Multiple sequence alignment - TraesCS3D01G329700

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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 TraesCS3D01G329700 chr3D 100.000 6221 0 0 1 6221 442505285 442499065 0.000000e+00 11489.0
1 TraesCS3D01G329700 chr3D 100.000 80 0 0 2410 2489 442502797 442502876 1.400000e-31 148.0
2 TraesCS3D01G329700 chr3D 92.188 64 4 1 6143 6206 497017114 497017176 8.590000e-14 89.8
3 TraesCS3D01G329700 chr3D 100.000 40 0 0 3087 3126 467570101 467570140 2.410000e-09 75.0
4 TraesCS3D01G329700 chr3B 94.111 1681 76 11 745 2415 580038807 580037140 0.000000e+00 2534.0
5 TraesCS3D01G329700 chr3B 95.984 747 28 2 2707 3452 580036875 580036130 0.000000e+00 1212.0
6 TraesCS3D01G329700 chr3B 89.857 769 57 7 4502 5265 580036142 580035390 0.000000e+00 968.0
7 TraesCS3D01G329700 chr3B 86.759 793 74 21 14 776 580039599 580038808 0.000000e+00 854.0
8 TraesCS3D01G329700 chr3B 93.450 229 13 2 2484 2711 580037143 580036916 7.720000e-89 339.0
9 TraesCS3D01G329700 chr3B 96.970 99 2 1 5817 5914 64321997 64322095 1.390000e-36 165.0
10 TraesCS3D01G329700 chr3B 87.413 143 18 0 5767 5909 580034374 580034232 1.390000e-36 165.0
11 TraesCS3D01G329700 chr3B 93.939 66 3 1 6143 6208 229307860 229307796 1.430000e-16 99.0
12 TraesCS3D01G329700 chr5D 98.861 1054 8 4 3453 4505 60160380 60161430 0.000000e+00 1877.0
13 TraesCS3D01G329700 chr5D 92.930 1174 70 9 1251 2415 209310808 209311977 0.000000e+00 1696.0
14 TraesCS3D01G329700 chr5D 89.024 656 49 9 2785 3425 209312293 209312940 0.000000e+00 791.0
15 TraesCS3D01G329700 chr5D 75.940 1276 140 88 5 1168 209309567 209310787 9.310000e-138 501.0
16 TraesCS3D01G329700 chr5D 87.119 427 45 5 4864 5287 209313463 209313882 5.640000e-130 475.0
17 TraesCS3D01G329700 chr5D 88.073 327 26 7 4535 4852 209312954 209313276 5.890000e-100 375.0
18 TraesCS3D01G329700 chr5D 96.939 98 1 1 5826 5921 444097055 444096958 4.990000e-36 163.0
19 TraesCS3D01G329700 chr5A 92.857 1218 77 6 1205 2415 270179051 270180265 0.000000e+00 1759.0
20 TraesCS3D01G329700 chr5A 87.645 777 69 13 4519 5287 270181233 270181990 0.000000e+00 878.0
21 TraesCS3D01G329700 chr5A 86.903 733 60 19 2707 3427 270180527 270181235 0.000000e+00 789.0
22 TraesCS3D01G329700 chr5A 86.800 250 19 9 950 1189 270178686 270178931 3.700000e-67 267.0
23 TraesCS3D01G329700 chr3A 95.749 1082 41 4 1337 2415 583707306 583706227 0.000000e+00 1738.0
24 TraesCS3D01G329700 chr3A 91.523 755 56 4 2709 3456 583705960 583705207 0.000000e+00 1033.0
25 TraesCS3D01G329700 chr3A 85.987 892 83 26 234 1108 583708203 583707337 0.000000e+00 917.0
26 TraesCS3D01G329700 chr3A 92.443 397 29 1 4895 5290 583704877 583704481 3.260000e-157 566.0
27 TraesCS3D01G329700 chr3A 93.429 350 20 2 4502 4850 583705223 583704876 3.320000e-142 516.0
28 TraesCS3D01G329700 chr3A 86.966 468 29 14 5783 6221 583704035 583703571 1.200000e-136 497.0
29 TraesCS3D01G329700 chr3A 90.086 232 20 3 2484 2713 583706230 583706000 1.310000e-76 298.0
30 TraesCS3D01G329700 chr5B 92.447 1218 73 12 1205 2415 222368676 222369881 0.000000e+00 1722.0
31 TraesCS3D01G329700 chr5B 87.415 731 60 14 2709 3427 222370149 222370859 0.000000e+00 811.0
32 TraesCS3D01G329700 chr5B 87.822 427 42 5 4864 5287 222371374 222371793 5.600000e-135 492.0
33 TraesCS3D01G329700 chr5B 88.462 338 29 8 4519 4852 222370857 222371188 3.490000e-107 399.0
34 TraesCS3D01G329700 chr5B 88.000 250 16 8 950 1189 222368311 222368556 3.670000e-72 283.0
35 TraesCS3D01G329700 chr4D 89.581 1075 84 13 3453 4504 4060933 4062002 0.000000e+00 1339.0
36 TraesCS3D01G329700 chr4D 88.616 1098 77 20 3453 4504 4058261 4059356 0.000000e+00 1291.0
37 TraesCS3D01G329700 chr4D 88.193 1101 78 24 3453 4504 4063349 4064446 0.000000e+00 1266.0
38 TraesCS3D01G329700 chr4D 86.818 1100 86 16 3453 4504 4053346 4054434 0.000000e+00 1173.0
39 TraesCS3D01G329700 chr4D 89.278 914 77 14 3594 4504 3873847 3874742 0.000000e+00 1125.0
40 TraesCS3D01G329700 chr4D 87.816 870 60 17 3677 4504 4056152 4057017 0.000000e+00 977.0
41 TraesCS3D01G329700 chr4D 87.661 543 55 10 3453 3991 4055597 4056131 6.850000e-174 621.0
42 TraesCS3D01G329700 chr7A 84.659 1069 100 34 3452 4504 578567200 578566180 0.000000e+00 1007.0
43 TraesCS3D01G329700 chr7A 96.907 97 2 1 5814 5909 696780477 696780381 1.790000e-35 161.0
44 TraesCS3D01G329700 chr6A 95.425 459 20 1 4045 4503 32691727 32691270 0.000000e+00 730.0
45 TraesCS3D01G329700 chr6A 100.000 91 0 0 5825 5915 125885166 125885256 1.070000e-37 169.0
46 TraesCS3D01G329700 chr6A 92.593 81 6 0 2406 2486 235083778 235083858 3.940000e-22 117.0
47 TraesCS3D01G329700 chrUn 95.238 462 16 4 4043 4504 10146913 10147368 0.000000e+00 726.0
48 TraesCS3D01G329700 chrUn 93.647 425 26 1 3453 3876 10145929 10146353 8.800000e-178 634.0
49 TraesCS3D01G329700 chrUn 96.491 57 1 1 6152 6208 268034004 268033949 6.640000e-15 93.5
50 TraesCS3D01G329700 chr1D 94.353 425 23 1 3453 3876 41449455 41449879 0.000000e+00 651.0
51 TraesCS3D01G329700 chr1D 85.944 498 50 11 3860 4347 378870383 378870870 1.200000e-141 514.0
52 TraesCS3D01G329700 chr1D 98.913 92 1 0 5824 5915 560760 560669 1.390000e-36 165.0
53 TraesCS3D01G329700 chr1D 94.872 78 2 1 2411 2486 464312357 464312434 3.050000e-23 121.0
