTCATACTT 57.458 30.769 7.22 0.00 0.00 2.24
3544 9340 8.440059 TGTTAACTAGCGTGATTTTCATACTTG 58.560 33.333 7.22 0.00 0.00 3.16
3545 9341 5.470845 ACTAGCGTGATTTTCATACTTGC 57.529 39.130 0.00 0.00 0.00 4.01
3546 9342 5.178797 ACTAGCGTGATTTTCATACTTGCT 58.821 37.500 0.00 0.00 0.00 3.91
3547 9343 6.338146 ACTAGCGTGATTTTCATACTTGCTA 58.662 36.000 0.00 0.00 0.00 3.49
3548 9344 6.816640 ACTAGCGTGATTTTCATACTTGCTAA 59.183 34.615 0.00 0.00 32.64 3.09
3549 9345 6.683974 AGCGTGATTTTCATACTTGCTAAT 57.316 33.333 0.00 0.00 0.00 1.73
3551 9347 7.855545 AGCGTGATTTTCATACTTGCTAATAG 58.144 34.615 0.00 0.00 0.00 1.73
3552 9348 7.710907 AGCGTGATTTTCATACTTGCTAATAGA 59.289 33.333 0.00 0.00 0.00 1.98
3553 9349 8.335356 GCGTGATTTTCATACTTGCTAATAGAA 58.665 33.333 0.00 0.00 0.00 2.10
3561 9357 8.327941 TCATACTTGCTAATAGAATGATTGCC 57.672 34.615 0.00 0.00 0.00 4.52
3562 9358 7.391554 TCATACTTGCTAATAGAATGATTGCCC 59.608 37.037 0.00 0.00 0.00 5.36
3563 9359 5.448654 ACTTGCTAATAGAATGATTGCCCA 58.551 37.500 0.00 0.00 0.00 5.36
3564 9360 6.073314 ACTTGCTAATAGAATGATTGCCCAT 58.927 36.000 0.00 0.00 0.00 4.00
3565 9361 5.970317 TGCTAATAGAATGATTGCCCATG 57.030 39.130 0.00 0.00 0.00 3.66
3566 9362 5.387788 TGCTAATAGAATGATTGCCCATGT 58.612 37.500 0.00 0.00 0.00 3.21
3567 9363 6.541907 TGCTAATAGAATGATTGCCCATGTA 58.458 36.000 0.00 0.00 0.00 2.29
3568 9364 6.430925 TGCTAATAGAATGATTGCCCATGTAC 59.569 38.462 0.00 0.00 0.00 2.90
3569 9365 6.127897 GCTAATAGAATGATTGCCCATGTACC 60.128 42.308 0.00 0.00 0.00 3.34
3570 9366 2.949447 AGAATGATTGCCCATGTACCC 58.051 47.619 0.00 0.00 0.00 3.69
3571 9367 2.515429 AGAATGATTGCCCATGTACCCT 59.485 45.455 0.00 0.00 0.00 4.34
3572 9368 3.052642 AGAATGATTGCCCATGTACCCTT 60.053 43.478 0.00 0.00 0.00 3.95
3573 9369 2.142356 TGATTGCCCATGTACCCTTG 57.858 50.000 0.00 0.00 0.00 3.61
3574 9370 1.638070 TGATTGCCCATGTACCCTTGA 59.362 47.619 0.00 0.00 0.00 3.02
3575 9371 2.024414 GATTGCCCATGTACCCTTGAC 58.976 52.381 0.00 0.00 0.00 3.18
3580 9376 0.249120 CCATGTACCCTTGACGCTCA 59.751 55.000 0.00 0.00 0.00 4.26
3606 9402 0.234884 GTAGCGTGAACTTGTGGTGC 59.765 55.000 0.00 0.00 0.00 5.01
3611 9407 1.603802 CGTGAACTTGTGGTGCTTGAT 59.396 47.619 0.00 0.00 0.00 2.57
3612 9408 2.033299 CGTGAACTTGTGGTGCTTGATT 59.967 45.455 0.00 0.00 0.00 2.57
3613 9409 3.489059 CGTGAACTTGTGGTGCTTGATTT 60.489 43.478 0.00 0.00 0.00 2.17
3614 9410 4.432712 GTGAACTTGTGGTGCTTGATTTT 58.567 39.130 0.00 0.00 0.00 1.82
3615 9411 4.869861 GTGAACTTGTGGTGCTTGATTTTT 59.130 37.500 0.00 0.00 0.00 1.94
3728 9527 6.538444 TGCACACACGTAATATACATTTGTG 58.462 36.000 0.00 10.18 38.51 3.33
3729 9528 5.963004 GCACACACGTAATATACATTTGTGG 59.037 40.000 13.80 7.63 37.65 4.17
3730 9529 6.402766 GCACACACGTAATATACATTTGTGGT 60.403 38.462 13.80 0.00 37.65 4.16
3732 9531 5.963004 CACACGTAATATACATTTGTGGTGC 59.037 40.000 0.00 0.00 35.35 5.01
3733 9532 5.194657 CACGTAATATACATTTGTGGTGCG 58.805 41.667 0.00 0.00 31.05 5.34
3734 9533 4.208355 CGTAATATACATTTGTGGTGCGC 58.792 43.478 0.00 0.00 0.00 6.09
3735 9534 4.025229 CGTAATATACATTTGTGGTGCGCT 60.025 41.667 9.73 0.00 0.00 5.92
3736 9535 4.552166 AATATACATTTGTGGTGCGCTC 57.448 40.909 9.73 4.47 0.00 5.03
3737 9536 0.726827 ATACATTTGTGGTGCGCTCG 59.273 50.000 9.73 0.00 0.00 5.03
3738 9537 1.906994 TACATTTGTGGTGCGCTCGC 61.907 55.000 9.73 7.38 42.35 5.03
3739 9538 4.088762 ATTTGTGGTGCGCTCGCG 62.089 61.111 9.73 6.98 45.51 5.87
3749 9548 2.781957 CGCTCGCGCCATTTGTAA 59.218 55.556 0.00 0.00 0.00 2.41
3750 9549 1.351707 CGCTCGCGCCATTTGTAAT 59.648 52.632 0.00 0.00 0.00 1.89
3751 9550 0.248054 CGCTCGCGCCATTTGTAATT 60.248 50.000 0.00 0.00 0.00 1.40
3752 9551 1.793714 CGCTCGCGCCATTTGTAATTT 60.794 47.619 0.00 0.00 0.00 1.82
3753 9552 1.846175 GCTCGCGCCATTTGTAATTTC 59.154 47.619 0.00 0.00 0.00 2.17
3754 9553 2.477863 GCTCGCGCCATTTGTAATTTCT 60.478 45.455 0.00 0.00 0.00 2.52
3755 9554 3.100817 CTCGCGCCATTTGTAATTTCTG 58.899 45.455 0.00 0.00 0.00 3.02
3756 9555 1.583404 CGCGCCATTTGTAATTTCTGC 59.417 47.619 0.00 0.00 0.00 4.26
3768 9567 2.697147 ATTTCTGCGTGGCCTGTGGT 62.697 55.000 3.32 0.00 0.00 4.16
3769 9568 2.902423 TTTCTGCGTGGCCTGTGGTT 62.902 55.000 3.32 0.00 0.00 3.67
3770 9569 2.031919 CTGCGTGGCCTGTGGTTA 59.968 61.111 3.32 0.00 0.00 2.85
3771 9570 2.281208 TGCGTGGCCTGTGGTTAC 60.281 61.111 3.32 0.00 0.00 2.50
3772 9571 2.281208 GCGTGGCCTGTGGTTACA 60.281 61.111 3.32 0.00 35.08 2.41
3773 9572 1.674322 GCGTGGCCTGTGGTTACAT 60.674 57.895 3.32 0.00 35.97 2.29
3774 9573 1.241315 GCGTGGCCTGTGGTTACATT 61.241 55.000 3.32 0.00 35.97 2.71
3776 9575 1.068610 CGTGGCCTGTGGTTACATTTG 60.069 52.381 3.32 0.00 35.97 2.32
3777 9576 1.960689 GTGGCCTGTGGTTACATTTGT 59.039 47.619 3.32 0.00 35.97 2.83
3778 9577 2.364002 GTGGCCTGTGGTTACATTTGTT 59.636 45.455 3.32 0.00 35.97 2.83
3780 9579 4.038162 GTGGCCTGTGGTTACATTTGTTTA 59.962 41.667 3.32 0.00 35.97 2.01
3781 9580 4.835615 TGGCCTGTGGTTACATTTGTTTAT 59.164 37.500 3.32 0.00 35.97 1.40
3782 9581 5.167845 GGCCTGTGGTTACATTTGTTTATG 58.832 41.667 0.00 0.00 35.97 1.90
3783 9582 4.625311 GCCTGTGGTTACATTTGTTTATGC 59.375 41.667 0.00 0.00 35.97 3.14
3799 9598 1.741327 ATGCGGCATGGCTGGATTTC 61.741 55.000 15.87 0.00 43.17 2.17
3835 9661 2.043551 TGGTTGCACCACAAGGCA 60.044 55.556 4.16 0.00 44.79 4.75
3866 9692 4.261572 GCTTGTTTTGAGTGTGCCTATTCA 60.262 41.667 0.00 0.00 0.00 2.57
3936 9762 4.633126 CAGTTGGATGACAATCTCGTTGAT 59.367 41.667 0.00 0.00 41.95 2.57
3992 9818 2.071540 TGTACGTACACGAGGACTCAG 58.928 52.381 24.10 0.00 43.02 3.35
4100 10134 6.015688 AGACATGCATTCAACTCTCACAAAAT 60.016 34.615 0.00 0.00 0.00 1.82