54 TraesCS3D01G329700 chr1D 94.872 78 2 1 2413 2488 464312434 464312357 3.050000e-23 121.0
55 TraesCS3D01G329700 chr2D 92.771 415 27 3 3450 3861 15511433 15511847 1.150000e-166 597.0
56 TraesCS3D01G329700 chr6B 98.925 93 0 1 5824 5915 189563993 189564085 1.390000e-36 165.0
57 TraesCS3D01G329700 chr6B 92.537 67 4 1 6142 6208 703681561 703681496 1.850000e-15 95.3
58 TraesCS3D01G329700 chr1A 98.913 92 1 0 5824 5915 3369134 3369043 1.390000e-36 165.0
59 TraesCS3D01G329700 chr1B 93.902 82 5 0 2405 2486 627152253 627152334 2.350000e-24 124.0
60 TraesCS3D01G329700 chr1B 92.537 67 4 1 6143 6209 553450263 553450198 1.850000e-15 95.3
61 TraesCS3D01G329700 chr1B 90.909 66 5 1 6143 6208 589055675 589055739 3.090000e-13 87.9
62 TraesCS3D01G329700 chr1B 88.462 52 4 2 502 551 31057482 31057533 1.870000e-05 62.1
63 TraesCS3D01G329700 chr7B 96.000 75 3 0 2413 2487 589938040 589938114 8.470000e-24 122.0
64 TraesCS3D01G329700 chr7B 96.000 75 3 0 2412 2486 589938114 589938040 8.470000e-24 122.0
65 TraesCS3D01G329700 chr7B 90.805 87 7 1 2413 2499 727632962 727633047 1.420000e-21 115.0
66 TraesCS3D01G329700 chr7B 91.045 67 6 0 6143 6209 119234561 119234495 2.390000e-14 91.6
67 TraesCS3D01G329700 chr7B 90.909 66 4 2 6143 6208 256020129 256020066 3.090000e-13 87.9
68 TraesCS3D01G329700 chr4A 92.683 82 6 0 2405 2486 236541816 236541735 1.100000e-22 119.0
69 TraesCS3D01G329700 chr4A 90.909 66 5 1 6143 6208 698165757 698165821 3.090000e-13 87.9


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 TraesCS3D01G329700 chr3D 442499065 442505285 6220 True 11489.000000 11489 100.000000 1 6221 1 chr3D.!!$R1 6220
1 TraesCS3D01G329700 chr3B 580034232 580039599 5367 True 1012.000000 2534 91.262333 14 5909 6 chr3B.!!$R2 5895
2 TraesCS3D01G329700 chr5D 60160380 60161430 1050 False 1877.000000 1877 98.861000 3453 4505 1 chr5D.!!$F1 1052
3 TraesCS3D01G329700 chr5D 209309567 209313882 4315 False 767.600000 1696 86.617200 5 5287 5 chr5D.!!$F2 5282
4 TraesCS3D01G329700 chr5A 270178686 270181990 3304 False 923.250000 1759 88.551250 950 5287 4 chr5A.!!$F1 4337
5 TraesCS3D01G329700 chr3A 583703571 583708203 4632 True 795.000000 1738 90.883286 234 6221 7 chr3A.!!$R1 5987
6 TraesCS3D01G329700 chr5B 222368311 222371793 3482 False 741.400000 1722 88.829200 950 5287 5 chr5B.!!$F1 4337
7 TraesCS3D01G329700 chr4D 3873847 3874742 895 False 1125.000000 1125 89.278000 3594 4504 1 chr4D.!!$F1 910
8 TraesCS3D01G329700 chr4D 4053346 4064446 11100 False 1111.166667 1339 88.114167 3453 4504 6 chr4D.!!$F2 1051
9 TraesCS3D01G329700 chr7A 578566180 578567200 1020 True 1007.000000 1007 84.659000 3452 4504 1 chr7A.!!$R1 1052
10 TraesCS3D01G329700 chrUn 10145929 10147368 1439 False 680.000000 726 94.442500 3453 4504 2 chrUn.!!$F1 1051

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
568 648 0.036732 TCTGTCTTCATGCCCACACC 59.963 55.0 0.00 0.0 0.00 4.16 F
2428 2698 0.115745 AGGTACTCCCTCCGTTCCAA 59.884 55.0 0.00 0.0 40.71 3.53 F
3181 3519 0.264955 GAGGGGTCCCAGAGGTATGA 59.735 60.0 10.98 0.0 38.92 2.15 F
3438 3778 0.034186 CCTTACTGAGCATTGGGCCA 60.034 55.0 0.00 0.0 46.50 5.36 F
5177 13819 0.740868 ATCGGGTCACTGCACATTCG 60.741 55.0 0.00 0.0 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2469 2739 0.115745 AGGTACTCCCTCCGTTCCAA 59.884 55.000 0.0 0.0 40.71 3.53 R
3299 3639 1.205655 TCTTCTGGATCTGGTTCTGCG 59.794 52.381 0.0 0.0 0.00 5.18 R
4870 13508 1.039068 TGCCCACATTTTGACCAGTG 58.961 50.000 0.0 0.0 0.00 3.66 R
5193 13835 0.042188 CTTGCGTTTCACACTGGTCG 60.042 55.000 0.0 0.0 0.00 4.79 R
6161 15370 3.118261 TGTTTGGGTTGCCATGCTTAAAA 60.118 39.130 0.0 0.0 0.00 1.52 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 1.300697 GGGCGACGTGTCAGTTCTT 60.301 57.895 0.00 0.00 0.00 2.52
65 66 2.431057 ACGTGTCAGTTCTTGAAGTCCT 59.569 45.455 0.00 0.00 37.61 3.85
66 67 3.118738 ACGTGTCAGTTCTTGAAGTCCTT 60.119 43.478 0.00 0.00 37.61 3.36
89 90 4.308458 CCGACACCTTCACCGCCA 62.308 66.667 0.00 0.00 0.00 5.69
114 115 4.056125 CTCCTCGTGCTGCCGTCA 62.056 66.667 9.66 0.00 0.00 4.35
121 122 4.662961 TGCTGCCGTCACCTGTCG 62.663 66.667 0.00 0.00 0.00 4.35
142 144 2.687566 CCGTAGTGGGGGCTTCCT 60.688 66.667 0.00 0.00 35.33 3.36
154 156 3.095347 GCTTCCTCCGCCTCCGATT 62.095 63.158 0.00 0.00 36.29 3.34
193 195 0.677842 GTGTCCGTGTCCCTTGTAGT 59.322 55.000 0.00 0.00 0.00 2.73
205 207 1.534476 TTGTAGTGGCGGAGGTGGA 60.534 57.895 0.00 0.00 0.00 4.02
268 287 3.062466 CGCCGTCACTCCCTCTCA 61.062 66.667 0.00 0.00 0.00 3.27
272 293 2.574399 GTCACTCCCTCTCACGGC 59.426 66.667 0.00 0.00 0.00 5.68
338 359 4.352887 CCTTTTTAACAGCGGTCGAAAAA 58.647 39.130 16.17 16.17 33.87 1.94
400 432 1.586154 GAATGGTCACACCGCCCAAG 61.586 60.000 0.00 0.00 42.58 3.61
503 562 2.516460 GCGACGGCCTCCTCTCTA 60.516 66.667 0.00 0.00 0.00 2.43
509 568 1.202952 ACGGCCTCCTCTCTATTCGAT 60.203 52.381 0.00 0.00 0.00 3.59
551 619 2.910688 TCACCTCGTTTTGCTTCTCT 57.089 45.000 0.00 0.00 0.00 3.10
568 648 0.036732 TCTGTCTTCATGCCCACACC 59.963 55.000 0.00 0.00 0.00 4.16
581 661 1.078759 CCACACCGATGAGCTCGTTC 61.079 60.000 10.42 8.12 46.18 3.95
588 668 0.820871 GATGAGCTCGTTCCTCCAGT 59.179 55.000 10.42 0.00 0.00 4.00
589 669 0.820871 ATGAGCTCGTTCCTCCAGTC 59.179 55.000 9.64 0.00 0.00 3.51
590 670 0.251386 TGAGCTCGTTCCTCCAGTCT 60.251 55.000 9.64 0.00 0.00 3.24
594 675 0.528470 CTCGTTCCTCCAGTCTCCAC 59.472 60.000 0.00 0.00 0.00 4.02
652 733 2.283617 CAGCTAATCGTCACATCACAGC 59.716 50.000 0.00 0.00 0.00 4.40
653 734 2.094026 AGCTAATCGTCACATCACAGCA 60.094 45.455 0.00 0.00 0.00 4.41
657 738 0.319813 TCGTCACATCACAGCACAGG 60.320 55.000 0.00 0.00 0.00 4.00
658 739 1.871772 GTCACATCACAGCACAGGC 59.128 57.895 0.00 0.00 41.61 4.85
777 891 7.081349 CACGCCACTTCAAAATCATTACTTAA 58.919 34.615 0.00 0.00 0.00 1.85
780 894 8.638565 CGCCACTTCAAAATCATTACTTAAAAG 58.361 33.333 0.00 0.00 0.00 2.27
833 947 6.644248 TCCATACGCTAGTGATTTAGCTAA 57.356 37.500 10.99 0.86 43.05 3.09
928 1064 9.745018 AGACTCTCTTTTCCATTAATGAATGAA 57.255 29.630 17.23 8.99 44.59 2.57
976 1120 3.560105 TGTTTCACACACAATGGATGGA 58.440 40.909 0.00 0.00 0.00 3.41
1097 1242 4.526438 AGCTTGGCCATAAGGTCTTTAT 57.474 40.909 6.09 0.00 41.31 1.40
1100 1245 4.276926 GCTTGGCCATAAGGTCTTTATCTG 59.723 45.833 6.09 0.00 41.31 2.90
1108 1255 7.500559 GCCATAAGGTCTTTATCTGATGAACTT 59.499 37.037 10.46 10.46 39.44 2.66
1121 1276 7.807977 TCTGATGAACTTTTATTATCCTGCC 57.192 36.000 0.00 0.00 0.00 4.85
1152 1307 6.722301 TGGTTCGAGAATGTAAGATAGTACG 58.278 40.000 0.00 0.00 0.00 3.67
1153 1308 6.539826 TGGTTCGAGAATGTAAGATAGTACGA 59.460 38.462 0.00 0.00 0.00 3.43
1175 1330 5.469760 CGATACTGGGTATGCATTTGATTCA 59.530 40.000 3.54 0.00 0.00 2.57
1181 1336 4.262164 GGGTATGCATTTGATTCATCCACC 60.262 45.833 3.54 0.88 0.00 4.61
1196 1351 1.593787 CACCCTCATCACTCTGCGT 59.406 57.895 0.00 0.00 0.00 5.24
1215 1474 2.286359 CGTTGTACCCATGAATGCATCG 60.286 50.000 0.00 0.00 30.68 3.84
1225 1484 4.266029 CCATGAATGCATCGTTTTTACTGC 59.734 41.667 0.00 0.00 30.68 4.40
1242 1501 2.224090 ACTGCATTTGTGAAGCATGCAA 60.224 40.909 21.98 4.19 41.04 4.08
1273 1532 7.015292 ACTGAGTTTCTGTTTGAGGATGTACTA 59.985 37.037 0.00 0.00 0.00 1.82
1280 1539 5.556915 TGTTTGAGGATGTACTACTTTGGG 58.443 41.667 0.00 0.00 0.00 4.12
1311 1570 7.383102 ACCTTCTAATGAACACAATAAGCAG 57.617 36.000 0.00 0.00 0.00 4.24
1503 1770 6.986231 TGATGCAGAATACACTACCTACATTG 59.014 38.462 0.00 0.00 0.00 2.82
1578 1845 2.412605 GCATGGACATCAGGCCTTC 58.587 57.895 0.00 0.00 46.35 3.46
1586 1853 2.485814 GACATCAGGCCTTCTCAACAAC 59.514 50.000 0.00 0.00 0.00 3.32
1764 2031 4.332543 CACACAAGCAAAGAGAACACTGTA 59.667 41.667 0.00 0.00 0.00 2.74
1844 2111 3.522553 CAATGTTTACTCCCTCCTCGAC 58.477 50.000 0.00 0.00 0.00 4.20
2101 2370 5.488262 TTGATCACTGTCATCCTTTCTGA 57.512 39.130 0.00 0.00 0.00 3.27
2170 2439 7.079182 TGTTTTGGTTCATACGTTATCATCC 57.921 36.000 0.00 0.00 0.00 3.51
2214 2484 9.654663 ACTCTATGTTGTTTTGGAGTTATAGTC 57.345 33.333 0.00 0.00 31.14 2.59
2215 2485 9.099454 CTCTATGTTGTTTTGGAGTTATAGTCC 57.901 37.037 0.00 0.00 38.22 3.85
2230 2500 8.511748 AGTTATAGTCCATTATGTTCCCTCAT 57.488 34.615 0.00 0.00 0.00 2.90
2279 2549 2.286418 CGCTTTATTGTTGGAGGCGATC 60.286 50.000 0.00 0.00 43.05 3.69
2334 2604 4.835284 GAGAAGTTCTCCCTTCAGGATT 57.165 45.455 20.40 0.00 46.33 3.01
2384 2654 4.098055 TGCTCAAGTACGATCTGTTCTC 57.902 45.455 0.00 0.00 0.00 2.87
2417 2687 9.708092 GGTCATATATTTCTTAACAGGTACTCC 57.292 37.037 0.00 0.00 34.60 3.85
2418 2688 9.708092 GTCATATATTTCTTAACAGGTACTCCC 57.292 37.037 0.00 0.00 34.60 4.30
2420 2690 9.930693 CATATATTTCTTAACAGGTACTCCCTC 57.069 37.037 0.00 0.00 43.86 4.30
2421 2691 5.695424 ATTTCTTAACAGGTACTCCCTCC 57.305 43.478 0.00 0.00 43.86 4.30
2422 2692 2.731572 TCTTAACAGGTACTCCCTCCG 58.268 52.381 0.00 0.00 43.86 4.63
2423 2693 2.042162 TCTTAACAGGTACTCCCTCCGT 59.958 50.000 0.00 0.00 43.86 4.69
2424 2694 2.610438 TAACAGGTACTCCCTCCGTT 57.390 50.000 0.00 0.00 43.86 4.44
2425 2695 1.264295 AACAGGTACTCCCTCCGTTC 58.736 55.000 0.00 0.00 43.86 3.95
2426 2696 0.614134 ACAGGTACTCCCTCCGTTCC 60.614 60.000 0.00 0.00 43.86 3.62
2427 2697 0.613853 CAGGTACTCCCTCCGTTCCA 60.614 60.000 0.00 0.00 43.86 3.53
2428 2698 0.115745 AGGTACTCCCTCCGTTCCAA 59.884 55.000 0.00 0.00 40.71 3.53
2429 2699 0.978907 GGTACTCCCTCCGTTCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
2430 2700 1.348696 GGTACTCCCTCCGTTCCAAAA 59.651 52.381 0.00 0.00 0.00 2.44
2431 2701 2.026542 GGTACTCCCTCCGTTCCAAAAT 60.027 50.000 0.00 0.00 0.00 1.82
2432 2702 3.198417 GGTACTCCCTCCGTTCCAAAATA 59.802 47.826 0.00 0.00 0.00 1.40
2433 2703 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2434 2704 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2435 2705 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2436 2706 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2437 2707 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2438 2708 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2439 2709 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2440 2710 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2441 2711 4.766375 TCCGTTCCAAAATAGATGACTCC 58.234 43.478 0.00 0.00 0.00 3.85
2442 2712 4.224147 TCCGTTCCAAAATAGATGACTCCA 59.776 41.667 0.00 0.00 0.00 3.86
2443 2713 4.332819 CCGTTCCAAAATAGATGACTCCAC 59.667 45.833 0.00 0.00 0.00 4.02
2444 2714 5.178797 CGTTCCAAAATAGATGACTCCACT 58.821 41.667 0.00 0.00 0.00 4.00
2445 2715 5.643777 CGTTCCAAAATAGATGACTCCACTT 59.356 40.000 0.00 0.00 0.00 3.16
2446 2716 6.149474 CGTTCCAAAATAGATGACTCCACTTT 59.851 38.462 0.00 0.00 0.00 2.66