4283 10318 3.119743 GCAAGTGCATAGCTCACATTTGA 60.120 43.478 17.42 0.00 41.59 2.69
4284 10319 4.616604 GCAAGTGCATAGCTCACATTTGAA 60.617 41.667 17.42 0.00 41.59 2.69
4285 10320 5.647589 CAAGTGCATAGCTCACATTTGAAT 58.352 37.500 11.15 0.00 36.93 2.57
4286 10321 5.496133 AGTGCATAGCTCACATTTGAATC 57.504 39.130 6.78 0.00 36.93 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
658 2164 8.866956 GCAATAATCCTTGAACATGAAGAAAAG 58.133 33.333 0.00 0.00 0.00 2.27
805 2311 4.326826 TGGGCAAGTACTTTCAGAATCAG 58.673 43.478 5.07 0.00 0.00 2.90
872 2378 1.806758 CGTTAAGTACACGGGCCGG 60.807 63.158 31.78 21.03 33.86 6.13
873 2379 1.080569 ACGTTAAGTACACGGGCCG 60.081 57.895 27.06 27.06 42.14 6.13
874 2380 2.448477 CACGTTAAGTACACGGGCC 58.552 57.895 8.80 0.00 42.14 5.80
876 2382 0.037975 AGGCACGTTAAGTACACGGG 60.038 55.000 8.80 5.73 44.22 5.28
877 2383 1.065358 CAGGCACGTTAAGTACACGG 58.935 55.000 8.80 0.33 42.14 4.94
878 2384 1.065358 CCAGGCACGTTAAGTACACG 58.935 55.000 2.95 2.95 43.52 4.49
879 2385 0.794473 GCCAGGCACGTTAAGTACAC 59.206 55.000 6.55 0.00 0.00 2.90
880 2386 0.320946 GGCCAGGCACGTTAAGTACA 60.321 55.000 15.19 0.00 0.00 2.90
881 2387 1.356527 CGGCCAGGCACGTTAAGTAC 61.357 60.000 15.19 0.00 0.00 2.73
882 2388 1.079681 CGGCCAGGCACGTTAAGTA 60.080 57.895 15.19 0.00 0.00 2.24
883 2389 2.358247 CGGCCAGGCACGTTAAGT 60.358 61.111 15.19 0.00 0.00 2.24
884 2390 3.124921 CCGGCCAGGCACGTTAAG 61.125 66.667 15.19 0.00 0.00 1.85
885 2391 4.708386 CCCGGCCAGGCACGTTAA 62.708 66.667 15.19 0.00 39.21 2.01
910 2416 2.632544 GGTTAAACGGGCCAGGCAC 61.633 63.158 15.19 9.32 0.00 5.01
911 2417 2.282603 GGTTAAACGGGCCAGGCA 60.283 61.111 15.19 0.00 0.00 4.75
912 2418 3.066190 GGGTTAAACGGGCCAGGC 61.066 66.667 8.08 1.26 0.00 4.85
913 2419 1.677633 CAGGGTTAAACGGGCCAGG 60.678 63.158 8.08 0.00 0.00 4.45
914 2420 1.677633 CCAGGGTTAAACGGGCCAG 60.678 63.158 4.39 1.85 0.00 4.85
915 2421 2.437002 CCAGGGTTAAACGGGCCA 59.563 61.111 4.39 0.00 0.00 5.36
916 2422 3.066190 GCCAGGGTTAAACGGGCC 61.066 66.667 12.52 0.00 38.70 5.80
917 2423 3.066190 GGCCAGGGTTAAACGGGC 61.066 66.667 14.64 14.64 43.86 6.13
918 2424 2.748647 CGGCCAGGGTTAAACGGG 60.749 66.667 2.24 0.00 0.00 5.28
919 2425 2.748647 CCGGCCAGGGTTAAACGG 60.749 66.667 2.24 0.00 35.97 4.44
942 2448 0.322997 TCAATACCTGGCCAAACGGG 60.323 55.000 7.01 7.12 42.81 5.28
943 2449 0.808755 GTCAATACCTGGCCAAACGG 59.191 55.000 7.01 7.56 0.00 4.44
944 2450 0.446222 CGTCAATACCTGGCCAAACG 59.554 55.000 7.01 4.65 0.00 3.60
945 2451 0.170339 GCGTCAATACCTGGCCAAAC 59.830 55.000 7.01 0.00 0.00 2.93
946 2452 0.963355 GGCGTCAATACCTGGCCAAA 60.963 55.000 7.01 0.00 43.23 3.28
947 2453 1.377987 GGCGTCAATACCTGGCCAA 60.378 57.895 7.01 0.00 43.23 4.52
948 2454 2.270850 GGCGTCAATACCTGGCCA 59.729 61.111 4.71 4.71 43.23 5.36
949 2455 2.895372 CGGCGTCAATACCTGGCC 60.895 66.667 0.00 0.00 40.36 5.36
950 2456 2.895372 CCGGCGTCAATACCTGGC 60.895 66.667 6.01 0.00 0.00 4.85
951 2457 0.675522 AAACCGGCGTCAATACCTGG 60.676 55.000 6.01 0.00 0.00 4.45
952 2458 0.725117 GAAACCGGCGTCAATACCTG 59.275 55.000 6.01 0.00 0.00 4.00
953 2459 0.392060 GGAAACCGGCGTCAATACCT 60.392 55.000 6.01 0.00 0.00 3.08
954 2460 1.371337 GGGAAACCGGCGTCAATACC 61.371 60.000 6.01 1.33 43.64 2.73
955 2461 2.092374 GGGAAACCGGCGTCAATAC 58.908 57.895 6.01 0.00 43.64 1.89
956 2462 4.621832 GGGAAACCGGCGTCAATA 57.378 55.556 6.01 0.00 43.64 1.90
990 2496 7.773690 GGATTTTTGCCTGGTAGTAGATCTAAA 59.226 37.037 3.40 0.00 0.00 1.85
999 2505 1.273041 GGGGGATTTTTGCCTGGTAGT 60.273 52.381 0.00 0.00 0.00 2.73
1009 2515 3.004000 AGGAAGGAGAAGGGGGATTTTT 58.996 45.455 0.00 0.00 0.00 1.94
1010 2516 2.583101 GAGGAAGGAGAAGGGGGATTTT 59.417 50.000 0.00 0.00 0.00 1.82
1048 2554 0.819582 AGGCAGCGATTTGATTTGGG 59.180 50.000 0.00 0.00 0.00 4.12
1050 2556 1.473677 TGGAGGCAGCGATTTGATTTG 59.526 47.619 0.00 0.00 0.00 2.32
1051 2557 1.474077 GTGGAGGCAGCGATTTGATTT 59.526 47.619 0.00 0.00 0.00 2.17
1052 2558 1.098050 GTGGAGGCAGCGATTTGATT 58.902 50.000 0.00 0.00 0.00 2.57
1053 2559 0.749454 GGTGGAGGCAGCGATTTGAT 60.749 55.000 0.00 0.00 0.00 2.57
1054 2560 1.377202 GGTGGAGGCAGCGATTTGA 60.377 57.895 0.00 0.00 0.00 2.69
1055 2561 2.409870 GGGTGGAGGCAGCGATTTG 61.410 63.158 0.00 0.00 0.00 2.32
1056 2562 1.271840 TAGGGTGGAGGCAGCGATTT 61.272 55.000 0.00 0.00 0.00 2.17
1057 2563 1.271840 TTAGGGTGGAGGCAGCGATT 61.272 55.000 0.00 0.00 0.00 3.34
1058 2564 1.689233 TTAGGGTGGAGGCAGCGAT 60.689 57.895 0.00 0.00 0.00 4.58
1060 2566 2.125106 GTTAGGGTGGAGGCAGCG 60.125 66.667 0.00 0.00 0.00 5.18
1064 2573 0.545171 GTTAGGGTTAGGGTGGAGGC 59.455 60.000 0.00 0.00 0.00 4.70
1479 5260 0.673644 CTCCCATCTCCGCAAACGTT 60.674 55.000 0.00 0.00 37.70 3.99
1558 5345 2.328473 CATGGCCATATACTCGTCGTG 58.672 52.381 20.30 0.00 0.00 4.35
1746 5566 5.121380 AGTGAATGGAGAAATACATGGCT 57.879 39.130 0.00 0.00 0.00 4.75
1753 5573 4.471904 AGCACGAGTGAATGGAGAAATA 57.528 40.909 7.50 0.00 0.00 1.40
1857 5686 0.813821 GGGGCAACTCAATGAAGCTC 59.186 55.000 0.00 0.00 36.63 4.09
2050 5963 4.567318 GCTTATGCTCCACCCTGG 57.433 61.111 0.00 0.00 39.43 4.45
2656 7187 4.083110 CGCTGACATCTTTGAATGGACTTT 60.083 41.667 0.00 0.00 0.00 2.66
2657 7188 3.438087 CGCTGACATCTTTGAATGGACTT 59.562 43.478 0.00 0.00 0.00 3.01
2658 7189 3.005554 CGCTGACATCTTTGAATGGACT 58.994 45.455 0.00 0.00 0.00 3.85
2659 7190 2.744202 ACGCTGACATCTTTGAATGGAC 59.256 45.455 0.00 0.00 0.00 4.02
2660 7191 3.057969 ACGCTGACATCTTTGAATGGA 57.942 42.857 0.00 0.00 0.00 3.41
2661 7192 4.333649 ACATACGCTGACATCTTTGAATGG 59.666 41.667 0.00 0.00 0.00 3.16
2662 7193 5.163824 ACACATACGCTGACATCTTTGAATG 60.164 40.000 0.00 0.00 0.00 2.67