2447 2717 7.308435 GTTCCAAAATAGATGACTCCACTTTG 58.692 38.462 0.00 0.00 0.00 2.77
2448 2718 6.542821 TCCAAAATAGATGACTCCACTTTGT 58.457 36.000 0.00 0.00 0.00 2.83
2449 2719 7.685481 TCCAAAATAGATGACTCCACTTTGTA 58.315 34.615 0.00 0.00 0.00 2.41
2450 2720 7.606456 TCCAAAATAGATGACTCCACTTTGTAC 59.394 37.037 0.00 0.00 0.00 2.90
2451 2721 7.390440 CCAAAATAGATGACTCCACTTTGTACA 59.610 37.037 0.00 0.00 0.00 2.90
2452 2722 8.783093 CAAAATAGATGACTCCACTTTGTACAA 58.217 33.333 3.59 3.59 0.00 2.41
2453 2723 8.918202 AAATAGATGACTCCACTTTGTACAAA 57.082 30.769 19.53 19.53 0.00 2.83
2468 2738 8.553459 CTTTGTACAAAGTGGAGTCATCTATT 57.447 34.615 31.55 0.00 42.02 1.73
2469 2739 8.918202 TTTGTACAAAGTGGAGTCATCTATTT 57.082 30.769 17.01 0.00 0.00 1.40
2470 2740 8.918202 TTGTACAAAGTGGAGTCATCTATTTT 57.082 30.769 5.64 0.00 0.00 1.82
2471 2741 8.322906 TGTACAAAGTGGAGTCATCTATTTTG 57.677 34.615 0.00 7.65 44.19 2.44
2472 2742 6.824305 ACAAAGTGGAGTCATCTATTTTGG 57.176 37.500 12.00 0.00 43.46 3.28
2473 2743 6.542821 ACAAAGTGGAGTCATCTATTTTGGA 58.457 36.000 12.00 0.00 43.46 3.53
2474 2744 7.004086 ACAAAGTGGAGTCATCTATTTTGGAA 58.996 34.615 12.00 0.00 43.46 3.53
2475 2745 7.040409 ACAAAGTGGAGTCATCTATTTTGGAAC 60.040 37.037 12.00 0.00 43.46 3.62
2476 2746 5.178797 AGTGGAGTCATCTATTTTGGAACG 58.821 41.667 0.00 0.00 0.00 3.95
2477 2747 4.332819 GTGGAGTCATCTATTTTGGAACGG 59.667 45.833 0.00 0.00 0.00 4.44
2478 2748 4.224147 TGGAGTCATCTATTTTGGAACGGA 59.776 41.667 0.00 0.00 0.00 4.69
2479 2749 4.811557 GGAGTCATCTATTTTGGAACGGAG 59.188 45.833 0.00 0.00 0.00 4.63
2480 2750 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2481 2751 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2482 2752 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2483 2753 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2484 2754 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2485 2755 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
2555 2826 6.135290 TGGTCATATATGTGCTTTTTCTGC 57.865 37.500 12.42 0.00 0.00 4.26
2659 2932 3.414549 TTGTTGCGACAAAGGAAGTTC 57.585 42.857 17.36 0.00 42.54 3.01
2699 2973 8.859090 TGTCCATTGAATTCTAAAAACTCATGT 58.141 29.630 7.05 0.00 0.00 3.21
2756 3077 2.351418 CGAACAGATATTTTGAGCCGCA 59.649 45.455 0.00 0.00 0.00 5.69
2760 3081 3.696051 ACAGATATTTTGAGCCGCATTGT 59.304 39.130 0.00 0.00 0.00 2.71
2768 3089 1.663643 TGAGCCGCATTGTATTCGTTC 59.336 47.619 0.00 0.00 0.00 3.95
2800 3121 4.013728 TGCACTTGGTCATATTTGTACCC 58.986 43.478 0.00 0.00 31.97 3.69
3169 3507 1.385756 GCACTAGAGTCGGAGGGGTC 61.386 65.000 0.00 0.00 0.00 4.46
3181 3519 0.264955 GAGGGGTCCCAGAGGTATGA 59.735 60.000 10.98 0.00 38.92 2.15
3249 3589 3.254166 AGCTAGTTGGACAATTTGCAGTG 59.746 43.478 13.99 0.00 32.98 3.66
3299 3639 4.333913 ACCAGATGACATGATAGTGCTC 57.666 45.455 0.00 0.00 0.00 4.26
3435 3775 2.636830 CTGACCTTACTGAGCATTGGG 58.363 52.381 0.00 0.00 0.00 4.12
3438 3778 0.034186 CCTTACTGAGCATTGGGCCA 60.034 55.000 0.00 0.00 46.50 5.36
3581 6172 4.392921 CACTGATCGGTGGATTAGTCTT 57.607 45.455 24.60 0.00 43.72 3.01
4506 12773 5.222631 GTGGTTTTCTGCAATTTACTCCAG 58.777 41.667 0.00 0.00 0.00 3.86
4508 12775 5.596361 TGGTTTTCTGCAATTTACTCCAGAA 59.404 36.000 0.00 0.00 41.16 3.02
4509 12776 6.097554 TGGTTTTCTGCAATTTACTCCAGAAA 59.902 34.615 9.76 9.76 46.56 2.52
4513 12780 4.766891 TCTGCAATTTACTCCAGAAAAGGG 59.233 41.667 0.00 0.00 31.90 3.95
4536 12803 1.609208 TCTGCACCAGCTTTTCCTTC 58.391 50.000 0.00 0.00 42.74 3.46
4552 12819 9.561270 GCTTTTCCTTCAGTAGAAAATTGATAC 57.439 33.333 0.00 0.00 40.25 2.24
4555 12822 6.403049 TCCTTCAGTAGAAAATTGATACGCA 58.597 36.000 0.00 0.00 32.35 5.24
4649 12917 5.649831 GGCCAAAAGAACAGAGATTGTCTAT 59.350 40.000 0.00 0.00 39.73 1.98
4740 13008 5.810587 GCACGGACTGTAAATTCATCTTCTA 59.189 40.000 0.00 0.00 0.00 2.10
4830 13109 9.874215 CATATATTGTCTGTCAAAGTGCTAATG 57.126 33.333 0.00 0.00 39.62 1.90
4881 13519 6.404954 GGTTAGTTTAGTTGCACTGGTCAAAA 60.405 38.462 0.00 0.00 0.00 2.44
4893 13531 3.900601 ACTGGTCAAAATGTGGGCAATAA 59.099 39.130 0.00 0.00 0.00 1.40
5056 13694 3.432890 GCCTTCTAGAATTCCTCCAGGTG 60.433 52.174 5.44 0.00 36.34 4.00
5160 13802 5.782845 AGGTATTGAAGAGGTCCCAGATATC 59.217 44.000 0.00 0.00 0.00 1.63
5164 13806 0.861155 AGAGGTCCCAGATATCGGGT 59.139 55.000 23.44 11.24 44.81 5.28
5177 13819 0.740868 ATCGGGTCACTGCACATTCG 60.741 55.000 0.00 0.00 0.00 3.34
5187 13829 2.095768 ACTGCACATTCGTTTGGATTCG 60.096 45.455 0.00 0.00 0.00 3.34
5193 13835 1.153353 TTCGTTTGGATTCGGCAGAC 58.847 50.000 0.00 0.00 0.00 3.51
5225 13867 4.142271 TGAAACGCAAGGAAATTGAACTGT 60.142 37.500 0.00 0.00 41.83 3.55
5261 13904 2.507058 TGGCATGGATCATATAGGAGGC 59.493 50.000 0.00 0.00 0.00 4.70
5268 13918 3.118112 GGATCATATAGGAGGCCATGGTG 60.118 52.174 14.67 0.00 0.00 4.17
5290 13940 2.849943 TCTATTTTAGGCTGGCTCCCAA 59.150 45.455 7.13 0.00 30.80 4.12
5292 13942 2.621556 TTTTAGGCTGGCTCCCAATT 57.378 45.000 7.13 0.00 30.80 2.32
5305 14049 6.819284 TGGCTCCCAATTATGAAATCATTTC 58.181 36.000 2.87 2.87 37.76 2.17
5309 14053 6.724263 TCCCAATTATGAAATCATTTCGTCG 58.276 36.000 8.17 0.00 42.55 5.12
5314 14058 2.147150 TGAAATCATTTCGTCGCACCA 58.853 42.857 5.64 0.00 42.55 4.17
5403 14148 7.994425 TCTTGTGTGATGTAATTGTATGGTT 57.006 32.000 0.00 0.00 0.00 3.67
5441 14186 3.554934 TGAACTGTCTCTTGTGCCAATT 58.445 40.909 0.00 0.00 0.00 2.32
5452 14197 2.440247 GCCAATTCTGGGACCCCG 60.440 66.667 8.45 0.61 43.74 5.73
5527 14316 5.782047 TGGAGACAGTTGGCATAAAATTTG 58.218 37.500 0.00 0.00 35.01 2.32
5550 14340 4.467735 GAAGCTCGTTTTGTCCTGAATTC 58.532 43.478 0.00 0.00 0.00 2.17
5561 14401 2.416893 GTCCTGAATTCGCTCTTGGTTC 59.583 50.000 0.04 0.00 0.00 3.62
5580 14420 4.094442 GGTTCGTCCATCCAAATTCAGTAC 59.906 45.833 0.00 0.00 35.97 2.73
5586 14426 5.815740 GTCCATCCAAATTCAGTACGTGTAT 59.184 40.000 0.00 0.00 0.00 2.29
5594 14434 7.439955 CCAAATTCAGTACGTGTATGCCTATTA 59.560 37.037 0.00 0.00 0.00 0.98
5595 14435 7.941795 AATTCAGTACGTGTATGCCTATTAC 57.058 36.000 0.00 0.00 0.00 1.89
5603 14611 4.149922 CGTGTATGCCTATTACCACATTCG 59.850 45.833 0.00 0.00 0.00 3.34
5609 14617 4.574421 TGCCTATTACCACATTCGAACATG 59.426 41.667 0.00 1.25 0.00 3.21
5612 14620 6.715464 CCTATTACCACATTCGAACATGAAC 58.285 40.000 0.00 0.00 0.00 3.18
5613 14621 4.655440 TTACCACATTCGAACATGAACG 57.345 40.909 0.00 4.76 0.00 3.95
5618 14626 3.428534 CACATTCGAACATGAACGAGACA 59.571 43.478 0.00 5.72 39.59 3.41
5623 14631 2.609491 CGAACATGAACGAGACAGGGAA 60.609 50.000 0.00 0.00 0.00 3.97
5627 14635 3.071023 ACATGAACGAGACAGGGAAAGAA 59.929 43.478 0.00 0.00 0.00 2.52
5628 14636 4.256920 CATGAACGAGACAGGGAAAGAAT 58.743 43.478 0.00 0.00 0.00 2.40
5632 14645 3.165875 ACGAGACAGGGAAAGAATGAGA 58.834 45.455 0.00 0.00 0.00 3.27
5650 14663 7.403231 AGAATGAGAGTGAGGATAAAAGGGTTA 59.597 37.037 0.00 0.00 0.00 2.85
5652 14665 6.261435 TGAGAGTGAGGATAAAAGGGTTAGA 58.739 40.000 0.00 0.00 0.00 2.10
5657 14670 4.720273 TGAGGATAAAAGGGTTAGAGGTCC 59.280 45.833 0.00 0.00 0.00 4.46
5669 14682 2.479566 AGAGGTCCGTGTACTCGTAA 57.520 50.000 15.43 1.60 36.40 3.18
5670 14683 2.996631 AGAGGTCCGTGTACTCGTAAT 58.003 47.619 15.43 0.00 36.40 1.89
5676 14689 4.427312 GTCCGTGTACTCGTAATTCCATT 58.573 43.478 15.43 0.00 0.00 3.16
5679 14692 4.100529 CGTGTACTCGTAATTCCATTCGT 58.899 43.478 9.11 0.00 0.00 3.85
5681 14694 5.170270 CGTGTACTCGTAATTCCATTCGTAC 59.830 44.000 9.11 0.00 0.00 3.67
5682 14695 5.456822 GTGTACTCGTAATTCCATTCGTACC 59.543 44.000 0.00 0.00 0.00 3.34
5684 14697 3.047796 CTCGTAATTCCATTCGTACCGG 58.952 50.000 0.00 0.00 0.00 5.28
5685 14698 1.523934 CGTAATTCCATTCGTACCGGC 59.476 52.381 0.00 0.00 0.00 6.13
5720 14899 4.189188 CTTCTGCTGCCGCCATGC 62.189 66.667 0.00 0.00 34.43 4.06
5730 14909 3.908081 CGCCATGCCCTTCCATGC 61.908 66.667 0.00 0.00 40.92 4.06
5743 14922 3.256631 CCTTCCATGCTAAAAGTTGCAGT 59.743 43.478 0.00 0.00 42.74 4.40
5746 14925 2.557924 CCATGCTAAAAGTTGCAGTGGA 59.442 45.455 0.00 0.00 42.74 4.02
5747 14926 3.194116 CCATGCTAAAAGTTGCAGTGGAT 59.806 43.478 0.00 0.00 42.74 3.41
5748 14927 4.322198 CCATGCTAAAAGTTGCAGTGGATT 60.322 41.667 0.00 0.00 42.74 3.01
5749 14928 4.241590 TGCTAAAAGTTGCAGTGGATTG 57.758 40.909 0.00 0.00 34.84 2.67
5750 14929 3.005684 TGCTAAAAGTTGCAGTGGATTGG 59.994 43.478 0.00 0.00 34.84 3.16
5751 14930 2.531522 AAAAGTTGCAGTGGATTGGC 57.468 45.000 0.00 0.00 0.00 4.52
5752 14931 1.412079 AAAGTTGCAGTGGATTGGCA 58.588 45.000 0.00 0.00 35.41 4.92
5753 14932 1.412079 AAGTTGCAGTGGATTGGCAA 58.588 45.000 0.68 0.68 44.50 4.52
5755 14934 3.130264 TTGCAGTGGATTGGCAACT 57.870 47.368 0.00 0.00 42.12 3.16
5756 14935 1.412079 TTGCAGTGGATTGGCAACTT 58.588 45.000 0.00 0.00 42.12 2.66
5757 14936 0.675083 TGCAGTGGATTGGCAACTTG 59.325 50.000 0.00 0.00 34.05 3.16
5758 14937 0.037975 GCAGTGGATTGGCAACTTGG 60.038 55.000 0.00 0.00 37.61 3.61
5759 14938 1.619654 CAGTGGATTGGCAACTTGGA 58.380 50.000 0.00 0.00 37.61 3.53
5763 14945 3.088532 GTGGATTGGCAACTTGGACATA 58.911 45.455 0.00 0.00 37.61 2.29
5765 14947 4.160252 GTGGATTGGCAACTTGGACATAAT 59.840 41.667 0.00 0.00 37.61 1.28
5779 14961 6.104146 TGGACATAATAATTAGGCACGCTA 57.896 37.500 0.00 0.00 0.00 4.26
5910 15095 3.329542 AATCCTGCCGACCACGCAT 62.330 57.895 0.00 0.00 38.29 4.73
5915 15100 1.003262 CTGCCGACCACGCATTTTTG 61.003 55.000 0.00 0.00 38.29 2.44
5917 15102 1.080839 CCGACCACGCATTTTTGGG 60.081 57.895 0.00 0.00 37.18 4.12
6002 15199 9.449719 AGAGTATTATTCCACGAATTTTGTTCT 57.550 29.630 0.00 0.00 33.95 3.01
6038 15235 4.713946 GGGTGACGAGATTGGCAA 57.286 55.556 0.68 0.68 0.00 4.52
6125 15334 9.715121 TTTATAACTCAGTTTTCGTTCACCTAT 57.285 29.630 0.00 0.00 0.00 2.57
6172 15381 3.757745 ACGTTCGGATTTTAAGCATGG 57.242 42.857 0.00 0.00 0.00 3.66
6178 15387 2.738321 CGGATTTTAAGCATGGCAACCC 60.738 50.000 0.00 0.00 0.00 4.11
6184 16301 1.058284 AAGCATGGCAACCCAAACAT 58.942 45.000 0.00 0.00 46.14 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.374252 GAACTGACACGTCGCCCAT 60.374 57.895 0.00 0.00 0.00 4.00
42 43 2.460918 ACTTCAAGAACTGACACGTCG 58.539 47.619 0.00 0.00 32.21 5.12
49 50 3.454447 TGTGGAAGGACTTCAAGAACTGA 59.546 43.478 13.51 0.00 41.20 3.41
57 58 0.391597 GTCGGTGTGGAAGGACTTCA 59.608 55.000 13.51 0.00 41.20 3.02
65 66 0.179067 GTGAAGGTGTCGGTGTGGAA 60.179 55.000 0.00 0.00 0.00 3.53
66 67 1.444250 GTGAAGGTGTCGGTGTGGA 59.556 57.895 0.00 0.00 0.00 4.02
89 90 3.474570 GCACGAGGAGGAGGGCAT 61.475 66.667 0.00 0.00 0.00 4.40
112 113 2.598099 TACGGTGGCGACAGGTGA 60.598 61.111 0.00 0.00 44.46 4.02
114 115 2.599578 ACTACGGTGGCGACAGGT 60.600 61.111 0.00 0.00 44.46 4.00