2663 7194 4.937620 ACACATACGCTGACATCTTTGAAT 59.062 37.500 0.00 0.00 0.00 2.57
2664 7195 4.314961 ACACATACGCTGACATCTTTGAA 58.685 39.130 0.00 0.00 0.00 2.69
2665 7196 3.925379 ACACATACGCTGACATCTTTGA 58.075 40.909 0.00 0.00 0.00 2.69
2666 7197 4.083855 ACAACACATACGCTGACATCTTTG 60.084 41.667 0.00 0.00 0.00 2.77
2667 7198 4.065088 ACAACACATACGCTGACATCTTT 58.935 39.130 0.00 0.00 0.00 2.52
2668 7199 3.664107 ACAACACATACGCTGACATCTT 58.336 40.909 0.00 0.00 0.00 2.40
2669 7200 3.254060 GACAACACATACGCTGACATCT 58.746 45.455 0.00 0.00 0.00 2.90
2671 7202 3.038788 TGACAACACATACGCTGACAT 57.961 42.857 0.00 0.00 0.00 3.06
2672 7203 2.517650 TGACAACACATACGCTGACA 57.482 45.000 0.00 0.00 0.00 3.58
2673 7204 4.492570 GCTAATGACAACACATACGCTGAC 60.493 45.833 0.00 0.00 0.00 3.51
2675 7206 3.618594 AGCTAATGACAACACATACGCTG 59.381 43.478 0.00 0.00 35.87 5.18
2676 7207 3.861840 AGCTAATGACAACACATACGCT 58.138 40.909 0.00 0.00 33.97 5.07
2677 7208 4.092821 TGAAGCTAATGACAACACATACGC 59.907 41.667 0.00 0.00 0.00 4.42
2678 7209 5.445939 GGTGAAGCTAATGACAACACATACG 60.446 44.000 0.00 0.00 0.00 3.06
2679 7210 5.163754 GGGTGAAGCTAATGACAACACATAC 60.164 44.000 0.00 0.00 0.00 2.39
2680 7211 4.941263 GGGTGAAGCTAATGACAACACATA 59.059 41.667 0.00 0.00 0.00 2.29
2806 7731 7.909121 CAGCTCTAGTTTGAAATTATGCTTCAG 59.091 37.037 5.74 0.00 34.41 3.02
2906 7832 8.772705 CAGTCTAGGATGCTCTGAATTAAAATC 58.227 37.037 0.00 0.00 0.00 2.17
3071 8689 6.506357 GCAAAAACGAAACAGAGATGTTTGTC 60.506 38.462 10.83 0.00 41.49 3.18
3072 8690 5.288472 GCAAAAACGAAACAGAGATGTTTGT 59.712 36.000 10.83 6.99 41.49 2.83
3073 8691 5.276348 GGCAAAAACGAAACAGAGATGTTTG 60.276 40.000 10.83 6.46 41.49 2.93
3074 8692 4.803613 GGCAAAAACGAAACAGAGATGTTT 59.196 37.500 6.08 6.08 43.77 2.83
3075 8693 4.142271 TGGCAAAAACGAAACAGAGATGTT 60.142 37.500 0.00 0.00 0.00 2.71
3076 8694 3.380004 TGGCAAAAACGAAACAGAGATGT 59.620 39.130 0.00 0.00 0.00 3.06
3077 8695 3.963665 TGGCAAAAACGAAACAGAGATG 58.036 40.909 0.00 0.00 0.00 2.90
3078 8696 3.882888 TCTGGCAAAAACGAAACAGAGAT 59.117 39.130 0.00 0.00 31.92 2.75
3079 8697 3.275143 TCTGGCAAAAACGAAACAGAGA 58.725 40.909 0.00 0.00 31.92 3.10
3080 8698 3.621794 CTCTGGCAAAAACGAAACAGAG 58.378 45.455 0.00 0.00 43.81 3.35
3081 8699 3.275143 TCTCTGGCAAAAACGAAACAGA 58.725 40.909 0.00 0.00 34.23 3.41
3082 8700 3.312421 TCTCTCTGGCAAAAACGAAACAG 59.688 43.478 0.00 0.00 0.00 3.16
3083 8701 3.275143 TCTCTCTGGCAAAAACGAAACA 58.725 40.909 0.00 0.00 0.00 2.83
3084 8702 3.560068 TCTCTCTCTGGCAAAAACGAAAC 59.440 43.478 0.00 0.00 0.00 2.78
3085 8703 3.804036 TCTCTCTCTGGCAAAAACGAAA 58.196 40.909 0.00 0.00 0.00 3.46
3086 8704 3.469008 TCTCTCTCTGGCAAAAACGAA 57.531 42.857 0.00 0.00 0.00 3.85
3087 8705 3.685139 ATCTCTCTCTGGCAAAAACGA 57.315 42.857 0.00 0.00 0.00 3.85