124 125 3.007323 GGAAGCCCCCACTACGGT 61.007 66.667 0.00 0.00 0.00 4.83
127 128 2.732619 CGGAGGAAGCCCCCACTAC 61.733 68.421 0.00 0.00 34.66 2.73
136 138 2.980213 GAATCGGAGGCGGAGGAAGC 62.980 65.000 0.00 0.00 0.00 3.86
139 141 2.838225 GGAATCGGAGGCGGAGGA 60.838 66.667 0.00 0.00 0.00 3.71
142 144 3.217017 CTCGGAATCGGAGGCGGA 61.217 66.667 9.64 0.00 36.95 5.54
177 179 1.823169 GCCACTACAAGGGACACGGA 61.823 60.000 0.00 0.00 0.00 4.69
188 190 2.118732 TCCACCTCCGCCACTACA 59.881 61.111 0.00 0.00 0.00 2.74
272 293 2.663852 ACGAACCGAAAGCCCACG 60.664 61.111 0.00 0.00 0.00 4.94
338 359 2.126071 CATCGGACGGTGAGCGTT 60.126 61.111 12.09 0.00 0.00 4.84
359 380 1.815421 CAGATCGAAGCCGTTGGGG 60.815 63.158 0.00 0.00 37.05 4.96
400 432 1.739562 CCACCTGAGAGAAGTGCGC 60.740 63.158 0.00 0.00 0.00 6.09
500 559 3.323979 GGGGCTAACCTTGATCGAATAGA 59.676 47.826 0.00 0.00 40.03 1.98
502 561 2.370849 GGGGGCTAACCTTGATCGAATA 59.629 50.000 0.00 0.00 40.03 1.75
503 562 1.143073 GGGGGCTAACCTTGATCGAAT 59.857 52.381 0.00 0.00 40.03 3.34
532 600 2.158957 ACAGAGAAGCAAAACGAGGTGA 60.159 45.455 0.00 0.00 0.00 4.02
551 619 1.302431 CGGTGTGGGCATGAAGACA 60.302 57.895 0.00 0.00 0.00 3.41
581 661 0.539051 GTGGATGTGGAGACTGGAGG 59.461 60.000 0.00 0.00 0.00 4.30
588 668 1.080093 GCGTTCGTGGATGTGGAGA 60.080 57.895 0.00 0.00 0.00 3.71
589 669 2.444624 CGCGTTCGTGGATGTGGAG 61.445 63.158 0.00 0.00 0.00 3.86
590 670 2.431771 CGCGTTCGTGGATGTGGA 60.432 61.111 0.00 0.00 0.00 4.02
652 733 1.066573 AGGAGAATGAACTCGCCTGTG 60.067 52.381 0.00 0.00 43.25 3.66
653 734 1.205893 GAGGAGAATGAACTCGCCTGT 59.794 52.381 0.29 0.00 44.70 4.00
657 738 3.305744 GGATAGGAGGAGAATGAACTCGC 60.306 52.174 0.00 0.00 37.74 5.03
658 739 3.257127 GGGATAGGAGGAGAATGAACTCG 59.743 52.174 0.00 0.00 37.74 4.18
662 743 4.675065 TCTAGGGGATAGGAGGAGAATGAA 59.325 45.833 0.00 0.00 31.83 2.57
665 750 5.122701 AGATCTAGGGGATAGGAGGAGAAT 58.877 45.833 0.00 0.00 34.33 2.40
777 891 9.495572 TTTTGAACATGAAAAGGTGTTAACTTT 57.504 25.926 7.22 0.00 39.69 2.66
833 947 7.201848 CCATATTGACACACCATGCTTAATCTT 60.202 37.037 0.00 0.00 0.00 2.40
926 1062 6.619801 ACCTGAAATAACATAAGCCGATTC 57.380 37.500 0.00 0.00 0.00 2.52
927 1063 7.122055 TGAAACCTGAAATAACATAAGCCGATT 59.878 33.333 0.00 0.00 0.00 3.34
928 1064 6.601613 TGAAACCTGAAATAACATAAGCCGAT 59.398 34.615 0.00 0.00 0.00 4.18
929 1065 5.941058 TGAAACCTGAAATAACATAAGCCGA 59.059 36.000 0.00 0.00 0.00 5.54
976 1120 2.875094 ATCCTGTGCTTTCTGCTCTT 57.125 45.000 0.00 0.00 43.37 2.85
1097 1242 6.772716 GGGCAGGATAATAAAAGTTCATCAGA 59.227 38.462 0.00 0.00 0.00 3.27
1100 1245 6.959639 TGGGCAGGATAATAAAAGTTCATC 57.040 37.500 0.00 0.00 0.00 2.92
1148 1303 5.294356 TCAAATGCATACCCAGTATCGTAC 58.706 41.667 0.00 0.00 0.00 3.67
1149 1304 5.538849 TCAAATGCATACCCAGTATCGTA 57.461 39.130 0.00 0.00 0.00 3.43
1150 1305 4.415881 TCAAATGCATACCCAGTATCGT 57.584 40.909 0.00 0.00 0.00 3.73
1151 1306 5.469760 TGAATCAAATGCATACCCAGTATCG 59.530 40.000 0.00 0.00 0.00 2.92
1152 1307 6.882610 TGAATCAAATGCATACCCAGTATC 57.117 37.500 0.00 0.00 0.00 2.24
1153 1308 6.435277 GGATGAATCAAATGCATACCCAGTAT 59.565 38.462 0.00 0.00 0.00 2.12
1175 1330 0.835941 GCAGAGTGATGAGGGTGGAT 59.164 55.000 0.00 0.00 0.00 3.41
1181 1336 2.263077 GTACAACGCAGAGTGATGAGG 58.737 52.381 0.00 0.00 0.00 3.86
1196 1351 2.997980 ACGATGCATTCATGGGTACAA 58.002 42.857 0.00 0.00 33.38 2.41
1215 1474 5.964887 TGCTTCACAAATGCAGTAAAAAC 57.035 34.783 0.00 0.00 32.55 2.43
1225 1484 7.703197 TCAGTATATTTGCATGCTTCACAAATG 59.297 33.333 20.33 10.02 42.38 2.32
1242 1501 9.388506 CATCCTCAAACAGAAACTCAGTATATT 57.611 33.333 0.00 0.00 0.00 1.28
1273 1532 2.714808 AGAAGGTAAGGTCCCCAAAGT 58.285 47.619 0.00 0.00 0.00 2.66
1280 1539 5.801380 TGTGTTCATTAGAAGGTAAGGTCC 58.199 41.667 0.00 0.00 33.63 4.46
1311 1570 8.535690 AGCATAAGTTACTCTGTACAAACTTC 57.464 34.615 21.03 11.22 40.38 3.01
1503 1770 9.736023 GTCCTTATAATTGGAAATGTCATGAAC 57.264 33.333 0.00 0.00 33.72 3.18
1578 1845 1.664016 GCTTCATGGCACGTTGTTGAG 60.664 52.381 0.00 0.00 0.00 3.02
1586 1853 1.835121 CATCAATGCTTCATGGCACG 58.165 50.000 0.00 0.00 45.36 5.34
1617 1884 5.310451 GTGAAGACAACTTTGTACCCCATA 58.690 41.667 0.00 0.00 42.43 2.74
1764 2031 4.140591 TCTGGAGATATCCCTGACCTCAAT 60.141 45.833 3.38 0.00 0.00 2.57
1844 2111 5.690990 TGATTTCATCACAGCTTAAGCGGG 61.691 45.833 27.58 22.24 40.56 6.13
2170 2439 7.819900 ACATAGAGTAAGAAAGTAAAGGTGCAG 59.180 37.037 0.00 0.00 0.00 4.41
2214 2484 9.918630 GATTTATTGAATGAGGGAACATAATGG 57.081 33.333 0.00 0.00 0.00 3.16
2293 2563 3.768757 CTCCCTCATCTCTTCAAGTCAGT 59.231 47.826 0.00 0.00 0.00 3.41
2295 2565 4.053009 TCTCCCTCATCTCTTCAAGTCA 57.947 45.455 0.00 0.00 0.00 3.41
2334 2604 2.237143 CAGCCCCTAACATCTCAACTCA 59.763 50.000 0.00 0.00 0.00 3.41
2414 2684 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2415 2685 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2416 2686 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2417 2687 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2418 2688 4.811557 GGAGTCATCTATTTTGGAACGGAG 59.188 45.833 0.00 0.00 0.00 4.63
2419 2689 4.224147 TGGAGTCATCTATTTTGGAACGGA 59.776 41.667 0.00 0.00 0.00 4.69
2420 2690 4.332819 GTGGAGTCATCTATTTTGGAACGG 59.667 45.833 0.00 0.00 0.00 4.44