3088 8706 4.748892 TCTATCTCTCTCTGGCAAAAACG 58.251 43.478 0.00 0.00 0.00 3.60
3089 8707 5.064579 GCTTCTATCTCTCTCTGGCAAAAAC 59.935 44.000 0.00 0.00 0.00 2.43
3125 8743 0.239347 CTTCTTTCCACTTGCGCCAG 59.761 55.000 4.18 5.76 0.00 4.85
3129 8747 1.497991 TCGTCTTCTTTCCACTTGCG 58.502 50.000 0.00 0.00 0.00 4.85
3321 9107 6.166279 CAAAAGAAGCCACTCACTAGACATA 58.834 40.000 0.00 0.00 0.00 2.29
3322 9108 4.899352 AAAGAAGCCACTCACTAGACAT 57.101 40.909 0.00 0.00 0.00 3.06
3323 9109 4.380531 CAAAAGAAGCCACTCACTAGACA 58.619 43.478 0.00 0.00 0.00 3.41
3324 9110 3.748568 CCAAAAGAAGCCACTCACTAGAC 59.251 47.826 0.00 0.00 0.00 2.59
3325 9111 3.646162 TCCAAAAGAAGCCACTCACTAGA 59.354 43.478 0.00 0.00 0.00 2.43
3326 9112 4.008074 TCCAAAAGAAGCCACTCACTAG 57.992 45.455 0.00 0.00 0.00 2.57
3327 9113 4.640771 ATCCAAAAGAAGCCACTCACTA 57.359 40.909 0.00 0.00 0.00 2.74
3328 9114 3.515602 ATCCAAAAGAAGCCACTCACT 57.484 42.857 0.00 0.00 0.00 3.41
3329 9115 3.319122 ACAATCCAAAAGAAGCCACTCAC 59.681 43.478 0.00 0.00 0.00 3.51
3330 9116 3.565307 ACAATCCAAAAGAAGCCACTCA 58.435 40.909 0.00 0.00 0.00 3.41
3331 9117 5.241728 AGTTACAATCCAAAAGAAGCCACTC 59.758 40.000 0.00 0.00 0.00 3.51
3405 9191 9.617975 GGCATCAAATTAGTTCTCTAATATTGC 57.382 33.333 0.00 7.75 43.52 3.56
3422 9214 0.625849 AACGGAGGGAGGCATCAAAT 59.374 50.000 0.00 0.00 0.00 2.32
3512 9308 8.346300 TGAAAATCACGCTAGTTAACAAATTGA 58.654 29.630 8.61 4.13 0.00 2.57
3527 9323 7.851508 TCTATTAGCAAGTATGAAAATCACGC 58.148 34.615 0.00 0.00 0.00 5.34
3536 9332 7.391554 GGGCAATCATTCTATTAGCAAGTATGA 59.608 37.037 0.00 0.00 35.89 2.15
3538 9334 7.233632 TGGGCAATCATTCTATTAGCAAGTAT 58.766 34.615 0.00 0.00 0.00 2.12
3539 9335 6.600388 TGGGCAATCATTCTATTAGCAAGTA 58.400 36.000 0.00 0.00 0.00 2.24
3540 9336 5.448654 TGGGCAATCATTCTATTAGCAAGT 58.551 37.500 0.00 0.00 0.00 3.16
3541 9337 6.015688 ACATGGGCAATCATTCTATTAGCAAG 60.016 38.462 0.00 0.00 0.00 4.01
3542 9338 5.834742 ACATGGGCAATCATTCTATTAGCAA 59.165 36.000 0.00 0.00 0.00 3.91
3543 9339 5.387788 ACATGGGCAATCATTCTATTAGCA 58.612 37.500 0.00 0.00 0.00 3.49
3544 9340 5.972107 ACATGGGCAATCATTCTATTAGC 57.028 39.130 0.00 0.00 0.00 3.09
3545 9341 6.375455 GGGTACATGGGCAATCATTCTATTAG 59.625 42.308 0.00 0.00 0.00 1.73
3546 9342 6.045459 AGGGTACATGGGCAATCATTCTATTA 59.955 38.462 0.00 0.00 0.00 0.98
3547 9343 5.079643 GGGTACATGGGCAATCATTCTATT 58.920 41.667 0.00 0.00 0.00 1.73
3548 9344 4.354987 AGGGTACATGGGCAATCATTCTAT 59.645 41.667 0.00 0.00 0.00 1.98
3549 9345 3.721575 AGGGTACATGGGCAATCATTCTA 59.278 43.478 0.00 0.00 0.00 2.10
3551 9347 2.949447 AGGGTACATGGGCAATCATTC 58.051 47.619 0.00 0.00 0.00 2.67
3552 9348 3.033184 CAAGGGTACATGGGCAATCATT 58.967 45.455 0.00 0.00 0.00 2.57