2421 2691 5.178797 AGTGGAGTCATCTATTTTGGAACG 58.821 41.667 0.00 0.00 0.00 3.95
2422 2692 7.040409 ACAAAGTGGAGTCATCTATTTTGGAAC 60.040 37.037 12.00 0.00 43.46 3.62
2423 2693 7.004086 ACAAAGTGGAGTCATCTATTTTGGAA 58.996 34.615 12.00 0.00 43.46 3.53
2424 2694 6.542821 ACAAAGTGGAGTCATCTATTTTGGA 58.457 36.000 12.00 0.00 43.46 3.53
2425 2695 6.824305 ACAAAGTGGAGTCATCTATTTTGG 57.176 37.500 12.00 0.00 43.46 3.28
2426 2696 8.322906 TGTACAAAGTGGAGTCATCTATTTTG 57.677 34.615 0.00 7.65 44.19 2.44
2427 2697 8.918202 TTGTACAAAGTGGAGTCATCTATTTT 57.082 30.769 5.64 0.00 0.00 1.82
2428 2698 8.918202 TTTGTACAAAGTGGAGTCATCTATTT 57.082 30.769 17.01 0.00 0.00 1.40
2429 2699 8.553459 CTTTGTACAAAGTGGAGTCATCTATT 57.447 34.615 31.55 0.00 42.02 1.73
2444 2714 8.918202 AAATAGATGACTCCACTTTGTACAAA 57.082 30.769 19.53 19.53 0.00 2.83
2445 2715 8.783093 CAAAATAGATGACTCCACTTTGTACAA 58.217 33.333 3.59 3.59 0.00 2.41
2446 2716 7.390440 CCAAAATAGATGACTCCACTTTGTACA 59.610 37.037 0.00 0.00 0.00 2.90
2447 2717 7.606456 TCCAAAATAGATGACTCCACTTTGTAC 59.394 37.037 0.00 0.00 0.00 2.90
2448 2718 7.685481 TCCAAAATAGATGACTCCACTTTGTA 58.315 34.615 0.00 0.00 0.00 2.41
2449 2719 6.542821 TCCAAAATAGATGACTCCACTTTGT 58.457 36.000 0.00 0.00 0.00 2.83
2450 2720 7.308435 GTTCCAAAATAGATGACTCCACTTTG 58.692 38.462 0.00 0.00 0.00 2.77
2451 2721 6.149474 CGTTCCAAAATAGATGACTCCACTTT 59.851 38.462 0.00 0.00 0.00 2.66
2452 2722 5.643777 CGTTCCAAAATAGATGACTCCACTT 59.356 40.000 0.00 0.00 0.00 3.16
2453 2723 5.178797 CGTTCCAAAATAGATGACTCCACT 58.821 41.667 0.00 0.00 0.00 4.00
2454 2724 4.332819 CCGTTCCAAAATAGATGACTCCAC 59.667 45.833 0.00 0.00 0.00 4.02
2455 2725 4.224147 TCCGTTCCAAAATAGATGACTCCA 59.776 41.667 0.00 0.00 0.00 3.86
2456 2726 4.766375 TCCGTTCCAAAATAGATGACTCC 58.234 43.478 0.00 0.00 0.00 3.85
2457 2727 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2458 2728 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2459 2729 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2460 2730 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2461 2731 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2462 2732 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2463 2733 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2464 2734 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2465 2735 3.198417 GGTACTCCCTCCGTTCCAAAATA 59.802 47.826 0.00 0.00 0.00 1.40
2466 2736 2.026542 GGTACTCCCTCCGTTCCAAAAT 60.027 50.000 0.00 0.00 0.00 1.82
2467 2737 1.348696 GGTACTCCCTCCGTTCCAAAA 59.651 52.381 0.00 0.00 0.00 2.44
2468 2738 0.978907 GGTACTCCCTCCGTTCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
2469 2739 0.115745 AGGTACTCCCTCCGTTCCAA 59.884 55.000 0.00 0.00 40.71 3.53
2470 2740 0.115745 AAGGTACTCCCTCCGTTCCA 59.884 55.000 0.00 0.00 45.47 3.53
2471 2741 1.206610 GAAAGGTACTCCCTCCGTTCC 59.793 57.143 0.00 0.00 45.47 3.62
2472 2742 2.094130 CAGAAAGGTACTCCCTCCGTTC 60.094 54.545 0.00 0.00 45.47 3.95
2473 2743 1.900486 CAGAAAGGTACTCCCTCCGTT 59.100 52.381 0.00 0.00 45.47 4.44
2474 2744 1.076677 TCAGAAAGGTACTCCCTCCGT 59.923 52.381 0.00 0.00 45.47 4.69
2475 2745 1.751924 CTCAGAAAGGTACTCCCTCCG 59.248 57.143 0.00 0.00 45.47 4.63
2476 2746 2.822697 ACTCAGAAAGGTACTCCCTCC 58.177 52.381 0.00 0.00 45.47 4.30
2477 2747 4.893829 AAACTCAGAAAGGTACTCCCTC 57.106 45.455 0.00 0.00 45.47 4.30
2526 2796 9.369904 GAAAAAGCACATATATGACCAACAATT 57.630 29.630 19.63 4.79 0.00 2.32
2536 2806 8.834465 AGTAAGAGCAGAAAAAGCACATATATG 58.166 33.333 11.29 11.29 0.00 1.78
2555 2826 9.535878 GATGGTAAAGTAGAAATCCAGTAAGAG 57.464 37.037 0.00 0.00 0.00 2.85
2659 2932 4.517453 TCAATGGACAAGTTCGGTAAAAGG 59.483 41.667 0.00 0.00 0.00 3.11
2699 2973 3.058293 GCATTCAAACATTCCACAGACGA 60.058 43.478 0.00 0.00 0.00 4.20
2756 3077 6.092122 TGCAGAAAAGATCGAACGAATACAAT 59.908 34.615 0.12 0.00 0.00 2.71
2760 3081 5.168569 AGTGCAGAAAAGATCGAACGAATA 58.831 37.500 0.12 0.00 0.00 1.75
2768 3089 2.807967 TGACCAAGTGCAGAAAAGATCG 59.192 45.455 0.00 0.00 0.00 3.69
2800 3121 8.458843 AGGTTAACAGGAACAATTCAATAATCG 58.541 33.333 8.10 0.00 0.00 3.34
2867 3191 7.503566 AGAAATATTCCCACAACATCAGTATGG 59.496 37.037 0.00 0.00 37.43 2.74
3016 3354 3.858040 GCGTTCTGCACAACTATCG 57.142 52.632 3.29 0.00 45.45 2.92
3042 3380 5.828859 AGCCTCACGTCTCAGTATTACTATT 59.171 40.000 0.00 0.00 0.00 1.73
3169 3507 8.159447 TGAAATCATAAAGATCATACCTCTGGG 58.841 37.037 0.00 0.00 35.39 4.45
3249 3589 5.335976 CCTGAAAAAGAGTCATTTGTAGGGC 60.336 44.000 12.45 0.00 0.00 5.19
3299 3639 1.205655 TCTTCTGGATCTGGTTCTGCG 59.794 52.381 0.00 0.00 0.00 5.18
3435 3775 1.349357 ACTCCCTTTTCTGAGAGTGGC 59.651 52.381 0.00 0.00 38.15 5.01
3438 3778 5.707764 GCAATTTACTCCCTTTTCTGAGAGT 59.292 40.000 0.00 0.00 42.13 3.24
3581 6172 1.867865 TGTCATAAACGCGCTCAAACA 59.132 42.857 5.73 0.76 0.00 2.83
3866 6464 3.110178 GGAAGCAACGACGACGGG 61.110 66.667 12.58 4.59 44.46 5.28
4536 12803 8.230486 AGAACTTTGCGTATCAATTTTCTACTG 58.770 33.333 0.00 0.00 35.79 2.74
4555 12822 9.822185 AGATTTGAATAAGCACAAAAGAACTTT 57.178 25.926 0.00 0.00 39.01 2.66
4649 12917 1.667212 GATGACTGCATTGCACGATCA 59.333 47.619 7.38 11.92 34.11 2.92
4781 13058 1.079503 GGACAGCTGACGATCCAAAC 58.920 55.000 23.35 0.00 0.00 2.93
4870 13508 1.039068 TGCCCACATTTTGACCAGTG 58.961 50.000 0.00 0.00 0.00 3.66
4893 13531 2.094494 TGTCGTTGCAAAAATGTGGTGT 60.094 40.909 0.00 0.00 0.00 4.16
5064 13704 5.511888 CCAGAAAATGAGAAAAGCATGGGTT 60.512 40.000 0.00 0.00 0.00 4.11
5160 13802 1.227999 AACGAATGTGCAGTGACCCG 61.228 55.000 0.00 0.00 0.00 5.28
5164 13806 1.960417 TCCAAACGAATGTGCAGTGA 58.040 45.000 0.00 0.00 0.00 3.41
5177 13819 2.835605 TCGTCTGCCGAATCCAAAC 58.164 52.632 0.00 0.00 44.03 2.93
5187 13829 0.531974 TTTCACACTGGTCGTCTGCC 60.532 55.000 0.00 0.00 0.00 4.85
5193 13835 0.042188 CTTGCGTTTCACACTGGTCG 60.042 55.000 0.00 0.00 0.00 4.79
5225 13867 3.474600 CATGCCACAATGGTTGGAAAAA 58.525 40.909 0.00 0.00 40.46 1.94
5261 13904 3.885297 CCAGCCTAAAATAGACACCATGG 59.115 47.826 11.19 11.19 0.00 3.66
5268 13918 2.172717 TGGGAGCCAGCCTAAAATAGAC 59.827 50.000 0.00 0.00 0.00 2.59
5290 13940 5.065859 TGGTGCGACGAAATGATTTCATAAT 59.934 36.000 17.14 0.43 39.63 1.28
5292 13942 3.935828 TGGTGCGACGAAATGATTTCATA 59.064 39.130 17.14 0.00 39.63 2.15
5305 14049 1.003851 ATTCCGTATTTGGTGCGACG 58.996 50.000 0.00 0.00 38.26 5.12
5309 14053 5.305139 ACTGTAAATTCCGTATTTGGTGC 57.695 39.130 3.71 0.00 37.07 5.01
5314 14058 6.595794 CAACACGACTGTAAATTCCGTATTT 58.404 36.000 0.00 0.00 39.69 1.40
5403 14148 3.697045 AGTTCAAACGAAAATGGTGGTGA 59.303 39.130 0.00 0.00 0.00 4.02
5409 14154 5.424121 AGAGACAGTTCAAACGAAAATGG 57.576 39.130 0.00 0.00 0.00 3.16
5410 14155 6.195244 CACAAGAGACAGTTCAAACGAAAATG 59.805 38.462 0.00 0.00 0.00 2.32
5449 14194 1.972872 ATATCAAAGAAGCAGCCGGG 58.027 50.000 2.18 0.00 0.00 5.73
5452 14197 5.751990 CCAAATCAATATCAAAGAAGCAGCC 59.248 40.000 0.00 0.00 0.00 4.85
5527 14316 1.878953 TCAGGACAAAACGAGCTTCC 58.121 50.000 0.00 0.00 0.00 3.46
5561 14401 3.062099 CACGTACTGAATTTGGATGGACG 59.938 47.826 0.00 0.00 0.00 4.79
5580 14420 4.149922 CGAATGTGGTAATAGGCATACACG 59.850 45.833 0.00 0.00 0.00 4.49
5586 14426 4.209307 TGTTCGAATGTGGTAATAGGCA 57.791 40.909 0.00 0.00 0.00 4.75
5594 14434 2.736721 CTCGTTCATGTTCGAATGTGGT 59.263 45.455 0.00 0.00 35.69 4.16
5595 14435 2.993220 TCTCGTTCATGTTCGAATGTGG 59.007 45.455 0.00 0.00 35.69 4.17
5603 14611 2.743636 TCCCTGTCTCGTTCATGTTC 57.256 50.000 0.00 0.00 0.00 3.18
5609 14617 3.926616 TCATTCTTTCCCTGTCTCGTTC 58.073 45.455 0.00 0.00 0.00 3.95
5612 14620 3.194542 ACTCTCATTCTTTCCCTGTCTCG 59.805 47.826 0.00 0.00 0.00 4.04
5613 14621 4.221703 TCACTCTCATTCTTTCCCTGTCTC 59.778 45.833 0.00 0.00 0.00 3.36
5618 14626 3.796111 TCCTCACTCTCATTCTTTCCCT 58.204 45.455 0.00 0.00 0.00 4.20
5623 14631 6.216456 ACCCTTTTATCCTCACTCTCATTCTT 59.784 38.462 0.00 0.00 0.00 2.52
5627 14635 6.903534 TCTAACCCTTTTATCCTCACTCTCAT 59.096 38.462 0.00 0.00 0.00 2.90
5628 14636 6.261435 TCTAACCCTTTTATCCTCACTCTCA 58.739 40.000 0.00 0.00 0.00 3.27
5632 14645 5.351405 ACCTCTAACCCTTTTATCCTCACT 58.649 41.667 0.00 0.00 0.00 3.41
5650 14663 2.479566 TTACGAGTACACGGACCTCT 57.520 50.000 16.97 0.00 37.61 3.69
5652 14665 2.424956 GGAATTACGAGTACACGGACCT 59.575 50.000 16.97 0.00 37.61 3.85
5657 14670 4.100529 ACGAATGGAATTACGAGTACACG 58.899 43.478 11.29 11.29 36.07 4.49
5679 14692 2.203972 CTTGTCTTCGACCGCCGGTA 62.204 60.000 9.73 0.00 35.25 4.02
5681 14694 2.809601 CTTGTCTTCGACCGCCGG 60.810 66.667 0.00 0.00 39.14 6.13
5682 14695 2.809601 CCTTGTCTTCGACCGCCG 60.810 66.667 0.00 0.00 40.25 6.46
5684 14697 3.479269 CGCCTTGTCTTCGACCGC 61.479 66.667 0.00 0.00 0.00 5.68
5685 14698 2.809601 CCGCCTTGTCTTCGACCG 60.810 66.667 0.00 0.00 0.00 4.79
5720 14899 2.562298 TGCAACTTTTAGCATGGAAGGG 59.438 45.455 0.00 0.00 35.51 3.95
5730 14909 3.005684 TGCCAATCCACTGCAACTTTTAG 59.994 43.478 0.00 0.00 30.85 1.85
5743 14922 2.307496 ATGTCCAAGTTGCCAATCCA 57.693 45.000 0.00 0.00 0.00 3.41
5746 14925 8.641541 CCTAATTATTATGTCCAAGTTGCCAAT 58.358 33.333 0.00 0.00 0.00 3.16
5747 14926 7.417342 GCCTAATTATTATGTCCAAGTTGCCAA 60.417 37.037 0.00 0.00 0.00 4.52
5748 14927 6.040391 GCCTAATTATTATGTCCAAGTTGCCA 59.960 38.462 0.00 0.00 0.00 4.92
5749 14928 6.040391 TGCCTAATTATTATGTCCAAGTTGCC 59.960 38.462 0.00 0.00 0.00 4.52
5750 14929 6.918022 GTGCCTAATTATTATGTCCAAGTTGC 59.082 38.462 0.00 0.00 0.00 4.17
5751 14930 7.132213 CGTGCCTAATTATTATGTCCAAGTTG 58.868 38.462 0.00 0.00 0.00 3.16
5752 14931 6.238648 GCGTGCCTAATTATTATGTCCAAGTT 60.239 38.462 0.00 0.00 0.00 2.66
5753 14932 5.238650 GCGTGCCTAATTATTATGTCCAAGT 59.761 40.000 0.00 0.00 0.00 3.16
5755 14934 5.373222 AGCGTGCCTAATTATTATGTCCAA 58.627 37.500 0.00 0.00 0.00 3.53
5756 14935 4.968259 AGCGTGCCTAATTATTATGTCCA 58.032 39.130 0.00 0.00 0.00 4.02
5757 14936 7.980099 ACTATAGCGTGCCTAATTATTATGTCC 59.020 37.037 0.00 0.00 0.00 4.02
5758 14937 8.928270 ACTATAGCGTGCCTAATTATTATGTC 57.072 34.615 0.00 0.00 0.00 3.06
5765 14947 9.017509 ACTAACATACTATAGCGTGCCTAATTA 57.982 33.333 0.00 0.00 0.00 1.40
5800 14982 9.150348 CTTTTGTGTATTTCCTTTGTTGTTTCT 57.850 29.630 0.00 0.00 0.00 2.52
5910 15095 3.037549 AGAGCACATTTGACCCCAAAAA 58.962 40.909 0.00 0.00 44.49 1.94
5915 15100 1.678101 GCATAGAGCACATTTGACCCC 59.322 52.381 0.00 0.00 44.79 4.95
6002 15199 7.648908 CGTCACCCGTAACAAATATGAGTTATA 59.351 37.037 4.22 0.00 33.30 0.98
6125 15334 4.866327 ATTTACGGGGGTCCTATTGAAA 57.134 40.909 0.00 0.00 0.00 2.69
6161 15370 3.118261 TGTTTGGGTTGCCATGCTTAAAA 60.118 39.130 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.