3553 9349 2.244510 TCAAGGGTACATGGGCAATCAT 59.755 45.455 0.00 0.00 0.00 2.45
3554 9350 1.638070 TCAAGGGTACATGGGCAATCA 59.362 47.619 0.00 0.00 0.00 2.57
3555 9351 2.024414 GTCAAGGGTACATGGGCAATC 58.976 52.381 0.00 0.00 0.00 2.67
3556 9352 1.681780 CGTCAAGGGTACATGGGCAAT 60.682 52.381 0.00 0.00 0.00 3.56
3557 9353 0.322098 CGTCAAGGGTACATGGGCAA 60.322 55.000 0.00 0.00 0.00 4.52
3558 9354 1.298340 CGTCAAGGGTACATGGGCA 59.702 57.895 0.00 0.00 0.00 5.36
3559 9355 2.112815 GCGTCAAGGGTACATGGGC 61.113 63.158 0.00 0.00 0.00 5.36
3560 9356 0.462047 GAGCGTCAAGGGTACATGGG 60.462 60.000 0.00 0.00 0.00 4.00
3561 9357 0.249120 TGAGCGTCAAGGGTACATGG 59.751 55.000 0.00 0.00 0.00 3.66
3562 9358 1.935873 CATGAGCGTCAAGGGTACATG 59.064 52.381 0.00 0.00 0.00 3.21
3563 9359 1.555075 ACATGAGCGTCAAGGGTACAT 59.445 47.619 0.00 0.00 0.00 2.29
3564 9360 0.973632 ACATGAGCGTCAAGGGTACA 59.026 50.000 0.00 0.00 0.00 2.90
3565 9361 2.000447 GAACATGAGCGTCAAGGGTAC 59.000 52.381 0.00 0.00 0.00 3.34
3566 9362 1.899814 AGAACATGAGCGTCAAGGGTA 59.100 47.619 0.00 0.00 0.00 3.69
3567 9363 0.687354 AGAACATGAGCGTCAAGGGT 59.313 50.000 0.00 0.00 0.00 4.34
3568 9364 1.081892 CAGAACATGAGCGTCAAGGG 58.918 55.000 0.00 0.00 0.00 3.95
3569 9365 1.800805 ACAGAACATGAGCGTCAAGG 58.199 50.000 0.00 0.00 0.00 3.61
3570 9366 2.346847 GCTACAGAACATGAGCGTCAAG 59.653 50.000 0.00 0.00 0.00 3.02
3571 9367 2.337583 GCTACAGAACATGAGCGTCAA 58.662 47.619 0.00 0.00 0.00 3.18
3572 9368 1.732405 CGCTACAGAACATGAGCGTCA 60.732 52.381 14.17 0.00 43.94 4.35
3573 9369 0.917259 CGCTACAGAACATGAGCGTC 59.083 55.000 14.17 0.34 43.94 5.19
3574 9370 3.036026 CGCTACAGAACATGAGCGT 57.964 52.632 14.17 2.40 43.94 5.07
3580 9376 3.494626 CACAAGTTCACGCTACAGAACAT 59.505 43.478 7.88 0.00 44.94 2.71
3734 9533 3.100817 CAGAAATTACAAATGGCGCGAG 58.899 45.455 12.10 0.00 0.00 5.03
3735 9534 2.730715 GCAGAAATTACAAATGGCGCGA 60.731 45.455 12.10 0.00 0.00 5.87
3736 9535 1.583404 GCAGAAATTACAAATGGCGCG 59.417 47.619 0.00 0.00 0.00 6.86
3737 9536 1.583404 CGCAGAAATTACAAATGGCGC 59.417 47.619 0.00 0.00 36.70 6.53
3739 9538 2.923020 CCACGCAGAAATTACAAATGGC 59.077 45.455 0.00 0.00 0.00 4.40
3740 9539 2.923020 GCCACGCAGAAATTACAAATGG 59.077 45.455 0.00 0.00 0.00 3.16
3741 9540 2.923020 GGCCACGCAGAAATTACAAATG 59.077 45.455 0.00 0.00 0.00 2.32
3742 9541 2.825532 AGGCCACGCAGAAATTACAAAT 59.174 40.909 5.01 0.00 0.00 2.32
3743 9542 2.030363 CAGGCCACGCAGAAATTACAAA 60.030 45.455 5.01 0.00 0.00 2.83
3744 9543 1.539388 CAGGCCACGCAGAAATTACAA 59.461 47.619 5.01 0.00 0.00 2.41
3745 9544 1.164411 CAGGCCACGCAGAAATTACA 58.836 50.000 5.01 0.00 0.00 2.41
3746 9545 1.135689 CACAGGCCACGCAGAAATTAC 60.136 52.381 5.01 0.00 0.00 1.89
3747 9546 1.164411 CACAGGCCACGCAGAAATTA 58.836 50.000 5.01 0.00 0.00 1.40
3748 9547 1.526575 CCACAGGCCACGCAGAAATT 61.527 55.000 5.01 0.00 0.00 1.82
3749 9548 1.973281 CCACAGGCCACGCAGAAAT 60.973 57.895 5.01 0.00 0.00 2.17
3750 9549 2.594303 CCACAGGCCACGCAGAAA 60.594 61.111 5.01 0.00 0.00 2.52
3751 9550 2.046009 TAACCACAGGCCACGCAGAA 62.046 55.000 5.01 0.00 0.00 3.02
3752 9551 2.512355 TAACCACAGGCCACGCAGA 61.512 57.895 5.01 0.00 0.00 4.26
3753 9552 2.031919 TAACCACAGGCCACGCAG 59.968 61.111 5.01 0.00 0.00 5.18
3754 9553 2.281208 GTAACCACAGGCCACGCA 60.281 61.111 5.01 0.00 0.00 5.24
3755 9554 1.241315 AATGTAACCACAGGCCACGC 61.241 55.000 5.01 0.00 38.30 5.34
3756 9555 1.068610 CAAATGTAACCACAGGCCACG 60.069 52.381 5.01 0.00 38.30 4.94
3768 9567 4.428209 CCATGCCGCATAAACAAATGTAA 58.572 39.130 5.31 0.00 0.00 2.41
3769 9568 3.736433 GCCATGCCGCATAAACAAATGTA 60.736 43.478 5.31 0.00 0.00 2.29
3770 9569 2.891112 CCATGCCGCATAAACAAATGT 58.109 42.857 5.31 0.00 0.00 2.71
3771 9570 1.593933 GCCATGCCGCATAAACAAATG 59.406 47.619 5.31 0.00 0.00 2.32
3772 9571 1.481772 AGCCATGCCGCATAAACAAAT 59.518 42.857 5.31 0.00 0.00 2.32
3773 9572 0.894141 AGCCATGCCGCATAAACAAA 59.106 45.000 5.31 0.00 0.00 2.83
3774 9573 0.173029 CAGCCATGCCGCATAAACAA 59.827 50.000 5.31 0.00 0.00 2.83
3776 9575 1.066257 CCAGCCATGCCGCATAAAC 59.934 57.895 5.31 0.00 0.00 2.01
3777 9576 0.467844 ATCCAGCCATGCCGCATAAA 60.468 50.000 5.31 0.00 0.00 1.40
3778 9577 0.467844 AATCCAGCCATGCCGCATAA 60.468 50.000 5.31 0.00 0.00 1.90
3780 9579 1.741327 GAAATCCAGCCATGCCGCAT 61.741 55.000 0.00 0.00 0.00 4.73
3781 9580 2.362760 AAATCCAGCCATGCCGCA 60.363 55.556 0.00 0.00 0.00 5.69
3782 9581 1.669999 AAGAAATCCAGCCATGCCGC 61.670 55.000 0.00 0.00 0.00 6.53
3783 9582 0.819582 AAAGAAATCCAGCCATGCCG 59.180 50.000 0.00 0.00 0.00 5.69
3835 9661 5.451908 CACACTCAAAACAAGCGATTGTAT 58.548 37.500 20.73 9.22 34.24 2.29
3992 9818 2.276201 GGTTTTGTTGCACCTTTGGTC 58.724 47.619 0.00 0.00 31.02 4.02
4100 10134 1.742146 CTAGATGGCCTGCTACGCA 59.258 57.895 3.32 0.00 36.92 5.24
4142 10177 7.360269 CCAAAATAACTGATTTCAAGCGCAATT 60.360 33.333 11.47 0.00 36.71 2.32
4283 10318 7.572523 TGAGACTTTTGTTGATGAAGTGATT 57.427 32.000 0.00 0.00 34.02 2.57
4284 10319 7.572523 TTGAGACTTTTGTTGATGAAGTGAT 57.427 32.000 0.00 0.00 34.02 3.06
4285 10320 7.518848 CGATTGAGACTTTTGTTGATGAAGTGA 60.519 37.037 0.00 0.00 34.02 3.41
4286 10321 6.576313 CGATTGAGACTTTTGTTGATGAAGTG 59.424 38.462 0.00 0.00 34.02 3.16
4371 10410 6.094048 GTGGCTGAGAAATATTTTCTAGCACA 59.906 38.462 22.06 17.16 32.21 4.57
4372 10411 6.458888 GGTGGCTGAGAAATATTTTCTAGCAC 60.459 42.308 22.06 18.48 32.21 4.40
4373 10412 5.590259 GGTGGCTGAGAAATATTTTCTAGCA 59.410 40.000 22.06 12.30 32.21 3.49
4388 10427 0.325933 TCTCATTGGTGGTGGCTGAG 59.674 55.000 0.00 0.00 35.71 3.35


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

AutoCloner maintained by Alex Coulton.